Multiple sequence alignment - TraesCS6A01G316900

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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 TraesCS6A01G316900 chr6A 100.000 3217 0 0 1 3217 553099149 553102365 0.000000e+00 5941.0
1 TraesCS6A01G316900 chr6A 78.904 858 162 18 1196 2046 553054971 553055816 6.020000e-157 564.0
2 TraesCS6A01G316900 chr6A 90.769 260 14 2 1 250 123502134 123502393 3.980000e-89 339.0
3 TraesCS6A01G316900 chr6A 81.410 156 29 0 2345 2500 51907443 51907598 9.370000e-26 128.0
4 TraesCS6A01G316900 chr6D 93.713 1670 68 11 574 2217 407579054 407580712 0.000000e+00 2468.0
5 TraesCS6A01G316900 chr6D 78.721 860 166 15 1196 2046 407522837 407523688 2.800000e-155 558.0
6 TraesCS6A01G316900 chr6B 94.654 1272 48 6 961 2217 611698221 611699487 0.000000e+00 1954.0
7 TraesCS6A01G316900 chr6B 79.391 854 156 19 1200 2046 611500148 611500988 4.620000e-163 584.0
8 TraesCS6A01G316900 chr6B 95.611 319 4 4 574 882 611697878 611698196 1.330000e-138 503.0
9 TraesCS6A01G316900 chr6B 76.842 190 44 0 2343 2532 3855555 3855744 1.220000e-19 108.0
10 TraesCS6A01G316900 chr7A 91.818 880 72 0 2338 3217 8322824 8321945 0.000000e+00 1227.0
11 TraesCS6A01G316900 chr7A 88.953 344 36 2 237 578 37181745 37181402 1.070000e-114 424.0
12 TraesCS6A01G316900 chr7A 92.032 251 19 1 1 250 581089666 581089916 5.110000e-93 351.0
13 TraesCS6A01G316900 chr3B 91.230 878 77 0 2340 3217 588178132 588177255 0.000000e+00 1195.0
14 TraesCS6A01G316900 chr3B 89.168 877 92 3 2343 3217 643994039 643994914 0.000000e+00 1090.0
15 TraesCS6A01G316900 chr2B 92.718 824 60 0 2394 3217 321653068 321653891 0.000000e+00 1190.0
16 TraesCS6A01G316900 chr2B 84.507 71 9 2 2460 2529 668769537 668769606 5.760000e-08 69.4
17 TraesCS6A01G316900 chr7B 89.396 877 89 4 2343 3217 615302173 615301299 0.000000e+00 1101.0
18 TraesCS6A01G316900 chr3D 84.607 877 105 10 2343 3217 294113913 294113065 0.000000e+00 845.0
19 TraesCS6A01G316900 chr3D 90.283 247 19 3 1 243 579521899 579521654 5.180000e-83 318.0
20 TraesCS6A01G316900 chr1B 89.074 659 71 1 2559 3217 89375777 89375120 0.000000e+00 817.0
21 TraesCS6A01G316900 chr1B 90.435 230 22 0 2344 2573 89433598 89433369 1.450000e-78 303.0
22 TraesCS6A01G316900 chr5B 91.339 381 32 1 2345 2724 193583484 193583104 1.320000e-143 520.0
23 TraesCS6A01G316900 chr5A 88.942 416 43 1 2802 3217 575162567 575162979 7.960000e-141 510.0
24 TraesCS6A01G316900 chr5A 89.474 342 32 4 236 575 690781932 690782271 2.290000e-116 429.0
25 TraesCS6A01G316900 chr5A 90.769 260 14 4 1 250 9375307 9375566 3.980000e-89 339.0
26 TraesCS6A01G316900 chr5A 81.356 118 14 5 1195 1307 502545044 502544930 4.420000e-14 89.8
27 TraesCS6A01G316900 chr2A 90.116 344 31 3 236 577 55940579 55940921 8.190000e-121 444.0
28 TraesCS6A01G316900 chr2A 89.941 338 31 3 236 573 83859081 83859415 1.770000e-117 433.0
29 TraesCS6A01G316900 chr7D 89.826 344 34 1 236 578 13069581 13069238 1.060000e-119 440.0
30 TraesCS6A01G316900 chr3A 89.766 342 33 2 236 575 742346680 742346339 1.370000e-118 436.0
31 TraesCS6A01G316900 chr2D 89.676 339 34 1 238 575 633084948 633084610 6.380000e-117 431.0
32 TraesCS6A01G316900 chr4A 88.921 343 35 3 236 575 464997378 464997720 1.380000e-113 420.0
33 TraesCS6A01G316900 chr4A 93.227 251 16 1 1 250 544069660 544069910 5.070000e-98 368.0
34 TraesCS6A01G316900 chr4A 92.430 251 17 2 1 250 77146434 77146683 1.100000e-94 357.0
35 TraesCS6A01G316900 chr4A 90.385 260 15 2 1 250 464997089 464997348 1.850000e-87 333.0
36 TraesCS6A01G316900 chr4A 89.552 268 15 4 1 255 124369592 124369325 8.610000e-86 327.0
37 TraesCS6A01G316900 chr1D 89.118 340 34 3 236 573 54945463 54945125 1.380000e-113 420.0
38 TraesCS6A01G316900 chr1D 86.471 340 37 2 2878 3217 58817982 58818312 6.560000e-97 364.0
39 TraesCS6A01G316900 chr1D 88.333 60 7 0 2343 2402 314655474 314655415 4.450000e-09 73.1
40 TraesCS6A01G316900 chr5D 90.769 260 14 4 1 250 409340970 409341229 3.980000e-89 339.0
41 TraesCS6A01G316900 chr1A 80.128 156 31 0 2345 2500 252330826 252330981 2.030000e-22 117.0
42 TraesCS6A01G316900 chrUn 80.000 145 25 3 2358 2500 49410339 49410481 1.580000e-18 104.0
43 TraesCS6A01G316900 chrUn 79.470 151 27 3 2364 2512 286750706 286750558 1.580000e-18 104.0
44 TraesCS6A01G316900 chrUn 80.000 145 25 3 2358 2500 295212409 295212551 1.580000e-18 104.0


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 TraesCS6A01G316900 chr6A 553099149 553102365 3216 False 5941.0 5941 100.0000 1 3217 1 chr6A.!!$F4 3216
1 TraesCS6A01G316900 chr6A 553054971 553055816 845 False 564.0 564 78.9040 1196 2046 1 chr6A.!!$F3 850
2 TraesCS6A01G316900 chr6D 407579054 407580712 1658 False 2468.0 2468 93.7130 574 2217 1 chr6D.!!$F2 1643
3 TraesCS6A01G316900 chr6D 407522837 407523688 851 False 558.0 558 78.7210 1196 2046 1 chr6D.!!$F1 850
4 TraesCS6A01G316900 chr6B 611697878 611699487 1609 False 1228.5 1954 95.1325 574 2217 2 chr6B.!!$F3 1643
5 TraesCS6A01G316900 chr6B 611500148 611500988 840 False 584.0 584 79.3910 1200 2046 1 chr6B.!!$F2 846
6 TraesCS6A01G316900 chr7A 8321945 8322824 879 True 1227.0 1227 91.8180 2338 3217 1 chr7A.!!$R1 879
7 TraesCS6A01G316900 chr3B 588177255 588178132 877 True 1195.0 1195 91.2300 2340 3217 1 chr3B.!!$R1 877
8 TraesCS6A01G316900 chr3B 643994039 643994914 875 False 1090.0 1090 89.1680 2343 3217 1 chr3B.!!$F1 874
9 TraesCS6A01G316900 chr2B 321653068 321653891 823 False 1190.0 1190 92.7180 2394 3217 1 chr2B.!!$F1 823
10 TraesCS6A01G316900 chr7B 615301299 615302173 874 True 1101.0 1101 89.3960 2343 3217 1 chr7B.!!$R1 874
11 TraesCS6A01G316900 chr3D 294113065 294113913 848 True 845.0 845 84.6070 2343 3217 1 chr3D.!!$R1 874
12 TraesCS6A01G316900 chr1B 89375120 89375777 657 True 817.0 817 89.0740 2559 3217 1 chr1B.!!$R1 658
13 TraesCS6A01G316900 chr4A 464997089 464997720 631 False 376.5 420 89.6530 1 575 2 chr4A.!!$F3 574

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
315 316 0.028505 CTTGCCATTGATTCCTCGCG 59.971 55.0 0.0 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 2502 0.180878 AAACCACGACCGAAAAGGGA 59.819 50.0 0.0 0.0 46.96 4.2 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
57 58 3.703001 TGGAACAGGAGTCAAGATTCC 57.297 47.619 3.61 3.61 37.47 3.01
117 118 2.835895 TCATCGCCGGGGAATCGA 60.836 61.111 26.33 18.44 36.63 3.59
181 182 2.516460 GCGCTCGAGGGAGGTAGA 60.516 66.667 31.36 0.00 40.80 2.59
182 183 2.548295 GCGCTCGAGGGAGGTAGAG 61.548 68.421 31.36 0.00 40.80 2.43
183 184 1.894756 CGCTCGAGGGAGGTAGAGG 60.895 68.421 24.08 0.00 40.80 3.69
184 185 1.529713 GCTCGAGGGAGGTAGAGGG 60.530 68.421 15.58 0.00 40.80 4.30
185 186 1.529713 CTCGAGGGAGGTAGAGGGC 60.530 68.421 3.91 0.00 36.61 5.19
186 187 2.907917 CGAGGGAGGTAGAGGGCG 60.908 72.222 0.00 0.00 0.00 6.13
187 188 2.522193 GAGGGAGGTAGAGGGCGG 60.522 72.222 0.00 0.00 0.00 6.13
188 189 4.159108 AGGGAGGTAGAGGGCGGG 62.159 72.222 0.00 0.00 0.00 6.13
190 191 4.862823 GGAGGTAGAGGGCGGGCT 62.863 72.222 0.26 0.00 0.00 5.19
191 192 2.197875 GAGGTAGAGGGCGGGCTA 59.802 66.667 0.26 0.00 0.00 3.93
192 193 1.904378 GAGGTAGAGGGCGGGCTAG 60.904 68.421 0.26 0.00 0.00 3.42
193 194 2.918276 GGTAGAGGGCGGGCTAGG 60.918 72.222 0.26 0.00 0.00 3.02
194 195 2.918276 GTAGAGGGCGGGCTAGGG 60.918 72.222 0.26 0.00 0.00 3.53
195 196 4.936081 TAGAGGGCGGGCTAGGGC 62.936 72.222 0.26 0.00 37.82 5.19
202 203 4.473520 CGGGCTAGGGCTGGTGTG 62.474 72.222 0.00 0.00 38.73 3.82
203 204 4.115199 GGGCTAGGGCTGGTGTGG 62.115 72.222 0.00 0.00 38.73 4.17
204 205 4.803908 GGCTAGGGCTGGTGTGGC 62.804 72.222 0.00 0.00 38.73 5.01
270 271 2.897350 CGCCGCCCTTGAGGAATC 60.897 66.667 0.00 0.00 38.24 2.52
271 272 2.272146 GCCGCCCTTGAGGAATCA 59.728 61.111 0.00 0.00 38.24 2.57
272 273 2.115291 GCCGCCCTTGAGGAATCAC 61.115 63.158 0.00 0.00 38.24 3.06
273 274 1.604378 CCGCCCTTGAGGAATCACT 59.396 57.895 0.00 0.00 38.24 3.41
274 275 0.745845 CCGCCCTTGAGGAATCACTG 60.746 60.000 0.00 0.00 38.24 3.66
275 276 0.745845 CGCCCTTGAGGAATCACTGG 60.746 60.000 0.00 0.00 38.24 4.00
276 277 0.329596 GCCCTTGAGGAATCACTGGT 59.670 55.000 0.00 0.00 38.24 4.00
277 278 1.559682 GCCCTTGAGGAATCACTGGTA 59.440 52.381 0.00 0.00 38.24 3.25
278 279 2.026262 GCCCTTGAGGAATCACTGGTAA 60.026 50.000 0.00 0.00 38.24 2.85
279 280 3.878778 CCCTTGAGGAATCACTGGTAAG 58.121 50.000 0.00 0.00 38.24 2.34
280 281 3.370953 CCCTTGAGGAATCACTGGTAAGG 60.371 52.174 0.00 0.00 38.24 2.69
281 282 3.274288 CTTGAGGAATCACTGGTAAGGC 58.726 50.000 0.00 0.00 0.00 4.35
282 283 2.551270 TGAGGAATCACTGGTAAGGCT 58.449 47.619 0.00 0.00 0.00 4.58
283 284 2.237143 TGAGGAATCACTGGTAAGGCTG 59.763 50.000 0.00 0.00 0.00 4.85
284 285 2.501723 GAGGAATCACTGGTAAGGCTGA 59.498 50.000 0.00 0.00 0.00 4.26
285 286 2.237392 AGGAATCACTGGTAAGGCTGAC 59.763 50.000 0.00 0.00 0.00 3.51
286 287 2.633488 GAATCACTGGTAAGGCTGACC 58.367 52.381 14.73 14.73 37.49 4.02
287 288 0.537188 ATCACTGGTAAGGCTGACCG 59.463 55.000 16.46 12.98 42.76 4.79
289 290 2.125106 CTGGTAAGGCTGACCGGC 60.125 66.667 17.16 0.00 42.76 6.13
290 291 4.077184 TGGTAAGGCTGACCGGCG 62.077 66.667 16.46 0.00 44.22 6.46
291 292 4.832608 GGTAAGGCTGACCGGCGG 62.833 72.222 27.06 27.06 44.22 6.13
309 310 3.357504 GCAGCCTTGCCATTGATTC 57.642 52.632 0.00 0.00 44.74 2.52
310 311 0.179092 GCAGCCTTGCCATTGATTCC 60.179 55.000 0.00 0.00 44.74 3.01
311 312 1.481871 CAGCCTTGCCATTGATTCCT 58.518 50.000 0.00 0.00 0.00 3.36
312 313 1.407979 CAGCCTTGCCATTGATTCCTC 59.592 52.381 0.00 0.00 0.00 3.71
313 314 0.383231 GCCTTGCCATTGATTCCTCG 59.617 55.000 0.00 0.00 0.00 4.63
314 315 0.383231 CCTTGCCATTGATTCCTCGC 59.617 55.000 0.00 0.00 0.00 5.03
315 316 0.028505 CTTGCCATTGATTCCTCGCG 59.971 55.000 0.00 0.00 0.00 5.87
316 317 1.375853 TTGCCATTGATTCCTCGCGG 61.376 55.000 6.13 0.00 0.00 6.46
317 318 2.546494 GCCATTGATTCCTCGCGGG 61.546 63.158 6.13 0.59 0.00 6.13
318 319 1.146041 CCATTGATTCCTCGCGGGA 59.854 57.895 8.08 10.34 43.41 5.14
339 340 4.814294 CGAGGCGTTCGGGGAAGG 62.814 72.222 3.92 0.00 45.54 3.46
340 341 3.387947 GAGGCGTTCGGGGAAGGA 61.388 66.667 2.55 0.00 30.17 3.36
341 342 3.372554 GAGGCGTTCGGGGAAGGAG 62.373 68.421 2.55 0.00 30.17 3.69
342 343 3.387947 GGCGTTCGGGGAAGGAGA 61.388 66.667 2.55 0.00 30.17 3.71
343 344 2.125633 GCGTTCGGGGAAGGAGAC 60.126 66.667 2.55 0.00 30.17 3.36
344 345 2.181021 CGTTCGGGGAAGGAGACG 59.819 66.667 0.00 0.00 30.17 4.18
345 346 2.125633 GTTCGGGGAAGGAGACGC 60.126 66.667 0.00 0.00 0.00 5.19
346 347 3.755628 TTCGGGGAAGGAGACGCG 61.756 66.667 3.53 3.53 43.27 6.01
352 353 4.719369 GAAGGAGACGCGCGGTGT 62.719 66.667 35.22 18.09 0.00 4.16
353 354 4.719369 AAGGAGACGCGCGGTGTC 62.719 66.667 35.22 24.95 42.60 3.67
460 461 3.199891 GTCCGCCGGCGCTAAATT 61.200 61.111 42.39 0.00 38.24 1.82
461 462 2.893404 TCCGCCGGCGCTAAATTC 60.893 61.111 42.39 0.75 38.24 2.17
462 463 4.293626 CCGCCGGCGCTAAATTCG 62.294 66.667 42.39 22.74 38.24 3.34
463 464 4.293626 CGCCGGCGCTAAATTCGG 62.294 66.667 38.48 15.00 44.70 4.30
464 465 3.199891 GCCGGCGCTAAATTCGGT 61.200 61.111 12.58 0.00 43.87 4.69
465 466 3.011583 CCGGCGCTAAATTCGGTC 58.988 61.111 7.64 0.00 37.92 4.79
466 467 2.531376 CCGGCGCTAAATTCGGTCC 61.531 63.158 7.64 0.00 37.92 4.46
467 468 1.812093 CGGCGCTAAATTCGGTCCA 60.812 57.895 7.64 0.00 0.00 4.02
468 469 1.762222 CGGCGCTAAATTCGGTCCAG 61.762 60.000 7.64 0.00 0.00 3.86
469 470 0.461339 GGCGCTAAATTCGGTCCAGA 60.461 55.000 7.64 0.00 0.00 3.86
470 471 1.583054 GCGCTAAATTCGGTCCAGAT 58.417 50.000 0.00 0.00 0.00 2.90
471 472 1.527311 GCGCTAAATTCGGTCCAGATC 59.473 52.381 0.00 0.00 0.00 2.75
472 473 1.787155 CGCTAAATTCGGTCCAGATCG 59.213 52.381 0.00 0.00 36.00 3.69
473 474 2.135933 GCTAAATTCGGTCCAGATCGG 58.864 52.381 0.00 0.00 35.26 4.18
474 475 2.483188 GCTAAATTCGGTCCAGATCGGT 60.483 50.000 0.00 0.00 35.26 4.69
475 476 3.243636 GCTAAATTCGGTCCAGATCGGTA 60.244 47.826 0.00 0.00 35.26 4.02
476 477 3.899052 AAATTCGGTCCAGATCGGTAA 57.101 42.857 0.00 0.00 35.26 2.85
477 478 3.899052 AATTCGGTCCAGATCGGTAAA 57.101 42.857 0.00 0.00 35.26 2.01
478 479 3.899052 ATTCGGTCCAGATCGGTAAAA 57.101 42.857 0.00 0.00 35.26 1.52
479 480 3.681593 TTCGGTCCAGATCGGTAAAAA 57.318 42.857 0.00 0.00 35.26 1.94
480 481 3.899052 TCGGTCCAGATCGGTAAAAAT 57.101 42.857 0.00 0.00 35.26 1.82
481 482 3.788937 TCGGTCCAGATCGGTAAAAATC 58.211 45.455 0.00 0.00 35.26 2.17
482 483 2.538449 CGGTCCAGATCGGTAAAAATCG 59.462 50.000 0.00 0.00 35.57 3.34
483 484 2.870411 GGTCCAGATCGGTAAAAATCGG 59.130 50.000 3.97 0.00 35.57 4.18
484 485 2.870411 GTCCAGATCGGTAAAAATCGGG 59.130 50.000 3.97 0.00 38.24 5.14
485 486 2.502538 TCCAGATCGGTAAAAATCGGGT 59.497 45.455 3.97 0.00 38.12 5.28
486 487 3.054948 TCCAGATCGGTAAAAATCGGGTT 60.055 43.478 3.97 0.00 38.12 4.11
487 488 3.311596 CCAGATCGGTAAAAATCGGGTTC 59.688 47.826 0.00 0.00 33.94 3.62
488 489 3.311596 CAGATCGGTAAAAATCGGGTTCC 59.688 47.826 0.00 0.00 0.00 3.62
489 490 3.199289 AGATCGGTAAAAATCGGGTTCCT 59.801 43.478 0.00 0.00 0.00 3.36
490 491 2.702261 TCGGTAAAAATCGGGTTCCTG 58.298 47.619 0.00 0.00 0.00 3.86
491 492 2.302445 TCGGTAAAAATCGGGTTCCTGA 59.698 45.455 2.65 2.65 0.00 3.86
492 493 3.075884 CGGTAAAAATCGGGTTCCTGAA 58.924 45.455 4.38 0.00 0.00 3.02
493 494 3.126343 CGGTAAAAATCGGGTTCCTGAAG 59.874 47.826 4.38 0.00 0.00 3.02
494 495 4.329392 GGTAAAAATCGGGTTCCTGAAGA 58.671 43.478 4.38 0.00 0.00 2.87
495 496 4.155462 GGTAAAAATCGGGTTCCTGAAGAC 59.845 45.833 4.38 0.00 0.00 3.01
496 497 2.094762 AAATCGGGTTCCTGAAGACG 57.905 50.000 4.38 0.00 0.00 4.18
497 498 0.974383 AATCGGGTTCCTGAAGACGT 59.026 50.000 4.38 0.00 0.00 4.34
498 499 0.246635 ATCGGGTTCCTGAAGACGTG 59.753 55.000 4.38 0.00 0.00 4.49
499 500 0.824595 TCGGGTTCCTGAAGACGTGA 60.825 55.000 0.00 0.00 0.00 4.35
500 501 0.666577 CGGGTTCCTGAAGACGTGAC 60.667 60.000 0.00 0.00 0.00 3.67
501 502 0.680061 GGGTTCCTGAAGACGTGACT 59.320 55.000 0.00 0.00 0.00 3.41
502 503 1.605712 GGGTTCCTGAAGACGTGACTG 60.606 57.143 0.00 0.00 0.00 3.51
503 504 1.605712 GGTTCCTGAAGACGTGACTGG 60.606 57.143 0.00 0.00 0.00 4.00
504 505 0.679505 TTCCTGAAGACGTGACTGGG 59.320 55.000 0.00 0.00 0.00 4.45
505 506 0.469331 TCCTGAAGACGTGACTGGGT 60.469 55.000 0.00 0.00 0.00 4.51
506 507 0.038159 CCTGAAGACGTGACTGGGTC 60.038 60.000 0.00 0.00 0.00 4.46
507 508 0.673985 CTGAAGACGTGACTGGGTCA 59.326 55.000 0.00 0.00 40.50 4.02
508 509 1.068588 CTGAAGACGTGACTGGGTCAA 59.931 52.381 0.00 0.00 44.49 3.18
509 510 1.691976 TGAAGACGTGACTGGGTCAAT 59.308 47.619 0.00 0.00 44.49 2.57
510 511 2.104111 TGAAGACGTGACTGGGTCAATT 59.896 45.455 0.00 0.00 44.49 2.32
511 512 2.930826 AGACGTGACTGGGTCAATTT 57.069 45.000 0.00 0.00 44.49 1.82
512 513 3.208747 AGACGTGACTGGGTCAATTTT 57.791 42.857 0.00 0.00 44.49 1.82
513 514 3.551846 AGACGTGACTGGGTCAATTTTT 58.448 40.909 0.00 0.00 44.49 1.94
546 547 4.494515 AAAAACGTCTGGGAGGCC 57.505 55.556 0.00 0.00 0.00 5.19
547 548 1.844130 AAAAACGTCTGGGAGGCCT 59.156 52.632 3.86 3.86 0.00 5.19
548 549 0.185175 AAAAACGTCTGGGAGGCCTT 59.815 50.000 6.77 0.00 0.00 4.35
549 550 0.185175 AAAACGTCTGGGAGGCCTTT 59.815 50.000 6.77 0.00 0.00 3.11
550 551 1.061546 AAACGTCTGGGAGGCCTTTA 58.938 50.000 6.77 0.00 0.00 1.85
551 552 1.286248 AACGTCTGGGAGGCCTTTAT 58.714 50.000 6.77 0.00 0.00 1.40
552 553 2.170012 ACGTCTGGGAGGCCTTTATA 57.830 50.000 6.77 0.00 0.00 0.98
553 554 2.040178 ACGTCTGGGAGGCCTTTATAG 58.960 52.381 6.77 3.66 0.00 1.31
554 555 1.344763 CGTCTGGGAGGCCTTTATAGG 59.655 57.143 6.77 0.00 45.02 2.57
555 556 1.700186 GTCTGGGAGGCCTTTATAGGG 59.300 57.143 6.77 0.00 42.25 3.53
556 557 1.068121 CTGGGAGGCCTTTATAGGGG 58.932 60.000 6.77 0.00 42.25 4.79
561 562 2.668550 GCCTTTATAGGGGCGCGG 60.669 66.667 8.83 0.00 42.25 6.46
562 563 2.668550 CCTTTATAGGGGCGCGGC 60.669 66.667 26.39 26.39 37.94 6.53
563 564 2.426023 CTTTATAGGGGCGCGGCT 59.574 61.111 32.30 16.42 0.00 5.52
564 565 1.961277 CTTTATAGGGGCGCGGCTG 60.961 63.158 32.30 8.55 0.00 4.85
565 566 3.469863 TTTATAGGGGCGCGGCTGG 62.470 63.158 32.30 0.00 0.00 4.85
566 567 4.926162 TATAGGGGCGCGGCTGGA 62.926 66.667 32.30 17.28 0.00 3.86
622 627 2.668632 CGCCCAAAGCTGACCCTA 59.331 61.111 0.00 0.00 40.39 3.53
683 688 2.100879 ATAGGCGACGGGAATCTGCC 62.101 60.000 0.00 0.00 46.07 4.85
884 895 4.562425 CCGCCACGCCATACCCAT 62.562 66.667 0.00 0.00 0.00 4.00
885 896 2.423874 CGCCACGCCATACCCATA 59.576 61.111 0.00 0.00 0.00 2.74
886 897 1.959226 CGCCACGCCATACCCATAC 60.959 63.158 0.00 0.00 0.00 2.39
887 898 1.599797 GCCACGCCATACCCATACC 60.600 63.158 0.00 0.00 0.00 2.73
888 899 1.833606 CCACGCCATACCCATACCA 59.166 57.895 0.00 0.00 0.00 3.25
889 900 0.534203 CCACGCCATACCCATACCAC 60.534 60.000 0.00 0.00 0.00 4.16
890 901 0.534203 CACGCCATACCCATACCACC 60.534 60.000 0.00 0.00 0.00 4.61
891 902 1.072505 CGCCATACCCATACCACCC 59.927 63.158 0.00 0.00 0.00 4.61
892 903 1.415672 CGCCATACCCATACCACCCT 61.416 60.000 0.00 0.00 0.00 4.34
893 904 0.850784 GCCATACCCATACCACCCTT 59.149 55.000 0.00 0.00 0.00 3.95
896 907 1.423921 CATACCCATACCACCCTTCCC 59.576 57.143 0.00 0.00 0.00 3.97
911 922 0.473117 TTCCCTCCCCGGATCATACC 60.473 60.000 0.73 0.00 33.16 2.73
912 923 1.158705 CCCTCCCCGGATCATACCT 59.841 63.158 0.73 0.00 33.16 3.08
913 924 0.473886 CCCTCCCCGGATCATACCTT 60.474 60.000 0.73 0.00 33.16 3.50
924 935 0.462375 TCATACCTTATGCCGCACGT 59.538 50.000 0.00 0.00 36.14 4.49
940 951 2.707902 CGTAGGACGGTAGGGGTAC 58.292 63.158 0.00 0.00 38.08 3.34
946 957 0.392998 GACGGTAGGGGTACACGAGA 60.393 60.000 0.00 0.00 0.00 4.04
1029 1040 3.142838 GCCATGAGCGGGTGCAAT 61.143 61.111 0.00 0.00 46.23 3.56
1069 1080 1.338973 CAGCACCAAGTCACAAGCAAT 59.661 47.619 0.00 0.00 0.00 3.56
1124 1150 3.371591 ACAGTTCGCAAGTGTTTCGTTTA 59.628 39.130 4.22 0.00 42.19 2.01
1335 1364 3.081133 CGCAAAGGTCCATCGTCG 58.919 61.111 0.00 0.00 0.00 5.12
1355 1384 4.044024 GACTTCGTCGTCTCGCTG 57.956 61.111 0.00 0.00 0.00 5.18
1430 1459 1.063327 CGAGCAGCTCTACCTGTCG 59.937 63.158 20.39 1.29 35.28 4.35
1433 1462 1.202582 GAGCAGCTCTACCTGTCGAAA 59.797 52.381 15.78 0.00 35.28 3.46
2073 2301 1.429463 CAACACGCTTGTCTAGTCCC 58.571 55.000 0.00 0.00 33.55 4.46
2074 2302 1.045407 AACACGCTTGTCTAGTCCCA 58.955 50.000 0.00 0.00 33.55 4.37
2175 2403 7.184106 TGGAAATTGCTTCGTTCGTTTATATC 58.816 34.615 0.00 0.00 34.56 1.63
2195 2423 1.148273 GCATCTGTTCCGGCCCATA 59.852 57.895 0.00 0.00 0.00 2.74
2286 2514 4.776795 TTTTGCTAATCCCTTTTCGGTC 57.223 40.909 0.00 0.00 0.00 4.79
2287 2515 2.018542 TGCTAATCCCTTTTCGGTCG 57.981 50.000 0.00 0.00 0.00 4.79
2288 2516 1.276989 TGCTAATCCCTTTTCGGTCGT 59.723 47.619 0.00 0.00 0.00 4.34
2289 2517 1.664151 GCTAATCCCTTTTCGGTCGTG 59.336 52.381 0.00 0.00 0.00 4.35
2290 2518 2.277084 CTAATCCCTTTTCGGTCGTGG 58.723 52.381 0.00 0.00 0.00 4.94
2291 2519 0.399075 AATCCCTTTTCGGTCGTGGT 59.601 50.000 0.00 0.00 0.00 4.16
2292 2520 0.399075 ATCCCTTTTCGGTCGTGGTT 59.601 50.000 0.00 0.00 0.00 3.67
2293 2521 0.180878 TCCCTTTTCGGTCGTGGTTT 59.819 50.000 0.00 0.00 0.00 3.27
2294 2522 1.026584 CCCTTTTCGGTCGTGGTTTT 58.973 50.000 0.00 0.00 0.00 2.43
2295 2523 1.406180 CCCTTTTCGGTCGTGGTTTTT 59.594 47.619 0.00 0.00 0.00 1.94
2320 2548 8.729529 TTCTTTAGCGAATACTATTCAGATCG 57.270 34.615 9.08 0.00 0.00 3.69
2321 2549 6.802348 TCTTTAGCGAATACTATTCAGATCGC 59.198 38.462 9.68 9.68 44.40 4.58
2322 2550 3.493272 AGCGAATACTATTCAGATCGCG 58.507 45.455 0.00 0.00 46.36 5.87
2323 2551 2.594654 GCGAATACTATTCAGATCGCGG 59.405 50.000 6.13 0.00 39.78 6.46
2324 2552 2.594654 CGAATACTATTCAGATCGCGGC 59.405 50.000 6.13 0.00 0.00 6.53
2325 2553 3.670895 CGAATACTATTCAGATCGCGGCT 60.671 47.826 6.13 0.45 0.00 5.52
2326 2554 4.436986 CGAATACTATTCAGATCGCGGCTA 60.437 45.833 6.13 0.00 0.00 3.93
2327 2555 5.583495 GAATACTATTCAGATCGCGGCTAT 58.417 41.667 6.13 0.00 0.00 2.97
2328 2556 6.511282 CGAATACTATTCAGATCGCGGCTATA 60.511 42.308 6.13 0.00 0.00 1.31
2329 2557 4.624336 ACTATTCAGATCGCGGCTATAG 57.376 45.455 6.13 11.27 0.00 1.31
2330 2558 4.262617 ACTATTCAGATCGCGGCTATAGA 58.737 43.478 6.13 0.00 0.00 1.98
2331 2559 4.884744 ACTATTCAGATCGCGGCTATAGAT 59.115 41.667 6.13 0.00 0.00 1.98
2332 2560 3.766676 TTCAGATCGCGGCTATAGATC 57.233 47.619 6.13 0.00 40.61 2.75
2333 2561 2.711542 TCAGATCGCGGCTATAGATCA 58.288 47.619 6.13 0.00 42.21 2.92
2334 2562 3.282885 TCAGATCGCGGCTATAGATCAT 58.717 45.455 6.13 0.00 42.21 2.45
2335 2563 3.696548 TCAGATCGCGGCTATAGATCATT 59.303 43.478 6.13 0.00 42.21 2.57
2336 2564 3.795639 CAGATCGCGGCTATAGATCATTG 59.204 47.826 6.13 5.04 42.21 2.82
2337 2565 3.445450 AGATCGCGGCTATAGATCATTGT 59.555 43.478 6.13 0.00 42.21 2.71
2338 2566 3.217599 TCGCGGCTATAGATCATTGTC 57.782 47.619 6.13 0.00 0.00 3.18
2339 2567 2.556622 TCGCGGCTATAGATCATTGTCA 59.443 45.455 6.13 0.00 0.00 3.58
2340 2568 2.919859 CGCGGCTATAGATCATTGTCAG 59.080 50.000 3.21 0.00 0.00 3.51
2341 2569 2.670414 GCGGCTATAGATCATTGTCAGC 59.330 50.000 3.21 0.00 0.00 4.26
2392 2621 8.788806 ACTTTATTCATCCGTCACAATGTTTAA 58.211 29.630 0.00 0.00 0.00 1.52
2409 2638 5.141910 TGTTTAAAGGGACGAAGGGAATTT 58.858 37.500 0.00 0.00 0.00 1.82
2458 2687 2.490991 GCCACGTCCAAGAGTTAAAGT 58.509 47.619 0.00 0.00 0.00 2.66
2471 2700 8.500773 CCAAGAGTTAAAGTATGTTTCGCTAAA 58.499 33.333 0.00 0.00 0.00 1.85
2482 2711 5.181690 TGTTTCGCTAAATTGTGAGCTTT 57.818 34.783 0.00 0.00 36.50 3.51
2500 2729 4.699257 AGCTTTGACATTTGAGCTCCTAAG 59.301 41.667 12.15 8.06 41.34 2.18
2516 2745 7.742556 GCTCCTAAGCTCATGATCTAAAAAT 57.257 36.000 0.00 0.00 45.55 1.82
2519 2748 9.504708 CTCCTAAGCTCATGATCTAAAAATCAT 57.495 33.333 0.00 0.00 45.17 2.45
2567 2796 2.526304 TCTCCCGAATAATTGCTCCG 57.474 50.000 0.00 0.00 0.00 4.63
2613 2842 3.661648 CCTGGACCACCCCCTTGG 61.662 72.222 0.00 0.00 43.04 3.61
2628 2857 4.270482 TGGAGTCGGACGCCATAT 57.730 55.556 26.72 0.00 43.20 1.78
2632 2861 3.423749 TGGAGTCGGACGCCATATATAA 58.576 45.455 26.72 5.22 43.20 0.98
2706 2935 2.184020 CTCCAATGTGGCTGGGTCGA 62.184 60.000 0.00 0.00 37.47 4.20
2786 3015 1.933853 GTAGCAACTGAACCATAGCGG 59.066 52.381 0.00 0.00 42.50 5.52
2832 3061 9.784531 CATCTACATTAATCTTGGAGTGGTATT 57.215 33.333 0.00 0.00 0.00 1.89
2860 3089 3.561120 CTAACCAACCAGCGGGGCA 62.561 63.158 8.08 0.00 42.05 5.36
2890 3119 5.131067 GGAAGTCACCCTTGTAACTTTCTT 58.869 41.667 0.00 0.00 32.34 2.52
2922 3151 6.359804 AGCACCTGAATATCTTGCAAATAGA 58.640 36.000 0.00 0.00 35.57 1.98
2981 3210 5.759059 TGGATGTCTTCATGGATAGCTTTT 58.241 37.500 0.00 0.00 34.06 2.27
3117 3347 8.260114 TCATACTTAGCTGATCAAGAATCACAA 58.740 33.333 0.00 0.00 39.52 3.33
3119 3349 6.233434 ACTTAGCTGATCAAGAATCACAACA 58.767 36.000 0.00 0.00 39.52 3.33
3161 3392 1.918293 TGAGACCGGGCAATCCAGT 60.918 57.895 11.69 0.00 34.36 4.00
3197 3428 0.738975 TATCACGAACTCCGCAGAGG 59.261 55.000 1.26 0.00 45.11 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.721718 CCGCGAACAGGAATCTTGAC 59.278 55.000 8.23 0.00 0.00 3.18
48 49 0.606096 TCCGCGAACAGGAATCTTGA 59.394 50.000 8.23 0.00 34.33 3.02
117 118 2.919856 CCTCTCCCGATGGCCGAT 60.920 66.667 0.00 0.00 41.76 4.18
128 129 2.015726 TCTCCCTCCCTCCCTCTCC 61.016 68.421 0.00 0.00 0.00 3.71
171 172 4.159108 CCCGCCCTCTACCTCCCT 62.159 72.222 0.00 0.00 0.00 4.20
173 174 3.447933 TAGCCCGCCCTCTACCTCC 62.448 68.421 0.00 0.00 0.00 4.30
185 186 4.473520 CACACCAGCCCTAGCCCG 62.474 72.222 0.00 0.00 41.25 6.13
186 187 4.115199 CCACACCAGCCCTAGCCC 62.115 72.222 0.00 0.00 41.25 5.19
187 188 4.803908 GCCACACCAGCCCTAGCC 62.804 72.222 0.00 0.00 41.25 3.93
188 189 4.803908 GGCCACACCAGCCCTAGC 62.804 72.222 0.00 0.00 45.16 3.42
204 205 2.044551 GGCTTCCCTTGCCTCTGG 60.045 66.667 0.00 0.00 46.38 3.86
253 254 2.897350 GATTCCTCAAGGGCGGCG 60.897 66.667 0.51 0.51 35.41 6.46
254 255 2.115291 GTGATTCCTCAAGGGCGGC 61.115 63.158 0.00 0.00 35.41 6.53
255 256 0.745845 CAGTGATTCCTCAAGGGCGG 60.746 60.000 0.00 0.00 35.41 6.13
256 257 0.745845 CCAGTGATTCCTCAAGGGCG 60.746 60.000 0.00 0.00 35.41 6.13
257 258 0.329596 ACCAGTGATTCCTCAAGGGC 59.670 55.000 0.00 0.00 34.62 5.19
258 259 3.370953 CCTTACCAGTGATTCCTCAAGGG 60.371 52.174 0.00 0.00 34.62 3.95
259 260 3.878778 CCTTACCAGTGATTCCTCAAGG 58.121 50.000 0.00 0.00 35.80 3.61
260 261 3.054802 AGCCTTACCAGTGATTCCTCAAG 60.055 47.826 0.00 0.00 31.85 3.02
261 262 2.912956 AGCCTTACCAGTGATTCCTCAA 59.087 45.455 0.00 0.00 31.85 3.02
262 263 2.237143 CAGCCTTACCAGTGATTCCTCA 59.763 50.000 0.00 0.00 0.00 3.86
263 264 2.501723 TCAGCCTTACCAGTGATTCCTC 59.498 50.000 0.00 0.00 0.00 3.71
264 265 2.237392 GTCAGCCTTACCAGTGATTCCT 59.763 50.000 0.00 0.00 0.00 3.36
265 266 2.633488 GTCAGCCTTACCAGTGATTCC 58.367 52.381 0.00 0.00 0.00 3.01
266 267 2.633488 GGTCAGCCTTACCAGTGATTC 58.367 52.381 0.00 0.00 36.96 2.52
267 268 1.066143 CGGTCAGCCTTACCAGTGATT 60.066 52.381 0.00 0.00 36.78 2.57
268 269 0.537188 CGGTCAGCCTTACCAGTGAT 59.463 55.000 0.00 0.00 36.78 3.06
269 270 1.541310 CCGGTCAGCCTTACCAGTGA 61.541 60.000 0.00 0.00 36.78 3.41
270 271 1.079127 CCGGTCAGCCTTACCAGTG 60.079 63.158 0.00 0.00 36.78 3.66
271 272 2.955881 GCCGGTCAGCCTTACCAGT 61.956 63.158 1.90 0.00 36.78 4.00
272 273 2.125106 GCCGGTCAGCCTTACCAG 60.125 66.667 1.90 0.00 36.78 4.00
273 274 4.077184 CGCCGGTCAGCCTTACCA 62.077 66.667 1.90 0.00 36.78 3.25
274 275 4.832608 CCGCCGGTCAGCCTTACC 62.833 72.222 1.90 0.00 0.00 2.85
292 293 1.407979 GAGGAATCAATGGCAAGGCTG 59.592 52.381 0.00 0.00 0.00 4.85
293 294 1.772836 GAGGAATCAATGGCAAGGCT 58.227 50.000 0.00 0.00 0.00 4.58
294 295 0.383231 CGAGGAATCAATGGCAAGGC 59.617 55.000 0.00 0.00 0.00 4.35
295 296 0.383231 GCGAGGAATCAATGGCAAGG 59.617 55.000 0.00 0.00 0.00 3.61
296 297 0.028505 CGCGAGGAATCAATGGCAAG 59.971 55.000 0.00 0.00 0.00 4.01
297 298 2.097444 CGCGAGGAATCAATGGCAA 58.903 52.632 0.00 0.00 0.00 4.52
298 299 3.812203 CGCGAGGAATCAATGGCA 58.188 55.556 0.00 0.00 0.00 4.92
315 316 3.116531 CGAACGCCTCGGTTTCCC 61.117 66.667 0.00 0.00 44.20 3.97
323 324 3.372554 CTCCTTCCCCGAACGCCTC 62.373 68.421 0.00 0.00 0.00 4.70
324 325 3.391382 CTCCTTCCCCGAACGCCT 61.391 66.667 0.00 0.00 0.00 5.52
325 326 3.387947 TCTCCTTCCCCGAACGCC 61.388 66.667 0.00 0.00 0.00 5.68
326 327 2.125633 GTCTCCTTCCCCGAACGC 60.126 66.667 0.00 0.00 0.00 4.84
327 328 2.181021 CGTCTCCTTCCCCGAACG 59.819 66.667 0.00 0.00 0.00 3.95
328 329 2.125633 GCGTCTCCTTCCCCGAAC 60.126 66.667 0.00 0.00 0.00 3.95
329 330 3.755628 CGCGTCTCCTTCCCCGAA 61.756 66.667 0.00 0.00 0.00 4.30
335 336 4.719369 ACACCGCGCGTCTCCTTC 62.719 66.667 29.95 0.00 0.00 3.46
336 337 4.719369 GACACCGCGCGTCTCCTT 62.719 66.667 29.95 6.15 0.00 3.36
443 444 3.164390 GAATTTAGCGCCGGCGGAC 62.164 63.158 45.81 31.88 46.35 4.79
444 445 2.893404 GAATTTAGCGCCGGCGGA 60.893 61.111 45.81 14.61 46.35 5.54
445 446 4.293626 CGAATTTAGCGCCGGCGG 62.294 66.667 45.81 29.29 46.35 6.13
446 447 4.293626 CCGAATTTAGCGCCGGCG 62.294 66.667 43.13 43.13 46.35 6.46
447 448 3.164390 GACCGAATTTAGCGCCGGC 62.164 63.158 19.07 19.07 45.29 6.13
448 449 2.531376 GGACCGAATTTAGCGCCGG 61.531 63.158 17.23 17.23 46.65 6.13
449 450 1.762222 CTGGACCGAATTTAGCGCCG 61.762 60.000 2.29 0.00 0.00 6.46
450 451 0.461339 TCTGGACCGAATTTAGCGCC 60.461 55.000 2.29 0.00 0.00 6.53
451 452 1.527311 GATCTGGACCGAATTTAGCGC 59.473 52.381 0.00 0.00 0.00 5.92
452 453 1.787155 CGATCTGGACCGAATTTAGCG 59.213 52.381 0.00 0.00 0.00 4.26
453 454 2.135933 CCGATCTGGACCGAATTTAGC 58.864 52.381 0.00 0.00 42.00 3.09
454 455 3.454371 ACCGATCTGGACCGAATTTAG 57.546 47.619 10.05 0.00 42.00 1.85
455 456 5.341872 TTTACCGATCTGGACCGAATTTA 57.658 39.130 10.05 0.00 42.00 1.40
456 457 3.899052 TTACCGATCTGGACCGAATTT 57.101 42.857 10.05 0.00 42.00 1.82
457 458 3.899052 TTTACCGATCTGGACCGAATT 57.101 42.857 10.05 0.00 42.00 2.17
458 459 3.899052 TTTTACCGATCTGGACCGAAT 57.101 42.857 10.05 0.00 42.00 3.34
459 460 3.681593 TTTTTACCGATCTGGACCGAA 57.318 42.857 10.05 0.00 42.00 4.30
460 461 3.735820 CGATTTTTACCGATCTGGACCGA 60.736 47.826 10.05 0.00 42.00 4.69
461 462 2.538449 CGATTTTTACCGATCTGGACCG 59.462 50.000 10.05 0.00 42.00 4.79
462 463 2.870411 CCGATTTTTACCGATCTGGACC 59.130 50.000 10.05 0.00 42.00 4.46
463 464 2.870411 CCCGATTTTTACCGATCTGGAC 59.130 50.000 10.05 0.00 42.00 4.02
464 465 2.502538 ACCCGATTTTTACCGATCTGGA 59.497 45.455 10.05 0.00 42.00 3.86
465 466 2.914059 ACCCGATTTTTACCGATCTGG 58.086 47.619 2.55 2.55 46.41 3.86
466 467 3.311596 GGAACCCGATTTTTACCGATCTG 59.688 47.826 0.00 0.00 0.00 2.90
467 468 3.199289 AGGAACCCGATTTTTACCGATCT 59.801 43.478 0.00 0.00 0.00 2.75
468 469 3.311596 CAGGAACCCGATTTTTACCGATC 59.688 47.826 0.00 0.00 0.00 3.69
469 470 3.054948 TCAGGAACCCGATTTTTACCGAT 60.055 43.478 0.00 0.00 0.00 4.18
470 471 2.302445 TCAGGAACCCGATTTTTACCGA 59.698 45.455 0.00 0.00 0.00 4.69
471 472 2.702261 TCAGGAACCCGATTTTTACCG 58.298 47.619 0.00 0.00 0.00 4.02
472 473 4.155462 GTCTTCAGGAACCCGATTTTTACC 59.845 45.833 0.00 0.00 0.00 2.85
473 474 4.142966 CGTCTTCAGGAACCCGATTTTTAC 60.143 45.833 0.00 0.00 0.00 2.01
474 475 3.998341 CGTCTTCAGGAACCCGATTTTTA 59.002 43.478 0.00 0.00 0.00 1.52
475 476 2.812011 CGTCTTCAGGAACCCGATTTTT 59.188 45.455 0.00 0.00 0.00 1.94
476 477 2.224450 ACGTCTTCAGGAACCCGATTTT 60.224 45.455 0.00 0.00 0.00 1.82
477 478 1.346722 ACGTCTTCAGGAACCCGATTT 59.653 47.619 0.00 0.00 0.00 2.17
478 479 0.974383 ACGTCTTCAGGAACCCGATT 59.026 50.000 0.00 0.00 0.00 3.34
479 480 0.246635 CACGTCTTCAGGAACCCGAT 59.753 55.000 0.00 0.00 0.00 4.18
480 481 0.824595 TCACGTCTTCAGGAACCCGA 60.825 55.000 0.00 0.00 0.00 5.14
481 482 0.666577 GTCACGTCTTCAGGAACCCG 60.667 60.000 0.00 0.00 0.00 5.28
482 483 0.680061 AGTCACGTCTTCAGGAACCC 59.320 55.000 0.00 0.00 0.00 4.11
483 484 1.605712 CCAGTCACGTCTTCAGGAACC 60.606 57.143 0.00 0.00 0.00 3.62
484 485 1.605712 CCCAGTCACGTCTTCAGGAAC 60.606 57.143 0.00 0.00 0.00 3.62
485 486 0.679505 CCCAGTCACGTCTTCAGGAA 59.320 55.000 0.00 0.00 0.00 3.36
486 487 0.469331 ACCCAGTCACGTCTTCAGGA 60.469 55.000 0.00 0.00 0.00 3.86
487 488 0.038159 GACCCAGTCACGTCTTCAGG 60.038 60.000 0.00 0.00 32.09 3.86
488 489 0.673985 TGACCCAGTCACGTCTTCAG 59.326 55.000 0.00 0.00 37.67 3.02
489 490 1.116308 TTGACCCAGTCACGTCTTCA 58.884 50.000 0.00 0.00 42.60 3.02
490 491 2.457366 ATTGACCCAGTCACGTCTTC 57.543 50.000 0.00 0.00 42.60 2.87
491 492 2.930826 AATTGACCCAGTCACGTCTT 57.069 45.000 0.00 0.00 42.60 3.01
492 493 2.930826 AAATTGACCCAGTCACGTCT 57.069 45.000 0.00 0.00 42.60 4.18
493 494 3.982576 AAAAATTGACCCAGTCACGTC 57.017 42.857 0.00 0.00 42.60 4.34
529 530 0.185175 AAGGCCTCCCAGACGTTTTT 59.815 50.000 5.23 0.00 0.00 1.94
530 531 0.185175 AAAGGCCTCCCAGACGTTTT 59.815 50.000 5.23 0.00 0.00 2.43
531 532 1.061546 TAAAGGCCTCCCAGACGTTT 58.938 50.000 5.23 0.00 0.00 3.60
532 533 1.286248 ATAAAGGCCTCCCAGACGTT 58.714 50.000 5.23 0.00 0.00 3.99
533 534 2.040178 CTATAAAGGCCTCCCAGACGT 58.960 52.381 5.23 0.00 0.00 4.34
534 535 1.344763 CCTATAAAGGCCTCCCAGACG 59.655 57.143 5.23 0.00 35.64 4.18
535 536 1.700186 CCCTATAAAGGCCTCCCAGAC 59.300 57.143 5.23 0.00 42.14 3.51
536 537 1.416013 CCCCTATAAAGGCCTCCCAGA 60.416 57.143 5.23 0.00 42.14 3.86
537 538 1.068121 CCCCTATAAAGGCCTCCCAG 58.932 60.000 5.23 0.65 42.14 4.45
538 539 1.065997 GCCCCTATAAAGGCCTCCCA 61.066 60.000 5.23 0.00 43.76 4.37
539 540 1.768349 GCCCCTATAAAGGCCTCCC 59.232 63.158 5.23 0.00 43.76 4.30
544 545 2.668550 CCGCGCCCCTATAAAGGC 60.669 66.667 0.00 3.07 46.17 4.35
545 546 2.668550 GCCGCGCCCCTATAAAGG 60.669 66.667 0.00 0.00 43.25 3.11
546 547 1.961277 CAGCCGCGCCCCTATAAAG 60.961 63.158 0.00 0.00 0.00 1.85
547 548 2.110213 CAGCCGCGCCCCTATAAA 59.890 61.111 0.00 0.00 0.00 1.40
548 549 3.936203 CCAGCCGCGCCCCTATAA 61.936 66.667 0.00 0.00 0.00 0.98
549 550 4.926162 TCCAGCCGCGCCCCTATA 62.926 66.667 0.00 0.00 0.00 1.31
622 627 0.035056 CGGAAGGTTCCCAAGAGCAT 60.035 55.000 3.08 0.00 44.67 3.79
683 688 4.131376 GGATGACGACATGGCTGG 57.869 61.111 4.80 0.00 36.82 4.85
882 893 1.353394 GGGGAGGGAAGGGTGGTATG 61.353 65.000 0.00 0.00 0.00 2.39
883 894 1.005690 GGGGAGGGAAGGGTGGTAT 59.994 63.158 0.00 0.00 0.00 2.73
884 895 2.457794 GGGGAGGGAAGGGTGGTA 59.542 66.667 0.00 0.00 0.00 3.25
887 898 4.733725 TCCGGGGAGGGAAGGGTG 62.734 72.222 0.00 0.00 41.52 4.61
888 899 3.707189 ATCCGGGGAGGGAAGGGT 61.707 66.667 0.00 0.00 40.09 4.34
889 900 2.849646 GATCCGGGGAGGGAAGGG 60.850 72.222 0.00 0.00 40.09 3.95
890 901 0.178903 TATGATCCGGGGAGGGAAGG 60.179 60.000 0.00 0.00 40.09 3.46
891 902 0.977395 GTATGATCCGGGGAGGGAAG 59.023 60.000 0.00 0.00 40.09 3.46
892 903 0.473117 GGTATGATCCGGGGAGGGAA 60.473 60.000 0.00 0.00 40.09 3.97
893 904 1.157751 GGTATGATCCGGGGAGGGA 59.842 63.158 0.00 0.00 41.52 4.20
896 907 2.093447 GCATAAGGTATGATCCGGGGAG 60.093 54.545 0.00 0.00 38.45 4.30
911 922 1.206745 CGTCCTACGTGCGGCATAAG 61.207 60.000 5.72 4.09 36.74 1.73
912 923 1.226745 CGTCCTACGTGCGGCATAA 60.227 57.895 5.72 0.00 36.74 1.90
913 924 2.410060 CGTCCTACGTGCGGCATA 59.590 61.111 5.72 0.00 36.74 3.14
924 935 0.107214 CGTGTACCCCTACCGTCCTA 60.107 60.000 0.00 0.00 0.00 2.94
939 950 3.047115 TCCTATCCTACTCCTCTCGTGT 58.953 50.000 0.00 0.00 0.00 4.49
940 951 3.773418 TCCTATCCTACTCCTCTCGTG 57.227 52.381 0.00 0.00 0.00 4.35
946 957 3.768878 CGATGGTTCCTATCCTACTCCT 58.231 50.000 0.00 0.00 0.00 3.69
1029 1040 1.281867 GTGGTGATGGGATGAGTGGAA 59.718 52.381 0.00 0.00 0.00 3.53
1069 1080 1.415289 TCGGTGATCGAGCTCCTACTA 59.585 52.381 18.58 0.38 43.74 1.82
1124 1150 0.322456 TAGCCATTGCCGACTTGCTT 60.322 50.000 0.00 0.00 38.69 3.91
1523 1558 2.285368 TCGATCTGGGCCAGGGTT 60.285 61.111 32.23 17.90 31.51 4.11
1685 1885 2.281484 TGCTTCACGGAGTTGCCC 60.281 61.111 0.00 0.00 41.61 5.36
2073 2301 4.854924 TGCCCGGATGGACGCATG 62.855 66.667 0.73 0.00 37.49 4.06
2074 2302 4.856801 GTGCCCGGATGGACGCAT 62.857 66.667 0.73 0.00 35.32 4.73
2093 2321 1.019805 GCGTACAGGGAAAGTCTGGC 61.020 60.000 0.00 0.00 36.62 4.85
2094 2322 0.608640 AGCGTACAGGGAAAGTCTGG 59.391 55.000 0.00 0.00 36.62 3.86
2264 2492 4.320641 CGACCGAAAAGGGATTAGCAAAAA 60.321 41.667 0.00 0.00 46.96 1.94
2265 2493 3.189702 CGACCGAAAAGGGATTAGCAAAA 59.810 43.478 0.00 0.00 46.96 2.44
2266 2494 2.745281 CGACCGAAAAGGGATTAGCAAA 59.255 45.455 0.00 0.00 46.96 3.68
2267 2495 2.289819 ACGACCGAAAAGGGATTAGCAA 60.290 45.455 0.00 0.00 46.96 3.91
2268 2496 1.276989 ACGACCGAAAAGGGATTAGCA 59.723 47.619 0.00 0.00 46.96 3.49
2269 2497 1.664151 CACGACCGAAAAGGGATTAGC 59.336 52.381 0.00 0.00 46.96 3.09
2270 2498 2.277084 CCACGACCGAAAAGGGATTAG 58.723 52.381 0.00 0.00 46.96 1.73
2271 2499 1.624813 ACCACGACCGAAAAGGGATTA 59.375 47.619 0.00 0.00 46.96 1.75
2272 2500 0.399075 ACCACGACCGAAAAGGGATT 59.601 50.000 0.00 0.00 46.96 3.01
2273 2501 0.399075 AACCACGACCGAAAAGGGAT 59.601 50.000 0.00 0.00 46.96 3.85
2274 2502 0.180878 AAACCACGACCGAAAAGGGA 59.819 50.000 0.00 0.00 46.96 4.20
2275 2503 1.026584 AAAACCACGACCGAAAAGGG 58.973 50.000 0.00 0.00 46.96 3.95
2294 2522 9.181805 CGATCTGAATAGTATTCGCTAAAGAAA 57.818 33.333 16.29 0.00 33.43 2.52
2295 2523 7.326305 GCGATCTGAATAGTATTCGCTAAAGAA 59.674 37.037 16.29 0.00 40.80 2.52
2296 2524 6.802348 GCGATCTGAATAGTATTCGCTAAAGA 59.198 38.462 16.29 13.21 40.80 2.52
2297 2525 6.237071 CGCGATCTGAATAGTATTCGCTAAAG 60.237 42.308 18.81 10.97 41.27 1.85
2298 2526 5.567915 CGCGATCTGAATAGTATTCGCTAAA 59.432 40.000 18.81 3.14 41.27 1.85
2299 2527 5.086727 CGCGATCTGAATAGTATTCGCTAA 58.913 41.667 18.81 6.66 41.27 3.09
2300 2528 4.436986 CCGCGATCTGAATAGTATTCGCTA 60.437 45.833 18.81 8.60 41.27 4.26
2301 2529 3.493272 CGCGATCTGAATAGTATTCGCT 58.507 45.455 18.81 7.63 41.27 4.93
2302 2530 2.594654 CCGCGATCTGAATAGTATTCGC 59.405 50.000 8.23 14.90 40.70 4.70
2303 2531 2.594654 GCCGCGATCTGAATAGTATTCG 59.405 50.000 8.23 11.69 0.00 3.34
2304 2532 3.839293 AGCCGCGATCTGAATAGTATTC 58.161 45.455 8.23 14.86 0.00 1.75
2305 2533 3.944055 AGCCGCGATCTGAATAGTATT 57.056 42.857 8.23 0.00 0.00 1.89
2306 2534 6.056236 TCTATAGCCGCGATCTGAATAGTAT 58.944 40.000 8.23 0.00 0.00 2.12
2307 2535 5.425630 TCTATAGCCGCGATCTGAATAGTA 58.574 41.667 8.23 0.00 0.00 1.82
2308 2536 4.262617 TCTATAGCCGCGATCTGAATAGT 58.737 43.478 8.23 0.00 0.00 2.12
2309 2537 4.884458 TCTATAGCCGCGATCTGAATAG 57.116 45.455 8.23 9.33 0.00 1.73
2310 2538 4.881850 TGATCTATAGCCGCGATCTGAATA 59.118 41.667 8.23 0.00 35.68 1.75
2311 2539 3.696548 TGATCTATAGCCGCGATCTGAAT 59.303 43.478 8.23 0.00 35.68 2.57
2312 2540 3.081804 TGATCTATAGCCGCGATCTGAA 58.918 45.455 8.23 0.00 35.68 3.02
2313 2541 2.711542 TGATCTATAGCCGCGATCTGA 58.288 47.619 8.23 0.00 35.68 3.27
2314 2542 3.706802 ATGATCTATAGCCGCGATCTG 57.293 47.619 8.23 0.00 35.68 2.90
2315 2543 3.445450 ACAATGATCTATAGCCGCGATCT 59.555 43.478 8.23 6.91 35.68 2.75
2316 2544 3.775202 ACAATGATCTATAGCCGCGATC 58.225 45.455 8.23 0.33 35.33 3.69
2317 2545 3.193479 TGACAATGATCTATAGCCGCGAT 59.807 43.478 8.23 0.00 0.00 4.58
2318 2546 2.556622 TGACAATGATCTATAGCCGCGA 59.443 45.455 8.23 0.00 0.00 5.87
2319 2547 2.919859 CTGACAATGATCTATAGCCGCG 59.080 50.000 0.00 0.00 0.00 6.46
2320 2548 2.670414 GCTGACAATGATCTATAGCCGC 59.330 50.000 0.00 0.00 0.00 6.53
2321 2549 4.185467 AGCTGACAATGATCTATAGCCG 57.815 45.455 0.00 0.00 0.00 5.52
2322 2550 6.874288 AAAAGCTGACAATGATCTATAGCC 57.126 37.500 0.00 0.00 0.00 3.93
2360 2588 5.760743 TGTGACGGATGAATAAAGTTTCACA 59.239 36.000 0.00 0.00 38.37 3.58
2362 2590 6.869315 TTGTGACGGATGAATAAAGTTTCA 57.131 33.333 0.00 0.00 39.77 2.69
2392 2621 3.739401 ATGAAATTCCCTTCGTCCCTT 57.261 42.857 0.00 0.00 0.00 3.95
2409 2638 1.306296 GGTTAGGCCAGCCCAATGA 59.694 57.895 5.01 0.00 37.17 2.57
2436 2665 0.759959 TTAACTCTTGGACGTGGCCA 59.240 50.000 0.00 0.00 35.78 5.36
2458 2687 6.494893 AAGCTCACAATTTAGCGAAACATA 57.505 33.333 0.00 0.00 43.63 2.29
2471 2700 4.280174 AGCTCAAATGTCAAAGCTCACAAT 59.720 37.500 0.00 0.00 41.05 2.71
2567 2796 0.250166 AGGGAAGTGCAACCACGTAC 60.250 55.000 7.87 0.00 46.62 3.67
2613 2842 4.430137 TGTTATATATGGCGTCCGACTC 57.570 45.455 0.00 0.00 0.00 3.36
2628 2857 9.778741 GATGGATTTGAACCTAGACATGTTATA 57.221 33.333 0.00 0.00 0.00 0.98
2632 2861 5.118990 CGATGGATTTGAACCTAGACATGT 58.881 41.667 0.00 0.00 0.00 3.21
2706 2935 3.149196 CTGCTATGGTGTTCAACTTGGT 58.851 45.455 0.00 0.00 0.00 3.67
2753 2982 2.812011 AGTTGCTACAATTTGTCGGGAC 59.188 45.455 5.07 2.18 0.00 4.46
2832 3061 0.111639 GGTTGGTTAGCACCCCAAGA 59.888 55.000 1.68 0.00 43.49 3.02
2849 3078 1.754745 CACTATATGCCCCGCTGGT 59.245 57.895 0.00 0.00 36.04 4.00
2854 3083 1.691976 TGACTTCCACTATATGCCCCG 59.308 52.381 0.00 0.00 0.00 5.73
2860 3089 6.672657 AGTTACAAGGGTGACTTCCACTATAT 59.327 38.462 0.00 0.00 40.60 0.86
2922 3151 4.440525 CGCCATCCACAGCTTTATCAATTT 60.441 41.667 0.00 0.00 0.00 1.82
3117 3347 4.033709 AGTACTTGGGCACTATCATCTGT 58.966 43.478 0.00 0.00 0.00 3.41
3119 3349 3.643792 GGAGTACTTGGGCACTATCATCT 59.356 47.826 0.00 0.00 0.00 2.90
3161 3392 4.441495 CGTGATACTTGGAGACATGCCTTA 60.441 45.833 0.00 0.00 42.32 2.69


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

AutoCloner maintained by Alex Coulton.