Multiple sequence alignment - TraesCS2D01G196900

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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 TraesCS2D01G196900 chr2D 100.000 8746 0 0 1 8746 143311676 143302931 0.000000e+00 16151.0
1 TraesCS2D01G196900 chr2D 80.417 623 66 29 106 710 602077899 602078483 2.920000e-114 424.0
2 TraesCS2D01G196900 chr2D 98.333 60 1 0 8687 8746 391812509 391812450 1.200000e-18 106.0
3 TraesCS2D01G196900 chr2D 98.305 59 1 0 8688 8746 424400057 424399999 4.320000e-18 104.0
4 TraesCS2D01G196900 chr2B 92.418 4392 190 65 3774 8096 201373249 201368932 0.000000e+00 6133.0
5 TraesCS2D01G196900 chr2B 93.333 2115 109 16 1594 3693 201375345 201373248 0.000000e+00 3096.0
6 TraesCS2D01G196900 chr2B 86.378 1615 112 34 1 1594 201377098 201375571 0.000000e+00 1664.0
7 TraesCS2D01G196900 chr2B 92.545 550 16 9 8153 8679 201368584 201368037 0.000000e+00 765.0
8 TraesCS2D01G196900 chr2B 76.182 571 90 31 155 710 732339628 732340167 8.710000e-65 259.0
9 TraesCS2D01G196900 chr2B 84.496 129 16 4 3649 3775 514342287 514342161 3.320000e-24 124.0
10 TraesCS2D01G196900 chr2B 96.825 63 2 0 8684 8746 134091512 134091574 1.200000e-18 106.0
11 TraesCS2D01G196900 chr2B 94.286 35 1 1 8222 8256 694094862 694094829 1.600000e-02 52.8
12 TraesCS2D01G196900 chr2A 94.814 3548 112 25 4630 8151 158044282 158047783 0.000000e+00 5467.0
13 TraesCS2D01G196900 chr2A 96.665 2039 48 9 2623 4646 158042234 158044267 0.000000e+00 3371.0
14 TraesCS2D01G196900 chr2A 94.665 1912 64 15 747 2634 158040183 158042080 0.000000e+00 2931.0
15 TraesCS2D01G196900 chr2A 87.852 461 23 15 8251 8689 158047858 158048307 2.180000e-140 510.0
16 TraesCS2D01G196900 chr6D 82.536 773 79 28 9 742 69903763 69904518 5.760000e-176 628.0
17 TraesCS2D01G196900 chr6D 80.848 637 71 29 38 652 359558219 359558826 3.720000e-123 453.0
18 TraesCS2D01G196900 chr6D 95.294 85 3 1 3692 3775 455738776 455738860 5.510000e-27 134.0
19 TraesCS2D01G196900 chr6D 93.103 87 5 1 3690 3775 103601940 103601854 9.220000e-25 126.0
20 TraesCS2D01G196900 chr6D 91.860 86 6 1 3691 3775 342467207 342467292 1.540000e-22 119.0
21 TraesCS2D01G196900 chr6D 90.805 87 6 2 3691 3775 420232194 420232108 2.000000e-21 115.0
22 TraesCS2D01G196900 chr6D 100.000 60 0 0 8685 8744 392512909 392512968 2.580000e-20 111.0
23 TraesCS2D01G196900 chr6D 98.305 59 1 0 8688 8746 21670806 21670748 4.320000e-18 104.0
24 TraesCS2D01G196900 chr6D 98.305 59 1 0 8688 8746 208781794 208781852 4.320000e-18 104.0
25 TraesCS2D01G196900 chr6D 98.305 59 1 0 8688 8746 473238382 473238324 4.320000e-18 104.0
26 TraesCS2D01G196900 chr6D 93.939 66 4 0 8681 8746 447248787 447248852 5.590000e-17 100.0
27 TraesCS2D01G196900 chr6D 92.857 70 2 3 8679 8746 470634200 470634132 2.010000e-16 99.0
28 TraesCS2D01G196900 chr6D 93.651 63 4 0 8684 8746 42565380 42565318 2.600000e-15 95.3
29 TraesCS2D01G196900 chr6D 91.304 69 6 0 8678 8746 359354769 359354837 2.600000e-15 95.3
30 TraesCS2D01G196900 chr6D 85.393 89 9 4 8660 8746 461485055 461485141 1.210000e-13 89.8
31 TraesCS2D01G196900 chr5A 80.601 732 93 31 44 742 574860187 574860902 3.620000e-143 520.0
32 TraesCS2D01G196900 chr1B 80.663 724 88 26 44 744 548831512 548832206 1.680000e-141 514.0
33 TraesCS2D01G196900 chr1B 81.717 361 44 17 44 393 129107902 129107553 1.860000e-71 281.0
34 TraesCS2D01G196900 chr1B 91.954 87 6 1 3691 3776 568524119 568524205 4.290000e-23 121.0
35 TraesCS2D01G196900 chr1B 96.825 63 2 0 8684 8746 136440160 136440098 1.200000e-18 106.0
36 TraesCS2D01G196900 chr1B 95.385 65 3 0 8682 8746 605929115 605929179 4.320000e-18 104.0
37 TraesCS2D01G196900 chr1B 100.000 28 0 0 8229 8256 32383102 32383129 1.600000e-02 52.8
38 TraesCS2D01G196900 chr5B 80.000 715 88 31 44 722 281435104 281435799 2.210000e-130 477.0
39 TraesCS2D01G196900 chr5B 84.416 308 25 13 44 338 626787513 626787216 1.860000e-71 281.0
40 TraesCS2D01G196900 chr5B 94.118 85 4 1 3692 3775 477498514 477498430 2.560000e-25 128.0
41 TraesCS2D01G196900 chr5B 89.286 84 4 5 8666 8746 48418462 48418543 5.590000e-17 100.0
42 TraesCS2D01G196900 chr5B 95.122 41 2 0 8213 8253 492449872 492449912 2.040000e-06 65.8
43 TraesCS2D01G196900 chr3D 78.737 776 92 33 1 742 442760156 442760892 1.340000e-122 451.0
44 TraesCS2D01G196900 chr3D 78.125 736 87 25 44 744 527706009 527706705 4.920000e-107 399.0
45 TraesCS2D01G196900 chr3D 77.690 632 92 19 149 744 58433354 58433972 3.020000e-89 340.0
46 TraesCS2D01G196900 chr3D 98.361 61 1 0 8686 8746 536788335 536788395 3.340000e-19 108.0
47 TraesCS2D01G196900 chr3D 94.203 69 4 0 8678 8746 540255715 540255647 1.200000e-18 106.0
48 TraesCS2D01G196900 chr4B 79.511 654 103 16 107 744 576748924 576749562 3.750000e-118 436.0
49 TraesCS2D01G196900 chr4B 94.186 86 4 1 3691 3775 179310446 179310361 7.130000e-26 130.0
50 TraesCS2D01G196900 chr4B 91.398 93 7 1 3685 3776 291854574 291854666 9.220000e-25 126.0
51 TraesCS2D01G196900 chr3B 78.464 729 95 30 67 750 367648686 367647975 3.780000e-113 420.0
52 TraesCS2D01G196900 chr3B 79.227 621 82 22 155 744 607818884 607819488 1.060000e-103 388.0
53 TraesCS2D01G196900 chr3B 87.218 266 17 14 18 276 230943481 230943226 4.000000e-73 287.0
54 TraesCS2D01G196900 chr3B 90.625 96 8 1 3685 3779 358847108 358847203 9.220000e-25 126.0
55 TraesCS2D01G196900 chr6A 83.553 456 57 13 295 744 89308407 89307964 2.270000e-110 411.0
56 TraesCS2D01G196900 chr6A 92.308 91 6 1 3689 3778 607960034 607959944 2.560000e-25 128.0
57 TraesCS2D01G196900 chr6A 93.902 82 2 3 3691 3770 88774744 88774824 4.290000e-23 121.0
58 TraesCS2D01G196900 chr6A 98.333 60 1 0 8687 8746 124305610 124305669 1.200000e-18 106.0
59 TraesCS2D01G196900 chr7D 79.962 524 63 26 105 621 637505214 637504726 1.810000e-91 348.0
60 TraesCS2D01G196900 chr7D 85.897 156 19 2 4141 4296 204452849 204452697 7.030000e-36 163.0
61 TraesCS2D01G196900 chr7D 98.333 60 1 0 8687 8746 36659736 36659795 1.200000e-18 106.0
62 TraesCS2D01G196900 chr7A 76.093 778 104 46 18 752 449452248 449452986 1.820000e-86 331.0
63 TraesCS2D01G196900 chr7A 82.235 349 39 13 52 394 132622235 132621904 6.690000e-71 279.0
64 TraesCS2D01G196900 chr7A 79.381 388 57 12 363 742 449455231 449454859 1.460000e-62 252.0
65 TraesCS2D01G196900 chr7A 100.000 60 0 0 8687 8746 532703756 532703697 2.580000e-20 111.0
66 TraesCS2D01G196900 chr7A 96.825 63 2 0 8684 8746 378440 378502 1.200000e-18 106.0
67 TraesCS2D01G196900 chr5D 75.421 712 113 35 47 742 540130274 540129609 1.110000e-73 289.0
68 TraesCS2D01G196900 chr5D 91.860 86 6 1 3692 3776 192552318 192552233 1.540000e-22 119.0
69 TraesCS2D01G196900 chr5D 98.333 60 1 0 8687 8746 398757404 398757345 1.200000e-18 106.0
70 TraesCS2D01G196900 chr7B 81.395 301 47 6 449 744 425361093 425361389 4.080000e-58 237.0
71 TraesCS2D01G196900 chr7B 85.897 156 19 2 4141 4296 168359496 168359344 7.030000e-36 163.0
72 TraesCS2D01G196900 chr6B 93.478 92 4 2 3687 3776 225523359 225523450 1.530000e-27 135.0
73 TraesCS2D01G196900 chr4D 93.258 89 4 2 3689 3776 160826820 160826733 7.130000e-26 130.0
74 TraesCS2D01G196900 chr4D 91.954 87 5 1 3692 3776 253767457 253767543 4.290000e-23 121.0
75 TraesCS2D01G196900 chr4D 91.765 85 6 1 3692 3775 359681564 359681480 5.550000e-22 117.0
76 TraesCS2D01G196900 chr4D 96.774 62 2 0 8685 8746 356873788 356873849 4.320000e-18 104.0
77 TraesCS2D01G196900 chr4D 92.857 70 3 2 8679 8746 505322499 505322430 5.590000e-17 100.0
78 TraesCS2D01G196900 chr4D 86.585 82 11 0 8665 8746 501060370 501060451 3.360000e-14 91.6
79 TraesCS2D01G196900 chr4A 93.258 89 5 1 3689 3776 697982984 697983072 7.130000e-26 130.0
80 TraesCS2D01G196900 chr4A 92.941 85 5 1 3692 3775 200089165 200089249 1.190000e-23 122.0
81 TraesCS2D01G196900 chr4A 92.941 85 5 1 3692 3775 200089249 200089165 1.190000e-23 122.0
82 TraesCS2D01G196900 chr1A 92.045 88 6 1 3689 3775 511621801 511621888 1.190000e-23 122.0
83 TraesCS2D01G196900 chr1A 98.333 60 1 0 8687 8746 15540159 15540100 1.200000e-18 106.0
84 TraesCS2D01G196900 chr1A 98.333 60 1 0 8687 8746 24075817 24075876 1.200000e-18 106.0
85 TraesCS2D01G196900 chr1A 89.412 85 8 1 3692 3775 237511065 237510981 1.200000e-18 106.0
86 TraesCS2D01G196900 chr1A 98.305 59 1 0 8688 8746 254349076 254349018 4.320000e-18 104.0
87 TraesCS2D01G196900 chr1A 96.774 31 1 0 714 744 321283545 321283575 1.600000e-02 52.8
88 TraesCS2D01G196900 chr1D 89.130 92 9 1 3692 3782 300011819 300011910 7.180000e-21 113.0
89 TraesCS2D01G196900 chr1D 90.698 86 6 1 3692 3775 459027003 459027088 7.180000e-21 113.0
90 TraesCS2D01G196900 chr1D 92.105 76 6 0 3691 3766 365051923 365051998 3.340000e-19 108.0
91 TraesCS2D01G196900 chr1D 89.412 85 8 1 3692 3775 100882986 100882902 1.200000e-18 106.0
92 TraesCS2D01G196900 chr1D 98.305 59 1 0 8688 8746 9666133 9666075 4.320000e-18 104.0
93 TraesCS2D01G196900 chr1D 96.774 62 2 0 8685 8746 126223507 126223446 4.320000e-18 104.0
94 TraesCS2D01G196900 chr1D 89.286 84 8 1 3692 3775 349250452 349250534 4.320000e-18 104.0
95 TraesCS2D01G196900 chrUn 98.305 59 1 0 8688 8746 21191900 21191842 4.320000e-18 104.0
96 TraesCS2D01G196900 chrUn 96.667 60 2 0 8686 8745 38135414 38135473 5.590000e-17 100.0
97 TraesCS2D01G196900 chrUn 87.500 88 10 1 3689 3775 326861589 326861676 5.590000e-17 100.0
98 TraesCS2D01G196900 chrUn 87.500 88 10 1 3689 3775 326864620 326864707 5.590000e-17 100.0
99 TraesCS2D01G196900 chrUn 88.235 85 9 1 3692 3775 371911705 371911621 5.590000e-17 100.0
100 TraesCS2D01G196900 chrUn 87.500 88 10 1 3689 3775 458243500 458243587 5.590000e-17 100.0
101 TraesCS2D01G196900 chrUn 96.610 59 2 0 8688 8746 31210741 31210799 2.010000e-16 99.0
102 TraesCS2D01G196900 chrUn 95.161 62 3 0 8685 8746 47449489 47449550 2.010000e-16 99.0
103 TraesCS2D01G196900 chrUn 95.000 60 3 0 8687 8746 100779962 100780021 2.600000e-15 95.3
104 TraesCS2D01G196900 chrUn 93.750 64 3 1 8684 8746 177149369 177149306 2.600000e-15 95.3
105 TraesCS2D01G196900 chrUn 95.000 60 3 0 8687 8746 243337449 243337390 2.600000e-15 95.3
106 TraesCS2D01G196900 chrUn 95.000 60 3 0 8687 8746 248708854 248708795 2.600000e-15 95.3
107 TraesCS2D01G196900 chrUn 92.308 65 5 0 8682 8746 11569608 11569672 9.350000e-15 93.5
108 TraesCS2D01G196900 chrUn 88.312 77 6 3 8671 8746 247001422 247001348 1.210000e-13 89.8


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 TraesCS2D01G196900 chr2D 143302931 143311676 8745 True 16151.00 16151 100.0000 1 8746 1 chr2D.!!$R1 8745
1 TraesCS2D01G196900 chr2D 602077899 602078483 584 False 424.00 424 80.4170 106 710 1 chr2D.!!$F1 604
2 TraesCS2D01G196900 chr2B 201368037 201377098 9061 True 2914.50 6133 91.1685 1 8679 4 chr2B.!!$R3 8678
3 TraesCS2D01G196900 chr2B 732339628 732340167 539 False 259.00 259 76.1820 155 710 1 chr2B.!!$F2 555
4 TraesCS2D01G196900 chr2A 158040183 158048307 8124 False 3069.75 5467 93.4990 747 8689 4 chr2A.!!$F1 7942
5 TraesCS2D01G196900 chr6D 69903763 69904518 755 False 628.00 628 82.5360 9 742 1 chr6D.!!$F1 733
6 TraesCS2D01G196900 chr6D 359558219 359558826 607 False 453.00 453 80.8480 38 652 1 chr6D.!!$F5 614
7 TraesCS2D01G196900 chr5A 574860187 574860902 715 False 520.00 520 80.6010 44 742 1 chr5A.!!$F1 698
8 TraesCS2D01G196900 chr1B 548831512 548832206 694 False 514.00 514 80.6630 44 744 1 chr1B.!!$F2 700
9 TraesCS2D01G196900 chr5B 281435104 281435799 695 False 477.00 477 80.0000 44 722 1 chr5B.!!$F2 678
10 TraesCS2D01G196900 chr3D 442760156 442760892 736 False 451.00 451 78.7370 1 742 1 chr3D.!!$F2 741
11 TraesCS2D01G196900 chr3D 527706009 527706705 696 False 399.00 399 78.1250 44 744 1 chr3D.!!$F3 700
12 TraesCS2D01G196900 chr3D 58433354 58433972 618 False 340.00 340 77.6900 149 744 1 chr3D.!!$F1 595
13 TraesCS2D01G196900 chr4B 576748924 576749562 638 False 436.00 436 79.5110 107 744 1 chr4B.!!$F2 637
14 TraesCS2D01G196900 chr3B 367647975 367648686 711 True 420.00 420 78.4640 67 750 1 chr3B.!!$R2 683
15 TraesCS2D01G196900 chr3B 607818884 607819488 604 False 388.00 388 79.2270 155 744 1 chr3B.!!$F2 589
16 TraesCS2D01G196900 chr7A 449452248 449452986 738 False 331.00 331 76.0930 18 752 1 chr7A.!!$F2 734
17 TraesCS2D01G196900 chr5D 540129609 540130274 665 True 289.00 289 75.4210 47 742 1 chr5D.!!$R3 695

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
864 1154 0.036858 GCTGGTTGGTCTCCACTCTC 60.037 60.000 0.00 0.00 30.78 3.20 F
866 1156 0.105194 TGGTTGGTCTCCACTCTCCA 60.105 55.000 0.00 0.00 30.78 3.86 F
1622 2157 0.524862 CCACTGGACAGCTGCAAATC 59.475 55.000 15.27 3.22 0.00 2.17 F
1688 2224 1.000955 GAGGGACAGAACGAGAAGCAA 59.999 52.381 0.00 0.00 0.00 3.91 F
2760 3473 1.299321 GGAGAGCCAAGCTGCTTCT 59.701 57.895 12.82 7.66 42.95 2.85 F
3328 4053 0.983467 TGTCTATGTGCCTCCTTGCA 59.017 50.000 0.00 0.00 39.37 4.08 F
3770 4497 2.090943 TCCTACATTATGGGACGGAGGT 60.091 50.000 0.00 0.00 31.72 3.85 F
4846 5634 2.599659 GTAAGCTGCAAAGTTCCATGC 58.400 47.619 1.02 0.00 42.86 4.06 F
5962 6760 2.160721 AGAATGCCGAGGAAGAGGTA 57.839 50.000 0.00 0.00 0.00 3.08 F
6412 7236 0.827089 CCCCAAAGCACATGGACACA 60.827 55.000 0.00 0.00 40.56 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2294 0.252375 TTCCTAGTACGTTGGGGCCT 60.252 55.000 0.84 0.0 0.00 5.19 R
2783 3499 1.135960 GAGGAGAAAGGATGAGGGGG 58.864 60.000 0.00 0.0 0.00 5.40 R
3264 3986 2.182312 AGATGGATAGGGCTCCCAGTAA 59.818 50.000 7.82 0.0 38.92 2.24 R
3328 4053 8.405418 TGTAGAGGAATATACAGAAATAGCGT 57.595 34.615 0.00 0.0 0.00 5.07 R
4713 5500 3.139077 CACCTTCTACTCAAACCACACC 58.861 50.000 0.00 0.0 0.00 4.16 R
4901 5689 4.696877 TGATATGCACTCTTTGAACACCAG 59.303 41.667 0.00 0.0 0.00 4.00 R
5097 5885 5.695363 GTGTACTGGACCTAGACTTTTTGTC 59.305 44.000 0.00 0.0 45.67 3.18 R
6367 7191 0.983467 TATGGCTGCAACAGGAGTCA 59.017 50.000 0.50 0.0 39.66 3.41 R
7493 8334 2.097142 GCACTTCATCATTCACTGGAGC 59.903 50.000 0.00 0.0 0.00 4.70 R
8155 9324 1.133915 AGAGAAAGAAAACCGCCACCA 60.134 47.619 0.00 0.0 0.00 4.17 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
252 404 0.041312 GCACGTCGTGAAAGCACAAT 60.041 50.000 28.83 0.00 45.41 2.71
276 428 1.226746 CCTCTCGCGGAAACAAAACT 58.773 50.000 6.13 0.00 0.00 2.66
277 429 2.409975 CCTCTCGCGGAAACAAAACTA 58.590 47.619 6.13 0.00 0.00 2.24
534 800 7.539712 TTTTTCACGCAAATATTTTTGACCA 57.460 28.000 12.18 0.00 44.11 4.02
655 944 1.595093 CCGGAGAAAGCGCCCAAAAT 61.595 55.000 2.29 0.00 0.00 1.82
801 1091 0.664761 CCATAACAATGGGCTGAGCG 59.335 55.000 0.00 0.00 38.04 5.03
860 1150 0.326264 ATCTGCTGGTTGGTCTCCAC 59.674 55.000 0.00 0.00 30.78 4.02
861 1151 0.764369 TCTGCTGGTTGGTCTCCACT 60.764 55.000 0.00 0.00 30.78 4.00
862 1152 0.321122 CTGCTGGTTGGTCTCCACTC 60.321 60.000 0.00 0.00 30.78 3.51
863 1153 0.764369 TGCTGGTTGGTCTCCACTCT 60.764 55.000 0.00 0.00 30.78 3.24
864 1154 0.036858 GCTGGTTGGTCTCCACTCTC 60.037 60.000 0.00 0.00 30.78 3.20
865 1155 0.610687 CTGGTTGGTCTCCACTCTCC 59.389 60.000 0.00 0.00 30.78 3.71
866 1156 0.105194 TGGTTGGTCTCCACTCTCCA 60.105 55.000 0.00 0.00 30.78 3.86
882 1172 2.666862 CAACTACGCGCCAACCCA 60.667 61.111 5.73 0.00 0.00 4.51
1348 1647 4.127171 GTTGAACTGAGCTGGAGTGTTTA 58.873 43.478 0.00 0.00 0.00 2.01
1373 1672 5.562623 GGATTTTCGTGTTCATTGTTCGTAC 59.437 40.000 0.00 0.00 0.00 3.67
1472 1776 8.099364 ACATAACTTACTTTGATCACAAGTGG 57.901 34.615 22.68 18.59 37.32 4.00
1511 1815 1.419012 TCCATTGGCCAGCTAGAGATG 59.581 52.381 5.11 4.80 0.00 2.90
1561 1865 6.016527 CCATATGGTTCATTGGACTTGATCAG 60.017 42.308 14.09 0.00 29.80 2.90
1620 2155 2.195567 GCCACTGGACAGCTGCAAA 61.196 57.895 15.27 0.00 0.00 3.68
1622 2157 0.524862 CCACTGGACAGCTGCAAATC 59.475 55.000 15.27 3.22 0.00 2.17
1643 2178 5.670792 TCGTAAGAGTATGGGTTCATTGT 57.329 39.130 0.00 0.00 45.01 2.71
1688 2224 1.000955 GAGGGACAGAACGAGAAGCAA 59.999 52.381 0.00 0.00 0.00 3.91
1729 2267 4.848357 ACATAGTTGGAATGAGGGTCTTG 58.152 43.478 0.00 0.00 0.00 3.02
1756 2294 7.335673 TGCGAACATGGATTCAAGACTATAAAA 59.664 33.333 0.00 0.00 0.00 1.52
1856 2395 3.695060 GTGACTGAGCTTAGGTGCTACTA 59.305 47.826 10.64 0.00 44.17 1.82
1918 2457 7.578310 AGTTCACATCATTATGGATTCCTTG 57.422 36.000 3.95 0.00 37.43 3.61
2105 2644 6.917477 GTCTTCTGTCACTCATATCTGATCAC 59.083 42.308 0.00 0.00 0.00 3.06
2150 2689 9.967451 TGTATATTTGTTCTTACTTTCCCATCA 57.033 29.630 0.00 0.00 0.00 3.07
2156 2695 6.074648 TGTTCTTACTTTCCCATCAATGGTT 58.925 36.000 8.19 0.00 46.65 3.67
2197 2737 6.323739 AGTTCACAACACAATGTTTAAGGGAT 59.676 34.615 0.00 0.00 38.77 3.85
2254 2799 2.233738 GCTTAGTTTCTGAAGCACGC 57.766 50.000 7.01 2.55 45.99 5.34
2255 2800 1.531149 GCTTAGTTTCTGAAGCACGCA 59.469 47.619 7.01 0.00 45.99 5.24
2316 2861 2.159338 GCAACAGCACCATGATACCTTG 60.159 50.000 0.00 0.00 0.00 3.61
2413 2958 3.120199 CCGTGACACTTCCAAATGTGATC 60.120 47.826 3.68 0.00 37.59 2.92
2508 3056 6.925610 TTGATGAAAGCAGCGACTTATTAT 57.074 33.333 0.00 0.00 28.24 1.28
2587 3135 8.231007 AGAGAAGAGGGAATATCTGAACTCATA 58.769 37.037 0.00 0.00 31.11 2.15
2733 3446 7.014326 CAGGAGACCATATGCTTGTTACTAGTA 59.986 40.741 0.00 0.00 0.00 1.82
2760 3473 1.299321 GGAGAGCCAAGCTGCTTCT 59.701 57.895 12.82 7.66 42.95 2.85
2768 3481 3.390639 AGCCAAGCTGCTTCTATCATAGT 59.609 43.478 12.82 0.00 38.85 2.12
2783 3499 7.827701 TCTATCATAGTACGAATTCACCATCC 58.172 38.462 6.22 0.00 0.00 3.51
2807 3523 2.170187 CCTCATCCTTTCTCCTCCACAG 59.830 54.545 0.00 0.00 0.00 3.66
2889 3610 5.755375 ACTCCGATGATGATGTGAACAATAC 59.245 40.000 0.00 0.00 0.00 1.89
3232 3954 7.361286 GGTGCTAAGGTGAATATTTATAGCTGC 60.361 40.741 0.00 0.00 36.23 5.25
3264 3986 5.426689 TTTGAGATTGGAGACAGCTGTAT 57.573 39.130 21.73 18.43 44.54 2.29
3328 4053 0.983467 TGTCTATGTGCCTCCTTGCA 59.017 50.000 0.00 0.00 39.37 4.08
3341 4066 3.521560 CTCCTTGCACGCTATTTCTGTA 58.478 45.455 0.00 0.00 0.00 2.74
3628 4353 7.773224 TCTCTACCAGTTGTTCAATTTCAAGAA 59.227 33.333 0.00 0.00 0.00 2.52
3660 4385 8.876275 ACGATTATATGCTTGCATTGATTTTT 57.124 26.923 13.52 0.00 0.00 1.94
3770 4497 2.090943 TCCTACATTATGGGACGGAGGT 60.091 50.000 0.00 0.00 31.72 3.85
4562 5300 5.731686 GCAATCCTGTTGAAGCAATACTAGC 60.732 44.000 0.00 0.00 0.00 3.42
4563 5301 4.551702 TCCTGTTGAAGCAATACTAGCA 57.448 40.909 0.00 0.00 0.00 3.49
4615 5353 3.365868 GCTGGCACATTGAACGACATAAA 60.366 43.478 0.00 0.00 38.20 1.40
4618 5356 4.517075 TGGCACATTGAACGACATAAAGAA 59.483 37.500 0.00 0.00 0.00 2.52
4713 5500 8.589338 AGTAGTATCCATGTATCTAAAGCTTGG 58.411 37.037 0.00 0.00 0.00 3.61
4846 5634 2.599659 GTAAGCTGCAAAGTTCCATGC 58.400 47.619 1.02 0.00 42.86 4.06
4901 5689 5.852282 TTTATTTCTTCCTTATGCCAGGC 57.148 39.130 3.66 3.66 33.35 4.85
5097 5885 9.719279 AACAATGCACAAATCAAATTTTTGTAG 57.281 25.926 6.45 3.97 43.51 2.74
5100 5888 8.659925 ATGCACAAATCAAATTTTTGTAGACA 57.340 26.923 6.45 6.41 43.51 3.41
5727 6525 9.831737 CAGATAAAGAGGTGTGTTAAGATTTTG 57.168 33.333 0.00 0.00 0.00 2.44
5728 6526 9.793259 AGATAAAGAGGTGTGTTAAGATTTTGA 57.207 29.630 0.00 0.00 0.00 2.69
5736 6534 8.912988 AGGTGTGTTAAGATTTTGATTTTGAGA 58.087 29.630 0.00 0.00 0.00 3.27
5871 6669 6.353323 TGTTGTTGAAAGAGATGGTTCAGTA 58.647 36.000 0.00 0.00 0.00 2.74
5962 6760 2.160721 AGAATGCCGAGGAAGAGGTA 57.839 50.000 0.00 0.00 0.00 3.08
6030 6834 6.751514 TTTGTTCTGAAAGTAGCAACTGAA 57.248 33.333 0.00 0.00 35.62 3.02
6056 6860 4.370364 TGCCACTTGAAGTTTCAAAGAC 57.630 40.909 8.48 0.00 45.61 3.01
6149 6973 7.597288 TGTGCTATAGCTAAGAAATACAGGA 57.403 36.000 24.61 0.00 42.66 3.86
6187 7011 6.428465 TGTTTCTGCTTGATAATGTTCCGTAA 59.572 34.615 0.00 0.00 0.00 3.18
6286 7110 4.793216 CAGTTGACTGGTTTTCGAAACAAG 59.207 41.667 10.79 11.03 40.20 3.16
6311 7135 6.095432 TGGGGTGTCATTTCATAAAAACAG 57.905 37.500 0.00 0.00 0.00 3.16
6378 7202 2.364632 TGGTTGTTGTGACTCCTGTTG 58.635 47.619 0.00 0.00 0.00 3.33
6412 7236 0.827089 CCCCAAAGCACATGGACACA 60.827 55.000 0.00 0.00 40.56 3.72
6693 7518 2.360165 GCGATGGCCAGAAATCAGAATT 59.640 45.455 13.05 0.00 0.00 2.17
6768 7593 2.993899 CTGCCGGTGTTAGTTTCTACTG 59.006 50.000 1.90 0.00 35.78 2.74
6770 7595 3.573538 TGCCGGTGTTAGTTTCTACTGTA 59.426 43.478 1.90 0.00 35.78 2.74
6771 7596 3.922850 GCCGGTGTTAGTTTCTACTGTAC 59.077 47.826 1.90 0.00 35.78 2.90
6772 7597 4.321527 GCCGGTGTTAGTTTCTACTGTACT 60.322 45.833 1.90 0.00 35.78 2.73
6773 7598 5.106157 GCCGGTGTTAGTTTCTACTGTACTA 60.106 44.000 1.90 0.00 35.78 1.82
6774 7599 6.317857 CCGGTGTTAGTTTCTACTGTACTAC 58.682 44.000 0.00 0.00 35.78 2.73
6864 7689 2.629017 ATCCCTTGGTCTTGGCAAAT 57.371 45.000 0.00 0.00 0.00 2.32
7139 7977 6.801862 GGGTGTAGATTTGTCAATTTCTTTCG 59.198 38.462 4.42 0.00 0.00 3.46
7172 8010 7.007116 TCACTAGGACATCTCTAATAGCACAT 58.993 38.462 0.00 0.00 0.00 3.21
7178 8016 6.015519 GGACATCTCTAATAGCACATCTCAGT 60.016 42.308 0.00 0.00 0.00 3.41
7200 8038 4.081087 GTCATTTCTTAGAGGGTGCCACTA 60.081 45.833 0.00 0.00 0.00 2.74
7232 8070 6.753107 TGTTCATGTAGACGAGAGAACATA 57.247 37.500 0.00 0.00 40.01 2.29
7348 8186 6.334202 TGTTTGTAAATTCAGTCCACCAAAC 58.666 36.000 0.00 0.00 40.27 2.93
7366 8204 4.881850 CCAAACTCTATTGGCGAGGTTAAT 59.118 41.667 0.00 0.00 43.11 1.40
7369 8207 7.312899 CAAACTCTATTGGCGAGGTTAATTTT 58.687 34.615 0.00 0.00 36.33 1.82
7371 8209 6.852664 ACTCTATTGGCGAGGTTAATTTTTG 58.147 36.000 0.00 0.00 32.83 2.44
7493 8334 1.519408 CCCTTTGGACCTGTTACACG 58.481 55.000 0.00 0.00 0.00 4.49
7750 8596 2.353357 TTTGCTGGCAGATGATAGGG 57.647 50.000 20.86 0.00 0.00 3.53
7874 8720 2.222027 GCCTGTGATAGCGGCTTAAAT 58.778 47.619 8.26 0.00 40.62 1.40
7875 8721 2.618709 GCCTGTGATAGCGGCTTAAATT 59.381 45.455 8.26 0.00 40.62 1.82
7876 8722 3.066760 GCCTGTGATAGCGGCTTAAATTT 59.933 43.478 8.26 0.00 40.62 1.82
7877 8723 4.440112 GCCTGTGATAGCGGCTTAAATTTT 60.440 41.667 8.26 0.00 40.62 1.82
8051 8899 4.113815 CCCCTGATTGAGCCGGCA 62.114 66.667 31.54 8.70 0.00 5.69
8090 8938 9.685828 GGACATATTCTACACATCTCTTAAGAC 57.314 37.037 0.00 0.00 33.32 3.01
8146 9315 2.507484 CTCTTGGTGGCAAATCACTCA 58.493 47.619 0.00 0.00 37.75 3.41
8151 9320 6.422333 TCTTGGTGGCAAATCACTCATTATA 58.578 36.000 0.00 0.00 37.75 0.98
8152 9321 7.062322 TCTTGGTGGCAAATCACTCATTATAT 58.938 34.615 0.00 0.00 37.75 0.86
8153 9322 6.882610 TGGTGGCAAATCACTCATTATATC 57.117 37.500 0.00 0.00 37.75 1.63
8155 9324 7.062322 TGGTGGCAAATCACTCATTATATCTT 58.938 34.615 0.00 0.00 37.75 2.40
8156 9325 7.013559 TGGTGGCAAATCACTCATTATATCTTG 59.986 37.037 0.00 0.00 37.75 3.02
8174 9371 1.314730 TGGTGGCGGTTTTCTTTCTC 58.685 50.000 0.00 0.00 0.00 2.87
8186 9383 3.864789 TTCTTTCTCTTGCTTCCACCT 57.135 42.857 0.00 0.00 0.00 4.00
8224 9421 1.339610 CCTCCGTGTGAATTGCCAAAA 59.660 47.619 0.00 0.00 0.00 2.44
8295 9493 2.984562 TGCTTGATTCCTGCGATGTTA 58.015 42.857 0.00 0.00 0.00 2.41
8403 9607 1.961277 CTTCGCGTGGAGGTTTGCT 60.961 57.895 5.77 0.00 0.00 3.91
8467 9682 4.988486 GCAGTTGGCAGCACGCAC 62.988 66.667 3.63 0.00 45.17 5.34
8569 9789 1.597854 TGCTGGTGCACTGTACTGC 60.598 57.895 17.98 15.13 45.31 4.40
8570 9790 2.328099 GCTGGTGCACTGTACTGCC 61.328 63.158 17.98 0.00 39.41 4.85
8572 9792 2.395988 CTGGTGCACTGTACTGCCCA 62.396 60.000 17.98 13.15 36.02 5.36
8573 9793 1.228124 GGTGCACTGTACTGCCCAA 60.228 57.895 17.98 0.00 36.21 4.12
8574 9794 1.237285 GGTGCACTGTACTGCCCAAG 61.237 60.000 17.98 0.00 36.21 3.61
8575 9795 1.073025 TGCACTGTACTGCCCAAGG 59.927 57.895 4.79 0.00 36.21 3.61
8576 9796 1.073199 GCACTGTACTGCCCAAGGT 59.927 57.895 0.00 0.00 0.00 3.50
8577 9797 1.237285 GCACTGTACTGCCCAAGGTG 61.237 60.000 0.00 0.00 0.00 4.00
8595 9819 2.649129 GGGTGGGTGCCTTCATTGC 61.649 63.158 0.00 0.00 0.00 3.56
8635 9859 3.000925 CGATGTGGAATTAGGCAACGTAC 59.999 47.826 0.00 0.00 46.39 3.67
8670 9894 7.862372 TCAGTGTGAGAATCTAAAACAAAATGC 59.138 33.333 0.00 0.00 34.92 3.56
8681 9905 7.838884 TCTAAAACAAAATGCCATCATCATCA 58.161 30.769 0.00 0.00 31.27 3.07
8689 9913 7.458409 AAATGCCATCATCATCAGGTAATAC 57.542 36.000 0.00 0.00 31.27 1.89
8690 9914 5.830799 TGCCATCATCATCAGGTAATACT 57.169 39.130 0.00 0.00 0.00 2.12
8691 9915 5.798132 TGCCATCATCATCAGGTAATACTC 58.202 41.667 0.00 0.00 0.00 2.59
8692 9916 5.181748 GCCATCATCATCAGGTAATACTCC 58.818 45.833 0.00 0.00 0.00 3.85
8693 9917 5.738909 CCATCATCATCAGGTAATACTCCC 58.261 45.833 0.00 0.00 0.00 4.30
8694 9918 5.486775 CCATCATCATCAGGTAATACTCCCT 59.513 44.000 0.00 0.00 0.00 4.20
8695 9919 6.351711 CCATCATCATCAGGTAATACTCCCTC 60.352 46.154 0.00 0.00 0.00 4.30
8696 9920 5.087323 TCATCATCAGGTAATACTCCCTCC 58.913 45.833 0.00 0.00 0.00 4.30
8697 9921 3.497332 TCATCAGGTAATACTCCCTCCG 58.503 50.000 0.00 0.00 0.00 4.63
8698 9922 3.117246 TCATCAGGTAATACTCCCTCCGT 60.117 47.826 0.00 0.00 0.00 4.69
8699 9923 3.393426 TCAGGTAATACTCCCTCCGTT 57.607 47.619 0.00 0.00 0.00 4.44
8700 9924 3.294214 TCAGGTAATACTCCCTCCGTTC 58.706 50.000 0.00 0.00 0.00 3.95
8701 9925 2.364647 CAGGTAATACTCCCTCCGTTCC 59.635 54.545 0.00 0.00 0.00 3.62
8702 9926 2.246849 AGGTAATACTCCCTCCGTTCCT 59.753 50.000 0.00 0.00 0.00 3.36
8703 9927 3.464833 AGGTAATACTCCCTCCGTTCCTA 59.535 47.826 0.00 0.00 0.00 2.94
8704 9928 4.078980 AGGTAATACTCCCTCCGTTCCTAA 60.079 45.833 0.00 0.00 0.00 2.69
8705 9929 4.651045 GGTAATACTCCCTCCGTTCCTAAA 59.349 45.833 0.00 0.00 0.00 1.85
8706 9930 5.306419 GGTAATACTCCCTCCGTTCCTAAAT 59.694 44.000 0.00 0.00 0.00 1.40
8707 9931 6.494835 GGTAATACTCCCTCCGTTCCTAAATA 59.505 42.308 0.00 0.00 0.00 1.40
8708 9932 7.179872 GGTAATACTCCCTCCGTTCCTAAATAT 59.820 40.741 0.00 0.00 0.00 1.28
8709 9933 9.247861 GTAATACTCCCTCCGTTCCTAAATATA 57.752 37.037 0.00 0.00 0.00 0.86
8710 9934 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
8711 9935 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
8712 9936 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
8713 9937 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
8714 9938 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
8715 9939 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
8716 9940 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
8717 9941 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
8718 9942 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
8737 9961 9.827411 GTCTTTGTAGAAATTTCACTATGAACC 57.173 33.333 19.99 6.84 31.84 3.62
8738 9962 9.567776 TCTTTGTAGAAATTTCACTATGAACCA 57.432 29.630 19.99 0.96 35.89 3.67
8739 9963 9.612620 CTTTGTAGAAATTTCACTATGAACCAC 57.387 33.333 19.99 3.25 35.89 4.16
8740 9964 8.684386 TTGTAGAAATTTCACTATGAACCACA 57.316 30.769 19.99 5.40 35.89 4.17
8741 9965 8.862325 TGTAGAAATTTCACTATGAACCACAT 57.138 30.769 19.99 0.00 35.89 3.21
8742 9966 9.952030 TGTAGAAATTTCACTATGAACCACATA 57.048 29.630 19.99 0.00 35.89 2.29
8744 9968 7.974675 AGAAATTTCACTATGAACCACATACG 58.025 34.615 19.99 0.00 35.89 3.06
8745 9969 6.677781 AATTTCACTATGAACCACATACGG 57.322 37.500 0.00 0.00 35.89 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 18 4.618460 GCCTCTTTCGGAAAGGGAAAAATC 60.618 45.833 27.71 11.55 41.66 2.17
16 19 3.258372 GCCTCTTTCGGAAAGGGAAAAAT 59.742 43.478 27.71 0.00 41.66 1.82
111 124 1.738099 CGTGCCTCCTCGGAAACAG 60.738 63.158 0.00 0.00 33.16 3.16
252 404 3.676605 TTTCCGCGAGAGGCACGA 61.677 61.111 8.23 0.00 43.84 4.35
269 421 2.832129 TCCGAGAGAGGCATAGTTTTGT 59.168 45.455 0.00 0.00 0.00 2.83
276 428 2.454336 TTCCTTCCGAGAGAGGCATA 57.546 50.000 0.00 0.00 0.00 3.14
277 429 1.573108 TTTCCTTCCGAGAGAGGCAT 58.427 50.000 0.00 0.00 0.00 4.40
398 619 4.930463 AACGGAAACAAAACGCATTTTT 57.070 31.818 0.00 0.00 35.79 1.94
534 800 5.195185 TCCACCGGTCTTCTTTAACTTTTT 58.805 37.500 2.59 0.00 0.00 1.94
544 810 3.719816 GGTTTTCCACCGGTCTTCT 57.280 52.632 2.59 0.00 40.31 2.85
676 965 1.967319 ACGTCATTTGGTGTGCTCTT 58.033 45.000 0.00 0.00 0.00 2.85
756 1045 2.437895 ATGCCCGTCTCTCGTCGA 60.438 61.111 0.00 0.00 37.94 4.20
801 1091 3.589495 AACACGAGCTACCTTTCTACC 57.411 47.619 0.00 0.00 0.00 3.18
860 1150 1.080093 TTGGCGCGTAGTTGGAGAG 60.080 57.895 8.43 0.00 0.00 3.20
861 1151 1.373748 GTTGGCGCGTAGTTGGAGA 60.374 57.895 8.43 0.00 0.00 3.71
862 1152 2.388232 GGTTGGCGCGTAGTTGGAG 61.388 63.158 8.43 0.00 0.00 3.86
863 1153 2.357760 GGTTGGCGCGTAGTTGGA 60.358 61.111 8.43 0.00 0.00 3.53
864 1154 3.428282 GGGTTGGCGCGTAGTTGG 61.428 66.667 8.43 0.00 0.00 3.77
865 1155 2.666862 TGGGTTGGCGCGTAGTTG 60.667 61.111 8.43 0.00 0.00 3.16
866 1156 2.667199 GTGGGTTGGCGCGTAGTT 60.667 61.111 8.43 0.00 0.00 2.24
882 1172 0.751643 AGGCCGTTGTTTCAGCAAGT 60.752 50.000 0.00 0.00 0.00 3.16
1348 1647 4.274950 ACGAACAATGAACACGAAAATCCT 59.725 37.500 0.00 0.00 0.00 3.24
1373 1672 4.708726 AAATGGAAGAATGGCTCTTTCG 57.291 40.909 0.00 0.00 44.82 3.46
1461 1765 6.034898 CAGTTTTGTTTGAACCACTTGTGATC 59.965 38.462 1.89 1.62 0.00 2.92
1511 1815 7.094463 GGTCCATCCATCTCATAAAATGTCATC 60.094 40.741 0.00 0.00 35.97 2.92
1561 1865 4.098349 TGATTGCTTAGATCATTTGCCCAC 59.902 41.667 0.00 0.00 0.00 4.61
1620 2155 6.235231 ACAATGAACCCATACTCTTACGAT 57.765 37.500 0.00 0.00 31.59 3.73
1622 2157 6.570692 AGTACAATGAACCCATACTCTTACG 58.429 40.000 0.00 0.00 31.59 3.18
1701 2239 3.181443 CCTCATTCCAACTATGTACCCCC 60.181 52.174 0.00 0.00 0.00 5.40
1702 2240 3.181443 CCCTCATTCCAACTATGTACCCC 60.181 52.174 0.00 0.00 0.00 4.95
1703 2241 3.458487 ACCCTCATTCCAACTATGTACCC 59.542 47.826 0.00 0.00 0.00 3.69
1729 2267 2.744202 AGTCTTGAATCCATGTTCGCAC 59.256 45.455 0.00 0.00 0.00 5.34
1756 2294 0.252375 TTCCTAGTACGTTGGGGCCT 60.252 55.000 0.84 0.00 0.00 5.19
2176 2716 6.331369 AGATCCCTTAAACATTGTGTTGTG 57.669 37.500 0.00 0.00 40.14 3.33
2316 2861 7.328277 TCTCAAAGAGATAGAGTTCACTAGC 57.672 40.000 0.00 0.00 33.35 3.42
2413 2958 4.692625 CCCTGTTTCACAATCACTCTACAG 59.307 45.833 0.00 0.00 33.39 2.74
2440 2985 5.220228 CGTATGTAAGCAGCAGTTTAGACAC 60.220 44.000 0.00 0.00 0.00 3.67
2443 2991 5.068234 ACGTATGTAAGCAGCAGTTTAGA 57.932 39.130 0.00 0.00 0.00 2.10
2508 3056 2.827755 TGCTCTCACCTACCAATGGTA 58.172 47.619 12.12 12.12 37.09 3.25
2592 3140 9.627123 CTATTGGAGGGTTTGATACTATTGAAA 57.373 33.333 0.00 0.00 0.00 2.69
2666 3379 2.957402 AAACTCATCTTGTGGGCTCA 57.043 45.000 0.00 0.00 0.00 4.26
2756 3469 9.347934 GATGGTGAATTCGTACTATGATAGAAG 57.652 37.037 6.45 0.00 0.00 2.85
2760 3473 6.070995 GGGGATGGTGAATTCGTACTATGATA 60.071 42.308 0.04 0.00 0.00 2.15
2783 3499 1.135960 GAGGAGAAAGGATGAGGGGG 58.864 60.000 0.00 0.00 0.00 5.40
2793 3509 4.891992 TTAGGAACTGTGGAGGAGAAAG 57.108 45.455 0.00 0.00 41.52 2.62
2807 3523 4.454728 TGCCAAATCAGCATTTAGGAAC 57.545 40.909 0.00 0.00 34.69 3.62
2889 3610 6.787085 AAGGACAAGAATAGTGAAGAAACG 57.213 37.500 0.00 0.00 0.00 3.60
3264 3986 2.182312 AGATGGATAGGGCTCCCAGTAA 59.818 50.000 7.82 0.00 38.92 2.24
3328 4053 8.405418 TGTAGAGGAATATACAGAAATAGCGT 57.595 34.615 0.00 0.00 0.00 5.07
3329 4054 9.862371 AATGTAGAGGAATATACAGAAATAGCG 57.138 33.333 0.00 0.00 35.49 4.26
3770 4497 9.787435 AGTAAAACAGGAAATTCACACATACTA 57.213 29.630 0.00 0.00 0.00 1.82
4562 5300 4.174411 TCTGACAAGACGTTAGGTGATG 57.826 45.455 0.00 0.00 32.14 3.07
4563 5301 4.707448 AGATCTGACAAGACGTTAGGTGAT 59.293 41.667 0.00 0.00 34.48 3.06
4615 5353 6.784969 AGTGATGCACTAAGATAGGGTATTCT 59.215 38.462 0.00 0.00 43.46 2.40
4713 5500 3.139077 CACCTTCTACTCAAACCACACC 58.861 50.000 0.00 0.00 0.00 4.16
4901 5689 4.696877 TGATATGCACTCTTTGAACACCAG 59.303 41.667 0.00 0.00 0.00 4.00
5097 5885 5.695363 GTGTACTGGACCTAGACTTTTTGTC 59.305 44.000 0.00 0.00 45.67 3.18
5100 5888 5.881923 TGTGTACTGGACCTAGACTTTTT 57.118 39.130 0.00 0.00 0.00 1.94
5566 6364 8.588472 CATGTGATAGGTAGGACATGAATCTTA 58.412 37.037 0.00 0.00 45.66 2.10
5805 6603 3.460857 AGAAGCTGAAGAGACGTTGTT 57.539 42.857 0.00 0.00 0.00 2.83
5806 6604 3.126831 CAAGAAGCTGAAGAGACGTTGT 58.873 45.455 0.00 0.00 0.00 3.32
5962 6760 1.645919 ACCAAGCAACTTATCCCCCAT 59.354 47.619 0.00 0.00 0.00 4.00
6056 6860 8.864024 CAGAGTATATTATGCAATAGAACACCG 58.136 37.037 0.00 0.00 30.22 4.94
6187 7011 5.883661 CATTGCGAATGTTAAAGATCAGGT 58.116 37.500 0.00 0.00 34.18 4.00
6241 7065 4.770010 TGCATACCTCGACATGTATCCATA 59.230 41.667 0.00 0.00 0.00 2.74
6248 7072 2.233676 TCAACTGCATACCTCGACATGT 59.766 45.455 0.00 0.00 0.00 3.21
6286 7110 6.284459 TGTTTTTATGAAATGACACCCCAAC 58.716 36.000 0.00 0.00 0.00 3.77
6367 7191 0.983467 TATGGCTGCAACAGGAGTCA 59.017 50.000 0.50 0.00 39.66 3.41
6368 7192 1.661341 CTATGGCTGCAACAGGAGTC 58.339 55.000 0.50 0.00 31.21 3.36
6412 7236 1.032014 GGGCACAGTGAAACATGTGT 58.968 50.000 4.15 0.00 43.28 3.72
6474 7298 8.923270 TGATGTGGTTTCTTTTCTATCCTTTTT 58.077 29.630 0.00 0.00 0.00 1.94
6479 7303 8.110860 TCTTTGATGTGGTTTCTTTTCTATCC 57.889 34.615 0.00 0.00 0.00 2.59
6693 7518 5.642063 ACGAGAGAAAAATCGCCAGATTAAA 59.358 36.000 0.00 0.00 45.66 1.52
6744 7569 5.295944 AGTAGAAACTAACACCGGCAGGTA 61.296 45.833 8.66 0.00 41.14 3.08
6864 7689 4.053295 GTCCGTGTAGTAAGCAAGAACAA 58.947 43.478 0.00 0.00 0.00 2.83
7051 7888 9.358872 GCTTTCTTATGAAACTTGGGATTTAAG 57.641 33.333 0.00 0.00 37.27 1.85
7139 7977 5.609423 AGAGATGTCCTAGTGAAATCATGC 58.391 41.667 11.67 3.99 39.82 4.06
7172 8010 4.081420 GCACCCTCTAAGAAATGACTGAGA 60.081 45.833 0.00 0.00 0.00 3.27
7178 8016 2.912956 AGTGGCACCCTCTAAGAAATGA 59.087 45.455 15.27 0.00 0.00 2.57
7200 8038 7.041721 TCTCGTCTACATGAACAAAATGCTAT 58.958 34.615 0.00 0.00 0.00 2.97
7348 8186 6.747280 CACAAAAATTAACCTCGCCAATAGAG 59.253 38.462 0.00 0.00 35.60 2.43
7366 8204 6.696411 ACAGATTGTTTCTTCACCACAAAAA 58.304 32.000 0.00 0.00 34.19 1.94
7369 8207 5.652014 AGAACAGATTGTTTCTTCACCACAA 59.348 36.000 0.00 0.00 41.28 3.33
7371 8209 5.757850 AGAACAGATTGTTTCTTCACCAC 57.242 39.130 0.00 0.00 41.28 4.16
7493 8334 2.097142 GCACTTCATCATTCACTGGAGC 59.903 50.000 0.00 0.00 0.00 4.70
7774 8620 2.621055 ACCAGTGCAGATATCTCGTCTC 59.379 50.000 1.03 0.00 0.00 3.36
7971 8819 6.515696 GCTTTTCCAGGGAAGCATCATTATAC 60.516 42.308 18.42 0.00 45.74 1.47
8046 8894 1.378882 CCCATCAGTGAACATGCCGG 61.379 60.000 0.00 0.00 0.00 6.13
8051 8899 6.257994 AGAATATGTCCCATCAGTGAACAT 57.742 37.500 11.79 11.79 0.00 2.71
8090 8938 9.231297 TCCATTACCATTTTCTTTTCAGAGTAG 57.769 33.333 0.00 0.00 0.00 2.57
8146 9315 5.445964 AGAAAACCGCCACCAAGATATAAT 58.554 37.500 0.00 0.00 0.00 1.28
8151 9320 1.995376 AAGAAAACCGCCACCAAGAT 58.005 45.000 0.00 0.00 0.00 2.40
8152 9321 1.679153 GAAAGAAAACCGCCACCAAGA 59.321 47.619 0.00 0.00 0.00 3.02
8153 9322 1.681264 AGAAAGAAAACCGCCACCAAG 59.319 47.619 0.00 0.00 0.00 3.61
8155 9324 1.133915 AGAGAAAGAAAACCGCCACCA 60.134 47.619 0.00 0.00 0.00 4.17
8156 9325 1.605753 AGAGAAAGAAAACCGCCACC 58.394 50.000 0.00 0.00 0.00 4.61
8174 9371 3.253188 TCGAAATCAAAGGTGGAAGCAAG 59.747 43.478 0.00 0.00 36.26 4.01
8186 9383 4.258543 GGAGGGTGTACATCGAAATCAAA 58.741 43.478 0.00 0.00 0.00 2.69
8224 9421 7.439108 ACCTCTGTTCCTAAATATAAGCTGT 57.561 36.000 0.00 0.00 0.00 4.40
8403 9607 3.392882 CATGTGCGGCATCTGATAAGTA 58.607 45.455 5.72 0.00 35.19 2.24
8430 9645 1.878088 CAAGCTAATCTCGGCATGCAT 59.122 47.619 21.36 0.42 0.00 3.96
8485 9700 4.855340 TGAAATTTATTCCTCTCCGGCTT 58.145 39.130 0.00 0.00 0.00 4.35
8570 9790 4.994756 GGCACCCACCCACCTTGG 62.995 72.222 0.00 0.00 37.25 3.61
8572 9792 3.110031 AAGGCACCCACCCACCTT 61.110 61.111 0.00 0.00 37.69 3.50
8573 9793 3.580319 GAAGGCACCCACCCACCT 61.580 66.667 0.00 0.00 0.00 4.00
8574 9794 2.730129 AATGAAGGCACCCACCCACC 62.730 60.000 0.00 0.00 0.00 4.61
8575 9795 1.228862 AATGAAGGCACCCACCCAC 60.229 57.895 0.00 0.00 0.00 4.61
8576 9796 1.228831 CAATGAAGGCACCCACCCA 60.229 57.895 0.00 0.00 0.00 4.51
8577 9797 2.649129 GCAATGAAGGCACCCACCC 61.649 63.158 0.00 0.00 0.00 4.61
8635 9859 5.662456 AGATTCTCACACTGATGATGACAG 58.338 41.667 0.00 0.00 40.68 3.51
8670 9894 5.486775 AGGGAGTATTACCTGATGATGATGG 59.513 44.000 0.00 0.00 35.30 3.51
8681 9905 2.246849 AGGAACGGAGGGAGTATTACCT 59.753 50.000 0.00 0.00 40.54 3.08
8689 9913 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
8690 9914 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
8691 9915 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
8692 9916 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
8693 9917 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
8711 9935 9.827411 GGTTCATAGTGAAATTTCTACAAAGAC 57.173 33.333 18.64 7.04 38.22 3.01
8712 9936 9.567776 TGGTTCATAGTGAAATTTCTACAAAGA 57.432 29.630 18.64 7.52 38.22 2.52
8713 9937 9.612620 GTGGTTCATAGTGAAATTTCTACAAAG 57.387 33.333 18.64 5.49 38.22 2.77
8714 9938 9.126151 TGTGGTTCATAGTGAAATTTCTACAAA 57.874 29.630 18.64 8.40 38.22 2.83
8715 9939 8.684386 TGTGGTTCATAGTGAAATTTCTACAA 57.316 30.769 18.64 3.14 38.22 2.41
8716 9940 8.862325 ATGTGGTTCATAGTGAAATTTCTACA 57.138 30.769 18.64 4.82 38.22 2.74
8718 9942 9.093970 CGTATGTGGTTCATAGTGAAATTTCTA 57.906 33.333 18.64 4.82 38.22 2.10
8719 9943 7.065803 CCGTATGTGGTTCATAGTGAAATTTCT 59.934 37.037 18.64 2.61 38.22 2.52
8720 9944 7.186804 CCGTATGTGGTTCATAGTGAAATTTC 58.813 38.462 11.41 11.41 38.22 2.17
8721 9945 7.083875 CCGTATGTGGTTCATAGTGAAATTT 57.916 36.000 0.00 0.00 38.22 1.82
8722 9946 6.677781 CCGTATGTGGTTCATAGTGAAATT 57.322 37.500 0.00 0.00 38.22 1.82


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

AutoCloner maintained by Alex Coulton.