Multiple sequence alignment - TraesCS5D01G056300

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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 TraesCS5D01G056300 chr5D 100.000 3278 0 0 1 3278 52319946 52323223 0.000000e+00 6054.0
1 TraesCS5D01G056300 chr5B 91.124 1780 118 12 559 2309 55421197 55422965 0.000000e+00 2375.0
2 TraesCS5D01G056300 chr5B 94.087 575 23 3 1 564 55420308 55420882 0.000000e+00 863.0
3 TraesCS5D01G056300 chr5B 84.531 640 90 8 1293 1928 236260892 236260258 2.780000e-175 625.0
4 TraesCS5D01G056300 chr5A 96.429 840 30 0 1187 2026 41439084 41439923 0.000000e+00 1386.0
5 TraesCS5D01G056300 chr5A 90.341 528 39 6 559 1083 41438572 41439090 0.000000e+00 682.0
6 TraesCS5D01G056300 chr5A 95.779 308 13 0 2018 2325 41451166 41451473 6.320000e-137 497.0
7 TraesCS5D01G056300 chr5A 81.947 637 48 24 2680 3276 41451756 41452365 8.230000e-131 477.0
8 TraesCS5D01G056300 chr5A 92.760 221 15 1 2338 2558 41451437 41451656 5.280000e-83 318.0
9 TraesCS5D01G056300 chr7A 86.332 1156 127 20 1188 2322 669089575 669088430 0.000000e+00 1230.0
10 TraesCS5D01G056300 chr7A 86.273 1151 137 14 1188 2322 669144530 669143385 0.000000e+00 1230.0
11 TraesCS5D01G056300 chr7A 86.246 1156 128 20 1188 2322 669188391 669187246 0.000000e+00 1225.0
12 TraesCS5D01G056300 chr7A 85.962 1154 134 18 1188 2322 669118102 669116958 0.000000e+00 1208.0
13 TraesCS5D01G056300 chr7A 85.825 1157 130 23 1188 2322 669170462 669169318 0.000000e+00 1197.0
14 TraesCS5D01G056300 chr7D 89.508 305 23 4 1 296 507301587 507301891 8.590000e-101 377.0
15 TraesCS5D01G056300 chr6A 86.786 280 23 4 29 294 515658371 515658092 1.910000e-77 300.0
16 TraesCS5D01G056300 chr2D 87.097 62 8 0 1576 1637 609267294 609267355 1.630000e-08 71.3


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 TraesCS5D01G056300 chr5D 52319946 52323223 3277 False 6054.000000 6054 100.0000 1 3278 1 chr5D.!!$F1 3277
1 TraesCS5D01G056300 chr5B 55420308 55422965 2657 False 1619.000000 2375 92.6055 1 2309 2 chr5B.!!$F1 2308
2 TraesCS5D01G056300 chr5B 236260258 236260892 634 True 625.000000 625 84.5310 1293 1928 1 chr5B.!!$R1 635
3 TraesCS5D01G056300 chr5A 41438572 41439923 1351 False 1034.000000 1386 93.3850 559 2026 2 chr5A.!!$F1 1467
4 TraesCS5D01G056300 chr5A 41451166 41452365 1199 False 430.666667 497 90.1620 2018 3276 3 chr5A.!!$F2 1258
5 TraesCS5D01G056300 chr7A 669088430 669089575 1145 True 1230.000000 1230 86.3320 1188 2322 1 chr7A.!!$R1 1134
6 TraesCS5D01G056300 chr7A 669143385 669144530 1145 True 1230.000000 1230 86.2730 1188 2322 1 chr7A.!!$R3 1134
7 TraesCS5D01G056300 chr7A 669187246 669188391 1145 True 1225.000000 1225 86.2460 1188 2322 1 chr7A.!!$R5 1134
8 TraesCS5D01G056300 chr7A 669116958 669118102 1144 True 1208.000000 1208 85.9620 1188 2322 1 chr7A.!!$R2 1134
9 TraesCS5D01G056300 chr7A 669169318 669170462 1144 True 1197.000000 1197 85.8250 1188 2322 1 chr7A.!!$R4 1134

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
138 148 0.179078 AGTGTTTGCGTTGACCGGTA 60.179 50.000 7.34 0.0 36.94 4.02 F
140 150 0.869068 TGTTTGCGTTGACCGGTATG 59.131 50.000 7.34 0.0 36.94 2.39 F
278 288 1.003580 ACTCACACAAATCATCCGGCT 59.996 47.619 0.00 0.0 0.00 5.52 F
599 931 1.078759 CAGGTTGAGACGATCCGTGC 61.079 60.000 0.00 0.0 41.37 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2229 0.167251 GTATTTGAACGTGCACGGGG 59.833 55.000 39.21 16.13 44.95 5.73 R
1984 2366 1.399440 CATTTCTCCACCATCGCAGTG 59.601 52.381 0.00 0.00 34.91 3.66 R
2175 2557 5.979517 AGCTTGACTTATGTTGCAAAGTTTC 59.020 36.000 0.00 0.00 36.10 2.78 R
2562 2944 3.768215 TGGCCAAGATTCATACATTTGCA 59.232 39.130 0.61 0.00 0.00 4.08 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
45 46 5.836603 CGACAATCGACGTGCTACTAGCA 62.837 52.174 6.66 6.66 45.99 3.49
116 126 6.313658 GGAAGAACAAAGCAAGAACAAAATGT 59.686 34.615 0.00 0.00 0.00 2.71
124 134 4.160252 AGCAAGAACAAAATGTGGAGTGTT 59.840 37.500 0.00 0.00 36.92 3.32
138 148 0.179078 AGTGTTTGCGTTGACCGGTA 60.179 50.000 7.34 0.00 36.94 4.02
139 149 0.869730 GTGTTTGCGTTGACCGGTAT 59.130 50.000 7.34 0.00 36.94 2.73
140 150 0.869068 TGTTTGCGTTGACCGGTATG 59.131 50.000 7.34 0.00 36.94 2.39
151 161 1.276989 GACCGGTATGACCACAAGGAA 59.723 52.381 7.34 0.00 38.47 3.36
161 171 3.071892 TGACCACAAGGAACGGTTAGATT 59.928 43.478 0.00 0.00 38.69 2.40
278 288 1.003580 ACTCACACAAATCATCCGGCT 59.996 47.619 0.00 0.00 0.00 5.52
344 354 9.102757 GTGATTTGATAGAGTTGAAAGCTATGA 57.897 33.333 0.00 0.00 0.00 2.15
387 397 4.018415 CCATAAAACTCCCTCTCCCAGAAA 60.018 45.833 0.00 0.00 0.00 2.52
412 423 6.940831 ACAATGGGGAAAAACATGAAAAAG 57.059 33.333 0.00 0.00 0.00 2.27
426 438 6.340522 ACATGAAAAAGTGAAACAAAGGGAG 58.659 36.000 0.00 0.00 41.43 4.30
452 464 1.856802 AACTAACCACAACCGTCGAC 58.143 50.000 5.18 5.18 0.00 4.20
523 535 2.228241 GCGATTGCGATTCGTCGGA 61.228 57.895 16.11 0.00 40.82 4.55
537 549 4.394712 CGGAGGACAGTGGGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
574 906 3.243873 CGCTAAGGACATGATTGAGCCTA 60.244 47.826 0.00 0.00 33.12 3.93
599 931 1.078759 CAGGTTGAGACGATCCGTGC 61.079 60.000 0.00 0.00 41.37 5.34
657 989 1.141019 GAACGCATCTCAGGCCGTA 59.859 57.895 0.00 0.00 0.00 4.02
732 1064 5.130292 ACTTGTCCAAATTCAGAGCATTG 57.870 39.130 0.00 0.00 0.00 2.82
930 1269 4.921547 AGTACATGCATGAGTACTGTACG 58.078 43.478 32.75 1.99 46.60 3.67
931 1270 4.638865 AGTACATGCATGAGTACTGTACGA 59.361 41.667 32.75 4.03 46.60 3.43
933 1272 3.694566 ACATGCATGAGTACTGTACGAGA 59.305 43.478 32.75 1.32 0.00 4.04
936 1275 5.324784 TGCATGAGTACTGTACGAGATTT 57.675 39.130 11.97 0.00 0.00 2.17
937 1276 5.102313 TGCATGAGTACTGTACGAGATTTG 58.898 41.667 11.97 7.03 0.00 2.32
938 1277 5.103000 GCATGAGTACTGTACGAGATTTGT 58.897 41.667 11.97 0.00 0.00 2.83
940 1279 4.966249 TGAGTACTGTACGAGATTTGTCG 58.034 43.478 11.97 0.00 45.76 4.35
1017 1358 2.497675 TGCAATGGAGGAGAGACTGTAC 59.502 50.000 0.00 0.00 0.00 2.90
1031 1372 2.262292 GTACGCCACCTACCGCAA 59.738 61.111 0.00 0.00 0.00 4.85
1038 1379 2.358737 ACCTACCGCAACAGCAGC 60.359 61.111 0.00 0.00 0.00 5.25
1039 1380 2.358615 CCTACCGCAACAGCAGCA 60.359 61.111 0.00 0.00 0.00 4.41
1040 1381 2.393768 CCTACCGCAACAGCAGCAG 61.394 63.158 0.00 0.00 0.00 4.24
1041 1382 3.031964 CTACCGCAACAGCAGCAGC 62.032 63.158 0.00 0.00 42.56 5.25
1042 1383 3.823397 TACCGCAACAGCAGCAGCA 62.823 57.895 3.17 0.00 45.49 4.41
1043 1384 4.400109 CCGCAACAGCAGCAGCAG 62.400 66.667 3.17 0.00 45.49 4.24
1052 1393 2.970974 GCAGCAGCAGGAACGGTTC 61.971 63.158 12.41 12.41 41.58 3.62
1075 1419 2.335712 GGCTGGACCTTCAAAGCCG 61.336 63.158 4.15 0.00 45.30 5.52
1155 1516 9.968870 GTACTCCATTAACTCGATTAATCTCTT 57.031 33.333 13.45 4.56 40.82 2.85
1163 1524 9.988350 TTAACTCGATTAATCTCTTCAATTTGC 57.012 29.630 13.45 0.00 0.00 3.68
1186 1547 9.719355 TTGCTTTCTACTCTTAATCAATGTGTA 57.281 29.630 0.00 0.00 0.00 2.90
1371 1747 3.447586 TGAAGTGGCCTCTCTATGTGTAC 59.552 47.826 7.99 0.00 0.00 2.90
1984 2366 3.248602 AGTTGTGTTGCTTGATTCTCGTC 59.751 43.478 0.00 0.00 0.00 4.20
2175 2557 3.197790 CATGTCAAGCTCGCCCCG 61.198 66.667 0.00 0.00 0.00 5.73
2317 2699 7.565029 ACCCTTGTATTACTAGTATACCGGTTT 59.435 37.037 15.04 7.86 0.00 3.27
2318 2700 8.424133 CCCTTGTATTACTAGTATACCGGTTTT 58.576 37.037 15.04 3.17 0.00 2.43
2319 2701 9.822185 CCTTGTATTACTAGTATACCGGTTTTT 57.178 33.333 15.04 0.08 0.00 1.94
2343 2725 8.918202 TTTGTATGGATCAGATATTTACACCC 57.082 34.615 0.00 0.00 0.00 4.61
2344 2726 7.872061 TGTATGGATCAGATATTTACACCCT 57.128 36.000 0.00 0.00 0.00 4.34
2345 2727 8.275187 TGTATGGATCAGATATTTACACCCTT 57.725 34.615 0.00 0.00 0.00 3.95
2346 2728 8.156820 TGTATGGATCAGATATTTACACCCTTG 58.843 37.037 0.00 0.00 0.00 3.61
2347 2729 5.376625 TGGATCAGATATTTACACCCTTGC 58.623 41.667 0.00 0.00 0.00 4.01
2348 2730 5.104151 TGGATCAGATATTTACACCCTTGCA 60.104 40.000 0.00 0.00 0.00 4.08
2349 2731 6.006449 GGATCAGATATTTACACCCTTGCAT 58.994 40.000 0.00 0.00 0.00 3.96
2350 2732 6.491403 GGATCAGATATTTACACCCTTGCATT 59.509 38.462 0.00 0.00 0.00 3.56
2351 2733 7.665559 GGATCAGATATTTACACCCTTGCATTA 59.334 37.037 0.00 0.00 0.00 1.90
2352 2734 7.801716 TCAGATATTTACACCCTTGCATTAC 57.198 36.000 0.00 0.00 0.00 1.89
2353 2735 7.573710 TCAGATATTTACACCCTTGCATTACT 58.426 34.615 0.00 0.00 0.00 2.24
2354 2736 8.710239 TCAGATATTTACACCCTTGCATTACTA 58.290 33.333 0.00 0.00 0.00 1.82
2355 2737 8.993121 CAGATATTTACACCCTTGCATTACTAG 58.007 37.037 0.00 0.00 0.00 2.57
2356 2738 8.714906 AGATATTTACACCCTTGCATTACTAGT 58.285 33.333 0.00 0.00 0.00 2.57
2357 2739 9.991906 GATATTTACACCCTTGCATTACTAGTA 57.008 33.333 0.00 0.00 0.00 1.82
2360 2742 9.774413 ATTTACACCCTTGCATTACTAGTATAC 57.226 33.333 2.79 0.00 0.00 1.47
2361 2743 6.170846 ACACCCTTGCATTACTAGTATACC 57.829 41.667 2.79 0.00 0.00 2.73
2362 2744 5.221382 ACACCCTTGCATTACTAGTATACCG 60.221 44.000 2.79 0.00 0.00 4.02
2363 2745 4.282703 ACCCTTGCATTACTAGTATACCGG 59.717 45.833 2.79 0.00 0.00 5.28
2364 2746 4.282703 CCCTTGCATTACTAGTATACCGGT 59.717 45.833 13.98 13.98 0.00 5.28
2365 2747 5.221581 CCCTTGCATTACTAGTATACCGGTT 60.222 44.000 15.04 3.05 0.00 4.44
2366 2748 6.285990 CCTTGCATTACTAGTATACCGGTTT 58.714 40.000 15.04 7.86 0.00 3.27
2433 2815 5.068987 TCGTACCCTGTTTTACAAGTACTGT 59.931 40.000 0.00 0.00 42.47 3.55
2551 2933 1.985473 TTTGATTGTGTCCAGCAGCT 58.015 45.000 0.00 0.00 0.00 4.24
2556 2938 2.566833 TTGTGTCCAGCAGCTGTATT 57.433 45.000 21.26 0.00 0.00 1.89
2557 2939 3.694043 TTGTGTCCAGCAGCTGTATTA 57.306 42.857 21.26 1.90 0.00 0.98
2558 2940 3.694043 TGTGTCCAGCAGCTGTATTAA 57.306 42.857 21.26 1.04 0.00 1.40
2559 2941 4.220693 TGTGTCCAGCAGCTGTATTAAT 57.779 40.909 21.26 0.00 0.00 1.40
2560 2942 4.588899 TGTGTCCAGCAGCTGTATTAATT 58.411 39.130 21.26 0.00 0.00 1.40
2561 2943 5.739959 TGTGTCCAGCAGCTGTATTAATTA 58.260 37.500 21.26 0.00 0.00 1.40
2562 2944 6.356556 TGTGTCCAGCAGCTGTATTAATTAT 58.643 36.000 21.26 0.00 0.00 1.28
2563 2945 6.260714 TGTGTCCAGCAGCTGTATTAATTATG 59.739 38.462 21.26 1.78 0.00 1.90
2564 2946 5.239306 TGTCCAGCAGCTGTATTAATTATGC 59.761 40.000 21.26 0.00 0.00 3.14
2565 2947 5.239306 GTCCAGCAGCTGTATTAATTATGCA 59.761 40.000 21.26 0.00 34.71 3.96
2566 2948 5.827267 TCCAGCAGCTGTATTAATTATGCAA 59.173 36.000 21.26 0.00 34.71 4.08
2567 2949 6.320926 TCCAGCAGCTGTATTAATTATGCAAA 59.679 34.615 21.26 0.00 34.71 3.68
2568 2950 7.014518 TCCAGCAGCTGTATTAATTATGCAAAT 59.985 33.333 21.26 0.00 34.71 2.32
2569 2951 7.115805 CCAGCAGCTGTATTAATTATGCAAATG 59.884 37.037 21.26 0.00 34.71 2.32
2570 2952 7.650504 CAGCAGCTGTATTAATTATGCAAATGT 59.349 33.333 16.64 0.00 34.71 2.71
2571 2953 8.849168 AGCAGCTGTATTAATTATGCAAATGTA 58.151 29.630 16.64 0.00 34.71 2.29
2572 2954 9.630098 GCAGCTGTATTAATTATGCAAATGTAT 57.370 29.630 16.64 0.00 32.58 2.29
2582 2964 8.597662 AATTATGCAAATGTATGAATCTTGGC 57.402 30.769 0.00 0.00 0.00 4.52
2583 2965 4.389890 TGCAAATGTATGAATCTTGGCC 57.610 40.909 0.00 0.00 0.00 5.36
2584 2966 3.768215 TGCAAATGTATGAATCTTGGCCA 59.232 39.130 0.00 0.00 0.00 5.36
2585 2967 4.222366 TGCAAATGTATGAATCTTGGCCAA 59.778 37.500 19.25 19.25 0.00 4.52
2586 2968 5.104859 TGCAAATGTATGAATCTTGGCCAAT 60.105 36.000 20.85 3.65 0.00 3.16
2587 2969 6.097981 TGCAAATGTATGAATCTTGGCCAATA 59.902 34.615 20.85 13.13 0.00 1.90
2588 2970 7.156673 GCAAATGTATGAATCTTGGCCAATAT 58.843 34.615 20.85 15.15 0.00 1.28
2589 2971 7.117236 GCAAATGTATGAATCTTGGCCAATATG 59.883 37.037 20.85 7.87 0.00 1.78
2590 2972 7.844493 AATGTATGAATCTTGGCCAATATGT 57.156 32.000 20.85 9.81 0.00 2.29
2591 2973 6.882610 TGTATGAATCTTGGCCAATATGTC 57.117 37.500 20.85 16.26 0.00 3.06
2592 2974 6.363882 TGTATGAATCTTGGCCAATATGTCA 58.636 36.000 20.85 20.55 0.00 3.58
2593 2975 7.005902 TGTATGAATCTTGGCCAATATGTCAT 58.994 34.615 26.06 26.06 0.00 3.06
2594 2976 6.989155 ATGAATCTTGGCCAATATGTCATT 57.011 33.333 20.85 10.17 0.00 2.57
2595 2977 6.151663 TGAATCTTGGCCAATATGTCATTG 57.848 37.500 20.85 3.71 0.00 2.82
2596 2978 5.657745 TGAATCTTGGCCAATATGTCATTGT 59.342 36.000 20.85 0.00 0.00 2.71
2597 2979 6.154877 TGAATCTTGGCCAATATGTCATTGTT 59.845 34.615 20.85 0.00 0.00 2.83
2598 2980 5.999205 TCTTGGCCAATATGTCATTGTTT 57.001 34.783 20.85 0.00 0.00 2.83
2599 2981 7.658525 ATCTTGGCCAATATGTCATTGTTTA 57.341 32.000 20.85 0.00 0.00 2.01
2600 2982 7.658525 TCTTGGCCAATATGTCATTGTTTAT 57.341 32.000 20.85 0.00 0.00 1.40
2601 2983 8.759481 TCTTGGCCAATATGTCATTGTTTATA 57.241 30.769 20.85 0.00 0.00 0.98
2602 2984 9.194972 TCTTGGCCAATATGTCATTGTTTATAA 57.805 29.630 20.85 0.00 0.00 0.98
2603 2985 9.985730 CTTGGCCAATATGTCATTGTTTATAAT 57.014 29.630 20.85 0.00 0.00 1.28
2604 2986 9.979578 TTGGCCAATATGTCATTGTTTATAATC 57.020 29.630 16.05 0.00 0.00 1.75
2605 2987 9.365906 TGGCCAATATGTCATTGTTTATAATCT 57.634 29.630 0.61 0.00 0.00 2.40
2606 2988 9.846248 GGCCAATATGTCATTGTTTATAATCTC 57.154 33.333 0.00 0.00 0.00 2.75
2623 3005 7.759489 ATAATCTCTAGGCTCTAGACACAAG 57.241 40.000 7.59 0.57 0.00 3.16
2649 3031 6.883744 ACTTGGGTTTCTCAGAAGATAGATC 58.116 40.000 0.00 0.00 0.00 2.75
2656 3038 7.433680 GTTTCTCAGAAGATAGATCCCTTCTC 58.566 42.308 15.57 4.92 45.09 2.87
2657 3039 6.529084 TCTCAGAAGATAGATCCCTTCTCT 57.471 41.667 15.57 0.45 45.09 3.10
2694 3106 3.194329 GCTGATGGGTATGATCGATCTGA 59.806 47.826 25.02 10.92 0.00 3.27
2698 3110 2.833943 TGGGTATGATCGATCTGATGGG 59.166 50.000 25.02 0.00 37.47 4.00
2701 3113 4.499183 GGTATGATCGATCTGATGGGAAC 58.501 47.826 25.02 11.24 37.47 3.62
2709 3121 0.251354 TCTGATGGGAACTGCTCTGC 59.749 55.000 0.00 0.00 0.00 4.26
2719 3131 2.775911 ACTGCTCTGCTTATTGCTGA 57.224 45.000 0.00 0.00 45.30 4.26
2720 3132 3.063510 ACTGCTCTGCTTATTGCTGAA 57.936 42.857 0.00 0.00 46.39 3.02
2721 3133 2.746362 ACTGCTCTGCTTATTGCTGAAC 59.254 45.455 0.00 0.00 46.39 3.18
2723 3135 2.002586 GCTCTGCTTATTGCTGAACGA 58.997 47.619 0.00 0.00 46.39 3.85
2724 3136 2.222908 GCTCTGCTTATTGCTGAACGAC 60.223 50.000 0.00 0.00 46.39 4.34
2725 3137 2.346803 TCTGCTTATTGCTGAACGACC 58.653 47.619 0.00 0.00 44.69 4.79
2726 3138 2.028112 TCTGCTTATTGCTGAACGACCT 60.028 45.455 0.00 0.00 44.69 3.85
2727 3139 3.194755 TCTGCTTATTGCTGAACGACCTA 59.805 43.478 0.00 0.00 44.69 3.08
2728 3140 3.521560 TGCTTATTGCTGAACGACCTAG 58.478 45.455 0.00 0.00 43.37 3.02
2729 3141 2.866762 GCTTATTGCTGAACGACCTAGG 59.133 50.000 7.41 7.41 38.95 3.02
2730 3142 2.596904 TATTGCTGAACGACCTAGGC 57.403 50.000 9.30 0.36 0.00 3.93
2731 3143 0.107654 ATTGCTGAACGACCTAGGCC 60.108 55.000 9.30 0.00 0.00 5.19
2732 3144 1.476845 TTGCTGAACGACCTAGGCCA 61.477 55.000 9.30 0.00 0.00 5.36
2733 3145 1.448013 GCTGAACGACCTAGGCCAC 60.448 63.158 9.30 0.00 0.00 5.01
2734 3146 1.218316 CTGAACGACCTAGGCCACC 59.782 63.158 9.30 0.00 0.00 4.61
2735 3147 1.534476 TGAACGACCTAGGCCACCA 60.534 57.895 9.30 0.00 0.00 4.17
2736 3148 1.079336 GAACGACCTAGGCCACCAC 60.079 63.158 9.30 0.00 0.00 4.16
2750 3162 0.389025 CACCACCCACCAGAAAAAGC 59.611 55.000 0.00 0.00 0.00 3.51
2766 3178 3.733443 AAAGCAAGATGGTTTGTGACC 57.267 42.857 6.72 0.00 45.13 4.02
2786 3198 7.148000 TGTGACCATCAATTTTGAGTTGTACAA 60.148 33.333 3.59 3.59 41.08 2.41
2799 3211 1.720805 TGTACAAGTGTATGCAGGCG 58.279 50.000 0.00 0.00 32.54 5.52
2822 3234 3.568007 TGTCAACTTGTTAATGGACTGCC 59.432 43.478 0.00 0.00 0.00 4.85
2836 3248 1.129437 GACTGCCGAGTGAATTGCTTC 59.871 52.381 0.00 0.00 30.16 3.86
2851 3266 9.101655 GTGAATTGCTTCCTTATTATGCAAAAT 57.898 29.630 0.00 0.00 44.90 1.82
2858 3273 8.204160 GCTTCCTTATTATGCAAAATAAAGGGT 58.796 33.333 14.52 0.00 32.41 4.34
2859 3274 9.750125 CTTCCTTATTATGCAAAATAAAGGGTC 57.250 33.333 14.52 0.00 32.41 4.46
2886 3303 8.660373 CAGACTTAATCAGTGGTATTCAGAAAC 58.340 37.037 0.00 0.00 35.01 2.78
2888 3305 8.779354 ACTTAATCAGTGGTATTCAGAAACTC 57.221 34.615 0.00 0.00 32.83 3.01
2905 3322 5.187772 AGAAACTCAATTAAATTGGAGCCCC 59.812 40.000 0.00 0.00 40.61 5.80
2914 3331 2.510664 TTGGAGCCCCAACAAACAC 58.489 52.632 0.00 0.00 46.94 3.32
2921 3353 2.365293 AGCCCCAACAAACACTTCATTC 59.635 45.455 0.00 0.00 0.00 2.67
2927 3359 5.394005 CCCAACAAACACTTCATTCTTCACA 60.394 40.000 0.00 0.00 0.00 3.58
2944 3377 7.408132 TCTTCACAAAACAAATCGAGTAGAG 57.592 36.000 0.00 0.00 0.00 2.43
2987 3422 8.049117 TGATCTTCATATTAAACTCCAAGCTGT 58.951 33.333 0.00 0.00 0.00 4.40
2992 3427 6.543465 TCATATTAAACTCCAAGCTGTCATGG 59.457 38.462 0.00 0.00 38.09 3.66
3002 3437 4.543692 CAAGCTGTCATGGAAGAAACAAG 58.456 43.478 0.00 0.00 0.00 3.16
3012 3447 3.130340 TGGAAGAAACAAGCCAGAAACAC 59.870 43.478 0.00 0.00 0.00 3.32
3036 3471 9.552114 CACTGAAAATGATCTTACATGTTTCTC 57.448 33.333 2.30 0.00 33.70 2.87
3039 3474 8.229811 TGAAAATGATCTTACATGTTTCTCGTG 58.770 33.333 2.30 0.00 38.86 4.35
3045 3480 0.531974 ACATGTTTCTCGTGTGCGGT 60.532 50.000 0.00 0.00 43.67 5.68
3053 3488 2.142418 CTCGTGTGCGGTCGTTTGAC 62.142 60.000 0.00 0.00 44.72 3.18
3063 3498 2.597305 CGGTCGTTTGACTACATACAGC 59.403 50.000 0.00 0.00 44.83 4.40
3066 3501 1.924524 CGTTTGACTACATACAGCCGG 59.075 52.381 0.00 0.00 0.00 6.13
3083 3518 2.432444 CCGGTTTGGCTAGTTTCATCA 58.568 47.619 0.00 0.00 0.00 3.07
3084 3519 2.817258 CCGGTTTGGCTAGTTTCATCAA 59.183 45.455 0.00 0.00 0.00 2.57
3085 3520 3.365969 CCGGTTTGGCTAGTTTCATCAAC 60.366 47.826 0.00 0.00 35.32 3.18
3086 3521 3.252215 CGGTTTGGCTAGTTTCATCAACA 59.748 43.478 0.00 0.00 37.93 3.33
3087 3522 4.613622 CGGTTTGGCTAGTTTCATCAACAG 60.614 45.833 0.00 0.00 37.93 3.16
3088 3523 4.321230 GGTTTGGCTAGTTTCATCAACAGG 60.321 45.833 0.00 0.00 37.93 4.00
3089 3524 2.436417 TGGCTAGTTTCATCAACAGGC 58.564 47.619 0.00 0.00 37.93 4.85
3090 3525 2.224744 TGGCTAGTTTCATCAACAGGCA 60.225 45.455 8.36 8.36 41.95 4.75
3091 3526 2.421424 GGCTAGTTTCATCAACAGGCAG 59.579 50.000 0.00 0.00 38.18 4.85
3092 3527 2.159462 GCTAGTTTCATCAACAGGCAGC 60.159 50.000 0.00 0.00 37.93 5.25
3093 3528 1.985473 AGTTTCATCAACAGGCAGCA 58.015 45.000 0.00 0.00 37.93 4.41
3094 3529 1.610522 AGTTTCATCAACAGGCAGCAC 59.389 47.619 0.00 0.00 37.93 4.40
3095 3530 1.337703 GTTTCATCAACAGGCAGCACA 59.662 47.619 0.00 0.00 35.18 4.57
3096 3531 1.689984 TTCATCAACAGGCAGCACAA 58.310 45.000 0.00 0.00 0.00 3.33
3097 3532 0.953727 TCATCAACAGGCAGCACAAC 59.046 50.000 0.00 0.00 0.00 3.32
3098 3533 0.669619 CATCAACAGGCAGCACAACA 59.330 50.000 0.00 0.00 0.00 3.33
3099 3534 0.670162 ATCAACAGGCAGCACAACAC 59.330 50.000 0.00 0.00 0.00 3.32
3100 3535 0.679321 TCAACAGGCAGCACAACACA 60.679 50.000 0.00 0.00 0.00 3.72
3101 3536 0.526096 CAACAGGCAGCACAACACAC 60.526 55.000 0.00 0.00 0.00 3.82
3102 3537 1.666209 AACAGGCAGCACAACACACC 61.666 55.000 0.00 0.00 0.00 4.16
3127 3562 7.095102 CCTGACACATGAATTTCCCAAAATTTC 60.095 37.037 0.00 0.00 43.48 2.17
3139 3574 6.126568 TCCCAAAATTTCGATCGATAAACC 57.873 37.500 20.18 0.00 0.00 3.27
3161 3596 4.203563 CCGCAAAAGTTTCGACAACTTTAC 59.796 41.667 25.08 20.90 46.33 2.01
3162 3597 4.789119 CGCAAAAGTTTCGACAACTTTACA 59.211 37.500 25.08 0.00 46.33 2.41
3163 3598 5.454232 CGCAAAAGTTTCGACAACTTTACAT 59.546 36.000 25.08 14.95 46.33 2.29
3171 3609 9.485206 AGTTTCGACAACTTTACATATACAACT 57.515 29.630 7.04 0.00 0.00 3.16
3174 3612 9.701098 TTCGACAACTTTACATATACAACTTCT 57.299 29.630 0.00 0.00 0.00 2.85
3205 3643 3.955650 AGACTTAGGTTGCGCTCTAAA 57.044 42.857 9.73 0.00 0.00 1.85
3207 3645 4.246458 AGACTTAGGTTGCGCTCTAAAAG 58.754 43.478 9.73 9.71 0.00 2.27
3209 3647 1.734163 TAGGTTGCGCTCTAAAAGGC 58.266 50.000 9.73 0.00 0.00 4.35
3230 3681 4.462483 GGCACTCCAATGTATTCTTCCAAA 59.538 41.667 0.00 0.00 0.00 3.28
3234 3685 7.523709 GCACTCCAATGTATTCTTCCAAAAAGA 60.524 37.037 0.00 0.00 0.00 2.52
3269 3720 4.686554 ACTCTTTAAGTTGATCGTGCAGAC 59.313 41.667 0.00 0.00 33.03 3.51
3271 3722 4.686091 TCTTTAAGTTGATCGTGCAGACTG 59.314 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.797249 AGTAGCACGTCGATTGTCGC 60.797 55.000 0.00 0.00 40.21 5.19
23 24 2.364128 CTAGTAGCACGTCGATTGTCG 58.636 52.381 0.00 0.00 42.10 4.35
45 46 3.276846 GGCACCGTCGCAACACTT 61.277 61.111 0.00 0.00 0.00 3.16
116 126 1.433053 CGGTCAACGCAAACACTCCA 61.433 55.000 0.00 0.00 34.82 3.86
124 134 0.671163 GGTCATACCGGTCAACGCAA 60.671 55.000 12.40 0.00 42.52 4.85
138 148 2.635915 TCTAACCGTTCCTTGTGGTCAT 59.364 45.455 0.00 0.00 34.11 3.06
139 149 2.040939 TCTAACCGTTCCTTGTGGTCA 58.959 47.619 0.00 0.00 34.11 4.02
140 150 2.825861 TCTAACCGTTCCTTGTGGTC 57.174 50.000 0.00 0.00 34.11 4.02
151 161 6.183360 CGCAAATGTCTCTTTAATCTAACCGT 60.183 38.462 0.00 0.00 0.00 4.83
161 171 5.940192 ATGTCAACGCAAATGTCTCTTTA 57.060 34.783 0.00 0.00 0.00 1.85
249 259 4.854399 TGATTTGTGTGAGTTTTAAGCCG 58.146 39.130 0.00 0.00 0.00 5.52
344 354 0.338467 GGTAAAAAGGGAGGGGGCAT 59.662 55.000 0.00 0.00 0.00 4.40
387 397 8.217111 ACTTTTTCATGTTTTTCCCCATTGTAT 58.783 29.630 0.00 0.00 0.00 2.29
412 423 0.875059 CTCGCCTCCCTTTGTTTCAC 59.125 55.000 0.00 0.00 0.00 3.18
426 438 1.534163 GGTTGTGGTTAGTTTCTCGCC 59.466 52.381 0.00 0.00 0.00 5.54
452 464 2.091610 TCCCTGTCAGATCCCTACTCTG 60.092 54.545 0.00 0.00 41.23 3.35
523 535 2.122413 TCTGCCACCCACTGTCCT 60.122 61.111 0.00 0.00 0.00 3.85
552 564 1.869767 GGCTCAATCATGTCCTTAGCG 59.130 52.381 0.00 0.00 0.00 4.26
557 569 2.507058 TGCTTAGGCTCAATCATGTCCT 59.493 45.455 0.00 0.00 39.59 3.85
574 906 0.322975 ATCGTCTCAACCTGCTGCTT 59.677 50.000 0.00 0.00 0.00 3.91
599 931 2.513204 CCACCTCCTGCATCTGCG 60.513 66.667 0.00 0.00 45.83 5.18
652 984 1.471676 CCTCTCCATGAGTTGTACGGC 60.472 57.143 0.00 0.00 41.11 5.68
657 989 2.569404 GTCTTCCCTCTCCATGAGTTGT 59.431 50.000 0.00 0.00 41.11 3.32
673 1005 4.109050 GAGATGTGGTTCGAGATGTCTTC 58.891 47.826 0.00 0.00 0.00 2.87
732 1064 0.723129 CGAATCCGATCTCGACGAGC 60.723 60.000 20.11 6.21 43.02 5.03
839 1171 2.711542 TCTTCTTTTCCTCGGCAATCC 58.288 47.619 0.00 0.00 0.00 3.01
927 1266 5.178061 TCCTACTGTACGACAAATCTCGTA 58.822 41.667 0.00 0.00 45.03 3.43
930 1269 4.639310 TCCTCCTACTGTACGACAAATCTC 59.361 45.833 0.00 0.00 0.00 2.75
931 1270 4.597004 TCCTCCTACTGTACGACAAATCT 58.403 43.478 0.00 0.00 0.00 2.40
933 1272 3.700038 CCTCCTCCTACTGTACGACAAAT 59.300 47.826 0.00 0.00 0.00 2.32
936 1275 1.911357 TCCTCCTCCTACTGTACGACA 59.089 52.381 0.00 0.00 0.00 4.35
937 1276 2.563702 CTCCTCCTCCTACTGTACGAC 58.436 57.143 0.00 0.00 0.00 4.34
938 1277 1.489649 CCTCCTCCTCCTACTGTACGA 59.510 57.143 0.00 0.00 0.00 3.43
940 1279 2.158579 CCTCCTCCTCCTCCTACTGTAC 60.159 59.091 0.00 0.00 0.00 2.90
942 1281 0.930726 CCTCCTCCTCCTCCTACTGT 59.069 60.000 0.00 0.00 0.00 3.55
943 1282 1.144913 CTCCTCCTCCTCCTCCTACTG 59.855 61.905 0.00 0.00 0.00 2.74
944 1283 1.011545 TCTCCTCCTCCTCCTCCTACT 59.988 57.143 0.00 0.00 0.00 2.57
945 1284 1.144298 GTCTCCTCCTCCTCCTCCTAC 59.856 61.905 0.00 0.00 0.00 3.18
946 1285 1.525175 GTCTCCTCCTCCTCCTCCTA 58.475 60.000 0.00 0.00 0.00 2.94
1017 1358 3.118454 CTGTTGCGGTAGGTGGCG 61.118 66.667 0.00 0.00 0.00 5.69
1031 1372 2.667536 CGTTCCTGCTGCTGCTGT 60.668 61.111 17.00 0.00 40.48 4.40
1038 1379 1.361668 CCGATGAACCGTTCCTGCTG 61.362 60.000 8.80 0.00 0.00 4.41
1039 1380 1.079127 CCGATGAACCGTTCCTGCT 60.079 57.895 8.80 0.00 0.00 4.24
1040 1381 2.106683 CCCGATGAACCGTTCCTGC 61.107 63.158 8.80 0.00 0.00 4.85
1041 1382 2.106683 GCCCGATGAACCGTTCCTG 61.107 63.158 8.80 0.00 0.00 3.86
1042 1383 2.267961 GCCCGATGAACCGTTCCT 59.732 61.111 8.80 0.00 0.00 3.36
1043 1384 2.106683 CAGCCCGATGAACCGTTCC 61.107 63.158 8.80 0.00 0.00 3.62
1052 1393 0.322456 TTTGAAGGTCCAGCCCGATG 60.322 55.000 0.00 0.00 38.26 3.84
1169 1530 9.896645 ACATGAATCTACACATTGATTAAGAGT 57.103 29.630 0.00 0.00 33.60 3.24
1186 1547 4.639310 GCTGTGAGGAATCAACATGAATCT 59.361 41.667 0.00 0.00 0.00 2.40
1285 1661 1.690985 TGGTCCCGGTGGCATGATA 60.691 57.895 0.00 0.00 0.00 2.15
1847 2229 0.167251 GTATTTGAACGTGCACGGGG 59.833 55.000 39.21 16.13 44.95 5.73
1984 2366 1.399440 CATTTCTCCACCATCGCAGTG 59.601 52.381 0.00 0.00 34.91 3.66
2175 2557 5.979517 AGCTTGACTTATGTTGCAAAGTTTC 59.020 36.000 0.00 0.00 36.10 2.78
2317 2699 9.349713 GGGTGTAAATATCTGATCCATACAAAA 57.650 33.333 0.00 0.00 0.00 2.44
2318 2700 8.723365 AGGGTGTAAATATCTGATCCATACAAA 58.277 33.333 0.00 0.00 0.00 2.83
2319 2701 8.275187 AGGGTGTAAATATCTGATCCATACAA 57.725 34.615 0.00 0.00 0.00 2.41
2320 2702 7.872061 AGGGTGTAAATATCTGATCCATACA 57.128 36.000 0.00 0.00 0.00 2.29
2321 2703 7.119846 GCAAGGGTGTAAATATCTGATCCATAC 59.880 40.741 0.00 0.00 0.00 2.39
2322 2704 7.168219 GCAAGGGTGTAAATATCTGATCCATA 58.832 38.462 0.00 0.00 0.00 2.74
2323 2705 6.006449 GCAAGGGTGTAAATATCTGATCCAT 58.994 40.000 0.00 0.00 0.00 3.41
2324 2706 5.104151 TGCAAGGGTGTAAATATCTGATCCA 60.104 40.000 0.00 0.00 0.00 3.41
2325 2707 5.376625 TGCAAGGGTGTAAATATCTGATCC 58.623 41.667 0.00 0.00 0.00 3.36
2326 2708 7.516198 AATGCAAGGGTGTAAATATCTGATC 57.484 36.000 0.00 0.00 0.00 2.92
2327 2709 8.220559 AGTAATGCAAGGGTGTAAATATCTGAT 58.779 33.333 0.00 0.00 0.00 2.90
2328 2710 7.573710 AGTAATGCAAGGGTGTAAATATCTGA 58.426 34.615 0.00 0.00 0.00 3.27
2329 2711 7.807977 AGTAATGCAAGGGTGTAAATATCTG 57.192 36.000 0.00 0.00 0.00 2.90
2330 2712 8.714906 ACTAGTAATGCAAGGGTGTAAATATCT 58.285 33.333 0.00 0.00 0.00 1.98
2331 2713 8.904099 ACTAGTAATGCAAGGGTGTAAATATC 57.096 34.615 0.00 0.00 0.00 1.63
2334 2716 9.774413 GTATACTAGTAATGCAAGGGTGTAAAT 57.226 33.333 6.70 0.00 0.00 1.40
2335 2717 8.206189 GGTATACTAGTAATGCAAGGGTGTAAA 58.794 37.037 6.70 0.00 0.00 2.01
2336 2718 7.470424 CGGTATACTAGTAATGCAAGGGTGTAA 60.470 40.741 6.70 0.00 0.00 2.41
2337 2719 6.016024 CGGTATACTAGTAATGCAAGGGTGTA 60.016 42.308 6.70 0.00 0.00 2.90
2338 2720 5.221382 CGGTATACTAGTAATGCAAGGGTGT 60.221 44.000 6.70 0.00 0.00 4.16
2339 2721 5.227908 CGGTATACTAGTAATGCAAGGGTG 58.772 45.833 6.70 0.00 0.00 4.61
2340 2722 4.282703 CCGGTATACTAGTAATGCAAGGGT 59.717 45.833 6.70 0.00 0.00 4.34
2341 2723 4.282703 ACCGGTATACTAGTAATGCAAGGG 59.717 45.833 4.49 5.14 0.00 3.95
2342 2724 5.464030 ACCGGTATACTAGTAATGCAAGG 57.536 43.478 4.49 8.48 0.00 3.61
2343 2725 7.781548 AAAACCGGTATACTAGTAATGCAAG 57.218 36.000 8.00 0.00 0.00 4.01
2393 2775 9.669887 ACAGGGTACGATACACAAATATTTAAA 57.330 29.630 0.00 0.00 33.51 1.52
2407 2789 7.039784 ACAGTACTTGTAAAACAGGGTACGATA 60.040 37.037 0.00 0.00 40.52 2.92
2410 2792 5.291971 ACAGTACTTGTAAAACAGGGTACG 58.708 41.667 0.00 12.37 40.52 3.67
2414 2796 6.859017 ACAAAACAGTACTTGTAAAACAGGG 58.141 36.000 0.00 0.00 39.73 4.45
2444 2826 8.908786 TCTGATCCATTCATAAATAGTTGGAC 57.091 34.615 0.00 0.00 32.72 4.02
2515 2897 8.918658 CACAATCAAAACAGAAATACTTCATGG 58.081 33.333 0.00 0.00 33.64 3.66
2556 2938 9.695526 GCCAAGATTCATACATTTGCATAATTA 57.304 29.630 0.00 0.00 0.00 1.40
2557 2939 7.658575 GGCCAAGATTCATACATTTGCATAATT 59.341 33.333 0.00 0.00 0.00 1.40
2558 2940 7.156673 GGCCAAGATTCATACATTTGCATAAT 58.843 34.615 0.00 0.00 0.00 1.28
2559 2941 6.097981 TGGCCAAGATTCATACATTTGCATAA 59.902 34.615 0.61 0.00 0.00 1.90
2560 2942 5.597594 TGGCCAAGATTCATACATTTGCATA 59.402 36.000 0.61 0.00 0.00 3.14
2561 2943 4.406326 TGGCCAAGATTCATACATTTGCAT 59.594 37.500 0.61 0.00 0.00 3.96
2562 2944 3.768215 TGGCCAAGATTCATACATTTGCA 59.232 39.130 0.61 0.00 0.00 4.08
2563 2945 4.389890 TGGCCAAGATTCATACATTTGC 57.610 40.909 0.61 0.00 0.00 3.68
2564 2946 8.145767 ACATATTGGCCAAGATTCATACATTTG 58.854 33.333 22.88 11.63 0.00 2.32
2565 2947 8.253867 ACATATTGGCCAAGATTCATACATTT 57.746 30.769 22.88 3.70 0.00 2.32
2566 2948 7.506599 TGACATATTGGCCAAGATTCATACATT 59.493 33.333 22.88 3.91 0.00 2.71
2567 2949 7.005902 TGACATATTGGCCAAGATTCATACAT 58.994 34.615 22.88 4.46 0.00 2.29
2568 2950 6.363882 TGACATATTGGCCAAGATTCATACA 58.636 36.000 22.88 14.47 0.00 2.29
2569 2951 6.882610 TGACATATTGGCCAAGATTCATAC 57.117 37.500 22.88 12.34 0.00 2.39
2570 2952 7.506599 ACAATGACATATTGGCCAAGATTCATA 59.493 33.333 29.89 18.39 33.56 2.15
2571 2953 6.325545 ACAATGACATATTGGCCAAGATTCAT 59.674 34.615 27.20 27.20 33.56 2.57
2572 2954 5.657745 ACAATGACATATTGGCCAAGATTCA 59.342 36.000 25.96 25.96 33.56 2.57
2573 2955 6.152932 ACAATGACATATTGGCCAAGATTC 57.847 37.500 22.88 20.89 33.56 2.52
2574 2956 6.549433 AACAATGACATATTGGCCAAGATT 57.451 33.333 22.88 14.05 33.56 2.40
2575 2957 6.549433 AAACAATGACATATTGGCCAAGAT 57.451 33.333 24.94 22.40 33.56 2.40
2576 2958 5.999205 AAACAATGACATATTGGCCAAGA 57.001 34.783 24.94 20.93 33.56 3.02
2577 2959 9.985730 ATTATAAACAATGACATATTGGCCAAG 57.014 29.630 24.94 13.02 33.56 3.61
2578 2960 9.979578 GATTATAAACAATGACATATTGGCCAA 57.020 29.630 23.00 23.00 33.56 4.52
2579 2961 9.365906 AGATTATAAACAATGACATATTGGCCA 57.634 29.630 0.00 0.00 33.56 5.36
2580 2962 9.846248 GAGATTATAAACAATGACATATTGGCC 57.154 33.333 0.00 0.00 33.56 5.36
2587 2969 9.717942 GAGCCTAGAGATTATAAACAATGACAT 57.282 33.333 0.00 0.00 0.00 3.06
2588 2970 8.928448 AGAGCCTAGAGATTATAAACAATGACA 58.072 33.333 0.00 0.00 0.00 3.58
2593 2975 9.642343 TGTCTAGAGCCTAGAGATTATAAACAA 57.358 33.333 10.98 0.00 0.00 2.83
2594 2976 9.069082 GTGTCTAGAGCCTAGAGATTATAAACA 57.931 37.037 10.98 2.83 0.00 2.83
2595 2977 9.069082 TGTGTCTAGAGCCTAGAGATTATAAAC 57.931 37.037 10.98 0.00 0.00 2.01
2596 2978 9.642343 TTGTGTCTAGAGCCTAGAGATTATAAA 57.358 33.333 10.98 2.13 0.00 1.40
2597 2979 9.290988 CTTGTGTCTAGAGCCTAGAGATTATAA 57.709 37.037 10.98 0.00 0.00 0.98
2598 2980 8.441572 ACTTGTGTCTAGAGCCTAGAGATTATA 58.558 37.037 10.98 0.00 0.00 0.98
2599 2981 7.294584 ACTTGTGTCTAGAGCCTAGAGATTAT 58.705 38.462 10.98 0.00 0.00 1.28
2600 2982 6.664714 ACTTGTGTCTAGAGCCTAGAGATTA 58.335 40.000 10.98 3.51 0.00 1.75
2601 2983 5.515106 ACTTGTGTCTAGAGCCTAGAGATT 58.485 41.667 10.98 0.00 0.00 2.40
2602 2984 5.124036 ACTTGTGTCTAGAGCCTAGAGAT 57.876 43.478 10.98 0.00 0.00 2.75
2603 2985 4.577988 ACTTGTGTCTAGAGCCTAGAGA 57.422 45.455 10.98 8.13 0.00 3.10
2604 2986 5.433526 AGTACTTGTGTCTAGAGCCTAGAG 58.566 45.833 10.98 4.02 0.00 2.43
2605 2987 5.438698 AGTACTTGTGTCTAGAGCCTAGA 57.561 43.478 7.59 7.59 0.00 2.43
2606 2988 5.163602 CCAAGTACTTGTGTCTAGAGCCTAG 60.164 48.000 29.05 9.07 38.85 3.02
2623 3005 7.171630 TCTATCTTCTGAGAAACCCAAGTAC 57.828 40.000 0.00 0.00 35.07 2.73
2631 3013 7.287696 AGAGAAGGGATCTATCTTCTGAGAAAC 59.712 40.741 21.87 11.97 46.61 2.78
2634 3016 6.529084 AGAGAAGGGATCTATCTTCTGAGA 57.471 41.667 21.87 0.00 46.61 3.27
2649 3031 6.004574 GCTGGGGTTATTTATAAGAGAAGGG 58.995 44.000 0.00 0.00 0.00 3.95
2656 3038 6.824305 CCATCAGCTGGGGTTATTTATAAG 57.176 41.667 15.13 0.00 41.82 1.73
2694 3106 3.285484 CAATAAGCAGAGCAGTTCCCAT 58.715 45.455 0.00 0.00 0.00 4.00
2709 3121 2.866762 GCCTAGGTCGTTCAGCAATAAG 59.133 50.000 11.31 0.00 0.00 1.73
2719 3131 2.590114 GGTGGTGGCCTAGGTCGTT 61.590 63.158 9.28 0.00 0.00 3.85
2720 3132 3.001406 GGTGGTGGCCTAGGTCGT 61.001 66.667 9.28 0.00 0.00 4.34
2721 3133 3.782443 GGGTGGTGGCCTAGGTCG 61.782 72.222 9.28 0.00 0.00 4.79
2723 3135 2.933834 GTGGGTGGTGGCCTAGGT 60.934 66.667 11.31 0.00 0.00 3.08
2724 3136 3.728373 GGTGGGTGGTGGCCTAGG 61.728 72.222 3.67 3.67 0.00 3.02
2725 3137 2.933287 TGGTGGGTGGTGGCCTAG 60.933 66.667 3.32 0.00 0.00 3.02
2726 3138 2.933287 CTGGTGGGTGGTGGCCTA 60.933 66.667 3.32 0.00 0.00 3.93
2727 3139 4.918360 TCTGGTGGGTGGTGGCCT 62.918 66.667 3.32 0.00 0.00 5.19
2728 3140 2.937959 TTTTCTGGTGGGTGGTGGCC 62.938 60.000 0.00 0.00 0.00 5.36
2729 3141 1.045911 TTTTTCTGGTGGGTGGTGGC 61.046 55.000 0.00 0.00 0.00 5.01
2730 3142 1.039856 CTTTTTCTGGTGGGTGGTGG 58.960 55.000 0.00 0.00 0.00 4.61
2731 3143 0.389025 GCTTTTTCTGGTGGGTGGTG 59.611 55.000 0.00 0.00 0.00 4.17
2732 3144 0.032615 TGCTTTTTCTGGTGGGTGGT 60.033 50.000 0.00 0.00 0.00 4.16
2733 3145 1.069049 CTTGCTTTTTCTGGTGGGTGG 59.931 52.381 0.00 0.00 0.00 4.61
2734 3146 2.031120 TCTTGCTTTTTCTGGTGGGTG 58.969 47.619 0.00 0.00 0.00 4.61
2735 3147 2.452600 TCTTGCTTTTTCTGGTGGGT 57.547 45.000 0.00 0.00 0.00 4.51
2736 3148 2.028748 CCATCTTGCTTTTTCTGGTGGG 60.029 50.000 0.00 0.00 0.00 4.61
2766 3178 9.897744 ATACACTTGTACAACTCAAAATTGATG 57.102 29.630 3.59 0.00 33.14 3.07
2776 3188 3.125316 GCCTGCATACACTTGTACAACTC 59.875 47.826 3.59 0.00 32.72 3.01
2786 3198 0.034756 TTGACACGCCTGCATACACT 59.965 50.000 0.00 0.00 0.00 3.55
2799 3211 4.537015 GCAGTCCATTAACAAGTTGACAC 58.463 43.478 10.54 0.00 0.00 3.67
2822 3234 6.138761 GCATAATAAGGAAGCAATTCACTCG 58.861 40.000 0.00 0.00 0.00 4.18
2836 3248 8.017418 TGGACCCTTTATTTTGCATAATAAGG 57.983 34.615 18.59 18.59 33.03 2.69
2851 3266 5.045869 CCACTGATTAAGTCTGGACCCTTTA 60.046 44.000 0.00 0.00 36.83 1.85
2858 3273 6.667848 TCTGAATACCACTGATTAAGTCTGGA 59.332 38.462 0.00 0.00 36.83 3.86
2859 3274 6.878317 TCTGAATACCACTGATTAAGTCTGG 58.122 40.000 0.00 0.00 36.83 3.86
2905 3322 7.579589 TTTGTGAAGAATGAAGTGTTTGTTG 57.420 32.000 0.00 0.00 0.00 3.33
2914 3331 7.645340 ACTCGATTTGTTTTGTGAAGAATGAAG 59.355 33.333 0.00 0.00 0.00 3.02
2921 3353 7.408132 TCTCTACTCGATTTGTTTTGTGAAG 57.592 36.000 0.00 0.00 0.00 3.02
2927 3359 8.398665 GGCATTATTCTCTACTCGATTTGTTTT 58.601 33.333 0.00 0.00 0.00 2.43
2944 3377 7.322664 TGAAGATCAACCTTTTGGCATTATTC 58.677 34.615 0.00 0.00 45.59 1.75
2987 3422 3.507162 TCTGGCTTGTTTCTTCCATGA 57.493 42.857 0.00 0.00 0.00 3.07
2992 3427 4.096382 TCAGTGTTTCTGGCTTGTTTCTTC 59.904 41.667 0.00 0.00 43.76 2.87
3002 3437 5.382618 AGATCATTTTCAGTGTTTCTGGC 57.617 39.130 0.00 0.00 43.76 4.85
3012 3447 8.446273 ACGAGAAACATGTAAGATCATTTTCAG 58.554 33.333 0.00 0.00 33.19 3.02
3016 3451 7.521529 CACACGAGAAACATGTAAGATCATTT 58.478 34.615 0.00 0.00 0.00 2.32
3028 3463 1.282248 CGACCGCACACGAGAAACAT 61.282 55.000 0.00 0.00 43.93 2.71
3036 3471 0.935831 TAGTCAAACGACCGCACACG 60.936 55.000 0.00 0.00 39.67 4.49
3039 3474 1.425412 ATGTAGTCAAACGACCGCAC 58.575 50.000 0.00 0.00 33.60 5.34
3045 3480 2.416296 CCGGCTGTATGTAGTCAAACGA 60.416 50.000 0.00 0.00 0.00 3.85
3063 3498 2.432444 TGATGAAACTAGCCAAACCGG 58.568 47.619 0.00 0.00 38.11 5.28
3066 3501 4.798574 CCTGTTGATGAAACTAGCCAAAC 58.201 43.478 0.00 0.00 39.70 2.93
3075 3510 1.337703 TGTGCTGCCTGTTGATGAAAC 59.662 47.619 0.00 0.00 39.41 2.78
3082 3517 0.526096 GTGTGTTGTGCTGCCTGTTG 60.526 55.000 0.00 0.00 0.00 3.33
3083 3518 1.666209 GGTGTGTTGTGCTGCCTGTT 61.666 55.000 0.00 0.00 0.00 3.16
3084 3519 2.120909 GGTGTGTTGTGCTGCCTGT 61.121 57.895 0.00 0.00 0.00 4.00
3085 3520 1.825191 AGGTGTGTTGTGCTGCCTG 60.825 57.895 0.00 0.00 0.00 4.85
3086 3521 1.825191 CAGGTGTGTTGTGCTGCCT 60.825 57.895 0.00 0.00 0.00 4.75
3087 3522 1.823470 TCAGGTGTGTTGTGCTGCC 60.823 57.895 0.00 0.00 0.00 4.85
3088 3523 1.356624 GTCAGGTGTGTTGTGCTGC 59.643 57.895 0.00 0.00 0.00 5.25
3089 3524 0.378257 GTGTCAGGTGTGTTGTGCTG 59.622 55.000 0.00 0.00 0.00 4.41
3090 3525 0.035534 TGTGTCAGGTGTGTTGTGCT 60.036 50.000 0.00 0.00 0.00 4.40
3091 3526 1.024271 ATGTGTCAGGTGTGTTGTGC 58.976 50.000 0.00 0.00 0.00 4.57
3092 3527 2.287769 TCATGTGTCAGGTGTGTTGTG 58.712 47.619 0.00 0.00 0.00 3.33
3093 3528 2.708216 TCATGTGTCAGGTGTGTTGT 57.292 45.000 0.00 0.00 0.00 3.32
3094 3529 4.572985 AATTCATGTGTCAGGTGTGTTG 57.427 40.909 0.00 0.00 0.00 3.33
3095 3530 4.037923 GGAAATTCATGTGTCAGGTGTGTT 59.962 41.667 0.00 0.00 0.00 3.32
3096 3531 3.569701 GGAAATTCATGTGTCAGGTGTGT 59.430 43.478 0.00 0.00 0.00 3.72
3097 3532 3.057315 GGGAAATTCATGTGTCAGGTGTG 60.057 47.826 0.00 0.00 0.00 3.82
3098 3533 3.157087 GGGAAATTCATGTGTCAGGTGT 58.843 45.455 0.00 0.00 0.00 4.16
3099 3534 3.156293 TGGGAAATTCATGTGTCAGGTG 58.844 45.455 0.00 0.00 0.00 4.00
3100 3535 3.524095 TGGGAAATTCATGTGTCAGGT 57.476 42.857 0.00 0.00 0.00 4.00
3101 3536 4.870123 TTTGGGAAATTCATGTGTCAGG 57.130 40.909 0.00 0.00 0.00 3.86
3102 3537 7.359431 CGAAATTTTGGGAAATTCATGTGTCAG 60.359 37.037 0.00 0.00 42.97 3.51
3127 3562 3.651562 ACTTTTGCGGTTTATCGATCG 57.348 42.857 9.36 9.36 0.00 3.69
3139 3574 4.789119 TGTAAAGTTGTCGAAACTTTTGCG 59.211 37.500 27.55 0.00 45.20 4.85
3205 3643 4.263905 TGGAAGAATACATTGGAGTGCCTT 60.264 41.667 0.00 0.00 34.31 4.35
3207 3645 3.620488 TGGAAGAATACATTGGAGTGCC 58.380 45.455 0.00 0.00 0.00 5.01
3209 3647 7.809806 GTCTTTTTGGAAGAATACATTGGAGTG 59.190 37.037 0.00 0.00 0.00 3.51
3247 3698 4.926238 AGTCTGCACGATCAACTTAAAGAG 59.074 41.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.