Multiple sequence alignment - TraesCS2D01G382800

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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 TraesCS2D01G382800 chr2D 100.000 6017 0 0 1 6017 487059982 487053966 0.000000e+00 11112.0
1 TraesCS2D01G382800 chr2D 94.805 77 4 0 5941 6017 585912651 585912575 2.950000e-23 121.0
2 TraesCS2D01G382800 chr2B 88.899 3441 188 89 164 3494 571767392 571764036 0.000000e+00 4060.0
3 TraesCS2D01G382800 chr2B 93.952 992 37 4 4047 5019 571763420 571762433 0.000000e+00 1478.0
4 TraesCS2D01G382800 chr2B 90.657 792 44 6 5229 6017 24105333 24104569 0.000000e+00 1026.0
5 TraesCS2D01G382800 chr2B 91.476 481 36 3 3561 4037 571764039 571763560 0.000000e+00 656.0
6 TraesCS2D01G382800 chr2B 93.500 200 11 2 5018 5215 571753892 571753693 4.560000e-76 296.0
7 TraesCS2D01G382800 chr2B 84.677 124 11 3 1 124 571767511 571767396 3.810000e-22 117.0
8 TraesCS2D01G382800 chr2A 92.556 2351 112 23 3562 5883 632293071 632290755 0.000000e+00 3314.0
9 TraesCS2D01G382800 chr2A 89.384 1347 103 15 1454 2783 632295132 632293809 0.000000e+00 1659.0
10 TraesCS2D01G382800 chr2A 93.713 668 33 4 2800 3464 632293753 632293092 0.000000e+00 992.0
11 TraesCS2D01G382800 chr2A 88.599 728 42 17 5216 5931 35472054 35472752 0.000000e+00 846.0
12 TraesCS2D01G382800 chr2A 88.038 744 29 22 692 1418 632296056 632295356 0.000000e+00 826.0
13 TraesCS2D01G382800 chr2A 87.461 646 25 12 45 671 632296950 632296342 0.000000e+00 693.0
14 TraesCS2D01G382800 chr2A 91.304 138 3 3 5880 6017 632290518 632290390 4.790000e-41 180.0
15 TraesCS2D01G382800 chr2A 78.000 250 33 15 2868 3109 699414975 699414740 2.920000e-28 137.0
16 TraesCS2D01G382800 chr4A 89.567 786 47 6 5232 6017 710015024 710015774 0.000000e+00 965.0
17 TraesCS2D01G382800 chr4A 82.072 251 32 6 2860 3109 570994682 570994920 1.020000e-47 202.0
18 TraesCS2D01G382800 chr4A 91.803 61 2 3 3505 3563 684637540 684637599 1.390000e-11 82.4
19 TraesCS2D01G382800 chr4A 95.238 42 2 0 3521 3562 647178185 647178144 3.890000e-07 67.6
20 TraesCS2D01G382800 chr4D 89.241 790 46 9 5232 6017 54384435 54383681 0.000000e+00 952.0
21 TraesCS2D01G382800 chr4D 82.470 251 31 6 2860 3109 31808752 31808514 2.200000e-49 207.0
22 TraesCS2D01G382800 chr7A 86.241 705 66 13 5232 5931 63572518 63573196 0.000000e+00 736.0
23 TraesCS2D01G382800 chr7A 89.641 502 41 8 5232 5724 577198210 577197711 3.960000e-176 628.0
24 TraesCS2D01G382800 chr7A 96.104 77 3 0 5941 6017 577197696 577197620 6.330000e-25 126.0
25 TraesCS2D01G382800 chr6D 86.409 699 63 7 5238 5931 76067274 76066603 0.000000e+00 736.0
26 TraesCS2D01G382800 chr6D 96.104 77 3 0 5941 6017 60509008 60509084 6.330000e-25 126.0
27 TraesCS2D01G382800 chr6D 97.500 40 1 0 3525 3564 470635952 470635913 1.080000e-07 69.4
28 TraesCS2D01G382800 chr6D 100.000 32 0 0 3692 3723 403795232 403795201 6.510000e-05 60.2
29 TraesCS2D01G382800 chr7D 85.714 707 67 16 5232 5931 152114516 152115195 0.000000e+00 715.0
30 TraesCS2D01G382800 chr7D 78.788 231 42 4 3737 3960 34445283 34445513 1.350000e-31 148.0
31 TraesCS2D01G382800 chr5A 90.249 482 40 5 5232 5708 607486105 607486584 1.840000e-174 623.0
32 TraesCS2D01G382800 chr5A 97.561 41 1 0 3525 3565 566709398 566709438 3.010000e-08 71.3
33 TraesCS2D01G382800 chr3A 90.041 482 41 5 5232 5708 691450308 691449829 8.570000e-173 617.0
34 TraesCS2D01G382800 chr3B 88.623 501 51 4 5228 5724 763044122 763043624 6.670000e-169 604.0
35 TraesCS2D01G382800 chr4B 88.189 508 52 6 5220 5724 654587504 654588006 3.100000e-167 599.0
36 TraesCS2D01G382800 chr4B 83.730 252 30 4 2859 3109 45507460 45507219 1.690000e-55 228.0
37 TraesCS2D01G382800 chr4B 92.537 67 3 2 3498 3562 400364631 400364697 1.790000e-15 95.3
38 TraesCS2D01G382800 chr4B 88.525 61 4 3 3505 3563 46216638 46216579 3.010000e-08 71.3
39 TraesCS2D01G382800 chrUn 86.799 553 42 7 5383 5931 382647090 382646565 6.720000e-164 588.0
40 TraesCS2D01G382800 chrUn 87.110 481 35 5 5451 5931 263443204 263442751 2.490000e-143 520.0
41 TraesCS2D01G382800 chr1D 92.966 327 20 1 5691 6017 39788759 39788436 1.960000e-129 473.0
42 TraesCS2D01G382800 chr1D 95.652 46 2 0 3518 3563 52358568 52358523 2.330000e-09 75.0
43 TraesCS2D01G382800 chr6B 89.783 323 21 5 5695 6017 716394836 716394526 2.610000e-108 403.0
44 TraesCS2D01G382800 chr3D 84.456 193 23 4 3620 3812 281599982 281600167 3.700000e-42 183.0
45 TraesCS2D01G382800 chr3D 100.000 43 0 0 3523 3565 598299594 598299636 5.000000e-11 80.5
46 TraesCS2D01G382800 chr6A 91.803 61 2 3 3505 3563 346634144 346634203 1.390000e-11 82.4
47 TraesCS2D01G382800 chr6A 100.000 32 0 0 3692 3723 550279832 550279801 6.510000e-05 60.2


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 TraesCS2D01G382800 chr2D 487053966 487059982 6016 True 11112.000000 11112 100.000000 1 6017 1 chr2D.!!$R1 6016
1 TraesCS2D01G382800 chr2B 571762433 571767511 5078 True 1577.750000 4060 89.751000 1 5019 4 chr2B.!!$R3 5018
2 TraesCS2D01G382800 chr2B 24104569 24105333 764 True 1026.000000 1026 90.657000 5229 6017 1 chr2B.!!$R1 788
3 TraesCS2D01G382800 chr2A 632290390 632296950 6560 True 1277.333333 3314 90.409333 45 6017 6 chr2A.!!$R2 5972
4 TraesCS2D01G382800 chr2A 35472054 35472752 698 False 846.000000 846 88.599000 5216 5931 1 chr2A.!!$F1 715
5 TraesCS2D01G382800 chr4A 710015024 710015774 750 False 965.000000 965 89.567000 5232 6017 1 chr4A.!!$F3 785
6 TraesCS2D01G382800 chr4D 54383681 54384435 754 True 952.000000 952 89.241000 5232 6017 1 chr4D.!!$R2 785
7 TraesCS2D01G382800 chr7A 63572518 63573196 678 False 736.000000 736 86.241000 5232 5931 1 chr7A.!!$F1 699
8 TraesCS2D01G382800 chr7A 577197620 577198210 590 True 377.000000 628 92.872500 5232 6017 2 chr7A.!!$R1 785
9 TraesCS2D01G382800 chr6D 76066603 76067274 671 True 736.000000 736 86.409000 5238 5931 1 chr6D.!!$R1 693
10 TraesCS2D01G382800 chr7D 152114516 152115195 679 False 715.000000 715 85.714000 5232 5931 1 chr7D.!!$F2 699
11 TraesCS2D01G382800 chr4B 654587504 654588006 502 False 599.000000 599 88.189000 5220 5724 1 chr4B.!!$F2 504
12 TraesCS2D01G382800 chrUn 382646565 382647090 525 True 588.000000 588 86.799000 5383 5931 1 chrUn.!!$R2 548

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
156 157 0.250513 CAGTAGTTGCCTCAGACCCC 59.749 60.0 0.00 0.00 0.00 4.95 F
409 449 0.391661 GTTGAAGGATCGGAGCAGCA 60.392 55.0 0.00 0.00 0.00 4.41 F
1511 2068 0.461548 TGCGATCTACTGCTTCTGGG 59.538 55.0 0.00 0.00 0.00 4.45 F
2593 3186 0.325577 AGATTGAAACCATGGGGCCC 60.326 55.0 18.17 18.17 37.90 5.80 F
3828 4487 0.251077 CTGCTGGTTTCTGGAAGGCT 60.251 55.0 0.00 0.00 0.00 4.58 F
4198 4987 0.693049 ACTCGCCCTTCTGGTTCAAT 59.307 50.0 0.00 0.00 36.04 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2586 0.037232 AACGTGGTGAAGCTAGAGGC 60.037 55.000 0.00 0.00 42.19 4.70 R
2273 2844 2.087646 GAGGCCTTGCTAAGAAAGTGG 58.912 52.381 6.77 0.00 0.00 4.00 R
2612 3205 0.250124 ATGTTCCCGTCAACAGCGAA 60.250 50.000 3.18 0.00 39.63 4.70 R
4460 5249 0.975040 ATCTCAGGCTGCCGAGAAGT 60.975 55.000 31.55 20.83 37.00 3.01 R
4873 5665 1.619827 CACCCTCCAAATTGTGCATGT 59.380 47.619 0.00 0.00 0.00 3.21 R
5752 6594 3.374988 TCGCAAGCTGGAATATGAAACTG 59.625 43.478 0.00 0.00 37.18 3.16 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
30 31 2.546368 CGTCCAACTTCGATGTTTTCCA 59.454 45.455 13.53 0.00 0.00 3.53
36 37 5.912955 CCAACTTCGATGTTTTCCAGTTTAC 59.087 40.000 13.53 0.00 0.00 2.01
40 41 6.987992 ACTTCGATGTTTTCCAGTTTACACTA 59.012 34.615 0.00 0.00 0.00 2.74
41 42 7.170998 ACTTCGATGTTTTCCAGTTTACACTAG 59.829 37.037 0.00 0.00 0.00 2.57
42 43 6.518493 TCGATGTTTTCCAGTTTACACTAGT 58.482 36.000 0.00 0.00 0.00 2.57
43 44 6.643770 TCGATGTTTTCCAGTTTACACTAGTC 59.356 38.462 0.00 0.00 0.00 2.59
92 93 6.367686 TCAGTGTACACGATGTATAACGAT 57.632 37.500 19.93 0.00 35.05 3.73
129 130 2.977914 GCAAGAGCAAGTACTCCATGA 58.022 47.619 0.00 0.00 41.58 3.07
130 131 2.935201 GCAAGAGCAAGTACTCCATGAG 59.065 50.000 0.00 0.00 41.58 2.90
131 132 3.529533 CAAGAGCAAGTACTCCATGAGG 58.470 50.000 0.00 0.00 37.39 3.86
132 133 2.114616 AGAGCAAGTACTCCATGAGGG 58.885 52.381 0.00 0.00 37.39 4.30
133 134 2.111384 GAGCAAGTACTCCATGAGGGA 58.889 52.381 0.00 0.00 45.89 4.20
134 135 1.834263 AGCAAGTACTCCATGAGGGAC 59.166 52.381 0.00 0.00 42.15 4.46
135 136 1.555075 GCAAGTACTCCATGAGGGACA 59.445 52.381 0.00 0.00 42.15 4.02
136 137 2.419297 GCAAGTACTCCATGAGGGACAG 60.419 54.545 0.00 0.00 42.15 3.51
137 138 1.490574 AGTACTCCATGAGGGACAGC 58.509 55.000 0.00 0.00 42.15 4.40
138 139 1.195115 GTACTCCATGAGGGACAGCA 58.805 55.000 0.00 0.00 42.15 4.41
139 140 1.137872 GTACTCCATGAGGGACAGCAG 59.862 57.143 0.00 0.00 42.15 4.24
140 141 0.546267 ACTCCATGAGGGACAGCAGT 60.546 55.000 0.00 0.00 42.15 4.40
141 142 1.273267 ACTCCATGAGGGACAGCAGTA 60.273 52.381 0.00 0.00 42.15 2.74
142 143 1.411977 CTCCATGAGGGACAGCAGTAG 59.588 57.143 0.00 0.00 42.15 2.57
143 144 1.198713 CCATGAGGGACAGCAGTAGT 58.801 55.000 0.00 0.00 40.01 2.73
144 145 1.556911 CCATGAGGGACAGCAGTAGTT 59.443 52.381 0.00 0.00 40.01 2.24
145 146 2.625737 CATGAGGGACAGCAGTAGTTG 58.374 52.381 0.00 0.00 0.00 3.16
155 156 3.842869 CAGTAGTTGCCTCAGACCC 57.157 57.895 0.00 0.00 0.00 4.46
156 157 0.250513 CAGTAGTTGCCTCAGACCCC 59.749 60.000 0.00 0.00 0.00 4.95
157 158 1.218316 GTAGTTGCCTCAGACCCCG 59.782 63.158 0.00 0.00 0.00 5.73
158 159 1.987855 TAGTTGCCTCAGACCCCGG 60.988 63.158 0.00 0.00 0.00 5.73
159 160 2.741878 TAGTTGCCTCAGACCCCGGT 62.742 60.000 0.00 0.00 0.00 5.28
160 161 3.319198 TTGCCTCAGACCCCGGTC 61.319 66.667 5.70 5.70 44.86 4.79
407 447 0.462759 GGGTTGAAGGATCGGAGCAG 60.463 60.000 0.00 0.00 0.00 4.24
408 448 1.092345 GGTTGAAGGATCGGAGCAGC 61.092 60.000 0.00 0.00 0.00 5.25
409 449 0.391661 GTTGAAGGATCGGAGCAGCA 60.392 55.000 0.00 0.00 0.00 4.41
436 476 4.201901 CCTTTACATCGTTACATGCATGCA 60.202 41.667 26.53 25.04 0.00 3.96
437 477 5.497635 TTTACATCGTTACATGCATGCAT 57.502 34.783 27.46 27.46 37.08 3.96
441 481 2.212652 TCGTTACATGCATGCATCCTC 58.787 47.619 30.07 18.09 33.90 3.71
445 485 0.467474 ACATGCATGCATCCTCCCTG 60.467 55.000 30.07 20.45 33.90 4.45
446 486 1.530891 ATGCATGCATCCTCCCTGC 60.531 57.895 27.46 0.00 40.10 4.85
447 487 2.910994 GCATGCATCCTCCCTGCC 60.911 66.667 14.21 0.00 38.89 4.85
565 621 2.094130 CCGAGTTAAGGAAGTGGAGTCC 60.094 54.545 0.73 0.73 35.17 3.85
569 625 1.263356 TAAGGAAGTGGAGTCCGTGG 58.737 55.000 4.30 0.00 40.36 4.94
584 640 1.671379 GTGGCACCCTTTCGGTCTC 60.671 63.158 6.29 0.00 43.58 3.36
721 1042 3.682858 CGAAGAAGGCCAATAGAAAACGA 59.317 43.478 5.01 0.00 0.00 3.85
724 1045 2.420058 AGGCCAATAGAAAACGAGGG 57.580 50.000 5.01 0.00 0.00 4.30
1004 1334 1.298264 CTCGAGTCTAGCTGCTGCG 60.298 63.158 13.43 8.20 45.42 5.18
1057 1387 2.123425 CGGGCCAGCTAGGGAGTA 60.123 66.667 4.39 0.00 38.09 2.59
1058 1388 1.760875 CGGGCCAGCTAGGGAGTAA 60.761 63.158 4.39 0.00 38.09 2.24
1059 1389 1.749334 CGGGCCAGCTAGGGAGTAAG 61.749 65.000 4.39 0.00 38.09 2.34
1134 1468 2.423898 CCGTGCGTCCTACCCAGAT 61.424 63.158 0.00 0.00 0.00 2.90
1184 1518 3.112709 GAGCGTGCTTCGTGGGTC 61.113 66.667 0.00 0.00 42.13 4.46
1218 1552 1.000607 CTTCGAGGTGTTTGTCGGAGA 60.001 52.381 0.00 0.00 43.40 3.71
1226 1560 3.454375 GTGTTTGTCGGAGAAGAAGACA 58.546 45.455 0.00 0.00 42.36 3.41
1227 1561 3.491267 GTGTTTGTCGGAGAAGAAGACAG 59.509 47.826 0.00 0.00 44.37 3.51
1233 1567 0.539518 GGAGAAGAAGACAGGGAGGC 59.460 60.000 0.00 0.00 0.00 4.70
1234 1568 1.270907 GAGAAGAAGACAGGGAGGCA 58.729 55.000 0.00 0.00 0.00 4.75
1240 1575 4.106925 GACAGGGAGGCAGGCAGG 62.107 72.222 0.00 0.00 0.00 4.85
1248 1583 2.118294 GGCAGGCAGGGAAAGGTT 59.882 61.111 0.00 0.00 0.00 3.50
1249 1584 1.533994 GGCAGGCAGGGAAAGGTTT 60.534 57.895 0.00 0.00 0.00 3.27
1250 1585 1.667722 GCAGGCAGGGAAAGGTTTG 59.332 57.895 0.00 0.00 0.00 2.93
1251 1586 1.667722 CAGGCAGGGAAAGGTTTGC 59.332 57.895 0.00 0.00 35.87 3.68
1256 1591 3.059982 GGGAAAGGTTTGCCCTGC 58.940 61.111 1.64 0.00 45.47 4.85
1295 1630 3.793144 GCGCTTGGCTGAACTCCG 61.793 66.667 0.00 0.00 39.11 4.63
1296 1631 3.793144 CGCTTGGCTGAACTCCGC 61.793 66.667 0.00 0.00 0.00 5.54
1297 1632 2.669569 GCTTGGCTGAACTCCGCA 60.670 61.111 0.00 0.00 0.00 5.69
1298 1633 2.970974 GCTTGGCTGAACTCCGCAC 61.971 63.158 0.00 0.00 0.00 5.34
1325 1672 1.004918 GTAGGCGTGGTGAAGCACT 60.005 57.895 10.60 0.00 34.40 4.40
1347 1703 2.159198 GGTACGTTCTTCCTCGCCATAA 60.159 50.000 0.00 0.00 0.00 1.90
1354 1710 5.502544 CGTTCTTCCTCGCCATAAATTCTTC 60.503 44.000 0.00 0.00 0.00 2.87
1441 1818 4.944962 ATACATGTTGGTGAATCGTGTG 57.055 40.909 2.30 0.00 34.02 3.82
1459 2015 3.764434 GTGTGAGTATGTTCTCTCCTCCA 59.236 47.826 0.00 0.00 35.68 3.86
1511 2068 0.461548 TGCGATCTACTGCTTCTGGG 59.538 55.000 0.00 0.00 0.00 4.45
1548 2105 0.531974 AGCTTCGTCCGCACAAAAGA 60.532 50.000 0.00 0.00 0.00 2.52
1552 2109 2.461897 TCGTCCGCACAAAAGAAAAC 57.538 45.000 0.00 0.00 0.00 2.43
1553 2110 1.064357 TCGTCCGCACAAAAGAAAACC 59.936 47.619 0.00 0.00 0.00 3.27
1556 2113 2.601314 GTCCGCACAAAAGAAAACCAAC 59.399 45.455 0.00 0.00 0.00 3.77
1557 2114 2.231478 TCCGCACAAAAGAAAACCAACA 59.769 40.909 0.00 0.00 0.00 3.33
1559 2116 3.620821 CCGCACAAAAGAAAACCAACAAT 59.379 39.130 0.00 0.00 0.00 2.71
1560 2117 4.806247 CCGCACAAAAGAAAACCAACAATA 59.194 37.500 0.00 0.00 0.00 1.90
1561 2118 5.051106 CCGCACAAAAGAAAACCAACAATAG 60.051 40.000 0.00 0.00 0.00 1.73
1562 2119 5.746245 CGCACAAAAGAAAACCAACAATAGA 59.254 36.000 0.00 0.00 0.00 1.98
1588 2145 2.226962 ATGGGGCTCAATCATATGGC 57.773 50.000 2.13 0.00 0.00 4.40
1644 2201 4.944962 TTCTGCCATGAGTTCGTAATTG 57.055 40.909 0.00 0.00 0.00 2.32
1752 2309 6.821616 ATCCCCATCCTTTATATAGAGCAG 57.178 41.667 0.00 0.00 0.00 4.24
1762 2319 9.080097 TCCTTTATATAGAGCAGAAGTTACCTC 57.920 37.037 0.00 0.00 0.00 3.85
1776 2333 9.720769 CAGAAGTTACCTCCATCTTTTTACTAA 57.279 33.333 0.00 0.00 0.00 2.24
1784 2341 7.060421 CCTCCATCTTTTTACTAAATGGCCTA 58.940 38.462 3.32 0.00 0.00 3.93
1801 2358 6.659745 TGGCCTAACGATGTATAGTTGTAT 57.340 37.500 3.32 0.00 0.00 2.29
1851 2409 7.948034 TTAACCATTGGAATAACCTAGGTTG 57.052 36.000 33.19 16.77 42.65 3.77
1880 2439 2.222678 CACATAGCAAAGCTAGGCATCG 59.777 50.000 10.22 2.41 45.23 3.84
1890 2450 3.412386 AGCTAGGCATCGAAACAAAAGT 58.588 40.909 0.00 0.00 0.00 2.66
1891 2451 3.821033 AGCTAGGCATCGAAACAAAAGTT 59.179 39.130 0.00 0.00 0.00 2.66
1916 2476 8.408043 TCATGAAAATTGTCCTAGAACATGTT 57.592 30.769 11.78 11.78 35.58 2.71
1917 2477 8.859090 TCATGAAAATTGTCCTAGAACATGTTT 58.141 29.630 13.36 5.60 35.58 2.83
1976 2537 7.646922 CCTAGAATTAAGCAAGCATTTGATGTC 59.353 37.037 0.00 0.00 36.36 3.06
2017 2586 6.989169 AGTATGCTATCACTTTTTCAGCTAGG 59.011 38.462 0.00 0.00 33.38 3.02
2034 2603 1.153549 GGCCTCTAGCTTCACCACG 60.154 63.158 0.00 0.00 43.05 4.94
2110 2679 6.521162 AGTTTTAAGTAAACAAAGGCCATGG 58.479 36.000 7.63 7.63 46.93 3.66
2134 2704 6.545298 GGAAATTGCCATAGAGATGAGAAAGT 59.455 38.462 0.00 0.00 34.73 2.66
2141 2712 8.435187 TGCCATAGAGATGAGAAAGTGAATATT 58.565 33.333 0.00 0.00 34.73 1.28
2167 2738 8.657074 AGGAAACATGCAATTTGATAATCATG 57.343 30.769 0.00 6.50 34.53 3.07
2195 2766 9.491675 ACTTGACAAATTCATTTCATTGCAATA 57.508 25.926 12.53 0.00 32.84 1.90
2273 2844 7.674471 AAGACTGATTTTTGGAGTAAGCTAC 57.326 36.000 0.00 0.00 0.00 3.58
2572 3165 7.312899 CACACACACTCACACAATATCTACTA 58.687 38.462 0.00 0.00 0.00 1.82
2593 3186 0.325577 AGATTGAAACCATGGGGCCC 60.326 55.000 18.17 18.17 37.90 5.80
2612 3205 3.889815 CCCCATGATCAACACATGTACT 58.110 45.455 0.00 0.00 42.16 2.73
2615 3208 4.034394 CCCATGATCAACACATGTACTTCG 59.966 45.833 0.00 0.00 42.16 3.79
2618 3211 3.679502 TGATCAACACATGTACTTCGCTG 59.320 43.478 0.00 0.00 0.00 5.18
2646 3239 3.443037 GGAACATCATCTCACTCTCACG 58.557 50.000 0.00 0.00 0.00 4.35
2656 3249 4.738124 TCTCACTCTCACGCTGAAATAAG 58.262 43.478 0.00 0.00 0.00 1.73
2671 3264 8.961092 CGCTGAAATAAGAATTCACATAAATGG 58.039 33.333 8.44 0.00 33.47 3.16
2712 3309 2.421725 AGGAGTAATCCATCATGGGCA 58.578 47.619 12.54 0.00 38.32 5.36
2744 3341 1.691434 TCACCCTCCAAAAATTGCACC 59.309 47.619 0.00 0.00 0.00 5.01
2749 3346 3.392882 CCTCCAAAAATTGCACCAGTTC 58.607 45.455 0.00 0.00 0.00 3.01
2754 3351 5.353678 TCCAAAAATTGCACCAGTTCTTTTG 59.646 36.000 0.00 0.00 0.00 2.44
2806 3442 6.084277 GCGTTGATCTAAAAGGGTTACAAAG 58.916 40.000 0.00 0.00 0.00 2.77
2838 3474 9.777297 TGACAAATGTAGAGCTGCATATTATAA 57.223 29.630 1.02 0.00 34.83 0.98
2867 3503 2.084546 GCAACAAATTCTACTCCCGCT 58.915 47.619 0.00 0.00 0.00 5.52
2915 3552 8.137745 TCCCATTTTTCAGATAGCAAGAAAAT 57.862 30.769 10.72 3.36 39.93 1.82
2986 3624 1.133792 CCTCCATGTTCCGGGCTAATT 60.134 52.381 0.00 0.00 0.00 1.40
3022 3660 3.055819 GTGGTGTCTCTTTCTCTATGGCA 60.056 47.826 0.00 0.00 0.00 4.92
3085 3728 7.177921 AGGCAAAAATCTGATCAATTCTTCTCA 59.822 33.333 0.00 0.00 0.00 3.27
3086 3729 7.980099 GGCAAAAATCTGATCAATTCTTCTCAT 59.020 33.333 0.00 0.00 0.00 2.90
3161 3808 3.259374 AGGGAGTATAAGATGGTCGCATG 59.741 47.826 0.00 0.00 0.00 4.06
3233 3882 7.288810 AGAATGTTTTTGTTTATCAGGCAGA 57.711 32.000 0.00 0.00 0.00 4.26
3264 3915 6.163135 ACTGTCAACTAACTTGCTTCTAGT 57.837 37.500 0.00 0.00 0.00 2.57
3350 4001 0.618680 TCCACCCCACTGATGAGGAG 60.619 60.000 0.00 0.00 0.00 3.69
3384 4035 1.707427 ACCTGAGGAAGAAGGTGCAAT 59.293 47.619 4.99 0.00 45.26 3.56
3397 4048 3.094572 AGGTGCAATTGAAGAGGATTGG 58.905 45.455 10.34 0.00 34.60 3.16
3464 4115 5.989477 TGGGATCTACAAGGTAATCACAAG 58.011 41.667 0.00 0.00 28.92 3.16
3465 4116 4.816925 GGGATCTACAAGGTAATCACAAGC 59.183 45.833 0.00 0.00 0.00 4.01
3466 4117 4.816925 GGATCTACAAGGTAATCACAAGCC 59.183 45.833 0.00 0.00 0.00 4.35
3467 4118 4.901197 TCTACAAGGTAATCACAAGCCA 57.099 40.909 0.00 0.00 0.00 4.75
3468 4119 4.575885 TCTACAAGGTAATCACAAGCCAC 58.424 43.478 0.00 0.00 0.00 5.01
3469 4120 3.222173 ACAAGGTAATCACAAGCCACA 57.778 42.857 0.00 0.00 0.00 4.17
3470 4121 3.561143 ACAAGGTAATCACAAGCCACAA 58.439 40.909 0.00 0.00 0.00 3.33
3491 4142 4.090761 ACTCCACTCATTCATGTTGTGT 57.909 40.909 0.00 0.00 34.35 3.72
3492 4143 5.227569 ACTCCACTCATTCATGTTGTGTA 57.772 39.130 0.00 0.82 34.35 2.90
3493 4144 4.997395 ACTCCACTCATTCATGTTGTGTAC 59.003 41.667 0.00 0.00 34.35 2.90
3494 4145 5.221722 ACTCCACTCATTCATGTTGTGTACT 60.222 40.000 0.00 0.00 34.35 2.73
3495 4146 5.237815 TCCACTCATTCATGTTGTGTACTC 58.762 41.667 0.00 0.00 34.35 2.59
3496 4147 4.393062 CCACTCATTCATGTTGTGTACTCC 59.607 45.833 0.00 0.00 34.35 3.85
3497 4148 4.996758 CACTCATTCATGTTGTGTACTCCA 59.003 41.667 0.00 0.00 32.90 3.86
3498 4149 5.645067 CACTCATTCATGTTGTGTACTCCAT 59.355 40.000 0.00 0.00 32.90 3.41
3499 4150 6.818142 CACTCATTCATGTTGTGTACTCCATA 59.182 38.462 0.00 0.00 32.90 2.74
3500 4151 7.334171 CACTCATTCATGTTGTGTACTCCATAA 59.666 37.037 0.00 0.00 32.90 1.90
3501 4152 7.550551 ACTCATTCATGTTGTGTACTCCATAAG 59.449 37.037 0.00 0.00 0.00 1.73
3502 4153 7.394016 TCATTCATGTTGTGTACTCCATAAGT 58.606 34.615 0.00 0.00 42.33 2.24
3503 4154 7.334171 TCATTCATGTTGTGTACTCCATAAGTG 59.666 37.037 0.00 0.00 39.11 3.16
3504 4155 6.353404 TCATGTTGTGTACTCCATAAGTGA 57.647 37.500 0.00 0.00 39.11 3.41
3505 4156 6.163476 TCATGTTGTGTACTCCATAAGTGAC 58.837 40.000 0.00 0.00 39.11 3.67
3506 4157 5.801531 TGTTGTGTACTCCATAAGTGACT 57.198 39.130 0.00 0.00 39.11 3.41
3507 4158 5.779922 TGTTGTGTACTCCATAAGTGACTC 58.220 41.667 0.00 0.00 39.11 3.36
3508 4159 5.303333 TGTTGTGTACTCCATAAGTGACTCA 59.697 40.000 0.00 0.00 39.11 3.41
3509 4160 6.183360 TGTTGTGTACTCCATAAGTGACTCAA 60.183 38.462 0.00 0.00 39.11 3.02
3510 4161 5.779922 TGTGTACTCCATAAGTGACTCAAC 58.220 41.667 0.00 0.00 39.11 3.18
3511 4162 5.538813 TGTGTACTCCATAAGTGACTCAACT 59.461 40.000 0.00 0.00 39.11 3.16
3512 4163 6.041637 TGTGTACTCCATAAGTGACTCAACTT 59.958 38.462 0.00 0.00 42.89 2.66
3513 4164 6.929606 GTGTACTCCATAAGTGACTCAACTTT 59.070 38.462 0.00 0.00 40.77 2.66
3514 4165 6.929049 TGTACTCCATAAGTGACTCAACTTTG 59.071 38.462 0.00 0.00 40.77 2.77
3515 4166 5.930135 ACTCCATAAGTGACTCAACTTTGT 58.070 37.500 0.00 0.00 40.77 2.83
3516 4167 7.062749 ACTCCATAAGTGACTCAACTTTGTA 57.937 36.000 0.00 0.00 40.77 2.41
3517 4168 6.929606 ACTCCATAAGTGACTCAACTTTGTAC 59.070 38.462 0.00 0.00 40.77 2.90
3518 4169 6.822442 TCCATAAGTGACTCAACTTTGTACA 58.178 36.000 0.00 0.00 40.77 2.90
3519 4170 7.276658 TCCATAAGTGACTCAACTTTGTACAA 58.723 34.615 3.59 3.59 40.77 2.41
3520 4171 7.771361 TCCATAAGTGACTCAACTTTGTACAAA 59.229 33.333 19.53 19.53 40.77 2.83
3521 4172 8.402472 CCATAAGTGACTCAACTTTGTACAAAA 58.598 33.333 20.89 6.40 40.77 2.44
3522 4173 9.950680 CATAAGTGACTCAACTTTGTACAAAAT 57.049 29.630 20.89 9.56 40.77 1.82
3523 4174 9.950680 ATAAGTGACTCAACTTTGTACAAAATG 57.049 29.630 20.89 20.44 40.77 2.32
3524 4175 6.795399 AGTGACTCAACTTTGTACAAAATGG 58.205 36.000 20.89 10.06 0.00 3.16
3525 4176 6.377146 AGTGACTCAACTTTGTACAAAATGGT 59.623 34.615 20.89 18.92 0.00 3.55
3526 4177 7.554835 AGTGACTCAACTTTGTACAAAATGGTA 59.445 33.333 20.89 8.23 0.00 3.25
3527 4178 7.642586 GTGACTCAACTTTGTACAAAATGGTAC 59.357 37.037 20.89 15.34 43.08 3.34
3547 4198 8.514330 TGGTACAAAGTTGAGTCACTTATTTT 57.486 30.769 0.00 0.00 35.87 1.82
3548 4199 8.962679 TGGTACAAAGTTGAGTCACTTATTTTT 58.037 29.630 0.00 0.00 35.87 1.94
3549 4200 9.233232 GGTACAAAGTTGAGTCACTTATTTTTG 57.767 33.333 0.00 1.16 35.87 2.44
3550 4201 9.233232 GTACAAAGTTGAGTCACTTATTTTTGG 57.767 33.333 0.00 0.00 35.87 3.28
3551 4202 8.062065 ACAAAGTTGAGTCACTTATTTTTGGA 57.938 30.769 0.00 0.00 35.87 3.53
3552 4203 8.695456 ACAAAGTTGAGTCACTTATTTTTGGAT 58.305 29.630 0.00 0.00 35.87 3.41
3553 4204 8.971321 CAAAGTTGAGTCACTTATTTTTGGATG 58.029 33.333 0.00 0.00 35.87 3.51
3554 4205 7.219484 AGTTGAGTCACTTATTTTTGGATGG 57.781 36.000 0.00 0.00 0.00 3.51
3555 4206 7.004086 AGTTGAGTCACTTATTTTTGGATGGA 58.996 34.615 0.00 0.00 0.00 3.41
3556 4207 7.175641 AGTTGAGTCACTTATTTTTGGATGGAG 59.824 37.037 0.00 0.00 0.00 3.86
3557 4208 5.945784 TGAGTCACTTATTTTTGGATGGAGG 59.054 40.000 0.00 0.00 0.00 4.30
3558 4209 5.264395 AGTCACTTATTTTTGGATGGAGGG 58.736 41.667 0.00 0.00 0.00 4.30
3559 4210 5.015178 AGTCACTTATTTTTGGATGGAGGGA 59.985 40.000 0.00 0.00 0.00 4.20
3560 4211 5.358160 GTCACTTATTTTTGGATGGAGGGAG 59.642 44.000 0.00 0.00 0.00 4.30
3565 4216 4.301072 TTTTTGGATGGAGGGAGTACAG 57.699 45.455 0.00 0.00 0.00 2.74
3570 4221 5.412617 TGGATGGAGGGAGTACAGTATAA 57.587 43.478 0.00 0.00 0.00 0.98
3576 4227 5.424252 TGGAGGGAGTACAGTATAACCAAAG 59.576 44.000 0.00 0.00 0.00 2.77
3594 4245 1.010685 GAAGCTTTCCTATGCGCGC 60.011 57.895 27.26 27.26 0.00 6.86
3596 4247 4.945433 GCTTTCCTATGCGCGCGC 62.945 66.667 45.02 45.02 42.35 6.86
3597 4248 4.633596 CTTTCCTATGCGCGCGCG 62.634 66.667 45.73 45.73 45.51 6.86
3637 4296 4.630111 ACTCTAGCATGATTAGCAGAAGC 58.370 43.478 0.00 0.00 42.56 3.86
3643 4302 3.314357 GCATGATTAGCAGAAGCATGACA 59.686 43.478 25.12 0.00 45.49 3.58
3647 4306 5.922053 TGATTAGCAGAAGCATGACATACT 58.078 37.500 0.00 0.00 45.49 2.12
3649 4308 7.500141 TGATTAGCAGAAGCATGACATACTAA 58.500 34.615 0.00 0.00 45.49 2.24
3674 4333 6.289834 TCCATGCATCAAATTCAGTTTTTGT 58.710 32.000 0.00 0.00 35.90 2.83
3678 4337 6.269315 TGCATCAAATTCAGTTTTTGTACGT 58.731 32.000 0.00 0.00 35.90 3.57
3780 4439 3.610911 CCACAAGGACAAGAAGTATCCC 58.389 50.000 0.00 0.00 36.89 3.85
3807 4466 1.341531 ACTCGCACTAACAGAGCAACT 59.658 47.619 0.00 0.00 35.56 3.16
3828 4487 0.251077 CTGCTGGTTTCTGGAAGGCT 60.251 55.000 0.00 0.00 0.00 4.58
4025 4684 2.100252 CTCCCAAAATGTGCATGCTAGG 59.900 50.000 20.33 9.50 0.00 3.02
4032 4691 6.262944 CCAAAATGTGCATGCTAGGAGTAATA 59.737 38.462 20.33 0.00 0.00 0.98
4037 4696 9.745018 AATGTGCATGCTAGGAGTAATAATTAT 57.255 29.630 20.33 0.00 0.00 1.28
4044 4833 9.804758 ATGCTAGGAGTAATAATTATTAGCGTC 57.195 33.333 16.53 13.21 0.00 5.19
4045 4834 8.799367 TGCTAGGAGTAATAATTATTAGCGTCA 58.201 33.333 16.53 7.41 0.00 4.35
4198 4987 0.693049 ACTCGCCCTTCTGGTTCAAT 59.307 50.000 0.00 0.00 36.04 2.57
4239 5028 4.400109 GCCTCACGTCGACTCGCA 62.400 66.667 14.70 0.00 0.00 5.10
4296 5085 1.407851 CCATCATGGACACCACCAGAG 60.408 57.143 0.00 0.00 40.96 3.35
4364 5153 3.640407 AGGAGCCGGCAAGCTTCA 61.640 61.111 31.54 0.00 45.15 3.02
4432 5221 1.140589 CGTAGCTGCCAGTCTCCAG 59.859 63.158 0.00 0.00 0.00 3.86
4460 5249 1.885388 CAGACACACGACGGCCAAA 60.885 57.895 2.24 0.00 0.00 3.28
4473 5262 2.982744 GCCAAACTTCTCGGCAGCC 61.983 63.158 0.00 0.00 45.52 4.85
4616 5405 3.036084 CCGCGCTGTCGTTTCAGT 61.036 61.111 5.56 0.00 37.70 3.41
4618 5407 2.016704 CGCGCTGTCGTTTCAGTCT 61.017 57.895 5.56 0.00 37.70 3.24
4712 5501 6.200665 GTGGAAATAACGTACGGCATATACAA 59.799 38.462 21.06 4.67 0.00 2.41
4809 5599 7.935338 TTAATGTACGTAAACATAGCTAGCC 57.065 36.000 12.13 0.00 39.16 3.93
4829 5619 3.185391 GCCGTGCTATTGATTAAGCTCTC 59.815 47.826 0.00 0.00 39.53 3.20
4956 5767 6.463897 GCTGTATAGTACTCCCAAAATGGCTA 60.464 42.308 0.00 0.00 35.79 3.93
4978 5789 2.276409 ATGGTCGGTGCCATGCAT 59.724 55.556 0.00 0.00 46.63 3.96
5015 5826 4.161333 CGCTTTCCAATTCAAGTGATGTC 58.839 43.478 0.00 0.00 33.12 3.06
5052 5864 6.155221 TGAGTAATTTCCTGATGCTAGACACT 59.845 38.462 0.00 0.00 0.00 3.55
5151 5963 5.964958 AATCTGGGTCACACACAAATAAG 57.035 39.130 0.00 0.00 26.79 1.73
5320 6133 4.157840 GTGTTTAAGTGGGACCCATTCATC 59.842 45.833 18.51 2.78 35.28 2.92
5464 6303 2.037251 TCCTCTCTCTCAAACAAACCCG 59.963 50.000 0.00 0.00 0.00 5.28
5466 6305 3.060602 CTCTCTCTCAAACAAACCCGTC 58.939 50.000 0.00 0.00 0.00 4.79
5502 6341 6.925211 TGTTTACATTTTTCGATGGCCAATA 58.075 32.000 10.96 0.00 0.00 1.90
5917 7001 5.140177 CGACTGTAATGTGCTTTCTGAAAC 58.860 41.667 0.00 0.00 0.00 2.78
5943 7027 8.641155 CGAGTGAAATGAGTGTAATACGTTTTA 58.359 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 8.797438 TGCATGAGGAGTTATAATAGACTAGTG 58.203 37.037 0.00 0.00 0.00 2.74
66 67 7.083230 TCGTTATACATCGTGTACACTGAAAA 58.917 34.615 23.01 11.66 35.42 2.29
67 68 6.610456 TCGTTATACATCGTGTACACTGAAA 58.390 36.000 23.01 10.07 35.42 2.69
68 69 6.180771 TCGTTATACATCGTGTACACTGAA 57.819 37.500 23.01 9.44 35.42 3.02
69 70 5.799681 TCGTTATACATCGTGTACACTGA 57.200 39.130 23.01 20.34 35.42 3.41
74 75 6.399669 GCATTCCATCGTTATACATCGTGTAC 60.400 42.308 0.88 0.00 35.42 2.90
142 143 3.607370 GACCGGGGTCTGAGGCAAC 62.607 68.421 6.32 0.00 41.57 4.17
143 144 3.319198 GACCGGGGTCTGAGGCAA 61.319 66.667 6.32 0.00 41.57 4.52
146 147 2.365635 ATGGACCGGGGTCTGAGG 60.366 66.667 16.86 0.00 44.04 3.86
147 148 2.903357 CATGGACCGGGGTCTGAG 59.097 66.667 16.86 4.12 44.04 3.35
148 149 3.399181 GCATGGACCGGGGTCTGA 61.399 66.667 16.86 5.35 44.04 3.27
149 150 3.047807 ATGCATGGACCGGGGTCTG 62.048 63.158 16.86 9.78 44.04 3.51
150 151 2.692368 ATGCATGGACCGGGGTCT 60.692 61.111 16.86 0.00 44.04 3.85
151 152 2.516930 CATGCATGGACCGGGGTC 60.517 66.667 19.40 9.40 43.87 4.46
152 153 4.820744 GCATGCATGGACCGGGGT 62.821 66.667 27.34 0.00 0.00 4.95
153 154 4.818863 TGCATGCATGGACCGGGG 62.819 66.667 27.34 0.11 0.00 5.73
154 155 2.520020 ATGCATGCATGGACCGGG 60.520 61.111 31.74 0.91 35.03 5.73
204 241 2.529619 GCTTTGCCGATCGAGGAGC 61.530 63.158 18.66 15.62 0.00 4.70
339 379 3.443099 GGTGGTACTCCATACGGTTAC 57.557 52.381 0.00 0.00 46.20 2.50
407 447 2.739913 TGTAACGATGTAAAGGTGCTGC 59.260 45.455 0.00 0.00 0.00 5.25
408 448 4.727734 GCATGTAACGATGTAAAGGTGCTG 60.728 45.833 0.00 0.00 0.00 4.41
409 449 3.374058 GCATGTAACGATGTAAAGGTGCT 59.626 43.478 0.00 0.00 0.00 4.40
445 485 1.766143 CTACTCAAATGCGCGGAGGC 61.766 60.000 8.83 0.00 32.98 4.70
446 486 0.179111 TCTACTCAAATGCGCGGAGG 60.179 55.000 8.83 0.00 32.98 4.30
447 487 1.640428 TTCTACTCAAATGCGCGGAG 58.360 50.000 8.83 8.10 34.85 4.63
486 538 1.153086 GCGAGGCTGGAATGATGGT 60.153 57.895 0.00 0.00 0.00 3.55
543 599 2.561858 GACTCCACTTCCTTAACTCGGT 59.438 50.000 0.00 0.00 0.00 4.69
584 640 3.496875 CTCCGATGAGCTCCAGCCG 62.497 68.421 12.15 9.01 43.38 5.52
721 1042 0.396417 CACGATCTCCCTCTCACCCT 60.396 60.000 0.00 0.00 0.00 4.34
724 1045 1.323271 TGCCACGATCTCCCTCTCAC 61.323 60.000 0.00 0.00 0.00 3.51
849 1170 6.158023 ACAAGCCGGGCTATATATATACAC 57.842 41.667 24.16 0.00 38.25 2.90
850 1171 5.303589 GGACAAGCCGGGCTATATATATACA 59.696 44.000 24.16 0.00 38.25 2.29
919 1242 2.243736 ACTTGAGCTAGCTACTCCTCCT 59.756 50.000 19.38 0.00 32.98 3.69
1053 1383 9.465985 GATGCTGGTTAACTATCTTACTTACTC 57.534 37.037 5.42 0.00 0.00 2.59
1055 1385 8.202137 TGGATGCTGGTTAACTATCTTACTTAC 58.798 37.037 5.42 0.00 0.00 2.34
1056 1386 8.313944 TGGATGCTGGTTAACTATCTTACTTA 57.686 34.615 5.42 0.00 0.00 2.24
1057 1387 7.195374 TGGATGCTGGTTAACTATCTTACTT 57.805 36.000 5.42 0.00 0.00 2.24
1058 1388 6.808321 TGGATGCTGGTTAACTATCTTACT 57.192 37.500 5.42 0.00 0.00 2.24
1059 1389 8.451908 AAATGGATGCTGGTTAACTATCTTAC 57.548 34.615 5.42 0.00 0.00 2.34
1122 1456 3.896272 CAGTAAGGGTATCTGGGTAGGAC 59.104 52.174 0.00 0.00 0.00 3.85
1124 1458 3.641906 CACAGTAAGGGTATCTGGGTAGG 59.358 52.174 0.00 0.00 34.02 3.18
1131 1465 2.774234 AGCATGCACAGTAAGGGTATCT 59.226 45.455 21.98 0.00 0.00 1.98
1134 1468 1.905894 TCAGCATGCACAGTAAGGGTA 59.094 47.619 21.98 0.00 34.76 3.69
1184 1518 2.680913 CGAAGCAAGCGAACCCCTG 61.681 63.158 0.00 0.00 0.00 4.45
1218 1552 1.846712 GCCTGCCTCCCTGTCTTCTT 61.847 60.000 0.00 0.00 0.00 2.52
1226 1560 4.682714 TTCCCTGCCTGCCTCCCT 62.683 66.667 0.00 0.00 0.00 4.20
1227 1561 3.651980 CTTTCCCTGCCTGCCTCCC 62.652 68.421 0.00 0.00 0.00 4.30
1233 1567 1.667722 GCAAACCTTTCCCTGCCTG 59.332 57.895 0.00 0.00 0.00 4.85
1234 1568 4.198087 GCAAACCTTTCCCTGCCT 57.802 55.556 0.00 0.00 0.00 4.75
1325 1672 1.180456 TGGCGAGGAAGAACGTACCA 61.180 55.000 0.00 0.00 0.00 3.25
1347 1703 3.138304 TGCACGCTTACAGTGAAGAATT 58.862 40.909 0.00 0.00 41.83 2.17
1354 1710 0.937304 ACACTTGCACGCTTACAGTG 59.063 50.000 10.21 10.21 42.15 3.66
1421 1789 3.993736 CTCACACGATTCACCAACATGTA 59.006 43.478 0.00 0.00 0.00 2.29
1422 1790 2.807967 CTCACACGATTCACCAACATGT 59.192 45.455 0.00 0.00 0.00 3.21
1423 1791 2.807967 ACTCACACGATTCACCAACATG 59.192 45.455 0.00 0.00 0.00 3.21
1424 1792 3.126001 ACTCACACGATTCACCAACAT 57.874 42.857 0.00 0.00 0.00 2.71
1429 1797 4.495422 AGAACATACTCACACGATTCACC 58.505 43.478 0.00 0.00 0.00 4.02
1430 1798 5.403246 AGAGAACATACTCACACGATTCAC 58.597 41.667 0.00 0.00 39.14 3.18
1431 1799 5.393135 GGAGAGAACATACTCACACGATTCA 60.393 44.000 0.00 0.00 39.14 2.57
1433 1801 4.707448 AGGAGAGAACATACTCACACGATT 59.293 41.667 0.00 0.00 39.14 3.34
1435 1803 3.687125 AGGAGAGAACATACTCACACGA 58.313 45.455 0.00 0.00 39.14 4.35
1436 1804 3.181495 GGAGGAGAGAACATACTCACACG 60.181 52.174 0.00 0.00 39.14 4.49
1437 1805 3.764434 TGGAGGAGAGAACATACTCACAC 59.236 47.826 0.00 0.00 39.14 3.82
1441 1818 4.038642 GGATGTGGAGGAGAGAACATACTC 59.961 50.000 0.00 0.00 33.51 2.59
1511 2068 7.189512 ACGAAGCTAAATTTAATGAGTGCATC 58.810 34.615 0.00 0.64 32.35 3.91
1588 2145 0.677288 TCGTATGTAGGATTGCCGGG 59.323 55.000 2.18 0.00 39.96 5.73
1762 2319 7.066525 TCGTTAGGCCATTTAGTAAAAAGATGG 59.933 37.037 5.01 8.16 0.00 3.51
1776 2333 5.925509 ACAACTATACATCGTTAGGCCATT 58.074 37.500 5.01 0.00 0.00 3.16
1851 2409 1.202348 GCTTTGCTATGTGTGGGGTTC 59.798 52.381 0.00 0.00 0.00 3.62
1880 2439 8.882736 AGGACAATTTTCATGAACTTTTGTTTC 58.117 29.630 21.51 17.87 43.66 2.78
1890 2450 8.408043 ACATGTTCTAGGACAATTTTCATGAA 57.592 30.769 8.23 3.38 35.58 2.57
1891 2451 8.408043 AACATGTTCTAGGACAATTTTCATGA 57.592 30.769 8.23 0.00 35.58 3.07
1926 2486 5.332506 GCAAACCAAGTTGAATTGTCGAATG 60.333 40.000 3.87 0.00 0.00 2.67
1976 2537 3.313526 GCATACTCTACATTGGTGCAAGG 59.686 47.826 0.00 0.00 0.00 3.61
2017 2586 0.037232 AACGTGGTGAAGCTAGAGGC 60.037 55.000 0.00 0.00 42.19 4.70
2110 2679 7.281774 TCACTTTCTCATCTCTATGGCAATTTC 59.718 37.037 0.00 0.00 33.61 2.17
2141 2712 9.752961 CATGATTATCAAATTGCATGTTTCCTA 57.247 29.630 0.00 0.00 29.21 2.94
2167 2738 6.075280 GCAATGAAATGAATTTGTCAAGTGC 58.925 36.000 0.00 0.00 40.50 4.40
2217 2788 9.401058 AGATGTTTAATTCTATGCAAACTAGCT 57.599 29.630 0.00 0.00 33.16 3.32
2251 2822 5.938125 TGGTAGCTTACTCCAAAAATCAGTC 59.062 40.000 0.00 0.00 0.00 3.51
2252 2823 5.705905 GTGGTAGCTTACTCCAAAAATCAGT 59.294 40.000 0.00 0.00 32.82 3.41
2273 2844 2.087646 GAGGCCTTGCTAAGAAAGTGG 58.912 52.381 6.77 0.00 0.00 4.00
2572 3165 1.908619 GGCCCCATGGTTTCAATCTTT 59.091 47.619 11.73 0.00 0.00 2.52
2593 3186 4.494690 GCGAAGTACATGTGTTGATCATGG 60.495 45.833 9.11 0.00 44.57 3.66
2612 3205 0.250124 ATGTTCCCGTCAACAGCGAA 60.250 50.000 3.18 0.00 39.63 4.70
2615 3208 1.398390 GATGATGTTCCCGTCAACAGC 59.602 52.381 5.30 5.30 42.00 4.40
2618 3211 2.673368 GTGAGATGATGTTCCCGTCAAC 59.327 50.000 0.00 0.00 39.94 3.18
2646 3239 9.252962 CCCATTTATGTGAATTCTTATTTCAGC 57.747 33.333 7.05 0.00 33.95 4.26
2656 3249 3.548014 CGCCGTCCCATTTATGTGAATTC 60.548 47.826 0.00 0.00 0.00 2.17
2671 3264 1.134694 GTTTGATGCTTCGCCGTCC 59.865 57.895 0.00 0.00 0.00 4.79
2783 3380 7.198306 ACTTTGTAACCCTTTTAGATCAACG 57.802 36.000 0.00 0.00 0.00 4.10
2806 3442 5.091431 GCAGCTCTACATTTGTCAATCAAC 58.909 41.667 0.00 0.00 35.61 3.18
2838 3474 6.547510 GGAGTAGAATTTGTTGCTATTGGGAT 59.452 38.462 0.00 0.00 0.00 3.85
2867 3503 6.072175 GGATAGTGGTCTTGTATGCAAAAACA 60.072 38.462 0.00 0.00 33.73 2.83
2915 3552 7.908827 TCGTGTTATTTATTAGTTGGCTTGA 57.091 32.000 0.00 0.00 0.00 3.02
2946 3583 9.889128 ATGGAGGTTTAATTTTCCATACAATTG 57.111 29.630 3.24 3.24 45.96 2.32
2947 3584 9.889128 CATGGAGGTTTAATTTTCCATACAATT 57.111 29.630 12.25 0.00 46.04 2.32
2948 3585 9.045745 ACATGGAGGTTTAATTTTCCATACAAT 57.954 29.630 12.25 1.30 46.04 2.71
2949 3586 8.429237 ACATGGAGGTTTAATTTTCCATACAA 57.571 30.769 12.25 0.00 46.04 2.41
2950 3587 8.429237 AACATGGAGGTTTAATTTTCCATACA 57.571 30.769 12.25 0.00 46.04 2.29
2986 3624 3.888323 AGACACCACATGCAACATGTTTA 59.112 39.130 8.77 1.19 0.00 2.01
3045 3688 2.526304 TTGCCTCGTATGATAGTGCC 57.474 50.000 0.00 0.00 0.00 5.01
3085 3728 7.805083 ATATACAAGCCCACTATCTCTTCAT 57.195 36.000 0.00 0.00 0.00 2.57
3086 3729 7.618019 AATATACAAGCCCACTATCTCTTCA 57.382 36.000 0.00 0.00 0.00 3.02
3161 3808 1.661341 GTCACTCCATCTCCATGCAC 58.339 55.000 0.00 0.00 0.00 4.57
3233 3882 5.163754 GCAAGTTAGTTGACAGTTGACACTT 60.164 40.000 3.69 0.00 38.60 3.16
3279 3930 4.882427 AGCATTCATCTTCTTCCACTGATG 59.118 41.667 0.00 0.00 38.03 3.07
3350 4001 2.103263 CCTCAGGTAGTAATCCACCAGC 59.897 54.545 0.00 0.00 37.28 4.85
3384 4035 4.908601 TGTCTAAGCCAATCCTCTTCAA 57.091 40.909 0.00 0.00 0.00 2.69
3464 4115 1.896220 TGAATGAGTGGAGTTGTGGC 58.104 50.000 0.00 0.00 0.00 5.01
3465 4116 3.415212 ACATGAATGAGTGGAGTTGTGG 58.585 45.455 0.00 0.00 0.00 4.17
3466 4117 4.276678 ACAACATGAATGAGTGGAGTTGTG 59.723 41.667 0.00 0.00 44.23 3.33
3467 4118 4.276678 CACAACATGAATGAGTGGAGTTGT 59.723 41.667 0.00 0.00 46.09 3.32
3468 4119 4.276678 ACACAACATGAATGAGTGGAGTTG 59.723 41.667 17.97 0.00 39.64 3.16
3469 4120 4.464008 ACACAACATGAATGAGTGGAGTT 58.536 39.130 17.97 0.00 39.64 3.01
3470 4121 4.090761 ACACAACATGAATGAGTGGAGT 57.909 40.909 17.97 8.33 39.64 3.85
3491 4142 7.062749 ACAAAGTTGAGTCACTTATGGAGTA 57.937 36.000 0.00 0.00 35.87 2.59
3492 4143 5.930135 ACAAAGTTGAGTCACTTATGGAGT 58.070 37.500 0.00 0.00 35.87 3.85
3493 4144 6.929049 TGTACAAAGTTGAGTCACTTATGGAG 59.071 38.462 0.00 0.00 35.87 3.86
3494 4145 6.822442 TGTACAAAGTTGAGTCACTTATGGA 58.178 36.000 0.00 0.00 35.87 3.41
3495 4146 7.490962 TTGTACAAAGTTGAGTCACTTATGG 57.509 36.000 5.64 0.00 35.87 2.74
3496 4147 9.950680 ATTTTGTACAAAGTTGAGTCACTTATG 57.049 29.630 19.72 4.76 35.87 1.90
3497 4148 9.950680 CATTTTGTACAAAGTTGAGTCACTTAT 57.049 29.630 19.72 4.60 35.87 1.73
3498 4149 8.402472 CCATTTTGTACAAAGTTGAGTCACTTA 58.598 33.333 24.10 8.35 35.87 2.24
3499 4150 7.093945 ACCATTTTGTACAAAGTTGAGTCACTT 60.094 33.333 24.10 0.00 38.74 3.16
3500 4151 6.377146 ACCATTTTGTACAAAGTTGAGTCACT 59.623 34.615 24.10 2.75 0.00 3.41
3501 4152 6.560711 ACCATTTTGTACAAAGTTGAGTCAC 58.439 36.000 24.10 0.00 0.00 3.67
3502 4153 6.767524 ACCATTTTGTACAAAGTTGAGTCA 57.232 33.333 24.10 10.07 0.00 3.41
3503 4154 7.699566 TGTACCATTTTGTACAAAGTTGAGTC 58.300 34.615 24.10 16.61 45.94 3.36
3504 4155 7.633193 TGTACCATTTTGTACAAAGTTGAGT 57.367 32.000 24.10 21.37 45.94 3.41
3513 4164 7.337184 TGACTCAACTTTGTACCATTTTGTACA 59.663 33.333 0.00 0.00 46.93 2.90
3514 4165 7.642586 GTGACTCAACTTTGTACCATTTTGTAC 59.357 37.037 0.00 0.00 41.18 2.90
3515 4166 7.554835 AGTGACTCAACTTTGTACCATTTTGTA 59.445 33.333 0.00 0.00 0.00 2.41
3516 4167 6.377146 AGTGACTCAACTTTGTACCATTTTGT 59.623 34.615 0.00 0.00 0.00 2.83
3517 4168 6.795399 AGTGACTCAACTTTGTACCATTTTG 58.205 36.000 0.00 0.00 0.00 2.44
3518 4169 7.404671 AAGTGACTCAACTTTGTACCATTTT 57.595 32.000 0.00 0.00 37.05 1.82
3519 4170 8.691661 ATAAGTGACTCAACTTTGTACCATTT 57.308 30.769 0.00 0.00 40.77 2.32
3520 4171 8.691661 AATAAGTGACTCAACTTTGTACCATT 57.308 30.769 0.00 0.00 40.77 3.16
3521 4172 8.691661 AAATAAGTGACTCAACTTTGTACCAT 57.308 30.769 0.00 0.00 40.77 3.55
3522 4173 8.514330 AAAATAAGTGACTCAACTTTGTACCA 57.486 30.769 0.00 0.00 40.77 3.25
3523 4174 9.233232 CAAAAATAAGTGACTCAACTTTGTACC 57.767 33.333 0.00 0.00 40.77 3.34
3524 4175 9.233232 CCAAAAATAAGTGACTCAACTTTGTAC 57.767 33.333 0.00 0.00 40.77 2.90
3525 4176 9.179909 TCCAAAAATAAGTGACTCAACTTTGTA 57.820 29.630 0.00 0.00 40.77 2.41
3526 4177 8.062065 TCCAAAAATAAGTGACTCAACTTTGT 57.938 30.769 0.00 0.00 40.77 2.83
3527 4178 8.971321 CATCCAAAAATAAGTGACTCAACTTTG 58.029 33.333 0.00 0.00 40.77 2.77
3528 4179 8.143835 CCATCCAAAAATAAGTGACTCAACTTT 58.856 33.333 0.00 0.00 40.77 2.66
3529 4180 7.505585 TCCATCCAAAAATAAGTGACTCAACTT 59.494 33.333 0.00 0.00 42.89 2.66
3530 4181 7.004086 TCCATCCAAAAATAAGTGACTCAACT 58.996 34.615 0.00 0.00 0.00 3.16
3531 4182 7.214467 TCCATCCAAAAATAAGTGACTCAAC 57.786 36.000 0.00 0.00 0.00 3.18
3532 4183 6.434028 CCTCCATCCAAAAATAAGTGACTCAA 59.566 38.462 0.00 0.00 0.00 3.02
3533 4184 5.945784 CCTCCATCCAAAAATAAGTGACTCA 59.054 40.000 0.00 0.00 0.00 3.41
3534 4185 5.358160 CCCTCCATCCAAAAATAAGTGACTC 59.642 44.000 0.00 0.00 0.00 3.36
3535 4186 5.015178 TCCCTCCATCCAAAAATAAGTGACT 59.985 40.000 0.00 0.00 0.00 3.41
3536 4187 5.261216 TCCCTCCATCCAAAAATAAGTGAC 58.739 41.667 0.00 0.00 0.00 3.67
3537 4188 5.015178 ACTCCCTCCATCCAAAAATAAGTGA 59.985 40.000 0.00 0.00 0.00 3.41
3538 4189 5.264395 ACTCCCTCCATCCAAAAATAAGTG 58.736 41.667 0.00 0.00 0.00 3.16
3539 4190 5.536497 ACTCCCTCCATCCAAAAATAAGT 57.464 39.130 0.00 0.00 0.00 2.24
3540 4191 6.423182 TGTACTCCCTCCATCCAAAAATAAG 58.577 40.000 0.00 0.00 0.00 1.73
3541 4192 6.011981 ACTGTACTCCCTCCATCCAAAAATAA 60.012 38.462 0.00 0.00 0.00 1.40
3542 4193 5.491078 ACTGTACTCCCTCCATCCAAAAATA 59.509 40.000 0.00 0.00 0.00 1.40
3543 4194 4.292306 ACTGTACTCCCTCCATCCAAAAAT 59.708 41.667 0.00 0.00 0.00 1.82
3544 4195 3.655777 ACTGTACTCCCTCCATCCAAAAA 59.344 43.478 0.00 0.00 0.00 1.94
3545 4196 3.256704 ACTGTACTCCCTCCATCCAAAA 58.743 45.455 0.00 0.00 0.00 2.44
3546 4197 2.915869 ACTGTACTCCCTCCATCCAAA 58.084 47.619 0.00 0.00 0.00 3.28
3547 4198 2.642171 ACTGTACTCCCTCCATCCAA 57.358 50.000 0.00 0.00 0.00 3.53
3548 4199 3.993658 ATACTGTACTCCCTCCATCCA 57.006 47.619 0.00 0.00 0.00 3.41
3549 4200 4.527427 GGTTATACTGTACTCCCTCCATCC 59.473 50.000 0.00 0.00 0.00 3.51
3550 4201 5.145564 TGGTTATACTGTACTCCCTCCATC 58.854 45.833 0.00 0.00 0.00 3.51
3551 4202 5.152306 TGGTTATACTGTACTCCCTCCAT 57.848 43.478 0.00 0.00 0.00 3.41
3552 4203 4.613265 TGGTTATACTGTACTCCCTCCA 57.387 45.455 0.00 0.00 0.00 3.86
3553 4204 5.659971 TCTTTGGTTATACTGTACTCCCTCC 59.340 44.000 0.00 0.00 0.00 4.30
3554 4205 6.786967 TCTTTGGTTATACTGTACTCCCTC 57.213 41.667 0.00 0.00 0.00 4.30
3555 4206 6.351966 GCTTCTTTGGTTATACTGTACTCCCT 60.352 42.308 0.00 0.00 0.00 4.20
3556 4207 5.816258 GCTTCTTTGGTTATACTGTACTCCC 59.184 44.000 0.00 0.00 0.00 4.30
3557 4208 6.641474 AGCTTCTTTGGTTATACTGTACTCC 58.359 40.000 0.00 0.00 0.00 3.85
3558 4209 8.549338 AAAGCTTCTTTGGTTATACTGTACTC 57.451 34.615 0.00 0.00 0.00 2.59
3559 4210 7.606839 GGAAAGCTTCTTTGGTTATACTGTACT 59.393 37.037 0.00 0.00 0.00 2.73
3560 4211 7.606839 AGGAAAGCTTCTTTGGTTATACTGTAC 59.393 37.037 0.00 0.00 0.00 2.90
3565 4216 7.418408 GCATAGGAAAGCTTCTTTGGTTATAC 58.582 38.462 0.00 0.00 0.00 1.47
3570 4221 2.749621 CGCATAGGAAAGCTTCTTTGGT 59.250 45.455 0.00 0.00 0.00 3.67
3576 4227 1.010685 GCGCGCATAGGAAAGCTTC 60.011 57.895 29.10 0.00 0.00 3.86
3594 4245 2.613691 AGTGTATTGGAAGGTTACGCG 58.386 47.619 3.53 3.53 32.89 6.01
3596 4247 6.205101 AGAGTAGTGTATTGGAAGGTTACG 57.795 41.667 0.00 0.00 0.00 3.18
3597 4248 7.147949 TGCTAGAGTAGTGTATTGGAAGGTTAC 60.148 40.741 0.00 0.00 0.00 2.50
3598 4249 6.893554 TGCTAGAGTAGTGTATTGGAAGGTTA 59.106 38.462 0.00 0.00 0.00 2.85
3599 4250 5.720041 TGCTAGAGTAGTGTATTGGAAGGTT 59.280 40.000 0.00 0.00 0.00 3.50
3605 4256 7.543868 GCTAATCATGCTAGAGTAGTGTATTGG 59.456 40.741 12.58 0.00 38.19 3.16
3637 4296 7.443259 TTGATGCATGGATTAGTATGTCATG 57.557 36.000 2.46 0.00 38.46 3.07
3643 4302 8.701908 ACTGAATTTGATGCATGGATTAGTAT 57.298 30.769 2.46 0.00 0.00 2.12
3647 4306 8.937884 CAAAAACTGAATTTGATGCATGGATTA 58.062 29.630 2.46 0.00 39.56 1.75
3649 4308 6.938030 ACAAAAACTGAATTTGATGCATGGAT 59.062 30.769 2.46 0.00 39.56 3.41
3659 4318 9.161684 GGTTAGTACGTACAAAAACTGAATTTG 57.838 33.333 26.55 7.87 42.18 2.32
3674 4333 5.645929 TCGTTTGAGGTATGGTTAGTACGTA 59.354 40.000 0.00 0.00 0.00 3.57
3678 4337 5.128171 AGCATCGTTTGAGGTATGGTTAGTA 59.872 40.000 0.00 0.00 0.00 1.82
3780 4439 2.048597 TTAGTGCGAGTGCCGGTG 60.049 61.111 1.90 0.00 41.78 4.94
3807 4466 1.271379 GCCTTCCAGAAACCAGCAGTA 60.271 52.381 0.00 0.00 0.00 2.74
4044 4833 2.174210 AGGGATGGAGTGGTCATGAATG 59.826 50.000 0.00 0.00 0.00 2.67
4045 4834 2.496297 AGGGATGGAGTGGTCATGAAT 58.504 47.619 0.00 0.00 0.00 2.57
4050 4839 1.191535 CGTTAGGGATGGAGTGGTCA 58.808 55.000 0.00 0.00 0.00 4.02
4056 4845 6.995511 TTAACATTTTCGTTAGGGATGGAG 57.004 37.500 0.00 0.00 33.11 3.86
4198 4987 4.673298 AACGCCGCATGGTCGTGA 62.673 61.111 0.00 0.00 43.78 4.35
4239 5028 4.341783 GGTGCACTGCCTGCCTCT 62.342 66.667 17.98 0.00 46.51 3.69
4432 5221 2.899838 TGTGTCTGGTTGCACGGC 60.900 61.111 0.00 0.00 38.36 5.68
4460 5249 0.975040 ATCTCAGGCTGCCGAGAAGT 60.975 55.000 31.55 20.83 37.00 3.01
4473 5262 2.223829 ACATAAACCGGCTCGATCTCAG 60.224 50.000 0.00 0.00 0.00 3.35
4594 5383 2.563086 GAAACGACAGCGCGGGATTG 62.563 60.000 13.26 1.71 42.48 2.67
4600 5389 2.016704 AGACTGAAACGACAGCGCG 61.017 57.895 0.00 0.00 42.48 6.86
4607 5396 1.618837 CTTCCCCTCAGACTGAAACGA 59.381 52.381 6.61 0.00 0.00 3.85
4616 5405 0.541998 TCTTCGTGCTTCCCCTCAGA 60.542 55.000 0.00 0.00 0.00 3.27
4618 5407 1.544825 CCTCTTCGTGCTTCCCCTCA 61.545 60.000 0.00 0.00 0.00 3.86
4712 5501 7.152645 AGTGTGTATCTTTTCGTATCTGTGTT 58.847 34.615 0.00 0.00 0.00 3.32
4873 5665 1.619827 CACCCTCCAAATTGTGCATGT 59.380 47.619 0.00 0.00 0.00 3.21
4978 5789 4.646040 TGGAAAGCGTATAACCACTAGCTA 59.354 41.667 0.00 0.00 34.24 3.32
5052 5864 7.489160 ACTGTAAAGAATATCGATACACTGCA 58.511 34.615 7.41 9.07 0.00 4.41
5062 5874 7.757097 AGCACTACAACTGTAAAGAATATCG 57.243 36.000 0.00 0.00 0.00 2.92
5118 5930 6.374053 TGTGTGACCCAGATTATATGTTGTTG 59.626 38.462 0.00 0.00 0.00 3.33
5151 5963 4.752101 ACGCTGCACAAAATCCTCTATATC 59.248 41.667 0.00 0.00 0.00 1.63
5320 6133 5.822519 ACTGCCACAATACATGGTTATACAG 59.177 40.000 0.00 0.00 39.63 2.74
5491 6330 5.347342 TGCTGTAAAAATTATTGGCCATCG 58.653 37.500 6.09 0.00 0.00 3.84
5752 6594 3.374988 TCGCAAGCTGGAATATGAAACTG 59.625 43.478 0.00 0.00 37.18 3.16
5917 7001 6.627690 AACGTATTACACTCATTTCACTCG 57.372 37.500 0.00 0.00 0.00 4.18
5968 7052 7.726079 TCAGAAAACGTATTACACTCATTTCG 58.274 34.615 0.00 0.00 31.40 3.46


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

AutoCloner maintained by Alex Coulton.