Multiple sequence alignment - TraesCS2B01G110300

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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 TraesCS2B01G110300 chr2B 100.000 4771 0 0 1 4771 71740392 71735622 0.000000e+00 8811.0
1 TraesCS2B01G110300 chr2B 93.394 439 20 5 1465 1896 72171632 72171196 4.030000e-180 641.0
2 TraesCS2B01G110300 chr2B 81.437 501 58 19 4278 4771 71696036 71695564 1.250000e-100 377.0
3 TraesCS2B01G110300 chr2B 78.858 473 38 29 935 1401 72172066 72171650 3.660000e-66 263.0
4 TraesCS2B01G110300 chr2B 77.297 370 60 15 4361 4727 71443586 71443238 3.770000e-46 196.0
5 TraesCS2B01G110300 chr2B 75.271 461 69 20 4295 4732 71532827 71532389 1.360000e-40 178.0
6 TraesCS2B01G110300 chr2B 76.389 360 51 23 4365 4715 71462307 71461973 3.820000e-36 163.0
7 TraesCS2B01G110300 chr2B 98.333 60 1 0 304 363 586239890 586239949 6.530000e-19 106.0
8 TraesCS2B01G110300 chr2B 95.312 64 1 2 304 365 104965827 104965764 3.040000e-17 100.0
9 TraesCS2B01G110300 chr2B 96.667 60 2 0 304 363 653603192 653603133 3.040000e-17 100.0
10 TraesCS2B01G110300 chr2D 89.694 3920 220 90 365 4216 44900154 44896351 0.000000e+00 4831.0
11 TraesCS2B01G110300 chr2D 88.566 551 35 13 4214 4754 44895725 44895193 1.120000e-180 643.0
12 TraesCS2B01G110300 chr2D 81.366 703 83 21 4061 4754 44891305 44890642 3.270000e-146 529.0
13 TraesCS2B01G110300 chr2D 82.709 561 49 11 4112 4671 44686591 44686078 5.630000e-124 455.0
14 TraesCS2B01G110300 chr2D 89.844 256 11 5 8 263 44900726 44900486 9.970000e-82 315.0
15 TraesCS2B01G110300 chr2D 80.241 415 40 12 4357 4771 44734096 44733724 1.690000e-69 274.0
16 TraesCS2B01G110300 chr2D 96.203 79 3 0 934 1012 45091168 45091090 3.870000e-26 130.0
17 TraesCS2B01G110300 chr2D 86.517 89 9 2 4683 4771 44686019 44685934 1.410000e-15 95.3
18 TraesCS2B01G110300 chr2D 81.915 94 5 4 1146 1227 45091015 45090922 8.570000e-08 69.4
19 TraesCS2B01G110300 chr2D 96.875 32 1 0 1848 1879 473171947 473171978 2.000000e-03 54.7
20 TraesCS2B01G110300 chr2A 93.630 2182 98 15 1352 3520 48658582 48660735 0.000000e+00 3221.0
21 TraesCS2B01G110300 chr2A 80.225 622 36 43 3668 4233 48660824 48661414 2.080000e-103 387.0
22 TraesCS2B01G110300 chr2A 81.336 509 62 18 4223 4724 48487789 48487307 2.690000e-102 383.0
23 TraesCS2B01G110300 chr2A 82.078 385 34 17 381 749 48785561 48785196 3.610000e-76 296.0
24 TraesCS2B01G110300 chr2A 75.163 612 77 32 4115 4697 48476249 48475684 8.040000e-53 219.0
25 TraesCS2B01G110300 chr2A 86.061 165 17 5 4493 4656 48494037 48493878 6.350000e-39 172.0
26 TraesCS2B01G110300 chr2A 83.708 178 14 10 1053 1225 48658298 48658465 2.300000e-33 154.0
27 TraesCS2B01G110300 chr2A 76.923 325 37 28 615 913 48657960 48658272 2.970000e-32 150.0
28 TraesCS2B01G110300 chr2A 83.673 147 11 7 116 251 48657619 48657763 5.010000e-25 126.0
29 TraesCS2B01G110300 chr2A 90.769 65 5 1 4168 4232 48661585 48661648 8.510000e-13 86.1
30 TraesCS2B01G110300 chr5A 93.428 1202 49 15 880 2062 376846296 376845106 0.000000e+00 1755.0
31 TraesCS2B01G110300 chr3A 92.909 832 42 9 1246 2062 435355491 435354662 0.000000e+00 1194.0
32 TraesCS2B01G110300 chr3A 95.906 342 7 4 880 1217 435355889 435355551 9.030000e-152 547.0
33 TraesCS2B01G110300 chr4D 79.980 1014 185 17 2138 3145 324894633 324895634 0.000000e+00 732.0
34 TraesCS2B01G110300 chr4A 79.614 1035 189 17 2143 3169 146727513 146726493 0.000000e+00 723.0
35 TraesCS2B01G110300 chr4B 79.467 1013 192 15 2138 3145 405053941 405054942 0.000000e+00 704.0
36 TraesCS2B01G110300 chr3B 80.360 555 49 24 1960 2497 797135216 797134705 2.710000e-97 366.0
37 TraesCS2B01G110300 chr3B 82.609 207 15 6 2173 2365 83312355 83312156 3.820000e-36 163.0
38 TraesCS2B01G110300 chr3B 96.721 61 2 0 304 364 167110083 167110143 8.450000e-18 102.0
39 TraesCS2B01G110300 chr3D 81.991 422 33 19 2047 2465 594157082 594156701 7.700000e-83 318.0
40 TraesCS2B01G110300 chr3D 98.276 58 1 0 2917 2974 126233188 126233245 8.450000e-18 102.0
41 TraesCS2B01G110300 chr5B 100.000 57 0 0 304 360 608625030 608624974 6.530000e-19 106.0
42 TraesCS2B01G110300 chr5B 100.000 57 0 0 304 360 653004832 653004776 6.530000e-19 106.0
43 TraesCS2B01G110300 chr7B 93.939 66 3 1 304 368 392644118 392644183 1.090000e-16 99.0
44 TraesCS2B01G110300 chr6B 95.238 63 2 1 304 365 164882971 164882909 1.090000e-16 99.0
45 TraesCS2B01G110300 chr1B 89.855 69 6 1 306 374 634288256 634288189 2.370000e-13 87.9
46 TraesCS2B01G110300 chr1D 100.000 29 0 0 1851 1879 22400425 22400453 2.000000e-03 54.7
47 TraesCS2B01G110300 chr1D 100.000 29 0 0 1851 1879 447336490 447336462 2.000000e-03 54.7
48 TraesCS2B01G110300 chr5D 100.000 28 0 0 1852 1879 330715183 330715156 9.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G110300 chr2B 71735622 71740392 4770 True 8811.00 8811 100.000000 1 4771 1 chr2B.!!$R5 4770
1 TraesCS2B01G110300 chr2B 72171196 72172066 870 True 452.00 641 86.126000 935 1896 2 chr2B.!!$R8 961
2 TraesCS2B01G110300 chr2D 44890642 44900726 10084 True 1579.50 4831 87.367500 8 4754 4 chr2D.!!$R3 4746
3 TraesCS2B01G110300 chr2D 44685934 44686591 657 True 275.15 455 84.613000 4112 4771 2 chr2D.!!$R2 659
4 TraesCS2B01G110300 chr2A 48657619 48661648 4029 False 687.35 3221 84.821333 116 4233 6 chr2A.!!$F1 4117
5 TraesCS2B01G110300 chr2A 48475684 48476249 565 True 219.00 219 75.163000 4115 4697 1 chr2A.!!$R1 582
6 TraesCS2B01G110300 chr5A 376845106 376846296 1190 True 1755.00 1755 93.428000 880 2062 1 chr5A.!!$R1 1182
7 TraesCS2B01G110300 chr3A 435354662 435355889 1227 True 870.50 1194 94.407500 880 2062 2 chr3A.!!$R1 1182
8 TraesCS2B01G110300 chr4D 324894633 324895634 1001 False 732.00 732 79.980000 2138 3145 1 chr4D.!!$F1 1007
9 TraesCS2B01G110300 chr4A 146726493 146727513 1020 True 723.00 723 79.614000 2143 3169 1 chr4A.!!$R1 1026
10 TraesCS2B01G110300 chr4B 405053941 405054942 1001 False 704.00 704 79.467000 2138 3145 1 chr4B.!!$F1 1007
11 TraesCS2B01G110300 chr3B 797134705 797135216 511 True 366.00 366 80.360000 1960 2497 1 chr3B.!!$R2 537

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
353 651 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.0 13.64 0.00 46.06 4.20 F
355 653 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.0 13.64 1.45 46.06 3.85 F
356 654 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.00 46.06 2.59 F
361 659 0.179936 CGGACGGAGGGAGTAGTACT 59.820 60.0 1.37 1.37 0.00 2.73 F
591 911 0.248289 GTACACCGTATGGGCACTGT 59.752 55.0 5.82 3.09 40.62 3.55 F
2128 2582 0.245539 GCAGTGCTGATTGCCATTGT 59.754 50.0 8.18 0.00 42.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1868 0.193069 ATCCCTCCTCCCTCATCAGG 59.807 60.000 0.00 0.00 39.98 3.86 R
1958 2406 0.319900 GTCGAAGCAGCAGAGGAACA 60.320 55.000 0.00 0.00 0.00 3.18 R
2050 2502 0.659957 GGCAATGGCGAGTGATTCTC 59.340 55.000 0.00 0.00 42.47 2.87 R
2128 2582 2.805671 CAAGTACCTGCACACGAATTGA 59.194 45.455 0.00 0.00 0.00 2.57 R
2328 2815 2.970974 GACGCCTGGCTGAACTTGC 61.971 63.158 17.92 0.00 0.00 4.01 R
3784 4285 0.037160 ACACAGAGGACATGCATGCA 59.963 50.000 26.53 25.04 0.00 3.96 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
33 34 3.498481 GGATGTTAGGCTGGATAATGGCA 60.498 47.826 0.00 0.00 0.00 4.92
86 87 2.813908 GTCGCCATGTGACCCGAC 60.814 66.667 4.42 0.00 42.39 4.79
87 88 4.077184 TCGCCATGTGACCCGACC 62.077 66.667 0.00 0.00 0.00 4.79
90 91 3.387091 CCATGTGACCCGACCCGA 61.387 66.667 0.00 0.00 0.00 5.14
91 92 2.125673 CATGTGACCCGACCCGAC 60.126 66.667 0.00 0.00 0.00 4.79
92 93 3.387947 ATGTGACCCGACCCGACC 61.388 66.667 0.00 0.00 0.00 4.79
116 117 3.989104 GATCGGTCGATCCAACCAT 57.011 52.632 19.21 5.19 43.71 3.55
117 118 1.784525 GATCGGTCGATCCAACCATC 58.215 55.000 19.21 9.33 43.71 3.51
118 119 0.393077 ATCGGTCGATCCAACCATCC 59.607 55.000 11.42 0.00 36.53 3.51
119 120 0.973496 TCGGTCGATCCAACCATCCA 60.973 55.000 11.42 0.00 36.53 3.41
120 121 0.810031 CGGTCGATCCAACCATCCAC 60.810 60.000 11.42 0.00 36.53 4.02
121 122 0.463833 GGTCGATCCAACCATCCACC 60.464 60.000 6.99 0.00 36.75 4.61
122 123 0.810031 GTCGATCCAACCATCCACCG 60.810 60.000 0.00 0.00 0.00 4.94
123 124 2.180204 CGATCCAACCATCCACCGC 61.180 63.158 0.00 0.00 0.00 5.68
124 125 2.124736 ATCCAACCATCCACCGCG 60.125 61.111 0.00 0.00 0.00 6.46
145 146 0.819582 CCTTCTCAAAATGCGCCCAT 59.180 50.000 4.18 0.00 0.00 4.00
203 214 2.485814 AGCTGGAAAGAAAAGACGCATC 59.514 45.455 0.00 0.00 0.00 3.91
235 246 1.141657 CACTGATGACGGGGATTGGAT 59.858 52.381 0.00 0.00 0.00 3.41
251 262 3.562567 TGGATTTTTCTTTTACCGCGG 57.437 42.857 26.86 26.86 0.00 6.46
256 267 0.606130 TTTCTTTTACCGCGGGGGAC 60.606 55.000 31.76 0.00 39.97 4.46
282 580 2.957491 TTTTTGCTAATGGCCGGATG 57.043 45.000 5.05 0.00 40.92 3.51
285 583 0.682532 TTGCTAATGGCCGGATGCAA 60.683 50.000 17.88 17.88 43.89 4.08
305 603 5.293324 TGCAATTTCGATTAGTACTTGCGAT 59.707 36.000 0.00 0.00 40.15 4.58
306 604 6.477360 TGCAATTTCGATTAGTACTTGCGATA 59.523 34.615 0.00 4.20 40.15 2.92
307 605 6.786103 GCAATTTCGATTAGTACTTGCGATAC 59.214 38.462 0.00 0.00 0.00 2.24
308 606 7.516155 GCAATTTCGATTAGTACTTGCGATACA 60.516 37.037 0.00 0.00 0.00 2.29
309 607 8.487970 CAATTTCGATTAGTACTTGCGATACAT 58.512 33.333 0.00 0.00 0.00 2.29
310 608 7.997107 TTTCGATTAGTACTTGCGATACATT 57.003 32.000 0.00 0.00 0.00 2.71
311 609 7.618964 TTCGATTAGTACTTGCGATACATTC 57.381 36.000 0.00 0.00 0.00 2.67
312 610 6.731164 TCGATTAGTACTTGCGATACATTCA 58.269 36.000 0.00 0.00 0.00 2.57
313 611 7.368059 TCGATTAGTACTTGCGATACATTCAT 58.632 34.615 0.00 0.00 0.00 2.57
314 612 7.865889 TCGATTAGTACTTGCGATACATTCATT 59.134 33.333 0.00 0.00 0.00 2.57
315 613 8.487970 CGATTAGTACTTGCGATACATTCATTT 58.512 33.333 0.00 0.00 0.00 2.32
318 616 7.609760 AGTACTTGCGATACATTCATTTTCA 57.390 32.000 0.00 0.00 0.00 2.69
319 617 8.213518 AGTACTTGCGATACATTCATTTTCAT 57.786 30.769 0.00 0.00 0.00 2.57
320 618 8.338259 AGTACTTGCGATACATTCATTTTCATC 58.662 33.333 0.00 0.00 0.00 2.92
321 619 6.498304 ACTTGCGATACATTCATTTTCATCC 58.502 36.000 0.00 0.00 0.00 3.51
322 620 6.095300 ACTTGCGATACATTCATTTTCATCCA 59.905 34.615 0.00 0.00 0.00 3.41
323 621 6.638096 TGCGATACATTCATTTTCATCCAT 57.362 33.333 0.00 0.00 0.00 3.41
324 622 7.041635 TGCGATACATTCATTTTCATCCATT 57.958 32.000 0.00 0.00 0.00 3.16
325 623 7.490840 TGCGATACATTCATTTTCATCCATTT 58.509 30.769 0.00 0.00 0.00 2.32
326 624 7.980662 TGCGATACATTCATTTTCATCCATTTT 59.019 29.630 0.00 0.00 0.00 1.82
327 625 8.270799 GCGATACATTCATTTTCATCCATTTTG 58.729 33.333 0.00 0.00 0.00 2.44
328 626 9.518906 CGATACATTCATTTTCATCCATTTTGA 57.481 29.630 0.00 0.00 0.00 2.69
342 640 8.469200 TCATCCATTTTGATGACAAGTAATTCC 58.531 33.333 0.00 0.00 44.65 3.01
343 641 6.851609 TCCATTTTGATGACAAGTAATTCCG 58.148 36.000 0.00 0.00 37.32 4.30
344 642 6.035843 CCATTTTGATGACAAGTAATTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
345 643 6.127758 CCATTTTGATGACAAGTAATTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
346 644 5.873179 TTTGATGACAAGTAATTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
347 645 3.517602 TGATGACAAGTAATTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
348 646 2.373540 TGACAAGTAATTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
349 647 1.894466 TGACAAGTAATTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
350 648 2.094390 TGACAAGTAATTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
351 649 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
352 650 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
353 651 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
354 652 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
355 653 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.000 13.64 1.45 46.06 3.85
356 654 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
357 655 0.467659 ATTCCGGACGGAGGGAGTAG 60.468 60.000 13.64 0.00 46.06 2.57
358 656 1.856539 TTCCGGACGGAGGGAGTAGT 61.857 60.000 13.64 0.00 46.06 2.73
359 657 0.982852 TCCGGACGGAGGGAGTAGTA 60.983 60.000 9.76 0.00 39.76 1.82
360 658 0.817229 CCGGACGGAGGGAGTAGTAC 60.817 65.000 4.40 0.00 37.50 2.73
361 659 0.179936 CGGACGGAGGGAGTAGTACT 59.820 60.000 1.37 1.37 0.00 2.73
362 660 1.414181 CGGACGGAGGGAGTAGTACTA 59.586 57.143 1.88 0.00 0.00 1.82
363 661 2.158900 CGGACGGAGGGAGTAGTACTAA 60.159 54.545 3.61 0.00 0.00 2.24
385 683 3.058160 GCTGGTGCTGTTGGCGAT 61.058 61.111 0.00 0.00 45.43 4.58
454 773 4.347453 GCAGGTTTGGCGCAGTGG 62.347 66.667 10.83 0.00 0.00 4.00
455 774 2.906897 CAGGTTTGGCGCAGTGGT 60.907 61.111 10.83 0.00 0.00 4.16
456 775 2.906897 AGGTTTGGCGCAGTGGTG 60.907 61.111 10.83 0.00 0.00 4.17
479 798 3.711086 CGTGAGGCGTAGTACTAGTAGA 58.289 50.000 1.87 0.00 35.54 2.59
480 799 3.489047 CGTGAGGCGTAGTACTAGTAGAC 59.511 52.174 1.87 3.94 35.54 2.59
481 800 4.437239 GTGAGGCGTAGTACTAGTAGACA 58.563 47.826 1.87 0.00 0.00 3.41
482 801 4.507388 GTGAGGCGTAGTACTAGTAGACAG 59.493 50.000 1.87 3.33 0.00 3.51
483 802 4.161189 TGAGGCGTAGTACTAGTAGACAGT 59.839 45.833 1.87 0.00 0.00 3.55
484 803 5.360999 TGAGGCGTAGTACTAGTAGACAGTA 59.639 44.000 1.87 0.00 0.00 2.74
567 887 0.958382 TGGCGGACAATTACAGTGCC 60.958 55.000 0.00 0.00 41.33 5.01
568 888 1.423845 GCGGACAATTACAGTGCCG 59.576 57.895 0.00 0.00 38.14 5.69
578 898 2.203972 TACAGTGCCGCGAGTACACC 62.204 60.000 8.23 0.00 37.07 4.16
580 900 4.712425 GTGCCGCGAGTACACCGT 62.712 66.667 8.23 0.00 32.10 4.83
582 902 2.409055 TGCCGCGAGTACACCGTAT 61.409 57.895 8.23 0.00 0.00 3.06
591 911 0.248289 GTACACCGTATGGGCACTGT 59.752 55.000 5.82 3.09 40.62 3.55
598 918 0.331616 GTATGGGCACTGTTCCCCTT 59.668 55.000 13.11 9.43 43.24 3.95
600 920 1.434513 ATGGGCACTGTTCCCCTTCA 61.435 55.000 13.11 0.00 43.24 3.02
602 922 1.966451 GGCACTGTTCCCCTTCACG 60.966 63.158 0.00 0.00 0.00 4.35
603 923 2.617274 GCACTGTTCCCCTTCACGC 61.617 63.158 0.00 0.00 0.00 5.34
604 924 1.071471 CACTGTTCCCCTTCACGCT 59.929 57.895 0.00 0.00 0.00 5.07
605 925 1.071471 ACTGTTCCCCTTCACGCTG 59.929 57.895 0.00 0.00 0.00 5.18
606 926 2.281484 TGTTCCCCTTCACGCTGC 60.281 61.111 0.00 0.00 0.00 5.25
608 928 3.565214 TTCCCCTTCACGCTGCCA 61.565 61.111 0.00 0.00 0.00 4.92
611 931 1.978617 CCCCTTCACGCTGCCAAAT 60.979 57.895 0.00 0.00 0.00 2.32
612 932 1.213537 CCCTTCACGCTGCCAAATG 59.786 57.895 0.00 0.00 0.00 2.32
622 947 2.034558 CGCTGCCAAATGGGGTAATTAG 59.965 50.000 0.90 0.00 37.04 1.73
624 949 3.068165 GCTGCCAAATGGGGTAATTAGAC 59.932 47.826 0.90 0.00 37.04 2.59
625 950 4.277476 CTGCCAAATGGGGTAATTAGACA 58.723 43.478 0.90 0.00 37.04 3.41
637 962 6.116126 GGGTAATTAGACACAGCAAATCTCT 58.884 40.000 0.00 0.00 0.00 3.10
638 963 6.258947 GGGTAATTAGACACAGCAAATCTCTC 59.741 42.308 0.00 0.00 0.00 3.20
641 966 0.723981 GACACAGCAAATCTCTCGCC 59.276 55.000 0.00 0.00 0.00 5.54
651 976 4.260948 GCAAATCTCTCGCCATAAAGGAAG 60.261 45.833 0.00 0.00 41.22 3.46
654 979 4.819105 TCTCTCGCCATAAAGGAAGAAA 57.181 40.909 0.00 0.00 41.22 2.52
695 1020 2.899838 GGGCACACGCAACACAGA 60.900 61.111 0.00 0.00 41.24 3.41
712 1051 3.053991 CACAGACCCTCTCTCTCCTCTTA 60.054 52.174 0.00 0.00 0.00 2.10
1066 1438 5.934402 CCCCCATATATATATACGCCTCC 57.066 47.826 4.54 0.00 0.00 4.30
1067 1439 5.590818 CCCCCATATATATATACGCCTCCT 58.409 45.833 4.54 0.00 0.00 3.69
1436 1868 5.357878 TGCTTCATTAATGTCCATTCTGGTC 59.642 40.000 14.97 0.00 39.03 4.02
1485 1918 3.069158 ACTCGTCTTTCTTTCCTCCGAAA 59.931 43.478 0.00 0.00 36.55 3.46
1498 1938 2.399611 CGAAATCTTGACGGCGGC 59.600 61.111 13.24 9.67 0.00 6.53
1505 1945 4.697756 TTGACGGCGGCTTGAGGG 62.698 66.667 16.45 0.00 0.00 4.30
1611 2053 1.446445 CAACGGGTACATCGGCGAA 60.446 57.895 15.93 0.00 0.00 4.70
1972 2420 1.537397 TCCCTGTTCCTCTGCTGCT 60.537 57.895 0.00 0.00 0.00 4.24
1980 2428 2.091112 CCTCTGCTGCTTCGACGTG 61.091 63.158 0.00 0.00 0.00 4.49
2021 2473 2.061578 TCGCCGGCCTATCCAAGAA 61.062 57.895 23.46 0.00 34.01 2.52
2028 2480 1.202545 GGCCTATCCAAGAACTCCGAC 60.203 57.143 0.00 0.00 34.01 4.79
2050 2502 0.818296 CGAGACCCAGTGGAGGTAAG 59.182 60.000 11.95 0.00 37.88 2.34
2128 2582 0.245539 GCAGTGCTGATTGCCATTGT 59.754 50.000 8.18 0.00 42.00 2.71
2407 2894 4.081030 CTGGCGCACGTGAAGCTG 62.081 66.667 27.19 19.21 0.00 4.24
2695 3185 4.899239 GCGATCCCCGACAGCCTG 62.899 72.222 0.00 0.00 41.76 4.85
3251 3741 4.170062 CGTCAGCGGCCATGCAAG 62.170 66.667 2.24 0.00 37.31 4.01
3254 3744 2.042259 TCAGCGGCCATGCAAGAAG 61.042 57.895 2.24 0.00 37.31 2.85
3269 3759 6.857777 TGCAAGAAGAAGAAGAAGAAGAAG 57.142 37.500 0.00 0.00 0.00 2.85
3295 3785 4.785453 GTGCCGGAGAGCCCCAAG 62.785 72.222 5.05 0.00 0.00 3.61
3334 3824 1.375396 CGAGAACATCCCGGTGCAA 60.375 57.895 0.00 0.00 0.00 4.08
3520 4010 4.432859 GCGATGAGCTGCTGATCA 57.567 55.556 24.99 14.09 43.13 2.92
3521 4011 1.222766 GGCGATGAGCTGCTGATCAG 61.223 60.000 24.99 18.84 42.19 2.90
3531 4021 3.786101 CTGATCAGCCGTCAACCG 58.214 61.111 10.38 0.00 0.00 4.44
3532 4022 1.079819 CTGATCAGCCGTCAACCGT 60.080 57.895 10.38 0.00 33.66 4.83
3533 4023 1.078759 CTGATCAGCCGTCAACCGTC 61.079 60.000 10.38 0.00 33.66 4.79
3534 4024 1.080093 GATCAGCCGTCAACCGTCA 60.080 57.895 0.00 0.00 33.66 4.35
3535 4025 0.669318 GATCAGCCGTCAACCGTCAA 60.669 55.000 0.00 0.00 33.66 3.18
3536 4026 0.949105 ATCAGCCGTCAACCGTCAAC 60.949 55.000 0.00 0.00 33.66 3.18
3537 4027 2.280592 AGCCGTCAACCGTCAACC 60.281 61.111 0.00 0.00 33.66 3.77
3541 4031 1.296056 CCGTCAACCGTCAACCATCC 61.296 60.000 0.00 0.00 33.66 3.51
3542 4032 1.623081 CGTCAACCGTCAACCATCCG 61.623 60.000 0.00 0.00 0.00 4.18
3544 4034 2.359478 AACCGTCAACCATCCGGC 60.359 61.111 0.00 0.00 45.49 6.13
3545 4035 4.752879 ACCGTCAACCATCCGGCG 62.753 66.667 0.00 0.00 45.49 6.46
3546 4036 4.444838 CCGTCAACCATCCGGCGA 62.445 66.667 9.30 0.00 34.62 5.54
3547 4037 2.202878 CGTCAACCATCCGGCGAT 60.203 61.111 9.30 0.00 34.57 4.58
3548 4038 2.525248 CGTCAACCATCCGGCGATG 61.525 63.158 9.30 10.36 44.80 3.84
3549 4039 2.513666 TCAACCATCCGGCGATGC 60.514 61.111 9.30 0.00 44.00 3.91
3550 4040 3.585990 CAACCATCCGGCGATGCC 61.586 66.667 9.30 0.00 44.00 4.40
3589 4079 2.727544 GCAAGCAGCGGGAAAACA 59.272 55.556 0.00 0.00 0.00 2.83
3607 4097 6.372937 GGAAAACAGAGAGGAAATTCGAAGAT 59.627 38.462 3.35 0.00 35.04 2.40
3611 4101 5.047021 ACAGAGAGGAAATTCGAAGATGTCA 60.047 40.000 3.35 0.00 35.04 3.58
3612 4102 6.047870 CAGAGAGGAAATTCGAAGATGTCAT 58.952 40.000 3.35 0.00 35.04 3.06
3613 4103 7.147828 ACAGAGAGGAAATTCGAAGATGTCATA 60.148 37.037 3.35 0.00 35.04 2.15
3620 4110 9.226345 GGAAATTCGAAGATGTCATATTCAAAC 57.774 33.333 17.90 5.20 35.04 2.93
3626 4116 6.747280 CGAAGATGTCATATTCAAACCCAAAC 59.253 38.462 17.90 0.00 31.12 2.93
3642 4132 2.005451 CAAACATTCGAGGAGCTGGAG 58.995 52.381 0.00 0.00 0.00 3.86
3643 4133 0.539051 AACATTCGAGGAGCTGGAGG 59.461 55.000 0.00 0.00 0.00 4.30
3644 4134 0.324738 ACATTCGAGGAGCTGGAGGA 60.325 55.000 0.00 0.00 0.00 3.71
3645 4135 0.103937 CATTCGAGGAGCTGGAGGAC 59.896 60.000 0.00 0.00 0.00 3.85
3653 4143 1.827399 GAGCTGGAGGACCGGTGAAA 61.827 60.000 14.63 0.00 43.99 2.69
3654 4144 1.671379 GCTGGAGGACCGGTGAAAC 60.671 63.158 14.63 0.00 43.99 2.78
3775 4276 6.549061 AGTAAAGTTTTGGTTTCGTCTTGAC 58.451 36.000 0.00 0.00 0.00 3.18
3779 4280 4.332819 AGTTTTGGTTTCGTCTTGACTCTG 59.667 41.667 0.00 0.00 0.00 3.35
3780 4281 3.812156 TTGGTTTCGTCTTGACTCTGA 57.188 42.857 0.00 0.00 0.00 3.27
3781 4282 4.336889 TTGGTTTCGTCTTGACTCTGAT 57.663 40.909 0.00 0.00 0.00 2.90
3783 4284 3.320826 TGGTTTCGTCTTGACTCTGATCA 59.679 43.478 0.00 0.00 0.00 2.92
3784 4285 4.021104 TGGTTTCGTCTTGACTCTGATCAT 60.021 41.667 0.00 0.00 0.00 2.45
3802 4306 1.065551 CATGCATGCATGTCCTCTGTG 59.934 52.381 40.30 21.81 46.20 3.66
3812 4318 1.067060 TGTCCTCTGTGTGTGAGTTCG 59.933 52.381 0.00 0.00 0.00 3.95
3875 4411 4.337060 TGGAGTGCACGACGACGG 62.337 66.667 12.01 1.93 44.46 4.79
3897 4433 4.567747 GGGCTGTTTATTCTTCCTCTTCCA 60.568 45.833 0.00 0.00 0.00 3.53
3935 4475 0.179004 TTCCGCTCTGCCTTTTCCAA 60.179 50.000 0.00 0.00 0.00 3.53
3962 4502 2.125391 GATGCTGGCTCAGACGCA 60.125 61.111 0.00 0.00 36.75 5.24
4064 4610 2.185238 GCGCTCGCCTCCTCTATAT 58.815 57.895 0.00 0.00 34.56 0.86
4068 4614 1.893210 GCTCGCCTCCTCTATATGGGT 60.893 57.143 0.00 0.00 0.00 4.51
4069 4615 2.620886 GCTCGCCTCCTCTATATGGGTA 60.621 54.545 0.00 0.00 0.00 3.69
4070 4616 3.018149 CTCGCCTCCTCTATATGGGTAC 58.982 54.545 0.00 0.00 0.00 3.34
4173 4724 5.816777 CACCTGTTTGTTTCCATGTGAAAAT 59.183 36.000 9.91 0.00 44.30 1.82
4201 4758 5.841957 AAATTTCAGTTCAAGACAGTGCT 57.158 34.783 0.00 0.00 0.00 4.40
4267 5452 5.972107 AATGAAGTCCAATGTTGAAGAGG 57.028 39.130 0.00 0.00 0.00 3.69
4271 5456 7.252612 TGAAGTCCAATGTTGAAGAGGTATA 57.747 36.000 0.00 0.00 0.00 1.47
4272 5457 7.861629 TGAAGTCCAATGTTGAAGAGGTATAT 58.138 34.615 0.00 0.00 0.00 0.86
4354 5544 3.933332 GCAGTTAGTTAGTGCCTTAGTGG 59.067 47.826 0.00 0.00 45.67 4.00
4355 5545 4.562963 GCAGTTAGTTAGTGCCTTAGTGGT 60.563 45.833 0.00 0.00 45.67 4.16
4356 5546 5.337009 GCAGTTAGTTAGTGCCTTAGTGGTA 60.337 44.000 0.00 0.00 45.67 3.25
4359 5549 4.803098 AGTTAGTGCCTTAGTGGTAGTG 57.197 45.455 0.00 0.00 35.63 2.74
4393 5585 0.764890 TCTGAAGAACACCACAGGGG 59.235 55.000 0.00 0.00 44.81 4.79
4449 5641 1.300931 TCTGCCGCTGACAGTTCAC 60.301 57.895 3.99 0.00 36.50 3.18
4456 5648 3.325870 CCGCTGACAGTTCACTAAATCA 58.674 45.455 3.99 0.00 0.00 2.57
4528 5745 6.248569 TGATCCCTTCCTATTGGTCTAAAC 57.751 41.667 0.00 0.00 34.23 2.01
4573 5791 3.072476 TGCCAGGGTATCCTATTAGCAAC 59.928 47.826 0.00 0.00 42.67 4.17
4604 5822 8.627403 CCTAATTTACTCGGTAAGTGAGATACA 58.373 37.037 0.00 0.00 39.11 2.29
4605 5823 9.666626 CTAATTTACTCGGTAAGTGAGATACAG 57.333 37.037 0.00 0.00 39.11 2.74
4606 5824 7.876936 ATTTACTCGGTAAGTGAGATACAGA 57.123 36.000 0.00 0.00 39.11 3.41
4607 5825 6.922247 TTACTCGGTAAGTGAGATACAGAG 57.078 41.667 10.79 10.79 45.31 3.35
4620 5838 6.377712 GTGAGATACAGAGTAGTACCAAACCT 59.622 42.308 0.00 0.00 0.00 3.50
4653 5872 1.349688 TCCGTGGTGAGGCTGTAAAAT 59.650 47.619 0.00 0.00 0.00 1.82
4669 5888 2.094762 AAATACGGTTGAGCGCTTCT 57.905 45.000 13.26 0.00 0.00 2.85
4726 5945 3.662247 GGATCCGATCCGTTCATACTT 57.338 47.619 11.76 0.00 40.13 2.24
4727 5946 4.778534 GGATCCGATCCGTTCATACTTA 57.221 45.455 11.76 0.00 40.13 2.24
4728 5947 5.130292 GGATCCGATCCGTTCATACTTAA 57.870 43.478 11.76 0.00 40.13 1.85
4729 5948 4.922103 GGATCCGATCCGTTCATACTTAAC 59.078 45.833 11.76 0.00 40.13 2.01
4730 5949 5.278858 GGATCCGATCCGTTCATACTTAACT 60.279 44.000 11.76 0.00 40.13 2.24
4731 5950 6.072286 GGATCCGATCCGTTCATACTTAACTA 60.072 42.308 11.76 0.00 40.13 2.24
4732 5951 6.309712 TCCGATCCGTTCATACTTAACTAG 57.690 41.667 0.00 0.00 0.00 2.57
4737 10557 7.519488 CGATCCGTTCATACTTAACTAGCACTA 60.519 40.741 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.120399 CAGCCTAACATCCGTAATAAACCA 58.880 41.667 0.00 0.00 0.00 3.67
1 2 4.514066 CCAGCCTAACATCCGTAATAAACC 59.486 45.833 0.00 0.00 0.00 3.27
2 3 5.362263 TCCAGCCTAACATCCGTAATAAAC 58.638 41.667 0.00 0.00 0.00 2.01
3 4 5.617528 TCCAGCCTAACATCCGTAATAAA 57.382 39.130 0.00 0.00 0.00 1.40
4 5 5.818678 ATCCAGCCTAACATCCGTAATAA 57.181 39.130 0.00 0.00 0.00 1.40
5 6 6.921486 TTATCCAGCCTAACATCCGTAATA 57.079 37.500 0.00 0.00 0.00 0.98
6 7 5.818678 TTATCCAGCCTAACATCCGTAAT 57.181 39.130 0.00 0.00 0.00 1.89
13 14 3.499202 CCTGCCATTATCCAGCCTAACAT 60.499 47.826 0.00 0.00 0.00 2.71
18 19 1.152368 GCCTGCCATTATCCAGCCT 59.848 57.895 0.00 0.00 0.00 4.58
115 116 4.162690 GAGAAGGGCGCGGTGGAT 62.163 66.667 8.83 0.00 0.00 3.41
117 118 4.697756 TTGAGAAGGGCGCGGTGG 62.698 66.667 8.83 0.00 0.00 4.61
118 119 1.586154 ATTTTGAGAAGGGCGCGGTG 61.586 55.000 8.83 0.00 0.00 4.94
119 120 1.303317 ATTTTGAGAAGGGCGCGGT 60.303 52.632 8.83 0.00 0.00 5.68
120 121 1.137404 CATTTTGAGAAGGGCGCGG 59.863 57.895 8.83 0.00 0.00 6.46
121 122 1.514873 GCATTTTGAGAAGGGCGCG 60.515 57.895 0.00 0.00 0.00 6.86
122 123 1.514873 CGCATTTTGAGAAGGGCGC 60.515 57.895 0.00 0.00 37.96 6.53
123 124 1.514873 GCGCATTTTGAGAAGGGCG 60.515 57.895 0.30 0.00 46.47 6.13
124 125 1.153765 GGCGCATTTTGAGAAGGGC 60.154 57.895 10.83 0.00 38.96 5.19
125 126 1.250154 TGGGCGCATTTTGAGAAGGG 61.250 55.000 10.83 0.00 0.00 3.95
203 214 3.047807 ATCAGTGGGCCGTGGATGG 62.048 63.158 0.00 0.00 0.00 3.51
235 246 0.960286 CCCCCGCGGTAAAAGAAAAA 59.040 50.000 26.12 0.00 0.00 1.94
263 274 1.134848 GCATCCGGCCATTAGCAAAAA 60.135 47.619 2.24 0.00 46.50 1.94
264 275 0.459489 GCATCCGGCCATTAGCAAAA 59.541 50.000 2.24 0.00 46.50 2.44
265 276 0.682532 TGCATCCGGCCATTAGCAAA 60.683 50.000 2.24 0.00 46.50 3.68
268 566 0.675633 AATTGCATCCGGCCATTAGC 59.324 50.000 2.24 1.29 43.89 3.09
275 573 2.290641 ACTAATCGAAATTGCATCCGGC 59.709 45.455 0.00 0.00 45.13 6.13
277 575 5.907197 AGTACTAATCGAAATTGCATCCG 57.093 39.130 0.00 0.00 0.00 4.18
282 580 5.138800 TCGCAAGTACTAATCGAAATTGC 57.861 39.130 8.69 8.69 38.48 3.56
285 583 8.589335 AATGTATCGCAAGTACTAATCGAAAT 57.411 30.769 14.92 8.74 39.48 2.17
317 615 7.433131 CGGAATTACTTGTCATCAAAATGGATG 59.567 37.037 0.00 0.00 44.78 3.51
318 616 7.416664 CCGGAATTACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
319 617 6.127758 CCGGAATTACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
320 618 6.035843 CCGGAATTACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
321 619 6.747280 GTCCGGAATTACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
322 620 6.403200 CGTCCGGAATTACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
323 621 5.106869 CGTCCGGAATTACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
324 622 4.390603 CGTCCGGAATTACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
325 623 3.930229 CGTCCGGAATTACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
326 624 3.517602 CGTCCGGAATTACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
327 625 2.864343 CCGTCCGGAATTACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
328 626 2.498481 TCCGTCCGGAATTACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
329 627 1.894466 TCCGTCCGGAATTACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
330 628 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
331 629 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
332 630 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
333 631 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
334 632 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
335 633 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
336 634 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
337 635 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
338 636 0.467659 CTACTCCCTCCGTCCGGAAT 60.468 60.000 5.23 0.00 44.66 3.01
339 637 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
340 638 0.982852 TACTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
341 639 0.817229 GTACTACTCCCTCCGTCCGG 60.817 65.000 0.00 0.00 0.00 5.14
342 640 0.179936 AGTACTACTCCCTCCGTCCG 59.820 60.000 0.00 0.00 0.00 4.79
343 641 3.567478 TTAGTACTACTCCCTCCGTCC 57.433 52.381 0.91 0.00 0.00 4.79
344 642 5.700373 CAGTATTAGTACTACTCCCTCCGTC 59.300 48.000 0.91 0.00 39.12 4.79
345 643 5.619220 CAGTATTAGTACTACTCCCTCCGT 58.381 45.833 0.91 0.00 39.12 4.69
346 644 4.455190 GCAGTATTAGTACTACTCCCTCCG 59.545 50.000 0.91 0.00 39.12 4.63
347 645 5.474189 CAGCAGTATTAGTACTACTCCCTCC 59.526 48.000 0.91 0.00 39.12 4.30
348 646 5.474189 CCAGCAGTATTAGTACTACTCCCTC 59.526 48.000 0.91 0.00 39.12 4.30
349 647 5.103601 ACCAGCAGTATTAGTACTACTCCCT 60.104 44.000 0.91 0.00 39.12 4.20
350 648 5.009811 CACCAGCAGTATTAGTACTACTCCC 59.990 48.000 0.91 0.00 39.12 4.30
351 649 5.507650 GCACCAGCAGTATTAGTACTACTCC 60.508 48.000 0.91 0.00 39.12 3.85
352 650 5.299782 AGCACCAGCAGTATTAGTACTACTC 59.700 44.000 0.91 0.00 45.49 2.59
353 651 5.067936 CAGCACCAGCAGTATTAGTACTACT 59.932 44.000 0.91 0.00 45.49 2.57
354 652 5.163540 ACAGCACCAGCAGTATTAGTACTAC 60.164 44.000 0.91 0.00 45.49 2.73
355 653 4.954202 ACAGCACCAGCAGTATTAGTACTA 59.046 41.667 0.00 0.00 45.49 1.82
356 654 3.769844 ACAGCACCAGCAGTATTAGTACT 59.230 43.478 0.00 0.00 45.49 2.73
357 655 4.124851 ACAGCACCAGCAGTATTAGTAC 57.875 45.455 0.00 0.00 45.49 2.73
358 656 4.503910 CAACAGCACCAGCAGTATTAGTA 58.496 43.478 0.00 0.00 45.49 1.82
359 657 3.338249 CAACAGCACCAGCAGTATTAGT 58.662 45.455 0.00 0.00 45.49 2.24
360 658 2.679837 CCAACAGCACCAGCAGTATTAG 59.320 50.000 0.00 0.00 45.49 1.73
361 659 2.710377 CCAACAGCACCAGCAGTATTA 58.290 47.619 0.00 0.00 45.49 0.98
362 660 1.538047 CCAACAGCACCAGCAGTATT 58.462 50.000 0.00 0.00 45.49 1.89
363 661 0.962356 GCCAACAGCACCAGCAGTAT 60.962 55.000 0.00 0.00 45.49 2.12
371 669 1.794222 GTACATCGCCAACAGCACC 59.206 57.895 0.00 0.00 44.04 5.01
385 683 1.874739 GCTGTTAACCAGTGCCGTACA 60.875 52.381 2.48 0.00 43.55 2.90
459 778 4.437239 TGTCTACTAGTACTACGCCTCAC 58.563 47.826 0.00 0.00 0.00 3.51
460 779 4.161189 ACTGTCTACTAGTACTACGCCTCA 59.839 45.833 0.00 0.00 0.00 3.86
461 780 4.692228 ACTGTCTACTAGTACTACGCCTC 58.308 47.826 0.00 0.00 0.00 4.70
462 781 4.751767 ACTGTCTACTAGTACTACGCCT 57.248 45.455 0.00 0.00 0.00 5.52
463 782 5.596845 ACTACTGTCTACTAGTACTACGCC 58.403 45.833 0.00 0.00 0.00 5.68
464 783 7.617533 GTACTACTGTCTACTAGTACTACGC 57.382 44.000 0.00 0.00 40.84 4.42
469 788 8.137437 CAGAGGAGTACTACTGTCTACTAGTAC 58.863 44.444 13.86 8.94 42.90 2.73
470 789 7.201902 GCAGAGGAGTACTACTGTCTACTAGTA 60.202 44.444 13.86 1.89 33.57 1.82
471 790 6.407299 GCAGAGGAGTACTACTGTCTACTAGT 60.407 46.154 13.86 0.00 33.57 2.57
472 791 5.987347 GCAGAGGAGTACTACTGTCTACTAG 59.013 48.000 13.86 0.00 33.57 2.57
473 792 5.451659 CGCAGAGGAGTACTACTGTCTACTA 60.452 48.000 13.86 0.00 33.57 1.82
474 793 4.681244 CGCAGAGGAGTACTACTGTCTACT 60.681 50.000 13.86 0.00 33.57 2.57
475 794 3.556775 CGCAGAGGAGTACTACTGTCTAC 59.443 52.174 13.86 0.00 33.57 2.59
476 795 3.431905 CCGCAGAGGAGTACTACTGTCTA 60.432 52.174 13.86 0.00 45.00 2.59
477 796 2.634600 CGCAGAGGAGTACTACTGTCT 58.365 52.381 13.86 1.02 33.57 3.41
478 797 1.671845 CCGCAGAGGAGTACTACTGTC 59.328 57.143 13.86 0.00 45.00 3.51
479 798 1.752683 CCGCAGAGGAGTACTACTGT 58.247 55.000 13.86 5.40 45.00 3.55
480 799 0.382515 GCCGCAGAGGAGTACTACTG 59.617 60.000 13.86 14.88 45.00 2.74
481 800 1.096386 CGCCGCAGAGGAGTACTACT 61.096 60.000 7.55 7.55 45.00 2.57
482 801 1.355916 CGCCGCAGAGGAGTACTAC 59.644 63.158 0.00 0.00 45.00 2.73
483 802 1.822613 CCGCCGCAGAGGAGTACTA 60.823 63.158 0.00 0.00 45.00 1.82
484 803 3.141488 CCGCCGCAGAGGAGTACT 61.141 66.667 0.00 0.00 45.00 2.73
510 830 2.033194 GTCCACGTGGGCTAACAGC 61.033 63.158 31.64 9.30 41.46 4.40
567 887 1.298863 CCCATACGGTGTACTCGCG 60.299 63.158 0.00 0.00 0.00 5.87
568 888 1.590792 GCCCATACGGTGTACTCGC 60.591 63.158 8.64 0.00 0.00 5.03
578 898 4.218722 GGGAACAGTGCCCATACG 57.781 61.111 12.63 0.00 45.31 3.06
591 911 2.632602 TTTGGCAGCGTGAAGGGGAA 62.633 55.000 0.00 0.00 0.00 3.97
598 918 2.130821 TACCCCATTTGGCAGCGTGA 62.131 55.000 0.00 0.00 0.00 4.35
600 920 0.324275 ATTACCCCATTTGGCAGCGT 60.324 50.000 0.00 0.00 0.00 5.07
602 922 3.068165 GTCTAATTACCCCATTTGGCAGC 59.932 47.826 0.00 0.00 0.00 5.25
603 923 4.097892 GTGTCTAATTACCCCATTTGGCAG 59.902 45.833 0.00 0.00 26.48 4.85
604 924 4.020543 GTGTCTAATTACCCCATTTGGCA 58.979 43.478 0.00 0.00 0.00 4.92
605 925 4.020543 TGTGTCTAATTACCCCATTTGGC 58.979 43.478 0.00 0.00 0.00 4.52
606 926 4.097892 GCTGTGTCTAATTACCCCATTTGG 59.902 45.833 0.00 0.00 0.00 3.28
608 928 4.929479 TGCTGTGTCTAATTACCCCATTT 58.071 39.130 0.00 0.00 0.00 2.32
611 931 4.374689 TTTGCTGTGTCTAATTACCCCA 57.625 40.909 0.00 0.00 0.00 4.96
612 932 5.193679 AGATTTGCTGTGTCTAATTACCCC 58.806 41.667 0.00 0.00 0.00 4.95
622 947 0.723981 GGCGAGAGATTTGCTGTGTC 59.276 55.000 0.00 0.00 36.37 3.67
624 949 1.376543 ATGGCGAGAGATTTGCTGTG 58.623 50.000 0.00 0.00 36.37 3.66
625 950 2.988010 TATGGCGAGAGATTTGCTGT 57.012 45.000 0.00 0.00 36.37 4.40
637 962 3.951680 GGGATTTTCTTCCTTTATGGCGA 59.048 43.478 0.00 0.00 35.97 5.54
638 963 3.068165 GGGGATTTTCTTCCTTTATGGCG 59.932 47.826 0.00 0.00 35.97 5.69
641 966 4.947388 TGACGGGGATTTTCTTCCTTTATG 59.053 41.667 0.00 0.00 35.97 1.90
651 976 2.939103 CTCAGTGATGACGGGGATTTTC 59.061 50.000 0.00 0.00 0.00 2.29
654 979 0.179000 GCTCAGTGATGACGGGGATT 59.821 55.000 0.00 0.00 0.00 3.01
724 1063 2.046507 CTGCTGCCCACCACTCTC 60.047 66.667 0.00 0.00 0.00 3.20
725 1064 3.644606 CCTGCTGCCCACCACTCT 61.645 66.667 0.00 0.00 0.00 3.24
726 1065 4.729918 CCCTGCTGCCCACCACTC 62.730 72.222 0.00 0.00 0.00 3.51
859 1221 2.892852 CTCCTTTTGTTGGATGCCTTGA 59.107 45.455 0.00 0.00 32.56 3.02
1057 1429 2.038557 GAGAGAGAGAGAGGAGGCGTAT 59.961 54.545 0.00 0.00 0.00 3.06
1058 1430 1.414919 GAGAGAGAGAGAGGAGGCGTA 59.585 57.143 0.00 0.00 0.00 4.42
1059 1431 0.180406 GAGAGAGAGAGAGGAGGCGT 59.820 60.000 0.00 0.00 0.00 5.68
1061 1433 2.576615 GAAGAGAGAGAGAGAGGAGGC 58.423 57.143 0.00 0.00 0.00 4.70
1064 1436 2.777692 GGAGGAAGAGAGAGAGAGAGGA 59.222 54.545 0.00 0.00 0.00 3.71
1065 1437 2.158608 GGGAGGAAGAGAGAGAGAGAGG 60.159 59.091 0.00 0.00 0.00 3.69
1066 1438 2.780010 AGGGAGGAAGAGAGAGAGAGAG 59.220 54.545 0.00 0.00 0.00 3.20
1067 1439 2.509548 CAGGGAGGAAGAGAGAGAGAGA 59.490 54.545 0.00 0.00 0.00 3.10
1257 1681 0.729140 CAAAGTCCAAATCGCGCCAC 60.729 55.000 0.00 0.00 0.00 5.01
1436 1868 0.193069 ATCCCTCCTCCCTCATCAGG 59.807 60.000 0.00 0.00 39.98 3.86
1485 1918 1.448540 CTCAAGCCGCCGTCAAGAT 60.449 57.895 0.00 0.00 0.00 2.40
1498 1938 2.367512 CCCCCTCCCTCCCTCAAG 60.368 72.222 0.00 0.00 0.00 3.02
1505 1945 2.069430 CAAGCTCTCCCCCTCCCTC 61.069 68.421 0.00 0.00 0.00 4.30
1506 1946 2.041928 CAAGCTCTCCCCCTCCCT 59.958 66.667 0.00 0.00 0.00 4.20
1509 1949 1.843206 AGAATTCAAGCTCTCCCCCTC 59.157 52.381 8.44 0.00 0.00 4.30
1510 1950 1.843206 GAGAATTCAAGCTCTCCCCCT 59.157 52.381 8.44 0.00 33.36 4.79
1845 2287 2.766229 GAGGAGGAGGAGGTGGCC 60.766 72.222 0.00 0.00 0.00 5.36
1952 2400 1.078567 CAGCAGAGGAACAGGGAGC 60.079 63.158 0.00 0.00 0.00 4.70
1958 2406 0.319900 GTCGAAGCAGCAGAGGAACA 60.320 55.000 0.00 0.00 0.00 3.18
1972 2420 0.876399 TTGATCTCGGACACGTCGAA 59.124 50.000 0.00 0.00 41.85 3.71
1980 2428 2.956964 CGGCGCTTGATCTCGGAC 60.957 66.667 7.64 0.00 0.00 4.79
2013 2465 1.218316 GGCGTCGGAGTTCTTGGAT 59.782 57.895 0.00 0.00 0.00 3.41
2028 2480 4.135153 CTCCACTGGGTCTCGGCG 62.135 72.222 0.00 0.00 34.93 6.46
2050 2502 0.659957 GGCAATGGCGAGTGATTCTC 59.340 55.000 0.00 0.00 42.47 2.87
2128 2582 2.805671 CAAGTACCTGCACACGAATTGA 59.194 45.455 0.00 0.00 0.00 2.57
2328 2815 2.970974 GACGCCTGGCTGAACTTGC 61.971 63.158 17.92 0.00 0.00 4.01
3251 3741 3.124466 GCCGCTTCTTCTTCTTCTTCTTC 59.876 47.826 0.00 0.00 0.00 2.87
3254 3744 2.414825 CTGCCGCTTCTTCTTCTTCTTC 59.585 50.000 0.00 0.00 0.00 2.87
3311 3801 2.185350 CGGGATGTTCTCGCAGCT 59.815 61.111 0.00 0.00 31.65 4.24
3334 3824 4.736896 GTTTCCGGCTCCGCGACT 62.737 66.667 8.23 0.00 38.24 4.18
3484 3974 2.741985 TCGCACTTGACCGCCATG 60.742 61.111 0.00 0.00 0.00 3.66
3524 4014 1.296056 CCGGATGGTTGACGGTTGAC 61.296 60.000 0.00 0.00 42.53 3.18
3525 4015 1.004320 CCGGATGGTTGACGGTTGA 60.004 57.895 0.00 0.00 42.53 3.18
3530 4020 2.202878 ATCGCCGGATGGTTGACG 60.203 61.111 5.05 0.00 37.67 4.35
3531 4021 3.409856 CATCGCCGGATGGTTGAC 58.590 61.111 5.05 0.00 45.15 3.18
3551 4041 3.947841 TGCTGTTGTTGCCGTCGC 61.948 61.111 0.00 0.00 0.00 5.19
3552 4042 2.052237 GTGCTGTTGTTGCCGTCG 60.052 61.111 0.00 0.00 0.00 5.12
3553 4043 2.331451 GGTGCTGTTGTTGCCGTC 59.669 61.111 0.00 0.00 0.00 4.79
3554 4044 2.439338 TGGTGCTGTTGTTGCCGT 60.439 55.556 0.00 0.00 0.00 5.68
3555 4045 2.332514 CTGGTGCTGTTGTTGCCG 59.667 61.111 0.00 0.00 0.00 5.69
3556 4046 2.028043 GCTGGTGCTGTTGTTGCC 59.972 61.111 0.00 0.00 36.03 4.52
3557 4047 0.872881 CTTGCTGGTGCTGTTGTTGC 60.873 55.000 0.00 0.00 40.48 4.17
3558 4048 0.872881 GCTTGCTGGTGCTGTTGTTG 60.873 55.000 0.00 0.00 40.48 3.33
3559 4049 1.321805 TGCTTGCTGGTGCTGTTGTT 61.322 50.000 0.00 0.00 40.48 2.83
3560 4050 1.731433 CTGCTTGCTGGTGCTGTTGT 61.731 55.000 0.00 0.00 40.48 3.32
3561 4051 1.007734 CTGCTTGCTGGTGCTGTTG 60.008 57.895 0.00 0.00 40.48 3.33
3562 4052 2.853290 GCTGCTTGCTGGTGCTGTT 61.853 57.895 0.00 0.00 40.48 3.16
3589 4079 5.667539 TGACATCTTCGAATTTCCTCTCT 57.332 39.130 0.00 0.00 0.00 3.10
3607 4097 6.207614 TCGAATGTTTGGGTTTGAATATGACA 59.792 34.615 0.00 0.00 0.00 3.58
3611 4101 5.949354 TCCTCGAATGTTTGGGTTTGAATAT 59.051 36.000 0.00 0.00 0.00 1.28
3612 4102 5.317808 TCCTCGAATGTTTGGGTTTGAATA 58.682 37.500 0.00 0.00 0.00 1.75
3613 4103 4.148838 TCCTCGAATGTTTGGGTTTGAAT 58.851 39.130 0.00 0.00 0.00 2.57
3620 4110 1.089920 CAGCTCCTCGAATGTTTGGG 58.910 55.000 0.00 0.00 0.00 4.12
3626 4116 0.103937 GTCCTCCAGCTCCTCGAATG 59.896 60.000 0.00 0.00 0.00 2.67
3669 4159 2.029288 CTGTACACTGCTGCCACGG 61.029 63.158 0.00 0.00 0.00 4.94
3783 4284 1.340697 ACACAGAGGACATGCATGCAT 60.341 47.619 27.46 27.46 37.08 3.96
3784 4285 0.037160 ACACAGAGGACATGCATGCA 59.963 50.000 26.53 25.04 0.00 3.96
3802 4306 0.507358 GCGAAGGAACGAACTCACAC 59.493 55.000 0.00 0.00 35.09 3.82
3855 4389 3.220658 TCGTCGTGCACTCCACCA 61.221 61.111 16.19 0.00 41.53 4.17
3875 4411 4.589908 TGGAAGAGGAAGAATAAACAGCC 58.410 43.478 0.00 0.00 0.00 4.85
3962 4502 2.657237 CAGCCCGGAAAGACGAGT 59.343 61.111 0.73 0.00 35.47 4.18
4029 4575 3.044059 GCCGCACAGATCCTGCAAC 62.044 63.158 12.27 1.44 34.37 4.17
4078 4624 2.016318 CACTCCTCAACAACAGCAACA 58.984 47.619 0.00 0.00 0.00 3.33
4105 4651 1.269726 GCAAATAATGGCCGGGTCATG 60.270 52.381 16.10 4.73 0.00 3.07
4110 4656 0.670162 CTCTGCAAATAATGGCCGGG 59.330 55.000 2.18 0.00 0.00 5.73
4173 4724 8.352201 CACTGTCTTGAACTGAAATTTATGGAA 58.648 33.333 0.00 0.00 0.00 3.53
4185 4742 5.065218 AGTTAAACAGCACTGTCTTGAACTG 59.935 40.000 3.32 0.00 44.13 3.16
4195 4752 5.734855 AGTAACACAGTTAAACAGCACTG 57.265 39.130 0.00 0.00 36.39 3.66
4263 5448 4.907875 AGTGCCACAACCATATATACCTCT 59.092 41.667 0.00 0.00 0.00 3.69
4267 5452 4.515191 CCACAGTGCCACAACCATATATAC 59.485 45.833 0.00 0.00 0.00 1.47
4271 5456 1.616725 CCCACAGTGCCACAACCATAT 60.617 52.381 0.00 0.00 0.00 1.78
4272 5457 0.251121 CCCACAGTGCCACAACCATA 60.251 55.000 0.00 0.00 0.00 2.74
4346 5536 5.535406 CCAGATACTACCACTACCACTAAGG 59.465 48.000 0.00 0.00 45.67 2.69
4347 5537 6.127793 ACCAGATACTACCACTACCACTAAG 58.872 44.000 0.00 0.00 0.00 2.18
4348 5538 6.083487 ACCAGATACTACCACTACCACTAA 57.917 41.667 0.00 0.00 0.00 2.24
4349 5539 5.722172 ACCAGATACTACCACTACCACTA 57.278 43.478 0.00 0.00 0.00 2.74
4350 5540 4.604784 ACCAGATACTACCACTACCACT 57.395 45.455 0.00 0.00 0.00 4.00
4351 5541 4.954826 AGAACCAGATACTACCACTACCAC 59.045 45.833 0.00 0.00 0.00 4.16
4352 5542 5.044328 AGAGAACCAGATACTACCACTACCA 60.044 44.000 0.00 0.00 0.00 3.25
4353 5543 5.299782 CAGAGAACCAGATACTACCACTACC 59.700 48.000 0.00 0.00 0.00 3.18
4354 5544 6.120905 TCAGAGAACCAGATACTACCACTAC 58.879 44.000 0.00 0.00 0.00 2.73
4355 5545 6.323210 TCAGAGAACCAGATACTACCACTA 57.677 41.667 0.00 0.00 0.00 2.74
4356 5546 5.194473 TCAGAGAACCAGATACTACCACT 57.806 43.478 0.00 0.00 0.00 4.00
4359 5549 6.777213 TTCTTCAGAGAACCAGATACTACC 57.223 41.667 0.00 0.00 36.99 3.18
4393 5585 6.235231 TCCCACATCTGTTTCCTATCTAAC 57.765 41.667 0.00 0.00 0.00 2.34
4395 5587 6.726299 CCTATCCCACATCTGTTTCCTATCTA 59.274 42.308 0.00 0.00 0.00 1.98
4396 5588 5.545723 CCTATCCCACATCTGTTTCCTATCT 59.454 44.000 0.00 0.00 0.00 1.98
4431 5623 1.300931 GTGAACTGTCAGCGGCAGA 60.301 57.895 15.33 0.00 37.40 4.26
4456 5648 8.562892 CAAGCAGTCGATTCCATAAGATTATTT 58.437 33.333 0.00 0.00 0.00 1.40
4473 5671 1.294659 GAGCAGGGAACAAGCAGTCG 61.295 60.000 0.00 0.00 36.26 4.18
4528 5745 7.792383 CATCAGTGCAATAGTTTTTCAAGAG 57.208 36.000 0.00 0.00 0.00 2.85
4553 5771 4.593206 TCAGTTGCTAATAGGATACCCTGG 59.407 45.833 0.00 0.00 44.15 4.45
4573 5791 7.713750 TCACTTACCGAGTAAATTAGGATCAG 58.286 38.462 0.00 0.00 36.65 2.90
4604 5822 3.646637 AGTGCAAGGTTTGGTACTACTCT 59.353 43.478 0.00 0.00 0.00 3.24
4605 5823 4.004196 AGTGCAAGGTTTGGTACTACTC 57.996 45.455 0.00 0.00 0.00 2.59
4606 5824 4.432980 AAGTGCAAGGTTTGGTACTACT 57.567 40.909 0.00 0.00 29.56 2.57
4607 5825 5.178809 CACTAAGTGCAAGGTTTGGTACTAC 59.821 44.000 0.00 0.00 29.56 2.73
4639 5857 3.998341 TCAACCGTATTTTACAGCCTCAC 59.002 43.478 0.00 0.00 0.00 3.51
4653 5872 0.454600 CCTAGAAGCGCTCAACCGTA 59.545 55.000 12.06 0.00 0.00 4.02
4680 5899 3.573772 TTCCTGCTGGTCACTCGCG 62.574 63.158 9.73 0.00 34.23 5.87
4688 5907 1.228367 CCTGCTTGTTCCTGCTGGT 60.228 57.895 9.73 0.00 41.41 4.00
4716 5935 8.371053 GTTTGTAGTGCTAGTTAAGTATGAACG 58.629 37.037 0.00 0.00 33.48 3.95
4726 5945 7.491372 GTGATGCATAGTTTGTAGTGCTAGTTA 59.509 37.037 0.00 0.00 38.37 2.24
4727 5946 6.313905 GTGATGCATAGTTTGTAGTGCTAGTT 59.686 38.462 0.00 0.00 38.37 2.24
4728 5947 5.812642 GTGATGCATAGTTTGTAGTGCTAGT 59.187 40.000 0.00 0.00 38.37 2.57
4729 5948 5.812127 TGTGATGCATAGTTTGTAGTGCTAG 59.188 40.000 0.00 0.00 38.37 3.42
4730 5949 5.580691 GTGTGATGCATAGTTTGTAGTGCTA 59.419 40.000 0.00 0.00 38.37 3.49
4731 5950 4.393062 GTGTGATGCATAGTTTGTAGTGCT 59.607 41.667 0.00 0.00 38.37 4.40
4732 5951 4.154015 TGTGTGATGCATAGTTTGTAGTGC 59.846 41.667 0.00 0.00 38.05 4.40
4737 10557 3.503363 CCTGTGTGTGATGCATAGTTTGT 59.497 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.