Multiple sequence alignment - TraesCS7D01G180000

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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 TraesCS7D01G180000 chr7D 100.000 3008 0 0 1 3008 133318928 133321935 0.000000e+00 5555.0
1 TraesCS7D01G180000 chr7D 80.263 380 57 15 1113 1486 133828174 133827807 1.370000e-68 270.0
2 TraesCS7D01G180000 chr7D 75.862 377 64 18 1113 1486 133664837 133665189 1.850000e-37 167.0
3 TraesCS7D01G180000 chr7D 83.019 106 16 2 551 655 15787238 15787134 8.880000e-16 95.3
4 TraesCS7D01G180000 chr7A 93.870 2349 92 15 1 2321 131868044 131870368 0.000000e+00 3493.0
5 TraesCS7D01G180000 chr7A 80.211 379 59 13 1113 1486 132619974 132619607 1.370000e-68 270.0
6 TraesCS7D01G180000 chr7A 79.630 378 63 12 1113 1486 132410707 132411074 2.970000e-65 259.0
7 TraesCS7D01G180000 chr7B 93.898 1737 62 21 861 2590 94607298 94608997 0.000000e+00 2580.0
8 TraesCS7D01G180000 chr7B 87.075 441 43 8 2574 3004 94609011 94609447 1.250000e-133 486.0
9 TraesCS7D01G180000 chr7B 80.526 380 56 15 1113 1486 95045489 95045856 2.950000e-70 276.0
10 TraesCS7D01G180000 chr7B 83.065 124 16 5 544 665 186110113 186109993 1.140000e-19 108.0
11 TraesCS7D01G180000 chr4D 83.333 216 34 2 2793 3008 307276997 307276784 6.580000e-47 198.0
12 TraesCS7D01G180000 chr6D 82.710 214 34 2 2795 3008 460588269 460588059 1.420000e-43 187.0
13 TraesCS7D01G180000 chr5B 84.324 185 26 3 2824 3008 386330729 386330548 8.570000e-41 178.0
14 TraesCS7D01G180000 chr5B 84.239 184 25 3 2824 3007 383464115 383463936 3.080000e-40 176.0
15 TraesCS7D01G180000 chr5B 81.683 202 34 2 2807 3008 239432364 239432166 6.670000e-37 165.0
16 TraesCS7D01G180000 chr5B 77.869 122 16 5 545 666 255774676 255774566 6.960000e-07 65.8
17 TraesCS7D01G180000 chr5A 81.951 205 35 1 2804 3008 397510139 397510341 3.990000e-39 172.0
18 TraesCS7D01G180000 chr5A 81.463 205 36 1 2804 3008 653289619 653289821 1.850000e-37 167.0
19 TraesCS7D01G180000 chr5A 80.132 151 20 7 2663 2803 426551274 426551424 1.480000e-18 104.0
20 TraesCS7D01G180000 chr5A 90.000 70 7 0 2565 2634 11277645 11277714 1.150000e-14 91.6
21 TraesCS7D01G180000 chr1D 80.995 221 38 3 2788 3008 454454736 454454952 3.990000e-39 172.0
22 TraesCS7D01G180000 chr1A 82.090 201 34 1 2804 3004 49263583 49263781 1.430000e-38 171.0
23 TraesCS7D01G180000 chr3D 83.740 123 19 1 544 666 522945159 522945280 6.810000e-22 115.0
24 TraesCS7D01G180000 chr2B 93.506 77 3 2 549 624 56531156 56531231 2.450000e-21 113.0
25 TraesCS7D01G180000 chr3A 91.250 80 5 2 549 627 728045421 728045343 1.140000e-19 108.0
26 TraesCS7D01G180000 chr3A 81.967 122 20 2 549 669 392860804 392860684 5.310000e-18 102.0
27 TraesCS7D01G180000 chr1B 89.610 77 8 0 548 624 563051778 563051854 6.860000e-17 99.0
28 TraesCS7D01G180000 chr4A 80.833 120 21 2 549 666 253868481 253868362 3.190000e-15 93.5
29 TraesCS7D01G180000 chr5D 79.508 122 14 5 545 666 539320302 539320192 3.220000e-10 76.8
30 TraesCS7D01G180000 chr6B 83.333 78 13 0 2557 2634 516869098 516869021 4.160000e-09 73.1
31 TraesCS7D01G180000 chr4B 77.869 122 16 5 545 666 443719789 443719679 6.960000e-07 65.8


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 TraesCS7D01G180000 chr7D 133318928 133321935 3007 False 5555 5555 100.0000 1 3008 1 chr7D.!!$F1 3007
1 TraesCS7D01G180000 chr7A 131868044 131870368 2324 False 3493 3493 93.8700 1 2321 1 chr7A.!!$F1 2320
2 TraesCS7D01G180000 chr7B 94607298 94609447 2149 False 1533 2580 90.4865 861 3004 2 chr7B.!!$F2 2143

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
829 836 0.032678 CAGTGTGTCGAGAAGCACCT 59.967 55.000 1.89 0.0 34.94 4.00 F
1041 1052 1.747145 CTCCGGATCTCATGCAGCT 59.253 57.895 3.57 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 1994 0.032217 CTGCCTCTTCTCCCTCCTCT 60.032 60.0 0.00 0.0 0.00 3.69 R
2496 2527 0.175531 AAAACCACTTGTGCACCAGC 59.824 50.0 17.37 0.0 42.57 4.85 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
36 37 2.099427 GAGACTCCTCACGGATACAACC 59.901 54.545 0.00 0.00 39.01 3.77
75 76 3.983821 AGAGTAACTAGAGGGTTCCTGG 58.016 50.000 0.00 0.00 31.76 4.45
112 113 3.132467 CCTCTAGAAGTTTCCTAACCCGG 59.868 52.174 0.00 0.00 34.71 5.73
128 129 6.208007 CCTAACCCGGTTTTTCTCTTTATGTT 59.792 38.462 8.44 0.00 0.00 2.71
436 441 7.951287 TGAAAAATGTTCATAATTGCATGACG 58.049 30.769 0.00 0.00 34.69 4.35
439 444 7.510428 AAATGTTCATAATTGCATGACGAAC 57.490 32.000 0.00 8.68 34.69 3.95
444 449 4.808364 TCATAATTGCATGACGAACGATCA 59.192 37.500 0.00 2.02 29.93 2.92
462 467 6.223852 ACGATCATGCGATTAACTAAGGATT 58.776 36.000 0.00 0.00 34.83 3.01
482 487 0.390866 AGTCAGCTGAGTCCAATGCG 60.391 55.000 18.89 0.00 0.00 4.73
557 564 3.648739 GGAGGACTTTGATACTCCCTCT 58.351 50.000 0.00 0.00 42.87 3.69
560 567 4.027437 AGGACTTTGATACTCCCTCTGTC 58.973 47.826 0.00 0.00 0.00 3.51
561 568 4.027437 GGACTTTGATACTCCCTCTGTCT 58.973 47.826 0.00 0.00 0.00 3.41
569 576 7.113658 TGATACTCCCTCTGTCTCAAATTAC 57.886 40.000 0.00 0.00 0.00 1.89
572 579 5.799213 ACTCCCTCTGTCTCAAATTACTTG 58.201 41.667 0.00 0.00 36.25 3.16
579 586 4.627058 TGTCTCAAATTACTTGTCGCAGA 58.373 39.130 0.00 0.00 36.34 4.26
587 594 8.726068 TCAAATTACTTGTCGCAGAAATGAATA 58.274 29.630 0.00 0.00 39.69 1.75
597 604 8.797438 TGTCGCAGAAATGAATATATCTAGACT 58.203 33.333 0.00 0.00 39.69 3.24
671 678 3.493699 CCAGACGAAGGGAGTACAAAACA 60.494 47.826 0.00 0.00 0.00 2.83
772 779 8.574196 ACTTGTGAAGTTTGGATTTTTAATCG 57.426 30.769 0.00 0.00 39.04 3.34
773 780 7.169140 ACTTGTGAAGTTTGGATTTTTAATCGC 59.831 33.333 0.00 0.00 39.04 4.58
774 781 5.923684 TGTGAAGTTTGGATTTTTAATCGCC 59.076 36.000 0.00 0.00 0.00 5.54
775 782 6.156519 GTGAAGTTTGGATTTTTAATCGCCT 58.843 36.000 0.00 0.00 0.00 5.52
776 783 6.308041 GTGAAGTTTGGATTTTTAATCGCCTC 59.692 38.462 0.00 0.00 0.00 4.70
777 784 6.208599 TGAAGTTTGGATTTTTAATCGCCTCT 59.791 34.615 0.00 0.00 0.00 3.69
778 785 6.196079 AGTTTGGATTTTTAATCGCCTCTC 57.804 37.500 0.00 0.00 0.00 3.20
779 786 5.946377 AGTTTGGATTTTTAATCGCCTCTCT 59.054 36.000 0.00 0.00 0.00 3.10
780 787 7.110155 AGTTTGGATTTTTAATCGCCTCTCTA 58.890 34.615 0.00 0.00 0.00 2.43
781 788 7.775561 AGTTTGGATTTTTAATCGCCTCTCTAT 59.224 33.333 0.00 0.00 0.00 1.98
782 789 7.730364 TTGGATTTTTAATCGCCTCTCTATC 57.270 36.000 0.00 0.00 0.00 2.08
783 790 6.826668 TGGATTTTTAATCGCCTCTCTATCA 58.173 36.000 0.00 0.00 0.00 2.15
784 791 7.279615 TGGATTTTTAATCGCCTCTCTATCAA 58.720 34.615 0.00 0.00 0.00 2.57
785 792 7.773224 TGGATTTTTAATCGCCTCTCTATCAAA 59.227 33.333 0.00 0.00 0.00 2.69
786 793 8.286097 GGATTTTTAATCGCCTCTCTATCAAAG 58.714 37.037 0.00 0.00 0.00 2.77
787 794 8.964476 ATTTTTAATCGCCTCTCTATCAAAGA 57.036 30.769 0.00 0.00 0.00 2.52
802 809 3.485394 TCAAAGACAATAGCACCAGCAA 58.515 40.909 0.00 0.00 45.49 3.91
819 826 1.334059 GCAACAACATCCAGTGTGTCG 60.334 52.381 0.00 0.00 41.14 4.35
826 833 0.969149 ATCCAGTGTGTCGAGAAGCA 59.031 50.000 0.00 0.00 0.00 3.91
829 836 0.032678 CAGTGTGTCGAGAAGCACCT 59.967 55.000 1.89 0.00 34.94 4.00
1041 1052 1.747145 CTCCGGATCTCATGCAGCT 59.253 57.895 3.57 0.00 0.00 4.24
2006 2020 1.479709 GGAGAAGAGGCAGAGCAGTA 58.520 55.000 0.00 0.00 0.00 2.74
2067 2081 1.335182 GAGGATCAACGATCGAGCTGA 59.665 52.381 24.34 19.87 39.72 4.26
2080 2094 1.654317 GAGCTGATTCTGGCTGTGAG 58.346 55.000 0.00 0.00 39.05 3.51
2082 2096 2.167281 GAGCTGATTCTGGCTGTGAGTA 59.833 50.000 0.00 0.00 39.05 2.59
2083 2097 2.093764 AGCTGATTCTGGCTGTGAGTAC 60.094 50.000 0.00 0.00 37.41 2.73
2086 2100 3.165071 TGATTCTGGCTGTGAGTACTGA 58.835 45.455 0.00 0.00 0.00 3.41
2087 2101 3.056536 TGATTCTGGCTGTGAGTACTGAC 60.057 47.826 5.42 5.42 34.59 3.51
2088 2102 2.294449 TCTGGCTGTGAGTACTGACT 57.706 50.000 13.79 0.00 39.20 3.41
2089 2103 3.434940 TCTGGCTGTGAGTACTGACTA 57.565 47.619 13.79 0.00 35.45 2.59
2135 2164 2.667969 TGCTTGATGAGTTTGTCGATCG 59.332 45.455 9.36 9.36 0.00 3.69
2137 2166 3.241804 GCTTGATGAGTTTGTCGATCGAC 60.242 47.826 35.46 35.46 44.77 4.20
2140 2169 2.060326 TGAGTTTGTCGATCGACCAC 57.940 50.000 37.58 32.28 43.97 4.16
2220 2250 0.981183 ATACGTGATGGGGTGTGTGT 59.019 50.000 0.00 0.00 0.00 3.72
2317 2348 0.249573 TGAGTTCGTTGTTCGGGGAC 60.250 55.000 0.00 0.00 40.32 4.46
2318 2349 0.249573 GAGTTCGTTGTTCGGGGACA 60.250 55.000 0.00 0.00 40.32 4.02
2319 2350 0.395312 AGTTCGTTGTTCGGGGACAT 59.605 50.000 0.00 0.00 40.32 3.06
2320 2351 0.515564 GTTCGTTGTTCGGGGACATG 59.484 55.000 0.00 0.00 40.32 3.21
2321 2352 0.604243 TTCGTTGTTCGGGGACATGG 60.604 55.000 0.00 0.00 40.32 3.66
2322 2353 1.004320 CGTTGTTCGGGGACATGGA 60.004 57.895 0.00 0.00 35.71 3.41
2323 2354 1.296056 CGTTGTTCGGGGACATGGAC 61.296 60.000 0.00 0.00 35.71 4.02
2324 2355 1.004320 TTGTTCGGGGACATGGACG 60.004 57.895 0.00 0.00 0.00 4.79
2325 2356 1.473497 TTGTTCGGGGACATGGACGA 61.473 55.000 0.00 0.00 0.00 4.20
2326 2357 1.153628 GTTCGGGGACATGGACGAG 60.154 63.158 0.00 0.00 36.65 4.18
2327 2358 2.355986 TTCGGGGACATGGACGAGG 61.356 63.158 0.00 0.00 36.65 4.63
2328 2359 2.758327 CGGGGACATGGACGAGGA 60.758 66.667 0.00 0.00 0.00 3.71
2336 2367 2.166459 GACATGGACGAGGAGAATGTCA 59.834 50.000 8.75 0.00 44.15 3.58
2352 2383 3.297620 CAGTGCCACTTGGGTGCC 61.298 66.667 0.00 0.00 41.75 5.01
2359 2390 1.821759 CACTTGGGTGCCAACGTGA 60.822 57.895 1.14 0.00 41.03 4.35
2380 2411 1.727880 CCGCAACAATTTTCATGGCTG 59.272 47.619 0.00 0.00 0.00 4.85
2395 2426 1.378250 GCTGGCTGTGGAATGCTCT 60.378 57.895 0.00 0.00 0.00 4.09
2399 2430 0.251354 GGCTGTGGAATGCTCTGAGA 59.749 55.000 9.28 0.00 0.00 3.27
2467 2498 9.561270 GATTTCTTAGTTGATTTACCAGCTTTC 57.439 33.333 0.00 0.00 0.00 2.62
2491 2522 6.270000 TCGAAGGTGGATTGAGATATACCATT 59.730 38.462 0.00 0.00 33.19 3.16
2504 2535 2.601067 CCATTGGTGGCTGGTGCA 60.601 61.111 0.00 0.00 39.01 4.57
2505 2536 2.652530 CATTGGTGGCTGGTGCAC 59.347 61.111 8.80 8.80 41.91 4.57
2525 2556 4.326009 GCACAAGTGGTTTTGTTGTTACTG 59.674 41.667 2.00 0.00 39.17 2.74
2549 2580 3.693300 CATGCAATGCACGTTTTCTTC 57.307 42.857 11.23 0.00 43.04 2.87
2552 2587 2.857152 TGCAATGCACGTTTTCTTCAAC 59.143 40.909 2.72 0.00 31.71 3.18
2557 2592 4.267357 TGCACGTTTTCTTCAACACTAC 57.733 40.909 0.00 0.00 0.00 2.73
2563 2598 5.750067 ACGTTTTCTTCAACACTACGTGTAT 59.250 36.000 0.00 0.00 46.79 2.29
2613 2678 6.861065 AATTGCACGTTGATATTAGGTAGG 57.139 37.500 0.00 0.00 0.00 3.18
2619 2684 7.396339 TGCACGTTGATATTAGGTAGGATATCT 59.604 37.037 2.05 0.00 36.60 1.98
2729 2794 7.703621 GCATGCTAAATATGTTGAACACTCATT 59.296 33.333 11.37 0.00 0.00 2.57
2730 2795 9.016623 CATGCTAAATATGTTGAACACTCATTG 57.983 33.333 0.00 0.00 0.00 2.82
2731 2796 8.109705 TGCTAAATATGTTGAACACTCATTGT 57.890 30.769 0.00 0.00 41.74 2.71
2742 2807 3.759581 ACACTCATTGTTGGAGCAATCT 58.240 40.909 0.00 0.00 37.00 2.40
2756 2821 5.059833 GGAGCAATCTAGATCGTTGGATTT 58.940 41.667 5.51 0.00 31.51 2.17
2758 2823 6.038714 GGAGCAATCTAGATCGTTGGATTTTT 59.961 38.462 5.51 0.00 31.51 1.94
2814 2888 9.516314 GGTCTTTTTATATTGACCAGTAAATGC 57.484 33.333 6.18 0.00 45.87 3.56
2819 2893 5.900339 ATATTGACCAGTAAATGCGTACG 57.100 39.130 11.84 11.84 0.00 3.67
2829 2903 1.373590 AATGCGTACGCCCAATCCAC 61.374 55.000 35.11 7.28 41.09 4.02
2830 2904 3.199891 GCGTACGCCCAATCCACC 61.200 66.667 29.51 0.00 34.56 4.61
2840 2914 5.697067 ACGCCCAATCCACCTTAATATTAA 58.303 37.500 7.66 7.66 0.00 1.40
2867 2941 8.686334 AGAGGAAATTAATTGCACGTTGATATT 58.314 29.630 8.47 0.00 0.00 1.28
2870 2944 9.944663 GGAAATTAATTGCACGTTGATATTAGA 57.055 29.630 8.47 0.00 0.00 2.10
2897 2971 8.603242 AGGATATCAATCACGTGTTAATTACC 57.397 34.615 16.51 11.26 33.41 2.85
2912 2986 8.700644 GTGTTAATTACCTGATTAGCATAGACG 58.299 37.037 0.00 0.00 35.90 4.18
2928 3002 5.007626 GCATAGACGTTGATATTTGGCAAGA 59.992 40.000 0.00 0.00 0.00 3.02
2929 3003 6.293626 GCATAGACGTTGATATTTGGCAAGAT 60.294 38.462 0.00 0.00 0.00 2.40
2957 3031 3.699779 TTGCACGCTAAACATGTTGAA 57.300 38.095 12.82 2.69 0.00 2.69
2958 3032 3.913548 TGCACGCTAAACATGTTGAAT 57.086 38.095 12.82 0.00 0.00 2.57
2959 3033 3.563508 TGCACGCTAAACATGTTGAATG 58.436 40.909 12.82 7.87 0.00 2.67
2965 3039 4.731961 CGCTAAACATGTTGAATGCTCATC 59.268 41.667 12.82 0.00 0.00 2.92
2969 3043 6.961359 AAACATGTTGAATGCTCATCATTG 57.039 33.333 12.82 0.00 44.95 2.82
2970 3044 5.006153 ACATGTTGAATGCTCATCATTGG 57.994 39.130 0.00 0.00 44.95 3.16
2982 3056 4.970711 CTCATCATTGGAGCAATCTAGGT 58.029 43.478 0.00 0.00 31.05 3.08
2984 3058 3.459232 TCATTGGAGCAATCTAGGTCG 57.541 47.619 0.00 0.00 36.90 4.79
2989 3063 1.480954 GGAGCAATCTAGGTCGTTGGA 59.519 52.381 0.00 0.00 36.90 3.53
2998 3072 3.767131 TCTAGGTCGTTGGATTGACATGA 59.233 43.478 0.00 0.00 36.83 3.07
3004 3078 5.088739 GTCGTTGGATTGACATGATTTGAC 58.911 41.667 0.00 0.00 35.20 3.18
3005 3079 4.090729 CGTTGGATTGACATGATTTGACG 58.909 43.478 0.00 0.00 0.00 4.35
3006 3080 4.414852 GTTGGATTGACATGATTTGACGG 58.585 43.478 0.00 0.00 0.00 4.79
3007 3081 2.423185 TGGATTGACATGATTTGACGGC 59.577 45.455 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.039941 CGTGAGGAGTCTCTTGTAATTATCCT 59.960 42.308 0.00 0.59 40.58 3.24
287 292 9.844257 TCAGAACAATGTTTAAAATTCCCAAAT 57.156 25.926 0.00 0.00 0.00 2.32
325 330 6.150396 TCAACATAATTTTGAACACGGGTT 57.850 33.333 0.56 0.56 40.76 4.11
326 331 5.776173 TCAACATAATTTTGAACACGGGT 57.224 34.783 2.69 0.00 29.89 5.28
412 417 8.172159 TCGTCATGCAATTATGAACATTTTTC 57.828 30.769 0.00 0.00 38.69 2.29
436 441 5.690409 TCCTTAGTTAATCGCATGATCGTTC 59.310 40.000 0.00 0.00 32.24 3.95
439 444 6.712241 AATCCTTAGTTAATCGCATGATCG 57.288 37.500 0.00 0.00 32.24 3.69
444 449 6.647067 GCTGACTAATCCTTAGTTAATCGCAT 59.353 38.462 1.40 0.00 46.01 4.73
462 467 1.134995 CGCATTGGACTCAGCTGACTA 60.135 52.381 13.74 0.00 0.00 2.59
473 478 8.651588 CAGATATAAGATAGAAACGCATTGGAC 58.348 37.037 0.00 0.00 0.00 4.02
507 514 7.361542 CCTCTGTGTTGTCTATGATTTTCCTTG 60.362 40.741 0.00 0.00 0.00 3.61
556 563 4.686091 TCTGCGACAAGTAATTTGAGACAG 59.314 41.667 0.00 0.00 39.21 3.51
557 564 4.627058 TCTGCGACAAGTAATTTGAGACA 58.373 39.130 0.00 0.00 39.21 3.41
560 567 6.602179 TCATTTCTGCGACAAGTAATTTGAG 58.398 36.000 0.00 0.00 39.21 3.02
561 568 6.552859 TCATTTCTGCGACAAGTAATTTGA 57.447 33.333 0.00 0.00 39.21 2.69
569 576 9.631452 TCTAGATATATTCATTTCTGCGACAAG 57.369 33.333 0.00 0.00 0.00 3.16
572 579 9.632807 AAGTCTAGATATATTCATTTCTGCGAC 57.367 33.333 0.00 0.00 31.66 5.19
692 699 7.437748 AGGAAGAAGACGATCGATATGATTTT 58.562 34.615 24.34 0.00 37.47 1.82
769 776 5.543507 ATTGTCTTTGATAGAGAGGCGAT 57.456 39.130 0.00 0.00 32.23 4.58
770 777 5.508153 GCTATTGTCTTTGATAGAGAGGCGA 60.508 44.000 0.00 0.00 32.23 5.54
771 778 4.683781 GCTATTGTCTTTGATAGAGAGGCG 59.316 45.833 0.00 0.00 32.23 5.52
772 779 5.465056 GTGCTATTGTCTTTGATAGAGAGGC 59.535 44.000 0.00 0.00 32.23 4.70
773 780 5.988561 GGTGCTATTGTCTTTGATAGAGAGG 59.011 44.000 0.00 0.00 32.23 3.69
774 781 6.577103 TGGTGCTATTGTCTTTGATAGAGAG 58.423 40.000 0.00 0.00 32.23 3.20
775 782 6.544928 TGGTGCTATTGTCTTTGATAGAGA 57.455 37.500 0.00 0.00 32.23 3.10
776 783 5.236047 GCTGGTGCTATTGTCTTTGATAGAG 59.764 44.000 0.00 0.00 32.66 2.43
777 784 5.118990 GCTGGTGCTATTGTCTTTGATAGA 58.881 41.667 0.00 0.00 36.03 1.98
778 785 4.877823 TGCTGGTGCTATTGTCTTTGATAG 59.122 41.667 0.00 0.00 40.48 2.08
779 786 4.842574 TGCTGGTGCTATTGTCTTTGATA 58.157 39.130 0.00 0.00 40.48 2.15
780 787 3.689347 TGCTGGTGCTATTGTCTTTGAT 58.311 40.909 0.00 0.00 40.48 2.57
781 788 3.138884 TGCTGGTGCTATTGTCTTTGA 57.861 42.857 0.00 0.00 40.48 2.69
782 789 3.004629 TGTTGCTGGTGCTATTGTCTTTG 59.995 43.478 0.00 0.00 40.48 2.77
783 790 3.221771 TGTTGCTGGTGCTATTGTCTTT 58.778 40.909 0.00 0.00 40.48 2.52
784 791 2.862541 TGTTGCTGGTGCTATTGTCTT 58.137 42.857 0.00 0.00 40.48 3.01
785 792 2.554032 GTTGTTGCTGGTGCTATTGTCT 59.446 45.455 0.00 0.00 40.48 3.41
786 793 2.293122 TGTTGTTGCTGGTGCTATTGTC 59.707 45.455 0.00 0.00 40.48 3.18
787 794 2.305928 TGTTGTTGCTGGTGCTATTGT 58.694 42.857 0.00 0.00 40.48 2.71
802 809 1.686587 TCTCGACACACTGGATGTTGT 59.313 47.619 0.00 0.00 40.64 3.32
819 826 4.454504 TGTTTATTTTCGGAGGTGCTTCTC 59.545 41.667 0.00 0.00 0.00 2.87
826 833 4.142182 CCATGCATGTTTATTTTCGGAGGT 60.142 41.667 24.58 0.00 0.00 3.85
829 836 5.651387 TTCCATGCATGTTTATTTTCGGA 57.349 34.783 24.58 8.36 0.00 4.55
1041 1052 2.073252 ATGGATGGTCTCGCACTCTA 57.927 50.000 0.00 0.00 0.00 2.43
1831 1842 4.197498 TACTACGGCCGCTTCGCC 62.197 66.667 28.58 0.00 46.13 5.54
1980 1994 0.032217 CTGCCTCTTCTCCCTCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
2006 2020 3.121030 GATGGCGTCGTTGCTGCT 61.121 61.111 0.00 0.00 34.52 4.24
2047 2061 1.335182 TCAGCTCGATCGTTGATCCTC 59.665 52.381 15.94 0.00 35.83 3.71
2048 2062 1.393603 TCAGCTCGATCGTTGATCCT 58.606 50.000 15.94 1.01 35.83 3.24
2049 2063 2.430546 ATCAGCTCGATCGTTGATCC 57.569 50.000 15.94 0.00 35.83 3.36
2067 2081 3.169099 AGTCAGTACTCACAGCCAGAAT 58.831 45.455 0.00 0.00 0.00 2.40
2080 2094 3.614616 GCAAGCACATCACTAGTCAGTAC 59.385 47.826 0.00 0.00 32.21 2.73
2082 2096 2.301296 AGCAAGCACATCACTAGTCAGT 59.699 45.455 0.00 0.00 34.42 3.41
2083 2097 2.671888 CAGCAAGCACATCACTAGTCAG 59.328 50.000 0.00 0.00 0.00 3.51
2086 2100 2.301296 AGTCAGCAAGCACATCACTAGT 59.699 45.455 0.00 0.00 0.00 2.57
2087 2101 2.969990 AGTCAGCAAGCACATCACTAG 58.030 47.619 0.00 0.00 0.00 2.57
2088 2102 3.069289 CAAGTCAGCAAGCACATCACTA 58.931 45.455 0.00 0.00 0.00 2.74
2089 2103 1.878088 CAAGTCAGCAAGCACATCACT 59.122 47.619 0.00 0.00 0.00 3.41
2317 2348 2.167281 ACTGACATTCTCCTCGTCCATG 59.833 50.000 0.00 0.00 0.00 3.66
2318 2349 2.167281 CACTGACATTCTCCTCGTCCAT 59.833 50.000 0.00 0.00 0.00 3.41
2319 2350 1.546029 CACTGACATTCTCCTCGTCCA 59.454 52.381 0.00 0.00 0.00 4.02
2320 2351 1.737363 GCACTGACATTCTCCTCGTCC 60.737 57.143 0.00 0.00 0.00 4.79
2321 2352 1.634702 GCACTGACATTCTCCTCGTC 58.365 55.000 0.00 0.00 0.00 4.20
2322 2353 0.247736 GGCACTGACATTCTCCTCGT 59.752 55.000 0.00 0.00 0.00 4.18
2323 2354 0.247460 TGGCACTGACATTCTCCTCG 59.753 55.000 0.00 0.00 0.00 4.63
2324 2355 1.277557 AGTGGCACTGACATTCTCCTC 59.722 52.381 21.37 0.00 0.00 3.71
2325 2356 1.356124 AGTGGCACTGACATTCTCCT 58.644 50.000 21.37 0.00 0.00 3.69
2326 2357 1.808945 CAAGTGGCACTGACATTCTCC 59.191 52.381 22.83 0.00 0.00 3.71
2327 2358 1.808945 CCAAGTGGCACTGACATTCTC 59.191 52.381 22.83 0.00 0.00 2.87
2328 2359 1.546323 CCCAAGTGGCACTGACATTCT 60.546 52.381 22.83 0.00 0.00 2.40
2352 2383 1.833860 AAATTGTTGCGGTCACGTTG 58.166 45.000 0.00 0.00 43.45 4.10
2359 2390 1.344114 AGCCATGAAAATTGTTGCGGT 59.656 42.857 0.00 0.00 0.00 5.68
2380 2411 0.251354 TCTCAGAGCATTCCACAGCC 59.749 55.000 0.00 0.00 0.00 4.85
2395 2426 5.448496 CGGTCACAACACAAGAAAAATCTCA 60.448 40.000 0.00 0.00 0.00 3.27
2399 2430 3.181480 CCCGGTCACAACACAAGAAAAAT 60.181 43.478 0.00 0.00 0.00 1.82
2435 2466 7.333423 TGGTAAATCAACTAAGAAATCCAGTCG 59.667 37.037 0.00 0.00 0.00 4.18
2467 2498 5.468540 TGGTATATCTCAATCCACCTTCG 57.531 43.478 0.00 0.00 0.00 3.79
2491 2522 2.519063 CTTGTGCACCAGCCACCA 60.519 61.111 15.69 0.00 41.13 4.17
2496 2527 0.175531 AAAACCACTTGTGCACCAGC 59.824 50.000 17.37 0.00 42.57 4.85
2497 2528 1.204467 ACAAAACCACTTGTGCACCAG 59.796 47.619 15.69 15.85 38.12 4.00
2498 2529 1.261480 ACAAAACCACTTGTGCACCA 58.739 45.000 15.69 1.44 38.12 4.17
2499 2530 1.999024 CAACAAAACCACTTGTGCACC 59.001 47.619 15.69 0.00 39.47 5.01
2500 2531 2.682836 ACAACAAAACCACTTGTGCAC 58.317 42.857 10.75 10.75 39.47 4.57
2501 2532 3.393089 AACAACAAAACCACTTGTGCA 57.607 38.095 0.00 0.00 39.47 4.57
2502 2533 4.326009 CAGTAACAACAAAACCACTTGTGC 59.674 41.667 0.00 0.00 39.47 4.57
2503 2534 4.862018 CCAGTAACAACAAAACCACTTGTG 59.138 41.667 0.00 0.00 39.47 3.33
2504 2535 4.525100 ACCAGTAACAACAAAACCACTTGT 59.475 37.500 0.00 0.00 41.31 3.16
2505 2536 5.066968 ACCAGTAACAACAAAACCACTTG 57.933 39.130 0.00 0.00 0.00 3.16
2563 2598 9.522804 AACTTTCTTTCAAATATTAACGTGCAA 57.477 25.926 0.00 0.00 0.00 4.08
2577 2612 7.030165 TCAACGTGCAATTAACTTTCTTTCAA 58.970 30.769 0.00 0.00 0.00 2.69
2579 2614 7.623268 ATCAACGTGCAATTAACTTTCTTTC 57.377 32.000 0.00 0.00 0.00 2.62
2580 2615 9.691362 AATATCAACGTGCAATTAACTTTCTTT 57.309 25.926 0.00 0.00 0.00 2.52
2590 2625 6.588204 TCCTACCTAATATCAACGTGCAATT 58.412 36.000 0.00 0.00 0.00 2.32
2591 2626 6.169557 TCCTACCTAATATCAACGTGCAAT 57.830 37.500 0.00 0.00 0.00 3.56
2594 2629 7.773149 AGATATCCTACCTAATATCAACGTGC 58.227 38.462 0.00 0.00 37.34 5.34
2729 2794 4.183865 CAACGATCTAGATTGCTCCAACA 58.816 43.478 18.44 0.00 0.00 3.33
2730 2795 3.557595 CCAACGATCTAGATTGCTCCAAC 59.442 47.826 18.44 0.00 0.00 3.77
2731 2796 3.450817 TCCAACGATCTAGATTGCTCCAA 59.549 43.478 18.44 0.20 0.00 3.53
2756 2821 4.408596 GGATCCAATTAATCCAGGCCAAAA 59.591 41.667 6.95 0.00 42.01 2.44
2758 2823 3.052262 TGGATCCAATTAATCCAGGCCAA 60.052 43.478 13.46 0.00 46.05 4.52
2759 2824 2.517553 TGGATCCAATTAATCCAGGCCA 59.482 45.455 13.46 0.00 46.05 5.36
2760 2825 3.243359 TGGATCCAATTAATCCAGGCC 57.757 47.619 13.46 0.00 46.05 5.19
2804 2878 0.741574 TGGGCGTACGCATTTACTGG 60.742 55.000 37.99 0.00 44.11 4.00
2814 2888 0.176219 TAAGGTGGATTGGGCGTACG 59.824 55.000 11.84 11.84 0.00 3.67
2819 2893 7.039714 CCTCTTTAATATTAAGGTGGATTGGGC 60.040 40.741 23.86 0.00 36.22 5.36
2840 2914 6.325919 TCAACGTGCAATTAATTTCCTCTT 57.674 33.333 0.00 0.00 0.00 2.85
2855 2929 9.803315 TTGATATCCTATCTAATATCAACGTGC 57.197 33.333 11.72 0.00 44.20 5.34
2883 2957 6.656314 TGCTAATCAGGTAATTAACACGTG 57.344 37.500 15.48 15.48 34.02 4.49
2894 2968 6.650427 ATCAACGTCTATGCTAATCAGGTA 57.350 37.500 0.00 0.00 0.00 3.08
2897 2971 8.438513 CCAAATATCAACGTCTATGCTAATCAG 58.561 37.037 0.00 0.00 0.00 2.90
2929 3003 9.444534 CAACATGTTTAGCGTGCAATTAATATA 57.555 29.630 8.77 0.00 37.62 0.86
2942 3016 4.082274 TGAGCATTCAACATGTTTAGCG 57.918 40.909 8.77 0.00 0.00 4.26
2965 3039 3.185246 ACGACCTAGATTGCTCCAATG 57.815 47.619 0.00 0.00 33.90 2.82
2969 3043 1.480954 TCCAACGACCTAGATTGCTCC 59.519 52.381 0.00 0.00 0.00 4.70
2970 3044 2.961526 TCCAACGACCTAGATTGCTC 57.038 50.000 0.00 0.00 0.00 4.26
2982 3056 4.142924 CGTCAAATCATGTCAATCCAACGA 60.143 41.667 0.00 0.00 0.00 3.85
2984 3058 4.414852 CCGTCAAATCATGTCAATCCAAC 58.585 43.478 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.