Multiple sequence alignment - TraesCS2D01G012000

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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 TraesCS2D01G012000 chr2D 100.000 4151 0 0 1 4151 5727121 5731271 0.000000e+00 7666.0
1 TraesCS2D01G012000 chr2D 91.343 335 24 2 7 338 460867340 460867008 1.760000e-123 453.0
2 TraesCS2D01G012000 chr2D 91.860 86 6 1 2351 2436 566557840 566557924 7.290000e-23 119.0
3 TraesCS2D01G012000 chr2D 97.368 38 1 0 3389 3426 121777058 121777021 9.630000e-07 65.8
4 TraesCS2D01G012000 chr2D 100.000 33 0 0 3390 3422 550804723 550804755 1.250000e-05 62.1
5 TraesCS2D01G012000 chr2A 89.670 3427 174 63 856 4151 4313974 4310597 0.000000e+00 4202.0
6 TraesCS2D01G012000 chr2A 97.368 38 1 0 3389 3426 125951696 125951659 9.630000e-07 65.8
7 TraesCS2D01G012000 chr2A 94.737 38 2 0 3389 3426 637977501 637977464 4.480000e-05 60.2
8 TraesCS2D01G012000 chr2B 87.927 878 78 10 1475 2347 5608894 5609748 0.000000e+00 1009.0
9 TraesCS2D01G012000 chr2B 89.696 757 33 15 2431 3185 5609750 5610463 0.000000e+00 924.0
10 TraesCS2D01G012000 chr2B 87.639 631 23 23 855 1448 5608290 5608902 0.000000e+00 682.0
11 TraesCS2D01G012000 chr2B 86.878 221 20 2 1067 1287 728409715 728409504 5.360000e-59 239.0
12 TraesCS2D01G012000 chr1A 87.538 666 52 12 18 658 412453525 412452866 0.000000e+00 741.0
13 TraesCS2D01G012000 chr1A 87.425 167 15 3 656 821 249129962 249129801 1.970000e-43 187.0
14 TraesCS2D01G012000 chr1A 84.211 171 23 2 652 821 507912015 507911848 3.320000e-36 163.0
15 TraesCS2D01G012000 chr1A 83.429 175 24 3 648 821 391234126 391234296 1.540000e-34 158.0
16 TraesCS2D01G012000 chr1A 94.231 52 1 2 1229 1279 548496005 548495955 1.240000e-10 78.7
17 TraesCS2D01G012000 chr7A 96.730 367 7 2 1223 1585 395487355 395487720 1.280000e-169 606.0
18 TraesCS2D01G012000 chr7A 85.185 459 40 18 376 812 137913177 137913629 2.940000e-121 446.0
19 TraesCS2D01G012000 chr7A 85.714 224 23 4 1064 1287 2372704 2372918 1.160000e-55 228.0
20 TraesCS2D01G012000 chr7A 90.217 92 7 2 2345 2436 171555467 171555378 7.290000e-23 119.0
21 TraesCS2D01G012000 chr5D 96.694 363 12 0 1223 1585 457376017 457375655 4.590000e-169 604.0
22 TraesCS2D01G012000 chr5D 93.731 335 17 2 7 338 344691614 344691281 2.230000e-137 499.0
23 TraesCS2D01G012000 chr5D 86.830 448 46 6 376 821 331514479 331514043 4.820000e-134 488.0
24 TraesCS2D01G012000 chr5D 87.824 386 30 12 4 377 431559589 431559969 1.770000e-118 436.0
25 TraesCS2D01G012000 chr5D 91.558 308 15 8 376 679 217061030 217061330 8.300000e-112 414.0
26 TraesCS2D01G012000 chr5D 90.879 307 19 7 376 679 35278738 35278438 1.800000e-108 403.0
27 TraesCS2D01G012000 chr5D 88.889 171 13 2 652 821 344690343 344690178 5.440000e-49 206.0
28 TraesCS2D01G012000 chr5D 86.875 160 15 4 653 811 224762420 224762266 1.530000e-39 174.0
29 TraesCS2D01G012000 chr5D 96.610 59 1 1 1223 1280 26628294 26628352 3.420000e-16 97.1
30 TraesCS2D01G012000 chr5D 97.297 37 1 0 3390 3426 43040922 43040958 3.460000e-06 63.9
31 TraesCS2D01G012000 chr3D 96.226 371 6 1 1223 1585 145735954 145736324 5.940000e-168 601.0
32 TraesCS2D01G012000 chr3D 89.211 380 31 8 4 377 406174479 406174854 2.260000e-127 466.0
33 TraesCS2D01G012000 chr3D 83.958 480 35 19 376 821 216460739 216461210 4.960000e-114 422.0
34 TraesCS2D01G012000 chr3D 91.531 307 20 6 376 679 126394429 126394732 6.420000e-113 418.0
35 TraesCS2D01G012000 chr3D 87.719 171 15 2 652 821 435710732 435710897 1.180000e-45 195.0
36 TraesCS2D01G012000 chr3D 87.578 161 14 2 652 811 126394735 126394890 9.170000e-42 182.0
37 TraesCS2D01G012000 chr3D 96.610 59 1 1 1223 1280 567955179 567955121 3.420000e-16 97.1
38 TraesCS2D01G012000 chr3D 93.750 64 1 3 1223 1283 510142401 510142338 4.420000e-15 93.5
39 TraesCS2D01G012000 chr4A 94.340 371 12 2 1223 1585 190529248 190528879 1.010000e-155 560.0
40 TraesCS2D01G012000 chr4A 85.843 332 33 9 3 331 106358840 106359160 1.430000e-89 340.0
41 TraesCS2D01G012000 chr4A 84.000 150 15 2 1064 1213 373805450 373805310 7.240000e-28 135.0
42 TraesCS2D01G012000 chr4A 84.000 150 15 2 1064 1213 606355840 606355700 7.240000e-28 135.0
43 TraesCS2D01G012000 chr4A 90.909 88 7 1 2351 2438 338747849 338747763 2.620000e-22 117.0
44 TraesCS2D01G012000 chr4A 100.000 29 0 0 3389 3417 714847514 714847486 2.000000e-03 54.7
45 TraesCS2D01G012000 chr3A 87.333 450 37 13 376 821 438774770 438775203 8.010000e-137 497.0
46 TraesCS2D01G012000 chr3A 91.011 89 6 2 2351 2439 550510612 550510698 7.290000e-23 119.0
47 TraesCS2D01G012000 chr3A 100.000 34 0 0 3390 3423 194704380 194704413 3.460000e-06 63.9
48 TraesCS2D01G012000 chr4D 86.667 450 42 12 376 821 73211461 73211896 2.240000e-132 483.0
49 TraesCS2D01G012000 chr4D 85.057 174 23 1 648 821 23271751 23271581 1.530000e-39 174.0
50 TraesCS2D01G012000 chr4D 83.125 160 22 2 662 821 99205970 99206124 1.560000e-29 141.0
51 TraesCS2D01G012000 chr4D 87.302 126 11 3 654 779 56946545 56946665 5.600000e-29 139.0
52 TraesCS2D01G012000 chr4D 87.640 89 10 1 2347 2435 291470250 291470163 7.340000e-18 102.0
53 TraesCS2D01G012000 chr4D 96.610 59 1 1 1223 1280 60090753 60090811 3.420000e-16 97.1
54 TraesCS2D01G012000 chr4D 97.222 36 1 0 2351 2386 12297235 12297270 1.250000e-05 62.1
55 TraesCS2D01G012000 chr4D 100.000 29 0 0 2350 2378 187246590 187246562 2.000000e-03 54.7
56 TraesCS2D01G012000 chr7D 91.617 334 25 2 8 338 66963699 66964032 3.780000e-125 459.0
57 TraesCS2D01G012000 chr7D 90.801 337 30 1 3 338 392216156 392216492 2.280000e-122 449.0
58 TraesCS2D01G012000 chr7D 87.240 384 27 17 7 377 565209772 565209398 6.420000e-113 418.0
59 TraesCS2D01G012000 chr7D 87.730 326 30 7 7 326 607550093 607549772 5.070000e-99 372.0
60 TraesCS2D01G012000 chr7D 87.059 170 19 1 652 821 66965581 66965747 5.480000e-44 189.0
61 TraesCS2D01G012000 chr7D 87.059 170 17 2 652 821 511939833 511939997 1.970000e-43 187.0
62 TraesCS2D01G012000 chr7D 100.000 37 0 0 3390 3426 388038989 388039025 7.450000e-08 69.4
63 TraesCS2D01G012000 chr7D 94.872 39 1 1 3389 3426 101098939 101098977 4.480000e-05 60.2
64 TraesCS2D01G012000 chr1D 91.291 333 22 5 11 338 484182327 484181997 8.190000e-122 448.0
65 TraesCS2D01G012000 chr1D 93.407 91 5 1 2351 2441 303314694 303314783 2.600000e-27 134.0
66 TraesCS2D01G012000 chr1D 88.889 90 7 3 2348 2436 122770082 122770169 1.580000e-19 108.0
67 TraesCS2D01G012000 chr1D 87.912 91 7 3 2351 2438 238320630 238320719 2.040000e-18 104.0
68 TraesCS2D01G012000 chr1D 94.915 59 2 1 1223 1280 164906987 164907045 1.590000e-14 91.6
69 TraesCS2D01G012000 chr4B 84.444 450 49 14 376 821 517365769 517365337 1.380000e-114 424.0
70 TraesCS2D01G012000 chr4B 83.047 466 51 19 376 821 400362454 400362911 8.360000e-107 398.0
71 TraesCS2D01G012000 chr4B 86.854 213 18 2 1067 1279 275996517 275996315 3.230000e-56 230.0
72 TraesCS2D01G012000 chr4B 86.735 98 9 4 2344 2439 144280460 144280555 5.680000e-19 106.0
73 TraesCS2D01G012000 chr4B 88.636 88 9 1 2351 2438 351614315 351614229 5.680000e-19 106.0
74 TraesCS2D01G012000 chr4B 96.364 55 1 1 1227 1280 475719321 475719267 5.720000e-14 89.8
75 TraesCS2D01G012000 chr6D 83.333 468 47 13 376 821 87469335 87468877 1.800000e-108 403.0
76 TraesCS2D01G012000 chr6D 81.562 461 58 11 376 821 452836727 452837175 5.100000e-94 355.0
77 TraesCS2D01G012000 chr6D 85.294 170 22 1 652 821 302581338 302581172 5.520000e-39 172.0
78 TraesCS2D01G012000 chr6D 87.356 87 8 3 2350 2436 91851806 91851889 3.420000e-16 97.1
79 TraesCS2D01G012000 chr6D 97.561 41 1 0 2351 2391 410152903 410152943 2.070000e-08 71.3
80 TraesCS2D01G012000 chr6D 92.000 50 3 1 2347 2396 82969859 82969907 7.450000e-08 69.4
81 TraesCS2D01G012000 chr6D 100.000 33 0 0 3389 3421 436862720 436862752 1.250000e-05 62.1
82 TraesCS2D01G012000 chr6D 94.595 37 2 0 3390 3426 12086451 12086415 1.610000e-04 58.4
83 TraesCS2D01G012000 chr6D 94.595 37 2 0 3390 3426 411950599 411950563 1.610000e-04 58.4
84 TraesCS2D01G012000 chr5B 86.878 221 20 2 1067 1287 22064372 22064161 5.360000e-59 239.0
85 TraesCS2D01G012000 chr5B 89.349 169 15 2 652 819 668818622 668818788 4.210000e-50 209.0
86 TraesCS2D01G012000 chr6B 85.714 224 23 4 1064 1287 653312179 653312393 1.160000e-55 228.0
87 TraesCS2D01G012000 chr6B 88.485 165 16 2 657 821 128883925 128884086 3.270000e-46 196.0
88 TraesCS2D01G012000 chr6B 97.403 77 1 1 1205 1280 83251318 83251242 3.370000e-26 130.0
89 TraesCS2D01G012000 chr6B 94.805 77 3 1 1205 1280 83264235 83264159 7.290000e-23 119.0
90 TraesCS2D01G012000 chr7B 79.880 333 30 14 4 329 724805340 724805642 4.210000e-50 209.0
91 TraesCS2D01G012000 chr7B 84.028 144 14 2 1064 1207 178408297 178408431 3.370000e-26 130.0
92 TraesCS2D01G012000 chrUn 86.335 161 18 1 652 812 108278456 108278300 5.520000e-39 172.0
93 TraesCS2D01G012000 chrUn 82.456 171 25 3 652 821 462207446 462207280 1.200000e-30 145.0
94 TraesCS2D01G012000 chrUn 90.217 92 7 2 2345 2436 82713410 82713321 7.290000e-23 119.0
95 TraesCS2D01G012000 chrUn 91.860 86 6 1 2351 2436 82713321 82713405 7.290000e-23 119.0
96 TraesCS2D01G012000 chrUn 92.063 63 2 3 1224 1283 114694965 114694903 7.390000e-13 86.1
97 TraesCS2D01G012000 chrUn 100.000 29 0 0 2417 2445 95593951 95593979 2.000000e-03 54.7
98 TraesCS2D01G012000 chrUn 100.000 29 0 0 3389 3417 328056416 328056388 2.000000e-03 54.7
99 TraesCS2D01G012000 chr1B 96.629 89 3 0 1064 1152 679326798 679326886 9.300000e-32 148.0
100 TraesCS2D01G012000 chr1B 84.000 150 15 2 1064 1213 258837704 258837564 7.240000e-28 135.0
101 TraesCS2D01G012000 chr1B 91.304 92 7 1 2351 2442 410793965 410794055 1.570000e-24 124.0
102 TraesCS2D01G012000 chr1B 87.500 96 10 2 2350 2444 549520555 549520461 4.390000e-20 110.0
103 TraesCS2D01G012000 chr6A 94.595 37 2 0 3390 3426 602667398 602667362 1.610000e-04 58.4


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 TraesCS2D01G012000 chr2D 5727121 5731271 4150 False 7666.000000 7666 100.000000 1 4151 1 chr2D.!!$F1 4150
1 TraesCS2D01G012000 chr2A 4310597 4313974 3377 True 4202.000000 4202 89.670000 856 4151 1 chr2A.!!$R1 3295
2 TraesCS2D01G012000 chr2B 5608290 5610463 2173 False 871.666667 1009 88.420667 855 3185 3 chr2B.!!$F1 2330
3 TraesCS2D01G012000 chr1A 412452866 412453525 659 True 741.000000 741 87.538000 18 658 1 chr1A.!!$R2 640
4 TraesCS2D01G012000 chr5D 344690178 344691614 1436 True 352.500000 499 91.310000 7 821 2 chr5D.!!$R5 814
5 TraesCS2D01G012000 chr7D 66963699 66965747 2048 False 324.000000 459 89.338000 8 821 2 chr7D.!!$F5 813

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
833 2650 0.037605 CGGACAAGCCCGTTAGAGTT 60.038 55.0 0.0 0.0 44.23 3.01 F
882 2700 0.178831 AATGTTCCCCCTCAGTCCCT 60.179 55.0 0.0 0.0 0.00 4.20 F
1360 3199 0.178995 TGTGCATCCAAGAACTGGCA 60.179 50.0 0.0 0.0 45.98 4.92 F
1502 3386 0.186386 TAGGGTGGGTTGGTTGGTTG 59.814 55.0 0.0 0.0 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2697 4593 0.178068 CCACGGAACTACCCCATCAG 59.822 60.000 0.00 0.0 34.64 2.90 R
2982 4878 6.183360 CCTCATACAAGTACCACGAGATGTAA 60.183 42.308 0.00 0.0 0.00 2.41 R
3059 4955 1.256812 TGCTGTCAAGATCGTGGAGA 58.743 50.000 8.84 0.0 0.00 3.71 R
3249 5183 1.948611 GCATCGGGTTCTGCAGGTAAA 60.949 52.381 15.13 0.0 38.28 2.01 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
68 73 1.354368 TCCACCACTTCCCTCCATTTC 59.646 52.381 0.00 0.00 0.00 2.17
83 88 1.176182 ATTTCCCCCAAAACCCTCCT 58.824 50.000 0.00 0.00 0.00 3.69
281 286 1.271840 AATAGCGGGCAAGGGAGTCA 61.272 55.000 0.00 0.00 0.00 3.41
409 2195 4.849813 TCATGAAGGTGGATCTCAACAT 57.150 40.909 0.00 0.00 34.94 2.71
494 2280 3.527427 TGATCTCGTGGCGGCGAT 61.527 61.111 12.98 0.00 40.29 4.58
630 2417 2.045926 AGTGCGCCAGGATGAACC 60.046 61.111 4.18 0.00 39.69 3.62
691 2508 4.384599 GCATGATCTATGGCCGCA 57.615 55.556 0.00 0.00 37.26 5.69
692 2509 2.864114 GCATGATCTATGGCCGCAT 58.136 52.632 0.00 0.00 37.26 4.73
695 2512 0.327259 ATGATCTATGGCCGCATGCT 59.673 50.000 17.13 0.00 40.92 3.79
700 2517 2.649190 TCTATGGCCGCATGCTTTTTA 58.351 42.857 17.13 0.00 40.92 1.52
701 2518 3.020274 TCTATGGCCGCATGCTTTTTAA 58.980 40.909 17.13 0.00 40.92 1.52
702 2519 2.758736 ATGGCCGCATGCTTTTTAAA 57.241 40.000 17.13 0.00 40.92 1.52
703 2520 2.533266 TGGCCGCATGCTTTTTAAAA 57.467 40.000 17.13 0.00 40.92 1.52
764 2581 1.743623 CGCACTGCCGACCCAAATA 60.744 57.895 0.00 0.00 0.00 1.40
779 2596 3.895041 CCCAAATATAAAACAGGGCGGAT 59.105 43.478 0.00 0.00 0.00 4.18
783 2600 4.986054 ATATAAAACAGGGCGGATACCA 57.014 40.909 0.00 0.00 0.00 3.25
794 2611 4.171103 GATACCAGGCGGGCGGTT 62.171 66.667 19.31 10.13 42.05 4.44
812 2629 2.480587 GGTTGACCCAAACGGACAAAAG 60.481 50.000 0.00 0.00 45.88 2.27
813 2630 2.421751 TGACCCAAACGGACAAAAGA 57.578 45.000 0.00 0.00 33.04 2.52
821 2638 1.578583 ACGGACAAAAGACGGACAAG 58.421 50.000 0.00 0.00 0.00 3.16
822 2639 0.234884 CGGACAAAAGACGGACAAGC 59.765 55.000 0.00 0.00 0.00 4.01
823 2640 0.591659 GGACAAAAGACGGACAAGCC 59.408 55.000 0.00 0.00 0.00 4.35
824 2641 0.591659 GACAAAAGACGGACAAGCCC 59.408 55.000 0.00 0.00 0.00 5.19
831 2648 4.496670 CGGACAAGCCCGTTAGAG 57.503 61.111 0.00 0.00 44.23 2.43
832 2649 1.590147 CGGACAAGCCCGTTAGAGT 59.410 57.895 0.00 0.00 44.23 3.24
833 2650 0.037605 CGGACAAGCCCGTTAGAGTT 60.038 55.000 0.00 0.00 44.23 3.01
834 2651 1.439679 GGACAAGCCCGTTAGAGTTG 58.560 55.000 0.00 0.00 0.00 3.16
835 2652 0.796927 GACAAGCCCGTTAGAGTTGC 59.203 55.000 0.00 0.00 0.00 4.17
836 2653 0.396811 ACAAGCCCGTTAGAGTTGCT 59.603 50.000 0.00 0.00 0.00 3.91
837 2654 1.079503 CAAGCCCGTTAGAGTTGCTC 58.920 55.000 0.00 0.00 0.00 4.26
838 2655 0.977395 AAGCCCGTTAGAGTTGCTCT 59.023 50.000 4.02 4.02 43.83 4.09
839 2656 1.848652 AGCCCGTTAGAGTTGCTCTA 58.151 50.000 2.07 2.07 41.50 2.43
840 2657 2.176889 AGCCCGTTAGAGTTGCTCTAA 58.823 47.619 12.89 12.89 46.70 2.10
850 2667 5.562298 AGAGTTGCTCTAAAAAGTACCCA 57.438 39.130 0.00 0.00 39.28 4.51
851 2668 5.937111 AGAGTTGCTCTAAAAAGTACCCAA 58.063 37.500 0.00 0.00 39.28 4.12
852 2669 5.763698 AGAGTTGCTCTAAAAAGTACCCAAC 59.236 40.000 0.00 0.00 39.28 3.77
853 2670 4.514066 AGTTGCTCTAAAAAGTACCCAACG 59.486 41.667 0.00 0.00 37.12 4.10
872 2689 1.473434 CGGAGTAGCTGAATGTTCCCC 60.473 57.143 0.00 0.00 0.00 4.81
882 2700 0.178831 AATGTTCCCCCTCAGTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
883 2701 0.621862 ATGTTCCCCCTCAGTCCCTC 60.622 60.000 0.00 0.00 0.00 4.30
890 2708 0.543749 CCCTCAGTCCCTCCACAATC 59.456 60.000 0.00 0.00 0.00 2.67
944 2767 0.755698 TCGATCTTTCCCCCTCCTCG 60.756 60.000 0.00 0.00 0.00 4.63
945 2768 0.755698 CGATCTTTCCCCCTCCTCGA 60.756 60.000 0.00 0.00 0.00 4.04
946 2769 1.044611 GATCTTTCCCCCTCCTCGAG 58.955 60.000 5.13 5.13 0.00 4.04
947 2770 0.637195 ATCTTTCCCCCTCCTCGAGA 59.363 55.000 15.71 0.00 0.00 4.04
948 2771 0.324460 TCTTTCCCCCTCCTCGAGAC 60.324 60.000 15.71 0.00 0.00 3.36
949 2772 0.324830 CTTTCCCCCTCCTCGAGACT 60.325 60.000 15.71 0.00 0.00 3.24
950 2773 0.324460 TTTCCCCCTCCTCGAGACTC 60.324 60.000 15.71 0.00 0.00 3.36
1295 3134 0.696501 TTTCCCCTTCCTCCCGAAAG 59.303 55.000 0.00 0.00 0.00 2.62
1346 3185 0.903924 CCCACCCATCCAAATGTGCA 60.904 55.000 0.00 0.00 0.00 4.57
1348 3187 1.137479 CCACCCATCCAAATGTGCATC 59.863 52.381 0.00 0.00 0.00 3.91
1349 3188 1.137479 CACCCATCCAAATGTGCATCC 59.863 52.381 0.00 0.00 0.00 3.51
1357 3196 3.256383 TCCAAATGTGCATCCAAGAACTG 59.744 43.478 0.00 0.00 0.00 3.16
1359 3198 1.180029 ATGTGCATCCAAGAACTGGC 58.820 50.000 0.00 0.00 45.98 4.85
1360 3199 0.178995 TGTGCATCCAAGAACTGGCA 60.179 50.000 0.00 0.00 45.98 4.92
1361 3200 0.524862 GTGCATCCAAGAACTGGCAG 59.475 55.000 14.16 14.16 45.98 4.85
1423 3295 1.392853 GCAGCTCTGTCTGATTGTTCG 59.607 52.381 0.00 0.00 36.19 3.95
1429 3301 3.381045 TCTGTCTGATTGTTCGTGTGTC 58.619 45.455 0.00 0.00 0.00 3.67
1451 3325 6.152323 TGTCATACTCTGTTAGGGTTCAGTAC 59.848 42.308 0.00 0.00 33.89 2.73
1452 3326 6.377712 GTCATACTCTGTTAGGGTTCAGTACT 59.622 42.308 0.00 0.00 33.89 2.73
1453 3327 6.952358 TCATACTCTGTTAGGGTTCAGTACTT 59.048 38.462 0.00 0.00 33.89 2.24
1454 3328 5.725325 ACTCTGTTAGGGTTCAGTACTTC 57.275 43.478 0.00 0.00 33.89 3.01
1455 3329 5.145564 ACTCTGTTAGGGTTCAGTACTTCA 58.854 41.667 0.00 0.00 33.89 3.02
1456 3330 5.244178 ACTCTGTTAGGGTTCAGTACTTCAG 59.756 44.000 0.00 0.00 33.89 3.02
1457 3331 5.145564 TCTGTTAGGGTTCAGTACTTCAGT 58.854 41.667 0.00 0.00 33.89 3.41
1458 3332 5.601313 TCTGTTAGGGTTCAGTACTTCAGTT 59.399 40.000 0.00 0.00 33.89 3.16
1461 3335 6.126997 TGTTAGGGTTCAGTACTTCAGTTTCA 60.127 38.462 0.00 0.00 0.00 2.69
1481 3355 3.509388 CACCGACAGTGTAGGGTTC 57.491 57.895 24.21 0.00 41.93 3.62
1482 3356 0.677288 CACCGACAGTGTAGGGTTCA 59.323 55.000 24.21 0.00 41.93 3.18
1483 3357 1.275291 CACCGACAGTGTAGGGTTCAT 59.725 52.381 24.21 2.23 41.93 2.57
1484 3358 2.494471 CACCGACAGTGTAGGGTTCATA 59.506 50.000 24.21 0.00 41.93 2.15
1489 3373 2.838202 ACAGTGTAGGGTTCATAGGGTG 59.162 50.000 0.00 0.00 0.00 4.61
1499 3383 0.701731 TCATAGGGTGGGTTGGTTGG 59.298 55.000 0.00 0.00 0.00 3.77
1502 3386 0.186386 TAGGGTGGGTTGGTTGGTTG 59.814 55.000 0.00 0.00 0.00 3.77
1510 3394 1.951602 GGTTGGTTGGTTGGTGTAGAC 59.048 52.381 0.00 0.00 0.00 2.59
1522 3406 2.656560 GTGTAGACTGGCACCTAGTG 57.343 55.000 0.00 0.00 36.51 2.74
1541 3425 7.618512 ACCTAGTGGTAGTGTATGTTTATCTGT 59.381 37.037 0.00 0.00 46.43 3.41
1630 3516 3.416414 AGGCTAGGTACCAACAGGTAT 57.584 47.619 15.94 0.00 39.92 2.73
1662 3548 2.427453 CAAGATAGTGTACTGCCGGACT 59.573 50.000 5.05 0.00 0.00 3.85
1664 3550 1.067212 GATAGTGTACTGCCGGACTGG 59.933 57.143 5.05 0.00 42.50 4.00
1666 3552 1.215647 GTGTACTGCCGGACTGGAG 59.784 63.158 5.05 1.37 42.00 3.86
1667 3553 2.184579 GTACTGCCGGACTGGAGC 59.815 66.667 5.05 0.00 42.00 4.70
1749 3635 0.669625 CGGTCTCCCTTGGTTTCGAC 60.670 60.000 0.00 0.00 0.00 4.20
1816 3702 6.294176 CCCATAGCCTAATGTTTAGTTGCATC 60.294 42.308 0.00 0.00 0.00 3.91
1817 3703 6.294176 CCATAGCCTAATGTTTAGTTGCATCC 60.294 42.308 0.00 0.00 0.00 3.51
1846 3732 3.006752 TGCAAAATGTGGGTTTCTGGATC 59.993 43.478 0.00 0.00 0.00 3.36
1881 3767 5.181748 AGTTGACTCCTGCAAATGATCTAC 58.818 41.667 0.00 0.00 0.00 2.59
1894 3780 4.909696 ATGATCTACTCTGACGGAACAG 57.090 45.455 0.00 0.00 39.02 3.16
1993 3879 8.680039 TTGTTATCTCATGCATATCATTCACA 57.320 30.769 0.00 0.00 31.79 3.58
1994 3880 8.319143 TGTTATCTCATGCATATCATTCACAG 57.681 34.615 0.00 0.00 31.79 3.66
1998 3884 5.038651 TCATGCATATCATTCACAGTGGA 57.961 39.130 0.00 0.00 31.79 4.02
2001 3887 5.612725 TGCATATCATTCACAGTGGAGTA 57.387 39.130 0.00 0.00 0.00 2.59
2066 3952 4.929819 AAGTGCGTAATTTGGTTTTCCT 57.070 36.364 0.00 0.00 41.38 3.36
2245 4131 7.701924 GTACATGTACAACCATTGATGGATTTG 59.298 37.037 27.37 12.94 41.72 2.32
2276 4162 2.819608 GCAAATGTCAAGTTAGCTGGGA 59.180 45.455 0.00 0.00 0.00 4.37
2296 4182 7.125792 TGGGACTTATAAAAGATGGAGTCTC 57.874 40.000 0.00 0.00 35.67 3.36
2447 4333 7.363617 GGGATGGAGGGAGTATTATTTAGTACG 60.364 44.444 0.00 0.00 0.00 3.67
2450 4336 5.479724 GGAGGGAGTATTATTTAGTACGGCT 59.520 44.000 0.00 0.00 0.00 5.52
2576 4464 9.799106 ATAGAGGTTCAATTATGATTTGGTAGG 57.201 33.333 0.00 0.00 34.96 3.18
2691 4587 6.346477 TGGTCTATATCTCTGTATTGTGGC 57.654 41.667 0.00 0.00 0.00 5.01
2982 4878 1.000283 GAGTATGCTGCTACCGATGCT 60.000 52.381 0.00 0.00 0.00 3.79
3064 4960 9.159254 TCTTATAAGCTGATATTCCTTTCTCCA 57.841 33.333 7.67 0.00 0.00 3.86
3065 4961 9.213799 CTTATAAGCTGATATTCCTTTCTCCAC 57.786 37.037 0.00 0.00 0.00 4.02
3066 4962 4.065321 AGCTGATATTCCTTTCTCCACG 57.935 45.455 0.00 0.00 0.00 4.94
3067 4963 3.706594 AGCTGATATTCCTTTCTCCACGA 59.293 43.478 0.00 0.00 0.00 4.35
3068 4964 4.346418 AGCTGATATTCCTTTCTCCACGAT 59.654 41.667 0.00 0.00 0.00 3.73
3069 4965 4.688413 GCTGATATTCCTTTCTCCACGATC 59.312 45.833 0.00 0.00 0.00 3.69
3070 4966 5.510520 GCTGATATTCCTTTCTCCACGATCT 60.511 44.000 0.00 0.00 0.00 2.75
3166 5076 5.913137 TGTTTAGGGAACATATTTGCAGG 57.087 39.130 0.00 0.00 43.13 4.85
3170 5080 8.275758 TGTTTAGGGAACATATTTGCAGGTATA 58.724 33.333 0.00 0.00 43.13 1.47
3185 5095 5.353123 TGCAGGTATACAAGAAATCGGAAAC 59.647 40.000 5.01 0.00 0.00 2.78
3186 5096 5.353123 GCAGGTATACAAGAAATCGGAAACA 59.647 40.000 5.01 0.00 0.00 2.83
3187 5097 6.128117 GCAGGTATACAAGAAATCGGAAACAA 60.128 38.462 5.01 0.00 0.00 2.83
3188 5098 7.574217 GCAGGTATACAAGAAATCGGAAACAAA 60.574 37.037 5.01 0.00 0.00 2.83
3189 5099 7.962918 CAGGTATACAAGAAATCGGAAACAAAG 59.037 37.037 5.01 0.00 0.00 2.77
3190 5100 7.120726 AGGTATACAAGAAATCGGAAACAAAGG 59.879 37.037 5.01 0.00 0.00 3.11
3224 5158 2.398588 TCACTTCTCAACCAGGTCAGT 58.601 47.619 0.00 0.00 0.00 3.41
3231 5165 5.304686 TCTCAACCAGGTCAGTAATGTTT 57.695 39.130 0.00 0.00 0.00 2.83
3262 5196 7.486802 TTACAGTTTACTTTACCTGCAGAAC 57.513 36.000 17.39 8.92 0.00 3.01
3287 5221 6.428159 CCCGATGCTAGCTATGACTTATTTTT 59.572 38.462 17.23 0.00 0.00 1.94
3292 5226 7.109501 TGCTAGCTATGACTTATTTTTCACCA 58.890 34.615 17.23 0.00 0.00 4.17
3303 5237 7.386059 ACTTATTTTTCACCACCAATGATTCC 58.614 34.615 0.00 0.00 0.00 3.01
3306 5240 5.822132 TTTTCACCACCAATGATTCCATT 57.178 34.783 0.00 0.00 43.37 3.16
3314 5248 5.186409 CCACCAATGATTCCATTCTGTCTTT 59.814 40.000 0.00 0.00 40.81 2.52
3318 5252 6.154021 CCAATGATTCCATTCTGTCTTTTCCT 59.846 38.462 0.00 0.00 40.81 3.36
3400 5334 9.582648 TTTTAAATTAGCTTTTACTCCCTCTGT 57.417 29.630 0.00 0.00 0.00 3.41
3404 5338 8.563123 AATTAGCTTTTACTCCCTCTGTAAAC 57.437 34.615 0.00 0.00 38.91 2.01
3405 5339 5.827326 AGCTTTTACTCCCTCTGTAAACT 57.173 39.130 0.00 0.00 38.91 2.66
3408 5342 7.061054 AGCTTTTACTCCCTCTGTAAACTTTT 58.939 34.615 0.00 0.00 38.91 2.27
3409 5343 8.215736 AGCTTTTACTCCCTCTGTAAACTTTTA 58.784 33.333 0.00 0.00 38.91 1.52
3410 5344 9.011095 GCTTTTACTCCCTCTGTAAACTTTTAT 57.989 33.333 0.00 0.00 38.91 1.40
3416 5350 8.319881 ACTCCCTCTGTAAACTTTTATAAGACC 58.680 37.037 0.00 0.00 35.30 3.85
3417 5351 8.445361 TCCCTCTGTAAACTTTTATAAGACCT 57.555 34.615 0.00 0.00 35.30 3.85
3418 5352 8.887393 TCCCTCTGTAAACTTTTATAAGACCTT 58.113 33.333 0.00 0.00 35.30 3.50
3419 5353 9.516546 CCCTCTGTAAACTTTTATAAGACCTTT 57.483 33.333 0.00 0.00 35.30 3.11
3436 5370 8.712228 AAGACCTTTTAGATCTCAAATGGTTT 57.288 30.769 22.02 17.84 41.15 3.27
3440 5374 9.807921 ACCTTTTAGATCTCAAATGGTTTAAGA 57.192 29.630 18.81 0.00 39.22 2.10
3458 5392 9.726232 GGTTTAAGACTAGTTTAGTTTTTGGTG 57.274 33.333 0.00 0.00 39.59 4.17
3509 5447 6.265422 TCTGAAAATCTTCCTTGAGAAAACCC 59.735 38.462 0.00 0.00 32.88 4.11
3534 5472 4.827692 ACTTGTTGGGTTTCCTTGTTTTC 58.172 39.130 0.00 0.00 0.00 2.29
3558 5496 8.402798 TCATCAAAAACTTGCTAGTTCCAATA 57.597 30.769 13.94 0.61 43.74 1.90
3559 5497 8.514594 TCATCAAAAACTTGCTAGTTCCAATAG 58.485 33.333 13.94 4.49 43.74 1.73
3579 5517 2.840651 AGGGTCTGTCATAAAGTCCCAG 59.159 50.000 8.19 0.00 43.25 4.45
3606 5544 1.462238 ACTCCCAGTGCTCCAACCT 60.462 57.895 0.00 0.00 0.00 3.50
3625 5566 3.243602 ACCTGTTCCGTTAAATTTGCCAC 60.244 43.478 0.00 0.00 0.00 5.01
3630 5571 4.974368 TCCGTTAAATTTGCCACATAGG 57.026 40.909 0.00 0.00 41.84 2.57
3660 5601 6.731467 ACCTGATGTGGAGGTACAATTAAAT 58.269 36.000 0.00 0.00 42.35 1.40
3731 5695 4.894784 TGTAGGTGGAACTGAGACAAATC 58.105 43.478 0.00 0.00 36.74 2.17
3754 5718 0.913924 TGCCATCCTGATCTCTTGCA 59.086 50.000 0.00 0.00 0.00 4.08
3773 5737 2.545946 GCACATATCCTCCTCGCTTTTC 59.454 50.000 0.00 0.00 0.00 2.29
3774 5738 3.742640 GCACATATCCTCCTCGCTTTTCT 60.743 47.826 0.00 0.00 0.00 2.52
3775 5739 4.446371 CACATATCCTCCTCGCTTTTCTT 58.554 43.478 0.00 0.00 0.00 2.52
3776 5740 4.878397 CACATATCCTCCTCGCTTTTCTTT 59.122 41.667 0.00 0.00 0.00 2.52
3794 5758 0.871722 TTTTCACTTGCCCATCGTCG 59.128 50.000 0.00 0.00 0.00 5.12
3809 5773 1.194547 TCGTCGTCGTAACCACAGTAC 59.805 52.381 1.33 0.00 38.33 2.73
3830 5794 1.926511 CTCATTGCCCAACCTGTCGC 61.927 60.000 0.00 0.00 0.00 5.19
3845 5809 0.603569 GTCGCTGTCCTCTCCTTTCA 59.396 55.000 0.00 0.00 0.00 2.69
3846 5810 0.891373 TCGCTGTCCTCTCCTTTCAG 59.109 55.000 0.00 0.00 0.00 3.02
3855 5819 1.349026 CTCTCCTTTCAGACCAAGCCA 59.651 52.381 0.00 0.00 0.00 4.75
3859 5823 1.477558 CCTTTCAGACCAAGCCACACT 60.478 52.381 0.00 0.00 0.00 3.55
3876 5840 4.321452 CCACACTGTCATCCCAATTCAAAG 60.321 45.833 0.00 0.00 0.00 2.77
3880 5844 1.818674 GTCATCCCAATTCAAAGCCGT 59.181 47.619 0.00 0.00 0.00 5.68
3883 5847 0.178975 TCCCAATTCAAAGCCGTGGT 60.179 50.000 0.00 0.00 0.00 4.16
3884 5848 0.678950 CCCAATTCAAAGCCGTGGTT 59.321 50.000 0.00 0.00 0.00 3.67
3921 5885 0.896940 AAGCCACCAGAGCCATTGTG 60.897 55.000 0.00 0.00 0.00 3.33
3930 5894 0.537143 GAGCCATTGTGTCCACACCA 60.537 55.000 7.38 0.00 45.88 4.17
3931 5895 0.823356 AGCCATTGTGTCCACACCAC 60.823 55.000 7.38 0.00 45.88 4.16
3934 5898 1.152830 ATTGTGTCCACACCACCCC 59.847 57.895 7.38 0.00 45.88 4.95
3944 5908 1.228793 CACCACCCCCAAAGTGTCA 59.771 57.895 0.00 0.00 33.20 3.58
3949 5913 0.850100 ACCCCCAAAGTGTCATGACA 59.150 50.000 24.56 24.56 39.32 3.58
3950 5914 1.202927 ACCCCCAAAGTGTCATGACAG 60.203 52.381 28.54 16.32 42.74 3.51
3951 5915 1.202927 CCCCCAAAGTGTCATGACAGT 60.203 52.381 28.54 27.76 46.18 3.55
3969 5957 2.351244 TTGTCCTCGCATCCTCGCT 61.351 57.895 0.00 0.00 0.00 4.93
3971 5959 2.755876 TCCTCGCATCCTCGCTGT 60.756 61.111 0.00 0.00 0.00 4.40
3998 5986 4.260355 CCGCTGGCATTGCATCCG 62.260 66.667 11.39 8.77 0.00 4.18
4000 5988 2.549198 CGCTGGCATTGCATCCGAT 61.549 57.895 11.39 0.00 0.00 4.18
4001 5989 1.285023 GCTGGCATTGCATCCGATC 59.715 57.895 11.39 0.00 0.00 3.69
4002 5990 1.449726 GCTGGCATTGCATCCGATCA 61.450 55.000 11.39 0.00 0.00 2.92
4013 6007 3.499537 TGCATCCGATCAACATGAATAGC 59.500 43.478 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 59 0.709992 TTGGGGGAAATGGAGGGAAG 59.290 55.000 0.00 0.00 0.00 3.46
68 73 2.283894 GCAGGAGGGTTTTGGGGG 60.284 66.667 0.00 0.00 0.00 5.40
119 124 2.435586 TCGAGGTCGAGGTCGTCC 60.436 66.667 14.24 7.48 44.22 4.79
230 235 0.746063 CCTTCTTTGGCTTGTGTGCA 59.254 50.000 0.00 0.00 34.04 4.57
260 265 1.271840 ACTCCCTTGCCCGCTATTCA 61.272 55.000 0.00 0.00 0.00 2.57
264 269 2.284331 TGACTCCCTTGCCCGCTA 60.284 61.111 0.00 0.00 0.00 4.26
281 286 3.721706 CGGCCCTTCCTCTTGGCT 61.722 66.667 0.00 0.00 44.71 4.75
384 1597 5.045359 TGTTGAGATCCACCTTCATGATCTT 60.045 40.000 0.00 0.00 43.90 2.40
409 2195 1.289066 CTCTTCCTTGGCGACACGA 59.711 57.895 0.00 0.00 42.67 4.35
510 2296 2.331893 GCACACAAGCCGGCATACA 61.332 57.895 31.54 0.00 0.00 2.29
533 2319 4.796231 ATCGCGGCTCGTGGTCAC 62.796 66.667 6.13 0.00 37.97 3.67
623 2410 5.560966 AAAATATCACCACACGGTTCATC 57.439 39.130 0.00 0.00 46.31 2.92
720 2537 1.933115 GCGCCGACCCATTTCATGTT 61.933 55.000 0.00 0.00 0.00 2.71
745 2562 2.457743 TATTTGGGTCGGCAGTGCGT 62.458 55.000 9.45 0.00 0.00 5.24
764 2581 2.158667 CCTGGTATCCGCCCTGTTTTAT 60.159 50.000 0.00 0.00 0.00 1.40
793 2610 2.424246 GTCTTTTGTCCGTTTGGGTCAA 59.576 45.455 0.00 0.00 41.22 3.18
794 2611 2.018515 GTCTTTTGTCCGTTTGGGTCA 58.981 47.619 0.00 0.00 37.00 4.02
821 2638 2.667473 TTAGAGCAACTCTAACGGGC 57.333 50.000 11.99 0.00 44.85 6.13
827 2644 6.675413 TGGGTACTTTTTAGAGCAACTCTA 57.325 37.500 0.16 0.16 41.50 2.43
828 2645 5.562298 TGGGTACTTTTTAGAGCAACTCT 57.438 39.130 2.23 2.23 43.83 3.24
829 2646 5.333875 CGTTGGGTACTTTTTAGAGCAACTC 60.334 44.000 0.00 0.00 0.00 3.01
830 2647 4.514066 CGTTGGGTACTTTTTAGAGCAACT 59.486 41.667 0.00 0.00 0.00 3.16
831 2648 4.319984 CCGTTGGGTACTTTTTAGAGCAAC 60.320 45.833 0.00 0.00 0.00 4.17
832 2649 3.816523 CCGTTGGGTACTTTTTAGAGCAA 59.183 43.478 0.00 0.00 0.00 3.91
833 2650 3.071312 TCCGTTGGGTACTTTTTAGAGCA 59.929 43.478 0.00 0.00 33.83 4.26
834 2651 3.667360 TCCGTTGGGTACTTTTTAGAGC 58.333 45.455 0.00 0.00 33.83 4.09
835 2652 4.891260 ACTCCGTTGGGTACTTTTTAGAG 58.109 43.478 0.00 0.00 33.83 2.43
836 2653 4.961438 ACTCCGTTGGGTACTTTTTAGA 57.039 40.909 0.00 0.00 33.83 2.10
837 2654 4.628766 GCTACTCCGTTGGGTACTTTTTAG 59.371 45.833 0.00 0.00 33.83 1.85
838 2655 4.284234 AGCTACTCCGTTGGGTACTTTTTA 59.716 41.667 0.00 0.00 33.83 1.52
839 2656 3.072038 AGCTACTCCGTTGGGTACTTTTT 59.928 43.478 0.00 0.00 33.83 1.94
840 2657 2.636403 AGCTACTCCGTTGGGTACTTTT 59.364 45.455 0.00 0.00 33.83 2.27
841 2658 2.028385 CAGCTACTCCGTTGGGTACTTT 60.028 50.000 0.00 0.00 33.83 2.66
842 2659 1.549170 CAGCTACTCCGTTGGGTACTT 59.451 52.381 0.00 0.00 33.83 2.24
843 2660 1.183549 CAGCTACTCCGTTGGGTACT 58.816 55.000 0.00 0.00 33.83 2.73
844 2661 1.180029 TCAGCTACTCCGTTGGGTAC 58.820 55.000 0.00 0.00 33.83 3.34
845 2662 1.927487 TTCAGCTACTCCGTTGGGTA 58.073 50.000 0.00 0.00 33.83 3.69
846 2663 1.066143 CATTCAGCTACTCCGTTGGGT 60.066 52.381 0.00 0.00 33.83 4.51
847 2664 1.066143 ACATTCAGCTACTCCGTTGGG 60.066 52.381 0.00 0.00 0.00 4.12
848 2665 2.386661 ACATTCAGCTACTCCGTTGG 57.613 50.000 0.00 0.00 0.00 3.77
849 2666 2.673368 GGAACATTCAGCTACTCCGTTG 59.327 50.000 0.00 0.00 0.00 4.10
850 2667 2.354805 GGGAACATTCAGCTACTCCGTT 60.355 50.000 0.00 0.00 0.00 4.44
851 2668 1.207329 GGGAACATTCAGCTACTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
852 2669 1.473434 GGGGAACATTCAGCTACTCCG 60.473 57.143 0.00 0.00 0.00 4.63
853 2670 1.134068 GGGGGAACATTCAGCTACTCC 60.134 57.143 0.00 0.00 0.00 3.85
872 2689 1.577736 AGATTGTGGAGGGACTGAGG 58.422 55.000 0.00 0.00 41.55 3.86
883 2701 9.814899 TGTATATTGCCAATTTTAAGATTGTGG 57.185 29.630 15.38 5.42 35.68 4.17
947 2770 2.154074 GGTGGTGGGACTTGGGAGT 61.154 63.158 0.00 0.00 39.32 3.85
948 2771 2.757077 GGTGGTGGGACTTGGGAG 59.243 66.667 0.00 0.00 0.00 4.30
949 2772 3.246112 CGGTGGTGGGACTTGGGA 61.246 66.667 0.00 0.00 0.00 4.37
950 2773 4.344865 CCGGTGGTGGGACTTGGG 62.345 72.222 0.00 0.00 0.00 4.12
1038 2861 0.514255 AGAAATCGTCGTCGTCGTCA 59.486 50.000 11.41 0.00 38.33 4.35
1295 3134 3.365364 CGATGAGTTCTTGGGTTCTTTGC 60.365 47.826 0.00 0.00 0.00 3.68
1335 3174 3.256383 CAGTTCTTGGATGCACATTTGGA 59.744 43.478 0.00 0.00 0.00 3.53
1336 3175 3.581755 CAGTTCTTGGATGCACATTTGG 58.418 45.455 0.00 0.00 0.00 3.28
1357 3196 2.783135 TCTTCCAAGTGATGAACTGCC 58.217 47.619 0.00 0.00 39.81 4.85
1359 3198 6.385033 GGATTTTCTTCCAAGTGATGAACTG 58.615 40.000 0.00 0.00 39.81 3.16
1360 3199 5.478332 GGGATTTTCTTCCAAGTGATGAACT 59.522 40.000 0.00 0.00 37.00 3.01
1361 3200 5.336770 GGGGATTTTCTTCCAAGTGATGAAC 60.337 44.000 0.00 0.00 37.00 3.18
1423 3295 4.803098 ACCCTAACAGAGTATGACACAC 57.197 45.455 0.00 0.00 0.00 3.82
1429 3301 6.777213 AGTACTGAACCCTAACAGAGTATG 57.223 41.667 0.00 0.00 37.54 2.39
1451 3325 3.393800 ACTGTCGGTGATGAAACTGAAG 58.606 45.455 0.00 0.00 37.20 3.02
1452 3326 3.469008 ACTGTCGGTGATGAAACTGAA 57.531 42.857 0.00 0.00 37.20 3.02
1474 3348 2.201830 CAACCCACCCTATGAACCCTA 58.798 52.381 0.00 0.00 0.00 3.53
1475 3349 0.999712 CAACCCACCCTATGAACCCT 59.000 55.000 0.00 0.00 0.00 4.34
1476 3350 0.033503 CCAACCCACCCTATGAACCC 60.034 60.000 0.00 0.00 0.00 4.11
1477 3351 0.702316 ACCAACCCACCCTATGAACC 59.298 55.000 0.00 0.00 0.00 3.62
1479 3353 1.076350 CCAACCAACCCACCCTATGAA 59.924 52.381 0.00 0.00 0.00 2.57
1481 3355 0.407918 ACCAACCAACCCACCCTATG 59.592 55.000 0.00 0.00 0.00 2.23
1482 3356 1.163408 AACCAACCAACCCACCCTAT 58.837 50.000 0.00 0.00 0.00 2.57
1483 3357 0.186386 CAACCAACCAACCCACCCTA 59.814 55.000 0.00 0.00 0.00 3.53
1484 3358 1.075600 CAACCAACCAACCCACCCT 60.076 57.895 0.00 0.00 0.00 4.34
1489 3373 1.133730 TCTACACCAACCAACCAACCC 60.134 52.381 0.00 0.00 0.00 4.11
1541 3425 6.720309 TGTCAATCCCACAAGATGATTAAGA 58.280 36.000 0.00 0.00 0.00 2.10
1549 3433 4.849813 TCAGATGTCAATCCCACAAGAT 57.150 40.909 0.00 0.00 32.77 2.40
1630 3516 2.093500 ACACTATCTTGCCGCTGAATGA 60.093 45.455 0.00 0.00 0.00 2.57
1662 3548 1.271054 GCTTTCTCCACTTCAGCTCCA 60.271 52.381 0.00 0.00 0.00 3.86
1664 3550 2.470983 AGCTTTCTCCACTTCAGCTC 57.529 50.000 0.00 0.00 35.95 4.09
1666 3552 2.739379 GTGTAGCTTTCTCCACTTCAGC 59.261 50.000 0.00 0.00 0.00 4.26
1667 3553 2.989840 CGTGTAGCTTTCTCCACTTCAG 59.010 50.000 0.00 0.00 28.15 3.02
1749 3635 1.809684 GAAAGGGTTTCCACTCGAGG 58.190 55.000 18.41 5.65 33.56 4.63
1816 3702 2.102925 ACCCACATTTTGCAGTTTGAGG 59.897 45.455 0.00 0.00 0.00 3.86
1817 3703 3.457610 ACCCACATTTTGCAGTTTGAG 57.542 42.857 0.00 0.00 0.00 3.02
1846 3732 5.691754 GCAGGAGTCAACTTAAAAACCATTG 59.308 40.000 0.00 0.00 0.00 2.82
1881 3767 1.081892 CAATGGCTGTTCCGTCAGAG 58.918 55.000 4.16 0.00 37.61 3.35
1908 3794 0.251341 AAGGCGGTTCTCCTGCAAAT 60.251 50.000 0.00 0.00 35.88 2.32
1954 3840 7.815840 TGAGATAACAATGAGTTTTGTCCAA 57.184 32.000 0.00 0.00 41.64 3.53
2001 3887 7.403231 TCCAAAAGAGACTTCAATATAGGAGGT 59.597 37.037 0.00 0.00 0.00 3.85
2007 3893 8.146053 TGTCCTCCAAAAGAGACTTCAATATA 57.854 34.615 0.00 0.00 46.50 0.86
2010 3896 5.163152 ACTGTCCTCCAAAAGAGACTTCAAT 60.163 40.000 0.00 0.00 46.50 2.57
2016 3902 4.073293 TGAACTGTCCTCCAAAAGAGAC 57.927 45.455 0.00 0.00 46.50 3.36
2066 3952 6.942005 TGGAGAAAGAAGCAAATGTCTTATGA 59.058 34.615 0.00 0.00 32.90 2.15
2130 4016 7.288810 ACAACAATGTCTTACATGACCAAAT 57.711 32.000 0.00 0.00 37.97 2.32
2223 4109 6.436847 TGACAAATCCATCAATGGTTGTACAT 59.563 34.615 14.55 0.00 43.20 2.29
2245 4131 4.423732 ACTTGACATTTGCAACAGTTGAC 58.576 39.130 17.99 8.90 0.00 3.18
2276 4162 6.276847 CAGCGAGACTCCATCTTTTATAAGT 58.723 40.000 0.00 0.00 38.00 2.24
2296 4182 2.823196 TCATTTCGGTTAATGCAGCG 57.177 45.000 0.00 0.00 35.86 5.18
2406 4292 6.073314 CCTCCATCCCAAAATGTAAGATCAT 58.927 40.000 0.00 0.00 0.00 2.45
2425 4311 5.244626 GCCGTACTAAATAATACTCCCTCCA 59.755 44.000 0.00 0.00 0.00 3.86
2576 4464 0.253044 TAGGCATCTGGGTGTTCTGC 59.747 55.000 0.00 0.00 0.00 4.26
2691 4587 2.301346 GAACTACCCCATCAGGCATTG 58.699 52.381 0.00 0.00 0.00 2.82
2697 4593 0.178068 CCACGGAACTACCCCATCAG 59.822 60.000 0.00 0.00 34.64 2.90
2982 4878 6.183360 CCTCATACAAGTACCACGAGATGTAA 60.183 42.308 0.00 0.00 0.00 2.41
3057 4953 2.037121 TGCTGTCAAGATCGTGGAGAAA 59.963 45.455 8.84 0.00 0.00 2.52
3058 4954 1.618343 TGCTGTCAAGATCGTGGAGAA 59.382 47.619 8.84 0.00 0.00 2.87
3059 4955 1.256812 TGCTGTCAAGATCGTGGAGA 58.743 50.000 8.84 0.00 0.00 3.71
3060 4956 2.084610 TTGCTGTCAAGATCGTGGAG 57.915 50.000 8.84 6.53 0.00 3.86
3061 4957 2.768253 ATTGCTGTCAAGATCGTGGA 57.232 45.000 8.84 0.00 35.37 4.02
3062 4958 3.935203 AGTAATTGCTGTCAAGATCGTGG 59.065 43.478 8.84 0.00 35.37 4.94
3063 4959 4.890378 CAGTAATTGCTGTCAAGATCGTG 58.110 43.478 14.75 1.76 35.37 4.35
3092 5002 3.521126 TGGAAGACTCCGTAGTACCTAGT 59.479 47.826 2.60 2.60 45.85 2.57
3166 5076 7.813645 ACCTTTGTTTCCGATTTCTTGTATAC 58.186 34.615 0.00 0.00 0.00 1.47
3170 5080 5.105513 ACAACCTTTGTTTCCGATTTCTTGT 60.106 36.000 0.00 0.00 42.22 3.16
3185 5095 6.436843 AGTGAAGTTACAGAACAACCTTTG 57.563 37.500 0.00 0.00 38.10 2.77
3186 5096 6.884836 AGAAGTGAAGTTACAGAACAACCTTT 59.115 34.615 0.00 0.00 38.10 3.11
3187 5097 6.415573 AGAAGTGAAGTTACAGAACAACCTT 58.584 36.000 0.00 0.00 38.10 3.50
3188 5098 5.990668 AGAAGTGAAGTTACAGAACAACCT 58.009 37.500 0.00 0.00 38.10 3.50
3189 5099 5.815740 TGAGAAGTGAAGTTACAGAACAACC 59.184 40.000 0.00 0.00 38.10 3.77
3190 5100 6.903883 TGAGAAGTGAAGTTACAGAACAAC 57.096 37.500 0.00 0.00 38.10 3.32
3249 5183 1.948611 GCATCGGGTTCTGCAGGTAAA 60.949 52.381 15.13 0.00 38.28 2.01
3262 5196 4.727507 ATAAGTCATAGCTAGCATCGGG 57.272 45.455 18.83 1.46 0.00 5.14
3287 5221 4.018490 CAGAATGGAATCATTGGTGGTGA 58.982 43.478 0.00 0.00 43.08 4.02
3292 5226 6.071165 GGAAAAGACAGAATGGAATCATTGGT 60.071 38.462 0.00 0.00 43.08 3.67
3318 5252 5.248477 AGAATCTTGTGCTAAACCCTGAGTA 59.752 40.000 0.00 0.00 0.00 2.59
3379 5313 8.383947 AGTTTACAGAGGGAGTAAAAGCTAATT 58.616 33.333 0.00 0.00 41.51 1.40
3393 5327 9.516546 AAAGGTCTTATAAAAGTTTACAGAGGG 57.483 33.333 0.00 0.00 34.13 4.30
3409 5343 9.981460 AACCATTTGAGATCTAAAAGGTCTTAT 57.019 29.630 19.20 7.93 37.93 1.73
3410 5344 9.807921 AAACCATTTGAGATCTAAAAGGTCTTA 57.192 29.630 19.20 0.00 37.93 2.10
3411 5345 8.712228 AAACCATTTGAGATCTAAAAGGTCTT 57.288 30.769 19.20 14.64 37.93 3.01
3412 5346 9.807921 TTAAACCATTTGAGATCTAAAAGGTCT 57.192 29.630 19.20 12.66 37.93 3.85
3414 5348 9.807921 TCTTAAACCATTTGAGATCTAAAAGGT 57.192 29.630 14.61 15.21 39.87 3.50
3436 5370 7.055378 TGCCACCAAAAACTAAACTAGTCTTA 58.945 34.615 0.00 0.00 38.26 2.10
3440 5374 6.724893 AATGCCACCAAAAACTAAACTAGT 57.275 33.333 0.00 0.00 41.73 2.57
3509 5447 4.200838 ACAAGGAAACCCAACAAGTTTG 57.799 40.909 0.00 0.00 37.55 2.93
3534 5472 7.756722 CCTATTGGAACTAGCAAGTTTTTGATG 59.243 37.037 0.00 0.00 46.09 3.07
3558 5496 2.840651 CTGGGACTTTATGACAGACCCT 59.159 50.000 8.61 0.00 44.19 4.34
3559 5497 2.681097 GCTGGGACTTTATGACAGACCC 60.681 54.545 0.00 0.00 44.15 4.46
3606 5544 4.592485 ATGTGGCAAATTTAACGGAACA 57.408 36.364 0.00 0.00 0.00 3.18
3625 5566 6.000219 CCTCCACATCAGGTTTAATCCTATG 59.000 44.000 4.73 10.92 35.87 2.23
3630 5571 5.741011 TGTACCTCCACATCAGGTTTAATC 58.259 41.667 0.00 0.00 41.95 1.75
3677 5618 8.804204 CGTATCTAAATCTAGGTATGGTTTCCT 58.196 37.037 0.00 0.00 37.80 3.36
3680 5621 9.364653 AGTCGTATCTAAATCTAGGTATGGTTT 57.635 33.333 0.00 0.00 31.14 3.27
3682 5623 8.384718 AGAGTCGTATCTAAATCTAGGTATGGT 58.615 37.037 0.00 0.00 31.14 3.55
3683 5624 8.795842 AGAGTCGTATCTAAATCTAGGTATGG 57.204 38.462 0.00 0.00 31.14 2.74
3685 5626 9.796180 ACAAGAGTCGTATCTAAATCTAGGTAT 57.204 33.333 0.00 0.00 0.00 2.73
3702 5666 2.557056 TCAGTTCCACCTACAAGAGTCG 59.443 50.000 0.00 0.00 0.00 4.18
3731 5695 3.243434 GCAAGAGATCAGGATGGCAAATG 60.243 47.826 0.00 0.00 36.16 2.32
3754 5718 4.762289 AAGAAAAGCGAGGAGGATATGT 57.238 40.909 0.00 0.00 0.00 2.29
3773 5737 2.665519 CGACGATGGGCAAGTGAAAAAG 60.666 50.000 0.00 0.00 0.00 2.27
3774 5738 1.265635 CGACGATGGGCAAGTGAAAAA 59.734 47.619 0.00 0.00 0.00 1.94
3775 5739 0.871722 CGACGATGGGCAAGTGAAAA 59.128 50.000 0.00 0.00 0.00 2.29
3776 5740 0.250124 ACGACGATGGGCAAGTGAAA 60.250 50.000 0.00 0.00 0.00 2.69
3794 5758 1.069022 TGAGCGTACTGTGGTTACGAC 60.069 52.381 6.11 0.00 39.31 4.34
3830 5794 2.251818 TGGTCTGAAAGGAGAGGACAG 58.748 52.381 0.00 0.00 0.00 3.51
3845 5809 0.767375 ATGACAGTGTGGCTTGGTCT 59.233 50.000 0.00 0.00 0.00 3.85
3846 5810 1.160137 GATGACAGTGTGGCTTGGTC 58.840 55.000 0.00 0.00 0.00 4.02
3855 5819 3.256631 GCTTTGAATTGGGATGACAGTGT 59.743 43.478 0.00 0.00 0.00 3.55
3859 5823 1.818060 CGGCTTTGAATTGGGATGACA 59.182 47.619 0.00 0.00 0.00 3.58
3876 5840 2.117941 GAGACAACAGCAACCACGGC 62.118 60.000 0.00 0.00 0.00 5.68
3880 5844 2.288666 GAACTGAGACAACAGCAACCA 58.711 47.619 0.00 0.00 41.06 3.67
3883 5847 2.595124 TCGAACTGAGACAACAGCAA 57.405 45.000 0.00 0.00 41.06 3.91
3884 5848 2.473816 CTTCGAACTGAGACAACAGCA 58.526 47.619 0.00 0.00 41.06 4.41
3921 5885 1.530655 CTTTGGGGGTGGTGTGGAC 60.531 63.158 0.00 0.00 0.00 4.02
3930 5894 0.850100 TGTCATGACACTTTGGGGGT 59.150 50.000 24.56 0.00 36.21 4.95
3931 5895 1.202927 ACTGTCATGACACTTTGGGGG 60.203 52.381 24.56 14.25 36.21 5.40
3934 5898 3.003689 GGACAACTGTCATGACACTTTGG 59.996 47.826 30.89 22.30 46.47 3.28
3944 5908 1.406069 GGATGCGAGGACAACTGTCAT 60.406 52.381 11.76 4.38 46.47 3.06
3949 5913 1.513158 CGAGGATGCGAGGACAACT 59.487 57.895 0.00 0.00 0.00 3.16
3950 5914 2.167861 GCGAGGATGCGAGGACAAC 61.168 63.158 0.00 0.00 0.00 3.32
3951 5915 2.184322 GCGAGGATGCGAGGACAA 59.816 61.111 0.00 0.00 0.00 3.18
3954 5918 2.755876 ACAGCGAGGATGCGAGGA 60.756 61.111 0.00 0.00 40.67 3.71
3955 5919 2.279120 GACAGCGAGGATGCGAGG 60.279 66.667 0.00 0.00 40.67 4.63
3956 5920 2.279120 GGACAGCGAGGATGCGAG 60.279 66.667 0.00 0.00 40.67 5.03
3982 5970 2.453773 GATCGGATGCAATGCCAGCG 62.454 60.000 1.53 0.00 33.85 5.18
3988 5976 3.974871 TCATGTTGATCGGATGCAATG 57.025 42.857 0.00 0.00 0.00 2.82
3998 5986 4.450080 TCATGCTCGCTATTCATGTTGATC 59.550 41.667 0.00 0.00 38.82 2.92
4000 5988 3.557185 GTCATGCTCGCTATTCATGTTGA 59.443 43.478 0.00 0.00 38.82 3.18
4001 5989 3.303593 GGTCATGCTCGCTATTCATGTTG 60.304 47.826 0.00 0.00 38.82 3.33
4002 5990 2.874701 GGTCATGCTCGCTATTCATGTT 59.125 45.455 0.00 0.00 38.82 2.71
4013 6007 0.249120 TGTTGGTAGGGTCATGCTCG 59.751 55.000 0.00 0.00 0.00 5.03
4072 6066 0.957888 GGCTGACAGGAGTTGAAGGC 60.958 60.000 4.26 0.00 34.45 4.35
4132 6126 2.177950 CACACTGCTGCCAGGAATC 58.822 57.895 0.00 0.00 43.53 2.52


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

AutoCloner maintained by Alex Coulton.