Multiple sequence alignment - TraesCS6A01G078300

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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 TraesCS6A01G078300 chr6A 100.000 3101 0 0 1 3101 48170460 48167360 0.000000e+00 5727.0
1 TraesCS6A01G078300 chr6D 88.530 2659 211 36 482 3101 36582622 36580019 0.000000e+00 3134.0
2 TraesCS6A01G078300 chr6D 86.345 498 54 12 2594 3084 126856338 126856828 5.890000e-147 531.0
3 TraesCS6A01G078300 chr6B 90.441 2312 135 46 1 2286 84850195 84847944 0.000000e+00 2966.0
4 TraesCS6A01G078300 chr7D 86.373 499 58 9 2593 3084 293186260 293185765 1.270000e-148 536.0
5 TraesCS6A01G078300 chr7D 87.879 66 4 3 101 164 112867933 112867870 1.190000e-09 75.0
6 TraesCS6A01G078300 chr3D 86.345 498 58 9 2594 3084 380470997 380471491 4.550000e-148 534.0
7 TraesCS6A01G078300 chr3D 86.373 499 57 10 2593 3084 446111012 446111506 4.550000e-148 534.0
8 TraesCS6A01G078300 chr3D 86.345 498 55 11 2594 3084 340901343 340901834 5.890000e-147 531.0
9 TraesCS6A01G078300 chr5D 86.318 497 57 9 2594 3084 502866603 502866112 5.890000e-147 531.0
10 TraesCS6A01G078300 chr5D 86.345 498 52 11 2594 3084 357388264 357387776 2.120000e-146 529.0
11 TraesCS6A01G078300 chr5B 85.323 511 68 7 2594 3098 497009360 497009869 3.540000e-144 521.0
12 TraesCS6A01G078300 chr3A 97.143 35 1 0 102 136 216198 216164 3.340000e-05 60.2


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 TraesCS6A01G078300 chr6A 48167360 48170460 3100 True 5727 5727 100.000 1 3101 1 chr6A.!!$R1 3100
1 TraesCS6A01G078300 chr6D 36580019 36582622 2603 True 3134 3134 88.530 482 3101 1 chr6D.!!$R1 2619
2 TraesCS6A01G078300 chr6B 84847944 84850195 2251 True 2966 2966 90.441 1 2286 1 chr6B.!!$R1 2285
3 TraesCS6A01G078300 chr5B 497009360 497009869 509 False 521 521 85.323 2594 3098 1 chr5B.!!$F1 504

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
951 973 0.030235 TCAACTGGTCACTCGACACG 59.97 55.0 0.0 0.0 44.54 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2441 2490 0.036952 CGGAGCCGGCATGAATCTAT 60.037 55.0 31.54 3.33 35.56 1.98 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
25 26 0.539986 CTGGGTGCCCGTATGTTACT 59.460 55.000 2.44 0.00 39.42 2.24
98 99 3.804036 TGTCTCCGACACATGAGTTTTT 58.196 40.909 0.00 0.00 37.67 1.94
104 105 4.036262 TCCGACACATGAGTTTTTGGAAAG 59.964 41.667 0.00 0.00 0.00 2.62
107 108 5.520376 ACACATGAGTTTTTGGAAAGAGG 57.480 39.130 0.00 0.00 0.00 3.69
146 147 3.753294 ATATTTAGGGCTGAGGTGACG 57.247 47.619 0.00 0.00 0.00 4.35
246 247 4.074970 GGATGGGTTCCATATGCTAAGTG 58.925 47.826 0.00 0.00 45.26 3.16
259 260 3.090037 TGCTAAGTGACTAGAGGGACAC 58.910 50.000 0.00 0.00 0.00 3.67
260 261 3.090037 GCTAAGTGACTAGAGGGACACA 58.910 50.000 0.00 0.00 35.97 3.72
279 280 1.086067 ATCGGCTTGAGACATGCACG 61.086 55.000 10.71 10.93 36.45 5.34
295 296 7.658982 AGACATGCACGTCATATTTCTCATTAT 59.341 33.333 16.21 0.00 38.43 1.28
296 297 8.831715 ACATGCACGTCATATTTCTCATTATA 57.168 30.769 0.00 0.00 33.19 0.98
297 298 8.712363 ACATGCACGTCATATTTCTCATTATAC 58.288 33.333 0.00 0.00 33.19 1.47
299 300 6.128929 TGCACGTCATATTTCTCATTATACGC 60.129 38.462 0.00 0.00 0.00 4.42
300 301 6.450276 CACGTCATATTTCTCATTATACGCG 58.550 40.000 3.53 3.53 0.00 6.01
301 302 6.304683 CACGTCATATTTCTCATTATACGCGA 59.695 38.462 15.93 0.00 0.00 5.87
302 303 6.304922 ACGTCATATTTCTCATTATACGCGAC 59.695 38.462 15.93 0.00 0.00 5.19
320 321 4.569162 CGCGACTAATGGAAGGAATTTGTA 59.431 41.667 0.00 0.00 0.00 2.41
437 439 8.801882 ATATTTGTGTAATTTCCTCTTTCGGA 57.198 30.769 0.00 0.00 0.00 4.55
617 638 3.941483 AGTAGAATTCCCGACAGCATTTG 59.059 43.478 0.65 0.00 0.00 2.32
662 684 4.202010 GCAGACAGCTTGACCAAGTAAAAA 60.202 41.667 10.96 0.00 40.45 1.94
852 874 3.753294 TCAAATCGATTCTAGGGCTCC 57.247 47.619 11.83 0.00 0.00 4.70
855 877 1.343069 ATCGATTCTAGGGCTCCACC 58.657 55.000 0.00 0.00 37.93 4.61
857 879 0.676736 CGATTCTAGGGCTCCACCTC 59.323 60.000 0.00 0.00 42.09 3.85
860 882 0.343372 TTCTAGGGCTCCACCTCCAT 59.657 55.000 0.00 0.00 42.09 3.41
861 883 0.343372 TCTAGGGCTCCACCTCCATT 59.657 55.000 0.00 0.00 42.09 3.16
862 884 1.578703 TCTAGGGCTCCACCTCCATTA 59.421 52.381 0.00 0.00 42.09 1.90
863 885 2.182312 TCTAGGGCTCCACCTCCATTAT 59.818 50.000 0.00 0.00 42.09 1.28
864 886 2.815357 AGGGCTCCACCTCCATTATA 57.185 50.000 0.00 0.00 35.43 0.98
868 890 2.028930 GGCTCCACCTCCATTATAGACG 60.029 54.545 0.00 0.00 34.51 4.18
895 917 9.558396 ACTATATATACGCTTCTCCACTATACC 57.442 37.037 0.00 0.00 0.00 2.73
914 936 1.552792 CCCTTCTCACCAGTTCTCTCC 59.447 57.143 0.00 0.00 0.00 3.71
915 937 2.534990 CCTTCTCACCAGTTCTCTCCT 58.465 52.381 0.00 0.00 0.00 3.69
916 938 2.495669 CCTTCTCACCAGTTCTCTCCTC 59.504 54.545 0.00 0.00 0.00 3.71
917 939 2.980246 TCTCACCAGTTCTCTCCTCA 57.020 50.000 0.00 0.00 0.00 3.86
918 940 2.801483 TCTCACCAGTTCTCTCCTCAG 58.199 52.381 0.00 0.00 0.00 3.35
919 941 2.109128 TCTCACCAGTTCTCTCCTCAGT 59.891 50.000 0.00 0.00 0.00 3.41
920 942 2.491693 CTCACCAGTTCTCTCCTCAGTC 59.508 54.545 0.00 0.00 0.00 3.51
948 970 1.071605 GCATCAACTGGTCACTCGAC 58.928 55.000 0.00 0.00 41.80 4.20
951 973 0.030235 TCAACTGGTCACTCGACACG 59.970 55.000 0.00 0.00 44.54 4.49
995 1017 4.671377 GCTGCATCGGTGATTAAATTTGA 58.329 39.130 0.00 0.00 0.00 2.69
1116 1138 1.300465 CATGATGCCTCGGAGGTCG 60.300 63.158 24.30 0.61 37.80 4.79
1169 1191 4.201970 GGACGACGAGAATGAGAAATCTCT 60.202 45.833 11.45 0.00 43.25 3.10
1218 1240 2.093658 TCATCTGGTTAAGAAGGTCCGC 60.094 50.000 0.00 0.00 38.79 5.54
1247 1278 1.940758 ATGAAATTCATGCGCGCGC 60.941 52.632 45.02 45.02 35.43 6.86
1262 1293 2.123428 GCGCATGAGATGGGGCTTT 61.123 57.895 0.30 0.00 42.79 3.51
1268 1299 0.627451 TGAGATGGGGCTTTGCTGAT 59.373 50.000 0.00 0.00 0.00 2.90
1315 1346 0.317479 CGAGTTCTTGGGGACGTTCT 59.683 55.000 0.00 0.00 0.00 3.01
1428 1459 3.188786 GTGCTCGTGATCGTGGCC 61.189 66.667 0.00 0.00 36.65 5.36
1540 1571 0.240145 CTACGTGTCCGCTCAGTTCA 59.760 55.000 0.00 0.00 37.70 3.18
1552 1583 4.015406 AGTTCATGGGCGCCGTCA 62.015 61.111 22.54 14.78 0.00 4.35
1702 1733 1.227350 CTCTTCGCCATCATCGCCA 60.227 57.895 0.00 0.00 0.00 5.69
1735 1766 1.270625 CCAAAGCAGTACGGAAGACCA 60.271 52.381 0.00 0.00 35.59 4.02
1776 1811 4.022416 GTCTCATTCACTCACTCACTCACT 60.022 45.833 0.00 0.00 0.00 3.41
1777 1812 4.217334 TCTCATTCACTCACTCACTCACTC 59.783 45.833 0.00 0.00 0.00 3.51
1778 1813 3.891366 TCATTCACTCACTCACTCACTCA 59.109 43.478 0.00 0.00 0.00 3.41
1779 1814 3.717400 TTCACTCACTCACTCACTCAC 57.283 47.619 0.00 0.00 0.00 3.51
1780 1815 2.937519 TCACTCACTCACTCACTCACT 58.062 47.619 0.00 0.00 0.00 3.41
1781 1816 2.881513 TCACTCACTCACTCACTCACTC 59.118 50.000 0.00 0.00 0.00 3.51
1782 1817 2.620585 CACTCACTCACTCACTCACTCA 59.379 50.000 0.00 0.00 0.00 3.41
1783 1818 2.621055 ACTCACTCACTCACTCACTCAC 59.379 50.000 0.00 0.00 0.00 3.51
1789 1824 3.291584 TCACTCACTCACTCACTGACTT 58.708 45.455 0.00 0.00 0.00 3.01
1791 1826 4.276183 TCACTCACTCACTCACTGACTTAC 59.724 45.833 0.00 0.00 0.00 2.34
1839 1874 1.002544 GTGAAGGAGCTGGTAGCAGTT 59.997 52.381 22.21 17.23 45.56 3.16
1923 1970 9.500785 TTCTACAGTTGTTTTCATATGATCACA 57.499 29.630 6.17 9.55 0.00 3.58
1953 2000 6.822667 AATGTTTAGTTGTGATCATGCAGA 57.177 33.333 0.00 0.00 0.00 4.26
1959 2006 4.840271 AGTTGTGATCATGCAGAGAATCA 58.160 39.130 0.00 0.00 37.82 2.57
1998 2045 2.741092 GCGAGGACACTGGGAACA 59.259 61.111 0.00 0.00 39.59 3.18
2222 2271 5.906073 AGAAATTCTTTTGGGACACTGTTG 58.094 37.500 0.00 0.00 39.29 3.33
2272 2321 4.456911 AGGTGTTGCAATGTCATGACTAAG 59.543 41.667 25.55 15.59 0.00 2.18
2274 2323 3.819902 TGTTGCAATGTCATGACTAAGCA 59.180 39.130 25.55 25.29 32.98 3.91
2275 2324 4.277921 TGTTGCAATGTCATGACTAAGCAA 59.722 37.500 30.31 30.31 38.43 3.91
2310 2359 3.348119 TGCACACGGATTTGCCTAAATA 58.652 40.909 0.00 0.00 36.66 1.40
2317 2366 5.799936 CACGGATTTGCCTAAATACAGTTTG 59.200 40.000 0.00 0.00 37.01 2.93
2336 2385 8.844244 ACAGTTTGATCATCAAAATATAGCCTC 58.156 33.333 14.56 0.00 46.53 4.70
2345 2394 8.448008 TCATCAAAATATAGCCTCTATGGGTTT 58.552 33.333 0.00 0.00 45.67 3.27
2346 2395 8.517878 CATCAAAATATAGCCTCTATGGGTTTG 58.482 37.037 0.00 5.13 45.67 2.93
2372 2421 7.852945 GGATACACTAGCAATTCAAAATTCTCG 59.147 37.037 0.00 0.00 0.00 4.04
2388 2437 1.948145 TCTCGATCTAAGTCTTCCGGC 59.052 52.381 0.00 0.00 0.00 6.13
2389 2438 1.001158 CTCGATCTAAGTCTTCCGGCC 60.001 57.143 0.00 0.00 0.00 6.13
2391 2440 1.001158 CGATCTAAGTCTTCCGGCCTC 60.001 57.143 0.00 0.00 0.00 4.70
2405 2454 1.522580 GCCTCCGATGCTCCTCAAC 60.523 63.158 0.00 0.00 0.00 3.18
2415 2464 1.412710 TGCTCCTCAACTTCGTCTGTT 59.587 47.619 0.00 0.00 0.00 3.16
2420 2469 2.135933 CTCAACTTCGTCTGTTGGGTC 58.864 52.381 14.19 0.00 43.36 4.46
2422 2471 0.249741 AACTTCGTCTGTTGGGTCGG 60.250 55.000 0.00 0.00 0.00 4.79
2436 2485 0.745468 GGTCGGATTAGACGGAGCTT 59.255 55.000 0.00 0.00 41.81 3.74
2441 2490 1.404391 GGATTAGACGGAGCTTCGACA 59.596 52.381 24.16 0.00 0.00 4.35
2460 2509 0.036952 ATAGATTCATGCCGGCTCCG 60.037 55.000 29.70 15.91 39.44 4.63
2486 2536 2.540145 CGCAAGCTTAGGGTTTCGT 58.460 52.632 0.00 0.00 35.57 3.85
2490 2540 2.489971 CAAGCTTAGGGTTTCGTGTCA 58.510 47.619 0.00 0.00 0.00 3.58
2498 2548 1.135024 GGGTTTCGTGTCAGGCGTATA 60.135 52.381 0.00 0.00 0.00 1.47
2532 2582 5.934402 ATCGGTGTTAGGTTATTCAGACT 57.066 39.130 0.00 0.00 0.00 3.24
2545 2595 6.094186 GGTTATTCAGACTGATTCAAGGGTTC 59.906 42.308 5.87 0.00 0.00 3.62
2548 2598 5.407407 TCAGACTGATTCAAGGGTTCTAC 57.593 43.478 0.00 0.00 0.00 2.59
2571 2621 0.379669 GACGATTACGGCTTCGAGGA 59.620 55.000 0.00 0.00 45.04 3.71
2573 2623 0.381089 CGATTACGGCTTCGAGGAGT 59.619 55.000 0.00 0.00 37.55 3.85
2609 2659 1.466360 GCACTGAAATGACGTGGATGC 60.466 52.381 0.00 0.00 0.00 3.91
2680 2734 3.940209 TTAGGCTTGAACAAATGCAGG 57.060 42.857 0.00 0.00 0.00 4.85
2682 2736 2.318908 AGGCTTGAACAAATGCAGGAA 58.681 42.857 0.00 0.00 0.00 3.36
2787 2841 7.759489 AGATAAACAACCAAGTGATAGCAAA 57.241 32.000 0.00 0.00 0.00 3.68
2844 2898 9.555727 AAAGTAAGTGCATAAGTAAAGAGTTCA 57.444 29.630 0.00 0.00 0.00 3.18
2854 2908 9.575783 CATAAGTAAAGAGTTCAGGTAAGAGAC 57.424 37.037 0.00 0.00 0.00 3.36
2866 2920 1.000506 GTAAGAGACAACCGAGGCACA 59.999 52.381 0.00 0.00 0.00 4.57
2870 2924 1.227556 GACAACCGAGGCACACTGT 60.228 57.895 0.00 0.00 0.00 3.55
2902 2956 4.841813 TGTATCCTGAAGTTCACACCCTTA 59.158 41.667 0.08 0.00 0.00 2.69
2924 2980 4.465886 ACAGATGCTAATCTCCGTAGAGT 58.534 43.478 0.00 0.00 41.43 3.24
2946 3002 2.952714 GTGAAGGCACAATGCTCCT 58.047 52.632 0.13 0.00 44.28 3.69
2955 3011 2.613691 CACAATGCTCCTCAAAATGCC 58.386 47.619 0.00 0.00 0.00 4.40
2960 3016 2.715046 TGCTCCTCAAAATGCCACTAG 58.285 47.619 0.00 0.00 0.00 2.57
2972 3028 1.445942 CCACTAGGGCCACCGTATG 59.554 63.158 6.18 0.00 43.47 2.39
2977 3033 4.564110 GGGCCACCGTATGCTCCC 62.564 72.222 4.39 0.00 33.90 4.30
2980 3036 3.120086 GCCACCGTATGCTCCCCAT 62.120 63.158 0.00 0.00 37.97 4.00
3079 3136 2.397413 CTTGGGGCAGTCACCGAACT 62.397 60.000 0.00 0.00 0.00 3.01
3084 3141 0.038892 GGCAGTCACCGAACTCGTAA 60.039 55.000 0.00 0.00 37.74 3.18
3091 3148 5.005394 CAGTCACCGAACTCGTAAATATTGG 59.995 44.000 0.00 0.00 37.74 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 5.549742 ATTTGTGCAATTTCCTCTTTCCA 57.450 34.783 0.00 0.00 0.00 3.53
104 105 8.931385 ATATTGTGTATTTGTGCAATTTCCTC 57.069 30.769 0.00 0.00 34.05 3.71
146 147 7.660208 TGATTAGTTCTAGAGTTGTGGTTTTCC 59.340 37.037 0.00 0.00 41.14 3.13
246 247 0.386113 GCCGATGTGTCCCTCTAGTC 59.614 60.000 0.00 0.00 0.00 2.59
259 260 0.376152 GTGCATGTCTCAAGCCGATG 59.624 55.000 0.00 0.00 0.00 3.84
260 261 1.086067 CGTGCATGTCTCAAGCCGAT 61.086 55.000 0.00 0.00 28.96 4.18
279 280 7.798486 AGTCGCGTATAATGAGAAATATGAC 57.202 36.000 5.77 0.00 0.00 3.06
295 296 4.395959 AATTCCTTCCATTAGTCGCGTA 57.604 40.909 5.77 0.00 0.00 4.42
296 297 2.981859 ATTCCTTCCATTAGTCGCGT 57.018 45.000 5.77 0.00 0.00 6.01
297 298 3.374058 ACAAATTCCTTCCATTAGTCGCG 59.626 43.478 0.00 0.00 0.00 5.87
299 300 8.438676 AAGATACAAATTCCTTCCATTAGTCG 57.561 34.615 0.00 0.00 0.00 4.18
320 321 9.606631 CTCAAGGACTAATAAGCTACAAAAGAT 57.393 33.333 0.00 0.00 0.00 2.40
326 327 7.097192 CACAACTCAAGGACTAATAAGCTACA 58.903 38.462 0.00 0.00 0.00 2.74
368 369 8.680001 GGTAACGAATAATCACAAATTTAGGGT 58.320 33.333 0.00 0.00 0.00 4.34
370 371 9.931210 GAGGTAACGAATAATCACAAATTTAGG 57.069 33.333 0.00 0.00 46.39 2.69
385 386 4.772886 ATTAAGGGCTGAGGTAACGAAT 57.227 40.909 0.00 0.00 46.39 3.34
388 389 5.365619 ACAATATTAAGGGCTGAGGTAACG 58.634 41.667 0.00 0.00 46.39 3.18
499 507 0.798009 CCACATGCGAATGCCGTTTC 60.798 55.000 2.30 0.00 41.78 2.78
541 549 9.090103 TCCTTATTCGATATGTATCTTCTTGGT 57.910 33.333 0.00 0.00 0.00 3.67
617 638 2.856222 CTCCAGGCCACCAAGATAATC 58.144 52.381 5.01 0.00 0.00 1.75
662 684 0.976641 TGTCGCTGGTTCATTCTCCT 59.023 50.000 0.00 0.00 0.00 3.69
706 728 6.916440 TCATTGTCCAATCAGAAAACTGATG 58.084 36.000 12.44 7.67 42.63 3.07
707 729 7.232127 AGTTCATTGTCCAATCAGAAAACTGAT 59.768 33.333 6.87 6.87 45.06 2.90
772 794 4.043750 ACGTGTGATGCTTGTTCAAATTG 58.956 39.130 0.00 0.00 0.00 2.32
845 867 2.182312 TCTATAATGGAGGTGGAGCCCT 59.818 50.000 0.00 0.00 38.26 5.19
846 868 2.303311 GTCTATAATGGAGGTGGAGCCC 59.697 54.545 0.00 0.00 38.26 5.19
849 871 4.145807 AGTCGTCTATAATGGAGGTGGAG 58.854 47.826 0.00 0.00 0.00 3.86
850 872 4.180377 AGTCGTCTATAATGGAGGTGGA 57.820 45.455 0.00 0.00 0.00 4.02
861 883 9.689976 GGAGAAGCGTATATATAGTCGTCTATA 57.310 37.037 11.05 11.05 41.51 1.31
862 884 8.202811 TGGAGAAGCGTATATATAGTCGTCTAT 58.797 37.037 7.35 7.35 39.77 1.98
863 885 7.490725 GTGGAGAAGCGTATATATAGTCGTCTA 59.509 40.741 8.54 0.00 0.00 2.59
864 886 6.313411 GTGGAGAAGCGTATATATAGTCGTCT 59.687 42.308 8.39 8.39 0.00 4.18
895 917 2.495669 GAGGAGAGAACTGGTGAGAAGG 59.504 54.545 0.00 0.00 0.00 3.46
914 936 1.277273 TGATGCTTGGTGAGGACTGAG 59.723 52.381 0.00 0.00 0.00 3.35
915 937 1.351076 TGATGCTTGGTGAGGACTGA 58.649 50.000 0.00 0.00 0.00 3.41
916 938 1.808945 GTTGATGCTTGGTGAGGACTG 59.191 52.381 0.00 0.00 0.00 3.51
917 939 1.701847 AGTTGATGCTTGGTGAGGACT 59.298 47.619 0.00 0.00 0.00 3.85
918 940 1.808945 CAGTTGATGCTTGGTGAGGAC 59.191 52.381 0.00 0.00 0.00 3.85
919 941 1.271543 CCAGTTGATGCTTGGTGAGGA 60.272 52.381 0.00 0.00 0.00 3.71
920 942 1.171308 CCAGTTGATGCTTGGTGAGG 58.829 55.000 0.00 0.00 0.00 3.86
995 1017 0.105555 CCTGCTCTCCTCCATCCTCT 60.106 60.000 0.00 0.00 0.00 3.69
1097 1119 1.070445 GACCTCCGAGGCATCATGG 59.930 63.158 14.86 0.00 39.63 3.66
1116 1138 0.992802 GCACGATCTTCACCGAAGTC 59.007 55.000 3.81 1.33 40.24 3.01
1229 1251 1.940758 GCGCGCGCATGAATTTCAT 60.941 52.632 46.11 6.06 37.65 2.57
1244 1267 2.123428 AAAGCCCCATCTCATGCGC 61.123 57.895 0.00 0.00 0.00 6.09
1245 1268 1.731700 CAAAGCCCCATCTCATGCG 59.268 57.895 0.00 0.00 0.00 4.73
1247 1278 0.744874 CAGCAAAGCCCCATCTCATG 59.255 55.000 0.00 0.00 0.00 3.07
1262 1293 5.068855 TGACAAGAAACATCCAAAATCAGCA 59.931 36.000 0.00 0.00 0.00 4.41
1268 1299 3.703556 TGCCTGACAAGAAACATCCAAAA 59.296 39.130 0.00 0.00 0.00 2.44
1315 1346 0.038251 AGCACGATGAAGACGAGCAA 60.038 50.000 0.00 0.00 46.08 3.91
1412 1443 3.356639 GAGGCCACGATCACGAGCA 62.357 63.158 5.01 0.00 41.28 4.26
1414 1445 2.278206 CGAGGCCACGATCACGAG 60.278 66.667 18.51 0.00 42.66 4.18
1428 1459 1.797933 CGACACGTGGAAGAGCGAG 60.798 63.158 21.57 0.00 0.00 5.03
1702 1733 1.153168 CTTTGGGATCGGTGGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
1776 1811 4.023963 CAGTTCGAGTAAGTCAGTGAGTGA 60.024 45.833 0.00 0.00 0.00 3.41
1777 1812 4.222886 CAGTTCGAGTAAGTCAGTGAGTG 58.777 47.826 0.00 0.00 0.00 3.51
1778 1813 3.304794 GCAGTTCGAGTAAGTCAGTGAGT 60.305 47.826 0.00 0.00 0.00 3.41
1779 1814 3.238441 GCAGTTCGAGTAAGTCAGTGAG 58.762 50.000 0.00 0.00 0.00 3.51
1780 1815 2.030185 GGCAGTTCGAGTAAGTCAGTGA 60.030 50.000 0.00 0.00 0.00 3.41
1781 1816 2.288213 TGGCAGTTCGAGTAAGTCAGTG 60.288 50.000 0.00 0.00 0.00 3.66
1782 1817 1.961394 TGGCAGTTCGAGTAAGTCAGT 59.039 47.619 0.00 0.00 0.00 3.41
1783 1818 2.724977 TGGCAGTTCGAGTAAGTCAG 57.275 50.000 0.00 0.00 0.00 3.51
1789 1824 4.471904 AGATCATTTGGCAGTTCGAGTA 57.528 40.909 0.00 0.00 0.00 2.59
1791 1826 4.691860 AAAGATCATTTGGCAGTTCGAG 57.308 40.909 0.00 0.00 0.00 4.04
1953 2000 3.133542 TCATCGATGCTCCTGTTGATTCT 59.866 43.478 20.81 0.00 0.00 2.40
1959 2006 2.804572 CGGATTCATCGATGCTCCTGTT 60.805 50.000 28.95 10.15 31.28 3.16
2106 2153 2.038689 TCGAGGCTATGACGGTCTAGAT 59.961 50.000 9.88 0.00 0.00 1.98
2107 2154 1.415289 TCGAGGCTATGACGGTCTAGA 59.585 52.381 9.88 0.00 0.00 2.43
2201 2248 5.675684 ACAACAGTGTCCCAAAAGAATTT 57.324 34.783 0.00 0.00 33.41 1.82
2222 2271 3.004106 GCTTGCTCATATGTCATCCCAAC 59.996 47.826 1.90 0.00 0.00 3.77
2310 2359 8.757982 AGGCTATATTTTGATGATCAAACTGT 57.242 30.769 19.30 14.69 45.03 3.55
2317 2366 8.270744 ACCCATAGAGGCTATATTTTGATGATC 58.729 37.037 0.00 0.00 35.39 2.92
2330 2379 4.347000 GTGTATCCAAACCCATAGAGGCTA 59.653 45.833 0.00 0.00 35.39 3.93
2336 2385 5.290493 TGCTAGTGTATCCAAACCCATAG 57.710 43.478 0.00 0.00 0.00 2.23
2345 2394 8.579850 AGAATTTTGAATTGCTAGTGTATCCA 57.420 30.769 0.00 0.00 0.00 3.41
2346 2395 7.852945 CGAGAATTTTGAATTGCTAGTGTATCC 59.147 37.037 0.00 0.00 0.00 2.59
2372 2421 1.341852 GGAGGCCGGAAGACTTAGATC 59.658 57.143 5.05 0.00 0.00 2.75
2388 2437 0.539051 AAGTTGAGGAGCATCGGAGG 59.461 55.000 0.00 0.00 34.37 4.30
2389 2438 1.800655 CGAAGTTGAGGAGCATCGGAG 60.801 57.143 0.00 0.00 34.37 4.63
2391 2440 0.108615 ACGAAGTTGAGGAGCATCGG 60.109 55.000 0.00 0.00 37.78 4.18
2405 2454 0.246635 ATCCGACCCAACAGACGAAG 59.753 55.000 0.00 0.00 0.00 3.79
2415 2464 1.389609 GCTCCGTCTAATCCGACCCA 61.390 60.000 0.00 0.00 0.00 4.51
2420 2469 0.661552 TCGAAGCTCCGTCTAATCCG 59.338 55.000 0.00 0.00 0.00 4.18
2422 2471 2.846039 TGTCGAAGCTCCGTCTAATC 57.154 50.000 0.00 0.00 0.00 1.75
2441 2490 0.036952 CGGAGCCGGCATGAATCTAT 60.037 55.000 31.54 3.33 35.56 1.98
2485 2535 1.916000 GTTGTCGTATACGCCTGACAC 59.084 52.381 20.42 12.31 40.75 3.67
2486 2536 1.466192 CGTTGTCGTATACGCCTGACA 60.466 52.381 20.42 15.76 39.42 3.58
2490 2540 1.372582 TCTCGTTGTCGTATACGCCT 58.627 50.000 20.42 0.00 39.60 5.52
2498 2548 0.313043 ACACCGATTCTCGTTGTCGT 59.687 50.000 0.00 0.00 41.65 4.34
2518 2568 6.443849 ACCCTTGAATCAGTCTGAATAACCTA 59.556 38.462 6.64 0.00 0.00 3.08
2532 2582 2.901192 TCACCGTAGAACCCTTGAATCA 59.099 45.455 0.00 0.00 0.00 2.57
2545 2595 0.379669 AGCCGTAATCGTCACCGTAG 59.620 55.000 0.00 0.00 35.01 3.51
2548 2598 1.469126 CGAAGCCGTAATCGTCACCG 61.469 60.000 0.00 0.00 34.48 4.94
2559 2609 2.156051 GACCAACTCCTCGAAGCCGT 62.156 60.000 0.00 0.00 37.05 5.68
2560 2610 1.446272 GACCAACTCCTCGAAGCCG 60.446 63.158 0.00 0.00 37.07 5.52
2571 2621 0.919710 GCCCCTGATAAGGACCAACT 59.080 55.000 0.00 0.00 0.00 3.16
2573 2623 0.623723 GTGCCCCTGATAAGGACCAA 59.376 55.000 0.00 0.00 0.00 3.67
2584 2634 0.606401 ACGTCATTTCAGTGCCCCTG 60.606 55.000 0.00 0.00 42.97 4.45
2598 2648 3.071837 TAGGCGGCATCCACGTCA 61.072 61.111 13.08 0.00 38.63 4.35
2733 2787 5.064198 AGCATAAATTGTTGATGCACATTGC 59.936 36.000 13.08 0.00 46.78 3.56
2750 2804 8.116651 TGGTTGTTTATCTTGCTTAGCATAAA 57.883 30.769 8.05 7.54 38.76 1.40
2787 2841 5.107065 GCCTTCGCGCTTGAAGTTATATATT 60.107 40.000 19.41 0.00 43.06 1.28
2844 2898 0.896226 GCCTCGGTTGTCTCTTACCT 59.104 55.000 0.00 0.00 32.08 3.08
2854 2908 1.227527 TCACAGTGTGCCTCGGTTG 60.228 57.895 18.80 0.00 32.98 3.77
2866 2920 3.954258 TCAGGATACATCATCGTCACAGT 59.046 43.478 0.00 0.00 41.41 3.55
2870 2924 5.127031 TGAACTTCAGGATACATCATCGTCA 59.873 40.000 0.00 0.00 41.41 4.35
2902 2956 4.277174 CACTCTACGGAGATTAGCATCTGT 59.723 45.833 0.00 0.00 40.14 3.41
2955 3011 1.227556 GCATACGGTGGCCCTAGTG 60.228 63.158 0.00 0.00 0.00 2.74
2960 3016 4.564110 GGGAGCATACGGTGGCCC 62.564 72.222 0.00 0.00 0.00 5.80
2990 3046 5.618561 GTGAAATCACGACACCTTACATTC 58.381 41.667 0.00 0.00 37.10 2.67
3068 3124 5.107133 CCAATATTTACGAGTTCGGTGACT 58.893 41.667 6.48 0.00 44.95 3.41


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

AutoCloner maintained by Alex Coulton.