Multiple sequence alignment - TraesCS7B01G300700

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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 TraesCS7B01G300700 chr7B 100.000 5026 0 0 1 5026 537832267 537827242 0.000000e+00 9282.0
1 TraesCS7B01G300700 chr7B 83.630 2920 371 63 1034 3905 537795894 537793034 0.000000e+00 2645.0
2 TraesCS7B01G300700 chr7B 83.097 2396 357 30 1159 3537 537676791 537674427 0.000000e+00 2137.0
3 TraesCS7B01G300700 chr7B 77.011 2362 471 50 1130 3456 538243303 538245627 0.000000e+00 1288.0
4 TraesCS7B01G300700 chr7B 90.083 363 15 2 3908 4249 537792922 537792560 7.670000e-123 451.0
5 TraesCS7B01G300700 chr7B 91.003 289 15 7 4738 5026 537792190 537791913 3.670000e-101 379.0
6 TraesCS7B01G300700 chr7B 96.216 185 6 1 4842 5026 537673206 537673023 8.180000e-78 302.0
7 TraesCS7B01G300700 chr7B 88.393 224 17 4 4329 4550 537792560 537792344 1.390000e-65 261.0
8 TraesCS7B01G300700 chr7B 76.000 600 89 28 3647 4233 537674288 537673731 4.990000e-65 259.0
9 TraesCS7B01G300700 chr7B 75.116 430 89 12 3003 3423 538203573 538203153 8.590000e-43 185.0
10 TraesCS7B01G300700 chr7B 86.441 118 7 5 4611 4727 537792346 537792237 2.460000e-23 121.0
11 TraesCS7B01G300700 chr7A 95.162 3142 129 7 423 3560 580510122 580507000 0.000000e+00 4939.0
12 TraesCS7B01G300700 chr7A 83.044 2359 359 28 1193 3537 580474377 580472046 0.000000e+00 2102.0
13 TraesCS7B01G300700 chr7A 76.949 2360 475 50 1132 3456 580693947 580696272 0.000000e+00 1280.0
14 TraesCS7B01G300700 chr7A 90.311 289 16 6 4738 5026 580506601 580506325 7.950000e-98 368.0
15 TraesCS7B01G300700 chr7A 95.676 185 7 1 4842 5026 580470854 580470671 3.800000e-76 296.0
16 TraesCS7B01G300700 chr7A 75.459 599 91 32 3647 4229 580471912 580471354 1.810000e-59 241.0
17 TraesCS7B01G300700 chr7A 88.182 110 11 1 422 529 238551433 238551542 4.080000e-26 130.0
18 TraesCS7B01G300700 chr7A 90.769 65 1 1 3560 3624 580506924 580506865 1.160000e-11 82.4
19 TraesCS7B01G300700 chr7D 86.517 3664 377 62 423 4031 509615376 509611775 0.000000e+00 3921.0
20 TraesCS7B01G300700 chr7D 80.827 2999 452 72 1159 4103 509559686 509556757 0.000000e+00 2239.0
21 TraesCS7B01G300700 chr7D 94.595 259 13 1 87 345 563842128 563841871 2.820000e-107 399.0
22 TraesCS7B01G300700 chr7D 91.724 290 18 5 4738 5026 509611429 509611145 1.010000e-106 398.0
23 TraesCS7B01G300700 chr7D 93.514 185 11 1 4842 5026 509556099 509555916 1.780000e-69 274.0
24 TraesCS7B01G300700 chr7D 90.000 50 2 1 1448 1494 509563257 509563208 1.510000e-05 62.1
25 TraesCS7B01G300700 chr6B 91.667 348 29 0 1 348 477697064 477697411 2.720000e-132 483.0
26 TraesCS7B01G300700 chr4D 93.502 277 18 0 72 348 328701541 328701265 3.620000e-111 412.0
27 TraesCS7B01G300700 chr4D 87.850 107 11 1 422 526 354880752 354880646 1.900000e-24 124.0
28 TraesCS7B01G300700 chr6D 89.634 328 23 9 32 349 1557227 1557553 1.680000e-109 407.0
29 TraesCS7B01G300700 chr6D 89.720 107 9 1 422 526 344175868 344175762 8.780000e-28 135.0
30 TraesCS7B01G300700 chr3A 91.638 287 24 0 63 349 94091799 94091513 1.010000e-106 398.0
31 TraesCS7B01G300700 chr3A 96.471 85 3 0 4246 4330 303756876 303756792 1.890000e-29 141.0
32 TraesCS7B01G300700 chr3A 93.846 65 3 1 365 428 420834215 420834151 4.140000e-16 97.1
33 TraesCS7B01G300700 chr1D 91.608 286 23 1 65 350 43188002 43187718 1.310000e-105 394.0
34 TraesCS7B01G300700 chr5B 91.697 277 23 0 72 348 41393208 41392932 7.890000e-103 385.0
35 TraesCS7B01G300700 chr5B 83.240 179 21 8 29 199 478923934 478924111 6.740000e-34 156.0
36 TraesCS7B01G300700 chr5B 92.553 94 7 0 4246 4339 293544285 293544192 8.780000e-28 135.0
37 TraesCS7B01G300700 chr5B 91.304 46 4 0 371 416 565540446 565540401 4.200000e-06 63.9
38 TraesCS7B01G300700 chr3B 97.170 212 6 0 137 348 602784832 602785043 4.780000e-95 359.0
39 TraesCS7B01G300700 chr3B 92.157 255 16 2 95 348 85079387 85079136 1.720000e-94 357.0
40 TraesCS7B01G300700 chr2B 92.308 130 10 0 4842 4971 126731380 126731509 8.590000e-43 185.0
41 TraesCS7B01G300700 chr1A 96.739 92 3 0 4239 4330 511001601 511001510 2.420000e-33 154.0
42 TraesCS7B01G300700 chr1A 92.553 94 6 1 4243 4335 527694853 527694946 3.160000e-27 134.0
43 TraesCS7B01G300700 chr1A 88.182 110 8 3 422 527 117188193 117188301 5.280000e-25 126.0
44 TraesCS7B01G300700 chr4A 96.591 88 3 0 4244 4331 82849272 82849185 4.050000e-31 147.0
45 TraesCS7B01G300700 chr4A 88.679 106 10 1 423 526 490599658 490599553 1.470000e-25 128.0
46 TraesCS7B01G300700 chr2A 96.591 88 3 0 4243 4330 636911452 636911539 4.050000e-31 147.0
47 TraesCS7B01G300700 chr2A 97.647 85 2 0 4246 4330 690329336 690329420 4.050000e-31 147.0
48 TraesCS7B01G300700 chr5D 96.552 87 3 0 4244 4330 231356275 231356361 1.460000e-30 145.0
49 TraesCS7B01G300700 chr5D 93.846 65 3 1 365 428 321599548 321599612 4.140000e-16 97.1
50 TraesCS7B01G300700 chr6A 90.196 102 10 0 4238 4339 47680567 47680668 3.160000e-27 134.0
51 TraesCS7B01G300700 chr4B 89.720 107 8 2 422 526 510827706 510827811 3.160000e-27 134.0
52 TraesCS7B01G300700 chr4B 88.785 107 10 1 422 526 613321929 613321823 4.080000e-26 130.0
53 TraesCS7B01G300700 chr2D 93.878 49 3 0 366 414 544336278 544336230 1.940000e-09 75.0


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 TraesCS7B01G300700 chr7B 537827242 537832267 5025 True 9282.000000 9282 100.000000 1 5026 1 chr7B.!!$R1 5025
1 TraesCS7B01G300700 chr7B 538243303 538245627 2324 False 1288.000000 1288 77.011000 1130 3456 1 chr7B.!!$F1 2326
2 TraesCS7B01G300700 chr7B 537673023 537676791 3768 True 899.333333 2137 85.104333 1159 5026 3 chr7B.!!$R3 3867
3 TraesCS7B01G300700 chr7B 537791913 537795894 3981 True 771.400000 2645 87.910000 1034 5026 5 chr7B.!!$R4 3992
4 TraesCS7B01G300700 chr7A 580506325 580510122 3797 True 1796.466667 4939 92.080667 423 5026 3 chr7A.!!$R2 4603
5 TraesCS7B01G300700 chr7A 580693947 580696272 2325 False 1280.000000 1280 76.949000 1132 3456 1 chr7A.!!$F2 2324
6 TraesCS7B01G300700 chr7A 580470671 580474377 3706 True 879.666667 2102 84.726333 1193 5026 3 chr7A.!!$R1 3833
7 TraesCS7B01G300700 chr7D 509611145 509615376 4231 True 2159.500000 3921 89.120500 423 5026 2 chr7D.!!$R3 4603
8 TraesCS7B01G300700 chr7D 509555916 509563257 7341 True 858.366667 2239 88.113667 1159 5026 3 chr7D.!!$R2 3867

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
897 900 0.106708 ACATTGTCTGTGACTGCCGT 59.893 50.0 0.00 0.00 36.48 5.68 F
1513 3942 0.252467 CTCCAGTTCCTCACCTCCCT 60.252 60.0 0.00 0.00 0.00 4.20 F
2477 4944 0.445436 CTCGACATTCCTGTTGCTGC 59.555 55.0 0.00 0.00 36.80 5.25 F
3497 5964 0.104855 TTCCATCGATGAAGGGAGCG 59.895 55.0 26.86 7.31 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 4617 0.323178 TCGGCGGAGTAGTTCTTCCT 60.323 55.0 7.21 0.0 0.00 3.36 R
3467 5934 0.392060 TCGATGGAAGAGGTCGACGA 60.392 55.0 9.92 0.0 39.22 4.20 R
3550 6093 0.242017 AGAAACGCAGCAGATTTGGC 59.758 50.0 0.00 0.0 0.00 4.52 R
4669 7656 0.817654 GGGGCCGGAAAGAAAATGAG 59.182 55.0 5.05 0.0 0.00 2.90 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
157 158 2.561373 GCAGGGGCGAAAAGAACG 59.439 61.111 0.00 0.00 0.00 3.95
162 163 3.633951 GGCGAAAAGAACGACCGT 58.366 55.556 0.00 0.00 32.13 4.83
163 164 1.490258 GGCGAAAAGAACGACCGTC 59.510 57.895 0.00 0.00 32.13 4.79
164 165 1.127225 GCGAAAAGAACGACCGTCG 59.873 57.895 19.24 19.24 46.93 5.12
166 167 0.661187 CGAAAAGAACGACCGTCGGA 60.661 55.000 24.03 0.00 45.59 4.55
167 168 1.058404 GAAAAGAACGACCGTCGGAG 58.942 55.000 24.03 13.87 45.59 4.63
168 169 0.670162 AAAAGAACGACCGTCGGAGA 59.330 50.000 24.03 0.00 45.59 3.71
187 188 4.620937 GGGCGCGGGTAGGGATTC 62.621 72.222 8.83 0.00 34.27 2.52
188 189 4.963428 GGCGCGGGTAGGGATTCG 62.963 72.222 8.83 0.00 34.27 3.34
189 190 4.963428 GCGCGGGTAGGGATTCGG 62.963 72.222 8.83 0.00 34.27 4.30
190 191 4.295119 CGCGGGTAGGGATTCGGG 62.295 72.222 0.00 0.00 34.27 5.14
192 193 3.135814 CGGGTAGGGATTCGGGTC 58.864 66.667 0.00 0.00 0.00 4.46
193 194 1.759299 CGGGTAGGGATTCGGGTCA 60.759 63.158 0.00 0.00 0.00 4.02
194 195 1.745320 CGGGTAGGGATTCGGGTCAG 61.745 65.000 0.00 0.00 0.00 3.51
195 196 1.408453 GGGTAGGGATTCGGGTCAGG 61.408 65.000 0.00 0.00 0.00 3.86
197 198 1.764854 TAGGGATTCGGGTCAGGGC 60.765 63.158 0.00 0.00 0.00 5.19
198 199 4.191015 GGGATTCGGGTCAGGGCC 62.191 72.222 0.00 0.00 0.00 5.80
199 200 3.090532 GGATTCGGGTCAGGGCCT 61.091 66.667 0.00 0.00 0.00 5.19
200 201 2.680370 GGATTCGGGTCAGGGCCTT 61.680 63.158 1.32 0.00 0.00 4.35
201 202 1.153147 GATTCGGGTCAGGGCCTTC 60.153 63.158 1.32 0.00 0.00 3.46
203 204 1.281925 ATTCGGGTCAGGGCCTTCAT 61.282 55.000 1.32 0.00 0.00 2.57
204 205 1.910580 TTCGGGTCAGGGCCTTCATC 61.911 60.000 1.32 0.00 0.00 2.92
205 206 2.597903 GGGTCAGGGCCTTCATCC 59.402 66.667 1.32 0.00 0.00 3.51
206 207 2.597903 GGTCAGGGCCTTCATCCC 59.402 66.667 1.32 0.00 44.25 3.85
209 210 4.195334 CAGGGCCTTCATCCCCGG 62.195 72.222 1.32 0.00 46.24 5.73
343 344 3.597728 GGAGTCGCGGGAGGCTAG 61.598 72.222 6.13 0.00 40.44 3.42
344 345 3.597728 GAGTCGCGGGAGGCTAGG 61.598 72.222 6.13 0.00 40.44 3.02
348 349 4.530857 CGCGGGAGGCTAGGGTTG 62.531 72.222 0.00 0.00 40.44 3.77
349 350 4.176752 GCGGGAGGCTAGGGTTGG 62.177 72.222 0.00 0.00 39.11 3.77
350 351 4.176752 CGGGAGGCTAGGGTTGGC 62.177 72.222 0.00 0.00 0.00 4.52
351 352 2.692741 GGGAGGCTAGGGTTGGCT 60.693 66.667 0.00 0.00 43.15 4.75
358 359 1.900545 GCTAGGGTTGGCTCTCGGTT 61.901 60.000 0.00 0.00 0.00 4.44
359 360 0.613777 CTAGGGTTGGCTCTCGGTTT 59.386 55.000 0.00 0.00 0.00 3.27
360 361 1.003233 CTAGGGTTGGCTCTCGGTTTT 59.997 52.381 0.00 0.00 0.00 2.43
361 362 0.537371 AGGGTTGGCTCTCGGTTTTG 60.537 55.000 0.00 0.00 0.00 2.44
362 363 0.822121 GGGTTGGCTCTCGGTTTTGT 60.822 55.000 0.00 0.00 0.00 2.83
363 364 1.029681 GGTTGGCTCTCGGTTTTGTT 58.970 50.000 0.00 0.00 0.00 2.83
368 369 2.875933 TGGCTCTCGGTTTTGTTACAAG 59.124 45.455 0.00 0.00 0.00 3.16
369 370 2.225727 GGCTCTCGGTTTTGTTACAAGG 59.774 50.000 0.00 0.00 0.00 3.61
370 371 2.876550 GCTCTCGGTTTTGTTACAAGGT 59.123 45.455 0.00 0.00 0.00 3.50
371 372 4.060205 GCTCTCGGTTTTGTTACAAGGTA 58.940 43.478 0.00 0.00 0.00 3.08
372 373 4.694037 GCTCTCGGTTTTGTTACAAGGTAT 59.306 41.667 0.00 0.00 0.00 2.73
373 374 5.163884 GCTCTCGGTTTTGTTACAAGGTATC 60.164 44.000 0.00 0.00 0.00 2.24
374 375 6.105397 TCTCGGTTTTGTTACAAGGTATCT 57.895 37.500 0.00 0.00 0.00 1.98
375 376 7.230849 TCTCGGTTTTGTTACAAGGTATCTA 57.769 36.000 0.00 0.00 0.00 1.98
376 377 7.844009 TCTCGGTTTTGTTACAAGGTATCTAT 58.156 34.615 0.00 0.00 0.00 1.98
377 378 8.316214 TCTCGGTTTTGTTACAAGGTATCTATT 58.684 33.333 0.00 0.00 0.00 1.73
379 380 9.941325 TCGGTTTTGTTACAAGGTATCTATTTA 57.059 29.630 0.00 0.00 0.00 1.40
380 381 9.977762 CGGTTTTGTTACAAGGTATCTATTTAC 57.022 33.333 0.00 0.00 0.00 2.01
385 386 8.360325 TGTTACAAGGTATCTATTTACATGCG 57.640 34.615 0.00 0.00 0.00 4.73
386 387 7.439955 TGTTACAAGGTATCTATTTACATGCGG 59.560 37.037 0.00 0.00 0.00 5.69
387 388 6.169557 ACAAGGTATCTATTTACATGCGGA 57.830 37.500 0.00 0.00 0.00 5.54
388 389 6.769512 ACAAGGTATCTATTTACATGCGGAT 58.230 36.000 0.00 0.00 0.00 4.18
389 390 7.224297 ACAAGGTATCTATTTACATGCGGATT 58.776 34.615 0.00 0.00 0.00 3.01
390 391 7.719633 ACAAGGTATCTATTTACATGCGGATTT 59.280 33.333 0.00 0.00 0.00 2.17
391 392 8.567948 CAAGGTATCTATTTACATGCGGATTTT 58.432 33.333 0.00 0.00 0.00 1.82
392 393 9.787435 AAGGTATCTATTTACATGCGGATTTTA 57.213 29.630 0.00 0.00 0.00 1.52
393 394 9.959721 AGGTATCTATTTACATGCGGATTTTAT 57.040 29.630 0.00 0.00 0.00 1.40
406 407 4.268797 GGATTTTATCCGACCTACCCTC 57.731 50.000 0.00 0.00 40.13 4.30
407 408 3.902467 GGATTTTATCCGACCTACCCTCT 59.098 47.826 0.00 0.00 40.13 3.69
410 411 4.803329 TTTATCCGACCTACCCTCTACT 57.197 45.455 0.00 0.00 0.00 2.57
412 413 1.588239 TCCGACCTACCCTCTACTCA 58.412 55.000 0.00 0.00 0.00 3.41
413 414 1.211457 TCCGACCTACCCTCTACTCAC 59.789 57.143 0.00 0.00 0.00 3.51
415 416 2.356947 CCGACCTACCCTCTACTCACTT 60.357 54.545 0.00 0.00 0.00 3.16
416 417 3.118112 CCGACCTACCCTCTACTCACTTA 60.118 52.174 0.00 0.00 0.00 2.24
417 418 4.446023 CCGACCTACCCTCTACTCACTTAT 60.446 50.000 0.00 0.00 0.00 1.73
419 420 5.686913 CGACCTACCCTCTACTCACTTATGA 60.687 48.000 0.00 0.00 0.00 2.15
420 421 5.447757 ACCTACCCTCTACTCACTTATGAC 58.552 45.833 0.00 0.00 0.00 3.06
421 422 4.515944 CCTACCCTCTACTCACTTATGACG 59.484 50.000 0.00 0.00 0.00 4.35
449 450 8.035394 ACTACATACGAACTGAAATGAGTGAAT 58.965 33.333 0.00 0.00 0.00 2.57
665 668 1.625818 AGCTAGTGTCACCTCCTTTGG 59.374 52.381 0.00 0.00 0.00 3.28
717 720 6.303839 TGCCCATCTAACTTAATTATCCACC 58.696 40.000 0.00 0.00 0.00 4.61
782 785 1.135972 CAAAAGTGCGATTCCGTCCAG 60.136 52.381 0.00 0.00 38.24 3.86
850 853 4.022589 CGGCAATCAAATTATCTCCTGCAT 60.023 41.667 0.00 0.00 0.00 3.96
897 900 0.106708 ACATTGTCTGTGACTGCCGT 59.893 50.000 0.00 0.00 36.48 5.68
930 933 4.866486 GGAATGCTTTGTTTTGGCTATCAG 59.134 41.667 0.00 0.00 0.00 2.90
1089 1095 1.074951 CCCTCTTTTTCCCGCCACT 59.925 57.895 0.00 0.00 0.00 4.00
1092 1098 0.890996 CTCTTTTTCCCGCCACTGCT 60.891 55.000 0.00 0.00 34.43 4.24
1167 3581 2.936919 AGCCAACAGACTCACAATCA 57.063 45.000 0.00 0.00 0.00 2.57
1381 3795 1.920734 ATGGCCACGGCACTATCCAA 61.921 55.000 8.16 0.00 41.84 3.53
1412 3832 3.782523 TCAAAGATGGTATGCTCTCCCTT 59.217 43.478 0.00 0.00 0.00 3.95
1513 3942 0.252467 CTCCAGTTCCTCACCTCCCT 60.252 60.000 0.00 0.00 0.00 4.20
1516 3945 1.920835 AGTTCCTCACCTCCCTGGC 60.921 63.158 0.00 0.00 40.22 4.85
1517 3946 1.920835 GTTCCTCACCTCCCTGGCT 60.921 63.158 0.00 0.00 40.22 4.75
1562 3991 0.822532 AGGATCCGACCGATACGCTT 60.823 55.000 5.98 0.00 36.84 4.68
1714 4161 3.570638 CGCTGGCAATCTGGCTCG 61.571 66.667 1.71 2.14 44.10 5.03
1810 4263 2.797278 CGCCGGGGCATCTCTACTT 61.797 63.158 5.22 0.00 42.06 2.24
1856 4309 5.678583 CATGACATGATACCTCCACTTCTT 58.321 41.667 10.03 0.00 0.00 2.52
2159 4617 3.244281 ATGCCGCAGAGCTGTGACA 62.244 57.895 16.28 9.48 43.32 3.58
2462 4926 2.697761 GCACTACTCGGTGGCTCGA 61.698 63.158 3.83 3.83 37.65 4.04
2477 4944 0.445436 CTCGACATTCCTGTTGCTGC 59.555 55.000 0.00 0.00 36.80 5.25
2480 4947 1.242076 GACATTCCTGTTGCTGCTGT 58.758 50.000 0.00 0.00 35.14 4.40
2481 4948 1.198637 GACATTCCTGTTGCTGCTGTC 59.801 52.381 0.00 0.00 35.14 3.51
2482 4949 0.524862 CATTCCTGTTGCTGCTGTCC 59.475 55.000 0.00 0.00 0.00 4.02
2495 4962 0.900421 GCTGTCCGGGGTAAGTAGTT 59.100 55.000 0.00 0.00 0.00 2.24
2497 4964 2.289882 GCTGTCCGGGGTAAGTAGTTTT 60.290 50.000 0.00 0.00 0.00 2.43
2716 5183 0.827925 ACAGTGAGAGGGAGTTCGCA 60.828 55.000 0.00 0.00 0.00 5.10
2719 5186 1.149148 GTGAGAGGGAGTTCGCAAAC 58.851 55.000 0.00 0.00 35.50 2.93
2773 5240 1.819632 CCTAGTCCGCATGGTTGGC 60.820 63.158 0.00 0.00 36.30 4.52
2932 5399 3.432326 GCCTGGAGTACTTACATGAAGGG 60.432 52.174 0.00 0.00 39.74 3.95
3091 5558 1.132201 AGGGGCACAAGGGGCTATATA 60.132 52.381 0.00 0.00 0.00 0.86
3274 5741 1.074775 GGTTGGTGATGGCAGGACA 59.925 57.895 0.00 0.00 0.00 4.02
3356 5823 2.661566 CGTGTTGCTCTCTGGTGCG 61.662 63.158 0.00 0.00 35.02 5.34
3385 5852 4.831307 CCTTCGCTCCGTCCGACG 62.831 72.222 14.15 14.15 42.11 5.12
3467 5934 3.759581 ACAAGCTCCAACTGTTCATCAT 58.240 40.909 0.00 0.00 0.00 2.45
3471 5938 2.349886 GCTCCAACTGTTCATCATCGTC 59.650 50.000 0.00 0.00 0.00 4.20
3481 5948 1.676529 TCATCATCGTCGACCTCTTCC 59.323 52.381 10.58 0.00 0.00 3.46
3482 5949 1.405463 CATCATCGTCGACCTCTTCCA 59.595 52.381 10.58 0.00 0.00 3.53
3487 5954 0.663688 CGTCGACCTCTTCCATCGAT 59.336 55.000 10.58 0.00 45.72 3.59
3488 5955 1.598183 CGTCGACCTCTTCCATCGATG 60.598 57.143 18.76 18.76 45.72 3.84
3489 5956 1.676529 GTCGACCTCTTCCATCGATGA 59.323 52.381 26.86 10.02 45.72 2.92
3490 5957 2.099263 GTCGACCTCTTCCATCGATGAA 59.901 50.000 26.86 16.47 45.72 2.57
3497 5964 0.104855 TTCCATCGATGAAGGGAGCG 59.895 55.000 26.86 7.31 0.00 5.03
3508 5975 2.771763 AAGGGAGCGCTCTGTTGTCG 62.772 60.000 34.46 0.00 0.00 4.35
3550 6093 9.944663 GAGATAGAGTGATTCTTACTGTACTTG 57.055 37.037 0.00 0.00 37.36 3.16
3551 6094 8.410141 AGATAGAGTGATTCTTACTGTACTTGC 58.590 37.037 0.00 0.00 37.36 4.01
3554 6097 5.865085 AGTGATTCTTACTGTACTTGCCAA 58.135 37.500 0.00 0.00 0.00 4.52
3555 6098 6.296026 AGTGATTCTTACTGTACTTGCCAAA 58.704 36.000 0.00 0.00 0.00 3.28
3556 6099 6.942576 AGTGATTCTTACTGTACTTGCCAAAT 59.057 34.615 0.00 0.00 0.00 2.32
3557 6100 7.119846 AGTGATTCTTACTGTACTTGCCAAATC 59.880 37.037 0.00 0.00 0.00 2.17
3599 6174 4.063689 GGACATCAGTCATGCATTCTAGG 58.936 47.826 0.00 0.00 46.80 3.02
3600 6175 4.063689 GACATCAGTCATGCATTCTAGGG 58.936 47.826 0.00 0.00 44.34 3.53
3601 6176 3.457380 ACATCAGTCATGCATTCTAGGGT 59.543 43.478 0.00 0.00 35.65 4.34
3602 6177 4.655649 ACATCAGTCATGCATTCTAGGGTA 59.344 41.667 0.00 0.00 35.65 3.69
3603 6178 4.944619 TCAGTCATGCATTCTAGGGTAG 57.055 45.455 0.00 0.00 0.00 3.18
3621 6196 6.611785 AGGGTAGCTACATACATGTCTTCTA 58.388 40.000 24.75 0.00 41.97 2.10
3622 6197 6.490721 AGGGTAGCTACATACATGTCTTCTAC 59.509 42.308 24.75 6.82 41.97 2.59
3623 6198 6.490721 GGGTAGCTACATACATGTCTTCTACT 59.509 42.308 24.75 0.00 41.97 2.57
3707 6447 6.441093 TGGTTTGAGCACTAATTCATCATC 57.559 37.500 0.00 0.00 0.00 2.92
3711 6451 7.013083 GGTTTGAGCACTAATTCATCATCAGAT 59.987 37.037 0.00 0.00 33.87 2.90
3738 6484 4.857871 TTGACACTTTTCTGAAGTCACG 57.142 40.909 9.03 0.00 38.77 4.35
3746 6492 7.116948 ACACTTTTCTGAAGTCACGAGATATTG 59.883 37.037 0.00 0.00 0.00 1.90
3800 6546 8.693120 TGTATAATGGTTTAGGAAAACACACA 57.307 30.769 3.66 0.00 45.68 3.72
3853 6602 7.756722 AGATTTGCTGAAAATTTCGTCAATAGG 59.243 33.333 11.28 0.00 38.64 2.57
3865 6615 5.661056 TCGTCAATAGGTCATTCAGTTCT 57.339 39.130 0.00 0.00 0.00 3.01
3866 6616 6.769134 TCGTCAATAGGTCATTCAGTTCTA 57.231 37.500 0.00 0.00 0.00 2.10
3867 6617 6.561614 TCGTCAATAGGTCATTCAGTTCTAC 58.438 40.000 0.00 0.00 0.00 2.59
3868 6618 6.377429 TCGTCAATAGGTCATTCAGTTCTACT 59.623 38.462 0.00 0.00 0.00 2.57
3869 6619 6.693545 CGTCAATAGGTCATTCAGTTCTACTC 59.306 42.308 0.00 0.00 0.00 2.59
3870 6620 6.693545 GTCAATAGGTCATTCAGTTCTACTCG 59.306 42.308 0.00 0.00 0.00 4.18
3878 6628 3.069079 TCAGTTCTACTCGTACCTGCT 57.931 47.619 0.00 0.00 0.00 4.24
3905 6655 5.823045 AGAGCAAAGTGTTAGCAAACTACTT 59.177 36.000 0.00 0.00 37.96 2.24
3906 6656 6.990349 AGAGCAAAGTGTTAGCAAACTACTTA 59.010 34.615 0.00 0.00 36.66 2.24
3949 6808 2.289002 CGGGCATTTCTCATAAGAGCAC 59.711 50.000 0.00 0.00 41.81 4.40
3957 6817 4.397481 TCTCATAAGAGCACCAGTCATG 57.603 45.455 0.00 0.00 41.81 3.07
3964 6824 2.012673 GAGCACCAGTCATGATTCACC 58.987 52.381 0.00 0.00 0.00 4.02
3999 6860 2.016318 TGCTTCACAGATATTTGGCCG 58.984 47.619 0.00 0.00 0.00 6.13
4052 6928 3.006247 GGAGCTTCTCACTCATTTGTCC 58.994 50.000 0.00 0.00 35.79 4.02
4141 7108 5.356426 CGGGTGAAAAGAAAATTTTGGAGT 58.644 37.500 8.47 0.00 0.00 3.85
4234 7208 1.664016 CGCTGCCATGTCACTCAAAAC 60.664 52.381 0.00 0.00 0.00 2.43
4249 7223 6.260050 TCACTCAAAACCATTGTGAAGTACTC 59.740 38.462 0.00 0.00 35.15 2.59
4250 7224 5.531287 ACTCAAAACCATTGTGAAGTACTCC 59.469 40.000 0.00 0.00 0.00 3.85
4252 7226 4.724279 AAACCATTGTGAAGTACTCCCT 57.276 40.909 0.00 0.00 0.00 4.20
4253 7227 3.983044 ACCATTGTGAAGTACTCCCTC 57.017 47.619 0.00 0.00 0.00 4.30
4254 7228 3.521727 ACCATTGTGAAGTACTCCCTCT 58.478 45.455 0.00 0.00 0.00 3.69
4255 7229 3.261897 ACCATTGTGAAGTACTCCCTCTG 59.738 47.826 0.00 0.00 0.00 3.35
4256 7230 3.261897 CCATTGTGAAGTACTCCCTCTGT 59.738 47.826 0.00 0.00 0.00 3.41
4257 7231 4.466370 CCATTGTGAAGTACTCCCTCTGTA 59.534 45.833 0.00 0.00 0.00 2.74
4258 7232 5.046591 CCATTGTGAAGTACTCCCTCTGTAA 60.047 44.000 0.00 0.00 0.00 2.41
4259 7233 6.464222 CATTGTGAAGTACTCCCTCTGTAAA 58.536 40.000 0.00 0.00 0.00 2.01
4260 7234 5.464030 TGTGAAGTACTCCCTCTGTAAAC 57.536 43.478 0.00 0.00 0.00 2.01
4261 7235 4.897076 TGTGAAGTACTCCCTCTGTAAACA 59.103 41.667 0.00 0.00 0.00 2.83
4262 7236 5.364446 TGTGAAGTACTCCCTCTGTAAACAA 59.636 40.000 0.00 0.00 0.00 2.83
4263 7237 6.126997 TGTGAAGTACTCCCTCTGTAAACAAA 60.127 38.462 0.00 0.00 0.00 2.83
4264 7238 6.935208 GTGAAGTACTCCCTCTGTAAACAAAT 59.065 38.462 0.00 0.00 0.00 2.32
4265 7239 8.092687 GTGAAGTACTCCCTCTGTAAACAAATA 58.907 37.037 0.00 0.00 0.00 1.40
4266 7240 8.822805 TGAAGTACTCCCTCTGTAAACAAATAT 58.177 33.333 0.00 0.00 0.00 1.28
4272 7246 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
4273 7247 6.984474 TCCCTCTGTAAACAAATATAAGAGCG 59.016 38.462 0.00 0.00 0.00 5.03
4274 7248 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
4275 7249 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
4276 7250 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
4284 7258 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
4325 7299 8.738645 ATGCTCTTATAAAAGTTTACAGAGGG 57.261 34.615 16.49 5.38 35.69 4.30
4326 7300 7.913789 TGCTCTTATAAAAGTTTACAGAGGGA 58.086 34.615 16.49 4.34 35.69 4.20
4327 7301 8.041323 TGCTCTTATAAAAGTTTACAGAGGGAG 58.959 37.037 16.49 0.00 35.69 4.30
4328 7302 8.041919 GCTCTTATAAAAGTTTACAGAGGGAGT 58.958 37.037 16.49 0.00 35.69 3.85
4433 7407 9.778741 TTCAGTTACTCAAGATCATGTTTACTT 57.221 29.630 0.00 0.00 0.00 2.24
4531 7515 2.986479 CAGATGACATGAACACGAACGA 59.014 45.455 0.00 0.00 0.00 3.85
4537 7521 4.798387 TGACATGAACACGAACGATGATAG 59.202 41.667 0.00 0.00 0.00 2.08
4539 7523 4.798907 ACATGAACACGAACGATGATAGTC 59.201 41.667 0.00 0.00 0.00 2.59
4553 7537 9.828852 AACGATGATAGTCGAAGATATACTTTC 57.171 33.333 3.09 0.00 44.06 2.62
4555 7539 9.268255 CGATGATAGTCGAAGATATACTTTCAC 57.732 37.037 0.00 0.00 44.06 3.18
4562 7546 8.740906 AGTCGAAGATATACTTTCACTCTTTCA 58.259 33.333 0.00 0.00 40.67 2.69
4563 7547 9.015577 GTCGAAGATATACTTTCACTCTTTCAG 57.984 37.037 0.00 0.00 40.67 3.02
4564 7548 8.191446 TCGAAGATATACTTTCACTCTTTCAGG 58.809 37.037 0.00 0.00 39.13 3.86
4565 7549 8.191446 CGAAGATATACTTTCACTCTTTCAGGA 58.809 37.037 0.00 0.00 39.13 3.86
4567 7551 9.829507 AAGATATACTTTCACTCTTTCAGGATG 57.170 33.333 0.00 0.00 34.94 3.51
4585 7569 6.828273 TCAGGATGAGGTACAAACCAATATTG 59.172 38.462 8.58 8.58 42.56 1.90
4595 7579 9.665719 GGTACAAACCAATATTGAAAATCCATT 57.334 29.630 17.23 0.00 45.98 3.16
4669 7656 5.560953 GCAGGCCAATAAGATAAACATCGAC 60.561 44.000 5.01 0.00 0.00 4.20
4682 7669 8.669243 AGATAAACATCGACTCATTTTCTTTCC 58.331 33.333 0.00 0.00 0.00 3.13
4707 7694 5.661312 GGCCCCTTTATCAAGAAATTTACCT 59.339 40.000 0.00 0.00 30.57 3.08
4708 7695 6.406961 GGCCCCTTTATCAAGAAATTTACCTG 60.407 42.308 0.00 0.00 30.57 4.00
4715 7702 6.916360 ATCAAGAAATTTACCTGCTCCAAA 57.084 33.333 0.00 0.00 0.00 3.28
4740 7763 5.542779 AGAGTGTGAAGGCTACTACAAAAG 58.457 41.667 0.00 0.00 0.00 2.27
4858 7884 2.839486 AGAGACCGAAACATCAAGCA 57.161 45.000 0.00 0.00 0.00 3.91
4982 8008 1.280133 CCTGCAGAACCCTCTTCATCA 59.720 52.381 17.39 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 135 4.722700 TTTCGCCCCTGCTGCTCC 62.723 66.667 0.00 0.00 34.43 4.70
135 136 2.672996 TTTTCGCCCCTGCTGCTC 60.673 61.111 0.00 0.00 34.43 4.26
136 137 2.674380 CTTTTCGCCCCTGCTGCT 60.674 61.111 0.00 0.00 34.43 4.24
137 138 2.268076 TTCTTTTCGCCCCTGCTGC 61.268 57.895 0.00 0.00 34.43 5.25
139 140 1.966451 CGTTCTTTTCGCCCCTGCT 60.966 57.895 0.00 0.00 34.43 4.24
141 142 1.574702 GGTCGTTCTTTTCGCCCCTG 61.575 60.000 0.00 0.00 0.00 4.45
143 144 2.674084 CGGTCGTTCTTTTCGCCCC 61.674 63.158 0.00 0.00 0.00 5.80
144 145 1.894223 GACGGTCGTTCTTTTCGCCC 61.894 60.000 0.00 0.00 0.00 6.13
145 146 1.490258 GACGGTCGTTCTTTTCGCC 59.510 57.895 0.00 0.00 0.00 5.54
146 147 1.127225 CGACGGTCGTTCTTTTCGC 59.873 57.895 21.68 0.00 34.72 4.70
147 148 0.661187 TCCGACGGTCGTTCTTTTCG 60.661 55.000 26.72 10.71 38.40 3.46
148 149 1.058404 CTCCGACGGTCGTTCTTTTC 58.942 55.000 26.72 0.00 38.40 2.29
149 150 0.670162 TCTCCGACGGTCGTTCTTTT 59.330 50.000 26.72 0.00 38.40 2.27
150 151 0.240411 CTCTCCGACGGTCGTTCTTT 59.760 55.000 26.72 0.00 38.40 2.52
151 152 1.584380 CCTCTCCGACGGTCGTTCTT 61.584 60.000 26.72 0.00 38.40 2.52
152 153 2.039405 CCTCTCCGACGGTCGTTCT 61.039 63.158 26.72 0.00 38.40 3.01
154 155 3.060615 CCCTCTCCGACGGTCGTT 61.061 66.667 26.72 0.00 38.40 3.85
171 172 4.963428 CGAATCCCTACCCGCGCC 62.963 72.222 0.00 0.00 0.00 6.53
172 173 4.963428 CCGAATCCCTACCCGCGC 62.963 72.222 0.00 0.00 0.00 6.86
173 174 4.295119 CCCGAATCCCTACCCGCG 62.295 72.222 0.00 0.00 0.00 6.46
174 175 3.159347 ACCCGAATCCCTACCCGC 61.159 66.667 0.00 0.00 0.00 6.13
176 177 1.408453 CCTGACCCGAATCCCTACCC 61.408 65.000 0.00 0.00 0.00 3.69
177 178 1.408453 CCCTGACCCGAATCCCTACC 61.408 65.000 0.00 0.00 0.00 3.18
178 179 2.041206 GCCCTGACCCGAATCCCTAC 62.041 65.000 0.00 0.00 0.00 3.18
179 180 1.764854 GCCCTGACCCGAATCCCTA 60.765 63.158 0.00 0.00 0.00 3.53
180 181 3.090532 GCCCTGACCCGAATCCCT 61.091 66.667 0.00 0.00 0.00 4.20
181 182 4.191015 GGCCCTGACCCGAATCCC 62.191 72.222 0.00 0.00 0.00 3.85
183 184 1.153147 GAAGGCCCTGACCCGAATC 60.153 63.158 0.00 0.00 0.00 2.52
184 185 1.281925 ATGAAGGCCCTGACCCGAAT 61.282 55.000 0.00 0.00 0.00 3.34
186 187 2.285368 ATGAAGGCCCTGACCCGA 60.285 61.111 0.00 0.00 0.00 5.14
187 188 2.190578 GATGAAGGCCCTGACCCG 59.809 66.667 0.00 0.00 0.00 5.28
188 189 2.597903 GGATGAAGGCCCTGACCC 59.402 66.667 0.00 0.00 0.00 4.46
189 190 2.597903 GGGATGAAGGCCCTGACC 59.402 66.667 0.00 0.00 42.56 4.02
190 191 2.597903 GGGGATGAAGGCCCTGAC 59.402 66.667 0.00 0.00 45.30 3.51
326 327 3.597728 CTAGCCTCCCGCGACTCC 61.598 72.222 8.23 0.00 44.76 3.85
327 328 3.597728 CCTAGCCTCCCGCGACTC 61.598 72.222 8.23 0.00 44.76 3.36
330 331 4.772231 AACCCTAGCCTCCCGCGA 62.772 66.667 8.23 0.00 44.76 5.87
331 332 4.530857 CAACCCTAGCCTCCCGCG 62.531 72.222 0.00 0.00 44.76 6.46
332 333 4.176752 CCAACCCTAGCCTCCCGC 62.177 72.222 0.00 0.00 37.98 6.13
333 334 4.176752 GCCAACCCTAGCCTCCCG 62.177 72.222 0.00 0.00 0.00 5.14
334 335 2.692741 AGCCAACCCTAGCCTCCC 60.693 66.667 0.00 0.00 0.00 4.30
335 336 1.690985 AGAGCCAACCCTAGCCTCC 60.691 63.158 0.00 0.00 0.00 4.30
336 337 1.826709 GAGAGCCAACCCTAGCCTC 59.173 63.158 0.00 0.00 0.00 4.70
337 338 2.060980 CGAGAGCCAACCCTAGCCT 61.061 63.158 0.00 0.00 0.00 4.58
339 340 1.900545 AACCGAGAGCCAACCCTAGC 61.901 60.000 0.00 0.00 0.00 3.42
340 341 0.613777 AAACCGAGAGCCAACCCTAG 59.386 55.000 0.00 0.00 0.00 3.02
341 342 1.061546 AAAACCGAGAGCCAACCCTA 58.938 50.000 0.00 0.00 0.00 3.53
343 344 0.822121 ACAAAACCGAGAGCCAACCC 60.822 55.000 0.00 0.00 0.00 4.11
344 345 1.029681 AACAAAACCGAGAGCCAACC 58.970 50.000 0.00 0.00 0.00 3.77
345 346 2.614983 TGTAACAAAACCGAGAGCCAAC 59.385 45.455 0.00 0.00 0.00 3.77
348 349 2.225727 CCTTGTAACAAAACCGAGAGCC 59.774 50.000 0.00 0.00 0.00 4.70
349 350 2.876550 ACCTTGTAACAAAACCGAGAGC 59.123 45.455 0.00 0.00 0.00 4.09
350 351 6.164176 AGATACCTTGTAACAAAACCGAGAG 58.836 40.000 0.00 0.00 0.00 3.20
351 352 6.105397 AGATACCTTGTAACAAAACCGAGA 57.895 37.500 0.00 0.00 0.00 4.04
352 353 8.488651 AATAGATACCTTGTAACAAAACCGAG 57.511 34.615 0.00 0.00 0.00 4.63
353 354 8.851541 AAATAGATACCTTGTAACAAAACCGA 57.148 30.769 0.00 0.00 0.00 4.69
359 360 8.822855 CGCATGTAAATAGATACCTTGTAACAA 58.177 33.333 0.00 0.00 0.00 2.83
360 361 7.439955 CCGCATGTAAATAGATACCTTGTAACA 59.560 37.037 0.00 0.00 0.00 2.41
361 362 7.654520 TCCGCATGTAAATAGATACCTTGTAAC 59.345 37.037 0.00 0.00 0.00 2.50
362 363 7.728148 TCCGCATGTAAATAGATACCTTGTAA 58.272 34.615 0.00 0.00 0.00 2.41
363 364 7.292713 TCCGCATGTAAATAGATACCTTGTA 57.707 36.000 0.00 0.00 0.00 2.41
385 386 3.902467 AGAGGGTAGGTCGGATAAAATCC 59.098 47.826 0.00 0.00 46.22 3.01
386 387 5.774184 AGTAGAGGGTAGGTCGGATAAAATC 59.226 44.000 0.00 0.00 0.00 2.17
387 388 5.713807 AGTAGAGGGTAGGTCGGATAAAAT 58.286 41.667 0.00 0.00 0.00 1.82
388 389 5.134725 AGTAGAGGGTAGGTCGGATAAAA 57.865 43.478 0.00 0.00 0.00 1.52
389 390 4.166725 TGAGTAGAGGGTAGGTCGGATAAA 59.833 45.833 0.00 0.00 0.00 1.40
390 391 3.718434 TGAGTAGAGGGTAGGTCGGATAA 59.282 47.826 0.00 0.00 0.00 1.75
391 392 3.072184 GTGAGTAGAGGGTAGGTCGGATA 59.928 52.174 0.00 0.00 0.00 2.59
392 393 2.133520 TGAGTAGAGGGTAGGTCGGAT 58.866 52.381 0.00 0.00 0.00 4.18
393 394 1.211457 GTGAGTAGAGGGTAGGTCGGA 59.789 57.143 0.00 0.00 0.00 4.55
394 395 1.212441 AGTGAGTAGAGGGTAGGTCGG 59.788 57.143 0.00 0.00 0.00 4.79
396 397 5.532032 GTCATAAGTGAGTAGAGGGTAGGTC 59.468 48.000 0.00 0.00 34.36 3.85
398 399 4.515944 CGTCATAAGTGAGTAGAGGGTAGG 59.484 50.000 0.00 0.00 34.36 3.18
400 401 4.164796 TCCGTCATAAGTGAGTAGAGGGTA 59.835 45.833 0.00 0.00 36.10 3.69
401 402 3.053842 TCCGTCATAAGTGAGTAGAGGGT 60.054 47.826 0.00 0.00 36.10 4.34
402 403 3.315749 GTCCGTCATAAGTGAGTAGAGGG 59.684 52.174 0.00 0.00 34.36 4.30
404 405 5.816258 TGTAGTCCGTCATAAGTGAGTAGAG 59.184 44.000 0.00 0.00 34.36 2.43
406 407 6.621316 ATGTAGTCCGTCATAAGTGAGTAG 57.379 41.667 0.00 0.00 34.36 2.57
407 408 6.201615 CGTATGTAGTCCGTCATAAGTGAGTA 59.798 42.308 0.00 0.00 34.36 2.59
410 411 5.118286 TCGTATGTAGTCCGTCATAAGTGA 58.882 41.667 0.00 0.00 31.56 3.41
412 413 5.587844 AGTTCGTATGTAGTCCGTCATAAGT 59.412 40.000 0.00 0.00 31.56 2.24
413 414 5.907945 CAGTTCGTATGTAGTCCGTCATAAG 59.092 44.000 0.00 0.00 0.00 1.73
415 416 5.118286 TCAGTTCGTATGTAGTCCGTCATA 58.882 41.667 0.00 0.00 0.00 2.15
416 417 3.943381 TCAGTTCGTATGTAGTCCGTCAT 59.057 43.478 0.00 0.00 0.00 3.06
417 418 3.337358 TCAGTTCGTATGTAGTCCGTCA 58.663 45.455 0.00 0.00 0.00 4.35
419 420 4.771590 TTTCAGTTCGTATGTAGTCCGT 57.228 40.909 0.00 0.00 0.00 4.69
420 421 5.337554 TCATTTCAGTTCGTATGTAGTCCG 58.662 41.667 0.00 0.00 0.00 4.79
421 422 6.253727 CACTCATTTCAGTTCGTATGTAGTCC 59.746 42.308 0.00 0.00 0.00 3.85
665 668 0.955428 TTGGCACGAACCATGAGCTC 60.955 55.000 6.82 6.82 40.13 4.09
717 720 1.328680 CGAGGTTCCATCAGCAAATCG 59.671 52.381 0.00 0.00 0.00 3.34
782 785 7.850982 CAGACTTGTTTAAACTACACACATGTC 59.149 37.037 18.72 13.70 40.35 3.06
850 853 5.396484 GTTAAGCGCCATATCTCATACGTA 58.604 41.667 2.29 0.00 0.00 3.57
897 900 2.463589 AAAGCATTCCACTCGCCGGA 62.464 55.000 5.05 0.00 0.00 5.14
930 933 5.353123 TGACACACACAGGAGAAAAGTTAAC 59.647 40.000 0.00 0.00 0.00 2.01
1089 1095 4.980702 CAGTGGGGCAAGGCAGCA 62.981 66.667 0.00 0.00 35.83 4.41
1092 1098 4.223125 AAGCAGTGGGGCAAGGCA 62.223 61.111 0.00 0.00 35.83 4.75
1167 3581 1.299976 GGGGCCTGAAAGTCGATGT 59.700 57.895 0.84 0.00 0.00 3.06
1513 3942 0.249699 CCACACGACAGTTGTAGCCA 60.250 55.000 0.00 0.00 0.00 4.75
1516 3945 1.611977 TCTCCCACACGACAGTTGTAG 59.388 52.381 0.00 0.00 0.00 2.74
1517 3946 1.611977 CTCTCCCACACGACAGTTGTA 59.388 52.381 0.00 0.00 0.00 2.41
1562 3991 2.063979 CATGTACTGCCCCGGGAGA 61.064 63.158 26.32 6.65 37.03 3.71
1714 4161 5.794894 CCCAGTATATGTTGTATGAGTCCC 58.205 45.833 0.00 0.00 0.00 4.46
1810 4263 0.953471 CGTGCCGTCCTTGATTTGGA 60.953 55.000 0.00 0.00 0.00 3.53
1839 4292 5.964477 TGGAGTTAAGAAGTGGAGGTATCAT 59.036 40.000 0.00 0.00 0.00 2.45
1856 4309 3.262405 GGTGGTAACTGATGGTGGAGTTA 59.738 47.826 0.00 0.00 34.28 2.24
1928 4382 0.463833 CTTCCCCGGCGCTATTCTTT 60.464 55.000 7.64 0.00 0.00 2.52
2159 4617 0.323178 TCGGCGGAGTAGTTCTTCCT 60.323 55.000 7.21 0.00 0.00 3.36
2462 4926 1.242076 GACAGCAGCAACAGGAATGT 58.758 50.000 0.00 0.00 0.00 2.71
2477 4944 3.690475 AAAACTACTTACCCCGGACAG 57.310 47.619 0.73 0.00 0.00 3.51
2480 4947 5.760484 AACATAAAACTACTTACCCCGGA 57.240 39.130 0.73 0.00 0.00 5.14
2481 4948 6.405538 TGTAACATAAAACTACTTACCCCGG 58.594 40.000 0.00 0.00 0.00 5.73
2482 4949 8.392612 CAATGTAACATAAAACTACTTACCCCG 58.607 37.037 0.00 0.00 0.00 5.73
2495 4962 9.391006 CTTCCTAAGGTAGCAATGTAACATAAA 57.609 33.333 0.00 0.00 0.00 1.40
2497 4964 8.313944 TCTTCCTAAGGTAGCAATGTAACATA 57.686 34.615 0.00 0.00 0.00 2.29
2716 5183 1.203994 CCGATGGACTGTACCTCGTTT 59.796 52.381 15.05 0.00 32.80 3.60
2719 5186 1.065928 GCCGATGGACTGTACCTCG 59.934 63.158 10.30 10.30 33.68 4.63
2773 5240 3.260740 CTGCTCCTTCTCTTTGCAGTAG 58.739 50.000 0.00 0.00 44.04 2.57
2794 5261 0.949105 ACTCGAACACCAACATCCGC 60.949 55.000 0.00 0.00 0.00 5.54
2932 5399 5.068198 ACAGTGGATGATTGGATAATTGCAC 59.932 40.000 0.00 0.00 30.16 4.57
2988 5455 8.579863 AGTCAGTAATCTTTGGATTTTTCTTGG 58.420 33.333 0.00 0.00 41.75 3.61
3091 5558 4.974438 TGGAACCACTCGGGGGCT 62.974 66.667 0.00 0.00 42.91 5.19
3274 5741 1.550524 TCGCTATGAAACAGCACCTCT 59.449 47.619 0.00 0.00 39.04 3.69
3356 5823 1.731720 AGCGAAGGATTCTGCTCAAC 58.268 50.000 0.00 0.00 46.37 3.18
3385 5852 4.324471 TGCACCACCTGATGCATC 57.676 55.556 20.14 20.14 46.63 3.91
3467 5934 0.392060 TCGATGGAAGAGGTCGACGA 60.392 55.000 9.92 0.00 39.22 4.20
3471 5938 2.544694 CCTTCATCGATGGAAGAGGTCG 60.545 54.545 24.61 9.86 43.46 4.79
3481 5948 0.943359 GAGCGCTCCCTTCATCGATG 60.943 60.000 27.22 19.61 0.00 3.84
3482 5949 1.112315 AGAGCGCTCCCTTCATCGAT 61.112 55.000 32.94 8.29 0.00 3.59
3487 5954 1.004560 CAACAGAGCGCTCCCTTCA 60.005 57.895 32.94 0.00 0.00 3.02
3488 5955 1.004440 ACAACAGAGCGCTCCCTTC 60.004 57.895 32.94 9.88 0.00 3.46
3489 5956 1.004440 GACAACAGAGCGCTCCCTT 60.004 57.895 32.94 21.04 0.00 3.95
3490 5957 2.659610 GACAACAGAGCGCTCCCT 59.340 61.111 32.94 16.12 0.00 4.20
3497 5964 2.031163 AGCACCCGACAACAGAGC 59.969 61.111 0.00 0.00 0.00 4.09
3508 5975 0.898320 TCTCAAGAGTAGCAGCACCC 59.102 55.000 0.00 0.00 0.00 4.61
3550 6093 0.242017 AGAAACGCAGCAGATTTGGC 59.758 50.000 0.00 0.00 0.00 4.52
3551 6094 1.267806 ACAGAAACGCAGCAGATTTGG 59.732 47.619 0.00 0.00 0.00 3.28
3554 6097 3.563808 TGTTTACAGAAACGCAGCAGATT 59.436 39.130 0.00 0.00 46.76 2.40
3555 6098 3.138304 TGTTTACAGAAACGCAGCAGAT 58.862 40.909 0.00 0.00 46.76 2.90
3556 6099 2.543848 CTGTTTACAGAAACGCAGCAGA 59.456 45.455 3.80 0.00 46.76 4.26
3557 6100 2.349817 CCTGTTTACAGAAACGCAGCAG 60.350 50.000 11.35 0.00 46.76 4.24
3599 6174 7.513371 AGTAGAAGACATGTATGTAGCTACC 57.487 40.000 21.01 6.55 41.95 3.18
3600 6175 9.275398 ACTAGTAGAAGACATGTATGTAGCTAC 57.725 37.037 17.30 17.30 41.95 3.58
3602 6177 9.848710 TTACTAGTAGAAGACATGTATGTAGCT 57.151 33.333 3.59 0.00 41.95 3.32
3621 6196 4.227197 AGGATATGCTGGCACTTACTAGT 58.773 43.478 0.00 0.00 34.00 2.57
3622 6197 4.881019 AGGATATGCTGGCACTTACTAG 57.119 45.455 0.00 0.00 0.00 2.57
3623 6198 5.780282 ACATAGGATATGCTGGCACTTACTA 59.220 40.000 7.05 0.00 0.00 1.82
3629 6204 5.491070 TGAATACATAGGATATGCTGGCAC 58.509 41.667 7.05 0.00 0.00 5.01
3722 6468 7.155328 ACAATATCTCGTGACTTCAGAAAAGT 58.845 34.615 0.00 0.00 0.00 2.66
3774 6520 9.132923 TGTGTGTTTTCCTAAACCATTATACAA 57.867 29.630 0.00 0.00 42.39 2.41
3797 6543 0.872881 GCTGCTTTGGCTGTGTTGTG 60.873 55.000 0.00 0.00 39.19 3.33
3800 6546 1.737816 CTGCTGCTTTGGCTGTGTT 59.262 52.632 0.00 0.00 39.19 3.32
3853 6602 5.333513 CAGGTACGAGTAGAACTGAATGAC 58.666 45.833 0.00 0.00 0.00 3.06
3878 6628 5.611374 AGTTTGCTAACACTTTGCTCTCTA 58.389 37.500 13.46 0.00 36.70 2.43
3905 6655 8.199449 CCCGACCAACTTCAGTTAGTAAATATA 58.801 37.037 0.00 0.00 36.32 0.86
3906 6656 7.046033 CCCGACCAACTTCAGTTAGTAAATAT 58.954 38.462 0.00 0.00 36.32 1.28
3949 6808 3.940852 TCATTTCGGTGAATCATGACTGG 59.059 43.478 0.00 0.00 0.00 4.00
3964 6824 2.749076 TGAAGCACCCAGATTCATTTCG 59.251 45.455 0.00 0.00 46.84 3.46
3999 6860 9.959749 TTTGTGAACTTATATTGGTTGTTCTTC 57.040 29.630 0.00 0.00 38.17 2.87
4052 6928 7.630242 ACTGTTGGTCTGTTATTATCCATTG 57.370 36.000 0.00 0.00 0.00 2.82
4234 7208 3.261897 ACAGAGGGAGTACTTCACAATGG 59.738 47.826 2.92 0.00 0.00 3.16
4249 7223 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
4250 7224 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
4258 7232 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
4299 7273 9.832445 CCCTCTGTAAACTTTTATAAGAGCATA 57.168 33.333 13.76 0.00 36.27 3.14
4300 7274 8.548877 TCCCTCTGTAAACTTTTATAAGAGCAT 58.451 33.333 13.76 0.00 36.27 3.79
4301 7275 7.913789 TCCCTCTGTAAACTTTTATAAGAGCA 58.086 34.615 13.76 0.00 36.27 4.26
4302 7276 8.041919 ACTCCCTCTGTAAACTTTTATAAGAGC 58.958 37.037 13.76 0.00 36.27 4.09
4309 7283 9.774413 CTTTTCTACTCCCTCTGTAAACTTTTA 57.226 33.333 0.00 0.00 0.00 1.52
4310 7284 8.491958 TCTTTTCTACTCCCTCTGTAAACTTTT 58.508 33.333 0.00 0.00 0.00 2.27
4311 7285 8.030913 TCTTTTCTACTCCCTCTGTAAACTTT 57.969 34.615 0.00 0.00 0.00 2.66
4312 7286 7.613551 TCTTTTCTACTCCCTCTGTAAACTT 57.386 36.000 0.00 0.00 0.00 2.66
4313 7287 7.290481 ACTTCTTTTCTACTCCCTCTGTAAACT 59.710 37.037 0.00 0.00 0.00 2.66
4314 7288 7.443477 ACTTCTTTTCTACTCCCTCTGTAAAC 58.557 38.462 0.00 0.00 0.00 2.01
4315 7289 7.613551 ACTTCTTTTCTACTCCCTCTGTAAA 57.386 36.000 0.00 0.00 0.00 2.01
4316 7290 7.289317 TGAACTTCTTTTCTACTCCCTCTGTAA 59.711 37.037 0.00 0.00 0.00 2.41
4317 7291 6.781014 TGAACTTCTTTTCTACTCCCTCTGTA 59.219 38.462 0.00 0.00 0.00 2.74
4318 7292 5.602978 TGAACTTCTTTTCTACTCCCTCTGT 59.397 40.000 0.00 0.00 0.00 3.41
4319 7293 6.102897 TGAACTTCTTTTCTACTCCCTCTG 57.897 41.667 0.00 0.00 0.00 3.35
4320 7294 6.498651 TGATGAACTTCTTTTCTACTCCCTCT 59.501 38.462 0.00 0.00 0.00 3.69
4321 7295 6.702329 TGATGAACTTCTTTTCTACTCCCTC 58.298 40.000 0.00 0.00 0.00 4.30
4322 7296 6.688073 TGATGAACTTCTTTTCTACTCCCT 57.312 37.500 0.00 0.00 0.00 4.20
4323 7297 7.745620 TTTGATGAACTTCTTTTCTACTCCC 57.254 36.000 0.00 0.00 0.00 4.30
4376 7350 6.064060 TGGTGAAACAAAGAGATCATTGACT 58.936 36.000 11.43 0.00 39.98 3.41
4377 7351 6.317789 TGGTGAAACAAAGAGATCATTGAC 57.682 37.500 11.43 1.76 39.98 3.18
4378 7352 6.957920 TTGGTGAAACAAAGAGATCATTGA 57.042 33.333 11.43 0.00 39.98 2.57
4379 7353 9.695526 TTATTTGGTGAAACAAAGAGATCATTG 57.304 29.630 0.00 0.00 42.91 2.82
4388 7362 8.702163 AACTGAACTTATTTGGTGAAACAAAG 57.298 30.769 0.00 0.00 42.91 2.77
4393 7367 8.740123 TGAGTAACTGAACTTATTTGGTGAAA 57.260 30.769 0.00 0.00 0.00 2.69
4433 7407 8.431910 AGAACCTGGACTCTATTAACTAACAA 57.568 34.615 0.00 0.00 0.00 2.83
4537 7521 8.912787 TGAAAGAGTGAAAGTATATCTTCGAC 57.087 34.615 0.00 0.00 35.02 4.20
4539 7523 8.191446 TCCTGAAAGAGTGAAAGTATATCTTCG 58.809 37.037 0.00 0.00 32.63 3.79
4553 7537 4.808414 TGTACCTCATCCTGAAAGAGTG 57.192 45.455 0.00 0.00 34.07 3.51
4555 7539 4.938226 GGTTTGTACCTCATCCTGAAAGAG 59.062 45.833 0.00 0.00 41.53 2.85
4556 7540 4.349636 TGGTTTGTACCTCATCCTGAAAGA 59.650 41.667 0.00 0.00 45.27 2.52
4557 7541 4.651778 TGGTTTGTACCTCATCCTGAAAG 58.348 43.478 0.00 0.00 45.27 2.62
4559 7543 4.715534 TTGGTTTGTACCTCATCCTGAA 57.284 40.909 0.00 0.00 45.27 3.02
4560 7544 4.927267 ATTGGTTTGTACCTCATCCTGA 57.073 40.909 0.00 0.00 45.27 3.86
4561 7545 6.828273 TCAATATTGGTTTGTACCTCATCCTG 59.172 38.462 15.36 0.00 45.27 3.86
4562 7546 6.969043 TCAATATTGGTTTGTACCTCATCCT 58.031 36.000 15.36 0.00 45.27 3.24
4563 7547 7.639113 TTCAATATTGGTTTGTACCTCATCC 57.361 36.000 15.36 0.00 45.27 3.51
4566 7550 8.527810 GGATTTTCAATATTGGTTTGTACCTCA 58.472 33.333 15.36 0.00 45.27 3.86
4567 7551 8.527810 TGGATTTTCAATATTGGTTTGTACCTC 58.472 33.333 15.36 1.64 45.27 3.85
4568 7552 8.429237 TGGATTTTCAATATTGGTTTGTACCT 57.571 30.769 15.36 0.00 45.27 3.08
4569 7553 9.665719 AATGGATTTTCAATATTGGTTTGTACC 57.334 29.630 15.36 10.56 45.26 3.34
4585 7569 9.874205 TGAAGACAAATGGATAAATGGATTTTC 57.126 29.630 0.00 0.00 0.00 2.29
4591 7575 6.377996 TGAGGTGAAGACAAATGGATAAATGG 59.622 38.462 0.00 0.00 0.00 3.16
4595 7579 6.122277 GGATGAGGTGAAGACAAATGGATAA 58.878 40.000 0.00 0.00 0.00 1.75
4599 7583 3.019564 GGGATGAGGTGAAGACAAATGG 58.980 50.000 0.00 0.00 0.00 3.16
4669 7656 0.817654 GGGGCCGGAAAGAAAATGAG 59.182 55.000 5.05 0.00 0.00 2.90
4677 7664 2.024414 CTTGATAAAGGGGCCGGAAAG 58.976 52.381 5.05 0.00 0.00 2.62
4681 7668 2.137810 TTTCTTGATAAAGGGGCCGG 57.862 50.000 0.00 0.00 0.00 6.13
4682 7669 4.736126 AAATTTCTTGATAAAGGGGCCG 57.264 40.909 0.00 0.00 0.00 6.13
4707 7694 2.951642 CCTTCACACTCTTTTTGGAGCA 59.048 45.455 0.00 0.00 36.87 4.26
4708 7695 2.287849 GCCTTCACACTCTTTTTGGAGC 60.288 50.000 0.00 0.00 36.87 4.70
4715 7702 5.546621 TTGTAGTAGCCTTCACACTCTTT 57.453 39.130 0.00 0.00 0.00 2.52
4740 7763 7.688578 CGAAGGAAAAACTCGATCTGAATAAAC 59.311 37.037 0.00 0.00 0.00 2.01
4858 7884 3.370840 TTCTGGCTAGGCAACATCAAT 57.629 42.857 20.64 0.00 41.41 2.57
4982 8008 3.314693 TGGAGTGTTCCTGGTTAAGACT 58.685 45.455 0.00 0.00 44.36 3.24


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

AutoCloner maintained by Alex Coulton.