Multiple sequence alignment - TraesCS3D01G468400

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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 TraesCS3D01G468400 chr3D 100.000 3968 0 0 1 3968 570800243 570804210 0.000000e+00 7328.0
1 TraesCS3D01G468400 chr3D 86.364 132 12 4 3157 3286 497869492 497869619 5.350000e-29 139.0
2 TraesCS3D01G468400 chr3D 91.525 59 5 0 1411 1469 395065178 395065120 9.140000e-12 82.4
3 TraesCS3D01G468400 chr3B 86.947 3754 235 113 341 3968 757917664 757921288 0.000000e+00 3982.0
4 TraesCS3D01G468400 chr3B 90.000 280 23 5 1 279 757916171 757916446 1.360000e-94 357.0
5 TraesCS3D01G468400 chr3B 94.949 99 3 2 3200 3296 685059075 685059173 1.910000e-33 154.0
6 TraesCS3D01G468400 chr3B 87.218 133 10 4 3163 3292 659067988 659068116 1.150000e-30 145.0
7 TraesCS3D01G468400 chr3B 87.805 123 11 2 3163 3285 658492358 658492476 1.490000e-29 141.0
8 TraesCS3D01G468400 chr3B 89.744 78 6 2 2426 2502 653152429 653152505 9.070000e-17 99.0
9 TraesCS3D01G468400 chr3B 90.476 63 6 0 1407 1469 103722470 103722408 2.540000e-12 84.2
10 TraesCS3D01G468400 chr3A 89.545 1913 107 41 1209 3086 703906112 703904258 0.000000e+00 2338.0
11 TraesCS3D01G468400 chr3A 90.361 498 28 11 3490 3968 703902347 703901851 1.560000e-178 636.0
12 TraesCS3D01G468400 chr3A 87.692 325 29 8 3182 3495 703902699 703902375 6.260000e-98 368.0
13 TraesCS3D01G468400 chr3A 89.167 120 6 7 3191 3307 655640140 655640255 4.130000e-30 143.0
14 TraesCS3D01G468400 chr5A 91.200 125 11 0 1423 1547 663379381 663379505 1.900000e-38 171.0
15 TraesCS3D01G468400 chr5A 88.525 61 7 0 1406 1466 436089389 436089449 1.530000e-09 75.0
16 TraesCS3D01G468400 chr4B 91.803 122 10 0 1426 1547 613754440 613754319 1.900000e-38 171.0
17 TraesCS3D01G468400 chr4D 88.971 136 15 0 1412 1547 483369422 483369557 6.820000e-38 169.0
18 TraesCS3D01G468400 chr4D 84.167 120 10 3 2621 2740 448154559 448154449 1.510000e-19 108.0
19 TraesCS3D01G468400 chr4D 84.167 120 10 3 2621 2740 448155157 448155047 1.510000e-19 108.0
20 TraesCS3D01G468400 chr5B 95.789 95 2 2 3196 3288 350371224 350371130 6.870000e-33 152.0
21 TraesCS3D01G468400 chr1A 92.453 106 5 3 3184 3286 481884938 481885043 8.880000e-32 148.0
22 TraesCS3D01G468400 chr1A 89.796 49 4 1 97 145 343611205 343611158 1.190000e-05 62.1
23 TraesCS3D01G468400 chr5D 88.525 61 7 0 1406 1466 334255458 334255518 1.530000e-09 75.0
24 TraesCS3D01G468400 chr6D 93.333 45 3 0 2455 2499 90869463 90869419 2.560000e-07 67.6
25 TraesCS3D01G468400 chr6B 85.938 64 7 2 2455 2517 172990129 172990067 2.560000e-07 67.6
26 TraesCS3D01G468400 chr6A 93.333 45 3 0 2455 2499 109114233 109114189 2.560000e-07 67.6
27 TraesCS3D01G468400 chr1B 94.737 38 2 0 108 145 343651068 343651031 4.280000e-05 60.2
28 TraesCS3D01G468400 chr2B 96.970 33 0 1 2471 2502 663180745 663180713 2.000000e-03 54.7


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 TraesCS3D01G468400 chr3D 570800243 570804210 3967 False 7328.0 7328 100.000000 1 3968 1 chr3D.!!$F2 3967
1 TraesCS3D01G468400 chr3B 757916171 757921288 5117 False 2169.5 3982 88.473500 1 3968 2 chr3B.!!$F5 3967
2 TraesCS3D01G468400 chr3A 703901851 703906112 4261 True 1114.0 2338 89.199333 1209 3968 3 chr3A.!!$R1 2759

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
250 251 0.038166 CTTGTTTGCAGCCTAGGGGA 59.962 55.0 11.72 0.0 33.58 4.81 F
289 290 0.107066 TCTGCCAGGCATACACCATG 60.107 55.0 16.64 0.0 38.13 3.66 F
290 291 0.107066 CTGCCAGGCATACACCATGA 60.107 55.0 16.64 0.0 38.13 3.07 F
1343 2515 0.250901 ACAAGGAATGCGGCAAGAGT 60.251 50.0 6.82 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 3411 0.184692 TTGTTGTGCCACATCTGGGA 59.815 50.0 0.0 0.0 38.13 4.37 R
2195 3412 0.314935 GTTGTTGTGCCACATCTGGG 59.685 55.0 0.0 0.0 38.13 4.45 R
2196 3413 0.314935 GGTTGTTGTGCCACATCTGG 59.685 55.0 0.0 0.0 41.13 3.86 R
3142 4392 0.099968 CCATGCGCACTTCAGGAATG 59.900 55.0 14.9 3.0 0.00 2.67 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
37 38 7.430441 ACTTTCTTAATGCAAAACACGGTTAT 58.570 30.769 0.00 0.00 0.00 1.89
38 39 7.593644 ACTTTCTTAATGCAAAACACGGTTATC 59.406 33.333 0.00 0.00 0.00 1.75
39 40 6.811253 TCTTAATGCAAAACACGGTTATCT 57.189 33.333 0.00 0.00 0.00 1.98
40 41 7.908827 TCTTAATGCAAAACACGGTTATCTA 57.091 32.000 0.00 0.00 0.00 1.98
41 42 7.970384 TCTTAATGCAAAACACGGTTATCTAG 58.030 34.615 0.00 0.00 0.00 2.43
42 43 5.560966 AATGCAAAACACGGTTATCTAGG 57.439 39.130 0.00 0.00 0.00 3.02
47 48 6.027749 GCAAAACACGGTTATCTAGGATTTG 58.972 40.000 0.00 0.00 0.00 2.32
151 152 1.074889 TCCTAAGTCAAACTTGGCCCC 59.925 52.381 0.00 0.00 39.11 5.80
166 167 1.228124 CCCCGCTCACAAAGGTTGA 60.228 57.895 0.00 0.00 0.00 3.18
188 189 4.856607 GGCTCGGAGCTTCGGTCG 62.857 72.222 27.47 4.72 41.99 4.79
217 218 4.277174 ACAATTCAGGTACAACGCAATCAA 59.723 37.500 0.00 0.00 0.00 2.57
218 219 4.685169 ATTCAGGTACAACGCAATCAAG 57.315 40.909 0.00 0.00 0.00 3.02
237 238 1.215423 AGTGGCTCCTTGGACTTGTTT 59.785 47.619 0.00 0.00 0.00 2.83
238 239 1.338020 GTGGCTCCTTGGACTTGTTTG 59.662 52.381 0.00 0.00 0.00 2.93
239 240 0.315251 GGCTCCTTGGACTTGTTTGC 59.685 55.000 0.00 0.00 0.00 3.68
240 241 1.032014 GCTCCTTGGACTTGTTTGCA 58.968 50.000 0.00 0.00 0.00 4.08
242 243 1.000938 CTCCTTGGACTTGTTTGCAGC 60.001 52.381 0.00 0.00 0.00 5.25
250 251 0.038166 CTTGTTTGCAGCCTAGGGGA 59.962 55.000 11.72 0.00 33.58 4.81
269 270 2.280628 GAAGTGTGGAATCGATCACCC 58.719 52.381 13.06 9.01 33.29 4.61
279 280 2.191641 GATCACCCTCTGCCAGGC 59.808 66.667 3.66 3.66 41.80 4.85
280 281 2.611800 ATCACCCTCTGCCAGGCA 60.612 61.111 15.23 15.23 41.80 4.75
281 282 1.992519 GATCACCCTCTGCCAGGCAT 61.993 60.000 16.64 0.00 41.80 4.40
282 283 0.695462 ATCACCCTCTGCCAGGCATA 60.695 55.000 16.64 7.03 41.80 3.14
283 284 1.153086 CACCCTCTGCCAGGCATAC 60.153 63.158 16.64 0.00 41.80 2.39
285 286 1.153086 CCCTCTGCCAGGCATACAC 60.153 63.158 16.64 0.00 41.80 2.90
286 287 1.153086 CCTCTGCCAGGCATACACC 60.153 63.158 16.64 0.00 38.13 4.16
287 288 1.603842 CTCTGCCAGGCATACACCA 59.396 57.895 16.64 0.00 38.13 4.17
289 290 0.107066 TCTGCCAGGCATACACCATG 60.107 55.000 16.64 0.00 38.13 3.66
290 291 0.107066 CTGCCAGGCATACACCATGA 60.107 55.000 16.64 0.00 38.13 3.07
291 292 0.330941 TGCCAGGCATACACCATGAA 59.669 50.000 11.22 0.00 36.69 2.57
292 293 1.027357 GCCAGGCATACACCATGAAG 58.973 55.000 6.55 0.00 36.69 3.02
294 295 2.019249 CCAGGCATACACCATGAAGTG 58.981 52.381 0.00 0.00 43.65 3.16
303 304 3.044235 CACCATGAAGTGTGCTACTCA 57.956 47.619 0.00 0.00 39.18 3.41
304 305 2.738846 CACCATGAAGTGTGCTACTCAC 59.261 50.000 0.00 0.00 45.82 3.51
311 312 4.617875 GTGCTACTCACGGGCATT 57.382 55.556 0.00 0.00 38.27 3.56
312 313 3.752796 GTGCTACTCACGGGCATTA 57.247 52.632 0.00 0.00 38.27 1.90
313 314 2.018542 GTGCTACTCACGGGCATTAA 57.981 50.000 0.00 0.00 38.27 1.40
314 315 1.664151 GTGCTACTCACGGGCATTAAC 59.336 52.381 0.00 0.00 38.27 2.01
315 316 1.276705 TGCTACTCACGGGCATTAACA 59.723 47.619 0.00 0.00 0.00 2.41
316 317 1.933853 GCTACTCACGGGCATTAACAG 59.066 52.381 0.00 0.00 0.00 3.16
319 320 0.999406 CTCACGGGCATTAACAGACG 59.001 55.000 0.00 0.00 0.00 4.18
321 322 0.719465 CACGGGCATTAACAGACGAC 59.281 55.000 0.00 0.00 0.00 4.34
322 323 0.606604 ACGGGCATTAACAGACGACT 59.393 50.000 0.00 0.00 0.00 4.18
324 325 1.403647 CGGGCATTAACAGACGACTGA 60.404 52.381 21.50 0.00 46.03 3.41
325 326 2.271800 GGGCATTAACAGACGACTGAG 58.728 52.381 21.50 6.76 46.03 3.35
326 327 1.661112 GGCATTAACAGACGACTGAGC 59.339 52.381 21.50 14.69 46.03 4.26
327 328 1.321743 GCATTAACAGACGACTGAGCG 59.678 52.381 21.50 6.13 46.03 5.03
329 330 2.046283 TTAACAGACGACTGAGCGTG 57.954 50.000 21.50 0.00 45.72 5.34
331 332 0.949397 AACAGACGACTGAGCGTGTA 59.051 50.000 21.50 0.00 45.72 2.90
332 333 1.166129 ACAGACGACTGAGCGTGTAT 58.834 50.000 21.50 0.00 45.72 2.29
333 334 1.135660 ACAGACGACTGAGCGTGTATG 60.136 52.381 21.50 0.24 45.72 2.39
335 336 0.525668 GACGACTGAGCGTGTATGGG 60.526 60.000 6.66 0.00 45.72 4.00
336 337 1.248785 ACGACTGAGCGTGTATGGGT 61.249 55.000 1.43 0.00 43.79 4.51
337 338 0.736636 CGACTGAGCGTGTATGGGTA 59.263 55.000 0.00 0.00 0.00 3.69
338 339 1.133598 CGACTGAGCGTGTATGGGTAA 59.866 52.381 0.00 0.00 0.00 2.85
339 340 2.223735 CGACTGAGCGTGTATGGGTAAT 60.224 50.000 0.00 0.00 0.00 1.89
368 1525 5.617528 TCCCTGCACGGTTAAATCTATTA 57.382 39.130 1.44 0.00 0.00 0.98
371 1528 6.053005 CCCTGCACGGTTAAATCTATTAGAA 58.947 40.000 0.00 0.00 0.00 2.10
389 1546 1.883926 GAATAGTTGTGCCCACGGTTT 59.116 47.619 0.00 0.00 0.00 3.27
390 1547 2.863132 ATAGTTGTGCCCACGGTTTA 57.137 45.000 0.00 0.00 0.00 2.01
395 1552 1.071814 GTGCCCACGGTTTAGGACA 59.928 57.895 0.00 0.00 0.00 4.02
403 1560 3.818773 CCACGGTTTAGGACAACTTGAAT 59.181 43.478 0.00 0.00 0.00 2.57
486 1645 6.030727 AGTGCCTTGGGGATTATTCTTAAT 57.969 37.500 0.00 0.00 33.58 1.40
495 1654 5.185828 GGGGATTATTCTTAATGGGTGATGC 59.814 44.000 0.00 0.00 0.00 3.91
496 1655 5.106157 GGGATTATTCTTAATGGGTGATGCG 60.106 44.000 0.00 0.00 0.00 4.73
497 1656 5.705441 GGATTATTCTTAATGGGTGATGCGA 59.295 40.000 0.00 0.00 0.00 5.10
498 1657 6.206634 GGATTATTCTTAATGGGTGATGCGAA 59.793 38.462 0.00 0.00 0.00 4.70
499 1658 7.255451 GGATTATTCTTAATGGGTGATGCGAAA 60.255 37.037 0.00 0.00 0.00 3.46
531 1690 2.456577 GGGGGCAAGATTGTGTTATGT 58.543 47.619 0.00 0.00 0.00 2.29
532 1691 3.626930 GGGGGCAAGATTGTGTTATGTA 58.373 45.455 0.00 0.00 0.00 2.29
533 1692 3.380320 GGGGGCAAGATTGTGTTATGTAC 59.620 47.826 0.00 0.00 0.00 2.90
541 1700 9.490663 GCAAGATTGTGTTATGTACTTATGTTC 57.509 33.333 0.00 0.00 0.00 3.18
543 1702 8.997621 AGATTGTGTTATGTACTTATGTTCGT 57.002 30.769 0.00 0.00 0.00 3.85
545 1704 6.397831 TGTGTTATGTACTTATGTTCGTGC 57.602 37.500 0.00 0.00 0.00 5.34
566 1725 5.832060 GTGCTTAGGTTAGGTGGATAGAGTA 59.168 44.000 0.00 0.00 0.00 2.59
570 1729 8.108364 GCTTAGGTTAGGTGGATAGAGTAGATA 58.892 40.741 0.00 0.00 0.00 1.98
576 1735 9.298250 GTTAGGTGGATAGAGTAGATATTGTCA 57.702 37.037 0.00 0.00 0.00 3.58
581 1740 9.019656 GTGGATAGAGTAGATATTGTCATGACT 57.980 37.037 25.55 9.97 0.00 3.41
611 1770 5.306160 CCAATATGGATGGCCTCAGATTTTT 59.694 40.000 3.32 0.00 40.96 1.94
691 1850 2.294233 GGTTGTGTGCATCACTCAATGT 59.706 45.455 14.71 0.00 45.18 2.71
696 1855 3.065786 GTGTGCATCACTCAATGTATGGG 59.934 47.826 10.87 0.00 43.13 4.00
698 1857 2.300433 GCATCACTCAATGTATGGGCA 58.700 47.619 0.00 0.00 30.00 5.36
751 1911 3.074538 AGTGTGCTACCAAAAAGGGATCT 59.925 43.478 0.00 0.00 43.89 2.75
785 1945 0.943673 CGCACGCATATCCCAATCAA 59.056 50.000 0.00 0.00 0.00 2.57
843 2003 6.431234 ACTGGTCAGTTTTGATTACCATTCTC 59.569 38.462 0.00 0.00 38.83 2.87
846 2006 7.505585 TGGTCAGTTTTGATTACCATTCTCTTT 59.494 33.333 0.00 0.00 35.39 2.52
877 2037 9.706691 CTAATTACTAGAGTTTCCTTCACACAA 57.293 33.333 0.00 0.00 0.00 3.33
897 2057 6.207417 ACACAACCTCATCTAACCTTCAAATG 59.793 38.462 0.00 0.00 0.00 2.32
899 2059 4.273318 ACCTCATCTAACCTTCAAATGGC 58.727 43.478 0.00 0.00 0.00 4.40
918 2078 2.210711 CCCCCATCTAGGAGCGTCC 61.211 68.421 0.00 0.00 41.22 4.79
940 2100 7.521585 CGTCCTACATATACACATGAACAGCTA 60.522 40.741 0.00 0.00 0.00 3.32
941 2101 7.810282 GTCCTACATATACACATGAACAGCTAG 59.190 40.741 0.00 0.00 0.00 3.42
942 2102 6.587990 CCTACATATACACATGAACAGCTAGC 59.412 42.308 6.62 6.62 0.00 3.42
943 2103 6.166984 ACATATACACATGAACAGCTAGCT 57.833 37.500 12.68 12.68 0.00 3.32
947 2107 2.564504 ACACATGAACAGCTAGCTGAGA 59.435 45.455 43.42 28.04 46.30 3.27
975 2135 1.134431 TGTCAGACACATGCACACACT 60.134 47.619 0.00 0.00 0.00 3.55
976 2136 1.528586 GTCAGACACATGCACACACTC 59.471 52.381 0.00 0.00 0.00 3.51
990 2150 1.214062 CACTCACACCGAGAGAGGC 59.786 63.158 0.00 0.00 45.45 4.70
995 2155 3.443925 CACCGAGAGAGGCGCAGA 61.444 66.667 10.83 0.00 33.69 4.26
998 2158 3.898509 CGAGAGAGGCGCAGAGGG 61.899 72.222 10.83 0.00 0.00 4.30
999 2159 2.441164 GAGAGAGGCGCAGAGGGA 60.441 66.667 10.83 0.00 0.00 4.20
1029 2189 3.063704 CCATGCTGCGCCAAGGAA 61.064 61.111 4.18 0.00 0.00 3.36
1098 2258 2.097036 TCCTACATCAACGATCACGGT 58.903 47.619 0.00 0.00 44.46 4.83
1113 2273 4.366684 GGTGAGGGCAAGTGGGGG 62.367 72.222 0.00 0.00 0.00 5.40
1119 2279 4.432741 GGCAAGTGGGGGAGCCTC 62.433 72.222 0.00 0.00 43.70 4.70
1142 2302 2.028385 CCAAACGAGCTGGTAGGTTACT 60.028 50.000 0.30 0.00 0.00 2.24
1163 2328 5.437946 ACTCACACCATCGTCTCTAATCTA 58.562 41.667 0.00 0.00 0.00 1.98
1168 2333 5.048364 ACACCATCGTCTCTAATCTATGCTC 60.048 44.000 0.00 0.00 0.00 4.26
1174 2339 5.703592 TCGTCTCTAATCTATGCTCTTCTCC 59.296 44.000 0.00 0.00 0.00 3.71
1197 2362 8.950208 TCCGAACATTACATCAATACATACAA 57.050 30.769 0.00 0.00 0.00 2.41
1212 2377 4.772434 ACATACAATTGTCGATTATGCGC 58.228 39.130 15.85 0.00 0.00 6.09
1229 2394 1.832402 GCGCGCGATTTTCTTTAAGTC 59.168 47.619 37.18 6.21 0.00 3.01
1232 2397 3.541516 CGCGCGATTTTCTTTAAGTCGAT 60.542 43.478 28.94 0.00 45.59 3.59
1237 2402 6.129535 CGCGATTTTCTTTAAGTCGATCGATA 60.130 38.462 22.50 7.78 45.59 2.92
1257 2422 6.381420 TCGATATCTCCTCCAAACTCTTTCTT 59.619 38.462 0.34 0.00 0.00 2.52
1343 2515 0.250901 ACAAGGAATGCGGCAAGAGT 60.251 50.000 6.82 0.00 0.00 3.24
1348 2520 1.661341 GAATGCGGCAAGAGTGAGAT 58.339 50.000 6.82 0.00 0.00 2.75
1351 2523 0.390340 TGCGGCAAGAGTGAGATCAC 60.390 55.000 0.00 4.77 46.77 3.06
1403 2588 0.599060 TGTTGACGGCGTGTGAGATA 59.401 50.000 21.19 0.00 0.00 1.98
1410 2595 1.999735 CGGCGTGTGAGATATTGTGTT 59.000 47.619 0.00 0.00 0.00 3.32
1523 2708 0.975040 AGGAGCTCATCGTCAGGCTT 60.975 55.000 17.19 0.00 35.01 4.35
1570 2759 5.569059 GCACATCTATGTTGTTTTCCTTTCG 59.431 40.000 0.00 0.00 39.39 3.46
1611 2807 4.452114 TCTGTTGTGTACATGATCAAGCAC 59.548 41.667 0.00 7.36 35.85 4.40
1617 2813 6.172630 TGTGTACATGATCAAGCACTGTATT 58.827 36.000 17.13 0.00 0.00 1.89
1618 2814 6.092533 TGTGTACATGATCAAGCACTGTATTG 59.907 38.462 17.13 4.62 0.00 1.90
1619 2815 4.627611 ACATGATCAAGCACTGTATTGC 57.372 40.909 0.00 0.00 43.34 3.56
1672 2876 8.492673 ACATGCATATTCCTAATGTAATACGG 57.507 34.615 0.00 0.00 29.93 4.02
1673 2877 7.552687 ACATGCATATTCCTAATGTAATACGGG 59.447 37.037 0.00 0.00 29.93 5.28
1674 2878 6.411376 TGCATATTCCTAATGTAATACGGGG 58.589 40.000 0.00 0.00 0.00 5.73
1710 2914 4.745125 AGTGTGAACGAAGATGTACAAGTG 59.255 41.667 0.00 0.00 0.00 3.16
1767 2975 7.913297 TCACACTTGCTTGACAAAATTTAGTAC 59.087 33.333 0.00 0.00 37.96 2.73
1876 3085 3.072330 TGATCAGACAAAGTAGGCCAACA 59.928 43.478 5.01 0.00 0.00 3.33
1880 3089 2.174854 AGACAAAGTAGGCCAACACCTT 59.825 45.455 5.01 0.00 41.50 3.50
1886 3095 4.017177 AGTAGGCCAACACCTTCTAAAC 57.983 45.455 5.01 0.00 41.50 2.01
1888 3097 1.142262 AGGCCAACACCTTCTAAACGT 59.858 47.619 5.01 0.00 36.28 3.99
1891 3100 4.223477 AGGCCAACACCTTCTAAACGTATA 59.777 41.667 5.01 0.00 36.28 1.47
1892 3101 5.104652 AGGCCAACACCTTCTAAACGTATAT 60.105 40.000 5.01 0.00 36.28 0.86
1893 3102 6.098695 AGGCCAACACCTTCTAAACGTATATA 59.901 38.462 5.01 0.00 36.28 0.86
1894 3103 6.762661 GGCCAACACCTTCTAAACGTATATAA 59.237 38.462 0.00 0.00 0.00 0.98
1895 3104 7.254556 GGCCAACACCTTCTAAACGTATATAAC 60.255 40.741 0.00 0.00 0.00 1.89
1896 3105 7.493645 GCCAACACCTTCTAAACGTATATAACT 59.506 37.037 0.00 0.00 0.00 2.24
1897 3106 9.374838 CCAACACCTTCTAAACGTATATAACTT 57.625 33.333 0.00 0.00 0.00 2.66
1960 3169 5.478332 CACCTACTATCCATATCAGTCAGCA 59.522 44.000 0.00 0.00 0.00 4.41
2029 3238 0.671781 GACAGCCTGAATGCGTGTCT 60.672 55.000 0.00 0.00 36.91 3.41
2086 3296 5.630061 CAAAGTTGATGATGACGTGCATTA 58.370 37.500 0.00 0.00 37.34 1.90
2092 3302 5.809464 TGATGATGACGTGCATTAATTCAC 58.191 37.500 8.03 8.03 37.34 3.18
2093 3303 5.585844 TGATGATGACGTGCATTAATTCACT 59.414 36.000 14.87 3.90 37.34 3.41
2094 3304 5.878332 TGATGACGTGCATTAATTCACTT 57.122 34.783 14.87 6.78 37.34 3.16
2131 3341 6.096036 CACAACCACTCTGATCTACTACAAG 58.904 44.000 0.00 0.00 0.00 3.16
2194 3411 1.915078 CGAAATGCCACTCCCTCCCT 61.915 60.000 0.00 0.00 0.00 4.20
2195 3412 0.106967 GAAATGCCACTCCCTCCCTC 60.107 60.000 0.00 0.00 0.00 4.30
2196 3413 1.575447 AAATGCCACTCCCTCCCTCC 61.575 60.000 0.00 0.00 0.00 4.30
2197 3414 4.741239 TGCCACTCCCTCCCTCCC 62.741 72.222 0.00 0.00 0.00 4.30
2198 3415 4.741239 GCCACTCCCTCCCTCCCA 62.741 72.222 0.00 0.00 0.00 4.37
2199 3416 2.366167 CCACTCCCTCCCTCCCAG 60.366 72.222 0.00 0.00 0.00 4.45
2200 3417 2.780693 CACTCCCTCCCTCCCAGA 59.219 66.667 0.00 0.00 0.00 3.86
2270 3491 2.164624 GCTCTGATCTACGACAACCACT 59.835 50.000 0.00 0.00 0.00 4.00
2272 3493 3.687125 TCTGATCTACGACAACCACTCT 58.313 45.455 0.00 0.00 0.00 3.24
2273 3494 3.440522 TCTGATCTACGACAACCACTCTG 59.559 47.826 0.00 0.00 0.00 3.35
2276 3497 2.578786 TCTACGACAACCACTCTGTCA 58.421 47.619 4.07 0.00 42.80 3.58
2288 3509 2.620585 CACTCTGTCAGTCAGACTGTCA 59.379 50.000 26.65 25.09 46.77 3.58
2370 3599 4.129380 TCGCTACTGCTAATCAATTGCAT 58.871 39.130 0.00 0.00 36.07 3.96
2378 3607 5.584442 TGCTAATCAATTGCATGTGCTTAG 58.416 37.500 12.84 12.84 42.66 2.18
2379 3608 4.443394 GCTAATCAATTGCATGTGCTTAGC 59.557 41.667 20.65 20.65 42.66 3.09
2380 3609 4.730949 AATCAATTGCATGTGCTTAGCT 57.269 36.364 5.60 0.00 42.66 3.32
2382 3611 5.840243 ATCAATTGCATGTGCTTAGCTAA 57.160 34.783 5.60 5.94 42.66 3.09
2384 3613 6.940831 TCAATTGCATGTGCTTAGCTAATA 57.059 33.333 6.64 0.00 42.66 0.98
2385 3614 6.962686 TCAATTGCATGTGCTTAGCTAATAG 58.037 36.000 6.64 0.00 42.66 1.73
2386 3615 6.543465 TCAATTGCATGTGCTTAGCTAATAGT 59.457 34.615 6.64 0.00 42.66 2.12
2387 3616 7.714813 TCAATTGCATGTGCTTAGCTAATAGTA 59.285 33.333 6.64 0.00 42.66 1.82
2390 3619 7.284919 TGCATGTGCTTAGCTAATAGTAGTA 57.715 36.000 6.64 0.00 42.66 1.82
2391 3620 7.722363 TGCATGTGCTTAGCTAATAGTAGTAA 58.278 34.615 6.64 0.00 42.66 2.24
2392 3621 7.652105 TGCATGTGCTTAGCTAATAGTAGTAAC 59.348 37.037 6.64 0.00 42.66 2.50
2393 3622 7.868415 GCATGTGCTTAGCTAATAGTAGTAACT 59.132 37.037 6.64 0.00 37.65 2.24
2402 3631 7.818642 AGCTAATAGTAGTAACTAATCCAGCG 58.181 38.462 0.00 0.00 41.49 5.18
2404 3633 7.750014 GCTAATAGTAGTAACTAATCCAGCGTC 59.250 40.741 0.00 0.00 41.49 5.19
2405 3634 7.578310 AATAGTAGTAACTAATCCAGCGTCA 57.422 36.000 0.00 0.00 41.49 4.35
2415 3644 2.654749 TCCAGCGTCAGATAACAGTG 57.345 50.000 0.00 0.00 0.00 3.66
2416 3645 2.167662 TCCAGCGTCAGATAACAGTGA 58.832 47.619 0.00 0.00 0.00 3.41
2417 3646 2.094700 TCCAGCGTCAGATAACAGTGAC 60.095 50.000 0.00 0.00 39.83 3.67
2519 3749 1.004560 CGCTGAGCAAGAGGAACCA 60.005 57.895 4.88 0.00 0.00 3.67
2876 4112 4.559063 CGGGGCTGAGGCTGATGG 62.559 72.222 5.84 0.00 38.73 3.51
2964 4206 2.050077 GAGTTGGCGTGGCTTTGC 60.050 61.111 0.00 0.00 0.00 3.68
2978 4221 0.321653 CTTTGCTAGCCGTGGGAACT 60.322 55.000 13.29 0.00 0.00 3.01
2988 4231 1.335872 CCGTGGGAACTGTCAAAATGC 60.336 52.381 0.00 0.00 0.00 3.56
2991 4234 1.962807 TGGGAACTGTCAAAATGCCAG 59.037 47.619 0.00 0.00 0.00 4.85
3015 4260 5.539582 TGTGTTTGGCGTGAAATATAGTC 57.460 39.130 0.00 0.00 0.00 2.59
3016 4261 4.092237 TGTGTTTGGCGTGAAATATAGTCG 59.908 41.667 0.00 0.00 0.00 4.18
3057 4304 7.730084 ACTTGCATAGCTCAGTTCATCTTATA 58.270 34.615 0.00 0.00 0.00 0.98
3086 4336 2.554370 TACAGGGTGGTGCTGTAAAC 57.446 50.000 0.00 0.00 31.58 2.01
3094 4344 3.881089 GGTGGTGCTGTAAACAAAGTACT 59.119 43.478 0.00 0.00 30.66 2.73
3095 4345 5.058490 GGTGGTGCTGTAAACAAAGTACTA 58.942 41.667 0.00 0.00 30.66 1.82
3112 4362 3.721087 ACTACTGCCAAATAAGCTGGT 57.279 42.857 0.00 0.00 36.24 4.00
3131 4381 1.067060 GTGTGCCTTGGTCTTGGTTTC 59.933 52.381 0.00 0.00 0.00 2.78
3142 4392 1.004745 TCTTGGTTTCAGCCATCCCTC 59.995 52.381 0.00 0.00 38.48 4.30
3174 5900 1.917252 GCGCATGGAAATCGATTCGTG 60.917 52.381 11.83 12.22 39.05 4.35
3178 5904 3.198068 CATGGAAATCGATTCGTGGAGT 58.802 45.455 11.83 0.00 39.05 3.85
3179 5905 4.368315 CATGGAAATCGATTCGTGGAGTA 58.632 43.478 11.83 0.00 39.05 2.59
3292 6022 1.019805 GCTAGACGGGCTGGTGTTTC 61.020 60.000 0.00 0.00 0.00 2.78
3296 6026 0.534203 GACGGGCTGGTGTTTCTGAA 60.534 55.000 0.00 0.00 0.00 3.02
3302 6032 2.033424 GGCTGGTGTTTCTGAAGTGTTC 59.967 50.000 0.00 0.00 0.00 3.18
3308 6038 7.581213 TGGTGTTTCTGAAGTGTTCATTTAT 57.419 32.000 0.00 0.00 39.30 1.40
3310 6040 7.920151 TGGTGTTTCTGAAGTGTTCATTTATTG 59.080 33.333 0.00 0.00 39.30 1.90
3311 6041 7.382218 GGTGTTTCTGAAGTGTTCATTTATTGG 59.618 37.037 0.00 0.00 39.30 3.16
3313 6043 7.920151 TGTTTCTGAAGTGTTCATTTATTGGTG 59.080 33.333 0.00 0.00 39.30 4.17
3314 6044 6.573664 TCTGAAGTGTTCATTTATTGGTGG 57.426 37.500 0.00 0.00 39.30 4.61
3315 6045 6.068010 TCTGAAGTGTTCATTTATTGGTGGT 58.932 36.000 0.00 0.00 39.30 4.16
3317 6047 7.888021 TCTGAAGTGTTCATTTATTGGTGGTAT 59.112 33.333 0.00 0.00 39.30 2.73
3319 6049 7.122055 TGAAGTGTTCATTTATTGGTGGTATCC 59.878 37.037 0.00 0.00 34.08 2.59
3320 6050 6.731467 AGTGTTCATTTATTGGTGGTATCCT 58.269 36.000 0.00 0.00 0.00 3.24
3321 6051 6.828785 AGTGTTCATTTATTGGTGGTATCCTC 59.171 38.462 0.00 0.00 0.00 3.71
3333 6070 1.270518 GGTATCCTCGCATGCACAGAT 60.271 52.381 19.57 16.96 0.00 2.90
3337 6074 0.179076 CCTCGCATGCACAGATGGTA 60.179 55.000 19.57 0.00 0.00 3.25
3380 6118 3.748568 CCTACAAGAAAGCCAACTCTGAC 59.251 47.826 0.00 0.00 0.00 3.51
3397 6135 7.391148 ACTCTGACAAAGAAAACAGCTAAAA 57.609 32.000 0.00 0.00 33.37 1.52
3399 6137 7.917505 ACTCTGACAAAGAAAACAGCTAAAATG 59.082 33.333 0.00 0.00 33.37 2.32
3525 6300 7.581213 ACACTGATTTGGTATTCAGAAACAA 57.419 32.000 6.91 0.00 41.53 2.83
3553 6328 5.106317 TGGAACAGTTCAAGTTTGACAAGTC 60.106 40.000 15.36 0.00 36.83 3.01
3587 6362 4.446051 ACAAAACAAACCAAGTTGACAACG 59.554 37.500 12.54 1.68 36.23 4.10
3609 6384 4.332819 CGATGGACAGAAACTAATCAACCC 59.667 45.833 0.00 0.00 0.00 4.11
3754 6540 3.579302 CCCAGGGACCAGCCAACA 61.579 66.667 0.00 0.00 38.95 3.33
3765 6551 2.884639 ACCAGCCAACAATCTACAACAC 59.115 45.455 0.00 0.00 0.00 3.32
3776 6570 5.592282 ACAATCTACAACACCAATGACACAA 59.408 36.000 0.00 0.00 0.00 3.33
3808 6602 2.027192 ACCAGCCAACGATCTACAACAT 60.027 45.455 0.00 0.00 0.00 2.71
3955 6752 2.592032 TTGCCCGTCTGATCCTGCA 61.592 57.895 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.515414 GTTTTGCATTAAGAAAGTACTCAGGAT 58.485 33.333 0.00 0.00 0.00 3.24
5 6 7.591426 GTGTTTTGCATTAAGAAAGTACTCAGG 59.409 37.037 0.00 0.00 0.00 3.86
16 17 6.811253 AGATAACCGTGTTTTGCATTAAGA 57.189 33.333 0.00 0.00 0.00 2.10
23 24 5.813080 AATCCTAGATAACCGTGTTTTGC 57.187 39.130 0.00 0.00 0.00 3.68
37 38 4.746535 TTCATACGTGGCAAATCCTAGA 57.253 40.909 0.00 0.00 35.26 2.43
38 39 5.569413 GTTTTCATACGTGGCAAATCCTAG 58.431 41.667 0.00 0.00 35.26 3.02
39 40 4.093703 CGTTTTCATACGTGGCAAATCCTA 59.906 41.667 0.00 0.00 36.80 2.94
40 41 3.119990 CGTTTTCATACGTGGCAAATCCT 60.120 43.478 0.00 0.00 36.80 3.24
41 42 3.168193 CGTTTTCATACGTGGCAAATCC 58.832 45.455 0.00 0.00 36.80 3.01
130 131 2.160205 GGGCCAAGTTTGACTTAGGAC 58.840 52.381 4.39 8.91 36.03 3.85
136 137 2.597510 GCGGGGCCAAGTTTGACT 60.598 61.111 4.39 0.00 0.00 3.41
151 152 0.868406 GGACTCAACCTTTGTGAGCG 59.132 55.000 1.41 0.00 33.30 5.03
188 189 3.432252 CGTTGTACCTGAATTGTGAGTCC 59.568 47.826 0.00 0.00 0.00 3.85
217 218 0.846693 AACAAGTCCAAGGAGCCACT 59.153 50.000 0.00 0.00 0.00 4.00
218 219 1.338020 CAAACAAGTCCAAGGAGCCAC 59.662 52.381 0.00 0.00 0.00 5.01
237 238 1.538876 ACACTTCCCCTAGGCTGCA 60.539 57.895 2.05 0.00 0.00 4.41
238 239 1.078143 CACACTTCCCCTAGGCTGC 60.078 63.158 2.05 0.00 0.00 5.25
239 240 0.909610 TCCACACTTCCCCTAGGCTG 60.910 60.000 2.05 0.00 0.00 4.85
240 241 0.178873 TTCCACACTTCCCCTAGGCT 60.179 55.000 2.05 0.00 0.00 4.58
242 243 1.139058 CGATTCCACACTTCCCCTAGG 59.861 57.143 0.06 0.06 0.00 3.02
250 251 1.909302 AGGGTGATCGATTCCACACTT 59.091 47.619 14.52 2.10 43.89 3.16
269 270 0.182061 ATGGTGTATGCCTGGCAGAG 59.818 55.000 27.20 7.37 43.65 3.35
283 284 2.738846 GTGAGTAGCACACTTCATGGTG 59.261 50.000 0.00 0.00 46.91 4.17
294 295 1.664151 GTTAATGCCCGTGAGTAGCAC 59.336 52.381 0.00 0.00 40.58 4.40
296 297 1.933853 CTGTTAATGCCCGTGAGTAGC 59.066 52.381 0.00 0.00 0.00 3.58
297 298 3.187700 GTCTGTTAATGCCCGTGAGTAG 58.812 50.000 0.00 0.00 0.00 2.57
299 300 1.671850 CGTCTGTTAATGCCCGTGAGT 60.672 52.381 0.00 0.00 0.00 3.41
300 301 0.999406 CGTCTGTTAATGCCCGTGAG 59.001 55.000 0.00 0.00 0.00 3.51
303 304 0.606604 AGTCGTCTGTTAATGCCCGT 59.393 50.000 0.00 0.00 0.00 5.28
304 305 0.999406 CAGTCGTCTGTTAATGCCCG 59.001 55.000 1.16 0.00 36.97 6.13
305 306 2.271800 CTCAGTCGTCTGTTAATGCCC 58.728 52.381 9.48 0.00 41.91 5.36
306 307 1.661112 GCTCAGTCGTCTGTTAATGCC 59.339 52.381 9.48 0.00 41.91 4.40
307 308 1.321743 CGCTCAGTCGTCTGTTAATGC 59.678 52.381 9.48 6.85 41.91 3.56
308 309 2.342651 CACGCTCAGTCGTCTGTTAATG 59.657 50.000 9.48 1.90 41.21 1.90
309 310 2.030185 ACACGCTCAGTCGTCTGTTAAT 60.030 45.455 9.48 0.00 41.21 1.40
310 311 1.335810 ACACGCTCAGTCGTCTGTTAA 59.664 47.619 9.48 0.00 41.21 2.01
311 312 0.949397 ACACGCTCAGTCGTCTGTTA 59.051 50.000 9.48 0.00 41.21 2.41
312 313 0.949397 TACACGCTCAGTCGTCTGTT 59.051 50.000 9.48 0.00 41.21 3.16
313 314 1.135660 CATACACGCTCAGTCGTCTGT 60.136 52.381 9.48 0.00 41.21 3.41
314 315 1.539341 CATACACGCTCAGTCGTCTG 58.461 55.000 3.03 3.03 41.21 3.51
315 316 0.452184 CCATACACGCTCAGTCGTCT 59.548 55.000 0.00 0.00 41.21 4.18
316 317 0.525668 CCCATACACGCTCAGTCGTC 60.526 60.000 0.00 0.00 41.21 4.20
319 320 2.953466 TTACCCATACACGCTCAGTC 57.047 50.000 0.00 0.00 0.00 3.51
321 322 3.452755 TCATTACCCATACACGCTCAG 57.547 47.619 0.00 0.00 0.00 3.35
322 323 3.727726 CATCATTACCCATACACGCTCA 58.272 45.455 0.00 0.00 0.00 4.26
323 324 2.480419 GCATCATTACCCATACACGCTC 59.520 50.000 0.00 0.00 0.00 5.03
324 325 2.158827 TGCATCATTACCCATACACGCT 60.159 45.455 0.00 0.00 0.00 5.07
325 326 2.217750 TGCATCATTACCCATACACGC 58.782 47.619 0.00 0.00 0.00 5.34
326 327 3.436704 GGATGCATCATTACCCATACACG 59.563 47.826 27.25 0.00 0.00 4.49
327 328 3.758554 GGGATGCATCATTACCCATACAC 59.241 47.826 27.25 5.69 40.20 2.90
329 330 4.012374 CAGGGATGCATCATTACCCATAC 58.988 47.826 27.25 6.39 42.62 2.39
331 332 2.820485 GCAGGGATGCATCATTACCCAT 60.820 50.000 27.25 5.07 42.62 4.00
332 333 1.479205 GCAGGGATGCATCATTACCCA 60.479 52.381 27.25 0.00 42.62 4.51
333 334 1.251251 GCAGGGATGCATCATTACCC 58.749 55.000 27.25 19.29 40.71 3.69
368 1525 0.690762 ACCGTGGGCACAACTATTCT 59.309 50.000 0.00 0.00 0.00 2.40
371 1528 2.617021 CCTAAACCGTGGGCACAACTAT 60.617 50.000 0.00 0.00 0.00 2.12
389 1546 9.739276 ATCAAGTAAATCATTCAAGTTGTCCTA 57.261 29.630 2.11 0.00 0.00 2.94
390 1547 8.641498 ATCAAGTAAATCATTCAAGTTGTCCT 57.359 30.769 2.11 0.00 0.00 3.85
447 1606 0.667993 CACTCACACGGTTGGCAAAT 59.332 50.000 0.00 0.00 0.00 2.32
448 1607 1.999071 GCACTCACACGGTTGGCAAA 61.999 55.000 0.00 0.00 0.00 3.68
449 1608 2.477176 GCACTCACACGGTTGGCAA 61.477 57.895 0.00 0.00 0.00 4.52
450 1609 2.899838 GCACTCACACGGTTGGCA 60.900 61.111 0.00 0.00 0.00 4.92
451 1610 3.660111 GGCACTCACACGGTTGGC 61.660 66.667 0.00 0.00 0.00 4.52
455 1614 2.111043 CCAAGGCACTCACACGGT 59.889 61.111 0.00 0.00 38.49 4.83
486 1645 2.354729 CCCCTTTCGCATCACCCA 59.645 61.111 0.00 0.00 0.00 4.51
513 1672 5.897377 AAGTACATAACACAATCTTGCCC 57.103 39.130 0.00 0.00 0.00 5.36
516 1675 9.689075 CGAACATAAGTACATAACACAATCTTG 57.311 33.333 0.00 0.00 0.00 3.02
517 1676 9.431887 ACGAACATAAGTACATAACACAATCTT 57.568 29.630 0.00 0.00 0.00 2.40
518 1677 8.869897 CACGAACATAAGTACATAACACAATCT 58.130 33.333 0.00 0.00 0.00 2.40
521 1680 6.647481 AGCACGAACATAAGTACATAACACAA 59.353 34.615 0.00 0.00 0.00 3.33
522 1681 6.160684 AGCACGAACATAAGTACATAACACA 58.839 36.000 0.00 0.00 0.00 3.72
523 1682 6.642683 AGCACGAACATAAGTACATAACAC 57.357 37.500 0.00 0.00 0.00 3.32
524 1683 7.490079 CCTAAGCACGAACATAAGTACATAACA 59.510 37.037 0.00 0.00 0.00 2.41
525 1684 7.490402 ACCTAAGCACGAACATAAGTACATAAC 59.510 37.037 0.00 0.00 0.00 1.89
526 1685 7.549839 ACCTAAGCACGAACATAAGTACATAA 58.450 34.615 0.00 0.00 0.00 1.90
527 1686 7.104043 ACCTAAGCACGAACATAAGTACATA 57.896 36.000 0.00 0.00 0.00 2.29
528 1687 5.974108 ACCTAAGCACGAACATAAGTACAT 58.026 37.500 0.00 0.00 0.00 2.29
529 1688 5.395682 ACCTAAGCACGAACATAAGTACA 57.604 39.130 0.00 0.00 0.00 2.90
530 1689 6.474751 CCTAACCTAAGCACGAACATAAGTAC 59.525 42.308 0.00 0.00 0.00 2.73
531 1690 6.153340 ACCTAACCTAAGCACGAACATAAGTA 59.847 38.462 0.00 0.00 0.00 2.24
532 1691 5.046807 ACCTAACCTAAGCACGAACATAAGT 60.047 40.000 0.00 0.00 0.00 2.24
533 1692 5.291128 CACCTAACCTAAGCACGAACATAAG 59.709 44.000 0.00 0.00 0.00 1.73
541 1700 2.981859 ATCCACCTAACCTAAGCACG 57.018 50.000 0.00 0.00 0.00 5.34
543 1702 4.880164 ACTCTATCCACCTAACCTAAGCA 58.120 43.478 0.00 0.00 0.00 3.91
570 1729 8.608598 TCCATATTGGATATGAGTCATGACAAT 58.391 33.333 27.02 23.29 42.67 2.71
660 1819 6.478512 TGATGCACACAACCATATACTCTA 57.521 37.500 0.00 0.00 0.00 2.43
661 1820 5.357742 TGATGCACACAACCATATACTCT 57.642 39.130 0.00 0.00 0.00 3.24
720 1880 5.606348 TTTGGTAGCACACTTCCATTTTT 57.394 34.783 0.00 0.00 42.33 1.94
724 1884 3.573967 CCTTTTTGGTAGCACACTTCCAT 59.426 43.478 0.00 0.00 42.33 3.41
725 1885 2.955660 CCTTTTTGGTAGCACACTTCCA 59.044 45.455 0.00 0.00 41.22 3.53
726 1886 2.296190 CCCTTTTTGGTAGCACACTTCC 59.704 50.000 0.00 0.00 34.04 3.46
727 1887 3.219281 TCCCTTTTTGGTAGCACACTTC 58.781 45.455 0.00 0.00 0.00 3.01
728 1888 3.306472 TCCCTTTTTGGTAGCACACTT 57.694 42.857 0.00 0.00 0.00 3.16
730 1890 3.421844 AGATCCCTTTTTGGTAGCACAC 58.578 45.455 0.00 0.00 0.00 3.82
731 1891 3.806949 AGATCCCTTTTTGGTAGCACA 57.193 42.857 0.00 0.00 0.00 4.57
733 1893 4.534500 TCTGTAGATCCCTTTTTGGTAGCA 59.466 41.667 0.00 0.00 0.00 3.49
734 1894 5.099042 TCTGTAGATCCCTTTTTGGTAGC 57.901 43.478 0.00 0.00 0.00 3.58
735 1895 6.889198 TCATCTGTAGATCCCTTTTTGGTAG 58.111 40.000 0.00 0.00 31.21 3.18
775 1935 4.472470 TCTCACTGTCAGATTGATTGGGAT 59.528 41.667 6.91 0.00 0.00 3.85
785 1945 1.280421 GGCCCTTTCTCACTGTCAGAT 59.720 52.381 6.91 0.00 0.00 2.90
822 1982 9.827411 GTAAAGAGAATGGTAATCAAAACTGAC 57.173 33.333 0.00 0.00 0.00 3.51
846 2006 9.537852 TGAAGGAAACTCTAGTAATTAGGTGTA 57.462 33.333 0.00 0.00 42.68 2.90
861 2021 3.541632 TGAGGTTGTGTGAAGGAAACTC 58.458 45.455 0.00 0.00 42.68 3.01
868 2028 4.899502 AGGTTAGATGAGGTTGTGTGAAG 58.100 43.478 0.00 0.00 0.00 3.02
877 2037 4.273318 GCCATTTGAAGGTTAGATGAGGT 58.727 43.478 0.00 0.00 0.00 3.85
913 2073 5.286438 TGTTCATGTGTATATGTAGGACGC 58.714 41.667 0.00 0.00 0.00 5.19
918 2078 7.328005 CAGCTAGCTGTTCATGTGTATATGTAG 59.672 40.741 32.46 3.88 39.10 2.74
941 2101 1.818060 TCTGACAGAGAAGCTCTCAGC 59.182 52.381 0.00 0.00 45.73 4.26
942 2102 2.819019 TGTCTGACAGAGAAGCTCTCAG 59.181 50.000 5.10 9.08 45.73 3.35
943 2103 2.556189 GTGTCTGACAGAGAAGCTCTCA 59.444 50.000 11.41 0.00 45.73 3.27
947 2107 2.612471 GCATGTGTCTGACAGAGAAGCT 60.612 50.000 11.41 0.00 38.23 3.74
951 2111 1.688197 TGTGCATGTGTCTGACAGAGA 59.312 47.619 11.41 0.73 38.23 3.10
975 2135 3.749064 GCGCCTCTCTCGGTGTGA 61.749 66.667 0.00 0.00 36.91 3.58
976 2136 3.978723 CTGCGCCTCTCTCGGTGTG 62.979 68.421 4.18 0.00 36.91 3.82
990 2150 2.507944 CTCCCCATTCCCTCTGCG 59.492 66.667 0.00 0.00 0.00 5.18
995 2155 2.009302 GGCTTCCTCCCCATTCCCT 61.009 63.158 0.00 0.00 0.00 4.20
998 2158 1.111715 GCATGGCTTCCTCCCCATTC 61.112 60.000 0.00 0.00 39.76 2.67
999 2159 1.075748 GCATGGCTTCCTCCCCATT 60.076 57.895 0.00 0.00 39.76 3.16
1029 2189 3.334054 GCCCCTCTGTTCAGGCCT 61.334 66.667 0.00 0.00 39.60 5.19
1098 2258 2.935481 CTCCCCCACTTGCCCTCA 60.935 66.667 0.00 0.00 0.00 3.86
1113 2273 2.436824 GCTCGTTTGGGGAGGCTC 60.437 66.667 5.78 5.78 32.10 4.70
1119 2279 1.078426 CCTACCAGCTCGTTTGGGG 60.078 63.158 0.00 0.00 40.11 4.96
1142 2302 5.278512 GCATAGATTAGAGACGATGGTGTGA 60.279 44.000 0.00 0.00 0.00 3.58
1163 2328 4.471904 TGTAATGTTCGGAGAAGAGCAT 57.528 40.909 0.00 0.00 45.90 3.79
1168 2333 7.770801 TGTATTGATGTAATGTTCGGAGAAG 57.229 36.000 0.00 0.00 45.90 2.85
1197 2362 1.201578 CGCGCGCATAATCGACAAT 59.798 52.632 32.61 0.00 0.00 2.71
1203 2368 2.300623 AGAAAATCGCGCGCATAATC 57.699 45.000 32.61 20.61 0.00 1.75
1212 2377 4.027945 TCGATCGACTTAAAGAAAATCGCG 60.028 41.667 15.15 0.00 35.68 5.87
1229 2394 4.457603 AGAGTTTGGAGGAGATATCGATCG 59.542 45.833 9.36 9.36 37.15 3.69
1232 2397 5.894393 AGAAAGAGTTTGGAGGAGATATCGA 59.106 40.000 0.00 0.00 0.00 3.59
1237 2402 4.331108 GCAAGAAAGAGTTTGGAGGAGAT 58.669 43.478 0.00 0.00 0.00 2.75
1318 2490 0.598065 GCCGCATTCCTTGTTTCAGT 59.402 50.000 0.00 0.00 0.00 3.41
1343 2515 5.178797 GCTAAAGCTAAACCAGTGATCTCA 58.821 41.667 0.00 0.00 38.21 3.27
1348 2520 4.876107 GCTATGCTAAAGCTAAACCAGTGA 59.124 41.667 3.26 0.00 42.66 3.41
1359 2531 2.992543 CCATCTCGAGCTATGCTAAAGC 59.007 50.000 7.81 0.00 39.88 3.51
1410 2595 2.124983 GCAGCGATTCAGCCCTGA 60.125 61.111 0.00 0.00 38.01 3.86
1523 2708 2.284331 TTGCCTAGGAGCCCGTGA 60.284 61.111 14.75 0.00 0.00 4.35
1611 2807 8.984764 TGTAAGTGTAAGTAAACAGCAATACAG 58.015 33.333 0.00 0.00 0.00 2.74
1617 2813 6.238266 GCAAGTGTAAGTGTAAGTAAACAGCA 60.238 38.462 0.00 0.00 0.00 4.41
1618 2814 6.134061 GCAAGTGTAAGTGTAAGTAAACAGC 58.866 40.000 0.00 0.00 0.00 4.40
1619 2815 7.241663 TGCAAGTGTAAGTGTAAGTAAACAG 57.758 36.000 0.00 0.00 0.00 3.16
1670 2874 5.237815 TCACACTATATACTACGTACCCCG 58.762 45.833 0.00 0.00 44.03 5.73
1671 2875 6.347725 CGTTCACACTATATACTACGTACCCC 60.348 46.154 0.00 0.00 0.00 4.95
1672 2876 6.423905 TCGTTCACACTATATACTACGTACCC 59.576 42.308 0.00 0.00 0.00 3.69
1673 2877 7.408132 TCGTTCACACTATATACTACGTACC 57.592 40.000 0.00 0.00 0.00 3.34
1674 2878 8.755941 TCTTCGTTCACACTATATACTACGTAC 58.244 37.037 0.00 0.00 0.00 3.67
1710 2914 1.003718 CCTCCACGACCAAAGACCC 60.004 63.158 0.00 0.00 0.00 4.46
1767 2975 6.823689 AGCATGACCTTGGTGTTTATTACTAG 59.176 38.462 0.00 0.00 0.00 2.57
1913 3122 6.818644 GTGTGTACAGGTGATCATGATAACTT 59.181 38.462 20.52 12.12 0.00 2.66
1960 3169 1.483415 GGCTGAATTGGGAACATGCAT 59.517 47.619 0.00 0.00 42.32 3.96
2029 3238 3.094572 CTCGTTTACCTCTTGGGGTAGA 58.905 50.000 0.00 0.00 42.04 2.59
2131 3341 7.121315 AGCCTTTTCAAGTTATGGTGTAGATTC 59.879 37.037 0.00 0.00 0.00 2.52
2194 3411 0.184692 TTGTTGTGCCACATCTGGGA 59.815 50.000 0.00 0.00 38.13 4.37
2195 3412 0.314935 GTTGTTGTGCCACATCTGGG 59.685 55.000 0.00 0.00 38.13 4.45
2196 3413 0.314935 GGTTGTTGTGCCACATCTGG 59.685 55.000 0.00 0.00 41.13 3.86
2197 3414 1.031235 TGGTTGTTGTGCCACATCTG 58.969 50.000 0.00 0.00 0.00 2.90
2198 3415 3.511362 TGGTTGTTGTGCCACATCT 57.489 47.368 0.00 0.00 0.00 2.90
2256 3477 2.552743 CTGACAGAGTGGTTGTCGTAGA 59.447 50.000 0.00 0.00 46.14 2.59
2261 3482 2.890808 TGACTGACAGAGTGGTTGTC 57.109 50.000 10.08 0.00 44.03 3.18
2276 3497 4.221482 TCTGCATATGTTGACAGTCTGACT 59.779 41.667 6.91 4.06 33.71 3.41
2378 3607 7.592051 ACGCTGGATTAGTTACTACTATTAGC 58.408 38.462 0.00 0.00 36.76 3.09
2379 3608 8.781196 TGACGCTGGATTAGTTACTACTATTAG 58.219 37.037 0.00 0.00 36.76 1.73
2380 3609 8.681486 TGACGCTGGATTAGTTACTACTATTA 57.319 34.615 0.00 0.00 36.76 0.98
2382 3611 6.996879 TCTGACGCTGGATTAGTTACTACTAT 59.003 38.462 0.00 0.00 36.76 2.12
2384 3613 5.191426 TCTGACGCTGGATTAGTTACTACT 58.809 41.667 0.00 0.00 38.44 2.57
2385 3614 5.496133 TCTGACGCTGGATTAGTTACTAC 57.504 43.478 0.00 0.00 0.00 2.73
2386 3615 7.283807 TGTTATCTGACGCTGGATTAGTTACTA 59.716 37.037 0.00 0.00 0.00 1.82
2387 3616 6.096423 TGTTATCTGACGCTGGATTAGTTACT 59.904 38.462 0.00 0.00 0.00 2.24
2390 3619 5.105310 ACTGTTATCTGACGCTGGATTAGTT 60.105 40.000 0.00 0.00 0.00 2.24
2391 3620 4.402793 ACTGTTATCTGACGCTGGATTAGT 59.597 41.667 0.00 0.00 0.00 2.24
2392 3621 4.742167 CACTGTTATCTGACGCTGGATTAG 59.258 45.833 0.00 0.00 0.00 1.73
2393 3622 4.401202 TCACTGTTATCTGACGCTGGATTA 59.599 41.667 0.00 0.00 0.00 1.75
2394 3623 3.195610 TCACTGTTATCTGACGCTGGATT 59.804 43.478 0.00 0.00 0.00 3.01
2395 3624 2.760650 TCACTGTTATCTGACGCTGGAT 59.239 45.455 0.00 0.00 0.00 3.41
2396 3625 2.094700 GTCACTGTTATCTGACGCTGGA 60.095 50.000 0.00 0.00 0.00 3.86
2397 3626 2.263077 GTCACTGTTATCTGACGCTGG 58.737 52.381 0.00 0.00 0.00 4.85
2402 3631 2.607187 CCACGGTCACTGTTATCTGAC 58.393 52.381 0.00 0.00 36.78 3.51
2404 3633 1.359848 GCCACGGTCACTGTTATCTG 58.640 55.000 0.00 0.00 0.00 2.90
2405 3634 0.249398 GGCCACGGTCACTGTTATCT 59.751 55.000 0.00 0.00 0.00 1.98
2726 3956 3.554342 CCCCCAGCTGATCCTCCG 61.554 72.222 17.39 0.00 0.00 4.63
2775 4005 3.160047 AGCTCGATGCCCTCCAGG 61.160 66.667 3.66 0.00 44.23 4.45
2863 4093 1.153208 CCAGACCATCAGCCTCAGC 60.153 63.158 0.00 0.00 40.32 4.26
2876 4112 2.493973 CGAGCAGCTCCTCCAGAC 59.506 66.667 17.16 0.00 0.00 3.51
2931 4173 4.753662 TCCAGGTCCCCGAGTCCG 62.754 72.222 0.00 0.00 0.00 4.79
2964 4206 0.320374 TTGACAGTTCCCACGGCTAG 59.680 55.000 0.00 0.00 0.00 3.42
2971 4214 2.079170 TGGCATTTTGACAGTTCCCA 57.921 45.000 0.00 0.00 28.05 4.37
2978 4221 4.370049 CAAACACATCTGGCATTTTGACA 58.630 39.130 0.00 0.00 32.24 3.58
2988 4231 0.950836 TTCACGCCAAACACATCTGG 59.049 50.000 0.00 0.00 35.67 3.86
2991 4234 6.119144 ACTATATTTCACGCCAAACACATC 57.881 37.500 0.00 0.00 0.00 3.06
3015 4260 3.300754 GCAAGTCGTAATTACTGTACGCG 60.301 47.826 13.56 3.53 43.13 6.01
3016 4261 3.609373 TGCAAGTCGTAATTACTGTACGC 59.391 43.478 13.56 10.60 43.13 4.42
3020 4265 5.661458 AGCTATGCAAGTCGTAATTACTGT 58.339 37.500 13.56 0.00 0.00 3.55
3057 4304 3.761752 GCACCACCCTGTAATTTGTACAT 59.238 43.478 0.00 0.00 0.00 2.29
3073 4323 5.756833 AGTAGTACTTTGTTTACAGCACCAC 59.243 40.000 0.00 0.00 0.00 4.16
3086 4336 6.403636 CCAGCTTATTTGGCAGTAGTACTTTG 60.404 42.308 0.00 1.41 0.00 2.77
3094 4344 3.081061 CACACCAGCTTATTTGGCAGTA 58.919 45.455 0.00 0.00 39.39 2.74
3095 4345 1.888512 CACACCAGCTTATTTGGCAGT 59.111 47.619 0.00 0.00 39.39 4.40
3112 4362 1.341482 TGAAACCAAGACCAAGGCACA 60.341 47.619 0.00 0.00 0.00 4.57
3131 4381 0.841961 TCAGGAATGAGGGATGGCTG 59.158 55.000 0.00 0.00 0.00 4.85
3142 4392 0.099968 CCATGCGCACTTCAGGAATG 59.900 55.000 14.90 3.00 0.00 2.67
3201 5930 1.033202 ACGGTGGGCGTTCTGTTTTT 61.033 50.000 0.00 0.00 0.00 1.94
3292 6022 6.331369 ACCACCAATAAATGAACACTTCAG 57.669 37.500 0.00 0.00 43.98 3.02
3296 6026 6.731467 AGGATACCACCAATAAATGAACACT 58.269 36.000 0.00 0.00 37.17 3.55
3302 6032 4.133820 TGCGAGGATACCACCAATAAATG 58.866 43.478 0.00 0.00 37.17 2.32
3308 6038 0.463654 GCATGCGAGGATACCACCAA 60.464 55.000 0.00 0.00 37.17 3.67
3310 6040 1.146041 TGCATGCGAGGATACCACC 59.854 57.895 14.09 0.00 37.17 4.61
3311 6041 0.461870 TGTGCATGCGAGGATACCAC 60.462 55.000 14.09 2.49 37.17 4.16
3313 6043 0.104855 TCTGTGCATGCGAGGATACC 59.895 55.000 14.09 0.00 37.17 2.73
3314 6044 1.797046 CATCTGTGCATGCGAGGATAC 59.203 52.381 14.09 4.85 0.00 2.24
3315 6045 1.270465 CCATCTGTGCATGCGAGGATA 60.270 52.381 14.09 0.00 0.00 2.59
3317 6047 1.153309 CCATCTGTGCATGCGAGGA 60.153 57.895 14.09 10.73 0.00 3.71
3319 6049 1.328680 GTTACCATCTGTGCATGCGAG 59.671 52.381 14.09 11.61 0.00 5.03
3320 6050 1.368641 GTTACCATCTGTGCATGCGA 58.631 50.000 14.09 4.56 0.00 5.10
3321 6051 0.378257 GGTTACCATCTGTGCATGCG 59.622 55.000 14.09 0.00 0.00 4.73
3337 6074 1.138228 GGAGGTGGTTAGGTGGGGTT 61.138 60.000 0.00 0.00 0.00 4.11
3344 6081 0.043637 TGTAGGGGGAGGTGGTTAGG 59.956 60.000 0.00 0.00 0.00 2.69
3346 6083 1.437945 TCTTGTAGGGGGAGGTGGTTA 59.562 52.381 0.00 0.00 0.00 2.85
3349 6086 1.282157 CTTTCTTGTAGGGGGAGGTGG 59.718 57.143 0.00 0.00 0.00 4.61
3380 6118 5.523188 TGCACCATTTTAGCTGTTTTCTTTG 59.477 36.000 0.00 0.00 0.00 2.77
3525 6300 5.184864 TGTCAAACTTGAACTGTTCCATTGT 59.815 36.000 17.26 8.17 39.21 2.71
3545 6320 4.681074 TGTAGATGGTGTTGACTTGTCA 57.319 40.909 0.00 0.00 0.00 3.58
3553 6328 5.655488 TGGTTTGTTTTGTAGATGGTGTTG 58.345 37.500 0.00 0.00 0.00 3.33
3556 6331 5.901552 ACTTGGTTTGTTTTGTAGATGGTG 58.098 37.500 0.00 0.00 0.00 4.17
3558 6333 6.475402 GTCAACTTGGTTTGTTTTGTAGATGG 59.525 38.462 0.00 0.00 0.00 3.51
3559 6334 7.032580 TGTCAACTTGGTTTGTTTTGTAGATG 58.967 34.615 0.00 0.00 0.00 2.90
3587 6362 4.332819 CGGGTTGATTAGTTTCTGTCCATC 59.667 45.833 0.00 0.00 0.00 3.51
3622 6397 5.925969 GCCTTGCAAATAAGTGTATGTTGTT 59.074 36.000 0.00 0.00 0.00 2.83
3699 6475 7.557719 CCTCCTATTTCACCATGTGATTAGTTT 59.442 37.037 0.00 0.00 42.40 2.66
3703 6479 5.690097 GCCCTCCTATTTCACCATGTGATTA 60.690 44.000 0.00 0.00 42.40 1.75
3705 6481 3.435601 GCCCTCCTATTTCACCATGTGAT 60.436 47.826 0.00 0.00 42.40 3.06
3706 6482 2.092429 GCCCTCCTATTTCACCATGTGA 60.092 50.000 0.00 0.00 41.09 3.58
3707 6483 2.301346 GCCCTCCTATTTCACCATGTG 58.699 52.381 0.00 0.00 34.45 3.21
3708 6484 1.134098 CGCCCTCCTATTTCACCATGT 60.134 52.381 0.00 0.00 0.00 3.21
3709 6485 1.140852 TCGCCCTCCTATTTCACCATG 59.859 52.381 0.00 0.00 0.00 3.66
3720 6496 1.979693 GGATCGCTATCGCCCTCCT 60.980 63.158 0.00 0.00 35.26 3.69
3754 6540 6.321181 ACTTTGTGTCATTGGTGTTGTAGATT 59.679 34.615 0.00 0.00 0.00 2.40
3765 6551 2.819608 CCCTGGTACTTTGTGTCATTGG 59.180 50.000 0.00 0.00 0.00 3.16
3776 6570 0.770557 TTGGCTGGTCCCTGGTACTT 60.771 55.000 0.00 0.00 0.00 2.24
3808 6602 0.325933 CTGAACATGGGCTGACTGGA 59.674 55.000 0.00 0.00 0.00 3.86
3943 6740 2.626840 GAACTCCTTGCAGGATCAGAC 58.373 52.381 0.00 0.00 44.81 3.51


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

AutoCloner maintained by Alex Coulton.