Multiple sequence alignment - TraesCS3D01G048800

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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 TraesCS3D01G048800 chr3D 100.000 5208 0 0 1 5208 18756464 18761671 0.000000e+00 9618.0
1 TraesCS3D01G048800 chr3D 81.516 1834 268 52 2230 4019 18908114 18909920 0.000000e+00 1443.0
2 TraesCS3D01G048800 chr3D 90.402 448 39 3 4763 5208 68032304 68032749 2.090000e-163 586.0
3 TraesCS3D01G048800 chr3D 80.028 721 123 16 110 821 539923769 539924477 1.000000e-141 514.0
4 TraesCS3D01G048800 chr3D 77.688 372 74 8 7 375 533143623 533143988 8.780000e-53 219.0
5 TraesCS3D01G048800 chr3D 77.273 374 72 10 7 375 77066806 77067171 1.900000e-49 207.0
6 TraesCS3D01G048800 chr3D 77.151 372 76 7 7 375 102232161 102232526 1.900000e-49 207.0
7 TraesCS3D01G048800 chr3D 100.000 28 0 0 2167 2194 553419282 553419309 9.000000e-03 52.8
8 TraesCS3D01G048800 chr3B 93.964 4208 214 21 942 5118 29419034 29414836 0.000000e+00 6327.0
9 TraesCS3D01G048800 chr3B 92.887 2896 168 25 1836 4711 75475368 75472491 0.000000e+00 4172.0
10 TraesCS3D01G048800 chr3B 86.695 1180 149 7 2846 4019 29782025 29783202 0.000000e+00 1303.0
11 TraesCS3D01G048800 chr3B 85.168 1281 172 13 2753 4019 29853937 29855213 0.000000e+00 1297.0
12 TraesCS3D01G048800 chr3B 93.511 601 39 0 1243 1843 75476237 75475637 0.000000e+00 894.0
13 TraesCS3D01G048800 chr3B 93.204 309 19 1 942 1250 75476914 75476608 2.210000e-123 453.0
14 TraesCS3D01G048800 chr3B 76.865 657 124 15 1116 1761 30470960 30471599 3.860000e-91 346.0
15 TraesCS3D01G048800 chr3B 78.144 334 61 6 1121 1451 30375380 30375704 8.840000e-48 202.0
16 TraesCS3D01G048800 chr3B 76.682 223 36 9 1395 1602 29780332 29780553 5.510000e-20 110.0
17 TraesCS3D01G048800 chr3B 76.233 223 37 12 1395 1602 30205177 30205398 2.570000e-18 104.0
18 TraesCS3D01G048800 chr3B 75.652 230 41 10 1398 1616 30515159 30515384 3.320000e-17 100.0
19 TraesCS3D01G048800 chr3A 80.806 1860 273 56 2208 4014 26205030 26206858 0.000000e+00 1380.0
20 TraesCS3D01G048800 chr3A 84.880 1336 174 21 2702 4015 26261472 26262801 0.000000e+00 1323.0
21 TraesCS3D01G048800 chr3A 81.103 1741 240 57 2327 4019 26232673 26234372 0.000000e+00 1310.0
22 TraesCS3D01G048800 chr3A 89.755 449 41 3 4763 5208 466817424 466816978 2.100000e-158 569.0
23 TraesCS3D01G048800 chr3A 88.172 465 48 6 4748 5208 147378438 147378899 9.860000e-152 547.0
24 TraesCS3D01G048800 chr3A 77.188 377 77 4 1118 1487 26476177 26476551 1.470000e-50 211.0
25 TraesCS3D01G048800 chr3A 75.771 227 39 9 1395 1608 26479915 26480138 3.320000e-17 100.0
26 TraesCS3D01G048800 chr3A 96.875 32 0 1 2164 2195 601398838 601398868 9.000000e-03 52.8
27 TraesCS3D01G048800 chr3A 96.875 32 0 1 2164 2195 601398917 601398887 9.000000e-03 52.8
28 TraesCS3D01G048800 chr7B 84.906 1325 175 18 2702 4009 64321540 64322856 0.000000e+00 1315.0
29 TraesCS3D01G048800 chr7D 89.755 449 41 3 4763 5208 50815691 50816137 2.100000e-158 569.0
30 TraesCS3D01G048800 chr7D 89.755 449 41 3 4763 5208 50898089 50898535 2.100000e-158 569.0
31 TraesCS3D01G048800 chr7D 89.310 449 43 3 4763 5208 50866304 50866750 4.560000e-155 558.0
32 TraesCS3D01G048800 chr7D 89.310 449 43 3 4763 5208 50930119 50930565 4.560000e-155 558.0
33 TraesCS3D01G048800 chr7D 89.087 449 44 3 4763 5208 50763251 50763697 2.120000e-153 553.0
34 TraesCS3D01G048800 chr7D 79.477 726 121 18 115 821 484990540 484991256 1.690000e-134 490.0
35 TraesCS3D01G048800 chr7D 78.462 260 46 6 593 846 477656929 477657184 1.500000e-35 161.0
36 TraesCS3D01G048800 chr4D 78.604 874 158 22 4 860 131275491 131274630 7.620000e-153 551.0
37 TraesCS3D01G048800 chr4D 77.748 373 73 9 7 375 335750618 335750984 2.440000e-53 220.0
38 TraesCS3D01G048800 chr4D 92.857 42 2 1 2154 2194 7830333 7830292 5.630000e-05 60.2
39 TraesCS3D01G048800 chrUn 78.465 808 147 20 94 883 101358938 101359736 2.160000e-138 503.0
40 TraesCS3D01G048800 chr4A 81.436 571 85 13 151 707 165413339 165412776 1.030000e-121 448.0
41 TraesCS3D01G048800 chr7A 77.793 752 146 16 56 801 610365081 610364345 1.330000e-120 444.0
42 TraesCS3D01G048800 chr2D 81.193 553 91 8 285 830 560324816 560325362 2.880000e-117 433.0
43 TraesCS3D01G048800 chr4B 80.551 581 91 10 212 780 123457438 123456868 1.340000e-115 427.0
44 TraesCS3D01G048800 chr2A 81.783 516 81 8 289 801 700082875 700083380 2.240000e-113 420.0
45 TraesCS3D01G048800 chr2A 100.000 30 0 0 2165 2194 205920524 205920553 7.290000e-04 56.5
46 TraesCS3D01G048800 chr1D 77.957 372 73 7 7 375 379633124 379633489 1.890000e-54 224.0
47 TraesCS3D01G048800 chr5D 77.358 371 73 9 9 375 304790479 304790116 5.280000e-50 209.0
48 TraesCS3D01G048800 chr5D 76.819 371 78 8 7 375 209405184 209404820 8.840000e-48 202.0
49 TraesCS3D01G048800 chr6A 96.875 32 0 1 2164 2195 400115545 400115515 9.000000e-03 52.8


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 TraesCS3D01G048800 chr3D 18756464 18761671 5207 False 9618.000000 9618 100.000000 1 5208 1 chr3D.!!$F1 5207
1 TraesCS3D01G048800 chr3D 18908114 18909920 1806 False 1443.000000 1443 81.516000 2230 4019 1 chr3D.!!$F2 1789
2 TraesCS3D01G048800 chr3D 539923769 539924477 708 False 514.000000 514 80.028000 110 821 1 chr3D.!!$F7 711
3 TraesCS3D01G048800 chr3B 29414836 29419034 4198 True 6327.000000 6327 93.964000 942 5118 1 chr3B.!!$R1 4176
4 TraesCS3D01G048800 chr3B 75472491 75476914 4423 True 1839.666667 4172 93.200667 942 4711 3 chr3B.!!$R2 3769
5 TraesCS3D01G048800 chr3B 29853937 29855213 1276 False 1297.000000 1297 85.168000 2753 4019 1 chr3B.!!$F1 1266
6 TraesCS3D01G048800 chr3B 29780332 29783202 2870 False 706.500000 1303 81.688500 1395 4019 2 chr3B.!!$F6 2624
7 TraesCS3D01G048800 chr3B 30470960 30471599 639 False 346.000000 346 76.865000 1116 1761 1 chr3B.!!$F4 645
8 TraesCS3D01G048800 chr3A 26205030 26206858 1828 False 1380.000000 1380 80.806000 2208 4014 1 chr3A.!!$F1 1806
9 TraesCS3D01G048800 chr3A 26261472 26262801 1329 False 1323.000000 1323 84.880000 2702 4015 1 chr3A.!!$F3 1313
10 TraesCS3D01G048800 chr3A 26232673 26234372 1699 False 1310.000000 1310 81.103000 2327 4019 1 chr3A.!!$F2 1692
11 TraesCS3D01G048800 chr7B 64321540 64322856 1316 False 1315.000000 1315 84.906000 2702 4009 1 chr7B.!!$F1 1307
12 TraesCS3D01G048800 chr7D 484990540 484991256 716 False 490.000000 490 79.477000 115 821 1 chr7D.!!$F7 706
13 TraesCS3D01G048800 chr4D 131274630 131275491 861 True 551.000000 551 78.604000 4 860 1 chr4D.!!$R2 856
14 TraesCS3D01G048800 chrUn 101358938 101359736 798 False 503.000000 503 78.465000 94 883 1 chrUn.!!$F1 789
15 TraesCS3D01G048800 chr4A 165412776 165413339 563 True 448.000000 448 81.436000 151 707 1 chr4A.!!$R1 556
16 TraesCS3D01G048800 chr7A 610364345 610365081 736 True 444.000000 444 77.793000 56 801 1 chr7A.!!$R1 745
17 TraesCS3D01G048800 chr2D 560324816 560325362 546 False 433.000000 433 81.193000 285 830 1 chr2D.!!$F1 545
18 TraesCS3D01G048800 chr4B 123456868 123457438 570 True 427.000000 427 80.551000 212 780 1 chr4B.!!$R1 568
19 TraesCS3D01G048800 chr2A 700082875 700083380 505 False 420.000000 420 81.783000 289 801 1 chr2A.!!$F2 512

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
919 945 0.029567 GATCAGACGCGTGTAGGAGG 59.970 60.0 20.70 0.0 0.00 4.30 F
929 955 0.035725 GTGTAGGAGGTTTTCGGGGG 60.036 60.0 0.00 0.0 0.00 5.40 F
1105 1131 0.530650 CACCACCACTATAGCTGCCG 60.531 60.0 0.00 0.0 0.00 5.69 F
1570 1995 0.957395 CATTTCGAGGCAGGTGCACT 60.957 55.0 17.98 0.0 44.36 4.40 F
2686 3910 1.187715 CGTTGCTTGGTTTTGACACG 58.812 50.0 0.00 0.0 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2667 3891 1.187715 CGTGTCAAAACCAAGCAACG 58.812 50.000 0.00 0.0 0.0 4.10 R
2774 4023 3.304057 GCTGTTACTGCCAAAACTGAGAC 60.304 47.826 2.72 0.0 0.0 3.36 R
3034 4289 0.240945 CAGCAACCAAACGACCATCC 59.759 55.000 0.00 0.0 0.0 3.51 R
3163 4418 0.873743 GAGCTCGCTTTGATCCCTCG 60.874 60.000 0.00 0.0 0.0 4.63 R
4297 5562 0.390124 CTTTGTTGGTGGTGCTGCAT 59.610 50.000 5.27 0.0 0.0 3.96 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
20 21 1.404391 CGTAGCCGGCTTCTTTCTCTA 59.596 52.381 37.74 10.57 0.00 2.43
22 23 0.537653 AGCCGGCTTCTTTCTCTACC 59.462 55.000 27.08 0.00 0.00 3.18
27 28 2.351455 GGCTTCTTTCTCTACCTGCAC 58.649 52.381 0.00 0.00 0.00 4.57
29 30 2.352814 GCTTCTTTCTCTACCTGCACGA 60.353 50.000 0.00 0.00 0.00 4.35
50 51 1.577616 CAGTTACGCGCGCATTGAC 60.578 57.895 32.58 22.49 0.00 3.18
163 165 0.767375 TCAGCCTGGAGAAACTTGCT 59.233 50.000 0.00 0.00 0.00 3.91
239 241 1.802636 CGGCAATTTGCTCCATCGT 59.197 52.632 20.06 0.00 44.28 3.73
251 253 2.490148 CCATCGTGCTAGGCGAGGA 61.490 63.158 0.96 0.00 41.80 3.71
253 255 0.179111 CATCGTGCTAGGCGAGGAAA 60.179 55.000 0.00 0.00 41.80 3.13
254 256 0.753262 ATCGTGCTAGGCGAGGAAAT 59.247 50.000 0.00 0.00 41.83 2.17
264 266 1.028868 GCGAGGAAATTGGAGCAGCT 61.029 55.000 0.00 0.00 0.00 4.24
267 269 2.159043 CGAGGAAATTGGAGCAGCTAGA 60.159 50.000 0.00 0.00 0.00 2.43
270 272 3.201708 AGGAAATTGGAGCAGCTAGATGT 59.798 43.478 10.15 0.00 0.00 3.06
279 281 0.940833 CAGCTAGATGTCTCGCTCGA 59.059 55.000 6.12 0.00 42.21 4.04
412 428 1.675641 GTGGTGCGATTCTTGCCCT 60.676 57.895 0.00 0.00 0.00 5.19
419 435 1.813513 CGATTCTTGCCCTGTGTCTT 58.186 50.000 0.00 0.00 0.00 3.01
421 437 2.783135 GATTCTTGCCCTGTGTCTTGA 58.217 47.619 0.00 0.00 0.00 3.02
425 441 0.836606 TTGCCCTGTGTCTTGACTCA 59.163 50.000 2.35 4.12 0.00 3.41
438 454 7.334421 TGTGTCTTGACTCATTTAAATAGAGGC 59.666 37.037 21.37 20.17 37.92 4.70
452 468 4.095400 AGGCCGGATGGGAGGAGT 62.095 66.667 5.05 0.00 38.47 3.85
454 470 2.506472 GCCGGATGGGAGGAGTTC 59.494 66.667 5.05 0.00 38.47 3.01
478 494 1.969256 CAGCGTTGTGTTTAATGTCGC 59.031 47.619 0.00 0.00 41.96 5.19
498 516 4.231753 CGCTTGTGAACGGACGTA 57.768 55.556 0.00 0.00 0.00 3.57
548 566 1.100510 GGGTTTAATGGAGGCGTTCC 58.899 55.000 1.61 1.61 46.98 3.62
561 579 4.179579 GTTCCAATGCGGCGAGGC 62.180 66.667 12.98 0.00 33.14 4.70
638 656 1.536943 GGCGGAGACAGTGAGAGGTT 61.537 60.000 0.00 0.00 31.66 3.50
732 752 1.003355 CAGGAAGCACACACGGGAT 60.003 57.895 0.00 0.00 0.00 3.85
733 753 1.003355 AGGAAGCACACACGGGATG 60.003 57.895 0.00 0.00 0.00 3.51
734 754 1.003839 GGAAGCACACACGGGATGA 60.004 57.895 0.00 0.00 0.00 2.92
738 759 0.036732 AGCACACACGGGATGAATGT 59.963 50.000 0.00 0.00 0.00 2.71
743 764 0.960364 ACACGGGATGAATGTGTGGC 60.960 55.000 0.00 0.00 44.59 5.01
754 775 2.017668 ATGTGTGGCTTTGGGTGGGA 62.018 55.000 0.00 0.00 0.00 4.37
757 778 1.456705 GTGGCTTTGGGTGGGACAA 60.457 57.895 0.00 0.00 44.16 3.18
762 783 0.179029 CTTTGGGTGGGACAAGACGT 60.179 55.000 0.00 0.00 44.16 4.34
821 847 2.028876 CCCCTGTTTGTCTTCGGTTTT 58.971 47.619 0.00 0.00 0.00 2.43
822 848 2.429250 CCCCTGTTTGTCTTCGGTTTTT 59.571 45.455 0.00 0.00 0.00 1.94
862 888 2.389386 GCATCGCGGACCAATACAA 58.611 52.632 6.13 0.00 0.00 2.41
865 891 2.780993 CATCGCGGACCAATACAAAAC 58.219 47.619 6.13 0.00 0.00 2.43
868 894 1.533731 CGCGGACCAATACAAAACAGT 59.466 47.619 0.00 0.00 0.00 3.55
869 895 2.737783 CGCGGACCAATACAAAACAGTA 59.262 45.455 0.00 0.00 0.00 2.74
870 896 3.372822 CGCGGACCAATACAAAACAGTAT 59.627 43.478 0.00 0.00 36.29 2.12
871 897 4.142773 CGCGGACCAATACAAAACAGTATT 60.143 41.667 0.00 0.00 43.51 1.89
882 908 9.777297 AATACAAAACAGTATTGAAATGGCTTT 57.223 25.926 0.00 0.00 41.72 3.51
883 909 7.481275 ACAAAACAGTATTGAAATGGCTTTG 57.519 32.000 0.00 0.00 32.01 2.77
884 910 6.482973 ACAAAACAGTATTGAAATGGCTTTGG 59.517 34.615 0.00 0.00 30.93 3.28
885 911 4.192429 ACAGTATTGAAATGGCTTTGGC 57.808 40.909 0.00 0.00 37.82 4.52
902 928 4.514577 CCTTCCGGACAGCGCGAT 62.515 66.667 12.10 0.00 0.00 4.58
903 929 2.956964 CTTCCGGACAGCGCGATC 60.957 66.667 12.10 3.12 0.00 3.69
904 930 3.699955 CTTCCGGACAGCGCGATCA 62.700 63.158 12.10 0.00 0.00 2.92
905 931 3.699955 TTCCGGACAGCGCGATCAG 62.700 63.158 12.10 10.82 0.00 2.90
906 932 4.193334 CCGGACAGCGCGATCAGA 62.193 66.667 12.10 0.00 0.00 3.27
907 933 2.951745 CGGACAGCGCGATCAGAC 60.952 66.667 12.10 0.00 0.00 3.51
908 934 2.951745 GGACAGCGCGATCAGACG 60.952 66.667 12.10 0.00 0.00 4.18
916 942 4.286967 CGATCAGACGCGTGTAGG 57.713 61.111 20.70 0.73 0.00 3.18
917 943 1.719709 CGATCAGACGCGTGTAGGA 59.280 57.895 20.70 7.88 0.00 2.94
918 944 0.316278 CGATCAGACGCGTGTAGGAG 60.316 60.000 20.70 0.00 0.00 3.69
919 945 0.029567 GATCAGACGCGTGTAGGAGG 59.970 60.000 20.70 0.00 0.00 4.30
920 946 0.680280 ATCAGACGCGTGTAGGAGGT 60.680 55.000 20.70 0.00 0.00 3.85
921 947 0.892358 TCAGACGCGTGTAGGAGGTT 60.892 55.000 20.70 0.00 0.00 3.50
922 948 0.038526 CAGACGCGTGTAGGAGGTTT 60.039 55.000 20.70 0.00 0.00 3.27
923 949 0.677842 AGACGCGTGTAGGAGGTTTT 59.322 50.000 20.70 0.00 0.00 2.43
924 950 1.066136 GACGCGTGTAGGAGGTTTTC 58.934 55.000 20.70 0.00 0.00 2.29
925 951 0.665369 ACGCGTGTAGGAGGTTTTCG 60.665 55.000 12.93 0.00 0.00 3.46
926 952 1.349259 CGCGTGTAGGAGGTTTTCGG 61.349 60.000 0.00 0.00 0.00 4.30
927 953 1.017701 GCGTGTAGGAGGTTTTCGGG 61.018 60.000 0.00 0.00 0.00 5.14
928 954 0.390735 CGTGTAGGAGGTTTTCGGGG 60.391 60.000 0.00 0.00 0.00 5.73
929 955 0.035725 GTGTAGGAGGTTTTCGGGGG 60.036 60.000 0.00 0.00 0.00 5.40
947 973 4.579127 GCGTTGGGATGCCCTTAT 57.421 55.556 0.00 0.00 45.70 1.73
948 974 2.807247 GCGTTGGGATGCCCTTATT 58.193 52.632 0.00 0.00 45.70 1.40
962 988 3.366374 GCCCTTATTCAGTTTGCACACTC 60.366 47.826 1.59 0.00 0.00 3.51
972 998 3.114527 TGCACACTCCACTTGCAAT 57.885 47.368 0.00 0.00 43.16 3.56
973 999 2.268762 TGCACACTCCACTTGCAATA 57.731 45.000 0.00 0.00 43.16 1.90
1023 1049 0.774908 ACCCGTTTCATTTCCCTGGA 59.225 50.000 0.00 0.00 0.00 3.86
1072 1098 0.829333 CATGCTCCTACTGCTCACCT 59.171 55.000 0.00 0.00 0.00 4.00
1105 1131 0.530650 CACCACCACTATAGCTGCCG 60.531 60.000 0.00 0.00 0.00 5.69
1109 1135 2.485479 CCACCACTATAGCTGCCGAAAT 60.485 50.000 0.00 0.00 0.00 2.17
1161 1187 2.106332 CTCCGCATCACGTACCCC 59.894 66.667 0.00 0.00 41.42 4.95
1202 1228 3.702048 GCCCGAGTGTGGCTACCA 61.702 66.667 0.00 0.00 45.70 3.25
1252 1656 3.911137 GCAGCAAGGCCTTACTCC 58.089 61.111 20.00 3.72 0.00 3.85
1265 1669 3.330267 CCTTACTCCAGCACTCAGTTTC 58.670 50.000 0.00 0.00 0.00 2.78
1266 1670 3.330267 CTTACTCCAGCACTCAGTTTCC 58.670 50.000 0.00 0.00 0.00 3.13
1323 1727 1.331138 TCGTTGCGGATCAAAAACGTT 59.669 42.857 19.11 0.00 44.25 3.99
1332 1736 3.423645 GGATCAAAAACGTTGAGCTCTCG 60.424 47.826 22.80 22.80 35.39 4.04
1348 1752 4.101790 CGGACGGCATGTGCAACC 62.102 66.667 7.36 5.92 44.36 3.77
1351 1755 4.594854 ACGGCATGTGCAACCCCA 62.595 61.111 7.36 0.00 44.36 4.96
1359 1769 1.607467 GTGCAACCCCAAGCTCCAT 60.607 57.895 0.00 0.00 0.00 3.41
1361 1771 3.010413 GCAACCCCAAGCTCCATGC 62.010 63.158 0.00 0.00 43.29 4.06
1544 1969 3.089838 TGCTGGGGCATACAAGCT 58.910 55.556 3.75 0.00 44.28 3.74
1570 1995 0.957395 CATTTCGAGGCAGGTGCACT 60.957 55.000 17.98 0.00 44.36 4.40
1587 2012 4.980805 TGGAACTGCACGGCGTCC 62.981 66.667 10.85 8.07 0.00 4.79
1977 3017 2.729156 GCAATTTCAACAGAGCTACCGC 60.729 50.000 0.00 0.00 0.00 5.68
1992 3032 3.364167 GCTACCGCTCTAGTACAGAATCG 60.364 52.174 0.00 3.36 31.12 3.34
2166 3361 9.603189 ACAGACATATAACTAATAAGTAGCCCT 57.397 33.333 0.00 0.00 33.75 5.19
2303 3501 4.085055 CGTCACTATCGTGCAATGTATTCC 60.085 45.833 0.00 0.00 40.99 3.01
2667 3891 9.045223 AGACCGTTAAATTTATCGTATTTACCC 57.955 33.333 21.19 6.75 29.67 3.69
2676 3900 2.348660 TCGTATTTACCCGTTGCTTGG 58.651 47.619 0.00 0.00 0.00 3.61
2682 3906 2.054232 TACCCGTTGCTTGGTTTTGA 57.946 45.000 0.00 0.00 36.04 2.69
2686 3910 1.187715 CGTTGCTTGGTTTTGACACG 58.812 50.000 0.00 0.00 0.00 4.49
2697 3921 3.377798 GGTTTTGACACGGTGTAAAGGAA 59.622 43.478 14.74 2.60 0.00 3.36
2774 4023 2.350522 AGGAAGTAACATCTGCTTGCG 58.649 47.619 0.00 0.00 41.91 4.85
2887 4142 2.464157 AGAAGACTAGCAGCAACACC 57.536 50.000 0.00 0.00 0.00 4.16
2947 4202 5.326069 TCCCTAGCTCCTACAAGATACATC 58.674 45.833 0.00 0.00 0.00 3.06
3034 4289 3.888930 TGGTTTTCAAAGGAAGGCTACAG 59.111 43.478 0.00 0.00 33.82 2.74
3088 4343 3.218453 TGATTGCAAAGGAAACGGAGAA 58.782 40.909 1.71 0.00 0.00 2.87
3163 4418 8.332464 GTTGTTAGCTTATTTGGGTTTTGTTTC 58.668 33.333 0.00 0.00 0.00 2.78
3235 4490 8.598916 TCCTTGGATAAGTACATTTACTCACAA 58.401 33.333 0.00 0.00 37.59 3.33
3273 4528 1.507300 AGGATGGGAGAGGCTCTATGT 59.493 52.381 18.75 3.87 0.00 2.29
3349 4604 8.689251 ATACTCGTATTGTCCATTTCGATATG 57.311 34.615 8.70 8.70 0.00 1.78
3488 4743 1.078708 GGGTTCATCGCTCCGGAAA 60.079 57.895 5.23 0.00 0.00 3.13
3511 4766 2.224305 CCACTCTCGAACCTTTGGAGTT 60.224 50.000 0.00 0.00 36.91 3.01
3595 4850 7.756722 GGTAGGAGAAATGTCAAATCAATTGTG 59.243 37.037 5.13 0.00 40.11 3.33
3666 4921 5.332743 TGCCCAAGATGAAGGATTAAAAGT 58.667 37.500 0.00 0.00 0.00 2.66
4179 5444 1.541233 GGAGATACGCCATGTCAAGGG 60.541 57.143 0.00 0.00 0.00 3.95
4216 5481 1.699634 GATATTGCCTAGGAGGTGCCA 59.300 52.381 14.75 0.00 37.80 4.92
4286 5551 2.563620 TGTTACTGTCACGGCTATGGAA 59.436 45.455 0.00 0.00 0.00 3.53
4291 5556 5.036117 ACTGTCACGGCTATGGAATATTT 57.964 39.130 0.00 0.00 0.00 1.40
4296 5561 4.102524 TCACGGCTATGGAATATTTCACCT 59.897 41.667 0.00 0.00 0.00 4.00
4297 5562 5.305902 TCACGGCTATGGAATATTTCACCTA 59.694 40.000 0.00 0.00 0.00 3.08
4362 5627 5.830457 TGTCAGGATAATCCTCTGTGAGTAG 59.170 44.000 0.00 0.00 45.66 2.57
4379 5644 5.701290 GTGAGTAGCTGTAAAGACCACAATT 59.299 40.000 0.00 0.00 0.00 2.32
4426 5691 3.203040 CCTCTCCATTTATCCAGTGGGTT 59.797 47.826 9.92 0.00 33.78 4.11
4501 5766 2.490115 GTGGCACGGTGATTTCCAATTA 59.510 45.455 13.29 0.00 0.00 1.40
4640 5905 8.682936 ATATCAGTTTTGTGTTCTCAAGTTCT 57.317 30.769 0.00 0.00 0.00 3.01
4717 5982 8.563732 TCGAGATCACAATAAACACAATTTTGA 58.436 29.630 0.00 0.00 30.12 2.69
4720 5985 7.872483 AGATCACAATAAACACAATTTTGACCC 59.128 33.333 0.00 0.00 28.72 4.46
4723 5988 8.356657 TCACAATAAACACAATTTTGACCCTAG 58.643 33.333 0.00 0.00 0.00 3.02
4732 5997 0.111639 TTTGACCCTAGTTGTGGCCC 59.888 55.000 0.00 0.00 0.00 5.80
4738 6003 1.569072 CCCTAGTTGTGGCCCCTAATT 59.431 52.381 0.00 0.00 0.00 1.40
4747 6012 3.768757 TGTGGCCCCTAATTTTTCAGATG 59.231 43.478 0.00 0.00 0.00 2.90
4777 6042 7.524717 AGTGTATATTGTTGGAAATATGCCC 57.475 36.000 0.00 0.00 35.46 5.36
4779 6044 7.231317 AGTGTATATTGTTGGAAATATGCCCTG 59.769 37.037 0.00 0.00 35.46 4.45
4780 6045 6.493115 TGTATATTGTTGGAAATATGCCCTGG 59.507 38.462 0.00 0.00 35.46 4.45
4782 6047 3.017048 TGTTGGAAATATGCCCTGGAG 57.983 47.619 0.00 0.00 0.00 3.86
4783 6048 2.310538 GTTGGAAATATGCCCTGGAGG 58.689 52.381 0.00 0.00 39.47 4.30
4875 6140 8.828751 TGATATGATCCTGGAATATGTGATTCA 58.171 33.333 0.00 0.00 0.00 2.57
4894 6159 5.627499 TTCAGTGGAAAACTCATATGCAC 57.373 39.130 0.00 0.00 36.83 4.57
4933 6198 8.696043 AACGGTTAAATAAAAGGTTCCTAGTT 57.304 30.769 0.00 0.00 0.00 2.24
4982 6247 2.556189 TGTTGGTGATCATGTTTTCCGG 59.444 45.455 0.00 0.00 0.00 5.14
4999 6264 7.661437 TGTTTTCCGGATCTTAGGATATCATTG 59.339 37.037 4.15 0.00 36.28 2.82
5052 6317 6.106673 AGATTATGACGTTGGAAGAACGATT 58.893 36.000 13.45 1.31 45.64 3.34
5078 6343 4.273480 ACTGAATCGACCAAAACTTGTCTG 59.727 41.667 0.00 0.00 0.00 3.51
5083 6348 7.658167 TGAATCGACCAAAACTTGTCTGTTATA 59.342 33.333 0.00 0.00 0.00 0.98
5121 6386 7.716768 TTGTCTGTAACGAATTGTAATCACA 57.283 32.000 0.00 0.00 0.00 3.58
5122 6387 7.899178 TGTCTGTAACGAATTGTAATCACAT 57.101 32.000 0.00 0.00 33.76 3.21
5123 6388 7.738345 TGTCTGTAACGAATTGTAATCACATG 58.262 34.615 0.00 0.00 33.76 3.21
5124 6389 7.148490 TGTCTGTAACGAATTGTAATCACATGG 60.148 37.037 0.00 0.00 33.76 3.66
5125 6390 7.064134 GTCTGTAACGAATTGTAATCACATGGA 59.936 37.037 0.00 0.00 33.76 3.41
5126 6391 7.277760 TCTGTAACGAATTGTAATCACATGGAG 59.722 37.037 0.00 0.00 33.76 3.86
5127 6392 6.876789 TGTAACGAATTGTAATCACATGGAGT 59.123 34.615 0.00 0.00 33.76 3.85
5138 6403 3.519908 CACATGGAGTGTTAACGTGTG 57.480 47.619 0.26 0.00 43.40 3.82
5139 6404 3.127589 CACATGGAGTGTTAACGTGTGA 58.872 45.455 9.89 0.00 43.40 3.58
5140 6405 3.558006 CACATGGAGTGTTAACGTGTGAA 59.442 43.478 9.89 0.00 43.40 3.18
5141 6406 4.213270 CACATGGAGTGTTAACGTGTGAAT 59.787 41.667 9.89 0.00 43.40 2.57
5142 6407 4.819630 ACATGGAGTGTTAACGTGTGAATT 59.180 37.500 0.26 0.00 38.01 2.17
5143 6408 5.298276 ACATGGAGTGTTAACGTGTGAATTT 59.702 36.000 0.26 0.00 38.01 1.82
5144 6409 5.821516 TGGAGTGTTAACGTGTGAATTTT 57.178 34.783 0.26 0.00 0.00 1.82
5145 6410 5.812652 TGGAGTGTTAACGTGTGAATTTTC 58.187 37.500 0.26 0.00 0.00 2.29
5146 6411 5.587043 TGGAGTGTTAACGTGTGAATTTTCT 59.413 36.000 0.26 0.00 0.00 2.52
5147 6412 6.134061 GGAGTGTTAACGTGTGAATTTTCTC 58.866 40.000 0.26 0.00 0.00 2.87
5148 6413 6.056428 AGTGTTAACGTGTGAATTTTCTCC 57.944 37.500 0.26 0.00 0.00 3.71
5149 6414 5.820947 AGTGTTAACGTGTGAATTTTCTCCT 59.179 36.000 0.26 0.00 0.00 3.69
5150 6415 6.317893 AGTGTTAACGTGTGAATTTTCTCCTT 59.682 34.615 0.26 0.00 0.00 3.36
5151 6416 7.496591 AGTGTTAACGTGTGAATTTTCTCCTTA 59.503 33.333 0.26 0.00 0.00 2.69
5152 6417 7.797123 GTGTTAACGTGTGAATTTTCTCCTTAG 59.203 37.037 0.26 0.00 0.00 2.18
5153 6418 7.711772 TGTTAACGTGTGAATTTTCTCCTTAGA 59.288 33.333 0.26 0.00 0.00 2.10
5154 6419 8.553696 GTTAACGTGTGAATTTTCTCCTTAGAA 58.446 33.333 0.00 0.00 40.03 2.10
5155 6420 6.541111 ACGTGTGAATTTTCTCCTTAGAAC 57.459 37.500 0.00 0.00 41.48 3.01
5156 6421 6.053005 ACGTGTGAATTTTCTCCTTAGAACA 58.947 36.000 0.00 0.00 41.48 3.18
5157 6422 6.710744 ACGTGTGAATTTTCTCCTTAGAACAT 59.289 34.615 0.00 0.00 41.48 2.71
5158 6423 7.017645 CGTGTGAATTTTCTCCTTAGAACATG 58.982 38.462 0.00 0.00 41.48 3.21
5159 6424 7.095229 CGTGTGAATTTTCTCCTTAGAACATGA 60.095 37.037 0.00 0.00 41.48 3.07
5160 6425 8.233190 GTGTGAATTTTCTCCTTAGAACATGAG 58.767 37.037 0.00 0.00 41.48 2.90
5161 6426 8.156820 TGTGAATTTTCTCCTTAGAACATGAGA 58.843 33.333 0.00 0.00 41.48 3.27
5162 6427 8.663911 GTGAATTTTCTCCTTAGAACATGAGAG 58.336 37.037 0.00 0.00 41.48 3.20
5163 6428 8.378565 TGAATTTTCTCCTTAGAACATGAGAGT 58.621 33.333 0.00 0.00 41.48 3.24
5164 6429 9.877178 GAATTTTCTCCTTAGAACATGAGAGTA 57.123 33.333 0.00 0.00 41.48 2.59
5167 6432 9.658799 TTTTCTCCTTAGAACATGAGAGTATTG 57.341 33.333 0.00 0.00 41.48 1.90
5168 6433 7.962995 TCTCCTTAGAACATGAGAGTATTGT 57.037 36.000 0.00 0.00 30.71 2.71
5169 6434 9.475620 TTCTCCTTAGAACATGAGAGTATTGTA 57.524 33.333 0.00 0.00 36.80 2.41
5170 6435 9.126151 TCTCCTTAGAACATGAGAGTATTGTAG 57.874 37.037 0.00 0.00 30.71 2.74
5171 6436 8.824756 TCCTTAGAACATGAGAGTATTGTAGT 57.175 34.615 0.00 0.00 0.00 2.73
5172 6437 8.904834 TCCTTAGAACATGAGAGTATTGTAGTC 58.095 37.037 0.00 0.00 0.00 2.59
5173 6438 8.687242 CCTTAGAACATGAGAGTATTGTAGTCA 58.313 37.037 0.00 0.00 0.00 3.41
5174 6439 9.509855 CTTAGAACATGAGAGTATTGTAGTCAC 57.490 37.037 0.00 0.00 0.00 3.67
5175 6440 7.710676 AGAACATGAGAGTATTGTAGTCACT 57.289 36.000 0.00 0.00 0.00 3.41
5176 6441 8.128322 AGAACATGAGAGTATTGTAGTCACTT 57.872 34.615 0.00 0.00 0.00 3.16
5177 6442 8.247562 AGAACATGAGAGTATTGTAGTCACTTC 58.752 37.037 0.00 0.00 0.00 3.01
5178 6443 7.710676 ACATGAGAGTATTGTAGTCACTTCT 57.289 36.000 0.00 0.00 0.00 2.85
5179 6444 8.128322 ACATGAGAGTATTGTAGTCACTTCTT 57.872 34.615 0.00 0.00 0.00 2.52
5180 6445 9.244292 ACATGAGAGTATTGTAGTCACTTCTTA 57.756 33.333 0.00 0.00 0.00 2.10
5181 6446 9.509855 CATGAGAGTATTGTAGTCACTTCTTAC 57.490 37.037 0.00 0.00 0.00 2.34
5182 6447 8.631480 TGAGAGTATTGTAGTCACTTCTTACA 57.369 34.615 0.00 0.00 0.00 2.41
5183 6448 8.731605 TGAGAGTATTGTAGTCACTTCTTACAG 58.268 37.037 0.00 0.00 0.00 2.74
5184 6449 8.638629 AGAGTATTGTAGTCACTTCTTACAGT 57.361 34.615 0.00 0.00 0.00 3.55
5185 6450 9.736414 AGAGTATTGTAGTCACTTCTTACAGTA 57.264 33.333 0.00 0.00 0.00 2.74
5186 6451 9.771915 GAGTATTGTAGTCACTTCTTACAGTAC 57.228 37.037 3.88 3.88 35.48 2.73
5187 6452 9.293404 AGTATTGTAGTCACTTCTTACAGTACA 57.707 33.333 11.57 0.00 36.76 2.90
5188 6453 9.557338 GTATTGTAGTCACTTCTTACAGTACAG 57.443 37.037 6.34 0.00 35.40 2.74
5189 6454 7.578310 TTGTAGTCACTTCTTACAGTACAGT 57.422 36.000 0.00 0.00 0.00 3.55
5190 6455 6.967135 TGTAGTCACTTCTTACAGTACAGTG 58.033 40.000 0.42 1.21 36.91 3.66
5191 6456 5.455056 AGTCACTTCTTACAGTACAGTGG 57.545 43.478 0.42 0.00 36.34 4.00
5192 6457 4.281182 AGTCACTTCTTACAGTACAGTGGG 59.719 45.833 0.42 0.00 36.34 4.61
5193 6458 3.006537 TCACTTCTTACAGTACAGTGGGC 59.993 47.826 0.42 0.00 36.34 5.36
5194 6459 3.006967 CACTTCTTACAGTACAGTGGGCT 59.993 47.826 0.42 0.00 32.74 5.19
5195 6460 3.646637 ACTTCTTACAGTACAGTGGGCTT 59.353 43.478 0.42 0.00 0.00 4.35
5196 6461 4.102681 ACTTCTTACAGTACAGTGGGCTTT 59.897 41.667 0.42 0.00 0.00 3.51
5197 6462 4.002906 TCTTACAGTACAGTGGGCTTTG 57.997 45.455 0.42 0.00 0.00 2.77
5198 6463 2.851263 TACAGTACAGTGGGCTTTGG 57.149 50.000 0.42 0.00 0.00 3.28
5199 6464 0.110486 ACAGTACAGTGGGCTTTGGG 59.890 55.000 0.00 0.00 0.00 4.12
5200 6465 0.609131 CAGTACAGTGGGCTTTGGGG 60.609 60.000 0.00 0.00 0.00 4.96
5201 6466 1.065997 AGTACAGTGGGCTTTGGGGT 61.066 55.000 0.00 0.00 0.00 4.95
5202 6467 0.178973 GTACAGTGGGCTTTGGGGTT 60.179 55.000 0.00 0.00 0.00 4.11
5203 6468 0.558712 TACAGTGGGCTTTGGGGTTT 59.441 50.000 0.00 0.00 0.00 3.27
5204 6469 0.759060 ACAGTGGGCTTTGGGGTTTC 60.759 55.000 0.00 0.00 0.00 2.78
5205 6470 0.469892 CAGTGGGCTTTGGGGTTTCT 60.470 55.000 0.00 0.00 0.00 2.52
5206 6471 0.178961 AGTGGGCTTTGGGGTTTCTC 60.179 55.000 0.00 0.00 0.00 2.87
5207 6472 0.469144 GTGGGCTTTGGGGTTTCTCA 60.469 55.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.173708 AGAGAAAGAAGCCGGCTACG 59.826 55.000 33.07 0.00 40.55 3.51
2 3 1.755380 GGTAGAGAAAGAAGCCGGCTA 59.245 52.381 33.07 7.71 0.00 3.93
15 16 2.875485 GCGTCGTGCAGGTAGAGA 59.125 61.111 6.26 0.00 45.45 3.10
39 40 4.834892 ATTGCCGTCAATGCGCGC 62.835 61.111 27.26 27.26 41.12 6.86
45 46 2.749865 CCGCGTCATTGCCGTCAAT 61.750 57.895 4.92 0.00 43.31 2.57
54 55 4.814294 GCCTCCGACCGCGTCATT 62.814 66.667 4.92 0.00 35.23 2.57
94 96 0.877649 ATCGCTGTCGTGGATGATGC 60.878 55.000 0.00 0.00 36.96 3.91
96 98 0.746659 TCATCGCTGTCGTGGATGAT 59.253 50.000 0.00 0.00 41.03 2.45
99 101 0.877649 GCATCATCGCTGTCGTGGAT 60.878 55.000 0.00 0.00 36.96 3.41
142 144 1.528129 CAAGTTTCTCCAGGCTGACC 58.472 55.000 17.94 0.00 0.00 4.02
163 165 2.829003 CCAGCTCGCGGAGGAGTA 60.829 66.667 6.13 0.00 36.41 2.59
182 184 1.154413 CAACAACTCGCCGCATCAC 60.154 57.895 0.00 0.00 0.00 3.06
185 187 1.574428 GTTCAACAACTCGCCGCAT 59.426 52.632 0.00 0.00 0.00 4.73
186 188 2.539338 GGTTCAACAACTCGCCGCA 61.539 57.895 0.00 0.00 32.50 5.69
239 241 0.908910 TCCAATTTCCTCGCCTAGCA 59.091 50.000 0.00 0.00 0.00 3.49
251 253 4.450053 GAGACATCTAGCTGCTCCAATTT 58.550 43.478 4.91 0.00 0.00 1.82
253 255 2.035704 CGAGACATCTAGCTGCTCCAAT 59.964 50.000 4.91 0.00 0.00 3.16
254 256 1.406898 CGAGACATCTAGCTGCTCCAA 59.593 52.381 4.91 0.00 0.00 3.53
264 266 2.550180 CCAGATTCGAGCGAGACATCTA 59.450 50.000 5.54 0.00 0.00 1.98
267 269 0.249238 GCCAGATTCGAGCGAGACAT 60.249 55.000 0.00 0.00 0.00 3.06
390 406 1.009829 GCAAGAATCGCACCACTAGG 58.990 55.000 0.00 0.00 42.21 3.02
391 407 1.009829 GGCAAGAATCGCACCACTAG 58.990 55.000 0.00 0.00 0.00 2.57
392 408 0.392461 GGGCAAGAATCGCACCACTA 60.392 55.000 0.00 0.00 0.00 2.74
393 409 1.675641 GGGCAAGAATCGCACCACT 60.676 57.895 0.00 0.00 0.00 4.00
412 428 7.334421 GCCTCTATTTAAATGAGTCAAGACACA 59.666 37.037 11.05 2.93 36.41 3.72
419 435 4.407621 TCCGGCCTCTATTTAAATGAGTCA 59.592 41.667 11.05 0.00 0.00 3.41
421 437 5.308825 CATCCGGCCTCTATTTAAATGAGT 58.691 41.667 11.05 0.00 0.00 3.41
425 441 3.655777 TCCCATCCGGCCTCTATTTAAAT 59.344 43.478 5.89 5.89 0.00 1.40
438 454 2.017559 GACGAACTCCTCCCATCCGG 62.018 65.000 0.00 0.00 0.00 5.14
498 516 3.545703 CCAAGAAATCTACTTCGGCCAT 58.454 45.455 2.24 0.00 0.00 4.40
561 579 3.357079 GCCTGGCTGAACACACGG 61.357 66.667 12.43 0.00 0.00 4.94
562 580 3.716006 CGCCTGGCTGAACACACG 61.716 66.667 17.92 0.00 0.00 4.49
687 705 2.116533 CAGCTGCCCGCATTCATGA 61.117 57.895 0.00 0.00 42.61 3.07
724 743 0.960364 GCCACACATTCATCCCGTGT 60.960 55.000 0.00 0.00 44.45 4.49
732 752 1.039068 CACCCAAAGCCACACATTCA 58.961 50.000 0.00 0.00 0.00 2.57
733 753 0.318120 CCACCCAAAGCCACACATTC 59.682 55.000 0.00 0.00 0.00 2.67
734 754 1.120795 CCCACCCAAAGCCACACATT 61.121 55.000 0.00 0.00 0.00 2.71
738 759 2.197324 GTCCCACCCAAAGCCACA 59.803 61.111 0.00 0.00 0.00 4.17
740 761 1.152567 CTTGTCCCACCCAAAGCCA 60.153 57.895 0.00 0.00 0.00 4.75
743 764 0.179029 ACGTCTTGTCCCACCCAAAG 60.179 55.000 0.00 0.00 0.00 2.77
754 775 0.600255 CCCGCTTCTGAACGTCTTGT 60.600 55.000 0.00 0.00 0.00 3.16
757 778 2.048127 GCCCGCTTCTGAACGTCT 60.048 61.111 0.00 0.00 0.00 4.18
762 783 4.697756 CCCACGCCCGCTTCTGAA 62.698 66.667 0.00 0.00 0.00 3.02
801 822 1.687563 AAACCGAAGACAAACAGGGG 58.312 50.000 0.00 0.00 0.00 4.79
804 830 6.698359 TTTTCAAAAACCGAAGACAAACAG 57.302 33.333 0.00 0.00 0.00 3.16
846 872 2.418628 CTGTTTTGTATTGGTCCGCGAT 59.581 45.455 8.23 0.00 0.00 4.58
856 882 9.777297 AAAGCCATTTCAATACTGTTTTGTATT 57.223 25.926 10.12 0.00 41.99 1.89
862 888 4.996758 GCCAAAGCCATTTCAATACTGTTT 59.003 37.500 0.00 0.00 0.00 2.83
886 912 2.956964 GATCGCGCTGTCCGGAAG 60.957 66.667 5.23 7.54 37.44 3.46
887 913 3.699955 CTGATCGCGCTGTCCGGAA 62.700 63.158 5.23 0.00 37.44 4.30
888 914 4.193334 CTGATCGCGCTGTCCGGA 62.193 66.667 5.56 0.00 37.44 5.14
889 915 4.193334 TCTGATCGCGCTGTCCGG 62.193 66.667 5.56 0.00 37.44 5.14
890 916 2.951745 GTCTGATCGCGCTGTCCG 60.952 66.667 5.56 0.00 40.75 4.79
891 917 2.951745 CGTCTGATCGCGCTGTCC 60.952 66.667 5.56 0.00 0.00 4.02
899 925 0.316278 CTCCTACACGCGTCTGATCG 60.316 60.000 9.86 0.00 0.00 3.69
900 926 0.029567 CCTCCTACACGCGTCTGATC 59.970 60.000 9.86 0.00 0.00 2.92
901 927 0.680280 ACCTCCTACACGCGTCTGAT 60.680 55.000 9.86 0.00 0.00 2.90
902 928 0.892358 AACCTCCTACACGCGTCTGA 60.892 55.000 9.86 2.24 0.00 3.27
903 929 0.038526 AAACCTCCTACACGCGTCTG 60.039 55.000 9.86 0.66 0.00 3.51
904 930 0.677842 AAAACCTCCTACACGCGTCT 59.322 50.000 9.86 0.00 0.00 4.18
905 931 1.066136 GAAAACCTCCTACACGCGTC 58.934 55.000 9.86 0.00 0.00 5.19
906 932 0.665369 CGAAAACCTCCTACACGCGT 60.665 55.000 5.58 5.58 0.00 6.01
907 933 1.349259 CCGAAAACCTCCTACACGCG 61.349 60.000 3.53 3.53 0.00 6.01
908 934 1.017701 CCCGAAAACCTCCTACACGC 61.018 60.000 0.00 0.00 0.00 5.34
909 935 0.390735 CCCCGAAAACCTCCTACACG 60.391 60.000 0.00 0.00 0.00 4.49
910 936 0.035725 CCCCCGAAAACCTCCTACAC 60.036 60.000 0.00 0.00 0.00 2.90
911 937 2.379288 CCCCCGAAAACCTCCTACA 58.621 57.895 0.00 0.00 0.00 2.74
935 961 2.101415 GCAAACTGAATAAGGGCATCCC 59.899 50.000 0.00 0.00 45.90 3.85
936 962 2.760092 TGCAAACTGAATAAGGGCATCC 59.240 45.455 0.00 0.00 29.89 3.51
937 963 3.193267 TGTGCAAACTGAATAAGGGCATC 59.807 43.478 0.00 0.00 35.13 3.91
938 964 3.056607 GTGTGCAAACTGAATAAGGGCAT 60.057 43.478 0.00 0.00 35.13 4.40
939 965 2.295909 GTGTGCAAACTGAATAAGGGCA 59.704 45.455 0.00 0.00 31.65 5.36
940 966 2.558359 AGTGTGCAAACTGAATAAGGGC 59.442 45.455 9.29 0.00 0.00 5.19
947 973 2.418368 AGTGGAGTGTGCAAACTGAA 57.582 45.000 16.08 0.00 0.00 3.02
948 974 2.016318 CAAGTGGAGTGTGCAAACTGA 58.984 47.619 16.08 0.00 0.00 3.41
962 988 3.866651 AGTAGCAGAGTATTGCAAGTGG 58.133 45.455 4.94 0.00 46.47 4.00
972 998 3.754850 TGCAACGTTCTAGTAGCAGAGTA 59.245 43.478 0.00 0.00 0.00 2.59
973 999 2.557056 TGCAACGTTCTAGTAGCAGAGT 59.443 45.455 0.00 0.00 0.00 3.24
1037 1063 0.392863 CATGGGTGAGCGGAACATGA 60.393 55.000 0.00 0.00 40.92 3.07
1072 1098 1.619977 GGTGGTGCTAGAGAGGAGGAA 60.620 57.143 0.00 0.00 0.00 3.36
1105 1131 3.861263 GCACGACGGCGGGATTTC 61.861 66.667 22.31 0.00 45.89 2.17
1252 1656 1.792949 GTACGTGGAAACTGAGTGCTG 59.207 52.381 0.00 0.00 0.00 4.41
1265 1669 0.381089 GTCGAGGATCTGGTACGTGG 59.619 60.000 0.00 0.00 0.00 4.94
1266 1670 1.092348 TGTCGAGGATCTGGTACGTG 58.908 55.000 0.00 0.00 0.00 4.49
1316 1720 1.499049 GTCCGAGAGCTCAACGTTTT 58.501 50.000 23.96 1.27 0.00 2.43
1323 1727 2.755876 ATGCCGTCCGAGAGCTCA 60.756 61.111 17.77 0.00 0.00 4.26
1332 1736 3.747976 GGGTTGCACATGCCGTCC 61.748 66.667 0.49 1.38 41.18 4.79
1348 1752 2.753966 CGTTCGCATGGAGCTTGGG 61.754 63.158 0.00 0.00 42.61 4.12
1351 1755 3.127533 GGCGTTCGCATGGAGCTT 61.128 61.111 18.46 0.00 42.61 3.74
1359 1769 3.621805 TTGGAGGAGGCGTTCGCA 61.622 61.111 18.46 0.00 0.00 5.10
1361 1771 2.434359 GGTTGGAGGAGGCGTTCG 60.434 66.667 0.00 0.00 0.00 3.95
1477 1900 1.549243 TTGGATCCAGTGGCGCAGTA 61.549 55.000 15.53 0.00 0.00 2.74
1512 1937 2.025441 GCAAGCCACGCAAACGAA 59.975 55.556 0.00 0.00 43.93 3.85
1570 1995 4.980805 GGACGCCGTGCAGTTCCA 62.981 66.667 3.13 0.00 0.00 3.53
1587 2012 2.184830 CCCGAGCACTGGCATCATG 61.185 63.158 0.00 0.00 44.61 3.07
1685 2110 4.783621 GGCTCTCCATGCACGCCA 62.784 66.667 0.00 0.00 40.41 5.69
1762 2187 2.416547 CGCAGATGTTGGACGAAGAAAT 59.583 45.455 0.00 0.00 0.00 2.17
1875 2596 8.660295 TTTTCTTGTAGAACTCCTCTATACCA 57.340 34.615 0.00 0.00 38.91 3.25
1903 2624 7.827236 TGTAGTAGTAATTAGCAGGCAATGTTT 59.173 33.333 0.00 0.00 0.00 2.83
1908 2629 9.489084 CATATTGTAGTAGTAATTAGCAGGCAA 57.511 33.333 0.00 0.00 0.00 4.52
1977 3017 7.542534 ACTTACTCACGATTCTGTACTAGAG 57.457 40.000 0.00 0.00 36.61 2.43
1984 3024 5.124138 CCTCTGTACTTACTCACGATTCTGT 59.876 44.000 0.00 0.00 0.00 3.41
1992 3032 5.348997 GCAAATGTCCTCTGTACTTACTCAC 59.651 44.000 0.00 0.00 0.00 3.51
2667 3891 1.187715 CGTGTCAAAACCAAGCAACG 58.812 50.000 0.00 0.00 0.00 4.10
2676 3900 4.619437 TTCCTTTACACCGTGTCAAAAC 57.381 40.909 7.63 0.00 0.00 2.43
2742 3983 9.774742 CAGATGTTACTTCCTTTAAATACAAGC 57.225 33.333 0.00 0.00 0.00 4.01
2774 4023 3.304057 GCTGTTACTGCCAAAACTGAGAC 60.304 47.826 2.72 0.00 0.00 3.36
2843 4098 5.307196 TGCTAAGGGGAATCCATAGTCTTAC 59.693 44.000 0.09 0.00 38.66 2.34
2887 4142 5.756195 TCATGGCCTCATAATTCTTTTCG 57.244 39.130 3.32 0.00 31.33 3.46
2947 4202 7.273320 TGTTATCTTCATTACCTCCGAGTAG 57.727 40.000 0.00 0.00 0.00 2.57
3034 4289 0.240945 CAGCAACCAAACGACCATCC 59.759 55.000 0.00 0.00 0.00 3.51
3088 4343 5.296151 TCAGAACCTCATTCACAAACTCT 57.704 39.130 0.00 0.00 40.09 3.24
3163 4418 0.873743 GAGCTCGCTTTGATCCCTCG 60.874 60.000 0.00 0.00 0.00 4.63
3235 4490 6.240147 CCCATCCTAAAATTTCTTTGGGGTTT 60.240 38.462 13.09 0.00 0.00 3.27
3349 4604 7.275920 TGTCTAGAAGGATATTTTGAGGCTTC 58.724 38.462 0.00 0.00 0.00 3.86
3437 4692 2.973945 AGTACCGGTCATTGAAAGCTC 58.026 47.619 12.40 0.00 0.00 4.09
3488 4743 2.234908 CTCCAAAGGTTCGAGAGTGGAT 59.765 50.000 6.03 0.00 34.75 3.41
3543 4798 5.418524 CCAACCATCTCCAACAACATCATTA 59.581 40.000 0.00 0.00 0.00 1.90
3666 4921 5.986741 TCAACTTCGCTTGTAACTTCACATA 59.013 36.000 0.00 0.00 0.00 2.29
3831 5086 7.038302 TGGGAGAAACATCTTACAGTAGTTCAT 60.038 37.037 0.00 0.00 0.00 2.57
3968 5230 2.583101 ACCTCCTCAGTCTCAGACCATA 59.417 50.000 0.00 0.00 32.18 2.74
4190 5455 2.982488 CCTCCTAGGCAATATCCCTTGT 59.018 50.000 2.96 0.00 33.88 3.16
4254 5519 4.082408 CGTGACAGTAACATACCCTCTTCA 60.082 45.833 0.00 0.00 0.00 3.02
4286 5551 3.885297 GTGGTGCTGCATAGGTGAAATAT 59.115 43.478 5.27 0.00 0.00 1.28
4291 5556 1.299648 GGTGGTGCTGCATAGGTGA 59.700 57.895 5.27 0.00 0.00 4.02
4296 5561 1.612950 CTTTGTTGGTGGTGCTGCATA 59.387 47.619 5.27 0.00 0.00 3.14
4297 5562 0.390124 CTTTGTTGGTGGTGCTGCAT 59.610 50.000 5.27 0.00 0.00 3.96
4362 5627 2.352715 GGGCAATTGTGGTCTTTACAGC 60.353 50.000 7.40 0.00 0.00 4.40
4379 5644 2.194597 GGGTGGATTATGCGGGCA 59.805 61.111 0.00 0.00 0.00 5.36
4426 5691 3.836562 GACTAGACTGTAAACTTGGGGGA 59.163 47.826 0.00 0.00 0.00 4.81
4487 5752 8.903820 AGTACAGCTAAATAATTGGAAATCACC 58.096 33.333 0.00 0.00 0.00 4.02
4515 5780 5.448632 GCTGGTTTAATTTCCCGATGTACTG 60.449 44.000 0.00 0.00 0.00 2.74
4619 5884 6.195165 GCTAGAACTTGAGAACACAAAACTG 58.805 40.000 0.00 0.00 0.00 3.16
4653 5918 4.157246 TGAAGGTCTTGGTAGCTTGTCTA 58.843 43.478 0.00 0.00 37.32 2.59
4717 5982 0.178855 TTAGGGGCCACAACTAGGGT 60.179 55.000 8.31 0.00 0.00 4.34
4720 5985 4.770010 TGAAAAATTAGGGGCCACAACTAG 59.230 41.667 8.31 0.00 0.00 2.57
4723 5988 3.576550 TCTGAAAAATTAGGGGCCACAAC 59.423 43.478 8.31 0.00 0.00 3.32
4868 6133 6.127925 TGCATATGAGTTTTCCACTGAATCAC 60.128 38.462 6.97 0.00 35.01 3.06
4870 6135 6.261118 GTGCATATGAGTTTTCCACTGAATC 58.739 40.000 6.97 0.00 35.01 2.52
4875 6140 3.436704 CACGTGCATATGAGTTTTCCACT 59.563 43.478 6.97 0.00 39.07 4.00
4894 6159 5.533533 TTAACCGTTTATCATTCCACACG 57.466 39.130 0.00 0.00 0.00 4.49
4933 6198 4.804597 TGAGCTAGTCCTATAGAGGCAAA 58.195 43.478 0.00 0.00 43.40 3.68
4947 6212 3.118408 TCACCAACAACACTTGAGCTAGT 60.118 43.478 0.00 0.00 0.00 2.57
4954 6219 4.572985 ACATGATCACCAACAACACTTG 57.427 40.909 0.00 0.00 0.00 3.16
4982 6247 9.347934 CGTTACACTCAATGATATCCTAAGATC 57.652 37.037 0.00 0.00 33.67 2.75
5021 6286 6.878923 TCTTCCAACGTCATAATCTCAATGTT 59.121 34.615 0.00 0.00 0.00 2.71
5023 6288 6.908870 TCTTCCAACGTCATAATCTCAATG 57.091 37.500 0.00 0.00 0.00 2.82
5052 6317 7.330946 CAGACAAGTTTTGGTCGATTCAGTATA 59.669 37.037 0.00 0.00 39.01 1.47
5063 6328 9.959749 TCAATTTATAACAGACAAGTTTTGGTC 57.040 29.630 0.00 0.00 33.07 4.02
5098 6363 7.148490 CCATGTGATTACAATTCGTTACAGACA 60.148 37.037 0.00 0.00 40.84 3.41
5119 6384 3.462483 TCACACGTTAACACTCCATGT 57.538 42.857 6.39 0.00 46.42 3.21
5120 6385 5.356882 AATTCACACGTTAACACTCCATG 57.643 39.130 6.39 0.00 0.00 3.66
5121 6386 6.262273 AGAAAATTCACACGTTAACACTCCAT 59.738 34.615 6.39 0.00 0.00 3.41
5122 6387 5.587043 AGAAAATTCACACGTTAACACTCCA 59.413 36.000 6.39 0.00 0.00 3.86
5123 6388 6.056428 AGAAAATTCACACGTTAACACTCC 57.944 37.500 6.39 0.00 0.00 3.85
5124 6389 6.018180 AGGAGAAAATTCACACGTTAACACTC 60.018 38.462 6.39 0.00 0.00 3.51
5125 6390 5.820947 AGGAGAAAATTCACACGTTAACACT 59.179 36.000 6.39 0.00 0.00 3.55
5126 6391 6.056428 AGGAGAAAATTCACACGTTAACAC 57.944 37.500 6.39 0.00 0.00 3.32
5127 6392 6.687081 AAGGAGAAAATTCACACGTTAACA 57.313 33.333 6.39 0.00 0.00 2.41
5128 6393 8.080083 TCTAAGGAGAAAATTCACACGTTAAC 57.920 34.615 0.00 0.00 0.00 2.01
5129 6394 8.553696 GTTCTAAGGAGAAAATTCACACGTTAA 58.446 33.333 0.00 0.00 43.38 2.01
5130 6395 7.711772 TGTTCTAAGGAGAAAATTCACACGTTA 59.288 33.333 0.00 0.00 43.38 3.18
5131 6396 6.540914 TGTTCTAAGGAGAAAATTCACACGTT 59.459 34.615 0.00 0.00 43.38 3.99
5132 6397 6.053005 TGTTCTAAGGAGAAAATTCACACGT 58.947 36.000 0.00 0.00 43.38 4.49
5133 6398 6.539649 TGTTCTAAGGAGAAAATTCACACG 57.460 37.500 0.00 0.00 43.38 4.49
5134 6399 8.099364 TCATGTTCTAAGGAGAAAATTCACAC 57.901 34.615 0.00 0.00 43.38 3.82
5135 6400 8.156820 TCTCATGTTCTAAGGAGAAAATTCACA 58.843 33.333 0.00 0.00 43.38 3.58
5136 6401 8.553459 TCTCATGTTCTAAGGAGAAAATTCAC 57.447 34.615 0.00 0.00 43.38 3.18
5137 6402 8.378565 ACTCTCATGTTCTAAGGAGAAAATTCA 58.621 33.333 0.00 0.00 43.38 2.57
5138 6403 8.785329 ACTCTCATGTTCTAAGGAGAAAATTC 57.215 34.615 0.00 0.00 43.38 2.17
5141 6406 9.658799 CAATACTCTCATGTTCTAAGGAGAAAA 57.341 33.333 0.00 0.00 43.38 2.29
5142 6407 8.816894 ACAATACTCTCATGTTCTAAGGAGAAA 58.183 33.333 0.00 0.00 43.38 2.52
5143 6408 8.367660 ACAATACTCTCATGTTCTAAGGAGAA 57.632 34.615 0.00 0.00 39.47 2.87
5144 6409 7.962995 ACAATACTCTCATGTTCTAAGGAGA 57.037 36.000 0.00 0.00 35.30 3.71
5145 6410 8.908903 ACTACAATACTCTCATGTTCTAAGGAG 58.091 37.037 0.00 0.00 0.00 3.69
5146 6411 8.824756 ACTACAATACTCTCATGTTCTAAGGA 57.175 34.615 0.00 0.00 0.00 3.36
5147 6412 8.687242 TGACTACAATACTCTCATGTTCTAAGG 58.313 37.037 0.00 0.00 0.00 2.69
5148 6413 9.509855 GTGACTACAATACTCTCATGTTCTAAG 57.490 37.037 0.00 0.00 0.00 2.18
5149 6414 9.244292 AGTGACTACAATACTCTCATGTTCTAA 57.756 33.333 0.00 0.00 0.00 2.10
5150 6415 8.809468 AGTGACTACAATACTCTCATGTTCTA 57.191 34.615 0.00 0.00 0.00 2.10
5151 6416 7.710676 AGTGACTACAATACTCTCATGTTCT 57.289 36.000 0.00 0.00 0.00 3.01
5152 6417 8.247562 AGAAGTGACTACAATACTCTCATGTTC 58.752 37.037 0.00 0.00 0.00 3.18
5153 6418 8.128322 AGAAGTGACTACAATACTCTCATGTT 57.872 34.615 0.00 0.00 0.00 2.71
5154 6419 7.710676 AGAAGTGACTACAATACTCTCATGT 57.289 36.000 0.00 0.00 0.00 3.21
5155 6420 9.509855 GTAAGAAGTGACTACAATACTCTCATG 57.490 37.037 0.00 0.00 0.00 3.07
5156 6421 9.244292 TGTAAGAAGTGACTACAATACTCTCAT 57.756 33.333 0.00 0.00 0.00 2.90
5157 6422 8.631480 TGTAAGAAGTGACTACAATACTCTCA 57.369 34.615 0.00 0.00 0.00 3.27
5158 6423 8.732531 ACTGTAAGAAGTGACTACAATACTCTC 58.267 37.037 0.00 0.00 37.43 3.20
5159 6424 8.638629 ACTGTAAGAAGTGACTACAATACTCT 57.361 34.615 0.00 0.00 37.43 3.24
5160 6425 9.771915 GTACTGTAAGAAGTGACTACAATACTC 57.228 37.037 0.00 0.00 37.43 2.59
5161 6426 9.293404 TGTACTGTAAGAAGTGACTACAATACT 57.707 33.333 6.45 0.00 37.43 2.12
5162 6427 9.557338 CTGTACTGTAAGAAGTGACTACAATAC 57.443 37.037 0.00 0.00 37.43 1.89
5163 6428 9.293404 ACTGTACTGTAAGAAGTGACTACAATA 57.707 33.333 3.21 0.00 37.43 1.90
5164 6429 8.082852 CACTGTACTGTAAGAAGTGACTACAAT 58.917 37.037 15.94 0.00 42.06 2.71
5165 6430 7.423199 CACTGTACTGTAAGAAGTGACTACAA 58.577 38.462 15.94 0.00 42.06 2.41
5166 6431 6.016527 CCACTGTACTGTAAGAAGTGACTACA 60.017 42.308 19.90 0.00 42.06 2.74
5167 6432 6.380190 CCACTGTACTGTAAGAAGTGACTAC 58.620 44.000 19.90 0.00 42.06 2.73
5168 6433 5.475909 CCCACTGTACTGTAAGAAGTGACTA 59.524 44.000 19.90 0.00 42.06 2.59
5169 6434 4.281182 CCCACTGTACTGTAAGAAGTGACT 59.719 45.833 19.90 0.00 42.06 3.41
5170 6435 4.557205 CCCACTGTACTGTAAGAAGTGAC 58.443 47.826 19.90 0.00 42.06 3.67
5171 6436 3.006537 GCCCACTGTACTGTAAGAAGTGA 59.993 47.826 19.90 0.00 42.06 3.41
5172 6437 3.006967 AGCCCACTGTACTGTAAGAAGTG 59.993 47.826 4.96 14.79 40.49 3.16
5173 6438 3.240302 AGCCCACTGTACTGTAAGAAGT 58.760 45.455 4.96 0.00 37.43 3.01
5174 6439 3.963428 AGCCCACTGTACTGTAAGAAG 57.037 47.619 4.96 0.00 37.43 2.85
5175 6440 4.385825 CAAAGCCCACTGTACTGTAAGAA 58.614 43.478 4.96 0.00 37.43 2.52
5176 6441 3.244422 CCAAAGCCCACTGTACTGTAAGA 60.244 47.826 4.96 0.00 37.43 2.10
5177 6442 3.074412 CCAAAGCCCACTGTACTGTAAG 58.926 50.000 4.96 1.49 42.29 2.34
5178 6443 2.224670 CCCAAAGCCCACTGTACTGTAA 60.225 50.000 4.96 0.00 0.00 2.41
5179 6444 1.349688 CCCAAAGCCCACTGTACTGTA 59.650 52.381 4.96 0.00 0.00 2.74
5180 6445 0.110486 CCCAAAGCCCACTGTACTGT 59.890 55.000 0.00 0.00 0.00 3.55
5181 6446 0.609131 CCCCAAAGCCCACTGTACTG 60.609 60.000 0.00 0.00 0.00 2.74
5182 6447 1.065997 ACCCCAAAGCCCACTGTACT 61.066 55.000 0.00 0.00 0.00 2.73
5183 6448 0.178973 AACCCCAAAGCCCACTGTAC 60.179 55.000 0.00 0.00 0.00 2.90
5184 6449 0.558712 AAACCCCAAAGCCCACTGTA 59.441 50.000 0.00 0.00 0.00 2.74
5185 6450 0.759060 GAAACCCCAAAGCCCACTGT 60.759 55.000 0.00 0.00 0.00 3.55
5186 6451 0.469892 AGAAACCCCAAAGCCCACTG 60.470 55.000 0.00 0.00 0.00 3.66
5187 6452 0.178961 GAGAAACCCCAAAGCCCACT 60.179 55.000 0.00 0.00 0.00 4.00
5188 6453 0.469144 TGAGAAACCCCAAAGCCCAC 60.469 55.000 0.00 0.00 0.00 4.61
5189 6454 1.934410 TGAGAAACCCCAAAGCCCA 59.066 52.632 0.00 0.00 0.00 5.36
5190 6455 4.943373 TGAGAAACCCCAAAGCCC 57.057 55.556 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.