Multiple sequence alignment - TraesCS5B01G186200

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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 TraesCS5B01G186200 chr5B 100.000 3398 0 0 1 3398 338480286 338483683 0.000000e+00 6276.0
1 TraesCS5B01G186200 chr5B 100.000 116 0 0 2623 2738 338483023 338482908 7.380000e-52 215.0
2 TraesCS5B01G186200 chr5B 92.000 125 8 2 2617 2739 38357005 38357129 1.250000e-39 174.0
3 TraesCS5B01G186200 chr5D 96.770 1424 34 5 151 1562 297736038 297737461 0.000000e+00 2364.0
4 TraesCS5B01G186200 chr5D 96.710 851 19 2 1560 2410 297737504 297738345 0.000000e+00 1408.0
5 TraesCS5B01G186200 chr5D 94.118 408 12 2 2736 3143 297738640 297739035 8.060000e-171 610.0
6 TraesCS5B01G186200 chr5D 98.174 219 4 0 2406 2624 297738424 297738642 1.910000e-102 383.0
7 TraesCS5B01G186200 chr5D 93.511 262 9 2 3137 3398 297749299 297749552 1.910000e-102 383.0
8 TraesCS5B01G186200 chr5D 80.189 106 16 5 14 117 9919788 9919686 1.310000e-09 75.0
9 TraesCS5B01G186200 chr5A 94.472 1429 37 9 151 1562 401318477 401317074 0.000000e+00 2163.0
10 TraesCS5B01G186200 chr5A 96.717 1066 28 3 1560 2624 401317031 401315972 0.000000e+00 1768.0
11 TraesCS5B01G186200 chr5A 94.428 664 27 4 2736 3398 401315974 401315320 0.000000e+00 1013.0
12 TraesCS5B01G186200 chrUn 83.140 860 130 8 1560 2409 250030954 250031808 0.000000e+00 771.0
13 TraesCS5B01G186200 chrUn 82.659 865 128 14 1560 2404 282476801 282475939 0.000000e+00 747.0
14 TraesCS5B01G186200 chrUn 82.093 860 132 14 1560 2399 267761385 267762242 0.000000e+00 715.0
15 TraesCS5B01G186200 chrUn 82.039 863 133 14 1560 2402 334500996 334500136 0.000000e+00 715.0
16 TraesCS5B01G186200 chrUn 80.593 371 64 6 1181 1546 311734916 311735283 2.580000e-71 279.0
17 TraesCS5B01G186200 chrUn 80.593 371 64 6 1181 1546 311738790 311739157 2.580000e-71 279.0
18 TraesCS5B01G186200 chr3D 78.086 972 158 39 1560 2496 570145995 570145044 6.370000e-157 564.0
19 TraesCS5B01G186200 chr3D 80.428 608 88 19 964 1554 520319268 520318675 5.210000e-118 435.0
20 TraesCS5B01G186200 chr3D 79.487 624 100 19 938 1556 570146641 570146041 5.240000e-113 418.0
21 TraesCS5B01G186200 chr3D 83.920 398 45 11 948 1327 520153028 520153424 2.490000e-96 363.0
22 TraesCS5B01G186200 chr3D 74.465 701 147 23 846 1534 497867458 497868138 1.200000e-69 274.0
23 TraesCS5B01G186200 chr3A 79.419 826 143 23 1560 2368 655886025 655885210 2.960000e-155 558.0
24 TraesCS5B01G186200 chr3A 76.851 851 168 20 1560 2398 701265532 701266365 1.440000e-123 453.0
25 TraesCS5B01G186200 chr3A 83.668 398 46 11 948 1327 655572389 655572785 1.160000e-94 357.0
26 TraesCS5B01G186200 chr3A 78.118 425 85 6 1560 1977 702915608 702915185 2.600000e-66 263.0
27 TraesCS5B01G186200 chr3A 74.643 631 116 26 1699 2311 702952076 702951472 4.380000e-59 239.0
28 TraesCS5B01G186200 chr3A 86.567 134 14 1 943 1072 702556043 702556176 9.830000e-31 145.0
29 TraesCS5B01G186200 chr3A 84.677 124 17 1 964 1085 655886632 655886509 4.600000e-24 122.0
30 TraesCS5B01G186200 chr1A 79.127 848 146 18 1564 2402 14109037 14108212 1.070000e-154 556.0
31 TraesCS5B01G186200 chr1D 78.333 840 151 18 1564 2394 12179104 12178287 6.500000e-142 514.0
32 TraesCS5B01G186200 chr1D 94.167 120 6 1 2620 2739 491052532 491052650 7.490000e-42 182.0
33 TraesCS5B01G186200 chr1D 93.966 116 6 1 2623 2738 491052649 491052535 1.250000e-39 174.0
34 TraesCS5B01G186200 chr1D 88.750 80 8 1 66 145 22040576 22040498 2.790000e-16 97.1
35 TraesCS5B01G186200 chr3B 78.344 785 150 16 1561 2333 684770494 684771270 1.100000e-134 490.0
36 TraesCS5B01G186200 chr3B 78.973 623 100 19 938 1553 756824215 756823617 2.460000e-106 396.0
37 TraesCS5B01G186200 chr3B 78.812 623 101 19 938 1553 756709083 756708485 1.140000e-104 390.0
38 TraesCS5B01G186200 chr3B 86.080 352 46 2 1636 1984 756656138 756656489 3.200000e-100 375.0
39 TraesCS5B01G186200 chr3B 83.827 371 60 0 2040 2410 756656509 756656879 1.500000e-93 353.0
40 TraesCS5B01G186200 chr3B 83.492 315 50 2 1233 1546 756613663 756613976 3.320000e-75 292.0
41 TraesCS5B01G186200 chr3B 74.925 666 142 20 879 1534 658489831 658490481 7.180000e-72 281.0
42 TraesCS5B01G186200 chr3B 81.212 330 59 3 1560 1887 756684098 756683770 2.600000e-66 263.0
43 TraesCS5B01G186200 chr3B 77.371 464 86 12 1899 2346 756682901 756682441 1.210000e-64 257.0
44 TraesCS5B01G186200 chr2D 96.094 128 5 0 1 128 16266344 16266217 3.440000e-50 209.0
45 TraesCS5B01G186200 chr7A 96.581 117 4 0 2622 2738 118166808 118166924 9.620000e-46 195.0
46 TraesCS5B01G186200 chr7A 96.581 117 4 0 2622 2738 118166925 118166809 9.620000e-46 195.0
47 TraesCS5B01G186200 chr7A 94.340 53 3 0 100 152 33059584 33059636 7.820000e-12 82.4
48 TraesCS5B01G186200 chr1B 95.868 121 2 1 2623 2740 658739072 658739192 3.460000e-45 193.0
49 TraesCS5B01G186200 chr1B 95.798 119 2 1 2623 2738 658739190 658739072 4.480000e-44 189.0
50 TraesCS5B01G186200 chr7D 91.736 121 10 0 2626 2746 78885197 78885077 5.830000e-38 169.0
51 TraesCS5B01G186200 chr7D 94.521 73 4 0 79 151 568314369 568314297 2.770000e-21 113.0
52 TraesCS5B01G186200 chr4A 90.196 51 4 1 101 151 13255789 13255838 7.870000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G186200 chr5B 338480286 338483683 3397 False 6276.00 6276 100.000000 1 3398 1 chr5B.!!$F2 3397
1 TraesCS5B01G186200 chr5D 297736038 297739035 2997 False 1191.25 2364 96.443000 151 3143 4 chr5D.!!$F2 2992
2 TraesCS5B01G186200 chr5A 401315320 401318477 3157 True 1648.00 2163 95.205667 151 3398 3 chr5A.!!$R1 3247
3 TraesCS5B01G186200 chrUn 250030954 250031808 854 False 771.00 771 83.140000 1560 2409 1 chrUn.!!$F1 849
4 TraesCS5B01G186200 chrUn 282475939 282476801 862 True 747.00 747 82.659000 1560 2404 1 chrUn.!!$R1 844
5 TraesCS5B01G186200 chrUn 267761385 267762242 857 False 715.00 715 82.093000 1560 2399 1 chrUn.!!$F2 839
6 TraesCS5B01G186200 chrUn 334500136 334500996 860 True 715.00 715 82.039000 1560 2402 1 chrUn.!!$R2 842
7 TraesCS5B01G186200 chrUn 311734916 311739157 4241 False 279.00 279 80.593000 1181 1546 2 chrUn.!!$F3 365
8 TraesCS5B01G186200 chr3D 570145044 570146641 1597 True 491.00 564 78.786500 938 2496 2 chr3D.!!$R2 1558
9 TraesCS5B01G186200 chr3D 520318675 520319268 593 True 435.00 435 80.428000 964 1554 1 chr3D.!!$R1 590
10 TraesCS5B01G186200 chr3D 497867458 497868138 680 False 274.00 274 74.465000 846 1534 1 chr3D.!!$F1 688
11 TraesCS5B01G186200 chr3A 701265532 701266365 833 False 453.00 453 76.851000 1560 2398 1 chr3A.!!$F2 838
12 TraesCS5B01G186200 chr3A 655885210 655886632 1422 True 340.00 558 82.048000 964 2368 2 chr3A.!!$R3 1404
13 TraesCS5B01G186200 chr3A 702951472 702952076 604 True 239.00 239 74.643000 1699 2311 1 chr3A.!!$R2 612
14 TraesCS5B01G186200 chr1A 14108212 14109037 825 True 556.00 556 79.127000 1564 2402 1 chr1A.!!$R1 838
15 TraesCS5B01G186200 chr1D 12178287 12179104 817 True 514.00 514 78.333000 1564 2394 1 chr1D.!!$R1 830
16 TraesCS5B01G186200 chr3B 684770494 684771270 776 False 490.00 490 78.344000 1561 2333 1 chr3B.!!$F2 772
17 TraesCS5B01G186200 chr3B 756823617 756824215 598 True 396.00 396 78.973000 938 1553 1 chr3B.!!$R2 615
18 TraesCS5B01G186200 chr3B 756708485 756709083 598 True 390.00 390 78.812000 938 1553 1 chr3B.!!$R1 615
19 TraesCS5B01G186200 chr3B 756656138 756656879 741 False 364.00 375 84.953500 1636 2410 2 chr3B.!!$F4 774
20 TraesCS5B01G186200 chr3B 658489831 658490481 650 False 281.00 281 74.925000 879 1534 1 chr3B.!!$F1 655
21 TraesCS5B01G186200 chr3B 756682441 756684098 1657 True 260.00 263 79.291500 1560 2346 2 chr3B.!!$R3 786

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 0.170339 GGGCCAATGTTAACTCGTGC 59.830 55.0 4.39 4.87 0.00 5.34 F
79 80 0.602638 TTGTACACAGAGGCGCCAAG 60.603 55.0 31.54 19.97 0.00 3.61 F
920 937 0.869730 TTCCGGTACTTTTTCAGCGC 59.130 50.0 0.00 0.00 34.48 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1074 1.763545 GAGAGGGGAACATACCTGGAC 59.236 57.143 0.0 0.0 37.18 4.02 R
1294 1329 3.230284 CCGCTTCTATCAGGGGCA 58.770 61.111 0.0 0.0 39.82 5.36 R
2621 6622 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.0 0.0 0.00 2.73 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.073475 AGACTACCAAATGTTATTTTGCTAACA 57.927 29.630 0.00 0.00 43.63 2.41
27 28 9.341899 GACTACCAAATGTTATTTTGCTAACAG 57.658 33.333 3.14 0.00 42.97 3.16
28 29 8.856103 ACTACCAAATGTTATTTTGCTAACAGT 58.144 29.630 3.14 0.00 42.97 3.55
31 32 9.073475 ACCAAATGTTATTTTGCTAACAGTAGA 57.927 29.630 3.14 0.00 42.97 2.59
32 33 9.559958 CCAAATGTTATTTTGCTAACAGTAGAG 57.440 33.333 3.14 0.00 42.97 2.43
33 34 9.559958 CAAATGTTATTTTGCTAACAGTAGAGG 57.440 33.333 3.14 0.00 42.97 3.69
34 35 7.865706 ATGTTATTTTGCTAACAGTAGAGGG 57.134 36.000 3.14 0.00 42.97 4.30
35 36 5.646360 TGTTATTTTGCTAACAGTAGAGGGC 59.354 40.000 0.00 0.00 36.84 5.19
36 37 2.781681 TTTGCTAACAGTAGAGGGCC 57.218 50.000 0.00 0.00 0.00 5.80
37 38 1.651737 TTGCTAACAGTAGAGGGCCA 58.348 50.000 6.18 0.00 0.00 5.36
38 39 1.651737 TGCTAACAGTAGAGGGCCAA 58.348 50.000 6.18 0.00 0.00 4.52
39 40 2.196595 TGCTAACAGTAGAGGGCCAAT 58.803 47.619 6.18 0.00 0.00 3.16
40 41 2.092968 TGCTAACAGTAGAGGGCCAATG 60.093 50.000 6.18 0.00 0.00 2.82
41 42 2.092914 GCTAACAGTAGAGGGCCAATGT 60.093 50.000 6.18 0.00 0.00 2.71
42 43 3.622455 GCTAACAGTAGAGGGCCAATGTT 60.622 47.826 6.18 9.90 35.28 2.71
43 44 4.383770 GCTAACAGTAGAGGGCCAATGTTA 60.384 45.833 6.18 10.56 33.31 2.41
44 45 4.650972 AACAGTAGAGGGCCAATGTTAA 57.349 40.909 6.18 0.00 0.00 2.01
45 46 3.951663 ACAGTAGAGGGCCAATGTTAAC 58.048 45.455 6.18 0.00 0.00 2.01
46 47 3.587506 ACAGTAGAGGGCCAATGTTAACT 59.412 43.478 6.18 0.00 0.00 2.24
47 48 4.192317 CAGTAGAGGGCCAATGTTAACTC 58.808 47.826 6.18 0.00 0.00 3.01
48 49 2.403252 AGAGGGCCAATGTTAACTCG 57.597 50.000 6.18 0.00 0.00 4.18
49 50 1.628846 AGAGGGCCAATGTTAACTCGT 59.371 47.619 6.18 0.00 0.00 4.18
50 51 1.737793 GAGGGCCAATGTTAACTCGTG 59.262 52.381 6.18 2.33 0.00 4.35
51 52 0.170339 GGGCCAATGTTAACTCGTGC 59.830 55.000 4.39 4.87 0.00 5.34
52 53 0.878416 GGCCAATGTTAACTCGTGCA 59.122 50.000 7.22 0.00 0.00 4.57
53 54 1.268352 GGCCAATGTTAACTCGTGCAA 59.732 47.619 7.22 0.00 0.00 4.08
54 55 2.584791 GCCAATGTTAACTCGTGCAAG 58.415 47.619 7.22 0.00 0.00 4.01
55 56 2.225491 GCCAATGTTAACTCGTGCAAGA 59.775 45.455 7.22 1.47 0.00 3.02
56 57 3.304391 GCCAATGTTAACTCGTGCAAGAA 60.304 43.478 7.22 0.00 0.00 2.52
57 58 4.615912 GCCAATGTTAACTCGTGCAAGAAT 60.616 41.667 7.22 0.00 0.00 2.40
58 59 4.853196 CCAATGTTAACTCGTGCAAGAATG 59.147 41.667 7.22 0.00 0.00 2.67
59 60 4.685169 ATGTTAACTCGTGCAAGAATGG 57.315 40.909 7.22 0.00 0.00 3.16
60 61 3.472652 TGTTAACTCGTGCAAGAATGGT 58.527 40.909 7.22 0.00 0.00 3.55
61 62 3.880490 TGTTAACTCGTGCAAGAATGGTT 59.120 39.130 7.22 7.31 0.00 3.67
62 63 4.219033 GTTAACTCGTGCAAGAATGGTTG 58.781 43.478 13.45 0.53 0.00 3.77
63 64 1.967319 ACTCGTGCAAGAATGGTTGT 58.033 45.000 3.39 0.00 0.00 3.32
64 65 3.120321 ACTCGTGCAAGAATGGTTGTA 57.880 42.857 3.39 0.00 0.00 2.41
65 66 2.806244 ACTCGTGCAAGAATGGTTGTAC 59.194 45.455 3.39 0.00 39.05 2.90
66 67 2.805671 CTCGTGCAAGAATGGTTGTACA 59.194 45.455 3.39 0.00 41.58 2.90
67 68 2.546368 TCGTGCAAGAATGGTTGTACAC 59.454 45.455 0.00 0.00 41.58 2.90
68 69 2.289274 CGTGCAAGAATGGTTGTACACA 59.711 45.455 0.00 0.00 41.58 3.72
69 70 3.606846 CGTGCAAGAATGGTTGTACACAG 60.607 47.826 0.00 0.00 41.58 3.66
70 71 3.563808 GTGCAAGAATGGTTGTACACAGA 59.436 43.478 0.00 0.00 41.26 3.41
71 72 3.814842 TGCAAGAATGGTTGTACACAGAG 59.185 43.478 0.00 0.00 0.00 3.35
72 73 3.189287 GCAAGAATGGTTGTACACAGAGG 59.811 47.826 0.00 0.00 0.00 3.69
73 74 3.059352 AGAATGGTTGTACACAGAGGC 57.941 47.619 0.00 0.00 0.00 4.70
74 75 1.732259 GAATGGTTGTACACAGAGGCG 59.268 52.381 0.00 0.00 0.00 5.52
75 76 0.673644 ATGGTTGTACACAGAGGCGC 60.674 55.000 0.00 0.00 0.00 6.53
76 77 2.033194 GGTTGTACACAGAGGCGCC 61.033 63.158 21.89 21.89 0.00 6.53
77 78 1.301401 GTTGTACACAGAGGCGCCA 60.301 57.895 31.54 1.71 0.00 5.69
78 79 0.882927 GTTGTACACAGAGGCGCCAA 60.883 55.000 31.54 7.70 0.00 4.52
79 80 0.602638 TTGTACACAGAGGCGCCAAG 60.603 55.000 31.54 19.97 0.00 3.61
80 81 1.741770 GTACACAGAGGCGCCAAGG 60.742 63.158 31.54 19.25 0.00 3.61
81 82 2.214216 TACACAGAGGCGCCAAGGT 61.214 57.895 31.54 19.98 0.00 3.50
82 83 2.449031 TACACAGAGGCGCCAAGGTG 62.449 60.000 30.47 30.47 0.00 4.00
100 101 2.110296 GCTCCAGCAATACAAGGGC 58.890 57.895 0.00 0.00 41.59 5.19
101 102 1.718757 GCTCCAGCAATACAAGGGCG 61.719 60.000 0.00 0.00 41.59 6.13
102 103 1.718757 CTCCAGCAATACAAGGGCGC 61.719 60.000 0.00 0.00 0.00 6.53
103 104 2.045708 CCAGCAATACAAGGGCGCA 61.046 57.895 10.83 0.00 0.00 6.09
104 105 1.137404 CAGCAATACAAGGGCGCAC 59.863 57.895 10.83 5.15 0.00 5.34
105 106 1.303236 AGCAATACAAGGGCGCACA 60.303 52.632 14.57 0.00 0.00 4.57
106 107 1.137404 GCAATACAAGGGCGCACAG 59.863 57.895 14.57 6.48 0.00 3.66
118 119 3.123620 GCACAGCTCCGCCTCAAG 61.124 66.667 0.00 0.00 0.00 3.02
119 120 2.659016 CACAGCTCCGCCTCAAGA 59.341 61.111 0.00 0.00 0.00 3.02
120 121 1.447489 CACAGCTCCGCCTCAAGAG 60.447 63.158 0.00 0.00 0.00 2.85
189 190 6.147164 GTGTCGACTGAAATATTCTTTGTCCA 59.853 38.462 17.92 0.00 0.00 4.02
318 322 9.241317 GTTTTGTCATGATATTCTGCCATTTAG 57.759 33.333 0.00 0.00 0.00 1.85
350 354 5.748402 TCTGATGCATCACTATTTGAAGGT 58.252 37.500 25.42 0.00 37.92 3.50
356 360 7.936496 TGCATCACTATTTGAAGGTTGAATA 57.064 32.000 0.00 0.00 37.92 1.75
514 524 7.596749 TGAAAAATCTACGCCAAAACAAAAA 57.403 28.000 0.00 0.00 0.00 1.94
647 657 1.153469 GCCTCTGCTAGTGACAGGC 60.153 63.158 7.97 7.97 42.87 4.85
653 663 2.231478 TCTGCTAGTGACAGGCTGTTAC 59.769 50.000 29.13 29.13 37.16 2.50
655 665 3.427573 TGCTAGTGACAGGCTGTTACTA 58.572 45.455 35.54 35.54 44.02 1.82
728 738 7.846066 AGAACAAGTCTGCTAATCTAATCTGT 58.154 34.615 0.00 0.00 34.29 3.41
920 937 0.869730 TTCCGGTACTTTTTCAGCGC 59.130 50.000 0.00 0.00 34.48 5.92
1054 1074 1.466167 GCTATGCACACAACTCCAGTG 59.534 52.381 0.00 0.00 42.56 3.66
1294 1329 1.472904 CGCTCAGCAGAACAGGATGAT 60.473 52.381 0.00 0.00 39.69 2.45
1550 1588 2.665185 GCCACGCTCCGTCAAAGT 60.665 61.111 0.00 0.00 38.32 2.66
1556 1594 1.862827 ACGCTCCGTCAAAGTAACAAC 59.137 47.619 0.00 0.00 33.69 3.32
1557 1595 1.862201 CGCTCCGTCAAAGTAACAACA 59.138 47.619 0.00 0.00 0.00 3.33
1558 1596 2.285756 CGCTCCGTCAAAGTAACAACAA 59.714 45.455 0.00 0.00 0.00 2.83
1812 1915 1.295792 TGCACGTCAGTTCAGGAAAC 58.704 50.000 0.00 0.00 38.21 2.78
2621 6622 5.745294 GCTATGCCTACAAAACATTGTGATG 59.255 40.000 4.55 0.00 39.25 3.07
2623 6624 6.832520 ATGCCTACAAAACATTGTGATGTA 57.167 33.333 11.99 11.99 45.58 2.29
2624 6625 6.007936 TGCCTACAAAACATTGTGATGTAC 57.992 37.500 9.62 0.00 45.58 2.90
2625 6626 5.767665 TGCCTACAAAACATTGTGATGTACT 59.232 36.000 9.62 0.00 45.58 2.73
2626 6627 6.072728 TGCCTACAAAACATTGTGATGTACTC 60.073 38.462 9.62 6.50 45.58 2.59
2627 6628 6.622896 GCCTACAAAACATTGTGATGTACTCC 60.623 42.308 9.62 0.00 45.58 3.85
2628 6629 5.705609 ACAAAACATTGTGATGTACTCCC 57.294 39.130 6.06 0.00 45.58 4.30
2629 6630 5.385198 ACAAAACATTGTGATGTACTCCCT 58.615 37.500 6.06 0.00 45.58 4.20
2630 6631 5.473504 ACAAAACATTGTGATGTACTCCCTC 59.526 40.000 6.06 0.00 45.58 4.30
2631 6632 3.914426 ACATTGTGATGTACTCCCTCC 57.086 47.619 0.00 0.00 44.51 4.30
2632 6633 2.168521 ACATTGTGATGTACTCCCTCCG 59.831 50.000 0.00 0.00 44.51 4.63
2633 6634 1.933021 TTGTGATGTACTCCCTCCGT 58.067 50.000 0.00 0.00 0.00 4.69
2634 6635 1.471119 TGTGATGTACTCCCTCCGTC 58.529 55.000 0.00 0.00 0.00 4.79
2635 6636 0.745468 GTGATGTACTCCCTCCGTCC 59.255 60.000 0.00 0.00 0.00 4.79
2636 6637 0.750546 TGATGTACTCCCTCCGTCCG 60.751 60.000 0.00 0.00 0.00 4.79
2637 6638 0.465097 GATGTACTCCCTCCGTCCGA 60.465 60.000 0.00 0.00 0.00 4.55
2638 6639 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
2639 6640 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
2640 6641 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
2641 6642 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
2642 6643 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2643 6644 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2644 6645 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2645 6646 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2646 6647 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2647 6648 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2648 6649 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2649 6650 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2650 6651 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2651 6652 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2652 6653 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2653 6654 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2654 6655 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2655 6656 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2656 6657 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2657 6658 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2658 6659 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
2659 6660 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
2660 6661 8.638565 CCGAAAATACTTGTCATCAAAATGAAC 58.361 33.333 0.00 0.00 43.42 3.18
2661 6662 9.179552 CGAAAATACTTGTCATCAAAATGAACA 57.820 29.630 0.00 0.00 43.42 3.18
2666 6667 7.775397 ACTTGTCATCAAAATGAACAAAAGG 57.225 32.000 0.87 0.00 43.42 3.11
2667 6668 6.762661 ACTTGTCATCAAAATGAACAAAAGGG 59.237 34.615 0.87 0.00 43.42 3.95
2668 6669 5.609423 TGTCATCAAAATGAACAAAAGGGG 58.391 37.500 0.00 0.00 43.42 4.79
2669 6670 5.365025 TGTCATCAAAATGAACAAAAGGGGA 59.635 36.000 0.00 0.00 43.42 4.81
2670 6671 6.043012 TGTCATCAAAATGAACAAAAGGGGAT 59.957 34.615 0.00 0.00 43.42 3.85
2671 6672 6.369615 GTCATCAAAATGAACAAAAGGGGATG 59.630 38.462 0.00 0.00 43.42 3.51
2672 6673 5.885449 TCAAAATGAACAAAAGGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
2673 6674 6.985653 TCAAAATGAACAAAAGGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
2674 6675 7.552050 TCAAAATGAACAAAAGGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
2675 6676 7.610865 TCAAAATGAACAAAAGGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
2676 6677 7.454380 TCAAAATGAACAAAAGGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
2677 6678 8.748412 CAAAATGAACAAAAGGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
2678 6679 8.525290 AAATGAACAAAAGGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
2679 6680 6.884472 TGAACAAAAGGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
2680 6681 7.451731 TGAACAAAAGGGGATGTATCTAGAT 57.548 36.000 10.73 10.73 0.00 1.98
2681 6682 7.509546 TGAACAAAAGGGGATGTATCTAGATC 58.490 38.462 8.95 2.00 0.00 2.75
2682 6683 7.348274 TGAACAAAAGGGGATGTATCTAGATCT 59.652 37.037 8.95 0.00 0.00 2.75
2683 6684 8.798975 AACAAAAGGGGATGTATCTAGATCTA 57.201 34.615 8.95 1.69 0.00 1.98
2684 6685 8.429237 ACAAAAGGGGATGTATCTAGATCTAG 57.571 38.462 21.81 21.81 34.56 2.43
2685 6686 8.235230 ACAAAAGGGGATGTATCTAGATCTAGA 58.765 37.037 29.94 29.94 45.24 2.43
2699 6700 8.657387 TCTAGATCTAGATACATCCCCTTTTG 57.343 38.462 25.54 0.00 37.28 2.44
2700 6701 8.235230 TCTAGATCTAGATACATCCCCTTTTGT 58.765 37.037 25.54 0.00 37.28 2.83
2701 6702 7.698163 AGATCTAGATACATCCCCTTTTGTT 57.302 36.000 4.89 0.00 0.00 2.83
2702 6703 7.740805 AGATCTAGATACATCCCCTTTTGTTC 58.259 38.462 4.89 0.00 0.00 3.18
2703 6704 6.884472 TCTAGATACATCCCCTTTTGTTCA 57.116 37.500 0.00 0.00 0.00 3.18
2704 6705 7.451731 TCTAGATACATCCCCTTTTGTTCAT 57.548 36.000 0.00 0.00 0.00 2.57
2705 6706 7.872138 TCTAGATACATCCCCTTTTGTTCATT 58.128 34.615 0.00 0.00 0.00 2.57
2706 6707 8.336235 TCTAGATACATCCCCTTTTGTTCATTT 58.664 33.333 0.00 0.00 0.00 2.32
2707 6708 7.797121 AGATACATCCCCTTTTGTTCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
2708 6709 7.614494 AGATACATCCCCTTTTGTTCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
2709 6710 5.885449 ACATCCCCTTTTGTTCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
2710 6711 6.438186 ACATCCCCTTTTGTTCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
2711 6712 6.232692 ACATCCCCTTTTGTTCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
2712 6713 6.043012 ACATCCCCTTTTGTTCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
2713 6714 5.852827 TCCCCTTTTGTTCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
2714 6715 5.365025 TCCCCTTTTGTTCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
2715 6716 6.054295 CCCCTTTTGTTCATTTTGATGACAA 58.946 36.000 0.00 0.00 0.00 3.18
2716 6717 6.203338 CCCCTTTTGTTCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.32 3.16
2717 6718 6.762661 CCCTTTTGTTCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.32 3.16
2718 6719 7.925483 CCCTTTTGTTCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.32 2.24
2719 6720 9.480053 CCTTTTGTTCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.32 2.12
2724 6725 9.179552 TGTTCATTTTGATGACAAGTATTTTCG 57.820 29.630 0.00 0.00 37.32 3.46
2725 6726 8.638565 GTTCATTTTGATGACAAGTATTTTCGG 58.361 33.333 0.00 0.00 37.32 4.30
2726 6727 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
2727 6728 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
2728 6729 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2729 6730 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2730 6731 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2731 6732 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2732 6733 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2733 6734 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2734 6735 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2941 6942 7.911651 AGAAATTCACAGAAGTTGATCTAGGA 58.088 34.615 0.00 0.00 0.00 2.94
3007 7008 8.936864 ACATAAGCTAAATACACTCACAAGTTC 58.063 33.333 0.00 0.00 31.71 3.01
3118 7120 0.304705 CTGATGAAATGCGGCGTACC 59.695 55.000 9.37 0.00 0.00 3.34
3119 7121 1.092921 TGATGAAATGCGGCGTACCC 61.093 55.000 9.37 0.00 0.00 3.69
3120 7122 0.814010 GATGAAATGCGGCGTACCCT 60.814 55.000 9.37 0.00 0.00 4.34
3186 7191 4.216257 TCTTGTGCAAGAAGTTCTATTGCC 59.784 41.667 21.35 14.93 46.82 4.52
3214 7219 2.757124 GGCCTTGTGGGGATCCGAT 61.757 63.158 5.45 0.00 35.24 4.18
3229 7234 2.917933 TCCGATTTGGATGGACATGTC 58.082 47.619 17.91 17.91 43.74 3.06
3296 7301 2.338984 GTCGAGCCGAACACACCT 59.661 61.111 0.00 0.00 37.72 4.00
3297 7302 2.022129 GTCGAGCCGAACACACCTG 61.022 63.158 0.00 0.00 37.72 4.00
3298 7303 2.029073 CGAGCCGAACACACCTGT 59.971 61.111 0.00 0.00 0.00 4.00
3299 7304 2.022129 CGAGCCGAACACACCTGTC 61.022 63.158 0.00 0.00 0.00 3.51
3300 7305 1.367840 GAGCCGAACACACCTGTCT 59.632 57.895 0.00 0.00 0.00 3.41
3301 7306 0.946221 GAGCCGAACACACCTGTCTG 60.946 60.000 0.00 0.00 0.00 3.51
3302 7307 2.607892 GCCGAACACACCTGTCTGC 61.608 63.158 0.00 0.00 0.00 4.26
3303 7308 1.961277 CCGAACACACCTGTCTGCC 60.961 63.158 0.00 0.00 0.00 4.85
3331 7336 4.448720 AAGGCTTTGTACCCTGTTACTT 57.551 40.909 0.00 0.00 0.00 2.24
3371 7376 1.352352 AGGTCTGTTGGTTCATGGGAG 59.648 52.381 0.00 0.00 0.00 4.30
3376 7381 2.041081 CTGTTGGTTCATGGGAGGGTTA 59.959 50.000 0.00 0.00 0.00 2.85
3386 7391 1.132500 GGGAGGGTTACAGGAGGATG 58.868 60.000 0.00 0.00 0.00 3.51
3391 7396 3.256704 AGGGTTACAGGAGGATGTTCAA 58.743 45.455 0.00 0.00 34.56 2.69
3392 7397 3.264450 AGGGTTACAGGAGGATGTTCAAG 59.736 47.826 0.00 0.00 34.56 3.02
3393 7398 3.009143 GGGTTACAGGAGGATGTTCAAGT 59.991 47.826 0.00 0.00 34.56 3.16
3394 7399 4.224370 GGGTTACAGGAGGATGTTCAAGTA 59.776 45.833 0.00 0.00 34.56 2.24
3396 7401 5.420409 GTTACAGGAGGATGTTCAAGTAGG 58.580 45.833 0.00 0.00 34.56 3.18
3397 7402 3.521727 ACAGGAGGATGTTCAAGTAGGT 58.478 45.455 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.559958 CTCTACTGTTAGCAAAATAACATTTGG 57.440 33.333 0.21 0.00 42.97 3.28
7 8 9.559958 CCTCTACTGTTAGCAAAATAACATTTG 57.440 33.333 0.21 0.00 42.97 2.32
8 9 8.739972 CCCTCTACTGTTAGCAAAATAACATTT 58.260 33.333 0.21 0.00 42.97 2.32
9 10 7.148069 GCCCTCTACTGTTAGCAAAATAACATT 60.148 37.037 0.21 0.00 42.97 2.71
10 11 6.318900 GCCCTCTACTGTTAGCAAAATAACAT 59.681 38.462 0.21 0.00 42.97 2.71
11 12 5.646360 GCCCTCTACTGTTAGCAAAATAACA 59.354 40.000 0.00 0.00 42.01 2.41
12 13 5.066117 GGCCCTCTACTGTTAGCAAAATAAC 59.934 44.000 0.00 0.00 36.40 1.89
13 14 5.190677 GGCCCTCTACTGTTAGCAAAATAA 58.809 41.667 0.00 0.00 0.00 1.40
14 15 4.226394 TGGCCCTCTACTGTTAGCAAAATA 59.774 41.667 0.00 0.00 0.00 1.40
15 16 3.010138 TGGCCCTCTACTGTTAGCAAAAT 59.990 43.478 0.00 0.00 0.00 1.82
16 17 2.373836 TGGCCCTCTACTGTTAGCAAAA 59.626 45.455 0.00 0.00 0.00 2.44
17 18 1.982226 TGGCCCTCTACTGTTAGCAAA 59.018 47.619 0.00 0.00 0.00 3.68
18 19 1.651737 TGGCCCTCTACTGTTAGCAA 58.348 50.000 0.00 0.00 0.00 3.91
19 20 1.651737 TTGGCCCTCTACTGTTAGCA 58.348 50.000 0.00 0.00 0.00 3.49
20 21 2.092914 ACATTGGCCCTCTACTGTTAGC 60.093 50.000 0.00 0.00 0.00 3.09
21 22 3.914426 ACATTGGCCCTCTACTGTTAG 57.086 47.619 0.00 0.00 0.00 2.34
22 23 5.249852 AGTTAACATTGGCCCTCTACTGTTA 59.750 40.000 8.61 0.00 0.00 2.41
23 24 4.042934 AGTTAACATTGGCCCTCTACTGTT 59.957 41.667 8.61 0.68 0.00 3.16
24 25 3.587506 AGTTAACATTGGCCCTCTACTGT 59.412 43.478 8.61 0.00 0.00 3.55
25 26 4.192317 GAGTTAACATTGGCCCTCTACTG 58.808 47.826 8.61 0.00 0.00 2.74
26 27 3.118738 CGAGTTAACATTGGCCCTCTACT 60.119 47.826 8.61 0.00 0.00 2.57
27 28 3.195661 CGAGTTAACATTGGCCCTCTAC 58.804 50.000 8.61 0.00 0.00 2.59
28 29 2.835764 ACGAGTTAACATTGGCCCTCTA 59.164 45.455 8.61 0.00 0.00 2.43
29 30 1.628846 ACGAGTTAACATTGGCCCTCT 59.371 47.619 8.61 0.00 0.00 3.69
30 31 1.737793 CACGAGTTAACATTGGCCCTC 59.262 52.381 8.61 0.00 0.00 4.30
31 32 1.821216 CACGAGTTAACATTGGCCCT 58.179 50.000 8.61 0.00 0.00 5.19
32 33 0.170339 GCACGAGTTAACATTGGCCC 59.830 55.000 8.61 0.00 0.00 5.80
33 34 0.878416 TGCACGAGTTAACATTGGCC 59.122 50.000 8.61 0.00 0.00 5.36
34 35 2.225491 TCTTGCACGAGTTAACATTGGC 59.775 45.455 8.61 6.86 0.00 4.52
35 36 4.481930 TTCTTGCACGAGTTAACATTGG 57.518 40.909 8.61 0.00 0.00 3.16
36 37 4.853196 CCATTCTTGCACGAGTTAACATTG 59.147 41.667 8.61 2.74 0.00 2.82
37 38 4.518970 ACCATTCTTGCACGAGTTAACATT 59.481 37.500 8.61 0.00 0.00 2.71
38 39 4.072131 ACCATTCTTGCACGAGTTAACAT 58.928 39.130 8.61 0.00 0.00 2.71
39 40 3.472652 ACCATTCTTGCACGAGTTAACA 58.527 40.909 8.61 0.00 0.00 2.41
40 41 4.219033 CAACCATTCTTGCACGAGTTAAC 58.781 43.478 0.00 0.00 0.00 2.01
41 42 3.880490 ACAACCATTCTTGCACGAGTTAA 59.120 39.130 0.00 0.00 0.00 2.01
42 43 3.472652 ACAACCATTCTTGCACGAGTTA 58.527 40.909 0.00 0.00 0.00 2.24
43 44 2.297701 ACAACCATTCTTGCACGAGTT 58.702 42.857 0.00 0.00 0.00 3.01
44 45 1.967319 ACAACCATTCTTGCACGAGT 58.033 45.000 0.00 0.00 0.00 4.18
45 46 2.805671 TGTACAACCATTCTTGCACGAG 59.194 45.455 0.00 0.00 0.00 4.18
46 47 2.546368 GTGTACAACCATTCTTGCACGA 59.454 45.455 0.00 0.00 0.00 4.35
47 48 2.289274 TGTGTACAACCATTCTTGCACG 59.711 45.455 0.00 0.00 0.00 5.34
48 49 3.563808 TCTGTGTACAACCATTCTTGCAC 59.436 43.478 0.00 0.00 0.00 4.57
49 50 3.814625 TCTGTGTACAACCATTCTTGCA 58.185 40.909 0.00 0.00 0.00 4.08
50 51 3.189287 CCTCTGTGTACAACCATTCTTGC 59.811 47.826 0.00 0.00 0.00 4.01
51 52 3.189287 GCCTCTGTGTACAACCATTCTTG 59.811 47.826 0.00 0.00 0.00 3.02
52 53 3.412386 GCCTCTGTGTACAACCATTCTT 58.588 45.455 0.00 0.00 0.00 2.52
53 54 2.612972 CGCCTCTGTGTACAACCATTCT 60.613 50.000 0.00 0.00 0.00 2.40
54 55 1.732259 CGCCTCTGTGTACAACCATTC 59.268 52.381 0.00 0.00 0.00 2.67
55 56 1.808411 CGCCTCTGTGTACAACCATT 58.192 50.000 0.00 0.00 0.00 3.16
56 57 0.673644 GCGCCTCTGTGTACAACCAT 60.674 55.000 0.00 0.00 0.00 3.55
57 58 1.301401 GCGCCTCTGTGTACAACCA 60.301 57.895 0.00 0.00 0.00 3.67
58 59 2.033194 GGCGCCTCTGTGTACAACC 61.033 63.158 22.15 0.00 0.00 3.77
59 60 0.882927 TTGGCGCCTCTGTGTACAAC 60.883 55.000 29.70 0.00 0.00 3.32
60 61 0.602638 CTTGGCGCCTCTGTGTACAA 60.603 55.000 29.70 9.04 0.00 2.41
61 62 1.005037 CTTGGCGCCTCTGTGTACA 60.005 57.895 29.70 0.00 0.00 2.90
62 63 1.741770 CCTTGGCGCCTCTGTGTAC 60.742 63.158 29.70 0.00 0.00 2.90
63 64 2.214216 ACCTTGGCGCCTCTGTGTA 61.214 57.895 29.70 1.01 0.00 2.90
64 65 3.560251 ACCTTGGCGCCTCTGTGT 61.560 61.111 29.70 14.49 0.00 3.72
65 66 3.052082 CACCTTGGCGCCTCTGTG 61.052 66.667 29.70 25.07 0.00 3.66
67 68 4.711949 AGCACCTTGGCGCCTCTG 62.712 66.667 29.70 17.56 39.27 3.35
68 69 4.400961 GAGCACCTTGGCGCCTCT 62.401 66.667 29.70 14.13 39.27 3.69
82 83 1.718757 CGCCCTTGTATTGCTGGAGC 61.719 60.000 0.00 0.00 42.50 4.70
83 84 1.718757 GCGCCCTTGTATTGCTGGAG 61.719 60.000 0.00 0.00 0.00 3.86
84 85 1.748879 GCGCCCTTGTATTGCTGGA 60.749 57.895 0.00 0.00 0.00 3.86
85 86 2.045708 TGCGCCCTTGTATTGCTGG 61.046 57.895 4.18 0.00 0.00 4.85
86 87 1.137404 GTGCGCCCTTGTATTGCTG 59.863 57.895 4.18 0.00 0.00 4.41
87 88 1.303236 TGTGCGCCCTTGTATTGCT 60.303 52.632 4.18 0.00 0.00 3.91
88 89 1.137404 CTGTGCGCCCTTGTATTGC 59.863 57.895 4.18 0.00 0.00 3.56
89 90 1.137404 GCTGTGCGCCCTTGTATTG 59.863 57.895 4.18 0.00 0.00 1.90
90 91 1.002134 AGCTGTGCGCCCTTGTATT 60.002 52.632 4.18 0.00 40.39 1.89
91 92 1.450312 GAGCTGTGCGCCCTTGTAT 60.450 57.895 4.18 0.00 40.39 2.29
92 93 2.047274 GAGCTGTGCGCCCTTGTA 60.047 61.111 4.18 0.00 40.39 2.41
113 114 3.494336 CTTGGCGCGCCTCTTGAG 61.494 66.667 45.79 30.27 36.94 3.02
139 140 3.801997 CTGGGCACTAGGGGCTGG 61.802 72.222 19.20 7.66 31.37 4.85
284 288 8.944029 CAGAATATCATGACAAAACTGAGAAGT 58.056 33.333 0.00 0.00 0.00 3.01
290 294 6.198650 TGGCAGAATATCATGACAAAACTG 57.801 37.500 0.00 6.02 29.43 3.16
318 322 5.368256 AGTGATGCATCAGAAGTGAAAAC 57.632 39.130 29.38 13.35 37.51 2.43
350 354 8.830580 GCAGCAAGATAATGAACTACTATTCAA 58.169 33.333 0.00 0.00 41.78 2.69
356 360 6.409704 TCAAGCAGCAAGATAATGAACTACT 58.590 36.000 0.00 0.00 0.00 2.57
509 519 2.283351 GCAGCACAGAAGCAACTTTTTG 59.717 45.455 0.00 0.00 36.85 2.44
514 524 1.396653 AAAGCAGCACAGAAGCAACT 58.603 45.000 0.00 0.00 36.85 3.16
655 665 8.618385 AGCATAGGATCCAGTGGAAATAATAAT 58.382 33.333 17.71 0.00 34.34 1.28
920 937 5.591472 TGCAGGAATCAAATTAGGATGACAG 59.409 40.000 0.00 0.00 0.00 3.51
1054 1074 1.763545 GAGAGGGGAACATACCTGGAC 59.236 57.143 0.00 0.00 37.18 4.02
1294 1329 3.230284 CCGCTTCTATCAGGGGCA 58.770 61.111 0.00 0.00 39.82 5.36
1550 1588 5.983720 GTCACTAGTGAAGAGCTTGTTGTTA 59.016 40.000 26.74 0.00 41.85 2.41
1556 1594 3.509575 AGGAGTCACTAGTGAAGAGCTTG 59.490 47.826 26.74 0.00 41.85 4.01
1557 1595 3.773560 AGGAGTCACTAGTGAAGAGCTT 58.226 45.455 26.74 10.14 41.85 3.74
1558 1596 3.449746 AGGAGTCACTAGTGAAGAGCT 57.550 47.619 26.74 18.85 41.85 4.09
1812 1915 5.649395 TCAGCTCCAGGAAAAGTATGAAATG 59.351 40.000 0.00 0.00 0.00 2.32
2558 6559 4.157656 GTGGGCAACAACATTCTGCTAATA 59.842 41.667 0.00 0.00 36.32 0.98
2601 6602 5.767665 AGTACATCACAATGTTTTGTAGGCA 59.232 36.000 5.67 0.00 43.74 4.75
2607 6608 5.106157 GGAGGGAGTACATCACAATGTTTTG 60.106 44.000 0.00 0.00 43.74 2.44
2621 6622 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
2622 6623 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2623 6624 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2624 6625 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2625 6626 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2626 6627 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2627 6628 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2628 6629 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2629 6630 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2630 6631 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2631 6632 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2632 6633 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
2633 6634 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
2634 6635 8.638565 GTTCATTTTGATGACAAGTATTTTCGG 58.361 33.333 0.00 0.00 37.32 4.30
2635 6636 9.179552 TGTTCATTTTGATGACAAGTATTTTCG 57.820 29.630 0.00 0.00 37.32 3.46
2640 6641 9.480053 CCTTTTGTTCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.32 2.12
2641 6642 7.925483 CCCTTTTGTTCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.32 2.24
2642 6643 6.762661 CCCTTTTGTTCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.32 3.16
2643 6644 6.203338 CCCCTTTTGTTCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.32 3.16
2644 6645 6.054295 CCCCTTTTGTTCATTTTGATGACAA 58.946 36.000 0.00 0.00 0.00 3.18
2645 6646 5.365025 TCCCCTTTTGTTCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
2646 6647 5.852827 TCCCCTTTTGTTCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
2647 6648 6.043012 ACATCCCCTTTTGTTCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
2648 6649 6.232692 ACATCCCCTTTTGTTCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
2649 6650 6.438186 ACATCCCCTTTTGTTCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
2650 6651 5.885449 ACATCCCCTTTTGTTCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
2651 6652 7.614494 AGATACATCCCCTTTTGTTCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
2652 6653 7.797121 AGATACATCCCCTTTTGTTCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
2653 6654 8.336235 TCTAGATACATCCCCTTTTGTTCATTT 58.664 33.333 0.00 0.00 0.00 2.32
2654 6655 7.872138 TCTAGATACATCCCCTTTTGTTCATT 58.128 34.615 0.00 0.00 0.00 2.57
2655 6656 7.451731 TCTAGATACATCCCCTTTTGTTCAT 57.548 36.000 0.00 0.00 0.00 2.57
2656 6657 6.884472 TCTAGATACATCCCCTTTTGTTCA 57.116 37.500 0.00 0.00 0.00 3.18
2657 6658 7.740805 AGATCTAGATACATCCCCTTTTGTTC 58.259 38.462 4.89 0.00 0.00 3.18
2658 6659 7.698163 AGATCTAGATACATCCCCTTTTGTT 57.302 36.000 4.89 0.00 0.00 2.83
2659 6660 8.235230 TCTAGATCTAGATACATCCCCTTTTGT 58.765 37.037 25.54 0.00 37.28 2.83
2660 6661 8.657387 TCTAGATCTAGATACATCCCCTTTTG 57.343 38.462 25.54 0.00 37.28 2.44
2674 6675 8.235230 ACAAAAGGGGATGTATCTAGATCTAGA 58.765 37.037 29.94 29.94 45.24 2.43
2675 6676 8.429237 ACAAAAGGGGATGTATCTAGATCTAG 57.571 38.462 21.81 21.81 34.56 2.43
2676 6677 8.798975 AACAAAAGGGGATGTATCTAGATCTA 57.201 34.615 8.95 1.69 0.00 1.98
2677 6678 7.348274 TGAACAAAAGGGGATGTATCTAGATCT 59.652 37.037 8.95 0.00 0.00 2.75
2678 6679 7.509546 TGAACAAAAGGGGATGTATCTAGATC 58.490 38.462 8.95 2.00 0.00 2.75
2679 6680 7.451731 TGAACAAAAGGGGATGTATCTAGAT 57.548 36.000 10.73 10.73 0.00 1.98
2680 6681 6.884472 TGAACAAAAGGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
2681 6682 8.525290 AAATGAACAAAAGGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
2682 6683 8.748412 CAAAATGAACAAAAGGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
2683 6684 7.454380 TCAAAATGAACAAAAGGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
2684 6685 7.610865 TCAAAATGAACAAAAGGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
2685 6686 7.552050 TCAAAATGAACAAAAGGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
2686 6687 6.985653 TCAAAATGAACAAAAGGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
2687 6688 5.885449 TCAAAATGAACAAAAGGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
2688 6689 6.369615 GTCATCAAAATGAACAAAAGGGGATG 59.630 38.462 0.00 0.00 43.42 3.51
2689 6690 6.043012 TGTCATCAAAATGAACAAAAGGGGAT 59.957 34.615 0.00 0.00 43.42 3.85
2690 6691 5.365025 TGTCATCAAAATGAACAAAAGGGGA 59.635 36.000 0.00 0.00 43.42 4.81
2691 6692 5.609423 TGTCATCAAAATGAACAAAAGGGG 58.391 37.500 0.00 0.00 43.42 4.79
2692 6693 6.762661 ACTTGTCATCAAAATGAACAAAAGGG 59.237 34.615 0.87 0.00 43.42 3.95
2693 6694 7.775397 ACTTGTCATCAAAATGAACAAAAGG 57.225 32.000 0.87 0.00 43.42 3.11
2698 6699 9.179552 CGAAAATACTTGTCATCAAAATGAACA 57.820 29.630 0.00 0.00 43.42 3.18
2699 6700 8.638565 CCGAAAATACTTGTCATCAAAATGAAC 58.361 33.333 0.00 0.00 43.42 3.18
2700 6701 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
2701 6702 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
2702 6703 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2703 6704 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2704 6705 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2705 6706 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2706 6707 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2707 6708 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2708 6709 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2709 6710 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2710 6711 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2711 6712 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2712 6713 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2713 6714 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2714 6715 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2715 6716 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2716 6717 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2717 6718 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2718 6719 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2719 6720 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
2720 6721 1.479323 CAATACTCCCTCCGTCCGAAA 59.521 52.381 0.00 0.00 0.00 3.46
2721 6722 1.108776 CAATACTCCCTCCGTCCGAA 58.891 55.000 0.00 0.00 0.00 4.30
2722 6723 1.389609 GCAATACTCCCTCCGTCCGA 61.390 60.000 0.00 0.00 0.00 4.55
2723 6724 1.067582 GCAATACTCCCTCCGTCCG 59.932 63.158 0.00 0.00 0.00 4.79
2724 6725 1.067582 CGCAATACTCCCTCCGTCC 59.932 63.158 0.00 0.00 0.00 4.79
2725 6726 1.591863 GCGCAATACTCCCTCCGTC 60.592 63.158 0.30 0.00 0.00 4.79
2726 6727 1.686325 ATGCGCAATACTCCCTCCGT 61.686 55.000 17.11 0.00 0.00 4.69
2727 6728 1.069765 ATGCGCAATACTCCCTCCG 59.930 57.895 17.11 0.00 0.00 4.63
2728 6729 1.510480 GCATGCGCAATACTCCCTCC 61.510 60.000 17.11 0.00 38.36 4.30
2729 6730 1.944778 GCATGCGCAATACTCCCTC 59.055 57.895 17.11 0.00 38.36 4.30
2730 6731 4.147701 GCATGCGCAATACTCCCT 57.852 55.556 17.11 0.00 38.36 4.20
2829 6830 1.948145 CGAGCAGTACTAGTAGGGGTG 59.052 57.143 1.87 0.36 0.00 4.61
2830 6831 1.749983 GCGAGCAGTACTAGTAGGGGT 60.750 57.143 1.87 4.00 0.00 4.95
2932 6933 3.671740 AGTGCACCTAGTCCTAGATCA 57.328 47.619 14.63 0.00 35.21 2.92
2941 6942 0.687354 CCAGACCAAGTGCACCTAGT 59.313 55.000 14.63 8.18 0.00 2.57
3007 7008 1.000385 TGGTTCTGCTTTTGCCATTCG 60.000 47.619 0.00 0.00 46.87 3.34
3099 7101 0.304705 GGTACGCCGCATTTCATCAG 59.695 55.000 0.00 0.00 0.00 2.90
3100 7102 1.092921 GGGTACGCCGCATTTCATCA 61.093 55.000 0.00 0.00 34.97 3.07
3157 7162 4.276926 AGAACTTCTTGCACAAGACAATCC 59.723 41.667 12.50 2.60 46.13 3.01
3214 7219 2.811431 GTCAACGACATGTCCATCCAAA 59.189 45.455 20.03 0.00 32.09 3.28
3229 7234 0.937304 CCCAGAACAGTGTGTCAACG 59.063 55.000 0.00 0.00 0.00 4.10
3296 7301 1.890894 GCCTTAGAGACGGCAGACA 59.109 57.895 0.00 0.00 45.59 3.41
3297 7302 4.816990 GCCTTAGAGACGGCAGAC 57.183 61.111 0.00 0.00 45.59 3.51
3301 7306 2.269172 GTACAAAGCCTTAGAGACGGC 58.731 52.381 0.00 0.00 46.65 5.68
3302 7307 2.418334 GGGTACAAAGCCTTAGAGACGG 60.418 54.545 0.00 0.00 40.33 4.79
3303 7308 2.889852 GGGTACAAAGCCTTAGAGACG 58.110 52.381 0.00 0.00 40.33 4.18
3371 7376 3.009143 ACTTGAACATCCTCCTGTAACCC 59.991 47.826 0.00 0.00 0.00 4.11
3376 7381 3.521727 ACCTACTTGAACATCCTCCTGT 58.478 45.455 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.