Multiple sequence alignment - TraesCS4A01G257600

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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 TraesCS4A01G257600 chr4A 100.000 5482 0 0 1 5482 570460424 570465905 0.000000e+00 10124.0
1 TraesCS4A01G257600 chr4D 93.757 4741 164 57 158 4832 32242534 32237860 0.000000e+00 6994.0
2 TraesCS4A01G257600 chr4D 79.227 414 49 17 5064 5455 32237677 32237279 2.530000e-63 254.0
3 TraesCS4A01G257600 chr4D 91.781 73 4 2 4868 4938 32237766 32237694 3.490000e-17 100.0
4 TraesCS4A01G257600 chr4B 93.356 3748 121 51 127 3802 46628309 46624618 0.000000e+00 5424.0
5 TraesCS4A01G257600 chr4B 89.283 1493 69 36 3871 5310 46624449 46622995 0.000000e+00 1786.0
6 TraesCS4A01G257600 chr4B 87.500 112 4 4 5351 5452 46622016 46621905 2.680000e-23 121.0
7 TraesCS4A01G257600 chr7B 97.917 48 0 1 3413 3459 162120855 162120808 1.270000e-11 82.4
8 TraesCS4A01G257600 chr7A 92.727 55 4 0 3401 3455 206943094 206943148 4.550000e-11 80.5
9 TraesCS4A01G257600 chr6D 100.000 43 0 0 3413 3455 128910425 128910383 4.550000e-11 80.5
10 TraesCS4A01G257600 chr6D 100.000 43 0 0 3413 3455 157930449 157930407 4.550000e-11 80.5
11 TraesCS4A01G257600 chr3D 100.000 43 0 0 3413 3455 609983851 609983809 4.550000e-11 80.5
12 TraesCS4A01G257600 chr1D 100.000 43 0 0 3413 3455 343363396 343363438 4.550000e-11 80.5
13 TraesCS4A01G257600 chr1A 100.000 43 0 0 3413 3455 496440027 496439985 4.550000e-11 80.5


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 TraesCS4A01G257600 chr4A 570460424 570465905 5481 False 10124.000000 10124 100.000000 1 5482 1 chr4A.!!$F1 5481
1 TraesCS4A01G257600 chr4D 32237279 32242534 5255 True 2449.333333 6994 88.255000 158 5455 3 chr4D.!!$R1 5297
2 TraesCS4A01G257600 chr4B 46621905 46628309 6404 True 2443.666667 5424 90.046333 127 5452 3 chr4B.!!$R1 5325

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
909 938 0.034059 GATTGATCATCCGGCGGACT 59.966 55.000 33.71 19.17 32.98 3.85 F
916 945 0.673985 CATCCGGCGGACTGAATCTA 59.326 55.000 33.71 5.54 32.98 1.98 F
1864 1902 1.129251 GCACACATCACTGGATCAACG 59.871 52.381 0.00 0.00 0.00 4.10 F
3056 3128 0.038709 AGCTGACGACTGAGCTTGTC 60.039 55.000 9.82 9.82 43.15 3.18 F
3068 3140 0.380733 AGCTTGTCGCATCATGCATG 59.619 50.000 21.07 21.07 45.36 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2416 2458 0.179116 CTCCGCAGAGACCACATCTG 60.179 60.000 0.00 0.0 45.71 2.90 R
2720 2792 1.147817 AGAACTTGGGAGGCCACAATT 59.852 47.619 5.01 0.0 0.00 2.32 R
3066 3138 0.700564 TTCTTTCAGGCTCAGGGCAT 59.299 50.000 0.00 0.0 44.01 4.40 R
4222 4421 0.108472 CAGCTCGATGAAGTCCTGCA 60.108 55.000 0.00 0.0 0.00 4.41 R
4865 5092 0.250793 ACCGTATCCAAATCCGCACA 59.749 50.000 0.00 0.0 0.00 4.57 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
24 25 7.582435 CGAAACTAGAGAGCAGATGTTTTAA 57.418 36.000 0.00 0.00 0.00 1.52
25 26 8.018677 CGAAACTAGAGAGCAGATGTTTTAAA 57.981 34.615 0.00 0.00 0.00 1.52
26 27 8.495949 CGAAACTAGAGAGCAGATGTTTTAAAA 58.504 33.333 0.00 0.00 0.00 1.52
27 28 9.600646 GAAACTAGAGAGCAGATGTTTTAAAAC 57.399 33.333 21.66 21.66 39.33 2.43
43 44 9.720769 TGTTTTAAAACATGTTTTTCACCCTAA 57.279 25.926 34.51 20.95 43.45 2.69
69 70 8.911247 AAAATGTGTTTTTCTTGTCTGTAGTC 57.089 30.769 0.00 0.00 33.89 2.59
70 71 6.619801 ATGTGTTTTTCTTGTCTGTAGTCC 57.380 37.500 0.00 0.00 0.00 3.85
71 72 5.492895 TGTGTTTTTCTTGTCTGTAGTCCA 58.507 37.500 0.00 0.00 0.00 4.02
72 73 5.584649 TGTGTTTTTCTTGTCTGTAGTCCAG 59.415 40.000 0.00 0.00 42.97 3.86
84 85 6.235231 TCTGTAGTCCAGACTTTTTGAACT 57.765 37.500 5.49 0.00 45.34 3.01
85 86 6.281405 TCTGTAGTCCAGACTTTTTGAACTC 58.719 40.000 5.49 0.00 45.34 3.01
86 87 5.365619 TGTAGTCCAGACTTTTTGAACTCC 58.634 41.667 5.49 0.00 42.54 3.85
87 88 4.779993 AGTCCAGACTTTTTGAACTCCT 57.220 40.909 0.00 0.00 38.83 3.69
88 89 4.709250 AGTCCAGACTTTTTGAACTCCTC 58.291 43.478 0.00 0.00 38.83 3.71
89 90 4.410555 AGTCCAGACTTTTTGAACTCCTCT 59.589 41.667 0.00 0.00 38.83 3.69
90 91 5.104318 AGTCCAGACTTTTTGAACTCCTCTT 60.104 40.000 0.00 0.00 38.83 2.85
91 92 5.008118 GTCCAGACTTTTTGAACTCCTCTTG 59.992 44.000 0.00 0.00 0.00 3.02
92 93 4.261363 CCAGACTTTTTGAACTCCTCTTGC 60.261 45.833 0.00 0.00 0.00 4.01
93 94 4.578105 CAGACTTTTTGAACTCCTCTTGCT 59.422 41.667 0.00 0.00 0.00 3.91
94 95 5.067023 CAGACTTTTTGAACTCCTCTTGCTT 59.933 40.000 0.00 0.00 0.00 3.91
95 96 5.654209 AGACTTTTTGAACTCCTCTTGCTTT 59.346 36.000 0.00 0.00 0.00 3.51
96 97 6.153510 AGACTTTTTGAACTCCTCTTGCTTTT 59.846 34.615 0.00 0.00 0.00 2.27
97 98 6.101997 ACTTTTTGAACTCCTCTTGCTTTTG 58.898 36.000 0.00 0.00 0.00 2.44
98 99 5.913137 TTTTGAACTCCTCTTGCTTTTGA 57.087 34.783 0.00 0.00 0.00 2.69
99 100 5.505173 TTTGAACTCCTCTTGCTTTTGAG 57.495 39.130 0.00 0.00 0.00 3.02
100 101 2.880890 TGAACTCCTCTTGCTTTTGAGC 59.119 45.455 0.00 0.00 0.00 4.26
101 102 2.645838 ACTCCTCTTGCTTTTGAGCA 57.354 45.000 0.00 0.00 43.81 4.26
111 112 2.877043 CTTTTGAGCAAAGCACACCT 57.123 45.000 0.00 0.00 35.66 4.00
112 113 3.169355 CTTTTGAGCAAAGCACACCTT 57.831 42.857 0.00 0.00 35.66 3.50
113 114 3.524541 CTTTTGAGCAAAGCACACCTTT 58.475 40.909 0.00 0.00 44.45 3.11
114 115 3.608316 TTTGAGCAAAGCACACCTTTT 57.392 38.095 0.00 0.00 41.75 2.27
115 116 3.608316 TTGAGCAAAGCACACCTTTTT 57.392 38.095 0.00 0.00 41.75 1.94
138 139 1.002033 CAGACAAGAGCAAAGCACACC 60.002 52.381 0.00 0.00 0.00 4.16
198 200 0.183731 CCCAAGGTAGAAGATGGGCC 59.816 60.000 0.00 0.00 45.56 5.80
213 215 2.207580 GGCCGGCCCATTAAAATGT 58.792 52.632 36.64 0.00 34.60 2.71
215 217 0.534873 GCCGGCCCATTAAAATGTGT 59.465 50.000 18.11 0.00 34.60 3.72
220 222 3.181497 CGGCCCATTAAAATGTGTCTCTG 60.181 47.826 0.00 0.00 34.60 3.35
244 246 2.298158 ATCAGACGTGACGGGCCATC 62.298 60.000 10.66 0.00 34.75 3.51
312 318 1.354368 GAAGAAACCACCATCCCCTCA 59.646 52.381 0.00 0.00 0.00 3.86
340 346 2.937799 ACTAAAACGACGCCAAGAAACA 59.062 40.909 0.00 0.00 0.00 2.83
343 349 2.182904 AACGACGCCAAGAAACAAAC 57.817 45.000 0.00 0.00 0.00 2.93
344 350 0.379316 ACGACGCCAAGAAACAAACC 59.621 50.000 0.00 0.00 0.00 3.27
346 352 1.202200 CGACGCCAAGAAACAAACCAA 60.202 47.619 0.00 0.00 0.00 3.67
347 353 2.732597 CGACGCCAAGAAACAAACCAAA 60.733 45.455 0.00 0.00 0.00 3.28
348 354 2.857748 GACGCCAAGAAACAAACCAAAG 59.142 45.455 0.00 0.00 0.00 2.77
349 355 2.494073 ACGCCAAGAAACAAACCAAAGA 59.506 40.909 0.00 0.00 0.00 2.52
350 356 2.857748 CGCCAAGAAACAAACCAAAGAC 59.142 45.455 0.00 0.00 0.00 3.01
645 651 0.095245 CGCGCGTGTCATCTCAATTT 59.905 50.000 24.19 0.00 0.00 1.82
713 742 1.414158 CTCCGGGCCTCTTGATTAGA 58.586 55.000 0.84 0.00 0.00 2.10
727 756 4.913335 TGATTAGACGCCGTATCTCTTT 57.087 40.909 0.00 0.00 0.00 2.52
784 813 4.275689 AGTGTGTCATTTCGCATCTCAAAA 59.724 37.500 0.00 0.00 0.00 2.44
789 818 5.412286 TGTCATTTCGCATCTCAAAAGATCA 59.588 36.000 0.00 0.00 40.38 2.92
799 828 6.749118 GCATCTCAAAAGATCACATTTGGTAC 59.251 38.462 14.69 0.00 40.38 3.34
810 839 4.332543 TCACATTTGGTACTGATTGATCGC 59.667 41.667 0.00 0.00 0.00 4.58
812 841 4.333649 ACATTTGGTACTGATTGATCGCAG 59.666 41.667 8.09 8.09 38.10 5.18
834 863 1.617850 TCAAAATGCAATCCGCCAAGT 59.382 42.857 0.00 0.00 41.33 3.16
897 926 4.024438 CGAACGTGCAGAATTGATTGATC 58.976 43.478 0.00 0.00 0.00 2.92
899 928 5.571784 AACGTGCAGAATTGATTGATCAT 57.428 34.783 0.00 0.00 36.56 2.45
900 929 5.165911 ACGTGCAGAATTGATTGATCATC 57.834 39.130 0.00 0.00 36.56 2.92
902 931 4.534168 GTGCAGAATTGATTGATCATCCG 58.466 43.478 0.00 0.00 36.56 4.18
903 932 3.566742 TGCAGAATTGATTGATCATCCGG 59.433 43.478 0.00 0.00 36.56 5.14
905 934 2.810274 AGAATTGATTGATCATCCGGCG 59.190 45.455 0.00 0.00 36.56 6.46
908 937 0.249868 TGATTGATCATCCGGCGGAC 60.250 55.000 33.71 19.29 32.98 4.79
909 938 0.034059 GATTGATCATCCGGCGGACT 59.966 55.000 33.71 19.17 32.98 3.85
912 941 1.326951 TGATCATCCGGCGGACTGAA 61.327 55.000 33.71 17.05 32.98 3.02
913 942 0.034059 GATCATCCGGCGGACTGAAT 59.966 55.000 33.71 21.05 32.98 2.57
916 945 0.673985 CATCCGGCGGACTGAATCTA 59.326 55.000 33.71 5.54 32.98 1.98
1308 1345 5.298777 GTCAAATTCCATCTCCCTCTGATTG 59.701 44.000 0.00 0.00 0.00 2.67
1312 1349 7.398289 AATTCCATCTCCCTCTGATTGATTA 57.602 36.000 0.00 0.00 0.00 1.75
1314 1351 6.179906 TCCATCTCCCTCTGATTGATTAAC 57.820 41.667 0.00 0.00 0.00 2.01
1340 1377 4.404073 ACCACCATTGTTTGCTTGTTTCTA 59.596 37.500 0.00 0.00 0.00 2.10
1346 1383 7.224557 ACCATTGTTTGCTTGTTTCTATGTTTC 59.775 33.333 0.00 0.00 0.00 2.78
1370 1407 7.535139 TCTTTTACTTACAATTACATGCTGCC 58.465 34.615 0.00 0.00 0.00 4.85
1380 1417 1.292223 CATGCTGCCTGCTTGCTTT 59.708 52.632 0.00 0.00 43.37 3.51
1571 1608 7.218963 GCAAGTAAGCTGCATCTTTATTTGTAC 59.781 37.037 8.30 0.00 0.00 2.90
1572 1609 7.321745 AGTAAGCTGCATCTTTATTTGTACC 57.678 36.000 8.30 0.00 0.00 3.34
1573 1610 5.582689 AAGCTGCATCTTTATTTGTACCC 57.417 39.130 1.02 0.00 0.00 3.69
1574 1611 3.627577 AGCTGCATCTTTATTTGTACCCG 59.372 43.478 1.02 0.00 0.00 5.28
1578 1615 5.432645 TGCATCTTTATTTGTACCCGATCA 58.567 37.500 0.00 0.00 0.00 2.92
1718 1756 3.042682 TCCAAGTAAGACCTGTCCACAA 58.957 45.455 0.00 0.00 0.00 3.33
1720 1758 4.841813 TCCAAGTAAGACCTGTCCACAATA 59.158 41.667 0.00 0.00 0.00 1.90
1721 1759 5.487488 TCCAAGTAAGACCTGTCCACAATAT 59.513 40.000 0.00 0.00 0.00 1.28
1722 1760 6.670464 TCCAAGTAAGACCTGTCCACAATATA 59.330 38.462 0.00 0.00 0.00 0.86
1864 1902 1.129251 GCACACATCACTGGATCAACG 59.871 52.381 0.00 0.00 0.00 4.10
2005 2043 6.368243 CACATCAGATGATCTATCGAAAAGGG 59.632 42.308 17.81 0.00 40.86 3.95
2257 2295 3.243035 CCGTTCAAATTCAGCTTGACACA 60.243 43.478 0.00 0.00 32.61 3.72
2416 2458 1.726853 ACATGCGGTCTAGCTTGAAC 58.273 50.000 2.80 2.80 42.63 3.18
2537 2579 3.596214 GAGGCTCAAAAGGTCATCGTTA 58.404 45.455 10.25 0.00 0.00 3.18
2637 2705 5.973651 TGTCTGAACGATTTCTATGCATC 57.026 39.130 0.19 0.00 32.36 3.91
2670 2738 3.778954 ATAAATCTAGTCCTGCTGCCC 57.221 47.619 0.00 0.00 0.00 5.36
2849 2921 2.216898 CAGATCTGGCTCCGGAAAATC 58.783 52.381 15.38 4.45 34.70 2.17
2969 3041 1.004440 AAACCTGAGAGGCGCACTC 60.004 57.895 21.36 21.36 46.98 3.51
3056 3128 0.038709 AGCTGACGACTGAGCTTGTC 60.039 55.000 9.82 9.82 43.15 3.18
3066 3138 0.674269 TGAGCTTGTCGCATCATGCA 60.674 50.000 11.00 0.00 45.36 3.96
3068 3140 0.380733 AGCTTGTCGCATCATGCATG 59.619 50.000 21.07 21.07 45.36 4.06
3099 3178 5.776744 CCTGAAAGAAAGAATCCCTTGTTG 58.223 41.667 0.00 0.00 34.07 3.33
3133 3212 1.136147 CGTGAGAGTCGTAACGGGG 59.864 63.158 7.22 0.00 32.55 5.73
3391 3470 0.539438 TGCCAAAGCAGGTAGGTTGG 60.539 55.000 0.00 0.00 46.52 3.77
3392 3471 0.539669 GCCAAAGCAGGTAGGTTGGT 60.540 55.000 3.96 0.00 38.12 3.67
3393 3472 1.995376 CCAAAGCAGGTAGGTTGGTT 58.005 50.000 0.00 0.00 38.12 3.67
3394 3473 2.316108 CCAAAGCAGGTAGGTTGGTTT 58.684 47.619 0.00 0.00 44.41 3.27
3395 3474 2.296190 CCAAAGCAGGTAGGTTGGTTTC 59.704 50.000 0.01 0.00 42.44 2.78
3396 3475 3.222603 CAAAGCAGGTAGGTTGGTTTCT 58.777 45.455 0.01 0.00 42.44 2.52
3397 3476 4.394729 CAAAGCAGGTAGGTTGGTTTCTA 58.605 43.478 0.01 0.00 42.44 2.10
3398 3477 3.983044 AGCAGGTAGGTTGGTTTCTAG 57.017 47.619 0.00 0.00 0.00 2.43
3399 3478 2.572104 AGCAGGTAGGTTGGTTTCTAGG 59.428 50.000 0.00 0.00 0.00 3.02
3400 3479 2.305052 GCAGGTAGGTTGGTTTCTAGGT 59.695 50.000 0.00 0.00 0.00 3.08
3401 3480 3.244805 GCAGGTAGGTTGGTTTCTAGGTT 60.245 47.826 0.00 0.00 0.00 3.50
3402 3481 4.576879 CAGGTAGGTTGGTTTCTAGGTTC 58.423 47.826 0.00 0.00 0.00 3.62
3403 3482 4.286291 CAGGTAGGTTGGTTTCTAGGTTCT 59.714 45.833 0.00 0.00 0.00 3.01
3404 3483 5.482878 CAGGTAGGTTGGTTTCTAGGTTCTA 59.517 44.000 0.00 0.00 0.00 2.10
3405 3484 5.720520 AGGTAGGTTGGTTTCTAGGTTCTAG 59.279 44.000 0.00 0.00 0.00 2.43
3406 3485 4.554960 AGGTTGGTTTCTAGGTTCTAGC 57.445 45.455 0.00 0.00 0.00 3.42
3407 3486 4.168883 AGGTTGGTTTCTAGGTTCTAGCT 58.831 43.478 0.00 0.00 0.00 3.32
3408 3487 5.339477 AGGTTGGTTTCTAGGTTCTAGCTA 58.661 41.667 0.00 0.00 0.00 3.32
3409 3488 5.422650 AGGTTGGTTTCTAGGTTCTAGCTAG 59.577 44.000 15.01 15.01 45.14 3.42
3410 3489 5.187381 GGTTGGTTTCTAGGTTCTAGCTAGT 59.813 44.000 20.10 3.77 44.37 2.57
3411 3490 5.916661 TGGTTTCTAGGTTCTAGCTAGTG 57.083 43.478 20.10 0.00 44.37 2.74
3454 3533 3.780850 ACTTATTTTGGATCGGAGGGAGT 59.219 43.478 0.00 0.00 0.00 3.85
3455 3534 4.227527 ACTTATTTTGGATCGGAGGGAGTT 59.772 41.667 0.00 0.00 0.00 3.01
3490 3569 8.650143 AACTAACTGATGATGGGTTTGTTAAT 57.350 30.769 0.00 0.00 37.23 1.40
3501 3580 4.872691 TGGGTTTGTTAATTGTGTGCTTTG 59.127 37.500 0.00 0.00 0.00 2.77
3528 3607 2.126346 GCATGGCAGGCAACGTTC 60.126 61.111 20.53 0.00 46.39 3.95
3747 3826 2.280457 GCGCCTCTCATACTGCCC 60.280 66.667 0.00 0.00 0.00 5.36
3802 3881 3.128349 GTGTACCGCAACCAGGTATATG 58.872 50.000 0.00 0.00 44.96 1.78
3804 3883 0.544223 ACCGCAACCAGGTATATGCA 59.456 50.000 14.00 0.00 40.80 3.96
3808 3969 2.031769 CGCAACCAGGTATATGCACATG 60.032 50.000 14.00 0.00 38.69 3.21
3826 3987 8.054152 TGCACATGTGTTAATAACTTGATCAT 57.946 30.769 26.01 0.28 0.00 2.45
3827 3988 8.183536 TGCACATGTGTTAATAACTTGATCATC 58.816 33.333 26.01 4.32 0.00 2.92
3846 4044 1.912731 TCCATCCATGAAAGGAACGGA 59.087 47.619 0.00 0.00 41.92 4.69
3859 4057 5.438761 AAGGAACGGACAATTTTCTTCTG 57.561 39.130 0.00 0.00 0.00 3.02
3860 4058 4.714632 AGGAACGGACAATTTTCTTCTGA 58.285 39.130 0.00 0.00 0.00 3.27
4068 4266 3.430929 GCACCATCCTCTTCAACGAGTAT 60.431 47.826 0.00 0.00 0.00 2.12
4130 4328 3.805108 GCCCAGGTCTCATCATCATACAC 60.805 52.174 0.00 0.00 0.00 2.90
4131 4329 3.389002 CCCAGGTCTCATCATCATACACA 59.611 47.826 0.00 0.00 0.00 3.72
4133 4331 4.141869 CCAGGTCTCATCATCATACACACA 60.142 45.833 0.00 0.00 0.00 3.72
4134 4332 5.454329 CCAGGTCTCATCATCATACACACAT 60.454 44.000 0.00 0.00 0.00 3.21
4138 4336 6.422100 GGTCTCATCATCATACACACATACAC 59.578 42.308 0.00 0.00 0.00 2.90
4143 4341 8.420222 TCATCATCATACACACATACACACATA 58.580 33.333 0.00 0.00 0.00 2.29
4151 4349 7.307493 ACACACATACACACATACATTCATC 57.693 36.000 0.00 0.00 0.00 2.92
4163 4362 6.484308 CACATACATTCATCCATAGCACTTCA 59.516 38.462 0.00 0.00 0.00 3.02
4180 4379 5.173854 GCACTTCATTTCCTCTTTGAAAACG 59.826 40.000 0.00 0.00 37.74 3.60
4191 4390 6.035542 TCCTCTTTGAAAACGAAATGCAAAAC 59.964 34.615 0.00 0.00 0.00 2.43
4195 4394 7.542477 TCTTTGAAAACGAAATGCAAAACTGTA 59.458 29.630 0.00 0.00 0.00 2.74
4213 4412 0.955178 TAAATGTTGGGCGTGTGTGG 59.045 50.000 0.00 0.00 0.00 4.17
4214 4413 1.040339 AAATGTTGGGCGTGTGTGGT 61.040 50.000 0.00 0.00 0.00 4.16
4215 4414 1.733402 AATGTTGGGCGTGTGTGGTG 61.733 55.000 0.00 0.00 0.00 4.17
4216 4415 2.826738 GTTGGGCGTGTGTGGTGT 60.827 61.111 0.00 0.00 0.00 4.16
4217 4416 2.515057 TTGGGCGTGTGTGGTGTC 60.515 61.111 0.00 0.00 0.00 3.67
4218 4417 4.555709 TGGGCGTGTGTGGTGTCC 62.556 66.667 0.00 0.00 0.00 4.02
4222 4421 2.664851 CGTGTGTGGTGTCCGCAT 60.665 61.111 5.34 0.00 46.11 4.73
4367 4566 2.040464 ATCATGGAGGACCCGGCT 60.040 61.111 0.00 0.00 37.93 5.52
4651 4852 3.437049 GGAGCTAACTAACTGGCTTGTTG 59.563 47.826 6.69 1.33 35.01 3.33
4751 4957 4.933400 TGGCTTACGATTTCACCTTCTTAC 59.067 41.667 0.00 0.00 0.00 2.34
4753 4959 4.860907 GCTTACGATTTCACCTTCTTACGA 59.139 41.667 0.00 0.00 0.00 3.43
4755 4961 6.035758 GCTTACGATTTCACCTTCTTACGATT 59.964 38.462 0.00 0.00 0.00 3.34
4756 4962 7.412672 GCTTACGATTTCACCTTCTTACGATTT 60.413 37.037 0.00 0.00 0.00 2.17
4804 5031 6.038356 TCGTCGATTAAGTATTTCCACTTCC 58.962 40.000 0.00 0.00 39.45 3.46
4832 5059 5.042463 TCGCAAATATAGGGATGAAACCA 57.958 39.130 0.00 0.00 0.00 3.67
4833 5060 4.819630 TCGCAAATATAGGGATGAAACCAC 59.180 41.667 0.00 0.00 0.00 4.16
4835 5062 5.299279 CGCAAATATAGGGATGAAACCACTT 59.701 40.000 0.00 0.00 0.00 3.16
4836 5063 6.513393 CGCAAATATAGGGATGAAACCACTTC 60.513 42.308 0.00 0.00 34.31 3.01
4849 5076 7.397892 TGAAACCACTTCAAGTAATCACAAA 57.602 32.000 0.00 0.00 41.21 2.83
4855 5082 8.879759 ACCACTTCAAGTAATCACAAATATACG 58.120 33.333 0.00 0.00 0.00 3.06
4856 5083 8.335356 CCACTTCAAGTAATCACAAATATACGG 58.665 37.037 0.00 0.00 0.00 4.02
4857 5084 9.093970 CACTTCAAGTAATCACAAATATACGGA 57.906 33.333 0.00 0.00 0.00 4.69
4858 5085 9.832445 ACTTCAAGTAATCACAAATATACGGAT 57.168 29.630 0.00 0.00 0.00 4.18
4861 5088 9.825109 TCAAGTAATCACAAATATACGGATGAA 57.175 29.630 0.00 0.00 0.00 2.57
4864 5091 9.052759 AGTAATCACAAATATACGGATGAAACC 57.947 33.333 0.00 0.00 0.00 3.27
4865 5092 9.052759 GTAATCACAAATATACGGATGAAACCT 57.947 33.333 0.00 0.00 0.00 3.50
4866 5093 6.918892 TCACAAATATACGGATGAAACCTG 57.081 37.500 0.00 0.00 0.00 4.00
4926 5213 2.262423 AACAGCCTCAAGTCAGAACC 57.738 50.000 0.00 0.00 0.00 3.62
4962 5249 4.752604 TGCATACACGGCGAACATATTATT 59.247 37.500 16.62 0.00 0.00 1.40
4997 5284 2.226262 CACAACTTAACCGATGTGCG 57.774 50.000 0.00 0.00 37.03 5.34
5001 5288 1.448985 ACTTAACCGATGTGCGCAAT 58.551 45.000 14.00 8.37 39.11 3.56
5010 5299 3.283256 CGATGTGCGCAATTACATCTTC 58.717 45.455 26.46 14.30 46.82 2.87
5018 5307 4.728882 GCGCAATTACATCTTCCAAGACAG 60.729 45.833 0.30 0.00 37.98 3.51
5021 5310 4.851639 ATTACATCTTCCAAGACAGCCT 57.148 40.909 0.00 0.00 37.98 4.58
5035 5324 7.047891 CCAAGACAGCCTTTATGTACAGAATA 58.952 38.462 3.34 0.00 31.42 1.75
5041 5330 5.815740 AGCCTTTATGTACAGAATACAACCG 59.184 40.000 3.34 0.00 0.00 4.44
5151 5441 3.782889 ACATAGGAAGCAAAAATCCGC 57.217 42.857 0.00 0.00 40.78 5.54
5154 5444 2.438868 AGGAAGCAAAAATCCGCAAC 57.561 45.000 0.00 0.00 40.78 4.17
5323 5635 6.341316 AGCATATACCATATCTTAGCAACCG 58.659 40.000 0.00 0.00 0.00 4.44
5324 5636 5.523916 GCATATACCATATCTTAGCAACCGG 59.476 44.000 0.00 0.00 0.00 5.28
5326 5638 3.470645 ACCATATCTTAGCAACCGGTC 57.529 47.619 8.04 0.00 0.00 4.79
5327 5639 3.039011 ACCATATCTTAGCAACCGGTCT 58.961 45.455 8.04 3.81 0.00 3.85
5329 5641 4.652421 ACCATATCTTAGCAACCGGTCTAA 59.348 41.667 8.04 11.64 0.00 2.10
5332 5644 4.820894 ATCTTAGCAACCGGTCTAAGTT 57.179 40.909 28.75 22.46 41.36 2.66
5333 5645 4.612264 TCTTAGCAACCGGTCTAAGTTT 57.388 40.909 28.75 5.10 41.36 2.66
5335 5647 1.792006 AGCAACCGGTCTAAGTTTCG 58.208 50.000 8.04 0.00 0.00 3.46
5338 5650 2.064014 CAACCGGTCTAAGTTTCGGAC 58.936 52.381 8.04 4.82 44.69 4.79
5340 5652 0.457337 CCGGTCTAAGTTTCGGACGG 60.457 60.000 0.00 0.00 44.69 4.79
5341 5653 0.523072 CGGTCTAAGTTTCGGACGGA 59.477 55.000 0.00 0.00 33.94 4.69
5342 5654 1.467035 CGGTCTAAGTTTCGGACGGAG 60.467 57.143 0.00 0.00 33.94 4.63
5421 6673 6.662865 TTTCAGGCAGAAATTAACCATTCA 57.337 33.333 0.44 0.00 41.17 2.57
5422 6674 5.643379 TCAGGCAGAAATTAACCATTCAC 57.357 39.130 0.00 0.00 0.00 3.18
5467 6728 2.256117 GCATCCCGCCAAGTAATACT 57.744 50.000 0.00 0.00 32.94 2.12
5468 6729 2.143925 GCATCCCGCCAAGTAATACTC 58.856 52.381 0.00 0.00 32.94 2.59
5469 6730 2.484770 GCATCCCGCCAAGTAATACTCA 60.485 50.000 0.00 0.00 32.94 3.41
5470 6731 2.973694 TCCCGCCAAGTAATACTCAC 57.026 50.000 0.00 0.00 0.00 3.51
5471 6732 1.135527 TCCCGCCAAGTAATACTCACG 59.864 52.381 0.00 0.00 0.00 4.35
5472 6733 1.567504 CCGCCAAGTAATACTCACGG 58.432 55.000 12.19 12.19 33.62 4.94
5473 6734 1.134907 CCGCCAAGTAATACTCACGGT 60.135 52.381 15.94 0.00 34.89 4.83
5474 6735 2.190981 CGCCAAGTAATACTCACGGTC 58.809 52.381 0.00 0.00 0.00 4.79
5475 6736 2.416296 CGCCAAGTAATACTCACGGTCA 60.416 50.000 0.00 0.00 0.00 4.02
5476 6737 2.928116 GCCAAGTAATACTCACGGTCAC 59.072 50.000 0.00 0.00 0.00 3.67
5478 6739 3.176708 CAAGTAATACTCACGGTCACGG 58.823 50.000 0.00 0.00 46.48 4.94
5479 6740 1.133790 AGTAATACTCACGGTCACGGC 59.866 52.381 0.00 0.00 46.48 5.68
5480 6741 1.133790 GTAATACTCACGGTCACGGCT 59.866 52.381 0.00 0.00 46.48 5.52
5481 6742 1.466856 AATACTCACGGTCACGGCTA 58.533 50.000 0.00 0.00 46.48 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.582435 TTAAAACATCTGCTCTCTAGTTTCG 57.418 36.000 0.00 0.00 0.00 3.46
1 2 9.600646 GTTTTAAAACATCTGCTCTCTAGTTTC 57.399 33.333 23.12 0.00 38.74 2.78
2 3 9.120538 TGTTTTAAAACATCTGCTCTCTAGTTT 57.879 29.630 26.05 0.00 43.45 2.66
3 4 8.677148 TGTTTTAAAACATCTGCTCTCTAGTT 57.323 30.769 26.05 0.00 43.45 2.24
44 45 7.973944 GGACTACAGACAAGAAAAACACATTTT 59.026 33.333 0.00 0.00 43.85 1.82
45 46 7.122055 TGGACTACAGACAAGAAAAACACATTT 59.878 33.333 0.00 0.00 0.00 2.32
46 47 6.601613 TGGACTACAGACAAGAAAAACACATT 59.398 34.615 0.00 0.00 0.00 2.71
47 48 6.119536 TGGACTACAGACAAGAAAAACACAT 58.880 36.000 0.00 0.00 0.00 3.21
48 49 5.492895 TGGACTACAGACAAGAAAAACACA 58.507 37.500 0.00 0.00 0.00 3.72
63 64 5.130477 AGGAGTTCAAAAAGTCTGGACTACA 59.870 40.000 3.54 0.00 41.58 2.74
64 65 5.612351 AGGAGTTCAAAAAGTCTGGACTAC 58.388 41.667 3.54 0.00 41.58 2.73
65 66 5.602978 AGAGGAGTTCAAAAAGTCTGGACTA 59.397 40.000 3.54 0.00 41.58 2.59
66 67 4.410555 AGAGGAGTTCAAAAAGTCTGGACT 59.589 41.667 0.00 0.00 44.94 3.85
67 68 4.709250 AGAGGAGTTCAAAAAGTCTGGAC 58.291 43.478 0.00 0.00 35.51 4.02
68 69 5.126067 CAAGAGGAGTTCAAAAAGTCTGGA 58.874 41.667 0.00 0.00 35.51 3.86
69 70 4.261363 GCAAGAGGAGTTCAAAAAGTCTGG 60.261 45.833 0.00 0.00 35.51 3.86
70 71 4.578105 AGCAAGAGGAGTTCAAAAAGTCTG 59.422 41.667 0.00 0.00 35.51 3.51
71 72 4.786425 AGCAAGAGGAGTTCAAAAAGTCT 58.214 39.130 0.00 0.00 35.51 3.24
72 73 5.506686 AAGCAAGAGGAGTTCAAAAAGTC 57.493 39.130 0.00 0.00 34.59 3.01
73 74 5.921962 AAAGCAAGAGGAGTTCAAAAAGT 57.078 34.783 0.00 0.00 0.00 2.66
74 75 6.332630 TCAAAAGCAAGAGGAGTTCAAAAAG 58.667 36.000 0.00 0.00 0.00 2.27
75 76 6.279513 TCAAAAGCAAGAGGAGTTCAAAAA 57.720 33.333 0.00 0.00 0.00 1.94
76 77 5.894807 CTCAAAAGCAAGAGGAGTTCAAAA 58.105 37.500 0.00 0.00 0.00 2.44
77 78 5.505173 CTCAAAAGCAAGAGGAGTTCAAA 57.495 39.130 0.00 0.00 0.00 2.69
92 93 2.877043 AGGTGTGCTTTGCTCAAAAG 57.123 45.000 0.00 0.00 46.90 2.27
93 94 3.608316 AAAGGTGTGCTTTGCTCAAAA 57.392 38.095 0.00 0.00 33.88 2.44
94 95 3.608316 AAAAGGTGTGCTTTGCTCAAA 57.392 38.095 0.00 0.00 33.88 2.69
95 96 3.608316 AAAAAGGTGTGCTTTGCTCAA 57.392 38.095 0.00 0.00 33.88 3.02
113 114 4.082300 TGTGCTTTGCTCTTGTCTGAAAAA 60.082 37.500 0.00 0.00 0.00 1.94
114 115 3.443329 TGTGCTTTGCTCTTGTCTGAAAA 59.557 39.130 0.00 0.00 0.00 2.29
115 116 3.016031 TGTGCTTTGCTCTTGTCTGAAA 58.984 40.909 0.00 0.00 0.00 2.69
116 117 2.355756 GTGTGCTTTGCTCTTGTCTGAA 59.644 45.455 0.00 0.00 0.00 3.02
117 118 1.942657 GTGTGCTTTGCTCTTGTCTGA 59.057 47.619 0.00 0.00 0.00 3.27
118 119 1.002033 GGTGTGCTTTGCTCTTGTCTG 60.002 52.381 0.00 0.00 0.00 3.51
119 120 1.133976 AGGTGTGCTTTGCTCTTGTCT 60.134 47.619 0.00 0.00 0.00 3.41
120 121 1.002033 CAGGTGTGCTTTGCTCTTGTC 60.002 52.381 0.00 0.00 0.00 3.18
121 122 1.027357 CAGGTGTGCTTTGCTCTTGT 58.973 50.000 0.00 0.00 0.00 3.16
122 123 1.027357 ACAGGTGTGCTTTGCTCTTG 58.973 50.000 0.00 0.00 0.00 3.02
123 124 1.027357 CACAGGTGTGCTTTGCTCTT 58.973 50.000 0.00 0.00 39.39 2.85
124 125 0.820891 CCACAGGTGTGCTTTGCTCT 60.821 55.000 4.48 0.00 44.34 4.09
125 126 0.819259 TCCACAGGTGTGCTTTGCTC 60.819 55.000 4.48 0.00 44.34 4.26
198 200 3.016736 AGAGACACATTTTAATGGGCCG 58.983 45.455 4.66 0.00 43.63 6.13
213 215 0.813821 CGTCTGATCCAGCAGAGACA 59.186 55.000 8.75 0.00 44.92 3.41
215 217 0.813821 CACGTCTGATCCAGCAGAGA 59.186 55.000 0.00 0.00 44.92 3.10
220 222 1.517257 CCGTCACGTCTGATCCAGC 60.517 63.158 0.00 0.00 0.00 4.85
283 289 1.606224 GGTGGTTTCTTCGCGTCCTAA 60.606 52.381 5.77 0.00 0.00 2.69
284 290 0.037975 GGTGGTTTCTTCGCGTCCTA 60.038 55.000 5.77 0.00 0.00 2.94
285 291 1.301479 GGTGGTTTCTTCGCGTCCT 60.301 57.895 5.77 0.00 0.00 3.85
286 292 0.953960 ATGGTGGTTTCTTCGCGTCC 60.954 55.000 5.77 1.30 0.00 4.79
321 327 4.097012 GTTTGTTTCTTGGCGTCGTTTTA 58.903 39.130 0.00 0.00 0.00 1.52
340 346 2.719354 GCGTGGCGTCTTTGGTTT 59.281 55.556 0.00 0.00 0.00 3.27
706 732 4.607955 CAAAGAGATACGGCGTCTAATCA 58.392 43.478 19.21 0.00 0.00 2.57
713 742 1.665679 CAATGCAAAGAGATACGGCGT 59.334 47.619 19.64 19.64 0.00 5.68
784 813 6.481313 CGATCAATCAGTACCAAATGTGATCT 59.519 38.462 14.65 0.00 38.52 2.75
789 818 4.260985 TGCGATCAATCAGTACCAAATGT 58.739 39.130 0.00 0.00 0.00 2.71
799 828 4.675565 GCATTTTGATCTGCGATCAATCAG 59.324 41.667 24.42 19.13 37.79 2.90
834 863 6.238566 GCATGCATCTTAAGAATTCTGCTGTA 60.239 38.462 22.73 10.54 0.00 2.74
897 926 0.673985 TAGATTCAGTCCGCCGGATG 59.326 55.000 10.04 9.15 32.73 3.51
899 928 1.187974 TTTAGATTCAGTCCGCCGGA 58.812 50.000 5.05 0.00 0.00 5.14
900 929 1.867233 CATTTAGATTCAGTCCGCCGG 59.133 52.381 0.00 0.00 0.00 6.13
902 931 5.066505 ACATTTCATTTAGATTCAGTCCGCC 59.933 40.000 0.00 0.00 0.00 6.13
903 932 6.124088 ACATTTCATTTAGATTCAGTCCGC 57.876 37.500 0.00 0.00 0.00 5.54
905 934 7.008628 CGCAAACATTTCATTTAGATTCAGTCC 59.991 37.037 0.00 0.00 0.00 3.85
908 937 7.660059 CACGCAAACATTTCATTTAGATTCAG 58.340 34.615 0.00 0.00 0.00 3.02
909 938 6.089283 GCACGCAAACATTTCATTTAGATTCA 59.911 34.615 0.00 0.00 0.00 2.57
912 941 4.558470 CGCACGCAAACATTTCATTTAGAT 59.442 37.500 0.00 0.00 0.00 1.98
913 942 3.911365 CGCACGCAAACATTTCATTTAGA 59.089 39.130 0.00 0.00 0.00 2.10
916 945 2.218302 CACGCACGCAAACATTTCATTT 59.782 40.909 0.00 0.00 0.00 2.32
1144 1181 1.205893 GGAGAAGTAGTCCACCTGCTG 59.794 57.143 0.00 0.00 36.13 4.41
1266 1303 0.107945 ACCTGAAGATGAAGAGGCGC 60.108 55.000 0.00 0.00 0.00 6.53
1308 1345 4.384547 GCAAACAATGGTGGTTCGTTAATC 59.615 41.667 0.00 0.00 29.90 1.75
1312 1349 1.754226 AGCAAACAATGGTGGTTCGTT 59.246 42.857 0.00 0.00 38.62 3.85
1314 1351 2.126467 CAAGCAAACAATGGTGGTTCG 58.874 47.619 1.49 0.00 40.33 3.95
1346 1383 7.485913 CAGGCAGCATGTAATTGTAAGTAAAAG 59.514 37.037 0.00 0.00 39.31 2.27
1370 1407 0.580104 GCAACAAGCAAAGCAAGCAG 59.420 50.000 0.00 0.00 44.79 4.24
1380 1417 1.855213 GCATCAGTCCGCAACAAGCA 61.855 55.000 0.00 0.00 46.13 3.91
1571 1608 4.100707 TCAGTAACTAAACGTGATCGGG 57.899 45.455 0.00 0.00 41.85 5.14
1572 1609 6.309494 TGAATTCAGTAACTAAACGTGATCGG 59.691 38.462 3.38 0.00 41.85 4.18
1573 1610 7.273188 TGAATTCAGTAACTAAACGTGATCG 57.727 36.000 3.38 0.00 43.34 3.69
1683 1721 8.722394 GGTCTTACTTGGAAAAGAAGAATACAG 58.278 37.037 0.00 0.00 33.70 2.74
1786 1824 7.933033 TGCAACATGAAGATGTATAATCAGCTA 59.067 33.333 0.00 0.00 42.30 3.32
2005 2043 6.503524 TCTTACCACAAAATTCTGCAACTTC 58.496 36.000 0.00 0.00 0.00 3.01
2305 2347 7.830099 AAACAGAGTTTGAGGAAATGATCTT 57.170 32.000 0.00 0.00 0.00 2.40
2416 2458 0.179116 CTCCGCAGAGACCACATCTG 60.179 60.000 0.00 0.00 45.71 2.90
2568 2610 4.808364 TGCTGGTCAAAACTTTAAACATGC 59.192 37.500 0.00 0.00 0.00 4.06
2637 2705 9.320295 AGGACTAGATTTATTTATGAGGAGAGG 57.680 37.037 0.00 0.00 0.00 3.69
2664 2732 3.368571 GCAGTCCTGTTGGGCAGC 61.369 66.667 0.00 0.00 42.97 5.25
2670 2738 1.601759 CACCTGGGCAGTCCTGTTG 60.602 63.158 0.00 0.00 36.20 3.33
2720 2792 1.147817 AGAACTTGGGAGGCCACAATT 59.852 47.619 5.01 0.00 0.00 2.32
3010 3082 5.784177 TGCAAACCTGTTAACAAAGTGAAA 58.216 33.333 10.03 0.00 0.00 2.69
3066 3138 0.700564 TTCTTTCAGGCTCAGGGCAT 59.299 50.000 0.00 0.00 44.01 4.40
3068 3140 1.172175 CTTTCTTTCAGGCTCAGGGC 58.828 55.000 0.00 0.00 40.90 5.19
3069 3141 2.867109 TCTTTCTTTCAGGCTCAGGG 57.133 50.000 0.00 0.00 0.00 4.45
3070 3142 3.693578 GGATTCTTTCTTTCAGGCTCAGG 59.306 47.826 0.00 0.00 0.00 3.86
3071 3143 3.693578 GGGATTCTTTCTTTCAGGCTCAG 59.306 47.826 0.00 0.00 0.00 3.35
3072 3144 3.331889 AGGGATTCTTTCTTTCAGGCTCA 59.668 43.478 0.00 0.00 0.00 4.26
3133 3212 3.001406 ACCACGCTGGGGAGGTAC 61.001 66.667 8.89 0.00 43.37 3.34
3391 3470 4.403113 AGGCACTAGCTAGAACCTAGAAAC 59.597 45.833 27.26 8.05 41.70 2.78
3392 3471 4.611367 AGGCACTAGCTAGAACCTAGAAA 58.389 43.478 27.26 0.00 41.70 2.52
3393 3472 4.252570 AGGCACTAGCTAGAACCTAGAA 57.747 45.455 27.26 0.00 41.70 2.10
3394 3473 3.955524 AGGCACTAGCTAGAACCTAGA 57.044 47.619 27.26 0.00 41.70 2.43
3395 3474 5.134661 ACTAAGGCACTAGCTAGAACCTAG 58.865 45.833 28.07 24.98 38.49 3.02
3396 3475 5.126699 ACTAAGGCACTAGCTAGAACCTA 57.873 43.478 28.07 18.92 38.49 3.08
3397 3476 3.983821 ACTAAGGCACTAGCTAGAACCT 58.016 45.455 27.45 25.78 38.49 3.50
3398 3477 4.159879 TGAACTAAGGCACTAGCTAGAACC 59.840 45.833 27.45 24.15 38.49 3.62
3399 3478 5.326200 TGAACTAAGGCACTAGCTAGAAC 57.674 43.478 27.45 16.95 38.49 3.01
3400 3479 5.995565 TTGAACTAAGGCACTAGCTAGAA 57.004 39.130 27.45 3.47 38.49 2.10
3401 3480 5.995565 TTTGAACTAAGGCACTAGCTAGA 57.004 39.130 27.45 2.47 38.49 2.43
3402 3481 6.091441 CAGTTTTGAACTAAGGCACTAGCTAG 59.909 42.308 19.44 19.44 40.46 3.42
3403 3482 5.932303 CAGTTTTGAACTAAGGCACTAGCTA 59.068 40.000 0.00 0.00 40.46 3.32
3404 3483 4.757149 CAGTTTTGAACTAAGGCACTAGCT 59.243 41.667 0.00 0.00 40.46 3.32
3405 3484 4.613850 GCAGTTTTGAACTAAGGCACTAGC 60.614 45.833 0.00 0.00 40.46 3.42
3406 3485 4.377431 CGCAGTTTTGAACTAAGGCACTAG 60.377 45.833 0.00 0.00 40.46 2.57
3407 3486 3.496884 CGCAGTTTTGAACTAAGGCACTA 59.503 43.478 0.00 0.00 40.46 2.74
3408 3487 2.290641 CGCAGTTTTGAACTAAGGCACT 59.709 45.455 0.00 0.00 40.46 4.40
3409 3488 2.289547 TCGCAGTTTTGAACTAAGGCAC 59.710 45.455 0.00 0.00 40.46 5.01
3410 3489 2.289547 GTCGCAGTTTTGAACTAAGGCA 59.710 45.455 0.00 0.00 40.46 4.75
3411 3490 2.289547 TGTCGCAGTTTTGAACTAAGGC 59.710 45.455 0.00 0.00 40.46 4.35
3455 3534 8.651389 CCCATCATCAGTTAGTTAATCCTTAGA 58.349 37.037 0.00 0.00 0.00 2.10
3490 3569 2.158986 CCCATCCAAACAAAGCACACAA 60.159 45.455 0.00 0.00 0.00 3.33
3501 3580 1.518774 CTGCCATGCCCATCCAAAC 59.481 57.895 0.00 0.00 0.00 2.93
3528 3607 2.492088 TGTGAGGACGTAGGTCATGAAG 59.508 50.000 16.80 0.00 45.28 3.02
3747 3826 3.120511 GGCAAAAGTAGACGAGCAAGAAG 60.121 47.826 0.00 0.00 0.00 2.85
3802 3881 7.645340 GGATGATCAAGTTATTAACACATGTGC 59.355 37.037 25.68 7.49 0.00 4.57
3804 3883 8.806429 TGGATGATCAAGTTATTAACACATGT 57.194 30.769 0.00 0.00 0.00 3.21
3808 3969 8.450578 TGGATGGATGATCAAGTTATTAACAC 57.549 34.615 0.00 0.00 31.91 3.32
3826 3987 1.912731 TCCGTTCCTTTCATGGATGGA 59.087 47.619 4.45 4.45 38.14 3.41
3827 3988 2.017049 GTCCGTTCCTTTCATGGATGG 58.983 52.381 0.00 0.00 35.83 3.51
3846 4044 5.992829 TGCATGCATTTCAGAAGAAAATTGT 59.007 32.000 18.46 0.00 46.06 2.71
3990 4188 0.169009 GCGCCTTCTTGATGGTGAAC 59.831 55.000 16.88 0.85 36.02 3.18
4068 4266 3.052082 GAGAAGCGCTGCCTGCAA 61.052 61.111 12.58 0.00 43.06 4.08
4130 4328 6.923928 TGGATGAATGTATGTGTGTATGTG 57.076 37.500 0.00 0.00 0.00 3.21
4131 4329 7.388776 GCTATGGATGAATGTATGTGTGTATGT 59.611 37.037 0.00 0.00 0.00 2.29
4133 4331 7.388776 GTGCTATGGATGAATGTATGTGTGTAT 59.611 37.037 0.00 0.00 0.00 2.29
4134 4332 6.705825 GTGCTATGGATGAATGTATGTGTGTA 59.294 38.462 0.00 0.00 0.00 2.90
4138 4336 6.484308 TGAAGTGCTATGGATGAATGTATGTG 59.516 38.462 0.00 0.00 0.00 3.21
4143 4341 6.040166 GGAAATGAAGTGCTATGGATGAATGT 59.960 38.462 0.00 0.00 0.00 2.71
4151 4349 5.649395 TCAAAGAGGAAATGAAGTGCTATGG 59.351 40.000 0.00 0.00 0.00 2.74
4163 4362 6.279882 TGCATTTCGTTTTCAAAGAGGAAAT 58.720 32.000 7.66 7.66 36.71 2.17
4180 4379 6.657888 CCCAACATTTACAGTTTTGCATTTC 58.342 36.000 0.00 0.00 0.00 2.17
4191 4390 1.606668 ACACACGCCCAACATTTACAG 59.393 47.619 0.00 0.00 0.00 2.74
4195 4394 1.040339 ACCACACACGCCCAACATTT 61.040 50.000 0.00 0.00 0.00 2.32
4216 4415 0.462581 GATGAAGTCCTGCATGCGGA 60.463 55.000 28.32 24.72 0.00 5.54
4217 4416 1.769098 CGATGAAGTCCTGCATGCGG 61.769 60.000 20.13 20.13 0.00 5.69
4218 4417 0.807275 TCGATGAAGTCCTGCATGCG 60.807 55.000 14.09 7.87 0.00 4.73
4219 4418 0.935898 CTCGATGAAGTCCTGCATGC 59.064 55.000 11.82 11.82 0.00 4.06
4220 4419 0.935898 GCTCGATGAAGTCCTGCATG 59.064 55.000 0.00 0.00 0.00 4.06
4221 4420 0.829333 AGCTCGATGAAGTCCTGCAT 59.171 50.000 0.00 0.00 0.00 3.96
4222 4421 0.108472 CAGCTCGATGAAGTCCTGCA 60.108 55.000 0.00 0.00 0.00 4.41
4367 4566 2.636412 CGAGTTGGACGCCTCCTGA 61.636 63.158 3.30 0.00 37.48 3.86
4485 4684 0.312102 AAAGAGAGCCAAAACGCAGC 59.688 50.000 0.00 0.00 0.00 5.25
4486 4685 2.781945 AAAAGAGAGCCAAAACGCAG 57.218 45.000 0.00 0.00 0.00 5.18
4543 4743 2.219445 CGAGATTCATCGACCGTACGTA 59.781 50.000 15.21 0.00 45.56 3.57
4544 4744 1.004185 CGAGATTCATCGACCGTACGT 60.004 52.381 15.21 2.02 45.56 3.57
4545 4745 1.259770 TCGAGATTCATCGACCGTACG 59.740 52.381 8.69 8.69 46.20 3.67
4651 4852 7.309867 CCTGTACCTACAACATACATAGGATCC 60.310 44.444 2.48 2.48 38.20 3.36
4696 4902 5.376854 AATTAATCTGCACAGTTGACACC 57.623 39.130 0.00 0.00 0.00 4.16
4697 4903 6.371548 TCCTAATTAATCTGCACAGTTGACAC 59.628 38.462 0.00 0.00 0.00 3.67
4698 4904 6.472016 TCCTAATTAATCTGCACAGTTGACA 58.528 36.000 0.00 0.00 0.00 3.58
4699 4905 6.985188 TCCTAATTAATCTGCACAGTTGAC 57.015 37.500 0.00 0.00 0.00 3.18
4701 4907 7.383102 AGTTCCTAATTAATCTGCACAGTTG 57.617 36.000 0.00 0.00 0.00 3.16
4751 4957 4.488126 ACAAATGTGTCAGGTGAAATCG 57.512 40.909 0.00 0.00 29.49 3.34
4753 4959 5.529430 TCGTTACAAATGTGTCAGGTGAAAT 59.471 36.000 0.00 0.00 39.30 2.17
4755 4961 4.443621 TCGTTACAAATGTGTCAGGTGAA 58.556 39.130 0.00 0.00 39.30 3.18
4756 4962 4.055360 CTCGTTACAAATGTGTCAGGTGA 58.945 43.478 0.00 0.00 39.30 4.02
4804 5031 7.905604 TTCATCCCTATATTTGCGATTACTG 57.094 36.000 0.00 0.00 0.00 2.74
4832 5059 9.832445 ATCCGTATATTTGTGATTACTTGAAGT 57.168 29.630 2.37 2.37 0.00 3.01
4835 5062 9.825109 TTCATCCGTATATTTGTGATTACTTGA 57.175 29.630 0.00 0.00 0.00 3.02
4839 5066 9.052759 AGGTTTCATCCGTATATTTGTGATTAC 57.947 33.333 0.00 0.00 0.00 1.89
4841 5068 7.556275 ACAGGTTTCATCCGTATATTTGTGATT 59.444 33.333 0.00 0.00 0.00 2.57
4842 5069 7.012327 CACAGGTTTCATCCGTATATTTGTGAT 59.988 37.037 0.00 0.00 34.54 3.06
4843 5070 6.315144 CACAGGTTTCATCCGTATATTTGTGA 59.685 38.462 0.00 0.00 34.54 3.58
4844 5071 6.486248 CACAGGTTTCATCCGTATATTTGTG 58.514 40.000 0.00 0.00 0.00 3.33
4845 5072 5.065988 GCACAGGTTTCATCCGTATATTTGT 59.934 40.000 0.00 0.00 0.00 2.83
4846 5073 5.510671 GCACAGGTTTCATCCGTATATTTG 58.489 41.667 0.00 0.00 0.00 2.32
4847 5074 4.272504 CGCACAGGTTTCATCCGTATATTT 59.727 41.667 0.00 0.00 0.00 1.40
4848 5075 3.807622 CGCACAGGTTTCATCCGTATATT 59.192 43.478 0.00 0.00 0.00 1.28
4849 5076 3.390135 CGCACAGGTTTCATCCGTATAT 58.610 45.455 0.00 0.00 0.00 0.86
4852 5079 0.390603 CCGCACAGGTTTCATCCGTA 60.391 55.000 0.00 0.00 34.51 4.02
4853 5080 1.671054 CCGCACAGGTTTCATCCGT 60.671 57.895 0.00 0.00 34.51 4.69
4854 5081 0.744414 ATCCGCACAGGTTTCATCCG 60.744 55.000 0.00 0.00 41.99 4.18
4855 5082 1.463674 AATCCGCACAGGTTTCATCC 58.536 50.000 0.00 0.00 41.99 3.51
4856 5083 2.415893 CCAAATCCGCACAGGTTTCATC 60.416 50.000 0.00 0.00 41.99 2.92
4857 5084 1.545582 CCAAATCCGCACAGGTTTCAT 59.454 47.619 0.00 0.00 41.99 2.57
4858 5085 0.958091 CCAAATCCGCACAGGTTTCA 59.042 50.000 0.00 0.00 41.99 2.69
4859 5086 1.243902 TCCAAATCCGCACAGGTTTC 58.756 50.000 0.00 0.00 41.99 2.78
4861 5088 2.365582 GTATCCAAATCCGCACAGGTT 58.634 47.619 0.00 0.00 41.99 3.50
4862 5089 1.742411 CGTATCCAAATCCGCACAGGT 60.742 52.381 0.00 0.00 41.99 4.00
4863 5090 0.937304 CGTATCCAAATCCGCACAGG 59.063 55.000 0.00 0.00 42.97 4.00
4864 5091 0.937304 CCGTATCCAAATCCGCACAG 59.063 55.000 0.00 0.00 0.00 3.66
4865 5092 0.250793 ACCGTATCCAAATCCGCACA 59.749 50.000 0.00 0.00 0.00 4.57
4866 5093 1.375551 AACCGTATCCAAATCCGCAC 58.624 50.000 0.00 0.00 0.00 5.34
4967 5254 4.180817 GGTTAAGTTGTGCTGCAGTTTTT 58.819 39.130 16.64 4.66 0.00 1.94
4996 5283 4.728882 GCTGTCTTGGAAGATGTAATTGCG 60.729 45.833 0.00 0.00 37.39 4.85
4997 5284 4.439289 GGCTGTCTTGGAAGATGTAATTGC 60.439 45.833 0.00 0.00 37.39 3.56
5001 5288 4.640771 AAGGCTGTCTTGGAAGATGTAA 57.359 40.909 0.00 0.00 37.39 2.41
5010 5299 4.832248 TCTGTACATAAAGGCTGTCTTGG 58.168 43.478 0.00 0.00 35.55 3.61
5018 5307 5.007332 CCGGTTGTATTCTGTACATAAAGGC 59.993 44.000 0.00 0.00 0.00 4.35
5021 5310 6.465948 ACACCGGTTGTATTCTGTACATAAA 58.534 36.000 2.97 0.00 36.32 1.40
5035 5324 9.452287 AAATATGTTAACTTATACACCGGTTGT 57.548 29.630 2.97 9.80 42.84 3.32
5081 5370 8.704234 GTGCATAAGTATTACTACTTGCTCATC 58.296 37.037 14.06 2.81 45.61 2.92
5151 5441 5.500610 GCACATGCTTGTTAGTGTTTTGTTG 60.501 40.000 1.83 0.00 38.21 3.33
5154 5444 4.697300 GCACATGCTTGTTAGTGTTTTG 57.303 40.909 1.83 0.00 38.21 2.44
5307 5619 3.753294 AGACCGGTTGCTAAGATATGG 57.247 47.619 9.42 0.00 0.00 2.74
5309 5621 6.481434 AACTTAGACCGGTTGCTAAGATAT 57.519 37.500 33.50 21.97 43.88 1.63
5314 5626 3.319755 CGAAACTTAGACCGGTTGCTAA 58.680 45.455 9.42 12.08 0.00 3.09
5317 5629 0.794473 CCGAAACTTAGACCGGTTGC 59.206 55.000 9.42 0.00 37.40 4.17
5319 5631 1.336240 CGTCCGAAACTTAGACCGGTT 60.336 52.381 9.42 0.87 42.34 4.44
5321 5633 0.457337 CCGTCCGAAACTTAGACCGG 60.457 60.000 0.00 0.00 43.02 5.28
5322 5634 0.523072 TCCGTCCGAAACTTAGACCG 59.477 55.000 0.00 0.00 0.00 4.79
5323 5635 1.543358 ACTCCGTCCGAAACTTAGACC 59.457 52.381 0.00 0.00 0.00 3.85
5324 5636 2.030451 ACACTCCGTCCGAAACTTAGAC 60.030 50.000 0.00 0.00 0.00 2.59
5326 5638 2.719426 ACACTCCGTCCGAAACTTAG 57.281 50.000 0.00 0.00 0.00 2.18
5327 5639 4.789012 AATACACTCCGTCCGAAACTTA 57.211 40.909 0.00 0.00 0.00 2.24
5329 5641 3.672767 AAATACACTCCGTCCGAAACT 57.327 42.857 0.00 0.00 0.00 2.66
5332 5644 4.400251 ACATCTAAATACACTCCGTCCGAA 59.600 41.667 0.00 0.00 0.00 4.30
5333 5645 3.949754 ACATCTAAATACACTCCGTCCGA 59.050 43.478 0.00 0.00 0.00 4.55
5335 5647 4.098960 TGGACATCTAAATACACTCCGTCC 59.901 45.833 0.00 0.00 40.63 4.79
5338 5650 6.986817 AGATTTGGACATCTAAATACACTCCG 59.013 38.462 3.48 0.00 37.20 4.63
5340 5652 9.606631 AAGAGATTTGGACATCTAAATACACTC 57.393 33.333 3.48 6.52 37.20 3.51
5341 5653 9.388506 CAAGAGATTTGGACATCTAAATACACT 57.611 33.333 3.48 0.00 37.20 3.55
5342 5654 8.125448 GCAAGAGATTTGGACATCTAAATACAC 58.875 37.037 3.48 0.21 37.20 2.90
5346 5658 6.660521 TGTGCAAGAGATTTGGACATCTAAAT 59.339 34.615 9.66 3.14 43.96 1.40
5348 5660 5.559770 TGTGCAAGAGATTTGGACATCTAA 58.440 37.500 9.66 0.00 43.96 2.10
5414 6666 2.289444 CCGTGAGTACTTGGTGAATGGT 60.289 50.000 0.00 0.00 0.00 3.55
5417 6669 1.671850 CGCCGTGAGTACTTGGTGAAT 60.672 52.381 14.68 0.00 33.86 2.57
5418 6670 0.319211 CGCCGTGAGTACTTGGTGAA 60.319 55.000 14.68 0.00 33.86 3.18
5419 6671 1.287815 CGCCGTGAGTACTTGGTGA 59.712 57.895 14.68 0.00 33.86 4.02
5421 6673 2.654877 CCGCCGTGAGTACTTGGT 59.345 61.111 0.00 0.00 0.00 3.67
5422 6674 2.125673 CCCGCCGTGAGTACTTGG 60.126 66.667 0.00 0.81 0.00 3.61
5455 6716 2.928116 GTGACCGTGAGTATTACTTGGC 59.072 50.000 0.00 0.00 0.00 4.52
5456 6717 3.176708 CGTGACCGTGAGTATTACTTGG 58.823 50.000 0.00 3.88 0.00 3.61
5457 6718 3.176708 CCGTGACCGTGAGTATTACTTG 58.823 50.000 0.00 0.00 0.00 3.16
5458 6719 2.416431 GCCGTGACCGTGAGTATTACTT 60.416 50.000 0.00 0.00 0.00 2.24
5459 6720 1.133790 GCCGTGACCGTGAGTATTACT 59.866 52.381 0.00 0.00 0.00 2.24
5460 6721 1.133790 AGCCGTGACCGTGAGTATTAC 59.866 52.381 0.00 0.00 0.00 1.89
5461 6722 1.466856 AGCCGTGACCGTGAGTATTA 58.533 50.000 0.00 0.00 0.00 0.98
5462 6723 1.466856 TAGCCGTGACCGTGAGTATT 58.533 50.000 0.00 0.00 0.00 1.89
5463 6724 3.179925 TAGCCGTGACCGTGAGTAT 57.820 52.632 0.00 0.00 0.00 2.12
5464 6725 4.720127 TAGCCGTGACCGTGAGTA 57.280 55.556 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.