Multiple sequence alignment - TraesCS5B01G423700

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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 TraesCS5B01G423700 chr5B 100.000 4519 0 0 1 4519 600053208 600057726 0.000000e+00 8346.0
1 TraesCS5B01G423700 chr5B 81.057 227 17 16 903 1112 599988696 599988913 1.680000e-34 158.0
2 TraesCS5B01G423700 chr5B 81.057 227 17 16 903 1112 600010193 600010410 1.680000e-34 158.0
3 TraesCS5B01G423700 chr5B 81.057 227 17 16 903 1112 600031587 600031804 1.680000e-34 158.0
4 TraesCS5B01G423700 chr5D 91.236 2111 113 47 666 2725 487467008 487469097 0.000000e+00 2808.0
5 TraesCS5B01G423700 chr5D 86.010 1158 87 35 2727 3861 487469142 487470247 0.000000e+00 1171.0
6 TraesCS5B01G423700 chr5D 84.630 527 65 12 47 568 487466492 487467007 1.120000e-140 510.0
7 TraesCS5B01G423700 chr5D 91.159 328 21 4 3342 3666 487494396 487494718 5.370000e-119 438.0
8 TraesCS5B01G423700 chr5D 78.561 695 86 26 3863 4519 487472113 487472782 2.530000e-107 399.0
9 TraesCS5B01G423700 chr5D 91.549 213 13 3 901 1111 487485351 487485560 5.720000e-74 289.0
10 TraesCS5B01G423700 chr5D 91.542 201 17 0 3865 4065 487494720 487494920 1.240000e-70 278.0
11 TraesCS5B01G423700 chr5D 89.503 181 13 3 669 845 487449551 487449729 1.640000e-54 224.0
12 TraesCS5B01G423700 chr5D 79.751 321 44 14 1 320 487449293 487449593 3.540000e-51 213.0
13 TraesCS5B01G423700 chr5D 83.796 216 26 2 4058 4265 487495371 487495157 3.570000e-46 196.0
14 TraesCS5B01G423700 chr5D 86.387 191 12 8 4331 4519 487495363 487495541 3.570000e-46 196.0
15 TraesCS5B01G423700 chr5D 80.435 230 23 15 901 1112 487449938 487450163 6.050000e-34 156.0
16 TraesCS5B01G423700 chr5D 84.967 153 11 5 669 809 487484773 487484925 1.310000e-30 145.0
17 TraesCS5B01G423700 chr5A 93.312 1271 52 17 880 2129 608031410 608032668 0.000000e+00 1845.0
18 TraesCS5B01G423700 chr5A 90.476 672 41 7 3763 4421 608063301 608063962 0.000000e+00 865.0
19 TraesCS5B01G423700 chr5A 89.365 677 49 11 3763 4424 608085761 608086429 0.000000e+00 830.0
20 TraesCS5B01G423700 chr5A 91.556 604 27 7 2728 3327 608033532 608034115 0.000000e+00 811.0
21 TraesCS5B01G423700 chr5A 94.605 519 15 4 2209 2727 608032984 608033489 0.000000e+00 791.0
22 TraesCS5B01G423700 chr5A 92.135 445 21 6 3329 3772 608059931 608060362 2.310000e-172 616.0
23 TraesCS5B01G423700 chr5A 91.648 443 23 6 3329 3771 608082400 608082828 6.470000e-168 601.0
24 TraesCS5B01G423700 chr5A 77.945 866 121 36 3695 4519 608039874 608040710 1.140000e-130 477.0
25 TraesCS5B01G423700 chr5A 91.549 213 13 3 901 1111 608082186 608082395 5.720000e-74 289.0
26 TraesCS5B01G423700 chr5A 90.741 216 12 4 901 1111 608059714 608059926 9.570000e-72 281.0
27 TraesCS5B01G423700 chr5A 87.975 158 9 3 678 825 608031158 608031315 1.290000e-40 178.0
28 TraesCS5B01G423700 chr1A 76.857 350 73 7 322 666 186665227 186664881 1.660000e-44 191.0
29 TraesCS5B01G423700 chr1A 87.500 80 7 3 2567 2645 520351806 520351729 6.230000e-14 89.8
30 TraesCS5B01G423700 chr6D 76.667 360 66 16 318 666 91389067 91388715 2.780000e-42 183.0
31 TraesCS5B01G423700 chr7D 76.023 342 70 11 322 655 153414108 153413771 2.800000e-37 167.0
32 TraesCS5B01G423700 chr4A 74.474 333 72 10 322 645 398489300 398488972 1.020000e-26 132.0
33 TraesCS5B01G423700 chr3B 77.249 189 32 10 322 504 49982222 49982039 2.880000e-17 100.0
34 TraesCS5B01G423700 chr3B 79.048 105 15 7 362 462 330601483 330601584 1.050000e-06 65.8
35 TraesCS5B01G423700 chr2D 83.871 93 8 6 2568 2659 446919527 446919441 1.040000e-11 82.4
36 TraesCS5B01G423700 chr2D 82.979 94 9 6 2567 2659 446904919 446904832 1.350000e-10 78.7
37 TraesCS5B01G423700 chr2D 76.923 143 27 5 366 505 406264632 406264771 4.850000e-10 76.8
38 TraesCS5B01G423700 chr2D 89.130 46 5 0 28 73 422755467 422755422 1.760000e-04 58.4
39 TraesCS5B01G423700 chrUn 80.189 106 18 3 363 466 35699777 35699673 4.850000e-10 76.8
40 TraesCS5B01G423700 chr3D 78.195 133 19 7 2564 2695 466752820 466752943 4.850000e-10 76.8
41 TraesCS5B01G423700 chr4B 88.333 60 6 1 322 381 189796324 189796382 2.260000e-08 71.3
42 TraesCS5B01G423700 chr2B 100.000 29 0 0 47 75 495921083 495921111 2.000000e-03 54.7
43 TraesCS5B01G423700 chr6A 94.286 35 1 1 4476 4509 603364647 603364681 8.000000e-03 52.8


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 TraesCS5B01G423700 chr5B 600053208 600057726 4518 False 8346.000000 8346 100.000000 1 4519 1 chr5B.!!$F4 4518
1 TraesCS5B01G423700 chr5D 487466492 487472782 6290 False 1222.000000 2808 85.109250 47 4519 4 chr5D.!!$F2 4472
2 TraesCS5B01G423700 chr5D 487494396 487495541 1145 False 304.000000 438 89.696000 3342 4519 3 chr5D.!!$F4 1177
3 TraesCS5B01G423700 chr5D 487484773 487485560 787 False 217.000000 289 88.258000 669 1111 2 chr5D.!!$F3 442
4 TraesCS5B01G423700 chr5A 608031158 608034115 2957 False 906.250000 1845 91.862000 678 3327 4 chr5A.!!$F2 2649
5 TraesCS5B01G423700 chr5A 608059714 608063962 4248 False 587.333333 865 91.117333 901 4421 3 chr5A.!!$F3 3520
6 TraesCS5B01G423700 chr5A 608082186 608086429 4243 False 573.333333 830 90.854000 901 4424 3 chr5A.!!$F4 3523
7 TraesCS5B01G423700 chr5A 608039874 608040710 836 False 477.000000 477 77.945000 3695 4519 1 chr5A.!!$F1 824

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
657 662 0.108186 CAGAATAGACCGGCTGTGCA 60.108 55.000 0.00 0.00 0.0 4.57 F
658 663 0.833287 AGAATAGACCGGCTGTGCAT 59.167 50.000 0.00 0.00 0.0 3.96 F
848 879 0.949105 TCCCGAAAAGTGAAGCTCGC 60.949 55.000 0.00 0.00 0.0 5.03 F
1586 2002 1.514553 GTGTCACCCTACTACGGCC 59.485 63.158 0.00 0.00 0.0 6.13 F
2443 3101 1.063174 GACATTAAAGGCTCAGCTGCG 59.937 52.381 9.47 3.41 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1899 0.024238 CGTTGAAGCTCTTGATCGCG 59.976 55.000 0.00 0.0 0.0 5.87 R
1573 1989 2.123982 CTCGGGCCGTAGTAGGGT 60.124 66.667 27.32 0.0 0.0 4.34 R
1979 2398 2.125512 GGCGTCGCTCCAGTCAAT 60.126 61.111 18.11 0.0 0.0 2.57 R
3107 3812 0.040425 ACAAGACATGCGGCGTTTTC 60.040 50.000 9.37 0.0 0.0 2.29 R
3518 4236 0.580104 GACACGAGACCAACAAACCG 59.420 55.000 0.00 0.0 0.0 4.44 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
17 18 3.326109 AACGGTTTGAGGCGTTCG 58.674 55.556 0.00 0.00 0.00 3.95
18 19 2.248835 AACGGTTTGAGGCGTTCGG 61.249 57.895 0.00 0.00 0.00 4.30
19 20 2.356553 CGGTTTGAGGCGTTCGGA 60.357 61.111 0.00 0.00 0.00 4.55
20 21 1.740296 CGGTTTGAGGCGTTCGGAT 60.740 57.895 0.00 0.00 0.00 4.18
21 22 1.794222 GGTTTGAGGCGTTCGGATG 59.206 57.895 0.00 0.00 0.00 3.51
22 23 1.644786 GGTTTGAGGCGTTCGGATGG 61.645 60.000 0.00 0.00 0.00 3.51
23 24 0.672401 GTTTGAGGCGTTCGGATGGA 60.672 55.000 0.00 0.00 0.00 3.41
24 25 0.251916 TTTGAGGCGTTCGGATGGAT 59.748 50.000 0.00 0.00 0.00 3.41
25 26 0.179084 TTGAGGCGTTCGGATGGATC 60.179 55.000 0.00 0.00 0.00 3.36
26 27 1.661821 GAGGCGTTCGGATGGATCG 60.662 63.158 0.00 0.00 40.10 3.69
27 28 2.661866 GGCGTTCGGATGGATCGG 60.662 66.667 0.00 0.00 38.11 4.18
28 29 2.106332 GCGTTCGGATGGATCGGT 59.894 61.111 0.00 0.00 38.11 4.69
29 30 1.520787 GCGTTCGGATGGATCGGTT 60.521 57.895 0.00 0.00 38.11 4.44
30 31 1.087771 GCGTTCGGATGGATCGGTTT 61.088 55.000 0.00 0.00 38.11 3.27
31 32 1.365699 CGTTCGGATGGATCGGTTTT 58.634 50.000 0.00 0.00 34.88 2.43
32 33 1.735571 CGTTCGGATGGATCGGTTTTT 59.264 47.619 0.00 0.00 34.88 1.94
79 80 0.313043 GTCCGGACGTTTGAGACTGA 59.687 55.000 20.85 0.00 0.00 3.41
94 95 1.212250 ACTGATTTAAGGCCCCCGGT 61.212 55.000 0.00 0.00 0.00 5.28
95 96 0.465642 CTGATTTAAGGCCCCCGGTC 60.466 60.000 0.00 0.00 0.00 4.79
96 97 1.208844 TGATTTAAGGCCCCCGGTCA 61.209 55.000 0.00 0.00 0.00 4.02
102 103 0.697854 AAGGCCCCCGGTCATAGATT 60.698 55.000 0.00 0.00 0.00 2.40
105 106 0.765510 GCCCCCGGTCATAGATTCTT 59.234 55.000 0.00 0.00 0.00 2.52
136 137 4.650734 TCTTGACTGTAATGCCATCACAA 58.349 39.130 0.00 0.00 0.00 3.33
137 138 5.255687 TCTTGACTGTAATGCCATCACAAT 58.744 37.500 0.00 0.00 0.00 2.71
141 142 5.942826 TGACTGTAATGCCATCACAATACAA 59.057 36.000 0.00 0.00 0.00 2.41
151 152 5.916883 GCCATCACAATACAAGAATATGCAC 59.083 40.000 0.00 0.00 0.00 4.57
170 171 6.122850 TGCACTGCATAAAATACATGACTC 57.877 37.500 0.00 0.00 31.71 3.36
185 186 9.486497 AATACATGACTCACTGATGAATATGTC 57.514 33.333 0.00 0.00 35.75 3.06
189 190 8.574737 CATGACTCACTGATGAATATGTCTCTA 58.425 37.037 0.00 0.00 33.30 2.43
191 192 8.409371 TGACTCACTGATGAATATGTCTCTAAC 58.591 37.037 0.00 0.00 33.30 2.34
229 231 6.937436 AACCTTCGTTTTCTTTGTCAGTAT 57.063 33.333 0.00 0.00 0.00 2.12
243 245 0.734253 CAGTATGATAGAGCGGCCGC 60.734 60.000 42.34 42.34 39.69 6.53
283 285 5.351465 TCACTTCTAGTTTGAATGATTCGGC 59.649 40.000 0.18 0.00 0.00 5.54
334 337 8.248117 ACTTGTCTAATTAAAAATACGCTCGT 57.752 30.769 0.00 0.00 0.00 4.18
337 340 6.957077 TGTCTAATTAAAAATACGCTCGTTGC 59.043 34.615 0.00 0.00 38.57 4.17
346 349 2.243957 CGCTCGTTGCCACTTGTCA 61.244 57.895 0.00 0.00 38.78 3.58
351 354 1.658409 GTTGCCACTTGTCAAGCGC 60.658 57.895 12.66 14.14 0.00 5.92
352 355 2.117779 TTGCCACTTGTCAAGCGCA 61.118 52.632 19.07 19.07 35.89 6.09
353 356 2.062361 TTGCCACTTGTCAAGCGCAG 62.062 55.000 20.91 0.72 38.05 5.18
379 382 9.797473 GCATTATTTTTGAAACTGCTCTTAAAC 57.203 29.630 0.00 0.00 0.00 2.01
392 395 7.051000 ACTGCTCTTAAACCATAAGGAATCTC 58.949 38.462 0.00 0.00 38.69 2.75
393 396 6.049149 TGCTCTTAAACCATAAGGAATCTCG 58.951 40.000 0.00 0.00 38.69 4.04
398 401 9.162764 TCTTAAACCATAAGGAATCTCGAAAAG 57.837 33.333 0.00 0.00 38.69 2.27
410 413 7.066284 AGGAATCTCGAAAAGTGTTCAATATGG 59.934 37.037 0.00 0.00 0.00 2.74
421 424 4.218417 GTGTTCAATATGGTGAAGTTGCCT 59.782 41.667 0.00 0.00 38.17 4.75
427 431 6.321181 TCAATATGGTGAAGTTGCCTTAATCC 59.679 38.462 0.00 0.00 0.00 3.01
440 444 5.457686 TGCCTTAATCCATAGCTTTCCAAT 58.542 37.500 0.00 0.00 0.00 3.16
444 448 6.293626 CCTTAATCCATAGCTTTCCAATGACG 60.294 42.308 0.00 0.00 0.00 4.35
445 449 3.627395 TCCATAGCTTTCCAATGACGT 57.373 42.857 0.00 0.00 0.00 4.34
451 455 6.873605 CCATAGCTTTCCAATGACGTATCATA 59.126 38.462 0.00 0.00 45.26 2.15
452 456 7.550551 CCATAGCTTTCCAATGACGTATCATAT 59.449 37.037 0.00 0.00 45.26 1.78
453 457 6.791887 AGCTTTCCAATGACGTATCATATG 57.208 37.500 0.00 0.00 45.26 1.78
454 458 5.180117 AGCTTTCCAATGACGTATCATATGC 59.820 40.000 0.00 0.00 45.26 3.14
455 459 5.049474 GCTTTCCAATGACGTATCATATGCA 60.049 40.000 0.00 0.00 45.26 3.96
456 460 6.348786 GCTTTCCAATGACGTATCATATGCAT 60.349 38.462 3.79 3.79 45.26 3.96
457 461 7.509141 TTTCCAATGACGTATCATATGCATT 57.491 32.000 3.54 0.00 45.26 3.56
458 462 6.484818 TCCAATGACGTATCATATGCATTG 57.515 37.500 17.63 17.63 45.26 2.82
459 463 5.997129 TCCAATGACGTATCATATGCATTGT 59.003 36.000 20.52 9.30 45.26 2.71
466 470 6.048509 ACGTATCATATGCATTGTTCAGACA 58.951 36.000 3.54 0.00 0.00 3.41
483 488 4.636648 TCAGACAAACGGTTAAAAAGCTGA 59.363 37.500 0.00 0.00 0.00 4.26
537 542 0.736053 TTTGCGACCACAAGTTCACC 59.264 50.000 0.00 0.00 0.00 4.02
543 548 1.342174 GACCACAAGTTCACCCGTCTA 59.658 52.381 0.00 0.00 0.00 2.59
545 550 2.171027 ACCACAAGTTCACCCGTCTAAA 59.829 45.455 0.00 0.00 0.00 1.85
561 566 5.753438 CCGTCTAAATATTGCAGTGCTCTTA 59.247 40.000 17.60 5.73 0.00 2.10
575 580 8.889717 TGCAGTGCTCTTACTTAAATAAATACC 58.110 33.333 17.60 0.00 0.00 2.73
576 581 8.062448 GCAGTGCTCTTACTTAAATAAATACCG 58.938 37.037 8.18 0.00 0.00 4.02
577 582 9.095065 CAGTGCTCTTACTTAAATAAATACCGT 57.905 33.333 0.00 0.00 0.00 4.83
578 583 9.095065 AGTGCTCTTACTTAAATAAATACCGTG 57.905 33.333 0.00 0.00 0.00 4.94
579 584 7.849515 GTGCTCTTACTTAAATAAATACCGTGC 59.150 37.037 0.00 0.00 0.00 5.34
580 585 7.549842 TGCTCTTACTTAAATAAATACCGTGCA 59.450 33.333 0.00 0.00 0.00 4.57
581 586 7.849515 GCTCTTACTTAAATAAATACCGTGCAC 59.150 37.037 6.82 6.82 0.00 4.57
582 587 9.095065 CTCTTACTTAAATAAATACCGTGCACT 57.905 33.333 16.19 0.00 0.00 4.40
583 588 9.439500 TCTTACTTAAATAAATACCGTGCACTT 57.561 29.630 16.19 4.31 0.00 3.16
584 589 9.485591 CTTACTTAAATAAATACCGTGCACTTG 57.514 33.333 16.19 8.50 0.00 3.16
585 590 6.319399 ACTTAAATAAATACCGTGCACTTGC 58.681 36.000 16.19 0.00 42.50 4.01
586 591 3.398954 AATAAATACCGTGCACTTGCG 57.601 42.857 16.19 0.67 45.83 4.85
587 592 1.798283 TAAATACCGTGCACTTGCGT 58.202 45.000 16.19 8.01 45.83 5.24
588 593 0.515564 AAATACCGTGCACTTGCGTC 59.484 50.000 16.19 0.00 45.83 5.19
589 594 1.623081 AATACCGTGCACTTGCGTCG 61.623 55.000 16.19 10.32 45.83 5.12
590 595 2.480853 ATACCGTGCACTTGCGTCGA 62.481 55.000 16.19 0.00 45.83 4.20
591 596 3.767230 CCGTGCACTTGCGTCGAG 61.767 66.667 16.19 0.00 45.83 4.04
592 597 4.415501 CGTGCACTTGCGTCGAGC 62.416 66.667 16.19 0.00 45.83 5.03
606 611 4.726975 CGTCGAGCATGCAATTTAAAAG 57.273 40.909 21.98 0.03 0.00 2.27
607 612 4.158384 CGTCGAGCATGCAATTTAAAAGT 58.842 39.130 21.98 0.00 0.00 2.66
608 613 4.029418 CGTCGAGCATGCAATTTAAAAGTG 59.971 41.667 21.98 0.00 0.00 3.16
609 614 4.917415 GTCGAGCATGCAATTTAAAAGTGT 59.083 37.500 21.98 0.00 0.00 3.55
610 615 4.916831 TCGAGCATGCAATTTAAAAGTGTG 59.083 37.500 21.98 0.00 0.00 3.82
611 616 4.681025 CGAGCATGCAATTTAAAAGTGTGT 59.319 37.500 21.98 0.00 0.00 3.72
612 617 5.164158 CGAGCATGCAATTTAAAAGTGTGTC 60.164 40.000 21.98 1.28 0.00 3.67
613 618 4.990426 AGCATGCAATTTAAAAGTGTGTCC 59.010 37.500 21.98 0.00 0.00 4.02
614 619 4.749099 GCATGCAATTTAAAAGTGTGTCCA 59.251 37.500 14.21 0.00 0.00 4.02
615 620 5.236047 GCATGCAATTTAAAAGTGTGTCCAA 59.764 36.000 14.21 0.00 0.00 3.53
616 621 6.238320 GCATGCAATTTAAAAGTGTGTCCAAA 60.238 34.615 14.21 0.00 0.00 3.28
617 622 6.654793 TGCAATTTAAAAGTGTGTCCAAAC 57.345 33.333 0.00 0.00 0.00 2.93
618 623 6.402222 TGCAATTTAAAAGTGTGTCCAAACT 58.598 32.000 0.00 0.00 0.00 2.66
619 624 7.548097 TGCAATTTAAAAGTGTGTCCAAACTA 58.452 30.769 0.00 0.00 0.00 2.24
620 625 8.200792 TGCAATTTAAAAGTGTGTCCAAACTAT 58.799 29.630 0.00 0.00 0.00 2.12
621 626 8.699749 GCAATTTAAAAGTGTGTCCAAACTATC 58.300 33.333 0.00 0.00 0.00 2.08
622 627 9.743057 CAATTTAAAAGTGTGTCCAAACTATCA 57.257 29.630 0.00 0.00 0.00 2.15
625 630 9.959749 TTTAAAAGTGTGTCCAAACTATCATTC 57.040 29.630 0.00 0.00 0.00 2.67
626 631 7.823745 AAAAGTGTGTCCAAACTATCATTCT 57.176 32.000 0.00 0.00 0.00 2.40
627 632 6.808008 AAGTGTGTCCAAACTATCATTCTG 57.192 37.500 0.00 0.00 0.00 3.02
628 633 4.697352 AGTGTGTCCAAACTATCATTCTGC 59.303 41.667 0.00 0.00 0.00 4.26
629 634 4.697352 GTGTGTCCAAACTATCATTCTGCT 59.303 41.667 0.00 0.00 0.00 4.24
630 635 5.874810 GTGTGTCCAAACTATCATTCTGCTA 59.125 40.000 0.00 0.00 0.00 3.49
631 636 6.540189 GTGTGTCCAAACTATCATTCTGCTAT 59.460 38.462 0.00 0.00 0.00 2.97
632 637 7.066284 GTGTGTCCAAACTATCATTCTGCTATT 59.934 37.037 0.00 0.00 0.00 1.73
633 638 8.264347 TGTGTCCAAACTATCATTCTGCTATTA 58.736 33.333 0.00 0.00 0.00 0.98
634 639 9.277783 GTGTCCAAACTATCATTCTGCTATTAT 57.722 33.333 0.00 0.00 0.00 1.28
635 640 9.851686 TGTCCAAACTATCATTCTGCTATTATT 57.148 29.630 0.00 0.00 0.00 1.40
652 657 5.746990 ATTATTAGCAGAATAGACCGGCT 57.253 39.130 0.00 1.78 38.55 5.52
653 658 2.890808 TTAGCAGAATAGACCGGCTG 57.109 50.000 0.00 0.00 36.10 4.85
654 659 1.776662 TAGCAGAATAGACCGGCTGT 58.223 50.000 0.00 0.00 36.10 4.40
655 660 0.176680 AGCAGAATAGACCGGCTGTG 59.823 55.000 0.00 0.00 32.76 3.66
656 661 1.432270 GCAGAATAGACCGGCTGTGC 61.432 60.000 0.00 5.16 0.00 4.57
657 662 0.108186 CAGAATAGACCGGCTGTGCA 60.108 55.000 0.00 0.00 0.00 4.57
658 663 0.833287 AGAATAGACCGGCTGTGCAT 59.167 50.000 0.00 0.00 0.00 3.96
659 664 2.039418 AGAATAGACCGGCTGTGCATA 58.961 47.619 0.00 0.00 0.00 3.14
660 665 2.634940 AGAATAGACCGGCTGTGCATAT 59.365 45.455 0.00 0.00 0.00 1.78
661 666 3.832490 AGAATAGACCGGCTGTGCATATA 59.168 43.478 0.00 0.00 0.00 0.86
662 667 4.467795 AGAATAGACCGGCTGTGCATATAT 59.532 41.667 0.00 0.00 0.00 0.86
663 668 5.656859 AGAATAGACCGGCTGTGCATATATA 59.343 40.000 0.00 0.00 0.00 0.86
664 669 6.325028 AGAATAGACCGGCTGTGCATATATAT 59.675 38.462 0.00 0.00 0.00 0.86
668 673 6.889198 AGACCGGCTGTGCATATATATAATT 58.111 36.000 0.00 0.00 0.00 1.40
692 697 7.651027 TTCGGTAGGCTTAGAGTATTTTAGT 57.349 36.000 0.00 0.00 0.00 2.24
771 788 1.667236 CAAGTCTGCAAGGTCACACA 58.333 50.000 0.00 0.00 0.00 3.72
776 793 2.480419 GTCTGCAAGGTCACACATACAC 59.520 50.000 0.00 0.00 0.00 2.90
845 876 3.010420 GCTATTCCCGAAAAGTGAAGCT 58.990 45.455 0.00 0.00 0.00 3.74
848 879 0.949105 TCCCGAAAAGTGAAGCTCGC 60.949 55.000 0.00 0.00 0.00 5.03
863 908 4.265630 CGCGCACGTAGGCATTCG 62.266 66.667 8.75 0.00 33.53 3.34
893 958 1.662446 AAAGGTGCACGTACGACCG 60.662 57.895 24.41 10.87 34.72 4.79
957 1336 4.796495 CCCAAGCTACCCGCCCAC 62.796 72.222 0.00 0.00 40.39 4.61
1016 1399 3.767673 ACCATACACACACCTACACCTAG 59.232 47.826 0.00 0.00 0.00 3.02
1151 1550 5.104693 TCGCTAGCTAGGCTCTATCTATCTT 60.105 44.000 22.10 0.00 40.44 2.40
1217 1618 3.885724 TGAGTTATGATTGCCTCGTCA 57.114 42.857 0.00 0.00 0.00 4.35
1218 1619 3.785486 TGAGTTATGATTGCCTCGTCAG 58.215 45.455 0.00 0.00 0.00 3.51
1219 1620 3.195610 TGAGTTATGATTGCCTCGTCAGT 59.804 43.478 0.00 0.00 0.00 3.41
1220 1621 4.401202 TGAGTTATGATTGCCTCGTCAGTA 59.599 41.667 0.00 0.00 0.00 2.74
1221 1622 4.938080 AGTTATGATTGCCTCGTCAGTAG 58.062 43.478 0.00 0.00 0.00 2.57
1570 1986 2.047844 CTCCACCACTGGCTCGTG 60.048 66.667 0.00 1.31 37.49 4.35
1573 1989 2.421314 CACCACTGGCTCGTGTCA 59.579 61.111 0.00 0.00 33.07 3.58
1586 2002 1.514553 GTGTCACCCTACTACGGCC 59.485 63.158 0.00 0.00 0.00 6.13
1587 2003 1.683365 TGTCACCCTACTACGGCCC 60.683 63.158 0.00 0.00 0.00 5.80
1588 2004 2.440796 TCACCCTACTACGGCCCG 60.441 66.667 0.00 0.00 0.00 6.13
1596 2015 4.849329 CTACGGCCCGAGCACGAC 62.849 72.222 11.71 0.00 42.56 4.34
1610 2029 2.508439 CGACCCCGATCACCAACG 60.508 66.667 0.00 0.00 38.22 4.10
1712 2131 2.190841 TACGGCATCGAGATCGGCA 61.191 57.895 1.91 0.00 40.29 5.69
1713 2132 1.730451 TACGGCATCGAGATCGGCAA 61.730 55.000 1.91 0.00 40.29 4.52
1816 2235 4.664677 ACCGAGTGCAGGTGCGAC 62.665 66.667 0.00 0.00 45.83 5.19
1979 2398 3.041701 GGTACACCGTGTCGTGGA 58.958 61.111 7.63 0.00 38.11 4.02
2107 2526 9.816787 TGTATATGTCTACTCTCTCTCTCTCTA 57.183 37.037 0.00 0.00 0.00 2.43
2169 2610 6.634436 GTGATTATAACACGGACTACTTACGG 59.366 42.308 0.00 0.00 0.00 4.02
2207 2648 9.719279 CAAGCATTAACAATTGTTGAAAAATGT 57.281 25.926 28.43 19.43 38.90 2.71
2443 3101 1.063174 GACATTAAAGGCTCAGCTGCG 59.937 52.381 9.47 3.41 0.00 5.18
2446 3104 3.976701 TAAAGGCTCAGCTGCGCCC 62.977 63.158 37.57 22.79 46.59 6.13
2595 3255 1.118965 TCCTGTTCAGCGAGACCCAA 61.119 55.000 0.00 0.00 0.00 4.12
2621 3281 6.992123 TCTATCATAATCATGCTCAAAACGGT 59.008 34.615 0.00 0.00 31.73 4.83
2631 3291 2.767505 CTCAAAACGGTCTAAGCCACT 58.232 47.619 0.00 0.00 0.00 4.00
2652 3314 5.399013 ACTGACTAGTGTTTTTGCAACAAC 58.601 37.500 19.25 19.25 35.34 3.32
2655 3317 5.861251 TGACTAGTGTTTTTGCAACAACAAG 59.139 36.000 27.69 23.82 34.70 3.16
2656 3318 6.019779 ACTAGTGTTTTTGCAACAACAAGA 57.980 33.333 27.69 18.65 34.70 3.02
2657 3319 6.451393 ACTAGTGTTTTTGCAACAACAAGAA 58.549 32.000 27.69 16.73 34.70 2.52
2658 3320 5.844301 AGTGTTTTTGCAACAACAAGAAG 57.156 34.783 27.69 0.00 34.70 2.85
2687 3349 7.201350 GCTTCAGAATTAGTAATTTTTGGCACG 60.201 37.037 9.47 0.00 0.00 5.34
3084 3789 5.824624 TGATTTGGTTCTATCTCATCTTGCC 59.175 40.000 0.00 0.00 0.00 4.52
3094 3799 7.937649 TCTATCTCATCTTGCCATTTGAAATG 58.062 34.615 10.84 10.84 0.00 2.32
3096 3801 6.203808 TCTCATCTTGCCATTTGAAATGAG 57.796 37.500 18.82 8.81 39.82 2.90
3097 3802 4.751060 TCATCTTGCCATTTGAAATGAGC 58.249 39.130 18.82 18.50 0.00 4.26
3098 3803 4.464951 TCATCTTGCCATTTGAAATGAGCT 59.535 37.500 18.82 0.00 0.00 4.09
3099 3804 4.877378 TCTTGCCATTTGAAATGAGCTT 57.123 36.364 18.82 0.00 0.00 3.74
3100 3805 4.562082 TCTTGCCATTTGAAATGAGCTTG 58.438 39.130 18.82 14.79 0.00 4.01
3101 3806 4.039488 TCTTGCCATTTGAAATGAGCTTGT 59.961 37.500 18.82 0.00 0.00 3.16
3102 3807 3.655486 TGCCATTTGAAATGAGCTTGTG 58.345 40.909 18.82 2.03 0.00 3.33
3103 3808 3.321396 TGCCATTTGAAATGAGCTTGTGA 59.679 39.130 18.82 2.72 0.00 3.58
3104 3809 4.202233 TGCCATTTGAAATGAGCTTGTGAA 60.202 37.500 18.82 2.11 0.00 3.18
3105 3810 4.933400 GCCATTTGAAATGAGCTTGTGAAT 59.067 37.500 18.82 0.00 0.00 2.57
3106 3811 5.410439 GCCATTTGAAATGAGCTTGTGAATT 59.590 36.000 18.82 0.00 0.00 2.17
3107 3812 6.619874 GCCATTTGAAATGAGCTTGTGAATTG 60.620 38.462 18.82 0.00 0.00 2.32
3108 3813 6.647481 CCATTTGAAATGAGCTTGTGAATTGA 59.353 34.615 18.82 0.00 0.00 2.57
3109 3814 7.171848 CCATTTGAAATGAGCTTGTGAATTGAA 59.828 33.333 18.82 0.00 0.00 2.69
3110 3815 8.552865 CATTTGAAATGAGCTTGTGAATTGAAA 58.447 29.630 12.37 0.00 0.00 2.69
3111 3816 8.489990 TTTGAAATGAGCTTGTGAATTGAAAA 57.510 26.923 0.00 0.00 0.00 2.29
3112 3817 7.467557 TGAAATGAGCTTGTGAATTGAAAAC 57.532 32.000 0.00 0.00 0.00 2.43
3125 3830 0.040514 TGAAAACGCCGCATGTCTTG 60.041 50.000 0.00 0.00 0.00 3.02
3128 3833 1.444119 AAACGCCGCATGTCTTGTGT 61.444 50.000 0.00 0.00 33.82 3.72
3130 3835 0.601576 ACGCCGCATGTCTTGTGTAA 60.602 50.000 0.00 0.00 33.82 2.41
3149 3854 4.832266 TGTAATGACATGGTTTCCTTGCTT 59.168 37.500 0.00 0.00 32.73 3.91
3153 3858 3.450457 TGACATGGTTTCCTTGCTTGTTT 59.550 39.130 0.00 0.00 32.73 2.83
3210 3915 2.405143 CAGCATGGATGTGGAGCAG 58.595 57.895 0.00 0.00 0.00 4.24
3226 3933 0.675837 GCAGCCAGATGTGAGAAGCA 60.676 55.000 0.00 0.00 0.00 3.91
3265 3976 8.755941 CAGTGAGTTATACATCATTTCCGTAAG 58.244 37.037 0.00 0.00 0.00 2.34
3267 3978 9.309516 GTGAGTTATACATCATTTCCGTAAGAA 57.690 33.333 0.00 0.00 43.02 2.52
3280 3991 6.827586 TTCCGTAAGAAAATGTAAGGCATT 57.172 33.333 0.00 0.00 45.42 3.56
3312 4023 4.058124 GCATGAATCCGCTATGTCACTAA 58.942 43.478 0.00 0.00 0.00 2.24
3327 4038 7.801716 ATGTCACTAAGTGTGTGTAATTTGT 57.198 32.000 0.00 0.00 46.27 2.83
3426 4141 2.831333 CAGGACGCAGCTGAGATAATT 58.169 47.619 25.03 0.02 0.00 1.40
3544 4262 2.283676 GGTCTCGTGTCCCTCCCA 60.284 66.667 0.00 0.00 0.00 4.37
3571 4291 7.155328 TGCACTTTCTGTTTTTCCTTTTGTAA 58.845 30.769 0.00 0.00 0.00 2.41
3573 4293 7.330946 GCACTTTCTGTTTTTCCTTTTGTAACT 59.669 33.333 0.00 0.00 0.00 2.24
3593 4315 2.668212 GTAGGCACGCTGGCACAA 60.668 61.111 12.56 0.00 46.46 3.33
3609 4331 3.498018 GGCACAACCATTTTCATTTGTCC 59.502 43.478 0.00 0.00 38.86 4.02
3611 4333 4.701765 CACAACCATTTTCATTTGTCCCA 58.298 39.130 0.00 0.00 29.65 4.37
3626 4348 7.836685 TCATTTGTCCCATACAGGCTTAATTAA 59.163 33.333 0.00 0.00 39.87 1.40
3627 4349 8.641541 CATTTGTCCCATACAGGCTTAATTAAT 58.358 33.333 0.00 0.00 39.87 1.40
3628 4350 7.817418 TTGTCCCATACAGGCTTAATTAATC 57.183 36.000 0.00 0.00 39.87 1.75
3629 4351 6.905736 TGTCCCATACAGGCTTAATTAATCA 58.094 36.000 0.00 0.00 35.39 2.57
3658 4382 6.978343 TCATCCGTTCGAAATAAATGTCTT 57.022 33.333 0.00 0.00 0.00 3.01
3784 7539 4.829064 TCCATGTTTTCCTTTCGACAAG 57.171 40.909 0.00 0.00 0.00 3.16
4013 9637 0.302288 TGCGGTCGTTGTTTCTTTCG 59.698 50.000 0.00 0.00 0.00 3.46
4030 9654 6.730960 TCTTTCGCTAATACAAAACCGAAT 57.269 33.333 0.00 0.00 35.11 3.34
4054 9678 6.615088 TGCATTGAGCTGATTCTTTCTTAAC 58.385 36.000 0.00 0.00 45.94 2.01
4056 9680 7.607607 TGCATTGAGCTGATTCTTTCTTAACTA 59.392 33.333 0.00 0.00 45.94 2.24
4132 9764 9.554724 TCGAATTCAAAATGTTTTATAGCTCAC 57.445 29.630 6.22 0.00 0.00 3.51
4142 9774 5.817296 TGTTTTATAGCTCACATCATCGCTT 59.183 36.000 0.00 0.00 34.14 4.68
4167 9799 5.834169 GGTTCAAAAACCGTCTTCCAATAA 58.166 37.500 0.00 0.00 45.33 1.40
4168 9800 6.274579 GGTTCAAAAACCGTCTTCCAATAAA 58.725 36.000 0.00 0.00 45.33 1.40
4169 9801 6.757478 GGTTCAAAAACCGTCTTCCAATAAAA 59.243 34.615 0.00 0.00 45.33 1.52
4170 9802 7.042992 GGTTCAAAAACCGTCTTCCAATAAAAG 60.043 37.037 0.00 0.00 45.33 2.27
4171 9803 6.508777 TCAAAAACCGTCTTCCAATAAAAGG 58.491 36.000 0.00 0.00 0.00 3.11
4200 9837 5.810587 TCATGACGATACTTTGGAAACTAGC 59.189 40.000 0.00 0.00 0.00 3.42
4212 9849 4.585879 TGGAAACTAGCTCCCATGTTAAC 58.414 43.478 8.61 0.00 31.32 2.01
4226 9863 3.374220 TGTTAACATGTTCCGACGACT 57.626 42.857 15.85 0.00 0.00 4.18
4290 10020 5.466819 TCACGTCTGTGGTTCATAAGTTAG 58.533 41.667 0.00 0.00 46.42 2.34
4297 10027 6.382859 TCTGTGGTTCATAAGTTAGCATCCTA 59.617 38.462 0.00 0.00 0.00 2.94
4301 10031 9.555727 GTGGTTCATAAGTTAGCATCCTATTTA 57.444 33.333 0.00 0.00 0.00 1.40
4302 10032 9.555727 TGGTTCATAAGTTAGCATCCTATTTAC 57.444 33.333 0.00 0.00 0.00 2.01
4303 10033 9.555727 GGTTCATAAGTTAGCATCCTATTTACA 57.444 33.333 0.00 0.00 0.00 2.41
4362 10325 3.668141 TCTCCCCACATACAAATGCAT 57.332 42.857 0.00 0.00 36.50 3.96
4390 10353 1.656095 CGAGAAAGTTGATGTCCTCGC 59.344 52.381 0.00 0.00 37.35 5.03
4437 10401 8.464770 TCAAAATATTTTGTAGCTCACATTGC 57.535 30.769 30.50 0.00 45.77 3.56
4444 10408 2.038952 TGTAGCTCACATTGCTGTTCCT 59.961 45.455 0.00 0.00 41.32 3.36
4503 10467 4.081586 ACGAGACCTTTGAAACTAGATCCC 60.082 45.833 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.444700 ATCCGAACGCCTCAAACCGT 62.445 55.000 0.00 0.00 39.70 4.83
2 3 1.740296 ATCCGAACGCCTCAAACCG 60.740 57.895 0.00 0.00 0.00 4.44
3 4 1.644786 CCATCCGAACGCCTCAAACC 61.645 60.000 0.00 0.00 0.00 3.27
4 5 0.672401 TCCATCCGAACGCCTCAAAC 60.672 55.000 0.00 0.00 0.00 2.93
6 7 0.179084 GATCCATCCGAACGCCTCAA 60.179 55.000 0.00 0.00 0.00 3.02
7 8 1.441729 GATCCATCCGAACGCCTCA 59.558 57.895 0.00 0.00 0.00 3.86
8 9 1.661821 CGATCCATCCGAACGCCTC 60.662 63.158 0.00 0.00 29.49 4.70
9 10 2.417516 CGATCCATCCGAACGCCT 59.582 61.111 0.00 0.00 29.49 5.52
10 11 2.661866 CCGATCCATCCGAACGCC 60.662 66.667 0.00 0.00 35.57 5.68
11 12 1.087771 AAACCGATCCATCCGAACGC 61.088 55.000 0.00 0.00 35.57 4.84
12 13 1.365699 AAAACCGATCCATCCGAACG 58.634 50.000 0.00 0.00 36.58 3.95
35 36 0.888619 GACCGGTCAGTGACTGATCA 59.111 55.000 29.93 0.00 41.28 2.92
36 37 0.888619 TGACCGGTCAGTGACTGATC 59.111 55.000 33.23 24.35 42.73 2.92
37 38 3.051617 TGACCGGTCAGTGACTGAT 57.948 52.632 33.23 16.69 42.73 2.90
38 39 4.591038 TGACCGGTCAGTGACTGA 57.409 55.556 33.23 11.93 41.05 3.41
61 62 1.254026 ATCAGTCTCAAACGTCCGGA 58.746 50.000 0.00 0.00 0.00 5.14
64 65 4.142881 GCCTTAAATCAGTCTCAAACGTCC 60.143 45.833 0.00 0.00 0.00 4.79
66 67 3.751698 GGCCTTAAATCAGTCTCAAACGT 59.248 43.478 0.00 0.00 0.00 3.99
76 77 0.465642 GACCGGGGGCCTTAAATCAG 60.466 60.000 6.32 0.00 0.00 2.90
77 78 1.208844 TGACCGGGGGCCTTAAATCA 61.209 55.000 6.32 0.00 0.00 2.57
79 80 1.423921 CTATGACCGGGGGCCTTAAAT 59.576 52.381 6.32 0.00 0.00 1.40
102 103 8.668353 GCATTACAGTCAAGATCATGTAAAAGA 58.332 33.333 0.00 0.00 40.42 2.52
105 106 6.883756 TGGCATTACAGTCAAGATCATGTAAA 59.116 34.615 0.00 0.00 40.42 2.01
124 125 7.149973 GCATATTCTTGTATTGTGATGGCATT 58.850 34.615 0.00 0.00 0.00 3.56
125 126 6.265876 TGCATATTCTTGTATTGTGATGGCAT 59.734 34.615 0.00 0.00 0.00 4.40
126 127 5.593502 TGCATATTCTTGTATTGTGATGGCA 59.406 36.000 0.00 0.00 0.00 4.92
151 152 7.543947 TCAGTGAGTCATGTATTTTATGCAG 57.456 36.000 0.00 0.00 0.00 4.41
160 161 8.868103 AGACATATTCATCAGTGAGTCATGTAT 58.132 33.333 0.00 0.00 34.63 2.29
185 186 8.095937 AGGTTTCGTTGGATTAAAAGTTAGAG 57.904 34.615 0.00 0.00 0.00 2.43
229 231 4.592192 GCTGCGGCCGCTCTATCA 62.592 66.667 45.79 27.01 42.51 2.15
243 245 0.109597 GTGAAAGCCGGACATTGCTG 60.110 55.000 5.05 0.00 38.00 4.41
249 251 1.968493 ACTAGAAGTGAAAGCCGGACA 59.032 47.619 5.05 0.00 0.00 4.02
251 253 3.070446 TCAAACTAGAAGTGAAAGCCGGA 59.930 43.478 5.05 0.00 0.00 5.14
252 254 3.399330 TCAAACTAGAAGTGAAAGCCGG 58.601 45.455 0.00 0.00 0.00 6.13
283 285 8.506168 TTATTGTCCAAAATACTCTAAGCCTG 57.494 34.615 0.00 0.00 0.00 4.85
313 316 7.346961 GCAACGAGCGTATTTTTAATTAGAC 57.653 36.000 0.00 0.00 0.00 2.59
334 337 2.062361 CTGCGCTTGACAAGTGGCAA 62.062 55.000 25.86 14.30 41.52 4.52
337 340 1.859427 ATGCTGCGCTTGACAAGTGG 61.859 55.000 25.86 15.16 39.38 4.00
346 349 4.990426 AGTTTCAAAAATAATGCTGCGCTT 59.010 33.333 9.73 0.00 0.00 4.68
351 354 7.647907 AAGAGCAGTTTCAAAAATAATGCTG 57.352 32.000 0.92 0.00 42.23 4.41
352 355 9.762933 TTTAAGAGCAGTTTCAAAAATAATGCT 57.237 25.926 0.00 0.00 44.65 3.79
353 356 9.797473 GTTTAAGAGCAGTTTCAAAAATAATGC 57.203 29.630 0.00 0.00 0.00 3.56
359 362 9.528018 CTTATGGTTTAAGAGCAGTTTCAAAAA 57.472 29.630 0.00 0.00 39.48 1.94
368 371 6.201806 CGAGATTCCTTATGGTTTAAGAGCAG 59.798 42.308 0.00 0.00 39.48 4.24
379 382 6.371548 TGAACACTTTTCGAGATTCCTTATGG 59.628 38.462 0.00 0.00 0.00 2.74
381 384 7.979444 TTGAACACTTTTCGAGATTCCTTAT 57.021 32.000 0.00 0.00 0.00 1.73
383 386 6.884280 ATTGAACACTTTTCGAGATTCCTT 57.116 33.333 0.00 0.00 0.00 3.36
392 395 6.668323 ACTTCACCATATTGAACACTTTTCG 58.332 36.000 0.00 0.00 32.02 3.46
393 396 7.096065 GCAACTTCACCATATTGAACACTTTTC 60.096 37.037 0.00 0.00 32.02 2.29
398 401 4.485163 GGCAACTTCACCATATTGAACAC 58.515 43.478 0.00 0.00 32.02 3.32
421 424 6.119536 ACGTCATTGGAAAGCTATGGATTAA 58.880 36.000 0.00 0.00 0.00 1.40
427 431 6.791887 ATGATACGTCATTGGAAAGCTATG 57.208 37.500 0.00 0.00 42.37 2.23
440 444 6.200854 GTCTGAACAATGCATATGATACGTCA 59.799 38.462 6.97 1.51 39.04 4.35
444 448 7.374228 CGTTTGTCTGAACAATGCATATGATAC 59.626 37.037 6.97 0.00 44.59 2.24
445 449 7.408910 CGTTTGTCTGAACAATGCATATGATA 58.591 34.615 6.97 0.00 44.59 2.15
451 455 2.622942 ACCGTTTGTCTGAACAATGCAT 59.377 40.909 0.00 0.00 44.59 3.96
452 456 2.020720 ACCGTTTGTCTGAACAATGCA 58.979 42.857 0.00 0.00 44.59 3.96
453 457 2.774439 ACCGTTTGTCTGAACAATGC 57.226 45.000 0.00 0.00 44.59 3.56
454 458 7.513190 TTTTTAACCGTTTGTCTGAACAATG 57.487 32.000 0.00 0.00 44.59 2.82
455 459 6.254804 GCTTTTTAACCGTTTGTCTGAACAAT 59.745 34.615 0.00 0.00 44.59 2.71
456 460 5.573669 GCTTTTTAACCGTTTGTCTGAACAA 59.426 36.000 0.00 0.00 43.58 2.83
457 461 5.096849 GCTTTTTAACCGTTTGTCTGAACA 58.903 37.500 0.00 0.00 0.00 3.18
458 462 5.229260 CAGCTTTTTAACCGTTTGTCTGAAC 59.771 40.000 0.00 0.00 0.00 3.18
459 463 5.124138 TCAGCTTTTTAACCGTTTGTCTGAA 59.876 36.000 0.00 0.00 0.00 3.02
521 526 2.604174 CGGGTGAACTTGTGGTCGC 61.604 63.158 0.00 0.00 0.00 5.19
526 531 6.542852 CAATATTTAGACGGGTGAACTTGTG 58.457 40.000 0.00 0.00 0.00 3.33
528 533 5.123186 TGCAATATTTAGACGGGTGAACTTG 59.877 40.000 0.00 0.00 0.00 3.16
537 542 4.122776 AGAGCACTGCAATATTTAGACGG 58.877 43.478 3.30 0.00 0.00 4.79
561 566 6.319399 GCAAGTGCACGGTATTTATTTAAGT 58.681 36.000 12.01 0.00 41.59 2.24
584 589 2.172593 TTAAATTGCATGCTCGACGC 57.827 45.000 20.33 0.58 39.77 5.19
585 590 4.029418 CACTTTTAAATTGCATGCTCGACG 59.971 41.667 20.33 1.21 0.00 5.12
586 591 4.917415 ACACTTTTAAATTGCATGCTCGAC 59.083 37.500 20.33 0.00 0.00 4.20
587 592 4.916831 CACACTTTTAAATTGCATGCTCGA 59.083 37.500 20.33 5.31 0.00 4.04
588 593 4.681025 ACACACTTTTAAATTGCATGCTCG 59.319 37.500 20.33 0.00 0.00 5.03
589 594 5.119125 GGACACACTTTTAAATTGCATGCTC 59.881 40.000 20.33 1.47 0.00 4.26
590 595 4.990426 GGACACACTTTTAAATTGCATGCT 59.010 37.500 20.33 0.00 0.00 3.79
591 596 4.749099 TGGACACACTTTTAAATTGCATGC 59.251 37.500 11.82 11.82 0.00 4.06
592 597 6.841443 TTGGACACACTTTTAAATTGCATG 57.159 33.333 0.00 0.00 0.00 4.06
593 598 7.047271 AGTTTGGACACACTTTTAAATTGCAT 58.953 30.769 0.00 0.00 0.00 3.96
594 599 6.402222 AGTTTGGACACACTTTTAAATTGCA 58.598 32.000 0.00 0.00 0.00 4.08
595 600 6.902224 AGTTTGGACACACTTTTAAATTGC 57.098 33.333 0.00 0.00 0.00 3.56
596 601 9.743057 TGATAGTTTGGACACACTTTTAAATTG 57.257 29.630 0.00 0.00 0.00 2.32
599 604 9.959749 GAATGATAGTTTGGACACACTTTTAAA 57.040 29.630 0.00 0.00 0.00 1.52
600 605 9.349713 AGAATGATAGTTTGGACACACTTTTAA 57.650 29.630 0.00 0.00 0.00 1.52
601 606 8.783093 CAGAATGATAGTTTGGACACACTTTTA 58.217 33.333 0.00 0.00 39.69 1.52
602 607 7.651808 CAGAATGATAGTTTGGACACACTTTT 58.348 34.615 0.00 0.00 39.69 2.27
603 608 6.294176 GCAGAATGATAGTTTGGACACACTTT 60.294 38.462 0.00 0.00 39.69 2.66
604 609 5.182001 GCAGAATGATAGTTTGGACACACTT 59.818 40.000 0.00 0.00 39.69 3.16
605 610 4.697352 GCAGAATGATAGTTTGGACACACT 59.303 41.667 0.00 0.00 39.69 3.55
606 611 4.697352 AGCAGAATGATAGTTTGGACACAC 59.303 41.667 0.00 0.00 39.69 3.82
607 612 4.910195 AGCAGAATGATAGTTTGGACACA 58.090 39.130 0.00 0.00 39.69 3.72
608 613 7.559590 AATAGCAGAATGATAGTTTGGACAC 57.440 36.000 0.00 0.00 41.98 3.67
609 614 9.851686 AATAATAGCAGAATGATAGTTTGGACA 57.148 29.630 0.00 0.00 41.98 4.02
628 633 6.754209 CAGCCGGTCTATTCTGCTAATAATAG 59.246 42.308 1.90 0.00 37.13 1.73
629 634 6.210784 ACAGCCGGTCTATTCTGCTAATAATA 59.789 38.462 1.90 0.00 0.00 0.98
630 635 5.012148 ACAGCCGGTCTATTCTGCTAATAAT 59.988 40.000 1.90 0.00 0.00 1.28
631 636 4.344102 ACAGCCGGTCTATTCTGCTAATAA 59.656 41.667 1.90 0.00 0.00 1.40
632 637 3.895656 ACAGCCGGTCTATTCTGCTAATA 59.104 43.478 1.90 0.00 0.00 0.98
633 638 2.700897 ACAGCCGGTCTATTCTGCTAAT 59.299 45.455 1.90 0.00 0.00 1.73
634 639 2.108168 ACAGCCGGTCTATTCTGCTAA 58.892 47.619 1.90 0.00 0.00 3.09
635 640 1.409064 CACAGCCGGTCTATTCTGCTA 59.591 52.381 1.90 0.00 0.00 3.49
636 641 0.176680 CACAGCCGGTCTATTCTGCT 59.823 55.000 1.90 0.00 0.00 4.24
637 642 1.432270 GCACAGCCGGTCTATTCTGC 61.432 60.000 1.90 2.82 0.00 4.26
638 643 0.108186 TGCACAGCCGGTCTATTCTG 60.108 55.000 1.90 2.75 0.00 3.02
639 644 0.833287 ATGCACAGCCGGTCTATTCT 59.167 50.000 1.90 0.00 0.00 2.40
640 645 2.526304 TATGCACAGCCGGTCTATTC 57.474 50.000 1.90 0.00 0.00 1.75
641 646 4.826274 ATATATGCACAGCCGGTCTATT 57.174 40.909 1.90 0.00 0.00 1.73
642 647 7.597288 TTATATATATGCACAGCCGGTCTAT 57.403 36.000 1.90 0.00 0.00 1.98
643 648 7.597288 ATTATATATATGCACAGCCGGTCTA 57.403 36.000 1.90 0.00 0.00 2.59
644 649 5.932619 TTATATATATGCACAGCCGGTCT 57.067 39.130 1.90 0.00 0.00 3.85
645 650 7.516785 CGAAATTATATATATGCACAGCCGGTC 60.517 40.741 1.90 0.00 0.00 4.79
646 651 6.257849 CGAAATTATATATATGCACAGCCGGT 59.742 38.462 1.90 0.00 0.00 5.28
647 652 6.292865 CCGAAATTATATATATGCACAGCCGG 60.293 42.308 5.44 0.00 0.00 6.13
648 653 6.257849 ACCGAAATTATATATATGCACAGCCG 59.742 38.462 5.44 1.40 0.00 5.52
649 654 7.553881 ACCGAAATTATATATATGCACAGCC 57.446 36.000 5.44 0.00 0.00 4.85
650 655 8.765219 CCTACCGAAATTATATATATGCACAGC 58.235 37.037 5.44 0.00 0.00 4.40
651 656 8.765219 GCCTACCGAAATTATATATATGCACAG 58.235 37.037 5.44 0.00 0.00 3.66
652 657 8.482943 AGCCTACCGAAATTATATATATGCACA 58.517 33.333 5.44 0.00 0.00 4.57
653 658 8.888579 AGCCTACCGAAATTATATATATGCAC 57.111 34.615 5.44 0.00 0.00 4.57
668 673 7.340232 TGACTAAAATACTCTAAGCCTACCGAA 59.660 37.037 0.00 0.00 0.00 4.30
724 729 8.672815 AGTCGGAACAAAGTCTATACTACTTAC 58.327 37.037 0.00 0.00 36.17 2.34
776 793 0.310854 GTTGAAGCCAAACCTCGTGG 59.689 55.000 0.99 0.99 39.33 4.94
845 876 2.883730 GAATGCCTACGTGCGCGA 60.884 61.111 28.73 9.16 42.00 5.87
858 889 3.242936 ACCTTTGTCGGTTTTCACGAATG 60.243 43.478 0.00 0.00 42.55 2.67
863 908 1.133407 TGCACCTTTGTCGGTTTTCAC 59.867 47.619 0.00 0.00 34.29 3.18
893 958 1.376812 CACTCCCAAAGGTACCCGC 60.377 63.158 8.74 0.00 0.00 6.13
898 1276 0.599558 CGTCGACACTCCCAAAGGTA 59.400 55.000 17.16 0.00 0.00 3.08
957 1336 1.599542 GCACCGCTGGCTCTTATAAAG 59.400 52.381 0.00 0.00 0.00 1.85
1284 1685 4.156190 TCGTCTTCATCTTGTCACCTACTC 59.844 45.833 0.00 0.00 0.00 2.59
1483 1899 0.024238 CGTTGAAGCTCTTGATCGCG 59.976 55.000 0.00 0.00 0.00 5.87
1570 1986 2.779033 CGGGCCGTAGTAGGGTGAC 61.779 68.421 19.97 2.08 0.00 3.67
1573 1989 2.123982 CTCGGGCCGTAGTAGGGT 60.124 66.667 27.32 0.00 0.00 4.34
1586 2002 4.570663 GATCGGGGTCGTGCTCGG 62.571 72.222 8.49 0.00 37.69 4.63
1587 2003 3.822192 TGATCGGGGTCGTGCTCG 61.822 66.667 0.81 0.81 37.69 5.03
1588 2004 2.202756 GTGATCGGGGTCGTGCTC 60.203 66.667 0.00 0.00 37.69 4.26
1629 2048 2.509336 CGAAGTACTGGCCCAGCG 60.509 66.667 11.63 1.47 34.37 5.18
1878 2297 2.438906 CTGTCGTAGCAGCAGTGTG 58.561 57.895 0.00 0.00 0.00 3.82
1979 2398 2.125512 GGCGTCGCTCCAGTCAAT 60.126 61.111 18.11 0.00 0.00 2.57
2150 2591 4.265073 ACTCCGTAAGTAGTCCGTGTTAT 58.735 43.478 0.00 0.00 36.07 1.89
2207 2648 6.017026 CACGATACTCTATCTGTAAAGCCAGA 60.017 42.308 0.00 0.00 45.06 3.86
2595 3255 7.663081 ACCGTTTTGAGCATGATTATGATAGAT 59.337 33.333 0.85 0.00 36.36 1.98
2631 3291 5.378292 TGTTGTTGCAAAAACACTAGTCA 57.622 34.783 27.60 6.76 31.52 3.41
2649 3311 7.869800 ACTAATTCTGAAGCTTCTTCTTGTTG 58.130 34.615 26.09 12.76 0.00 3.33
2658 3320 8.864024 GCCAAAAATTACTAATTCTGAAGCTTC 58.136 33.333 19.89 19.89 0.00 3.86
3084 3789 7.646446 TCAATTCACAAGCTCATTTCAAATG 57.354 32.000 3.46 3.46 0.00 2.32
3094 3799 2.726241 GGCGTTTTCAATTCACAAGCTC 59.274 45.455 0.00 0.00 0.00 4.09
3096 3801 1.451651 CGGCGTTTTCAATTCACAAGC 59.548 47.619 0.00 0.00 0.00 4.01
3097 3802 1.451651 GCGGCGTTTTCAATTCACAAG 59.548 47.619 9.37 0.00 0.00 3.16
3098 3803 1.202302 TGCGGCGTTTTCAATTCACAA 60.202 42.857 9.37 0.00 0.00 3.33
3099 3804 0.382158 TGCGGCGTTTTCAATTCACA 59.618 45.000 9.37 0.00 0.00 3.58
3100 3805 1.386412 CATGCGGCGTTTTCAATTCAC 59.614 47.619 9.37 0.00 0.00 3.18
3101 3806 1.000827 ACATGCGGCGTTTTCAATTCA 60.001 42.857 9.37 0.00 0.00 2.57
3102 3807 1.648681 GACATGCGGCGTTTTCAATTC 59.351 47.619 9.37 0.00 0.00 2.17
3103 3808 1.269448 AGACATGCGGCGTTTTCAATT 59.731 42.857 9.37 0.00 0.00 2.32
3104 3809 0.881118 AGACATGCGGCGTTTTCAAT 59.119 45.000 9.37 0.00 0.00 2.57
3105 3810 0.665835 AAGACATGCGGCGTTTTCAA 59.334 45.000 9.37 0.00 0.00 2.69
3106 3811 0.040514 CAAGACATGCGGCGTTTTCA 60.041 50.000 9.37 0.00 0.00 2.69
3107 3812 0.040425 ACAAGACATGCGGCGTTTTC 60.040 50.000 9.37 0.00 0.00 2.29
3108 3813 0.317770 CACAAGACATGCGGCGTTTT 60.318 50.000 9.37 0.00 0.00 2.43
3109 3814 1.282570 CACAAGACATGCGGCGTTT 59.717 52.632 9.37 0.00 0.00 3.60
3110 3815 0.601576 TACACAAGACATGCGGCGTT 60.602 50.000 9.37 0.00 0.00 4.84
3111 3816 0.601576 TTACACAAGACATGCGGCGT 60.602 50.000 9.37 0.00 0.00 5.68
3112 3817 0.726827 ATTACACAAGACATGCGGCG 59.273 50.000 0.51 0.51 0.00 6.46
3125 3830 4.218417 AGCAAGGAAACCATGTCATTACAC 59.782 41.667 0.00 0.00 38.78 2.90
3128 3833 4.832266 ACAAGCAAGGAAACCATGTCATTA 59.168 37.500 0.00 0.00 0.00 1.90
3130 3835 3.233507 ACAAGCAAGGAAACCATGTCAT 58.766 40.909 0.00 0.00 0.00 3.06
3153 3858 9.162764 CAATAGTATCCGGAAGAAGAAGAAAAA 57.837 33.333 9.01 0.00 0.00 1.94
3190 3895 2.487532 GCTCCACATCCATGCTGGC 61.488 63.158 0.00 0.00 37.47 4.85
3193 3898 1.453379 GCTGCTCCACATCCATGCT 60.453 57.895 0.00 0.00 0.00 3.79
3242 3949 9.878667 TTTCTTACGGAAATGATGTATAACTCA 57.121 29.630 0.00 0.00 38.81 3.41
3255 3964 6.827586 TGCCTTACATTTTCTTACGGAAAT 57.172 33.333 0.00 0.00 42.63 2.17
3270 3981 7.508687 TCATGCTCTAATAAGAATGCCTTACA 58.491 34.615 0.00 0.00 39.93 2.41
3271 3982 7.969536 TCATGCTCTAATAAGAATGCCTTAC 57.030 36.000 0.00 0.00 39.93 2.34
3280 3991 5.474578 AGCGGATTCATGCTCTAATAAGA 57.525 39.130 0.00 0.00 36.53 2.10
3312 4023 6.751514 TGAACAAGACAAATTACACACACT 57.248 33.333 0.00 0.00 0.00 3.55
3327 4038 3.565482 GCAGGTCATCAACTTGAACAAGA 59.435 43.478 19.35 0.19 40.79 3.02
3394 4105 1.437986 CGTCCTGCTACTAGTGGCC 59.562 63.158 26.23 11.31 36.12 5.36
3518 4236 0.580104 GACACGAGACCAACAAACCG 59.420 55.000 0.00 0.00 0.00 4.44
3525 4243 1.911766 GGGAGGGACACGAGACCAA 60.912 63.158 3.68 0.00 0.00 3.67
3544 4262 5.405935 AAAGGAAAAACAGAAAGTGCAGT 57.594 34.783 0.00 0.00 0.00 4.40
3571 4291 1.966451 GCCAGCGTGCCTACAAAGT 60.966 57.895 0.00 0.00 0.00 2.66
3573 4293 2.112087 TGCCAGCGTGCCTACAAA 59.888 55.556 0.00 0.00 0.00 2.83
3626 4348 8.657074 TTATTTCGAACGGATGAAATACTGAT 57.343 30.769 14.04 0.00 43.20 2.90
3627 4349 8.481974 TTTATTTCGAACGGATGAAATACTGA 57.518 30.769 14.04 2.82 43.20 3.41
3628 4350 9.158364 CATTTATTTCGAACGGATGAAATACTG 57.842 33.333 14.04 11.72 43.20 2.74
3629 4351 8.889717 ACATTTATTTCGAACGGATGAAATACT 58.110 29.630 14.04 6.12 43.20 2.12
3804 7559 9.288576 TGAGATTGATCTAAAAATGAACAGTGT 57.711 29.630 0.00 0.00 37.25 3.55
4013 9637 6.033341 TCAATGCATTCGGTTTTGTATTAGC 58.967 36.000 9.53 0.00 28.86 3.09
4030 9654 6.432162 AGTTAAGAAAGAATCAGCTCAATGCA 59.568 34.615 0.00 0.00 45.94 3.96
4132 9764 3.469899 TTTTGAACCGAAGCGATGATG 57.530 42.857 0.00 0.00 0.00 3.07
4134 9766 2.031508 GGTTTTTGAACCGAAGCGATGA 60.032 45.455 0.00 0.00 32.47 2.92
4158 9790 6.719365 GTCATGACGATCCTTTTATTGGAAG 58.281 40.000 10.69 0.00 37.13 3.46
4185 9822 4.288626 ACATGGGAGCTAGTTTCCAAAGTA 59.711 41.667 11.12 0.00 36.40 2.24
4191 9828 4.585879 TGTTAACATGGGAGCTAGTTTCC 58.414 43.478 3.59 0.00 0.00 3.13
4245 9884 8.417106 CGTGATAACTTATCCTATGCCTCATAT 58.583 37.037 6.37 0.00 34.26 1.78
4290 10020 6.694411 CAGTCATTGCTTTGTAAATAGGATGC 59.306 38.462 0.00 0.00 0.00 3.91
4301 10031 9.768662 ATTTTTATTTCTCAGTCATTGCTTTGT 57.231 25.926 0.00 0.00 0.00 2.83
4303 10033 9.211485 CCATTTTTATTTCTCAGTCATTGCTTT 57.789 29.630 0.00 0.00 0.00 3.51
4362 10325 3.574396 ACATCAACTTTCTCGTCCTCTCA 59.426 43.478 0.00 0.00 0.00 3.27
4390 10353 7.094805 TTTGAAGTTCCAAATACGGAGAATCTG 60.095 37.037 0.00 0.00 38.05 2.90
4434 10398 4.211125 TGGTGTTTCAATAGGAACAGCAA 58.789 39.130 16.53 3.82 39.60 3.91
4437 10401 7.382218 GTGAAAATGGTGTTTCAATAGGAACAG 59.618 37.037 2.14 0.00 46.28 3.16


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

AutoCloner maintained by Alex Coulton.