Multiple sequence alignment - TraesCS1D01G431400

Loading Multiple Alignment...

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 TraesCS1D01G431400 chr1D 100.000 5060 0 0 1 5060 481560731 481555672 0.000000e+00 9345.0
1 TraesCS1D01G431400 chr1D 94.969 1272 45 6 698 1957 481480170 481481434 0.000000e+00 1977.0
2 TraesCS1D01G431400 chr1D 92.691 1245 71 16 2930 4159 481482298 481483537 0.000000e+00 1777.0
3 TraesCS1D01G431400 chr1D 92.503 747 43 9 4319 5060 481485123 481485861 0.000000e+00 1057.0
4 TraesCS1D01G431400 chr1D 90.448 670 57 5 4392 5060 481489308 481489971 0.000000e+00 876.0
5 TraesCS1D01G431400 chr1D 91.843 613 45 3 84 694 481479457 481480066 0.000000e+00 850.0
6 TraesCS1D01G431400 chr1D 86.199 442 41 18 2037 2470 481481417 481481846 1.280000e-125 460.0
7 TraesCS1D01G431400 chr1D 93.985 266 11 3 2661 2925 481481986 481482247 1.020000e-106 398.0
8 TraesCS1D01G431400 chr1D 100.000 125 0 0 2520 2644 72884447 72884323 1.100000e-56 231.0
9 TraesCS1D01G431400 chr1D 93.684 95 5 1 4187 4280 481484766 481484860 1.900000e-29 141.0
10 TraesCS1D01G431400 chr1D 95.745 47 2 0 4280 4326 481556267 481556221 5.430000e-10 76.8
11 TraesCS1D01G431400 chr1D 95.745 47 2 0 4465 4511 481556452 481556406 5.430000e-10 76.8
12 TraesCS1D01G431400 chr1A 96.210 1583 56 3 2926 4508 578015796 578014218 0.000000e+00 2588.0
13 TraesCS1D01G431400 chr1A 93.308 1330 60 9 698 2006 578018000 578016679 0.000000e+00 1936.0
14 TraesCS1D01G431400 chr1A 95.053 566 21 5 4490 5053 578013691 578013131 0.000000e+00 883.0
15 TraesCS1D01G431400 chr1A 90.145 690 47 7 9 697 578018766 578018097 0.000000e+00 878.0
16 TraesCS1D01G431400 chr1A 92.259 478 23 4 2048 2524 578016569 578016105 0.000000e+00 665.0
17 TraesCS1D01G431400 chr1A 94.485 272 15 0 2654 2925 578016108 578015837 2.180000e-113 420.0
18 TraesCS1D01G431400 chr1A 78.678 605 98 20 1 597 65236033 65236614 1.720000e-99 374.0
19 TraesCS1D01G431400 chr1A 93.617 47 3 0 4465 4511 578014446 578014400 2.530000e-08 71.3
20 TraesCS1D01G431400 chr1A 97.297 37 1 0 4280 4316 578014261 578014225 4.230000e-06 63.9
21 TraesCS1D01G431400 chr1B 92.254 1291 84 12 2926 4209 670154224 670152943 0.000000e+00 1816.0
22 TraesCS1D01G431400 chr1B 92.917 833 58 1 1127 1959 670155864 670155033 0.000000e+00 1210.0
23 TraesCS1D01G431400 chr1B 90.574 488 29 7 2041 2519 670155037 670154558 9.240000e-177 630.0
24 TraesCS1D01G431400 chr1B 94.681 282 15 0 2644 2925 670154566 670154285 6.010000e-119 438.0
25 TraesCS1D01G431400 chr1B 84.466 309 45 2 1088 1396 669939166 669938861 8.230000e-78 302.0
26 TraesCS1D01G431400 chrUn 94.175 309 17 1 3051 3359 34767637 34767944 2.130000e-128 470.0
27 TraesCS1D01G431400 chr4D 79.873 631 102 11 3 628 502028771 502028161 6.010000e-119 438.0
28 TraesCS1D01G431400 chr7A 76.361 643 104 21 1 636 71111240 71111841 8.230000e-78 302.0
29 TraesCS1D01G431400 chr7A 100.000 125 0 0 2519 2643 124067306 124067182 1.100000e-56 231.0
30 TraesCS1D01G431400 chr2B 88.584 219 25 0 2685 2903 245318955 245318737 3.000000e-67 267.0
31 TraesCS1D01G431400 chr2B 100.000 126 0 0 2519 2644 24197149 24197274 3.050000e-57 233.0
32 TraesCS1D01G431400 chr2B 80.000 245 44 5 3714 3957 245687169 245686929 5.210000e-40 176.0
33 TraesCS1D01G431400 chr2B 97.849 93 1 1 1954 2045 785216426 785216334 5.240000e-35 159.0
34 TraesCS1D01G431400 chr2A 87.892 223 24 1 2699 2921 203256661 203256442 5.030000e-65 259.0
35 TraesCS1D01G431400 chr2A 85.259 251 35 2 3104 3353 203255991 203255742 1.810000e-64 257.0
36 TraesCS1D01G431400 chr2A 94.059 101 4 2 1951 2050 79496766 79496865 8.770000e-33 152.0
37 TraesCS1D01G431400 chr2D 86.498 237 29 1 2685 2921 189296482 189296249 1.810000e-64 257.0
38 TraesCS1D01G431400 chr2D 95.000 100 2 3 1955 2052 13895159 13895061 2.440000e-33 154.0
39 TraesCS1D01G431400 chr2D 77.251 211 42 5 3148 3354 189528503 189528295 8.900000e-23 119.0
40 TraesCS1D01G431400 chr7B 99.231 130 0 1 2516 2644 336360957 336361086 3.050000e-57 233.0
41 TraesCS1D01G431400 chr7B 100.000 124 0 0 2519 2642 534538234 534538111 3.940000e-56 230.0
42 TraesCS1D01G431400 chr7B 100.000 124 0 0 2520 2643 733885648 733885525 3.940000e-56 230.0
43 TraesCS1D01G431400 chr4A 100.000 125 0 0 2519 2643 8592557 8592681 1.100000e-56 231.0
44 TraesCS1D01G431400 chr4A 99.213 127 1 0 2519 2645 46560411 46560537 3.940000e-56 230.0
45 TraesCS1D01G431400 chr5A 98.450 129 2 0 2520 2648 608862350 608862222 1.420000e-55 228.0
46 TraesCS1D01G431400 chr5A 81.349 252 41 5 3110 3356 546307079 546306829 3.090000e-47 200.0
47 TraesCS1D01G431400 chr5A 94.175 103 2 4 1957 2058 48918165 48918066 2.440000e-33 154.0
48 TraesCS1D01G431400 chr7D 92.373 118 5 4 1935 2050 405186272 405186387 1.130000e-36 165.0
49 TraesCS1D01G431400 chr4B 96.842 95 1 2 1950 2042 286079579 286079485 1.890000e-34 158.0
50 TraesCS1D01G431400 chr6B 95.876 97 2 2 1951 2045 132894360 132894264 6.780000e-34 156.0
51 TraesCS1D01G431400 chr5D 95.000 100 3 2 1958 2055 413056177 413056276 6.780000e-34 156.0
52 TraesCS1D01G431400 chr5D 92.593 108 7 1 1941 2047 333986476 333986369 2.440000e-33 154.0


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 TraesCS1D01G431400 chr1D 481555672 481560731 5059 True 9345.00 9345 100.00000 1 5060 1 chr1D.!!$R2 5059
1 TraesCS1D01G431400 chr1D 481479457 481489971 10514 False 942.00 1977 92.04025 84 5060 8 chr1D.!!$F1 4976
2 TraesCS1D01G431400 chr1A 578013131 578018766 5635 True 938.15 2588 94.04675 9 5053 8 chr1A.!!$R1 5044
3 TraesCS1D01G431400 chr1A 65236033 65236614 581 False 374.00 374 78.67800 1 597 1 chr1A.!!$F1 596
4 TraesCS1D01G431400 chr1B 670152943 670155864 2921 True 1023.50 1816 92.60650 1127 4209 4 chr1B.!!$R2 3082
5 TraesCS1D01G431400 chr4D 502028161 502028771 610 True 438.00 438 79.87300 3 628 1 chr4D.!!$R1 625
6 TraesCS1D01G431400 chr7A 71111240 71111841 601 False 302.00 302 76.36100 1 636 1 chr7A.!!$F1 635
7 TraesCS1D01G431400 chr2A 203255742 203256661 919 True 258.00 259 86.57550 2699 3353 2 chr2A.!!$R1 654

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
51 52 0.037326 TGCTCCGACGCTGAAAAGAT 60.037 50.0 0.00 0.0 0.00 2.40 F
1138 1268 0.316522 CGTCCTCGCCATGATCATCT 59.683 55.0 4.86 0.0 0.00 2.90 F
2567 2881 0.179048 TGCAGTTGGGTCACTGACAG 60.179 55.0 11.34 0.0 46.29 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 2014 0.679002 GAAGCTGGAGCATTGCCTGA 60.679 55.0 4.70 0.00 45.16 3.86 R
2612 2926 0.109086 CTCTGACGTACTGCAGGGTG 60.109 60.0 19.93 9.21 33.05 4.61 R
4079 4686 0.179156 CAAACATGACATGGCCGCTC 60.179 55.0 19.39 0.00 33.60 5.03 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
32 33 1.143073 ACGCTGGTCCTCCTTTTCTTT 59.857 47.619 0.00 0.00 34.23 2.52
43 44 0.868406 CTTTTCTTTGCTCCGACGCT 59.132 50.000 0.00 0.00 0.00 5.07
51 52 0.037326 TGCTCCGACGCTGAAAAGAT 60.037 50.000 0.00 0.00 0.00 2.40
77 78 0.964860 ACACAAGTGCAGCCAACACA 60.965 50.000 0.00 0.00 40.59 3.72
87 88 0.969917 AGCCAACACACCTGCAACAA 60.970 50.000 0.00 0.00 0.00 2.83
128 129 1.889829 GAGTATCGCTAGATGTGCCCT 59.110 52.381 0.00 0.00 37.70 5.19
274 276 7.630242 ACATCAGAAAAATCATACCAACGAT 57.370 32.000 0.00 0.00 0.00 3.73
285 290 6.724893 TCATACCAACGATGAGGAAGAATA 57.275 37.500 0.00 0.00 0.00 1.75
286 291 7.119709 TCATACCAACGATGAGGAAGAATAA 57.880 36.000 0.00 0.00 0.00 1.40
287 292 7.735917 TCATACCAACGATGAGGAAGAATAAT 58.264 34.615 0.00 0.00 0.00 1.28
300 305 5.011533 AGGAAGAATAATCTCCATCTCCACG 59.988 44.000 0.00 0.00 33.77 4.94
472 477 4.682860 GGAAAACTTATTCAGACACGACGA 59.317 41.667 0.00 0.00 0.00 4.20
482 487 2.803670 CACGACGACACCGCGATT 60.804 61.111 8.23 0.00 39.95 3.34
560 569 2.044620 GTTCCCCCTCCCTCCCAT 59.955 66.667 0.00 0.00 0.00 4.00
723 835 2.832201 CCGTCGGTAGAGGGGGAC 60.832 72.222 2.08 0.00 45.91 4.46
823 936 2.597510 GGACAGGTTGGGCACACC 60.598 66.667 0.00 0.00 40.81 4.16
847 960 4.457496 AGCTGTCATGCGGGTCCG 62.457 66.667 4.85 4.85 43.09 4.79
942 1055 1.289694 CCAAAATTGCGGCTCTGCA 59.710 52.632 0.00 0.00 44.61 4.41
973 1097 1.676006 CAACTTTGACTCCTTTGGCGT 59.324 47.619 0.00 0.00 0.00 5.68
1051 1181 1.495584 GCTCTGTCGTCGTGCCAAAA 61.496 55.000 0.00 0.00 0.00 2.44
1057 1187 2.161808 TGTCGTCGTGCCAAAAGAAAAA 59.838 40.909 0.00 0.00 0.00 1.94
1064 1194 1.478510 TGCCAAAAGAAAAACGAGCCA 59.521 42.857 0.00 0.00 0.00 4.75
1082 1212 4.716977 GTCCACCGGTCTCCCCCT 62.717 72.222 2.59 0.00 0.00 4.79
1083 1213 4.715130 TCCACCGGTCTCCCCCTG 62.715 72.222 2.59 0.00 0.00 4.45
1138 1268 0.316522 CGTCCTCGCCATGATCATCT 59.683 55.000 4.86 0.00 0.00 2.90
1878 2014 3.524606 CGGCCCATCTACGACGGT 61.525 66.667 0.00 0.00 0.00 4.83
1927 2063 1.144936 CCGCCATCTCCTTCTGTCC 59.855 63.158 0.00 0.00 0.00 4.02
1931 2067 1.969240 GCCATCTCCTTCTGTCCCTCT 60.969 57.143 0.00 0.00 0.00 3.69
1953 2089 3.297391 GCATGGAGCAGGTAGTAGC 57.703 57.895 0.00 0.00 44.79 3.58
1954 2090 0.755686 GCATGGAGCAGGTAGTAGCT 59.244 55.000 0.00 0.00 45.25 3.32
1955 2091 1.964223 GCATGGAGCAGGTAGTAGCTA 59.036 52.381 0.60 0.00 42.04 3.32
1956 2092 2.029470 GCATGGAGCAGGTAGTAGCTAG 60.029 54.545 0.60 0.00 42.04 3.42
1970 2115 2.055684 AGCTAGTACTCCCTCCGTTC 57.944 55.000 0.00 0.00 0.00 3.95
2028 2226 8.934023 AGTAAAAGTTGGGTCATCTATTTTGA 57.066 30.769 0.00 0.00 0.00 2.69
2031 2229 8.887036 AAAAGTTGGGTCATCTATTTTGAAAC 57.113 30.769 0.00 0.00 0.00 2.78
2042 2240 5.974108 TCTATTTTGAAACGGAGGGAGTAG 58.026 41.667 0.00 0.00 0.00 2.57
2045 2243 4.796038 TTTGAAACGGAGGGAGTAGTAG 57.204 45.455 0.00 0.00 0.00 2.57
2084 2300 4.844085 TCAGTTCCCCTTCTTATCTGAACA 59.156 41.667 0.00 0.00 35.68 3.18
2085 2301 5.309543 TCAGTTCCCCTTCTTATCTGAACAA 59.690 40.000 0.00 0.00 35.68 2.83
2086 2302 5.645497 CAGTTCCCCTTCTTATCTGAACAAG 59.355 44.000 0.00 0.00 35.68 3.16
2087 2303 5.310857 AGTTCCCCTTCTTATCTGAACAAGT 59.689 40.000 0.00 0.00 35.68 3.16
2140 2362 8.634335 TTTATCATCATTCAGGAAACACAAGA 57.366 30.769 0.00 0.00 0.00 3.02
2142 2364 6.317789 TCATCATTCAGGAAACACAAGAAC 57.682 37.500 0.00 0.00 0.00 3.01
2269 2491 7.114247 GCTGAAGATGATAATCGTGAGTAGAAC 59.886 40.741 0.00 0.00 0.00 3.01
2323 2551 5.049267 GCCGGACTTTTGTTTACTGATAACA 60.049 40.000 5.05 0.00 33.92 2.41
2421 2649 1.487482 GCAACCGGAAACTTTTCAGC 58.513 50.000 9.46 0.00 38.92 4.26
2425 2653 0.667993 CCGGAAACTTTTCAGCAGCA 59.332 50.000 0.00 0.00 38.92 4.41
2489 2798 4.103365 TGAAAACAAGCAAGAAAGCGAA 57.897 36.364 0.00 0.00 40.15 4.70
2518 2832 4.557695 AAGGAGTCGATGTATCGCTCATTC 60.558 45.833 25.14 15.67 44.92 2.67
2519 2833 7.762678 AAGGAGTCGATGTATCGCTCATTCG 62.763 48.000 25.14 0.00 44.92 3.34
2521 2835 2.331809 CGATGTATCGCTCATTCGGA 57.668 50.000 0.92 0.00 43.84 4.55
2522 2836 1.979469 CGATGTATCGCTCATTCGGAC 59.021 52.381 0.92 0.00 43.84 4.79
2523 2837 2.350868 CGATGTATCGCTCATTCGGACT 60.351 50.000 0.92 0.00 43.84 3.85
2524 2838 2.776312 TGTATCGCTCATTCGGACTC 57.224 50.000 0.00 0.00 0.00 3.36
2525 2839 1.002792 TGTATCGCTCATTCGGACTCG 60.003 52.381 0.00 0.00 37.82 4.18
2526 2840 0.591659 TATCGCTCATTCGGACTCGG 59.408 55.000 0.00 0.00 36.95 4.63
2527 2841 2.685387 ATCGCTCATTCGGACTCGGC 62.685 60.000 0.00 0.00 36.95 5.54
2528 2842 2.496817 GCTCATTCGGACTCGGCT 59.503 61.111 0.00 0.00 36.95 5.52
2529 2843 1.590259 GCTCATTCGGACTCGGCTC 60.590 63.158 0.00 0.00 36.95 4.70
2530 2844 1.066587 CTCATTCGGACTCGGCTCC 59.933 63.158 0.00 0.00 36.95 4.70
2531 2845 2.107141 CATTCGGACTCGGCTCCC 59.893 66.667 0.00 0.00 36.95 4.30
2532 2846 3.155167 ATTCGGACTCGGCTCCCC 61.155 66.667 0.00 0.00 36.95 4.81
2533 2847 3.680920 ATTCGGACTCGGCTCCCCT 62.681 63.158 0.00 0.00 36.95 4.79
2536 2850 3.462678 GGACTCGGCTCCCCTGAC 61.463 72.222 0.00 0.00 0.00 3.51
2537 2851 3.827898 GACTCGGCTCCCCTGACG 61.828 72.222 0.00 0.00 40.31 4.35
2538 2852 4.680537 ACTCGGCTCCCCTGACGT 62.681 66.667 0.00 0.00 39.83 4.34
2539 2853 2.439701 CTCGGCTCCCCTGACGTA 60.440 66.667 0.00 0.00 39.83 3.57
2540 2854 2.753043 TCGGCTCCCCTGACGTAC 60.753 66.667 0.00 0.00 39.83 3.67
2541 2855 2.754658 CGGCTCCCCTGACGTACT 60.755 66.667 0.00 0.00 33.11 2.73
2542 2856 2.893398 GGCTCCCCTGACGTACTG 59.107 66.667 0.00 0.00 0.00 2.74
2543 2857 2.184579 GCTCCCCTGACGTACTGC 59.815 66.667 0.00 0.00 0.00 4.40
2544 2858 2.646175 GCTCCCCTGACGTACTGCA 61.646 63.158 0.00 0.00 0.00 4.41
2545 2859 1.513158 CTCCCCTGACGTACTGCAG 59.487 63.158 13.48 13.48 0.00 4.41
2548 2862 3.377656 CCTGACGTACTGCAGGGT 58.622 61.111 19.93 12.80 46.24 4.34
2549 2863 1.079819 CCTGACGTACTGCAGGGTG 60.080 63.158 19.93 9.21 46.24 4.61
2550 2864 1.738099 CTGACGTACTGCAGGGTGC 60.738 63.158 19.93 0.92 45.29 5.01
2559 2873 2.985847 GCAGGGTGCAGTTGGGTC 60.986 66.667 0.00 0.00 44.26 4.46
2560 2874 2.515398 CAGGGTGCAGTTGGGTCA 59.485 61.111 0.00 0.00 0.00 4.02
2561 2875 1.898574 CAGGGTGCAGTTGGGTCAC 60.899 63.158 0.00 0.00 0.00 3.67
2562 2876 2.078665 AGGGTGCAGTTGGGTCACT 61.079 57.895 0.00 0.00 0.00 3.41
2563 2877 1.898574 GGGTGCAGTTGGGTCACTG 60.899 63.158 0.00 0.00 46.15 3.66
2564 2878 1.148273 GGTGCAGTTGGGTCACTGA 59.852 57.895 5.01 0.00 46.29 3.41
2565 2879 1.166531 GGTGCAGTTGGGTCACTGAC 61.167 60.000 5.01 0.00 46.29 3.51
2566 2880 0.463654 GTGCAGTTGGGTCACTGACA 60.464 55.000 11.34 0.35 46.29 3.58
2567 2881 0.179048 TGCAGTTGGGTCACTGACAG 60.179 55.000 11.34 0.00 46.29 3.51
2568 2882 0.886490 GCAGTTGGGTCACTGACAGG 60.886 60.000 11.34 0.00 46.29 4.00
2569 2883 0.469917 CAGTTGGGTCACTGACAGGT 59.530 55.000 11.34 0.00 46.29 4.00
2570 2884 0.469917 AGTTGGGTCACTGACAGGTG 59.530 55.000 11.34 3.26 38.44 4.00
2571 2885 0.535102 GTTGGGTCACTGACAGGTGG 60.535 60.000 11.34 0.00 37.75 4.61
2572 2886 1.705002 TTGGGTCACTGACAGGTGGG 61.705 60.000 11.34 0.00 37.75 4.61
2573 2887 2.032681 GGTCACTGACAGGTGGGC 59.967 66.667 11.34 0.00 37.75 5.36
2574 2888 2.032681 GTCACTGACAGGTGGGCC 59.967 66.667 7.51 0.00 37.75 5.80
2575 2889 2.447572 TCACTGACAGGTGGGCCA 60.448 61.111 0.00 0.00 37.75 5.36
2576 2890 2.075566 TCACTGACAGGTGGGCCAA 61.076 57.895 8.40 0.00 37.75 4.52
2577 2891 1.898574 CACTGACAGGTGGGCCAAC 60.899 63.158 15.52 15.52 37.19 3.77
2578 2892 2.078665 ACTGACAGGTGGGCCAACT 61.079 57.895 21.01 21.01 37.19 3.16
2579 2893 1.151450 CTGACAGGTGGGCCAACTT 59.849 57.895 24.60 13.86 37.19 2.66
2580 2894 1.152777 TGACAGGTGGGCCAACTTG 60.153 57.895 24.60 20.50 37.19 3.16
2581 2895 2.521708 ACAGGTGGGCCAACTTGC 60.522 61.111 24.60 0.90 37.19 4.01
2582 2896 2.203538 CAGGTGGGCCAACTTGCT 60.204 61.111 24.60 0.00 37.19 3.91
2583 2897 1.833934 CAGGTGGGCCAACTTGCTT 60.834 57.895 24.60 0.00 37.19 3.91
2584 2898 1.075301 AGGTGGGCCAACTTGCTTT 60.075 52.632 21.01 0.00 37.19 3.51
2585 2899 1.115326 AGGTGGGCCAACTTGCTTTC 61.115 55.000 21.01 0.00 37.19 2.62
2586 2900 1.007387 GTGGGCCAACTTGCTTTCG 60.007 57.895 8.40 0.00 0.00 3.46
2587 2901 2.199652 TGGGCCAACTTGCTTTCGG 61.200 57.895 2.13 0.00 0.00 4.30
2588 2902 2.650778 GGCCAACTTGCTTTCGGG 59.349 61.111 0.00 0.00 0.00 5.14
2589 2903 2.049156 GCCAACTTGCTTTCGGGC 60.049 61.111 0.00 0.00 0.00 6.13
2590 2904 2.650778 CCAACTTGCTTTCGGGCC 59.349 61.111 0.00 0.00 0.00 5.80
2591 2905 2.650778 CAACTTGCTTTCGGGCCC 59.349 61.111 13.57 13.57 0.00 5.80
2592 2906 2.197324 AACTTGCTTTCGGGCCCA 59.803 55.556 24.92 6.15 0.00 5.36
2593 2907 2.200337 AACTTGCTTTCGGGCCCAC 61.200 57.895 24.92 5.64 0.00 4.61
2594 2908 3.373565 CTTGCTTTCGGGCCCACC 61.374 66.667 24.92 4.81 0.00 4.61
2595 2909 3.868200 CTTGCTTTCGGGCCCACCT 62.868 63.158 24.92 0.00 36.97 4.00
2596 2910 4.659172 TGCTTTCGGGCCCACCTG 62.659 66.667 24.92 10.12 44.63 4.00
2597 2911 4.660938 GCTTTCGGGCCCACCTGT 62.661 66.667 24.92 0.00 43.58 4.00
2598 2912 2.359975 CTTTCGGGCCCACCTGTC 60.360 66.667 24.92 0.00 43.58 3.51
2599 2913 3.172106 TTTCGGGCCCACCTGTCA 61.172 61.111 24.92 0.00 43.58 3.58
2600 2914 3.190738 TTTCGGGCCCACCTGTCAG 62.191 63.158 24.92 1.98 43.58 3.51
2601 2915 4.954118 TCGGGCCCACCTGTCAGT 62.954 66.667 24.92 0.00 43.58 3.41
2602 2916 4.704833 CGGGCCCACCTGTCAGTG 62.705 72.222 24.92 0.00 37.57 3.66
2608 2922 2.515398 CACCTGTCAGTGGCCCAA 59.485 61.111 0.00 0.00 33.95 4.12
2609 2923 1.898574 CACCTGTCAGTGGCCCAAC 60.899 63.158 0.00 0.00 33.95 3.77
2610 2924 2.078665 ACCTGTCAGTGGCCCAACT 61.079 57.895 0.00 0.00 0.00 3.16
2612 2926 2.203337 TGTCAGTGGCCCAACTGC 60.203 61.111 16.60 12.53 45.93 4.40
2613 2927 2.203337 GTCAGTGGCCCAACTGCA 60.203 61.111 16.60 5.16 45.93 4.41
2614 2928 2.203337 TCAGTGGCCCAACTGCAC 60.203 61.111 16.60 0.00 45.93 4.57
2615 2929 3.297620 CAGTGGCCCAACTGCACC 61.298 66.667 10.07 0.00 41.05 5.01
2616 2930 4.603535 AGTGGCCCAACTGCACCC 62.604 66.667 0.00 0.00 0.00 4.61
2617 2931 4.603535 GTGGCCCAACTGCACCCT 62.604 66.667 0.00 0.00 0.00 4.34
2618 2932 4.601794 TGGCCCAACTGCACCCTG 62.602 66.667 0.00 0.00 0.00 4.45
2628 2942 2.342279 GCACCCTGCAGTACGTCA 59.658 61.111 13.81 0.00 44.26 4.35
2629 2943 1.738099 GCACCCTGCAGTACGTCAG 60.738 63.158 13.81 9.54 44.26 3.51
2630 2944 1.964448 CACCCTGCAGTACGTCAGA 59.036 57.895 13.81 0.00 32.26 3.27
2631 2945 0.109086 CACCCTGCAGTACGTCAGAG 60.109 60.000 13.81 7.84 32.26 3.35
2632 2946 1.251527 ACCCTGCAGTACGTCAGAGG 61.252 60.000 13.81 15.90 32.26 3.69
2633 2947 0.965866 CCCTGCAGTACGTCAGAGGA 60.966 60.000 13.81 0.00 32.26 3.71
2634 2948 0.453793 CCTGCAGTACGTCAGAGGAG 59.546 60.000 13.81 0.00 32.26 3.69
2635 2949 0.179150 CTGCAGTACGTCAGAGGAGC 60.179 60.000 5.25 0.00 32.26 4.70
2636 2950 1.139947 GCAGTACGTCAGAGGAGCC 59.860 63.158 0.00 0.00 0.00 4.70
2637 2951 1.316706 GCAGTACGTCAGAGGAGCCT 61.317 60.000 0.00 0.00 0.00 4.58
2638 2952 0.736053 CAGTACGTCAGAGGAGCCTC 59.264 60.000 8.50 8.50 43.03 4.70
2639 2953 0.745128 AGTACGTCAGAGGAGCCTCG 60.745 60.000 10.69 6.49 46.90 4.63
2640 2954 1.025647 GTACGTCAGAGGAGCCTCGT 61.026 60.000 10.69 8.30 46.90 4.18
2641 2955 0.743701 TACGTCAGAGGAGCCTCGTC 60.744 60.000 10.69 6.30 46.90 4.20
2642 2956 2.766400 CGTCAGAGGAGCCTCGTCC 61.766 68.421 10.64 2.33 46.90 4.79
2643 2957 2.043852 TCAGAGGAGCCTCGTCCC 60.044 66.667 10.64 0.00 46.90 4.46
2652 2966 2.107141 CCTCGTCCCGCTCATTCC 59.893 66.667 0.00 0.00 0.00 3.01
2663 2977 0.178068 GCTCATTCCGGCCTTGTCTA 59.822 55.000 0.00 0.00 0.00 2.59
2925 3239 9.981460 ATTTATTTTCCTCTCCATTCACTACTT 57.019 29.630 0.00 0.00 0.00 2.24
2926 3240 8.792830 TTATTTTCCTCTCCATTCACTACTTG 57.207 34.615 0.00 0.00 0.00 3.16
2929 3243 7.496346 TTTCCTCTCCATTCACTACTTGTAT 57.504 36.000 0.00 0.00 0.00 2.29
2931 3245 7.496346 TCCTCTCCATTCACTACTTGTATTT 57.504 36.000 0.00 0.00 0.00 1.40
3042 3636 6.547510 ACTTCTTCAGGCAAGTGAGTATTTTT 59.452 34.615 0.00 0.00 31.82 1.94
3046 3640 9.077885 TCTTCAGGCAAGTGAGTATTTTTATTT 57.922 29.630 0.00 0.00 33.27 1.40
3047 3641 9.346725 CTTCAGGCAAGTGAGTATTTTTATTTC 57.653 33.333 0.00 0.00 0.00 2.17
3048 3642 7.526608 TCAGGCAAGTGAGTATTTTTATTTCG 58.473 34.615 0.00 0.00 0.00 3.46
3049 3643 6.251376 CAGGCAAGTGAGTATTTTTATTTCGC 59.749 38.462 0.00 0.00 0.00 4.70
3430 4031 3.770625 TTCACTTCGTGAAGGTGCA 57.229 47.368 13.73 0.00 45.88 4.57
3433 4034 1.872952 TCACTTCGTGAAGGTGCATTG 59.127 47.619 13.73 2.59 39.78 2.82
3485 4086 2.416244 ATATGGCACCGGAGTACGCG 62.416 60.000 9.46 3.53 42.52 6.01
3542 4143 5.209818 TCAGTTTTGGTGTACTAGTCCTG 57.790 43.478 0.00 0.00 0.00 3.86
3961 4562 1.110442 ATCTCCAGCTTCTCCACGAG 58.890 55.000 0.00 0.00 0.00 4.18
4000 4607 1.133823 TGCATGGCCGACCTGATTTAT 60.134 47.619 0.00 0.00 36.63 1.40
4073 4680 3.626670 CCTAGGTGATATACGATCCGGAC 59.373 52.174 6.12 0.00 0.00 4.79
4079 4686 3.756963 TGATATACGATCCGGACTCTTGG 59.243 47.826 6.12 0.00 0.00 3.61
4153 5902 1.391485 CGTCTTCATTGCGAGTCTTGG 59.609 52.381 0.00 0.00 0.00 3.61
4317 6126 4.097589 TGCATAATCGACAATGGAATGCAA 59.902 37.500 4.72 0.00 39.20 4.08
4438 6475 3.426695 GCCAACAATAGATGTGTCTGTGC 60.427 47.826 0.00 0.00 42.99 4.57
4532 7113 3.560896 TGTGCATCACCAATATCATGACG 59.439 43.478 0.00 0.00 32.73 4.35
4570 7151 4.923281 GCACTTAATGTTGGATGTTGTTCC 59.077 41.667 0.00 0.00 36.24 3.62
5053 7636 5.989777 TCTTGGAGAGTAACTTGCAACTAAC 59.010 40.000 0.00 0.00 0.00 2.34
5054 7637 5.546621 TGGAGAGTAACTTGCAACTAACT 57.453 39.130 0.00 0.00 0.00 2.24
5055 7638 5.539048 TGGAGAGTAACTTGCAACTAACTC 58.461 41.667 16.89 16.89 34.85 3.01
5056 7639 5.069914 TGGAGAGTAACTTGCAACTAACTCA 59.930 40.000 22.60 8.55 36.63 3.41
5057 7640 5.635700 GGAGAGTAACTTGCAACTAACTCAG 59.364 44.000 22.60 5.02 36.63 3.35
5059 7642 5.070580 AGAGTAACTTGCAACTAACTCAGGT 59.929 40.000 22.60 3.90 36.63 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.037326 ATCTTTTCAGCGTCGGAGCA 60.037 50.000 5.88 0.00 40.15 4.26
43 44 5.008613 GCACTTGTGTGTCCTTATCTTTTCA 59.991 40.000 2.61 0.00 45.44 2.69
51 52 1.593196 GCTGCACTTGTGTGTCCTTA 58.407 50.000 0.00 0.00 45.44 2.69
77 78 0.033601 TGGTGAAGGTTGTTGCAGGT 60.034 50.000 0.00 0.00 0.00 4.00
113 114 0.178068 GGAAAGGGCACATCTAGCGA 59.822 55.000 0.00 0.00 0.00 4.93
128 129 7.993183 GGATCCTAGTTCACTTTCATATGGAAA 59.007 37.037 3.84 2.03 43.07 3.13
190 192 1.303309 CTGCTTGGTCCGGATGATTC 58.697 55.000 7.81 0.00 0.00 2.52
201 203 4.257890 AGGGATGTCCTGCTTGGT 57.742 55.556 0.00 0.00 46.07 3.67
274 276 6.042552 GTGGAGATGGAGATTATTCTTCCTCA 59.957 42.308 0.00 0.00 30.30 3.86
285 290 1.407437 GGTTGCGTGGAGATGGAGATT 60.407 52.381 0.00 0.00 0.00 2.40
286 291 0.179000 GGTTGCGTGGAGATGGAGAT 59.821 55.000 0.00 0.00 0.00 2.75
287 292 1.191489 TGGTTGCGTGGAGATGGAGA 61.191 55.000 0.00 0.00 0.00 3.71
300 305 0.394352 ATCGGAAGGGATGTGGTTGC 60.394 55.000 0.00 0.00 0.00 4.17
427 432 0.598065 GGCTCCGTTTGCAGTCAAAT 59.402 50.000 0.00 0.00 43.32 2.32
472 477 2.680913 GCTGAAGCAATCGCGGTGT 61.681 57.895 6.13 0.00 45.49 4.16
607 616 3.076916 GGGTCCCTTTGCATGCCC 61.077 66.667 16.68 6.80 0.00 5.36
723 835 0.467474 AGCCATGGCATGTCCTGATG 60.467 55.000 37.18 9.67 44.88 3.07
823 936 2.220224 CGCATGACAGCTCTCGTCG 61.220 63.158 0.00 0.00 36.11 5.12
847 960 2.771089 TCAGGAGTGCACACAAGATTC 58.229 47.619 21.04 5.49 0.00 2.52
942 1055 1.963515 GTCAAAGTTGATTGGCCACCT 59.036 47.619 3.88 0.00 39.73 4.00
945 1058 2.158475 AGGAGTCAAAGTTGATTGGCCA 60.158 45.455 0.00 0.00 39.73 5.36
997 1121 2.599848 GCGACGCACCATTTGTCATATC 60.600 50.000 16.42 0.00 32.91 1.63
1051 1181 1.594331 GTGGACTGGCTCGTTTTTCT 58.406 50.000 0.00 0.00 0.00 2.52
1167 1297 1.078848 GTCGCACTCCATTGAGGCT 60.079 57.895 0.00 0.00 43.29 4.58
1878 2014 0.679002 GAAGCTGGAGCATTGCCTGA 60.679 55.000 4.70 0.00 45.16 3.86
1927 2063 1.067749 CTGCTCCATGCTCGAGAGG 59.932 63.158 18.75 14.37 43.37 3.69
1931 2067 0.684479 ACTACCTGCTCCATGCTCGA 60.684 55.000 0.00 0.00 43.37 4.04
1952 2088 1.031235 GGAACGGAGGGAGTACTAGC 58.969 60.000 0.00 0.00 0.00 3.42
1953 2089 2.431954 TGGAACGGAGGGAGTACTAG 57.568 55.000 0.00 0.00 0.00 2.57
1954 2090 2.905415 TTGGAACGGAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
1955 2091 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
1956 2092 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1970 2115 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2006 2151 7.651704 CGTTTCAAAATAGATGACCCAACTTTT 59.348 33.333 0.00 0.00 0.00 2.27
2007 2152 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
2008 2153 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
2009 2154 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
2010 2155 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
2011 2156 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
2013 2158 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
2014 2159 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
2015 2160 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2018 2163 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2019 2164 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2020 2165 5.731591 ACTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
2028 2226 2.528673 AGCTACTACTCCCTCCGTTT 57.471 50.000 0.00 0.00 0.00 3.60
2031 2229 1.072648 AGCTAGCTACTACTCCCTCCG 59.927 57.143 17.69 0.00 0.00 4.63
2112 2330 9.859427 TTGTGTTTCCTGAATGATGATAAAATC 57.141 29.630 0.00 0.00 0.00 2.17
2113 2331 9.865321 CTTGTGTTTCCTGAATGATGATAAAAT 57.135 29.630 0.00 0.00 0.00 1.82
2115 2333 8.634335 TCTTGTGTTTCCTGAATGATGATAAA 57.366 30.769 0.00 0.00 0.00 1.40
2116 2334 8.514594 GTTCTTGTGTTTCCTGAATGATGATAA 58.485 33.333 0.00 0.00 0.00 1.75
2117 2335 7.884877 AGTTCTTGTGTTTCCTGAATGATGATA 59.115 33.333 0.00 0.00 0.00 2.15
2118 2336 6.718454 AGTTCTTGTGTTTCCTGAATGATGAT 59.282 34.615 0.00 0.00 0.00 2.45
2119 2337 6.016860 CAGTTCTTGTGTTTCCTGAATGATGA 60.017 38.462 0.00 0.00 0.00 2.92
2140 2362 3.689347 TGCATAGATTCCTGTTGCAGTT 58.311 40.909 0.00 0.00 37.69 3.16
2142 2364 3.965292 CTGCATAGATTCCTGTTGCAG 57.035 47.619 8.60 8.60 45.57 4.41
2323 2551 8.186821 GCTAGTGTCATATGAAAAGCAAGAAAT 58.813 33.333 7.07 0.00 0.00 2.17
2421 2649 3.760684 ACCTTCTCCAAGCTTATTTGCTG 59.239 43.478 0.00 0.00 43.24 4.41
2425 2653 4.388577 ACCACCTTCTCCAAGCTTATTT 57.611 40.909 0.00 0.00 0.00 1.40
2511 2825 1.590259 GAGCCGAGTCCGAATGAGC 60.590 63.158 0.00 0.00 38.22 4.26
2512 2826 1.066587 GGAGCCGAGTCCGAATGAG 59.933 63.158 0.00 0.00 38.22 2.90
2513 2827 2.423898 GGGAGCCGAGTCCGAATGA 61.424 63.158 0.00 0.00 37.50 2.57
2514 2828 2.107141 GGGAGCCGAGTCCGAATG 59.893 66.667 0.00 0.00 37.50 2.67
2515 2829 3.155167 GGGGAGCCGAGTCCGAAT 61.155 66.667 0.00 0.00 37.50 3.34
2516 2830 4.377760 AGGGGAGCCGAGTCCGAA 62.378 66.667 0.00 0.00 37.50 4.30
2519 2833 3.462678 GTCAGGGGAGCCGAGTCC 61.463 72.222 0.00 0.00 35.64 3.85
2520 2834 3.827898 CGTCAGGGGAGCCGAGTC 61.828 72.222 0.00 0.00 0.00 3.36
2521 2835 3.278072 TACGTCAGGGGAGCCGAGT 62.278 63.158 0.00 0.00 0.00 4.18
2522 2836 2.439701 TACGTCAGGGGAGCCGAG 60.440 66.667 0.00 0.00 0.00 4.63
2523 2837 2.753043 GTACGTCAGGGGAGCCGA 60.753 66.667 0.00 0.00 0.00 5.54
2524 2838 2.754658 AGTACGTCAGGGGAGCCG 60.755 66.667 0.00 0.00 0.00 5.52
2525 2839 2.893398 CAGTACGTCAGGGGAGCC 59.107 66.667 0.00 0.00 0.00 4.70
2526 2840 2.184579 GCAGTACGTCAGGGGAGC 59.815 66.667 0.00 0.00 0.00 4.70
2527 2841 1.513158 CTGCAGTACGTCAGGGGAG 59.487 63.158 5.25 0.00 0.00 4.30
2528 2842 1.982395 CCTGCAGTACGTCAGGGGA 60.982 63.158 21.58 0.00 44.64 4.81
2529 2843 2.579201 CCTGCAGTACGTCAGGGG 59.421 66.667 21.58 5.35 44.64 4.79
2532 2846 1.738099 GCACCCTGCAGTACGTCAG 60.738 63.158 13.81 9.54 44.26 3.51
2533 2847 2.342279 GCACCCTGCAGTACGTCA 59.658 61.111 13.81 0.00 44.26 4.35
2542 2856 2.985847 GACCCAACTGCACCCTGC 60.986 66.667 0.00 0.00 45.29 4.85
2543 2857 1.898574 GTGACCCAACTGCACCCTG 60.899 63.158 0.00 0.00 0.00 4.45
2544 2858 2.078665 AGTGACCCAACTGCACCCT 61.079 57.895 0.00 0.00 33.14 4.34
2545 2859 1.898574 CAGTGACCCAACTGCACCC 60.899 63.158 0.00 0.00 41.05 4.61
2546 2860 1.148273 TCAGTGACCCAACTGCACC 59.852 57.895 0.00 0.00 45.93 5.01
2547 2861 0.463654 TGTCAGTGACCCAACTGCAC 60.464 55.000 20.43 0.00 45.93 4.57
2548 2862 0.179048 CTGTCAGTGACCCAACTGCA 60.179 55.000 20.43 0.00 45.93 4.41
2549 2863 0.886490 CCTGTCAGTGACCCAACTGC 60.886 60.000 20.43 0.00 45.93 4.40
2551 2865 0.469917 CACCTGTCAGTGACCCAACT 59.530 55.000 20.43 0.00 40.34 3.16
2552 2866 0.535102 CCACCTGTCAGTGACCCAAC 60.535 60.000 20.43 0.00 40.34 3.77
2553 2867 1.705002 CCCACCTGTCAGTGACCCAA 61.705 60.000 20.43 1.10 40.34 4.12
2554 2868 2.146724 CCCACCTGTCAGTGACCCA 61.147 63.158 20.43 1.94 40.34 4.51
2555 2869 2.750350 CCCACCTGTCAGTGACCC 59.250 66.667 20.43 0.00 40.34 4.46
2556 2870 2.032681 GCCCACCTGTCAGTGACC 59.967 66.667 20.43 3.45 40.34 4.02
2557 2871 2.032681 GGCCCACCTGTCAGTGAC 59.967 66.667 16.68 16.68 40.34 3.67
2558 2872 2.075566 TTGGCCCACCTGTCAGTGA 61.076 57.895 0.00 0.00 40.34 3.41
2559 2873 1.898574 GTTGGCCCACCTGTCAGTG 60.899 63.158 0.00 0.00 36.63 3.66
2560 2874 1.645402 AAGTTGGCCCACCTGTCAGT 61.645 55.000 2.72 0.00 36.63 3.41
2561 2875 1.151450 AAGTTGGCCCACCTGTCAG 59.849 57.895 2.72 0.00 36.63 3.51
2562 2876 1.152777 CAAGTTGGCCCACCTGTCA 60.153 57.895 2.72 0.00 36.63 3.58
2563 2877 2.564721 GCAAGTTGGCCCACCTGTC 61.565 63.158 2.72 0.00 36.63 3.51
2564 2878 2.521708 GCAAGTTGGCCCACCTGT 60.522 61.111 2.72 0.00 36.63 4.00
2565 2879 1.402107 AAAGCAAGTTGGCCCACCTG 61.402 55.000 2.72 1.84 36.63 4.00
2566 2880 1.075301 AAAGCAAGTTGGCCCACCT 60.075 52.632 2.72 0.00 36.63 4.00
2567 2881 1.367471 GAAAGCAAGTTGGCCCACC 59.633 57.895 2.72 0.00 0.00 4.61
2568 2882 1.007387 CGAAAGCAAGTTGGCCCAC 60.007 57.895 0.00 0.00 0.00 4.61
2569 2883 2.199652 CCGAAAGCAAGTTGGCCCA 61.200 57.895 0.00 0.00 0.00 5.36
2570 2884 2.650778 CCGAAAGCAAGTTGGCCC 59.349 61.111 0.00 0.00 0.00 5.80
2571 2885 2.650778 CCCGAAAGCAAGTTGGCC 59.349 61.111 4.75 0.00 0.00 5.36
2572 2886 2.049156 GCCCGAAAGCAAGTTGGC 60.049 61.111 4.75 0.00 0.00 4.52
2573 2887 2.650778 GGCCCGAAAGCAAGTTGG 59.349 61.111 4.75 0.00 0.00 3.77
2574 2888 2.199652 TGGGCCCGAAAGCAAGTTG 61.200 57.895 19.37 0.00 0.00 3.16
2575 2889 2.197324 TGGGCCCGAAAGCAAGTT 59.803 55.556 19.37 0.00 0.00 2.66
2576 2890 2.597510 GTGGGCCCGAAAGCAAGT 60.598 61.111 19.37 0.00 0.00 3.16
2577 2891 3.373565 GGTGGGCCCGAAAGCAAG 61.374 66.667 19.37 0.00 0.00 4.01
2578 2892 3.897122 AGGTGGGCCCGAAAGCAA 61.897 61.111 19.37 0.00 38.74 3.91
2579 2893 4.659172 CAGGTGGGCCCGAAAGCA 62.659 66.667 19.37 0.00 38.74 3.91
2580 2894 4.660938 ACAGGTGGGCCCGAAAGC 62.661 66.667 19.37 9.80 38.74 3.51
2581 2895 2.359975 GACAGGTGGGCCCGAAAG 60.360 66.667 19.37 10.07 38.74 2.62
2582 2896 3.172106 TGACAGGTGGGCCCGAAA 61.172 61.111 19.37 0.00 38.74 3.46
2583 2897 3.636231 CTGACAGGTGGGCCCGAA 61.636 66.667 19.37 0.00 38.74 4.30
2584 2898 4.954118 ACTGACAGGTGGGCCCGA 62.954 66.667 19.37 3.06 38.74 5.14
2585 2899 4.704833 CACTGACAGGTGGGCCCG 62.705 72.222 19.37 4.81 38.74 6.13
2591 2905 1.898574 GTTGGGCCACTGACAGGTG 60.899 63.158 5.23 2.99 37.00 4.00
2592 2906 2.078665 AGTTGGGCCACTGACAGGT 61.079 57.895 5.23 0.00 0.00 4.00
2593 2907 1.601759 CAGTTGGGCCACTGACAGG 60.602 63.158 23.45 7.08 46.29 4.00
2594 2908 2.263741 GCAGTTGGGCCACTGACAG 61.264 63.158 28.71 15.14 46.29 3.51
2595 2909 2.203337 GCAGTTGGGCCACTGACA 60.203 61.111 28.71 5.60 46.29 3.58
2596 2910 2.203337 TGCAGTTGGGCCACTGAC 60.203 61.111 28.71 21.80 46.29 3.51
2597 2911 2.203337 GTGCAGTTGGGCCACTGA 60.203 61.111 28.71 16.56 46.29 3.41
2598 2912 3.297620 GGTGCAGTTGGGCCACTG 61.298 66.667 23.47 23.47 46.15 3.66
2599 2913 4.603535 GGGTGCAGTTGGGCCACT 62.604 66.667 5.23 3.94 0.00 4.00
2600 2914 4.603535 AGGGTGCAGTTGGGCCAC 62.604 66.667 5.23 1.08 0.00 5.01
2601 2915 4.601794 CAGGGTGCAGTTGGGCCA 62.602 66.667 0.00 0.00 0.00 5.36
2611 2925 1.738099 CTGACGTACTGCAGGGTGC 60.738 63.158 19.93 0.92 45.29 5.01
2612 2926 0.109086 CTCTGACGTACTGCAGGGTG 60.109 60.000 19.93 9.21 33.05 4.61
2613 2927 1.251527 CCTCTGACGTACTGCAGGGT 61.252 60.000 19.93 12.80 30.57 4.34
2614 2928 0.965866 TCCTCTGACGTACTGCAGGG 60.966 60.000 19.93 9.39 33.05 4.45
2615 2929 0.453793 CTCCTCTGACGTACTGCAGG 59.546 60.000 19.93 2.38 33.05 4.85
2616 2930 0.179150 GCTCCTCTGACGTACTGCAG 60.179 60.000 13.48 13.48 0.00 4.41
2617 2931 1.595993 GGCTCCTCTGACGTACTGCA 61.596 60.000 0.00 0.00 0.00 4.41
2618 2932 1.139947 GGCTCCTCTGACGTACTGC 59.860 63.158 0.00 0.00 0.00 4.40
2619 2933 0.736053 GAGGCTCCTCTGACGTACTG 59.264 60.000 2.15 0.00 39.80 2.74
2620 2934 0.745128 CGAGGCTCCTCTGACGTACT 60.745 60.000 9.32 0.00 40.69 2.73
2621 2935 1.025647 ACGAGGCTCCTCTGACGTAC 61.026 60.000 9.32 0.00 40.69 3.67
2622 2936 0.743701 GACGAGGCTCCTCTGACGTA 60.744 60.000 9.32 0.00 40.69 3.57
2623 2937 2.034376 ACGAGGCTCCTCTGACGT 59.966 61.111 9.32 4.69 40.69 4.34
2624 2938 2.766400 GGACGAGGCTCCTCTGACG 61.766 68.421 9.32 4.08 40.69 4.35
2625 2939 2.419739 GGGACGAGGCTCCTCTGAC 61.420 68.421 9.32 7.69 40.69 3.51
2626 2940 2.043852 GGGACGAGGCTCCTCTGA 60.044 66.667 9.32 0.00 40.69 3.27
2641 2955 4.489771 AAGGCCGGAATGAGCGGG 62.490 66.667 5.05 0.00 0.00 6.13
2642 2956 3.204827 CAAGGCCGGAATGAGCGG 61.205 66.667 5.05 0.00 0.00 5.52
2643 2957 2.436646 ACAAGGCCGGAATGAGCG 60.437 61.111 5.05 0.00 0.00 5.03
2683 2997 1.348064 CCATCCGGCAGTATTCCCTA 58.652 55.000 0.00 0.00 0.00 3.53
3013 3591 5.437060 ACTCACTTGCCTGAAGAAGTTTAA 58.563 37.500 0.00 0.00 35.42 1.52
3042 3636 7.386848 CCCGAAAGATAAATAAGGAGCGAAATA 59.613 37.037 0.00 0.00 0.00 1.40
3046 3640 4.342951 TCCCGAAAGATAAATAAGGAGCGA 59.657 41.667 0.00 0.00 0.00 4.93
3047 3641 4.628074 TCCCGAAAGATAAATAAGGAGCG 58.372 43.478 0.00 0.00 0.00 5.03
3048 3642 6.231211 TGATCCCGAAAGATAAATAAGGAGC 58.769 40.000 0.00 0.00 0.00 4.70
3049 3643 8.317679 AGATGATCCCGAAAGATAAATAAGGAG 58.682 37.037 0.00 0.00 0.00 3.69
3249 3850 2.186532 TAGGATCCATCTCCTCGTCG 57.813 55.000 15.82 0.00 42.12 5.12
3419 4020 0.387622 CTTGGCAATGCACCTTCACG 60.388 55.000 7.79 0.00 0.00 4.35
3430 4031 2.459644 TGAGCAATTAGGCTTGGCAAT 58.540 42.857 0.00 0.00 45.99 3.56
3433 4034 1.339291 GGATGAGCAATTAGGCTTGGC 59.661 52.381 0.00 0.00 45.99 4.52
3542 4143 7.283354 CAGTTCCTTCTCCTGGTTATAATTTCC 59.717 40.741 0.00 0.00 0.00 3.13
3675 4276 7.934457 ACATGGATGATGCTTTTAGATACAAC 58.066 34.615 0.00 0.00 35.15 3.32
3802 4403 2.821366 CAGCAGCCCGATGTGGAC 60.821 66.667 0.00 0.00 42.00 4.02
4079 4686 0.179156 CAAACATGACATGGCCGCTC 60.179 55.000 19.39 0.00 33.60 5.03
4247 6056 8.615211 GTTTCATTGATTATGATGCTGACACTA 58.385 33.333 0.00 0.00 42.69 2.74
4426 6463 2.907910 GATGTTGGCACAGACACATC 57.092 50.000 12.09 12.09 43.69 3.06
4438 6475 5.411977 GGAGCATGAGATTATGAGATGTTGG 59.588 44.000 0.00 0.00 0.00 3.77
4532 7113 7.639945 ACATTAAGTGCAAGTTAGTCTCAAAC 58.360 34.615 0.00 0.00 32.47 2.93
4570 7151 5.041191 AGCTTAAGATTAGGTGGGTGATG 57.959 43.478 6.67 0.00 0.00 3.07
4862 7444 9.890629 TTAGCCAACATGGAATATATCTGATAC 57.109 33.333 0.00 0.00 40.96 2.24
4958 7541 8.681806 TCGATTATCCATGTGCAAAGAAAATAA 58.318 29.630 0.00 0.00 0.00 1.40
4959 7542 8.219546 TCGATTATCCATGTGCAAAGAAAATA 57.780 30.769 0.00 0.00 0.00 1.40
4960 7543 7.067372 TCTCGATTATCCATGTGCAAAGAAAAT 59.933 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.