Multiple sequence alignment - TraesCS2D01G376200

Loading Multiple Alignment...

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 TraesCS2D01G376200 chr2D 100.000 3395 0 0 1 3395 480511743 480508349 0.000000e+00 6270
1 TraesCS2D01G376200 chr2D 81.633 245 31 8 14 246 278370155 278370397 1.240000e-44 191
2 TraesCS2D01G376200 chr2D 90.000 90 8 1 242 331 480511412 480511324 7.700000e-22 115
3 TraesCS2D01G376200 chr2D 90.000 90 8 1 332 420 480511502 480511413 7.700000e-22 115
4 TraesCS2D01G376200 chr2A 96.298 2215 55 13 724 2928 623088676 623086479 0.000000e+00 3611
5 TraesCS2D01G376200 chr2A 94.512 164 7 2 3194 3356 623086269 623086107 5.620000e-63 252
6 TraesCS2D01G376200 chr2B 96.512 2179 61 7 752 2928 563312413 563310248 0.000000e+00 3589
7 TraesCS2D01G376200 chr2B 97.826 138 2 1 2962 3099 563309984 563309848 1.570000e-58 237
8 TraesCS2D01G376200 chr3B 87.842 329 29 6 13 331 681090192 681090519 3.200000e-100 375
9 TraesCS2D01G376200 chr3B 82.164 342 53 7 315 651 681090411 681090749 1.540000e-73 287
10 TraesCS2D01G376200 chr3B 80.328 305 39 12 14 304 532211769 532211472 9.540000e-51 211
11 TraesCS2D01G376200 chr7A 87.456 287 31 4 355 640 127068885 127069167 3.270000e-85 326
12 TraesCS2D01G376200 chr7A 82.915 199 26 7 140 331 127068752 127068949 4.500000e-39 172
13 TraesCS2D01G376200 chr6D 85.897 312 27 10 14 310 4737729 4737420 1.970000e-82 316
14 TraesCS2D01G376200 chr1B 85.892 241 29 5 406 645 560181573 560181809 5.620000e-63 252
15 TraesCS2D01G376200 chr5B 80.731 301 41 11 14 304 511017270 511017563 5.700000e-53 219
16 TraesCS2D01G376200 chr4D 80.000 320 40 15 1 304 47658133 47657822 7.380000e-52 215
17 TraesCS2D01G376200 chr7D 85.644 202 16 8 140 331 124847694 124847892 2.070000e-47 200
18 TraesCS2D01G376200 chr7D 87.006 177 22 1 342 518 124847815 124847990 7.430000e-47 198
19 TraesCS2D01G376200 chr3D 86.705 173 14 5 3187 3356 335674381 335674215 2.080000e-42 183
20 TraesCS2D01G376200 chr4A 81.223 229 25 9 3137 3351 60740524 60740300 5.830000e-38 169
21 TraesCS2D01G376200 chr4A 78.715 249 36 11 66 304 741965118 741965359 2.110000e-32 150
22 TraesCS2D01G376200 chr6A 86.620 142 19 0 3137 3278 16349106 16349247 1.260000e-34 158
23 TraesCS2D01G376200 chr3A 86.713 143 18 1 3137 3279 140954946 140955087 1.260000e-34 158
24 TraesCS2D01G376200 chr1A 76.176 319 50 19 1 304 13940845 13941152 9.820000e-31 145


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 TraesCS2D01G376200 chr2D 480508349 480511743 3394 True 2166.666667 6270 93.333333 1 3395 3 chr2D.!!$R1 3394
1 TraesCS2D01G376200 chr2A 623086107 623088676 2569 True 1931.500000 3611 95.405000 724 3356 2 chr2A.!!$R1 2632
2 TraesCS2D01G376200 chr2B 563309848 563312413 2565 True 1913.000000 3589 97.169000 752 3099 2 chr2B.!!$R1 2347
3 TraesCS2D01G376200 chr3B 681090192 681090749 557 False 331.000000 375 85.003000 13 651 2 chr3B.!!$F1 638

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
485 495 0.032813 ACGCCCTAGCCAGTAGGTTA 60.033 55.0 0.0 0.0 46.66 2.85 F
1701 1722 0.107945 ATGCTTTCCTCTCCACGCTC 60.108 55.0 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2389 0.384725 CGCTTCAACCTTCGTGCAAG 60.385 55.0 0.00 0.0 0.0 4.01 R
3118 3371 0.035739 GTGCCCGGGTCTACTTTCAA 59.964 55.0 24.63 0.0 0.0 2.69 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
111 112 4.634012 AGTACCAACTAAAGGTGCATCA 57.366 40.909 0.00 0.00 43.25 3.07
118 119 6.266558 ACCAACTAAAGGTGCATCATAAACAA 59.733 34.615 0.00 0.00 38.13 2.83
191 198 9.997482 TTTTTCTGAGCGGTTTTCATATATAAC 57.003 29.630 0.00 0.00 0.00 1.89
286 296 2.675658 AAAAAGTAGCTGGGCCAAGA 57.324 45.000 12.85 0.00 0.00 3.02
287 297 2.907458 AAAAGTAGCTGGGCCAAGAT 57.093 45.000 12.85 7.43 0.00 2.40
288 298 4.316025 AAAAAGTAGCTGGGCCAAGATA 57.684 40.909 12.85 6.03 0.00 1.98
289 299 4.316025 AAAAGTAGCTGGGCCAAGATAA 57.684 40.909 12.85 0.00 0.00 1.75
290 300 4.526438 AAAGTAGCTGGGCCAAGATAAT 57.474 40.909 12.85 5.11 0.00 1.28
291 301 5.646692 AAAGTAGCTGGGCCAAGATAATA 57.353 39.130 12.85 0.00 0.00 0.98
292 302 5.850046 AAGTAGCTGGGCCAAGATAATAT 57.150 39.130 12.85 0.00 0.00 1.28
293 303 5.428184 AGTAGCTGGGCCAAGATAATATC 57.572 43.478 12.85 0.00 0.00 1.63
294 304 4.846367 AGTAGCTGGGCCAAGATAATATCA 59.154 41.667 12.85 0.00 0.00 2.15
295 305 4.942363 AGCTGGGCCAAGATAATATCAT 57.058 40.909 12.85 0.00 0.00 2.45
296 306 6.673978 AGTAGCTGGGCCAAGATAATATCATA 59.326 38.462 12.85 0.00 0.00 2.15
297 307 5.749462 AGCTGGGCCAAGATAATATCATAC 58.251 41.667 12.85 0.00 0.00 2.39
298 308 5.490357 AGCTGGGCCAAGATAATATCATACT 59.510 40.000 12.85 0.00 0.00 2.12
299 309 6.673978 AGCTGGGCCAAGATAATATCATACTA 59.326 38.462 12.85 0.00 0.00 1.82
300 310 7.349330 AGCTGGGCCAAGATAATATCATACTAT 59.651 37.037 12.85 0.00 0.00 2.12
301 311 8.651389 GCTGGGCCAAGATAATATCATACTATA 58.349 37.037 12.85 0.00 0.00 1.31
303 313 9.951866 TGGGCCAAGATAATATCATACTATAGA 57.048 33.333 2.13 0.00 0.00 1.98
321 331 8.578448 ACTATAGATATACGGGGAGAAAACTC 57.422 38.462 6.78 0.00 0.00 3.01
322 332 8.168725 ACTATAGATATACGGGGAGAAAACTCA 58.831 37.037 6.78 0.00 0.00 3.41
323 333 5.793030 AGATATACGGGGAGAAAACTCAG 57.207 43.478 0.00 0.00 0.00 3.35
324 334 2.693267 ATACGGGGAGAAAACTCAGC 57.307 50.000 0.00 0.00 0.00 4.26
325 335 1.344065 TACGGGGAGAAAACTCAGCA 58.656 50.000 0.00 0.00 0.00 4.41
326 336 0.472471 ACGGGGAGAAAACTCAGCAA 59.528 50.000 0.00 0.00 0.00 3.91
327 337 1.133915 ACGGGGAGAAAACTCAGCAAA 60.134 47.619 0.00 0.00 0.00 3.68
328 338 1.953686 CGGGGAGAAAACTCAGCAAAA 59.046 47.619 0.00 0.00 0.00 2.44
329 339 2.360801 CGGGGAGAAAACTCAGCAAAAA 59.639 45.455 0.00 0.00 0.00 1.94
412 422 9.219603 CTATAGATATTCGGGAAGAAAATGCAA 57.780 33.333 0.00 0.00 42.91 4.08
454 464 0.328258 ATCAAACCCAACTCTCCCCG 59.672 55.000 0.00 0.00 0.00 5.73
459 469 2.190578 CCAACTCTCCCCGATGGC 59.809 66.667 0.00 0.00 0.00 4.40
460 470 2.669133 CCAACTCTCCCCGATGGCA 61.669 63.158 0.00 0.00 0.00 4.92
461 471 1.153289 CAACTCTCCCCGATGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
478 488 2.512515 GAGCAACGCCCTAGCCAG 60.513 66.667 0.00 0.00 34.57 4.85
483 493 1.305887 AACGCCCTAGCCAGTAGGT 60.306 57.895 0.00 0.00 46.66 3.08
485 495 0.032813 ACGCCCTAGCCAGTAGGTTA 60.033 55.000 0.00 0.00 46.66 2.85
491 501 3.132467 CCCTAGCCAGTAGGTTACTTGTC 59.868 52.174 0.00 0.00 46.66 3.18
495 505 4.675038 AGCCAGTAGGTTACTTGTCTACT 58.325 43.478 0.00 0.00 42.89 2.57
497 507 5.047235 AGCCAGTAGGTTACTTGTCTACTTG 60.047 44.000 0.00 0.00 40.95 3.16
499 509 6.388278 CCAGTAGGTTACTTGTCTACTTGTC 58.612 44.000 0.00 0.00 40.95 3.18
504 514 9.351570 GTAGGTTACTTGTCTACTTGTCATAAC 57.648 37.037 0.00 0.00 32.84 1.89
505 515 7.088905 AGGTTACTTGTCTACTTGTCATAACG 58.911 38.462 0.00 0.00 0.00 3.18
507 517 7.383300 GGTTACTTGTCTACTTGTCATAACGTT 59.617 37.037 5.88 5.88 0.00 3.99
512 522 5.477984 TGTCTACTTGTCATAACGTTAGGGT 59.522 40.000 18.87 11.47 0.00 4.34
519 529 4.097437 TGTCATAACGTTAGGGTCTAGCTG 59.903 45.833 18.87 6.76 0.00 4.24
528 538 5.921408 CGTTAGGGTCTAGCTGTAAATGATC 59.079 44.000 0.00 0.00 0.00 2.92
530 540 3.322254 AGGGTCTAGCTGTAAATGATCCG 59.678 47.826 0.00 0.00 33.47 4.18
531 541 3.555168 GGGTCTAGCTGTAAATGATCCGG 60.555 52.174 0.00 0.00 0.00 5.14
536 546 1.934589 CTGTAAATGATCCGGACGCA 58.065 50.000 6.12 9.14 0.00 5.24
558 568 1.096416 CGGCGGCCACCTAATAAAAA 58.904 50.000 20.71 0.00 0.00 1.94
585 596 4.822036 TCATTTTTGTCACTTACGGGTG 57.178 40.909 0.00 0.00 38.44 4.61
591 602 0.802494 GTCACTTACGGGTGGCATTG 59.198 55.000 0.00 0.00 41.00 2.82
592 603 0.398696 TCACTTACGGGTGGCATTGT 59.601 50.000 0.00 0.00 37.75 2.71
600 611 0.606096 GGGTGGCATTGTTGGGTAAC 59.394 55.000 0.00 0.00 37.32 2.50
603 614 2.029380 GGTGGCATTGTTGGGTAACTTC 60.029 50.000 0.00 0.00 37.68 3.01
607 618 5.185056 GTGGCATTGTTGGGTAACTTCTATT 59.815 40.000 0.00 0.00 37.68 1.73
610 621 7.617723 TGGCATTGTTGGGTAACTTCTATTAAT 59.382 33.333 0.00 0.00 37.68 1.40
612 623 9.869757 GCATTGTTGGGTAACTTCTATTAATTT 57.130 29.630 0.00 0.00 37.68 1.82
651 663 3.622630 ACTACGACCAGAAGCAGTAGAT 58.377 45.455 7.77 0.00 38.40 1.98
652 664 2.949451 ACGACCAGAAGCAGTAGATG 57.051 50.000 0.00 0.00 0.00 2.90
663 675 2.871182 CAGTAGATGCTACCGCTCAA 57.129 50.000 0.00 0.00 36.97 3.02
664 676 3.165058 CAGTAGATGCTACCGCTCAAA 57.835 47.619 0.00 0.00 36.97 2.69
665 677 3.521560 CAGTAGATGCTACCGCTCAAAA 58.478 45.455 0.00 0.00 36.97 2.44
666 678 3.932710 CAGTAGATGCTACCGCTCAAAAA 59.067 43.478 0.00 0.00 36.97 1.94
721 733 6.820470 TTTTTCCAATTAAGCGAAACACAG 57.180 33.333 0.00 0.00 0.00 3.66
722 734 5.508200 TTTCCAATTAAGCGAAACACAGT 57.492 34.783 0.00 0.00 0.00 3.55
728 740 0.935196 AAGCGAAACACAGTCGTTCC 59.065 50.000 0.00 0.00 40.64 3.62
751 763 2.086869 CATTATTGGGCTAGGATGCGG 58.913 52.381 0.00 0.00 0.00 5.69
754 766 0.773644 ATTGGGCTAGGATGCGGAAT 59.226 50.000 0.00 0.00 0.00 3.01
843 856 3.644399 GACGGAGGCCCAAGACGAC 62.644 68.421 0.00 0.00 0.00 4.34
927 945 3.602205 AGGAGGGCCAAAATTAGGATC 57.398 47.619 6.18 0.00 36.29 3.36
946 964 4.828387 GGATCGACAGTAGGAGTAGGATTT 59.172 45.833 0.00 0.00 0.00 2.17
1183 1204 1.968493 TCAAGTCCGAAACCTGCTACT 59.032 47.619 0.00 0.00 0.00 2.57
1184 1205 2.029290 TCAAGTCCGAAACCTGCTACTC 60.029 50.000 0.00 0.00 0.00 2.59
1185 1206 0.896226 AGTCCGAAACCTGCTACTCC 59.104 55.000 0.00 0.00 0.00 3.85
1701 1722 0.107945 ATGCTTTCCTCTCCACGCTC 60.108 55.000 0.00 0.00 0.00 5.03
1729 1750 1.228657 GGACCAGTTCAACGAGGCAC 61.229 60.000 2.30 0.00 0.00 5.01
2091 2112 4.400961 AACGAGCAGCTGCCCTCC 62.401 66.667 34.39 19.50 43.38 4.30
2160 2181 1.301716 ATCTGCCGCAGTTGACGTT 60.302 52.632 19.77 0.00 32.61 3.99
2215 2236 3.347077 CTGAGGAATCAGCCAAAGAGT 57.653 47.619 0.00 0.00 0.00 3.24
2305 2326 0.251787 GGGAATTGAGTTGCCCCAGT 60.252 55.000 0.00 0.00 42.12 4.00
2368 2389 1.472480 GGCACCACACATATGACCAAC 59.528 52.381 10.38 0.00 0.00 3.77
2460 2481 1.686052 GGATGCCACTGGTTGTTTTGA 59.314 47.619 0.00 0.00 0.00 2.69
2530 2551 3.054802 CACTTCCTCATTAGGCCTCAAGT 60.055 47.826 9.68 4.55 43.31 3.16
2598 2619 7.765149 TGGCCTATATATTGTTAGCCCTATT 57.235 36.000 3.32 0.00 0.00 1.73
2636 2657 4.286297 TGAGAAACCATGAGGAATCGTT 57.714 40.909 0.00 0.00 38.69 3.85
2637 2658 4.002982 TGAGAAACCATGAGGAATCGTTG 58.997 43.478 0.00 0.00 38.69 4.10
2672 2694 4.266714 TGAAGTTTTGTTCGAAAGGAGGT 58.733 39.130 0.00 0.00 0.00 3.85
2704 2726 4.567971 CAGTTGCATTGCCTAATTTTGGA 58.432 39.130 6.12 0.00 0.00 3.53
2712 2734 6.458210 CATTGCCTAATTTTGGAAAGTCTGT 58.542 36.000 0.73 0.00 0.00 3.41
2758 2780 0.909610 GGAGGGTGGAGATGGTGTGA 60.910 60.000 0.00 0.00 0.00 3.58
2769 2791 1.906574 GATGGTGTGACTAGGGGTTGA 59.093 52.381 0.00 0.00 0.00 3.18
2797 2819 6.745794 AGAGAGGATAATTTTGAGGAGGAG 57.254 41.667 0.00 0.00 0.00 3.69
2906 2929 6.978659 CCTAAGAAAAAGGAACACAAAACTCC 59.021 38.462 0.00 0.00 36.08 3.85
2928 2951 4.445735 CCGGAATATGGAAAAGAGGCCTAA 60.446 45.833 4.42 0.00 0.00 2.69
2929 2952 4.515567 CGGAATATGGAAAAGAGGCCTAAC 59.484 45.833 4.42 0.00 0.00 2.34
2930 2953 5.687706 CGGAATATGGAAAAGAGGCCTAACT 60.688 44.000 4.42 0.00 0.00 2.24
2931 2954 6.129874 GGAATATGGAAAAGAGGCCTAACTT 58.870 40.000 4.42 2.20 0.00 2.66
2932 2955 6.039829 GGAATATGGAAAAGAGGCCTAACTTG 59.960 42.308 4.42 0.00 0.00 3.16
2933 2956 3.154827 TGGAAAAGAGGCCTAACTTGG 57.845 47.619 4.42 0.00 0.00 3.61
2934 2957 2.225017 TGGAAAAGAGGCCTAACTTGGG 60.225 50.000 4.42 0.00 0.00 4.12
2935 2958 2.447443 GAAAAGAGGCCTAACTTGGGG 58.553 52.381 4.42 0.00 0.00 4.96
2936 2959 0.704664 AAAGAGGCCTAACTTGGGGG 59.295 55.000 4.42 0.00 0.00 5.40
3010 3263 6.790232 ATTTCTTCCCTTCAAAACAGTTCA 57.210 33.333 0.00 0.00 0.00 3.18
3059 3312 1.212935 TCAAAGCCTTGCCTAGATCCC 59.787 52.381 0.00 0.00 32.14 3.85
3062 3315 2.029666 CCTTGCCTAGATCCCGCG 59.970 66.667 0.00 0.00 0.00 6.46
3099 3352 3.955551 ACCACCACCTTTTATTGAACGTT 59.044 39.130 0.00 0.00 0.00 3.99
3100 3353 4.403113 ACCACCACCTTTTATTGAACGTTT 59.597 37.500 0.46 0.00 0.00 3.60
3101 3354 5.105269 ACCACCACCTTTTATTGAACGTTTT 60.105 36.000 0.46 0.00 0.00 2.43
3102 3355 5.460748 CCACCACCTTTTATTGAACGTTTTC 59.539 40.000 0.46 0.00 0.00 2.29
3103 3356 6.270064 CACCACCTTTTATTGAACGTTTTCT 58.730 36.000 0.46 0.00 32.36 2.52
3104 3357 6.198216 CACCACCTTTTATTGAACGTTTTCTG 59.802 38.462 0.46 0.00 32.36 3.02
3105 3358 5.174943 CCACCTTTTATTGAACGTTTTCTGC 59.825 40.000 0.46 0.00 32.36 4.26
3106 3359 5.174943 CACCTTTTATTGAACGTTTTCTGCC 59.825 40.000 0.46 0.00 32.36 4.85
3107 3360 5.163499 ACCTTTTATTGAACGTTTTCTGCCA 60.163 36.000 0.46 0.00 32.36 4.92
3108 3361 5.925969 CCTTTTATTGAACGTTTTCTGCCAT 59.074 36.000 0.46 0.00 32.36 4.40
3109 3362 7.087639 CCTTTTATTGAACGTTTTCTGCCATA 58.912 34.615 0.46 0.00 32.36 2.74
3110 3363 7.596995 CCTTTTATTGAACGTTTTCTGCCATAA 59.403 33.333 0.46 0.00 32.36 1.90
3111 3364 8.873215 TTTTATTGAACGTTTTCTGCCATAAA 57.127 26.923 0.46 1.12 32.36 1.40
3112 3365 9.482627 TTTTATTGAACGTTTTCTGCCATAAAT 57.517 25.926 0.46 0.00 32.36 1.40
3114 3367 9.781834 TTATTGAACGTTTTCTGCCATAAATAG 57.218 29.630 0.46 0.00 32.36 1.73
3115 3368 6.189677 TGAACGTTTTCTGCCATAAATAGG 57.810 37.500 0.46 0.00 32.36 2.57
3116 3369 5.941058 TGAACGTTTTCTGCCATAAATAGGA 59.059 36.000 0.46 0.00 32.36 2.94
3117 3370 5.813080 ACGTTTTCTGCCATAAATAGGAC 57.187 39.130 0.00 0.00 0.00 3.85
3118 3371 5.497474 ACGTTTTCTGCCATAAATAGGACT 58.503 37.500 0.00 0.00 0.00 3.85
3119 3372 5.944007 ACGTTTTCTGCCATAAATAGGACTT 59.056 36.000 0.00 0.00 0.00 3.01
3120 3373 6.128007 ACGTTTTCTGCCATAAATAGGACTTG 60.128 38.462 0.00 0.00 0.00 3.16
3121 3374 6.093495 CGTTTTCTGCCATAAATAGGACTTGA 59.907 38.462 0.00 0.00 0.00 3.02
3122 3375 7.361713 CGTTTTCTGCCATAAATAGGACTTGAA 60.362 37.037 0.00 0.00 0.00 2.69
3123 3376 8.303876 GTTTTCTGCCATAAATAGGACTTGAAA 58.696 33.333 0.00 0.00 0.00 2.69
3124 3377 7.630242 TTCTGCCATAAATAGGACTTGAAAG 57.370 36.000 0.00 0.00 0.00 2.62
3125 3378 6.721318 TCTGCCATAAATAGGACTTGAAAGT 58.279 36.000 0.00 0.00 43.16 2.66
3126 3379 7.857456 TCTGCCATAAATAGGACTTGAAAGTA 58.143 34.615 0.00 0.00 39.88 2.24
3127 3380 7.987458 TCTGCCATAAATAGGACTTGAAAGTAG 59.013 37.037 0.00 0.00 39.88 2.57
3128 3381 7.857456 TGCCATAAATAGGACTTGAAAGTAGA 58.143 34.615 0.00 0.00 39.88 2.59
3129 3382 7.769044 TGCCATAAATAGGACTTGAAAGTAGAC 59.231 37.037 0.00 0.00 39.88 2.59
3130 3383 7.226918 GCCATAAATAGGACTTGAAAGTAGACC 59.773 40.741 0.00 0.00 39.88 3.85
3131 3384 7.715686 CCATAAATAGGACTTGAAAGTAGACCC 59.284 40.741 0.00 0.00 39.88 4.46
3132 3385 5.340439 AATAGGACTTGAAAGTAGACCCG 57.660 43.478 0.00 0.00 39.88 5.28
3133 3386 1.900486 AGGACTTGAAAGTAGACCCGG 59.100 52.381 0.00 0.00 39.88 5.73
3134 3387 1.066358 GGACTTGAAAGTAGACCCGGG 60.066 57.143 22.25 22.25 39.88 5.73
3135 3388 0.323957 ACTTGAAAGTAGACCCGGGC 59.676 55.000 24.08 14.21 37.52 6.13
3136 3389 0.323629 CTTGAAAGTAGACCCGGGCA 59.676 55.000 24.08 4.39 0.00 5.36
3137 3390 0.035739 TTGAAAGTAGACCCGGGCAC 59.964 55.000 24.08 16.67 0.00 5.01
3138 3391 1.122632 TGAAAGTAGACCCGGGCACA 61.123 55.000 24.08 1.39 0.00 4.57
3139 3392 0.252197 GAAAGTAGACCCGGGCACAT 59.748 55.000 24.08 6.38 0.00 3.21
3140 3393 0.252197 AAAGTAGACCCGGGCACATC 59.748 55.000 24.08 11.13 0.00 3.06
3141 3394 1.623542 AAGTAGACCCGGGCACATCC 61.624 60.000 24.08 3.58 0.00 3.51
3163 3416 4.394712 CGGGCTCGGGCTCAGTTT 62.395 66.667 8.49 0.00 39.29 2.66
3164 3417 2.034221 GGGCTCGGGCTCAGTTTT 59.966 61.111 7.48 0.00 39.12 2.43
3165 3418 1.603739 GGGCTCGGGCTCAGTTTTT 60.604 57.895 7.48 0.00 39.12 1.94
3166 3419 1.587043 GGGCTCGGGCTCAGTTTTTC 61.587 60.000 7.48 0.00 39.12 2.29
3167 3420 0.606673 GGCTCGGGCTCAGTTTTTCT 60.607 55.000 7.48 0.00 38.73 2.52
3168 3421 0.519077 GCTCGGGCTCAGTTTTTCTG 59.481 55.000 0.00 0.00 44.85 3.02
3169 3422 0.519077 CTCGGGCTCAGTTTTTCTGC 59.481 55.000 0.00 0.00 43.32 4.26
3170 3423 0.889186 TCGGGCTCAGTTTTTCTGCC 60.889 55.000 0.00 0.00 43.32 4.85
3171 3424 0.890996 CGGGCTCAGTTTTTCTGCCT 60.891 55.000 0.00 0.00 43.32 4.75
3172 3425 0.600057 GGGCTCAGTTTTTCTGCCTG 59.400 55.000 0.00 0.00 43.32 4.85
3173 3426 1.609208 GGCTCAGTTTTTCTGCCTGA 58.391 50.000 0.00 0.00 43.32 3.86
3174 3427 1.956477 GGCTCAGTTTTTCTGCCTGAA 59.044 47.619 0.00 0.00 43.32 3.02
3175 3428 2.030451 GGCTCAGTTTTTCTGCCTGAAG 60.030 50.000 0.00 0.00 43.32 3.02
3176 3429 2.606551 GCTCAGTTTTTCTGCCTGAAGC 60.607 50.000 0.00 0.00 43.32 3.86
3177 3430 2.883386 CTCAGTTTTTCTGCCTGAAGCT 59.117 45.455 0.00 0.00 43.32 3.74
3178 3431 3.290710 TCAGTTTTTCTGCCTGAAGCTT 58.709 40.909 0.00 0.00 43.32 3.74
3179 3432 3.067180 TCAGTTTTTCTGCCTGAAGCTTG 59.933 43.478 2.10 0.00 43.32 4.01
3180 3433 3.067180 CAGTTTTTCTGCCTGAAGCTTGA 59.933 43.478 2.10 0.00 44.23 3.02
3181 3434 3.067320 AGTTTTTCTGCCTGAAGCTTGAC 59.933 43.478 2.10 0.00 44.23 3.18
3182 3435 1.609208 TTTCTGCCTGAAGCTTGACC 58.391 50.000 2.10 0.00 44.23 4.02
3183 3436 0.250901 TTCTGCCTGAAGCTTGACCC 60.251 55.000 2.10 0.00 44.23 4.46
3184 3437 1.073722 CTGCCTGAAGCTTGACCCA 59.926 57.895 2.10 0.00 44.23 4.51
3185 3438 0.538057 CTGCCTGAAGCTTGACCCAA 60.538 55.000 2.10 0.00 44.23 4.12
3186 3439 0.106268 TGCCTGAAGCTTGACCCAAA 60.106 50.000 2.10 0.00 44.23 3.28
3187 3440 1.039856 GCCTGAAGCTTGACCCAAAA 58.960 50.000 2.10 0.00 38.99 2.44
3188 3441 1.000171 GCCTGAAGCTTGACCCAAAAG 60.000 52.381 2.10 0.00 38.99 2.27
3192 3445 2.650778 GCTTGACCCAAAAGCCCG 59.349 61.111 0.00 0.00 43.45 6.13
3199 3452 1.530655 CCCAAAAGCCCGAACAGGT 60.531 57.895 0.00 0.00 38.74 4.00
3210 3463 2.943033 CCCGAACAGGTCATAAATCACC 59.057 50.000 0.00 0.00 38.74 4.02
3215 3468 6.350110 CCGAACAGGTCATAAATCACCATTTT 60.350 38.462 0.00 0.00 34.80 1.82
3217 3470 8.405531 CGAACAGGTCATAAATCACCATTTTAT 58.594 33.333 0.00 0.00 34.80 1.40
3302 3556 0.958091 CTTTCATGTGTTTCGGGCCA 59.042 50.000 4.39 0.00 0.00 5.36
3333 3587 1.004745 GGCTTGGGATTTGAGGTCAGA 59.995 52.381 0.00 0.00 0.00 3.27
3356 3610 2.282462 CAAAGCCCGGCCTGAACT 60.282 61.111 5.55 0.00 0.00 3.01
3357 3611 1.903404 CAAAGCCCGGCCTGAACTT 60.903 57.895 5.55 0.00 0.00 2.66
3358 3612 0.608035 CAAAGCCCGGCCTGAACTTA 60.608 55.000 5.55 0.00 0.00 2.24
3359 3613 0.608308 AAAGCCCGGCCTGAACTTAC 60.608 55.000 5.55 0.00 0.00 2.34
3360 3614 1.489560 AAGCCCGGCCTGAACTTACT 61.490 55.000 5.55 0.00 0.00 2.24
3361 3615 1.002502 GCCCGGCCTGAACTTACTT 60.003 57.895 0.00 0.00 0.00 2.24
3362 3616 1.305930 GCCCGGCCTGAACTTACTTG 61.306 60.000 0.00 0.00 0.00 3.16
3363 3617 0.323629 CCCGGCCTGAACTTACTTGA 59.676 55.000 0.00 0.00 0.00 3.02
3364 3618 1.271163 CCCGGCCTGAACTTACTTGAA 60.271 52.381 0.00 0.00 0.00 2.69
3365 3619 2.500229 CCGGCCTGAACTTACTTGAAA 58.500 47.619 0.00 0.00 0.00 2.69
3366 3620 2.484264 CCGGCCTGAACTTACTTGAAAG 59.516 50.000 0.00 0.00 0.00 2.62
3367 3621 2.484264 CGGCCTGAACTTACTTGAAAGG 59.516 50.000 0.00 0.00 0.00 3.11
3368 3622 2.229062 GGCCTGAACTTACTTGAAAGGC 59.771 50.000 0.00 2.15 46.39 4.35
3369 3623 3.149981 GCCTGAACTTACTTGAAAGGCT 58.850 45.455 3.58 0.00 44.26 4.58
3370 3624 3.570125 GCCTGAACTTACTTGAAAGGCTT 59.430 43.478 0.00 0.00 44.26 4.35
3371 3625 4.038042 GCCTGAACTTACTTGAAAGGCTTT 59.962 41.667 13.25 13.25 44.26 3.51
3372 3626 5.523369 CCTGAACTTACTTGAAAGGCTTTG 58.477 41.667 18.79 5.70 0.00 2.77
3373 3627 4.932146 TGAACTTACTTGAAAGGCTTTGC 58.068 39.130 18.79 9.59 0.00 3.68
3374 3628 3.626028 ACTTACTTGAAAGGCTTTGCG 57.374 42.857 18.79 7.64 0.00 4.85
3375 3629 2.293399 ACTTACTTGAAAGGCTTTGCGG 59.707 45.455 18.79 8.93 0.00 5.69
3376 3630 1.975660 TACTTGAAAGGCTTTGCGGT 58.024 45.000 18.79 14.01 0.00 5.68
3377 3631 1.111277 ACTTGAAAGGCTTTGCGGTT 58.889 45.000 18.79 0.00 0.00 4.44
3378 3632 1.202405 ACTTGAAAGGCTTTGCGGTTG 60.202 47.619 18.79 4.12 0.00 3.77
3379 3633 0.103937 TTGAAAGGCTTTGCGGTTGG 59.896 50.000 18.79 0.00 0.00 3.77
3380 3634 0.753479 TGAAAGGCTTTGCGGTTGGA 60.753 50.000 18.79 0.00 0.00 3.53
3381 3635 0.387565 GAAAGGCTTTGCGGTTGGAA 59.612 50.000 18.79 0.00 0.00 3.53
3382 3636 0.389025 AAAGGCTTTGCGGTTGGAAG 59.611 50.000 12.53 0.00 0.00 3.46
3383 3637 0.755327 AAGGCTTTGCGGTTGGAAGT 60.755 50.000 0.00 0.00 0.00 3.01
3384 3638 0.109723 AGGCTTTGCGGTTGGAAGTA 59.890 50.000 0.00 0.00 0.00 2.24
3385 3639 1.173913 GGCTTTGCGGTTGGAAGTAT 58.826 50.000 0.00 0.00 0.00 2.12
3386 3640 2.026636 AGGCTTTGCGGTTGGAAGTATA 60.027 45.455 0.00 0.00 0.00 1.47
3387 3641 2.354821 GGCTTTGCGGTTGGAAGTATAG 59.645 50.000 0.00 0.00 0.00 1.31
3388 3642 3.007635 GCTTTGCGGTTGGAAGTATAGT 58.992 45.455 0.00 0.00 0.00 2.12
3389 3643 3.063588 GCTTTGCGGTTGGAAGTATAGTC 59.936 47.826 0.00 0.00 0.00 2.59
3390 3644 4.504858 CTTTGCGGTTGGAAGTATAGTCT 58.495 43.478 0.00 0.00 0.00 3.24
3391 3645 4.546829 TTGCGGTTGGAAGTATAGTCTT 57.453 40.909 0.00 0.00 0.00 3.01
3392 3646 3.857052 TGCGGTTGGAAGTATAGTCTTG 58.143 45.455 0.00 0.00 0.00 3.02
3393 3647 3.195661 GCGGTTGGAAGTATAGTCTTGG 58.804 50.000 0.00 0.00 0.00 3.61
3394 3648 3.195661 CGGTTGGAAGTATAGTCTTGGC 58.804 50.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 8.586570 TTTTGTTTATGATGCACCTTTAGTTG 57.413 30.769 0.00 0.00 0.00 3.16
170 177 8.087982 ACATGTTATATATGAAAACCGCTCAG 57.912 34.615 0.00 0.00 0.00 3.35
269 279 4.526438 ATTATCTTGGCCCAGCTACTTT 57.474 40.909 0.00 0.00 0.00 2.66
270 280 5.310594 TGATATTATCTTGGCCCAGCTACTT 59.689 40.000 0.00 0.00 0.00 2.24
271 281 4.846367 TGATATTATCTTGGCCCAGCTACT 59.154 41.667 0.00 0.00 0.00 2.57
272 282 5.165961 TGATATTATCTTGGCCCAGCTAC 57.834 43.478 0.00 0.00 0.00 3.58
273 283 6.673978 AGTATGATATTATCTTGGCCCAGCTA 59.326 38.462 0.00 0.00 0.00 3.32
274 284 4.942363 ATGATATTATCTTGGCCCAGCT 57.058 40.909 0.00 0.00 0.00 4.24
275 285 5.749462 AGTATGATATTATCTTGGCCCAGC 58.251 41.667 0.00 0.00 0.00 4.85
277 287 9.951866 TCTATAGTATGATATTATCTTGGCCCA 57.048 33.333 0.00 0.00 0.00 5.36
295 305 9.678260 GAGTTTTCTCCCCGTATATCTATAGTA 57.322 37.037 0.00 0.00 40.79 1.82
296 306 8.168725 TGAGTTTTCTCCCCGTATATCTATAGT 58.831 37.037 0.00 0.00 45.63 2.12
297 307 8.577048 TGAGTTTTCTCCCCGTATATCTATAG 57.423 38.462 0.00 0.00 45.63 1.31
298 308 7.122353 GCTGAGTTTTCTCCCCGTATATCTATA 59.878 40.741 0.00 0.00 45.63 1.31
299 309 6.071278 GCTGAGTTTTCTCCCCGTATATCTAT 60.071 42.308 0.00 0.00 45.63 1.98
300 310 5.243283 GCTGAGTTTTCTCCCCGTATATCTA 59.757 44.000 0.00 0.00 45.63 1.98
301 311 4.039366 GCTGAGTTTTCTCCCCGTATATCT 59.961 45.833 0.00 0.00 45.63 1.98
302 312 4.202223 TGCTGAGTTTTCTCCCCGTATATC 60.202 45.833 0.00 0.00 45.63 1.63
303 313 3.709653 TGCTGAGTTTTCTCCCCGTATAT 59.290 43.478 0.00 0.00 45.63 0.86
304 314 3.101437 TGCTGAGTTTTCTCCCCGTATA 58.899 45.455 0.00 0.00 45.63 1.47
305 315 1.906574 TGCTGAGTTTTCTCCCCGTAT 59.093 47.619 0.00 0.00 45.63 3.06
306 316 1.344065 TGCTGAGTTTTCTCCCCGTA 58.656 50.000 0.00 0.00 45.63 4.02
307 317 0.472471 TTGCTGAGTTTTCTCCCCGT 59.528 50.000 0.00 0.00 45.63 5.28
308 318 1.604604 TTTGCTGAGTTTTCTCCCCG 58.395 50.000 0.00 0.00 45.63 5.73
344 354 8.304596 GCCCAGCTACTTCTTTTAACTTTTATT 58.695 33.333 0.00 0.00 0.00 1.40
345 355 7.093902 GGCCCAGCTACTTCTTTTAACTTTTAT 60.094 37.037 0.00 0.00 0.00 1.40
346 356 6.208007 GGCCCAGCTACTTCTTTTAACTTTTA 59.792 38.462 0.00 0.00 0.00 1.52
347 357 5.010719 GGCCCAGCTACTTCTTTTAACTTTT 59.989 40.000 0.00 0.00 0.00 2.27
348 358 4.523173 GGCCCAGCTACTTCTTTTAACTTT 59.477 41.667 0.00 0.00 0.00 2.66
349 359 4.079970 GGCCCAGCTACTTCTTTTAACTT 58.920 43.478 0.00 0.00 0.00 2.66
350 360 3.073946 TGGCCCAGCTACTTCTTTTAACT 59.926 43.478 0.00 0.00 0.00 2.24
351 361 3.418047 TGGCCCAGCTACTTCTTTTAAC 58.582 45.455 0.00 0.00 0.00 2.01
352 362 3.799432 TGGCCCAGCTACTTCTTTTAA 57.201 42.857 0.00 0.00 0.00 1.52
353 363 3.329520 TCTTGGCCCAGCTACTTCTTTTA 59.670 43.478 0.00 0.00 0.00 1.52
354 364 2.108250 TCTTGGCCCAGCTACTTCTTTT 59.892 45.455 0.00 0.00 0.00 2.27
355 365 1.705186 TCTTGGCCCAGCTACTTCTTT 59.295 47.619 0.00 0.00 0.00 2.52
356 366 1.362224 TCTTGGCCCAGCTACTTCTT 58.638 50.000 0.00 0.00 0.00 2.52
357 367 1.589414 ATCTTGGCCCAGCTACTTCT 58.411 50.000 0.00 0.00 0.00 2.85
358 368 3.560636 TTATCTTGGCCCAGCTACTTC 57.439 47.619 0.00 0.00 0.00 3.01
423 433 1.354368 GGGTTTGATCCCAGGTTCTGA 59.646 52.381 0.00 0.00 46.30 3.27
424 434 1.839424 GGGTTTGATCCCAGGTTCTG 58.161 55.000 0.00 0.00 46.30 3.02
459 469 2.512515 GGCTAGGGCGTTGCTCTG 60.513 66.667 12.87 0.00 40.83 3.35
460 470 3.003173 TGGCTAGGGCGTTGCTCT 61.003 61.111 12.87 0.00 44.12 4.09
461 471 1.956629 TACTGGCTAGGGCGTTGCTC 61.957 60.000 12.87 4.75 39.81 4.26
478 488 9.351570 GTTATGACAAGTAGACAAGTAACCTAC 57.648 37.037 0.00 0.00 34.52 3.18
483 493 9.616634 CTAACGTTATGACAAGTAGACAAGTAA 57.383 33.333 8.76 0.00 0.00 2.24
485 495 7.088905 CCTAACGTTATGACAAGTAGACAAGT 58.911 38.462 8.76 0.00 0.00 3.16
491 501 6.205101 AGACCCTAACGTTATGACAAGTAG 57.795 41.667 8.76 0.00 0.00 2.57
495 505 4.708421 AGCTAGACCCTAACGTTATGACAA 59.292 41.667 8.76 0.00 0.00 3.18
497 507 4.097589 ACAGCTAGACCCTAACGTTATGAC 59.902 45.833 8.76 4.17 0.00 3.06
499 509 4.650754 ACAGCTAGACCCTAACGTTATG 57.349 45.455 8.76 6.03 0.00 1.90
504 514 5.258456 TCATTTACAGCTAGACCCTAACG 57.742 43.478 0.00 0.00 0.00 3.18
505 515 6.224584 GGATCATTTACAGCTAGACCCTAAC 58.775 44.000 0.00 0.00 0.00 2.34
507 517 4.523173 CGGATCATTTACAGCTAGACCCTA 59.477 45.833 0.00 0.00 0.00 3.53
512 522 3.004419 CGTCCGGATCATTTACAGCTAGA 59.996 47.826 7.81 0.00 0.00 2.43
519 529 1.329599 GGTTGCGTCCGGATCATTTAC 59.670 52.381 7.81 4.54 0.00 2.01
536 546 1.912826 TTATTAGGTGGCCGCCGGTT 61.913 55.000 29.37 19.19 0.00 4.44
558 568 6.699642 CCCGTAAGTGACAAAAATGATTTGTT 59.300 34.615 7.86 0.00 42.11 2.83
566 576 2.295070 GCCACCCGTAAGTGACAAAAAT 59.705 45.455 0.00 0.00 40.34 1.82
574 585 1.068610 CAACAATGCCACCCGTAAGTG 60.069 52.381 0.00 0.00 37.51 3.16
575 586 1.243902 CAACAATGCCACCCGTAAGT 58.756 50.000 0.00 0.00 0.00 2.24
585 596 5.914898 AATAGAAGTTACCCAACAATGCC 57.085 39.130 0.00 0.00 37.10 4.40
627 638 1.269998 ACTGCTTCTGGTCGTAGTCAC 59.730 52.381 0.00 0.00 0.00 3.67
698 710 6.334202 ACTGTGTTTCGCTTAATTGGAAAAA 58.666 32.000 0.00 0.00 32.08 1.94
699 711 5.897050 ACTGTGTTTCGCTTAATTGGAAAA 58.103 33.333 0.00 0.00 32.08 2.29
700 712 5.508200 ACTGTGTTTCGCTTAATTGGAAA 57.492 34.783 0.00 0.00 0.00 3.13
701 713 4.319190 CGACTGTGTTTCGCTTAATTGGAA 60.319 41.667 0.00 0.00 0.00 3.53
702 714 3.185594 CGACTGTGTTTCGCTTAATTGGA 59.814 43.478 0.00 0.00 0.00 3.53
703 715 3.059188 ACGACTGTGTTTCGCTTAATTGG 60.059 43.478 0.00 0.00 40.24 3.16
704 716 4.128554 ACGACTGTGTTTCGCTTAATTG 57.871 40.909 0.00 0.00 40.24 2.32
705 717 4.319261 GGAACGACTGTGTTTCGCTTAATT 60.319 41.667 0.00 0.00 40.24 1.40
706 718 3.185797 GGAACGACTGTGTTTCGCTTAAT 59.814 43.478 0.00 0.00 40.24 1.40
707 719 2.540931 GGAACGACTGTGTTTCGCTTAA 59.459 45.455 0.00 0.00 40.24 1.85
708 720 2.129607 GGAACGACTGTGTTTCGCTTA 58.870 47.619 0.00 0.00 40.24 3.09
709 721 0.935196 GGAACGACTGTGTTTCGCTT 59.065 50.000 0.00 0.00 40.24 4.68
710 722 0.878961 GGGAACGACTGTGTTTCGCT 60.879 55.000 0.00 0.00 40.24 4.93
711 723 1.155424 TGGGAACGACTGTGTTTCGC 61.155 55.000 0.00 7.65 40.24 4.70
712 724 0.580104 GTGGGAACGACTGTGTTTCG 59.420 55.000 0.00 0.00 42.36 3.46
713 725 1.658994 TGTGGGAACGACTGTGTTTC 58.341 50.000 0.00 0.00 30.75 2.78
714 726 2.341846 ATGTGGGAACGACTGTGTTT 57.658 45.000 0.00 0.00 30.75 2.83
715 727 2.341846 AATGTGGGAACGACTGTGTT 57.658 45.000 0.00 0.00 34.02 3.32
716 728 3.695830 ATAATGTGGGAACGACTGTGT 57.304 42.857 0.00 0.00 0.00 3.72
717 729 3.126858 CCAATAATGTGGGAACGACTGTG 59.873 47.826 0.00 0.00 34.77 3.66
718 730 3.343617 CCAATAATGTGGGAACGACTGT 58.656 45.455 0.00 0.00 34.77 3.55
728 740 2.821969 GCATCCTAGCCCAATAATGTGG 59.178 50.000 0.00 0.00 38.51 4.17
742 754 4.404394 TGACTAACTTCATTCCGCATCCTA 59.596 41.667 0.00 0.00 0.00 2.94
751 763 2.673368 CCACGGCTGACTAACTTCATTC 59.327 50.000 0.00 0.00 0.00 2.67
754 766 0.320374 CCCACGGCTGACTAACTTCA 59.680 55.000 0.00 0.00 0.00 3.02
784 797 5.405935 AATCTGGCCTGTTTATTGGTTTC 57.594 39.130 3.32 0.00 0.00 2.78
822 835 2.920912 TCTTGGGCCTCCGTCGTT 60.921 61.111 4.53 0.00 35.24 3.85
828 841 2.232298 CTCTGTCGTCTTGGGCCTCC 62.232 65.000 4.53 0.00 0.00 4.30
843 856 6.632834 CGTGTTTGTAAAATCCTCAAACTCTG 59.367 38.462 16.82 9.03 45.99 3.35
927 945 4.519730 CCCTAAATCCTACTCCTACTGTCG 59.480 50.000 0.00 0.00 0.00 4.35
946 964 0.646055 CCCCCTCTACTTTCCCCCTA 59.354 60.000 0.00 0.00 0.00 3.53
968 986 1.396301 GTGCTTTCTTCGATCTGCAGG 59.604 52.381 15.13 0.00 0.00 4.85
1008 1026 1.587054 CTCCGTGCTCTTCTCCGTT 59.413 57.895 0.00 0.00 0.00 4.44
1171 1192 1.449778 GGCGGGAGTAGCAGGTTTC 60.450 63.158 0.00 0.00 36.08 2.78
1701 1722 3.934391 GAACTGGTCCCCTCGCACG 62.934 68.421 0.00 0.00 0.00 5.34
1729 1750 2.938756 GCATCACCTGGAGGAACTTGAG 60.939 54.545 0.00 0.00 41.55 3.02
1731 1752 1.457346 GCATCACCTGGAGGAACTTG 58.543 55.000 0.00 0.00 41.55 3.16
2091 2112 3.730761 GCAGCACAGTTGGAGGCG 61.731 66.667 0.00 0.00 0.00 5.52
2160 2181 1.672030 CTCCACGATGCAGTGCCAA 60.672 57.895 13.72 0.00 40.59 4.52
2215 2236 3.031736 AGTCGAGAAGCCCAGCTATTAA 58.968 45.455 0.00 0.00 38.25 1.40
2368 2389 0.384725 CGCTTCAACCTTCGTGCAAG 60.385 55.000 0.00 0.00 0.00 4.01
2460 2481 7.388437 AGTTTCACACAATAAATGGCAATCAT 58.612 30.769 0.00 0.00 37.79 2.45
2598 2619 9.639563 TGGTTTCTCAAAATGAATATATAGCCA 57.360 29.630 0.00 0.00 0.00 4.75
2636 2657 1.073722 CTTCAAGCAGTGGAGCCCA 59.926 57.895 0.00 0.00 34.23 5.36
2637 2658 0.538287 AACTTCAAGCAGTGGAGCCC 60.538 55.000 0.00 0.00 36.08 5.19
2672 2694 3.525537 GCAATGCAACTGCTAGAGTCTA 58.474 45.455 15.04 0.00 42.66 2.59
2712 2734 3.334691 CACGGGACATAGCAGAAAAAGA 58.665 45.455 0.00 0.00 0.00 2.52
2758 2780 3.445987 CTCTCTTCCTTCAACCCCTAGT 58.554 50.000 0.00 0.00 0.00 2.57
2769 2791 7.366371 CCTCCTCAAAATTATCCTCTCTTCCTT 60.366 40.741 0.00 0.00 0.00 3.36
2797 2819 1.416401 TCTCCCGTTTATCAGCCATCC 59.584 52.381 0.00 0.00 0.00 3.51
2906 2929 3.214696 AGGCCTCTTTTCCATATTCCG 57.785 47.619 0.00 0.00 0.00 4.30
2945 2968 3.391382 GAGGGGTCACCGGGTCAG 61.391 72.222 6.32 0.00 46.96 3.51
2946 2969 2.976284 AAAGAGGGGTCACCGGGTCA 62.976 60.000 6.32 0.00 46.96 4.02
2947 2970 1.775934 AAAAGAGGGGTCACCGGGTC 61.776 60.000 6.32 0.00 46.96 4.46
2948 2971 0.474273 TAAAAGAGGGGTCACCGGGT 60.474 55.000 6.32 0.00 46.96 5.28
2949 2972 0.916809 ATAAAAGAGGGGTCACCGGG 59.083 55.000 6.32 0.00 46.96 5.73
2950 2973 2.290705 ACAATAAAAGAGGGGTCACCGG 60.291 50.000 0.00 0.00 46.96 5.28
2951 2974 3.067684 ACAATAAAAGAGGGGTCACCG 57.932 47.619 0.00 0.00 46.96 4.94
2952 2975 5.184479 GGTTAACAATAAAAGAGGGGTCACC 59.816 44.000 8.10 0.00 40.67 4.02
2953 2976 6.008331 AGGTTAACAATAAAAGAGGGGTCAC 58.992 40.000 8.10 0.00 0.00 3.67
2954 2977 6.007703 CAGGTTAACAATAAAAGAGGGGTCA 58.992 40.000 8.10 0.00 0.00 4.02
2955 2978 5.417894 CCAGGTTAACAATAAAAGAGGGGTC 59.582 44.000 8.10 0.00 0.00 4.46
2956 2979 5.330233 CCAGGTTAACAATAAAAGAGGGGT 58.670 41.667 8.10 0.00 0.00 4.95
2957 2980 4.159693 GCCAGGTTAACAATAAAAGAGGGG 59.840 45.833 8.10 0.00 0.00 4.79
2958 2981 4.770010 TGCCAGGTTAACAATAAAAGAGGG 59.230 41.667 8.10 0.00 0.00 4.30
2959 2982 5.975693 TGCCAGGTTAACAATAAAAGAGG 57.024 39.130 8.10 0.00 0.00 3.69
2960 2983 8.519526 TGTTATGCCAGGTTAACAATAAAAGAG 58.480 33.333 8.10 0.00 35.86 2.85
3059 3312 0.110192 GTCTTGCTTCCTTTTCCGCG 60.110 55.000 0.00 0.00 0.00 6.46
3062 3315 1.613925 GGTGGTCTTGCTTCCTTTTCC 59.386 52.381 0.00 0.00 0.00 3.13
3099 3352 7.669722 ACTTTCAAGTCCTATTTATGGCAGAAA 59.330 33.333 10.01 10.01 32.86 2.52
3100 3353 7.175104 ACTTTCAAGTCCTATTTATGGCAGAA 58.825 34.615 0.00 0.00 32.86 3.02
3101 3354 6.721318 ACTTTCAAGTCCTATTTATGGCAGA 58.279 36.000 0.00 0.00 32.86 4.26
3102 3355 7.987458 TCTACTTTCAAGTCCTATTTATGGCAG 59.013 37.037 0.00 0.00 40.37 4.85
3103 3356 7.769044 GTCTACTTTCAAGTCCTATTTATGGCA 59.231 37.037 0.00 0.00 40.37 4.92
3104 3357 7.226918 GGTCTACTTTCAAGTCCTATTTATGGC 59.773 40.741 0.00 0.00 40.37 4.40
3105 3358 7.715686 GGGTCTACTTTCAAGTCCTATTTATGG 59.284 40.741 0.00 0.00 40.37 2.74
3106 3359 7.438459 CGGGTCTACTTTCAAGTCCTATTTATG 59.562 40.741 0.00 0.00 40.37 1.90
3107 3360 7.418712 CCGGGTCTACTTTCAAGTCCTATTTAT 60.419 40.741 0.00 0.00 40.37 1.40
3108 3361 6.127253 CCGGGTCTACTTTCAAGTCCTATTTA 60.127 42.308 0.00 0.00 40.37 1.40
3109 3362 5.338137 CCGGGTCTACTTTCAAGTCCTATTT 60.338 44.000 0.00 0.00 40.37 1.40
3110 3363 4.161754 CCGGGTCTACTTTCAAGTCCTATT 59.838 45.833 0.00 0.00 40.37 1.73
3111 3364 3.705072 CCGGGTCTACTTTCAAGTCCTAT 59.295 47.826 0.00 0.00 40.37 2.57
3112 3365 3.094572 CCGGGTCTACTTTCAAGTCCTA 58.905 50.000 0.00 0.00 40.37 2.94
3113 3366 1.900486 CCGGGTCTACTTTCAAGTCCT 59.100 52.381 0.00 0.00 40.37 3.85
3114 3367 1.066358 CCCGGGTCTACTTTCAAGTCC 60.066 57.143 14.18 0.00 40.37 3.85
3115 3368 1.675116 GCCCGGGTCTACTTTCAAGTC 60.675 57.143 24.63 0.00 40.37 3.01
3116 3369 0.323957 GCCCGGGTCTACTTTCAAGT 59.676 55.000 24.63 0.00 42.91 3.16
3117 3370 0.323629 TGCCCGGGTCTACTTTCAAG 59.676 55.000 24.63 0.00 0.00 3.02
3118 3371 0.035739 GTGCCCGGGTCTACTTTCAA 59.964 55.000 24.63 0.00 0.00 2.69
3119 3372 1.122632 TGTGCCCGGGTCTACTTTCA 61.123 55.000 24.63 5.60 0.00 2.69
3120 3373 0.252197 ATGTGCCCGGGTCTACTTTC 59.748 55.000 24.63 2.41 0.00 2.62
3121 3374 0.252197 GATGTGCCCGGGTCTACTTT 59.748 55.000 24.63 10.73 0.00 2.66
3122 3375 1.623542 GGATGTGCCCGGGTCTACTT 61.624 60.000 24.63 16.37 0.00 2.24
3123 3376 2.064581 GGATGTGCCCGGGTCTACT 61.065 63.158 24.63 8.98 0.00 2.57
3124 3377 2.504519 GGATGTGCCCGGGTCTAC 59.495 66.667 24.63 18.96 0.00 2.59
3125 3378 3.151710 CGGATGTGCCCGGGTCTA 61.152 66.667 24.63 8.90 45.43 2.59
3146 3399 3.901797 AAAACTGAGCCCGAGCCCG 62.902 63.158 0.00 0.00 41.25 6.13
3147 3400 1.587043 GAAAAACTGAGCCCGAGCCC 61.587 60.000 0.00 0.00 41.25 5.19
3148 3401 0.606673 AGAAAAACTGAGCCCGAGCC 60.607 55.000 0.00 0.00 41.25 4.70
3149 3402 2.934083 AGAAAAACTGAGCCCGAGC 58.066 52.632 0.00 0.00 40.32 5.03
3159 3412 3.067320 GTCAAGCTTCAGGCAGAAAAACT 59.933 43.478 0.00 0.00 44.79 2.66
3160 3413 3.375642 GTCAAGCTTCAGGCAGAAAAAC 58.624 45.455 0.00 0.00 44.79 2.43
3161 3414 2.362077 GGTCAAGCTTCAGGCAGAAAAA 59.638 45.455 0.00 0.00 44.79 1.94
3162 3415 1.956477 GGTCAAGCTTCAGGCAGAAAA 59.044 47.619 0.00 0.00 44.79 2.29
3163 3416 1.609208 GGTCAAGCTTCAGGCAGAAA 58.391 50.000 0.00 0.00 44.79 2.52
3164 3417 0.250901 GGGTCAAGCTTCAGGCAGAA 60.251 55.000 0.00 0.00 44.79 3.02
3165 3418 1.376466 GGGTCAAGCTTCAGGCAGA 59.624 57.895 0.00 0.00 44.79 4.26
3166 3419 0.538057 TTGGGTCAAGCTTCAGGCAG 60.538 55.000 0.00 0.00 44.79 4.85
3167 3420 0.106268 TTTGGGTCAAGCTTCAGGCA 60.106 50.000 0.00 0.00 44.79 4.75
3168 3421 1.000171 CTTTTGGGTCAAGCTTCAGGC 60.000 52.381 0.00 0.00 42.19 4.85
3169 3422 1.000171 GCTTTTGGGTCAAGCTTCAGG 60.000 52.381 0.00 0.00 42.95 3.86
3170 3423 1.000171 GGCTTTTGGGTCAAGCTTCAG 60.000 52.381 0.00 0.00 45.18 3.02
3171 3424 1.039856 GGCTTTTGGGTCAAGCTTCA 58.960 50.000 0.00 0.00 45.18 3.02
3172 3425 0.318441 GGGCTTTTGGGTCAAGCTTC 59.682 55.000 0.00 0.00 45.18 3.86
3173 3426 1.463553 CGGGCTTTTGGGTCAAGCTT 61.464 55.000 0.00 0.00 45.18 3.74
3174 3427 1.903404 CGGGCTTTTGGGTCAAGCT 60.903 57.895 4.75 0.00 45.18 3.74
3175 3428 1.460273 TTCGGGCTTTTGGGTCAAGC 61.460 55.000 0.00 0.00 45.13 4.01
3176 3429 0.313987 GTTCGGGCTTTTGGGTCAAG 59.686 55.000 0.00 0.00 0.00 3.02
3177 3430 0.395862 TGTTCGGGCTTTTGGGTCAA 60.396 50.000 0.00 0.00 0.00 3.18
3178 3431 0.821711 CTGTTCGGGCTTTTGGGTCA 60.822 55.000 0.00 0.00 0.00 4.02
3179 3432 1.524008 CCTGTTCGGGCTTTTGGGTC 61.524 60.000 0.00 0.00 0.00 4.46
3180 3433 1.530655 CCTGTTCGGGCTTTTGGGT 60.531 57.895 0.00 0.00 0.00 4.51
3181 3434 1.524008 GACCTGTTCGGGCTTTTGGG 61.524 60.000 0.00 0.00 38.04 4.12
3182 3435 0.821711 TGACCTGTTCGGGCTTTTGG 60.822 55.000 0.00 0.00 43.44 3.28
3183 3436 1.247567 ATGACCTGTTCGGGCTTTTG 58.752 50.000 0.00 0.00 43.44 2.44
3184 3437 2.871096 TATGACCTGTTCGGGCTTTT 57.129 45.000 0.00 0.00 43.44 2.27
3185 3438 2.871096 TTATGACCTGTTCGGGCTTT 57.129 45.000 0.00 0.00 43.44 3.51
3186 3439 2.871096 TTTATGACCTGTTCGGGCTT 57.129 45.000 0.00 0.00 43.44 4.35
3187 3440 2.238646 TGATTTATGACCTGTTCGGGCT 59.761 45.455 0.00 0.00 43.44 5.19
3188 3441 2.354821 GTGATTTATGACCTGTTCGGGC 59.645 50.000 0.00 0.00 43.30 6.13
3189 3442 2.943033 GGTGATTTATGACCTGTTCGGG 59.057 50.000 0.00 0.00 36.97 5.14
3190 3443 3.605634 TGGTGATTTATGACCTGTTCGG 58.394 45.455 0.18 0.00 34.92 4.30
3191 3444 5.818136 AATGGTGATTTATGACCTGTTCG 57.182 39.130 0.18 0.00 34.92 3.95
3307 3561 2.039462 AAATCCCAAGCCCAGCCC 59.961 61.111 0.00 0.00 0.00 5.19
3333 3587 3.615709 GGCCGGGCTTTGCAAAGT 61.616 61.111 33.47 0.00 38.28 2.66
3356 3610 2.303175 ACCGCAAAGCCTTTCAAGTAA 58.697 42.857 0.00 0.00 0.00 2.24
3357 3611 1.975660 ACCGCAAAGCCTTTCAAGTA 58.024 45.000 0.00 0.00 0.00 2.24
3358 3612 1.111277 AACCGCAAAGCCTTTCAAGT 58.889 45.000 0.00 0.00 0.00 3.16
3359 3613 1.490621 CAACCGCAAAGCCTTTCAAG 58.509 50.000 0.00 0.00 0.00 3.02
3360 3614 0.103937 CCAACCGCAAAGCCTTTCAA 59.896 50.000 0.00 0.00 0.00 2.69
3361 3615 0.753479 TCCAACCGCAAAGCCTTTCA 60.753 50.000 0.00 0.00 0.00 2.69
3362 3616 0.387565 TTCCAACCGCAAAGCCTTTC 59.612 50.000 0.00 0.00 0.00 2.62
3363 3617 0.389025 CTTCCAACCGCAAAGCCTTT 59.611 50.000 0.00 0.00 0.00 3.11
3364 3618 0.755327 ACTTCCAACCGCAAAGCCTT 60.755 50.000 0.00 0.00 0.00 4.35
3365 3619 0.109723 TACTTCCAACCGCAAAGCCT 59.890 50.000 0.00 0.00 0.00 4.58
3366 3620 1.173913 ATACTTCCAACCGCAAAGCC 58.826 50.000 0.00 0.00 0.00 4.35
3367 3621 3.007635 ACTATACTTCCAACCGCAAAGC 58.992 45.455 0.00 0.00 0.00 3.51
3368 3622 4.504858 AGACTATACTTCCAACCGCAAAG 58.495 43.478 0.00 0.00 0.00 2.77
3369 3623 4.546829 AGACTATACTTCCAACCGCAAA 57.453 40.909 0.00 0.00 0.00 3.68
3370 3624 4.250464 CAAGACTATACTTCCAACCGCAA 58.750 43.478 0.00 0.00 0.00 4.85
3371 3625 3.369052 CCAAGACTATACTTCCAACCGCA 60.369 47.826 0.00 0.00 0.00 5.69
3372 3626 3.195661 CCAAGACTATACTTCCAACCGC 58.804 50.000 0.00 0.00 0.00 5.68
3373 3627 3.195661 GCCAAGACTATACTTCCAACCG 58.804 50.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.