Multiple sequence alignment - TraesCS3A01G310300

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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 TraesCS3A01G310300 chr3A 100.000 4417 0 0 939 5355 549332356 549336772 0.000000e+00 8157.0
1 TraesCS3A01G310300 chr3A 100.000 648 0 0 1 648 549331418 549332065 0.000000e+00 1197.0
2 TraesCS3A01G310300 chr3A 92.692 561 35 2 7 561 456383849 456383289 0.000000e+00 804.0
3 TraesCS3A01G310300 chr3A 83.333 594 54 15 3712 4289 576276834 576277398 1.720000e-139 507.0
4 TraesCS3A01G310300 chr3A 97.024 168 4 1 5030 5196 549341656 549341823 1.140000e-71 281.0
5 TraesCS3A01G310300 chr3A 96.341 164 6 0 5192 5355 549341860 549342023 2.460000e-68 270.0
6 TraesCS3A01G310300 chr3A 93.567 171 8 2 5029 5198 8633579 8633747 8.900000e-63 252.0
7 TraesCS3A01G310300 chr3A 89.634 164 13 2 5195 5355 30152140 30152302 7.030000e-49 206.0
8 TraesCS3A01G310300 chr3A 83.412 211 20 4 2608 2804 77717295 77717086 1.180000e-41 182.0
9 TraesCS3A01G310300 chr5B 97.017 2313 52 6 2000 4297 509672875 509675185 0.000000e+00 3873.0
10 TraesCS3A01G310300 chr5B 97.259 839 21 1 1046 1884 509672039 509672875 0.000000e+00 1421.0
11 TraesCS3A01G310300 chr5B 91.624 585 41 4 1 578 339092256 339091673 0.000000e+00 802.0
12 TraesCS3A01G310300 chr5B 87.642 615 45 5 56 648 3891729 3891124 0.000000e+00 686.0
13 TraesCS3A01G310300 chr3B 96.555 2293 72 4 939 3229 599816406 599814119 0.000000e+00 3790.0
14 TraesCS3A01G310300 chr3B 95.161 310 13 2 3989 4297 599814105 599813797 6.230000e-134 488.0
15 TraesCS3A01G310300 chr3B 91.102 236 14 3 3730 3959 573490603 573490837 4.030000e-81 313.0
16 TraesCS3A01G310300 chr3B 90.213 235 15 4 3794 4024 304244217 304243987 3.130000e-77 300.0
17 TraesCS3A01G310300 chr3D 96.060 1066 30 4 3249 4305 42347417 42348479 0.000000e+00 1725.0
18 TraesCS3A01G310300 chr3D 83.446 592 52 14 3716 4289 438050186 438050749 4.780000e-140 508.0
19 TraesCS3A01G310300 chr3D 91.667 168 11 2 5021 5187 29994489 29994654 4.170000e-56 230.0
20 TraesCS3A01G310300 chr3D 91.613 155 10 1 5195 5346 1054632 1054786 1.510000e-50 211.0
21 TraesCS3A01G310300 chr3D 94.805 77 4 0 4302 4378 42348580 42348656 2.620000e-23 121.0
22 TraesCS3A01G310300 chr2A 97.227 649 13 2 4386 5029 759962212 759961564 0.000000e+00 1094.0
23 TraesCS3A01G310300 chr2A 92.130 648 41 4 7 648 777249808 777250451 0.000000e+00 905.0
24 TraesCS3A01G310300 chr2A 87.593 669 56 6 7 648 619920277 619919609 0.000000e+00 750.0
25 TraesCS3A01G310300 chr2A 86.538 676 60 7 1 648 693416966 693417638 0.000000e+00 715.0
26 TraesCS3A01G310300 chr2A 94.083 169 7 2 5029 5196 755528984 755528818 2.480000e-63 254.0
27 TraesCS3A01G310300 chr2A 91.716 169 11 3 5189 5355 464938070 464938237 1.160000e-56 231.0
28 TraesCS3A01G310300 chr2A 92.169 166 10 3 5192 5355 464953550 464953714 1.160000e-56 231.0
29 TraesCS3A01G310300 chr2A 83.212 137 21 2 2673 2808 628693026 628692891 2.030000e-24 124.0
30 TraesCS3A01G310300 chr2A 78.109 201 25 12 2136 2326 207107658 207107849 5.670000e-20 110.0
31 TraesCS3A01G310300 chr4D 96.923 650 14 3 4386 5029 105378142 105378791 0.000000e+00 1085.0
32 TraesCS3A01G310300 chr4D 86.858 662 78 7 3015 3669 97931290 97930631 0.000000e+00 732.0
33 TraesCS3A01G310300 chr4D 92.308 273 20 1 3892 4163 97909942 97909670 2.340000e-103 387.0
34 TraesCS3A01G310300 chr4D 85.217 345 39 7 3956 4297 346197435 346197770 1.430000e-90 344.0
35 TraesCS3A01G310300 chr4D 84.713 314 30 9 1676 1986 435015002 435014704 1.130000e-76 298.0
36 TraesCS3A01G310300 chr2B 95.327 642 24 3 4393 5029 319359076 319358436 0.000000e+00 1014.0
37 TraesCS3A01G310300 chr2B 89.530 659 39 6 1 630 51894041 51894698 0.000000e+00 808.0
38 TraesCS3A01G310300 chr2B 85.922 689 53 21 1 648 11336249 11336934 0.000000e+00 695.0
39 TraesCS3A01G310300 chr2B 84.789 664 81 6 4386 5029 794313945 794314608 0.000000e+00 649.0
40 TraesCS3A01G310300 chr5A 91.259 675 26 13 1 648 568896649 568895981 0.000000e+00 889.0
41 TraesCS3A01G310300 chr5A 94.972 537 21 2 1 531 638077089 638076553 0.000000e+00 837.0
42 TraesCS3A01G310300 chr5A 88.640 669 48 7 7 648 565702029 565701362 0.000000e+00 789.0
43 TraesCS3A01G310300 chr5A 85.686 510 52 13 3812 4304 4129937 4129432 7.950000e-143 518.0
44 TraesCS3A01G310300 chr5A 94.611 167 7 1 5030 5196 679162535 679162371 1.910000e-64 257.0
45 TraesCS3A01G310300 chr7A 88.971 680 65 8 3016 3688 621322480 621321804 0.000000e+00 832.0
46 TraesCS3A01G310300 chr7A 89.598 423 37 4 3792 4209 621321768 621321348 1.020000e-146 531.0
47 TraesCS3A01G310300 chr7A 89.844 256 26 0 3016 3271 678001526 678001781 4.000000e-86 329.0
48 TraesCS3A01G310300 chr7A 82.111 341 34 15 4615 4929 47562825 47563164 3.180000e-67 267.0
49 TraesCS3A01G310300 chr7A 91.061 179 10 6 5018 5196 127868538 127868710 2.490000e-58 237.0
50 TraesCS3A01G310300 chr7A 91.304 69 6 0 4308 4376 621321311 621321243 1.590000e-15 95.3
51 TraesCS3A01G310300 chr6D 92.573 579 35 4 7 578 5673270 5672693 0.000000e+00 824.0
52 TraesCS3A01G310300 chr7D 91.980 586 39 5 1 578 162192216 162192801 0.000000e+00 815.0
53 TraesCS3A01G310300 chr7D 86.144 599 60 13 3726 4304 40697014 40696419 4.550000e-175 625.0
54 TraesCS3A01G310300 chr7D 84.553 492 41 12 939 1421 30298583 30298118 6.320000e-124 455.0
55 TraesCS3A01G310300 chr7D 94.048 168 9 1 5030 5196 115019464 115019297 2.480000e-63 254.0
56 TraesCS3A01G310300 chr5D 88.939 669 47 11 7 648 493682450 493681782 0.000000e+00 800.0
57 TraesCS3A01G310300 chr5D 94.410 161 9 0 5195 5355 415277959 415277799 1.150000e-61 248.0
58 TraesCS3A01G310300 chr5D 93.168 161 8 1 5195 5355 415291516 415291359 3.220000e-57 233.0
59 TraesCS3A01G310300 chr5D 90.062 161 15 1 5195 5355 504179643 504179484 1.950000e-49 207.0
60 TraesCS3A01G310300 chr5D 90.062 161 15 1 5195 5355 504185248 504185089 1.950000e-49 207.0
61 TraesCS3A01G310300 chr5D 82.979 188 20 11 5006 5188 313776593 313776773 5.550000e-35 159.0
62 TraesCS3A01G310300 chr4A 88.633 651 63 6 3016 3659 47137247 47137893 0.000000e+00 782.0
63 TraesCS3A01G310300 chr4A 87.740 677 53 12 1 648 685852105 685851430 0.000000e+00 763.0
64 TraesCS3A01G310300 chr4A 90.191 418 32 6 3797 4209 47138144 47138557 2.190000e-148 536.0
65 TraesCS3A01G310300 chr4A 88.889 72 8 0 4305 4376 47138591 47138662 7.390000e-14 89.8
66 TraesCS3A01G310300 chr6B 88.293 615 48 3 56 648 580246820 580246208 0.000000e+00 715.0
67 TraesCS3A01G310300 chr6B 80.106 377 50 19 2136 2496 72385341 72384974 1.910000e-64 257.0
68 TraesCS3A01G310300 chr6B 81.752 274 44 3 3016 3284 637398913 637399185 1.940000e-54 224.0
69 TraesCS3A01G310300 chr6B 93.407 91 6 0 2810 2900 72384627 72384537 9.360000e-28 135.0
70 TraesCS3A01G310300 chr6B 82.716 81 10 4 1203 1281 4467140 4467218 9.620000e-08 69.4
71 TraesCS3A01G310300 chr2D 85.090 664 79 6 4386 5029 636387812 636388475 0.000000e+00 660.0
72 TraesCS3A01G310300 chr2D 94.083 169 7 2 5029 5196 96788073 96787907 2.480000e-63 254.0
73 TraesCS3A01G310300 chr2D 82.938 211 21 5 2608 2804 37137456 37137665 5.510000e-40 176.0
74 TraesCS3A01G310300 chr2D 77.114 201 27 13 2136 2326 107760014 107760205 1.230000e-16 99.0
75 TraesCS3A01G310300 chr2D 94.737 57 3 0 5030 5086 638450565 638450509 7.390000e-14 89.8
76 TraesCS3A01G310300 chr6A 89.883 257 25 1 3016 3271 485779096 485778840 4.000000e-86 329.0
77 TraesCS3A01G310300 chr6A 79.381 388 59 16 2129 2504 39191762 39191384 2.480000e-63 254.0
78 TraesCS3A01G310300 chr6A 91.176 102 8 1 2810 2910 39190953 39190852 2.600000e-28 137.0
79 TraesCS3A01G310300 chr4B 84.615 312 30 9 1676 1984 535088456 535088160 1.460000e-75 294.0
80 TraesCS3A01G310300 chr4B 81.340 209 24 4 2610 2804 537204819 537205026 7.180000e-34 156.0
81 TraesCS3A01G310300 chr1D 94.643 168 7 2 5030 5196 47716496 47716662 5.320000e-65 259.0
82 TraesCS3A01G310300 chr1D 94.643 168 7 2 5030 5196 47721618 47721784 5.320000e-65 259.0
83 TraesCS3A01G310300 chrUn 94.048 168 9 1 5030 5196 259875680 259875847 2.480000e-63 254.0
84 TraesCS3A01G310300 chrUn 82.716 81 10 4 1203 1281 462448849 462448927 9.620000e-08 69.4
85 TraesCS3A01G310300 chr1A 74.359 351 76 14 2673 3012 44060883 44061230 2.600000e-28 137.0
86 TraesCS3A01G310300 chr7B 84.058 138 16 6 3095 3231 65341232 65341364 1.570000e-25 128.0
87 TraesCS3A01G310300 chr7B 79.213 178 16 9 2012 2188 62405104 62404947 2.640000e-18 104.0
88 TraesCS3A01G310300 chr7B 89.157 83 9 0 2012 2094 633919754 633919836 2.640000e-18 104.0
89 TraesCS3A01G310300 chr1B 88.095 84 9 1 2012 2094 122972549 122972466 1.230000e-16 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G310300 chr3A 549331418 549336772 5354 False 4677.000000 8157 100.000000 1 5355 2 chr3A.!!$F4 5354
1 TraesCS3A01G310300 chr3A 456383289 456383849 560 True 804.000000 804 92.692000 7 561 1 chr3A.!!$R2 554
2 TraesCS3A01G310300 chr3A 576276834 576277398 564 False 507.000000 507 83.333000 3712 4289 1 chr3A.!!$F3 577
3 TraesCS3A01G310300 chr5B 509672039 509675185 3146 False 2647.000000 3873 97.138000 1046 4297 2 chr5B.!!$F1 3251
4 TraesCS3A01G310300 chr5B 339091673 339092256 583 True 802.000000 802 91.624000 1 578 1 chr5B.!!$R2 577
5 TraesCS3A01G310300 chr5B 3891124 3891729 605 True 686.000000 686 87.642000 56 648 1 chr5B.!!$R1 592
6 TraesCS3A01G310300 chr3B 599813797 599816406 2609 True 2139.000000 3790 95.858000 939 4297 2 chr3B.!!$R2 3358
7 TraesCS3A01G310300 chr3D 42347417 42348656 1239 False 923.000000 1725 95.432500 3249 4378 2 chr3D.!!$F4 1129
8 TraesCS3A01G310300 chr3D 438050186 438050749 563 False 508.000000 508 83.446000 3716 4289 1 chr3D.!!$F3 573
9 TraesCS3A01G310300 chr2A 759961564 759962212 648 True 1094.000000 1094 97.227000 4386 5029 1 chr2A.!!$R4 643
10 TraesCS3A01G310300 chr2A 777249808 777250451 643 False 905.000000 905 92.130000 7 648 1 chr2A.!!$F5 641
11 TraesCS3A01G310300 chr2A 619919609 619920277 668 True 750.000000 750 87.593000 7 648 1 chr2A.!!$R1 641
12 TraesCS3A01G310300 chr2A 693416966 693417638 672 False 715.000000 715 86.538000 1 648 1 chr2A.!!$F4 647
13 TraesCS3A01G310300 chr4D 105378142 105378791 649 False 1085.000000 1085 96.923000 4386 5029 1 chr4D.!!$F1 643
14 TraesCS3A01G310300 chr4D 97930631 97931290 659 True 732.000000 732 86.858000 3015 3669 1 chr4D.!!$R2 654
15 TraesCS3A01G310300 chr2B 319358436 319359076 640 True 1014.000000 1014 95.327000 4393 5029 1 chr2B.!!$R1 636
16 TraesCS3A01G310300 chr2B 51894041 51894698 657 False 808.000000 808 89.530000 1 630 1 chr2B.!!$F2 629
17 TraesCS3A01G310300 chr2B 11336249 11336934 685 False 695.000000 695 85.922000 1 648 1 chr2B.!!$F1 647
18 TraesCS3A01G310300 chr2B 794313945 794314608 663 False 649.000000 649 84.789000 4386 5029 1 chr2B.!!$F3 643
19 TraesCS3A01G310300 chr5A 568895981 568896649 668 True 889.000000 889 91.259000 1 648 1 chr5A.!!$R3 647
20 TraesCS3A01G310300 chr5A 638076553 638077089 536 True 837.000000 837 94.972000 1 531 1 chr5A.!!$R4 530
21 TraesCS3A01G310300 chr5A 565701362 565702029 667 True 789.000000 789 88.640000 7 648 1 chr5A.!!$R2 641
22 TraesCS3A01G310300 chr5A 4129432 4129937 505 True 518.000000 518 85.686000 3812 4304 1 chr5A.!!$R1 492
23 TraesCS3A01G310300 chr7A 621321243 621322480 1237 True 486.100000 832 89.957667 3016 4376 3 chr7A.!!$R1 1360
24 TraesCS3A01G310300 chr6D 5672693 5673270 577 True 824.000000 824 92.573000 7 578 1 chr6D.!!$R1 571
25 TraesCS3A01G310300 chr7D 162192216 162192801 585 False 815.000000 815 91.980000 1 578 1 chr7D.!!$F1 577
26 TraesCS3A01G310300 chr7D 40696419 40697014 595 True 625.000000 625 86.144000 3726 4304 1 chr7D.!!$R2 578
27 TraesCS3A01G310300 chr5D 493681782 493682450 668 True 800.000000 800 88.939000 7 648 1 chr5D.!!$R3 641
28 TraesCS3A01G310300 chr4A 685851430 685852105 675 True 763.000000 763 87.740000 1 648 1 chr4A.!!$R1 647
29 TraesCS3A01G310300 chr4A 47137247 47138662 1415 False 469.266667 782 89.237667 3016 4376 3 chr4A.!!$F1 1360
30 TraesCS3A01G310300 chr6B 580246208 580246820 612 True 715.000000 715 88.293000 56 648 1 chr6B.!!$R1 592
31 TraesCS3A01G310300 chr2D 636387812 636388475 663 False 660.000000 660 85.090000 4386 5029 1 chr2D.!!$F3 643

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
962 1010 0.317103 CTACGTCGATCTGAAGCCCG 60.317 60.0 0.0 0.0 0.00 6.13 F
963 1011 2.332362 TACGTCGATCTGAAGCCCGC 62.332 60.0 0.0 0.0 0.00 6.13 F
2358 2413 0.535780 TGCTTCCAGTCACTTGCCTG 60.536 55.0 0.0 0.0 0.00 4.85 F
3001 3058 2.751806 CTCATTTTCTTCCACTCTGGCC 59.248 50.0 0.0 0.0 37.47 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1896 1.004610 CATGCTAATCTGAACCACGCG 60.005 52.381 3.53 3.53 0.00 6.01 R
2451 2506 2.266055 GGAGGCGAGTGAACCCTG 59.734 66.667 0.00 0.00 0.00 4.45 R
4250 4539 0.103026 CTAGCGTAGGAGCATGCACA 59.897 55.000 21.98 0.00 40.15 4.57 R
4986 5401 2.161855 GATGATGTGCAACCAGTGGAA 58.838 47.619 18.40 0.00 34.36 3.53 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
82 90 0.981183 ACATGGACCCGAGCAAGTTA 59.019 50.000 0.00 0.00 0.00 2.24
131 139 2.357034 CCGTCGAACCACCACCAG 60.357 66.667 0.00 0.00 0.00 4.00
324 334 0.320771 GACATCTTCAGTGTGGCCGT 60.321 55.000 0.00 0.00 0.00 5.68
409 419 0.536460 AAAACAGCGACCGGAACCAT 60.536 50.000 9.46 0.00 0.00 3.55
421 432 0.991920 GGAACCATCAGGAACAGGGA 59.008 55.000 0.00 0.00 38.69 4.20
962 1010 0.317103 CTACGTCGATCTGAAGCCCG 60.317 60.000 0.00 0.00 0.00 6.13
963 1011 2.332362 TACGTCGATCTGAAGCCCGC 62.332 60.000 0.00 0.00 0.00 6.13
964 1012 2.586357 GTCGATCTGAAGCCCGCC 60.586 66.667 0.00 0.00 0.00 6.13
965 1013 4.207281 TCGATCTGAAGCCCGCCG 62.207 66.667 0.00 0.00 0.00 6.46
1243 1291 3.070159 TCCATCGTCCATTCATTCCTCTC 59.930 47.826 0.00 0.00 0.00 3.20
1272 1320 4.376920 CGCACACATTCTAATTCGTTGTCA 60.377 41.667 0.00 0.00 0.00 3.58
1400 1448 3.921119 TTGTTGCATCATGTTCCTGAC 57.079 42.857 0.00 0.00 0.00 3.51
1418 1466 7.956328 TCCTGACATAGAGTTGTATACTTGT 57.044 36.000 4.17 0.00 37.17 3.16
1419 1467 9.470399 TTCCTGACATAGAGTTGTATACTTGTA 57.530 33.333 4.17 0.00 37.17 2.41
1480 1528 8.715191 TTTGTTTAATTGCTGTTTCATGAAGT 57.285 26.923 8.41 0.00 0.00 3.01
1495 1543 8.336806 GTTTCATGAAGTGATCTCAATCTGATC 58.663 37.037 8.41 0.00 40.34 2.92
1517 1565 6.353404 TCATGTATCTAATTGCCGTATCCA 57.647 37.500 0.00 0.00 0.00 3.41
1529 1577 5.398603 TGCCGTATCCATTTTGTTTGATT 57.601 34.783 0.00 0.00 0.00 2.57
1602 1650 3.228453 CAGCAAAGAGGGGAATATGCAT 58.772 45.455 3.79 3.79 36.30 3.96
1633 1681 5.749462 CCATCTCCTAATGTTTGGTTCTCT 58.251 41.667 0.00 0.00 0.00 3.10
1848 1896 6.012658 TGTTTAACTGATCATCCTTTGTGC 57.987 37.500 0.00 0.00 0.00 4.57
1942 1990 2.444700 ATCGGTGACACGACCCAACC 62.445 60.000 0.00 0.00 46.64 3.77
1966 2014 5.468072 CCATACCAAGCATCTTCACATCTAC 59.532 44.000 0.00 0.00 0.00 2.59
1974 2022 3.801114 TCTTCACATCTACCATGACCG 57.199 47.619 0.00 0.00 0.00 4.79
2018 2066 4.871933 TTCTTCCCTGAAGCAAAATTCC 57.128 40.909 0.00 0.00 39.29 3.01
2358 2413 0.535780 TGCTTCCAGTCACTTGCCTG 60.536 55.000 0.00 0.00 0.00 4.85
2428 2483 5.984233 TTCCTCATGTATACAAATCACGC 57.016 39.130 10.14 0.00 0.00 5.34
2451 2506 5.119125 GCTGTGGTTTGCACAAATATTCTTC 59.881 40.000 0.00 0.00 32.36 2.87
2495 2550 5.221362 TGTTCAACTCGTTGTCCAATCTAGA 60.221 40.000 9.38 0.00 41.16 2.43
2704 2759 6.601741 TTCTTGCAAGTTTTTATTTGCCAG 57.398 33.333 25.19 5.54 46.91 4.85
2869 2926 4.427438 GCATTTGCGTCAATTGATAAGC 57.573 40.909 12.12 16.99 29.53 3.09
3001 3058 2.751806 CTCATTTTCTTCCACTCTGGCC 59.248 50.000 0.00 0.00 37.47 5.36
3238 3295 6.531021 AGTTAAGCTAAGTTTCTTGTGGCTA 58.469 36.000 0.00 0.00 0.00 3.93
3288 3345 4.072131 AGTTGAACCATGACGCTTGTTAT 58.928 39.130 0.00 0.00 0.00 1.89
3297 3354 5.008019 CCATGACGCTTGTTATGCTAATCTT 59.992 40.000 0.00 0.00 38.05 2.40
4180 4469 9.429359 GTATAGTTGCATAGCTGATTCAGTTAT 57.571 33.333 15.06 15.06 38.16 1.89
4182 4471 7.959689 AGTTGCATAGCTGATTCAGTTATAG 57.040 36.000 18.95 14.85 36.11 1.31
4187 4476 8.300286 TGCATAGCTGATTCAGTTATAGTAGTC 58.700 37.037 18.95 8.11 36.11 2.59
4366 4759 2.046314 CACCGGACCGCCTCAAAT 60.046 61.111 9.46 0.00 0.00 2.32
4378 4771 3.386867 CTCAAATGACGCGCCCAGC 62.387 63.158 5.73 0.00 43.95 4.85
4379 4772 4.481112 CAAATGACGCGCCCAGCC 62.481 66.667 5.73 0.00 44.76 4.85
4504 4897 3.913548 TCACCACCAAACAATTCATCG 57.086 42.857 0.00 0.00 0.00 3.84
4572 4965 5.355350 GCTTGCCTACATCAACATTAGAACT 59.645 40.000 0.00 0.00 0.00 3.01
4986 5401 9.917887 ATCACTGGAATTCTCATTCTAATCTTT 57.082 29.630 5.23 0.00 39.17 2.52
5029 5444 3.445008 TCCTTGAGTATGAGCAGACCTT 58.555 45.455 0.00 0.00 0.00 3.50
5030 5445 3.196469 TCCTTGAGTATGAGCAGACCTTG 59.804 47.826 0.00 0.00 0.00 3.61
5031 5446 3.055530 CCTTGAGTATGAGCAGACCTTGT 60.056 47.826 0.00 0.00 0.00 3.16
5032 5447 4.564406 CCTTGAGTATGAGCAGACCTTGTT 60.564 45.833 0.00 0.00 0.00 2.83
5033 5448 5.337571 CCTTGAGTATGAGCAGACCTTGTTA 60.338 44.000 0.00 0.00 0.00 2.41
5034 5449 5.330455 TGAGTATGAGCAGACCTTGTTAG 57.670 43.478 0.00 0.00 0.00 2.34
5036 5451 4.353777 AGTATGAGCAGACCTTGTTAGGA 58.646 43.478 0.00 0.00 45.05 2.94
5037 5452 4.965532 AGTATGAGCAGACCTTGTTAGGAT 59.034 41.667 0.00 0.00 45.05 3.24
5038 5453 3.616956 TGAGCAGACCTTGTTAGGATG 57.383 47.619 0.00 0.00 45.05 3.51
5039 5454 3.173151 TGAGCAGACCTTGTTAGGATGA 58.827 45.455 0.00 0.00 45.05 2.92
5040 5455 3.776969 TGAGCAGACCTTGTTAGGATGAT 59.223 43.478 0.00 0.00 45.05 2.45
5041 5456 4.141846 TGAGCAGACCTTGTTAGGATGATC 60.142 45.833 0.00 5.56 45.05 2.92
5042 5457 4.036518 AGCAGACCTTGTTAGGATGATCT 58.963 43.478 0.00 0.00 45.05 2.75
5043 5458 4.100808 AGCAGACCTTGTTAGGATGATCTC 59.899 45.833 0.00 0.00 45.05 2.75
5044 5459 4.742138 GCAGACCTTGTTAGGATGATCTCC 60.742 50.000 0.00 0.00 45.05 3.71
5052 5467 3.369381 GGATGATCTCCACCGTGTG 57.631 57.895 0.00 0.00 44.26 3.82
5080 5495 3.331293 CCCACCGGGCCTTTAGAT 58.669 61.111 6.32 0.00 35.35 1.98
5081 5496 1.148498 CCCACCGGGCCTTTAGATC 59.852 63.158 6.32 0.00 35.35 2.75
5082 5497 1.148498 CCACCGGGCCTTTAGATCC 59.852 63.158 6.32 0.00 0.00 3.36
5083 5498 1.632018 CCACCGGGCCTTTAGATCCA 61.632 60.000 6.32 0.00 0.00 3.41
5084 5499 0.463833 CACCGGGCCTTTAGATCCAC 60.464 60.000 6.32 0.00 0.00 4.02
5085 5500 1.227556 CCGGGCCTTTAGATCCACG 60.228 63.158 0.84 0.00 0.00 4.94
5086 5501 1.227556 CGGGCCTTTAGATCCACGG 60.228 63.158 0.84 0.00 0.00 4.94
5087 5502 1.526225 GGGCCTTTAGATCCACGGC 60.526 63.158 0.84 2.17 39.98 5.68
5088 5503 4.142780 GCCTTTAGATCCACGGCC 57.857 61.111 0.00 0.00 34.75 6.13
5089 5504 1.527370 GCCTTTAGATCCACGGCCT 59.473 57.895 0.00 0.00 34.75 5.19
5090 5505 0.815615 GCCTTTAGATCCACGGCCTG 60.816 60.000 0.00 0.00 34.75 4.85
5091 5506 0.830648 CCTTTAGATCCACGGCCTGA 59.169 55.000 0.00 0.00 0.00 3.86
5092 5507 1.417890 CCTTTAGATCCACGGCCTGAT 59.582 52.381 0.00 0.00 0.00 2.90
5093 5508 2.548920 CCTTTAGATCCACGGCCTGATC 60.549 54.545 15.31 15.31 38.10 2.92
5094 5509 0.673985 TTAGATCCACGGCCTGATCG 59.326 55.000 16.46 0.20 41.76 3.69
5095 5510 1.179174 TAGATCCACGGCCTGATCGG 61.179 60.000 16.46 0.00 41.76 4.18
5096 5511 3.521529 GATCCACGGCCTGATCGGG 62.522 68.421 16.98 16.98 0.00 5.14
5104 5519 4.161295 CCTGATCGGGGCGCTCAA 62.161 66.667 10.74 0.00 31.82 3.02
5105 5520 2.892425 CTGATCGGGGCGCTCAAC 60.892 66.667 10.74 0.00 31.82 3.18
5106 5521 4.467084 TGATCGGGGCGCTCAACC 62.467 66.667 10.74 0.00 29.16 3.77
5113 5528 3.813596 GGCGCTCAACCCACTATG 58.186 61.111 7.64 0.00 0.00 2.23
5114 5529 1.819632 GGCGCTCAACCCACTATGG 60.820 63.158 7.64 0.00 37.25 2.74
5125 5540 3.087906 ACTATGGGTGACGGGCCC 61.088 66.667 13.57 13.57 46.26 5.80
5126 5541 3.873812 CTATGGGTGACGGGCCCC 61.874 72.222 18.66 2.97 45.49 5.80
5127 5542 4.424867 TATGGGTGACGGGCCCCT 62.425 66.667 18.66 3.90 45.49 4.79
5139 5554 3.958860 GCCCCTGTCACCTGCACT 61.959 66.667 0.00 0.00 0.00 4.40
5140 5555 2.592993 GCCCCTGTCACCTGCACTA 61.593 63.158 0.00 0.00 0.00 2.74
5141 5556 1.915078 GCCCCTGTCACCTGCACTAT 61.915 60.000 0.00 0.00 0.00 2.12
5142 5557 1.496060 CCCCTGTCACCTGCACTATA 58.504 55.000 0.00 0.00 0.00 1.31
5143 5558 2.050144 CCCCTGTCACCTGCACTATAT 58.950 52.381 0.00 0.00 0.00 0.86
5144 5559 3.239449 CCCCTGTCACCTGCACTATATA 58.761 50.000 0.00 0.00 0.00 0.86
5145 5560 3.840666 CCCCTGTCACCTGCACTATATAT 59.159 47.826 0.00 0.00 0.00 0.86
5146 5561 5.023452 CCCCTGTCACCTGCACTATATATA 58.977 45.833 0.00 0.00 0.00 0.86
5147 5562 5.483937 CCCCTGTCACCTGCACTATATATAA 59.516 44.000 0.00 0.00 0.00 0.98
5148 5563 6.013725 CCCCTGTCACCTGCACTATATATAAA 60.014 42.308 0.00 0.00 0.00 1.40
5149 5564 7.099764 CCCTGTCACCTGCACTATATATAAAG 58.900 42.308 0.00 0.00 0.00 1.85
5150 5565 7.039011 CCCTGTCACCTGCACTATATATAAAGA 60.039 40.741 0.00 0.00 0.00 2.52
5151 5566 8.031864 CCTGTCACCTGCACTATATATAAAGAG 58.968 40.741 0.00 0.00 0.00 2.85
5152 5567 7.896811 TGTCACCTGCACTATATATAAAGAGG 58.103 38.462 0.00 0.00 0.00 3.69
5153 5568 7.509318 TGTCACCTGCACTATATATAAAGAGGT 59.491 37.037 0.00 0.00 0.00 3.85
5154 5569 7.815068 GTCACCTGCACTATATATAAAGAGGTG 59.185 40.741 21.12 21.12 46.20 4.00
5155 5570 7.039011 TCACCTGCACTATATATAAAGAGGTGG 60.039 40.741 23.74 14.22 45.31 4.61
5156 5571 6.213600 ACCTGCACTATATATAAAGAGGTGGG 59.786 42.308 9.75 6.87 30.04 4.61
5157 5572 6.352222 CCTGCACTATATATAAAGAGGTGGGG 60.352 46.154 9.75 0.00 0.00 4.96
5158 5573 5.487488 TGCACTATATATAAAGAGGTGGGGG 59.513 44.000 9.75 0.00 0.00 5.40
5159 5574 5.629366 GCACTATATATAAAGAGGTGGGGGC 60.629 48.000 9.75 0.00 0.00 5.80
5160 5575 5.037598 ACTATATATAAAGAGGTGGGGGCC 58.962 45.833 0.00 0.00 0.00 5.80
5161 5576 1.064825 ATATAAAGAGGTGGGGGCCG 58.935 55.000 0.00 0.00 0.00 6.13
5162 5577 1.057851 TATAAAGAGGTGGGGGCCGG 61.058 60.000 0.00 0.00 0.00 6.13
5188 5603 2.218953 GGATTACGAGGTTCATCGCA 57.781 50.000 6.78 0.00 46.60 5.10
5189 5604 2.546778 GGATTACGAGGTTCATCGCAA 58.453 47.619 6.78 1.11 46.60 4.85
5190 5605 2.284417 GGATTACGAGGTTCATCGCAAC 59.716 50.000 6.78 0.00 46.60 4.17
5191 5606 1.342555 TTACGAGGTTCATCGCAACG 58.657 50.000 6.78 0.00 46.60 4.10
5192 5607 1.074319 TACGAGGTTCATCGCAACGC 61.074 55.000 6.78 0.00 46.60 4.84
5193 5608 2.785258 GAGGTTCATCGCAACGCC 59.215 61.111 0.00 0.00 0.00 5.68
5194 5609 3.083600 GAGGTTCATCGCAACGCCG 62.084 63.158 0.00 0.00 0.00 6.46
5195 5610 3.419759 GGTTCATCGCAACGCCGT 61.420 61.111 0.00 0.00 0.00 5.68
5196 5611 2.202171 GTTCATCGCAACGCCGTG 60.202 61.111 0.00 0.00 0.00 4.94
5197 5612 4.083600 TTCATCGCAACGCCGTGC 62.084 61.111 0.00 0.00 41.32 5.34
5199 5614 4.799473 CATCGCAACGCCGTGCTG 62.799 66.667 9.33 0.00 42.62 4.41
5202 5617 4.799473 CGCAACGCCGTGCTGATG 62.799 66.667 9.33 0.00 42.62 3.07
5203 5618 4.465512 GCAACGCCGTGCTGATGG 62.466 66.667 0.00 0.00 41.51 3.51
5204 5619 3.803082 CAACGCCGTGCTGATGGG 61.803 66.667 0.00 0.00 0.00 4.00
5205 5620 4.015406 AACGCCGTGCTGATGGGA 62.015 61.111 0.00 0.00 0.00 4.37
5206 5621 3.545124 AACGCCGTGCTGATGGGAA 62.545 57.895 0.00 0.00 0.00 3.97
5207 5622 3.197790 CGCCGTGCTGATGGGAAG 61.198 66.667 0.00 0.00 0.00 3.46
5208 5623 3.512516 GCCGTGCTGATGGGAAGC 61.513 66.667 0.00 0.00 41.22 3.86
5212 5627 2.046023 TGCTGATGGGAAGCACCG 60.046 61.111 0.00 0.00 45.50 4.94
5213 5628 3.512516 GCTGATGGGAAGCACCGC 61.513 66.667 0.00 0.00 40.52 5.68
5214 5629 2.825836 CTGATGGGAAGCACCGCC 60.826 66.667 0.00 0.00 40.11 6.13
5215 5630 3.626996 CTGATGGGAAGCACCGCCA 62.627 63.158 0.00 0.00 40.11 5.69
5216 5631 3.134127 GATGGGAAGCACCGCCAC 61.134 66.667 0.00 0.00 40.11 5.01
5217 5632 4.740822 ATGGGAAGCACCGCCACC 62.741 66.667 0.00 0.00 40.11 4.61
5221 5636 4.643387 GAAGCACCGCCACCACCT 62.643 66.667 0.00 0.00 0.00 4.00
5222 5637 4.643387 AAGCACCGCCACCACCTC 62.643 66.667 0.00 0.00 0.00 3.85
5230 5645 3.000819 CCACCACCTCGCCCACTA 61.001 66.667 0.00 0.00 0.00 2.74
5231 5646 2.264794 CACCACCTCGCCCACTAC 59.735 66.667 0.00 0.00 0.00 2.73
5232 5647 2.119832 ACCACCTCGCCCACTACT 59.880 61.111 0.00 0.00 0.00 2.57
5233 5648 1.982938 ACCACCTCGCCCACTACTC 60.983 63.158 0.00 0.00 0.00 2.59
5234 5649 1.682684 CCACCTCGCCCACTACTCT 60.683 63.158 0.00 0.00 0.00 3.24
5235 5650 1.668101 CCACCTCGCCCACTACTCTC 61.668 65.000 0.00 0.00 0.00 3.20
5236 5651 0.681564 CACCTCGCCCACTACTCTCT 60.682 60.000 0.00 0.00 0.00 3.10
5237 5652 0.681564 ACCTCGCCCACTACTCTCTG 60.682 60.000 0.00 0.00 0.00 3.35
5238 5653 1.435515 CTCGCCCACTACTCTCTGC 59.564 63.158 0.00 0.00 0.00 4.26
5239 5654 2.010582 CTCGCCCACTACTCTCTGCC 62.011 65.000 0.00 0.00 0.00 4.85
5240 5655 2.351244 CGCCCACTACTCTCTGCCA 61.351 63.158 0.00 0.00 0.00 4.92
5241 5656 1.680522 CGCCCACTACTCTCTGCCAT 61.681 60.000 0.00 0.00 0.00 4.40
5242 5657 0.105778 GCCCACTACTCTCTGCCATC 59.894 60.000 0.00 0.00 0.00 3.51
5243 5658 1.489481 CCCACTACTCTCTGCCATCA 58.511 55.000 0.00 0.00 0.00 3.07
5244 5659 1.137872 CCCACTACTCTCTGCCATCAC 59.862 57.143 0.00 0.00 0.00 3.06
5245 5660 2.106566 CCACTACTCTCTGCCATCACT 58.893 52.381 0.00 0.00 0.00 3.41
5246 5661 2.159128 CCACTACTCTCTGCCATCACTG 60.159 54.545 0.00 0.00 0.00 3.66
5247 5662 2.106566 ACTACTCTCTGCCATCACTGG 58.893 52.381 0.00 0.00 46.17 4.00
5255 5670 2.436646 CCATCACTGGCCACCGTC 60.437 66.667 0.00 0.00 35.23 4.79
5256 5671 2.347114 CATCACTGGCCACCGTCA 59.653 61.111 0.00 0.00 0.00 4.35
5257 5672 2.034879 CATCACTGGCCACCGTCAC 61.035 63.158 0.00 0.00 0.00 3.67
5258 5673 3.254024 ATCACTGGCCACCGTCACC 62.254 63.158 0.00 0.00 0.00 4.02
5259 5674 4.248842 CACTGGCCACCGTCACCA 62.249 66.667 0.00 0.00 0.00 4.17
5260 5675 3.249189 ACTGGCCACCGTCACCAT 61.249 61.111 0.00 0.00 31.79 3.55
5261 5676 2.747460 CTGGCCACCGTCACCATG 60.747 66.667 0.00 0.00 31.79 3.66
5262 5677 4.343323 TGGCCACCGTCACCATGG 62.343 66.667 11.19 11.19 36.51 3.66
5284 5699 4.135153 CACCGGTGGCTCCTCGAG 62.135 72.222 27.57 5.13 0.00 4.04
5293 5708 3.700109 CTCCTCGAGCCACAAGGA 58.300 61.111 6.99 0.00 37.61 3.36
5294 5709 1.975327 CTCCTCGAGCCACAAGGAA 59.025 57.895 6.99 0.00 38.69 3.36
5295 5710 0.321671 CTCCTCGAGCCACAAGGAAA 59.678 55.000 6.99 0.00 38.69 3.13
5296 5711 0.762418 TCCTCGAGCCACAAGGAAAA 59.238 50.000 6.99 0.00 36.27 2.29
5297 5712 1.160137 CCTCGAGCCACAAGGAAAAG 58.840 55.000 6.99 0.00 36.89 2.27
5298 5713 1.160137 CTCGAGCCACAAGGAAAAGG 58.840 55.000 0.00 0.00 36.89 3.11
5299 5714 0.472471 TCGAGCCACAAGGAAAAGGT 59.528 50.000 0.00 0.00 36.89 3.50
5300 5715 1.695242 TCGAGCCACAAGGAAAAGGTA 59.305 47.619 0.00 0.00 36.89 3.08
5301 5716 2.105134 TCGAGCCACAAGGAAAAGGTAA 59.895 45.455 0.00 0.00 36.89 2.85
5302 5717 3.081804 CGAGCCACAAGGAAAAGGTAAT 58.918 45.455 0.00 0.00 36.89 1.89
5303 5718 4.020039 TCGAGCCACAAGGAAAAGGTAATA 60.020 41.667 0.00 0.00 36.89 0.98
5304 5719 4.094442 CGAGCCACAAGGAAAAGGTAATAC 59.906 45.833 0.00 0.00 36.89 1.89
5305 5720 4.341487 AGCCACAAGGAAAAGGTAATACC 58.659 43.478 0.07 0.07 36.07 2.73
5306 5721 4.044191 AGCCACAAGGAAAAGGTAATACCT 59.956 41.667 6.06 6.06 44.84 3.08
5307 5722 5.252164 AGCCACAAGGAAAAGGTAATACCTA 59.748 40.000 13.03 0.00 42.87 3.08
5308 5723 6.069029 AGCCACAAGGAAAAGGTAATACCTAT 60.069 38.462 13.03 4.87 42.87 2.57
5309 5724 6.262496 GCCACAAGGAAAAGGTAATACCTATC 59.738 42.308 13.03 13.44 42.87 2.08
5310 5725 7.343357 CCACAAGGAAAAGGTAATACCTATCA 58.657 38.462 13.03 0.00 42.87 2.15
5311 5726 7.282450 CCACAAGGAAAAGGTAATACCTATCAC 59.718 40.741 13.03 8.43 42.87 3.06
5318 5733 4.004196 GGTAATACCTATCACCACTGCC 57.996 50.000 1.41 0.00 34.73 4.85
5319 5734 2.910688 AATACCTATCACCACTGCCG 57.089 50.000 0.00 0.00 0.00 5.69
5320 5735 1.048601 ATACCTATCACCACTGCCGG 58.951 55.000 0.00 0.00 0.00 6.13
5321 5736 0.032912 TACCTATCACCACTGCCGGA 60.033 55.000 5.05 0.00 0.00 5.14
5322 5737 0.907704 ACCTATCACCACTGCCGGAA 60.908 55.000 5.05 0.00 0.00 4.30
5323 5738 0.469917 CCTATCACCACTGCCGGAAT 59.530 55.000 5.05 0.00 0.00 3.01
5324 5739 1.541233 CCTATCACCACTGCCGGAATC 60.541 57.143 5.05 0.00 0.00 2.52
5325 5740 0.468226 TATCACCACTGCCGGAATCC 59.532 55.000 5.05 0.00 0.00 3.01
5326 5741 2.270874 ATCACCACTGCCGGAATCCC 62.271 60.000 5.05 0.00 0.00 3.85
5327 5742 3.728373 ACCACTGCCGGAATCCCC 61.728 66.667 5.05 0.00 0.00 4.81
5328 5743 3.727258 CCACTGCCGGAATCCCCA 61.727 66.667 5.05 0.00 34.14 4.96
5329 5744 2.597340 CACTGCCGGAATCCCCAT 59.403 61.111 5.05 0.00 34.14 4.00
5330 5745 1.825191 CACTGCCGGAATCCCCATG 60.825 63.158 5.05 0.00 34.14 3.66
5331 5746 2.908940 CTGCCGGAATCCCCATGC 60.909 66.667 5.05 0.00 34.05 4.06
5332 5747 4.521292 TGCCGGAATCCCCATGCC 62.521 66.667 5.05 0.00 32.87 4.40
5334 5749 3.819652 CCGGAATCCCCATGCCCA 61.820 66.667 0.00 0.00 34.14 5.36
5335 5750 2.519302 CGGAATCCCCATGCCCAC 60.519 66.667 0.00 0.00 34.14 4.61
5336 5751 3.018901 GGAATCCCCATGCCCACT 58.981 61.111 0.00 0.00 34.14 4.00
5337 5752 1.456331 GGAATCCCCATGCCCACTG 60.456 63.158 0.00 0.00 34.14 3.66
5338 5753 1.456331 GAATCCCCATGCCCACTGG 60.456 63.158 0.00 0.00 0.00 4.00
5339 5754 1.935400 AATCCCCATGCCCACTGGA 60.935 57.895 0.00 0.00 35.70 3.86
5340 5755 1.298906 AATCCCCATGCCCACTGGAT 61.299 55.000 0.00 0.00 37.42 3.41
5341 5756 1.723128 ATCCCCATGCCCACTGGATC 61.723 60.000 0.00 0.00 35.70 3.36
5342 5757 2.692824 CCCCATGCCCACTGGATCA 61.693 63.158 0.00 0.00 35.70 2.92
5343 5758 1.307309 CCCATGCCCACTGGATCAA 59.693 57.895 0.00 0.00 35.70 2.57
5344 5759 1.039233 CCCATGCCCACTGGATCAAC 61.039 60.000 0.00 0.00 35.70 3.18
5345 5760 0.323633 CCATGCCCACTGGATCAACA 60.324 55.000 0.00 0.00 35.70 3.33
5346 5761 1.100510 CATGCCCACTGGATCAACAG 58.899 55.000 0.00 0.00 44.03 3.16
5347 5762 0.994247 ATGCCCACTGGATCAACAGA 59.006 50.000 6.04 0.00 40.97 3.41
5348 5763 0.994247 TGCCCACTGGATCAACAGAT 59.006 50.000 6.04 0.00 40.97 2.90
5349 5764 1.355381 TGCCCACTGGATCAACAGATT 59.645 47.619 6.04 0.00 40.97 2.40
5350 5765 2.019984 GCCCACTGGATCAACAGATTC 58.980 52.381 6.04 0.00 40.97 2.52
5351 5766 2.356535 GCCCACTGGATCAACAGATTCT 60.357 50.000 6.04 0.00 40.97 2.40
5352 5767 3.118261 GCCCACTGGATCAACAGATTCTA 60.118 47.826 6.04 0.00 40.97 2.10
5353 5768 4.445448 GCCCACTGGATCAACAGATTCTAT 60.445 45.833 6.04 0.00 40.97 1.98
5354 5769 5.303971 CCCACTGGATCAACAGATTCTATC 58.696 45.833 6.04 0.00 40.97 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 90 3.099905 TGGTCTGATCTTCATCTTCGGT 58.900 45.455 0.00 0.00 0.00 4.69
131 139 1.968540 GCTCAAGTGGTGGTGGAGC 60.969 63.158 0.00 0.00 43.41 4.70
349 359 2.835895 GGTGGTTGGGTGCGGTTT 60.836 61.111 0.00 0.00 0.00 3.27
351 361 4.579384 CTGGTGGTTGGGTGCGGT 62.579 66.667 0.00 0.00 0.00 5.68
409 419 3.691342 CGCCGTCCCTGTTCCTGA 61.691 66.667 0.00 0.00 0.00 3.86
1082 1130 3.320541 GGATCTGATGAGTCGAGGACAAT 59.679 47.826 0.00 0.00 34.60 2.71
1243 1291 5.288712 ACGAATTAGAATGTGTGCGAGTTAG 59.711 40.000 0.00 0.00 0.00 2.34
1272 1320 5.021033 TGCAGAAAACACACATGGAAAAT 57.979 34.783 0.00 0.00 0.00 1.82
1418 1466 7.461043 ACAGGATAATTGAGCACCCCTAATATA 59.539 37.037 0.00 0.00 0.00 0.86
1419 1467 6.275618 ACAGGATAATTGAGCACCCCTAATAT 59.724 38.462 0.00 0.00 0.00 1.28
1495 1543 7.615582 AATGGATACGGCAATTAGATACATG 57.384 36.000 0.00 0.00 42.51 3.21
1500 1548 6.959639 ACAAAATGGATACGGCAATTAGAT 57.040 33.333 0.00 0.00 42.51 1.98
1517 1565 6.013466 ACCCTGCTTGGATAATCAAACAAAAT 60.013 34.615 0.00 0.00 38.35 1.82
1529 1577 3.719871 TCTCAAGTACCCTGCTTGGATA 58.280 45.455 5.39 0.00 42.44 2.59
1633 1681 8.715088 CGATGTATTATGATGCAGAAATTCAGA 58.285 33.333 0.00 0.00 31.23 3.27
1848 1896 1.004610 CATGCTAATCTGAACCACGCG 60.005 52.381 3.53 3.53 0.00 6.01
1942 1990 4.458397 AGATGTGAAGATGCTTGGTATGG 58.542 43.478 0.00 0.00 0.00 2.74
1966 2014 5.068723 GGGTATATATGTACCTCGGTCATGG 59.931 48.000 23.35 0.00 43.02 3.66
1974 2022 9.102453 AGAAAGGAAAGGGTATATATGTACCTC 57.898 37.037 23.35 15.13 43.02 3.85
2451 2506 2.266055 GGAGGCGAGTGAACCCTG 59.734 66.667 0.00 0.00 0.00 4.45
2495 2550 4.563337 TCGTTGTCGCTATTAGTGCTAT 57.437 40.909 0.00 0.00 36.96 2.97
2869 2926 6.631016 TGTTTACATGACTAAGTAGCTCTGG 58.369 40.000 0.00 0.00 0.00 3.86
3001 3058 3.469008 TTACAAGTAGATGGATGGGCG 57.531 47.619 0.00 0.00 0.00 6.13
3124 3181 7.600375 CGCTAGTACCAAAATATGATCTCATGT 59.400 37.037 2.92 0.00 37.15 3.21
3145 3202 3.179443 TCATGGTTTAGGCTTCGCTAG 57.821 47.619 0.00 0.00 0.00 3.42
3238 3295 6.153756 GCAACTACCAACATCCGTTTTATTT 58.846 36.000 0.00 0.00 31.13 1.40
3288 3345 9.093458 TGATAGTCCAGATCAATAAGATTAGCA 57.907 33.333 0.00 0.00 37.00 3.49
3297 3354 9.904198 TGTGATTTTTGATAGTCCAGATCAATA 57.096 29.630 0.00 0.00 41.66 1.90
3307 3364 4.943705 TGGCTCCTGTGATTTTTGATAGTC 59.056 41.667 0.00 0.00 0.00 2.59
3311 3368 5.750352 AAATGGCTCCTGTGATTTTTGAT 57.250 34.783 0.00 0.00 0.00 2.57
4090 4379 9.429359 CAGACCAACTTTCTTATATAGCATAGG 57.571 37.037 0.00 0.00 0.00 2.57
4180 4469 6.229936 ACAAACACTTGTTCTGGACTACTA 57.770 37.500 0.00 0.00 43.45 1.82
4182 4471 6.929606 AGATACAAACACTTGTTCTGGACTAC 59.070 38.462 0.00 0.00 43.45 2.73
4187 4476 8.553459 AAGATAGATACAAACACTTGTTCTGG 57.447 34.615 0.00 0.00 43.45 3.86
4250 4539 0.103026 CTAGCGTAGGAGCATGCACA 59.897 55.000 21.98 0.00 40.15 4.57
4297 4586 6.493458 AGGGCACTTATGTACAATTCTTGTTT 59.507 34.615 0.00 0.00 42.22 2.83
4306 4699 5.765576 TCCTTAAGGGCACTTATGTACAA 57.234 39.130 21.53 0.00 38.87 2.41
4378 4771 9.140286 CGGTTTGATATACATTCATACTAGTGG 57.860 37.037 5.39 0.00 0.00 4.00
4379 4772 9.908152 TCGGTTTGATATACATTCATACTAGTG 57.092 33.333 5.39 0.00 0.00 2.74
4383 4776 9.832445 AGTTTCGGTTTGATATACATTCATACT 57.168 29.630 0.00 0.00 0.00 2.12
4504 4897 4.246458 GTGGGTATGTGTCTTGTTCTCTC 58.754 47.826 0.00 0.00 0.00 3.20
4509 4902 2.708861 TCCTGTGGGTATGTGTCTTGTT 59.291 45.455 0.00 0.00 0.00 2.83
4602 4996 4.782019 TGGATATGTTGGCAAAAGTGTC 57.218 40.909 0.00 0.00 0.00 3.67
4843 5238 8.023021 ACATATTCTTGTTAGTGCTAGATGGA 57.977 34.615 0.00 0.00 0.00 3.41
4986 5401 2.161855 GATGATGTGCAACCAGTGGAA 58.838 47.619 18.40 0.00 34.36 3.53
5064 5479 1.148498 GGATCTAAAGGCCCGGTGG 59.852 63.158 0.00 0.00 0.00 4.61
5065 5480 0.463833 GTGGATCTAAAGGCCCGGTG 60.464 60.000 0.00 0.00 0.00 4.94
5066 5481 1.912971 GTGGATCTAAAGGCCCGGT 59.087 57.895 0.00 0.00 0.00 5.28
5067 5482 1.227556 CGTGGATCTAAAGGCCCGG 60.228 63.158 0.00 0.00 0.00 5.73
5068 5483 1.227556 CCGTGGATCTAAAGGCCCG 60.228 63.158 0.00 0.00 0.00 6.13
5069 5484 1.526225 GCCGTGGATCTAAAGGCCC 60.526 63.158 13.67 0.00 41.81 5.80
5070 5485 4.142780 GCCGTGGATCTAAAGGCC 57.857 61.111 13.67 0.00 41.81 5.19
5071 5486 0.815615 CAGGCCGTGGATCTAAAGGC 60.816 60.000 15.61 15.61 46.51 4.35
5072 5487 0.830648 TCAGGCCGTGGATCTAAAGG 59.169 55.000 0.00 0.00 0.00 3.11
5073 5488 2.760374 GATCAGGCCGTGGATCTAAAG 58.240 52.381 20.92 0.00 37.52 1.85
5074 5489 1.068588 CGATCAGGCCGTGGATCTAAA 59.931 52.381 23.60 0.00 38.18 1.85
5075 5490 0.673985 CGATCAGGCCGTGGATCTAA 59.326 55.000 23.60 0.00 38.18 2.10
5076 5491 1.179174 CCGATCAGGCCGTGGATCTA 61.179 60.000 23.60 0.00 38.18 1.98
5077 5492 2.502492 CCGATCAGGCCGTGGATCT 61.502 63.158 23.60 1.89 38.18 2.75
5078 5493 2.029666 CCGATCAGGCCGTGGATC 59.970 66.667 19.25 19.25 37.22 3.36
5079 5494 3.550431 CCCGATCAGGCCGTGGAT 61.550 66.667 7.24 7.24 39.21 3.41
5094 5509 3.043999 ATAGTGGGTTGAGCGCCCC 62.044 63.158 12.14 12.14 45.49 5.80
5095 5510 1.819632 CATAGTGGGTTGAGCGCCC 60.820 63.158 2.29 0.00 46.26 6.13
5096 5511 1.819632 CCATAGTGGGTTGAGCGCC 60.820 63.158 2.29 0.00 32.67 6.53
5097 5512 3.813596 CCATAGTGGGTTGAGCGC 58.186 61.111 0.00 0.00 32.67 5.92
5115 5530 4.699522 GTGACAGGGGCCCGTCAC 62.700 72.222 39.18 39.18 43.96 3.67
5122 5537 1.915078 ATAGTGCAGGTGACAGGGGC 61.915 60.000 0.00 0.00 0.00 5.80
5123 5538 1.496060 TATAGTGCAGGTGACAGGGG 58.504 55.000 0.00 0.00 0.00 4.79
5124 5539 6.605471 TTATATATAGTGCAGGTGACAGGG 57.395 41.667 0.00 0.00 0.00 4.45
5125 5540 7.896811 TCTTTATATATAGTGCAGGTGACAGG 58.103 38.462 0.00 0.00 0.00 4.00
5126 5541 8.031864 CCTCTTTATATATAGTGCAGGTGACAG 58.968 40.741 0.00 0.00 0.00 3.51
5127 5542 7.509318 ACCTCTTTATATATAGTGCAGGTGACA 59.491 37.037 9.75 0.00 30.35 3.58
5128 5543 7.897864 ACCTCTTTATATATAGTGCAGGTGAC 58.102 38.462 9.75 0.00 30.35 3.67
5130 5545 7.099764 CCACCTCTTTATATATAGTGCAGGTG 58.900 42.308 20.89 20.89 45.39 4.00
5131 5546 6.213600 CCCACCTCTTTATATATAGTGCAGGT 59.786 42.308 6.36 6.36 31.67 4.00
5132 5547 6.352222 CCCCACCTCTTTATATATAGTGCAGG 60.352 46.154 0.00 3.43 0.00 4.85
5133 5548 6.352222 CCCCCACCTCTTTATATATAGTGCAG 60.352 46.154 0.00 0.07 0.00 4.41
5134 5549 5.487488 CCCCCACCTCTTTATATATAGTGCA 59.513 44.000 4.35 0.00 0.00 4.57
5135 5550 5.629366 GCCCCCACCTCTTTATATATAGTGC 60.629 48.000 4.35 0.00 0.00 4.40
5136 5551 5.104485 GGCCCCCACCTCTTTATATATAGTG 60.104 48.000 0.00 3.28 0.00 2.74
5137 5552 5.037598 GGCCCCCACCTCTTTATATATAGT 58.962 45.833 0.00 0.00 0.00 2.12
5138 5553 4.101119 CGGCCCCCACCTCTTTATATATAG 59.899 50.000 0.00 0.00 0.00 1.31
5139 5554 4.035112 CGGCCCCCACCTCTTTATATATA 58.965 47.826 0.00 0.00 0.00 0.86
5140 5555 2.844348 CGGCCCCCACCTCTTTATATAT 59.156 50.000 0.00 0.00 0.00 0.86
5141 5556 2.262637 CGGCCCCCACCTCTTTATATA 58.737 52.381 0.00 0.00 0.00 0.86
5142 5557 1.064825 CGGCCCCCACCTCTTTATAT 58.935 55.000 0.00 0.00 0.00 0.86
5143 5558 1.057851 CCGGCCCCCACCTCTTTATA 61.058 60.000 0.00 0.00 0.00 0.98
5144 5559 2.383601 CCGGCCCCCACCTCTTTAT 61.384 63.158 0.00 0.00 0.00 1.40
5145 5560 3.012722 CCGGCCCCCACCTCTTTA 61.013 66.667 0.00 0.00 0.00 1.85
5160 5575 4.260355 TCGTAATCCGAGCCGCCG 62.260 66.667 0.00 0.00 41.60 6.46
5167 5582 1.268896 GCGATGAACCTCGTAATCCGA 60.269 52.381 0.00 0.00 45.00 4.55
5168 5583 1.129326 GCGATGAACCTCGTAATCCG 58.871 55.000 0.00 0.00 40.73 4.18
5169 5584 2.218953 TGCGATGAACCTCGTAATCC 57.781 50.000 0.00 0.00 40.73 3.01
5170 5585 2.034842 CGTTGCGATGAACCTCGTAATC 60.035 50.000 6.36 1.84 43.35 1.75
5171 5586 1.924524 CGTTGCGATGAACCTCGTAAT 59.075 47.619 6.36 0.00 43.35 1.89
5172 5587 1.342555 CGTTGCGATGAACCTCGTAA 58.657 50.000 0.00 0.00 40.20 3.18
5173 5588 1.074319 GCGTTGCGATGAACCTCGTA 61.074 55.000 0.00 0.00 40.73 3.43
5174 5589 2.380410 GCGTTGCGATGAACCTCGT 61.380 57.895 0.00 0.00 40.73 4.18
5175 5590 2.395690 GCGTTGCGATGAACCTCG 59.604 61.111 0.00 0.00 41.54 4.63
5176 5591 2.785258 GGCGTTGCGATGAACCTC 59.215 61.111 0.00 0.00 0.00 3.85
5177 5592 3.118454 CGGCGTTGCGATGAACCT 61.118 61.111 0.00 0.00 0.00 3.50
5178 5593 3.419759 ACGGCGTTGCGATGAACC 61.420 61.111 6.77 0.00 0.00 3.62
5179 5594 2.202171 CACGGCGTTGCGATGAAC 60.202 61.111 11.19 0.00 0.00 3.18
5180 5595 4.083600 GCACGGCGTTGCGATGAA 62.084 61.111 11.19 0.00 31.51 2.57
5186 5601 4.465512 CCATCAGCACGGCGTTGC 62.466 66.667 21.23 21.23 43.34 4.17
5187 5602 3.803082 CCCATCAGCACGGCGTTG 61.803 66.667 11.19 7.77 0.00 4.10
5188 5603 3.545124 TTCCCATCAGCACGGCGTT 62.545 57.895 11.19 0.00 0.00 4.84
5189 5604 3.958147 CTTCCCATCAGCACGGCGT 62.958 63.158 6.77 6.77 0.00 5.68
5190 5605 3.197790 CTTCCCATCAGCACGGCG 61.198 66.667 4.80 4.80 0.00 6.46
5191 5606 3.512516 GCTTCCCATCAGCACGGC 61.513 66.667 0.00 0.00 37.22 5.68
5192 5607 2.046023 TGCTTCCCATCAGCACGG 60.046 61.111 0.00 0.00 42.49 4.94
5195 5610 2.046023 CGGTGCTTCCCATCAGCA 60.046 61.111 0.00 0.00 45.21 4.41
5196 5611 3.512516 GCGGTGCTTCCCATCAGC 61.513 66.667 0.00 0.00 37.82 4.26
5197 5612 2.825836 GGCGGTGCTTCCCATCAG 60.826 66.667 0.00 0.00 0.00 2.90
5198 5613 3.645660 TGGCGGTGCTTCCCATCA 61.646 61.111 0.00 0.00 0.00 3.07
5199 5614 3.134127 GTGGCGGTGCTTCCCATC 61.134 66.667 0.00 0.00 0.00 3.51
5200 5615 4.740822 GGTGGCGGTGCTTCCCAT 62.741 66.667 0.00 0.00 0.00 4.00
5204 5619 4.643387 AGGTGGTGGCGGTGCTTC 62.643 66.667 0.00 0.00 0.00 3.86
5205 5620 4.643387 GAGGTGGTGGCGGTGCTT 62.643 66.667 0.00 0.00 0.00 3.91
5213 5628 3.000819 TAGTGGGCGAGGTGGTGG 61.001 66.667 0.00 0.00 0.00 4.61
5214 5629 2.227089 GAGTAGTGGGCGAGGTGGTG 62.227 65.000 0.00 0.00 0.00 4.17
5215 5630 1.982938 GAGTAGTGGGCGAGGTGGT 60.983 63.158 0.00 0.00 0.00 4.16
5216 5631 1.668101 GAGAGTAGTGGGCGAGGTGG 61.668 65.000 0.00 0.00 0.00 4.61
5217 5632 0.681564 AGAGAGTAGTGGGCGAGGTG 60.682 60.000 0.00 0.00 0.00 4.00
5218 5633 0.681564 CAGAGAGTAGTGGGCGAGGT 60.682 60.000 0.00 0.00 0.00 3.85
5219 5634 2.010582 GCAGAGAGTAGTGGGCGAGG 62.011 65.000 0.00 0.00 0.00 4.63
5220 5635 1.435515 GCAGAGAGTAGTGGGCGAG 59.564 63.158 0.00 0.00 0.00 5.03
5221 5636 2.052690 GGCAGAGAGTAGTGGGCGA 61.053 63.158 0.00 0.00 0.00 5.54
5222 5637 1.680522 ATGGCAGAGAGTAGTGGGCG 61.681 60.000 0.00 0.00 0.00 6.13
5223 5638 0.105778 GATGGCAGAGAGTAGTGGGC 59.894 60.000 0.00 0.00 0.00 5.36
5224 5639 1.137872 GTGATGGCAGAGAGTAGTGGG 59.862 57.143 0.00 0.00 0.00 4.61
5225 5640 2.106566 AGTGATGGCAGAGAGTAGTGG 58.893 52.381 0.00 0.00 0.00 4.00
5226 5641 2.159128 CCAGTGATGGCAGAGAGTAGTG 60.159 54.545 0.00 0.00 0.00 2.74
5227 5642 2.106566 CCAGTGATGGCAGAGAGTAGT 58.893 52.381 0.00 0.00 0.00 2.73
5228 5643 2.886862 CCAGTGATGGCAGAGAGTAG 57.113 55.000 0.00 0.00 0.00 2.57
5238 5653 2.436646 GACGGTGGCCAGTGATGG 60.437 66.667 5.11 0.00 0.00 3.51
5239 5654 2.034879 GTGACGGTGGCCAGTGATG 61.035 63.158 5.11 0.00 0.00 3.07
5240 5655 2.347490 GTGACGGTGGCCAGTGAT 59.653 61.111 5.11 0.00 0.00 3.06
5241 5656 3.936203 GGTGACGGTGGCCAGTGA 61.936 66.667 5.11 0.00 0.00 3.41
5242 5657 3.551496 ATGGTGACGGTGGCCAGTG 62.551 63.158 5.11 3.55 35.56 3.66
5243 5658 3.249189 ATGGTGACGGTGGCCAGT 61.249 61.111 5.11 0.00 35.56 4.00
5244 5659 2.747460 CATGGTGACGGTGGCCAG 60.747 66.667 5.11 0.00 35.56 4.85
5245 5660 4.343323 CCATGGTGACGGTGGCCA 62.343 66.667 0.00 0.00 36.64 5.36
5267 5682 4.135153 CTCGAGGAGCCACCGGTG 62.135 72.222 28.26 28.26 44.74 4.94
5278 5693 1.160137 CTTTTCCTTGTGGCTCGAGG 58.840 55.000 15.58 15.41 46.55 4.63
5279 5694 1.160137 CCTTTTCCTTGTGGCTCGAG 58.840 55.000 8.45 8.45 0.00 4.04
5280 5695 0.472471 ACCTTTTCCTTGTGGCTCGA 59.528 50.000 0.00 0.00 0.00 4.04
5281 5696 2.178912 TACCTTTTCCTTGTGGCTCG 57.821 50.000 0.00 0.00 0.00 5.03
5282 5697 4.398358 GGTATTACCTTTTCCTTGTGGCTC 59.602 45.833 5.56 0.00 34.73 4.70
5283 5698 4.341487 GGTATTACCTTTTCCTTGTGGCT 58.659 43.478 5.56 0.00 34.73 4.75
5284 5699 4.713824 GGTATTACCTTTTCCTTGTGGC 57.286 45.455 5.56 0.00 34.73 5.01
5297 5712 3.554337 CGGCAGTGGTGATAGGTATTACC 60.554 52.174 4.57 4.57 41.33 2.85
5298 5713 3.554337 CCGGCAGTGGTGATAGGTATTAC 60.554 52.174 0.00 0.00 0.00 1.89
5299 5714 2.631062 CCGGCAGTGGTGATAGGTATTA 59.369 50.000 0.00 0.00 0.00 0.98
5300 5715 1.416401 CCGGCAGTGGTGATAGGTATT 59.584 52.381 0.00 0.00 0.00 1.89
5301 5716 1.048601 CCGGCAGTGGTGATAGGTAT 58.951 55.000 0.00 0.00 0.00 2.73
5302 5717 0.032912 TCCGGCAGTGGTGATAGGTA 60.033 55.000 0.00 0.00 0.00 3.08
5303 5718 0.907704 TTCCGGCAGTGGTGATAGGT 60.908 55.000 0.00 0.00 0.00 3.08
5304 5719 0.469917 ATTCCGGCAGTGGTGATAGG 59.530 55.000 0.00 0.00 0.00 2.57
5305 5720 1.541233 GGATTCCGGCAGTGGTGATAG 60.541 57.143 0.00 0.00 0.00 2.08
5306 5721 0.468226 GGATTCCGGCAGTGGTGATA 59.532 55.000 0.00 0.00 0.00 2.15
5307 5722 1.224592 GGATTCCGGCAGTGGTGAT 59.775 57.895 0.00 0.00 0.00 3.06
5308 5723 2.668632 GGATTCCGGCAGTGGTGA 59.331 61.111 0.00 0.00 0.00 4.02
5309 5724 2.438434 GGGATTCCGGCAGTGGTG 60.438 66.667 0.00 0.00 0.00 4.17
5310 5725 3.728373 GGGGATTCCGGCAGTGGT 61.728 66.667 0.00 0.00 0.00 4.16
5311 5726 3.060614 ATGGGGATTCCGGCAGTGG 62.061 63.158 0.00 0.00 38.76 4.00
5312 5727 1.825191 CATGGGGATTCCGGCAGTG 60.825 63.158 0.00 0.00 38.76 3.66
5313 5728 2.597340 CATGGGGATTCCGGCAGT 59.403 61.111 0.00 0.00 38.76 4.40
5314 5729 2.908940 GCATGGGGATTCCGGCAG 60.909 66.667 0.00 0.00 38.05 4.85
5315 5730 4.521292 GGCATGGGGATTCCGGCA 62.521 66.667 0.00 0.00 39.37 5.69
5317 5732 3.819652 TGGGCATGGGGATTCCGG 61.820 66.667 0.00 0.00 38.76 5.14
5318 5733 2.519302 GTGGGCATGGGGATTCCG 60.519 66.667 0.00 0.00 38.76 4.30
5319 5734 1.456331 CAGTGGGCATGGGGATTCC 60.456 63.158 0.00 0.00 0.00 3.01
5320 5735 1.456331 CCAGTGGGCATGGGGATTC 60.456 63.158 0.00 0.00 33.94 2.52
5321 5736 1.298906 ATCCAGTGGGCATGGGGATT 61.299 55.000 9.92 0.00 38.44 3.01
5322 5737 1.702491 ATCCAGTGGGCATGGGGAT 60.702 57.895 9.92 0.00 38.44 3.85
5323 5738 2.287117 ATCCAGTGGGCATGGGGA 60.287 61.111 9.92 0.00 38.44 4.81
5324 5739 2.196776 GATCCAGTGGGCATGGGG 59.803 66.667 9.92 0.00 38.44 4.96
5325 5740 1.039233 GTTGATCCAGTGGGCATGGG 61.039 60.000 9.92 0.00 38.44 4.00
5326 5741 0.323633 TGTTGATCCAGTGGGCATGG 60.324 55.000 9.92 0.00 39.33 3.66
5327 5742 1.100510 CTGTTGATCCAGTGGGCATG 58.899 55.000 9.92 0.00 0.00 4.06
5328 5743 0.994247 TCTGTTGATCCAGTGGGCAT 59.006 50.000 9.92 0.00 34.02 4.40
5329 5744 0.994247 ATCTGTTGATCCAGTGGGCA 59.006 50.000 9.92 5.39 34.02 5.36
5330 5745 2.019984 GAATCTGTTGATCCAGTGGGC 58.980 52.381 9.92 2.46 34.02 5.36
5331 5746 3.641434 AGAATCTGTTGATCCAGTGGG 57.359 47.619 9.92 0.00 34.02 4.61


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

AutoCloner maintained by Alex Coulton.