Multiple sequence alignment - TraesCS3B01G541300

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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 TraesCS3B01G541300 chr3B 100.000 4302 0 0 1 4302 779580923 779576622 0.000000e+00 7945.0
1 TraesCS3B01G541300 chr3B 88.591 1788 137 34 1693 3448 725114749 725116501 0.000000e+00 2109.0
2 TraesCS3B01G541300 chr3B 84.075 584 67 12 2349 2913 725113691 725114267 1.360000e-149 540.0
3 TraesCS3B01G541300 chr3B 89.937 159 8 5 1437 1595 725114265 725114415 9.440000e-47 198.0
4 TraesCS3B01G541300 chr3B 74.848 330 53 24 275 594 524770712 524771021 5.840000e-24 122.0
5 TraesCS3B01G541300 chr3B 72.840 405 70 32 2663 3050 779281178 779281559 7.610000e-18 102.0
6 TraesCS3B01G541300 chr1B 92.032 866 54 10 3448 4302 508887492 508886631 0.000000e+00 1203.0
7 TraesCS3B01G541300 chr1B 92.005 863 51 8 3449 4300 508894004 508893149 0.000000e+00 1195.0
8 TraesCS3B01G541300 chr1B 90.187 856 72 6 3459 4302 116030022 116029167 0.000000e+00 1105.0
9 TraesCS3B01G541300 chr1B 89.552 871 77 6 3445 4302 361785232 361786101 0.000000e+00 1092.0
10 TraesCS3B01G541300 chr1B 81.004 558 44 22 988 1521 121889896 121890415 1.880000e-103 387.0
11 TraesCS3B01G541300 chr1B 76.780 646 95 40 245 861 573626355 573625736 1.160000e-80 311.0
12 TraesCS3B01G541300 chr1B 77.922 539 78 30 101 615 640224681 640225202 9.040000e-77 298.0
13 TraesCS3B01G541300 chr1B 80.833 120 17 6 60 176 40988627 40988743 5.930000e-14 89.8
14 TraesCS3B01G541300 chr6B 91.264 870 63 9 3445 4302 603117742 603118610 0.000000e+00 1173.0
15 TraesCS3B01G541300 chr6B 88.161 397 34 6 1038 1432 39012669 39013054 1.090000e-125 460.0
16 TraesCS3B01G541300 chr2B 89.942 865 72 10 3449 4302 408103114 408103974 0.000000e+00 1101.0
17 TraesCS3B01G541300 chr2B 85.658 509 36 17 1038 1521 222490093 222489597 6.420000e-138 501.0
18 TraesCS3B01G541300 chr2B 80.709 508 39 27 1038 1521 292867317 292867789 1.480000e-89 340.0
19 TraesCS3B01G541300 chr2B 77.572 593 95 27 97 664 738275165 738275744 1.490000e-84 324.0
20 TraesCS3B01G541300 chr4B 89.504 867 78 7 3445 4302 486561171 486562033 0.000000e+00 1085.0
21 TraesCS3B01G541300 chr4B 79.310 667 96 30 25 664 664330917 664330266 3.070000e-116 429.0
22 TraesCS3B01G541300 chr4B 75.052 481 77 27 190 645 101835160 101834698 2.640000e-42 183.0
23 TraesCS3B01G541300 chr4B 78.462 195 32 10 178 367 7841363 7841552 7.560000e-23 119.0
24 TraesCS3B01G541300 chr5B 89.041 876 74 10 3448 4302 387463628 387462754 0.000000e+00 1066.0
25 TraesCS3B01G541300 chr5B 75.889 759 96 48 106 852 157047249 157047932 1.500000e-79 307.0
26 TraesCS3B01G541300 chr7B 89.029 875 75 11 3449 4302 180788952 180789826 0.000000e+00 1064.0
27 TraesCS3B01G541300 chr3D 90.887 823 23 21 859 1660 581982319 581983110 0.000000e+00 1057.0
28 TraesCS3B01G541300 chr3D 88.520 784 56 14 4 759 581976332 581977109 0.000000e+00 918.0
29 TraesCS3B01G541300 chr3D 85.052 863 94 14 2335 3174 581984325 581985175 0.000000e+00 846.0
30 TraesCS3B01G541300 chr3D 81.684 475 51 15 1823 2281 581983724 581984178 3.160000e-96 363.0
31 TraesCS3B01G541300 chr3D 82.697 393 31 19 1224 1592 349056210 349056589 8.980000e-82 315.0
32 TraesCS3B01G541300 chr3D 97.761 134 3 0 1691 1824 581983313 581983446 9.300000e-57 231.0
33 TraesCS3B01G541300 chr3D 74.627 402 69 26 2663 3050 582216929 582216547 3.470000e-31 147.0
34 TraesCS3B01G541300 chr3D 75.986 279 40 20 332 593 454978258 454978526 7.560000e-23 119.0
35 TraesCS3B01G541300 chr5D 79.014 710 108 32 67 748 5225817 5225121 8.490000e-122 448.0
36 TraesCS3B01G541300 chr5D 76.042 864 132 54 25 853 13636728 13635905 3.140000e-101 379.0
37 TraesCS3B01G541300 chr5D 77.229 729 100 47 25 729 478284572 478283886 2.440000e-97 366.0
38 TraesCS3B01G541300 chr5D 84.068 295 38 9 25 313 522105565 522105274 4.240000e-70 276.0
39 TraesCS3B01G541300 chr5D 79.070 258 30 10 2214 2462 27446715 27446957 5.760000e-34 156.0
40 TraesCS3B01G541300 chr5D 77.660 282 46 13 85 361 286170479 286170210 5.760000e-34 156.0
41 TraesCS3B01G541300 chr5D 86.364 110 8 6 438 546 294287146 294287249 3.520000e-21 113.0
42 TraesCS3B01G541300 chr5D 78.804 184 24 11 238 417 466651508 466651680 4.550000e-20 110.0
43 TraesCS3B01G541300 chr5D 73.482 313 58 18 308 613 539723683 539723389 1.270000e-15 95.3
44 TraesCS3B01G541300 chr5A 77.949 712 102 38 25 711 533565459 533566140 1.120000e-105 394.0
45 TraesCS3B01G541300 chr5A 83.150 273 39 7 30 297 679114273 679114003 4.300000e-60 243.0
46 TraesCS3B01G541300 chr5A 77.177 333 44 20 195 506 123575984 123575663 9.570000e-37 165.0
47 TraesCS3B01G541300 chr2A 76.649 758 104 46 25 759 138534335 138535042 6.840000e-93 351.0
48 TraesCS3B01G541300 chr7D 84.123 359 29 16 1258 1592 34208642 34208996 5.370000e-84 322.0
49 TraesCS3B01G541300 chr7D 82.697 393 31 19 1224 1592 138842495 138842874 8.980000e-82 315.0
50 TraesCS3B01G541300 chr7D 81.566 396 36 19 1224 1595 107543703 107543321 4.210000e-75 292.0
51 TraesCS3B01G541300 chr7D 79.297 256 31 10 2214 2462 116089868 116090108 4.450000e-35 159.0
52 TraesCS3B01G541300 chr7D 77.519 258 34 10 2214 2462 39144093 39143851 2.700000e-27 134.0
53 TraesCS3B01G541300 chr7D 80.208 192 26 9 537 724 58888024 58887841 2.700000e-27 134.0
54 TraesCS3B01G541300 chr7D 77.778 198 28 11 393 581 461903061 461903251 1.640000e-19 108.0
55 TraesCS3B01G541300 chr2D 82.828 396 31 19 1224 1595 475939605 475939223 1.930000e-83 320.0
56 TraesCS3B01G541300 chr2D 81.955 399 29 19 1224 1595 77944606 77944224 9.040000e-77 298.0
57 TraesCS3B01G541300 chr2D 81.934 393 34 19 1224 1592 136901704 136902083 9.040000e-77 298.0
58 TraesCS3B01G541300 chr2D 73.724 666 111 46 85 717 4233335 4233969 7.290000e-48 202.0
59 TraesCS3B01G541300 chr2D 77.657 367 56 13 85 432 6953001 6953360 2.620000e-47 200.0
60 TraesCS3B01G541300 chr2D 76.856 229 33 14 238 458 562227947 562228163 1.260000e-20 111.0
61 TraesCS3B01G541300 chr1A 81.606 386 58 12 39 413 322787577 322787194 1.500000e-79 307.0
62 TraesCS3B01G541300 chr1A 75.636 275 44 15 451 724 128640569 128640821 9.780000e-22 115.0
63 TraesCS3B01G541300 chr1A 82.524 103 11 7 60 159 26946677 26946775 2.760000e-12 84.2
64 TraesCS3B01G541300 chr1A 71.631 423 74 33 204 614 443136616 443137004 1.660000e-09 75.0
65 TraesCS3B01G541300 chr1A 82.609 69 11 1 308 375 556165723 556165655 4.650000e-05 60.2
66 TraesCS3B01G541300 chr1A 94.444 36 2 0 324 359 358846638 358846673 6.010000e-04 56.5
67 TraesCS3B01G541300 chr1D 77.069 580 90 25 21 576 35669554 35668994 1.170000e-75 294.0
68 TraesCS3B01G541300 chr1D 80.660 212 37 4 395 604 375973193 375973402 1.240000e-35 161.0
69 TraesCS3B01G541300 chr1D 79.457 258 29 10 2214 2462 482238529 482238771 1.240000e-35 161.0
70 TraesCS3B01G541300 chr1D 74.781 456 60 36 85 506 233788536 233788102 2.070000e-33 154.0
71 TraesCS3B01G541300 chr1D 72.509 291 48 25 331 613 287615202 287615468 9.990000e-07 65.8
72 TraesCS3B01G541300 chr1D 100.000 28 0 0 331 358 291101871 291101898 8.000000e-03 52.8
73 TraesCS3B01G541300 chr6A 80.000 415 67 14 25 434 50934342 50933939 4.210000e-75 292.0
74 TraesCS3B01G541300 chr6D 81.544 298 34 19 376 663 301121728 301121442 4.330000e-55 226.0
75 TraesCS3B01G541300 chr6D 80.546 293 39 12 25 312 386407459 386407180 4.360000e-50 209.0
76 TraesCS3B01G541300 chr6D 73.819 508 76 47 25 506 103008460 103007984 9.640000e-32 148.0
77 TraesCS3B01G541300 chr6D 79.104 134 23 5 238 368 461457438 461457569 2.130000e-13 87.9
78 TraesCS3B01G541300 chr6D 82.653 98 8 6 281 374 393412178 393412270 1.280000e-10 78.7
79 TraesCS3B01G541300 chr6D 74.138 232 34 20 281 506 114846486 114846697 5.970000e-09 73.1
80 TraesCS3B01G541300 chr6D 90.000 50 3 2 326 375 387720285 387720238 3.590000e-06 63.9
81 TraesCS3B01G541300 chr6D 77.228 101 16 7 267 361 44932555 44932456 8.000000e-03 52.8
82 TraesCS3B01G541300 chr4D 79.524 210 30 13 384 588 53791907 53791706 2.090000e-28 137.0
83 TraesCS3B01G541300 chr4D 79.641 167 28 5 137 300 411555495 411555658 9.780000e-22 115.0
84 TraesCS3B01G541300 chr4D 74.832 298 47 20 85 375 434533357 434533633 4.550000e-20 110.0
85 TraesCS3B01G541300 chr4D 73.107 383 62 29 192 548 396955366 396954999 9.850000e-17 99.0


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 TraesCS3B01G541300 chr3B 779576622 779580923 4301 True 7945.00 7945 100.000000 1 4302 1 chr3B.!!$R1 4301
1 TraesCS3B01G541300 chr3B 725113691 725116501 2810 False 949.00 2109 87.534333 1437 3448 3 chr3B.!!$F3 2011
2 TraesCS3B01G541300 chr1B 508886631 508887492 861 True 1203.00 1203 92.032000 3448 4302 1 chr1B.!!$R2 854
3 TraesCS3B01G541300 chr1B 508893149 508894004 855 True 1195.00 1195 92.005000 3449 4300 1 chr1B.!!$R3 851
4 TraesCS3B01G541300 chr1B 116029167 116030022 855 True 1105.00 1105 90.187000 3459 4302 1 chr1B.!!$R1 843
5 TraesCS3B01G541300 chr1B 361785232 361786101 869 False 1092.00 1092 89.552000 3445 4302 1 chr1B.!!$F3 857
6 TraesCS3B01G541300 chr1B 121889896 121890415 519 False 387.00 387 81.004000 988 1521 1 chr1B.!!$F2 533
7 TraesCS3B01G541300 chr1B 573625736 573626355 619 True 311.00 311 76.780000 245 861 1 chr1B.!!$R4 616
8 TraesCS3B01G541300 chr1B 640224681 640225202 521 False 298.00 298 77.922000 101 615 1 chr1B.!!$F4 514
9 TraesCS3B01G541300 chr6B 603117742 603118610 868 False 1173.00 1173 91.264000 3445 4302 1 chr6B.!!$F2 857
10 TraesCS3B01G541300 chr2B 408103114 408103974 860 False 1101.00 1101 89.942000 3449 4302 1 chr2B.!!$F2 853
11 TraesCS3B01G541300 chr2B 738275165 738275744 579 False 324.00 324 77.572000 97 664 1 chr2B.!!$F3 567
12 TraesCS3B01G541300 chr4B 486561171 486562033 862 False 1085.00 1085 89.504000 3445 4302 1 chr4B.!!$F2 857
13 TraesCS3B01G541300 chr4B 664330266 664330917 651 True 429.00 429 79.310000 25 664 1 chr4B.!!$R2 639
14 TraesCS3B01G541300 chr5B 387462754 387463628 874 True 1066.00 1066 89.041000 3448 4302 1 chr5B.!!$R1 854
15 TraesCS3B01G541300 chr5B 157047249 157047932 683 False 307.00 307 75.889000 106 852 1 chr5B.!!$F1 746
16 TraesCS3B01G541300 chr7B 180788952 180789826 874 False 1064.00 1064 89.029000 3449 4302 1 chr7B.!!$F1 853
17 TraesCS3B01G541300 chr3D 581976332 581977109 777 False 918.00 918 88.520000 4 759 1 chr3D.!!$F3 755
18 TraesCS3B01G541300 chr3D 581982319 581985175 2856 False 624.25 1057 88.846000 859 3174 4 chr3D.!!$F4 2315
19 TraesCS3B01G541300 chr5D 5225121 5225817 696 True 448.00 448 79.014000 67 748 1 chr5D.!!$R1 681
20 TraesCS3B01G541300 chr5D 13635905 13636728 823 True 379.00 379 76.042000 25 853 1 chr5D.!!$R2 828
21 TraesCS3B01G541300 chr5D 478283886 478284572 686 True 366.00 366 77.229000 25 729 1 chr5D.!!$R4 704
22 TraesCS3B01G541300 chr5A 533565459 533566140 681 False 394.00 394 77.949000 25 711 1 chr5A.!!$F1 686
23 TraesCS3B01G541300 chr2A 138534335 138535042 707 False 351.00 351 76.649000 25 759 1 chr2A.!!$F1 734
24 TraesCS3B01G541300 chr2D 4233335 4233969 634 False 202.00 202 73.724000 85 717 1 chr2D.!!$F1 632
25 TraesCS3B01G541300 chr1D 35668994 35669554 560 True 294.00 294 77.069000 21 576 1 chr1D.!!$R1 555

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
939 1434 1.527433 GCTTTTGTGTGGGAGGGAGC 61.527 60.0 0.0 0.0 0.00 4.70 F
1666 2258 0.108233 CAACTCTGCCTCTGAGCCTC 60.108 60.0 0.0 0.0 33.65 4.70 F
1667 2259 0.252193 AACTCTGCCTCTGAGCCTCT 60.252 55.0 0.0 0.0 33.65 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 3105 0.107800 CCTCCTCCTGTGCAGACATG 60.108 60.000 0.02 0.0 0.00 3.21 R
2681 3883 0.381801 AACGAAACAGCAGCTTGTGG 59.618 50.000 0.00 0.0 0.00 4.17 R
3639 4863 1.077212 CCCTGAGGCAATCCACCAG 60.077 63.158 0.00 0.0 36.03 4.00 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
466 892 8.638565 GTGTGTATAGAAAAATGTTGAACATGC 58.361 33.333 12.09 2.49 37.97 4.06
743 1238 8.828029 TGAAAAATAAAACCGAAAAACAATGC 57.172 26.923 0.00 0.00 0.00 3.56
744 1239 8.450964 TGAAAAATAAAACCGAAAAACAATGCA 58.549 25.926 0.00 0.00 0.00 3.96
745 1240 9.278734 GAAAAATAAAACCGAAAAACAATGCAA 57.721 25.926 0.00 0.00 0.00 4.08
746 1241 9.626045 AAAAATAAAACCGAAAAACAATGCAAA 57.374 22.222 0.00 0.00 0.00 3.68
747 1242 9.626045 AAAATAAAACCGAAAAACAATGCAAAA 57.374 22.222 0.00 0.00 0.00 2.44
748 1243 9.626045 AAATAAAACCGAAAAACAATGCAAAAA 57.374 22.222 0.00 0.00 0.00 1.94
749 1244 6.919687 AAAACCGAAAAACAATGCAAAAAC 57.080 29.167 0.00 0.00 0.00 2.43
750 1245 5.613358 AACCGAAAAACAATGCAAAAACA 57.387 30.435 0.00 0.00 0.00 2.83
751 1246 5.613358 ACCGAAAAACAATGCAAAAACAA 57.387 30.435 0.00 0.00 0.00 2.83
752 1247 6.002062 ACCGAAAAACAATGCAAAAACAAA 57.998 29.167 0.00 0.00 0.00 2.83
753 1248 6.616017 ACCGAAAAACAATGCAAAAACAAAT 58.384 28.000 0.00 0.00 0.00 2.32
754 1249 6.525976 ACCGAAAAACAATGCAAAAACAAATG 59.474 30.769 0.00 0.00 0.00 2.32
755 1250 6.744537 CCGAAAAACAATGCAAAAACAAATGA 59.255 30.769 0.00 0.00 0.00 2.57
756 1251 7.272084 CCGAAAAACAATGCAAAAACAAATGAA 59.728 29.630 0.00 0.00 0.00 2.57
757 1252 8.633408 CGAAAAACAATGCAAAAACAAATGAAA 58.367 25.926 0.00 0.00 0.00 2.69
767 1262 9.823647 TGCAAAAACAAATGAAAATAACTAGGA 57.176 25.926 0.00 0.00 0.00 2.94
781 1276 9.811995 AAAATAACTAGGAAAACAGTGAAAACC 57.188 29.630 0.00 0.00 0.00 3.27
782 1277 8.528044 AATAACTAGGAAAACAGTGAAAACCA 57.472 30.769 0.00 0.00 0.00 3.67
783 1278 6.844097 AACTAGGAAAACAGTGAAAACCAA 57.156 33.333 0.00 0.00 0.00 3.67
784 1279 7.418337 AACTAGGAAAACAGTGAAAACCAAT 57.582 32.000 0.00 0.00 0.00 3.16
785 1280 8.528044 AACTAGGAAAACAGTGAAAACCAATA 57.472 30.769 0.00 0.00 0.00 1.90
786 1281 8.528044 ACTAGGAAAACAGTGAAAACCAATAA 57.472 30.769 0.00 0.00 0.00 1.40
787 1282 8.973182 ACTAGGAAAACAGTGAAAACCAATAAA 58.027 29.630 0.00 0.00 0.00 1.40
788 1283 9.463443 CTAGGAAAACAGTGAAAACCAATAAAG 57.537 33.333 0.00 0.00 0.00 1.85
789 1284 8.073467 AGGAAAACAGTGAAAACCAATAAAGA 57.927 30.769 0.00 0.00 0.00 2.52
790 1285 8.197439 AGGAAAACAGTGAAAACCAATAAAGAG 58.803 33.333 0.00 0.00 0.00 2.85
791 1286 8.194769 GGAAAACAGTGAAAACCAATAAAGAGA 58.805 33.333 0.00 0.00 0.00 3.10
792 1287 9.581099 GAAAACAGTGAAAACCAATAAAGAGAA 57.419 29.630 0.00 0.00 0.00 2.87
793 1288 9.936759 AAAACAGTGAAAACCAATAAAGAGAAA 57.063 25.926 0.00 0.00 0.00 2.52
794 1289 9.936759 AAACAGTGAAAACCAATAAAGAGAAAA 57.063 25.926 0.00 0.00 0.00 2.29
795 1290 9.586435 AACAGTGAAAACCAATAAAGAGAAAAG 57.414 29.630 0.00 0.00 0.00 2.27
796 1291 8.197439 ACAGTGAAAACCAATAAAGAGAAAAGG 58.803 33.333 0.00 0.00 0.00 3.11
797 1292 8.413229 CAGTGAAAACCAATAAAGAGAAAAGGA 58.587 33.333 0.00 0.00 0.00 3.36
798 1293 8.977412 AGTGAAAACCAATAAAGAGAAAAGGAA 58.023 29.630 0.00 0.00 0.00 3.36
799 1294 9.764363 GTGAAAACCAATAAAGAGAAAAGGAAT 57.236 29.630 0.00 0.00 0.00 3.01
828 1323 9.793259 ACTATAGAAACATTGAACCAAGAAAGA 57.207 29.630 6.78 0.00 0.00 2.52
831 1326 9.750125 ATAGAAACATTGAACCAAGAAAGAAAC 57.250 29.630 0.00 0.00 0.00 2.78
832 1327 7.610865 AGAAACATTGAACCAAGAAAGAAACA 58.389 30.769 0.00 0.00 0.00 2.83
833 1328 8.093927 AGAAACATTGAACCAAGAAAGAAACAA 58.906 29.630 0.00 0.00 0.00 2.83
834 1329 8.614469 AAACATTGAACCAAGAAAGAAACAAA 57.386 26.923 0.00 0.00 0.00 2.83
835 1330 8.614469 AACATTGAACCAAGAAAGAAACAAAA 57.386 26.923 0.00 0.00 0.00 2.44
836 1331 8.614469 ACATTGAACCAAGAAAGAAACAAAAA 57.386 26.923 0.00 0.00 0.00 1.94
837 1332 8.503196 ACATTGAACCAAGAAAGAAACAAAAAC 58.497 29.630 0.00 0.00 0.00 2.43
838 1333 8.502387 CATTGAACCAAGAAAGAAACAAAAACA 58.498 29.630 0.00 0.00 0.00 2.83
839 1334 8.438676 TTGAACCAAGAAAGAAACAAAAACAA 57.561 26.923 0.00 0.00 0.00 2.83
840 1335 8.438676 TGAACCAAGAAAGAAACAAAAACAAA 57.561 26.923 0.00 0.00 0.00 2.83
841 1336 8.893727 TGAACCAAGAAAGAAACAAAAACAAAA 58.106 25.926 0.00 0.00 0.00 2.44
842 1337 9.381027 GAACCAAGAAAGAAACAAAAACAAAAG 57.619 29.630 0.00 0.00 0.00 2.27
843 1338 7.870826 ACCAAGAAAGAAACAAAAACAAAAGG 58.129 30.769 0.00 0.00 0.00 3.11
844 1339 7.717436 ACCAAGAAAGAAACAAAAACAAAAGGA 59.283 29.630 0.00 0.00 0.00 3.36
845 1340 8.563732 CCAAGAAAGAAACAAAAACAAAAGGAA 58.436 29.630 0.00 0.00 0.00 3.36
846 1341 9.943163 CAAGAAAGAAACAAAAACAAAAGGAAA 57.057 25.926 0.00 0.00 0.00 3.13
854 1349 9.522804 AAACAAAAACAAAAGGAAAAAGAAACC 57.477 25.926 0.00 0.00 0.00 3.27
855 1350 8.226819 ACAAAAACAAAAGGAAAAAGAAACCA 57.773 26.923 0.00 0.00 0.00 3.67
856 1351 8.132362 ACAAAAACAAAAGGAAAAAGAAACCAC 58.868 29.630 0.00 0.00 0.00 4.16
857 1352 8.349245 CAAAAACAAAAGGAAAAAGAAACCACT 58.651 29.630 0.00 0.00 0.00 4.00
858 1353 7.433708 AAACAAAAGGAAAAAGAAACCACTG 57.566 32.000 0.00 0.00 0.00 3.66
859 1354 6.353404 ACAAAAGGAAAAAGAAACCACTGA 57.647 33.333 0.00 0.00 0.00 3.41
860 1355 6.764379 ACAAAAGGAAAAAGAAACCACTGAA 58.236 32.000 0.00 0.00 0.00 3.02
861 1356 7.220740 ACAAAAGGAAAAAGAAACCACTGAAA 58.779 30.769 0.00 0.00 0.00 2.69
862 1357 7.717436 ACAAAAGGAAAAAGAAACCACTGAAAA 59.283 29.630 0.00 0.00 0.00 2.29
863 1358 8.563732 CAAAAGGAAAAAGAAACCACTGAAAAA 58.436 29.630 0.00 0.00 0.00 1.94
939 1434 1.527433 GCTTTTGTGTGGGAGGGAGC 61.527 60.000 0.00 0.00 0.00 4.70
943 1438 3.775654 GTGTGGGAGGGAGCGAGG 61.776 72.222 0.00 0.00 0.00 4.63
947 1442 4.475135 GGGAGGGAGCGAGGCAAC 62.475 72.222 0.00 0.00 0.00 4.17
950 1445 3.959991 GAGGGAGCGAGGCAACCAC 62.960 68.421 0.00 0.00 37.17 4.16
1003 1513 1.152139 GGAGGGGAGAGGAGGATGG 60.152 68.421 0.00 0.00 0.00 3.51
1004 1514 1.841103 GAGGGGAGAGGAGGATGGC 60.841 68.421 0.00 0.00 0.00 4.40
1005 1515 2.040464 GGGGAGAGGAGGATGGCA 60.040 66.667 0.00 0.00 0.00 4.92
1008 1518 2.420890 GAGAGGAGGATGGCAGCG 59.579 66.667 0.00 0.00 0.00 5.18
1275 1785 0.740737 GTCCGGATTGGCTTGGATTG 59.259 55.000 7.81 0.00 37.80 2.67
1276 1786 0.395586 TCCGGATTGGCTTGGATTGG 60.396 55.000 0.00 0.00 37.80 3.16
1277 1787 0.395586 CCGGATTGGCTTGGATTGGA 60.396 55.000 0.00 0.00 0.00 3.53
1278 1788 0.740737 CGGATTGGCTTGGATTGGAC 59.259 55.000 0.00 0.00 0.00 4.02
1279 1789 1.683011 CGGATTGGCTTGGATTGGACT 60.683 52.381 0.00 0.00 0.00 3.85
1301 1811 3.908712 TTGGGTGGCTGGATCCCCT 62.909 63.158 9.90 0.00 40.41 4.79
1321 1831 0.599558 TCTGTTTGCTGGCTGATTGC 59.400 50.000 0.00 0.00 41.94 3.56
1322 1832 0.731514 CTGTTTGCTGGCTGATTGCG 60.732 55.000 0.00 0.00 44.05 4.85
1331 1841 1.469703 TGGCTGATTGCGATTCTGTTG 59.530 47.619 0.00 0.00 44.05 3.33
1358 1870 2.811317 GTCGTGCAGCTTCCGGAG 60.811 66.667 3.34 0.00 0.00 4.63
1376 1888 0.394352 AGGACATCCGGTGGCATTTC 60.394 55.000 11.31 0.00 37.70 2.17
1413 1925 2.484264 AGCAACAAGGTGAAATCGCTAC 59.516 45.455 0.00 0.00 0.00 3.58
1420 1932 4.915158 AGGTGAAATCGCTACTAGGTAC 57.085 45.455 0.00 0.00 0.00 3.34
1424 1936 3.313526 TGAAATCGCTACTAGGTACGGTC 59.686 47.826 0.00 0.00 0.00 4.79
1432 1944 5.280164 GCTACTAGGTACGGTCAAGATTTC 58.720 45.833 0.00 0.00 0.00 2.17
1435 1947 2.262637 AGGTACGGTCAAGATTTCCCA 58.737 47.619 0.00 0.00 0.00 4.37
1522 2057 3.282021 GCCATAACACCACATCTCACAT 58.718 45.455 0.00 0.00 0.00 3.21
1523 2058 3.313526 GCCATAACACCACATCTCACATC 59.686 47.826 0.00 0.00 0.00 3.06
1524 2059 4.774124 CCATAACACCACATCTCACATCT 58.226 43.478 0.00 0.00 0.00 2.90
1525 2060 4.813161 CCATAACACCACATCTCACATCTC 59.187 45.833 0.00 0.00 0.00 2.75
1526 2061 5.422145 CATAACACCACATCTCACATCTCA 58.578 41.667 0.00 0.00 0.00 3.27
1527 2062 3.325293 ACACCACATCTCACATCTCAC 57.675 47.619 0.00 0.00 0.00 3.51
1528 2063 2.634453 ACACCACATCTCACATCTCACA 59.366 45.455 0.00 0.00 0.00 3.58
1581 2119 5.254115 AGGGGAACAGCAAAGTTAGATAAC 58.746 41.667 0.00 0.00 36.46 1.89
1660 2252 2.434428 AGCATTTCAACTCTGCCTCTG 58.566 47.619 0.00 0.00 36.56 3.35
1661 2253 2.039480 AGCATTTCAACTCTGCCTCTGA 59.961 45.455 0.00 0.00 36.56 3.27
1662 2254 2.419324 GCATTTCAACTCTGCCTCTGAG 59.581 50.000 0.00 0.00 35.91 3.35
1663 2255 2.175878 TTTCAACTCTGCCTCTGAGC 57.824 50.000 0.00 0.00 33.65 4.26
1664 2256 0.322975 TTCAACTCTGCCTCTGAGCC 59.677 55.000 0.00 0.00 33.65 4.70
1665 2257 0.543883 TCAACTCTGCCTCTGAGCCT 60.544 55.000 0.00 0.00 33.65 4.58
1666 2258 0.108233 CAACTCTGCCTCTGAGCCTC 60.108 60.000 0.00 0.00 33.65 4.70
1667 2259 0.252193 AACTCTGCCTCTGAGCCTCT 60.252 55.000 0.00 0.00 33.65 3.69
1668 2260 0.684153 ACTCTGCCTCTGAGCCTCTC 60.684 60.000 0.00 0.00 33.65 3.20
1669 2261 1.727511 CTCTGCCTCTGAGCCTCTCG 61.728 65.000 0.00 0.00 32.35 4.04
1670 2262 2.036414 TGCCTCTGAGCCTCTCGT 59.964 61.111 0.00 0.00 32.35 4.18
1671 2263 0.749818 CTGCCTCTGAGCCTCTCGTA 60.750 60.000 0.00 0.00 32.35 3.43
1672 2264 0.323451 TGCCTCTGAGCCTCTCGTAA 60.323 55.000 0.00 0.00 32.35 3.18
1673 2265 0.818296 GCCTCTGAGCCTCTCGTAAA 59.182 55.000 0.00 0.00 32.35 2.01
1674 2266 1.470112 GCCTCTGAGCCTCTCGTAAAC 60.470 57.143 0.00 0.00 32.35 2.01
1680 2272 2.095059 TGAGCCTCTCGTAAACCGTAAC 60.095 50.000 0.00 0.00 37.94 2.50
1792 2582 2.443632 TGAAACTCAACCCCCATACACA 59.556 45.455 0.00 0.00 0.00 3.72
1854 2923 8.149647 TCTAATTTTCTAACCAACTAACCGTCA 58.850 33.333 0.00 0.00 0.00 4.35
1858 2927 1.589803 AACCAACTAACCGTCACAGC 58.410 50.000 0.00 0.00 0.00 4.40
1872 2941 2.028876 TCACAGCCGCTATACTGCTTA 58.971 47.619 0.00 0.00 36.60 3.09
1878 2947 3.385111 AGCCGCTATACTGCTTAGACTTT 59.615 43.478 0.00 0.00 34.87 2.66
1982 3051 4.036027 AGCAGCAACAGACATATGTTATGC 59.964 41.667 19.74 19.74 45.84 3.14
1987 3056 7.641411 CAGCAACAGACATATGTTATGCTTAAC 59.359 37.037 24.04 14.02 41.41 2.01
2002 3071 5.050644 TGCTTAACAGTTGAATGCATCTG 57.949 39.130 9.86 9.86 43.98 2.90
2007 3076 2.485426 ACAGTTGAATGCATCTGAACCG 59.515 45.455 17.24 8.13 42.02 4.44
2008 3077 1.470098 AGTTGAATGCATCTGAACCGC 59.530 47.619 0.00 0.00 0.00 5.68
2009 3078 1.199789 GTTGAATGCATCTGAACCGCA 59.800 47.619 0.00 2.84 40.50 5.69
2011 3080 2.916640 TGAATGCATCTGAACCGCATA 58.083 42.857 0.00 0.00 45.33 3.14
2013 3082 2.916702 ATGCATCTGAACCGCATAGA 57.083 45.000 9.87 0.00 44.28 1.98
2014 3083 2.229675 TGCATCTGAACCGCATAGAG 57.770 50.000 0.00 0.00 0.00 2.43
2015 3084 0.864455 GCATCTGAACCGCATAGAGC 59.136 55.000 0.00 0.00 40.87 4.09
2017 3086 2.288457 GCATCTGAACCGCATAGAGCTA 60.288 50.000 0.00 0.00 42.61 3.32
2018 3087 3.573598 CATCTGAACCGCATAGAGCTAG 58.426 50.000 0.00 0.00 42.61 3.42
2019 3088 2.656002 TCTGAACCGCATAGAGCTAGT 58.344 47.619 0.00 0.00 42.61 2.57
2020 3089 3.816994 TCTGAACCGCATAGAGCTAGTA 58.183 45.455 0.00 0.00 42.61 1.82
2021 3090 4.399219 TCTGAACCGCATAGAGCTAGTAT 58.601 43.478 0.00 0.00 42.61 2.12
2022 3091 4.216472 TCTGAACCGCATAGAGCTAGTATG 59.784 45.833 10.12 10.12 42.61 2.39
2023 3092 4.142038 TGAACCGCATAGAGCTAGTATGA 58.858 43.478 16.41 0.00 42.61 2.15
2024 3093 4.583073 TGAACCGCATAGAGCTAGTATGAA 59.417 41.667 16.41 0.00 42.61 2.57
2025 3094 5.243954 TGAACCGCATAGAGCTAGTATGAAT 59.756 40.000 16.41 1.96 42.61 2.57
2026 3095 5.730296 ACCGCATAGAGCTAGTATGAATT 57.270 39.130 16.41 0.67 42.61 2.17
2027 3096 6.102897 ACCGCATAGAGCTAGTATGAATTT 57.897 37.500 16.41 0.00 42.61 1.82
2028 3097 7.228314 ACCGCATAGAGCTAGTATGAATTTA 57.772 36.000 16.41 0.00 42.61 1.40
2029 3098 7.841956 ACCGCATAGAGCTAGTATGAATTTAT 58.158 34.615 16.41 0.00 42.61 1.40
2030 3099 8.967918 ACCGCATAGAGCTAGTATGAATTTATA 58.032 33.333 16.41 0.00 42.61 0.98
2031 3100 9.973450 CCGCATAGAGCTAGTATGAATTTATAT 57.027 33.333 16.41 0.00 42.61 0.86
2048 3117 6.667007 TTTATATGTGACATGTCTGCACAG 57.333 37.500 25.55 0.00 40.33 3.66
2049 3118 1.817357 ATGTGACATGTCTGCACAGG 58.183 50.000 25.55 0.00 40.33 4.00
2054 3123 0.612229 ACATGTCTGCACAGGAGGAG 59.388 55.000 0.00 0.00 36.34 3.69
2057 3126 0.902048 TGTCTGCACAGGAGGAGGAG 60.902 60.000 0.00 0.00 0.00 3.69
2075 3144 7.013220 AGGAGGAGAATACTGATTACAGCATA 58.987 38.462 0.00 0.00 46.95 3.14
2098 3179 3.845781 TGTTCATCCTTATCTGCTCCC 57.154 47.619 0.00 0.00 0.00 4.30
2099 3180 2.439507 TGTTCATCCTTATCTGCTCCCC 59.560 50.000 0.00 0.00 0.00 4.81
2100 3181 2.708325 GTTCATCCTTATCTGCTCCCCT 59.292 50.000 0.00 0.00 0.00 4.79
2104 3185 3.066208 TCCTTATCTGCTCCCCTTGAT 57.934 47.619 0.00 0.00 0.00 2.57
2105 3186 3.397527 TCCTTATCTGCTCCCCTTGATT 58.602 45.455 0.00 0.00 0.00 2.57
2106 3187 4.566837 TCCTTATCTGCTCCCCTTGATTA 58.433 43.478 0.00 0.00 0.00 1.75
2117 3198 9.167311 CTGCTCCCCTTGATTATATTACATAAC 57.833 37.037 0.00 0.00 0.00 1.89
2120 3201 7.107542 TCCCCTTGATTATATTACATAACGCC 58.892 38.462 0.00 0.00 0.00 5.68
2122 3203 6.592607 CCCTTGATTATATTACATAACGCCGT 59.407 38.462 0.00 0.00 0.00 5.68
2139 3220 1.202222 CCGTCATGCTTTCAGATTGCC 60.202 52.381 0.00 0.00 0.00 4.52
2172 3253 1.671054 TGCTGTCGTTAGCTTGGGC 60.671 57.895 13.19 0.00 44.01 5.36
2236 3320 6.096141 TGGAGAAGAATGTGAGTACAGAGATC 59.904 42.308 0.00 0.00 40.79 2.75
2242 3326 9.646427 AAGAATGTGAGTACAGAGATCTTAAAC 57.354 33.333 0.00 0.00 40.79 2.01
2286 3371 7.329746 TGGTTTTAGGATATATCTTCCCAGG 57.670 40.000 12.42 0.00 33.45 4.45
2287 3372 6.855061 TGGTTTTAGGATATATCTTCCCAGGT 59.145 38.462 12.42 0.00 33.45 4.00
2288 3373 7.168905 GGTTTTAGGATATATCTTCCCAGGTG 58.831 42.308 12.42 0.00 33.45 4.00
2304 3392 4.451900 CCAGGTGTTTCAAGTAGTCAGTT 58.548 43.478 0.00 0.00 0.00 3.16
2309 3397 6.537660 AGGTGTTTCAAGTAGTCAGTTGTTAC 59.462 38.462 0.00 0.00 36.60 2.50
2310 3398 6.537660 GGTGTTTCAAGTAGTCAGTTGTTACT 59.462 38.462 0.00 0.00 36.60 2.24
2321 3409 6.725246 AGTCAGTTGTTACTTGCATTTACAC 58.275 36.000 0.00 0.00 30.26 2.90
2378 3558 7.041644 CCATTATTTCAAAAGCCATGCCATAAG 60.042 37.037 0.00 0.00 0.00 1.73
2424 3604 1.859427 AAGTCGCTGCCATGCTGTTG 61.859 55.000 0.00 0.00 0.00 3.33
2434 3614 4.459330 TGCCATGCTGTTGTATATTGCTA 58.541 39.130 0.00 0.00 0.00 3.49
2436 3616 5.181811 TGCCATGCTGTTGTATATTGCTATC 59.818 40.000 0.00 0.00 0.00 2.08
2440 3620 7.361542 CCATGCTGTTGTATATTGCTATCCTTC 60.362 40.741 0.00 0.00 0.00 3.46
2441 3621 5.997746 TGCTGTTGTATATTGCTATCCTTCC 59.002 40.000 0.00 0.00 0.00 3.46
2442 3622 5.997746 GCTGTTGTATATTGCTATCCTTCCA 59.002 40.000 0.00 0.00 0.00 3.53
2443 3623 6.073003 GCTGTTGTATATTGCTATCCTTCCAC 60.073 42.308 0.00 0.00 0.00 4.02
2482 3681 8.394971 TGATGAATTCACTGATGTAACACTTT 57.605 30.769 11.07 0.00 0.00 2.66
2483 3682 8.291740 TGATGAATTCACTGATGTAACACTTTG 58.708 33.333 11.07 0.00 0.00 2.77
2487 3686 8.458573 AATTCACTGATGTAACACTTTGGTTA 57.541 30.769 0.00 0.00 32.29 2.85
2581 3780 6.404734 GCCCAAACTTAATATTGTCAGGACTG 60.405 42.308 0.00 0.00 0.00 3.51
2608 3807 7.210174 TGACAATAGGGATGAAAGATTACTCG 58.790 38.462 0.00 0.00 0.00 4.18
2681 3883 8.559536 TGAATAATCTTTCTGTGTTGACACTTC 58.440 33.333 14.66 7.08 46.55 3.01
2697 3899 1.678101 ACTTCCACAAGCTGCTGTTTC 59.322 47.619 1.35 0.00 32.09 2.78
2942 4152 6.239120 CCATTAATCCTCGGAGCAAATTTGAT 60.239 38.462 22.31 16.26 0.00 2.57
2954 4164 7.009540 CGGAGCAAATTTGATATTTCCTGTTTC 59.990 37.037 22.31 0.00 0.00 2.78
3014 4224 4.526650 GTGAGGGTTGGGTCAACAATATTT 59.473 41.667 12.06 0.00 45.11 1.40
3073 4283 2.267174 ACATGTGCTTCTTGTGCTCT 57.733 45.000 0.00 0.00 33.98 4.09
3115 4325 6.880529 CCTATGTGCATTGTATGTATGATGGA 59.119 38.462 0.00 0.00 0.00 3.41
3185 4395 0.605589 AAGGACACTGGAAGAGAGCG 59.394 55.000 0.00 0.00 37.43 5.03
3217 4427 2.689983 CCATTACTAAGGGCAGCCTTTG 59.310 50.000 19.01 10.94 0.00 2.77
3246 4456 9.314321 CTGAATGAACATATTCGGGGTATATAC 57.686 37.037 4.14 4.14 38.96 1.47
3277 4487 9.679661 TGGTATTGCATTATTAAGAGTGAAGAA 57.320 29.630 0.00 0.00 0.00 2.52
3516 4726 2.106683 GCACGGAAATCACTCCCCG 61.107 63.158 0.00 0.00 46.65 5.73
3571 4795 3.402628 AGGCTACACGAAGAACAACAT 57.597 42.857 0.00 0.00 0.00 2.71
3639 4863 6.541934 AATACCCTACTCTAGTTTGTGGTC 57.458 41.667 0.00 0.00 0.00 4.02
3742 4975 1.154197 GCTAAGGTTTGACCGGTCAC 58.846 55.000 36.40 24.99 44.90 3.67
3819 5074 3.374042 TCCCAAATATTGAGCGGGAAA 57.626 42.857 11.07 0.00 43.02 3.13
3964 5219 1.230635 CCGTTCTGCTGGTCTTGGTG 61.231 60.000 0.00 0.00 0.00 4.17
3973 5228 1.682854 CTGGTCTTGGTGTTGTTGCAT 59.317 47.619 0.00 0.00 0.00 3.96
4253 5516 0.107703 GTGTCGATGAAGATGGGCCA 60.108 55.000 9.61 9.61 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
639 1134 9.089601 GGTTTTCTTTGATTCTTTCGGTTTTTA 57.910 29.630 0.00 0.00 0.00 1.52
640 1135 7.065324 GGGTTTTCTTTGATTCTTTCGGTTTTT 59.935 33.333 0.00 0.00 0.00 1.94
721 1216 9.626045 TTTTGCATTGTTTTTCGGTTTTATTTT 57.374 22.222 0.00 0.00 0.00 1.82
725 1220 7.581476 TGTTTTTGCATTGTTTTTCGGTTTTA 58.419 26.923 0.00 0.00 0.00 1.52
730 1225 6.744537 TCATTTGTTTTTGCATTGTTTTTCGG 59.255 30.769 0.00 0.00 0.00 4.30
731 1226 7.716738 TCATTTGTTTTTGCATTGTTTTTCG 57.283 28.000 0.00 0.00 0.00 3.46
741 1236 9.823647 TCCTAGTTATTTTCATTTGTTTTTGCA 57.176 25.926 0.00 0.00 0.00 4.08
755 1250 9.811995 GGTTTTCACTGTTTTCCTAGTTATTTT 57.188 29.630 0.00 0.00 0.00 1.82
756 1251 8.973182 TGGTTTTCACTGTTTTCCTAGTTATTT 58.027 29.630 0.00 0.00 0.00 1.40
757 1252 8.528044 TGGTTTTCACTGTTTTCCTAGTTATT 57.472 30.769 0.00 0.00 0.00 1.40
758 1253 8.528044 TTGGTTTTCACTGTTTTCCTAGTTAT 57.472 30.769 0.00 0.00 0.00 1.89
759 1254 7.941431 TTGGTTTTCACTGTTTTCCTAGTTA 57.059 32.000 0.00 0.00 0.00 2.24
760 1255 6.844097 TTGGTTTTCACTGTTTTCCTAGTT 57.156 33.333 0.00 0.00 0.00 2.24
761 1256 8.528044 TTATTGGTTTTCACTGTTTTCCTAGT 57.472 30.769 0.00 0.00 0.00 2.57
762 1257 9.463443 CTTTATTGGTTTTCACTGTTTTCCTAG 57.537 33.333 0.00 0.00 0.00 3.02
763 1258 9.191479 TCTTTATTGGTTTTCACTGTTTTCCTA 57.809 29.630 0.00 0.00 0.00 2.94
764 1259 8.073467 TCTTTATTGGTTTTCACTGTTTTCCT 57.927 30.769 0.00 0.00 0.00 3.36
765 1260 8.194769 TCTCTTTATTGGTTTTCACTGTTTTCC 58.805 33.333 0.00 0.00 0.00 3.13
766 1261 9.581099 TTCTCTTTATTGGTTTTCACTGTTTTC 57.419 29.630 0.00 0.00 0.00 2.29
767 1262 9.936759 TTTCTCTTTATTGGTTTTCACTGTTTT 57.063 25.926 0.00 0.00 0.00 2.43
768 1263 9.936759 TTTTCTCTTTATTGGTTTTCACTGTTT 57.063 25.926 0.00 0.00 0.00 2.83
769 1264 9.586435 CTTTTCTCTTTATTGGTTTTCACTGTT 57.414 29.630 0.00 0.00 0.00 3.16
770 1265 8.197439 CCTTTTCTCTTTATTGGTTTTCACTGT 58.803 33.333 0.00 0.00 0.00 3.55
771 1266 8.413229 TCCTTTTCTCTTTATTGGTTTTCACTG 58.587 33.333 0.00 0.00 0.00 3.66
772 1267 8.533569 TCCTTTTCTCTTTATTGGTTTTCACT 57.466 30.769 0.00 0.00 0.00 3.41
773 1268 9.764363 ATTCCTTTTCTCTTTATTGGTTTTCAC 57.236 29.630 0.00 0.00 0.00 3.18
802 1297 9.793259 TCTTTCTTGGTTCAATGTTTCTATAGT 57.207 29.630 0.00 0.00 0.00 2.12
805 1300 9.750125 GTTTCTTTCTTGGTTCAATGTTTCTAT 57.250 29.630 0.00 0.00 0.00 1.98
806 1301 8.744652 TGTTTCTTTCTTGGTTCAATGTTTCTA 58.255 29.630 0.00 0.00 0.00 2.10
807 1302 7.610865 TGTTTCTTTCTTGGTTCAATGTTTCT 58.389 30.769 0.00 0.00 0.00 2.52
808 1303 7.826260 TGTTTCTTTCTTGGTTCAATGTTTC 57.174 32.000 0.00 0.00 0.00 2.78
809 1304 8.614469 TTTGTTTCTTTCTTGGTTCAATGTTT 57.386 26.923 0.00 0.00 0.00 2.83
810 1305 8.614469 TTTTGTTTCTTTCTTGGTTCAATGTT 57.386 26.923 0.00 0.00 0.00 2.71
811 1306 8.503196 GTTTTTGTTTCTTTCTTGGTTCAATGT 58.497 29.630 0.00 0.00 0.00 2.71
812 1307 8.502387 TGTTTTTGTTTCTTTCTTGGTTCAATG 58.498 29.630 0.00 0.00 0.00 2.82
813 1308 8.614469 TGTTTTTGTTTCTTTCTTGGTTCAAT 57.386 26.923 0.00 0.00 0.00 2.57
814 1309 8.438676 TTGTTTTTGTTTCTTTCTTGGTTCAA 57.561 26.923 0.00 0.00 0.00 2.69
815 1310 8.438676 TTTGTTTTTGTTTCTTTCTTGGTTCA 57.561 26.923 0.00 0.00 0.00 3.18
816 1311 9.381027 CTTTTGTTTTTGTTTCTTTCTTGGTTC 57.619 29.630 0.00 0.00 0.00 3.62
817 1312 8.349245 CCTTTTGTTTTTGTTTCTTTCTTGGTT 58.651 29.630 0.00 0.00 0.00 3.67
818 1313 7.717436 TCCTTTTGTTTTTGTTTCTTTCTTGGT 59.283 29.630 0.00 0.00 0.00 3.67
819 1314 8.093659 TCCTTTTGTTTTTGTTTCTTTCTTGG 57.906 30.769 0.00 0.00 0.00 3.61
820 1315 9.943163 TTTCCTTTTGTTTTTGTTTCTTTCTTG 57.057 25.926 0.00 0.00 0.00 3.02
828 1323 9.522804 GGTTTCTTTTTCCTTTTGTTTTTGTTT 57.477 25.926 0.00 0.00 0.00 2.83
829 1324 8.687242 TGGTTTCTTTTTCCTTTTGTTTTTGTT 58.313 25.926 0.00 0.00 0.00 2.83
830 1325 8.132362 GTGGTTTCTTTTTCCTTTTGTTTTTGT 58.868 29.630 0.00 0.00 0.00 2.83
831 1326 8.349245 AGTGGTTTCTTTTTCCTTTTGTTTTTG 58.651 29.630 0.00 0.00 0.00 2.44
832 1327 8.349245 CAGTGGTTTCTTTTTCCTTTTGTTTTT 58.651 29.630 0.00 0.00 0.00 1.94
833 1328 7.717436 TCAGTGGTTTCTTTTTCCTTTTGTTTT 59.283 29.630 0.00 0.00 0.00 2.43
834 1329 7.220740 TCAGTGGTTTCTTTTTCCTTTTGTTT 58.779 30.769 0.00 0.00 0.00 2.83
835 1330 6.764379 TCAGTGGTTTCTTTTTCCTTTTGTT 58.236 32.000 0.00 0.00 0.00 2.83
836 1331 6.353404 TCAGTGGTTTCTTTTTCCTTTTGT 57.647 33.333 0.00 0.00 0.00 2.83
837 1332 7.665561 TTTCAGTGGTTTCTTTTTCCTTTTG 57.334 32.000 0.00 0.00 0.00 2.44
838 1333 8.684386 TTTTTCAGTGGTTTCTTTTTCCTTTT 57.316 26.923 0.00 0.00 0.00 2.27
860 1355 3.067601 CAGGCCGTAAAGAACACCTTTTT 59.932 43.478 0.00 0.00 42.13 1.94
861 1356 2.621526 CAGGCCGTAAAGAACACCTTTT 59.378 45.455 0.00 0.00 42.13 2.27
862 1357 2.227194 CAGGCCGTAAAGAACACCTTT 58.773 47.619 0.00 0.00 46.21 3.11
863 1358 1.544759 CCAGGCCGTAAAGAACACCTT 60.545 52.381 0.00 0.00 33.10 3.50
906 1401 2.360801 ACAAAAGCAAAAGCTTAGCCGA 59.639 40.909 17.34 0.00 0.00 5.54
916 1411 1.484240 CCCTCCCACACAAAAGCAAAA 59.516 47.619 0.00 0.00 0.00 2.44
939 1434 3.357079 GTGCTGGTGGTTGCCTCG 61.357 66.667 0.00 0.00 0.00 4.63
943 1438 3.297620 CCTGGTGCTGGTGGTTGC 61.298 66.667 0.00 0.00 0.00 4.17
944 1439 0.754957 TTTCCTGGTGCTGGTGGTTG 60.755 55.000 0.00 0.00 0.00 3.77
946 1441 0.032615 TTTTTCCTGGTGCTGGTGGT 60.033 50.000 0.00 0.00 0.00 4.16
947 1442 0.389025 GTTTTTCCTGGTGCTGGTGG 59.611 55.000 0.00 0.00 0.00 4.61
950 1445 0.593128 CTCGTTTTTCCTGGTGCTGG 59.407 55.000 0.00 0.00 0.00 4.85
1253 1763 0.035439 TCCAAGCCAATCCGGACTTC 60.035 55.000 6.12 0.00 36.56 3.01
1254 1764 0.625849 ATCCAAGCCAATCCGGACTT 59.374 50.000 6.12 1.96 36.56 3.01
1255 1765 0.625849 AATCCAAGCCAATCCGGACT 59.374 50.000 6.12 0.00 36.56 3.85
1256 1766 0.740737 CAATCCAAGCCAATCCGGAC 59.259 55.000 6.12 0.00 36.56 4.79
1267 1777 2.291800 ACCCAATCCAGTCCAATCCAAG 60.292 50.000 0.00 0.00 0.00 3.61
1275 1785 1.379044 CAGCCACCCAATCCAGTCC 60.379 63.158 0.00 0.00 0.00 3.85
1276 1786 1.379044 CCAGCCACCCAATCCAGTC 60.379 63.158 0.00 0.00 0.00 3.51
1277 1787 1.217057 ATCCAGCCACCCAATCCAGT 61.217 55.000 0.00 0.00 0.00 4.00
1278 1788 0.466922 GATCCAGCCACCCAATCCAG 60.467 60.000 0.00 0.00 0.00 3.86
1279 1789 1.614711 GATCCAGCCACCCAATCCA 59.385 57.895 0.00 0.00 0.00 3.41
1301 1811 1.000060 GCAATCAGCCAGCAAACAGAA 60.000 47.619 0.00 0.00 37.23 3.02
1321 1831 3.393800 ACAGGAGAACACAACAGAATCG 58.606 45.455 0.00 0.00 0.00 3.34
1322 1832 3.430218 CGACAGGAGAACACAACAGAATC 59.570 47.826 0.00 0.00 0.00 2.52
1331 1841 2.522060 CTGCACGACAGGAGAACAC 58.478 57.895 0.00 0.00 43.19 3.32
1358 1870 1.714899 CGAAATGCCACCGGATGTCC 61.715 60.000 9.46 0.00 0.00 4.02
1376 1888 3.114616 CTCTGCAAGTGCCCGACG 61.115 66.667 0.00 0.00 41.18 5.12
1413 1925 3.449737 TGGGAAATCTTGACCGTACCTAG 59.550 47.826 0.00 0.00 0.00 3.02
1420 1932 0.740737 GCCATGGGAAATCTTGACCG 59.259 55.000 15.13 0.00 0.00 4.79
1424 1936 0.179129 GCACGCCATGGGAAATCTTG 60.179 55.000 15.13 1.04 0.00 3.02
1450 1984 0.871722 TCAAATCCTCCGTGCAAACG 59.128 50.000 0.00 0.00 0.00 3.60
1554 2092 2.861147 ACTTTGCTGTTCCCCTACTC 57.139 50.000 0.00 0.00 0.00 2.59
1581 2119 9.570488 GAGTACAAGGTTTGTATCACTAACTAG 57.430 37.037 5.10 0.00 46.73 2.57
1669 2261 9.321590 GACTGATAAAACATTGTTACGGTTTAC 57.678 33.333 1.76 0.00 33.91 2.01
1670 2262 9.275398 AGACTGATAAAACATTGTTACGGTTTA 57.725 29.630 1.76 0.00 33.91 2.01
1671 2263 8.073768 CAGACTGATAAAACATTGTTACGGTTT 58.926 33.333 1.76 0.00 36.37 3.27
1672 2264 7.581476 CAGACTGATAAAACATTGTTACGGTT 58.419 34.615 1.76 0.00 0.00 4.44
1673 2265 6.348213 GCAGACTGATAAAACATTGTTACGGT 60.348 38.462 6.65 6.35 0.00 4.83
1674 2266 6.021596 GCAGACTGATAAAACATTGTTACGG 58.978 40.000 6.65 3.49 0.00 4.02
1680 2272 5.375417 TGGTGCAGACTGATAAAACATTG 57.625 39.130 6.65 0.00 0.00 2.82
1765 2555 6.782988 TGTATGGGGGTTGAGTTTCAAAATAA 59.217 34.615 0.00 0.00 38.22 1.40
1792 2582 3.709987 GGACACGTGTGTACTTACAGTT 58.290 45.455 28.82 0.00 45.05 3.16
1841 2910 1.289109 CGGCTGTGACGGTTAGTTGG 61.289 60.000 0.00 0.00 0.00 3.77
1858 2927 7.948278 AATTAAAGTCTAAGCAGTATAGCGG 57.052 36.000 0.00 0.00 40.15 5.52
1872 2941 5.411669 CGGCAGAAACAGGTAATTAAAGTCT 59.588 40.000 0.00 0.00 0.00 3.24
1878 2947 5.764131 CAAAACGGCAGAAACAGGTAATTA 58.236 37.500 0.00 0.00 0.00 1.40
1975 3044 6.324561 TGCATTCAACTGTTAAGCATAACA 57.675 33.333 13.43 13.43 46.96 2.41
1982 3051 6.088824 GGTTCAGATGCATTCAACTGTTAAG 58.911 40.000 0.00 0.00 41.93 1.85
1987 3056 2.730090 GCGGTTCAGATGCATTCAACTG 60.730 50.000 15.73 15.73 42.42 3.16
1992 3061 3.133691 TCTATGCGGTTCAGATGCATTC 58.866 45.455 0.00 0.00 46.55 2.67
2018 3087 9.817365 GCAGACATGTCACATATAAATTCATAC 57.183 33.333 27.02 0.00 0.00 2.39
2019 3088 9.558396 TGCAGACATGTCACATATAAATTCATA 57.442 29.630 27.02 0.00 0.00 2.15
2020 3089 8.347771 GTGCAGACATGTCACATATAAATTCAT 58.652 33.333 27.02 0.00 35.12 2.57
2021 3090 7.336427 TGTGCAGACATGTCACATATAAATTCA 59.664 33.333 27.02 12.77 38.03 2.57
2022 3091 7.696755 TGTGCAGACATGTCACATATAAATTC 58.303 34.615 27.02 10.65 38.03 2.17
2023 3092 7.201758 CCTGTGCAGACATGTCACATATAAATT 60.202 37.037 27.02 0.00 40.33 1.82
2024 3093 6.261603 CCTGTGCAGACATGTCACATATAAAT 59.738 38.462 27.02 0.42 40.33 1.40
2025 3094 5.585844 CCTGTGCAGACATGTCACATATAAA 59.414 40.000 27.02 8.97 40.33 1.40
2026 3095 5.104982 TCCTGTGCAGACATGTCACATATAA 60.105 40.000 27.02 10.94 40.33 0.98
2027 3096 4.405358 TCCTGTGCAGACATGTCACATATA 59.595 41.667 27.02 13.47 40.33 0.86
2028 3097 3.198417 TCCTGTGCAGACATGTCACATAT 59.802 43.478 27.02 3.53 40.33 1.78
2029 3098 2.566724 TCCTGTGCAGACATGTCACATA 59.433 45.455 27.02 19.91 40.33 2.29
2030 3099 1.348696 TCCTGTGCAGACATGTCACAT 59.651 47.619 27.02 4.33 40.33 3.21
2031 3100 0.758123 TCCTGTGCAGACATGTCACA 59.242 50.000 27.02 20.73 39.50 3.58
2032 3101 1.436600 CTCCTGTGCAGACATGTCAC 58.563 55.000 27.02 18.49 35.40 3.67
2033 3102 0.322648 CCTCCTGTGCAGACATGTCA 59.677 55.000 27.02 5.05 0.00 3.58
2034 3103 0.610174 TCCTCCTGTGCAGACATGTC 59.390 55.000 18.47 18.47 0.00 3.06
2035 3104 0.612229 CTCCTCCTGTGCAGACATGT 59.388 55.000 0.00 0.00 0.00 3.21
2036 3105 0.107800 CCTCCTCCTGTGCAGACATG 60.108 60.000 0.02 0.00 0.00 3.21
2037 3106 0.252421 TCCTCCTCCTGTGCAGACAT 60.252 55.000 0.02 0.00 0.00 3.06
2038 3107 0.902048 CTCCTCCTCCTGTGCAGACA 60.902 60.000 0.02 0.00 0.00 3.41
2039 3108 0.613292 TCTCCTCCTCCTGTGCAGAC 60.613 60.000 0.02 0.00 0.00 3.51
2043 3112 2.102252 CAGTATTCTCCTCCTCCTGTGC 59.898 54.545 0.00 0.00 0.00 4.57
2048 3117 5.279256 GCTGTAATCAGTATTCTCCTCCTCC 60.279 48.000 0.00 0.00 43.05 4.30
2049 3118 5.303078 TGCTGTAATCAGTATTCTCCTCCTC 59.697 44.000 0.00 0.00 43.05 3.71
2054 3123 9.277783 ACAAATATGCTGTAATCAGTATTCTCC 57.722 33.333 4.42 0.00 42.66 3.71
2071 3140 7.211966 AGCAGATAAGGATGAACAAATATGC 57.788 36.000 0.00 0.00 0.00 3.14
2075 3144 5.136105 GGGAGCAGATAAGGATGAACAAAT 58.864 41.667 0.00 0.00 0.00 2.32
2098 3179 7.329962 TGACGGCGTTATGTAATATAATCAAGG 59.670 37.037 16.19 0.00 0.00 3.61
2099 3180 8.234887 TGACGGCGTTATGTAATATAATCAAG 57.765 34.615 16.19 0.00 0.00 3.02
2100 3181 8.652463 CATGACGGCGTTATGTAATATAATCAA 58.348 33.333 29.74 0.00 0.00 2.57
2104 3185 6.160684 AGCATGACGGCGTTATGTAATATAA 58.839 36.000 34.88 0.00 39.27 0.98
2105 3186 5.716094 AGCATGACGGCGTTATGTAATATA 58.284 37.500 34.88 7.15 39.27 0.86
2106 3187 4.566004 AGCATGACGGCGTTATGTAATAT 58.434 39.130 34.88 19.14 39.27 1.28
2117 3198 0.729116 AATCTGAAAGCATGACGGCG 59.271 50.000 4.80 4.80 39.27 6.46
2120 3201 1.469703 TGGCAATCTGAAAGCATGACG 59.530 47.619 0.00 0.00 30.91 4.35
2122 3203 3.764972 TGATTGGCAATCTGAAAGCATGA 59.235 39.130 33.21 12.43 38.72 3.07
2139 3220 2.543012 GACAGCACGATCCAGATGATTG 59.457 50.000 4.53 0.00 40.28 2.67
2172 3253 5.016831 ACCATAACTTTTAAAGGCTCCCTG 58.983 41.667 9.64 0.00 32.13 4.45
2184 3265 7.107639 AGTGTTTACTTGCACCATAACTTTT 57.892 32.000 0.00 0.00 36.35 2.27
2263 3348 7.168905 CACCTGGGAAGATATATCCTAAAACC 58.831 42.308 9.18 4.70 37.14 3.27
2281 3366 3.181454 ACTGACTACTTGAAACACCTGGG 60.181 47.826 0.00 0.00 0.00 4.45
2282 3367 4.073293 ACTGACTACTTGAAACACCTGG 57.927 45.455 0.00 0.00 0.00 4.45
2283 3368 4.876107 ACAACTGACTACTTGAAACACCTG 59.124 41.667 0.00 0.00 0.00 4.00
2285 3370 5.813080 AACAACTGACTACTTGAAACACC 57.187 39.130 0.00 0.00 0.00 4.16
2286 3371 7.535489 AGTAACAACTGACTACTTGAAACAC 57.465 36.000 0.00 0.00 0.00 3.32
2304 3392 8.615878 AGATTGTAGTGTAAATGCAAGTAACA 57.384 30.769 0.00 0.00 40.33 2.41
2349 3437 5.065090 GGCATGGCTTTTGAAATAATGGAAC 59.935 40.000 12.86 0.00 0.00 3.62
2351 3439 4.224594 TGGCATGGCTTTTGAAATAATGGA 59.775 37.500 21.08 0.00 0.00 3.41
2352 3440 4.515361 TGGCATGGCTTTTGAAATAATGG 58.485 39.130 21.08 0.00 0.00 3.16
2358 3538 5.680594 ATCTTATGGCATGGCTTTTGAAA 57.319 34.783 21.08 4.54 0.00 2.69
2363 3543 8.654485 TTGAATATATCTTATGGCATGGCTTT 57.346 30.769 21.08 10.42 0.00 3.51
2436 3616 9.948964 TCATCATAACATAATCATAGTGGAAGG 57.051 33.333 0.00 0.00 0.00 3.46
2453 3633 9.708222 GTGTTACATCAGTGAATTCATCATAAC 57.292 33.333 12.12 13.75 40.97 1.89
2466 3665 7.433708 TCATAACCAAAGTGTTACATCAGTG 57.566 36.000 0.00 0.00 33.78 3.66
2482 3681 5.716228 ACCAGATTTTGCTGAATCATAACCA 59.284 36.000 12.86 0.00 38.27 3.67
2483 3682 6.212888 ACCAGATTTTGCTGAATCATAACC 57.787 37.500 12.86 0.00 38.27 2.85
2487 3686 7.649533 TCAATACCAGATTTTGCTGAATCAT 57.350 32.000 12.86 3.70 38.27 2.45
2581 3780 9.213799 GAGTAATCTTTCATCCCTATTGTCATC 57.786 37.037 0.00 0.00 0.00 2.92
2608 3807 5.460748 CACCTTAAAATTTTCCGGTGTTGAC 59.539 40.000 27.34 0.00 36.59 3.18
2681 3883 0.381801 AACGAAACAGCAGCTTGTGG 59.618 50.000 0.00 0.00 0.00 4.17
2697 3899 3.935203 AGTGCCTGTATTCAGATCAAACG 59.065 43.478 0.12 0.00 43.76 3.60
2891 4101 5.048991 GGTCCAAGAATTGTATCACGTTTGT 60.049 40.000 0.00 0.00 46.99 2.83
2942 4152 6.385649 ACAAAGAAAGCGAAACAGGAAATA 57.614 33.333 0.00 0.00 0.00 1.40
2954 4164 4.629200 AGCTCTATCTGAACAAAGAAAGCG 59.371 41.667 0.00 0.00 0.00 4.68
3014 4224 2.307686 GTTTGGATACTCCCTTGGTCCA 59.692 50.000 0.00 0.00 35.03 4.02
3185 4395 6.381420 TGCCCTTAGTAATGGAGCTATATCTC 59.619 42.308 8.29 0.00 0.00 2.75
3217 4427 2.554032 CCCGAATATGTTCATTCAGGGC 59.446 50.000 2.95 0.00 39.55 5.19
3246 4456 6.772716 ACTCTTAATAATGCAATACCAGGGTG 59.227 38.462 0.06 0.00 0.00 4.61
3277 4487 5.680594 TTGAAGAAAATGGGCTGCAATAT 57.319 34.783 0.50 0.00 0.00 1.28
3282 4492 3.006217 ACTCTTTGAAGAAAATGGGCTGC 59.994 43.478 0.00 0.00 34.03 5.25
3322 4532 7.989826 GCATATAGGAGGTAAAATGCCATTAG 58.010 38.462 0.00 0.00 34.95 1.73
3516 4726 2.099831 CGAGACGTGAGCCGGTAC 59.900 66.667 1.90 0.00 42.24 3.34
3571 4795 8.439964 AACTAGTATAAACCTTGTGTCCCTTA 57.560 34.615 0.00 0.00 0.00 2.69
3639 4863 1.077212 CCCTGAGGCAATCCACCAG 60.077 63.158 0.00 0.00 36.03 4.00
3742 4975 3.825623 GGCAGGGGGATTGGAGGG 61.826 72.222 0.00 0.00 0.00 4.30
3841 5096 3.700038 AGTGTACTAGATGTTCCCCTTCG 59.300 47.826 0.00 0.00 0.00 3.79
3964 5219 2.155539 GCAACCATTTCGATGCAACAAC 59.844 45.455 1.67 0.00 38.63 3.32
3973 5228 1.327303 AGCAAAGGCAACCATTTCGA 58.673 45.000 0.00 0.00 44.61 3.71
4083 5345 2.741985 CGCAAGCCATGACGACCA 60.742 61.111 0.00 0.00 32.61 4.02
4253 5516 1.207791 CTCAAGGAGTGGCCCAGTAT 58.792 55.000 0.00 0.00 37.37 2.12


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

AutoCloner maintained by Alex Coulton.