Multiple sequence alignment - TraesCS7D01G149300

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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 TraesCS7D01G149300 chr7D 100.000 3035 0 0 1 3035 98294620 98291586 0.000000e+00 5605.0
1 TraesCS7D01G149300 chr7D 76.496 234 42 10 65 295 554344556 554344779 6.880000e-22 115.0
2 TraesCS7D01G149300 chr7B 96.121 2320 65 10 729 3035 52911626 52909319 0.000000e+00 3762.0
3 TraesCS7D01G149300 chr7B 96.713 1369 32 5 1068 2428 615162050 615163413 0.000000e+00 2266.0
4 TraesCS7D01G149300 chr7B 92.833 293 21 0 2740 3032 615163591 615163883 2.800000e-115 425.0
5 TraesCS7D01G149300 chr7B 94.595 259 8 2 826 1078 615161691 615161949 2.190000e-106 396.0
6 TraesCS7D01G149300 chr7B 94.037 218 13 0 2523 2740 615163413 615163630 6.270000e-87 331.0
7 TraesCS7D01G149300 chr7B 93.750 48 2 1 731 778 615161629 615161675 1.510000e-08 71.3
8 TraesCS7D01G149300 chr7A 84.388 474 44 15 40 512 100599195 100598751 3.590000e-119 438.0
9 TraesCS7D01G149300 chr7A 81.667 180 19 12 61 236 534134526 534134695 1.470000e-28 137.0
10 TraesCS7D01G149300 chr4D 82.833 233 32 8 65 296 59424099 59424324 5.130000e-48 202.0
11 TraesCS7D01G149300 chr4D 76.786 224 38 10 65 280 506882544 506882327 2.470000e-21 113.0
12 TraesCS7D01G149300 chr3B 82.051 234 34 6 65 295 756679561 756679789 3.090000e-45 193.0
13 TraesCS7D01G149300 chr2A 79.424 243 33 14 65 297 35970908 35970673 4.050000e-34 156.0
14 TraesCS7D01G149300 chr2A 77.953 254 32 20 255 501 749000347 749000111 1.470000e-28 137.0
15 TraesCS7D01G149300 chr3D 75.521 384 51 28 70 448 25989137 25988792 6.780000e-32 148.0
16 TraesCS7D01G149300 chr6B 80.198 202 32 8 167 366 93823375 93823570 8.770000e-31 145.0
17 TraesCS7D01G149300 chr3A 85.507 138 16 4 70 207 111078356 111078223 1.130000e-29 141.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G149300 chr7D 98291586 98294620 3034 True 5605.00 5605 100.0000 1 3035 1 chr7D.!!$R1 3034
1 TraesCS7D01G149300 chr7B 52909319 52911626 2307 True 3762.00 3762 96.1210 729 3035 1 chr7B.!!$R1 2306
2 TraesCS7D01G149300 chr7B 615161629 615163883 2254 False 697.86 2266 94.3856 731 3032 5 chr7B.!!$F1 2301

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
576 577 0.179161 CTTCCCTACGTCTCGCTGTG 60.179 60.0 0.00 0.0 0.0 3.66 F
591 592 0.248661 CTGTGAGCGAGACATACGGG 60.249 60.0 0.00 0.0 0.0 5.28 F
683 684 0.319900 CGATCGGGCCATCACTAAGG 60.320 60.0 7.38 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1851 0.033405 CTTCCACCTCCTCCTCGGTA 60.033 60.000 0.0 0.0 30.91 4.02 R
1871 2000 1.000771 GCCTCCCCTTTCTTCCCAC 60.001 63.158 0.0 0.0 0.00 4.61 R
2632 2769 2.621486 GGAGTCCCCTTAGGCATGT 58.379 57.895 0.0 0.0 34.51 3.21 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
32 33 7.899648 TTTTTGTTGGGAAACATAGTAGGAA 57.100 32.000 0.00 0.00 32.01 3.36
33 34 7.899648 TTTTGTTGGGAAACATAGTAGGAAA 57.100 32.000 0.00 0.00 32.01 3.13
34 35 7.899648 TTTGTTGGGAAACATAGTAGGAAAA 57.100 32.000 0.00 0.00 32.01 2.29
35 36 7.899648 TTGTTGGGAAACATAGTAGGAAAAA 57.100 32.000 0.00 0.00 32.01 1.94
60 61 9.713684 AAACATCCTATGAATAAATTCCAAGGA 57.286 29.630 18.24 18.24 44.15 3.36
61 62 9.887862 AACATCCTATGAATAAATTCCAAGGAT 57.112 29.630 20.07 20.07 46.90 3.24
62 63 9.525826 ACATCCTATGAATAAATTCCAAGGATC 57.474 33.333 21.61 0.00 45.04 3.36
63 64 9.524496 CATCCTATGAATAAATTCCAAGGATCA 57.476 33.333 21.61 7.38 45.04 2.92
68 69 8.696043 ATGAATAAATTCCAAGGATCATTCGA 57.304 30.769 0.00 0.00 35.97 3.71
69 70 8.518430 TGAATAAATTCCAAGGATCATTCGAA 57.482 30.769 0.00 0.00 35.97 3.71
70 71 8.965819 TGAATAAATTCCAAGGATCATTCGAAA 58.034 29.630 0.00 0.00 35.97 3.46
71 72 9.971922 GAATAAATTCCAAGGATCATTCGAAAT 57.028 29.630 0.00 0.00 0.00 2.17
74 75 7.880160 AATTCCAAGGATCATTCGAAATACA 57.120 32.000 0.00 0.00 0.00 2.29
75 76 7.880160 ATTCCAAGGATCATTCGAAATACAA 57.120 32.000 0.00 0.00 0.00 2.41
76 77 7.695480 TTCCAAGGATCATTCGAAATACAAA 57.305 32.000 0.00 0.00 0.00 2.83
77 78 7.695480 TCCAAGGATCATTCGAAATACAAAA 57.305 32.000 0.00 0.00 0.00 2.44
78 79 8.292444 TCCAAGGATCATTCGAAATACAAAAT 57.708 30.769 0.00 0.00 0.00 1.82
79 80 8.748412 TCCAAGGATCATTCGAAATACAAAATT 58.252 29.630 0.00 0.00 0.00 1.82
118 119 8.458573 ACAAGGTCAACATTTTTGTCTATACA 57.541 30.769 0.00 0.00 0.00 2.29
119 120 9.077885 ACAAGGTCAACATTTTTGTCTATACAT 57.922 29.630 0.00 0.00 34.97 2.29
159 160 9.968870 AAATGCTTGATTTACATTTTTGCAAAT 57.031 22.222 13.65 0.00 40.20 2.32
185 186 9.734620 TGCAAGATTAGCATATTTTGAATACAC 57.265 29.630 5.78 0.00 37.02 2.90
186 187 8.895845 GCAAGATTAGCATATTTTGAATACACG 58.104 33.333 5.78 0.00 0.00 4.49
187 188 9.385902 CAAGATTAGCATATTTTGAATACACGG 57.614 33.333 0.00 0.00 0.00 4.94
188 189 8.677148 AGATTAGCATATTTTGAATACACGGT 57.323 30.769 0.00 0.00 0.00 4.83
189 190 8.559536 AGATTAGCATATTTTGAATACACGGTG 58.440 33.333 6.58 6.58 0.00 4.94
190 191 7.851387 TTAGCATATTTTGAATACACGGTGA 57.149 32.000 16.29 0.00 0.00 4.02
191 192 6.751514 AGCATATTTTGAATACACGGTGAA 57.248 33.333 16.29 0.00 0.00 3.18
192 193 7.333528 AGCATATTTTGAATACACGGTGAAT 57.666 32.000 16.29 4.78 0.00 2.57
193 194 8.445275 AGCATATTTTGAATACACGGTGAATA 57.555 30.769 16.29 6.86 0.00 1.75
194 195 8.342634 AGCATATTTTGAATACACGGTGAATAC 58.657 33.333 16.29 4.41 0.00 1.89
195 196 8.342634 GCATATTTTGAATACACGGTGAATACT 58.657 33.333 16.29 0.00 0.00 2.12
199 200 9.974980 ATTTTGAATACACGGTGAATACTTTTT 57.025 25.926 16.29 0.00 0.00 1.94
200 201 9.453325 TTTTGAATACACGGTGAATACTTTTTC 57.547 29.630 16.29 3.19 0.00 2.29
201 202 7.972832 TGAATACACGGTGAATACTTTTTCT 57.027 32.000 16.29 0.00 0.00 2.52
202 203 9.491675 TTGAATACACGGTGAATACTTTTTCTA 57.508 29.630 16.29 0.00 0.00 2.10
203 204 9.661563 TGAATACACGGTGAATACTTTTTCTAT 57.338 29.630 16.29 0.00 0.00 1.98
207 208 8.248117 ACACGGTGAATACTTTTTCTATACAC 57.752 34.615 16.29 0.00 0.00 2.90
208 209 7.874016 ACACGGTGAATACTTTTTCTATACACA 59.126 33.333 16.29 0.00 0.00 3.72
209 210 8.879759 CACGGTGAATACTTTTTCTATACACAT 58.120 33.333 0.74 0.00 0.00 3.21
210 211 9.444600 ACGGTGAATACTTTTTCTATACACATT 57.555 29.630 0.00 0.00 0.00 2.71
211 212 9.916397 CGGTGAATACTTTTTCTATACACATTC 57.084 33.333 0.00 0.00 0.00 2.67
222 223 8.996024 TTTCTATACACATTCATCGTTTCTCA 57.004 30.769 0.00 0.00 0.00 3.27
223 224 8.996024 TTCTATACACATTCATCGTTTCTCAA 57.004 30.769 0.00 0.00 0.00 3.02
224 225 8.996024 TCTATACACATTCATCGTTTCTCAAA 57.004 30.769 0.00 0.00 0.00 2.69
225 226 9.599866 TCTATACACATTCATCGTTTCTCAAAT 57.400 29.630 0.00 0.00 0.00 2.32
226 227 9.642312 CTATACACATTCATCGTTTCTCAAATG 57.358 33.333 0.00 0.00 0.00 2.32
227 228 5.156355 ACACATTCATCGTTTCTCAAATGC 58.844 37.500 0.00 0.00 0.00 3.56
228 229 5.048504 ACACATTCATCGTTTCTCAAATGCT 60.049 36.000 0.00 0.00 0.00 3.79
229 230 5.860182 CACATTCATCGTTTCTCAAATGCTT 59.140 36.000 0.00 0.00 0.00 3.91
230 231 5.860182 ACATTCATCGTTTCTCAAATGCTTG 59.140 36.000 0.00 0.00 0.00 4.01
231 232 5.687770 TTCATCGTTTCTCAAATGCTTGA 57.312 34.783 0.00 0.00 39.30 3.02
232 233 5.885230 TCATCGTTTCTCAAATGCTTGAT 57.115 34.783 0.00 0.00 40.78 2.57
233 234 6.258230 TCATCGTTTCTCAAATGCTTGATT 57.742 33.333 0.00 0.00 40.78 2.57
234 235 7.376435 TCATCGTTTCTCAAATGCTTGATTA 57.624 32.000 0.00 0.00 40.78 1.75
235 236 7.988737 TCATCGTTTCTCAAATGCTTGATTAT 58.011 30.769 0.00 0.00 40.78 1.28
236 237 8.124823 TCATCGTTTCTCAAATGCTTGATTATC 58.875 33.333 0.00 0.00 40.78 1.75
237 238 7.376435 TCGTTTCTCAAATGCTTGATTATCA 57.624 32.000 0.00 0.00 40.78 2.15
238 239 7.988737 TCGTTTCTCAAATGCTTGATTATCAT 58.011 30.769 0.00 0.00 40.78 2.45
239 240 8.461222 TCGTTTCTCAAATGCTTGATTATCATT 58.539 29.630 0.00 0.00 40.78 2.57
240 241 9.079833 CGTTTCTCAAATGCTTGATTATCATTT 57.920 29.630 0.00 0.00 40.78 2.32
318 319 8.746922 ACATGATCAAATATTTTCACACACAC 57.253 30.769 0.00 0.00 0.00 3.82
319 320 8.579006 ACATGATCAAATATTTTCACACACACT 58.421 29.630 0.00 0.00 0.00 3.55
320 321 8.856247 CATGATCAAATATTTTCACACACACTG 58.144 33.333 0.00 0.00 0.00 3.66
321 322 7.939782 TGATCAAATATTTTCACACACACTGT 58.060 30.769 0.00 0.00 0.00 3.55
322 323 9.061435 TGATCAAATATTTTCACACACACTGTA 57.939 29.630 0.00 0.00 0.00 2.74
354 355 7.633361 TCGTATAGGTGAGAAATATTTTCGC 57.367 36.000 1.43 8.34 0.00 4.70
355 356 7.431249 TCGTATAGGTGAGAAATATTTTCGCT 58.569 34.615 1.43 0.00 0.00 4.93
356 357 8.570488 TCGTATAGGTGAGAAATATTTTCGCTA 58.430 33.333 1.43 4.70 0.00 4.26
357 358 9.355215 CGTATAGGTGAGAAATATTTTCGCTAT 57.645 33.333 1.43 9.78 0.00 2.97
508 509 4.725790 AAGAAAATAATGAGGCTGTGGC 57.274 40.909 0.00 0.00 37.82 5.01
518 519 3.286751 GCTGTGGCCTTCAACGCA 61.287 61.111 3.32 0.00 0.00 5.24
519 520 2.639286 CTGTGGCCTTCAACGCAC 59.361 61.111 3.32 0.00 0.00 5.34
520 521 2.904866 TGTGGCCTTCAACGCACC 60.905 61.111 3.32 0.00 0.00 5.01
521 522 2.594592 GTGGCCTTCAACGCACCT 60.595 61.111 3.32 0.00 0.00 4.00
522 523 1.302192 GTGGCCTTCAACGCACCTA 60.302 57.895 3.32 0.00 0.00 3.08
523 524 1.003839 TGGCCTTCAACGCACCTAG 60.004 57.895 3.32 0.00 0.00 3.02
524 525 1.745489 GGCCTTCAACGCACCTAGG 60.745 63.158 7.41 7.41 0.00 3.02
525 526 2.399356 GCCTTCAACGCACCTAGGC 61.399 63.158 9.30 0.00 43.96 3.93
526 527 1.745489 CCTTCAACGCACCTAGGCC 60.745 63.158 9.30 0.00 0.00 5.19
527 528 2.047655 TTCAACGCACCTAGGCCG 60.048 61.111 17.93 17.93 0.00 6.13
528 529 3.599285 TTCAACGCACCTAGGCCGG 62.599 63.158 21.94 0.00 0.00 6.13
534 535 4.256180 CACCTAGGCCGGCCCATC 62.256 72.222 41.72 17.85 36.58 3.51
535 536 4.499116 ACCTAGGCCGGCCCATCT 62.499 66.667 41.72 25.97 36.58 2.90
536 537 3.171388 CCTAGGCCGGCCCATCTT 61.171 66.667 41.72 25.55 36.58 2.40
537 538 2.111878 CTAGGCCGGCCCATCTTG 59.888 66.667 41.72 20.36 36.58 3.02
538 539 4.189580 TAGGCCGGCCCATCTTGC 62.190 66.667 41.72 14.89 36.58 4.01
541 542 4.496336 GCCGGCCCATCTTGCTCT 62.496 66.667 18.11 0.00 0.00 4.09
542 543 2.515523 CCGGCCCATCTTGCTCTG 60.516 66.667 0.00 0.00 0.00 3.35
543 544 3.207669 CGGCCCATCTTGCTCTGC 61.208 66.667 0.00 0.00 0.00 4.26
544 545 2.832201 GGCCCATCTTGCTCTGCC 60.832 66.667 0.00 0.00 0.00 4.85
545 546 2.832201 GCCCATCTTGCTCTGCCC 60.832 66.667 0.00 0.00 0.00 5.36
546 547 3.004951 CCCATCTTGCTCTGCCCT 58.995 61.111 0.00 0.00 0.00 5.19
547 548 1.305623 CCCATCTTGCTCTGCCCTT 59.694 57.895 0.00 0.00 0.00 3.95
548 549 1.035932 CCCATCTTGCTCTGCCCTTG 61.036 60.000 0.00 0.00 0.00 3.61
549 550 1.664321 CCATCTTGCTCTGCCCTTGC 61.664 60.000 0.00 0.00 38.26 4.01
550 551 1.379576 ATCTTGCTCTGCCCTTGCC 60.380 57.895 0.00 0.00 36.33 4.52
551 552 3.437795 CTTGCTCTGCCCTTGCCG 61.438 66.667 0.00 0.00 36.33 5.69
567 568 3.823330 CGCGAGGCTTCCCTACGT 61.823 66.667 0.00 0.00 43.12 3.57
568 569 2.104530 GCGAGGCTTCCCTACGTC 59.895 66.667 0.00 0.00 43.12 4.34
569 570 2.416432 GCGAGGCTTCCCTACGTCT 61.416 63.158 0.00 0.00 43.12 4.18
570 571 1.728672 CGAGGCTTCCCTACGTCTC 59.271 63.158 0.00 0.00 43.12 3.36
571 572 1.728672 GAGGCTTCCCTACGTCTCG 59.271 63.158 0.00 0.00 43.12 4.04
572 573 2.104530 GGCTTCCCTACGTCTCGC 59.895 66.667 0.00 0.00 0.00 5.03
573 574 2.416432 GGCTTCCCTACGTCTCGCT 61.416 63.158 0.00 0.00 0.00 4.93
574 575 1.226717 GCTTCCCTACGTCTCGCTG 60.227 63.158 0.00 0.00 0.00 5.18
575 576 1.935327 GCTTCCCTACGTCTCGCTGT 61.935 60.000 0.00 0.00 0.00 4.40
576 577 0.179161 CTTCCCTACGTCTCGCTGTG 60.179 60.000 0.00 0.00 0.00 3.66
577 578 0.607217 TTCCCTACGTCTCGCTGTGA 60.607 55.000 0.00 0.00 0.00 3.58
578 579 1.025113 TCCCTACGTCTCGCTGTGAG 61.025 60.000 11.93 11.93 46.72 3.51
579 580 1.226435 CCTACGTCTCGCTGTGAGC 60.226 63.158 13.25 7.77 44.86 4.26
589 590 2.571528 GCTGTGAGCGAGACATACG 58.428 57.895 0.00 0.00 0.00 3.06
590 591 0.867753 GCTGTGAGCGAGACATACGG 60.868 60.000 0.00 0.00 0.00 4.02
591 592 0.248661 CTGTGAGCGAGACATACGGG 60.249 60.000 0.00 0.00 0.00 5.28
592 593 1.589196 GTGAGCGAGACATACGGGC 60.589 63.158 0.00 0.00 0.00 6.13
593 594 2.353607 GAGCGAGACATACGGGCG 60.354 66.667 0.00 0.00 0.00 6.13
594 595 3.122250 GAGCGAGACATACGGGCGT 62.122 63.158 0.00 0.00 0.00 5.68
595 596 2.654404 GCGAGACATACGGGCGTC 60.654 66.667 0.00 0.00 0.00 5.19
596 597 2.025727 CGAGACATACGGGCGTCC 59.974 66.667 0.00 0.00 32.33 4.79
616 617 3.155167 GGCGGAACCGGATCCTCT 61.155 66.667 26.42 0.00 40.19 3.69
617 618 2.732619 GGCGGAACCGGATCCTCTT 61.733 63.158 26.42 0.18 40.19 2.85
618 619 1.221021 GCGGAACCGGATCCTCTTT 59.779 57.895 26.42 0.00 40.19 2.52
619 620 0.462789 GCGGAACCGGATCCTCTTTA 59.537 55.000 26.42 0.00 40.19 1.85
620 621 1.070289 GCGGAACCGGATCCTCTTTAT 59.930 52.381 26.42 0.00 40.19 1.40
621 622 2.298163 GCGGAACCGGATCCTCTTTATA 59.702 50.000 26.42 0.00 40.19 0.98
622 623 3.614390 GCGGAACCGGATCCTCTTTATAG 60.614 52.174 26.42 10.83 40.19 1.31
623 624 3.614390 CGGAACCGGATCCTCTTTATAGC 60.614 52.174 26.42 0.00 37.34 2.97
624 625 3.323979 GGAACCGGATCCTCTTTATAGCA 59.676 47.826 22.87 0.00 36.50 3.49
625 626 4.561105 GAACCGGATCCTCTTTATAGCAG 58.439 47.826 9.46 0.00 0.00 4.24
626 627 2.900546 ACCGGATCCTCTTTATAGCAGG 59.099 50.000 9.46 1.11 0.00 4.85
627 628 2.900546 CCGGATCCTCTTTATAGCAGGT 59.099 50.000 10.75 0.00 0.00 4.00
628 629 4.087182 CCGGATCCTCTTTATAGCAGGTA 58.913 47.826 10.75 0.00 0.00 3.08
629 630 4.158764 CCGGATCCTCTTTATAGCAGGTAG 59.841 50.000 10.75 0.00 0.00 3.18
630 631 4.381079 CGGATCCTCTTTATAGCAGGTAGC 60.381 50.000 10.75 0.00 46.19 3.58
642 643 2.979240 GCAGGTAGCTAGATAATGGGC 58.021 52.381 0.00 0.00 41.15 5.36
643 644 2.569404 GCAGGTAGCTAGATAATGGGCT 59.431 50.000 0.00 0.00 41.15 5.19
644 645 3.618507 GCAGGTAGCTAGATAATGGGCTG 60.619 52.174 0.00 0.00 41.15 4.85
645 646 3.055530 CAGGTAGCTAGATAATGGGCTGG 60.056 52.174 0.00 0.00 36.40 4.85
646 647 2.355209 GGTAGCTAGATAATGGGCTGGC 60.355 54.545 0.00 0.00 38.70 4.85
647 648 0.695347 AGCTAGATAATGGGCTGGCC 59.305 55.000 14.23 14.23 39.15 5.36
660 661 2.449518 TGGCCCAACCCAGACTCA 60.450 61.111 0.00 0.00 37.83 3.41
661 662 2.352805 GGCCCAACCCAGACTCAG 59.647 66.667 0.00 0.00 0.00 3.35
662 663 2.360475 GCCCAACCCAGACTCAGC 60.360 66.667 0.00 0.00 0.00 4.26
663 664 2.900106 GCCCAACCCAGACTCAGCT 61.900 63.158 0.00 0.00 0.00 4.24
664 665 1.298014 CCCAACCCAGACTCAGCTC 59.702 63.158 0.00 0.00 0.00 4.09
665 666 1.079543 CCAACCCAGACTCAGCTCG 60.080 63.158 0.00 0.00 0.00 5.03
666 667 1.536073 CCAACCCAGACTCAGCTCGA 61.536 60.000 0.00 0.00 0.00 4.04
667 668 0.534412 CAACCCAGACTCAGCTCGAT 59.466 55.000 0.00 0.00 0.00 3.59
668 669 0.820871 AACCCAGACTCAGCTCGATC 59.179 55.000 0.00 0.00 0.00 3.69
669 670 1.358402 CCCAGACTCAGCTCGATCG 59.642 63.158 9.36 9.36 0.00 3.69
670 671 1.358402 CCAGACTCAGCTCGATCGG 59.642 63.158 16.41 7.26 0.00 4.18
671 672 1.358402 CAGACTCAGCTCGATCGGG 59.642 63.158 16.41 14.14 0.00 5.14
672 673 2.026879 GACTCAGCTCGATCGGGC 59.973 66.667 32.41 32.41 43.08 6.13
673 674 3.492311 GACTCAGCTCGATCGGGCC 62.492 68.421 35.16 16.72 43.99 5.80
674 675 3.531207 CTCAGCTCGATCGGGCCA 61.531 66.667 35.16 21.57 43.99 5.36
675 676 2.839632 TCAGCTCGATCGGGCCAT 60.840 61.111 35.16 16.61 43.99 4.40
676 677 2.356793 CAGCTCGATCGGGCCATC 60.357 66.667 35.16 9.43 43.99 3.51
677 678 2.839632 AGCTCGATCGGGCCATCA 60.840 61.111 35.16 3.00 43.99 3.07
678 679 2.663188 GCTCGATCGGGCCATCAC 60.663 66.667 29.70 0.00 35.11 3.06
679 680 3.133014 CTCGATCGGGCCATCACT 58.867 61.111 16.41 0.00 0.00 3.41
680 681 1.806461 GCTCGATCGGGCCATCACTA 61.806 60.000 29.70 0.00 35.11 2.74
681 682 0.673985 CTCGATCGGGCCATCACTAA 59.326 55.000 16.41 0.00 0.00 2.24
682 683 0.673985 TCGATCGGGCCATCACTAAG 59.326 55.000 16.41 0.00 0.00 2.18
683 684 0.319900 CGATCGGGCCATCACTAAGG 60.320 60.000 7.38 0.00 0.00 2.69
714 715 4.058797 AAAAACCTGAGCCGTCCG 57.941 55.556 0.00 0.00 0.00 4.79
715 716 1.599797 AAAAACCTGAGCCGTCCGG 60.600 57.895 0.24 0.24 38.57 5.14
725 726 4.371975 CCGTCCGGCTCAAAAGAA 57.628 55.556 0.00 0.00 0.00 2.52
726 727 2.624169 CCGTCCGGCTCAAAAGAAA 58.376 52.632 0.00 0.00 0.00 2.52
727 728 0.948678 CCGTCCGGCTCAAAAGAAAA 59.051 50.000 0.00 0.00 0.00 2.29
782 783 1.664956 AAACTCCCAACCCAAGGCCT 61.665 55.000 0.00 0.00 0.00 5.19
801 802 1.966451 CAGACAAACCGAGCCCACC 60.966 63.158 0.00 0.00 0.00 4.61
911 922 3.195002 CGCACCGCACCGAATCAT 61.195 61.111 0.00 0.00 0.00 2.45
912 923 2.709475 GCACCGCACCGAATCATC 59.291 61.111 0.00 0.00 0.00 2.92
913 924 2.823829 GCACCGCACCGAATCATCC 61.824 63.158 0.00 0.00 0.00 3.51
914 925 2.180204 CACCGCACCGAATCATCCC 61.180 63.158 0.00 0.00 0.00 3.85
915 926 2.967076 CCGCACCGAATCATCCCG 60.967 66.667 0.00 0.00 0.00 5.14
916 927 2.106131 CGCACCGAATCATCCCGA 59.894 61.111 0.00 0.00 0.00 5.14
917 928 1.300931 CGCACCGAATCATCCCGAT 60.301 57.895 0.00 0.00 35.12 4.18
918 929 1.284982 CGCACCGAATCATCCCGATC 61.285 60.000 0.00 0.00 31.11 3.69
919 930 0.951040 GCACCGAATCATCCCGATCC 60.951 60.000 0.00 0.00 31.11 3.36
933 946 3.227792 GATCCCCCATCGTCTCCGC 62.228 68.421 0.00 0.00 0.00 5.54
1662 1791 1.899142 GCTCTCAAGGAGGTGAAGTCT 59.101 52.381 0.00 0.00 42.08 3.24
1722 1851 2.381911 GACAAGATGCCCATCAATGGT 58.618 47.619 10.58 3.23 46.65 3.55
1871 2000 1.543802 AGACGCTGAGAAGTTGGAGAG 59.456 52.381 0.00 0.00 0.00 3.20
2022 2151 3.326385 ATGCCGGTCACTCCCCCTA 62.326 63.158 1.90 0.00 0.00 3.53
2060 2189 1.999295 TGTTGGGGAGATTCCAATGGA 59.001 47.619 0.00 0.00 44.87 3.41
2061 2190 2.586838 TGTTGGGGAGATTCCAATGGAT 59.413 45.455 1.39 0.00 44.87 3.41
2292 2429 4.855388 GCAATTTGTCTGAGTAATGCTGTG 59.145 41.667 0.00 0.00 0.00 3.66
2308 2445 4.401022 TGCTGTGGTTTTCATTCAGAGAT 58.599 39.130 0.00 0.00 0.00 2.75
2364 2501 8.415950 AATATGTAATGGTTGAAACAGTTGGA 57.584 30.769 0.00 0.00 0.00 3.53
2488 2625 6.449698 ACAAGCCTTTGATCAACAATTACTG 58.550 36.000 7.89 3.00 38.36 2.74
2632 2769 4.284234 GCGGAGGGGGTACTAATTTATGTA 59.716 45.833 0.00 0.00 0.00 2.29
2706 2843 2.560981 TGCAACTTCCACTGTATCTCGA 59.439 45.455 0.00 0.00 0.00 4.04
2709 2846 4.142447 GCAACTTCCACTGTATCTCGACTA 60.142 45.833 0.00 0.00 0.00 2.59
2794 2931 9.237187 TGTTTGAATAAGGCTGTGATTTATACA 57.763 29.630 0.00 0.00 0.00 2.29
2806 2943 4.730042 GTGATTTATACACATGCGCAAGTG 59.270 41.667 36.20 36.20 41.40 3.16
2904 3041 3.967203 AATTTGCATTGCGCTTGTTTT 57.033 33.333 9.73 0.00 43.06 2.43
2951 3088 4.312231 GCGCGCAAAGACAGTGCA 62.312 61.111 29.10 0.00 42.33 4.57
3032 3169 3.767278 GCTCTTTGCATGCTTCTTTAGG 58.233 45.455 20.33 3.01 42.31 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.899648 TTCCTACTATGTTTCCCAACAAAAA 57.100 32.000 0.00 0.00 46.17 1.94
9 10 7.899648 TTTCCTACTATGTTTCCCAACAAAA 57.100 32.000 0.00 0.00 46.17 2.44
10 11 7.899648 TTTTCCTACTATGTTTCCCAACAAA 57.100 32.000 0.00 0.00 46.17 2.83
11 12 7.899648 TTTTTCCTACTATGTTTCCCAACAA 57.100 32.000 0.00 0.00 46.17 2.83
34 35 9.713684 TCCTTGGAATTTATTCATAGGATGTTT 57.286 29.630 15.29 0.00 40.18 2.83
35 36 9.887862 ATCCTTGGAATTTATTCATAGGATGTT 57.112 29.630 23.08 10.82 46.00 2.71
36 37 9.525826 GATCCTTGGAATTTATTCATAGGATGT 57.474 33.333 25.95 14.44 46.76 3.06
37 38 9.524496 TGATCCTTGGAATTTATTCATAGGATG 57.476 33.333 25.95 6.78 46.76 3.51
42 43 9.791801 TCGAATGATCCTTGGAATTTATTCATA 57.208 29.630 4.97 0.00 38.53 2.15
43 44 8.696043 TCGAATGATCCTTGGAATTTATTCAT 57.304 30.769 4.97 0.00 38.53 2.57
44 45 8.518430 TTCGAATGATCCTTGGAATTTATTCA 57.482 30.769 4.47 0.00 38.53 2.57
45 46 9.971922 ATTTCGAATGATCCTTGGAATTTATTC 57.028 29.630 8.54 2.02 36.08 1.75
48 49 9.402320 TGTATTTCGAATGATCCTTGGAATTTA 57.598 29.630 8.54 3.19 0.00 1.40
49 50 8.292444 TGTATTTCGAATGATCCTTGGAATTT 57.708 30.769 8.54 3.92 0.00 1.82
50 51 7.880160 TGTATTTCGAATGATCCTTGGAATT 57.120 32.000 8.54 8.01 0.00 2.17
51 52 7.880160 TTGTATTTCGAATGATCCTTGGAAT 57.120 32.000 8.54 1.28 0.00 3.01
52 53 7.695480 TTTGTATTTCGAATGATCCTTGGAA 57.305 32.000 0.00 4.47 0.00 3.53
53 54 7.695480 TTTTGTATTTCGAATGATCCTTGGA 57.305 32.000 0.00 0.00 0.00 3.53
54 55 8.931385 AATTTTGTATTTCGAATGATCCTTGG 57.069 30.769 0.00 0.00 0.00 3.61
92 93 9.562408 TGTATAGACAAAAATGTTGACCTTGTA 57.438 29.630 0.00 0.00 30.62 2.41
93 94 8.458573 TGTATAGACAAAAATGTTGACCTTGT 57.541 30.769 0.00 0.00 33.07 3.16
133 134 9.968870 ATTTGCAAAAATGTAAATCAAGCATTT 57.031 22.222 17.19 0.00 42.46 2.32
134 135 9.400638 CATTTGCAAAAATGTAAATCAAGCATT 57.599 25.926 17.19 0.00 35.88 3.56
135 136 7.539366 GCATTTGCAAAAATGTAAATCAAGCAT 59.461 29.630 17.19 0.00 41.09 3.79
136 137 6.856938 GCATTTGCAAAAATGTAAATCAAGCA 59.143 30.769 17.19 0.00 41.09 3.91
137 138 7.255770 GCATTTGCAAAAATGTAAATCAAGC 57.744 32.000 17.19 0.00 41.09 4.01
159 160 9.734620 GTGTATTCAAAATATGCTAATCTTGCA 57.265 29.630 0.00 0.00 44.95 4.08
160 161 8.895845 CGTGTATTCAAAATATGCTAATCTTGC 58.104 33.333 0.00 0.00 0.00 4.01
161 162 9.385902 CCGTGTATTCAAAATATGCTAATCTTG 57.614 33.333 0.00 0.00 0.00 3.02
162 163 9.120538 ACCGTGTATTCAAAATATGCTAATCTT 57.879 29.630 0.00 0.00 0.00 2.40
163 164 8.559536 CACCGTGTATTCAAAATATGCTAATCT 58.440 33.333 0.00 0.00 0.00 2.40
164 165 8.556194 TCACCGTGTATTCAAAATATGCTAATC 58.444 33.333 0.00 0.00 0.00 1.75
165 166 8.445275 TCACCGTGTATTCAAAATATGCTAAT 57.555 30.769 0.00 0.00 0.00 1.73
166 167 7.851387 TCACCGTGTATTCAAAATATGCTAA 57.149 32.000 0.00 0.00 0.00 3.09
167 168 7.851387 TTCACCGTGTATTCAAAATATGCTA 57.149 32.000 0.00 0.00 0.00 3.49
168 169 6.751514 TTCACCGTGTATTCAAAATATGCT 57.248 33.333 0.00 0.00 0.00 3.79
169 170 8.342634 AGTATTCACCGTGTATTCAAAATATGC 58.657 33.333 0.00 0.00 0.00 3.14
173 174 9.974980 AAAAAGTATTCACCGTGTATTCAAAAT 57.025 25.926 0.00 0.00 0.00 1.82
174 175 9.453325 GAAAAAGTATTCACCGTGTATTCAAAA 57.547 29.630 0.00 0.00 0.00 2.44
175 176 8.842280 AGAAAAAGTATTCACCGTGTATTCAAA 58.158 29.630 0.00 0.00 0.00 2.69
176 177 8.385898 AGAAAAAGTATTCACCGTGTATTCAA 57.614 30.769 0.00 0.00 0.00 2.69
177 178 7.972832 AGAAAAAGTATTCACCGTGTATTCA 57.027 32.000 0.00 0.00 0.00 2.57
181 182 9.357652 GTGTATAGAAAAAGTATTCACCGTGTA 57.642 33.333 0.00 0.00 0.00 2.90
182 183 7.874016 TGTGTATAGAAAAAGTATTCACCGTGT 59.126 33.333 0.00 0.00 30.89 4.49
183 184 8.246908 TGTGTATAGAAAAAGTATTCACCGTG 57.753 34.615 0.00 0.00 30.89 4.94
184 185 9.444600 AATGTGTATAGAAAAAGTATTCACCGT 57.555 29.630 0.00 0.00 30.89 4.83
185 186 9.916397 GAATGTGTATAGAAAAAGTATTCACCG 57.084 33.333 0.00 0.00 30.89 4.94
196 197 9.430623 TGAGAAACGATGAATGTGTATAGAAAA 57.569 29.630 0.00 0.00 0.00 2.29
197 198 8.996024 TGAGAAACGATGAATGTGTATAGAAA 57.004 30.769 0.00 0.00 0.00 2.52
198 199 8.996024 TTGAGAAACGATGAATGTGTATAGAA 57.004 30.769 0.00 0.00 0.00 2.10
199 200 8.996024 TTTGAGAAACGATGAATGTGTATAGA 57.004 30.769 0.00 0.00 0.00 1.98
200 201 9.642312 CATTTGAGAAACGATGAATGTGTATAG 57.358 33.333 0.00 0.00 0.00 1.31
201 202 8.122330 GCATTTGAGAAACGATGAATGTGTATA 58.878 33.333 0.00 0.00 0.00 1.47
202 203 6.968904 GCATTTGAGAAACGATGAATGTGTAT 59.031 34.615 0.00 0.00 0.00 2.29
203 204 6.149308 AGCATTTGAGAAACGATGAATGTGTA 59.851 34.615 0.00 0.00 0.00 2.90
204 205 5.048504 AGCATTTGAGAAACGATGAATGTGT 60.049 36.000 0.00 0.00 0.00 3.72
205 206 5.396484 AGCATTTGAGAAACGATGAATGTG 58.604 37.500 0.00 0.00 0.00 3.21
206 207 5.633830 AGCATTTGAGAAACGATGAATGT 57.366 34.783 0.00 0.00 0.00 2.71
207 208 6.088173 TCAAGCATTTGAGAAACGATGAATG 58.912 36.000 0.00 0.00 38.37 2.67
208 209 6.258230 TCAAGCATTTGAGAAACGATGAAT 57.742 33.333 0.00 0.00 38.37 2.57
209 210 5.687770 TCAAGCATTTGAGAAACGATGAA 57.312 34.783 0.00 0.00 38.37 2.57
210 211 5.885230 ATCAAGCATTTGAGAAACGATGA 57.115 34.783 0.00 0.00 45.89 2.92
211 212 7.911727 TGATAATCAAGCATTTGAGAAACGATG 59.088 33.333 0.00 0.00 45.89 3.84
212 213 7.988737 TGATAATCAAGCATTTGAGAAACGAT 58.011 30.769 0.00 0.00 45.89 3.73
213 214 7.376435 TGATAATCAAGCATTTGAGAAACGA 57.624 32.000 0.00 0.00 45.89 3.85
214 215 8.624701 AATGATAATCAAGCATTTGAGAAACG 57.375 30.769 0.00 0.00 45.89 3.60
292 293 9.838975 GTGTGTGTGAAAATATTTGATCATGTA 57.161 29.630 0.39 0.00 0.00 2.29
293 294 8.579006 AGTGTGTGTGAAAATATTTGATCATGT 58.421 29.630 0.39 0.00 0.00 3.21
294 295 8.856247 CAGTGTGTGTGAAAATATTTGATCATG 58.144 33.333 0.39 0.00 0.00 3.07
295 296 8.579006 ACAGTGTGTGTGAAAATATTTGATCAT 58.421 29.630 0.39 0.00 38.28 2.45
296 297 7.939782 ACAGTGTGTGTGAAAATATTTGATCA 58.060 30.769 0.39 0.00 38.28 2.92
328 329 8.545420 GCGAAAATATTTCTCACCTATACGAAA 58.455 33.333 0.10 0.00 0.00 3.46
329 330 7.924412 AGCGAAAATATTTCTCACCTATACGAA 59.076 33.333 0.10 0.00 0.00 3.85
330 331 7.431249 AGCGAAAATATTTCTCACCTATACGA 58.569 34.615 0.10 0.00 0.00 3.43
331 332 7.639162 AGCGAAAATATTTCTCACCTATACG 57.361 36.000 0.10 0.00 0.00 3.06
484 485 5.934043 GCCACAGCCTCATTATTTTCTTTTT 59.066 36.000 0.00 0.00 0.00 1.94
485 486 5.482006 GCCACAGCCTCATTATTTTCTTTT 58.518 37.500 0.00 0.00 0.00 2.27
486 487 5.077134 GCCACAGCCTCATTATTTTCTTT 57.923 39.130 0.00 0.00 0.00 2.52
487 488 4.725790 GCCACAGCCTCATTATTTTCTT 57.274 40.909 0.00 0.00 0.00 2.52
501 502 3.286751 TGCGTTGAAGGCCACAGC 61.287 61.111 5.01 6.10 38.76 4.40
502 503 2.639286 GTGCGTTGAAGGCCACAG 59.361 61.111 5.01 0.00 0.00 3.66
503 504 2.046009 TAGGTGCGTTGAAGGCCACA 62.046 55.000 5.01 1.11 0.00 4.17
504 505 1.298859 CTAGGTGCGTTGAAGGCCAC 61.299 60.000 5.01 5.78 0.00 5.01
505 506 1.003839 CTAGGTGCGTTGAAGGCCA 60.004 57.895 5.01 0.00 0.00 5.36
506 507 1.745489 CCTAGGTGCGTTGAAGGCC 60.745 63.158 7.45 0.00 0.00 5.19
507 508 2.399356 GCCTAGGTGCGTTGAAGGC 61.399 63.158 11.31 2.45 45.37 4.35
508 509 1.745489 GGCCTAGGTGCGTTGAAGG 60.745 63.158 11.31 0.00 0.00 3.46
509 510 2.100631 CGGCCTAGGTGCGTTGAAG 61.101 63.158 11.31 0.00 0.00 3.02
510 511 2.047655 CGGCCTAGGTGCGTTGAA 60.048 61.111 11.31 0.00 0.00 2.69
511 512 4.077184 CCGGCCTAGGTGCGTTGA 62.077 66.667 11.31 0.00 0.00 3.18
517 518 4.256180 GATGGGCCGGCCTAGGTG 62.256 72.222 42.70 3.25 36.10 4.00
518 519 4.499116 AGATGGGCCGGCCTAGGT 62.499 66.667 42.70 25.58 36.10 3.08
519 520 3.171388 AAGATGGGCCGGCCTAGG 61.171 66.667 42.70 3.67 36.10 3.02
520 521 2.111878 CAAGATGGGCCGGCCTAG 59.888 66.667 42.70 22.98 36.10 3.02
521 522 4.189580 GCAAGATGGGCCGGCCTA 62.190 66.667 42.70 39.29 36.10 3.93
524 525 4.496336 AGAGCAAGATGGGCCGGC 62.496 66.667 21.18 21.18 0.00 6.13
525 526 2.515523 CAGAGCAAGATGGGCCGG 60.516 66.667 0.00 0.00 0.00 6.13
526 527 3.207669 GCAGAGCAAGATGGGCCG 61.208 66.667 0.00 0.00 0.00 6.13
527 528 2.832201 GGCAGAGCAAGATGGGCC 60.832 66.667 0.00 0.00 0.00 5.80
528 529 2.832201 GGGCAGAGCAAGATGGGC 60.832 66.667 0.00 0.00 0.00 5.36
529 530 1.035932 CAAGGGCAGAGCAAGATGGG 61.036 60.000 0.00 0.00 0.00 4.00
530 531 1.664321 GCAAGGGCAGAGCAAGATGG 61.664 60.000 0.00 0.00 40.72 3.51
531 532 1.664321 GGCAAGGGCAGAGCAAGATG 61.664 60.000 0.00 0.00 43.71 2.90
532 533 1.379576 GGCAAGGGCAGAGCAAGAT 60.380 57.895 0.00 0.00 43.71 2.40
533 534 2.034687 GGCAAGGGCAGAGCAAGA 59.965 61.111 0.00 0.00 43.71 3.02
534 535 3.437795 CGGCAAGGGCAGAGCAAG 61.438 66.667 0.00 0.00 43.71 4.01
549 550 4.570663 CGTAGGGAAGCCTCGCGG 62.571 72.222 6.13 0.00 39.45 6.46
550 551 3.753070 GACGTAGGGAAGCCTCGCG 62.753 68.421 0.00 0.00 39.45 5.87
551 552 2.104530 GACGTAGGGAAGCCTCGC 59.895 66.667 0.00 0.00 34.75 5.03
552 553 1.728672 GAGACGTAGGGAAGCCTCG 59.271 63.158 0.00 0.00 0.00 4.63
553 554 1.728672 CGAGACGTAGGGAAGCCTC 59.271 63.158 0.00 0.00 0.00 4.70
554 555 2.416432 GCGAGACGTAGGGAAGCCT 61.416 63.158 0.00 0.00 0.00 4.58
555 556 2.104530 GCGAGACGTAGGGAAGCC 59.895 66.667 0.00 0.00 0.00 4.35
556 557 1.226717 CAGCGAGACGTAGGGAAGC 60.227 63.158 0.00 0.00 0.00 3.86
557 558 0.179161 CACAGCGAGACGTAGGGAAG 60.179 60.000 0.00 0.00 0.00 3.46
558 559 0.607217 TCACAGCGAGACGTAGGGAA 60.607 55.000 0.00 0.00 0.00 3.97
559 560 1.002990 TCACAGCGAGACGTAGGGA 60.003 57.895 0.00 0.00 0.00 4.20
560 561 1.429825 CTCACAGCGAGACGTAGGG 59.570 63.158 0.00 0.00 45.45 3.53
561 562 1.226435 GCTCACAGCGAGACGTAGG 60.226 63.158 0.00 0.00 45.45 3.18
562 563 4.368756 GCTCACAGCGAGACGTAG 57.631 61.111 0.00 0.00 45.45 3.51
571 572 0.867753 CCGTATGTCTCGCTCACAGC 60.868 60.000 0.00 0.00 38.02 4.40
572 573 0.248661 CCCGTATGTCTCGCTCACAG 60.249 60.000 0.00 0.00 0.00 3.66
573 574 1.807226 CCCGTATGTCTCGCTCACA 59.193 57.895 0.00 0.00 0.00 3.58
574 575 1.589196 GCCCGTATGTCTCGCTCAC 60.589 63.158 0.00 0.00 0.00 3.51
575 576 2.805546 GCCCGTATGTCTCGCTCA 59.194 61.111 0.00 0.00 0.00 4.26
576 577 2.353607 CGCCCGTATGTCTCGCTC 60.354 66.667 0.00 0.00 0.00 5.03
577 578 3.122250 GACGCCCGTATGTCTCGCT 62.122 63.158 0.00 0.00 32.37 4.93
578 579 2.654404 GACGCCCGTATGTCTCGC 60.654 66.667 0.00 0.00 32.37 5.03
579 580 2.025727 GGACGCCCGTATGTCTCG 59.974 66.667 0.00 0.00 35.45 4.04
599 600 2.253403 AAAGAGGATCCGGTTCCGCC 62.253 60.000 26.20 20.34 40.94 6.13
600 601 0.462789 TAAAGAGGATCCGGTTCCGC 59.537 55.000 23.52 23.52 40.94 5.54
601 602 3.614390 GCTATAAAGAGGATCCGGTTCCG 60.614 52.174 22.98 9.57 40.94 4.30
602 603 3.323979 TGCTATAAAGAGGATCCGGTTCC 59.676 47.826 22.05 22.05 33.66 3.62
603 604 4.561105 CTGCTATAAAGAGGATCCGGTTC 58.439 47.826 5.98 1.67 33.66 3.62
604 605 3.325135 CCTGCTATAAAGAGGATCCGGTT 59.675 47.826 5.98 4.51 33.66 4.44
605 606 2.900546 CCTGCTATAAAGAGGATCCGGT 59.099 50.000 5.98 0.00 33.66 5.28
606 607 2.900546 ACCTGCTATAAAGAGGATCCGG 59.099 50.000 5.98 0.00 33.66 5.14
607 608 4.381079 GCTACCTGCTATAAAGAGGATCCG 60.381 50.000 5.98 0.00 38.95 4.18
608 609 5.079689 GCTACCTGCTATAAAGAGGATCC 57.920 47.826 2.48 2.48 38.95 3.36
622 623 2.569404 AGCCCATTATCTAGCTACCTGC 59.431 50.000 0.00 0.00 43.29 4.85
623 624 3.055530 CCAGCCCATTATCTAGCTACCTG 60.056 52.174 0.00 0.00 33.33 4.00
624 625 3.177228 CCAGCCCATTATCTAGCTACCT 58.823 50.000 0.00 0.00 33.33 3.08
625 626 2.355209 GCCAGCCCATTATCTAGCTACC 60.355 54.545 0.00 0.00 33.33 3.18
626 627 2.355209 GGCCAGCCCATTATCTAGCTAC 60.355 54.545 0.00 0.00 33.33 3.58
627 628 1.909302 GGCCAGCCCATTATCTAGCTA 59.091 52.381 0.00 0.00 33.33 3.32
628 629 0.695347 GGCCAGCCCATTATCTAGCT 59.305 55.000 0.00 0.00 35.52 3.32
629 630 3.256281 GGCCAGCCCATTATCTAGC 57.744 57.895 0.00 0.00 0.00 3.42
641 642 3.927481 GAGTCTGGGTTGGGCCAGC 62.927 68.421 12.53 12.53 39.65 4.85
642 643 2.352805 GAGTCTGGGTTGGGCCAG 59.647 66.667 6.23 0.00 39.65 4.85
643 644 2.449518 TGAGTCTGGGTTGGGCCA 60.450 61.111 0.00 0.00 39.65 5.36
644 645 2.352805 CTGAGTCTGGGTTGGGCC 59.647 66.667 0.00 0.00 0.00 5.80
645 646 2.360475 GCTGAGTCTGGGTTGGGC 60.360 66.667 0.00 0.00 0.00 5.36
646 647 1.298014 GAGCTGAGTCTGGGTTGGG 59.702 63.158 0.00 0.00 0.00 4.12
647 648 1.079543 CGAGCTGAGTCTGGGTTGG 60.080 63.158 0.00 0.00 0.00 3.77
648 649 0.534412 ATCGAGCTGAGTCTGGGTTG 59.466 55.000 0.00 0.00 0.00 3.77
649 650 0.820871 GATCGAGCTGAGTCTGGGTT 59.179 55.000 0.00 0.00 0.00 4.11
650 651 1.380403 CGATCGAGCTGAGTCTGGGT 61.380 60.000 10.26 0.00 0.00 4.51
651 652 1.358402 CGATCGAGCTGAGTCTGGG 59.642 63.158 10.26 0.00 0.00 4.45
652 653 1.358402 CCGATCGAGCTGAGTCTGG 59.642 63.158 18.66 0.00 0.00 3.86
653 654 1.358402 CCCGATCGAGCTGAGTCTG 59.642 63.158 18.66 0.00 0.00 3.51
654 655 2.485795 GCCCGATCGAGCTGAGTCT 61.486 63.158 18.66 0.00 0.00 3.24
655 656 2.026879 GCCCGATCGAGCTGAGTC 59.973 66.667 18.66 0.00 0.00 3.36
656 657 3.532155 GGCCCGATCGAGCTGAGT 61.532 66.667 21.29 0.00 0.00 3.41
657 658 2.762006 GATGGCCCGATCGAGCTGAG 62.762 65.000 21.29 0.46 0.00 3.35
658 659 2.839632 ATGGCCCGATCGAGCTGA 60.840 61.111 21.29 8.83 0.00 4.26
659 660 2.356793 GATGGCCCGATCGAGCTG 60.357 66.667 21.29 5.63 0.00 4.24
660 661 2.839632 TGATGGCCCGATCGAGCT 60.840 61.111 21.29 1.84 0.00 4.09
661 662 1.806461 TAGTGATGGCCCGATCGAGC 61.806 60.000 18.66 16.18 0.00 5.03
662 663 0.673985 TTAGTGATGGCCCGATCGAG 59.326 55.000 18.66 3.84 0.00 4.04
663 664 0.673985 CTTAGTGATGGCCCGATCGA 59.326 55.000 18.66 0.00 0.00 3.59
664 665 0.319900 CCTTAGTGATGGCCCGATCG 60.320 60.000 8.51 8.51 0.00 3.69
665 666 0.603975 GCCTTAGTGATGGCCCGATC 60.604 60.000 0.00 0.00 43.11 3.69
666 667 1.451936 GCCTTAGTGATGGCCCGAT 59.548 57.895 0.00 0.00 43.11 4.18
667 668 2.908015 GCCTTAGTGATGGCCCGA 59.092 61.111 0.00 0.00 43.11 5.14
672 673 2.159099 TCGCTTACTGCCTTAGTGATGG 60.159 50.000 0.00 0.00 40.65 3.51
673 674 3.165058 TCGCTTACTGCCTTAGTGATG 57.835 47.619 0.00 0.00 40.65 3.07
674 675 3.887621 TTCGCTTACTGCCTTAGTGAT 57.112 42.857 0.00 0.00 40.65 3.06
675 676 3.671008 TTTCGCTTACTGCCTTAGTGA 57.329 42.857 0.00 0.00 40.65 3.41
676 677 4.742438 TTTTTCGCTTACTGCCTTAGTG 57.258 40.909 0.00 0.00 40.65 2.74
697 698 1.599797 CCGGACGGCTCAGGTTTTT 60.600 57.895 0.00 0.00 0.00 1.94
698 699 2.032071 CCGGACGGCTCAGGTTTT 59.968 61.111 0.00 0.00 0.00 2.43
708 709 0.948678 TTTTCTTTTGAGCCGGACGG 59.051 50.000 5.05 6.35 38.57 4.79
709 710 2.032924 ACTTTTTCTTTTGAGCCGGACG 59.967 45.455 5.05 0.00 0.00 4.79
710 711 3.066203 TGACTTTTTCTTTTGAGCCGGAC 59.934 43.478 5.05 0.00 0.00 4.79
711 712 3.283751 TGACTTTTTCTTTTGAGCCGGA 58.716 40.909 5.05 0.00 0.00 5.14
712 713 3.708563 TGACTTTTTCTTTTGAGCCGG 57.291 42.857 0.00 0.00 0.00 6.13
713 714 4.672409 AGTTGACTTTTTCTTTTGAGCCG 58.328 39.130 0.00 0.00 0.00 5.52
714 715 6.199154 GCTAAGTTGACTTTTTCTTTTGAGCC 59.801 38.462 1.20 0.00 37.40 4.70
715 716 6.199154 GGCTAAGTTGACTTTTTCTTTTGAGC 59.801 38.462 1.20 1.98 37.40 4.26
716 717 6.414987 CGGCTAAGTTGACTTTTTCTTTTGAG 59.585 38.462 1.20 0.00 37.40 3.02
717 718 6.262601 CGGCTAAGTTGACTTTTTCTTTTGA 58.737 36.000 1.20 0.00 37.40 2.69
718 719 5.458779 CCGGCTAAGTTGACTTTTTCTTTTG 59.541 40.000 1.20 0.00 37.40 2.44
719 720 5.588240 CCGGCTAAGTTGACTTTTTCTTTT 58.412 37.500 1.20 0.00 37.40 2.27
720 721 4.499188 GCCGGCTAAGTTGACTTTTTCTTT 60.499 41.667 22.15 0.00 37.40 2.52
721 722 3.004419 GCCGGCTAAGTTGACTTTTTCTT 59.996 43.478 22.15 0.00 37.40 2.52
722 723 2.552743 GCCGGCTAAGTTGACTTTTTCT 59.447 45.455 22.15 0.00 37.40 2.52
723 724 2.351447 GGCCGGCTAAGTTGACTTTTTC 60.351 50.000 28.56 0.00 37.40 2.29
724 725 1.611977 GGCCGGCTAAGTTGACTTTTT 59.388 47.619 28.56 0.00 37.40 1.94
725 726 1.244816 GGCCGGCTAAGTTGACTTTT 58.755 50.000 28.56 0.00 37.40 2.27
726 727 0.608308 GGGCCGGCTAAGTTGACTTT 60.608 55.000 28.56 0.00 37.40 2.66
727 728 1.002502 GGGCCGGCTAAGTTGACTT 60.003 57.895 28.56 1.60 39.85 3.01
782 783 1.070786 GTGGGCTCGGTTTGTCTGA 59.929 57.895 0.00 0.00 0.00 3.27
901 912 0.320771 GGGATCGGGATGATTCGGTG 60.321 60.000 0.00 0.00 37.47 4.94
905 916 0.995024 ATGGGGGATCGGGATGATTC 59.005 55.000 0.00 0.00 37.47 2.52
906 917 0.995024 GATGGGGGATCGGGATGATT 59.005 55.000 0.00 0.00 37.47 2.57
907 918 2.702093 GATGGGGGATCGGGATGAT 58.298 57.895 0.00 0.00 41.06 2.45
908 919 4.232905 GATGGGGGATCGGGATGA 57.767 61.111 0.00 0.00 0.00 2.92
1098 1227 1.513622 GAAGCTGAGGAGGTCGGAC 59.486 63.158 0.00 0.00 32.51 4.79
1626 1755 2.666190 GCCTTCACGCTCAGCACA 60.666 61.111 0.00 0.00 0.00 4.57
1662 1791 0.534203 GGCAGACCAAACACGAGGAA 60.534 55.000 0.00 0.00 35.26 3.36
1722 1851 0.033405 CTTCCACCTCCTCCTCGGTA 60.033 60.000 0.00 0.00 30.91 4.02
1871 2000 1.000771 GCCTCCCCTTTCTTCCCAC 60.001 63.158 0.00 0.00 0.00 4.61
2022 2151 5.594317 CCCAACATCGATTTAATTCCTTCCT 59.406 40.000 0.00 0.00 0.00 3.36
2060 2189 5.127194 TCGCTGAATCAGTACAAGAGGTTAT 59.873 40.000 12.29 0.00 33.43 1.89
2061 2190 4.461431 TCGCTGAATCAGTACAAGAGGTTA 59.539 41.667 12.29 0.00 33.43 2.85
2213 2350 7.195646 ACAGCCATTACATATTTCACAAATCG 58.804 34.615 0.00 0.00 32.38 3.34
2292 2429 9.674824 CATATTGCTTATCTCTGAATGAAAACC 57.325 33.333 0.00 0.00 0.00 3.27
2326 2463 8.931385 ACCATTACATATTTCACAAAGCATTC 57.069 30.769 0.00 0.00 0.00 2.67
2364 2501 3.118531 AGACTGGACCCAATGATAAGCT 58.881 45.455 0.00 0.00 0.00 3.74
2445 2582 5.649831 GCTTGTCCTGATGAGACCTAAAATT 59.350 40.000 0.00 0.00 33.09 1.82
2448 2585 3.055094 GGCTTGTCCTGATGAGACCTAAA 60.055 47.826 0.00 0.00 33.09 1.85
2632 2769 2.621486 GGAGTCCCCTTAGGCATGT 58.379 57.895 0.00 0.00 34.51 3.21
2706 2843 6.816640 ACAAGTTGTATGTACGATTGCATAGT 59.183 34.615 6.75 0.00 31.64 2.12
2709 2846 6.494893 AACAAGTTGTATGTACGATTGCAT 57.505 33.333 9.37 0.00 32.13 3.96
2794 2931 0.593128 GAAAGTCCACTTGCGCATGT 59.407 50.000 21.97 21.97 36.12 3.21
2806 2943 9.710900 AAACCATTTGATTTATCTTGAAAGTCC 57.289 29.630 0.00 0.00 0.00 3.85
2904 3041 5.048782 GTGCTTCATGGACAACTAAACATCA 60.049 40.000 0.00 0.00 36.96 3.07
2951 3088 1.303091 GCCGCCAAATGTTCTACCGT 61.303 55.000 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.