Multiple sequence alignment - TraesCS7D01G064400

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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 TraesCS7D01G064400 chr7D 100.000 5614 0 0 1 5614 35605143 35599530 0.000000e+00 10368.0
1 TraesCS7D01G064400 chr7D 100.000 30 0 0 1091 1120 35322191 35322220 7.860000e-04 56.5
2 TraesCS7D01G064400 chr4A 92.220 4203 192 40 839 4979 688091899 688096028 0.000000e+00 5825.0
3 TraesCS7D01G064400 chr4A 84.160 1250 130 30 4 1221 688386933 688385720 0.000000e+00 1149.0
4 TraesCS7D01G064400 chr4A 86.082 776 92 11 3 773 688091105 688091869 0.000000e+00 821.0
5 TraesCS7D01G064400 chr4A 86.227 697 54 13 1147 1828 216171686 216172355 0.000000e+00 717.0
6 TraesCS7D01G064400 chr4A 79.107 560 67 22 924 1452 688338796 688338256 1.940000e-89 340.0
7 TraesCS7D01G064400 chr4A 80.658 486 54 18 987 1452 688383871 688383406 1.940000e-89 340.0
8 TraesCS7D01G064400 chr4A 88.073 109 11 2 1604 1710 688338126 688338018 1.640000e-25 128.0
9 TraesCS7D01G064400 chr7A 92.564 2945 125 41 2470 5396 35772596 35769728 0.000000e+00 4139.0
10 TraesCS7D01G064400 chr7A 86.024 1846 166 37 25 1828 35774978 35773183 0.000000e+00 1895.0
11 TraesCS7D01G064400 chr7A 90.748 508 40 5 1972 2473 35773204 35772698 0.000000e+00 671.0
12 TraesCS7D01G064400 chr7A 89.773 88 2 3 5531 5611 35769487 35769400 7.690000e-19 106.0
13 TraesCS7D01G064400 chr7A 100.000 31 0 0 1091 1121 36097808 36097778 2.180000e-04 58.4
14 TraesCS7D01G064400 chr5D 84.182 550 50 12 1147 1681 556631486 556632013 3.020000e-137 499.0
15 TraesCS7D01G064400 chr2A 86.589 343 46 0 2557 2899 513843442 513843784 4.100000e-101 379.0
16 TraesCS7D01G064400 chr2A 80.258 233 27 9 1984 2216 484993283 484993070 2.090000e-34 158.0
17 TraesCS7D01G064400 chr3A 92.453 159 3 2 1834 1983 80090634 80090476 9.470000e-53 219.0
18 TraesCS7D01G064400 chr3A 83.436 163 6 8 1829 1982 387286018 387286168 1.270000e-26 132.0
19 TraesCS7D01G064400 chr2D 80.632 253 30 9 1984 2236 576108154 576108387 1.610000e-40 178.0
20 TraesCS7D01G064400 chr3D 87.117 163 11 2 1829 1982 292035540 292035379 5.780000e-40 176.0
21 TraesCS7D01G064400 chr1B 87.097 155 7 4 1829 1983 530658856 530658997 4.500000e-36 163.0
22 TraesCS7D01G064400 chrUn 88.182 110 12 1 1981 2090 766470 766362 4.560000e-26 130.0
23 TraesCS7D01G064400 chrUn 88.182 110 12 1 1981 2090 71270776 71270884 4.560000e-26 130.0
24 TraesCS7D01G064400 chrUn 88.182 110 12 1 1981 2090 370168385 370168277 4.560000e-26 130.0
25 TraesCS7D01G064400 chr2B 88.182 110 12 1 1981 2090 6771092 6770984 4.560000e-26 130.0
26 TraesCS7D01G064400 chr2B 88.182 110 12 1 1981 2090 6819053 6818945 4.560000e-26 130.0
27 TraesCS7D01G064400 chr2B 88.182 110 12 1 1981 2090 6906524 6906416 4.560000e-26 130.0
28 TraesCS7D01G064400 chr1D 96.203 79 3 0 1905 1983 14986812 14986890 4.560000e-26 130.0
29 TraesCS7D01G064400 chr1D 92.941 85 4 1 1829 1913 392020231 392020149 7.640000e-24 122.0
30 TraesCS7D01G064400 chr1A 88.182 110 12 1 1981 2090 74242624 74242732 4.560000e-26 130.0
31 TraesCS7D01G064400 chr1A 83.217 143 11 2 1829 1969 493272946 493273077 9.880000e-23 119.0


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 TraesCS7D01G064400 chr7D 35599530 35605143 5613 True 10368.00 10368 100.00000 1 5614 1 chr7D.!!$R1 5613
1 TraesCS7D01G064400 chr4A 688091105 688096028 4923 False 3323.00 5825 89.15100 3 4979 2 chr4A.!!$F2 4976
2 TraesCS7D01G064400 chr4A 688383406 688386933 3527 True 744.50 1149 82.40900 4 1452 2 chr4A.!!$R2 1448
3 TraesCS7D01G064400 chr4A 216171686 216172355 669 False 717.00 717 86.22700 1147 1828 1 chr4A.!!$F1 681
4 TraesCS7D01G064400 chr4A 688338018 688338796 778 True 234.00 340 83.59000 924 1710 2 chr4A.!!$R1 786
5 TraesCS7D01G064400 chr7A 35769400 35774978 5578 True 1702.75 4139 89.77725 25 5611 4 chr7A.!!$R2 5586
6 TraesCS7D01G064400 chr5D 556631486 556632013 527 False 499.00 499 84.18200 1147 1681 1 chr5D.!!$F1 534

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
160 161 0.179113 CTTTGCCAGGCACAACGTTT 60.179 50.000 15.89 0.0 38.71 3.60 F
1129 3246 0.178068 TTCTGCTAGGCCGTCCAATC 59.822 55.000 0.00 0.0 33.74 2.67 F
1570 3735 0.109597 CACAATCTTGCGTTGAGGCC 60.110 55.000 0.00 0.0 0.00 5.19 F
1590 3755 0.119155 TGAGGGGAGGAGTTGGTGAT 59.881 55.000 0.00 0.0 0.00 3.06 F
1949 4128 1.003718 GTTAGAGCGGGTGGTGCTT 60.004 57.895 0.00 0.0 44.18 3.91 F
3014 5318 1.021390 AAGAGGCTGTGAAATCCGCG 61.021 55.000 0.00 0.0 0.00 6.46 F
4306 6614 0.389391 AACCGGGAGATGCTCATACG 59.611 55.000 6.32 0.0 31.08 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 3671 0.321564 TGCATCCAGTGTGTAGTGCC 60.322 55.000 0.00 0.0 0.00 5.01 R
2853 5155 0.322816 AAGTACTGACCTCGCCCGTA 60.323 55.000 0.00 0.0 0.00 4.02 R
3353 5657 0.650512 AATAACGTGAGAATGCCGCG 59.349 50.000 0.00 0.0 42.51 6.46 R
3480 5784 1.429930 TAACAAGTGACTGGCCTGGA 58.570 50.000 14.82 0.0 0.00 3.86 R
3657 5963 3.854666 AGAGCACACACAGCTAGTTATG 58.145 45.455 0.00 0.0 43.58 1.90 R
4422 6733 0.321653 AGGAACACCGGCATGAAGAC 60.322 55.000 0.00 0.0 0.00 3.01 R
5198 7513 0.037877 AGTCATGCAAAGAGCCAGCT 59.962 50.000 0.00 0.0 44.83 4.24 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 1.056660 GTCCCCTCCTTGTTGTCTCA 58.943 55.000 0.00 0.00 0.00 3.27
160 161 0.179113 CTTTGCCAGGCACAACGTTT 60.179 50.000 15.89 0.00 38.71 3.60
161 162 0.247736 TTTGCCAGGCACAACGTTTT 59.752 45.000 15.89 0.00 38.71 2.43
162 163 0.459237 TTGCCAGGCACAACGTTTTG 60.459 50.000 15.89 10.08 38.71 2.44
164 165 0.382515 GCCAGGCACAACGTTTTGTA 59.617 50.000 15.34 0.00 44.57 2.41
170 171 3.058501 AGGCACAACGTTTTGTATAGCAC 60.059 43.478 15.34 0.00 44.57 4.40
190 191 3.123621 CACGTAGCATCAACCACTCTTTC 59.876 47.826 0.00 0.00 0.00 2.62
202 203 2.290577 CCACTCTTTCTTCCTCAAGGGG 60.291 54.545 0.00 0.00 35.41 4.79
331 332 6.546403 TGTTTGCTTGTTACCACCATAGTTTA 59.454 34.615 0.00 0.00 0.00 2.01
380 381 6.581171 AGATCGCAGTATTCAGATGTATCA 57.419 37.500 0.00 0.00 0.00 2.15
392 393 3.883489 CAGATGTATCAGGTACACGAGGA 59.117 47.826 0.00 0.00 45.59 3.71
406 407 3.007940 ACACGAGGAAATTGGAGACATCA 59.992 43.478 0.00 0.00 42.32 3.07
412 413 4.725810 AGGAAATTGGAGACATCAGGAGAT 59.274 41.667 0.00 0.00 42.32 2.75
463 464 7.560368 ACAACCTAATATCTTCTCAGGTTCTG 58.440 38.462 1.40 0.00 45.55 3.02
531 532 2.943036 TTTCTTGAAAGGCGGTAGGT 57.057 45.000 0.00 0.00 0.00 3.08
540 541 1.153229 GGCGGTAGGTCCATGAACC 60.153 63.158 0.00 0.00 39.80 3.62
579 580 2.090400 GCTCTTGACAGCTCACATCA 57.910 50.000 0.00 0.00 36.38 3.07
674 676 0.329261 TGGTGAAGCCATTCCTCCTG 59.671 55.000 0.00 0.00 43.61 3.86
680 682 0.984230 AGCCATTCCTCCTGTTCGAA 59.016 50.000 0.00 0.00 0.00 3.71
688 690 5.477607 TTCCTCCTGTTCGAAAGATTGTA 57.522 39.130 0.00 0.00 41.60 2.41
699 701 5.163513 TCGAAAGATTGTACCCGTAACTTC 58.836 41.667 0.00 0.00 33.31 3.01
702 704 4.895668 AGATTGTACCCGTAACTTCCAA 57.104 40.909 0.00 0.00 0.00 3.53
709 711 4.577834 ACCCGTAACTTCCAAAACAATG 57.422 40.909 0.00 0.00 0.00 2.82
716 718 2.043411 CTTCCAAAACAATGTCGTGCG 58.957 47.619 0.00 0.00 0.00 5.34
722 724 1.781025 AACAATGTCGTGCGGTGTGG 61.781 55.000 0.00 0.00 0.00 4.17
726 728 2.357034 GTCGTGCGGTGTGGTCAT 60.357 61.111 0.00 0.00 0.00 3.06
745 747 9.573133 GTGGTCATTACTTTCTGAAATTTATGG 57.427 33.333 15.03 2.69 0.00 2.74
783 786 0.251297 TGCCAGGAGAAACACATGGG 60.251 55.000 0.00 0.00 0.00 4.00
808 811 9.136323 GGGACCTTACATAAATCAAGAATTCAT 57.864 33.333 8.44 0.00 0.00 2.57
890 917 1.623686 ACCCCAGGCCCAGAATCAT 60.624 57.895 0.00 0.00 0.00 2.45
894 921 1.396653 CCAGGCCCAGAATCATCAAC 58.603 55.000 0.00 0.00 0.00 3.18
895 922 1.341285 CCAGGCCCAGAATCATCAACA 60.341 52.381 0.00 0.00 0.00 3.33
896 923 2.022195 CAGGCCCAGAATCATCAACAG 58.978 52.381 0.00 0.00 0.00 3.16
957 996 2.622962 CGAACGAACCCCCAAAGCC 61.623 63.158 0.00 0.00 0.00 4.35
958 997 2.596338 AACGAACCCCCAAAGCCG 60.596 61.111 0.00 0.00 0.00 5.52
961 1000 2.915137 GAACCCCCAAAGCCGCAA 60.915 61.111 0.00 0.00 0.00 4.85
962 1001 3.220999 GAACCCCCAAAGCCGCAAC 62.221 63.158 0.00 0.00 0.00 4.17
963 1002 3.749284 AACCCCCAAAGCCGCAACT 62.749 57.895 0.00 0.00 0.00 3.16
1121 3238 1.134371 CAGGTAGGTTTCTGCTAGGCC 60.134 57.143 0.00 0.00 0.00 5.19
1128 3245 0.618458 TTTCTGCTAGGCCGTCCAAT 59.382 50.000 0.00 0.00 33.74 3.16
1129 3246 0.178068 TTCTGCTAGGCCGTCCAATC 59.822 55.000 0.00 0.00 33.74 2.67
1132 3249 1.367840 GCTAGGCCGTCCAATCGAT 59.632 57.895 0.00 0.00 33.74 3.59
1133 3250 0.667792 GCTAGGCCGTCCAATCGATC 60.668 60.000 0.00 0.00 33.74 3.69
1134 3251 0.387367 CTAGGCCGTCCAATCGATCG 60.387 60.000 9.36 9.36 33.74 3.69
1135 3252 0.820482 TAGGCCGTCCAATCGATCGA 60.820 55.000 21.86 21.86 33.74 3.59
1136 3253 1.006102 GGCCGTCCAATCGATCGAT 60.006 57.895 24.60 24.60 36.23 3.59
1137 3254 1.009389 GGCCGTCCAATCGATCGATC 61.009 60.000 29.48 15.68 33.08 3.69
1372 3517 2.174107 CGTGTGAATGGCTGTGCG 59.826 61.111 0.00 0.00 0.00 5.34
1373 3518 2.316867 CGTGTGAATGGCTGTGCGA 61.317 57.895 0.00 0.00 0.00 5.10
1459 3604 2.680577 ACGAACCGTGTTTATCTCCAC 58.319 47.619 0.00 0.00 39.18 4.02
1465 3618 4.457466 ACCGTGTTTATCTCCACTGTTTT 58.543 39.130 0.00 0.00 0.00 2.43
1479 3637 8.137437 TCTCCACTGTTTTTCTCAAATTGATTC 58.863 33.333 0.00 0.00 0.00 2.52
1564 3729 1.174712 AGCCTGCACAATCTTGCGTT 61.175 50.000 0.00 0.00 46.20 4.84
1565 3730 1.005294 GCCTGCACAATCTTGCGTTG 61.005 55.000 0.00 0.00 46.20 4.10
1566 3731 0.592637 CCTGCACAATCTTGCGTTGA 59.407 50.000 0.00 0.00 46.20 3.18
1567 3732 1.400629 CCTGCACAATCTTGCGTTGAG 60.401 52.381 0.00 0.00 46.20 3.02
1568 3733 0.592637 TGCACAATCTTGCGTTGAGG 59.407 50.000 0.00 0.00 46.20 3.86
1569 3734 0.730494 GCACAATCTTGCGTTGAGGC 60.730 55.000 0.00 0.00 31.51 4.70
1570 3735 0.109597 CACAATCTTGCGTTGAGGCC 60.110 55.000 0.00 0.00 0.00 5.19
1590 3755 0.119155 TGAGGGGAGGAGTTGGTGAT 59.881 55.000 0.00 0.00 0.00 3.06
1591 3756 1.364678 TGAGGGGAGGAGTTGGTGATA 59.635 52.381 0.00 0.00 0.00 2.15
1592 3757 1.763545 GAGGGGAGGAGTTGGTGATAC 59.236 57.143 0.00 0.00 0.00 2.24
1596 3764 2.168728 GGGAGGAGTTGGTGATACTGTC 59.831 54.545 0.00 0.00 0.00 3.51
1601 3769 3.997021 GGAGTTGGTGATACTGTCTTGTG 59.003 47.826 0.00 0.00 0.00 3.33
1645 3815 5.466728 TGAGCTCAACTGTTAACAAGATGTC 59.533 40.000 15.67 7.98 0.00 3.06
1743 3913 4.709397 AGTCTGAGGAGAGTTGGTGATAAG 59.291 45.833 0.00 0.00 0.00 1.73
1808 3978 4.516698 ACAAACACTTCCTGCTGTAGATTG 59.483 41.667 0.00 0.00 0.00 2.67
1949 4128 1.003718 GTTAGAGCGGGTGGTGCTT 60.004 57.895 0.00 0.00 44.18 3.91
1993 4172 7.365741 GCTTTATAAACCATGATCCATGAGTG 58.634 38.462 8.38 0.00 43.81 3.51
2070 4250 6.036191 GCTATTCACTAAGTACCTGTTTCTGC 59.964 42.308 0.00 0.00 0.00 4.26
2104 4284 9.462174 CATTTTTCTATCACAAGCTGTTAAACA 57.538 29.630 0.00 0.00 0.00 2.83
2132 4315 5.365025 TGTTTTTGGTGAATTTGGGAGATCA 59.635 36.000 0.00 0.00 0.00 2.92
2159 4342 4.473196 TCCATTGTCCTCAACTAAGCCATA 59.527 41.667 0.00 0.00 36.33 2.74
2188 4371 5.790593 AGTTCTTATTCGAGGTTAACAGCA 58.209 37.500 8.10 0.00 0.00 4.41
2189 4372 5.869888 AGTTCTTATTCGAGGTTAACAGCAG 59.130 40.000 8.10 0.00 0.00 4.24
2260 4443 6.387465 CGGCTCCGTGAAGATAAGATATTTA 58.613 40.000 0.00 0.00 34.35 1.40
2419 4610 8.754080 AGTATTCAGATGCTACTAGTTCACTTT 58.246 33.333 0.00 0.00 0.00 2.66
2455 4646 8.699130 TGCAGAGAGAATTATCAGTCTTCATTA 58.301 33.333 2.42 0.00 0.00 1.90
2819 5121 9.760077 TGAAGAGTTTAGTGGAGTTTTAGTTAG 57.240 33.333 0.00 0.00 0.00 2.34
2853 5155 4.699257 GCTCTTGATGATCTTTGTGGTCTT 59.301 41.667 0.00 0.00 0.00 3.01
2949 5253 3.506455 TCTGCTTCTGCTTACGTCTTACT 59.494 43.478 0.00 0.00 40.48 2.24
2999 5303 4.508662 CCTTGCCTGGTTACTTAGAAGAG 58.491 47.826 0.00 0.00 0.00 2.85
3014 5318 1.021390 AAGAGGCTGTGAAATCCGCG 61.021 55.000 0.00 0.00 0.00 6.46
3050 5354 6.040166 ACATGACATATCTGGAATCTTTTGGC 59.960 38.462 0.00 0.00 0.00 4.52
3095 5399 2.283529 GGTGGAGAGCGAGTTGGGA 61.284 63.158 0.00 0.00 0.00 4.37
3221 5525 9.562408 TCTTATACCAGTCTCTATTGTAGTCTG 57.438 37.037 0.00 0.00 0.00 3.51
3222 5526 9.344772 CTTATACCAGTCTCTATTGTAGTCTGT 57.655 37.037 0.00 0.00 0.00 3.41
3353 5657 9.341899 CTTTTTGTGCAAGGTGTTTCTATATAC 57.658 33.333 0.00 0.00 0.00 1.47
3480 5784 4.827284 CCAAGGGGCAAAGTATCGAATATT 59.173 41.667 0.00 0.00 0.00 1.28
3557 5861 6.407525 GGTGATATAGACCAGAAAAGACAGCT 60.408 42.308 0.00 0.00 33.25 4.24
3561 5865 4.899352 AGACCAGAAAAGACAGCTGTAT 57.101 40.909 21.73 15.20 0.00 2.29
3581 5885 8.066595 GCTGTATCTTACAATTGCTATGAACAG 58.933 37.037 17.48 17.48 38.38 3.16
3610 5914 7.941053 ACCTTGTCTAACAACCCCATATATA 57.059 36.000 0.00 0.00 33.96 0.86
3611 5915 8.520119 ACCTTGTCTAACAACCCCATATATAT 57.480 34.615 0.00 0.00 33.96 0.86
3675 5981 3.997021 AGAACATAACTAGCTGTGTGTGC 59.003 43.478 0.00 1.35 31.53 4.57
3734 6042 8.332996 TGCTAACTGTACTAGCTATATACCAC 57.667 38.462 12.32 0.00 41.96 4.16
3748 6056 9.627123 AGCTATATACCACAGAAAATTTGCTTA 57.373 29.630 0.00 0.00 0.00 3.09
3817 6125 1.476891 ACGTGTCGCATCCTAATGACT 59.523 47.619 0.00 0.00 34.61 3.41
3875 6183 3.297830 ACCAAAATAAGCGCCTGTTTC 57.702 42.857 2.29 0.00 0.00 2.78
3886 6194 1.310904 GCCTGTTTCGTTACCACCAA 58.689 50.000 0.00 0.00 0.00 3.67
4035 6343 1.605753 AGTTTCTCTTTCCCGCAACC 58.394 50.000 0.00 0.00 0.00 3.77
4094 6402 6.015772 TGGTTAATTCCTAGCCAGTTGTTTTC 60.016 38.462 0.00 0.00 36.06 2.29
4114 6422 3.314693 TCTAGCGTTCCCCCATATTCTT 58.685 45.455 0.00 0.00 0.00 2.52
4148 6456 0.615850 ACCTCTAGAAACTGGGCAGC 59.384 55.000 0.00 0.00 0.00 5.25
4224 6532 4.503714 TTATGGGGTAAAGGCTCTTCTG 57.496 45.455 0.00 0.00 0.00 3.02
4246 6554 3.531982 CAGTGTTACTGTTTTCTTCGCG 58.468 45.455 0.00 0.00 41.19 5.87
4278 6586 0.615331 TGGTCAAGCCATCCTGAGTC 59.385 55.000 0.00 0.00 43.61 3.36
4303 6611 1.153086 GCAACCGGGAGATGCTCAT 60.153 57.895 6.32 0.00 38.76 2.90
4306 6614 0.389391 AACCGGGAGATGCTCATACG 59.611 55.000 6.32 0.00 31.08 3.06
4407 6718 9.559958 GCATGTGTGGATTAATGTTATATAAGC 57.440 33.333 0.00 0.00 0.00 3.09
4503 6814 4.393371 GCTGATTTCCTGGTCTGAAGTTAC 59.607 45.833 0.00 0.00 0.00 2.50
4511 6822 5.652891 TCCTGGTCTGAAGTTACTAGACATC 59.347 44.000 14.80 2.48 41.93 3.06
4518 6829 3.428746 AGTTACTAGACATCGCTGCTG 57.571 47.619 0.00 0.00 0.00 4.41
4537 6848 6.598457 GCTGCTGGATTCAGTATATTCATGAT 59.402 38.462 2.16 0.00 42.78 2.45
4539 6850 6.373495 TGCTGGATTCAGTATATTCATGATGC 59.627 38.462 2.16 0.00 42.78 3.91
4652 6963 2.433664 CCGTGGCCTAACACCGAC 60.434 66.667 3.32 0.00 38.11 4.79
4660 6971 0.815734 CCTAACACCGACGGTCTGAT 59.184 55.000 18.72 4.43 31.02 2.90
4702 7013 1.963172 GAACCAGGTGTTCCGTTTCT 58.037 50.000 0.00 0.00 46.35 2.52
4729 7040 8.777578 TTTATCTTTCCTCTGTAGCTACCATA 57.222 34.615 21.01 5.66 0.00 2.74
4730 7041 8.958060 TTATCTTTCCTCTGTAGCTACCATAT 57.042 34.615 21.01 4.80 0.00 1.78
4758 7070 3.518634 ACAAGGCAAACGTCAAAACAT 57.481 38.095 0.00 0.00 0.00 2.71
4783 7096 4.170256 GTGCACTCACTTAAGTAGCTCTC 58.830 47.826 10.32 0.00 40.03 3.20
4878 7192 5.199982 TGGTATTTATTGGGCTTTCAGGA 57.800 39.130 0.00 0.00 0.00 3.86
4887 7201 1.836802 GGGCTTTCAGGATCAGTCTCT 59.163 52.381 0.00 0.00 0.00 3.10
4888 7202 3.034635 GGGCTTTCAGGATCAGTCTCTA 58.965 50.000 0.00 0.00 0.00 2.43
4898 7212 6.665248 TCAGGATCAGTCTCTAATGTTGAGAA 59.335 38.462 0.00 0.00 41.52 2.87
4949 7263 3.701205 TTGTGCATGGTCTGTCTATGT 57.299 42.857 0.00 0.00 37.35 2.29
5001 7316 6.373779 TCAATCGATTCTGAAAAGCAACTTC 58.626 36.000 7.92 0.00 0.00 3.01
5043 7358 2.286294 CAGCTGAGAATTATCACACCGC 59.714 50.000 8.42 1.34 0.00 5.68
5053 7368 7.081976 AGAATTATCACACCGCTTTGTTTTAC 58.918 34.615 0.00 0.00 0.00 2.01
5079 7394 0.322546 GACCACCGCTTTGAGGGAAT 60.323 55.000 0.00 0.00 0.00 3.01
5091 7406 1.078143 AGGGAATGAGGTTGCGCTC 60.078 57.895 9.73 1.18 0.00 5.03
5103 7418 0.110419 TTGCGCTCGATTTTTCACCG 60.110 50.000 9.73 0.00 0.00 4.94
5105 7420 0.110373 GCGCTCGATTTTTCACCGTT 60.110 50.000 0.00 0.00 0.00 4.44
5153 7468 1.159285 TGGTGAAAGCAAGAGCGATG 58.841 50.000 0.00 0.00 44.10 3.84
5204 7519 7.625828 TTTTAGGAAGTATTTAGAAGCTGGC 57.374 36.000 0.00 0.00 0.00 4.85
5205 7520 6.561519 TTAGGAAGTATTTAGAAGCTGGCT 57.438 37.500 0.00 0.00 0.00 4.75
5206 7521 5.029807 AGGAAGTATTTAGAAGCTGGCTC 57.970 43.478 0.00 0.00 0.00 4.70
5207 7522 4.719273 AGGAAGTATTTAGAAGCTGGCTCT 59.281 41.667 0.00 0.00 0.00 4.09
5208 7523 5.190726 AGGAAGTATTTAGAAGCTGGCTCTT 59.809 40.000 0.00 0.00 0.00 2.85
5210 7525 6.183360 GGAAGTATTTAGAAGCTGGCTCTTTG 60.183 42.308 0.00 0.00 0.00 2.77
5213 7528 2.795231 TAGAAGCTGGCTCTTTGCAT 57.205 45.000 0.00 0.00 45.15 3.96
5214 7529 1.174783 AGAAGCTGGCTCTTTGCATG 58.825 50.000 0.00 0.00 45.15 4.06
5215 7530 1.171308 GAAGCTGGCTCTTTGCATGA 58.829 50.000 0.00 0.00 45.15 3.07
5216 7531 0.886563 AAGCTGGCTCTTTGCATGAC 59.113 50.000 0.00 0.00 45.15 3.06
5217 7532 0.037877 AGCTGGCTCTTTGCATGACT 59.962 50.000 0.00 0.00 45.15 3.41
5218 7533 0.886563 GCTGGCTCTTTGCATGACTT 59.113 50.000 0.00 0.00 45.15 3.01
5220 7535 2.159462 GCTGGCTCTTTGCATGACTTAC 60.159 50.000 0.00 0.00 45.15 2.34
5221 7536 3.076621 CTGGCTCTTTGCATGACTTACA 58.923 45.455 0.00 0.00 45.15 2.41
5223 7538 4.081406 TGGCTCTTTGCATGACTTACATT 58.919 39.130 0.00 0.00 45.15 2.71
5224 7539 5.252547 TGGCTCTTTGCATGACTTACATTA 58.747 37.500 0.00 0.00 45.15 1.90
5225 7540 5.709631 TGGCTCTTTGCATGACTTACATTAA 59.290 36.000 0.00 0.00 45.15 1.40
5226 7541 6.208402 TGGCTCTTTGCATGACTTACATTAAA 59.792 34.615 0.00 0.00 45.15 1.52
5227 7542 7.093814 TGGCTCTTTGCATGACTTACATTAAAT 60.094 33.333 0.00 0.00 45.15 1.40
5228 7543 8.405531 GGCTCTTTGCATGACTTACATTAAATA 58.594 33.333 0.00 0.00 45.15 1.40
5229 7544 9.787532 GCTCTTTGCATGACTTACATTAAATAA 57.212 29.630 0.00 0.00 42.31 1.40
5237 7552 9.013490 CATGACTTACATTAAATAAGTTGCTGC 57.987 33.333 13.76 0.00 41.80 5.25
5273 7589 7.949903 TTAAATAAGTTTAGTGCGTCACAGA 57.050 32.000 11.58 0.00 36.74 3.41
5277 7593 2.361119 AGTTTAGTGCGTCACAGACTCA 59.639 45.455 11.58 0.00 36.74 3.41
5311 7627 5.010719 AGCAAACTGAGCAAGTAGTACTGTA 59.989 40.000 5.39 0.00 38.56 2.74
5312 7628 5.118817 GCAAACTGAGCAAGTAGTACTGTAC 59.881 44.000 9.93 9.93 38.56 2.90
5313 7629 6.448006 CAAACTGAGCAAGTAGTACTGTACT 58.552 40.000 22.72 22.72 38.56 2.73
5325 7646 8.363761 AGTAGTACTGTACTAGCAAGGAAAAT 57.636 34.615 24.09 2.42 41.59 1.82
5332 7653 7.819900 ACTGTACTAGCAAGGAAAATAGTGAAG 59.180 37.037 0.00 0.00 31.25 3.02
5335 7656 5.645497 ACTAGCAAGGAAAATAGTGAAGCTG 59.355 40.000 0.00 0.00 0.00 4.24
5359 7680 1.895707 GCCATGATCGCTCCCCTTG 60.896 63.158 0.00 0.00 0.00 3.61
5377 7699 0.590984 TGCGTCATTTGTTGTGTGCG 60.591 50.000 0.00 0.00 0.00 5.34
5382 7704 3.371168 GTCATTTGTTGTGTGCGTTGAT 58.629 40.909 0.00 0.00 0.00 2.57
5396 7718 1.740380 CGTTGATCTTGGCGGTCATCT 60.740 52.381 0.00 0.00 0.00 2.90
5397 7719 1.667724 GTTGATCTTGGCGGTCATCTG 59.332 52.381 0.00 0.00 0.00 2.90
5398 7720 0.904649 TGATCTTGGCGGTCATCTGT 59.095 50.000 0.00 0.00 0.00 3.41
5400 7722 0.904649 ATCTTGGCGGTCATCTGTCA 59.095 50.000 0.00 0.00 32.24 3.58
5401 7723 0.904649 TCTTGGCGGTCATCTGTCAT 59.095 50.000 0.00 0.00 34.34 3.06
5402 7724 1.278985 TCTTGGCGGTCATCTGTCATT 59.721 47.619 0.00 0.00 34.34 2.57
5403 7725 2.086869 CTTGGCGGTCATCTGTCATTT 58.913 47.619 0.00 0.00 34.34 2.32
5404 7726 1.737838 TGGCGGTCATCTGTCATTTC 58.262 50.000 0.00 0.00 28.75 2.17
5405 7727 1.017387 GGCGGTCATCTGTCATTTCC 58.983 55.000 0.00 0.00 0.00 3.13
5407 7729 1.667724 GCGGTCATCTGTCATTTCCTG 59.332 52.381 0.00 0.00 0.00 3.86
5408 7730 2.283298 CGGTCATCTGTCATTTCCTGG 58.717 52.381 0.00 0.00 0.00 4.45
5409 7731 2.355108 CGGTCATCTGTCATTTCCTGGT 60.355 50.000 0.00 0.00 0.00 4.00
5410 7732 3.690460 GGTCATCTGTCATTTCCTGGTT 58.310 45.455 0.00 0.00 0.00 3.67
5411 7733 3.441572 GGTCATCTGTCATTTCCTGGTTG 59.558 47.826 0.00 0.00 0.00 3.77
5412 7734 4.074970 GTCATCTGTCATTTCCTGGTTGT 58.925 43.478 0.00 0.00 0.00 3.32
5413 7735 4.074259 TCATCTGTCATTTCCTGGTTGTG 58.926 43.478 0.00 0.00 0.00 3.33
5415 7737 3.476552 TCTGTCATTTCCTGGTTGTGTC 58.523 45.455 0.00 0.00 0.00 3.67
5451 7868 3.130819 ATCGCGCCGCCATTTTGA 61.131 55.556 2.28 0.00 0.00 2.69
5480 7934 1.656652 CTAGGTGTTCCTCCATTGCG 58.343 55.000 0.00 0.00 43.94 4.85
5485 7939 0.871722 TGTTCCTCCATTGCGAAACG 59.128 50.000 0.00 0.00 0.00 3.60
5490 7944 0.871722 CTCCATTGCGAAACGGTGAA 59.128 50.000 0.00 0.00 0.00 3.18
5491 7945 0.589223 TCCATTGCGAAACGGTGAAC 59.411 50.000 0.00 0.00 0.00 3.18
5494 7948 2.307049 CATTGCGAAACGGTGAACTTC 58.693 47.619 0.00 0.00 0.00 3.01
5503 7957 4.870190 GTGAACTTCACGGTGGGT 57.130 55.556 8.50 5.16 37.67 4.51
5505 7959 1.147376 TGAACTTCACGGTGGGTGG 59.853 57.895 8.50 0.00 46.96 4.61
5506 7960 2.203294 AACTTCACGGTGGGTGGC 60.203 61.111 8.50 0.00 46.96 5.01
5507 7961 4.619227 ACTTCACGGTGGGTGGCG 62.619 66.667 8.50 0.00 46.96 5.69
5508 7962 4.308458 CTTCACGGTGGGTGGCGA 62.308 66.667 8.50 0.00 46.96 5.54
5509 7963 3.605749 CTTCACGGTGGGTGGCGAT 62.606 63.158 8.50 0.00 46.96 4.58
5510 7964 3.185299 TTCACGGTGGGTGGCGATT 62.185 57.895 8.50 0.00 46.96 3.34
5511 7965 3.124921 CACGGTGGGTGGCGATTC 61.125 66.667 0.00 0.00 43.16 2.52
5512 7966 4.404098 ACGGTGGGTGGCGATTCC 62.404 66.667 0.00 0.00 0.00 3.01
5532 7986 2.824041 CGCAGGCGGCAACCTATT 60.824 61.111 13.08 0.00 45.17 1.73
5533 7987 2.406616 CGCAGGCGGCAACCTATTT 61.407 57.895 13.08 0.00 45.17 1.40
5582 8043 2.032528 CGAAGCTGCCACCTCCAA 59.967 61.111 0.00 0.00 0.00 3.53
5587 8048 1.228245 GCTGCCACCTCCAAGAACA 60.228 57.895 0.00 0.00 0.00 3.18
5611 8072 4.967084 AAAATGTACCTTTGAAACCCCC 57.033 40.909 0.00 0.00 0.00 5.40
5612 8073 3.621682 AATGTACCTTTGAAACCCCCA 57.378 42.857 0.00 0.00 0.00 4.96
5613 8074 2.368311 TGTACCTTTGAAACCCCCAC 57.632 50.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.282455 TGTTGGTTGTCATTAAGTTTCACTTA 57.718 30.769 0.00 0.00 39.51 2.24
54 55 1.454479 ATGCCCGGAAGATTGCCAG 60.454 57.895 0.73 0.00 0.00 4.85
139 140 0.464735 ACGTTGTGCCTGGCAAAGTA 60.465 50.000 25.23 7.52 41.47 2.24
160 161 4.116961 GGTTGATGCTACGTGCTATACAA 58.883 43.478 0.00 3.64 43.37 2.41
161 162 3.131400 TGGTTGATGCTACGTGCTATACA 59.869 43.478 0.00 0.00 43.37 2.29
162 163 3.489785 GTGGTTGATGCTACGTGCTATAC 59.510 47.826 0.00 0.00 43.37 1.47
164 165 2.168521 AGTGGTTGATGCTACGTGCTAT 59.831 45.455 0.00 0.00 43.37 2.97
170 171 3.589988 AGAAAGAGTGGTTGATGCTACG 58.410 45.455 0.00 0.00 0.00 3.51
224 225 0.674581 CTTCGCCTTCTGTGCCATGA 60.675 55.000 0.00 0.00 0.00 3.07
243 244 5.411053 AGATGCTTTGTCTTTCTACAAGAGC 59.589 40.000 12.67 12.67 40.29 4.09
354 355 9.396022 TGATACATCTGAATACTGCGATCTATA 57.604 33.333 0.00 0.00 0.00 1.31
380 381 3.056035 GTCTCCAATTTCCTCGTGTACCT 60.056 47.826 0.00 0.00 0.00 3.08
392 393 6.060788 GCTTATCTCCTGATGTCTCCAATTT 58.939 40.000 0.00 0.00 34.32 1.82
406 407 4.162320 TCGAGAAATGGTTGCTTATCTCCT 59.838 41.667 0.00 0.00 31.78 3.69
412 413 3.306917 TCGTCGAGAAATGGTTGCTTA 57.693 42.857 0.00 0.00 0.00 3.09
463 464 3.066760 GGCATATTTGTTGGACTGCCTAC 59.933 47.826 4.19 0.00 44.47 3.18
523 524 4.534401 GGTTCATGGACCTACCGC 57.466 61.111 16.69 0.00 42.61 5.68
531 532 5.222027 TGACCTTGTCAATTAGGTTCATGGA 60.222 40.000 0.00 0.00 44.65 3.41
569 570 4.291047 CGCAAGGTGATGTGAGCT 57.709 55.556 0.00 0.00 32.55 4.09
674 676 4.925646 AGTTACGGGTACAATCTTTCGAAC 59.074 41.667 0.00 0.00 0.00 3.95
680 682 4.895668 TGGAAGTTACGGGTACAATCTT 57.104 40.909 0.00 0.00 0.00 2.40
688 690 3.955551 ACATTGTTTTGGAAGTTACGGGT 59.044 39.130 0.00 0.00 0.00 5.28
699 701 0.030101 ACCGCACGACATTGTTTTGG 59.970 50.000 0.00 0.00 0.00 3.28
702 704 0.028770 CACACCGCACGACATTGTTT 59.971 50.000 0.00 0.00 0.00 2.83
709 711 0.668096 TAATGACCACACCGCACGAC 60.668 55.000 0.00 0.00 0.00 4.34
716 718 6.575162 ATTTCAGAAAGTAATGACCACACC 57.425 37.500 1.28 0.00 0.00 4.16
765 767 0.967380 CCCCATGTGTTTCTCCTGGC 60.967 60.000 0.00 0.00 0.00 4.85
890 917 1.371183 CCCTGTTCGGCTCTGTTGA 59.629 57.895 0.00 0.00 0.00 3.18
958 997 0.451792 CTCTTTCGCTTGCGAGTTGC 60.452 55.000 17.06 0.00 46.70 4.17
959 998 1.125748 CTCTCTTTCGCTTGCGAGTTG 59.874 52.381 17.06 11.46 0.00 3.16
960 999 1.423395 CTCTCTTTCGCTTGCGAGTT 58.577 50.000 17.06 0.00 0.00 3.01
961 1000 0.389166 CCTCTCTTTCGCTTGCGAGT 60.389 55.000 17.06 0.00 0.00 4.18
962 1001 0.109086 TCCTCTCTTTCGCTTGCGAG 60.109 55.000 17.06 7.75 0.00 5.03
963 1002 0.317160 TTCCTCTCTTTCGCTTGCGA 59.683 50.000 13.93 13.93 0.00 5.10
973 1012 6.755542 TTTTCTCTTCTTCCTTCCTCTCTT 57.244 37.500 0.00 0.00 0.00 2.85
1372 3517 2.908626 CGCAAATTTTACTCCGCAGTTC 59.091 45.455 0.00 0.00 33.62 3.01
1373 3518 2.292292 ACGCAAATTTTACTCCGCAGTT 59.708 40.909 0.00 0.00 33.62 3.16
1379 3524 6.555315 AGATCAATCACGCAAATTTTACTCC 58.445 36.000 0.00 0.00 0.00 3.85
1459 3604 6.762333 AGGGGAATCAATTTGAGAAAAACAG 58.238 36.000 5.21 0.00 0.00 3.16
1465 3618 6.068260 AGGGATTAGGGGAATCAATTTGAGAA 60.068 38.462 5.21 0.00 45.15 2.87
1479 3637 1.700186 GCTCTTGGTAGGGATTAGGGG 59.300 57.143 0.00 0.00 0.00 4.79
1511 3670 1.361668 GCATCCAGTGTGTAGTGCCG 61.362 60.000 0.00 0.00 0.00 5.69
1512 3671 0.321564 TGCATCCAGTGTGTAGTGCC 60.322 55.000 0.00 0.00 0.00 5.01
1564 3729 3.284251 TCCTCCCCTCAGGCCTCA 61.284 66.667 0.00 0.00 32.91 3.86
1565 3730 2.445654 CTCCTCCCCTCAGGCCTC 60.446 72.222 0.00 0.00 32.91 4.70
1566 3731 2.886636 AACTCCTCCCCTCAGGCCT 61.887 63.158 0.00 0.00 32.91 5.19
1567 3732 2.285743 AACTCCTCCCCTCAGGCC 60.286 66.667 0.00 0.00 32.91 5.19
1568 3733 2.674220 CCAACTCCTCCCCTCAGGC 61.674 68.421 0.00 0.00 32.91 4.85
1569 3734 1.229658 ACCAACTCCTCCCCTCAGG 60.230 63.158 0.00 0.00 34.40 3.86
1570 3735 0.545309 TCACCAACTCCTCCCCTCAG 60.545 60.000 0.00 0.00 0.00 3.35
1590 3755 4.062293 GCCATACACAACACAAGACAGTA 58.938 43.478 0.00 0.00 0.00 2.74
1591 3756 2.878406 GCCATACACAACACAAGACAGT 59.122 45.455 0.00 0.00 0.00 3.55
1592 3757 3.141398 AGCCATACACAACACAAGACAG 58.859 45.455 0.00 0.00 0.00 3.51
1596 3764 4.305989 ACAAAGCCATACACAACACAAG 57.694 40.909 0.00 0.00 0.00 3.16
1601 3769 4.677584 TCAACAACAAAGCCATACACAAC 58.322 39.130 0.00 0.00 0.00 3.32
1645 3815 8.043710 AGGAATCACACTCTTATTTCTAGGTTG 58.956 37.037 0.00 0.00 0.00 3.77
1743 3913 5.335127 AGTTATTCATGAATTCGCAAGTGC 58.665 37.500 25.26 3.53 33.49 4.40
1777 3947 3.491447 GCAGGAAGTGTTTGTTCAGCATT 60.491 43.478 0.00 0.00 0.00 3.56
1881 4060 1.068954 GGCAAATATCTAAGGCGCTGC 60.069 52.381 7.64 4.69 0.00 5.25
1949 4128 1.717194 CGGTAAAGCGACCTAAAGCA 58.283 50.000 0.00 0.00 37.34 3.91
2044 4223 6.253727 CAGAAACAGGTACTTAGTGAATAGCG 59.746 42.308 0.00 0.00 34.60 4.26
2104 4284 6.099557 TCTCCCAAATTCACCAAAAACAAGAT 59.900 34.615 0.00 0.00 0.00 2.40
2132 4315 5.396884 GGCTTAGTTGAGGACAATGGATACT 60.397 44.000 0.00 0.00 38.32 2.12
2159 4342 8.038944 TGTTAACCTCGAATAAGAACTAATGCT 58.961 33.333 2.48 0.00 0.00 3.79
2260 4443 6.255294 TGAGCTACTACTATGAAGTCCTCT 57.745 41.667 0.00 0.00 37.15 3.69
2351 4542 5.011329 ACACTGATCAAAGTTCAATTGCCAT 59.989 36.000 0.00 0.00 0.00 4.40
2419 4610 7.553760 TGATAATTCTCTCTGCATTTTGCTACA 59.446 33.333 0.75 0.00 45.31 2.74
2455 4646 4.711355 ACCAAGGTACAATATTTGCAGCAT 59.289 37.500 0.00 0.00 0.00 3.79
2853 5155 0.322816 AAGTACTGACCTCGCCCGTA 60.323 55.000 0.00 0.00 0.00 4.02
2949 5253 3.844211 ACATTCTGCAGGAGTTAGGGTTA 59.156 43.478 15.13 0.00 0.00 2.85
2999 5303 1.792949 CTATACGCGGATTTCACAGCC 59.207 52.381 10.26 0.00 0.00 4.85
3014 5318 7.013369 TCCAGATATGTCATGTATCGGCTATAC 59.987 40.741 2.40 2.40 40.87 1.47
3050 5354 2.294791 CCGTAGATAGTGCTCTTCAGGG 59.705 54.545 0.00 0.00 0.00 4.45
3095 5399 8.961294 TCATTTTCAGGTGAATCATTTTTGTT 57.039 26.923 0.00 0.00 33.54 2.83
3235 5539 3.751175 ACCCACACAACAAAGATGTATCG 59.249 43.478 0.00 0.00 39.40 2.92
3353 5657 0.650512 AATAACGTGAGAATGCCGCG 59.349 50.000 0.00 0.00 42.51 6.46
3480 5784 1.429930 TAACAAGTGACTGGCCTGGA 58.570 50.000 14.82 0.00 0.00 3.86
3557 5861 9.448438 AACTGTTCATAGCAATTGTAAGATACA 57.552 29.630 7.40 5.10 36.79 2.29
3581 5885 4.888823 TGGGGTTGTTAGACAAGGTTTAAC 59.111 41.667 3.61 3.61 39.00 2.01
3610 5914 7.830697 TGAACAAGACCATGATCATACTTGAAT 59.169 33.333 32.16 25.30 38.30 2.57
3611 5915 7.119699 GTGAACAAGACCATGATCATACTTGAA 59.880 37.037 32.16 22.36 38.30 2.69
3657 5963 3.854666 AGAGCACACACAGCTAGTTATG 58.145 45.455 0.00 0.00 43.58 1.90
3729 6037 6.398234 TTGCTAAGCAAATTTTCTGTGGTA 57.602 33.333 0.00 0.00 45.96 3.25
3817 6125 6.698380 AGAGGAAAGCGAGAAAGTGTTATTA 58.302 36.000 0.00 0.00 0.00 0.98
3886 6194 6.831664 AAATATGGAACCTCAGACATACCT 57.168 37.500 0.00 0.00 0.00 3.08
3917 6225 5.622770 AATTCCAAACTGTTTAGTAGCCG 57.377 39.130 5.31 0.00 35.69 5.52
3949 6257 4.079970 TCAACCTATCTCGCCTATTCGAT 58.920 43.478 0.00 0.00 37.87 3.59
4035 6343 6.563422 TGTGTTTTCTGAATTTCTGGTGAAG 58.437 36.000 3.79 0.00 33.28 3.02
4081 6389 2.256117 ACGCTAGAAAACAACTGGCT 57.744 45.000 0.00 0.00 39.18 4.75
4087 6395 1.143277 TGGGGGAACGCTAGAAAACAA 59.857 47.619 0.00 0.00 45.02 2.83
4094 6402 3.557264 GGAAGAATATGGGGGAACGCTAG 60.557 52.174 0.00 0.00 45.02 3.42
4148 6456 1.131883 GTTATTGCTGAGCTGCCAGTG 59.868 52.381 5.83 0.00 36.57 3.66
4244 6552 1.687494 GACCAACACTCGATCTGCGC 61.687 60.000 0.00 0.00 40.61 6.09
4246 6554 1.728971 CTTGACCAACACTCGATCTGC 59.271 52.381 0.00 0.00 0.00 4.26
4272 6580 1.393539 CCGGTTGCAATAACGACTCAG 59.606 52.381 18.56 0.00 0.00 3.35
4278 6586 1.330521 CATCTCCCGGTTGCAATAACG 59.669 52.381 0.59 8.28 0.00 3.18
4329 6640 8.437742 CACTTTCATCAGGAAACATTTTAATGC 58.562 33.333 2.46 0.00 40.51 3.56
4368 6679 7.969536 ATCCACACATGCTTATATACTTGTC 57.030 36.000 0.00 0.00 0.00 3.18
4400 6711 9.578576 AAGACATTAATCCACACATGCTTATAT 57.421 29.630 0.00 0.00 0.00 0.86
4401 6712 8.978874 AAGACATTAATCCACACATGCTTATA 57.021 30.769 0.00 0.00 0.00 0.98
4402 6713 7.557358 TGAAGACATTAATCCACACATGCTTAT 59.443 33.333 0.00 0.00 0.00 1.73
4403 6714 6.883756 TGAAGACATTAATCCACACATGCTTA 59.116 34.615 0.00 0.00 0.00 3.09
4404 6715 5.711506 TGAAGACATTAATCCACACATGCTT 59.288 36.000 0.00 0.00 0.00 3.91
4405 6716 5.255687 TGAAGACATTAATCCACACATGCT 58.744 37.500 0.00 0.00 0.00 3.79
4406 6717 5.565592 TGAAGACATTAATCCACACATGC 57.434 39.130 0.00 0.00 0.00 4.06
4407 6718 5.975344 GCATGAAGACATTAATCCACACATG 59.025 40.000 0.00 0.00 34.15 3.21
4408 6719 5.068198 GGCATGAAGACATTAATCCACACAT 59.932 40.000 0.00 0.00 34.15 3.21
4409 6720 4.398988 GGCATGAAGACATTAATCCACACA 59.601 41.667 0.00 0.00 34.15 3.72
4410 6721 4.496341 CGGCATGAAGACATTAATCCACAC 60.496 45.833 0.00 0.00 34.15 3.82
4411 6722 3.627123 CGGCATGAAGACATTAATCCACA 59.373 43.478 0.00 0.00 34.15 4.17
4412 6723 3.003689 CCGGCATGAAGACATTAATCCAC 59.996 47.826 0.00 0.00 34.15 4.02
4413 6724 3.213506 CCGGCATGAAGACATTAATCCA 58.786 45.455 0.00 0.00 34.15 3.41
4414 6725 3.003689 CACCGGCATGAAGACATTAATCC 59.996 47.826 0.00 0.00 34.15 3.01
4415 6726 3.627577 ACACCGGCATGAAGACATTAATC 59.372 43.478 0.00 0.00 34.15 1.75
4416 6727 3.620488 ACACCGGCATGAAGACATTAAT 58.380 40.909 0.00 0.00 34.15 1.40
4417 6728 3.066291 ACACCGGCATGAAGACATTAA 57.934 42.857 0.00 0.00 34.15 1.40
4418 6729 2.779755 ACACCGGCATGAAGACATTA 57.220 45.000 0.00 0.00 34.15 1.90
4419 6730 1.812571 GAACACCGGCATGAAGACATT 59.187 47.619 0.00 0.00 34.15 2.71
4420 6731 1.453155 GAACACCGGCATGAAGACAT 58.547 50.000 0.00 0.00 37.19 3.06
4421 6732 0.605319 GGAACACCGGCATGAAGACA 60.605 55.000 0.00 0.00 0.00 3.41
4422 6733 0.321653 AGGAACACCGGCATGAAGAC 60.322 55.000 0.00 0.00 0.00 3.01
4503 6814 2.223900 TGAATCCAGCAGCGATGTCTAG 60.224 50.000 1.22 0.00 0.00 2.43
4511 6822 4.309933 TGAATATACTGAATCCAGCAGCG 58.690 43.478 0.00 0.00 44.16 5.18
4518 6829 9.569167 CAATTGCATCATGAATATACTGAATCC 57.431 33.333 0.00 0.00 0.00 3.01
4537 6848 2.030371 TCTGCAGGAACAACAATTGCA 58.970 42.857 15.13 0.00 41.97 4.08
4539 6850 4.232221 GTGATCTGCAGGAACAACAATTG 58.768 43.478 15.13 3.24 0.00 2.32
4652 6963 1.817099 GCAGCTTCCCATCAGACCG 60.817 63.158 0.00 0.00 0.00 4.79
4660 6971 3.070878 TGATATTGATACGCAGCTTCCCA 59.929 43.478 0.00 0.00 0.00 4.37
4702 7013 7.913789 TGGTAGCTACAGAGGAAAGATAAAAA 58.086 34.615 24.75 0.00 0.00 1.94
4745 7057 5.181690 AGTGCACATATGTTTTGACGTTT 57.818 34.783 21.04 0.00 0.00 3.60
4747 7059 3.812609 TGAGTGCACATATGTTTTGACGT 59.187 39.130 21.04 0.00 0.00 4.34
4783 7096 1.379044 AGGAAAATCTGGGGCGCAG 60.379 57.895 24.22 24.22 0.00 5.18
4860 7174 5.522641 ACTGATCCTGAAAGCCCAATAAAT 58.477 37.500 0.00 0.00 0.00 1.40
4906 7220 8.137437 ACAAAACAGACAAATCCTATTCAAGTG 58.863 33.333 0.00 0.00 0.00 3.16
4949 7263 3.218453 TGAAAATTTCAAGCGACTGGGA 58.782 40.909 5.87 0.00 36.59 4.37
5001 7316 1.975660 TTTCTGGAAGGTGGAAACCG 58.024 50.000 0.00 0.00 34.28 4.44
5043 7358 5.389098 CGGTGGTCGATACAGTAAAACAAAG 60.389 44.000 0.00 0.00 42.43 2.77
5053 7368 0.999406 CAAAGCGGTGGTCGATACAG 59.001 55.000 0.00 0.00 42.43 2.74
5079 7394 1.196808 GAAAAATCGAGCGCAACCTCA 59.803 47.619 11.47 0.00 0.00 3.86
5091 7406 4.602995 TGAAAAGGAACGGTGAAAAATCG 58.397 39.130 0.00 0.00 0.00 3.34
5171 7486 9.101655 TCTAAATACTTCCTAAAATACAACGGC 57.898 33.333 0.00 0.00 0.00 5.68
5198 7513 0.037877 AGTCATGCAAAGAGCCAGCT 59.962 50.000 0.00 0.00 44.83 4.24
5199 7514 0.886563 AAGTCATGCAAAGAGCCAGC 59.113 50.000 0.00 0.00 44.83 4.85
5200 7515 3.076621 TGTAAGTCATGCAAAGAGCCAG 58.923 45.455 0.00 0.00 44.83 4.85
5203 7518 9.787532 TTATTTAATGTAAGTCATGCAAAGAGC 57.212 29.630 0.00 0.00 45.96 4.09
5208 7523 9.352784 GCAACTTATTTAATGTAAGTCATGCAA 57.647 29.630 19.99 0.00 41.28 4.08
5210 7525 9.013490 CAGCAACTTATTTAATGTAAGTCATGC 57.987 33.333 18.70 18.70 41.60 4.06
5213 7528 8.236586 CAGCAGCAACTTATTTAATGTAAGTCA 58.763 33.333 11.84 0.00 40.49 3.41
5214 7529 7.218963 GCAGCAGCAACTTATTTAATGTAAGTC 59.781 37.037 11.84 4.27 40.49 3.01
5215 7530 7.029563 GCAGCAGCAACTTATTTAATGTAAGT 58.970 34.615 0.00 7.58 42.53 2.24
5216 7531 7.441878 GCAGCAGCAACTTATTTAATGTAAG 57.558 36.000 0.00 6.60 41.58 2.34
5231 7546 7.541783 CTTATTTAATAAGTTGTGCAGCAGCAA 59.458 33.333 4.94 0.36 43.53 3.91
5232 7547 7.028962 CTTATTTAATAAGTTGTGCAGCAGCA 58.971 34.615 14.63 0.00 41.76 4.41
5268 7583 3.871006 TGCTGTTAAACTGTGAGTCTGTG 59.129 43.478 0.00 0.00 0.00 3.66
5269 7584 4.137116 TGCTGTTAAACTGTGAGTCTGT 57.863 40.909 0.00 0.00 0.00 3.41
5304 7620 8.248945 TCACTATTTTCCTTGCTAGTACAGTAC 58.751 37.037 2.05 2.05 0.00 2.73
5307 7623 7.201565 GCTTCACTATTTTCCTTGCTAGTACAG 60.202 40.741 0.00 0.00 0.00 2.74
5311 7627 5.645497 CAGCTTCACTATTTTCCTTGCTAGT 59.355 40.000 0.00 0.00 0.00 2.57
5312 7628 5.645497 ACAGCTTCACTATTTTCCTTGCTAG 59.355 40.000 0.00 0.00 0.00 3.42
5313 7629 5.560724 ACAGCTTCACTATTTTCCTTGCTA 58.439 37.500 0.00 0.00 0.00 3.49
5335 7656 0.659957 GGAGCGATCATGGCTGAAAC 59.340 55.000 0.00 0.00 41.72 2.78
5350 7671 1.244019 ACAAATGACGCAAGGGGAGC 61.244 55.000 0.00 0.00 46.39 4.70
5359 7680 0.591236 ACGCACACAACAAATGACGC 60.591 50.000 0.00 0.00 0.00 5.19
5377 7699 1.667724 CAGATGACCGCCAAGATCAAC 59.332 52.381 0.00 0.00 0.00 3.18
5382 7704 0.904649 ATGACAGATGACCGCCAAGA 59.095 50.000 0.00 0.00 0.00 3.02
5396 7718 2.217750 CGACACAACCAGGAAATGACA 58.782 47.619 0.00 0.00 0.00 3.58
5397 7719 1.069227 GCGACACAACCAGGAAATGAC 60.069 52.381 0.00 0.00 0.00 3.06
5398 7720 1.234821 GCGACACAACCAGGAAATGA 58.765 50.000 0.00 0.00 0.00 2.57
5400 7722 1.909700 ATGCGACACAACCAGGAAAT 58.090 45.000 0.00 0.00 0.00 2.17
5401 7723 1.336440 CAATGCGACACAACCAGGAAA 59.664 47.619 0.00 0.00 0.00 3.13
5402 7724 0.950836 CAATGCGACACAACCAGGAA 59.049 50.000 0.00 0.00 0.00 3.36
5403 7725 0.107643 TCAATGCGACACAACCAGGA 59.892 50.000 0.00 0.00 0.00 3.86
5404 7726 1.131126 GATCAATGCGACACAACCAGG 59.869 52.381 0.00 0.00 0.00 4.45
5405 7727 2.079158 AGATCAATGCGACACAACCAG 58.921 47.619 0.00 0.00 0.00 4.00
5407 7729 2.414559 CCAAGATCAATGCGACACAACC 60.415 50.000 0.00 0.00 0.00 3.77
5408 7730 2.855180 CCAAGATCAATGCGACACAAC 58.145 47.619 0.00 0.00 0.00 3.32
5409 7731 1.199789 GCCAAGATCAATGCGACACAA 59.800 47.619 0.00 0.00 0.00 3.33
5410 7732 0.804364 GCCAAGATCAATGCGACACA 59.196 50.000 0.00 0.00 0.00 3.72
5411 7733 3.611433 GCCAAGATCAATGCGACAC 57.389 52.632 0.00 0.00 0.00 3.67
5415 7737 1.353103 GACCGCCAAGATCAATGCG 59.647 57.895 13.67 13.67 46.14 4.73
5439 7856 2.729360 GTGTAAGTTTCAAAATGGCGGC 59.271 45.455 0.00 0.00 0.00 6.53
5467 7921 0.168128 CCGTTTCGCAATGGAGGAAC 59.832 55.000 0.00 0.00 41.23 3.62
5473 7927 0.591170 AGTTCACCGTTTCGCAATGG 59.409 50.000 4.36 4.36 44.02 3.16
5480 7934 1.004292 CACCGTGAAGTTCACCGTTTC 60.004 52.381 26.37 4.81 44.20 2.78
5485 7939 1.147600 ACCCACCGTGAAGTTCACC 59.852 57.895 26.37 11.73 44.20 4.02
5490 7944 4.619227 CGCCACCCACCGTGAAGT 62.619 66.667 0.00 0.00 46.20 3.01
5491 7945 3.605749 ATCGCCACCCACCGTGAAG 62.606 63.158 0.00 0.00 46.20 3.02
5494 7948 3.124921 GAATCGCCACCCACCGTG 61.125 66.667 0.00 0.00 42.62 4.94
5515 7969 2.322999 GAAATAGGTTGCCGCCTGCG 62.323 60.000 4.20 4.20 45.60 5.18
5516 7970 1.433471 GAAATAGGTTGCCGCCTGC 59.567 57.895 6.44 0.00 39.60 4.85
5517 7971 1.714899 CCGAAATAGGTTGCCGCCTG 61.715 60.000 6.44 0.00 39.60 4.85
5518 7972 1.451387 CCGAAATAGGTTGCCGCCT 60.451 57.895 1.70 1.70 42.43 5.52
5519 7973 3.107447 CCGAAATAGGTTGCCGCC 58.893 61.111 0.00 0.00 0.00 6.13
5520 7974 2.407616 GCCGAAATAGGTTGCCGC 59.592 61.111 0.00 0.00 0.00 6.53
5521 7975 3.107447 GGCCGAAATAGGTTGCCG 58.893 61.111 0.00 0.00 31.55 5.69
5522 7976 3.107447 CGGCCGAAATAGGTTGCC 58.893 61.111 24.07 0.00 38.74 4.52
5523 7977 2.407616 GCGGCCGAAATAGGTTGC 59.592 61.111 33.48 1.90 0.00 4.17
5524 7978 1.029947 AAGGCGGCCGAAATAGGTTG 61.030 55.000 33.48 0.00 0.00 3.77
5525 7979 1.029947 CAAGGCGGCCGAAATAGGTT 61.030 55.000 33.48 7.27 0.00 3.50
5526 7980 1.451387 CAAGGCGGCCGAAATAGGT 60.451 57.895 33.48 2.23 0.00 3.08
5527 7981 0.746563 TTCAAGGCGGCCGAAATAGG 60.747 55.000 33.48 12.59 0.00 2.57
5528 7982 0.377203 GTTCAAGGCGGCCGAAATAG 59.623 55.000 33.48 14.15 0.00 1.73
5529 7983 0.321741 TGTTCAAGGCGGCCGAAATA 60.322 50.000 33.48 9.55 0.00 1.40
5530 7984 1.602323 TGTTCAAGGCGGCCGAAAT 60.602 52.632 33.48 10.88 0.00 2.17
5531 7985 2.203224 TGTTCAAGGCGGCCGAAA 60.203 55.556 33.48 11.32 0.00 3.46
5532 7986 2.975799 GTGTTCAAGGCGGCCGAA 60.976 61.111 33.48 11.42 0.00 4.30
5582 8043 7.547722 GGTTTCAAAGGTACATTTTTGTGTTCT 59.452 33.333 2.09 0.00 36.09 3.01
5587 8048 5.396996 GGGGGTTTCAAAGGTACATTTTTGT 60.397 40.000 2.09 0.00 36.09 2.83


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

AutoCloner maintained by Alex Coulton.