Multiple sequence alignment - TraesCS3A01G439500

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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 TraesCS3A01G439500 chr3A 100.000 2207 0 0 1 2207 682480641 682478435 0.000000e+00 4076.0
1 TraesCS3A01G439500 chr3A 100.000 2105 0 0 3188 5292 682477454 682475350 0.000000e+00 3888.0
2 TraesCS3A01G439500 chr3A 100.000 635 0 0 2338 2972 682478304 682477670 0.000000e+00 1173.0
3 TraesCS3A01G439500 chr3A 80.155 388 62 8 1 376 654077431 654077815 5.220000e-70 276.0
4 TraesCS3A01G439500 chr3A 85.043 234 35 0 1400 1633 225894569 225894336 6.850000e-59 239.0
5 TraesCS3A01G439500 chr3A 90.278 72 5 2 1256 1326 225894945 225894875 5.640000e-15 93.5
6 TraesCS3A01G439500 chr3D 94.143 1605 66 10 499 2095 546199820 546198236 0.000000e+00 2418.0
7 TraesCS3A01G439500 chr3D 93.299 582 21 10 3379 3955 546197298 546196730 0.000000e+00 843.0
8 TraesCS3A01G439500 chr3D 93.346 526 28 3 3968 4488 546196551 546196028 0.000000e+00 771.0
9 TraesCS3A01G439500 chr3D 89.237 511 34 4 1 506 546203779 546203285 2.090000e-173 619.0
10 TraesCS3A01G439500 chr3D 76.860 726 137 20 4575 5292 465037299 465036597 1.080000e-101 381.0
11 TraesCS3A01G439500 chr3D 76.029 680 116 33 4618 5286 554717757 554718400 5.150000e-80 309.0
12 TraesCS3A01G439500 chr3D 80.256 390 62 9 1 378 125294969 125294583 4.040000e-71 279.0
13 TraesCS3A01G439500 chr3D 85.470 234 34 0 1400 1633 180470744 180470511 1.470000e-60 244.0
14 TraesCS3A01G439500 chr3D 87.805 123 5 3 2080 2202 546198224 546198112 9.240000e-28 135.0
15 TraesCS3A01G439500 chr3D 85.185 108 12 4 1220 1325 180471139 180471034 2.020000e-19 108.0
16 TraesCS3A01G439500 chr3B 92.487 1677 71 30 542 2202 722591765 722590128 0.000000e+00 2348.0
17 TraesCS3A01G439500 chr3B 91.275 1169 51 21 3354 4488 722588770 722587619 0.000000e+00 1546.0
18 TraesCS3A01G439500 chr3B 91.882 542 38 3 1 537 722592859 722592319 0.000000e+00 752.0
19 TraesCS3A01G439500 chr3B 79.845 387 65 10 1 376 731559361 731558977 2.430000e-68 270.0
20 TraesCS3A01G439500 chr3B 84.188 234 37 0 1400 1633 258721284 258721051 1.480000e-55 228.0
21 TraesCS3A01G439500 chr3B 84.259 108 13 4 1220 1325 258721665 258721560 9.380000e-18 102.0
22 TraesCS3A01G439500 chr3B 100.000 28 0 0 4491 4518 24698716 24698743 1.000000e-02 52.8
23 TraesCS3A01G439500 chr7A 83.914 746 88 11 4561 5289 101465697 101464967 0.000000e+00 684.0
24 TraesCS3A01G439500 chr7A 80.990 384 61 9 1 378 420662777 420662400 1.440000e-75 294.0
25 TraesCS3A01G439500 chr5A 77.688 744 119 27 4570 5289 706652345 706651625 1.370000e-110 411.0
26 TraesCS3A01G439500 chr5A 75.034 737 146 20 4570 5286 531524279 531523561 1.850000e-79 307.0
27 TraesCS3A01G439500 chr5D 76.757 740 134 28 4567 5289 394143555 394142837 3.870000e-101 379.0
28 TraesCS3A01G439500 chr5D 76.178 743 130 29 4567 5286 197427046 197427764 1.090000e-91 348.0
29 TraesCS3A01G439500 chr1A 76.455 739 138 19 4567 5286 500849359 500850080 8.370000e-98 368.0
30 TraesCS3A01G439500 chr7D 75.908 743 135 29 4567 5286 461209283 461210004 1.830000e-89 340.0
31 TraesCS3A01G439500 chr4B 82.768 383 48 13 1 376 610568344 610567973 5.110000e-85 326.0
32 TraesCS3A01G439500 chr4D 82.292 384 56 10 1 378 392542762 392542385 6.610000e-84 322.0
33 TraesCS3A01G439500 chr7B 83.191 351 47 5 1 340 646991131 646991480 1.430000e-80 311.0
34 TraesCS3A01G439500 chrUn 75.034 737 143 27 4568 5284 51015125 51014410 2.390000e-78 303.0
35 TraesCS3A01G439500 chr4A 75.034 737 143 27 4568 5284 720181113 720180398 2.390000e-78 303.0
36 TraesCS3A01G439500 chr4A 74.627 737 143 29 4569 5283 720108544 720107830 8.670000e-73 285.0
37 TraesCS3A01G439500 chr2D 75.868 634 123 19 4667 5289 534746870 534746256 4.010000e-76 296.0
38 TraesCS3A01G439500 chr6A 75.901 527 92 25 4778 5289 52378856 52378350 2.460000e-58 237.0
39 TraesCS3A01G439500 chr2B 74.454 595 118 28 4700 5278 612862823 612863399 5.330000e-55 226.0


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 TraesCS3A01G439500 chr3A 682475350 682480641 5291 True 3045.666667 4076 100.000000 1 5292 3 chr3A.!!$R2 5291
1 TraesCS3A01G439500 chr3D 546196028 546203779 7751 True 957.200000 2418 91.566000 1 4488 5 chr3D.!!$R4 4487
2 TraesCS3A01G439500 chr3D 465036597 465037299 702 True 381.000000 381 76.860000 4575 5292 1 chr3D.!!$R2 717
3 TraesCS3A01G439500 chr3D 554717757 554718400 643 False 309.000000 309 76.029000 4618 5286 1 chr3D.!!$F1 668
4 TraesCS3A01G439500 chr3B 722587619 722592859 5240 True 1548.666667 2348 91.881333 1 4488 3 chr3B.!!$R3 4487
5 TraesCS3A01G439500 chr7A 101464967 101465697 730 True 684.000000 684 83.914000 4561 5289 1 chr7A.!!$R1 728
6 TraesCS3A01G439500 chr5A 706651625 706652345 720 True 411.000000 411 77.688000 4570 5289 1 chr5A.!!$R2 719
7 TraesCS3A01G439500 chr5A 531523561 531524279 718 True 307.000000 307 75.034000 4570 5286 1 chr5A.!!$R1 716
8 TraesCS3A01G439500 chr5D 394142837 394143555 718 True 379.000000 379 76.757000 4567 5289 1 chr5D.!!$R1 722
9 TraesCS3A01G439500 chr5D 197427046 197427764 718 False 348.000000 348 76.178000 4567 5286 1 chr5D.!!$F1 719
10 TraesCS3A01G439500 chr1A 500849359 500850080 721 False 368.000000 368 76.455000 4567 5286 1 chr1A.!!$F1 719
11 TraesCS3A01G439500 chr7D 461209283 461210004 721 False 340.000000 340 75.908000 4567 5286 1 chr7D.!!$F1 719
12 TraesCS3A01G439500 chrUn 51014410 51015125 715 True 303.000000 303 75.034000 4568 5284 1 chrUn.!!$R1 716
13 TraesCS3A01G439500 chr4A 720180398 720181113 715 True 303.000000 303 75.034000 4568 5284 1 chr4A.!!$R2 716
14 TraesCS3A01G439500 chr4A 720107830 720108544 714 True 285.000000 285 74.627000 4569 5283 1 chr4A.!!$R1 714
15 TraesCS3A01G439500 chr2D 534746256 534746870 614 True 296.000000 296 75.868000 4667 5289 1 chr2D.!!$R1 622
16 TraesCS3A01G439500 chr6A 52378350 52378856 506 True 237.000000 237 75.901000 4778 5289 1 chr6A.!!$R1 511
17 TraesCS3A01G439500 chr2B 612862823 612863399 576 False 226.000000 226 74.454000 4700 5278 1 chr2B.!!$F1 578


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
446 452 0.036164 TAGCATCACCACTTGCCGTT 59.964 50.0 0.00 0.00 39.72 4.44 F
921 4954 0.811616 CAACCGCCTAGGCACTGATC 60.812 60.0 32.47 2.22 46.52 2.92 F
2607 6694 0.244450 AATTGCCATGTCGCCAACTG 59.756 50.0 0.00 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 5922 0.250124 TGGTGGTGACGGTGATGAAC 60.250 55.0 0.00 0.0 0.00 3.18 R
2666 6760 0.245266 TCATAACTGGCGAGCGTTCA 59.755 50.0 0.00 0.0 0.00 3.18 R
4529 9517 0.036010 ATCCGTGCTGGGAACTTCAG 60.036 55.0 0.37 0.0 40.09 3.02 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
34 35 7.148540 GCAAATCAGCTTATGAAATTTCTGCAA 60.149 33.333 18.64 9.02 42.53 4.08
38 39 7.604549 TCAGCTTATGAAATTTCTGCAAATGA 58.395 30.769 18.64 12.77 34.02 2.57
68 69 1.185315 TCGAGATCATCAGGTGCACA 58.815 50.000 20.43 0.00 0.00 4.57
71 72 0.610174 AGATCATCAGGTGCACACGT 59.390 50.000 20.43 0.00 0.00 4.49
73 74 2.159184 AGATCATCAGGTGCACACGTAG 60.159 50.000 20.43 5.33 0.00 3.51
89 90 6.495706 CACACGTAGCTACTCATTGATCTTA 58.504 40.000 21.20 0.00 0.00 2.10
201 202 7.958567 CGGTATCAACATTTGTTATTTACGTGT 59.041 33.333 0.00 0.00 36.32 4.49
216 217 2.811855 ACGTGTGACATTGACGTGTAA 58.188 42.857 0.00 0.00 44.27 2.41
246 252 2.470821 GCATGGATTTGCATGAAGAGC 58.529 47.619 15.21 0.00 42.31 4.09
247 253 2.100916 GCATGGATTTGCATGAAGAGCT 59.899 45.455 15.21 0.00 42.31 4.09
271 277 0.403655 TTTGAGGTATGTGGCTGCCA 59.596 50.000 19.30 19.30 0.00 4.92
272 278 0.403655 TTGAGGTATGTGGCTGCCAA 59.596 50.000 25.23 14.16 34.18 4.52
360 366 0.608035 TGACCGGATTTGCCAAGTCC 60.608 55.000 9.46 8.84 38.31 3.85
361 367 0.608035 GACCGGATTTGCCAAGTCCA 60.608 55.000 17.84 0.00 34.85 4.02
365 371 2.421388 CCGGATTTGCCAAGTCCAGATA 60.421 50.000 17.84 0.00 35.94 1.98
404 410 6.896883 AGGTAAAACACTTTCTCCACTAACT 58.103 36.000 0.00 0.00 0.00 2.24
444 450 1.131126 CTTTAGCATCACCACTTGCCG 59.869 52.381 0.00 0.00 39.72 5.69
446 452 0.036164 TAGCATCACCACTTGCCGTT 59.964 50.000 0.00 0.00 39.72 4.44
457 463 3.013921 CACTTGCCGTTTATACATGGGT 58.986 45.455 0.00 0.00 0.00 4.51
476 482 7.609532 ACATGGGTCTCTTTGAGATTTTAGAAG 59.390 37.037 0.00 0.00 40.98 2.85
519 3997 9.357652 CCCATTATGTTTAACATTTCAGTCAAG 57.642 33.333 16.08 0.00 39.88 3.02
708 4735 0.825425 TCTAGGAGCTCCGCATCCAG 60.825 60.000 26.95 16.76 42.08 3.86
788 4815 1.818060 CACTGTGAGAGCTCTAGCACT 59.182 52.381 26.84 12.23 44.44 4.40
920 4953 1.221840 CAACCGCCTAGGCACTGAT 59.778 57.895 32.47 12.69 46.52 2.90
921 4954 0.811616 CAACCGCCTAGGCACTGATC 60.812 60.000 32.47 2.22 46.52 2.92
922 4955 1.264749 AACCGCCTAGGCACTGATCA 61.265 55.000 32.47 0.00 46.52 2.92
993 5026 1.605058 ATTAGGTCGACGCTGGCTGT 61.605 55.000 9.92 0.00 0.00 4.40
994 5027 2.209064 TTAGGTCGACGCTGGCTGTC 62.209 60.000 9.92 7.22 0.00 3.51
1009 5042 1.306911 TGTCCTGGGATGCCTAGCA 60.307 57.895 4.35 0.00 44.86 3.49
1130 5163 3.752796 GCACGGCCACTATAGACAA 57.247 52.632 6.78 0.00 0.00 3.18
1208 5241 2.283604 TAGCGGACAGTCCAGGCA 60.284 61.111 20.13 4.35 35.91 4.75
1209 5242 1.685765 TAGCGGACAGTCCAGGCAT 60.686 57.895 20.13 8.15 35.91 4.40
1272 5305 1.868251 CGAACTCGTGGCGCTCTAC 60.868 63.158 7.64 3.48 34.11 2.59
1334 5367 1.899814 GAGATCCGGTATGTATGGCCA 59.100 52.381 8.56 8.56 0.00 5.36
1335 5368 2.301870 GAGATCCGGTATGTATGGCCAA 59.698 50.000 10.96 0.00 0.00 4.52
1352 5385 1.302033 AAGCCACCGTGCTCTTCAG 60.302 57.895 0.00 0.00 41.80 3.02
1398 5437 6.367969 ACGTCTAACTTTTTATGCGTGAGATT 59.632 34.615 0.00 0.00 30.90 2.40
1472 5511 4.831307 CGCCCGTTCTCCGACGAG 62.831 72.222 0.00 0.00 45.47 4.18
1717 5756 3.095278 CGACGTCGTTGGTCACCG 61.095 66.667 29.08 0.11 34.04 4.94
1874 5913 4.352009 TGTTCCCCGGTGAGTAACTTATA 58.648 43.478 0.00 0.00 0.00 0.98
1883 5922 8.191446 CCCGGTGAGTAACTTATATATCATCAG 58.809 40.741 0.00 0.00 0.00 2.90
1884 5923 8.740906 CCGGTGAGTAACTTATATATCATCAGT 58.259 37.037 0.00 0.00 0.00 3.41
1893 5932 9.645059 AACTTATATATCATCAGTTCATCACCG 57.355 33.333 0.00 0.00 0.00 4.94
1910 5949 2.592864 GTCACCACCACCACCACA 59.407 61.111 0.00 0.00 0.00 4.17
2195 6276 3.436761 CCAAACACCCCTTTAGTACCCAA 60.437 47.826 0.00 0.00 0.00 4.12
2196 6277 3.513909 AACACCCCTTTAGTACCCAAC 57.486 47.619 0.00 0.00 0.00 3.77
2197 6278 2.420705 ACACCCCTTTAGTACCCAACA 58.579 47.619 0.00 0.00 0.00 3.33
2198 6279 2.990998 ACACCCCTTTAGTACCCAACAT 59.009 45.455 0.00 0.00 0.00 2.71
2199 6280 3.399983 ACACCCCTTTAGTACCCAACATT 59.600 43.478 0.00 0.00 0.00 2.71
2200 6281 4.140876 ACACCCCTTTAGTACCCAACATTT 60.141 41.667 0.00 0.00 0.00 2.32
2201 6282 4.836175 CACCCCTTTAGTACCCAACATTTT 59.164 41.667 0.00 0.00 0.00 1.82
2202 6283 5.305902 CACCCCTTTAGTACCCAACATTTTT 59.694 40.000 0.00 0.00 0.00 1.94
2354 6435 4.592426 AAGCGAAGGCGAAGTACC 57.408 55.556 0.00 0.00 46.35 3.34
2355 6436 1.079336 AAGCGAAGGCGAAGTACCC 60.079 57.895 0.00 0.00 46.35 3.69
2356 6437 1.823169 AAGCGAAGGCGAAGTACCCA 61.823 55.000 0.00 0.00 46.35 4.51
2376 6457 5.046663 ACCCAACATTTTATAGGGCAAACAG 60.047 40.000 0.00 0.00 43.47 3.16
2391 6473 4.441356 GGCAAACAGAAACAATCCTTCACA 60.441 41.667 0.00 0.00 0.00 3.58
2405 6487 5.512942 TCCTTCACACCCATTAAGATTGA 57.487 39.130 0.00 0.00 0.00 2.57
2439 6522 2.963498 AAAGAAAACTAGGCGAACGC 57.037 45.000 10.81 10.81 41.06 4.84
2440 6523 1.873698 AAGAAAACTAGGCGAACGCA 58.126 45.000 20.16 0.44 44.11 5.24
2441 6524 1.429463 AGAAAACTAGGCGAACGCAG 58.571 50.000 20.16 12.33 44.11 5.18
2443 6526 1.796459 GAAAACTAGGCGAACGCAGAA 59.204 47.619 20.16 4.63 44.11 3.02
2444 6527 2.094762 AAACTAGGCGAACGCAGAAT 57.905 45.000 20.16 6.18 44.11 2.40
2456 6543 7.904489 GCGAACGCAGAATGGTAATGTTACC 62.904 48.000 14.26 13.75 45.58 2.85
2474 6561 0.461548 CCTAGCTGACATTCGCTGGA 59.538 55.000 0.00 0.00 36.95 3.86
2498 6585 0.889186 GGGTGACAAGTGAACGCCAT 60.889 55.000 0.00 0.00 36.11 4.40
2499 6586 1.609580 GGGTGACAAGTGAACGCCATA 60.610 52.381 0.00 0.00 36.11 2.74
2500 6587 2.356135 GGTGACAAGTGAACGCCATAT 58.644 47.619 0.00 0.00 34.76 1.78
2501 6588 2.747446 GGTGACAAGTGAACGCCATATT 59.253 45.455 0.00 0.00 34.76 1.28
2502 6589 3.936453 GGTGACAAGTGAACGCCATATTA 59.064 43.478 0.00 0.00 34.76 0.98
2503 6590 4.574828 GGTGACAAGTGAACGCCATATTAT 59.425 41.667 0.00 0.00 34.76 1.28
2504 6591 5.501715 GTGACAAGTGAACGCCATATTATG 58.498 41.667 0.00 0.00 0.00 1.90
2505 6592 5.064707 GTGACAAGTGAACGCCATATTATGT 59.935 40.000 3.10 0.00 0.00 2.29
2506 6593 5.064579 TGACAAGTGAACGCCATATTATGTG 59.935 40.000 3.10 0.00 0.00 3.21
2507 6594 5.182487 ACAAGTGAACGCCATATTATGTGA 58.818 37.500 3.10 0.00 0.00 3.58
2508 6595 5.645929 ACAAGTGAACGCCATATTATGTGAA 59.354 36.000 3.10 0.00 0.00 3.18
2509 6596 5.734855 AGTGAACGCCATATTATGTGAAC 57.265 39.130 3.10 0.00 0.00 3.18
2515 6602 3.682377 CGCCATATTATGTGAACGCCATA 59.318 43.478 3.10 0.00 0.00 2.74
2522 6609 5.922739 TTATGTGAACGCCATATGATGAC 57.077 39.130 3.65 0.00 0.00 3.06
2537 6624 8.896744 CCATATGATGACAGTTTTAGTTGTGAT 58.103 33.333 3.65 0.00 0.00 3.06
2550 6637 9.515020 GTTTTAGTTGTGATGAAAGATCAAACA 57.485 29.630 0.00 0.00 39.49 2.83
2551 6638 9.734620 TTTTAGTTGTGATGAAAGATCAAACAG 57.265 29.630 0.00 0.00 39.49 3.16
2585 6672 5.712152 AAACGAAAAATGCCTTCTCTGAT 57.288 34.783 0.00 0.00 0.00 2.90
2590 6677 6.071728 ACGAAAAATGCCTTCTCTGATGAAAT 60.072 34.615 0.00 0.00 0.00 2.17
2593 6680 4.650754 ATGCCTTCTCTGATGAAATTGC 57.349 40.909 0.00 0.00 0.00 3.56
2600 6687 3.624410 TCTCTGATGAAATTGCCATGTCG 59.376 43.478 0.00 0.00 0.00 4.35
2602 6689 1.134753 TGATGAAATTGCCATGTCGCC 59.865 47.619 0.00 0.00 0.00 5.54
2603 6690 1.134753 GATGAAATTGCCATGTCGCCA 59.865 47.619 0.00 0.00 0.00 5.69
2604 6691 0.964700 TGAAATTGCCATGTCGCCAA 59.035 45.000 0.00 0.00 0.00 4.52
2605 6692 1.336702 TGAAATTGCCATGTCGCCAAC 60.337 47.619 0.00 0.00 0.00 3.77
2606 6693 0.968405 AAATTGCCATGTCGCCAACT 59.032 45.000 0.00 0.00 0.00 3.16
2607 6694 0.244450 AATTGCCATGTCGCCAACTG 59.756 50.000 0.00 0.00 0.00 3.16
2609 6696 1.106351 TTGCCATGTCGCCAACTGTT 61.106 50.000 0.00 0.00 0.00 3.16
2618 6712 1.377987 GCCAACTGTTATCCCCGCA 60.378 57.895 0.00 0.00 0.00 5.69
2665 6759 1.593265 CAAATGCCACCCTTCCTGC 59.407 57.895 0.00 0.00 0.00 4.85
2666 6760 0.901580 CAAATGCCACCCTTCCTGCT 60.902 55.000 0.00 0.00 0.00 4.24
2672 6766 2.032681 ACCCTTCCTGCTGAACGC 59.967 61.111 0.00 0.00 39.77 4.84
2710 6812 4.998672 CGTCCTAACAGAATTGGGTAAACA 59.001 41.667 0.00 0.00 0.00 2.83
2711 6813 5.106830 CGTCCTAACAGAATTGGGTAAACAC 60.107 44.000 0.00 0.00 0.00 3.32
2712 6814 5.766174 GTCCTAACAGAATTGGGTAAACACA 59.234 40.000 0.00 0.00 0.00 3.72
2713 6815 6.433093 GTCCTAACAGAATTGGGTAAACACAT 59.567 38.462 0.00 0.00 0.00 3.21
2714 6816 7.007723 TCCTAACAGAATTGGGTAAACACATT 58.992 34.615 0.00 0.00 0.00 2.71
2715 6817 7.040062 TCCTAACAGAATTGGGTAAACACATTG 60.040 37.037 0.00 0.00 0.00 2.82
2716 6818 6.478512 AACAGAATTGGGTAAACACATTGT 57.521 33.333 0.00 0.00 0.00 2.71
2717 6819 6.084326 ACAGAATTGGGTAAACACATTGTC 57.916 37.500 0.00 0.00 0.00 3.18
2727 6830 4.751767 AAACACATTGTCCCACAACATT 57.248 36.364 0.00 0.00 41.40 2.71
2739 6842 2.481104 CCACAACATTTTTCGCCACACT 60.481 45.455 0.00 0.00 0.00 3.55
2757 6860 2.230994 CTGCTAACTCCAGCGAGCCA 62.231 60.000 0.00 0.00 44.88 4.75
2787 6890 2.928988 ATCGACCATCTCTCCGCCCA 62.929 60.000 0.00 0.00 0.00 5.36
2793 6896 2.739996 ATCTCTCCGCCCAAGCCTG 61.740 63.158 0.00 0.00 34.57 4.85
2813 6916 3.227276 CCCATCGCCGCTACCTCT 61.227 66.667 0.00 0.00 0.00 3.69
2815 6918 2.490148 CCATCGCCGCTACCTCTCA 61.490 63.158 0.00 0.00 0.00 3.27
2830 6933 2.838286 CTCAACACTGAGCCAGAGC 58.162 57.895 8.91 0.00 42.66 4.09
2831 6934 0.673022 CTCAACACTGAGCCAGAGCC 60.673 60.000 8.91 0.00 42.66 4.70
2832 6935 1.071987 CAACACTGAGCCAGAGCCA 59.928 57.895 8.91 0.00 41.25 4.75
2833 6936 0.954449 CAACACTGAGCCAGAGCCAG 60.954 60.000 8.91 0.00 41.25 4.85
2850 6953 2.435586 GTGCTCATGGCTGTCGCT 60.436 61.111 7.54 0.00 42.39 4.93
2892 7594 0.850100 TTTTGAGCCTCCTCCCACAA 59.150 50.000 0.00 0.00 37.29 3.33
2894 7596 1.779061 TTGAGCCTCCTCCCACAACC 61.779 60.000 0.00 0.00 37.29 3.77
2909 7611 2.890766 AACCCGAGGCACATTCCGT 61.891 57.895 0.00 0.00 0.00 4.69
2931 7633 2.259204 CTTACGCCGTCACCCGAA 59.741 61.111 0.00 0.00 39.56 4.30
2941 7643 3.039588 CACCCGAACCGAACCACG 61.040 66.667 0.00 0.00 42.18 4.94
2961 7663 0.601046 GCCATGATCATCGCCGAGAA 60.601 55.000 13.75 0.00 0.00 2.87
2963 7665 1.730612 CCATGATCATCGCCGAGAATG 59.269 52.381 4.86 0.00 0.00 2.67
2970 7672 1.265095 CATCGCCGAGAATGGGAATTG 59.735 52.381 0.00 0.00 35.02 2.32
2971 7673 0.463654 TCGCCGAGAATGGGAATTGG 60.464 55.000 0.00 0.00 35.02 3.16
3205 7908 2.610694 CGCACTCACTGGCCTTGTG 61.611 63.158 19.01 19.01 36.82 3.33
3208 7911 1.526917 ACTCACTGGCCTTGTGCAC 60.527 57.895 19.89 10.75 43.89 4.57
3209 7912 2.591429 TCACTGGCCTTGTGCACG 60.591 61.111 19.89 0.00 43.89 5.34
3220 7923 2.095314 CCTTGTGCACGCAATATGTTCA 60.095 45.455 13.13 0.00 0.00 3.18
3290 7993 7.563888 AGTGAAAGTGTAGTTTTTAGTTCCC 57.436 36.000 0.00 0.00 0.00 3.97
3291 7994 6.544931 AGTGAAAGTGTAGTTTTTAGTTCCCC 59.455 38.462 0.00 0.00 0.00 4.81
3292 7995 5.528320 TGAAAGTGTAGTTTTTAGTTCCCCG 59.472 40.000 0.00 0.00 0.00 5.73
3293 7996 3.405831 AGTGTAGTTTTTAGTTCCCCGC 58.594 45.455 0.00 0.00 0.00 6.13
3294 7997 3.140623 GTGTAGTTTTTAGTTCCCCGCA 58.859 45.455 0.00 0.00 0.00 5.69
3295 7998 3.565063 GTGTAGTTTTTAGTTCCCCGCAA 59.435 43.478 0.00 0.00 0.00 4.85
3296 7999 4.036616 GTGTAGTTTTTAGTTCCCCGCAAA 59.963 41.667 0.00 0.00 0.00 3.68
3297 8000 4.643784 TGTAGTTTTTAGTTCCCCGCAAAA 59.356 37.500 0.00 0.00 0.00 2.44
3298 8001 4.739587 AGTTTTTAGTTCCCCGCAAAAA 57.260 36.364 0.00 0.00 0.00 1.94
3340 8043 9.901172 AGTAGTGAAAGTATAGTTAAAATGGGG 57.099 33.333 0.00 0.00 0.00 4.96
3377 8141 4.455877 ACAAAAGAGGTGCGAATTAGAAGG 59.544 41.667 0.00 0.00 0.00 3.46
3378 8142 2.990066 AGAGGTGCGAATTAGAAGGG 57.010 50.000 0.00 0.00 0.00 3.95
3383 8170 3.756963 AGGTGCGAATTAGAAGGGAAAAC 59.243 43.478 0.00 0.00 0.00 2.43
3387 8174 4.019141 TGCGAATTAGAAGGGAAAACCCTA 60.019 41.667 8.30 0.00 39.63 3.53
3391 8178 6.483640 CGAATTAGAAGGGAAAACCCTAGATG 59.516 42.308 8.30 0.00 39.63 2.90
3534 8321 2.554272 CGGCCTTTTCGTCGGTTG 59.446 61.111 0.00 0.00 0.00 3.77
3579 8368 0.996462 TAAATGCCTCGCTCGAAACG 59.004 50.000 1.24 1.24 0.00 3.60
3669 8458 2.880719 TTTTGCCACGCACAGCACAC 62.881 55.000 0.00 0.00 38.71 3.82
3713 8502 3.558411 GCACGCTCAGTCCATCGC 61.558 66.667 0.00 0.00 0.00 4.58
3720 8509 2.653448 CAGTCCATCGCTCGCTCG 60.653 66.667 0.00 0.00 0.00 5.03
3940 8730 4.752514 GGTTGACGATCCCGATCC 57.247 61.111 0.00 0.00 39.50 3.36
3955 8746 3.587923 CCGATCCAGTTTTTACCGTGTA 58.412 45.455 0.00 0.00 0.00 2.90
3956 8747 3.615496 CCGATCCAGTTTTTACCGTGTAG 59.385 47.826 0.00 0.00 0.00 2.74
3957 8748 4.240096 CGATCCAGTTTTTACCGTGTAGT 58.760 43.478 0.00 0.00 0.00 2.73
3958 8749 5.401550 CGATCCAGTTTTTACCGTGTAGTA 58.598 41.667 0.00 0.00 0.00 1.82
3959 8750 5.514204 CGATCCAGTTTTTACCGTGTAGTAG 59.486 44.000 0.00 0.00 0.00 2.57
3991 8948 4.746115 AGTAATGTTTCGCTCGTGTGTTTA 59.254 37.500 0.00 0.00 0.00 2.01
3995 8952 4.911053 TGTTTCGCTCGTGTGTTTATTTT 58.089 34.783 0.00 0.00 0.00 1.82
4103 9060 2.818274 GAGGTGGCGGCCTTTACG 60.818 66.667 21.46 0.00 39.34 3.18
4279 9236 4.720273 ACTTACATAGATTTCCTCGGGGTT 59.280 41.667 0.00 0.00 0.00 4.11
4458 9446 4.748102 TGCCACTCTACTTGTTTTAACTCG 59.252 41.667 0.00 0.00 0.00 4.18
4488 9476 3.713858 TGAACATCAGCTTGTGTTTGG 57.286 42.857 13.15 0.00 38.57 3.28
4489 9477 3.286353 TGAACATCAGCTTGTGTTTGGA 58.714 40.909 13.15 0.00 38.57 3.53
4490 9478 3.698539 TGAACATCAGCTTGTGTTTGGAA 59.301 39.130 13.15 0.84 38.57 3.53
4491 9479 4.341806 TGAACATCAGCTTGTGTTTGGAAT 59.658 37.500 13.15 0.00 38.57 3.01
4492 9480 4.510038 ACATCAGCTTGTGTTTGGAATC 57.490 40.909 0.00 0.00 0.00 2.52
4493 9481 3.890756 ACATCAGCTTGTGTTTGGAATCA 59.109 39.130 0.00 0.00 0.00 2.57
4494 9482 4.341806 ACATCAGCTTGTGTTTGGAATCAA 59.658 37.500 0.00 0.00 0.00 2.57
4495 9483 4.305989 TCAGCTTGTGTTTGGAATCAAC 57.694 40.909 0.00 0.00 31.78 3.18
4496 9484 3.068024 TCAGCTTGTGTTTGGAATCAACC 59.932 43.478 0.00 0.00 31.78 3.77
4497 9485 3.030291 AGCTTGTGTTTGGAATCAACCA 58.970 40.909 0.00 0.00 38.24 3.67
4498 9486 3.450457 AGCTTGTGTTTGGAATCAACCAA 59.550 39.130 0.00 0.00 46.44 3.67
4504 9492 6.623916 TGTGTTTGGAATCAACCAATCCACA 61.624 40.000 19.52 19.52 46.79 4.17
4505 9493 8.353282 TGTGTTTGGAATCAACCAATCCACAG 62.353 42.308 19.52 0.00 45.68 3.66
4506 9494 3.524095 TGGAATCAACCAATCCACAGT 57.476 42.857 0.00 0.00 38.30 3.55
4507 9495 3.843422 TGGAATCAACCAATCCACAGTT 58.157 40.909 0.00 0.00 38.30 3.16
4508 9496 3.826157 TGGAATCAACCAATCCACAGTTC 59.174 43.478 0.00 0.00 38.30 3.01
4509 9497 3.119849 GGAATCAACCAATCCACAGTTCG 60.120 47.826 0.00 0.00 33.30 3.95
4510 9498 1.234821 TCAACCAATCCACAGTTCGC 58.765 50.000 0.00 0.00 0.00 4.70
4511 9499 0.110238 CAACCAATCCACAGTTCGCG 60.110 55.000 0.00 0.00 0.00 5.87
4512 9500 1.234615 AACCAATCCACAGTTCGCGG 61.235 55.000 6.13 0.00 0.00 6.46
4513 9501 1.671054 CCAATCCACAGTTCGCGGT 60.671 57.895 6.13 0.00 0.00 5.68
4514 9502 1.497278 CAATCCACAGTTCGCGGTG 59.503 57.895 6.13 6.22 41.83 4.94
4518 9506 2.738521 CACAGTTCGCGGTGGAGG 60.739 66.667 6.13 0.00 39.17 4.30
4519 9507 2.915659 ACAGTTCGCGGTGGAGGA 60.916 61.111 6.13 0.00 0.00 3.71
4520 9508 2.283529 ACAGTTCGCGGTGGAGGAT 61.284 57.895 6.13 0.00 0.00 3.24
4521 9509 1.811266 CAGTTCGCGGTGGAGGATG 60.811 63.158 6.13 0.00 0.00 3.51
4522 9510 2.511600 GTTCGCGGTGGAGGATGG 60.512 66.667 6.13 0.00 0.00 3.51
4523 9511 2.682136 TTCGCGGTGGAGGATGGA 60.682 61.111 6.13 0.00 0.00 3.41
4524 9512 2.287274 TTCGCGGTGGAGGATGGAA 61.287 57.895 6.13 0.00 0.00 3.53
4525 9513 1.832719 TTCGCGGTGGAGGATGGAAA 61.833 55.000 6.13 0.00 0.00 3.13
4526 9514 2.106683 CGCGGTGGAGGATGGAAAC 61.107 63.158 0.00 0.00 0.00 2.78
4527 9515 1.299976 GCGGTGGAGGATGGAAACT 59.700 57.895 0.00 0.00 0.00 2.66
4528 9516 1.026718 GCGGTGGAGGATGGAAACTG 61.027 60.000 0.00 0.00 0.00 3.16
4529 9517 1.026718 CGGTGGAGGATGGAAACTGC 61.027 60.000 0.00 0.00 0.00 4.40
4530 9518 0.329596 GGTGGAGGATGGAAACTGCT 59.670 55.000 0.00 0.00 0.00 4.24
4531 9519 1.457346 GTGGAGGATGGAAACTGCTG 58.543 55.000 0.00 0.00 0.00 4.41
4532 9520 1.003580 GTGGAGGATGGAAACTGCTGA 59.996 52.381 0.00 0.00 0.00 4.26
4533 9521 1.704628 TGGAGGATGGAAACTGCTGAA 59.295 47.619 0.00 0.00 0.00 3.02
4534 9522 2.290514 TGGAGGATGGAAACTGCTGAAG 60.291 50.000 0.00 0.00 0.00 3.02
4535 9523 2.290577 GGAGGATGGAAACTGCTGAAGT 60.291 50.000 0.00 0.00 42.60 3.01
4542 9530 3.027419 AACTGCTGAAGTTCCCAGC 57.973 52.632 16.33 13.06 46.60 4.85
4546 9534 3.972227 CTGAAGTTCCCAGCACGG 58.028 61.111 0.00 0.00 0.00 4.94
4547 9535 1.371183 CTGAAGTTCCCAGCACGGA 59.629 57.895 0.00 0.00 36.56 4.69
4548 9536 0.036010 CTGAAGTTCCCAGCACGGAT 60.036 55.000 0.00 0.00 36.56 4.18
4549 9537 0.321564 TGAAGTTCCCAGCACGGATG 60.322 55.000 0.00 0.00 36.56 3.51
4550 9538 0.036388 GAAGTTCCCAGCACGGATGA 60.036 55.000 0.00 0.00 36.56 2.92
4551 9539 0.620556 AAGTTCCCAGCACGGATGAT 59.379 50.000 0.00 0.00 36.56 2.45
4552 9540 0.107508 AGTTCCCAGCACGGATGATG 60.108 55.000 0.00 0.00 42.12 3.07
4556 9544 2.512286 CAGCACGGATGATGGCGT 60.512 61.111 0.00 0.00 38.63 5.68
4557 9545 2.108514 CAGCACGGATGATGGCGTT 61.109 57.895 0.00 0.00 38.63 4.84
4558 9546 2.108514 AGCACGGATGATGGCGTTG 61.109 57.895 0.00 0.00 0.00 4.10
4559 9547 2.404789 CACGGATGATGGCGTTGC 59.595 61.111 0.00 0.00 0.00 4.17
4600 9588 3.771160 GACACGGTGGGCGATCCT 61.771 66.667 13.48 0.00 36.20 3.24
4664 9652 0.248289 GGTAAAGCTGCTCCGGTACA 59.752 55.000 1.00 0.00 0.00 2.90
4750 9738 2.819550 GTGGACACACGGACCAGT 59.180 61.111 0.00 0.00 37.94 4.00
4762 9750 1.198759 GGACCAGTGGAGGGCTTGTA 61.199 60.000 18.40 0.00 36.69 2.41
4763 9751 0.690762 GACCAGTGGAGGGCTTGTAA 59.309 55.000 18.40 0.00 32.29 2.41
4765 9753 1.710809 ACCAGTGGAGGGCTTGTAATT 59.289 47.619 18.40 0.00 0.00 1.40
4891 9879 4.980592 TGGAGAGGGGCTGTGGCA 62.981 66.667 0.00 0.00 40.87 4.92
4906 9894 1.497286 GTGGCAGGTGGGGGATTAATA 59.503 52.381 0.00 0.00 0.00 0.98
4972 9972 2.378634 CCACACCCCATCTCCTCCC 61.379 68.421 0.00 0.00 0.00 4.30
5013 10025 1.309950 GATGGTGGAGATCGACGAGA 58.690 55.000 3.01 0.00 0.00 4.04
5153 10165 0.757188 ATCTTCGAGGGGCTGACGAT 60.757 55.000 0.00 0.00 36.02 3.73
5199 10211 4.021925 GGAAGACGCAGGCACCCT 62.022 66.667 0.00 0.00 0.00 4.34
5286 10299 0.320374 TGGCGTTCACCTCTTTCGAT 59.680 50.000 0.00 0.00 0.00 3.59
5289 10302 2.416972 GGCGTTCACCTCTTTCGATACT 60.417 50.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.781196 CACCTGATGATCTCGAAAATTATGATT 58.219 33.333 0.00 0.00 0.00 2.57
47 48 2.028203 TGTGCACCTGATGATCTCGAAA 60.028 45.455 15.69 0.00 0.00 3.46
68 69 6.490381 TCCATAAGATCAATGAGTAGCTACGT 59.510 38.462 17.99 6.88 0.00 3.57
71 72 6.494835 TGCTCCATAAGATCAATGAGTAGCTA 59.505 38.462 19.02 0.00 31.41 3.32
73 74 5.545588 TGCTCCATAAGATCAATGAGTAGC 58.454 41.667 9.09 12.88 0.00 3.58
89 90 1.521764 TGGGTCCACATATGCTCCAT 58.478 50.000 1.58 0.00 0.00 3.41
175 176 7.958567 ACACGTAAATAACAAATGTTGATACCG 59.041 33.333 8.99 8.07 38.90 4.02
180 181 7.694886 TGTCACACGTAAATAACAAATGTTGA 58.305 30.769 8.99 0.00 38.90 3.18
201 202 4.242475 GTCCATCTTACACGTCAATGTCA 58.758 43.478 0.00 0.00 33.85 3.58
216 217 2.019249 CAAATCCATGCACGTCCATCT 58.981 47.619 0.00 0.00 0.00 2.90
241 242 3.452627 ACATACCTCAAATCCGAGCTCTT 59.547 43.478 12.85 0.00 0.00 2.85
246 252 2.158900 AGCCACATACCTCAAATCCGAG 60.159 50.000 0.00 0.00 0.00 4.63
247 253 1.837439 AGCCACATACCTCAAATCCGA 59.163 47.619 0.00 0.00 0.00 4.55
271 277 1.767759 GCCCCTCATATGTTGTGCTT 58.232 50.000 1.90 0.00 0.00 3.91
272 278 0.464373 CGCCCCTCATATGTTGTGCT 60.464 55.000 1.90 0.00 0.00 4.40
276 282 0.535102 GGACCGCCCCTCATATGTTG 60.535 60.000 1.90 0.00 0.00 3.33
327 333 0.099259 CGGTCAACTATACGTCCGCA 59.901 55.000 0.00 0.00 0.00 5.69
404 410 8.086522 GCTAAAGTTTACTCCCATATCGATACA 58.913 37.037 7.41 0.00 0.00 2.29
444 450 8.738645 AATCTCAAAGAGACCCATGTATAAAC 57.261 34.615 0.00 0.00 41.76 2.01
519 3997 7.280876 CCGGGGTAAAAAGTTAAGAAGGTATAC 59.719 40.741 0.00 0.00 0.00 1.47
731 4758 0.654683 CTAAATGCAGGAGTCGCAGC 59.345 55.000 0.00 0.00 43.88 5.25
788 4815 5.068067 GCTTTTCTTAACCCAAACCTACACA 59.932 40.000 0.00 0.00 0.00 3.72
912 4945 1.227380 CGGGCTAGTGATCAGTGCC 60.227 63.158 24.51 24.51 42.56 5.01
913 4946 1.884926 GCGGGCTAGTGATCAGTGC 60.885 63.158 13.54 13.48 0.00 4.40
920 4953 2.882876 GAACGAGCGGGCTAGTGA 59.117 61.111 7.19 0.00 32.42 3.41
921 4954 2.337749 ATCGAACGAGCGGGCTAGTG 62.338 60.000 7.19 0.00 32.42 2.74
922 4955 1.664321 AATCGAACGAGCGGGCTAGT 61.664 55.000 0.32 0.32 33.42 2.57
970 5003 1.467342 GCCAGCGTCGACCTAATTTTT 59.533 47.619 10.58 0.00 0.00 1.94
971 5004 1.084289 GCCAGCGTCGACCTAATTTT 58.916 50.000 10.58 0.00 0.00 1.82
972 5005 0.249398 AGCCAGCGTCGACCTAATTT 59.751 50.000 10.58 0.00 0.00 1.82
989 5022 1.449353 CTAGGCATCCCAGGACAGC 59.551 63.158 4.74 4.74 0.00 4.40
993 5026 2.434843 CGTGCTAGGCATCCCAGGA 61.435 63.158 0.00 0.00 41.91 3.86
994 5027 2.109799 CGTGCTAGGCATCCCAGG 59.890 66.667 0.00 0.00 41.91 4.45
995 5028 1.227380 GACGTGCTAGGCATCCCAG 60.227 63.158 0.00 0.00 41.91 4.45
1176 5209 1.143620 GCTACTGCTGCTCTCCTGG 59.856 63.158 0.00 0.00 36.03 4.45
1272 5305 3.646715 TTCCAGTTCTGGGGGCCG 61.647 66.667 17.37 0.00 0.00 6.13
1334 5367 1.302033 CTGAAGAGCACGGTGGCTT 60.302 57.895 10.60 0.00 45.99 4.35
1348 5381 7.706607 GTCATAGTGTTATGTACATGAGCTGAA 59.293 37.037 18.81 0.33 39.39 3.02
1352 5385 5.977725 ACGTCATAGTGTTATGTACATGAGC 59.022 40.000 18.81 8.61 39.39 4.26
1355 5388 8.955002 GTTAGACGTCATAGTGTTATGTACATG 58.045 37.037 19.50 0.35 39.39 3.21
1364 5397 8.440833 GCATAAAAAGTTAGACGTCATAGTGTT 58.559 33.333 19.50 6.36 0.00 3.32
1387 5426 1.833630 TCTTCCCTGAATCTCACGCAT 59.166 47.619 0.00 0.00 0.00 4.73
1398 5437 2.650116 GCCGACAGCTCTTCCCTGA 61.650 63.158 0.00 0.00 38.99 3.86
1472 5511 1.120795 CCATCAGCCTCTCCTCCTCC 61.121 65.000 0.00 0.00 0.00 4.30
1562 5601 1.133823 ACATGCCAGTGGTTCTTGACA 60.134 47.619 11.74 0.00 0.00 3.58
1717 5756 2.282462 CCAGGAGGTGGTTGTGGC 60.282 66.667 0.00 0.00 42.17 5.01
1755 5794 1.447314 CGTAGGGGTCCGCAAAGAC 60.447 63.158 8.89 0.06 35.95 3.01
1874 5913 5.292765 GTGACGGTGATGAACTGATGATAT 58.707 41.667 0.00 0.00 38.65 1.63
1883 5922 0.250124 TGGTGGTGACGGTGATGAAC 60.250 55.000 0.00 0.00 0.00 3.18
1884 5923 0.250124 GTGGTGGTGACGGTGATGAA 60.250 55.000 0.00 0.00 0.00 2.57
1885 5924 1.369692 GTGGTGGTGACGGTGATGA 59.630 57.895 0.00 0.00 0.00 2.92
1886 5925 1.671054 GGTGGTGGTGACGGTGATG 60.671 63.158 0.00 0.00 0.00 3.07
1887 5926 2.144078 TGGTGGTGGTGACGGTGAT 61.144 57.895 0.00 0.00 0.00 3.06
1888 5927 2.764547 TGGTGGTGGTGACGGTGA 60.765 61.111 0.00 0.00 0.00 4.02
1889 5928 2.590575 GTGGTGGTGGTGACGGTG 60.591 66.667 0.00 0.00 0.00 4.94
1890 5929 3.868985 GGTGGTGGTGGTGACGGT 61.869 66.667 0.00 0.00 0.00 4.83
1891 5930 3.867783 TGGTGGTGGTGGTGACGG 61.868 66.667 0.00 0.00 0.00 4.79
1892 5931 2.590575 GTGGTGGTGGTGGTGACG 60.591 66.667 0.00 0.00 0.00 4.35
1893 5932 1.077357 TTGTGGTGGTGGTGGTGAC 60.077 57.895 0.00 0.00 0.00 3.67
1910 5949 5.301298 AGAAAATCTACCGCCTCTATACGTT 59.699 40.000 0.00 0.00 0.00 3.99
2076 6126 7.398332 ACCCTCCTAAGAAAACGTAGAAATCTA 59.602 37.037 0.00 0.00 0.00 1.98
2144 6225 8.917414 AGTTAGATGCCTTATAATCCCAGATA 57.083 34.615 0.00 0.00 0.00 1.98
2146 6227 7.633018 AAGTTAGATGCCTTATAATCCCAGA 57.367 36.000 0.00 0.00 0.00 3.86
2156 6237 6.826741 GGTGTTTGGATAAGTTAGATGCCTTA 59.173 38.462 0.00 0.00 0.00 2.69
2337 6418 1.079336 GGGTACTTCGCCTTCGCTT 60.079 57.895 0.00 0.00 35.26 4.68
2338 6419 1.823169 TTGGGTACTTCGCCTTCGCT 61.823 55.000 0.00 0.00 35.26 4.93
2339 6420 1.375013 TTGGGTACTTCGCCTTCGC 60.375 57.895 0.00 0.00 35.26 4.70
2340 6421 0.320073 TGTTGGGTACTTCGCCTTCG 60.320 55.000 0.00 0.00 0.00 3.79
2341 6422 2.109425 ATGTTGGGTACTTCGCCTTC 57.891 50.000 0.00 0.00 0.00 3.46
2342 6423 2.579410 AATGTTGGGTACTTCGCCTT 57.421 45.000 0.00 0.00 0.00 4.35
2343 6424 2.579410 AAATGTTGGGTACTTCGCCT 57.421 45.000 0.00 0.00 0.00 5.52
2344 6425 4.976224 ATAAAATGTTGGGTACTTCGCC 57.024 40.909 0.00 0.00 0.00 5.54
2345 6426 5.008316 CCCTATAAAATGTTGGGTACTTCGC 59.992 44.000 0.00 0.00 33.49 4.70
2346 6427 5.008316 GCCCTATAAAATGTTGGGTACTTCG 59.992 44.000 0.00 0.00 39.97 3.79
2347 6428 5.889289 TGCCCTATAAAATGTTGGGTACTTC 59.111 40.000 0.00 0.00 39.97 3.01
2348 6429 5.833340 TGCCCTATAAAATGTTGGGTACTT 58.167 37.500 0.00 0.00 39.97 2.24
2349 6430 5.459982 TGCCCTATAAAATGTTGGGTACT 57.540 39.130 0.00 0.00 39.97 2.73
2350 6431 6.071278 TGTTTGCCCTATAAAATGTTGGGTAC 60.071 38.462 0.00 0.00 39.97 3.34
2351 6432 6.017192 TGTTTGCCCTATAAAATGTTGGGTA 58.983 36.000 0.00 0.00 39.97 3.69
2352 6433 4.841246 TGTTTGCCCTATAAAATGTTGGGT 59.159 37.500 0.00 0.00 39.97 4.51
2353 6434 5.186797 TCTGTTTGCCCTATAAAATGTTGGG 59.813 40.000 0.00 0.00 40.74 4.12
2354 6435 6.279513 TCTGTTTGCCCTATAAAATGTTGG 57.720 37.500 0.00 0.00 0.00 3.77
2355 6436 7.655328 TGTTTCTGTTTGCCCTATAAAATGTTG 59.345 33.333 0.00 0.00 0.00 3.33
2356 6437 7.731054 TGTTTCTGTTTGCCCTATAAAATGTT 58.269 30.769 0.00 0.00 0.00 2.71
2376 6457 4.871933 AATGGGTGTGAAGGATTGTTTC 57.128 40.909 0.00 0.00 0.00 2.78
2391 6473 4.220602 GGTGTTTGCTCAATCTTAATGGGT 59.779 41.667 0.00 0.00 0.00 4.51
2456 6543 2.159184 TCTTCCAGCGAATGTCAGCTAG 60.159 50.000 0.00 0.00 42.52 3.42
2457 6544 1.824852 TCTTCCAGCGAATGTCAGCTA 59.175 47.619 0.00 0.00 42.52 3.32
2465 6552 0.909610 TCACCCCTCTTCCAGCGAAT 60.910 55.000 0.00 0.00 0.00 3.34
2468 6555 2.111999 TTGTCACCCCTCTTCCAGCG 62.112 60.000 0.00 0.00 0.00 5.18
2474 6561 1.202651 CGTTCACTTGTCACCCCTCTT 60.203 52.381 0.00 0.00 0.00 2.85
2498 6585 7.158021 TGTCATCATATGGCGTTCACATAATA 58.842 34.615 2.13 0.00 37.81 0.98
2499 6586 5.997129 TGTCATCATATGGCGTTCACATAAT 59.003 36.000 2.13 0.00 37.81 1.28
2500 6587 5.363939 TGTCATCATATGGCGTTCACATAA 58.636 37.500 2.13 0.00 37.81 1.90
2501 6588 4.954875 TGTCATCATATGGCGTTCACATA 58.045 39.130 2.13 0.00 37.81 2.29
2502 6589 3.807553 TGTCATCATATGGCGTTCACAT 58.192 40.909 2.13 0.00 37.81 3.21
2503 6590 3.197265 CTGTCATCATATGGCGTTCACA 58.803 45.455 2.13 0.00 37.81 3.58
2504 6591 3.198068 ACTGTCATCATATGGCGTTCAC 58.802 45.455 2.13 0.00 37.81 3.18
2505 6592 3.541996 ACTGTCATCATATGGCGTTCA 57.458 42.857 2.13 0.00 37.81 3.18
2506 6593 4.882671 AAACTGTCATCATATGGCGTTC 57.117 40.909 2.13 0.00 37.81 3.95
2507 6594 5.880332 ACTAAAACTGTCATCATATGGCGTT 59.120 36.000 2.13 0.00 37.81 4.84
2508 6595 5.428253 ACTAAAACTGTCATCATATGGCGT 58.572 37.500 2.13 0.00 37.81 5.68
2509 6596 5.991328 ACTAAAACTGTCATCATATGGCG 57.009 39.130 2.13 0.00 37.81 5.69
2515 6602 7.984422 TCATCACAACTAAAACTGTCATCAT 57.016 32.000 0.00 0.00 0.00 2.45
2522 6609 9.734620 TTTGATCTTTCATCACAACTAAAACTG 57.265 29.630 0.00 0.00 0.00 3.16
2537 6624 3.466836 ACTGTCGCTGTTTGATCTTTCA 58.533 40.909 0.00 0.00 0.00 2.69
2550 6637 6.507299 GCATTTTTCGTTTTAAAACTGTCGCT 60.507 34.615 24.57 6.80 36.77 4.93
2551 6638 5.610013 GCATTTTTCGTTTTAAAACTGTCGC 59.390 36.000 24.57 15.12 36.77 5.19
2593 6680 1.670811 GGATAACAGTTGGCGACATGG 59.329 52.381 7.78 0.00 42.32 3.66
2600 6687 1.377987 TGCGGGGATAACAGTTGGC 60.378 57.895 0.00 0.00 0.00 4.52
2602 6689 1.199097 GTTGTGCGGGGATAACAGTTG 59.801 52.381 0.00 0.00 0.00 3.16
2603 6690 1.073284 AGTTGTGCGGGGATAACAGTT 59.927 47.619 3.02 0.00 0.00 3.16
2604 6691 0.690762 AGTTGTGCGGGGATAACAGT 59.309 50.000 3.02 0.00 0.00 3.55
2605 6692 2.684001 TAGTTGTGCGGGGATAACAG 57.316 50.000 3.02 0.00 0.00 3.16
2606 6693 3.420300 TTTAGTTGTGCGGGGATAACA 57.580 42.857 3.02 0.00 0.00 2.41
2607 6694 4.769859 TTTTTAGTTGTGCGGGGATAAC 57.230 40.909 0.00 0.00 0.00 1.89
2609 6696 3.129638 GCATTTTTAGTTGTGCGGGGATA 59.870 43.478 0.00 0.00 0.00 2.59
2618 6712 7.430441 ACGTTTTAGATGGCATTTTTAGTTGT 58.570 30.769 0.00 0.00 0.00 3.32
2665 6759 0.647410 CATAACTGGCGAGCGTTCAG 59.353 55.000 0.00 11.56 34.91 3.02
2666 6760 0.245266 TCATAACTGGCGAGCGTTCA 59.755 50.000 0.00 0.00 0.00 3.18
2710 6812 4.367450 CGAAAAATGTTGTGGGACAATGT 58.633 39.130 0.00 0.00 44.16 2.71
2711 6813 3.184178 GCGAAAAATGTTGTGGGACAATG 59.816 43.478 0.00 0.00 44.16 2.82
2712 6814 3.389221 GCGAAAAATGTTGTGGGACAAT 58.611 40.909 0.00 0.00 44.16 2.71
2713 6815 2.482142 GGCGAAAAATGTTGTGGGACAA 60.482 45.455 0.00 0.00 44.16 3.18
2714 6816 1.067821 GGCGAAAAATGTTGTGGGACA 59.932 47.619 0.00 0.00 0.00 4.02
2715 6817 1.067821 TGGCGAAAAATGTTGTGGGAC 59.932 47.619 0.00 0.00 0.00 4.46
2716 6818 1.067821 GTGGCGAAAAATGTTGTGGGA 59.932 47.619 0.00 0.00 0.00 4.37
2717 6819 1.202463 TGTGGCGAAAAATGTTGTGGG 60.202 47.619 0.00 0.00 0.00 4.61
2727 6830 1.871039 GAGTTAGCAGTGTGGCGAAAA 59.129 47.619 0.00 0.00 39.27 2.29
2739 6842 1.617018 ATGGCTCGCTGGAGTTAGCA 61.617 55.000 0.00 0.00 43.87 3.49
2787 6890 4.496336 GGCGATGGGAGCAGGCTT 62.496 66.667 0.00 0.00 36.08 4.35
2793 6896 4.971125 GGTAGCGGCGATGGGAGC 62.971 72.222 12.98 0.00 0.00 4.70
2813 6916 1.372683 GGCTCTGGCTCAGTGTTGA 59.627 57.895 2.68 0.00 38.73 3.18
2815 6918 1.374190 CTGGCTCTGGCTCAGTGTT 59.626 57.895 2.68 0.00 38.73 3.32
2856 6959 2.864770 AAAGTTGGCGGTGGTTGGGT 62.865 55.000 0.00 0.00 0.00 4.51
2892 7594 3.319198 ACGGAATGTGCCTCGGGT 61.319 61.111 0.00 0.00 0.00 5.28
2920 7622 2.735857 GTTCGGTTCGGGTGACGG 60.736 66.667 0.00 0.00 44.45 4.79
2923 7625 2.422591 GTGGTTCGGTTCGGGTGA 59.577 61.111 0.00 0.00 0.00 4.02
2934 7636 0.947244 GATGATCATGGCCGTGGTTC 59.053 55.000 24.78 20.39 0.00 3.62
2945 7647 1.338484 CCCATTCTCGGCGATGATCAT 60.338 52.381 11.27 8.25 0.00 2.45
2946 7648 0.033920 CCCATTCTCGGCGATGATCA 59.966 55.000 11.27 0.00 0.00 2.92
3187 7889 2.281070 ACAAGGCCAGTGAGTGCG 60.281 61.111 5.01 0.00 0.00 5.34
3205 7908 3.419264 TCCATTGAACATATTGCGTGC 57.581 42.857 0.00 0.00 0.00 5.34
3208 7911 6.063640 TCTCATTCCATTGAACATATTGCG 57.936 37.500 0.00 0.00 32.13 4.85
3209 7912 9.784680 GATATCTCATTCCATTGAACATATTGC 57.215 33.333 0.00 0.00 32.13 3.56
3264 7967 9.281371 GGGAACTAAAAACTACACTTTCACTAT 57.719 33.333 0.00 0.00 0.00 2.12
3265 7968 7.716560 GGGGAACTAAAAACTACACTTTCACTA 59.283 37.037 0.00 0.00 0.00 2.74
3266 7969 6.544931 GGGGAACTAAAAACTACACTTTCACT 59.455 38.462 0.00 0.00 0.00 3.41
3267 7970 6.512253 CGGGGAACTAAAAACTACACTTTCAC 60.512 42.308 0.00 0.00 0.00 3.18
3268 7971 5.528320 CGGGGAACTAAAAACTACACTTTCA 59.472 40.000 0.00 0.00 0.00 2.69
3269 7972 5.561532 GCGGGGAACTAAAAACTACACTTTC 60.562 44.000 0.00 0.00 0.00 2.62
3270 7973 4.276678 GCGGGGAACTAAAAACTACACTTT 59.723 41.667 0.00 0.00 0.00 2.66
3271 7974 3.817084 GCGGGGAACTAAAAACTACACTT 59.183 43.478 0.00 0.00 0.00 3.16
3272 7975 3.181452 TGCGGGGAACTAAAAACTACACT 60.181 43.478 0.00 0.00 0.00 3.55
3273 7976 3.140623 TGCGGGGAACTAAAAACTACAC 58.859 45.455 0.00 0.00 0.00 2.90
3274 7977 3.488778 TGCGGGGAACTAAAAACTACA 57.511 42.857 0.00 0.00 0.00 2.74
3275 7978 4.834357 TTTGCGGGGAACTAAAAACTAC 57.166 40.909 0.00 0.00 0.00 2.73
3276 7979 5.848833 TTTTTGCGGGGAACTAAAAACTA 57.151 34.783 0.00 0.00 29.87 2.24
3277 7980 4.739587 TTTTTGCGGGGAACTAAAAACT 57.260 36.364 0.00 0.00 29.87 2.66
3315 8018 9.676861 ACCCCATTTTAACTATACTTTCACTAC 57.323 33.333 0.00 0.00 0.00 2.73
3346 8049 6.621316 TTCGCACCTCTTTTGTATGTAAAA 57.379 33.333 0.00 0.00 0.00 1.52
3347 8050 6.811253 ATTCGCACCTCTTTTGTATGTAAA 57.189 33.333 0.00 0.00 0.00 2.01
3377 8141 6.071896 CCTCAAAACTTCATCTAGGGTTTTCC 60.072 42.308 0.00 0.00 39.04 3.13
3378 8142 6.715264 TCCTCAAAACTTCATCTAGGGTTTTC 59.285 38.462 0.00 0.00 39.04 2.29
3383 8170 4.578105 GCATCCTCAAAACTTCATCTAGGG 59.422 45.833 0.00 0.00 0.00 3.53
3387 8174 4.699257 GTCAGCATCCTCAAAACTTCATCT 59.301 41.667 0.00 0.00 0.00 2.90
3391 8178 2.413371 GCGTCAGCATCCTCAAAACTTC 60.413 50.000 0.00 0.00 44.35 3.01
3583 8372 3.127533 GTCTCACGCCCACATGCC 61.128 66.667 0.00 0.00 0.00 4.40
3669 8458 2.202797 CGGGAGGATCACTGTGCG 60.203 66.667 2.12 0.00 35.27 5.34
3698 8487 2.492090 GAGCGATGGACTGAGCGT 59.508 61.111 0.00 0.00 34.34 5.07
3700 8489 2.959071 GCGAGCGATGGACTGAGC 60.959 66.667 0.00 0.00 0.00 4.26
3701 8490 1.299014 GAGCGAGCGATGGACTGAG 60.299 63.158 0.00 0.00 0.00 3.35
3702 8491 2.801421 GAGCGAGCGATGGACTGA 59.199 61.111 0.00 0.00 0.00 3.41
3703 8492 2.653448 CGAGCGAGCGATGGACTG 60.653 66.667 0.00 0.00 0.00 3.51
3704 8493 4.560856 GCGAGCGAGCGATGGACT 62.561 66.667 1.41 0.00 0.00 3.85
3933 8723 1.735571 CACGGTAAAAACTGGATCGGG 59.264 52.381 0.00 0.00 0.00 5.14
3940 8730 8.642020 GTTCATACTACTACACGGTAAAAACTG 58.358 37.037 0.00 0.00 0.00 3.16
3991 8948 1.538687 GCCCTGCAGCCAGACAAAAT 61.539 55.000 8.66 0.00 41.77 1.82
4122 9079 4.452733 CGCCGGTCCAACCTCCTC 62.453 72.222 1.90 0.00 35.66 3.71
4150 9107 2.306805 AGAGTTGAACCATGCCATCTCA 59.693 45.455 15.26 1.30 33.69 3.27
4160 9117 0.596600 GCGTCGTCAGAGTTGAACCA 60.597 55.000 0.00 0.00 34.49 3.67
4166 9123 1.148310 CCATTTGCGTCGTCAGAGTT 58.852 50.000 0.00 0.00 0.00 3.01
4260 9217 2.172717 CCAACCCCGAGGAAATCTATGT 59.827 50.000 0.00 0.00 36.73 2.29
4279 9236 2.297315 GTCTATCCATCATGTCGCTCCA 59.703 50.000 0.00 0.00 0.00 3.86
4394 9382 1.139853 AGAGCCAACATAGCTAGTGCC 59.860 52.381 0.00 0.00 41.75 5.01
4488 9476 3.670627 GCGAACTGTGGATTGGTTGATTC 60.671 47.826 0.00 0.00 0.00 2.52
4489 9477 2.228822 GCGAACTGTGGATTGGTTGATT 59.771 45.455 0.00 0.00 0.00 2.57
4490 9478 1.812571 GCGAACTGTGGATTGGTTGAT 59.187 47.619 0.00 0.00 0.00 2.57
4491 9479 1.234821 GCGAACTGTGGATTGGTTGA 58.765 50.000 0.00 0.00 0.00 3.18
4492 9480 0.110238 CGCGAACTGTGGATTGGTTG 60.110 55.000 0.00 0.00 0.00 3.77
4493 9481 2.244000 CGCGAACTGTGGATTGGTT 58.756 52.632 0.00 0.00 0.00 3.67
4494 9482 3.966215 CGCGAACTGTGGATTGGT 58.034 55.556 0.00 0.00 0.00 3.67
4501 9489 2.507110 ATCCTCCACCGCGAACTGTG 62.507 60.000 8.23 7.01 0.00 3.66
4502 9490 2.283529 ATCCTCCACCGCGAACTGT 61.284 57.895 8.23 0.00 0.00 3.55
4503 9491 1.811266 CATCCTCCACCGCGAACTG 60.811 63.158 8.23 0.00 0.00 3.16
4504 9492 2.579201 CATCCTCCACCGCGAACT 59.421 61.111 8.23 0.00 0.00 3.01
4505 9493 2.511600 CCATCCTCCACCGCGAAC 60.512 66.667 8.23 0.00 0.00 3.95
4506 9494 1.832719 TTTCCATCCTCCACCGCGAA 61.833 55.000 8.23 0.00 0.00 4.70
4507 9495 2.287274 TTTCCATCCTCCACCGCGA 61.287 57.895 8.23 0.00 0.00 5.87
4508 9496 2.106683 GTTTCCATCCTCCACCGCG 61.107 63.158 0.00 0.00 0.00 6.46
4509 9497 1.026718 CAGTTTCCATCCTCCACCGC 61.027 60.000 0.00 0.00 0.00 5.68
4510 9498 1.026718 GCAGTTTCCATCCTCCACCG 61.027 60.000 0.00 0.00 0.00 4.94
4511 9499 0.329596 AGCAGTTTCCATCCTCCACC 59.670 55.000 0.00 0.00 0.00 4.61
4512 9500 1.003580 TCAGCAGTTTCCATCCTCCAC 59.996 52.381 0.00 0.00 0.00 4.02
4513 9501 1.361204 TCAGCAGTTTCCATCCTCCA 58.639 50.000 0.00 0.00 0.00 3.86
4514 9502 2.290577 ACTTCAGCAGTTTCCATCCTCC 60.291 50.000 0.00 0.00 27.32 4.30
4515 9503 3.064900 ACTTCAGCAGTTTCCATCCTC 57.935 47.619 0.00 0.00 27.32 3.71
4516 9504 3.416156 GAACTTCAGCAGTTTCCATCCT 58.584 45.455 0.00 0.00 46.53 3.24
4517 9505 2.489722 GGAACTTCAGCAGTTTCCATCC 59.510 50.000 0.00 0.00 46.53 3.51
4518 9506 3.839051 GGAACTTCAGCAGTTTCCATC 57.161 47.619 0.00 0.00 46.53 3.51
4529 9517 0.036010 ATCCGTGCTGGGAACTTCAG 60.036 55.000 0.37 0.00 40.09 3.02
4530 9518 0.321564 CATCCGTGCTGGGAACTTCA 60.322 55.000 0.37 0.00 40.09 3.02
4531 9519 0.036388 TCATCCGTGCTGGGAACTTC 60.036 55.000 0.37 0.00 40.09 3.01
4532 9520 0.620556 ATCATCCGTGCTGGGAACTT 59.379 50.000 0.37 0.00 40.09 2.66
4533 9521 0.107508 CATCATCCGTGCTGGGAACT 60.108 55.000 0.37 0.00 40.09 3.01
4534 9522 1.097547 CCATCATCCGTGCTGGGAAC 61.098 60.000 0.37 0.00 40.09 3.62
4535 9523 1.224315 CCATCATCCGTGCTGGGAA 59.776 57.895 0.37 0.00 40.09 3.97
4536 9524 2.910360 CCATCATCCGTGCTGGGA 59.090 61.111 0.00 0.00 37.85 4.37
4537 9525 2.903855 GCCATCATCCGTGCTGGG 60.904 66.667 1.10 0.00 41.03 4.45
4538 9526 3.274586 CGCCATCATCCGTGCTGG 61.275 66.667 0.00 0.00 43.07 4.85
4539 9527 2.108514 AACGCCATCATCCGTGCTG 61.109 57.895 0.00 0.00 37.79 4.41
4540 9528 2.108514 CAACGCCATCATCCGTGCT 61.109 57.895 0.00 0.00 37.79 4.40
4541 9529 2.404789 CAACGCCATCATCCGTGC 59.595 61.111 0.00 0.00 37.79 5.34
4542 9530 2.404789 GCAACGCCATCATCCGTG 59.595 61.111 0.00 0.00 37.79 4.94
4554 9542 3.698463 GTGTCGTGTCGGGCAACG 61.698 66.667 0.00 0.00 46.11 4.10
4555 9543 3.698463 CGTGTCGTGTCGGGCAAC 61.698 66.667 0.00 0.00 0.00 4.17
4556 9544 4.210093 ACGTGTCGTGTCGGGCAA 62.210 61.111 0.00 0.00 39.18 4.52
4557 9545 4.634133 GACGTGTCGTGTCGGGCA 62.634 66.667 0.00 0.00 41.37 5.36
4558 9546 4.338539 AGACGTGTCGTGTCGGGC 62.339 66.667 0.00 0.00 41.37 6.13
4559 9547 2.126965 GAGACGTGTCGTGTCGGG 60.127 66.667 0.00 0.00 40.02 5.14
4565 9553 2.955402 GCCAGAGAGACGTGTCGT 59.045 61.111 7.10 0.00 45.10 4.34
4750 9738 3.281332 GGCAATTACAAGCCCTCCA 57.719 52.632 0.00 0.00 45.18 3.86
4762 9750 2.604382 GTGGCACCAGGGGCAATT 60.604 61.111 17.91 0.00 45.54 2.32
4884 9872 1.570857 TAATCCCCCACCTGCCACAG 61.571 60.000 0.00 0.00 0.00 3.66
4891 9879 3.204382 CACCAAGTATTAATCCCCCACCT 59.796 47.826 0.00 0.00 0.00 4.00
4906 9894 0.482446 TTGGGGCAATCTCACCAAGT 59.518 50.000 0.00 0.00 38.02 3.16
5013 10025 1.002430 TGCGAACCTCTGCATCTTCTT 59.998 47.619 0.00 0.00 35.90 2.52
5109 10121 2.029666 GCCTCCGCATACATCGCT 59.970 61.111 0.00 0.00 34.03 4.93
5110 10122 3.406361 CGCCTCCGCATACATCGC 61.406 66.667 0.00 0.00 34.03 4.58
5111 10123 2.734723 CCGCCTCCGCATACATCG 60.735 66.667 0.00 0.00 34.03 3.84
5153 10165 3.219928 GCGATCTCTCCTCCGCCA 61.220 66.667 0.00 0.00 41.59 5.69
5199 10211 1.483595 CCCACAGCAGAACCTCCAGA 61.484 60.000 0.00 0.00 0.00 3.86
5253 10265 2.116125 GCCACCCACTTCCTTGCT 59.884 61.111 0.00 0.00 0.00 3.91



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

AutoCloner maintained by Alex Coulton.