Multiple sequence alignment - TraesCS1D01G341200

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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 TraesCS1D01G341200 chr1D 100.000 3333 0 0 1 3333 431424950 431428282 0.000000e+00 6156.0
1 TraesCS1D01G341200 chr1D 81.159 138 24 2 2125 2261 357214920 357215056 3.520000e-20 110.0
2 TraesCS1D01G341200 chr1D 86.207 87 10 1 2849 2933 431427649 431427735 3.540000e-15 93.5
3 TraesCS1D01G341200 chr1D 86.207 87 10 1 2700 2786 431427798 431427882 3.540000e-15 93.5
4 TraesCS1D01G341200 chr1A 90.325 2646 146 39 745 3333 529664008 529666600 0.000000e+00 3367.0
5 TraesCS1D01G341200 chr1A 81.159 138 24 2 2125 2261 458396824 458396960 3.520000e-20 110.0
6 TraesCS1D01G341200 chr1A 85.057 87 11 1 2700 2786 529666117 529666201 1.650000e-13 87.9
7 TraesCS1D01G341200 chr1B 92.935 2010 77 25 1335 3333 582544219 582546174 0.000000e+00 2865.0
8 TraesCS1D01G341200 chr1B 81.030 738 61 31 573 1255 582543462 582544175 6.380000e-142 514.0
9 TraesCS1D01G341200 chr1B 84.310 529 37 21 5 515 582542953 582543453 3.010000e-130 475.0
10 TraesCS1D01G341200 chr1B 88.312 231 27 0 1596 1826 79410285 79410515 9.110000e-71 278.0
11 TraesCS1D01G341200 chr1B 85.057 87 11 1 2849 2933 582545555 582545641 1.650000e-13 87.9
12 TraesCS1D01G341200 chr1B 85.057 87 11 1 2700 2786 582545704 582545788 1.650000e-13 87.9
13 TraesCS1D01G341200 chr3A 78.493 730 138 18 1603 2324 511754583 511753865 8.430000e-126 460.0
14 TraesCS1D01G341200 chr3A 85.957 235 29 4 1613 1845 502166738 502166506 7.140000e-62 248.0
15 TraesCS1D01G341200 chr3A 86.111 216 25 4 2119 2333 502166034 502165823 9.300000e-56 228.0
16 TraesCS1D01G341200 chr3A 90.588 170 16 0 1083 1252 502167839 502167670 3.350000e-55 226.0
17 TraesCS1D01G341200 chr3A 85.849 212 26 4 1042 1251 511755640 511755431 4.330000e-54 222.0
18 TraesCS1D01G341200 chr3A 87.407 135 13 4 1371 1503 511754805 511754673 5.760000e-33 152.0
19 TraesCS1D01G341200 chr3A 88.095 126 13 2 2125 2249 56591877 56592001 7.450000e-32 148.0
20 TraesCS1D01G341200 chr3A 95.556 45 2 0 388 432 726761628 726761672 4.610000e-09 73.1
21 TraesCS1D01G341200 chr3B 78.818 694 127 18 1603 2288 508709728 508709047 1.820000e-122 449.0
22 TraesCS1D01G341200 chr3B 85.306 245 32 4 1603 1845 492612081 492611839 1.990000e-62 250.0
23 TraesCS1D01G341200 chr3B 90.751 173 16 0 1083 1255 492613153 492612981 7.190000e-57 231.0
24 TraesCS1D01G341200 chr3B 83.539 243 30 9 1015 1251 508710833 508710595 5.600000e-53 219.0
25 TraesCS1D01G341200 chr3B 85.507 207 27 3 2128 2333 492611388 492611184 2.600000e-51 213.0
26 TraesCS1D01G341200 chr3B 85.926 135 15 4 1371 1503 508709937 508709805 1.250000e-29 141.0
27 TraesCS1D01G341200 chr3B 81.560 141 20 4 1106 1240 69643979 69644119 9.770000e-21 111.0
28 TraesCS1D01G341200 chr3B 95.556 45 2 0 388 432 677777929 677777885 4.610000e-09 73.1
29 TraesCS1D01G341200 chr3D 78.644 693 130 17 1603 2288 391599271 391598590 8.490000e-121 444.0
30 TraesCS1D01G341200 chr3D 84.836 244 33 4 1604 1845 378035117 378034876 3.320000e-60 243.0
31 TraesCS1D01G341200 chr3D 91.176 170 15 0 1083 1252 378036169 378036000 7.190000e-57 231.0
32 TraesCS1D01G341200 chr3D 86.111 216 25 4 2119 2333 378032922 378032711 9.300000e-56 228.0
33 TraesCS1D01G341200 chr3D 89.349 169 18 0 1083 1251 391600440 391600272 2.600000e-51 213.0
34 TraesCS1D01G341200 chr3D 85.816 141 16 4 1371 1509 391599473 391599335 2.680000e-31 147.0
35 TraesCS1D01G341200 chr3D 93.750 48 3 0 385 432 98597798 98597751 4.610000e-09 73.1
36 TraesCS1D01G341200 chr5B 83.575 207 23 8 3136 3333 106150001 106149797 2.040000e-42 183.0
37 TraesCS1D01G341200 chr7B 95.833 48 2 0 385 432 43705703 43705750 9.910000e-11 78.7
38 TraesCS1D01G341200 chr4A 97.727 44 1 0 389 432 4599738 4599695 3.570000e-10 76.8
39 TraesCS1D01G341200 chr4A 95.833 48 1 1 386 432 701953662 701953709 3.570000e-10 76.8
40 TraesCS1D01G341200 chr4B 95.652 46 2 0 387 432 559266360 559266405 1.280000e-09 75.0
41 TraesCS1D01G341200 chr6B 95.556 45 2 0 388 432 678542359 678542315 4.610000e-09 73.1
42 TraesCS1D01G341200 chr2A 92.157 51 2 2 384 432 180995547 180995597 1.660000e-08 71.3


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 TraesCS1D01G341200 chr1D 431424950 431428282 3332 False 2114.333333 6156 90.804667 1 3333 3 chr1D.!!$F2 3332
1 TraesCS1D01G341200 chr1A 529664008 529666600 2592 False 1727.450000 3367 87.691000 745 3333 2 chr1A.!!$F2 2588
2 TraesCS1D01G341200 chr1B 582542953 582546174 3221 False 805.960000 2865 85.677800 5 3333 5 chr1B.!!$F2 3328
3 TraesCS1D01G341200 chr3A 511753865 511755640 1775 True 278.000000 460 83.916333 1042 2324 3 chr3A.!!$R2 1282
4 TraesCS1D01G341200 chr3A 502165823 502167839 2016 True 234.000000 248 87.552000 1083 2333 3 chr3A.!!$R1 1250
5 TraesCS1D01G341200 chr3B 508709047 508710833 1786 True 269.666667 449 82.761000 1015 2288 3 chr3B.!!$R3 1273
6 TraesCS1D01G341200 chr3B 492611184 492613153 1969 True 231.333333 250 87.188000 1083 2333 3 chr3B.!!$R2 1250
7 TraesCS1D01G341200 chr3D 391598590 391600440 1850 True 268.000000 444 84.603000 1083 2288 3 chr3D.!!$R3 1205
8 TraesCS1D01G341200 chr3D 378032711 378036169 3458 True 234.000000 243 87.374333 1083 2333 3 chr3D.!!$R2 1250

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
364 377 0.164217 GCGGTCGATCGACTAGCTAG 59.836 60.0 37.11 26.37 44.04 3.42 F
578 598 0.179124 GCATCTCTCCAGTCACCGTC 60.179 60.0 0.00 0.00 0.00 4.79 F
1301 1717 0.376852 GCAAAATGCATGCATGGCAG 59.623 50.0 32.79 22.25 45.68 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 2674 0.390340 ACAGAGCGCATGGTGTACAG 60.390 55.0 11.47 0.00 0.0 2.74 R
1530 2678 1.014044 CGTAACAGAGCGCATGGTGT 61.014 55.0 11.47 3.92 0.0 4.16 R
2647 5563 0.033920 GCCCCAAGCTTTTCCTTGTG 59.966 55.0 0.00 0.00 40.4 3.33 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
36 37 1.881252 GGCGACGCCGTTCATATGT 60.881 57.895 25.24 0.00 39.62 2.29
37 38 1.272715 GCGACGCCGTTCATATGTG 59.727 57.895 9.14 0.00 38.24 3.21
40 41 1.515631 CGACGCCGTTCATATGTGTAC 59.484 52.381 1.90 0.00 0.00 2.90
55 56 1.396996 GTGTACGCATGTGGAATGTCC 59.603 52.381 11.65 0.00 36.96 4.02
56 57 0.650512 GTACGCATGTGGAATGTCCG 59.349 55.000 11.65 0.00 40.17 4.79
63 65 4.015406 TGGAATGTCCGGCGTGCT 62.015 61.111 6.01 0.00 40.17 4.40
64 66 3.195698 GGAATGTCCGGCGTGCTC 61.196 66.667 6.01 0.00 0.00 4.26
91 93 5.363292 TGGGTTATTGGATGTTGATGATTGG 59.637 40.000 0.00 0.00 0.00 3.16
166 175 1.152525 AGTCTGTCTGGTGTCCGGT 60.153 57.895 0.00 0.00 0.00 5.28
220 233 1.595993 ATGATCGGACGGGGCGATAG 61.596 60.000 0.00 0.00 0.00 2.08
307 320 1.884235 ACTGGAGTACAAACAGCAGC 58.116 50.000 10.27 0.00 35.70 5.25
308 321 1.140852 ACTGGAGTACAAACAGCAGCA 59.859 47.619 10.27 0.00 35.70 4.41
309 322 1.802960 CTGGAGTACAAACAGCAGCAG 59.197 52.381 0.00 0.00 0.00 4.24
310 323 0.519077 GGAGTACAAACAGCAGCAGC 59.481 55.000 0.00 0.00 42.56 5.25
311 324 1.229428 GAGTACAAACAGCAGCAGCA 58.771 50.000 3.17 0.00 45.49 4.41
312 325 0.947244 AGTACAAACAGCAGCAGCAC 59.053 50.000 3.17 0.00 45.49 4.40
313 326 0.947244 GTACAAACAGCAGCAGCACT 59.053 50.000 3.17 0.00 45.49 4.40
314 327 1.069636 GTACAAACAGCAGCAGCACTC 60.070 52.381 3.17 0.00 45.49 3.51
315 328 1.285023 CAAACAGCAGCAGCACTCC 59.715 57.895 3.17 0.00 45.49 3.85
316 329 1.152902 AAACAGCAGCAGCACTCCA 60.153 52.632 3.17 0.00 45.49 3.86
317 330 1.170919 AAACAGCAGCAGCACTCCAG 61.171 55.000 3.17 0.00 45.49 3.86
318 331 2.032223 CAGCAGCAGCACTCCAGT 59.968 61.111 3.17 0.00 45.49 4.00
319 332 1.294459 CAGCAGCAGCACTCCAGTA 59.706 57.895 3.17 0.00 45.49 2.74
338 351 4.642885 CAGTAAGCAGTAACTAGCTCCTCT 59.357 45.833 0.00 0.00 40.90 3.69
355 368 1.874019 CTGTTGAGGCGGTCGATCG 60.874 63.158 15.15 15.15 0.00 3.69
361 374 2.051166 GGCGGTCGATCGACTAGC 60.051 66.667 36.98 36.98 44.04 3.42
362 375 2.544698 GGCGGTCGATCGACTAGCT 61.545 63.158 39.41 0.00 44.04 3.32
363 376 1.226686 GGCGGTCGATCGACTAGCTA 61.227 60.000 39.41 15.21 44.04 3.32
364 377 0.164217 GCGGTCGATCGACTAGCTAG 59.836 60.000 37.11 26.37 44.04 3.42
367 380 2.408032 CGGTCGATCGACTAGCTAGTAC 59.592 54.545 38.48 22.05 44.04 2.73
373 386 1.135139 TCGACTAGCTAGTACGTCGGT 59.865 52.381 26.11 1.73 46.50 4.69
390 403 3.972502 GTCGGTGTTGCTCAAAATTGTAC 59.027 43.478 0.00 0.00 0.00 2.90
392 405 3.649073 GGTGTTGCTCAAAATTGTACCC 58.351 45.455 0.00 0.00 0.00 3.69
393 406 3.554129 GGTGTTGCTCAAAATTGTACCCC 60.554 47.826 0.00 0.00 0.00 4.95
395 408 2.897326 GTTGCTCAAAATTGTACCCCCT 59.103 45.455 0.00 0.00 0.00 4.79
396 409 2.802719 TGCTCAAAATTGTACCCCCTC 58.197 47.619 0.00 0.00 0.00 4.30
398 411 2.365582 CTCAAAATTGTACCCCCTCCG 58.634 52.381 0.00 0.00 0.00 4.63
399 412 1.706305 TCAAAATTGTACCCCCTCCGT 59.294 47.619 0.00 0.00 0.00 4.69
400 413 2.108601 TCAAAATTGTACCCCCTCCGTT 59.891 45.455 0.00 0.00 0.00 4.44
401 414 2.490509 CAAAATTGTACCCCCTCCGTTC 59.509 50.000 0.00 0.00 0.00 3.95
402 415 0.251073 AATTGTACCCCCTCCGTTCG 59.749 55.000 0.00 0.00 0.00 3.95
403 416 1.619807 ATTGTACCCCCTCCGTTCGG 61.620 60.000 4.74 4.74 0.00 4.30
405 418 1.984026 GTACCCCCTCCGTTCGGAA 60.984 63.158 14.79 0.00 33.41 4.30
406 419 1.002017 TACCCCCTCCGTTCGGAAT 59.998 57.895 14.79 2.09 33.41 3.01
411 424 1.208776 CCCCTCCGTTCGGAATTACTT 59.791 52.381 14.79 0.00 33.41 2.24
412 425 2.431782 CCCCTCCGTTCGGAATTACTTA 59.568 50.000 14.79 0.00 33.41 2.24
413 426 3.070590 CCCCTCCGTTCGGAATTACTTAT 59.929 47.826 14.79 0.00 33.41 1.73
414 427 4.304939 CCCTCCGTTCGGAATTACTTATC 58.695 47.826 14.79 0.00 33.41 1.75
415 428 4.038883 CCCTCCGTTCGGAATTACTTATCT 59.961 45.833 14.79 0.00 33.41 1.98
416 429 5.221130 CCTCCGTTCGGAATTACTTATCTC 58.779 45.833 14.79 0.00 33.41 2.75
417 430 4.852138 TCCGTTCGGAATTACTTATCTCG 58.148 43.478 11.66 0.00 0.00 4.04
418 431 4.576053 TCCGTTCGGAATTACTTATCTCGA 59.424 41.667 11.66 0.00 0.00 4.04
420 433 5.745294 CCGTTCGGAATTACTTATCTCGAAA 59.255 40.000 5.19 0.00 34.61 3.46
421 434 6.254157 CCGTTCGGAATTACTTATCTCGAAAA 59.746 38.462 5.19 0.00 34.61 2.29
422 435 7.042925 CCGTTCGGAATTACTTATCTCGAAAAT 60.043 37.037 5.19 0.00 34.61 1.82
423 436 7.787935 CGTTCGGAATTACTTATCTCGAAAATG 59.212 37.037 0.00 0.00 34.61 2.32
424 437 7.709269 TCGGAATTACTTATCTCGAAAATGG 57.291 36.000 0.00 0.00 0.00 3.16
425 438 7.494211 TCGGAATTACTTATCTCGAAAATGGA 58.506 34.615 0.00 0.00 0.00 3.41
437 450 3.935828 TCGAAAATGGATGTATCGCACAA 59.064 39.130 0.00 0.00 41.55 3.33
439 452 4.495472 CGAAAATGGATGTATCGCACAAAC 59.505 41.667 0.00 0.00 41.55 2.93
440 453 3.673746 AATGGATGTATCGCACAAACG 57.326 42.857 0.00 0.00 41.55 3.60
441 454 2.087501 TGGATGTATCGCACAAACGT 57.912 45.000 0.00 0.00 41.55 3.99
442 455 3.233684 TGGATGTATCGCACAAACGTA 57.766 42.857 0.00 0.00 41.55 3.57
452 465 2.256174 GCACAAACGTATAGCTCGACA 58.744 47.619 0.00 0.00 0.00 4.35
462 475 0.388134 TAGCTCGACACGCTTTGGTC 60.388 55.000 2.73 0.00 38.86 4.02
467 480 4.555709 ACACGCTTTGGTCGCCCA 62.556 61.111 0.00 0.00 39.65 5.36
481 495 1.079612 GCCCAATCAGCAAGCAACC 60.080 57.895 0.00 0.00 0.00 3.77
537 557 3.455195 CGTGCGTACGGTGTGTCG 61.455 66.667 18.81 0.00 46.23 4.35
538 558 2.051076 GTGCGTACGGTGTGTCGA 60.051 61.111 18.39 0.00 0.00 4.20
539 559 1.443194 GTGCGTACGGTGTGTCGAT 60.443 57.895 18.39 0.00 0.00 3.59
540 560 0.179192 GTGCGTACGGTGTGTCGATA 60.179 55.000 18.39 0.00 0.00 2.92
541 561 0.734309 TGCGTACGGTGTGTCGATAT 59.266 50.000 18.39 0.00 0.00 1.63
542 562 1.268184 TGCGTACGGTGTGTCGATATC 60.268 52.381 18.39 0.00 0.00 1.63
543 563 1.655587 CGTACGGTGTGTCGATATCG 58.344 55.000 19.14 19.14 41.45 2.92
559 579 7.221828 TCGATATCGACTCTCAACATTTTTG 57.778 36.000 23.48 0.00 44.22 2.44
560 580 5.898606 CGATATCGACTCTCAACATTTTTGC 59.101 40.000 20.50 0.00 43.02 3.68
561 581 6.455513 CGATATCGACTCTCAACATTTTTGCA 60.456 38.462 20.50 0.00 43.02 4.08
562 582 5.633830 ATCGACTCTCAACATTTTTGCAT 57.366 34.783 0.00 0.00 0.00 3.96
563 583 5.034554 TCGACTCTCAACATTTTTGCATC 57.965 39.130 0.00 0.00 0.00 3.91
564 584 4.756642 TCGACTCTCAACATTTTTGCATCT 59.243 37.500 0.00 0.00 0.00 2.90
565 585 5.084722 CGACTCTCAACATTTTTGCATCTC 58.915 41.667 0.00 0.00 0.00 2.75
566 586 5.106791 CGACTCTCAACATTTTTGCATCTCT 60.107 40.000 0.00 0.00 0.00 3.10
567 587 6.251655 ACTCTCAACATTTTTGCATCTCTC 57.748 37.500 0.00 0.00 0.00 3.20
568 588 5.182760 ACTCTCAACATTTTTGCATCTCTCC 59.817 40.000 0.00 0.00 0.00 3.71
569 589 5.072055 TCTCAACATTTTTGCATCTCTCCA 58.928 37.500 0.00 0.00 0.00 3.86
570 590 5.182570 TCTCAACATTTTTGCATCTCTCCAG 59.817 40.000 0.00 0.00 0.00 3.86
571 591 4.828939 TCAACATTTTTGCATCTCTCCAGT 59.171 37.500 0.00 0.00 0.00 4.00
572 592 5.048504 TCAACATTTTTGCATCTCTCCAGTC 60.049 40.000 0.00 0.00 0.00 3.51
573 593 4.401022 ACATTTTTGCATCTCTCCAGTCA 58.599 39.130 0.00 0.00 0.00 3.41
574 594 4.217118 ACATTTTTGCATCTCTCCAGTCAC 59.783 41.667 0.00 0.00 0.00 3.67
575 595 2.479566 TTTGCATCTCTCCAGTCACC 57.520 50.000 0.00 0.00 0.00 4.02
576 596 0.247460 TTGCATCTCTCCAGTCACCG 59.753 55.000 0.00 0.00 0.00 4.94
577 597 0.900182 TGCATCTCTCCAGTCACCGT 60.900 55.000 0.00 0.00 0.00 4.83
578 598 0.179124 GCATCTCTCCAGTCACCGTC 60.179 60.000 0.00 0.00 0.00 4.79
579 599 1.177401 CATCTCTCCAGTCACCGTCA 58.823 55.000 0.00 0.00 0.00 4.35
580 600 1.133982 CATCTCTCCAGTCACCGTCAG 59.866 57.143 0.00 0.00 0.00 3.51
587 607 2.822215 AGTCACCGTCAGGACTGTT 58.178 52.632 0.00 0.00 42.49 3.16
604 624 2.096248 TGTTCCCCAAACTGTGTGTTC 58.904 47.619 0.00 0.00 38.03 3.18
614 634 4.445452 AACTGTGTGTTCGTCCGTATAT 57.555 40.909 0.00 0.00 32.63 0.86
617 637 5.575957 ACTGTGTGTTCGTCCGTATATAAG 58.424 41.667 0.00 0.00 0.00 1.73
623 643 4.024893 TGTTCGTCCGTATATAAGTCCGTC 60.025 45.833 0.00 0.00 0.00 4.79
637 667 2.660552 CGTCGTGCCGGTCTTTGT 60.661 61.111 1.90 0.00 0.00 2.83
638 668 2.241880 CGTCGTGCCGGTCTTTGTT 61.242 57.895 1.90 0.00 0.00 2.83
642 672 0.938713 CGTGCCGGTCTTTGTTTACA 59.061 50.000 1.90 0.00 0.00 2.41
645 675 2.032290 GTGCCGGTCTTTGTTTACACTC 60.032 50.000 1.90 0.00 0.00 3.51
647 677 2.479275 GCCGGTCTTTGTTTACACTCTC 59.521 50.000 1.90 0.00 0.00 3.20
653 683 3.994392 TCTTTGTTTACACTCTCCGCATC 59.006 43.478 0.00 0.00 0.00 3.91
661 691 2.223595 ACACTCTCCGCATCGTAGATTG 60.224 50.000 0.00 0.00 45.12 2.67
662 692 2.025155 ACTCTCCGCATCGTAGATTGT 58.975 47.619 0.00 0.00 45.12 2.71
663 693 3.003378 CACTCTCCGCATCGTAGATTGTA 59.997 47.826 0.00 0.00 45.12 2.41
664 694 3.821600 ACTCTCCGCATCGTAGATTGTAT 59.178 43.478 0.00 0.00 45.12 2.29
665 695 4.083217 ACTCTCCGCATCGTAGATTGTATC 60.083 45.833 0.00 0.00 45.12 2.24
666 696 3.120304 TCTCCGCATCGTAGATTGTATCG 60.120 47.826 0.00 0.00 45.12 2.92
668 698 3.747529 TCCGCATCGTAGATTGTATCGTA 59.252 43.478 0.00 0.00 45.12 3.43
670 700 4.142966 CCGCATCGTAGATTGTATCGTAGA 60.143 45.833 0.00 0.00 45.12 2.59
674 704 7.460249 CGCATCGTAGATTGTATCGTAGATTTG 60.460 40.741 0.00 0.00 42.55 2.32
678 708 9.577110 TCGTAGATTGTATCGTAGATTTGTTTT 57.423 29.630 0.00 0.00 45.12 2.43
816 878 5.443230 AAAAACCCAATCCTCTCTCTAGG 57.557 43.478 0.00 0.00 38.06 3.02
875 945 7.228507 CAGCCCTATAAATAACACACAAGCATA 59.771 37.037 0.00 0.00 0.00 3.14
902 975 1.134401 CGCATATCCCCTCTGTGTGTT 60.134 52.381 0.00 0.00 0.00 3.32
953 1040 4.478371 CTCCATCCAGCAGCGGCA 62.478 66.667 12.44 0.00 44.61 5.69
976 1063 5.939353 CACTCACAGTGTCACCGAGAAGG 62.939 56.522 17.20 6.54 41.19 3.46
977 1064 0.946221 CACAGTGTCACCGAGAAGGC 60.946 60.000 0.00 0.00 46.52 4.35
978 1065 1.734477 CAGTGTCACCGAGAAGGCG 60.734 63.158 0.00 0.00 46.52 5.52
979 1066 1.901948 AGTGTCACCGAGAAGGCGA 60.902 57.895 0.00 0.00 46.52 5.54
980 1067 1.444553 GTGTCACCGAGAAGGCGAG 60.445 63.158 0.00 0.00 46.52 5.03
981 1068 1.602605 TGTCACCGAGAAGGCGAGA 60.603 57.895 0.00 0.00 46.52 4.04
982 1069 1.176619 TGTCACCGAGAAGGCGAGAA 61.177 55.000 0.00 0.00 46.52 2.87
983 1070 0.456995 GTCACCGAGAAGGCGAGAAG 60.457 60.000 0.00 0.00 46.52 2.85
984 1071 1.153745 CACCGAGAAGGCGAGAAGG 60.154 63.158 0.00 0.00 46.52 3.46
1301 1717 0.376852 GCAAAATGCATGCATGGCAG 59.623 50.000 32.79 22.25 45.68 4.85
1302 1718 2.009542 GCAAAATGCATGCATGGCAGA 61.010 47.619 32.79 3.69 45.68 4.26
1303 1719 2.560504 CAAAATGCATGCATGGCAGAT 58.439 42.857 32.79 14.12 45.68 2.90
1306 1722 0.389025 ATGCATGCATGGCAGATGTG 59.611 50.000 31.74 0.94 45.68 3.21
1341 2477 3.805807 GCCTTGCTTCCACTGTACTACAA 60.806 47.826 0.00 0.00 0.00 2.41
1503 2651 4.181010 CCGGGCAGCAGCTGGTAT 62.181 66.667 24.13 0.00 41.70 2.73
1521 2669 2.899838 GCACGGTGCACTCCAACA 60.900 61.111 27.10 0.00 44.26 3.33
1526 2674 1.586154 CGGTGCACTCCAACATTCCC 61.586 60.000 17.98 0.00 0.00 3.97
1528 2676 0.883833 GTGCACTCCAACATTCCCTG 59.116 55.000 10.32 0.00 0.00 4.45
1530 2678 1.702401 TGCACTCCAACATTCCCTGTA 59.298 47.619 0.00 0.00 36.98 2.74
1534 2683 2.039879 ACTCCAACATTCCCTGTACACC 59.960 50.000 0.00 0.00 36.98 4.16
1536 2685 2.647299 TCCAACATTCCCTGTACACCAT 59.353 45.455 0.00 0.00 36.98 3.55
1579 2731 4.653801 TCTCGAATCCCATGTCAATTCCTA 59.346 41.667 0.00 0.00 0.00 2.94
1585 2737 2.954318 CCCATGTCAATTCCTAAGCCTG 59.046 50.000 0.00 0.00 0.00 4.85
2344 5248 2.783288 CCTCTAGCCCGGTCGTTCC 61.783 68.421 0.00 0.00 0.00 3.62
2383 5294 3.637714 CCGTTGGTGTCGGTGAAG 58.362 61.111 0.00 0.00 42.62 3.02
2394 5305 3.741344 GTGTCGGTGAAGGATATGCATAC 59.259 47.826 8.99 3.26 0.00 2.39
2412 5323 0.036952 ACTTCTGATCCTGCGGTGTG 60.037 55.000 0.00 0.00 0.00 3.82
2461 5375 4.554723 GCGTCTGAATTTTGCAACTGTACT 60.555 41.667 0.00 0.00 0.00 2.73
2467 5381 6.728200 TGAATTTTGCAACTGTACTCTCTTG 58.272 36.000 0.00 0.00 0.00 3.02
2482 5396 2.432146 TCTCTTGCTCAGTTCACAGTGT 59.568 45.455 0.00 0.00 0.00 3.55
2485 5399 4.009675 TCTTGCTCAGTTCACAGTGTTTT 58.990 39.130 0.00 0.00 0.00 2.43
2523 5437 2.333926 TGTACTACGATTGTGCAGCAC 58.666 47.619 19.37 19.37 34.56 4.40
2598 5514 7.141363 GCAGTTCACAGAATTCATTAGTTTGT 58.859 34.615 8.44 0.00 0.00 2.83
2618 5534 4.326826 TGTTGGGAGAATTTAGTCTGCAG 58.673 43.478 7.63 7.63 37.69 4.41
2621 5537 4.836825 TGGGAGAATTTAGTCTGCAGAAG 58.163 43.478 20.19 0.00 37.69 2.85
2643 5559 4.711892 TGCGTAGGAATGCAGCAA 57.288 50.000 0.00 0.00 42.73 3.91
2644 5560 2.170738 TGCGTAGGAATGCAGCAAC 58.829 52.632 0.00 0.00 42.73 4.17
2645 5561 0.605050 TGCGTAGGAATGCAGCAACA 60.605 50.000 0.00 0.00 42.73 3.33
2646 5562 0.521291 GCGTAGGAATGCAGCAACAA 59.479 50.000 0.00 0.00 37.58 2.83
2647 5563 1.729149 GCGTAGGAATGCAGCAACAAC 60.729 52.381 0.00 0.00 37.58 3.32
2648 5564 1.535028 CGTAGGAATGCAGCAACAACA 59.465 47.619 0.00 0.00 0.00 3.33
2649 5565 2.665519 CGTAGGAATGCAGCAACAACAC 60.666 50.000 0.00 0.00 0.00 3.32
2650 5566 1.401761 AGGAATGCAGCAACAACACA 58.598 45.000 0.00 0.00 0.00 3.72
2651 5567 1.755959 AGGAATGCAGCAACAACACAA 59.244 42.857 0.00 0.00 0.00 3.33
2652 5568 2.129607 GGAATGCAGCAACAACACAAG 58.870 47.619 0.00 0.00 0.00 3.16
2653 5569 2.129607 GAATGCAGCAACAACACAAGG 58.870 47.619 0.00 0.00 0.00 3.61
2654 5570 1.401761 ATGCAGCAACAACACAAGGA 58.598 45.000 0.00 0.00 0.00 3.36
2655 5571 1.180907 TGCAGCAACAACACAAGGAA 58.819 45.000 0.00 0.00 0.00 3.36
2683 5599 0.036765 GGCTTCGTATCACCACCACA 60.037 55.000 0.00 0.00 0.00 4.17
2696 5612 1.269726 CCACCACAGCCAAAATCACAC 60.270 52.381 0.00 0.00 0.00 3.82
2705 5621 3.049912 GCCAAAATCACACGAGGAAAAC 58.950 45.455 0.00 0.00 0.00 2.43
2824 5740 6.642683 ATCGATCGAAAACAAACTAACGAT 57.357 33.333 23.50 0.00 41.83 3.73
3128 6050 4.920640 TTCTTCAGGATTAGCTAGTCCG 57.079 45.455 24.85 19.95 37.20 4.79
3129 6051 4.166246 TCTTCAGGATTAGCTAGTCCGA 57.834 45.455 24.85 21.49 37.20 4.55
3130 6052 4.730966 TCTTCAGGATTAGCTAGTCCGAT 58.269 43.478 24.85 9.90 37.20 4.18
3131 6053 4.520874 TCTTCAGGATTAGCTAGTCCGATG 59.479 45.833 24.85 23.13 37.20 3.84
3132 6054 4.100279 TCAGGATTAGCTAGTCCGATGA 57.900 45.455 24.85 21.20 37.20 2.92
3133 6055 4.075682 TCAGGATTAGCTAGTCCGATGAG 58.924 47.826 24.85 15.39 37.20 2.90
3198 6120 1.598962 GCAGCTTCAGCACAGGTCA 60.599 57.895 0.75 0.00 45.16 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.073056 GACATTCCACATGCGTACACA 58.927 47.619 0.00 0.00 0.00 3.72
36 37 1.732941 GGACATTCCACATGCGTACA 58.267 50.000 0.00 0.00 36.28 2.90
37 38 0.650512 CGGACATTCCACATGCGTAC 59.349 55.000 0.00 0.00 35.91 3.67
40 41 3.101209 CCGGACATTCCACATGCG 58.899 61.111 0.00 0.00 35.91 4.73
55 56 2.971428 ATAACCCATCGAGCACGCCG 62.971 60.000 0.00 0.00 39.58 6.46
56 57 0.814010 AATAACCCATCGAGCACGCC 60.814 55.000 0.00 0.00 39.58 5.68
63 65 4.495690 TCAACATCCAATAACCCATCGA 57.504 40.909 0.00 0.00 0.00 3.59
64 66 4.821260 TCATCAACATCCAATAACCCATCG 59.179 41.667 0.00 0.00 0.00 3.84
72 74 4.806892 AGGCCAATCATCAACATCCAATA 58.193 39.130 5.01 0.00 0.00 1.90
91 93 3.564225 CCATAAAACCGGAACAGATAGGC 59.436 47.826 9.46 0.00 0.00 3.93
133 142 2.202878 ACTGTGAACGCGCACACT 60.203 55.556 27.25 13.13 43.35 3.55
134 143 2.237751 AGACTGTGAACGCGCACAC 61.238 57.895 23.01 23.01 43.35 3.82
220 233 1.666189 GCAAGTTACCGGATCTTGAGC 59.334 52.381 27.68 16.89 40.35 4.26
231 244 3.501062 GTCCAGTTTACCAGCAAGTTACC 59.499 47.826 0.00 0.00 0.00 2.85
299 312 1.600076 CTGGAGTGCTGCTGCTGTT 60.600 57.895 17.00 2.12 40.48 3.16
300 313 1.475169 TACTGGAGTGCTGCTGCTGT 61.475 55.000 17.00 14.11 46.14 4.40
302 315 0.036577 CTTACTGGAGTGCTGCTGCT 60.037 55.000 17.00 0.00 40.48 4.24
303 316 1.642952 GCTTACTGGAGTGCTGCTGC 61.643 60.000 8.89 8.89 40.20 5.25
304 317 0.321034 TGCTTACTGGAGTGCTGCTG 60.321 55.000 0.00 0.00 0.00 4.41
305 318 0.036577 CTGCTTACTGGAGTGCTGCT 60.037 55.000 0.00 0.00 0.00 4.24
306 319 0.321122 ACTGCTTACTGGAGTGCTGC 60.321 55.000 0.00 0.00 45.78 5.25
307 320 2.996621 GTTACTGCTTACTGGAGTGCTG 59.003 50.000 0.21 0.00 46.90 4.41
308 321 2.900546 AGTTACTGCTTACTGGAGTGCT 59.099 45.455 0.21 0.00 46.90 4.40
309 322 3.320673 AGTTACTGCTTACTGGAGTGC 57.679 47.619 0.21 0.00 46.90 4.40
310 323 4.158764 AGCTAGTTACTGCTTACTGGAGTG 59.841 45.833 0.00 0.00 46.90 3.51
312 325 4.202070 GGAGCTAGTTACTGCTTACTGGAG 60.202 50.000 9.80 0.00 39.91 3.86
313 326 3.700038 GGAGCTAGTTACTGCTTACTGGA 59.300 47.826 9.80 0.00 39.91 3.86
314 327 3.702045 AGGAGCTAGTTACTGCTTACTGG 59.298 47.826 9.80 0.00 39.91 4.00
315 328 4.642885 AGAGGAGCTAGTTACTGCTTACTG 59.357 45.833 0.00 0.00 39.91 2.74
316 329 4.642885 CAGAGGAGCTAGTTACTGCTTACT 59.357 45.833 0.00 10.69 39.91 2.24
317 330 4.399934 ACAGAGGAGCTAGTTACTGCTTAC 59.600 45.833 0.00 7.25 39.91 2.34
318 331 4.601084 ACAGAGGAGCTAGTTACTGCTTA 58.399 43.478 0.00 0.00 39.91 3.09
319 332 3.436243 ACAGAGGAGCTAGTTACTGCTT 58.564 45.455 0.00 0.00 39.91 3.91
338 351 2.180769 CGATCGACCGCCTCAACA 59.819 61.111 10.26 0.00 0.00 3.33
355 368 2.275318 ACACCGACGTACTAGCTAGTC 58.725 52.381 29.28 18.72 37.73 2.59
359 372 0.109412 GCAACACCGACGTACTAGCT 60.109 55.000 0.00 0.00 0.00 3.32
360 373 0.109412 AGCAACACCGACGTACTAGC 60.109 55.000 0.00 0.00 0.00 3.42
361 374 1.198408 TGAGCAACACCGACGTACTAG 59.802 52.381 0.00 0.00 0.00 2.57
362 375 1.237533 TGAGCAACACCGACGTACTA 58.762 50.000 0.00 0.00 0.00 1.82
363 376 0.386476 TTGAGCAACACCGACGTACT 59.614 50.000 0.00 0.00 0.00 2.73
364 377 1.210870 TTTGAGCAACACCGACGTAC 58.789 50.000 0.00 0.00 0.00 3.67
367 380 2.043411 CAATTTTGAGCAACACCGACG 58.957 47.619 0.00 0.00 0.00 5.12
373 386 2.630580 GGGGGTACAATTTTGAGCAACA 59.369 45.455 0.00 0.00 0.00 3.33
390 403 0.179065 GTAATTCCGAACGGAGGGGG 60.179 60.000 15.34 0.00 46.06 5.40
392 405 2.685850 AAGTAATTCCGAACGGAGGG 57.314 50.000 15.34 0.00 46.06 4.30
393 406 5.197682 AGATAAGTAATTCCGAACGGAGG 57.802 43.478 15.34 0.00 46.06 4.30
395 408 4.576053 TCGAGATAAGTAATTCCGAACGGA 59.424 41.667 12.04 12.04 43.52 4.69
396 409 4.852138 TCGAGATAAGTAATTCCGAACGG 58.148 43.478 6.94 6.94 0.00 4.44
398 411 8.062448 CCATTTTCGAGATAAGTAATTCCGAAC 58.938 37.037 0.00 0.00 34.02 3.95
399 412 7.982919 TCCATTTTCGAGATAAGTAATTCCGAA 59.017 33.333 0.00 0.00 33.11 4.30
400 413 7.494211 TCCATTTTCGAGATAAGTAATTCCGA 58.506 34.615 0.00 0.00 0.00 4.55
401 414 7.709269 TCCATTTTCGAGATAAGTAATTCCG 57.291 36.000 0.00 0.00 0.00 4.30
402 415 9.057089 ACATCCATTTTCGAGATAAGTAATTCC 57.943 33.333 0.00 0.00 0.00 3.01
406 419 9.406828 CGATACATCCATTTTCGAGATAAGTAA 57.593 33.333 0.00 0.00 31.74 2.24
411 424 5.633601 GTGCGATACATCCATTTTCGAGATA 59.366 40.000 0.00 0.00 31.74 1.98
412 425 4.449068 GTGCGATACATCCATTTTCGAGAT 59.551 41.667 0.00 0.00 31.74 2.75
413 426 3.802139 GTGCGATACATCCATTTTCGAGA 59.198 43.478 0.00 0.00 31.74 4.04
414 427 3.555547 TGTGCGATACATCCATTTTCGAG 59.444 43.478 0.00 0.00 33.42 4.04
415 428 3.526534 TGTGCGATACATCCATTTTCGA 58.473 40.909 0.00 0.00 33.42 3.71
416 429 3.942539 TGTGCGATACATCCATTTTCG 57.057 42.857 0.00 0.00 33.42 3.46
417 430 4.495472 CGTTTGTGCGATACATCCATTTTC 59.505 41.667 0.00 0.00 39.48 2.29
418 431 4.083003 ACGTTTGTGCGATACATCCATTTT 60.083 37.500 0.00 0.00 39.48 1.82
420 433 3.006940 ACGTTTGTGCGATACATCCATT 58.993 40.909 0.00 0.00 39.48 3.16
421 434 2.627945 ACGTTTGTGCGATACATCCAT 58.372 42.857 0.00 0.00 39.48 3.41
422 435 2.087501 ACGTTTGTGCGATACATCCA 57.912 45.000 0.00 0.00 39.48 3.41
423 436 4.143389 GCTATACGTTTGTGCGATACATCC 60.143 45.833 0.00 0.00 39.48 3.51
424 437 4.680110 AGCTATACGTTTGTGCGATACATC 59.320 41.667 0.00 0.00 39.48 3.06
425 438 4.617959 AGCTATACGTTTGTGCGATACAT 58.382 39.130 0.00 0.00 39.48 2.29
429 442 2.117137 CGAGCTATACGTTTGTGCGAT 58.883 47.619 0.00 0.00 35.59 4.58
430 443 1.130938 TCGAGCTATACGTTTGTGCGA 59.869 47.619 0.00 0.00 35.59 5.10
437 450 0.731417 AGCGTGTCGAGCTATACGTT 59.269 50.000 7.48 0.00 44.05 3.99
439 452 1.513178 CAAAGCGTGTCGAGCTATACG 59.487 52.381 1.78 1.78 45.31 3.06
440 453 1.852895 CCAAAGCGTGTCGAGCTATAC 59.147 52.381 0.00 0.00 45.31 1.47
441 454 1.475280 ACCAAAGCGTGTCGAGCTATA 59.525 47.619 0.00 0.00 45.31 1.31
442 455 0.246635 ACCAAAGCGTGTCGAGCTAT 59.753 50.000 0.00 0.00 45.31 2.97
462 475 1.444895 GTTGCTTGCTGATTGGGCG 60.445 57.895 0.00 0.00 0.00 6.13
463 476 1.079612 GGTTGCTTGCTGATTGGGC 60.080 57.895 0.00 0.00 0.00 5.36
464 477 1.213537 CGGTTGCTTGCTGATTGGG 59.786 57.895 0.00 0.00 0.00 4.12
467 480 1.577328 CCGTCGGTTGCTTGCTGATT 61.577 55.000 2.08 0.00 0.00 2.57
469 482 2.664851 CCGTCGGTTGCTTGCTGA 60.665 61.111 2.08 0.00 0.00 4.26
481 495 1.082038 CGATGTAGCTAGCCCGTCG 60.082 63.158 23.80 23.80 0.00 5.12
523 543 1.392756 GATATCGACACACCGTACGC 58.607 55.000 10.49 0.00 0.00 4.42
536 556 5.898606 GCAAAAATGTTGAGAGTCGATATCG 59.101 40.000 19.14 19.14 41.45 2.92
537 557 6.775088 TGCAAAAATGTTGAGAGTCGATATC 58.225 36.000 0.00 0.00 0.00 1.63
538 558 6.741992 TGCAAAAATGTTGAGAGTCGATAT 57.258 33.333 0.00 0.00 0.00 1.63
539 559 6.595326 AGATGCAAAAATGTTGAGAGTCGATA 59.405 34.615 0.00 0.00 0.00 2.92
540 560 5.413833 AGATGCAAAAATGTTGAGAGTCGAT 59.586 36.000 0.00 0.00 0.00 3.59
541 561 4.756642 AGATGCAAAAATGTTGAGAGTCGA 59.243 37.500 0.00 0.00 0.00 4.20
542 562 5.039480 AGATGCAAAAATGTTGAGAGTCG 57.961 39.130 0.00 0.00 0.00 4.18
543 563 6.251655 AGAGATGCAAAAATGTTGAGAGTC 57.748 37.500 0.00 0.00 0.00 3.36
544 564 5.182760 GGAGAGATGCAAAAATGTTGAGAGT 59.817 40.000 0.00 0.00 0.00 3.24
545 565 5.182570 TGGAGAGATGCAAAAATGTTGAGAG 59.817 40.000 0.00 0.00 0.00 3.20
546 566 5.072055 TGGAGAGATGCAAAAATGTTGAGA 58.928 37.500 0.00 0.00 0.00 3.27
547 567 5.048224 ACTGGAGAGATGCAAAAATGTTGAG 60.048 40.000 0.00 0.00 0.00 3.02
548 568 4.828939 ACTGGAGAGATGCAAAAATGTTGA 59.171 37.500 0.00 0.00 0.00 3.18
549 569 5.130292 ACTGGAGAGATGCAAAAATGTTG 57.870 39.130 0.00 0.00 0.00 3.33
550 570 4.828939 TGACTGGAGAGATGCAAAAATGTT 59.171 37.500 0.00 0.00 0.00 2.71
551 571 4.217118 GTGACTGGAGAGATGCAAAAATGT 59.783 41.667 0.00 0.00 0.00 2.71
552 572 4.380233 GGTGACTGGAGAGATGCAAAAATG 60.380 45.833 0.00 0.00 0.00 2.32
553 573 3.760684 GGTGACTGGAGAGATGCAAAAAT 59.239 43.478 0.00 0.00 0.00 1.82
554 574 3.149196 GGTGACTGGAGAGATGCAAAAA 58.851 45.455 0.00 0.00 0.00 1.94
555 575 2.783135 GGTGACTGGAGAGATGCAAAA 58.217 47.619 0.00 0.00 0.00 2.44
556 576 1.338105 CGGTGACTGGAGAGATGCAAA 60.338 52.381 0.00 0.00 0.00 3.68
557 577 0.247460 CGGTGACTGGAGAGATGCAA 59.753 55.000 0.00 0.00 0.00 4.08
558 578 0.900182 ACGGTGACTGGAGAGATGCA 60.900 55.000 0.00 0.00 0.00 3.96
559 579 0.179124 GACGGTGACTGGAGAGATGC 60.179 60.000 0.00 0.00 0.00 3.91
560 580 1.133982 CTGACGGTGACTGGAGAGATG 59.866 57.143 0.00 0.00 0.00 2.90
561 581 1.468985 CTGACGGTGACTGGAGAGAT 58.531 55.000 0.00 0.00 0.00 2.75
562 582 0.609406 CCTGACGGTGACTGGAGAGA 60.609 60.000 0.00 0.00 0.00 3.10
563 583 0.609406 TCCTGACGGTGACTGGAGAG 60.609 60.000 0.00 0.00 32.95 3.20
564 584 0.894184 GTCCTGACGGTGACTGGAGA 60.894 60.000 0.00 0.00 36.38 3.71
565 585 0.896019 AGTCCTGACGGTGACTGGAG 60.896 60.000 0.00 0.00 40.23 3.86
566 586 1.153061 AGTCCTGACGGTGACTGGA 59.847 57.895 0.00 0.00 40.23 3.86
567 587 3.778955 AGTCCTGACGGTGACTGG 58.221 61.111 0.00 0.00 40.23 4.00
569 589 0.674534 GAACAGTCCTGACGGTGACT 59.325 55.000 3.87 0.00 42.41 3.41
570 590 0.319641 GGAACAGTCCTGACGGTGAC 60.320 60.000 3.87 2.59 41.24 3.67
571 591 1.469335 GGGAACAGTCCTGACGGTGA 61.469 60.000 3.87 0.00 44.28 4.02
572 592 1.004918 GGGAACAGTCCTGACGGTG 60.005 63.158 3.87 0.00 44.28 4.94
573 593 2.214920 GGGGAACAGTCCTGACGGT 61.215 63.158 0.40 0.00 44.28 4.83
574 594 1.764571 TTGGGGAACAGTCCTGACGG 61.765 60.000 0.40 0.00 44.28 4.79
575 595 0.107831 TTTGGGGAACAGTCCTGACG 59.892 55.000 0.40 0.00 44.28 4.35
576 596 1.143073 AGTTTGGGGAACAGTCCTGAC 59.857 52.381 0.40 0.00 44.28 3.51
577 597 1.142870 CAGTTTGGGGAACAGTCCTGA 59.857 52.381 0.40 0.00 44.28 3.86
578 598 1.133792 ACAGTTTGGGGAACAGTCCTG 60.134 52.381 0.00 0.00 44.28 3.86
579 599 1.133792 CACAGTTTGGGGAACAGTCCT 60.134 52.381 0.00 0.00 44.28 3.85
580 600 1.318576 CACAGTTTGGGGAACAGTCC 58.681 55.000 0.00 0.00 44.10 3.85
587 607 0.253610 ACGAACACACAGTTTGGGGA 59.746 50.000 0.00 0.00 44.49 4.81
604 624 2.476619 ACGACGGACTTATATACGGACG 59.523 50.000 0.00 0.00 36.75 4.79
637 667 3.011818 TCTACGATGCGGAGAGTGTAAA 58.988 45.455 0.00 0.00 42.31 2.01
638 668 2.635714 TCTACGATGCGGAGAGTGTAA 58.364 47.619 0.00 0.00 42.31 2.41
645 675 3.164358 CGATACAATCTACGATGCGGAG 58.836 50.000 0.00 0.00 39.48 4.63
647 677 2.929960 ACGATACAATCTACGATGCGG 58.070 47.619 0.00 0.00 0.00 5.69
686 716 9.292195 TCAGTCCATCTACGATACAATATGTTA 57.708 33.333 0.00 0.00 0.00 2.41
687 717 8.178313 TCAGTCCATCTACGATACAATATGTT 57.822 34.615 0.00 0.00 0.00 2.71
689 719 7.704047 CCATCAGTCCATCTACGATACAATATG 59.296 40.741 0.00 0.00 0.00 1.78
690 720 7.615757 TCCATCAGTCCATCTACGATACAATAT 59.384 37.037 0.00 0.00 0.00 1.28
691 721 6.946009 TCCATCAGTCCATCTACGATACAATA 59.054 38.462 0.00 0.00 0.00 1.90
692 722 5.775195 TCCATCAGTCCATCTACGATACAAT 59.225 40.000 0.00 0.00 0.00 2.71
694 724 4.725490 TCCATCAGTCCATCTACGATACA 58.275 43.478 0.00 0.00 0.00 2.29
700 730 3.243704 GCTCACTCCATCAGTCCATCTAC 60.244 52.174 0.00 0.00 30.26 2.59
701 731 2.961741 GCTCACTCCATCAGTCCATCTA 59.038 50.000 0.00 0.00 30.26 1.98
702 732 1.761784 GCTCACTCCATCAGTCCATCT 59.238 52.381 0.00 0.00 30.26 2.90
703 733 1.483827 TGCTCACTCCATCAGTCCATC 59.516 52.381 0.00 0.00 30.26 3.51
705 735 0.900421 CTGCTCACTCCATCAGTCCA 59.100 55.000 0.00 0.00 30.26 4.02
706 736 0.461693 GCTGCTCACTCCATCAGTCC 60.462 60.000 0.00 0.00 30.26 3.85
707 737 0.536260 AGCTGCTCACTCCATCAGTC 59.464 55.000 0.00 0.00 30.26 3.51
798 842 1.940957 ACCCTAGAGAGAGGATTGGGT 59.059 52.381 0.00 0.00 41.19 4.51
799 843 2.604139 GACCCTAGAGAGAGGATTGGG 58.396 57.143 0.00 0.00 39.15 4.12
802 846 4.488770 GATTGGACCCTAGAGAGAGGATT 58.511 47.826 0.00 0.00 39.15 3.01
804 848 2.178106 GGATTGGACCCTAGAGAGAGGA 59.822 54.545 0.00 0.00 39.15 3.71
816 878 3.134127 GCGGTGCTGGATTGGACC 61.134 66.667 0.00 0.00 43.70 4.46
845 907 4.578928 GTGTGTTATTTATAGGGCTGGTGG 59.421 45.833 0.00 0.00 0.00 4.61
875 945 2.365617 CAGAGGGGATATGCGTACTGTT 59.634 50.000 0.00 0.00 0.00 3.16
902 975 0.031449 TGTGATCGCGACAACACAGA 59.969 50.000 28.57 15.64 38.14 3.41
976 1063 3.552294 GCACTAACAAGTATCCTTCTCGC 59.448 47.826 0.00 0.00 0.00 5.03
977 1064 4.744570 TGCACTAACAAGTATCCTTCTCG 58.255 43.478 0.00 0.00 0.00 4.04
978 1065 6.037610 CCATTGCACTAACAAGTATCCTTCTC 59.962 42.308 0.00 0.00 31.96 2.87
979 1066 5.882557 CCATTGCACTAACAAGTATCCTTCT 59.117 40.000 0.00 0.00 31.96 2.85
980 1067 5.449177 GCCATTGCACTAACAAGTATCCTTC 60.449 44.000 0.00 0.00 37.47 3.46
981 1068 4.399303 GCCATTGCACTAACAAGTATCCTT 59.601 41.667 0.00 0.00 37.47 3.36
982 1069 3.947834 GCCATTGCACTAACAAGTATCCT 59.052 43.478 0.00 0.00 37.47 3.24
983 1070 3.242739 CGCCATTGCACTAACAAGTATCC 60.243 47.826 0.00 0.00 37.32 2.59
984 1071 3.242739 CCGCCATTGCACTAACAAGTATC 60.243 47.826 0.00 0.00 37.32 2.24
992 1079 2.753849 GCCCCGCCATTGCACTAA 60.754 61.111 0.00 0.00 37.32 2.24
1081 1171 2.830704 AAGTAGCACGGTACCTGCGC 62.831 60.000 22.49 19.68 39.79 6.09
1089 1179 0.662374 CGAACACGAAGTAGCACGGT 60.662 55.000 0.00 0.00 41.61 4.83
1200 1290 3.379445 GAGAAGCGTCCGGTGGGA 61.379 66.667 0.00 0.00 41.08 4.37
1297 1713 1.787847 GTACGTGCACACATCTGCC 59.212 57.895 18.64 0.00 36.21 4.85
1301 1717 2.776072 GCCGTACGTGCACACATC 59.224 61.111 18.64 3.06 0.00 3.06
1302 1718 3.109547 CGCCGTACGTGCACACAT 61.110 61.111 18.64 3.95 36.87 3.21
1320 1736 3.678056 TGTAGTACAGTGGAAGCAAGG 57.322 47.619 0.00 0.00 0.00 3.61
1341 2477 3.065925 GCAAAAACAGAGCAAGACTGACT 59.934 43.478 0.00 0.00 38.55 3.41
1521 2669 0.748005 GCGCATGGTGTACAGGGAAT 60.748 55.000 0.30 0.00 0.00 3.01
1526 2674 0.390340 ACAGAGCGCATGGTGTACAG 60.390 55.000 11.47 0.00 0.00 2.74
1528 2676 1.659098 GTAACAGAGCGCATGGTGTAC 59.341 52.381 11.47 8.59 0.00 2.90
1530 2678 1.014044 CGTAACAGAGCGCATGGTGT 61.014 55.000 11.47 3.92 0.00 4.16
1534 2683 2.526077 TCTTACGTAACAGAGCGCATG 58.474 47.619 11.47 11.02 0.00 4.06
1536 2685 2.710220 TTCTTACGTAACAGAGCGCA 57.290 45.000 11.47 0.00 0.00 6.09
1553 2705 5.049129 GGAATTGACATGGGATTCGAGATTC 60.049 44.000 0.00 0.00 32.03 2.52
1708 2904 1.642037 CGGTGAAGATGCACTGGCTG 61.642 60.000 0.00 0.00 40.62 4.85
1807 3003 2.670934 AGGTCGTCGGCGTACTGT 60.671 61.111 10.18 0.00 39.49 3.55
1984 3294 1.503542 GAGCCGCTGGTTGAACATG 59.496 57.895 0.00 0.00 0.00 3.21
2143 5047 4.323477 TGCCCGTTGTTCCTCCCG 62.323 66.667 0.00 0.00 0.00 5.14
2383 5294 4.874966 GCAGGATCAGAAGTATGCATATCC 59.125 45.833 10.16 11.62 33.92 2.59
2402 5313 3.964875 GTGTTGGCACACCGCAGG 61.965 66.667 8.44 0.00 46.84 4.85
2412 5323 4.570772 ACGTATCATCTTGTATGTGTTGGC 59.429 41.667 0.00 0.00 0.00 4.52
2461 5375 2.432146 ACACTGTGAACTGAGCAAGAGA 59.568 45.455 15.86 0.00 0.00 3.10
2467 5381 5.334414 CCATCTAAAACACTGTGAACTGAGC 60.334 44.000 15.86 0.00 0.00 4.26
2482 5396 2.964209 TGGTTGGTTGCCCATCTAAAA 58.036 42.857 0.00 0.00 41.49 1.52
2485 5399 1.357420 ACATGGTTGGTTGCCCATCTA 59.643 47.619 0.00 0.00 41.49 1.98
2598 5514 4.908601 TCTGCAGACTAAATTCTCCCAA 57.091 40.909 13.74 0.00 0.00 4.12
2618 5534 2.807967 TGCATTCCTACGCATATGCTTC 59.192 45.455 24.56 3.27 42.85 3.86
2621 5537 1.135859 GCTGCATTCCTACGCATATGC 60.136 52.381 18.08 18.08 42.75 3.14
2628 5544 1.535028 TGTTGTTGCTGCATTCCTACG 59.465 47.619 1.84 0.00 0.00 3.51
2629 5545 2.293122 TGTGTTGTTGCTGCATTCCTAC 59.707 45.455 1.84 0.00 0.00 3.18
2640 5556 2.892374 AGCTTTTCCTTGTGTTGTTGC 58.108 42.857 0.00 0.00 0.00 4.17
2642 5558 3.369366 CCCAAGCTTTTCCTTGTGTTGTT 60.369 43.478 0.00 0.00 40.40 2.83
2643 5559 2.168313 CCCAAGCTTTTCCTTGTGTTGT 59.832 45.455 0.00 0.00 40.40 3.32
2644 5560 2.483538 CCCCAAGCTTTTCCTTGTGTTG 60.484 50.000 0.00 0.00 40.40 3.33
2645 5561 1.762370 CCCCAAGCTTTTCCTTGTGTT 59.238 47.619 0.00 0.00 40.40 3.32
2646 5562 1.413118 CCCCAAGCTTTTCCTTGTGT 58.587 50.000 0.00 0.00 40.40 3.72
2647 5563 0.033920 GCCCCAAGCTTTTCCTTGTG 59.966 55.000 0.00 0.00 40.40 3.33
2648 5564 2.440946 GCCCCAAGCTTTTCCTTGT 58.559 52.632 0.00 0.00 40.40 3.16
2683 5599 2.270352 TTCCTCGTGTGATTTTGGCT 57.730 45.000 0.00 0.00 0.00 4.75
2705 5621 4.020839 AGCATTGGAAGGGAAAATCTGTTG 60.021 41.667 0.00 0.00 0.00 3.33
2824 5740 6.462207 CCCAACTGTTCATGTTGAAACCATTA 60.462 38.462 8.01 0.00 45.27 1.90
2987 5903 7.342581 TCCCTATTGTTGTTGTAATATGCTCA 58.657 34.615 0.00 0.00 0.00 4.26
3128 6050 4.030753 GTCTTTTCGTCGTCATCACTCATC 59.969 45.833 0.00 0.00 0.00 2.92
3129 6051 3.921021 GTCTTTTCGTCGTCATCACTCAT 59.079 43.478 0.00 0.00 0.00 2.90
3130 6052 3.004419 AGTCTTTTCGTCGTCATCACTCA 59.996 43.478 0.00 0.00 0.00 3.41
3131 6053 3.566523 AGTCTTTTCGTCGTCATCACTC 58.433 45.455 0.00 0.00 0.00 3.51
3132 6054 3.004419 TGAGTCTTTTCGTCGTCATCACT 59.996 43.478 0.00 0.00 0.00 3.41
3133 6055 3.305964 TGAGTCTTTTCGTCGTCATCAC 58.694 45.455 0.00 0.00 0.00 3.06
3198 6120 3.093057 AGTAGGTGCATCGAAGAAGACT 58.907 45.455 0.00 0.00 43.58 3.24


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

AutoCloner maintained by Alex Coulton.