Multiple sequence alignment - TraesCS4B01G084700

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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 TraesCS4B01G084700 chr4B 100.000 7850 0 0 1 7850 83059776 83051927 0.000000e+00 14497.0
1 TraesCS4B01G084700 chr4D 91.378 2366 152 22 5501 7850 56027153 56024824 0.000000e+00 3192.0
2 TraesCS4B01G084700 chr4D 95.472 1789 75 3 1 1789 56031083 56029301 0.000000e+00 2850.0
3 TraesCS4B01G084700 chr4D 90.747 2183 133 31 3309 5451 56029302 56027149 0.000000e+00 2848.0
4 TraesCS4B01G084700 chr4D 87.757 1217 110 24 2109 3314 80971761 80970573 0.000000e+00 1386.0
5 TraesCS4B01G084700 chr4D 84.150 1306 174 23 2026 3308 497418013 497416718 0.000000e+00 1234.0
6 TraesCS4B01G084700 chr4D 83.869 1308 175 26 2026 3308 497441728 497440432 0.000000e+00 1214.0
7 TraesCS4B01G084700 chr4D 100.000 31 0 0 5150 5180 56027490 56027460 3.060000e-04 58.4
8 TraesCS4B01G084700 chr4A 89.252 2540 159 52 5152 7658 540601957 540599499 0.000000e+00 3073.0
9 TraesCS4B01G084700 chr4A 95.084 1790 85 3 1 1789 540605472 540603685 0.000000e+00 2815.0
10 TraesCS4B01G084700 chr4A 94.141 1519 51 17 1816 3315 85895349 85893850 0.000000e+00 2278.0
11 TraesCS4B01G084700 chr4A 92.494 1359 85 9 1904 3260 640210015 640211358 0.000000e+00 1929.0
12 TraesCS4B01G084700 chr4A 90.856 853 62 7 3309 4147 540603686 540602836 0.000000e+00 1129.0
13 TraesCS4B01G084700 chr4A 89.853 887 56 18 4274 5126 540602828 540601942 0.000000e+00 1109.0
14 TraesCS4B01G084700 chr4A 94.697 132 7 0 7719 7850 540599515 540599384 1.030000e-48 206.0
15 TraesCS4B01G084700 chr4A 85.965 171 7 6 1830 1983 571357090 571357260 4.870000e-37 167.0
16 TraesCS4B01G084700 chr4A 83.696 184 11 4 1818 1983 713622590 713622772 1.050000e-33 156.0
17 TraesCS4B01G084700 chr4A 92.708 96 7 0 2092 2187 571357296 571357391 1.060000e-28 139.0
18 TraesCS4B01G084700 chr4A 91.667 96 8 0 2092 2187 713622808 713622903 4.940000e-27 134.0
19 TraesCS4B01G084700 chr2B 94.632 1509 63 4 1819 3309 752877922 752876414 0.000000e+00 2322.0
20 TraesCS4B01G084700 chr2B 82.399 1534 197 44 1820 3309 194643839 194645343 0.000000e+00 1269.0
21 TraesCS4B01G084700 chr3A 91.029 1516 113 8 1813 3307 15488006 15489519 0.000000e+00 2025.0
22 TraesCS4B01G084700 chr7B 82.595 1534 195 40 1820 3309 693836405 693837910 0.000000e+00 1288.0
23 TraesCS4B01G084700 chr7A 86.486 185 8 1 1816 1983 32181081 32181265 3.740000e-43 187.0
24 TraesCS4B01G084700 chr6B 86.667 180 7 6 1821 1983 54769739 54769560 4.840000e-42 183.0
25 TraesCS4B01G084700 chr6B 92.708 96 7 0 2092 2187 54769524 54769429 1.060000e-28 139.0
26 TraesCS4B01G084700 chr5A 85.870 184 8 2 1816 1982 600698707 600698889 6.260000e-41 180.0
27 TraesCS4B01G084700 chr5A 85.106 188 11 1 1813 1983 600073203 600073390 8.100000e-40 176.0
28 TraesCS4B01G084700 chr5A 91.667 96 8 0 2092 2187 600073426 600073521 4.940000e-27 134.0
29 TraesCS4B01G084700 chr3B 85.326 184 10 10 1816 1982 804987589 804987772 2.910000e-39 174.0
30 TraesCS4B01G084700 chr3B 84.103 195 14 2 1806 1983 799186608 799186414 1.050000e-38 172.0
31 TraesCS4B01G084700 chr5B 85.714 161 6 1 1840 1983 633909889 633910049 3.790000e-33 154.0
32 TraesCS4B01G084700 chr1B 93.750 96 6 0 2092 2187 473870709 473870804 2.280000e-30 145.0
33 TraesCS4B01G084700 chr2D 80.000 160 31 1 7067 7226 35037933 35038091 4.980000e-22 117.0


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 TraesCS4B01G084700 chr4B 83051927 83059776 7849 True 14497.0 14497 100.00000 1 7850 1 chr4B.!!$R1 7849
1 TraesCS4B01G084700 chr4D 56024824 56031083 6259 True 2237.1 3192 94.39925 1 7850 4 chr4D.!!$R4 7849
2 TraesCS4B01G084700 chr4D 80970573 80971761 1188 True 1386.0 1386 87.75700 2109 3314 1 chr4D.!!$R1 1205
3 TraesCS4B01G084700 chr4D 497416718 497418013 1295 True 1234.0 1234 84.15000 2026 3308 1 chr4D.!!$R2 1282
4 TraesCS4B01G084700 chr4D 497440432 497441728 1296 True 1214.0 1214 83.86900 2026 3308 1 chr4D.!!$R3 1282
5 TraesCS4B01G084700 chr4A 85893850 85895349 1499 True 2278.0 2278 94.14100 1816 3315 1 chr4A.!!$R1 1499
6 TraesCS4B01G084700 chr4A 640210015 640211358 1343 False 1929.0 1929 92.49400 1904 3260 1 chr4A.!!$F1 1356
7 TraesCS4B01G084700 chr4A 540599384 540605472 6088 True 1666.4 3073 91.94840 1 7850 5 chr4A.!!$R2 7849
8 TraesCS4B01G084700 chr2B 752876414 752877922 1508 True 2322.0 2322 94.63200 1819 3309 1 chr2B.!!$R1 1490
9 TraesCS4B01G084700 chr2B 194643839 194645343 1504 False 1269.0 1269 82.39900 1820 3309 1 chr2B.!!$F1 1489
10 TraesCS4B01G084700 chr3A 15488006 15489519 1513 False 2025.0 2025 91.02900 1813 3307 1 chr3A.!!$F1 1494
11 TraesCS4B01G084700 chr7B 693836405 693837910 1505 False 1288.0 1288 82.59500 1820 3309 1 chr7B.!!$F1 1489

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
375 377 0.679002 CATTGGGACAGGCCAGTCTG 60.679 60.000 25.53 13.52 42.39 3.51 F
411 413 1.838112 TTAAAGACCGCCTCGACCTA 58.162 50.000 0.00 0.00 0.00 3.08 F
1811 1814 1.134560 CTTTAGAACCCGTCTCTCCCG 59.865 57.143 0.00 0.00 37.84 5.14 F
2666 2705 0.318762 GCTCCGTGTTCTTGTCTCCT 59.681 55.000 0.00 0.00 0.00 3.69 F
3738 3789 0.033228 GATCGACCTCAGCATCCCAG 59.967 60.000 0.00 0.00 0.00 4.45 F
5025 5149 0.318445 GACGTTCCCCGATATCGTGG 60.318 60.000 19.34 19.34 40.70 4.94 F
5809 5948 0.034574 CGAAACCCCATCACCATCCA 60.035 55.000 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1796 0.329261 TCGGGAGAGACGGGTTCTAA 59.671 55.000 0.00 0.00 33.22 2.10 R
2021 2042 1.081833 ACAGATCCCAGGCTCCAGT 59.918 57.895 0.00 0.00 0.00 4.00 R
2822 2862 0.246635 CGATCCACTCCAAACGGACT 59.753 55.000 0.00 0.00 0.00 3.85 R
4537 4628 0.097150 CGACGTTGAGATCGCAGAGA 59.903 55.000 0.00 0.00 43.63 3.10 R
5208 5333 0.179065 CCTGCCTTCATCTGCGATCA 60.179 55.000 0.00 0.00 0.00 2.92 R
6580 6738 0.179100 CATCAAGCGGATCCGTCTGT 60.179 55.000 33.33 17.64 42.09 3.41 R
7771 7935 0.108585 ACCAGCAAAGAAGAAGGCGA 59.891 50.000 0.00 0.00 0.00 5.54 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
49 50 7.942341 TGCACTTTTCCTCTTAAAATTCTCCTA 59.058 33.333 0.00 0.00 0.00 2.94
103 104 9.498176 GTAGAGTTAAAAAGTAGAAACCATGGA 57.502 33.333 21.47 0.00 0.00 3.41
171 172 3.182972 GCAAAAATGCATGTATCATCGCC 59.817 43.478 0.00 0.00 34.41 5.54
186 187 2.586258 TCGCCTTGACTGATAAGAGC 57.414 50.000 0.00 0.00 0.00 4.09
213 214 2.425102 GGAGGTAGATGTGGAGCTAGGT 60.425 54.545 0.00 0.00 0.00 3.08
309 310 7.124573 TGACCATATCACTAGTAATGCAACT 57.875 36.000 0.00 0.00 29.99 3.16
363 365 7.669722 GTCCCATATAAATTTCTAGCATTGGGA 59.330 37.037 14.34 14.34 45.10 4.37
372 374 1.207488 TAGCATTGGGACAGGCCAGT 61.207 55.000 5.01 1.34 42.39 4.00
375 377 0.679002 CATTGGGACAGGCCAGTCTG 60.679 60.000 25.53 13.52 42.39 3.51
404 406 5.253330 TGATCTGAAATTTAAAGACCGCCT 58.747 37.500 5.44 0.00 0.00 5.52
411 413 1.838112 TTAAAGACCGCCTCGACCTA 58.162 50.000 0.00 0.00 0.00 3.08
412 414 1.838112 TAAAGACCGCCTCGACCTAA 58.162 50.000 0.00 0.00 0.00 2.69
423 426 4.000988 GCCTCGACCTAAATTGTCTTTCA 58.999 43.478 0.00 0.00 0.00 2.69
510 513 3.541711 GTTGCGTATGTTGTGACACTTC 58.458 45.455 7.20 0.69 38.91 3.01
637 640 9.590451 GCATTGATTTTGATTTCTAGGAAATCA 57.410 29.630 23.36 23.36 42.82 2.57
888 891 2.577606 ACCACAATGGATGAAACGGA 57.422 45.000 0.84 0.00 40.96 4.69
896 899 3.147553 TGGATGAAACGGATTTGGACA 57.852 42.857 0.00 0.00 0.00 4.02
914 917 4.707934 TGGACAGTATAGACATTTCCGTCA 59.292 41.667 0.00 0.00 38.43 4.35
1201 1204 6.145696 GTGGAGACGATATTGCATTTACCTAC 59.854 42.308 0.00 0.00 0.00 3.18
1308 1311 7.439655 TGTTGTTGTGTCCAAAATAATAAAGGC 59.560 33.333 0.00 0.00 30.94 4.35
1351 1354 5.070862 CGTTTAATTGAAGTCGTTTCTCCG 58.929 41.667 0.00 0.00 36.71 4.63
1463 1466 9.606631 AGTTCACATATAAATCAACTTCTCTCC 57.393 33.333 0.00 0.00 0.00 3.71
1750 1753 3.327757 TCCACTATTGTCAGTTCCTTGCT 59.672 43.478 0.00 0.00 0.00 3.91
1786 1789 8.422577 TCAGTAAATTCTAGAGCTATGGCATA 57.577 34.615 7.06 7.06 41.70 3.14
1787 1790 8.870116 TCAGTAAATTCTAGAGCTATGGCATAA 58.130 33.333 8.79 0.00 41.70 1.90
1788 1791 8.930760 CAGTAAATTCTAGAGCTATGGCATAAC 58.069 37.037 8.79 4.10 41.70 1.89
1789 1792 8.875168 AGTAAATTCTAGAGCTATGGCATAACT 58.125 33.333 10.08 10.08 41.70 2.24
1790 1793 9.495572 GTAAATTCTAGAGCTATGGCATAACTT 57.504 33.333 11.46 5.24 41.70 2.66
1791 1794 8.614469 AAATTCTAGAGCTATGGCATAACTTC 57.386 34.615 11.46 7.87 41.70 3.01
1792 1795 6.985653 TTCTAGAGCTATGGCATAACTTCT 57.014 37.500 11.46 13.69 41.70 2.85
1793 1796 6.985653 TCTAGAGCTATGGCATAACTTCTT 57.014 37.500 11.46 4.40 41.70 2.52
1794 1797 7.366847 TCTAGAGCTATGGCATAACTTCTTT 57.633 36.000 11.46 3.77 41.70 2.52
1795 1798 8.478775 TCTAGAGCTATGGCATAACTTCTTTA 57.521 34.615 11.46 4.57 41.70 1.85
1796 1799 8.580720 TCTAGAGCTATGGCATAACTTCTTTAG 58.419 37.037 11.46 11.93 41.70 1.85
1797 1800 7.366847 AGAGCTATGGCATAACTTCTTTAGA 57.633 36.000 11.46 0.00 41.70 2.10
1798 1801 7.796054 AGAGCTATGGCATAACTTCTTTAGAA 58.204 34.615 11.46 0.00 41.70 2.10
1799 1802 7.713073 AGAGCTATGGCATAACTTCTTTAGAAC 59.287 37.037 11.46 0.00 41.70 3.01
1800 1803 6.768381 AGCTATGGCATAACTTCTTTAGAACC 59.232 38.462 8.79 0.00 41.70 3.62
1801 1804 6.017026 GCTATGGCATAACTTCTTTAGAACCC 60.017 42.308 8.79 0.00 38.54 4.11
1802 1805 4.258543 TGGCATAACTTCTTTAGAACCCG 58.741 43.478 0.00 0.00 0.00 5.28
1803 1806 4.259356 GGCATAACTTCTTTAGAACCCGT 58.741 43.478 0.00 0.00 0.00 5.28
1804 1807 4.331992 GGCATAACTTCTTTAGAACCCGTC 59.668 45.833 0.00 0.00 0.00 4.79
1805 1808 5.176592 GCATAACTTCTTTAGAACCCGTCT 58.823 41.667 0.00 0.00 40.71 4.18
1806 1809 5.291371 GCATAACTTCTTTAGAACCCGTCTC 59.709 44.000 0.00 0.00 37.84 3.36
1807 1810 6.631962 CATAACTTCTTTAGAACCCGTCTCT 58.368 40.000 0.00 0.00 37.84 3.10
1808 1811 4.787260 ACTTCTTTAGAACCCGTCTCTC 57.213 45.455 0.00 0.00 37.84 3.20
1809 1812 3.510753 ACTTCTTTAGAACCCGTCTCTCC 59.489 47.826 0.00 0.00 37.84 3.71
1810 1813 2.454538 TCTTTAGAACCCGTCTCTCCC 58.545 52.381 0.00 0.00 37.84 4.30
1811 1814 1.134560 CTTTAGAACCCGTCTCTCCCG 59.865 57.143 0.00 0.00 37.84 5.14
1814 1817 1.678300 GAACCCGTCTCTCCCGAGT 60.678 63.158 0.00 0.00 38.45 4.18
1873 1877 4.109675 AAACCCTAGCGCCGCCAT 62.110 61.111 4.98 0.00 0.00 4.40
1881 1885 4.221422 GCGCCGCCATAGTCCTCA 62.221 66.667 0.00 0.00 0.00 3.86
2010 2031 2.130426 AGCGCGTCCATGGAGATCT 61.130 57.895 16.81 7.29 0.00 2.75
2021 2042 2.417516 GAGATCTGCCGGCGCTTA 59.582 61.111 23.90 7.16 35.36 3.09
2159 2184 4.402528 CGTCGATGGGGTTGGGCA 62.403 66.667 0.00 0.00 0.00 5.36
2445 2483 4.385405 GTCGCCAGCAGTGCTCCT 62.385 66.667 16.58 0.00 36.40 3.69
2666 2705 0.318762 GCTCCGTGTTCTTGTCTCCT 59.681 55.000 0.00 0.00 0.00 3.69
2699 2738 1.734117 GCAATGGTGGCGTCTTTGC 60.734 57.895 12.16 12.16 37.84 3.68
2758 2797 0.524862 CTGGTGTTGGAAGCATCTGC 59.475 55.000 0.00 0.00 42.49 4.26
2822 2862 0.966875 GCATGGAGCATTGGTGGTGA 60.967 55.000 0.00 0.00 44.79 4.02
3033 3074 2.279918 GACGGTTGTCGGTGTGCT 60.280 61.111 0.00 0.00 44.45 4.40
3042 3083 1.139256 TGTCGGTGTGCTCTTTGGTAA 59.861 47.619 0.00 0.00 0.00 2.85
3090 3131 1.187087 GTGTGTTGTGGGGTTTTGGA 58.813 50.000 0.00 0.00 0.00 3.53
3107 3148 1.409427 TGGATTTCCGGCGTTTTTGTT 59.591 42.857 6.01 0.00 39.43 2.83
3196 3237 0.618458 ACCGAGCAGCCCTATTTTCA 59.382 50.000 0.00 0.00 0.00 2.69
3247 3291 0.251787 GTGCATTCCTCCTTTGGGGT 60.252 55.000 0.00 0.00 36.25 4.95
3482 3530 6.892691 ACTACACACTTACTGTAGACGTAAC 58.107 40.000 11.59 0.00 42.58 2.50
3517 3565 4.949856 TGCAGTTTTCCTTCATATTCCCTC 59.050 41.667 0.00 0.00 0.00 4.30
3522 3570 8.897752 CAGTTTTCCTTCATATTCCCTCTTTAG 58.102 37.037 0.00 0.00 0.00 1.85
3536 3584 9.674068 ATTCCCTCTTTAGATTCTGTTTTAGAC 57.326 33.333 0.00 0.00 34.43 2.59
3727 3778 2.037901 AGTGCATGATGAGATCGACCT 58.962 47.619 0.00 0.00 0.00 3.85
3738 3789 0.033228 GATCGACCTCAGCATCCCAG 59.967 60.000 0.00 0.00 0.00 4.45
3739 3790 0.689080 ATCGACCTCAGCATCCCAGT 60.689 55.000 0.00 0.00 0.00 4.00
3755 3806 2.738846 CCCAGTCGATGACAAAGACTTG 59.261 50.000 11.92 9.50 42.65 3.16
3780 3831 3.047280 GCAACACGGGCACGATGA 61.047 61.111 19.19 0.00 44.60 2.92
3814 3865 1.153449 TTGCTACCGCGGATGAAGG 60.153 57.895 35.90 14.93 39.65 3.46
3823 3874 2.035449 CCGCGGATGAAGGTATTACTGA 59.965 50.000 24.07 0.00 0.00 3.41
3840 3891 1.068250 GATGCCGGGAGTGCTAGTC 59.932 63.158 2.18 0.00 0.00 2.59
3880 3931 1.793258 CATGCAAACCGCCAAATTCA 58.207 45.000 0.00 0.00 41.33 2.57
3906 3957 7.064253 AGGAACTTGAAGCGTATGTATAAACAC 59.936 37.037 0.00 0.00 33.75 3.32
4025 4087 1.073897 GCCCTCAGCAAGAAGGTGT 59.926 57.895 0.00 0.00 45.77 4.16
4120 4182 8.662369 TTAATTTTCGATTGATGTTTACCACG 57.338 30.769 0.00 0.00 0.00 4.94
4141 4203 8.692710 ACCACGAGATTTGATCAAGTACTAATA 58.307 33.333 8.41 0.00 0.00 0.98
4183 4248 9.571810 GAAATCATGTATGCTTGTTTTGACATA 57.428 29.630 9.44 0.00 0.00 2.29
4266 4354 5.429957 GGTTTAGCACCTCAATCATCATC 57.570 43.478 0.00 0.00 43.29 2.92
4271 4359 8.623903 GTTTAGCACCTCAATCATCATCAAATA 58.376 33.333 0.00 0.00 0.00 1.40
4338 4426 3.004419 CGGACGGAGAACATTATGCTAGA 59.996 47.826 0.00 0.00 0.00 2.43
4412 4500 0.609131 CAAAGGCCCGATGGTGTTCT 60.609 55.000 0.00 0.00 0.00 3.01
4416 4504 1.065418 AGGCCCGATGGTGTTCTTTAG 60.065 52.381 0.00 0.00 0.00 1.85
4458 4549 1.421410 CGCCTACACATGGAGAACGC 61.421 60.000 0.00 0.00 0.00 4.84
4465 4556 1.448540 CATGGAGAACGCGAGGCTT 60.449 57.895 15.93 0.00 0.00 4.35
4482 4573 0.902531 CTTAAGGCCGAACTCCTCCA 59.097 55.000 0.00 0.00 32.45 3.86
4537 4628 2.125512 GCAGGCTCGTCACGGATT 60.126 61.111 0.00 0.00 0.00 3.01
4565 4656 2.906388 TCAACGTCGACCCCGTCA 60.906 61.111 10.58 0.00 37.61 4.35
4573 4664 4.778143 GACCCCGTCATGCCGCTT 62.778 66.667 0.00 0.00 32.09 4.68
4694 4791 4.057428 ACGTCCTCGCTGCACTCC 62.057 66.667 0.00 0.00 41.18 3.85
4783 4880 0.963856 TCGACCACCAGCTGTATCGT 60.964 55.000 13.81 2.72 36.58 3.73
4856 4953 4.008933 GCACTCGGGACACTGGCT 62.009 66.667 0.00 0.00 0.00 4.75
4910 5007 3.587797 TCTTCATGGACGAGGTAACAC 57.412 47.619 0.00 0.00 41.41 3.32
4912 5009 2.736144 TCATGGACGAGGTAACACAC 57.264 50.000 0.00 0.00 41.41 3.82
4913 5010 1.964933 TCATGGACGAGGTAACACACA 59.035 47.619 0.00 0.00 41.41 3.72
4915 5012 3.764972 TCATGGACGAGGTAACACACATA 59.235 43.478 0.00 0.00 41.41 2.29
4921 5026 3.445096 ACGAGGTAACACACATACTACCC 59.555 47.826 0.00 0.00 35.39 3.69
4925 5030 6.712095 CGAGGTAACACACATACTACCCTATA 59.288 42.308 0.00 0.00 35.39 1.31
4942 5047 7.569599 ACCCTATATCTCATCCCGTAATTTT 57.430 36.000 0.00 0.00 0.00 1.82
5001 5125 1.392589 CTGTTGGCAGAACTGTTGGT 58.607 50.000 0.00 0.00 45.28 3.67
5002 5126 1.334869 CTGTTGGCAGAACTGTTGGTC 59.665 52.381 0.00 0.00 45.28 4.02
5025 5149 0.318445 GACGTTCCCCGATATCGTGG 60.318 60.000 19.34 19.34 40.70 4.94
5041 5165 2.975799 GGCAAGTGTTTCCGCCGA 60.976 61.111 0.00 0.00 34.26 5.54
5105 5229 3.189702 TGGTAAGTTCCGCTGCAAAATAC 59.810 43.478 0.00 1.42 0.00 1.89
5106 5230 3.189702 GGTAAGTTCCGCTGCAAAATACA 59.810 43.478 0.00 0.00 0.00 2.29
5107 5231 4.142469 GGTAAGTTCCGCTGCAAAATACAT 60.142 41.667 0.00 0.00 0.00 2.29
5108 5232 5.065474 GGTAAGTTCCGCTGCAAAATACATA 59.935 40.000 0.00 0.00 0.00 2.29
5222 5347 2.222976 GCACACTTGATCGCAGATGAAG 60.223 50.000 13.15 13.15 45.12 3.02
5262 5387 2.738521 CAGGGGTGTCGAGTTGCG 60.739 66.667 0.00 0.00 42.69 4.85
5337 5462 0.037326 GGACGTGTCTCTTGATGCCA 60.037 55.000 0.00 0.00 0.00 4.92
5451 5576 4.346730 TGGCTACTGCAAGGTAACTAGTA 58.653 43.478 0.00 0.00 44.27 1.82
5455 5580 8.342470 GGCTACTGCAAGGTAACTAGTACTCC 62.342 50.000 0.00 0.00 44.27 3.85
5468 5593 3.648507 AGTACTCCCATCTCTACACGT 57.351 47.619 0.00 0.00 0.00 4.49
5473 5598 4.342359 ACTCCCATCTCTACACGTACTTT 58.658 43.478 0.00 0.00 0.00 2.66
5485 5610 5.416271 ACACGTACTTTAGGAATGTGGAT 57.584 39.130 0.00 0.00 0.00 3.41
5486 5611 5.801380 ACACGTACTTTAGGAATGTGGATT 58.199 37.500 0.00 0.00 0.00 3.01
5487 5612 5.642063 ACACGTACTTTAGGAATGTGGATTG 59.358 40.000 0.00 0.00 0.00 2.67
5490 5615 7.010183 CACGTACTTTAGGAATGTGGATTGTAG 59.990 40.741 0.00 0.00 0.00 2.74
5491 5616 6.479001 CGTACTTTAGGAATGTGGATTGTAGG 59.521 42.308 0.00 0.00 0.00 3.18
5492 5617 6.636454 ACTTTAGGAATGTGGATTGTAGGA 57.364 37.500 0.00 0.00 0.00 2.94
5493 5618 6.653989 ACTTTAGGAATGTGGATTGTAGGAG 58.346 40.000 0.00 0.00 0.00 3.69
5495 5620 7.402071 ACTTTAGGAATGTGGATTGTAGGAGTA 59.598 37.037 0.00 0.00 0.00 2.59
5497 5622 6.426646 AGGAATGTGGATTGTAGGAGTATC 57.573 41.667 0.00 0.00 0.00 2.24
5498 5623 6.146760 AGGAATGTGGATTGTAGGAGTATCT 58.853 40.000 0.00 0.00 33.73 1.98
5500 5625 6.931840 GGAATGTGGATTGTAGGAGTATCTTC 59.068 42.308 0.00 0.00 33.73 2.87
5501 5626 7.202047 GGAATGTGGATTGTAGGAGTATCTTCT 60.202 40.741 0.00 0.00 33.73 2.85
5502 5627 8.783660 AATGTGGATTGTAGGAGTATCTTCTA 57.216 34.615 0.00 0.00 33.73 2.10
5503 5628 7.825331 TGTGGATTGTAGGAGTATCTTCTAG 57.175 40.000 0.00 0.00 33.73 2.43
5505 5630 7.285629 TGTGGATTGTAGGAGTATCTTCTAGTG 59.714 40.741 0.00 0.00 33.73 2.74
5506 5631 7.285858 GTGGATTGTAGGAGTATCTTCTAGTGT 59.714 40.741 0.00 0.00 33.73 3.55
5602 5741 9.017509 CATATATGTCTAATCCCTTGCACATTT 57.982 33.333 4.43 0.00 0.00 2.32
5653 5792 0.739462 TACGACAAGGGCTTCATGCG 60.739 55.000 0.00 0.00 44.05 4.73
5655 5794 1.675641 GACAAGGGCTTCATGCGGT 60.676 57.895 0.00 0.00 44.05 5.68
5690 5829 3.067091 CTGAGCTCAGGGCACACT 58.933 61.111 32.30 0.00 44.79 3.55
5806 5945 0.695924 TCACGAAACCCCATCACCAT 59.304 50.000 0.00 0.00 0.00 3.55
5807 5946 1.094785 CACGAAACCCCATCACCATC 58.905 55.000 0.00 0.00 0.00 3.51
5809 5948 0.034574 CGAAACCCCATCACCATCCA 60.035 55.000 0.00 0.00 0.00 3.41
5810 5949 1.474330 GAAACCCCATCACCATCCAC 58.526 55.000 0.00 0.00 0.00 4.02
5811 5950 0.041090 AAACCCCATCACCATCCACC 59.959 55.000 0.00 0.00 0.00 4.61
5813 5952 2.192979 CCCATCACCATCCACCCG 59.807 66.667 0.00 0.00 0.00 5.28
5814 5953 2.679342 CCCATCACCATCCACCCGT 61.679 63.158 0.00 0.00 0.00 5.28
5815 5954 1.341913 CCCATCACCATCCACCCGTA 61.342 60.000 0.00 0.00 0.00 4.02
5816 5955 0.764890 CCATCACCATCCACCCGTAT 59.235 55.000 0.00 0.00 0.00 3.06
5818 5957 1.056660 ATCACCATCCACCCGTATCC 58.943 55.000 0.00 0.00 0.00 2.59
5819 5958 1.069090 CACCATCCACCCGTATCCG 59.931 63.158 0.00 0.00 0.00 4.18
5820 5959 1.382146 ACCATCCACCCGTATCCGT 60.382 57.895 0.00 0.00 0.00 4.69
5821 5960 0.106066 ACCATCCACCCGTATCCGTA 60.106 55.000 0.00 0.00 0.00 4.02
5822 5961 1.263356 CCATCCACCCGTATCCGTAT 58.737 55.000 0.00 0.00 0.00 3.06
5823 5962 1.067142 CCATCCACCCGTATCCGTATG 60.067 57.143 0.00 0.00 0.00 2.39
5824 5963 0.606604 ATCCACCCGTATCCGTATGC 59.393 55.000 0.00 0.00 0.00 3.14
5825 5964 0.756070 TCCACCCGTATCCGTATGCA 60.756 55.000 0.00 0.00 0.00 3.96
5826 5965 0.320374 CCACCCGTATCCGTATGCAT 59.680 55.000 3.79 3.79 0.00 3.96
5828 5967 0.606604 ACCCGTATCCGTATGCATCC 59.393 55.000 0.19 0.00 0.00 3.51
5829 5968 0.606096 CCCGTATCCGTATGCATCCA 59.394 55.000 0.19 0.00 0.00 3.41
5830 5969 1.404181 CCCGTATCCGTATGCATCCAG 60.404 57.143 0.19 0.00 0.00 3.86
5831 5970 1.544246 CCGTATCCGTATGCATCCAGA 59.456 52.381 0.19 0.00 0.00 3.86
5833 5972 3.368427 CCGTATCCGTATGCATCCAGAAT 60.368 47.826 0.19 0.00 0.00 2.40
5843 5982 1.612463 GCATCCAGAATTCCAGATGGC 59.388 52.381 25.37 17.86 37.25 4.40
5866 6005 5.231702 CCATGCAATTCTGAAACATTCACA 58.768 37.500 0.00 0.00 35.46 3.58
5944 6083 3.821600 GGATGACGGAGAGCTTCTATGTA 59.178 47.826 0.00 0.00 0.00 2.29
6244 6389 2.529389 ACGGCCCAGTTCCCTCTT 60.529 61.111 0.00 0.00 0.00 2.85
6246 6391 1.221021 CGGCCCAGTTCCCTCTTAC 59.779 63.158 0.00 0.00 0.00 2.34
6298 6443 4.088634 TGGTTTGCATCCTAGCTTCAAAT 58.911 39.130 0.00 0.00 34.99 2.32
6316 6465 8.765219 GCTTCAAATATTCTTATCGCTACTTCA 58.235 33.333 0.00 0.00 0.00 3.02
6321 6470 4.650754 TTCTTATCGCTACTTCAGTCCC 57.349 45.455 0.00 0.00 0.00 4.46
6333 6482 0.107703 TCAGTCCCCATTGTGATCGC 60.108 55.000 0.00 0.00 0.00 4.58
6334 6483 1.153369 AGTCCCCATTGTGATCGCG 60.153 57.895 0.00 0.00 0.00 5.87
6352 6509 2.413112 CGCGCCAATGTGGATATCTAAG 59.587 50.000 0.00 0.00 40.96 2.18
6398 6556 3.612681 AGGGTCGTGGTCGTGGTG 61.613 66.667 0.00 0.00 38.33 4.17
6482 6640 1.515519 GCGTACGCTCCGATTGACA 60.516 57.895 31.95 0.00 38.26 3.58
6490 6648 3.474806 CCGATTGACACGGCAGAC 58.525 61.111 0.00 0.00 43.74 3.51
6493 6651 1.354337 CGATTGACACGGCAGACCTG 61.354 60.000 0.00 0.00 0.00 4.00
6585 6743 2.222217 GCGTCGGCGACATACAGAC 61.222 63.158 35.62 14.16 41.33 3.51
6586 6744 1.933041 CGTCGGCGACATACAGACG 60.933 63.158 35.62 18.68 46.32 4.18
6641 6799 1.690845 CCATAGACCACCAGAGGAGCT 60.691 57.143 0.00 0.00 0.00 4.09
6665 6823 1.333619 GATCTCTCGTCTCTGTCCTGC 59.666 57.143 0.00 0.00 0.00 4.85
6673 6831 2.601666 TCTGTCCTGCGGCAGACT 60.602 61.111 30.52 0.00 36.89 3.24
6675 6833 2.917227 TGTCCTGCGGCAGACTCA 60.917 61.111 30.52 20.96 32.44 3.41
6716 6874 1.299926 GCACAGACCGTCGACAACT 60.300 57.895 17.16 8.26 0.00 3.16
6760 6918 3.188667 CCATCATGAAGATCAAGGATGCG 59.811 47.826 0.00 8.39 39.17 4.73
6811 6969 1.436983 GCGCCTTCTACCATTTCCGG 61.437 60.000 0.00 0.00 0.00 5.14
6820 6978 7.221450 CCTTCTACCATTTCCGGTTCATAATA 58.779 38.462 0.00 0.00 40.67 0.98
6870 7028 7.359595 TGAGAATAAATTTGTGGACTTCGTTG 58.640 34.615 0.00 0.00 0.00 4.10
6874 7032 3.791973 ATTTGTGGACTTCGTTGCAAA 57.208 38.095 0.00 0.00 0.00 3.68
6919 7082 3.814625 TGTAGACATTGAACTGCACCAA 58.185 40.909 0.00 0.00 0.00 3.67
7095 7259 6.515272 AATGCACCATAAGTCCTAAAAGTG 57.485 37.500 0.00 0.00 0.00 3.16
7099 7263 5.472137 GCACCATAAGTCCTAAAAGTGTTCA 59.528 40.000 0.00 0.00 0.00 3.18
7110 7274 4.434713 AAAAGTGTTCAAGGTGTGTCAC 57.565 40.909 0.00 0.00 35.24 3.67
7135 7299 8.666821 ACCTAGGTCCTAAAAGTTCTAAAATGT 58.333 33.333 9.21 0.00 0.00 2.71
7284 7448 6.547141 CCAGAGCTGTTGGGAATATTTCATTA 59.453 38.462 0.00 0.00 31.87 1.90
7358 7522 1.478510 TCAACTCTTCTCTCGCATCCC 59.521 52.381 0.00 0.00 0.00 3.85
7406 7570 7.218228 TGTTCACAACAAATAGATGCAGAAT 57.782 32.000 0.00 0.00 38.72 2.40
7493 7657 8.839310 AGCAATAAGGTCTACATCATTATGAC 57.161 34.615 0.00 0.00 36.54 3.06
7494 7658 8.432013 AGCAATAAGGTCTACATCATTATGACA 58.568 33.333 0.00 0.00 36.54 3.58
7540 7704 8.478877 TCTCAGATAAGGTCTAAATTCAGGTTC 58.521 37.037 0.00 0.00 34.69 3.62
7615 7779 0.804364 TCAACGGCTTCATGCATGAC 59.196 50.000 28.72 17.82 45.15 3.06
7640 7804 3.925379 TCGCTACACACATCATGTCTTT 58.075 40.909 0.00 0.00 40.64 2.52
7642 7806 4.152223 TCGCTACACACATCATGTCTTTTG 59.848 41.667 0.00 0.00 40.64 2.44
7647 7811 4.276678 ACACACATCATGTCTTTTGTCCTG 59.723 41.667 0.00 0.00 40.64 3.86
7651 7815 2.766313 TCATGTCTTTTGTCCTGTCCG 58.234 47.619 0.00 0.00 0.00 4.79
7652 7816 1.806542 CATGTCTTTTGTCCTGTCCGG 59.193 52.381 0.00 0.00 0.00 5.14
7654 7818 1.202604 TGTCTTTTGTCCTGTCCGGTC 60.203 52.381 0.00 0.00 0.00 4.79
7656 7820 0.107831 CTTTTGTCCTGTCCGGTCCA 59.892 55.000 0.00 0.00 0.00 4.02
7664 7828 0.240945 CTGTCCGGTCCAAAATGCAC 59.759 55.000 0.00 0.00 0.00 4.57
7676 7840 4.405358 TCCAAAATGCACAACTTTCTTCCT 59.595 37.500 0.00 0.00 0.00 3.36
7681 7845 7.530426 AAATGCACAACTTTCTTCCTCTATT 57.470 32.000 0.00 0.00 0.00 1.73
7688 7852 9.403110 CACAACTTTCTTCCTCTATTCAAAATG 57.597 33.333 0.00 0.00 0.00 2.32
7701 7865 8.578308 TCTATTCAAAATGCACAACTTTCTTG 57.422 30.769 0.00 0.00 0.00 3.02
7703 7867 3.870419 TCAAAATGCACAACTTTCTTGCC 59.130 39.130 0.00 0.00 35.26 4.52
7704 7868 2.531522 AATGCACAACTTTCTTGCCC 57.468 45.000 0.00 0.00 35.26 5.36
7705 7869 1.708341 ATGCACAACTTTCTTGCCCT 58.292 45.000 0.00 0.00 35.26 5.19
7706 7870 0.746063 TGCACAACTTTCTTGCCCTG 59.254 50.000 0.00 0.00 35.26 4.45
7707 7871 0.746659 GCACAACTTTCTTGCCCTGT 59.253 50.000 0.00 0.00 0.00 4.00
7709 7873 1.002468 CACAACTTTCTTGCCCTGTCG 60.002 52.381 0.00 0.00 0.00 4.35
7712 7876 2.341846 ACTTTCTTGCCCTGTCGAAA 57.658 45.000 0.00 0.00 0.00 3.46
7713 7877 2.650322 ACTTTCTTGCCCTGTCGAAAA 58.350 42.857 0.00 0.00 0.00 2.29
7738 7902 2.158755 ACACCTTCTCCTGTCCAAGTTG 60.159 50.000 0.00 0.00 0.00 3.16
7771 7935 2.634453 CAGAACCATTTGCCTTTCCCTT 59.366 45.455 0.00 0.00 0.00 3.95
7814 7978 1.910580 CTACCCACAATGGCCTCGGT 61.911 60.000 3.32 2.75 35.79 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.452813 AGGAGAATTTTAAGAGGAAAAGTGCAT 59.547 33.333 0.00 0.00 32.06 3.96
49 50 9.010029 CCTTTGTAATTGTAGACAAACATAGGT 57.990 33.333 18.82 0.00 38.95 3.08
171 172 4.340666 TCCTAGCTGCTCTTATCAGTCAAG 59.659 45.833 4.91 0.00 34.21 3.02
186 187 2.890311 CTCCACATCTACCTCCTAGCTG 59.110 54.545 0.00 0.00 0.00 4.24
213 214 2.445525 GCCCCTCCCCTGATTATGTAAA 59.554 50.000 0.00 0.00 0.00 2.01
423 426 0.952497 CATGCCTCGTTGTGCAGTCT 60.952 55.000 0.00 0.00 41.46 3.24
510 513 6.686630 TGGCAACCATATTCTTGTTAAACAG 58.313 36.000 0.00 0.00 0.00 3.16
680 683 9.034800 TGATGCCCTTCTTCAAAATTTTACTAT 57.965 29.630 2.44 0.00 0.00 2.12
888 891 6.650120 ACGGAAATGTCTATACTGTCCAAAT 58.350 36.000 0.00 0.00 0.00 2.32
896 899 5.171147 CGACTGACGGAAATGTCTATACT 57.829 43.478 0.00 0.00 39.64 2.12
914 917 3.743269 CGGTATTTAAAGGCCATCCGACT 60.743 47.826 5.01 0.00 39.17 4.18
1132 1135 0.179234 TGTCAAAGAACCCACGCTCA 59.821 50.000 0.00 0.00 0.00 4.26
1201 1204 3.054361 TCTTAAAGCTTGCTTAGGGGAGG 60.054 47.826 8.36 0.00 0.00 4.30
1257 1260 9.722184 CACAATCAGATCTATAGAATCAACCAT 57.278 33.333 6.52 0.00 0.00 3.55
1343 1346 5.063564 GTGATGTTTGATCCTACGGAGAAAC 59.936 44.000 0.00 0.00 37.95 2.78
1351 1354 6.349363 GGAAACCAAGTGATGTTTGATCCTAC 60.349 42.308 0.00 0.00 34.97 3.18
1463 1466 4.156008 AGCAAAGCCAAAACCTATTACTCG 59.844 41.667 0.00 0.00 0.00 4.18
1561 1564 9.903682 CCAATAACTCATATATTGCCTCAAAAG 57.096 33.333 0.00 0.00 38.72 2.27
1565 1568 8.995027 AAACCAATAACTCATATATTGCCTCA 57.005 30.769 0.00 0.00 38.72 3.86
1786 1789 4.021280 GGAGAGACGGGTTCTAAAGAAGTT 60.021 45.833 0.00 0.00 33.22 2.66
1787 1790 3.510753 GGAGAGACGGGTTCTAAAGAAGT 59.489 47.826 0.00 0.00 33.22 3.01
1788 1791 3.119065 GGGAGAGACGGGTTCTAAAGAAG 60.119 52.174 0.00 0.00 33.22 2.85
1789 1792 2.830321 GGGAGAGACGGGTTCTAAAGAA 59.170 50.000 0.00 0.00 33.22 2.52
1790 1793 2.454538 GGGAGAGACGGGTTCTAAAGA 58.545 52.381 0.00 0.00 33.22 2.52
1791 1794 1.134560 CGGGAGAGACGGGTTCTAAAG 59.865 57.143 0.00 0.00 33.22 1.85
1792 1795 1.180029 CGGGAGAGACGGGTTCTAAA 58.820 55.000 0.00 0.00 33.22 1.85
1793 1796 0.329261 TCGGGAGAGACGGGTTCTAA 59.671 55.000 0.00 0.00 33.22 2.10
1794 1797 1.993653 TCGGGAGAGACGGGTTCTA 59.006 57.895 0.00 0.00 33.22 2.10
1795 1798 2.761844 TCGGGAGAGACGGGTTCT 59.238 61.111 0.00 0.00 37.23 3.01
1805 1808 4.437587 GGGTCGGGACTCGGGAGA 62.438 72.222 2.08 0.00 39.77 3.71
1838 1841 3.697747 CTACCCCCGTGTCGCCAA 61.698 66.667 0.00 0.00 0.00 4.52
1873 1877 2.643808 GGGGAGGGGGTGAGGACTA 61.644 68.421 0.00 0.00 0.00 2.59
2010 2031 4.451150 CTCCAGTAAGCGCCGGCA 62.451 66.667 28.98 2.89 43.41 5.69
2021 2042 1.081833 ACAGATCCCAGGCTCCAGT 59.918 57.895 0.00 0.00 0.00 4.00
2060 2081 3.418913 CCACGGACGCGAAATGCA 61.419 61.111 15.93 0.00 46.97 3.96
2063 2084 3.118454 CAGCCACGGACGCGAAAT 61.118 61.111 15.93 0.00 0.00 2.17
2445 2483 1.098129 TGCACCGCACAAAACTAGCA 61.098 50.000 0.00 0.00 31.71 3.49
2666 2705 1.107114 ATTGCACACGGTTTTCACCA 58.893 45.000 0.00 0.00 44.53 4.17
2699 2738 3.252215 TGCTTCCAACAAAGTAATGACGG 59.748 43.478 0.00 0.00 0.00 4.79
2758 2797 1.827789 CCACCACACCACCACCAAG 60.828 63.158 0.00 0.00 0.00 3.61
2822 2862 0.246635 CGATCCACTCCAAACGGACT 59.753 55.000 0.00 0.00 0.00 3.85
2874 2915 0.933097 CTGGCGCTACTTGCATACAG 59.067 55.000 7.64 0.00 43.06 2.74
3033 3074 1.670674 CGCCTACGCTGTTACCAAAGA 60.671 52.381 0.00 0.00 0.00 2.52
3090 3131 4.623002 ACATAAACAAAAACGCCGGAAAT 58.377 34.783 5.05 0.00 0.00 2.17
3107 3148 4.980573 AGGACTAAAGCACCACAACATAA 58.019 39.130 0.00 0.00 0.00 1.90
3247 3291 9.436957 GATCAGAAGAAGGTATTACAAGAACAA 57.563 33.333 0.00 0.00 0.00 2.83
3442 3490 9.893305 AAGTGTGTAGTTTTATTGCATAAACTC 57.107 29.630 19.27 13.75 34.68 3.01
3482 3530 6.017400 AGGAAAACTGCACATGATTAACAG 57.983 37.500 0.00 1.78 0.00 3.16
3658 3709 1.135402 CCATGGCGACCTGCTTAAAAC 60.135 52.381 0.00 0.00 45.43 2.43
3727 3778 0.461548 GTCATCGACTGGGATGCTGA 59.538 55.000 0.00 0.00 42.78 4.26
3738 3789 4.328440 CCAGATCAAGTCTTTGTCATCGAC 59.672 45.833 0.00 0.00 34.00 4.20
3739 3790 4.220602 TCCAGATCAAGTCTTTGTCATCGA 59.779 41.667 0.00 0.00 34.00 3.59
3755 3806 2.109126 GCCCGTGTTGCTCCAGATC 61.109 63.158 0.00 0.00 0.00 2.75
3780 3831 5.237996 CGGTAGCAACATCTTCATCATCATT 59.762 40.000 0.00 0.00 0.00 2.57
3814 3865 2.755650 CACTCCCGGCATCAGTAATAC 58.244 52.381 0.00 0.00 0.00 1.89
3823 3874 1.685765 TGACTAGCACTCCCGGCAT 60.686 57.895 0.00 0.00 0.00 4.40
3840 3891 0.107312 CTGCCCCTCTTCCTCATGTG 60.107 60.000 0.00 0.00 0.00 3.21
3880 3931 7.064253 GTGTTTATACATACGCTTCAAGTTCCT 59.936 37.037 0.00 0.00 36.50 3.36
3922 3973 4.751767 TTGGCTCAAGTTGTTTTTGGAT 57.248 36.364 2.11 0.00 0.00 3.41
3923 3974 4.442753 GGATTGGCTCAAGTTGTTTTTGGA 60.443 41.667 2.11 0.00 0.00 3.53
3924 3975 3.809279 GGATTGGCTCAAGTTGTTTTTGG 59.191 43.478 2.11 0.00 0.00 3.28
3925 3976 4.270808 GTGGATTGGCTCAAGTTGTTTTTG 59.729 41.667 2.11 0.00 0.00 2.44
3926 3977 4.162131 AGTGGATTGGCTCAAGTTGTTTTT 59.838 37.500 2.11 0.00 0.00 1.94
3927 3978 3.706086 AGTGGATTGGCTCAAGTTGTTTT 59.294 39.130 2.11 0.00 0.00 2.43
3928 3979 3.299503 AGTGGATTGGCTCAAGTTGTTT 58.700 40.909 2.11 0.00 0.00 2.83
3930 3981 2.107204 AGAGTGGATTGGCTCAAGTTGT 59.893 45.455 2.11 0.00 34.39 3.32
3931 3982 2.787994 AGAGTGGATTGGCTCAAGTTG 58.212 47.619 0.00 0.00 34.39 3.16
3934 3985 2.486982 CACAAGAGTGGATTGGCTCAAG 59.513 50.000 0.00 0.00 42.13 3.02
3935 3986 2.106338 TCACAAGAGTGGATTGGCTCAA 59.894 45.455 0.00 0.00 45.91 3.02
3939 4001 2.163010 CACATCACAAGAGTGGATTGGC 59.837 50.000 0.00 0.00 45.91 4.52
4025 4087 0.982852 ACCCGAAGAGGATCCATGCA 60.983 55.000 15.82 0.00 45.00 3.96
4263 4351 8.461222 TCTGGTTCTGCATTTAGTTATTTGATG 58.539 33.333 0.00 0.00 0.00 3.07
4264 4352 8.579850 TCTGGTTCTGCATTTAGTTATTTGAT 57.420 30.769 0.00 0.00 0.00 2.57
4265 4353 7.994425 TCTGGTTCTGCATTTAGTTATTTGA 57.006 32.000 0.00 0.00 0.00 2.69
4266 4354 9.079833 CATTCTGGTTCTGCATTTAGTTATTTG 57.920 33.333 0.00 0.00 0.00 2.32
4271 4359 5.105997 GCTCATTCTGGTTCTGCATTTAGTT 60.106 40.000 0.00 0.00 0.00 2.24
4328 4416 7.090173 GCTCGATTCTCTTCTTCTAGCATAAT 58.910 38.462 0.00 0.00 0.00 1.28
4338 4426 4.440880 CTTCATGGCTCGATTCTCTTCTT 58.559 43.478 0.00 0.00 0.00 2.52
4363 4451 2.349886 GCAGGTCTTCTTCAGTATTGCG 59.650 50.000 0.00 0.00 0.00 4.85
4366 4454 2.239907 GGGGCAGGTCTTCTTCAGTATT 59.760 50.000 0.00 0.00 0.00 1.89
4369 4457 0.768221 TGGGGCAGGTCTTCTTCAGT 60.768 55.000 0.00 0.00 0.00 3.41
4412 4500 4.090588 CGGGGTCAGCGGCCTAAA 62.091 66.667 0.00 0.00 0.00 1.85
4465 4556 0.543410 TGTGGAGGAGTTCGGCCTTA 60.543 55.000 0.00 0.00 35.44 2.69
4482 4573 2.363925 GGAGGTAGGCCGTCCTGT 60.364 66.667 22.96 3.93 44.08 4.00
4537 4628 0.097150 CGACGTTGAGATCGCAGAGA 59.903 55.000 0.00 0.00 43.63 3.10
4578 4669 0.668535 CATGAGATCGTCCTGGCGTA 59.331 55.000 9.66 0.00 0.00 4.42
4694 4791 0.944788 ATCAGCATCATGAGCTCGCG 60.945 55.000 9.64 0.00 41.14 5.87
4695 4792 0.513385 CATCAGCATCATGAGCTCGC 59.487 55.000 9.64 5.80 41.14 5.03
4856 4953 1.533625 GCTCCAGTGCACATAACCAA 58.466 50.000 21.04 0.00 0.00 3.67
4910 5007 6.263392 CGGGATGAGATATAGGGTAGTATGTG 59.737 46.154 0.00 0.00 0.00 3.21
4912 5009 6.366340 ACGGGATGAGATATAGGGTAGTATG 58.634 44.000 0.00 0.00 0.00 2.39
4913 5010 6.593759 ACGGGATGAGATATAGGGTAGTAT 57.406 41.667 0.00 0.00 0.00 2.12
4915 5012 4.949966 ACGGGATGAGATATAGGGTAGT 57.050 45.455 0.00 0.00 0.00 2.73
4942 5047 5.483937 ACACACAGGGAGAAGTCATATGTAA 59.516 40.000 1.90 0.00 0.00 2.41
5001 5125 2.228059 GATATCGGGGAACGTCTCAGA 58.772 52.381 0.00 0.00 44.69 3.27
5002 5126 1.069159 CGATATCGGGGAACGTCTCAG 60.069 57.143 17.51 0.00 44.69 3.35
5025 5149 2.054140 TTGTCGGCGGAAACACTTGC 62.054 55.000 7.21 0.00 0.00 4.01
5040 5164 1.964373 AACCGTGGCCGATGTTGTC 60.964 57.895 0.00 0.00 35.63 3.18
5041 5165 2.112297 AACCGTGGCCGATGTTGT 59.888 55.556 0.00 0.00 35.63 3.32
5139 5263 9.862371 CTACTAGTATGAGAGCTTCTTTCAAAA 57.138 33.333 2.33 0.00 28.70 2.44
5142 5266 8.462811 CAACTACTAGTATGAGAGCTTCTTTCA 58.537 37.037 2.33 0.00 0.00 2.69
5143 5267 7.918562 CCAACTACTAGTATGAGAGCTTCTTTC 59.081 40.741 2.33 0.00 0.00 2.62
5144 5268 7.397761 ACCAACTACTAGTATGAGAGCTTCTTT 59.602 37.037 2.33 0.00 0.00 2.52
5145 5269 6.893005 ACCAACTACTAGTATGAGAGCTTCTT 59.107 38.462 2.33 0.00 0.00 2.52
5146 5270 6.428295 ACCAACTACTAGTATGAGAGCTTCT 58.572 40.000 2.33 0.00 0.00 2.85
5147 5271 6.702716 ACCAACTACTAGTATGAGAGCTTC 57.297 41.667 2.33 0.00 0.00 3.86
5148 5272 8.770010 ATAACCAACTACTAGTATGAGAGCTT 57.230 34.615 2.33 0.00 0.00 3.74
5206 5331 1.598132 CTGCCTTCATCTGCGATCAAG 59.402 52.381 0.00 0.00 0.00 3.02
5208 5333 0.179065 CCTGCCTTCATCTGCGATCA 60.179 55.000 0.00 0.00 0.00 2.92
5262 5387 1.795768 TGCCTCACGAACTTCACATC 58.204 50.000 0.00 0.00 0.00 3.06
5337 5462 2.039818 CTGAGCTCAGATGTGCCATT 57.960 50.000 35.69 0.00 46.59 3.16
5399 5524 3.650942 TGTCCTTGATAAGACACCCACTT 59.349 43.478 0.00 0.00 0.00 3.16
5451 5576 3.648507 AGTACGTGTAGAGATGGGAGT 57.351 47.619 0.00 0.00 0.00 3.85
5455 5580 6.446781 TTCCTAAAGTACGTGTAGAGATGG 57.553 41.667 0.00 0.00 0.00 3.51
5468 5593 7.402071 ACTCCTACAATCCACATTCCTAAAGTA 59.598 37.037 0.00 0.00 0.00 2.24
5473 5598 7.306013 AGATACTCCTACAATCCACATTCCTA 58.694 38.462 0.00 0.00 0.00 2.94
5490 5615 9.344772 TGAGAATTCTACACTAGAAGATACTCC 57.655 37.037 8.25 0.00 46.90 3.85
5579 5713 6.835488 ACAAATGTGCAAGGGATTAGACATAT 59.165 34.615 0.00 0.00 0.00 1.78
5585 5724 4.220382 TGGAACAAATGTGCAAGGGATTAG 59.780 41.667 0.00 0.00 31.92 1.73
5597 5736 1.786937 TTGCCACCTGGAACAAATGT 58.213 45.000 0.00 0.00 38.70 2.71
5602 5741 1.838112 GATCATTGCCACCTGGAACA 58.162 50.000 0.00 0.00 37.39 3.18
5813 5952 4.631813 GGAATTCTGGATGCATACGGATAC 59.368 45.833 21.34 14.28 0.00 2.24
5814 5953 4.285775 TGGAATTCTGGATGCATACGGATA 59.714 41.667 21.34 12.31 0.00 2.59
5815 5954 3.072915 TGGAATTCTGGATGCATACGGAT 59.927 43.478 21.34 7.45 0.00 4.18
5816 5955 2.437651 TGGAATTCTGGATGCATACGGA 59.562 45.455 16.96 16.96 0.00 4.69
5818 5957 3.732212 TCTGGAATTCTGGATGCATACG 58.268 45.455 4.01 0.00 0.00 3.06
5819 5958 4.458295 CCATCTGGAATTCTGGATGCATAC 59.542 45.833 23.19 0.42 37.39 2.39
5820 5959 4.659115 CCATCTGGAATTCTGGATGCATA 58.341 43.478 23.19 3.04 37.39 3.14
5821 5960 3.497332 CCATCTGGAATTCTGGATGCAT 58.503 45.455 23.19 0.00 37.39 3.96
5822 5961 2.940158 CCATCTGGAATTCTGGATGCA 58.060 47.619 23.19 0.00 37.39 3.96
5823 5962 1.612463 GCCATCTGGAATTCTGGATGC 59.388 52.381 23.19 17.99 37.39 3.91
5824 5963 2.236766 GGCCATCTGGAATTCTGGATG 58.763 52.381 22.36 22.36 37.39 3.51
5825 5964 1.854939 TGGCCATCTGGAATTCTGGAT 59.145 47.619 14.06 10.57 37.39 3.41
5826 5965 1.297968 TGGCCATCTGGAATTCTGGA 58.702 50.000 14.06 8.93 37.39 3.86
5828 5967 1.340248 GCATGGCCATCTGGAATTCTG 59.660 52.381 17.61 2.83 37.39 3.02
5829 5968 1.063492 TGCATGGCCATCTGGAATTCT 60.063 47.619 17.61 0.00 37.39 2.40
5830 5969 1.405872 TGCATGGCCATCTGGAATTC 58.594 50.000 17.61 0.00 37.39 2.17
5831 5970 1.868713 TTGCATGGCCATCTGGAATT 58.131 45.000 17.61 0.00 37.39 2.17
5833 5972 1.758280 GAATTGCATGGCCATCTGGAA 59.242 47.619 17.61 15.89 37.39 3.53
5843 5982 5.231702 TGTGAATGTTTCAGAATTGCATGG 58.768 37.500 0.00 0.00 41.01 3.66
5944 6083 4.172512 CTGGGCGCAGAGATGGCT 62.173 66.667 25.55 0.00 0.00 4.75
6011 6150 4.821589 CTGGAAGGACTCGCCGCC 62.822 72.222 0.00 0.00 43.43 6.13
6013 6152 3.764466 AGCTGGAAGGACTCGCCG 61.764 66.667 0.00 0.00 43.43 6.46
6014 6153 2.125350 CAGCTGGAAGGACTCGCC 60.125 66.667 5.57 0.00 0.00 5.54
6244 6389 1.380785 AAGGATGGAGACGCCGGTA 60.381 57.895 1.90 0.00 40.66 4.02
6246 6391 2.107141 GAAGGATGGAGACGCCGG 59.893 66.667 0.00 0.00 40.66 6.13
6298 6443 5.243283 GGGGACTGAAGTAGCGATAAGAATA 59.757 44.000 0.00 0.00 0.00 1.75
6316 6465 1.153369 CGCGATCACAATGGGGACT 60.153 57.895 0.00 0.00 0.00 3.85
6321 6470 0.593008 CATTGGCGCGATCACAATGG 60.593 55.000 25.14 14.30 44.63 3.16
6333 6482 3.244561 ACCCTTAGATATCCACATTGGCG 60.245 47.826 0.00 0.00 37.47 5.69
6334 6483 4.373156 ACCCTTAGATATCCACATTGGC 57.627 45.455 0.00 0.00 37.47 4.52
6352 6509 0.811281 CGAAGAAAGATGGCCAACCC 59.189 55.000 10.96 1.57 33.59 4.11
6398 6556 0.670162 TTCTTGTTGCAGCTGCTTCC 59.330 50.000 36.61 24.14 42.66 3.46
6482 6640 2.932234 CGTCCTTCAGGTCTGCCGT 61.932 63.158 0.00 0.00 40.50 5.68
6486 6644 2.001812 CATCACGTCCTTCAGGTCTG 57.998 55.000 0.00 0.00 36.34 3.51
6490 6648 1.012086 CATGCATCACGTCCTTCAGG 58.988 55.000 0.00 0.00 0.00 3.86
6493 6651 1.097547 CCCCATGCATCACGTCCTTC 61.098 60.000 0.00 0.00 0.00 3.46
6517 6675 1.680651 CAGGGAGAGAGAGGCACGT 60.681 63.158 0.00 0.00 0.00 4.49
6551 6709 2.721167 CGCCGTCAGGAAGGATGGA 61.721 63.158 5.40 0.00 45.13 3.41
6580 6738 0.179100 CATCAAGCGGATCCGTCTGT 60.179 55.000 33.33 17.64 42.09 3.41
6641 6799 0.393132 ACAGAGACGAGAGATCCGCA 60.393 55.000 0.00 0.00 0.00 5.69
6665 6823 0.742281 CCAATCAGGTGAGTCTGCCG 60.742 60.000 0.00 0.00 34.91 5.69
6673 6831 0.991920 GGTTCCCTCCAATCAGGTGA 59.008 55.000 0.00 0.00 39.02 4.02
6675 6833 1.290134 GAGGTTCCCTCCAATCAGGT 58.710 55.000 0.00 0.00 44.36 4.00
6716 6874 2.112998 ACCGGAGACATTATTCCCGAA 58.887 47.619 9.46 0.00 42.49 4.30
6760 6918 0.623723 TAACCCTCTTGGCATGGACC 59.376 55.000 0.00 0.00 37.83 4.46
6820 6978 7.387397 CAGTTTCTCTTCTGAGTGCTTATTCTT 59.613 37.037 0.00 0.00 40.98 2.52
6837 6995 8.787852 GTCCACAAATTTATTCTCAGTTTCTCT 58.212 33.333 0.00 0.00 0.00 3.10
6842 7000 7.228706 ACGAAGTCCACAAATTTATTCTCAGTT 59.771 33.333 0.00 0.00 29.74 3.16
6891 7049 5.122239 TGCAGTTCAATGTCTACAATGTAGC 59.878 40.000 15.17 10.85 0.00 3.58
7021 7185 4.090786 CCCGTCTTTCACAACAACAAAAAC 59.909 41.667 0.00 0.00 0.00 2.43
7080 7244 7.228706 CACACCTTGAACACTTTTAGGACTTAT 59.771 37.037 0.00 0.00 0.00 1.73
7245 7409 0.466922 CTCTGGGTGGGATCATTGCC 60.467 60.000 0.00 0.00 0.00 4.52
7358 7522 3.364549 TCACATTTTTAGAGGCCATGGG 58.635 45.455 15.13 0.00 0.00 4.00
7493 7657 9.295214 CTGAGATGTTAGAAACTAGTGTATGTG 57.705 37.037 0.00 0.00 0.00 3.21
7494 7658 9.244292 TCTGAGATGTTAGAAACTAGTGTATGT 57.756 33.333 0.00 0.00 0.00 2.29
7540 7704 9.226606 TCTTTTGTGTGGTTCTATTGTAATAGG 57.773 33.333 10.77 0.00 39.06 2.57
7569 7733 7.013750 TGTTGGTTTACTTGCACATCTTTGATA 59.986 33.333 0.00 0.00 0.00 2.15
7615 7779 2.411748 ACATGATGTGTGTAGCGAAACG 59.588 45.455 0.00 0.00 40.28 3.60
7640 7804 0.547075 TTTTGGACCGGACAGGACAA 59.453 50.000 9.46 0.00 45.00 3.18
7642 7806 1.165270 CATTTTGGACCGGACAGGAC 58.835 55.000 9.46 0.00 45.00 3.85
7647 7811 0.671251 TTGTGCATTTTGGACCGGAC 59.329 50.000 9.46 0.00 37.97 4.79
7651 7815 4.058721 AGAAAGTTGTGCATTTTGGACC 57.941 40.909 0.00 0.00 37.97 4.46
7652 7816 4.507756 GGAAGAAAGTTGTGCATTTTGGAC 59.492 41.667 0.00 0.00 39.30 4.02
7654 7818 4.696455 AGGAAGAAAGTTGTGCATTTTGG 58.304 39.130 0.00 0.00 0.00 3.28
7656 7820 5.859205 AGAGGAAGAAAGTTGTGCATTTT 57.141 34.783 0.00 0.00 0.00 1.82
7664 7828 8.084073 TGCATTTTGAATAGAGGAAGAAAGTTG 58.916 33.333 0.00 0.00 0.00 3.16
7676 7840 7.169645 GCAAGAAAGTTGTGCATTTTGAATAGA 59.830 33.333 0.00 0.00 38.19 1.98
7681 7845 3.870419 GGCAAGAAAGTTGTGCATTTTGA 59.130 39.130 8.27 0.00 40.12 2.69
7688 7852 0.746659 ACAGGGCAAGAAAGTTGTGC 59.253 50.000 0.00 0.00 37.55 4.57
7701 7865 0.387239 GTGTGCATTTTCGACAGGGC 60.387 55.000 0.00 0.00 0.00 5.19
7703 7867 1.238439 AGGTGTGCATTTTCGACAGG 58.762 50.000 0.00 0.00 0.00 4.00
7704 7868 2.549754 AGAAGGTGTGCATTTTCGACAG 59.450 45.455 0.00 0.00 0.00 3.51
7705 7869 2.548057 GAGAAGGTGTGCATTTTCGACA 59.452 45.455 0.00 0.00 0.00 4.35
7706 7870 2.095718 GGAGAAGGTGTGCATTTTCGAC 60.096 50.000 0.00 0.00 0.00 4.20
7707 7871 2.151202 GGAGAAGGTGTGCATTTTCGA 58.849 47.619 0.00 0.00 0.00 3.71
7709 7873 2.887152 ACAGGAGAAGGTGTGCATTTTC 59.113 45.455 0.00 0.00 0.00 2.29
7712 7876 1.271597 GGACAGGAGAAGGTGTGCATT 60.272 52.381 0.00 0.00 35.27 3.56
7713 7877 0.326264 GGACAGGAGAAGGTGTGCAT 59.674 55.000 0.00 0.00 35.27 3.96
7753 7917 1.618343 CGAAGGGAAAGGCAAATGGTT 59.382 47.619 0.00 0.00 0.00 3.67
7757 7921 0.251787 AGGCGAAGGGAAAGGCAAAT 60.252 50.000 0.00 0.00 0.00 2.32
7771 7935 0.108585 ACCAGCAAAGAAGAAGGCGA 59.891 50.000 0.00 0.00 0.00 5.54
7814 7978 0.609151 CAAGGGATGCATTGCCACAA 59.391 50.000 6.12 0.00 38.58 3.33


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

AutoCloner maintained by Alex Coulton.