Multiple sequence alignment - TraesCS3B01G250800

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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 TraesCS3B01G250800 chr3B 100.000 5347 0 0 1 5347 401026590 401031936 0.000000e+00 9875.0
1 TraesCS3B01G250800 chr3B 94.681 94 5 0 4932 5025 401031436 401031529 4.320000e-31 147.0
2 TraesCS3B01G250800 chr3B 94.681 94 5 0 4847 4940 401031521 401031614 4.320000e-31 147.0
3 TraesCS3B01G250800 chr3D 94.594 5309 197 44 63 5347 318576312 318571070 0.000000e+00 8131.0
4 TraesCS3B01G250800 chr3D 93.617 94 6 0 4847 4940 318571471 318571378 2.010000e-29 141.0
5 TraesCS3B01G250800 chr3D 92.553 94 7 0 4932 5025 318571556 318571463 9.340000e-28 135.0
6 TraesCS3B01G250800 chr3A 95.821 3900 126 24 1057 4940 407423144 407427022 0.000000e+00 6264.0
7 TraesCS3B01G250800 chr3A 89.226 594 62 2 428 1020 407422235 407422827 0.000000e+00 741.0
8 TraesCS3B01G250800 chr3A 92.344 418 23 5 4932 5347 407426929 407427339 2.150000e-163 586.0
9 TraesCS3B01G250800 chr3A 83.951 81 5 7 21 101 69478143 69478071 2.670000e-08 71.3
10 TraesCS3B01G250800 chr3A 97.561 41 1 0 21 61 225603360 225603400 2.670000e-08 71.3
11 TraesCS3B01G250800 chr6D 86.145 166 18 5 63 226 137094590 137094752 1.980000e-39 174.0
12 TraesCS3B01G250800 chr6D 83.636 165 22 5 56 217 444084161 444084323 3.340000e-32 150.0
13 TraesCS3B01G250800 chr6D 82.424 165 26 3 63 226 87492307 87492145 2.010000e-29 141.0
14 TraesCS3B01G250800 chr7D 86.620 142 18 1 86 226 259829984 259829843 7.170000e-34 156.0
15 TraesCS3B01G250800 chr7D 84.091 132 19 2 228 358 54055722 54055852 5.620000e-25 126.0
16 TraesCS3B01G250800 chr2D 84.906 159 19 5 63 220 564479631 564479785 7.170000e-34 156.0
17 TraesCS3B01G250800 chr2D 97.826 46 1 0 21 66 427235486 427235531 4.440000e-11 80.5
18 TraesCS3B01G250800 chr4B 84.768 151 22 1 77 226 43597445 43597595 3.340000e-32 150.0
19 TraesCS3B01G250800 chr4B 95.833 48 2 0 21 68 279360676 279360629 1.600000e-10 78.7
20 TraesCS3B01G250800 chr5D 83.133 166 24 4 63 226 477882055 477881892 1.200000e-31 148.0
21 TraesCS3B01G250800 chr6B 82.390 159 24 4 63 219 668531418 668531574 9.340000e-28 135.0
22 TraesCS3B01G250800 chr7B 94.340 53 1 2 21 73 199384760 199384710 4.440000e-11 80.5
23 TraesCS3B01G250800 chr7B 81.250 96 16 2 263 357 331023857 331023763 5.740000e-10 76.8
24 TraesCS3B01G250800 chr4D 92.727 55 4 0 21 75 45102295 45102241 4.440000e-11 80.5
25 TraesCS3B01G250800 chr4D 97.826 46 1 0 21 66 458313357 458313312 4.440000e-11 80.5
26 TraesCS3B01G250800 chr5A 95.833 48 2 0 21 68 45336526 45336479 1.600000e-10 78.7
27 TraesCS3B01G250800 chr5A 92.453 53 2 2 20 72 66335989 66335939 2.070000e-09 75.0


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 TraesCS3B01G250800 chr3B 401026590 401031936 5346 False 3389.666667 9875 96.454000 1 5347 3 chr3B.!!$F1 5346
1 TraesCS3B01G250800 chr3D 318571070 318576312 5242 True 8131.000000 8131 94.594000 63 5347 1 chr3D.!!$R1 5284
2 TraesCS3B01G250800 chr3A 407422235 407427339 5104 False 2530.333333 6264 92.463667 428 5347 3 chr3A.!!$F2 4919

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
843 847 0.038526 CACGCAACTCGAAGTAGGGT 60.039 55.000 0.00 0.00 41.67 4.34 F
1347 1651 0.035630 CCCCTGCAAAGAGAGGTCTG 60.036 60.000 0.00 0.00 31.37 3.51 F
1941 2248 2.624316 TACGACCGTGCTAACAGAAG 57.376 50.000 5.20 0.00 0.00 2.85 F
3763 4071 1.003116 CAGTTTGAGCTGCTGTCACAC 60.003 52.381 7.01 3.35 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2486 0.392998 AGGAATGGCCAGCAGTAACG 60.393 55.000 13.05 0.0 40.02 3.18 R
3057 3364 0.531974 TGCGTTCAAAGTTCCGAGCT 60.532 50.000 0.00 0.0 0.00 4.09 R
3815 4123 1.612950 ACTCATTTTGCCGCATGAACA 59.387 42.857 0.00 0.0 0.00 3.18 R
4716 5029 0.327867 AGGCCCTCAAGGATGGATCA 60.328 55.000 0.00 0.0 38.24 2.92 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
19 20 2.121291 TGCCAGTTTTGACACTGACA 57.879 45.000 2.32 0.00 46.29 3.58
20 21 2.441410 TGCCAGTTTTGACACTGACAA 58.559 42.857 2.32 0.00 46.29 3.18
21 22 3.023119 TGCCAGTTTTGACACTGACAAT 58.977 40.909 2.32 0.00 46.29 2.71
22 23 3.181488 TGCCAGTTTTGACACTGACAATG 60.181 43.478 2.32 0.00 46.29 2.82
23 24 3.796504 GCCAGTTTTGACACTGACAATGG 60.797 47.826 2.32 7.57 46.29 3.16
24 25 3.631686 CCAGTTTTGACACTGACAATGGA 59.368 43.478 2.32 0.00 46.29 3.41
25 26 4.097741 CCAGTTTTGACACTGACAATGGAA 59.902 41.667 2.32 0.00 46.29 3.53
26 27 5.036737 CAGTTTTGACACTGACAATGGAAC 58.963 41.667 0.00 0.00 46.29 3.62
27 28 5.392919 CAGTTTTGACACTGACAATGGAACA 60.393 40.000 8.81 0.00 46.29 3.18
28 29 6.845064 CAGTTTTGACACTGACAATGGAACAA 60.845 38.462 8.81 0.00 46.29 2.83
29 30 8.777531 CAGTTTTGACACTGACAATGGAACAAC 61.778 40.741 8.81 4.26 46.29 3.32
75 76 3.071023 ACGTATCAATACCCCATCCACAG 59.929 47.826 0.00 0.00 0.00 3.66
96 97 7.310664 CACAGTCAATACATTCAAAGCAGAAT 58.689 34.615 0.00 0.00 38.72 2.40
110 112 6.430000 TCAAAGCAGAATGTAGGTTTTACCTC 59.570 38.462 0.79 0.00 41.82 3.85
129 131 1.229209 TTCGAGAGGGCCTGAACCT 60.229 57.895 12.95 0.00 42.18 3.50
160 162 1.244019 GGTGTCCCCTTGTGTCATGC 61.244 60.000 0.00 0.00 0.00 4.06
168 170 2.092753 CCCTTGTGTCATGCTACCATCT 60.093 50.000 0.00 0.00 0.00 2.90
181 183 5.756918 TGCTACCATCTAGTCAAGACTACT 58.243 41.667 5.86 0.00 42.54 2.57
209 211 2.683768 GACCCCCTACATGAGATCTGT 58.316 52.381 0.00 0.00 0.00 3.41
234 236 2.131709 CGATTCCGTCCCCTAGCCA 61.132 63.158 0.00 0.00 0.00 4.75
235 237 1.446366 GATTCCGTCCCCTAGCCAC 59.554 63.158 0.00 0.00 0.00 5.01
256 258 1.876799 CGCCACACCATTTAGAACACA 59.123 47.619 0.00 0.00 0.00 3.72
261 263 5.248640 CCACACCATTTAGAACACAGAGAT 58.751 41.667 0.00 0.00 0.00 2.75
270 272 9.474920 CATTTAGAACACAGAGATAAGAGATCC 57.525 37.037 0.00 0.00 0.00 3.36
273 275 6.430864 AGAACACAGAGATAAGAGATCCAGA 58.569 40.000 0.00 0.00 0.00 3.86
274 276 6.547141 AGAACACAGAGATAAGAGATCCAGAG 59.453 42.308 0.00 0.00 0.00 3.35
275 277 6.012337 ACACAGAGATAAGAGATCCAGAGA 57.988 41.667 0.00 0.00 0.00 3.10
309 311 4.386711 CGGAGACCCTTCTAGTTTTGTTT 58.613 43.478 0.00 0.00 29.47 2.83
323 326 6.590234 AGTTTTGTTTTCCATCTCCATACC 57.410 37.500 0.00 0.00 0.00 2.73
339 342 6.332635 TCTCCATACCCATATTCATTTCACCT 59.667 38.462 0.00 0.00 0.00 4.00
348 351 7.287466 CCCATATTCATTTCACCTTCACCATTA 59.713 37.037 0.00 0.00 0.00 1.90
474 477 7.689559 GCAGCTACATATTTACCTACTCCCTTT 60.690 40.741 0.00 0.00 0.00 3.11
606 609 4.812476 CCACTTGGGCGCGATCGA 62.812 66.667 21.57 0.00 38.10 3.59
610 613 2.125310 TTGGGCGCGATCGAACAT 60.125 55.556 21.57 0.00 38.10 2.71
636 639 3.471806 GCGGGACCTTCTCTCCCC 61.472 72.222 0.00 0.00 44.40 4.81
670 673 1.137594 TCCCCCGAACACTTCCCATT 61.138 55.000 0.00 0.00 0.00 3.16
685 688 0.756442 CCATTGCCCATCGGGTTGAT 60.756 55.000 0.06 0.00 46.51 2.57
753 756 2.408022 CGTCCTGATCCCGTCGAC 59.592 66.667 5.18 5.18 0.00 4.20
780 783 0.859232 GACGATTATTGCGATGGCGT 59.141 50.000 9.41 9.41 44.10 5.68
782 785 0.110688 CGATTATTGCGATGGCGTGG 60.111 55.000 0.00 0.00 44.10 4.94
800 803 1.180029 GGTGATGCTGCTTCAATGGT 58.820 50.000 18.30 0.00 0.00 3.55
806 809 0.524862 GCTGCTTCAATGGTGACTGG 59.475 55.000 0.00 0.00 31.90 4.00
829 833 1.822114 TTTCCTCATCGGGACACGCA 61.822 55.000 0.00 0.00 43.86 5.24
832 836 1.079819 CTCATCGGGACACGCAACT 60.080 57.895 0.00 0.00 43.86 3.16
835 839 2.632544 ATCGGGACACGCAACTCGA 61.633 57.895 0.00 0.00 43.04 4.04
838 842 1.300697 GGGACACGCAACTCGAAGT 60.301 57.895 0.00 0.00 41.67 3.01
843 847 0.038526 CACGCAACTCGAAGTAGGGT 60.039 55.000 0.00 0.00 41.67 4.34
847 851 1.270678 GCAACTCGAAGTAGGGTGGTT 60.271 52.381 0.00 0.00 0.00 3.67
861 865 1.529010 TGGTTGGTGCAGAGCAAGG 60.529 57.895 0.00 0.00 41.47 3.61
870 874 1.005748 CAGAGCAAGGCAGTCGACA 60.006 57.895 19.50 0.00 0.00 4.35
891 895 5.316327 CACAATGAGTGTAGCTGAGACTA 57.684 43.478 0.00 0.00 43.40 2.59
892 896 5.714047 CACAATGAGTGTAGCTGAGACTAA 58.286 41.667 0.00 0.00 43.40 2.24
899 903 4.956700 AGTGTAGCTGAGACTAATGGCTAA 59.043 41.667 0.00 0.00 37.27 3.09
975 980 4.133796 GGCAGTGGGAAATGCGGC 62.134 66.667 0.00 0.00 43.49 6.53
1028 1327 1.468736 CGTCGAGCTAAGTGGTTACCC 60.469 57.143 0.00 0.00 0.00 3.69
1032 1331 1.450848 GCTAAGTGGTTACCCCGGC 60.451 63.158 0.00 0.00 35.15 6.13
1039 1338 2.136229 GGTTACCCCGGCGATAGGT 61.136 63.158 9.30 14.93 37.69 3.08
1048 1347 2.792947 GGCGATAGGTGCGGGAGAA 61.793 63.158 0.00 0.00 0.00 2.87
1051 1350 1.749033 GATAGGTGCGGGAGAAGGG 59.251 63.158 0.00 0.00 0.00 3.95
1054 1353 2.465010 TAGGTGCGGGAGAAGGGGAA 62.465 60.000 0.00 0.00 0.00 3.97
1055 1354 2.269241 GTGCGGGAGAAGGGGAAG 59.731 66.667 0.00 0.00 0.00 3.46
1056 1355 3.009115 TGCGGGAGAAGGGGAAGG 61.009 66.667 0.00 0.00 0.00 3.46
1057 1356 3.798511 GCGGGAGAAGGGGAAGGG 61.799 72.222 0.00 0.00 0.00 3.95
1058 1357 3.090532 CGGGAGAAGGGGAAGGGG 61.091 72.222 0.00 0.00 0.00 4.79
1059 1358 2.459710 GGGAGAAGGGGAAGGGGA 59.540 66.667 0.00 0.00 0.00 4.81
1060 1359 1.694525 GGGAGAAGGGGAAGGGGAG 60.695 68.421 0.00 0.00 0.00 4.30
1061 1360 1.396594 GGAGAAGGGGAAGGGGAGA 59.603 63.158 0.00 0.00 0.00 3.71
1062 1361 0.692756 GGAGAAGGGGAAGGGGAGAG 60.693 65.000 0.00 0.00 0.00 3.20
1074 1373 1.460497 GGGAGAGGGGGAGGATCAC 60.460 68.421 0.00 0.00 38.30 3.06
1081 1380 4.530857 GGGAGGATCACACGGCCG 62.531 72.222 26.86 26.86 39.41 6.13
1212 1511 1.410083 CCTCAGTCTCTCCCCTCTCAG 60.410 61.905 0.00 0.00 0.00 3.35
1248 1552 1.202891 TCCTCTTCACACTCCGTCTCA 60.203 52.381 0.00 0.00 0.00 3.27
1268 1572 0.179073 CCACATTCGGAGCTCGGATT 60.179 55.000 22.92 16.95 34.23 3.01
1306 1610 0.773644 CCCGATCCCTCCCAAATCAT 59.226 55.000 0.00 0.00 0.00 2.45
1347 1651 0.035630 CCCCTGCAAAGAGAGGTCTG 60.036 60.000 0.00 0.00 31.37 3.51
1486 1790 6.465084 GTCTATCTGGTATTCGCCCTAATTT 58.535 40.000 0.00 0.00 0.00 1.82
1498 1802 4.585162 TCGCCCTAATTTTCTTTGGTTTCA 59.415 37.500 0.00 0.00 0.00 2.69
1524 1828 3.070018 CAATCTAGTGATGGGGATTCGC 58.930 50.000 0.00 0.00 32.44 4.70
1876 2183 6.025896 CGAGTGATGGATTGAACATCTTTTG 58.974 40.000 6.92 0.00 43.88 2.44
1941 2248 2.624316 TACGACCGTGCTAACAGAAG 57.376 50.000 5.20 0.00 0.00 2.85
2443 2750 4.965119 ACCTGAAACGATTCTTATTGCC 57.035 40.909 6.98 0.00 36.48 4.52
2501 2808 5.584551 AGGTGATAACTTGTCTTTCCCTT 57.415 39.130 0.00 0.00 0.00 3.95
2641 2948 3.559069 AGATGGTGAGCATGGTATTTGG 58.441 45.455 0.12 0.00 0.00 3.28
2737 3044 8.581057 AGAAGCATGACAATTCTTACTATACG 57.419 34.615 0.00 0.00 28.99 3.06
2912 3219 4.771577 ACATGAATGTTTCCCATGCAAGTA 59.228 37.500 0.00 0.00 42.56 2.24
2934 3241 3.543665 AGTCCACGACCAGAGACTATAC 58.456 50.000 0.00 0.00 36.03 1.47
3300 3607 3.197549 TGGTGCAGCACTATGAGAATACA 59.802 43.478 24.75 7.54 34.40 2.29
3413 3720 8.125978 AGAAATGAATTAAAGCTTGGTCATGA 57.874 30.769 0.00 0.00 0.00 3.07
3416 3723 6.748333 TGAATTAAAGCTTGGTCATGAGAG 57.252 37.500 0.00 0.00 0.00 3.20
3762 4070 1.134431 TCAGTTTGAGCTGCTGTCACA 60.134 47.619 7.01 0.00 36.49 3.58
3763 4071 1.003116 CAGTTTGAGCTGCTGTCACAC 60.003 52.381 7.01 3.35 0.00 3.82
3977 4288 0.947244 AAGAAAGTGGCAGCAAGACG 59.053 50.000 0.00 0.00 0.00 4.18
4163 4474 2.983592 GAACAACCAGGCACCGGG 60.984 66.667 6.32 4.11 37.31 5.73
4174 4485 4.864334 CACCGGGGATGCTGGAGC 62.864 72.222 6.32 0.00 42.50 4.70
4628 4941 7.201644 GCCAAGAAAAGAAAGAAAGAAAAAGGG 60.202 37.037 0.00 0.00 0.00 3.95
4654 4967 4.237843 AGAGCCAGATCCTATCCAATTCA 58.762 43.478 0.00 0.00 0.00 2.57
4715 5028 5.105797 CGAAACATCATCCCAGATTGGAAAA 60.106 40.000 0.00 0.00 40.96 2.29
4716 5029 6.406177 CGAAACATCATCCCAGATTGGAAAAT 60.406 38.462 0.00 0.00 40.96 1.82
4718 5031 5.521696 ACATCATCCCAGATTGGAAAATGA 58.478 37.500 10.31 3.97 40.96 2.57
4719 5032 6.141083 ACATCATCCCAGATTGGAAAATGAT 58.859 36.000 11.48 11.48 40.96 2.45
4721 5034 5.142639 TCATCCCAGATTGGAAAATGATCC 58.857 41.667 0.00 0.00 40.96 3.36
4778 5091 4.351111 ACTGTGAATTAGAAGGGTCAGGTT 59.649 41.667 0.00 0.00 0.00 3.50
4909 5230 1.821136 CTTGGGAAACTTCTGATGGGC 59.179 52.381 0.00 0.00 0.00 5.36
4914 5235 3.454812 GGGAAACTTCTGATGGGCTAGTA 59.545 47.826 0.00 0.00 0.00 1.82
4996 5317 1.272092 TGGGAAACTTCTGATGGGCTG 60.272 52.381 0.00 0.00 0.00 4.85
5002 5323 3.073274 ACTTCTGATGGGCTGGTAAAC 57.927 47.619 0.00 0.00 0.00 2.01
5045 5366 7.988028 AGTTCCTCTTTGCCTATAAGTGATTAC 59.012 37.037 0.00 0.00 0.00 1.89
5075 5396 4.592426 GTCCCGAGGAAAAGGACG 57.408 61.111 0.00 0.00 40.65 4.79
5193 5515 2.437651 TGTGTTGACCCTGTCATGAAGA 59.562 45.455 0.00 0.00 42.40 2.87
5273 5596 2.636893 AGATCTTGTGTGCTTCCACTCT 59.363 45.455 0.00 0.00 42.54 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.631686 TCCATTGTCAGTGTCAAAACTGG 59.368 43.478 12.37 12.37 46.27 4.00
4 5 4.704540 TGTTCCATTGTCAGTGTCAAAACT 59.295 37.500 6.89 0.00 0.00 2.66
5 6 4.992688 TGTTCCATTGTCAGTGTCAAAAC 58.007 39.130 6.89 7.76 0.00 2.43
6 7 5.047731 TGTTGTTCCATTGTCAGTGTCAAAA 60.048 36.000 6.89 0.00 0.00 2.44
7 8 4.460731 TGTTGTTCCATTGTCAGTGTCAAA 59.539 37.500 6.89 0.00 0.00 2.69
8 9 4.013050 TGTTGTTCCATTGTCAGTGTCAA 58.987 39.130 5.27 5.27 0.00 3.18
9 10 3.615155 TGTTGTTCCATTGTCAGTGTCA 58.385 40.909 0.00 0.00 0.00 3.58
10 11 4.630894 TTGTTGTTCCATTGTCAGTGTC 57.369 40.909 0.00 0.00 0.00 3.67
11 12 5.398603 TTTTGTTGTTCCATTGTCAGTGT 57.601 34.783 0.00 0.00 0.00 3.55
46 47 5.779529 TGGGGTATTGATACGTCTCTAAC 57.220 43.478 0.00 0.00 34.11 2.34
47 48 5.479375 GGATGGGGTATTGATACGTCTCTAA 59.521 44.000 0.00 0.00 34.11 2.10
48 49 5.014858 GGATGGGGTATTGATACGTCTCTA 58.985 45.833 0.00 0.00 34.11 2.43
49 50 3.833070 GGATGGGGTATTGATACGTCTCT 59.167 47.826 0.00 0.00 34.11 3.10
50 51 3.576982 TGGATGGGGTATTGATACGTCTC 59.423 47.826 0.00 0.00 34.11 3.36
51 52 3.323979 GTGGATGGGGTATTGATACGTCT 59.676 47.826 0.00 0.00 34.11 4.18
52 53 3.070446 TGTGGATGGGGTATTGATACGTC 59.930 47.826 0.00 0.00 34.11 4.34
53 54 3.042682 TGTGGATGGGGTATTGATACGT 58.957 45.455 0.00 0.00 34.11 3.57
54 55 3.071023 ACTGTGGATGGGGTATTGATACG 59.929 47.826 0.00 0.00 34.11 3.06
55 56 4.102524 TGACTGTGGATGGGGTATTGATAC 59.897 45.833 0.00 0.00 0.00 2.24
56 57 4.302930 TGACTGTGGATGGGGTATTGATA 58.697 43.478 0.00 0.00 0.00 2.15
57 58 3.122480 TGACTGTGGATGGGGTATTGAT 58.878 45.455 0.00 0.00 0.00 2.57
58 59 2.556766 TGACTGTGGATGGGGTATTGA 58.443 47.619 0.00 0.00 0.00 2.57
59 60 3.364460 TTGACTGTGGATGGGGTATTG 57.636 47.619 0.00 0.00 0.00 1.90
60 61 4.476846 TGTATTGACTGTGGATGGGGTATT 59.523 41.667 0.00 0.00 0.00 1.89
61 62 4.044308 TGTATTGACTGTGGATGGGGTAT 58.956 43.478 0.00 0.00 0.00 2.73
110 112 1.219393 GGTTCAGGCCCTCTCGAAG 59.781 63.158 0.00 0.00 0.00 3.79
123 125 1.700739 ACCGATGTTTACCCAGGTTCA 59.299 47.619 0.00 0.00 0.00 3.18
129 131 0.325602 GGGACACCGATGTTTACCCA 59.674 55.000 0.10 0.00 39.30 4.51
168 170 5.454471 GGTCCCGATCTAGTAGTCTTGACTA 60.454 48.000 6.41 6.41 0.00 2.59
219 221 2.686106 GGTGGCTAGGGGACGGAA 60.686 66.667 0.00 0.00 0.00 4.30
234 236 1.202830 TGTTCTAAATGGTGTGGCGGT 60.203 47.619 0.00 0.00 0.00 5.68
235 237 1.199097 GTGTTCTAAATGGTGTGGCGG 59.801 52.381 0.00 0.00 0.00 6.13
256 258 7.815383 TCTTCTTCTCTGGATCTCTTATCTCT 58.185 38.462 0.00 0.00 0.00 3.10
261 263 6.153680 GTGGTTCTTCTTCTCTGGATCTCTTA 59.846 42.308 0.00 0.00 0.00 2.10
270 272 1.618837 TCCGGTGGTTCTTCTTCTCTG 59.381 52.381 0.00 0.00 0.00 3.35
273 275 1.619332 GTCTCCGGTGGTTCTTCTTCT 59.381 52.381 0.00 0.00 0.00 2.85
274 276 1.337917 GGTCTCCGGTGGTTCTTCTTC 60.338 57.143 0.00 0.00 0.00 2.87
275 277 0.685660 GGTCTCCGGTGGTTCTTCTT 59.314 55.000 0.00 0.00 0.00 2.52
309 311 6.975471 ATGAATATGGGTATGGAGATGGAA 57.025 37.500 0.00 0.00 0.00 3.53
323 326 6.720112 ATGGTGAAGGTGAAATGAATATGG 57.280 37.500 0.00 0.00 0.00 2.74
395 398 3.546009 GCCAGGACCAGGCGTATA 58.454 61.111 12.76 0.00 43.15 1.47
448 451 5.246429 AGGGAGTAGGTAAATATGTAGCTGC 59.754 44.000 13.85 12.46 35.27 5.25
474 477 6.662755 AGAAGGTATGGATTAAAGTGATGCA 58.337 36.000 0.00 0.00 0.00 3.96
508 511 0.990818 TAGGGCATGGGCATGTACCA 60.991 55.000 12.66 12.66 43.71 3.25
603 606 2.359850 GCACCCCAGCATGTTCGA 60.360 61.111 0.00 0.00 0.00 3.71
659 662 0.680921 CGATGGGCAATGGGAAGTGT 60.681 55.000 0.00 0.00 0.00 3.55
753 756 1.267334 CGCAATAATCGTCACCGGTTG 60.267 52.381 2.97 0.00 38.06 3.77
768 771 1.451927 ATCACCACGCCATCGCAAT 60.452 52.632 0.00 0.00 39.84 3.56
775 778 3.848301 AAGCAGCATCACCACGCCA 62.848 57.895 0.00 0.00 0.00 5.69
780 783 1.179152 CCATTGAAGCAGCATCACCA 58.821 50.000 0.00 0.00 0.00 4.17
782 785 1.814394 TCACCATTGAAGCAGCATCAC 59.186 47.619 0.00 0.00 0.00 3.06
829 833 1.346722 CCAACCACCCTACTTCGAGTT 59.653 52.381 0.00 0.00 0.00 3.01
832 836 0.682852 CACCAACCACCCTACTTCGA 59.317 55.000 0.00 0.00 0.00 3.71
835 839 0.110486 CTGCACCAACCACCCTACTT 59.890 55.000 0.00 0.00 0.00 2.24
838 842 2.066340 CTCTGCACCAACCACCCTA 58.934 57.895 0.00 0.00 0.00 3.53
843 847 1.529010 CCTTGCTCTGCACCAACCA 60.529 57.895 0.00 0.00 38.71 3.67
847 851 2.281970 CTGCCTTGCTCTGCACCA 60.282 61.111 0.00 0.00 38.71 4.17
870 874 5.984695 TTAGTCTCAGCTACACTCATTGT 57.015 39.130 0.00 0.00 42.84 2.71
908 912 2.190170 ACAAATTCGTGGCGGCACA 61.190 52.632 36.79 22.22 0.00 4.57
953 957 1.312371 GCATTTCCCACTGCCGCTTA 61.312 55.000 0.00 0.00 32.15 3.09
991 996 2.776072 GTTTGGCATCGTCGTCGG 59.224 61.111 1.55 0.00 37.69 4.79
1003 1008 1.068474 CCACTTAGCTCGACGTTTGG 58.932 55.000 0.00 0.00 0.00 3.28
1032 1331 1.364171 CCTTCTCCCGCACCTATCG 59.636 63.158 0.00 0.00 0.00 2.92
1039 1338 3.009115 CCTTCCCCTTCTCCCGCA 61.009 66.667 0.00 0.00 0.00 5.69
1048 1347 3.711782 CCCCTCTCCCCTTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
1051 1350 2.040359 CTCCCCCTCTCCCCTTCC 60.040 72.222 0.00 0.00 0.00 3.46
1054 1353 2.289979 ATCCTCCCCCTCTCCCCT 60.290 66.667 0.00 0.00 0.00 4.79
1055 1354 2.205749 GATCCTCCCCCTCTCCCC 59.794 72.222 0.00 0.00 0.00 4.81
1056 1355 1.460497 GTGATCCTCCCCCTCTCCC 60.460 68.421 0.00 0.00 0.00 4.30
1057 1356 1.051556 GTGTGATCCTCCCCCTCTCC 61.052 65.000 0.00 0.00 0.00 3.71
1058 1357 1.395826 CGTGTGATCCTCCCCCTCTC 61.396 65.000 0.00 0.00 0.00 3.20
1059 1358 1.381872 CGTGTGATCCTCCCCCTCT 60.382 63.158 0.00 0.00 0.00 3.69
1060 1359 2.435693 CCGTGTGATCCTCCCCCTC 61.436 68.421 0.00 0.00 0.00 4.30
1061 1360 2.365635 CCGTGTGATCCTCCCCCT 60.366 66.667 0.00 0.00 0.00 4.79
1062 1361 4.176752 GCCGTGTGATCCTCCCCC 62.177 72.222 0.00 0.00 0.00 5.40
1085 1384 1.265462 CGTTAGATGAGAGAGCGCGC 61.265 60.000 26.66 26.66 0.00 6.86
1087 1386 0.318275 CCCGTTAGATGAGAGAGCGC 60.318 60.000 0.00 0.00 0.00 5.92
1088 1387 0.318275 GCCCGTTAGATGAGAGAGCG 60.318 60.000 0.00 0.00 0.00 5.03
1089 1388 0.747255 TGCCCGTTAGATGAGAGAGC 59.253 55.000 0.00 0.00 0.00 4.09
1090 1389 1.339610 CCTGCCCGTTAGATGAGAGAG 59.660 57.143 0.00 0.00 0.00 3.20
1091 1390 1.403814 CCTGCCCGTTAGATGAGAGA 58.596 55.000 0.00 0.00 0.00 3.10
1137 1436 0.976641 TGAGAGTTGGCCTTGTCGAT 59.023 50.000 3.32 0.00 0.00 3.59
1212 1511 2.603580 GAGGGATCCTTTGGGGGC 59.396 66.667 12.58 0.00 31.76 5.80
1248 1552 1.330655 ATCCGAGCTCCGAATGTGGT 61.331 55.000 8.47 0.00 41.76 4.16
1268 1572 1.004277 GGTGGGATAAGCAGTGGTTGA 59.996 52.381 17.67 2.63 0.00 3.18
1325 1629 1.077858 CCTCTCTTTGCAGGGGAGC 60.078 63.158 11.68 0.00 0.00 4.70
1347 1651 1.202615 GCCGAATCAAGGTAGGGGTAC 60.203 57.143 0.00 0.00 0.00 3.34
1486 1790 7.012327 CACTAGATTGTCACTGAAACCAAAGAA 59.988 37.037 0.00 0.00 0.00 2.52
1498 1802 3.724478 TCCCCATCACTAGATTGTCACT 58.276 45.455 0.00 0.00 30.20 3.41
1737 2041 1.144913 ACAAGGCCTGCAACCTTTAGA 59.855 47.619 16.22 0.00 45.39 2.10
1941 2248 7.621796 TGTAGGATTTCCTTCCTAGTCTTTTC 58.378 38.462 4.08 0.00 46.57 2.29
2179 2486 0.392998 AGGAATGGCCAGCAGTAACG 60.393 55.000 13.05 0.00 40.02 3.18
2407 2714 5.869888 CGTTTCAGGTTCTGCTAATAGAGTT 59.130 40.000 0.00 0.00 0.00 3.01
2443 2750 4.032900 ACGCGAAGTACAAAATATCTGCAG 59.967 41.667 15.93 7.63 0.00 4.41
2530 2837 7.490000 GGCTAAACTCAGCAGTAAGTAGAATA 58.510 38.462 0.00 0.00 43.67 1.75
2641 2948 4.210955 GCTCAGCATCTCAATACTACTTGC 59.789 45.833 0.00 0.00 0.00 4.01
2737 3044 3.200593 CTGACGCCCATCTGCAGC 61.201 66.667 9.47 0.00 0.00 5.25
2880 3187 5.481122 TGGGAAACATTCATGTGACAATCAT 59.519 36.000 0.00 0.00 41.61 2.45
2881 3188 4.831710 TGGGAAACATTCATGTGACAATCA 59.168 37.500 0.00 0.00 41.61 2.57
2912 3219 2.581216 TAGTCTCTGGTCGTGGACTT 57.419 50.000 0.00 0.00 39.39 3.01
3027 3334 4.161189 AGTGACCTGACTGGATTCATGTAG 59.839 45.833 5.22 0.00 39.71 2.74
3057 3364 0.531974 TGCGTTCAAAGTTCCGAGCT 60.532 50.000 0.00 0.00 0.00 4.09
3062 3369 1.673920 TGGAAGTGCGTTCAAAGTTCC 59.326 47.619 2.89 2.89 36.82 3.62
3252 3559 2.755650 TCAGCGGTCTTCTTCTTGTTC 58.244 47.619 0.00 0.00 0.00 3.18
3300 3607 6.692849 TTGAGGCTATAATCCACTGATGAT 57.307 37.500 0.00 0.00 0.00 2.45
3372 3679 8.744568 ATTCATTTCTCCTGGAATAAGAAGTC 57.255 34.615 0.00 0.00 33.53 3.01
3520 3828 6.962311 AGAAATCATATATGCTACTCCCTCCA 59.038 38.462 7.92 0.00 0.00 3.86
3562 3870 6.959639 ACTGTGCATCTTAAAGAGGAAAAA 57.040 33.333 0.00 0.00 0.00 1.94
3815 4123 1.612950 ACTCATTTTGCCGCATGAACA 59.387 42.857 0.00 0.00 0.00 3.18
3862 4170 7.775397 ATCAAAGGCATGCATACAAATTTAC 57.225 32.000 21.36 0.00 0.00 2.01
3977 4288 4.325472 CCTTGCTCGAAAAATGCAGATTTC 59.675 41.667 14.07 14.07 38.01 2.17
4029 4340 0.755327 GTGGCCTCCTTGGTGTTTGT 60.755 55.000 3.32 0.00 38.35 2.83
4181 4492 2.645838 ACTCTGCTTTGAAAGGAGCA 57.354 45.000 19.88 5.76 45.49 4.26
4518 4830 4.935808 AGAATGTTTCCATCCACGTAGAAC 59.064 41.667 0.00 0.00 0.00 3.01
4519 4831 4.935205 CAGAATGTTTCCATCCACGTAGAA 59.065 41.667 0.00 0.00 0.00 2.10
4520 4832 4.503910 CAGAATGTTTCCATCCACGTAGA 58.496 43.478 0.00 0.00 0.00 2.59
4521 4833 3.623060 CCAGAATGTTTCCATCCACGTAG 59.377 47.826 0.00 0.00 0.00 3.51
4522 4834 3.262151 TCCAGAATGTTTCCATCCACGTA 59.738 43.478 0.00 0.00 0.00 3.57
4591 4904 8.126700 TCTTTCTTTTCTTGGCTACTTTTTACG 58.873 33.333 0.00 0.00 0.00 3.18
4628 4941 4.696479 TGGATAGGATCTGGCTCTTTTC 57.304 45.455 0.00 0.00 0.00 2.29
4715 5028 0.776176 GGCCCTCAAGGATGGATCAT 59.224 55.000 0.00 0.00 38.24 2.45
4716 5029 0.327867 AGGCCCTCAAGGATGGATCA 60.328 55.000 0.00 0.00 38.24 2.92
4718 5031 0.625683 ACAGGCCCTCAAGGATGGAT 60.626 55.000 0.00 0.00 38.24 3.41
4719 5032 0.846427 AACAGGCCCTCAAGGATGGA 60.846 55.000 0.00 0.00 38.24 3.41
4721 5034 0.329261 TGAACAGGCCCTCAAGGATG 59.671 55.000 0.00 0.00 38.24 3.51
4778 5091 9.807921 AGAAATTCCTGGAAATACTTACTCAAA 57.192 29.630 14.03 0.00 0.00 2.69
4826 5147 8.773033 ACTTATGGATTCTAAGAAATGGCAAT 57.227 30.769 0.00 0.00 31.89 3.56
4943 5264 9.574577 TGGACATGGATATAATTATTCTAGGGT 57.425 33.333 2.68 3.15 0.00 4.34
4983 5304 3.054802 AGAGTTTACCAGCCCATCAGAAG 60.055 47.826 0.00 0.00 0.00 2.85
5037 5358 1.985159 TGTTGGGCCTCTGTAATCACT 59.015 47.619 4.53 0.00 0.00 3.41
5045 5366 2.352805 GGGACTGTTGGGCCTCTG 59.647 66.667 4.53 4.92 44.42 3.35
5224 5547 1.581934 CTCTGGAAACGTGCTGACAA 58.418 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.