Multiple sequence alignment - TraesCS5D01G494500

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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 TraesCS5D01G494500 chr5D 100.000 5073 0 0 1 5073 526501256 526496184 0.000000e+00 9369.0
1 TraesCS5D01G494500 chr5D 87.172 2440 259 32 2146 4563 525583270 525585677 0.000000e+00 2723.0
2 TraesCS5D01G494500 chr5D 84.968 785 87 14 1171 1939 525581785 525582554 0.000000e+00 767.0
3 TraesCS5D01G494500 chr5D 93.519 324 13 4 4731 5054 479213237 479212922 5.210000e-130 475.0
4 TraesCS5D01G494500 chr5D 100.000 187 0 0 5561 5747 526495696 526495510 4.260000e-91 346.0
5 TraesCS5D01G494500 chr5D 97.391 115 2 1 5633 5747 479212312 479212199 1.630000e-45 195.0
6 TraesCS5D01G494500 chr5B 93.313 3679 170 43 931 4564 661909286 661905639 0.000000e+00 5361.0
7 TraesCS5D01G494500 chr5B 91.592 2129 170 8 2304 4430 659970998 659973119 0.000000e+00 2931.0
8 TraesCS5D01G494500 chr5B 89.351 770 65 14 1171 1930 659969119 659969881 0.000000e+00 952.0
9 TraesCS5D01G494500 chr5B 96.341 164 5 1 4557 4719 661905318 661905155 9.490000e-68 268.0
10 TraesCS5D01G494500 chr5B 84.337 166 12 8 2128 2292 659970751 659970903 3.590000e-32 150.0
11 TraesCS5D01G494500 chr5A 93.272 2839 143 22 1915 4728 653703060 653700245 0.000000e+00 4141.0
12 TraesCS5D01G494500 chr5A 90.357 2157 187 14 2427 4567 651853320 651855471 0.000000e+00 2811.0
13 TraesCS5D01G494500 chr5A 88.286 1272 74 27 785 2002 653704285 653703035 0.000000e+00 1454.0
14 TraesCS5D01G494500 chr5A 89.673 765 70 8 1171 1930 651851477 651852237 0.000000e+00 966.0
15 TraesCS5D01G494500 chr7B 84.762 525 46 15 148 653 634153986 634154495 4.000000e-136 496.0
16 TraesCS5D01G494500 chr7B 84.762 525 42 21 150 653 634250075 634250582 5.170000e-135 492.0
17 TraesCS5D01G494500 chr7B 93.956 182 11 0 1 182 134526764 134526945 5.670000e-70 276.0
18 TraesCS5D01G494500 chr7B 88.060 67 5 3 512 576 198489326 198489261 6.170000e-10 76.8
19 TraesCS5D01G494500 chr2D 93.294 343 9 6 4731 5073 189678625 189678953 1.440000e-135 494.0
20 TraesCS5D01G494500 chr2D 89.275 345 18 9 4731 5073 617535809 617535482 1.150000e-111 414.0
21 TraesCS5D01G494500 chr1D 92.151 344 13 4 4731 5073 4679650 4679980 1.870000e-129 473.0
22 TraesCS5D01G494500 chr1D 100.000 29 0 0 1383 1411 475197209 475197181 3.000000e-03 54.7
23 TraesCS5D01G494500 chr2A 91.789 341 18 2 4731 5071 737466367 737466037 3.140000e-127 466.0
24 TraesCS5D01G494500 chr2A 88.630 343 16 11 4731 5073 311190326 311190007 4.170000e-106 396.0
25 TraesCS5D01G494500 chr2A 90.099 101 9 1 190 290 521186425 521186524 4.670000e-26 130.0
26 TraesCS5D01G494500 chr2A 91.304 46 2 1 741 784 104321891 104321936 1.730000e-05 62.1
27 TraesCS5D01G494500 chr7D 92.470 332 12 6 4731 5062 159025556 159025238 4.060000e-126 462.0
28 TraesCS5D01G494500 chr7D 95.341 279 13 0 4731 5009 69380362 69380640 1.470000e-120 444.0
29 TraesCS5D01G494500 chr7D 97.126 174 5 0 5574 5747 159024791 159024618 1.570000e-75 294.0
30 TraesCS5D01G494500 chr7D 85.517 290 28 7 1 290 184375096 184375371 2.030000e-74 291.0
31 TraesCS5D01G494500 chr7D 96.522 115 3 1 5633 5747 69381145 69381258 7.600000e-44 189.0
32 TraesCS5D01G494500 chr7D 91.919 99 7 1 193 290 112320935 112321033 2.790000e-28 137.0
33 TraesCS5D01G494500 chr1A 92.835 321 18 3 4731 5050 91560939 91561255 1.460000e-125 460.0
34 TraesCS5D01G494500 chr1A 100.000 29 0 0 1383 1411 570880495 570880467 3.000000e-03 54.7
35 TraesCS5D01G494500 chr1B 79.848 660 84 29 4 655 422986400 422985782 2.460000e-118 436.0
36 TraesCS5D01G494500 chr1B 86.538 104 13 1 553 655 180694520 180694417 4.710000e-21 113.0
37 TraesCS5D01G494500 chr1B 100.000 29 0 0 1383 1411 660881872 660881844 3.000000e-03 54.7
38 TraesCS5D01G494500 chr1B 100.000 29 0 0 1383 1411 661019126 661019098 3.000000e-03 54.7
39 TraesCS5D01G494500 chr2B 84.081 446 37 14 229 655 749957570 749958000 3.230000e-107 399.0
40 TraesCS5D01G494500 chr2B 83.981 412 35 11 149 547 118609972 118609579 3.270000e-97 366.0
41 TraesCS5D01G494500 chr2B 91.176 102 8 1 190 290 464903851 464903750 2.790000e-28 137.0
42 TraesCS5D01G494500 chr2B 100.000 31 0 0 754 784 17067187 17067217 2.240000e-04 58.4
43 TraesCS5D01G494500 chr3B 81.637 452 48 22 1 430 763287635 763288073 5.510000e-90 342.0
44 TraesCS5D01G494500 chr3B 89.427 227 17 7 4731 4954 570061892 570061670 4.380000e-71 279.0
45 TraesCS5D01G494500 chr3B 84.483 290 37 7 7 290 605914621 605914334 4.380000e-71 279.0
46 TraesCS5D01G494500 chr3D 88.194 288 29 5 7 290 529132585 529132871 7.130000e-89 339.0
47 TraesCS5D01G494500 chr3D 84.192 291 36 9 7 290 538123541 538123254 2.040000e-69 274.0
48 TraesCS5D01G494500 chr3A 76.877 666 103 37 1 636 69244536 69245180 4.290000e-86 329.0
49 TraesCS5D01G494500 chr6A 84.932 292 31 9 368 656 276291952 276291671 3.390000e-72 283.0
50 TraesCS5D01G494500 chr6B 93.407 182 11 1 1 182 584115966 584115786 9.490000e-68 268.0
51 TraesCS5D01G494500 chr6D 94.872 156 6 2 4919 5072 311580122 311579967 5.750000e-60 243.0
52 TraesCS5D01G494500 chr6D 97.391 115 2 1 5633 5747 311579526 311579413 1.630000e-45 195.0


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 TraesCS5D01G494500 chr5D 526495510 526501256 5746 True 4857.500000 9369 100.000000 1 5747 2 chr5D.!!$R2 5746
1 TraesCS5D01G494500 chr5D 525581785 525585677 3892 False 1745.000000 2723 86.070000 1171 4563 2 chr5D.!!$F1 3392
2 TraesCS5D01G494500 chr5D 479212199 479213237 1038 True 335.000000 475 95.455000 4731 5747 2 chr5D.!!$R1 1016
3 TraesCS5D01G494500 chr5B 661905155 661909286 4131 True 2814.500000 5361 94.827000 931 4719 2 chr5B.!!$R1 3788
4 TraesCS5D01G494500 chr5B 659969119 659973119 4000 False 1344.333333 2931 88.426667 1171 4430 3 chr5B.!!$F1 3259
5 TraesCS5D01G494500 chr5A 653700245 653704285 4040 True 2797.500000 4141 90.779000 785 4728 2 chr5A.!!$R1 3943
6 TraesCS5D01G494500 chr5A 651851477 651855471 3994 False 1888.500000 2811 90.015000 1171 4567 2 chr5A.!!$F1 3396
7 TraesCS5D01G494500 chr7B 634153986 634154495 509 False 496.000000 496 84.762000 148 653 1 chr7B.!!$F2 505
8 TraesCS5D01G494500 chr7B 634250075 634250582 507 False 492.000000 492 84.762000 150 653 1 chr7B.!!$F3 503
9 TraesCS5D01G494500 chr7D 159024618 159025556 938 True 378.000000 462 94.798000 4731 5747 2 chr7D.!!$R1 1016
10 TraesCS5D01G494500 chr7D 69380362 69381258 896 False 316.500000 444 95.931500 4731 5747 2 chr7D.!!$F3 1016
11 TraesCS5D01G494500 chr1B 422985782 422986400 618 True 436.000000 436 79.848000 4 655 1 chr1B.!!$R2 651
12 TraesCS5D01G494500 chr3A 69244536 69245180 644 False 329.000000 329 76.877000 1 636 1 chr3A.!!$F1 635
13 TraesCS5D01G494500 chr6D 311579413 311580122 709 True 219.000000 243 96.131500 4919 5747 2 chr6D.!!$R1 828

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
534 695 0.036010 ACTGAAGTCCAATCGGCCAG 60.036 55.0 2.24 0.00 0.00 4.85 F
566 727 0.106868 TGGATCCAATCAGCCAGCTG 60.107 55.0 13.46 13.54 44.86 4.24 F
677 838 0.108585 AACGGCCATGTGTCTGTTCT 59.891 50.0 2.24 0.00 0.00 3.01 F
679 840 0.320683 CGGCCATGTGTCTGTTCTGA 60.321 55.0 2.24 0.00 0.00 3.27 F
1149 1366 0.537188 AGGGGTTCGCATGTAGACTG 59.463 55.0 0.00 0.00 0.00 3.51 F
1369 1586 0.825840 CCTCTGGGTCCGAGATCTCC 60.826 65.0 17.13 3.30 0.00 3.71 F
3131 4694 0.519961 ATCTTAACGGTGCGGCAAAC 59.480 50.0 3.23 0.00 0.00 2.93 F
3861 5427 0.606604 GCAACTCCCTCAGTTCCGTA 59.393 55.0 0.00 0.00 44.14 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 2102 0.038618 CATGTTCGGTGTCGTCTCCA 60.039 55.000 1.90 0.00 37.69 3.86 R
1864 2112 0.317160 TCAGTCGAAGCATGTTCGGT 59.683 50.000 21.78 12.21 41.78 4.69 R
2633 4193 2.887151 AAACCTGGCTTGTGCTATCT 57.113 45.000 0.00 0.00 39.59 1.98 R
2798 4358 2.887568 CTGACAGGATGGTCGCGC 60.888 66.667 0.00 0.00 43.62 6.86 R
2837 4397 0.959372 CAAGTCCTTCAGCCAGCCAG 60.959 60.000 0.00 0.00 0.00 4.85 R
3425 4988 1.425066 TGGAGGACTTCAATTGGCAGT 59.575 47.619 5.42 8.19 0.00 4.40 R
4543 6149 0.372679 GCAGCACACACATCATCGAG 59.627 55.000 0.00 0.00 0.00 4.04 R
4963 6986 2.365768 TACATAGCGGGGTGGGCA 60.366 61.111 0.00 0.00 0.00 5.36 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
90 91 2.613691 CTTACCAACGTTAGTGCCGAT 58.386 47.619 9.74 0.00 0.00 4.18
124 125 3.363178 GTTGAGAACACAAAGAAAGGCG 58.637 45.455 0.00 0.00 0.00 5.52
125 126 1.946768 TGAGAACACAAAGAAAGGCGG 59.053 47.619 0.00 0.00 0.00 6.13
126 127 1.266989 GAGAACACAAAGAAAGGCGGG 59.733 52.381 0.00 0.00 0.00 6.13
127 128 1.133915 AGAACACAAAGAAAGGCGGGA 60.134 47.619 0.00 0.00 0.00 5.14
128 129 1.679153 GAACACAAAGAAAGGCGGGAA 59.321 47.619 0.00 0.00 0.00 3.97
129 130 1.029681 ACACAAAGAAAGGCGGGAAC 58.970 50.000 0.00 0.00 0.00 3.62
130 131 1.318576 CACAAAGAAAGGCGGGAACT 58.681 50.000 0.00 0.00 0.00 3.01
131 132 1.266989 CACAAAGAAAGGCGGGAACTC 59.733 52.381 0.00 0.00 0.00 3.01
132 133 0.517316 CAAAGAAAGGCGGGAACTCG 59.483 55.000 0.00 0.00 0.00 4.18
133 134 0.605589 AAAGAAAGGCGGGAACTCGG 60.606 55.000 0.00 0.00 0.00 4.63
134 135 1.477685 AAGAAAGGCGGGAACTCGGA 61.478 55.000 0.00 0.00 0.00 4.55
135 136 1.004200 GAAAGGCGGGAACTCGGAA 60.004 57.895 0.00 0.00 0.00 4.30
136 137 1.003718 AAAGGCGGGAACTCGGAAG 60.004 57.895 0.00 0.00 0.00 3.46
137 138 3.607370 AAGGCGGGAACTCGGAAGC 62.607 63.158 0.00 0.00 0.00 3.86
140 141 4.814294 CGGGAACTCGGAAGCGGG 62.814 72.222 0.00 0.00 0.00 6.13
141 142 4.468689 GGGAACTCGGAAGCGGGG 62.469 72.222 0.00 0.00 0.00 5.73
142 143 3.387947 GGAACTCGGAAGCGGGGA 61.388 66.667 0.00 0.00 0.00 4.81
143 144 2.660802 GAACTCGGAAGCGGGGAA 59.339 61.111 0.00 0.00 0.00 3.97
144 145 1.004200 GAACTCGGAAGCGGGGAAA 60.004 57.895 0.00 0.00 0.00 3.13
145 146 0.392595 GAACTCGGAAGCGGGGAAAT 60.393 55.000 0.00 0.00 0.00 2.17
146 147 0.906775 AACTCGGAAGCGGGGAAATA 59.093 50.000 0.00 0.00 0.00 1.40
183 184 0.107831 CGGGAAAATATGGCGGGAGA 59.892 55.000 0.00 0.00 0.00 3.71
184 185 1.605753 GGGAAAATATGGCGGGAGAC 58.394 55.000 0.00 0.00 39.51 3.36
191 192 4.680237 TGGCGGGAGACACTTGCG 62.680 66.667 0.00 0.00 43.08 4.85
194 195 3.691342 CGGGAGACACTTGCGGGA 61.691 66.667 0.00 0.00 0.00 5.14
195 196 2.747686 GGGAGACACTTGCGGGAA 59.252 61.111 0.00 0.00 0.00 3.97
196 197 1.671379 GGGAGACACTTGCGGGAAC 60.671 63.158 0.00 0.00 0.00 3.62
197 198 1.371558 GGAGACACTTGCGGGAACT 59.628 57.895 0.00 0.00 0.00 3.01
198 199 0.606604 GGAGACACTTGCGGGAACTA 59.393 55.000 0.00 0.00 0.00 2.24
199 200 1.404315 GGAGACACTTGCGGGAACTAG 60.404 57.143 0.00 0.00 0.00 2.57
200 201 1.544691 GAGACACTTGCGGGAACTAGA 59.455 52.381 0.00 0.00 0.00 2.43
201 202 1.546476 AGACACTTGCGGGAACTAGAG 59.454 52.381 0.00 0.00 0.00 2.43
202 203 1.544691 GACACTTGCGGGAACTAGAGA 59.455 52.381 0.00 0.00 0.00 3.10
203 204 1.546476 ACACTTGCGGGAACTAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
204 205 1.134965 CACTTGCGGGAACTAGAGAGG 60.135 57.143 0.00 0.00 0.00 3.69
205 206 0.461961 CTTGCGGGAACTAGAGAGGG 59.538 60.000 0.00 0.00 0.00 4.30
206 207 0.976073 TTGCGGGAACTAGAGAGGGG 60.976 60.000 0.00 0.00 0.00 4.79
207 208 1.076192 GCGGGAACTAGAGAGGGGA 60.076 63.158 0.00 0.00 0.00 4.81
208 209 0.686769 GCGGGAACTAGAGAGGGGAA 60.687 60.000 0.00 0.00 0.00 3.97
209 210 1.861982 CGGGAACTAGAGAGGGGAAA 58.138 55.000 0.00 0.00 0.00 3.13
210 211 2.185387 CGGGAACTAGAGAGGGGAAAA 58.815 52.381 0.00 0.00 0.00 2.29
211 212 2.772515 CGGGAACTAGAGAGGGGAAAAT 59.227 50.000 0.00 0.00 0.00 1.82
212 213 3.965347 CGGGAACTAGAGAGGGGAAAATA 59.035 47.826 0.00 0.00 0.00 1.40
213 214 4.593634 CGGGAACTAGAGAGGGGAAAATAT 59.406 45.833 0.00 0.00 0.00 1.28
214 215 5.511545 CGGGAACTAGAGAGGGGAAAATATG 60.512 48.000 0.00 0.00 0.00 1.78
215 216 5.221945 GGGAACTAGAGAGGGGAAAATATGG 60.222 48.000 0.00 0.00 0.00 2.74
216 217 4.984146 ACTAGAGAGGGGAAAATATGGC 57.016 45.455 0.00 0.00 0.00 4.40
217 218 2.938956 AGAGAGGGGAAAATATGGCG 57.061 50.000 0.00 0.00 0.00 5.69
218 219 1.421646 AGAGAGGGGAAAATATGGCGG 59.578 52.381 0.00 0.00 0.00 6.13
219 220 0.478507 AGAGGGGAAAATATGGCGGG 59.521 55.000 0.00 0.00 0.00 6.13
220 221 0.476771 GAGGGGAAAATATGGCGGGA 59.523 55.000 0.00 0.00 0.00 5.14
221 222 0.478507 AGGGGAAAATATGGCGGGAG 59.521 55.000 0.00 0.00 0.00 4.30
249 250 1.950909 CGGGAACTAGAGAGCGAGAAT 59.049 52.381 0.00 0.00 0.00 2.40
255 256 6.183360 GGGAACTAGAGAGCGAGAATATATGG 60.183 46.154 0.00 0.00 0.00 2.74
293 376 2.223711 GCGAAAATATGGCGGGAAATGT 60.224 45.455 0.00 0.00 0.00 2.71
325 408 2.834034 TAAGCGGGAAACGTACGGGC 62.834 60.000 21.06 12.10 46.52 6.13
327 410 2.125431 CGGGAAACGTACGGGCAT 60.125 61.111 21.06 1.92 37.93 4.40
328 411 1.141449 CGGGAAACGTACGGGCATA 59.859 57.895 21.06 0.00 37.93 3.14
329 412 0.872881 CGGGAAACGTACGGGCATAG 60.873 60.000 21.06 2.95 37.93 2.23
330 413 0.461135 GGGAAACGTACGGGCATAGA 59.539 55.000 21.06 0.00 0.00 1.98
334 417 3.624410 GGAAACGTACGGGCATAGAAAAT 59.376 43.478 21.06 0.00 0.00 1.82
335 418 4.495184 GGAAACGTACGGGCATAGAAAATG 60.495 45.833 21.06 0.00 0.00 2.32
365 448 0.041238 ACCAGTAGGCCTACAGCTGA 59.959 55.000 37.94 5.24 43.05 4.26
375 458 3.198872 GCCTACAGCTGACCAATTAGTC 58.801 50.000 23.35 0.00 38.99 2.59
382 514 5.189736 ACAGCTGACCAATTAGTCCTAATCA 59.810 40.000 23.35 0.00 34.90 2.57
390 522 6.330250 ACCAATTAGTCCTAATCAGCCTACAT 59.670 38.462 0.26 0.00 34.90 2.29
403 535 3.611766 GCCTACATATGGCCGATTAGT 57.388 47.619 7.80 0.00 44.32 2.24
411 543 1.271856 TGGCCGATTAGTTCCAGTCA 58.728 50.000 0.00 0.00 0.00 3.41
417 549 2.158900 CGATTAGTTCCAGTCAGCCCAT 60.159 50.000 0.00 0.00 0.00 4.00
430 562 2.831770 CCCATAGCTGGCCGACAT 59.168 61.111 0.00 0.00 41.64 3.06
436 568 0.676184 TAGCTGGCCGACATGATCTC 59.324 55.000 0.00 0.00 0.00 2.75
437 569 1.047596 AGCTGGCCGACATGATCTCT 61.048 55.000 0.00 0.00 0.00 3.10
510 642 3.063704 CCAATCGGCCAGCAGCAA 61.064 61.111 2.24 0.00 46.50 3.91
521 653 2.866028 GCAGCAAGCCGACTGAAG 59.134 61.111 1.90 0.00 35.90 3.02
522 654 1.963338 GCAGCAAGCCGACTGAAGT 60.963 57.895 1.90 0.00 35.90 3.01
526 687 0.884704 GCAAGCCGACTGAAGTCCAA 60.885 55.000 4.90 0.00 41.86 3.53
534 695 0.036010 ACTGAAGTCCAATCGGCCAG 60.036 55.000 2.24 0.00 0.00 4.85
551 712 2.437359 GCAGCAAGCCGACTGGAT 60.437 61.111 0.00 0.00 37.49 3.41
552 713 2.467826 GCAGCAAGCCGACTGGATC 61.468 63.158 0.00 0.00 37.49 3.36
553 714 1.817099 CAGCAAGCCGACTGGATCC 60.817 63.158 4.20 4.20 37.49 3.36
554 715 2.268920 GCAAGCCGACTGGATCCA 59.731 61.111 15.27 15.27 37.49 3.41
555 716 1.377202 GCAAGCCGACTGGATCCAA 60.377 57.895 17.00 0.00 37.49 3.53
556 717 0.749454 GCAAGCCGACTGGATCCAAT 60.749 55.000 17.00 5.36 37.49 3.16
557 718 1.303309 CAAGCCGACTGGATCCAATC 58.697 55.000 17.00 15.09 37.49 2.67
558 719 0.911769 AAGCCGACTGGATCCAATCA 59.088 50.000 22.29 0.00 37.49 2.57
559 720 0.467384 AGCCGACTGGATCCAATCAG 59.533 55.000 22.29 12.80 37.49 2.90
560 721 1.162800 GCCGACTGGATCCAATCAGC 61.163 60.000 22.29 18.79 37.49 4.26
561 722 0.533755 CCGACTGGATCCAATCAGCC 60.534 60.000 22.29 0.00 37.49 4.85
562 723 0.178767 CGACTGGATCCAATCAGCCA 59.821 55.000 22.29 0.00 34.57 4.75
564 725 2.716814 CTGGATCCAATCAGCCAGC 58.283 57.895 17.00 0.00 41.17 4.85
565 726 0.183014 CTGGATCCAATCAGCCAGCT 59.817 55.000 17.00 0.00 41.17 4.24
566 727 0.106868 TGGATCCAATCAGCCAGCTG 60.107 55.000 13.46 13.54 44.86 4.24
567 728 1.453762 GGATCCAATCAGCCAGCTGC 61.454 60.000 14.86 3.91 43.31 5.25
584 745 3.995199 GCTGCTAGCTGATGGTGTATTA 58.005 45.455 24.19 0.00 38.45 0.98
664 825 2.341318 AAAAATTAGCGTGAACGGCC 57.659 45.000 4.84 0.00 40.23 6.13
665 826 1.240256 AAAATTAGCGTGAACGGCCA 58.760 45.000 2.24 0.00 40.23 5.36
666 827 1.459450 AAATTAGCGTGAACGGCCAT 58.541 45.000 2.24 0.00 40.23 4.40
667 828 0.732571 AATTAGCGTGAACGGCCATG 59.267 50.000 2.24 0.00 40.23 3.66
668 829 0.392461 ATTAGCGTGAACGGCCATGT 60.392 50.000 2.24 0.00 40.23 3.21
669 830 1.295357 TTAGCGTGAACGGCCATGTG 61.295 55.000 2.24 0.00 40.23 3.21
670 831 2.443260 TAGCGTGAACGGCCATGTGT 62.443 55.000 2.24 0.00 40.23 3.72
671 832 2.860293 CGTGAACGGCCATGTGTC 59.140 61.111 2.24 0.00 35.37 3.67
672 833 1.667830 CGTGAACGGCCATGTGTCT 60.668 57.895 2.24 0.00 35.37 3.41
673 834 1.868997 GTGAACGGCCATGTGTCTG 59.131 57.895 2.24 0.00 0.00 3.51
674 835 0.884704 GTGAACGGCCATGTGTCTGT 60.885 55.000 2.24 0.00 0.00 3.41
675 836 0.179032 TGAACGGCCATGTGTCTGTT 60.179 50.000 2.24 0.00 34.75 3.16
676 837 0.517316 GAACGGCCATGTGTCTGTTC 59.483 55.000 2.24 12.66 40.17 3.18
677 838 0.108585 AACGGCCATGTGTCTGTTCT 59.891 50.000 2.24 0.00 0.00 3.01
678 839 0.603707 ACGGCCATGTGTCTGTTCTG 60.604 55.000 2.24 0.00 0.00 3.02
679 840 0.320683 CGGCCATGTGTCTGTTCTGA 60.321 55.000 2.24 0.00 0.00 3.27
680 841 1.877680 CGGCCATGTGTCTGTTCTGAA 60.878 52.381 2.24 0.00 0.00 3.02
681 842 2.229792 GGCCATGTGTCTGTTCTGAAA 58.770 47.619 0.00 0.00 0.00 2.69
682 843 2.227388 GGCCATGTGTCTGTTCTGAAAG 59.773 50.000 0.00 0.00 0.00 2.62
683 844 3.141398 GCCATGTGTCTGTTCTGAAAGA 58.859 45.455 0.00 0.00 44.68 2.52
768 929 9.823647 TTTTTGAATAGTTTGAATTGCTTACCA 57.176 25.926 0.00 0.00 0.00 3.25
769 930 9.995003 TTTTGAATAGTTTGAATTGCTTACCAT 57.005 25.926 0.00 0.00 0.00 3.55
775 936 7.466746 AGTTTGAATTGCTTACCATATGTGT 57.533 32.000 1.24 2.24 0.00 3.72
776 937 7.538575 AGTTTGAATTGCTTACCATATGTGTC 58.461 34.615 1.24 0.00 0.00 3.67
777 938 7.176515 AGTTTGAATTGCTTACCATATGTGTCA 59.823 33.333 1.24 0.00 0.00 3.58
778 939 6.435430 TGAATTGCTTACCATATGTGTCAC 57.565 37.500 1.24 0.00 0.00 3.67
779 940 5.942826 TGAATTGCTTACCATATGTGTCACA 59.057 36.000 8.40 8.40 0.00 3.58
780 941 6.602803 TGAATTGCTTACCATATGTGTCACAT 59.397 34.615 21.70 21.70 42.35 3.21
781 942 5.816449 TTGCTTACCATATGTGTCACATG 57.184 39.130 25.63 13.24 39.53 3.21
782 943 4.198530 TGCTTACCATATGTGTCACATGG 58.801 43.478 25.63 22.49 44.04 3.66
796 957 7.394016 TGTGTCACATGGTATAATTTCAGAGT 58.606 34.615 0.18 0.00 0.00 3.24
826 987 7.847096 ACCAAAGAAAAATAACCAGTTTGTCT 58.153 30.769 0.00 0.00 35.23 3.41
828 989 9.810545 CCAAAGAAAAATAACCAGTTTGTCTAA 57.189 29.630 0.00 0.00 33.17 2.10
927 1112 1.826385 AAGCTAATCCACACACTGCC 58.174 50.000 0.00 0.00 0.00 4.85
1003 1201 1.264295 ACTAGTCCACCCTTTCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
1006 1204 2.019807 AGTCCACCCTTTCGTCCTTA 57.980 50.000 0.00 0.00 0.00 2.69
1011 1209 0.893447 ACCCTTTCGTCCTTACCTCG 59.107 55.000 0.00 0.00 0.00 4.63
1012 1210 1.180029 CCCTTTCGTCCTTACCTCGA 58.820 55.000 0.00 0.00 0.00 4.04
1013 1211 1.135170 CCCTTTCGTCCTTACCTCGAC 60.135 57.143 0.00 0.00 33.38 4.20
1018 1221 2.757099 TCCTTACCTCGACCGCCC 60.757 66.667 0.00 0.00 0.00 6.13
1047 1250 4.704833 GCCTGCTCAACTCCGGCA 62.705 66.667 0.00 0.00 40.41 5.69
1096 1299 1.825341 CCGCATCCACTGGAGATGA 59.175 57.895 3.62 0.00 43.15 2.92
1098 1301 1.509703 CGCATCCACTGGAGATGATG 58.490 55.000 3.62 0.00 43.15 3.07
1100 1303 2.932855 CATCCACTGGAGATGATGCT 57.067 50.000 3.62 0.00 43.15 3.79
1101 1304 2.768698 CATCCACTGGAGATGATGCTC 58.231 52.381 3.62 0.00 43.15 4.26
1102 1305 2.171568 TCCACTGGAGATGATGCTCT 57.828 50.000 0.00 0.00 35.26 4.09
1103 1306 1.761198 TCCACTGGAGATGATGCTCTG 59.239 52.381 0.00 0.00 35.26 3.35
1149 1366 0.537188 AGGGGTTCGCATGTAGACTG 59.463 55.000 0.00 0.00 0.00 3.51
1168 1385 5.194740 AGACTGGCTAGCTAGGGATATATCA 59.805 44.000 29.06 7.31 0.00 2.15
1369 1586 0.825840 CCTCTGGGTCCGAGATCTCC 60.826 65.000 17.13 3.30 0.00 3.71
1570 1802 1.032794 CAACGATCAGGATCCGGAGA 58.967 55.000 19.66 13.06 34.40 3.71
1611 1852 2.419198 CGGAGCCAATCGGAGGAG 59.581 66.667 0.00 0.00 0.00 3.69
1612 1853 2.825264 GGAGCCAATCGGAGGAGG 59.175 66.667 0.00 0.00 0.00 4.30
1627 1868 2.612115 AGGGGAGGCTCAAGGTGG 60.612 66.667 17.69 0.00 0.00 4.61
1854 2102 5.579047 TCCAAAATCATACCACAGGTCAAT 58.421 37.500 0.00 0.00 37.09 2.57
1864 2112 1.000843 CACAGGTCAATGGAGACGACA 59.999 52.381 0.00 0.00 39.42 4.35
2033 3391 7.487829 TGCTTTCAAGTTTCAACAGTGTTATTC 59.512 33.333 8.49 0.31 0.00 1.75
2036 3394 9.567848 TTTCAAGTTTCAACAGTGTTATTCTTC 57.432 29.630 8.49 0.00 0.00 2.87
2152 3617 3.568538 CAAAACTGCGGAATGAGGAAAG 58.431 45.455 0.00 0.00 0.00 2.62
2332 3891 5.244626 AGAGCTAAATTGGTGTCAGCATTTT 59.755 36.000 21.74 21.74 34.73 1.82
2379 3938 7.101652 AGAATCGACTAGTAAGATTGCAAGA 57.898 36.000 23.02 0.00 35.06 3.02
2409 3968 3.665544 GCTTCAAAGCCTGCAACAA 57.334 47.368 3.27 0.00 46.20 2.83
2633 4193 1.216977 CGGTTCACCACTCGCCATA 59.783 57.895 0.00 0.00 35.14 2.74
2798 4358 2.223340 GCTGTATTTCTGCATGTTCCCG 60.223 50.000 0.00 0.00 40.09 5.14
2837 4397 0.606673 GGAATCCCCTGATAAGGCGC 60.607 60.000 0.00 0.00 0.00 6.53
2978 4538 5.749462 AGGAACTATGGAAATGTGAAGAGG 58.251 41.667 0.00 0.00 36.02 3.69
3131 4694 0.519961 ATCTTAACGGTGCGGCAAAC 59.480 50.000 3.23 0.00 0.00 2.93
3214 4777 1.063006 CAAATGTCGCCAGGCATCG 59.937 57.895 13.30 0.00 42.75 3.84
3341 4904 2.411904 CTCAAATATCTGAGCCTCGGC 58.588 52.381 0.00 0.00 36.67 5.54
3425 4988 1.149288 AGGAGAACCCAGGTAGTGACA 59.851 52.381 0.00 0.00 37.41 3.58
3491 5054 5.278022 CCTTGGAAAGTTTCAGCTAGTTGAC 60.278 44.000 17.16 0.00 44.25 3.18
3499 5062 2.786777 TCAGCTAGTTGACGGTGACTA 58.213 47.619 5.01 0.00 33.23 2.59
3515 5081 3.738282 GTGACTACACACAGAAGAAGCTG 59.262 47.826 0.00 0.00 45.32 4.24
3861 5427 0.606604 GCAACTCCCTCAGTTCCGTA 59.393 55.000 0.00 0.00 44.14 4.02
4091 5657 0.694771 TCCAAGATGAAGCTGTGCCT 59.305 50.000 0.00 0.00 0.00 4.75
4287 5853 1.688735 TCCATCATGCTAACTCCTCGG 59.311 52.381 0.00 0.00 0.00 4.63
4403 5972 4.680237 TCTCGTGCACGGCCAAGG 62.680 66.667 36.41 19.48 40.29 3.61
4509 6113 2.884012 TGACGTTGGTGCATCTTTGATT 59.116 40.909 0.00 0.00 0.00 2.57
4521 6125 2.071540 TCTTTGATTGTCTGCAGAGCG 58.928 47.619 18.89 0.00 0.00 5.03
4543 6149 1.274596 CTTTTGCATCCATTCGCTGC 58.725 50.000 0.00 0.00 36.45 5.25
4625 6627 0.539051 GCTGCTGGTGGTGAGTAGAT 59.461 55.000 0.00 0.00 0.00 1.98
4645 6647 3.361281 TTGAGATGATGCAGCCTCTTT 57.639 42.857 11.15 0.00 0.00 2.52
4661 6664 6.485648 CAGCCTCTTTGTGATGATTGATGATA 59.514 38.462 0.00 0.00 0.00 2.15
4709 6712 1.282817 CGCCGATAACGTTTCATGGA 58.717 50.000 5.91 0.00 37.88 3.41
4711 6714 2.285602 CGCCGATAACGTTTCATGGAAG 60.286 50.000 5.91 0.00 37.88 3.46
4715 6718 4.491924 CCGATAACGTTTCATGGAAGAACG 60.492 45.833 5.91 16.92 37.88 3.95
4725 6728 7.011109 CGTTTCATGGAAGAACGGAGTAAATAT 59.989 37.037 13.14 0.00 45.00 1.28
4728 6731 7.152645 TCATGGAAGAACGGAGTAAATATAGC 58.847 38.462 0.00 0.00 45.00 2.97
4729 6732 5.850614 TGGAAGAACGGAGTAAATATAGCC 58.149 41.667 0.00 0.00 45.00 3.93
4760 6763 0.981277 CGGTAGACCCCCTCCAACAT 60.981 60.000 0.00 0.00 0.00 2.71
4797 6800 3.465832 TGTCCCATACCCCTTCATAACA 58.534 45.455 0.00 0.00 0.00 2.41
5725 8146 4.194720 GACCCGCGCTCGTCTCAT 62.195 66.667 5.56 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.935789 CCTTTTGATCGTAGTTTTCACCCTA 59.064 40.000 0.00 0.00 0.00 3.53
5 6 5.934935 TCCTTTTGATCGTAGTTTTCACC 57.065 39.130 0.00 0.00 0.00 4.02
90 91 6.358178 TGTGTTCTCAACCTATAAAACACCA 58.642 36.000 12.14 0.82 43.49 4.17
124 125 4.468689 CCCCGCTTCCGAGTTCCC 62.469 72.222 0.00 0.00 36.29 3.97
125 126 2.459202 TTTCCCCGCTTCCGAGTTCC 62.459 60.000 0.00 0.00 36.29 3.62
126 127 0.392595 ATTTCCCCGCTTCCGAGTTC 60.393 55.000 0.00 0.00 36.29 3.01
127 128 0.906775 TATTTCCCCGCTTCCGAGTT 59.093 50.000 0.00 0.00 36.29 3.01
128 129 1.129058 ATATTTCCCCGCTTCCGAGT 58.871 50.000 0.00 0.00 36.29 4.18
129 130 1.512926 CATATTTCCCCGCTTCCGAG 58.487 55.000 0.00 0.00 36.29 4.63
130 131 0.107831 CCATATTTCCCCGCTTCCGA 59.892 55.000 0.00 0.00 36.29 4.55
131 132 1.515521 GCCATATTTCCCCGCTTCCG 61.516 60.000 0.00 0.00 0.00 4.30
132 133 1.515521 CGCCATATTTCCCCGCTTCC 61.516 60.000 0.00 0.00 0.00 3.46
133 134 1.515521 CCGCCATATTTCCCCGCTTC 61.516 60.000 0.00 0.00 0.00 3.86
134 135 1.528309 CCGCCATATTTCCCCGCTT 60.528 57.895 0.00 0.00 0.00 4.68
135 136 2.113139 CCGCCATATTTCCCCGCT 59.887 61.111 0.00 0.00 0.00 5.52
136 137 2.969300 TTCCCGCCATATTTCCCCGC 62.969 60.000 0.00 0.00 0.00 6.13
137 138 1.149627 TTCCCGCCATATTTCCCCG 59.850 57.895 0.00 0.00 0.00 5.73
138 139 0.185175 AGTTCCCGCCATATTTCCCC 59.815 55.000 0.00 0.00 0.00 4.81
139 140 1.605753 GAGTTCCCGCCATATTTCCC 58.394 55.000 0.00 0.00 0.00 3.97
140 141 1.226746 CGAGTTCCCGCCATATTTCC 58.773 55.000 0.00 0.00 0.00 3.13
141 142 1.202604 TCCGAGTTCCCGCCATATTTC 60.203 52.381 0.00 0.00 0.00 2.17
142 143 0.834612 TCCGAGTTCCCGCCATATTT 59.165 50.000 0.00 0.00 0.00 1.40
143 144 0.834612 TTCCGAGTTCCCGCCATATT 59.165 50.000 0.00 0.00 0.00 1.28
144 145 0.393077 CTTCCGAGTTCCCGCCATAT 59.607 55.000 0.00 0.00 0.00 1.78
145 146 1.820581 CTTCCGAGTTCCCGCCATA 59.179 57.895 0.00 0.00 0.00 2.74
146 147 2.584608 CTTCCGAGTTCCCGCCAT 59.415 61.111 0.00 0.00 0.00 4.40
183 184 1.546476 CTCTCTAGTTCCCGCAAGTGT 59.454 52.381 0.00 0.00 0.00 3.55
184 185 1.134965 CCTCTCTAGTTCCCGCAAGTG 60.135 57.143 0.00 0.00 0.00 3.16
185 186 1.187087 CCTCTCTAGTTCCCGCAAGT 58.813 55.000 0.00 0.00 0.00 3.16
186 187 0.461961 CCCTCTCTAGTTCCCGCAAG 59.538 60.000 0.00 0.00 0.00 4.01
187 188 0.976073 CCCCTCTCTAGTTCCCGCAA 60.976 60.000 0.00 0.00 0.00 4.85
188 189 1.381327 CCCCTCTCTAGTTCCCGCA 60.381 63.158 0.00 0.00 0.00 5.69
189 190 0.686769 TTCCCCTCTCTAGTTCCCGC 60.687 60.000 0.00 0.00 0.00 6.13
190 191 1.861982 TTTCCCCTCTCTAGTTCCCG 58.138 55.000 0.00 0.00 0.00 5.14
191 192 5.221945 CCATATTTTCCCCTCTCTAGTTCCC 60.222 48.000 0.00 0.00 0.00 3.97
192 193 5.746361 GCCATATTTTCCCCTCTCTAGTTCC 60.746 48.000 0.00 0.00 0.00 3.62
193 194 5.309638 GCCATATTTTCCCCTCTCTAGTTC 58.690 45.833 0.00 0.00 0.00 3.01
194 195 4.202367 CGCCATATTTTCCCCTCTCTAGTT 60.202 45.833 0.00 0.00 0.00 2.24
195 196 3.325135 CGCCATATTTTCCCCTCTCTAGT 59.675 47.826 0.00 0.00 0.00 2.57
196 197 3.307059 CCGCCATATTTTCCCCTCTCTAG 60.307 52.174 0.00 0.00 0.00 2.43
197 198 2.637872 CCGCCATATTTTCCCCTCTCTA 59.362 50.000 0.00 0.00 0.00 2.43
198 199 1.421646 CCGCCATATTTTCCCCTCTCT 59.578 52.381 0.00 0.00 0.00 3.10
199 200 1.545651 CCCGCCATATTTTCCCCTCTC 60.546 57.143 0.00 0.00 0.00 3.20
200 201 0.478507 CCCGCCATATTTTCCCCTCT 59.521 55.000 0.00 0.00 0.00 3.69
201 202 0.476771 TCCCGCCATATTTTCCCCTC 59.523 55.000 0.00 0.00 0.00 4.30
202 203 0.478507 CTCCCGCCATATTTTCCCCT 59.521 55.000 0.00 0.00 0.00 4.79
203 204 0.476771 TCTCCCGCCATATTTTCCCC 59.523 55.000 0.00 0.00 0.00 4.81
204 205 2.586648 ATCTCCCGCCATATTTTCCC 57.413 50.000 0.00 0.00 0.00 3.97
205 206 4.003648 CAGTATCTCCCGCCATATTTTCC 58.996 47.826 0.00 0.00 0.00 3.13
206 207 4.003648 CCAGTATCTCCCGCCATATTTTC 58.996 47.826 0.00 0.00 0.00 2.29
207 208 3.810743 GCCAGTATCTCCCGCCATATTTT 60.811 47.826 0.00 0.00 0.00 1.82
208 209 2.290323 GCCAGTATCTCCCGCCATATTT 60.290 50.000 0.00 0.00 0.00 1.40
209 210 1.279271 GCCAGTATCTCCCGCCATATT 59.721 52.381 0.00 0.00 0.00 1.28
210 211 0.905357 GCCAGTATCTCCCGCCATAT 59.095 55.000 0.00 0.00 0.00 1.78
211 212 1.532604 CGCCAGTATCTCCCGCCATA 61.533 60.000 0.00 0.00 0.00 2.74
212 213 2.872388 CGCCAGTATCTCCCGCCAT 61.872 63.158 0.00 0.00 0.00 4.40
213 214 3.536917 CGCCAGTATCTCCCGCCA 61.537 66.667 0.00 0.00 0.00 5.69
214 215 4.301027 CCGCCAGTATCTCCCGCC 62.301 72.222 0.00 0.00 0.00 6.13
215 216 4.301027 CCCGCCAGTATCTCCCGC 62.301 72.222 0.00 0.00 0.00 6.13
216 217 2.131709 TTCCCGCCAGTATCTCCCG 61.132 63.158 0.00 0.00 0.00 5.14
217 218 1.049289 AGTTCCCGCCAGTATCTCCC 61.049 60.000 0.00 0.00 0.00 4.30
218 219 1.614413 CTAGTTCCCGCCAGTATCTCC 59.386 57.143 0.00 0.00 0.00 3.71
219 220 2.554893 CTCTAGTTCCCGCCAGTATCTC 59.445 54.545 0.00 0.00 0.00 2.75
220 221 2.175069 TCTCTAGTTCCCGCCAGTATCT 59.825 50.000 0.00 0.00 0.00 1.98
221 222 2.554893 CTCTCTAGTTCCCGCCAGTATC 59.445 54.545 0.00 0.00 0.00 2.24
249 250 0.753867 TTGCTCGTTCCCGCCATATA 59.246 50.000 0.00 0.00 0.00 0.86
255 256 2.556287 CACTTTGCTCGTTCCCGC 59.444 61.111 0.00 0.00 0.00 6.13
263 264 2.854185 GCCATATTTTCGCACTTTGCTC 59.146 45.455 0.00 0.00 42.25 4.26
266 267 2.184448 CCGCCATATTTTCGCACTTTG 58.816 47.619 0.00 0.00 0.00 2.77
267 268 1.134175 CCCGCCATATTTTCGCACTTT 59.866 47.619 0.00 0.00 0.00 2.66
271 354 1.464734 TTTCCCGCCATATTTTCGCA 58.535 45.000 0.00 0.00 0.00 5.10
273 356 3.628017 GACATTTCCCGCCATATTTTCG 58.372 45.455 0.00 0.00 0.00 3.46
293 376 1.592400 CCGCTTATATCTCGGGCCGA 61.592 60.000 29.14 29.14 39.52 5.54
325 408 2.431419 TGCATGCACCCCATTTTCTATG 59.569 45.455 18.46 0.00 29.71 2.23
326 409 2.431782 GTGCATGCACCCCATTTTCTAT 59.568 45.455 35.69 0.00 40.79 1.98
327 410 1.824230 GTGCATGCACCCCATTTTCTA 59.176 47.619 35.69 0.00 40.79 2.10
328 411 0.609662 GTGCATGCACCCCATTTTCT 59.390 50.000 35.69 0.00 40.79 2.52
329 412 3.142124 GTGCATGCACCCCATTTTC 57.858 52.632 35.69 11.32 40.79 2.29
352 435 0.995024 AATTGGTCAGCTGTAGGCCT 59.005 50.000 11.78 11.78 43.05 5.19
365 448 5.665812 TGTAGGCTGATTAGGACTAATTGGT 59.334 40.000 6.08 0.00 36.02 3.67
390 522 3.035363 TGACTGGAACTAATCGGCCATA 58.965 45.455 2.24 0.00 0.00 2.74
417 549 0.676184 GAGATCATGTCGGCCAGCTA 59.324 55.000 2.24 0.00 0.00 3.32
430 562 3.510531 ATCGGCCACTAGTAGAGATCA 57.489 47.619 2.24 0.00 0.00 2.92
436 568 2.161030 GGACCTATCGGCCACTAGTAG 58.839 57.143 2.24 0.00 0.00 2.57
437 569 1.544093 CGGACCTATCGGCCACTAGTA 60.544 57.143 2.24 0.00 0.00 1.82
456 588 1.065928 GCCACCGACAGACCTATCG 59.934 63.158 0.00 0.00 38.08 2.92
457 589 1.327690 TGGCCACCGACAGACCTATC 61.328 60.000 0.00 0.00 0.00 2.08
458 590 1.305802 TGGCCACCGACAGACCTAT 60.306 57.895 0.00 0.00 0.00 2.57
459 591 1.982395 CTGGCCACCGACAGACCTA 60.982 63.158 0.00 0.00 36.86 3.08
460 592 3.314331 CTGGCCACCGACAGACCT 61.314 66.667 0.00 0.00 36.86 3.85
461 593 2.788191 CTTCTGGCCACCGACAGACC 62.788 65.000 0.00 0.00 42.91 3.85
462 594 1.374758 CTTCTGGCCACCGACAGAC 60.375 63.158 0.00 0.00 42.91 3.51
463 595 2.583441 CCTTCTGGCCACCGACAGA 61.583 63.158 0.00 0.00 41.63 3.41
504 636 1.905922 GACTTCAGTCGGCTTGCTGC 61.906 60.000 0.00 0.00 36.75 5.25
509 641 2.100605 GATTGGACTTCAGTCGGCTT 57.899 50.000 0.00 0.00 45.65 4.35
510 642 3.842869 GATTGGACTTCAGTCGGCT 57.157 52.632 0.83 0.00 45.65 5.52
522 654 3.565961 TTGCTGCTGGCCGATTGGA 62.566 57.895 1.98 0.00 40.92 3.53
534 695 2.437359 ATCCAGTCGGCTTGCTGC 60.437 61.111 0.00 0.00 41.94 5.25
547 708 0.106868 CAGCTGGCTGATTGGATCCA 60.107 55.000 11.44 11.44 46.30 3.41
548 709 1.453762 GCAGCTGGCTGATTGGATCC 61.454 60.000 24.40 4.20 46.30 3.36
549 710 2.031360 GCAGCTGGCTGATTGGATC 58.969 57.895 24.40 2.97 46.30 3.36
550 711 4.254721 GCAGCTGGCTGATTGGAT 57.745 55.556 24.40 0.00 46.30 3.41
563 724 2.540265 ATACACCATCAGCTAGCAGC 57.460 50.000 18.83 0.00 42.84 5.25
564 725 7.502120 AAAATAATACACCATCAGCTAGCAG 57.498 36.000 18.83 9.54 0.00 4.24
565 726 7.555914 TCAAAAATAATACACCATCAGCTAGCA 59.444 33.333 18.83 0.00 0.00 3.49
566 727 7.930217 TCAAAAATAATACACCATCAGCTAGC 58.070 34.615 6.62 6.62 0.00 3.42
645 806 1.609555 TGGCCGTTCACGCTAATTTTT 59.390 42.857 0.00 0.00 38.18 1.94
646 807 1.240256 TGGCCGTTCACGCTAATTTT 58.760 45.000 0.00 0.00 38.18 1.82
647 808 1.132262 CATGGCCGTTCACGCTAATTT 59.868 47.619 0.00 0.00 38.18 1.82
648 809 0.732571 CATGGCCGTTCACGCTAATT 59.267 50.000 0.00 0.00 38.18 1.40
649 810 0.392461 ACATGGCCGTTCACGCTAAT 60.392 50.000 0.00 0.00 38.18 1.73
650 811 1.004320 ACATGGCCGTTCACGCTAA 60.004 52.632 0.00 0.00 38.18 3.09
651 812 1.739929 CACATGGCCGTTCACGCTA 60.740 57.895 0.00 0.00 38.18 4.26
652 813 3.049674 CACATGGCCGTTCACGCT 61.050 61.111 0.00 0.00 38.18 5.07
653 814 3.308878 GACACATGGCCGTTCACGC 62.309 63.158 0.00 0.00 38.18 5.34
654 815 1.667830 AGACACATGGCCGTTCACG 60.668 57.895 0.00 0.00 39.44 4.35
655 816 0.884704 ACAGACACATGGCCGTTCAC 60.885 55.000 0.00 0.00 0.00 3.18
656 817 0.179032 AACAGACACATGGCCGTTCA 60.179 50.000 0.00 0.00 0.00 3.18
657 818 0.517316 GAACAGACACATGGCCGTTC 59.483 55.000 0.00 0.00 0.00 3.95
658 819 0.108585 AGAACAGACACATGGCCGTT 59.891 50.000 0.00 0.00 0.00 4.44
659 820 0.603707 CAGAACAGACACATGGCCGT 60.604 55.000 0.00 0.00 0.00 5.68
660 821 0.320683 TCAGAACAGACACATGGCCG 60.321 55.000 0.00 0.00 0.00 6.13
661 822 1.896220 TTCAGAACAGACACATGGCC 58.104 50.000 0.00 0.00 0.00 5.36
662 823 3.058639 GTCTTTCAGAACAGACACATGGC 60.059 47.826 15.26 0.00 39.49 4.40
663 824 4.129380 TGTCTTTCAGAACAGACACATGG 58.871 43.478 17.41 0.00 43.63 3.66
669 830 6.851222 TGAGAAATGTCTTTCAGAACAGAC 57.149 37.500 14.08 14.08 42.71 3.51
670 831 9.730705 ATAATGAGAAATGTCTTTCAGAACAGA 57.269 29.630 0.00 0.00 42.71 3.41
742 903 9.823647 TGGTAAGCAATTCAAACTATTCAAAAA 57.176 25.926 0.00 0.00 0.00 1.94
743 904 9.995003 ATGGTAAGCAATTCAAACTATTCAAAA 57.005 25.926 0.00 0.00 0.00 2.44
749 910 9.189156 ACACATATGGTAAGCAATTCAAACTAT 57.811 29.630 7.80 0.00 0.00 2.12
750 911 8.574251 ACACATATGGTAAGCAATTCAAACTA 57.426 30.769 7.80 0.00 0.00 2.24
751 912 7.176515 TGACACATATGGTAAGCAATTCAAACT 59.823 33.333 7.80 0.00 0.00 2.66
752 913 7.273381 GTGACACATATGGTAAGCAATTCAAAC 59.727 37.037 7.80 0.00 0.00 2.93
753 914 7.040132 TGTGACACATATGGTAAGCAATTCAAA 60.040 33.333 3.56 0.00 0.00 2.69
754 915 6.432472 TGTGACACATATGGTAAGCAATTCAA 59.568 34.615 3.56 0.00 0.00 2.69
755 916 5.942826 TGTGACACATATGGTAAGCAATTCA 59.057 36.000 3.56 0.00 0.00 2.57
756 917 6.435430 TGTGACACATATGGTAAGCAATTC 57.565 37.500 3.56 0.00 0.00 2.17
757 918 6.183360 CCATGTGACACATATGGTAAGCAATT 60.183 38.462 20.42 0.00 44.49 2.32
758 919 5.300034 CCATGTGACACATATGGTAAGCAAT 59.700 40.000 20.42 0.00 44.49 3.56
759 920 4.639755 CCATGTGACACATATGGTAAGCAA 59.360 41.667 20.42 0.00 44.49 3.91
760 921 4.198530 CCATGTGACACATATGGTAAGCA 58.801 43.478 20.42 1.13 44.49 3.91
761 922 4.818534 CCATGTGACACATATGGTAAGC 57.181 45.455 20.42 0.00 44.49 3.09
769 930 9.546428 CTCTGAAATTATACCATGTGACACATA 57.454 33.333 20.42 6.37 36.53 2.29
770 931 8.049117 ACTCTGAAATTATACCATGTGACACAT 58.951 33.333 15.48 15.48 39.91 3.21
771 932 7.394016 ACTCTGAAATTATACCATGTGACACA 58.606 34.615 11.41 11.41 0.00 3.72
772 933 7.849804 ACTCTGAAATTATACCATGTGACAC 57.150 36.000 0.00 0.00 0.00 3.67
833 994 3.131755 GCAGGTGTACGGTATTCTTAGGT 59.868 47.826 0.00 0.00 0.00 3.08
835 996 4.380841 TGCAGGTGTACGGTATTCTTAG 57.619 45.455 0.00 0.00 0.00 2.18
836 997 4.804868 TTGCAGGTGTACGGTATTCTTA 57.195 40.909 0.00 0.00 0.00 2.10
838 999 3.688694 TTTGCAGGTGTACGGTATTCT 57.311 42.857 0.00 0.00 0.00 2.40
839 1000 3.064820 CCATTTGCAGGTGTACGGTATTC 59.935 47.826 0.00 0.00 0.00 1.75
841 1002 2.026636 ACCATTTGCAGGTGTACGGTAT 60.027 45.455 0.00 0.00 38.13 2.73
909 1094 0.692476 TGGCAGTGTGTGGATTAGCT 59.308 50.000 0.00 0.00 0.00 3.32
1003 1201 1.017701 GTTTGGGCGGTCGAGGTAAG 61.018 60.000 0.00 0.00 0.00 2.34
1006 1204 3.239253 AGTTTGGGCGGTCGAGGT 61.239 61.111 0.00 0.00 0.00 3.85
1149 1366 6.014669 CCATCTTGATATATCCCTAGCTAGCC 60.015 46.154 15.74 0.00 0.00 3.93
1168 1385 1.002134 CCACCGCAACCTCCATCTT 60.002 57.895 0.00 0.00 0.00 2.40
1225 1442 2.438021 TCCTTTTCCCATCTATCACCGG 59.562 50.000 0.00 0.00 0.00 5.28
1290 1507 0.247460 CTTGGATCGACTGCAGGTCA 59.753 55.000 19.93 0.34 44.70 4.02
1446 1663 1.730501 TCTTCAGCTTGGCGATCTTG 58.269 50.000 0.00 0.00 0.00 3.02
1473 1690 0.100503 GCTGCTCGAGAGTCTCCTTC 59.899 60.000 18.75 4.18 0.00 3.46
1610 1851 2.612115 CCACCTTGAGCCTCCCCT 60.612 66.667 0.00 0.00 0.00 4.79
1611 1852 2.936032 ACCACCTTGAGCCTCCCC 60.936 66.667 0.00 0.00 0.00 4.81
1612 1853 1.904990 GAGACCACCTTGAGCCTCCC 61.905 65.000 0.00 0.00 0.00 4.30
1854 2102 0.038618 CATGTTCGGTGTCGTCTCCA 60.039 55.000 1.90 0.00 37.69 3.86
1864 2112 0.317160 TCAGTCGAAGCATGTTCGGT 59.683 50.000 21.78 12.21 41.78 4.69
2013 2801 8.397906 TCAGAAGAATAACACTGTTGAAACTTG 58.602 33.333 4.57 0.00 0.00 3.16
2015 2803 8.398665 GTTCAGAAGAATAACACTGTTGAAACT 58.601 33.333 4.57 0.00 35.92 2.66
2016 2804 8.398665 AGTTCAGAAGAATAACACTGTTGAAAC 58.601 33.333 4.57 0.00 35.92 2.78
2033 3391 6.609237 TCATGTCTTCAACAAGTTCAGAAG 57.391 37.500 6.67 6.67 42.37 2.85
2036 3394 7.076362 CAGAATCATGTCTTCAACAAGTTCAG 58.924 38.462 11.53 0.00 42.37 3.02
2152 3617 9.704098 GCATGTACTATGTTTTAGAGCTTAAAC 57.296 33.333 11.10 11.10 35.38 2.01
2277 3753 5.991606 CCTACTTGTGAACTTCATTGAGTCA 59.008 40.000 0.00 0.00 0.00 3.41
2278 3754 6.223852 TCCTACTTGTGAACTTCATTGAGTC 58.776 40.000 0.00 0.00 0.00 3.36
2279 3755 6.174720 TCCTACTTGTGAACTTCATTGAGT 57.825 37.500 0.00 3.04 0.00 3.41
2355 3914 7.101652 TCTTGCAATCTTACTAGTCGATTCT 57.898 36.000 14.22 0.00 0.00 2.40
2633 4193 2.887151 AAACCTGGCTTGTGCTATCT 57.113 45.000 0.00 0.00 39.59 1.98
2798 4358 2.887568 CTGACAGGATGGTCGCGC 60.888 66.667 0.00 0.00 43.62 6.86
2837 4397 0.959372 CAAGTCCTTCAGCCAGCCAG 60.959 60.000 0.00 0.00 0.00 4.85
3131 4694 1.814772 TTGGCAAATTCAGTGGCCCG 61.815 55.000 0.00 0.00 45.83 6.13
3214 4777 5.917462 ACTTGGCATAATTCAAATTAGCCC 58.083 37.500 20.77 14.53 40.50 5.19
3246 4809 4.133820 TCTTTGAGATCCAAAACTCGCAA 58.866 39.130 9.64 0.00 43.50 4.85
3341 4904 3.659786 TGGAACCTTGTCAATACTGTCG 58.340 45.455 0.00 0.00 0.00 4.35
3425 4988 1.425066 TGGAGGACTTCAATTGGCAGT 59.575 47.619 5.42 8.19 0.00 4.40
3491 5054 3.309388 CTTCTTCTGTGTGTAGTCACCG 58.691 50.000 0.00 0.00 43.26 4.94
3499 5062 2.042464 TCTCCAGCTTCTTCTGTGTGT 58.958 47.619 0.00 0.00 32.32 3.72
3515 5081 2.755650 TCTTTTGACACGAGCTTCTCC 58.244 47.619 0.00 0.00 0.00 3.71
3525 5091 5.466728 TCTGCAGTTCACTATCTTTTGACAC 59.533 40.000 14.67 0.00 0.00 3.67
3861 5427 3.258372 TCCTCGATGTAGTTCAGCTTTGT 59.742 43.478 0.00 0.00 0.00 2.83
4091 5657 5.804639 AGCATATGAAGTGACACAAGGTAA 58.195 37.500 6.97 0.00 0.00 2.85
4197 5763 5.582665 GCCATCCATCCTTTATCGTATCTTC 59.417 44.000 0.00 0.00 0.00 2.87
4310 5879 4.440112 CGATTTACAATTTCCCCTGCTTCC 60.440 45.833 0.00 0.00 0.00 3.46
4312 5881 3.447229 CCGATTTACAATTTCCCCTGCTT 59.553 43.478 0.00 0.00 0.00 3.91
4314 5883 3.020984 TCCGATTTACAATTTCCCCTGC 58.979 45.455 0.00 0.00 0.00 4.85
4403 5972 1.467734 CTTGCTTCAGTGCATCAGGAC 59.532 52.381 0.00 0.00 42.96 3.85
4509 6113 1.599071 CAAAAGTTCGCTCTGCAGACA 59.401 47.619 13.74 0.00 0.00 3.41
4521 6125 2.919229 CAGCGAATGGATGCAAAAGTTC 59.081 45.455 0.00 0.00 0.00 3.01
4543 6149 0.372679 GCAGCACACACATCATCGAG 59.627 55.000 0.00 0.00 0.00 4.04
4625 6627 3.014623 CAAAGAGGCTGCATCATCTCAA 58.985 45.455 17.19 0.00 0.00 3.02
4661 6664 7.946655 TCGCTCGTAAATTTCTTATCATGAT 57.053 32.000 13.81 13.81 0.00 2.45
4709 6712 5.365895 AGTGGGCTATATTTACTCCGTTCTT 59.634 40.000 0.00 0.00 0.00 2.52
4711 6714 5.211174 AGTGGGCTATATTTACTCCGTTC 57.789 43.478 0.00 0.00 0.00 3.95
4715 6718 4.566987 CGGAAGTGGGCTATATTTACTCC 58.433 47.826 0.00 0.00 0.00 3.85
4725 6728 2.577059 CGAAGCGGAAGTGGGCTA 59.423 61.111 0.00 0.00 38.88 3.93
4760 6763 2.433239 GGGACAATCTTAGCCGTCCTTA 59.567 50.000 7.32 0.00 45.94 2.69
4797 6800 2.424842 TTTTGCCCATCGTGCCCTCT 62.425 55.000 0.00 0.00 0.00 3.69
4963 6986 2.365768 TACATAGCGGGGTGGGCA 60.366 61.111 0.00 0.00 0.00 5.36
5017 7048 4.410400 GCAGCAGGGCCCGTAACT 62.410 66.667 18.44 9.77 0.00 2.24
5725 8146 2.664398 GGGTCGGGGCGTTTTCTA 59.336 61.111 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.