Multiple sequence alignment - TraesCS5A01G008800

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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 TraesCS5A01G008800 chr5A 100.000 3790 0 0 1 3790 6410107 6413896 0.000000e+00 6999.0
1 TraesCS5A01G008800 chr5A 78.901 564 98 15 977 1531 6422144 6422695 2.780000e-96 363.0
2 TraesCS5A01G008800 chr5A 88.679 106 11 1 2995 3100 705285345 705285241 1.110000e-25 128.0
3 TraesCS5A01G008800 chr5D 93.232 2497 143 17 507 2994 8019542 8022021 0.000000e+00 3651.0
4 TraesCS5A01G008800 chr5D 84.192 563 62 17 3249 3790 8022214 8022770 4.340000e-144 521.0
5 TraesCS5A01G008800 chr5D 91.765 340 22 5 34 370 8019093 8019429 5.730000e-128 468.0
6 TraesCS5A01G008800 chr5D 90.909 99 9 0 2995 3093 61485358 61485456 2.380000e-27 134.0
7 TraesCS5A01G008800 chr5B 91.705 2616 154 38 395 2990 8342020 8344592 0.000000e+00 3570.0
8 TraesCS5A01G008800 chr5B 89.080 348 23 9 34 370 8341702 8342045 5.860000e-113 418.0
9 TraesCS5A01G008800 chr5B 81.937 382 24 11 3453 3790 8344944 8345324 8.020000e-72 281.0
10 TraesCS5A01G008800 chr5B 77.974 227 44 6 506 728 399775244 399775468 1.840000e-28 137.0
11 TraesCS5A01G008800 chr5B 95.238 63 2 1 3148 3210 8344650 8344711 8.660000e-17 99.0
12 TraesCS5A01G008800 chr6D 84.862 218 28 4 515 728 116945822 116945606 8.250000e-52 215.0
13 TraesCS5A01G008800 chr6D 90.909 99 9 0 2995 3093 13176126 13176028 2.380000e-27 134.0
14 TraesCS5A01G008800 chr1B 91.919 99 7 1 2995 3093 120889318 120889221 1.840000e-28 137.0
15 TraesCS5A01G008800 chr7D 91.000 100 9 0 2995 3094 531825368 531825269 6.600000e-28 135.0
16 TraesCS5A01G008800 chr7D 81.098 164 23 5 160 319 58353493 58353652 1.430000e-24 124.0
17 TraesCS5A01G008800 chr7D 79.042 167 28 5 506 668 139303372 139303209 1.440000e-19 108.0
18 TraesCS5A01G008800 chr4D 84.028 144 19 3 518 658 84771013 84770871 6.600000e-28 135.0
19 TraesCS5A01G008800 chr4B 91.000 100 9 0 2995 3094 171186025 171185926 6.600000e-28 135.0
20 TraesCS5A01G008800 chr2A 91.000 100 9 0 2995 3094 98897512 98897413 6.600000e-28 135.0
21 TraesCS5A01G008800 chr2A 78.065 155 31 3 516 667 120471143 120471297 1.120000e-15 95.3
22 TraesCS5A01G008800 chr4A 90.909 99 9 0 2995 3093 16983981 16984079 2.380000e-27 134.0
23 TraesCS5A01G008800 chr4A 80.952 105 19 1 515 618 36401505 36401609 8.730000e-12 82.4
24 TraesCS5A01G008800 chr3B 91.000 100 8 1 2995 3094 779368988 779368890 2.380000e-27 134.0
25 TraesCS5A01G008800 chr1D 85.000 100 15 0 591 690 219476214 219476115 6.700000e-18 102.0


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 TraesCS5A01G008800 chr5A 6410107 6413896 3789 False 6999.000000 6999 100.000000 1 3790 1 chr5A.!!$F1 3789
1 TraesCS5A01G008800 chr5A 6422144 6422695 551 False 363.000000 363 78.901000 977 1531 1 chr5A.!!$F2 554
2 TraesCS5A01G008800 chr5D 8019093 8022770 3677 False 1546.666667 3651 89.729667 34 3790 3 chr5D.!!$F2 3756
3 TraesCS5A01G008800 chr5B 8341702 8345324 3622 False 1092.000000 3570 89.490000 34 3790 4 chr5B.!!$F2 3756

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
588 628 0.323360 AAGTTGCCACATACGCCCAT 60.323 50.0 0.00 0.0 0.0 4.00 F
1659 1713 0.321653 AAGATCCGTGAGTTGGCCAC 60.322 55.0 3.88 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1732 0.179000 GGAGCTCCGTCATGTCCAAT 59.821 55.0 19.06 0.0 0.0 3.16 R
2926 2992 0.106167 TAGAGGATCCCACAGGTCCG 60.106 60.0 8.55 0.0 38.0 4.79 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
21 22 3.938289 AGACAAGAGGTTCGTCTTACC 57.062 47.619 7.31 0.00 36.62 2.85
22 23 2.561858 AGACAAGAGGTTCGTCTTACCC 59.438 50.000 7.31 1.83 36.62 3.69
23 24 2.298163 GACAAGAGGTTCGTCTTACCCA 59.702 50.000 7.31 0.00 34.90 4.51
24 25 2.299297 ACAAGAGGTTCGTCTTACCCAG 59.701 50.000 7.31 0.00 34.90 4.45
25 26 2.299297 CAAGAGGTTCGTCTTACCCAGT 59.701 50.000 7.31 0.00 34.90 4.00
26 27 3.446442 AGAGGTTCGTCTTACCCAGTA 57.554 47.619 0.00 0.00 36.27 2.74
27 28 3.771216 AGAGGTTCGTCTTACCCAGTAA 58.229 45.455 0.00 0.00 36.27 2.24
28 29 4.154942 AGAGGTTCGTCTTACCCAGTAAA 58.845 43.478 0.00 0.00 36.27 2.01
29 30 4.776308 AGAGGTTCGTCTTACCCAGTAAAT 59.224 41.667 0.00 0.00 36.27 1.40
30 31 4.828829 AGGTTCGTCTTACCCAGTAAATG 58.171 43.478 0.00 0.00 36.27 2.32
31 32 4.529377 AGGTTCGTCTTACCCAGTAAATGA 59.471 41.667 0.00 0.00 36.27 2.57
32 33 4.868734 GGTTCGTCTTACCCAGTAAATGAG 59.131 45.833 0.00 0.00 0.00 2.90
33 34 4.730949 TCGTCTTACCCAGTAAATGAGG 57.269 45.455 0.00 0.00 0.00 3.86
34 35 4.346730 TCGTCTTACCCAGTAAATGAGGA 58.653 43.478 0.00 0.00 0.00 3.71
35 36 4.960469 TCGTCTTACCCAGTAAATGAGGAT 59.040 41.667 0.00 0.00 0.00 3.24
36 37 6.131264 TCGTCTTACCCAGTAAATGAGGATA 58.869 40.000 0.00 0.00 0.00 2.59
37 38 6.781014 TCGTCTTACCCAGTAAATGAGGATAT 59.219 38.462 0.00 0.00 0.00 1.63
41 42 9.615660 TCTTACCCAGTAAATGAGGATATACAT 57.384 33.333 0.00 0.00 0.00 2.29
63 64 6.209986 ACATCATTCAACATGAGGTCAACAAT 59.790 34.615 0.00 0.00 38.48 2.71
73 78 1.476488 AGGTCAACAATTATTGCGGCC 59.524 47.619 9.70 9.70 32.81 6.13
82 87 1.384525 TTATTGCGGCCCATACACAC 58.615 50.000 0.00 0.00 0.00 3.82
124 129 4.966965 TTGTTCAAGTTTCCGTGCTAAA 57.033 36.364 0.00 0.00 0.00 1.85
129 134 5.759506 TCAAGTTTCCGTGCTAAAATGAA 57.240 34.783 0.00 0.00 0.00 2.57
170 175 5.485708 ACCAGACTAGGTGCTTTTAAGATCT 59.514 40.000 0.00 0.00 41.30 2.75
198 203 9.685276 TGGATGTATAAAACTTGATGAACATCT 57.315 29.630 14.50 0.00 40.96 2.90
289 300 7.716612 AGTTAAAGTTTGTCAAAGGAATGAGG 58.283 34.615 0.00 0.00 0.00 3.86
290 301 7.559897 AGTTAAAGTTTGTCAAAGGAATGAGGA 59.440 33.333 0.00 0.00 0.00 3.71
291 302 6.396829 AAAGTTTGTCAAAGGAATGAGGAG 57.603 37.500 0.00 0.00 0.00 3.69
304 315 2.530151 AGGAGCTGGACAAGGGCA 60.530 61.111 0.00 0.00 0.00 5.36
354 365 1.680338 ATAGGGACAATTCGCAAGCC 58.320 50.000 0.00 0.00 37.15 4.35
362 373 2.884639 ACAATTCGCAAGCCTTAACTGT 59.115 40.909 0.00 0.00 37.18 3.55
366 377 0.605319 CGCAAGCCTTAACTGTCCCA 60.605 55.000 0.00 0.00 0.00 4.37
370 381 3.378427 GCAAGCCTTAACTGTCCCAATAG 59.622 47.826 0.00 0.00 0.00 1.73
372 383 4.489306 AGCCTTAACTGTCCCAATAGAC 57.511 45.455 0.00 0.00 37.28 2.59
373 384 4.104831 AGCCTTAACTGTCCCAATAGACT 58.895 43.478 0.00 0.00 37.66 3.24
374 385 5.278061 AGCCTTAACTGTCCCAATAGACTA 58.722 41.667 0.00 0.00 37.66 2.59
375 386 5.364157 AGCCTTAACTGTCCCAATAGACTAG 59.636 44.000 0.00 0.00 37.66 2.57
376 387 5.602628 CCTTAACTGTCCCAATAGACTAGC 58.397 45.833 0.00 0.00 37.66 3.42
377 388 5.128827 CCTTAACTGTCCCAATAGACTAGCA 59.871 44.000 0.00 0.00 37.66 3.49
378 389 6.183361 CCTTAACTGTCCCAATAGACTAGCAT 60.183 42.308 0.00 0.00 37.66 3.79
379 390 7.015292 CCTTAACTGTCCCAATAGACTAGCATA 59.985 40.741 0.00 0.00 37.66 3.14
380 391 5.793030 ACTGTCCCAATAGACTAGCATAC 57.207 43.478 0.00 0.00 37.66 2.39
381 392 5.208890 ACTGTCCCAATAGACTAGCATACA 58.791 41.667 0.00 0.00 37.66 2.29
382 393 5.069251 ACTGTCCCAATAGACTAGCATACAC 59.931 44.000 0.00 0.00 37.66 2.90
383 394 5.208890 TGTCCCAATAGACTAGCATACACT 58.791 41.667 0.00 0.00 37.66 3.55
384 395 5.661312 TGTCCCAATAGACTAGCATACACTT 59.339 40.000 0.00 0.00 37.66 3.16
385 396 6.837048 TGTCCCAATAGACTAGCATACACTTA 59.163 38.462 0.00 0.00 37.66 2.24
386 397 7.509318 TGTCCCAATAGACTAGCATACACTTAT 59.491 37.037 0.00 0.00 37.66 1.73
387 398 8.030106 GTCCCAATAGACTAGCATACACTTATC 58.970 40.741 0.00 0.00 33.79 1.75
388 399 7.178628 TCCCAATAGACTAGCATACACTTATCC 59.821 40.741 0.00 0.00 0.00 2.59
389 400 7.324178 CCAATAGACTAGCATACACTTATCCC 58.676 42.308 0.00 0.00 0.00 3.85
390 401 7.179338 CCAATAGACTAGCATACACTTATCCCT 59.821 40.741 0.00 0.00 0.00 4.20
391 402 9.244292 CAATAGACTAGCATACACTTATCCCTA 57.756 37.037 0.00 0.00 0.00 3.53
392 403 9.998752 AATAGACTAGCATACACTTATCCCTAT 57.001 33.333 0.00 0.00 0.00 2.57
393 404 7.710676 AGACTAGCATACACTTATCCCTATG 57.289 40.000 0.00 0.00 0.00 2.23
394 405 7.471041 AGACTAGCATACACTTATCCCTATGA 58.529 38.462 0.00 0.00 0.00 2.15
395 406 7.950684 AGACTAGCATACACTTATCCCTATGAA 59.049 37.037 0.00 0.00 0.00 2.57
396 407 8.671987 ACTAGCATACACTTATCCCTATGAAT 57.328 34.615 0.00 0.00 0.00 2.57
397 408 9.105844 ACTAGCATACACTTATCCCTATGAATT 57.894 33.333 0.00 0.00 0.00 2.17
398 409 9.593134 CTAGCATACACTTATCCCTATGAATTC 57.407 37.037 0.00 0.00 0.00 2.17
399 410 7.099764 AGCATACACTTATCCCTATGAATTCG 58.900 38.462 0.04 0.00 0.00 3.34
400 411 6.183360 GCATACACTTATCCCTATGAATTCGC 60.183 42.308 0.04 0.00 0.00 4.70
401 412 5.290493 ACACTTATCCCTATGAATTCGCA 57.710 39.130 0.04 0.00 0.00 5.10
402 413 5.680619 ACACTTATCCCTATGAATTCGCAA 58.319 37.500 0.04 0.00 0.00 4.85
403 414 5.760253 ACACTTATCCCTATGAATTCGCAAG 59.240 40.000 0.04 0.00 0.00 4.01
404 415 4.757149 ACTTATCCCTATGAATTCGCAAGC 59.243 41.667 0.04 0.00 37.18 4.01
405 416 1.967319 TCCCTATGAATTCGCAAGCC 58.033 50.000 0.04 0.00 37.18 4.35
406 417 1.490490 TCCCTATGAATTCGCAAGCCT 59.510 47.619 0.04 0.00 37.18 4.58
407 418 2.092429 TCCCTATGAATTCGCAAGCCTT 60.092 45.455 0.04 0.00 37.18 4.35
408 419 3.135712 TCCCTATGAATTCGCAAGCCTTA 59.864 43.478 0.04 0.00 37.18 2.69
409 420 3.882888 CCCTATGAATTCGCAAGCCTTAA 59.117 43.478 0.04 0.00 37.18 1.85
410 421 4.520492 CCCTATGAATTCGCAAGCCTTAAT 59.480 41.667 0.04 0.00 37.18 1.40
411 422 5.010012 CCCTATGAATTCGCAAGCCTTAATT 59.990 40.000 0.04 0.00 37.18 1.40
412 423 5.916883 CCTATGAATTCGCAAGCCTTAATTG 59.083 40.000 0.04 0.00 37.18 2.32
418 429 2.781945 GCAAGCCTTAATTGCGCTAT 57.218 45.000 9.73 2.86 43.15 2.97
419 430 3.896648 GCAAGCCTTAATTGCGCTATA 57.103 42.857 9.73 0.00 43.15 1.31
420 431 3.814945 GCAAGCCTTAATTGCGCTATAG 58.185 45.455 9.73 1.40 43.15 1.31
421 432 3.498397 GCAAGCCTTAATTGCGCTATAGA 59.502 43.478 9.73 0.00 43.15 1.98
422 433 4.154918 GCAAGCCTTAATTGCGCTATAGAT 59.845 41.667 9.73 0.00 43.15 1.98
430 441 9.539825 CCTTAATTGCGCTATAGATGAAGATAT 57.460 33.333 9.73 0.00 0.00 1.63
448 459 9.507329 TGAAGATATTTTCCTGGTTATATCTGC 57.493 33.333 19.06 18.18 39.21 4.26
449 460 8.553459 AAGATATTTTCCTGGTTATATCTGCG 57.447 34.615 19.06 0.00 39.21 5.18
485 496 2.323939 TTTTTAGCACGGCACAATCG 57.676 45.000 0.00 0.00 0.00 3.34
491 502 1.565156 GCACGGCACAATCGAAGTCA 61.565 55.000 0.00 0.00 0.00 3.41
502 513 5.287274 CACAATCGAAGTCACTCACATAGAC 59.713 44.000 0.00 0.00 0.00 2.59
504 515 2.418976 TCGAAGTCACTCACATAGACGG 59.581 50.000 0.00 0.00 37.36 4.79
532 572 5.281314 ACACTTATCCCTATGAACACCTCT 58.719 41.667 0.00 0.00 0.00 3.69
544 584 3.508012 TGAACACCTCTAAGAGACAGAGC 59.492 47.826 0.00 0.00 38.58 4.09
546 586 2.225142 ACACCTCTAAGAGACAGAGCCA 60.225 50.000 0.00 0.00 38.58 4.75
561 601 3.311871 CAGAGCCAGCACATTATCTTGAC 59.688 47.826 0.00 0.00 0.00 3.18
562 602 3.054875 AGAGCCAGCACATTATCTTGACA 60.055 43.478 0.00 0.00 0.00 3.58
567 607 5.221185 GCCAGCACATTATCTTGACATTGAT 60.221 40.000 0.00 0.00 0.00 2.57
568 608 6.206498 CCAGCACATTATCTTGACATTGATG 58.794 40.000 0.00 0.00 0.00 3.07
573 613 7.972277 GCACATTATCTTGACATTGATGAAGTT 59.028 33.333 0.00 0.00 0.00 2.66
580 620 3.827876 TGACATTGATGAAGTTGCCACAT 59.172 39.130 0.00 0.00 0.00 3.21
586 626 0.958382 TGAAGTTGCCACATACGCCC 60.958 55.000 0.00 0.00 0.00 6.13
587 627 0.958382 GAAGTTGCCACATACGCCCA 60.958 55.000 0.00 0.00 0.00 5.36
588 628 0.323360 AAGTTGCCACATACGCCCAT 60.323 50.000 0.00 0.00 0.00 4.00
598 640 1.040893 ATACGCCCATGGTCGACAGA 61.041 55.000 23.95 4.24 0.00 3.41
602 644 1.635663 GCCCATGGTCGACAGAAACG 61.636 60.000 18.91 0.64 0.00 3.60
610 652 1.536331 GTCGACAGAAACGTCTCCTCT 59.464 52.381 11.55 0.00 33.54 3.69
619 661 1.982660 ACGTCTCCTCTCACTGAACA 58.017 50.000 0.00 0.00 0.00 3.18
647 689 4.466015 TCACCAAAAGGCCTGGAATAAATC 59.534 41.667 16.13 0.00 37.40 2.17
695 737 4.862371 AGTTTGGGACTTGAACTTTGGTA 58.138 39.130 0.00 0.00 33.92 3.25
698 740 2.160205 GGGACTTGAACTTTGGTAGGC 58.840 52.381 0.00 0.00 0.00 3.93
703 745 1.440618 TGAACTTTGGTAGGCAGGGA 58.559 50.000 0.00 0.00 0.00 4.20
704 746 1.992557 TGAACTTTGGTAGGCAGGGAT 59.007 47.619 0.00 0.00 0.00 3.85
705 747 3.186283 TGAACTTTGGTAGGCAGGGATA 58.814 45.455 0.00 0.00 0.00 2.59
706 748 3.054655 TGAACTTTGGTAGGCAGGGATAC 60.055 47.826 0.00 0.00 0.00 2.24
728 771 4.656112 ACCAATGTCCTCCTAACTATCCAG 59.344 45.833 0.00 0.00 0.00 3.86
732 775 3.039011 GTCCTCCTAACTATCCAGCCAA 58.961 50.000 0.00 0.00 0.00 4.52
818 862 4.593597 ATTTAATGTCACGCTGGTAACG 57.406 40.909 0.00 0.00 42.51 3.18
911 959 1.069090 GACAAGTCGTGTGGCTGGA 59.931 57.895 0.00 0.00 41.96 3.86
912 960 0.946221 GACAAGTCGTGTGGCTGGAG 60.946 60.000 0.00 0.00 41.96 3.86
913 961 2.031163 AAGTCGTGTGGCTGGAGC 59.969 61.111 0.00 0.00 41.14 4.70
914 962 2.511452 AAGTCGTGTGGCTGGAGCT 61.511 57.895 0.00 0.00 41.70 4.09
954 1002 4.477780 GGTGTGCTTATATAGAGAGCGTC 58.522 47.826 1.49 0.00 39.23 5.19
967 1015 2.946329 GAGAGCGTCTGATGAGTAGGAA 59.054 50.000 0.00 0.00 0.00 3.36
968 1016 2.948979 AGAGCGTCTGATGAGTAGGAAG 59.051 50.000 0.00 0.00 0.00 3.46
1141 1189 2.747460 CCACCACCACCGCATCAG 60.747 66.667 0.00 0.00 0.00 2.90
1176 1230 3.155167 CTCCCGCCTACACCTCCC 61.155 72.222 0.00 0.00 0.00 4.30
1185 1239 1.305465 TACACCTCCCGGCAAGCTA 60.305 57.895 0.00 0.00 0.00 3.32
1209 1263 2.610859 ATCGGCCACCTCCACCTT 60.611 61.111 2.24 0.00 0.00 3.50
1233 1287 4.242586 TCCCACCCCCACGTCTCA 62.243 66.667 0.00 0.00 0.00 3.27
1543 1597 7.416551 GCGAAGAAGAGGTACCTAACTAAAGAT 60.417 40.741 16.29 0.00 0.00 2.40
1545 1599 8.667592 AAGAAGAGGTACCTAACTAAAGATGT 57.332 34.615 16.29 0.00 0.00 3.06
1546 1600 9.765295 AAGAAGAGGTACCTAACTAAAGATGTA 57.235 33.333 16.29 0.00 0.00 2.29
1547 1601 9.187996 AGAAGAGGTACCTAACTAAAGATGTAC 57.812 37.037 16.29 0.00 0.00 2.90
1599 1653 4.071961 ACAAACACAGATGCTCACACTA 57.928 40.909 0.00 0.00 0.00 2.74
1659 1713 0.321653 AAGATCCGTGAGTTGGCCAC 60.322 55.000 3.88 0.00 0.00 5.01
1660 1714 1.003839 GATCCGTGAGTTGGCCACA 60.004 57.895 3.88 0.00 34.36 4.17
1663 1717 2.281070 CGTGAGTTGGCCACAGCT 60.281 61.111 3.88 3.68 41.16 4.24
1708 1762 3.851128 GAGCTCCTGGGCGGGTAC 61.851 72.222 0.87 0.00 37.29 3.34
1751 1805 1.554583 GGTCCTTGGAGAGTCCCACC 61.555 65.000 0.26 0.00 35.03 4.61
1757 1811 1.305046 GGAGAGTCCCACCGGAAGA 60.305 63.158 9.46 0.00 40.92 2.87
1993 2047 5.018695 ACTTCGTACATCTTTTGCTTTCG 57.981 39.130 0.00 0.00 0.00 3.46
2414 2468 1.594293 CACCAACGACTGCGAGGTT 60.594 57.895 0.00 0.00 43.57 3.50
2417 2471 1.001633 ACCAACGACTGCGAGGTTAAT 59.998 47.619 0.00 0.00 43.15 1.40
2513 2567 0.683504 GAGCGGAGGAGTTCTACCCA 60.684 60.000 0.00 0.00 0.00 4.51
2561 2615 1.858091 CAGAGGTCGACATGTATGGC 58.142 55.000 18.91 0.00 0.00 4.40
2573 2627 4.326826 ACATGTATGGCAAAGATATCCGG 58.673 43.478 0.00 0.00 0.00 5.14
2585 2639 3.279434 AGATATCCGGTTTGTGCCTTTC 58.721 45.455 0.00 0.00 0.00 2.62
2651 2705 0.729116 CTGTTGAGGTAATGCTGGCG 59.271 55.000 0.00 0.00 0.00 5.69
2723 2777 1.742831 GGCGCAAAGGTTGATATGTCA 59.257 47.619 10.83 0.00 0.00 3.58
2741 2795 1.351017 TCAGACCAGTTTGGGATGACC 59.649 52.381 0.00 0.00 43.37 4.02
2847 2901 5.028549 CTGATAGGTCAGCTAACCATTGT 57.971 43.478 9.27 0.00 44.86 2.71
2922 2988 1.098712 TCGGGAGTTTGTTGCACACC 61.099 55.000 0.00 0.00 0.00 4.16
2923 2989 1.739667 GGGAGTTTGTTGCACACCC 59.260 57.895 0.00 0.00 37.81 4.61
2926 2992 0.028902 GAGTTTGTTGCACACCCGAC 59.971 55.000 0.00 0.00 0.00 4.79
2994 3066 9.706691 ATAAAAGTATGGTTGTATGGTAGATCG 57.293 33.333 0.00 0.00 0.00 3.69
2995 3067 6.726490 AAGTATGGTTGTATGGTAGATCGT 57.274 37.500 0.00 0.00 0.00 3.73
2996 3068 6.085555 AGTATGGTTGTATGGTAGATCGTG 57.914 41.667 0.00 0.00 0.00 4.35
2997 3069 3.812156 TGGTTGTATGGTAGATCGTGG 57.188 47.619 0.00 0.00 0.00 4.94
2998 3070 3.101437 TGGTTGTATGGTAGATCGTGGT 58.899 45.455 0.00 0.00 0.00 4.16
2999 3071 3.131577 TGGTTGTATGGTAGATCGTGGTC 59.868 47.826 0.00 0.00 0.00 4.02
3000 3072 3.383825 GGTTGTATGGTAGATCGTGGTCT 59.616 47.826 0.00 0.00 0.00 3.85
3001 3073 4.581824 GGTTGTATGGTAGATCGTGGTCTA 59.418 45.833 0.00 0.00 0.00 2.59
3002 3074 5.243283 GGTTGTATGGTAGATCGTGGTCTAT 59.757 44.000 0.00 0.00 33.58 1.98
3003 3075 5.959618 TGTATGGTAGATCGTGGTCTATG 57.040 43.478 0.00 0.00 33.58 2.23
3004 3076 4.765339 TGTATGGTAGATCGTGGTCTATGG 59.235 45.833 0.00 0.00 33.58 2.74
3005 3077 3.588210 TGGTAGATCGTGGTCTATGGA 57.412 47.619 0.00 0.00 33.58 3.41
3006 3078 4.114015 TGGTAGATCGTGGTCTATGGAT 57.886 45.455 0.00 0.00 33.58 3.41
3007 3079 4.480115 TGGTAGATCGTGGTCTATGGATT 58.520 43.478 0.00 0.00 33.58 3.01
3008 3080 4.899457 TGGTAGATCGTGGTCTATGGATTT 59.101 41.667 0.00 0.00 33.58 2.17
3009 3081 5.365605 TGGTAGATCGTGGTCTATGGATTTT 59.634 40.000 0.00 0.00 33.58 1.82
3010 3082 5.696724 GGTAGATCGTGGTCTATGGATTTTG 59.303 44.000 0.00 0.00 33.58 2.44
3011 3083 5.614324 AGATCGTGGTCTATGGATTTTGA 57.386 39.130 0.00 0.00 0.00 2.69
3012 3084 6.179906 AGATCGTGGTCTATGGATTTTGAT 57.820 37.500 0.00 0.00 0.00 2.57
3013 3085 5.994054 AGATCGTGGTCTATGGATTTTGATG 59.006 40.000 0.00 0.00 0.00 3.07
3014 3086 5.097742 TCGTGGTCTATGGATTTTGATGT 57.902 39.130 0.00 0.00 0.00 3.06
3015 3087 6.228616 TCGTGGTCTATGGATTTTGATGTA 57.771 37.500 0.00 0.00 0.00 2.29
3016 3088 6.645306 TCGTGGTCTATGGATTTTGATGTAA 58.355 36.000 0.00 0.00 0.00 2.41
3017 3089 7.279615 TCGTGGTCTATGGATTTTGATGTAAT 58.720 34.615 0.00 0.00 0.00 1.89
3018 3090 7.773224 TCGTGGTCTATGGATTTTGATGTAATT 59.227 33.333 0.00 0.00 0.00 1.40
3019 3091 8.405531 CGTGGTCTATGGATTTTGATGTAATTT 58.594 33.333 0.00 0.00 0.00 1.82
3045 3117 9.500864 TTTATTGTTTTTAGTGTTCGTTGTACC 57.499 29.630 0.00 0.00 0.00 3.34
3046 3118 6.492007 TTGTTTTTAGTGTTCGTTGTACCA 57.508 33.333 0.00 0.00 0.00 3.25
3047 3119 5.867166 TGTTTTTAGTGTTCGTTGTACCAC 58.133 37.500 0.00 0.00 0.00 4.16
3048 3120 5.163774 TGTTTTTAGTGTTCGTTGTACCACC 60.164 40.000 0.00 0.00 0.00 4.61
3049 3121 3.815856 TTAGTGTTCGTTGTACCACCA 57.184 42.857 0.00 0.00 0.00 4.17
3050 3122 2.922740 AGTGTTCGTTGTACCACCAT 57.077 45.000 0.00 0.00 0.00 3.55
3051 3123 2.489971 AGTGTTCGTTGTACCACCATG 58.510 47.619 0.00 0.00 0.00 3.66
3052 3124 2.103432 AGTGTTCGTTGTACCACCATGA 59.897 45.455 0.00 0.00 0.00 3.07
3053 3125 3.071479 GTGTTCGTTGTACCACCATGAT 58.929 45.455 0.00 0.00 0.00 2.45
3054 3126 3.500680 GTGTTCGTTGTACCACCATGATT 59.499 43.478 0.00 0.00 0.00 2.57
3055 3127 3.500299 TGTTCGTTGTACCACCATGATTG 59.500 43.478 0.00 0.00 0.00 2.67
3056 3128 3.686916 TCGTTGTACCACCATGATTGA 57.313 42.857 0.00 0.00 0.00 2.57
3057 3129 4.009370 TCGTTGTACCACCATGATTGAA 57.991 40.909 0.00 0.00 0.00 2.69
3058 3130 4.000325 TCGTTGTACCACCATGATTGAAG 59.000 43.478 0.00 0.00 0.00 3.02
3059 3131 4.000325 CGTTGTACCACCATGATTGAAGA 59.000 43.478 0.00 0.00 0.00 2.87
3060 3132 4.635765 CGTTGTACCACCATGATTGAAGAT 59.364 41.667 0.00 0.00 0.00 2.40
3061 3133 5.447683 CGTTGTACCACCATGATTGAAGATG 60.448 44.000 0.00 0.00 0.00 2.90
3062 3134 5.434182 TGTACCACCATGATTGAAGATGA 57.566 39.130 0.00 0.00 0.00 2.92
3063 3135 5.814481 TGTACCACCATGATTGAAGATGAA 58.186 37.500 0.00 0.00 0.00 2.57
3064 3136 6.425735 TGTACCACCATGATTGAAGATGAAT 58.574 36.000 0.00 0.00 0.00 2.57
3065 3137 7.572814 TGTACCACCATGATTGAAGATGAATA 58.427 34.615 0.00 0.00 0.00 1.75
3066 3138 7.716560 TGTACCACCATGATTGAAGATGAATAG 59.283 37.037 0.00 0.00 0.00 1.73
3067 3139 6.903516 ACCACCATGATTGAAGATGAATAGA 58.096 36.000 0.00 0.00 0.00 1.98
3068 3140 7.524290 ACCACCATGATTGAAGATGAATAGAT 58.476 34.615 0.00 0.00 0.00 1.98
3069 3141 8.003044 ACCACCATGATTGAAGATGAATAGATT 58.997 33.333 0.00 0.00 0.00 2.40
3070 3142 8.297426 CCACCATGATTGAAGATGAATAGATTG 58.703 37.037 0.00 0.00 0.00 2.67
3071 3143 9.063615 CACCATGATTGAAGATGAATAGATTGA 57.936 33.333 0.00 0.00 0.00 2.57
3072 3144 9.636789 ACCATGATTGAAGATGAATAGATTGAA 57.363 29.630 0.00 0.00 0.00 2.69
3113 3188 7.497925 AAAAAGATCACAGGTTCTCAACTAC 57.502 36.000 0.00 0.00 0.00 2.73
3122 3197 4.081586 CAGGTTCTCAACTACCCTTACTCC 60.082 50.000 0.00 0.00 34.90 3.85
3138 3213 0.588252 CTCCGCTATTTGGAATGCCG 59.412 55.000 0.00 0.00 34.44 5.69
3178 3253 4.938832 CCATATAAACACTCGTGTCCCAAA 59.061 41.667 2.81 0.00 44.13 3.28
3214 3315 4.393062 TCTTCTCTTGGAATTTCATGCGTC 59.607 41.667 0.00 0.00 33.01 5.19
3223 3324 5.525012 TGGAATTTCATGCGTCAGAGATAAG 59.475 40.000 0.00 0.00 0.00 1.73
3224 3325 5.415415 AATTTCATGCGTCAGAGATAAGC 57.585 39.130 0.00 0.00 0.00 3.09
3225 3326 3.808466 TTCATGCGTCAGAGATAAGCT 57.192 42.857 0.00 0.00 0.00 3.74
3226 3327 4.918810 TTCATGCGTCAGAGATAAGCTA 57.081 40.909 0.00 0.00 0.00 3.32
3227 3328 4.918810 TCATGCGTCAGAGATAAGCTAA 57.081 40.909 0.00 0.00 0.00 3.09
3228 3329 5.459536 TCATGCGTCAGAGATAAGCTAAT 57.540 39.130 0.00 0.00 0.00 1.73
3229 3330 6.575162 TCATGCGTCAGAGATAAGCTAATA 57.425 37.500 0.00 0.00 0.00 0.98
3230 3331 6.382608 TCATGCGTCAGAGATAAGCTAATAC 58.617 40.000 0.00 0.00 0.00 1.89
3241 3342 7.883833 AGAGATAAGCTAATACTACCGTCATCA 59.116 37.037 0.00 0.00 0.00 3.07
3250 3351 2.251818 CTACCGTCATCATCCTCCCAT 58.748 52.381 0.00 0.00 0.00 4.00
3253 3355 1.066573 CCGTCATCATCCTCCCATAGC 60.067 57.143 0.00 0.00 0.00 2.97
3254 3356 1.403382 CGTCATCATCCTCCCATAGCG 60.403 57.143 0.00 0.00 0.00 4.26
3297 3439 2.250031 TGAAAAATCAGCATGCCCACT 58.750 42.857 15.66 0.00 34.76 4.00
3314 3456 5.938125 TGCCCACTACTGAGAAATAAAGAAC 59.062 40.000 0.00 0.00 0.00 3.01
3371 3515 9.341899 GACGAAAAAGCATAACAATTACTGAAT 57.658 29.630 0.00 0.00 0.00 2.57
3379 3523 9.407380 AGCATAACAATTACTGAATATTCCACA 57.593 29.630 12.90 0.00 0.00 4.17
3393 3537 3.502191 TTCCACAACACTTGTCTTTGC 57.498 42.857 0.00 0.00 43.23 3.68
3404 3548 1.581934 TGTCTTTGCAGAGTTCACCG 58.418 50.000 3.90 0.00 0.00 4.94
3408 3552 0.817634 TTTGCAGAGTTCACCGTGGG 60.818 55.000 0.00 0.00 0.00 4.61
3409 3553 3.050275 GCAGAGTTCACCGTGGGC 61.050 66.667 0.00 0.00 0.00 5.36
3421 3579 1.005450 ACCGTGGGCCAACTTAATGAT 59.995 47.619 8.40 0.00 0.00 2.45
3422 3580 1.676006 CCGTGGGCCAACTTAATGATC 59.324 52.381 8.40 0.00 0.00 2.92
3424 3582 2.097466 CGTGGGCCAACTTAATGATCAC 59.903 50.000 8.40 0.00 0.00 3.06
3429 3587 4.578928 GGGCCAACTTAATGATCACGTAAT 59.421 41.667 4.39 0.00 0.00 1.89
3448 3606 9.901724 CACGTAATTAATAACATCAGTCTTGAC 57.098 33.333 0.00 0.00 35.83 3.18
3472 3630 8.075593 ACATTTTTATGCATGAAAAGTCACAC 57.924 30.769 26.93 0.00 36.31 3.82
3475 3633 3.542712 ATGCATGAAAAGTCACACGTC 57.457 42.857 0.00 0.00 36.31 4.34
3543 3703 7.547019 TGTGTAGCTAATGTTCATTCTCTCTTG 59.453 37.037 0.00 0.00 0.00 3.02
3669 3860 0.604780 GTCCTCATCATCATGGGCGG 60.605 60.000 0.00 0.00 0.00 6.13
3675 3866 0.694771 ATCATCATGGGCGGCTACAT 59.305 50.000 9.56 1.28 0.00 2.29
3738 3941 9.225682 AGAAATATTGGACCCTTAGATGTCTTA 57.774 33.333 0.00 0.00 0.00 2.10
3739 3942 9.495572 GAAATATTGGACCCTTAGATGTCTTAG 57.504 37.037 0.00 0.00 0.00 2.18
3742 3945 5.934402 TGGACCCTTAGATGTCTTAGAAC 57.066 43.478 0.00 0.00 0.00 3.01
3747 3950 7.119407 GGACCCTTAGATGTCTTAGAACAAAAC 59.881 40.741 0.00 0.00 31.81 2.43
3777 3980 7.966246 AGATCTCATTGTGAGCTATGATTTC 57.034 36.000 4.78 0.00 43.95 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.298163 TGGGTAAGACGAACCTCTTGTC 59.702 50.000 0.00 0.00 37.18 3.18
4 5 2.299297 ACTGGGTAAGACGAACCTCTTG 59.701 50.000 0.00 0.00 37.18 3.02
5 6 2.606378 ACTGGGTAAGACGAACCTCTT 58.394 47.619 0.00 0.00 37.18 2.85
6 7 2.305858 ACTGGGTAAGACGAACCTCT 57.694 50.000 0.00 0.00 37.18 3.69
7 8 4.525912 TTTACTGGGTAAGACGAACCTC 57.474 45.455 0.00 0.00 37.18 3.85
8 9 4.529377 TCATTTACTGGGTAAGACGAACCT 59.471 41.667 0.00 0.00 37.18 3.50
9 10 4.824289 TCATTTACTGGGTAAGACGAACC 58.176 43.478 0.00 0.00 36.19 3.62
10 11 4.868734 CCTCATTTACTGGGTAAGACGAAC 59.131 45.833 0.00 0.00 29.41 3.95
11 12 4.773674 TCCTCATTTACTGGGTAAGACGAA 59.226 41.667 0.00 0.00 29.41 3.85
12 13 4.346730 TCCTCATTTACTGGGTAAGACGA 58.653 43.478 0.00 0.00 29.41 4.20
13 14 4.730949 TCCTCATTTACTGGGTAAGACG 57.269 45.455 0.00 0.00 29.41 4.18
14 15 8.867097 TGTATATCCTCATTTACTGGGTAAGAC 58.133 37.037 0.00 0.00 29.41 3.01
15 16 9.615660 ATGTATATCCTCATTTACTGGGTAAGA 57.384 33.333 0.00 0.00 29.41 2.10
16 17 9.877178 GATGTATATCCTCATTTACTGGGTAAG 57.123 37.037 0.00 0.00 29.41 2.34
17 18 9.387397 TGATGTATATCCTCATTTACTGGGTAA 57.613 33.333 0.00 0.00 32.09 2.85
18 19 8.966155 TGATGTATATCCTCATTTACTGGGTA 57.034 34.615 0.00 0.00 32.09 3.69
19 20 7.872061 TGATGTATATCCTCATTTACTGGGT 57.128 36.000 0.00 0.00 32.09 4.51
20 21 9.388506 GAATGATGTATATCCTCATTTACTGGG 57.611 37.037 8.08 0.00 39.96 4.45
21 22 9.948964 TGAATGATGTATATCCTCATTTACTGG 57.051 33.333 8.08 0.00 39.96 4.00
28 29 9.668497 CTCATGTTGAATGATGTATATCCTCAT 57.332 33.333 0.00 0.00 33.89 2.90
29 30 8.098912 CCTCATGTTGAATGATGTATATCCTCA 58.901 37.037 0.00 0.00 32.09 3.86
30 31 8.099537 ACCTCATGTTGAATGATGTATATCCTC 58.900 37.037 0.00 0.00 32.09 3.71
31 32 7.982252 ACCTCATGTTGAATGATGTATATCCT 58.018 34.615 0.00 0.00 32.09 3.24
32 33 7.879677 TGACCTCATGTTGAATGATGTATATCC 59.120 37.037 0.00 0.00 32.09 2.59
33 34 8.837788 TGACCTCATGTTGAATGATGTATATC 57.162 34.615 0.00 0.00 29.28 1.63
34 35 9.060347 GTTGACCTCATGTTGAATGATGTATAT 57.940 33.333 0.00 0.00 29.28 0.86
35 36 8.046107 TGTTGACCTCATGTTGAATGATGTATA 58.954 33.333 0.00 0.00 29.28 1.47
36 37 6.885918 TGTTGACCTCATGTTGAATGATGTAT 59.114 34.615 0.00 0.00 29.28 2.29
37 38 6.237154 TGTTGACCTCATGTTGAATGATGTA 58.763 36.000 0.00 0.00 29.28 2.29
41 42 6.653526 AATTGTTGACCTCATGTTGAATGA 57.346 33.333 0.00 0.00 0.00 2.57
63 64 1.340114 TGTGTGTATGGGCCGCAATAA 60.340 47.619 0.00 0.00 0.00 1.40
73 78 3.485378 CGCTTTTGTGTTTGTGTGTATGG 59.515 43.478 0.00 0.00 0.00 2.74
82 87 0.934436 CCTCGCCGCTTTTGTGTTTG 60.934 55.000 0.00 0.00 0.00 2.93
124 129 3.804036 TGTCCGTGTCAAAGACTTCATT 58.196 40.909 5.39 0.00 33.15 2.57
129 134 1.208535 TGGTTGTCCGTGTCAAAGACT 59.791 47.619 5.39 0.00 36.30 3.24
190 195 4.887071 ACTACCAAAAGCAACAGATGTTCA 59.113 37.500 0.00 0.00 35.83 3.18
198 203 3.948473 TGCAACTACTACCAAAAGCAACA 59.052 39.130 0.00 0.00 0.00 3.33
289 300 1.376553 GTCTGCCCTTGTCCAGCTC 60.377 63.158 0.00 0.00 0.00 4.09
290 301 1.495579 ATGTCTGCCCTTGTCCAGCT 61.496 55.000 0.00 0.00 0.00 4.24
291 302 0.610232 AATGTCTGCCCTTGTCCAGC 60.610 55.000 0.00 0.00 0.00 4.85
354 365 6.222038 TGCTAGTCTATTGGGACAGTTAAG 57.778 41.667 0.00 0.00 42.39 1.85
362 373 7.178628 GGATAAGTGTATGCTAGTCTATTGGGA 59.821 40.741 0.00 0.00 0.00 4.37
366 377 9.998752 ATAGGGATAAGTGTATGCTAGTCTATT 57.001 33.333 0.00 0.00 0.00 1.73
370 381 7.704578 TCATAGGGATAAGTGTATGCTAGTC 57.295 40.000 0.00 0.00 0.00 2.59
372 383 9.593134 GAATTCATAGGGATAAGTGTATGCTAG 57.407 37.037 0.00 0.00 0.00 3.42
373 384 8.251026 CGAATTCATAGGGATAAGTGTATGCTA 58.749 37.037 6.22 0.00 0.00 3.49
374 385 7.099764 CGAATTCATAGGGATAAGTGTATGCT 58.900 38.462 6.22 0.00 0.00 3.79
375 386 6.183360 GCGAATTCATAGGGATAAGTGTATGC 60.183 42.308 6.22 0.00 0.00 3.14
376 387 6.873605 TGCGAATTCATAGGGATAAGTGTATG 59.126 38.462 6.22 0.00 0.00 2.39
377 388 7.004555 TGCGAATTCATAGGGATAAGTGTAT 57.995 36.000 6.22 0.00 0.00 2.29
378 389 6.413783 TGCGAATTCATAGGGATAAGTGTA 57.586 37.500 6.22 0.00 0.00 2.90
379 390 5.290493 TGCGAATTCATAGGGATAAGTGT 57.710 39.130 6.22 0.00 0.00 3.55
380 391 5.334414 GCTTGCGAATTCATAGGGATAAGTG 60.334 44.000 6.22 0.00 0.00 3.16
381 392 4.757149 GCTTGCGAATTCATAGGGATAAGT 59.243 41.667 6.22 0.00 0.00 2.24
382 393 4.154918 GGCTTGCGAATTCATAGGGATAAG 59.845 45.833 6.22 0.00 0.00 1.73
383 394 4.072131 GGCTTGCGAATTCATAGGGATAA 58.928 43.478 6.22 0.00 0.00 1.75
384 395 3.327757 AGGCTTGCGAATTCATAGGGATA 59.672 43.478 6.22 0.00 0.00 2.59
385 396 2.107204 AGGCTTGCGAATTCATAGGGAT 59.893 45.455 6.22 0.00 0.00 3.85
386 397 1.490490 AGGCTTGCGAATTCATAGGGA 59.510 47.619 6.22 0.00 0.00 4.20
387 398 1.972872 AGGCTTGCGAATTCATAGGG 58.027 50.000 6.22 0.00 0.00 3.53
388 399 5.695851 ATTAAGGCTTGCGAATTCATAGG 57.304 39.130 10.69 0.00 0.00 2.57
389 400 5.400485 GCAATTAAGGCTTGCGAATTCATAG 59.600 40.000 10.69 0.48 39.57 2.23
390 401 5.280945 GCAATTAAGGCTTGCGAATTCATA 58.719 37.500 10.69 0.00 39.57 2.15
391 402 4.114794 GCAATTAAGGCTTGCGAATTCAT 58.885 39.130 10.69 0.00 39.57 2.57
392 403 3.510719 GCAATTAAGGCTTGCGAATTCA 58.489 40.909 10.69 0.00 39.57 2.57
399 410 2.781945 ATAGCGCAATTAAGGCTTGC 57.218 45.000 11.47 4.20 44.32 4.01
400 411 5.409520 TCATCTATAGCGCAATTAAGGCTTG 59.590 40.000 11.47 0.00 38.19 4.01
401 412 5.551233 TCATCTATAGCGCAATTAAGGCTT 58.449 37.500 11.47 4.58 38.19 4.35
402 413 5.152623 TCATCTATAGCGCAATTAAGGCT 57.847 39.130 11.47 3.08 40.68 4.58
403 414 5.639506 TCTTCATCTATAGCGCAATTAAGGC 59.360 40.000 11.47 0.00 0.00 4.35
404 415 7.840342 ATCTTCATCTATAGCGCAATTAAGG 57.160 36.000 11.47 0.00 0.00 2.69
409 420 8.887717 GGAAAATATCTTCATCTATAGCGCAAT 58.112 33.333 11.47 0.00 0.00 3.56
410 421 8.097038 AGGAAAATATCTTCATCTATAGCGCAA 58.903 33.333 11.47 0.00 0.00 4.85
411 422 7.547019 CAGGAAAATATCTTCATCTATAGCGCA 59.453 37.037 11.47 0.00 0.00 6.09
412 423 7.010923 CCAGGAAAATATCTTCATCTATAGCGC 59.989 40.741 0.00 0.00 0.00 5.92
413 424 8.037758 ACCAGGAAAATATCTTCATCTATAGCG 58.962 37.037 0.00 0.00 0.00 4.26
414 425 9.732130 AACCAGGAAAATATCTTCATCTATAGC 57.268 33.333 0.00 0.00 0.00 2.97
422 433 9.507329 GCAGATATAACCAGGAAAATATCTTCA 57.493 33.333 14.97 0.00 38.83 3.02
430 441 6.827586 AAAACGCAGATATAACCAGGAAAA 57.172 33.333 0.00 0.00 0.00 2.29
472 483 1.132640 GACTTCGATTGTGCCGTGC 59.867 57.895 0.00 0.00 0.00 5.34
476 487 1.461127 GTGAGTGACTTCGATTGTGCC 59.539 52.381 0.00 0.00 0.00 5.01
485 496 2.735762 GCCCGTCTATGTGAGTGACTTC 60.736 54.545 0.00 0.00 0.00 3.01
491 502 2.100916 GTGTATGCCCGTCTATGTGAGT 59.899 50.000 0.00 0.00 0.00 3.41
502 513 3.513912 TCATAGGGATAAGTGTATGCCCG 59.486 47.826 1.09 0.00 46.79 6.13
504 515 5.701290 GTGTTCATAGGGATAAGTGTATGCC 59.299 44.000 0.00 0.00 46.13 4.40
532 572 1.632589 TGTGCTGGCTCTGTCTCTTA 58.367 50.000 0.00 0.00 0.00 2.10
544 584 5.823209 TCAATGTCAAGATAATGTGCTGG 57.177 39.130 0.00 0.00 0.00 4.85
546 586 7.338703 ACTTCATCAATGTCAAGATAATGTGCT 59.661 33.333 0.06 0.00 0.00 4.40
561 601 4.345288 CGTATGTGGCAACTTCATCAATG 58.655 43.478 0.00 0.00 34.71 2.82
562 602 3.181497 GCGTATGTGGCAACTTCATCAAT 60.181 43.478 0.00 0.00 34.71 2.57
567 607 0.958382 GGGCGTATGTGGCAACTTCA 60.958 55.000 0.00 0.00 35.84 3.02
568 608 0.958382 TGGGCGTATGTGGCAACTTC 60.958 55.000 0.00 0.00 35.84 3.01
573 613 2.124362 CCATGGGCGTATGTGGCA 60.124 61.111 2.85 0.00 35.84 4.92
580 620 1.252215 TTCTGTCGACCATGGGCGTA 61.252 55.000 37.84 26.28 0.00 4.42
586 626 1.986378 GAGACGTTTCTGTCGACCATG 59.014 52.381 14.12 3.49 43.70 3.66
587 627 1.067776 GGAGACGTTTCTGTCGACCAT 60.068 52.381 14.12 0.00 43.70 3.55
588 628 0.313043 GGAGACGTTTCTGTCGACCA 59.687 55.000 14.12 0.01 43.70 4.02
598 640 2.693591 TGTTCAGTGAGAGGAGACGTTT 59.306 45.455 0.00 0.00 0.00 3.60
602 644 2.362397 TGTGTGTTCAGTGAGAGGAGAC 59.638 50.000 0.00 0.00 0.00 3.36
610 652 2.998316 TGGTGATGTGTGTTCAGTGA 57.002 45.000 0.00 0.00 0.00 3.41
619 661 1.331214 CAGGCCTTTTGGTGATGTGT 58.669 50.000 0.00 0.00 42.99 3.72
657 699 6.096846 GTCCCAAACTTGATATTGGTGCTTAT 59.903 38.462 4.06 0.00 43.71 1.73
690 732 3.742422 TGGTATCCCTGCCTACCAA 57.258 52.632 0.00 0.00 43.33 3.67
695 737 0.846693 GGACATTGGTATCCCTGCCT 59.153 55.000 0.00 0.00 0.00 4.75
698 740 2.412591 AGGAGGACATTGGTATCCCTG 58.587 52.381 0.00 0.00 34.82 4.45
703 745 6.390504 TGGATAGTTAGGAGGACATTGGTAT 58.609 40.000 0.00 0.00 0.00 2.73
704 746 5.784023 TGGATAGTTAGGAGGACATTGGTA 58.216 41.667 0.00 0.00 0.00 3.25
705 747 4.631234 TGGATAGTTAGGAGGACATTGGT 58.369 43.478 0.00 0.00 0.00 3.67
706 748 4.503991 GCTGGATAGTTAGGAGGACATTGG 60.504 50.000 0.00 0.00 0.00 3.16
710 752 2.023404 TGGCTGGATAGTTAGGAGGACA 60.023 50.000 0.00 0.00 0.00 4.02
761 804 9.566530 TTTTGTCCATATGAAACATTGATTACG 57.433 29.630 3.65 0.00 0.00 3.18
802 846 2.953466 ATACGTTACCAGCGTGACAT 57.047 45.000 0.00 0.00 42.87 3.06
911 959 3.111098 CCGTAACGTTTATTCGCTAGCT 58.889 45.455 13.93 0.00 0.00 3.32
912 960 2.217167 CCCGTAACGTTTATTCGCTAGC 59.783 50.000 5.91 4.06 0.00 3.42
913 961 3.241322 CACCCGTAACGTTTATTCGCTAG 59.759 47.826 5.91 2.13 0.00 3.42
914 962 3.178267 CACCCGTAACGTTTATTCGCTA 58.822 45.455 5.91 0.00 0.00 4.26
954 1002 1.202627 GGCTGGCTTCCTACTCATCAG 60.203 57.143 0.00 0.00 0.00 2.90
967 1015 0.835941 CTGACTAGGAATGGCTGGCT 59.164 55.000 2.00 0.00 0.00 4.75
968 1016 0.817229 GCTGACTAGGAATGGCTGGC 60.817 60.000 0.00 0.00 0.00 4.85
1176 1230 1.224069 CGATGATGGGTAGCTTGCCG 61.224 60.000 0.00 0.00 0.00 5.69
1185 1239 2.692368 AGGTGGCCGATGATGGGT 60.692 61.111 0.00 0.00 0.00 4.51
1209 1263 4.096816 TGGGGGTGGGAGCCGATA 62.097 66.667 0.00 0.00 36.39 2.92
1365 1419 2.676265 GGGGTTACGTGGCCTGGAT 61.676 63.158 3.32 0.00 0.00 3.41
1554 1608 6.723131 ACCGTGTTTCTATAAAAGAAGAGC 57.277 37.500 0.00 0.00 44.95 4.09
1599 1653 5.127845 ACCTACAGTGATCATTGAGTCGATT 59.872 40.000 23.48 3.17 0.00 3.34
1678 1732 0.179000 GGAGCTCCGTCATGTCCAAT 59.821 55.000 19.06 0.00 0.00 3.16
1708 1762 2.249309 CACACAAAGTCGCTGGCG 59.751 61.111 8.80 8.80 41.35 5.69
1738 1792 1.609501 CTTCCGGTGGGACTCTCCA 60.610 63.158 0.00 0.00 43.74 3.86
1751 1805 2.461110 CGTTCCGGCCATTCTTCCG 61.461 63.158 2.24 0.00 44.89 4.30
1757 1811 0.893727 AAAAGCTCGTTCCGGCCATT 60.894 50.000 2.24 0.00 0.00 3.16
1993 2047 3.191791 AGAGACCGTACTCTTTCTTCAGC 59.808 47.826 3.31 0.00 43.62 4.26
2063 2117 6.913673 GCAACATGCATGAAAACTTCAAATTT 59.086 30.769 32.75 8.99 44.26 1.82
2064 2118 6.432107 GCAACATGCATGAAAACTTCAAATT 58.568 32.000 32.75 9.19 44.26 1.82
2099 2153 9.909644 GTATCGATTATCAATTGTGTACCTACT 57.090 33.333 1.71 0.00 0.00 2.57
2131 2185 9.114952 TGTTCTGTTACAAGATGACACAAATAA 57.885 29.630 0.00 0.00 0.00 1.40
2132 2186 8.669946 TGTTCTGTTACAAGATGACACAAATA 57.330 30.769 0.00 0.00 0.00 1.40
2274 2328 4.103103 GTCCAGCTTTTCGCCGCC 62.103 66.667 0.00 0.00 40.39 6.13
2275 2329 4.103103 GGTCCAGCTTTTCGCCGC 62.103 66.667 0.00 0.00 40.39 6.53
2316 2370 1.152881 CCTTGAGGTAGGGCATGCC 60.153 63.158 29.47 29.47 0.00 4.40
2324 2378 0.824109 TGATGGTCGCCTTGAGGTAG 59.176 55.000 0.00 0.00 37.57 3.18
2432 2486 1.227704 AATGACACGTGTTCCCGCA 60.228 52.632 24.26 15.90 0.00 5.69
2513 2567 2.304470 GCCTTCTTGGAGAAACCTCTCT 59.696 50.000 2.39 0.00 46.45 3.10
2561 2615 3.016736 AGGCACAAACCGGATATCTTTG 58.983 45.455 9.46 10.94 33.69 2.77
2612 2666 2.921614 GCGATCGCGAAAGTAGCC 59.078 61.111 26.12 0.00 40.82 3.93
2651 2705 5.696724 CCAGTCGAAATGGTATATGAGGTTC 59.303 44.000 9.32 0.00 32.85 3.62
2741 2795 2.202623 CTCTCCGTTCGGCGAAGG 60.203 66.667 29.42 29.42 44.77 3.46
2800 2854 6.402766 GCCGATACAAATAACACAAAGCTACA 60.403 38.462 0.00 0.00 0.00 2.74
2847 2901 4.682778 AATAGGCAGCTAACATAACGGA 57.317 40.909 0.00 0.00 0.00 4.69
2922 2988 3.075005 ATCCCACAGGTCCGTCGG 61.075 66.667 4.39 4.39 0.00 4.79
2923 2989 2.494918 GATCCCACAGGTCCGTCG 59.505 66.667 0.00 0.00 0.00 5.12
2926 2992 0.106167 TAGAGGATCCCACAGGTCCG 60.106 60.000 8.55 0.00 38.00 4.79
3019 3091 9.500864 GGTACAACGAACACTAAAAACAATAAA 57.499 29.630 0.00 0.00 0.00 1.40
3020 3092 8.671921 TGGTACAACGAACACTAAAAACAATAA 58.328 29.630 0.00 0.00 31.92 1.40
3021 3093 8.121708 GTGGTACAACGAACACTAAAAACAATA 58.878 33.333 0.00 0.00 44.16 1.90
3022 3094 6.968335 GTGGTACAACGAACACTAAAAACAAT 59.032 34.615 0.00 0.00 44.16 2.71
3023 3095 6.313252 GTGGTACAACGAACACTAAAAACAA 58.687 36.000 0.00 0.00 44.16 2.83
3024 3096 5.163774 GGTGGTACAACGAACACTAAAAACA 60.164 40.000 0.00 0.00 44.16 2.83
3025 3097 5.265477 GGTGGTACAACGAACACTAAAAAC 58.735 41.667 0.00 0.00 44.16 2.43
3026 3098 5.482686 GGTGGTACAACGAACACTAAAAA 57.517 39.130 0.00 0.00 44.16 1.94
3039 3111 5.814481 TCATCTTCAATCATGGTGGTACAA 58.186 37.500 0.00 0.00 44.16 2.41
3040 3112 5.434182 TCATCTTCAATCATGGTGGTACA 57.566 39.130 0.00 0.00 0.00 2.90
3041 3113 6.949352 ATTCATCTTCAATCATGGTGGTAC 57.051 37.500 0.00 0.00 0.00 3.34
3042 3114 8.033178 TCTATTCATCTTCAATCATGGTGGTA 57.967 34.615 0.00 0.00 0.00 3.25
3043 3115 6.903516 TCTATTCATCTTCAATCATGGTGGT 58.096 36.000 0.00 0.00 0.00 4.16
3044 3116 7.997773 ATCTATTCATCTTCAATCATGGTGG 57.002 36.000 0.00 0.00 0.00 4.61
3045 3117 9.063615 TCAATCTATTCATCTTCAATCATGGTG 57.936 33.333 0.00 0.00 0.00 4.17
3046 3118 9.636789 TTCAATCTATTCATCTTCAATCATGGT 57.363 29.630 0.00 0.00 0.00 3.55
3089 3161 6.486993 GGTAGTTGAGAACCTGTGATCTTTTT 59.513 38.462 0.00 0.00 32.72 1.94
3090 3162 5.998363 GGTAGTTGAGAACCTGTGATCTTTT 59.002 40.000 0.00 0.00 32.72 2.27
3099 3171 4.081586 GGAGTAAGGGTAGTTGAGAACCTG 60.082 50.000 0.00 0.00 35.97 4.00
3100 3172 4.095211 GGAGTAAGGGTAGTTGAGAACCT 58.905 47.826 0.00 0.00 35.97 3.50
3113 3188 3.553828 TTCCAAATAGCGGAGTAAGGG 57.446 47.619 0.00 0.00 33.01 3.95
3122 3197 1.603802 ACATCGGCATTCCAAATAGCG 59.396 47.619 0.00 0.00 0.00 4.26
3138 3213 4.489249 GCTGCACATTGCCACATC 57.511 55.556 0.00 0.00 44.23 3.06
3146 3221 4.035558 CGAGTGTTTATATGGCTGCACATT 59.964 41.667 0.50 0.00 32.39 2.71
3178 3253 6.113411 TCCAAGAGAAGAAAGTTTTCGAACT 58.887 36.000 0.00 0.00 41.92 3.01
3189 3264 5.241506 ACGCATGAAATTCCAAGAGAAGAAA 59.758 36.000 0.00 0.00 38.07 2.52
3214 3315 7.436430 TGACGGTAGTATTAGCTTATCTCTG 57.564 40.000 0.00 0.00 0.00 3.35
3223 3324 5.393243 GGAGGATGATGACGGTAGTATTAGC 60.393 48.000 0.00 0.00 0.00 3.09
3224 3325 5.125739 GGGAGGATGATGACGGTAGTATTAG 59.874 48.000 0.00 0.00 0.00 1.73
3225 3326 5.014858 GGGAGGATGATGACGGTAGTATTA 58.985 45.833 0.00 0.00 0.00 0.98
3226 3327 3.833070 GGGAGGATGATGACGGTAGTATT 59.167 47.826 0.00 0.00 0.00 1.89
3227 3328 3.181422 TGGGAGGATGATGACGGTAGTAT 60.181 47.826 0.00 0.00 0.00 2.12
3228 3329 2.176148 TGGGAGGATGATGACGGTAGTA 59.824 50.000 0.00 0.00 0.00 1.82
3229 3330 1.063190 TGGGAGGATGATGACGGTAGT 60.063 52.381 0.00 0.00 0.00 2.73
3230 3331 1.704641 TGGGAGGATGATGACGGTAG 58.295 55.000 0.00 0.00 0.00 3.18
3250 3351 1.271840 ATGCCTTCTGGTTCCCGCTA 61.272 55.000 0.00 0.00 35.27 4.26
3253 3355 2.348411 ATTATGCCTTCTGGTTCCCG 57.652 50.000 0.00 0.00 35.27 5.14
3254 3356 5.420725 AAAAATTATGCCTTCTGGTTCCC 57.579 39.130 0.00 0.00 35.27 3.97
3275 3417 3.071312 AGTGGGCATGCTGATTTTTCAAA 59.929 39.130 18.92 0.00 0.00 2.69
3291 3433 5.938125 TGTTCTTTATTTCTCAGTAGTGGGC 59.062 40.000 0.00 0.00 0.00 5.36
3294 3436 8.833231 TCCTTGTTCTTTATTTCTCAGTAGTG 57.167 34.615 0.00 0.00 0.00 2.74
3371 3515 4.642437 TGCAAAGACAAGTGTTGTGGAATA 59.358 37.500 0.00 0.00 45.52 1.75
3379 3523 4.009675 TGAACTCTGCAAAGACAAGTGTT 58.990 39.130 0.00 0.00 0.00 3.32
3380 3524 3.375299 GTGAACTCTGCAAAGACAAGTGT 59.625 43.478 0.00 0.00 0.00 3.55
3381 3525 3.242870 GGTGAACTCTGCAAAGACAAGTG 60.243 47.826 0.00 0.00 0.00 3.16
3393 3537 2.358737 GGCCCACGGTGAACTCTG 60.359 66.667 10.28 0.00 0.00 3.35
3404 3548 2.097466 CGTGATCATTAAGTTGGCCCAC 59.903 50.000 0.00 0.00 0.00 4.61
3421 3579 9.863845 TCAAGACTGATGTTATTAATTACGTGA 57.136 29.630 4.12 0.00 0.00 4.35
3422 3580 9.901724 GTCAAGACTGATGTTATTAATTACGTG 57.098 33.333 4.12 0.00 33.05 4.49
3444 3602 8.763356 GTGACTTTTCATGCATAAAAATGTCAA 58.237 29.630 31.14 22.06 43.04 3.18
3448 3606 7.096106 ACGTGTGACTTTTCATGCATAAAAATG 60.096 33.333 8.20 11.56 33.11 2.32
3450 3608 6.269315 ACGTGTGACTTTTCATGCATAAAAA 58.731 32.000 7.52 7.52 33.11 1.94
3451 3609 5.826586 ACGTGTGACTTTTCATGCATAAAA 58.173 33.333 0.00 0.00 33.11 1.52
3472 3630 3.820689 TCGCTTGAAAATCCATTTGACG 58.179 40.909 0.00 0.00 0.00 4.35
3509 3667 2.672874 ACATTAGCTACACATGTGCACG 59.327 45.455 25.68 14.50 29.74 5.34
3543 3703 9.691362 TTTCTTGAAAATAGTGTGAAATAAGGC 57.309 29.630 0.00 0.00 0.00 4.35
3635 3825 9.075678 GATGATGAGGACCAATATGAAATTTCT 57.924 33.333 18.64 7.42 0.00 2.52
3669 3860 7.095910 AGATTGCACATATACTCTCATGTAGC 58.904 38.462 0.00 0.00 33.66 3.58
3709 3900 9.847224 GACATCTAAGGGTCCAATATTTCTTAA 57.153 33.333 0.00 0.00 0.00 1.85
3710 3901 9.225682 AGACATCTAAGGGTCCAATATTTCTTA 57.774 33.333 0.00 0.00 34.58 2.10


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

AutoCloner maintained by Alex Coulton.