Multiple sequence alignment - TraesCS3D01G417900

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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 TraesCS3D01G417900 chr3D 100.000 2522 0 0 1 2522 529772914 529775435 0.000000e+00 4658.0
1 TraesCS3D01G417900 chr3B 90.671 954 42 20 710 1647 700362146 700363068 0.000000e+00 1225.0
2 TraesCS3D01G417900 chr3B 86.643 569 54 9 1 566 700361311 700361860 5.960000e-171 610.0
3 TraesCS3D01G417900 chr3B 96.296 108 4 0 2415 2522 742143338 742143445 7.170000e-41 178.0
4 TraesCS3D01G417900 chr3B 88.235 85 10 0 603 687 700361862 700361946 4.440000e-18 102.0
5 TraesCS3D01G417900 chr3A 87.252 957 46 20 911 1822 663577334 663578259 0.000000e+00 1022.0
6 TraesCS3D01G417900 chr2D 93.128 422 23 2 1838 2253 488992397 488991976 4.610000e-172 614.0
7 TraesCS3D01G417900 chr2D 91.534 189 11 5 2238 2425 492514631 492514447 3.220000e-64 255.0
8 TraesCS3D01G417900 chr2D 76.765 340 65 13 120 450 44940482 44940816 7.170000e-41 178.0
9 TraesCS3D01G417900 chr2D 81.395 86 14 2 280 364 35536405 35536321 4.500000e-08 69.4
10 TraesCS3D01G417900 chr1D 97.721 351 8 0 1838 2188 1857140 1856790 2.780000e-169 604.0
11 TraesCS3D01G417900 chr1D 99.083 109 1 0 2414 2522 1855979 1855871 1.980000e-46 196.0
12 TraesCS3D01G417900 chr1B 96.866 351 11 0 1838 2188 568003285 568003635 2.790000e-164 588.0
13 TraesCS3D01G417900 chr1B 92.571 175 12 1 2251 2425 268402864 268402691 1.500000e-62 250.0
14 TraesCS3D01G417900 chr1B 98.148 108 2 0 2415 2522 568004952 568005059 3.310000e-44 189.0
15 TraesCS3D01G417900 chr7A 96.866 351 10 1 1838 2188 596392815 596392466 1.010000e-163 586.0
16 TraesCS3D01G417900 chr7A 93.143 175 11 1 2252 2425 593795432 593795606 3.220000e-64 255.0
17 TraesCS3D01G417900 chr7A 93.567 171 10 1 2252 2422 48903752 48903921 1.160000e-63 254.0
18 TraesCS3D01G417900 chr7A 99.074 108 1 0 2415 2522 596379296 596379189 7.120000e-46 195.0
19 TraesCS3D01G417900 chr5D 92.000 425 23 4 1838 2253 423353680 423353258 1.010000e-163 586.0
20 TraesCS3D01G417900 chr4A 96.591 352 12 0 1837 2188 731594709 731595060 3.620000e-163 584.0
21 TraesCS3D01G417900 chr4A 99.074 108 1 0 2415 2522 731599513 731599620 7.120000e-46 195.0
22 TraesCS3D01G417900 chr4A 95.652 46 1 1 280 324 2178713 2178668 3.480000e-09 73.1
23 TraesCS3D01G417900 chr2A 89.183 416 25 4 1842 2253 622863844 622864243 3.750000e-138 501.0
24 TraesCS3D01G417900 chr2A 78.086 324 57 11 95 406 504051050 504050729 2.560000e-45 193.0
25 TraesCS3D01G417900 chr2A 96.296 108 4 0 2415 2522 454872003 454871896 7.170000e-41 178.0
26 TraesCS3D01G417900 chr2A 73.251 486 103 23 120 589 417101084 417100610 4.350000e-33 152.0
27 TraesCS3D01G417900 chr6A 88.361 421 28 10 1838 2253 313950287 313950691 1.050000e-133 486.0
28 TraesCS3D01G417900 chr6A 92.767 318 19 4 1838 2151 107608658 107608975 8.220000e-125 457.0
29 TraesCS3D01G417900 chr6A 95.370 108 5 0 2415 2522 313950690 313950797 3.340000e-39 172.0
30 TraesCS3D01G417900 chr6A 95.370 108 5 0 2415 2522 428840967 428840860 3.340000e-39 172.0
31 TraesCS3D01G417900 chr6B 93.478 276 17 1 1838 2112 622017118 622016843 2.340000e-110 409.0
32 TraesCS3D01G417900 chr6B 92.780 277 17 3 1838 2112 621580056 621580331 5.060000e-107 398.0
33 TraesCS3D01G417900 chr6B 93.750 176 11 0 2249 2424 226362477 226362652 5.350000e-67 265.0
34 TraesCS3D01G417900 chr6B 87.143 70 9 0 127 196 224860212 224860143 2.080000e-11 80.5
35 TraesCS3D01G417900 chr6B 70.874 309 82 8 280 584 532268798 532269102 5.820000e-07 65.8
36 TraesCS3D01G417900 chr4D 93.725 255 15 1 2000 2253 268081959 268081705 5.090000e-102 381.0
37 TraesCS3D01G417900 chr5A 87.197 289 18 4 1969 2253 3389609 3389336 6.770000e-81 311.0
38 TraesCS3D01G417900 chr5A 96.296 108 4 0 2415 2522 3389337 3389230 7.170000e-41 178.0
39 TraesCS3D01G417900 chrUn 95.181 166 8 0 2251 2416 74119450 74119615 1.920000e-66 263.0
40 TraesCS3D01G417900 chr7B 94.706 170 7 2 2251 2420 186866685 186866518 1.920000e-66 263.0
41 TraesCS3D01G417900 chr7B 95.349 43 2 0 282 324 199260455 199260413 4.500000e-08 69.4
42 TraesCS3D01G417900 chr4B 94.611 167 9 0 2252 2418 512755248 512755414 2.490000e-65 259.0
43 TraesCS3D01G417900 chr4B 88.571 175 15 3 2079 2253 299747836 299748005 9.140000e-50 207.0
44 TraesCS3D01G417900 chr5B 94.048 168 10 0 2252 2419 528369527 528369360 3.220000e-64 255.0
45 TraesCS3D01G417900 chr2B 80.838 167 23 8 89 249 731040522 731040359 3.410000e-24 122.0
46 TraesCS3D01G417900 chr7D 74.643 280 54 13 121 389 44671027 44671300 9.540000e-20 108.0
47 TraesCS3D01G417900 chr6D 84.211 95 13 2 272 364 347702288 347702194 9.610000e-15 91.6


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 TraesCS3D01G417900 chr3D 529772914 529775435 2521 False 4658.000000 4658 100.000000 1 2522 1 chr3D.!!$F1 2521
1 TraesCS3D01G417900 chr3B 700361311 700363068 1757 False 645.666667 1225 88.516333 1 1647 3 chr3B.!!$F2 1646
2 TraesCS3D01G417900 chr3A 663577334 663578259 925 False 1022.000000 1022 87.252000 911 1822 1 chr3A.!!$F1 911
3 TraesCS3D01G417900 chr1D 1855871 1857140 1269 True 400.000000 604 98.402000 1838 2522 2 chr1D.!!$R1 684
4 TraesCS3D01G417900 chr1B 568003285 568005059 1774 False 388.500000 588 97.507000 1838 2522 2 chr1B.!!$F1 684
5 TraesCS3D01G417900 chr6A 313950287 313950797 510 False 329.000000 486 91.865500 1838 2522 2 chr6A.!!$F2 684

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
507 511 0.179045 GGAGGGTGCATATGCGAAGT 60.179 55.0 22.21 7.62 45.83 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 3701 0.4546 GACCGGCTCGAAGTACATGA 59.545 55.0 0.0 0.0 0.0 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
18 19 1.296715 GGTTGACGAGCCTGATGGT 59.703 57.895 0.00 0.00 35.27 3.55
19 20 1.021390 GGTTGACGAGCCTGATGGTG 61.021 60.000 0.00 0.00 35.27 4.17
39 40 2.135139 GACATTGTCTTCACTCGTGCA 58.865 47.619 9.59 0.00 0.00 4.57
42 43 3.565482 ACATTGTCTTCACTCGTGCAATT 59.435 39.130 0.00 0.00 0.00 2.32
68 69 5.991328 TCACAAAACTTCATGACTGAGTC 57.009 39.130 5.47 5.47 31.68 3.36
72 73 6.690098 CACAAAACTTCATGACTGAGTCAAAG 59.310 38.462 20.26 20.10 45.96 2.77
73 74 6.599244 ACAAAACTTCATGACTGAGTCAAAGA 59.401 34.615 25.61 20.33 45.96 2.52
74 75 7.284034 ACAAAACTTCATGACTGAGTCAAAGAT 59.716 33.333 25.61 15.71 45.96 2.40
96 98 1.924524 GTGTACCACCGATGATTCACG 59.075 52.381 0.00 0.00 0.00 4.35
111 113 0.466543 TCACGTGCAAGTTGTAGGGT 59.533 50.000 11.67 5.39 0.00 4.34
144 147 3.512329 TCCTCATGAAACAAAGCATGCAT 59.488 39.130 21.98 4.57 41.18 3.96
161 164 2.559440 GCATGTTTTGCCAAAAGGTCA 58.441 42.857 2.15 0.00 46.15 4.02
177 181 1.281287 GGTCAAGTCCCCTTCCCTTAC 59.719 57.143 0.00 0.00 0.00 2.34
242 246 1.219469 TCATCCTTCCCGAGTATCCCA 59.781 52.381 0.00 0.00 0.00 4.37
257 261 5.497474 AGTATCCCAGCGTCATTTTACTTT 58.503 37.500 0.00 0.00 0.00 2.66
268 272 6.892430 GCGTCATTTTACTTTTGAAACAACAC 59.108 34.615 0.00 0.00 0.00 3.32
270 274 7.007546 CGTCATTTTACTTTTGAAACAACACGA 59.992 33.333 0.00 0.00 0.00 4.35
271 275 8.640291 GTCATTTTACTTTTGAAACAACACGAA 58.360 29.630 0.00 0.00 0.00 3.85
272 276 9.193133 TCATTTTACTTTTGAAACAACACGAAA 57.807 25.926 0.00 0.00 0.00 3.46
273 277 9.459276 CATTTTACTTTTGAAACAACACGAAAG 57.541 29.630 0.00 0.00 40.94 2.62
303 307 5.534207 AAAAGCTCAATGACATTTGACCA 57.466 34.783 0.00 0.00 32.39 4.02
307 311 4.341806 AGCTCAATGACATTTGACCAAACA 59.658 37.500 0.00 0.00 32.39 2.83
308 312 4.445385 GCTCAATGACATTTGACCAAACAC 59.555 41.667 0.00 0.00 32.39 3.32
309 313 4.942852 TCAATGACATTTGACCAAACACC 58.057 39.130 0.00 0.00 30.82 4.16
310 314 4.648762 TCAATGACATTTGACCAAACACCT 59.351 37.500 0.00 0.00 30.82 4.00
313 317 3.380004 TGACATTTGACCAAACACCTGTC 59.620 43.478 14.92 14.92 37.23 3.51
314 318 2.357637 ACATTTGACCAAACACCTGTCG 59.642 45.455 0.00 0.00 32.51 4.35
315 319 1.384525 TTTGACCAAACACCTGTCGG 58.615 50.000 0.00 0.00 0.00 4.79
325 329 3.462169 CCTGTCGGGTGTGGTGTA 58.538 61.111 0.00 0.00 0.00 2.90
326 330 1.980052 CCTGTCGGGTGTGGTGTAT 59.020 57.895 0.00 0.00 0.00 2.29
327 331 0.391130 CCTGTCGGGTGTGGTGTATG 60.391 60.000 0.00 0.00 0.00 2.39
338 342 3.122948 GTGTGGTGTATGTCATGAACGAC 59.877 47.826 0.00 0.00 36.40 4.34
352 356 1.130186 GAACGACGTCAGTAGAGGGAC 59.870 57.143 17.16 0.00 34.03 4.46
360 364 1.918262 TCAGTAGAGGGACGAAGGGTA 59.082 52.381 0.00 0.00 0.00 3.69
374 378 4.170947 GGTACCTATCCGCGGACT 57.829 61.111 33.75 21.55 0.00 3.85
379 383 1.120530 ACCTATCCGCGGACTGATTT 58.879 50.000 33.75 16.74 0.00 2.17
390 394 2.162681 GGACTGATTTTGGGTGGACAG 58.837 52.381 0.00 0.00 0.00 3.51
393 397 0.893270 TGATTTTGGGTGGACAGCGG 60.893 55.000 0.00 0.00 0.00 5.52
411 415 1.367840 GCATAGTCCAGGCGGGTAG 59.632 63.158 2.94 0.00 38.11 3.18
438 442 4.966787 TGGGGGCTGCAAACGTCC 62.967 66.667 0.50 0.00 0.00 4.79
442 446 2.357034 GGCTGCAAACGTCCGAGA 60.357 61.111 0.50 0.00 0.00 4.04
443 447 1.959226 GGCTGCAAACGTCCGAGAA 60.959 57.895 0.50 0.00 0.00 2.87
452 456 1.519455 CGTCCGAGAATGCCTGGTC 60.519 63.158 0.00 0.00 0.00 4.02
456 460 0.179089 CCGAGAATGCCTGGTCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
472 476 0.941963 AGAGGCCAGGGAGGTACATA 59.058 55.000 5.01 0.00 40.61 2.29
477 481 1.048601 CCAGGGAGGTACATATGCGT 58.951 55.000 1.58 0.00 0.00 5.24
490 494 3.068064 TGCGTCGGCAGATGAGGA 61.068 61.111 10.48 0.00 46.21 3.71
507 511 0.179045 GGAGGGTGCATATGCGAAGT 60.179 55.000 22.21 7.62 45.83 3.01
512 516 1.873591 GGTGCATATGCGAAGTAAGGG 59.126 52.381 22.21 0.00 45.83 3.95
530 534 1.676014 GGGAACTCATGAACGGAGTGG 60.676 57.143 0.00 0.00 45.00 4.00
532 536 2.289444 GGAACTCATGAACGGAGTGGAA 60.289 50.000 0.00 0.00 45.00 3.53
542 546 1.271379 ACGGAGTGGAAGAACAATGGG 60.271 52.381 0.00 0.00 42.51 4.00
551 555 0.328258 AGAACAATGGGACGGGGAAG 59.672 55.000 0.00 0.00 0.00 3.46
566 570 2.356227 GGGGAAGAGATTTGAGTGGGTC 60.356 54.545 0.00 0.00 0.00 4.46
567 571 2.305927 GGGAAGAGATTTGAGTGGGTCA 59.694 50.000 0.00 0.00 0.00 4.02
568 572 3.244911 GGGAAGAGATTTGAGTGGGTCAA 60.245 47.826 0.00 0.00 43.82 3.18
569 573 4.006319 GGAAGAGATTTGAGTGGGTCAAG 58.994 47.826 0.00 0.00 46.09 3.02
570 574 3.710209 AGAGATTTGAGTGGGTCAAGG 57.290 47.619 0.00 0.00 46.09 3.61
571 575 3.251484 AGAGATTTGAGTGGGTCAAGGA 58.749 45.455 0.00 0.00 46.09 3.36
572 576 3.848975 AGAGATTTGAGTGGGTCAAGGAT 59.151 43.478 0.00 0.00 46.09 3.24
573 577 3.944015 GAGATTTGAGTGGGTCAAGGATG 59.056 47.826 0.00 0.00 46.09 3.51
574 578 3.331889 AGATTTGAGTGGGTCAAGGATGT 59.668 43.478 0.00 0.00 46.09 3.06
575 579 2.859165 TTGAGTGGGTCAAGGATGTC 57.141 50.000 0.00 0.00 40.45 3.06
576 580 1.728323 TGAGTGGGTCAAGGATGTCA 58.272 50.000 0.00 0.00 29.64 3.58
577 581 1.625315 TGAGTGGGTCAAGGATGTCAG 59.375 52.381 0.00 0.00 29.64 3.51
578 582 1.902508 GAGTGGGTCAAGGATGTCAGA 59.097 52.381 0.00 0.00 0.00 3.27
579 583 1.905215 AGTGGGTCAAGGATGTCAGAG 59.095 52.381 0.00 0.00 0.00 3.35
580 584 1.625818 GTGGGTCAAGGATGTCAGAGT 59.374 52.381 0.00 0.00 0.00 3.24
581 585 1.902508 TGGGTCAAGGATGTCAGAGTC 59.097 52.381 0.00 0.00 0.00 3.36
582 586 1.208293 GGGTCAAGGATGTCAGAGTCC 59.792 57.143 0.00 0.00 34.64 3.85
583 587 2.183679 GGTCAAGGATGTCAGAGTCCT 58.816 52.381 0.00 0.00 46.63 3.85
584 588 3.366396 GGTCAAGGATGTCAGAGTCCTA 58.634 50.000 4.98 0.00 43.94 2.94
585 589 3.131400 GGTCAAGGATGTCAGAGTCCTAC 59.869 52.174 4.98 1.81 43.94 3.18
586 590 3.017442 TCAAGGATGTCAGAGTCCTACG 58.983 50.000 4.98 1.36 43.94 3.51
587 591 2.755655 CAAGGATGTCAGAGTCCTACGT 59.244 50.000 4.98 0.00 43.94 3.57
588 592 2.370349 AGGATGTCAGAGTCCTACGTG 58.630 52.381 0.00 0.00 42.93 4.49
589 593 2.026169 AGGATGTCAGAGTCCTACGTGA 60.026 50.000 0.00 0.00 42.93 4.35
590 594 2.097791 GGATGTCAGAGTCCTACGTGAC 59.902 54.545 0.00 0.00 37.42 3.67
591 595 1.154197 TGTCAGAGTCCTACGTGACG 58.846 55.000 2.24 2.24 38.78 4.35
592 596 0.447011 GTCAGAGTCCTACGTGACGG 59.553 60.000 10.66 0.00 40.26 4.79
593 597 1.136984 CAGAGTCCTACGTGACGGC 59.863 63.158 10.66 0.00 40.26 5.68
594 598 2.099831 GAGTCCTACGTGACGGCG 59.900 66.667 10.66 4.80 40.26 6.46
595 599 3.392595 GAGTCCTACGTGACGGCGG 62.393 68.421 13.24 9.26 40.26 6.13
596 600 3.741476 GTCCTACGTGACGGCGGT 61.741 66.667 13.24 0.00 35.98 5.68
597 601 3.434319 TCCTACGTGACGGCGGTC 61.434 66.667 16.90 16.90 43.71 4.79
598 602 4.487412 CCTACGTGACGGCGGTCC 62.487 72.222 20.34 11.35 42.73 4.46
599 603 3.740397 CTACGTGACGGCGGTCCA 61.740 66.667 20.34 2.99 42.73 4.02
600 604 3.678717 CTACGTGACGGCGGTCCAG 62.679 68.421 20.34 15.96 42.73 3.86
604 608 3.770040 TGACGGCGGTCCAGATGG 61.770 66.667 20.34 0.00 42.73 3.51
620 624 4.629779 GGGTACCGTGTTGGATGG 57.370 61.111 5.65 0.00 40.86 3.51
629 633 4.801019 CCGTGTTGGATGGCAAATTGCA 62.801 50.000 20.27 6.44 43.13 4.08
671 675 3.317993 ACAGTTGTATGTGTTTTGAGGGC 59.682 43.478 0.00 0.00 30.46 5.19
672 676 2.890945 AGTTGTATGTGTTTTGAGGGCC 59.109 45.455 0.00 0.00 0.00 5.80
673 677 1.917872 TGTATGTGTTTTGAGGGCCC 58.082 50.000 16.46 16.46 0.00 5.80
676 680 2.597510 GTGTTTTGAGGGCCCGCT 60.598 61.111 27.03 4.81 0.00 5.52
687 691 1.319614 GGGCCCGCTTTAAAGATGCA 61.320 55.000 19.48 0.00 0.00 3.96
688 692 0.746659 GGCCCGCTTTAAAGATGCAT 59.253 50.000 19.48 0.00 0.00 3.96
693 697 4.267690 GCCCGCTTTAAAGATGCATTAAAC 59.732 41.667 19.48 0.00 31.08 2.01
694 698 5.406649 CCCGCTTTAAAGATGCATTAAACA 58.593 37.500 19.48 0.00 31.08 2.83
695 699 5.288472 CCCGCTTTAAAGATGCATTAAACAC 59.712 40.000 19.48 0.00 31.08 3.32
697 701 6.033831 CCGCTTTAAAGATGCATTAAACACTG 59.966 38.462 19.48 0.00 31.08 3.66
700 704 9.787532 GCTTTAAAGATGCATTAAACACTGATA 57.212 29.630 19.48 0.00 31.08 2.15
748 929 6.071616 GGTGGACATTATAAAGTTGAAGCCAA 60.072 38.462 0.00 0.00 0.00 4.52
773 954 5.859205 AAAAGACTGACAAAAGCCAGAAT 57.141 34.783 0.00 0.00 34.65 2.40
777 958 4.889409 AGACTGACAAAAGCCAGAATCAAA 59.111 37.500 0.00 0.00 34.65 2.69
801 982 2.581354 AGGCCATCTGCGTCACTC 59.419 61.111 5.01 0.00 42.61 3.51
893 1075 2.155194 CAGACAGAGTAGCGCACGC 61.155 63.158 11.47 6.99 42.33 5.34
936 1118 4.502016 GAAGCTGTAGTGTAAACCCTACC 58.498 47.826 0.00 0.00 34.04 3.18
944 1126 7.642186 TGTAGTGTAAACCCTACCTATACTCA 58.358 38.462 1.13 0.00 34.04 3.41
1075 1277 4.697756 ACCACCACCGCATCCACG 62.698 66.667 0.00 0.00 0.00 4.94
1166 1368 0.818296 ACATCGGTTCCTCTTCCTCG 59.182 55.000 0.00 0.00 0.00 4.63
1174 1376 2.359967 CCTCTTCCTCGTCCCCACC 61.360 68.421 0.00 0.00 0.00 4.61
1321 1529 2.445654 GGGCAGAGGAGGAGGAGG 60.446 72.222 0.00 0.00 0.00 4.30
1322 1530 2.693017 GGCAGAGGAGGAGGAGGA 59.307 66.667 0.00 0.00 0.00 3.71
1323 1531 1.457455 GGCAGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1324 1532 1.457455 GCAGAGGAGGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1325 1533 1.943730 GCAGAGGAGGAGGAGGAGGA 61.944 65.000 0.00 0.00 0.00 3.71
1326 1534 0.633921 CAGAGGAGGAGGAGGAGGAA 59.366 60.000 0.00 0.00 0.00 3.36
1433 1657 1.211949 CCCTCGCTAATTTCTCCCCAA 59.788 52.381 0.00 0.00 0.00 4.12
1439 1663 2.879026 GCTAATTTCTCCCCAATCCGTC 59.121 50.000 0.00 0.00 0.00 4.79
1480 1714 2.938451 TGTGTCTTCTGCAACTCTGTTG 59.062 45.455 6.12 6.12 0.00 3.33
1482 1716 2.092968 TGTCTTCTGCAACTCTGTTGGT 60.093 45.455 11.64 0.00 0.00 3.67
1546 1780 3.918220 GCGGCTCAAGCGACGATG 61.918 66.667 0.00 0.00 43.26 3.84
1547 1781 3.257561 CGGCTCAAGCGACGATGG 61.258 66.667 0.00 0.00 43.26 3.51
1548 1782 2.184322 GGCTCAAGCGACGATGGA 59.816 61.111 0.00 0.00 43.26 3.41
1549 1783 1.880340 GGCTCAAGCGACGATGGAG 60.880 63.158 13.19 13.19 43.26 3.86
1550 1784 1.153745 GCTCAAGCGACGATGGAGT 60.154 57.895 18.18 0.00 0.00 3.85
1551 1785 0.737715 GCTCAAGCGACGATGGAGTT 60.738 55.000 18.18 0.00 0.00 3.01
1647 1883 3.616956 TTTTGCGAGAGGAGATGACAT 57.383 42.857 0.00 0.00 0.00 3.06
1648 1884 3.616956 TTTGCGAGAGGAGATGACATT 57.383 42.857 0.00 0.00 0.00 2.71
1649 1885 4.736126 TTTGCGAGAGGAGATGACATTA 57.264 40.909 0.00 0.00 0.00 1.90
1650 1886 4.944619 TTGCGAGAGGAGATGACATTAT 57.055 40.909 0.00 0.00 0.00 1.28
1651 1887 4.944619 TGCGAGAGGAGATGACATTATT 57.055 40.909 0.00 0.00 0.00 1.40
1652 1888 4.876125 TGCGAGAGGAGATGACATTATTC 58.124 43.478 0.00 0.00 0.00 1.75
1653 1889 4.342092 TGCGAGAGGAGATGACATTATTCA 59.658 41.667 0.00 0.00 0.00 2.57
1654 1890 5.163416 TGCGAGAGGAGATGACATTATTCAA 60.163 40.000 0.00 0.00 0.00 2.69
1655 1891 5.755375 GCGAGAGGAGATGACATTATTCAAA 59.245 40.000 0.00 0.00 0.00 2.69
1656 1892 6.258727 GCGAGAGGAGATGACATTATTCAAAA 59.741 38.462 0.00 0.00 0.00 2.44
1657 1893 7.041508 GCGAGAGGAGATGACATTATTCAAAAT 60.042 37.037 0.00 0.00 0.00 1.82
1658 1894 9.481340 CGAGAGGAGATGACATTATTCAAAATA 57.519 33.333 0.00 0.00 0.00 1.40
1666 1902 9.455847 GATGACATTATTCAAAATACTTCTGGC 57.544 33.333 0.00 0.00 0.00 4.85
1694 1930 2.240500 GCTCAGCGGGCAGTATTCG 61.241 63.158 0.00 0.00 0.00 3.34
1723 1959 0.320334 TGATGCTCCGCGTTGAGAAA 60.320 50.000 15.39 4.07 34.11 2.52
1726 1962 0.796312 TGCTCCGCGTTGAGAAATTC 59.204 50.000 15.39 0.00 34.11 2.17
1737 1973 5.603452 CGTTGAGAAATTCTGTTTCGAGAG 58.397 41.667 0.00 0.00 33.86 3.20
1742 1978 4.284746 AGAAATTCTGTTTCGAGAGGGAGT 59.715 41.667 0.00 0.00 33.86 3.85
1763 1999 6.596106 GGAGTTTGGTTTTTGCCTTTTAAGAA 59.404 34.615 0.00 0.00 0.00 2.52
1764 2000 7.282224 GGAGTTTGGTTTTTGCCTTTTAAGAAT 59.718 33.333 0.00 0.00 0.00 2.40
1765 2001 9.320352 GAGTTTGGTTTTTGCCTTTTAAGAATA 57.680 29.630 0.00 0.00 0.00 1.75
1767 2003 7.701809 TTGGTTTTTGCCTTTTAAGAATACG 57.298 32.000 0.00 0.00 0.00 3.06
1771 2007 5.455056 TTTGCCTTTTAAGAATACGCCAA 57.545 34.783 0.00 0.00 0.00 4.52
1825 2061 7.532682 TCATAAAGGAAAACAGTGTTTTTGC 57.467 32.000 29.49 19.56 37.14 3.68
1826 2062 4.919677 AAAGGAAAACAGTGTTTTTGCG 57.080 36.364 29.49 0.00 40.60 4.85
1827 2063 3.586100 AGGAAAACAGTGTTTTTGCGT 57.414 38.095 29.49 18.47 40.60 5.24
1828 2064 3.249917 AGGAAAACAGTGTTTTTGCGTG 58.750 40.909 29.49 0.00 40.60 5.34
1829 2065 2.990514 GGAAAACAGTGTTTTTGCGTGT 59.009 40.909 29.49 10.51 28.77 4.49
1830 2066 4.082679 AGGAAAACAGTGTTTTTGCGTGTA 60.083 37.500 29.49 0.00 40.60 2.90
1831 2067 4.621886 GGAAAACAGTGTTTTTGCGTGTAA 59.378 37.500 29.49 0.00 28.77 2.41
1832 2068 5.289917 GGAAAACAGTGTTTTTGCGTGTAAT 59.710 36.000 29.49 8.45 28.77 1.89
1833 2069 6.472808 GGAAAACAGTGTTTTTGCGTGTAATA 59.527 34.615 29.49 0.00 28.77 0.98
1834 2070 7.009357 GGAAAACAGTGTTTTTGCGTGTAATAA 59.991 33.333 29.49 0.00 28.77 1.40
1835 2071 6.799786 AACAGTGTTTTTGCGTGTAATAAC 57.200 33.333 1.64 0.00 0.00 1.89
1836 2072 6.126568 ACAGTGTTTTTGCGTGTAATAACT 57.873 33.333 0.00 0.00 0.00 2.24
1900 2136 6.270463 TGAAAACCACAGTATTACTCTGGGTA 59.730 38.462 18.79 0.00 32.77 3.69
2214 3737 2.727916 CGGTCCTAAATTCTTTGTGCGC 60.728 50.000 0.00 0.00 0.00 6.09
2260 3783 1.541379 GCTAGCTAGCTACTCCCTCC 58.459 60.000 33.71 5.30 45.62 4.30
2261 3784 1.816074 CTAGCTAGCTACTCCCTCCG 58.184 60.000 20.67 4.73 0.00 4.63
2262 3785 1.072648 CTAGCTAGCTACTCCCTCCGT 59.927 57.143 20.67 0.00 0.00 4.69
2263 3786 0.259356 AGCTAGCTACTCCCTCCGTT 59.741 55.000 17.69 0.00 0.00 4.44
2264 3787 0.669619 GCTAGCTACTCCCTCCGTTC 59.330 60.000 7.70 0.00 0.00 3.95
2265 3788 1.320507 CTAGCTACTCCCTCCGTTCC 58.679 60.000 0.00 0.00 0.00 3.62
2266 3789 0.465097 TAGCTACTCCCTCCGTTCCG 60.465 60.000 0.00 0.00 0.00 4.30
2267 3790 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
2268 3791 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
2269 3792 1.180029 CTACTCCCTCCGTTCCGAAA 58.820 55.000 0.00 0.00 0.00 3.46
2270 3793 1.755380 CTACTCCCTCCGTTCCGAAAT 59.245 52.381 0.00 0.00 0.00 2.17
2271 3794 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2272 3795 2.395619 ACTCCCTCCGTTCCGAAATAT 58.604 47.619 0.00 0.00 0.00 1.28
2273 3796 2.770232 ACTCCCTCCGTTCCGAAATATT 59.230 45.455 0.00 0.00 0.00 1.28
2274 3797 3.199289 ACTCCCTCCGTTCCGAAATATTT 59.801 43.478 0.00 0.00 0.00 1.40
2275 3798 3.537580 TCCCTCCGTTCCGAAATATTTG 58.462 45.455 5.17 0.00 0.00 2.32
2276 3799 3.054948 TCCCTCCGTTCCGAAATATTTGT 60.055 43.478 5.17 0.00 0.00 2.83
2277 3800 3.692593 CCCTCCGTTCCGAAATATTTGTT 59.307 43.478 5.17 0.00 0.00 2.83
2278 3801 4.157105 CCCTCCGTTCCGAAATATTTGTTT 59.843 41.667 5.17 0.00 0.00 2.83
2279 3802 5.336134 CCCTCCGTTCCGAAATATTTGTTTT 60.336 40.000 5.17 0.00 0.00 2.43
2280 3803 6.153756 CCTCCGTTCCGAAATATTTGTTTTT 58.846 36.000 5.17 0.00 0.00 1.94
2281 3804 6.307077 CCTCCGTTCCGAAATATTTGTTTTTC 59.693 38.462 5.17 0.00 0.00 2.29
2282 3805 6.972722 TCCGTTCCGAAATATTTGTTTTTCT 58.027 32.000 5.17 0.00 31.20 2.52
2283 3806 8.097078 TCCGTTCCGAAATATTTGTTTTTCTA 57.903 30.769 5.17 0.00 31.20 2.10
2284 3807 8.231837 TCCGTTCCGAAATATTTGTTTTTCTAG 58.768 33.333 5.17 0.00 31.20 2.43
2285 3808 8.019094 CCGTTCCGAAATATTTGTTTTTCTAGT 58.981 33.333 5.17 0.00 31.20 2.57
2286 3809 9.047871 CGTTCCGAAATATTTGTTTTTCTAGTC 57.952 33.333 5.17 0.00 31.20 2.59
2287 3810 9.887406 GTTCCGAAATATTTGTTTTTCTAGTCA 57.113 29.630 5.17 0.00 31.20 3.41
2299 3822 9.528018 TTGTTTTTCTAGTCATTTCAAATGGAC 57.472 29.630 10.30 7.30 0.00 4.02
2300 3823 8.912988 TGTTTTTCTAGTCATTTCAAATGGACT 58.087 29.630 10.30 13.37 42.76 3.85
2303 3826 8.561738 TTTCTAGTCATTTCAAATGGACTACC 57.438 34.615 10.30 0.00 40.76 3.18
2358 3881 8.261492 AGTGTAGATTCACTTATTTTGCTCTG 57.739 34.615 0.00 0.00 44.92 3.35
2359 3882 7.880195 AGTGTAGATTCACTTATTTTGCTCTGT 59.120 33.333 0.00 0.00 44.92 3.41
2360 3883 9.151471 GTGTAGATTCACTTATTTTGCTCTGTA 57.849 33.333 0.00 0.00 35.68 2.74
2361 3884 9.890629 TGTAGATTCACTTATTTTGCTCTGTAT 57.109 29.630 0.00 0.00 0.00 2.29
2363 3886 8.798859 AGATTCACTTATTTTGCTCTGTATGT 57.201 30.769 0.00 0.00 0.00 2.29
2364 3887 9.890629 AGATTCACTTATTTTGCTCTGTATGTA 57.109 29.630 0.00 0.00 0.00 2.29
2366 3889 9.672673 ATTCACTTATTTTGCTCTGTATGTAGT 57.327 29.630 0.00 0.00 0.00 2.73
2367 3890 8.703604 TCACTTATTTTGCTCTGTATGTAGTC 57.296 34.615 0.00 0.00 0.00 2.59
2368 3891 8.311109 TCACTTATTTTGCTCTGTATGTAGTCA 58.689 33.333 0.00 0.00 0.00 3.41
2369 3892 9.102757 CACTTATTTTGCTCTGTATGTAGTCAT 57.897 33.333 0.00 0.00 38.00 3.06
2370 3893 9.672673 ACTTATTTTGCTCTGTATGTAGTCATT 57.327 29.630 0.00 0.00 35.70 2.57
2373 3896 7.744087 TTTTGCTCTGTATGTAGTCATTTGT 57.256 32.000 0.00 0.00 35.70 2.83
2374 3897 7.744087 TTTGCTCTGTATGTAGTCATTTGTT 57.256 32.000 0.00 0.00 35.70 2.83
2375 3898 6.726258 TGCTCTGTATGTAGTCATTTGTTG 57.274 37.500 0.00 0.00 35.70 3.33
2376 3899 6.463360 TGCTCTGTATGTAGTCATTTGTTGA 58.537 36.000 0.00 0.00 35.70 3.18
2377 3900 6.934083 TGCTCTGTATGTAGTCATTTGTTGAA 59.066 34.615 0.00 0.00 35.70 2.69
2378 3901 7.443879 TGCTCTGTATGTAGTCATTTGTTGAAA 59.556 33.333 0.00 0.00 35.70 2.69
2379 3902 8.454106 GCTCTGTATGTAGTCATTTGTTGAAAT 58.546 33.333 0.00 0.00 35.70 2.17
2410 3933 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2411 3934 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2412 3935 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.318332 GAGTGAAGACAATGTCACCATCA 58.682 43.478 16.38 10.86 44.30 3.07
18 19 2.135139 GCACGAGTGAAGACAATGTCA 58.865 47.619 16.38 0.00 34.60 3.58
19 20 2.135139 TGCACGAGTGAAGACAATGTC 58.865 47.619 5.02 5.02 0.00 3.06
39 40 6.422701 CAGTCATGAAGTTTTGTGATGCAATT 59.577 34.615 0.00 0.00 36.89 2.32
42 43 4.579753 TCAGTCATGAAGTTTTGTGATGCA 59.420 37.500 0.00 0.00 30.61 3.96
91 93 1.134340 ACCCTACAACTTGCACGTGAA 60.134 47.619 22.23 5.66 0.00 3.18
93 95 0.586319 CACCCTACAACTTGCACGTG 59.414 55.000 12.28 12.28 0.00 4.49
96 98 1.961793 TCACACCCTACAACTTGCAC 58.038 50.000 0.00 0.00 0.00 4.57
123 126 3.306917 TGCATGCTTTGTTTCATGAGG 57.693 42.857 20.33 0.00 41.82 3.86
127 130 5.753744 CAAAACATGCATGCTTTGTTTCAT 58.246 33.333 32.87 23.47 38.42 2.57
144 147 3.368948 GGACTTGACCTTTTGGCAAAACA 60.369 43.478 20.81 14.64 45.59 2.83
159 162 2.785972 GCGTAAGGGAAGGGGACTTGA 61.786 57.143 0.00 0.00 46.13 3.02
160 163 0.392595 GCGTAAGGGAAGGGGACTTG 60.393 60.000 0.00 0.00 46.13 3.16
201 205 2.353030 GTTTGCGTGCGTGGAACC 60.353 61.111 0.00 0.00 0.00 3.62
202 206 1.226435 TTGTTTGCGTGCGTGGAAC 60.226 52.632 0.00 0.00 0.00 3.62
242 246 6.809196 TGTTGTTTCAAAAGTAAAATGACGCT 59.191 30.769 0.00 0.00 0.00 5.07
257 261 5.109662 TGTTGACTTTCGTGTTGTTTCAA 57.890 34.783 0.00 0.00 0.00 2.69
308 312 0.391130 CATACACCACACCCGACAGG 60.391 60.000 0.00 0.00 43.78 4.00
309 313 0.320374 ACATACACCACACCCGACAG 59.680 55.000 0.00 0.00 0.00 3.51
310 314 0.319083 GACATACACCACACCCGACA 59.681 55.000 0.00 0.00 0.00 4.35
313 317 1.066502 TCATGACATACACCACACCCG 60.067 52.381 0.00 0.00 0.00 5.28
314 318 2.747446 GTTCATGACATACACCACACCC 59.253 50.000 0.00 0.00 0.00 4.61
315 319 2.415168 CGTTCATGACATACACCACACC 59.585 50.000 0.00 0.00 0.00 4.16
318 322 2.344441 CGTCGTTCATGACATACACCAC 59.656 50.000 0.00 0.00 38.84 4.16
320 324 2.597305 GACGTCGTTCATGACATACACC 59.403 50.000 0.00 0.00 38.84 4.16
321 325 3.239254 TGACGTCGTTCATGACATACAC 58.761 45.455 11.62 0.00 38.84 2.90
322 326 3.057806 ACTGACGTCGTTCATGACATACA 60.058 43.478 11.62 0.00 38.84 2.29
323 327 3.499048 ACTGACGTCGTTCATGACATAC 58.501 45.455 11.62 0.00 38.84 2.39
324 328 3.842732 ACTGACGTCGTTCATGACATA 57.157 42.857 11.62 0.00 38.84 2.29
325 329 2.724977 ACTGACGTCGTTCATGACAT 57.275 45.000 11.62 0.00 38.84 3.06
326 330 2.809696 TCTACTGACGTCGTTCATGACA 59.190 45.455 11.62 0.00 38.84 3.58
327 331 3.418094 CTCTACTGACGTCGTTCATGAC 58.582 50.000 11.62 0.00 35.49 3.06
352 356 1.285023 CGCGGATAGGTACCCTTCG 59.715 63.158 8.74 8.39 34.61 3.79
360 364 1.120530 AAATCAGTCCGCGGATAGGT 58.879 50.000 33.58 20.43 0.00 3.08
364 368 0.748005 CCCAAAATCAGTCCGCGGAT 60.748 55.000 33.58 17.55 0.00 4.18
367 371 1.501741 CACCCAAAATCAGTCCGCG 59.498 57.895 0.00 0.00 0.00 6.46
374 378 0.893270 CCGCTGTCCACCCAAAATCA 60.893 55.000 0.00 0.00 0.00 2.57
379 383 2.535485 CTATGCCGCTGTCCACCCAA 62.535 60.000 0.00 0.00 0.00 4.12
393 397 1.367840 CTACCCGCCTGGACTATGC 59.632 63.158 0.00 0.00 37.49 3.14
417 421 2.438795 GTTTGCAGCCCCCACCTA 59.561 61.111 0.00 0.00 0.00 3.08
438 442 0.179089 CCTCTGACCAGGCATTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
452 456 0.692419 ATGTACCTCCCTGGCCTCTG 60.692 60.000 3.32 0.00 40.22 3.35
456 460 0.036875 GCATATGTACCTCCCTGGCC 59.963 60.000 4.29 0.00 40.22 5.36
460 464 0.959553 CGACGCATATGTACCTCCCT 59.040 55.000 4.29 0.00 0.00 4.20
472 476 2.107750 CCTCATCTGCCGACGCAT 59.892 61.111 0.00 0.00 46.11 4.73
477 481 2.060383 CACCCTCCTCATCTGCCGA 61.060 63.158 0.00 0.00 0.00 5.54
482 486 1.350351 GCATATGCACCCTCCTCATCT 59.650 52.381 22.84 0.00 41.59 2.90
490 494 2.485479 CCTTACTTCGCATATGCACCCT 60.485 50.000 26.52 9.02 42.21 4.34
507 511 3.056107 CACTCCGTTCATGAGTTCCCTTA 60.056 47.826 0.00 0.00 41.02 2.69
512 516 2.743636 TCCACTCCGTTCATGAGTTC 57.256 50.000 0.00 0.00 41.02 3.01
530 534 0.326927 TCCCCGTCCCATTGTTCTTC 59.673 55.000 0.00 0.00 0.00 2.87
532 536 0.328258 CTTCCCCGTCCCATTGTTCT 59.672 55.000 0.00 0.00 0.00 3.01
542 546 2.622436 CACTCAAATCTCTTCCCCGTC 58.378 52.381 0.00 0.00 0.00 4.79
551 555 3.703001 TCCTTGACCCACTCAAATCTC 57.297 47.619 0.00 0.00 38.47 2.75
566 570 2.755655 ACGTAGGACTCTGACATCCTTG 59.244 50.000 10.24 7.12 43.09 3.61
567 571 2.755655 CACGTAGGACTCTGACATCCTT 59.244 50.000 10.24 0.00 43.09 3.36
569 573 2.097791 GTCACGTAGGACTCTGACATCC 59.902 54.545 0.00 0.00 34.38 3.51
570 574 2.223066 CGTCACGTAGGACTCTGACATC 60.223 54.545 4.72 0.00 35.63 3.06
571 575 1.738350 CGTCACGTAGGACTCTGACAT 59.262 52.381 4.72 0.00 35.63 3.06
572 576 1.154197 CGTCACGTAGGACTCTGACA 58.846 55.000 4.72 0.00 35.63 3.58
573 577 0.447011 CCGTCACGTAGGACTCTGAC 59.553 60.000 0.00 0.00 35.63 3.51
574 578 1.303799 GCCGTCACGTAGGACTCTGA 61.304 60.000 7.92 0.00 35.63 3.27
575 579 1.136984 GCCGTCACGTAGGACTCTG 59.863 63.158 7.92 0.00 35.63 3.35
576 580 2.396955 CGCCGTCACGTAGGACTCT 61.397 63.158 7.92 0.00 35.63 3.24
577 581 2.099831 CGCCGTCACGTAGGACTC 59.900 66.667 7.92 0.00 35.63 3.36
578 582 3.437795 CCGCCGTCACGTAGGACT 61.438 66.667 2.26 0.00 35.63 3.85
579 583 3.673867 GACCGCCGTCACGTAGGAC 62.674 68.421 14.23 5.22 38.99 3.85
580 584 3.434319 GACCGCCGTCACGTAGGA 61.434 66.667 14.23 0.00 38.99 2.94
581 585 4.487412 GGACCGCCGTCACGTAGG 62.487 72.222 7.50 6.64 41.13 3.18
582 586 3.678717 CTGGACCGCCGTCACGTAG 62.679 68.421 7.50 0.00 41.13 3.51
583 587 3.740397 CTGGACCGCCGTCACGTA 61.740 66.667 7.50 0.00 41.13 3.57
585 589 4.129737 ATCTGGACCGCCGTCACG 62.130 66.667 7.50 0.00 41.13 4.35
586 590 2.509336 CATCTGGACCGCCGTCAC 60.509 66.667 7.50 0.00 41.13 3.67
587 591 3.770040 CCATCTGGACCGCCGTCA 61.770 66.667 7.50 0.00 41.13 4.35
588 592 4.530857 CCCATCTGGACCGCCGTC 62.531 72.222 0.00 0.00 37.39 4.79
589 593 3.968837 TACCCATCTGGACCGCCGT 62.969 63.158 0.00 0.00 37.39 5.68
590 594 3.151710 TACCCATCTGGACCGCCG 61.152 66.667 0.00 0.00 37.39 6.46
591 595 2.504519 GTACCCATCTGGACCGCC 59.495 66.667 0.00 0.00 37.39 6.13
592 596 2.504519 GGTACCCATCTGGACCGC 59.495 66.667 0.00 0.00 37.39 5.68
593 597 2.812499 CGGTACCCATCTGGACCG 59.188 66.667 13.21 13.21 45.11 4.79
594 598 1.262640 ACACGGTACCCATCTGGACC 61.263 60.000 6.25 0.00 37.39 4.46
595 599 0.611714 AACACGGTACCCATCTGGAC 59.388 55.000 6.25 0.00 37.39 4.02
596 600 0.611200 CAACACGGTACCCATCTGGA 59.389 55.000 6.25 0.00 37.39 3.86
597 601 0.392461 CCAACACGGTACCCATCTGG 60.392 60.000 6.25 4.86 41.37 3.86
598 602 0.611200 TCCAACACGGTACCCATCTG 59.389 55.000 6.25 0.00 35.57 2.90
599 603 1.209504 CATCCAACACGGTACCCATCT 59.790 52.381 6.25 0.00 35.57 2.90
600 604 1.663695 CATCCAACACGGTACCCATC 58.336 55.000 6.25 0.00 35.57 3.51
601 605 0.254747 CCATCCAACACGGTACCCAT 59.745 55.000 6.25 0.00 35.57 4.00
604 608 0.606944 TTGCCATCCAACACGGTACC 60.607 55.000 0.16 0.16 35.57 3.34
611 615 2.492012 GTTGCAATTTGCCATCCAACA 58.508 42.857 18.27 0.00 44.23 3.33
620 624 0.508213 GCTGTTCGGTTGCAATTTGC 59.492 50.000 14.49 14.49 45.29 3.68
629 633 0.888619 TCAGATCGAGCTGTTCGGTT 59.111 50.000 28.24 2.30 44.20 4.44
634 638 3.062763 CAACTGTTCAGATCGAGCTGTT 58.937 45.455 28.24 13.48 44.18 3.16
636 640 2.681706 ACAACTGTTCAGATCGAGCTG 58.318 47.619 24.40 24.40 37.24 4.24
671 675 5.288472 GTGTTTAATGCATCTTTAAAGCGGG 59.712 40.000 10.51 3.63 31.19 6.13
672 676 6.033831 CAGTGTTTAATGCATCTTTAAAGCGG 59.966 38.462 10.51 6.02 31.19 5.52
673 677 6.801377 TCAGTGTTTAATGCATCTTTAAAGCG 59.199 34.615 10.51 5.33 31.19 4.68
703 707 8.626526 GTCCACCTGAATTTCTTTTAAGTAACA 58.373 33.333 0.00 0.00 0.00 2.41
704 708 8.626526 TGTCCACCTGAATTTCTTTTAAGTAAC 58.373 33.333 0.00 0.00 0.00 2.50
705 709 8.754991 TGTCCACCTGAATTTCTTTTAAGTAA 57.245 30.769 0.00 0.00 0.00 2.24
706 710 8.934023 ATGTCCACCTGAATTTCTTTTAAGTA 57.066 30.769 0.00 0.00 0.00 2.24
707 711 7.839680 ATGTCCACCTGAATTTCTTTTAAGT 57.160 32.000 0.00 0.00 0.00 2.24
715 896 9.573133 CAACTTTATAATGTCCACCTGAATTTC 57.427 33.333 4.61 0.00 0.00 2.17
766 947 2.098770 GCCTCAGATGTTTGATTCTGGC 59.901 50.000 0.00 0.00 39.84 4.85
773 954 2.942752 GCAGATGGCCTCAGATGTTTGA 60.943 50.000 3.32 0.00 36.11 2.69
777 958 1.145598 CGCAGATGGCCTCAGATGT 59.854 57.895 3.32 0.00 40.31 3.06
837 1018 4.154195 GCCTCGCTCTAAAATCACAGAAAA 59.846 41.667 0.00 0.00 0.00 2.29
893 1075 2.429236 AGAACGTCAGAGCACGCG 60.429 61.111 3.53 3.53 43.93 6.01
936 1118 1.400371 CCGCGCTACTGCTGAGTATAG 60.400 57.143 5.56 0.00 34.05 1.31
944 1126 4.477975 GACGTCCGCGCTACTGCT 62.478 66.667 5.56 0.00 42.83 4.24
955 1141 1.135731 CTCTCTGTCTGCGACGTCC 59.864 63.158 10.58 3.43 34.95 4.79
957 1143 1.302383 CTCCTCTCTGTCTGCGACGT 61.302 60.000 0.00 0.00 34.95 4.34
974 1160 3.043340 GCTCTGTTTCTCGAGCCTC 57.957 57.895 7.81 0.58 45.21 4.70
1075 1277 4.699522 GTGGTGGCGGAGGTGGAC 62.700 72.222 0.00 0.00 0.00 4.02
1129 1331 1.150308 TGTGGTGGTGGTGGTGATG 59.850 57.895 0.00 0.00 0.00 3.07
1130 1332 1.150536 GTGTGGTGGTGGTGGTGAT 59.849 57.895 0.00 0.00 0.00 3.06
1131 1333 1.640593 ATGTGTGGTGGTGGTGGTGA 61.641 55.000 0.00 0.00 0.00 4.02
1307 1515 0.633921 TTCCTCCTCCTCCTCCTCTG 59.366 60.000 0.00 0.00 0.00 3.35
1325 1533 1.068585 GTCAGGACGAACACCGGTT 59.931 57.895 2.97 0.00 43.93 4.44
1326 1534 2.732658 GTCAGGACGAACACCGGT 59.267 61.111 0.00 0.00 43.93 5.28
1433 1657 2.315925 ATCGAACAAGCATGACGGAT 57.684 45.000 0.00 0.00 33.51 4.18
1439 1663 5.914635 ACACAAAAGTTATCGAACAAGCATG 59.085 36.000 0.00 0.00 38.10 4.06
1545 1779 0.615331 GGTCTGCATCTCCAACTCCA 59.385 55.000 0.00 0.00 0.00 3.86
1546 1780 0.460987 CGGTCTGCATCTCCAACTCC 60.461 60.000 0.00 0.00 0.00 3.85
1547 1781 0.460987 CCGGTCTGCATCTCCAACTC 60.461 60.000 0.00 0.00 0.00 3.01
1548 1782 0.904865 TCCGGTCTGCATCTCCAACT 60.905 55.000 0.00 0.00 0.00 3.16
1549 1783 0.741221 GTCCGGTCTGCATCTCCAAC 60.741 60.000 0.00 0.00 0.00 3.77
1550 1784 1.191489 TGTCCGGTCTGCATCTCCAA 61.191 55.000 0.00 0.00 0.00 3.53
1551 1785 1.607801 CTGTCCGGTCTGCATCTCCA 61.608 60.000 0.00 0.00 0.00 3.86
1647 1883 8.862325 TCAAGAGCCAGAAGTATTTTGAATAA 57.138 30.769 0.00 0.00 0.00 1.40
1648 1884 9.113838 GATCAAGAGCCAGAAGTATTTTGAATA 57.886 33.333 0.00 0.00 0.00 1.75
1649 1885 7.613022 TGATCAAGAGCCAGAAGTATTTTGAAT 59.387 33.333 0.00 0.00 0.00 2.57
1650 1886 6.942005 TGATCAAGAGCCAGAAGTATTTTGAA 59.058 34.615 0.00 0.00 0.00 2.69
1651 1887 6.475504 TGATCAAGAGCCAGAAGTATTTTGA 58.524 36.000 0.00 0.00 0.00 2.69
1652 1888 6.677431 GCTGATCAAGAGCCAGAAGTATTTTG 60.677 42.308 0.00 0.00 0.00 2.44
1653 1889 5.356470 GCTGATCAAGAGCCAGAAGTATTTT 59.644 40.000 0.00 0.00 0.00 1.82
1654 1890 4.880696 GCTGATCAAGAGCCAGAAGTATTT 59.119 41.667 0.00 0.00 0.00 1.40
1655 1891 4.163839 AGCTGATCAAGAGCCAGAAGTATT 59.836 41.667 0.00 0.00 37.12 1.89
1656 1892 3.710677 AGCTGATCAAGAGCCAGAAGTAT 59.289 43.478 0.00 0.00 37.12 2.12
1657 1893 3.102972 AGCTGATCAAGAGCCAGAAGTA 58.897 45.455 0.00 0.00 37.12 2.24
1658 1894 1.907936 AGCTGATCAAGAGCCAGAAGT 59.092 47.619 0.00 0.00 37.12 3.01
1659 1895 2.093606 TGAGCTGATCAAGAGCCAGAAG 60.094 50.000 0.00 0.00 37.12 2.85
1666 1902 0.530211 CCCGCTGAGCTGATCAAGAG 60.530 60.000 1.78 0.00 37.52 2.85
1712 1948 2.896410 CGAAACAGAATTTCTCAACGCG 59.104 45.455 3.53 3.53 0.00 6.01
1723 1959 4.319177 CAAACTCCCTCTCGAAACAGAAT 58.681 43.478 0.00 0.00 0.00 2.40
1726 1962 2.224305 ACCAAACTCCCTCTCGAAACAG 60.224 50.000 0.00 0.00 0.00 3.16
1737 1973 3.275617 AAAGGCAAAAACCAAACTCCC 57.724 42.857 0.00 0.00 0.00 4.30
1742 1978 7.254488 GCGTATTCTTAAAAGGCAAAAACCAAA 60.254 33.333 0.00 0.00 0.00 3.28
1763 1999 7.364970 GGATATAAAATTCCGTTTTGGCGTAT 58.635 34.615 0.00 0.00 40.17 3.06
1764 2000 6.727215 GGATATAAAATTCCGTTTTGGCGTA 58.273 36.000 0.00 0.00 40.17 4.42
1765 2001 5.584442 GGATATAAAATTCCGTTTTGGCGT 58.416 37.500 0.00 0.00 40.17 5.68
1818 2054 8.889000 CAAACTAGAGTTATTACACGCAAAAAC 58.111 33.333 0.00 0.00 37.25 2.43
1822 2058 5.121142 GCCAAACTAGAGTTATTACACGCAA 59.879 40.000 0.00 0.00 37.25 4.85
1823 2059 4.628333 GCCAAACTAGAGTTATTACACGCA 59.372 41.667 0.00 0.00 37.25 5.24
1824 2060 4.628333 TGCCAAACTAGAGTTATTACACGC 59.372 41.667 0.00 0.00 37.25 5.34
1825 2061 5.220416 GCTGCCAAACTAGAGTTATTACACG 60.220 44.000 0.00 0.00 37.25 4.49
1826 2062 5.642063 TGCTGCCAAACTAGAGTTATTACAC 59.358 40.000 0.00 0.00 37.25 2.90
1827 2063 5.800296 TGCTGCCAAACTAGAGTTATTACA 58.200 37.500 0.00 0.00 37.25 2.41
1828 2064 6.737254 TTGCTGCCAAACTAGAGTTATTAC 57.263 37.500 0.00 0.00 37.25 1.89
1829 2065 6.940298 ACTTTGCTGCCAAACTAGAGTTATTA 59.060 34.615 0.00 0.00 37.25 0.98
1830 2066 5.770162 ACTTTGCTGCCAAACTAGAGTTATT 59.230 36.000 0.00 0.00 37.25 1.40
1831 2067 5.316987 ACTTTGCTGCCAAACTAGAGTTAT 58.683 37.500 0.00 0.00 37.25 1.89
1832 2068 4.714632 ACTTTGCTGCCAAACTAGAGTTA 58.285 39.130 0.00 0.00 37.25 2.24
1833 2069 3.555966 ACTTTGCTGCCAAACTAGAGTT 58.444 40.909 0.00 0.00 40.50 3.01
1834 2070 3.214696 ACTTTGCTGCCAAACTAGAGT 57.785 42.857 0.00 0.00 36.09 3.24
1835 2071 4.574599 AAACTTTGCTGCCAAACTAGAG 57.425 40.909 0.00 0.00 36.09 2.43
1836 2072 5.337578 AAAAACTTTGCTGCCAAACTAGA 57.662 34.783 0.00 0.00 36.09 2.43
1900 2136 5.557866 AGAAAACCGTAGTATTCTTTGCCT 58.442 37.500 0.00 0.00 0.00 4.75
2052 2289 5.308976 AGGATGGTATTATGTGTGCATGA 57.691 39.130 0.00 0.00 36.58 3.07
2178 3701 0.454600 GACCGGCTCGAAGTACATGA 59.545 55.000 0.00 0.00 0.00 3.07
2214 3737 6.505039 TTCAGTATAAATGACGCATGTACG 57.495 37.500 0.00 0.00 39.50 3.67
2261 3784 9.887406 TGACTAGAAAAACAAATATTTCGGAAC 57.113 29.630 0.00 0.00 39.83 3.62
2273 3796 9.528018 GTCCATTTGAAATGACTAGAAAAACAA 57.472 29.630 18.82 0.00 0.00 2.83
2274 3797 8.912988 AGTCCATTTGAAATGACTAGAAAAACA 58.087 29.630 18.82 0.00 0.00 2.83
2277 3800 9.010029 GGTAGTCCATTTGAAATGACTAGAAAA 57.990 33.333 18.82 3.52 0.00 2.29
2278 3801 8.160765 TGGTAGTCCATTTGAAATGACTAGAAA 58.839 33.333 18.82 9.60 39.03 2.52
2279 3802 7.606456 GTGGTAGTCCATTTGAAATGACTAGAA 59.394 37.037 18.82 11.44 46.20 2.10
2280 3803 7.103641 GTGGTAGTCCATTTGAAATGACTAGA 58.896 38.462 18.82 5.13 46.20 2.43
2281 3804 6.878923 TGTGGTAGTCCATTTGAAATGACTAG 59.121 38.462 18.82 2.80 46.20 2.57
2282 3805 6.774673 TGTGGTAGTCCATTTGAAATGACTA 58.225 36.000 18.82 18.27 46.20 2.59
2283 3806 5.630121 TGTGGTAGTCCATTTGAAATGACT 58.370 37.500 18.82 19.11 46.20 3.41
2284 3807 5.957842 TGTGGTAGTCCATTTGAAATGAC 57.042 39.130 18.82 13.92 46.20 3.06
2285 3808 7.336679 CAGTATGTGGTAGTCCATTTGAAATGA 59.663 37.037 18.82 3.09 46.20 2.57
2286 3809 7.336679 TCAGTATGTGGTAGTCCATTTGAAATG 59.663 37.037 10.84 10.84 46.20 2.32
2287 3810 7.402054 TCAGTATGTGGTAGTCCATTTGAAAT 58.598 34.615 0.00 0.00 46.20 2.17
2288 3811 6.774673 TCAGTATGTGGTAGTCCATTTGAAA 58.225 36.000 0.00 0.00 46.20 2.69
2289 3812 6.367374 TCAGTATGTGGTAGTCCATTTGAA 57.633 37.500 0.00 0.00 46.20 2.69
2290 3813 6.070251 ACATCAGTATGTGGTAGTCCATTTGA 60.070 38.462 0.00 0.00 44.79 2.69
2291 3814 6.115446 ACATCAGTATGTGGTAGTCCATTTG 58.885 40.000 0.00 0.00 44.79 2.32
2292 3815 6.313519 ACATCAGTATGTGGTAGTCCATTT 57.686 37.500 0.00 0.00 44.79 2.32
2293 3816 5.957771 ACATCAGTATGTGGTAGTCCATT 57.042 39.130 0.00 0.00 44.79 3.16
2334 3857 8.034058 ACAGAGCAAAATAAGTGAATCTACAC 57.966 34.615 0.00 0.00 40.60 2.90
2335 3858 9.890629 ATACAGAGCAAAATAAGTGAATCTACA 57.109 29.630 0.00 0.00 0.00 2.74
2337 3860 9.890629 ACATACAGAGCAAAATAAGTGAATCTA 57.109 29.630 0.00 0.00 0.00 1.98
2338 3861 8.798859 ACATACAGAGCAAAATAAGTGAATCT 57.201 30.769 0.00 0.00 0.00 2.40
2340 3863 9.672673 ACTACATACAGAGCAAAATAAGTGAAT 57.327 29.630 0.00 0.00 0.00 2.57
2341 3864 9.151471 GACTACATACAGAGCAAAATAAGTGAA 57.849 33.333 0.00 0.00 0.00 3.18
2342 3865 8.311109 TGACTACATACAGAGCAAAATAAGTGA 58.689 33.333 0.00 0.00 0.00 3.41
2343 3866 8.479313 TGACTACATACAGAGCAAAATAAGTG 57.521 34.615 0.00 0.00 0.00 3.16
2344 3867 9.672673 AATGACTACATACAGAGCAAAATAAGT 57.327 29.630 0.00 0.00 35.50 2.24
2347 3870 9.448438 ACAAATGACTACATACAGAGCAAAATA 57.552 29.630 0.00 0.00 35.50 1.40
2348 3871 8.340618 ACAAATGACTACATACAGAGCAAAAT 57.659 30.769 0.00 0.00 35.50 1.82
2349 3872 7.744087 ACAAATGACTACATACAGAGCAAAA 57.256 32.000 0.00 0.00 35.50 2.44
2350 3873 7.443879 TCAACAAATGACTACATACAGAGCAAA 59.556 33.333 0.00 0.00 35.50 3.68
2351 3874 6.934083 TCAACAAATGACTACATACAGAGCAA 59.066 34.615 0.00 0.00 35.50 3.91
2352 3875 6.463360 TCAACAAATGACTACATACAGAGCA 58.537 36.000 0.00 0.00 35.50 4.26
2353 3876 6.968131 TCAACAAATGACTACATACAGAGC 57.032 37.500 0.00 0.00 35.50 4.09
2384 3907 9.338622 CCTCCGTTCCTAAATATTTGTCTTTAT 57.661 33.333 11.05 0.00 0.00 1.40
2385 3908 7.771826 CCCTCCGTTCCTAAATATTTGTCTTTA 59.228 37.037 11.05 0.00 0.00 1.85
2386 3909 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2387 3910 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2388 3911 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2389 3912 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2390 3913 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2391 3914 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2392 3915 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2393 3916 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2394 3917 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2395 3918 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2396 3919 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2397 3920 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2398 3921 4.803329 ATACTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
2399 3922 7.761981 ATATATACTACTCCCTCCGTTCCTA 57.238 40.000 0.00 0.00 0.00 2.94
2400 3923 6.655376 ATATATACTACTCCCTCCGTTCCT 57.345 41.667 0.00 0.00 0.00 3.36
2401 3924 7.284261 GGTTATATATACTACTCCCTCCGTTCC 59.716 44.444 0.00 0.00 0.00 3.62
2402 3925 8.052141 AGGTTATATATACTACTCCCTCCGTTC 58.948 40.741 0.00 0.00 0.00 3.95
2403 3926 7.833183 CAGGTTATATATACTACTCCCTCCGTT 59.167 40.741 0.00 0.00 0.00 4.44
2404 3927 7.344913 CAGGTTATATATACTACTCCCTCCGT 58.655 42.308 0.00 0.00 0.00 4.69
2405 3928 6.262720 GCAGGTTATATATACTACTCCCTCCG 59.737 46.154 0.00 0.00 0.00 4.63
2406 3929 7.285858 CAGCAGGTTATATATACTACTCCCTCC 59.714 44.444 0.00 0.00 0.00 4.30
2407 3930 7.201839 GCAGCAGGTTATATATACTACTCCCTC 60.202 44.444 0.00 0.00 0.00 4.30
2408 3931 6.608002 GCAGCAGGTTATATATACTACTCCCT 59.392 42.308 0.00 0.00 0.00 4.20
2409 3932 6.608002 AGCAGCAGGTTATATATACTACTCCC 59.392 42.308 0.00 0.00 0.00 4.30
2410 3933 7.648039 AGCAGCAGGTTATATATACTACTCC 57.352 40.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.