Multiple sequence alignment - TraesCS1B01G073800

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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 TraesCS1B01G073800 chr1B 100.000 4500 0 0 1 4500 57614167 57618666 0.000000e+00 8311.0
1 TraesCS1B01G073800 chr1B 97.222 108 3 0 3969 4076 626498463 626498570 2.760000e-42 183.0
2 TraesCS1B01G073800 chr1B 95.536 112 5 0 3964 4075 229263157 229263268 3.580000e-41 180.0
3 TraesCS1B01G073800 chr1B 96.296 108 3 1 3969 4076 159922531 159922637 4.630000e-40 176.0
4 TraesCS1B01G073800 chr1B 95.556 90 3 1 3969 4058 583085872 583085784 4.690000e-30 143.0
5 TraesCS1B01G073800 chr1D 93.825 2154 91 19 810 2941 37879802 37881935 0.000000e+00 3203.0
6 TraesCS1B01G073800 chr1D 95.810 1050 31 6 2903 3949 37882866 37883905 0.000000e+00 1683.0
7 TraesCS1B01G073800 chr1D 97.190 427 12 0 4074 4500 37884085 37884511 0.000000e+00 723.0
8 TraesCS1B01G073800 chr1D 96.288 431 12 3 5 431 37878625 37879055 0.000000e+00 704.0
9 TraesCS1B01G073800 chr1D 90.421 261 19 4 532 788 37879558 37879816 5.580000e-89 339.0
10 TraesCS1B01G073800 chr1D 96.842 95 3 0 437 531 37879202 37879296 4.660000e-35 159.0
11 TraesCS1B01G073800 chr6B 82.249 1859 238 52 2025 3849 75422509 75420709 0.000000e+00 1520.0
12 TraesCS1B01G073800 chr6B 84.153 1546 188 39 2322 3849 75045487 75043981 0.000000e+00 1445.0
13 TraesCS1B01G073800 chr6B 81.753 1118 143 32 855 1951 75423615 75422538 0.000000e+00 878.0
14 TraesCS1B01G073800 chr6B 82.711 937 136 16 1026 1944 75526303 75525375 0.000000e+00 809.0
15 TraesCS1B01G073800 chr6B 84.388 711 77 23 3147 3851 75524577 75523895 0.000000e+00 667.0
16 TraesCS1B01G073800 chr6B 78.593 995 155 34 1026 1970 75268450 75267464 4.980000e-169 604.0
17 TraesCS1B01G073800 chr6B 92.188 64 2 3 855 915 75510481 75510418 2.230000e-13 87.9
18 TraesCS1B01G073800 chr6B 97.917 48 1 0 3924 3971 65120339 65120292 2.880000e-12 84.2
19 TraesCS1B01G073800 chr1A 90.109 1193 74 18 2178 3357 36790141 36791302 0.000000e+00 1509.0
20 TraesCS1B01G073800 chr1A 92.620 664 28 7 1336 1984 36789149 36789806 0.000000e+00 935.0
21 TraesCS1B01G073800 chr1A 95.082 427 21 0 4074 4500 36791824 36792250 0.000000e+00 673.0
22 TraesCS1B01G073800 chr1A 92.778 360 18 5 437 788 36783927 36784286 8.630000e-142 514.0
23 TraesCS1B01G073800 chr1A 93.656 331 17 3 1026 1352 36785376 36785706 4.040000e-135 492.0
24 TraesCS1B01G073800 chr1A 91.239 331 25 2 1888 2215 36789812 36790141 8.880000e-122 448.0
25 TraesCS1B01G073800 chr1A 92.544 228 12 5 3745 3971 36791603 36791826 5.620000e-84 322.0
26 TraesCS1B01G073800 chr1A 92.697 178 13 0 5 182 36783400 36783577 1.610000e-64 257.0
27 TraesCS1B01G073800 chr1A 92.814 167 11 1 269 435 36783576 36783741 1.620000e-59 241.0
28 TraesCS1B01G073800 chr1A 94.643 112 5 1 3968 4079 6762195 6762085 5.980000e-39 172.0
29 TraesCS1B01G073800 chr1A 89.516 124 8 2 828 946 36784313 36784436 7.800000e-33 152.0
30 TraesCS1B01G073800 chr6D 85.415 1097 131 22 2759 3849 35716311 35715238 0.000000e+00 1112.0
31 TraesCS1B01G073800 chr6D 79.684 1329 176 43 2030 3328 35641103 35639839 0.000000e+00 872.0
32 TraesCS1B01G073800 chr6D 85.059 763 80 23 3103 3851 36083438 36082696 0.000000e+00 747.0
33 TraesCS1B01G073800 chr6D 80.450 977 153 23 1026 1969 35667506 35666535 0.000000e+00 712.0
34 TraesCS1B01G073800 chr6D 81.571 662 104 13 3062 3715 36073555 36072904 8.570000e-147 531.0
35 TraesCS1B01G073800 chr6D 83.333 564 86 5 1388 1944 36084580 36084018 8.630000e-142 514.0
36 TraesCS1B01G073800 chr6D 80.142 564 77 19 2022 2569 36083979 36083435 5.460000e-104 388.0
37 TraesCS1B01G073800 chr6D 82.069 435 58 15 971 1392 36090502 36090075 1.990000e-93 353.0
38 TraesCS1B01G073800 chr6D 83.289 377 45 15 933 1306 35886323 35885962 9.330000e-87 331.0
39 TraesCS1B01G073800 chr6D 84.459 296 41 5 2492 2782 35716618 35716323 2.050000e-73 287.0
40 TraesCS1B01G073800 chr6D 80.299 401 60 12 2030 2417 35666519 35666125 7.370000e-73 285.0
41 TraesCS1B01G073800 chr6D 79.241 448 63 17 2016 2452 35717050 35716622 7.370000e-73 285.0
42 TraesCS1B01G073800 chr6D 83.388 307 45 1 1623 1923 36105451 36105145 3.430000e-71 279.0
43 TraesCS1B01G073800 chr6D 83.471 121 17 3 3441 3560 28325614 28325496 4.760000e-20 110.0
44 TraesCS1B01G073800 chr6A 82.086 1323 184 28 2030 3328 39590049 39588756 0.000000e+00 1081.0
45 TraesCS1B01G073800 chr6A 81.434 1325 193 28 2030 3328 39547936 39546639 0.000000e+00 1035.0
46 TraesCS1B01G073800 chr6A 81.344 1324 194 26 2030 3328 39637843 39636548 0.000000e+00 1027.0
47 TraesCS1B01G073800 chr6A 82.090 938 146 13 1026 1944 39670757 39669823 0.000000e+00 782.0
48 TraesCS1B01G073800 chr6A 82.131 929 140 17 1037 1944 39628954 39628031 0.000000e+00 773.0
49 TraesCS1B01G073800 chr6A 81.376 945 148 19 1025 1944 39581184 39580243 0.000000e+00 745.0
50 TraesCS1B01G073800 chr6A 84.831 712 80 21 3147 3851 39669213 39668523 0.000000e+00 691.0
51 TraesCS1B01G073800 chr6A 84.129 712 85 22 3147 3851 39627421 39626731 0.000000e+00 664.0
52 TraesCS1B01G073800 chr6A 79.880 999 126 41 981 1923 39878026 39877047 0.000000e+00 662.0
53 TraesCS1B01G073800 chr6A 87.216 485 56 6 3369 3849 39546641 39546159 8.510000e-152 547.0
54 TraesCS1B01G073800 chr6A 79.433 564 83 18 2022 2569 39669784 39669238 7.110000e-98 368.0
55 TraesCS1B01G073800 chr6A 78.938 565 84 20 2022 2569 39627992 39627446 7.160000e-93 351.0
56 TraesCS1B01G073800 chr6A 78.230 565 89 22 2022 2569 39580204 39579657 9.330000e-87 331.0
57 TraesCS1B01G073800 chr6A 79.817 327 51 14 4179 4499 39587922 39587605 1.630000e-54 224.0
58 TraesCS1B01G073800 chr6A 79.817 327 50 15 4179 4499 39635714 39635398 1.630000e-54 224.0
59 TraesCS1B01G073800 chr6A 79.511 327 51 14 4179 4499 39545804 39545488 7.580000e-53 219.0
60 TraesCS1B01G073800 chr6A 93.966 116 7 0 3963 4078 17663913 17663798 4.630000e-40 176.0
61 TraesCS1B01G073800 chr6A 89.231 130 12 2 3966 4095 404989759 404989632 1.300000e-35 161.0
62 TraesCS1B01G073800 chr6A 92.424 66 4 1 3907 3971 496236807 496236742 4.790000e-15 93.5
63 TraesCS1B01G073800 chr2A 97.248 109 3 0 3967 4075 660176862 660176754 7.690000e-43 185.0
64 TraesCS1B01G073800 chr2A 97.087 103 3 0 4074 4176 86445956 86445854 1.660000e-39 174.0
65 TraesCS1B01G073800 chr2A 97.980 99 2 0 4074 4172 107386603 107386505 5.980000e-39 172.0
66 TraesCS1B01G073800 chr2A 90.625 128 10 2 3948 4075 660176735 660176860 7.740000e-38 169.0
67 TraesCS1B01G073800 chr2A 93.651 63 3 1 3910 3971 754429831 754429893 4.790000e-15 93.5
68 TraesCS1B01G073800 chr5B 94.783 115 6 0 3969 4083 511610743 511610857 3.580000e-41 180.0
69 TraesCS1B01G073800 chr7B 98.990 99 1 0 4074 4172 372327726 372327628 1.290000e-40 178.0
70 TraesCS1B01G073800 chr7B 95.082 61 3 0 3911 3971 104977698 104977638 3.710000e-16 97.1
71 TraesCS1B01G073800 chr7B 94.915 59 3 0 3913 3971 102234611 102234553 4.790000e-15 93.5
72 TraesCS1B01G073800 chr7A 98.000 100 2 0 4074 4173 130229639 130229540 1.660000e-39 174.0
73 TraesCS1B01G073800 chr7A 92.500 120 7 2 3957 4076 347252600 347252483 2.150000e-38 171.0
74 TraesCS1B01G073800 chr7D 97.980 99 2 0 4074 4172 377606745 377606647 5.980000e-39 172.0
75 TraesCS1B01G073800 chr7D 91.935 62 2 3 3913 3971 28445322 28445261 2.880000e-12 84.2
76 TraesCS1B01G073800 chr3A 93.860 114 7 0 3969 4082 671629484 671629371 5.980000e-39 172.0
77 TraesCS1B01G073800 chr5A 93.162 117 7 1 3967 4082 645629928 645629812 2.150000e-38 171.0
78 TraesCS1B01G073800 chr2D 96.117 103 4 0 4074 4176 86086061 86085959 7.740000e-38 169.0
79 TraesCS1B01G073800 chr2D 92.784 97 6 1 254 350 635586121 635586216 6.070000e-29 139.0
80 TraesCS1B01G073800 chr3B 86.486 148 12 6 3987 4128 70295894 70296039 6.030000e-34 156.0
81 TraesCS1B01G073800 chrUn 92.929 99 5 2 252 350 93415567 93415663 4.690000e-30 143.0
82 TraesCS1B01G073800 chrUn 92.784 97 5 2 254 350 93413201 93413295 6.070000e-29 139.0
83 TraesCS1B01G073800 chrUn 92.784 97 5 2 254 350 425406400 425406494 6.070000e-29 139.0
84 TraesCS1B01G073800 chr2B 92.929 99 5 2 252 350 369624480 369624384 4.690000e-30 143.0
85 TraesCS1B01G073800 chr5D 92.784 97 5 2 254 350 503214650 503214556 6.070000e-29 139.0
86 TraesCS1B01G073800 chr3D 92.784 97 5 2 254 350 24168243 24168149 6.070000e-29 139.0
87 TraesCS1B01G073800 chr3D 95.122 41 2 0 3913 3953 23172771 23172731 1.040000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G073800 chr1B 57614167 57618666 4499 False 8311.000000 8311 100.000000 1 4500 1 chr1B.!!$F1 4499
1 TraesCS1B01G073800 chr1D 37878625 37884511 5886 False 1135.166667 3203 95.062667 5 4500 6 chr1D.!!$F1 4495
2 TraesCS1B01G073800 chr6B 75043981 75045487 1506 True 1445.000000 1445 84.153000 2322 3849 1 chr6B.!!$R2 1527
3 TraesCS1B01G073800 chr6B 75420709 75423615 2906 True 1199.000000 1520 82.001000 855 3849 2 chr6B.!!$R5 2994
4 TraesCS1B01G073800 chr6B 75523895 75526303 2408 True 738.000000 809 83.549500 1026 3851 2 chr6B.!!$R6 2825
5 TraesCS1B01G073800 chr6B 75267464 75268450 986 True 604.000000 604 78.593000 1026 1970 1 chr6B.!!$R3 944
6 TraesCS1B01G073800 chr1A 36783400 36792250 8850 False 554.300000 1509 92.305500 5 4500 10 chr1A.!!$F1 4495
7 TraesCS1B01G073800 chr6D 35639839 35641103 1264 True 872.000000 872 79.684000 2030 3328 1 chr6D.!!$R2 1298
8 TraesCS1B01G073800 chr6D 35715238 35717050 1812 True 561.333333 1112 83.038333 2016 3849 3 chr6D.!!$R8 1833
9 TraesCS1B01G073800 chr6D 36082696 36084580 1884 True 549.666667 747 82.844667 1388 3851 3 chr6D.!!$R9 2463
10 TraesCS1B01G073800 chr6D 36072904 36073555 651 True 531.000000 531 81.571000 3062 3715 1 chr6D.!!$R4 653
11 TraesCS1B01G073800 chr6D 35666125 35667506 1381 True 498.500000 712 80.374500 1026 2417 2 chr6D.!!$R7 1391
12 TraesCS1B01G073800 chr6A 39877047 39878026 979 True 662.000000 662 79.880000 981 1923 1 chr6A.!!$R2 942
13 TraesCS1B01G073800 chr6A 39587605 39590049 2444 True 652.500000 1081 80.951500 2030 4499 2 chr6A.!!$R7 2469
14 TraesCS1B01G073800 chr6A 39635398 39637843 2445 True 625.500000 1027 80.580500 2030 4499 2 chr6A.!!$R9 2469
15 TraesCS1B01G073800 chr6A 39668523 39670757 2234 True 613.666667 782 82.118000 1026 3851 3 chr6A.!!$R10 2825
16 TraesCS1B01G073800 chr6A 39545488 39547936 2448 True 600.333333 1035 82.720333 2030 4499 3 chr6A.!!$R5 2469
17 TraesCS1B01G073800 chr6A 39626731 39628954 2223 True 596.000000 773 81.732667 1037 3851 3 chr6A.!!$R8 2814
18 TraesCS1B01G073800 chr6A 39579657 39581184 1527 True 538.000000 745 79.803000 1025 2569 2 chr6A.!!$R6 1544

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
768 1228 0.953471 TGGTTCTGTGCACATACGGC 60.953 55.000 22.0 10.12 0.00 5.68 F
1248 2648 1.078426 CGAGGGCTTCCGTTTCCAT 60.078 57.895 0.0 0.00 35.17 3.41 F
1634 6549 1.434188 TCCAGACTTCCCAGCAAGAA 58.566 50.000 0.0 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 6772 2.948979 CCATAACTGGGCGCTGAATTTA 59.051 45.455 14.63 3.54 39.04 1.40 R
2823 8166 4.115516 CCTATTCGACATCTCACTTGGTG 58.884 47.826 0.00 0.00 34.45 4.17 R
3584 9980 3.424703 TCAATGAAGCAGAAGAAAGGGG 58.575 45.455 0.00 0.00 0.00 4.79 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
50 51 2.949177 AAGGTGTGATGGCTTGTGTA 57.051 45.000 0.00 0.00 0.00 2.90
216 217 3.736252 GGTCACAATGGATTAGATCGACG 59.264 47.826 0.00 0.00 0.00 5.12
244 245 5.649831 GCCATCCACATCTTTTCTTCTAAGT 59.350 40.000 0.00 0.00 0.00 2.24
475 663 9.461312 AGTTTGTTTGATTCCTATGCATACTTA 57.539 29.630 1.16 0.00 0.00 2.24
548 997 5.213597 AAGCACGTATGTGTTTGTCTGTCA 61.214 41.667 15.42 0.00 46.14 3.58
566 1015 3.704566 TGTCATGAAGTTAGGGTCGCTAT 59.295 43.478 0.00 0.00 0.00 2.97
574 1023 1.452953 TAGGGTCGCTATGCCGTGAG 61.453 60.000 0.00 0.00 0.00 3.51
715 1166 7.255139 CCGTTGAATCTTGTAGGAGTTTTTCTT 60.255 37.037 0.00 0.00 0.00 2.52
716 1167 8.770828 CGTTGAATCTTGTAGGAGTTTTTCTTA 58.229 33.333 0.00 0.00 0.00 2.10
768 1228 0.953471 TGGTTCTGTGCACATACGGC 60.953 55.000 22.00 10.12 0.00 5.68
777 1237 1.212616 GCACATACGGCTAGCTTCTG 58.787 55.000 15.72 9.74 0.00 3.02
778 1238 1.202417 GCACATACGGCTAGCTTCTGA 60.202 52.381 15.72 0.00 0.00 3.27
779 1239 2.738643 GCACATACGGCTAGCTTCTGAA 60.739 50.000 15.72 0.00 0.00 3.02
780 1240 3.521560 CACATACGGCTAGCTTCTGAAA 58.478 45.455 15.72 0.00 0.00 2.69
781 1241 3.932710 CACATACGGCTAGCTTCTGAAAA 59.067 43.478 15.72 0.00 0.00 2.29
782 1242 4.572389 CACATACGGCTAGCTTCTGAAAAT 59.428 41.667 15.72 0.00 0.00 1.82
783 1243 4.811557 ACATACGGCTAGCTTCTGAAAATC 59.188 41.667 15.72 0.00 0.00 2.17
784 1244 3.334583 ACGGCTAGCTTCTGAAAATCA 57.665 42.857 15.72 0.00 0.00 2.57
785 1245 3.674997 ACGGCTAGCTTCTGAAAATCAA 58.325 40.909 15.72 0.00 0.00 2.57
786 1246 4.265073 ACGGCTAGCTTCTGAAAATCAAT 58.735 39.130 15.72 0.00 0.00 2.57
787 1247 4.333926 ACGGCTAGCTTCTGAAAATCAATC 59.666 41.667 15.72 0.00 0.00 2.67
788 1248 4.574013 CGGCTAGCTTCTGAAAATCAATCT 59.426 41.667 15.72 0.00 0.00 2.40
789 1249 5.277250 CGGCTAGCTTCTGAAAATCAATCTC 60.277 44.000 15.72 0.00 0.00 2.75
790 1250 5.821995 GGCTAGCTTCTGAAAATCAATCTCT 59.178 40.000 15.72 0.00 0.00 3.10
791 1251 6.018016 GGCTAGCTTCTGAAAATCAATCTCTC 60.018 42.308 15.72 0.00 0.00 3.20
792 1252 6.762661 GCTAGCTTCTGAAAATCAATCTCTCT 59.237 38.462 7.70 0.00 0.00 3.10
793 1253 7.280652 GCTAGCTTCTGAAAATCAATCTCTCTT 59.719 37.037 7.70 0.00 0.00 2.85
794 1254 7.999450 AGCTTCTGAAAATCAATCTCTCTTT 57.001 32.000 0.00 0.00 0.00 2.52
795 1255 8.406730 AGCTTCTGAAAATCAATCTCTCTTTT 57.593 30.769 0.00 0.00 0.00 2.27
796 1256 8.858094 AGCTTCTGAAAATCAATCTCTCTTTTT 58.142 29.630 0.00 0.00 0.00 1.94
902 1386 4.500116 GAGCTCTCGTGGGCCGTC 62.500 72.222 6.43 0.00 37.94 4.79
919 1407 2.294074 CGTCTCTTCTCTCTCCGGATT 58.706 52.381 3.57 0.00 0.00 3.01
962 1455 3.379445 ATTGTGGGCTGCTGCTGC 61.379 61.111 21.42 21.42 39.59 5.25
969 1462 3.797546 GCTGCTGCTGCTTCGACC 61.798 66.667 22.10 0.00 40.48 4.79
1248 2648 1.078426 CGAGGGCTTCCGTTTCCAT 60.078 57.895 0.00 0.00 35.17 3.41
1254 2654 1.664873 GCTTCCGTTTCCATCCTACC 58.335 55.000 0.00 0.00 0.00 3.18
1354 5024 2.832498 GCCATGGCCTCCTACTCC 59.168 66.667 27.24 0.00 34.56 3.85
1355 5025 2.072487 GCCATGGCCTCCTACTCCA 61.072 63.158 27.24 0.00 34.56 3.86
1619 6510 4.694760 TCTCAACACCATATCCATCCAG 57.305 45.455 0.00 0.00 0.00 3.86
1628 6543 3.008813 CCATATCCATCCAGACTTCCCAG 59.991 52.174 0.00 0.00 0.00 4.45
1634 6549 1.434188 TCCAGACTTCCCAGCAAGAA 58.566 50.000 0.00 0.00 0.00 2.52
1636 6551 2.376518 TCCAGACTTCCCAGCAAGAATT 59.623 45.455 0.00 0.00 0.00 2.17
1851 6772 4.767409 GGCCTTGGTATTCTCTTTCTGTTT 59.233 41.667 0.00 0.00 0.00 2.83
1886 6809 2.103263 AGTTATGGAAGATGGAGACCGC 59.897 50.000 0.00 0.00 0.00 5.68
1944 6873 2.731976 CGTTGAACTGGACAAGCTACTC 59.268 50.000 0.00 0.00 0.00 2.59
1952 6881 1.616628 ACAAGCTACTCCCCCTGGG 60.617 63.158 5.50 5.50 46.11 4.45
1994 7034 2.562298 CAGAAGAGGAGTGCTCAGAAGT 59.438 50.000 14.66 0.00 0.00 3.01
2007 7047 4.160439 TGCTCAGAAGTGGAAGATAACGAT 59.840 41.667 0.00 0.00 0.00 3.73
2254 7339 8.830580 TGATCGAATTCTATTTTCACATCCTTC 58.169 33.333 3.52 0.00 0.00 3.46
2258 7343 4.487714 TCTATTTTCACATCCTTCCGCT 57.512 40.909 0.00 0.00 0.00 5.52
2384 7479 4.382291 TGTGTGGTGGTGTTCTATGTAAC 58.618 43.478 0.00 0.00 0.00 2.50
2399 7494 8.885722 GTTCTATGTAACGGTTATGATTTGGAA 58.114 33.333 3.59 1.52 0.00 3.53
2433 7530 1.825474 GTGGTAGCTAGCCAGTTCTGA 59.175 52.381 19.78 0.00 36.57 3.27
2457 7554 8.602424 TGATTTTCTGGAGAGGTGATTTTACTA 58.398 33.333 0.00 0.00 0.00 1.82
2548 7653 9.771915 AAAATGTAGCAATGTTTTTCTTTGTTG 57.228 25.926 0.00 0.00 34.83 3.33
2569 7863 9.817809 TTGTTGTTCTCATACTCTATTATGGAC 57.182 33.333 0.00 0.00 31.33 4.02
2647 7950 8.733458 TCATCCTAGAATGAAACAATGACAAAG 58.267 33.333 0.00 0.00 32.80 2.77
2750 8055 8.573885 ACGTTAGTATTAATGCATAGCTACAGA 58.426 33.333 0.00 0.00 30.38 3.41
2807 8148 6.801539 TGGAAATTGAGACAACTACATGAC 57.198 37.500 0.00 0.00 0.00 3.06
2851 8194 7.429633 CAAGTGAGATGTCGAATAGGTAGATT 58.570 38.462 0.00 0.00 0.00 2.40
2906 8250 8.642908 TCAATATTGTTATCACTGGTCTTACG 57.357 34.615 14.97 0.00 0.00 3.18
3117 9452 3.071580 GCATGGAGCGAGCTTAAGT 57.928 52.632 4.02 0.00 0.00 2.24
3267 9608 9.737427 GATGGGTATATGTTTATCTACTCATCG 57.263 37.037 8.82 0.00 40.75 3.84
3269 9610 8.737175 TGGGTATATGTTTATCTACTCATCGTC 58.263 37.037 0.00 0.00 25.63 4.20
3366 9759 8.047911 TCCCCTCGTATCTACTTAATCTGATAG 58.952 40.741 0.00 0.00 0.00 2.08
3594 9990 6.758416 GCACAATGAAATATTCCCCTTTCTTC 59.242 38.462 0.00 0.00 33.50 2.87
3702 10100 3.572255 TGTGATTTTAAGTTGTCCCCTGC 59.428 43.478 0.00 0.00 0.00 4.85
3741 10140 3.511146 CCCAACAATACTGAGCATTTGGT 59.489 43.478 0.00 0.00 0.00 3.67
3976 10818 9.832445 TTCAAAATATTGACTACATACTCCCTC 57.168 33.333 0.00 0.00 45.01 4.30
3977 10819 8.429641 TCAAAATATTGACTACATACTCCCTCC 58.570 37.037 0.00 0.00 40.59 4.30
3978 10820 6.591750 AATATTGACTACATACTCCCTCCG 57.408 41.667 0.00 0.00 0.00 4.63
3979 10821 3.377253 TTGACTACATACTCCCTCCGT 57.623 47.619 0.00 0.00 0.00 4.69
3980 10822 2.928334 TGACTACATACTCCCTCCGTC 58.072 52.381 0.00 0.00 0.00 4.79
3981 10823 2.228925 GACTACATACTCCCTCCGTCC 58.771 57.143 0.00 0.00 0.00 4.79
3982 10824 1.236628 CTACATACTCCCTCCGTCCG 58.763 60.000 0.00 0.00 0.00 4.79
3983 10825 0.179009 TACATACTCCCTCCGTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
3984 10826 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
3985 10827 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
3986 10828 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3987 10829 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
3988 10830 1.218316 CTCCCTCCGTCCGGAAAAG 59.782 63.158 5.23 3.59 44.66 2.27
3989 10831 2.436115 CCCTCCGTCCGGAAAAGC 60.436 66.667 5.23 0.00 44.66 3.51
3990 10832 2.663196 CCTCCGTCCGGAAAAGCT 59.337 61.111 5.23 0.00 44.66 3.74
3991 10833 1.003718 CCTCCGTCCGGAAAAGCTT 60.004 57.895 5.23 0.00 44.66 3.74
3992 10834 1.298859 CCTCCGTCCGGAAAAGCTTG 61.299 60.000 5.23 0.00 44.66 4.01
3993 10835 0.602905 CTCCGTCCGGAAAAGCTTGT 60.603 55.000 5.23 0.00 44.66 3.16
3994 10836 0.601841 TCCGTCCGGAAAAGCTTGTC 60.602 55.000 5.23 8.23 42.05 3.18
3995 10837 1.574702 CCGTCCGGAAAAGCTTGTCC 61.575 60.000 24.00 24.00 37.50 4.02
3996 10838 1.574702 CGTCCGGAAAAGCTTGTCCC 61.575 60.000 26.94 13.97 0.00 4.46
3997 10839 0.250770 GTCCGGAAAAGCTTGTCCCT 60.251 55.000 26.94 0.00 0.00 4.20
3998 10840 0.036306 TCCGGAAAAGCTTGTCCCTC 59.964 55.000 26.94 5.77 0.00 4.30
3999 10841 0.250727 CCGGAAAAGCTTGTCCCTCA 60.251 55.000 26.94 0.00 0.00 3.86
4000 10842 1.604604 CGGAAAAGCTTGTCCCTCAA 58.395 50.000 26.94 0.00 34.61 3.02
4001 10843 1.953686 CGGAAAAGCTTGTCCCTCAAA 59.046 47.619 26.94 0.00 35.48 2.69
4002 10844 2.558359 CGGAAAAGCTTGTCCCTCAAAT 59.442 45.455 26.94 0.00 35.48 2.32
4003 10845 3.612479 CGGAAAAGCTTGTCCCTCAAATG 60.612 47.826 26.94 9.69 35.48 2.32
4004 10846 3.306294 GGAAAAGCTTGTCCCTCAAATGG 60.306 47.826 23.49 0.00 35.48 3.16
4005 10847 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
4006 10848 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
4007 10849 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
4008 10850 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
4009 10851 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
4010 10852 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
4011 10853 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
4012 10854 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
4013 10855 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
4014 10856 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
4015 10857 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
4016 10858 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
4017 10859 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
4018 10860 4.999950 CCTCAAATGGATGTATCTAGCACC 59.000 45.833 0.00 0.00 0.00 5.01
4019 10861 5.455183 CCTCAAATGGATGTATCTAGCACCA 60.455 44.000 0.00 0.00 0.00 4.17
4020 10862 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
4021 10863 6.057533 TCAAATGGATGTATCTAGCACCAAG 58.942 40.000 0.00 0.00 0.00 3.61
4022 10864 5.636903 AATGGATGTATCTAGCACCAAGT 57.363 39.130 0.00 0.00 0.00 3.16
4023 10865 5.636903 ATGGATGTATCTAGCACCAAGTT 57.363 39.130 0.00 0.00 0.00 2.66
4024 10866 6.747414 ATGGATGTATCTAGCACCAAGTTA 57.253 37.500 0.00 0.00 0.00 2.24
4025 10867 6.161855 TGGATGTATCTAGCACCAAGTTAG 57.838 41.667 0.00 0.00 32.79 2.34
4026 10868 5.661312 TGGATGTATCTAGCACCAAGTTAGT 59.339 40.000 0.00 0.00 33.25 2.24
4027 10869 5.986135 GGATGTATCTAGCACCAAGTTAGTG 59.014 44.000 0.00 0.00 38.30 2.74
4039 10881 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
4040 10882 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
4041 10883 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
4042 10884 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
4043 10885 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
4044 10886 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
4045 10887 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
4046 10888 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
4047 10889 6.737720 AGTGCTAGATACATCCATTTGAGA 57.262 37.500 0.00 0.00 0.00 3.27
4048 10890 6.757237 AGTGCTAGATACATCCATTTGAGAG 58.243 40.000 0.00 0.00 0.00 3.20
4049 10891 6.552725 AGTGCTAGATACATCCATTTGAGAGA 59.447 38.462 0.00 0.00 0.00 3.10
4050 10892 6.644592 GTGCTAGATACATCCATTTGAGAGAC 59.355 42.308 0.00 0.00 0.00 3.36
4051 10893 6.324770 TGCTAGATACATCCATTTGAGAGACA 59.675 38.462 0.00 0.00 0.00 3.41
4052 10894 7.147672 TGCTAGATACATCCATTTGAGAGACAA 60.148 37.037 0.00 0.00 36.65 3.18
4053 10895 7.384660 GCTAGATACATCCATTTGAGAGACAAG 59.615 40.741 0.00 0.00 39.77 3.16
4054 10896 6.054295 AGATACATCCATTTGAGAGACAAGC 58.946 40.000 0.00 0.00 39.77 4.01
4055 10897 4.298103 ACATCCATTTGAGAGACAAGCT 57.702 40.909 0.00 0.00 39.77 3.74
4056 10898 4.660168 ACATCCATTTGAGAGACAAGCTT 58.340 39.130 0.00 0.00 39.77 3.74
4057 10899 5.075493 ACATCCATTTGAGAGACAAGCTTT 58.925 37.500 0.00 0.00 39.77 3.51
4058 10900 5.537674 ACATCCATTTGAGAGACAAGCTTTT 59.462 36.000 0.00 0.00 39.77 2.27
4059 10901 6.041296 ACATCCATTTGAGAGACAAGCTTTTT 59.959 34.615 0.00 0.00 39.77 1.94
4060 10902 6.076981 TCCATTTGAGAGACAAGCTTTTTC 57.923 37.500 0.00 0.00 39.77 2.29
4061 10903 4.913924 CCATTTGAGAGACAAGCTTTTTCG 59.086 41.667 0.00 0.00 39.77 3.46
4062 10904 4.552166 TTTGAGAGACAAGCTTTTTCGG 57.448 40.909 0.00 0.00 39.77 4.30
4063 10905 3.469008 TGAGAGACAAGCTTTTTCGGA 57.531 42.857 0.00 0.00 0.00 4.55
4064 10906 3.131396 TGAGAGACAAGCTTTTTCGGAC 58.869 45.455 0.00 0.00 0.00 4.79
4065 10907 2.135933 AGAGACAAGCTTTTTCGGACG 58.864 47.619 0.00 0.00 0.00 4.79
4066 10908 1.194772 GAGACAAGCTTTTTCGGACGG 59.805 52.381 0.00 0.00 0.00 4.79
4067 10909 1.202604 AGACAAGCTTTTTCGGACGGA 60.203 47.619 0.00 0.00 0.00 4.69
4068 10910 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
4069 10911 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
4070 10912 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
4071 10913 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
4072 10914 1.019805 GCTTTTTCGGACGGAGGGAG 61.020 60.000 0.00 0.00 0.00 4.30
4073 10915 0.320697 CTTTTTCGGACGGAGGGAGT 59.679 55.000 0.00 0.00 0.00 3.85
4074 10916 1.547372 CTTTTTCGGACGGAGGGAGTA 59.453 52.381 0.00 0.00 0.00 2.59
4075 10917 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
4200 11042 7.116662 TGAGATTGAAAGCATGCAAAACATTAC 59.883 33.333 21.98 5.49 36.64 1.89
4270 11112 8.918202 AATATTCTCACTGTAGTTTTTCACCA 57.082 30.769 0.00 0.00 0.00 4.17
4469 11313 4.731313 AACCTCTTCCAAGATTCACCTT 57.269 40.909 0.00 0.00 33.93 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.449423 ACCCAAGTTAGATATATATGGCTTGA 57.551 34.615 18.82 0.00 35.47 3.02
8 9 9.614792 CCTTAACCCAAGTTAGATATATATGGC 57.385 37.037 0.00 0.00 39.58 4.40
50 51 7.394359 AGTGTCACATGCTACCATTTTATTTCT 59.606 33.333 5.62 0.00 0.00 2.52
216 217 2.494870 AGAAAAGATGTGGATGGCTTGC 59.505 45.455 0.00 0.00 0.00 4.01
423 428 3.340928 TGAAGGACATGAAGAGCACATG 58.659 45.455 0.00 0.00 46.96 3.21
435 440 4.942761 AACAAACTTGCATGAAGGACAT 57.057 36.364 6.60 0.00 40.17 3.06
548 997 2.224305 GGCATAGCGACCCTAACTTCAT 60.224 50.000 0.00 0.00 0.00 2.57
585 1034 1.813513 CCCCTAATGTGATCGCCATC 58.186 55.000 3.31 0.00 0.00 3.51
597 1047 2.031870 GAAAATTCAGCCGCCCCTAAT 58.968 47.619 0.00 0.00 0.00 1.73
602 1052 0.603065 ACAAGAAAATTCAGCCGCCC 59.397 50.000 0.00 0.00 0.00 6.13
732 1189 9.030301 CACAGAACCAACAAAAATAGTAAAAGG 57.970 33.333 0.00 0.00 0.00 3.11
768 1228 8.721019 AAGAGAGATTGATTTTCAGAAGCTAG 57.279 34.615 0.00 0.00 0.00 3.42
804 1264 9.059260 CCCTTTTGATTGATTTTCACAATTTCT 57.941 29.630 0.00 0.00 37.96 2.52
805 1265 7.804600 GCCCTTTTGATTGATTTTCACAATTTC 59.195 33.333 0.00 0.00 37.96 2.17
806 1266 7.284944 TGCCCTTTTGATTGATTTTCACAATTT 59.715 29.630 0.00 0.00 37.96 1.82
807 1267 6.771749 TGCCCTTTTGATTGATTTTCACAATT 59.228 30.769 0.00 0.00 37.96 2.32
808 1268 6.297582 TGCCCTTTTGATTGATTTTCACAAT 58.702 32.000 0.00 0.00 40.08 2.71
809 1269 5.678583 TGCCCTTTTGATTGATTTTCACAA 58.321 33.333 0.00 0.00 0.00 3.33
810 1270 5.287674 TGCCCTTTTGATTGATTTTCACA 57.712 34.783 0.00 0.00 0.00 3.58
811 1271 6.616774 TTTGCCCTTTTGATTGATTTTCAC 57.383 33.333 0.00 0.00 0.00 3.18
812 1272 7.636150 TTTTTGCCCTTTTGATTGATTTTCA 57.364 28.000 0.00 0.00 0.00 2.69
902 1386 3.020274 TGTCAATCCGGAGAGAGAAGAG 58.980 50.000 11.34 0.00 0.00 2.85
903 1387 3.087370 TGTCAATCCGGAGAGAGAAGA 57.913 47.619 11.34 0.00 0.00 2.87
919 1407 4.442706 GAGTGACACTCCTTTCTTTGTCA 58.557 43.478 22.77 0.00 44.68 3.58
946 1434 4.591399 AGCAGCAGCAGCCCACAA 62.591 61.111 6.10 0.00 45.49 3.33
947 1435 4.591399 AAGCAGCAGCAGCCCACA 62.591 61.111 6.10 0.00 45.49 4.17
948 1436 3.745803 GAAGCAGCAGCAGCCCAC 61.746 66.667 6.10 0.00 45.49 4.61
951 1439 3.797546 GTCGAAGCAGCAGCAGCC 61.798 66.667 6.10 0.00 45.49 4.85
952 1440 3.797546 GGTCGAAGCAGCAGCAGC 61.798 66.667 3.17 0.46 45.49 5.25
953 1441 3.123620 GGGTCGAAGCAGCAGCAG 61.124 66.667 3.17 0.00 45.49 4.24
962 1455 2.663196 GAGGTGGTGGGGTCGAAG 59.337 66.667 0.00 0.00 0.00 3.79
1354 5024 0.107831 TTCCCTGTTCCGTGGAAGTG 59.892 55.000 0.53 0.00 33.33 3.16
1355 5025 0.108019 GTTCCCTGTTCCGTGGAAGT 59.892 55.000 0.53 0.00 38.77 3.01
1619 6510 4.096984 CCATACAATTCTTGCTGGGAAGTC 59.903 45.833 2.09 0.00 34.71 3.01
1628 6543 5.358160 AGAGTAAAGCCCATACAATTCTTGC 59.642 40.000 0.00 0.00 0.00 4.01
1634 6549 5.045578 ACACTCAGAGTAAAGCCCATACAAT 60.046 40.000 1.67 0.00 0.00 2.71
1636 6551 3.838317 ACACTCAGAGTAAAGCCCATACA 59.162 43.478 1.67 0.00 0.00 2.29
1851 6772 2.948979 CCATAACTGGGCGCTGAATTTA 59.051 45.455 14.63 3.54 39.04 1.40
1952 6881 6.177610 TCTGAGTTCTCTTCCTCTTCTAGAC 58.822 44.000 0.00 0.00 0.00 2.59
1994 7034 5.130350 GGAATGGGAAATCGTTATCTTCCA 58.870 41.667 2.74 0.00 40.42 3.53
2007 7047 4.079443 CCTTGTATACCTGGGAATGGGAAA 60.079 45.833 0.00 0.00 0.00 3.13
2232 7317 6.422223 CGGAAGGATGTGAAAATAGAATTCG 58.578 40.000 0.00 0.00 0.00 3.34
2237 7322 4.162320 AGAGCGGAAGGATGTGAAAATAGA 59.838 41.667 0.00 0.00 0.00 1.98
2399 7494 7.423199 GCTAGCTACCACTAAAAGTTGTTTTT 58.577 34.615 7.70 0.00 41.68 1.94
2457 7554 9.901172 AACTAAGGGAACTAAAAATCACGATAT 57.099 29.630 0.00 0.00 42.68 1.63
2569 7863 7.770433 TCACACCTCTGATTCAAACCATATAAG 59.230 37.037 0.00 0.00 0.00 1.73
2725 8030 8.965986 TCTGTAGCTATGCATTAATACTAACG 57.034 34.615 3.54 0.00 0.00 3.18
2823 8166 4.115516 CCTATTCGACATCTCACTTGGTG 58.884 47.826 0.00 0.00 34.45 4.17
2851 8194 5.709631 TGAAAGCTTCATAATGTGCCAACTA 59.290 36.000 0.00 0.00 34.08 2.24
3067 9382 9.507280 CGGATAAAATAAAATATAGCCATGCTG 57.493 33.333 0.00 0.00 40.10 4.41
3117 9452 8.337739 TGAAGGGGCAAGTTACCTAAAATTATA 58.662 33.333 0.00 0.00 33.37 0.98
3324 9667 5.105752 CGAGGGGAAATCGATGAGATATTC 58.894 45.833 0.00 0.00 42.76 1.75
3366 9759 6.591834 CAGCTATGCACTAATAGTACCATTCC 59.408 42.308 9.85 4.19 33.42 3.01
3584 9980 3.424703 TCAATGAAGCAGAAGAAAGGGG 58.575 45.455 0.00 0.00 0.00 4.79
3702 10100 4.236935 GTTGGGCATCAATTACTTGTGTG 58.763 43.478 0.00 0.00 37.73 3.82
3758 10158 7.057894 TGGCAATTTATATAGGTCCGAGTTTT 58.942 34.615 0.00 0.00 0.00 2.43
3767 10167 9.985730 CAATGTGAAATGGCAATTTATATAGGT 57.014 29.630 0.00 0.00 36.10 3.08
3858 10540 6.867662 AGAGTTACTGAAAACAACCAGATG 57.132 37.500 0.00 0.00 34.65 2.90
3971 10813 2.951101 GCTTTTCCGGACGGAGGGA 61.951 63.158 13.64 1.83 46.06 4.20
3972 10814 2.436115 GCTTTTCCGGACGGAGGG 60.436 66.667 13.64 8.97 46.06 4.30
3973 10815 1.003718 AAGCTTTTCCGGACGGAGG 60.004 57.895 13.64 9.30 46.06 4.30
3974 10816 0.602905 ACAAGCTTTTCCGGACGGAG 60.603 55.000 13.64 3.27 46.06 4.63
3975 10817 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69
3976 10818 1.574702 GGACAAGCTTTTCCGGACGG 61.575 60.000 15.65 3.96 0.00 4.79
3977 10819 1.574702 GGGACAAGCTTTTCCGGACG 61.575 60.000 22.30 0.00 32.00 4.79
3978 10820 0.250770 AGGGACAAGCTTTTCCGGAC 60.251 55.000 22.30 11.02 32.00 4.79
3979 10821 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.000 22.30 0.00 32.00 5.14
3980 10822 0.250727 TGAGGGACAAGCTTTTCCGG 60.251 55.000 22.30 0.00 32.00 5.14
3981 10823 1.604604 TTGAGGGACAAGCTTTTCCG 58.395 50.000 22.30 2.85 34.20 4.30
3982 10824 3.306294 CCATTTGAGGGACAAGCTTTTCC 60.306 47.826 21.34 21.34 39.77 3.13
3983 10825 3.573967 TCCATTTGAGGGACAAGCTTTTC 59.426 43.478 3.91 3.91 39.77 2.29
3984 10826 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
3985 10827 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
3986 10828 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
3987 10829 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
3988 10830 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
3989 10831 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
3990 10832 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
3991 10833 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
3992 10834 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
3993 10835 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
3994 10836 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
3995 10837 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
3996 10838 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
3997 10839 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
3998 10840 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
3999 10841 6.006275 ACTTGGTGCTAGATACATCCATTT 57.994 37.500 0.00 0.00 0.00 2.32
4000 10842 5.636903 ACTTGGTGCTAGATACATCCATT 57.363 39.130 0.00 0.00 0.00 3.16
4001 10843 5.636903 AACTTGGTGCTAGATACATCCAT 57.363 39.130 0.00 0.00 0.00 3.41
4002 10844 5.661312 ACTAACTTGGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
4003 10845 5.986135 CACTAACTTGGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
4015 10857 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
4016 10858 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
4017 10859 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
4018 10860 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
4019 10861 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
4020 10862 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
4021 10863 8.144478 TCTCAAATGGATGTATCTAGCACTAAC 58.856 37.037 0.00 0.00 0.00 2.34
4022 10864 8.250143 TCTCAAATGGATGTATCTAGCACTAA 57.750 34.615 0.00 0.00 0.00 2.24
4023 10865 7.725844 TCTCTCAAATGGATGTATCTAGCACTA 59.274 37.037 0.00 0.00 0.00 2.74
4024 10866 6.552725 TCTCTCAAATGGATGTATCTAGCACT 59.447 38.462 0.00 0.00 0.00 4.40
4025 10867 6.644592 GTCTCTCAAATGGATGTATCTAGCAC 59.355 42.308 0.00 0.00 0.00 4.40
4026 10868 6.324770 TGTCTCTCAAATGGATGTATCTAGCA 59.675 38.462 0.00 0.00 0.00 3.49
4027 10869 6.753180 TGTCTCTCAAATGGATGTATCTAGC 58.247 40.000 0.00 0.00 0.00 3.42
4028 10870 7.384660 GCTTGTCTCTCAAATGGATGTATCTAG 59.615 40.741 0.00 0.00 35.48 2.43
4029 10871 7.070447 AGCTTGTCTCTCAAATGGATGTATCTA 59.930 37.037 0.00 0.00 35.48 1.98
4030 10872 6.054295 GCTTGTCTCTCAAATGGATGTATCT 58.946 40.000 0.00 0.00 35.48 1.98
4031 10873 6.054295 AGCTTGTCTCTCAAATGGATGTATC 58.946 40.000 0.00 0.00 35.48 2.24
4032 10874 5.999044 AGCTTGTCTCTCAAATGGATGTAT 58.001 37.500 0.00 0.00 35.48 2.29
4033 10875 5.426689 AGCTTGTCTCTCAAATGGATGTA 57.573 39.130 0.00 0.00 35.48 2.29
4034 10876 4.298103 AGCTTGTCTCTCAAATGGATGT 57.702 40.909 0.00 0.00 35.48 3.06
4035 10877 5.640189 AAAGCTTGTCTCTCAAATGGATG 57.360 39.130 0.00 0.00 35.48 3.51
4036 10878 6.569226 CGAAAAAGCTTGTCTCTCAAATGGAT 60.569 38.462 0.00 0.00 35.48 3.41
4037 10879 5.277974 CGAAAAAGCTTGTCTCTCAAATGGA 60.278 40.000 0.00 0.00 35.48 3.41
4038 10880 4.913924 CGAAAAAGCTTGTCTCTCAAATGG 59.086 41.667 0.00 0.00 35.48 3.16
4039 10881 4.913924 CCGAAAAAGCTTGTCTCTCAAATG 59.086 41.667 0.00 0.00 35.48 2.32
4040 10882 4.821805 TCCGAAAAAGCTTGTCTCTCAAAT 59.178 37.500 0.00 0.00 35.48 2.32
4041 10883 4.035208 GTCCGAAAAAGCTTGTCTCTCAAA 59.965 41.667 0.00 0.00 35.48 2.69
4042 10884 3.560068 GTCCGAAAAAGCTTGTCTCTCAA 59.440 43.478 0.00 0.00 34.61 3.02
4043 10885 3.131396 GTCCGAAAAAGCTTGTCTCTCA 58.869 45.455 0.00 0.00 0.00 3.27
4044 10886 2.155924 CGTCCGAAAAAGCTTGTCTCTC 59.844 50.000 0.00 0.00 0.00 3.20
4045 10887 2.135933 CGTCCGAAAAAGCTTGTCTCT 58.864 47.619 0.00 0.00 0.00 3.10
4046 10888 1.194772 CCGTCCGAAAAAGCTTGTCTC 59.805 52.381 0.00 0.00 0.00 3.36
4047 10889 1.202604 TCCGTCCGAAAAAGCTTGTCT 60.203 47.619 0.00 0.00 0.00 3.41
4048 10890 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
4049 10891 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
4050 10892 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
4051 10893 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
4052 10894 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
4053 10895 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
4054 10896 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
4055 10897 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
4056 10898 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
4057 10899 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
4058 10900 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
4059 10901 0.839277 TATGTACTCCCTCCGTCCGA 59.161 55.000 0.00 0.00 0.00 4.55
4060 10902 0.950116 GTATGTACTCCCTCCGTCCG 59.050 60.000 0.00 0.00 0.00 4.79
4061 10903 2.361643 AGTATGTACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
4062 10904 5.841957 TTTTAGTATGTACTCCCTCCGTC 57.158 43.478 0.00 0.00 37.73 4.79
4063 10905 5.895534 TCATTTTAGTATGTACTCCCTCCGT 59.104 40.000 0.00 0.00 37.73 4.69
4064 10906 6.040616 ACTCATTTTAGTATGTACTCCCTCCG 59.959 42.308 0.00 0.00 37.73 4.63
4065 10907 7.069578 TCACTCATTTTAGTATGTACTCCCTCC 59.930 40.741 0.00 0.00 37.73 4.30
4066 10908 8.008513 TCACTCATTTTAGTATGTACTCCCTC 57.991 38.462 0.00 0.00 37.73 4.30
4067 10909 7.973048 TCACTCATTTTAGTATGTACTCCCT 57.027 36.000 0.00 0.00 37.73 4.20
4068 10910 8.038944 TGTTCACTCATTTTAGTATGTACTCCC 58.961 37.037 0.00 0.00 37.73 4.30
4069 10911 8.997621 TGTTCACTCATTTTAGTATGTACTCC 57.002 34.615 0.00 0.00 37.73 3.85
4200 11042 9.749490 CAAAATTGTATTTGCAAGATTTAGCTG 57.251 29.630 0.00 0.00 33.90 4.24
4257 11099 8.403236 AGTTACAAACTGATGGTGAAAAACTAC 58.597 33.333 0.00 0.00 41.01 2.73
4469 11313 5.247110 GGAGAGAGCATAAGGGATGTATTCA 59.753 44.000 0.00 0.00 37.90 2.57


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

AutoCloner maintained by Alex Coulton.