Multiple sequence alignment - TraesCS7B01G150700

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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 TraesCS7B01G150700 chr7B 100.000 3352 0 0 1 3352 199857720 199854369 0.000000e+00 6191.0
1 TraesCS7B01G150700 chr7B 100.000 35 0 0 1978 2012 577372462 577372428 7.760000e-07 65.8
2 TraesCS7B01G150700 chr7D 92.624 2820 108 36 43 2791 228987832 228985042 0.000000e+00 3964.0
3 TraesCS7B01G150700 chr7D 92.635 353 15 6 3004 3352 228984821 228984476 6.460000e-137 497.0
4 TraesCS7B01G150700 chr7D 100.000 35 0 0 1978 2012 535658825 535658791 7.760000e-07 65.8
5 TraesCS7B01G150700 chr7A 90.960 2832 120 41 43 2792 240958668 240955891 0.000000e+00 3687.0
6 TraesCS7B01G150700 chr7A 89.130 276 7 7 3099 3352 240955213 240954939 4.170000e-84 322.0
7 TraesCS7B01G150700 chr7A 97.143 35 1 0 1978 2012 617949478 617949512 3.610000e-05 60.2
8 TraesCS7B01G150700 chr5B 83.590 195 26 2 1906 2097 462883340 462883149 9.560000e-41 178.0
9 TraesCS7B01G150700 chr5D 80.465 215 36 2 1886 2097 385604671 385604460 3.460000e-35 159.0
10 TraesCS7B01G150700 chr5A 80.465 215 36 3 1886 2097 487365619 487365408 3.460000e-35 159.0


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 TraesCS7B01G150700 chr7B 199854369 199857720 3351 True 6191.0 6191 100.0000 1 3352 1 chr7B.!!$R1 3351
1 TraesCS7B01G150700 chr7D 228984476 228987832 3356 True 2230.5 3964 92.6295 43 3352 2 chr7D.!!$R2 3309
2 TraesCS7B01G150700 chr7A 240954939 240958668 3729 True 2004.5 3687 90.0450 43 3352 2 chr7A.!!$R1 3309

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
40 41 0.179018 AAAGATGACCCGGCCTATGC 60.179 55.0 0.00 0.0 0.00 3.14 F
228 239 0.674895 GCCGGAGCATCAAGTCAAGT 60.675 55.0 5.05 0.0 39.53 3.16 F
1266 1341 1.038130 CCACGTCGGAGAAGGAGGAT 61.038 60.0 0.00 0.0 41.22 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1720 0.180406 AGTTCAACAGAACGGGCAGT 59.820 50.0 3.04 0.00 44.89 4.40 R
1753 1835 0.393808 TGCCCGGGATTTCAGCTAAC 60.394 55.0 29.31 1.17 0.00 2.34 R
2457 2565 0.034059 AAGAGGCCAACAGACAGACG 59.966 55.0 5.01 0.00 0.00 4.18 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
32 33 4.742438 TTTCGAAAAGAAAGATGACCCG 57.258 40.909 8.44 0.00 43.35 5.28
33 34 2.695359 TCGAAAAGAAAGATGACCCGG 58.305 47.619 0.00 0.00 0.00 5.73
34 35 1.130561 CGAAAAGAAAGATGACCCGGC 59.869 52.381 0.00 0.00 0.00 6.13
35 36 1.472878 GAAAAGAAAGATGACCCGGCC 59.527 52.381 0.00 0.00 0.00 6.13
36 37 0.698818 AAAGAAAGATGACCCGGCCT 59.301 50.000 0.00 0.00 0.00 5.19
37 38 1.580059 AAGAAAGATGACCCGGCCTA 58.420 50.000 0.00 0.00 0.00 3.93
38 39 1.807814 AGAAAGATGACCCGGCCTAT 58.192 50.000 0.00 0.00 0.00 2.57
39 40 1.417890 AGAAAGATGACCCGGCCTATG 59.582 52.381 0.00 0.00 0.00 2.23
40 41 0.179018 AAAGATGACCCGGCCTATGC 60.179 55.000 0.00 0.00 0.00 3.14
41 42 1.344953 AAGATGACCCGGCCTATGCA 61.345 55.000 0.00 0.00 40.13 3.96
106 107 1.311859 CACACACAGTGCAAGGTCAT 58.688 50.000 0.00 0.00 42.15 3.06
114 115 3.257393 CAGTGCAAGGTCATCTCAGTAC 58.743 50.000 0.00 0.00 0.00 2.73
119 120 3.447586 GCAAGGTCATCTCAGTACCAGTA 59.552 47.826 0.00 0.00 35.64 2.74
121 122 3.280295 AGGTCATCTCAGTACCAGTACG 58.720 50.000 2.43 0.00 40.80 3.67
224 235 2.109126 GTGGCCGGAGCATCAAGTC 61.109 63.158 5.05 0.00 42.56 3.01
225 236 2.268920 GGCCGGAGCATCAAGTCA 59.731 61.111 5.05 0.00 42.56 3.41
226 237 1.377202 GGCCGGAGCATCAAGTCAA 60.377 57.895 5.05 0.00 42.56 3.18
227 238 1.372087 GGCCGGAGCATCAAGTCAAG 61.372 60.000 5.05 0.00 42.56 3.02
228 239 0.674895 GCCGGAGCATCAAGTCAAGT 60.675 55.000 5.05 0.00 39.53 3.16
232 243 4.693283 CCGGAGCATCAAGTCAAGTATAA 58.307 43.478 0.00 0.00 36.25 0.98
244 255 5.183228 AGTCAAGTATAACATCAAACCGGG 58.817 41.667 6.32 0.00 0.00 5.73
247 258 3.275999 AGTATAACATCAAACCGGGCAC 58.724 45.455 6.32 0.00 0.00 5.01
278 289 3.007940 TGATTGTGAATCGGACCACTTCT 59.992 43.478 11.86 0.32 40.84 2.85
353 364 2.503061 CCATCCAGAGACCCTGCG 59.497 66.667 0.00 0.00 41.57 5.18
356 367 3.991924 ATCCAGAGACCCTGCGGCT 62.992 63.158 0.00 0.00 41.57 5.52
497 530 4.735132 CCCACACGTGCGATCCGT 62.735 66.667 17.22 0.00 39.52 4.69
558 595 6.601613 CCGTATACTTACCCCGTATACCATAA 59.398 42.308 12.23 0.00 43.16 1.90
567 604 4.084287 CCCGTATACCATAAGCTCTACCA 58.916 47.826 0.00 0.00 0.00 3.25
592 630 2.217847 CACGTACAGCAATACCGTATGC 59.782 50.000 0.00 0.00 42.87 3.14
1128 1203 1.670083 CCCCAACGGGTTCTTCGTC 60.670 63.158 0.00 0.00 45.50 4.20
1173 1248 4.722535 AGGGAGGAGCTGCGGGAA 62.723 66.667 0.00 0.00 0.00 3.97
1266 1341 1.038130 CCACGTCGGAGAAGGAGGAT 61.038 60.000 0.00 0.00 41.22 3.24
1393 1468 4.538089 AGTAAGCTTTCTTCTTCCCCATCT 59.462 41.667 3.20 0.00 33.85 2.90
1394 1469 3.643199 AGCTTTCTTCTTCCCCATCTC 57.357 47.619 0.00 0.00 0.00 2.75
1396 1471 2.911484 CTTTCTTCTTCCCCATCTCCG 58.089 52.381 0.00 0.00 0.00 4.63
1421 1499 8.745837 CGTGCTCCTTGCTTTATTAATTAATTG 58.254 33.333 15.64 8.19 43.37 2.32
1426 1504 6.983890 CCTTGCTTTATTAATTAATTGCCGGT 59.016 34.615 15.64 0.00 0.00 5.28
1428 1506 6.868622 TGCTTTATTAATTAATTGCCGGTGT 58.131 32.000 15.64 0.00 0.00 4.16
1429 1507 7.324178 TGCTTTATTAATTAATTGCCGGTGTT 58.676 30.769 15.64 0.00 0.00 3.32
1430 1508 7.819900 TGCTTTATTAATTAATTGCCGGTGTTT 59.180 29.630 15.64 0.00 0.00 2.83
1469 1548 9.468532 TTGTATGATCTTGTTATGATCTCTTCG 57.531 33.333 0.00 0.00 40.51 3.79
1616 1696 3.570125 TCATTGGGCTCTAGTAGATCACG 59.430 47.826 0.00 0.00 0.00 4.35
1630 1710 2.428890 AGATCACGAAACTGGAGCTAGG 59.571 50.000 0.00 0.00 0.00 3.02
1634 1714 3.070446 TCACGAAACTGGAGCTAGGAAAA 59.930 43.478 0.00 0.00 0.00 2.29
1636 1716 3.071167 ACGAAACTGGAGCTAGGAAAACT 59.929 43.478 0.00 0.00 0.00 2.66
1637 1717 4.282703 ACGAAACTGGAGCTAGGAAAACTA 59.717 41.667 0.00 0.00 0.00 2.24
1753 1835 7.093988 TGGATGGATTTAATTTGGTGTGTGTAG 60.094 37.037 0.00 0.00 0.00 2.74
1783 1865 1.149174 CCCGGGCATGTGAATAGCT 59.851 57.895 8.08 0.00 0.00 3.32
1822 1907 3.194116 ACAGGCCAAATACTCTGCAAATG 59.806 43.478 5.01 0.00 0.00 2.32
1823 1908 2.167075 AGGCCAAATACTCTGCAAATGC 59.833 45.455 5.01 0.00 42.50 3.56
1866 1959 1.737793 GCCCTGAACATTAACTGACCG 59.262 52.381 0.00 0.00 0.00 4.79
1879 1972 6.721571 TTAACTGACCGAGATGAATGAAAC 57.278 37.500 0.00 0.00 0.00 2.78
2066 2159 3.233980 AGCTCGCTGGTCACCACA 61.234 61.111 0.00 0.00 0.00 4.17
2272 2371 3.525537 CAAGCGTCATGAGTAGGAACAT 58.474 45.455 0.00 0.00 0.00 2.71
2273 2372 3.170791 AGCGTCATGAGTAGGAACATG 57.829 47.619 0.00 0.00 43.31 3.21
2282 2381 5.955961 TGAGTAGGAACATGATCAATCCA 57.044 39.130 21.06 9.48 34.30 3.41
2321 2420 3.776731 TCTCCAAGGTCATTCTCCCTA 57.223 47.619 0.00 0.00 0.00 3.53
2324 2423 3.969976 CTCCAAGGTCATTCTCCCTATCA 59.030 47.826 0.00 0.00 0.00 2.15
2368 2467 0.454600 TAGCTGAAACGTAGGCCGAG 59.545 55.000 0.00 0.00 40.70 4.63
2383 2482 0.739813 CCGAGTTTAGGTTGGCGAGG 60.740 60.000 0.00 0.00 0.00 4.63
2387 2495 0.605589 GTTTAGGTTGGCGAGGTGCT 60.606 55.000 0.00 0.00 45.43 4.40
2456 2564 8.406172 ACATTAATTTGTTGTGTTTGTCTGTC 57.594 30.769 0.00 0.00 0.00 3.51
2457 2565 7.491048 ACATTAATTTGTTGTGTTTGTCTGTCC 59.509 33.333 0.00 0.00 0.00 4.02
2458 2566 3.479505 TTTGTTGTGTTTGTCTGTCCG 57.520 42.857 0.00 0.00 0.00 4.79
2459 2567 2.102070 TGTTGTGTTTGTCTGTCCGT 57.898 45.000 0.00 0.00 0.00 4.69
2460 2568 2.004017 TGTTGTGTTTGTCTGTCCGTC 58.996 47.619 0.00 0.00 0.00 4.79
2490 2598 2.026822 GGCCTCTTCTTGAATCACCTGA 60.027 50.000 0.00 0.00 0.00 3.86
2574 2686 5.794894 AGTTCTTAACCATGTTCTCATCGT 58.205 37.500 0.00 0.00 31.15 3.73
2603 2715 6.363065 AGGATAATGATGTTGAGCTGATGTT 58.637 36.000 0.00 0.00 0.00 2.71
2751 2868 1.227002 CGACTCGCTTTAGGCCTCC 60.227 63.158 9.68 0.00 37.74 4.30
2783 2900 4.278975 GCTACCATTAGCCAGCTAATCT 57.721 45.455 19.51 11.53 44.61 2.40
2784 2901 5.407407 GCTACCATTAGCCAGCTAATCTA 57.593 43.478 19.51 11.96 44.61 1.98
2785 2902 5.794894 GCTACCATTAGCCAGCTAATCTAA 58.205 41.667 19.51 8.72 44.61 2.10
2786 2903 6.231211 GCTACCATTAGCCAGCTAATCTAAA 58.769 40.000 19.51 7.28 44.61 1.85
2787 2904 6.710744 GCTACCATTAGCCAGCTAATCTAAAA 59.289 38.462 19.51 5.86 44.61 1.52
2788 2905 7.095017 GCTACCATTAGCCAGCTAATCTAAAAG 60.095 40.741 19.51 13.78 44.61 2.27
2789 2906 5.532779 ACCATTAGCCAGCTAATCTAAAAGC 59.467 40.000 19.51 0.00 44.61 3.51
2791 2908 6.264067 CCATTAGCCAGCTAATCTAAAAGCTT 59.736 38.462 19.51 0.00 46.82 3.74
2792 2909 7.201857 CCATTAGCCAGCTAATCTAAAAGCTTT 60.202 37.037 19.51 5.69 46.82 3.51
2793 2910 7.703058 TTAGCCAGCTAATCTAAAAGCTTTT 57.297 32.000 26.50 26.50 46.82 2.27
2794 2911 6.596309 AGCCAGCTAATCTAAAAGCTTTTT 57.404 33.333 28.21 13.68 46.82 1.94
2833 2950 2.695359 TCTAAAAGCTTAGCACACGGG 58.305 47.619 7.07 0.00 35.42 5.28
2874 2993 3.797039 TCAGAGGTGGCATAATCTTTCG 58.203 45.455 0.00 0.00 0.00 3.46
2879 2998 2.288666 GTGGCATAATCTTTCGCTCCA 58.711 47.619 0.00 0.00 0.00 3.86
2880 2999 2.880890 GTGGCATAATCTTTCGCTCCAT 59.119 45.455 0.00 0.00 0.00 3.41
2881 3000 2.880268 TGGCATAATCTTTCGCTCCATG 59.120 45.455 0.00 0.00 0.00 3.66
2882 3001 2.227388 GGCATAATCTTTCGCTCCATGG 59.773 50.000 4.97 4.97 0.00 3.66
2884 3003 3.058639 GCATAATCTTTCGCTCCATGGAC 60.059 47.826 11.44 7.30 0.00 4.02
2886 3005 0.179073 ATCTTTCGCTCCATGGACGG 60.179 55.000 26.01 15.82 0.00 4.79
2887 3006 2.435938 TTTCGCTCCATGGACGGC 60.436 61.111 26.01 21.09 0.00 5.68
2888 3007 3.247056 TTTCGCTCCATGGACGGCA 62.247 57.895 26.01 15.93 0.00 5.69
2889 3008 3.664025 TTCGCTCCATGGACGGCAG 62.664 63.158 26.01 18.06 0.00 4.85
2891 3010 2.268920 GCTCCATGGACGGCAGAA 59.731 61.111 18.58 0.00 0.00 3.02
2914 3075 1.935873 GCAAACGCTCTGCAGATCATA 59.064 47.619 18.63 0.00 39.69 2.15
2916 3077 3.003068 GCAAACGCTCTGCAGATCATATT 59.997 43.478 18.63 4.93 39.69 1.28
2919 3080 1.126296 CGCTCTGCAGATCATATTGCG 59.874 52.381 23.77 23.77 43.13 4.85
2921 3082 1.126296 CTCTGCAGATCATATTGCGCG 59.874 52.381 18.63 0.00 43.13 6.86
2940 3101 2.877691 GCAACGGCTTCCATGGAC 59.122 61.111 15.91 3.47 36.96 4.02
2943 3104 2.890766 AACGGCTTCCATGGACGGT 61.891 57.895 22.71 16.25 0.00 4.83
2944 3105 1.546589 AACGGCTTCCATGGACGGTA 61.547 55.000 22.71 6.00 0.00 4.02
2946 3107 1.087771 CGGCTTCCATGGACGGTAAC 61.088 60.000 15.91 0.00 0.00 2.50
2947 3108 0.746923 GGCTTCCATGGACGGTAACC 60.747 60.000 15.91 5.37 0.00 2.85
2950 3111 2.081462 CTTCCATGGACGGTAACCAAC 58.919 52.381 15.91 0.00 40.93 3.77
2952 3113 1.700739 TCCATGGACGGTAACCAACTT 59.299 47.619 11.44 0.00 40.93 2.66
2956 3117 4.081531 CCATGGACGGTAACCAACTTACTA 60.082 45.833 5.56 0.00 40.93 1.82
2966 3159 8.299570 CGGTAACCAACTTACTACTAGAAAGAA 58.700 37.037 0.00 0.00 35.84 2.52
2967 3160 9.416794 GGTAACCAACTTACTACTAGAAAGAAC 57.583 37.037 0.00 0.00 35.84 3.01
2973 3166 8.697960 CAACTTACTACTAGAAAGAACGGAAAC 58.302 37.037 0.00 0.00 0.00 2.78
2987 3180 2.682155 GGAAACCGAGAAGCTCAGAT 57.318 50.000 0.00 0.00 0.00 2.90
2988 3181 2.545731 GGAAACCGAGAAGCTCAGATC 58.454 52.381 0.00 0.00 0.00 2.75
3045 3265 2.478890 GGAGAGAACCGCGATCCGA 61.479 63.158 8.23 0.00 40.02 4.55
3046 3266 1.432251 GAGAGAACCGCGATCCGAA 59.568 57.895 8.23 0.00 40.02 4.30
3047 3267 0.866483 GAGAGAACCGCGATCCGAAC 60.866 60.000 8.23 0.00 40.02 3.95
3048 3268 1.139095 GAGAACCGCGATCCGAACT 59.861 57.895 8.23 0.00 40.02 3.01
3049 3269 0.379669 GAGAACCGCGATCCGAACTA 59.620 55.000 8.23 0.00 40.02 2.24
3052 3272 0.381089 AACCGCGATCCGAACTAGAG 59.619 55.000 8.23 0.00 40.02 2.43
3070 3290 2.117051 GAGTAGTTAACCTGGGGAGGG 58.883 57.143 0.88 0.00 0.00 4.30
3107 3665 2.484889 GCGGATCACACCTTAATCTCC 58.515 52.381 0.00 0.00 0.00 3.71
3109 3667 2.545952 CGGATCACACCTTAATCTCCCG 60.546 54.545 0.00 0.00 0.00 5.14
3220 3787 7.866898 TGTGATGATGATGTTGTTTAAGGTTTG 59.133 33.333 0.00 0.00 0.00 2.93
3238 3818 2.123982 GAAGGGGCAGGCAGATGG 60.124 66.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.506649 CCGGGTCATCTTTCTTTTCGAAAAA 60.507 40.000 22.67 9.34 40.87 1.94
10 11 4.023536 CCGGGTCATCTTTCTTTTCGAAAA 60.024 41.667 21.35 21.35 40.87 2.29
11 12 3.500680 CCGGGTCATCTTTCTTTTCGAAA 59.499 43.478 6.47 6.47 39.23 3.46
12 13 3.071479 CCGGGTCATCTTTCTTTTCGAA 58.929 45.455 0.00 0.00 0.00 3.71
13 14 2.695359 CCGGGTCATCTTTCTTTTCGA 58.305 47.619 0.00 0.00 0.00 3.71
14 15 1.130561 GCCGGGTCATCTTTCTTTTCG 59.869 52.381 2.18 0.00 0.00 3.46
15 16 1.472878 GGCCGGGTCATCTTTCTTTTC 59.527 52.381 2.18 0.00 0.00 2.29
16 17 1.075536 AGGCCGGGTCATCTTTCTTTT 59.924 47.619 2.18 0.00 0.00 2.27
17 18 0.698818 AGGCCGGGTCATCTTTCTTT 59.301 50.000 2.18 0.00 0.00 2.52
18 19 1.580059 TAGGCCGGGTCATCTTTCTT 58.420 50.000 2.18 0.00 0.00 2.52
19 20 1.417890 CATAGGCCGGGTCATCTTTCT 59.582 52.381 2.18 0.00 0.00 2.52
20 21 1.884235 CATAGGCCGGGTCATCTTTC 58.116 55.000 2.18 0.00 0.00 2.62
21 22 0.179018 GCATAGGCCGGGTCATCTTT 60.179 55.000 2.18 0.00 0.00 2.52
22 23 1.344953 TGCATAGGCCGGGTCATCTT 61.345 55.000 2.18 0.00 40.13 2.40
23 24 1.130054 ATGCATAGGCCGGGTCATCT 61.130 55.000 2.18 0.00 40.13 2.90
24 25 0.957395 CATGCATAGGCCGGGTCATC 60.957 60.000 2.18 0.00 40.13 2.92
25 26 1.073722 CATGCATAGGCCGGGTCAT 59.926 57.895 2.18 0.00 40.13 3.06
26 27 2.510411 CATGCATAGGCCGGGTCA 59.490 61.111 2.18 0.00 40.13 4.02
27 28 2.281761 CCATGCATAGGCCGGGTC 60.282 66.667 2.18 0.00 40.13 4.46
28 29 3.096495 ACCATGCATAGGCCGGGT 61.096 61.111 2.18 6.26 39.69 5.28
29 30 2.281761 GACCATGCATAGGCCGGG 60.282 66.667 2.18 7.28 40.13 5.73
30 31 1.152984 TTGACCATGCATAGGCCGG 60.153 57.895 13.19 0.00 40.13 6.13
31 32 1.168407 CCTTGACCATGCATAGGCCG 61.168 60.000 13.19 0.00 40.13 6.13
32 33 0.106519 ACCTTGACCATGCATAGGCC 60.107 55.000 11.65 0.00 40.13 5.19
33 34 2.638480 TACCTTGACCATGCATAGGC 57.362 50.000 11.65 1.29 41.68 3.93
34 35 6.016276 GGTTAATTACCTTGACCATGCATAGG 60.016 42.308 10.38 10.38 41.90 2.57
35 36 6.545666 TGGTTAATTACCTTGACCATGCATAG 59.454 38.462 0.00 0.00 45.72 2.23
36 37 6.427441 TGGTTAATTACCTTGACCATGCATA 58.573 36.000 0.00 0.00 45.72 3.14
37 38 5.268387 TGGTTAATTACCTTGACCATGCAT 58.732 37.500 0.00 0.00 45.72 3.96
38 39 4.667573 TGGTTAATTACCTTGACCATGCA 58.332 39.130 2.43 0.00 45.72 3.96
72 73 2.197605 TGTGCTGTGCATGCTGCTT 61.198 52.632 20.33 0.00 45.31 3.91
88 89 1.141657 AGATGACCTTGCACTGTGTGT 59.858 47.619 9.86 2.19 35.75 3.72
106 107 1.816835 CAAGGCGTACTGGTACTGAGA 59.183 52.381 8.89 0.00 34.04 3.27
114 115 1.600023 TTTGGTTCAAGGCGTACTGG 58.400 50.000 0.00 0.00 0.00 4.00
119 120 1.039856 AGCATTTTGGTTCAAGGCGT 58.960 45.000 0.00 0.00 0.00 5.68
121 122 2.407090 GACAGCATTTTGGTTCAAGGC 58.593 47.619 0.00 0.00 0.00 4.35
224 235 3.692101 TGCCCGGTTTGATGTTATACTTG 59.308 43.478 0.00 0.00 0.00 3.16
225 236 3.692593 GTGCCCGGTTTGATGTTATACTT 59.307 43.478 0.00 0.00 0.00 2.24
226 237 3.275999 GTGCCCGGTTTGATGTTATACT 58.724 45.455 0.00 0.00 0.00 2.12
227 238 2.356695 GGTGCCCGGTTTGATGTTATAC 59.643 50.000 0.00 0.00 0.00 1.47
228 239 2.240160 AGGTGCCCGGTTTGATGTTATA 59.760 45.455 0.00 0.00 0.00 0.98
232 243 0.893727 GAAGGTGCCCGGTTTGATGT 60.894 55.000 0.00 0.00 0.00 3.06
244 255 4.909200 GATTCACAATCAAGCAGAAGGTGC 60.909 45.833 7.99 0.00 44.04 5.01
247 258 3.181503 CCGATTCACAATCAAGCAGAAGG 60.182 47.826 0.00 0.00 37.78 3.46
278 289 2.191908 CCCCGGCATCGATCCAAA 59.808 61.111 0.00 0.00 39.00 3.28
353 364 0.038310 AAACCCAGGTTCAGCTAGCC 59.962 55.000 12.13 0.00 37.35 3.93
356 367 0.404040 CCCAAACCCAGGTTCAGCTA 59.596 55.000 1.78 0.00 37.35 3.32
493 526 2.283529 GCTTGGTCTCCTGGACGGA 61.284 63.158 0.00 0.00 45.35 4.69
495 528 2.266055 GGCTTGGTCTCCTGGACG 59.734 66.667 0.00 0.00 45.35 4.79
497 530 2.822643 ATCCGGCTTGGTCTCCTGGA 62.823 60.000 0.00 0.00 39.52 3.86
558 595 3.253677 GCTGTACGTGATATGGTAGAGCT 59.746 47.826 14.85 0.00 46.56 4.09
567 604 4.579454 ACGGTATTGCTGTACGTGATAT 57.421 40.909 0.00 0.00 36.32 1.63
592 630 4.785453 GGCGGGCTGACCTGAAGG 62.785 72.222 0.00 0.00 46.41 3.46
908 979 2.278857 CGTCCGCCGAGAGATTGG 60.279 66.667 0.00 0.00 39.56 3.16
1124 1199 2.590645 CCTCCTCCTCCTCGACGA 59.409 66.667 0.00 0.00 0.00 4.20
1128 1203 3.430497 TCCCCCTCCTCCTCCTCG 61.430 72.222 0.00 0.00 0.00 4.63
1173 1248 2.196925 CGATAGCGCCTCCTCCAGT 61.197 63.158 2.29 0.00 0.00 4.00
1266 1341 1.700368 CACCTCCTCCTCCTCTCCA 59.300 63.158 0.00 0.00 0.00 3.86
1430 1508 9.906660 ACAAGATCATACAAATTTAGCGAAAAA 57.093 25.926 0.00 0.00 0.00 1.94
1616 1696 5.795972 ACTAGTTTTCCTAGCTCCAGTTTC 58.204 41.667 0.00 0.00 46.10 2.78
1630 1710 3.678548 CAGAACGGGCAGTACTAGTTTTC 59.321 47.826 0.00 0.00 0.00 2.29
1634 1714 1.920610 ACAGAACGGGCAGTACTAGT 58.079 50.000 0.00 0.00 0.00 2.57
1636 1716 2.241160 TCAACAGAACGGGCAGTACTA 58.759 47.619 0.00 0.00 0.00 1.82
1637 1717 1.045407 TCAACAGAACGGGCAGTACT 58.955 50.000 0.00 0.00 0.00 2.73
1638 1718 1.529865 GTTCAACAGAACGGGCAGTAC 59.470 52.381 0.00 0.00 33.10 2.73
1639 1719 1.414919 AGTTCAACAGAACGGGCAGTA 59.585 47.619 3.04 0.00 44.89 2.74
1640 1720 0.180406 AGTTCAACAGAACGGGCAGT 59.820 50.000 3.04 0.00 44.89 4.40
1753 1835 0.393808 TGCCCGGGATTTCAGCTAAC 60.394 55.000 29.31 1.17 0.00 2.34
1783 1865 2.553602 CCTGTTGTTGATGCACAGCTAA 59.446 45.455 0.00 0.00 0.00 3.09
1822 1907 3.886123 ACACTCCATGGGTACTAATTGC 58.114 45.455 13.02 0.00 0.00 3.56
1823 1908 5.393027 GCAAACACTCCATGGGTACTAATTG 60.393 44.000 13.02 10.00 0.00 2.32
1824 1909 4.705023 GCAAACACTCCATGGGTACTAATT 59.295 41.667 13.02 0.00 0.00 1.40
1825 1910 4.270008 GCAAACACTCCATGGGTACTAAT 58.730 43.478 13.02 0.00 0.00 1.73
1826 1911 3.560453 GGCAAACACTCCATGGGTACTAA 60.560 47.826 13.02 0.00 0.00 2.24
1866 1959 5.755375 TCCTGCGATTAGTTTCATTCATCTC 59.245 40.000 0.00 0.00 0.00 2.75
1879 1972 2.143419 AGGCCCCTCCTGCGATTAG 61.143 63.158 0.00 0.00 45.54 1.73
1964 2057 2.125147 TTGGCGATCTCCTTGGCG 60.125 61.111 2.88 0.00 36.58 5.69
2066 2159 2.365635 AGGAGTGGCGGCAGGTAT 60.366 61.111 13.91 0.00 0.00 2.73
2252 2351 3.195610 TCATGTTCCTACTCATGACGCTT 59.804 43.478 0.00 0.00 43.29 4.68
2272 2371 3.002791 GAGCTCGTGTTTGGATTGATCA 58.997 45.455 0.00 0.00 0.00 2.92
2273 2372 3.002791 TGAGCTCGTGTTTGGATTGATC 58.997 45.455 9.64 0.00 0.00 2.92
2282 2381 2.093973 AGATCGGAATGAGCTCGTGTTT 60.094 45.455 9.75 0.00 39.78 2.83
2368 2467 0.605589 AGCACCTCGCCAACCTAAAC 60.606 55.000 0.00 0.00 44.04 2.01
2383 2482 0.390340 TACAGTAGCAGCAGCAGCAC 60.390 55.000 12.92 8.21 45.49 4.40
2387 2495 4.670896 TGATTATACAGTAGCAGCAGCA 57.329 40.909 3.17 0.00 45.49 4.41
2456 2564 1.374758 GAGGCCAACAGACAGACGG 60.375 63.158 5.01 0.00 0.00 4.79
2457 2565 0.034059 AAGAGGCCAACAGACAGACG 59.966 55.000 5.01 0.00 0.00 4.18
2458 2566 1.346068 AGAAGAGGCCAACAGACAGAC 59.654 52.381 5.01 0.00 0.00 3.51
2459 2567 1.722034 AGAAGAGGCCAACAGACAGA 58.278 50.000 5.01 0.00 0.00 3.41
2460 2568 2.149578 CAAGAAGAGGCCAACAGACAG 58.850 52.381 5.01 0.00 0.00 3.51
2490 2598 5.047590 CCATTGCCATGTCATGCTATTGTAT 60.048 40.000 7.35 0.00 0.00 2.29
2574 2686 8.806429 TCAGCTCAACATCATTATCCTTTAAA 57.194 30.769 0.00 0.00 0.00 1.52
2603 2715 8.862325 ATTAAACCACTAATCTGTCATCAACA 57.138 30.769 0.00 0.00 36.18 3.33
2656 2768 0.610174 TTCTACCTGTCTGCTGCCAG 59.390 55.000 0.00 0.00 40.54 4.85
2799 2916 6.722092 AGCTTTTAGATTAGCTCCAGCGCA 62.722 45.833 11.47 0.00 44.05 6.09
2800 2917 4.294452 AGCTTTTAGATTAGCTCCAGCGC 61.294 47.826 0.00 0.00 44.05 5.92
2801 2918 3.462021 AGCTTTTAGATTAGCTCCAGCG 58.538 45.455 0.00 0.00 44.05 5.18
2802 2919 6.538189 CTAAGCTTTTAGATTAGCTCCAGC 57.462 41.667 3.20 0.00 46.53 4.85
2809 2926 5.006746 CCCGTGTGCTAAGCTTTTAGATTAG 59.993 44.000 3.20 7.22 44.58 1.73
2810 2927 4.873827 CCCGTGTGCTAAGCTTTTAGATTA 59.126 41.667 3.20 0.00 0.00 1.75
2811 2928 3.689649 CCCGTGTGCTAAGCTTTTAGATT 59.310 43.478 3.20 0.00 0.00 2.40
2852 2969 3.806521 CGAAAGATTATGCCACCTCTGAG 59.193 47.826 0.00 0.00 0.00 3.35
2868 2987 1.218047 CCGTCCATGGAGCGAAAGA 59.782 57.895 27.55 0.32 0.00 2.52
2874 2993 2.109126 GTTCTGCCGTCCATGGAGC 61.109 63.158 16.81 16.96 0.00 4.70
2879 2998 0.537143 TTTGCTGTTCTGCCGTCCAT 60.537 50.000 0.00 0.00 0.00 3.41
2880 2999 1.153066 TTTGCTGTTCTGCCGTCCA 60.153 52.632 0.00 0.00 0.00 4.02
2881 3000 1.282875 GTTTGCTGTTCTGCCGTCC 59.717 57.895 0.00 0.00 0.00 4.79
2882 3001 1.082756 CGTTTGCTGTTCTGCCGTC 60.083 57.895 0.00 0.00 0.00 4.79
2884 3003 2.427410 GCGTTTGCTGTTCTGCCG 60.427 61.111 0.00 0.00 38.39 5.69
2927 3088 1.087771 GTTACCGTCCATGGAAGCCG 61.088 60.000 18.20 16.05 0.00 5.52
2936 3097 4.151883 AGTAGTAAGTTGGTTACCGTCCA 58.848 43.478 0.00 0.00 41.96 4.02
2937 3098 4.790765 AGTAGTAAGTTGGTTACCGTCC 57.209 45.455 0.00 0.00 41.96 4.79
2939 3100 7.448469 TCTTTCTAGTAGTAAGTTGGTTACCGT 59.552 37.037 14.16 0.00 41.96 4.83
2940 3101 7.820648 TCTTTCTAGTAGTAAGTTGGTTACCG 58.179 38.462 14.16 0.00 41.96 4.02
2943 3104 8.299570 CCGTTCTTTCTAGTAGTAAGTTGGTTA 58.700 37.037 14.16 0.00 0.00 2.85
2944 3105 7.014615 TCCGTTCTTTCTAGTAGTAAGTTGGTT 59.985 37.037 14.16 0.00 0.00 3.67
2946 3107 6.917533 TCCGTTCTTTCTAGTAGTAAGTTGG 58.082 40.000 14.16 13.62 0.00 3.77
2947 3108 8.697960 GTTTCCGTTCTTTCTAGTAGTAAGTTG 58.302 37.037 14.16 7.18 0.00 3.16
2950 3111 6.525976 CGGTTTCCGTTCTTTCTAGTAGTAAG 59.474 42.308 9.63 9.63 42.73 2.34
2952 3113 5.942872 CGGTTTCCGTTCTTTCTAGTAGTA 58.057 41.667 0.00 0.00 42.73 1.82
2973 3166 2.794282 CGTCAAGATCTGAGCTTCTCGG 60.794 54.545 4.99 0.00 38.15 4.63
2984 3177 1.982395 TGGCGACCCGTCAAGATCT 60.982 57.895 0.00 0.00 38.94 2.75
2985 3178 1.810030 GTGGCGACCCGTCAAGATC 60.810 63.158 0.00 0.00 44.86 2.75
2986 3179 2.264794 GTGGCGACCCGTCAAGAT 59.735 61.111 0.00 0.00 44.86 2.40
2987 3180 4.351938 CGTGGCGACCCGTCAAGA 62.352 66.667 0.95 0.00 44.86 3.02
2988 3181 3.271706 TACGTGGCGACCCGTCAAG 62.272 63.158 0.00 5.45 44.86 3.02
3045 3265 5.813704 CCTCCCCAGGTTAACTACTCTAGTT 60.814 48.000 5.42 0.58 42.22 2.24
3046 3266 4.325974 CCTCCCCAGGTTAACTACTCTAGT 60.326 50.000 5.42 0.00 36.32 2.57
3047 3267 4.216708 CCTCCCCAGGTTAACTACTCTAG 58.783 52.174 5.42 0.00 34.60 2.43
3048 3268 3.052338 CCCTCCCCAGGTTAACTACTCTA 60.052 52.174 5.42 0.00 38.30 2.43
3049 3269 2.292984 CCCTCCCCAGGTTAACTACTCT 60.293 54.545 5.42 0.00 38.30 3.24
3052 3272 1.210538 CCCCTCCCCAGGTTAACTAC 58.789 60.000 5.42 0.00 38.30 2.73
3070 3290 0.521735 CGCCTGCTGTTTAGTTTCCC 59.478 55.000 0.00 0.00 0.00 3.97
3107 3665 5.859521 ACTACGAGCTATACTAATCACGG 57.140 43.478 0.00 0.00 0.00 4.94
3220 3787 2.123982 CATCTGCCTGCCCCTTCC 60.124 66.667 0.00 0.00 0.00 3.46
3238 3818 1.432270 CGCCCGAAGAAAGCTCATCC 61.432 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.