Multiple sequence alignment - TraesCS3A01G462000

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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 TraesCS3A01G462000 chr3A 100.000 5092 0 0 1 5092 697475693 697470602 0.000000e+00 9404.0
1 TraesCS3A01G462000 chr3A 89.530 1022 88 16 1778 2794 697492924 697491917 0.000000e+00 1277.0
2 TraesCS3A01G462000 chr3A 93.548 496 26 2 4597 5091 697480719 697480229 0.000000e+00 734.0
3 TraesCS3A01G462000 chr3A 89.060 585 31 8 3920 4489 697491377 697490811 0.000000e+00 695.0
4 TraesCS3A01G462000 chr3A 92.483 439 26 2 3482 3920 697491874 697491443 5.600000e-174 621.0
5 TraesCS3A01G462000 chr3A 83.333 576 45 28 1061 1631 697493556 697493027 7.670000e-133 484.0
6 TraesCS3A01G462000 chr3A 88.889 135 12 2 3342 3476 659015496 659015627 4.080000e-36 163.0
7 TraesCS3A01G462000 chr3A 85.217 115 8 4 910 1017 697493665 697493553 5.390000e-20 110.0
8 TraesCS3A01G462000 chr3D 92.103 1950 116 25 1348 3280 561892816 561890888 0.000000e+00 2713.0
9 TraesCS3A01G462000 chr3D 87.338 1698 119 49 1137 2802 561764056 561762423 0.000000e+00 1857.0
10 TraesCS3A01G462000 chr3D 93.589 1123 30 11 3475 4584 561890748 561889655 0.000000e+00 1637.0
11 TraesCS3A01G462000 chr3D 93.358 1069 49 3 1 1058 561751576 561750519 0.000000e+00 1561.0
12 TraesCS3A01G462000 chr3D 91.797 1024 64 14 1778 2794 561749662 561748652 0.000000e+00 1408.0
13 TraesCS3A01G462000 chr3D 89.225 1123 60 16 3478 4584 561748614 561747537 0.000000e+00 1347.0
14 TraesCS3A01G462000 chr3D 85.088 912 109 19 3 889 37787742 37788651 0.000000e+00 905.0
15 TraesCS3A01G462000 chr3D 90.520 654 28 10 3920 4561 561761926 561761295 0.000000e+00 833.0
16 TraesCS3A01G462000 chr3D 99.134 462 3 1 1322 1782 561750160 561749699 0.000000e+00 830.0
17 TraesCS3A01G462000 chr3D 98.268 462 8 0 4631 5092 561889535 561889074 0.000000e+00 809.0
18 TraesCS3A01G462000 chr3D 92.073 492 34 4 4603 5091 561761121 561760632 0.000000e+00 688.0
19 TraesCS3A01G462000 chr3D 90.455 440 35 3 3481 3920 561762424 561761992 1.590000e-159 573.0
20 TraesCS3A01G462000 chr3D 86.325 117 9 5 905 1017 561764272 561764159 2.490000e-23 121.0
21 TraesCS3A01G462000 chr3D 85.345 116 8 4 909 1017 561898713 561898600 1.500000e-20 111.0
22 TraesCS3A01G462000 chr3B 91.057 1532 110 12 1278 2802 749092992 749091481 0.000000e+00 2045.0
23 TraesCS3A01G462000 chr3B 89.691 970 82 13 1826 2794 749148411 749147459 0.000000e+00 1221.0
24 TraesCS3A01G462000 chr3B 91.206 796 58 6 1826 2619 749313600 749312815 0.000000e+00 1072.0
25 TraesCS3A01G462000 chr3B 90.704 753 59 6 360 1108 749093846 749093101 0.000000e+00 992.0
26 TraesCS3A01G462000 chr3B 87.405 659 41 16 3919 4565 749146917 749146289 0.000000e+00 719.0
27 TraesCS3A01G462000 chr3B 93.722 446 15 4 3481 3920 749091482 749091044 0.000000e+00 656.0
28 TraesCS3A01G462000 chr3B 84.583 707 53 24 1063 1738 749314321 749313640 0.000000e+00 651.0
29 TraesCS3A01G462000 chr3B 88.247 519 36 6 3920 4437 749090851 749090357 9.440000e-167 597.0
30 TraesCS3A01G462000 chr3B 90.625 448 33 4 3475 3921 749312062 749311623 2.040000e-163 586.0
31 TraesCS3A01G462000 chr3B 88.211 492 41 6 4601 5092 749078275 749077801 5.720000e-159 571.0
32 TraesCS3A01G462000 chr3B 87.751 498 47 7 4597 5092 749309605 749309120 2.060000e-158 569.0
33 TraesCS3A01G462000 chr3B 88.518 479 35 8 4597 5075 749146128 749145670 3.440000e-156 562.0
34 TraesCS3A01G462000 chr3B 85.487 565 53 19 1137 1678 749149171 749148613 3.440000e-156 562.0
35 TraesCS3A01G462000 chr3B 89.556 450 36 6 3475 3920 749147424 749146982 1.240000e-155 560.0
36 TraesCS3A01G462000 chr3B 90.220 409 27 4 3920 4316 749311558 749311151 5.840000e-144 521.0
37 TraesCS3A01G462000 chr3B 79.855 690 85 29 2598 3249 749312750 749312077 6.010000e-124 455.0
38 TraesCS3A01G462000 chr3B 83.711 485 50 20 1053 1520 749099176 749098704 1.010000e-116 431.0
39 TraesCS3A01G462000 chr3B 89.615 260 13 2 4325 4584 749309962 749309717 8.230000e-83 318.0
40 TraesCS3A01G462000 chr3B 86.972 284 34 1 3608 3891 749098708 749098428 2.960000e-82 316.0
41 TraesCS3A01G462000 chr3B 89.941 169 12 1 3975 4138 749098061 749097893 3.990000e-51 213.0
42 TraesCS3A01G462000 chr3B 98.182 110 2 0 3370 3479 20487500 20487391 5.200000e-45 193.0
43 TraesCS3A01G462000 chr3B 93.277 119 5 3 1149 1264 749093092 749092974 6.780000e-39 172.0
44 TraesCS3A01G462000 chr3B 80.916 131 9 4 4433 4563 749078556 749078442 7.020000e-14 89.8
45 TraesCS3A01G462000 chr7D 87.733 913 87 13 1 889 7338796 7339707 0.000000e+00 1042.0
46 TraesCS3A01G462000 chr7D 85.957 883 94 16 31 890 35795231 35796106 0.000000e+00 917.0
47 TraesCS3A01G462000 chr7D 87.183 749 88 7 145 891 294035493 294034751 0.000000e+00 845.0
48 TraesCS3A01G462000 chr5D 87.514 913 84 13 1 890 159641771 159640866 0.000000e+00 1027.0
49 TraesCS3A01G462000 chr5D 86.747 913 88 13 1 889 486670175 486671078 0.000000e+00 985.0
50 TraesCS3A01G462000 chr5D 86.339 915 101 12 1 891 545985591 545986505 0.000000e+00 976.0
51 TraesCS3A01G462000 chr5D 82.090 134 20 4 3369 3500 505374624 505374493 1.500000e-20 111.0
52 TraesCS3A01G462000 chr7A 86.181 919 95 11 1 889 5009186 5008270 0.000000e+00 965.0
53 TraesCS3A01G462000 chr7A 85.509 904 105 11 1 880 239776684 239775783 0.000000e+00 920.0
54 TraesCS3A01G462000 chr7A 100.000 109 0 0 3245 3353 685837621 685837729 8.640000e-48 202.0
55 TraesCS3A01G462000 chr4B 85.872 906 110 14 1 890 27942374 27941471 0.000000e+00 948.0
56 TraesCS3A01G462000 chr6A 85.542 913 96 18 1 890 560128656 560129555 0.000000e+00 922.0
57 TraesCS3A01G462000 chr6A 100.000 108 0 0 3246 3353 579148319 579148212 3.110000e-47 200.0
58 TraesCS3A01G462000 chr6A 94.262 122 7 0 3356 3477 108945300 108945421 2.420000e-43 187.0
59 TraesCS3A01G462000 chr6A 86.364 132 13 4 3369 3500 472356740 472356614 6.870000e-29 139.0
60 TraesCS3A01G462000 chr5A 85.542 913 97 11 1 890 41130287 41131187 0.000000e+00 922.0
61 TraesCS3A01G462000 chr5A 88.235 153 18 0 1 153 295073448 295073600 3.130000e-42 183.0
62 TraesCS3A01G462000 chr5A 85.185 135 18 2 3340 3473 206731003 206731136 2.470000e-28 137.0
63 TraesCS3A01G462000 chr6D 84.337 913 95 18 1 890 417697124 417698011 0.000000e+00 850.0
64 TraesCS3A01G462000 chr1D 87.764 711 60 6 1 688 338925448 338926154 0.000000e+00 806.0
65 TraesCS3A01G462000 chr1D 98.198 111 2 0 3367 3477 349422922 349423032 1.450000e-45 195.0
66 TraesCS3A01G462000 chr1D 96.522 115 4 0 3362 3476 48024737 48024623 1.870000e-44 191.0
67 TraesCS3A01G462000 chr2D 99.107 112 1 0 3242 3353 326217473 326217584 8.640000e-48 202.0
68 TraesCS3A01G462000 chr4A 96.639 119 4 0 3240 3358 54358915 54359033 1.120000e-46 198.0
69 TraesCS3A01G462000 chrUn 97.414 116 2 1 3238 3353 94014624 94014510 4.020000e-46 196.0
70 TraesCS3A01G462000 chr6B 98.198 111 2 0 3369 3479 197245559 197245669 1.450000e-45 195.0
71 TraesCS3A01G462000 chr6B 92.308 130 8 2 3351 3479 544804623 544804495 3.130000e-42 183.0
72 TraesCS3A01G462000 chr6B 92.857 126 8 1 3352 3476 633918939 633919064 1.130000e-41 182.0
73 TraesCS3A01G462000 chr6B 82.051 156 25 2 3328 3483 191540654 191540502 4.140000e-26 130.0
74 TraesCS3A01G462000 chr2A 94.400 125 7 0 3229 3353 647958055 647957931 5.200000e-45 193.0
75 TraesCS3A01G462000 chr5B 94.400 125 5 2 3244 3367 711156457 711156334 1.870000e-44 191.0
76 TraesCS3A01G462000 chr5B 85.517 145 16 5 3339 3480 515669428 515669570 4.110000e-31 147.0
77 TraesCS3A01G462000 chr5B 81.481 108 16 4 3340 3445 515669472 515669367 9.080000e-13 86.1
78 TraesCS3A01G462000 chr2B 94.400 125 6 1 3234 3358 621062516 621062639 1.870000e-44 191.0
79 TraesCS3A01G462000 chr1B 93.077 130 7 2 3230 3358 659332770 659332898 6.730000e-44 189.0
80 TraesCS3A01G462000 chr1A 95.082 122 3 3 3357 3476 531866979 531867099 6.730000e-44 189.0
81 TraesCS3A01G462000 chr1A 92.913 127 8 1 3356 3481 441238227 441238353 3.130000e-42 183.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G462000 chr3A 697470602 697475693 5091 True 9404.000000 9404 100.000000 1 5092 1 chr3A.!!$R1 5091
1 TraesCS3A01G462000 chr3A 697490811 697493665 2854 True 637.400000 1277 87.924600 910 4489 5 chr3A.!!$R3 3579
2 TraesCS3A01G462000 chr3D 561889074 561892816 3742 True 1719.666667 2713 94.653333 1348 5092 3 chr3D.!!$R4 3744
3 TraesCS3A01G462000 chr3D 561747537 561751576 4039 True 1286.500000 1561 93.378500 1 4584 4 chr3D.!!$R2 4583
4 TraesCS3A01G462000 chr3D 37787742 37788651 909 False 905.000000 905 85.088000 3 889 1 chr3D.!!$F1 886
5 TraesCS3A01G462000 chr3D 561760632 561764272 3640 True 814.400000 1857 89.342200 905 5091 5 chr3D.!!$R3 4186
6 TraesCS3A01G462000 chr3B 749090357 749093846 3489 True 892.400000 2045 91.401400 360 4437 5 chr3B.!!$R3 4077
7 TraesCS3A01G462000 chr3B 749145670 749149171 3501 True 724.800000 1221 88.131400 1137 5075 5 chr3B.!!$R5 3938
8 TraesCS3A01G462000 chr3B 749309120 749314321 5201 True 596.000000 1072 87.693571 1063 5092 7 chr3B.!!$R6 4029
9 TraesCS3A01G462000 chr3B 749077801 749078556 755 True 330.400000 571 84.563500 4433 5092 2 chr3B.!!$R2 659
10 TraesCS3A01G462000 chr3B 749097893 749099176 1283 True 320.000000 431 86.874667 1053 4138 3 chr3B.!!$R4 3085
11 TraesCS3A01G462000 chr7D 7338796 7339707 911 False 1042.000000 1042 87.733000 1 889 1 chr7D.!!$F1 888
12 TraesCS3A01G462000 chr7D 35795231 35796106 875 False 917.000000 917 85.957000 31 890 1 chr7D.!!$F2 859
13 TraesCS3A01G462000 chr7D 294034751 294035493 742 True 845.000000 845 87.183000 145 891 1 chr7D.!!$R1 746
14 TraesCS3A01G462000 chr5D 159640866 159641771 905 True 1027.000000 1027 87.514000 1 890 1 chr5D.!!$R1 889
15 TraesCS3A01G462000 chr5D 486670175 486671078 903 False 985.000000 985 86.747000 1 889 1 chr5D.!!$F1 888
16 TraesCS3A01G462000 chr5D 545985591 545986505 914 False 976.000000 976 86.339000 1 891 1 chr5D.!!$F2 890
17 TraesCS3A01G462000 chr7A 5008270 5009186 916 True 965.000000 965 86.181000 1 889 1 chr7A.!!$R1 888
18 TraesCS3A01G462000 chr7A 239775783 239776684 901 True 920.000000 920 85.509000 1 880 1 chr7A.!!$R2 879
19 TraesCS3A01G462000 chr4B 27941471 27942374 903 True 948.000000 948 85.872000 1 890 1 chr4B.!!$R1 889
20 TraesCS3A01G462000 chr6A 560128656 560129555 899 False 922.000000 922 85.542000 1 890 1 chr6A.!!$F2 889
21 TraesCS3A01G462000 chr5A 41130287 41131187 900 False 922.000000 922 85.542000 1 890 1 chr5A.!!$F1 889
22 TraesCS3A01G462000 chr6D 417697124 417698011 887 False 850.000000 850 84.337000 1 890 1 chr6D.!!$F1 889
23 TraesCS3A01G462000 chr1D 338925448 338926154 706 False 806.000000 806 87.764000 1 688 1 chr1D.!!$F1 687

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
64 65 0.319555 CGGTCCGACACACACTCAAT 60.320 55.000 4.91 0.0 0.00 2.57 F
311 344 1.004044 CTCCACCTGCATTTCCTCTGT 59.996 52.381 0.00 0.0 0.00 3.41 F
2183 2529 1.072266 ATGGTGGGGAAACACTGCTA 58.928 50.000 0.00 0.0 41.09 3.49 F
3261 3737 0.251653 TGCTACTCCCTCCGTTCACT 60.252 55.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2369 1.006832 CCGTTCTCAAGTTATGGGCG 58.993 55.000 0.00 0.00 0.00 6.13 R
2235 2581 3.238597 TCCTTGCTTGGCCTAATTTGTT 58.761 40.909 3.32 0.00 0.00 2.83 R
3458 3988 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 R
4489 6710 1.205655 TCTCTGGTCAAAGATGCTCGG 59.794 52.381 0.00 0.00 0.00 4.63 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
64 65 0.319555 CGGTCCGACACACACTCAAT 60.320 55.000 4.91 0.00 0.00 2.57
311 344 1.004044 CTCCACCTGCATTTCCTCTGT 59.996 52.381 0.00 0.00 0.00 3.41
410 449 5.045869 TCCGAAGAGGATTGTAGGTTTTCAT 60.046 40.000 0.00 0.00 45.98 2.57
423 462 7.629157 TGTAGGTTTTCATCCAACATGAGATA 58.371 34.615 0.00 0.00 0.00 1.98
907 978 9.050601 CCTCATCCTTTTAGTTTTAGCTCATAG 57.949 37.037 0.00 0.00 0.00 2.23
1227 1346 2.154462 CATGACGTTTGGCTTTCTCCT 58.846 47.619 0.00 0.00 0.00 3.69
1249 1379 2.817258 CTCAGAACGTTCTCCAGTCTCT 59.183 50.000 27.54 0.81 34.74 3.10
1253 1383 2.871096 ACGTTCTCCAGTCTCTCTCT 57.129 50.000 0.00 0.00 0.00 3.10
1257 1387 3.369471 CGTTCTCCAGTCTCTCTCTCTCT 60.369 52.174 0.00 0.00 0.00 3.10
1272 1402 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1273 1403 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1274 1404 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1275 1405 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1276 1406 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1277 1407 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1278 1408 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1279 1409 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1512 1720 1.822990 AGCAAGCCATGGATGAAACAG 59.177 47.619 18.40 0.00 0.00 3.16
1745 2045 7.391620 TCATTACTTAATTCGGTCTGTCCTTT 58.608 34.615 0.00 0.00 0.00 3.11
2183 2529 1.072266 ATGGTGGGGAAACACTGCTA 58.928 50.000 0.00 0.00 41.09 3.49
2314 2660 0.735471 CGTCGAGCTCTCCATCAGAA 59.265 55.000 12.85 0.00 0.00 3.02
2604 3035 0.606401 CCGCACCCTTGTGAGTCAAT 60.606 55.000 0.00 0.00 45.76 2.57
2815 3258 7.038659 TGAAGTTTGTCTTACCCAAAACAATG 58.961 34.615 0.00 0.00 36.40 2.82
2892 3349 2.739849 TTCCTGTCGCGGGATTTGCA 62.740 55.000 6.13 0.00 38.86 4.08
2952 3418 2.159490 GGTGTTTGTTGTAGTGCGTGTT 60.159 45.455 0.00 0.00 0.00 3.32
2978 3444 6.885922 AGTAGAAGTTGGTTGTAGTCTTGTT 58.114 36.000 0.00 0.00 0.00 2.83
2980 3446 8.142551 AGTAGAAGTTGGTTGTAGTCTTGTTAG 58.857 37.037 0.00 0.00 0.00 2.34
2995 3469 8.154649 AGTCTTGTTAGAAGTGTTTGGTTATG 57.845 34.615 0.00 0.00 30.65 1.90
3188 3662 3.181499 CCAGTGAGCTCTTATCGTTACGT 60.181 47.826 16.19 0.00 0.00 3.57
3259 3735 1.275291 CTTTGCTACTCCCTCCGTTCA 59.725 52.381 0.00 0.00 0.00 3.18
3260 3736 0.606604 TTGCTACTCCCTCCGTTCAC 59.393 55.000 0.00 0.00 0.00 3.18
3261 3737 0.251653 TGCTACTCCCTCCGTTCACT 60.252 55.000 0.00 0.00 0.00 3.41
3262 3738 0.896226 GCTACTCCCTCCGTTCACTT 59.104 55.000 0.00 0.00 0.00 3.16
3263 3739 1.275573 GCTACTCCCTCCGTTCACTTT 59.724 52.381 0.00 0.00 0.00 2.66
3272 3748 4.124238 CCTCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
3276 3752 6.721321 TCCGTTCACTTTTGTAAGTCATTTC 58.279 36.000 0.00 0.00 42.67 2.17
3280 3756 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
3281 3757 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
3282 3758 8.275015 TCACTTTTGTAAGTCATTTCAGACAA 57.725 30.769 0.00 0.00 42.67 3.18
3283 3759 8.181573 TCACTTTTGTAAGTCATTTCAGACAAC 58.818 33.333 0.00 0.00 42.67 3.32
3284 3760 8.184192 CACTTTTGTAAGTCATTTCAGACAACT 58.816 33.333 0.00 0.00 42.67 3.16
3287 3763 7.857734 TTGTAAGTCATTTCAGACAACTCAA 57.142 32.000 0.00 0.00 40.98 3.02
3288 3764 7.857734 TGTAAGTCATTTCAGACAACTCAAA 57.142 32.000 0.00 0.00 40.98 2.69
3292 3768 6.742109 AGTCATTTCAGACAACTCAAAATGG 58.258 36.000 0.00 0.00 40.98 3.16
3293 3769 5.922544 GTCATTTCAGACAACTCAAAATGGG 59.077 40.000 0.00 0.00 37.16 4.00
3296 3772 2.886523 TCAGACAACTCAAAATGGGCTG 59.113 45.455 0.00 0.00 0.00 4.85
3297 3773 2.624838 CAGACAACTCAAAATGGGCTGT 59.375 45.455 0.00 0.00 0.00 4.40
3298 3774 3.068590 CAGACAACTCAAAATGGGCTGTT 59.931 43.478 0.00 0.00 0.00 3.16
3300 3776 4.162131 AGACAACTCAAAATGGGCTGTTTT 59.838 37.500 0.00 0.00 0.00 2.43
3301 3777 4.190772 ACAACTCAAAATGGGCTGTTTTG 58.809 39.130 16.38 16.38 44.10 2.44
3302 3778 4.190772 CAACTCAAAATGGGCTGTTTTGT 58.809 39.130 19.52 6.52 43.52 2.83
3303 3779 5.105146 ACAACTCAAAATGGGCTGTTTTGTA 60.105 36.000 19.52 10.81 43.52 2.41
3304 3780 4.944048 ACTCAAAATGGGCTGTTTTGTAC 58.056 39.130 19.52 0.00 43.52 2.90
3305 3781 4.404073 ACTCAAAATGGGCTGTTTTGTACA 59.596 37.500 19.52 0.00 43.52 2.90
3306 3782 5.070313 ACTCAAAATGGGCTGTTTTGTACAT 59.930 36.000 19.52 7.99 43.52 2.29
3307 3783 5.923204 TCAAAATGGGCTGTTTTGTACATT 58.077 33.333 19.52 0.00 43.52 2.71
3308 3784 5.757320 TCAAAATGGGCTGTTTTGTACATTG 59.243 36.000 19.52 0.00 43.52 2.82
3309 3785 4.953940 AATGGGCTGTTTTGTACATTGT 57.046 36.364 0.00 0.00 35.85 2.71
3310 3786 4.519540 ATGGGCTGTTTTGTACATTGTC 57.480 40.909 0.00 0.00 35.85 3.18
3317 3847 6.144402 GGCTGTTTTGTACATTGTCTGAAATG 59.856 38.462 0.00 9.50 42.21 2.32
3319 3849 7.096477 GCTGTTTTGTACATTGTCTGAAATGTC 60.096 37.037 16.13 11.24 45.47 3.06
3321 3851 8.465999 TGTTTTGTACATTGTCTGAAATGTCTT 58.534 29.630 16.13 2.61 45.47 3.01
3322 3852 8.958043 GTTTTGTACATTGTCTGAAATGTCTTC 58.042 33.333 16.13 11.26 45.47 2.87
3325 3855 7.864686 TGTACATTGTCTGAAATGTCTTCAAG 58.135 34.615 16.13 0.00 45.47 3.02
3327 3857 5.829924 ACATTGTCTGAAATGTCTTCAAGGT 59.170 36.000 10.41 0.00 45.47 3.50
3332 3862 7.453393 TGTCTGAAATGTCTTCAAGGTCTTAT 58.547 34.615 0.00 0.00 0.00 1.73
3334 3864 9.436957 GTCTGAAATGTCTTCAAGGTCTTATAA 57.563 33.333 0.00 0.00 0.00 0.98
3343 3873 9.052759 GTCTTCAAGGTCTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 34.13 3.18
3351 3881 7.387643 GTCTTATAAAAGTGAACAGAGGGAGT 58.612 38.462 0.00 0.00 34.13 3.85
3352 3882 8.529476 GTCTTATAAAAGTGAACAGAGGGAGTA 58.471 37.037 0.00 0.00 34.13 2.59
3353 3883 8.529476 TCTTATAAAAGTGAACAGAGGGAGTAC 58.471 37.037 0.00 0.00 34.13 2.73
3379 3909 9.627395 CTATACTACAAAATGATACTCCCTTCG 57.373 37.037 0.00 0.00 0.00 3.79
3380 3910 6.295719 ACTACAAAATGATACTCCCTTCGT 57.704 37.500 0.00 0.00 0.00 3.85
3381 3911 6.708285 ACTACAAAATGATACTCCCTTCGTT 58.292 36.000 0.00 0.00 0.00 3.85
3382 3912 6.817140 ACTACAAAATGATACTCCCTTCGTTC 59.183 38.462 0.00 0.00 0.00 3.95
3383 3913 4.630069 ACAAAATGATACTCCCTTCGTTCG 59.370 41.667 0.00 0.00 0.00 3.95
3384 3914 3.454371 AATGATACTCCCTTCGTTCGG 57.546 47.619 0.00 0.00 0.00 4.30
3385 3915 2.133281 TGATACTCCCTTCGTTCGGA 57.867 50.000 0.00 0.00 0.00 4.55
3386 3916 2.449464 TGATACTCCCTTCGTTCGGAA 58.551 47.619 0.00 0.00 0.00 4.30
3387 3917 3.028850 TGATACTCCCTTCGTTCGGAAT 58.971 45.455 0.00 0.00 33.26 3.01
3388 3918 3.449737 TGATACTCCCTTCGTTCGGAATT 59.550 43.478 0.00 0.00 33.26 2.17
3389 3919 4.646040 TGATACTCCCTTCGTTCGGAATTA 59.354 41.667 0.00 0.00 33.26 1.40
3390 3920 3.242549 ACTCCCTTCGTTCGGAATTAC 57.757 47.619 0.00 0.00 33.26 1.89
3391 3921 2.830321 ACTCCCTTCGTTCGGAATTACT 59.170 45.455 0.00 0.00 33.26 2.24
3392 3922 3.260128 ACTCCCTTCGTTCGGAATTACTT 59.740 43.478 0.00 0.00 33.26 2.24
3393 3923 3.592059 TCCCTTCGTTCGGAATTACTTG 58.408 45.455 0.00 0.00 33.26 3.16
3394 3924 3.007182 TCCCTTCGTTCGGAATTACTTGT 59.993 43.478 0.00 0.00 33.26 3.16
3395 3925 3.370061 CCCTTCGTTCGGAATTACTTGTC 59.630 47.826 0.00 0.00 33.26 3.18
3396 3926 3.060363 CCTTCGTTCGGAATTACTTGTCG 59.940 47.826 0.00 0.00 33.26 4.35
3397 3927 1.987770 TCGTTCGGAATTACTTGTCGC 59.012 47.619 0.00 0.00 0.00 5.19
3398 3928 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3399 3929 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3400 3930 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3401 3931 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3402 3932 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3403 3933 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3404 3934 5.412640 TCGGAATTACTTGTCGCAGAAATA 58.587 37.500 0.00 0.00 39.69 1.40
3405 3935 5.518847 TCGGAATTACTTGTCGCAGAAATAG 59.481 40.000 0.00 0.00 39.69 1.73
3406 3936 5.518847 CGGAATTACTTGTCGCAGAAATAGA 59.481 40.000 0.00 0.00 39.69 1.98
3407 3937 6.201044 CGGAATTACTTGTCGCAGAAATAGAT 59.799 38.462 0.00 0.00 39.69 1.98
3408 3938 7.348201 GGAATTACTTGTCGCAGAAATAGATG 58.652 38.462 0.00 0.00 39.69 2.90
3409 3939 7.011482 GGAATTACTTGTCGCAGAAATAGATGT 59.989 37.037 0.00 0.00 39.69 3.06
3410 3940 8.942338 AATTACTTGTCGCAGAAATAGATGTA 57.058 30.769 0.00 0.00 39.69 2.29
3411 3941 9.547753 AATTACTTGTCGCAGAAATAGATGTAT 57.452 29.630 0.00 0.00 39.69 2.29
3412 3942 8.575565 TTACTTGTCGCAGAAATAGATGTATC 57.424 34.615 0.00 0.00 39.69 2.24
3413 3943 6.810911 ACTTGTCGCAGAAATAGATGTATCT 58.189 36.000 0.00 0.00 39.69 1.98
3414 3944 7.941919 ACTTGTCGCAGAAATAGATGTATCTA 58.058 34.615 4.22 4.22 40.45 1.98
3415 3945 8.079203 ACTTGTCGCAGAAATAGATGTATCTAG 58.921 37.037 7.57 0.00 39.84 2.43
3416 3946 7.745620 TGTCGCAGAAATAGATGTATCTAGA 57.254 36.000 7.57 0.00 39.84 2.43
3417 3947 8.341892 TGTCGCAGAAATAGATGTATCTAGAT 57.658 34.615 10.73 10.73 39.84 1.98
3418 3948 8.239998 TGTCGCAGAAATAGATGTATCTAGATG 58.760 37.037 15.79 0.00 39.84 2.90
3419 3949 8.240682 GTCGCAGAAATAGATGTATCTAGATGT 58.759 37.037 15.79 1.25 39.84 3.06
3420 3950 9.449719 TCGCAGAAATAGATGTATCTAGATGTA 57.550 33.333 15.79 4.44 42.20 2.29
3447 3977 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
3448 3978 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
3449 3979 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
3450 3980 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
3451 3981 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
3452 3982 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
3453 3983 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
3454 3984 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
3455 3985 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3456 3986 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3457 3987 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
3458 3988 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
3459 3989 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
3460 3990 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
3461 3991 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
3462 3992 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
3463 3993 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
3464 3994 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
3465 3995 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
3466 3996 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
3467 3997 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3468 3998 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
3469 3999 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3470 4000 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3471 4001 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3472 4002 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3473 4003 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3521 4051 6.000840 TCACTACACCATGATGTTTGCTTTA 58.999 36.000 0.00 0.00 33.85 1.85
3522 4052 6.658816 TCACTACACCATGATGTTTGCTTTAT 59.341 34.615 0.00 0.00 33.85 1.40
3523 4053 6.968904 CACTACACCATGATGTTTGCTTTATC 59.031 38.462 0.00 0.00 33.85 1.75
3524 4054 5.981088 ACACCATGATGTTTGCTTTATCA 57.019 34.783 0.00 0.00 35.52 2.15
3525 4055 5.957798 ACACCATGATGTTTGCTTTATCAG 58.042 37.500 0.00 0.00 34.64 2.90
3526 4056 5.477984 ACACCATGATGTTTGCTTTATCAGT 59.522 36.000 0.00 0.00 34.64 3.41
3527 4057 6.032094 CACCATGATGTTTGCTTTATCAGTC 58.968 40.000 0.00 0.00 34.64 3.51
3981 4969 3.715315 TCTCCAGGAAATGAGCATCTGAT 59.285 43.478 0.00 0.00 34.92 2.90
4196 5203 3.958147 TGAACTGTAGTGTCAGACAGGAA 59.042 43.478 2.53 0.00 46.05 3.36
4233 5241 3.885297 GGTTATTGCATGGATGTACTGCT 59.115 43.478 5.73 0.00 36.84 4.24
4244 5252 4.019771 TGGATGTACTGCTGGTTATGTCAA 60.020 41.667 0.00 0.00 0.00 3.18
4252 5260 3.324846 TGCTGGTTATGTCAAGACAGAGT 59.675 43.478 8.99 0.00 45.48 3.24
4317 6538 4.435137 CCTGGGATATACCTGGGTATCAA 58.565 47.826 20.13 0.73 43.69 2.57
4441 6662 7.503902 GCCCTATCTAACAAGATTGAGGAAATT 59.496 37.037 0.00 0.00 29.62 1.82
4489 6710 8.811378 CAAGAAACAAAAGGAGATTTCTTTGAC 58.189 33.333 7.83 0.00 44.87 3.18
4490 6711 7.492524 AGAAACAAAAGGAGATTTCTTTGACC 58.507 34.615 5.34 0.00 38.01 4.02
4491 6712 5.438761 ACAAAAGGAGATTTCTTTGACCG 57.561 39.130 5.34 0.00 34.99 4.79
4492 6713 5.130350 ACAAAAGGAGATTTCTTTGACCGA 58.870 37.500 5.34 0.00 34.99 4.69
4493 6714 5.239525 ACAAAAGGAGATTTCTTTGACCGAG 59.760 40.000 5.34 0.00 34.99 4.63
4494 6715 2.979240 AGGAGATTTCTTTGACCGAGC 58.021 47.619 0.00 0.00 0.00 5.03
4495 6716 2.303022 AGGAGATTTCTTTGACCGAGCA 59.697 45.455 0.00 0.00 0.00 4.26
4496 6717 3.054802 AGGAGATTTCTTTGACCGAGCAT 60.055 43.478 0.00 0.00 0.00 3.79
4497 6718 3.311048 GGAGATTTCTTTGACCGAGCATC 59.689 47.826 0.00 0.00 0.00 3.91
4498 6719 4.187694 GAGATTTCTTTGACCGAGCATCT 58.812 43.478 0.00 0.00 0.00 2.90
4499 6720 4.583871 AGATTTCTTTGACCGAGCATCTT 58.416 39.130 0.00 0.00 0.00 2.40
4500 6721 5.006386 AGATTTCTTTGACCGAGCATCTTT 58.994 37.500 0.00 0.00 0.00 2.52
4501 6722 4.488126 TTTCTTTGACCGAGCATCTTTG 57.512 40.909 0.00 0.00 0.00 2.77
4502 6723 3.401033 TCTTTGACCGAGCATCTTTGA 57.599 42.857 0.00 0.00 0.00 2.69
4503 6724 3.067106 TCTTTGACCGAGCATCTTTGAC 58.933 45.455 0.00 0.00 0.00 3.18
4578 6830 6.441924 TCTTCCCTCTGTCTAGAATGACAATT 59.558 38.462 0.00 0.00 44.98 2.32
4584 6836 9.829507 CCTCTGTCTAGAATGACAATTTATTCT 57.170 33.333 0.00 11.79 44.98 2.40
4588 6840 9.383519 TGTCTAGAATGACAATTTATTCTGTCC 57.616 33.333 14.89 6.88 43.08 4.02
4589 6841 9.606631 GTCTAGAATGACAATTTATTCTGTCCT 57.393 33.333 14.89 0.11 42.08 3.85
4597 6849 9.396022 TGACAATTTATTCTGTCCTTTATCCTC 57.604 33.333 0.12 0.00 41.07 3.71
4598 6850 9.396022 GACAATTTATTCTGTCCTTTATCCTCA 57.604 33.333 0.00 0.00 36.72 3.86
4599 6851 9.178758 ACAATTTATTCTGTCCTTTATCCTCAC 57.821 33.333 0.00 0.00 0.00 3.51
4608 6968 5.119694 GTCCTTTATCCTCACTGATTGGTC 58.880 45.833 0.00 0.00 0.00 4.02
5061 7424 2.386661 AGTGGATAGTGCAAAGGTCG 57.613 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.608662 GTGTGTCGGACCGGTGGA 61.609 66.667 14.63 6.28 0.00 4.02
311 344 2.686106 GGGGCTCGGTTGGGAGTA 60.686 66.667 0.00 0.00 36.41 2.59
410 449 2.126882 CCACCCCTATCTCATGTTGGA 58.873 52.381 0.00 0.00 0.00 3.53
423 462 2.006991 GCCCAATCTACCCACCCCT 61.007 63.158 0.00 0.00 0.00 4.79
545 585 2.359169 GGCTCCGGTGATGGTGAGA 61.359 63.158 7.92 0.00 0.00 3.27
628 670 2.897846 CGGTTTGGTGTCACGGCA 60.898 61.111 0.00 0.00 0.00 5.69
1189 1306 5.053145 GTCATGGAGATTAGGCAAGTAGTG 58.947 45.833 0.00 0.00 0.00 2.74
1227 1346 2.814919 GAGACTGGAGAACGTTCTGAGA 59.185 50.000 34.23 16.33 37.73 3.27
1249 1379 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1253 1383 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1257 1387 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1272 1402 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1273 1403 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1274 1404 4.892345 TCAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1275 1405 4.871822 TCAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
1276 1406 5.604758 TTCAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.00 0.00 3.20
1277 1407 5.901853 AGATTCAGAGAGAGAGAGAGAGAGA 59.098 44.000 0.00 0.00 0.00 3.10
1278 1408 6.172136 AGATTCAGAGAGAGAGAGAGAGAG 57.828 45.833 0.00 0.00 0.00 3.20
1279 1409 5.070981 GGAGATTCAGAGAGAGAGAGAGAGA 59.929 48.000 0.00 0.00 0.00 3.10
1512 1720 1.646189 GATGTTCGTCCAGCTCCTTC 58.354 55.000 0.00 0.00 0.00 3.46
2023 2369 1.006832 CCGTTCTCAAGTTATGGGCG 58.993 55.000 0.00 0.00 0.00 6.13
2183 2529 5.574891 TTGTGACAAGTGTTTACAATGCT 57.425 34.783 0.00 0.00 33.57 3.79
2235 2581 3.238597 TCCTTGCTTGGCCTAATTTGTT 58.761 40.909 3.32 0.00 0.00 2.83
2314 2660 5.889853 ACATTGTGAATCATAACCTGCTGAT 59.110 36.000 0.00 0.00 33.59 2.90
2604 3035 6.773200 ACAGTATCCATTCGAGAACAGAGATA 59.227 38.462 0.00 0.00 0.00 1.98
2815 3258 7.865706 ATACAATCAACAGGGTAAGATGAAC 57.134 36.000 0.00 0.00 0.00 3.18
2892 3349 3.278574 CCATCCACACAAATACACGGAT 58.721 45.455 0.00 0.00 33.52 4.18
2952 3418 8.015185 ACAAGACTACAACCAACTTCTACTAA 57.985 34.615 0.00 0.00 0.00 2.24
2978 3444 3.998341 GCCGACATAACCAAACACTTCTA 59.002 43.478 0.00 0.00 0.00 2.10
2980 3446 2.095415 GGCCGACATAACCAAACACTTC 60.095 50.000 0.00 0.00 0.00 3.01
2995 3469 2.187163 GCCCAAGACTAGGCCGAC 59.813 66.667 0.00 0.00 43.76 4.79
3188 3662 0.461548 CGCCCAGCTTACATGAGAGA 59.538 55.000 0.00 0.00 0.00 3.10
3232 3706 4.382685 CGGAGGGAGTAGCAAAGTTCATTA 60.383 45.833 0.00 0.00 0.00 1.90
3235 3709 1.275291 CGGAGGGAGTAGCAAAGTTCA 59.725 52.381 0.00 0.00 0.00 3.18
3236 3710 1.275573 ACGGAGGGAGTAGCAAAGTTC 59.724 52.381 0.00 0.00 0.00 3.01
3238 3712 1.275573 GAACGGAGGGAGTAGCAAAGT 59.724 52.381 0.00 0.00 0.00 2.66
3239 3713 1.275291 TGAACGGAGGGAGTAGCAAAG 59.725 52.381 0.00 0.00 0.00 2.77
3242 3716 0.251653 AGTGAACGGAGGGAGTAGCA 60.252 55.000 0.00 0.00 0.00 3.49
3243 3717 0.896226 AAGTGAACGGAGGGAGTAGC 59.104 55.000 0.00 0.00 0.00 3.58
3260 3736 8.397906 TGAGTTGTCTGAAATGACTTACAAAAG 58.602 33.333 0.00 0.00 37.79 2.27
3261 3737 8.275015 TGAGTTGTCTGAAATGACTTACAAAA 57.725 30.769 0.00 0.00 37.79 2.44
3262 3738 7.857734 TGAGTTGTCTGAAATGACTTACAAA 57.142 32.000 0.00 0.00 37.79 2.83
3263 3739 7.857734 TTGAGTTGTCTGAAATGACTTACAA 57.142 32.000 0.00 0.00 37.79 2.41
3272 3748 4.590222 AGCCCATTTTGAGTTGTCTGAAAT 59.410 37.500 0.00 0.00 0.00 2.17
3276 3752 2.624838 ACAGCCCATTTTGAGTTGTCTG 59.375 45.455 0.00 0.00 0.00 3.51
3280 3756 4.190772 ACAAAACAGCCCATTTTGAGTTG 58.809 39.130 19.09 6.15 45.75 3.16
3281 3757 4.486125 ACAAAACAGCCCATTTTGAGTT 57.514 36.364 19.09 0.99 45.75 3.01
3282 3758 4.404073 TGTACAAAACAGCCCATTTTGAGT 59.596 37.500 19.09 5.72 45.75 3.41
3283 3759 4.942852 TGTACAAAACAGCCCATTTTGAG 58.057 39.130 19.09 1.00 45.75 3.02
3284 3760 5.543507 ATGTACAAAACAGCCCATTTTGA 57.456 34.783 19.09 3.50 45.75 2.69
3287 3763 5.070313 AGACAATGTACAAAACAGCCCATTT 59.930 36.000 0.00 0.00 42.70 2.32
3288 3764 4.588528 AGACAATGTACAAAACAGCCCATT 59.411 37.500 0.00 0.00 42.70 3.16
3292 3768 4.829064 TCAGACAATGTACAAAACAGCC 57.171 40.909 0.00 0.00 42.70 4.85
3293 3769 6.697019 ACATTTCAGACAATGTACAAAACAGC 59.303 34.615 0.00 0.00 44.08 4.40
3296 3772 8.856490 AAGACATTTCAGACAATGTACAAAAC 57.144 30.769 0.00 0.00 45.55 2.43
3297 3773 8.681806 TGAAGACATTTCAGACAATGTACAAAA 58.318 29.630 0.00 0.00 45.55 2.44
3298 3774 8.219546 TGAAGACATTTCAGACAATGTACAAA 57.780 30.769 0.00 0.00 45.55 2.83
3300 3776 7.041167 CCTTGAAGACATTTCAGACAATGTACA 60.041 37.037 0.00 0.00 45.55 2.90
3301 3777 7.041098 ACCTTGAAGACATTTCAGACAATGTAC 60.041 37.037 9.58 0.00 45.55 2.90
3302 3778 6.998074 ACCTTGAAGACATTTCAGACAATGTA 59.002 34.615 9.58 0.00 45.55 2.29
3304 3780 6.206243 AGACCTTGAAGACATTTCAGACAATG 59.794 38.462 0.00 0.00 39.67 2.82
3305 3781 6.302269 AGACCTTGAAGACATTTCAGACAAT 58.698 36.000 0.00 0.00 0.00 2.71
3306 3782 5.684704 AGACCTTGAAGACATTTCAGACAA 58.315 37.500 0.00 0.00 0.00 3.18
3307 3783 5.296151 AGACCTTGAAGACATTTCAGACA 57.704 39.130 0.00 0.00 0.00 3.41
3308 3784 7.913674 ATAAGACCTTGAAGACATTTCAGAC 57.086 36.000 0.00 0.00 0.00 3.51
3317 3847 9.052759 TGTTCACTTTTATAAGACCTTGAAGAC 57.947 33.333 0.00 0.00 35.30 3.01
3319 3849 9.273016 TCTGTTCACTTTTATAAGACCTTGAAG 57.727 33.333 0.00 0.00 35.30 3.02
3321 3851 7.878127 CCTCTGTTCACTTTTATAAGACCTTGA 59.122 37.037 0.00 0.00 35.30 3.02
3322 3852 7.119846 CCCTCTGTTCACTTTTATAAGACCTTG 59.880 40.741 0.00 0.00 35.30 3.61
3325 3855 6.708285 TCCCTCTGTTCACTTTTATAAGACC 58.292 40.000 0.00 0.00 35.30 3.85
3327 3857 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
3332 3862 8.964772 GTATAGTACTCCCTCTGTTCACTTTTA 58.035 37.037 0.00 0.00 0.00 1.52
3334 3864 7.183460 AGTATAGTACTCCCTCTGTTCACTTT 58.817 38.462 0.00 0.00 32.47 2.66
3335 3865 6.733509 AGTATAGTACTCCCTCTGTTCACTT 58.266 40.000 0.00 0.00 32.47 3.16
3336 3866 6.330178 AGTATAGTACTCCCTCTGTTCACT 57.670 41.667 0.00 0.00 32.47 3.41
3337 3867 7.052873 TGTAGTATAGTACTCCCTCTGTTCAC 58.947 42.308 16.79 0.00 40.14 3.18
3338 3868 7.204243 TGTAGTATAGTACTCCCTCTGTTCA 57.796 40.000 16.79 0.00 40.14 3.18
3343 3873 9.884814 ATCATTTTGTAGTATAGTACTCCCTCT 57.115 33.333 16.79 0.00 40.14 3.69
3353 3883 9.627395 CGAAGGGAGTATCATTTTGTAGTATAG 57.373 37.037 0.00 0.00 36.25 1.31
3371 3901 3.521947 AGTAATTCCGAACGAAGGGAG 57.478 47.619 0.00 0.00 32.78 4.30
3373 3903 3.332034 ACAAGTAATTCCGAACGAAGGG 58.668 45.455 0.00 0.00 32.78 3.95
3374 3904 3.060363 CGACAAGTAATTCCGAACGAAGG 59.940 47.826 0.00 0.00 32.78 3.46
3376 3906 2.409378 GCGACAAGTAATTCCGAACGAA 59.591 45.455 0.00 0.00 34.14 3.85
3377 3907 1.987770 GCGACAAGTAATTCCGAACGA 59.012 47.619 0.00 0.00 0.00 3.85
3378 3908 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3379 3909 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
3380 3910 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
3381 3911 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
3382 3912 4.600012 ATTTCTGCGACAAGTAATTCCG 57.400 40.909 0.00 0.00 0.00 4.30
3383 3913 6.903883 TCTATTTCTGCGACAAGTAATTCC 57.096 37.500 0.00 0.00 0.00 3.01
3384 3914 7.910304 ACATCTATTTCTGCGACAAGTAATTC 58.090 34.615 0.00 0.00 0.00 2.17
3385 3915 7.849804 ACATCTATTTCTGCGACAAGTAATT 57.150 32.000 0.00 0.00 0.00 1.40
3386 3916 9.197694 GATACATCTATTTCTGCGACAAGTAAT 57.802 33.333 0.00 0.00 0.00 1.89
3387 3917 8.414003 AGATACATCTATTTCTGCGACAAGTAA 58.586 33.333 0.00 0.00 34.85 2.24
3388 3918 7.941919 AGATACATCTATTTCTGCGACAAGTA 58.058 34.615 0.00 0.00 34.85 2.24
3389 3919 6.810911 AGATACATCTATTTCTGCGACAAGT 58.189 36.000 0.00 0.00 34.85 3.16
3390 3920 8.293157 TCTAGATACATCTATTTCTGCGACAAG 58.707 37.037 0.00 0.00 38.60 3.16
3391 3921 8.166422 TCTAGATACATCTATTTCTGCGACAA 57.834 34.615 0.00 0.00 38.60 3.18
3392 3922 7.745620 TCTAGATACATCTATTTCTGCGACA 57.254 36.000 0.00 0.00 38.60 4.35
3393 3923 8.240682 ACATCTAGATACATCTATTTCTGCGAC 58.759 37.037 4.54 0.00 38.60 5.19
3394 3924 8.341892 ACATCTAGATACATCTATTTCTGCGA 57.658 34.615 4.54 0.00 38.60 5.10
3421 3951 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
3422 3952 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
3423 3953 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
3424 3954 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
3425 3955 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
3426 3956 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
3427 3957 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
3428 3958 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
3429 3959 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
3430 3960 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
3431 3961 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
3432 3962 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
3433 3963 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
3434 3964 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
3435 3965 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
3436 3966 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
3437 3967 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
3438 3968 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
3439 3969 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
3440 3970 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
3441 3971 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
3442 3972 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
3443 3973 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
3444 3974 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
3445 3975 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
3446 3976 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3447 3977 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
3448 3978 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3449 3979 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3450 3980 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3451 3981 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3452 3982 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3453 3983 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3454 3984 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3455 3985 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3456 3986 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3457 3987 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
3458 3988 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
3459 3989 0.911769 TACTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
3460 3990 1.307097 CTACTACTCCCTCCGTTCGG 58.693 60.000 4.74 4.74 0.00 4.30
3461 3991 0.662085 GCTACTACTCCCTCCGTTCG 59.338 60.000 0.00 0.00 0.00 3.95
3462 3992 1.677052 CAGCTACTACTCCCTCCGTTC 59.323 57.143 0.00 0.00 0.00 3.95
3463 3993 1.685491 CCAGCTACTACTCCCTCCGTT 60.685 57.143 0.00 0.00 0.00 4.44
3464 3994 0.106619 CCAGCTACTACTCCCTCCGT 60.107 60.000 0.00 0.00 0.00 4.69
3465 3995 0.183014 TCCAGCTACTACTCCCTCCG 59.817 60.000 0.00 0.00 0.00 4.63
3466 3996 1.694844 GTCCAGCTACTACTCCCTCC 58.305 60.000 0.00 0.00 0.00 4.30
3467 3997 1.310904 CGTCCAGCTACTACTCCCTC 58.689 60.000 0.00 0.00 0.00 4.30
3468 3998 0.624785 ACGTCCAGCTACTACTCCCT 59.375 55.000 0.00 0.00 0.00 4.20
3469 3999 0.739561 CACGTCCAGCTACTACTCCC 59.260 60.000 0.00 0.00 0.00 4.30
3470 4000 1.461559 ACACGTCCAGCTACTACTCC 58.538 55.000 0.00 0.00 0.00 3.85
3471 4001 3.005554 TGTACACGTCCAGCTACTACTC 58.994 50.000 0.00 0.00 0.00 2.59
3472 4002 3.063510 TGTACACGTCCAGCTACTACT 57.936 47.619 0.00 0.00 0.00 2.57
3473 4003 4.574013 ACTATGTACACGTCCAGCTACTAC 59.426 45.833 0.00 0.00 0.00 2.73
3981 4969 1.999648 ATCTTGTGGCCAGCTTTTCA 58.000 45.000 5.11 0.00 0.00 2.69
4220 5228 4.164030 TGACATAACCAGCAGTACATCCAT 59.836 41.667 0.00 0.00 0.00 3.41
4233 5241 6.413783 TGTAACTCTGTCTTGACATAACCA 57.586 37.500 3.79 0.00 0.00 3.67
4244 5252 6.859112 ACTGACCATAATGTAACTCTGTCT 57.141 37.500 0.00 0.00 0.00 3.41
4252 5260 5.804639 ACTGAGCAACTGACCATAATGTAA 58.195 37.500 0.00 0.00 0.00 2.41
4489 6710 1.205655 TCTCTGGTCAAAGATGCTCGG 59.794 52.381 0.00 0.00 0.00 4.63
4490 6711 2.662006 TCTCTGGTCAAAGATGCTCG 57.338 50.000 0.00 0.00 0.00 5.03
4491 6712 5.275067 AGTATCTCTGGTCAAAGATGCTC 57.725 43.478 0.13 0.00 39.76 4.26
4492 6713 5.690464 AAGTATCTCTGGTCAAAGATGCT 57.310 39.130 0.13 0.13 43.88 3.79
4493 6714 7.849804 TTTAAGTATCTCTGGTCAAAGATGC 57.150 36.000 0.00 0.00 35.57 3.91
4578 6830 7.733773 TCAGTGAGGATAAAGGACAGAATAA 57.266 36.000 0.00 0.00 0.00 1.40
4584 6836 4.536090 ACCAATCAGTGAGGATAAAGGACA 59.464 41.667 5.46 0.00 0.00 4.02
4585 6837 5.104259 ACCAATCAGTGAGGATAAAGGAC 57.896 43.478 5.46 0.00 0.00 3.85
4586 6838 5.032846 AGACCAATCAGTGAGGATAAAGGA 58.967 41.667 5.46 0.00 0.00 3.36
4587 6839 5.104776 TGAGACCAATCAGTGAGGATAAAGG 60.105 44.000 5.46 0.00 0.00 3.11
4588 6840 5.982356 TGAGACCAATCAGTGAGGATAAAG 58.018 41.667 5.46 0.00 0.00 1.85
4589 6841 6.373005 TTGAGACCAATCAGTGAGGATAAA 57.627 37.500 5.46 0.00 0.00 1.40
4590 6842 6.373005 TTTGAGACCAATCAGTGAGGATAA 57.627 37.500 5.46 0.00 31.46 1.75
4591 6843 5.627735 GCTTTGAGACCAATCAGTGAGGATA 60.628 44.000 5.46 0.00 31.46 2.59
4593 6845 3.557898 GCTTTGAGACCAATCAGTGAGGA 60.558 47.826 5.46 0.00 31.46 3.71
4594 6846 2.746362 GCTTTGAGACCAATCAGTGAGG 59.254 50.000 0.00 0.00 31.46 3.86
4595 6847 3.405831 TGCTTTGAGACCAATCAGTGAG 58.594 45.455 0.00 0.00 31.46 3.51
4597 6849 4.778534 AATGCTTTGAGACCAATCAGTG 57.221 40.909 0.00 0.00 31.46 3.66
4598 6850 5.316167 TGTAATGCTTTGAGACCAATCAGT 58.684 37.500 0.00 0.00 31.46 3.41
4599 6851 5.885230 TGTAATGCTTTGAGACCAATCAG 57.115 39.130 0.00 0.00 31.46 2.90
4685 7046 2.359900 CATCCTCCCTTCTTTGTTCCG 58.640 52.381 0.00 0.00 0.00 4.30
4716 7077 5.297527 TGGCTTCACTAAAGTGCATCATATG 59.702 40.000 5.21 0.00 45.25 1.78


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

AutoCloner maintained by Alex Coulton.