Multiple sequence alignment - TraesCS7D01G235100

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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 TraesCS7D01G235100 chr7D 100.000 3362 0 0 1 3362 197878742 197875381 0.000000e+00 6209.0
1 TraesCS7D01G235100 chr7D 100.000 39 0 0 2896 2934 197875806 197875768 4.650000e-09 73.1
2 TraesCS7D01G235100 chr7A 93.180 2610 92 35 1 2594 206938346 206935807 0.000000e+00 3755.0
3 TraesCS7D01G235100 chr7B 93.161 2047 96 19 571 2594 162115228 162113203 0.000000e+00 2964.0
4 TraesCS7D01G235100 chr7B 97.565 575 13 1 1 574 162115880 162115306 0.000000e+00 983.0
5 TraesCS7D01G235100 chr7B 89.583 768 32 21 2605 3362 74813415 74814144 0.000000e+00 931.0
6 TraesCS7D01G235100 chr7B 90.000 430 22 5 2937 3362 750595214 750595626 1.370000e-148 536.0
7 TraesCS7D01G235100 chr7B 91.086 359 15 6 2592 2934 750594895 750595252 1.410000e-128 470.0
8 TraesCS7D01G235100 chr3B 90.128 780 29 28 2593 3362 53580434 53581175 0.000000e+00 970.0
9 TraesCS7D01G235100 chr3B 79.070 258 27 14 2593 2829 36015519 36015770 5.810000e-33 152.0
10 TraesCS7D01G235100 chr3B 85.047 107 6 5 2606 2702 66829681 66829787 2.130000e-17 100.0
11 TraesCS7D01G235100 chr5B 88.745 773 34 24 2605 3362 587754694 587755428 0.000000e+00 896.0
12 TraesCS7D01G235100 chr5B 79.245 212 21 14 2605 2798 465521702 465521908 3.520000e-25 126.0
13 TraesCS7D01G235100 chr6B 88.303 778 34 20 2605 3362 719905614 719906354 0.000000e+00 880.0
14 TraesCS7D01G235100 chr6B 89.486 428 24 8 2939 3362 24756290 24756700 3.840000e-144 521.0
15 TraesCS7D01G235100 chr6B 90.415 313 18 5 2606 2907 24755973 24756284 5.230000e-108 401.0
16 TraesCS7D01G235100 chr2A 86.369 785 57 16 2592 3362 243530169 243530917 0.000000e+00 811.0
17 TraesCS7D01G235100 chrUn 86.719 768 29 20 2605 3362 33328482 33327778 0.000000e+00 785.0
18 TraesCS7D01G235100 chrUn 85.130 538 23 14 2825 3362 469209726 469209246 6.480000e-137 497.0
19 TraesCS7D01G235100 chr3A 86.328 768 32 20 2605 3362 725166530 725165826 0.000000e+00 769.0
20 TraesCS7D01G235100 chr1B 87.279 566 25 6 2595 3154 24644226 24644750 1.330000e-168 603.0
21 TraesCS7D01G235100 chr1B 91.736 363 12 7 2589 2934 730132 729771 3.900000e-134 488.0
22 TraesCS7D01G235100 chr1B 97.590 166 2 1 2937 3100 729809 729644 1.970000e-72 283.0
23 TraesCS7D01G235100 chr1B 90.050 201 10 5 3162 3362 729642 729452 5.570000e-63 252.0
24 TraesCS7D01G235100 chr1B 79.412 204 30 7 2605 2798 30012406 30012607 2.100000e-27 134.0
25 TraesCS7D01G235100 chr5A 88.158 304 19 5 3059 3362 689478896 689479182 2.480000e-91 346.0
26 TraesCS7D01G235100 chr5A 91.429 210 12 5 3155 3362 703236973 703236768 1.970000e-72 283.0
27 TraesCS7D01G235100 chr1A 79.612 206 26 9 2605 2798 29117978 29118179 2.100000e-27 134.0


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 TraesCS7D01G235100 chr7D 197875381 197878742 3361 True 3141.05 6209 100.000000 1 3362 2 chr7D.!!$R1 3361
1 TraesCS7D01G235100 chr7A 206935807 206938346 2539 True 3755.00 3755 93.180000 1 2594 1 chr7A.!!$R1 2593
2 TraesCS7D01G235100 chr7B 162113203 162115880 2677 True 1973.50 2964 95.363000 1 2594 2 chr7B.!!$R1 2593
3 TraesCS7D01G235100 chr7B 74813415 74814144 729 False 931.00 931 89.583000 2605 3362 1 chr7B.!!$F1 757
4 TraesCS7D01G235100 chr7B 750594895 750595626 731 False 503.00 536 90.543000 2592 3362 2 chr7B.!!$F2 770
5 TraesCS7D01G235100 chr3B 53580434 53581175 741 False 970.00 970 90.128000 2593 3362 1 chr3B.!!$F2 769
6 TraesCS7D01G235100 chr5B 587754694 587755428 734 False 896.00 896 88.745000 2605 3362 1 chr5B.!!$F2 757
7 TraesCS7D01G235100 chr6B 719905614 719906354 740 False 880.00 880 88.303000 2605 3362 1 chr6B.!!$F1 757
8 TraesCS7D01G235100 chr6B 24755973 24756700 727 False 461.00 521 89.950500 2606 3362 2 chr6B.!!$F2 756
9 TraesCS7D01G235100 chr2A 243530169 243530917 748 False 811.00 811 86.369000 2592 3362 1 chr2A.!!$F1 770
10 TraesCS7D01G235100 chrUn 33327778 33328482 704 True 785.00 785 86.719000 2605 3362 1 chrUn.!!$R1 757
11 TraesCS7D01G235100 chr3A 725165826 725166530 704 True 769.00 769 86.328000 2605 3362 1 chr3A.!!$R1 757
12 TraesCS7D01G235100 chr1B 24644226 24644750 524 False 603.00 603 87.279000 2595 3154 1 chr1B.!!$F1 559
13 TraesCS7D01G235100 chr1B 729452 730132 680 True 341.00 488 93.125333 2589 3362 3 chr1B.!!$R1 773

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
984 1075 1.517242 CTCACAGGCACAGGAAGAAC 58.483 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2956 3139 0.031414 AGCCGGTCTTGTAGGGGTAT 60.031 55.0 1.9 0.0 0.0 2.73 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
410 412 1.550524 CACTGACTCTGGATTCCGGAA 59.449 52.381 21.37 21.37 38.58 4.30
702 785 9.710818 ATACTGTATTTCCTAGAGTACCAGAAA 57.289 33.333 0.00 0.00 38.58 2.52
703 786 8.068892 ACTGTATTTCCTAGAGTACCAGAAAG 57.931 38.462 0.00 0.00 32.43 2.62
754 837 6.950860 ATTAAAACCATTGAGGGGAAATGT 57.049 33.333 0.00 0.00 43.89 2.71
755 838 6.755542 TTAAAACCATTGAGGGGAAATGTT 57.244 33.333 0.00 0.00 43.89 2.71
756 839 5.645056 AAAACCATTGAGGGGAAATGTTT 57.355 34.783 0.00 0.00 43.89 2.83
757 840 5.645056 AAACCATTGAGGGGAAATGTTTT 57.355 34.783 0.00 0.00 43.89 2.43
758 841 4.622260 ACCATTGAGGGGAAATGTTTTG 57.378 40.909 0.00 0.00 43.89 2.44
759 842 4.230455 ACCATTGAGGGGAAATGTTTTGA 58.770 39.130 0.00 0.00 43.89 2.69
760 843 4.040339 ACCATTGAGGGGAAATGTTTTGAC 59.960 41.667 0.00 0.00 43.89 3.18
808 891 8.495949 ACGTGCAGTTATAATGTAAATATCAGC 58.504 33.333 0.00 0.00 0.00 4.26
841 925 4.380973 GCTTTTTGGTCCTCTCCTTTATGC 60.381 45.833 0.00 0.00 0.00 3.14
942 1027 6.931840 AGCAAATATCCGAAGAGAGTTTATCC 59.068 38.462 0.00 0.00 0.00 2.59
984 1075 1.517242 CTCACAGGCACAGGAAGAAC 58.483 55.000 0.00 0.00 0.00 3.01
1015 1106 1.740025 GAGAAATGGCAGGGTTCTTCG 59.260 52.381 10.95 0.00 31.80 3.79
1157 1248 3.583526 GGGAAGACAAGAAGGGACTACTT 59.416 47.826 0.00 0.00 38.49 2.24
1261 1352 0.036164 TATTGCTGGCGACAAGGTGT 59.964 50.000 0.00 0.00 42.06 4.16
1366 1460 3.746045 AAACTCGACAAGGAGCAACTA 57.254 42.857 0.00 0.00 37.57 2.24
1398 1492 6.579292 CGTGTTAGATATCAGATCGGTTCTTC 59.421 42.308 5.32 0.00 29.93 2.87
1466 1560 4.830765 GGCCATGACCACGCGCTA 62.831 66.667 5.73 0.00 0.00 4.26
1641 1735 3.621268 TGAGAACAAATGCATAGGTACGC 59.379 43.478 0.00 0.00 0.00 4.42
1688 1782 3.324846 ACACCAGTGCTTCAGAGATACAA 59.675 43.478 0.00 0.00 0.00 2.41
1764 1858 3.338249 CATGGACGATGTTCTTGGAAGT 58.662 45.455 0.00 0.00 0.00 3.01
1864 1959 2.930950 TGGCACTAGTTGAGCTGTTTT 58.069 42.857 0.00 0.00 32.77 2.43
1873 1968 8.556194 CACTAGTTGAGCTGTTTTAAACACATA 58.444 33.333 6.41 0.00 36.25 2.29
1878 1973 5.121221 AGCTGTTTTAAACACATACAGGC 57.879 39.130 15.37 7.09 37.33 4.85
1908 2019 6.992063 ATCTGCTGAATATTTTCGACTTGT 57.008 33.333 0.00 0.00 34.39 3.16
1912 2023 8.604035 TCTGCTGAATATTTTCGACTTGTAATC 58.396 33.333 0.00 0.00 34.39 1.75
1964 2075 2.078452 CATCCACTGGGTTGGGAGT 58.922 57.895 0.00 0.00 37.24 3.85
1997 2108 3.197790 CTGGAGTTCATGGCGCGG 61.198 66.667 8.83 0.00 0.00 6.46
2024 2135 3.315949 AAGGAAGGGCACGGCGTA 61.316 61.111 14.22 0.00 0.00 4.42
2095 2206 1.989165 CTTCGCCAAGAAACTCGAGAG 59.011 52.381 21.68 0.00 38.57 3.20
2140 2251 2.064014 GGGCGCAAACGGTAGTATATC 58.936 52.381 10.83 0.00 40.57 1.63
2149 2260 5.609533 AACGGTAGTATATCCAGCTGTTT 57.390 39.130 13.81 1.63 0.00 2.83
2161 2272 5.353394 TCCAGCTGTTTATTCCTACGAAT 57.647 39.130 13.81 0.00 41.67 3.34
2162 2273 5.357257 TCCAGCTGTTTATTCCTACGAATC 58.643 41.667 13.81 0.00 39.49 2.52
2210 2333 7.502177 CTGAAAGTTCATGCATGATTTGTAC 57.498 36.000 29.13 22.44 36.56 2.90
2211 2334 7.218228 TGAAAGTTCATGCATGATTTGTACT 57.782 32.000 29.13 24.18 36.56 2.73
2212 2335 8.334263 TGAAAGTTCATGCATGATTTGTACTA 57.666 30.769 29.13 11.80 36.56 1.82
2213 2336 8.236586 TGAAAGTTCATGCATGATTTGTACTAC 58.763 33.333 29.13 20.41 36.56 2.73
2214 2337 7.686438 AAGTTCATGCATGATTTGTACTACA 57.314 32.000 29.13 8.22 36.56 2.74
2215 2338 7.686438 AGTTCATGCATGATTTGTACTACAA 57.314 32.000 29.13 7.68 36.56 2.41
2216 2339 8.284945 AGTTCATGCATGATTTGTACTACAAT 57.715 30.769 29.13 7.48 36.56 2.71
2217 2340 8.186163 AGTTCATGCATGATTTGTACTACAATG 58.814 33.333 29.13 0.00 36.56 2.82
2218 2341 7.628769 TCATGCATGATTTGTACTACAATGT 57.371 32.000 25.42 0.00 38.00 2.71
2219 2342 8.054152 TCATGCATGATTTGTACTACAATGTT 57.946 30.769 25.42 0.00 38.00 2.71
2386 2509 1.009829 CAATGGCTAGTCGCTGGTTC 58.990 55.000 0.00 0.00 39.13 3.62
2452 2577 5.185249 ACGTGCTGTAATACCTGGGATATAG 59.815 44.000 0.00 0.00 0.00 1.31
2453 2578 5.394224 CGTGCTGTAATACCTGGGATATAGG 60.394 48.000 0.00 0.00 41.22 2.57
2454 2579 5.720041 GTGCTGTAATACCTGGGATATAGGA 59.280 44.000 0.00 0.00 38.71 2.94
2455 2580 5.958380 TGCTGTAATACCTGGGATATAGGAG 59.042 44.000 0.00 0.00 38.71 3.69
2482 2607 4.422073 TGGAAGATGACACAGAACAACT 57.578 40.909 0.00 0.00 0.00 3.16
2483 2608 4.780815 TGGAAGATGACACAGAACAACTT 58.219 39.130 0.00 0.00 33.23 2.66
2484 2609 5.192927 TGGAAGATGACACAGAACAACTTT 58.807 37.500 0.00 0.00 31.34 2.66
2485 2610 5.652014 TGGAAGATGACACAGAACAACTTTT 59.348 36.000 0.00 0.00 31.34 2.27
2518 2643 2.224769 TGAGAATTCTCGCCCCACTTTT 60.225 45.455 26.32 0.00 45.72 2.27
2550 2678 7.450014 TCAACAAAATGTCCATAGGTACAATGT 59.550 33.333 0.00 0.00 0.00 2.71
2566 2696 6.071391 GGTACAATGTTTGGATCATGAGGTTT 60.071 38.462 0.09 0.00 34.12 3.27
2585 2715 3.443145 TTCCCCAACCAAATATGACGT 57.557 42.857 0.00 0.00 0.00 4.34
2752 2903 1.883084 GAATGGACCGGCTAGCACG 60.883 63.158 18.24 16.86 0.00 5.34
2916 3099 7.094032 GGATTTTCTGAATCTGACTGTTGGAAT 60.094 37.037 0.00 0.00 0.00 3.01
2917 3100 8.868522 ATTTTCTGAATCTGACTGTTGGAATA 57.131 30.769 0.00 0.00 0.00 1.75
2918 3101 7.672983 TTTCTGAATCTGACTGTTGGAATAC 57.327 36.000 0.00 0.00 0.00 1.89
2919 3102 5.734720 TCTGAATCTGACTGTTGGAATACC 58.265 41.667 0.00 0.00 0.00 2.73
2920 3103 4.843728 TGAATCTGACTGTTGGAATACCC 58.156 43.478 0.00 0.00 34.81 3.69
2921 3104 3.933861 ATCTGACTGTTGGAATACCCC 57.066 47.619 0.00 0.00 34.81 4.95
2922 3105 2.915869 TCTGACTGTTGGAATACCCCT 58.084 47.619 0.00 0.00 34.81 4.79
2923 3106 4.069312 TCTGACTGTTGGAATACCCCTA 57.931 45.455 0.00 0.00 34.81 3.53
2924 3107 3.773119 TCTGACTGTTGGAATACCCCTAC 59.227 47.826 0.00 0.00 34.81 3.18
2925 3108 3.517901 CTGACTGTTGGAATACCCCTACA 59.482 47.826 0.00 0.00 39.09 2.74
2926 3109 3.911260 TGACTGTTGGAATACCCCTACAA 59.089 43.478 0.00 0.00 40.41 2.41
2927 3110 4.019681 TGACTGTTGGAATACCCCTACAAG 60.020 45.833 0.00 0.00 40.41 3.16
2928 3111 4.172807 ACTGTTGGAATACCCCTACAAGA 58.827 43.478 0.00 0.00 40.41 3.02
2929 3112 4.019591 ACTGTTGGAATACCCCTACAAGAC 60.020 45.833 0.00 0.00 40.41 3.01
2930 3113 3.264964 TGTTGGAATACCCCTACAAGACC 59.735 47.826 0.00 0.00 38.60 3.85
2931 3114 2.112998 TGGAATACCCCTACAAGACCG 58.887 52.381 0.00 0.00 34.81 4.79
2932 3115 1.415289 GGAATACCCCTACAAGACCGG 59.585 57.143 0.00 0.00 0.00 5.28
2933 3116 0.835276 AATACCCCTACAAGACCGGC 59.165 55.000 0.00 0.00 0.00 6.13
2934 3117 0.325860 ATACCCCTACAAGACCGGCA 60.326 55.000 0.00 0.00 0.00 5.69
2935 3118 1.259840 TACCCCTACAAGACCGGCAC 61.260 60.000 0.00 0.00 0.00 5.01
2936 3119 2.291043 CCCCTACAAGACCGGCACT 61.291 63.158 0.00 0.00 0.00 4.40
2937 3120 1.677552 CCCTACAAGACCGGCACTT 59.322 57.895 0.00 4.80 0.00 3.16
2938 3121 0.391263 CCCTACAAGACCGGCACTTC 60.391 60.000 0.00 0.00 0.00 3.01
2939 3122 0.608640 CCTACAAGACCGGCACTTCT 59.391 55.000 0.00 0.00 0.00 2.85
2940 3123 1.673033 CCTACAAGACCGGCACTTCTG 60.673 57.143 0.00 0.16 0.00 3.02
2941 3124 1.272490 CTACAAGACCGGCACTTCTGA 59.728 52.381 0.00 0.00 0.00 3.27
2942 3125 0.468226 ACAAGACCGGCACTTCTGAA 59.532 50.000 0.00 0.00 0.00 3.02
2943 3126 1.072331 ACAAGACCGGCACTTCTGAAT 59.928 47.619 0.00 0.00 0.00 2.57
2944 3127 1.734465 CAAGACCGGCACTTCTGAATC 59.266 52.381 0.00 0.00 0.00 2.52
2945 3128 1.270907 AGACCGGCACTTCTGAATCT 58.729 50.000 0.00 0.00 0.00 2.40
2946 3129 1.066573 AGACCGGCACTTCTGAATCTG 60.067 52.381 0.00 0.00 0.00 2.90
2947 3130 0.976641 ACCGGCACTTCTGAATCTGA 59.023 50.000 0.00 0.00 0.00 3.27
2948 3131 1.338200 ACCGGCACTTCTGAATCTGAC 60.338 52.381 0.00 0.00 0.00 3.51
2949 3132 1.066573 CCGGCACTTCTGAATCTGACT 60.067 52.381 0.00 0.00 0.00 3.41
2950 3133 1.998315 CGGCACTTCTGAATCTGACTG 59.002 52.381 0.00 0.00 0.00 3.51
2951 3134 2.611473 CGGCACTTCTGAATCTGACTGT 60.611 50.000 0.00 0.00 0.00 3.55
2952 3135 3.406764 GGCACTTCTGAATCTGACTGTT 58.593 45.455 0.00 0.00 0.00 3.16
2953 3136 3.188048 GGCACTTCTGAATCTGACTGTTG 59.812 47.826 0.00 0.00 0.00 3.33
2954 3137 3.188048 GCACTTCTGAATCTGACTGTTGG 59.812 47.826 0.00 0.00 0.00 3.77
2955 3138 4.635223 CACTTCTGAATCTGACTGTTGGA 58.365 43.478 0.00 0.00 0.00 3.53
2956 3139 5.059161 CACTTCTGAATCTGACTGTTGGAA 58.941 41.667 0.00 0.00 0.00 3.53
3030 3227 4.260170 TCTCTCCGTAACAACTAGTCCTC 58.740 47.826 0.00 0.00 0.00 3.71
3102 3299 4.025401 CGGAGGTTGTGTTGGCGC 62.025 66.667 0.00 0.00 0.00 6.53
3134 3331 3.003113 GCCGACCTACGTGCTCCTT 62.003 63.158 0.00 0.00 40.78 3.36
3176 3373 6.398095 ACACTCGACAGATGAATGAACATAA 58.602 36.000 0.00 0.00 0.00 1.90
3208 3405 6.935240 TCTCTCCTGTTATTCCTTCTTTCA 57.065 37.500 0.00 0.00 0.00 2.69
3209 3406 6.702329 TCTCTCCTGTTATTCCTTCTTTCAC 58.298 40.000 0.00 0.00 0.00 3.18
3210 3407 6.498651 TCTCTCCTGTTATTCCTTCTTTCACT 59.501 38.462 0.00 0.00 0.00 3.41
3211 3408 6.702329 TCTCCTGTTATTCCTTCTTTCACTC 58.298 40.000 0.00 0.00 0.00 3.51
3212 3409 6.270000 TCTCCTGTTATTCCTTCTTTCACTCA 59.730 38.462 0.00 0.00 0.00 3.41
3213 3410 6.231211 TCCTGTTATTCCTTCTTTCACTCAC 58.769 40.000 0.00 0.00 0.00 3.51
3214 3411 5.120830 CCTGTTATTCCTTCTTTCACTCACG 59.879 44.000 0.00 0.00 0.00 4.35
3215 3412 5.849510 TGTTATTCCTTCTTTCACTCACGA 58.150 37.500 0.00 0.00 0.00 4.35
3216 3413 6.285224 TGTTATTCCTTCTTTCACTCACGAA 58.715 36.000 0.00 0.00 0.00 3.85
3326 3533 0.323360 TGGTGCCCAGTTATTCCTGC 60.323 55.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 191 5.009911 CAGATCCTCACCATTAGAGTCTGAG 59.990 48.000 1.86 0.24 37.95 3.35
471 473 2.834549 CACTACTCCCTCAACATCCTGT 59.165 50.000 0.00 0.00 0.00 4.00
550 552 0.388649 ACTCTACAACTTGAGCCGCG 60.389 55.000 0.00 0.00 33.92 6.46
702 785 7.309255 GGTCATATTCCTGATCGTACATACACT 60.309 40.741 0.00 0.00 0.00 3.55
703 786 6.807230 GGTCATATTCCTGATCGTACATACAC 59.193 42.308 0.00 0.00 0.00 2.90
742 825 5.423610 TCAAAAGTCAAAACATTTCCCCTCA 59.576 36.000 0.00 0.00 0.00 3.86
758 841 9.638300 CGTGTAAATATAGATTGCTCAAAAGTC 57.362 33.333 0.00 0.00 0.00 3.01
759 842 9.162764 ACGTGTAAATATAGATTGCTCAAAAGT 57.837 29.630 0.00 0.00 0.00 2.66
760 843 9.425893 CACGTGTAAATATAGATTGCTCAAAAG 57.574 33.333 7.58 0.00 0.00 2.27
808 891 2.544486 GGACCAAAAAGCAAGCAGACTG 60.544 50.000 0.00 0.00 0.00 3.51
841 925 4.487714 TTCATACCTTCTAGCTGTTGGG 57.512 45.455 0.00 0.00 0.00 4.12
942 1027 2.352805 GACTCCTGGGCAACTGGG 59.647 66.667 0.00 0.00 38.62 4.45
984 1075 1.815003 GCCATTTCTCACCTCAGGTTG 59.185 52.381 0.00 0.00 31.02 3.77
992 1083 1.177401 GAACCCTGCCATTTCTCACC 58.823 55.000 0.00 0.00 0.00 4.02
1131 1222 1.985895 TCCCTTCTTGTCTTCCCCTTC 59.014 52.381 0.00 0.00 0.00 3.46
1157 1248 2.024176 TGCTACTCCAAGAACCTGGA 57.976 50.000 0.00 0.00 43.45 3.86
1366 1460 7.382488 CCGATCTGATATCTAACACGACAAAAT 59.618 37.037 3.98 0.00 0.00 1.82
1398 1492 0.107017 AGATTCCACGATGCAAGGGG 60.107 55.000 7.46 7.46 0.00 4.79
1439 1533 0.038166 GGTCATGGCCCTGAACAGAA 59.962 55.000 20.07 0.00 32.90 3.02
1440 1534 1.133181 TGGTCATGGCCCTGAACAGA 61.133 55.000 23.27 3.32 37.92 3.41
1466 1560 3.136763 CTCATACGCCTCATTCAGCAAT 58.863 45.455 0.00 0.00 0.00 3.56
1641 1735 8.660373 GTTCTTTGGTCAGAAATATCAGTACTG 58.340 37.037 17.17 17.17 34.50 2.74
1764 1858 4.273257 TGGACTTCGACGTGCGCA 62.273 61.111 5.66 5.66 40.61 6.09
1864 1959 7.012327 GCAGATTAAGATGCCTGTATGTGTTTA 59.988 37.037 3.81 0.00 36.41 2.01
1873 1968 3.920231 TCAGCAGATTAAGATGCCTGT 57.080 42.857 10.24 0.00 43.60 4.00
1878 1973 9.591404 GTCGAAAATATTCAGCAGATTAAGATG 57.409 33.333 0.00 0.00 35.15 2.90
1964 2075 2.604686 AGCACCGGGAGCTCTTCA 60.605 61.111 16.86 0.00 38.01 3.02
1997 2108 3.741476 CCTTCCTTGCGCTGTGGC 61.741 66.667 9.73 0.00 0.00 5.01
2095 2206 2.034687 TTTCCTGCTGCTCCTGCC 59.965 61.111 0.00 0.00 38.71 4.85
2140 2251 4.209288 CGATTCGTAGGAATAAACAGCTGG 59.791 45.833 19.93 0.00 42.86 4.85
2149 2260 5.301045 ACATGGTTCTCGATTCGTAGGAATA 59.699 40.000 10.51 0.00 42.86 1.75
2161 2272 3.320826 TCTGAACTTCACATGGTTCTCGA 59.679 43.478 12.04 7.26 41.42 4.04
2162 2273 3.653344 TCTGAACTTCACATGGTTCTCG 58.347 45.455 12.04 5.59 41.42 4.04
2206 2329 3.417101 CCCCTGCAAACATTGTAGTACA 58.583 45.455 0.00 0.00 41.13 2.90
2207 2330 2.752903 CCCCCTGCAAACATTGTAGTAC 59.247 50.000 7.29 0.00 41.13 2.73
2208 2331 2.377193 ACCCCCTGCAAACATTGTAGTA 59.623 45.455 7.29 0.00 41.13 1.82
2209 2332 1.146982 ACCCCCTGCAAACATTGTAGT 59.853 47.619 7.29 0.00 41.13 2.73
2210 2333 1.545582 CACCCCCTGCAAACATTGTAG 59.454 52.381 1.76 1.76 42.18 2.74
2211 2334 1.145945 TCACCCCCTGCAAACATTGTA 59.854 47.619 0.00 0.00 0.00 2.41
2212 2335 0.105760 TCACCCCCTGCAAACATTGT 60.106 50.000 0.00 0.00 0.00 2.71
2213 2336 1.001181 CTTCACCCCCTGCAAACATTG 59.999 52.381 0.00 0.00 0.00 2.82
2214 2337 1.133199 TCTTCACCCCCTGCAAACATT 60.133 47.619 0.00 0.00 0.00 2.71
2215 2338 0.482446 TCTTCACCCCCTGCAAACAT 59.518 50.000 0.00 0.00 0.00 2.71
2216 2339 0.482446 ATCTTCACCCCCTGCAAACA 59.518 50.000 0.00 0.00 0.00 2.83
2217 2340 0.890683 CATCTTCACCCCCTGCAAAC 59.109 55.000 0.00 0.00 0.00 2.93
2218 2341 0.482446 ACATCTTCACCCCCTGCAAA 59.518 50.000 0.00 0.00 0.00 3.68
2219 2342 0.251297 CACATCTTCACCCCCTGCAA 60.251 55.000 0.00 0.00 0.00 4.08
2386 2509 0.792640 GCAGTCTTCACACCATCACG 59.207 55.000 0.00 0.00 0.00 4.35
2452 2577 5.127845 TCTGTGTCATCTTCCATCTTACTCC 59.872 44.000 0.00 0.00 0.00 3.85
2453 2578 6.214191 TCTGTGTCATCTTCCATCTTACTC 57.786 41.667 0.00 0.00 0.00 2.59
2454 2579 6.014242 TGTTCTGTGTCATCTTCCATCTTACT 60.014 38.462 0.00 0.00 0.00 2.24
2455 2580 6.166279 TGTTCTGTGTCATCTTCCATCTTAC 58.834 40.000 0.00 0.00 0.00 2.34
2498 2623 2.115343 AAAGTGGGGCGAGAATTCTC 57.885 50.000 23.20 23.20 39.55 2.87
2521 2646 9.521841 TTGTACCTATGGACATTTTGTTGAATA 57.478 29.630 0.00 0.00 0.00 1.75
2566 2696 2.356330 GGACGTCATATTTGGTTGGGGA 60.356 50.000 18.91 0.00 0.00 4.81
2670 2820 2.434359 CGGAAACAGGACCGCTCC 60.434 66.667 0.00 0.00 42.55 4.70
2752 2903 2.680913 GCACACATGGACGCTGGTC 61.681 63.158 0.00 0.00 42.66 4.02
2762 2913 2.429571 GCAGCAACCGCACACATG 60.430 61.111 0.00 0.00 42.27 3.21
2916 3099 1.078891 TGCCGGTCTTGTAGGGGTA 59.921 57.895 1.90 0.00 0.00 3.69
2917 3100 2.203877 TGCCGGTCTTGTAGGGGT 60.204 61.111 1.90 0.00 0.00 4.95
2918 3101 1.838073 AAGTGCCGGTCTTGTAGGGG 61.838 60.000 1.90 0.00 0.00 4.79
2919 3102 0.391263 GAAGTGCCGGTCTTGTAGGG 60.391 60.000 16.33 0.00 0.00 3.53
2920 3103 0.608640 AGAAGTGCCGGTCTTGTAGG 59.391 55.000 16.33 0.00 0.00 3.18
2921 3104 1.272490 TCAGAAGTGCCGGTCTTGTAG 59.728 52.381 16.33 9.08 0.00 2.74
2922 3105 1.334160 TCAGAAGTGCCGGTCTTGTA 58.666 50.000 16.33 2.28 0.00 2.41
2923 3106 0.468226 TTCAGAAGTGCCGGTCTTGT 59.532 50.000 16.33 10.95 0.00 3.16
2924 3107 1.734465 GATTCAGAAGTGCCGGTCTTG 59.266 52.381 16.33 6.49 0.00 3.02
2925 3108 1.625818 AGATTCAGAAGTGCCGGTCTT 59.374 47.619 1.90 8.61 0.00 3.01
2926 3109 1.066573 CAGATTCAGAAGTGCCGGTCT 60.067 52.381 1.90 0.00 0.00 3.85
2927 3110 1.066858 TCAGATTCAGAAGTGCCGGTC 60.067 52.381 1.90 0.00 0.00 4.79
2928 3111 0.976641 TCAGATTCAGAAGTGCCGGT 59.023 50.000 1.90 0.00 0.00 5.28
2929 3112 1.066573 AGTCAGATTCAGAAGTGCCGG 60.067 52.381 0.00 0.00 0.00 6.13
2930 3113 1.998315 CAGTCAGATTCAGAAGTGCCG 59.002 52.381 0.00 0.00 0.00 5.69
2931 3114 3.051081 ACAGTCAGATTCAGAAGTGCC 57.949 47.619 0.00 0.00 0.00 5.01
2932 3115 3.188048 CCAACAGTCAGATTCAGAAGTGC 59.812 47.826 0.00 0.00 0.00 4.40
2933 3116 4.635223 TCCAACAGTCAGATTCAGAAGTG 58.365 43.478 0.00 0.00 0.00 3.16
2934 3117 4.963318 TCCAACAGTCAGATTCAGAAGT 57.037 40.909 0.00 0.00 0.00 3.01
2935 3118 6.314896 GGTATTCCAACAGTCAGATTCAGAAG 59.685 42.308 0.00 0.00 0.00 2.85
2936 3119 6.173339 GGTATTCCAACAGTCAGATTCAGAA 58.827 40.000 0.00 0.00 0.00 3.02
2937 3120 5.338381 GGGTATTCCAACAGTCAGATTCAGA 60.338 44.000 0.00 0.00 35.00 3.27
2938 3121 4.878397 GGGTATTCCAACAGTCAGATTCAG 59.122 45.833 0.00 0.00 35.00 3.02
2939 3122 4.324254 GGGGTATTCCAACAGTCAGATTCA 60.324 45.833 0.00 0.00 37.22 2.57
2940 3123 4.080299 AGGGGTATTCCAACAGTCAGATTC 60.080 45.833 0.00 0.00 37.22 2.52
2941 3124 3.852578 AGGGGTATTCCAACAGTCAGATT 59.147 43.478 0.00 0.00 37.22 2.40
2942 3125 3.464828 AGGGGTATTCCAACAGTCAGAT 58.535 45.455 0.00 0.00 37.22 2.90
2943 3126 2.915869 AGGGGTATTCCAACAGTCAGA 58.084 47.619 0.00 0.00 37.22 3.27
2944 3127 3.517901 TGTAGGGGTATTCCAACAGTCAG 59.482 47.826 0.00 0.00 37.22 3.51
2945 3128 3.522759 TGTAGGGGTATTCCAACAGTCA 58.477 45.455 0.00 0.00 37.22 3.41
2946 3129 4.224370 TCTTGTAGGGGTATTCCAACAGTC 59.776 45.833 0.00 0.00 35.34 3.51
2947 3130 4.019591 GTCTTGTAGGGGTATTCCAACAGT 60.020 45.833 0.00 0.00 35.34 3.55
2948 3131 4.514401 GTCTTGTAGGGGTATTCCAACAG 58.486 47.826 0.00 0.00 35.34 3.16
2949 3132 3.264964 GGTCTTGTAGGGGTATTCCAACA 59.735 47.826 0.00 0.00 37.22 3.33
2950 3133 3.680754 CGGTCTTGTAGGGGTATTCCAAC 60.681 52.174 0.00 0.00 37.22 3.77
2951 3134 2.502538 CGGTCTTGTAGGGGTATTCCAA 59.497 50.000 0.00 0.00 37.22 3.53
2952 3135 2.112998 CGGTCTTGTAGGGGTATTCCA 58.887 52.381 0.00 0.00 37.22 3.53
2953 3136 1.415289 CCGGTCTTGTAGGGGTATTCC 59.585 57.143 0.00 0.00 0.00 3.01
2954 3137 1.202615 GCCGGTCTTGTAGGGGTATTC 60.203 57.143 1.90 0.00 0.00 1.75
2955 3138 0.835276 GCCGGTCTTGTAGGGGTATT 59.165 55.000 1.90 0.00 0.00 1.89
2956 3139 0.031414 AGCCGGTCTTGTAGGGGTAT 60.031 55.000 1.90 0.00 0.00 2.73
3124 3321 3.963428 ATACAGAGAAAAGGAGCACGT 57.037 42.857 0.00 0.00 0.00 4.49
3134 3331 8.396390 GTCGAGTGTTACAGATATACAGAGAAA 58.604 37.037 0.00 0.00 0.00 2.52
3208 3405 2.858344 CAGTTTCGTCAGTTTCGTGAGT 59.142 45.455 0.00 0.00 0.00 3.41
3209 3406 3.061139 GTCAGTTTCGTCAGTTTCGTGAG 60.061 47.826 0.00 0.00 0.00 3.51
3210 3407 2.855963 GTCAGTTTCGTCAGTTTCGTGA 59.144 45.455 0.00 0.00 0.00 4.35
3211 3408 2.601314 TGTCAGTTTCGTCAGTTTCGTG 59.399 45.455 0.00 0.00 0.00 4.35
3212 3409 2.883574 TGTCAGTTTCGTCAGTTTCGT 58.116 42.857 0.00 0.00 0.00 3.85
3213 3410 3.787826 CATGTCAGTTTCGTCAGTTTCG 58.212 45.455 0.00 0.00 0.00 3.46
3214 3411 3.545633 GCATGTCAGTTTCGTCAGTTTC 58.454 45.455 0.00 0.00 0.00 2.78
3215 3412 2.032894 CGCATGTCAGTTTCGTCAGTTT 60.033 45.455 0.00 0.00 0.00 2.66
3216 3413 1.526887 CGCATGTCAGTTTCGTCAGTT 59.473 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.