Multiple sequence alignment - TraesCS3D01G325100

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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 TraesCS3D01G325100 chr3D 100.000 1823 0 0 975 2797 437966538 437968360 0.000000e+00 3367
1 TraesCS3D01G325100 chr3D 100.000 622 0 0 1 622 437965564 437966185 0.000000e+00 1149
2 TraesCS3D01G325100 chr3D 92.600 473 19 3 11 467 512695369 512695841 0.000000e+00 665
3 TraesCS3D01G325100 chr3B 88.612 641 26 25 2099 2735 573404050 573404647 0.000000e+00 736
4 TraesCS3D01G325100 chr3B 97.143 280 6 1 975 1252 573403706 573403985 3.260000e-129 472
5 TraesCS3D01G325100 chr3B 94.631 149 8 0 474 622 573403510 573403658 6.030000e-57 231
6 TraesCS3D01G325100 chr5D 92.812 473 18 3 11 467 65104949 65105421 0.000000e+00 671
7 TraesCS3D01G325100 chr5D 94.872 273 14 0 11 283 65995313 65995585 7.160000e-116 427
8 TraesCS3D01G325100 chr5D 92.473 186 12 2 284 467 65997663 65997848 5.940000e-67 265
9 TraesCS3D01G325100 chr5D 82.879 257 35 3 995 1245 529845178 529845431 3.630000e-54 222
10 TraesCS3D01G325100 chr5D 81.905 210 23 8 1037 1244 529815854 529816050 2.230000e-36 163
11 TraesCS3D01G325100 chr5D 77.186 263 34 17 996 1244 529800917 529801167 2.260000e-26 130
12 TraesCS3D01G325100 chr3A 90.688 494 25 9 1461 1935 576209735 576210226 3.040000e-179 638
13 TraesCS3D01G325100 chr3A 95.486 288 6 4 2099 2386 576210277 576210557 1.180000e-123 453
14 TraesCS3D01G325100 chr3A 95.763 236 10 0 975 1210 576208929 576209164 5.650000e-102 381
15 TraesCS3D01G325100 chr3A 89.247 279 16 3 2406 2675 576210546 576210819 1.240000e-88 337
16 TraesCS3D01G325100 chr3A 95.973 149 6 0 474 622 576208733 576208881 2.780000e-60 243
17 TraesCS3D01G325100 chr3A 92.174 115 7 2 1348 1462 576209546 576209658 8.020000e-36 161
18 TraesCS3D01G325100 chr3A 88.525 122 6 6 2675 2795 576212104 576212218 1.040000e-29 141
19 TraesCS3D01G325100 chr5B 89.362 470 35 3 13 467 139154508 139154039 6.720000e-161 577
20 TraesCS3D01G325100 chr5B 88.298 470 40 3 13 467 474269644 474269175 1.460000e-152 549
21 TraesCS3D01G325100 chr5B 83.812 383 52 9 93 467 680681186 680681566 3.430000e-94 355
22 TraesCS3D01G325100 chr4D 89.083 458 35 3 11 453 489155380 489154923 3.150000e-154 555
23 TraesCS3D01G325100 chr4D 88.136 472 40 9 11 467 461842647 461842177 5.270000e-152 547
24 TraesCS3D01G325100 chr6B 87.686 471 42 3 13 467 695842475 695842005 4.100000e-148 534
25 TraesCS3D01G325100 chr2D 85.684 475 49 5 11 467 622249459 622248986 1.510000e-132 483
26 TraesCS3D01G325100 chr1D 89.607 356 21 8 11 352 467103940 467104293 3.310000e-119 438
27 TraesCS3D01G325100 chr6D 87.644 348 22 7 141 467 448707651 448707998 4.370000e-103 385
28 TraesCS3D01G325100 chr6A 88.679 318 21 2 161 463 15691140 15690823 9.460000e-100 374
29 TraesCS3D01G325100 chr5A 82.212 208 24 6 1038 1244 657757044 657757239 1.720000e-37 167
30 TraesCS3D01G325100 chr5A 77.947 263 37 13 997 1244 657725193 657725449 8.070000e-31 145
31 TraesCS3D01G325100 chr5A 80.102 196 26 4 1038 1223 657760367 657760559 1.750000e-27 134


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 TraesCS3D01G325100 chr3D 437965564 437968360 2796 False 2258.000000 3367 100.000000 1 2797 2 chr3D.!!$F2 2796
1 TraesCS3D01G325100 chr3B 573403510 573404647 1137 False 479.666667 736 93.462000 474 2735 3 chr3B.!!$F1 2261
2 TraesCS3D01G325100 chr5D 65995313 65997848 2535 False 346.000000 427 93.672500 11 467 2 chr5D.!!$F5 456
3 TraesCS3D01G325100 chr3A 576208733 576212218 3485 False 336.285714 638 92.550857 474 2795 7 chr3A.!!$F1 2321


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
303 2381 1.197910 GTACTTATCCACGTCAGCGC 58.802 55.0 0.00 0.0 42.83 5.92 F
1291 3393 0.033504 GCGAGTGAGGTCCAACTGAA 59.966 55.0 2.11 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 3408 0.321564 TTGTGGATCCAACAGCTCGG 60.322 55.000 18.2 0.0 0.0 4.63 R
2571 5000 1.546029 AGCAGCTCGAACATCACAGTA 59.454 47.619 0.0 0.0 0.0 2.74 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
30 31 2.847234 CTACCGCCAGCCCCCATA 60.847 66.667 0.00 0.00 0.00 2.74
40 41 2.122547 CCCCCATAGCGGTAGGGT 60.123 66.667 22.40 0.00 41.16 4.34
74 75 1.407712 GGGCCCTTGCACTTATCGTTA 60.408 52.381 17.04 0.00 38.13 3.18
151 152 3.706373 ACACAGCCTACCGCCAGG 61.706 66.667 0.00 0.00 45.13 4.45
193 194 4.415150 CCGCCAGGTCCACTGCAT 62.415 66.667 0.00 0.00 46.14 3.96
216 217 7.675637 GCATATTTCGTTACAGAAGGGTTGTAC 60.676 40.741 0.00 0.00 31.17 2.90
303 2381 1.197910 GTACTTATCCACGTCAGCGC 58.802 55.000 0.00 0.00 42.83 5.92
348 2426 3.636929 TTGCACCCTACCGCCATGG 62.637 63.158 7.63 7.63 46.41 3.66
349 2427 4.875713 GCACCCTACCGCCATGGG 62.876 72.222 15.13 3.37 44.64 4.00
379 2457 2.466547 AGGCTGTATAACCCTACCGT 57.533 50.000 0.00 0.00 0.00 4.83
382 2460 2.035576 GGCTGTATAACCCTACCGTCAG 59.964 54.545 0.00 0.00 0.00 3.51
391 2469 1.388065 CCTACCGTCAGAGCCTCTGG 61.388 65.000 21.14 8.40 44.39 3.86
407 2485 2.678336 CTCTGGCGATAACAAAAGGGTC 59.322 50.000 0.00 0.00 0.00 4.46
444 2522 1.335132 GCAACCGGGGTCAGATCCTA 61.335 60.000 6.32 0.00 0.00 2.94
455 2533 6.826741 CGGGGTCAGATCCTAAATTTCTTAAA 59.173 38.462 0.00 0.00 0.00 1.52
614 2692 3.760035 CTCCGGAGTGTCCCCACG 61.760 72.222 24.04 0.00 46.56 4.94
1060 3138 1.875813 CTGCTCTTGCTACTCGCCG 60.876 63.158 0.00 0.00 40.48 6.46
1273 3375 2.485124 CCTCTCTCATGTTCATCCCTGC 60.485 54.545 0.00 0.00 0.00 4.85
1282 3384 0.904865 TTCATCCCTGCGAGTGAGGT 60.905 55.000 0.00 0.00 0.00 3.85
1286 3388 2.583441 CCCTGCGAGTGAGGTCCAA 61.583 63.158 0.00 0.00 0.00 3.53
1287 3389 1.374758 CCTGCGAGTGAGGTCCAAC 60.375 63.158 0.00 0.00 0.00 3.77
1288 3390 1.668294 CTGCGAGTGAGGTCCAACT 59.332 57.895 0.00 0.00 0.00 3.16
1289 3391 0.668706 CTGCGAGTGAGGTCCAACTG 60.669 60.000 2.11 0.00 0.00 3.16
1290 3392 1.112916 TGCGAGTGAGGTCCAACTGA 61.113 55.000 2.11 0.00 0.00 3.41
1291 3393 0.033504 GCGAGTGAGGTCCAACTGAA 59.966 55.000 2.11 0.00 0.00 3.02
1292 3394 1.338200 GCGAGTGAGGTCCAACTGAAT 60.338 52.381 2.11 0.00 0.00 2.57
1293 3395 2.611518 CGAGTGAGGTCCAACTGAATC 58.388 52.381 2.11 0.00 0.00 2.52
1294 3396 2.232452 CGAGTGAGGTCCAACTGAATCT 59.768 50.000 2.11 0.00 0.00 2.40
1295 3397 3.594134 GAGTGAGGTCCAACTGAATCTG 58.406 50.000 2.11 0.00 0.00 2.90
1296 3398 2.975489 AGTGAGGTCCAACTGAATCTGT 59.025 45.455 0.00 0.00 0.00 3.41
1297 3399 3.070018 GTGAGGTCCAACTGAATCTGTG 58.930 50.000 0.00 0.00 0.00 3.66
1298 3400 2.705658 TGAGGTCCAACTGAATCTGTGT 59.294 45.455 0.00 0.00 0.00 3.72
1299 3401 3.136443 TGAGGTCCAACTGAATCTGTGTT 59.864 43.478 0.00 0.00 0.00 3.32
1300 3402 4.346709 TGAGGTCCAACTGAATCTGTGTTA 59.653 41.667 0.00 0.00 0.00 2.41
1301 3403 4.642429 AGGTCCAACTGAATCTGTGTTAC 58.358 43.478 0.00 0.00 0.00 2.50
1302 3404 4.102524 AGGTCCAACTGAATCTGTGTTACA 59.897 41.667 0.00 0.00 0.00 2.41
1303 3405 4.213482 GGTCCAACTGAATCTGTGTTACAC 59.787 45.833 8.76 8.76 34.56 2.90
1304 3406 4.814234 GTCCAACTGAATCTGTGTTACACA 59.186 41.667 17.67 17.67 42.45 3.72
1311 3413 4.354155 TGTGTTACACAGCCGAGC 57.646 55.556 14.73 0.00 39.62 5.03
1312 3414 1.745890 TGTGTTACACAGCCGAGCT 59.254 52.632 14.73 0.00 39.62 4.09
1321 3423 2.586792 AGCCGAGCTGTTGGATCC 59.413 61.111 4.20 4.20 37.57 3.36
1322 3424 2.268920 GCCGAGCTGTTGGATCCA 59.731 61.111 11.44 11.44 0.00 3.41
1323 3425 2.109126 GCCGAGCTGTTGGATCCAC 61.109 63.158 15.91 10.58 0.00 4.02
1324 3426 1.296392 CCGAGCTGTTGGATCCACA 59.704 57.895 15.91 14.69 0.00 4.17
1325 3427 0.321564 CCGAGCTGTTGGATCCACAA 60.322 55.000 15.91 4.49 0.00 3.33
1326 3428 1.522668 CGAGCTGTTGGATCCACAAA 58.477 50.000 15.91 0.00 31.17 2.83
1327 3429 1.466167 CGAGCTGTTGGATCCACAAAG 59.534 52.381 15.91 13.18 31.17 2.77
1328 3430 1.200948 GAGCTGTTGGATCCACAAAGC 59.799 52.381 25.13 25.13 36.07 3.51
1329 3431 1.202976 AGCTGTTGGATCCACAAAGCT 60.203 47.619 27.76 27.76 38.62 3.74
1330 3432 1.615392 GCTGTTGGATCCACAAAGCTT 59.385 47.619 25.18 0.00 34.57 3.74
1331 3433 2.036346 GCTGTTGGATCCACAAAGCTTT 59.964 45.455 25.18 5.69 34.57 3.51
1332 3434 3.645884 CTGTTGGATCCACAAAGCTTTG 58.354 45.455 32.53 32.53 43.62 2.77
1333 3435 2.364970 TGTTGGATCCACAAAGCTTTGG 59.635 45.455 35.65 24.11 42.34 3.28
1334 3436 2.365293 GTTGGATCCACAAAGCTTTGGT 59.635 45.455 35.65 21.81 42.34 3.67
1335 3437 2.676748 TGGATCCACAAAGCTTTGGTT 58.323 42.857 35.65 19.59 42.34 3.67
1336 3438 3.838565 TGGATCCACAAAGCTTTGGTTA 58.161 40.909 35.65 22.98 42.34 2.85
1337 3439 3.572255 TGGATCCACAAAGCTTTGGTTAC 59.428 43.478 35.65 23.33 42.34 2.50
1338 3440 3.572255 GGATCCACAAAGCTTTGGTTACA 59.428 43.478 35.65 18.85 42.34 2.41
1339 3441 4.321230 GGATCCACAAAGCTTTGGTTACAG 60.321 45.833 35.65 20.03 42.34 2.74
1340 3442 2.955660 TCCACAAAGCTTTGGTTACAGG 59.044 45.455 35.65 26.01 42.34 4.00
1341 3443 2.545742 CCACAAAGCTTTGGTTACAGGC 60.546 50.000 35.65 0.00 42.34 4.85
1342 3444 1.686587 ACAAAGCTTTGGTTACAGGCC 59.313 47.619 35.65 0.00 42.34 5.19
1343 3445 1.000843 CAAAGCTTTGGTTACAGGCCC 59.999 52.381 28.12 0.00 34.59 5.80
1344 3446 0.482887 AAGCTTTGGTTACAGGCCCT 59.517 50.000 0.00 0.00 0.00 5.19
1345 3447 0.482887 AGCTTTGGTTACAGGCCCTT 59.517 50.000 0.00 0.00 0.00 3.95
1346 3448 0.888619 GCTTTGGTTACAGGCCCTTC 59.111 55.000 0.00 0.00 0.00 3.46
1349 3671 3.230976 CTTTGGTTACAGGCCCTTCTTT 58.769 45.455 0.00 0.00 0.00 2.52
1353 3675 3.396611 TGGTTACAGGCCCTTCTTTACTT 59.603 43.478 0.00 0.00 0.00 2.24
1373 3695 9.545105 TTTACTTTTACACCGATCTAAGTTGAA 57.455 29.630 0.00 0.00 0.00 2.69
1400 3722 4.697352 GGCCGCTGTAAATCATATGAATCT 59.303 41.667 9.99 0.00 0.00 2.40
1404 3726 6.075918 CGCTGTAAATCATATGAATCTGTGC 58.924 40.000 9.99 9.69 0.00 4.57
1451 3773 4.576106 TTTTCGCAACAAAAAGCAAGAC 57.424 36.364 0.00 0.00 0.00 3.01
1470 3870 7.716998 AGCAAGACATGAAGTATATTTGGTAGG 59.283 37.037 0.00 0.00 0.00 3.18
1475 3875 8.029782 ACATGAAGTATATTTGGTAGGCAGTA 57.970 34.615 0.00 0.00 0.00 2.74
1504 3904 4.281182 ACAGTGCTCCTCCTATATTTACCG 59.719 45.833 0.00 0.00 0.00 4.02
1506 3906 3.056035 GTGCTCCTCCTATATTTACCGGG 60.056 52.174 6.32 0.00 0.00 5.73
1518 3924 8.905850 CCTATATTTACCGGGTTTGTATTTGTT 58.094 33.333 4.31 0.00 0.00 2.83
1520 3926 5.450592 TTTACCGGGTTTGTATTTGTTCC 57.549 39.130 4.31 0.00 0.00 3.62
1523 3929 3.319689 ACCGGGTTTGTATTTGTTCCAAG 59.680 43.478 6.32 0.00 0.00 3.61
1532 3938 6.968263 TGTATTTGTTCCAAGAATTGTCCA 57.032 33.333 0.00 0.00 46.99 4.02
1533 3939 6.980593 TGTATTTGTTCCAAGAATTGTCCAG 58.019 36.000 0.00 0.00 46.99 3.86
1545 3951 5.476614 AGAATTGTCCAGTAGTACGTTTCC 58.523 41.667 0.00 0.00 0.00 3.13
1547 3953 1.895131 TGTCCAGTAGTACGTTTCCCC 59.105 52.381 0.00 0.00 0.00 4.81
1548 3954 1.895131 GTCCAGTAGTACGTTTCCCCA 59.105 52.381 0.00 0.00 0.00 4.96
1549 3955 2.498885 GTCCAGTAGTACGTTTCCCCAT 59.501 50.000 0.00 0.00 0.00 4.00
1550 3956 2.498481 TCCAGTAGTACGTTTCCCCATG 59.502 50.000 0.00 0.00 0.00 3.66
1551 3957 2.498481 CCAGTAGTACGTTTCCCCATGA 59.502 50.000 0.00 0.00 0.00 3.07
1552 3958 3.518590 CAGTAGTACGTTTCCCCATGAC 58.481 50.000 0.00 0.00 0.00 3.06
1574 3983 6.057321 ACATGGAGGTTTTTAGTCCGATTA 57.943 37.500 0.00 0.00 32.51 1.75
1625 4034 0.390472 CCCTGCTGGAGTTCGAGAAC 60.390 60.000 11.88 7.83 41.45 3.01
1635 4044 0.507358 GTTCGAGAACGTGGTGAAGC 59.493 55.000 0.00 0.00 40.69 3.86
1679 4088 4.414852 GCACGATGCACTTCATTACAATT 58.585 39.130 0.00 0.00 44.26 2.32
1771 4180 0.036858 AAGCTCGAGGAGTTCAAGCC 60.037 55.000 15.58 0.00 31.39 4.35
1789 4198 2.045926 GGTGGAGGACGCTGCAAT 60.046 61.111 0.00 0.00 0.00 3.56
1806 4222 5.422666 TGCAATCGCATAAGGTAAGATTG 57.577 39.130 10.92 10.92 45.36 2.67
1830 4249 3.186909 CTCTGTTTCACACTGAACGTCA 58.813 45.455 0.00 0.00 35.89 4.35
1833 4252 4.073169 TGTTTCACACTGAACGTCAAAC 57.927 40.909 0.00 0.00 35.89 2.93
1852 4271 7.493313 GTCAAACAAAATTGCGTCTATTTCAG 58.507 34.615 0.00 0.00 0.00 3.02
1897 4316 9.617523 TGATTCTTGTTTCAAGAGCATATCATA 57.382 29.630 14.89 1.20 0.00 2.15
1901 4320 9.049523 TCTTGTTTCAAGAGCATATCATATCAC 57.950 33.333 7.92 0.00 0.00 3.06
1906 4325 7.781324 TCAAGAGCATATCATATCACCTGTA 57.219 36.000 0.00 0.00 0.00 2.74
1935 4354 2.290832 TGGTTGAATCATGCAGGCTGTA 60.291 45.455 17.16 12.83 0.00 2.74
1936 4355 2.098117 GGTTGAATCATGCAGGCTGTAC 59.902 50.000 17.16 0.20 0.00 2.90
1937 4356 2.749076 GTTGAATCATGCAGGCTGTACA 59.251 45.455 17.16 6.83 0.00 2.90
1938 4357 3.286329 TGAATCATGCAGGCTGTACAT 57.714 42.857 17.16 9.05 0.00 2.29
1939 4358 3.623703 TGAATCATGCAGGCTGTACATT 58.376 40.909 17.16 13.13 0.00 2.71
1940 4359 4.018490 TGAATCATGCAGGCTGTACATTT 58.982 39.130 17.16 5.94 0.00 2.32
1941 4360 4.463539 TGAATCATGCAGGCTGTACATTTT 59.536 37.500 17.16 7.82 0.00 1.82
1942 4361 4.644103 ATCATGCAGGCTGTACATTTTC 57.356 40.909 17.16 0.00 0.00 2.29
1943 4362 3.419943 TCATGCAGGCTGTACATTTTCA 58.580 40.909 17.16 2.89 0.00 2.69
1944 4363 3.825585 TCATGCAGGCTGTACATTTTCAA 59.174 39.130 17.16 0.00 0.00 2.69
1945 4364 4.280425 TCATGCAGGCTGTACATTTTCAAA 59.720 37.500 17.16 0.00 0.00 2.69
1946 4365 4.662468 TGCAGGCTGTACATTTTCAAAA 57.338 36.364 17.16 0.00 0.00 2.44
1947 4366 5.016051 TGCAGGCTGTACATTTTCAAAAA 57.984 34.783 17.16 0.00 0.00 1.94
2017 4439 7.862274 ATTGATCATCAGGACTATAAGGTCA 57.138 36.000 0.00 0.00 37.91 4.02
2018 4440 7.675161 TTGATCATCAGGACTATAAGGTCAA 57.325 36.000 0.00 0.00 37.91 3.18
2019 4441 7.055667 TGATCATCAGGACTATAAGGTCAAC 57.944 40.000 0.00 0.00 37.91 3.18
2020 4442 6.841229 TGATCATCAGGACTATAAGGTCAACT 59.159 38.462 0.00 0.00 37.91 3.16
2021 4443 7.345653 TGATCATCAGGACTATAAGGTCAACTT 59.654 37.037 0.00 0.00 43.28 2.66
2022 4444 7.113658 TCATCAGGACTATAAGGTCAACTTC 57.886 40.000 0.00 0.00 40.64 3.01
2023 4445 6.897966 TCATCAGGACTATAAGGTCAACTTCT 59.102 38.462 0.00 0.00 40.64 2.85
2024 4446 8.059461 TCATCAGGACTATAAGGTCAACTTCTA 58.941 37.037 0.00 0.00 40.64 2.10
2025 4447 8.696374 CATCAGGACTATAAGGTCAACTTCTAA 58.304 37.037 0.00 0.00 40.64 2.10
2026 4448 8.660295 TCAGGACTATAAGGTCAACTTCTAAA 57.340 34.615 0.00 0.00 40.64 1.85
2027 4449 9.096823 TCAGGACTATAAGGTCAACTTCTAAAA 57.903 33.333 0.00 0.00 40.64 1.52
2028 4450 9.720769 CAGGACTATAAGGTCAACTTCTAAAAA 57.279 33.333 0.00 0.00 40.64 1.94
2051 4473 9.545105 AAAAAGCTTGTGATGTTCATATGAAAA 57.455 25.926 19.55 15.18 35.58 2.29
2052 4474 9.715121 AAAAGCTTGTGATGTTCATATGAAAAT 57.285 25.926 19.19 19.19 34.81 1.82
2053 4475 8.697846 AAGCTTGTGATGTTCATATGAAAATG 57.302 30.769 23.18 11.09 32.38 2.32
2054 4476 6.755141 AGCTTGTGATGTTCATATGAAAATGC 59.245 34.615 23.18 18.74 32.38 3.56
2055 4477 6.019318 GCTTGTGATGTTCATATGAAAATGCC 60.019 38.462 23.18 14.09 32.38 4.40
2056 4478 6.527057 TGTGATGTTCATATGAAAATGCCA 57.473 33.333 23.18 16.11 32.38 4.92
2057 4479 6.566141 TGTGATGTTCATATGAAAATGCCAG 58.434 36.000 23.18 0.00 32.38 4.85
2058 4480 5.461078 GTGATGTTCATATGAAAATGCCAGC 59.539 40.000 23.18 17.05 32.38 4.85
2059 4481 5.127356 TGATGTTCATATGAAAATGCCAGCA 59.873 36.000 23.18 19.08 32.38 4.41
2060 4482 5.402997 TGTTCATATGAAAATGCCAGCAA 57.597 34.783 19.55 0.00 35.58 3.91
2061 4483 5.979993 TGTTCATATGAAAATGCCAGCAAT 58.020 33.333 19.55 0.00 35.58 3.56
2062 4484 6.408035 TGTTCATATGAAAATGCCAGCAATT 58.592 32.000 19.55 0.00 35.58 2.32
2063 4485 6.879993 TGTTCATATGAAAATGCCAGCAATTT 59.120 30.769 19.55 5.39 35.58 1.82
2064 4486 8.039538 TGTTCATATGAAAATGCCAGCAATTTA 58.960 29.630 19.55 0.00 35.58 1.40
2065 4487 9.048446 GTTCATATGAAAATGCCAGCAATTTAT 57.952 29.630 19.55 5.20 35.58 1.40
2066 4488 8.821147 TCATATGAAAATGCCAGCAATTTATC 57.179 30.769 1.98 0.00 30.20 1.75
2067 4489 8.422566 TCATATGAAAATGCCAGCAATTTATCA 58.577 29.630 1.98 2.06 30.20 2.15
2068 4490 9.214957 CATATGAAAATGCCAGCAATTTATCAT 57.785 29.630 5.69 8.68 30.20 2.45
2069 4491 6.912203 TGAAAATGCCAGCAATTTATCATG 57.088 33.333 5.69 0.00 30.20 3.07
2070 4492 5.818336 TGAAAATGCCAGCAATTTATCATGG 59.182 36.000 5.69 0.00 30.20 3.66
2071 4493 4.345859 AATGCCAGCAATTTATCATGGG 57.654 40.909 0.00 0.00 0.00 4.00
2072 4494 3.029483 TGCCAGCAATTTATCATGGGA 57.971 42.857 0.00 0.00 0.00 4.37
2073 4495 2.694628 TGCCAGCAATTTATCATGGGAC 59.305 45.455 0.00 0.00 0.00 4.46
2074 4496 2.036346 GCCAGCAATTTATCATGGGACC 59.964 50.000 0.00 0.00 0.00 4.46
2075 4497 2.629617 CCAGCAATTTATCATGGGACCC 59.370 50.000 2.45 2.45 0.00 4.46
2076 4498 3.569491 CAGCAATTTATCATGGGACCCT 58.431 45.455 13.00 0.00 0.00 4.34
2077 4499 3.319972 CAGCAATTTATCATGGGACCCTG 59.680 47.826 13.00 7.83 0.00 4.45
2078 4500 2.036346 GCAATTTATCATGGGACCCTGC 59.964 50.000 13.00 5.94 0.00 4.85
2079 4501 3.569491 CAATTTATCATGGGACCCTGCT 58.431 45.455 13.00 2.01 0.00 4.24
2080 4502 3.962718 CAATTTATCATGGGACCCTGCTT 59.037 43.478 13.00 0.00 0.00 3.91
2081 4503 5.139727 CAATTTATCATGGGACCCTGCTTA 58.860 41.667 13.00 0.00 0.00 3.09
2082 4504 5.605540 ATTTATCATGGGACCCTGCTTAT 57.394 39.130 13.00 1.16 0.00 1.73
2083 4505 4.640771 TTATCATGGGACCCTGCTTATC 57.359 45.455 13.00 0.00 0.00 1.75
2084 4506 1.891933 TCATGGGACCCTGCTTATCA 58.108 50.000 13.00 0.00 0.00 2.15
2085 4507 2.421725 TCATGGGACCCTGCTTATCAT 58.578 47.619 13.00 0.00 0.00 2.45
2086 4508 2.373169 TCATGGGACCCTGCTTATCATC 59.627 50.000 13.00 0.00 0.00 2.92
2087 4509 1.891933 TGGGACCCTGCTTATCATCA 58.108 50.000 13.00 0.00 0.00 3.07
2088 4510 2.204463 TGGGACCCTGCTTATCATCAA 58.796 47.619 13.00 0.00 0.00 2.57
2089 4511 2.785269 TGGGACCCTGCTTATCATCAAT 59.215 45.455 13.00 0.00 0.00 2.57
2090 4512 3.205056 TGGGACCCTGCTTATCATCAATT 59.795 43.478 13.00 0.00 0.00 2.32
2091 4513 4.415179 TGGGACCCTGCTTATCATCAATTA 59.585 41.667 13.00 0.00 0.00 1.40
2092 4514 5.074929 TGGGACCCTGCTTATCATCAATTAT 59.925 40.000 13.00 0.00 0.00 1.28
2093 4515 6.274436 TGGGACCCTGCTTATCATCAATTATA 59.726 38.462 13.00 0.00 0.00 0.98
2094 4516 6.825721 GGGACCCTGCTTATCATCAATTATAG 59.174 42.308 2.09 0.00 0.00 1.31
2095 4517 7.311297 GGGACCCTGCTTATCATCAATTATAGA 60.311 40.741 2.09 0.00 0.00 1.98
2096 4518 8.103305 GGACCCTGCTTATCATCAATTATAGAA 58.897 37.037 0.00 0.00 0.00 2.10
2097 4519 9.678260 GACCCTGCTTATCATCAATTATAGAAT 57.322 33.333 0.00 0.00 0.00 2.40
2311 4733 1.156736 TAAGTCCGCTTCTTGCAAGC 58.843 50.000 21.99 10.33 43.06 4.01
2315 4737 1.081641 CCGCTTCTTGCAAGCTGTG 60.082 57.895 21.99 19.94 43.06 3.66
2318 4740 1.534595 CGCTTCTTGCAAGCTGTGTTT 60.535 47.619 21.99 0.00 43.06 2.83
2319 4741 2.122564 GCTTCTTGCAAGCTGTGTTTC 58.877 47.619 21.99 1.21 42.31 2.78
2320 4742 2.480073 GCTTCTTGCAAGCTGTGTTTCA 60.480 45.455 21.99 0.00 42.31 2.69
2321 4743 3.772932 CTTCTTGCAAGCTGTGTTTCAA 58.227 40.909 21.99 6.43 0.00 2.69
2322 4744 3.149436 TCTTGCAAGCTGTGTTTCAAC 57.851 42.857 21.99 0.00 0.00 3.18
2325 4747 1.135141 TGCAAGCTGTGTTTCAACCAC 60.135 47.619 0.00 0.00 0.00 4.16
2326 4748 1.135141 GCAAGCTGTGTTTCAACCACA 60.135 47.619 0.00 0.00 0.00 4.17
2327 4749 2.481795 GCAAGCTGTGTTTCAACCACAT 60.482 45.455 0.00 0.00 0.00 3.21
2328 4750 3.374745 CAAGCTGTGTTTCAACCACATC 58.625 45.455 0.00 0.00 0.00 3.06
2329 4751 2.936202 AGCTGTGTTTCAACCACATCT 58.064 42.857 0.00 0.00 0.00 2.90
2330 4752 2.620115 AGCTGTGTTTCAACCACATCTG 59.380 45.455 0.00 0.00 0.00 2.90
2331 4753 2.618241 GCTGTGTTTCAACCACATCTGA 59.382 45.455 0.00 0.00 0.00 3.27
2373 4798 9.461312 TCAGTATTATTGTATTTTGTTCTGCCT 57.539 29.630 0.00 0.00 0.00 4.75
2378 4803 9.995003 ATTATTGTATTTTGTTCTGCCTTTTGA 57.005 25.926 0.00 0.00 0.00 2.69
2379 4804 9.995003 TTATTGTATTTTGTTCTGCCTTTTGAT 57.005 25.926 0.00 0.00 0.00 2.57
2380 4805 8.907222 ATTGTATTTTGTTCTGCCTTTTGATT 57.093 26.923 0.00 0.00 0.00 2.57
2381 4806 7.712264 TGTATTTTGTTCTGCCTTTTGATTG 57.288 32.000 0.00 0.00 0.00 2.67
2382 4807 7.495901 TGTATTTTGTTCTGCCTTTTGATTGA 58.504 30.769 0.00 0.00 0.00 2.57
2383 4808 6.849588 ATTTTGTTCTGCCTTTTGATTGAC 57.150 33.333 0.00 0.00 0.00 3.18
2384 4809 5.596836 TTTGTTCTGCCTTTTGATTGACT 57.403 34.783 0.00 0.00 0.00 3.41
2385 4810 5.596836 TTGTTCTGCCTTTTGATTGACTT 57.403 34.783 0.00 0.00 0.00 3.01
2386 4811 5.596836 TGTTCTGCCTTTTGATTGACTTT 57.403 34.783 0.00 0.00 0.00 2.66
2387 4812 5.976458 TGTTCTGCCTTTTGATTGACTTTT 58.024 33.333 0.00 0.00 0.00 2.27
2388 4813 7.106439 TGTTCTGCCTTTTGATTGACTTTTA 57.894 32.000 0.00 0.00 0.00 1.52
2389 4814 6.978080 TGTTCTGCCTTTTGATTGACTTTTAC 59.022 34.615 0.00 0.00 0.00 2.01
2390 4815 6.959639 TCTGCCTTTTGATTGACTTTTACT 57.040 33.333 0.00 0.00 0.00 2.24
2391 4816 7.346751 TCTGCCTTTTGATTGACTTTTACTT 57.653 32.000 0.00 0.00 0.00 2.24
2392 4817 7.781056 TCTGCCTTTTGATTGACTTTTACTTT 58.219 30.769 0.00 0.00 0.00 2.66
2393 4818 8.257306 TCTGCCTTTTGATTGACTTTTACTTTT 58.743 29.630 0.00 0.00 0.00 2.27
2394 4819 8.195617 TGCCTTTTGATTGACTTTTACTTTTG 57.804 30.769 0.00 0.00 0.00 2.44
2395 4820 7.125755 GCCTTTTGATTGACTTTTACTTTTGC 58.874 34.615 0.00 0.00 0.00 3.68
2396 4821 7.336975 CCTTTTGATTGACTTTTACTTTTGCG 58.663 34.615 0.00 0.00 0.00 4.85
2397 4822 7.221838 CCTTTTGATTGACTTTTACTTTTGCGA 59.778 33.333 0.00 0.00 0.00 5.10
2398 4823 8.467402 TTTTGATTGACTTTTACTTTTGCGAA 57.533 26.923 0.00 0.00 0.00 4.70
2425 4850 6.127196 TGCCTTTTGATTGACTTGTTTTACCT 60.127 34.615 0.00 0.00 0.00 3.08
2544 4969 5.012239 AGTTGATTTAGCTTTGCCTGATGA 58.988 37.500 0.00 0.00 0.00 2.92
2548 4973 6.567050 TGATTTAGCTTTGCCTGATGATTTC 58.433 36.000 0.00 0.00 0.00 2.17
2552 4977 3.695060 AGCTTTGCCTGATGATTTCTCTG 59.305 43.478 0.00 0.00 0.00 3.35
2571 5000 1.147191 TGGTATGAGAGGGATAGCCGT 59.853 52.381 0.00 0.00 33.83 5.68
2591 5020 0.319728 ACTGTGATGTTCGAGCTGCT 59.680 50.000 0.00 0.00 0.00 4.24
2619 5048 1.195115 TCCAGGAAATAGCAGCGAGT 58.805 50.000 0.00 0.00 0.00 4.18
2776 6497 7.986085 AGGTATACCTGCATTTTGATCATAC 57.014 36.000 24.01 0.00 46.55 2.39
2777 6498 7.517320 AGGTATACCTGCATTTTGATCATACA 58.483 34.615 24.01 0.00 46.55 2.29
2786 6507 8.235359 TGCATTTTGATCATACATTCATACCA 57.765 30.769 0.00 0.00 0.00 3.25
2787 6508 8.693625 TGCATTTTGATCATACATTCATACCAA 58.306 29.630 0.00 0.00 0.00 3.67
2795 6516 8.806429 ATCATACATTCATACCAAGTTTGTCA 57.194 30.769 0.00 0.00 0.00 3.58
2796 6517 8.806429 TCATACATTCATACCAAGTTTGTCAT 57.194 30.769 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.250597 GCGGTAGGGTCCTGTGTTTT 60.251 55.000 0.00 0.00 0.00 2.43
1 2 1.373812 GCGGTAGGGTCCTGTGTTT 59.626 57.895 0.00 0.00 0.00 2.83
2 3 2.590114 GGCGGTAGGGTCCTGTGTT 61.590 63.158 0.00 0.00 0.00 3.32
3 4 3.001406 GGCGGTAGGGTCCTGTGT 61.001 66.667 0.00 0.00 0.00 3.72
4 5 3.000819 TGGCGGTAGGGTCCTGTG 61.001 66.667 0.00 0.00 0.00 3.66
5 6 2.683933 CTGGCGGTAGGGTCCTGT 60.684 66.667 0.00 0.00 0.00 4.00
6 7 4.162690 GCTGGCGGTAGGGTCCTG 62.163 72.222 0.00 0.00 0.00 3.86
30 31 2.038329 TAGGTGCACCCTACCGCT 59.962 61.111 32.29 14.48 43.87 5.52
68 69 6.518493 TCCAGTGTAAAGTTTCTGTAACGAT 58.482 36.000 0.00 0.00 41.78 3.73
74 75 6.207810 TGTGTTTTCCAGTGTAAAGTTTCTGT 59.792 34.615 0.00 0.00 0.00 3.41
116 117 3.851128 GACCCTACCGCCAGAGCC 61.851 72.222 0.00 0.00 34.57 4.70
117 118 3.075005 TGACCCTACCGCCAGAGC 61.075 66.667 0.00 0.00 0.00 4.09
151 152 3.087906 ACCCTACCGTCATGGGGC 61.088 66.667 2.61 0.00 44.30 5.80
156 157 2.537633 TAGGTTCACCCTACCGTCAT 57.462 50.000 0.00 0.00 43.87 3.06
180 181 2.632377 ACGAAATATGCAGTGGACCTG 58.368 47.619 0.00 0.00 44.53 4.00
193 194 5.863397 CGTACAACCCTTCTGTAACGAAATA 59.137 40.000 0.00 0.00 31.27 1.40
254 255 0.040794 AGGCTGTCTAACCCTACCGT 59.959 55.000 0.00 0.00 0.00 4.83
331 2409 4.108299 CCATGGCGGTAGGGTGCA 62.108 66.667 0.00 0.00 0.00 4.57
391 2469 4.421058 GGATTTGACCCTTTTGTTATCGC 58.579 43.478 0.00 0.00 0.00 4.58
455 2533 2.422597 GCGGCTAAATTTTGCCCTTTT 58.577 42.857 29.80 0.00 44.58 2.27
459 2537 0.177836 ATGGCGGCTAAATTTTGCCC 59.822 50.000 29.80 23.17 44.58 5.36
506 2584 1.610554 GAATCCCGAGGGGTTGACGA 61.611 60.000 12.08 0.00 44.74 4.20
528 2606 1.895231 GTCCCCGTGCCGACTTTTT 60.895 57.895 0.00 0.00 0.00 1.94
1264 3364 1.305297 ACCTCACTCGCAGGGATGA 60.305 57.895 0.00 0.00 35.01 2.92
1273 3375 2.232452 AGATTCAGTTGGACCTCACTCG 59.768 50.000 0.00 0.00 0.00 4.18
1282 3384 5.029807 TGTGTAACACAGATTCAGTTGGA 57.970 39.130 0.00 0.00 45.67 3.53
1294 3396 1.745890 AGCTCGGCTGTGTAACACA 59.254 52.632 0.00 0.00 45.67 3.72
1295 3397 4.675404 AGCTCGGCTGTGTAACAC 57.325 55.556 0.00 0.00 45.67 3.32
1304 3406 2.293318 TGGATCCAACAGCTCGGCT 61.293 57.895 13.46 0.00 40.77 5.52
1305 3407 2.109126 GTGGATCCAACAGCTCGGC 61.109 63.158 18.20 0.00 0.00 5.54
1306 3408 0.321564 TTGTGGATCCAACAGCTCGG 60.322 55.000 18.20 0.00 0.00 4.63
1307 3409 1.466167 CTTTGTGGATCCAACAGCTCG 59.534 52.381 18.20 0.00 0.00 5.03
1308 3410 1.200948 GCTTTGTGGATCCAACAGCTC 59.799 52.381 24.44 11.15 31.58 4.09
1309 3411 1.202976 AGCTTTGTGGATCCAACAGCT 60.203 47.619 27.05 27.05 35.70 4.24
1310 3412 1.251251 AGCTTTGTGGATCCAACAGC 58.749 50.000 24.37 24.37 33.01 4.40
1311 3413 3.553508 CCAAAGCTTTGTGGATCCAACAG 60.554 47.826 31.67 13.47 37.03 3.16
1312 3414 2.364970 CCAAAGCTTTGTGGATCCAACA 59.635 45.455 31.67 14.14 37.03 3.33
1313 3415 2.365293 ACCAAAGCTTTGTGGATCCAAC 59.635 45.455 31.67 11.54 38.36 3.77
1314 3416 2.676748 ACCAAAGCTTTGTGGATCCAA 58.323 42.857 31.67 4.13 38.36 3.53
1315 3417 2.380064 ACCAAAGCTTTGTGGATCCA 57.620 45.000 31.67 11.44 38.36 3.41
1316 3418 3.572255 TGTAACCAAAGCTTTGTGGATCC 59.428 43.478 31.67 17.27 38.36 3.36
1317 3419 4.321230 CCTGTAACCAAAGCTTTGTGGATC 60.321 45.833 31.67 19.63 38.36 3.36
1318 3420 3.573967 CCTGTAACCAAAGCTTTGTGGAT 59.426 43.478 31.67 18.99 38.36 3.41
1319 3421 2.955660 CCTGTAACCAAAGCTTTGTGGA 59.044 45.455 31.67 16.74 38.36 4.02
1320 3422 2.545742 GCCTGTAACCAAAGCTTTGTGG 60.546 50.000 31.67 23.52 41.00 4.17
1321 3423 2.545742 GGCCTGTAACCAAAGCTTTGTG 60.546 50.000 31.67 25.27 36.45 3.33
1322 3424 1.686587 GGCCTGTAACCAAAGCTTTGT 59.313 47.619 31.67 19.93 36.45 2.83
1323 3425 1.000843 GGGCCTGTAACCAAAGCTTTG 59.999 52.381 28.69 28.69 37.90 2.77
1324 3426 1.133167 AGGGCCTGTAACCAAAGCTTT 60.133 47.619 4.50 5.69 0.00 3.51
1325 3427 0.482887 AGGGCCTGTAACCAAAGCTT 59.517 50.000 4.50 0.00 0.00 3.74
1326 3428 0.482887 AAGGGCCTGTAACCAAAGCT 59.517 50.000 6.92 0.00 0.00 3.74
1327 3429 0.888619 GAAGGGCCTGTAACCAAAGC 59.111 55.000 6.92 0.00 0.00 3.51
1328 3430 2.586648 AGAAGGGCCTGTAACCAAAG 57.413 50.000 6.92 0.00 0.00 2.77
1329 3431 3.322191 AAAGAAGGGCCTGTAACCAAA 57.678 42.857 6.92 0.00 0.00 3.28
1330 3432 3.396611 AGTAAAGAAGGGCCTGTAACCAA 59.603 43.478 6.92 0.00 0.00 3.67
1331 3433 2.983898 AGTAAAGAAGGGCCTGTAACCA 59.016 45.455 6.92 0.00 0.00 3.67
1332 3434 3.715638 AGTAAAGAAGGGCCTGTAACC 57.284 47.619 6.92 0.00 0.00 2.85
1333 3435 6.487668 TGTAAAAGTAAAGAAGGGCCTGTAAC 59.512 38.462 6.92 1.40 0.00 2.50
1334 3436 6.487668 GTGTAAAAGTAAAGAAGGGCCTGTAA 59.512 38.462 6.92 0.00 0.00 2.41
1335 3437 5.999600 GTGTAAAAGTAAAGAAGGGCCTGTA 59.000 40.000 6.92 0.00 0.00 2.74
1336 3438 4.825634 GTGTAAAAGTAAAGAAGGGCCTGT 59.174 41.667 6.92 0.00 0.00 4.00
1337 3439 4.217767 GGTGTAAAAGTAAAGAAGGGCCTG 59.782 45.833 6.92 0.00 0.00 4.85
1338 3440 4.404640 GGTGTAAAAGTAAAGAAGGGCCT 58.595 43.478 0.00 0.00 0.00 5.19
1339 3441 3.189910 CGGTGTAAAAGTAAAGAAGGGCC 59.810 47.826 0.00 0.00 0.00 5.80
1340 3442 4.067192 TCGGTGTAAAAGTAAAGAAGGGC 58.933 43.478 0.00 0.00 0.00 5.19
1341 3443 6.171213 AGATCGGTGTAAAAGTAAAGAAGGG 58.829 40.000 0.00 0.00 0.00 3.95
1342 3444 8.767478 TTAGATCGGTGTAAAAGTAAAGAAGG 57.233 34.615 0.00 0.00 0.00 3.46
1343 3445 9.420551 ACTTAGATCGGTGTAAAAGTAAAGAAG 57.579 33.333 0.00 0.00 0.00 2.85
1344 3446 9.768662 AACTTAGATCGGTGTAAAAGTAAAGAA 57.231 29.630 0.00 0.00 0.00 2.52
1345 3447 9.199982 CAACTTAGATCGGTGTAAAAGTAAAGA 57.800 33.333 0.00 0.00 0.00 2.52
1346 3448 9.199982 TCAACTTAGATCGGTGTAAAAGTAAAG 57.800 33.333 0.00 0.00 0.00 1.85
1349 3671 9.715121 AATTCAACTTAGATCGGTGTAAAAGTA 57.285 29.630 0.00 0.00 0.00 2.24
1353 3675 6.311935 CCGAATTCAACTTAGATCGGTGTAAA 59.688 38.462 6.22 0.00 43.51 2.01
1373 3695 1.967319 ATGATTTACAGCGGCCGAAT 58.033 45.000 33.48 19.65 0.00 3.34
1378 3700 5.180117 ACAGATTCATATGATTTACAGCGGC 59.820 40.000 6.17 0.00 0.00 6.53
1400 3722 2.777094 TGGTTCAGATCAAATCGCACA 58.223 42.857 0.00 0.00 0.00 4.57
1404 3726 5.526479 AGACATCATGGTTCAGATCAAATCG 59.474 40.000 0.00 0.00 0.00 3.34
1446 3768 7.498900 TGCCTACCAAATATACTTCATGTCTTG 59.501 37.037 0.00 0.00 0.00 3.02
1449 3771 6.992715 ACTGCCTACCAAATATACTTCATGTC 59.007 38.462 0.00 0.00 0.00 3.06
1450 3772 6.900194 ACTGCCTACCAAATATACTTCATGT 58.100 36.000 0.00 0.00 0.00 3.21
1451 3773 7.931407 TGTACTGCCTACCAAATATACTTCATG 59.069 37.037 0.00 0.00 0.00 3.07
1470 3870 2.028930 AGGAGCACTGTAGTTGTACTGC 60.029 50.000 0.00 0.00 32.82 4.40
1475 3875 2.016905 AGGAGGAGCACTGTAGTTGT 57.983 50.000 0.00 0.00 0.00 3.32
1518 3924 4.525487 ACGTACTACTGGACAATTCTTGGA 59.475 41.667 0.00 0.00 34.12 3.53
1520 3926 6.128634 GGAAACGTACTACTGGACAATTCTTG 60.129 42.308 0.00 0.00 0.00 3.02
1523 3929 4.628766 GGGAAACGTACTACTGGACAATTC 59.371 45.833 0.00 0.00 0.00 2.17
1532 3938 3.167485 TGTCATGGGGAAACGTACTACT 58.833 45.455 0.00 0.00 0.00 2.57
1533 3939 3.598019 TGTCATGGGGAAACGTACTAC 57.402 47.619 0.00 0.00 0.00 2.73
1547 3953 4.094887 CGGACTAAAAACCTCCATGTCATG 59.905 45.833 5.79 5.79 0.00 3.07
1548 3954 4.019681 TCGGACTAAAAACCTCCATGTCAT 60.020 41.667 0.00 0.00 0.00 3.06
1549 3955 3.325425 TCGGACTAAAAACCTCCATGTCA 59.675 43.478 0.00 0.00 0.00 3.58
1550 3956 3.934068 TCGGACTAAAAACCTCCATGTC 58.066 45.455 0.00 0.00 0.00 3.06
1551 3957 4.569719 ATCGGACTAAAAACCTCCATGT 57.430 40.909 0.00 0.00 0.00 3.21
1552 3958 6.995511 TTAATCGGACTAAAAACCTCCATG 57.004 37.500 0.00 0.00 0.00 3.66
1592 4001 2.437359 AGGGCATTCTGCGACAGC 60.437 61.111 2.45 0.00 46.21 4.40
1625 4034 0.514691 GCTTCTTCAGCTTCACCACG 59.485 55.000 0.00 0.00 46.27 4.94
1648 4057 2.192187 TGCATCGTGCCAGCAACAA 61.192 52.632 0.00 0.00 44.23 2.83
1669 4078 4.545208 TCAGTGACCCGAATTGTAATGA 57.455 40.909 0.00 0.00 0.00 2.57
1771 4180 3.958147 ATTGCAGCGTCCTCCACCG 62.958 63.158 0.00 0.00 0.00 4.94
1789 4198 2.438021 AGGGCAATCTTACCTTATGCGA 59.562 45.455 0.00 0.00 37.88 5.10
1830 4249 5.405269 GCCTGAAATAGACGCAATTTTGTTT 59.595 36.000 0.00 0.00 0.00 2.83
1833 4252 3.543494 CGCCTGAAATAGACGCAATTTTG 59.457 43.478 0.00 0.00 0.00 2.44
1852 4271 1.135402 CAACCTTGATACTTTGCCGCC 60.135 52.381 0.00 0.00 0.00 6.13
1897 4316 1.640670 ACCAGGGCAAATACAGGTGAT 59.359 47.619 0.00 0.00 0.00 3.06
1901 4320 2.214376 TCAACCAGGGCAAATACAGG 57.786 50.000 0.00 0.00 0.00 4.00
1906 4325 2.093341 GCATGATTCAACCAGGGCAAAT 60.093 45.455 0.00 0.00 0.00 2.32
1951 4370 9.701098 CATAATTATTTACAGCCTGCATGATTT 57.299 29.630 0.00 0.00 0.00 2.17
1952 4371 8.863086 ACATAATTATTTACAGCCTGCATGATT 58.137 29.630 0.00 0.00 0.00 2.57
1953 4372 8.413309 ACATAATTATTTACAGCCTGCATGAT 57.587 30.769 0.00 0.00 0.00 2.45
1954 4373 7.040478 GGACATAATTATTTACAGCCTGCATGA 60.040 37.037 0.00 0.00 0.00 3.07
1955 4374 7.086376 GGACATAATTATTTACAGCCTGCATG 58.914 38.462 0.00 0.00 0.00 4.06
1956 4375 6.777091 TGGACATAATTATTTACAGCCTGCAT 59.223 34.615 0.00 0.00 0.00 3.96
1957 4376 6.125719 TGGACATAATTATTTACAGCCTGCA 58.874 36.000 0.00 0.00 0.00 4.41
1958 4377 6.633500 TGGACATAATTATTTACAGCCTGC 57.367 37.500 0.00 0.00 0.00 4.85
2025 4447 9.545105 TTTTCATATGAACATCACAAGCTTTTT 57.455 25.926 17.76 0.00 33.13 1.94
2026 4448 9.715121 ATTTTCATATGAACATCACAAGCTTTT 57.285 25.926 17.76 0.00 33.13 2.27
2027 4449 9.146984 CATTTTCATATGAACATCACAAGCTTT 57.853 29.630 17.76 0.00 33.13 3.51
2028 4450 7.277098 GCATTTTCATATGAACATCACAAGCTT 59.723 33.333 17.76 0.00 33.13 3.74
2029 4451 6.755141 GCATTTTCATATGAACATCACAAGCT 59.245 34.615 17.76 0.00 33.13 3.74
2030 4452 6.019318 GGCATTTTCATATGAACATCACAAGC 60.019 38.462 17.76 14.37 33.13 4.01
2031 4453 7.036829 TGGCATTTTCATATGAACATCACAAG 58.963 34.615 17.76 6.16 33.13 3.16
2032 4454 6.932947 TGGCATTTTCATATGAACATCACAA 58.067 32.000 17.76 8.82 33.13 3.33
2033 4455 6.527057 TGGCATTTTCATATGAACATCACA 57.473 33.333 17.76 13.69 33.13 3.58
2034 4456 5.461078 GCTGGCATTTTCATATGAACATCAC 59.539 40.000 17.76 11.56 33.13 3.06
2035 4457 5.127356 TGCTGGCATTTTCATATGAACATCA 59.873 36.000 17.76 10.70 33.13 3.07
2036 4458 5.593968 TGCTGGCATTTTCATATGAACATC 58.406 37.500 17.76 8.42 33.13 3.06
2037 4459 5.601583 TGCTGGCATTTTCATATGAACAT 57.398 34.783 17.76 13.94 33.13 2.71
2038 4460 5.402997 TTGCTGGCATTTTCATATGAACA 57.597 34.783 17.76 12.12 33.13 3.18
2039 4461 6.913873 AATTGCTGGCATTTTCATATGAAC 57.086 33.333 17.76 6.46 33.13 3.18
2040 4462 9.263538 GATAAATTGCTGGCATTTTCATATGAA 57.736 29.630 14.23 14.23 33.42 2.57
2041 4463 8.422566 TGATAAATTGCTGGCATTTTCATATGA 58.577 29.630 15.52 0.00 33.42 2.15
2042 4464 8.596271 TGATAAATTGCTGGCATTTTCATATG 57.404 30.769 15.52 0.00 33.42 1.78
2043 4465 9.214957 CATGATAAATTGCTGGCATTTTCATAT 57.785 29.630 15.52 7.27 33.42 1.78
2044 4466 7.658167 CCATGATAAATTGCTGGCATTTTCATA 59.342 33.333 15.52 6.91 33.42 2.15
2045 4467 6.485313 CCATGATAAATTGCTGGCATTTTCAT 59.515 34.615 15.52 12.26 33.42 2.57
2046 4468 5.818336 CCATGATAAATTGCTGGCATTTTCA 59.182 36.000 15.52 10.93 33.42 2.69
2047 4469 5.237779 CCCATGATAAATTGCTGGCATTTTC 59.762 40.000 15.52 6.77 33.42 2.29
2048 4470 5.104444 TCCCATGATAAATTGCTGGCATTTT 60.104 36.000 16.08 16.08 34.94 1.82
2049 4471 4.409574 TCCCATGATAAATTGCTGGCATTT 59.590 37.500 0.00 0.00 0.00 2.32
2050 4472 3.968649 TCCCATGATAAATTGCTGGCATT 59.031 39.130 0.00 0.00 0.00 3.56
2051 4473 3.322828 GTCCCATGATAAATTGCTGGCAT 59.677 43.478 0.00 0.00 0.00 4.40
2052 4474 2.694628 GTCCCATGATAAATTGCTGGCA 59.305 45.455 0.00 0.00 0.00 4.92
2053 4475 2.036346 GGTCCCATGATAAATTGCTGGC 59.964 50.000 0.00 0.00 0.00 4.85
2054 4476 2.629617 GGGTCCCATGATAAATTGCTGG 59.370 50.000 1.78 0.00 0.00 4.85
2055 4477 3.319972 CAGGGTCCCATGATAAATTGCTG 59.680 47.826 11.55 0.00 0.00 4.41
2056 4478 3.569491 CAGGGTCCCATGATAAATTGCT 58.431 45.455 11.55 0.00 0.00 3.91
2057 4479 2.036346 GCAGGGTCCCATGATAAATTGC 59.964 50.000 11.55 3.81 0.00 3.56
2058 4480 3.569491 AGCAGGGTCCCATGATAAATTG 58.431 45.455 11.55 0.00 0.00 2.32
2059 4481 3.979501 AGCAGGGTCCCATGATAAATT 57.020 42.857 11.55 0.00 0.00 1.82
2060 4482 3.979501 AAGCAGGGTCCCATGATAAAT 57.020 42.857 11.55 0.00 0.00 1.40
2061 4483 4.415179 TGATAAGCAGGGTCCCATGATAAA 59.585 41.667 11.55 0.00 0.00 1.40
2062 4484 3.980022 TGATAAGCAGGGTCCCATGATAA 59.020 43.478 11.55 0.00 0.00 1.75
2063 4485 3.597182 TGATAAGCAGGGTCCCATGATA 58.403 45.455 11.55 0.00 0.00 2.15
2064 4486 2.421725 TGATAAGCAGGGTCCCATGAT 58.578 47.619 11.55 1.19 0.00 2.45
2065 4487 1.891933 TGATAAGCAGGGTCCCATGA 58.108 50.000 11.55 0.00 0.00 3.07
2066 4488 2.107031 TGATGATAAGCAGGGTCCCATG 59.893 50.000 11.55 6.84 0.00 3.66
2067 4489 2.421725 TGATGATAAGCAGGGTCCCAT 58.578 47.619 11.55 0.00 0.00 4.00
2068 4490 1.891933 TGATGATAAGCAGGGTCCCA 58.108 50.000 11.55 0.00 0.00 4.37
2069 4491 3.515602 ATTGATGATAAGCAGGGTCCC 57.484 47.619 0.00 0.00 0.00 4.46
2070 4492 7.624549 TCTATAATTGATGATAAGCAGGGTCC 58.375 38.462 0.00 0.00 0.00 4.46
2071 4493 9.678260 ATTCTATAATTGATGATAAGCAGGGTC 57.322 33.333 0.00 0.00 0.00 4.46
2091 4513 8.830580 CGAGTAATTCATGGTGAACAATTCTAT 58.169 33.333 0.00 0.00 39.45 1.98
2092 4514 8.038351 TCGAGTAATTCATGGTGAACAATTCTA 58.962 33.333 0.00 0.00 39.45 2.10
2093 4515 6.878923 TCGAGTAATTCATGGTGAACAATTCT 59.121 34.615 0.00 0.00 39.45 2.40
2094 4516 7.064609 TCTCGAGTAATTCATGGTGAACAATTC 59.935 37.037 13.13 0.00 39.45 2.17
2095 4517 6.878923 TCTCGAGTAATTCATGGTGAACAATT 59.121 34.615 13.13 0.00 39.45 2.32
2096 4518 6.406370 TCTCGAGTAATTCATGGTGAACAAT 58.594 36.000 13.13 0.00 39.45 2.71
2097 4519 5.789521 TCTCGAGTAATTCATGGTGAACAA 58.210 37.500 13.13 0.00 39.45 2.83
2315 4737 6.861065 TTTAGAGTCAGATGTGGTTGAAAC 57.139 37.500 0.00 0.00 0.00 2.78
2318 4740 9.739276 ATTTTATTTAGAGTCAGATGTGGTTGA 57.261 29.630 0.00 0.00 0.00 3.18
2321 4743 9.965902 AGAATTTTATTTAGAGTCAGATGTGGT 57.034 29.630 0.00 0.00 0.00 4.16
2368 4793 8.330302 CAAAAGTAAAAGTCAATCAAAAGGCAG 58.670 33.333 0.00 0.00 0.00 4.85
2370 4795 7.125755 GCAAAAGTAAAAGTCAATCAAAAGGC 58.874 34.615 0.00 0.00 0.00 4.35
2373 4798 8.467402 TTCGCAAAAGTAAAAGTCAATCAAAA 57.533 26.923 0.00 0.00 0.00 2.44
2374 4799 8.641499 ATTCGCAAAAGTAAAAGTCAATCAAA 57.359 26.923 0.00 0.00 0.00 2.69
2375 4800 8.538856 CAATTCGCAAAAGTAAAAGTCAATCAA 58.461 29.630 0.00 0.00 0.00 2.57
2376 4801 7.306515 GCAATTCGCAAAAGTAAAAGTCAATCA 60.307 33.333 0.00 0.00 41.79 2.57
2377 4802 7.003648 GCAATTCGCAAAAGTAAAAGTCAATC 58.996 34.615 0.00 0.00 41.79 2.67
2378 4803 6.073819 GGCAATTCGCAAAAGTAAAAGTCAAT 60.074 34.615 2.98 0.00 45.17 2.57
2379 4804 5.233263 GGCAATTCGCAAAAGTAAAAGTCAA 59.767 36.000 2.98 0.00 45.17 3.18
2380 4805 4.742659 GGCAATTCGCAAAAGTAAAAGTCA 59.257 37.500 2.98 0.00 45.17 3.41
2381 4806 4.982295 AGGCAATTCGCAAAAGTAAAAGTC 59.018 37.500 0.00 0.00 45.17 3.01
2382 4807 4.944048 AGGCAATTCGCAAAAGTAAAAGT 58.056 34.783 0.00 0.00 45.17 2.66
2383 4808 5.905480 AAGGCAATTCGCAAAAGTAAAAG 57.095 34.783 0.00 0.00 45.17 2.27
2384 4809 6.313905 TCAAAAGGCAATTCGCAAAAGTAAAA 59.686 30.769 0.00 0.00 45.17 1.52
2385 4810 5.812642 TCAAAAGGCAATTCGCAAAAGTAAA 59.187 32.000 0.00 0.00 45.17 2.01
2386 4811 5.352284 TCAAAAGGCAATTCGCAAAAGTAA 58.648 33.333 0.00 0.00 45.17 2.24
2387 4812 4.938080 TCAAAAGGCAATTCGCAAAAGTA 58.062 34.783 0.00 0.00 45.17 2.24
2388 4813 3.791245 TCAAAAGGCAATTCGCAAAAGT 58.209 36.364 0.00 0.00 45.17 2.66
2389 4814 4.996062 ATCAAAAGGCAATTCGCAAAAG 57.004 36.364 0.00 0.00 45.17 2.27
2390 4815 4.813161 TCAATCAAAAGGCAATTCGCAAAA 59.187 33.333 0.00 0.00 45.17 2.44
2391 4816 4.210955 GTCAATCAAAAGGCAATTCGCAAA 59.789 37.500 0.00 0.00 45.17 3.68
2392 4817 3.740321 GTCAATCAAAAGGCAATTCGCAA 59.260 39.130 0.00 0.00 45.17 4.85
2393 4818 3.005684 AGTCAATCAAAAGGCAATTCGCA 59.994 39.130 0.00 0.00 45.17 5.10
2394 4819 3.578688 AGTCAATCAAAAGGCAATTCGC 58.421 40.909 0.00 0.00 41.28 4.70
2395 4820 4.984161 ACAAGTCAATCAAAAGGCAATTCG 59.016 37.500 0.00 0.00 0.00 3.34
2396 4821 6.849588 AACAAGTCAATCAAAAGGCAATTC 57.150 33.333 0.00 0.00 0.00 2.17
2397 4822 7.628769 AAAACAAGTCAATCAAAAGGCAATT 57.371 28.000 0.00 0.00 0.00 2.32
2398 4823 7.226523 GGTAAAACAAGTCAATCAAAAGGCAAT 59.773 33.333 0.00 0.00 0.00 3.56
2425 4850 3.298619 ACATATGCTAATTGCTGCCCAA 58.701 40.909 1.58 0.00 43.37 4.12
2441 4866 4.865905 TGGGCAGGTTAATGTGAACATAT 58.134 39.130 0.00 0.00 35.10 1.78
2442 4867 4.308526 TGGGCAGGTTAATGTGAACATA 57.691 40.909 0.00 0.00 35.10 2.29
2513 4938 6.368516 GGCAAAGCTAAATCAACTGCATTAAA 59.631 34.615 0.00 0.00 0.00 1.52
2544 4969 5.483583 GCTATCCCTCTCATACCAGAGAAAT 59.516 44.000 0.00 0.00 43.58 2.17
2548 4973 3.096092 GGCTATCCCTCTCATACCAGAG 58.904 54.545 0.00 0.00 39.89 3.35
2552 4977 1.926108 ACGGCTATCCCTCTCATACC 58.074 55.000 0.00 0.00 0.00 2.73
2571 5000 1.546029 AGCAGCTCGAACATCACAGTA 59.454 47.619 0.00 0.00 0.00 2.74
2591 5020 1.776667 CTATTTCCTGGATCCCTGGCA 59.223 52.381 9.90 0.00 41.59 4.92
2619 5048 5.794894 CAGCCAGTTCCTACTTCTTTTCTA 58.205 41.667 0.00 0.00 30.26 2.10
2707 6428 8.992073 ACATCAAGAAATAAAGGTTGCATTTTC 58.008 29.630 0.00 0.00 0.00 2.29
2761 6482 8.235359 TGGTATGAATGTATGATCAAAATGCA 57.765 30.769 0.00 0.00 0.00 3.96
2762 6483 9.188588 CTTGGTATGAATGTATGATCAAAATGC 57.811 33.333 0.00 0.00 0.00 3.56
2767 6488 9.241919 ACAAACTTGGTATGAATGTATGATCAA 57.758 29.630 0.00 0.00 0.00 2.57
2768 6489 8.806429 ACAAACTTGGTATGAATGTATGATCA 57.194 30.769 0.00 0.00 0.00 2.92
2769 6490 8.892723 TGACAAACTTGGTATGAATGTATGATC 58.107 33.333 0.00 0.00 0.00 2.92
2770 6491 8.806429 TGACAAACTTGGTATGAATGTATGAT 57.194 30.769 0.00 0.00 0.00 2.45
2771 6492 8.806429 ATGACAAACTTGGTATGAATGTATGA 57.194 30.769 0.00 0.00 0.00 2.15



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

AutoCloner maintained by Alex Coulton.