Multiple sequence alignment - TraesCS4D01G108200

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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 TraesCS4D01G108200 chr4D 100.000 3994 0 0 1 3994 87713214 87717207 0.000000e+00 7376.0
1 TraesCS4D01G108200 chr4D 100.000 64 0 0 3251 3314 87716527 87716590 7.010000e-23 119.0
2 TraesCS4D01G108200 chr4A 91.481 2606 100 44 718 3242 500349381 500351945 0.000000e+00 3470.0
3 TraesCS4D01G108200 chr4A 90.894 593 32 7 3406 3992 500352034 500352610 0.000000e+00 776.0
4 TraesCS4D01G108200 chr4A 78.889 180 37 1 215 394 729614851 729615029 1.950000e-23 121.0
5 TraesCS4D01G108200 chr4B 93.240 1287 41 15 740 1993 124017542 124018815 0.000000e+00 1853.0
6 TraesCS4D01G108200 chr4B 91.375 1229 69 19 1994 3191 124018915 124020137 0.000000e+00 1648.0
7 TraesCS4D01G108200 chr4B 90.404 594 32 12 3408 3993 124020340 124020916 0.000000e+00 758.0
8 TraesCS4D01G108200 chr4B 89.431 123 11 2 3338 3459 658773185 658773064 1.920000e-33 154.0
9 TraesCS4D01G108200 chr2D 78.824 765 95 35 14 722 629255414 629254661 1.690000e-123 453.0
10 TraesCS4D01G108200 chr5B 92.905 296 21 0 1361 1656 207577667 207577962 7.930000e-117 431.0
11 TraesCS4D01G108200 chr5B 82.879 257 29 5 1362 1618 11061134 11061375 2.420000e-52 217.0
12 TraesCS4D01G108200 chr5B 88.889 126 11 3 3337 3461 405716055 405715932 6.910000e-33 152.0
13 TraesCS4D01G108200 chr5B 90.476 105 7 2 1029 1133 207577347 207577448 6.960000e-28 135.0
14 TraesCS4D01G108200 chr5A 92.230 296 23 0 1361 1656 244450135 244449840 1.720000e-113 420.0
15 TraesCS4D01G108200 chr5A 90.323 124 8 4 3338 3459 86662050 86662171 4.130000e-35 159.0
16 TraesCS4D01G108200 chr5A 91.176 102 6 2 1032 1133 244450452 244450354 6.960000e-28 135.0
17 TraesCS4D01G108200 chr5A 90.476 42 4 0 3225 3266 559092878 559092837 5.580000e-04 56.5
18 TraesCS4D01G108200 chr5D 91.892 296 24 0 1361 1656 204871866 204871571 7.990000e-112 414.0
19 TraesCS4D01G108200 chr5D 88.889 126 10 3 3337 3461 491586717 491586595 6.910000e-33 152.0
20 TraesCS4D01G108200 chr5D 93.407 91 6 0 1032 1122 204872183 204872093 6.960000e-28 135.0
21 TraesCS4D01G108200 chr5D 90.476 42 4 0 3225 3266 443066741 443066700 5.580000e-04 56.5
22 TraesCS4D01G108200 chr5D 100.000 30 0 0 3237 3266 510093333 510093304 5.580000e-04 56.5
23 TraesCS4D01G108200 chr1D 91.497 294 25 0 1362 1655 7921310 7921017 4.810000e-109 405.0
24 TraesCS4D01G108200 chr1B 91.497 294 25 0 1362 1655 10113708 10113415 4.810000e-109 405.0
25 TraesCS4D01G108200 chr1B 77.005 187 40 3 215 401 430892591 430892408 1.960000e-18 104.0
26 TraesCS4D01G108200 chr1B 94.737 57 3 0 1051 1107 10114115 10114059 5.500000e-14 89.8
27 TraesCS4D01G108200 chr1A 91.126 293 26 0 1363 1655 9589136 9588844 8.040000e-107 398.0
28 TraesCS4D01G108200 chr1A 92.857 70 5 0 1051 1120 9589279 9589210 7.060000e-18 102.0
29 TraesCS4D01G108200 chr7A 91.667 120 8 2 3342 3460 206959976 206959858 8.880000e-37 165.0
30 TraesCS4D01G108200 chr7A 100.000 30 0 0 3237 3266 734515596 734515625 5.580000e-04 56.5
31 TraesCS4D01G108200 chr7D 90.833 120 9 2 3342 3460 197927125 197927007 4.130000e-35 159.0
32 TraesCS4D01G108200 chr7D 89.431 123 11 2 3338 3459 34756987 34756866 1.920000e-33 154.0
33 TraesCS4D01G108200 chr7D 89.130 46 1 3 3225 3266 498284607 498284562 2.000000e-03 54.7
34 TraesCS4D01G108200 chr7B 89.516 124 11 2 3338 3460 369872750 369872872 5.340000e-34 156.0
35 TraesCS4D01G108200 chr3A 87.786 131 13 3 3332 3460 589797292 589797421 2.490000e-32 150.0
36 TraesCS4D01G108200 chr6D 100.000 30 0 0 3237 3266 168686101 168686130 5.580000e-04 56.5
37 TraesCS4D01G108200 chr3D 100.000 30 0 0 3237 3266 267028083 267028054 5.580000e-04 56.5
38 TraesCS4D01G108200 chrUn 100.000 29 0 0 3238 3266 105368174 105368202 2.000000e-03 54.7


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 TraesCS4D01G108200 chr4D 87713214 87717207 3993 False 3747.500000 7376 100.0000 1 3994 2 chr4D.!!$F1 3993
1 TraesCS4D01G108200 chr4A 500349381 500352610 3229 False 2123.000000 3470 91.1875 718 3992 2 chr4A.!!$F2 3274
2 TraesCS4D01G108200 chr4B 124017542 124020916 3374 False 1419.666667 1853 91.6730 740 3993 3 chr4B.!!$F1 3253
3 TraesCS4D01G108200 chr2D 629254661 629255414 753 True 453.000000 453 78.8240 14 722 1 chr2D.!!$R1 708
4 TraesCS4D01G108200 chr5B 207577347 207577962 615 False 283.000000 431 91.6905 1029 1656 2 chr5B.!!$F2 627
5 TraesCS4D01G108200 chr5A 244449840 244450452 612 True 277.500000 420 91.7030 1032 1656 2 chr5A.!!$R2 624
6 TraesCS4D01G108200 chr5D 204871571 204872183 612 True 274.500000 414 92.6495 1032 1656 2 chr5D.!!$R4 624
7 TraesCS4D01G108200 chr1B 10113415 10114115 700 True 247.400000 405 93.1170 1051 1655 2 chr1B.!!$R2 604

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
492 520 0.179023 AAAACGGAAGGGCGGTGTTA 60.179 50.0 0.0 0.0 0.0 2.41 F
644 682 0.257328 TTGCCTGAGGTGGTGTTTGA 59.743 50.0 0.0 0.0 0.0 2.69 F
645 683 0.478072 TGCCTGAGGTGGTGTTTGAT 59.522 50.0 0.0 0.0 0.0 2.57 F
1580 1897 0.741326 GCTACGCTCACCTCTCATCA 59.259 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 2050 3.930229 CCGTAATGCACAGCACTAACTAA 59.070 43.478 0.0 0.0 43.04 2.24 R
2567 3036 3.328505 CCCTGCAATCAAAATCCACAAC 58.671 45.455 0.0 0.0 0.00 3.32 R
2939 3422 5.282055 TGCATGTTTTTATTCACCACCAA 57.718 34.783 0.0 0.0 0.00 3.67 R
3648 4217 1.133823 ACAGACAGCACATTGAACCCA 60.134 47.619 0.0 0.0 0.00 4.51 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
29 30 1.271597 GGGAGTGTGAGGAACAATGCT 60.272 52.381 0.00 0.00 43.79 3.79
31 32 2.227388 GGAGTGTGAGGAACAATGCTTG 59.773 50.000 0.00 0.00 41.42 4.01
56 57 8.700051 TGTTTTGTGGGAAGAAAGAATCAATTA 58.300 29.630 0.00 0.00 0.00 1.40
58 59 9.541143 TTTTGTGGGAAGAAAGAATCAATTAAC 57.459 29.630 0.00 0.00 0.00 2.01
84 86 2.014010 TTTTCCAATGCCCTCTTGCT 57.986 45.000 0.00 0.00 0.00 3.91
90 92 3.071602 TCCAATGCCCTCTTGCTAGATAC 59.928 47.826 0.00 0.00 0.00 2.24
106 108 4.890158 AGATACATGTGGAGTGTTGTGA 57.110 40.909 9.11 0.00 0.00 3.58
109 111 5.480422 AGATACATGTGGAGTGTTGTGAGTA 59.520 40.000 9.11 0.00 0.00 2.59
110 112 3.995199 ACATGTGGAGTGTTGTGAGTAG 58.005 45.455 0.00 0.00 0.00 2.57
111 113 3.244215 ACATGTGGAGTGTTGTGAGTAGG 60.244 47.826 0.00 0.00 0.00 3.18
112 114 1.691976 TGTGGAGTGTTGTGAGTAGGG 59.308 52.381 0.00 0.00 0.00 3.53
113 115 1.692519 GTGGAGTGTTGTGAGTAGGGT 59.307 52.381 0.00 0.00 0.00 4.34
114 116 1.691976 TGGAGTGTTGTGAGTAGGGTG 59.308 52.381 0.00 0.00 0.00 4.61
115 117 1.608283 GGAGTGTTGTGAGTAGGGTGC 60.608 57.143 0.00 0.00 0.00 5.01
116 118 0.396811 AGTGTTGTGAGTAGGGTGCC 59.603 55.000 0.00 0.00 0.00 5.01
117 119 0.605589 GTGTTGTGAGTAGGGTGCCC 60.606 60.000 0.00 0.00 0.00 5.36
150 161 8.761575 TTTTTGATCTGGATTCATGCTTTAAC 57.238 30.769 0.00 0.00 0.00 2.01
156 167 5.066375 TCTGGATTCATGCTTTAACGATTGG 59.934 40.000 0.00 0.00 0.00 3.16
211 224 2.497675 TCAGTAGGAGTTGCTGCCTTAG 59.502 50.000 0.00 0.00 39.16 2.18
215 228 2.508526 AGGAGTTGCTGCCTTAGTTTG 58.491 47.619 0.00 0.00 0.00 2.93
221 234 1.247567 GCTGCCTTAGTTTGGAGCAA 58.752 50.000 0.00 0.00 32.14 3.91
222 235 1.821136 GCTGCCTTAGTTTGGAGCAAT 59.179 47.619 0.00 0.00 32.14 3.56
224 237 3.841643 CTGCCTTAGTTTGGAGCAATTG 58.158 45.455 0.00 0.00 32.14 2.32
226 239 2.675032 GCCTTAGTTTGGAGCAATTGGC 60.675 50.000 7.72 0.00 45.30 4.52
244 257 3.172339 TGGCAAATTAGGAACATGGCTT 58.828 40.909 0.00 0.00 37.45 4.35
253 266 3.037549 AGGAACATGGCTTTGTTTCCAA 58.962 40.909 10.58 0.00 39.85 3.53
255 268 2.507339 ACATGGCTTTGTTTCCAACG 57.493 45.000 0.00 0.00 35.75 4.10
256 269 1.068434 ACATGGCTTTGTTTCCAACGG 59.932 47.619 0.00 0.00 35.75 4.44
273 286 1.103398 CGGGTTTGGCCATCTGATCC 61.103 60.000 6.09 1.85 39.65 3.36
274 287 0.259938 GGGTTTGGCCATCTGATCCT 59.740 55.000 6.09 0.00 39.65 3.24
275 288 1.494721 GGGTTTGGCCATCTGATCCTA 59.505 52.381 6.09 0.00 39.65 2.94
276 289 2.487986 GGGTTTGGCCATCTGATCCTAG 60.488 54.545 6.09 0.00 39.65 3.02
277 290 2.173569 GGTTTGGCCATCTGATCCTAGT 59.826 50.000 6.09 0.00 37.17 2.57
278 291 3.209410 GTTTGGCCATCTGATCCTAGTG 58.791 50.000 6.09 0.00 0.00 2.74
328 341 7.039152 TGGATTAATGATTGGAGTCTTTTGCAA 60.039 33.333 0.00 0.00 32.84 4.08
333 346 4.276678 TGATTGGAGTCTTTTGCAAGTGAG 59.723 41.667 0.00 0.00 31.79 3.51
339 352 1.774254 TCTTTTGCAAGTGAGGGAGGA 59.226 47.619 0.00 0.00 0.00 3.71
341 354 0.843309 TTTGCAAGTGAGGGAGGACA 59.157 50.000 0.00 0.00 0.00 4.02
346 359 2.498167 CAAGTGAGGGAGGACACAAAG 58.502 52.381 0.00 0.00 39.18 2.77
376 389 3.529533 ACTACTATGCTCAAAGCTGCTG 58.470 45.455 1.35 0.00 42.97 4.41
380 393 1.848652 ATGCTCAAAGCTGCTGGATT 58.151 45.000 1.35 0.00 42.97 3.01
385 398 2.419324 CTCAAAGCTGCTGGATTGAGTC 59.581 50.000 24.39 0.00 42.28 3.36
387 400 0.610174 AAGCTGCTGGATTGAGTCGA 59.390 50.000 1.35 0.00 0.00 4.20
390 403 1.941209 GCTGCTGGATTGAGTCGACAA 60.941 52.381 19.50 4.43 0.00 3.18
401 414 6.019156 GGATTGAGTCGACAATGAGATCTTTC 60.019 42.308 19.50 2.14 40.03 2.62
403 416 5.783111 TGAGTCGACAATGAGATCTTTCAA 58.217 37.500 19.50 0.00 0.00 2.69
404 417 5.866092 TGAGTCGACAATGAGATCTTTCAAG 59.134 40.000 19.50 0.00 0.00 3.02
405 418 4.629200 AGTCGACAATGAGATCTTTCAAGC 59.371 41.667 19.50 0.00 0.00 4.01
406 419 4.629200 GTCGACAATGAGATCTTTCAAGCT 59.371 41.667 11.55 0.00 0.00 3.74
407 420 5.121454 GTCGACAATGAGATCTTTCAAGCTT 59.879 40.000 11.55 0.00 0.00 3.74
409 422 5.638783 GACAATGAGATCTTTCAAGCTTGG 58.361 41.667 25.73 10.56 0.00 3.61
410 423 5.319453 ACAATGAGATCTTTCAAGCTTGGA 58.681 37.500 25.73 15.86 0.00 3.53
411 424 5.415077 ACAATGAGATCTTTCAAGCTTGGAG 59.585 40.000 25.73 21.73 0.00 3.86
431 444 1.076705 GGGTGGGCTTCCTGGATTC 60.077 63.158 0.00 0.00 0.00 2.52
437 450 1.039785 GGCTTCCTGGATTCCAAGGC 61.040 60.000 12.19 12.19 30.80 4.35
461 474 4.023279 TGGAAAATGTTTGATCGTGGTCAG 60.023 41.667 0.00 0.00 0.00 3.51
473 486 2.367241 TCGTGGTCAGTCAAGATGGAAA 59.633 45.455 0.00 0.00 0.00 3.13
474 487 3.138304 CGTGGTCAGTCAAGATGGAAAA 58.862 45.455 0.00 0.00 0.00 2.29
475 488 3.563808 CGTGGTCAGTCAAGATGGAAAAA 59.436 43.478 0.00 0.00 0.00 1.94
492 520 0.179023 AAAACGGAAGGGCGGTGTTA 60.179 50.000 0.00 0.00 0.00 2.41
499 527 2.433436 GAAGGGCGGTGTTAGTTGATT 58.567 47.619 0.00 0.00 0.00 2.57
503 531 1.401018 GGCGGTGTTAGTTGATTGTGC 60.401 52.381 0.00 0.00 0.00 4.57
507 535 3.146066 GGTGTTAGTTGATTGTGCTGGA 58.854 45.455 0.00 0.00 0.00 3.86
509 537 4.037446 GGTGTTAGTTGATTGTGCTGGAAA 59.963 41.667 0.00 0.00 0.00 3.13
519 548 1.493022 TGTGCTGGAAACTAGGTGGTT 59.507 47.619 0.00 0.00 0.00 3.67
522 551 3.939592 GTGCTGGAAACTAGGTGGTTATC 59.060 47.826 0.00 0.00 0.00 1.75
527 556 6.195600 TGGAAACTAGGTGGTTATCAGTTT 57.804 37.500 0.00 0.00 40.99 2.66
530 559 6.315642 GGAAACTAGGTGGTTATCAGTTTAGC 59.684 42.308 0.00 0.00 39.02 3.09
533 562 7.729124 ACTAGGTGGTTATCAGTTTAGCTTA 57.271 36.000 0.00 0.00 0.00 3.09
534 563 8.142485 ACTAGGTGGTTATCAGTTTAGCTTAA 57.858 34.615 0.00 0.00 0.00 1.85
536 565 7.017319 AGGTGGTTATCAGTTTAGCTTAAGT 57.983 36.000 4.02 0.00 0.00 2.24
542 571 9.000486 GGTTATCAGTTTAGCTTAAGTGAGTTT 58.000 33.333 23.09 12.55 39.94 2.66
549 578 8.560374 AGTTTAGCTTAAGTGAGTTTTAGCTTG 58.440 33.333 12.50 0.00 36.70 4.01
553 582 5.853810 GCTTAAGTGAGTTTTAGCTTGCTTC 59.146 40.000 4.02 0.00 0.00 3.86
554 583 4.837896 AAGTGAGTTTTAGCTTGCTTCC 57.162 40.909 0.00 0.00 0.00 3.46
555 584 3.149981 AGTGAGTTTTAGCTTGCTTCCC 58.850 45.455 0.00 0.00 0.00 3.97
559 588 1.819288 GTTTTAGCTTGCTTCCCCCTC 59.181 52.381 0.00 0.00 0.00 4.30
573 602 3.803340 TCCCCCTCTTCACTTGTATTCT 58.197 45.455 0.00 0.00 0.00 2.40
574 603 3.775316 TCCCCCTCTTCACTTGTATTCTC 59.225 47.826 0.00 0.00 0.00 2.87
578 607 3.447586 CCTCTTCACTTGTATTCTCCGGA 59.552 47.826 2.93 2.93 0.00 5.14
580 609 5.011090 TCTTCACTTGTATTCTCCGGATG 57.989 43.478 3.57 0.00 0.00 3.51
596 632 0.908198 GATGAGAGGGGTGAGTGCTT 59.092 55.000 0.00 0.00 0.00 3.91
597 633 1.280421 GATGAGAGGGGTGAGTGCTTT 59.720 52.381 0.00 0.00 0.00 3.51
598 634 0.397941 TGAGAGGGGTGAGTGCTTTG 59.602 55.000 0.00 0.00 0.00 2.77
599 635 0.398318 GAGAGGGGTGAGTGCTTTGT 59.602 55.000 0.00 0.00 0.00 2.83
603 641 2.430694 GAGGGGTGAGTGCTTTGTTTTT 59.569 45.455 0.00 0.00 0.00 1.94
608 646 2.093711 GTGAGTGCTTTGTTTTTGGGGT 60.094 45.455 0.00 0.00 0.00 4.95
623 661 2.051345 GGTTGTTGTTGCCTCGCG 60.051 61.111 0.00 0.00 0.00 5.87
627 665 2.427410 GTTGTTGCCTCGCGCTTG 60.427 61.111 5.56 0.00 38.78 4.01
628 666 4.326766 TTGTTGCCTCGCGCTTGC 62.327 61.111 5.56 5.71 38.78 4.01
635 673 4.749310 CTCGCGCTTGCCTGAGGT 62.749 66.667 5.56 0.00 34.11 3.85
639 677 3.052082 CGCTTGCCTGAGGTGGTG 61.052 66.667 0.00 0.00 0.00 4.17
640 678 2.113986 GCTTGCCTGAGGTGGTGT 59.886 61.111 0.00 0.00 0.00 4.16
641 679 1.529244 GCTTGCCTGAGGTGGTGTT 60.529 57.895 0.00 0.00 0.00 3.32
642 680 1.109323 GCTTGCCTGAGGTGGTGTTT 61.109 55.000 0.00 0.00 0.00 2.83
643 681 0.670162 CTTGCCTGAGGTGGTGTTTG 59.330 55.000 0.00 0.00 0.00 2.93
644 682 0.257328 TTGCCTGAGGTGGTGTTTGA 59.743 50.000 0.00 0.00 0.00 2.69
645 683 0.478072 TGCCTGAGGTGGTGTTTGAT 59.522 50.000 0.00 0.00 0.00 2.57
646 684 0.883833 GCCTGAGGTGGTGTTTGATG 59.116 55.000 0.00 0.00 0.00 3.07
647 685 1.819305 GCCTGAGGTGGTGTTTGATGT 60.819 52.381 0.00 0.00 0.00 3.06
648 686 1.881973 CCTGAGGTGGTGTTTGATGTG 59.118 52.381 0.00 0.00 0.00 3.21
649 687 2.575532 CTGAGGTGGTGTTTGATGTGT 58.424 47.619 0.00 0.00 0.00 3.72
650 688 2.951642 CTGAGGTGGTGTTTGATGTGTT 59.048 45.455 0.00 0.00 0.00 3.32
651 689 3.360867 TGAGGTGGTGTTTGATGTGTTT 58.639 40.909 0.00 0.00 0.00 2.83
652 690 3.766591 TGAGGTGGTGTTTGATGTGTTTT 59.233 39.130 0.00 0.00 0.00 2.43
653 691 4.111916 GAGGTGGTGTTTGATGTGTTTTG 58.888 43.478 0.00 0.00 0.00 2.44
654 692 3.118811 AGGTGGTGTTTGATGTGTTTTGG 60.119 43.478 0.00 0.00 0.00 3.28
655 693 3.368948 GGTGGTGTTTGATGTGTTTTGGT 60.369 43.478 0.00 0.00 0.00 3.67
656 694 4.249661 GTGGTGTTTGATGTGTTTTGGTT 58.750 39.130 0.00 0.00 0.00 3.67
657 695 4.092675 GTGGTGTTTGATGTGTTTTGGTTG 59.907 41.667 0.00 0.00 0.00 3.77
658 696 4.249661 GGTGTTTGATGTGTTTTGGTTGT 58.750 39.130 0.00 0.00 0.00 3.32
659 697 5.047306 TGGTGTTTGATGTGTTTTGGTTGTA 60.047 36.000 0.00 0.00 0.00 2.41
660 698 6.045955 GGTGTTTGATGTGTTTTGGTTGTAT 58.954 36.000 0.00 0.00 0.00 2.29
661 699 6.019156 GGTGTTTGATGTGTTTTGGTTGTATG 60.019 38.462 0.00 0.00 0.00 2.39
662 700 6.533367 GTGTTTGATGTGTTTTGGTTGTATGT 59.467 34.615 0.00 0.00 0.00 2.29
663 701 6.754209 TGTTTGATGTGTTTTGGTTGTATGTC 59.246 34.615 0.00 0.00 0.00 3.06
664 702 6.456795 TTGATGTGTTTTGGTTGTATGTCA 57.543 33.333 0.00 0.00 0.00 3.58
665 703 6.070897 TGATGTGTTTTGGTTGTATGTCAG 57.929 37.500 0.00 0.00 0.00 3.51
666 704 4.909696 TGTGTTTTGGTTGTATGTCAGG 57.090 40.909 0.00 0.00 0.00 3.86
667 705 4.527944 TGTGTTTTGGTTGTATGTCAGGA 58.472 39.130 0.00 0.00 0.00 3.86
668 706 4.336993 TGTGTTTTGGTTGTATGTCAGGAC 59.663 41.667 0.00 0.00 0.00 3.85
669 707 4.578928 GTGTTTTGGTTGTATGTCAGGACT 59.421 41.667 0.65 0.00 0.00 3.85
670 708 5.761234 GTGTTTTGGTTGTATGTCAGGACTA 59.239 40.000 0.65 0.00 0.00 2.59
671 709 5.761234 TGTTTTGGTTGTATGTCAGGACTAC 59.239 40.000 0.65 2.45 0.00 2.73
672 710 5.818678 TTTGGTTGTATGTCAGGACTACT 57.181 39.130 0.65 0.00 0.00 2.57
673 711 5.818678 TTGGTTGTATGTCAGGACTACTT 57.181 39.130 0.65 0.00 0.00 2.24
674 712 5.147330 TGGTTGTATGTCAGGACTACTTG 57.853 43.478 0.65 0.00 0.00 3.16
675 713 4.020573 TGGTTGTATGTCAGGACTACTTGG 60.021 45.833 0.65 0.00 0.00 3.61
676 714 4.020485 GGTTGTATGTCAGGACTACTTGGT 60.020 45.833 0.65 0.00 0.00 3.67
677 715 5.512576 GGTTGTATGTCAGGACTACTTGGTT 60.513 44.000 0.65 0.00 0.00 3.67
678 716 5.818678 TGTATGTCAGGACTACTTGGTTT 57.181 39.130 0.65 0.00 0.00 3.27
679 717 5.790593 TGTATGTCAGGACTACTTGGTTTC 58.209 41.667 0.65 0.00 0.00 2.78
680 718 3.764237 TGTCAGGACTACTTGGTTTCC 57.236 47.619 0.65 0.00 0.00 3.13
681 719 3.314693 TGTCAGGACTACTTGGTTTCCT 58.685 45.455 0.65 0.00 39.17 3.36
682 720 3.714798 TGTCAGGACTACTTGGTTTCCTT 59.285 43.478 0.65 0.00 36.26 3.36
683 721 4.903049 TGTCAGGACTACTTGGTTTCCTTA 59.097 41.667 0.65 0.00 36.26 2.69
684 722 5.367352 TGTCAGGACTACTTGGTTTCCTTAA 59.633 40.000 0.65 0.00 36.26 1.85
685 723 6.043938 TGTCAGGACTACTTGGTTTCCTTAAT 59.956 38.462 0.65 0.00 36.26 1.40
686 724 6.371825 GTCAGGACTACTTGGTTTCCTTAATG 59.628 42.308 0.00 0.00 36.26 1.90
687 725 6.271391 TCAGGACTACTTGGTTTCCTTAATGA 59.729 38.462 0.00 0.00 36.26 2.57
688 726 6.940298 CAGGACTACTTGGTTTCCTTAATGAA 59.060 38.462 0.00 0.00 36.26 2.57
689 727 7.447238 CAGGACTACTTGGTTTCCTTAATGAAA 59.553 37.037 2.19 2.19 36.26 2.69
690 728 8.170730 AGGACTACTTGGTTTCCTTAATGAAAT 58.829 33.333 8.83 0.00 34.65 2.17
691 729 8.459635 GGACTACTTGGTTTCCTTAATGAAATC 58.540 37.037 8.83 8.90 36.68 2.17
692 730 8.934023 ACTACTTGGTTTCCTTAATGAAATCA 57.066 30.769 13.28 13.28 42.13 2.57
693 731 9.014297 ACTACTTGGTTTCCTTAATGAAATCAG 57.986 33.333 15.76 13.10 43.94 2.90
694 732 7.232118 ACTTGGTTTCCTTAATGAAATCAGG 57.768 36.000 19.90 19.90 43.94 3.86
695 733 7.010160 ACTTGGTTTCCTTAATGAAATCAGGA 58.990 34.615 25.06 11.09 43.94 3.86
696 734 7.508977 ACTTGGTTTCCTTAATGAAATCAGGAA 59.491 33.333 25.06 9.21 43.94 3.36
697 735 7.847711 TGGTTTCCTTAATGAAATCAGGAAA 57.152 32.000 13.28 7.93 45.96 3.13
860 909 1.692519 ACCAAGGAGTCACACCTGTAC 59.307 52.381 0.00 0.00 37.85 2.90
866 915 2.607282 GGAGTCACACCTGTACACTTCG 60.607 54.545 0.00 0.00 0.00 3.79
1021 1077 2.430382 AAGAAGCGCGACCGGAGAAA 62.430 55.000 12.10 0.00 34.32 2.52
1211 1270 2.544844 TTAGATGTCCGAGGGGTTCT 57.455 50.000 0.00 0.00 33.83 3.01
1223 1282 1.076192 GGGTTCTCTCTCCCCGCTA 60.076 63.158 0.00 0.00 37.89 4.26
1577 1894 2.407428 CGGCTACGCTCACCTCTCA 61.407 63.158 0.00 0.00 0.00 3.27
1580 1897 0.741326 GCTACGCTCACCTCTCATCA 59.259 55.000 0.00 0.00 0.00 3.07
1733 2050 1.337071 CGGTATGTGGATGCTCGTAGT 59.663 52.381 0.00 0.00 0.00 2.73
1832 2150 3.768468 TTTCCAAAACAGACGTGGTTC 57.232 42.857 0.00 0.00 29.78 3.62
1968 2300 6.720309 TGATATTGTGGATCCTTCTGTTTGA 58.280 36.000 14.23 0.00 0.00 2.69
1988 2320 6.564709 TTGAAGTCCATGCAATCTATATGC 57.435 37.500 0.00 0.00 44.08 3.14
1989 2321 5.872963 TGAAGTCCATGCAATCTATATGCT 58.127 37.500 0.00 0.00 44.14 3.79
1990 2322 7.008021 TGAAGTCCATGCAATCTATATGCTA 57.992 36.000 0.00 0.00 44.14 3.49
1991 2323 6.875726 TGAAGTCCATGCAATCTATATGCTAC 59.124 38.462 0.00 0.00 44.14 3.58
1992 2324 6.617782 AGTCCATGCAATCTATATGCTACT 57.382 37.500 0.00 0.00 44.14 2.57
2055 2487 6.149308 TGCTTGTACTTGTGACTATGGAATTG 59.851 38.462 0.00 0.00 0.00 2.32
2098 2531 8.755696 AAATTTAATACAGAAAGCATCGCAAA 57.244 26.923 0.00 0.00 0.00 3.68
2197 2630 5.527214 TGCTGATATTGCGCTTATGTAGTTT 59.473 36.000 9.73 0.00 0.00 2.66
2321 2766 7.361894 ACATTTTGCCTGCAATATTTTTGAAC 58.638 30.769 5.25 0.00 35.70 3.18
2367 2812 6.456988 CGAAAGTACATGTTCTTGGATAAGCC 60.457 42.308 17.24 1.56 33.82 4.35
2499 2968 6.089417 GTGTTTCCTTCACAGTTTTTCAGTTG 59.911 38.462 0.00 0.00 36.05 3.16
2560 3029 3.265791 CTCCTACAGTTGAATCCAGTGC 58.734 50.000 0.00 0.00 0.00 4.40
2567 3036 1.808945 GTTGAATCCAGTGCTGACCTG 59.191 52.381 0.02 0.00 0.00 4.00
2939 3422 7.422562 CCTGGGAATATGGGTTTTAATCCTACT 60.423 40.741 0.00 0.00 0.00 2.57
2958 3441 7.007723 TCCTACTTGGTGGTGAATAAAAACAT 58.992 34.615 0.00 0.00 37.07 2.71
3058 3541 4.761739 TCCTACTCTTTTTCTGCATGGTTG 59.238 41.667 0.00 0.00 0.00 3.77
3060 3543 3.299503 ACTCTTTTTCTGCATGGTTGGT 58.700 40.909 0.00 0.00 0.00 3.67
3061 3544 4.469657 ACTCTTTTTCTGCATGGTTGGTA 58.530 39.130 0.00 0.00 0.00 3.25
3062 3545 4.520492 ACTCTTTTTCTGCATGGTTGGTAG 59.480 41.667 0.00 0.00 0.00 3.18
3087 3570 7.986889 AGAAATTAATGTGGTTTGTCTGCTTTT 59.013 29.630 0.00 0.00 0.00 2.27
3094 3577 4.022849 GTGGTTTGTCTGCTTTTCTGCTAT 60.023 41.667 0.00 0.00 0.00 2.97
3115 3599 6.813152 GCTATACATTTGTTGAAGCCACAAAT 59.187 34.615 5.40 5.40 42.60 2.32
3223 3758 5.634020 GTCTGTTCACTGTTCTAATACGCTT 59.366 40.000 0.00 0.00 0.00 4.68
3228 3763 3.791887 CACTGTTCTAATACGCTTCTCCG 59.208 47.826 0.00 0.00 0.00 4.63
3231 3766 3.693085 TGTTCTAATACGCTTCTCCGTCT 59.307 43.478 0.00 0.00 42.20 4.18
3266 3828 6.071463 GTCGCTGATTTAGTACAAAGTTGTG 58.929 40.000 6.94 0.00 42.31 3.33
3267 3829 5.986741 TCGCTGATTTAGTACAAAGTTGTGA 59.013 36.000 6.94 0.00 42.31 3.58
3271 3833 7.041372 GCTGATTTAGTACAAAGTTGTGAAGGA 60.041 37.037 6.94 0.00 42.31 3.36
3273 3835 9.349713 TGATTTAGTACAAAGTTGTGAAGGAAT 57.650 29.630 6.94 1.82 42.31 3.01
3328 3894 7.922837 ACGCATTTAGTTTAGTACAAAGTTGT 58.077 30.769 1.75 1.75 44.86 3.32
3329 3895 7.853929 ACGCATTTAGTTTAGTACAAAGTTGTG 59.146 33.333 6.94 2.76 42.31 3.33
3330 3896 8.065407 CGCATTTAGTTTAGTACAAAGTTGTGA 58.935 33.333 6.94 0.00 42.31 3.58
3331 3897 9.724839 GCATTTAGTTTAGTACAAAGTTGTGAA 57.275 29.630 6.94 0.00 42.31 3.18
3334 3900 9.669887 TTTAGTTTAGTACAAAGTTGTGAAGGA 57.330 29.630 6.94 0.00 42.31 3.36
3335 3901 9.669887 TTAGTTTAGTACAAAGTTGTGAAGGAA 57.330 29.630 6.94 0.00 42.31 3.36
3336 3902 8.747538 AGTTTAGTACAAAGTTGTGAAGGAAT 57.252 30.769 6.94 0.00 42.31 3.01
3337 3903 9.185680 AGTTTAGTACAAAGTTGTGAAGGAATT 57.814 29.630 6.94 0.00 42.31 2.17
3390 3956 6.966021 ACGCATTTAGTGTATTTTGTTCACT 58.034 32.000 0.00 0.00 43.46 3.41
3391 3957 7.075741 ACGCATTTAGTGTATTTTGTTCACTC 58.924 34.615 0.00 0.00 41.66 3.51
3392 3958 7.075121 CGCATTTAGTGTATTTTGTTCACTCA 58.925 34.615 0.00 0.00 41.66 3.41
3393 3959 7.750458 CGCATTTAGTGTATTTTGTTCACTCAT 59.250 33.333 0.00 0.00 41.66 2.90
3394 3960 9.410556 GCATTTAGTGTATTTTGTTCACTCATT 57.589 29.630 0.00 0.00 41.66 2.57
3399 3965 8.225603 AGTGTATTTTGTTCACTCATTTCAGT 57.774 30.769 0.00 0.00 37.84 3.41
3400 3966 8.345565 AGTGTATTTTGTTCACTCATTTCAGTC 58.654 33.333 0.00 0.00 37.84 3.51
3401 3967 7.591426 GTGTATTTTGTTCACTCATTTCAGTCC 59.409 37.037 0.00 0.00 0.00 3.85
3402 3968 4.811555 TTTGTTCACTCATTTCAGTCCG 57.188 40.909 0.00 0.00 0.00 4.79
3403 3969 3.469008 TGTTCACTCATTTCAGTCCGT 57.531 42.857 0.00 0.00 0.00 4.69
3404 3970 4.594123 TGTTCACTCATTTCAGTCCGTA 57.406 40.909 0.00 0.00 0.00 4.02
3412 3978 5.652891 ACTCATTTCAGTCCGTATGTAGTCT 59.347 40.000 0.00 0.00 0.00 3.24
3477 4043 6.258947 GGGAGTACATTCTAAAAGCTGATGTC 59.741 42.308 0.00 0.00 0.00 3.06
3556 4125 5.926663 ACTCATATGTGAATCATGACAGCT 58.073 37.500 11.60 0.00 37.91 4.24
3584 4153 4.664688 AGGGATGTTCCATGAGAAGTTT 57.335 40.909 0.00 0.00 38.64 2.66
3585 4154 5.779241 AGGGATGTTCCATGAGAAGTTTA 57.221 39.130 0.00 0.00 38.64 2.01
3623 4192 3.748048 GGATCGCTAGCTGAAATGCAATA 59.252 43.478 13.93 0.00 34.99 1.90
3643 4212 8.664798 TGCAATAGTAAATCATCAAGTACACAC 58.335 33.333 0.00 0.00 0.00 3.82
3646 4215 9.719355 AATAGTAAATCATCAAGTACACACACA 57.281 29.630 0.00 0.00 0.00 3.72
3647 4216 7.421530 AGTAAATCATCAAGTACACACACAC 57.578 36.000 0.00 0.00 0.00 3.82
3648 4217 7.217200 AGTAAATCATCAAGTACACACACACT 58.783 34.615 0.00 0.00 0.00 3.55
3649 4218 5.929697 AATCATCAAGTACACACACACTG 57.070 39.130 0.00 0.00 0.00 3.66
3650 4219 3.727726 TCATCAAGTACACACACACTGG 58.272 45.455 0.00 0.00 0.00 4.00
3658 4227 2.023673 ACACACACACTGGGTTCAATG 58.976 47.619 0.00 0.00 29.07 2.82
3674 4243 1.723542 CAATGTGCTGTCTGTCTCGAC 59.276 52.381 0.00 0.00 34.52 4.20
3675 4244 0.961753 ATGTGCTGTCTGTCTCGACA 59.038 50.000 0.00 0.00 41.33 4.35
3676 4245 0.030773 TGTGCTGTCTGTCTCGACAC 59.969 55.000 0.00 0.00 38.89 3.67
3677 4246 0.312416 GTGCTGTCTGTCTCGACACT 59.688 55.000 0.00 0.00 38.89 3.55
3678 4247 0.312102 TGCTGTCTGTCTCGACACTG 59.688 55.000 0.00 0.00 38.89 3.66
3679 4248 0.312416 GCTGTCTGTCTCGACACTGT 59.688 55.000 0.00 0.00 38.89 3.55
3680 4249 1.664588 GCTGTCTGTCTCGACACTGTC 60.665 57.143 0.00 0.00 38.89 3.51
3681 4250 0.952280 TGTCTGTCTCGACACTGTCC 59.048 55.000 3.50 0.00 38.89 4.02
3682 4251 0.952280 GTCTGTCTCGACACTGTCCA 59.048 55.000 3.50 0.00 36.21 4.02
3683 4252 1.068885 GTCTGTCTCGACACTGTCCAG 60.069 57.143 3.50 5.42 36.21 3.86
3684 4253 0.955178 CTGTCTCGACACTGTCCAGT 59.045 55.000 3.50 0.00 43.61 4.00
3714 4293 7.588854 CACTGTTTGAAATACAACACATGAGAG 59.411 37.037 0.00 0.00 38.29 3.20
3750 4330 7.178628 TTGCTAACAAAGGTAGACTATCTGTCT 59.821 37.037 0.00 3.76 44.72 3.41
3993 4574 6.376978 CCTGAAGAACAATTTAGAGCAACAG 58.623 40.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.698818 ATTGTTCCTCACACTCCCCC 59.301 55.000 0.00 0.00 33.98 5.40
8 9 1.826385 CATTGTTCCTCACACTCCCC 58.174 55.000 0.00 0.00 33.98 4.81
9 10 1.168714 GCATTGTTCCTCACACTCCC 58.831 55.000 0.00 0.00 33.98 4.30
10 11 2.191128 AGCATTGTTCCTCACACTCC 57.809 50.000 0.00 0.00 33.98 3.85
11 12 3.549299 CAAGCATTGTTCCTCACACTC 57.451 47.619 0.00 0.00 42.34 3.51
29 30 6.537453 TGATTCTTTCTTCCCACAAAACAA 57.463 33.333 0.00 0.00 0.00 2.83
31 32 9.541143 TTAATTGATTCTTTCTTCCCACAAAAC 57.459 29.630 0.00 0.00 0.00 2.43
75 77 3.643320 TCCACATGTATCTAGCAAGAGGG 59.357 47.826 0.00 0.00 34.49 4.30
77 79 5.163468 ACACTCCACATGTATCTAGCAAGAG 60.163 44.000 0.00 0.00 34.49 2.85
84 86 5.480422 ACTCACAACACTCCACATGTATCTA 59.520 40.000 0.00 0.00 0.00 1.98
90 92 3.329386 CCTACTCACAACACTCCACATG 58.671 50.000 0.00 0.00 0.00 3.21
180 191 7.330700 GCAGCAACTCCTACTGAATATAATCTC 59.669 40.741 0.00 0.00 33.10 2.75
192 205 2.541466 ACTAAGGCAGCAACTCCTACT 58.459 47.619 0.00 0.00 31.24 2.57
195 208 2.508526 CAAACTAAGGCAGCAACTCCT 58.491 47.619 0.00 0.00 0.00 3.69
211 224 4.392754 CCTAATTTGCCAATTGCTCCAAAC 59.607 41.667 14.97 0.00 42.00 2.93
215 228 4.183865 GTTCCTAATTTGCCAATTGCTCC 58.816 43.478 6.03 0.00 42.00 4.70
221 234 3.776417 AGCCATGTTCCTAATTTGCCAAT 59.224 39.130 0.00 0.00 0.00 3.16
222 235 3.172339 AGCCATGTTCCTAATTTGCCAA 58.828 40.909 0.00 0.00 0.00 4.52
224 237 3.893326 AAGCCATGTTCCTAATTTGCC 57.107 42.857 0.00 0.00 0.00 4.52
226 239 6.147656 GGAAACAAAGCCATGTTCCTAATTTG 59.852 38.462 5.30 0.00 42.49 2.32
230 243 4.219115 TGGAAACAAAGCCATGTTCCTAA 58.781 39.130 9.60 0.00 42.49 2.69
253 266 0.394352 GATCAGATGGCCAAACCCGT 60.394 55.000 10.96 0.00 37.83 5.28
255 268 0.259938 AGGATCAGATGGCCAAACCC 59.740 55.000 10.96 5.66 37.83 4.11
256 269 2.173569 ACTAGGATCAGATGGCCAAACC 59.826 50.000 10.96 0.29 39.84 3.27
290 303 9.386010 CCAATCATTAATCCAATGTGACATTTT 57.614 29.630 8.30 3.61 43.88 1.82
312 325 3.571401 CCTCACTTGCAAAAGACTCCAAT 59.429 43.478 0.00 0.00 0.00 3.16
319 332 1.774254 TCCTCCCTCACTTGCAAAAGA 59.226 47.619 0.00 0.08 0.00 2.52
320 333 1.882623 GTCCTCCCTCACTTGCAAAAG 59.117 52.381 0.00 0.00 0.00 2.27
328 341 0.398318 GCTTTGTGTCCTCCCTCACT 59.602 55.000 0.00 0.00 35.82 3.41
333 346 0.322008 CTCCAGCTTTGTGTCCTCCC 60.322 60.000 0.00 0.00 0.00 4.30
346 359 3.569250 GAGCATAGTAGTAGCTCCAGC 57.431 52.381 13.73 0.00 46.82 4.85
357 370 2.501316 TCCAGCAGCTTTGAGCATAGTA 59.499 45.455 0.00 0.00 45.56 1.82
360 373 2.686405 CAATCCAGCAGCTTTGAGCATA 59.314 45.455 0.00 0.00 45.56 3.14
365 378 2.430465 GACTCAATCCAGCAGCTTTGA 58.570 47.619 7.62 7.62 0.00 2.69
369 382 0.108424 GTCGACTCAATCCAGCAGCT 60.108 55.000 8.70 0.00 0.00 4.24
370 383 0.390340 TGTCGACTCAATCCAGCAGC 60.390 55.000 17.92 0.00 0.00 5.25
376 389 4.942852 AGATCTCATTGTCGACTCAATCC 58.057 43.478 17.92 0.00 36.10 3.01
380 393 5.391312 TGAAAGATCTCATTGTCGACTCA 57.609 39.130 17.92 4.39 0.00 3.41
385 398 5.322310 CAAGCTTGAAAGATCTCATTGTCG 58.678 41.667 22.31 0.00 0.00 4.35
387 400 5.319453 TCCAAGCTTGAAAGATCTCATTGT 58.681 37.500 28.05 0.00 0.00 2.71
390 403 4.525024 CCTCCAAGCTTGAAAGATCTCAT 58.475 43.478 28.05 0.00 0.00 2.90
401 414 2.036256 CCACCCCCTCCAAGCTTG 59.964 66.667 19.93 19.93 0.00 4.01
405 418 3.268032 AAGCCCACCCCCTCCAAG 61.268 66.667 0.00 0.00 0.00 3.61
406 419 3.264845 GAAGCCCACCCCCTCCAA 61.265 66.667 0.00 0.00 0.00 3.53
409 422 3.732849 CAGGAAGCCCACCCCCTC 61.733 72.222 0.00 0.00 33.88 4.30
431 444 3.749665 TCAAACATTTTCCAGCCTTGG 57.250 42.857 0.00 0.00 46.49 3.61
437 450 4.023279 TGACCACGATCAAACATTTTCCAG 60.023 41.667 0.00 0.00 0.00 3.86
442 455 4.133820 TGACTGACCACGATCAAACATTT 58.866 39.130 0.00 0.00 0.00 2.32
443 456 3.738982 TGACTGACCACGATCAAACATT 58.261 40.909 0.00 0.00 0.00 2.71
445 458 2.900716 TGACTGACCACGATCAAACA 57.099 45.000 0.00 0.00 0.00 2.83
446 459 3.390135 TCTTGACTGACCACGATCAAAC 58.610 45.455 0.00 0.00 31.00 2.93
450 463 2.166459 TCCATCTTGACTGACCACGATC 59.834 50.000 0.00 0.00 0.00 3.69
473 486 0.179023 TAACACCGCCCTTCCGTTTT 60.179 50.000 0.00 0.00 0.00 2.43
474 487 0.604511 CTAACACCGCCCTTCCGTTT 60.605 55.000 0.00 0.00 0.00 3.60
475 488 1.004200 CTAACACCGCCCTTCCGTT 60.004 57.895 0.00 0.00 0.00 4.44
477 490 1.004200 AACTAACACCGCCCTTCCG 60.004 57.895 0.00 0.00 0.00 4.30
478 491 0.035739 TCAACTAACACCGCCCTTCC 59.964 55.000 0.00 0.00 0.00 3.46
482 495 1.199097 CACAATCAACTAACACCGCCC 59.801 52.381 0.00 0.00 0.00 6.13
483 496 1.401018 GCACAATCAACTAACACCGCC 60.401 52.381 0.00 0.00 0.00 6.13
485 513 2.095768 CCAGCACAATCAACTAACACCG 60.096 50.000 0.00 0.00 0.00 4.94
492 520 4.074970 CCTAGTTTCCAGCACAATCAACT 58.925 43.478 0.00 0.00 0.00 3.16
499 527 1.136828 ACCACCTAGTTTCCAGCACA 58.863 50.000 0.00 0.00 0.00 4.57
503 531 5.422214 ACTGATAACCACCTAGTTTCCAG 57.578 43.478 0.00 0.00 35.68 3.86
507 535 7.017319 AGCTAAACTGATAACCACCTAGTTT 57.983 36.000 0.00 0.00 42.34 2.66
509 537 6.622427 AAGCTAAACTGATAACCACCTAGT 57.378 37.500 0.00 0.00 0.00 2.57
522 551 8.089115 AGCTAAAACTCACTTAAGCTAAACTG 57.911 34.615 1.29 0.00 0.00 3.16
527 556 6.231211 AGCAAGCTAAAACTCACTTAAGCTA 58.769 36.000 1.29 0.00 0.00 3.32
530 559 6.374578 GGAAGCAAGCTAAAACTCACTTAAG 58.625 40.000 0.00 0.00 0.00 1.85
533 562 3.570125 GGGAAGCAAGCTAAAACTCACTT 59.430 43.478 0.00 0.00 0.00 3.16
534 563 3.149981 GGGAAGCAAGCTAAAACTCACT 58.850 45.455 0.00 0.00 0.00 3.41
536 565 2.514803 GGGGAAGCAAGCTAAAACTCA 58.485 47.619 0.00 0.00 0.00 3.41
542 571 1.282157 GAAGAGGGGGAAGCAAGCTAA 59.718 52.381 0.00 0.00 0.00 3.09
549 578 0.402121 ACAAGTGAAGAGGGGGAAGC 59.598 55.000 0.00 0.00 0.00 3.86
553 582 3.118223 GGAGAATACAAGTGAAGAGGGGG 60.118 52.174 0.00 0.00 0.00 5.40
554 583 3.430929 CGGAGAATACAAGTGAAGAGGGG 60.431 52.174 0.00 0.00 0.00 4.79
555 584 3.430929 CCGGAGAATACAAGTGAAGAGGG 60.431 52.174 0.00 0.00 0.00 4.30
559 588 5.011090 TCATCCGGAGAATACAAGTGAAG 57.989 43.478 11.34 0.00 0.00 3.02
573 602 1.075970 CTCACCCCTCTCATCCGGA 60.076 63.158 6.61 6.61 0.00 5.14
574 603 1.381872 ACTCACCCCTCTCATCCGG 60.382 63.158 0.00 0.00 0.00 5.14
578 607 1.004044 CAAAGCACTCACCCCTCTCAT 59.996 52.381 0.00 0.00 0.00 2.90
580 609 0.398318 ACAAAGCACTCACCCCTCTC 59.602 55.000 0.00 0.00 0.00 3.20
596 632 2.814336 GCAACAACAACCCCAAAAACAA 59.186 40.909 0.00 0.00 0.00 2.83
597 633 2.427506 GCAACAACAACCCCAAAAACA 58.572 42.857 0.00 0.00 0.00 2.83
598 634 1.740585 GGCAACAACAACCCCAAAAAC 59.259 47.619 0.00 0.00 0.00 2.43
599 635 1.630878 AGGCAACAACAACCCCAAAAA 59.369 42.857 0.00 0.00 41.41 1.94
603 641 1.826054 CGAGGCAACAACAACCCCA 60.826 57.895 0.00 0.00 41.41 4.96
623 661 1.109323 AAACACCACCTCAGGCAAGC 61.109 55.000 0.00 0.00 0.00 4.01
627 665 0.883833 CATCAAACACCACCTCAGGC 59.116 55.000 0.00 0.00 0.00 4.85
628 666 1.881973 CACATCAAACACCACCTCAGG 59.118 52.381 0.00 0.00 0.00 3.86
631 669 4.111916 CAAAACACATCAAACACCACCTC 58.888 43.478 0.00 0.00 0.00 3.85
632 670 3.118811 CCAAAACACATCAAACACCACCT 60.119 43.478 0.00 0.00 0.00 4.00
633 671 3.194062 CCAAAACACATCAAACACCACC 58.806 45.455 0.00 0.00 0.00 4.61
634 672 3.855858 ACCAAAACACATCAAACACCAC 58.144 40.909 0.00 0.00 0.00 4.16
635 673 4.248859 CAACCAAAACACATCAAACACCA 58.751 39.130 0.00 0.00 0.00 4.17
636 674 4.249661 ACAACCAAAACACATCAAACACC 58.750 39.130 0.00 0.00 0.00 4.16
637 675 6.533367 ACATACAACCAAAACACATCAAACAC 59.467 34.615 0.00 0.00 0.00 3.32
638 676 6.634805 ACATACAACCAAAACACATCAAACA 58.365 32.000 0.00 0.00 0.00 2.83
639 677 6.754209 TGACATACAACCAAAACACATCAAAC 59.246 34.615 0.00 0.00 0.00 2.93
640 678 6.867550 TGACATACAACCAAAACACATCAAA 58.132 32.000 0.00 0.00 0.00 2.69
641 679 6.456795 TGACATACAACCAAAACACATCAA 57.543 33.333 0.00 0.00 0.00 2.57
642 680 5.009510 CCTGACATACAACCAAAACACATCA 59.990 40.000 0.00 0.00 0.00 3.07
643 681 5.240623 TCCTGACATACAACCAAAACACATC 59.759 40.000 0.00 0.00 0.00 3.06
644 682 5.009610 GTCCTGACATACAACCAAAACACAT 59.990 40.000 0.00 0.00 0.00 3.21
645 683 4.336993 GTCCTGACATACAACCAAAACACA 59.663 41.667 0.00 0.00 0.00 3.72
646 684 4.578928 AGTCCTGACATACAACCAAAACAC 59.421 41.667 0.00 0.00 0.00 3.32
647 685 4.787551 AGTCCTGACATACAACCAAAACA 58.212 39.130 0.00 0.00 0.00 2.83
648 686 5.995897 AGTAGTCCTGACATACAACCAAAAC 59.004 40.000 0.00 0.00 0.00 2.43
649 687 6.182507 AGTAGTCCTGACATACAACCAAAA 57.817 37.500 0.00 0.00 0.00 2.44
650 688 5.818678 AGTAGTCCTGACATACAACCAAA 57.181 39.130 0.00 0.00 0.00 3.28
651 689 5.512404 CCAAGTAGTCCTGACATACAACCAA 60.512 44.000 0.00 0.00 0.00 3.67
652 690 4.020573 CCAAGTAGTCCTGACATACAACCA 60.021 45.833 0.00 0.00 0.00 3.67
653 691 4.020485 ACCAAGTAGTCCTGACATACAACC 60.020 45.833 0.00 0.00 0.00 3.77
654 692 5.148651 ACCAAGTAGTCCTGACATACAAC 57.851 43.478 0.00 0.00 0.00 3.32
655 693 5.818678 AACCAAGTAGTCCTGACATACAA 57.181 39.130 0.00 0.00 0.00 2.41
656 694 5.279809 GGAAACCAAGTAGTCCTGACATACA 60.280 44.000 0.00 0.00 0.00 2.29
657 695 5.046520 AGGAAACCAAGTAGTCCTGACATAC 60.047 44.000 0.00 0.51 39.09 2.39
658 696 5.091552 AGGAAACCAAGTAGTCCTGACATA 58.908 41.667 0.00 0.00 39.09 2.29
659 697 3.910627 AGGAAACCAAGTAGTCCTGACAT 59.089 43.478 0.00 0.00 39.09 3.06
660 698 3.314693 AGGAAACCAAGTAGTCCTGACA 58.685 45.455 0.00 0.00 39.09 3.58
661 699 4.353383 AAGGAAACCAAGTAGTCCTGAC 57.647 45.455 0.00 0.00 39.65 3.51
662 700 6.271391 TCATTAAGGAAACCAAGTAGTCCTGA 59.729 38.462 0.00 0.00 39.65 3.86
663 701 6.472887 TCATTAAGGAAACCAAGTAGTCCTG 58.527 40.000 0.00 0.00 39.65 3.86
664 702 6.697641 TCATTAAGGAAACCAAGTAGTCCT 57.302 37.500 0.00 0.00 42.45 3.85
665 703 7.754851 TTTCATTAAGGAAACCAAGTAGTCC 57.245 36.000 11.06 0.00 32.12 3.85
666 704 9.010029 TGATTTCATTAAGGAAACCAAGTAGTC 57.990 33.333 16.79 8.99 39.40 2.59
667 705 8.934023 TGATTTCATTAAGGAAACCAAGTAGT 57.066 30.769 16.79 0.00 39.40 2.73
668 706 8.462016 CCTGATTTCATTAAGGAAACCAAGTAG 58.538 37.037 16.79 2.70 39.40 2.57
669 707 8.167392 TCCTGATTTCATTAAGGAAACCAAGTA 58.833 33.333 16.79 0.29 39.40 2.24
670 708 7.010160 TCCTGATTTCATTAAGGAAACCAAGT 58.990 34.615 16.79 1.62 39.40 3.16
671 709 7.466746 TCCTGATTTCATTAAGGAAACCAAG 57.533 36.000 16.79 8.19 39.40 3.61
672 710 7.847711 TTCCTGATTTCATTAAGGAAACCAA 57.152 32.000 16.79 5.68 43.99 3.67
677 715 8.971073 GGATCTTTTCCTGATTTCATTAAGGAA 58.029 33.333 0.00 0.00 44.99 3.36
678 716 7.561356 GGGATCTTTTCCTGATTTCATTAAGGA 59.439 37.037 0.00 0.00 44.75 3.36
679 717 7.562821 AGGGATCTTTTCCTGATTTCATTAAGG 59.437 37.037 0.00 0.00 44.75 2.69
680 718 8.530804 AGGGATCTTTTCCTGATTTCATTAAG 57.469 34.615 0.00 0.00 44.75 1.85
681 719 8.899887 AAGGGATCTTTTCCTGATTTCATTAA 57.100 30.769 0.00 0.00 44.75 1.40
682 720 8.899887 AAAGGGATCTTTTCCTGATTTCATTA 57.100 30.769 0.00 0.00 44.75 1.90
683 721 7.677319 AGAAAGGGATCTTTTCCTGATTTCATT 59.323 33.333 15.16 0.00 44.75 2.57
684 722 7.187676 AGAAAGGGATCTTTTCCTGATTTCAT 58.812 34.615 15.16 0.00 44.75 2.57
685 723 6.555711 AGAAAGGGATCTTTTCCTGATTTCA 58.444 36.000 15.16 0.00 44.75 2.69
686 724 7.473735 AAGAAAGGGATCTTTTCCTGATTTC 57.526 36.000 15.16 5.55 44.75 2.17
687 725 7.510343 TGAAAGAAAGGGATCTTTTCCTGATTT 59.490 33.333 15.16 10.98 46.77 2.17
688 726 7.012607 TGAAAGAAAGGGATCTTTTCCTGATT 58.987 34.615 15.16 8.82 46.77 2.57
689 727 6.555711 TGAAAGAAAGGGATCTTTTCCTGAT 58.444 36.000 15.16 0.00 46.77 2.90
690 728 5.952387 TGAAAGAAAGGGATCTTTTCCTGA 58.048 37.500 15.16 1.36 46.77 3.86
691 729 6.655078 TTGAAAGAAAGGGATCTTTTCCTG 57.345 37.500 15.16 0.00 46.77 3.86
692 730 7.675161 TTTTGAAAGAAAGGGATCTTTTCCT 57.325 32.000 15.16 1.91 46.77 3.36
716 754 6.894339 ATCTCCGGGCGATTTAATATTTTT 57.106 33.333 0.00 0.00 0.00 1.94
720 758 6.894339 AAAAATCTCCGGGCGATTTAATAT 57.106 33.333 21.65 6.93 39.46 1.28
760 799 1.611006 CCATCGGATCAGATCTCACGT 59.389 52.381 10.36 0.00 0.00 4.49
860 909 9.716507 TCTTGAAAAATAAAAACTCTCGAAGTG 57.283 29.630 1.80 0.00 38.58 3.16
1021 1077 4.021544 ACGACATCTTGCTCTTCTTCTTCT 60.022 41.667 0.00 0.00 0.00 2.85
1159 1218 1.310904 TTTCGTAAAAGGTGCCGCTT 58.689 45.000 0.00 0.00 0.00 4.68
1211 1270 2.124403 GACGGTAGCGGGGAGAGA 60.124 66.667 19.72 0.00 0.00 3.10
1697 2014 6.128007 CCACATACCGCTTAAAAGTCAAAGAT 60.128 38.462 0.00 0.00 0.00 2.40
1733 2050 3.930229 CCGTAATGCACAGCACTAACTAA 59.070 43.478 0.00 0.00 43.04 2.24
1776 2093 5.199723 TGCTCATTGGGCATAAACTAATGA 58.800 37.500 7.23 0.00 36.60 2.57
1926 2257 9.607333 ACAATATCATGTAGGATTCTAGGAAGA 57.393 33.333 0.00 0.00 0.00 2.87
1927 2258 9.650539 CACAATATCATGTAGGATTCTAGGAAG 57.349 37.037 0.00 0.00 30.84 3.46
1968 2300 7.013823 AGTAGCATATAGATTGCATGGACTT 57.986 36.000 0.00 0.00 42.62 3.01
1970 2302 7.551585 ACTAGTAGCATATAGATTGCATGGAC 58.448 38.462 0.00 0.00 42.62 4.02
2089 2521 7.948137 TGTTAAATTAAAGTCATTTGCGATGC 58.052 30.769 0.00 0.00 0.00 3.91
2197 2630 5.163591 CCTCAATATTTGCTGCTCACATCAA 60.164 40.000 0.00 0.00 30.33 2.57
2321 2766 8.854979 TTTCGAATGTAAATCTGCAATATTGG 57.145 30.769 17.02 1.65 0.00 3.16
2394 2839 9.935682 ATAGTCGACATTAAACATTTATTGCAG 57.064 29.630 19.50 2.64 30.91 4.41
2499 2968 7.370383 CCCCATACAAAACAGTATCAATATGC 58.630 38.462 0.00 0.00 32.56 3.14
2560 3029 5.224888 CAATCAAAATCCACAACAGGTCAG 58.775 41.667 0.00 0.00 0.00 3.51
2567 3036 3.328505 CCCTGCAATCAAAATCCACAAC 58.671 45.455 0.00 0.00 0.00 3.32
2939 3422 5.282055 TGCATGTTTTTATTCACCACCAA 57.718 34.783 0.00 0.00 0.00 3.67
3058 3541 6.806739 GCAGACAAACCACATTAATTTCTACC 59.193 38.462 0.00 0.00 0.00 3.18
3060 3543 7.759489 AGCAGACAAACCACATTAATTTCTA 57.241 32.000 0.00 0.00 0.00 2.10
3061 3544 6.655078 AGCAGACAAACCACATTAATTTCT 57.345 33.333 0.00 0.00 0.00 2.52
3062 3545 7.713764 AAAGCAGACAAACCACATTAATTTC 57.286 32.000 0.00 0.00 0.00 2.17
3087 3570 5.123820 GTGGCTTCAACAAATGTATAGCAGA 59.876 40.000 13.11 1.67 33.65 4.26
3094 3577 6.238320 GCAAATTTGTGGCTTCAACAAATGTA 60.238 34.615 19.03 0.00 41.47 2.29
3115 3599 7.838079 ATTGGTAGCCTATATGAATTGCAAA 57.162 32.000 1.71 0.00 0.00 3.68
3181 3666 7.709182 TGAACAGACGAAAGAGTATGAGAAAAA 59.291 33.333 0.00 0.00 36.87 1.94
3191 3676 3.802948 ACAGTGAACAGACGAAAGAGT 57.197 42.857 0.00 0.00 0.00 3.24
3223 3758 4.421058 CGACAATTATGAACAGACGGAGA 58.579 43.478 0.00 0.00 0.00 3.71
3228 3763 5.725110 ATCAGCGACAATTATGAACAGAC 57.275 39.130 0.00 0.00 0.00 3.51
3231 3766 7.609760 ACTAAATCAGCGACAATTATGAACA 57.390 32.000 0.00 0.00 0.00 3.18
3302 3868 9.044150 ACAACTTTGTACTAAACTAAATGCGTA 57.956 29.630 0.00 0.00 40.16 4.42
3311 3877 8.747538 ATTCCTTCACAACTTTGTACTAAACT 57.252 30.769 0.00 0.00 39.91 2.66
3363 3929 9.976255 GTGAACAAAATACACTAAATGCGTATA 57.024 29.630 0.00 0.00 0.00 1.47
3364 3930 8.726988 AGTGAACAAAATACACTAAATGCGTAT 58.273 29.630 0.00 0.00 42.01 3.06
3365 3931 8.090250 AGTGAACAAAATACACTAAATGCGTA 57.910 30.769 0.00 0.00 42.01 4.42
3366 3932 6.966021 AGTGAACAAAATACACTAAATGCGT 58.034 32.000 0.00 0.00 42.01 5.24
3367 3933 7.075121 TGAGTGAACAAAATACACTAAATGCG 58.925 34.615 0.00 0.00 43.49 4.73
3368 3934 8.970691 ATGAGTGAACAAAATACACTAAATGC 57.029 30.769 0.00 0.00 43.49 3.56
3373 3939 9.337396 ACTGAAATGAGTGAACAAAATACACTA 57.663 29.630 0.00 0.00 43.49 2.74
3374 3940 8.225603 ACTGAAATGAGTGAACAAAATACACT 57.774 30.769 0.00 0.00 45.62 3.55
3375 3941 7.591426 GGACTGAAATGAGTGAACAAAATACAC 59.409 37.037 0.00 0.00 35.15 2.90
3376 3942 7.519809 CGGACTGAAATGAGTGAACAAAATACA 60.520 37.037 0.00 0.00 0.00 2.29
3377 3943 6.797033 CGGACTGAAATGAGTGAACAAAATAC 59.203 38.462 0.00 0.00 0.00 1.89
3378 3944 6.485313 ACGGACTGAAATGAGTGAACAAAATA 59.515 34.615 0.00 0.00 0.00 1.40
3379 3945 5.299279 ACGGACTGAAATGAGTGAACAAAAT 59.701 36.000 0.00 0.00 0.00 1.82
3380 3946 4.638421 ACGGACTGAAATGAGTGAACAAAA 59.362 37.500 0.00 0.00 0.00 2.44
3381 3947 4.196193 ACGGACTGAAATGAGTGAACAAA 58.804 39.130 0.00 0.00 0.00 2.83
3382 3948 3.804036 ACGGACTGAAATGAGTGAACAA 58.196 40.909 0.00 0.00 0.00 2.83
3383 3949 3.469008 ACGGACTGAAATGAGTGAACA 57.531 42.857 0.00 0.00 0.00 3.18
3384 3950 4.929808 ACATACGGACTGAAATGAGTGAAC 59.070 41.667 7.93 0.00 0.00 3.18
3385 3951 5.147330 ACATACGGACTGAAATGAGTGAA 57.853 39.130 7.93 0.00 0.00 3.18
3386 3952 4.801330 ACATACGGACTGAAATGAGTGA 57.199 40.909 7.93 0.00 0.00 3.41
3387 3953 5.651530 ACTACATACGGACTGAAATGAGTG 58.348 41.667 7.93 0.00 0.00 3.51
3388 3954 5.652891 AGACTACATACGGACTGAAATGAGT 59.347 40.000 7.93 7.04 0.00 3.41
3389 3955 6.137794 AGACTACATACGGACTGAAATGAG 57.862 41.667 7.93 4.83 0.00 2.90
3390 3956 7.818997 ATAGACTACATACGGACTGAAATGA 57.181 36.000 7.93 0.00 0.00 2.57
3393 3959 9.346005 TCAATATAGACTACATACGGACTGAAA 57.654 33.333 0.00 0.00 0.00 2.69
3394 3960 8.913487 TCAATATAGACTACATACGGACTGAA 57.087 34.615 0.00 0.00 0.00 3.02
3395 3961 8.913487 TTCAATATAGACTACATACGGACTGA 57.087 34.615 0.00 0.00 0.00 3.41
3441 4007 8.654485 TTAGAATGTACTCCCACTGTTAACTA 57.346 34.615 7.22 0.00 0.00 2.24
3445 4011 6.877322 GCTTTTAGAATGTACTCCCACTGTTA 59.123 38.462 0.00 0.00 0.00 2.41
3529 4098 5.881443 TGTCATGATTCACATATGAGTTGCA 59.119 36.000 10.38 2.46 37.46 4.08
3531 4100 6.260271 AGCTGTCATGATTCACATATGAGTTG 59.740 38.462 10.38 0.00 37.46 3.16
3584 4153 4.278669 GCGATCCTGTTCTCCTCAGTTATA 59.721 45.833 0.00 0.00 0.00 0.98
3585 4154 3.068873 GCGATCCTGTTCTCCTCAGTTAT 59.931 47.826 0.00 0.00 0.00 1.89
3623 4192 7.171508 CAGTGTGTGTGTACTTGATGATTTACT 59.828 37.037 0.00 0.00 0.00 2.24
3646 4215 1.143684 AGACAGCACATTGAACCCAGT 59.856 47.619 0.00 0.00 0.00 4.00
3647 4216 1.538512 CAGACAGCACATTGAACCCAG 59.461 52.381 0.00 0.00 0.00 4.45
3648 4217 1.133823 ACAGACAGCACATTGAACCCA 60.134 47.619 0.00 0.00 0.00 4.51
3649 4218 1.537202 GACAGACAGCACATTGAACCC 59.463 52.381 0.00 0.00 0.00 4.11
3650 4219 2.481952 GAGACAGACAGCACATTGAACC 59.518 50.000 0.00 0.00 0.00 3.62
3682 4251 5.650266 TGTTGTATTTCAAACAGTGGACACT 59.350 36.000 0.00 0.00 38.89 3.55
3683 4252 5.741982 GTGTTGTATTTCAAACAGTGGACAC 59.258 40.000 0.00 0.00 37.81 3.67
3684 4253 5.416013 TGTGTTGTATTTCAAACAGTGGACA 59.584 36.000 0.00 0.00 37.81 4.02
3685 4254 5.885881 TGTGTTGTATTTCAAACAGTGGAC 58.114 37.500 0.00 0.00 37.81 4.02
3700 4277 6.119536 AGAACAAAACCTCTCATGTGTTGTA 58.880 36.000 0.00 0.00 42.00 2.41
3739 4318 8.988934 TGTGTTTCAAACAATAGACAGATAGTC 58.011 33.333 4.02 0.00 44.72 2.59
3750 4330 7.766283 TCATCTGTGTTGTGTTTCAAACAATA 58.234 30.769 4.02 0.00 44.16 1.90
3752 4332 6.018589 TCATCTGTGTTGTGTTTCAAACAA 57.981 33.333 4.02 0.00 44.16 2.83
3756 4336 4.522114 TCCTCATCTGTGTTGTGTTTCAA 58.478 39.130 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.