Multiple sequence alignment - TraesCS3B01G481200

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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 TraesCS3B01G481200 chr3B 100.000 4141 0 0 1 4141 728891743 728887603 0.000000e+00 7648.0
1 TraesCS3B01G481200 chr3B 83.616 1239 172 15 1062 2286 728754011 728752790 0.000000e+00 1134.0
2 TraesCS3B01G481200 chr3B 82.545 1289 157 39 991 2249 728585864 728584614 0.000000e+00 1072.0
3 TraesCS3B01G481200 chr3B 80.553 1265 192 29 992 2222 727786511 727787755 0.000000e+00 924.0
4 TraesCS3B01G481200 chr3B 81.217 1150 175 25 1169 2299 605912628 605911501 0.000000e+00 889.0
5 TraesCS3B01G481200 chr3B 82.800 843 87 31 2977 3787 728803576 728802760 0.000000e+00 701.0
6 TraesCS3B01G481200 chr3B 83.131 741 115 8 1397 2132 727794133 727794868 0.000000e+00 667.0
7 TraesCS3B01G481200 chr3B 77.326 763 119 39 2191 2914 728503055 728502308 6.450000e-108 401.0
8 TraesCS3B01G481200 chr3B 79.754 568 83 14 2341 2891 605911485 605910933 2.340000e-102 383.0
9 TraesCS3B01G481200 chr3B 79.821 446 59 16 2985 3407 727742495 727742932 3.130000e-76 296.0
10 TraesCS3B01G481200 chr3B 80.601 366 54 10 2527 2891 728752552 728752203 2.450000e-67 267.0
11 TraesCS3B01G481200 chr3B 97.248 109 3 0 3784 3892 728802729 728802621 7.070000e-43 185.0
12 TraesCS3B01G481200 chr3B 80.000 270 20 20 858 1110 605913263 605913011 7.120000e-38 169.0
13 TraesCS3B01G481200 chr3B 81.148 122 15 6 3353 3474 728615840 728615727 1.590000e-14 91.6
14 TraesCS3B01G481200 chr3A 93.031 2798 129 27 836 3614 686750005 686747255 0.000000e+00 4026.0
15 TraesCS3B01G481200 chr3A 79.403 1908 281 65 1003 2891 686539264 686537450 0.000000e+00 1243.0
16 TraesCS3B01G481200 chr3A 81.449 1477 204 40 856 2299 601134129 601132690 0.000000e+00 1146.0
17 TraesCS3B01G481200 chr3A 78.552 1865 289 65 1076 2891 686617383 686615581 0.000000e+00 1125.0
18 TraesCS3B01G481200 chr3A 92.966 526 27 5 3612 4129 686747140 686746617 0.000000e+00 758.0
19 TraesCS3B01G481200 chr3A 85.622 619 57 16 922 1523 686551716 686551113 4.550000e-174 621.0
20 TraesCS3B01G481200 chr3A 82.353 459 60 16 3037 3482 601131968 601131518 3.020000e-101 379.0
21 TraesCS3B01G481200 chr3A 76.938 529 69 34 2976 3478 686184904 686185405 6.870000e-63 252.0
22 TraesCS3B01G481200 chr3A 87.565 193 23 1 2699 2891 686708909 686708718 5.390000e-54 222.0
23 TraesCS3B01G481200 chr3A 95.455 44 2 0 3513 3556 601130938 601130895 2.070000e-08 71.3
24 TraesCS3B01G481200 chr7B 89.000 1900 185 20 1004 2895 543186975 543188858 0.000000e+00 2329.0
25 TraesCS3B01G481200 chr7B 80.995 563 64 25 3374 3908 543190400 543190947 1.390000e-109 407.0
26 TraesCS3B01G481200 chr3D 93.937 1204 53 7 945 2148 549468070 549466887 0.000000e+00 1801.0
27 TraesCS3B01G481200 chr3D 91.423 1096 46 19 3047 4129 549463476 549462416 0.000000e+00 1459.0
28 TraesCS3B01G481200 chr3D 80.590 1865 263 60 1062 2891 549127180 549125380 0.000000e+00 1347.0
29 TraesCS3B01G481200 chr3D 80.507 1893 248 64 1032 2883 548694352 548696164 0.000000e+00 1339.0
30 TraesCS3B01G481200 chr3D 83.495 1442 192 20 856 2287 549349956 549348551 0.000000e+00 1303.0
31 TraesCS3B01G481200 chr3D 82.309 1334 177 40 986 2299 458885969 458884675 0.000000e+00 1101.0
32 TraesCS3B01G481200 chr3D 93.906 640 34 3 2140 2774 549464203 549463564 0.000000e+00 961.0
33 TraesCS3B01G481200 chr3D 82.095 525 71 18 2972 3482 458884066 458883551 1.060000e-115 427.0
34 TraesCS3B01G481200 chr3D 80.998 521 75 12 2380 2891 458884613 458884108 3.880000e-105 392.0
35 TraesCS3B01G481200 chr3D 80.000 520 69 20 2985 3478 548706184 548706694 6.590000e-93 351.0
36 TraesCS3B01G481200 chr3D 80.279 502 68 17 2333 2821 548713151 548713634 2.370000e-92 350.0
37 TraesCS3B01G481200 chr3D 79.511 532 75 15 2972 3480 549107974 549107454 8.520000e-92 348.0
38 TraesCS3B01G481200 chr3D 80.448 491 47 28 3176 3649 549347841 549347383 3.090000e-86 329.0
39 TraesCS3B01G481200 chr3D 81.361 338 49 9 2563 2888 549348481 549348146 3.170000e-66 263.0
40 TraesCS3B01G481200 chr3D 83.333 252 16 19 667 895 549468771 549468523 4.190000e-50 209.0
41 TraesCS3B01G481200 chr3D 95.181 83 4 0 2882 2964 549463576 549463494 9.340000e-27 132.0
42 TraesCS3B01G481200 chr3D 83.838 99 14 1 3513 3609 458882976 458882878 4.410000e-15 93.5
43 TraesCS3B01G481200 chrUn 80.889 675 84 26 11 658 309969640 309968984 1.340000e-134 490.0
44 TraesCS3B01G481200 chr1B 82.440 541 74 14 129 661 566549161 566548634 1.760000e-123 453.0
45 TraesCS3B01G481200 chr1B 86.632 389 44 6 3 389 566549327 566548945 1.380000e-114 424.0
46 TraesCS3B01G481200 chr5B 86.632 389 45 7 3 387 258474081 258474466 1.380000e-114 424.0
47 TraesCS3B01G481200 chr4A 87.105 380 40 9 9 387 722781862 722782233 4.950000e-114 422.0


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 TraesCS3B01G481200 chr3B 728887603 728891743 4140 True 7648.000000 7648 100.000000 1 4141 1 chr3B.!!$R4 4140
1 TraesCS3B01G481200 chr3B 728584614 728585864 1250 True 1072.000000 1072 82.545000 991 2249 1 chr3B.!!$R2 1258
2 TraesCS3B01G481200 chr3B 727786511 727787755 1244 False 924.000000 924 80.553000 992 2222 1 chr3B.!!$F2 1230
3 TraesCS3B01G481200 chr3B 728752203 728754011 1808 True 700.500000 1134 82.108500 1062 2891 2 chr3B.!!$R6 1829
4 TraesCS3B01G481200 chr3B 727794133 727794868 735 False 667.000000 667 83.131000 1397 2132 1 chr3B.!!$F3 735
5 TraesCS3B01G481200 chr3B 605910933 605913263 2330 True 480.333333 889 80.323667 858 2891 3 chr3B.!!$R5 2033
6 TraesCS3B01G481200 chr3B 728802621 728803576 955 True 443.000000 701 90.024000 2977 3892 2 chr3B.!!$R7 915
7 TraesCS3B01G481200 chr3B 728502308 728503055 747 True 401.000000 401 77.326000 2191 2914 1 chr3B.!!$R1 723
8 TraesCS3B01G481200 chr3A 686746617 686750005 3388 True 2392.000000 4026 92.998500 836 4129 2 chr3A.!!$R6 3293
9 TraesCS3B01G481200 chr3A 686537450 686539264 1814 True 1243.000000 1243 79.403000 1003 2891 1 chr3A.!!$R1 1888
10 TraesCS3B01G481200 chr3A 686615581 686617383 1802 True 1125.000000 1125 78.552000 1076 2891 1 chr3A.!!$R3 1815
11 TraesCS3B01G481200 chr3A 686551113 686551716 603 True 621.000000 621 85.622000 922 1523 1 chr3A.!!$R2 601
12 TraesCS3B01G481200 chr3A 601130895 601134129 3234 True 532.100000 1146 86.419000 856 3556 3 chr3A.!!$R5 2700
13 TraesCS3B01G481200 chr3A 686184904 686185405 501 False 252.000000 252 76.938000 2976 3478 1 chr3A.!!$F1 502
14 TraesCS3B01G481200 chr7B 543186975 543190947 3972 False 1368.000000 2329 84.997500 1004 3908 2 chr7B.!!$F1 2904
15 TraesCS3B01G481200 chr3D 549125380 549127180 1800 True 1347.000000 1347 80.590000 1062 2891 1 chr3D.!!$R2 1829
16 TraesCS3B01G481200 chr3D 548694352 548696164 1812 False 1339.000000 1339 80.507000 1032 2883 1 chr3D.!!$F1 1851
17 TraesCS3B01G481200 chr3D 549462416 549468771 6355 True 912.400000 1801 91.556000 667 4129 5 chr3D.!!$R5 3462
18 TraesCS3B01G481200 chr3D 549347383 549349956 2573 True 631.666667 1303 81.768000 856 3649 3 chr3D.!!$R4 2793
19 TraesCS3B01G481200 chr3D 458882878 458885969 3091 True 503.375000 1101 82.310000 986 3609 4 chr3D.!!$R3 2623
20 TraesCS3B01G481200 chr3D 548706184 548706694 510 False 351.000000 351 80.000000 2985 3478 1 chr3D.!!$F2 493
21 TraesCS3B01G481200 chr3D 549107454 549107974 520 True 348.000000 348 79.511000 2972 3480 1 chr3D.!!$R1 508
22 TraesCS3B01G481200 chrUn 309968984 309969640 656 True 490.000000 490 80.889000 11 658 1 chrUn.!!$R1 647
23 TraesCS3B01G481200 chr1B 566548634 566549327 693 True 438.500000 453 84.536000 3 661 2 chr1B.!!$R1 658

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
648 670 0.251916 TGGGCCGAGTGTAGAATTGG 59.748 55.0 0.00 0.00 0.00 3.16 F
668 690 0.537371 CCCACAAAGAGCTCCCGTTT 60.537 55.0 10.93 1.42 0.00 3.60 F
1581 2426 0.532573 CCCGTGACAGAGCATGTACT 59.467 55.0 0.00 0.00 44.17 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 2391 1.215647 CTCTGTCACGGGCTACCAC 59.784 63.158 0.00 0.0 36.13 4.16 R
2625 6324 3.185797 ACAGTTCACGCGGAAGAAAATAC 59.814 43.478 12.47 0.6 35.82 1.89 R
3497 8712 1.557269 GGATCCTCACTGGCCACACT 61.557 60.000 0.00 0.0 35.26 3.55 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
27 28 4.450080 GGTCGTTCGTTTTCCTCTTGTATT 59.550 41.667 0.00 0.00 0.00 1.89
37 38 7.376072 CGTTTTCCTCTTGTATTTCTTTGTCAC 59.624 37.037 0.00 0.00 0.00 3.67
56 57 5.566016 TGTCACTTCGTTTTGTTCTTTTTCG 59.434 36.000 0.00 0.00 0.00 3.46
61 62 7.790216 CACTTCGTTTTGTTCTTTTTCGTTTTT 59.210 29.630 0.00 0.00 0.00 1.94
354 376 9.610705 TTTGATGAACTTTTTCCAAATTGATGA 57.389 25.926 0.00 0.00 0.00 2.92
355 377 9.781633 TTGATGAACTTTTTCCAAATTGATGAT 57.218 25.926 0.00 0.00 0.00 2.45
356 378 9.781633 TGATGAACTTTTTCCAAATTGATGATT 57.218 25.926 0.00 0.00 0.00 2.57
386 408 8.824159 TTCAAAATTGAACAGACTGTTTTTCA 57.176 26.923 21.42 12.70 41.28 2.69
387 409 9.434420 TTCAAAATTGAACAGACTGTTTTTCAT 57.566 25.926 21.42 8.96 41.28 2.57
388 410 9.434420 TCAAAATTGAACAGACTGTTTTTCATT 57.566 25.926 21.42 13.60 41.28 2.57
456 478 9.561069 AAATCTTAGTGGTATAGTAAATGGCTG 57.439 33.333 0.00 0.00 0.00 4.85
457 479 7.907841 TCTTAGTGGTATAGTAAATGGCTGA 57.092 36.000 0.00 0.00 0.00 4.26
458 480 7.952671 TCTTAGTGGTATAGTAAATGGCTGAG 58.047 38.462 0.00 0.00 0.00 3.35
459 481 7.563924 TCTTAGTGGTATAGTAAATGGCTGAGT 59.436 37.037 0.00 0.00 0.00 3.41
460 482 5.918608 AGTGGTATAGTAAATGGCTGAGTG 58.081 41.667 0.00 0.00 0.00 3.51
461 483 5.661312 AGTGGTATAGTAAATGGCTGAGTGA 59.339 40.000 0.00 0.00 0.00 3.41
462 484 6.327626 AGTGGTATAGTAAATGGCTGAGTGAT 59.672 38.462 0.00 0.00 0.00 3.06
463 485 7.509318 AGTGGTATAGTAAATGGCTGAGTGATA 59.491 37.037 0.00 0.00 0.00 2.15
464 486 8.148351 GTGGTATAGTAAATGGCTGAGTGATAA 58.852 37.037 0.00 0.00 0.00 1.75
465 487 8.710239 TGGTATAGTAAATGGCTGAGTGATAAA 58.290 33.333 0.00 0.00 0.00 1.40
466 488 9.726438 GGTATAGTAAATGGCTGAGTGATAAAT 57.274 33.333 0.00 0.00 0.00 1.40
469 491 7.736447 AGTAAATGGCTGAGTGATAAATAGC 57.264 36.000 0.00 0.00 0.00 2.97
470 492 5.679734 AAATGGCTGAGTGATAAATAGCG 57.320 39.130 0.00 0.00 35.31 4.26
471 493 3.819564 TGGCTGAGTGATAAATAGCGT 57.180 42.857 0.00 0.00 35.31 5.07
472 494 3.457234 TGGCTGAGTGATAAATAGCGTG 58.543 45.455 0.00 0.00 35.31 5.34
473 495 3.118775 TGGCTGAGTGATAAATAGCGTGT 60.119 43.478 0.00 0.00 35.31 4.49
474 496 3.871594 GGCTGAGTGATAAATAGCGTGTT 59.128 43.478 0.00 0.00 35.31 3.32
475 497 4.260375 GGCTGAGTGATAAATAGCGTGTTG 60.260 45.833 0.00 0.00 35.31 3.33
476 498 4.783450 GCTGAGTGATAAATAGCGTGTTGC 60.783 45.833 0.00 0.00 46.98 4.17
490 512 3.846335 GCGTGTTGCATTAGTTCTAAAGC 59.154 43.478 11.30 11.30 45.45 3.51
491 513 4.612712 GCGTGTTGCATTAGTTCTAAAGCA 60.613 41.667 15.33 15.33 45.45 3.91
492 514 5.448438 CGTGTTGCATTAGTTCTAAAGCAA 58.552 37.500 22.48 22.48 40.07 3.91
493 515 6.086222 CGTGTTGCATTAGTTCTAAAGCAAT 58.914 36.000 26.24 0.32 42.80 3.56
494 516 6.582295 CGTGTTGCATTAGTTCTAAAGCAATT 59.418 34.615 26.24 0.00 42.80 2.32
495 517 7.201266 CGTGTTGCATTAGTTCTAAAGCAATTC 60.201 37.037 26.24 21.54 42.80 2.17
496 518 6.801377 TGTTGCATTAGTTCTAAAGCAATTCG 59.199 34.615 26.24 0.00 42.80 3.34
497 519 6.494893 TGCATTAGTTCTAAAGCAATTCGT 57.505 33.333 16.47 0.00 31.80 3.85
498 520 6.314018 TGCATTAGTTCTAAAGCAATTCGTG 58.686 36.000 16.47 1.50 31.80 4.35
499 521 6.072728 TGCATTAGTTCTAAAGCAATTCGTGT 60.073 34.615 16.47 0.00 31.80 4.49
500 522 6.801862 GCATTAGTTCTAAAGCAATTCGTGTT 59.198 34.615 12.76 0.00 0.00 3.32
501 523 7.201266 GCATTAGTTCTAAAGCAATTCGTGTTG 60.201 37.037 12.76 0.00 0.00 3.33
512 534 4.810125 CAATTCGTGTTGCTTTTGTTCAC 58.190 39.130 0.00 0.00 0.00 3.18
513 535 3.840890 TTCGTGTTGCTTTTGTTCACT 57.159 38.095 0.00 0.00 0.00 3.41
514 536 4.948608 TTCGTGTTGCTTTTGTTCACTA 57.051 36.364 0.00 0.00 0.00 2.74
515 537 4.267357 TCGTGTTGCTTTTGTTCACTAC 57.733 40.909 0.00 0.00 0.00 2.73
516 538 3.064271 TCGTGTTGCTTTTGTTCACTACC 59.936 43.478 0.00 0.00 0.00 3.18
517 539 3.359654 GTGTTGCTTTTGTTCACTACCG 58.640 45.455 0.00 0.00 0.00 4.02
518 540 2.356382 TGTTGCTTTTGTTCACTACCGG 59.644 45.455 0.00 0.00 0.00 5.28
519 541 2.335316 TGCTTTTGTTCACTACCGGT 57.665 45.000 13.98 13.98 0.00 5.28
520 542 3.472283 TGCTTTTGTTCACTACCGGTA 57.528 42.857 14.95 14.95 0.00 4.02
521 543 3.132925 TGCTTTTGTTCACTACCGGTAC 58.867 45.455 11.16 3.46 0.00 3.34
535 557 3.900446 GGTACGTTGCTGTAGTGGT 57.100 52.632 0.00 0.00 0.00 4.16
536 558 2.159327 GGTACGTTGCTGTAGTGGTT 57.841 50.000 0.00 0.00 0.00 3.67
537 559 3.302365 GGTACGTTGCTGTAGTGGTTA 57.698 47.619 0.00 0.00 0.00 2.85
538 560 3.652274 GGTACGTTGCTGTAGTGGTTAA 58.348 45.455 0.00 0.00 0.00 2.01
539 561 3.676646 GGTACGTTGCTGTAGTGGTTAAG 59.323 47.826 0.00 0.00 0.00 1.85
540 562 2.140717 ACGTTGCTGTAGTGGTTAAGC 58.859 47.619 0.00 0.00 36.18 3.09
541 563 1.126113 CGTTGCTGTAGTGGTTAAGCG 59.874 52.381 0.00 0.00 38.53 4.68
542 564 2.409975 GTTGCTGTAGTGGTTAAGCGA 58.590 47.619 0.00 0.00 38.53 4.93
543 565 2.803956 GTTGCTGTAGTGGTTAAGCGAA 59.196 45.455 0.00 0.00 38.53 4.70
544 566 2.683968 TGCTGTAGTGGTTAAGCGAAG 58.316 47.619 0.00 0.00 38.53 3.79
545 567 2.297880 TGCTGTAGTGGTTAAGCGAAGA 59.702 45.455 0.00 0.00 38.53 2.87
546 568 3.243941 TGCTGTAGTGGTTAAGCGAAGAA 60.244 43.478 0.00 0.00 38.53 2.52
547 569 3.368236 GCTGTAGTGGTTAAGCGAAGAAG 59.632 47.826 0.00 0.00 0.00 2.85
548 570 4.557205 CTGTAGTGGTTAAGCGAAGAAGT 58.443 43.478 0.00 0.00 0.00 3.01
549 571 4.952460 TGTAGTGGTTAAGCGAAGAAGTT 58.048 39.130 0.00 0.00 0.00 2.66
550 572 4.748102 TGTAGTGGTTAAGCGAAGAAGTTG 59.252 41.667 0.00 0.00 0.00 3.16
551 573 2.548480 AGTGGTTAAGCGAAGAAGTTGC 59.452 45.455 0.00 0.00 0.00 4.17
552 574 2.289547 GTGGTTAAGCGAAGAAGTTGCA 59.710 45.455 0.00 0.00 0.00 4.08
553 575 2.946329 TGGTTAAGCGAAGAAGTTGCAA 59.054 40.909 0.00 0.00 0.00 4.08
554 576 3.003275 TGGTTAAGCGAAGAAGTTGCAAG 59.997 43.478 0.00 0.00 0.00 4.01
555 577 2.969443 TAAGCGAAGAAGTTGCAAGC 57.031 45.000 0.00 0.00 0.00 4.01
556 578 1.024271 AAGCGAAGAAGTTGCAAGCA 58.976 45.000 0.00 0.00 0.00 3.91
557 579 1.024271 AGCGAAGAAGTTGCAAGCAA 58.976 45.000 0.00 2.89 0.00 3.91
558 580 1.405105 AGCGAAGAAGTTGCAAGCAAA 59.595 42.857 9.32 0.00 37.70 3.68
559 581 2.035066 AGCGAAGAAGTTGCAAGCAAAT 59.965 40.909 9.32 5.37 37.70 2.32
560 582 2.154389 GCGAAGAAGTTGCAAGCAAATG 59.846 45.455 9.32 0.00 37.70 2.32
561 583 2.154389 CGAAGAAGTTGCAAGCAAATGC 59.846 45.455 9.32 7.10 46.58 3.56
571 593 2.793946 GCAAATGCGGCGTGAGAT 59.206 55.556 9.37 0.00 0.00 2.75
572 594 1.297893 GCAAATGCGGCGTGAGATC 60.298 57.895 9.37 0.00 0.00 2.75
573 595 1.980951 GCAAATGCGGCGTGAGATCA 61.981 55.000 9.37 0.00 0.00 2.92
574 596 0.447406 CAAATGCGGCGTGAGATCAA 59.553 50.000 9.37 0.00 0.00 2.57
575 597 1.135717 CAAATGCGGCGTGAGATCAAA 60.136 47.619 9.37 0.00 0.00 2.69
576 598 1.382522 AATGCGGCGTGAGATCAAAT 58.617 45.000 9.37 0.00 0.00 2.32
577 599 0.940126 ATGCGGCGTGAGATCAAATC 59.060 50.000 9.37 0.00 0.00 2.17
578 600 1.089481 TGCGGCGTGAGATCAAATCC 61.089 55.000 9.37 0.00 0.00 3.01
579 601 1.776034 GCGGCGTGAGATCAAATCCC 61.776 60.000 9.37 0.00 0.00 3.85
580 602 1.160329 CGGCGTGAGATCAAATCCCC 61.160 60.000 0.00 0.00 0.00 4.81
581 603 1.160329 GGCGTGAGATCAAATCCCCG 61.160 60.000 0.00 0.00 0.00 5.73
582 604 0.462047 GCGTGAGATCAAATCCCCGT 60.462 55.000 0.00 0.00 0.00 5.28
583 605 2.012051 GCGTGAGATCAAATCCCCGTT 61.012 52.381 0.00 0.00 0.00 4.44
584 606 1.933853 CGTGAGATCAAATCCCCGTTC 59.066 52.381 0.00 0.00 0.00 3.95
585 607 2.418746 CGTGAGATCAAATCCCCGTTCT 60.419 50.000 0.00 0.00 0.00 3.01
586 608 2.939103 GTGAGATCAAATCCCCGTTCTG 59.061 50.000 0.00 0.00 0.00 3.02
587 609 2.571653 TGAGATCAAATCCCCGTTCTGT 59.428 45.455 0.00 0.00 0.00 3.41
588 610 3.198872 GAGATCAAATCCCCGTTCTGTC 58.801 50.000 0.00 0.00 0.00 3.51
589 611 2.571653 AGATCAAATCCCCGTTCTGTCA 59.428 45.455 0.00 0.00 0.00 3.58
590 612 2.940994 TCAAATCCCCGTTCTGTCAA 57.059 45.000 0.00 0.00 0.00 3.18
591 613 3.216187 TCAAATCCCCGTTCTGTCAAA 57.784 42.857 0.00 0.00 0.00 2.69
592 614 3.556999 TCAAATCCCCGTTCTGTCAAAA 58.443 40.909 0.00 0.00 0.00 2.44
593 615 4.148838 TCAAATCCCCGTTCTGTCAAAAT 58.851 39.130 0.00 0.00 0.00 1.82
594 616 4.586841 TCAAATCCCCGTTCTGTCAAAATT 59.413 37.500 0.00 0.00 0.00 1.82
595 617 5.069781 TCAAATCCCCGTTCTGTCAAAATTT 59.930 36.000 0.00 0.00 0.00 1.82
596 618 5.545063 AATCCCCGTTCTGTCAAAATTTT 57.455 34.783 0.00 0.00 0.00 1.82
597 619 4.314740 TCCCCGTTCTGTCAAAATTTTG 57.685 40.909 22.40 22.40 39.48 2.44
598 620 2.799978 CCCCGTTCTGTCAAAATTTTGC 59.200 45.455 23.36 18.42 38.05 3.68
599 621 2.470999 CCCGTTCTGTCAAAATTTTGCG 59.529 45.455 23.36 18.76 38.05 4.85
600 622 3.112580 CCGTTCTGTCAAAATTTTGCGT 58.887 40.909 23.36 0.00 38.05 5.24
601 623 3.061271 CCGTTCTGTCAAAATTTTGCGTG 60.061 43.478 23.36 15.32 38.05 5.34
602 624 3.599116 CGTTCTGTCAAAATTTTGCGTGC 60.599 43.478 23.36 14.16 38.05 5.34
603 625 3.435105 TCTGTCAAAATTTTGCGTGCT 57.565 38.095 23.36 0.00 38.05 4.40
604 626 3.779759 TCTGTCAAAATTTTGCGTGCTT 58.220 36.364 23.36 0.00 38.05 3.91
605 627 4.180057 TCTGTCAAAATTTTGCGTGCTTT 58.820 34.783 23.36 0.00 38.05 3.51
606 628 4.629200 TCTGTCAAAATTTTGCGTGCTTTT 59.371 33.333 23.36 0.00 38.05 2.27
607 629 5.121454 TCTGTCAAAATTTTGCGTGCTTTTT 59.879 32.000 23.36 0.00 38.05 1.94
628 650 5.418310 TTTTTCGTGAATGACTCTGTTCC 57.582 39.130 0.00 0.00 0.00 3.62
629 651 4.336889 TTTCGTGAATGACTCTGTTCCT 57.663 40.909 0.00 0.00 0.00 3.36
630 652 3.303881 TCGTGAATGACTCTGTTCCTG 57.696 47.619 0.00 0.00 0.00 3.86
631 653 2.029020 TCGTGAATGACTCTGTTCCTGG 60.029 50.000 0.00 0.00 0.00 4.45
632 654 2.704572 GTGAATGACTCTGTTCCTGGG 58.295 52.381 0.00 0.00 0.00 4.45
633 655 1.003580 TGAATGACTCTGTTCCTGGGC 59.996 52.381 0.00 0.00 0.00 5.36
634 656 0.329596 AATGACTCTGTTCCTGGGCC 59.670 55.000 0.00 0.00 0.00 5.80
635 657 1.903877 ATGACTCTGTTCCTGGGCCG 61.904 60.000 0.00 0.00 0.00 6.13
636 658 2.203788 ACTCTGTTCCTGGGCCGA 60.204 61.111 0.00 0.00 0.00 5.54
637 659 2.232298 GACTCTGTTCCTGGGCCGAG 62.232 65.000 7.99 7.99 0.00 4.63
638 660 2.203788 TCTGTTCCTGGGCCGAGT 60.204 61.111 14.30 0.00 0.00 4.18
639 661 2.046892 CTGTTCCTGGGCCGAGTG 60.047 66.667 14.30 5.51 0.00 3.51
640 662 2.847234 TGTTCCTGGGCCGAGTGT 60.847 61.111 14.30 0.00 0.00 3.55
641 663 1.534476 TGTTCCTGGGCCGAGTGTA 60.534 57.895 14.30 0.00 0.00 2.90
642 664 1.218316 GTTCCTGGGCCGAGTGTAG 59.782 63.158 14.30 0.00 0.00 2.74
643 665 1.077805 TTCCTGGGCCGAGTGTAGA 59.922 57.895 14.30 0.50 0.00 2.59
644 666 0.543410 TTCCTGGGCCGAGTGTAGAA 60.543 55.000 14.30 7.02 0.00 2.10
645 667 0.325296 TCCTGGGCCGAGTGTAGAAT 60.325 55.000 14.30 0.00 0.00 2.40
646 668 0.541863 CCTGGGCCGAGTGTAGAATT 59.458 55.000 14.30 0.00 0.00 2.17
647 669 1.656652 CTGGGCCGAGTGTAGAATTG 58.343 55.000 6.60 0.00 0.00 2.32
648 670 0.251916 TGGGCCGAGTGTAGAATTGG 59.748 55.000 0.00 0.00 0.00 3.16
649 671 1.095807 GGGCCGAGTGTAGAATTGGC 61.096 60.000 10.04 10.04 44.14 4.52
650 672 2.394604 GCCGAGTGTAGAATTGGCC 58.605 57.895 7.34 0.00 39.71 5.36
651 673 1.095807 GCCGAGTGTAGAATTGGCCC 61.096 60.000 7.34 0.00 39.71 5.80
652 674 0.251916 CCGAGTGTAGAATTGGCCCA 59.748 55.000 0.00 0.00 0.00 5.36
653 675 1.369625 CGAGTGTAGAATTGGCCCAC 58.630 55.000 0.00 0.00 0.00 4.61
654 676 1.338674 CGAGTGTAGAATTGGCCCACA 60.339 52.381 0.00 0.00 0.00 4.17
655 677 2.790433 GAGTGTAGAATTGGCCCACAA 58.210 47.619 0.00 0.00 44.54 3.33
656 678 3.153919 GAGTGTAGAATTGGCCCACAAA 58.846 45.455 0.00 0.00 43.46 2.83
657 679 3.157087 AGTGTAGAATTGGCCCACAAAG 58.843 45.455 0.00 0.00 43.46 2.77
658 680 3.153919 GTGTAGAATTGGCCCACAAAGA 58.846 45.455 0.00 0.00 43.46 2.52
659 681 3.191371 GTGTAGAATTGGCCCACAAAGAG 59.809 47.826 0.00 0.00 43.46 2.85
660 682 1.260544 AGAATTGGCCCACAAAGAGC 58.739 50.000 0.00 0.00 43.46 4.09
661 683 1.203100 AGAATTGGCCCACAAAGAGCT 60.203 47.619 0.00 0.00 43.46 4.09
662 684 1.203287 GAATTGGCCCACAAAGAGCTC 59.797 52.381 5.27 5.27 43.46 4.09
663 685 0.613012 ATTGGCCCACAAAGAGCTCC 60.613 55.000 10.93 0.00 43.46 4.70
664 686 2.361737 GGCCCACAAAGAGCTCCC 60.362 66.667 10.93 0.00 0.00 4.30
665 687 2.747855 GCCCACAAAGAGCTCCCG 60.748 66.667 10.93 1.15 0.00 5.14
666 688 2.750350 CCCACAAAGAGCTCCCGT 59.250 61.111 10.93 1.88 0.00 5.28
667 689 1.073199 CCCACAAAGAGCTCCCGTT 59.927 57.895 10.93 0.00 0.00 4.44
668 690 0.537371 CCCACAAAGAGCTCCCGTTT 60.537 55.000 10.93 1.42 0.00 3.60
669 691 1.318576 CCACAAAGAGCTCCCGTTTT 58.681 50.000 10.93 1.01 0.00 2.43
670 692 1.681264 CCACAAAGAGCTCCCGTTTTT 59.319 47.619 10.93 0.59 0.00 1.94
671 693 2.287608 CCACAAAGAGCTCCCGTTTTTC 60.288 50.000 10.93 0.00 0.00 2.29
672 694 2.618709 CACAAAGAGCTCCCGTTTTTCT 59.381 45.455 10.93 0.00 0.00 2.52
684 706 6.575649 GCTCCCGTTTTTCTGGGCTATATATA 60.576 42.308 0.00 0.00 45.60 0.86
685 707 7.504926 TCCCGTTTTTCTGGGCTATATATAT 57.495 36.000 0.00 0.00 45.60 0.86
687 709 9.220906 TCCCGTTTTTCTGGGCTATATATATAT 57.779 33.333 10.10 10.10 45.60 0.86
723 746 8.637281 AAAATAAAAATAGATAAAACGGGCCG 57.363 30.769 27.06 27.06 0.00 6.13
744 767 3.807538 CATGCCAGCCTGCGTGTC 61.808 66.667 8.69 0.00 42.12 3.67
745 768 4.334118 ATGCCAGCCTGCGTGTCA 62.334 61.111 0.00 0.00 0.00 3.58
746 769 3.848301 ATGCCAGCCTGCGTGTCAA 62.848 57.895 0.00 0.00 0.00 3.18
747 770 3.730761 GCCAGCCTGCGTGTCAAG 61.731 66.667 0.00 0.00 0.00 3.02
750 773 3.946201 AGCCTGCGTGTCAAGCCT 61.946 61.111 8.33 0.00 32.55 4.58
751 774 2.980233 GCCTGCGTGTCAAGCCTT 60.980 61.111 8.33 0.00 0.00 4.35
753 776 1.234615 GCCTGCGTGTCAAGCCTTTA 61.235 55.000 8.33 0.00 0.00 1.85
754 777 0.798776 CCTGCGTGTCAAGCCTTTAG 59.201 55.000 8.33 0.00 0.00 1.85
790 816 0.739813 GCACGACCCATTTAGCTCGT 60.740 55.000 0.00 0.00 39.90 4.18
820 873 4.937431 GGCACGGCCCAGATAGCC 62.937 72.222 0.00 0.00 44.06 3.93
959 1426 1.986413 CCCAGACCAGTCTTCCCAG 59.014 63.158 0.00 0.00 37.98 4.45
1149 1648 4.089757 CCTTCCTCCCTCCCCCGA 62.090 72.222 0.00 0.00 0.00 5.14
1472 2299 2.304056 CCCCACCTGAGCTGGACAT 61.304 63.158 0.00 0.00 0.00 3.06
1537 2364 2.633509 GGCCAAGGCTGCAGTTCAG 61.634 63.158 16.64 3.53 45.62 3.02
1581 2426 0.532573 CCCGTGACAGAGCATGTACT 59.467 55.000 0.00 0.00 44.17 2.73
1715 2595 2.388232 GCTGGTTACTTCCGGTGCG 61.388 63.158 0.00 0.00 36.33 5.34
1795 2681 0.837272 GCCAGCACCTATAGAACCCA 59.163 55.000 0.00 0.00 0.00 4.51
1925 2817 3.772387 TGGATGTTTGGGTGCTCAATAA 58.228 40.909 0.00 0.00 0.00 1.40
2132 3027 8.908786 TTTGAATATTTCTATCCTGCAGGTAG 57.091 34.615 31.58 27.55 36.34 3.18
2227 5829 7.373617 TGCCTATCATATCCTTGAGTGTTAA 57.626 36.000 0.00 0.00 0.00 2.01
2399 6044 3.679389 CCTTGTGTGCCTATCTGAAGTT 58.321 45.455 0.00 0.00 0.00 2.66
2532 6220 7.835181 TGGGAAACATAACCGGAACTTATTATT 59.165 33.333 9.46 0.00 0.00 1.40
2750 6479 2.549332 GCTGAGACCAAACCAGCTC 58.451 57.895 0.00 0.00 46.96 4.09
2774 6515 6.318648 TCAATGTATAACTCCATTGGCACTTC 59.681 38.462 11.24 0.00 45.05 3.01
2802 6550 9.403110 CGAAACTTAAAGCTAGTTACACTCTTA 57.597 33.333 0.84 0.00 34.88 2.10
2832 6580 3.492337 AGCTGAAACCGGTGGAATAAAA 58.508 40.909 8.52 0.00 0.00 1.52
2837 6585 6.869388 GCTGAAACCGGTGGAATAAAATTAAA 59.131 34.615 8.52 0.00 0.00 1.52
2945 6696 6.010219 ACCAGCTTAATGTGTAACTCCATTT 58.990 36.000 0.00 0.00 38.04 2.32
3128 6937 2.026822 ACATGGTGGAGATGAGGTGTTC 60.027 50.000 0.00 0.00 0.00 3.18
3334 7205 3.450904 AGGAATCCACTACTGTGCCTAA 58.549 45.455 0.61 0.00 42.54 2.69
3335 7206 3.452627 AGGAATCCACTACTGTGCCTAAG 59.547 47.826 0.61 0.00 42.54 2.18
3336 7207 3.197983 GGAATCCACTACTGTGCCTAAGT 59.802 47.826 0.00 0.00 42.54 2.24
3337 7208 4.404715 GGAATCCACTACTGTGCCTAAGTA 59.595 45.833 0.00 0.00 42.54 2.24
3338 7209 5.105064 GGAATCCACTACTGTGCCTAAGTAA 60.105 44.000 0.00 0.00 42.54 2.24
3339 7210 6.408206 GGAATCCACTACTGTGCCTAAGTAAT 60.408 42.308 0.00 0.00 42.54 1.89
3486 8701 5.786401 ACTTGATCACGAGTAGATTTTGC 57.214 39.130 6.16 0.00 38.81 3.68
3497 8712 4.069304 AGTAGATTTTGCGTTTGCTGGTA 58.931 39.130 0.00 0.00 43.34 3.25
3598 9287 6.258507 GCAGGAATGAACTGTTTGAATTGTTT 59.741 34.615 0.00 0.00 38.22 2.83
3680 9638 3.261897 CCATGAGTCTGTCCCTTGTACTT 59.738 47.826 0.00 0.00 0.00 2.24
3712 9680 6.877322 AGTGGTTCGTTTGCTTATGTATAGTT 59.123 34.615 0.00 0.00 0.00 2.24
3714 9682 6.651643 TGGTTCGTTTGCTTATGTATAGTTGT 59.348 34.615 0.00 0.00 0.00 3.32
3715 9683 7.818446 TGGTTCGTTTGCTTATGTATAGTTGTA 59.182 33.333 0.00 0.00 0.00 2.41
3734 9702 1.247567 AAGAATTGGTGGGTTGCTCG 58.752 50.000 0.00 0.00 0.00 5.03
3749 9717 1.613925 TGCTCGTGCTAGTTTCAGAGT 59.386 47.619 11.19 0.00 40.48 3.24
3768 9740 1.333619 GTCTAGCTTCTCTCTCTGCCG 59.666 57.143 0.00 0.00 0.00 5.69
3871 9889 1.460504 TAGATGGTCTCGTGCGAGTT 58.539 50.000 19.20 5.44 42.49 3.01
3901 9926 3.407698 TGGTTCATCTTGCGCTTCTTTA 58.592 40.909 9.73 0.00 0.00 1.85
3926 9951 4.307432 CCCACAAGATGACGATGTATACC 58.693 47.826 0.00 0.00 0.00 2.73
4036 10065 0.107800 CAGATGTCCTGGCTGGTCTG 60.108 60.000 10.44 11.85 39.23 3.51
4090 10119 1.235281 GGAGGTCCGTGGACTTTTGC 61.235 60.000 17.99 6.72 44.04 3.68
4093 10122 0.534203 GGTCCGTGGACTTTTGCTGA 60.534 55.000 17.99 0.00 44.04 4.26
4096 10125 1.021202 CCGTGGACTTTTGCTGACAA 58.979 50.000 0.00 0.00 0.00 3.18
4098 10127 2.811431 CCGTGGACTTTTGCTGACAATA 59.189 45.455 0.00 0.00 35.21 1.90
4115 10144 3.894427 ACAATACTGTTTTGATGGTGCCA 59.106 39.130 16.18 0.00 28.57 4.92
4119 10148 4.989279 ACTGTTTTGATGGTGCCATATC 57.011 40.909 3.37 0.00 36.70 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.411612 AGAGGAAAACGAACGACCAGT 59.588 47.619 0.14 0.00 0.00 4.00
7 8 6.224420 AGAAATACAAGAGGAAAACGAACG 57.776 37.500 0.00 0.00 0.00 3.95
18 19 7.178712 ACGAAGTGACAAAGAAATACAAGAG 57.821 36.000 0.00 0.00 42.51 2.85
27 28 6.249035 AGAACAAAACGAAGTGACAAAGAA 57.751 33.333 0.00 0.00 45.00 2.52
90 91 7.010091 CCCGCGCATTTAAGAAAAAGATAAAAT 59.990 33.333 8.75 0.00 0.00 1.82
94 95 4.396790 ACCCGCGCATTTAAGAAAAAGATA 59.603 37.500 8.75 0.00 0.00 1.98
95 96 3.192633 ACCCGCGCATTTAAGAAAAAGAT 59.807 39.130 8.75 0.00 0.00 2.40
112 113 2.642995 GTTCACGAACTAAAAACCCGC 58.357 47.619 2.63 0.00 38.25 6.13
284 285 9.203421 GGATTTGATAAAGGTTTACTGGTTTTG 57.797 33.333 0.00 0.00 0.00 2.44
292 293 8.674607 AGTTCATCGGATTTGATAAAGGTTTAC 58.325 33.333 0.00 0.00 0.00 2.01
294 295 7.703058 AGTTCATCGGATTTGATAAAGGTTT 57.297 32.000 0.00 0.00 0.00 3.27
330 352 9.781633 AATCATCAATTTGGAAAAAGTTCATCA 57.218 25.926 0.00 0.00 35.25 3.07
361 383 8.824159 TGAAAAACAGTCTGTTCAATTTTGAA 57.176 26.923 18.42 1.66 40.14 2.69
362 384 9.434420 AATGAAAAACAGTCTGTTCAATTTTGA 57.566 25.926 18.42 9.87 40.14 2.69
430 452 9.561069 CAGCCATTTACTATACCACTAAGATTT 57.439 33.333 0.00 0.00 0.00 2.17
431 453 8.934697 TCAGCCATTTACTATACCACTAAGATT 58.065 33.333 0.00 0.00 0.00 2.40
432 454 8.492415 TCAGCCATTTACTATACCACTAAGAT 57.508 34.615 0.00 0.00 0.00 2.40
433 455 7.563924 ACTCAGCCATTTACTATACCACTAAGA 59.436 37.037 0.00 0.00 0.00 2.10
434 456 7.653713 CACTCAGCCATTTACTATACCACTAAG 59.346 40.741 0.00 0.00 0.00 2.18
435 457 7.343574 TCACTCAGCCATTTACTATACCACTAA 59.656 37.037 0.00 0.00 0.00 2.24
436 458 6.837048 TCACTCAGCCATTTACTATACCACTA 59.163 38.462 0.00 0.00 0.00 2.74
437 459 5.661312 TCACTCAGCCATTTACTATACCACT 59.339 40.000 0.00 0.00 0.00 4.00
438 460 5.914033 TCACTCAGCCATTTACTATACCAC 58.086 41.667 0.00 0.00 0.00 4.16
439 461 6.747414 ATCACTCAGCCATTTACTATACCA 57.253 37.500 0.00 0.00 0.00 3.25
440 462 9.726438 ATTTATCACTCAGCCATTTACTATACC 57.274 33.333 0.00 0.00 0.00 2.73
443 465 9.442047 GCTATTTATCACTCAGCCATTTACTAT 57.558 33.333 0.00 0.00 0.00 2.12
444 466 7.598869 CGCTATTTATCACTCAGCCATTTACTA 59.401 37.037 0.00 0.00 0.00 1.82
445 467 6.425114 CGCTATTTATCACTCAGCCATTTACT 59.575 38.462 0.00 0.00 0.00 2.24
446 468 6.202954 ACGCTATTTATCACTCAGCCATTTAC 59.797 38.462 0.00 0.00 0.00 2.01
447 469 6.202762 CACGCTATTTATCACTCAGCCATTTA 59.797 38.462 0.00 0.00 0.00 1.40
448 470 5.008019 CACGCTATTTATCACTCAGCCATTT 59.992 40.000 0.00 0.00 0.00 2.32
449 471 4.512944 CACGCTATTTATCACTCAGCCATT 59.487 41.667 0.00 0.00 0.00 3.16
450 472 4.060900 CACGCTATTTATCACTCAGCCAT 58.939 43.478 0.00 0.00 0.00 4.40
451 473 3.118775 ACACGCTATTTATCACTCAGCCA 60.119 43.478 0.00 0.00 0.00 4.75
452 474 3.458189 ACACGCTATTTATCACTCAGCC 58.542 45.455 0.00 0.00 0.00 4.85
453 475 4.783450 GCAACACGCTATTTATCACTCAGC 60.783 45.833 0.00 0.00 37.77 4.26
454 476 4.329801 TGCAACACGCTATTTATCACTCAG 59.670 41.667 0.00 0.00 43.06 3.35
455 477 4.249661 TGCAACACGCTATTTATCACTCA 58.750 39.130 0.00 0.00 43.06 3.41
456 478 4.857871 TGCAACACGCTATTTATCACTC 57.142 40.909 0.00 0.00 43.06 3.51
457 479 5.818136 AATGCAACACGCTATTTATCACT 57.182 34.783 0.00 0.00 43.06 3.41
458 480 6.715464 ACTAATGCAACACGCTATTTATCAC 58.285 36.000 0.00 0.00 43.06 3.06
459 481 6.918892 ACTAATGCAACACGCTATTTATCA 57.081 33.333 0.00 0.00 43.06 2.15
460 482 7.630924 AGAACTAATGCAACACGCTATTTATC 58.369 34.615 0.00 0.00 43.06 1.75
461 483 7.553881 AGAACTAATGCAACACGCTATTTAT 57.446 32.000 0.00 0.00 43.06 1.40
462 484 6.978343 AGAACTAATGCAACACGCTATTTA 57.022 33.333 0.00 0.00 43.06 1.40
463 485 5.880054 AGAACTAATGCAACACGCTATTT 57.120 34.783 0.00 0.00 43.06 1.40
464 486 6.978343 TTAGAACTAATGCAACACGCTATT 57.022 33.333 0.00 0.00 43.06 1.73
465 487 6.456988 GCTTTAGAACTAATGCAACACGCTAT 60.457 38.462 19.99 0.00 42.36 2.97
466 488 5.163893 GCTTTAGAACTAATGCAACACGCTA 60.164 40.000 19.99 0.00 42.36 4.26
467 489 4.378459 GCTTTAGAACTAATGCAACACGCT 60.378 41.667 19.99 0.00 42.36 5.07
468 490 3.846335 GCTTTAGAACTAATGCAACACGC 59.154 43.478 19.99 0.00 42.36 5.34
469 491 5.029650 TGCTTTAGAACTAATGCAACACG 57.970 39.130 23.15 0.00 46.32 4.49
475 497 6.314784 ACACGAATTGCTTTAGAACTAATGC 58.685 36.000 18.85 18.85 42.81 3.56
476 498 8.150300 CAACACGAATTGCTTTAGAACTAATG 57.850 34.615 0.00 0.00 0.00 1.90
490 512 4.562394 AGTGAACAAAAGCAACACGAATTG 59.438 37.500 0.00 0.00 36.71 2.32
491 513 4.743493 AGTGAACAAAAGCAACACGAATT 58.257 34.783 0.00 0.00 36.71 2.17
492 514 4.370364 AGTGAACAAAAGCAACACGAAT 57.630 36.364 0.00 0.00 36.71 3.34
493 515 3.840890 AGTGAACAAAAGCAACACGAA 57.159 38.095 0.00 0.00 36.71 3.85
494 516 3.064271 GGTAGTGAACAAAAGCAACACGA 59.936 43.478 0.00 0.00 36.71 4.35
495 517 3.359654 GGTAGTGAACAAAAGCAACACG 58.640 45.455 0.00 0.00 36.71 4.49
496 518 3.359654 CGGTAGTGAACAAAAGCAACAC 58.640 45.455 0.00 0.00 0.00 3.32
497 519 2.356382 CCGGTAGTGAACAAAAGCAACA 59.644 45.455 0.00 0.00 0.00 3.33
498 520 2.356695 ACCGGTAGTGAACAAAAGCAAC 59.643 45.455 4.49 0.00 0.00 4.17
499 521 2.645802 ACCGGTAGTGAACAAAAGCAA 58.354 42.857 4.49 0.00 0.00 3.91
500 522 2.335316 ACCGGTAGTGAACAAAAGCA 57.665 45.000 4.49 0.00 0.00 3.91
501 523 2.156310 CGTACCGGTAGTGAACAAAAGC 59.844 50.000 16.41 0.00 0.00 3.51
502 524 3.383761 ACGTACCGGTAGTGAACAAAAG 58.616 45.455 16.41 0.00 0.00 2.27
503 525 3.451141 ACGTACCGGTAGTGAACAAAA 57.549 42.857 16.41 0.00 0.00 2.44
504 526 3.122297 CAACGTACCGGTAGTGAACAAA 58.878 45.455 16.41 0.00 0.00 2.83
505 527 2.741612 CAACGTACCGGTAGTGAACAA 58.258 47.619 16.41 0.00 0.00 2.83
506 528 1.602668 GCAACGTACCGGTAGTGAACA 60.603 52.381 16.41 0.00 0.00 3.18
507 529 1.063031 GCAACGTACCGGTAGTGAAC 58.937 55.000 16.41 4.16 0.00 3.18
508 530 0.961019 AGCAACGTACCGGTAGTGAA 59.039 50.000 16.41 0.00 0.00 3.18
509 531 0.241749 CAGCAACGTACCGGTAGTGA 59.758 55.000 16.41 0.00 0.00 3.41
510 532 0.038892 ACAGCAACGTACCGGTAGTG 60.039 55.000 16.41 14.43 0.00 2.74
511 533 1.470098 CTACAGCAACGTACCGGTAGT 59.530 52.381 16.41 12.46 0.00 2.73
512 534 1.470098 ACTACAGCAACGTACCGGTAG 59.530 52.381 16.41 17.67 35.53 3.18
513 535 1.199789 CACTACAGCAACGTACCGGTA 59.800 52.381 11.16 11.16 0.00 4.02
514 536 0.038892 CACTACAGCAACGTACCGGT 60.039 55.000 13.98 13.98 0.00 5.28
515 537 0.734942 CCACTACAGCAACGTACCGG 60.735 60.000 0.00 0.00 0.00 5.28
516 538 0.038892 ACCACTACAGCAACGTACCG 60.039 55.000 0.00 0.00 0.00 4.02
517 539 2.159327 AACCACTACAGCAACGTACC 57.841 50.000 0.00 0.00 0.00 3.34
518 540 3.122445 GCTTAACCACTACAGCAACGTAC 59.878 47.826 0.00 0.00 32.17 3.67
519 541 3.319755 GCTTAACCACTACAGCAACGTA 58.680 45.455 0.00 0.00 32.17 3.57
520 542 2.140717 GCTTAACCACTACAGCAACGT 58.859 47.619 0.00 0.00 32.17 3.99
521 543 1.126113 CGCTTAACCACTACAGCAACG 59.874 52.381 0.00 0.00 32.17 4.10
522 544 2.409975 TCGCTTAACCACTACAGCAAC 58.590 47.619 0.00 0.00 32.17 4.17
523 545 2.823924 TCGCTTAACCACTACAGCAA 57.176 45.000 0.00 0.00 32.17 3.91
524 546 2.297880 TCTTCGCTTAACCACTACAGCA 59.702 45.455 0.00 0.00 32.17 4.41
525 547 2.955614 TCTTCGCTTAACCACTACAGC 58.044 47.619 0.00 0.00 0.00 4.40
526 548 4.557205 ACTTCTTCGCTTAACCACTACAG 58.443 43.478 0.00 0.00 0.00 2.74
527 549 4.595762 ACTTCTTCGCTTAACCACTACA 57.404 40.909 0.00 0.00 0.00 2.74
528 550 4.377124 GCAACTTCTTCGCTTAACCACTAC 60.377 45.833 0.00 0.00 0.00 2.73
529 551 3.744426 GCAACTTCTTCGCTTAACCACTA 59.256 43.478 0.00 0.00 0.00 2.74
530 552 2.548480 GCAACTTCTTCGCTTAACCACT 59.452 45.455 0.00 0.00 0.00 4.00
531 553 2.289547 TGCAACTTCTTCGCTTAACCAC 59.710 45.455 0.00 0.00 0.00 4.16
532 554 2.566913 TGCAACTTCTTCGCTTAACCA 58.433 42.857 0.00 0.00 0.00 3.67
533 555 3.555518 CTTGCAACTTCTTCGCTTAACC 58.444 45.455 0.00 0.00 0.00 2.85
534 556 2.973879 GCTTGCAACTTCTTCGCTTAAC 59.026 45.455 0.00 0.00 0.00 2.01
535 557 2.616376 TGCTTGCAACTTCTTCGCTTAA 59.384 40.909 0.00 0.00 0.00 1.85
536 558 2.217750 TGCTTGCAACTTCTTCGCTTA 58.782 42.857 0.00 0.00 0.00 3.09
537 559 1.024271 TGCTTGCAACTTCTTCGCTT 58.976 45.000 0.00 0.00 0.00 4.68
538 560 1.024271 TTGCTTGCAACTTCTTCGCT 58.976 45.000 3.70 0.00 0.00 4.93
539 561 1.838913 TTTGCTTGCAACTTCTTCGC 58.161 45.000 7.60 0.00 0.00 4.70
540 562 2.154389 GCATTTGCTTGCAACTTCTTCG 59.846 45.455 7.60 0.00 42.31 3.79
541 563 2.154389 CGCATTTGCTTGCAACTTCTTC 59.846 45.455 7.60 0.00 42.91 2.87
542 564 2.129607 CGCATTTGCTTGCAACTTCTT 58.870 42.857 7.60 0.00 42.91 2.52
543 565 1.603678 CCGCATTTGCTTGCAACTTCT 60.604 47.619 7.60 0.00 42.91 2.85
544 566 0.785979 CCGCATTTGCTTGCAACTTC 59.214 50.000 7.60 0.00 42.91 3.01
545 567 1.223417 GCCGCATTTGCTTGCAACTT 61.223 50.000 7.60 0.00 42.91 2.66
546 568 1.665599 GCCGCATTTGCTTGCAACT 60.666 52.632 7.60 0.00 42.91 3.16
547 569 2.855325 GCCGCATTTGCTTGCAAC 59.145 55.556 7.60 0.00 42.91 4.17
548 570 2.733969 CGCCGCATTTGCTTGCAA 60.734 55.556 3.70 3.70 42.91 4.08
549 571 3.976000 ACGCCGCATTTGCTTGCA 61.976 55.556 12.39 0.00 42.91 4.08
550 572 3.472298 CACGCCGCATTTGCTTGC 61.472 61.111 0.51 2.78 39.32 4.01
551 573 1.798725 CTCACGCCGCATTTGCTTG 60.799 57.895 0.51 0.00 39.32 4.01
552 574 1.308069 ATCTCACGCCGCATTTGCTT 61.308 50.000 0.51 0.00 39.32 3.91
553 575 1.709147 GATCTCACGCCGCATTTGCT 61.709 55.000 0.51 0.00 39.32 3.91
554 576 1.297893 GATCTCACGCCGCATTTGC 60.298 57.895 0.00 0.00 37.78 3.68
555 577 0.447406 TTGATCTCACGCCGCATTTG 59.553 50.000 0.00 0.00 0.00 2.32
556 578 1.164411 TTTGATCTCACGCCGCATTT 58.836 45.000 0.00 0.00 0.00 2.32
557 579 1.331756 GATTTGATCTCACGCCGCATT 59.668 47.619 0.00 0.00 0.00 3.56
558 580 0.940126 GATTTGATCTCACGCCGCAT 59.060 50.000 0.00 0.00 0.00 4.73
559 581 1.089481 GGATTTGATCTCACGCCGCA 61.089 55.000 0.00 0.00 0.00 5.69
560 582 1.643832 GGATTTGATCTCACGCCGC 59.356 57.895 0.00 0.00 0.00 6.53
561 583 1.160329 GGGGATTTGATCTCACGCCG 61.160 60.000 0.00 0.00 0.00 6.46
562 584 1.160329 CGGGGATTTGATCTCACGCC 61.160 60.000 0.00 0.00 0.00 5.68
563 585 0.462047 ACGGGGATTTGATCTCACGC 60.462 55.000 0.00 0.00 32.16 5.34
564 586 1.933853 GAACGGGGATTTGATCTCACG 59.066 52.381 0.00 0.00 34.17 4.35
565 587 2.939103 CAGAACGGGGATTTGATCTCAC 59.061 50.000 0.00 0.00 0.00 3.51
566 588 2.571653 ACAGAACGGGGATTTGATCTCA 59.428 45.455 0.00 0.00 0.00 3.27
567 589 3.198872 GACAGAACGGGGATTTGATCTC 58.801 50.000 0.00 0.00 0.00 2.75
568 590 2.571653 TGACAGAACGGGGATTTGATCT 59.428 45.455 0.00 0.00 0.00 2.75
569 591 2.985896 TGACAGAACGGGGATTTGATC 58.014 47.619 0.00 0.00 0.00 2.92
570 592 3.433306 TTGACAGAACGGGGATTTGAT 57.567 42.857 0.00 0.00 0.00 2.57
571 593 2.940994 TTGACAGAACGGGGATTTGA 57.059 45.000 0.00 0.00 0.00 2.69
572 594 4.519540 ATTTTGACAGAACGGGGATTTG 57.480 40.909 0.00 0.00 0.00 2.32
573 595 5.545063 AAATTTTGACAGAACGGGGATTT 57.455 34.783 0.00 0.00 0.00 2.17
574 596 5.296748 CAAAATTTTGACAGAACGGGGATT 58.703 37.500 23.72 0.00 40.55 3.01
575 597 4.799255 GCAAAATTTTGACAGAACGGGGAT 60.799 41.667 30.40 0.00 40.55 3.85
576 598 3.491792 GCAAAATTTTGACAGAACGGGGA 60.492 43.478 30.40 0.00 40.55 4.81
577 599 2.799978 GCAAAATTTTGACAGAACGGGG 59.200 45.455 30.40 3.92 40.55 5.73
578 600 2.470999 CGCAAAATTTTGACAGAACGGG 59.529 45.455 30.40 8.79 40.55 5.28
579 601 3.061271 CACGCAAAATTTTGACAGAACGG 60.061 43.478 30.40 14.41 40.55 4.44
580 602 3.599116 GCACGCAAAATTTTGACAGAACG 60.599 43.478 30.40 23.74 40.55 3.95
581 603 3.551485 AGCACGCAAAATTTTGACAGAAC 59.449 39.130 30.40 15.28 40.55 3.01
582 604 3.779759 AGCACGCAAAATTTTGACAGAA 58.220 36.364 30.40 0.00 40.55 3.02
583 605 3.435105 AGCACGCAAAATTTTGACAGA 57.565 38.095 30.40 0.00 40.55 3.41
584 606 4.519191 AAAGCACGCAAAATTTTGACAG 57.481 36.364 30.40 21.90 40.55 3.51
585 607 4.935885 AAAAGCACGCAAAATTTTGACA 57.064 31.818 30.40 0.00 40.55 3.58
606 628 5.007626 CAGGAACAGAGTCATTCACGAAAAA 59.992 40.000 8.83 0.00 0.00 1.94
607 629 4.511454 CAGGAACAGAGTCATTCACGAAAA 59.489 41.667 8.83 0.00 0.00 2.29
608 630 4.058124 CAGGAACAGAGTCATTCACGAAA 58.942 43.478 8.83 0.00 0.00 3.46
609 631 3.554960 CCAGGAACAGAGTCATTCACGAA 60.555 47.826 8.83 0.00 0.00 3.85
610 632 2.029020 CCAGGAACAGAGTCATTCACGA 60.029 50.000 8.83 0.00 0.00 4.35
611 633 2.341257 CCAGGAACAGAGTCATTCACG 58.659 52.381 8.83 0.00 0.00 4.35
612 634 2.704572 CCCAGGAACAGAGTCATTCAC 58.295 52.381 8.83 0.68 0.00 3.18
613 635 1.003580 GCCCAGGAACAGAGTCATTCA 59.996 52.381 8.83 0.00 0.00 2.57
614 636 1.680249 GGCCCAGGAACAGAGTCATTC 60.680 57.143 0.00 0.00 0.00 2.67
615 637 0.329596 GGCCCAGGAACAGAGTCATT 59.670 55.000 0.00 0.00 0.00 2.57
616 638 1.903877 CGGCCCAGGAACAGAGTCAT 61.904 60.000 0.00 0.00 0.00 3.06
617 639 2.583441 CGGCCCAGGAACAGAGTCA 61.583 63.158 0.00 0.00 0.00 3.41
618 640 2.232298 CTCGGCCCAGGAACAGAGTC 62.232 65.000 0.00 0.00 0.00 3.36
619 641 2.203788 TCGGCCCAGGAACAGAGT 60.204 61.111 0.00 0.00 0.00 3.24
620 642 2.286523 ACTCGGCCCAGGAACAGAG 61.287 63.158 1.31 0.07 0.00 3.35
621 643 2.203788 ACTCGGCCCAGGAACAGA 60.204 61.111 1.31 0.00 0.00 3.41
622 644 1.541310 TACACTCGGCCCAGGAACAG 61.541 60.000 1.31 0.00 0.00 3.16
623 645 1.534476 TACACTCGGCCCAGGAACA 60.534 57.895 1.31 0.00 0.00 3.18
624 646 1.218316 CTACACTCGGCCCAGGAAC 59.782 63.158 1.31 0.00 0.00 3.62
625 647 0.543410 TTCTACACTCGGCCCAGGAA 60.543 55.000 1.31 0.00 0.00 3.36
626 648 0.325296 ATTCTACACTCGGCCCAGGA 60.325 55.000 1.31 0.00 0.00 3.86
627 649 0.541863 AATTCTACACTCGGCCCAGG 59.458 55.000 1.31 0.00 0.00 4.45
628 650 1.656652 CAATTCTACACTCGGCCCAG 58.343 55.000 0.00 0.00 0.00 4.45
629 651 0.251916 CCAATTCTACACTCGGCCCA 59.748 55.000 0.00 0.00 0.00 5.36
630 652 1.095807 GCCAATTCTACACTCGGCCC 61.096 60.000 0.00 0.00 33.31 5.80
631 653 2.394604 GCCAATTCTACACTCGGCC 58.605 57.895 0.00 0.00 33.31 6.13
632 654 1.095807 GGGCCAATTCTACACTCGGC 61.096 60.000 4.39 0.00 38.85 5.54
633 655 0.251916 TGGGCCAATTCTACACTCGG 59.748 55.000 2.13 0.00 0.00 4.63
634 656 1.338674 TGTGGGCCAATTCTACACTCG 60.339 52.381 8.40 0.00 33.44 4.18
635 657 2.489938 TGTGGGCCAATTCTACACTC 57.510 50.000 8.40 0.00 33.44 3.51
636 658 2.969821 TTGTGGGCCAATTCTACACT 57.030 45.000 8.40 0.00 33.44 3.55
637 659 3.153919 TCTTTGTGGGCCAATTCTACAC 58.846 45.455 8.40 1.49 31.81 2.90
638 660 3.420893 CTCTTTGTGGGCCAATTCTACA 58.579 45.455 8.40 0.00 31.81 2.74
639 661 2.164422 GCTCTTTGTGGGCCAATTCTAC 59.836 50.000 8.40 0.00 31.81 2.59
640 662 2.041620 AGCTCTTTGTGGGCCAATTCTA 59.958 45.455 8.40 0.00 31.81 2.10
641 663 1.203100 AGCTCTTTGTGGGCCAATTCT 60.203 47.619 8.40 0.00 31.81 2.40
642 664 1.203287 GAGCTCTTTGTGGGCCAATTC 59.797 52.381 8.40 0.00 31.81 2.17
643 665 1.260544 GAGCTCTTTGTGGGCCAATT 58.739 50.000 8.40 0.00 31.81 2.32
644 666 0.613012 GGAGCTCTTTGTGGGCCAAT 60.613 55.000 8.40 0.00 31.81 3.16
645 667 1.228552 GGAGCTCTTTGTGGGCCAA 60.229 57.895 8.40 0.00 0.00 4.52
646 668 2.436109 GGAGCTCTTTGTGGGCCA 59.564 61.111 14.64 0.00 0.00 5.36
647 669 2.361737 GGGAGCTCTTTGTGGGCC 60.362 66.667 14.64 0.00 0.00 5.80
648 670 2.747855 CGGGAGCTCTTTGTGGGC 60.748 66.667 14.64 0.00 0.00 5.36
649 671 0.537371 AAACGGGAGCTCTTTGTGGG 60.537 55.000 14.64 0.00 0.00 4.61
650 672 1.318576 AAAACGGGAGCTCTTTGTGG 58.681 50.000 14.64 0.00 0.00 4.17
651 673 2.618709 AGAAAAACGGGAGCTCTTTGTG 59.381 45.455 14.64 1.85 0.00 3.33
652 674 2.618709 CAGAAAAACGGGAGCTCTTTGT 59.381 45.455 14.64 6.94 0.00 2.83
653 675 2.030805 CCAGAAAAACGGGAGCTCTTTG 60.031 50.000 14.64 6.27 35.91 2.77
654 676 2.230660 CCAGAAAAACGGGAGCTCTTT 58.769 47.619 14.64 5.60 35.91 2.52
655 677 1.545651 CCCAGAAAAACGGGAGCTCTT 60.546 52.381 14.64 0.00 46.34 2.85
656 678 0.036875 CCCAGAAAAACGGGAGCTCT 59.963 55.000 14.64 0.00 46.34 4.09
657 679 1.587043 GCCCAGAAAAACGGGAGCTC 61.587 60.000 4.71 4.71 46.34 4.09
658 680 1.603739 GCCCAGAAAAACGGGAGCT 60.604 57.895 0.00 0.00 46.34 4.09
659 681 0.322187 TAGCCCAGAAAAACGGGAGC 60.322 55.000 0.00 0.00 46.34 4.70
660 682 2.420058 ATAGCCCAGAAAAACGGGAG 57.580 50.000 0.00 0.00 46.34 4.30
661 683 5.836024 ATATATAGCCCAGAAAAACGGGA 57.164 39.130 0.00 0.00 46.34 5.14
819 872 3.379880 CCAACCTGGCCAACATGG 58.620 61.111 7.01 11.50 41.55 3.66
959 1426 0.583438 CGATGTGTGATTCGGATGGC 59.417 55.000 0.00 0.00 0.00 4.40
1149 1648 2.604686 TTGCAGACGAGGGAGGCT 60.605 61.111 0.00 0.00 0.00 4.58
1472 2299 1.554617 TGAAGATGAACATCTGCCCGA 59.445 47.619 16.46 0.00 46.75 5.14
1555 2391 1.215647 CTCTGTCACGGGCTACCAC 59.784 63.158 0.00 0.00 36.13 4.16
1581 2426 4.789807 AGTAAAGGCATACGGAGACTCTA 58.210 43.478 1.74 0.00 0.00 2.43
1715 2595 6.467723 ACTCAAGTATGACATTTTGACGAC 57.532 37.500 9.69 0.00 0.00 4.34
1795 2681 8.188139 CGGCACAATCCATAACTTTTTATAGTT 58.812 33.333 0.00 0.00 41.13 2.24
1925 2817 5.503927 TGAGCTCCTCAAAATCAATAGCTT 58.496 37.500 12.15 0.00 38.85 3.74
2227 5829 4.461431 TGATTTGAACTGCAATCATCAGCT 59.539 37.500 2.95 0.00 36.15 4.24
2330 5936 8.826710 CGCATATTACCAATAGAGAAGAACAAA 58.173 33.333 0.00 0.00 0.00 2.83
2349 5986 9.202273 ACATTTGAAACACAATTTACGCATATT 57.798 25.926 0.00 0.00 38.36 1.28
2517 6205 8.398878 TGACAAGAAAAATAATAAGTTCCGGT 57.601 30.769 0.00 0.00 0.00 5.28
2551 6242 5.696724 AGAACGAACTAAGACATGACAAAGG 59.303 40.000 0.00 0.00 0.00 3.11
2552 6243 6.584954 CAGAACGAACTAAGACATGACAAAG 58.415 40.000 0.00 0.00 0.00 2.77
2616 6309 5.697633 ACGCGGAAGAAAATACACTTTCTAA 59.302 36.000 12.47 0.00 43.33 2.10
2625 6324 3.185797 ACAGTTCACGCGGAAGAAAATAC 59.814 43.478 12.47 0.60 35.82 1.89
2802 6550 1.613437 CCGGTTTCAGCTTCCAAATGT 59.387 47.619 0.00 0.00 0.00 2.71
2945 6696 5.308014 ACATGAGACATACAGAAAAGTGCA 58.692 37.500 0.00 0.00 0.00 4.57
3128 6937 8.667076 TCAGACAACCATCTCATATATTGTTG 57.333 34.615 0.00 0.00 36.53 3.33
3486 8701 1.574428 GCCACACTACCAGCAAACG 59.426 57.895 0.00 0.00 0.00 3.60
3497 8712 1.557269 GGATCCTCACTGGCCACACT 61.557 60.000 0.00 0.00 35.26 3.55
3598 9287 0.824109 CCGAAGTCATAGTGGGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
3680 9638 1.202245 GCAAACGAACCACTGAAAGCA 60.202 47.619 0.00 0.00 37.60 3.91
3712 9680 3.153919 GAGCAACCCACCAATTCTTACA 58.846 45.455 0.00 0.00 0.00 2.41
3714 9682 2.224670 ACGAGCAACCCACCAATTCTTA 60.225 45.455 0.00 0.00 0.00 2.10
3715 9683 1.247567 CGAGCAACCCACCAATTCTT 58.752 50.000 0.00 0.00 0.00 2.52
3749 9717 1.210722 TCGGCAGAGAGAGAAGCTAGA 59.789 52.381 0.00 0.00 0.00 2.43
3871 9889 4.625028 CGCAAGATGAACCAGATCAGATA 58.375 43.478 0.00 0.00 43.02 1.98
3901 9926 1.065199 ACATCGTCATCTTGTGGGCAT 60.065 47.619 0.00 0.00 0.00 4.40
3926 9951 1.154093 CCAAACATCTGCAGCAGCG 60.154 57.895 18.43 13.34 46.23 5.18
4047 10076 0.898320 ATCACCTTGTCCCAGTCTCG 59.102 55.000 0.00 0.00 0.00 4.04
4090 10119 5.156355 GCACCATCAAAACAGTATTGTCAG 58.844 41.667 0.00 0.00 36.23 3.51
4093 10122 3.894427 TGGCACCATCAAAACAGTATTGT 59.106 39.130 0.00 0.00 39.87 2.71
4096 10125 6.128486 TGATATGGCACCATCAAAACAGTAT 58.872 36.000 5.20 0.00 37.82 2.12
4098 10127 4.343231 TGATATGGCACCATCAAAACAGT 58.657 39.130 5.20 0.00 37.82 3.55


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

AutoCloner maintained by Alex Coulton.