Multiple sequence alignment - TraesCS6B01G084000

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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 TraesCS6B01G084000 chr6B 100.000 5537 0 0 1 5537 60865573 60860037 0.000000e+00 10226.0
1 TraesCS6B01G084000 chr6B 92.681 1339 88 5 3204 4538 61224767 61226099 0.000000e+00 1921.0
2 TraesCS6B01G084000 chr6B 87.308 780 65 19 1441 2211 61223923 61224677 0.000000e+00 861.0
3 TraesCS6B01G084000 chr6B 84.934 531 43 21 931 1448 61223323 61223829 2.300000e-138 503.0
4 TraesCS6B01G084000 chr6B 94.382 89 5 0 2298 2386 61224670 61224758 2.690000e-28 137.0
5 TraesCS6B01G084000 chr6A 90.761 2327 153 36 3231 5519 33541262 33538960 0.000000e+00 3049.0
6 TraesCS6B01G084000 chr6A 92.720 1305 80 9 3239 4538 33584604 33585898 0.000000e+00 1869.0
7 TraesCS6B01G084000 chr6A 98.985 788 7 1 2401 3188 447185146 447185932 0.000000e+00 1410.0
8 TraesCS6B01G084000 chr6A 86.672 1178 69 51 721 1858 33543063 33541934 0.000000e+00 1225.0
9 TraesCS6B01G084000 chr6A 85.677 775 62 29 1441 2211 33583745 33584474 0.000000e+00 771.0
10 TraesCS6B01G084000 chr6A 90.745 443 15 4 1920 2357 33541725 33541304 8.050000e-158 568.0
11 TraesCS6B01G084000 chr6A 85.687 531 44 20 931 1442 33583131 33583648 1.060000e-146 531.0
12 TraesCS6B01G084000 chr6A 93.500 200 11 2 270 468 33543517 33543319 4.190000e-76 296.0
13 TraesCS6B01G084000 chr6A 95.506 89 4 0 2298 2386 33584467 33584555 5.780000e-30 143.0
14 TraesCS6B01G084000 chr6D 94.038 1560 76 8 3198 4744 29000081 29001636 0.000000e+00 2350.0
15 TraesCS6B01G084000 chr6D 92.937 1161 76 2 3378 4538 28941154 28940000 0.000000e+00 1685.0
16 TraesCS6B01G084000 chr6D 88.003 1292 65 29 197 1448 28997825 28999066 0.000000e+00 1445.0
17 TraesCS6B01G084000 chr6D 90.628 971 35 19 1441 2398 28999152 29000079 0.000000e+00 1238.0
18 TraesCS6B01G084000 chr6D 90.069 433 28 8 1935 2367 28941848 28941431 1.050000e-151 547.0
19 TraesCS6B01G084000 chr6D 86.635 419 29 15 1441 1856 28942403 28942009 6.590000e-119 438.0
20 TraesCS6B01G084000 chr6D 97.468 237 6 0 1206 1442 28942794 28942558 6.680000e-109 405.0
21 TraesCS6B01G084000 chr6D 89.340 197 16 2 939 1135 28943299 28943108 5.540000e-60 243.0
22 TraesCS6B01G084000 chr6D 92.258 155 8 3 3226 3380 28941399 28941249 3.360000e-52 217.0
23 TraesCS6B01G084000 chr6D 97.500 40 1 0 3145 3184 427726893 427726854 9.950000e-08 69.4
24 TraesCS6B01G084000 chr3D 88.559 1180 115 10 3378 4538 574918521 574919699 0.000000e+00 1413.0
25 TraesCS6B01G084000 chr3D 84.082 779 87 26 1441 2211 574917431 574918180 0.000000e+00 717.0
26 TraesCS6B01G084000 chr3D 82.311 424 58 14 1021 1442 574916934 574917342 8.830000e-93 351.0
27 TraesCS6B01G084000 chr3D 87.755 147 13 3 3234 3380 574918301 574918442 3.430000e-37 167.0
28 TraesCS6B01G084000 chr3D 96.721 61 2 0 2298 2358 574918173 574918233 9.810000e-18 102.0
29 TraesCS6B01G084000 chr3B 87.521 1186 125 9 3378 4541 765003173 765001989 0.000000e+00 1349.0
30 TraesCS6B01G084000 chr3B 83.107 515 66 12 4745 5244 761703919 761703411 3.040000e-122 449.0
31 TraesCS6B01G084000 chr3B 91.633 251 21 0 1447 1697 765004553 765004303 1.140000e-91 348.0
32 TraesCS6B01G084000 chr3B 88.968 281 30 1 1931 2211 765003832 765003553 4.110000e-91 346.0
33 TraesCS6B01G084000 chr3B 82.033 423 44 19 1022 1442 765005047 765004655 1.150000e-86 331.0
34 TraesCS6B01G084000 chr3B 83.810 210 26 5 4745 4946 562783760 562783969 5.660000e-45 193.0
35 TraesCS6B01G084000 chr3B 91.736 121 10 0 3260 3380 765003372 765003252 9.540000e-38 169.0
36 TraesCS6B01G084000 chr3A 95.911 807 13 9 2397 3194 163805603 163804808 0.000000e+00 1290.0
37 TraesCS6B01G084000 chr3A 95.975 795 15 6 2401 3187 46568922 46568137 0.000000e+00 1275.0
38 TraesCS6B01G084000 chr3A 95.208 793 21 6 2401 3184 717836829 717836045 0.000000e+00 1238.0
39 TraesCS6B01G084000 chr3A 89.258 903 95 2 3378 4279 710700175 710699274 0.000000e+00 1129.0
40 TraesCS6B01G084000 chr3A 91.633 251 21 0 1444 1694 710701335 710701085 1.140000e-91 348.0
41 TraesCS6B01G084000 chr3A 88.929 280 30 1 1931 2210 710700816 710700538 1.480000e-90 344.0
42 TraesCS6B01G084000 chr3A 90.086 232 23 0 1211 1442 710701655 710701424 9.010000e-78 302.0
43 TraesCS6B01G084000 chr3A 85.926 270 38 0 4272 4541 710699254 710698985 7.020000e-74 289.0
44 TraesCS6B01G084000 chr3A 88.312 154 14 2 3227 3380 710700403 710700254 1.230000e-41 182.0
45 TraesCS6B01G084000 chr3A 95.082 61 3 0 2298 2358 710700544 710700484 4.570000e-16 97.1
46 TraesCS6B01G084000 chr3A 84.270 89 14 0 1021 1109 710701803 710701715 2.750000e-13 87.9
47 TraesCS6B01G084000 chr3A 85.915 71 9 1 1637 1707 689132944 689133013 2.140000e-09 75.0
48 TraesCS6B01G084000 chr4B 95.844 794 14 7 2401 3184 124596539 124595755 0.000000e+00 1266.0
49 TraesCS6B01G084000 chr4B 85.323 804 68 17 2407 3184 489368781 489368002 0.000000e+00 785.0
50 TraesCS6B01G084000 chr7B 95.833 792 15 7 2401 3184 522602208 522602989 0.000000e+00 1264.0
51 TraesCS6B01G084000 chr7B 75.180 556 101 21 4926 5464 716374290 716373755 1.550000e-55 228.0
52 TraesCS6B01G084000 chr7B 74.011 531 85 28 5043 5537 525928729 525929242 3.430000e-37 167.0
53 TraesCS6B01G084000 chr4A 93.765 818 15 16 2401 3184 5968914 5968099 0.000000e+00 1195.0
54 TraesCS6B01G084000 chr1A 98.049 615 10 1 2570 3184 581941106 581941718 0.000000e+00 1068.0
55 TraesCS6B01G084000 chr5B 88.199 805 64 15 2400 3184 71794491 71795284 0.000000e+00 931.0
56 TraesCS6B01G084000 chr5D 85.135 814 87 21 4745 5537 114916238 114917038 0.000000e+00 802.0
57 TraesCS6B01G084000 chr5D 78.534 382 63 12 4926 5304 124540826 124540461 3.340000e-57 233.0
58 TraesCS6B01G084000 chr1B 83.866 595 44 27 2400 2957 657186214 657186793 2.290000e-143 520.0
59 TraesCS6B01G084000 chr2D 84.821 448 44 9 4745 5168 39206589 39207036 3.960000e-116 429.0
60 TraesCS6B01G084000 chr2B 76.021 563 95 28 4926 5464 692145061 692145607 7.120000e-64 255.0
61 TraesCS6B01G084000 chr2B 82.192 219 37 2 1225 1442 394364270 394364053 2.630000e-43 187.0
62 TraesCS6B01G084000 chr1D 76.351 444 77 12 5042 5469 96400694 96401125 4.350000e-51 213.0


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 TraesCS6B01G084000 chr6B 60860037 60865573 5536 True 10226.000000 10226 100.000000 1 5537 1 chr6B.!!$R1 5536
1 TraesCS6B01G084000 chr6B 61223323 61226099 2776 False 855.500000 1921 89.826250 931 4538 4 chr6B.!!$F1 3607
2 TraesCS6B01G084000 chr6A 447185146 447185932 786 False 1410.000000 1410 98.985000 2401 3188 1 chr6A.!!$F1 787
3 TraesCS6B01G084000 chr6A 33538960 33543517 4557 True 1284.500000 3049 90.419500 270 5519 4 chr6A.!!$R1 5249
4 TraesCS6B01G084000 chr6A 33583131 33585898 2767 False 828.500000 1869 89.897500 931 4538 4 chr6A.!!$F2 3607
5 TraesCS6B01G084000 chr6D 28997825 29001636 3811 False 1677.666667 2350 90.889667 197 4744 3 chr6D.!!$F1 4547
6 TraesCS6B01G084000 chr6D 28940000 28943299 3299 True 589.166667 1685 91.451167 939 4538 6 chr6D.!!$R2 3599
7 TraesCS6B01G084000 chr3D 574916934 574919699 2765 False 550.000000 1413 87.885600 1021 4538 5 chr3D.!!$F1 3517
8 TraesCS6B01G084000 chr3B 765001989 765005047 3058 True 508.600000 1349 88.378200 1022 4541 5 chr3B.!!$R2 3519
9 TraesCS6B01G084000 chr3B 761703411 761703919 508 True 449.000000 449 83.107000 4745 5244 1 chr3B.!!$R1 499
10 TraesCS6B01G084000 chr3A 163804808 163805603 795 True 1290.000000 1290 95.911000 2397 3194 1 chr3A.!!$R2 797
11 TraesCS6B01G084000 chr3A 46568137 46568922 785 True 1275.000000 1275 95.975000 2401 3187 1 chr3A.!!$R1 786
12 TraesCS6B01G084000 chr3A 717836045 717836829 784 True 1238.000000 1238 95.208000 2401 3184 1 chr3A.!!$R3 783
13 TraesCS6B01G084000 chr3A 710698985 710701803 2818 True 347.375000 1129 89.187000 1021 4541 8 chr3A.!!$R4 3520
14 TraesCS6B01G084000 chr4B 124595755 124596539 784 True 1266.000000 1266 95.844000 2401 3184 1 chr4B.!!$R1 783
15 TraesCS6B01G084000 chr4B 489368002 489368781 779 True 785.000000 785 85.323000 2407 3184 1 chr4B.!!$R2 777
16 TraesCS6B01G084000 chr7B 522602208 522602989 781 False 1264.000000 1264 95.833000 2401 3184 1 chr7B.!!$F1 783
17 TraesCS6B01G084000 chr7B 716373755 716374290 535 True 228.000000 228 75.180000 4926 5464 1 chr7B.!!$R1 538
18 TraesCS6B01G084000 chr4A 5968099 5968914 815 True 1195.000000 1195 93.765000 2401 3184 1 chr4A.!!$R1 783
19 TraesCS6B01G084000 chr1A 581941106 581941718 612 False 1068.000000 1068 98.049000 2570 3184 1 chr1A.!!$F1 614
20 TraesCS6B01G084000 chr5B 71794491 71795284 793 False 931.000000 931 88.199000 2400 3184 1 chr5B.!!$F1 784
21 TraesCS6B01G084000 chr5D 114916238 114917038 800 False 802.000000 802 85.135000 4745 5537 1 chr5D.!!$F1 792
22 TraesCS6B01G084000 chr1B 657186214 657186793 579 False 520.000000 520 83.866000 2400 2957 1 chr1B.!!$F1 557
23 TraesCS6B01G084000 chr2B 692145061 692145607 546 False 255.000000 255 76.021000 4926 5464 1 chr2B.!!$F1 538

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
154 155 0.032615 GCAGGAGAAGAGGAGGAGGA 60.033 60.000 0.00 0.0 0.0 3.71 F
1201 1593 0.107848 GACTTCCGTATGTGGGGTGG 60.108 60.000 0.00 0.0 0.0 4.61 F
1202 1594 1.223487 CTTCCGTATGTGGGGTGGG 59.777 63.158 0.00 0.0 0.0 4.61 F
2281 3492 1.240256 TTTATTTCCCTGCGCAACGT 58.760 45.000 13.05 0.0 0.0 3.99 F
3257 4582 1.000385 TCTTCATTTTGCGGCCTGTTG 60.000 47.619 0.00 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 2582 1.111116 ACTGCAGCAACACAGCCATT 61.111 50.000 15.27 0.0 37.42 3.16 R
2284 3495 0.458025 GTGCCTGCAGGAGTACGTAC 60.458 60.000 37.21 18.1 37.39 3.67 R
2551 3792 1.472480 TCTCGTGTCGATCAATCAGCA 59.528 47.619 0.00 0.0 34.61 4.41 R
3585 5009 1.218316 GAAGGCGAGGGTGACGATT 59.782 57.895 0.00 0.0 0.00 3.34 R
5109 6625 1.133945 TGGAGCTAGACATCTCTCGCT 60.134 52.381 0.00 0.0 45.83 4.93 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
19 20 0.868406 GACGGCAAGTGTCTGAAAGG 59.132 55.000 0.00 0.00 33.54 3.11
20 21 0.468226 ACGGCAAGTGTCTGAAAGGA 59.532 50.000 0.00 0.00 0.00 3.36
21 22 0.868406 CGGCAAGTGTCTGAAAGGAC 59.132 55.000 0.00 0.00 36.81 3.85
22 23 0.868406 GGCAAGTGTCTGAAAGGACG 59.132 55.000 0.00 0.00 38.91 4.79
23 24 1.583054 GCAAGTGTCTGAAAGGACGT 58.417 50.000 0.00 0.00 38.91 4.34
24 25 1.261619 GCAAGTGTCTGAAAGGACGTG 59.738 52.381 0.00 0.00 38.91 4.49
25 26 2.550978 CAAGTGTCTGAAAGGACGTGT 58.449 47.619 0.00 0.00 38.91 4.49
26 27 2.510768 AGTGTCTGAAAGGACGTGTC 57.489 50.000 0.00 0.00 38.91 3.67
36 37 2.746277 GACGTGTCCATGGGGTGC 60.746 66.667 13.02 0.72 34.93 5.01
37 38 4.344865 ACGTGTCCATGGGGTGCC 62.345 66.667 13.02 0.00 34.93 5.01
38 39 4.343323 CGTGTCCATGGGGTGCCA 62.343 66.667 13.02 0.00 34.93 4.92
39 40 2.676471 GTGTCCATGGGGTGCCAC 60.676 66.667 13.02 7.67 34.93 5.01
40 41 3.181530 TGTCCATGGGGTGCCACA 61.182 61.111 13.02 4.59 34.93 4.17
41 42 2.360191 GTCCATGGGGTGCCACAT 59.640 61.111 13.02 0.00 34.93 3.21
42 43 1.210885 TGTCCATGGGGTGCCACATA 61.211 55.000 13.02 0.00 34.93 2.29
43 44 0.466189 GTCCATGGGGTGCCACATAG 60.466 60.000 13.02 0.00 34.93 2.23
44 45 1.152694 CCATGGGGTGCCACATAGG 60.153 63.158 5.55 6.60 41.84 2.57
53 54 2.890474 CCACATAGGCGTGCGGAC 60.890 66.667 0.00 0.00 35.47 4.79
54 55 2.184322 CACATAGGCGTGCGGACT 59.816 61.111 5.27 0.00 38.01 3.85
55 56 2.167219 CACATAGGCGTGCGGACTG 61.167 63.158 5.27 0.00 34.13 3.51
56 57 2.348104 ACATAGGCGTGCGGACTGA 61.348 57.895 5.27 0.00 34.13 3.41
57 58 1.068083 CATAGGCGTGCGGACTGAT 59.932 57.895 5.27 0.00 34.13 2.90
58 59 1.068083 ATAGGCGTGCGGACTGATG 59.932 57.895 5.27 0.00 34.13 3.07
59 60 1.391933 ATAGGCGTGCGGACTGATGA 61.392 55.000 5.27 0.00 34.13 2.92
60 61 2.279502 TAGGCGTGCGGACTGATGAC 62.280 60.000 5.27 0.00 34.13 3.06
61 62 3.188786 GCGTGCGGACTGATGACC 61.189 66.667 5.27 0.00 0.00 4.02
62 63 2.261361 CGTGCGGACTGATGACCA 59.739 61.111 5.27 0.00 0.00 4.02
63 64 1.153568 CGTGCGGACTGATGACCAT 60.154 57.895 5.27 0.00 0.00 3.55
64 65 0.740868 CGTGCGGACTGATGACCATT 60.741 55.000 5.27 0.00 0.00 3.16
65 66 0.729116 GTGCGGACTGATGACCATTG 59.271 55.000 0.00 0.00 0.00 2.82
66 67 0.612744 TGCGGACTGATGACCATTGA 59.387 50.000 0.00 0.00 0.00 2.57
67 68 1.009829 GCGGACTGATGACCATTGAC 58.990 55.000 0.00 0.00 0.00 3.18
68 69 1.280982 CGGACTGATGACCATTGACG 58.719 55.000 0.00 0.00 0.00 4.35
69 70 1.656652 GGACTGATGACCATTGACGG 58.343 55.000 0.00 0.00 0.00 4.79
70 71 1.066143 GGACTGATGACCATTGACGGT 60.066 52.381 0.00 0.00 43.91 4.83
76 77 3.806591 GACCATTGACGGTCGAAGA 57.193 52.632 1.47 0.00 45.77 2.87
96 97 4.362476 GCAACCGGCTTGGGCTTG 62.362 66.667 0.00 0.00 44.64 4.01
97 98 4.362476 CAACCGGCTTGGGCTTGC 62.362 66.667 0.00 0.00 44.64 4.01
102 103 4.372999 GGCTTGGGCTTGCCTCCT 62.373 66.667 11.71 0.00 45.26 3.69
103 104 2.677228 GCTTGGGCTTGCCTCCTA 59.323 61.111 11.71 0.00 35.22 2.94
104 105 1.228510 GCTTGGGCTTGCCTCCTAT 59.771 57.895 11.71 0.00 35.22 2.57
105 106 0.474184 GCTTGGGCTTGCCTCCTATA 59.526 55.000 11.71 0.00 35.22 1.31
106 107 1.544314 GCTTGGGCTTGCCTCCTATAG 60.544 57.143 11.71 0.00 35.22 1.31
107 108 2.050144 CTTGGGCTTGCCTCCTATAGA 58.950 52.381 11.71 0.00 0.00 1.98
108 109 2.190398 TGGGCTTGCCTCCTATAGAA 57.810 50.000 11.71 0.00 0.00 2.10
109 110 2.487775 TGGGCTTGCCTCCTATAGAAA 58.512 47.619 11.71 0.00 0.00 2.52
110 111 2.849943 TGGGCTTGCCTCCTATAGAAAA 59.150 45.455 11.71 0.00 0.00 2.29
111 112 3.215151 GGGCTTGCCTCCTATAGAAAAC 58.785 50.000 11.71 0.00 0.00 2.43
112 113 2.872858 GGCTTGCCTCCTATAGAAAACG 59.127 50.000 0.00 0.00 0.00 3.60
113 114 2.288186 GCTTGCCTCCTATAGAAAACGC 59.712 50.000 0.00 0.00 0.00 4.84
114 115 2.218953 TGCCTCCTATAGAAAACGCG 57.781 50.000 3.53 3.53 0.00 6.01
115 116 1.479323 TGCCTCCTATAGAAAACGCGT 59.521 47.619 5.58 5.58 0.00 6.01
116 117 2.125685 GCCTCCTATAGAAAACGCGTC 58.874 52.381 14.44 0.00 0.00 5.19
117 118 2.223758 GCCTCCTATAGAAAACGCGTCT 60.224 50.000 14.44 8.42 0.00 4.18
118 119 3.372954 CCTCCTATAGAAAACGCGTCTG 58.627 50.000 14.44 0.00 0.00 3.51
119 120 3.372954 CTCCTATAGAAAACGCGTCTGG 58.627 50.000 14.44 3.50 0.00 3.86
120 121 1.859080 CCTATAGAAAACGCGTCTGGC 59.141 52.381 14.44 2.32 38.69 4.85
131 132 4.681978 GTCTGGCGGGCAGTCGTT 62.682 66.667 27.88 0.00 0.00 3.85
132 133 3.936203 TCTGGCGGGCAGTCGTTT 61.936 61.111 27.88 0.00 0.00 3.60
133 134 3.423154 CTGGCGGGCAGTCGTTTC 61.423 66.667 22.22 0.00 0.00 2.78
134 135 3.883744 CTGGCGGGCAGTCGTTTCT 62.884 63.158 22.22 0.00 0.00 2.52
135 136 3.423154 GGCGGGCAGTCGTTTCTG 61.423 66.667 0.00 0.00 38.35 3.02
142 143 3.894257 CAGTCGTTTCTGCAGGAGA 57.106 52.632 15.13 5.59 0.00 3.71
143 144 2.154854 CAGTCGTTTCTGCAGGAGAA 57.845 50.000 15.13 0.00 39.05 2.87
144 145 2.064762 CAGTCGTTTCTGCAGGAGAAG 58.935 52.381 15.13 0.17 41.86 2.85
145 146 1.964223 AGTCGTTTCTGCAGGAGAAGA 59.036 47.619 15.13 2.85 41.86 2.87
146 147 2.029470 AGTCGTTTCTGCAGGAGAAGAG 60.029 50.000 15.13 3.67 41.86 2.85
147 148 1.273606 TCGTTTCTGCAGGAGAAGAGG 59.726 52.381 15.13 0.00 41.86 3.69
148 149 1.273606 CGTTTCTGCAGGAGAAGAGGA 59.726 52.381 15.13 0.00 41.86 3.71
149 150 2.673610 CGTTTCTGCAGGAGAAGAGGAG 60.674 54.545 15.13 0.00 41.86 3.69
150 151 1.566211 TTCTGCAGGAGAAGAGGAGG 58.434 55.000 15.13 0.00 35.64 4.30
151 152 0.707024 TCTGCAGGAGAAGAGGAGGA 59.293 55.000 15.13 0.00 0.00 3.71
152 153 1.113788 CTGCAGGAGAAGAGGAGGAG 58.886 60.000 5.57 0.00 0.00 3.69
153 154 0.325110 TGCAGGAGAAGAGGAGGAGG 60.325 60.000 0.00 0.00 0.00 4.30
154 155 0.032615 GCAGGAGAAGAGGAGGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
155 156 1.775385 CAGGAGAAGAGGAGGAGGAC 58.225 60.000 0.00 0.00 0.00 3.85
156 157 1.287739 CAGGAGAAGAGGAGGAGGACT 59.712 57.143 0.00 0.00 0.00 3.85
157 158 1.569072 AGGAGAAGAGGAGGAGGACTC 59.431 57.143 0.00 0.00 45.84 3.36
165 166 2.185238 GAGGAGGACTCAGGACACG 58.815 63.158 1.32 0.00 45.85 4.49
166 167 1.939769 GAGGAGGACTCAGGACACGC 61.940 65.000 1.32 0.00 45.85 5.34
167 168 2.179517 GAGGACTCAGGACACGCG 59.820 66.667 3.53 3.53 0.00 6.01
168 169 3.343788 GAGGACTCAGGACACGCGG 62.344 68.421 12.47 1.27 0.00 6.46
169 170 4.436998 GGACTCAGGACACGCGGG 62.437 72.222 6.92 6.92 0.00 6.13
170 171 4.436998 GACTCAGGACACGCGGGG 62.437 72.222 15.46 5.78 0.00 5.73
182 183 3.347168 GCGGGGCGTACAAGTTTT 58.653 55.556 0.00 0.00 0.00 2.43
183 184 2.542432 GCGGGGCGTACAAGTTTTA 58.458 52.632 0.00 0.00 0.00 1.52
184 185 0.166597 GCGGGGCGTACAAGTTTTAC 59.833 55.000 0.00 0.00 0.00 2.01
185 186 1.510776 CGGGGCGTACAAGTTTTACA 58.489 50.000 0.45 0.00 0.00 2.41
186 187 2.078392 CGGGGCGTACAAGTTTTACAT 58.922 47.619 0.45 0.00 0.00 2.29
187 188 3.260740 CGGGGCGTACAAGTTTTACATA 58.739 45.455 0.45 0.00 0.00 2.29
188 189 3.062504 CGGGGCGTACAAGTTTTACATAC 59.937 47.826 0.45 0.00 0.00 2.39
189 190 3.062504 GGGGCGTACAAGTTTTACATACG 59.937 47.826 0.45 0.00 41.13 3.06
192 193 3.903259 CGTACAAGTTTTACATACGCGG 58.097 45.455 12.47 0.00 33.08 6.46
193 194 3.607641 CGTACAAGTTTTACATACGCGGA 59.392 43.478 12.47 0.00 33.08 5.54
194 195 4.259135 CGTACAAGTTTTACATACGCGGAG 60.259 45.833 12.47 1.42 33.08 4.63
195 196 3.656559 ACAAGTTTTACATACGCGGAGT 58.343 40.909 12.47 8.42 0.00 3.85
206 207 1.349627 CGCGGAGTGATGAATGTGC 59.650 57.895 0.00 0.00 43.07 4.57
209 210 2.279741 GCGGAGTGATGAATGTGCTTA 58.720 47.619 0.00 0.00 0.00 3.09
212 213 3.242543 CGGAGTGATGAATGTGCTTAAGC 60.243 47.826 20.84 20.84 42.50 3.09
247 248 4.395959 AGGCGAGTAAATACGGAAATGA 57.604 40.909 0.00 0.00 0.00 2.57
249 250 4.750098 AGGCGAGTAAATACGGAAATGATG 59.250 41.667 0.00 0.00 0.00 3.07
251 252 4.084013 GCGAGTAAATACGGAAATGATGGG 60.084 45.833 0.00 0.00 0.00 4.00
252 253 4.451096 CGAGTAAATACGGAAATGATGGGG 59.549 45.833 0.00 0.00 0.00 4.96
254 255 5.374071 AGTAAATACGGAAATGATGGGGTC 58.626 41.667 0.00 0.00 0.00 4.46
255 256 2.951229 ATACGGAAATGATGGGGTCC 57.049 50.000 0.00 0.00 0.00 4.46
256 257 1.887797 TACGGAAATGATGGGGTCCT 58.112 50.000 0.00 0.00 0.00 3.85
257 258 0.999712 ACGGAAATGATGGGGTCCTT 59.000 50.000 0.00 0.00 0.00 3.36
258 259 1.340991 ACGGAAATGATGGGGTCCTTG 60.341 52.381 0.00 0.00 0.00 3.61
259 260 1.340991 CGGAAATGATGGGGTCCTTGT 60.341 52.381 0.00 0.00 0.00 3.16
260 261 2.102578 GGAAATGATGGGGTCCTTGTG 58.897 52.381 0.00 0.00 0.00 3.33
261 262 2.102578 GAAATGATGGGGTCCTTGTGG 58.897 52.381 0.00 0.00 0.00 4.17
262 263 0.324645 AATGATGGGGTCCTTGTGGC 60.325 55.000 0.00 0.00 0.00 5.01
263 264 2.043953 GATGGGGTCCTTGTGGCC 60.044 66.667 0.00 0.00 0.00 5.36
264 265 3.662117 GATGGGGTCCTTGTGGCCC 62.662 68.421 0.00 0.00 44.09 5.80
266 267 3.909651 GGGGTCCTTGTGGCCCAA 61.910 66.667 0.00 3.07 45.55 4.12
275 276 0.251165 TTGTGGCCCAAGCTAGTTCC 60.251 55.000 0.00 0.00 39.73 3.62
350 351 2.203625 GCCCCTGCCTGGACAAAA 60.204 61.111 0.00 0.00 38.35 2.44
424 426 3.489738 GGGTGGAGAAATCATTCGCATTG 60.490 47.826 0.00 0.00 40.63 2.82
505 546 2.161486 CCTGCAGCTTCTACGCGTC 61.161 63.158 18.63 0.00 34.40 5.19
619 669 4.090588 CAGGGCCGGCGTAAGGAA 62.091 66.667 22.54 0.00 38.28 3.36
675 726 3.522731 CAGACCTCTCCTCGCCCG 61.523 72.222 0.00 0.00 0.00 6.13
714 767 3.173965 TCCCTCTTCATTTCTTCCGTCT 58.826 45.455 0.00 0.00 0.00 4.18
715 768 3.195825 TCCCTCTTCATTTCTTCCGTCTC 59.804 47.826 0.00 0.00 0.00 3.36
743 796 0.250295 TGCCACTCGTTTTCTCTGGG 60.250 55.000 0.00 0.00 0.00 4.45
792 846 2.004017 TGGTGGTTCATACGAAATCGC 58.996 47.619 2.15 0.00 44.43 4.58
839 893 7.637709 AGTGTTTTGAGTTTTGAGTTTTGAC 57.362 32.000 0.00 0.00 0.00 3.18
1110 1211 4.115199 GGCTCCGGGGTCAGCAAT 62.115 66.667 14.20 0.00 37.38 3.56
1130 1238 5.163488 GCAATCAAATCATCCATCACCTTGA 60.163 40.000 0.00 0.00 0.00 3.02
1131 1239 6.270815 CAATCAAATCATCCATCACCTTGAC 58.729 40.000 0.00 0.00 0.00 3.18
1133 1241 5.573219 TCAAATCATCCATCACCTTGACTT 58.427 37.500 0.00 0.00 0.00 3.01
1134 1242 6.720309 TCAAATCATCCATCACCTTGACTTA 58.280 36.000 0.00 0.00 0.00 2.24
1137 1245 9.123902 CAAATCATCCATCACCTTGACTTATTA 57.876 33.333 0.00 0.00 0.00 0.98
1138 1246 9.699410 AAATCATCCATCACCTTGACTTATTAA 57.301 29.630 0.00 0.00 0.00 1.40
1153 1544 8.851541 TGACTTATTAACTTGTTAATTCCCGT 57.148 30.769 19.61 13.01 0.00 5.28
1172 1563 4.021631 CGGCTGCTGTGCTGTGTG 62.022 66.667 0.00 0.00 34.82 3.82
1173 1564 4.338539 GGCTGCTGTGCTGTGTGC 62.339 66.667 0.00 0.00 43.25 4.57
1179 1570 1.820906 CTGTGCTGTGTGCCTGTGT 60.821 57.895 0.00 0.00 42.00 3.72
1187 1578 1.221414 GTGTGCCTGTGTCTGACTTC 58.779 55.000 9.51 3.30 0.00 3.01
1198 1590 1.134788 GTCTGACTTCCGTATGTGGGG 60.135 57.143 0.00 0.00 0.00 4.96
1199 1591 0.902531 CTGACTTCCGTATGTGGGGT 59.097 55.000 0.00 0.00 0.00 4.95
1200 1592 0.611200 TGACTTCCGTATGTGGGGTG 59.389 55.000 0.00 0.00 0.00 4.61
1201 1593 0.107848 GACTTCCGTATGTGGGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
1202 1594 1.223487 CTTCCGTATGTGGGGTGGG 59.777 63.158 0.00 0.00 0.00 4.61
1307 1700 1.734748 GCCGCTCTACACCTACTCC 59.265 63.158 0.00 0.00 0.00 3.85
1723 2521 3.058914 ACGTACATTCAGCAACTTCAAGC 60.059 43.478 0.00 0.00 0.00 4.01
1728 2526 4.202182 ACATTCAGCAACTTCAAGCACATT 60.202 37.500 0.00 0.00 0.00 2.71
1731 2529 4.136796 TCAGCAACTTCAAGCACATTACT 58.863 39.130 0.00 0.00 0.00 2.24
1738 2536 7.534239 GCAACTTCAAGCACATTACTAGTTTAC 59.466 37.037 0.00 0.00 0.00 2.01
1865 2675 4.083217 TGACCCAATGTACGTATGTTTTGC 60.083 41.667 0.00 0.00 0.00 3.68
2141 3269 2.754552 CAACCCCATGTACATTGTGGAG 59.245 50.000 14.39 4.92 34.94 3.86
2145 3273 3.194861 CCCATGTACATTGTGGAGTACG 58.805 50.000 14.39 0.00 42.62 3.67
2259 3470 6.606768 CATGCCTTTCTTTCTTTCTACTGAC 58.393 40.000 0.00 0.00 0.00 3.51
2275 3486 3.016736 ACTGACCATTTATTTCCCTGCG 58.983 45.455 0.00 0.00 0.00 5.18
2276 3487 1.748493 TGACCATTTATTTCCCTGCGC 59.252 47.619 0.00 0.00 0.00 6.09
2277 3488 1.748493 GACCATTTATTTCCCTGCGCA 59.252 47.619 10.98 10.98 0.00 6.09
2278 3489 2.165437 GACCATTTATTTCCCTGCGCAA 59.835 45.455 13.05 0.00 0.00 4.85
2279 3490 2.094234 ACCATTTATTTCCCTGCGCAAC 60.094 45.455 13.05 0.00 0.00 4.17
2280 3491 2.184448 CATTTATTTCCCTGCGCAACG 58.816 47.619 13.05 3.96 0.00 4.10
2281 3492 1.240256 TTTATTTCCCTGCGCAACGT 58.760 45.000 13.05 0.00 0.00 3.99
2282 3493 2.096220 TTATTTCCCTGCGCAACGTA 57.904 45.000 13.05 0.00 0.00 3.57
2283 3494 1.361793 TATTTCCCTGCGCAACGTAC 58.638 50.000 13.05 0.00 0.00 3.67
2284 3495 1.632046 ATTTCCCTGCGCAACGTACG 61.632 55.000 13.05 15.01 0.00 3.67
2285 3496 2.974935 TTTCCCTGCGCAACGTACGT 62.975 55.000 16.72 16.72 0.00 3.57
2286 3497 2.126385 CCCTGCGCAACGTACGTA 60.126 61.111 23.12 4.28 0.00 3.57
2287 3498 2.438954 CCCTGCGCAACGTACGTAC 61.439 63.158 23.12 15.90 0.00 3.67
2385 3600 7.012894 CACTACCAGTTTTTCACTCCATTTGTA 59.987 37.037 0.00 0.00 30.92 2.41
2387 3602 5.068591 ACCAGTTTTTCACTCCATTTGTACC 59.931 40.000 0.00 0.00 30.92 3.34
2396 3611 5.882000 TCACTCCATTTGTACCATTGATCTG 59.118 40.000 0.00 0.00 0.00 2.90
2397 3612 5.649395 CACTCCATTTGTACCATTGATCTGT 59.351 40.000 0.00 0.00 0.00 3.41
2398 3613 6.823182 CACTCCATTTGTACCATTGATCTGTA 59.177 38.462 0.00 0.00 0.00 2.74
2551 3792 1.069159 CGTTAGTCTCTGCGTCTGTGT 60.069 52.381 0.00 0.00 0.00 3.72
2651 3927 1.004080 CCATCAGCCATCGCCTAGG 60.004 63.158 3.67 3.67 34.57 3.02
3187 4495 1.133761 TCCTAGCTACGCCACTGATCT 60.134 52.381 0.00 0.00 0.00 2.75
3188 4496 1.000827 CCTAGCTACGCCACTGATCTG 60.001 57.143 0.00 0.00 0.00 2.90
3189 4497 1.678627 CTAGCTACGCCACTGATCTGT 59.321 52.381 0.00 0.00 0.00 3.41
3190 4498 1.763968 AGCTACGCCACTGATCTGTA 58.236 50.000 4.78 0.00 0.00 2.74
3191 4499 1.678627 AGCTACGCCACTGATCTGTAG 59.321 52.381 4.78 0.00 36.47 2.74
3192 4500 1.405821 GCTACGCCACTGATCTGTAGT 59.594 52.381 4.78 8.49 35.94 2.73
3193 4501 2.617308 GCTACGCCACTGATCTGTAGTA 59.383 50.000 4.78 9.10 35.94 1.82
3219 4538 9.409918 ACTAGTACATTAGTAATTCAGAGCAGA 57.590 33.333 0.00 0.00 32.25 4.26
3257 4582 1.000385 TCTTCATTTTGCGGCCTGTTG 60.000 47.619 0.00 0.00 0.00 3.33
3345 4672 4.874534 CTGCACAAATTCCCGCAG 57.125 55.556 8.11 8.11 45.17 5.18
4143 5567 3.737172 GCCGAGCACCGCATGTTT 61.737 61.111 0.00 0.00 36.84 2.83
4438 5892 0.963962 GAGGGTCGTGGTCAACTACA 59.036 55.000 0.00 0.00 0.00 2.74
4497 5951 3.439540 GCGCTCGCCATTCCCAAA 61.440 61.111 0.00 0.00 34.56 3.28
4511 5965 1.065636 TCCCAAAGATCAGCTGCTCAG 60.066 52.381 19.13 8.64 0.00 3.35
4605 6073 5.581605 TCTTTTGCAGAACTTGTTGATGAC 58.418 37.500 0.00 0.00 0.00 3.06
4620 6088 7.640616 TGTTGATGACGACGACTTATTTTTA 57.359 32.000 0.00 0.00 33.40 1.52
4621 6089 7.726079 TGTTGATGACGACGACTTATTTTTAG 58.274 34.615 0.00 0.00 33.40 1.85
4622 6090 6.327177 TGATGACGACGACTTATTTTTAGC 57.673 37.500 0.00 0.00 0.00 3.09
4623 6091 5.865013 TGATGACGACGACTTATTTTTAGCA 59.135 36.000 0.00 0.00 0.00 3.49
4660 6128 5.239306 CAGTGTAAACCTCTGAATTCTGCAA 59.761 40.000 7.05 0.00 0.00 4.08
4686 6158 1.679680 GGATGATCCTGTGCACCAATG 59.320 52.381 15.69 1.80 32.53 2.82
4758 6230 2.270434 AGGAAGGGTGAATAGCTCCA 57.730 50.000 0.00 0.00 31.65 3.86
4851 6332 6.546034 GGCAACAATAGTTCCTATGTAACCAT 59.454 38.462 0.00 0.00 35.28 3.55
4855 6336 8.562949 ACAATAGTTCCTATGTAACCATACCT 57.437 34.615 0.00 0.00 32.29 3.08
4860 6342 8.159229 AGTTCCTATGTAACCATACCTTCTTT 57.841 34.615 0.00 0.00 32.29 2.52
4862 6344 9.895138 GTTCCTATGTAACCATACCTTCTTTAA 57.105 33.333 0.00 0.00 32.29 1.52
4924 6411 4.767255 CCACCTCACCTCAGCGCC 62.767 72.222 2.29 0.00 0.00 6.53
4998 6485 2.866762 CGTAAGCCATTACAAGAGGAGC 59.133 50.000 0.00 0.00 41.22 4.70
5040 6556 2.285024 GCCATTGCCCTTGCCTGAA 61.285 57.895 0.00 0.00 36.33 3.02
5132 6648 2.548057 CGAGAGATGTCTAGCTCCAGTC 59.452 54.545 0.00 0.00 40.18 3.51
5172 6688 2.584608 GCGGTATGGTCCAGTGCT 59.415 61.111 0.00 0.00 0.00 4.40
5221 6737 1.600916 GGAGCCACTGAAGCGGTTT 60.601 57.895 0.00 0.00 34.64 3.27
5249 6765 1.425066 TGAAGGAAGACCATGGCAACT 59.575 47.619 13.04 6.25 38.94 3.16
5289 6805 2.031012 CGAGAGCAGGCCACAACA 59.969 61.111 5.01 0.00 0.00 3.33
5304 6820 1.710809 ACAACAGGGGCAGGTTAGATT 59.289 47.619 0.00 0.00 0.00 2.40
5314 6830 4.162509 GGGCAGGTTAGATTTGAGTACTCT 59.837 45.833 23.01 3.50 0.00 3.24
5317 6833 6.166982 GCAGGTTAGATTTGAGTACTCTGTT 58.833 40.000 23.01 7.94 0.00 3.16
5320 6836 5.351740 GGTTAGATTTGAGTACTCTGTTGGC 59.648 44.000 23.01 8.33 0.00 4.52
5355 6871 7.370383 TGATTTCTCCCGATTTCTTTCTTTTG 58.630 34.615 0.00 0.00 0.00 2.44
5386 6905 9.135189 CATTGAATTTGGAATCTAGGGTTCATA 57.865 33.333 9.86 0.00 0.00 2.15
5408 6935 1.574428 CGCCGTTTTCAGGTTCTGG 59.426 57.895 0.00 0.00 31.51 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.468226 TCCTTTCAGACACTTGCCGT 59.532 50.000 0.00 0.00 0.00 5.68
2 3 0.868406 GTCCTTTCAGACACTTGCCG 59.132 55.000 0.00 0.00 36.73 5.69
4 5 1.261619 CACGTCCTTTCAGACACTTGC 59.738 52.381 0.00 0.00 36.52 4.01
6 7 2.483188 GGACACGTCCTTTCAGACACTT 60.483 50.000 9.04 0.00 46.16 3.16
7 8 1.068741 GGACACGTCCTTTCAGACACT 59.931 52.381 9.04 0.00 46.16 3.55
8 9 1.499049 GGACACGTCCTTTCAGACAC 58.501 55.000 9.04 0.00 46.16 3.67
9 10 3.980583 GGACACGTCCTTTCAGACA 57.019 52.632 9.04 0.00 46.16 3.41
19 20 2.746277 GCACCCCATGGACACGTC 60.746 66.667 15.22 0.00 34.81 4.34
20 21 4.344865 GGCACCCCATGGACACGT 62.345 66.667 15.22 0.14 34.81 4.49
21 22 4.343323 TGGCACCCCATGGACACG 62.343 66.667 15.22 0.00 35.79 4.49
22 23 2.676471 GTGGCACCCCATGGACAC 60.676 66.667 15.22 10.19 44.51 3.67
23 24 1.210885 TATGTGGCACCCCATGGACA 61.211 55.000 15.22 8.90 44.51 4.02
24 25 0.466189 CTATGTGGCACCCCATGGAC 60.466 60.000 15.22 2.18 44.51 4.02
25 26 1.644437 CCTATGTGGCACCCCATGGA 61.644 60.000 15.22 0.00 44.51 3.41
26 27 1.152694 CCTATGTGGCACCCCATGG 60.153 63.158 16.26 4.14 44.51 3.66
27 28 4.585070 CCTATGTGGCACCCCATG 57.415 61.111 16.26 0.89 44.51 3.66
37 38 2.167219 CAGTCCGCACGCCTATGTG 61.167 63.158 0.00 0.00 42.81 3.21
38 39 1.676678 ATCAGTCCGCACGCCTATGT 61.677 55.000 0.00 0.00 0.00 2.29
39 40 1.068083 ATCAGTCCGCACGCCTATG 59.932 57.895 0.00 0.00 0.00 2.23
40 41 1.068083 CATCAGTCCGCACGCCTAT 59.932 57.895 0.00 0.00 0.00 2.57
41 42 2.049767 TCATCAGTCCGCACGCCTA 61.050 57.895 0.00 0.00 0.00 3.93
42 43 3.381983 TCATCAGTCCGCACGCCT 61.382 61.111 0.00 0.00 0.00 5.52
43 44 3.188786 GTCATCAGTCCGCACGCC 61.189 66.667 0.00 0.00 0.00 5.68
44 45 3.188786 GGTCATCAGTCCGCACGC 61.189 66.667 0.00 0.00 0.00 5.34
45 46 0.740868 AATGGTCATCAGTCCGCACG 60.741 55.000 0.00 0.00 0.00 5.34
46 47 0.729116 CAATGGTCATCAGTCCGCAC 59.271 55.000 0.00 0.00 0.00 5.34
47 48 0.612744 TCAATGGTCATCAGTCCGCA 59.387 50.000 0.00 0.00 0.00 5.69
48 49 1.009829 GTCAATGGTCATCAGTCCGC 58.990 55.000 0.00 0.00 0.00 5.54
49 50 1.280982 CGTCAATGGTCATCAGTCCG 58.719 55.000 0.00 0.00 0.00 4.79
50 51 1.066143 ACCGTCAATGGTCATCAGTCC 60.066 52.381 0.00 0.00 37.91 3.85
51 52 2.386661 ACCGTCAATGGTCATCAGTC 57.613 50.000 0.00 0.00 37.91 3.51
60 61 1.076533 CCGTCTTCGACCGTCAATGG 61.077 60.000 0.00 0.00 39.71 3.16
61 62 1.683790 GCCGTCTTCGACCGTCAATG 61.684 60.000 0.00 0.00 39.71 2.82
62 63 1.445582 GCCGTCTTCGACCGTCAAT 60.446 57.895 0.00 0.00 39.71 2.57
63 64 2.049802 GCCGTCTTCGACCGTCAA 60.050 61.111 0.00 0.00 39.71 3.18
64 65 2.847754 TTGCCGTCTTCGACCGTCA 61.848 57.895 0.00 0.00 39.71 4.35
65 66 2.049802 TTGCCGTCTTCGACCGTC 60.050 61.111 0.00 0.00 39.71 4.79
66 67 2.355481 GTTGCCGTCTTCGACCGT 60.355 61.111 0.00 0.00 39.71 4.83
67 68 3.110178 GGTTGCCGTCTTCGACCG 61.110 66.667 0.00 0.00 39.71 4.79
68 69 3.110178 CGGTTGCCGTCTTCGACC 61.110 66.667 0.00 0.00 42.73 4.79
69 70 3.110178 CCGGTTGCCGTCTTCGAC 61.110 66.667 6.82 0.00 46.80 4.20
72 73 2.668550 AAGCCGGTTGCCGTCTTC 60.669 61.111 1.90 0.00 41.45 2.87
73 74 2.978010 CAAGCCGGTTGCCGTCTT 60.978 61.111 1.90 2.33 46.24 3.01
79 80 4.362476 CAAGCCCAAGCCGGTTGC 62.362 66.667 1.90 0.00 41.25 4.17
80 81 4.362476 GCAAGCCCAAGCCGGTTG 62.362 66.667 1.90 6.55 41.25 3.77
86 87 0.474184 TATAGGAGGCAAGCCCAAGC 59.526 55.000 7.62 0.00 40.32 4.01
87 88 2.050144 TCTATAGGAGGCAAGCCCAAG 58.950 52.381 7.62 0.00 36.58 3.61
88 89 2.190398 TCTATAGGAGGCAAGCCCAA 57.810 50.000 7.62 0.00 36.58 4.12
89 90 2.190398 TTCTATAGGAGGCAAGCCCA 57.810 50.000 7.62 0.00 36.58 5.36
90 91 3.215151 GTTTTCTATAGGAGGCAAGCCC 58.785 50.000 7.62 0.00 36.58 5.19
91 92 2.872858 CGTTTTCTATAGGAGGCAAGCC 59.127 50.000 2.02 2.02 0.00 4.35
92 93 2.288186 GCGTTTTCTATAGGAGGCAAGC 59.712 50.000 0.00 0.00 0.00 4.01
93 94 2.540101 CGCGTTTTCTATAGGAGGCAAG 59.460 50.000 0.00 0.00 0.00 4.01
94 95 2.093869 ACGCGTTTTCTATAGGAGGCAA 60.094 45.455 5.58 0.00 0.00 4.52
95 96 1.479323 ACGCGTTTTCTATAGGAGGCA 59.521 47.619 5.58 0.00 0.00 4.75
96 97 2.125685 GACGCGTTTTCTATAGGAGGC 58.874 52.381 15.53 3.59 0.00 4.70
97 98 3.372954 CAGACGCGTTTTCTATAGGAGG 58.627 50.000 15.53 0.00 0.00 4.30
98 99 3.372954 CCAGACGCGTTTTCTATAGGAG 58.627 50.000 15.53 0.00 0.00 3.69
99 100 2.480759 GCCAGACGCGTTTTCTATAGGA 60.481 50.000 15.53 0.00 0.00 2.94
100 101 1.859080 GCCAGACGCGTTTTCTATAGG 59.141 52.381 15.53 5.08 0.00 2.57
114 115 4.681978 AACGACTGCCCGCCAGAC 62.682 66.667 8.11 1.88 44.64 3.51
115 116 3.876589 GAAACGACTGCCCGCCAGA 62.877 63.158 8.11 0.00 44.64 3.86
117 118 3.936203 AGAAACGACTGCCCGCCA 61.936 61.111 0.00 0.00 0.00 5.69
118 119 3.423154 CAGAAACGACTGCCCGCC 61.423 66.667 0.00 0.00 0.00 6.13
124 125 2.064762 CTTCTCCTGCAGAAACGACTG 58.935 52.381 17.39 0.00 40.83 3.51
125 126 1.964223 TCTTCTCCTGCAGAAACGACT 59.036 47.619 17.39 0.00 40.83 4.18
126 127 2.333014 CTCTTCTCCTGCAGAAACGAC 58.667 52.381 17.39 0.00 40.83 4.34
127 128 1.273606 CCTCTTCTCCTGCAGAAACGA 59.726 52.381 17.39 2.35 40.83 3.85
128 129 1.273606 TCCTCTTCTCCTGCAGAAACG 59.726 52.381 17.39 0.00 40.83 3.60
129 130 2.354604 CCTCCTCTTCTCCTGCAGAAAC 60.355 54.545 17.39 0.00 40.83 2.78
130 131 1.905215 CCTCCTCTTCTCCTGCAGAAA 59.095 52.381 17.39 5.64 40.83 2.52
131 132 1.077828 TCCTCCTCTTCTCCTGCAGAA 59.922 52.381 17.39 0.22 38.95 3.02
132 133 0.707024 TCCTCCTCTTCTCCTGCAGA 59.293 55.000 17.39 0.00 0.00 4.26
133 134 1.113788 CTCCTCCTCTTCTCCTGCAG 58.886 60.000 6.78 6.78 0.00 4.41
134 135 0.325110 CCTCCTCCTCTTCTCCTGCA 60.325 60.000 0.00 0.00 0.00 4.41
135 136 0.032615 TCCTCCTCCTCTTCTCCTGC 60.033 60.000 0.00 0.00 0.00 4.85
136 137 1.287739 AGTCCTCCTCCTCTTCTCCTG 59.712 57.143 0.00 0.00 0.00 3.86
137 138 1.569072 GAGTCCTCCTCCTCTTCTCCT 59.431 57.143 0.00 0.00 33.79 3.69
138 139 1.286553 TGAGTCCTCCTCCTCTTCTCC 59.713 57.143 0.00 0.00 39.65 3.71
139 140 2.654863 CTGAGTCCTCCTCCTCTTCTC 58.345 57.143 0.00 0.00 39.65 2.87
140 141 1.287739 CCTGAGTCCTCCTCCTCTTCT 59.712 57.143 0.00 0.00 39.65 2.85
141 142 1.286553 TCCTGAGTCCTCCTCCTCTTC 59.713 57.143 0.00 0.00 39.65 2.87
142 143 1.006639 GTCCTGAGTCCTCCTCCTCTT 59.993 57.143 0.00 0.00 39.65 2.85
143 144 0.629058 GTCCTGAGTCCTCCTCCTCT 59.371 60.000 0.00 0.00 39.65 3.69
144 145 0.333312 TGTCCTGAGTCCTCCTCCTC 59.667 60.000 0.00 0.00 39.65 3.71
145 146 0.040499 GTGTCCTGAGTCCTCCTCCT 59.960 60.000 0.00 0.00 39.65 3.69
146 147 1.316706 CGTGTCCTGAGTCCTCCTCC 61.317 65.000 0.00 0.00 39.65 4.30
147 148 1.939769 GCGTGTCCTGAGTCCTCCTC 61.940 65.000 0.00 0.00 40.89 3.71
148 149 1.979693 GCGTGTCCTGAGTCCTCCT 60.980 63.158 0.00 0.00 0.00 3.69
149 150 2.574399 GCGTGTCCTGAGTCCTCC 59.426 66.667 0.00 0.00 0.00 4.30
150 151 2.179517 CGCGTGTCCTGAGTCCTC 59.820 66.667 0.00 0.00 0.00 3.71
151 152 3.374402 CCGCGTGTCCTGAGTCCT 61.374 66.667 4.92 0.00 0.00 3.85
152 153 4.436998 CCCGCGTGTCCTGAGTCC 62.437 72.222 4.92 0.00 0.00 3.85
153 154 4.436998 CCCCGCGTGTCCTGAGTC 62.437 72.222 4.92 0.00 0.00 3.36
165 166 0.166597 GTAAAACTTGTACGCCCCGC 59.833 55.000 0.00 0.00 0.00 6.13
166 167 1.510776 TGTAAAACTTGTACGCCCCG 58.489 50.000 0.00 0.00 0.00 5.73
167 168 3.062504 CGTATGTAAAACTTGTACGCCCC 59.937 47.826 0.00 0.00 32.93 5.80
168 169 4.249181 CGTATGTAAAACTTGTACGCCC 57.751 45.455 0.00 0.00 32.93 6.13
171 172 3.607641 TCCGCGTATGTAAAACTTGTACG 59.392 43.478 4.92 0.00 40.59 3.67
172 173 4.622740 ACTCCGCGTATGTAAAACTTGTAC 59.377 41.667 4.92 0.00 0.00 2.90
173 174 4.622313 CACTCCGCGTATGTAAAACTTGTA 59.378 41.667 4.92 0.00 0.00 2.41
174 175 3.430895 CACTCCGCGTATGTAAAACTTGT 59.569 43.478 4.92 0.00 0.00 3.16
175 176 3.676172 TCACTCCGCGTATGTAAAACTTG 59.324 43.478 4.92 0.00 0.00 3.16
176 177 3.916761 TCACTCCGCGTATGTAAAACTT 58.083 40.909 4.92 0.00 0.00 2.66
177 178 3.581024 TCACTCCGCGTATGTAAAACT 57.419 42.857 4.92 0.00 0.00 2.66
178 179 3.861113 TCATCACTCCGCGTATGTAAAAC 59.139 43.478 4.92 0.00 0.00 2.43
179 180 4.112716 TCATCACTCCGCGTATGTAAAA 57.887 40.909 4.92 0.00 0.00 1.52
180 181 3.786516 TCATCACTCCGCGTATGTAAA 57.213 42.857 4.92 0.00 0.00 2.01
181 182 3.786516 TTCATCACTCCGCGTATGTAA 57.213 42.857 4.92 0.00 0.00 2.41
182 183 3.067601 ACATTCATCACTCCGCGTATGTA 59.932 43.478 4.92 0.00 0.00 2.29
183 184 2.159099 ACATTCATCACTCCGCGTATGT 60.159 45.455 4.92 0.00 0.00 2.29
184 185 2.219445 CACATTCATCACTCCGCGTATG 59.781 50.000 4.92 0.00 0.00 2.39
185 186 2.473816 CACATTCATCACTCCGCGTAT 58.526 47.619 4.92 0.00 0.00 3.06
186 187 1.921243 CACATTCATCACTCCGCGTA 58.079 50.000 4.92 0.00 0.00 4.42
187 188 1.361668 GCACATTCATCACTCCGCGT 61.362 55.000 4.92 0.00 0.00 6.01
188 189 1.086067 AGCACATTCATCACTCCGCG 61.086 55.000 0.00 0.00 0.00 6.46
189 190 1.089920 AAGCACATTCATCACTCCGC 58.910 50.000 0.00 0.00 0.00 5.54
190 191 3.242543 GCTTAAGCACATTCATCACTCCG 60.243 47.826 22.59 0.00 41.59 4.63
191 192 3.242543 CGCTTAAGCACATTCATCACTCC 60.243 47.826 26.29 0.00 42.21 3.85
192 193 3.786818 GCGCTTAAGCACATTCATCACTC 60.787 47.826 26.29 0.00 42.21 3.51
193 194 2.096496 GCGCTTAAGCACATTCATCACT 59.904 45.455 26.29 0.00 42.21 3.41
194 195 2.159531 TGCGCTTAAGCACATTCATCAC 60.160 45.455 26.29 3.75 42.92 3.06
195 196 2.083002 TGCGCTTAAGCACATTCATCA 58.917 42.857 26.29 8.08 42.92 3.07
206 207 3.066760 CCTTCCCCTATTTTGCGCTTAAG 59.933 47.826 9.73 0.00 0.00 1.85
209 210 1.474330 CCTTCCCCTATTTTGCGCTT 58.526 50.000 9.73 0.00 0.00 4.68
212 213 0.746563 TCGCCTTCCCCTATTTTGCG 60.747 55.000 0.00 0.00 41.68 4.85
221 222 1.539712 CCGTATTTACTCGCCTTCCCC 60.540 57.143 0.00 0.00 0.00 4.81
256 257 0.251165 GGAACTAGCTTGGGCCACAA 60.251 55.000 5.23 5.72 39.73 3.33
257 258 1.378762 GGAACTAGCTTGGGCCACA 59.621 57.895 5.23 0.00 39.73 4.17
258 259 0.678048 CTGGAACTAGCTTGGGCCAC 60.678 60.000 5.23 0.00 39.73 5.01
259 260 1.133809 ACTGGAACTAGCTTGGGCCA 61.134 55.000 0.00 0.00 39.73 5.36
260 261 0.678048 CACTGGAACTAGCTTGGGCC 60.678 60.000 0.00 0.00 39.73 5.80
261 262 1.308783 GCACTGGAACTAGCTTGGGC 61.309 60.000 0.00 0.00 39.06 5.36
262 263 0.036732 TGCACTGGAACTAGCTTGGG 59.963 55.000 0.00 0.00 0.00 4.12
263 264 1.160137 GTGCACTGGAACTAGCTTGG 58.840 55.000 10.32 0.00 0.00 3.61
264 265 1.160137 GGTGCACTGGAACTAGCTTG 58.840 55.000 17.98 0.00 0.00 4.01
265 266 0.320771 CGGTGCACTGGAACTAGCTT 60.321 55.000 18.43 0.00 0.00 3.74
266 267 1.293498 CGGTGCACTGGAACTAGCT 59.707 57.895 18.43 0.00 0.00 3.32
267 268 2.391389 GCGGTGCACTGGAACTAGC 61.391 63.158 26.55 10.68 0.00 3.42
347 348 2.034001 CGCGTTCGTCTCTTTCTGTTTT 60.034 45.455 0.00 0.00 0.00 2.43
350 351 0.663568 CCGCGTTCGTCTCTTTCTGT 60.664 55.000 4.92 0.00 0.00 3.41
492 533 2.254703 CTGACGGACGCGTAGAAGCT 62.255 60.000 13.97 0.00 34.40 3.74
495 536 1.499056 GTCTGACGGACGCGTAGAA 59.501 57.895 13.97 3.09 35.07 2.10
505 546 1.107114 ATACAGGCAGAGTCTGACGG 58.893 55.000 22.88 22.88 45.59 4.79
551 592 1.738432 GACGACGGATCCCTTACCC 59.262 63.158 6.06 0.00 0.00 3.69
552 593 1.358046 CGACGACGGATCCCTTACC 59.642 63.158 6.06 0.00 35.72 2.85
554 595 0.107508 AGACGACGACGGATCCCTTA 60.108 55.000 12.58 0.00 44.46 2.69
647 697 2.106566 GAGAGGTCTGATCTGAGGCAA 58.893 52.381 2.02 0.00 0.00 4.52
675 726 0.179108 GATAGATCATACCGGCCGGC 60.179 60.000 43.58 25.95 39.32 6.13
714 767 0.832135 ACGAGTGGCAAGGAGAAGGA 60.832 55.000 0.00 0.00 0.00 3.36
715 768 0.035458 AACGAGTGGCAAGGAGAAGG 59.965 55.000 0.00 0.00 0.00 3.46
743 796 1.068816 CCGGACAAAATCGTGGGAAAC 60.069 52.381 0.00 0.00 0.00 2.78
792 846 0.109319 CAAACCGGAATTCGCAAGGG 60.109 55.000 9.46 0.00 37.59 3.95
839 893 3.754965 TCCACAACAGATCCTCCAAAAG 58.245 45.455 0.00 0.00 0.00 2.27
888 969 6.988622 TCTGGTTTTTGAAGACTTTACGAA 57.011 33.333 0.00 0.00 0.00 3.85
1110 1211 5.183530 AGTCAAGGTGATGGATGATTTGA 57.816 39.130 0.00 0.00 0.00 2.69
1130 1238 7.064966 CGGACGGGAATTAACAAGTTAATAAGT 59.935 37.037 16.13 13.39 42.91 2.24
1131 1239 7.404203 CGGACGGGAATTAACAAGTTAATAAG 58.596 38.462 16.13 11.10 42.91 1.73
1133 1241 5.816777 CCGGACGGGAATTAACAAGTTAATA 59.183 40.000 16.13 0.00 42.91 0.98
1134 1242 4.637091 CCGGACGGGAATTAACAAGTTAAT 59.363 41.667 11.38 11.38 44.89 1.40
1137 1245 2.429478 CCGGACGGGAATTAACAAGTT 58.571 47.619 0.00 0.00 38.47 2.66
1138 1246 1.947212 GCCGGACGGGAATTAACAAGT 60.947 52.381 5.05 0.00 38.47 3.16
1153 1544 4.994471 CACAGCACAGCAGCCGGA 62.994 66.667 5.05 0.00 34.23 5.14
1172 1563 1.367840 ACGGAAGTCAGACACAGGC 59.632 57.895 2.66 0.00 44.19 4.85
1187 1578 3.804329 CCCCCACCCCACATACGG 61.804 72.222 0.00 0.00 0.00 4.02
1526 2098 1.833630 TCCTGGATGCTGTAGTTGGAG 59.166 52.381 0.00 0.00 0.00 3.86
1781 2582 1.111116 ACTGCAGCAACACAGCCATT 61.111 50.000 15.27 0.00 37.42 3.16
1865 2675 7.316640 ACAGCTCTTGACAATTAGTAGTAGTG 58.683 38.462 0.00 0.00 0.00 2.74
1910 2925 8.458052 ACATACATACATACAACAAACCACATG 58.542 33.333 0.00 0.00 0.00 3.21
2259 3470 2.539476 GTTGCGCAGGGAAATAAATGG 58.461 47.619 11.31 0.00 0.00 3.16
2280 3491 4.686745 GCCTGCAGGAGTACGTACGTAC 62.687 59.091 38.76 38.76 42.17 3.67
2281 3492 1.372582 CCTGCAGGAGTACGTACGTA 58.627 55.000 29.88 23.60 37.39 3.57
2282 3493 1.930908 GCCTGCAGGAGTACGTACGT 61.931 60.000 37.21 25.98 37.39 3.57
2283 3494 1.226603 GCCTGCAGGAGTACGTACG 60.227 63.158 37.21 15.01 37.39 3.67
2284 3495 0.458025 GTGCCTGCAGGAGTACGTAC 60.458 60.000 37.21 18.10 37.39 3.67
2285 3496 1.888018 GTGCCTGCAGGAGTACGTA 59.112 57.895 37.21 9.44 37.39 3.57
2286 3497 2.657237 GTGCCTGCAGGAGTACGT 59.343 61.111 37.21 0.00 37.39 3.57
2287 3498 2.507102 CGTGCCTGCAGGAGTACG 60.507 66.667 37.21 32.71 37.39 3.67
2288 3499 2.125512 CCGTGCCTGCAGGAGTAC 60.126 66.667 37.21 26.72 37.39 2.73
2289 3500 2.283604 TCCGTGCCTGCAGGAGTA 60.284 61.111 37.21 18.37 37.39 2.59
2290 3501 3.699894 CTCCGTGCCTGCAGGAGT 61.700 66.667 37.21 0.00 44.79 3.85
2385 3600 2.681976 GCCACTGCTACAGATCAATGGT 60.682 50.000 0.78 0.00 35.18 3.55
2387 3602 1.596260 CGCCACTGCTACAGATCAATG 59.404 52.381 0.78 0.00 35.18 2.82
2396 3611 1.519455 CCAGCTACGCCACTGCTAC 60.519 63.158 0.00 0.00 35.05 3.58
2397 3612 1.667154 CTCCAGCTACGCCACTGCTA 61.667 60.000 0.00 0.00 35.05 3.49
2398 3613 2.997315 TCCAGCTACGCCACTGCT 60.997 61.111 0.00 0.00 37.56 4.24
2551 3792 1.472480 TCTCGTGTCGATCAATCAGCA 59.528 47.619 0.00 0.00 34.61 4.41
3084 4379 8.158169 ACCAACATATGCATACAGAAATACAG 57.842 34.615 8.99 0.00 0.00 2.74
3086 4381 9.236691 CAAACCAACATATGCATACAGAAATAC 57.763 33.333 8.99 0.00 0.00 1.89
3088 4383 7.839907 ACAAACCAACATATGCATACAGAAAT 58.160 30.769 8.99 0.00 0.00 2.17
3193 4501 9.409918 TCTGCTCTGAATTACTAATGTACTAGT 57.590 33.333 0.00 0.00 36.16 2.57
3208 4527 3.047115 AGTCCATGGATCTGCTCTGAAT 58.953 45.455 19.62 0.00 0.00 2.57
3219 4538 7.729124 ATGAAGAAAAATTCAGTCCATGGAT 57.271 32.000 19.62 4.19 42.20 3.41
3345 4672 2.431942 AATGTGTCGCCGACGTCC 60.432 61.111 13.18 3.66 41.18 4.79
3585 5009 1.218316 GAAGGCGAGGGTGACGATT 59.782 57.895 0.00 0.00 0.00 3.34
4020 5444 1.723870 GTGCACCGATGGCATCTTC 59.276 57.895 23.97 11.04 44.11 2.87
4044 5468 4.893608 TCTTGATGGACATGAAGACGAAA 58.106 39.130 9.63 0.00 36.40 3.46
4408 5862 1.141881 CGACCCTCTTCATCACCGG 59.858 63.158 0.00 0.00 0.00 5.28
4497 5951 1.674764 CGACCCTGAGCAGCTGATCT 61.675 60.000 30.29 13.46 0.00 2.75
4511 5965 1.453762 CTCGTAGGTGATCCCGACCC 61.454 65.000 7.54 0.00 35.55 4.46
4550 6004 3.454371 AGACACTAGAAACGCACAAGT 57.546 42.857 0.00 0.00 0.00 3.16
4555 6009 2.404215 GAGCAAGACACTAGAAACGCA 58.596 47.619 0.00 0.00 0.00 5.24
4605 6073 6.248420 CCATTTGTGCTAAAAATAAGTCGTCG 59.752 38.462 0.00 0.00 0.00 5.12
4620 6088 3.424703 ACACTGCTAATCCATTTGTGCT 58.575 40.909 0.00 0.00 0.00 4.40
4621 6089 3.855689 ACACTGCTAATCCATTTGTGC 57.144 42.857 0.00 0.00 0.00 4.57
4622 6090 6.071952 AGGTTTACACTGCTAATCCATTTGTG 60.072 38.462 0.00 0.00 0.00 3.33
4623 6091 6.010219 AGGTTTACACTGCTAATCCATTTGT 58.990 36.000 0.00 0.00 0.00 2.83
4660 6128 1.453235 CACAGGATCATCCGGGCAT 59.547 57.895 8.86 0.00 42.75 4.40
4696 6168 4.344968 AGCTTGTAGGCAATCCAAAGTTTT 59.655 37.500 0.00 0.00 33.65 2.43
4697 6169 3.897505 AGCTTGTAGGCAATCCAAAGTTT 59.102 39.130 0.00 0.00 33.65 2.66
4716 6188 3.354948 TTAGATCATGCCACAACAGCT 57.645 42.857 0.00 0.00 0.00 4.24
4758 6230 2.976589 TCATGTCAATGATGTCGCACT 58.023 42.857 0.00 0.00 37.91 4.40
4845 6326 9.218440 CGTTTTAGGTTAAAGAAGGTATGGTTA 57.782 33.333 0.00 0.00 0.00 2.85
4846 6327 7.308770 GCGTTTTAGGTTAAAGAAGGTATGGTT 60.309 37.037 0.00 0.00 0.00 3.67
4851 6332 6.991531 TCTTGCGTTTTAGGTTAAAGAAGGTA 59.008 34.615 0.00 0.00 0.00 3.08
4855 6336 6.539464 TGTCTCTTGCGTTTTAGGTTAAAGAA 59.461 34.615 0.00 0.00 0.00 2.52
4860 6342 4.753107 CCTTGTCTCTTGCGTTTTAGGTTA 59.247 41.667 0.00 0.00 0.00 2.85
4862 6344 3.139077 CCTTGTCTCTTGCGTTTTAGGT 58.861 45.455 0.00 0.00 0.00 3.08
4911 6395 4.504916 CTCCGGCGCTGAGGTGAG 62.505 72.222 20.25 11.89 0.00 3.51
4924 6411 1.338674 TGTGGATTAGTTGTGGCTCCG 60.339 52.381 0.00 0.00 0.00 4.63
5040 6556 1.544151 GGAAGGAAAGGGGAGGGGT 60.544 63.158 0.00 0.00 0.00 4.95
5109 6625 1.133945 TGGAGCTAGACATCTCTCGCT 60.134 52.381 0.00 0.00 45.83 4.93
5132 6648 2.389449 ATGATGGGTGGGAGGCTGG 61.389 63.158 0.00 0.00 0.00 4.85
5172 6688 2.046023 CGGGGCATCTTGTCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
5209 6725 3.259876 TCACATAGGTAAACCGCTTCAGT 59.740 43.478 0.00 0.00 42.08 3.41
5221 6737 4.408921 CCATGGTCTTCCTTCACATAGGTA 59.591 45.833 2.57 0.00 36.63 3.08
5249 6765 3.115892 GACGAAATCGCGCCCACA 61.116 61.111 0.00 0.00 44.43 4.17
5287 6803 1.992557 TCAAATCTAACCTGCCCCTGT 59.007 47.619 0.00 0.00 0.00 4.00
5289 6805 2.279173 ACTCAAATCTAACCTGCCCCT 58.721 47.619 0.00 0.00 0.00 4.79
5304 6820 4.820897 CATACAGCCAACAGAGTACTCAA 58.179 43.478 24.44 0.00 0.00 3.02
5320 6836 3.068732 TCGGGAGAAATCAGAGCATACAG 59.931 47.826 0.00 0.00 34.75 2.74
5355 6871 8.314021 ACCCTAGATTCCAAATTCAATGAAAAC 58.686 33.333 0.00 0.00 0.00 2.43
5372 6891 2.290323 GGCGGCATATGAACCCTAGATT 60.290 50.000 6.97 0.00 0.00 2.40
5386 6905 1.862602 GAACCTGAAAACGGCGGCAT 61.863 55.000 13.24 0.00 0.00 4.40
5439 6966 5.045942 TCCAATTGTAGCCTCTCAATGTACA 60.046 40.000 4.43 0.00 34.98 2.90


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

AutoCloner maintained by Alex Coulton.