Multiple sequence alignment - TraesCS4B01G004600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G004600 chr4B 100.000 5009 0 0 1 5009 3312452 3307444 0.000000e+00 9250.0
1 TraesCS4B01G004600 chr4B 90.617 3485 255 33 1390 4842 85268921 85265477 0.000000e+00 4558.0
2 TraesCS4B01G004600 chr4B 87.755 3487 338 57 1390 4851 669752918 669749496 0.000000e+00 3991.0
3 TraesCS4B01G004600 chr4B 88.087 3408 334 52 1390 4780 24466117 24462765 0.000000e+00 3978.0
4 TraesCS4B01G004600 chr4B 85.609 3523 368 96 1390 4874 145158559 145155138 0.000000e+00 3568.0
5 TraesCS4B01G004600 chr4B 84.902 3537 392 90 1392 4882 447592535 447589095 0.000000e+00 3443.0
6 TraesCS4B01G004600 chr4B 84.765 3538 398 89 1390 4882 447585181 447581740 0.000000e+00 3417.0
7 TraesCS4B01G004600 chr4B 100.000 1726 0 0 5353 7078 3307100 3305375 0.000000e+00 3188.0
8 TraesCS4B01G004600 chr4B 83.036 3419 437 88 1390 4728 640616340 640612985 0.000000e+00 2968.0
9 TraesCS4B01G004600 chr4B 84.260 2465 277 64 2471 4915 446304656 446302283 0.000000e+00 2300.0
10 TraesCS4B01G004600 chr4B 89.773 616 54 7 5401 6010 523083111 523083723 0.000000e+00 780.0
11 TraesCS4B01G004600 chr4B 93.524 525 30 3 5490 6011 121270822 121271345 0.000000e+00 778.0
12 TraesCS4B01G004600 chr4B 89.756 615 52 10 5401 6010 517151928 517151320 0.000000e+00 776.0
13 TraesCS4B01G004600 chr4B 90.541 592 47 9 5424 6010 129001243 129001830 0.000000e+00 774.0
14 TraesCS4B01G004600 chr4B 89.610 616 54 10 5399 6009 515201920 515202530 0.000000e+00 774.0
15 TraesCS4B01G004600 chr4B 89.448 616 52 13 5401 6009 126951879 126951270 0.000000e+00 765.0
16 TraesCS4B01G004600 chr4B 89.379 612 56 9 5402 6010 430316023 430316628 0.000000e+00 761.0
17 TraesCS4B01G004600 chr4B 89.439 606 55 8 5408 6009 519691001 519691601 0.000000e+00 756.0
18 TraesCS4B01G004600 chr4B 89.034 611 58 9 5402 6009 430323003 430323607 0.000000e+00 749.0
19 TraesCS4B01G004600 chr4B 77.867 750 128 24 4083 4823 182442692 182441972 1.410000e-116 431.0
20 TraesCS4B01G004600 chr4B 85.714 392 48 8 4455 4842 667960102 667960489 2.380000e-109 407.0
21 TraesCS4B01G004600 chr4B 76.637 779 140 29 4083 4850 125198640 125197893 6.660000e-105 392.0
22 TraesCS4B01G004600 chr4B 81.328 482 65 21 4439 4907 52662772 52662303 1.120000e-97 368.0
23 TraesCS4B01G004600 chr4B 85.583 326 45 2 6752 7076 3713200 3712876 2.450000e-89 340.0
24 TraesCS4B01G004600 chr4B 97.059 34 0 1 4976 5009 372297803 372297771 1.000000e-03 56.5
25 TraesCS4B01G004600 chr7B 93.284 3648 203 34 1390 5009 716282993 716279360 0.000000e+00 5341.0
26 TraesCS4B01G004600 chr7B 94.216 657 36 2 5353 6009 716279029 716278375 0.000000e+00 1002.0
27 TraesCS4B01G004600 chr7B 91.133 609 42 12 5408 6010 417071304 417071906 0.000000e+00 815.0
28 TraesCS4B01G004600 chr7B 90.359 612 51 8 5401 6009 452783028 452782422 0.000000e+00 797.0
29 TraesCS4B01G004600 chr7B 90.212 613 52 8 5401 6010 452789980 452789373 0.000000e+00 793.0
30 TraesCS4B01G004600 chr7B 89.507 629 56 8 5385 6010 88001798 88001177 0.000000e+00 787.0
31 TraesCS4B01G004600 chr7B 89.082 632 57 10 5383 6009 711909719 711910343 0.000000e+00 774.0
32 TraesCS4B01G004600 chr7B 87.746 661 67 13 5355 6009 573222979 573223631 0.000000e+00 760.0
33 TraesCS4B01G004600 chr7B 82.430 535 70 17 4456 4982 427448146 427448664 5.040000e-121 446.0
34 TraesCS4B01G004600 chr7B 77.535 779 123 38 4082 4842 569298998 569299742 8.490000e-114 422.0
35 TraesCS4B01G004600 chr7B 78.979 666 98 28 4295 4948 212507757 212507122 3.950000e-112 416.0
36 TraesCS4B01G004600 chr7B 86.301 73 8 2 494 565 485843455 485843384 2.120000e-10 78.7
37 TraesCS4B01G004600 chr5B 89.326 3504 307 47 1390 4876 522283025 522286478 0.000000e+00 4337.0
38 TraesCS4B01G004600 chr5B 88.166 3490 280 82 1387 4818 652103345 652106759 0.000000e+00 4034.0
39 TraesCS4B01G004600 chr5B 87.874 3480 299 74 1387 4818 652110741 652114145 0.000000e+00 3975.0
40 TraesCS4B01G004600 chr5B 90.706 2819 215 29 1390 4196 522276082 522278865 0.000000e+00 3711.0
41 TraesCS4B01G004600 chr5B 85.900 3078 318 73 1924 4955 700860493 700863500 0.000000e+00 3173.0
42 TraesCS4B01G004600 chr5B 91.653 611 47 4 5402 6009 195443335 195443944 0.000000e+00 843.0
43 TraesCS4B01G004600 chr5B 90.690 623 53 5 5391 6010 110771084 110770464 0.000000e+00 824.0
44 TraesCS4B01G004600 chr5B 90.656 610 53 4 5404 6010 195405141 195405749 0.000000e+00 808.0
45 TraesCS4B01G004600 chr5B 89.984 619 57 5 5393 6009 243314173 243314788 0.000000e+00 795.0
46 TraesCS4B01G004600 chr5B 89.920 625 48 14 5391 6009 451210055 451210670 0.000000e+00 791.0
47 TraesCS4B01G004600 chr5B 80.215 1117 169 42 3872 4964 625343252 625342164 0.000000e+00 791.0
48 TraesCS4B01G004600 chr5B 80.215 1117 169 42 3872 4964 628980238 628979150 0.000000e+00 791.0
49 TraesCS4B01G004600 chr5B 79.892 1114 175 39 3872 4961 632945948 632947036 0.000000e+00 771.0
50 TraesCS4B01G004600 chr5B 79.892 1114 171 41 3872 4961 628987368 628986284 0.000000e+00 767.0
51 TraesCS4B01G004600 chr5B 83.313 803 119 12 3872 4666 625363822 625363027 0.000000e+00 726.0
52 TraesCS4B01G004600 chr5B 87.296 307 35 4 6757 7061 41907258 41907562 1.460000e-91 348.0
53 TraesCS4B01G004600 chr5B 78.537 205 37 6 1065 1266 597303117 597302917 2.070000e-25 128.0
54 TraesCS4B01G004600 chr2B 87.358 3615 331 82 1390 4970 508856778 508860300 0.000000e+00 4028.0
55 TraesCS4B01G004600 chr2B 87.084 3484 342 67 1388 4847 221531291 221527892 0.000000e+00 3842.0
56 TraesCS4B01G004600 chr2B 90.319 1694 99 31 1390 3051 750647076 750648736 0.000000e+00 2159.0
57 TraesCS4B01G004600 chr2B 91.135 643 49 8 5371 6010 668699024 668698387 0.000000e+00 865.0
58 TraesCS4B01G004600 chr2B 90.726 647 54 6 5371 6015 668692025 668691383 0.000000e+00 857.0
59 TraesCS4B01G004600 chr2B 89.362 658 54 15 5361 6010 230921844 230921195 0.000000e+00 813.0
60 TraesCS4B01G004600 chr2B 78.029 883 145 39 4091 4956 213516229 213515379 1.760000e-140 510.0
61 TraesCS4B01G004600 chr2B 87.226 274 35 0 6784 7057 718588613 718588340 5.330000e-81 313.0
62 TraesCS4B01G004600 chr6B 86.820 3513 348 67 1390 4873 213426676 213423250 0.000000e+00 3816.0
63 TraesCS4B01G004600 chr6B 89.676 649 53 12 5367 6009 138596056 138595416 0.000000e+00 815.0
64 TraesCS4B01G004600 chr6B 89.231 650 59 10 5367 6010 138604964 138604320 0.000000e+00 802.0
65 TraesCS4B01G004600 chr6B 83.425 543 72 16 4455 4988 639260912 639260379 8.250000e-134 488.0
66 TraesCS4B01G004600 chr6B 89.024 82 8 1 485 565 24968394 24968313 4.520000e-17 100.0
67 TraesCS4B01G004600 chr4D 85.138 3620 417 78 1390 4951 191220448 191224004 0.000000e+00 3592.0
68 TraesCS4B01G004600 chr4D 84.842 3635 385 105 1392 4955 202393936 202390397 0.000000e+00 3507.0
69 TraesCS4B01G004600 chr4D 84.641 3633 415 98 1390 4955 419662944 419666500 0.000000e+00 3485.0
70 TraesCS4B01G004600 chr4D 84.798 3447 381 87 1581 4955 179542447 179539072 0.000000e+00 3330.0
71 TraesCS4B01G004600 chr4D 91.013 523 44 3 5488 6009 107195385 107195905 0.000000e+00 702.0
72 TraesCS4B01G004600 chr4D 85.533 629 70 17 5391 6010 260115978 260116594 7.740000e-179 638.0
73 TraesCS4B01G004600 chr4D 85.484 620 79 10 5394 6009 189654333 189653721 2.780000e-178 636.0
74 TraesCS4B01G004600 chr4D 85.150 633 77 15 5384 6010 154904037 154903416 3.600000e-177 632.0
75 TraesCS4B01G004600 chr4D 85.072 623 82 11 5391 6009 192684240 192684855 6.030000e-175 625.0
76 TraesCS4B01G004600 chr4D 85.024 621 83 9 5396 6011 93435674 93435059 2.170000e-174 623.0
77 TraesCS4B01G004600 chr4D 84.863 621 84 10 5394 6010 189662026 189661412 1.010000e-172 617.0
78 TraesCS4B01G004600 chr4D 85.161 620 71 17 5408 6018 260140622 260141229 3.630000e-172 616.0
79 TraesCS4B01G004600 chr4D 84.786 631 75 16 5391 6014 173144283 173143667 1.300000e-171 614.0
80 TraesCS4B01G004600 chr4D 88.123 522 55 7 5492 6010 222361750 222361233 1.300000e-171 614.0
81 TraesCS4B01G004600 chr4D 84.848 627 76 18 5391 6009 332190730 332191345 1.300000e-171 614.0
82 TraesCS4B01G004600 chr4D 84.967 612 83 8 5401 6009 386954331 386953726 4.690000e-171 612.0
83 TraesCS4B01G004600 chr4D 84.543 634 78 17 5384 6010 157290511 157291131 1.690000e-170 610.0
84 TraesCS4B01G004600 chr4D 78.277 801 127 33 4173 4955 419645437 419646208 8.310000e-129 472.0
85 TraesCS4B01G004600 chr4D 90.214 327 32 0 6752 7078 1697799 1698125 1.820000e-115 427.0
86 TraesCS4B01G004600 chr4D 83.665 251 41 0 6803 7053 2130716 2130466 3.300000e-58 237.0
87 TraesCS4B01G004600 chr2D 85.011 3616 419 76 1390 4942 30708225 30704670 0.000000e+00 3561.0
88 TraesCS4B01G004600 chr2D 88.455 615 58 13 5401 6009 520276665 520277272 0.000000e+00 730.0
89 TraesCS4B01G004600 chr2D 85.873 630 76 11 5384 6010 478446331 478446950 0.000000e+00 658.0
90 TraesCS4B01G004600 chr2D 86.861 274 36 0 6784 7057 592621030 592620757 2.480000e-79 307.0
91 TraesCS4B01G004600 chr3D 85.848 3420 392 62 1389 4772 128521162 128524525 0.000000e+00 3550.0
92 TraesCS4B01G004600 chr3D 90.619 533 36 7 47 566 19298761 19299292 0.000000e+00 695.0
93 TraesCS4B01G004600 chr3D 83.923 311 48 2 6755 7065 13179917 13179609 5.370000e-76 296.0
94 TraesCS4B01G004600 chr1D 84.789 3642 416 86 1385 4960 8671230 8674799 0.000000e+00 3530.0
95 TraesCS4B01G004600 chr1D 85.407 3351 390 71 1390 4707 478614171 478617455 0.000000e+00 3387.0
96 TraesCS4B01G004600 chr1D 89.925 536 46 8 5478 6009 93170112 93169581 0.000000e+00 684.0
97 TraesCS4B01G004600 chr1D 79.635 987 153 37 3994 4960 214683049 214682091 0.000000e+00 665.0
98 TraesCS4B01G004600 chr1D 85.829 621 75 13 5394 6009 357641917 357641305 0.000000e+00 647.0
99 TraesCS4B01G004600 chr1D 85.761 611 79 8 5402 6009 283802877 283802272 2.150000e-179 640.0
100 TraesCS4B01G004600 chr1D 80.395 811 120 34 4162 4955 441701497 441702285 1.320000e-161 580.0
101 TraesCS4B01G004600 chr1D 76.004 971 206 25 3835 4794 301770701 301769747 1.790000e-130 477.0
102 TraesCS4B01G004600 chr1D 75.876 970 204 28 3828 4783 188140245 188141198 1.080000e-127 468.0
103 TraesCS4B01G004600 chr1D 75.689 979 203 32 3828 4790 48419597 48418638 2.330000e-124 457.0
104 TraesCS4B01G004600 chr1D 78.969 718 108 33 4263 4960 214698006 214697312 3.890000e-122 449.0
105 TraesCS4B01G004600 chr1D 75.305 984 209 32 3828 4794 369676746 369677712 2.340000e-119 440.0
106 TraesCS4B01G004600 chr1D 75.202 988 203 36 3828 4790 156096511 156095541 5.070000e-116 429.0
107 TraesCS4B01G004600 chr1D 75.177 987 203 36 3828 4796 239698701 239697739 1.820000e-115 427.0
108 TraesCS4B01G004600 chr1D 73.443 1220 259 47 3616 4794 440540568 440541763 1.430000e-106 398.0
109 TraesCS4B01G004600 chr3B 92.696 2437 155 19 1390 3814 9122008 9124433 0.000000e+00 3493.0
110 TraesCS4B01G004600 chr3B 87.016 3150 313 68 1789 4909 9131675 9134757 0.000000e+00 3463.0
111 TraesCS4B01G004600 chr3B 84.566 311 47 1 6755 7065 18861140 18860831 2.480000e-79 307.0
112 TraesCS4B01G004600 chr4A 85.595 3367 379 60 1387 4703 632540407 632543717 0.000000e+00 3434.0
113 TraesCS4B01G004600 chr4A 88.203 1263 114 18 3391 4625 736955893 736957148 0.000000e+00 1474.0
114 TraesCS4B01G004600 chr4A 95.063 709 34 1 6010 6718 603044358 603045065 0.000000e+00 1114.0
115 TraesCS4B01G004600 chr4A 89.186 823 63 12 577 1389 603043556 603044362 0.000000e+00 1003.0
116 TraesCS4B01G004600 chr4A 86.867 533 38 7 39 567 571552732 571553236 1.030000e-157 568.0
117 TraesCS4B01G004600 chr4A 93.767 369 22 1 6710 7078 603045260 603045627 2.890000e-153 553.0
118 TraesCS4B01G004600 chr5D 84.408 3630 395 104 1390 4942 86828049 86831584 0.000000e+00 3410.0
119 TraesCS4B01G004600 chr5D 84.182 2219 273 53 2775 4942 66568172 66565981 0.000000e+00 2082.0
120 TraesCS4B01G004600 chr5D 89.194 620 56 8 5396 6010 126153878 126154491 0.000000e+00 763.0
121 TraesCS4B01G004600 chr5D 85.915 284 34 5 6781 7061 43962387 43962667 1.490000e-76 298.0
122 TraesCS4B01G004600 chr5D 90.411 73 7 0 495 567 544793764 544793692 5.840000e-16 97.1
123 TraesCS4B01G004600 chr1B 87.689 1259 119 19 3391 4624 17714052 17712805 0.000000e+00 1434.0
124 TraesCS4B01G004600 chr1B 90.123 648 49 13 5370 6010 137399261 137398622 0.000000e+00 828.0
125 TraesCS4B01G004600 chr1B 90.894 615 46 9 5402 6011 295429418 295428809 0.000000e+00 817.0
126 TraesCS4B01G004600 chr1B 89.953 637 50 14 5383 6010 27110501 27109870 0.000000e+00 809.0
127 TraesCS4B01G004600 chr1B 88.939 669 55 17 5355 6013 27105065 27104406 0.000000e+00 808.0
128 TraesCS4B01G004600 chr2A 90.400 625 49 11 5391 6010 406484878 406485496 0.000000e+00 811.0
129 TraesCS4B01G004600 chr2A 91.913 507 30 8 62 566 705594789 705594292 0.000000e+00 699.0
130 TraesCS4B01G004600 chr2A 90.385 104 6 2 465 567 346203064 346203164 4.450000e-27 134.0
131 TraesCS4B01G004600 chr7D 89.362 611 58 7 5403 6010 333950032 333950638 0.000000e+00 761.0
132 TraesCS4B01G004600 chrUn 92.381 525 37 3 5488 6010 397464486 397465009 0.000000e+00 745.0
133 TraesCS4B01G004600 chrUn 88.562 612 61 9 5402 6009 64404716 64405322 0.000000e+00 734.0
134 TraesCS4B01G004600 chrUn 91.794 524 39 4 5490 6010 122447409 122446887 0.000000e+00 726.0
135 TraesCS4B01G004600 chrUn 91.619 525 38 6 5490 6010 122454658 122454136 0.000000e+00 721.0
136 TraesCS4B01G004600 chrUn 92.023 514 38 3 5497 6009 279022373 279022884 0.000000e+00 719.0
137 TraesCS4B01G004600 chrUn 91.603 524 37 4 5491 6010 461897614 461898134 0.000000e+00 717.0
138 TraesCS4B01G004600 chrUn 91.571 522 36 8 5496 6012 121508157 121508675 0.000000e+00 713.0
139 TraesCS4B01G004600 chrUn 91.506 518 39 5 5494 6009 217719185 217718671 0.000000e+00 708.0
140 TraesCS4B01G004600 chrUn 87.745 612 66 9 5402 6009 64397162 64397768 0.000000e+00 706.0
141 TraesCS4B01G004600 chrUn 91.221 524 39 4 5491 6010 461995164 461995684 0.000000e+00 706.0
142 TraesCS4B01G004600 chrUn 87.480 615 65 10 5402 6009 64521642 64522251 0.000000e+00 699.0
143 TraesCS4B01G004600 chrUn 87.419 620 61 16 5402 6012 77203903 77203292 0.000000e+00 697.0
144 TraesCS4B01G004600 chrUn 86.977 622 64 14 5395 6009 5414497 5415108 0.000000e+00 684.0
145 TraesCS4B01G004600 chrUn 79.240 684 90 34 4295 4961 437038685 437039333 5.070000e-116 429.0
146 TraesCS4B01G004600 chrUn 79.094 684 91 34 4295 4961 439174870 439175518 2.360000e-114 424.0
147 TraesCS4B01G004600 chrUn 82.402 483 59 21 4456 4924 54322393 54321923 1.430000e-106 398.0
148 TraesCS4B01G004600 chrUn 76.456 824 130 48 4151 4952 432090998 432091779 8.610000e-104 388.0
149 TraesCS4B01G004600 chrUn 79.117 589 83 23 4295 4874 411937704 411938261 3.120000e-98 370.0
150 TraesCS4B01G004600 chrUn 86.890 328 40 3 6752 7078 47949851 47950176 1.450000e-96 364.0
151 TraesCS4B01G004600 chrUn 75.145 688 126 33 4295 4969 467086287 467086942 1.500000e-71 281.0
152 TraesCS4B01G004600 chrUn 83.556 225 32 5 4651 4873 474932063 474932284 9.310000e-49 206.0
153 TraesCS4B01G004600 chr5A 76.940 928 182 30 3872 4784 684456667 684457577 3.810000e-137 499.0
154 TraesCS4B01G004600 chr5A 76.782 926 183 30 3872 4782 682313326 682312418 2.290000e-134 490.0
155 TraesCS4B01G004600 chr5A 76.273 805 162 27 3832 4622 53849169 53848380 1.110000e-107 401.0
156 TraesCS4B01G004600 chr5A 74.280 1007 229 29 3829 4821 130668486 130669476 1.430000e-106 398.0
157 TraesCS4B01G004600 chr5A 85.484 310 39 5 6755 7061 33929432 33929738 1.150000e-82 318.0
158 TraesCS4B01G004600 chr5A 85.000 100 11 2 467 565 635282585 635282489 1.620000e-16 99.0
159 TraesCS4B01G004600 chr5A 96.970 33 1 0 4977 5009 375443841 375443873 1.000000e-03 56.5
160 TraesCS4B01G004600 chr1A 75.485 1134 210 52 3854 4955 551073603 551074700 6.380000e-135 492.0
161 TraesCS4B01G004600 chr1A 72.743 1152 253 55 3872 4987 441421635 441422761 1.470000e-86 331.0
162 TraesCS4B01G004600 chr1A 97.059 34 0 1 4976 5009 37552493 37552525 1.000000e-03 56.5
163 TraesCS4B01G004600 chr6A 86.176 340 43 3 6725 7061 9577978 9577640 1.450000e-96 364.0
164 TraesCS4B01G004600 chr6A 81.586 391 67 5 1000 1389 614960450 614960836 1.150000e-82 318.0
165 TraesCS4B01G004600 chr6A 72.984 707 137 45 4295 4971 477533352 477534034 1.560000e-46 198.0
166 TraesCS4B01G004600 chr6A 75.635 394 86 9 1001 1389 27108778 27108390 3.370000e-43 187.0
167 TraesCS4B01G004600 chr6A 94.118 102 4 2 466 565 4728993 4728892 3.420000e-33 154.0
168 TraesCS4B01G004600 chr6A 100.000 30 0 0 4980 5009 236780510 236780481 1.000000e-03 56.5
169 TraesCS4B01G004600 chr6D 81.841 391 66 5 1000 1389 470297965 470297579 2.460000e-84 324.0
170 TraesCS4B01G004600 chr6D 83.721 86 5 6 4916 5000 237713282 237713205 9.850000e-09 73.1
171 TraesCS4B01G004600 chr3A 84.566 311 47 1 6755 7065 24012213 24012522 2.480000e-79 307.0
172 TraesCS4B01G004600 chr3A 100.000 28 0 0 4982 5009 253590584 253590611 1.300000e-02 52.8
173 TraesCS4B01G004600 chr7A 100.000 31 0 0 4979 5009 224733579 224733609 2.760000e-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 TraesCS4B01G004600 chr4B 3305375 3312452 7077 True 6219.0 9250 100.0000 1 7078 2 chr4B.!!$R14 7077
1 TraesCS4B01G004600 chr4B 85265477 85268921 3444 True 4558.0 4558 90.6170 1390 4842 1 chr4B.!!$R4 3452
2 TraesCS4B01G004600 chr4B 669749496 669752918 3422 True 3991.0 3991 87.7550 1390 4851 1 chr4B.!!$R13 3461
3 TraesCS4B01G004600 chr4B 24462765 24466117 3352 True 3978.0 3978 88.0870 1390 4780 1 chr4B.!!$R2 3390
4 TraesCS4B01G004600 chr4B 145155138 145158559 3421 True 3568.0 3568 85.6090 1390 4874 1 chr4B.!!$R7 3484
5 TraesCS4B01G004600 chr4B 447581740 447592535 10795 True 3430.0 3443 84.8335 1390 4882 2 chr4B.!!$R15 3492
6 TraesCS4B01G004600 chr4B 640612985 640616340 3355 True 2968.0 2968 83.0360 1390 4728 1 chr4B.!!$R12 3338
7 TraesCS4B01G004600 chr4B 446302283 446304656 2373 True 2300.0 2300 84.2600 2471 4915 1 chr4B.!!$R10 2444
8 TraesCS4B01G004600 chr4B 523083111 523083723 612 False 780.0 780 89.7730 5401 6010 1 chr4B.!!$F7 609
9 TraesCS4B01G004600 chr4B 121270822 121271345 523 False 778.0 778 93.5240 5490 6011 1 chr4B.!!$F1 521
10 TraesCS4B01G004600 chr4B 517151320 517151928 608 True 776.0 776 89.7560 5401 6010 1 chr4B.!!$R11 609
11 TraesCS4B01G004600 chr4B 129001243 129001830 587 False 774.0 774 90.5410 5424 6010 1 chr4B.!!$F2 586
12 TraesCS4B01G004600 chr4B 515201920 515202530 610 False 774.0 774 89.6100 5399 6009 1 chr4B.!!$F5 610
13 TraesCS4B01G004600 chr4B 126951270 126951879 609 True 765.0 765 89.4480 5401 6009 1 chr4B.!!$R6 608
14 TraesCS4B01G004600 chr4B 430316023 430316628 605 False 761.0 761 89.3790 5402 6010 1 chr4B.!!$F3 608
15 TraesCS4B01G004600 chr4B 519691001 519691601 600 False 756.0 756 89.4390 5408 6009 1 chr4B.!!$F6 601
16 TraesCS4B01G004600 chr4B 430323003 430323607 604 False 749.0 749 89.0340 5402 6009 1 chr4B.!!$F4 607
17 TraesCS4B01G004600 chr4B 182441972 182442692 720 True 431.0 431 77.8670 4083 4823 1 chr4B.!!$R8 740
18 TraesCS4B01G004600 chr4B 125197893 125198640 747 True 392.0 392 76.6370 4083 4850 1 chr4B.!!$R5 767
19 TraesCS4B01G004600 chr7B 716278375 716282993 4618 True 3171.5 5341 93.7500 1390 6009 2 chr7B.!!$R6 4619
20 TraesCS4B01G004600 chr7B 417071304 417071906 602 False 815.0 815 91.1330 5408 6010 1 chr7B.!!$F1 602
21 TraesCS4B01G004600 chr7B 452782422 452783028 606 True 797.0 797 90.3590 5401 6009 1 chr7B.!!$R3 608
22 TraesCS4B01G004600 chr7B 452789373 452789980 607 True 793.0 793 90.2120 5401 6010 1 chr7B.!!$R4 609
23 TraesCS4B01G004600 chr7B 88001177 88001798 621 True 787.0 787 89.5070 5385 6010 1 chr7B.!!$R1 625
24 TraesCS4B01G004600 chr7B 711909719 711910343 624 False 774.0 774 89.0820 5383 6009 1 chr7B.!!$F5 626
25 TraesCS4B01G004600 chr7B 573222979 573223631 652 False 760.0 760 87.7460 5355 6009 1 chr7B.!!$F4 654
26 TraesCS4B01G004600 chr7B 427448146 427448664 518 False 446.0 446 82.4300 4456 4982 1 chr7B.!!$F2 526
27 TraesCS4B01G004600 chr7B 569298998 569299742 744 False 422.0 422 77.5350 4082 4842 1 chr7B.!!$F3 760
28 TraesCS4B01G004600 chr7B 212507122 212507757 635 True 416.0 416 78.9790 4295 4948 1 chr7B.!!$R2 653
29 TraesCS4B01G004600 chr5B 522283025 522286478 3453 False 4337.0 4337 89.3260 1390 4876 1 chr5B.!!$F7 3486
30 TraesCS4B01G004600 chr5B 652103345 652114145 10800 False 4004.5 4034 88.0200 1387 4818 2 chr5B.!!$F10 3431
31 TraesCS4B01G004600 chr5B 522276082 522278865 2783 False 3711.0 3711 90.7060 1390 4196 1 chr5B.!!$F6 2806
32 TraesCS4B01G004600 chr5B 700860493 700863500 3007 False 3173.0 3173 85.9000 1924 4955 1 chr5B.!!$F9 3031
33 TraesCS4B01G004600 chr5B 195443335 195443944 609 False 843.0 843 91.6530 5402 6009 1 chr5B.!!$F3 607
34 TraesCS4B01G004600 chr5B 110770464 110771084 620 True 824.0 824 90.6900 5391 6010 1 chr5B.!!$R1 619
35 TraesCS4B01G004600 chr5B 195405141 195405749 608 False 808.0 808 90.6560 5404 6010 1 chr5B.!!$F2 606
36 TraesCS4B01G004600 chr5B 243314173 243314788 615 False 795.0 795 89.9840 5393 6009 1 chr5B.!!$F4 616
37 TraesCS4B01G004600 chr5B 451210055 451210670 615 False 791.0 791 89.9200 5391 6009 1 chr5B.!!$F5 618
38 TraesCS4B01G004600 chr5B 625342164 625343252 1088 True 791.0 791 80.2150 3872 4964 1 chr5B.!!$R3 1092
39 TraesCS4B01G004600 chr5B 628979150 628980238 1088 True 791.0 791 80.2150 3872 4964 1 chr5B.!!$R5 1092
40 TraesCS4B01G004600 chr5B 632945948 632947036 1088 False 771.0 771 79.8920 3872 4961 1 chr5B.!!$F8 1089
41 TraesCS4B01G004600 chr5B 628986284 628987368 1084 True 767.0 767 79.8920 3872 4961 1 chr5B.!!$R6 1089
42 TraesCS4B01G004600 chr5B 625363027 625363822 795 True 726.0 726 83.3130 3872 4666 1 chr5B.!!$R4 794
43 TraesCS4B01G004600 chr2B 508856778 508860300 3522 False 4028.0 4028 87.3580 1390 4970 1 chr2B.!!$F1 3580
44 TraesCS4B01G004600 chr2B 221527892 221531291 3399 True 3842.0 3842 87.0840 1388 4847 1 chr2B.!!$R2 3459
45 TraesCS4B01G004600 chr2B 750647076 750648736 1660 False 2159.0 2159 90.3190 1390 3051 1 chr2B.!!$F2 1661
46 TraesCS4B01G004600 chr2B 668698387 668699024 637 True 865.0 865 91.1350 5371 6010 1 chr2B.!!$R5 639
47 TraesCS4B01G004600 chr2B 668691383 668692025 642 True 857.0 857 90.7260 5371 6015 1 chr2B.!!$R4 644
48 TraesCS4B01G004600 chr2B 230921195 230921844 649 True 813.0 813 89.3620 5361 6010 1 chr2B.!!$R3 649
49 TraesCS4B01G004600 chr2B 213515379 213516229 850 True 510.0 510 78.0290 4091 4956 1 chr2B.!!$R1 865
50 TraesCS4B01G004600 chr6B 213423250 213426676 3426 True 3816.0 3816 86.8200 1390 4873 1 chr6B.!!$R4 3483
51 TraesCS4B01G004600 chr6B 138595416 138596056 640 True 815.0 815 89.6760 5367 6009 1 chr6B.!!$R2 642
52 TraesCS4B01G004600 chr6B 138604320 138604964 644 True 802.0 802 89.2310 5367 6010 1 chr6B.!!$R3 643
53 TraesCS4B01G004600 chr6B 639260379 639260912 533 True 488.0 488 83.4250 4455 4988 1 chr6B.!!$R5 533
54 TraesCS4B01G004600 chr4D 191220448 191224004 3556 False 3592.0 3592 85.1380 1390 4951 1 chr4D.!!$F4 3561
55 TraesCS4B01G004600 chr4D 202390397 202393936 3539 True 3507.0 3507 84.8420 1392 4955 1 chr4D.!!$R8 3563
56 TraesCS4B01G004600 chr4D 419662944 419666500 3556 False 3485.0 3485 84.6410 1390 4955 1 chr4D.!!$F10 3565
57 TraesCS4B01G004600 chr4D 179539072 179542447 3375 True 3330.0 3330 84.7980 1581 4955 1 chr4D.!!$R5 3374
58 TraesCS4B01G004600 chr4D 107195385 107195905 520 False 702.0 702 91.0130 5488 6009 1 chr4D.!!$F2 521
59 TraesCS4B01G004600 chr4D 260115978 260116594 616 False 638.0 638 85.5330 5391 6010 1 chr4D.!!$F6 619
60 TraesCS4B01G004600 chr4D 189653721 189654333 612 True 636.0 636 85.4840 5394 6009 1 chr4D.!!$R6 615
61 TraesCS4B01G004600 chr4D 154903416 154904037 621 True 632.0 632 85.1500 5384 6010 1 chr4D.!!$R3 626
62 TraesCS4B01G004600 chr4D 192684240 192684855 615 False 625.0 625 85.0720 5391 6009 1 chr4D.!!$F5 618
63 TraesCS4B01G004600 chr4D 93435059 93435674 615 True 623.0 623 85.0240 5396 6011 1 chr4D.!!$R2 615
64 TraesCS4B01G004600 chr4D 189661412 189662026 614 True 617.0 617 84.8630 5394 6010 1 chr4D.!!$R7 616
65 TraesCS4B01G004600 chr4D 260140622 260141229 607 False 616.0 616 85.1610 5408 6018 1 chr4D.!!$F7 610
66 TraesCS4B01G004600 chr4D 173143667 173144283 616 True 614.0 614 84.7860 5391 6014 1 chr4D.!!$R4 623
67 TraesCS4B01G004600 chr4D 222361233 222361750 517 True 614.0 614 88.1230 5492 6010 1 chr4D.!!$R9 518
68 TraesCS4B01G004600 chr4D 332190730 332191345 615 False 614.0 614 84.8480 5391 6009 1 chr4D.!!$F8 618
69 TraesCS4B01G004600 chr4D 386953726 386954331 605 True 612.0 612 84.9670 5401 6009 1 chr4D.!!$R10 608
70 TraesCS4B01G004600 chr4D 157290511 157291131 620 False 610.0 610 84.5430 5384 6010 1 chr4D.!!$F3 626
71 TraesCS4B01G004600 chr4D 419645437 419646208 771 False 472.0 472 78.2770 4173 4955 1 chr4D.!!$F9 782
72 TraesCS4B01G004600 chr2D 30704670 30708225 3555 True 3561.0 3561 85.0110 1390 4942 1 chr2D.!!$R1 3552
73 TraesCS4B01G004600 chr2D 520276665 520277272 607 False 730.0 730 88.4550 5401 6009 1 chr2D.!!$F2 608
74 TraesCS4B01G004600 chr2D 478446331 478446950 619 False 658.0 658 85.8730 5384 6010 1 chr2D.!!$F1 626
75 TraesCS4B01G004600 chr3D 128521162 128524525 3363 False 3550.0 3550 85.8480 1389 4772 1 chr3D.!!$F2 3383
76 TraesCS4B01G004600 chr3D 19298761 19299292 531 False 695.0 695 90.6190 47 566 1 chr3D.!!$F1 519
77 TraesCS4B01G004600 chr1D 8671230 8674799 3569 False 3530.0 3530 84.7890 1385 4960 1 chr1D.!!$F1 3575
78 TraesCS4B01G004600 chr1D 478614171 478617455 3284 False 3387.0 3387 85.4070 1390 4707 1 chr1D.!!$F6 3317
79 TraesCS4B01G004600 chr1D 93169581 93170112 531 True 684.0 684 89.9250 5478 6009 1 chr1D.!!$R2 531
80 TraesCS4B01G004600 chr1D 214682091 214683049 958 True 665.0 665 79.6350 3994 4960 1 chr1D.!!$R4 966
81 TraesCS4B01G004600 chr1D 357641305 357641917 612 True 647.0 647 85.8290 5394 6009 1 chr1D.!!$R9 615
82 TraesCS4B01G004600 chr1D 283802272 283802877 605 True 640.0 640 85.7610 5402 6009 1 chr1D.!!$R7 607
83 TraesCS4B01G004600 chr1D 441701497 441702285 788 False 580.0 580 80.3950 4162 4955 1 chr1D.!!$F5 793
84 TraesCS4B01G004600 chr1D 301769747 301770701 954 True 477.0 477 76.0040 3835 4794 1 chr1D.!!$R8 959
85 TraesCS4B01G004600 chr1D 188140245 188141198 953 False 468.0 468 75.8760 3828 4783 1 chr1D.!!$F2 955
86 TraesCS4B01G004600 chr1D 48418638 48419597 959 True 457.0 457 75.6890 3828 4790 1 chr1D.!!$R1 962
87 TraesCS4B01G004600 chr1D 214697312 214698006 694 True 449.0 449 78.9690 4263 4960 1 chr1D.!!$R5 697
88 TraesCS4B01G004600 chr1D 369676746 369677712 966 False 440.0 440 75.3050 3828 4794 1 chr1D.!!$F3 966
89 TraesCS4B01G004600 chr1D 156095541 156096511 970 True 429.0 429 75.2020 3828 4790 1 chr1D.!!$R3 962
90 TraesCS4B01G004600 chr1D 239697739 239698701 962 True 427.0 427 75.1770 3828 4796 1 chr1D.!!$R6 968
91 TraesCS4B01G004600 chr1D 440540568 440541763 1195 False 398.0 398 73.4430 3616 4794 1 chr1D.!!$F4 1178
92 TraesCS4B01G004600 chr3B 9122008 9124433 2425 False 3493.0 3493 92.6960 1390 3814 1 chr3B.!!$F1 2424
93 TraesCS4B01G004600 chr3B 9131675 9134757 3082 False 3463.0 3463 87.0160 1789 4909 1 chr3B.!!$F2 3120
94 TraesCS4B01G004600 chr4A 632540407 632543717 3310 False 3434.0 3434 85.5950 1387 4703 1 chr4A.!!$F2 3316
95 TraesCS4B01G004600 chr4A 736955893 736957148 1255 False 1474.0 1474 88.2030 3391 4625 1 chr4A.!!$F3 1234
96 TraesCS4B01G004600 chr4A 603043556 603045627 2071 False 890.0 1114 92.6720 577 7078 3 chr4A.!!$F4 6501
97 TraesCS4B01G004600 chr4A 571552732 571553236 504 False 568.0 568 86.8670 39 567 1 chr4A.!!$F1 528
98 TraesCS4B01G004600 chr5D 86828049 86831584 3535 False 3410.0 3410 84.4080 1390 4942 1 chr5D.!!$F2 3552
99 TraesCS4B01G004600 chr5D 66565981 66568172 2191 True 2082.0 2082 84.1820 2775 4942 1 chr5D.!!$R1 2167
100 TraesCS4B01G004600 chr5D 126153878 126154491 613 False 763.0 763 89.1940 5396 6010 1 chr5D.!!$F3 614
101 TraesCS4B01G004600 chr1B 17712805 17714052 1247 True 1434.0 1434 87.6890 3391 4624 1 chr1B.!!$R1 1233
102 TraesCS4B01G004600 chr1B 137398622 137399261 639 True 828.0 828 90.1230 5370 6010 1 chr1B.!!$R4 640
103 TraesCS4B01G004600 chr1B 295428809 295429418 609 True 817.0 817 90.8940 5402 6011 1 chr1B.!!$R5 609
104 TraesCS4B01G004600 chr1B 27109870 27110501 631 True 809.0 809 89.9530 5383 6010 1 chr1B.!!$R3 627
105 TraesCS4B01G004600 chr1B 27104406 27105065 659 True 808.0 808 88.9390 5355 6013 1 chr1B.!!$R2 658
106 TraesCS4B01G004600 chr2A 406484878 406485496 618 False 811.0 811 90.4000 5391 6010 1 chr2A.!!$F2 619
107 TraesCS4B01G004600 chr7D 333950032 333950638 606 False 761.0 761 89.3620 5403 6010 1 chr7D.!!$F1 607
108 TraesCS4B01G004600 chrUn 397464486 397465009 523 False 745.0 745 92.3810 5488 6010 1 chrUn.!!$F8 522
109 TraesCS4B01G004600 chrUn 64404716 64405322 606 False 734.0 734 88.5620 5402 6009 1 chrUn.!!$F4 607
110 TraesCS4B01G004600 chrUn 122446887 122447409 522 True 726.0 726 91.7940 5490 6010 1 chrUn.!!$R3 520
111 TraesCS4B01G004600 chrUn 122454136 122454658 522 True 721.0 721 91.6190 5490 6010 1 chrUn.!!$R4 520
112 TraesCS4B01G004600 chrUn 279022373 279022884 511 False 719.0 719 92.0230 5497 6009 1 chrUn.!!$F7 512
113 TraesCS4B01G004600 chrUn 461897614 461898134 520 False 717.0 717 91.6030 5491 6010 1 chrUn.!!$F13 519
114 TraesCS4B01G004600 chrUn 121508157 121508675 518 False 713.0 713 91.5710 5496 6012 1 chrUn.!!$F6 516
115 TraesCS4B01G004600 chrUn 217718671 217719185 514 True 708.0 708 91.5060 5494 6009 1 chrUn.!!$R5 515
116 TraesCS4B01G004600 chrUn 64397162 64397768 606 False 706.0 706 87.7450 5402 6009 1 chrUn.!!$F3 607
117 TraesCS4B01G004600 chrUn 461995164 461995684 520 False 706.0 706 91.2210 5491 6010 1 chrUn.!!$F14 519
118 TraesCS4B01G004600 chrUn 64521642 64522251 609 False 699.0 699 87.4800 5402 6009 1 chrUn.!!$F5 607
119 TraesCS4B01G004600 chrUn 77203292 77203903 611 True 697.0 697 87.4190 5402 6012 1 chrUn.!!$R2 610
120 TraesCS4B01G004600 chrUn 5414497 5415108 611 False 684.0 684 86.9770 5395 6009 1 chrUn.!!$F1 614
121 TraesCS4B01G004600 chrUn 437038685 437039333 648 False 429.0 429 79.2400 4295 4961 1 chrUn.!!$F11 666
122 TraesCS4B01G004600 chrUn 439174870 439175518 648 False 424.0 424 79.0940 4295 4961 1 chrUn.!!$F12 666
123 TraesCS4B01G004600 chrUn 432090998 432091779 781 False 388.0 388 76.4560 4151 4952 1 chrUn.!!$F10 801
124 TraesCS4B01G004600 chrUn 411937704 411938261 557 False 370.0 370 79.1170 4295 4874 1 chrUn.!!$F9 579
125 TraesCS4B01G004600 chrUn 467086287 467086942 655 False 281.0 281 75.1450 4295 4969 1 chrUn.!!$F15 674
126 TraesCS4B01G004600 chr5A 684456667 684457577 910 False 499.0 499 76.9400 3872 4784 1 chr5A.!!$F4 912
127 TraesCS4B01G004600 chr5A 682312418 682313326 908 True 490.0 490 76.7820 3872 4782 1 chr5A.!!$R3 910
128 TraesCS4B01G004600 chr5A 53848380 53849169 789 True 401.0 401 76.2730 3832 4622 1 chr5A.!!$R1 790
129 TraesCS4B01G004600 chr5A 130668486 130669476 990 False 398.0 398 74.2800 3829 4821 1 chr5A.!!$F2 992
130 TraesCS4B01G004600 chr1A 551073603 551074700 1097 False 492.0 492 75.4850 3854 4955 1 chr1A.!!$F3 1101
131 TraesCS4B01G004600 chr1A 441421635 441422761 1126 False 331.0 331 72.7430 3872 4987 1 chr1A.!!$F2 1115

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
88 89 0.179012 CCTCCCGACCTACTCCTCTC 60.179 65.000 0.00 0.0 0.00 3.20 F
943 966 0.240945 CGCCTTTCAATCCACACCAC 59.759 55.000 0.00 0.0 0.00 4.16 F
1347 1371 0.101219 GCTTCACCCATGAAATCGGC 59.899 55.000 0.00 0.0 44.28 5.54 F
2004 2064 0.753262 CCTCTCGATCAACCCCGAAT 59.247 55.000 0.00 0.0 34.17 3.34 F
2362 2433 0.457337 GCGTACAGGAACCGACGAAT 60.457 55.000 15.84 0.0 37.50 3.34 F
3271 3454 1.135112 GCAAGTTTAAATGAGGCCGGG 60.135 52.381 2.18 0.0 0.00 5.73 F
3278 3461 1.241315 AAATGAGGCCGGGAACAACG 61.241 55.000 2.18 0.0 0.00 4.10 F
3714 3906 2.681344 CCCAACGTAATAACAGAAGGCC 59.319 50.000 0.00 0.0 0.00 5.19 F
5824 6984 0.469917 ACATAGGAGTGCCGGATTGG 59.530 55.000 5.05 0.0 39.96 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1276 1300 0.033796 CAGCATCCAATGTCTGGGGT 60.034 55.000 0.00 0.00 46.44 4.95 R
2004 2064 1.466167 GCGTAACCGTGAGTGTCTCTA 59.534 52.381 0.00 0.00 36.15 2.43 R
2362 2433 1.969923 CCATTTCCTTGGCAACTTGGA 59.030 47.619 0.00 0.00 37.00 3.53 R
3708 3900 0.183492 TACATCATGCCCAGGCCTTC 59.817 55.000 0.00 0.00 41.09 3.46 R
3714 3906 3.558931 TTACCTGTACATCATGCCCAG 57.441 47.619 0.00 0.00 0.00 4.45 R
4956 5279 1.065928 CGTTCGCTCCGGCTAGATT 59.934 57.895 0.00 0.00 36.09 2.40 R
5824 6984 1.023502 TTTCCCCGTTGTCCGTTTTC 58.976 50.000 0.00 0.00 33.66 2.29 R
6067 10992 0.178950 AGCACTGGGTCAGACTCTCA 60.179 55.000 1.07 0.00 35.18 3.27 R
6900 14275 1.606885 CCCCAAGCATGGCGTGATTT 61.607 55.000 11.71 0.78 46.09 2.17 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
36 37 4.069232 CGTCGCTGCCTCCAGGAA 62.069 66.667 0.00 0.00 39.54 3.36
37 38 2.435059 GTCGCTGCCTCCAGGAAC 60.435 66.667 0.00 0.00 39.54 3.62
40 41 4.021925 GCTGCCTCCAGGAACCGT 62.022 66.667 0.00 0.00 39.54 4.83
44 45 2.671070 CCTCCAGGAACCGTGCAT 59.329 61.111 0.00 0.00 37.39 3.96
51 52 1.197721 CAGGAACCGTGCATCAAGAAC 59.802 52.381 0.00 0.00 0.00 3.01
55 56 3.305335 GGAACCGTGCATCAAGAACAATT 60.305 43.478 0.00 0.00 0.00 2.32
60 61 2.912967 GTGCATCAAGAACAATTGCTCG 59.087 45.455 5.05 0.00 34.47 5.03
76 77 3.154473 CGCCTGGAATCCTCCCGA 61.154 66.667 0.00 0.00 41.64 5.14
87 88 0.623911 TCCTCCCGACCTACTCCTCT 60.624 60.000 0.00 0.00 0.00 3.69
88 89 0.179012 CCTCCCGACCTACTCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
142 143 3.610911 GGACCTGCAATATATAGCACCC 58.389 50.000 0.00 0.00 36.62 4.61
156 163 1.593296 GCACCCTCGTCGGTTACTCT 61.593 60.000 0.00 0.00 32.17 3.24
168 175 3.315470 TCGGTTACTCTTGGATCGATCTG 59.685 47.826 23.96 14.51 0.00 2.90
181 188 5.051153 GGATCGATCTGTTTCCTTCCTTAC 58.949 45.833 23.96 0.00 0.00 2.34
219 230 8.469309 ACAGGAGGTTGATGAATAATATTTGG 57.531 34.615 0.00 0.00 0.00 3.28
311 325 8.040132 GGAAACAATATATGAGAGGATGAGGAG 58.960 40.741 0.00 0.00 0.00 3.69
330 344 4.041198 AGGAGTAAGATTTGGTGGAAACGA 59.959 41.667 0.00 0.00 0.00 3.85
371 385 8.996651 AAATTAATGGGTGGGAGAGTAATTAG 57.003 34.615 0.00 0.00 0.00 1.73
438 452 3.008375 TGGAACAGATGTTTCAGGAGAGG 59.992 47.826 2.46 0.00 38.53 3.69
518 535 3.638627 CTGAGGTGGACTATCTGCATGTA 59.361 47.826 0.00 0.00 0.00 2.29
554 571 3.876309 AGTGGGGAGCAACTTCTTAAA 57.124 42.857 0.00 0.00 0.00 1.52
574 591 9.807921 TCTTAAAAATGTAAGATTCTGGAAGGT 57.192 29.630 0.00 0.00 35.61 3.50
591 608 3.577805 AGGTTAGGTTCACAAACTGCT 57.422 42.857 0.00 0.00 35.61 4.24
612 629 4.273480 GCTTGTGCTCTTCTTTAGTTCACA 59.727 41.667 0.00 0.00 36.32 3.58
629 646 4.054780 TCACACCAAGACAAGTGAGTAC 57.945 45.455 0.00 0.00 36.20 2.73
630 647 3.131396 CACACCAAGACAAGTGAGTACC 58.869 50.000 0.00 0.00 37.43 3.34
632 649 3.181465 ACACCAAGACAAGTGAGTACCAG 60.181 47.826 0.00 0.00 37.43 4.00
633 650 2.224305 ACCAAGACAAGTGAGTACCAGC 60.224 50.000 0.00 0.00 0.00 4.85
634 651 2.224281 CCAAGACAAGTGAGTACCAGCA 60.224 50.000 0.00 0.00 0.00 4.41
635 652 2.802816 CAAGACAAGTGAGTACCAGCAC 59.197 50.000 3.63 3.63 35.30 4.40
636 653 2.039418 AGACAAGTGAGTACCAGCACA 58.961 47.619 12.01 0.00 37.48 4.57
673 692 2.761809 ACAGATGAGAGGAAGAGGCAT 58.238 47.619 0.00 0.00 0.00 4.40
674 693 3.921104 ACAGATGAGAGGAAGAGGCATA 58.079 45.455 0.00 0.00 0.00 3.14
675 694 3.896888 ACAGATGAGAGGAAGAGGCATAG 59.103 47.826 0.00 0.00 0.00 2.23
676 695 2.899256 AGATGAGAGGAAGAGGCATAGC 59.101 50.000 0.00 0.00 0.00 2.97
694 717 1.003696 AGCCTAGCCCAAGACAGTTTC 59.996 52.381 0.00 0.00 0.00 2.78
725 748 1.968540 GGCGGCTTCAGCAAAGACT 60.969 57.895 0.00 0.00 41.29 3.24
750 773 2.117156 GGCACTCATGGCGCAAGAT 61.117 57.895 10.83 0.00 42.22 2.40
774 797 3.127589 ACCAAGCAAAATTACAAACGCC 58.872 40.909 0.00 0.00 0.00 5.68
777 800 1.338655 AGCAAAATTACAAACGCCGGT 59.661 42.857 1.90 0.00 0.00 5.28
778 801 1.453900 GCAAAATTACAAACGCCGGTG 59.546 47.619 14.93 14.93 0.00 4.94
779 802 2.055100 CAAAATTACAAACGCCGGTGG 58.945 47.619 21.14 6.53 0.00 4.61
781 804 0.594110 AATTACAAACGCCGGTGGTG 59.406 50.000 21.14 18.63 39.41 4.17
785 808 4.887190 AAACGCCGGTGGTGCCTT 62.887 61.111 21.14 0.24 36.54 4.35
797 820 1.312371 GGTGCCTTGCCAGCGATTTA 61.312 55.000 0.00 0.00 0.00 1.40
896 919 3.122971 GACCCGGCCGCTACAAAC 61.123 66.667 22.85 2.17 0.00 2.93
897 920 3.887335 GACCCGGCCGCTACAAACA 62.887 63.158 22.85 0.00 0.00 2.83
903 926 2.399356 GCCGCTACAAACAGGGAGC 61.399 63.158 0.00 0.00 0.00 4.70
910 933 3.194968 GCTACAAACAGGGAGCACTACTA 59.805 47.826 0.00 0.00 34.96 1.82
943 966 0.240945 CGCCTTTCAATCCACACCAC 59.759 55.000 0.00 0.00 0.00 4.16
944 967 0.603065 GCCTTTCAATCCACACCACC 59.397 55.000 0.00 0.00 0.00 4.61
945 968 1.823250 GCCTTTCAATCCACACCACCT 60.823 52.381 0.00 0.00 0.00 4.00
946 969 1.888512 CCTTTCAATCCACACCACCTG 59.111 52.381 0.00 0.00 0.00 4.00
947 970 1.888512 CTTTCAATCCACACCACCTGG 59.111 52.381 0.00 0.00 42.17 4.45
986 1010 1.984570 CGTCCCCTGAGAGCAAGGA 60.985 63.158 0.00 0.00 0.00 3.36
992 1016 1.566211 CCTGAGAGCAAGGAGGAGAA 58.434 55.000 0.00 0.00 0.00 2.87
1009 1033 5.624159 AGGAGAAATTAATCATGGCGATGA 58.376 37.500 14.13 14.13 42.92 2.92
1035 1059 2.104530 GCCTTCGCGTCCTACCTC 59.895 66.667 5.77 0.00 0.00 3.85
1092 1116 1.663074 GATGATGCTCGGCGTCTCC 60.663 63.158 6.85 6.94 44.07 3.71
1149 1173 2.026449 CCTCAAGAACCTCCTTGCTGAT 60.026 50.000 0.00 0.00 42.34 2.90
1170 1194 2.895680 GAGAGGAGGCGCATCACA 59.104 61.111 24.79 0.00 0.00 3.58
1179 1203 0.795085 GGCGCATCACAGATGATAGC 59.205 55.000 10.83 11.20 44.13 2.97
1221 1245 2.433491 AAGCGCGCCATGTACGAA 60.433 55.556 30.33 0.00 0.00 3.85
1236 1260 1.079127 CGAAGCCACCGACATCCTT 60.079 57.895 0.00 0.00 0.00 3.36
1247 1271 0.615331 GACATCCTTGACCTCTGCCA 59.385 55.000 0.00 0.00 0.00 4.92
1254 1278 0.473755 TTGACCTCTGCCAGCTCAAA 59.526 50.000 0.00 0.00 0.00 2.69
1255 1279 0.473755 TGACCTCTGCCAGCTCAAAA 59.526 50.000 0.00 0.00 0.00 2.44
1256 1280 1.074405 TGACCTCTGCCAGCTCAAAAT 59.926 47.619 0.00 0.00 0.00 1.82
1257 1281 1.742268 GACCTCTGCCAGCTCAAAATC 59.258 52.381 0.00 0.00 0.00 2.17
1272 1296 3.144506 CAAAATCATGGAGAGGGGATCG 58.855 50.000 0.00 0.00 0.00 3.69
1276 1300 1.780919 TCATGGAGAGGGGATCGTCTA 59.219 52.381 0.00 0.00 38.14 2.59
1278 1302 0.185416 TGGAGAGGGGATCGTCTACC 59.815 60.000 0.00 0.00 37.81 3.18
1315 1339 2.125773 CAATCCCTTGCTCTTCTGCT 57.874 50.000 0.00 0.00 0.00 4.24
1318 1342 1.059098 TCCCTTGCTCTTCTGCTTGA 58.941 50.000 0.00 0.00 0.00 3.02
1333 1357 0.253044 CTTGAGGAATCCCCGCTTCA 59.747 55.000 0.00 0.00 40.87 3.02
1347 1371 0.101219 GCTTCACCCATGAAATCGGC 59.899 55.000 0.00 0.00 44.28 5.54
1351 1375 2.516930 CCCATGAAATCGGCGGCT 60.517 61.111 7.21 0.00 0.00 5.52
1464 1489 2.396590 AGACCCGCATATTGAAACGT 57.603 45.000 0.00 0.00 0.00 3.99
1667 1713 1.275666 TCCCCTGATCGAAGAAGCAA 58.724 50.000 0.00 0.00 43.58 3.91
1787 1838 3.053395 ACTCAGCAATCCCATTACCATGT 60.053 43.478 0.00 0.00 0.00 3.21
2004 2064 0.753262 CCTCTCGATCAACCCCGAAT 59.247 55.000 0.00 0.00 34.17 3.34
2362 2433 0.457337 GCGTACAGGAACCGACGAAT 60.457 55.000 15.84 0.00 37.50 3.34
2377 2448 1.202879 ACGAATCCAAGTTGCCAAGGA 60.203 47.619 0.00 0.00 34.12 3.36
2378 2449 1.885887 CGAATCCAAGTTGCCAAGGAA 59.114 47.619 0.00 0.00 33.17 3.36
2458 2539 5.163023 GGGGGCTAAATAAAGATGACCCTTA 60.163 44.000 1.98 0.00 36.31 2.69
2656 2742 2.165437 GGCAAGAGTGGAACAAAACACA 59.835 45.455 0.00 0.00 44.16 3.72
2859 2957 2.496111 CGGTAACCTAGCCAAACAACA 58.504 47.619 0.00 0.00 0.00 3.33
2965 3116 4.106029 AGCGATAGAACGAAGCAACTAA 57.894 40.909 0.00 0.00 39.76 2.24
3271 3454 1.135112 GCAAGTTTAAATGAGGCCGGG 60.135 52.381 2.18 0.00 0.00 5.73
3278 3461 1.241315 AAATGAGGCCGGGAACAACG 61.241 55.000 2.18 0.00 0.00 4.10
3325 3508 7.546358 TCATATGCAAATTTCGAAATTGGTCT 58.454 30.769 31.04 21.79 38.53 3.85
3708 3900 3.938963 ACAGCATCCCAACGTAATAACAG 59.061 43.478 0.00 0.00 0.00 3.16
3714 3906 2.681344 CCCAACGTAATAACAGAAGGCC 59.319 50.000 0.00 0.00 0.00 5.19
3794 3987 8.800332 AGAAATCACTAGAACATGCTCAAAATT 58.200 29.630 0.00 0.00 0.00 1.82
3847 4063 9.173939 GTTTCAGACTTGTCAGAAAATAACATG 57.826 33.333 18.26 0.00 32.44 3.21
3850 4066 7.933577 TCAGACTTGTCAGAAAATAACATGAGT 59.066 33.333 0.00 0.00 0.00 3.41
4134 4370 3.153919 GGCATGAGAAGGTAACCAACAA 58.846 45.455 0.00 0.00 37.17 2.83
4257 4499 4.641989 AGGCTGACAGCAACATTATTTAGG 59.358 41.667 27.87 0.00 44.75 2.69
4709 4977 7.663081 GGCATCTAGATGACCTCAAATGAATAA 59.337 37.037 32.38 0.00 40.97 1.40
4956 5279 4.770362 TCTCATCCACCCGCCCGA 62.770 66.667 0.00 0.00 0.00 5.14
5824 6984 0.469917 ACATAGGAGTGCCGGATTGG 59.530 55.000 5.05 0.00 39.96 3.16
6075 11000 5.009631 CCTATGAAGATCGGATGAGAGTCT 58.990 45.833 0.00 0.00 0.00 3.24
6104 11029 0.392193 CTGCTTGCCGGAAGACAGAT 60.392 55.000 5.05 0.00 37.71 2.90
6107 11032 0.250234 CTTGCCGGAAGACAGATCCA 59.750 55.000 5.05 0.00 36.74 3.41
6164 11695 7.637511 AGATTGAAGATGATACAAGAACCCTT 58.362 34.615 0.00 0.00 0.00 3.95
6186 13353 5.499139 TGTGGAAAAGCTCACTAACAAAG 57.501 39.130 5.05 0.00 35.15 2.77
6221 13388 1.018752 TCATGTTGGTCGCCATCGTG 61.019 55.000 16.59 16.59 39.97 4.35
6227 13394 3.118454 GTCGCCATCGTGGGTGTG 61.118 66.667 8.17 0.00 38.19 3.82
6324 13495 6.560253 AGATATGGTTGAGTGTCACAAAAC 57.440 37.500 5.62 8.74 0.00 2.43
6337 13508 2.053627 CACAAAACAATTCAGCGAGGC 58.946 47.619 0.00 0.00 0.00 4.70
6439 13610 1.366111 GCTCTTGCCGTCGCCATAAA 61.366 55.000 0.00 0.00 0.00 1.40
6513 13684 0.535102 CAACTTGCTCAAGGACCCGT 60.535 55.000 13.48 0.00 42.53 5.28
6521 13692 0.606604 TCAAGGACCCGTTCAGCTAC 59.393 55.000 0.00 0.00 0.00 3.58
6531 13702 1.751544 TTCAGCTACGGCGCTCCTA 60.752 57.895 6.90 0.00 44.37 2.94
6593 13764 3.361174 GGCCTAAAAGCCGTGCAA 58.639 55.556 0.00 0.00 44.57 4.08
6596 13767 1.584495 CCTAAAAGCCGTGCAACCC 59.416 57.895 0.00 0.00 0.00 4.11
6597 13768 1.209127 CTAAAAGCCGTGCAACCCG 59.791 57.895 0.00 0.00 0.00 5.28
6598 13769 1.512156 CTAAAAGCCGTGCAACCCGT 61.512 55.000 0.00 0.00 0.00 5.28
6599 13770 0.250209 TAAAAGCCGTGCAACCCGTA 60.250 50.000 0.00 0.00 0.00 4.02
6600 13771 1.788067 AAAAGCCGTGCAACCCGTAC 61.788 55.000 0.00 0.00 0.00 3.67
6645 13816 4.885907 CCTGAAGATGCATGGTCATTACTT 59.114 41.667 2.46 0.00 0.00 2.24
6648 13819 5.822519 TGAAGATGCATGGTCATTACTTACC 59.177 40.000 2.46 0.00 36.24 2.85
6670 13841 4.318332 CAAGCAGGTGAGAGTTACATCAA 58.682 43.478 0.00 0.00 0.00 2.57
6907 14282 2.099141 TGCCAGAAGGAGAAATCACG 57.901 50.000 0.00 0.00 36.89 4.35
6939 14314 3.181489 GGGAAAGCTCTTGAATGATGCTG 60.181 47.826 0.00 0.00 33.96 4.41
6940 14315 3.436496 GAAAGCTCTTGAATGATGCTGC 58.564 45.455 0.00 0.00 33.96 5.25
6953 14328 2.149578 GATGCTGCATGGTCAGTATCC 58.850 52.381 21.53 0.00 44.86 2.59
6962 14337 1.922447 TGGTCAGTATCCCAAATGCCT 59.078 47.619 0.00 0.00 0.00 4.75
6965 14340 3.620488 GTCAGTATCCCAAATGCCTGAA 58.380 45.455 0.00 0.00 31.38 3.02
6973 14348 3.091545 CCCAAATGCCTGAAGAGCTAAA 58.908 45.455 0.00 0.00 0.00 1.85
7004 14379 9.311916 GCAATATATCTTAGCTATGAGGACTTG 57.688 37.037 14.03 14.11 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.069232 TTCCTGGAGGCAGCGACG 62.069 66.667 0.00 0.00 34.44 5.12
20 21 2.435059 GTTCCTGGAGGCAGCGAC 60.435 66.667 0.00 0.00 34.44 5.19
21 22 3.706373 GGTTCCTGGAGGCAGCGA 61.706 66.667 0.00 0.00 34.44 4.93
23 24 4.021925 ACGGTTCCTGGAGGCAGC 62.022 66.667 0.00 0.00 34.44 5.25
24 25 2.046892 CACGGTTCCTGGAGGCAG 60.047 66.667 0.00 0.00 34.44 4.85
25 26 4.329545 GCACGGTTCCTGGAGGCA 62.330 66.667 0.00 0.00 34.44 4.75
26 27 3.628646 ATGCACGGTTCCTGGAGGC 62.629 63.158 0.00 0.00 34.44 4.70
27 28 1.450312 GATGCACGGTTCCTGGAGG 60.450 63.158 0.00 0.00 0.00 4.30
28 29 0.321564 TTGATGCACGGTTCCTGGAG 60.322 55.000 0.00 0.00 0.00 3.86
29 30 0.321564 CTTGATGCACGGTTCCTGGA 60.322 55.000 0.00 0.00 0.00 3.86
30 31 0.321564 TCTTGATGCACGGTTCCTGG 60.322 55.000 0.00 0.00 0.00 4.45
31 32 1.197721 GTTCTTGATGCACGGTTCCTG 59.802 52.381 0.00 0.00 0.00 3.86
32 33 1.202758 TGTTCTTGATGCACGGTTCCT 60.203 47.619 0.00 0.00 0.00 3.36
33 34 1.234821 TGTTCTTGATGCACGGTTCC 58.765 50.000 0.00 0.00 0.00 3.62
34 35 3.559238 ATTGTTCTTGATGCACGGTTC 57.441 42.857 0.00 0.00 0.00 3.62
35 36 3.641648 CAATTGTTCTTGATGCACGGTT 58.358 40.909 0.00 0.00 0.00 4.44
36 37 2.607771 GCAATTGTTCTTGATGCACGGT 60.608 45.455 7.40 0.00 37.00 4.83
37 38 1.987770 GCAATTGTTCTTGATGCACGG 59.012 47.619 7.40 0.00 37.00 4.94
40 41 2.669113 GCGAGCAATTGTTCTTGATGCA 60.669 45.455 18.55 0.00 39.42 3.96
44 45 1.536766 CAGGCGAGCAATTGTTCTTGA 59.463 47.619 18.55 0.00 0.00 3.02
51 52 0.383231 GGATTCCAGGCGAGCAATTG 59.617 55.000 0.00 0.00 0.00 2.32
55 56 2.735772 GGAGGATTCCAGGCGAGCA 61.736 63.158 5.29 0.00 43.45 4.26
60 61 2.506472 GTCGGGAGGATTCCAGGC 59.494 66.667 5.29 0.00 45.98 4.85
76 77 0.039911 AAGGTGCGAGAGGAGTAGGT 59.960 55.000 0.00 0.00 0.00 3.08
142 143 2.539142 CGATCCAAGAGTAACCGACGAG 60.539 54.545 0.00 0.00 0.00 4.18
156 163 3.519510 AGGAAGGAAACAGATCGATCCAA 59.480 43.478 21.66 0.00 34.30 3.53
181 188 7.938140 TCAACCTCCTGTTAATATTTTCCAG 57.062 36.000 0.00 0.00 34.69 3.86
196 207 7.506938 CCACCAAATATTATTCATCAACCTCCT 59.493 37.037 0.00 0.00 0.00 3.69
219 230 4.086706 TCTTCCTTTTCACCTTCTCCAC 57.913 45.455 0.00 0.00 0.00 4.02
304 318 5.779241 TTCCACCAAATCTTACTCCTCAT 57.221 39.130 0.00 0.00 0.00 2.90
311 325 9.931210 CTATTTATCGTTTCCACCAAATCTTAC 57.069 33.333 0.00 0.00 0.00 2.34
330 344 9.828691 CCCATTAATTTCCCTCTTCCTATTTAT 57.171 33.333 0.00 0.00 0.00 1.40
371 385 3.137533 GCACCTCTAATCTTCTCCATGC 58.862 50.000 0.00 0.00 0.00 4.06
518 535 3.772025 CCCCACTACAAGTCATTCTCTCT 59.228 47.826 0.00 0.00 0.00 3.10
554 571 7.699878 ACCTAACCTTCCAGAATCTTACATTT 58.300 34.615 0.00 0.00 0.00 2.32
567 584 4.204012 CAGTTTGTGAACCTAACCTTCCA 58.796 43.478 0.00 0.00 36.39 3.53
568 585 3.004419 GCAGTTTGTGAACCTAACCTTCC 59.996 47.826 0.00 0.00 36.39 3.46
569 586 3.883489 AGCAGTTTGTGAACCTAACCTTC 59.117 43.478 0.00 0.00 36.39 3.46
570 587 3.898482 AGCAGTTTGTGAACCTAACCTT 58.102 40.909 0.00 0.00 36.39 3.50
571 588 3.577805 AGCAGTTTGTGAACCTAACCT 57.422 42.857 0.00 0.00 36.39 3.50
572 589 3.964909 CAAGCAGTTTGTGAACCTAACC 58.035 45.455 0.00 0.00 36.39 2.85
591 608 4.574828 GGTGTGAACTAAAGAAGAGCACAA 59.425 41.667 0.00 0.00 41.14 3.33
596 613 6.049149 TGTCTTGGTGTGAACTAAAGAAGAG 58.951 40.000 0.00 0.00 0.00 2.85
612 629 2.224305 GCTGGTACTCACTTGTCTTGGT 60.224 50.000 0.00 0.00 0.00 3.67
629 646 0.871163 CAGTTTTTGCCGTGTGCTGG 60.871 55.000 0.00 0.00 42.00 4.85
630 647 0.100325 TCAGTTTTTGCCGTGTGCTG 59.900 50.000 0.00 0.00 42.00 4.41
632 649 1.208642 GCTCAGTTTTTGCCGTGTGC 61.209 55.000 0.00 0.00 41.77 4.57
633 650 0.100325 TGCTCAGTTTTTGCCGTGTG 59.900 50.000 0.00 0.00 0.00 3.82
634 651 0.814457 TTGCTCAGTTTTTGCCGTGT 59.186 45.000 0.00 0.00 0.00 4.49
635 652 1.199624 GTTGCTCAGTTTTTGCCGTG 58.800 50.000 0.00 0.00 0.00 4.94
636 653 0.814457 TGTTGCTCAGTTTTTGCCGT 59.186 45.000 0.00 0.00 0.00 5.68
642 661 4.070716 CCTCTCATCTGTTGCTCAGTTTT 58.929 43.478 8.75 0.00 43.97 2.43
673 692 1.952621 AACTGTCTTGGGCTAGGCTA 58.047 50.000 16.80 7.37 0.00 3.93
674 693 1.003696 GAAACTGTCTTGGGCTAGGCT 59.996 52.381 16.80 0.00 0.00 4.58
675 694 1.454201 GAAACTGTCTTGGGCTAGGC 58.546 55.000 8.00 8.00 0.00 3.93
676 695 1.630878 AGGAAACTGTCTTGGGCTAGG 59.369 52.381 0.00 0.00 41.13 3.02
677 696 2.675317 CGAGGAAACTGTCTTGGGCTAG 60.675 54.545 0.00 0.00 44.43 3.42
679 698 0.035458 CGAGGAAACTGTCTTGGGCT 59.965 55.000 0.00 0.00 44.43 5.19
680 699 1.578206 GCGAGGAAACTGTCTTGGGC 61.578 60.000 0.00 0.00 44.43 5.36
681 700 0.035458 AGCGAGGAAACTGTCTTGGG 59.965 55.000 0.00 0.00 44.43 4.12
750 773 4.363999 CGTTTGTAATTTTGCTTGGTCCA 58.636 39.130 0.00 0.00 0.00 4.02
777 800 3.866379 AATCGCTGGCAAGGCACCA 62.866 57.895 0.00 0.00 35.40 4.17
778 801 1.312371 TAAATCGCTGGCAAGGCACC 61.312 55.000 0.00 0.00 0.00 5.01
779 802 0.740737 ATAAATCGCTGGCAAGGCAC 59.259 50.000 0.00 0.00 0.00 5.01
781 804 0.312102 GGATAAATCGCTGGCAAGGC 59.688 55.000 0.00 0.00 0.00 4.35
783 806 2.542411 GCTTGGATAAATCGCTGGCAAG 60.542 50.000 0.00 0.00 0.00 4.01
784 807 1.405105 GCTTGGATAAATCGCTGGCAA 59.595 47.619 0.00 0.00 0.00 4.52
785 808 1.024271 GCTTGGATAAATCGCTGGCA 58.976 50.000 0.00 0.00 0.00 4.92
786 809 1.024271 TGCTTGGATAAATCGCTGGC 58.976 50.000 0.00 0.00 0.00 4.85
787 810 3.489738 CCTTTGCTTGGATAAATCGCTGG 60.490 47.826 0.00 0.00 0.00 4.85
788 811 3.378112 TCCTTTGCTTGGATAAATCGCTG 59.622 43.478 0.00 0.00 0.00 5.18
793 816 4.095946 TGCCTTCCTTTGCTTGGATAAAT 58.904 39.130 0.00 0.00 33.09 1.40
797 820 2.105766 GATGCCTTCCTTTGCTTGGAT 58.894 47.619 0.00 0.00 33.09 3.41
896 919 2.555199 GCAATGTAGTAGTGCTCCCTG 58.445 52.381 0.00 0.00 46.32 4.45
897 920 2.990066 GCAATGTAGTAGTGCTCCCT 57.010 50.000 0.00 0.00 46.32 4.20
903 926 4.492570 GCGTAAAGCTGCAATGTAGTAGTG 60.493 45.833 1.02 0.00 44.04 2.74
947 970 1.040339 TTGGTTGGTTGGGTCACAGC 61.040 55.000 0.00 0.00 0.00 4.40
986 1010 5.624159 TCATCGCCATGATTAATTTCTCCT 58.376 37.500 0.00 0.00 33.80 3.69
992 1016 4.082408 CCAGCATCATCGCCATGATTAATT 60.082 41.667 3.82 0.00 46.07 1.40
1027 1051 2.439701 CAGGTCGCCGAGGTAGGA 60.440 66.667 0.00 0.00 0.00 2.94
1028 1052 4.208686 GCAGGTCGCCGAGGTAGG 62.209 72.222 0.00 0.00 32.94 3.18
1029 1053 3.127352 GAGCAGGTCGCCGAGGTAG 62.127 68.421 0.00 0.00 44.04 3.18
1030 1054 3.138798 GAGCAGGTCGCCGAGGTA 61.139 66.667 0.00 0.00 44.04 3.08
1032 1056 3.997064 CTTGAGCAGGTCGCCGAGG 62.997 68.421 0.00 0.00 44.04 4.63
1033 1057 2.507992 CTTGAGCAGGTCGCCGAG 60.508 66.667 0.00 0.00 44.04 4.63
1034 1058 4.742201 GCTTGAGCAGGTCGCCGA 62.742 66.667 0.00 0.00 44.04 5.54
1092 1116 0.374758 CCATCTTGTCAATGTCGCCG 59.625 55.000 0.00 0.00 0.00 6.46
1096 1120 1.398390 GACGCCCATCTTGTCAATGTC 59.602 52.381 0.00 0.00 32.91 3.06
1127 1151 0.037447 AGCAAGGAGGTTCTTGAGGC 59.963 55.000 1.90 0.00 44.98 4.70
1170 1194 1.871676 CATTGCTGCACGCTATCATCT 59.128 47.619 0.00 0.00 40.11 2.90
1179 1203 2.562912 GTCACCCATTGCTGCACG 59.437 61.111 0.00 0.00 0.00 5.34
1209 1233 2.461110 GGTGGCTTCGTACATGGCG 61.461 63.158 0.00 1.17 0.00 5.69
1221 1245 1.296715 GTCAAGGATGTCGGTGGCT 59.703 57.895 0.00 0.00 0.00 4.75
1247 1271 2.091994 CCCCTCTCCATGATTTTGAGCT 60.092 50.000 0.00 0.00 0.00 4.09
1254 1278 1.974236 GACGATCCCCTCTCCATGATT 59.026 52.381 0.00 0.00 0.00 2.57
1255 1279 1.148867 AGACGATCCCCTCTCCATGAT 59.851 52.381 0.00 0.00 0.00 2.45
1256 1280 0.558220 AGACGATCCCCTCTCCATGA 59.442 55.000 0.00 0.00 0.00 3.07
1257 1281 1.889829 GTAGACGATCCCCTCTCCATG 59.110 57.143 0.00 0.00 0.00 3.66
1276 1300 0.033796 CAGCATCCAATGTCTGGGGT 60.034 55.000 0.00 0.00 46.44 4.95
1278 1302 0.681887 TGCAGCATCCAATGTCTGGG 60.682 55.000 0.00 0.00 46.44 4.45
1281 1305 2.029623 GGATTGCAGCATCCAATGTCT 58.970 47.619 11.83 0.00 36.95 3.41
1284 1308 1.410004 AGGGATTGCAGCATCCAATG 58.590 50.000 17.31 0.00 38.68 2.82
1285 1309 1.760613 CAAGGGATTGCAGCATCCAAT 59.239 47.619 17.31 4.56 38.68 3.16
1286 1310 1.187974 CAAGGGATTGCAGCATCCAA 58.812 50.000 17.31 0.00 38.68 3.53
1287 1311 1.324740 GCAAGGGATTGCAGCATCCA 61.325 55.000 17.31 0.00 46.60 3.41
1299 1323 1.002888 CTCAAGCAGAAGAGCAAGGGA 59.997 52.381 0.00 0.00 36.85 4.20
1315 1339 0.035439 GTGAAGCGGGGATTCCTCAA 60.035 55.000 2.89 0.00 0.00 3.02
1318 1342 2.680370 GGGTGAAGCGGGGATTCCT 61.680 63.158 2.01 0.00 0.00 3.36
1333 1357 2.828549 GCCGCCGATTTCATGGGT 60.829 61.111 0.00 0.00 0.00 4.51
1347 1371 1.022982 TGAGCTTCTTGATGCAGCCG 61.023 55.000 0.00 0.00 35.52 5.52
1351 1375 2.156917 CTGGTTGAGCTTCTTGATGCA 58.843 47.619 10.39 0.00 0.00 3.96
1365 1389 1.444553 GGAGTCGAGCGTCTGGTTG 60.445 63.158 0.00 0.00 0.00 3.77
1464 1489 7.473735 TGTAATGATATCCACCTTGCAAAAA 57.526 32.000 0.00 0.00 0.00 1.94
1509 1537 6.016360 GCAATTGTGCCTTATGTATGTATCCA 60.016 38.462 7.40 0.00 45.68 3.41
1531 1560 4.462508 TGTTGATGTTTTCTTGTGGCAA 57.537 36.364 0.00 0.00 0.00 4.52
1667 1713 5.659440 TGCTTGTTTTGGAGTTCTTCTTT 57.341 34.783 0.00 0.00 0.00 2.52
1787 1838 7.334421 CCTTTAAGCTTTGCTAGTCTTGATACA 59.666 37.037 3.20 0.00 38.25 2.29
2004 2064 1.466167 GCGTAACCGTGAGTGTCTCTA 59.534 52.381 0.00 0.00 36.15 2.43
2234 2299 8.155821 TGTTTTACCATTGTCGAAATGTCTTA 57.844 30.769 14.81 5.33 0.00 2.10
2362 2433 1.969923 CCATTTCCTTGGCAACTTGGA 59.030 47.619 0.00 0.00 37.00 3.53
2377 2448 2.671619 CACCGTGCGGGACCATTT 60.672 61.111 15.44 0.00 39.97 2.32
2397 2468 5.991861 TGTCTAAGTGTTGGTCCAAACTAA 58.008 37.500 5.69 0.60 0.00 2.24
2458 2539 5.315109 ACTTTCCCTTGGGAGTAATTAACCT 59.685 40.000 8.55 0.00 0.00 3.50
2859 2957 3.788227 TGACACCATTCCTAGCAAACT 57.212 42.857 0.00 0.00 0.00 2.66
2965 3116 7.452813 TGGATCTCACTACTATCATTGCTATGT 59.547 37.037 8.01 0.00 33.34 2.29
3271 3454 5.535043 ACCGGAATTGTTATACGTTGTTC 57.465 39.130 9.46 0.00 0.00 3.18
3278 3461 6.576185 TGAGGACTTACCGGAATTGTTATAC 58.424 40.000 9.46 0.00 44.74 1.47
3708 3900 0.183492 TACATCATGCCCAGGCCTTC 59.817 55.000 0.00 0.00 41.09 3.46
3714 3906 3.558931 TTACCTGTACATCATGCCCAG 57.441 47.619 0.00 0.00 0.00 4.45
3847 4063 9.840427 TTTAATAGCTCTAAACATTGCAAACTC 57.160 29.630 1.71 0.00 0.00 3.01
3850 4066 9.973450 TTGTTTAATAGCTCTAAACATTGCAAA 57.027 25.926 24.08 12.53 44.52 3.68
4134 4370 8.565896 TTAGCTTCATGTTTATGTCATCTTGT 57.434 30.769 0.00 0.00 35.73 3.16
4257 4499 6.072112 TGTTGTTATCTTGCTCCAAACTTC 57.928 37.500 0.00 0.00 0.00 3.01
4661 4927 5.460646 CCTGATTTATCGTTGCAAAAGTGT 58.539 37.500 0.00 0.00 0.00 3.55
4679 4947 3.854437 TGAGGTCATCTAGATGCCTGAT 58.146 45.455 34.33 21.11 41.78 2.90
4709 4977 8.677300 AGTACATAATTTCATTTCATTGCGTCT 58.323 29.630 0.00 0.00 0.00 4.18
4956 5279 1.065928 CGTTCGCTCCGGCTAGATT 59.934 57.895 0.00 0.00 36.09 2.40
5824 6984 1.023502 TTTCCCCGTTGTCCGTTTTC 58.976 50.000 0.00 0.00 33.66 2.29
6027 7188 3.055530 GTGAGATTGAGGAAGCTGAAGGA 60.056 47.826 0.00 0.00 0.00 3.36
6062 7223 0.331616 TGGGTCAGACTCTCATCCGA 59.668 55.000 1.07 0.00 0.00 4.55
6063 7224 0.743688 CTGGGTCAGACTCTCATCCG 59.256 60.000 1.07 0.00 32.44 4.18
6067 10992 0.178950 AGCACTGGGTCAGACTCTCA 60.179 55.000 1.07 0.00 35.18 3.27
6075 11000 2.595463 GCAAGCAGCACTGGGTCA 60.595 61.111 0.00 0.00 44.79 4.02
6107 11032 4.335647 CCCAACCGCTCCAGCACT 62.336 66.667 0.00 0.00 42.21 4.40
6122 11047 0.836400 TCTTCTCTCCCACCACACCC 60.836 60.000 0.00 0.00 0.00 4.61
6164 11695 5.189928 TCTTTGTTAGTGAGCTTTTCCACA 58.810 37.500 6.11 0.00 35.84 4.17
6207 13374 3.632080 ACCCACGATGGCGACCAA 61.632 61.111 2.68 0.00 41.64 3.67
6221 13388 4.109675 CCGATCCCACCCACACCC 62.110 72.222 0.00 0.00 0.00 4.61
6227 13394 2.124695 GTCTTGCCGATCCCACCC 60.125 66.667 0.00 0.00 0.00 4.61
6337 13508 1.547820 TGGCAGTCTTGAGTAGCTCAG 59.452 52.381 0.00 0.00 41.75 3.35
6344 13515 2.355513 GGTGATGATGGCAGTCTTGAGT 60.356 50.000 0.00 0.00 0.00 3.41
6394 13565 6.199908 CGGCACAAGTAGAGATTTATCTTGAG 59.800 42.308 9.63 3.87 38.82 3.02
6531 13702 0.889306 GTGACAAGGACTCGGCTACT 59.111 55.000 0.00 0.00 0.00 2.57
6593 13764 0.035739 GTCAACATGGTGGTACGGGT 59.964 55.000 11.68 0.00 0.00 5.28
6596 13767 4.225984 CAATTTGTCAACATGGTGGTACG 58.774 43.478 11.68 0.00 0.00 3.67
6597 13768 4.555262 CCAATTTGTCAACATGGTGGTAC 58.445 43.478 11.68 2.99 0.00 3.34
6598 13769 3.576118 CCCAATTTGTCAACATGGTGGTA 59.424 43.478 11.68 0.00 0.00 3.25
6599 13770 2.368221 CCCAATTTGTCAACATGGTGGT 59.632 45.455 11.68 0.00 0.00 4.16
6600 13771 2.632028 TCCCAATTTGTCAACATGGTGG 59.368 45.455 11.68 0.00 0.00 4.61
6645 13816 9.827422 GTTGATGTAACTCTCACCTGCTTGGTA 62.827 44.444 1.80 0.00 40.68 3.25
6648 13819 3.930336 TGATGTAACTCTCACCTGCTTG 58.070 45.455 0.00 0.00 0.00 4.01
6704 13875 9.712359 AATTTCTTGACTCGTTAAACTGTTAAC 57.288 29.630 0.00 0.00 43.82 2.01
6718 13889 6.603095 AGTGAACGCATAAATTTCTTGACTC 58.397 36.000 0.00 0.00 0.00 3.36
6719 13890 6.560253 AGTGAACGCATAAATTTCTTGACT 57.440 33.333 0.00 0.00 0.00 3.41
6720 13891 8.788813 CAATAGTGAACGCATAAATTTCTTGAC 58.211 33.333 0.00 0.00 0.00 3.18
6721 13892 8.726068 TCAATAGTGAACGCATAAATTTCTTGA 58.274 29.630 0.00 0.00 0.00 3.02
6722 13893 8.788813 GTCAATAGTGAACGCATAAATTTCTTG 58.211 33.333 0.00 0.00 34.87 3.02
6723 13894 8.730680 AGTCAATAGTGAACGCATAAATTTCTT 58.269 29.630 0.00 0.00 34.87 2.52
6725 13896 8.391106 AGAGTCAATAGTGAACGCATAAATTTC 58.609 33.333 0.00 0.00 34.87 2.17
6726 13897 8.177663 CAGAGTCAATAGTGAACGCATAAATTT 58.822 33.333 0.00 0.00 34.87 1.82
6886 14261 3.797039 CGTGATTTCTCCTTCTGGCATA 58.203 45.455 0.00 0.00 0.00 3.14
6887 14262 2.636830 CGTGATTTCTCCTTCTGGCAT 58.363 47.619 0.00 0.00 0.00 4.40
6900 14275 1.606885 CCCCAAGCATGGCGTGATTT 61.607 55.000 11.71 0.78 46.09 2.17
6939 14314 2.035066 GCATTTGGGATACTGACCATGC 59.965 50.000 0.00 0.00 36.48 4.06
6940 14315 2.624838 GGCATTTGGGATACTGACCATG 59.375 50.000 0.00 0.00 36.48 3.66
6953 14328 4.996788 ATTTAGCTCTTCAGGCATTTGG 57.003 40.909 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.