Multiple sequence alignment - TraesCS1D01G446100

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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 TraesCS1D01G446100 chr1D 100.000 5771 0 0 1 5771 488753638 488759408 0.000000e+00 10658.0
1 TraesCS1D01G446100 chr1D 95.136 884 41 2 3479 4360 782946 783829 0.000000e+00 1393.0
2 TraesCS1D01G446100 chr1D 92.142 649 41 5 5127 5771 22880445 22879803 0.000000e+00 907.0
3 TraesCS1D01G446100 chr1D 91.564 652 45 6 5124 5771 445402621 445403266 0.000000e+00 891.0
4 TraesCS1D01G446100 chr1D 89.764 508 46 3 4619 5121 490121239 490120733 0.000000e+00 645.0
5 TraesCS1D01G446100 chr1D 86.696 451 50 6 3037 3478 490121680 490121231 5.200000e-135 492.0
6 TraesCS1D01G446100 chr1D 87.607 234 20 6 742 975 490122515 490122291 4.430000e-66 263.0
7 TraesCS1D01G446100 chr1D 89.241 158 11 1 974 1125 490122251 490122094 5.900000e-45 193.0
8 TraesCS1D01G446100 chr1D 86.885 61 5 1 1006 1066 488589546 488589603 1.340000e-06 65.8
9 TraesCS1D01G446100 chr4D 94.444 1350 65 6 1176 2520 464995111 464993767 0.000000e+00 2069.0
10 TraesCS1D01G446100 chr4D 91.345 1167 62 7 3477 4609 477495727 477496888 0.000000e+00 1559.0
11 TraesCS1D01G446100 chr4D 94.207 656 35 3 5118 5771 84976382 84975728 0.000000e+00 998.0
12 TraesCS1D01G446100 chr7D 93.718 1353 77 3 1176 2522 131825364 131826714 0.000000e+00 2021.0
13 TraesCS1D01G446100 chr7D 90.978 1186 56 6 3474 4609 594016997 594018181 0.000000e+00 1550.0
14 TraesCS1D01G446100 chr7D 93.682 1013 61 3 1176 2188 71625831 71624822 0.000000e+00 1513.0
15 TraesCS1D01G446100 chr7D 86.614 254 20 10 4351 4595 6964502 6964750 9.530000e-68 268.0
16 TraesCS1D01G446100 chr2D 92.973 1352 87 3 1177 2522 66854238 66852889 0.000000e+00 1964.0
17 TraesCS1D01G446100 chr2D 93.872 1028 51 11 3478 4498 9755127 9754105 0.000000e+00 1539.0
18 TraesCS1D01G446100 chr2D 90.649 663 50 7 5114 5771 424834108 424834763 0.000000e+00 870.0
19 TraesCS1D01G446100 chr1A 93.039 1336 85 3 1192 2521 534140889 534142222 0.000000e+00 1945.0
20 TraesCS1D01G446100 chr1A 95.647 850 35 2 2629 3477 588015195 588016043 0.000000e+00 1363.0
21 TraesCS1D01G446100 chr1A 93.046 302 17 3 216 513 588014011 588014312 6.870000e-119 438.0
22 TraesCS1D01G446100 chr1A 86.445 391 34 7 4749 5121 588258937 588259326 1.500000e-110 411.0
23 TraesCS1D01G446100 chr1A 93.927 247 15 0 4618 4864 588016035 588016281 1.960000e-99 374.0
24 TraesCS1D01G446100 chr1A 89.956 229 20 3 2 228 588010420 588010647 5.660000e-75 292.0
25 TraesCS1D01G446100 chr1A 89.956 229 20 3 2 228 588226497 588226724 5.660000e-75 292.0
26 TraesCS1D01G446100 chr1A 96.000 50 1 1 5072 5121 588016283 588016331 4.790000e-11 80.5
27 TraesCS1D01G446100 chr2B 91.581 1354 105 4 1176 2522 774540925 774539574 0.000000e+00 1860.0
28 TraesCS1D01G446100 chr2B 90.217 1288 124 2 1206 2491 792411326 792410039 0.000000e+00 1679.0
29 TraesCS1D01G446100 chr4A 92.223 1183 91 1 1176 2358 702527927 702529108 0.000000e+00 1674.0
30 TraesCS1D01G446100 chr6D 92.203 1180 39 5 3481 4609 27988149 27986972 0.000000e+00 1620.0
31 TraesCS1D01G446100 chr6D 93.682 1013 61 3 1176 2188 3458125 3457116 0.000000e+00 1513.0
32 TraesCS1D01G446100 chr6D 93.939 660 36 4 5114 5771 72109244 72109901 0.000000e+00 994.0
33 TraesCS1D01G446100 chr3D 91.716 1171 46 9 3475 4596 12113171 12114339 0.000000e+00 1578.0
34 TraesCS1D01G446100 chr3D 96.092 870 32 1 3479 4346 485199181 485198312 0.000000e+00 1417.0
35 TraesCS1D01G446100 chr3D 91.254 1029 48 10 3466 4457 498099107 498098084 0.000000e+00 1363.0
36 TraesCS1D01G446100 chr3D 91.834 649 43 5 5127 5771 568230492 568229850 0.000000e+00 896.0
37 TraesCS1D01G446100 chr3D 91.185 658 47 6 5118 5771 596087984 596087334 0.000000e+00 883.0
38 TraesCS1D01G446100 chr7A 91.982 1135 65 17 3480 4599 183836777 183835654 0.000000e+00 1568.0
39 TraesCS1D01G446100 chr5D 95.696 883 36 1 3480 4360 443062023 443061141 0.000000e+00 1419.0
40 TraesCS1D01G446100 chr5D 91.061 660 48 6 5116 5771 1546322 1546974 0.000000e+00 881.0
41 TraesCS1D01G446100 chr5D 90.084 595 58 1 1897 2491 525730610 525731203 0.000000e+00 771.0
42 TraesCS1D01G446100 chr5D 98.246 57 1 0 1125 1181 559237729 559237673 3.680000e-17 100.0
43 TraesCS1D01G446100 chrUn 87.221 1166 101 31 3480 4601 255785262 255784101 0.000000e+00 1284.0
44 TraesCS1D01G446100 chrUn 87.221 1166 101 31 3480 4601 353514944 353513783 0.000000e+00 1284.0
45 TraesCS1D01G446100 chrUn 86.844 1163 105 30 3480 4598 241989051 241990209 0.000000e+00 1256.0
46 TraesCS1D01G446100 chrUn 86.621 1166 108 30 3480 4601 334824824 334823663 0.000000e+00 1245.0
47 TraesCS1D01G446100 chrUn 93.760 657 37 3 5116 5769 35649713 35650368 0.000000e+00 983.0
48 TraesCS1D01G446100 chrUn 85.006 787 72 28 3855 4598 410176569 410177352 0.000000e+00 758.0
49 TraesCS1D01G446100 chrUn 85.932 263 24 8 4352 4601 463695304 463695042 9.530000e-68 268.0
50 TraesCS1D01G446100 chr1B 90.767 834 60 10 2654 3478 680998904 680998079 0.000000e+00 1098.0
51 TraesCS1D01G446100 chr1B 93.725 510 26 5 2973 3478 681001682 681001175 0.000000e+00 760.0
52 TraesCS1D01G446100 chr1B 91.971 548 33 9 2 541 681002906 681002362 0.000000e+00 758.0
53 TraesCS1D01G446100 chr1B 90.132 456 33 7 4619 5065 680998087 680997635 3.000000e-162 582.0
54 TraesCS1D01G446100 chr1B 88.889 414 33 8 4619 5021 681001183 681000772 1.120000e-136 497.0
55 TraesCS1D01G446100 chr1B 87.016 439 39 10 698 1126 681002309 681001879 4.040000e-131 479.0
56 TraesCS1D01G446100 chr1B 95.918 196 6 1 2523 2718 681001891 681001698 3.360000e-82 316.0
57 TraesCS1D01G446100 chr1B 84.314 306 19 9 833 1125 680999202 680998913 7.370000e-69 272.0
58 TraesCS1D01G446100 chr6A 89.231 65 5 1 2738 2802 32872891 32872829 4.790000e-11 80.5


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 TraesCS1D01G446100 chr1D 488753638 488759408 5770 False 10658.00 10658 100.0000 1 5771 1 chr1D.!!$F4 5770
1 TraesCS1D01G446100 chr1D 782946 783829 883 False 1393.00 1393 95.1360 3479 4360 1 chr1D.!!$F1 881
2 TraesCS1D01G446100 chr1D 22879803 22880445 642 True 907.00 907 92.1420 5127 5771 1 chr1D.!!$R1 644
3 TraesCS1D01G446100 chr1D 445402621 445403266 645 False 891.00 891 91.5640 5124 5771 1 chr1D.!!$F2 647
4 TraesCS1D01G446100 chr1D 490120733 490122515 1782 True 398.25 645 88.3270 742 5121 4 chr1D.!!$R2 4379
5 TraesCS1D01G446100 chr4D 464993767 464995111 1344 True 2069.00 2069 94.4440 1176 2520 1 chr4D.!!$R2 1344
6 TraesCS1D01G446100 chr4D 477495727 477496888 1161 False 1559.00 1559 91.3450 3477 4609 1 chr4D.!!$F1 1132
7 TraesCS1D01G446100 chr4D 84975728 84976382 654 True 998.00 998 94.2070 5118 5771 1 chr4D.!!$R1 653
8 TraesCS1D01G446100 chr7D 131825364 131826714 1350 False 2021.00 2021 93.7180 1176 2522 1 chr7D.!!$F2 1346
9 TraesCS1D01G446100 chr7D 594016997 594018181 1184 False 1550.00 1550 90.9780 3474 4609 1 chr7D.!!$F3 1135
10 TraesCS1D01G446100 chr7D 71624822 71625831 1009 True 1513.00 1513 93.6820 1176 2188 1 chr7D.!!$R1 1012
11 TraesCS1D01G446100 chr2D 66852889 66854238 1349 True 1964.00 1964 92.9730 1177 2522 1 chr2D.!!$R2 1345
12 TraesCS1D01G446100 chr2D 9754105 9755127 1022 True 1539.00 1539 93.8720 3478 4498 1 chr2D.!!$R1 1020
13 TraesCS1D01G446100 chr2D 424834108 424834763 655 False 870.00 870 90.6490 5114 5771 1 chr2D.!!$F1 657
14 TraesCS1D01G446100 chr1A 534140889 534142222 1333 False 1945.00 1945 93.0390 1192 2521 1 chr1A.!!$F1 1329
15 TraesCS1D01G446100 chr1A 588010420 588016331 5911 False 509.50 1363 93.7152 2 5121 5 chr1A.!!$F4 5119
16 TraesCS1D01G446100 chr2B 774539574 774540925 1351 True 1860.00 1860 91.5810 1176 2522 1 chr2B.!!$R1 1346
17 TraesCS1D01G446100 chr2B 792410039 792411326 1287 True 1679.00 1679 90.2170 1206 2491 1 chr2B.!!$R2 1285
18 TraesCS1D01G446100 chr4A 702527927 702529108 1181 False 1674.00 1674 92.2230 1176 2358 1 chr4A.!!$F1 1182
19 TraesCS1D01G446100 chr6D 27986972 27988149 1177 True 1620.00 1620 92.2030 3481 4609 1 chr6D.!!$R2 1128
20 TraesCS1D01G446100 chr6D 3457116 3458125 1009 True 1513.00 1513 93.6820 1176 2188 1 chr6D.!!$R1 1012
21 TraesCS1D01G446100 chr6D 72109244 72109901 657 False 994.00 994 93.9390 5114 5771 1 chr6D.!!$F1 657
22 TraesCS1D01G446100 chr3D 12113171 12114339 1168 False 1578.00 1578 91.7160 3475 4596 1 chr3D.!!$F1 1121
23 TraesCS1D01G446100 chr3D 485198312 485199181 869 True 1417.00 1417 96.0920 3479 4346 1 chr3D.!!$R1 867
24 TraesCS1D01G446100 chr3D 498098084 498099107 1023 True 1363.00 1363 91.2540 3466 4457 1 chr3D.!!$R2 991
25 TraesCS1D01G446100 chr3D 568229850 568230492 642 True 896.00 896 91.8340 5127 5771 1 chr3D.!!$R3 644
26 TraesCS1D01G446100 chr3D 596087334 596087984 650 True 883.00 883 91.1850 5118 5771 1 chr3D.!!$R4 653
27 TraesCS1D01G446100 chr7A 183835654 183836777 1123 True 1568.00 1568 91.9820 3480 4599 1 chr7A.!!$R1 1119
28 TraesCS1D01G446100 chr5D 443061141 443062023 882 True 1419.00 1419 95.6960 3480 4360 1 chr5D.!!$R1 880
29 TraesCS1D01G446100 chr5D 1546322 1546974 652 False 881.00 881 91.0610 5116 5771 1 chr5D.!!$F1 655
30 TraesCS1D01G446100 chr5D 525730610 525731203 593 False 771.00 771 90.0840 1897 2491 1 chr5D.!!$F2 594
31 TraesCS1D01G446100 chrUn 255784101 255785262 1161 True 1284.00 1284 87.2210 3480 4601 1 chrUn.!!$R1 1121
32 TraesCS1D01G446100 chrUn 353513783 353514944 1161 True 1284.00 1284 87.2210 3480 4601 1 chrUn.!!$R3 1121
33 TraesCS1D01G446100 chrUn 241989051 241990209 1158 False 1256.00 1256 86.8440 3480 4598 1 chrUn.!!$F2 1118
34 TraesCS1D01G446100 chrUn 334823663 334824824 1161 True 1245.00 1245 86.6210 3480 4601 1 chrUn.!!$R2 1121
35 TraesCS1D01G446100 chrUn 35649713 35650368 655 False 983.00 983 93.7600 5116 5769 1 chrUn.!!$F1 653
36 TraesCS1D01G446100 chrUn 410176569 410177352 783 False 758.00 758 85.0060 3855 4598 1 chrUn.!!$F3 743
37 TraesCS1D01G446100 chr1B 680997635 681002906 5271 True 595.25 1098 90.3415 2 5065 8 chr1B.!!$R1 5063

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
832 4216 0.179153 CTGCGTCGCTCTCAATCTCA 60.179 55.0 19.50 0.0 0.00 3.27 F
2218 5730 0.595095 GGCAAGAATGATGCGGATCC 59.405 55.0 14.82 0.0 44.75 3.36 F
2432 6065 2.484770 GCTTCGGGTGGCTTGATGTATA 60.485 50.0 0.00 0.0 0.00 1.47 F
3715 10239 0.471617 CCTCCAAGAAGGGATGCGAT 59.528 55.0 0.00 0.0 36.09 4.58 F
4602 11208 0.168348 CGGTCGCGAGAGAGAAAGAA 59.832 55.0 10.24 0.0 42.92 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2467 6101 0.317854 CAATCGATGCATGCAGCCAG 60.318 55.000 28.76 16.64 44.83 4.85 R
3329 9848 1.251251 ACGTACCTAAGAGTGGCGTT 58.749 50.000 0.00 0.00 31.77 4.84 R
4015 10540 1.375908 GATGTTGCTGCTCCCGTCA 60.376 57.895 0.00 0.00 0.00 4.35 R
4610 11216 0.039527 AAAGAACCGCATGAAACGCC 60.040 50.000 0.00 0.00 0.00 5.68 R
5684 12306 0.517316 GTGTTGATGACAGGCGTTCC 59.483 55.000 0.00 0.00 39.39 3.62 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
32 33 6.014840 TCTGTTAGTTATGGAGTTTCTCGGTT 60.015 38.462 0.00 0.00 0.00 4.44
132 136 6.317893 TCCTTCAACTTCTAAACCAGACAAAC 59.682 38.462 0.00 0.00 31.12 2.93
146 150 6.126409 ACCAGACAAACTTAATCCTTCAACA 58.874 36.000 0.00 0.00 0.00 3.33
319 3698 1.276138 CGGTAGCATCATGGCCATCTA 59.724 52.381 17.61 11.61 0.00 1.98
350 3729 4.442038 TGACTGGTCAGCTCCGAT 57.558 55.556 0.00 0.00 34.14 4.18
460 3842 9.612066 AAAAGTTTAAGGATTTGAAATTGCTCA 57.388 25.926 0.00 0.00 0.00 4.26
466 3848 3.869246 GGATTTGAAATTGCTCAGCCATG 59.131 43.478 0.00 0.00 0.00 3.66
468 3850 1.258676 TGAAATTGCTCAGCCATGCA 58.741 45.000 0.00 0.00 37.42 3.96
622 4006 5.751990 AGTAAAAACTGAGATAATACCGGCG 59.248 40.000 0.00 0.00 0.00 6.46
629 4013 3.128349 GAGATAATACCGGCGCAGAAAA 58.872 45.455 10.83 0.00 0.00 2.29
631 4015 4.134563 AGATAATACCGGCGCAGAAAATT 58.865 39.130 10.83 8.33 0.00 1.82
632 4016 2.559998 AATACCGGCGCAGAAAATTG 57.440 45.000 10.83 0.00 0.00 2.32
633 4017 1.745232 ATACCGGCGCAGAAAATTGA 58.255 45.000 10.83 0.00 0.00 2.57
636 4020 1.586154 CCGGCGCAGAAAATTGACCT 61.586 55.000 10.83 0.00 0.00 3.85
637 4021 0.179189 CGGCGCAGAAAATTGACCTC 60.179 55.000 10.83 0.00 0.00 3.85
639 4023 2.356135 GGCGCAGAAAATTGACCTCTA 58.644 47.619 10.83 0.00 0.00 2.43
640 4024 2.352960 GGCGCAGAAAATTGACCTCTAG 59.647 50.000 10.83 0.00 0.00 2.43
641 4025 3.262420 GCGCAGAAAATTGACCTCTAGA 58.738 45.455 0.30 0.00 0.00 2.43
642 4026 3.684788 GCGCAGAAAATTGACCTCTAGAA 59.315 43.478 0.30 0.00 0.00 2.10
643 4027 4.201763 GCGCAGAAAATTGACCTCTAGAAG 60.202 45.833 0.30 0.00 0.00 2.85
644 4028 5.171476 CGCAGAAAATTGACCTCTAGAAGA 58.829 41.667 0.00 0.00 0.00 2.87
645 4029 5.814705 CGCAGAAAATTGACCTCTAGAAGAT 59.185 40.000 0.00 0.00 0.00 2.40
646 4030 6.314896 CGCAGAAAATTGACCTCTAGAAGATT 59.685 38.462 0.00 0.00 0.00 2.40
647 4031 7.148340 CGCAGAAAATTGACCTCTAGAAGATTT 60.148 37.037 0.00 0.00 0.00 2.17
648 4032 8.180920 GCAGAAAATTGACCTCTAGAAGATTTC 58.819 37.037 0.00 0.25 0.00 2.17
649 4033 8.672815 CAGAAAATTGACCTCTAGAAGATTTCC 58.327 37.037 0.00 0.00 0.00 3.13
650 4034 8.386264 AGAAAATTGACCTCTAGAAGATTTCCA 58.614 33.333 0.00 0.00 0.00 3.53
651 4035 8.940397 AAAATTGACCTCTAGAAGATTTCCAA 57.060 30.769 0.00 0.00 0.00 3.53
652 4036 8.940397 AAATTGACCTCTAGAAGATTTCCAAA 57.060 30.769 0.00 0.00 0.00 3.28
653 4037 8.940397 AATTGACCTCTAGAAGATTTCCAAAA 57.060 30.769 0.00 0.00 0.00 2.44
654 4038 8.940397 ATTGACCTCTAGAAGATTTCCAAAAA 57.060 30.769 0.00 0.00 0.00 1.94
675 4059 3.953542 AAAATAGTTAGGGCTCAGGGG 57.046 47.619 0.00 0.00 0.00 4.79
676 4060 2.588925 AATAGTTAGGGCTCAGGGGT 57.411 50.000 0.00 0.00 0.00 4.95
677 4061 3.719368 AATAGTTAGGGCTCAGGGGTA 57.281 47.619 0.00 0.00 0.00 3.69
678 4062 2.769602 TAGTTAGGGCTCAGGGGTAG 57.230 55.000 0.00 0.00 0.00 3.18
679 4063 1.016415 AGTTAGGGCTCAGGGGTAGA 58.984 55.000 0.00 0.00 0.00 2.59
680 4064 1.121378 GTTAGGGCTCAGGGGTAGAC 58.879 60.000 0.00 0.00 0.00 2.59
681 4065 1.016415 TTAGGGCTCAGGGGTAGACT 58.984 55.000 0.00 0.00 0.00 3.24
682 4066 1.917099 TAGGGCTCAGGGGTAGACTA 58.083 55.000 0.00 0.00 0.00 2.59
683 4067 1.246294 AGGGCTCAGGGGTAGACTAT 58.754 55.000 0.00 0.00 0.00 2.12
684 4068 1.581149 AGGGCTCAGGGGTAGACTATT 59.419 52.381 0.00 0.00 0.00 1.73
685 4069 2.795960 AGGGCTCAGGGGTAGACTATTA 59.204 50.000 0.00 0.00 0.00 0.98
686 4070 3.406498 AGGGCTCAGGGGTAGACTATTAT 59.594 47.826 0.00 0.00 0.00 1.28
687 4071 4.140423 AGGGCTCAGGGGTAGACTATTATT 60.140 45.833 0.00 0.00 0.00 1.40
688 4072 4.597940 GGGCTCAGGGGTAGACTATTATTT 59.402 45.833 0.00 0.00 0.00 1.40
689 4073 5.513267 GGGCTCAGGGGTAGACTATTATTTG 60.513 48.000 0.00 0.00 0.00 2.32
690 4074 5.513267 GGCTCAGGGGTAGACTATTATTTGG 60.513 48.000 0.00 0.00 0.00 3.28
691 4075 5.513267 GCTCAGGGGTAGACTATTATTTGGG 60.513 48.000 0.00 0.00 0.00 4.12
692 4076 5.544682 TCAGGGGTAGACTATTATTTGGGT 58.455 41.667 0.00 0.00 0.00 4.51
693 4077 5.605488 TCAGGGGTAGACTATTATTTGGGTC 59.395 44.000 0.00 0.00 0.00 4.46
694 4078 4.591924 AGGGGTAGACTATTATTTGGGTCG 59.408 45.833 0.00 0.00 34.34 4.79
695 4079 4.262765 GGGGTAGACTATTATTTGGGTCGG 60.263 50.000 0.00 0.00 34.34 4.79
696 4080 4.346127 GGGTAGACTATTATTTGGGTCGGT 59.654 45.833 0.00 0.00 34.34 4.69
697 4081 5.510349 GGGTAGACTATTATTTGGGTCGGTC 60.510 48.000 0.00 0.00 34.34 4.79
698 4082 4.684484 AGACTATTATTTGGGTCGGTCC 57.316 45.455 0.00 0.00 34.34 4.46
726 4110 0.474184 AATCCTGTATGAAGGGCCGG 59.526 55.000 0.00 0.00 37.96 6.13
750 4134 0.739112 GCCGTGCTTCTCAAGGAGAG 60.739 60.000 1.18 0.00 45.67 3.20
793 4177 2.492940 GGATAGGATTCCTCGAAGGGGA 60.493 54.545 8.94 0.00 35.59 4.81
814 4198 5.597182 GGGAAAGGGAAAGTAAAACTTGTCT 59.403 40.000 0.00 0.00 38.66 3.41
826 4210 1.081175 CTTGTCTGCGTCGCTCTCA 60.081 57.895 19.50 11.21 0.00 3.27
832 4216 0.179153 CTGCGTCGCTCTCAATCTCA 60.179 55.000 19.50 0.00 0.00 3.27
862 4246 4.277672 CGACGGAGACCAATAAGAATCCTA 59.722 45.833 0.00 0.00 0.00 2.94
863 4247 5.047943 CGACGGAGACCAATAAGAATCCTAT 60.048 44.000 0.00 0.00 0.00 2.57
900 4289 5.856455 CGCTCACCAAAATCTACGAAATTTT 59.144 36.000 0.00 0.00 36.91 1.82
903 4292 7.542130 GCTCACCAAAATCTACGAAATTTTCAT 59.458 33.333 9.66 0.00 34.84 2.57
905 4294 9.834628 TCACCAAAATCTACGAAATTTTCATAC 57.165 29.630 9.66 0.00 34.84 2.39
968 4357 2.340328 GCGGTGGTGACCAAATCCC 61.340 63.158 5.57 1.73 43.33 3.85
986 4416 4.568072 TCCCTAACTAATTGCTTGCAGA 57.432 40.909 0.00 0.00 0.00 4.26
1066 4496 3.989787 TGCTCCAGCGAACGCAGA 61.990 61.111 20.66 14.99 45.83 4.26
1071 4501 3.470567 CAGCGAACGCAGACGGAC 61.471 66.667 20.66 0.00 46.04 4.79
1072 4502 4.719369 AGCGAACGCAGACGGACC 62.719 66.667 20.66 0.00 46.04 4.46
1132 4568 7.918076 TGAGGTATCTCAACCAAAGAATTAGT 58.082 34.615 2.30 0.00 46.08 2.24
1133 4569 7.824289 TGAGGTATCTCAACCAAAGAATTAGTG 59.176 37.037 2.30 0.00 46.08 2.74
1134 4570 7.918076 AGGTATCTCAACCAAAGAATTAGTGA 58.082 34.615 0.00 0.00 42.40 3.41
1135 4571 8.043710 AGGTATCTCAACCAAAGAATTAGTGAG 58.956 37.037 0.00 0.00 42.40 3.51
1136 4572 7.824779 GGTATCTCAACCAAAGAATTAGTGAGT 59.175 37.037 0.00 0.00 39.50 3.41
1137 4573 9.220767 GTATCTCAACCAAAGAATTAGTGAGTT 57.779 33.333 0.00 0.00 0.00 3.01
1138 4574 8.697507 ATCTCAACCAAAGAATTAGTGAGTTT 57.302 30.769 0.00 0.00 0.00 2.66
1139 4575 8.519799 TCTCAACCAAAGAATTAGTGAGTTTT 57.480 30.769 0.00 0.00 0.00 2.43
1140 4576 8.405531 TCTCAACCAAAGAATTAGTGAGTTTTG 58.594 33.333 0.00 0.00 0.00 2.44
1141 4577 8.287439 TCAACCAAAGAATTAGTGAGTTTTGA 57.713 30.769 0.00 0.00 0.00 2.69
1142 4578 8.188139 TCAACCAAAGAATTAGTGAGTTTTGAC 58.812 33.333 0.00 0.00 0.00 3.18
1143 4579 7.639113 ACCAAAGAATTAGTGAGTTTTGACA 57.361 32.000 0.00 0.00 0.00 3.58
1144 4580 7.480810 ACCAAAGAATTAGTGAGTTTTGACAC 58.519 34.615 0.00 0.00 37.30 3.67
1145 4581 7.122055 ACCAAAGAATTAGTGAGTTTTGACACA 59.878 33.333 0.00 0.00 39.18 3.72
1146 4582 7.973388 CCAAAGAATTAGTGAGTTTTGACACAA 59.027 33.333 0.00 0.00 39.18 3.33
1147 4583 9.352784 CAAAGAATTAGTGAGTTTTGACACAAA 57.647 29.630 0.00 0.00 39.18 2.83
1148 4584 9.921637 AAAGAATTAGTGAGTTTTGACACAAAA 57.078 25.926 5.70 5.70 39.18 2.44
1150 4586 9.736023 AGAATTAGTGAGTTTTGACACAAAATC 57.264 29.630 11.75 10.61 39.18 2.17
1151 4587 8.560576 AATTAGTGAGTTTTGACACAAAATCG 57.439 30.769 11.75 0.00 39.18 3.34
1152 4588 5.560966 AGTGAGTTTTGACACAAAATCGT 57.439 34.783 11.75 2.35 39.18 3.73
1153 4589 6.671614 AGTGAGTTTTGACACAAAATCGTA 57.328 33.333 11.75 0.00 39.18 3.43
1154 4590 6.715464 AGTGAGTTTTGACACAAAATCGTAG 58.285 36.000 11.75 0.00 39.18 3.51
1155 4591 6.537301 AGTGAGTTTTGACACAAAATCGTAGA 59.463 34.615 11.75 0.00 39.31 2.59
1156 4592 7.065324 AGTGAGTTTTGACACAAAATCGTAGAA 59.935 33.333 11.75 0.00 38.76 2.10
1157 4593 7.163682 GTGAGTTTTGACACAAAATCGTAGAAC 59.836 37.037 11.75 0.00 37.21 3.01
1158 4594 7.065324 TGAGTTTTGACACAAAATCGTAGAACT 59.935 33.333 11.75 4.03 43.58 3.01
1159 4595 7.186804 AGTTTTGACACAAAATCGTAGAACTG 58.813 34.615 11.75 0.00 43.58 3.16
1160 4596 6.671614 TTTGACACAAAATCGTAGAACTGT 57.328 33.333 0.00 0.00 43.58 3.55
1161 4597 5.651172 TGACACAAAATCGTAGAACTGTG 57.349 39.130 0.00 0.00 44.51 3.66
1162 4598 4.509970 TGACACAAAATCGTAGAACTGTGG 59.490 41.667 5.15 0.00 43.79 4.17
1163 4599 4.448210 ACACAAAATCGTAGAACTGTGGT 58.552 39.130 5.15 0.00 43.79 4.16
1164 4600 4.879545 ACACAAAATCGTAGAACTGTGGTT 59.120 37.500 5.15 0.00 43.79 3.67
1165 4601 5.355910 ACACAAAATCGTAGAACTGTGGTTT 59.644 36.000 5.15 0.00 43.79 3.27
1166 4602 5.907391 CACAAAATCGTAGAACTGTGGTTTC 59.093 40.000 0.00 0.00 43.58 2.78
1167 4603 5.820947 ACAAAATCGTAGAACTGTGGTTTCT 59.179 36.000 0.00 0.00 43.58 2.52
1168 4604 5.924475 AAATCGTAGAACTGTGGTTTCTG 57.076 39.130 0.00 0.00 43.58 3.02
1169 4605 2.750948 TCGTAGAACTGTGGTTTCTGC 58.249 47.619 0.00 0.00 35.58 4.26
1170 4606 2.101750 TCGTAGAACTGTGGTTTCTGCA 59.898 45.455 0.00 0.00 35.58 4.41
1171 4607 2.869801 CGTAGAACTGTGGTTTCTGCAA 59.130 45.455 0.00 0.00 35.58 4.08
1172 4608 3.303132 CGTAGAACTGTGGTTTCTGCAAC 60.303 47.826 0.00 0.00 35.58 4.17
1185 4621 2.187163 GCAACCCTACCCTCTCGC 59.813 66.667 0.00 0.00 0.00 5.03
1328 4764 4.270577 GGGTTCCCTTCCCCTTCT 57.729 61.111 0.00 0.00 39.08 2.85
1709 5146 3.622206 GCAGATGGAGATTGGTGGTACAA 60.622 47.826 0.00 0.00 44.16 2.41
1922 5360 2.356667 GTCTTGGGAGGCTTGGGG 59.643 66.667 0.00 0.00 0.00 4.96
1931 5439 4.522975 GGCTTGGGGATTCGGGGG 62.523 72.222 0.00 0.00 0.00 5.40
1932 5440 3.416880 GCTTGGGGATTCGGGGGA 61.417 66.667 0.00 0.00 0.00 4.81
1951 5461 2.501723 GGAGAGTTGCTATGGGTGAAGA 59.498 50.000 0.00 0.00 0.00 2.87
1975 5485 1.368950 GTGTGTCAGCTCCAGCAGA 59.631 57.895 0.48 0.00 45.16 4.26
2017 5527 1.511768 GAGGAGCGGCGTTCTAACT 59.488 57.895 22.65 11.84 0.00 2.24
2133 5643 2.142357 CTTCCAGAGTGTCCGCGTCA 62.142 60.000 4.92 0.46 0.00 4.35
2141 5651 2.058001 TGTCCGCGTCAGGATGGAT 61.058 57.895 4.92 0.00 43.04 3.41
2218 5730 0.595095 GGCAAGAATGATGCGGATCC 59.405 55.000 14.82 0.00 44.75 3.36
2279 5791 2.489971 CCTCTAAAACGTGTGCAAGGA 58.510 47.619 0.00 0.00 0.00 3.36
2390 6023 4.701765 GTGAGAGCACTCCACATTATCAT 58.298 43.478 8.77 0.00 41.84 2.45
2432 6065 2.484770 GCTTCGGGTGGCTTGATGTATA 60.485 50.000 0.00 0.00 0.00 1.47
2438 6072 4.821805 CGGGTGGCTTGATGTATATTCTTT 59.178 41.667 0.00 0.00 0.00 2.52
2444 6078 8.677300 GTGGCTTGATGTATATTCTTTTCAGAA 58.323 33.333 0.00 0.00 43.45 3.02
2666 6308 8.996651 ACTTTTCTTCTCCTTTCTATTTGGAA 57.003 30.769 0.00 0.00 0.00 3.53
3329 9848 3.680458 GCAAAAAGTCGTTCCAAAACCAA 59.320 39.130 0.00 0.00 31.27 3.67
3331 9850 5.613812 CAAAAAGTCGTTCCAAAACCAAAC 58.386 37.500 0.00 0.00 31.27 2.93
3379 9900 8.693120 ATCAGAGAATCAAATAAGATGCATGT 57.307 30.769 2.46 0.00 37.82 3.21
3381 9902 9.049523 TCAGAGAATCAAATAAGATGCATGTAC 57.950 33.333 2.46 0.00 37.82 2.90
3392 9913 9.882996 AATAAGATGCATGTACATACAAAATCG 57.117 29.630 12.70 0.00 39.99 3.34
3396 9917 5.331098 TGCATGTACATACAAAATCGCTTG 58.669 37.500 8.32 0.00 39.99 4.01
3413 9934 6.235231 TCGCTTGGTCTATTCTTCCTTAAT 57.765 37.500 0.00 0.00 0.00 1.40
3419 9940 8.589701 TTGGTCTATTCTTCCTTAATTTTCCC 57.410 34.615 0.00 0.00 0.00 3.97
3478 10002 1.264749 TAGGACCTGCATGCGGTTCT 61.265 55.000 31.56 31.56 42.95 3.01
3479 10003 1.675641 GGACCTGCATGCGGTTCTT 60.676 57.895 27.12 10.43 34.19 2.52
3532 10056 2.552315 CAAAGCAACCAACACCGAGTAT 59.448 45.455 0.00 0.00 0.00 2.12
3539 10063 5.989777 GCAACCAACACCGAGTATAGATAAT 59.010 40.000 0.00 0.00 0.00 1.28
3626 10150 2.745884 CAAAGCGCGGATGACCCA 60.746 61.111 8.83 0.00 34.14 4.51
3633 10157 3.702048 CGGATGACCCACCACCGT 61.702 66.667 0.00 0.00 38.97 4.83
3715 10239 0.471617 CCTCCAAGAAGGGATGCGAT 59.528 55.000 0.00 0.00 36.09 4.58
3757 10281 1.192146 CGAGTCCTCAGGTTTCCCCA 61.192 60.000 0.00 0.00 34.66 4.96
4015 10540 0.616111 ACCGGAGAGAAGCTCACCAT 60.616 55.000 9.46 0.00 45.81 3.55
4529 11135 0.340208 GGAGGAAGAAGGGAGGAGGA 59.660 60.000 0.00 0.00 0.00 3.71
4544 11150 3.093172 GGAAGCCTGGAGGGAGGG 61.093 72.222 0.00 0.00 37.23 4.30
4601 11207 1.794864 CGGTCGCGAGAGAGAAAGA 59.205 57.895 10.24 0.00 42.92 2.52
4602 11208 0.168348 CGGTCGCGAGAGAGAAAGAA 59.832 55.000 10.24 0.00 42.92 2.52
4621 11227 3.758931 GGGGGTGGCGTTTCATGC 61.759 66.667 0.00 0.00 0.00 4.06
4622 11228 4.114997 GGGGTGGCGTTTCATGCG 62.115 66.667 0.00 0.00 0.00 4.73
4623 11229 4.114997 GGGTGGCGTTTCATGCGG 62.115 66.667 0.00 0.00 0.00 5.69
4624 11230 3.361977 GGTGGCGTTTCATGCGGT 61.362 61.111 0.00 0.00 0.00 5.68
4625 11231 2.642700 GTGGCGTTTCATGCGGTT 59.357 55.556 0.00 0.00 0.00 4.44
4626 11232 1.442017 GTGGCGTTTCATGCGGTTC 60.442 57.895 0.00 0.00 0.00 3.62
4627 11233 1.599518 TGGCGTTTCATGCGGTTCT 60.600 52.632 0.00 0.00 0.00 3.01
4628 11234 1.169661 TGGCGTTTCATGCGGTTCTT 61.170 50.000 0.00 0.00 0.00 2.52
4647 11253 4.897140 TCTTTACAAGGGCTAACGCTTTA 58.103 39.130 0.00 0.00 46.07 1.85
4648 11254 5.493809 TCTTTACAAGGGCTAACGCTTTAT 58.506 37.500 0.00 0.00 46.07 1.40
4674 11280 0.673333 CAGCTGCCCACGTGACAATA 60.673 55.000 19.30 0.00 0.00 1.90
4711 11317 1.072331 CTGTTGTGGTTAGAGCCAGGT 59.928 52.381 0.00 0.00 39.53 4.00
4776 11382 6.327365 ACCAGGGAAGTCAAGATTGAAAATTT 59.673 34.615 0.00 0.00 39.21 1.82
4914 11527 7.831690 TCTCTATCTATCCGAGTAGATTGCATT 59.168 37.037 12.67 0.00 40.79 3.56
4927 11540 9.178427 GAGTAGATTGCATTTATGAATGAAAGC 57.822 33.333 14.00 12.13 44.17 3.51
4929 11542 6.880484 AGATTGCATTTATGAATGAAAGCCA 58.120 32.000 13.90 0.57 44.67 4.75
4932 11545 8.827177 ATTGCATTTATGAATGAAAGCCATAG 57.173 30.769 14.00 0.00 42.61 2.23
4934 11547 6.324512 TGCATTTATGAATGAAAGCCATAGGT 59.675 34.615 14.00 0.00 44.37 3.08
4945 11558 9.435688 AATGAAAGCCATAGGTTATTTTTGTTC 57.564 29.630 0.00 0.00 34.45 3.18
4956 11569 7.327214 AGGTTATTTTTGTTCTGCTGTTTCAA 58.673 30.769 0.00 0.00 0.00 2.69
4957 11570 7.492344 AGGTTATTTTTGTTCTGCTGTTTCAAG 59.508 33.333 0.00 0.00 0.00 3.02
4960 11573 6.890663 TTTTTGTTCTGCTGTTTCAAGATG 57.109 33.333 0.00 0.00 0.00 2.90
4961 11574 5.833406 TTTGTTCTGCTGTTTCAAGATGA 57.167 34.783 0.00 0.00 0.00 2.92
4969 11582 3.190118 GCTGTTTCAAGATGACCCAGAAG 59.810 47.826 8.75 0.00 30.21 2.85
4975 11588 5.378230 TCAAGATGACCCAGAAGCATATT 57.622 39.130 0.00 0.00 0.00 1.28
4997 11610 0.999406 CTAGTGACAAATGCGTCCCG 59.001 55.000 0.00 0.00 34.88 5.14
5004 11617 3.268103 AAATGCGTCCCGAGGCCTT 62.268 57.895 6.77 1.06 41.13 4.35
5023 11636 2.354729 CCCTGTCGGGCCATTGAA 59.645 61.111 4.39 0.00 45.33 2.69
5066 11683 2.724977 CAGGTAGTGCTGAGAAACGA 57.275 50.000 0.00 0.00 0.00 3.85
5113 11731 7.050377 CCATACTCTTGTGTAAAGATGGATGT 58.950 38.462 0.00 0.00 29.62 3.06
5121 11739 8.684386 TTGTGTAAAGATGGATGTTCAAGTTA 57.316 30.769 0.00 0.00 0.00 2.24
5152 11771 0.106116 TTTAGGGTTTTGCGTGGGGT 60.106 50.000 0.00 0.00 0.00 4.95
5278 11900 1.134068 GCCCCCTCAATCTGAACTACC 60.134 57.143 0.00 0.00 0.00 3.18
5285 11907 5.395768 CCCTCAATCTGAACTACCTACAAGG 60.396 48.000 0.00 0.00 42.49 3.61
5318 11940 1.406898 CTGAAGCGGTCTAGCATCTGA 59.593 52.381 0.00 0.00 36.40 3.27
5320 11942 1.407258 GAAGCGGTCTAGCATCTGACT 59.593 52.381 0.00 0.00 40.15 3.41
5321 11943 0.743688 AGCGGTCTAGCATCTGACTG 59.256 55.000 0.00 0.00 41.19 3.51
5347 11969 4.122046 GCGGGTTTAGTAAATACATCCGT 58.878 43.478 17.21 0.00 37.55 4.69
5596 12218 4.235079 TGGCCAATGCTTTATACTCTGT 57.765 40.909 0.61 0.00 37.74 3.41
5667 12289 6.542370 AGATATAAGATTGGGTCCAACAAACG 59.458 38.462 4.37 0.00 38.88 3.60
5682 12304 1.954362 AAACGCAGCAAAGCCACCAA 61.954 50.000 0.00 0.00 0.00 3.67
5684 12306 1.735198 CGCAGCAAAGCCACCAATG 60.735 57.895 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.220767 GAAACTCCATAACTAACAGACAAAGAT 57.779 33.333 0.00 0.00 0.00 2.40
32 33 6.921307 CCAACTACGTATAAGTATCATGCACA 59.079 38.462 0.00 0.00 0.00 4.57
70 74 4.383173 TCCGTAAAGTTGAGGGAGAAAAC 58.617 43.478 0.00 0.00 0.00 2.43
106 110 5.996644 TGTCTGGTTTAGAAGTTGAAGGAA 58.003 37.500 0.00 0.00 37.12 3.36
146 150 7.718314 AGGGACGAAAAGTATCAGTTTTTAACT 59.282 33.333 0.00 0.00 44.06 2.24
156 160 3.194968 GGTCTGAGGGACGAAAAGTATCA 59.805 47.826 0.00 0.00 45.35 2.15
319 3698 1.178276 CAGTCAGAACCTAGCCGAGT 58.822 55.000 0.00 0.00 0.00 4.18
442 3824 3.579586 TGGCTGAGCAATTTCAAATCCTT 59.420 39.130 6.82 0.00 0.00 3.36
532 3916 9.810545 TCACGTTTTCATTCTAATTTTTCCTTT 57.189 25.926 0.00 0.00 0.00 3.11
533 3917 9.810545 TTCACGTTTTCATTCTAATTTTTCCTT 57.189 25.926 0.00 0.00 0.00 3.36
534 3918 9.810545 TTTCACGTTTTCATTCTAATTTTTCCT 57.189 25.926 0.00 0.00 0.00 3.36
535 3919 9.843874 GTTTCACGTTTTCATTCTAATTTTTCC 57.156 29.630 0.00 0.00 0.00 3.13
536 3920 9.549923 CGTTTCACGTTTTCATTCTAATTTTTC 57.450 29.630 0.00 0.00 36.74 2.29
537 3921 9.291664 TCGTTTCACGTTTTCATTCTAATTTTT 57.708 25.926 0.00 0.00 43.14 1.94
538 3922 8.844441 TCGTTTCACGTTTTCATTCTAATTTT 57.156 26.923 0.00 0.00 43.14 1.82
539 3923 8.844441 TTCGTTTCACGTTTTCATTCTAATTT 57.156 26.923 0.00 0.00 43.14 1.82
540 3924 8.739461 GTTTCGTTTCACGTTTTCATTCTAATT 58.261 29.630 0.00 0.00 43.14 1.40
541 3925 7.911205 TGTTTCGTTTCACGTTTTCATTCTAAT 59.089 29.630 0.00 0.00 43.14 1.73
542 3926 7.242079 TGTTTCGTTTCACGTTTTCATTCTAA 58.758 30.769 0.00 0.00 43.14 2.10
543 3927 6.773080 TGTTTCGTTTCACGTTTTCATTCTA 58.227 32.000 0.00 0.00 43.14 2.10
575 3959 4.027572 TGTTTTTCTCGCTGGTTTTCTG 57.972 40.909 0.00 0.00 0.00 3.02
622 4006 7.622893 AATCTTCTAGAGGTCAATTTTCTGC 57.377 36.000 1.31 0.00 0.00 4.26
629 4013 8.940397 TTTTTGGAAATCTTCTAGAGGTCAAT 57.060 30.769 1.31 0.00 0.00 2.57
654 4038 3.596500 ACCCCTGAGCCCTAACTATTTTT 59.403 43.478 0.00 0.00 0.00 1.94
655 4039 3.198827 ACCCCTGAGCCCTAACTATTTT 58.801 45.455 0.00 0.00 0.00 1.82
656 4040 2.859951 ACCCCTGAGCCCTAACTATTT 58.140 47.619 0.00 0.00 0.00 1.40
657 4041 2.588925 ACCCCTGAGCCCTAACTATT 57.411 50.000 0.00 0.00 0.00 1.73
658 4042 2.795960 TCTACCCCTGAGCCCTAACTAT 59.204 50.000 0.00 0.00 0.00 2.12
659 4043 2.091444 GTCTACCCCTGAGCCCTAACTA 60.091 54.545 0.00 0.00 0.00 2.24
660 4044 1.016415 TCTACCCCTGAGCCCTAACT 58.984 55.000 0.00 0.00 0.00 2.24
661 4045 1.121378 GTCTACCCCTGAGCCCTAAC 58.879 60.000 0.00 0.00 0.00 2.34
662 4046 1.016415 AGTCTACCCCTGAGCCCTAA 58.984 55.000 0.00 0.00 0.00 2.69
663 4047 1.917099 TAGTCTACCCCTGAGCCCTA 58.083 55.000 0.00 0.00 0.00 3.53
664 4048 1.246294 ATAGTCTACCCCTGAGCCCT 58.754 55.000 0.00 0.00 0.00 5.19
665 4049 2.104669 AATAGTCTACCCCTGAGCCC 57.895 55.000 0.00 0.00 0.00 5.19
666 4050 5.513267 CCAAATAATAGTCTACCCCTGAGCC 60.513 48.000 0.00 0.00 0.00 4.70
667 4051 5.513267 CCCAAATAATAGTCTACCCCTGAGC 60.513 48.000 0.00 0.00 0.00 4.26
668 4052 5.607171 ACCCAAATAATAGTCTACCCCTGAG 59.393 44.000 0.00 0.00 0.00 3.35
669 4053 5.544682 ACCCAAATAATAGTCTACCCCTGA 58.455 41.667 0.00 0.00 0.00 3.86
670 4054 5.510861 CGACCCAAATAATAGTCTACCCCTG 60.511 48.000 0.00 0.00 0.00 4.45
671 4055 4.591924 CGACCCAAATAATAGTCTACCCCT 59.408 45.833 0.00 0.00 0.00 4.79
672 4056 4.262765 CCGACCCAAATAATAGTCTACCCC 60.263 50.000 0.00 0.00 0.00 4.95
673 4057 4.346127 ACCGACCCAAATAATAGTCTACCC 59.654 45.833 0.00 0.00 0.00 3.69
674 4058 5.510349 GGACCGACCCAAATAATAGTCTACC 60.510 48.000 0.00 0.00 0.00 3.18
675 4059 5.536260 GGACCGACCCAAATAATAGTCTAC 58.464 45.833 0.00 0.00 0.00 2.59
676 4060 5.796424 GGACCGACCCAAATAATAGTCTA 57.204 43.478 0.00 0.00 0.00 2.59
677 4061 4.684484 GGACCGACCCAAATAATAGTCT 57.316 45.455 0.00 0.00 0.00 3.24
690 4074 3.054582 AGGATTTCTAAAAGGGACCGACC 60.055 47.826 0.00 0.00 38.08 4.79
691 4075 3.939592 CAGGATTTCTAAAAGGGACCGAC 59.060 47.826 0.00 0.00 0.00 4.79
692 4076 3.585732 ACAGGATTTCTAAAAGGGACCGA 59.414 43.478 0.00 0.00 0.00 4.69
693 4077 3.951663 ACAGGATTTCTAAAAGGGACCG 58.048 45.455 0.00 0.00 0.00 4.79
694 4078 6.659824 TCATACAGGATTTCTAAAAGGGACC 58.340 40.000 0.00 0.00 0.00 4.46
695 4079 7.283354 CCTTCATACAGGATTTCTAAAAGGGAC 59.717 40.741 0.00 0.00 35.71 4.46
696 4080 7.346471 CCTTCATACAGGATTTCTAAAAGGGA 58.654 38.462 0.00 0.00 35.71 4.20
697 4081 6.547510 CCCTTCATACAGGATTTCTAAAAGGG 59.452 42.308 0.00 0.00 42.22 3.95
698 4082 6.039829 GCCCTTCATACAGGATTTCTAAAAGG 59.960 42.308 0.00 0.00 35.71 3.11
699 4083 6.039829 GGCCCTTCATACAGGATTTCTAAAAG 59.960 42.308 0.00 0.00 35.71 2.27
700 4084 5.891551 GGCCCTTCATACAGGATTTCTAAAA 59.108 40.000 0.00 0.00 35.71 1.52
701 4085 5.445964 GGCCCTTCATACAGGATTTCTAAA 58.554 41.667 0.00 0.00 35.71 1.85
702 4086 4.444306 CGGCCCTTCATACAGGATTTCTAA 60.444 45.833 0.00 0.00 35.71 2.10
703 4087 3.071023 CGGCCCTTCATACAGGATTTCTA 59.929 47.826 0.00 0.00 35.71 2.10
726 4110 1.301677 CTTGAGAAGCACGGCCCTTC 61.302 60.000 11.19 11.19 39.13 3.46
750 4134 1.729284 TTCGATACAAAAGCGGGGAC 58.271 50.000 0.00 0.00 0.00 4.46
793 4177 5.449999 CGCAGACAAGTTTTACTTTCCCTTT 60.450 40.000 0.00 0.00 36.03 3.11
814 4198 0.179153 CTGAGATTGAGAGCGACGCA 60.179 55.000 23.70 0.00 0.00 5.24
826 4210 1.517257 CCGTCGCTTCGCTGAGATT 60.517 57.895 0.00 0.00 0.00 2.40
832 4216 4.117661 GGTCTCCGTCGCTTCGCT 62.118 66.667 0.00 0.00 0.00 4.93
838 4222 2.288961 TTCTTATTGGTCTCCGTCGC 57.711 50.000 0.00 0.00 0.00 5.19
839 4223 3.068307 AGGATTCTTATTGGTCTCCGTCG 59.932 47.826 0.00 0.00 0.00 5.12
840 4224 4.674281 AGGATTCTTATTGGTCTCCGTC 57.326 45.455 0.00 0.00 0.00 4.79
841 4225 7.038941 CCTTATAGGATTCTTATTGGTCTCCGT 60.039 40.741 0.00 0.00 37.67 4.69
842 4226 7.178628 TCCTTATAGGATTCTTATTGGTCTCCG 59.821 40.741 0.00 0.00 40.06 4.63
862 4246 1.757699 GTGAGCGTTCCTCCTCCTTAT 59.242 52.381 0.00 0.00 39.98 1.73
863 4247 1.183549 GTGAGCGTTCCTCCTCCTTA 58.816 55.000 0.00 0.00 39.98 2.69
900 4289 7.514784 TCGATCGGGTTTTAATCTAGTATGA 57.485 36.000 16.41 0.00 0.00 2.15
903 4292 8.627208 ACTATCGATCGGGTTTTAATCTAGTA 57.373 34.615 16.41 0.00 0.00 1.82
904 4293 7.521871 ACTATCGATCGGGTTTTAATCTAGT 57.478 36.000 16.41 0.00 0.00 2.57
912 4301 5.047519 CCACCTATACTATCGATCGGGTTTT 60.048 44.000 16.41 6.30 0.00 2.43
968 4357 3.063997 CCGGTCTGCAAGCAATTAGTTAG 59.936 47.826 0.00 0.00 0.00 2.34
986 4416 1.144057 GACATGGATCTTCGCCGGT 59.856 57.895 1.90 0.00 0.00 5.28
1066 4496 3.441290 CGAGAAGAGCCGGTCCGT 61.441 66.667 11.06 0.00 0.00 4.69
1126 4562 8.188139 ACGATTTTGTGTCAAAACTCACTAATT 58.812 29.630 9.33 0.00 35.82 1.40
1127 4563 7.703328 ACGATTTTGTGTCAAAACTCACTAAT 58.297 30.769 9.33 0.00 35.82 1.73
1128 4564 7.079182 ACGATTTTGTGTCAAAACTCACTAA 57.921 32.000 9.33 0.00 35.82 2.24
1129 4565 6.671614 ACGATTTTGTGTCAAAACTCACTA 57.328 33.333 9.33 0.00 35.82 2.74
1130 4566 5.560966 ACGATTTTGTGTCAAAACTCACT 57.439 34.783 9.33 0.00 35.82 3.41
1131 4567 6.711579 TCTACGATTTTGTGTCAAAACTCAC 58.288 36.000 9.33 0.00 35.43 3.51
1132 4568 6.912203 TCTACGATTTTGTGTCAAAACTCA 57.088 33.333 9.33 0.00 0.00 3.41
1133 4569 7.373441 CAGTTCTACGATTTTGTGTCAAAACTC 59.627 37.037 9.33 7.93 0.00 3.01
1134 4570 7.148306 ACAGTTCTACGATTTTGTGTCAAAACT 60.148 33.333 9.33 0.00 0.00 2.66
1135 4571 6.964934 ACAGTTCTACGATTTTGTGTCAAAAC 59.035 34.615 9.33 4.47 0.00 2.43
1136 4572 6.964370 CACAGTTCTACGATTTTGTGTCAAAA 59.036 34.615 9.52 9.52 33.21 2.44
1137 4573 6.457663 CCACAGTTCTACGATTTTGTGTCAAA 60.458 38.462 0.00 0.00 35.39 2.69
1138 4574 5.007234 CCACAGTTCTACGATTTTGTGTCAA 59.993 40.000 0.00 0.00 35.39 3.18
1139 4575 4.509970 CCACAGTTCTACGATTTTGTGTCA 59.490 41.667 0.00 0.00 35.39 3.58
1140 4576 4.510340 ACCACAGTTCTACGATTTTGTGTC 59.490 41.667 0.00 0.00 35.39 3.67
1141 4577 4.448210 ACCACAGTTCTACGATTTTGTGT 58.552 39.130 0.00 0.00 35.39 3.72
1142 4578 5.418310 AACCACAGTTCTACGATTTTGTG 57.582 39.130 0.00 0.00 36.56 3.33
1143 4579 5.820947 AGAAACCACAGTTCTACGATTTTGT 59.179 36.000 0.00 0.00 34.19 2.83
1144 4580 6.136071 CAGAAACCACAGTTCTACGATTTTG 58.864 40.000 0.00 0.00 34.19 2.44
1145 4581 5.277828 GCAGAAACCACAGTTCTACGATTTT 60.278 40.000 0.00 0.00 34.19 1.82
1146 4582 4.213482 GCAGAAACCACAGTTCTACGATTT 59.787 41.667 0.00 0.00 34.19 2.17
1147 4583 3.746492 GCAGAAACCACAGTTCTACGATT 59.254 43.478 0.00 0.00 34.19 3.34
1148 4584 3.244078 TGCAGAAACCACAGTTCTACGAT 60.244 43.478 0.00 0.00 34.19 3.73
1149 4585 2.101750 TGCAGAAACCACAGTTCTACGA 59.898 45.455 0.00 0.00 34.19 3.43
1150 4586 2.479837 TGCAGAAACCACAGTTCTACG 58.520 47.619 0.00 0.00 34.19 3.51
1151 4587 4.210832 GTTGCAGAAACCACAGTTCTAC 57.789 45.455 0.00 0.00 34.19 2.59
1162 4598 1.351350 AGAGGGTAGGGTTGCAGAAAC 59.649 52.381 0.00 0.00 38.12 2.78
1163 4599 1.628846 GAGAGGGTAGGGTTGCAGAAA 59.371 52.381 0.00 0.00 0.00 2.52
1164 4600 1.276622 GAGAGGGTAGGGTTGCAGAA 58.723 55.000 0.00 0.00 0.00 3.02
1165 4601 0.970937 CGAGAGGGTAGGGTTGCAGA 60.971 60.000 0.00 0.00 0.00 4.26
1166 4602 1.517832 CGAGAGGGTAGGGTTGCAG 59.482 63.158 0.00 0.00 0.00 4.41
1167 4603 2.656069 GCGAGAGGGTAGGGTTGCA 61.656 63.158 0.00 0.00 0.00 4.08
1168 4604 2.187163 GCGAGAGGGTAGGGTTGC 59.813 66.667 0.00 0.00 0.00 4.17
1169 4605 2.494918 CGCGAGAGGGTAGGGTTG 59.505 66.667 0.00 0.00 39.50 3.77
1209 4645 3.782443 CCGGCGGCTAGGGTTTCT 61.782 66.667 15.42 0.00 0.00 2.52
1233 4669 2.317149 GAAGGAGATGCGGGGGAGTG 62.317 65.000 0.00 0.00 0.00 3.51
1314 4750 2.656069 CGCGAGAAGGGGAAGGGAA 61.656 63.158 0.00 0.00 0.00 3.97
1401 4838 4.240103 TCGCGGCCAGGATCCATG 62.240 66.667 15.82 9.25 0.00 3.66
1470 4907 2.982130 GCGACCACCAGATCCAGT 59.018 61.111 0.00 0.00 0.00 4.00
1709 5146 1.196012 GTTTCCTCCGGTCCTCATCT 58.804 55.000 0.00 0.00 0.00 2.90
1873 5311 0.883833 GAGGTTACGACACGAAGGGA 59.116 55.000 0.00 0.00 0.00 4.20
1922 5360 1.120530 TAGCAACTCTCCCCCGAATC 58.879 55.000 0.00 0.00 0.00 2.52
1931 5439 3.791245 CTCTTCACCCATAGCAACTCTC 58.209 50.000 0.00 0.00 0.00 3.20
1932 5440 2.093235 GCTCTTCACCCATAGCAACTCT 60.093 50.000 0.00 0.00 35.05 3.24
1975 5485 0.540365 CAACCTCCACACCATTGCCT 60.540 55.000 0.00 0.00 0.00 4.75
2133 5643 1.747145 CTCTGCGCTCATCCATCCT 59.253 57.895 9.73 0.00 0.00 3.24
2218 5730 1.761784 CTGTCCCATCTTCAGGAGAGG 59.238 57.143 0.00 0.00 39.34 3.69
2242 5754 2.031516 GGCCGCCATCATCATCGAG 61.032 63.158 3.91 0.00 0.00 4.04
2279 5791 2.806244 CAGCAAACCTAAAGCGTACACT 59.194 45.455 0.00 0.00 0.00 3.55
2390 6023 2.420827 CCACCACTCACACCTACAAACA 60.421 50.000 0.00 0.00 0.00 2.83
2432 6065 6.884280 ATTTCACGAGGTTCTGAAAAGAAT 57.116 33.333 1.40 0.00 39.28 2.40
2444 6078 8.621286 CCAGCTTTATTAATTATTTCACGAGGT 58.379 33.333 0.00 0.00 0.00 3.85
2467 6101 0.317854 CAATCGATGCATGCAGCCAG 60.318 55.000 28.76 16.64 44.83 4.85
2522 6163 7.472334 AAAATATGTCAGCTTTGGTTGAGAT 57.528 32.000 0.00 0.00 39.29 2.75
2523 6164 6.899393 AAAATATGTCAGCTTTGGTTGAGA 57.101 33.333 0.00 0.00 33.52 3.27
2524 6165 7.029563 GGTAAAATATGTCAGCTTTGGTTGAG 58.970 38.462 0.00 0.00 33.52 3.02
2525 6166 6.719370 AGGTAAAATATGTCAGCTTTGGTTGA 59.281 34.615 0.00 0.00 0.00 3.18
2526 6167 6.924111 AGGTAAAATATGTCAGCTTTGGTTG 58.076 36.000 0.00 0.00 0.00 3.77
2527 6168 6.719370 TGAGGTAAAATATGTCAGCTTTGGTT 59.281 34.615 0.00 0.00 0.00 3.67
2528 6169 6.245408 TGAGGTAAAATATGTCAGCTTTGGT 58.755 36.000 0.00 0.00 0.00 3.67
2529 6170 6.757897 TGAGGTAAAATATGTCAGCTTTGG 57.242 37.500 0.00 0.00 0.00 3.28
2530 6171 7.988737 TCATGAGGTAAAATATGTCAGCTTTG 58.011 34.615 0.00 0.00 0.00 2.77
2531 6172 8.757982 ATCATGAGGTAAAATATGTCAGCTTT 57.242 30.769 0.09 0.00 0.00 3.51
2532 6173 8.757982 AATCATGAGGTAAAATATGTCAGCTT 57.242 30.769 0.09 0.00 0.00 3.74
2533 6174 8.757982 AAATCATGAGGTAAAATATGTCAGCT 57.242 30.769 0.09 0.00 0.00 4.24
2534 6175 9.455847 GAAAATCATGAGGTAAAATATGTCAGC 57.544 33.333 0.09 0.00 0.00 4.26
2666 6308 7.169158 TCAAAAACATTCAAACTTGTCTCCT 57.831 32.000 0.00 0.00 0.00 3.69
2816 9318 3.369366 CCCTCTGTGCCAAACTTTTTGTT 60.369 43.478 0.00 0.00 41.29 2.83
2824 9326 1.348036 AGTACTCCCTCTGTGCCAAAC 59.652 52.381 0.00 0.00 0.00 2.93
2830 9332 4.995487 GGTTAAACAAGTACTCCCTCTGTG 59.005 45.833 0.00 0.00 0.00 3.66
3280 9799 1.974236 AGATATGGGAGTGCTAGTGGC 59.026 52.381 0.00 0.00 42.22 5.01
3329 9848 1.251251 ACGTACCTAAGAGTGGCGTT 58.749 50.000 0.00 0.00 31.77 4.84
3331 9850 3.492421 TTTACGTACCTAAGAGTGGCG 57.508 47.619 0.00 0.00 0.00 5.69
3368 9889 7.226523 AGCGATTTTGTATGTACATGCATCTTA 59.773 33.333 24.57 9.37 35.89 2.10
3379 9900 7.985184 AGAATAGACCAAGCGATTTTGTATGTA 59.015 33.333 0.00 0.00 0.00 2.29
3381 9902 7.251704 AGAATAGACCAAGCGATTTTGTATG 57.748 36.000 0.00 0.00 0.00 2.39
3392 9913 8.191446 GGAAAATTAAGGAAGAATAGACCAAGC 58.809 37.037 0.00 0.00 0.00 4.01
3396 9917 6.827251 ACGGGAAAATTAAGGAAGAATAGACC 59.173 38.462 0.00 0.00 0.00 3.85
3413 9934 4.785511 TCTTGTCAAACAAACGGGAAAA 57.214 36.364 0.00 0.00 37.69 2.29
3419 9940 3.862267 TGCCAATTCTTGTCAAACAAACG 59.138 39.130 0.00 0.00 37.69 3.60
3532 10056 1.412343 TGCTCGCCACAGCATTATCTA 59.588 47.619 0.00 0.00 44.73 1.98
4015 10540 1.375908 GATGTTGCTGCTCCCGTCA 60.376 57.895 0.00 0.00 0.00 4.35
4223 10748 3.964221 GATGCGACGCGTGACTGGA 62.964 63.158 20.70 5.09 0.00 3.86
4228 10753 4.492160 GGGAGATGCGACGCGTGA 62.492 66.667 20.70 0.00 0.00 4.35
4446 11039 2.615288 CTCCTGGCCCTTCCCCTT 60.615 66.667 0.00 0.00 0.00 3.95
4529 11135 4.767892 CCCCCTCCCTCCAGGCTT 62.768 72.222 0.00 0.00 34.51 4.35
4609 11215 1.169661 AAGAACCGCATGAAACGCCA 61.170 50.000 0.00 0.00 0.00 5.69
4610 11216 0.039527 AAAGAACCGCATGAAACGCC 60.040 50.000 0.00 0.00 0.00 5.68
4611 11217 2.239201 GTAAAGAACCGCATGAAACGC 58.761 47.619 0.00 0.00 0.00 4.84
4612 11218 3.529634 TGTAAAGAACCGCATGAAACG 57.470 42.857 0.00 0.00 0.00 3.60
4621 11227 5.249637 GCGTTAGCCCTTGTAAAGAACCG 62.250 52.174 0.00 0.00 45.77 4.44
4622 11228 2.161012 GCGTTAGCCCTTGTAAAGAACC 59.839 50.000 0.00 0.00 45.77 3.62
4623 11229 3.072211 AGCGTTAGCCCTTGTAAAGAAC 58.928 45.455 0.00 0.00 46.64 3.01
4624 11230 3.412237 AGCGTTAGCCCTTGTAAAGAA 57.588 42.857 0.00 0.00 46.64 2.52
4625 11231 3.412237 AAGCGTTAGCCCTTGTAAAGA 57.588 42.857 0.00 0.00 46.64 2.52
4626 11232 5.813080 ATAAAGCGTTAGCCCTTGTAAAG 57.187 39.130 0.00 0.00 46.67 1.85
4627 11233 5.106078 CCAATAAAGCGTTAGCCCTTGTAAA 60.106 40.000 0.00 0.00 46.67 2.01
4628 11234 4.396790 CCAATAAAGCGTTAGCCCTTGTAA 59.603 41.667 0.00 0.00 46.67 2.41
4647 11253 2.056223 GTGGGCAGCTGCATCCAAT 61.056 57.895 37.63 0.00 44.36 3.16
4648 11254 2.677524 GTGGGCAGCTGCATCCAA 60.678 61.111 37.63 18.57 44.36 3.53
4667 11273 6.205853 AGCAGTAACCAAAACGAATATTGTCA 59.794 34.615 0.00 0.00 0.00 3.58
4674 11280 4.097286 ACAACAGCAGTAACCAAAACGAAT 59.903 37.500 0.00 0.00 0.00 3.34
4711 11317 1.882989 GCTTTTACCCCAATGCCGCA 61.883 55.000 0.00 0.00 0.00 5.69
4927 11540 6.924111 ACAGCAGAACAAAAATAACCTATGG 58.076 36.000 0.00 0.00 0.00 2.74
4929 11542 8.637986 TGAAACAGCAGAACAAAAATAACCTAT 58.362 29.630 0.00 0.00 0.00 2.57
4932 11545 7.491048 TCTTGAAACAGCAGAACAAAAATAACC 59.509 33.333 0.00 0.00 0.00 2.85
4934 11547 9.033481 CATCTTGAAACAGCAGAACAAAAATAA 57.967 29.630 0.00 0.00 0.00 1.40
4945 11558 2.486982 CTGGGTCATCTTGAAACAGCAG 59.513 50.000 0.00 0.00 29.74 4.24
4969 11582 7.692387 GACGCATTTGTCACTAGCAAATATGC 61.692 42.308 6.51 7.67 42.54 3.14
4975 11588 1.804151 GGACGCATTTGTCACTAGCAA 59.196 47.619 0.00 0.00 40.72 3.91
4997 11610 3.787001 CCGACAGGGGAAGGCCTC 61.787 72.222 5.23 0.00 33.50 4.70
5023 11636 8.183104 TGCTCATTGCTATCTACTAGTACAAT 57.817 34.615 0.00 4.36 43.37 2.71
5066 11683 6.717289 TGGCTTTGTACCTAAACTATGTGAT 58.283 36.000 0.00 0.00 0.00 3.06
5113 11731 7.503230 CCCTAAACCTACCTGTTTTAACTTGAA 59.497 37.037 0.00 0.00 39.15 2.69
5121 11739 5.163385 GCAAAACCCTAAACCTACCTGTTTT 60.163 40.000 0.00 0.00 39.15 2.43
5152 11771 2.521126 TGAGACGTGAGGTGGATGTAA 58.479 47.619 0.00 0.00 0.00 2.41
5318 11940 4.831674 ATTTACTAAACCCGCTACCAGT 57.168 40.909 0.00 0.00 0.00 4.00
5320 11942 5.674052 TGTATTTACTAAACCCGCTACCA 57.326 39.130 0.00 0.00 0.00 3.25
5321 11943 5.698089 GGATGTATTTACTAAACCCGCTACC 59.302 44.000 0.00 0.00 0.00 3.18
5347 11969 7.148188 GGTTCATTTCAACAGATGATCAGCTAA 60.148 37.037 14.17 4.28 38.03 3.09
5585 12207 5.434408 TCTAGCACCGAGACAGAGTATAAA 58.566 41.667 0.00 0.00 0.00 1.40
5596 12218 1.872388 CTCGAGATCTAGCACCGAGA 58.128 55.000 20.41 0.87 46.62 4.04
5667 12289 1.375013 CCATTGGTGGCTTTGCTGC 60.375 57.895 0.00 0.00 39.01 5.25
5682 12304 1.271325 TGTTGATGACAGGCGTTCCAT 60.271 47.619 0.00 0.00 33.40 3.41
5684 12306 0.517316 GTGTTGATGACAGGCGTTCC 59.483 55.000 0.00 0.00 39.39 3.62


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

AutoCloner maintained by Alex Coulton.