Multiple sequence alignment - TraesCS5B01G453800

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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 TraesCS5B01G453800 chr5B 100.000 3335 0 0 1 3335 626336289 626339623 0.000000e+00 6159.0
1 TraesCS5B01G453800 chr5B 91.788 2813 133 47 13 2772 631462707 631465474 0.000000e+00 3825.0
2 TraesCS5B01G453800 chr5B 92.887 239 3 3 3111 3335 626350768 626351006 5.330000e-88 335.0
3 TraesCS5B01G453800 chr5B 84.022 363 30 10 2899 3258 631465472 631465809 1.150000e-84 324.0
4 TraesCS5B01G453800 chr5B 87.000 100 13 0 1948 2047 115419192 115419291 2.720000e-21 113.0
5 TraesCS5B01G453800 chr5B 84.404 109 15 2 1939 2046 79804916 79804809 4.550000e-19 106.0
6 TraesCS5B01G453800 chr5B 88.060 67 5 2 2908 2974 631596625 631596688 3.570000e-10 76.8
7 TraesCS5B01G453800 chr5D 90.305 2816 190 42 1 2770 502594511 502597289 0.000000e+00 3611.0
8 TraesCS5B01G453800 chr5D 85.849 106 15 0 1948 2053 106520267 106520162 2.720000e-21 113.0
9 TraesCS5B01G453800 chr5A 94.073 1721 63 17 678 2380 631329134 631330833 0.000000e+00 2577.0
10 TraesCS5B01G453800 chr5A 84.384 365 37 13 2427 2772 631330841 631331204 1.150000e-89 340.0
11 TraesCS5B01G453800 chr5A 87.000 100 13 0 1948 2047 109966829 109966928 2.720000e-21 113.0
12 TraesCS5B01G453800 chr5A 100.000 40 0 0 2899 2938 631331202 631331241 1.280000e-09 75.0
13 TraesCS5B01G453800 chr4D 81.995 411 22 20 1019 1422 344359697 344360062 5.410000e-78 302.0
14 TraesCS5B01G453800 chr2A 96.212 132 5 0 2770 2901 20004649 20004780 2.010000e-52 217.0
15 TraesCS5B01G453800 chr2A 95.455 132 5 1 2770 2901 36139461 36139591 3.370000e-50 209.0
16 TraesCS5B01G453800 chr2A 92.958 142 8 2 2761 2901 538689393 538689533 4.360000e-49 206.0
17 TraesCS5B01G453800 chr7A 94.815 135 7 0 2774 2908 653596638 653596772 9.370000e-51 211.0
18 TraesCS5B01G453800 chr1A 95.489 133 5 1 2770 2902 354945664 354945795 9.370000e-51 211.0
19 TraesCS5B01G453800 chr1A 96.094 128 5 0 2775 2902 10231903 10232030 3.370000e-50 209.0
20 TraesCS5B01G453800 chr1A 93.478 138 7 2 2765 2901 202073503 202073639 1.570000e-48 204.0
21 TraesCS5B01G453800 chr3A 96.094 128 5 0 2775 2902 547195988 547196115 3.370000e-50 209.0
22 TraesCS5B01G453800 chr3A 94.737 38 0 2 3018 3053 741036547 741036510 1.290000e-04 58.4
23 TraesCS5B01G453800 chr3A 92.683 41 1 2 3015 3053 741898039 741898079 1.290000e-04 58.4
24 TraesCS5B01G453800 chr4B 91.333 150 11 2 2759 2907 210282742 210282890 1.570000e-48 204.0
25 TraesCS5B01G453800 chr4B 94.595 37 0 1 3020 3054 328971882 328971846 4.650000e-04 56.5
26 TraesCS5B01G453800 chr3D 86.598 97 13 0 1939 2035 17843166 17843262 1.270000e-19 108.0
27 TraesCS5B01G453800 chrUn 83.036 112 19 0 1939 2050 37382230 37382119 5.890000e-18 102.0
28 TraesCS5B01G453800 chr6D 96.970 33 1 0 1307 1339 457644689 457644721 4.650000e-04 56.5
29 TraesCS5B01G453800 chr1B 100.000 29 0 0 3019 3047 284020068 284020096 2.000000e-03 54.7
30 TraesCS5B01G453800 chr1B 100.000 29 0 0 3019 3047 285833513 285833541 2.000000e-03 54.7
31 TraesCS5B01G453800 chr1B 100.000 28 0 0 3020 3047 414776222 414776195 6.000000e-03 52.8
32 TraesCS5B01G453800 chr1B 100.000 28 0 0 3020 3047 645519601 645519574 6.000000e-03 52.8
33 TraesCS5B01G453800 chr3B 100.000 28 0 0 3088 3115 304221888 304221861 6.000000e-03 52.8
34 TraesCS5B01G453800 chr2D 100.000 28 0 0 3020 3047 172575957 172575930 6.000000e-03 52.8
35 TraesCS5B01G453800 chr2D 100.000 28 0 0 3088 3115 443481917 443481944 6.000000e-03 52.8
36 TraesCS5B01G453800 chr2B 100.000 28 0 0 3020 3047 38236807 38236834 6.000000e-03 52.8


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 TraesCS5B01G453800 chr5B 626336289 626339623 3334 False 6159.000000 6159 100.000 1 3335 1 chr5B.!!$F2 3334
1 TraesCS5B01G453800 chr5B 631462707 631465809 3102 False 2074.500000 3825 87.905 13 3258 2 chr5B.!!$F5 3245
2 TraesCS5B01G453800 chr5D 502594511 502597289 2778 False 3611.000000 3611 90.305 1 2770 1 chr5D.!!$F1 2769
3 TraesCS5B01G453800 chr5A 631329134 631331241 2107 False 997.333333 2577 92.819 678 2938 3 chr5A.!!$F2 2260

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
164 168 0.180406 TGCTATCCTTTTCGGGGCTC 59.820 55.0 0.0 0.0 0.0 4.70 F
521 536 1.216064 CCTCCCATCCTCATTGTCCA 58.784 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1887 1.08437 CCGCCTCCACGAAGATGTTC 61.084 60.0 0.00 0.0 34.06 3.18 R
2430 2493 0.39034 ATGCAACGATCAGTGCGACT 60.390 50.0 11.75 0.0 32.22 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 48 3.736252 GCTACTGGTACGACTTATGCATG 59.264 47.826 10.16 0.00 0.00 4.06
53 56 5.106869 GGTACGACTTATGCATGTTTCAACA 60.107 40.000 10.16 0.00 44.06 3.33
59 62 6.902341 ACTTATGCATGTTTCAACACTACAG 58.098 36.000 10.16 0.00 42.51 2.74
75 78 2.559381 ACAGTCCTCCTCTTGGCTAT 57.441 50.000 0.00 0.00 0.00 2.97
89 92 1.764854 GCTATCCCCTTCCCCGTCA 60.765 63.158 0.00 0.00 0.00 4.35
108 112 0.696501 AAGTCCCACGCCTAACCAAT 59.303 50.000 0.00 0.00 0.00 3.16
120 124 3.758554 GCCTAACCAATGTCATCAACACT 59.241 43.478 0.00 0.00 41.75 3.55
123 127 6.238484 GCCTAACCAATGTCATCAACACTATC 60.238 42.308 0.00 0.00 41.75 2.08
128 132 4.864916 ATGTCATCAACACTATCGTTGC 57.135 40.909 0.00 0.00 44.80 4.17
135 139 0.458543 ACACTATCGTTGCTGCCTCG 60.459 55.000 0.00 2.01 0.00 4.63
136 140 0.458543 CACTATCGTTGCTGCCTCGT 60.459 55.000 11.81 4.55 0.00 4.18
137 141 0.246635 ACTATCGTTGCTGCCTCGTT 59.753 50.000 11.81 7.57 0.00 3.85
142 146 1.891919 GTTGCTGCCTCGTTGACCA 60.892 57.895 0.00 0.00 0.00 4.02
149 153 0.320421 GCCTCGTTGACCACTTGCTA 60.320 55.000 0.00 0.00 0.00 3.49
156 160 3.502211 CGTTGACCACTTGCTATCCTTTT 59.498 43.478 0.00 0.00 0.00 2.27
164 168 0.180406 TGCTATCCTTTTCGGGGCTC 59.820 55.000 0.00 0.00 0.00 4.70
185 189 2.036475 CGTGAGACATATGGAGAAGGGG 59.964 54.545 7.80 0.00 0.00 4.79
209 213 7.130269 GGGTTTAATGTACATATTTGAGTCGC 58.870 38.462 9.21 0.54 0.00 5.19
224 228 7.915293 TTTGAGTCGCTAAAATTTCCAGATA 57.085 32.000 0.00 0.00 0.00 1.98
235 239 9.277565 CTAAAATTTCCAGATATGTTCGTGTTG 57.722 33.333 0.00 0.00 0.00 3.33
243 247 6.237942 CCAGATATGTTCGTGTTGACTCATTC 60.238 42.308 0.00 0.00 0.00 2.67
247 251 3.498018 TGTTCGTGTTGACTCATTCATGG 59.502 43.478 0.00 0.00 32.84 3.66
283 287 5.047847 GGTCGATCGGAATTTCAGATACAA 58.952 41.667 16.41 0.00 31.57 2.41
308 312 2.368221 CCTTTGATTTGAACAAGGGGCA 59.632 45.455 0.00 0.00 39.65 5.36
335 339 4.471904 TCCTTCAATCACACTCGCTTAT 57.528 40.909 0.00 0.00 0.00 1.73
336 340 4.433615 TCCTTCAATCACACTCGCTTATC 58.566 43.478 0.00 0.00 0.00 1.75
339 346 3.521560 TCAATCACACTCGCTTATCCAC 58.478 45.455 0.00 0.00 0.00 4.02
352 359 3.312890 CTTATCCACCACTCATCCTCCT 58.687 50.000 0.00 0.00 0.00 3.69
401 413 2.951457 TGCCAATCTCATGCAATGTG 57.049 45.000 0.00 0.00 46.80 3.21
419 434 4.159377 TGTGGTCGAAATTGAGATTTGC 57.841 40.909 0.00 0.00 35.65 3.68
477 492 1.552578 ACCATACCACTACTCGCACA 58.447 50.000 0.00 0.00 0.00 4.57
493 508 4.512484 TCGCACAAGTTATGGATCATTCA 58.488 39.130 0.00 0.00 0.00 2.57
500 515 6.094603 ACAAGTTATGGATCATTCAAGCACTC 59.905 38.462 0.00 0.00 0.00 3.51
521 536 1.216064 CCTCCCATCCTCATTGTCCA 58.784 55.000 0.00 0.00 0.00 4.02
527 542 3.276857 CCATCCTCATTGTCCAACTCAG 58.723 50.000 0.00 0.00 0.00 3.35
610 625 2.045045 CCATCCTTGCCGCCTCAA 60.045 61.111 0.00 0.00 0.00 3.02
665 688 2.618559 GCCCCGTCAACCCTACAATTTA 60.619 50.000 0.00 0.00 0.00 1.40
1824 1887 4.813526 CGCGACGTCACCTCCTCG 62.814 72.222 17.16 0.00 0.00 4.63
2149 2212 3.071206 GCGAGCTGAGGGAGGTGA 61.071 66.667 0.00 0.00 30.42 4.02
2367 2430 1.207570 CAGATCAGAACTGAGCCAGCT 59.792 52.381 14.98 0.00 46.32 4.24
2382 2445 1.676916 CCAGCTCTGCAAAATCTCGGA 60.677 52.381 0.00 0.00 0.00 4.55
2393 2456 4.107622 CAAAATCTCGGATTGTTGATGGC 58.892 43.478 0.70 0.00 0.00 4.40
2394 2457 3.287867 AATCTCGGATTGTTGATGGCT 57.712 42.857 0.00 0.00 0.00 4.75
2396 2459 0.379669 CTCGGATTGTTGATGGCTGC 59.620 55.000 0.00 0.00 0.00 5.25
2398 2461 1.434696 GGATTGTTGATGGCTGCGG 59.565 57.895 0.00 0.00 0.00 5.69
2400 2463 0.527565 GATTGTTGATGGCTGCGGTT 59.472 50.000 0.00 0.00 0.00 4.44
2404 2467 0.313672 GTTGATGGCTGCGGTTCAAA 59.686 50.000 10.68 0.00 30.51 2.69
2405 2468 1.067635 GTTGATGGCTGCGGTTCAAAT 60.068 47.619 10.68 0.00 30.51 2.32
2407 2470 0.101219 GATGGCTGCGGTTCAAATCC 59.899 55.000 0.00 0.00 0.00 3.01
2408 2471 0.323725 ATGGCTGCGGTTCAAATCCT 60.324 50.000 0.00 0.00 0.00 3.24
2409 2472 1.243342 TGGCTGCGGTTCAAATCCTG 61.243 55.000 0.00 0.00 0.00 3.86
2410 2473 0.960364 GGCTGCGGTTCAAATCCTGA 60.960 55.000 0.00 0.00 0.00 3.86
2412 2475 1.064654 GCTGCGGTTCAAATCCTGATC 59.935 52.381 0.00 0.00 32.78 2.92
2413 2476 2.636830 CTGCGGTTCAAATCCTGATCT 58.363 47.619 0.00 0.00 32.78 2.75
2414 2477 2.611292 CTGCGGTTCAAATCCTGATCTC 59.389 50.000 0.00 0.00 32.78 2.75
2415 2478 2.237143 TGCGGTTCAAATCCTGATCTCT 59.763 45.455 0.00 0.00 32.78 3.10
2430 2493 5.396101 CCTGATCTCTTTGGCTGACAGATTA 60.396 44.000 6.65 0.00 0.00 1.75
2437 2500 1.281899 GGCTGACAGATTAGTCGCAC 58.718 55.000 6.65 0.00 41.41 5.34
2439 2502 1.923204 GCTGACAGATTAGTCGCACTG 59.077 52.381 6.65 0.00 41.41 3.66
2573 2644 3.385111 AGATCAATCAACGGTAGGAGGAC 59.615 47.826 0.00 0.00 0.00 3.85
2589 2660 4.463186 AGGAGGACACTGTGACAGTAATAC 59.537 45.833 18.99 10.45 43.43 1.89
2596 2667 4.324669 CACTGTGACAGTAATACGAGCTTG 59.675 45.833 18.99 0.00 43.43 4.01
2597 2668 4.217767 ACTGTGACAGTAATACGAGCTTGA 59.782 41.667 17.91 0.00 43.46 3.02
2604 2677 5.577164 ACAGTAATACGAGCTTGATTGTGTC 59.423 40.000 8.31 0.00 0.00 3.67
2630 2703 1.273606 TGTGAGCTCAAGGAGTAGCAC 59.726 52.381 20.19 2.72 41.32 4.40
2644 2724 1.949847 TAGCACGAGCAAGCTCCTCC 61.950 60.000 15.81 4.74 45.49 4.30
2649 2729 4.093291 AGCAAGCTCCTCCGCCTG 62.093 66.667 0.00 0.00 0.00 4.85
2664 2744 0.528249 GCCTGTTGTGTTTGGCAGTG 60.528 55.000 0.00 0.00 44.34 3.66
2686 2766 5.049167 TGGCTTGTGATCAAAATGAACAAC 58.951 37.500 0.00 0.00 30.93 3.32
2691 2771 7.596248 GCTTGTGATCAAAATGAACAACTGTAT 59.404 33.333 0.00 0.00 30.93 2.29
2692 2772 8.800231 TTGTGATCAAAATGAACAACTGTATG 57.200 30.769 0.00 0.00 30.93 2.39
2693 2773 7.939782 TGTGATCAAAATGAACAACTGTATGT 58.060 30.769 0.00 0.00 30.93 2.29
2694 2774 9.061435 TGTGATCAAAATGAACAACTGTATGTA 57.939 29.630 0.00 0.00 30.93 2.29
2696 2776 9.891828 TGATCAAAATGAACAACTGTATGTAAC 57.108 29.630 0.00 0.00 32.02 2.50
2697 2777 9.891828 GATCAAAATGAACAACTGTATGTAACA 57.108 29.630 0.00 0.00 36.42 2.41
2703 2783 7.675962 TGAACAACTGTATGTAACATAACCC 57.324 36.000 0.00 0.00 37.50 4.11
2704 2784 6.369340 TGAACAACTGTATGTAACATAACCCG 59.631 38.462 0.00 0.00 37.50 5.28
2707 2798 3.135994 CTGTATGTAACATAACCCGGCC 58.864 50.000 0.00 0.00 37.50 6.13
2761 2852 5.106908 GGTTCTGTAGTCAAGAAACTGATGC 60.107 44.000 0.00 0.00 0.00 3.91
2763 2854 5.858381 TCTGTAGTCAAGAAACTGATGCTT 58.142 37.500 0.00 0.00 0.00 3.91
2770 2861 3.402628 AGAAACTGATGCTTGGTACGT 57.597 42.857 0.00 0.00 0.00 3.57
2771 2862 4.530710 AGAAACTGATGCTTGGTACGTA 57.469 40.909 0.00 0.00 0.00 3.57
2772 2863 4.243270 AGAAACTGATGCTTGGTACGTAC 58.757 43.478 17.56 17.56 0.00 3.67
2773 2864 2.273370 ACTGATGCTTGGTACGTACG 57.727 50.000 18.98 15.01 0.00 3.67
2774 2865 1.542915 ACTGATGCTTGGTACGTACGT 59.457 47.619 25.98 25.98 0.00 3.57
2775 2866 2.749076 ACTGATGCTTGGTACGTACGTA 59.251 45.455 23.60 23.60 0.00 3.57
2784 2875 0.931005 GTACGTACGTACTCCCTCCG 59.069 60.000 38.40 10.64 45.30 4.63
2785 2876 0.535335 TACGTACGTACTCCCTCCGT 59.465 55.000 23.60 15.61 38.53 4.69
2786 2877 0.321653 ACGTACGTACTCCCTCCGTT 60.322 55.000 21.41 0.00 36.12 4.44
2787 2878 0.375106 CGTACGTACTCCCTCCGTTC 59.625 60.000 22.55 0.00 36.12 3.95
2788 2879 0.735471 GTACGTACTCCCTCCGTTCC 59.265 60.000 18.47 0.00 36.12 3.62
2789 2880 0.744414 TACGTACTCCCTCCGTTCCG 60.744 60.000 0.00 0.00 36.12 4.30
2790 2881 1.746615 CGTACTCCCTCCGTTCCGA 60.747 63.158 0.00 0.00 0.00 4.55
2791 2882 1.308069 CGTACTCCCTCCGTTCCGAA 61.308 60.000 0.00 0.00 0.00 4.30
2792 2883 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
2793 2884 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2794 2885 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2795 2886 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2796 2887 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2797 2888 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2798 2889 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2799 2890 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2800 2891 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2801 2892 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2802 2893 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2803 2894 4.634199 TCCGTTCCGAATTACTTGTCTTT 58.366 39.130 0.00 0.00 0.00 2.52
2804 2895 4.449743 TCCGTTCCGAATTACTTGTCTTTG 59.550 41.667 0.00 0.00 0.00 2.77
2805 2896 4.449743 CCGTTCCGAATTACTTGTCTTTGA 59.550 41.667 0.00 0.00 0.00 2.69
2806 2897 5.121768 CCGTTCCGAATTACTTGTCTTTGAT 59.878 40.000 0.00 0.00 0.00 2.57
2807 2898 6.348213 CCGTTCCGAATTACTTGTCTTTGATT 60.348 38.462 0.00 0.00 0.00 2.57
2808 2899 7.075741 CGTTCCGAATTACTTGTCTTTGATTT 58.924 34.615 0.00 0.00 0.00 2.17
2809 2900 7.059488 CGTTCCGAATTACTTGTCTTTGATTTG 59.941 37.037 0.00 0.00 0.00 2.32
2810 2901 7.504924 TCCGAATTACTTGTCTTTGATTTGT 57.495 32.000 0.00 0.00 0.00 2.83
2811 2902 7.581476 TCCGAATTACTTGTCTTTGATTTGTC 58.419 34.615 0.00 0.00 0.00 3.18
2812 2903 7.444183 TCCGAATTACTTGTCTTTGATTTGTCT 59.556 33.333 0.00 0.00 0.00 3.41
2813 2904 8.717821 CCGAATTACTTGTCTTTGATTTGTCTA 58.282 33.333 0.00 0.00 0.00 2.59
2814 2905 9.746711 CGAATTACTTGTCTTTGATTTGTCTAG 57.253 33.333 0.00 0.00 0.00 2.43
2819 2910 8.467402 ACTTGTCTTTGATTTGTCTAGATACG 57.533 34.615 0.00 0.00 0.00 3.06
2820 2911 7.545965 ACTTGTCTTTGATTTGTCTAGATACGG 59.454 37.037 0.00 0.00 0.00 4.02
2821 2912 7.165460 TGTCTTTGATTTGTCTAGATACGGA 57.835 36.000 0.00 0.00 0.00 4.69
2822 2913 7.782049 TGTCTTTGATTTGTCTAGATACGGAT 58.218 34.615 0.00 0.00 0.00 4.18
2823 2914 7.706607 TGTCTTTGATTTGTCTAGATACGGATG 59.293 37.037 0.00 0.00 0.00 3.51
2824 2915 7.707035 GTCTTTGATTTGTCTAGATACGGATGT 59.293 37.037 0.00 0.00 0.00 3.06
2825 2916 8.909923 TCTTTGATTTGTCTAGATACGGATGTA 58.090 33.333 0.00 0.00 34.45 2.29
2826 2917 9.698309 CTTTGATTTGTCTAGATACGGATGTAT 57.302 33.333 0.00 0.00 43.97 2.29
2843 2934 8.794553 ACGGATGTATCTAGTACTAAAATGAGG 58.205 37.037 3.76 0.00 34.27 3.86
2844 2935 7.755822 CGGATGTATCTAGTACTAAAATGAGGC 59.244 40.741 3.76 0.00 34.27 4.70
2845 2936 8.808092 GGATGTATCTAGTACTAAAATGAGGCT 58.192 37.037 3.76 0.00 34.27 4.58
2855 2946 9.594936 AGTACTAAAATGAGGCTAGATACATCT 57.405 33.333 0.00 0.00 40.86 2.90
2856 2947 9.632807 GTACTAAAATGAGGCTAGATACATCTG 57.367 37.037 1.88 0.00 37.76 2.90
2857 2948 8.256356 ACTAAAATGAGGCTAGATACATCTGT 57.744 34.615 1.88 0.00 37.76 3.41
2858 2949 9.368416 ACTAAAATGAGGCTAGATACATCTGTA 57.632 33.333 1.88 0.00 37.76 2.74
2891 2982 9.746711 CAAATCTAAGACAAGTAATTCAGAACG 57.253 33.333 0.00 0.00 0.00 3.95
2892 2983 8.480643 AATCTAAGACAAGTAATTCAGAACGG 57.519 34.615 0.00 0.00 0.00 4.44
2893 2984 7.223260 TCTAAGACAAGTAATTCAGAACGGA 57.777 36.000 0.00 0.00 0.00 4.69
2894 2985 7.313646 TCTAAGACAAGTAATTCAGAACGGAG 58.686 38.462 0.00 0.00 0.00 4.63
2895 2986 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
2896 2987 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2897 2988 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2942 3033 5.811399 TTGGGTTCTTGTTATATCGCAAG 57.189 39.130 11.03 11.03 42.32 4.01
2943 3034 4.839121 TGGGTTCTTGTTATATCGCAAGT 58.161 39.130 14.80 0.00 41.83 3.16
2944 3035 4.634004 TGGGTTCTTGTTATATCGCAAGTG 59.366 41.667 14.80 0.00 41.83 3.16
2983 3074 8.849543 TCTCCATGATGATGATTATCCTATCA 57.150 34.615 0.00 3.81 38.78 2.15
2984 3075 9.448587 TCTCCATGATGATGATTATCCTATCAT 57.551 33.333 7.47 7.47 45.51 2.45
3000 3091 4.141620 CCTATCATACAGTTGACTTGGCCT 60.142 45.833 3.32 0.00 0.00 5.19
3019 3110 5.007682 GGCCTGGAAAATGTTCAGTACTTA 58.992 41.667 0.00 0.00 35.25 2.24
3022 3113 6.877322 GCCTGGAAAATGTTCAGTACTTAGTA 59.123 38.462 0.00 0.00 35.25 1.82
3025 3116 9.141400 CTGGAAAATGTTCAGTACTTAGTACTC 57.859 37.037 20.80 11.50 44.86 2.59
3026 3117 8.092687 TGGAAAATGTTCAGTACTTAGTACTCC 58.907 37.037 20.80 15.72 44.86 3.85
3027 3118 7.548427 GGAAAATGTTCAGTACTTAGTACTCCC 59.452 40.741 20.80 12.32 44.86 4.30
3028 3119 7.793948 AAATGTTCAGTACTTAGTACTCCCT 57.206 36.000 20.80 0.00 44.86 4.20
3029 3120 7.407393 AATGTTCAGTACTTAGTACTCCCTC 57.593 40.000 20.80 12.39 44.86 4.30
3030 3121 5.259632 TGTTCAGTACTTAGTACTCCCTCC 58.740 45.833 20.80 8.99 44.86 4.30
3031 3122 4.148128 TCAGTACTTAGTACTCCCTCCG 57.852 50.000 20.80 9.92 44.86 4.63
3033 3124 3.876320 CAGTACTTAGTACTCCCTCCGTC 59.124 52.174 20.80 0.00 44.86 4.79
3034 3125 2.433662 ACTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
3035 3126 1.307097 CTTAGTACTCCCTCCGTCCG 58.693 60.000 0.00 0.00 0.00 4.79
3036 3127 0.107017 TTAGTACTCCCTCCGTCCGG 60.107 60.000 0.00 0.00 0.00 5.14
3037 3128 1.987807 TAGTACTCCCTCCGTCCGGG 61.988 65.000 0.00 0.00 43.38 5.73
3042 3133 3.135814 CCCTCCGTCCGGGAATAC 58.864 66.667 0.00 0.00 46.61 1.89
3043 3134 1.457079 CCCTCCGTCCGGGAATACT 60.457 63.158 0.00 0.00 46.61 2.12
3044 3135 1.047034 CCCTCCGTCCGGGAATACTT 61.047 60.000 0.00 0.00 46.61 2.24
3045 3136 0.104304 CCTCCGTCCGGGAATACTTG 59.896 60.000 0.00 0.00 46.61 3.16
3046 3137 0.822164 CTCCGTCCGGGAATACTTGT 59.178 55.000 0.00 0.00 46.61 3.16
3060 3151 7.749126 CGGGAATACTTGTTTGAAATACTTGTC 59.251 37.037 0.00 0.00 0.00 3.18
3061 3152 8.573035 GGGAATACTTGTTTGAAATACTTGTCA 58.427 33.333 0.00 0.00 0.00 3.58
3065 3156 9.778741 ATACTTGTTTGAAATACTTGTCAGAGA 57.221 29.630 0.00 0.00 0.00 3.10
3066 3157 8.147642 ACTTGTTTGAAATACTTGTCAGAGAG 57.852 34.615 0.00 0.00 0.00 3.20
3067 3158 7.987458 ACTTGTTTGAAATACTTGTCAGAGAGA 59.013 33.333 0.00 0.00 0.00 3.10
3068 3159 7.953158 TGTTTGAAATACTTGTCAGAGAGAG 57.047 36.000 0.00 0.00 0.00 3.20
3069 3160 7.726216 TGTTTGAAATACTTGTCAGAGAGAGA 58.274 34.615 0.00 0.00 0.00 3.10
3070 3161 7.869937 TGTTTGAAATACTTGTCAGAGAGAGAG 59.130 37.037 0.00 0.00 0.00 3.20
3071 3162 7.767250 TTGAAATACTTGTCAGAGAGAGAGA 57.233 36.000 0.00 0.00 0.00 3.10
3072 3163 7.389803 TGAAATACTTGTCAGAGAGAGAGAG 57.610 40.000 0.00 0.00 0.00 3.20
3073 3164 7.171653 TGAAATACTTGTCAGAGAGAGAGAGA 58.828 38.462 0.00 0.00 0.00 3.10
3082 3173 5.360714 GTCAGAGAGAGAGAGAAATGGATGT 59.639 44.000 0.00 0.00 0.00 3.06
3085 3176 5.363580 AGAGAGAGAGAGAAATGGATGTTCC 59.636 44.000 0.00 0.00 36.96 3.62
3096 3187 4.900635 ATGGATGTTCCGCAAGTATTTC 57.099 40.909 0.00 0.00 40.17 2.17
3099 3190 1.444836 TGTTCCGCAAGTATTTCCGG 58.555 50.000 0.00 0.00 40.56 5.14
3100 3191 1.002201 TGTTCCGCAAGTATTTCCGGA 59.998 47.619 0.00 0.00 44.50 5.14
3101 3192 2.285977 GTTCCGCAAGTATTTCCGGAT 58.714 47.619 4.15 0.00 45.18 4.18
3103 3194 1.483004 TCCGCAAGTATTTCCGGATGA 59.517 47.619 4.15 0.00 42.31 2.92
3114 3205 2.471815 TCCGGATGAAGGGAGTACAT 57.528 50.000 0.00 0.00 0.00 2.29
3119 3210 4.344102 CCGGATGAAGGGAGTACATTTCTA 59.656 45.833 0.00 0.00 0.00 2.10
3139 3231 9.798994 ATTTCTATCTCTTGCATGTTGATTTTC 57.201 29.630 12.85 0.00 0.00 2.29
3186 3280 5.099042 AGTTTAATTATGTGCCTCCTCGT 57.901 39.130 0.00 0.00 0.00 4.18
3196 3290 2.673368 GTGCCTCCTCGTTTTCACATAG 59.327 50.000 0.00 0.00 0.00 2.23
3211 3305 1.618343 ACATAGGTTTGGTTGCTTGCC 59.382 47.619 0.00 0.00 0.00 4.52
3226 3320 1.165907 TTGCCAGCGTCAAACCTCTG 61.166 55.000 0.00 0.00 0.00 3.35
3237 3331 4.872691 CGTCAAACCTCTGATAGAGCAAAT 59.127 41.667 0.31 0.00 40.98 2.32
3238 3332 5.006165 CGTCAAACCTCTGATAGAGCAAATC 59.994 44.000 0.31 0.00 40.98 2.17
3242 3336 4.437239 ACCTCTGATAGAGCAAATCAACG 58.563 43.478 0.31 0.00 40.98 4.10
3254 3348 4.083484 AGCAAATCAACGCTAGTTACCAAC 60.083 41.667 0.00 0.00 38.79 3.77
3258 3352 5.909621 ATCAACGCTAGTTACCAACTCTA 57.090 39.130 0.00 0.00 41.77 2.43
3259 3353 5.909621 TCAACGCTAGTTACCAACTCTAT 57.090 39.130 0.00 0.00 41.77 1.98
3260 3354 5.888105 TCAACGCTAGTTACCAACTCTATC 58.112 41.667 0.00 0.00 41.77 2.08
3261 3355 4.915158 ACGCTAGTTACCAACTCTATCC 57.085 45.455 0.00 0.00 41.77 2.59
3262 3356 4.275810 ACGCTAGTTACCAACTCTATCCA 58.724 43.478 0.00 0.00 41.77 3.41
3263 3357 4.894114 ACGCTAGTTACCAACTCTATCCAT 59.106 41.667 0.00 0.00 41.77 3.41
3264 3358 6.066690 ACGCTAGTTACCAACTCTATCCATA 58.933 40.000 0.00 0.00 41.77 2.74
3265 3359 6.016443 ACGCTAGTTACCAACTCTATCCATAC 60.016 42.308 0.00 0.00 41.77 2.39
3266 3360 6.016527 CGCTAGTTACCAACTCTATCCATACA 60.017 42.308 0.00 0.00 41.77 2.29
3267 3361 7.146648 GCTAGTTACCAACTCTATCCATACAC 58.853 42.308 0.00 0.00 41.77 2.90
3268 3362 7.201884 GCTAGTTACCAACTCTATCCATACACA 60.202 40.741 0.00 0.00 41.77 3.72
3269 3363 7.113658 AGTTACCAACTCTATCCATACACAG 57.886 40.000 0.00 0.00 37.02 3.66
3270 3364 4.408182 ACCAACTCTATCCATACACAGC 57.592 45.455 0.00 0.00 0.00 4.40
3271 3365 3.774766 ACCAACTCTATCCATACACAGCA 59.225 43.478 0.00 0.00 0.00 4.41
3272 3366 4.122776 CCAACTCTATCCATACACAGCAC 58.877 47.826 0.00 0.00 0.00 4.40
3273 3367 4.383010 CCAACTCTATCCATACACAGCACA 60.383 45.833 0.00 0.00 0.00 4.57
3274 3368 5.363101 CAACTCTATCCATACACAGCACAT 58.637 41.667 0.00 0.00 0.00 3.21
3275 3369 5.620738 ACTCTATCCATACACAGCACATT 57.379 39.130 0.00 0.00 0.00 2.71
3276 3370 6.731292 ACTCTATCCATACACAGCACATTA 57.269 37.500 0.00 0.00 0.00 1.90
3277 3371 7.308450 ACTCTATCCATACACAGCACATTAT 57.692 36.000 0.00 0.00 0.00 1.28
3278 3372 7.157347 ACTCTATCCATACACAGCACATTATG 58.843 38.462 0.00 0.00 0.00 1.90
3279 3373 7.066307 TCTATCCATACACAGCACATTATGT 57.934 36.000 0.00 0.00 0.00 2.29
3280 3374 7.508687 TCTATCCATACACAGCACATTATGTT 58.491 34.615 0.00 0.00 0.00 2.71
3281 3375 6.624352 ATCCATACACAGCACATTATGTTC 57.376 37.500 0.00 0.00 0.00 3.18
3282 3376 5.495640 TCCATACACAGCACATTATGTTCA 58.504 37.500 0.00 0.00 0.00 3.18
3283 3377 5.353956 TCCATACACAGCACATTATGTTCAC 59.646 40.000 0.00 0.00 0.00 3.18
3284 3378 5.355071 CCATACACAGCACATTATGTTCACT 59.645 40.000 0.00 0.00 0.00 3.41
3285 3379 6.538381 CCATACACAGCACATTATGTTCACTA 59.462 38.462 0.00 0.00 0.00 2.74
3286 3380 7.254556 CCATACACAGCACATTATGTTCACTAG 60.255 40.741 0.00 0.00 0.00 2.57
3287 3381 5.793817 ACACAGCACATTATGTTCACTAGA 58.206 37.500 0.00 0.00 0.00 2.43
3288 3382 6.409704 ACACAGCACATTATGTTCACTAGAT 58.590 36.000 0.00 0.00 0.00 1.98
3289 3383 7.555965 ACACAGCACATTATGTTCACTAGATA 58.444 34.615 0.00 0.00 0.00 1.98
3290 3384 8.040727 ACACAGCACATTATGTTCACTAGATAA 58.959 33.333 0.00 0.00 0.00 1.75
3291 3385 8.546244 CACAGCACATTATGTTCACTAGATAAG 58.454 37.037 0.00 0.00 0.00 1.73
3292 3386 8.478066 ACAGCACATTATGTTCACTAGATAAGA 58.522 33.333 0.00 0.00 0.00 2.10
3293 3387 9.486497 CAGCACATTATGTTCACTAGATAAGAT 57.514 33.333 0.00 0.00 0.00 2.40
3314 3408 7.962995 AGATATACTGTCAAACCAAGAGAGA 57.037 36.000 0.00 0.00 31.44 3.10
3315 3409 8.006298 AGATATACTGTCAAACCAAGAGAGAG 57.994 38.462 0.00 0.00 31.44 3.20
3316 3410 7.836685 AGATATACTGTCAAACCAAGAGAGAGA 59.163 37.037 0.00 0.00 31.44 3.10
3317 3411 4.329462 ACTGTCAAACCAAGAGAGAGAC 57.671 45.455 0.00 0.00 31.44 3.36
3318 3412 3.070302 ACTGTCAAACCAAGAGAGAGACC 59.930 47.826 0.00 0.00 31.44 3.85
3319 3413 3.038280 TGTCAAACCAAGAGAGAGACCA 58.962 45.455 0.00 0.00 0.00 4.02
3320 3414 3.454447 TGTCAAACCAAGAGAGAGACCAA 59.546 43.478 0.00 0.00 0.00 3.67
3321 3415 4.080582 TGTCAAACCAAGAGAGAGACCAAA 60.081 41.667 0.00 0.00 0.00 3.28
3322 3416 5.066593 GTCAAACCAAGAGAGAGACCAAAT 58.933 41.667 0.00 0.00 0.00 2.32
3323 3417 5.049129 GTCAAACCAAGAGAGAGACCAAATG 60.049 44.000 0.00 0.00 0.00 2.32
3324 3418 4.982241 AACCAAGAGAGAGACCAAATGA 57.018 40.909 0.00 0.00 0.00 2.57
3325 3419 4.982241 ACCAAGAGAGAGACCAAATGAA 57.018 40.909 0.00 0.00 0.00 2.57
3326 3420 5.310409 ACCAAGAGAGAGACCAAATGAAA 57.690 39.130 0.00 0.00 0.00 2.69
3327 3421 5.312079 ACCAAGAGAGAGACCAAATGAAAG 58.688 41.667 0.00 0.00 0.00 2.62
3328 3422 5.072329 ACCAAGAGAGAGACCAAATGAAAGA 59.928 40.000 0.00 0.00 0.00 2.52
3329 3423 6.179040 CCAAGAGAGAGACCAAATGAAAGAT 58.821 40.000 0.00 0.00 0.00 2.40
3330 3424 6.093771 CCAAGAGAGAGACCAAATGAAAGATG 59.906 42.308 0.00 0.00 0.00 2.90
3331 3425 6.371595 AGAGAGAGACCAAATGAAAGATGT 57.628 37.500 0.00 0.00 0.00 3.06
3332 3426 6.405538 AGAGAGAGACCAAATGAAAGATGTC 58.594 40.000 0.00 0.00 0.00 3.06
3333 3427 6.013898 AGAGAGAGACCAAATGAAAGATGTCA 60.014 38.462 0.00 0.00 0.00 3.58
3334 3428 6.537355 AGAGAGACCAAATGAAAGATGTCAA 58.463 36.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.163642 CCAGTAGCGTCATTGTCTAGTAGTT 60.164 44.000 0.00 0.00 0.00 2.24
45 48 4.039366 AGAGGAGGACTGTAGTGTTGAAAC 59.961 45.833 0.00 0.00 0.00 2.78
53 56 1.077993 AGCCAAGAGGAGGACTGTAGT 59.922 52.381 0.00 0.00 36.89 2.73
59 62 1.052617 GGGATAGCCAAGAGGAGGAC 58.947 60.000 0.00 0.00 36.89 3.85
75 78 1.916777 GACTTGACGGGGAAGGGGA 60.917 63.158 0.00 0.00 0.00 4.81
89 92 0.696501 ATTGGTTAGGCGTGGGACTT 59.303 50.000 0.00 0.00 30.49 3.01
120 124 0.245266 TCAACGAGGCAGCAACGATA 59.755 50.000 15.52 0.50 0.00 2.92
123 127 2.551270 GTCAACGAGGCAGCAACG 59.449 61.111 8.56 8.56 0.00 4.10
128 132 1.845809 GCAAGTGGTCAACGAGGCAG 61.846 60.000 0.00 0.00 0.00 4.85
135 139 4.378459 CGAAAAGGATAGCAAGTGGTCAAC 60.378 45.833 0.00 0.00 0.00 3.18
136 140 3.751175 CGAAAAGGATAGCAAGTGGTCAA 59.249 43.478 0.00 0.00 0.00 3.18
137 141 3.334691 CGAAAAGGATAGCAAGTGGTCA 58.665 45.455 0.00 0.00 0.00 4.02
142 146 1.682087 GCCCCGAAAAGGATAGCAAGT 60.682 52.381 0.00 0.00 45.00 3.16
149 153 1.078426 CACGAGCCCCGAAAAGGAT 60.078 57.895 2.99 0.00 45.00 3.24
156 160 0.467474 ATATGTCTCACGAGCCCCGA 60.467 55.000 2.99 0.00 41.76 5.14
164 168 2.036475 CCCCTTCTCCATATGTCTCACG 59.964 54.545 1.24 0.00 0.00 4.35
185 189 7.916552 AGCGACTCAAATATGTACATTAAACC 58.083 34.615 14.77 0.00 0.00 3.27
209 213 9.277565 CAACACGAACATATCTGGAAATTTTAG 57.722 33.333 0.00 0.00 0.00 1.85
224 228 4.154737 CCATGAATGAGTCAACACGAACAT 59.845 41.667 0.00 0.00 40.50 2.71
235 239 0.815615 GGGCGGTCCATGAATGAGTC 60.816 60.000 0.00 0.00 35.00 3.36
283 287 5.279960 GCCCCTTGTTCAAATCAAAGGTTAT 60.280 40.000 0.00 0.00 0.00 1.89
308 312 4.691175 CGAGTGTGATTGAAGGATCAGAT 58.309 43.478 0.00 0.00 36.76 2.90
335 339 0.117140 ACAGGAGGATGAGTGGTGGA 59.883 55.000 0.00 0.00 0.00 4.02
336 340 0.251354 CACAGGAGGATGAGTGGTGG 59.749 60.000 0.00 0.00 0.00 4.61
352 359 4.075682 TGTGTCTCACAAAAGAAACCACA 58.924 39.130 0.00 0.00 41.69 4.17
401 413 2.477863 CGGGCAAATCTCAATTTCGACC 60.478 50.000 0.00 0.00 32.69 4.79
419 434 2.833631 AACTATCCGGATTTAGCGGG 57.166 50.000 24.71 7.01 0.00 6.13
477 492 6.094603 GTGAGTGCTTGAATGATCCATAACTT 59.905 38.462 0.00 0.00 0.00 2.66
493 508 0.548682 AGGATGGGAGGTGAGTGCTT 60.549 55.000 0.00 0.00 0.00 3.91
500 515 1.133976 GGACAATGAGGATGGGAGGTG 60.134 57.143 0.00 0.00 0.00 4.00
521 536 1.893919 GCCGAGAAGGGAGCTGAGTT 61.894 60.000 0.00 0.00 41.48 3.01
527 542 1.614241 TTGTAGGCCGAGAAGGGAGC 61.614 60.000 0.00 0.00 41.48 4.70
665 688 6.926826 TGTGTACACAATTATGTCGAGAAACT 59.073 34.615 26.07 0.00 37.82 2.66
723 746 5.705441 TCCATGTGTACAATGGACTTTCTTC 59.295 40.000 24.19 1.32 39.36 2.87
784 807 3.003173 CCGGGTCTCCTCTTGGCA 61.003 66.667 0.00 0.00 0.00 4.92
785 808 2.683933 TCCGGGTCTCCTCTTGGC 60.684 66.667 0.00 0.00 0.00 4.52
1200 1257 3.461773 TAGAGCAGGAGCACGGCC 61.462 66.667 0.00 0.00 45.49 6.13
1422 1485 1.805910 GAGGTAGACCGTCCCGAAC 59.194 63.158 0.00 0.00 42.08 3.95
1434 1497 3.429925 GGGAGGTACGCGAGGTAG 58.570 66.667 15.93 0.00 0.00 3.18
1824 1887 1.084370 CCGCCTCCACGAAGATGTTC 61.084 60.000 0.00 0.00 34.06 3.18
2367 2430 4.071423 TCAACAATCCGAGATTTTGCAGA 58.929 39.130 0.00 0.00 0.00 4.26
2382 2445 0.527565 GAACCGCAGCCATCAACAAT 59.472 50.000 0.00 0.00 0.00 2.71
2393 2456 2.611292 GAGATCAGGATTTGAACCGCAG 59.389 50.000 0.00 0.00 39.77 5.18
2394 2457 2.237143 AGAGATCAGGATTTGAACCGCA 59.763 45.455 0.00 0.00 39.77 5.69
2396 2459 4.095483 CCAAAGAGATCAGGATTTGAACCG 59.905 45.833 11.32 0.00 39.77 4.44
2398 2461 4.704057 AGCCAAAGAGATCAGGATTTGAAC 59.296 41.667 11.32 5.70 39.77 3.18
2400 2463 4.019051 TCAGCCAAAGAGATCAGGATTTGA 60.019 41.667 11.32 0.00 40.85 2.69
2404 2467 2.842496 TGTCAGCCAAAGAGATCAGGAT 59.158 45.455 0.00 0.00 0.00 3.24
2405 2468 2.235650 CTGTCAGCCAAAGAGATCAGGA 59.764 50.000 0.00 0.00 0.00 3.86
2407 2470 3.606595 TCTGTCAGCCAAAGAGATCAG 57.393 47.619 0.00 0.00 0.00 2.90
2408 2471 4.564782 AATCTGTCAGCCAAAGAGATCA 57.435 40.909 0.00 0.00 0.00 2.92
2409 2472 5.669477 ACTAATCTGTCAGCCAAAGAGATC 58.331 41.667 0.00 0.00 0.00 2.75
2410 2473 5.669477 GACTAATCTGTCAGCCAAAGAGAT 58.331 41.667 0.00 0.00 36.97 2.75
2412 2475 3.862267 CGACTAATCTGTCAGCCAAAGAG 59.138 47.826 0.00 0.00 36.82 2.85
2413 2476 3.849911 CGACTAATCTGTCAGCCAAAGA 58.150 45.455 0.00 0.00 36.82 2.52
2414 2477 2.349886 GCGACTAATCTGTCAGCCAAAG 59.650 50.000 0.00 0.00 36.82 2.77
2415 2478 2.289382 TGCGACTAATCTGTCAGCCAAA 60.289 45.455 0.00 0.00 36.46 3.28
2430 2493 0.390340 ATGCAACGATCAGTGCGACT 60.390 50.000 11.75 0.00 32.22 4.18
2437 2500 3.123453 TCTTCGACAAATGCAACGATCAG 59.877 43.478 0.00 0.00 34.85 2.90
2439 2502 3.408150 GTCTTCGACAAATGCAACGATC 58.592 45.455 0.00 0.00 34.85 3.69
2573 2644 4.098055 AGCTCGTATTACTGTCACAGTG 57.902 45.455 21.37 3.12 45.01 3.66
2589 2660 1.126846 GAACCGACACAATCAAGCTCG 59.873 52.381 0.00 0.00 0.00 5.03
2596 2667 1.461127 GCTCACAGAACCGACACAATC 59.539 52.381 0.00 0.00 0.00 2.67
2597 2668 1.070758 AGCTCACAGAACCGACACAAT 59.929 47.619 0.00 0.00 0.00 2.71
2604 2677 0.318441 TCCTTGAGCTCACAGAACCG 59.682 55.000 18.03 5.01 0.00 4.44
2649 2729 0.175531 AAGCCACTGCCAAACACAAC 59.824 50.000 0.00 0.00 38.69 3.32
2664 2744 5.176223 CAGTTGTTCATTTTGATCACAAGCC 59.824 40.000 0.00 0.00 37.32 4.35
2686 2766 3.135994 GGCCGGGTTATGTTACATACAG 58.864 50.000 2.18 0.00 40.83 2.74
2691 2771 0.324285 AACGGCCGGGTTATGTTACA 59.676 50.000 31.76 0.00 0.00 2.41
2692 2772 1.009078 GAACGGCCGGGTTATGTTAC 58.991 55.000 31.76 3.37 0.00 2.50
2693 2773 0.903942 AGAACGGCCGGGTTATGTTA 59.096 50.000 31.76 0.00 0.00 2.41
2694 2774 0.037160 AAGAACGGCCGGGTTATGTT 59.963 50.000 31.76 12.91 0.00 2.71
2696 2776 0.675522 ACAAGAACGGCCGGGTTATG 60.676 55.000 31.76 22.19 0.00 1.90
2697 2777 0.392060 GACAAGAACGGCCGGGTTAT 60.392 55.000 31.76 10.31 0.00 1.89
2698 2778 1.004679 GACAAGAACGGCCGGGTTA 60.005 57.895 31.76 0.00 0.00 2.85
2699 2779 2.281276 GACAAGAACGGCCGGGTT 60.281 61.111 31.76 16.36 0.00 4.11
2700 2780 3.109592 TTGACAAGAACGGCCGGGT 62.110 57.895 31.76 17.71 0.00 5.28
2701 2781 2.281208 TTGACAAGAACGGCCGGG 60.281 61.111 31.76 15.31 0.00 5.73
2702 2782 0.673644 ATCTTGACAAGAACGGCCGG 60.674 55.000 31.76 13.93 41.63 6.13
2703 2783 0.443869 CATCTTGACAAGAACGGCCG 59.556 55.000 26.86 26.86 41.63 6.13
2704 2784 1.808411 TCATCTTGACAAGAACGGCC 58.192 50.000 21.29 0.00 41.63 6.13
2707 2798 3.809832 AGGTGTTCATCTTGACAAGAACG 59.190 43.478 21.29 15.15 42.35 3.95
2770 2861 3.175133 GGAACGGAGGGAGTACGTA 57.825 57.895 0.00 0.00 40.31 3.57
2771 2862 4.009015 GGAACGGAGGGAGTACGT 57.991 61.111 0.00 0.00 43.43 3.57
2784 2875 7.860872 ACAAATCAAAGACAAGTAATTCGGAAC 59.139 33.333 0.00 0.00 0.00 3.62
2785 2876 7.936584 ACAAATCAAAGACAAGTAATTCGGAA 58.063 30.769 0.00 0.00 0.00 4.30
2786 2877 7.444183 AGACAAATCAAAGACAAGTAATTCGGA 59.556 33.333 0.00 0.00 0.00 4.55
2787 2878 7.584987 AGACAAATCAAAGACAAGTAATTCGG 58.415 34.615 0.00 0.00 0.00 4.30
2788 2879 9.746711 CTAGACAAATCAAAGACAAGTAATTCG 57.253 33.333 0.00 0.00 0.00 3.34
2793 2884 9.569167 CGTATCTAGACAAATCAAAGACAAGTA 57.431 33.333 0.00 0.00 0.00 2.24
2794 2885 7.545965 CCGTATCTAGACAAATCAAAGACAAGT 59.454 37.037 0.00 0.00 0.00 3.16
2795 2886 7.759886 TCCGTATCTAGACAAATCAAAGACAAG 59.240 37.037 0.00 0.00 0.00 3.16
2796 2887 7.608153 TCCGTATCTAGACAAATCAAAGACAA 58.392 34.615 0.00 0.00 0.00 3.18
2797 2888 7.165460 TCCGTATCTAGACAAATCAAAGACA 57.835 36.000 0.00 0.00 0.00 3.41
2798 2889 7.707035 ACATCCGTATCTAGACAAATCAAAGAC 59.293 37.037 0.00 0.00 0.00 3.01
2799 2890 7.782049 ACATCCGTATCTAGACAAATCAAAGA 58.218 34.615 0.00 0.00 0.00 2.52
2800 2891 9.698309 ATACATCCGTATCTAGACAAATCAAAG 57.302 33.333 0.00 0.00 32.66 2.77
2817 2908 8.794553 CCTCATTTTAGTACTAGATACATCCGT 58.205 37.037 2.23 0.00 36.09 4.69
2818 2909 7.755822 GCCTCATTTTAGTACTAGATACATCCG 59.244 40.741 2.23 0.00 36.09 4.18
2819 2910 8.808092 AGCCTCATTTTAGTACTAGATACATCC 58.192 37.037 2.23 0.00 36.09 3.51
2829 2920 9.594936 AGATGTATCTAGCCTCATTTTAGTACT 57.405 33.333 0.00 0.00 34.85 2.73
2830 2921 9.632807 CAGATGTATCTAGCCTCATTTTAGTAC 57.367 37.037 0.00 0.00 34.85 2.73
2831 2922 9.368416 ACAGATGTATCTAGCCTCATTTTAGTA 57.632 33.333 0.00 0.00 34.85 1.82
2832 2923 8.256356 ACAGATGTATCTAGCCTCATTTTAGT 57.744 34.615 0.00 0.00 34.85 2.24
2865 2956 9.746711 CGTTCTGAATTACTTGTCTTAGATTTG 57.253 33.333 0.00 0.00 0.00 2.32
2866 2957 8.936864 CCGTTCTGAATTACTTGTCTTAGATTT 58.063 33.333 0.00 0.00 0.00 2.17
2867 2958 8.311836 TCCGTTCTGAATTACTTGTCTTAGATT 58.688 33.333 0.00 0.00 0.00 2.40
2868 2959 7.837863 TCCGTTCTGAATTACTTGTCTTAGAT 58.162 34.615 0.00 0.00 0.00 1.98
2869 2960 7.223260 TCCGTTCTGAATTACTTGTCTTAGA 57.777 36.000 0.00 0.00 0.00 2.10
2870 2961 6.531948 CCTCCGTTCTGAATTACTTGTCTTAG 59.468 42.308 0.00 0.00 0.00 2.18
2871 2962 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.00 0.00 2.10
2872 2963 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
2873 2964 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2874 2965 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2875 2966 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2876 2967 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2877 2968 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2878 2969 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2879 2970 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2880 2971 5.205821 TCATACTCCCTCCGTTCTGAATTA 58.794 41.667 0.00 0.00 0.00 1.40
2881 2972 4.030913 TCATACTCCCTCCGTTCTGAATT 58.969 43.478 0.00 0.00 0.00 2.17
2882 2973 3.639094 CTCATACTCCCTCCGTTCTGAAT 59.361 47.826 0.00 0.00 0.00 2.57
2883 2974 3.024547 CTCATACTCCCTCCGTTCTGAA 58.975 50.000 0.00 0.00 0.00 3.02
2884 2975 2.241430 TCTCATACTCCCTCCGTTCTGA 59.759 50.000 0.00 0.00 0.00 3.27
2885 2976 2.359531 GTCTCATACTCCCTCCGTTCTG 59.640 54.545 0.00 0.00 0.00 3.02
2886 2977 2.025226 TGTCTCATACTCCCTCCGTTCT 60.025 50.000 0.00 0.00 0.00 3.01
2887 2978 2.359531 CTGTCTCATACTCCCTCCGTTC 59.640 54.545 0.00 0.00 0.00 3.95
2888 2979 2.379972 CTGTCTCATACTCCCTCCGTT 58.620 52.381 0.00 0.00 0.00 4.44
2889 2980 1.410365 CCTGTCTCATACTCCCTCCGT 60.410 57.143 0.00 0.00 0.00 4.69
2890 2981 1.323412 CCTGTCTCATACTCCCTCCG 58.677 60.000 0.00 0.00 0.00 4.63
2891 2982 1.044611 GCCTGTCTCATACTCCCTCC 58.955 60.000 0.00 0.00 0.00 4.30
2892 2983 1.410882 GTGCCTGTCTCATACTCCCTC 59.589 57.143 0.00 0.00 0.00 4.30
2893 2984 1.490574 GTGCCTGTCTCATACTCCCT 58.509 55.000 0.00 0.00 0.00 4.20
2894 2985 0.466124 GGTGCCTGTCTCATACTCCC 59.534 60.000 0.00 0.00 0.00 4.30
2895 2986 0.466124 GGGTGCCTGTCTCATACTCC 59.534 60.000 0.00 0.00 0.00 3.85
2896 2987 0.466124 GGGGTGCCTGTCTCATACTC 59.534 60.000 0.00 0.00 0.00 2.59
2897 2988 0.252696 TGGGGTGCCTGTCTCATACT 60.253 55.000 0.00 0.00 0.00 2.12
2972 3063 7.880195 GCCAAGTCAACTGTATGATAGGATAAT 59.120 37.037 0.00 0.00 0.00 1.28
2973 3064 7.217200 GCCAAGTCAACTGTATGATAGGATAA 58.783 38.462 0.00 0.00 0.00 1.75
2980 3071 3.614092 CAGGCCAAGTCAACTGTATGAT 58.386 45.455 5.01 0.00 0.00 2.45
2983 3074 1.985159 TCCAGGCCAAGTCAACTGTAT 59.015 47.619 5.01 0.00 0.00 2.29
2984 3075 1.429930 TCCAGGCCAAGTCAACTGTA 58.570 50.000 5.01 0.00 0.00 2.74
2986 3077 1.691196 TTTCCAGGCCAAGTCAACTG 58.309 50.000 5.01 0.00 0.00 3.16
3019 3110 2.274760 CCGGACGGAGGGAGTACT 59.725 66.667 4.40 0.00 37.50 2.73
3026 3117 0.104304 CAAGTATTCCCGGACGGAGG 59.896 60.000 13.13 0.00 43.39 4.30
3027 3118 0.822164 ACAAGTATTCCCGGACGGAG 59.178 55.000 13.13 2.58 43.39 4.63
3028 3119 1.269012 AACAAGTATTCCCGGACGGA 58.731 50.000 13.13 0.00 39.68 4.69
3029 3120 1.735571 CAAACAAGTATTCCCGGACGG 59.264 52.381 0.73 3.25 0.00 4.79
3030 3121 2.690786 TCAAACAAGTATTCCCGGACG 58.309 47.619 0.73 0.00 0.00 4.79
3031 3122 5.638596 ATTTCAAACAAGTATTCCCGGAC 57.361 39.130 0.73 0.00 0.00 4.79
3033 3124 6.753107 AGTATTTCAAACAAGTATTCCCGG 57.247 37.500 0.00 0.00 0.00 5.73
3034 3125 7.590279 ACAAGTATTTCAAACAAGTATTCCCG 58.410 34.615 0.00 0.00 0.00 5.14
3035 3126 8.573035 TGACAAGTATTTCAAACAAGTATTCCC 58.427 33.333 0.00 0.00 0.00 3.97
3036 3127 9.612620 CTGACAAGTATTTCAAACAAGTATTCC 57.387 33.333 0.00 0.00 0.00 3.01
3039 3130 9.778741 TCTCTGACAAGTATTTCAAACAAGTAT 57.221 29.630 0.00 0.00 0.00 2.12
3040 3131 9.261180 CTCTCTGACAAGTATTTCAAACAAGTA 57.739 33.333 0.00 0.00 0.00 2.24
3041 3132 7.987458 TCTCTCTGACAAGTATTTCAAACAAGT 59.013 33.333 0.00 0.00 0.00 3.16
3042 3133 8.370493 TCTCTCTGACAAGTATTTCAAACAAG 57.630 34.615 0.00 0.00 0.00 3.16
3043 3134 8.204160 TCTCTCTCTGACAAGTATTTCAAACAA 58.796 33.333 0.00 0.00 0.00 2.83
3044 3135 7.726216 TCTCTCTCTGACAAGTATTTCAAACA 58.274 34.615 0.00 0.00 0.00 2.83
3045 3136 8.085296 TCTCTCTCTCTGACAAGTATTTCAAAC 58.915 37.037 0.00 0.00 0.00 2.93
3046 3137 8.183104 TCTCTCTCTCTGACAAGTATTTCAAA 57.817 34.615 0.00 0.00 0.00 2.69
3060 3151 5.857471 ACATCCATTTCTCTCTCTCTCTG 57.143 43.478 0.00 0.00 0.00 3.35
3061 3152 5.363580 GGAACATCCATTTCTCTCTCTCTCT 59.636 44.000 0.00 0.00 36.28 3.10
3065 3156 3.431486 GCGGAACATCCATTTCTCTCTCT 60.431 47.826 0.00 0.00 35.91 3.10
3066 3157 2.869192 GCGGAACATCCATTTCTCTCTC 59.131 50.000 0.00 0.00 35.91 3.20
3067 3158 2.237143 TGCGGAACATCCATTTCTCTCT 59.763 45.455 0.00 0.00 35.91 3.10
3068 3159 2.632377 TGCGGAACATCCATTTCTCTC 58.368 47.619 0.00 0.00 35.91 3.20
3069 3160 2.787473 TGCGGAACATCCATTTCTCT 57.213 45.000 0.00 0.00 35.91 3.10
3070 3161 2.749621 ACTTGCGGAACATCCATTTCTC 59.250 45.455 0.00 0.00 35.91 2.87
3071 3162 2.795329 ACTTGCGGAACATCCATTTCT 58.205 42.857 0.00 0.00 35.91 2.52
3072 3163 4.900635 ATACTTGCGGAACATCCATTTC 57.099 40.909 0.00 0.00 35.91 2.17
3073 3164 5.394115 GGAAATACTTGCGGAACATCCATTT 60.394 40.000 0.00 0.00 35.91 2.32
3085 3176 2.287915 CCTTCATCCGGAAATACTTGCG 59.712 50.000 9.01 0.00 45.09 4.85
3096 3187 3.134804 AGAAATGTACTCCCTTCATCCGG 59.865 47.826 0.00 0.00 0.00 5.14
3099 3190 8.189119 AGAGATAGAAATGTACTCCCTTCATC 57.811 38.462 0.00 0.00 0.00 2.92
3100 3191 8.428063 CAAGAGATAGAAATGTACTCCCTTCAT 58.572 37.037 0.00 0.00 0.00 2.57
3101 3192 7.633772 GCAAGAGATAGAAATGTACTCCCTTCA 60.634 40.741 0.00 0.00 0.00 3.02
3103 3194 6.156949 TGCAAGAGATAGAAATGTACTCCCTT 59.843 38.462 0.00 0.00 0.00 3.95
3114 3205 8.246180 GGAAAATCAACATGCAAGAGATAGAAA 58.754 33.333 0.00 0.00 0.00 2.52
3119 3210 5.105473 CCTGGAAAATCAACATGCAAGAGAT 60.105 40.000 0.00 0.00 0.00 2.75
3186 3280 5.355596 CAAGCAACCAAACCTATGTGAAAA 58.644 37.500 0.00 0.00 0.00 2.29
3196 3290 4.756630 CTGGCAAGCAACCAAACC 57.243 55.556 0.00 0.00 36.56 3.27
3211 3305 3.443037 CTCTATCAGAGGTTTGACGCTG 58.557 50.000 0.00 0.00 38.67 5.18
3216 3310 6.053632 TGATTTGCTCTATCAGAGGTTTGA 57.946 37.500 5.40 0.00 42.54 2.69
3226 3320 5.975410 AACTAGCGTTGATTTGCTCTATC 57.025 39.130 0.00 0.00 42.48 2.08
3237 3331 5.163581 GGATAGAGTTGGTAACTAGCGTTGA 60.164 44.000 0.00 0.00 43.03 3.18
3238 3332 5.041940 GGATAGAGTTGGTAACTAGCGTTG 58.958 45.833 0.00 0.00 43.03 4.10
3242 3336 7.146648 GTGTATGGATAGAGTTGGTAACTAGC 58.853 42.308 0.00 0.00 43.03 3.42
3254 3348 7.157347 ACATAATGTGCTGTGTATGGATAGAG 58.843 38.462 0.00 0.00 0.00 2.43
3258 3352 6.038603 GTGAACATAATGTGCTGTGTATGGAT 59.961 38.462 0.00 0.00 0.00 3.41
3259 3353 5.353956 GTGAACATAATGTGCTGTGTATGGA 59.646 40.000 0.00 0.00 0.00 3.41
3260 3354 5.355071 AGTGAACATAATGTGCTGTGTATGG 59.645 40.000 0.00 0.00 0.00 2.74
3261 3355 6.426980 AGTGAACATAATGTGCTGTGTATG 57.573 37.500 0.00 0.00 0.00 2.39
3262 3356 7.555965 TCTAGTGAACATAATGTGCTGTGTAT 58.444 34.615 0.00 0.00 0.00 2.29
3263 3357 6.930731 TCTAGTGAACATAATGTGCTGTGTA 58.069 36.000 0.00 0.00 0.00 2.90
3264 3358 5.793817 TCTAGTGAACATAATGTGCTGTGT 58.206 37.500 0.00 0.00 0.00 3.72
3265 3359 6.915544 ATCTAGTGAACATAATGTGCTGTG 57.084 37.500 0.00 0.00 0.00 3.66
3266 3360 8.478066 TCTTATCTAGTGAACATAATGTGCTGT 58.522 33.333 0.00 0.00 0.00 4.40
3267 3361 8.877808 TCTTATCTAGTGAACATAATGTGCTG 57.122 34.615 0.00 0.00 0.00 4.41
3288 3382 9.475620 TCTCTCTTGGTTTGACAGTATATCTTA 57.524 33.333 0.00 0.00 0.00 2.10
3289 3383 8.367660 TCTCTCTTGGTTTGACAGTATATCTT 57.632 34.615 0.00 0.00 0.00 2.40
3290 3384 7.836685 TCTCTCTCTTGGTTTGACAGTATATCT 59.163 37.037 0.00 0.00 0.00 1.98
3291 3385 7.918562 GTCTCTCTCTTGGTTTGACAGTATATC 59.081 40.741 0.00 0.00 0.00 1.63
3292 3386 7.147811 GGTCTCTCTCTTGGTTTGACAGTATAT 60.148 40.741 0.00 0.00 0.00 0.86
3293 3387 6.153000 GGTCTCTCTCTTGGTTTGACAGTATA 59.847 42.308 0.00 0.00 0.00 1.47
3294 3388 5.046950 GGTCTCTCTCTTGGTTTGACAGTAT 60.047 44.000 0.00 0.00 0.00 2.12
3295 3389 4.281182 GGTCTCTCTCTTGGTTTGACAGTA 59.719 45.833 0.00 0.00 0.00 2.74
3296 3390 3.070302 GGTCTCTCTCTTGGTTTGACAGT 59.930 47.826 0.00 0.00 0.00 3.55
3297 3391 3.070159 TGGTCTCTCTCTTGGTTTGACAG 59.930 47.826 0.00 0.00 0.00 3.51
3298 3392 3.038280 TGGTCTCTCTCTTGGTTTGACA 58.962 45.455 0.00 0.00 0.00 3.58
3299 3393 3.753294 TGGTCTCTCTCTTGGTTTGAC 57.247 47.619 0.00 0.00 0.00 3.18
3300 3394 4.771114 TTTGGTCTCTCTCTTGGTTTGA 57.229 40.909 0.00 0.00 0.00 2.69
3301 3395 5.065914 TCATTTGGTCTCTCTCTTGGTTTG 58.934 41.667 0.00 0.00 0.00 2.93
3302 3396 5.310409 TCATTTGGTCTCTCTCTTGGTTT 57.690 39.130 0.00 0.00 0.00 3.27
3303 3397 4.982241 TCATTTGGTCTCTCTCTTGGTT 57.018 40.909 0.00 0.00 0.00 3.67
3304 3398 4.982241 TTCATTTGGTCTCTCTCTTGGT 57.018 40.909 0.00 0.00 0.00 3.67
3305 3399 5.555017 TCTTTCATTTGGTCTCTCTCTTGG 58.445 41.667 0.00 0.00 0.00 3.61
3306 3400 6.654161 ACATCTTTCATTTGGTCTCTCTCTTG 59.346 38.462 0.00 0.00 0.00 3.02
3307 3401 6.777782 ACATCTTTCATTTGGTCTCTCTCTT 58.222 36.000 0.00 0.00 0.00 2.85
3308 3402 6.013898 TGACATCTTTCATTTGGTCTCTCTCT 60.014 38.462 0.00 0.00 0.00 3.10
3309 3403 6.169094 TGACATCTTTCATTTGGTCTCTCTC 58.831 40.000 0.00 0.00 0.00 3.20
3310 3404 6.119240 TGACATCTTTCATTTGGTCTCTCT 57.881 37.500 0.00 0.00 0.00 3.10
3311 3405 6.808008 TTGACATCTTTCATTTGGTCTCTC 57.192 37.500 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.