Multiple sequence alignment - TraesCS6D01G112900

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 TraesCS6D01G112900 chr6D 100.000 7731 0 0 1 7731 79716064 79723794 0.000000e+00 14277
1 TraesCS6D01G112900 chr6A 96.193 6015 163 25 1635 7620 96441204 96447181 0.000000e+00 9779
2 TraesCS6D01G112900 chr6A 91.236 1643 112 19 12 1638 96439513 96441139 0.000000e+00 2207
3 TraesCS6D01G112900 chr6A 92.683 82 6 0 2383 2464 311856997 311856916 1.360000e-22 119
4 TraesCS6D01G112900 chr6B 96.823 3305 77 12 3274 6573 152084100 152087381 0.000000e+00 5496
5 TraesCS6D01G112900 chr6B 89.720 1644 125 19 12 1634 152078414 152080034 0.000000e+00 2060
6 TraesCS6D01G112900 chr6B 96.748 1230 27 3 2050 3275 152082798 152084018 0.000000e+00 2037
7 TraesCS6D01G112900 chr6B 93.263 1039 36 9 6614 7633 152087380 152088403 0.000000e+00 1500
8 TraesCS6D01G112900 chr6B 97.381 420 9 2 1632 2049 152082221 152082640 0.000000e+00 713
9 TraesCS6D01G112900 chr6B 80.110 181 22 14 13 185 187778036 187778210 1.050000e-23 122
10 TraesCS6D01G112900 chr6B 79.781 183 25 12 13 188 555347640 555347463 1.050000e-23 122
11 TraesCS6D01G112900 chr5D 86.286 175 18 4 13 183 422694573 422694745 1.320000e-42 185
12 TraesCS6D01G112900 chr5D 93.023 86 6 0 2386 2471 420277225 420277140 8.140000e-25 126
13 TraesCS6D01G112900 chr5D 78.866 194 22 19 1 185 301983053 301982870 6.340000e-21 113
14 TraesCS6D01G112900 chr7A 93.519 108 7 0 7353 7460 628642655 628642548 2.230000e-35 161
15 TraesCS6D01G112900 chr7A 89.815 108 9 2 7353 7460 169958644 169958749 3.760000e-28 137
16 TraesCS6D01G112900 chr2A 92.523 107 8 0 7353 7459 377131673 377131779 3.740000e-33 154
17 TraesCS6D01G112900 chr2A 89.362 94 8 2 2383 2475 79308231 79308139 4.900000e-22 117
18 TraesCS6D01G112900 chr7B 91.667 108 9 0 7353 7460 589732907 589732800 4.830000e-32 150
19 TraesCS6D01G112900 chr3D 84.667 150 22 1 36 184 96417497 96417646 1.740000e-31 148
20 TraesCS6D01G112900 chr3D 91.579 95 6 2 2379 2473 157099352 157099444 6.300000e-26 130
21 TraesCS6D01G112900 chr3D 93.671 79 5 0 7650 7728 513464550 513464628 1.360000e-22 119
22 TraesCS6D01G112900 chr3D 93.671 79 5 0 7650 7728 513504881 513504959 1.360000e-22 119
23 TraesCS6D01G112900 chr2B 91.589 107 7 2 7353 7459 358770088 358770192 6.250000e-31 147
24 TraesCS6D01G112900 chr2B 90.588 85 8 0 2387 2471 723392895 723392979 6.340000e-21 113
25 TraesCS6D01G112900 chr5B 96.341 82 3 0 7650 7731 176229737 176229656 1.350000e-27 135
26 TraesCS6D01G112900 chr3A 81.461 178 21 12 13 184 413990831 413991002 1.350000e-27 135
27 TraesCS6D01G112900 chr2D 82.099 162 25 4 13 172 17845693 17845852 1.350000e-27 135
28 TraesCS6D01G112900 chr2D 91.753 97 7 1 7353 7449 300884572 300884667 4.870000e-27 134
29 TraesCS6D01G112900 chr1B 90.385 104 9 1 2375 2477 331096882 331096985 1.350000e-27 135
30 TraesCS6D01G112900 chr1B 79.558 181 24 13 13 186 510783417 510783591 4.900000e-22 117
31 TraesCS6D01G112900 chr3B 88.542 96 9 2 2379 2474 228206181 228206274 1.760000e-21 115
32 TraesCS6D01G112900 chr1A 90.244 82 5 1 7650 7731 364642081 364642003 3.820000e-18 104


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 TraesCS6D01G112900 chr6D 79716064 79723794 7730 False 14277.0 14277 100.0000 1 7731 1 chr6D.!!$F1 7730
1 TraesCS6D01G112900 chr6A 96439513 96447181 7668 False 5993.0 9779 93.7145 12 7620 2 chr6A.!!$F1 7608
2 TraesCS6D01G112900 chr6B 152078414 152088403 9989 False 2361.2 5496 94.7870 12 7633 5 chr6B.!!$F2 7621

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
390 402 0.175760 GTGGCTTCGGAGTCATGCTA 59.824 55.000 0.00 0.0 40.15 3.49 F
1381 1404 0.452184 CGATCTACTCGTGTGCAGGT 59.548 55.000 0.00 0.0 42.56 4.00 F
1435 1458 0.889186 ATGTCGCGGCCTGTTTTCTT 60.889 50.000 8.89 0.0 0.00 2.52 F
1506 1529 2.042464 CTGCAGCAGAAGAGGGGTATA 58.958 52.381 18.42 0.0 32.44 1.47 F
2400 4777 1.134580 TGTACTACTCCCTCCGTCTCG 60.135 57.143 0.00 0.0 0.00 4.04 F
2557 4934 0.184933 CAACACCCAAGTTCCCTGGA 59.815 55.000 0.00 0.0 0.00 3.86 F
3225 5606 0.189822 AAGCCCTTTTAGGTGGCCAA 59.810 50.000 7.24 0.0 46.55 4.52 F
4993 7472 0.248702 GCGACGTTTGCCTCCAAAAA 60.249 50.000 2.57 0.0 42.19 1.94 F
5917 8396 0.976073 TGGCCTGCTCTACCTACACC 60.976 60.000 3.32 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1449 0.316204 CCAGCTGGGCAAGAAAACAG 59.684 55.000 26.14 0.00 0.00 3.16 R
2379 4756 2.563702 GAGACGGAGGGAGTAGTACAG 58.436 57.143 2.52 0.00 0.00 2.74 R
2398 4775 2.654749 ATCAGCGACACTCATTTCGA 57.345 45.000 0.00 0.00 37.43 3.71 R
2448 4825 4.251103 ACTCCCTCCATCCCAAAATAAC 57.749 45.455 0.00 0.00 0.00 1.89 R
4125 6604 1.016130 GTGTGTCGACATCAGCCTGG 61.016 60.000 23.12 0.00 33.63 4.45 R
4853 7332 0.597377 GTTTTGCTTTGGGCCACGAG 60.597 55.000 5.23 8.93 40.92 4.18 R
5015 7494 1.270732 CCTCTGGAGCAGGTGCATATC 60.271 57.143 4.48 0.00 45.16 1.63 R
5985 8464 0.807275 CATCGGCGATCTTGCAGACA 60.807 55.000 21.25 0.00 41.74 3.41 R
7694 10196 0.179045 GGCATGTATCCGGTTCTGCT 60.179 55.000 0.00 0.00 0.00 4.24 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
27 28 6.650427 TGTAGAGTAGTCTTGAAGCTTTGA 57.350 37.500 5.16 0.00 33.84 2.69
28 29 7.050970 TGTAGAGTAGTCTTGAAGCTTTGAA 57.949 36.000 5.16 0.00 33.84 2.69
37 38 7.099120 AGTCTTGAAGCTTTGAAAATGTTTGT 58.901 30.769 0.00 0.00 0.00 2.83
70 73 2.237143 TGAGGGTCCACATTCACATCTC 59.763 50.000 0.00 0.00 0.00 2.75
75 78 3.379372 GGTCCACATTCACATCTCATTGG 59.621 47.826 0.00 0.00 0.00 3.16
86 89 5.011431 TCACATCTCATTGGCATACCTAGAG 59.989 44.000 0.00 0.00 36.63 2.43
95 98 5.086104 TGGCATACCTAGAGTGAACTTTC 57.914 43.478 0.00 0.00 36.63 2.62
96 99 4.777896 TGGCATACCTAGAGTGAACTTTCT 59.222 41.667 0.00 0.00 36.63 2.52
101 104 7.064016 GCATACCTAGAGTGAACTTTCTTGAAG 59.936 40.741 0.00 0.00 41.32 3.02
164 168 7.782897 TGTTATGAATTATCAAAACCACCCA 57.217 32.000 0.00 0.00 39.49 4.51
172 176 4.625225 ATCAAAACCACCCAGGGATTAT 57.375 40.909 14.54 0.00 43.89 1.28
195 199 9.868277 TTATTTGCATTTTCAAAGGTACTATGG 57.132 29.630 0.00 0.00 38.49 2.74
211 215 1.115467 ATGGTCTTCTCCTGCTACGG 58.885 55.000 0.00 0.00 0.00 4.02
212 216 0.251653 TGGTCTTCTCCTGCTACGGT 60.252 55.000 0.00 0.00 0.00 4.83
228 232 0.251916 CGGTGAAGTCTTATGGGGCA 59.748 55.000 0.00 0.00 0.00 5.36
236 240 1.140312 TCTTATGGGGCAGGACCATC 58.860 55.000 0.00 0.00 45.33 3.51
239 243 1.121407 TATGGGGCAGGACCATCGAG 61.121 60.000 0.00 0.00 45.33 4.04
250 254 0.456221 ACCATCGAGCGAGGTAGTTG 59.544 55.000 10.73 0.00 32.92 3.16
257 261 0.889306 AGCGAGGTAGTTGGTGTCTC 59.111 55.000 0.00 0.00 0.00 3.36
273 277 1.045407 TCTCTGTAGGTTTGGTGCGT 58.955 50.000 0.00 0.00 0.00 5.24
275 279 0.753867 TCTGTAGGTTTGGTGCGTCA 59.246 50.000 0.00 0.00 0.00 4.35
284 288 1.315981 TTGGTGCGTCAAACCTTGCA 61.316 50.000 0.00 0.00 38.60 4.08
302 306 6.128007 ACCTTGCAGATTTTAGGTTTATGTCG 60.128 38.462 0.00 0.00 37.75 4.35
304 308 7.201732 CCTTGCAGATTTTAGGTTTATGTCGAT 60.202 37.037 0.00 0.00 0.00 3.59
305 309 7.624360 TGCAGATTTTAGGTTTATGTCGATT 57.376 32.000 0.00 0.00 0.00 3.34
307 311 7.335673 TGCAGATTTTAGGTTTATGTCGATTCA 59.664 33.333 0.00 0.00 0.00 2.57
308 312 8.345565 GCAGATTTTAGGTTTATGTCGATTCAT 58.654 33.333 0.00 0.00 0.00 2.57
315 327 9.825109 TTAGGTTTATGTCGATTCATTCATACA 57.175 29.630 0.00 0.00 0.00 2.29
316 328 8.731275 AGGTTTATGTCGATTCATTCATACAA 57.269 30.769 0.00 0.00 0.00 2.41
323 335 8.667076 TGTCGATTCATTCATACAAATCTGAT 57.333 30.769 0.00 0.00 0.00 2.90
330 342 8.658499 TCATTCATACAAATCTGATGAGTCTG 57.342 34.615 0.00 0.00 31.50 3.51
350 362 9.640963 GAGTCTGTGTTAGTGTTTTATATGTCT 57.359 33.333 0.00 0.00 0.00 3.41
364 376 6.561737 TTATATGTCTTTTTGTTGGTGCGA 57.438 33.333 0.00 0.00 0.00 5.10
374 386 2.355197 TGTTGGTGCGATCTATTGTGG 58.645 47.619 0.00 0.00 0.00 4.17
378 390 1.599542 GGTGCGATCTATTGTGGCTTC 59.400 52.381 0.00 0.00 0.00 3.86
387 399 1.742761 ATTGTGGCTTCGGAGTCATG 58.257 50.000 0.00 0.00 40.15 3.07
390 402 0.175760 GTGGCTTCGGAGTCATGCTA 59.824 55.000 0.00 0.00 40.15 3.49
393 405 1.506493 GCTTCGGAGTCATGCTATGG 58.494 55.000 0.00 0.00 0.00 2.74
396 408 2.313172 CGGAGTCATGCTATGGCGC 61.313 63.158 0.00 0.00 40.53 6.53
398 410 0.948141 GGAGTCATGCTATGGCGCTC 60.948 60.000 7.64 0.00 40.53 5.03
400 412 1.270826 GAGTCATGCTATGGCGCTCTA 59.729 52.381 7.64 0.00 40.53 2.43
418 430 6.244275 CGCTCTATTAAAGTTCTTGTGCTTC 58.756 40.000 0.00 0.00 0.00 3.86
434 446 1.682087 GCTTCGATGCCCCCTACTTTT 60.682 52.381 12.05 0.00 0.00 2.27
442 454 2.923629 TGCCCCCTACTTTTAGGTGATT 59.076 45.455 0.00 0.00 43.41 2.57
443 455 4.113085 TGCCCCCTACTTTTAGGTGATTA 58.887 43.478 0.00 0.00 43.41 1.75
444 456 4.729881 TGCCCCCTACTTTTAGGTGATTAT 59.270 41.667 0.00 0.00 43.41 1.28
447 459 5.222068 CCCCCTACTTTTAGGTGATTATCCC 60.222 48.000 0.00 0.00 43.41 3.85
448 460 5.512576 CCCCTACTTTTAGGTGATTATCCCG 60.513 48.000 0.00 0.00 43.41 5.14
449 461 5.512576 CCCTACTTTTAGGTGATTATCCCGG 60.513 48.000 0.00 0.00 43.41 5.73
462 475 1.244019 ATCCCGGCAAGCACTTTGAC 61.244 55.000 0.00 0.00 41.71 3.18
471 484 1.597742 AGCACTTTGACGCTCATGTT 58.402 45.000 0.00 0.00 31.16 2.71
525 538 6.126409 AGGGTTTCAGTCAAATTTGTGTAGA 58.874 36.000 17.47 9.11 0.00 2.59
532 545 3.603770 GTCAAATTTGTGTAGATGCACGC 59.396 43.478 17.47 0.00 41.94 5.34
550 563 1.215655 GCGTGACAGTGTCGCTTCTT 61.216 55.000 28.91 0.00 45.29 2.52
573 586 6.971726 TCAACCTAACTACAGTCTCTTTCA 57.028 37.500 0.00 0.00 0.00 2.69
737 754 9.997482 TTCACAAGTTTGAATAAAGTTACAGAC 57.003 29.630 0.00 0.00 37.34 3.51
738 755 8.617809 TCACAAGTTTGAATAAAGTTACAGACC 58.382 33.333 0.00 0.00 37.34 3.85
739 756 8.621286 CACAAGTTTGAATAAAGTTACAGACCT 58.379 33.333 0.00 0.00 37.34 3.85
740 757 9.185680 ACAAGTTTGAATAAAGTTACAGACCTT 57.814 29.630 0.00 0.00 37.34 3.50
908 930 1.364317 TTTGATCCCCACCACCACCA 61.364 55.000 0.00 0.00 0.00 4.17
1289 1311 1.152383 GGTACGCTCTCGATTTGGGC 61.152 60.000 0.00 0.00 39.41 5.36
1357 1380 7.329717 GGTACGGAATTATAGCAGATTCTCAAG 59.670 40.741 0.00 0.00 33.75 3.02
1358 1381 5.698545 ACGGAATTATAGCAGATTCTCAAGC 59.301 40.000 0.00 0.00 33.75 4.01
1370 1393 3.808466 TTCTCAAGCATGCGATCTACT 57.192 42.857 13.01 0.00 0.00 2.57
1381 1404 0.452184 CGATCTACTCGTGTGCAGGT 59.548 55.000 0.00 0.00 42.56 4.00
1426 1449 4.899239 CAGGAGGATGTCGCGGCC 62.899 72.222 8.89 4.01 0.00 6.13
1435 1458 0.889186 ATGTCGCGGCCTGTTTTCTT 60.889 50.000 8.89 0.00 0.00 2.52
1506 1529 2.042464 CTGCAGCAGAAGAGGGGTATA 58.958 52.381 18.42 0.00 32.44 1.47
1580 1607 5.788450 CAAATTATTGTGCCCCTGTGTTTA 58.212 37.500 0.00 0.00 0.00 2.01
1965 4185 5.769662 TGGAACAGATGTGTCAAAAGCTATT 59.230 36.000 0.00 0.00 35.08 1.73
2032 4252 5.277876 GGAGCATCATCTAAGAGTGCATTTG 60.278 44.000 0.00 0.00 38.23 2.32
2091 4468 8.244494 TCTGCGTATCATTATCTCTTATTTGC 57.756 34.615 0.00 0.00 0.00 3.68
2103 4480 9.601217 TTATCTCTTATTTGCTGGTACTCTTTC 57.399 33.333 0.00 0.00 0.00 2.62
2201 4578 6.892658 TGTGGCTACATCTGTTACAAAAAT 57.107 33.333 0.00 0.00 0.00 1.82
2220 4597 2.842208 TTGCACCAAACTTCTGTTCG 57.158 45.000 0.00 0.00 34.96 3.95
2398 4775 1.408544 GCTGTACTACTCCCTCCGTCT 60.409 57.143 0.00 0.00 0.00 4.18
2400 4777 1.134580 TGTACTACTCCCTCCGTCTCG 60.135 57.143 0.00 0.00 0.00 4.04
2448 4825 4.056050 ACTTTGTACTAAACCAGCGACAG 58.944 43.478 0.00 0.00 0.00 3.51
2460 4837 3.016736 CCAGCGACAGTTATTTTGGGAT 58.983 45.455 0.00 0.00 0.00 3.85
2557 4934 0.184933 CAACACCCAAGTTCCCTGGA 59.815 55.000 0.00 0.00 0.00 3.86
2601 4978 7.231722 GTGAGTCTACATCCCTAACTATCACAT 59.768 40.741 0.00 0.00 0.00 3.21
2622 4999 6.151985 CACATATAGGGTGATAGACAGGTCTC 59.848 46.154 5.00 0.00 38.51 3.36
2797 5178 3.587498 TGAGGATATACAGGGAAGGGTG 58.413 50.000 0.00 0.00 0.00 4.61
3052 5433 8.087982 TCAAGTTTTCTGTGCTTTCATACTAG 57.912 34.615 0.00 0.00 0.00 2.57
3221 5602 0.541764 TGCCAAGCCCTTTTAGGTGG 60.542 55.000 0.00 0.00 33.45 4.61
3222 5603 1.888436 GCCAAGCCCTTTTAGGTGGC 61.888 60.000 9.30 9.30 44.46 5.01
3223 5604 1.257750 CCAAGCCCTTTTAGGTGGCC 61.258 60.000 0.00 0.00 46.55 5.36
3224 5605 0.541764 CAAGCCCTTTTAGGTGGCCA 60.542 55.000 0.00 0.00 46.55 5.36
3225 5606 0.189822 AAGCCCTTTTAGGTGGCCAA 59.810 50.000 7.24 0.00 46.55 4.52
3226 5607 0.413434 AGCCCTTTTAGGTGGCCAAT 59.587 50.000 7.24 0.79 46.55 3.16
3227 5608 0.536724 GCCCTTTTAGGTGGCCAATG 59.463 55.000 7.24 0.00 39.30 2.82
3451 5915 5.074515 TCCTTTTGGTGTCTTTCCCTTCTAT 59.925 40.000 0.00 0.00 41.38 1.98
3559 6023 9.775854 ACAATGGATTTAACATTCAAAACATGA 57.224 25.926 0.00 0.00 36.47 3.07
3800 6268 7.647715 AGTGTTTACGTTTGATCATTTCCAAAG 59.352 33.333 0.00 0.00 33.52 2.77
3905 6373 5.864418 AAAATATGACCGTAGCCAGTAGA 57.136 39.130 0.00 0.00 0.00 2.59
3906 6374 6.420913 AAAATATGACCGTAGCCAGTAGAT 57.579 37.500 0.00 0.00 0.00 1.98
3907 6375 5.646577 AATATGACCGTAGCCAGTAGATC 57.353 43.478 0.00 0.00 0.00 2.75
3908 6376 2.430248 TGACCGTAGCCAGTAGATCA 57.570 50.000 0.00 0.00 0.00 2.92
3909 6377 2.945456 TGACCGTAGCCAGTAGATCAT 58.055 47.619 0.00 0.00 0.00 2.45
4125 6604 5.455056 TCTTACTCTATTTGATCTCGGGC 57.545 43.478 0.00 0.00 0.00 6.13
4746 7225 4.051661 AGGAAGCATTCTTTTGGGATCA 57.948 40.909 0.00 0.00 46.56 2.92
4875 7354 1.044611 GTGGCCCAAAGCAAAACCTA 58.955 50.000 0.00 0.00 46.50 3.08
4980 7459 1.264826 GTTAACCCAATGTTGCGACGT 59.735 47.619 0.00 0.00 37.83 4.34
4993 7472 0.248702 GCGACGTTTGCCTCCAAAAA 60.249 50.000 2.57 0.00 42.19 1.94
5015 7494 9.846248 AAAAATTTTCTCACCTCGAAATGATAG 57.154 29.630 3.41 0.00 31.17 2.08
5021 7500 6.625362 TCTCACCTCGAAATGATAGATATGC 58.375 40.000 0.00 0.00 0.00 3.14
5023 7502 6.159293 TCACCTCGAAATGATAGATATGCAC 58.841 40.000 0.00 0.00 0.00 4.57
5917 8396 0.976073 TGGCCTGCTCTACCTACACC 60.976 60.000 3.32 0.00 0.00 4.16
5985 8464 2.879103 TCCTCCTTGGCGAAGATTTT 57.121 45.000 10.40 0.00 35.26 1.82
6415 8894 1.303309 GCCATCTGAACATCCTTCCG 58.697 55.000 0.00 0.00 0.00 4.30
6555 9034 6.037726 GGAAACACCGAAATTGTAACAAAGT 58.962 36.000 0.00 0.00 0.00 2.66
6630 9109 5.148651 TGTCTCACCTAGGCTTTTAACTC 57.851 43.478 9.30 0.00 0.00 3.01
6631 9110 4.838986 TGTCTCACCTAGGCTTTTAACTCT 59.161 41.667 9.30 0.00 0.00 3.24
6632 9111 5.307196 TGTCTCACCTAGGCTTTTAACTCTT 59.693 40.000 9.30 0.00 0.00 2.85
6633 9112 6.183361 TGTCTCACCTAGGCTTTTAACTCTTT 60.183 38.462 9.30 0.00 0.00 2.52
6668 9147 8.593945 ACTAGGAATGCAGGATTTAATTTTGA 57.406 30.769 0.00 0.00 0.00 2.69
6754 9233 1.019650 ATGAGGACCAGGAGTAGGGT 58.980 55.000 0.00 0.00 40.96 4.34
6756 9235 0.041386 GAGGACCAGGAGTAGGGTGT 59.959 60.000 0.00 0.00 37.57 4.16
6757 9236 0.252284 AGGACCAGGAGTAGGGTGTG 60.252 60.000 0.00 0.00 37.57 3.82
6758 9237 0.544595 GGACCAGGAGTAGGGTGTGT 60.545 60.000 0.00 0.00 37.57 3.72
6759 9238 0.896226 GACCAGGAGTAGGGTGTGTC 59.104 60.000 0.00 0.00 37.57 3.67
6760 9239 0.190069 ACCAGGAGTAGGGTGTGTCA 59.810 55.000 0.00 0.00 35.67 3.58
6761 9240 0.898320 CCAGGAGTAGGGTGTGTCAG 59.102 60.000 0.00 0.00 0.00 3.51
6762 9241 0.898320 CAGGAGTAGGGTGTGTCAGG 59.102 60.000 0.00 0.00 0.00 3.86
6763 9242 0.905337 AGGAGTAGGGTGTGTCAGGC 60.905 60.000 0.00 0.00 0.00 4.85
6810 9290 4.787598 CAGCTGTTCCAACTTTGATGTAC 58.212 43.478 5.25 0.00 0.00 2.90
6834 9315 3.434309 ACTGCACTATCCCAGCAAAAAT 58.566 40.909 0.00 0.00 37.89 1.82
6860 9341 6.826668 TCAGATTGTTGTAGTTCTTTCTCCA 58.173 36.000 0.00 0.00 0.00 3.86
6940 9421 4.022242 TGCTAGTACAGAAGAACTCACACC 60.022 45.833 0.00 0.00 0.00 4.16
6953 9434 0.692476 TCACACCTTCATGACCTGGG 59.308 55.000 0.00 0.00 0.00 4.45
6967 9448 1.100510 CCTGGGTCAATCACATGCTG 58.899 55.000 0.00 0.00 0.00 4.41
7140 9622 0.739813 ACTCGGTCGCACCTAATTGC 60.740 55.000 4.21 0.00 35.66 3.56
7259 9757 2.039084 ACCCAAGTACAAGCTTCAGGAG 59.961 50.000 0.00 0.00 0.00 3.69
7270 9768 2.494073 AGCTTCAGGAGGTAGAGAAACG 59.506 50.000 0.00 0.00 33.44 3.60
7271 9769 2.231721 GCTTCAGGAGGTAGAGAAACGT 59.768 50.000 0.00 0.00 0.00 3.99
7358 9856 4.530553 TCAAATCCACTAGCTGTTACTCCA 59.469 41.667 0.00 0.00 0.00 3.86
7364 9862 2.688958 ACTAGCTGTTACTCCATCCGTC 59.311 50.000 0.00 0.00 0.00 4.79
7435 9933 6.426327 CGTGTCTGAAATGTGTAAAACATCA 58.574 36.000 0.00 0.00 44.51 3.07
7462 9963 3.207044 AGGGAACAGAGGGAGTACATT 57.793 47.619 0.00 0.00 0.00 2.71
7495 9997 6.540189 TGAAAAATATCAGGTAGAGCTTGCTC 59.460 38.462 14.16 14.16 0.00 4.26
7549 10051 4.683781 GGATAACACTCTCGCAATCAGATC 59.316 45.833 0.00 0.00 0.00 2.75
7633 10135 1.666553 CAGCCGTAAGCACGTCCAA 60.667 57.895 0.00 0.00 46.96 3.53
7634 10136 1.070105 AGCCGTAAGCACGTCCAAA 59.930 52.632 0.00 0.00 46.96 3.28
7635 10137 0.533308 AGCCGTAAGCACGTCCAAAA 60.533 50.000 0.00 0.00 46.96 2.44
7636 10138 0.519961 GCCGTAAGCACGTCCAAAAT 59.480 50.000 0.00 0.00 46.96 1.82
7637 10139 1.068816 GCCGTAAGCACGTCCAAAATT 60.069 47.619 0.00 0.00 46.96 1.82
7638 10140 2.580589 CCGTAAGCACGTCCAAAATTG 58.419 47.619 0.00 0.00 46.96 2.32
7639 10141 2.224549 CCGTAAGCACGTCCAAAATTGA 59.775 45.455 0.00 0.00 46.96 2.57
7640 10142 3.119990 CCGTAAGCACGTCCAAAATTGAT 60.120 43.478 0.00 0.00 46.96 2.57
7641 10143 4.472286 CGTAAGCACGTCCAAAATTGATT 58.528 39.130 0.00 0.00 43.31 2.57
7642 10144 4.320690 CGTAAGCACGTCCAAAATTGATTG 59.679 41.667 0.00 0.00 43.31 2.67
7643 10145 2.676076 AGCACGTCCAAAATTGATTGC 58.324 42.857 0.00 0.00 0.00 3.56
7644 10146 1.386412 GCACGTCCAAAATTGATTGCG 59.614 47.619 0.00 0.00 0.00 4.85
7645 10147 1.386412 CACGTCCAAAATTGATTGCGC 59.614 47.619 0.00 0.00 0.00 6.09
7646 10148 0.991344 CGTCCAAAATTGATTGCGCC 59.009 50.000 4.18 0.00 0.00 6.53
7647 10149 1.668337 CGTCCAAAATTGATTGCGCCA 60.668 47.619 4.18 0.00 0.00 5.69
7648 10150 2.620242 GTCCAAAATTGATTGCGCCAT 58.380 42.857 4.18 0.00 0.00 4.40
7649 10151 3.733380 CGTCCAAAATTGATTGCGCCATA 60.733 43.478 4.18 0.00 0.00 2.74
7650 10152 4.370917 GTCCAAAATTGATTGCGCCATAT 58.629 39.130 4.18 0.00 0.00 1.78
7651 10153 4.209703 GTCCAAAATTGATTGCGCCATATG 59.790 41.667 4.18 0.00 0.00 1.78
7652 10154 3.059461 CCAAAATTGATTGCGCCATATGC 60.059 43.478 4.18 0.00 0.00 3.14
7662 10164 1.641677 GCCATATGCGAACACGTCC 59.358 57.895 0.00 0.00 0.00 4.79
7663 10165 0.810031 GCCATATGCGAACACGTCCT 60.810 55.000 0.00 0.00 0.00 3.85
7664 10166 1.651987 CCATATGCGAACACGTCCTT 58.348 50.000 0.00 0.00 0.00 3.36
7665 10167 1.593006 CCATATGCGAACACGTCCTTC 59.407 52.381 0.00 0.00 0.00 3.46
7666 10168 2.540515 CATATGCGAACACGTCCTTCT 58.459 47.619 0.00 0.00 0.00 2.85
7667 10169 2.736144 TATGCGAACACGTCCTTCTT 57.264 45.000 0.00 0.00 0.00 2.52
7668 10170 1.429463 ATGCGAACACGTCCTTCTTC 58.571 50.000 0.00 0.00 0.00 2.87
7669 10171 0.599204 TGCGAACACGTCCTTCTTCC 60.599 55.000 0.00 0.00 0.00 3.46
7670 10172 0.599204 GCGAACACGTCCTTCTTCCA 60.599 55.000 0.00 0.00 0.00 3.53
7671 10173 1.939838 GCGAACACGTCCTTCTTCCAT 60.940 52.381 0.00 0.00 0.00 3.41
7672 10174 1.993370 CGAACACGTCCTTCTTCCATC 59.007 52.381 0.00 0.00 0.00 3.51
7673 10175 1.993370 GAACACGTCCTTCTTCCATCG 59.007 52.381 0.00 0.00 0.00 3.84
7674 10176 0.389948 ACACGTCCTTCTTCCATCGC 60.390 55.000 0.00 0.00 0.00 4.58
7675 10177 1.084370 CACGTCCTTCTTCCATCGCC 61.084 60.000 0.00 0.00 0.00 5.54
7676 10178 1.218047 CGTCCTTCTTCCATCGCCA 59.782 57.895 0.00 0.00 0.00 5.69
7677 10179 0.391130 CGTCCTTCTTCCATCGCCAA 60.391 55.000 0.00 0.00 0.00 4.52
7678 10180 1.743772 CGTCCTTCTTCCATCGCCAAT 60.744 52.381 0.00 0.00 0.00 3.16
7679 10181 1.672881 GTCCTTCTTCCATCGCCAATG 59.327 52.381 0.00 0.00 34.93 2.82
7680 10182 0.383231 CCTTCTTCCATCGCCAATGC 59.617 55.000 0.00 0.00 33.71 3.56
7681 10183 1.097232 CTTCTTCCATCGCCAATGCA 58.903 50.000 0.00 0.00 37.32 3.96
7682 10184 0.810648 TTCTTCCATCGCCAATGCAC 59.189 50.000 0.00 0.00 37.32 4.57
7683 10185 1.031571 TCTTCCATCGCCAATGCACC 61.032 55.000 0.00 0.00 37.32 5.01
7684 10186 1.001020 TTCCATCGCCAATGCACCT 60.001 52.632 0.00 0.00 37.32 4.00
7685 10187 0.254462 TTCCATCGCCAATGCACCTA 59.746 50.000 0.00 0.00 37.32 3.08
7686 10188 0.463654 TCCATCGCCAATGCACCTAC 60.464 55.000 0.00 0.00 37.32 3.18
7687 10189 1.447317 CCATCGCCAATGCACCTACC 61.447 60.000 0.00 0.00 37.32 3.18
7688 10190 1.523711 ATCGCCAATGCACCTACCG 60.524 57.895 0.00 0.00 37.32 4.02
7689 10191 3.876198 CGCCAATGCACCTACCGC 61.876 66.667 0.00 0.00 37.32 5.68
7690 10192 2.749839 GCCAATGCACCTACCGCA 60.750 61.111 0.00 0.00 44.94 5.69
7691 10193 2.339556 GCCAATGCACCTACCGCAA 61.340 57.895 0.00 0.00 43.84 4.85
7692 10194 1.802636 CCAATGCACCTACCGCAAG 59.197 57.895 0.00 0.00 43.84 4.01
7693 10195 1.137404 CAATGCACCTACCGCAAGC 59.863 57.895 0.00 0.00 43.84 4.01
7694 10196 1.303236 AATGCACCTACCGCAAGCA 60.303 52.632 0.00 0.00 43.84 3.91
7695 10197 1.308069 AATGCACCTACCGCAAGCAG 61.308 55.000 0.00 0.00 43.84 4.24
7696 10198 3.804193 GCACCTACCGCAAGCAGC 61.804 66.667 0.00 0.00 40.87 5.25
7697 10199 2.358615 CACCTACCGCAAGCAGCA 60.359 61.111 0.00 0.00 46.13 4.41
7698 10200 2.046892 ACCTACCGCAAGCAGCAG 60.047 61.111 0.00 0.00 46.13 4.24
7699 10201 2.265739 CCTACCGCAAGCAGCAGA 59.734 61.111 0.00 0.00 46.13 4.26
7700 10202 1.375908 CCTACCGCAAGCAGCAGAA 60.376 57.895 0.00 0.00 46.13 3.02
7701 10203 1.639298 CCTACCGCAAGCAGCAGAAC 61.639 60.000 0.00 0.00 46.13 3.01
7702 10204 1.639298 CTACCGCAAGCAGCAGAACC 61.639 60.000 0.00 0.00 46.13 3.62
7703 10205 4.093952 CCGCAAGCAGCAGAACCG 62.094 66.667 0.00 0.00 46.13 4.44
7704 10206 4.093952 CGCAAGCAGCAGAACCGG 62.094 66.667 0.00 0.00 46.13 5.28
7705 10207 2.669569 GCAAGCAGCAGAACCGGA 60.670 61.111 9.46 0.00 44.79 5.14
7706 10208 2.042831 GCAAGCAGCAGAACCGGAT 61.043 57.895 9.46 0.00 44.79 4.18
7707 10209 0.744414 GCAAGCAGCAGAACCGGATA 60.744 55.000 9.46 0.00 44.79 2.59
7708 10210 1.009829 CAAGCAGCAGAACCGGATAC 58.990 55.000 9.46 0.00 0.00 2.24
7709 10211 0.613260 AAGCAGCAGAACCGGATACA 59.387 50.000 9.46 0.00 0.00 2.29
7710 10212 0.833287 AGCAGCAGAACCGGATACAT 59.167 50.000 9.46 0.00 0.00 2.29
7711 10213 0.940126 GCAGCAGAACCGGATACATG 59.060 55.000 9.46 0.15 0.00 3.21
7712 10214 0.940126 CAGCAGAACCGGATACATGC 59.060 55.000 9.46 11.10 0.00 4.06
7713 10215 0.179045 AGCAGAACCGGATACATGCC 60.179 55.000 9.46 0.00 34.24 4.40
7714 10216 1.166531 GCAGAACCGGATACATGCCC 61.167 60.000 9.46 0.00 0.00 5.36
7715 10217 0.469917 CAGAACCGGATACATGCCCT 59.530 55.000 9.46 0.00 0.00 5.19
7716 10218 0.469917 AGAACCGGATACATGCCCTG 59.530 55.000 9.46 0.00 0.00 4.45
7717 10219 0.535102 GAACCGGATACATGCCCTGG 60.535 60.000 9.46 0.00 0.00 4.45
7718 10220 1.279025 AACCGGATACATGCCCTGGT 61.279 55.000 9.46 7.14 33.17 4.00
7719 10221 1.227943 CCGGATACATGCCCTGGTG 60.228 63.158 0.00 0.00 0.00 4.17
7720 10222 1.227943 CGGATACATGCCCTGGTGG 60.228 63.158 0.00 0.00 37.09 4.61
7721 10223 1.922821 GGATACATGCCCTGGTGGT 59.077 57.895 0.00 0.00 36.04 4.16
7722 10224 0.258774 GGATACATGCCCTGGTGGTT 59.741 55.000 0.00 0.00 36.04 3.67
7723 10225 1.392589 GATACATGCCCTGGTGGTTG 58.607 55.000 0.00 0.00 36.04 3.77
7724 10226 0.998928 ATACATGCCCTGGTGGTTGA 59.001 50.000 0.00 0.00 36.04 3.18
7725 10227 0.998928 TACATGCCCTGGTGGTTGAT 59.001 50.000 0.00 0.00 36.04 2.57
7726 10228 0.612732 ACATGCCCTGGTGGTTGATG 60.613 55.000 0.00 0.00 36.04 3.07
7727 10229 1.000739 ATGCCCTGGTGGTTGATGG 59.999 57.895 0.00 0.00 36.04 3.51
7728 10230 3.070576 GCCCTGGTGGTTGATGGC 61.071 66.667 0.00 0.00 36.04 4.40
7729 10231 2.751436 CCCTGGTGGTTGATGGCG 60.751 66.667 0.00 0.00 0.00 5.69
7730 10232 3.443045 CCTGGTGGTTGATGGCGC 61.443 66.667 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.475137 AAGCTTCAAGACTACTCTACATCTT 57.525 36.000 0.00 0.00 31.53 2.40
1 2 7.177568 TCAAAGCTTCAAGACTACTCTACATCT 59.822 37.037 0.00 0.00 0.00 2.90
2 3 7.316640 TCAAAGCTTCAAGACTACTCTACATC 58.683 38.462 0.00 0.00 0.00 3.06
3 4 7.233389 TCAAAGCTTCAAGACTACTCTACAT 57.767 36.000 0.00 0.00 0.00 2.29
4 5 6.650427 TCAAAGCTTCAAGACTACTCTACA 57.350 37.500 0.00 0.00 0.00 2.74
5 6 7.948278 TTTCAAAGCTTCAAGACTACTCTAC 57.052 36.000 0.00 0.00 0.00 2.59
6 7 8.993121 CATTTTCAAAGCTTCAAGACTACTCTA 58.007 33.333 0.00 0.00 0.00 2.43
7 8 7.500559 ACATTTTCAAAGCTTCAAGACTACTCT 59.499 33.333 0.00 0.00 0.00 3.24
8 9 7.643579 ACATTTTCAAAGCTTCAAGACTACTC 58.356 34.615 0.00 0.00 0.00 2.59
9 10 7.573968 ACATTTTCAAAGCTTCAAGACTACT 57.426 32.000 0.00 0.00 0.00 2.57
10 11 8.534778 CAAACATTTTCAAAGCTTCAAGACTAC 58.465 33.333 0.00 0.00 0.00 2.73
19 20 5.519927 CGAAGGACAAACATTTTCAAAGCTT 59.480 36.000 0.00 0.00 0.00 3.74
27 28 5.814705 TCAAAATGCGAAGGACAAACATTTT 59.185 32.000 6.26 6.26 46.39 1.82
28 29 5.355596 TCAAAATGCGAAGGACAAACATTT 58.644 33.333 0.00 0.00 41.40 2.32
37 38 1.613255 GGACCCTCAAAATGCGAAGGA 60.613 52.381 0.00 0.00 0.00 3.36
70 73 5.028549 AGTTCACTCTAGGTATGCCAATG 57.971 43.478 1.54 0.00 37.19 2.82
75 78 6.398918 TCAAGAAAGTTCACTCTAGGTATGC 58.601 40.000 0.00 0.00 0.00 3.14
86 89 9.657121 CTCAAAGAATACTTCAAGAAAGTTCAC 57.343 33.333 0.00 0.00 46.26 3.18
95 98 7.856145 ATGCCTACTCAAAGAATACTTCAAG 57.144 36.000 0.00 0.00 35.05 3.02
96 99 9.733556 TTAATGCCTACTCAAAGAATACTTCAA 57.266 29.630 0.00 0.00 35.05 2.69
108 111 8.911965 TGCATCATTAAATTAATGCCTACTCAA 58.088 29.630 18.19 2.28 43.97 3.02
164 168 7.019656 ACCTTTGAAAATGCAAATAATCCCT 57.980 32.000 0.00 0.00 37.16 4.20
172 176 7.232534 AGACCATAGTACCTTTGAAAATGCAAA 59.767 33.333 0.00 0.00 36.43 3.68
192 196 1.115467 CCGTAGCAGGAGAAGACCAT 58.885 55.000 0.00 0.00 0.00 3.55
195 199 1.174783 TCACCGTAGCAGGAGAAGAC 58.825 55.000 0.00 0.00 34.73 3.01
211 215 1.559682 TCCTGCCCCATAAGACTTCAC 59.440 52.381 0.00 0.00 0.00 3.18
212 216 1.559682 GTCCTGCCCCATAAGACTTCA 59.440 52.381 0.00 0.00 0.00 3.02
228 232 0.820074 CTACCTCGCTCGATGGTCCT 60.820 60.000 13.70 0.00 35.48 3.85
236 240 0.456312 GACACCAACTACCTCGCTCG 60.456 60.000 0.00 0.00 0.00 5.03
239 243 0.889306 AGAGACACCAACTACCTCGC 59.111 55.000 0.00 0.00 0.00 5.03
250 254 2.767505 CACCAAACCTACAGAGACACC 58.232 52.381 0.00 0.00 0.00 4.16
257 261 1.588674 TTGACGCACCAAACCTACAG 58.411 50.000 0.00 0.00 0.00 2.74
304 308 9.106070 CAGACTCATCAGATTTGTATGAATGAA 57.894 33.333 2.52 0.00 0.00 2.57
305 309 8.262933 ACAGACTCATCAGATTTGTATGAATGA 58.737 33.333 11.88 0.00 0.00 2.57
307 311 8.045507 ACACAGACTCATCAGATTTGTATGAAT 58.954 33.333 11.88 0.89 0.00 2.57
308 312 7.389232 ACACAGACTCATCAGATTTGTATGAA 58.611 34.615 11.88 0.00 0.00 2.57
309 313 6.939622 ACACAGACTCATCAGATTTGTATGA 58.060 36.000 11.88 0.00 0.00 2.15
310 314 7.606858 AACACAGACTCATCAGATTTGTATG 57.393 36.000 5.91 5.91 0.00 2.39
315 327 6.763355 ACACTAACACAGACTCATCAGATTT 58.237 36.000 0.00 0.00 0.00 2.17
316 328 6.352016 ACACTAACACAGACTCATCAGATT 57.648 37.500 0.00 0.00 0.00 2.40
323 335 9.419297 GACATATAAAACACTAACACAGACTCA 57.581 33.333 0.00 0.00 0.00 3.41
350 362 5.218885 CACAATAGATCGCACCAACAAAAA 58.781 37.500 0.00 0.00 0.00 1.94
355 367 1.064060 GCCACAATAGATCGCACCAAC 59.936 52.381 0.00 0.00 0.00 3.77
359 371 1.258982 CGAAGCCACAATAGATCGCAC 59.741 52.381 0.00 0.00 0.00 5.34
364 376 2.766263 TGACTCCGAAGCCACAATAGAT 59.234 45.455 0.00 0.00 0.00 1.98
374 386 1.506493 CCATAGCATGACTCCGAAGC 58.494 55.000 0.00 0.00 0.00 3.86
378 390 2.313172 GCGCCATAGCATGACTCCG 61.313 63.158 0.00 0.00 39.83 4.63
387 399 4.991687 AGAACTTTAATAGAGCGCCATAGC 59.008 41.667 2.29 0.00 37.41 2.97
390 402 5.065218 CACAAGAACTTTAATAGAGCGCCAT 59.935 40.000 2.29 0.00 0.00 4.40
393 405 4.093556 AGCACAAGAACTTTAATAGAGCGC 59.906 41.667 0.00 0.00 0.00 5.92
396 408 7.582435 TCGAAGCACAAGAACTTTAATAGAG 57.418 36.000 0.00 0.00 0.00 2.43
398 410 6.684555 GCATCGAAGCACAAGAACTTTAATAG 59.315 38.462 7.93 0.00 0.00 1.73
400 412 5.393962 GCATCGAAGCACAAGAACTTTAAT 58.606 37.500 7.93 0.00 0.00 1.40
418 430 2.256117 CCTAAAAGTAGGGGGCATCG 57.744 55.000 0.00 0.00 43.07 3.84
434 446 1.071699 GCTTGCCGGGATAATCACCTA 59.928 52.381 2.18 0.00 0.00 3.08
442 454 0.326595 TCAAAGTGCTTGCCGGGATA 59.673 50.000 2.18 0.00 34.76 2.59
443 455 1.074775 TCAAAGTGCTTGCCGGGAT 59.925 52.632 2.18 0.00 34.76 3.85
444 456 1.896660 GTCAAAGTGCTTGCCGGGA 60.897 57.895 2.18 0.00 34.76 5.14
447 459 2.427410 GCGTCAAAGTGCTTGCCG 60.427 61.111 0.00 0.00 39.36 5.69
448 460 1.081840 GAGCGTCAAAGTGCTTGCC 60.082 57.895 0.00 0.00 42.60 4.52
449 461 0.239347 ATGAGCGTCAAAGTGCTTGC 59.761 50.000 0.00 0.00 42.60 4.01
462 475 6.801367 CATAAAGATGGAAAAACATGAGCG 57.199 37.500 0.00 0.00 0.00 5.03
492 505 8.990163 AATTTGACTGAAACCCTCTTAAGTTA 57.010 30.769 1.63 0.00 0.00 2.24
496 509 7.123547 ACACAAATTTGACTGAAACCCTCTTAA 59.876 33.333 24.64 0.00 0.00 1.85
525 538 2.280119 ACACTGTCACGCGTGCAT 60.280 55.556 33.63 19.23 34.58 3.96
532 545 0.778815 GAAGAAGCGACACTGTCACG 59.221 55.000 9.84 0.00 32.09 4.35
550 563 6.322969 TGTGAAAGAGACTGTAGTTAGGTTGA 59.677 38.462 0.00 0.00 0.00 3.18
573 586 2.802774 CGAAATGTTGCCAAGGCTTTGT 60.803 45.455 12.96 0.00 42.51 2.83
678 693 7.773224 AGTACAATGATTTGGATCGTAAATCCA 59.227 33.333 21.57 2.63 45.71 3.41
686 701 9.840427 AAAACTAAAGTACAATGATTTGGATCG 57.160 29.630 0.00 0.00 37.15 3.69
713 730 8.621286 AGGTCTGTAACTTTATTCAAACTTGTG 58.379 33.333 0.00 0.00 0.00 3.33
750 772 9.574641 CAGGCATGGCATGTTTTTCTTGAAAAG 62.575 40.741 26.94 0.00 39.42 2.27
783 805 1.212229 GGTTGGGTCTCGACTCGAC 59.788 63.158 8.51 8.51 43.87 4.20
1331 1354 6.688578 TGAGAATCTGCTATAATTCCGTACC 58.311 40.000 0.00 0.00 33.29 3.34
1370 1393 2.425592 CTTCCCACCTGCACACGA 59.574 61.111 0.00 0.00 0.00 4.35
1381 1404 1.371183 CGTGGAGAACTGCTTCCCA 59.629 57.895 0.00 0.00 0.00 4.37
1426 1449 0.316204 CCAGCTGGGCAAGAAAACAG 59.684 55.000 26.14 0.00 0.00 3.16
1435 1458 0.911045 TCTGAAGATCCAGCTGGGCA 60.911 55.000 32.23 15.19 36.21 5.36
1506 1529 8.567948 ACAAAGTGATGATGAAATAAGAAACGT 58.432 29.630 0.00 0.00 0.00 3.99
2070 4447 8.539770 ACCAGCAAATAAGAGATAATGATACG 57.460 34.615 0.00 0.00 0.00 3.06
2201 4578 2.842208 CGAACAGAAGTTTGGTGCAA 57.158 45.000 0.00 0.00 38.30 4.08
2220 4597 4.782019 TCCTTTTGCAATCACATACACC 57.218 40.909 0.00 0.00 0.00 4.16
2379 4756 2.563702 GAGACGGAGGGAGTAGTACAG 58.436 57.143 2.52 0.00 0.00 2.74
2398 4775 2.654749 ATCAGCGACACTCATTTCGA 57.345 45.000 0.00 0.00 37.43 3.71
2400 4777 5.786401 ACTAAATCAGCGACACTCATTTC 57.214 39.130 0.00 0.00 0.00 2.17
2448 4825 4.251103 ACTCCCTCCATCCCAAAATAAC 57.749 45.455 0.00 0.00 0.00 1.89
2460 4837 9.535170 CTAGAGATAAATATTGTACTCCCTCCA 57.465 37.037 0.00 0.00 0.00 3.86
2601 4978 4.920749 AGGAGACCTGTCTATCACCCTATA 59.079 45.833 0.00 0.00 40.61 1.31
2622 4999 4.372656 GCAGGTAAGTAGAGCATTGTAGG 58.627 47.826 0.00 0.00 0.00 3.18
2797 5178 5.397534 CCTGTACATGTAGTATTTACGCGAC 59.602 44.000 15.93 0.00 34.67 5.19
3052 5433 4.683832 ACTGTCTCGTGCATAATTCTACC 58.316 43.478 0.00 0.00 0.00 3.18
3227 5608 5.830991 TCATGGTTTTTAGTATGGTATGGCC 59.169 40.000 0.00 0.00 37.90 5.36
3724 6192 3.091545 GGAGCCAATGACATCCTTCAAA 58.908 45.455 0.00 0.00 0.00 2.69
3727 6195 2.425143 TGGAGCCAATGACATCCTTC 57.575 50.000 0.00 0.00 32.79 3.46
3800 6268 4.642445 TGCACATGATCCATCAACATTC 57.358 40.909 0.00 0.00 40.69 2.67
3905 6373 9.052759 GTCGTGAATAGTTGGGTTTATTATGAT 57.947 33.333 0.00 0.00 0.00 2.45
3906 6374 7.496591 GGTCGTGAATAGTTGGGTTTATTATGA 59.503 37.037 0.00 0.00 0.00 2.15
3907 6375 7.281324 TGGTCGTGAATAGTTGGGTTTATTATG 59.719 37.037 0.00 0.00 0.00 1.90
3908 6376 7.340256 TGGTCGTGAATAGTTGGGTTTATTAT 58.660 34.615 0.00 0.00 0.00 1.28
3909 6377 6.709281 TGGTCGTGAATAGTTGGGTTTATTA 58.291 36.000 0.00 0.00 0.00 0.98
4108 6587 2.289320 CCTGGCCCGAGATCAAATAGAG 60.289 54.545 0.00 0.00 0.00 2.43
4125 6604 1.016130 GTGTGTCGACATCAGCCTGG 61.016 60.000 23.12 0.00 33.63 4.45
4853 7332 0.597377 GTTTTGCTTTGGGCCACGAG 60.597 55.000 5.23 8.93 40.92 4.18
4875 7354 7.444183 TCGGAAGATAAAGTTTCAAGTGTCAAT 59.556 33.333 0.00 0.00 33.31 2.57
4980 7459 5.104569 AGGTGAGAAAATTTTTGGAGGCAAA 60.105 36.000 4.63 0.00 0.00 3.68
5015 7494 1.270732 CCTCTGGAGCAGGTGCATATC 60.271 57.143 4.48 0.00 45.16 1.63
5985 8464 0.807275 CATCGGCGATCTTGCAGACA 60.807 55.000 21.25 0.00 41.74 3.41
6605 9084 2.969628 AAAGCCTAGGTGAGACATCG 57.030 50.000 11.31 0.00 0.00 3.84
6668 9147 5.113446 AGAATCTCAGACAAGCCATCAAT 57.887 39.130 0.00 0.00 0.00 2.57
6700 9179 1.123077 ATGATCCTGCCTTCGCACTA 58.877 50.000 0.00 0.00 41.12 2.74
6754 9233 1.070275 CAGCTGACAGCCTGACACA 59.930 57.895 23.74 0.00 43.77 3.72
6756 9235 1.368950 GACAGCTGACAGCCTGACA 59.631 57.895 23.35 0.00 43.77 3.58
6757 9236 1.735920 CGACAGCTGACAGCCTGAC 60.736 63.158 23.35 18.00 43.77 3.51
6758 9237 2.653115 CGACAGCTGACAGCCTGA 59.347 61.111 23.35 0.00 43.77 3.86
6759 9238 3.117171 GCGACAGCTGACAGCCTG 61.117 66.667 23.35 21.00 43.77 4.85
6760 9239 3.619767 TGCGACAGCTGACAGCCT 61.620 61.111 23.35 9.42 43.77 4.58
6761 9240 3.418068 GTGCGACAGCTGACAGCC 61.418 66.667 23.35 8.68 43.77 4.85
6762 9241 2.356793 AGTGCGACAGCTGACAGC 60.357 61.111 23.35 20.12 45.42 4.40
6763 9242 2.025969 CCAGTGCGACAGCTGACAG 61.026 63.158 23.35 11.91 45.42 3.51
6810 9290 2.916702 TGCTGGGATAGTGCAGTATG 57.083 50.000 18.80 5.60 40.87 2.39
6834 9315 7.773224 TGGAGAAAGAACTACAACAATCTGAAA 59.227 33.333 0.00 0.00 0.00 2.69
6953 9434 2.490903 AGGAAAGCAGCATGTGATTGAC 59.509 45.455 0.00 0.00 34.11 3.18
7114 9595 1.006571 GTGCGACCGAGTCTTCCAA 60.007 57.895 0.00 0.00 0.00 3.53
7169 9651 3.063997 CACTAAAATGGCCGAGTAGCTTG 59.936 47.826 0.00 0.00 0.00 4.01
7259 9757 7.497249 TGAGATAGTTAGGTACGTTTCTCTACC 59.503 40.741 0.00 0.00 34.64 3.18
7270 9768 5.753921 GTGGCACATTGAGATAGTTAGGTAC 59.246 44.000 13.86 0.00 44.52 3.34
7271 9769 5.163343 GGTGGCACATTGAGATAGTTAGGTA 60.163 44.000 20.82 0.00 44.52 3.08
7277 9775 1.831106 TCGGTGGCACATTGAGATAGT 59.169 47.619 20.82 0.00 44.52 2.12
7281 9779 1.811965 CAATTCGGTGGCACATTGAGA 59.188 47.619 20.82 7.37 44.52 3.27
7435 9933 6.906901 TGTACTCCCTCTGTTCCCTTTTATAT 59.093 38.462 0.00 0.00 0.00 0.86
7462 9963 7.337938 TCTACCTGATATTTTTCATGACTGCA 58.662 34.615 0.00 0.00 0.00 4.41
7495 9997 2.679837 GTGATGGTGGTGTATCAGCAAG 59.320 50.000 0.74 0.00 46.23 4.01
7549 10051 3.193263 GGAGCCATATGATCATACTGCG 58.807 50.000 17.60 6.88 31.94 5.18
7644 10146 0.810031 AGGACGTGTTCGCATATGGC 60.810 55.000 4.56 0.00 41.18 4.40
7645 10147 1.593006 GAAGGACGTGTTCGCATATGG 59.407 52.381 4.56 0.00 41.18 2.74
7646 10148 2.540515 AGAAGGACGTGTTCGCATATG 58.459 47.619 0.00 0.00 41.18 1.78
7647 10149 2.961526 AGAAGGACGTGTTCGCATAT 57.038 45.000 0.00 0.00 41.18 1.78
7648 10150 2.602878 GAAGAAGGACGTGTTCGCATA 58.397 47.619 0.00 0.00 41.18 3.14
7649 10151 1.429463 GAAGAAGGACGTGTTCGCAT 58.571 50.000 0.00 0.00 41.18 4.73
7650 10152 0.599204 GGAAGAAGGACGTGTTCGCA 60.599 55.000 0.00 0.00 41.18 5.10
7651 10153 0.599204 TGGAAGAAGGACGTGTTCGC 60.599 55.000 0.00 0.00 41.18 4.70
7652 10154 1.993370 GATGGAAGAAGGACGTGTTCG 59.007 52.381 0.00 0.00 43.34 3.95
7653 10155 1.993370 CGATGGAAGAAGGACGTGTTC 59.007 52.381 0.00 0.00 0.00 3.18
7654 10156 1.939838 GCGATGGAAGAAGGACGTGTT 60.940 52.381 0.00 0.00 0.00 3.32
7655 10157 0.389948 GCGATGGAAGAAGGACGTGT 60.390 55.000 0.00 0.00 0.00 4.49
7656 10158 1.084370 GGCGATGGAAGAAGGACGTG 61.084 60.000 0.00 0.00 0.00 4.49
7657 10159 1.218316 GGCGATGGAAGAAGGACGT 59.782 57.895 0.00 0.00 0.00 4.34
7658 10160 0.391130 TTGGCGATGGAAGAAGGACG 60.391 55.000 0.00 0.00 0.00 4.79
7659 10161 1.672881 CATTGGCGATGGAAGAAGGAC 59.327 52.381 6.84 0.00 31.83 3.85
7660 10162 2.018644 GCATTGGCGATGGAAGAAGGA 61.019 52.381 16.33 0.00 36.21 3.36
7661 10163 0.383231 GCATTGGCGATGGAAGAAGG 59.617 55.000 16.33 0.00 36.21 3.46
7662 10164 1.097232 TGCATTGGCGATGGAAGAAG 58.903 50.000 16.33 0.00 45.35 2.85
7663 10165 0.810648 GTGCATTGGCGATGGAAGAA 59.189 50.000 16.33 0.00 45.35 2.52
7664 10166 1.031571 GGTGCATTGGCGATGGAAGA 61.032 55.000 16.33 0.00 45.35 2.87
7665 10167 1.033746 AGGTGCATTGGCGATGGAAG 61.034 55.000 16.33 0.00 45.35 3.46
7666 10168 0.254462 TAGGTGCATTGGCGATGGAA 59.746 50.000 16.33 0.00 45.35 3.53
7667 10169 0.463654 GTAGGTGCATTGGCGATGGA 60.464 55.000 16.33 10.96 45.35 3.41
7668 10170 1.447317 GGTAGGTGCATTGGCGATGG 61.447 60.000 16.33 0.00 45.35 3.51
7669 10171 1.775039 CGGTAGGTGCATTGGCGATG 61.775 60.000 10.52 10.52 45.35 3.84
7670 10172 1.523711 CGGTAGGTGCATTGGCGAT 60.524 57.895 0.00 0.00 45.35 4.58
7671 10173 2.125310 CGGTAGGTGCATTGGCGA 60.125 61.111 0.00 0.00 45.35 5.54
7672 10174 3.876198 GCGGTAGGTGCATTGGCG 61.876 66.667 0.00 0.00 45.35 5.69
7673 10175 2.270297 CTTGCGGTAGGTGCATTGGC 62.270 60.000 0.00 0.00 42.84 4.52
7674 10176 1.802636 CTTGCGGTAGGTGCATTGG 59.197 57.895 0.00 0.00 42.84 3.16
7675 10177 1.137404 GCTTGCGGTAGGTGCATTG 59.863 57.895 0.00 0.00 42.84 2.82
7676 10178 1.303236 TGCTTGCGGTAGGTGCATT 60.303 52.632 0.00 0.00 42.84 3.56
7677 10179 1.746615 CTGCTTGCGGTAGGTGCAT 60.747 57.895 0.00 0.00 42.84 3.96
7678 10180 2.358615 CTGCTTGCGGTAGGTGCA 60.359 61.111 0.00 0.00 41.38 4.57
7679 10181 3.804193 GCTGCTTGCGGTAGGTGC 61.804 66.667 3.26 0.00 0.00 5.01
7680 10182 2.358615 TGCTGCTTGCGGTAGGTG 60.359 61.111 0.00 0.00 46.63 4.00
7681 10183 2.046892 CTGCTGCTTGCGGTAGGT 60.047 61.111 10.94 0.00 46.63 3.08
7687 10189 4.093952 CCGGTTCTGCTGCTTGCG 62.094 66.667 0.00 0.00 46.63 4.85
7688 10190 0.744414 TATCCGGTTCTGCTGCTTGC 60.744 55.000 0.00 0.00 43.25 4.01
7689 10191 1.009829 GTATCCGGTTCTGCTGCTTG 58.990 55.000 0.00 0.00 0.00 4.01
7690 10192 0.613260 TGTATCCGGTTCTGCTGCTT 59.387 50.000 0.00 0.00 0.00 3.91
7691 10193 0.833287 ATGTATCCGGTTCTGCTGCT 59.167 50.000 0.00 0.00 0.00 4.24
7692 10194 0.940126 CATGTATCCGGTTCTGCTGC 59.060 55.000 0.00 0.00 0.00 5.25
7693 10195 0.940126 GCATGTATCCGGTTCTGCTG 59.060 55.000 0.00 0.00 0.00 4.41
7694 10196 0.179045 GGCATGTATCCGGTTCTGCT 60.179 55.000 0.00 0.00 0.00 4.24
7695 10197 1.166531 GGGCATGTATCCGGTTCTGC 61.167 60.000 0.00 5.04 0.00 4.26
7696 10198 0.469917 AGGGCATGTATCCGGTTCTG 59.530 55.000 0.00 0.00 0.00 3.02
7697 10199 0.469917 CAGGGCATGTATCCGGTTCT 59.530 55.000 0.00 0.00 0.00 3.01
7698 10200 0.535102 CCAGGGCATGTATCCGGTTC 60.535 60.000 0.00 0.00 0.00 3.62
7699 10201 1.279025 ACCAGGGCATGTATCCGGTT 61.279 55.000 0.00 0.00 30.05 4.44
7700 10202 1.692749 ACCAGGGCATGTATCCGGT 60.693 57.895 0.00 4.06 0.00 5.28
7701 10203 1.227943 CACCAGGGCATGTATCCGG 60.228 63.158 0.00 0.00 0.00 5.14
7702 10204 1.227943 CCACCAGGGCATGTATCCG 60.228 63.158 0.00 0.00 0.00 4.18
7703 10205 0.258774 AACCACCAGGGCATGTATCC 59.741 55.000 0.00 0.00 42.05 2.59
7704 10206 1.064758 TCAACCACCAGGGCATGTATC 60.065 52.381 0.00 0.00 42.05 2.24
7705 10207 0.998928 TCAACCACCAGGGCATGTAT 59.001 50.000 0.00 0.00 42.05 2.29
7706 10208 0.998928 ATCAACCACCAGGGCATGTA 59.001 50.000 0.00 0.00 42.05 2.29
7707 10209 0.612732 CATCAACCACCAGGGCATGT 60.613 55.000 0.00 0.00 42.05 3.21
7708 10210 1.324740 CCATCAACCACCAGGGCATG 61.325 60.000 0.00 0.00 42.05 4.06
7709 10211 1.000739 CCATCAACCACCAGGGCAT 59.999 57.895 0.00 0.00 42.05 4.40
7710 10212 2.440147 CCATCAACCACCAGGGCA 59.560 61.111 0.00 0.00 42.05 5.36
7711 10213 3.070576 GCCATCAACCACCAGGGC 61.071 66.667 0.00 0.00 42.05 5.19
7712 10214 2.751436 CGCCATCAACCACCAGGG 60.751 66.667 0.00 0.00 44.81 4.45
7713 10215 3.443045 GCGCCATCAACCACCAGG 61.443 66.667 0.00 0.00 42.21 4.45


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

AutoCloner maintained by Alex Coulton.