Multiple sequence alignment - TraesCS4A01G298400

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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 TraesCS4A01G298400 chr4A 100.000 3749 0 0 1 3749 597051406 597055154 0.000000e+00 6924.0
1 TraesCS4A01G298400 chr4A 90.381 551 42 5 2357 2900 597030715 597030169 0.000000e+00 713.0
2 TraesCS4A01G298400 chr4A 77.444 399 49 20 34 394 667108644 667108249 2.280000e-47 200.0
3 TraesCS4A01G298400 chr4A 87.421 159 10 5 2012 2163 597030943 597030788 1.380000e-39 174.0
4 TraesCS4A01G298400 chr4A 95.385 65 2 1 2936 3000 597030168 597030105 6.620000e-18 102.0
5 TraesCS4A01G298400 chr4A 92.157 51 3 1 3224 3273 597029869 597029819 1.870000e-08 71.3
6 TraesCS4A01G298400 chr4A 97.561 41 1 0 2245 2285 597030750 597030710 1.870000e-08 71.3
7 TraesCS4A01G298400 chr4D 87.840 3125 184 65 602 3585 6283133 6286202 0.000000e+00 3485.0
8 TraesCS4A01G298400 chr4D 87.024 1102 82 28 2207 3281 6269704 6268637 0.000000e+00 1186.0
9 TraesCS4A01G298400 chr4D 80.992 242 42 4 361 602 6282867 6283104 4.940000e-44 189.0
10 TraesCS4A01G298400 chr4D 84.422 199 21 10 2011 2203 6269856 6269662 1.780000e-43 187.0
11 TraesCS4A01G298400 chr4D 72.964 577 118 20 19 591 471813301 471812759 2.320000e-37 167.0
12 TraesCS4A01G298400 chr4D 84.884 86 4 2 3463 3539 6268485 6268400 1.120000e-10 78.7
13 TraesCS4A01G298400 chr4D 91.071 56 4 1 3284 3339 6268595 6268541 1.440000e-09 75.0
14 TraesCS4A01G298400 chr4B 89.585 2554 151 44 905 3396 11433328 11435828 0.000000e+00 3136.0
15 TraesCS4A01G298400 chr4B 79.719 641 100 22 1198 1817 575771043 575771674 1.600000e-118 436.0
16 TraesCS4A01G298400 chr4B 86.921 367 41 3 2390 2756 11410200 11409841 4.510000e-109 405.0
17 TraesCS4A01G298400 chr4B 87.000 200 22 3 2771 2966 11409764 11409565 4.870000e-54 222.0
18 TraesCS4A01G298400 chr4B 87.719 114 13 1 3284 3397 11407752 11407640 8.450000e-27 132.0
19 TraesCS4A01G298400 chr4B 83.065 124 10 5 3419 3531 11405837 11405714 6.620000e-18 102.0
20 TraesCS4A01G298400 chr4B 79.487 156 19 6 3133 3281 11407940 11407791 8.570000e-17 99.0
21 TraesCS4A01G298400 chr4B 100.000 45 0 0 3024 3068 11409565 11409521 2.400000e-12 84.2
22 TraesCS4A01G298400 chr4B 97.500 40 1 0 3485 3524 11435915 11435954 6.720000e-08 69.4
23 TraesCS4A01G298400 chr1B 83.260 1362 160 37 1646 2979 409833874 409832553 0.000000e+00 1190.0
24 TraesCS4A01G298400 chr1B 75.593 590 104 26 7 593 480443887 480443335 4.810000e-64 255.0
25 TraesCS4A01G298400 chr7D 82.952 1355 142 45 1646 2979 406315156 406313870 0.000000e+00 1140.0
26 TraesCS4A01G298400 chr7D 86.014 143 20 0 39 181 63077651 63077509 1.800000e-33 154.0
27 TraesCS4A01G298400 chr3A 85.073 1092 127 17 1646 2718 358903490 358904564 0.000000e+00 1081.0
28 TraesCS4A01G298400 chr3A 84.456 193 30 0 7 199 225448188 225448380 1.370000e-44 191.0
29 TraesCS4A01G298400 chr3B 80.826 1283 140 56 1717 2979 722586400 722585204 0.000000e+00 909.0
30 TraesCS4A01G298400 chr3B 88.889 63 7 0 1561 1623 722586516 722586454 1.120000e-10 78.7
31 TraesCS4A01G298400 chr5A 87.708 480 45 4 2159 2638 667024614 667024149 7.080000e-152 547.0
32 TraesCS4A01G298400 chr5A 79.444 647 97 21 1198 1817 19067414 19068051 3.460000e-115 425.0
33 TraesCS4A01G298400 chr5D 80.655 641 94 19 1198 1817 28024304 28024935 1.580000e-128 470.0
34 TraesCS4A01G298400 chr5D 79.811 634 100 23 1198 1817 27861511 27860892 1.600000e-118 436.0
35 TraesCS4A01G298400 chr5D 92.857 70 5 0 1978 2047 28025075 28025144 6.620000e-18 102.0
36 TraesCS4A01G298400 chr1D 74.958 595 109 25 1 593 356934187 356933631 1.740000e-58 237.0
37 TraesCS4A01G298400 chr1D 87.413 143 18 0 39 181 32361230 32361372 8.330000e-37 165.0
38 TraesCS4A01G298400 chr7B 79.078 282 27 17 3014 3281 735913028 735913291 8.330000e-37 165.0
39 TraesCS4A01G298400 chr7A 85.430 151 22 0 65 215 549565826 549565976 1.390000e-34 158.0
40 TraesCS4A01G298400 chr2D 86.014 143 20 0 39 181 38908238 38908380 1.800000e-33 154.0
41 TraesCS4A01G298400 chr2D 86.014 143 20 0 39 181 102446528 102446670 1.800000e-33 154.0
42 TraesCS4A01G298400 chr1A 71.101 436 106 18 168 591 363065424 363065851 5.160000e-14 89.8


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 TraesCS4A01G298400 chr4A 597051406 597055154 3748 False 6924.000 6924 100.00000 1 3749 1 chr4A.!!$F1 3748
1 TraesCS4A01G298400 chr4A 597029819 597030943 1124 True 226.320 713 92.58100 2012 3273 5 chr4A.!!$R2 1261
2 TraesCS4A01G298400 chr4D 6282867 6286202 3335 False 1837.000 3485 84.41600 361 3585 2 chr4D.!!$F1 3224
3 TraesCS4A01G298400 chr4D 6268400 6269856 1456 True 381.675 1186 86.85025 2011 3539 4 chr4D.!!$R2 1528
4 TraesCS4A01G298400 chr4B 11433328 11435954 2626 False 1602.700 3136 93.54250 905 3524 2 chr4B.!!$F2 2619
5 TraesCS4A01G298400 chr4B 575771043 575771674 631 False 436.000 436 79.71900 1198 1817 1 chr4B.!!$F1 619
6 TraesCS4A01G298400 chr1B 409832553 409833874 1321 True 1190.000 1190 83.26000 1646 2979 1 chr1B.!!$R1 1333
7 TraesCS4A01G298400 chr1B 480443335 480443887 552 True 255.000 255 75.59300 7 593 1 chr1B.!!$R2 586
8 TraesCS4A01G298400 chr7D 406313870 406315156 1286 True 1140.000 1140 82.95200 1646 2979 1 chr7D.!!$R2 1333
9 TraesCS4A01G298400 chr3A 358903490 358904564 1074 False 1081.000 1081 85.07300 1646 2718 1 chr3A.!!$F2 1072
10 TraesCS4A01G298400 chr3B 722585204 722586516 1312 True 493.850 909 84.85750 1561 2979 2 chr3B.!!$R1 1418
11 TraesCS4A01G298400 chr5A 19067414 19068051 637 False 425.000 425 79.44400 1198 1817 1 chr5A.!!$F1 619
12 TraesCS4A01G298400 chr5D 27860892 27861511 619 True 436.000 436 79.81100 1198 1817 1 chr5D.!!$R1 619
13 TraesCS4A01G298400 chr5D 28024304 28025144 840 False 286.000 470 86.75600 1198 2047 2 chr5D.!!$F1 849
14 TraesCS4A01G298400 chr1D 356933631 356934187 556 True 237.000 237 74.95800 1 593 1 chr1D.!!$R1 592

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
840 894 0.034477 GGACCCGACCCATCACAAAT 60.034 55.0 0.0 0.0 0.0 2.32 F
843 897 0.255890 CCCGACCCATCACAAATCCT 59.744 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 1903 0.107993 TCCAGACGAGGACGACGTAT 60.108 55.0 0.0 0.0 43.97 3.06 R
2825 3159 0.834687 GTGTCCCCCTCCACTGTACA 60.835 60.0 0.0 0.0 0.00 2.90 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
22 23 0.107214 CGGGTACATGGGCAACAGAT 60.107 55.000 0.00 0.00 39.74 2.90
35 36 1.135859 CAACAGATGCAACTTCGGCTC 60.136 52.381 0.00 0.00 0.00 4.70
58 59 4.824515 CGGCCTCCGTCTCCTCCT 62.825 72.222 0.00 0.00 42.73 3.69
59 60 2.601868 GGCCTCCGTCTCCTCCTA 59.398 66.667 0.00 0.00 0.00 2.94
60 61 1.154221 GGCCTCCGTCTCCTCCTAT 59.846 63.158 0.00 0.00 0.00 2.57
63 64 0.468214 CCTCCGTCTCCTCCTATGCA 60.468 60.000 0.00 0.00 0.00 3.96
68 69 1.271934 CGTCTCCTCCTATGCATCCAG 59.728 57.143 0.19 0.00 0.00 3.86
84 85 2.355837 AGCTCGTCGAAAAGCGCA 60.356 55.556 11.47 0.00 43.37 6.09
88 89 2.020016 CGTCGAAAAGCGCATCGG 59.980 61.111 23.60 10.07 39.45 4.18
89 90 2.276680 GTCGAAAAGCGCATCGGC 60.277 61.111 23.60 20.37 39.45 5.54
101 102 2.020131 CATCGGCCTCTGCATGTTC 58.980 57.895 0.00 0.00 40.13 3.18
106 107 0.964358 GGCCTCTGCATGTTCTTGCT 60.964 55.000 0.00 0.00 43.18 3.91
107 108 0.170561 GCCTCTGCATGTTCTTGCTG 59.829 55.000 10.95 10.39 43.18 4.41
153 154 1.135094 ACGCCTCATCTTGGATGGAT 58.865 50.000 7.54 0.00 0.00 3.41
155 156 2.092212 ACGCCTCATCTTGGATGGATTT 60.092 45.455 7.54 0.00 0.00 2.17
156 157 2.551459 CGCCTCATCTTGGATGGATTTC 59.449 50.000 7.54 0.00 0.00 2.17
159 160 4.142790 CCTCATCTTGGATGGATTTCAGG 58.857 47.826 7.54 2.95 0.00 3.86
168 169 2.806945 TGGATTTCAGGATGGTGGTC 57.193 50.000 0.00 0.00 36.16 4.02
170 171 3.459828 TGGATTTCAGGATGGTGGTCTA 58.540 45.455 0.00 0.00 36.16 2.59
171 172 3.199946 TGGATTTCAGGATGGTGGTCTAC 59.800 47.826 0.00 0.00 36.16 2.59
172 173 3.456277 GGATTTCAGGATGGTGGTCTACT 59.544 47.826 0.00 0.00 36.16 2.57
173 174 4.443598 GGATTTCAGGATGGTGGTCTACTC 60.444 50.000 0.00 0.00 36.16 2.59
174 175 2.160721 TCAGGATGGTGGTCTACTCC 57.839 55.000 0.00 0.00 36.16 3.85
211 212 4.753877 CGAGCGCGAACTCCGACA 62.754 66.667 12.10 0.00 41.76 4.35
215 216 2.126071 CGCGAACTCCGACATGGT 60.126 61.111 0.00 0.00 41.76 3.55
222 223 1.450312 CTCCGACATGGTGAAGCCC 60.450 63.158 0.00 0.00 39.52 5.19
232 233 4.269523 TGAAGCCCGCAACCAGCT 62.270 61.111 0.00 0.00 42.61 4.24
254 261 2.202492 CTCCGTCGCGTCTTCCTG 60.202 66.667 5.77 0.00 0.00 3.86
262 269 2.182030 CGTCTTCCTGCTCCGGAC 59.818 66.667 0.00 0.00 31.44 4.79
264 271 2.683933 TCTTCCTGCTCCGGACCC 60.684 66.667 0.00 0.00 31.44 4.46
265 272 4.148825 CTTCCTGCTCCGGACCCG 62.149 72.222 0.00 0.66 39.44 5.28
283 290 4.455137 CCCCCTCCATGGACCCCT 62.455 72.222 11.44 0.00 38.35 4.79
284 291 2.774351 CCCCTCCATGGACCCCTC 60.774 72.222 11.44 0.00 38.35 4.30
287 294 1.768077 CCTCCATGGACCCCTCCTC 60.768 68.421 11.44 0.00 37.48 3.71
288 295 1.316266 CTCCATGGACCCCTCCTCT 59.684 63.158 11.44 0.00 37.48 3.69
290 297 0.326618 TCCATGGACCCCTCCTCTTC 60.327 60.000 11.44 0.00 37.48 2.87
294 301 1.156322 TGGACCCCTCCTCTTCCTCT 61.156 60.000 0.00 0.00 37.48 3.69
295 302 0.043485 GGACCCCTCCTCTTCCTCTT 59.957 60.000 0.00 0.00 33.07 2.85
296 303 1.199615 GACCCCTCCTCTTCCTCTTG 58.800 60.000 0.00 0.00 0.00 3.02
303 310 0.829990 CCTCTTCCTCTTGCTCCTCC 59.170 60.000 0.00 0.00 0.00 4.30
311 318 2.187100 CTCTTGCTCCTCCTCCTTCTT 58.813 52.381 0.00 0.00 0.00 2.52
313 320 0.898320 TTGCTCCTCCTCCTTCTTCG 59.102 55.000 0.00 0.00 0.00 3.79
314 321 0.972983 TGCTCCTCCTCCTTCTTCGG 60.973 60.000 0.00 0.00 0.00 4.30
316 323 2.010582 CTCCTCCTCCTTCTTCGGCG 62.011 65.000 0.00 0.00 0.00 6.46
317 324 2.052690 CCTCCTCCTTCTTCGGCGA 61.053 63.158 4.99 4.99 0.00 5.54
318 325 1.435515 CTCCTCCTTCTTCGGCGAG 59.564 63.158 10.46 4.79 0.00 5.03
319 326 1.304217 TCCTCCTTCTTCGGCGAGT 60.304 57.895 10.46 0.00 0.00 4.18
320 327 0.898789 TCCTCCTTCTTCGGCGAGTT 60.899 55.000 10.46 0.00 0.00 3.01
327 334 1.741770 CTTCGGCGAGTTTGGAGGG 60.742 63.158 10.46 0.00 0.00 4.30
371 378 1.611965 GCCTTGCCCAGATCTCCTT 59.388 57.895 0.00 0.00 0.00 3.36
384 391 3.779183 AGATCTCCTTCTGCATCTGGAAA 59.221 43.478 0.00 0.00 0.00 3.13
385 392 3.623906 TCTCCTTCTGCATCTGGAAAG 57.376 47.619 0.00 0.00 0.00 2.62
386 393 2.909006 TCTCCTTCTGCATCTGGAAAGT 59.091 45.455 0.00 0.00 0.00 2.66
389 396 2.553904 CCTTCTGCATCTGGAAAGTGGT 60.554 50.000 0.00 0.00 0.00 4.16
395 402 1.067295 ATCTGGAAAGTGGTGCTCCA 58.933 50.000 2.64 2.64 42.05 3.86
396 403 0.843309 TCTGGAAAGTGGTGCTCCAA 59.157 50.000 9.53 0.00 46.15 3.53
398 405 0.817634 TGGAAAGTGGTGCTCCAACG 60.818 55.000 9.53 0.00 46.15 4.10
401 408 2.215196 GAAAGTGGTGCTCCAACGTTA 58.785 47.619 9.53 0.00 46.15 3.18
402 409 2.335316 AAGTGGTGCTCCAACGTTAA 57.665 45.000 9.53 0.00 46.15 2.01
406 413 3.068560 GTGGTGCTCCAACGTTAACATA 58.931 45.455 9.53 0.00 46.15 2.29
412 419 6.199719 GGTGCTCCAACGTTAACATAGTATAC 59.800 42.308 0.00 0.00 0.00 1.47
413 420 6.753279 GTGCTCCAACGTTAACATAGTATACA 59.247 38.462 0.00 0.00 0.00 2.29
416 423 7.650504 GCTCCAACGTTAACATAGTATACATGA 59.349 37.037 17.00 0.00 0.00 3.07
418 425 9.471084 TCCAACGTTAACATAGTATACATGATG 57.529 33.333 17.00 13.42 0.00 3.07
438 445 2.084546 GTTGTTCTACTGGGCCATGAC 58.915 52.381 6.72 2.25 0.00 3.06
440 447 0.535335 GTTCTACTGGGCCATGACGA 59.465 55.000 6.72 0.00 0.00 4.20
447 454 1.450312 GGGCCATGACGAAGACAGG 60.450 63.158 4.39 0.00 34.76 4.00
463 470 4.840005 GGCGGCGAGGAAAGAGGG 62.840 72.222 12.98 0.00 0.00 4.30
468 475 1.258445 GGCGAGGAAAGAGGGAGACA 61.258 60.000 0.00 0.00 0.00 3.41
469 476 0.174617 GCGAGGAAAGAGGGAGACAG 59.825 60.000 0.00 0.00 0.00 3.51
473 480 2.758423 GAGGAAAGAGGGAGACAGAGAC 59.242 54.545 0.00 0.00 0.00 3.36
481 488 2.241176 AGGGAGACAGAGACGAAGAGAT 59.759 50.000 0.00 0.00 0.00 2.75
482 489 3.456644 AGGGAGACAGAGACGAAGAGATA 59.543 47.826 0.00 0.00 0.00 1.98
487 494 5.630121 AGACAGAGACGAAGAGATATGGAT 58.370 41.667 0.00 0.00 0.00 3.41
491 498 2.564947 AGACGAAGAGATATGGATGGGC 59.435 50.000 0.00 0.00 0.00 5.36
498 505 2.235898 GAGATATGGATGGGCTCAGACC 59.764 54.545 0.00 0.00 0.00 3.85
501 508 2.764128 GGATGGGCTCAGACCGGA 60.764 66.667 9.46 0.00 29.56 5.14
515 522 4.082523 CGGAGGCGCAAAGGAGGA 62.083 66.667 10.83 0.00 0.00 3.71
516 523 2.592308 GGAGGCGCAAAGGAGGAT 59.408 61.111 10.83 0.00 0.00 3.24
519 526 0.392998 GAGGCGCAAAGGAGGATGAA 60.393 55.000 10.83 0.00 0.00 2.57
533 540 5.598005 AGGAGGATGAAGAAGATGTGACTAG 59.402 44.000 0.00 0.00 0.00 2.57
537 544 3.445008 TGAAGAAGATGTGACTAGGGCT 58.555 45.455 0.00 0.00 0.00 5.19
540 547 3.571590 AGAAGATGTGACTAGGGCTAGG 58.428 50.000 0.00 0.00 37.49 3.02
579 586 1.389609 TAGCCGGACTTTAGCCTCGG 61.390 60.000 5.05 0.00 43.13 4.63
603 610 3.857038 GAGCCGGCGTATCCCCAA 61.857 66.667 23.20 0.00 0.00 4.12
608 644 1.444119 CCGGCGTATCCCCAACATTG 61.444 60.000 6.01 0.00 0.00 2.82
626 662 2.607892 GCCACAGTTGAGGCGTGTC 61.608 63.158 4.85 0.00 41.64 3.67
629 665 1.227556 ACAGTTGAGGCGTGTCCAC 60.228 57.895 0.00 0.00 37.29 4.02
656 692 4.456253 CGTCCGTCCGGAGACACG 62.456 72.222 20.28 16.74 46.16 4.49
665 701 1.584495 CGGAGACACGGACACATCA 59.416 57.895 0.00 0.00 0.00 3.07
694 730 2.809601 GTAGCACGGCGTCCACAG 60.810 66.667 10.85 0.00 0.00 3.66
700 736 4.436998 CGGCGTCCACAGAGTCCC 62.437 72.222 0.00 0.00 0.00 4.46
716 752 1.449246 CCCGGAGCAGCAGAAGAAG 60.449 63.158 0.73 0.00 0.00 2.85
717 753 1.449246 CCGGAGCAGCAGAAGAAGG 60.449 63.158 0.00 0.00 0.00 3.46
718 754 1.593787 CGGAGCAGCAGAAGAAGGA 59.406 57.895 0.00 0.00 0.00 3.36
730 766 2.234414 AGAAGAAGGAGCAGAAGAGCAG 59.766 50.000 0.00 0.00 36.85 4.24
751 787 2.877975 GTGGCCTCCACGTAGTAGA 58.122 57.895 3.32 0.00 44.95 2.59
752 788 0.455005 GTGGCCTCCACGTAGTAGAC 59.545 60.000 3.32 0.00 44.95 2.59
777 814 3.998672 GCCCACGTTCCCACTCGA 61.999 66.667 0.00 0.00 0.00 4.04
833 887 4.096003 CGCAAGGACCCGACCCAT 62.096 66.667 0.00 0.00 0.00 4.00
840 894 0.034477 GGACCCGACCCATCACAAAT 60.034 55.000 0.00 0.00 0.00 2.32
843 897 0.255890 CCCGACCCATCACAAATCCT 59.744 55.000 0.00 0.00 0.00 3.24
847 901 2.743183 CGACCCATCACAAATCCTCTCC 60.743 54.545 0.00 0.00 0.00 3.71
848 902 2.239654 GACCCATCACAAATCCTCTCCA 59.760 50.000 0.00 0.00 0.00 3.86
851 908 3.539604 CCATCACAAATCCTCTCCACTC 58.460 50.000 0.00 0.00 0.00 3.51
879 936 4.467084 GCCGAGCATTCCCCGACA 62.467 66.667 0.00 0.00 0.00 4.35
880 937 2.511600 CCGAGCATTCCCCGACAC 60.512 66.667 0.00 0.00 0.00 3.67
885 960 2.186903 CATTCCCCGACACCTCCG 59.813 66.667 0.00 0.00 0.00 4.63
926 1018 3.459965 CGCTCAGCCTCAGCCTCT 61.460 66.667 0.00 0.00 41.25 3.69
987 1079 4.185286 GCCCGATTTAGCCCCCGT 62.185 66.667 0.00 0.00 0.00 5.28
1305 1411 3.197614 CGCCTCTTCTACTGCGGA 58.802 61.111 0.00 0.00 43.08 5.54
1779 1903 0.741927 TCGTCTCCATCTACGTCGCA 60.742 55.000 0.00 0.00 39.99 5.10
1878 2036 0.459237 TCCTAGAGGACGACGACGAC 60.459 60.000 15.32 7.84 39.78 4.34
1879 2037 1.630026 CTAGAGGACGACGACGACG 59.370 63.158 17.60 17.60 42.66 5.12
1880 2038 0.799917 CTAGAGGACGACGACGACGA 60.800 60.000 25.15 1.75 42.66 4.20
1881 2039 1.073216 TAGAGGACGACGACGACGAC 61.073 60.000 25.15 18.64 42.66 4.34
1908 2066 4.554363 CCGCTGCCGTCCTACTCG 62.554 72.222 0.00 0.00 0.00 4.18
2825 3159 1.065273 CGGCGATGTACGTAGGCTT 59.935 57.895 17.44 0.00 44.60 4.35
2828 3162 1.066002 GGCGATGTACGTAGGCTTGTA 59.934 52.381 13.45 0.00 44.60 2.41
2829 3163 2.114825 GCGATGTACGTAGGCTTGTAC 58.885 52.381 17.81 17.81 44.60 2.90
2839 3176 1.201429 AGGCTTGTACAGTGGAGGGG 61.201 60.000 0.00 0.00 0.00 4.79
2909 3254 0.940126 GCGATCAGCCATTAGGTGTG 59.060 55.000 0.00 0.00 44.62 3.82
2966 3323 4.774124 TGATTGTTTTGGTTGGCATCAAA 58.226 34.783 10.98 10.98 34.28 2.69
3006 3363 5.028428 GGTACGTACCGAGAGATGAATAC 57.972 47.826 28.00 1.18 36.50 1.89
3010 3367 4.579340 ACGTACCGAGAGATGAATACATGT 59.421 41.667 2.69 2.69 36.82 3.21
3012 3369 6.078479 CGTACCGAGAGATGAATACATGTAC 58.922 44.000 7.96 0.00 36.82 2.90
3021 3408 8.228464 AGAGATGAATACATGTACGTACGTATG 58.772 37.037 29.05 25.79 36.82 2.39
3032 3419 4.238761 ACGTACGTATGGATCTGGATTG 57.761 45.455 21.41 0.00 0.00 2.67
3068 3473 4.253273 GCTCGACGTTGCGATCGC 62.253 66.667 32.48 32.48 39.85 4.58
3131 3536 1.067283 GGCCATCGATCGATCATCTGT 60.067 52.381 27.20 3.21 31.62 3.41
3195 3614 2.190841 CCGTTTCACCCGGCTTGTT 61.191 57.895 0.00 0.00 38.85 2.83
3203 3622 3.426615 TCACCCGGCTTGTTTTGATAAT 58.573 40.909 0.00 0.00 0.00 1.28
3205 3624 3.925913 CACCCGGCTTGTTTTGATAATTG 59.074 43.478 0.00 0.00 0.00 2.32
3206 3625 3.056179 ACCCGGCTTGTTTTGATAATTGG 60.056 43.478 0.00 0.00 0.00 3.16
3207 3626 2.929398 CCGGCTTGTTTTGATAATTGGC 59.071 45.455 0.00 0.00 0.00 4.52
3222 3644 3.512516 GGCTTGCCTCGTCATGCC 61.513 66.667 4.11 12.92 45.74 4.40
3223 3645 2.437359 GCTTGCCTCGTCATGCCT 60.437 61.111 0.00 0.00 32.82 4.75
3234 3656 4.530857 CATGCCTCCGTCCGTCCC 62.531 72.222 0.00 0.00 0.00 4.46
3235 3657 4.779733 ATGCCTCCGTCCGTCCCT 62.780 66.667 0.00 0.00 0.00 4.20
3272 3718 2.351726 GCGCCGACAGACAAAATCTAAT 59.648 45.455 0.00 0.00 35.15 1.73
3273 3719 3.544244 GCGCCGACAGACAAAATCTAATC 60.544 47.826 0.00 0.00 35.15 1.75
3275 3721 3.938963 GCCGACAGACAAAATCTAATCCA 59.061 43.478 0.00 0.00 35.15 3.41
3278 3724 5.874810 CCGACAGACAAAATCTAATCCAAGA 59.125 40.000 0.00 0.00 35.15 3.02
3279 3725 6.183360 CCGACAGACAAAATCTAATCCAAGAC 60.183 42.308 0.00 0.00 35.15 3.01
3280 3726 6.368791 CGACAGACAAAATCTAATCCAAGACA 59.631 38.462 0.00 0.00 35.15 3.41
3281 3727 7.065085 CGACAGACAAAATCTAATCCAAGACAT 59.935 37.037 0.00 0.00 35.15 3.06
3282 3728 8.048534 ACAGACAAAATCTAATCCAAGACATG 57.951 34.615 0.00 0.00 35.15 3.21
3283 3729 7.884877 ACAGACAAAATCTAATCCAAGACATGA 59.115 33.333 0.00 0.00 35.15 3.07
3286 3732 8.408043 ACAAAATCTAATCCAAGACATGAACA 57.592 30.769 0.00 0.00 0.00 3.18
3350 3835 2.483876 GCCGAATCTAGCAGCATGTTA 58.516 47.619 0.00 0.00 39.31 2.41
3368 3853 7.872483 AGCATGTTAGTTTTGTTCCCTTAAATG 59.128 33.333 0.00 0.00 0.00 2.32
3402 3887 4.205587 GCATGATTCTCCCTTCTTGATGT 58.794 43.478 0.00 0.00 0.00 3.06
3407 3892 5.250543 TGATTCTCCCTTCTTGATGTTGGTA 59.749 40.000 0.00 0.00 0.00 3.25
3408 3893 4.553330 TCTCCCTTCTTGATGTTGGTAC 57.447 45.455 0.00 0.00 0.00 3.34
3411 3896 3.650942 TCCCTTCTTGATGTTGGTACTGT 59.349 43.478 0.00 0.00 0.00 3.55
3412 3897 3.753272 CCCTTCTTGATGTTGGTACTGTG 59.247 47.826 0.00 0.00 0.00 3.66
3413 3898 3.189287 CCTTCTTGATGTTGGTACTGTGC 59.811 47.826 0.00 0.00 0.00 4.57
3414 3899 2.778299 TCTTGATGTTGGTACTGTGCC 58.222 47.619 8.09 8.09 0.00 5.01
3440 3949 0.756070 TGGCATACACGTATCCGGGA 60.756 55.000 0.00 0.00 41.01 5.14
3458 3967 4.066139 GGAGGGGGCAGGCACAAT 62.066 66.667 0.00 0.00 0.00 2.71
3460 3969 1.610379 GAGGGGGCAGGCACAATTT 60.610 57.895 0.00 0.00 0.00 1.82
3461 3970 1.891722 GAGGGGGCAGGCACAATTTG 61.892 60.000 0.00 0.00 0.00 2.32
3477 3986 1.484038 TTTGGTGCTTTGCTCCTGTT 58.516 45.000 11.18 0.00 42.02 3.16
3489 4002 0.674895 CTCCTGTTGTACTGCCCTGC 60.675 60.000 0.00 0.00 0.00 4.85
3555 4073 0.522495 CGCGGGCGGAAATAAACAAG 60.522 55.000 4.92 0.00 35.56 3.16
3585 4103 2.363147 GGACCGTCCTGCTCCTCT 60.363 66.667 10.59 0.00 32.53 3.69
3586 4104 2.419739 GGACCGTCCTGCTCCTCTC 61.420 68.421 10.59 0.00 32.53 3.20
3587 4105 2.363147 ACCGTCCTGCTCCTCTCC 60.363 66.667 0.00 0.00 0.00 3.71
3588 4106 2.363018 CCGTCCTGCTCCTCTCCA 60.363 66.667 0.00 0.00 0.00 3.86
3589 4107 2.716017 CCGTCCTGCTCCTCTCCAC 61.716 68.421 0.00 0.00 0.00 4.02
3590 4108 2.888863 GTCCTGCTCCTCTCCACG 59.111 66.667 0.00 0.00 0.00 4.94
3591 4109 3.071206 TCCTGCTCCTCTCCACGC 61.071 66.667 0.00 0.00 0.00 5.34
3592 4110 4.504916 CCTGCTCCTCTCCACGCG 62.505 72.222 3.53 3.53 0.00 6.01
3595 4113 3.518998 GCTCCTCTCCACGCGCTA 61.519 66.667 5.73 0.00 0.00 4.26
3596 4114 2.718731 CTCCTCTCCACGCGCTAG 59.281 66.667 5.73 0.37 0.00 3.42
3597 4115 3.477224 CTCCTCTCCACGCGCTAGC 62.477 68.421 5.73 4.06 40.74 3.42
3598 4116 3.826754 CCTCTCCACGCGCTAGCA 61.827 66.667 16.45 0.00 45.49 3.49
3599 4117 2.580867 CTCTCCACGCGCTAGCAC 60.581 66.667 16.45 3.62 45.49 4.40
3600 4118 3.342370 CTCTCCACGCGCTAGCACA 62.342 63.158 16.45 0.00 45.49 4.57
3601 4119 3.181967 CTCCACGCGCTAGCACAC 61.182 66.667 16.45 2.22 45.49 3.82
3626 4144 3.541713 CCTAGCTCCACCCGGCTC 61.542 72.222 0.00 0.00 39.65 4.70
3627 4145 3.905678 CTAGCTCCACCCGGCTCG 61.906 72.222 0.00 0.00 39.65 5.03
3628 4146 4.753662 TAGCTCCACCCGGCTCGT 62.754 66.667 0.00 0.00 39.65 4.18
3641 4159 2.251371 CTCGTCGTCGTGCAGTGA 59.749 61.111 1.33 0.00 38.33 3.41
3642 4160 1.154207 CTCGTCGTCGTGCAGTGAT 60.154 57.895 1.33 0.00 38.33 3.06
3643 4161 1.128724 CTCGTCGTCGTGCAGTGATC 61.129 60.000 1.33 0.00 38.33 2.92
3644 4162 2.152699 CGTCGTCGTGCAGTGATCC 61.153 63.158 0.00 0.00 0.00 3.36
3645 4163 1.080772 GTCGTCGTGCAGTGATCCA 60.081 57.895 0.00 0.00 0.00 3.41
3646 4164 1.080772 TCGTCGTGCAGTGATCCAC 60.081 57.895 0.00 0.00 34.10 4.02
3650 4168 2.436646 GTGCAGTGATCCACGGGG 60.437 66.667 0.00 0.00 39.64 5.73
3663 4181 2.281208 CGGGGAACGGTTGCTTCA 60.281 61.111 12.19 0.00 39.42 3.02
3664 4182 2.325082 CGGGGAACGGTTGCTTCAG 61.325 63.158 12.19 0.00 39.42 3.02
3665 4183 1.072505 GGGGAACGGTTGCTTCAGA 59.927 57.895 12.19 0.00 0.00 3.27
3666 4184 0.536460 GGGGAACGGTTGCTTCAGAA 60.536 55.000 12.19 0.00 0.00 3.02
3667 4185 0.875059 GGGAACGGTTGCTTCAGAAG 59.125 55.000 12.19 5.72 0.00 2.85
3668 4186 0.875059 GGAACGGTTGCTTCAGAAGG 59.125 55.000 12.30 0.00 0.00 3.46
3669 4187 1.542547 GGAACGGTTGCTTCAGAAGGA 60.543 52.381 12.30 6.26 0.00 3.36
3670 4188 1.531578 GAACGGTTGCTTCAGAAGGAC 59.468 52.381 12.30 4.34 0.00 3.85
3671 4189 0.600255 ACGGTTGCTTCAGAAGGACG 60.600 55.000 12.30 11.91 0.00 4.79
3672 4190 0.600255 CGGTTGCTTCAGAAGGACGT 60.600 55.000 12.30 0.00 0.00 4.34
3673 4191 0.868406 GGTTGCTTCAGAAGGACGTG 59.132 55.000 12.30 0.00 0.00 4.49
3674 4192 0.235926 GTTGCTTCAGAAGGACGTGC 59.764 55.000 12.30 0.00 0.00 5.34
3675 4193 0.106708 TTGCTTCAGAAGGACGTGCT 59.893 50.000 12.30 2.68 0.00 4.40
3676 4194 0.319900 TGCTTCAGAAGGACGTGCTC 60.320 55.000 10.99 4.17 0.00 4.26
3677 4195 0.319900 GCTTCAGAAGGACGTGCTCA 60.320 55.000 10.99 0.00 0.00 4.26
3678 4196 1.873903 GCTTCAGAAGGACGTGCTCAA 60.874 52.381 10.99 0.36 0.00 3.02
3679 4197 2.693069 CTTCAGAAGGACGTGCTCAAT 58.307 47.619 10.99 0.00 0.00 2.57
3680 4198 2.839486 TCAGAAGGACGTGCTCAATT 57.161 45.000 10.99 0.00 0.00 2.32
3681 4199 2.416747 TCAGAAGGACGTGCTCAATTG 58.583 47.619 10.99 6.87 0.00 2.32
3682 4200 2.146342 CAGAAGGACGTGCTCAATTGT 58.854 47.619 10.99 0.00 0.00 2.71
3683 4201 2.549754 CAGAAGGACGTGCTCAATTGTT 59.450 45.455 10.99 0.00 0.00 2.83
3684 4202 2.808543 AGAAGGACGTGCTCAATTGTTC 59.191 45.455 10.99 1.92 0.00 3.18
3685 4203 2.254546 AGGACGTGCTCAATTGTTCA 57.745 45.000 2.68 1.95 0.00 3.18
3686 4204 1.873591 AGGACGTGCTCAATTGTTCAC 59.126 47.619 2.68 17.03 0.00 3.18
3687 4205 1.069227 GGACGTGCTCAATTGTTCACC 60.069 52.381 19.40 11.11 0.00 4.02
3688 4206 0.586319 ACGTGCTCAATTGTTCACCG 59.414 50.000 19.40 17.07 0.00 4.94
3689 4207 0.865111 CGTGCTCAATTGTTCACCGA 59.135 50.000 19.40 0.00 0.00 4.69
3690 4208 1.398451 CGTGCTCAATTGTTCACCGAC 60.398 52.381 19.40 4.73 0.00 4.79
3691 4209 1.069227 GTGCTCAATTGTTCACCGACC 60.069 52.381 16.50 0.00 0.00 4.79
3692 4210 0.521735 GCTCAATTGTTCACCGACCC 59.478 55.000 5.13 0.00 0.00 4.46
3693 4211 1.890876 CTCAATTGTTCACCGACCCA 58.109 50.000 5.13 0.00 0.00 4.51
3694 4212 1.535462 CTCAATTGTTCACCGACCCAC 59.465 52.381 5.13 0.00 0.00 4.61
3695 4213 0.237235 CAATTGTTCACCGACCCACG 59.763 55.000 0.00 0.00 42.18 4.94
3718 4236 2.817834 GCGCACGCAACCATCCTA 60.818 61.111 10.65 0.00 41.49 2.94
3719 4237 2.395360 GCGCACGCAACCATCCTAA 61.395 57.895 10.65 0.00 41.49 2.69
3720 4238 1.917782 GCGCACGCAACCATCCTAAA 61.918 55.000 10.65 0.00 41.49 1.85
3721 4239 0.519519 CGCACGCAACCATCCTAAAA 59.480 50.000 0.00 0.00 0.00 1.52
3722 4240 1.068885 CGCACGCAACCATCCTAAAAA 60.069 47.619 0.00 0.00 0.00 1.94
3742 4260 3.575965 AAAAAGCCGCTCATTTCGAAT 57.424 38.095 0.00 0.00 0.00 3.34
3743 4261 4.695217 AAAAAGCCGCTCATTTCGAATA 57.305 36.364 0.00 0.00 0.00 1.75
3744 4262 4.900635 AAAAGCCGCTCATTTCGAATAT 57.099 36.364 0.00 0.00 0.00 1.28
3745 4263 4.900635 AAAGCCGCTCATTTCGAATATT 57.099 36.364 0.00 0.00 0.00 1.28
3746 4264 4.900635 AAGCCGCTCATTTCGAATATTT 57.099 36.364 0.00 0.00 0.00 1.40
3747 4265 4.474226 AGCCGCTCATTTCGAATATTTC 57.526 40.909 0.00 0.00 0.00 2.17
3748 4266 3.876914 AGCCGCTCATTTCGAATATTTCA 59.123 39.130 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.160137 GAGCCGAAGTTGCATCTGTT 58.840 50.000 0.00 0.00 0.00 3.16
42 43 1.154221 ATAGGAGGAGACGGAGGCC 59.846 63.158 0.00 0.00 0.00 5.19
49 50 1.001860 GCTGGATGCATAGGAGGAGAC 59.998 57.143 0.00 0.00 42.31 3.36
55 56 0.676184 GACGAGCTGGATGCATAGGA 59.324 55.000 1.44 0.00 45.94 2.94
56 57 0.665670 CGACGAGCTGGATGCATAGG 60.666 60.000 1.44 0.00 45.94 2.57
57 58 0.312102 TCGACGAGCTGGATGCATAG 59.688 55.000 1.44 0.00 45.94 2.23
58 59 0.744281 TTCGACGAGCTGGATGCATA 59.256 50.000 1.44 0.00 45.94 3.14
59 60 0.108186 TTTCGACGAGCTGGATGCAT 60.108 50.000 0.00 0.00 45.94 3.96
60 61 0.320334 TTTTCGACGAGCTGGATGCA 60.320 50.000 1.44 0.00 45.94 3.96
63 64 1.078759 CGCTTTTCGACGAGCTGGAT 61.079 55.000 15.00 0.00 41.67 3.41
68 69 1.296216 GATGCGCTTTTCGACGAGC 60.296 57.895 9.73 8.74 41.67 5.03
84 85 0.254178 AAGAACATGCAGAGGCCGAT 59.746 50.000 0.00 0.00 40.13 4.18
96 97 1.741706 CGCTTCATCCAGCAAGAACAT 59.258 47.619 0.00 0.00 40.09 2.71
101 102 2.796651 GGCGCTTCATCCAGCAAG 59.203 61.111 7.64 0.00 40.09 4.01
106 107 2.745884 CAACCGGCGCTTCATCCA 60.746 61.111 7.64 0.00 0.00 3.41
107 108 3.508840 CCAACCGGCGCTTCATCC 61.509 66.667 7.64 0.00 0.00 3.51
153 154 2.838202 GGAGTAGACCACCATCCTGAAA 59.162 50.000 0.00 0.00 0.00 2.69
155 156 1.685180 CGGAGTAGACCACCATCCTGA 60.685 57.143 0.00 0.00 0.00 3.86
156 157 0.747255 CGGAGTAGACCACCATCCTG 59.253 60.000 0.00 0.00 0.00 3.86
159 160 1.327690 TGGCGGAGTAGACCACCATC 61.328 60.000 0.00 0.00 37.24 3.51
168 169 2.336809 GCGGAGATGGCGGAGTAG 59.663 66.667 0.00 0.00 0.00 2.57
197 198 3.554692 CCATGTCGGAGTTCGCGC 61.555 66.667 0.00 0.00 39.05 6.86
199 200 0.669318 TTCACCATGTCGGAGTTCGC 60.669 55.000 0.00 0.00 38.63 4.70
209 210 2.115052 TTGCGGGCTTCACCATGT 59.885 55.556 0.00 0.00 42.05 3.21
211 212 2.676471 GGTTGCGGGCTTCACCAT 60.676 61.111 0.00 0.00 42.05 3.55
236 243 4.117661 AGGAAGACGCGACGGAGC 62.118 66.667 15.93 0.00 0.00 4.70
237 244 2.202492 CAGGAAGACGCGACGGAG 60.202 66.667 15.93 0.00 0.00 4.63
238 245 4.415332 GCAGGAAGACGCGACGGA 62.415 66.667 15.93 0.00 0.00 4.69
239 246 4.421479 AGCAGGAAGACGCGACGG 62.421 66.667 15.93 0.00 0.00 4.79
240 247 2.876645 GAGCAGGAAGACGCGACG 60.877 66.667 15.93 0.00 0.00 5.12
241 248 2.507324 GGAGCAGGAAGACGCGAC 60.507 66.667 15.93 6.86 0.00 5.19
242 249 4.116328 CGGAGCAGGAAGACGCGA 62.116 66.667 15.93 0.00 0.00 5.87
244 251 3.760035 TCCGGAGCAGGAAGACGC 61.760 66.667 0.00 0.00 37.36 5.19
245 252 2.182030 GTCCGGAGCAGGAAGACG 59.818 66.667 3.06 0.00 42.77 4.18
246 253 2.579738 GGTCCGGAGCAGGAAGAC 59.420 66.667 28.27 1.80 42.77 3.01
247 254 2.683933 GGGTCCGGAGCAGGAAGA 60.684 66.667 32.94 0.00 42.77 2.87
248 255 4.148825 CGGGTCCGGAGCAGGAAG 62.149 72.222 32.94 15.34 42.77 3.46
283 290 1.621072 GGAGGAGCAAGAGGAAGAGGA 60.621 57.143 0.00 0.00 0.00 3.71
284 291 0.829990 GGAGGAGCAAGAGGAAGAGG 59.170 60.000 0.00 0.00 0.00 3.69
287 294 0.829990 GGAGGAGGAGCAAGAGGAAG 59.170 60.000 0.00 0.00 0.00 3.46
288 295 0.415429 AGGAGGAGGAGCAAGAGGAA 59.585 55.000 0.00 0.00 0.00 3.36
290 297 0.829990 GAAGGAGGAGGAGCAAGAGG 59.170 60.000 0.00 0.00 0.00 3.69
294 301 0.898320 CGAAGAAGGAGGAGGAGCAA 59.102 55.000 0.00 0.00 0.00 3.91
295 302 0.972983 CCGAAGAAGGAGGAGGAGCA 60.973 60.000 0.00 0.00 0.00 4.26
296 303 1.819905 CCGAAGAAGGAGGAGGAGC 59.180 63.158 0.00 0.00 0.00 4.70
303 310 1.071605 CAAACTCGCCGAAGAAGGAG 58.928 55.000 0.00 0.00 0.00 3.69
311 318 2.602267 TCCCTCCAAACTCGCCGA 60.602 61.111 0.00 0.00 0.00 5.54
313 320 2.269241 CCTCCCTCCAAACTCGCC 59.731 66.667 0.00 0.00 0.00 5.54
314 321 2.436824 GCCTCCCTCCAAACTCGC 60.437 66.667 0.00 0.00 0.00 5.03
316 323 2.269241 CGGCCTCCCTCCAAACTC 59.731 66.667 0.00 0.00 0.00 3.01
317 324 3.330720 CCGGCCTCCCTCCAAACT 61.331 66.667 0.00 0.00 0.00 2.66
353 360 0.465278 GAAGGAGATCTGGGCAAGGC 60.465 60.000 0.00 0.00 0.00 4.35
357 364 0.911045 TGCAGAAGGAGATCTGGGCA 60.911 55.000 0.00 0.00 45.60 5.36
358 365 0.473326 ATGCAGAAGGAGATCTGGGC 59.527 55.000 0.00 0.00 45.60 5.36
371 378 1.883638 GCACCACTTTCCAGATGCAGA 60.884 52.381 0.00 0.00 33.27 4.26
384 391 1.134340 TGTTAACGTTGGAGCACCACT 60.134 47.619 11.99 0.00 46.80 4.00
385 392 1.301423 TGTTAACGTTGGAGCACCAC 58.699 50.000 11.99 0.00 46.80 4.16
386 393 2.264005 ATGTTAACGTTGGAGCACCA 57.736 45.000 11.99 0.00 45.34 4.17
389 396 6.865411 TGTATACTATGTTAACGTTGGAGCA 58.135 36.000 11.99 0.00 0.00 4.26
396 403 9.811995 ACAACATCATGTATACTATGTTAACGT 57.188 29.630 21.06 15.78 39.80 3.99
406 413 7.500992 CCCAGTAGAACAACATCATGTATACT 58.499 38.462 4.17 0.00 36.85 2.12
412 419 2.684881 GGCCCAGTAGAACAACATCATG 59.315 50.000 0.00 0.00 0.00 3.07
413 420 2.308570 TGGCCCAGTAGAACAACATCAT 59.691 45.455 0.00 0.00 0.00 2.45
416 423 2.308570 TCATGGCCCAGTAGAACAACAT 59.691 45.455 0.00 0.00 0.00 2.71
418 425 2.084546 GTCATGGCCCAGTAGAACAAC 58.915 52.381 0.00 0.00 0.00 3.32
426 433 1.296715 GTCTTCGTCATGGCCCAGT 59.703 57.895 0.00 0.00 0.00 4.00
428 435 1.296392 CTGTCTTCGTCATGGCCCA 59.704 57.895 0.00 0.00 0.00 5.36
440 447 2.788191 CTTTCCTCGCCGCCTGTCTT 62.788 60.000 0.00 0.00 0.00 3.01
447 454 3.724914 CTCCCTCTTTCCTCGCCGC 62.725 68.421 0.00 0.00 0.00 6.53
463 470 5.060506 TCCATATCTCTTCGTCTCTGTCTC 58.939 45.833 0.00 0.00 0.00 3.36
468 475 4.085733 CCCATCCATATCTCTTCGTCTCT 58.914 47.826 0.00 0.00 0.00 3.10
469 476 3.367910 GCCCATCCATATCTCTTCGTCTC 60.368 52.174 0.00 0.00 0.00 3.36
473 480 2.564504 TGAGCCCATCCATATCTCTTCG 59.435 50.000 0.00 0.00 0.00 3.79
481 488 1.121407 CCGGTCTGAGCCCATCCATA 61.121 60.000 0.63 0.00 0.00 2.74
482 489 2.446848 CCGGTCTGAGCCCATCCAT 61.447 63.158 0.63 0.00 0.00 3.41
491 498 3.589654 TTTGCGCCTCCGGTCTGAG 62.590 63.158 4.18 0.00 34.32 3.35
498 505 3.391665 ATCCTCCTTTGCGCCTCCG 62.392 63.158 4.18 0.00 37.57 4.63
501 508 0.393537 CTTCATCCTCCTTTGCGCCT 60.394 55.000 4.18 0.00 0.00 5.52
505 512 4.096081 CACATCTTCTTCATCCTCCTTTGC 59.904 45.833 0.00 0.00 0.00 3.68
507 514 5.250313 AGTCACATCTTCTTCATCCTCCTTT 59.750 40.000 0.00 0.00 0.00 3.11
508 515 4.782156 AGTCACATCTTCTTCATCCTCCTT 59.218 41.667 0.00 0.00 0.00 3.36
511 518 5.221422 CCCTAGTCACATCTTCTTCATCCTC 60.221 48.000 0.00 0.00 0.00 3.71
514 521 4.100808 AGCCCTAGTCACATCTTCTTCATC 59.899 45.833 0.00 0.00 0.00 2.92
515 522 4.036518 AGCCCTAGTCACATCTTCTTCAT 58.963 43.478 0.00 0.00 0.00 2.57
516 523 3.445008 AGCCCTAGTCACATCTTCTTCA 58.555 45.455 0.00 0.00 0.00 3.02
519 526 3.571590 CCTAGCCCTAGTCACATCTTCT 58.428 50.000 1.99 0.00 0.00 2.85
593 600 0.738389 GTGGCAATGTTGGGGATACG 59.262 55.000 0.00 0.00 37.60 3.06
597 604 0.105760 AACTGTGGCAATGTTGGGGA 60.106 50.000 5.71 0.00 0.00 4.81
623 659 4.429212 CGGTGCGATCGGTGGACA 62.429 66.667 18.30 2.43 0.00 4.02
649 685 1.670087 CCTGTGATGTGTCCGTGTCTC 60.670 57.143 0.00 0.00 0.00 3.36
656 692 2.436646 CCGCCCTGTGATGTGTCC 60.437 66.667 0.00 0.00 0.00 4.02
659 695 3.434319 GTGCCGCCCTGTGATGTG 61.434 66.667 0.00 0.00 0.00 3.21
683 719 4.436998 GGGACTCTGTGGACGCCG 62.437 72.222 0.00 0.00 0.00 6.46
694 730 2.570582 CTTCTGCTGCTCCGGGACTC 62.571 65.000 0.00 0.00 0.00 3.36
700 736 0.459934 CTCCTTCTTCTGCTGCTCCG 60.460 60.000 0.00 0.00 0.00 4.63
716 752 2.511145 CCGCTGCTCTTCTGCTCC 60.511 66.667 0.00 0.00 37.48 4.70
717 753 2.099431 CACCGCTGCTCTTCTGCTC 61.099 63.158 0.00 0.00 37.48 4.26
718 754 2.047465 CACCGCTGCTCTTCTGCT 60.047 61.111 0.00 0.00 37.48 4.24
747 783 4.129737 TGGGCTCTGCGCGTCTAC 62.130 66.667 8.43 0.00 44.57 2.59
748 784 4.129737 GTGGGCTCTGCGCGTCTA 62.130 66.667 8.43 0.00 44.57 2.59
755 791 4.329545 TGGGAACGTGGGCTCTGC 62.330 66.667 0.00 0.00 0.00 4.26
756 792 2.358737 GTGGGAACGTGGGCTCTG 60.359 66.667 0.00 0.00 0.00 3.35
757 793 2.526873 AGTGGGAACGTGGGCTCT 60.527 61.111 0.00 0.00 0.00 4.09
758 794 2.047179 GAGTGGGAACGTGGGCTC 60.047 66.667 0.00 0.00 0.00 4.70
804 841 3.306571 GGGTCCTTGCGAGTTAAGTAAGT 60.307 47.826 0.00 0.00 30.90 2.24
833 887 2.834549 GAGGAGTGGAGAGGATTTGTGA 59.165 50.000 0.00 0.00 0.00 3.58
840 894 0.333312 GAGTGGAGGAGTGGAGAGGA 59.667 60.000 0.00 0.00 0.00 3.71
843 897 1.000771 CGGAGTGGAGGAGTGGAGA 60.001 63.158 0.00 0.00 0.00 3.71
847 901 3.775654 GGCCGGAGTGGAGGAGTG 61.776 72.222 5.05 0.00 42.00 3.51
865 922 1.153349 GAGGTGTCGGGGAATGCTC 60.153 63.158 0.00 0.00 0.00 4.26
986 1078 2.656002 GCTCCATAAAAGAAGGGGGAC 58.344 52.381 0.00 0.00 0.00 4.46
987 1079 1.569072 GGCTCCATAAAAGAAGGGGGA 59.431 52.381 0.00 0.00 0.00 4.81
1669 1793 3.184683 GAAGCAGAGGTCGCGCAG 61.185 66.667 8.75 0.00 0.00 5.18
1758 1882 1.002684 GCGACGTAGATGGAGACGAAT 60.003 52.381 0.00 0.00 41.60 3.34
1779 1903 0.107993 TCCAGACGAGGACGACGTAT 60.108 55.000 0.00 0.00 43.97 3.06
1878 2036 3.494336 AGCGGAGGTACGTCGTCG 61.494 66.667 0.00 9.19 43.34 5.12
1879 2037 2.099831 CAGCGGAGGTACGTCGTC 59.900 66.667 0.00 3.95 35.08 4.20
1880 2038 4.112341 GCAGCGGAGGTACGTCGT 62.112 66.667 9.33 2.21 35.08 4.34
1881 2039 4.849329 GGCAGCGGAGGTACGTCG 62.849 72.222 9.33 6.32 35.08 5.12
1882 2040 4.849329 CGGCAGCGGAGGTACGTC 62.849 72.222 7.03 7.03 35.08 4.34
1893 2051 2.102553 GACGAGTAGGACGGCAGC 59.897 66.667 0.00 0.00 38.75 5.25
1998 2156 1.227674 GATGTCCGGGATGGTGAGC 60.228 63.158 0.00 0.00 39.52 4.26
2394 2596 2.915659 ACCAGGTCGCCGAGTGAA 60.916 61.111 0.00 0.00 0.00 3.18
2397 2599 3.063084 GAGACCAGGTCGCCGAGT 61.063 66.667 14.32 0.00 37.67 4.18
2825 3159 0.834687 GTGTCCCCCTCCACTGTACA 60.835 60.000 0.00 0.00 0.00 2.90
2828 3162 1.151810 ATGTGTCCCCCTCCACTGT 60.152 57.895 0.00 0.00 32.76 3.55
2829 3163 1.300963 CATGTGTCCCCCTCCACTG 59.699 63.158 0.00 0.00 32.76 3.66
2831 3165 2.044946 GCATGTGTCCCCCTCCAC 60.045 66.667 0.00 0.00 0.00 4.02
2839 3176 2.552743 CTGATGATCCATGCATGTGTCC 59.447 50.000 24.58 11.41 0.00 4.02
2900 3245 3.971305 TCCATCGGTAATCCACACCTAAT 59.029 43.478 0.00 0.00 33.62 1.73
2901 3246 3.376636 TCCATCGGTAATCCACACCTAA 58.623 45.455 0.00 0.00 33.62 2.69
2909 3254 5.411781 CACTAGCTAATCCATCGGTAATCC 58.588 45.833 0.00 0.00 0.00 3.01
2966 3323 1.916181 ACCGTGGAGGGAAAATCATCT 59.084 47.619 0.00 0.00 46.96 2.90
3000 3357 6.616774 TCCATACGTACGTACATGTATTCA 57.383 37.500 28.99 6.46 33.01 2.57
3001 3358 7.480855 CAGATCCATACGTACGTACATGTATTC 59.519 40.741 28.99 18.72 33.01 1.75
3004 3361 5.179929 CCAGATCCATACGTACGTACATGTA 59.820 44.000 28.99 18.51 33.01 2.29
3006 3363 4.214758 TCCAGATCCATACGTACGTACATG 59.785 45.833 28.99 23.75 33.01 3.21
3010 3367 5.065235 TCAATCCAGATCCATACGTACGTA 58.935 41.667 28.62 28.62 34.87 3.57
3012 3369 4.499037 TCAATCCAGATCCATACGTACG 57.501 45.455 15.01 15.01 0.00 3.67
3021 3408 2.149578 CCGAGCAATCAATCCAGATCC 58.850 52.381 0.00 0.00 0.00 3.36
3032 3419 0.876342 CTAACTCCGGCCGAGCAATC 60.876 60.000 30.73 0.00 43.01 2.67
3131 3536 2.583298 ATCCTGGGATCCGTCGTCCA 62.583 60.000 5.45 0.00 37.49 4.02
3183 3602 3.866883 ATTATCAAAACAAGCCGGGTG 57.133 42.857 7.07 4.00 0.00 4.61
3184 3603 3.056179 CCAATTATCAAAACAAGCCGGGT 60.056 43.478 0.00 0.00 0.00 5.28
3195 3614 3.088532 ACGAGGCAAGCCAATTATCAAA 58.911 40.909 14.40 0.00 38.92 2.69
3203 3622 2.334946 GCATGACGAGGCAAGCCAA 61.335 57.895 14.40 0.00 38.92 4.52
3205 3624 3.512516 GGCATGACGAGGCAAGCC 61.513 66.667 9.56 9.56 44.17 4.35
3206 3625 2.437359 AGGCATGACGAGGCAAGC 60.437 61.111 0.00 0.00 0.00 4.01
3207 3626 1.817099 GGAGGCATGACGAGGCAAG 60.817 63.158 0.00 0.00 0.00 4.01
3222 3644 1.455217 ATACCAGGGACGGACGGAG 60.455 63.158 0.00 0.00 0.00 4.63
3223 3645 1.755395 CATACCAGGGACGGACGGA 60.755 63.158 0.00 0.00 0.00 4.69
3234 3656 1.785041 CGCCGGCAAATCCATACCAG 61.785 60.000 28.98 0.12 34.01 4.00
3235 3657 1.821759 CGCCGGCAAATCCATACCA 60.822 57.895 28.98 0.00 34.01 3.25
3237 3659 2.331451 GCGCCGGCAAATCCATAC 59.669 61.111 28.98 0.00 39.62 2.39
3238 3660 2.904866 GGCGCCGGCAAATCCATA 60.905 61.111 28.98 0.00 42.47 2.74
3272 3718 2.618241 GCAACTGTGTTCATGTCTTGGA 59.382 45.455 0.00 0.00 0.00 3.53
3273 3719 2.287788 GGCAACTGTGTTCATGTCTTGG 60.288 50.000 0.00 0.00 0.00 3.61
3275 3721 1.956477 GGGCAACTGTGTTCATGTCTT 59.044 47.619 0.00 0.00 0.00 3.01
3278 3724 0.179032 TCGGGCAACTGTGTTCATGT 60.179 50.000 0.00 0.00 45.94 3.21
3279 3725 1.167851 ATCGGGCAACTGTGTTCATG 58.832 50.000 0.00 0.00 45.94 3.07
3280 3726 1.812571 GAATCGGGCAACTGTGTTCAT 59.187 47.619 0.00 0.00 45.94 2.57
3281 3727 1.234821 GAATCGGGCAACTGTGTTCA 58.765 50.000 0.00 0.00 45.94 3.18
3282 3728 0.521735 GGAATCGGGCAACTGTGTTC 59.478 55.000 0.00 0.00 45.94 3.18
3283 3729 1.234615 CGGAATCGGGCAACTGTGTT 61.235 55.000 0.00 0.00 45.94 3.32
3286 3732 1.072505 AACGGAATCGGGCAACTGT 59.927 52.632 0.00 0.00 45.94 3.55
3359 3844 8.423349 TCATGCCTGATTAATTTCATTTAAGGG 58.577 33.333 0.00 0.00 0.00 3.95
3414 3899 5.591643 GGATACGTGTATGCCATAAACTG 57.408 43.478 0.00 0.51 0.00 3.16
3431 3940 2.203803 CCCCCTCCTCCCGGATAC 60.204 72.222 0.73 0.00 39.01 2.24
3458 3967 1.136695 CAACAGGAGCAAAGCACCAAA 59.863 47.619 8.14 0.00 41.64 3.28
3460 3969 0.395586 ACAACAGGAGCAAAGCACCA 60.396 50.000 8.14 0.00 41.64 4.17
3461 3970 1.266989 GTACAACAGGAGCAAAGCACC 59.733 52.381 0.00 0.00 39.54 5.01
3477 3986 0.606130 CATGTGTGCAGGGCAGTACA 60.606 55.000 9.65 9.65 40.08 2.90
3489 4002 1.586154 GGGGACCGAAAGCATGTGTG 61.586 60.000 0.00 0.00 40.86 3.82
3541 4059 2.414957 CCGAACCCTTGTTTATTTCCGC 60.415 50.000 0.00 0.00 33.97 5.54
3542 4060 2.815503 ACCGAACCCTTGTTTATTTCCG 59.184 45.455 0.00 0.00 33.97 4.30
3543 4061 4.614306 CGAACCGAACCCTTGTTTATTTCC 60.614 45.833 0.00 0.00 33.97 3.13
3544 4062 4.213906 TCGAACCGAACCCTTGTTTATTTC 59.786 41.667 0.00 0.00 33.97 2.17
3555 4073 2.263852 GGTCCTCGAACCGAACCC 59.736 66.667 0.00 0.00 34.74 4.11
3609 4127 3.541713 GAGCCGGGTGGAGCTAGG 61.542 72.222 12.94 0.00 40.11 3.02
3610 4128 3.905678 CGAGCCGGGTGGAGCTAG 61.906 72.222 12.94 0.00 40.11 3.42
3611 4129 4.753662 ACGAGCCGGGTGGAGCTA 62.754 66.667 23.12 0.00 40.11 3.32
3624 4142 1.128724 GATCACTGCACGACGACGAG 61.129 60.000 15.32 7.39 42.66 4.18
3625 4143 1.154282 GATCACTGCACGACGACGA 60.154 57.895 15.32 0.00 42.66 4.20
3626 4144 2.152699 GGATCACTGCACGACGACG 61.153 63.158 5.58 5.58 45.75 5.12
3627 4145 1.080772 TGGATCACTGCACGACGAC 60.081 57.895 0.00 0.00 0.00 4.34
3628 4146 1.080772 GTGGATCACTGCACGACGA 60.081 57.895 0.00 0.00 33.83 4.20
3629 4147 3.463505 GTGGATCACTGCACGACG 58.536 61.111 0.00 0.00 33.83 5.12
3633 4151 2.436646 CCCCGTGGATCACTGCAC 60.437 66.667 0.00 0.00 40.09 4.57
3634 4152 2.220586 TTCCCCGTGGATCACTGCA 61.221 57.895 0.00 0.00 41.40 4.41
3635 4153 1.745489 GTTCCCCGTGGATCACTGC 60.745 63.158 0.00 0.00 41.40 4.40
3636 4154 1.447838 CGTTCCCCGTGGATCACTG 60.448 63.158 0.00 0.00 41.40 3.66
3637 4155 2.656069 CCGTTCCCCGTGGATCACT 61.656 63.158 0.00 0.00 41.40 3.41
3638 4156 2.125269 CCGTTCCCCGTGGATCAC 60.125 66.667 0.00 0.00 41.40 3.06
3639 4157 2.218454 AACCGTTCCCCGTGGATCA 61.218 57.895 0.00 0.00 41.40 2.92
3640 4158 1.743995 CAACCGTTCCCCGTGGATC 60.744 63.158 0.00 0.00 41.40 3.36
3641 4159 2.349755 CAACCGTTCCCCGTGGAT 59.650 61.111 0.00 0.00 41.40 3.41
3642 4160 4.629523 GCAACCGTTCCCCGTGGA 62.630 66.667 0.00 0.00 39.54 4.02
3643 4161 4.636435 AGCAACCGTTCCCCGTGG 62.636 66.667 0.00 0.00 33.66 4.94
3644 4162 2.593436 AAGCAACCGTTCCCCGTG 60.593 61.111 0.00 0.00 33.66 4.94
3645 4163 2.281276 GAAGCAACCGTTCCCCGT 60.281 61.111 0.00 0.00 33.66 5.28
3646 4164 2.281208 TGAAGCAACCGTTCCCCG 60.281 61.111 0.00 0.00 0.00 5.73
3647 4165 0.536460 TTCTGAAGCAACCGTTCCCC 60.536 55.000 0.00 0.00 0.00 4.81
3648 4166 0.875059 CTTCTGAAGCAACCGTTCCC 59.125 55.000 4.20 0.00 0.00 3.97
3649 4167 0.875059 CCTTCTGAAGCAACCGTTCC 59.125 55.000 11.93 0.00 0.00 3.62
3650 4168 1.531578 GTCCTTCTGAAGCAACCGTTC 59.468 52.381 11.93 0.00 0.00 3.95
3651 4169 1.594331 GTCCTTCTGAAGCAACCGTT 58.406 50.000 11.93 0.00 0.00 4.44
3652 4170 0.600255 CGTCCTTCTGAAGCAACCGT 60.600 55.000 11.93 0.00 0.00 4.83
3653 4171 0.600255 ACGTCCTTCTGAAGCAACCG 60.600 55.000 11.93 11.84 0.00 4.44
3654 4172 0.868406 CACGTCCTTCTGAAGCAACC 59.132 55.000 11.93 0.00 0.00 3.77
3655 4173 0.235926 GCACGTCCTTCTGAAGCAAC 59.764 55.000 11.93 10.64 0.00 4.17
3656 4174 0.106708 AGCACGTCCTTCTGAAGCAA 59.893 50.000 11.93 0.00 0.00 3.91
3657 4175 0.319900 GAGCACGTCCTTCTGAAGCA 60.320 55.000 11.93 0.00 0.00 3.91
3658 4176 0.319900 TGAGCACGTCCTTCTGAAGC 60.320 55.000 11.93 0.52 0.00 3.86
3659 4177 2.154854 TTGAGCACGTCCTTCTGAAG 57.845 50.000 10.46 10.46 0.00 3.02
3660 4178 2.807967 CAATTGAGCACGTCCTTCTGAA 59.192 45.455 0.00 0.00 0.00 3.02
3661 4179 2.224281 ACAATTGAGCACGTCCTTCTGA 60.224 45.455 13.59 0.00 0.00 3.27
3662 4180 2.146342 ACAATTGAGCACGTCCTTCTG 58.854 47.619 13.59 0.00 0.00 3.02
3663 4181 2.550830 ACAATTGAGCACGTCCTTCT 57.449 45.000 13.59 0.00 0.00 2.85
3664 4182 2.548057 TGAACAATTGAGCACGTCCTTC 59.452 45.455 13.59 2.69 0.00 3.46
3665 4183 2.290641 GTGAACAATTGAGCACGTCCTT 59.709 45.455 13.59 0.00 0.00 3.36
3666 4184 1.873591 GTGAACAATTGAGCACGTCCT 59.126 47.619 13.59 0.00 0.00 3.85
3667 4185 1.069227 GGTGAACAATTGAGCACGTCC 60.069 52.381 13.59 3.95 32.24 4.79
3668 4186 1.398451 CGGTGAACAATTGAGCACGTC 60.398 52.381 13.59 6.96 32.24 4.34
3669 4187 0.586319 CGGTGAACAATTGAGCACGT 59.414 50.000 13.59 0.00 32.24 4.49
3670 4188 0.865111 TCGGTGAACAATTGAGCACG 59.135 50.000 13.59 14.04 32.24 5.34
3671 4189 1.069227 GGTCGGTGAACAATTGAGCAC 60.069 52.381 13.59 17.64 0.00 4.40
3672 4190 1.234821 GGTCGGTGAACAATTGAGCA 58.765 50.000 13.59 6.67 0.00 4.26
3673 4191 0.521735 GGGTCGGTGAACAATTGAGC 59.478 55.000 13.59 3.90 0.00 4.26
3674 4192 1.535462 GTGGGTCGGTGAACAATTGAG 59.465 52.381 13.59 0.00 0.00 3.02
3675 4193 1.600023 GTGGGTCGGTGAACAATTGA 58.400 50.000 13.59 0.00 0.00 2.57
3676 4194 0.237235 CGTGGGTCGGTGAACAATTG 59.763 55.000 3.24 3.24 35.71 2.32
3677 4195 2.624169 CGTGGGTCGGTGAACAATT 58.376 52.632 0.00 0.00 35.71 2.32
3678 4196 4.371975 CGTGGGTCGGTGAACAAT 57.628 55.556 0.00 0.00 35.71 2.71
3701 4219 1.917782 TTTAGGATGGTTGCGTGCGC 61.918 55.000 9.85 9.85 42.35 6.09
3702 4220 0.519519 TTTTAGGATGGTTGCGTGCG 59.480 50.000 0.00 0.00 0.00 5.34
3703 4221 2.715737 TTTTTAGGATGGTTGCGTGC 57.284 45.000 0.00 0.00 0.00 5.34
3722 4240 3.575965 ATTCGAAATGAGCGGCTTTTT 57.424 38.095 2.97 7.75 0.00 1.94
3723 4241 4.900635 ATATTCGAAATGAGCGGCTTTT 57.099 36.364 2.97 0.94 0.00 2.27
3724 4242 4.900635 AATATTCGAAATGAGCGGCTTT 57.099 36.364 2.97 0.00 0.00 3.51
3725 4243 4.335315 TGAAATATTCGAAATGAGCGGCTT 59.665 37.500 2.97 0.00 0.00 4.35
3726 4244 3.876914 TGAAATATTCGAAATGAGCGGCT 59.123 39.130 0.00 0.00 0.00 5.52
3727 4245 4.209452 TGAAATATTCGAAATGAGCGGC 57.791 40.909 0.00 0.00 0.00 6.53


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

AutoCloner maintained by Alex Coulton.