Multiple sequence alignment - TraesCS7B01G266000

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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 TraesCS7B01G266000 chr7B 100.000 5582 0 0 1 5582 488415395 488409814 0.000000e+00 10309.0
1 TraesCS7B01G266000 chr7B 88.596 114 11 2 1731 1842 729729604 729729491 2.710000e-28 137.0
2 TraesCS7B01G266000 chr7B 90.278 72 6 1 1663 1734 508824496 508824566 5.950000e-15 93.5
3 TraesCS7B01G266000 chr7B 90.000 70 6 1 1664 1733 231203905 231203837 7.700000e-14 89.8
4 TraesCS7B01G266000 chr7A 88.703 2691 157 58 3001 5582 536982262 536979610 0.000000e+00 3149.0
5 TraesCS7B01G266000 chr7A 90.621 1674 83 30 81 1737 536985121 536983505 0.000000e+00 2154.0
6 TraesCS7B01G266000 chr7A 96.517 1177 38 2 1815 2990 536983502 536982328 0.000000e+00 1943.0
7 TraesCS7B01G266000 chr7A 88.889 72 7 1 1663 1734 549715129 549715199 2.770000e-13 87.9
8 TraesCS7B01G266000 chr7D 89.082 2070 111 33 3588 5578 463264130 463266163 0.000000e+00 2464.0
9 TraesCS7B01G266000 chr7D 89.417 1682 83 26 81 1733 463260745 463262360 0.000000e+00 2032.0
10 TraesCS7B01G266000 chr7D 91.235 1004 57 8 2526 3526 463263156 463264131 0.000000e+00 1338.0
11 TraesCS7B01G266000 chr7D 94.678 714 35 3 1815 2527 463262363 463263074 0.000000e+00 1105.0
12 TraesCS7B01G266000 chr7D 94.030 67 4 0 3 69 463260695 463260761 9.890000e-18 102.0
13 TraesCS7B01G266000 chrUn 91.743 109 6 3 1741 1848 404803970 404804076 1.250000e-31 148.0
14 TraesCS7B01G266000 chrUn 91.743 109 6 3 1741 1848 475571272 475571378 1.250000e-31 148.0
15 TraesCS7B01G266000 chrUn 90.278 72 6 1 1663 1734 81694185 81694115 5.950000e-15 93.5
16 TraesCS7B01G266000 chr5B 93.750 96 6 0 1729 1824 446414412 446414507 1.620000e-30 145.0
17 TraesCS7B01G266000 chr5B 89.908 109 8 3 1741 1848 440653519 440653625 2.710000e-28 137.0
18 TraesCS7B01G266000 chr3B 95.556 90 4 0 1729 1818 797463911 797464000 1.620000e-30 145.0
19 TraesCS7B01G266000 chr3B 89.908 109 8 3 1741 1848 211109463 211109569 2.710000e-28 137.0
20 TraesCS7B01G266000 chr3A 88.235 119 13 1 1729 1847 469077472 469077589 2.100000e-29 141.0
21 TraesCS7B01G266000 chr1B 92.000 100 8 0 1729 1828 659725990 659725891 2.100000e-29 141.0
22 TraesCS7B01G266000 chr1A 90.278 72 6 1 1663 1734 382249611 382249541 5.950000e-15 93.5
23 TraesCS7B01G266000 chr1A 86.585 82 9 2 1663 1744 357769337 357769416 7.700000e-14 89.8
24 TraesCS7B01G266000 chr2B 90.000 70 6 1 1664 1733 157801867 157801799 7.700000e-14 89.8
25 TraesCS7B01G266000 chr5D 83.951 81 8 4 1664 1744 55700917 55700842 7.760000e-09 73.1
26 TraesCS7B01G266000 chr4A 97.368 38 1 0 1816 1853 514080043 514080006 1.300000e-06 65.8


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 TraesCS7B01G266000 chr7B 488409814 488415395 5581 True 10309.000000 10309 100.0000 1 5582 1 chr7B.!!$R2 5581
1 TraesCS7B01G266000 chr7A 536979610 536985121 5511 True 2415.333333 3149 91.9470 81 5582 3 chr7A.!!$R1 5501
2 TraesCS7B01G266000 chr7D 463260695 463266163 5468 False 1408.200000 2464 91.6884 3 5578 5 chr7D.!!$F1 5575

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
772 777 0.590195 GAGGGCTAGCGATGCAAATG 59.410 55.000 9.00 0.00 0.00 2.32 F
1316 1355 0.102481 ATAGACGTGCATCGGACCAC 59.898 55.000 12.18 1.65 44.69 4.16 F
1812 1884 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
1813 1885 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30 F
1814 1886 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 F
1815 1887 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59 F
1993 2065 0.530870 GATTAGGTGCTCCCGTCTGC 60.531 60.000 0.00 0.00 38.74 4.26 F
2462 2535 1.077212 ACCCTATGCTGCTTGGCTG 60.077 57.895 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1865 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
2317 2390 0.673333 CCGTCAGGCAAGCACATACA 60.673 55.000 0.00 0.0 0.00 2.29 R
3413 3629 1.344763 AGCGAGCACCCCATCTATAAC 59.655 52.381 0.00 0.0 0.00 1.89 R
3414 3630 1.717032 AGCGAGCACCCCATCTATAA 58.283 50.000 0.00 0.0 0.00 0.98 R
3561 3796 5.308497 TCCCTCCATAACAAACTGTAAGACA 59.692 40.000 0.00 0.0 37.43 3.41 R
3996 4246 3.780294 TGCACAGGGAGTTACTTATGGAT 59.220 43.478 0.00 0.0 0.00 3.41 R
4056 4307 9.177608 TGATTAAGTTCTGTAATCTTTGGGATG 57.822 33.333 5.92 0.0 38.33 3.51 R
4607 4883 0.257328 TGTGCCCTTCAGGTTGAACA 59.743 50.000 0.00 0.0 38.26 3.18 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
56 57 3.887621 CCTAACTGGCACTACTAAGCA 57.112 47.619 0.00 0.00 0.00 3.91
57 58 4.408182 CCTAACTGGCACTACTAAGCAT 57.592 45.455 0.00 0.00 0.00 3.79
58 59 5.531122 CCTAACTGGCACTACTAAGCATA 57.469 43.478 0.00 0.00 0.00 3.14
59 60 6.102897 CCTAACTGGCACTACTAAGCATAT 57.897 41.667 0.00 0.00 0.00 1.78
60 61 7.228314 CCTAACTGGCACTACTAAGCATATA 57.772 40.000 0.00 0.00 0.00 0.86
61 62 7.316640 CCTAACTGGCACTACTAAGCATATAG 58.683 42.308 0.00 0.00 0.00 1.31
62 63 6.978674 AACTGGCACTACTAAGCATATAGA 57.021 37.500 0.00 0.00 0.00 1.98
63 64 6.582677 ACTGGCACTACTAAGCATATAGAG 57.417 41.667 0.00 0.00 0.00 2.43
64 65 6.307776 ACTGGCACTACTAAGCATATAGAGA 58.692 40.000 0.00 0.00 0.00 3.10
65 66 6.778069 ACTGGCACTACTAAGCATATAGAGAA 59.222 38.462 0.00 0.00 0.00 2.87
66 67 6.982852 TGGCACTACTAAGCATATAGAGAAC 58.017 40.000 0.00 0.00 0.00 3.01
67 68 6.549736 TGGCACTACTAAGCATATAGAGAACA 59.450 38.462 0.00 0.00 0.00 3.18
68 69 7.233553 TGGCACTACTAAGCATATAGAGAACAT 59.766 37.037 0.00 0.00 0.00 2.71
69 70 7.543868 GGCACTACTAAGCATATAGAGAACATG 59.456 40.741 0.00 0.00 0.00 3.21
70 71 7.062839 GCACTACTAAGCATATAGAGAACATGC 59.937 40.741 0.00 0.00 44.29 4.06
105 106 4.262249 GCACATAGAGAACATCCTAGACCC 60.262 50.000 0.00 0.00 0.00 4.46
152 154 7.031372 CAGCATGTACAATCTTTACAAAGCAT 58.969 34.615 0.00 0.00 37.17 3.79
172 174 9.846248 AAAGCATTGATAACAGTATTCTTGTTC 57.154 29.630 0.00 0.00 0.00 3.18
185 187 8.049721 CAGTATTCTTGTTCCCTAATCTCCTTT 58.950 37.037 0.00 0.00 0.00 3.11
274 276 3.814842 TCACAAGTCACAATGCGAGAAAT 59.185 39.130 0.00 0.00 0.00 2.17
277 279 2.002586 AGTCACAATGCGAGAAATCGG 58.997 47.619 0.00 0.00 0.00 4.18
382 384 2.283894 TTCGGCAGAGCAGGAGGA 60.284 61.111 0.00 0.00 0.00 3.71
393 395 2.614969 AGGAGGAGGCATGCCCAA 60.615 61.111 33.14 0.00 36.58 4.12
404 406 1.083706 ATGCCCAACTCCCTCTCCT 59.916 57.895 0.00 0.00 0.00 3.69
471 473 2.202987 GGATCGTCAGCAGGGCAG 60.203 66.667 0.00 0.00 0.00 4.85
684 689 4.035792 CGGCGGTGGATATTTTACATTCAA 59.964 41.667 0.00 0.00 0.00 2.69
707 712 1.728425 ACCGTTCTTCCGCGTAAATTC 59.272 47.619 4.92 0.00 0.00 2.17
711 716 4.977963 CCGTTCTTCCGCGTAAATTCTATA 59.022 41.667 4.92 0.00 0.00 1.31
738 743 2.682269 GCTCCAAACTCCAGAGATTCCC 60.682 54.545 0.70 0.00 0.00 3.97
741 746 2.363683 CAAACTCCAGAGATTCCCTGC 58.636 52.381 0.70 0.00 0.00 4.85
772 777 0.590195 GAGGGCTAGCGATGCAAATG 59.410 55.000 9.00 0.00 0.00 2.32
806 811 3.060602 AGCACTCTCTCGCAAAAAGTAC 58.939 45.455 0.00 0.00 0.00 2.73
944 967 3.518998 CGAGACCGAGGCGACCAT 61.519 66.667 0.00 0.00 38.22 3.55
945 968 2.413765 GAGACCGAGGCGACCATC 59.586 66.667 0.00 0.00 0.00 3.51
946 969 3.140225 GAGACCGAGGCGACCATCC 62.140 68.421 0.00 0.00 0.00 3.51
947 970 4.222847 GACCGAGGCGACCATCCC 62.223 72.222 0.00 0.00 0.00 3.85
1118 1150 2.583441 CGGGCTCCAAGGTCAGTCA 61.583 63.158 0.00 0.00 0.00 3.41
1125 1157 1.811266 CAAGGTCAGTCATCCGGCG 60.811 63.158 0.00 0.00 0.00 6.46
1136 1168 4.137615 TCCGGCGGGGAGATGAGA 62.138 66.667 27.98 0.00 40.94 3.27
1137 1169 2.919856 CCGGCGGGGAGATGAGAT 60.920 66.667 20.56 0.00 38.47 2.75
1147 1179 0.602562 GAGATGAGATGCTCCTCCGG 59.397 60.000 0.00 0.00 32.32 5.14
1264 1303 0.392729 AAGATGTGAGCTGCTCTGCC 60.393 55.000 28.04 16.86 0.00 4.85
1316 1355 0.102481 ATAGACGTGCATCGGACCAC 59.898 55.000 12.18 1.65 44.69 4.16
1625 1689 5.012871 GGTACTAGTTTCTCAGGGGAAGTTT 59.987 44.000 0.00 0.00 0.00 2.66
1638 1702 2.496070 GGGAAGTTTAATTGGTGGCCTC 59.504 50.000 3.32 0.00 0.00 4.70
1696 1768 4.908736 ACTGAAATGAGTGAACAAACACG 58.091 39.130 0.00 0.00 44.35 4.49
1702 1774 4.530094 TGAGTGAACAAACACGCTAAAG 57.470 40.909 0.00 0.00 44.35 1.85
1719 1791 6.872670 GCTAAAGGCGTGTCTATATACATC 57.127 41.667 0.00 0.00 0.00 3.06
1795 1867 9.918630 CCTCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
1802 1874 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
1803 1875 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
1804 1876 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
1805 1877 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1806 1878 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1807 1879 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
1808 1880 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1809 1881 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1810 1882 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1811 1883 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1812 1884 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1813 1885 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1814 1886 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1815 1887 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1816 1888 0.682209 TTTCCGGACGGAGGGAGTAG 60.682 60.000 13.64 0.00 46.06 2.57
1822 1894 2.747467 CGGACGGAGGGAGTAGAACATA 60.747 54.545 0.00 0.00 0.00 2.29
1831 1903 9.587772 CGGAGGGAGTAGAACATATTATATTTG 57.412 37.037 0.00 0.00 0.00 2.32
1862 1934 2.221055 GGAGTAGCAAATTACGATGGCG 59.779 50.000 0.00 0.00 44.79 5.69
1902 1974 4.906618 TGTTTTATCTCAGGTTCCTCCAC 58.093 43.478 0.00 0.00 39.02 4.02
1907 1979 3.544698 TCTCAGGTTCCTCCACTAACT 57.455 47.619 0.00 0.00 39.02 2.24
1993 2065 0.530870 GATTAGGTGCTCCCGTCTGC 60.531 60.000 0.00 0.00 38.74 4.26
2118 2190 1.910722 GCTTGAGAGAGGATGGGCA 59.089 57.895 0.00 0.00 0.00 5.36
2294 2367 7.768120 AGAAACTATGTTCCTTAATCTCTGCAG 59.232 37.037 7.63 7.63 0.00 4.41
2300 2373 6.810911 TGTTCCTTAATCTCTGCAGACTATC 58.189 40.000 13.74 0.00 0.00 2.08
2317 2390 7.227512 GCAGACTATCTGTTTGGCTTATACAAT 59.772 37.037 7.62 0.00 45.94 2.71
2462 2535 1.077212 ACCCTATGCTGCTTGGCTG 60.077 57.895 0.00 0.00 0.00 4.85
2482 2555 4.081862 GCTGGTTACCTAGTACATGTGTGA 60.082 45.833 9.11 0.00 0.00 3.58
2796 2952 4.569943 TCTAGAATTCTTGTCACACCTGC 58.430 43.478 14.36 0.00 0.00 4.85
2999 3158 2.118313 CATCCAGTTCAGATGGTGCA 57.882 50.000 0.00 0.00 37.96 4.57
3036 3250 7.653767 ACCAGAACTAAAAGAACAGTAATCG 57.346 36.000 0.00 0.00 0.00 3.34
3048 3262 2.231478 ACAGTAATCGCAGCTGTGTACT 59.769 45.455 25.68 22.18 41.33 2.73
3054 3268 5.880054 AATCGCAGCTGTGTACTTAAATT 57.120 34.783 25.68 13.62 0.00 1.82
3095 3309 6.560003 TGATATCTATGACACCCACTGTTT 57.440 37.500 3.98 0.00 31.03 2.83
3158 3372 9.986833 TTCAGTCATTGTGTATTATCATTTTCG 57.013 29.630 0.00 0.00 0.00 3.46
3253 3467 8.831715 TGCTAAGCGATATATTGATCAGAAAA 57.168 30.769 3.97 0.00 0.00 2.29
3279 3493 7.715657 TCGAGTTAGTTGTAAGTTGGACTTTA 58.284 34.615 0.00 0.00 39.51 1.85
3438 3654 2.047061 AGATGGGGTGCTCGCTAATAA 58.953 47.619 2.72 0.00 0.00 1.40
3500 3716 6.708285 TCTTAGGGACAAATAGGTGAAAGAC 58.292 40.000 0.00 0.00 0.00 3.01
3510 3726 8.715088 ACAAATAGGTGAAAGACGTTATGTTAC 58.285 33.333 0.00 0.00 0.00 2.50
3530 3746 8.570068 TGTTACGTGCCATATATGATACTAGA 57.430 34.615 14.54 0.00 0.00 2.43
3531 3747 8.674607 TGTTACGTGCCATATATGATACTAGAG 58.325 37.037 14.54 3.25 0.00 2.43
3532 3748 8.675504 GTTACGTGCCATATATGATACTAGAGT 58.324 37.037 14.54 8.05 0.00 3.24
3533 3749 9.895138 TTACGTGCCATATATGATACTAGAGTA 57.105 33.333 14.54 7.26 34.67 2.59
3534 3750 8.211116 ACGTGCCATATATGATACTAGAGTAC 57.789 38.462 14.54 3.85 32.72 2.73
3536 3752 8.552865 CGTGCCATATATGATACTAGAGTACTC 58.447 40.741 15.41 15.41 32.72 2.59
3537 3753 9.621629 GTGCCATATATGATACTAGAGTACTCT 57.378 37.037 27.72 27.72 43.40 3.24
3551 3767 9.039165 ACTAGAGTACTCTATGATACTACCTCC 57.961 40.741 28.52 0.00 40.97 4.30
3552 3768 7.875338 AGAGTACTCTATGATACTACCTCCA 57.125 40.000 24.04 0.00 38.35 3.86
3554 3770 9.563593 AGAGTACTCTATGATACTACCTCCATA 57.436 37.037 24.04 0.00 38.35 2.74
3555 3771 9.603921 GAGTACTCTATGATACTACCTCCATAC 57.396 40.741 15.91 0.00 31.69 2.39
3556 3772 8.550585 AGTACTCTATGATACTACCTCCATACC 58.449 40.741 0.00 0.00 29.70 2.73
3561 3796 9.615660 TCTATGATACTACCTCCATACCAAAAT 57.384 33.333 0.00 0.00 0.00 1.82
3682 3921 9.541143 TTAGAATGTGATGTAAAAGCATCGATA 57.459 29.630 0.00 0.00 45.98 2.92
3734 3974 6.015010 TGTTCAACTGAAAAGGAGGTTTGAAA 60.015 34.615 0.00 0.00 35.58 2.69
3735 3975 6.790232 TCAACTGAAAAGGAGGTTTGAAAT 57.210 33.333 0.00 0.00 0.00 2.17
3797 4044 9.588096 ACTTTCCCTTTAACTATTCATTCTTGT 57.412 29.630 0.00 0.00 0.00 3.16
3891 4141 1.209504 TCGCCCAAACTAGATTCCAGG 59.790 52.381 0.00 0.00 0.00 4.45
4056 4307 8.345565 CAACCTGCATAATTTTCTAGTGGTATC 58.654 37.037 0.00 0.00 0.00 2.24
4061 4312 7.665559 TGCATAATTTTCTAGTGGTATCATCCC 59.334 37.037 0.00 0.00 0.00 3.85
4093 4344 6.349300 ACAGAACTTAATCATGAACGCCTAT 58.651 36.000 0.00 0.00 0.00 2.57
4186 4444 1.923356 ACTGGAAAATGATTGGGCGT 58.077 45.000 0.00 0.00 0.00 5.68
4264 4537 4.884164 GCTTCTGTTCCCTGCACTAATTAT 59.116 41.667 0.00 0.00 0.00 1.28
4270 4543 7.335924 TCTGTTCCCTGCACTAATTATTGTTAC 59.664 37.037 4.91 0.00 0.00 2.50
4271 4544 6.376018 TGTTCCCTGCACTAATTATTGTTACC 59.624 38.462 4.91 0.00 0.00 2.85
4477 4750 2.008268 GATTTGCTCATGCCCCACCG 62.008 60.000 0.00 0.00 38.71 4.94
4515 4791 2.988549 GAAGTCGAGCGCACGTGTG 61.989 63.158 25.76 24.45 34.70 3.82
4578 4854 2.212327 GCTAGGTAGCCAGCCAGAA 58.788 57.895 0.42 0.00 43.39 3.02
4583 4859 3.283259 AGGTAGCCAGCCAGAATAAAC 57.717 47.619 0.00 0.00 0.00 2.01
4598 4874 1.945354 TAAACGAGGAGCCTCTGCCG 61.945 60.000 14.19 4.59 40.69 5.69
4607 4883 4.335647 CCTCTGCCGCCCACAAGT 62.336 66.667 0.00 0.00 0.00 3.16
4675 4957 5.542779 AGAGGTTTGCCGTTCTATCATATC 58.457 41.667 0.00 0.00 40.50 1.63
4685 4970 6.019237 GCCGTTCTATCATATCAGCATGTATG 60.019 42.308 0.00 0.00 37.40 2.39
4686 4971 6.478016 CCGTTCTATCATATCAGCATGTATGG 59.522 42.308 0.00 0.00 37.40 2.74
4691 4976 9.155785 TCTATCATATCAGCATGTATGGATCAT 57.844 33.333 0.00 0.00 37.40 2.45
4692 4977 9.209175 CTATCATATCAGCATGTATGGATCATG 57.791 37.037 0.00 0.00 43.58 3.07
4739 5024 3.161866 TGTCATAAGGCCTTTGTTTCCC 58.838 45.455 26.08 6.28 0.00 3.97
4763 5048 0.668535 GATTACGCAATGGGGAAGCC 59.331 55.000 0.00 0.00 0.00 4.35
4804 5089 2.167487 GAGAGACAACACCTGGAGATCC 59.833 54.545 0.00 0.00 0.00 3.36
4820 5105 0.697511 ATCCCCGTTGATCCCCATCA 60.698 55.000 0.00 0.00 37.24 3.07
4833 5118 6.772605 TGATCCCCATCATCAAACTATACTG 58.227 40.000 0.00 0.00 33.80 2.74
4851 5144 4.248691 ACTGTACGGGTTTCAGTTACTC 57.751 45.455 6.65 0.00 39.00 2.59
4852 5145 3.006217 ACTGTACGGGTTTCAGTTACTCC 59.994 47.826 6.65 0.00 39.00 3.85
4853 5146 3.233507 TGTACGGGTTTCAGTTACTCCT 58.766 45.455 0.00 0.00 0.00 3.69
4861 5154 6.313164 CGGGTTTCAGTTACTCCTATTTTCTC 59.687 42.308 0.00 0.00 0.00 2.87
4950 5245 6.475727 AGAGATACGGTATGATGTTTTTGTCG 59.524 38.462 5.18 0.00 0.00 4.35
4951 5246 3.465122 ACGGTATGATGTTTTTGTCGC 57.535 42.857 0.00 0.00 0.00 5.19
4983 5288 1.226128 GCAAGACGGCTTTCATCGC 60.226 57.895 0.00 0.00 30.14 4.58
5000 5305 2.275380 GCCGGCTTGTTGGATGGTT 61.275 57.895 22.15 0.00 0.00 3.67
5084 5397 1.801913 CTCTCGGCGGAAAGACACG 60.802 63.158 7.21 0.00 0.00 4.49
5105 5418 2.559440 GATAGTTGAAGCTGCCAGGAG 58.441 52.381 0.00 0.00 0.00 3.69
5155 5495 2.641305 GAGCTTCATCATCCAGTGCTT 58.359 47.619 0.00 0.00 0.00 3.91
5170 5510 3.057104 CAGTGCTTGAATTTGATGCCAGA 60.057 43.478 0.00 0.00 0.00 3.86
5220 5563 2.321719 CCTAGAGCCCTAGACCTTTCC 58.678 57.143 3.42 0.00 44.00 3.13
5221 5564 2.090999 CCTAGAGCCCTAGACCTTTCCT 60.091 54.545 3.42 0.00 44.00 3.36
5222 5565 2.651642 AGAGCCCTAGACCTTTCCTT 57.348 50.000 0.00 0.00 0.00 3.36
5236 5579 6.067217 ACCTTTCCTTGCTCATATACTGTT 57.933 37.500 0.00 0.00 0.00 3.16
5242 5585 5.069648 TCCTTGCTCATATACTGTTCAGGAG 59.930 44.000 4.82 2.55 0.00 3.69
5250 5593 0.765510 ACTGTTCAGGAGGTTGACCC 59.234 55.000 4.82 0.00 36.42 4.46
5252 5595 0.764890 TGTTCAGGAGGTTGACCCAG 59.235 55.000 0.00 0.00 36.42 4.45
5255 5598 0.768221 TCAGGAGGTTGACCCAGCTT 60.768 55.000 0.00 0.00 36.42 3.74
5293 5636 6.502136 AAGGAGAATTTCAGAAAACCGATC 57.498 37.500 0.00 0.00 0.00 3.69
5318 5661 5.518848 TCTCATGTCAAAACTGCAACATT 57.481 34.783 0.00 0.00 30.16 2.71
5327 5670 2.292828 ACTGCAACATTAGGCCTTGT 57.707 45.000 12.58 7.62 0.00 3.16
5353 5704 6.282199 AGACGACAAGTAACCAACTATCAT 57.718 37.500 0.00 0.00 37.50 2.45
5362 5713 6.711277 AGTAACCAACTATCATCAAGCTGAA 58.289 36.000 0.00 0.00 36.36 3.02
5380 5731 6.921914 AGCTGAAGACTACGTTACACTAAAT 58.078 36.000 0.00 0.00 0.00 1.40
5381 5732 8.048534 AGCTGAAGACTACGTTACACTAAATA 57.951 34.615 0.00 0.00 0.00 1.40
5382 5733 8.182881 AGCTGAAGACTACGTTACACTAAATAG 58.817 37.037 0.00 0.00 0.00 1.73
5404 5757 2.025321 GGGCCTTCAATCTAGACCCAAA 60.025 50.000 0.84 0.00 35.84 3.28
5415 5768 5.223449 TCTAGACCCAAACACTACCAAAG 57.777 43.478 0.00 0.00 0.00 2.77
5424 5785 5.451798 CCAAACACTACCAAAGCTCAACAAT 60.452 40.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.924650 GGATACCACATAAGATAATTCGTACTT 57.075 33.333 0.00 0.00 0.00 2.24
5 6 9.310449 AGGATACCACATAAGATAATTCGTACT 57.690 33.333 0.00 0.00 37.17 2.73
6 7 9.355215 CAGGATACCACATAAGATAATTCGTAC 57.645 37.037 0.00 0.00 37.17 3.67
8 9 6.874134 GCAGGATACCACATAAGATAATTCGT 59.126 38.462 0.00 0.00 37.17 3.85
9 10 6.873605 TGCAGGATACCACATAAGATAATTCG 59.126 38.462 0.00 0.00 37.17 3.34
10 11 7.148340 GCTGCAGGATACCACATAAGATAATTC 60.148 40.741 17.12 0.00 37.17 2.17
11 12 6.656693 GCTGCAGGATACCACATAAGATAATT 59.343 38.462 17.12 0.00 37.17 1.40
13 14 5.513094 GGCTGCAGGATACCACATAAGATAA 60.513 44.000 17.12 0.00 37.17 1.75
14 15 4.020218 GGCTGCAGGATACCACATAAGATA 60.020 45.833 17.12 0.00 37.17 1.98
77 78 7.550906 GTCTAGGATGTTCTCTATGTGCTTTTT 59.449 37.037 0.00 0.00 0.00 1.94
78 79 7.044798 GTCTAGGATGTTCTCTATGTGCTTTT 58.955 38.462 0.00 0.00 0.00 2.27
79 80 6.407525 GGTCTAGGATGTTCTCTATGTGCTTT 60.408 42.308 0.00 0.00 0.00 3.51
80 81 5.069781 GGTCTAGGATGTTCTCTATGTGCTT 59.930 44.000 0.00 0.00 0.00 3.91
81 82 4.586841 GGTCTAGGATGTTCTCTATGTGCT 59.413 45.833 0.00 0.00 0.00 4.40
82 83 4.262249 GGGTCTAGGATGTTCTCTATGTGC 60.262 50.000 0.00 0.00 0.00 4.57
85 86 4.526262 CCAGGGTCTAGGATGTTCTCTATG 59.474 50.000 0.00 0.00 0.00 2.23
89 90 2.696187 GACCAGGGTCTAGGATGTTCTC 59.304 54.545 11.21 0.00 41.57 2.87
105 106 6.583806 GCTGTTCTGAATGTAAAATTGACCAG 59.416 38.462 0.00 0.00 0.00 4.00
204 206 2.031245 TGCATTGTACCAGTTTGAAGCG 60.031 45.455 0.00 0.00 0.00 4.68
274 276 3.733883 TTCTCCTCCTCTTAGTTCCGA 57.266 47.619 0.00 0.00 0.00 4.55
382 384 2.943265 AGGGAGTTGGGCATGCCT 60.943 61.111 34.70 16.75 36.10 4.75
471 473 4.000557 CACACACACTGCGCGGTC 62.001 66.667 21.45 0.00 0.00 4.79
635 637 1.007849 GGGATTCGCTCTCGCTCTC 60.008 63.158 0.00 0.00 35.26 3.20
636 638 2.494530 GGGGATTCGCTCTCGCTCT 61.495 63.158 0.40 0.00 35.26 4.09
660 665 2.695127 TGTAAAATATCCACCGCCGT 57.305 45.000 0.00 0.00 0.00 5.68
684 689 2.086251 TTACGCGGAAGAACGGTGGT 62.086 55.000 12.47 0.00 34.40 4.16
707 712 3.187700 GGAGTTTGGAGCACACGTATAG 58.812 50.000 0.00 0.00 0.00 1.31
711 716 0.532862 CTGGAGTTTGGAGCACACGT 60.533 55.000 0.00 0.00 0.00 4.49
738 743 1.378250 CCTCCTTCCCTTGCTGCAG 60.378 63.158 10.11 10.11 0.00 4.41
741 746 1.274703 TAGCCCTCCTTCCCTTGCTG 61.275 60.000 0.00 0.00 0.00 4.41
772 777 3.063485 GAGAGTGCTTCTGAAGTTGGAC 58.937 50.000 17.97 10.08 35.87 4.02
868 889 2.726822 CTTATTACCTCCCGCGGGGC 62.727 65.000 42.36 0.00 43.94 5.80
869 890 1.370064 CTTATTACCTCCCGCGGGG 59.630 63.158 42.36 31.16 46.11 5.73
870 891 1.301479 GCTTATTACCTCCCGCGGG 60.301 63.158 39.13 39.13 0.00 6.13
871 892 1.663702 CGCTTATTACCTCCCGCGG 60.664 63.158 21.04 21.04 37.25 6.46
872 893 1.663702 CCGCTTATTACCTCCCGCG 60.664 63.158 0.00 0.00 40.22 6.46
873 894 1.959738 GCCGCTTATTACCTCCCGC 60.960 63.158 0.00 0.00 0.00 6.13
874 895 0.179067 TTGCCGCTTATTACCTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
875 896 1.306148 GTTGCCGCTTATTACCTCCC 58.694 55.000 0.00 0.00 0.00 4.30
876 897 1.669265 GTGTTGCCGCTTATTACCTCC 59.331 52.381 0.00 0.00 0.00 4.30
877 898 2.352388 TGTGTTGCCGCTTATTACCTC 58.648 47.619 0.00 0.00 0.00 3.85
878 899 2.483014 TGTGTTGCCGCTTATTACCT 57.517 45.000 0.00 0.00 0.00 3.08
879 900 2.726681 CGTTGTGTTGCCGCTTATTACC 60.727 50.000 0.00 0.00 0.00 2.85
880 901 2.501881 CGTTGTGTTGCCGCTTATTAC 58.498 47.619 0.00 0.00 0.00 1.89
881 902 1.135916 GCGTTGTGTTGCCGCTTATTA 60.136 47.619 0.00 0.00 43.81 0.98
882 903 0.386731 GCGTTGTGTTGCCGCTTATT 60.387 50.000 0.00 0.00 43.81 1.40
883 904 1.209127 GCGTTGTGTTGCCGCTTAT 59.791 52.632 0.00 0.00 43.81 1.73
904 925 4.704103 TCGCTCTGGGCTGGGAGT 62.704 66.667 0.00 0.00 39.13 3.85
1118 1150 2.738510 ATCTCATCTCCCCGCCGGAT 62.739 60.000 5.05 0.00 41.00 4.18
1147 1179 4.157120 CGGGTGATCGGGGGTGAC 62.157 72.222 0.00 0.00 0.00 3.67
1165 1204 1.003545 CAATCGCAGCCACGGATTAAG 60.004 52.381 0.00 0.00 0.00 1.85
1264 1303 2.726351 GGTGGAGAAGAGGCGGGAG 61.726 68.421 0.00 0.00 0.00 4.30
1625 1689 5.376625 GAGTATCAATGAGGCCACCAATTA 58.623 41.667 5.01 0.00 33.17 1.40
1638 1702 3.118775 TGTGAACGGAGGGAGTATCAATG 60.119 47.826 0.00 0.00 36.25 2.82
1696 1768 5.805994 GGATGTATATAGACACGCCTTTAGC 59.194 44.000 1.52 0.00 38.52 3.09
1702 1774 4.634184 ATCGGATGTATATAGACACGCC 57.366 45.455 1.52 6.74 30.52 5.68
1769 1841 9.918630 ACTTGTCATCAAAATGAATAAAAGAGG 57.081 29.630 0.00 0.00 43.42 3.69
1777 1849 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
1778 1850 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
1779 1851 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
1780 1852 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1781 1853 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1782 1854 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1783 1855 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1784 1856 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1785 1857 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1786 1858 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1787 1859 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1788 1860 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1789 1861 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1790 1862 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1791 1863 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1792 1864 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1793 1865 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1794 1866 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1795 1867 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1796 1868 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1797 1869 0.682209 CTACTCCCTCCGTCCGGAAA 60.682 60.000 5.23 0.00 44.66 3.13
1798 1870 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
1799 1871 1.565390 TTCTACTCCCTCCGTCCGGA 61.565 60.000 0.00 0.00 42.90 5.14
1800 1872 1.077212 TTCTACTCCCTCCGTCCGG 60.077 63.158 0.00 0.00 0.00 5.14
1801 1873 0.679002 TGTTCTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
1802 1874 1.777941 ATGTTCTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
1803 1875 6.837471 ATAATATGTTCTACTCCCTCCGTC 57.163 41.667 0.00 0.00 0.00 4.79
1804 1876 8.896722 AATATAATATGTTCTACTCCCTCCGT 57.103 34.615 0.00 0.00 0.00 4.69
1805 1877 9.587772 CAAATATAATATGTTCTACTCCCTCCG 57.412 37.037 0.00 0.00 0.00 4.63
1815 1887 9.273016 CCTCCGTTCACAAATATAATATGTTCT 57.727 33.333 0.00 0.00 0.00 3.01
1816 1888 8.504005 CCCTCCGTTCACAAATATAATATGTTC 58.496 37.037 0.00 0.00 0.00 3.18
1822 1894 6.248569 ACTCCCTCCGTTCACAAATATAAT 57.751 37.500 0.00 0.00 0.00 1.28
1831 1903 0.606604 TTGCTACTCCCTCCGTTCAC 59.393 55.000 0.00 0.00 0.00 3.18
1862 1934 1.463444 ACATCTCGTTTAGCAAACCGC 59.537 47.619 6.29 0.00 38.14 5.68
1993 2065 2.571212 TGCACCTGGTACTTTTCAGTG 58.429 47.619 0.00 0.00 34.06 3.66
2062 2134 0.045623 ATGGACCCACCCACCTATGA 59.954 55.000 0.00 0.00 39.34 2.15
2118 2190 3.732048 AACCCTCCACCGACATTAATT 57.268 42.857 0.00 0.00 0.00 1.40
2294 2367 8.438676 ACATTGTATAAGCCAAACAGATAGTC 57.561 34.615 0.00 0.00 0.00 2.59
2300 2373 6.692681 GCACATACATTGTATAAGCCAAACAG 59.307 38.462 8.95 0.00 36.57 3.16
2317 2390 0.673333 CCGTCAGGCAAGCACATACA 60.673 55.000 0.00 0.00 0.00 2.29
2462 2535 4.081862 TGCTCACACATGTACTAGGTAACC 60.082 45.833 0.00 0.00 37.17 2.85
2905 3064 2.280797 GCTCAACACCAGGACGCA 60.281 61.111 0.00 0.00 0.00 5.24
2907 3066 2.002586 CTTATGCTCAACACCAGGACG 58.997 52.381 0.00 0.00 0.00 4.79
2998 3157 9.921637 TTTTAGTTCTGGTAAATGCCTATTTTG 57.078 29.630 0.00 0.00 37.64 2.44
3033 3247 6.978343 TTAATTTAAGTACACAGCTGCGAT 57.022 33.333 15.27 1.40 0.00 4.58
3095 3309 8.988934 GTGACAATAACAACAGACTAATCTTCA 58.011 33.333 0.00 0.00 30.42 3.02
3253 3467 6.342338 AGTCCAACTTACAACTAACTCGAT 57.658 37.500 0.00 0.00 0.00 3.59
3279 3493 8.579006 TGAAGAAAAATATGATCAACAGCTTGT 58.421 29.630 0.00 0.00 0.00 3.16
3329 3543 4.022589 CACTCTGAAAATGCACAATGGAGT 60.023 41.667 0.00 0.00 32.70 3.85
3331 3545 3.256383 CCACTCTGAAAATGCACAATGGA 59.744 43.478 0.00 0.00 0.00 3.41
3413 3629 1.344763 AGCGAGCACCCCATCTATAAC 59.655 52.381 0.00 0.00 0.00 1.89
3414 3630 1.717032 AGCGAGCACCCCATCTATAA 58.283 50.000 0.00 0.00 0.00 0.98
3510 3726 8.439993 AGTACTCTAGTATCATATATGGCACG 57.560 38.462 12.78 2.07 32.54 5.34
3529 3745 9.603921 GTATGGAGGTAGTATCATAGAGTACTC 57.396 40.741 15.41 15.41 33.48 2.59
3530 3746 8.550585 GGTATGGAGGTAGTATCATAGAGTACT 58.449 40.741 0.00 0.00 35.47 2.73
3531 3747 8.327271 TGGTATGGAGGTAGTATCATAGAGTAC 58.673 40.741 0.00 0.00 0.00 2.73
3532 3748 8.458951 TGGTATGGAGGTAGTATCATAGAGTA 57.541 38.462 0.00 0.00 0.00 2.59
3533 3749 7.344599 TGGTATGGAGGTAGTATCATAGAGT 57.655 40.000 0.00 0.00 0.00 3.24
3534 3750 8.651589 TTTGGTATGGAGGTAGTATCATAGAG 57.348 38.462 0.00 0.00 0.00 2.43
3536 3752 9.658799 CATTTTGGTATGGAGGTAGTATCATAG 57.341 37.037 0.00 0.00 0.00 2.23
3537 3753 9.166222 ACATTTTGGTATGGAGGTAGTATCATA 57.834 33.333 0.00 0.00 0.00 2.15
3538 3754 8.045720 ACATTTTGGTATGGAGGTAGTATCAT 57.954 34.615 0.00 0.00 0.00 2.45
3539 3755 7.347222 AGACATTTTGGTATGGAGGTAGTATCA 59.653 37.037 0.00 0.00 0.00 2.15
3540 3756 7.736893 AGACATTTTGGTATGGAGGTAGTATC 58.263 38.462 0.00 0.00 0.00 2.24
3541 3757 7.691993 AGACATTTTGGTATGGAGGTAGTAT 57.308 36.000 0.00 0.00 0.00 2.12
3542 3758 7.504926 AAGACATTTTGGTATGGAGGTAGTA 57.495 36.000 0.00 0.00 0.00 1.82
3543 3759 6.388619 AAGACATTTTGGTATGGAGGTAGT 57.611 37.500 0.00 0.00 0.00 2.73
3544 3760 7.335627 TGTAAGACATTTTGGTATGGAGGTAG 58.664 38.462 0.00 0.00 0.00 3.18
3547 3763 6.180472 ACTGTAAGACATTTTGGTATGGAGG 58.820 40.000 0.00 0.00 37.43 4.30
3548 3764 7.687941 AACTGTAAGACATTTTGGTATGGAG 57.312 36.000 0.00 0.00 37.43 3.86
3549 3765 7.504238 ACAAACTGTAAGACATTTTGGTATGGA 59.496 33.333 19.96 0.00 46.48 3.41
3550 3766 7.657336 ACAAACTGTAAGACATTTTGGTATGG 58.343 34.615 19.96 2.34 46.48 2.74
3554 3770 8.141268 CCATAACAAACTGTAAGACATTTTGGT 58.859 33.333 19.96 17.47 46.48 3.67
3555 3771 8.356657 TCCATAACAAACTGTAAGACATTTTGG 58.643 33.333 19.96 9.02 46.48 3.28
3561 3796 5.308497 TCCCTCCATAACAAACTGTAAGACA 59.692 40.000 0.00 0.00 37.43 3.41
3996 4246 3.780294 TGCACAGGGAGTTACTTATGGAT 59.220 43.478 0.00 0.00 0.00 3.41
4056 4307 9.177608 TGATTAAGTTCTGTAATCTTTGGGATG 57.822 33.333 5.92 0.00 38.33 3.51
4216 4474 9.264719 GCAAAATAAAGGCAATAATATGCTCTT 57.735 29.630 0.00 0.00 45.68 2.85
4217 4475 8.645110 AGCAAAATAAAGGCAATAATATGCTCT 58.355 29.630 0.00 0.00 45.68 4.09
4218 4476 8.822652 AGCAAAATAAAGGCAATAATATGCTC 57.177 30.769 0.00 0.00 45.68 4.26
4219 4477 9.264719 GAAGCAAAATAAAGGCAATAATATGCT 57.735 29.630 0.00 0.00 45.68 3.79
4220 4478 9.264719 AGAAGCAAAATAAAGGCAATAATATGC 57.735 29.630 0.00 0.00 45.67 3.14
4224 4482 9.154847 GAACAGAAGCAAAATAAAGGCAATAAT 57.845 29.630 0.00 0.00 0.00 1.28
4225 4483 7.602265 GGAACAGAAGCAAAATAAAGGCAATAA 59.398 33.333 0.00 0.00 0.00 1.40
4226 4484 7.096551 GGAACAGAAGCAAAATAAAGGCAATA 58.903 34.615 0.00 0.00 0.00 1.90
4227 4485 5.934043 GGAACAGAAGCAAAATAAAGGCAAT 59.066 36.000 0.00 0.00 0.00 3.56
4228 4486 5.296748 GGAACAGAAGCAAAATAAAGGCAA 58.703 37.500 0.00 0.00 0.00 4.52
4236 4509 2.036346 GTGCAGGGAACAGAAGCAAAAT 59.964 45.455 0.00 0.00 36.91 1.82
4270 4543 1.667724 GCAGCAGCAGTATAACAGTGG 59.332 52.381 0.00 0.00 41.58 4.00
4446 4719 5.734220 GCATGAGCAAATCGGTATGTGATTT 60.734 40.000 0.00 0.00 44.60 2.17
4578 4854 0.466124 GGCAGAGGCTCCTCGTTTAT 59.534 55.000 11.71 0.00 46.90 1.40
4598 4874 0.385390 CAGGTTGAACACTTGTGGGC 59.615 55.000 5.72 0.00 0.00 5.36
4607 4883 0.257328 TGTGCCCTTCAGGTTGAACA 59.743 50.000 0.00 0.00 38.26 3.18
4644 4926 2.767505 ACGGCAAACCTCTTCTTACAG 58.232 47.619 0.00 0.00 0.00 2.74
4660 4942 4.248859 ACATGCTGATATGATAGAACGGC 58.751 43.478 0.00 0.00 0.00 5.68
4662 4944 7.260603 TCCATACATGCTGATATGATAGAACG 58.739 38.462 0.00 0.00 31.54 3.95
4675 4957 6.262496 AGACTTTTCATGATCCATACATGCTG 59.738 38.462 0.00 0.00 43.03 4.41
4685 4970 5.006386 AGGTGACAAGACTTTTCATGATCC 58.994 41.667 7.29 4.38 0.00 3.36
4686 4971 6.016777 ACAAGGTGACAAGACTTTTCATGATC 60.017 38.462 7.29 0.00 0.00 2.92
4691 4976 5.492895 TGTACAAGGTGACAAGACTTTTCA 58.507 37.500 0.00 0.00 0.00 2.69
4692 4977 6.619801 ATGTACAAGGTGACAAGACTTTTC 57.380 37.500 0.00 0.00 0.00 2.29
4739 5024 2.917933 TCCCCATTGCGTAATCTTCTG 58.082 47.619 0.00 0.00 0.00 3.02
4763 5048 0.807275 TTGTCATCATGGCGCTCTCG 60.807 55.000 7.64 0.00 39.07 4.04
4804 5089 0.473755 TGATGATGGGGATCAACGGG 59.526 55.000 0.00 0.00 33.83 5.28
4820 5105 6.938507 TGAAACCCGTACAGTATAGTTTGAT 58.061 36.000 9.21 0.00 0.00 2.57
4833 5118 3.949842 AGGAGTAACTGAAACCCGTAC 57.050 47.619 0.00 0.00 0.00 3.67
4851 5144 2.289565 GGCTTCCCACGAGAAAATAGG 58.710 52.381 0.00 0.00 0.00 2.57
4852 5145 2.985896 TGGCTTCCCACGAGAAAATAG 58.014 47.619 0.00 0.00 35.79 1.73
4853 5146 3.426787 TTGGCTTCCCACGAGAAAATA 57.573 42.857 0.00 0.00 41.97 1.40
4861 5154 3.243068 GCAGTATTTATTGGCTTCCCACG 60.243 47.826 0.00 0.00 41.97 4.94
4933 5226 2.173964 GCGCGACAAAAACATCATACC 58.826 47.619 12.10 0.00 0.00 2.73
4965 5260 1.226128 GCGATGAAAGCCGTCTTGC 60.226 57.895 0.00 0.00 31.78 4.01
4983 5288 1.201414 GTAAACCATCCAACAAGCCGG 59.799 52.381 0.00 0.00 0.00 6.13
5052 5360 2.932622 GCCGAGAGCTGTCATCAAAAGA 60.933 50.000 11.90 0.00 38.99 2.52
5058 5366 2.279120 CCGCCGAGAGCTGTCATC 60.279 66.667 11.90 0.61 40.39 2.92
5081 5394 1.009829 GGCAGCTTCAACTATCCGTG 58.990 55.000 0.00 0.00 0.00 4.94
5084 5397 1.210478 TCCTGGCAGCTTCAACTATCC 59.790 52.381 9.56 0.00 0.00 2.59
5155 5495 5.759059 AGGAATAGTCTGGCATCAAATTCA 58.241 37.500 12.08 0.00 0.00 2.57
5170 5510 8.903820 CGAGGAATTTTATTGGAAAGGAATAGT 58.096 33.333 0.00 0.00 0.00 2.12
5220 5563 5.163364 ACCTCCTGAACAGTATATGAGCAAG 60.163 44.000 1.18 0.00 0.00 4.01
5221 5564 4.716784 ACCTCCTGAACAGTATATGAGCAA 59.283 41.667 1.18 0.00 0.00 3.91
5222 5565 4.290093 ACCTCCTGAACAGTATATGAGCA 58.710 43.478 1.18 0.00 0.00 4.26
5236 5579 0.768221 AAGCTGGGTCAACCTCCTGA 60.768 55.000 0.00 0.00 41.11 3.86
5250 5593 0.179078 TTTTGCTGGCACCAAAGCTG 60.179 50.000 7.91 0.00 40.21 4.24
5252 5595 3.077617 TTTTTGCTGGCACCAAAGC 57.922 47.368 7.91 0.00 39.96 3.51
5275 5618 6.094048 TGAGATGGATCGGTTTTCTGAAATTC 59.906 38.462 3.31 1.07 38.81 2.17
5278 5621 4.905429 TGAGATGGATCGGTTTTCTGAAA 58.095 39.130 0.00 0.00 38.81 2.69
5293 5636 4.232221 GTTGCAGTTTTGACATGAGATGG 58.768 43.478 0.00 0.00 33.60 3.51
5318 5661 4.913335 CTTGTCGTCTATACAAGGCCTA 57.087 45.455 5.16 0.00 46.52 3.93
5327 5670 8.510243 TGATAGTTGGTTACTTGTCGTCTATA 57.490 34.615 0.00 0.00 38.33 1.31
5344 5687 6.198029 CGTAGTCTTCAGCTTGATGATAGTTG 59.802 42.308 0.00 0.00 33.89 3.16
5353 5704 4.277672 AGTGTAACGTAGTCTTCAGCTTGA 59.722 41.667 0.00 0.00 45.00 3.02
5362 5713 5.068329 GCCCCTATTTAGTGTAACGTAGTCT 59.932 44.000 0.00 0.00 45.00 3.24
5380 5731 2.690840 GGTCTAGATTGAAGGCCCCTA 58.309 52.381 0.00 0.00 32.25 3.53
5381 5732 1.512735 GGTCTAGATTGAAGGCCCCT 58.487 55.000 0.00 0.00 32.25 4.79
5404 5757 7.165485 TGTATATTGTTGAGCTTTGGTAGTGT 58.835 34.615 0.00 0.00 0.00 3.55
5415 5768 9.884465 GTCTTTTATCCATGTATATTGTTGAGC 57.116 33.333 0.00 0.00 0.00 4.26
5480 5842 3.064900 AGGCAGGAAAATGACTCTGTC 57.935 47.619 0.00 0.00 30.65 3.51


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

AutoCloner maintained by Alex Coulton.