Multiple sequence alignment - TraesCS2A01G569800

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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 TraesCS2A01G569800 chr2A 100.000 6102 0 0 1 6102 767558066 767564167 0.000000e+00 11269.0
1 TraesCS2A01G569800 chr2A 95.597 1181 39 8 2020 3193 767486167 767484993 0.000000e+00 1881.0
2 TraesCS2A01G569800 chr2A 95.230 608 20 4 4876 5483 767479823 767479225 0.000000e+00 953.0
3 TraesCS2A01G569800 chr2A 97.889 521 11 0 4291 4811 767480341 767479821 0.000000e+00 902.0
4 TraesCS2A01G569800 chr2A 86.118 778 98 6 2231 3005 767138519 767139289 0.000000e+00 830.0
5 TraesCS2A01G569800 chr2A 94.329 529 24 3 3893 4417 767480866 767480340 0.000000e+00 806.0
6 TraesCS2A01G569800 chr2A 90.647 556 46 5 60 613 767465249 767464698 0.000000e+00 734.0
7 TraesCS2A01G569800 chr2A 83.543 796 83 21 2071 2826 766714566 766715353 0.000000e+00 701.0
8 TraesCS2A01G569800 chr2A 97.409 386 10 0 3514 3899 767481495 767481110 0.000000e+00 658.0
9 TraesCS2A01G569800 chr2A 80.510 667 117 9 4418 5076 767140100 767140761 3.280000e-137 499.0
10 TraesCS2A01G569800 chr2A 80.704 653 99 15 4436 5086 766717445 766718072 3.310000e-132 483.0
11 TraesCS2A01G569800 chr2A 97.473 277 7 0 3514 3790 767483268 767482992 1.990000e-129 473.0
12 TraesCS2A01G569800 chr2A 81.077 613 90 13 959 1570 767137134 767137721 3.330000e-127 466.0
13 TraesCS2A01G569800 chr2A 77.778 612 107 24 4287 4882 767789173 767788575 3.500000e-92 350.0
14 TraesCS2A01G569800 chr2A 92.917 240 6 3 3185 3423 767482840 767482611 7.580000e-89 339.0
15 TraesCS2A01G569800 chr2A 78.759 532 83 16 2351 2868 767570697 767571212 4.560000e-86 329.0
16 TraesCS2A01G569800 chr2A 91.111 180 6 2 3244 3423 767484552 767484383 1.020000e-57 235.0
17 TraesCS2A01G569800 chr2A 95.763 118 4 1 1837 1954 16796703 16796587 8.070000e-44 189.0
18 TraesCS2A01G569800 chr2A 93.600 125 5 3 604 727 767463559 767463437 3.760000e-42 183.0
19 TraesCS2A01G569800 chr2A 91.538 130 10 1 1833 1961 529797311 529797182 1.750000e-40 178.0
20 TraesCS2A01G569800 chr2A 98.333 60 1 0 3463 3522 767484386 767484327 8.360000e-19 106.0
21 TraesCS2A01G569800 chr2A 100.000 56 0 0 3467 3522 767482609 767482554 3.010000e-18 104.0
22 TraesCS2A01G569800 chr2A 86.250 80 7 4 591 666 766711703 766711782 3.920000e-12 84.2
23 TraesCS2A01G569800 chr2A 93.617 47 2 1 4181 4226 767789416 767789370 1.100000e-07 69.4
24 TraesCS2A01G569800 chr2D 94.027 1808 74 12 4313 6102 642417508 642419299 0.000000e+00 2710.0
25 TraesCS2A01G569800 chr2D 92.971 1252 64 12 1952 3193 642415223 642416460 0.000000e+00 1803.0
26 TraesCS2A01G569800 chr2D 90.510 980 63 13 3307 4270 642416544 642417509 0.000000e+00 1267.0
27 TraesCS2A01G569800 chr2D 91.001 889 31 15 965 1848 642414380 642415224 0.000000e+00 1153.0
28 TraesCS2A01G569800 chr2D 91.803 793 54 10 1 786 642406429 642407217 0.000000e+00 1094.0
29 TraesCS2A01G569800 chr2D 82.238 822 92 30 2049 2826 641611846 641612657 0.000000e+00 660.0
30 TraesCS2A01G569800 chr2D 81.944 648 104 9 4436 5075 642239403 642238761 2.500000e-148 536.0
31 TraesCS2A01G569800 chr2D 77.726 853 118 37 3785 4604 642941218 642942031 2.000000e-124 457.0
32 TraesCS2A01G569800 chr2D 79.570 651 110 6 4436 5086 641613402 641614029 1.560000e-120 444.0
33 TraesCS2A01G569800 chr2D 82.353 527 76 9 1048 1573 642241662 642241152 5.610000e-120 442.0
34 TraesCS2A01G569800 chr2D 87.728 383 31 7 5721 6088 24875271 24874890 3.380000e-117 433.0
35 TraesCS2A01G569800 chr2D 79.113 541 82 17 2342 2868 642500403 642500926 1.630000e-90 344.0
36 TraesCS2A01G569800 chr2D 93.333 150 3 4 786 934 642414237 642414380 1.330000e-51 215.0
37 TraesCS2A01G569800 chr2D 85.000 80 8 4 591 666 641609055 641609134 1.820000e-10 78.7
38 TraesCS2A01G569800 chr2B 93.288 1311 81 4 4313 5621 799285305 799284000 0.000000e+00 1927.0
39 TraesCS2A01G569800 chr2B 92.456 1246 47 21 1952 3193 799287549 799286347 0.000000e+00 1736.0
40 TraesCS2A01G569800 chr2B 90.609 1001 45 14 874 1848 799288525 799287548 0.000000e+00 1282.0
41 TraesCS2A01G569800 chr2B 90.082 978 65 16 3307 4270 799286263 799285304 0.000000e+00 1240.0
42 TraesCS2A01G569800 chr2B 85.604 778 102 7 2231 3005 799352727 799351957 0.000000e+00 808.0
43 TraesCS2A01G569800 chr2B 81.459 658 109 9 4436 5085 799351155 799350503 1.510000e-145 527.0
44 TraesCS2A01G569800 chr2B 76.136 1144 192 55 3785 4882 799252196 799251088 5.420000e-145 525.0
45 TraesCS2A01G569800 chr2B 79.710 552 95 9 1023 1573 799353643 799353108 3.450000e-102 383.0
46 TraesCS2A01G569800 chr2B 90.545 275 24 2 71 343 195612966 195613240 4.500000e-96 363.0
47 TraesCS2A01G569800 chr2B 82.692 104 9 5 5245 5348 799350432 799350338 3.920000e-12 84.2
48 TraesCS2A01G569800 chrUn 93.485 614 26 6 5019 5628 31455983 31456586 0.000000e+00 900.0
49 TraesCS2A01G569800 chrUn 93.617 47 2 1 4181 4226 31528099 31528053 1.100000e-07 69.4
50 TraesCS2A01G569800 chr4D 92.468 385 15 2 5731 6102 71374510 71374127 6.960000e-149 538.0
51 TraesCS2A01G569800 chr4D 89.974 389 26 6 5727 6102 413039057 413038669 1.980000e-134 490.0
52 TraesCS2A01G569800 chr4D 94.355 124 6 1 1838 1960 80469904 80470027 8.070000e-44 189.0
53 TraesCS2A01G569800 chr1D 92.487 386 14 3 5731 6102 10289118 10289502 6.960000e-149 538.0
54 TraesCS2A01G569800 chr7D 92.428 383 15 2 5733 6102 76537614 76537233 9.000000e-148 534.0
55 TraesCS2A01G569800 chr7D 90.979 388 20 6 5729 6102 580313056 580313442 5.460000e-140 508.0
56 TraesCS2A01G569800 chr7D 85.714 399 34 9 5720 6102 31138233 31137842 3.430000e-107 399.0
57 TraesCS2A01G569800 chr7D 91.667 276 20 3 72 345 282878112 282878386 4.460000e-101 379.0
58 TraesCS2A01G569800 chr7D 99.074 108 1 0 1847 1954 598013057 598012950 1.740000e-45 195.0
59 TraesCS2A01G569800 chr6D 91.969 386 15 3 5732 6102 468570662 468571046 1.510000e-145 527.0
60 TraesCS2A01G569800 chr6D 87.234 423 33 11 5695 6102 423443791 423443375 4.310000e-126 462.0
61 TraesCS2A01G569800 chr6D 91.860 258 7 2 5858 6102 429343608 429343352 1.260000e-91 348.0
62 TraesCS2A01G569800 chr5A 91.753 388 17 3 5729 6102 36009251 36009637 5.420000e-145 525.0
63 TraesCS2A01G569800 chr5A 87.586 290 21 7 5720 5995 688138022 688138310 7.630000e-84 322.0
64 TraesCS2A01G569800 chr1A 89.268 410 23 11 5710 6101 495647965 495647559 1.530000e-135 494.0
65 TraesCS2A01G569800 chr1A 88.071 394 30 9 5718 6096 514118083 514118474 9.330000e-123 451.0
66 TraesCS2A01G569800 chr1B 89.844 384 23 7 5733 6102 534745218 534744837 4.280000e-131 479.0
67 TraesCS2A01G569800 chr3A 89.817 383 24 3 5730 6098 154736416 154736797 1.540000e-130 477.0
68 TraesCS2A01G569800 chr3A 92.126 127 10 0 1844 1970 571330242 571330116 4.860000e-41 180.0
69 TraesCS2A01G569800 chr3A 77.434 226 39 5 3785 4006 719828986 719829203 2.310000e-24 124.0
70 TraesCS2A01G569800 chr7B 88.974 390 24 7 5730 6102 672840164 672839777 1.200000e-126 464.0
71 TraesCS2A01G569800 chr7B 89.722 360 33 3 5736 6094 199997144 199997500 2.000000e-124 457.0
72 TraesCS2A01G569800 chr3D 87.591 411 35 8 5707 6102 20700338 20700747 4.310000e-126 462.0
73 TraesCS2A01G569800 chr3D 91.200 250 20 2 5854 6102 497807408 497807160 7.580000e-89 339.0
74 TraesCS2A01G569800 chr6B 86.990 392 33 8 5720 6096 42601848 42602236 5.650000e-115 425.0
75 TraesCS2A01G569800 chr6B 90.909 275 23 2 71 343 662616424 662616150 9.660000e-98 368.0
76 TraesCS2A01G569800 chr6B 90.288 278 24 3 72 346 226389852 226390129 1.620000e-95 361.0
77 TraesCS2A01G569800 chr6B 86.154 65 3 4 4072 4134 181132532 181132592 1.420000e-06 65.8
78 TraesCS2A01G569800 chr7A 86.290 372 45 4 5732 6102 260012735 260012369 3.430000e-107 399.0
79 TraesCS2A01G569800 chr7A 96.552 116 3 1 1839 1954 381253916 381254030 2.240000e-44 191.0
80 TraesCS2A01G569800 chr7A 77.434 226 39 7 3785 4006 581693104 581692887 2.310000e-24 124.0
81 TraesCS2A01G569800 chr3B 90.614 277 22 4 72 345 607429239 607429514 1.250000e-96 364.0
82 TraesCS2A01G569800 chr3B 90.580 276 23 3 72 345 708943246 708942972 4.500000e-96 363.0
83 TraesCS2A01G569800 chr5B 90.580 276 22 3 72 345 320411184 320410911 4.500000e-96 363.0
84 TraesCS2A01G569800 chr6A 99.074 108 1 0 1846 1953 12457478 12457585 1.740000e-45 195.0
85 TraesCS2A01G569800 chr6A 93.220 118 8 0 1838 1955 99966791 99966908 2.260000e-39 174.0
86 TraesCS2A01G569800 chr6A 74.586 362 63 20 3785 4134 530594292 530594636 1.380000e-26 132.0
87 TraesCS2A01G569800 chr4A 96.552 116 4 0 1840 1955 278329147 278329262 6.240000e-45 193.0


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 TraesCS2A01G569800 chr2A 767558066 767564167 6101 False 11269.000000 11269 100.000000 1 6102 1 chr2A.!!$F1 6101
1 TraesCS2A01G569800 chr2A 767479225 767486167 6942 True 645.700000 1881 96.028800 2020 5483 10 chr2A.!!$R4 3463
2 TraesCS2A01G569800 chr2A 767137134 767140761 3627 False 598.333333 830 82.568333 959 5076 3 chr2A.!!$F4 4117
3 TraesCS2A01G569800 chr2A 767463437 767465249 1812 True 458.500000 734 92.123500 60 727 2 chr2A.!!$R3 667
4 TraesCS2A01G569800 chr2A 766711703 766718072 6369 False 422.733333 701 83.499000 591 5086 3 chr2A.!!$F3 4495
5 TraesCS2A01G569800 chr2A 767570697 767571212 515 False 329.000000 329 78.759000 2351 2868 1 chr2A.!!$F2 517
6 TraesCS2A01G569800 chr2A 767788575 767789416 841 True 209.700000 350 85.697500 4181 4882 2 chr2A.!!$R5 701
7 TraesCS2A01G569800 chr2D 642414237 642419299 5062 False 1429.600000 2710 92.368400 786 6102 5 chr2D.!!$F5 5316
8 TraesCS2A01G569800 chr2D 642406429 642407217 788 False 1094.000000 1094 91.803000 1 786 1 chr2D.!!$F1 785
9 TraesCS2A01G569800 chr2D 642238761 642241662 2901 True 489.000000 536 82.148500 1048 5075 2 chr2D.!!$R2 4027
10 TraesCS2A01G569800 chr2D 642941218 642942031 813 False 457.000000 457 77.726000 3785 4604 1 chr2D.!!$F3 819
11 TraesCS2A01G569800 chr2D 641609055 641614029 4974 False 394.233333 660 82.269333 591 5086 3 chr2D.!!$F4 4495
12 TraesCS2A01G569800 chr2D 642500403 642500926 523 False 344.000000 344 79.113000 2342 2868 1 chr2D.!!$F2 526
13 TraesCS2A01G569800 chr2B 799284000 799288525 4525 True 1546.250000 1927 91.608750 874 5621 4 chr2B.!!$R2 4747
14 TraesCS2A01G569800 chr2B 799251088 799252196 1108 True 525.000000 525 76.136000 3785 4882 1 chr2B.!!$R1 1097
15 TraesCS2A01G569800 chr2B 799350338 799353643 3305 True 450.550000 808 82.366250 1023 5348 4 chr2B.!!$R3 4325
16 TraesCS2A01G569800 chrUn 31455983 31456586 603 False 900.000000 900 93.485000 5019 5628 1 chrUn.!!$F1 609

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
915 3639 0.040058 TATATCCTAGGCGGCGGGAA 59.960 55.000 24.63 16.33 32.53 3.97 F
1015 3748 0.179000 GAAGATGGACATGAGGGCGT 59.821 55.000 0.00 0.00 0.00 5.68 F
1886 5372 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06 F
3307 9203 0.409876 TAGAGGGGCTCAGTGTCTGT 59.590 55.000 0.00 0.00 32.06 3.41 F
4069 12598 0.177141 TAGGTACTTGGGCACGCATC 59.823 55.000 0.00 0.00 41.75 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 5421 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.0 0.0 0.0 0.00 4.30 R
1936 5422 0.329261 TTCTACTCCCTCCGTTCCGA 59.671 55.0 0.0 0.0 0.00 4.55 R
3389 10500 0.181114 TTCTTGCTGCTGACCAGTGT 59.819 50.0 0.0 0.0 43.71 3.55 R
4150 12689 0.412244 TCAGGTGTAGGCACTAGGGT 59.588 55.0 0.0 0.0 44.14 4.34 R
5755 14587 0.757188 CTCCCAGATACAGAGCCCGT 60.757 60.0 0.0 0.0 0.00 5.28 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
34 35 1.625818 ACTGTTGAGGGAGAAGCGAAT 59.374 47.619 0.00 0.00 0.00 3.34
52 53 3.879295 CGAATGAGTGGCTATGGATTGTT 59.121 43.478 0.00 0.00 0.00 2.83
97 98 6.770785 GGGCATGTACAATGGTTCTATCTTAA 59.229 38.462 0.00 0.00 0.00 1.85
129 130 4.524714 CGTAGGATAATGATGAGGTGGAGT 59.475 45.833 0.00 0.00 0.00 3.85
218 219 4.669197 GCACAATATGTCTCACCACGTTTC 60.669 45.833 0.00 0.00 0.00 2.78
229 230 4.744570 TCACCACGTTTCTAGAATAGCTG 58.255 43.478 5.89 5.09 38.99 4.24
239 240 8.879759 CGTTTCTAGAATAGCTGGTTATTGAAA 58.120 33.333 5.89 5.31 38.99 2.69
252 253 8.466798 GCTGGTTATTGAAAATAAGGCTAAGAA 58.533 33.333 0.00 0.00 0.00 2.52
268 269 6.064717 GGCTAAGAAATGACCCATTGTAGAT 58.935 40.000 0.00 0.00 34.04 1.98
271 272 9.289782 GCTAAGAAATGACCCATTGTAGATAAT 57.710 33.333 0.00 0.00 34.04 1.28
353 354 8.587608 CCATTATACATGCCCTAATGAAACATT 58.412 33.333 17.54 0.00 35.72 2.71
392 393 9.912634 AAAAAGTGTGGATAAATGAATGTACAG 57.087 29.630 0.33 0.00 0.00 2.74
422 424 3.317711 CGTCAGATGAGAAGCACTCCTAT 59.682 47.826 8.13 0.00 44.34 2.57
507 509 9.758651 AAATTTAGCCAAAGTTTACGAAGATTT 57.241 25.926 0.00 0.00 27.90 2.17
662 3298 1.065418 CGGAGAACTGGGCCATACTTT 60.065 52.381 6.72 0.00 0.00 2.66
689 3348 0.955919 GGCACTTCTTCTTGGACGGG 60.956 60.000 0.00 0.00 0.00 5.28
694 3353 3.056107 CACTTCTTCTTGGACGGGATACA 60.056 47.826 0.00 0.00 39.74 2.29
742 3460 3.132824 CCACTTTGGTTGAAGCCTTTTCT 59.867 43.478 0.00 0.00 31.35 2.52
808 3531 9.725019 AAAGAAAAGAAAAAGACTTGGTTGAAT 57.275 25.926 0.00 0.00 0.00 2.57
913 3637 1.991121 TATATATCCTAGGCGGCGGG 58.009 55.000 9.78 15.65 0.00 6.13
914 3638 0.260816 ATATATCCTAGGCGGCGGGA 59.739 55.000 23.54 23.54 0.00 5.14
915 3639 0.040058 TATATCCTAGGCGGCGGGAA 59.960 55.000 24.63 16.33 32.53 3.97
916 3640 1.542187 ATATCCTAGGCGGCGGGAAC 61.542 60.000 24.63 0.00 32.53 3.62
937 3661 4.409187 ACCGGGAAGAGAGATCCTATAAC 58.591 47.826 6.32 0.00 37.14 1.89
940 3664 5.304614 CCGGGAAGAGAGATCCTATAACAAA 59.695 44.000 0.00 0.00 37.14 2.83
941 3665 6.451393 CGGGAAGAGAGATCCTATAACAAAG 58.549 44.000 0.00 0.00 37.14 2.77
1015 3748 0.179000 GAAGATGGACATGAGGGCGT 59.821 55.000 0.00 0.00 0.00 5.68
1212 3945 4.268687 CTGGTCGAGCACTTGTCC 57.731 61.111 14.39 0.00 0.00 4.02
1213 3946 1.374758 CTGGTCGAGCACTTGTCCC 60.375 63.158 14.39 0.00 0.00 4.46
1214 3947 1.821061 CTGGTCGAGCACTTGTCCCT 61.821 60.000 14.39 0.00 0.00 4.20
1215 3948 1.079750 GGTCGAGCACTTGTCCCTC 60.080 63.158 10.30 0.00 0.00 4.30
1515 4254 3.414700 CGCCGTGTCAGCTGGAAC 61.415 66.667 15.13 11.50 0.00 3.62
1561 4300 1.073025 TGTGGCGGCTTCAATGACT 59.927 52.632 11.43 0.00 0.00 3.41
1710 4575 4.044426 TCTCAATCAGTGCAATCGTATCG 58.956 43.478 0.00 0.00 0.00 2.92
1732 4597 1.321474 TGCTGCCTTTCCTTCTTGTG 58.679 50.000 0.00 0.00 0.00 3.33
1797 5283 7.236019 TGGGGAAACTCATTGTACTAGTTTAGA 59.764 37.037 0.00 0.00 42.06 2.10
1830 5316 5.175673 GTGCTTGTGCCAGAAATTAGAAAAC 59.824 40.000 0.00 0.00 38.71 2.43
1847 5333 3.621682 AAACCCCACACCAAATTCCTA 57.378 42.857 0.00 0.00 0.00 2.94
1848 5334 2.597578 ACCCCACACCAAATTCCTAC 57.402 50.000 0.00 0.00 0.00 3.18
1849 5335 2.070573 ACCCCACACCAAATTCCTACT 58.929 47.619 0.00 0.00 0.00 2.57
1850 5336 2.041216 ACCCCACACCAAATTCCTACTC 59.959 50.000 0.00 0.00 0.00 2.59
1851 5337 2.620627 CCCCACACCAAATTCCTACTCC 60.621 54.545 0.00 0.00 0.00 3.85
1852 5338 2.620627 CCCACACCAAATTCCTACTCCC 60.621 54.545 0.00 0.00 0.00 4.30
1853 5339 2.308866 CCACACCAAATTCCTACTCCCT 59.691 50.000 0.00 0.00 0.00 4.20
1854 5340 3.610911 CACACCAAATTCCTACTCCCTC 58.389 50.000 0.00 0.00 0.00 4.30
1855 5341 2.576648 ACACCAAATTCCTACTCCCTCC 59.423 50.000 0.00 0.00 0.00 4.30
1856 5342 1.838077 ACCAAATTCCTACTCCCTCCG 59.162 52.381 0.00 0.00 0.00 4.63
1857 5343 1.838077 CCAAATTCCTACTCCCTCCGT 59.162 52.381 0.00 0.00 0.00 4.69
1858 5344 2.238898 CCAAATTCCTACTCCCTCCGTT 59.761 50.000 0.00 0.00 0.00 4.44
1859 5345 3.308188 CCAAATTCCTACTCCCTCCGTTT 60.308 47.826 0.00 0.00 0.00 3.60
1860 5346 3.908643 AATTCCTACTCCCTCCGTTTC 57.091 47.619 0.00 0.00 0.00 2.78
1861 5347 2.314071 TTCCTACTCCCTCCGTTTCA 57.686 50.000 0.00 0.00 0.00 2.69
1862 5348 2.314071 TCCTACTCCCTCCGTTTCAA 57.686 50.000 0.00 0.00 0.00 2.69
1863 5349 2.612000 TCCTACTCCCTCCGTTTCAAA 58.388 47.619 0.00 0.00 0.00 2.69
1864 5350 3.178865 TCCTACTCCCTCCGTTTCAAAT 58.821 45.455 0.00 0.00 0.00 2.32
1865 5351 3.585732 TCCTACTCCCTCCGTTTCAAATT 59.414 43.478 0.00 0.00 0.00 1.82
1866 5352 4.778958 TCCTACTCCCTCCGTTTCAAATTA 59.221 41.667 0.00 0.00 0.00 1.40
1867 5353 4.874396 CCTACTCCCTCCGTTTCAAATTAC 59.126 45.833 0.00 0.00 0.00 1.89
1868 5354 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
1869 5355 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
1870 5356 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
1871 5357 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
1872 5358 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
1873 5359 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
1874 5360 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
1875 5361 2.156117 CCGTTTCAAATTACTCGTCGCA 59.844 45.455 0.00 0.00 0.00 5.10
1876 5362 3.395671 CGTTTCAAATTACTCGTCGCAG 58.604 45.455 0.00 0.00 0.00 5.18
1877 5363 3.120616 CGTTTCAAATTACTCGTCGCAGA 59.879 43.478 0.00 0.00 0.00 4.26
1878 5364 4.375606 CGTTTCAAATTACTCGTCGCAGAA 60.376 41.667 0.00 0.00 39.69 3.02
1879 5365 5.437263 GTTTCAAATTACTCGTCGCAGAAA 58.563 37.500 0.00 0.00 39.69 2.52
1880 5366 5.856126 TTCAAATTACTCGTCGCAGAAAT 57.144 34.783 0.00 0.00 39.69 2.17
1881 5367 5.203358 TCAAATTACTCGTCGCAGAAATG 57.797 39.130 0.00 0.00 39.69 2.32
1882 5368 4.092821 TCAAATTACTCGTCGCAGAAATGG 59.907 41.667 0.00 0.00 39.69 3.16
1883 5369 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
1884 5370 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
1885 5371 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
1886 5372 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
1887 5373 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
1888 5374 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
1889 5375 3.792401 TCGTCGCAGAAATGGATGTATT 58.208 40.909 0.00 0.00 39.69 1.89
1890 5376 4.188462 TCGTCGCAGAAATGGATGTATTT 58.812 39.130 0.00 0.00 39.69 1.40
1891 5377 5.353111 TCGTCGCAGAAATGGATGTATTTA 58.647 37.500 0.00 0.00 39.69 1.40
1892 5378 5.462068 TCGTCGCAGAAATGGATGTATTTAG 59.538 40.000 0.00 0.00 39.69 1.85
1893 5379 5.462068 CGTCGCAGAAATGGATGTATTTAGA 59.538 40.000 0.00 0.00 39.69 2.10
1894 5380 6.019075 CGTCGCAGAAATGGATGTATTTAGAA 60.019 38.462 0.00 0.00 39.69 2.10
1895 5381 7.126398 GTCGCAGAAATGGATGTATTTAGAAC 58.874 38.462 0.00 0.00 39.69 3.01
1896 5382 7.011482 GTCGCAGAAATGGATGTATTTAGAACT 59.989 37.037 0.00 0.00 39.69 3.01
1897 5383 8.201464 TCGCAGAAATGGATGTATTTAGAACTA 58.799 33.333 0.00 0.00 30.78 2.24
1898 5384 8.826710 CGCAGAAATGGATGTATTTAGAACTAA 58.173 33.333 0.00 0.00 30.78 2.24
1926 5412 7.867305 ACATCTAGATACATCCATACCTACG 57.133 40.000 4.54 0.00 0.00 3.51
1927 5413 7.631007 ACATCTAGATACATCCATACCTACGA 58.369 38.462 4.54 0.00 0.00 3.43
1928 5414 7.553402 ACATCTAGATACATCCATACCTACGAC 59.447 40.741 4.54 0.00 0.00 4.34
1929 5415 7.012661 TCTAGATACATCCATACCTACGACA 57.987 40.000 0.00 0.00 0.00 4.35
1930 5416 7.455891 TCTAGATACATCCATACCTACGACAA 58.544 38.462 0.00 0.00 0.00 3.18
1931 5417 6.576662 AGATACATCCATACCTACGACAAG 57.423 41.667 0.00 0.00 0.00 3.16
1932 5418 6.069331 AGATACATCCATACCTACGACAAGT 58.931 40.000 0.00 0.00 0.00 3.16
1933 5419 7.229308 AGATACATCCATACCTACGACAAGTA 58.771 38.462 0.00 0.00 0.00 2.24
1934 5420 7.722728 AGATACATCCATACCTACGACAAGTAA 59.277 37.037 0.00 0.00 34.45 2.24
1935 5421 6.726490 ACATCCATACCTACGACAAGTAAT 57.274 37.500 0.00 0.00 34.45 1.89
1936 5422 7.120923 ACATCCATACCTACGACAAGTAATT 57.879 36.000 0.00 0.00 34.45 1.40
1937 5423 7.208080 ACATCCATACCTACGACAAGTAATTC 58.792 38.462 0.00 0.00 34.45 2.17
1938 5424 5.824429 TCCATACCTACGACAAGTAATTCG 58.176 41.667 0.00 0.00 41.14 3.34
1939 5425 4.980434 CCATACCTACGACAAGTAATTCGG 59.020 45.833 0.00 0.00 39.63 4.30
1940 5426 5.221106 CCATACCTACGACAAGTAATTCGGA 60.221 44.000 0.00 0.00 39.63 4.55
1941 5427 4.789012 ACCTACGACAAGTAATTCGGAA 57.211 40.909 0.00 0.00 39.63 4.30
1942 5428 4.488879 ACCTACGACAAGTAATTCGGAAC 58.511 43.478 0.00 0.00 39.63 3.62
1943 5429 3.545078 CCTACGACAAGTAATTCGGAACG 59.455 47.826 0.00 0.00 44.64 3.95
1944 5430 3.500982 TACGACAAGTAATTCGGAACGG 58.499 45.455 0.00 0.00 42.34 4.44
1964 5450 6.591750 ACGGAGGGAGTAGAATATAATGTG 57.408 41.667 0.00 0.00 0.00 3.21
2060 5556 8.211629 AGTGAGTAATTACCAAGGGTATTGATC 58.788 37.037 12.05 0.00 38.05 2.92
2159 5655 4.537135 TTAGCTGTTGGAAGGTAGTGAG 57.463 45.455 0.00 0.00 32.11 3.51
2176 5674 7.013655 AGGTAGTGAGTAACGAAGTAAAGTCAA 59.986 37.037 0.00 0.00 45.00 3.18
2227 5752 1.073177 GTGATACGGGTGGTGAAACG 58.927 55.000 0.00 0.00 38.12 3.60
2256 5850 2.034558 ACCTGCACAAATACACACAAGC 59.965 45.455 0.00 0.00 0.00 4.01
2257 5851 2.034432 CCTGCACAAATACACACAAGCA 59.966 45.455 0.00 0.00 0.00 3.91
2826 6454 3.682718 CGATATGGCTCTGGTGGTTCTTT 60.683 47.826 0.00 0.00 0.00 2.52
2931 6576 6.739331 ACACACCAAGGAAATGGAATTAAA 57.261 33.333 0.00 0.00 43.54 1.52
2949 6594 2.969628 AACTCAGCAGGATTAGTCGG 57.030 50.000 0.00 0.00 0.00 4.79
3063 6800 4.893524 TCTGGCCGAAGTCAAGATCTATTA 59.106 41.667 0.00 0.00 0.00 0.98
3081 6818 8.874744 ATCTATTATGGATTAATGCAAGCAGT 57.125 30.769 14.00 0.00 32.66 4.40
3181 6918 7.543947 TTGATACATATCTCAACAACAGCAG 57.456 36.000 0.82 0.00 33.88 4.24
3182 6919 5.525012 TGATACATATCTCAACAACAGCAGC 59.475 40.000 0.82 0.00 33.88 5.25
3184 6921 4.074259 ACATATCTCAACAACAGCAGCAA 58.926 39.130 0.00 0.00 0.00 3.91
3185 6922 4.703575 ACATATCTCAACAACAGCAGCAAT 59.296 37.500 0.00 0.00 0.00 3.56
3307 9203 0.409876 TAGAGGGGCTCAGTGTCTGT 59.590 55.000 0.00 0.00 32.06 3.41
3385 10496 9.987272 TTCAGAGATATAATCCATTGTACTGTG 57.013 33.333 0.00 0.00 0.00 3.66
3386 10497 8.588472 TCAGAGATATAATCCATTGTACTGTGG 58.412 37.037 9.91 9.91 36.82 4.17
3387 10498 8.370940 CAGAGATATAATCCATTGTACTGTGGT 58.629 37.037 14.20 2.58 36.84 4.16
3388 10499 8.589338 AGAGATATAATCCATTGTACTGTGGTC 58.411 37.037 14.20 6.19 36.84 4.02
3389 10500 8.262601 AGATATAATCCATTGTACTGTGGTCA 57.737 34.615 14.20 0.66 36.84 4.02
3390 10501 8.150945 AGATATAATCCATTGTACTGTGGTCAC 58.849 37.037 14.20 0.00 36.84 3.67
3391 10502 4.365514 AATCCATTGTACTGTGGTCACA 57.634 40.909 14.20 3.64 39.32 3.58
3442 10553 9.426837 CAAACAATCAATGTGACCATTAATTCT 57.573 29.630 0.00 0.00 42.99 2.40
3465 10578 2.611518 GTGCTCTGTCCATCAGTACAC 58.388 52.381 0.00 0.00 43.97 2.90
3524 11704 2.851824 GCGTTTCAAACAAACAGACAGG 59.148 45.455 0.22 0.00 0.00 4.00
3570 11753 3.197265 GCAGGCAACAAATCAACAAACT 58.803 40.909 0.00 0.00 41.41 2.66
3576 11759 5.450412 GGCAACAAATCAACAAACTCTCTCA 60.450 40.000 0.00 0.00 0.00 3.27
3928 12452 8.747538 AATAAGTAGACATTTGATTGGTACCC 57.252 34.615 10.07 0.00 0.00 3.69
4060 12588 7.256012 GGAAAGACATCCTATCTAGGTACTTGG 60.256 44.444 3.25 0.00 44.02 3.61
4069 12598 0.177141 TAGGTACTTGGGCACGCATC 59.823 55.000 0.00 0.00 41.75 3.91
4150 12689 7.565323 AAGAAAATTTATGCAGGCACAAAAA 57.435 28.000 1.49 1.88 0.00 1.94
4272 12938 6.070021 TCCAGAATGAACATGTCTTGTAGGAT 60.070 38.462 0.00 0.00 39.69 3.24
4277 12943 9.553064 GAATGAACATGTCTTGTAGGATAGAAT 57.447 33.333 0.00 0.00 37.68 2.40
4302 12980 9.944376 ATCTTTATGCTCTCTAGTTTGTTTACA 57.056 29.630 0.00 0.00 0.00 2.41
4420 13225 9.716507 CCTTTGTAATACTTTCCATGTTATTCG 57.283 33.333 0.00 0.00 0.00 3.34
4612 13433 5.313712 AGTTCTACTAACCACCACCATTTG 58.686 41.667 0.00 0.00 0.00 2.32
4736 13564 2.567169 GTTGGAGGGGGATTTCCTTTTG 59.433 50.000 0.00 0.00 34.21 2.44
4737 13565 2.077803 TGGAGGGGGATTTCCTTTTGA 58.922 47.619 0.00 0.00 34.21 2.69
4738 13566 2.452823 TGGAGGGGGATTTCCTTTTGAA 59.547 45.455 0.00 0.00 34.21 2.69
4739 13567 3.078918 TGGAGGGGGATTTCCTTTTGAAT 59.921 43.478 0.00 0.00 34.21 2.57
4775 13603 2.924290 GCTTGTTCATCGTCTACTGGAC 59.076 50.000 0.00 0.00 41.28 4.02
4835 13663 6.073058 GCTTGATTCTGTTGAAAAATTTCCCC 60.073 38.462 3.60 0.00 36.36 4.81
5390 14218 3.763057 ACCTACATTTGAGTTTGGGTCC 58.237 45.455 0.00 0.00 0.00 4.46
5403 14231 1.173043 TGGGTCCAATTGACGAATGC 58.827 50.000 7.12 0.00 45.46 3.56
5712 14544 7.392953 TGGAACAACTTCAGCATATGATTTACA 59.607 33.333 6.97 0.00 33.76 2.41
5718 14550 8.839310 ACTTCAGCATATGATTTACAGTATCC 57.161 34.615 6.97 0.00 37.89 2.59
5759 14591 0.328258 AAAAGGAGGATGACCACGGG 59.672 55.000 0.00 0.00 38.94 5.28
5765 14597 2.660064 GGATGACCACGGGCTCTGT 61.660 63.158 0.00 0.00 35.97 3.41
5778 14610 2.324541 GGCTCTGTATCTGGGAGATGT 58.675 52.381 0.00 0.00 35.37 3.06
5845 14677 3.620488 ACAACAATATGCCTGAATCCGT 58.380 40.909 0.00 0.00 0.00 4.69
5851 14683 2.540265 ATGCCTGAATCCGTCATCTC 57.460 50.000 0.00 0.00 35.07 2.75
5853 14685 0.385751 GCCTGAATCCGTCATCTCGA 59.614 55.000 0.00 0.00 35.07 4.04
5895 14727 3.726557 TCCATATGATGAAGGGATGCC 57.273 47.619 3.65 0.00 0.00 4.40
5898 14730 3.245158 CCATATGATGAAGGGATGCCAGT 60.245 47.826 5.86 0.00 0.00 4.00
6033 14878 0.389166 CACAGGTCCGTCTTCAGAGC 60.389 60.000 0.00 0.00 0.00 4.09
6077 14925 2.265739 GCCACTCTGCCATCGACA 59.734 61.111 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.623311 TCATTCGCTTCTCCCTCAACA 59.377 47.619 0.00 0.00 0.00 3.33
34 35 2.308570 ACCAACAATCCATAGCCACTCA 59.691 45.455 0.00 0.00 0.00 3.41
52 53 3.636231 CCAGGCCGTCTCCAACCA 61.636 66.667 0.00 0.00 0.00 3.67
187 188 5.982516 GGTGAGACATATTGTGCTAAGAGAG 59.017 44.000 0.00 0.00 0.00 3.20
239 240 6.897413 ACAATGGGTCATTTCTTAGCCTTATT 59.103 34.615 0.00 0.00 31.05 1.40
332 333 7.422465 AACAATGTTTCATTAGGGCATGTAT 57.578 32.000 0.00 0.00 0.00 2.29
507 509 8.355169 GGTGCTTACCGATATTATCCGAATATA 58.645 37.037 0.00 0.00 0.00 0.86
662 3298 1.722034 AGAAGAAGTGCCCAGAGACA 58.278 50.000 0.00 0.00 0.00 3.41
689 3348 0.105778 GCTCAGTCCAGCCCTGTATC 59.894 60.000 0.00 0.00 32.76 2.24
694 3353 3.076092 CAAGCTCAGTCCAGCCCT 58.924 61.111 0.00 0.00 40.65 5.19
786 3509 7.851228 AGGATTCAACCAAGTCTTTTTCTTTT 58.149 30.769 0.00 0.00 0.00 2.27
787 3510 7.423844 AGGATTCAACCAAGTCTTTTTCTTT 57.576 32.000 0.00 0.00 0.00 2.52
792 3515 7.670364 CCAATTAGGATTCAACCAAGTCTTTT 58.330 34.615 0.00 0.00 41.22 2.27
793 3516 6.295292 GCCAATTAGGATTCAACCAAGTCTTT 60.295 38.462 0.00 0.00 41.22 2.52
794 3517 5.185828 GCCAATTAGGATTCAACCAAGTCTT 59.814 40.000 0.00 0.00 41.22 3.01
795 3518 4.706962 GCCAATTAGGATTCAACCAAGTCT 59.293 41.667 0.00 0.00 41.22 3.24
796 3519 4.438744 CGCCAATTAGGATTCAACCAAGTC 60.439 45.833 0.00 0.00 41.22 3.01
808 3531 0.534203 GATTCCGCCGCCAATTAGGA 60.534 55.000 0.00 0.00 41.22 2.94
913 3637 1.783071 AGGATCTCTCTTCCCGGTTC 58.217 55.000 0.00 0.00 33.45 3.62
914 3638 3.621682 ATAGGATCTCTCTTCCCGGTT 57.378 47.619 0.00 0.00 33.45 4.44
915 3639 4.140994 TGTTATAGGATCTCTCTTCCCGGT 60.141 45.833 0.00 0.00 33.45 5.28
916 3640 4.408276 TGTTATAGGATCTCTCTTCCCGG 58.592 47.826 0.00 0.00 33.45 5.73
1124 3857 1.296727 GTAATCCTTCTTTCCGGCGG 58.703 55.000 22.51 22.51 0.00 6.13
1204 3937 0.764890 TGGTTCTGGAGGGACAAGTG 59.235 55.000 0.00 0.00 0.00 3.16
1205 3938 1.059913 CTGGTTCTGGAGGGACAAGT 58.940 55.000 0.00 0.00 0.00 3.16
1206 3939 1.352083 TCTGGTTCTGGAGGGACAAG 58.648 55.000 0.00 0.00 0.00 3.16
1207 3940 1.814429 TTCTGGTTCTGGAGGGACAA 58.186 50.000 0.00 0.00 0.00 3.18
1208 3941 1.699634 CTTTCTGGTTCTGGAGGGACA 59.300 52.381 0.00 0.00 0.00 4.02
1209 3942 1.700186 ACTTTCTGGTTCTGGAGGGAC 59.300 52.381 0.00 0.00 0.00 4.46
1210 3943 1.978580 GACTTTCTGGTTCTGGAGGGA 59.021 52.381 0.00 0.00 0.00 4.20
1211 3944 1.338200 CGACTTTCTGGTTCTGGAGGG 60.338 57.143 0.00 0.00 0.00 4.30
1212 3945 1.941668 GCGACTTTCTGGTTCTGGAGG 60.942 57.143 0.00 0.00 0.00 4.30
1213 3946 1.433534 GCGACTTTCTGGTTCTGGAG 58.566 55.000 0.00 0.00 0.00 3.86
1214 3947 0.319555 CGCGACTTTCTGGTTCTGGA 60.320 55.000 0.00 0.00 0.00 3.86
1215 3948 0.319555 TCGCGACTTTCTGGTTCTGG 60.320 55.000 3.71 0.00 0.00 3.86
1561 4300 4.811969 TGGATGAACGGCTCTTACTTAA 57.188 40.909 0.00 0.00 0.00 1.85
1710 4575 0.964700 AAGAAGGAAAGGCAGCAAGC 59.035 50.000 0.00 0.00 44.65 4.01
1766 5246 5.091552 AGTACAATGAGTTTCCCCAGAGTA 58.908 41.667 0.00 0.00 0.00 2.59
1797 5283 1.075374 TGGCACAAGCACTAATTCCCT 59.925 47.619 0.00 0.00 44.61 4.20
1830 5316 2.620627 GGAGTAGGAATTTGGTGTGGGG 60.621 54.545 0.00 0.00 0.00 4.96
1847 5333 4.576879 GAGTAATTTGAAACGGAGGGAGT 58.423 43.478 0.00 0.00 0.00 3.85
1848 5334 3.617263 CGAGTAATTTGAAACGGAGGGAG 59.383 47.826 0.00 0.00 0.00 4.30
1849 5335 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
1850 5336 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
1851 5337 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
1852 5338 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
1853 5339 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
1854 5340 2.156117 TGCGACGAGTAATTTGAAACGG 59.844 45.455 0.00 0.00 0.00 4.44
1855 5341 3.120616 TCTGCGACGAGTAATTTGAAACG 59.879 43.478 0.00 0.00 0.00 3.60
1856 5342 4.640805 TCTGCGACGAGTAATTTGAAAC 57.359 40.909 0.00 0.00 0.00 2.78
1857 5343 5.660629 TTTCTGCGACGAGTAATTTGAAA 57.339 34.783 0.00 0.00 0.00 2.69
1858 5344 5.390461 CCATTTCTGCGACGAGTAATTTGAA 60.390 40.000 0.00 0.00 0.00 2.69
1859 5345 4.092821 CCATTTCTGCGACGAGTAATTTGA 59.907 41.667 0.00 0.00 0.00 2.69
1860 5346 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
1861 5347 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
1862 5348 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
1863 5349 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
1864 5350 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
1865 5351 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
1866 5352 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
1867 5353 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
1868 5354 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
1869 5355 4.536364 AAATACATCCATTTCTGCGACG 57.464 40.909 0.00 0.00 0.00 5.12
1870 5356 6.844696 TCTAAATACATCCATTTCTGCGAC 57.155 37.500 0.00 0.00 30.84 5.19
1871 5357 7.047891 AGTTCTAAATACATCCATTTCTGCGA 58.952 34.615 0.00 0.00 30.84 5.10
1872 5358 7.251704 AGTTCTAAATACATCCATTTCTGCG 57.748 36.000 0.00 0.00 30.84 5.18
1900 5386 9.562408 CGTAGGTATGGATGTATCTAGATGTAT 57.438 37.037 15.79 9.11 0.00 2.29
1901 5387 8.765517 TCGTAGGTATGGATGTATCTAGATGTA 58.234 37.037 15.79 4.44 0.00 2.29
1902 5388 7.553402 GTCGTAGGTATGGATGTATCTAGATGT 59.447 40.741 15.79 1.25 0.00 3.06
1903 5389 7.553044 TGTCGTAGGTATGGATGTATCTAGATG 59.447 40.741 15.79 0.00 0.00 2.90
1904 5390 7.631007 TGTCGTAGGTATGGATGTATCTAGAT 58.369 38.462 10.73 10.73 0.00 1.98
1905 5391 7.012661 TGTCGTAGGTATGGATGTATCTAGA 57.987 40.000 0.00 0.00 0.00 2.43
1906 5392 7.390996 ACTTGTCGTAGGTATGGATGTATCTAG 59.609 40.741 0.00 0.00 0.00 2.43
1907 5393 7.229308 ACTTGTCGTAGGTATGGATGTATCTA 58.771 38.462 0.00 0.00 0.00 1.98
1908 5394 6.069331 ACTTGTCGTAGGTATGGATGTATCT 58.931 40.000 0.00 0.00 0.00 1.98
1909 5395 6.328641 ACTTGTCGTAGGTATGGATGTATC 57.671 41.667 0.00 0.00 0.00 2.24
1910 5396 7.828508 TTACTTGTCGTAGGTATGGATGTAT 57.171 36.000 0.00 0.00 0.00 2.29
1911 5397 7.828508 ATTACTTGTCGTAGGTATGGATGTA 57.171 36.000 0.00 0.00 0.00 2.29
1912 5398 6.726490 ATTACTTGTCGTAGGTATGGATGT 57.274 37.500 0.00 0.00 0.00 3.06
1913 5399 6.362551 CGAATTACTTGTCGTAGGTATGGATG 59.637 42.308 0.00 0.00 32.61 3.51
1914 5400 6.444633 CGAATTACTTGTCGTAGGTATGGAT 58.555 40.000 0.00 0.00 32.61 3.41
1915 5401 5.221106 CCGAATTACTTGTCGTAGGTATGGA 60.221 44.000 0.00 0.00 35.48 3.41
1916 5402 4.980434 CCGAATTACTTGTCGTAGGTATGG 59.020 45.833 0.00 0.00 35.48 2.74
1917 5403 5.824429 TCCGAATTACTTGTCGTAGGTATG 58.176 41.667 0.00 0.00 35.48 2.39
1918 5404 6.268566 GTTCCGAATTACTTGTCGTAGGTAT 58.731 40.000 0.00 0.00 35.48 2.73
1919 5405 5.640732 GTTCCGAATTACTTGTCGTAGGTA 58.359 41.667 0.00 0.00 35.48 3.08
1920 5406 4.488879 GTTCCGAATTACTTGTCGTAGGT 58.511 43.478 0.00 0.00 35.48 3.08
1921 5407 3.545078 CGTTCCGAATTACTTGTCGTAGG 59.455 47.826 0.00 0.00 35.48 3.18
1922 5408 3.545078 CCGTTCCGAATTACTTGTCGTAG 59.455 47.826 0.00 0.00 35.48 3.51
1923 5409 3.190327 TCCGTTCCGAATTACTTGTCGTA 59.810 43.478 0.00 0.00 35.48 3.43
1924 5410 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
1925 5411 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1926 5412 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1927 5413 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1928 5414 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1929 5415 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1930 5416 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1931 5417 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1932 5418 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1933 5419 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
1934 5420 1.064166 TCTACTCCCTCCGTTCCGAAT 60.064 52.381 0.00 0.00 0.00 3.34
1935 5421 0.329261 TCTACTCCCTCCGTTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
1936 5422 0.329261 TTCTACTCCCTCCGTTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
1937 5423 1.400737 ATTCTACTCCCTCCGTTCCG 58.599 55.000 0.00 0.00 0.00 4.30
1938 5424 6.210984 ACATTATATTCTACTCCCTCCGTTCC 59.789 42.308 0.00 0.00 0.00 3.62
1939 5425 7.039923 TCACATTATATTCTACTCCCTCCGTTC 60.040 40.741 0.00 0.00 0.00 3.95
1940 5426 6.781014 TCACATTATATTCTACTCCCTCCGTT 59.219 38.462 0.00 0.00 0.00 4.44
1941 5427 6.312529 TCACATTATATTCTACTCCCTCCGT 58.687 40.000 0.00 0.00 0.00 4.69
1942 5428 6.434652 ACTCACATTATATTCTACTCCCTCCG 59.565 42.308 0.00 0.00 0.00 4.63
1943 5429 7.233757 ACACTCACATTATATTCTACTCCCTCC 59.766 40.741 0.00 0.00 0.00 4.30
1944 5430 8.184304 ACACTCACATTATATTCTACTCCCTC 57.816 38.462 0.00 0.00 0.00 4.30
1945 5431 9.080097 GTACACTCACATTATATTCTACTCCCT 57.920 37.037 0.00 0.00 0.00 4.20
1946 5432 9.080097 AGTACACTCACATTATATTCTACTCCC 57.920 37.037 0.00 0.00 0.00 4.30
2060 5556 8.558700 CCTCTGAGAGACATATGTATATGATCG 58.441 40.741 11.82 0.00 42.05 3.69
2159 5655 7.859875 ACTGTAGTCTTGACTTTACTTCGTTAC 59.140 37.037 8.66 0.00 0.00 2.50
2176 5674 4.973168 TCCTTTCAAATGCACTGTAGTCT 58.027 39.130 0.00 0.00 0.00 3.24
2227 5752 5.995282 TGTGTATTTGTGCAGGTATATAGCC 59.005 40.000 8.31 1.32 0.00 3.93
2256 5850 2.051334 TCCACTTGGGAAACTGTGTG 57.949 50.000 0.00 0.00 44.80 3.82
2861 6499 6.223120 ACTTTGCTTCACTCAAACTGTTTTT 58.777 32.000 2.41 0.00 31.05 1.94
2931 6576 1.115467 CCCGACTAATCCTGCTGAGT 58.885 55.000 0.00 0.00 0.00 3.41
2949 6594 4.003648 AGTTTGTTATCTGCTGTGCTACC 58.996 43.478 0.00 0.00 0.00 3.18
3063 6800 4.467082 TGGAAACTGCTTGCATTAATCCAT 59.533 37.500 12.79 0.00 29.08 3.41
3081 6818 3.071874 CTGGAAGGTGCAGTATGGAAA 57.928 47.619 0.00 0.00 39.09 3.13
3217 9113 2.345876 CCGGCCATTTTCATTTTGGTC 58.654 47.619 2.24 0.00 32.90 4.02
3285 9181 1.923850 AGACACTGAGCCCCTCTACTA 59.076 52.381 0.00 0.00 0.00 1.82
3307 9203 0.538977 AGGTCGAAACGGGAGACTGA 60.539 55.000 0.00 0.00 41.09 3.41
3374 10485 2.807967 CCAGTGTGACCACAGTACAATG 59.192 50.000 9.85 0.00 42.66 2.82
3384 10495 1.447217 CTGCTGACCAGTGTGACCA 59.553 57.895 0.00 0.00 36.79 4.02
3385 10496 1.963338 GCTGCTGACCAGTGTGACC 60.963 63.158 0.00 0.00 43.71 4.02
3386 10497 0.815213 TTGCTGCTGACCAGTGTGAC 60.815 55.000 0.00 0.00 43.71 3.67
3387 10498 0.533531 CTTGCTGCTGACCAGTGTGA 60.534 55.000 0.00 0.00 43.71 3.58
3388 10499 0.533531 TCTTGCTGCTGACCAGTGTG 60.534 55.000 0.00 0.00 43.71 3.82
3389 10500 0.181114 TTCTTGCTGCTGACCAGTGT 59.819 50.000 0.00 0.00 43.71 3.55
3390 10501 0.873054 CTTCTTGCTGCTGACCAGTG 59.127 55.000 0.00 0.00 43.71 3.66
3391 10502 0.761187 TCTTCTTGCTGCTGACCAGT 59.239 50.000 0.00 0.00 43.71 4.00
3392 10503 1.534595 GTTCTTCTTGCTGCTGACCAG 59.465 52.381 0.00 0.00 44.67 4.00
3465 10578 6.423182 TGGTATTCCCTTCCTATGAGTTTTG 58.577 40.000 0.00 0.00 0.00 2.44
3524 11704 5.220416 CGTGCTTAATTTACAGAGGTGCTAC 60.220 44.000 0.00 0.00 0.00 3.58
3570 11753 9.507329 AAAATACTGATACTTTGCTTTGAGAGA 57.493 29.630 0.00 0.00 0.00 3.10
3657 11840 1.241165 TGCTTGCAAGGTCATGTGAG 58.759 50.000 27.10 0.00 0.00 3.51
4053 12577 1.421410 CTCGATGCGTGCCCAAGTAC 61.421 60.000 0.00 0.00 0.00 2.73
4056 12580 3.869272 GCTCGATGCGTGCCCAAG 61.869 66.667 2.82 0.00 39.88 3.61
4060 12588 0.657840 ATTTAAGCTCGATGCGTGCC 59.342 50.000 9.80 0.00 45.54 5.01
4150 12689 0.412244 TCAGGTGTAGGCACTAGGGT 59.588 55.000 0.00 0.00 44.14 4.34
4162 12701 4.814771 GCTACTTGTGTTTTACTCAGGTGT 59.185 41.667 6.83 0.00 33.82 4.16
4277 12943 9.424319 CTGTAAACAAACTAGAGAGCATAAAGA 57.576 33.333 0.00 0.00 0.00 2.52
4302 12980 6.904626 ACAGAACATAAAGCTCCCATATTCT 58.095 36.000 0.00 0.00 0.00 2.40
4340 13144 7.703328 TGTTTAGGAACAAACTCAATGACTTC 58.297 34.615 0.00 0.00 42.54 3.01
4612 13433 2.789409 AAAGAGCAGTATCACCACCC 57.211 50.000 0.00 0.00 0.00 4.61
4736 13564 3.282831 AGCAACTTGTACGCCAAATTC 57.717 42.857 0.00 0.00 31.20 2.17
4737 13565 3.380142 CAAGCAACTTGTACGCCAAATT 58.620 40.909 0.00 0.00 36.79 1.82
4738 13566 3.011949 CAAGCAACTTGTACGCCAAAT 57.988 42.857 0.00 0.00 36.79 2.32
4739 13567 2.483583 CAAGCAACTTGTACGCCAAA 57.516 45.000 0.00 0.00 36.79 3.28
4835 13663 5.878406 AGGTAACCATCTAGTCCATCTTG 57.122 43.478 0.00 0.00 37.17 3.02
5197 14025 6.619744 TCACACAAGCCAACATAAACATATG 58.380 36.000 0.00 0.00 0.00 1.78
5212 14040 3.565482 TCTTCAGGTTTGATCACACAAGC 59.435 43.478 13.73 6.98 32.27 4.01
5390 14218 5.640218 AAAACAACTGCATTCGTCAATTG 57.360 34.783 0.00 0.00 0.00 2.32
5403 14231 6.098679 TCATGTCTTTGACCAAAAACAACTG 58.901 36.000 5.83 2.12 0.00 3.16
5557 14389 6.154877 TGCATCCCAAATGTGATTAATCAAGT 59.845 34.615 19.55 8.65 38.75 3.16
5737 14569 2.500098 CCGTGGTCATCCTCCTTTTCTA 59.500 50.000 0.00 0.00 34.23 2.10
5755 14587 0.757188 CTCCCAGATACAGAGCCCGT 60.757 60.000 0.00 0.00 0.00 5.28
5759 14591 4.620332 GCATACATCTCCCAGATACAGAGC 60.620 50.000 0.00 0.00 32.12 4.09
5765 14597 1.550524 GCCGCATACATCTCCCAGATA 59.449 52.381 0.00 0.00 32.12 1.98
5778 14610 6.714810 AGAATAATCAATAAAGTGGCCGCATA 59.285 34.615 20.59 11.66 0.00 3.14
5845 14677 3.132824 AGTGGCATATGTTGTCGAGATGA 59.867 43.478 4.29 0.00 30.28 2.92
5851 14683 3.123804 GGAGTAGTGGCATATGTTGTCG 58.876 50.000 4.29 0.00 30.28 4.35
5853 14685 5.012148 GGATAGGAGTAGTGGCATATGTTGT 59.988 44.000 4.29 0.00 0.00 3.32
5903 14735 2.618045 GGTGAGTGGTCTGGGTATTTGG 60.618 54.545 0.00 0.00 0.00 3.28
5941 14786 2.495409 CCGGTATGTGGCTCGGCTA 61.495 63.158 0.00 0.00 35.95 3.93
5999 14844 2.203070 GTGGAAGATGGCGGCGAT 60.203 61.111 12.98 0.00 0.00 4.58
6033 14878 5.923204 ACAAGGTAGAAGCCTCAATATCTG 58.077 41.667 0.00 0.00 38.03 2.90
6077 14925 2.347490 GTCTGGCGTCATGGTGGT 59.653 61.111 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.