Multiple sequence alignment - TraesCS5B01G296300

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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 TraesCS5B01G296300 chr5B 100.000 6182 0 0 1 6182 479638894 479645075 0.000000e+00 11417.0
1 TraesCS5B01G296300 chr5B 97.531 81 0 1 6102 6182 479697521 479697599 3.010000e-28 137.0
2 TraesCS5B01G296300 chr5B 97.368 76 0 2 4647 4721 479643614 479643540 1.810000e-25 128.0
3 TraesCS5B01G296300 chr5B 92.000 75 3 1 4647 4721 661232215 661232286 1.100000e-17 102.0
4 TraesCS5B01G296300 chr5B 87.209 86 3 6 4644 4721 54455493 54455408 2.370000e-14 91.6
5 TraesCS5B01G296300 chr5D 93.650 4646 188 48 59 4647 399285189 399289784 0.000000e+00 6846.0
6 TraesCS5B01G296300 chr5D 91.020 2294 110 33 319 2559 399299496 399297246 0.000000e+00 3007.0
7 TraesCS5B01G296300 chr5D 87.798 1508 113 32 1 1491 399249471 399250924 0.000000e+00 1700.0
8 TraesCS5B01G296300 chr5D 91.231 707 30 10 4685 5381 399289784 399290468 0.000000e+00 933.0
9 TraesCS5B01G296300 chr5D 85.573 506 39 15 6 509 399248273 399248746 3.330000e-137 499.0
10 TraesCS5B01G296300 chr5D 90.331 362 19 10 5746 6102 399293260 399293610 1.570000e-125 460.0
11 TraesCS5B01G296300 chr5D 89.058 329 28 3 5420 5745 399292527 399292850 9.650000e-108 401.0
12 TraesCS5B01G296300 chr5D 96.296 81 1 1 6102 6182 41904778 41904856 1.400000e-26 132.0
13 TraesCS5B01G296300 chr5D 96.296 81 1 1 6102 6182 461601947 461601869 1.400000e-26 132.0
14 TraesCS5B01G296300 chr5D 89.474 76 5 2 4646 4721 483574147 483574219 6.600000e-15 93.5
15 TraesCS5B01G296300 chr5A 92.975 3744 161 42 1 3692 504875127 504878820 0.000000e+00 5363.0
16 TraesCS5B01G296300 chr5A 95.316 982 35 8 3670 4647 504879877 504880851 0.000000e+00 1548.0
17 TraesCS5B01G296300 chr5A 86.945 766 53 15 1 756 504883096 504882368 0.000000e+00 817.0
18 TraesCS5B01G296300 chr5A 86.385 639 50 21 4685 5295 504880851 504881480 0.000000e+00 664.0
19 TraesCS5B01G296300 chr5A 89.130 46 3 2 4632 4676 291594468 291594512 8.660000e-04 56.5
20 TraesCS5B01G296300 chr2B 96.341 82 1 1 6101 6182 161201783 161201704 3.890000e-27 134.0
21 TraesCS5B01G296300 chr7D 96.296 81 1 1 6102 6182 231405532 231405610 1.400000e-26 132.0
22 TraesCS5B01G296300 chr7B 96.296 81 1 1 6102 6182 48241764 48241686 1.400000e-26 132.0
23 TraesCS5B01G296300 chr3B 96.296 81 1 1 6102 6182 647896305 647896383 1.400000e-26 132.0
24 TraesCS5B01G296300 chr3B 96.296 81 1 1 6102 6182 824145924 824146002 1.400000e-26 132.0
25 TraesCS5B01G296300 chr2A 96.296 81 1 1 6102 6182 87556580 87556658 1.400000e-26 132.0
26 TraesCS5B01G296300 chr2A 90.909 44 4 0 6059 6102 79731364 79731321 6.690000e-05 60.2
27 TraesCS5B01G296300 chr3D 96.053 76 2 1 4647 4721 457058548 457058473 8.420000e-24 122.0
28 TraesCS5B01G296300 chr3D 94.872 78 3 1 4645 4721 457058471 457058548 3.030000e-23 121.0
29 TraesCS5B01G296300 chr6D 93.590 78 2 3 4647 4722 305173998 305174074 5.060000e-21 113.0
30 TraesCS5B01G296300 chr6A 93.333 75 4 1 4647 4721 39289661 39289734 6.550000e-20 110.0
31 TraesCS5B01G296300 chr6A 91.026 78 4 2 4646 4722 39289735 39289660 1.100000e-17 102.0
32 TraesCS5B01G296300 chr1A 83.333 96 5 5 4636 4721 436259643 436259737 1.850000e-10 78.7
33 TraesCS5B01G296300 chr7A 86.076 79 2 1 425 503 725645351 725645420 6.650000e-10 76.8
34 TraesCS5B01G296300 chr1B 86.792 53 5 2 4635 4685 278472054 278472106 2.410000e-04 58.4


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 TraesCS5B01G296300 chr5B 479638894 479645075 6181 False 11417.0 11417 100.000000 1 6182 1 chr5B.!!$F1 6181
1 TraesCS5B01G296300 chr5D 399297246 399299496 2250 True 3007.0 3007 91.020000 319 2559 1 chr5D.!!$R1 2240
2 TraesCS5B01G296300 chr5D 399285189 399293610 8421 False 2160.0 6846 91.067500 59 6102 4 chr5D.!!$F4 6043
3 TraesCS5B01G296300 chr5D 399248273 399250924 2651 False 1099.5 1700 86.685500 1 1491 2 chr5D.!!$F3 1490
4 TraesCS5B01G296300 chr5A 504875127 504881480 6353 False 2525.0 5363 91.558667 1 5295 3 chr5A.!!$F2 5294
5 TraesCS5B01G296300 chr5A 504882368 504883096 728 True 817.0 817 86.945000 1 756 1 chr5A.!!$R1 755

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
661 1889 1.142748 GTGGATCCTCACTCGGCAG 59.857 63.158 14.23 0.00 34.98 4.85 F
1189 2430 0.724453 CGATGAAACGTTTGGGTGCG 60.724 55.000 20.10 10.62 0.00 5.34 F
1346 2601 0.749454 CTGGGTGAGTGGGCTTATGC 60.749 60.000 0.00 0.00 38.76 3.14 F
1900 3159 0.759346 ATGAGGAATCACGGGGCTAC 59.241 55.000 0.00 0.00 0.00 3.58 F
1905 3164 1.483415 GGAATCACGGGGCTACAACTA 59.517 52.381 0.00 0.00 0.00 2.24 F
2102 3361 3.678056 ATTCCGTAACTGCTGAGTTCA 57.322 42.857 0.00 0.00 41.75 3.18 F
3939 6312 2.219674 CGCCGTATTCTTGAGAATGCTC 59.780 50.000 14.82 0.00 43.90 4.26 F
4665 7042 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 2900 1.968493 TGTCCCTATCCTGTTATCCGC 59.032 52.381 0.00 0.00 0.00 5.54 R
3178 4463 2.170166 GATTGATGGGCACTCAACCAA 58.830 47.619 3.42 0.00 40.73 3.67 R
3210 4495 4.285863 TCCACTCAAAGTTTGGATTTGGT 58.714 39.130 15.47 3.38 38.04 3.67 R
3410 4696 1.462731 AAATGAGCTTGCGTGGCCAA 61.463 50.000 7.24 0.00 0.00 4.52 R
3543 4831 4.969484 ACCCTGACTGTCGAAAGTAAAAT 58.031 39.130 8.61 0.00 0.00 1.82 R
4098 6471 3.134623 TGATGAATCTCACGCACCCTAAT 59.865 43.478 0.00 0.00 0.00 1.73 R
4740 7117 0.039165 AGCTTAGCGCACCAAAAAGC 60.039 50.000 11.47 13.99 42.21 3.51 R
5763 10605 0.118346 ACACAGGGTGACATAGGGGA 59.882 55.000 2.98 0.00 36.96 4.81 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.746711 CTTTCGTGAAATACATCTTTAGTTCAG 57.253 33.333 0.00 0.00 36.88 3.02
73 74 2.479566 TCAGAAAGGCATGTCTGACC 57.520 50.000 17.14 0.00 44.12 4.02
128 1332 8.897872 ATTCTTGCATGAATCTTCTTTGTTTT 57.102 26.923 19.23 0.00 31.72 2.43
129 1333 9.985730 ATTCTTGCATGAATCTTCTTTGTTTTA 57.014 25.926 19.23 0.00 31.72 1.52
130 1334 9.814899 TTCTTGCATGAATCTTCTTTGTTTTAA 57.185 25.926 10.76 0.00 0.00 1.52
131 1335 9.985730 TCTTGCATGAATCTTCTTTGTTTTAAT 57.014 25.926 0.00 0.00 0.00 1.40
153 1357 7.625828 AATTTAGTGGTACTTTAGTGGATGC 57.374 36.000 0.00 0.00 0.00 3.91
203 1407 2.614057 ACACCAAGAAAAAGAGTGCGAG 59.386 45.455 0.00 0.00 31.58 5.03
215 1422 1.300697 GTGCGAGGTTGACGAGGTT 60.301 57.895 0.00 0.00 0.00 3.50
272 1479 4.250464 ACGTCACAAAACTCAGTTTCTCA 58.750 39.130 2.45 0.00 34.43 3.27
499 1716 4.038080 GTTTGCGTCCTTGCCGGG 62.038 66.667 2.18 0.00 0.00 5.73
572 1789 3.368635 CCTGCGGCGGTATGGTATTATTA 60.369 47.826 9.78 0.00 0.00 0.98
636 1864 1.259770 TCTGTCGTATCGATCGAACCG 59.740 52.381 23.50 24.46 38.42 4.44
642 1870 1.727511 TATCGATCGAACCGCCCGTT 61.728 55.000 23.50 4.51 37.41 4.44
653 1881 2.668632 GCCCGTTGTGGATCCTCA 59.331 61.111 14.23 13.32 42.00 3.86
661 1889 1.142748 GTGGATCCTCACTCGGCAG 59.857 63.158 14.23 0.00 34.98 4.85
1183 2424 2.966708 CAGCTGTTCGATGAAACGTTTG 59.033 45.455 20.10 3.83 34.70 2.93
1189 2430 0.724453 CGATGAAACGTTTGGGTGCG 60.724 55.000 20.10 10.62 0.00 5.34
1221 2472 2.726821 TGATTGATTGAGGTGGCTTCC 58.273 47.619 0.00 0.00 0.00 3.46
1234 2489 1.600916 GCTTCCGGTGGCTTCTTGT 60.601 57.895 0.00 0.00 0.00 3.16
1240 2495 2.647297 GTGGCTTCTTGTGCAGGC 59.353 61.111 0.00 0.00 36.13 4.85
1346 2601 0.749454 CTGGGTGAGTGGGCTTATGC 60.749 60.000 0.00 0.00 38.76 3.14
1381 2636 8.467598 TCAGTGAATGGAGTTGAATAGTACTAC 58.532 37.037 4.31 0.00 0.00 2.73
1405 2660 3.671928 TCTTTTCTTCCGTTCGTTCGATC 59.328 43.478 0.00 0.00 0.00 3.69
1406 2661 3.293311 TTTCTTCCGTTCGTTCGATCT 57.707 42.857 0.00 0.00 0.00 2.75
1407 2662 3.293311 TTCTTCCGTTCGTTCGATCTT 57.707 42.857 0.00 0.00 0.00 2.40
1408 2663 2.860062 TCTTCCGTTCGTTCGATCTTC 58.140 47.619 0.00 0.00 0.00 2.87
1409 2664 1.578023 CTTCCGTTCGTTCGATCTTCG 59.422 52.381 0.00 0.00 42.10 3.79
1477 2736 1.304134 ATGGCCGGTGGGAGTTTTC 60.304 57.895 1.90 0.00 34.06 2.29
1478 2737 3.053896 GGCCGGTGGGAGTTTTCG 61.054 66.667 1.90 0.00 34.06 3.46
1498 2757 2.514458 GGGGGTGATTCTTGTGACAT 57.486 50.000 0.00 0.00 0.00 3.06
1641 2900 3.699038 AGCTTACTAGTGCTCTTGGAGAG 59.301 47.826 5.39 0.61 45.04 3.20
1671 2930 1.322442 GATAGGGACAGGCATTTGGC 58.678 55.000 0.00 0.00 43.74 4.52
1853 3112 4.913335 ATACATGCTTTGGCTCATGAAG 57.087 40.909 8.93 0.00 41.82 3.02
1856 3115 1.250328 TGCTTTGGCTCATGAAGTGG 58.750 50.000 0.00 0.00 39.59 4.00
1893 3152 6.856895 TCTATGCAGTATATGAGGAATCACG 58.143 40.000 0.00 0.00 0.00 4.35
1900 3159 0.759346 ATGAGGAATCACGGGGCTAC 59.241 55.000 0.00 0.00 0.00 3.58
1905 3164 1.483415 GGAATCACGGGGCTACAACTA 59.517 52.381 0.00 0.00 0.00 2.24
1931 3190 5.259632 AGCTAAAAATGGAGCATTGAGACT 58.740 37.500 0.00 0.00 41.36 3.24
1957 3216 7.285172 TGTGATAATACATGCCAAGTTGCTAAT 59.715 33.333 0.00 0.00 0.00 1.73
1985 3244 6.417044 GCTTGCATGTCATATCAACAAGATTC 59.583 38.462 0.00 0.00 37.56 2.52
2102 3361 3.678056 ATTCCGTAACTGCTGAGTTCA 57.322 42.857 0.00 0.00 41.75 3.18
2106 3365 4.385825 TCCGTAACTGCTGAGTTCAAAAT 58.614 39.130 0.00 0.00 41.75 1.82
2188 3447 8.846943 TGTTATCTTAGCTTTTGATCTGAACA 57.153 30.769 0.00 0.00 0.00 3.18
2345 3627 5.569355 TGATTTGTGCCCATCTCTCTTAAA 58.431 37.500 0.00 0.00 0.00 1.52
2567 3852 6.808704 GGCTTAGCCTAAAACATTTTCTCTTG 59.191 38.462 17.16 0.00 46.69 3.02
3178 4463 5.717178 TCTCTGCCTCTTCACTTTATGTAGT 59.283 40.000 0.00 0.00 0.00 2.73
3210 4495 4.065088 GCCCATCAATCTACGAAATGCTA 58.935 43.478 0.00 0.00 0.00 3.49
3455 4741 4.892433 AGAGACAAGAAACATCCAGACAG 58.108 43.478 0.00 0.00 0.00 3.51
3457 4743 4.636249 AGACAAGAAACATCCAGACAGAC 58.364 43.478 0.00 0.00 0.00 3.51
3458 4744 4.346418 AGACAAGAAACATCCAGACAGACT 59.654 41.667 0.00 0.00 0.00 3.24
3459 4745 5.041191 ACAAGAAACATCCAGACAGACTT 57.959 39.130 0.00 0.00 0.00 3.01
3460 4746 4.818546 ACAAGAAACATCCAGACAGACTTG 59.181 41.667 0.00 0.00 38.34 3.16
3658 4949 8.788806 TCCTTTGATTGTTATGTCGTGTTTAAT 58.211 29.630 0.00 0.00 0.00 1.40
3777 6150 4.582869 TGATGTAACTCTTGCATGAAGCT 58.417 39.130 0.00 0.00 45.94 3.74
3778 6151 5.733676 TGATGTAACTCTTGCATGAAGCTA 58.266 37.500 0.00 0.00 45.94 3.32
3869 6242 6.929049 TGTAGCTCAATTATAATGGGAAGACG 59.071 38.462 0.00 0.00 0.00 4.18
3939 6312 2.219674 CGCCGTATTCTTGAGAATGCTC 59.780 50.000 14.82 0.00 43.90 4.26
4053 6426 5.142635 ACTAACGTCGTGTGTTTTTAACC 57.857 39.130 0.00 0.00 0.00 2.85
4087 6460 9.462174 CTGTTCTAGAAATGATAGTGTGAGATC 57.538 37.037 6.78 0.00 0.00 2.75
4106 6479 9.388506 GTGAGATCCATCATTATTATTAGGGTG 57.611 37.037 0.00 0.00 0.00 4.61
4119 6492 2.890808 TAGGGTGCGTGAGATTCATC 57.109 50.000 0.00 0.00 0.00 2.92
4157 6530 5.764131 ACTATAACTCTAGCGTTGCTCATC 58.236 41.667 8.37 0.00 40.44 2.92
4264 6639 5.343249 ACTTAAGCTTCAAAACAAGTGCTG 58.657 37.500 0.00 0.00 0.00 4.41
4286 6661 8.830580 TGCTGTCAGCTTATATTTCAGTATTTC 58.169 33.333 24.76 0.00 42.97 2.17
4319 6694 4.025229 TGCAACGATAACACAGAGTTGTTC 60.025 41.667 8.16 0.00 42.72 3.18
4348 6723 9.436957 TTTTAGGTAAGTTTAGAAGCTGATGAG 57.563 33.333 0.00 0.00 0.00 2.90
4368 6743 6.286240 TGAGTCTGATAGCAAATGTACTGT 57.714 37.500 0.00 0.00 0.00 3.55
4450 6825 2.495270 GAGATCTCTCAGAAGTGTGCCA 59.505 50.000 15.80 0.00 42.42 4.92
4475 6850 2.560105 AGTGGTACTGTCTTCCGTTACC 59.440 50.000 0.00 0.00 0.00 2.85
4622 6999 2.993899 CACGGTAACCATTCTCTGTCAC 59.006 50.000 0.00 0.00 0.00 3.67
4647 7024 7.560262 ACAGTGAAGTATGCCAACTATCTAGTA 59.440 37.037 0.00 0.00 34.99 1.82
4648 7025 7.863375 CAGTGAAGTATGCCAACTATCTAGTAC 59.137 40.741 0.00 0.00 34.99 2.73
4649 7026 7.780745 AGTGAAGTATGCCAACTATCTAGTACT 59.219 37.037 0.00 0.00 34.99 2.73
4650 7027 8.077386 GTGAAGTATGCCAACTATCTAGTACTC 58.923 40.741 0.00 0.00 34.99 2.59
4651 7028 7.230913 TGAAGTATGCCAACTATCTAGTACTCC 59.769 40.741 0.00 0.00 34.99 3.85
4652 7029 6.011481 AGTATGCCAACTATCTAGTACTCCC 58.989 44.000 0.00 0.00 34.99 4.30
4653 7030 4.537945 TGCCAACTATCTAGTACTCCCT 57.462 45.455 0.00 0.00 34.99 4.20
4654 7031 4.471548 TGCCAACTATCTAGTACTCCCTC 58.528 47.826 0.00 0.00 34.99 4.30
4655 7032 3.827876 GCCAACTATCTAGTACTCCCTCC 59.172 52.174 0.00 0.00 34.99 4.30
4656 7033 4.073549 CCAACTATCTAGTACTCCCTCCG 58.926 52.174 0.00 0.00 34.99 4.63
4657 7034 4.446023 CCAACTATCTAGTACTCCCTCCGT 60.446 50.000 0.00 0.00 34.99 4.69
4658 7035 4.622260 ACTATCTAGTACTCCCTCCGTC 57.378 50.000 0.00 0.00 34.13 4.79
4659 7036 2.955342 ATCTAGTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
4660 7037 0.842635 TCTAGTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
4661 7038 0.549950 CTAGTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
4662 7039 0.257039 TAGTACTCCCTCCGTCCCAC 59.743 60.000 0.00 0.00 0.00 4.61
4663 7040 1.304713 GTACTCCCTCCGTCCCACA 60.305 63.158 0.00 0.00 0.00 4.17
4664 7041 0.901580 GTACTCCCTCCGTCCCACAA 60.902 60.000 0.00 0.00 0.00 3.33
4665 7042 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
4666 7043 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
4667 7044 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
4668 7045 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
4669 7046 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
4670 7047 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
4671 7048 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
4672 7049 3.583086 CCCTCCGTCCCACAATATAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
4673 7050 4.563580 CCCTCCGTCCCACAATATAAGATG 60.564 50.000 0.00 0.00 0.00 2.90
4674 7051 4.040461 CCTCCGTCCCACAATATAAGATGT 59.960 45.833 0.00 0.00 0.00 3.06
4675 7052 5.454755 CCTCCGTCCCACAATATAAGATGTT 60.455 44.000 0.00 0.00 0.00 2.71
4676 7053 5.996644 TCCGTCCCACAATATAAGATGTTT 58.003 37.500 0.00 0.00 0.00 2.83
4677 7054 6.419791 TCCGTCCCACAATATAAGATGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
4678 7055 6.887545 TCCGTCCCACAATATAAGATGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
4679 7056 6.972328 CCGTCCCACAATATAAGATGTTTTTG 59.028 38.462 0.00 0.00 0.00 2.44
4680 7057 6.472163 CGTCCCACAATATAAGATGTTTTTGC 59.528 38.462 0.00 0.00 0.00 3.68
4681 7058 7.319646 GTCCCACAATATAAGATGTTTTTGCA 58.680 34.615 0.00 0.00 0.00 4.08
4682 7059 7.489113 GTCCCACAATATAAGATGTTTTTGCAG 59.511 37.037 0.00 0.00 0.00 4.41
4683 7060 6.256321 CCCACAATATAAGATGTTTTTGCAGC 59.744 38.462 0.00 0.00 0.00 5.25
4684 7061 7.037438 CCACAATATAAGATGTTTTTGCAGCT 58.963 34.615 0.00 0.00 36.59 4.24
4725 7102 1.465200 GGGACGGAGGGAGTATCTGC 61.465 65.000 0.00 0.00 33.73 4.26
4732 7109 4.120589 CGGAGGGAGTATCTGCTTTAAAC 58.879 47.826 0.00 0.00 33.73 2.01
4733 7110 4.382685 CGGAGGGAGTATCTGCTTTAAACA 60.383 45.833 0.00 0.00 33.73 2.83
4734 7111 5.119694 GGAGGGAGTATCTGCTTTAAACAG 58.880 45.833 9.98 9.98 36.44 3.16
4735 7112 5.338463 GGAGGGAGTATCTGCTTTAAACAGT 60.338 44.000 13.77 7.39 36.50 3.55
4736 7113 6.127140 GGAGGGAGTATCTGCTTTAAACAGTA 60.127 42.308 13.77 6.75 36.50 2.74
4737 7114 6.879400 AGGGAGTATCTGCTTTAAACAGTAG 58.121 40.000 13.77 2.86 36.50 2.57
4739 7116 7.180408 AGGGAGTATCTGCTTTAAACAGTAGAA 59.820 37.037 13.77 1.10 38.79 2.10
4740 7117 7.492994 GGGAGTATCTGCTTTAAACAGTAGAAG 59.507 40.741 13.77 0.00 38.79 2.85
4741 7118 7.010645 GGAGTATCTGCTTTAAACAGTAGAAGC 59.989 40.741 13.77 8.00 38.79 3.86
4742 7119 7.616313 AGTATCTGCTTTAAACAGTAGAAGCT 58.384 34.615 13.53 6.80 43.60 3.74
4743 7120 8.097662 AGTATCTGCTTTAAACAGTAGAAGCTT 58.902 33.333 0.00 0.00 43.60 3.74
4752 7129 2.290641 ACAGTAGAAGCTTTTTGGTGCG 59.709 45.455 0.00 0.00 0.00 5.34
4760 7137 3.133673 AGCTTTTTGGTGCGCTAAGCTA 61.134 45.455 19.88 3.54 46.92 3.32
4870 7249 8.918202 ACATTCTTATGTGTTTCTGTTCCTTA 57.082 30.769 0.00 0.00 43.29 2.69
4874 7253 7.608153 TCTTATGTGTTTCTGTTCCTTATCGA 58.392 34.615 0.00 0.00 0.00 3.59
4948 7334 4.964262 ACCTTGCCATTCACAATATTGGAT 59.036 37.500 19.37 7.72 0.00 3.41
5074 7460 5.125356 TGTGTGATGAGAATGTGTTCAAGT 58.875 37.500 0.00 0.00 36.79 3.16
5240 7649 5.656549 TTTGGTCCTTTCCCTTAAGAGAA 57.343 39.130 3.36 0.00 0.00 2.87
5275 7684 6.932356 TGTACCGGTAATTGTGTACAAAAA 57.068 33.333 17.78 0.00 40.24 1.94
5321 7730 6.262944 TGTGAAACACTTCATGGGCATATATC 59.737 38.462 0.00 0.00 45.67 1.63
5324 7733 5.308976 ACACTTCATGGGCATATATCACA 57.691 39.130 0.00 0.00 0.00 3.58
5325 7734 5.693961 ACACTTCATGGGCATATATCACAA 58.306 37.500 0.00 0.00 0.00 3.33
5331 7740 7.019656 TCATGGGCATATATCACAATGTAGT 57.980 36.000 0.00 0.00 0.00 2.73
5332 7741 8.144862 TCATGGGCATATATCACAATGTAGTA 57.855 34.615 0.00 0.00 0.00 1.82
5333 7742 8.040727 TCATGGGCATATATCACAATGTAGTAC 58.959 37.037 0.00 0.00 0.00 2.73
5334 7743 7.309770 TGGGCATATATCACAATGTAGTACA 57.690 36.000 5.24 5.24 0.00 2.90
5370 7779 4.225942 TCATATGAGCCTGGAAACTTCTGT 59.774 41.667 0.00 0.00 0.00 3.41
5371 7780 3.515602 ATGAGCCTGGAAACTTCTGTT 57.484 42.857 0.00 0.00 38.16 3.16
5377 7786 7.175104 TGAGCCTGGAAACTTCTGTTAAATAT 58.825 34.615 0.00 0.00 34.96 1.28
5381 7790 7.755373 GCCTGGAAACTTCTGTTAAATATTGTC 59.245 37.037 0.00 0.00 34.96 3.18
5382 7791 8.792633 CCTGGAAACTTCTGTTAAATATTGTCA 58.207 33.333 0.00 0.00 34.96 3.58
5384 7793 9.349713 TGGAAACTTCTGTTAAATATTGTCACT 57.650 29.630 0.00 0.00 34.96 3.41
5393 8620 7.722336 TGTTAAATATTGTCACTGTAACGACG 58.278 34.615 0.00 0.00 34.78 5.12
5413 8640 1.674322 CTTCGTCCACCGGCCATTT 60.674 57.895 0.00 0.00 37.11 2.32
5416 8643 2.355115 GTCCACCGGCCATTTCCT 59.645 61.111 0.00 0.00 0.00 3.36
5468 9898 1.209747 GCATCTACCGGGTTTCCTCTT 59.790 52.381 4.31 0.00 0.00 2.85
5475 9905 1.675552 CGGGTTTCCTCTTGTTGTGT 58.324 50.000 0.00 0.00 0.00 3.72
5478 9908 1.748493 GGTTTCCTCTTGTTGTGTGCA 59.252 47.619 0.00 0.00 0.00 4.57
5482 9912 2.288666 TCCTCTTGTTGTGTGCACTTC 58.711 47.619 19.41 11.68 0.00 3.01
5508 9938 7.838879 CGTGCTTTGTGTTTTACTGTATTTTTG 59.161 33.333 0.00 0.00 0.00 2.44
5542 9972 2.668212 TGGAGAAGCCGCCGTTTG 60.668 61.111 0.00 0.00 40.66 2.93
5564 9994 5.313712 TGAAAATAAGTTTCTCCGGCTTCT 58.686 37.500 0.00 0.00 45.14 2.85
5573 10003 3.702048 CCGGCTTCTTCCCCGTCA 61.702 66.667 0.00 0.00 42.87 4.35
5575 10005 1.521681 CGGCTTCTTCCCCGTCATC 60.522 63.158 0.00 0.00 39.67 2.92
5581 10011 3.664025 CTTCCCCGTCATCGCAGCA 62.664 63.158 0.00 0.00 35.54 4.41
5592 10022 0.678395 ATCGCAGCATCTTCTCCGAT 59.322 50.000 0.00 0.00 0.00 4.18
5593 10023 0.249197 TCGCAGCATCTTCTCCGATG 60.249 55.000 0.00 0.00 42.83 3.84
5596 10026 0.883814 CAGCATCTTCTCCGATGGCC 60.884 60.000 0.00 0.00 40.82 5.36
5608 10038 1.077212 GATGGCCAGGCTGATGTGT 60.077 57.895 17.94 0.00 0.00 3.72
5610 10040 1.855441 ATGGCCAGGCTGATGTGTGA 61.855 55.000 17.94 0.00 0.00 3.58
5658 10089 2.277969 TCTCACGCGGTGTTTAAAACA 58.722 42.857 12.47 0.00 39.52 2.83
5659 10090 2.873472 TCTCACGCGGTGTTTAAAACAT 59.127 40.909 12.47 0.00 44.35 2.71
5660 10091 4.056740 TCTCACGCGGTGTTTAAAACATA 58.943 39.130 12.47 0.00 44.35 2.29
5661 10092 4.150980 TCTCACGCGGTGTTTAAAACATAG 59.849 41.667 12.47 0.00 44.35 2.23
5662 10093 4.056740 TCACGCGGTGTTTAAAACATAGA 58.943 39.130 12.47 0.00 44.35 1.98
5676 10107 9.520515 TTTAAAACATAGAGAAGATTCAGGCTT 57.479 29.630 0.00 0.00 0.00 4.35
5693 10124 3.494045 GCTTGTGGATAAGCCTTTGTC 57.506 47.619 0.00 0.00 45.62 3.18
5695 10126 3.119708 GCTTGTGGATAAGCCTTTGTCAG 60.120 47.826 0.00 0.00 45.62 3.51
5696 10127 3.788227 TGTGGATAAGCCTTTGTCAGT 57.212 42.857 0.00 0.00 37.63 3.41
5697 10128 4.098914 TGTGGATAAGCCTTTGTCAGTT 57.901 40.909 0.00 0.00 37.63 3.16
5698 10129 4.469657 TGTGGATAAGCCTTTGTCAGTTT 58.530 39.130 0.00 0.00 37.63 2.66
5763 10605 7.566658 AATATATTAAGCTCTCTGGGAAGCT 57.433 36.000 0.00 0.00 39.55 3.74
5777 10619 0.470341 GAAGCTCCCCTATGTCACCC 59.530 60.000 0.00 0.00 0.00 4.61
5778 10620 0.044855 AAGCTCCCCTATGTCACCCT 59.955 55.000 0.00 0.00 0.00 4.34
5779 10621 0.692419 AGCTCCCCTATGTCACCCTG 60.692 60.000 0.00 0.00 0.00 4.45
5786 10628 2.346803 CCTATGTCACCCTGTGTTTCG 58.653 52.381 0.00 0.00 34.79 3.46
5819 10664 3.666001 AGACGCATTTAACAATTACGCG 58.334 40.909 3.53 3.53 46.14 6.01
5848 10695 1.697982 GTTTCACCGGCCCTAGGATAT 59.302 52.381 11.48 0.00 0.00 1.63
5860 10707 5.442391 GCCCTAGGATATGTGGTTTTGTTA 58.558 41.667 11.48 0.00 0.00 2.41
5924 10771 7.744087 TGACATGTTAGTTTCATATATGGCC 57.256 36.000 12.78 0.00 0.00 5.36
5925 10772 7.286313 TGACATGTTAGTTTCATATATGGCCA 58.714 34.615 8.56 8.56 0.00 5.36
5926 10773 7.944000 TGACATGTTAGTTTCATATATGGCCAT 59.056 33.333 24.45 24.45 0.00 4.40
5927 10774 9.448438 GACATGTTAGTTTCATATATGGCCATA 57.552 33.333 27.36 27.36 0.00 2.74
5928 10775 9.453572 ACATGTTAGTTTCATATATGGCCATAG 57.546 33.333 28.58 16.48 0.00 2.23
5929 10776 9.453572 CATGTTAGTTTCATATATGGCCATAGT 57.546 33.333 28.58 17.76 0.00 2.12
5930 10777 9.672673 ATGTTAGTTTCATATATGGCCATAGTC 57.327 33.333 28.58 13.71 0.00 2.59
5931 10778 7.817478 TGTTAGTTTCATATATGGCCATAGTCG 59.183 37.037 28.58 18.77 0.00 4.18
5932 10779 5.734720 AGTTTCATATATGGCCATAGTCGG 58.265 41.667 28.58 17.93 0.00 4.79
5933 10780 5.483937 AGTTTCATATATGGCCATAGTCGGA 59.516 40.000 28.58 19.66 0.00 4.55
5947 10794 5.416083 CATAGTCGGATAGTCCAAACAACA 58.584 41.667 0.00 0.00 35.91 3.33
5969 10816 4.553330 TTTCTAACGCTCCTCCATTCTT 57.447 40.909 0.00 0.00 0.00 2.52
5971 10818 2.099263 TCTAACGCTCCTCCATTCTTCG 59.901 50.000 0.00 0.00 0.00 3.79
5990 10837 5.691305 TCTTCGCCAAATTTCATGAAAACAG 59.309 36.000 23.91 15.38 33.56 3.16
6016 10863 1.305718 GAGAGAGTGTGGGAGCCCT 60.306 63.158 7.16 0.00 36.94 5.19
6031 10878 2.505819 GAGCCCTGGATCTTTGGTTCTA 59.494 50.000 0.00 0.00 0.00 2.10
6044 10891 6.946340 TCTTTGGTTCTAGCATGAAGATACA 58.054 36.000 0.00 0.00 0.00 2.29
6068 10915 2.203153 AGTTCTTGGCGGCGTTGT 60.203 55.556 9.37 0.00 0.00 3.32
6102 10949 1.149174 CCGGAGTTCCATCCCCATG 59.851 63.158 0.00 0.00 35.82 3.66
6103 10950 1.635817 CCGGAGTTCCATCCCCATGT 61.636 60.000 0.00 0.00 35.82 3.21
6104 10951 0.255890 CGGAGTTCCATCCCCATGTT 59.744 55.000 0.00 0.00 35.82 2.71
6105 10952 1.767759 GGAGTTCCATCCCCATGTTG 58.232 55.000 0.00 0.00 35.64 3.33
6106 10953 1.686115 GGAGTTCCATCCCCATGTTGG 60.686 57.143 0.00 0.00 35.47 3.77
6107 10954 1.284785 GAGTTCCATCCCCATGTTGGA 59.715 52.381 3.87 3.87 40.96 3.53
6108 10955 1.715931 AGTTCCATCCCCATGTTGGAA 59.284 47.619 10.78 10.78 46.08 3.53
6110 10957 3.266477 TTCCATCCCCATGTTGGAAAA 57.734 42.857 11.89 3.57 45.56 2.29
6111 10958 3.266477 TCCATCCCCATGTTGGAAAAA 57.734 42.857 5.40 0.00 40.96 1.94
6112 10959 3.800924 TCCATCCCCATGTTGGAAAAAT 58.199 40.909 5.40 0.00 40.96 1.82
6113 10960 4.952845 TCCATCCCCATGTTGGAAAAATA 58.047 39.130 5.40 0.00 40.96 1.40
6114 10961 5.536951 TCCATCCCCATGTTGGAAAAATAT 58.463 37.500 5.40 0.00 40.96 1.28
6115 10962 5.366186 TCCATCCCCATGTTGGAAAAATATG 59.634 40.000 5.40 0.00 40.96 1.78
6116 10963 5.366186 CCATCCCCATGTTGGAAAAATATGA 59.634 40.000 5.40 0.00 40.96 2.15
6117 10964 6.463331 CCATCCCCATGTTGGAAAAATATGAG 60.463 42.308 5.40 0.00 40.96 2.90
6118 10965 4.405358 TCCCCATGTTGGAAAAATATGAGC 59.595 41.667 0.00 0.00 40.96 4.26
6119 10966 4.161942 CCCCATGTTGGAAAAATATGAGCA 59.838 41.667 0.00 0.00 40.96 4.26
6120 10967 5.338219 CCCCATGTTGGAAAAATATGAGCAA 60.338 40.000 0.00 0.00 40.96 3.91
6121 10968 6.350906 CCCATGTTGGAAAAATATGAGCAAT 58.649 36.000 0.00 0.00 40.96 3.56
6122 10969 6.824704 CCCATGTTGGAAAAATATGAGCAATT 59.175 34.615 0.00 0.00 40.96 2.32
6123 10970 7.337436 CCCATGTTGGAAAAATATGAGCAATTT 59.663 33.333 0.00 0.00 40.96 1.82
6124 10971 9.381033 CCATGTTGGAAAAATATGAGCAATTTA 57.619 29.630 0.00 0.00 40.96 1.40
6126 10973 8.770438 TGTTGGAAAAATATGAGCAATTTACC 57.230 30.769 0.00 0.00 0.00 2.85
6127 10974 8.370940 TGTTGGAAAAATATGAGCAATTTACCA 58.629 29.630 0.00 0.00 34.32 3.25
6128 10975 9.382275 GTTGGAAAAATATGAGCAATTTACCAT 57.618 29.630 0.00 0.00 35.20 3.55
6165 11012 8.421673 AACGGAAATACTAGATAAAGCAAGAC 57.578 34.615 0.00 0.00 0.00 3.01
6166 11013 7.783042 ACGGAAATACTAGATAAAGCAAGACT 58.217 34.615 0.00 0.00 0.00 3.24
6167 11014 8.910944 ACGGAAATACTAGATAAAGCAAGACTA 58.089 33.333 0.00 0.00 0.00 2.59
6168 11015 9.745880 CGGAAATACTAGATAAAGCAAGACTAA 57.254 33.333 0.00 0.00 0.00 2.24
6178 11025 9.323985 AGATAAAGCAAGACTAAAATAGCAGAG 57.676 33.333 0.00 0.00 0.00 3.35
6179 11026 9.319143 GATAAAGCAAGACTAAAATAGCAGAGA 57.681 33.333 0.00 0.00 0.00 3.10
6180 11027 9.844257 ATAAAGCAAGACTAAAATAGCAGAGAT 57.156 29.630 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.307514 CGAAAGGTTTGCAACAGTACAGTATTA 60.308 37.037 0.00 0.00 0.00 0.98
24 25 4.902443 TGTATTTCACGAAAGGTTTGCA 57.098 36.364 0.00 0.00 33.32 4.08
57 58 0.798776 CACGGTCAGACATGCCTTTC 59.201 55.000 2.17 0.00 0.00 2.62
128 1332 7.493320 CGCATCCACTAAAGTACCACTAAATTA 59.507 37.037 0.00 0.00 0.00 1.40
129 1333 6.315393 CGCATCCACTAAAGTACCACTAAATT 59.685 38.462 0.00 0.00 0.00 1.82
130 1334 5.815740 CGCATCCACTAAAGTACCACTAAAT 59.184 40.000 0.00 0.00 0.00 1.40
131 1335 5.172934 CGCATCCACTAAAGTACCACTAAA 58.827 41.667 0.00 0.00 0.00 1.85
132 1336 4.221262 ACGCATCCACTAAAGTACCACTAA 59.779 41.667 0.00 0.00 0.00 2.24
133 1337 3.765511 ACGCATCCACTAAAGTACCACTA 59.234 43.478 0.00 0.00 0.00 2.74
134 1338 2.565834 ACGCATCCACTAAAGTACCACT 59.434 45.455 0.00 0.00 0.00 4.00
135 1339 2.928116 GACGCATCCACTAAAGTACCAC 59.072 50.000 0.00 0.00 0.00 4.16
136 1340 2.093869 GGACGCATCCACTAAAGTACCA 60.094 50.000 0.00 0.00 45.47 3.25
137 1341 2.547826 GGACGCATCCACTAAAGTACC 58.452 52.381 0.00 0.00 45.47 3.34
153 1357 2.223386 CGAGGCTCTTCTCTTTAGGACG 60.223 54.545 13.50 0.00 0.00 4.79
203 1407 2.865551 TCGTTTTACAACCTCGTCAACC 59.134 45.455 0.00 0.00 0.00 3.77
215 1422 6.847289 GCTCTTGTTTTATCGTTCGTTTTACA 59.153 34.615 0.00 0.00 0.00 2.41
257 1464 6.487299 AGTACCTCTGAGAAACTGAGTTTT 57.513 37.500 12.37 2.48 41.11 2.43
272 1479 4.038883 ACAACACGCTCTTTTAGTACCTCT 59.961 41.667 0.00 0.00 0.00 3.69
604 1821 8.903570 ATCGATACGACAGAATATTCTCAATC 57.096 34.615 15.24 11.76 39.18 2.67
605 1822 7.694367 CGATCGATACGACAGAATATTCTCAAT 59.306 37.037 15.24 4.19 39.18 2.57
621 1849 1.728426 GGGCGGTTCGATCGATACG 60.728 63.158 27.26 27.26 0.00 3.06
636 1864 1.745489 GTGAGGATCCACAACGGGC 60.745 63.158 13.92 0.00 37.04 6.13
642 1870 1.607801 CTGCCGAGTGAGGATCCACA 61.608 60.000 15.82 11.78 39.42 4.17
653 1881 4.719369 GGTTCGCGTCTGCCGAGT 62.719 66.667 5.77 0.00 39.56 4.18
661 1889 2.948134 GATCCGACGGTTCGCGTC 60.948 66.667 14.79 4.25 44.43 5.19
766 1994 2.994186 TGGGGCTCTAATAAACGGAC 57.006 50.000 0.00 0.00 0.00 4.79
767 1995 2.105821 CCATGGGGCTCTAATAAACGGA 59.894 50.000 2.85 0.00 0.00 4.69
1189 2430 0.041090 ATCAATCAACCACCCCCACC 59.959 55.000 0.00 0.00 0.00 4.61
1221 2472 2.620112 CCTGCACAAGAAGCCACCG 61.620 63.158 0.00 0.00 0.00 4.94
1234 2489 0.541392 ACGATTCCACATAGCCTGCA 59.459 50.000 0.00 0.00 0.00 4.41
1240 2495 3.159353 TCGTCCAACGATTCCACATAG 57.841 47.619 0.00 0.00 46.73 2.23
1346 2601 3.261897 ACTCCATTCACTGACCTAACAGG 59.738 47.826 0.00 0.00 41.59 4.00
1347 2602 4.543590 ACTCCATTCACTGACCTAACAG 57.456 45.455 0.00 0.00 42.78 3.16
1350 2605 5.560722 TTCAACTCCATTCACTGACCTAA 57.439 39.130 0.00 0.00 0.00 2.69
1354 2609 7.324178 AGTACTATTCAACTCCATTCACTGAC 58.676 38.462 0.00 0.00 0.00 3.51
1381 2636 3.427528 TCGAACGAACGGAAGAAAAGATG 59.572 43.478 0.00 0.00 0.00 2.90
1405 2660 2.316792 CCAGTGTACAGTTCGTCGAAG 58.683 52.381 8.18 0.00 0.00 3.79
1406 2661 1.601162 GCCAGTGTACAGTTCGTCGAA 60.601 52.381 2.90 2.90 0.00 3.71
1407 2662 0.039798 GCCAGTGTACAGTTCGTCGA 60.040 55.000 0.00 0.00 0.00 4.20
1408 2663 0.318360 TGCCAGTGTACAGTTCGTCG 60.318 55.000 0.00 0.00 0.00 5.12
1409 2664 1.269621 ACTGCCAGTGTACAGTTCGTC 60.270 52.381 9.61 0.00 44.59 4.20
1410 2665 0.750850 ACTGCCAGTGTACAGTTCGT 59.249 50.000 9.61 0.00 44.59 3.85
1411 2666 2.596452 CTACTGCCAGTGTACAGTTCG 58.404 52.381 18.08 8.84 44.59 3.95
1498 2757 2.630580 GCCCCAATTAACAGACACCAAA 59.369 45.455 0.00 0.00 0.00 3.28
1641 2900 1.968493 TGTCCCTATCCTGTTATCCGC 59.032 52.381 0.00 0.00 0.00 5.54
1642 2901 2.563179 CCTGTCCCTATCCTGTTATCCG 59.437 54.545 0.00 0.00 0.00 4.18
1671 2930 9.454585 CTAAATGCAATTTACAGTCCATATGTG 57.545 33.333 1.24 0.00 46.47 3.21
1776 3035 7.831193 ACAAATTTGATGGACTACAATAGCTCT 59.169 33.333 24.64 0.00 0.00 4.09
1833 3092 3.441222 CACTTCATGAGCCAAAGCATGTA 59.559 43.478 0.00 0.00 43.56 2.29
1834 3093 2.230508 CACTTCATGAGCCAAAGCATGT 59.769 45.455 0.00 0.00 43.56 3.21
1853 3112 6.039047 ACTGCATAGATCATTTGATTGACCAC 59.961 38.462 0.00 0.00 34.37 4.16
1900 3159 6.985188 TGCTCCATTTTTAGCTACTAGTTG 57.015 37.500 0.00 0.00 39.53 3.16
1905 3164 6.317391 GTCTCAATGCTCCATTTTTAGCTACT 59.683 38.462 0.00 0.00 39.53 2.57
1912 3171 4.828939 TCACAGTCTCAATGCTCCATTTTT 59.171 37.500 0.00 0.00 31.05 1.94
1931 3190 4.949238 AGCAACTTGGCATGTATTATCACA 59.051 37.500 6.44 0.00 35.83 3.58
1957 3216 6.543100 TCTTGTTGATATGACATGCAAGCATA 59.457 34.615 7.29 8.39 35.39 3.14
1985 3244 4.955590 CGATGGATTAATTGTTCGAACACG 59.044 41.667 29.74 20.51 38.92 4.49
2165 3424 9.507329 ACTTGTTCAGATCAAAAGCTAAGATAA 57.493 29.630 0.00 0.00 0.00 1.75
2176 3435 7.336679 TCTTGAAGTGAACTTGTTCAGATCAAA 59.663 33.333 26.10 19.62 36.14 2.69
2182 3441 7.475015 TGAATTCTTGAAGTGAACTTGTTCAG 58.525 34.615 15.44 4.55 36.11 3.02
2183 3442 7.389803 TGAATTCTTGAAGTGAACTTGTTCA 57.610 32.000 11.62 11.62 36.11 3.18
2184 3443 7.380602 CCATGAATTCTTGAAGTGAACTTGTTC 59.619 37.037 19.94 6.56 36.11 3.18
2185 3444 7.205297 CCATGAATTCTTGAAGTGAACTTGTT 58.795 34.615 19.94 0.00 36.11 2.83
2187 3446 6.016024 TCCCATGAATTCTTGAAGTGAACTTG 60.016 38.462 19.94 2.51 36.11 3.16
2188 3447 6.070656 TCCCATGAATTCTTGAAGTGAACTT 58.929 36.000 19.94 0.00 39.23 2.66
2281 3544 5.277825 TCTTTGCAACAACTGGTTAAATCG 58.722 37.500 0.00 0.00 37.72 3.34
2284 3547 4.429108 GCTCTTTGCAACAACTGGTTAAA 58.571 39.130 0.00 0.00 42.31 1.52
2345 3627 5.152623 TGCAGTAGCTCTACAAACTGAAT 57.847 39.130 14.78 0.00 41.47 2.57
2942 4227 5.525378 CACCTGCCAAGATATGAGAACTAAC 59.475 44.000 0.00 0.00 0.00 2.34
3139 4424 7.810260 AGAGGCAGAGATTATTTTTAGATGGT 58.190 34.615 0.00 0.00 0.00 3.55
3178 4463 2.170166 GATTGATGGGCACTCAACCAA 58.830 47.619 3.42 0.00 40.73 3.67
3210 4495 4.285863 TCCACTCAAAGTTTGGATTTGGT 58.714 39.130 15.47 3.38 38.04 3.67
3410 4696 1.462731 AAATGAGCTTGCGTGGCCAA 61.463 50.000 7.24 0.00 0.00 4.52
3455 4741 7.748683 TGATTTTCATGCGTATTACAACAAGTC 59.251 33.333 0.00 0.00 0.00 3.01
3457 4743 7.536964 TGTGATTTTCATGCGTATTACAACAAG 59.463 33.333 0.00 0.00 0.00 3.16
3458 4744 7.363431 TGTGATTTTCATGCGTATTACAACAA 58.637 30.769 0.00 0.00 0.00 2.83
3459 4745 6.903419 TGTGATTTTCATGCGTATTACAACA 58.097 32.000 0.00 0.00 0.00 3.33
3460 4746 7.484641 ACATGTGATTTTCATGCGTATTACAAC 59.515 33.333 0.00 0.00 44.26 3.32
3543 4831 4.969484 ACCCTGACTGTCGAAAGTAAAAT 58.031 39.130 8.61 0.00 0.00 1.82
3795 6168 5.394224 AACAAGTAGCTGACTAAGAGTCC 57.606 43.478 0.00 0.00 44.44 3.85
3869 6242 6.262944 TGGACATATTGAATGGTAGTGCAATC 59.737 38.462 0.00 0.00 33.45 2.67
3939 6312 4.451629 AACTCACGGTATCTGGTAGTTG 57.548 45.455 0.00 0.00 0.00 3.16
4037 6410 9.161684 CAGTATAAAAGGTTAAAAACACACGAC 57.838 33.333 0.00 0.00 0.00 4.34
4087 6460 5.937540 TCACGCACCCTAATAATAATGATGG 59.062 40.000 0.00 0.00 0.00 3.51
4098 6471 3.134623 TGATGAATCTCACGCACCCTAAT 59.865 43.478 0.00 0.00 0.00 1.73
4106 6479 7.293745 CCTAACAATAATGATGAATCTCACGC 58.706 38.462 0.00 0.00 0.00 5.34
4147 6520 1.081892 CTCCCAACTGATGAGCAACG 58.918 55.000 0.00 0.00 0.00 4.10
4157 6530 1.207089 TGTATCGGAAGCTCCCAACTG 59.793 52.381 0.00 0.00 31.13 3.16
4170 6543 6.856895 TCAATCATATCAGCTACTGTATCGG 58.143 40.000 0.00 0.00 32.61 4.18
4213 6586 4.377021 ACTGTGAAGCGAACATTAACAGA 58.623 39.130 9.62 0.00 40.32 3.41
4219 6592 2.987149 CGACTACTGTGAAGCGAACATT 59.013 45.455 0.00 0.00 0.00 2.71
4286 6661 5.147162 GTGTTATCGTTGCAGAAGGAAAAG 58.853 41.667 0.00 0.00 30.07 2.27
4319 6694 9.660180 ATCAGCTTCTAAACTTACCTAAAAGAG 57.340 33.333 0.00 0.00 0.00 2.85
4328 6703 7.316640 TCAGACTCATCAGCTTCTAAACTTAC 58.683 38.462 0.00 0.00 0.00 2.34
4332 6707 6.420604 GCTATCAGACTCATCAGCTTCTAAAC 59.579 42.308 0.00 0.00 0.00 2.01
4335 6710 5.136105 TGCTATCAGACTCATCAGCTTCTA 58.864 41.667 0.00 0.00 0.00 2.10
4348 6723 6.727824 AACACAGTACATTTGCTATCAGAC 57.272 37.500 0.00 0.00 0.00 3.51
4368 6743 2.978156 AAGCCAGGAGGAATGAAACA 57.022 45.000 0.00 0.00 36.89 2.83
4475 6850 5.277683 CCAACAAGAACATGTCAGACTTCAG 60.278 44.000 0.00 0.00 31.81 3.02
4622 6999 6.810911 ACTAGATAGTTGGCATACTTCACTG 58.189 40.000 0.00 1.36 31.13 3.66
4647 7024 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
4648 7025 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4649 7026 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
4650 7027 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
4651 7028 4.040461 ACATCTTATATTGTGGGACGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
4652 7029 5.215252 ACATCTTATATTGTGGGACGGAG 57.785 43.478 0.00 0.00 0.00 4.63
4653 7030 5.623956 AACATCTTATATTGTGGGACGGA 57.376 39.130 0.00 0.00 0.00 4.69
4654 7031 6.693315 AAAACATCTTATATTGTGGGACGG 57.307 37.500 0.00 0.00 0.00 4.79
4655 7032 6.472163 GCAAAAACATCTTATATTGTGGGACG 59.528 38.462 0.00 0.00 0.00 4.79
4656 7033 7.319646 TGCAAAAACATCTTATATTGTGGGAC 58.680 34.615 0.00 0.00 0.00 4.46
4657 7034 7.473735 TGCAAAAACATCTTATATTGTGGGA 57.526 32.000 0.00 0.00 0.00 4.37
4658 7035 6.256321 GCTGCAAAAACATCTTATATTGTGGG 59.744 38.462 0.00 0.00 0.00 4.61
4659 7036 7.037438 AGCTGCAAAAACATCTTATATTGTGG 58.963 34.615 1.02 0.00 0.00 4.17
4660 7037 8.377681 CAAGCTGCAAAAACATCTTATATTGTG 58.622 33.333 1.02 0.00 0.00 3.33
4661 7038 7.063780 GCAAGCTGCAAAAACATCTTATATTGT 59.936 33.333 1.02 0.00 44.26 2.71
4662 7039 7.396419 GCAAGCTGCAAAAACATCTTATATTG 58.604 34.615 1.02 0.00 44.26 1.90
4663 7040 7.529880 GCAAGCTGCAAAAACATCTTATATT 57.470 32.000 1.02 0.00 44.26 1.28
4679 7056 7.063780 ACAATATAAGATGTTTTTGCAAGCTGC 59.936 33.333 0.00 0.00 45.29 5.25
4680 7057 8.377681 CACAATATAAGATGTTTTTGCAAGCTG 58.622 33.333 0.00 0.00 0.00 4.24
4681 7058 7.546667 CCACAATATAAGATGTTTTTGCAAGCT 59.453 33.333 0.00 0.00 0.00 3.74
4682 7059 7.201548 CCCACAATATAAGATGTTTTTGCAAGC 60.202 37.037 0.00 0.00 0.00 4.01
4683 7060 8.034215 TCCCACAATATAAGATGTTTTTGCAAG 58.966 33.333 0.00 0.00 0.00 4.01
4684 7061 7.816995 GTCCCACAATATAAGATGTTTTTGCAA 59.183 33.333 0.00 0.00 0.00 4.08
4725 7102 7.043391 GCACCAAAAAGCTTCTACTGTTTAAAG 60.043 37.037 0.00 0.00 0.00 1.85
4732 7109 2.918131 GCGCACCAAAAAGCTTCTACTG 60.918 50.000 0.30 0.00 0.00 2.74
4733 7110 1.266989 GCGCACCAAAAAGCTTCTACT 59.733 47.619 0.30 0.00 0.00 2.57
4734 7111 1.266989 AGCGCACCAAAAAGCTTCTAC 59.733 47.619 11.47 0.00 36.41 2.59
4735 7112 1.604604 AGCGCACCAAAAAGCTTCTA 58.395 45.000 11.47 0.00 36.41 2.10
4736 7113 1.604604 TAGCGCACCAAAAAGCTTCT 58.395 45.000 11.47 0.00 40.73 2.85
4737 7114 2.319472 CTTAGCGCACCAAAAAGCTTC 58.681 47.619 11.47 0.00 40.73 3.86
4739 7116 0.039165 GCTTAGCGCACCAAAAAGCT 60.039 50.000 11.47 0.00 39.51 3.74
4740 7117 0.039165 AGCTTAGCGCACCAAAAAGC 60.039 50.000 11.47 13.99 42.21 3.51
4741 7118 3.764885 ATAGCTTAGCGCACCAAAAAG 57.235 42.857 11.47 4.28 42.61 2.27
4742 7119 4.258543 AGTATAGCTTAGCGCACCAAAAA 58.741 39.130 11.47 0.00 42.61 1.94
4743 7120 3.869065 AGTATAGCTTAGCGCACCAAAA 58.131 40.909 11.47 0.00 42.61 2.44
4779 7156 3.588569 GGACCCCATGTTAGAGGAGTAT 58.411 50.000 0.00 0.00 0.00 2.12
4780 7157 2.688817 CGGACCCCATGTTAGAGGAGTA 60.689 54.545 0.00 0.00 0.00 2.59
4781 7158 1.880941 GGACCCCATGTTAGAGGAGT 58.119 55.000 0.00 0.00 0.00 3.85
4782 7159 0.753262 CGGACCCCATGTTAGAGGAG 59.247 60.000 0.00 0.00 0.00 3.69
4852 7229 6.309494 CGTTCGATAAGGAACAGAAACACATA 59.691 38.462 6.30 0.00 45.12 2.29
4874 7253 8.301720 TCGGTTGTAAATAGATATGCTATCGTT 58.698 33.333 0.00 0.00 38.88 3.85
4948 7334 1.960689 GTGCAGGGGAAGCTTGTAAAA 59.039 47.619 2.10 0.00 0.00 1.52
5074 7460 1.812571 GCCGAGCCATTTCTTGAGAAA 59.187 47.619 8.48 8.48 46.60 2.52
5240 7649 2.584608 GGTACATCTGCGTGCCCT 59.415 61.111 0.00 0.00 35.77 5.19
5275 7684 5.584649 CACAATGTTCCACACGGTAGATAAT 59.415 40.000 0.00 0.00 0.00 1.28
5303 7712 6.208007 ACATTGTGATATATGCCCATGAAGTG 59.792 38.462 0.00 0.00 0.00 3.16
5354 7763 7.451566 ACAATATTTAACAGAAGTTTCCAGGCT 59.548 33.333 0.00 0.00 39.15 4.58
5370 7779 6.183360 GCCGTCGTTACAGTGACAATATTTAA 60.183 38.462 0.00 0.00 34.78 1.52
5371 7780 5.289193 GCCGTCGTTACAGTGACAATATTTA 59.711 40.000 0.00 0.00 34.78 1.40
5377 7786 0.386476 AGCCGTCGTTACAGTGACAA 59.614 50.000 0.00 0.00 34.78 3.18
5381 7790 2.059575 CGAAGCCGTCGTTACAGTG 58.940 57.895 0.00 0.00 45.09 3.66
5382 7791 4.546637 CGAAGCCGTCGTTACAGT 57.453 55.556 0.00 0.00 45.09 3.55
5399 8626 2.046285 CAGGAAATGGCCGGTGGAC 61.046 63.158 1.90 0.00 0.00 4.02
5410 8637 0.322546 GCAAGGGGACGACAGGAAAT 60.323 55.000 0.00 0.00 0.00 2.17
5413 8640 3.319198 GGCAAGGGGACGACAGGA 61.319 66.667 0.00 0.00 0.00 3.86
5416 8643 2.449967 TAGGAGGCAAGGGGACGACA 62.450 60.000 0.00 0.00 0.00 4.35
5457 9887 1.067060 GCACACAACAAGAGGAAACCC 59.933 52.381 0.00 0.00 0.00 4.11
5482 9912 7.444558 AAAATACAGTAAAACACAAAGCACG 57.555 32.000 0.00 0.00 0.00 5.34
5492 9922 9.141400 TGGACACAAACAAAAATACAGTAAAAC 57.859 29.630 0.00 0.00 0.00 2.43
5508 9938 0.314935 CCACTGCCATGGACACAAAC 59.685 55.000 18.40 0.00 43.02 2.93
5535 9965 4.615541 CGGAGAAACTTATTTTCAAACGGC 59.384 41.667 0.00 0.00 45.50 5.68
5542 9972 5.881777 AGAAGCCGGAGAAACTTATTTTC 57.118 39.130 5.05 0.00 43.67 2.29
5564 9994 2.923426 GATGCTGCGATGACGGGGAA 62.923 60.000 0.00 0.00 40.15 3.97
5581 10011 2.049627 GCCTGGCCATCGGAGAAGAT 62.050 60.000 15.14 0.00 43.58 2.40
5592 10022 2.034532 CACACATCAGCCTGGCCA 59.965 61.111 16.57 4.71 0.00 5.36
5593 10023 1.303561 TTCACACATCAGCCTGGCC 60.304 57.895 16.57 0.00 0.00 5.36
5596 10026 1.300971 CCCGTTCACACATCAGCCTG 61.301 60.000 0.00 0.00 0.00 4.85
5608 10038 3.068881 CAGAGGCTTCCCCGTTCA 58.931 61.111 0.00 0.00 39.21 3.18
5610 10040 4.035102 GGCAGAGGCTTCCCCGTT 62.035 66.667 0.00 0.00 40.87 4.44
5637 10067 2.873472 TGTTTTAAACACCGCGTGAGAT 59.127 40.909 6.41 0.00 36.25 2.75
5641 10072 4.150980 TCTCTATGTTTTAAACACCGCGTG 59.849 41.667 13.01 6.23 45.50 5.34
5658 10089 4.718774 TCCACAAGCCTGAATCTTCTCTAT 59.281 41.667 0.00 0.00 0.00 1.98
5659 10090 4.096681 TCCACAAGCCTGAATCTTCTCTA 58.903 43.478 0.00 0.00 0.00 2.43
5660 10091 2.909006 TCCACAAGCCTGAATCTTCTCT 59.091 45.455 0.00 0.00 0.00 3.10
5661 10092 3.340814 TCCACAAGCCTGAATCTTCTC 57.659 47.619 0.00 0.00 0.00 2.87
5662 10093 5.435291 CTTATCCACAAGCCTGAATCTTCT 58.565 41.667 0.00 0.00 0.00 2.85
5676 10107 3.788227 ACTGACAAAGGCTTATCCACA 57.212 42.857 0.00 0.00 37.29 4.17
5741 10174 5.482175 GGAGCTTCCCAGAGAGCTTAATATA 59.518 44.000 0.00 0.00 37.79 0.86
5747 10589 2.295904 GGAGCTTCCCAGAGAGCTT 58.704 57.895 0.00 0.00 37.79 3.74
5763 10605 0.118346 ACACAGGGTGACATAGGGGA 59.882 55.000 2.98 0.00 36.96 4.81
5777 10619 6.419771 GTCTAAGAAGAAAACCGAAACACAG 58.580 40.000 0.00 0.00 32.16 3.66
5778 10620 5.005971 CGTCTAAGAAGAAAACCGAAACACA 59.994 40.000 0.00 0.00 32.16 3.72
5779 10621 5.429615 CGTCTAAGAAGAAAACCGAAACAC 58.570 41.667 0.00 0.00 32.16 3.32
5786 10628 7.357303 TGTTAAATGCGTCTAAGAAGAAAACC 58.643 34.615 0.00 0.00 32.16 3.27
5816 10661 1.154413 GTGAAACTCATGCCACGCG 60.154 57.895 3.53 3.53 0.00 6.01
5819 10664 1.875963 CCGGTGAAACTCATGCCAC 59.124 57.895 0.00 0.00 36.74 5.01
5820 10665 1.971167 GCCGGTGAAACTCATGCCA 60.971 57.895 1.90 0.00 36.74 4.92
5848 10695 2.747989 TCAACGCACTAACAAAACCACA 59.252 40.909 0.00 0.00 0.00 4.17
5876 10723 2.236146 AGTTTGATGGCACGTATCTCCA 59.764 45.455 0.00 0.00 0.00 3.86
5910 10757 5.730550 TCCGACTATGGCCATATATGAAAC 58.269 41.667 25.62 10.73 0.00 2.78
5919 10766 2.180276 GGACTATCCGACTATGGCCAT 58.820 52.381 24.45 24.45 0.00 4.40
5920 10767 1.133294 TGGACTATCCGACTATGGCCA 60.133 52.381 8.56 8.56 40.17 5.36
5921 10768 1.629043 TGGACTATCCGACTATGGCC 58.371 55.000 0.00 0.00 40.17 5.36
5922 10769 3.181469 TGTTTGGACTATCCGACTATGGC 60.181 47.826 0.00 0.00 40.17 4.40
5923 10770 4.665833 TGTTTGGACTATCCGACTATGG 57.334 45.455 0.00 0.00 40.17 2.74
5924 10771 5.416083 TGTTGTTTGGACTATCCGACTATG 58.584 41.667 0.00 0.00 40.17 2.23
5925 10772 5.670792 TGTTGTTTGGACTATCCGACTAT 57.329 39.130 0.00 0.00 40.17 2.12
5926 10773 5.670792 ATGTTGTTTGGACTATCCGACTA 57.329 39.130 0.00 0.00 40.17 2.59
5927 10774 4.553330 ATGTTGTTTGGACTATCCGACT 57.447 40.909 0.00 0.00 40.17 4.18
5928 10775 5.411669 AGAAATGTTGTTTGGACTATCCGAC 59.588 40.000 0.00 0.00 40.17 4.79
5929 10776 5.556915 AGAAATGTTGTTTGGACTATCCGA 58.443 37.500 0.00 0.00 40.17 4.55
5930 10777 5.880054 AGAAATGTTGTTTGGACTATCCG 57.120 39.130 0.00 0.00 40.17 4.18
5931 10778 7.241376 CGTTAGAAATGTTGTTTGGACTATCC 58.759 38.462 0.00 0.00 36.96 2.59
5932 10779 6.741358 GCGTTAGAAATGTTGTTTGGACTATC 59.259 38.462 0.00 0.00 0.00 2.08
5933 10780 6.430000 AGCGTTAGAAATGTTGTTTGGACTAT 59.570 34.615 0.00 0.00 0.00 2.12
5947 10794 4.762289 AGAATGGAGGAGCGTTAGAAAT 57.238 40.909 0.00 0.00 0.00 2.17
5969 10816 5.009510 TCTCTGTTTTCATGAAATTTGGCGA 59.990 36.000 21.10 10.97 0.00 5.54
5971 10818 5.406477 GGTCTCTGTTTTCATGAAATTTGGC 59.594 40.000 21.10 11.20 0.00 4.52
5990 10837 0.523966 CCACACTCTCTCGTGGTCTC 59.476 60.000 0.00 0.00 46.31 3.36
6016 10863 4.842531 TCATGCTAGAACCAAAGATCCA 57.157 40.909 0.00 0.00 0.00 3.41
6031 10878 4.551671 ACTCCTACCTGTATCTTCATGCT 58.448 43.478 0.00 0.00 0.00 3.79
6044 10891 1.900545 GCCGCCAAGAACTCCTACCT 61.901 60.000 0.00 0.00 0.00 3.08
6068 10915 1.562008 TCCGGCAACATTATTCCTCCA 59.438 47.619 0.00 0.00 0.00 3.86
6102 10949 8.770438 TGGTAAATTGCTCATATTTTTCCAAC 57.230 30.769 0.00 0.00 31.43 3.77
6139 10986 9.525409 GTCTTGCTTTATCTAGTATTTCCGTTA 57.475 33.333 0.00 0.00 0.00 3.18
6140 10987 8.258708 AGTCTTGCTTTATCTAGTATTTCCGTT 58.741 33.333 0.00 0.00 0.00 4.44
6141 10988 7.783042 AGTCTTGCTTTATCTAGTATTTCCGT 58.217 34.615 0.00 0.00 0.00 4.69
6142 10989 9.745880 TTAGTCTTGCTTTATCTAGTATTTCCG 57.254 33.333 0.00 0.00 0.00 4.30
6152 10999 9.323985 CTCTGCTATTTTAGTCTTGCTTTATCT 57.676 33.333 0.00 0.00 0.00 1.98
6153 11000 9.319143 TCTCTGCTATTTTAGTCTTGCTTTATC 57.681 33.333 0.00 0.00 0.00 1.75
6154 11001 9.844257 ATCTCTGCTATTTTAGTCTTGCTTTAT 57.156 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.