Multiple sequence alignment - TraesCS1A01G288200

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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 TraesCS1A01G288200 chr1A 100.000 5330 0 0 1 5330 485339616 485344945 0.000000e+00 9843
1 TraesCS1A01G288200 chr1B 92.743 3266 163 22 1 3231 517903674 517906900 0.000000e+00 4650
2 TraesCS1A01G288200 chr1B 92.342 888 38 11 3334 4219 517906898 517907757 0.000000e+00 1236
3 TraesCS1A01G288200 chr1B 89.587 605 35 11 4340 4920 517907986 517908586 0.000000e+00 743
4 TraesCS1A01G288200 chr1B 89.764 254 16 3 5084 5330 517908588 517908838 3.100000e-82 316
5 TraesCS1A01G288200 chr1B 97.581 124 3 0 4213 4336 517907801 517907924 4.180000e-51 213
6 TraesCS1A01G288200 chr1D 91.533 3307 141 51 1 3231 385617360 385620603 0.000000e+00 4427
7 TraesCS1A01G288200 chr1D 95.847 891 19 8 3334 4217 385620601 385621480 0.000000e+00 1424
8 TraesCS1A01G288200 chr1D 88.977 1134 55 17 4213 5282 385621527 385622654 0.000000e+00 1338
9 TraesCS1A01G288200 chr2D 95.868 121 3 2 3218 3336 68867347 68867467 1.510000e-45 195
10 TraesCS1A01G288200 chr2D 95.726 117 5 0 3223 3339 65564833 65564717 7.050000e-44 189
11 TraesCS1A01G288200 chr3D 96.552 116 3 1 3222 3336 419583118 419583003 1.960000e-44 191
12 TraesCS1A01G288200 chr3A 96.522 115 4 0 3222 3336 585501077 585500963 1.960000e-44 191
13 TraesCS1A01G288200 chr3A 94.958 119 6 0 3218 3336 583676579 583676697 2.530000e-43 187
14 TraesCS1A01G288200 chr7D 95.726 117 3 2 3221 3336 568753358 568753473 2.530000e-43 187
15 TraesCS1A01G288200 chr2B 95.690 116 5 0 3230 3345 5665454 5665569 2.530000e-43 187
16 TraesCS1A01G288200 chr3B 92.913 127 7 2 3212 3336 627610750 627610624 3.280000e-42 183
17 TraesCS1A01G288200 chr4D 91.603 131 10 1 3210 3340 491951660 491951531 4.240000e-41 180


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 TraesCS1A01G288200 chr1A 485339616 485344945 5329 False 9843.000000 9843 100.0000 1 5330 1 chr1A.!!$F1 5329
1 TraesCS1A01G288200 chr1B 517903674 517908838 5164 False 1431.600000 4650 92.4034 1 5330 5 chr1B.!!$F1 5329
2 TraesCS1A01G288200 chr1D 385617360 385622654 5294 False 2396.333333 4427 92.1190 1 5282 3 chr1D.!!$F1 5281

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
648 712 0.240145 CGCCTTCTATGCCGTCGATA 59.760 55.0 0.00 0.00 0.0 2.92 F
1442 1509 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.0 0.00 0.00 0.0 3.71 F
1588 1655 0.319211 TCTACTGCGTGTTGGTTCCG 60.319 55.0 0.00 0.00 0.0 4.30 F
3245 3321 0.251297 TTGTACTCCCTCCGTTCGGA 60.251 55.0 13.34 13.34 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 1530 0.304705 GTCGGCGGCAATATTCTGTG 59.695 55.000 6.63 0.0 0.0 3.66 R
2889 2959 0.802494 GTGCAGTGGGGTTTACATCG 59.198 55.000 0.00 0.0 0.0 3.84 R
3307 3383 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.0 0.0 5.19 R
4586 4827 0.108567 GGGCGAGAGAGTGAGGTTTC 60.109 60.000 0.00 0.0 0.0 2.78 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
84 88 2.738521 GAGCGCTGCGACTTGGAA 60.739 61.111 28.07 0.00 0.00 3.53
85 89 3.016474 GAGCGCTGCGACTTGGAAC 62.016 63.158 28.07 4.97 0.00 3.62
93 97 0.893727 GCGACTTGGAACCCACCATT 60.894 55.000 0.00 0.00 39.82 3.16
97 101 2.296190 GACTTGGAACCCACCATTGTTC 59.704 50.000 0.00 0.00 39.82 3.18
117 121 4.099170 CTCGCTCGTCGTTCCGGT 62.099 66.667 0.00 0.00 39.67 5.28
275 300 1.884926 GCCGGCTTCTTGGATCGAG 60.885 63.158 22.15 0.00 0.00 4.04
338 363 3.165058 TCGATGAAGACGGGAGAATTG 57.835 47.619 0.00 0.00 0.00 2.32
405 449 2.818132 GACGGGCTCAGGATCCTG 59.182 66.667 32.60 32.60 44.86 3.86
450 495 2.204448 TTCCCCATTGCCCCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
454 499 4.431131 CCATTGCCCCCTCTGCGT 62.431 66.667 0.00 0.00 0.00 5.24
468 513 2.089201 TCTGCGTTCTTCACCTATCGA 58.911 47.619 0.00 0.00 0.00 3.59
480 526 5.444663 TCACCTATCGATGAGATGACAAG 57.555 43.478 8.54 0.00 40.40 3.16
534 580 2.987413 TGATGTTTACGGCAGCAAAG 57.013 45.000 0.00 0.00 28.71 2.77
544 590 1.030457 GGCAGCAAAGCTAGCATCAT 58.970 50.000 18.83 0.00 36.40 2.45
545 591 1.407979 GGCAGCAAAGCTAGCATCATT 59.592 47.619 18.83 3.36 36.40 2.57
546 592 2.543238 GGCAGCAAAGCTAGCATCATTC 60.543 50.000 18.83 0.56 36.40 2.67
547 593 2.543238 GCAGCAAAGCTAGCATCATTCC 60.543 50.000 18.83 0.00 36.40 3.01
548 594 2.686405 CAGCAAAGCTAGCATCATTCCA 59.314 45.455 18.83 0.00 36.40 3.53
552 598 4.037684 GCAAAGCTAGCATCATTCCAATCT 59.962 41.667 18.83 0.00 0.00 2.40
568 618 4.080413 TCCAATCTACATTGCCACAGATCA 60.080 41.667 0.00 0.00 38.53 2.92
585 635 7.121272 CACAGATCAAGCAAAACAAAAATGTC 58.879 34.615 0.00 0.00 0.00 3.06
591 641 6.203530 TCAAGCAAAACAAAAATGTCAACACA 59.796 30.769 0.00 0.00 36.78 3.72
597 647 8.494347 CAAAACAAAAATGTCAACACAAGAGAA 58.506 29.630 0.00 0.00 35.64 2.87
598 648 8.600449 AAACAAAAATGTCAACACAAGAGAAA 57.400 26.923 0.00 0.00 35.64 2.52
599 649 7.816945 ACAAAAATGTCAACACAAGAGAAAG 57.183 32.000 0.00 0.00 35.64 2.62
600 650 7.601856 ACAAAAATGTCAACACAAGAGAAAGA 58.398 30.769 0.00 0.00 35.64 2.52
601 651 7.756722 ACAAAAATGTCAACACAAGAGAAAGAG 59.243 33.333 0.00 0.00 35.64 2.85
602 652 7.630242 AAAATGTCAACACAAGAGAAAGAGA 57.370 32.000 0.00 0.00 35.64 3.10
603 653 7.814264 AAATGTCAACACAAGAGAAAGAGAT 57.186 32.000 0.00 0.00 35.64 2.75
604 654 7.432350 AATGTCAACACAAGAGAAAGAGATC 57.568 36.000 0.00 0.00 35.64 2.75
605 655 5.917462 TGTCAACACAAGAGAAAGAGATCA 58.083 37.500 0.00 0.00 0.00 2.92
648 712 0.240145 CGCCTTCTATGCCGTCGATA 59.760 55.000 0.00 0.00 0.00 2.92
649 713 1.729472 CGCCTTCTATGCCGTCGATAG 60.729 57.143 0.00 0.00 0.00 2.08
821 885 1.574147 CGTGATAAACGCGCACACG 60.574 57.895 21.47 21.47 46.99 4.49
1185 1252 2.379005 GATTGGGGATTTCGAGGCTTT 58.621 47.619 0.00 0.00 0.00 3.51
1186 1253 3.551846 GATTGGGGATTTCGAGGCTTTA 58.448 45.455 0.00 0.00 0.00 1.85
1187 1254 3.443145 TTGGGGATTTCGAGGCTTTAA 57.557 42.857 0.00 0.00 0.00 1.52
1188 1255 3.662759 TGGGGATTTCGAGGCTTTAAT 57.337 42.857 0.00 0.00 0.00 1.40
1193 1260 6.040391 TGGGGATTTCGAGGCTTTAATTAATG 59.960 38.462 0.00 2.78 0.00 1.90
1200 1267 2.757868 AGGCTTTAATTAATGTGCGCCA 59.242 40.909 4.18 2.31 38.71 5.69
1204 1271 4.031652 GCTTTAATTAATGTGCGCCAACTG 59.968 41.667 4.18 0.00 0.00 3.16
1207 1274 1.598882 TTAATGTGCGCCAACTGACA 58.401 45.000 4.18 0.61 0.00 3.58
1239 1306 4.383118 CCAATTCCACAGATTCGAGTAGGT 60.383 45.833 0.00 0.00 0.00 3.08
1297 1364 4.348495 GGGTGGAGGGAGGGGTGA 62.348 72.222 0.00 0.00 0.00 4.02
1389 1456 1.019278 TCGGCGAGGCAGATTTTGAC 61.019 55.000 4.99 0.00 33.75 3.18
1431 1498 3.393970 TTGCAGGGCGAGGAGGAG 61.394 66.667 0.00 0.00 0.00 3.69
1442 1509 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1463 1530 1.227002 GTAGTAGCCTGGCGCAGAC 60.227 63.158 13.96 10.20 41.38 3.51
1514 1581 0.755698 TCTGATCCTGCCGTACCTCC 60.756 60.000 0.00 0.00 0.00 4.30
1518 1585 1.614241 ATCCTGCCGTACCTCCACAC 61.614 60.000 0.00 0.00 0.00 3.82
1577 1644 3.119291 CTGGTTAGCTTGATCTACTGCG 58.881 50.000 0.00 0.00 0.00 5.18
1588 1655 0.319211 TCTACTGCGTGTTGGTTCCG 60.319 55.000 0.00 0.00 0.00 4.30
1596 1663 3.733960 GTTGGTTCCGCGCCCTTC 61.734 66.667 0.00 0.00 0.00 3.46
1597 1664 4.257654 TTGGTTCCGCGCCCTTCA 62.258 61.111 0.00 0.00 0.00 3.02
1614 1681 4.383118 CCCTTCATCCTTCGACTTGTATGT 60.383 45.833 0.00 0.00 0.00 2.29
1621 1688 4.462834 TCCTTCGACTTGTATGTCATCACT 59.537 41.667 0.00 0.00 36.82 3.41
1649 1716 4.572985 TCAGTTTTTGTGATCTTGCAGG 57.427 40.909 0.00 0.00 0.00 4.85
1773 1840 0.320683 GGTGGCCTGGTGCAATTTTC 60.321 55.000 3.32 0.00 43.89 2.29
1782 1849 2.161410 TGGTGCAATTTTCGATCCTTCG 59.839 45.455 0.00 0.00 46.87 3.79
1868 1935 1.166531 GGCTCTTTTGCGTGGTGTCT 61.167 55.000 0.00 0.00 0.00 3.41
1943 2010 2.231964 GCAATTCTGATGCCTTCACCAA 59.768 45.455 0.00 0.00 37.85 3.67
1955 2022 4.769488 TGCCTTCACCAATGCAGTTAATTA 59.231 37.500 0.00 0.00 30.47 1.40
2077 2144 1.676967 GGGCTCAAGGCTGGAGTTG 60.677 63.158 19.88 0.00 41.46 3.16
2093 2160 3.935828 GGAGTTGCTTGCTCTAAGGTTAG 59.064 47.826 0.00 0.00 36.87 2.34
2304 2371 3.055819 AGGATAGCATCGACACAACTGTT 60.056 43.478 0.00 0.00 0.00 3.16
2389 2459 3.181486 GCCTGACGATGACATAGAGTTGA 60.181 47.826 2.24 0.00 0.00 3.18
2490 2560 2.266554 GACATCTCTGTGAAGAAGCCG 58.733 52.381 0.00 0.00 35.14 5.52
2499 2569 1.336755 GTGAAGAAGCCGGCAAAAAGA 59.663 47.619 31.54 4.97 0.00 2.52
2628 2698 3.732212 AGAGTGGAAATTTTTGCCTTGC 58.268 40.909 0.00 0.00 0.00 4.01
2753 2823 1.306148 CCGATACGTAGGCAGAGACA 58.694 55.000 0.08 0.00 0.00 3.41
2763 2833 2.861006 CAGAGACAGACGCGACGA 59.139 61.111 15.93 0.00 0.00 4.20
2786 2856 2.014335 TGTGCACCTTCATCAGATCG 57.986 50.000 15.69 0.00 0.00 3.69
2800 2870 3.643237 TCAGATCGTTCTTCCCCTGTAT 58.357 45.455 0.00 0.00 0.00 2.29
2801 2871 3.384789 TCAGATCGTTCTTCCCCTGTATG 59.615 47.826 0.00 0.00 0.00 2.39
2802 2872 3.133003 CAGATCGTTCTTCCCCTGTATGT 59.867 47.826 0.00 0.00 0.00 2.29
2803 2873 3.133003 AGATCGTTCTTCCCCTGTATGTG 59.867 47.826 0.00 0.00 0.00 3.21
2825 2895 1.526575 ATGCAGCCTGAAACGTTGGG 61.527 55.000 0.00 6.20 0.00 4.12
2839 2909 2.946990 ACGTTGGGTGTTAACAGAAAGG 59.053 45.455 8.98 11.29 0.00 3.11
2889 2959 2.338500 GTTGACGAGAAGATGGTCCAC 58.662 52.381 0.00 0.00 35.89 4.02
2892 2962 1.405821 GACGAGAAGATGGTCCACGAT 59.594 52.381 0.00 0.00 30.85 3.73
3171 3241 6.927294 AGAACGACTGAATTGAATTATCCC 57.073 37.500 0.00 0.00 0.00 3.85
3197 3273 4.972875 CCCTGAAGGCATGGAGAC 57.027 61.111 0.00 0.00 32.08 3.36
3205 3281 1.222936 GGCATGGAGACTCCTGGTG 59.777 63.158 22.14 17.50 37.46 4.17
3210 3286 2.030027 TGGAGACTCCTGGTGAACAT 57.970 50.000 22.14 0.00 37.46 2.71
3236 3312 9.862149 TTTCTTTCTCTTAAATTTGTACTCCCT 57.138 29.630 0.00 0.00 0.00 4.20
3237 3313 9.503399 TTCTTTCTCTTAAATTTGTACTCCCTC 57.497 33.333 0.00 0.00 0.00 4.30
3238 3314 8.101419 TCTTTCTCTTAAATTTGTACTCCCTCC 58.899 37.037 0.00 0.00 0.00 4.30
3239 3315 5.974108 TCTCTTAAATTTGTACTCCCTCCG 58.026 41.667 0.00 0.00 0.00 4.63
3240 3316 5.482878 TCTCTTAAATTTGTACTCCCTCCGT 59.517 40.000 0.00 0.00 0.00 4.69
3241 3317 6.013984 TCTCTTAAATTTGTACTCCCTCCGTT 60.014 38.462 0.00 0.00 0.00 4.44
3242 3318 6.168389 TCTTAAATTTGTACTCCCTCCGTTC 58.832 40.000 0.00 0.00 0.00 3.95
3243 3319 2.667473 ATTTGTACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
3244 3320 0.604578 TTTGTACTCCCTCCGTTCGG 59.395 55.000 4.74 4.74 0.00 4.30
3245 3321 0.251297 TTGTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55
3246 3322 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
3247 3323 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3248 3324 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
3249 3325 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3250 3326 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3251 3327 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3252 3328 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3253 3329 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3254 3330 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3255 3331 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3256 3332 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3257 3333 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
3258 3334 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3259 3335 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
3260 3336 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
3261 3337 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
3262 3338 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
3263 3339 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
3264 3340 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
3265 3341 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
3266 3342 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
3267 3343 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
3268 3344 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
3269 3345 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
3270 3346 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
3271 3347 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
3272 3348 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
3273 3349 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
3274 3350 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
3275 3351 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
3276 3352 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
3277 3353 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
3278 3354 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
3279 3355 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
3280 3356 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
3281 3357 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
3282 3358 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
3283 3359 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
3308 3384 8.749841 ATACGTCTAGATACATTCATTTCTGC 57.250 34.615 0.00 0.00 0.00 4.26
3309 3385 5.687730 ACGTCTAGATACATTCATTTCTGCG 59.312 40.000 0.00 0.00 0.00 5.18
3310 3386 5.915196 CGTCTAGATACATTCATTTCTGCGA 59.085 40.000 0.00 0.00 0.00 5.10
3311 3387 6.129326 CGTCTAGATACATTCATTTCTGCGAC 60.129 42.308 0.00 0.00 0.00 5.19
3312 3388 6.697455 GTCTAGATACATTCATTTCTGCGACA 59.303 38.462 0.00 0.00 0.00 4.35
3313 3389 7.222805 GTCTAGATACATTCATTTCTGCGACAA 59.777 37.037 0.00 0.00 0.00 3.18
3314 3390 6.355397 AGATACATTCATTTCTGCGACAAG 57.645 37.500 0.00 0.00 0.00 3.16
3315 3391 5.877012 AGATACATTCATTTCTGCGACAAGT 59.123 36.000 0.00 0.00 0.00 3.16
3316 3392 7.041721 AGATACATTCATTTCTGCGACAAGTA 58.958 34.615 0.00 0.00 0.00 2.24
3317 3393 5.940192 ACATTCATTTCTGCGACAAGTAA 57.060 34.783 0.00 0.00 0.00 2.24
3318 3394 6.500684 ACATTCATTTCTGCGACAAGTAAT 57.499 33.333 0.00 0.00 0.00 1.89
3319 3395 6.913170 ACATTCATTTCTGCGACAAGTAATT 58.087 32.000 0.00 0.00 0.00 1.40
3320 3396 7.023575 ACATTCATTTCTGCGACAAGTAATTC 58.976 34.615 0.00 0.00 0.00 2.17
3321 3397 5.545658 TCATTTCTGCGACAAGTAATTCC 57.454 39.130 0.00 0.00 0.00 3.01
3322 3398 4.092821 TCATTTCTGCGACAAGTAATTCCG 59.907 41.667 0.00 0.00 0.00 4.30
3323 3399 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
3324 3400 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
3325 3401 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
3326 3402 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3327 3403 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3328 3404 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3392 3468 7.875327 ACAGTACCTTTTGTATGTGTTTTCT 57.125 32.000 0.00 0.00 29.66 2.52
3393 3469 8.288689 ACAGTACCTTTTGTATGTGTTTTCTT 57.711 30.769 0.00 0.00 29.66 2.52
3394 3470 9.398538 ACAGTACCTTTTGTATGTGTTTTCTTA 57.601 29.630 0.00 0.00 29.66 2.10
3435 3514 1.527034 GAGTTGCACTGGATTCTGCA 58.473 50.000 0.00 0.00 41.68 4.41
3629 3708 3.846588 ACTGGAATTGTAGATGACACCCT 59.153 43.478 0.00 0.00 37.96 4.34
3706 3785 6.479972 TGGAAGTTGATAATACGGATGAGT 57.520 37.500 0.00 0.00 0.00 3.41
3717 3796 2.712709 ACGGATGAGTCTCGAGAAGAA 58.287 47.619 18.55 5.64 35.21 2.52
3720 3799 3.127895 CGGATGAGTCTCGAGAAGAAACT 59.872 47.826 18.55 10.27 35.21 2.66
3730 3809 3.699538 TCGAGAAGAAACTAGCATGCCTA 59.300 43.478 15.66 5.40 0.00 3.93
3731 3810 4.159693 TCGAGAAGAAACTAGCATGCCTAA 59.840 41.667 15.66 0.00 0.00 2.69
3917 3997 2.639327 GCAGCCAAACCAGCGGATT 61.639 57.895 1.50 0.00 34.64 3.01
3918 3998 1.312371 GCAGCCAAACCAGCGGATTA 61.312 55.000 1.50 0.00 34.64 1.75
3953 4033 1.079543 CTGACAAGACTCTGGGCGG 60.080 63.158 0.00 0.00 0.00 6.13
3983 4064 3.638160 ACTGTTGCATTTGATGGACAAGT 59.362 39.130 0.00 0.00 39.77 3.16
3984 4065 3.979948 TGTTGCATTTGATGGACAAGTG 58.020 40.909 0.00 0.00 45.05 3.16
3986 4067 1.894466 TGCATTTGATGGACAAGTGGG 59.106 47.619 0.00 0.00 43.35 4.61
3987 4068 1.895131 GCATTTGATGGACAAGTGGGT 59.105 47.619 0.00 0.00 43.35 4.51
4082 4163 6.903419 TGTATGATGCGTTCTGTATAGAGAG 58.097 40.000 0.00 0.00 33.70 3.20
4323 4506 3.063510 TGAATTTCTGCCTGGTGAGAG 57.936 47.619 0.00 0.00 0.00 3.20
4336 4519 5.163301 GCCTGGTGAGAGAATAGGAAATACA 60.163 44.000 0.00 0.00 0.00 2.29
4337 4520 6.632672 GCCTGGTGAGAGAATAGGAAATACAA 60.633 42.308 0.00 0.00 0.00 2.41
4338 4521 7.512992 CCTGGTGAGAGAATAGGAAATACAAT 58.487 38.462 0.00 0.00 0.00 2.71
4339 4522 8.651389 CCTGGTGAGAGAATAGGAAATACAATA 58.349 37.037 0.00 0.00 0.00 1.90
4395 4636 3.935203 AGGTATGAGTTGCATCTCAAACG 59.065 43.478 26.73 0.00 45.65 3.60
4406 4647 0.596577 TCTCAAACGGAGTGGACTCG 59.403 55.000 0.74 0.00 45.00 4.18
4408 4649 0.824595 TCAAACGGAGTGGACTCGGA 60.825 55.000 18.24 1.81 45.00 4.55
4409 4650 0.032952 CAAACGGAGTGGACTCGGAA 59.967 55.000 18.24 0.00 45.00 4.30
4446 4687 9.034800 TCTATTCTAAATTCTTTGGGTGCAATT 57.965 29.630 0.00 0.00 0.00 2.32
4454 4695 1.337118 TTGGGTGCAATTGTTCCTCC 58.663 50.000 7.40 1.02 0.00 4.30
4530 4771 5.168647 TGTTTTTAGGCGGGAAGAGATTA 57.831 39.130 0.00 0.00 0.00 1.75
4532 4773 5.646360 TGTTTTTAGGCGGGAAGAGATTAAG 59.354 40.000 0.00 0.00 0.00 1.85
4534 4775 2.176247 AGGCGGGAAGAGATTAAGGA 57.824 50.000 0.00 0.00 0.00 3.36
5059 5335 2.393768 CCAGCGATGTGGACACTGC 61.394 63.158 0.00 5.57 40.44 4.40
5070 5346 3.202906 GTGGACACTGCTCAAGTTGTAA 58.797 45.455 2.11 0.00 36.83 2.41
5156 5432 3.753434 CGCGGTGCTCCTCTCTGT 61.753 66.667 0.00 0.00 0.00 3.41
5169 5445 5.243730 GCTCCTCTCTGTAGAATGCTTCTAT 59.756 44.000 8.31 0.00 43.59 1.98
5214 5490 4.456535 TCCAGAAGGACAAAAACGATCAA 58.543 39.130 0.00 0.00 39.61 2.57
5215 5491 4.884744 TCCAGAAGGACAAAAACGATCAAA 59.115 37.500 0.00 0.00 39.61 2.69
5247 5530 0.742635 GGAAGCTACACTCAGGCAGC 60.743 60.000 0.00 0.00 0.00 5.25
5248 5531 0.742635 GAAGCTACACTCAGGCAGCC 60.743 60.000 1.84 1.84 34.49 4.85
5249 5532 1.197430 AAGCTACACTCAGGCAGCCT 61.197 55.000 8.70 8.70 34.49 4.58
5257 5540 0.179078 CTCAGGCAGCCTCATCTGAC 60.179 60.000 12.53 0.00 42.42 3.51
5312 5595 2.508526 ACAAACCAGCATCTGAAGGTC 58.491 47.619 0.00 0.00 32.44 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 88 0.606401 CGAGCAGAACAATGGTGGGT 60.606 55.000 0.00 0.00 0.00 4.51
85 89 1.926511 GCGAGCAGAACAATGGTGGG 61.927 60.000 0.00 0.00 0.00 4.61
93 97 2.126850 CGACGAGCGAGCAGAACA 60.127 61.111 0.00 0.00 44.57 3.18
97 101 2.876645 GGAACGACGAGCGAGCAG 60.877 66.667 0.00 0.00 44.57 4.24
117 121 2.045045 CTGCGGAGGCCAAATCCA 60.045 61.111 5.01 0.00 38.85 3.41
241 266 4.539881 GCCGAGAGACCGACGAGC 62.540 72.222 0.00 0.00 0.00 5.03
286 311 0.040958 GCAAATGACCGATCCGCATC 60.041 55.000 0.00 0.00 0.00 3.91
287 312 1.775039 CGCAAATGACCGATCCGCAT 61.775 55.000 0.00 0.00 0.00 4.73
288 313 2.460275 CGCAAATGACCGATCCGCA 61.460 57.895 0.00 0.00 0.00 5.69
417 461 1.271434 GGGAAGAAGGTGAGGTGGTTC 60.271 57.143 0.00 0.00 0.00 3.62
468 513 7.165460 TGATTTTTGCATCTTGTCATCTCAT 57.835 32.000 0.00 0.00 0.00 2.90
480 526 7.359765 CCACTTGTTCTTGATGATTTTTGCATC 60.360 37.037 0.00 0.00 41.87 3.91
534 580 6.609533 CAATGTAGATTGGAATGATGCTAGC 58.390 40.000 8.10 8.10 36.12 3.42
544 590 4.299586 TCTGTGGCAATGTAGATTGGAA 57.700 40.909 13.92 0.00 39.62 3.53
545 591 3.998913 TCTGTGGCAATGTAGATTGGA 57.001 42.857 13.92 0.31 39.62 3.53
546 592 4.201657 TGATCTGTGGCAATGTAGATTGG 58.798 43.478 13.92 0.00 39.62 3.16
547 593 5.732528 GCTTGATCTGTGGCAATGTAGATTG 60.733 44.000 8.21 8.21 41.82 2.67
548 594 4.337555 GCTTGATCTGTGGCAATGTAGATT 59.662 41.667 0.00 0.00 30.49 2.40
552 598 3.070476 TGCTTGATCTGTGGCAATGTA 57.930 42.857 0.00 0.00 0.00 2.29
568 618 6.551385 TGTGTTGACATTTTTGTTTTGCTT 57.449 29.167 0.00 0.00 0.00 3.91
585 635 5.303971 AGGTGATCTCTTTCTCTTGTGTTG 58.696 41.667 0.00 0.00 0.00 3.33
591 641 6.269769 ACAGAAGAAGGTGATCTCTTTCTCTT 59.730 38.462 18.84 7.77 30.52 2.85
597 647 5.779771 AGAAGACAGAAGAAGGTGATCTCTT 59.220 40.000 0.00 0.00 0.00 2.85
598 648 5.185635 CAGAAGACAGAAGAAGGTGATCTCT 59.814 44.000 0.00 0.00 0.00 3.10
599 649 5.410067 CAGAAGACAGAAGAAGGTGATCTC 58.590 45.833 0.00 0.00 0.00 2.75
600 650 4.322650 GCAGAAGACAGAAGAAGGTGATCT 60.323 45.833 0.00 0.00 0.00 2.75
601 651 3.932089 GCAGAAGACAGAAGAAGGTGATC 59.068 47.826 0.00 0.00 0.00 2.92
602 652 3.307339 GGCAGAAGACAGAAGAAGGTGAT 60.307 47.826 0.00 0.00 0.00 3.06
603 653 2.037772 GGCAGAAGACAGAAGAAGGTGA 59.962 50.000 0.00 0.00 0.00 4.02
604 654 2.421619 GGCAGAAGACAGAAGAAGGTG 58.578 52.381 0.00 0.00 0.00 4.00
605 655 1.001406 CGGCAGAAGACAGAAGAAGGT 59.999 52.381 0.00 0.00 0.00 3.50
633 697 0.386858 GCGCTATCGACGGCATAGAA 60.387 55.000 0.00 0.00 38.10 2.10
832 896 2.102420 GTGGGCTGGTTTTGCTTAACTT 59.898 45.455 2.38 0.00 0.00 2.66
838 902 1.454847 TTCGTGGGCTGGTTTTGCT 60.455 52.632 0.00 0.00 0.00 3.91
1121 1187 2.893398 CGAGGTACCTCAGGCACC 59.107 66.667 35.32 4.65 42.86 5.01
1185 1252 3.753797 TGTCAGTTGGCGCACATTAATTA 59.246 39.130 10.83 0.00 0.00 1.40
1186 1253 2.556189 TGTCAGTTGGCGCACATTAATT 59.444 40.909 10.83 0.00 0.00 1.40
1187 1254 2.158559 TGTCAGTTGGCGCACATTAAT 58.841 42.857 10.83 0.00 0.00 1.40
1188 1255 1.598882 TGTCAGTTGGCGCACATTAA 58.401 45.000 10.83 0.00 0.00 1.40
1193 1260 1.639298 GGAGATGTCAGTTGGCGCAC 61.639 60.000 10.83 0.00 0.00 5.34
1200 1267 1.488705 TTGGGGCGGAGATGTCAGTT 61.489 55.000 0.00 0.00 0.00 3.16
1204 1271 0.819666 GGAATTGGGGCGGAGATGTC 60.820 60.000 0.00 0.00 0.00 3.06
1207 1274 1.227383 GTGGAATTGGGGCGGAGAT 59.773 57.895 0.00 0.00 0.00 2.75
1400 1467 1.303236 TGCAACCCACCAGATTCCG 60.303 57.895 0.00 0.00 0.00 4.30
1423 1490 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1424 1491 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1425 1492 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1426 1493 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1431 1498 1.426215 CTACTACCCTCCTCCTCCTCC 59.574 61.905 0.00 0.00 0.00 4.30
1442 1509 3.155167 GCGCCAGGCTACTACCCT 61.155 66.667 10.54 0.00 39.11 4.34
1463 1530 0.304705 GTCGGCGGCAATATTCTGTG 59.695 55.000 6.63 0.00 0.00 3.66
1514 1581 2.743752 CCGGCTTCAGCATCGTGTG 61.744 63.158 0.30 0.00 44.36 3.82
1518 1585 1.766143 GCTTACCGGCTTCAGCATCG 61.766 60.000 0.00 0.00 44.36 3.84
1564 1631 2.688507 ACCAACACGCAGTAGATCAAG 58.311 47.619 0.00 0.00 41.61 3.02
1588 1655 2.174319 GTCGAAGGATGAAGGGCGC 61.174 63.158 0.00 0.00 0.00 6.53
1590 1657 1.339151 ACAAGTCGAAGGATGAAGGGC 60.339 52.381 0.00 0.00 0.00 5.19
1596 1663 5.233050 GTGATGACATACAAGTCGAAGGATG 59.767 44.000 4.84 4.84 41.41 3.51
1597 1664 5.127845 AGTGATGACATACAAGTCGAAGGAT 59.872 40.000 0.00 0.00 41.41 3.24
1621 1688 7.013178 TGCAAGATCACAAAAACTGATTAGTCA 59.987 33.333 0.00 0.00 35.69 3.41
1630 1697 4.083110 CGATCCTGCAAGATCACAAAAACT 60.083 41.667 22.09 0.00 42.40 2.66
1639 1706 2.209838 TCGTTCGATCCTGCAAGATC 57.790 50.000 14.31 14.31 39.47 2.75
1649 1716 1.855360 GCTGACCATCTTCGTTCGATC 59.145 52.381 0.00 0.00 0.00 3.69
1782 1849 0.537600 ATGCCAGCTCAGATGCATCC 60.538 55.000 23.06 7.80 40.21 3.51
1845 1912 2.250939 CCACGCAAAAGAGCCGTCA 61.251 57.895 0.00 0.00 0.00 4.35
1851 1918 0.588252 CCAGACACCACGCAAAAGAG 59.412 55.000 0.00 0.00 0.00 2.85
1868 1935 1.075601 AGGCTTCAACTGGGATTCCA 58.924 50.000 4.80 0.00 41.58 3.53
1943 2010 4.898829 TGAAGCGCATAATTAACTGCAT 57.101 36.364 11.47 0.00 38.30 3.96
1955 2022 2.462456 TGAGAGTTCTTGAAGCGCAT 57.538 45.000 11.47 0.00 0.00 4.73
2077 2144 2.284190 CTGGCTAACCTTAGAGCAAGC 58.716 52.381 0.00 0.00 40.64 4.01
2093 2160 1.683943 TTGCAATATCTCAGCCTGGC 58.316 50.000 11.65 11.65 0.00 4.85
2287 2354 2.224185 TGGTAACAGTTGTGTCGATGCT 60.224 45.455 0.00 0.00 46.17 3.79
2304 2371 2.571653 ACTAGGCTGCACTTCATTGGTA 59.428 45.455 0.50 0.00 0.00 3.25
2377 2447 4.142049 CCTTCCCTCTGTCAACTCTATGTC 60.142 50.000 0.00 0.00 0.00 3.06
2490 2560 1.215014 GCACACGCCTTCTTTTTGCC 61.215 55.000 0.00 0.00 0.00 4.52
2628 2698 3.072211 GTCCGTTGTTTCTTCCTTAGGG 58.928 50.000 0.00 0.00 0.00 3.53
2747 2817 1.207085 GTTCGTCGCGTCTGTCTCT 59.793 57.895 5.77 0.00 0.00 3.10
2753 2823 2.372690 GCACATGTTCGTCGCGTCT 61.373 57.895 5.77 0.00 0.00 4.18
2763 2833 3.144657 TCTGATGAAGGTGCACATGTT 57.855 42.857 20.43 8.65 0.00 2.71
2786 2856 4.757149 GCATATCACATACAGGGGAAGAAC 59.243 45.833 0.00 0.00 0.00 3.01
2800 2870 2.009051 CGTTTCAGGCTGCATATCACA 58.991 47.619 10.34 0.00 0.00 3.58
2801 2871 2.009774 ACGTTTCAGGCTGCATATCAC 58.990 47.619 10.34 0.00 0.00 3.06
2802 2872 2.401583 ACGTTTCAGGCTGCATATCA 57.598 45.000 10.34 0.00 0.00 2.15
2803 2873 2.223340 CCAACGTTTCAGGCTGCATATC 60.223 50.000 10.34 0.00 0.00 1.63
2825 2895 7.964604 ATCACTTCTACCTTTCTGTTAACAC 57.035 36.000 3.59 0.00 0.00 3.32
2889 2959 0.802494 GTGCAGTGGGGTTTACATCG 59.198 55.000 0.00 0.00 0.00 3.84
2892 2962 1.064314 ACAAGTGCAGTGGGGTTTACA 60.064 47.619 0.00 0.00 0.00 2.41
3197 3273 5.312079 AGAGAAAGAAATGTTCACCAGGAG 58.688 41.667 0.00 0.00 0.00 3.69
3210 3286 9.862149 AGGGAGTACAAATTTAAGAGAAAGAAA 57.138 29.630 0.00 0.00 0.00 2.52
3231 3307 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3232 3308 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3233 3309 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3234 3310 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3235 3311 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3236 3312 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
3237 3313 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3238 3314 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
3239 3315 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
3240 3316 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
3241 3317 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
3242 3318 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
3243 3319 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
3244 3320 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
3245 3321 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
3246 3322 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
3247 3323 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
3248 3324 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3249 3325 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3250 3326 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
3251 3327 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
3252 3328 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
3253 3329 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
3254 3330 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
3255 3331 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
3256 3332 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
3257 3333 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
3282 3358 9.197694 GCAGAAATGAATGTATCTAGACGTATT 57.802 33.333 0.00 0.00 0.00 1.89
3283 3359 7.539022 CGCAGAAATGAATGTATCTAGACGTAT 59.461 37.037 0.00 0.00 0.00 3.06
3284 3360 6.856426 CGCAGAAATGAATGTATCTAGACGTA 59.144 38.462 0.00 0.00 0.00 3.57
3285 3361 5.687730 CGCAGAAATGAATGTATCTAGACGT 59.312 40.000 0.00 0.00 0.00 4.34
3286 3362 5.915196 TCGCAGAAATGAATGTATCTAGACG 59.085 40.000 0.00 0.00 0.00 4.18
3287 3363 6.697455 TGTCGCAGAAATGAATGTATCTAGAC 59.303 38.462 0.00 0.00 39.69 2.59
3288 3364 6.805713 TGTCGCAGAAATGAATGTATCTAGA 58.194 36.000 0.00 0.00 39.69 2.43
3289 3365 7.223582 ACTTGTCGCAGAAATGAATGTATCTAG 59.776 37.037 0.00 0.00 39.69 2.43
3290 3366 7.041721 ACTTGTCGCAGAAATGAATGTATCTA 58.958 34.615 0.00 0.00 39.69 1.98
3291 3367 5.877012 ACTTGTCGCAGAAATGAATGTATCT 59.123 36.000 0.00 0.00 39.69 1.98
3292 3368 6.111768 ACTTGTCGCAGAAATGAATGTATC 57.888 37.500 0.00 0.00 39.69 2.24
3293 3369 7.609760 TTACTTGTCGCAGAAATGAATGTAT 57.390 32.000 0.00 0.00 39.69 2.29
3294 3370 7.609760 ATTACTTGTCGCAGAAATGAATGTA 57.390 32.000 0.00 0.00 39.69 2.29
3295 3371 5.940192 TTACTTGTCGCAGAAATGAATGT 57.060 34.783 0.00 0.00 39.69 2.71
3296 3372 6.470235 GGAATTACTTGTCGCAGAAATGAATG 59.530 38.462 0.00 0.00 39.69 2.67
3297 3373 6.555315 GGAATTACTTGTCGCAGAAATGAAT 58.445 36.000 0.00 0.00 39.69 2.57
3298 3374 5.390461 CGGAATTACTTGTCGCAGAAATGAA 60.390 40.000 0.00 0.00 39.69 2.57
3299 3375 4.092821 CGGAATTACTTGTCGCAGAAATGA 59.907 41.667 0.00 0.00 39.69 2.57
3300 3376 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3301 3377 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3302 3378 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3303 3379 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3304 3380 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3305 3381 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3306 3382 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3307 3383 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3308 3384 2.598589 TCCGTTCGGAATTACTTGTCG 58.401 47.619 11.66 0.00 0.00 4.35
3309 3385 3.370061 CCTTCCGTTCGGAATTACTTGTC 59.630 47.826 23.69 0.00 42.61 3.18
3310 3386 3.007182 TCCTTCCGTTCGGAATTACTTGT 59.993 43.478 23.69 0.00 42.61 3.16
3311 3387 3.592059 TCCTTCCGTTCGGAATTACTTG 58.408 45.455 23.69 12.71 42.61 3.16
3312 3388 3.260128 ACTCCTTCCGTTCGGAATTACTT 59.740 43.478 23.69 7.92 42.61 2.24
3313 3389 2.830321 ACTCCTTCCGTTCGGAATTACT 59.170 45.455 23.69 7.58 42.61 2.24
3314 3390 3.242549 ACTCCTTCCGTTCGGAATTAC 57.757 47.619 23.69 0.00 42.61 1.89
3315 3391 5.404466 TTTACTCCTTCCGTTCGGAATTA 57.596 39.130 23.69 14.90 42.61 1.40
3316 3392 3.967332 TTACTCCTTCCGTTCGGAATT 57.033 42.857 23.69 12.73 42.61 2.17
3317 3393 3.967332 TTTACTCCTTCCGTTCGGAAT 57.033 42.857 23.69 13.41 42.61 3.01
3318 3394 3.749665 TTTTACTCCTTCCGTTCGGAA 57.250 42.857 22.42 22.42 41.48 4.30
3319 3395 3.368739 GGATTTTACTCCTTCCGTTCGGA 60.369 47.826 10.00 10.00 32.18 4.55
3320 3396 2.934553 GGATTTTACTCCTTCCGTTCGG 59.065 50.000 4.74 4.74 32.18 4.30
3321 3397 3.592059 TGGATTTTACTCCTTCCGTTCG 58.408 45.455 0.00 0.00 36.20 3.95
3322 3398 4.392138 CACTGGATTTTACTCCTTCCGTTC 59.608 45.833 0.00 0.00 36.20 3.95
3323 3399 4.041198 TCACTGGATTTTACTCCTTCCGTT 59.959 41.667 0.00 0.00 36.20 4.44
3324 3400 3.581332 TCACTGGATTTTACTCCTTCCGT 59.419 43.478 0.00 0.00 36.20 4.69
3325 3401 4.184629 CTCACTGGATTTTACTCCTTCCG 58.815 47.826 0.00 0.00 36.20 4.30
3326 3402 3.942115 GCTCACTGGATTTTACTCCTTCC 59.058 47.826 0.00 0.00 36.20 3.46
3327 3403 4.837972 AGCTCACTGGATTTTACTCCTTC 58.162 43.478 0.00 0.00 36.20 3.46
3328 3404 4.917906 AGCTCACTGGATTTTACTCCTT 57.082 40.909 0.00 0.00 36.20 3.36
3329 3405 6.374417 TTTAGCTCACTGGATTTTACTCCT 57.626 37.500 0.00 0.00 36.20 3.69
3330 3406 8.778358 CATATTTAGCTCACTGGATTTTACTCC 58.222 37.037 0.00 0.00 35.74 3.85
3331 3407 8.286097 GCATATTTAGCTCACTGGATTTTACTC 58.714 37.037 0.00 0.00 0.00 2.59
3332 3408 7.995488 AGCATATTTAGCTCACTGGATTTTACT 59.005 33.333 0.00 0.00 38.01 2.24
3333 3409 8.159344 AGCATATTTAGCTCACTGGATTTTAC 57.841 34.615 0.00 0.00 38.01 2.01
3334 3410 8.752005 AAGCATATTTAGCTCACTGGATTTTA 57.248 30.769 0.00 0.00 42.53 1.52
3335 3411 7.651027 AAGCATATTTAGCTCACTGGATTTT 57.349 32.000 0.00 0.00 42.53 1.82
3392 3468 6.842280 TCCAGACACCCTACAAGCTATAATAA 59.158 38.462 0.00 0.00 0.00 1.40
3393 3469 6.378745 TCCAGACACCCTACAAGCTATAATA 58.621 40.000 0.00 0.00 0.00 0.98
3394 3470 5.216622 TCCAGACACCCTACAAGCTATAAT 58.783 41.667 0.00 0.00 0.00 1.28
3435 3514 4.772434 CTTTGTCGACGATGTCAATTTGT 58.228 39.130 11.62 0.00 32.09 2.83
3706 3785 3.429547 GGCATGCTAGTTTCTTCTCGAGA 60.430 47.826 18.92 12.08 0.00 4.04
3717 3796 2.171448 CAGGTCCTTAGGCATGCTAGTT 59.829 50.000 18.92 3.79 0.00 2.24
3720 3799 2.042464 CTCAGGTCCTTAGGCATGCTA 58.958 52.381 18.92 5.20 0.00 3.49
3730 3809 0.612744 GCTTGAGCTCTCAGGTCCTT 59.387 55.000 16.19 0.00 41.77 3.36
3731 3810 2.285824 GCTTGAGCTCTCAGGTCCT 58.714 57.895 16.19 0.00 41.77 3.85
3757 3836 5.063438 CCACAGACTGTTTTGGTACATATCG 59.937 44.000 5.04 0.00 39.30 2.92
3917 3997 8.812972 TCTTGTCAGCTTCTTTAGTTTCCTATA 58.187 33.333 0.00 0.00 0.00 1.31
3918 3998 7.604545 GTCTTGTCAGCTTCTTTAGTTTCCTAT 59.395 37.037 0.00 0.00 0.00 2.57
3953 4033 2.713927 AAATGCAACAGTTGGGCCGC 62.714 55.000 15.28 0.48 0.00 6.53
3964 4044 3.319755 CCACTTGTCCATCAAATGCAAC 58.680 45.455 0.00 0.00 32.72 4.17
3965 4045 2.299582 CCCACTTGTCCATCAAATGCAA 59.700 45.455 0.00 0.00 32.72 4.08
3986 4067 6.018994 CAGTTCAATATAAGCTGGTTCGGTAC 60.019 42.308 0.00 0.00 0.00 3.34
3987 4068 6.046593 CAGTTCAATATAAGCTGGTTCGGTA 58.953 40.000 0.00 0.00 0.00 4.02
4120 4201 1.202394 TGTCAATGCTGTTGTTGCCAC 60.202 47.619 3.03 0.00 0.00 5.01
4128 4209 1.603802 CACGAAGGTGTCAATGCTGTT 59.396 47.619 0.00 0.00 39.38 3.16
4179 4260 0.508641 CAGTTGTGCACGCTAGACAC 59.491 55.000 13.13 0.13 34.86 3.67
4342 4525 9.593134 ACAATAAACAAACAGAAGCAAACAATA 57.407 25.926 0.00 0.00 0.00 1.90
4383 4624 0.684535 TCCACTCCGTTTGAGATGCA 59.315 50.000 0.00 0.00 44.42 3.96
4395 4636 1.825474 TGAGAATTCCGAGTCCACTCC 59.175 52.381 0.65 0.00 39.79 3.85
4406 4647 9.495572 AATTTAGAATAGACGGATGAGAATTCC 57.504 33.333 0.65 0.00 0.00 3.01
4421 4662 9.090692 CAATTGCACCCAAAGAATTTAGAATAG 57.909 33.333 0.00 0.00 35.03 1.73
4446 4687 5.778241 TGTTCTCACTACTATTGGAGGAACA 59.222 40.000 5.88 5.88 31.45 3.18
4454 4695 6.873605 TCACAATGGTGTTCTCACTACTATTG 59.126 38.462 0.00 9.97 45.45 1.90
4499 4740 9.629878 TCTTCCCGCCTAAAAACAATTATATAA 57.370 29.630 0.00 0.00 0.00 0.98
4586 4827 0.108567 GGGCGAGAGAGTGAGGTTTC 60.109 60.000 0.00 0.00 0.00 2.78
4613 4857 1.544917 AAGGGGAGGAGGCAATGGT 60.545 57.895 0.00 0.00 0.00 3.55
4617 4861 1.616628 GAGGAAGGGGAGGAGGCAA 60.617 63.158 0.00 0.00 0.00 4.52
4622 4866 3.010226 CGGGAGAGGAAGGGGAGGA 62.010 68.421 0.00 0.00 0.00 3.71
4623 4867 2.444895 CGGGAGAGGAAGGGGAGG 60.445 72.222 0.00 0.00 0.00 4.30
4974 5250 3.865164 TGTATCGCATGCTGTTTGTCTAG 59.135 43.478 17.13 0.00 0.00 2.43
5029 5305 1.200716 CATCGCTGGTGCTGAATTTGT 59.799 47.619 0.00 0.00 36.97 2.83
5070 5346 4.183101 CAATGTCCTGCTTGTTGTTTGTT 58.817 39.130 0.00 0.00 0.00 2.83
5075 5351 3.550820 TGTACAATGTCCTGCTTGTTGT 58.449 40.909 0.00 0.00 36.92 3.32
5112 5388 5.523188 GCAGAATGAGACCTCAATCTACTTG 59.477 44.000 15.03 7.26 45.27 3.16
5169 5445 9.134055 TGGAATTCAGATGCATATGTTGAAATA 57.866 29.630 20.12 0.00 0.00 1.40
5214 5490 3.990959 AGCTTCCGGAGAAAGAAGATT 57.009 42.857 3.34 0.00 0.00 2.40
5215 5491 3.769844 TGTAGCTTCCGGAGAAAGAAGAT 59.230 43.478 3.34 0.00 0.00 2.40
5247 5530 2.092914 GGGTAAAGGGTGTCAGATGAGG 60.093 54.545 0.00 0.00 0.00 3.86
5248 5531 2.571653 TGGGTAAAGGGTGTCAGATGAG 59.428 50.000 0.00 0.00 0.00 2.90
5249 5532 2.626785 TGGGTAAAGGGTGTCAGATGA 58.373 47.619 0.00 0.00 0.00 2.92
5257 5540 1.633432 TCTGTGGATGGGTAAAGGGTG 59.367 52.381 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.