Multiple sequence alignment - TraesCS1D01G090700

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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 TraesCS1D01G090700 chr1D 100.000 5402 0 0 1 5402 77014601 77009200 0.000000e+00 9976
1 TraesCS1D01G090700 chr1B 93.410 5417 203 46 1 5330 120659063 120653714 0.000000e+00 7884
2 TraesCS1D01G090700 chr1B 87.156 2032 166 48 1834 3847 157277355 157275401 0.000000e+00 2218
3 TraesCS1D01G090700 chr1B 91.331 646 49 5 3844 4485 157275353 157274711 0.000000e+00 876
4 TraesCS1D01G090700 chr1B 94.595 148 6 1 179 324 157285452 157285305 1.510000e-55 228
5 TraesCS1D01G090700 chr1B 97.183 71 1 1 5332 5401 473556852 473556922 9.500000e-23 119
6 TraesCS1D01G090700 chr1B 94.667 75 4 0 307 381 157285291 157285217 3.420000e-22 117
7 TraesCS1D01G090700 chr1B 95.833 72 2 1 5332 5402 518057419 518057490 1.230000e-21 115
8 TraesCS1D01G090700 chr1B 92.105 76 6 0 963 1038 157285143 157285218 2.060000e-19 108
9 TraesCS1D01G090700 chr1B 90.000 80 7 1 1749 1828 157277465 157277387 9.570000e-18 102
10 TraesCS1D01G090700 chr2D 92.135 89 7 0 1147 1235 557267268 557267180 5.680000e-25 126
11 TraesCS1D01G090700 chr3B 92.941 85 6 0 1149 1233 680423382 680423298 2.040000e-24 124
12 TraesCS1D01G090700 chr3B 89.000 100 9 2 1134 1233 126580052 126580149 7.350000e-24 122
13 TraesCS1D01G090700 chr3B 95.833 72 2 1 5332 5402 39155329 39155400 1.230000e-21 115
14 TraesCS1D01G090700 chr3B 95.833 72 2 1 5332 5402 240081470 240081399 1.230000e-21 115
15 TraesCS1D01G090700 chr2A 93.023 86 5 1 1149 1233 593655909 593655994 2.040000e-24 124
16 TraesCS1D01G090700 chr7D 91.954 87 7 0 1156 1242 78306060 78305974 7.350000e-24 122
17 TraesCS1D01G090700 chr4A 91.111 90 8 0 1145 1234 590111635 590111546 7.350000e-24 122
18 TraesCS1D01G090700 chr7A 91.765 85 7 0 1149 1233 398924516 398924432 9.500000e-23 119
19 TraesCS1D01G090700 chr5B 95.946 74 2 1 5329 5401 540321059 540320986 9.500000e-23 119
20 TraesCS1D01G090700 chr3D 97.183 71 1 1 5333 5402 44972619 44972549 9.500000e-23 119
21 TraesCS1D01G090700 chr3D 89.247 93 10 0 1149 1241 428242731 428242639 3.420000e-22 117
22 TraesCS1D01G090700 chr7B 95.833 72 2 1 5332 5402 443325896 443325825 1.230000e-21 115
23 TraesCS1D01G090700 chr6B 95.833 72 2 1 5332 5402 533239619 533239548 1.230000e-21 115
24 TraesCS1D01G090700 chr6B 95.833 72 2 1 5332 5402 593122855 593122784 1.230000e-21 115


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 TraesCS1D01G090700 chr1D 77009200 77014601 5401 True 9976.000000 9976 100.000000 1 5402 1 chr1D.!!$R1 5401
1 TraesCS1D01G090700 chr1B 120653714 120659063 5349 True 7884.000000 7884 93.410000 1 5330 1 chr1B.!!$R1 5329
2 TraesCS1D01G090700 chr1B 157274711 157277465 2754 True 1065.333333 2218 89.495667 1749 4485 3 chr1B.!!$R2 2736

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
253 263 0.032130 TGAAGACACGGTCACTGAGC 59.968 55.000 0.00 0.00 34.6 4.26 F
254 264 0.032130 GAAGACACGGTCACTGAGCA 59.968 55.000 8.89 0.00 34.6 4.26 F
255 265 0.032678 AAGACACGGTCACTGAGCAG 59.967 55.000 8.89 3.09 34.6 4.24 F
310 320 0.034616 AGCTTGCAGACAGAGTCACC 59.965 55.000 0.00 0.00 34.6 4.02 F
2142 2264 0.103937 GCTAGATCGAGCTGCCTGTT 59.896 55.000 19.36 0.00 39.5 3.16 F
2150 2272 1.067565 CGAGCTGCCTGTTCTCACTAA 60.068 52.381 0.00 0.00 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1574 0.343372 AGAGGAGGGAGTATTGGCCA 59.657 55.000 0.00 0.00 0.00 5.36 R
2184 2306 1.731720 GCCTTCTGCTGTAGTTCTGG 58.268 55.000 0.00 0.00 36.87 3.86 R
2542 2670 3.186119 CCAAAGCAACGACAACAAACAT 58.814 40.909 0.00 0.00 0.00 2.71 R
2729 2857 5.698545 AGAAAGAAGATCAGAAAGAACACCG 59.301 40.000 0.00 0.00 0.00 4.94 R
4194 4430 0.326264 ACATGGTTCTGGCAGGAGTC 59.674 55.000 15.73 1.67 0.00 3.36 R
4501 4741 0.759346 CTTCCCTAACCAGATCCCCG 59.241 60.000 0.00 0.00 0.00 5.73 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
44 45 3.644606 CCTGCTGCTGACTGGGGT 61.645 66.667 8.20 0.00 0.00 4.95
45 46 2.359602 CTGCTGCTGACTGGGGTG 60.360 66.667 0.00 0.00 0.00 4.61
46 47 2.848679 TGCTGCTGACTGGGGTGA 60.849 61.111 0.00 0.00 0.00 4.02
47 48 2.359230 GCTGCTGACTGGGGTGAC 60.359 66.667 0.00 0.00 0.00 3.67
52 53 2.529136 TGACTGGGGTGACTGGGG 60.529 66.667 0.00 0.00 0.00 4.96
53 54 2.529389 GACTGGGGTGACTGGGGT 60.529 66.667 0.00 0.00 0.00 4.95
57 58 2.691252 GGGGTGACTGGGGTAGGG 60.691 72.222 0.00 0.00 0.00 3.53
61 62 1.344701 GGGTGACTGGGGTAGGGAATA 60.345 57.143 0.00 0.00 0.00 1.75
82 83 0.038892 GTCCGTTCGCAGGTTACTCA 60.039 55.000 0.00 0.00 0.00 3.41
139 140 1.671261 GCAGGCACACTCACAGAGTAG 60.671 57.143 0.00 0.00 41.37 2.57
145 146 3.744530 GCACACTCACAGAGTAGGGTTTT 60.745 47.826 0.00 0.00 41.37 2.43
173 183 1.269102 GCAGATGATGATGCAGGTTGC 60.269 52.381 0.00 0.00 45.29 4.17
232 242 0.798776 GAACCATTCGACAGTGCAGG 59.201 55.000 0.00 0.00 0.00 4.85
233 243 0.108585 AACCATTCGACAGTGCAGGT 59.891 50.000 0.00 0.00 0.00 4.00
234 244 0.108585 ACCATTCGACAGTGCAGGTT 59.891 50.000 0.00 0.00 0.00 3.50
235 245 0.518636 CCATTCGACAGTGCAGGTTG 59.481 55.000 0.00 0.00 0.00 3.77
236 246 1.511850 CATTCGACAGTGCAGGTTGA 58.488 50.000 4.61 4.61 0.00 3.18
237 247 1.872952 CATTCGACAGTGCAGGTTGAA 59.127 47.619 18.55 18.55 41.52 2.69
238 248 1.581934 TTCGACAGTGCAGGTTGAAG 58.418 50.000 14.29 2.89 34.53 3.02
239 249 0.750249 TCGACAGTGCAGGTTGAAGA 59.250 50.000 6.02 0.34 0.00 2.87
240 250 0.861837 CGACAGTGCAGGTTGAAGAC 59.138 55.000 0.00 0.00 0.00 3.01
241 251 1.806247 CGACAGTGCAGGTTGAAGACA 60.806 52.381 0.00 0.00 0.00 3.41
242 252 1.599542 GACAGTGCAGGTTGAAGACAC 59.400 52.381 0.00 0.00 0.00 3.67
243 253 0.583438 CAGTGCAGGTTGAAGACACG 59.417 55.000 0.00 0.00 36.38 4.49
244 254 0.532862 AGTGCAGGTTGAAGACACGG 60.533 55.000 0.00 0.00 36.38 4.94
245 255 0.814010 GTGCAGGTTGAAGACACGGT 60.814 55.000 0.00 0.00 0.00 4.83
246 256 0.531974 TGCAGGTTGAAGACACGGTC 60.532 55.000 0.00 0.00 0.00 4.79
247 257 0.531974 GCAGGTTGAAGACACGGTCA 60.532 55.000 6.78 0.00 34.60 4.02
248 258 1.217882 CAGGTTGAAGACACGGTCAC 58.782 55.000 6.78 2.06 34.60 3.67
249 259 1.120530 AGGTTGAAGACACGGTCACT 58.879 50.000 6.78 0.00 34.60 3.41
250 260 1.202533 AGGTTGAAGACACGGTCACTG 60.203 52.381 6.78 0.00 34.60 3.66
251 261 1.202486 GGTTGAAGACACGGTCACTGA 60.202 52.381 0.00 0.00 34.60 3.41
252 262 2.128035 GTTGAAGACACGGTCACTGAG 58.872 52.381 0.00 0.00 34.60 3.35
253 263 0.032130 TGAAGACACGGTCACTGAGC 59.968 55.000 0.00 0.00 34.60 4.26
254 264 0.032130 GAAGACACGGTCACTGAGCA 59.968 55.000 8.89 0.00 34.60 4.26
255 265 0.032678 AAGACACGGTCACTGAGCAG 59.967 55.000 8.89 3.09 34.60 4.24
256 266 0.823769 AGACACGGTCACTGAGCAGA 60.824 55.000 8.89 0.00 34.60 4.26
257 267 0.387878 GACACGGTCACTGAGCAGAG 60.388 60.000 8.89 0.00 32.09 3.35
258 268 1.109920 ACACGGTCACTGAGCAGAGT 61.110 55.000 8.89 3.88 0.00 3.24
259 269 0.032678 CACGGTCACTGAGCAGAGTT 59.967 55.000 8.89 0.00 0.00 3.01
260 270 1.269723 CACGGTCACTGAGCAGAGTTA 59.730 52.381 8.89 0.00 0.00 2.24
261 271 1.269998 ACGGTCACTGAGCAGAGTTAC 59.730 52.381 8.89 0.00 0.00 2.50
262 272 1.542030 CGGTCACTGAGCAGAGTTACT 59.458 52.381 8.89 0.00 0.00 2.24
275 285 5.152623 CAGAGTTACTGTCCAAATCAGGA 57.847 43.478 0.00 0.00 41.30 3.86
276 286 5.551233 CAGAGTTACTGTCCAAATCAGGAA 58.449 41.667 0.00 0.00 39.92 3.36
279 289 4.394729 GTTACTGTCCAAATCAGGAACCA 58.605 43.478 9.15 0.00 45.63 3.67
280 290 3.814504 ACTGTCCAAATCAGGAACCAT 57.185 42.857 0.00 0.00 39.92 3.55
281 291 4.118168 ACTGTCCAAATCAGGAACCATT 57.882 40.909 0.00 0.00 39.92 3.16
282 292 5.255397 ACTGTCCAAATCAGGAACCATTA 57.745 39.130 0.00 0.00 39.92 1.90
283 293 5.256474 ACTGTCCAAATCAGGAACCATTAG 58.744 41.667 0.00 0.00 39.92 1.73
284 294 5.014123 ACTGTCCAAATCAGGAACCATTAGA 59.986 40.000 0.00 0.00 39.92 2.10
285 295 5.253330 TGTCCAAATCAGGAACCATTAGAC 58.747 41.667 0.00 0.00 39.92 2.59
286 296 5.222027 TGTCCAAATCAGGAACCATTAGACA 60.222 40.000 0.00 0.00 39.92 3.41
287 297 5.355350 GTCCAAATCAGGAACCATTAGACAG 59.645 44.000 0.00 0.00 39.92 3.51
288 298 5.014123 TCCAAATCAGGAACCATTAGACAGT 59.986 40.000 0.00 0.00 33.93 3.55
289 299 5.124457 CCAAATCAGGAACCATTAGACAGTG 59.876 44.000 0.00 0.00 0.00 3.66
290 300 3.334583 TCAGGAACCATTAGACAGTGC 57.665 47.619 0.00 0.00 0.00 4.40
291 301 2.637382 TCAGGAACCATTAGACAGTGCA 59.363 45.455 0.00 0.00 0.00 4.57
292 302 3.005554 CAGGAACCATTAGACAGTGCAG 58.994 50.000 0.00 0.00 0.00 4.41
308 318 0.602106 GCAGCTTGCAGACAGAGTCA 60.602 55.000 0.00 0.00 44.26 3.41
310 320 0.034616 AGCTTGCAGACAGAGTCACC 59.965 55.000 0.00 0.00 34.60 4.02
335 383 3.924686 GCAGATTTTGAGGTGCATTGAAG 59.075 43.478 0.00 0.00 35.91 3.02
363 411 1.736681 GCTTTCATGTGAGCTCAGACC 59.263 52.381 18.89 6.23 36.01 3.85
364 412 2.614987 GCTTTCATGTGAGCTCAGACCT 60.615 50.000 18.89 0.00 36.01 3.85
365 413 3.672808 CTTTCATGTGAGCTCAGACCTT 58.327 45.455 18.89 0.00 0.00 3.50
366 414 2.756840 TCATGTGAGCTCAGACCTTG 57.243 50.000 18.89 11.64 0.00 3.61
386 434 3.515630 TGCTTCAGCGAGTGATTTAGAG 58.484 45.455 0.00 0.00 45.83 2.43
395 443 4.985409 GCGAGTGATTTAGAGGATTAGTGG 59.015 45.833 0.00 0.00 0.00 4.00
399 447 5.726793 AGTGATTTAGAGGATTAGTGGTGGT 59.273 40.000 0.00 0.00 0.00 4.16
400 448 6.215636 AGTGATTTAGAGGATTAGTGGTGGTT 59.784 38.462 0.00 0.00 0.00 3.67
413 461 3.875134 AGTGGTGGTTCGTTTACTTTCTG 59.125 43.478 0.00 0.00 0.00 3.02
414 462 3.872771 GTGGTGGTTCGTTTACTTTCTGA 59.127 43.478 0.00 0.00 0.00 3.27
445 493 7.961325 ACTTCAGAAGAAAAGTTCAGATCTC 57.039 36.000 17.56 0.00 31.81 2.75
495 544 3.975992 GCTGTAAATCAGGTGCGTG 57.024 52.632 0.00 0.00 43.78 5.34
498 547 0.250510 TGTAAATCAGGTGCGTGCCA 60.251 50.000 0.59 0.00 0.00 4.92
508 557 1.227793 TGCGTGCCATCAAGTGTCA 60.228 52.632 0.00 0.00 0.00 3.58
531 580 9.028185 GTCAAAACATAGTAAATACTACCTCCG 57.972 37.037 2.54 0.00 41.18 4.63
536 585 6.543831 ACATAGTAAATACTACCTCCGTTCGT 59.456 38.462 2.54 0.00 41.18 3.85
548 597 3.255725 CTCCGTTCGTAAATAAGTGGCA 58.744 45.455 0.00 0.00 0.00 4.92
553 602 4.493545 CGTTCGTAAATAAGTGGCATGGTC 60.494 45.833 0.00 0.00 0.00 4.02
554 603 3.537580 TCGTAAATAAGTGGCATGGTCC 58.462 45.455 0.00 0.00 0.00 4.46
555 604 3.055021 TCGTAAATAAGTGGCATGGTCCA 60.055 43.478 0.00 0.00 0.00 4.02
568 640 3.429410 GCATGGTCCAAGCCACTTATTTC 60.429 47.826 7.92 0.00 41.94 2.17
574 646 3.081804 CCAAGCCACTTATTTCCGAACT 58.918 45.455 0.00 0.00 0.00 3.01
581 653 4.184629 CACTTATTTCCGAACTGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
589 661 2.944349 CCGAACTGAGGGAGTAGTACTC 59.056 54.545 20.24 20.24 44.32 2.59
595 667 4.043059 ACTGAGGGAGTAGTACTCTGTTCA 59.957 45.833 25.70 22.58 44.46 3.18
718 790 4.527816 TGCCCATAAAATCCATTATCTGCC 59.472 41.667 0.00 0.00 0.00 4.85
726 798 4.581309 ATCCATTATCTGCCCATACAGG 57.419 45.455 0.00 0.00 38.26 4.00
750 825 1.165270 AAACACTACTGGCGAATGGC 58.835 50.000 0.00 0.00 42.51 4.40
797 875 0.680921 ATGAACTTCCACCCGGCATG 60.681 55.000 0.00 0.00 0.00 4.06
837 915 1.164411 TCAACATGACATGCCCGTTC 58.836 50.000 15.49 0.00 0.00 3.95
922 1000 3.055819 TGATGGACTCCGAAGAAAGAAGG 60.056 47.826 0.00 0.00 0.00 3.46
924 1002 3.173965 TGGACTCCGAAGAAAGAAGGAT 58.826 45.455 0.00 0.00 31.66 3.24
930 1008 2.436173 CCGAAGAAAGAAGGATAGGGCT 59.564 50.000 0.00 0.00 0.00 5.19
934 1012 2.774809 AGAAAGAAGGATAGGGCTGACC 59.225 50.000 0.00 0.00 40.67 4.02
1037 1115 9.739276 TTCTGTTTGTAGATTTTCCAGTGATAT 57.261 29.630 0.00 0.00 0.00 1.63
1040 1118 9.166173 TGTTTGTAGATTTTCCAGTGATATGAG 57.834 33.333 0.00 0.00 0.00 2.90
1046 1124 8.461249 AGATTTTCCAGTGATATGAGATTTGG 57.539 34.615 0.00 0.00 0.00 3.28
1088 1166 8.050778 TCTCTTCACGTTTGCCATAATTATTT 57.949 30.769 0.00 0.00 0.00 1.40
1089 1167 7.967854 TCTCTTCACGTTTGCCATAATTATTTG 59.032 33.333 0.00 0.00 0.00 2.32
1112 1190 2.154462 CATCACTTCCAACTCCACACC 58.846 52.381 0.00 0.00 0.00 4.16
1196 1274 6.015688 AGACGTTTTTAGAGTCCATGACAGTA 60.016 38.462 0.00 0.00 34.60 2.74
1283 1361 3.509967 GTCATTTTCTTGTTCCCCGGAAT 59.490 43.478 0.73 0.00 36.45 3.01
1288 1366 3.449746 TCTTGTTCCCCGGAATCATTT 57.550 42.857 0.73 0.00 36.45 2.32
1310 1388 4.695217 TTTTCTTCCATATGTTCGCCAC 57.305 40.909 1.24 0.00 0.00 5.01
1384 1462 9.841295 ATATTCTTGCTCATGCCATTAAATTTT 57.159 25.926 0.00 0.00 38.71 1.82
1423 1502 8.959548 TCGTGTAATTAGTGAACCTTACATAGA 58.040 33.333 0.00 0.00 36.70 1.98
1424 1503 9.577110 CGTGTAATTAGTGAACCTTACATAGAA 57.423 33.333 0.00 0.00 36.70 2.10
1437 1516 8.102484 ACCTTACATAGAATAGAATGTTGGGT 57.898 34.615 0.00 0.00 37.50 4.51
1495 1574 3.616721 AGGTTGGCGAGCACGAGT 61.617 61.111 8.01 0.00 42.66 4.18
1513 1592 0.470341 GTGGCCAATACTCCCTCCTC 59.530 60.000 7.24 0.00 0.00 3.71
1526 1605 5.746284 ACTCCCTCCTCTTTTGTTTATAGC 58.254 41.667 0.00 0.00 0.00 2.97
1539 1618 7.753309 TTTGTTTATAGCGCACCCAATATAT 57.247 32.000 11.47 0.00 0.00 0.86
1548 1627 6.795399 AGCGCACCCAATATATATATTTTGC 58.205 36.000 21.12 21.12 32.44 3.68
1595 1674 3.301794 TGGATGTGAGGCATAGCAATT 57.698 42.857 0.00 0.00 38.06 2.32
1662 1742 7.956420 AATTTATGTGATTGCATGCCATTAG 57.044 32.000 16.68 0.00 0.00 1.73
1680 1760 6.127619 GCCATTAGGGATAGACCATTAATTGC 60.128 42.308 0.00 0.00 40.01 3.56
1689 1769 8.103305 GGATAGACCATTAATTGCCTTGATCTA 58.897 37.037 0.00 0.00 38.79 1.98
1720 1804 5.231357 TGCGTTGATCTAAGTTGTATTAGCG 59.769 40.000 0.00 0.00 33.57 4.26
1733 1817 6.202954 AGTTGTATTAGCGGAATTACATGCTC 59.797 38.462 0.00 0.00 38.82 4.26
1739 1823 3.627577 AGCGGAATTACATGCTCGAAAAT 59.372 39.130 0.00 0.00 30.37 1.82
1773 1857 2.242196 AGCCTGGGTGCACTATAAACAT 59.758 45.455 17.98 0.00 0.00 2.71
1828 1913 2.341846 ATTGGTGTCCGTCAAACACT 57.658 45.000 6.38 0.00 45.05 3.55
1855 1966 3.780294 AGTATGCCCTCTGTCCAAACATA 59.220 43.478 0.00 0.00 34.13 2.29
1862 1973 5.009631 CCCTCTGTCCAAACATATTTGTCA 58.990 41.667 0.00 0.00 43.23 3.58
2100 2222 2.553602 TGTATGCTTGGCTCACACTTTG 59.446 45.455 0.00 0.00 0.00 2.77
2101 2223 1.696063 ATGCTTGGCTCACACTTTGT 58.304 45.000 0.00 0.00 0.00 2.83
2102 2224 2.340210 TGCTTGGCTCACACTTTGTA 57.660 45.000 0.00 0.00 0.00 2.41
2103 2225 2.862541 TGCTTGGCTCACACTTTGTAT 58.137 42.857 0.00 0.00 0.00 2.29
2104 2226 3.221771 TGCTTGGCTCACACTTTGTATT 58.778 40.909 0.00 0.00 0.00 1.89
2115 2237 8.383619 GCTCACACTTTGTATTGTACTTCATAG 58.616 37.037 0.00 0.00 0.00 2.23
2120 2242 9.424319 CACTTTGTATTGTACTTCATAGTCAGT 57.576 33.333 0.00 0.00 35.78 3.41
2142 2264 0.103937 GCTAGATCGAGCTGCCTGTT 59.896 55.000 19.36 0.00 39.50 3.16
2150 2272 1.067565 CGAGCTGCCTGTTCTCACTAA 60.068 52.381 0.00 0.00 0.00 2.24
2184 2306 3.133003 TCCATCTAGCCAAGCTGAACTAC 59.867 47.826 0.00 0.00 40.10 2.73
2433 2561 2.810274 CAGCATCAATAGCGCCTATGTT 59.190 45.455 2.29 0.00 37.01 2.71
2449 2577 5.548406 CCTATGTTAAGTACCCACTATGGC 58.452 45.833 0.00 0.00 35.79 4.40
2542 2670 5.265191 AGACCAAATCTCTGCTCACTACTA 58.735 41.667 0.00 0.00 28.16 1.82
2729 2857 1.410517 TCTCATTCACTCCCTGATCGC 59.589 52.381 0.00 0.00 0.00 4.58
2733 2861 2.202797 CACTCCCTGATCGCGGTG 60.203 66.667 6.13 0.00 0.00 4.94
2778 2906 1.909700 TGAATGGTGGAAGGACTTGC 58.090 50.000 0.00 0.00 0.00 4.01
2967 3122 3.848975 AGGAGAAGATTGTGGAGGTGAAT 59.151 43.478 0.00 0.00 0.00 2.57
3078 3263 8.530804 AAAATGATAATGAAAAGGAGGAGGAG 57.469 34.615 0.00 0.00 0.00 3.69
3102 3287 1.645710 TGGAGGTGAAGGAGAAGGAC 58.354 55.000 0.00 0.00 0.00 3.85
3115 3300 4.021280 AGGAGAAGGACGATGATGATGATG 60.021 45.833 0.00 0.00 0.00 3.07
3220 3405 7.764901 AGAAGGACGATGATAATGATGATGATG 59.235 37.037 0.00 0.00 0.00 3.07
3221 3406 7.179076 AGGACGATGATAATGATGATGATGA 57.821 36.000 0.00 0.00 0.00 2.92
3222 3407 7.793036 AGGACGATGATAATGATGATGATGAT 58.207 34.615 0.00 0.00 0.00 2.45
3468 3653 5.542616 CGAAGCTTCAGAAAACTCATGAT 57.457 39.130 25.47 0.00 0.00 2.45
3716 3901 4.127171 GAGTCTCTCAGCTCACCTAGTAG 58.873 52.174 0.00 0.00 0.00 2.57
3832 4017 2.040178 CCGACTGGGCTAAGGTAGAAT 58.960 52.381 0.00 0.00 0.00 2.40
3862 4098 2.287668 CGGCTTCCAGGACTATACTTCG 60.288 54.545 0.00 0.00 0.00 3.79
3936 4172 5.506317 GCACTCGCTAATTAAGGATTTGCAT 60.506 40.000 0.00 0.00 43.70 3.96
3998 4234 9.185192 GTCTTATTTGTTTCAGTCCTTTCATTG 57.815 33.333 0.00 0.00 0.00 2.82
4194 4430 1.596603 TATGGGCATGCAATCACGAG 58.403 50.000 21.36 0.00 0.00 4.18
4262 4501 4.252878 TGTGTCATCGCACAATGTAAGAT 58.747 39.130 0.00 0.00 45.17 2.40
4309 4548 2.726821 ACCATCATACTGTTGCCCAAG 58.273 47.619 0.00 0.00 0.00 3.61
4349 4588 3.772932 CATATTTGATGGCGTTTGTGCT 58.227 40.909 0.00 0.00 34.52 4.40
4354 4593 2.710377 TGATGGCGTTTGTGCTAGAAT 58.290 42.857 0.00 0.00 34.52 2.40
4455 4695 0.653636 GACGCCGTTTGAGAAACACA 59.346 50.000 0.00 0.00 41.44 3.72
4559 4799 2.167281 AGATGACAGTCGGTGGAAGATG 59.833 50.000 0.00 0.00 0.00 2.90
4569 4809 1.684248 GGTGGAAGATGCTGGCAGATT 60.684 52.381 20.86 6.54 0.00 2.40
4593 4833 7.770801 TTCTGGACTGAAATGATATTGTACG 57.229 36.000 0.00 0.00 0.00 3.67
4594 4834 5.753438 TCTGGACTGAAATGATATTGTACGC 59.247 40.000 0.00 0.00 0.00 4.42
4652 4892 2.158475 TCTGGCAAATGGAGGTGAGTTT 60.158 45.455 0.00 0.00 0.00 2.66
4720 4960 2.353357 GATCAACAGATCCATGGCCA 57.647 50.000 8.56 8.56 33.58 5.36
4722 4962 2.353357 TCAACAGATCCATGGCCATC 57.647 50.000 17.61 5.44 0.00 3.51
4723 4963 1.133699 TCAACAGATCCATGGCCATCC 60.134 52.381 17.61 5.54 0.00 3.51
4724 4964 1.133575 CAACAGATCCATGGCCATCCT 60.134 52.381 17.61 7.94 0.00 3.24
4725 4965 0.769873 ACAGATCCATGGCCATCCTC 59.230 55.000 17.61 12.67 0.00 3.71
4726 4966 0.037877 CAGATCCATGGCCATCCTCC 59.962 60.000 17.61 5.92 0.00 4.30
4727 4967 0.104037 AGATCCATGGCCATCCTCCT 60.104 55.000 17.61 8.32 0.00 3.69
4728 4968 0.037877 GATCCATGGCCATCCTCCTG 59.962 60.000 17.61 4.78 0.00 3.86
4729 4969 2.077842 ATCCATGGCCATCCTCCTGC 62.078 60.000 17.61 0.00 0.00 4.85
4732 4972 1.695239 ATGGCCATCCTCCTGCAGA 60.695 57.895 17.39 0.00 0.00 4.26
4734 4974 1.284111 TGGCCATCCTCCTGCAGAAT 61.284 55.000 17.39 0.00 0.00 2.40
4735 4975 0.822532 GGCCATCCTCCTGCAGAATG 60.823 60.000 17.39 12.53 40.87 2.67
4736 4976 0.106819 GCCATCCTCCTGCAGAATGT 60.107 55.000 17.39 0.00 39.31 2.71
4739 4979 3.094572 CCATCCTCCTGCAGAATGTTTT 58.905 45.455 17.39 0.00 39.31 2.43
4888 5129 2.951457 TCAATGGAGCGTCGTATTGA 57.049 45.000 10.23 10.23 37.25 2.57
4920 5161 0.538057 TTCAAGCTCCACCAAGCAGG 60.538 55.000 0.00 0.00 45.00 4.85
4926 5167 2.360852 CCACCAAGCAGGCCTGAG 60.361 66.667 37.21 23.12 43.14 3.35
4952 5193 3.742433 AAGTGTGAGGTCTCTTCACTG 57.258 47.619 20.20 0.00 41.28 3.66
4955 5196 2.362397 GTGTGAGGTCTCTTCACTGTCA 59.638 50.000 11.89 0.00 35.59 3.58
5004 5245 8.148351 TCAGTTGTTTGCTAGTACTAGTCAATT 58.852 33.333 26.76 19.41 35.65 2.32
5102 5352 5.648092 GCCTTTCACTCTGTAATATGGTTGT 59.352 40.000 0.00 0.00 0.00 3.32
5124 5374 5.006386 GTGATTTCCACTCAAGAAGATGGT 58.994 41.667 0.00 0.00 42.44 3.55
5140 5390 5.376854 AGATGGTTGTGATTTGTTAGTGC 57.623 39.130 0.00 0.00 0.00 4.40
5141 5391 4.218417 AGATGGTTGTGATTTGTTAGTGCC 59.782 41.667 0.00 0.00 0.00 5.01
5172 5448 4.961438 TGCTGATATGGATGCTAACTGA 57.039 40.909 0.00 0.00 0.00 3.41
5218 5494 5.535406 TGGGTTTGGTCAAATATGTTTACGT 59.465 36.000 0.00 0.00 32.36 3.57
5245 5521 1.210155 GCAGGGCAACACGTGATTC 59.790 57.895 25.01 4.37 39.74 2.52
5253 5529 0.038166 AACACGTGATTCCCCATGCT 59.962 50.000 25.01 0.00 0.00 3.79
5254 5530 0.038166 ACACGTGATTCCCCATGCTT 59.962 50.000 25.01 0.00 0.00 3.91
5273 5549 9.696917 CCATGCTTTTTATTATAAGTTGATCCC 57.303 33.333 0.00 0.00 0.00 3.85
5310 5586 2.758423 AGGTTCGCAATGGTTATTTCCC 59.242 45.455 0.00 0.00 0.00 3.97
5316 5592 2.831526 GCAATGGTTATTTCCCCTGTGT 59.168 45.455 0.00 0.00 0.00 3.72
5317 5593 3.260632 GCAATGGTTATTTCCCCTGTGTT 59.739 43.478 0.00 0.00 0.00 3.32
5318 5594 4.620567 GCAATGGTTATTTCCCCTGTGTTC 60.621 45.833 0.00 0.00 0.00 3.18
5322 5598 4.141135 TGGTTATTTCCCCTGTGTTCTTGA 60.141 41.667 0.00 0.00 0.00 3.02
5330 5606 2.816087 CCCTGTGTTCTTGATCCAAGTG 59.184 50.000 6.59 0.00 41.66 3.16
5331 5607 3.480470 CCTGTGTTCTTGATCCAAGTGT 58.520 45.455 6.59 0.00 41.66 3.55
5332 5608 3.885297 CCTGTGTTCTTGATCCAAGTGTT 59.115 43.478 6.59 0.00 41.66 3.32
5333 5609 4.339247 CCTGTGTTCTTGATCCAAGTGTTT 59.661 41.667 6.59 0.00 41.66 2.83
5334 5610 5.163519 CCTGTGTTCTTGATCCAAGTGTTTT 60.164 40.000 6.59 0.00 41.66 2.43
5335 5611 6.279513 TGTGTTCTTGATCCAAGTGTTTTT 57.720 33.333 6.59 0.00 41.66 1.94
5355 5631 2.024176 TTACGGGCAAATCAGAGAGC 57.976 50.000 0.00 0.00 0.00 4.09
5356 5632 1.195115 TACGGGCAAATCAGAGAGCT 58.805 50.000 0.00 0.00 0.00 4.09
5357 5633 0.326264 ACGGGCAAATCAGAGAGCTT 59.674 50.000 0.00 0.00 0.00 3.74
5358 5634 1.271597 ACGGGCAAATCAGAGAGCTTT 60.272 47.619 0.00 0.00 0.00 3.51
5359 5635 2.027192 ACGGGCAAATCAGAGAGCTTTA 60.027 45.455 0.00 0.00 0.00 1.85
5360 5636 3.209410 CGGGCAAATCAGAGAGCTTTAT 58.791 45.455 0.00 0.00 0.00 1.40
5361 5637 3.629398 CGGGCAAATCAGAGAGCTTTATT 59.371 43.478 0.00 0.00 0.00 1.40
5362 5638 4.260948 CGGGCAAATCAGAGAGCTTTATTC 60.261 45.833 0.00 0.00 0.00 1.75
5363 5639 4.641989 GGGCAAATCAGAGAGCTTTATTCA 59.358 41.667 0.00 0.00 0.00 2.57
5364 5640 5.126061 GGGCAAATCAGAGAGCTTTATTCAA 59.874 40.000 0.00 0.00 0.00 2.69
5365 5641 6.032717 GGCAAATCAGAGAGCTTTATTCAAC 58.967 40.000 0.00 0.00 0.00 3.18
5366 5642 6.349611 GGCAAATCAGAGAGCTTTATTCAACA 60.350 38.462 0.00 0.00 0.00 3.33
5367 5643 7.086376 GCAAATCAGAGAGCTTTATTCAACAA 58.914 34.615 0.00 0.00 0.00 2.83
5368 5644 7.596248 GCAAATCAGAGAGCTTTATTCAACAAA 59.404 33.333 0.00 0.00 0.00 2.83
5369 5645 9.467258 CAAATCAGAGAGCTTTATTCAACAAAA 57.533 29.630 0.00 0.00 0.00 2.44
5370 5646 9.688592 AAATCAGAGAGCTTTATTCAACAAAAG 57.311 29.630 0.00 0.00 36.09 2.27
5371 5647 7.807977 TCAGAGAGCTTTATTCAACAAAAGT 57.192 32.000 0.00 0.00 35.56 2.66
5372 5648 7.642669 TCAGAGAGCTTTATTCAACAAAAGTG 58.357 34.615 0.00 0.00 35.56 3.16
5373 5649 7.283127 TCAGAGAGCTTTATTCAACAAAAGTGT 59.717 33.333 0.00 0.00 40.75 3.55
5375 5651 8.131731 AGAGAGCTTTATTCAACAAAAGTGTTC 58.868 33.333 0.00 0.00 45.00 3.18
5376 5652 7.203218 AGAGCTTTATTCAACAAAAGTGTTCC 58.797 34.615 0.00 0.00 45.00 3.62
5377 5653 6.280643 AGCTTTATTCAACAAAAGTGTTCCC 58.719 36.000 0.00 0.00 45.00 3.97
5378 5654 5.174943 GCTTTATTCAACAAAAGTGTTCCCG 59.825 40.000 0.00 0.00 45.00 5.14
5379 5655 3.726291 ATTCAACAAAAGTGTTCCCGG 57.274 42.857 0.00 0.00 45.00 5.73
5380 5656 1.394618 TCAACAAAAGTGTTCCCGGG 58.605 50.000 16.85 16.85 45.00 5.73
5381 5657 0.249280 CAACAAAAGTGTTCCCGGGC 60.249 55.000 18.49 2.59 45.00 6.13
5382 5658 0.684805 AACAAAAGTGTTCCCGGGCA 60.685 50.000 18.49 0.00 45.00 5.36
5383 5659 0.684805 ACAAAAGTGTTCCCGGGCAA 60.685 50.000 18.49 8.60 32.58 4.52
5384 5660 0.678950 CAAAAGTGTTCCCGGGCAAT 59.321 50.000 18.49 5.19 0.00 3.56
5385 5661 0.966179 AAAAGTGTTCCCGGGCAATC 59.034 50.000 18.49 6.53 0.00 2.67
5386 5662 0.178975 AAAGTGTTCCCGGGCAATCA 60.179 50.000 18.49 9.15 0.00 2.57
5387 5663 0.609131 AAGTGTTCCCGGGCAATCAG 60.609 55.000 18.49 0.00 0.00 2.90
5388 5664 2.361104 TGTTCCCGGGCAATCAGC 60.361 61.111 18.49 0.00 44.65 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.995626 CCTACCCCAGTCACCCCAG 60.996 68.421 0.00 0.00 0.00 4.45
39 40 2.124085 CCTACCCCAGTCACCCCA 59.876 66.667 0.00 0.00 0.00 4.96
40 41 2.691252 CCCTACCCCAGTCACCCC 60.691 72.222 0.00 0.00 0.00 4.95
41 42 0.623617 ATTCCCTACCCCAGTCACCC 60.624 60.000 0.00 0.00 0.00 4.61
42 43 2.185663 TATTCCCTACCCCAGTCACC 57.814 55.000 0.00 0.00 0.00 4.02
43 44 3.046374 ACATATTCCCTACCCCAGTCAC 58.954 50.000 0.00 0.00 0.00 3.67
44 45 3.314693 GACATATTCCCTACCCCAGTCA 58.685 50.000 0.00 0.00 0.00 3.41
45 46 2.638363 GGACATATTCCCTACCCCAGTC 59.362 54.545 0.00 0.00 38.70 3.51
46 47 2.702748 GGACATATTCCCTACCCCAGT 58.297 52.381 0.00 0.00 38.70 4.00
47 48 1.623811 CGGACATATTCCCTACCCCAG 59.376 57.143 0.00 0.00 42.27 4.45
52 53 2.223876 TGCGAACGGACATATTCCCTAC 60.224 50.000 0.00 0.00 42.27 3.18
53 54 2.033372 TGCGAACGGACATATTCCCTA 58.967 47.619 0.00 0.00 42.27 3.53
57 58 1.935933 ACCTGCGAACGGACATATTC 58.064 50.000 0.00 0.00 0.00 1.75
61 62 0.606604 AGTAACCTGCGAACGGACAT 59.393 50.000 0.00 0.00 0.00 3.06
69 70 2.565391 TCCATTCTTGAGTAACCTGCGA 59.435 45.455 0.00 0.00 0.00 5.10
82 83 3.011032 ACCTTCTGCCTGAATCCATTCTT 59.989 43.478 1.13 0.00 37.67 2.52
128 129 3.368116 CCCGTAAAACCCTACTCTGTGAG 60.368 52.174 0.00 0.00 35.52 3.51
132 133 1.276989 TGCCCGTAAAACCCTACTCTG 59.723 52.381 0.00 0.00 0.00 3.35
139 140 0.679960 ATCTGCTGCCCGTAAAACCC 60.680 55.000 0.00 0.00 0.00 4.11
145 146 1.051008 ATCATCATCTGCTGCCCGTA 58.949 50.000 0.00 0.00 0.00 4.02
173 183 1.339291 TCTGCTCTGTGACTGTGTCTG 59.661 52.381 0.00 0.00 33.15 3.51
177 187 2.522836 AACTCTGCTCTGTGACTGTG 57.477 50.000 0.00 0.00 0.00 3.66
232 242 2.128035 CTCAGTGACCGTGTCTTCAAC 58.872 52.381 0.00 0.00 33.15 3.18
233 243 1.538204 GCTCAGTGACCGTGTCTTCAA 60.538 52.381 0.00 0.00 33.15 2.69
234 244 0.032130 GCTCAGTGACCGTGTCTTCA 59.968 55.000 0.00 0.00 33.15 3.02
235 245 0.032130 TGCTCAGTGACCGTGTCTTC 59.968 55.000 0.00 0.68 33.15 2.87
236 246 0.032678 CTGCTCAGTGACCGTGTCTT 59.967 55.000 0.00 0.00 33.15 3.01
237 247 0.823769 TCTGCTCAGTGACCGTGTCT 60.824 55.000 0.00 0.00 33.15 3.41
238 248 0.387878 CTCTGCTCAGTGACCGTGTC 60.388 60.000 0.00 0.00 0.00 3.67
239 249 1.109920 ACTCTGCTCAGTGACCGTGT 61.110 55.000 6.02 0.00 0.00 4.49
240 250 0.032678 AACTCTGCTCAGTGACCGTG 59.967 55.000 6.02 0.00 0.00 4.94
241 251 1.269998 GTAACTCTGCTCAGTGACCGT 59.730 52.381 6.02 0.00 0.00 4.83
242 252 1.542030 AGTAACTCTGCTCAGTGACCG 59.458 52.381 6.02 0.00 28.52 4.79
243 253 2.953020 CAGTAACTCTGCTCAGTGACC 58.047 52.381 6.02 0.00 37.36 4.02
254 264 5.513267 GGTTCCTGATTTGGACAGTAACTCT 60.513 44.000 0.00 0.00 35.55 3.24
255 265 4.695928 GGTTCCTGATTTGGACAGTAACTC 59.304 45.833 0.00 0.00 35.55 3.01
256 266 4.104102 TGGTTCCTGATTTGGACAGTAACT 59.896 41.667 0.00 0.00 35.55 2.24
257 267 4.394729 TGGTTCCTGATTTGGACAGTAAC 58.605 43.478 0.00 0.00 35.58 2.50
258 268 4.715534 TGGTTCCTGATTTGGACAGTAA 57.284 40.909 0.00 0.00 35.58 2.24
259 269 4.927267 ATGGTTCCTGATTTGGACAGTA 57.073 40.909 0.00 0.00 35.58 2.74
260 270 3.814504 ATGGTTCCTGATTTGGACAGT 57.185 42.857 0.00 0.00 35.58 3.55
261 271 5.355350 GTCTAATGGTTCCTGATTTGGACAG 59.645 44.000 0.00 0.00 35.58 3.51
262 272 5.222027 TGTCTAATGGTTCCTGATTTGGACA 60.222 40.000 0.00 0.00 35.58 4.02
263 273 5.253330 TGTCTAATGGTTCCTGATTTGGAC 58.747 41.667 0.00 0.00 35.58 4.02
264 274 5.014123 ACTGTCTAATGGTTCCTGATTTGGA 59.986 40.000 0.00 0.00 0.00 3.53
265 275 5.124457 CACTGTCTAATGGTTCCTGATTTGG 59.876 44.000 0.00 0.00 0.00 3.28
266 276 5.392380 GCACTGTCTAATGGTTCCTGATTTG 60.392 44.000 0.00 0.00 0.00 2.32
267 277 4.702131 GCACTGTCTAATGGTTCCTGATTT 59.298 41.667 0.00 0.00 0.00 2.17
268 278 4.263462 TGCACTGTCTAATGGTTCCTGATT 60.263 41.667 0.00 0.00 0.00 2.57
269 279 3.264193 TGCACTGTCTAATGGTTCCTGAT 59.736 43.478 0.00 0.00 0.00 2.90
270 280 2.637382 TGCACTGTCTAATGGTTCCTGA 59.363 45.455 0.00 0.00 0.00 3.86
271 281 3.005554 CTGCACTGTCTAATGGTTCCTG 58.994 50.000 0.00 0.00 0.00 3.86
272 282 2.616510 GCTGCACTGTCTAATGGTTCCT 60.617 50.000 0.00 0.00 0.00 3.36
273 283 1.740025 GCTGCACTGTCTAATGGTTCC 59.260 52.381 0.00 0.00 0.00 3.62
274 284 2.704572 AGCTGCACTGTCTAATGGTTC 58.295 47.619 1.02 0.00 0.00 3.62
275 285 2.816087 CAAGCTGCACTGTCTAATGGTT 59.184 45.455 1.02 0.00 0.00 3.67
276 286 2.430465 CAAGCTGCACTGTCTAATGGT 58.570 47.619 1.02 0.00 0.00 3.55
277 287 1.131883 GCAAGCTGCACTGTCTAATGG 59.868 52.381 1.02 0.00 44.26 3.16
278 288 2.539346 GCAAGCTGCACTGTCTAATG 57.461 50.000 1.02 0.00 44.26 1.90
289 299 0.602106 TGACTCTGTCTGCAAGCTGC 60.602 55.000 0.00 0.00 45.29 5.25
290 300 1.146637 GTGACTCTGTCTGCAAGCTG 58.853 55.000 0.00 0.00 33.15 4.24
291 301 0.034616 GGTGACTCTGTCTGCAAGCT 59.965 55.000 0.00 0.00 33.15 3.74
292 302 1.287730 CGGTGACTCTGTCTGCAAGC 61.288 60.000 0.00 0.00 33.15 4.01
298 308 0.250945 TCTGCTCGGTGACTCTGTCT 60.251 55.000 0.00 0.00 33.15 3.41
308 318 1.813513 CACCTCAAAATCTGCTCGGT 58.186 50.000 0.00 0.00 0.00 4.69
310 320 1.159285 TGCACCTCAAAATCTGCTCG 58.841 50.000 0.00 0.00 0.00 5.03
335 383 0.953727 TCACATGAAAGCACCACAGC 59.046 50.000 0.00 0.00 0.00 4.40
363 411 3.928992 TCTAAATCACTCGCTGAAGCAAG 59.071 43.478 2.79 0.00 42.21 4.01
364 412 3.925379 TCTAAATCACTCGCTGAAGCAA 58.075 40.909 2.79 0.00 42.21 3.91
365 413 3.515630 CTCTAAATCACTCGCTGAAGCA 58.484 45.455 2.79 0.00 42.21 3.91
366 414 2.863137 CCTCTAAATCACTCGCTGAAGC 59.137 50.000 0.00 0.00 37.78 3.86
382 430 3.705051 ACGAACCACCACTAATCCTCTA 58.295 45.455 0.00 0.00 0.00 2.43
386 434 4.572909 AGTAAACGAACCACCACTAATCC 58.427 43.478 0.00 0.00 0.00 3.01
395 443 4.448060 CCTCTCAGAAAGTAAACGAACCAC 59.552 45.833 0.00 0.00 0.00 4.16
399 447 4.330944 TGCCTCTCAGAAAGTAAACGAA 57.669 40.909 0.00 0.00 0.00 3.85
400 448 4.056050 GTTGCCTCTCAGAAAGTAAACGA 58.944 43.478 0.00 0.00 0.00 3.85
413 461 4.819088 ACTTTTCTTCTGAAGTTGCCTCTC 59.181 41.667 16.43 0.00 32.43 3.20
414 462 4.786425 ACTTTTCTTCTGAAGTTGCCTCT 58.214 39.130 16.43 0.00 32.43 3.69
469 518 4.455877 GCACCTGATTTACAGCTAACACTT 59.544 41.667 0.00 0.00 44.52 3.16
495 544 5.376854 ACTATGTTTTGACACTTGATGGC 57.623 39.130 0.00 0.00 36.53 4.40
508 557 9.591792 GAACGGAGGTAGTATTTACTATGTTTT 57.408 33.333 1.05 0.00 40.55 2.43
531 580 4.201881 GGACCATGCCACTTATTTACGAAC 60.202 45.833 0.00 0.00 0.00 3.95
536 585 3.699038 GCTTGGACCATGCCACTTATTTA 59.301 43.478 19.29 0.00 37.75 1.40
548 597 3.365472 GGAAATAAGTGGCTTGGACCAT 58.635 45.455 0.00 0.00 43.01 3.55
553 602 3.081804 AGTTCGGAAATAAGTGGCTTGG 58.918 45.455 0.00 0.00 0.00 3.61
554 603 3.751175 TCAGTTCGGAAATAAGTGGCTTG 59.249 43.478 0.00 0.00 0.00 4.01
555 604 4.003648 CTCAGTTCGGAAATAAGTGGCTT 58.996 43.478 0.00 0.00 0.00 4.35
568 640 2.944349 GAGTACTACTCCCTCAGTTCGG 59.056 54.545 5.01 0.00 39.28 4.30
574 646 4.652679 TGAACAGAGTACTACTCCCTCA 57.347 45.455 11.94 9.55 46.18 3.86
648 720 8.572855 AAGCATGTCTTCTAATAAAGCTTTCT 57.427 30.769 16.57 2.47 36.50 2.52
750 825 1.669115 CAGCACCCTCACCGTCTTG 60.669 63.158 0.00 0.00 0.00 3.02
868 946 0.606673 GTCACAGGGCAAAGGAGACC 60.607 60.000 0.00 0.00 0.00 3.85
1064 1142 7.754924 ACAAATAATTATGGCAAACGTGAAGAG 59.245 33.333 0.00 0.00 0.00 2.85
1070 1148 8.031864 TGATGAACAAATAATTATGGCAAACGT 58.968 29.630 0.00 0.00 0.00 3.99
1088 1166 3.118075 TGTGGAGTTGGAAGTGATGAACA 60.118 43.478 0.00 0.00 0.00 3.18
1089 1167 3.251004 GTGTGGAGTTGGAAGTGATGAAC 59.749 47.826 0.00 0.00 0.00 3.18
1112 1190 9.838339 AGGAATATCACATACCTTTTTCTACAG 57.162 33.333 0.00 0.00 0.00 2.74
1139 1217 9.725206 AAAGTTACAGAGGGAGTATATTCCTAA 57.275 33.333 13.49 2.30 37.40 2.69
1140 1218 9.725206 AAAAGTTACAGAGGGAGTATATTCCTA 57.275 33.333 13.49 0.00 37.40 2.94
1141 1219 8.625467 AAAAGTTACAGAGGGAGTATATTCCT 57.375 34.615 13.49 3.08 37.40 3.36
1149 1227 8.033626 CGTCTTATAAAAAGTTACAGAGGGAGT 58.966 37.037 0.00 0.00 0.00 3.85
1150 1228 8.033626 ACGTCTTATAAAAAGTTACAGAGGGAG 58.966 37.037 0.00 0.00 29.65 4.30
1151 1229 7.899973 ACGTCTTATAAAAAGTTACAGAGGGA 58.100 34.615 0.00 0.00 29.65 4.20
1205 1283 4.695455 GCCTCTGCAACTTAATACAAGACA 59.305 41.667 0.00 0.00 37.47 3.41
1206 1284 4.695455 TGCCTCTGCAACTTAATACAAGAC 59.305 41.667 0.00 0.00 46.66 3.01
1288 1366 4.520874 TGTGGCGAACATATGGAAGAAAAA 59.479 37.500 7.80 0.00 32.36 1.94
1293 1371 4.096231 TGAATTGTGGCGAACATATGGAAG 59.904 41.667 7.80 0.00 38.99 3.46
1302 1380 6.088085 CACTAAAATTCTGAATTGTGGCGAAC 59.912 38.462 15.80 0.00 0.00 3.95
1348 1426 6.456853 GCATGAGCAAGAATATACGTGAAACA 60.457 38.462 0.00 0.00 41.58 2.83
1384 1462 8.286800 CACTAATTACACGAACTTTCATGGAAA 58.713 33.333 0.00 0.00 25.87 3.13
1387 1465 7.359262 TCACTAATTACACGAACTTTCATGG 57.641 36.000 0.00 0.00 0.00 3.66
1389 1467 7.660208 AGGTTCACTAATTACACGAACTTTCAT 59.340 33.333 12.91 0.00 36.91 2.57
1390 1468 6.987992 AGGTTCACTAATTACACGAACTTTCA 59.012 34.615 12.91 0.00 36.91 2.69
1391 1469 7.417496 AGGTTCACTAATTACACGAACTTTC 57.583 36.000 12.91 2.61 36.91 2.62
1423 1502 3.541632 CACCGCTACCCAACATTCTATT 58.458 45.455 0.00 0.00 0.00 1.73
1424 1503 2.745152 GCACCGCTACCCAACATTCTAT 60.745 50.000 0.00 0.00 0.00 1.98
1425 1504 1.406341 GCACCGCTACCCAACATTCTA 60.406 52.381 0.00 0.00 0.00 2.10
1426 1505 0.676782 GCACCGCTACCCAACATTCT 60.677 55.000 0.00 0.00 0.00 2.40
1427 1506 1.800681 GCACCGCTACCCAACATTC 59.199 57.895 0.00 0.00 0.00 2.67
1428 1507 2.038269 CGCACCGCTACCCAACATT 61.038 57.895 0.00 0.00 0.00 2.71
1495 1574 0.343372 AGAGGAGGGAGTATTGGCCA 59.657 55.000 0.00 0.00 0.00 5.36
1513 1592 3.840890 TGGGTGCGCTATAAACAAAAG 57.159 42.857 9.73 0.00 0.00 2.27
1662 1742 5.385198 TCAAGGCAATTAATGGTCTATCCC 58.615 41.667 0.00 0.00 34.77 3.85
1680 1760 8.031864 AGATCAACGCATAATACTAGATCAAGG 58.968 37.037 0.00 0.00 34.58 3.61
1689 1769 9.982651 ATACAACTTAGATCAACGCATAATACT 57.017 29.630 0.00 0.00 0.00 2.12
1720 1804 7.581011 AACAAATTTTCGAGCATGTAATTCC 57.419 32.000 0.00 0.00 0.00 3.01
1733 1817 7.290118 CCAGGCTAAAATCAAACAAATTTTCG 58.710 34.615 0.00 0.00 37.47 3.46
1739 1823 4.742138 GCACCCAGGCTAAAATCAAACAAA 60.742 41.667 0.00 0.00 0.00 2.83
1790 1875 7.112122 CACCAATATGCTATGGCCTAATCTTA 58.888 38.462 3.32 0.00 40.51 2.10
1828 1913 4.741928 TGGACAGAGGGCATACTCTATA 57.258 45.455 4.75 0.00 45.71 1.31
1855 1966 5.105675 TGCATGCTCAATGTATGTGACAAAT 60.106 36.000 20.33 0.00 42.78 2.32
1862 1973 4.381185 CCAAGTTGCATGCTCAATGTATGT 60.381 41.667 20.33 0.00 40.27 2.29
2102 2224 9.409918 TCTAGCTTACTGACTATGAAGTACAAT 57.590 33.333 0.00 0.00 35.56 2.71
2103 2225 8.803397 TCTAGCTTACTGACTATGAAGTACAA 57.197 34.615 0.00 0.00 35.56 2.41
2104 2226 8.982091 ATCTAGCTTACTGACTATGAAGTACA 57.018 34.615 0.00 0.00 35.56 2.90
2142 2264 9.647918 AGATGGAATAATCAGTAGTTAGTGAGA 57.352 33.333 3.36 0.00 38.88 3.27
2150 2272 7.618019 TTGGCTAGATGGAATAATCAGTAGT 57.382 36.000 0.00 0.00 0.00 2.73
2184 2306 1.731720 GCCTTCTGCTGTAGTTCTGG 58.268 55.000 0.00 0.00 36.87 3.86
2542 2670 3.186119 CCAAAGCAACGACAACAAACAT 58.814 40.909 0.00 0.00 0.00 2.71
2729 2857 5.698545 AGAAAGAAGATCAGAAAGAACACCG 59.301 40.000 0.00 0.00 0.00 4.94
2733 2861 6.708054 TGGTCAGAAAGAAGATCAGAAAGAAC 59.292 38.462 0.00 0.00 0.00 3.01
2778 2906 3.251729 AGCTACTTGCCATGATATTTGCG 59.748 43.478 0.00 0.00 44.23 4.85
2940 3068 3.008375 CCTCCACAATCTTCTCCTGTTCA 59.992 47.826 0.00 0.00 0.00 3.18
2967 3122 4.654724 AGCTTCTCCTCATCATCATTCTCA 59.345 41.667 0.00 0.00 0.00 3.27
3065 3250 3.715834 CTCCATGATCTCCTCCTCCTTTT 59.284 47.826 0.00 0.00 0.00 2.27
3078 3263 3.181456 CCTTCTCCTTCACCTCCATGATC 60.181 52.174 0.00 0.00 0.00 2.92
3102 3287 4.159879 TCCTCCTCATCATCATCATCATCG 59.840 45.833 0.00 0.00 0.00 3.84
3115 3300 1.688197 CTTCTGCTCCTCCTCCTCATC 59.312 57.143 0.00 0.00 0.00 2.92
3220 3405 1.688197 CTTCTGCTCCTCCTCCTCATC 59.312 57.143 0.00 0.00 0.00 2.92
3221 3406 1.792115 CTTCTGCTCCTCCTCCTCAT 58.208 55.000 0.00 0.00 0.00 2.90
3222 3407 0.975040 GCTTCTGCTCCTCCTCCTCA 60.975 60.000 0.00 0.00 36.03 3.86
3468 3653 4.171234 AGAGGAATCCTTTGAAGACCAGA 58.829 43.478 2.09 0.00 31.76 3.86
3716 3901 1.682344 GTTCTTCCCCATGGCACCC 60.682 63.158 6.09 0.00 0.00 4.61
3936 4172 3.378112 GGTCAGCGATGAATGATTTTCCA 59.622 43.478 4.22 0.00 0.00 3.53
3998 4234 3.068307 TCGAGGGAAAGCTGAAGTATAGC 59.932 47.826 0.00 0.00 41.43 2.97
4194 4430 0.326264 ACATGGTTCTGGCAGGAGTC 59.674 55.000 15.73 1.67 0.00 3.36
4254 4490 6.648192 AGTTTCTAGCTCTGCAATCTTACAT 58.352 36.000 0.00 0.00 0.00 2.29
4262 4501 3.820557 ACCAAAGTTTCTAGCTCTGCAA 58.179 40.909 0.00 0.00 0.00 4.08
4349 4588 2.303022 GGATGATCCGGGAGCAATTCTA 59.697 50.000 20.09 0.00 29.85 2.10
4354 4593 0.918983 AAAGGATGATCCGGGAGCAA 59.081 50.000 20.09 2.89 42.75 3.91
4455 4695 4.700213 CCGGTGATAGGTTTTCATCTTTGT 59.300 41.667 0.00 0.00 0.00 2.83
4501 4741 0.759346 CTTCCCTAACCAGATCCCCG 59.241 60.000 0.00 0.00 0.00 5.73
4559 4799 1.093159 CAGTCCAGAAATCTGCCAGC 58.907 55.000 4.87 0.00 42.47 4.85
4569 4809 6.257849 GCGTACAATATCATTTCAGTCCAGAA 59.742 38.462 0.00 0.00 0.00 3.02
4593 4833 2.020131 CATTGTCCGATGGAGCTGC 58.980 57.895 0.00 0.00 29.39 5.25
4594 4834 0.745486 TGCATTGTCCGATGGAGCTG 60.745 55.000 0.00 0.00 29.39 4.24
4652 4892 1.369692 CGCCCACAGGTGTGTTAGA 59.630 57.895 9.22 0.00 44.21 2.10
4720 4960 2.494870 GCAAAACATTCTGCAGGAGGAT 59.505 45.455 14.91 0.00 38.48 3.24
4722 4962 1.614903 TGCAAAACATTCTGCAGGAGG 59.385 47.619 15.13 10.07 43.44 4.30
4727 4967 1.001487 CGAGGTGCAAAACATTCTGCA 60.001 47.619 0.00 0.00 46.01 4.41
4728 4968 1.689959 CGAGGTGCAAAACATTCTGC 58.310 50.000 0.00 0.00 39.09 4.26
4729 4969 1.689959 GCGAGGTGCAAAACATTCTG 58.310 50.000 0.00 0.00 45.45 3.02
4732 4972 0.665835 TTCGCGAGGTGCAAAACATT 59.334 45.000 9.59 0.00 46.97 2.71
4734 4974 1.646540 CTTCGCGAGGTGCAAAACA 59.353 52.632 9.59 0.00 46.97 2.83
4735 4975 1.725973 GCTTCGCGAGGTGCAAAAC 60.726 57.895 19.98 0.00 46.97 2.43
4736 4976 1.719725 TTGCTTCGCGAGGTGCAAAA 61.720 50.000 29.76 17.25 46.97 2.44
4739 4979 3.345808 GTTGCTTCGCGAGGTGCA 61.346 61.111 22.87 22.87 46.97 4.57
4775 5016 2.448726 GCTGATCATTTCTGCACGTC 57.551 50.000 0.00 0.00 45.73 4.34
4841 5082 0.393820 TTTCTACCTCCGTTTGCCGT 59.606 50.000 0.00 0.00 33.66 5.68
4844 5085 3.125316 CAGTCATTTCTACCTCCGTTTGC 59.875 47.826 0.00 0.00 0.00 3.68
4878 5119 8.592155 TGAAACTTCAGAAATATCAATACGACG 58.408 33.333 0.00 0.00 32.50 5.12
4888 5129 6.151817 GGTGGAGCTTGAAACTTCAGAAATAT 59.848 38.462 0.00 0.00 38.61 1.28
4920 5161 3.265791 CCTCACACTTATTCACTCAGGC 58.734 50.000 0.00 0.00 0.00 4.85
4926 5167 5.635700 GTGAAGAGACCTCACACTTATTCAC 59.364 44.000 14.92 12.02 36.73 3.18
4952 5193 6.879458 ACTCTCACAATTTTATACCACCTGAC 59.121 38.462 0.00 0.00 0.00 3.51
4955 5196 7.458397 TGAACTCTCACAATTTTATACCACCT 58.542 34.615 0.00 0.00 0.00 4.00
5004 5245 2.665165 ACAACTGGAGGCATCAAACAA 58.335 42.857 0.00 0.00 0.00 2.83
5102 5352 5.246981 ACCATCTTCTTGAGTGGAAATCA 57.753 39.130 0.00 0.00 40.30 2.57
5124 5374 3.320256 TGCATGGCACTAACAAATCACAA 59.680 39.130 0.00 0.00 31.71 3.33
5172 5448 7.235399 ACCCAATGTTTCCTGAAAATCATAGTT 59.765 33.333 0.00 0.00 31.33 2.24
5218 5494 2.030363 CGTGTTGCCCTGCATTTTCTTA 60.030 45.455 0.00 0.00 38.76 2.10
5245 5521 9.696917 GATCAACTTATAATAAAAAGCATGGGG 57.303 33.333 0.00 0.00 0.00 4.96
5253 5529 7.841729 TGGGCAGGGATCAACTTATAATAAAAA 59.158 33.333 0.00 0.00 0.00 1.94
5254 5530 7.358263 TGGGCAGGGATCAACTTATAATAAAA 58.642 34.615 0.00 0.00 0.00 1.52
5310 5586 3.480470 ACACTTGGATCAAGAACACAGG 58.520 45.455 13.74 0.00 43.42 4.00
5333 5609 3.190535 GCTCTCTGATTTGCCCGTAAAAA 59.809 43.478 0.00 0.00 0.00 1.94
5334 5610 2.747446 GCTCTCTGATTTGCCCGTAAAA 59.253 45.455 0.00 0.00 0.00 1.52
5335 5611 2.027192 AGCTCTCTGATTTGCCCGTAAA 60.027 45.455 0.00 0.00 0.00 2.01
5336 5612 1.555075 AGCTCTCTGATTTGCCCGTAA 59.445 47.619 0.00 0.00 0.00 3.18
5337 5613 1.195115 AGCTCTCTGATTTGCCCGTA 58.805 50.000 0.00 0.00 0.00 4.02
5338 5614 0.326264 AAGCTCTCTGATTTGCCCGT 59.674 50.000 0.00 0.00 0.00 5.28
5339 5615 1.457346 AAAGCTCTCTGATTTGCCCG 58.543 50.000 0.00 0.00 32.52 6.13
5340 5616 4.641989 TGAATAAAGCTCTCTGATTTGCCC 59.358 41.667 0.00 0.00 34.88 5.36
5341 5617 5.824904 TGAATAAAGCTCTCTGATTTGCC 57.175 39.130 0.00 0.00 34.88 4.52
5342 5618 6.615088 TGTTGAATAAAGCTCTCTGATTTGC 58.385 36.000 0.00 0.00 34.88 3.68
5343 5619 9.467258 TTTTGTTGAATAAAGCTCTCTGATTTG 57.533 29.630 0.00 0.00 34.88 2.32
5344 5620 9.688592 CTTTTGTTGAATAAAGCTCTCTGATTT 57.311 29.630 0.00 0.00 37.99 2.17
5345 5621 8.854117 ACTTTTGTTGAATAAAGCTCTCTGATT 58.146 29.630 0.00 0.00 35.31 2.57
5346 5622 8.295288 CACTTTTGTTGAATAAAGCTCTCTGAT 58.705 33.333 0.00 0.00 35.31 2.90
5347 5623 7.283127 ACACTTTTGTTGAATAAAGCTCTCTGA 59.717 33.333 0.00 0.00 35.31 3.27
5348 5624 7.420800 ACACTTTTGTTGAATAAAGCTCTCTG 58.579 34.615 0.00 0.00 35.31 3.35
5349 5625 7.573968 ACACTTTTGTTGAATAAAGCTCTCT 57.426 32.000 0.00 0.00 35.31 3.10
5350 5626 7.379797 GGAACACTTTTGTTGAATAAAGCTCTC 59.620 37.037 0.00 0.00 46.43 3.20
5351 5627 7.203218 GGAACACTTTTGTTGAATAAAGCTCT 58.797 34.615 0.00 0.00 46.43 4.09
5352 5628 6.420903 GGGAACACTTTTGTTGAATAAAGCTC 59.579 38.462 0.00 0.00 46.43 4.09
5353 5629 6.280643 GGGAACACTTTTGTTGAATAAAGCT 58.719 36.000 0.00 0.00 46.43 3.74
5354 5630 5.174943 CGGGAACACTTTTGTTGAATAAAGC 59.825 40.000 0.00 0.00 46.43 3.51
5355 5631 5.689961 CCGGGAACACTTTTGTTGAATAAAG 59.310 40.000 0.00 0.00 46.43 1.85
5356 5632 5.452077 CCCGGGAACACTTTTGTTGAATAAA 60.452 40.000 18.48 0.00 46.43 1.40
5357 5633 4.038162 CCCGGGAACACTTTTGTTGAATAA 59.962 41.667 18.48 0.00 46.43 1.40
5358 5634 3.570550 CCCGGGAACACTTTTGTTGAATA 59.429 43.478 18.48 0.00 46.43 1.75
5359 5635 2.364002 CCCGGGAACACTTTTGTTGAAT 59.636 45.455 18.48 0.00 46.43 2.57
5360 5636 1.751924 CCCGGGAACACTTTTGTTGAA 59.248 47.619 18.48 0.00 46.43 2.69
5361 5637 1.394618 CCCGGGAACACTTTTGTTGA 58.605 50.000 18.48 0.00 46.43 3.18
5362 5638 0.249280 GCCCGGGAACACTTTTGTTG 60.249 55.000 29.31 0.00 46.43 3.33
5364 5640 0.684805 TTGCCCGGGAACACTTTTGT 60.685 50.000 29.31 0.00 37.67 2.83
5365 5641 0.678950 ATTGCCCGGGAACACTTTTG 59.321 50.000 29.31 0.00 0.00 2.44
5366 5642 0.966179 GATTGCCCGGGAACACTTTT 59.034 50.000 29.31 0.00 0.00 2.27
5367 5643 0.178975 TGATTGCCCGGGAACACTTT 60.179 50.000 29.31 0.00 0.00 2.66
5368 5644 0.609131 CTGATTGCCCGGGAACACTT 60.609 55.000 29.31 3.31 0.00 3.16
5369 5645 1.002134 CTGATTGCCCGGGAACACT 60.002 57.895 29.31 7.83 0.00 3.55
5370 5646 2.700773 GCTGATTGCCCGGGAACAC 61.701 63.158 29.31 11.34 35.15 3.32
5371 5647 2.361104 GCTGATTGCCCGGGAACA 60.361 61.111 29.31 11.51 35.15 3.18


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

AutoCloner maintained by Alex Coulton.