Multiple sequence alignment - TraesCS3D01G412000

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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 TraesCS3D01G412000 chr3D 100.000 4520 0 0 1 4520 524649203 524644684 0.000000e+00 8347.0
1 TraesCS3D01G412000 chr3D 90.531 1130 82 16 807 1922 524311516 524310398 0.000000e+00 1471.0
2 TraesCS3D01G412000 chr3D 88.108 370 29 11 1848 2205 524310382 524310016 4.180000e-115 425.0
3 TraesCS3D01G412000 chr3D 85.904 376 21 15 2529 2892 524309461 524309106 5.520000e-99 372.0
4 TraesCS3D01G412000 chr3D 81.087 460 77 7 4064 4514 611585814 611586272 4.300000e-95 359.0
5 TraesCS3D01G412000 chr3D 90.411 219 16 2 3192 3410 157364362 157364575 2.660000e-72 283.0
6 TraesCS3D01G412000 chr3D 94.253 174 8 2 699 871 524311674 524311502 9.640000e-67 265.0
7 TraesCS3D01G412000 chr3D 89.266 177 16 3 525 701 524312062 524311889 7.610000e-53 219.0
8 TraesCS3D01G412000 chr3D 92.857 56 4 0 4005 4060 120323805 120323860 1.040000e-11 82.4
9 TraesCS3D01G412000 chr3D 100.000 32 0 0 3953 3984 165904561 165904530 4.880000e-05 60.2
10 TraesCS3D01G412000 chr3D 100.000 32 0 0 3953 3984 407306049 407306018 4.880000e-05 60.2
11 TraesCS3D01G412000 chr3A 86.638 1654 137 48 629 2236 658907470 658905855 0.000000e+00 1753.0
12 TraesCS3D01G412000 chr3A 90.108 1021 84 10 3504 4520 658983026 658982019 0.000000e+00 1310.0
13 TraesCS3D01G412000 chr3A 95.074 812 31 5 1431 2236 658984596 658983788 0.000000e+00 1269.0
14 TraesCS3D01G412000 chr3A 85.587 1013 57 33 1946 2916 658983988 658983023 0.000000e+00 979.0
15 TraesCS3D01G412000 chr3A 83.818 859 113 16 1 852 658986563 658985724 0.000000e+00 793.0
16 TraesCS3D01G412000 chr3A 87.698 504 16 19 885 1382 658985063 658984600 3.070000e-151 545.0
17 TraesCS3D01G412000 chr3A 86.038 265 21 7 2532 2792 658905376 658905124 2.070000e-68 270.0
18 TraesCS3D01G412000 chr3A 88.360 189 13 5 679 862 658985712 658985528 7.610000e-53 219.0
19 TraesCS3D01G412000 chr3A 95.588 68 3 0 1810 1877 658906242 658906175 4.780000e-20 110.0
20 TraesCS3D01G412000 chr3B 86.842 1254 104 30 691 1922 691752559 691751345 0.000000e+00 1345.0
21 TraesCS3D01G412000 chr3B 90.022 912 49 18 1364 2236 691923782 691922874 0.000000e+00 1142.0
22 TraesCS3D01G412000 chr3B 85.681 859 91 15 66 917 691925048 691924215 0.000000e+00 876.0
23 TraesCS3D01G412000 chr3B 83.642 972 56 38 1946 2856 691923074 691922145 0.000000e+00 819.0
24 TraesCS3D01G412000 chr3B 90.585 393 20 8 895 1273 691924169 691923780 5.220000e-139 505.0
25 TraesCS3D01G412000 chr3B 87.534 369 18 13 2532 2892 691750441 691750093 7.040000e-108 401.0
26 TraesCS3D01G412000 chr3B 79.274 468 90 5 4050 4516 684418340 684418801 2.030000e-83 320.0
27 TraesCS3D01G412000 chr3B 85.000 300 17 15 1848 2133 691751284 691750999 3.440000e-71 279.0
28 TraesCS3D01G412000 chr5D 89.655 377 29 8 3510 3882 501436425 501436795 5.290000e-129 472.0
29 TraesCS3D01G412000 chr5D 91.349 289 23 2 3192 3479 363847481 363847768 1.180000e-105 394.0
30 TraesCS3D01G412000 chr5D 82.641 409 65 6 4108 4514 476045284 476045688 1.550000e-94 357.0
31 TraesCS3D01G412000 chr2B 95.848 289 11 1 3192 3479 795755832 795756120 2.460000e-127 466.0
32 TraesCS3D01G412000 chr2B 82.587 402 63 7 4115 4514 706526907 706526511 9.310000e-92 348.0
33 TraesCS3D01G412000 chr2B 89.083 229 11 1 2982 3196 795755065 795755293 5.760000e-69 272.0
34 TraesCS3D01G412000 chr2B 85.714 231 31 2 3250 3479 210700733 210700504 4.520000e-60 243.0
35 TraesCS3D01G412000 chr2B 89.091 55 4 2 2985 3038 49377213 49377160 2.920000e-07 67.6
36 TraesCS3D01G412000 chr4D 89.034 383 27 12 3506 3884 101440166 101440537 1.150000e-125 460.0
37 TraesCS3D01G412000 chr4D 91.696 289 22 2 3192 3479 364048967 364048680 2.530000e-107 399.0
38 TraesCS3D01G412000 chr4A 88.773 383 33 9 3505 3883 639057281 639056905 1.150000e-125 460.0
39 TraesCS3D01G412000 chr6B 89.362 376 21 15 3506 3871 48550684 48550318 5.330000e-124 455.0
40 TraesCS3D01G412000 chr6B 82.090 469 79 5 4050 4515 81029568 81029102 3.280000e-106 396.0
41 TraesCS3D01G412000 chr6B 96.875 32 1 0 3970 4001 34925969 34925938 2.000000e-03 54.7
42 TraesCS3D01G412000 chr4B 95.156 289 13 1 3192 3479 641406057 641406345 5.330000e-124 455.0
43 TraesCS3D01G412000 chr4B 89.700 233 9 2 2979 3196 641405336 641405568 2.660000e-72 283.0
44 TraesCS3D01G412000 chr5B 94.810 289 14 1 3192 3479 240327868 240327580 2.480000e-122 449.0
45 TraesCS3D01G412000 chr5B 90.265 226 8 4 2985 3196 240328582 240328357 2.660000e-72 283.0
46 TraesCS3D01G412000 chr7A 88.421 380 32 10 3506 3882 10020860 10021230 8.920000e-122 448.0
47 TraesCS3D01G412000 chr7B 88.189 381 31 10 3506 3882 202508737 202508367 4.150000e-120 442.0
48 TraesCS3D01G412000 chr7B 83.234 167 26 2 4012 4177 742072868 742073033 7.830000e-33 152.0
49 TraesCS3D01G412000 chr7B 90.909 55 5 0 3947 4001 643459558 643459504 1.740000e-09 75.0
50 TraesCS3D01G412000 chr6D 88.329 377 32 11 3510 3882 457095606 457095974 4.150000e-120 442.0
51 TraesCS3D01G412000 chr6D 87.895 380 35 8 3506 3880 428885139 428884766 1.930000e-118 436.0
52 TraesCS3D01G412000 chr6D 80.508 472 64 17 4053 4516 380995190 380994739 2.010000e-88 337.0
53 TraesCS3D01G412000 chr6D 93.443 61 4 0 2921 2981 134335451 134335391 1.730000e-14 91.6
54 TraesCS3D01G412000 chr6D 90.000 50 5 0 3949 3998 361544961 361545010 1.050000e-06 65.8
55 TraesCS3D01G412000 chr6A 92.150 293 20 2 3192 3481 101522358 101522650 1.170000e-110 411.0
56 TraesCS3D01G412000 chr6A 89.686 223 10 1 2987 3196 101521407 101521629 5.760000e-69 272.0
57 TraesCS3D01G412000 chr2D 91.349 289 23 2 3192 3479 242224695 242224408 1.180000e-105 394.0
58 TraesCS3D01G412000 chr2D 91.667 60 5 0 4005 4064 215848444 215848503 2.900000e-12 84.2
59 TraesCS3D01G412000 chr2D 92.857 56 4 0 4008 4063 481447193 481447138 1.040000e-11 82.4
60 TraesCS3D01G412000 chr2D 91.071 56 5 0 3943 3998 11028155 11028210 4.850000e-10 76.8
61 TraesCS3D01G412000 chr2D 90.244 41 4 0 3483 3523 395603750 395603790 2.000000e-03 54.7
62 TraesCS3D01G412000 chr2A 84.085 377 55 4 4148 4520 748291520 748291895 4.300000e-95 359.0
63 TraesCS3D01G412000 chr2A 75.261 287 52 7 4050 4336 652287232 652286965 7.940000e-23 119.0
64 TraesCS3D01G412000 chr2A 94.643 56 3 0 4005 4060 306178116 306178171 2.240000e-13 87.9
65 TraesCS3D01G412000 chr2A 94.340 53 3 0 4008 4060 666033965 666034017 1.040000e-11 82.4
66 TraesCS3D01G412000 chr2A 90.909 55 5 0 4006 4060 651511832 651511886 1.740000e-09 75.0
67 TraesCS3D01G412000 chr1A 81.106 434 80 1 4050 4481 521606781 521607214 3.350000e-91 346.0
68 TraesCS3D01G412000 chr7D 89.706 68 7 0 2914 2981 1357000 1357067 2.240000e-13 87.9
69 TraesCS3D01G412000 chr7D 87.500 56 7 0 3947 4002 626479224 626479279 1.050000e-06 65.8
70 TraesCS3D01G412000 chr1B 88.889 54 4 2 3945 3997 363445891 363445943 1.050000e-06 65.8
71 TraesCS3D01G412000 chr1B 84.127 63 8 2 2977 3038 373118794 373118733 4.880000e-05 60.2


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 TraesCS3D01G412000 chr3D 524644684 524649203 4519 True 8347.0 8347 100.000000 1 4520 1 chr3D.!!$R3 4519
1 TraesCS3D01G412000 chr3D 524309106 524312062 2956 True 550.4 1471 89.612400 525 2892 5 chr3D.!!$R4 2367
2 TraesCS3D01G412000 chr3A 658982019 658986563 4544 True 852.5 1310 88.440833 1 4520 6 chr3A.!!$R2 4519
3 TraesCS3D01G412000 chr3A 658905124 658907470 2346 True 711.0 1753 89.421333 629 2792 3 chr3A.!!$R1 2163
4 TraesCS3D01G412000 chr3B 691922145 691925048 2903 True 835.5 1142 87.482500 66 2856 4 chr3B.!!$R2 2790
5 TraesCS3D01G412000 chr3B 691750093 691752559 2466 True 675.0 1345 86.458667 691 2892 3 chr3B.!!$R1 2201
6 TraesCS3D01G412000 chr2B 795755065 795756120 1055 False 369.0 466 92.465500 2982 3479 2 chr2B.!!$F1 497
7 TraesCS3D01G412000 chr4B 641405336 641406345 1009 False 369.0 455 92.428000 2979 3479 2 chr4B.!!$F1 500
8 TraesCS3D01G412000 chr5B 240327580 240328582 1002 True 366.0 449 92.537500 2985 3479 2 chr5B.!!$R1 494
9 TraesCS3D01G412000 chr6A 101521407 101522650 1243 False 341.5 411 90.918000 2987 3481 2 chr6A.!!$F1 494

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
733 954 0.105658 AGTAAGCATCCCCGCTAGGA 60.106 55.0 0.0 0.0 42.89 2.94 F
1463 2457 0.455464 CGTCGTCGTACCAGCATGAA 60.455 55.0 0.0 0.0 39.69 2.57 F
1818 2812 0.471780 TCTCCACCAGGACAGCAAGA 60.472 55.0 0.0 0.0 39.61 3.02 F
3429 5743 0.252057 TCAGGGATTGGACGTGAGGA 60.252 55.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 2812 0.107456 CCGTAGCCATGCTTCTGGAT 59.893 55.0 4.93 1.27 40.44 3.41 R
2837 4397 0.388520 CACGACGACCATCAAGAGCA 60.389 55.0 0.00 0.00 0.00 4.26 R
3488 5802 0.407139 GGTACTCCCTCCGCCCTATA 59.593 60.0 0.00 0.00 0.00 1.31 R
4264 6581 0.614697 TCTCGAGGTTCATGGCCTGA 60.615 55.0 13.56 2.06 36.29 3.86 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
24 25 2.754552 GACATGCCATTTACTTGCCTCA 59.245 45.455 0.00 0.00 0.00 3.86
30 31 3.181493 GCCATTTACTTGCCTCATGTCAG 60.181 47.826 0.00 0.00 0.00 3.51
53 54 7.890127 TCAGTTTTCTATTGGATTGTGGAAGAT 59.110 33.333 0.00 0.00 0.00 2.40
56 57 4.464008 TCTATTGGATTGTGGAAGATGCC 58.536 43.478 0.00 0.00 0.00 4.40
60 61 1.396653 GATTGTGGAAGATGCCAGGG 58.603 55.000 0.00 0.00 38.95 4.45
61 62 0.706433 ATTGTGGAAGATGCCAGGGT 59.294 50.000 0.00 0.00 38.95 4.34
62 63 0.251297 TTGTGGAAGATGCCAGGGTG 60.251 55.000 0.00 0.00 38.95 4.61
64 65 1.852157 TGGAAGATGCCAGGGTGGT 60.852 57.895 0.00 0.00 40.46 4.16
158 159 3.119173 CCATGTACCGCAATTCATTGGTT 60.119 43.478 1.77 0.00 38.21 3.67
181 182 8.978539 GGTTATTCTCATTTGTTGTTTCCTTTC 58.021 33.333 0.00 0.00 0.00 2.62
182 183 9.528018 GTTATTCTCATTTGTTGTTTCCTTTCA 57.472 29.630 0.00 0.00 0.00 2.69
189 190 9.447157 TCATTTGTTGTTTCCTTTCAAAAGAAT 57.553 25.926 4.06 0.00 38.28 2.40
191 192 8.614469 TTTGTTGTTTCCTTTCAAAAGAATGT 57.386 26.923 4.06 0.00 38.28 2.71
192 193 9.712305 TTTGTTGTTTCCTTTCAAAAGAATGTA 57.288 25.926 4.06 0.00 38.28 2.29
194 195 9.883142 TGTTGTTTCCTTTCAAAAGAATGTATT 57.117 25.926 4.06 0.00 38.28 1.89
198 199 8.978539 GTTTCCTTTCAAAAGAATGTATTGTCC 58.021 33.333 4.06 0.00 38.28 4.02
199 200 7.831691 TCCTTTCAAAAGAATGTATTGTCCA 57.168 32.000 4.06 0.00 38.28 4.02
200 201 7.885297 TCCTTTCAAAAGAATGTATTGTCCAG 58.115 34.615 4.06 0.00 38.28 3.86
201 202 7.723616 TCCTTTCAAAAGAATGTATTGTCCAGA 59.276 33.333 4.06 0.00 38.28 3.86
205 206 9.695526 TTCAAAAGAATGTATTGTCCAGATTTG 57.304 29.630 0.00 0.00 0.00 2.32
216 217 7.649533 ATTGTCCAGATTTGAATGCAAGATA 57.350 32.000 0.00 0.00 35.04 1.98
217 218 6.441093 TGTCCAGATTTGAATGCAAGATAC 57.559 37.500 0.00 0.00 35.04 2.24
218 219 5.357878 TGTCCAGATTTGAATGCAAGATACC 59.642 40.000 0.00 0.00 35.04 2.73
258 259 5.124457 GGTTGTGTCAGCTGATTATTGATGT 59.876 40.000 21.47 0.00 0.00 3.06
270 271 7.767659 GCTGATTATTGATGTATCATGCCTCTA 59.232 37.037 0.00 0.00 36.56 2.43
275 276 4.020751 TTGATGTATCATGCCTCTAGGCTC 60.021 45.833 21.15 8.77 46.26 4.70
293 294 2.027625 CGAACAAGGTGTCCCTCGC 61.028 63.158 0.00 0.00 41.56 5.03
299 300 1.536943 AAGGTGTCCCTCGCTGACTC 61.537 60.000 0.00 0.00 41.56 3.36
300 301 2.574399 GTGTCCCTCGCTGACTCC 59.426 66.667 0.00 0.00 33.83 3.85
325 326 0.250684 TGGCGAATGCAGAAGACCAA 60.251 50.000 0.00 0.00 45.35 3.67
333 334 3.228188 TGCAGAAGACCAAGGTTGAAT 57.772 42.857 0.00 0.00 0.00 2.57
337 338 4.279420 GCAGAAGACCAAGGTTGAATCTTT 59.721 41.667 9.33 0.00 35.18 2.52
338 339 5.766222 CAGAAGACCAAGGTTGAATCTTTG 58.234 41.667 9.33 0.00 35.18 2.77
373 374 1.818060 TCAATTGGCTATGTGTGTGGC 59.182 47.619 5.42 0.00 0.00 5.01
383 384 1.656587 TGTGTGTGGCCCTATCTTCT 58.343 50.000 0.00 0.00 0.00 2.85
393 394 2.764269 CCCTATCTTCTGTGGGAGGAA 58.236 52.381 0.00 0.00 42.11 3.36
395 396 3.718956 CCCTATCTTCTGTGGGAGGAAAT 59.281 47.826 0.00 0.00 42.11 2.17
397 398 3.550437 ATCTTCTGTGGGAGGAAATCG 57.450 47.619 0.00 0.00 33.76 3.34
399 400 1.279271 CTTCTGTGGGAGGAAATCGGT 59.721 52.381 0.00 0.00 0.00 4.69
413 415 1.126488 ATCGGTCATGCATGGACTCT 58.874 50.000 25.97 6.52 35.61 3.24
425 427 1.717032 TGGACTCTAGGTGCAACTGT 58.283 50.000 16.44 3.11 43.13 3.55
433 435 0.179018 AGGTGCAACTGTTGGGAGAC 60.179 55.000 21.01 5.53 36.74 3.36
439 441 0.834612 AACTGTTGGGAGACGGTCAA 59.165 50.000 11.27 0.00 38.15 3.18
480 483 3.550437 AGATTAGTGACACATGAGGCC 57.450 47.619 8.59 0.00 0.00 5.19
483 486 2.238084 TAGTGACACATGAGGCCTCT 57.762 50.000 32.28 15.91 0.00 3.69
484 487 1.356124 AGTGACACATGAGGCCTCTT 58.644 50.000 32.28 24.06 0.00 2.85
485 488 1.002888 AGTGACACATGAGGCCTCTTG 59.997 52.381 35.34 35.34 39.69 3.02
486 489 0.325933 TGACACATGAGGCCTCTTGG 59.674 55.000 37.85 30.37 38.58 3.61
487 490 0.615331 GACACATGAGGCCTCTTGGA 59.385 55.000 37.85 20.62 38.58 3.53
491 494 1.064166 ACATGAGGCCTCTTGGAATGG 60.064 52.381 37.85 21.20 38.58 3.16
517 520 6.912051 TCATGTGTTCTTTTCGATTGTTTCAG 59.088 34.615 0.00 0.00 0.00 3.02
528 531 4.759693 TCGATTGTTTCAGCCTTGTTATGT 59.240 37.500 0.00 0.00 0.00 2.29
603 606 5.067023 TGCGATAATGGAATGTTGCATACAA 59.933 36.000 0.06 0.00 40.89 2.41
620 623 1.065491 ACAACTATTCGATGCAGGGCA 60.065 47.619 0.00 0.00 44.86 5.36
685 690 5.933187 ATGTGACACGTTAGCACAAATTA 57.067 34.783 15.95 0.00 44.62 1.40
729 950 1.000955 CGATAAGTAAGCATCCCCGCT 59.999 52.381 0.00 0.00 46.67 5.52
733 954 0.105658 AGTAAGCATCCCCGCTAGGA 60.106 55.000 0.00 0.00 42.89 2.94
876 1780 5.745294 CGAGGATGCTTGGAAATTTACATTG 59.255 40.000 3.35 1.90 0.00 2.82
988 1966 1.288508 AATGCTATGGCTCCCACCCA 61.289 55.000 1.68 0.00 35.80 4.51
1029 2007 2.094675 CCTACCTTCCAAAGCCACATG 58.905 52.381 0.00 0.00 0.00 3.21
1226 2220 2.355481 GTGACCACCGTCGTGACC 60.355 66.667 0.00 0.00 43.14 4.02
1304 2298 2.581354 CAGAAGACGGCCTCCCTG 59.419 66.667 0.00 4.76 0.00 4.45
1428 2422 3.545481 CGCAGAAGCACGGCTACG 61.545 66.667 0.00 0.00 38.25 3.51
1429 2423 3.188786 GCAGAAGCACGGCTACGG 61.189 66.667 0.00 0.00 46.48 4.02
1463 2457 0.455464 CGTCGTCGTACCAGCATGAA 60.455 55.000 0.00 0.00 39.69 2.57
1818 2812 0.471780 TCTCCACCAGGACAGCAAGA 60.472 55.000 0.00 0.00 39.61 3.02
1839 2833 1.450134 CAGAAGCATGGCTACGGCA 60.450 57.895 0.00 0.00 38.25 5.69
2044 3269 3.740397 CGACGCCGTCCACCACTA 61.740 66.667 12.26 0.00 0.00 2.74
2045 3270 2.126189 GACGCCGTCCACCACTAC 60.126 66.667 5.81 0.00 0.00 2.73
2180 3411 2.046314 GGGCAGAAGGCTTACGCA 60.046 61.111 18.71 0.00 44.01 5.24
2209 3554 1.692749 ATGGCGGAGGGTACACCAT 60.693 57.895 0.00 0.00 43.89 3.55
2300 3726 2.386660 GCTCGTCCAGAAGCAGCAC 61.387 63.158 0.00 0.00 0.00 4.40
2301 3727 2.049156 TCGTCCAGAAGCAGCACG 60.049 61.111 0.00 0.00 0.00 5.34
2302 3728 3.114616 CGTCCAGAAGCAGCACGG 61.115 66.667 0.00 0.00 0.00 4.94
2303 3729 2.743928 GTCCAGAAGCAGCACGGG 60.744 66.667 0.00 0.00 0.00 5.28
2304 3730 4.020617 TCCAGAAGCAGCACGGGG 62.021 66.667 0.00 0.00 0.00 5.73
2305 3731 4.020617 CCAGAAGCAGCACGGGGA 62.021 66.667 0.00 0.00 0.00 4.81
2649 4198 4.037208 CGTGATACAATCCTACCTACGGTT 59.963 45.833 0.00 0.00 37.09 4.44
2650 4199 5.239306 CGTGATACAATCCTACCTACGGTTA 59.761 44.000 0.00 0.00 37.09 2.85
2651 4200 6.442112 GTGATACAATCCTACCTACGGTTAC 58.558 44.000 0.00 0.00 37.09 2.50
2653 4202 2.689983 ACAATCCTACCTACGGTTACGG 59.310 50.000 0.00 0.00 46.48 4.02
2654 4203 2.689983 CAATCCTACCTACGGTTACGGT 59.310 50.000 0.55 0.55 46.48 4.83
2834 4394 0.740868 GCGCCTCACTCTGCAACATA 60.741 55.000 0.00 0.00 0.00 2.29
2835 4395 1.002366 CGCCTCACTCTGCAACATAC 58.998 55.000 0.00 0.00 0.00 2.39
2836 4396 1.672737 CGCCTCACTCTGCAACATACA 60.673 52.381 0.00 0.00 0.00 2.29
2837 4397 2.636830 GCCTCACTCTGCAACATACAT 58.363 47.619 0.00 0.00 0.00 2.29
2917 4478 4.694760 AACGTTTGGTTCCTAGGTACTT 57.305 40.909 17.10 1.17 34.60 2.24
2919 4480 3.899980 ACGTTTGGTTCCTAGGTACTTCT 59.100 43.478 17.10 0.00 41.75 2.85
2920 4481 4.346127 ACGTTTGGTTCCTAGGTACTTCTT 59.654 41.667 17.10 0.00 41.75 2.52
2921 4482 4.928020 CGTTTGGTTCCTAGGTACTTCTTC 59.072 45.833 17.10 2.21 41.75 2.87
2922 4483 5.279356 CGTTTGGTTCCTAGGTACTTCTTCT 60.279 44.000 17.10 0.00 41.75 2.85
2923 4484 5.997384 TTGGTTCCTAGGTACTTCTTCTC 57.003 43.478 17.10 0.90 41.75 2.87
2924 4485 5.272405 TGGTTCCTAGGTACTTCTTCTCT 57.728 43.478 17.10 0.00 41.75 3.10
2925 4486 5.262804 TGGTTCCTAGGTACTTCTTCTCTC 58.737 45.833 17.10 0.00 41.75 3.20
2926 4487 4.646040 GGTTCCTAGGTACTTCTTCTCTCC 59.354 50.000 17.10 0.00 41.75 3.71
2927 4488 4.523168 TCCTAGGTACTTCTTCTCTCCC 57.477 50.000 9.08 0.00 41.75 4.30
2928 4489 3.856813 TCCTAGGTACTTCTTCTCTCCCA 59.143 47.826 9.08 0.00 41.75 4.37
2929 4490 4.294168 TCCTAGGTACTTCTTCTCTCCCAA 59.706 45.833 9.08 0.00 41.75 4.12
2930 4491 5.024118 CCTAGGTACTTCTTCTCTCCCAAA 58.976 45.833 0.00 0.00 41.75 3.28
2931 4492 5.484290 CCTAGGTACTTCTTCTCTCCCAAAA 59.516 44.000 0.00 0.00 41.75 2.44
2932 4493 6.157123 CCTAGGTACTTCTTCTCTCCCAAAAT 59.843 42.308 0.00 0.00 41.75 1.82
2933 4494 7.344871 CCTAGGTACTTCTTCTCTCCCAAAATA 59.655 40.741 0.00 0.00 41.75 1.40
2934 4495 7.757242 AGGTACTTCTTCTCTCCCAAAATAT 57.243 36.000 0.00 0.00 27.25 1.28
2935 4496 8.855804 AGGTACTTCTTCTCTCCCAAAATATA 57.144 34.615 0.00 0.00 27.25 0.86
2936 4497 9.280456 AGGTACTTCTTCTCTCCCAAAATATAA 57.720 33.333 0.00 0.00 27.25 0.98
2937 4498 9.901172 GGTACTTCTTCTCTCCCAAAATATAAA 57.099 33.333 0.00 0.00 0.00 1.40
2941 4502 9.774742 CTTCTTCTCTCCCAAAATATAAAAACG 57.225 33.333 0.00 0.00 0.00 3.60
2942 4503 8.857694 TCTTCTCTCCCAAAATATAAAAACGT 57.142 30.769 0.00 0.00 0.00 3.99
2943 4504 9.292195 TCTTCTCTCCCAAAATATAAAAACGTT 57.708 29.630 0.00 0.00 0.00 3.99
2944 4505 9.908152 CTTCTCTCCCAAAATATAAAAACGTTT 57.092 29.630 7.96 7.96 0.00 3.60
2946 4507 9.902196 TCTCTCCCAAAATATAAAAACGTTTTC 57.098 29.630 25.37 0.00 0.00 2.29
2947 4508 9.908152 CTCTCCCAAAATATAAAAACGTTTTCT 57.092 29.630 25.37 17.76 0.00 2.52
2960 4521 8.707938 AAAAACGTTTTCTACACTACACTAGT 57.292 30.769 25.37 2.41 40.28 2.57
2961 4522 9.801873 AAAAACGTTTTCTACACTACACTAGTA 57.198 29.630 25.37 0.00 37.23 1.82
2962 4523 9.971922 AAAACGTTTTCTACACTACACTAGTAT 57.028 29.630 20.26 0.00 37.23 2.12
3007 4568 9.965824 GAATGAAGTCTGATTTAAACCTTGAAA 57.034 29.630 0.00 0.00 0.00 2.69
3022 4583 5.690865 ACCTTGAAATTGTAGAGGTTGTCA 58.309 37.500 0.00 0.00 37.44 3.58
3158 4733 8.914011 AGCAGGAGAAGTAAATAACAAGTTTTT 58.086 29.630 0.00 0.00 0.00 1.94
3379 5692 7.931407 CCTAAAAAGGCATCAAGGTTAAAAACT 59.069 33.333 0.00 0.00 0.00 2.66
3383 5696 5.390387 AGGCATCAAGGTTAAAAACTACCA 58.610 37.500 0.00 0.00 36.87 3.25
3429 5743 0.252057 TCAGGGATTGGACGTGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
3438 5752 3.880047 TGGACGTGAGGATTCGTTTAT 57.120 42.857 0.00 0.00 40.39 1.40
3502 5816 6.956102 TTTTTATATTATAGGGCGGAGGGA 57.044 37.500 0.00 0.00 0.00 4.20
3503 5817 6.555463 TTTTATATTATAGGGCGGAGGGAG 57.445 41.667 0.00 0.00 0.00 4.30
3504 5818 3.778622 ATATTATAGGGCGGAGGGAGT 57.221 47.619 0.00 0.00 0.00 3.85
3505 5819 4.894252 ATATTATAGGGCGGAGGGAGTA 57.106 45.455 0.00 0.00 0.00 2.59
3506 5820 2.299326 TTATAGGGCGGAGGGAGTAC 57.701 55.000 0.00 0.00 0.00 2.73
3507 5821 0.407139 TATAGGGCGGAGGGAGTACC 59.593 60.000 0.00 0.00 40.67 3.34
3637 5951 9.788960 ACAAAACTAAAATCACTCTTTGACTTC 57.211 29.630 0.00 0.00 36.92 3.01
3641 5955 9.620259 AACTAAAATCACTCTTTGACTTCTTCT 57.380 29.630 0.00 0.00 36.92 2.85
3642 5956 9.620259 ACTAAAATCACTCTTTGACTTCTTCTT 57.380 29.630 0.00 0.00 36.92 2.52
3645 5959 9.578439 AAAATCACTCTTTGACTTCTTCTTTTG 57.422 29.630 0.00 0.00 36.92 2.44
3686 6000 4.387862 CGGTCAAAATAGTGTGGTAGTGAC 59.612 45.833 0.00 0.00 34.71 3.67
3866 6181 9.219603 CATATGGGTGTATATACAACAAGGAAG 57.780 37.037 27.77 12.03 45.51 3.46
3871 6186 7.068226 GGGTGTATATACAACAAGGAAGCAAAT 59.932 37.037 27.77 0.00 45.51 2.32
3881 6196 5.793817 ACAAGGAAGCAAATTGTATTTCCC 58.206 37.500 16.52 3.84 38.42 3.97
3909 6224 3.083293 GCTTCCGCTATACTAGTAGGCT 58.917 50.000 20.78 0.00 0.00 4.58
3920 6235 3.300388 ACTAGTAGGCTGCTGCTATTCA 58.700 45.455 15.86 0.00 39.59 2.57
3937 6252 6.769341 TGCTATTCATGAACAATACTGAGCAT 59.231 34.615 11.07 0.00 0.00 3.79
3940 6255 9.264719 CTATTCATGAACAATACTGAGCATGTA 57.735 33.333 11.07 0.00 38.07 2.29
3941 6256 7.920160 TTCATGAACAATACTGAGCATGTAA 57.080 32.000 3.38 0.00 38.07 2.41
3942 6257 7.307493 TCATGAACAATACTGAGCATGTAAC 57.693 36.000 0.00 0.00 38.07 2.50
3943 6258 6.878389 TCATGAACAATACTGAGCATGTAACA 59.122 34.615 0.00 0.00 38.07 2.41
3944 6259 7.553760 TCATGAACAATACTGAGCATGTAACAT 59.446 33.333 0.00 0.00 38.07 2.71
3945 6260 8.829612 CATGAACAATACTGAGCATGTAACATA 58.170 33.333 0.00 0.00 35.18 2.29
3950 6265 4.844349 ACTGAGCATGTAACATAAGGGT 57.156 40.909 0.00 0.00 0.00 4.34
3982 6299 1.248101 AACCGGCAAATTTCCTCCCG 61.248 55.000 0.00 8.39 38.71 5.14
3987 6304 1.471501 GGCAAATTTCCTCCCGCATTC 60.472 52.381 0.00 0.00 0.00 2.67
4028 6345 0.961019 GGCATCTTCAACTGCAACCA 59.039 50.000 0.00 0.00 40.18 3.67
4050 6367 1.472480 CAAATTTTCTCCCGCATCCGT 59.528 47.619 0.00 0.00 0.00 4.69
4065 6382 2.725641 CGTCCGCGGACATGGATA 59.274 61.111 46.26 16.89 44.77 2.59
4067 6384 1.660575 GTCCGCGGACATGGATACG 60.661 63.158 44.88 8.87 44.02 3.06
4073 6390 1.371558 GGACATGGATACGGGAGGC 59.628 63.158 0.00 0.00 42.51 4.70
4076 6393 3.626924 ATGGATACGGGAGGCCGC 61.627 66.667 0.00 0.00 42.51 6.53
4080 6397 3.168528 ATACGGGAGGCCGCCATT 61.169 61.111 28.06 15.34 36.58 3.16
4085 6402 3.508840 GGAGGCCGCCATTCAACG 61.509 66.667 22.24 0.00 0.00 4.10
4088 6405 4.481112 GGCCGCCATTCAACGCTG 62.481 66.667 3.91 0.00 0.00 5.18
4101 6418 1.089481 AACGCTGCCCACATACATCG 61.089 55.000 0.00 0.00 0.00 3.84
4124 6441 4.173256 GGCCAACAATTCAAACTAATCGG 58.827 43.478 0.00 0.00 0.00 4.18
4143 6460 3.059188 TCGGAAGAAATTCGCTCAAACAC 60.059 43.478 1.67 0.00 37.03 3.32
4147 6464 2.223377 AGAAATTCGCTCAAACACGACC 59.777 45.455 0.00 0.00 38.17 4.79
4168 6485 6.201997 CGACCGGATTTCATATAAACATGACA 59.798 38.462 9.46 0.00 34.69 3.58
4169 6486 7.496529 ACCGGATTTCATATAAACATGACAG 57.503 36.000 9.46 0.00 34.69 3.51
4205 6522 7.578310 TTTATATCAACTACGGTGCTAGTCT 57.422 36.000 0.00 0.00 0.00 3.24
4207 6524 2.511659 TCAACTACGGTGCTAGTCTGT 58.488 47.619 0.00 6.73 0.00 3.41
4210 6527 2.085320 ACTACGGTGCTAGTCTGTCTG 58.915 52.381 5.14 3.86 0.00 3.51
4275 6592 2.350895 CCCGTGTCAGGCCATGAA 59.649 61.111 5.01 0.00 40.43 2.57
4286 6603 0.250513 GGCCATGAACCTCGAGAACT 59.749 55.000 15.71 0.00 0.00 3.01
4287 6604 1.480954 GGCCATGAACCTCGAGAACTA 59.519 52.381 15.71 0.00 0.00 2.24
4317 6634 4.459089 GTCCAGCTCCACCTCGGC 62.459 72.222 0.00 0.00 33.14 5.54
4336 6653 2.720134 GCTCTCCAGCTCCGCTTCT 61.720 63.158 0.00 0.00 43.09 2.85
4337 6654 1.141449 CTCTCCAGCTCCGCTTCTG 59.859 63.158 0.00 0.00 36.40 3.02
4376 6693 1.070289 ACCCGAGAAGTGAAGTTGTCC 59.930 52.381 0.00 0.00 0.00 4.02
4411 6728 1.226773 CAAGCAGCTAATTGGCCGC 60.227 57.895 13.63 13.63 36.03 6.53
4463 6780 3.003763 AGGGGAGGAGCGGTGTTC 61.004 66.667 0.00 0.00 0.00 3.18
4468 6785 1.079057 GAGGAGCGGTGTTCTTCCC 60.079 63.158 0.00 0.00 0.00 3.97
4473 6790 2.047560 CGGTGTTCTTCCCGGGAC 60.048 66.667 26.87 13.65 40.54 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.701651 CCAATAGAAAACTGACATGAGGCA 59.298 41.667 0.00 0.00 0.00 4.75
19 20 4.943705 TCCAATAGAAAACTGACATGAGGC 59.056 41.667 0.00 0.00 0.00 4.70
24 25 6.947733 TCCACAATCCAATAGAAAACTGACAT 59.052 34.615 0.00 0.00 0.00 3.06
30 31 6.753744 GCATCTTCCACAATCCAATAGAAAAC 59.246 38.462 0.00 0.00 0.00 2.43
60 61 1.607148 GTGGCAAAGTAAGGTGACCAC 59.393 52.381 3.63 0.00 35.94 4.16
61 62 1.477923 GGTGGCAAAGTAAGGTGACCA 60.478 52.381 3.63 0.00 0.00 4.02
62 63 1.202891 AGGTGGCAAAGTAAGGTGACC 60.203 52.381 0.00 0.00 0.00 4.02
64 65 2.054799 AGAGGTGGCAAAGTAAGGTGA 58.945 47.619 0.00 0.00 0.00 4.02
78 79 3.260380 ACCAATCTGTGAGAGAAGAGGTG 59.740 47.826 1.28 0.00 33.95 4.00
181 182 9.695526 TTCAAATCTGGACAATACATTCTTTTG 57.304 29.630 0.00 0.00 0.00 2.44
189 190 6.433716 TCTTGCATTCAAATCTGGACAATACA 59.566 34.615 0.00 0.00 0.00 2.29
191 192 7.649533 ATCTTGCATTCAAATCTGGACAATA 57.350 32.000 0.00 0.00 0.00 1.90
192 193 5.988310 TCTTGCATTCAAATCTGGACAAT 57.012 34.783 0.00 0.00 0.00 2.71
194 195 5.357878 GGTATCTTGCATTCAAATCTGGACA 59.642 40.000 0.00 0.00 0.00 4.02
198 199 5.125900 TGGTGGTATCTTGCATTCAAATCTG 59.874 40.000 0.00 0.00 0.00 2.90
199 200 5.263599 TGGTGGTATCTTGCATTCAAATCT 58.736 37.500 0.00 0.00 0.00 2.40
200 201 5.126061 ACTGGTGGTATCTTGCATTCAAATC 59.874 40.000 0.00 0.00 0.00 2.17
201 202 5.018809 ACTGGTGGTATCTTGCATTCAAAT 58.981 37.500 0.00 0.00 0.00 2.32
205 206 3.129287 CCAACTGGTGGTATCTTGCATTC 59.871 47.826 2.79 0.00 43.20 2.67
234 235 5.124457 ACATCAATAATCAGCTGACACAACC 59.876 40.000 20.97 0.00 0.00 3.77
270 271 1.371558 GGACACCTTGTTCGAGCCT 59.628 57.895 0.00 0.00 0.00 4.58
293 294 0.820226 TTCGCCATCTCAGGAGTCAG 59.180 55.000 0.00 0.00 0.00 3.51
299 300 0.179065 TCTGCATTCGCCATCTCAGG 60.179 55.000 0.00 0.00 37.32 3.86
300 301 1.598132 CTTCTGCATTCGCCATCTCAG 59.402 52.381 0.00 0.00 37.32 3.35
325 326 4.524328 CAGGGTTTAGCAAAGATTCAACCT 59.476 41.667 0.00 0.00 35.09 3.50
333 334 2.373335 TTGCCAGGGTTTAGCAAAGA 57.627 45.000 0.00 0.00 43.14 2.52
337 338 2.300956 TTGATTGCCAGGGTTTAGCA 57.699 45.000 0.00 0.00 33.97 3.49
338 339 3.524541 CAATTGATTGCCAGGGTTTAGC 58.475 45.455 0.00 0.00 0.00 3.09
373 374 2.478872 TCCTCCCACAGAAGATAGGG 57.521 55.000 0.00 0.00 42.86 3.53
383 384 1.065491 CATGACCGATTTCCTCCCACA 60.065 52.381 0.00 0.00 0.00 4.17
393 394 1.487976 AGAGTCCATGCATGACCGATT 59.512 47.619 28.31 13.17 0.00 3.34
395 396 1.683385 CTAGAGTCCATGCATGACCGA 59.317 52.381 28.31 13.85 0.00 4.69
397 398 1.765314 ACCTAGAGTCCATGCATGACC 59.235 52.381 28.31 16.71 0.00 4.02
399 400 1.139654 GCACCTAGAGTCCATGCATGA 59.860 52.381 28.31 11.26 36.30 3.07
413 415 1.071699 GTCTCCCAACAGTTGCACCTA 59.928 52.381 7.88 0.00 0.00 3.08
423 425 0.037697 CGATTGACCGTCTCCCAACA 60.038 55.000 0.00 0.00 0.00 3.33
425 427 1.189524 ACCGATTGACCGTCTCCCAA 61.190 55.000 0.00 0.00 0.00 4.12
433 435 2.136728 TGTGTTGTAACCGATTGACCG 58.863 47.619 0.00 0.00 0.00 4.79
480 483 4.330250 AGAACACATGACCATTCCAAGAG 58.670 43.478 0.00 0.00 0.00 2.85
483 486 5.507149 CGAAAAGAACACATGACCATTCCAA 60.507 40.000 0.00 0.00 0.00 3.53
484 487 4.023279 CGAAAAGAACACATGACCATTCCA 60.023 41.667 0.00 0.00 0.00 3.53
485 488 4.215399 TCGAAAAGAACACATGACCATTCC 59.785 41.667 0.00 0.00 0.00 3.01
486 489 5.356882 TCGAAAAGAACACATGACCATTC 57.643 39.130 0.00 0.00 0.00 2.67
487 490 5.964958 ATCGAAAAGAACACATGACCATT 57.035 34.783 0.00 0.00 0.00 3.16
491 494 6.690957 TGAAACAATCGAAAAGAACACATGAC 59.309 34.615 0.00 0.00 0.00 3.06
517 520 8.863049 CAAGATCAATTAAACACATAACAAGGC 58.137 33.333 0.00 0.00 0.00 4.35
528 531 8.421249 AAATGGAGGACAAGATCAATTAAACA 57.579 30.769 0.00 0.00 0.00 2.83
685 690 9.599866 TCGTATCTTACAGTGAAATGATTTGAT 57.400 29.630 0.00 0.00 0.00 2.57
729 950 2.039879 GGCCTGTTTTCTTCCACTCCTA 59.960 50.000 0.00 0.00 0.00 2.94
733 954 2.158475 TGATGGCCTGTTTTCTTCCACT 60.158 45.455 3.32 0.00 0.00 4.00
1029 2007 2.730094 CTTTGTGCTGGTGTGCCC 59.270 61.111 0.00 0.00 0.00 5.36
1226 2220 0.879400 GGCTCATGTGGCTGATCTCG 60.879 60.000 13.55 0.00 0.00 4.04
1425 2419 2.126228 CTTCTGTTCGCCGCCGTA 60.126 61.111 0.00 0.00 35.54 4.02
1436 2430 1.208614 GTACGACGACGCCTTCTGT 59.791 57.895 7.30 0.00 43.96 3.41
1478 2472 1.741770 GTGGTGAAGGGCGCTGTAG 60.742 63.158 7.64 0.00 0.00 2.74
1487 2481 1.291877 CGGAGCTTTCGTGGTGAAGG 61.292 60.000 0.00 0.00 37.99 3.46
1489 2483 1.444250 ACGGAGCTTTCGTGGTGAA 59.556 52.632 13.88 0.00 39.55 3.18
1490 2484 3.134879 ACGGAGCTTTCGTGGTGA 58.865 55.556 13.88 0.00 39.55 4.02
1818 2812 0.107456 CCGTAGCCATGCTTCTGGAT 59.893 55.000 4.93 1.27 40.44 3.41
1839 2833 1.815421 CATAGCCGTGCGCCTTCTT 60.815 57.895 4.18 0.00 38.78 2.52
1856 2850 3.378602 TACGCCTTCTGCTCGCCA 61.379 61.111 0.00 0.00 38.05 5.69
2043 3268 0.391228 TTCTGCACCGAGCTGTTGTA 59.609 50.000 0.00 0.00 45.94 2.41
2044 3269 0.882042 CTTCTGCACCGAGCTGTTGT 60.882 55.000 0.00 0.00 45.94 3.32
2045 3270 1.864862 CTTCTGCACCGAGCTGTTG 59.135 57.895 0.00 0.00 45.94 3.33
2066 3291 2.764547 GCCTTCTCCCCGTAGCCT 60.765 66.667 0.00 0.00 0.00 4.58
2180 3411 2.512286 CCGCCATCAGCATCGTGT 60.512 61.111 0.00 0.00 44.04 4.49
2194 3425 1.092348 GAAAATGGTGTACCCTCCGC 58.908 55.000 0.00 0.00 34.29 5.54
2209 3554 2.739287 CGCCGCCGTGGTAGAAAA 60.739 61.111 0.00 0.00 41.21 2.29
2454 3904 3.403558 GCCCACCACCTCCTCCTC 61.404 72.222 0.00 0.00 0.00 3.71
2649 4198 2.022195 GAGCAGATAGGTGTCACCGTA 58.978 52.381 16.44 9.57 44.90 4.02
2650 4199 0.818296 GAGCAGATAGGTGTCACCGT 59.182 55.000 16.44 9.40 44.90 4.83
2651 4200 0.817654 TGAGCAGATAGGTGTCACCG 59.182 55.000 16.44 2.97 44.90 4.94
2652 4201 1.550524 TGTGAGCAGATAGGTGTCACC 59.449 52.381 14.68 14.68 37.35 4.02
2653 4202 3.193263 CATGTGAGCAGATAGGTGTCAC 58.807 50.000 0.00 0.00 38.41 3.67
2654 4203 2.419159 GCATGTGAGCAGATAGGTGTCA 60.419 50.000 0.00 0.00 0.00 3.58
2834 4394 1.737029 CGACGACCATCAAGAGCATGT 60.737 52.381 0.00 0.00 0.00 3.21
2835 4395 0.926155 CGACGACCATCAAGAGCATG 59.074 55.000 0.00 0.00 0.00 4.06
2836 4396 0.532573 ACGACGACCATCAAGAGCAT 59.467 50.000 0.00 0.00 0.00 3.79
2837 4397 0.388520 CACGACGACCATCAAGAGCA 60.389 55.000 0.00 0.00 0.00 4.26
2907 4468 4.252570 TGGGAGAGAAGAAGTACCTAGG 57.747 50.000 7.41 7.41 0.00 3.02
2910 4471 7.757242 ATATTTTGGGAGAGAAGAAGTACCT 57.243 36.000 0.00 0.00 0.00 3.08
2916 4477 9.292195 ACGTTTTTATATTTTGGGAGAGAAGAA 57.708 29.630 0.00 0.00 0.00 2.52
2917 4478 8.857694 ACGTTTTTATATTTTGGGAGAGAAGA 57.142 30.769 0.00 0.00 0.00 2.87
2920 4481 9.902196 GAAAACGTTTTTATATTTTGGGAGAGA 57.098 29.630 25.86 0.00 0.00 3.10
2921 4482 9.908152 AGAAAACGTTTTTATATTTTGGGAGAG 57.092 29.630 25.86 0.00 0.00 3.20
2934 4495 9.801873 ACTAGTGTAGTGTAGAAAACGTTTTTA 57.198 29.630 25.86 16.64 37.69 1.52
2935 4496 8.707938 ACTAGTGTAGTGTAGAAAACGTTTTT 57.292 30.769 25.86 17.52 37.69 1.94
2936 4497 9.971922 ATACTAGTGTAGTGTAGAAAACGTTTT 57.028 29.630 25.46 25.46 39.81 2.43
2978 4539 9.918630 CAAGGTTTAAATCAGACTTCATTCAAT 57.081 29.630 0.43 0.00 0.00 2.57
2979 4540 9.130661 TCAAGGTTTAAATCAGACTTCATTCAA 57.869 29.630 0.43 0.00 0.00 2.69
2980 4541 8.690203 TCAAGGTTTAAATCAGACTTCATTCA 57.310 30.769 0.43 0.00 0.00 2.57
3007 4568 5.209818 TCGTTTCTGACAACCTCTACAAT 57.790 39.130 0.00 0.00 0.00 2.71
3022 4583 7.215085 GGTATATATTGTGAGGGTTCGTTTCT 58.785 38.462 0.00 0.00 0.00 2.52
3379 5692 6.039415 ACCCTATACTCTTTGATCCTGGTA 57.961 41.667 0.00 0.00 0.00 3.25
3383 5696 6.778559 GTCTGTACCCTATACTCTTTGATCCT 59.221 42.308 0.00 0.00 0.00 3.24
3429 5743 8.915036 AGATTGTAGAGGTAGTCATAAACGAAT 58.085 33.333 0.00 0.00 0.00 3.34
3438 5752 5.580998 ACCTTGAGATTGTAGAGGTAGTCA 58.419 41.667 0.00 0.00 38.88 3.41
3481 5795 5.596763 ACTCCCTCCGCCCTATAATATAAA 58.403 41.667 0.00 0.00 0.00 1.40
3482 5796 5.216665 ACTCCCTCCGCCCTATAATATAA 57.783 43.478 0.00 0.00 0.00 0.98
3483 5797 4.894252 ACTCCCTCCGCCCTATAATATA 57.106 45.455 0.00 0.00 0.00 0.86
3484 5798 3.778622 ACTCCCTCCGCCCTATAATAT 57.221 47.619 0.00 0.00 0.00 1.28
3485 5799 3.309410 GGTACTCCCTCCGCCCTATAATA 60.309 52.174 0.00 0.00 0.00 0.98
3486 5800 2.559252 GGTACTCCCTCCGCCCTATAAT 60.559 54.545 0.00 0.00 0.00 1.28
3487 5801 1.203100 GGTACTCCCTCCGCCCTATAA 60.203 57.143 0.00 0.00 0.00 0.98
3488 5802 0.407139 GGTACTCCCTCCGCCCTATA 59.593 60.000 0.00 0.00 0.00 1.31
3489 5803 1.155624 GGTACTCCCTCCGCCCTAT 59.844 63.158 0.00 0.00 0.00 2.57
3490 5804 1.587522 AAGGTACTCCCTCCGCCCTA 61.588 60.000 0.00 0.00 45.47 3.53
3491 5805 1.587522 TAAGGTACTCCCTCCGCCCT 61.588 60.000 0.00 0.00 45.47 5.19
3492 5806 0.471401 ATAAGGTACTCCCTCCGCCC 60.471 60.000 0.00 0.00 45.47 6.13
3493 5807 2.299326 TATAAGGTACTCCCTCCGCC 57.701 55.000 0.00 0.00 45.47 6.13
3494 5808 2.496470 CCATATAAGGTACTCCCTCCGC 59.504 54.545 0.00 0.00 45.47 5.54
3495 5809 4.043608 TCCATATAAGGTACTCCCTCCG 57.956 50.000 0.00 0.00 45.47 4.63
3496 5810 6.758806 TTTTCCATATAAGGTACTCCCTCC 57.241 41.667 0.00 0.00 45.47 4.30
3653 5967 7.096230 CCACACTATTTTGACCGAAAATTTGTC 60.096 37.037 0.00 0.00 40.73 3.18
3835 6150 8.679344 TGTTGTATATACACCCATATGAGGAT 57.321 34.615 15.20 5.32 35.64 3.24
3836 6151 8.499288 TTGTTGTATATACACCCATATGAGGA 57.501 34.615 15.20 0.00 35.64 3.71
3838 6153 8.593679 TCCTTGTTGTATATACACCCATATGAG 58.406 37.037 15.20 8.87 35.64 2.90
3839 6154 8.499288 TCCTTGTTGTATATACACCCATATGA 57.501 34.615 15.20 8.81 35.64 2.15
3840 6155 9.219603 CTTCCTTGTTGTATATACACCCATATG 57.780 37.037 15.20 0.00 35.64 1.78
3841 6156 7.883311 GCTTCCTTGTTGTATATACACCCATAT 59.117 37.037 15.20 0.00 35.64 1.78
3842 6157 7.147461 TGCTTCCTTGTTGTATATACACCCATA 60.147 37.037 15.20 0.00 35.64 2.74
3843 6158 6.062095 GCTTCCTTGTTGTATATACACCCAT 58.938 40.000 15.20 0.00 35.64 4.00
3844 6159 5.045505 TGCTTCCTTGTTGTATATACACCCA 60.046 40.000 15.20 11.83 35.64 4.51
3866 6181 3.020984 TCCCGAGGGAAATACAATTTGC 58.979 45.455 8.71 0.00 42.05 3.68
3871 6186 1.580059 AGCTCCCGAGGGAAATACAA 58.420 50.000 12.54 0.00 44.66 2.41
3909 6224 6.114767 TCAGTATTGTTCATGAATAGCAGCA 58.885 36.000 12.12 0.47 0.00 4.41
3920 6235 7.870509 ATGTTACATGCTCAGTATTGTTCAT 57.129 32.000 0.00 0.00 0.00 2.57
3937 6252 6.631766 GCAGTTGGAGATACCCTTATGTTACA 60.632 42.308 0.00 0.00 38.00 2.41
3940 6255 4.227300 TGCAGTTGGAGATACCCTTATGTT 59.773 41.667 0.00 0.00 38.00 2.71
3941 6256 3.780294 TGCAGTTGGAGATACCCTTATGT 59.220 43.478 0.00 0.00 38.00 2.29
3942 6257 4.422073 TGCAGTTGGAGATACCCTTATG 57.578 45.455 0.00 0.00 38.00 1.90
3943 6258 4.385310 GGTTGCAGTTGGAGATACCCTTAT 60.385 45.833 0.00 0.00 38.00 1.73
3944 6259 3.054655 GGTTGCAGTTGGAGATACCCTTA 60.055 47.826 0.00 0.00 38.00 2.69
3945 6260 2.290960 GGTTGCAGTTGGAGATACCCTT 60.291 50.000 0.00 0.00 38.00 3.95
3950 6265 0.392461 GCCGGTTGCAGTTGGAGATA 60.392 55.000 1.90 0.00 40.77 1.98
3997 6314 0.541863 AAGATGCCCTTACGGACCAG 59.458 55.000 0.00 0.00 32.24 4.00
4003 6320 1.398390 GCAGTTGAAGATGCCCTTACG 59.602 52.381 0.00 0.00 36.41 3.18
4004 6321 2.436417 TGCAGTTGAAGATGCCCTTAC 58.564 47.619 0.48 0.00 41.85 2.34
4028 6345 1.478105 GGATGCGGGAGAAAATTTGCT 59.522 47.619 0.00 0.00 0.00 3.91
4050 6367 2.725641 CGTATCCATGTCCGCGGA 59.274 61.111 27.28 27.28 35.27 5.54
4054 6371 1.666011 CCTCCCGTATCCATGTCCG 59.334 63.158 0.00 0.00 0.00 4.79
4067 6384 3.140814 GTTGAATGGCGGCCTCCC 61.141 66.667 21.46 5.77 0.00 4.30
4073 6390 4.481112 GGCAGCGTTGAATGGCGG 62.481 66.667 2.38 0.00 31.92 6.13
4076 6393 1.597797 ATGTGGGCAGCGTTGAATGG 61.598 55.000 2.38 0.00 0.00 3.16
4080 6397 0.035534 ATGTATGTGGGCAGCGTTGA 60.036 50.000 2.38 0.00 0.00 3.18
4085 6402 1.893808 CCCGATGTATGTGGGCAGC 60.894 63.158 0.00 0.00 35.82 5.25
4101 6418 4.173256 CGATTAGTTTGAATTGTTGGCCC 58.827 43.478 0.00 0.00 0.00 5.80
4124 6441 3.900703 GTCGTGTTTGAGCGAATTTCTTC 59.099 43.478 0.00 0.00 38.91 2.87
4134 6451 0.872388 AAATCCGGTCGTGTTTGAGC 59.128 50.000 0.00 0.00 0.00 4.26
4135 6452 2.139917 TGAAATCCGGTCGTGTTTGAG 58.860 47.619 0.00 0.00 0.00 3.02
4143 6460 6.201997 TGTCATGTTTATATGAAATCCGGTCG 59.798 38.462 0.00 0.00 38.69 4.79
4174 6491 8.988934 AGCACCGTAGTTGATATAAATGTAATG 58.011 33.333 0.00 0.00 0.00 1.90
4197 6514 2.294449 ACTCCACAGACAGACTAGCA 57.706 50.000 0.00 0.00 0.00 3.49
4264 6581 0.614697 TCTCGAGGTTCATGGCCTGA 60.615 55.000 13.56 2.06 36.29 3.86
4286 6603 4.505039 GGAGCTGGACAAGGAGAAGTTTTA 60.505 45.833 0.00 0.00 0.00 1.52
4287 6604 3.481453 GAGCTGGACAAGGAGAAGTTTT 58.519 45.455 0.00 0.00 0.00 2.43
4336 6653 3.072468 CCGGAGGCGGAGGTTACA 61.072 66.667 0.00 0.00 46.14 2.41
4398 6715 1.893808 CATCGGCGGCCAATTAGCT 60.894 57.895 20.71 0.00 0.00 3.32
4411 6728 1.303236 TTGGTGGGCTCAACATCGG 60.303 57.895 4.39 0.00 40.73 4.18
4436 6753 1.612442 TCCTCCCCTCCCTTTGACG 60.612 63.158 0.00 0.00 0.00 4.35
4489 6806 3.728268 CGAAGAAGAGTAGTGCACGGTAG 60.728 52.174 12.01 0.00 0.00 3.18
4490 6807 2.161012 CGAAGAAGAGTAGTGCACGGTA 59.839 50.000 12.01 0.00 0.00 4.02
4494 6811 1.989165 CAGCGAAGAAGAGTAGTGCAC 59.011 52.381 9.40 9.40 0.00 4.57


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

AutoCloner maintained by Alex Coulton.