Multiple sequence alignment - TraesCS3D01G081100

Loading Multiple Alignment...

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 TraesCS3D01G081100 chr3D 100.000 4111 0 0 1 4111 40755868 40751758 0.000000e+00 7592.0
1 TraesCS3D01G081100 chr3D 71.599 588 114 36 1706 2265 23230456 23229894 1.210000e-20 111.0
2 TraesCS3D01G081100 chr3D 79.389 131 27 0 1449 1579 23730927 23730797 4.380000e-15 93.5
3 TraesCS3D01G081100 chr3D 88.158 76 9 0 2203 2278 501162931 501162856 1.570000e-14 91.6
4 TraesCS3D01G081100 chr3D 79.832 119 24 0 1437 1555 23857931 23858049 2.040000e-13 87.9
5 TraesCS3D01G081100 chr3B 92.749 2579 132 27 1045 3599 64314611 64317158 0.000000e+00 3675.0
6 TraesCS3D01G081100 chr3B 90.385 312 20 4 3798 4108 64317384 64317686 6.400000e-108 401.0
7 TraesCS3D01G081100 chr3B 76.967 699 70 43 1 647 64310318 64310977 8.580000e-82 315.0
8 TraesCS3D01G081100 chr3B 92.500 80 4 2 3657 3736 64317271 64317348 3.360000e-21 113.0
9 TraesCS3D01G081100 chr3B 71.218 542 116 28 1744 2265 42125807 42126328 2.610000e-17 100.0
10 TraesCS3D01G081100 chr3B 80.672 119 23 0 1437 1555 41800438 41800556 4.380000e-15 93.5
11 TraesCS3D01G081100 chr3B 80.000 125 25 0 1443 1567 42048068 42047944 4.380000e-15 93.5
12 TraesCS3D01G081100 chr3B 88.000 75 3 3 853 922 64311253 64311326 2.630000e-12 84.2
13 TraesCS3D01G081100 chr3A 92.084 2577 126 34 1063 3590 52457493 52460040 0.000000e+00 3557.0
14 TraesCS3D01G081100 chr3A 89.056 466 37 6 3657 4111 52460641 52461103 2.140000e-157 566.0
15 TraesCS3D01G081100 chr3A 92.035 113 4 2 853 965 52457244 52457351 1.980000e-33 154.0
16 TraesCS3D01G081100 chr3A 83.784 148 17 7 503 647 52456216 52456359 2.580000e-27 134.0
17 TraesCS3D01G081100 chr3A 79.839 124 25 0 1444 1567 32876385 32876262 1.570000e-14 91.6
18 TraesCS3D01G081100 chr3A 72.697 304 65 15 1744 2038 32876109 32875815 7.320000e-13 86.1
19 TraesCS3D01G081100 chr3A 80.292 137 7 8 731 864 52457082 52457201 7.320000e-13 86.1
20 TraesCS3D01G081100 chr6B 88.206 602 46 12 1841 2426 157534744 157535336 0.000000e+00 695.0
21 TraesCS3D01G081100 chr1B 88.462 182 18 2 2198 2379 168586365 168586543 2.490000e-52 217.0
22 TraesCS3D01G081100 chr4B 71.289 613 130 35 1698 2278 672129512 672128914 9.340000e-22 115.0
23 TraesCS3D01G081100 chrUn 70.903 598 137 26 1698 2269 100089955 100090541 5.620000e-19 106.0
24 TraesCS3D01G081100 chrUn 80.000 125 25 0 1443 1567 373565392 373565268 4.380000e-15 93.5
25 TraesCS3D01G081100 chr5A 92.647 68 5 0 2202 2269 658990156 658990223 9.400000e-17 99.0
26 TraesCS3D01G081100 chr5B 86.842 76 10 0 2203 2278 426559059 426558984 7.320000e-13 86.1
27 TraesCS3D01G081100 chr6D 91.667 60 2 2 2320 2379 19349237 19349293 3.410000e-11 80.5
28 TraesCS3D01G081100 chr7D 91.228 57 2 2 2323 2379 49493304 49493251 1.580000e-09 75.0
29 TraesCS3D01G081100 chr7D 89.091 55 3 2 2325 2379 49427280 49427229 9.540000e-07 65.8
30 TraesCS3D01G081100 chr5D 90.000 60 3 1 2320 2379 561620146 561620090 1.580000e-09 75.0
31 TraesCS3D01G081100 chr5D 81.443 97 10 8 1488 1579 528587519 528587612 5.700000e-09 73.1


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 TraesCS3D01G081100 chr3D 40751758 40755868 4110 True 7592.00 7592 100.0000 1 4111 1 chr3D.!!$R3 4110
1 TraesCS3D01G081100 chr3B 64310318 64317686 7368 False 917.64 3675 88.1202 1 4108 5 chr3B.!!$F3 4107
2 TraesCS3D01G081100 chr3A 52456216 52461103 4887 False 899.42 3557 87.4502 503 4111 5 chr3A.!!$F1 3608
3 TraesCS3D01G081100 chr6B 157534744 157535336 592 False 695.00 695 88.2060 1841 2426 1 chr6B.!!$F1 585

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
498 547 0.042188 CAAGTCCGTGCAACTTGTCG 60.042 55.000 17.82 3.68 45.46 4.35 F
1000 5010 0.178932 CCCGTCTCCATGGATCCCTA 60.179 60.000 16.63 0.00 0.00 3.53 F
1053 5101 0.529337 CATCTGCGCAACCTCTCGAT 60.529 55.000 13.05 5.82 0.00 3.59 F
1176 5227 1.226547 CAAGACGAGCTCGCTCTCC 60.227 63.158 34.83 18.37 44.43 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 5860 0.321996 AGAGGTTGAAGAAGCGGTCC 59.678 55.000 0.00 0.0 34.60 4.46 R
2923 7007 0.608640 AGGAAGACGGCGAAGTTGAT 59.391 50.000 16.62 0.0 0.00 2.57 R
3030 7114 0.817634 CACTTCACTTGTGGCCGGAA 60.818 55.000 5.05 0.0 0.00 4.30 R
3156 7249 2.113433 GGGCTGCTGCTCTGTCATG 61.113 63.158 15.64 0.0 36.57 3.07 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
92 93 2.270874 AATCCAAAGCTCCCGCCGAT 62.271 55.000 0.00 0.00 36.60 4.18
93 94 2.666596 ATCCAAAGCTCCCGCCGATC 62.667 60.000 0.00 0.00 36.60 3.69
146 148 0.846427 ACAGGGAGGGCATTCAAGGA 60.846 55.000 0.00 0.00 0.00 3.36
147 149 0.554792 CAGGGAGGGCATTCAAGGAT 59.445 55.000 0.00 0.00 0.00 3.24
148 150 0.554792 AGGGAGGGCATTCAAGGATG 59.445 55.000 0.00 0.00 0.00 3.51
149 151 0.552848 GGGAGGGCATTCAAGGATGA 59.447 55.000 0.00 0.00 0.00 2.92
171 173 1.485480 GGTAGGTTAAGGCTGTCCTCC 59.515 57.143 8.33 6.98 43.40 4.30
187 189 1.306141 TCCAACGATCTCCCCTGCT 60.306 57.895 0.00 0.00 0.00 4.24
192 194 0.616111 ACGATCTCCCCTGCTTCTGT 60.616 55.000 0.00 0.00 0.00 3.41
194 196 1.494960 GATCTCCCCTGCTTCTGTCT 58.505 55.000 0.00 0.00 0.00 3.41
195 197 1.138661 GATCTCCCCTGCTTCTGTCTG 59.861 57.143 0.00 0.00 0.00 3.51
197 199 1.834856 CTCCCCTGCTTCTGTCTGCA 61.835 60.000 0.00 0.00 37.63 4.41
198 200 1.203441 TCCCCTGCTTCTGTCTGCAT 61.203 55.000 0.00 0.00 38.59 3.96
200 202 1.093159 CCCTGCTTCTGTCTGCATTC 58.907 55.000 0.00 0.00 38.59 2.67
203 205 0.401356 TGCTTCTGTCTGCATTCCCA 59.599 50.000 0.00 0.00 33.94 4.37
204 206 1.005097 TGCTTCTGTCTGCATTCCCAT 59.995 47.619 0.00 0.00 33.94 4.00
205 207 2.097825 GCTTCTGTCTGCATTCCCATT 58.902 47.619 0.00 0.00 0.00 3.16
206 208 2.494870 GCTTCTGTCTGCATTCCCATTT 59.505 45.455 0.00 0.00 0.00 2.32
207 209 3.428589 GCTTCTGTCTGCATTCCCATTTC 60.429 47.826 0.00 0.00 0.00 2.17
210 212 4.410099 TCTGTCTGCATTCCCATTTCTTT 58.590 39.130 0.00 0.00 0.00 2.52
218 224 6.713276 TGCATTCCCATTTCTTTCATTCATT 58.287 32.000 0.00 0.00 0.00 2.57
219 225 6.596106 TGCATTCCCATTTCTTTCATTCATTG 59.404 34.615 0.00 0.00 0.00 2.82
222 228 9.042008 CATTCCCATTTCTTTCATTCATTGATC 57.958 33.333 0.00 0.00 33.34 2.92
255 265 5.458069 GGATTCAGTTGGATCCATCCCAATA 60.458 44.000 17.06 0.00 46.59 1.90
275 285 6.258727 CCAATAGGCAGTAACACATAACTGAG 59.741 42.308 6.65 0.00 44.79 3.35
276 286 4.891992 AGGCAGTAACACATAACTGAGT 57.108 40.909 6.65 0.00 44.79 3.41
277 287 5.228945 AGGCAGTAACACATAACTGAGTT 57.771 39.130 2.37 2.37 44.79 3.01
278 288 5.621193 AGGCAGTAACACATAACTGAGTTT 58.379 37.500 1.97 0.00 44.79 2.66
279 289 5.470098 AGGCAGTAACACATAACTGAGTTTG 59.530 40.000 1.97 4.67 44.79 2.93
280 290 5.238650 GGCAGTAACACATAACTGAGTTTGT 59.761 40.000 1.97 5.31 44.79 2.83
281 291 6.425721 GGCAGTAACACATAACTGAGTTTGTA 59.574 38.462 1.97 0.00 44.79 2.41
282 292 7.288672 GCAGTAACACATAACTGAGTTTGTAC 58.711 38.462 1.97 4.07 44.79 2.90
283 293 7.170998 GCAGTAACACATAACTGAGTTTGTACT 59.829 37.037 1.97 6.07 44.79 2.73
284 294 9.687210 CAGTAACACATAACTGAGTTTGTACTA 57.313 33.333 1.97 1.25 44.79 1.82
285 295 9.688592 AGTAACACATAACTGAGTTTGTACTAC 57.311 33.333 1.97 11.27 37.38 2.73
286 296 7.633361 AACACATAACTGAGTTTGTACTACG 57.367 36.000 1.97 0.00 33.11 3.51
287 297 6.742109 ACACATAACTGAGTTTGTACTACGT 58.258 36.000 1.97 0.00 33.84 3.57
291 301 5.424121 AACTGAGTTTGTACTACGTACGT 57.576 39.130 25.98 25.98 41.41 3.57
311 321 4.681025 ACGTTACGTACTGGTTGTGTAATG 59.319 41.667 9.22 0.00 38.73 1.90
313 323 3.756933 ACGTACTGGTTGTGTAATGGT 57.243 42.857 0.00 0.00 0.00 3.55
329 339 2.425143 TGGTAGTACCAGGGACTACG 57.575 55.000 29.08 0.00 44.79 3.51
330 340 1.064463 TGGTAGTACCAGGGACTACGG 60.064 57.143 29.08 0.00 44.79 4.02
331 341 1.685148 GTAGTACCAGGGACTACGGG 58.315 60.000 24.08 0.00 39.81 5.28
332 342 1.064389 GTAGTACCAGGGACTACGGGT 60.064 57.143 24.08 0.00 39.81 5.28
333 343 1.298953 AGTACCAGGGACTACGGGTA 58.701 55.000 0.72 0.00 36.02 3.69
334 344 1.393603 GTACCAGGGACTACGGGTAC 58.606 60.000 9.29 9.29 46.17 3.34
364 395 4.375272 CGATCCATTATCACTTCACTGCT 58.625 43.478 0.00 0.00 33.87 4.24
365 396 4.813161 CGATCCATTATCACTTCACTGCTT 59.187 41.667 0.00 0.00 33.87 3.91
366 397 5.277202 CGATCCATTATCACTTCACTGCTTG 60.277 44.000 0.00 0.00 33.87 4.01
367 398 3.691118 TCCATTATCACTTCACTGCTTGC 59.309 43.478 0.00 0.00 0.00 4.01
368 399 3.693085 CCATTATCACTTCACTGCTTGCT 59.307 43.478 0.00 0.00 0.00 3.91
369 400 4.438336 CCATTATCACTTCACTGCTTGCTG 60.438 45.833 0.00 0.00 0.00 4.41
370 401 1.531423 ATCACTTCACTGCTTGCTGG 58.469 50.000 4.64 0.00 0.00 4.85
371 402 1.168407 TCACTTCACTGCTTGCTGGC 61.168 55.000 4.64 0.00 0.00 4.85
372 403 1.900498 ACTTCACTGCTTGCTGGCC 60.900 57.895 0.00 0.00 0.00 5.36
373 404 2.974489 CTTCACTGCTTGCTGGCCG 61.974 63.158 0.00 0.00 0.00 6.13
384 415 2.900337 CTGGCCGGCCGGTTAATC 60.900 66.667 41.29 26.58 39.42 1.75
398 429 5.508489 GCCGGTTAATCAGCTATAGTGTACA 60.508 44.000 1.90 0.00 0.00 2.90
399 430 5.919141 CCGGTTAATCAGCTATAGTGTACAC 59.081 44.000 18.56 18.56 0.00 2.90
400 431 5.624081 CGGTTAATCAGCTATAGTGTACACG 59.376 44.000 19.93 7.27 36.20 4.49
401 432 6.501781 GGTTAATCAGCTATAGTGTACACGT 58.498 40.000 19.93 14.95 36.20 4.49
402 433 7.518848 CGGTTAATCAGCTATAGTGTACACGTA 60.519 40.741 19.93 15.26 36.20 3.57
405 436 4.516323 TCAGCTATAGTGTACACGTACCA 58.484 43.478 19.93 5.22 35.26 3.25
406 437 4.333649 TCAGCTATAGTGTACACGTACCAC 59.666 45.833 19.93 9.63 35.26 4.16
430 467 8.998989 CACGTACATACATGTGATTTTCATTTC 58.001 33.333 9.11 0.00 41.89 2.17
441 478 6.424509 TGTGATTTTCATTTCATTTCAGTGGC 59.575 34.615 0.00 0.00 0.00 5.01
445 482 2.749076 TCATTTCATTTCAGTGGCGGAG 59.251 45.455 0.00 0.00 0.00 4.63
460 506 1.091771 CGGAGGCATTAGCAGTGGTG 61.092 60.000 4.76 0.00 44.61 4.17
472 521 1.771565 CAGTGGTGCCATGGATCATT 58.228 50.000 18.40 3.75 0.00 2.57
480 529 3.130869 GTGCCATGGATCATTAACAAGCA 59.869 43.478 18.40 0.00 0.00 3.91
482 531 4.142116 TGCCATGGATCATTAACAAGCAAG 60.142 41.667 18.40 0.00 0.00 4.01
483 532 4.142093 GCCATGGATCATTAACAAGCAAGT 60.142 41.667 18.40 0.00 0.00 3.16
484 533 5.585390 CCATGGATCATTAACAAGCAAGTC 58.415 41.667 5.56 0.00 0.00 3.01
485 534 5.450965 CCATGGATCATTAACAAGCAAGTCC 60.451 44.000 5.56 0.00 0.00 3.85
486 535 3.689161 TGGATCATTAACAAGCAAGTCCG 59.311 43.478 0.00 0.00 0.00 4.79
487 536 3.689649 GGATCATTAACAAGCAAGTCCGT 59.310 43.478 0.00 0.00 0.00 4.69
488 537 4.437390 GGATCATTAACAAGCAAGTCCGTG 60.437 45.833 0.00 0.00 0.00 4.94
489 538 2.225491 TCATTAACAAGCAAGTCCGTGC 59.775 45.455 0.00 0.00 45.28 5.34
497 546 3.825812 CAAGTCCGTGCAACTTGTC 57.174 52.632 17.82 0.00 45.46 3.18
498 547 0.042188 CAAGTCCGTGCAACTTGTCG 60.042 55.000 17.82 3.68 45.46 4.35
500 549 0.874607 AGTCCGTGCAACTTGTCGTC 60.875 55.000 0.00 0.00 31.75 4.20
501 550 1.142097 TCCGTGCAACTTGTCGTCA 59.858 52.632 0.00 0.00 31.75 4.35
521 575 0.678684 TGTCGATCGTGGTGAGGCTA 60.679 55.000 15.94 0.00 0.00 3.93
529 583 1.401670 CGTGGTGAGGCTAGATATCGC 60.402 57.143 0.00 0.00 0.00 4.58
536 590 5.336849 GGTGAGGCTAGATATCGCTGTTTAT 60.337 44.000 0.00 0.00 0.00 1.40
537 591 6.127703 GGTGAGGCTAGATATCGCTGTTTATA 60.128 42.308 0.00 0.00 0.00 0.98
543 600 9.834628 GGCTAGATATCGCTGTTTATATAGATC 57.165 37.037 0.00 0.00 0.00 2.75
566 623 0.534873 GTGGCCAGGTGTTGTTGTTT 59.465 50.000 5.11 0.00 0.00 2.83
571 628 2.028130 CCAGGTGTTGTTGTTTGCCTA 58.972 47.619 0.00 0.00 0.00 3.93
573 631 2.034558 CAGGTGTTGTTGTTTGCCTAGG 59.965 50.000 3.67 3.67 0.00 3.02
582 640 1.003839 TTTGCCTAGGCGTGGTGAG 60.004 57.895 28.28 0.00 45.51 3.51
583 641 1.764571 TTTGCCTAGGCGTGGTGAGT 61.765 55.000 28.28 0.00 45.51 3.41
584 642 2.125512 GCCTAGGCGTGGTGAGTG 60.126 66.667 20.16 0.00 0.00 3.51
585 643 2.125512 CCTAGGCGTGGTGAGTGC 60.126 66.667 0.00 0.00 0.00 4.40
586 644 2.507102 CTAGGCGTGGTGAGTGCG 60.507 66.667 0.00 0.00 0.00 5.34
634 698 5.334957 GCGTGCATGCTAGTAATCTACTCTA 60.335 44.000 23.72 0.00 40.14 2.43
647 711 2.438392 TCTACTCTATCAGCTCGGTCCA 59.562 50.000 0.00 0.00 0.00 4.02
649 713 0.958091 CTCTATCAGCTCGGTCCAGG 59.042 60.000 0.00 0.00 0.00 4.45
650 714 1.109920 TCTATCAGCTCGGTCCAGGC 61.110 60.000 0.00 0.00 0.00 4.85
652 716 2.589610 TATCAGCTCGGTCCAGGCCT 62.590 60.000 0.00 0.00 0.00 5.19
653 717 4.463879 CAGCTCGGTCCAGGCCTG 62.464 72.222 26.87 26.87 0.00 4.85
656 720 4.767255 CTCGGTCCAGGCCTGCAC 62.767 72.222 28.39 23.92 0.00 4.57
658 722 4.767255 CGGTCCAGGCCTGCACTC 62.767 72.222 25.90 14.94 0.00 3.51
659 723 4.416738 GGTCCAGGCCTGCACTCC 62.417 72.222 25.90 19.38 0.00 3.85
660 724 3.325753 GTCCAGGCCTGCACTCCT 61.326 66.667 28.39 0.00 0.00 3.69
661 725 3.005539 TCCAGGCCTGCACTCCTC 61.006 66.667 28.39 0.00 0.00 3.71
662 726 3.007920 CCAGGCCTGCACTCCTCT 61.008 66.667 28.39 0.00 0.00 3.69
663 727 2.268280 CAGGCCTGCACTCCTCTG 59.732 66.667 22.33 0.00 0.00 3.35
664 728 3.715097 AGGCCTGCACTCCTCTGC 61.715 66.667 3.11 0.00 37.70 4.26
665 729 4.792804 GGCCTGCACTCCTCTGCC 62.793 72.222 0.00 0.00 36.21 4.85
687 751 2.142761 TGCACCACTGCCTCTGTCT 61.143 57.895 0.00 0.00 43.51 3.41
688 752 0.831711 TGCACCACTGCCTCTGTCTA 60.832 55.000 0.00 0.00 43.51 2.59
693 757 1.169577 CACTGCCTCTGTCTACGAGT 58.830 55.000 0.00 0.00 0.00 4.18
707 771 5.404366 TGTCTACGAGTGTGTTTCATTTAGC 59.596 40.000 0.00 0.00 0.00 3.09
708 772 3.788434 ACGAGTGTGTTTCATTTAGCG 57.212 42.857 0.00 0.00 0.00 4.26
709 773 3.386486 ACGAGTGTGTTTCATTTAGCGA 58.614 40.909 0.00 0.00 0.00 4.93
710 774 3.183775 ACGAGTGTGTTTCATTTAGCGAC 59.816 43.478 0.00 0.00 0.00 5.19
711 775 3.423123 CGAGTGTGTTTCATTTAGCGACC 60.423 47.826 0.00 0.00 0.00 4.79
728 1448 2.046988 CACGGCCTCATGTGAGCA 60.047 61.111 0.00 0.00 40.75 4.26
762 1497 3.104519 TCATTCATTTCATGGGCTGGT 57.895 42.857 0.00 0.00 0.00 4.00
780 1515 1.477553 GTTCATGGCCATGGTGTGAT 58.522 50.000 38.81 5.54 39.24 3.06
783 1518 1.285667 TCATGGCCATGGTGTGATTCT 59.714 47.619 38.81 3.28 39.24 2.40
803 1545 5.462530 TCTAGTTTAGTTACTGCACAGCA 57.537 39.130 0.00 0.00 36.92 4.41
804 1546 5.227908 TCTAGTTTAGTTACTGCACAGCAC 58.772 41.667 0.00 0.00 33.79 4.40
805 1547 3.804036 AGTTTAGTTACTGCACAGCACA 58.196 40.909 0.00 0.00 33.79 4.57
806 1548 3.809832 AGTTTAGTTACTGCACAGCACAG 59.190 43.478 0.00 0.00 41.08 3.66
807 1549 1.795768 TAGTTACTGCACAGCACAGC 58.204 50.000 0.00 0.00 38.79 4.40
808 1550 0.179048 AGTTACTGCACAGCACAGCA 60.179 50.000 0.00 0.00 38.79 4.41
816 1558 1.376942 ACAGCACAGCAGCTCCATC 60.377 57.895 0.00 0.00 44.54 3.51
822 1564 0.469070 ACAGCAGCTCCATCTCCATC 59.531 55.000 0.00 0.00 0.00 3.51
823 1565 0.759959 CAGCAGCTCCATCTCCATCT 59.240 55.000 0.00 0.00 0.00 2.90
824 1566 1.050204 AGCAGCTCCATCTCCATCTC 58.950 55.000 0.00 0.00 0.00 2.75
826 1568 1.421480 CAGCTCCATCTCCATCTCCA 58.579 55.000 0.00 0.00 0.00 3.86
827 1569 1.979308 CAGCTCCATCTCCATCTCCAT 59.021 52.381 0.00 0.00 0.00 3.41
828 1570 1.979308 AGCTCCATCTCCATCTCCATG 59.021 52.381 0.00 0.00 0.00 3.66
829 1571 1.698532 GCTCCATCTCCATCTCCATGT 59.301 52.381 0.00 0.00 0.00 3.21
830 1572 2.289569 GCTCCATCTCCATCTCCATGTC 60.290 54.545 0.00 0.00 0.00 3.06
831 1573 3.241156 CTCCATCTCCATCTCCATGTCT 58.759 50.000 0.00 0.00 0.00 3.41
832 1574 4.414677 CTCCATCTCCATCTCCATGTCTA 58.585 47.826 0.00 0.00 0.00 2.59
833 1575 5.020941 TCCATCTCCATCTCCATGTCTAT 57.979 43.478 0.00 0.00 0.00 1.98
834 1576 4.776308 TCCATCTCCATCTCCATGTCTATG 59.224 45.833 0.00 0.00 0.00 2.23
869 1666 2.940410 TCGTTCCACTTCCAACTTCAAC 59.060 45.455 0.00 0.00 0.00 3.18
976 4986 1.352352 CCATCCTCCGCCATAAATCCT 59.648 52.381 0.00 0.00 0.00 3.24
977 4987 2.224867 CCATCCTCCGCCATAAATCCTT 60.225 50.000 0.00 0.00 0.00 3.36
995 5005 0.982852 TTGCTCCCGTCTCCATGGAT 60.983 55.000 16.63 0.00 0.00 3.41
997 5007 2.053618 CTCCCGTCTCCATGGATCC 58.946 63.158 16.63 4.20 0.00 3.36
1000 5010 0.178932 CCCGTCTCCATGGATCCCTA 60.179 60.000 16.63 0.00 0.00 3.53
1002 5012 1.203063 CCGTCTCCATGGATCCCTAGA 60.203 57.143 16.63 4.82 0.00 2.43
1003 5013 2.598565 CGTCTCCATGGATCCCTAGAA 58.401 52.381 16.63 0.00 0.00 2.10
1004 5014 2.560542 CGTCTCCATGGATCCCTAGAAG 59.439 54.545 16.63 6.43 0.00 2.85
1006 5016 2.090550 TCTCCATGGATCCCTAGAAGCA 60.091 50.000 16.63 0.00 0.00 3.91
1008 5018 2.090550 TCCATGGATCCCTAGAAGCAGA 60.091 50.000 11.44 0.00 0.00 4.26
1010 5020 1.403814 TGGATCCCTAGAAGCAGACG 58.596 55.000 9.90 0.00 0.00 4.18
1013 5061 1.403687 ATCCCTAGAAGCAGACGCCC 61.404 60.000 0.00 0.00 39.83 6.13
1026 5074 2.172483 GACGCCCCTCTCTTCTTGCA 62.172 60.000 0.00 0.00 0.00 4.08
1027 5075 1.222936 CGCCCCTCTCTTCTTGCAT 59.777 57.895 0.00 0.00 0.00 3.96
1029 5077 1.134401 CGCCCCTCTCTTCTTGCATAA 60.134 52.381 0.00 0.00 0.00 1.90
1034 5082 5.451103 GCCCCTCTCTTCTTGCATAATTTTC 60.451 44.000 0.00 0.00 0.00 2.29
1039 5087 8.129840 CCTCTCTTCTTGCATAATTTTCATCTG 58.870 37.037 0.00 0.00 0.00 2.90
1041 5089 6.260377 TCTTCTTGCATAATTTTCATCTGCG 58.740 36.000 0.00 0.00 35.63 5.18
1043 5091 3.779271 TGCATAATTTTCATCTGCGCA 57.221 38.095 10.98 10.98 35.63 6.09
1044 5092 4.107363 TGCATAATTTTCATCTGCGCAA 57.893 36.364 13.05 2.72 35.63 4.85
1046 5094 3.243643 GCATAATTTTCATCTGCGCAACC 59.756 43.478 13.05 0.00 0.00 3.77
1047 5095 4.675510 CATAATTTTCATCTGCGCAACCT 58.324 39.130 13.05 0.00 0.00 3.50
1048 5096 2.927553 ATTTTCATCTGCGCAACCTC 57.072 45.000 13.05 0.00 0.00 3.85
1049 5097 1.896220 TTTTCATCTGCGCAACCTCT 58.104 45.000 13.05 0.00 0.00 3.69
1051 5099 0.737367 TTCATCTGCGCAACCTCTCG 60.737 55.000 13.05 0.00 0.00 4.04
1052 5100 1.153765 CATCTGCGCAACCTCTCGA 60.154 57.895 13.05 3.15 0.00 4.04
1053 5101 0.529337 CATCTGCGCAACCTCTCGAT 60.529 55.000 13.05 5.82 0.00 3.59
1141 5192 3.411418 GAGATCAAGTCGCCGCCGA 62.411 63.158 0.00 0.00 42.01 5.54
1176 5227 1.226547 CAAGACGAGCTCGCTCTCC 60.227 63.158 34.83 18.37 44.43 3.71
1242 5293 3.109547 CGCCGCTTCTACAACGCA 61.110 61.111 0.00 0.00 0.00 5.24
1243 5294 2.452813 CGCCGCTTCTACAACGCAT 61.453 57.895 0.00 0.00 0.00 4.73
2352 6436 2.356553 TACACGCTCAACACCGGC 60.357 61.111 0.00 0.00 0.00 6.13
2530 6614 3.068691 TGGGCCTCGTCTTCTCCG 61.069 66.667 4.53 0.00 0.00 4.63
2685 6769 4.324991 GGGGTCGCCGAGGTGTTT 62.325 66.667 2.35 0.00 0.00 2.83
3030 7114 2.214920 GGTGGAGGTCTCGGTGGTT 61.215 63.158 0.00 0.00 0.00 3.67
3077 7164 9.903682 ATGAATGAAATACTTGAACAGAACTTG 57.096 29.630 0.00 0.00 0.00 3.16
3156 7249 9.630098 AGTACACAATTTGATCATCATTTTCAC 57.370 29.630 2.79 0.00 0.00 3.18
3239 7342 5.507817 CCAGCAGAAGTTATCTCAGCTAGAG 60.508 48.000 0.00 6.79 46.14 2.43
3352 7457 7.611147 TAACCACTGTTGATCGAAATCCGATG 61.611 42.308 4.59 0.00 45.25 3.84
3362 7467 2.604914 CGAAATCCGATGTCACCTCAAG 59.395 50.000 0.00 0.00 41.76 3.02
3364 7469 5.957092 CGAAATCCGATGTCACCTCAAGTG 61.957 50.000 0.00 0.00 44.11 3.16
3379 7485 4.165036 CTCAAGTGTGATCGTCTTCTCAG 58.835 47.826 0.00 0.00 31.85 3.35
3395 7501 4.192429 TCTCAGAGATGAACATTCGCAA 57.808 40.909 0.00 0.00 0.00 4.85
3406 7512 1.408702 ACATTCGCAAGCCAAAACTGT 59.591 42.857 0.00 0.00 37.18 3.55
3476 7582 5.276536 GCAAACAAATTCTGCTCAACTGAAC 60.277 40.000 0.00 0.00 38.82 3.18
3482 7588 4.341366 TTCTGCTCAACTGAACATCTGA 57.659 40.909 0.00 0.00 31.90 3.27
3483 7589 4.341366 TCTGCTCAACTGAACATCTGAA 57.659 40.909 0.00 0.00 0.00 3.02
3489 7595 3.817084 TCAACTGAACATCTGAAGCCAAG 59.183 43.478 0.00 0.00 0.00 3.61
3490 7596 3.498774 ACTGAACATCTGAAGCCAAGT 57.501 42.857 0.00 0.00 0.00 3.16
3517 7635 4.201891 GCATCAATACAAGCAAGGAGTCAG 60.202 45.833 0.00 0.00 0.00 3.51
3520 7638 4.040339 TCAATACAAGCAAGGAGTCAGTCA 59.960 41.667 0.00 0.00 0.00 3.41
3521 7639 4.623932 ATACAAGCAAGGAGTCAGTCAA 57.376 40.909 0.00 0.00 0.00 3.18
3522 7640 3.498774 ACAAGCAAGGAGTCAGTCAAT 57.501 42.857 0.00 0.00 0.00 2.57
3523 7641 3.406764 ACAAGCAAGGAGTCAGTCAATC 58.593 45.455 0.00 0.00 0.00 2.67
3524 7642 3.072184 ACAAGCAAGGAGTCAGTCAATCT 59.928 43.478 0.00 0.00 0.00 2.40
3525 7643 3.331478 AGCAAGGAGTCAGTCAATCTG 57.669 47.619 0.00 0.00 44.85 2.90
3526 7644 2.027377 AGCAAGGAGTCAGTCAATCTGG 60.027 50.000 0.00 0.00 43.76 3.86
3527 7645 2.289945 GCAAGGAGTCAGTCAATCTGGT 60.290 50.000 0.00 0.00 43.76 4.00
3528 7646 3.055819 GCAAGGAGTCAGTCAATCTGGTA 60.056 47.826 0.00 0.00 43.76 3.25
3529 7647 4.563580 GCAAGGAGTCAGTCAATCTGGTAA 60.564 45.833 0.00 0.00 43.76 2.85
3530 7648 5.174395 CAAGGAGTCAGTCAATCTGGTAAG 58.826 45.833 0.00 0.00 43.76 2.34
3531 7649 4.421131 AGGAGTCAGTCAATCTGGTAAGT 58.579 43.478 0.00 0.00 43.76 2.24
3532 7650 4.221703 AGGAGTCAGTCAATCTGGTAAGTG 59.778 45.833 0.00 0.00 43.76 3.16
3533 7651 4.220821 GGAGTCAGTCAATCTGGTAAGTGA 59.779 45.833 0.00 0.00 43.76 3.41
3534 7652 5.140747 AGTCAGTCAATCTGGTAAGTGAC 57.859 43.478 0.00 0.00 43.76 3.67
3535 7653 4.588951 AGTCAGTCAATCTGGTAAGTGACA 59.411 41.667 10.72 0.00 42.10 3.58
3536 7654 4.926238 GTCAGTCAATCTGGTAAGTGACAG 59.074 45.833 7.16 0.00 42.29 3.51
3537 7655 4.021104 TCAGTCAATCTGGTAAGTGACAGG 60.021 45.833 7.16 0.09 42.29 4.00
3538 7656 3.904339 AGTCAATCTGGTAAGTGACAGGT 59.096 43.478 7.16 0.00 42.29 4.00
3539 7657 4.021016 AGTCAATCTGGTAAGTGACAGGTC 60.021 45.833 7.16 0.00 42.29 3.85
3540 7658 3.901222 TCAATCTGGTAAGTGACAGGTCA 59.099 43.478 0.00 0.00 37.24 4.02
3591 7714 8.879342 TCAAAACACGATAATTTCAACCAAAT 57.121 26.923 0.00 0.00 36.12 2.32
3613 7761 2.554032 AGCACTACACCAGTTTCAATGC 59.446 45.455 0.00 0.00 34.26 3.56
3690 8352 5.869344 TGAAGAAGGTATGTTCAGTCATTCG 59.131 40.000 0.00 0.00 36.47 3.34
3698 8360 6.978659 GGTATGTTCAGTCATTCGAGTTCATA 59.021 38.462 0.00 0.00 0.00 2.15
3699 8361 6.893958 ATGTTCAGTCATTCGAGTTCATAC 57.106 37.500 0.00 0.00 0.00 2.39
3768 8440 6.531503 TGACTAGAAGGAACAATACAGGAG 57.468 41.667 0.00 0.00 0.00 3.69
3793 8465 3.560025 CCTGATTGTGTAACCTTGGCTCT 60.560 47.826 0.00 0.00 34.36 4.09
3806 8478 3.703052 CCTTGGCTCTGCATAAAAAGGAT 59.297 43.478 8.79 0.00 35.73 3.24
3812 8485 6.210385 TGGCTCTGCATAAAAAGGATACAAAA 59.790 34.615 0.00 0.00 41.41 2.44
3813 8486 6.753744 GGCTCTGCATAAAAAGGATACAAAAG 59.246 38.462 0.00 0.00 41.41 2.27
3834 8507 7.946381 AAAGAAGAAGAAAATCCATACCTCC 57.054 36.000 0.00 0.00 0.00 4.30
3837 8510 5.779241 AGAAGAAAATCCATACCTCCACA 57.221 39.130 0.00 0.00 0.00 4.17
3842 8515 4.494091 AAATCCATACCTCCACAGTGAG 57.506 45.455 0.62 0.00 0.00 3.51
3845 8518 0.904649 CATACCTCCACAGTGAGCCA 59.095 55.000 0.62 0.00 0.00 4.75
3849 8522 1.145738 ACCTCCACAGTGAGCCAAAAT 59.854 47.619 0.62 0.00 0.00 1.82
3853 8526 3.937706 CTCCACAGTGAGCCAAAATAGAG 59.062 47.826 0.62 0.00 0.00 2.43
3854 8527 3.582647 TCCACAGTGAGCCAAAATAGAGA 59.417 43.478 0.62 0.00 0.00 3.10
3871 8544 4.630644 AGAGACCACTGAATGACACAAT 57.369 40.909 0.00 0.00 0.00 2.71
3877 8550 6.652481 AGACCACTGAATGACACAATAAGAAG 59.348 38.462 0.00 0.00 0.00 2.85
3893 8566 4.762956 AAGAAGCATCTTCAAACTGCTC 57.237 40.909 0.00 0.00 45.10 4.26
3910 8590 1.873591 GCTCACCGTTCAGTGTTCATT 59.126 47.619 0.00 0.00 38.91 2.57
3911 8591 2.349817 GCTCACCGTTCAGTGTTCATTG 60.350 50.000 0.00 0.00 38.91 2.82
3912 8592 2.872245 CTCACCGTTCAGTGTTCATTGT 59.128 45.455 0.00 0.00 38.91 2.71
3913 8593 3.275143 TCACCGTTCAGTGTTCATTGTT 58.725 40.909 0.00 0.00 38.91 2.83
3914 8594 3.311322 TCACCGTTCAGTGTTCATTGTTC 59.689 43.478 0.00 0.00 38.91 3.18
3915 8595 3.064682 CACCGTTCAGTGTTCATTGTTCA 59.935 43.478 0.00 0.00 32.89 3.18
3916 8596 3.882888 ACCGTTCAGTGTTCATTGTTCAT 59.117 39.130 0.00 0.00 0.00 2.57
3996 8676 2.294512 CTCTGAGGTGCACGATATAGCA 59.705 50.000 11.45 0.17 38.65 3.49
4026 8706 3.870419 GCATCTCAGTCAATCTGTCCTTC 59.130 47.826 0.00 0.00 43.97 3.46
4029 8709 2.232452 CTCAGTCAATCTGTCCTTCGGT 59.768 50.000 0.00 0.00 43.97 4.69
4032 8712 2.028930 AGTCAATCTGTCCTTCGGTGAC 60.029 50.000 0.00 0.00 0.00 3.67
4047 8727 1.339097 GTGACGTATCCCATAGCCCT 58.661 55.000 0.00 0.00 0.00 5.19
4059 8739 2.103941 CCATAGCCCTGGAGAGAAGAAC 59.896 54.545 0.00 0.00 38.69 3.01
4071 8751 0.034059 AGAAGAACTCACTGGTGCGG 59.966 55.000 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.313091 GGCCAACGGTCCTTCCATTC 61.313 60.000 0.00 0.00 35.57 2.67
18 19 1.304134 GGCCAACGGTCCTTCCATT 60.304 57.895 0.00 0.00 35.57 3.16
19 20 2.355115 GGCCAACGGTCCTTCCAT 59.645 61.111 0.00 0.00 35.57 3.41
20 21 4.323477 CGGCCAACGGTCCTTCCA 62.323 66.667 2.24 0.00 39.42 3.53
21 22 3.837570 AACGGCCAACGGTCCTTCC 62.838 63.158 2.24 0.00 39.00 3.46
22 23 2.281276 AACGGCCAACGGTCCTTC 60.281 61.111 2.24 0.00 39.00 3.46
42 43 2.431942 CGTCTGCCACCGGTGTAC 60.432 66.667 31.80 23.45 0.00 2.90
107 108 3.907260 TTTGCCAGCGCTCCCAGAG 62.907 63.158 7.13 0.00 35.36 3.35
108 109 3.907260 CTTTGCCAGCGCTCCCAGA 62.907 63.158 7.13 1.48 35.36 3.86
109 110 3.437795 CTTTGCCAGCGCTCCCAG 61.438 66.667 7.13 0.00 35.36 4.45
110 111 3.952508 TCTTTGCCAGCGCTCCCA 61.953 61.111 7.13 4.32 35.36 4.37
111 112 3.435186 GTCTTTGCCAGCGCTCCC 61.435 66.667 7.13 0.94 35.36 4.30
132 134 2.305009 CCTTCATCCTTGAATGCCCTC 58.695 52.381 0.00 0.00 40.95 4.30
146 148 3.200165 GGACAGCCTTAACCTACCTTCAT 59.800 47.826 0.00 0.00 0.00 2.57
147 149 2.570302 GGACAGCCTTAACCTACCTTCA 59.430 50.000 0.00 0.00 0.00 3.02
148 150 2.838813 AGGACAGCCTTAACCTACCTTC 59.161 50.000 0.00 0.00 43.90 3.46
149 151 2.917205 AGGACAGCCTTAACCTACCTT 58.083 47.619 0.00 0.00 43.90 3.50
150 152 2.644060 AGGACAGCCTTAACCTACCT 57.356 50.000 0.00 0.00 43.90 3.08
169 171 0.909610 AAGCAGGGGAGATCGTTGGA 60.910 55.000 0.00 0.00 0.00 3.53
171 173 0.539051 AGAAGCAGGGGAGATCGTTG 59.461 55.000 0.00 0.00 0.00 4.10
187 189 4.038271 AGAAATGGGAATGCAGACAGAA 57.962 40.909 0.00 0.00 0.00 3.02
192 194 5.481122 TGAATGAAAGAAATGGGAATGCAGA 59.519 36.000 0.00 0.00 0.00 4.26
194 196 5.741962 TGAATGAAAGAAATGGGAATGCA 57.258 34.783 0.00 0.00 0.00 3.96
195 197 6.819649 TCAATGAATGAAAGAAATGGGAATGC 59.180 34.615 0.00 0.00 34.30 3.56
197 199 8.208903 GGATCAATGAATGAAAGAAATGGGAAT 58.791 33.333 0.00 0.00 42.54 3.01
198 200 7.180587 TGGATCAATGAATGAAAGAAATGGGAA 59.819 33.333 0.00 0.00 42.54 3.97
200 202 6.880484 TGGATCAATGAATGAAAGAAATGGG 58.120 36.000 0.00 0.00 42.54 4.00
203 205 7.919091 CGACATGGATCAATGAATGAAAGAAAT 59.081 33.333 17.33 0.00 42.54 2.17
204 206 7.252708 CGACATGGATCAATGAATGAAAGAAA 58.747 34.615 17.33 0.00 42.54 2.52
205 207 6.678655 GCGACATGGATCAATGAATGAAAGAA 60.679 38.462 17.33 0.00 42.54 2.52
206 208 5.220912 GCGACATGGATCAATGAATGAAAGA 60.221 40.000 17.33 0.00 42.54 2.52
207 209 4.974275 GCGACATGGATCAATGAATGAAAG 59.026 41.667 17.33 1.46 42.54 2.62
210 212 2.545106 CGCGACATGGATCAATGAATGA 59.455 45.455 17.33 0.00 43.67 2.57
218 224 0.463620 TGAATCCGCGACATGGATCA 59.536 50.000 8.23 0.00 45.46 2.92
219 225 1.143305 CTGAATCCGCGACATGGATC 58.857 55.000 8.23 0.00 45.46 3.36
222 228 0.374758 CAACTGAATCCGCGACATGG 59.625 55.000 8.23 0.00 0.00 3.66
255 265 4.891992 ACTCAGTTATGTGTTACTGCCT 57.108 40.909 0.00 0.00 41.16 4.75
287 297 3.980646 ACACAACCAGTACGTAACGTA 57.019 42.857 0.00 0.00 41.54 3.57
291 301 5.212532 ACCATTACACAACCAGTACGTAA 57.787 39.130 0.00 0.00 0.00 3.18
311 321 1.685148 CCGTAGTCCCTGGTACTACC 58.315 60.000 20.01 6.51 44.19 3.18
313 323 1.298953 ACCCGTAGTCCCTGGTACTA 58.701 55.000 0.00 0.00 0.00 1.82
321 331 1.137675 GTTGATGGTACCCGTAGTCCC 59.862 57.143 10.07 0.00 0.00 4.46
323 333 1.202336 CGGTTGATGGTACCCGTAGTC 60.202 57.143 10.07 0.65 35.78 2.59
329 339 0.834612 TGGATCGGTTGATGGTACCC 59.165 55.000 10.07 0.00 34.09 3.69
330 340 2.930826 ATGGATCGGTTGATGGTACC 57.069 50.000 4.43 4.43 34.09 3.34
331 341 5.408604 GTGATAATGGATCGGTTGATGGTAC 59.591 44.000 0.00 0.00 37.38 3.34
332 342 5.306937 AGTGATAATGGATCGGTTGATGGTA 59.693 40.000 0.00 0.00 37.38 3.25
333 343 4.103153 AGTGATAATGGATCGGTTGATGGT 59.897 41.667 0.00 0.00 37.38 3.55
334 344 4.645535 AGTGATAATGGATCGGTTGATGG 58.354 43.478 0.00 0.00 37.38 3.51
339 370 5.118990 CAGTGAAGTGATAATGGATCGGTT 58.881 41.667 0.00 0.00 37.38 4.44
367 398 2.900337 GATTAACCGGCCGGCCAG 60.900 66.667 43.58 35.59 39.32 4.85
368 399 3.690685 CTGATTAACCGGCCGGCCA 62.691 63.158 43.58 28.74 39.32 5.36
369 400 2.900337 CTGATTAACCGGCCGGCC 60.900 66.667 43.58 36.69 39.32 6.13
370 401 2.653953 TAGCTGATTAACCGGCCGGC 62.654 60.000 43.58 26.98 39.18 6.13
371 402 0.034896 ATAGCTGATTAACCGGCCGG 59.965 55.000 42.17 42.17 39.18 6.13
372 403 2.029290 ACTATAGCTGATTAACCGGCCG 60.029 50.000 21.04 21.04 39.18 6.13
373 404 3.244112 ACACTATAGCTGATTAACCGGCC 60.244 47.826 0.00 0.00 39.18 6.13
374 405 3.991367 ACACTATAGCTGATTAACCGGC 58.009 45.455 0.00 0.00 38.68 6.13
375 406 5.919141 GTGTACACTATAGCTGATTAACCGG 59.081 44.000 18.92 0.00 0.00 5.28
376 407 5.624081 CGTGTACACTATAGCTGATTAACCG 59.376 44.000 23.01 0.51 0.00 4.44
377 408 6.501781 ACGTGTACACTATAGCTGATTAACC 58.498 40.000 23.01 0.00 0.00 2.85
378 409 7.589221 GGTACGTGTACACTATAGCTGATTAAC 59.411 40.741 23.01 3.99 37.78 2.01
379 410 7.282901 TGGTACGTGTACACTATAGCTGATTAA 59.717 37.037 23.01 6.19 37.78 1.40
380 411 6.767423 TGGTACGTGTACACTATAGCTGATTA 59.233 38.462 23.01 6.78 37.78 1.75
381 412 5.591472 TGGTACGTGTACACTATAGCTGATT 59.409 40.000 23.01 0.00 37.78 2.57
382 413 5.008415 GTGGTACGTGTACACTATAGCTGAT 59.992 44.000 23.01 1.18 37.78 2.90
383 414 4.333649 GTGGTACGTGTACACTATAGCTGA 59.666 45.833 23.01 7.98 37.78 4.26
384 415 4.595116 GTGGTACGTGTACACTATAGCTG 58.405 47.826 23.01 8.65 37.78 4.24
399 430 4.018649 TCACATGTATGTACGTGGTACG 57.981 45.455 14.84 0.00 45.19 3.67
400 431 6.897259 AAATCACATGTATGTACGTGGTAC 57.103 37.500 14.84 0.00 45.19 3.34
401 432 7.097834 TGAAAATCACATGTATGTACGTGGTA 58.902 34.615 14.84 4.90 45.19 3.25
402 433 5.935206 TGAAAATCACATGTATGTACGTGGT 59.065 36.000 14.84 0.00 45.19 4.16
405 436 8.726068 TGAAATGAAAATCACATGTATGTACGT 58.274 29.630 0.00 0.00 39.39 3.57
406 437 9.720667 ATGAAATGAAAATCACATGTATGTACG 57.279 29.630 0.00 0.00 39.39 3.67
413 444 8.984764 CACTGAAATGAAATGAAAATCACATGT 58.015 29.630 0.00 0.00 0.00 3.21
414 445 8.440059 CCACTGAAATGAAATGAAAATCACATG 58.560 33.333 0.00 0.00 0.00 3.21
415 446 7.118680 GCCACTGAAATGAAATGAAAATCACAT 59.881 33.333 0.00 0.00 0.00 3.21
430 467 1.033746 ATGCCTCCGCCACTGAAATG 61.034 55.000 0.00 0.00 0.00 2.32
441 478 1.091771 CACCACTGCTAATGCCTCCG 61.092 60.000 0.00 0.00 38.71 4.63
460 506 4.142093 ACTTGCTTGTTAATGATCCATGGC 60.142 41.667 6.96 0.00 0.00 4.40
472 521 1.332375 GTTGCACGGACTTGCTTGTTA 59.668 47.619 2.49 0.00 43.41 2.41
480 529 0.461339 ACGACAAGTTGCACGGACTT 60.461 50.000 21.06 0.00 37.82 3.01
482 531 1.149361 TGACGACAAGTTGCACGGAC 61.149 55.000 21.06 16.02 0.00 4.79
483 532 0.249699 ATGACGACAAGTTGCACGGA 60.250 50.000 21.06 11.45 0.00 4.69
484 533 0.110688 CATGACGACAAGTTGCACGG 60.111 55.000 21.06 5.16 0.00 4.94
485 534 0.581529 ACATGACGACAAGTTGCACG 59.418 50.000 17.36 17.36 0.00 5.34
486 535 1.397190 CGACATGACGACAAGTTGCAC 60.397 52.381 12.27 0.00 35.09 4.57
487 536 0.858583 CGACATGACGACAAGTTGCA 59.141 50.000 12.27 0.00 35.09 4.08
488 537 1.136690 TCGACATGACGACAAGTTGC 58.863 50.000 16.10 0.00 37.37 4.17
489 538 2.026860 CGATCGACATGACGACAAGTTG 59.973 50.000 21.81 7.04 44.84 3.16
490 539 2.251040 CGATCGACATGACGACAAGTT 58.749 47.619 21.81 6.38 44.84 2.66
491 540 1.199327 ACGATCGACATGACGACAAGT 59.801 47.619 24.34 17.60 44.84 3.16
492 541 1.579361 CACGATCGACATGACGACAAG 59.421 52.381 24.34 17.02 44.84 3.16
493 542 1.613270 CACGATCGACATGACGACAA 58.387 50.000 24.34 1.03 44.84 3.18
494 543 0.179174 CCACGATCGACATGACGACA 60.179 55.000 24.34 1.79 44.84 4.35
497 546 0.179174 TCACCACGATCGACATGACG 60.179 55.000 24.34 11.41 0.00 4.35
498 547 1.550065 CTCACCACGATCGACATGAC 58.450 55.000 24.34 0.00 0.00 3.06
500 549 1.148157 GCCTCACCACGATCGACATG 61.148 60.000 24.34 15.58 0.00 3.21
501 550 1.141881 GCCTCACCACGATCGACAT 59.858 57.895 24.34 2.76 0.00 3.06
529 583 8.037758 CCTGGCCACTAAGATCTATATAAACAG 58.962 40.741 0.00 0.95 0.00 3.16
536 590 4.816126 ACACCTGGCCACTAAGATCTATA 58.184 43.478 0.00 0.00 0.00 1.31
537 591 3.658725 ACACCTGGCCACTAAGATCTAT 58.341 45.455 0.00 0.00 0.00 1.98
543 600 1.608590 CAACAACACCTGGCCACTAAG 59.391 52.381 0.00 0.00 0.00 2.18
544 601 1.064314 ACAACAACACCTGGCCACTAA 60.064 47.619 0.00 0.00 0.00 2.24
566 623 2.603473 ACTCACCACGCCTAGGCA 60.603 61.111 32.47 11.76 42.06 4.75
634 698 3.474570 GGCCTGGACCGAGCTGAT 61.475 66.667 0.00 0.00 0.00 2.90
647 711 3.715097 GCAGAGGAGTGCAGGCCT 61.715 66.667 0.00 0.00 43.41 5.19
671 735 0.109086 CGTAGACAGAGGCAGTGGTG 60.109 60.000 0.00 0.00 0.00 4.17
672 736 0.251209 TCGTAGACAGAGGCAGTGGT 60.251 55.000 0.00 0.00 0.00 4.16
673 737 0.453793 CTCGTAGACAGAGGCAGTGG 59.546 60.000 0.00 0.00 32.38 4.00
674 738 1.135546 CACTCGTAGACAGAGGCAGTG 60.136 57.143 0.00 0.00 39.90 3.66
675 739 1.169577 CACTCGTAGACAGAGGCAGT 58.830 55.000 0.00 0.00 39.90 4.40
676 740 1.135546 CACACTCGTAGACAGAGGCAG 60.136 57.143 0.00 0.00 39.90 4.85
677 741 0.881796 CACACTCGTAGACAGAGGCA 59.118 55.000 0.00 0.00 39.90 4.75
678 742 0.882474 ACACACTCGTAGACAGAGGC 59.118 55.000 0.00 0.00 39.90 4.70
679 743 3.004419 TGAAACACACTCGTAGACAGAGG 59.996 47.826 0.00 0.00 39.90 3.69
687 751 4.383649 GTCGCTAAATGAAACACACTCGTA 59.616 41.667 0.00 0.00 0.00 3.43
688 752 3.183775 GTCGCTAAATGAAACACACTCGT 59.816 43.478 0.00 0.00 0.00 4.18
693 757 2.222213 CGTGGTCGCTAAATGAAACACA 59.778 45.455 0.00 0.00 0.00 3.72
707 771 2.815211 CACATGAGGCCGTGGTCG 60.815 66.667 0.00 0.00 33.64 4.79
708 772 1.448540 CTCACATGAGGCCGTGGTC 60.449 63.158 0.00 0.00 38.48 4.02
709 773 2.665000 CTCACATGAGGCCGTGGT 59.335 61.111 0.00 0.00 38.48 4.16
710 774 2.821366 GCTCACATGAGGCCGTGG 60.821 66.667 10.81 1.79 42.29 4.94
711 775 1.450848 ATGCTCACATGAGGCCGTG 60.451 57.895 10.81 0.00 42.29 4.94
762 1497 2.101783 GAATCACACCATGGCCATGAA 58.898 47.619 41.32 22.82 41.20 2.57
780 1515 5.694910 GTGCTGTGCAGTAACTAAACTAGAA 59.305 40.000 0.00 0.00 40.08 2.10
783 1518 4.951254 TGTGCTGTGCAGTAACTAAACTA 58.049 39.130 0.00 0.00 40.08 2.24
803 1545 0.469070 GATGGAGATGGAGCTGCTGT 59.531 55.000 7.01 0.00 0.00 4.40
804 1546 0.759959 AGATGGAGATGGAGCTGCTG 59.240 55.000 7.01 0.00 0.00 4.41
805 1547 1.050204 GAGATGGAGATGGAGCTGCT 58.950 55.000 6.82 0.00 0.00 4.24
806 1548 0.035176 GGAGATGGAGATGGAGCTGC 59.965 60.000 0.00 0.00 0.00 5.25
807 1549 1.421480 TGGAGATGGAGATGGAGCTG 58.579 55.000 0.00 0.00 0.00 4.24
808 1550 1.979308 CATGGAGATGGAGATGGAGCT 59.021 52.381 0.00 0.00 0.00 4.09
826 1568 1.139058 GGAAGTGCCGTCCATAGACAT 59.861 52.381 3.04 0.00 43.73 3.06
827 1569 0.535335 GGAAGTGCCGTCCATAGACA 59.465 55.000 3.04 0.00 43.73 3.41
828 1570 0.179081 GGGAAGTGCCGTCCATAGAC 60.179 60.000 8.82 0.00 36.83 2.59
829 1571 0.325296 AGGGAAGTGCCGTCCATAGA 60.325 55.000 8.82 0.00 36.83 1.98
830 1572 0.105039 GAGGGAAGTGCCGTCCATAG 59.895 60.000 0.00 0.00 44.08 2.23
831 1573 1.672854 CGAGGGAAGTGCCGTCCATA 61.673 60.000 4.17 0.00 46.48 2.74
832 1574 2.990479 GAGGGAAGTGCCGTCCAT 59.010 61.111 0.00 2.53 44.08 3.41
833 1575 3.691342 CGAGGGAAGTGCCGTCCA 61.691 66.667 4.17 0.00 46.48 4.02
834 1576 3.236003 AACGAGGGAAGTGCCGTCC 62.236 63.158 4.17 0.00 46.48 4.79
869 1666 4.389576 GGCACGCCACGCTTCAAG 62.390 66.667 2.36 0.00 35.81 3.02
891 1688 0.321475 TGACAAGGACGATGCATGCA 60.321 50.000 25.04 25.04 0.00 3.96
892 1689 0.804364 TTGACAAGGACGATGCATGC 59.196 50.000 11.82 11.82 0.00 4.06
976 4986 0.982852 ATCCATGGAGACGGGAGCAA 60.983 55.000 21.33 0.00 39.43 3.91
977 4987 1.383109 ATCCATGGAGACGGGAGCA 60.383 57.895 21.33 0.00 39.43 4.26
995 5005 2.058595 GGGCGTCTGCTTCTAGGGA 61.059 63.158 0.00 0.00 42.25 4.20
997 5007 2.022240 GAGGGGCGTCTGCTTCTAGG 62.022 65.000 0.00 0.00 42.25 3.02
1000 5010 2.284258 AGAGGGGCGTCTGCTTCT 60.284 61.111 0.00 0.00 42.25 2.85
1002 5012 1.893919 GAAGAGAGGGGCGTCTGCTT 61.894 60.000 0.00 0.00 42.25 3.91
1003 5013 2.284258 AAGAGAGGGGCGTCTGCT 60.284 61.111 0.00 0.00 42.25 4.24
1004 5014 1.893919 AAGAAGAGAGGGGCGTCTGC 61.894 60.000 0.00 0.00 41.71 4.26
1006 5016 1.893919 GCAAGAAGAGAGGGGCGTCT 61.894 60.000 0.00 0.00 0.00 4.18
1008 5018 1.557269 ATGCAAGAAGAGAGGGGCGT 61.557 55.000 0.00 0.00 0.00 5.68
1010 5020 2.717639 TTATGCAAGAAGAGAGGGGC 57.282 50.000 0.00 0.00 0.00 5.80
1013 5061 8.129840 CAGATGAAAATTATGCAAGAAGAGAGG 58.870 37.037 0.00 0.00 0.00 3.69
1026 5074 4.641989 AGAGGTTGCGCAGATGAAAATTAT 59.358 37.500 11.31 0.00 0.00 1.28
1027 5075 4.009675 AGAGGTTGCGCAGATGAAAATTA 58.990 39.130 11.31 0.00 0.00 1.40
1029 5077 2.421424 GAGAGGTTGCGCAGATGAAAAT 59.579 45.455 11.31 0.00 0.00 1.82
1034 5082 0.529337 ATCGAGAGGTTGCGCAGATG 60.529 55.000 11.31 0.00 0.00 2.90
1039 5087 0.872021 ATTCGATCGAGAGGTTGCGC 60.872 55.000 18.54 0.00 0.00 6.09
1051 5099 1.927895 ACAGTTGAGGCGATTCGATC 58.072 50.000 10.88 7.46 0.00 3.69
1052 5100 2.799917 GCTACAGTTGAGGCGATTCGAT 60.800 50.000 10.88 0.00 0.00 3.59
1053 5101 1.469251 GCTACAGTTGAGGCGATTCGA 60.469 52.381 10.88 0.00 0.00 3.71
1061 5109 2.509336 CGGCGGCTACAGTTGAGG 60.509 66.667 7.61 0.00 0.00 3.86
1064 5112 1.447838 ATCACGGCGGCTACAGTTG 60.448 57.895 13.24 0.00 0.00 3.16
1120 5168 1.590259 GCGGCGACTTGATCTCCTC 60.590 63.158 12.98 0.00 28.98 3.71
1148 5199 2.683933 TCGTCTTGAGGGCCTCCC 60.684 66.667 30.03 14.23 45.90 4.30
1149 5200 2.896443 CTCGTCTTGAGGGCCTCC 59.104 66.667 30.03 13.89 41.29 4.30
1150 5201 2.185608 GCTCGTCTTGAGGGCCTC 59.814 66.667 26.95 26.95 45.38 4.70
1151 5202 2.284258 AGCTCGTCTTGAGGGCCT 60.284 61.111 5.25 5.25 45.38 5.19
1152 5203 2.185608 GAGCTCGTCTTGAGGGCC 59.814 66.667 0.00 0.00 45.38 5.80
1153 5204 2.202676 CGAGCTCGTCTTGAGGGC 60.203 66.667 27.79 0.00 45.38 5.19
1160 5211 2.826738 GGGAGAGCGAGCTCGTCT 60.827 66.667 34.46 31.30 46.90 4.18
1237 5288 2.427245 CGGAGGAGGAGGATGCGTT 61.427 63.158 0.00 0.00 0.00 4.84
1238 5289 2.835431 CGGAGGAGGAGGATGCGT 60.835 66.667 0.00 0.00 0.00 5.24
1623 5674 4.680237 TTGTCGCAGCCGTCCTGG 62.680 66.667 2.99 0.00 42.03 4.45
1746 5797 1.663702 CCCGAACGAGGACACACAC 60.664 63.158 0.00 0.00 0.00 3.82
1749 5800 3.998672 GCCCCGAACGAGGACACA 61.999 66.667 0.00 0.00 0.00 3.72
1809 5860 0.321996 AGAGGTTGAAGAAGCGGTCC 59.678 55.000 0.00 0.00 34.60 4.46
2193 6277 4.796231 CGCCACGGGTCCTCTTCG 62.796 72.222 0.00 0.00 0.00 3.79
2585 6669 4.143333 CCAGGTACCCGTGCTCCG 62.143 72.222 8.74 0.00 0.00 4.63
2607 6691 2.892425 GGCATCGGCGACAGGAAG 60.892 66.667 13.76 0.00 42.47 3.46
2775 6859 2.792947 GGCCATGAAGCAGCCCATG 61.793 63.158 15.16 15.16 41.00 3.66
2923 7007 0.608640 AGGAAGACGGCGAAGTTGAT 59.391 50.000 16.62 0.00 0.00 2.57
2998 7082 1.529010 CCACCTTGCTGCTGTTGGA 60.529 57.895 0.00 0.00 0.00 3.53
2999 7083 1.521450 CTCCACCTTGCTGCTGTTGG 61.521 60.000 0.00 2.41 0.00 3.77
3030 7114 0.817634 CACTTCACTTGTGGCCGGAA 60.818 55.000 5.05 0.00 0.00 4.30
3035 7119 3.988379 TTCATTCACTTCACTTGTGGC 57.012 42.857 0.64 0.00 36.21 5.01
3085 7172 2.529780 CCAAGTGAAATTTGGCTGCA 57.470 45.000 0.50 0.00 46.98 4.41
3156 7249 2.113433 GGGCTGCTGCTCTGTCATG 61.113 63.158 15.64 0.00 36.57 3.07
3186 7289 2.480073 CCCAACGGCATCACAATGATTC 60.480 50.000 0.00 0.00 34.28 2.52
3196 7299 1.471287 GGTTCTAAACCCAACGGCATC 59.529 52.381 0.00 0.00 46.12 3.91
3218 7321 4.298332 GCTCTAGCTGAGATAACTTCTGC 58.702 47.826 14.86 0.00 45.39 4.26
3274 7377 6.485313 TGTAGTATCTTTTGTTGTTGGTGAGG 59.515 38.462 0.00 0.00 0.00 3.86
3341 7446 2.293677 TGAGGTGACATCGGATTTCG 57.706 50.000 0.00 0.00 40.90 3.46
3352 7457 2.029828 AGACGATCACACTTGAGGTGAC 60.030 50.000 0.38 0.00 46.99 3.67
3362 7467 4.095632 TCATCTCTGAGAAGACGATCACAC 59.904 45.833 12.00 0.00 0.00 3.82
3364 7469 4.891627 TCATCTCTGAGAAGACGATCAC 57.108 45.455 12.00 0.00 0.00 3.06
3369 7474 4.498681 CGAATGTTCATCTCTGAGAAGACG 59.501 45.833 12.00 8.24 31.68 4.18
3379 7485 1.739466 TGGCTTGCGAATGTTCATCTC 59.261 47.619 0.00 0.00 0.00 2.75
3395 7501 3.547746 TCTTTCCGTTACAGTTTTGGCT 58.452 40.909 0.00 0.00 0.00 4.75
3406 7512 7.422399 CCTGATCTTTGTTTTTCTTTCCGTTA 58.578 34.615 0.00 0.00 0.00 3.18
3489 7595 4.640201 TCCTTGCTTGTATTGATGCCTAAC 59.360 41.667 0.00 0.00 0.00 2.34
3490 7596 4.854173 TCCTTGCTTGTATTGATGCCTAA 58.146 39.130 0.00 0.00 0.00 2.69
3517 7635 4.246458 GACCTGTCACTTACCAGATTGAC 58.754 47.826 0.00 0.00 39.09 3.18
3531 7649 0.686789 CATCCACCTGTGACCTGTCA 59.313 55.000 0.00 0.00 37.24 3.58
3532 7650 0.976641 TCATCCACCTGTGACCTGTC 59.023 55.000 0.00 0.00 0.00 3.51
3533 7651 0.979665 CTCATCCACCTGTGACCTGT 59.020 55.000 0.00 0.00 0.00 4.00
3534 7652 0.979665 ACTCATCCACCTGTGACCTG 59.020 55.000 0.00 0.00 0.00 4.00
3535 7653 1.734655 AACTCATCCACCTGTGACCT 58.265 50.000 0.00 0.00 0.00 3.85
3536 7654 2.554032 CAAAACTCATCCACCTGTGACC 59.446 50.000 0.00 0.00 0.00 4.02
3537 7655 3.214328 ACAAAACTCATCCACCTGTGAC 58.786 45.455 0.00 0.00 0.00 3.67
3538 7656 3.576078 ACAAAACTCATCCACCTGTGA 57.424 42.857 0.00 0.00 0.00 3.58
3539 7657 4.654091 AAACAAAACTCATCCACCTGTG 57.346 40.909 0.00 0.00 0.00 3.66
3540 7658 4.466015 ACAAAACAAAACTCATCCACCTGT 59.534 37.500 0.00 0.00 0.00 4.00
3541 7659 5.009854 ACAAAACAAAACTCATCCACCTG 57.990 39.130 0.00 0.00 0.00 4.00
3591 7714 3.751175 GCATTGAAACTGGTGTAGTGCTA 59.249 43.478 0.00 0.00 40.26 3.49
3613 7761 6.889722 TCAAGTTTAGATTGGTAATTCCTGGG 59.110 38.462 0.00 0.00 37.07 4.45
3690 8352 6.284459 AGGAGGATCAATTTCGTATGAACTC 58.716 40.000 0.00 0.00 36.25 3.01
3698 8360 7.703058 ACATTAAAAGGAGGATCAATTTCGT 57.297 32.000 0.00 0.00 36.25 3.85
3699 8361 8.863049 CAAACATTAAAAGGAGGATCAATTTCG 58.137 33.333 0.00 0.00 36.25 3.46
3704 8366 8.713708 TTACCAAACATTAAAAGGAGGATCAA 57.286 30.769 0.00 0.00 36.25 2.57
3768 8440 3.057526 GCCAAGGTTACACAATCAGGTTC 60.058 47.826 0.00 0.00 0.00 3.62
3782 8454 3.259123 CCTTTTTATGCAGAGCCAAGGTT 59.741 43.478 0.00 0.00 0.00 3.50
3793 8465 9.912634 CTTCTTCTTTTGTATCCTTTTTATGCA 57.087 29.630 0.00 0.00 0.00 3.96
3806 8478 9.807921 AGGTATGGATTTTCTTCTTCTTTTGTA 57.192 29.630 0.00 0.00 0.00 2.41
3812 8485 6.012508 TGTGGAGGTATGGATTTTCTTCTTCT 60.013 38.462 0.00 0.00 0.00 2.85
3813 8486 6.180472 TGTGGAGGTATGGATTTTCTTCTTC 58.820 40.000 0.00 0.00 0.00 2.87
3834 8507 3.686726 GGTCTCTATTTTGGCTCACTGTG 59.313 47.826 0.17 0.17 0.00 3.66
3837 8510 3.584848 AGTGGTCTCTATTTTGGCTCACT 59.415 43.478 0.00 0.00 0.00 3.41
3842 8515 4.943705 TCATTCAGTGGTCTCTATTTTGGC 59.056 41.667 0.00 0.00 0.00 4.52
3845 8518 6.533730 TGTGTCATTCAGTGGTCTCTATTTT 58.466 36.000 0.00 0.00 0.00 1.82
3849 8522 5.745312 ATTGTGTCATTCAGTGGTCTCTA 57.255 39.130 0.00 0.00 0.00 2.43
3853 8526 6.621596 GCTTCTTATTGTGTCATTCAGTGGTC 60.622 42.308 0.00 0.00 0.00 4.02
3854 8527 5.182001 GCTTCTTATTGTGTCATTCAGTGGT 59.818 40.000 0.00 0.00 0.00 4.16
3877 8550 1.135859 CGGTGAGCAGTTTGAAGATGC 60.136 52.381 0.00 0.00 40.29 3.91
3893 8566 3.064682 TGAACAATGAACACTGAACGGTG 59.935 43.478 11.58 11.58 42.34 4.94
3910 8590 5.509501 GGTTGAAGCAATTGAGGAATGAACA 60.510 40.000 10.34 0.00 0.00 3.18
3911 8591 4.925646 GGTTGAAGCAATTGAGGAATGAAC 59.074 41.667 10.34 2.11 0.00 3.18
3912 8592 4.834496 AGGTTGAAGCAATTGAGGAATGAA 59.166 37.500 10.34 0.00 0.00 2.57
3913 8593 4.410099 AGGTTGAAGCAATTGAGGAATGA 58.590 39.130 10.34 0.00 0.00 2.57
3914 8594 4.796038 AGGTTGAAGCAATTGAGGAATG 57.204 40.909 10.34 0.00 0.00 2.67
3915 8595 4.562143 GCAAGGTTGAAGCAATTGAGGAAT 60.562 41.667 10.34 0.00 0.00 3.01
3916 8596 3.243839 GCAAGGTTGAAGCAATTGAGGAA 60.244 43.478 10.34 0.00 0.00 3.36
4026 8706 0.038526 GGCTATGGGATACGTCACCG 60.039 60.000 0.00 0.00 40.83 4.94
4029 8709 1.338107 CAGGGCTATGGGATACGTCA 58.662 55.000 0.00 0.00 37.60 4.35
4032 8712 0.898320 CTCCAGGGCTATGGGATACG 59.102 60.000 9.01 0.00 41.01 3.06
4044 8724 2.233431 CAGTGAGTTCTTCTCTCCAGGG 59.767 54.545 0.00 0.00 43.13 4.45
4047 8727 2.630098 CACCAGTGAGTTCTTCTCTCCA 59.370 50.000 0.00 0.00 43.13 3.86
4059 8739 1.374758 GGAAGACCGCACCAGTGAG 60.375 63.158 0.99 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.