Multiple sequence alignment - TraesCS2A01G236800

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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 TraesCS2A01G236800 chr2A 100.000 6222 0 0 1 6222 305830045 305823824 0.000000e+00 11490
1 TraesCS2A01G236800 chr2A 96.715 2770 85 6 1669 4435 374483438 374486204 0.000000e+00 4606
2 TraesCS2A01G236800 chr2A 96.573 2772 89 6 1669 4435 628569566 628572336 0.000000e+00 4588
3 TraesCS2A01G236800 chr2A 94.032 1709 90 7 3806 5509 756945365 756943664 0.000000e+00 2580
4 TraesCS2A01G236800 chr2A 94.353 726 35 3 5503 6222 252023151 252022426 0.000000e+00 1109
5 TraesCS2A01G236800 chr2A 94.306 720 37 1 5507 6222 252013248 252012529 0.000000e+00 1099
6 TraesCS2A01G236800 chr2A 93.889 720 40 1 5507 6222 358474318 358475037 0.000000e+00 1083
7 TraesCS2A01G236800 chr2A 93.434 731 38 7 5500 6222 240258518 240257790 0.000000e+00 1075
8 TraesCS2A01G236800 chr2A 98.611 72 1 0 1 72 367681501 367681430 1.820000e-25 128
9 TraesCS2A01G236800 chr5B 98.550 5449 65 6 66 5511 411791677 411797114 0.000000e+00 9612
10 TraesCS2A01G236800 chr5B 87.092 736 51 21 65 766 629258822 629258097 0.000000e+00 793
11 TraesCS2A01G236800 chr5B 86.290 744 51 16 65 766 629346867 629346133 0.000000e+00 761
12 TraesCS2A01G236800 chr7B 98.912 4412 41 7 71 4478 630138613 630134205 0.000000e+00 7875
13 TraesCS2A01G236800 chr7B 89.806 206 20 1 1028 1232 713956087 713956292 4.780000e-66 263
14 TraesCS2A01G236800 chr4B 92.479 3962 247 20 1560 5509 256160213 256156291 0.000000e+00 5618
15 TraesCS2A01G236800 chr4B 89.447 976 77 16 65 1023 256161455 256160489 0.000000e+00 1208
16 TraesCS2A01G236800 chr4B 90.074 272 16 3 1233 1493 256160495 256160224 5.970000e-90 342
17 TraesCS2A01G236800 chr2D 93.416 3569 193 20 1233 4784 276940565 276944108 0.000000e+00 5251
18 TraesCS2A01G236800 chr2D 90.333 931 60 13 104 1023 276939660 276940571 0.000000e+00 1194
19 TraesCS2A01G236800 chr2D 89.855 207 16 2 1025 1226 634854604 634854398 1.720000e-65 261
20 TraesCS2A01G236800 chr5A 94.634 3187 143 15 1269 4435 272284070 272287248 0.000000e+00 4913
21 TraesCS2A01G236800 chr7A 94.847 3144 127 11 1233 4356 607605791 607608919 0.000000e+00 4876
22 TraesCS2A01G236800 chr7A 94.552 1707 82 7 3806 5509 2870254 2871952 0.000000e+00 2627
23 TraesCS2A01G236800 chr7A 93.860 1710 92 7 3806 5509 85878818 85877116 0.000000e+00 2564
24 TraesCS2A01G236800 chr7A 93.333 960 52 7 68 1024 607604848 607605798 0.000000e+00 1408
25 TraesCS2A01G236800 chr7A 94.036 721 38 2 5507 6222 512730771 512730051 0.000000e+00 1088
26 TraesCS2A01G236800 chr7A 90.286 350 15 5 1233 1567 2869909 2870254 2.060000e-119 440
27 TraesCS2A01G236800 chr7A 89.714 350 17 5 1233 1567 85879163 85878818 4.460000e-116 429
28 TraesCS2A01G236800 chr1B 96.751 2770 86 4 1669 4435 95491803 95494571 0.000000e+00 4614
29 TraesCS2A01G236800 chr1B 96.751 2770 86 4 1669 4435 530764362 530761594 0.000000e+00 4614
30 TraesCS2A01G236800 chr6A 94.204 1708 88 7 3806 5509 604391783 604393483 0.000000e+00 2595
31 TraesCS2A01G236800 chr6A 86.278 634 58 15 65 682 604390281 604390901 0.000000e+00 662
32 TraesCS2A01G236800 chr6A 97.222 72 2 0 1 72 66794703 66794774 8.470000e-24 122
33 TraesCS2A01G236800 chr6A 97.222 72 2 0 1 72 135348332 135348261 8.470000e-24 122
34 TraesCS2A01G236800 chr6A 97.222 72 2 0 1 72 249116689 249116760 8.470000e-24 122
35 TraesCS2A01G236800 chr6A 97.222 72 2 0 1 72 328790391 328790320 8.470000e-24 122
36 TraesCS2A01G236800 chr6A 97.222 72 2 0 1 72 346605178 346605249 8.470000e-24 122
37 TraesCS2A01G236800 chr6A 93.750 80 3 2 1 78 571717716 571717795 1.100000e-22 119
38 TraesCS2A01G236800 chr3A 93.966 1707 92 7 3806 5509 26421876 26420178 0.000000e+00 2571
39 TraesCS2A01G236800 chr3A 94.306 720 37 1 5507 6222 279319318 279320037 0.000000e+00 1099
40 TraesCS2A01G236800 chr3A 94.036 721 37 3 5507 6222 143840582 143841301 0.000000e+00 1088
41 TraesCS2A01G236800 chr3A 87.279 621 50 16 78 682 26423365 26422758 0.000000e+00 682
42 TraesCS2A01G236800 chr3A 89.714 350 17 5 1233 1567 26422221 26421876 4.460000e-116 429
43 TraesCS2A01G236800 chr4A 93.918 1710 91 7 3806 5509 684408419 684410121 0.000000e+00 2569
44 TraesCS2A01G236800 chr4A 94.452 721 34 3 5507 6222 415822224 415822943 0.000000e+00 1105
45 TraesCS2A01G236800 chr4A 94.036 721 38 2 5507 6222 234064175 234064895 0.000000e+00 1088
46 TraesCS2A01G236800 chr4A 90.000 350 16 5 1233 1567 684408074 684408419 9.580000e-118 435
47 TraesCS2A01G236800 chr6B 94.979 1195 57 3 4309 5501 519185413 519186606 0.000000e+00 1871
48 TraesCS2A01G236800 chr7D 88.935 723 44 16 66 763 474676198 474676909 0.000000e+00 859
49 TraesCS2A01G236800 chr7D 89.541 545 35 11 1256 1784 364737430 364737968 0.000000e+00 671
50 TraesCS2A01G236800 chr7D 89.809 471 33 7 553 1022 364736985 364737441 1.930000e-164 590
51 TraesCS2A01G236800 chr7D 90.110 182 17 1 1025 1205 93614300 93614119 1.040000e-57 235
52 TraesCS2A01G236800 chr2B 90.351 342 18 3 1269 1595 244700936 244701277 9.580000e-118 435
53 TraesCS2A01G236800 chr5D 91.429 210 17 1 1024 1232 422430321 422430530 2.840000e-73 287
54 TraesCS2A01G236800 chr3D 86.730 211 23 2 1024 1229 431320307 431320097 4.850000e-56 230
55 TraesCS2A01G236800 chr1A 97.222 72 2 0 1 72 31259604 31259533 8.470000e-24 122
56 TraesCS2A01G236800 chr1A 93.750 80 3 2 1 78 269271790 269271711 1.100000e-22 119


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 TraesCS2A01G236800 chr2A 305823824 305830045 6221 True 11490.000000 11490 100.000000 1 6222 1 chr2A.!!$R4 6221
1 TraesCS2A01G236800 chr2A 374483438 374486204 2766 False 4606.000000 4606 96.715000 1669 4435 1 chr2A.!!$F2 2766
2 TraesCS2A01G236800 chr2A 628569566 628572336 2770 False 4588.000000 4588 96.573000 1669 4435 1 chr2A.!!$F3 2766
3 TraesCS2A01G236800 chr2A 756943664 756945365 1701 True 2580.000000 2580 94.032000 3806 5509 1 chr2A.!!$R6 1703
4 TraesCS2A01G236800 chr2A 252022426 252023151 725 True 1109.000000 1109 94.353000 5503 6222 1 chr2A.!!$R3 719
5 TraesCS2A01G236800 chr2A 252012529 252013248 719 True 1099.000000 1099 94.306000 5507 6222 1 chr2A.!!$R2 715
6 TraesCS2A01G236800 chr2A 358474318 358475037 719 False 1083.000000 1083 93.889000 5507 6222 1 chr2A.!!$F1 715
7 TraesCS2A01G236800 chr2A 240257790 240258518 728 True 1075.000000 1075 93.434000 5500 6222 1 chr2A.!!$R1 722
8 TraesCS2A01G236800 chr5B 411791677 411797114 5437 False 9612.000000 9612 98.550000 66 5511 1 chr5B.!!$F1 5445
9 TraesCS2A01G236800 chr5B 629258097 629258822 725 True 793.000000 793 87.092000 65 766 1 chr5B.!!$R1 701
10 TraesCS2A01G236800 chr5B 629346133 629346867 734 True 761.000000 761 86.290000 65 766 1 chr5B.!!$R2 701
11 TraesCS2A01G236800 chr7B 630134205 630138613 4408 True 7875.000000 7875 98.912000 71 4478 1 chr7B.!!$R1 4407
12 TraesCS2A01G236800 chr4B 256156291 256161455 5164 True 2389.333333 5618 90.666667 65 5509 3 chr4B.!!$R1 5444
13 TraesCS2A01G236800 chr2D 276939660 276944108 4448 False 3222.500000 5251 91.874500 104 4784 2 chr2D.!!$F1 4680
14 TraesCS2A01G236800 chr5A 272284070 272287248 3178 False 4913.000000 4913 94.634000 1269 4435 1 chr5A.!!$F1 3166
15 TraesCS2A01G236800 chr7A 607604848 607608919 4071 False 3142.000000 4876 94.090000 68 4356 2 chr7A.!!$F2 4288
16 TraesCS2A01G236800 chr7A 2869909 2871952 2043 False 1533.500000 2627 92.419000 1233 5509 2 chr7A.!!$F1 4276
17 TraesCS2A01G236800 chr7A 85877116 85879163 2047 True 1496.500000 2564 91.787000 1233 5509 2 chr7A.!!$R2 4276
18 TraesCS2A01G236800 chr7A 512730051 512730771 720 True 1088.000000 1088 94.036000 5507 6222 1 chr7A.!!$R1 715
19 TraesCS2A01G236800 chr1B 95491803 95494571 2768 False 4614.000000 4614 96.751000 1669 4435 1 chr1B.!!$F1 2766
20 TraesCS2A01G236800 chr1B 530761594 530764362 2768 True 4614.000000 4614 96.751000 1669 4435 1 chr1B.!!$R1 2766
21 TraesCS2A01G236800 chr6A 604390281 604393483 3202 False 1628.500000 2595 90.241000 65 5509 2 chr6A.!!$F5 5444
22 TraesCS2A01G236800 chr3A 26420178 26423365 3187 True 1227.333333 2571 90.319667 78 5509 3 chr3A.!!$R1 5431
23 TraesCS2A01G236800 chr3A 279319318 279320037 719 False 1099.000000 1099 94.306000 5507 6222 1 chr3A.!!$F2 715
24 TraesCS2A01G236800 chr3A 143840582 143841301 719 False 1088.000000 1088 94.036000 5507 6222 1 chr3A.!!$F1 715
25 TraesCS2A01G236800 chr4A 684408074 684410121 2047 False 1502.000000 2569 91.959000 1233 5509 2 chr4A.!!$F3 4276
26 TraesCS2A01G236800 chr4A 415822224 415822943 719 False 1105.000000 1105 94.452000 5507 6222 1 chr4A.!!$F2 715
27 TraesCS2A01G236800 chr4A 234064175 234064895 720 False 1088.000000 1088 94.036000 5507 6222 1 chr4A.!!$F1 715
28 TraesCS2A01G236800 chr6B 519185413 519186606 1193 False 1871.000000 1871 94.979000 4309 5501 1 chr6B.!!$F1 1192
29 TraesCS2A01G236800 chr7D 474676198 474676909 711 False 859.000000 859 88.935000 66 763 1 chr7D.!!$F1 697
30 TraesCS2A01G236800 chr7D 364736985 364737968 983 False 630.500000 671 89.675000 553 1784 2 chr7D.!!$F2 1231

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
37 38 1.135721 GGCAAAGCAAGGCCTAGAATG 59.864 52.381 5.16 0.41 46.74 2.67 F
1034 1612 0.035152 TCTTCATGGCAGTGGCGAAT 60.035 50.000 12.58 0.00 42.47 3.34 F
1156 1734 0.032267 GGCTAGGCCTAACTAGTGCG 59.968 60.000 14.85 0.12 46.69 5.34 F
1213 1791 0.183492 TTGAGCCTGTTCAAGCCTGT 59.817 50.000 0.00 0.00 32.39 4.00 F
1216 1794 0.183492 AGCCTGTTCAAGCCTGTTGA 59.817 50.000 0.00 0.00 0.00 3.18 F
1880 2489 0.191064 TAGGGAGCGGAGGATTCCAT 59.809 55.000 5.29 0.00 44.26 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1620 0.255890 TCAGCCTACCCTCCATTTGC 59.744 55.000 0.00 0.0 0.00 3.68 R
2972 3583 1.589803 TGATGAGCAATGGCATCTCG 58.410 50.000 0.00 0.0 44.61 4.04 R
3332 3957 1.002430 TCCATTGCGCTCTGTCTTCTT 59.998 47.619 9.73 0.0 0.00 2.52 R
4427 5062 7.631717 AAATAGAAGCAGAATTTGAGTACCC 57.368 36.000 0.00 0.0 0.00 3.69 R
4892 5531 5.989551 ACTTTTGGCAATCAACAATCAAC 57.010 34.783 0.00 0.0 34.67 3.18 R
5406 6050 1.230050 ACCCCTACCATTCCCCGTT 60.230 57.895 0.00 0.0 0.00 4.44 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
22 23 5.957842 CTACAGGAACTTAACATGGCAAA 57.042 39.130 0.00 0.00 34.60 3.68
23 24 4.853924 ACAGGAACTTAACATGGCAAAG 57.146 40.909 0.00 0.00 34.60 2.77
24 25 3.005791 ACAGGAACTTAACATGGCAAAGC 59.994 43.478 0.00 0.00 34.60 3.51
25 26 3.005684 CAGGAACTTAACATGGCAAAGCA 59.994 43.478 0.00 0.00 34.60 3.91
26 27 3.640967 AGGAACTTAACATGGCAAAGCAA 59.359 39.130 0.00 0.00 27.25 3.91
27 28 3.989817 GGAACTTAACATGGCAAAGCAAG 59.010 43.478 0.00 0.00 0.00 4.01
28 29 3.665745 ACTTAACATGGCAAAGCAAGG 57.334 42.857 0.00 0.00 0.00 3.61
29 30 2.289010 ACTTAACATGGCAAAGCAAGGC 60.289 45.455 0.00 0.00 0.00 4.35
34 35 4.743018 GGCAAAGCAAGGCCTAGA 57.257 55.556 5.16 0.00 46.74 2.43
35 36 2.961424 GGCAAAGCAAGGCCTAGAA 58.039 52.632 5.16 0.00 46.74 2.10
36 37 1.478631 GGCAAAGCAAGGCCTAGAAT 58.521 50.000 5.16 0.00 46.74 2.40
37 38 1.135721 GGCAAAGCAAGGCCTAGAATG 59.864 52.381 5.16 0.41 46.74 2.67
38 39 2.094675 GCAAAGCAAGGCCTAGAATGA 58.905 47.619 5.16 0.00 0.00 2.57
39 40 2.493278 GCAAAGCAAGGCCTAGAATGAA 59.507 45.455 5.16 0.00 0.00 2.57
40 41 3.428589 GCAAAGCAAGGCCTAGAATGAAG 60.429 47.826 5.16 0.00 0.00 3.02
41 42 2.049888 AGCAAGGCCTAGAATGAAGC 57.950 50.000 5.16 0.20 0.00 3.86
42 43 1.563410 AGCAAGGCCTAGAATGAAGCT 59.437 47.619 5.16 2.79 0.00 3.74
43 44 2.774234 AGCAAGGCCTAGAATGAAGCTA 59.226 45.455 5.16 0.00 0.00 3.32
44 45 2.875317 GCAAGGCCTAGAATGAAGCTAC 59.125 50.000 5.16 0.00 0.00 3.58
45 46 3.432890 GCAAGGCCTAGAATGAAGCTACT 60.433 47.826 5.16 0.00 0.00 2.57
46 47 4.376146 CAAGGCCTAGAATGAAGCTACTC 58.624 47.826 5.16 0.00 0.00 2.59
47 48 3.647636 AGGCCTAGAATGAAGCTACTCA 58.352 45.455 1.29 0.00 0.00 3.41
48 49 4.033709 AGGCCTAGAATGAAGCTACTCAA 58.966 43.478 1.29 0.00 0.00 3.02
49 50 4.471386 AGGCCTAGAATGAAGCTACTCAAA 59.529 41.667 1.29 0.00 0.00 2.69
50 51 4.813697 GGCCTAGAATGAAGCTACTCAAAG 59.186 45.833 0.00 0.00 0.00 2.77
51 52 4.272261 GCCTAGAATGAAGCTACTCAAAGC 59.728 45.833 0.00 0.00 43.11 3.51
52 53 5.423015 CCTAGAATGAAGCTACTCAAAGCA 58.577 41.667 0.00 0.00 45.30 3.91
53 54 5.293079 CCTAGAATGAAGCTACTCAAAGCAC 59.707 44.000 0.00 0.00 45.30 4.40
54 55 4.904241 AGAATGAAGCTACTCAAAGCACT 58.096 39.130 0.00 0.00 45.30 4.40
55 56 5.312079 AGAATGAAGCTACTCAAAGCACTT 58.688 37.500 0.00 0.00 45.30 3.16
56 57 6.467677 AGAATGAAGCTACTCAAAGCACTTA 58.532 36.000 0.00 0.00 45.30 2.24
57 58 6.936900 AGAATGAAGCTACTCAAAGCACTTAA 59.063 34.615 0.00 0.00 45.30 1.85
58 59 5.924475 TGAAGCTACTCAAAGCACTTAAC 57.076 39.130 0.00 0.00 45.30 2.01
59 60 5.364778 TGAAGCTACTCAAAGCACTTAACA 58.635 37.500 0.00 0.00 45.30 2.41
60 61 5.820423 TGAAGCTACTCAAAGCACTTAACAA 59.180 36.000 0.00 0.00 45.30 2.83
61 62 6.317642 TGAAGCTACTCAAAGCACTTAACAAA 59.682 34.615 0.00 0.00 45.30 2.83
62 63 6.693315 AGCTACTCAAAGCACTTAACAAAA 57.307 33.333 0.00 0.00 45.30 2.44
63 64 6.729187 AGCTACTCAAAGCACTTAACAAAAG 58.271 36.000 0.00 0.00 45.30 2.27
310 319 4.877619 TCTCCCGAGCGAGGCGAT 62.878 66.667 0.00 0.00 0.00 4.58
544 579 4.548513 CTCTCCCCCTCCCCCTCG 62.549 77.778 0.00 0.00 0.00 4.63
1024 1602 8.894768 AGTATATAAGTTGTTCTCTTCATGGC 57.105 34.615 0.00 0.00 0.00 4.40
1025 1603 8.486210 AGTATATAAGTTGTTCTCTTCATGGCA 58.514 33.333 0.00 0.00 0.00 4.92
1026 1604 7.798596 ATATAAGTTGTTCTCTTCATGGCAG 57.201 36.000 0.00 0.00 0.00 4.85
1027 1605 3.498774 AGTTGTTCTCTTCATGGCAGT 57.501 42.857 0.00 0.00 0.00 4.40
1028 1606 3.144506 AGTTGTTCTCTTCATGGCAGTG 58.855 45.455 0.00 0.00 0.00 3.66
1029 1607 2.189594 TGTTCTCTTCATGGCAGTGG 57.810 50.000 0.00 0.00 0.00 4.00
1030 1608 0.807496 GTTCTCTTCATGGCAGTGGC 59.193 55.000 10.30 10.30 40.13 5.01
1031 1609 0.674581 TTCTCTTCATGGCAGTGGCG 60.675 55.000 12.58 0.00 42.47 5.69
1032 1610 1.078918 CTCTTCATGGCAGTGGCGA 60.079 57.895 12.58 0.88 42.47 5.54
1033 1611 0.674581 CTCTTCATGGCAGTGGCGAA 60.675 55.000 12.58 9.27 42.47 4.70
1034 1612 0.035152 TCTTCATGGCAGTGGCGAAT 60.035 50.000 12.58 0.00 42.47 3.34
1035 1613 0.379669 CTTCATGGCAGTGGCGAATC 59.620 55.000 12.58 0.00 42.47 2.52
1036 1614 0.035152 TTCATGGCAGTGGCGAATCT 60.035 50.000 12.58 0.00 42.47 2.40
1037 1615 0.829990 TCATGGCAGTGGCGAATCTA 59.170 50.000 12.58 0.00 42.47 1.98
1038 1616 1.202568 TCATGGCAGTGGCGAATCTAG 60.203 52.381 12.58 0.00 42.47 2.43
1039 1617 0.107456 ATGGCAGTGGCGAATCTAGG 59.893 55.000 12.58 0.00 42.47 3.02
1040 1618 0.975556 TGGCAGTGGCGAATCTAGGA 60.976 55.000 12.58 0.00 42.47 2.94
1041 1619 0.530870 GGCAGTGGCGAATCTAGGAC 60.531 60.000 0.00 0.00 42.47 3.85
1042 1620 0.872021 GCAGTGGCGAATCTAGGACG 60.872 60.000 0.00 0.00 0.00 4.79
1050 1628 2.821546 CGAATCTAGGACGCAAATGGA 58.178 47.619 0.00 0.00 0.00 3.41
1051 1629 2.797156 CGAATCTAGGACGCAAATGGAG 59.203 50.000 0.00 0.00 0.00 3.86
1052 1630 2.918712 ATCTAGGACGCAAATGGAGG 57.081 50.000 0.00 0.00 0.00 4.30
1053 1631 0.830648 TCTAGGACGCAAATGGAGGG 59.169 55.000 0.00 0.00 0.00 4.30
1054 1632 0.541863 CTAGGACGCAAATGGAGGGT 59.458 55.000 0.00 0.00 34.62 4.34
1055 1633 1.760613 CTAGGACGCAAATGGAGGGTA 59.239 52.381 0.00 0.00 31.85 3.69
1056 1634 0.541863 AGGACGCAAATGGAGGGTAG 59.458 55.000 0.00 0.00 31.85 3.18
1057 1635 0.463833 GGACGCAAATGGAGGGTAGG 60.464 60.000 0.00 0.00 31.85 3.18
1058 1636 1.077716 ACGCAAATGGAGGGTAGGC 60.078 57.895 0.00 0.00 0.00 3.93
1059 1637 1.224592 CGCAAATGGAGGGTAGGCT 59.775 57.895 0.00 0.00 0.00 4.58
1060 1638 1.097547 CGCAAATGGAGGGTAGGCTG 61.098 60.000 0.00 0.00 0.00 4.85
1061 1639 0.255890 GCAAATGGAGGGTAGGCTGA 59.744 55.000 0.00 0.00 0.00 4.26
1062 1640 1.340991 GCAAATGGAGGGTAGGCTGAA 60.341 52.381 0.00 0.00 0.00 3.02
1063 1641 2.369394 CAAATGGAGGGTAGGCTGAAC 58.631 52.381 0.00 0.00 0.00 3.18
1064 1642 1.972588 AATGGAGGGTAGGCTGAACT 58.027 50.000 0.00 0.00 0.00 3.01
1065 1643 1.972588 ATGGAGGGTAGGCTGAACTT 58.027 50.000 0.00 0.00 0.00 2.66
1066 1644 0.984230 TGGAGGGTAGGCTGAACTTG 59.016 55.000 0.00 0.00 0.00 3.16
1067 1645 1.276622 GGAGGGTAGGCTGAACTTGA 58.723 55.000 0.00 0.00 0.00 3.02
1068 1646 1.628846 GGAGGGTAGGCTGAACTTGAA 59.371 52.381 0.00 0.00 0.00 2.69
1069 1647 2.039879 GGAGGGTAGGCTGAACTTGAAA 59.960 50.000 0.00 0.00 0.00 2.69
1070 1648 3.308473 GGAGGGTAGGCTGAACTTGAAAT 60.308 47.826 0.00 0.00 0.00 2.17
1071 1649 4.080526 GGAGGGTAGGCTGAACTTGAAATA 60.081 45.833 0.00 0.00 0.00 1.40
1072 1650 4.844884 AGGGTAGGCTGAACTTGAAATAC 58.155 43.478 0.00 0.00 0.00 1.89
1073 1651 3.621715 GGGTAGGCTGAACTTGAAATACG 59.378 47.826 0.00 0.00 0.00 3.06
1074 1652 4.251268 GGTAGGCTGAACTTGAAATACGT 58.749 43.478 0.00 0.00 0.00 3.57
1075 1653 4.694037 GGTAGGCTGAACTTGAAATACGTT 59.306 41.667 0.00 0.00 0.00 3.99
1076 1654 5.870978 GGTAGGCTGAACTTGAAATACGTTA 59.129 40.000 0.00 0.00 0.00 3.18
1077 1655 6.369615 GGTAGGCTGAACTTGAAATACGTTAA 59.630 38.462 0.00 0.00 0.00 2.01
1078 1656 7.065443 GGTAGGCTGAACTTGAAATACGTTAAT 59.935 37.037 0.00 0.00 0.00 1.40
1079 1657 7.448748 AGGCTGAACTTGAAATACGTTAATT 57.551 32.000 0.00 0.00 0.00 1.40
1080 1658 7.882179 AGGCTGAACTTGAAATACGTTAATTT 58.118 30.769 0.00 0.00 0.00 1.82
1081 1659 8.357402 AGGCTGAACTTGAAATACGTTAATTTT 58.643 29.630 0.00 0.00 0.00 1.82
1082 1660 8.974408 GGCTGAACTTGAAATACGTTAATTTTT 58.026 29.630 0.00 0.00 0.00 1.94
1083 1661 9.777843 GCTGAACTTGAAATACGTTAATTTTTG 57.222 29.630 0.00 0.00 0.00 2.44
1088 1666 9.804758 ACTTGAAATACGTTAATTTTTGTTGGA 57.195 25.926 0.00 0.00 0.00 3.53
1090 1668 8.804688 TGAAATACGTTAATTTTTGTTGGAGG 57.195 30.769 0.00 0.00 0.00 4.30
1091 1669 7.382759 TGAAATACGTTAATTTTTGTTGGAGGC 59.617 33.333 0.00 0.00 0.00 4.70
1092 1670 4.657436 ACGTTAATTTTTGTTGGAGGCA 57.343 36.364 0.00 0.00 0.00 4.75
1093 1671 4.616953 ACGTTAATTTTTGTTGGAGGCAG 58.383 39.130 0.00 0.00 0.00 4.85
1094 1672 4.098807 ACGTTAATTTTTGTTGGAGGCAGT 59.901 37.500 0.00 0.00 0.00 4.40
1095 1673 4.444056 CGTTAATTTTTGTTGGAGGCAGTG 59.556 41.667 0.00 0.00 0.00 3.66
1096 1674 2.531522 ATTTTTGTTGGAGGCAGTGC 57.468 45.000 6.55 6.55 0.00 4.40
1097 1675 1.189752 TTTTTGTTGGAGGCAGTGCA 58.810 45.000 18.61 0.00 0.00 4.57
1098 1676 0.746063 TTTTGTTGGAGGCAGTGCAG 59.254 50.000 18.61 0.00 0.00 4.41
1099 1677 0.395586 TTTGTTGGAGGCAGTGCAGT 60.396 50.000 18.61 2.65 0.00 4.40
1100 1678 1.102809 TTGTTGGAGGCAGTGCAGTG 61.103 55.000 18.61 17.56 0.00 3.66
1101 1679 1.526917 GTTGGAGGCAGTGCAGTGT 60.527 57.895 22.22 3.74 0.00 3.55
1102 1680 1.526686 TTGGAGGCAGTGCAGTGTG 60.527 57.895 22.22 4.86 0.00 3.82
1103 1681 1.981951 TTGGAGGCAGTGCAGTGTGA 61.982 55.000 22.22 0.26 0.00 3.58
1104 1682 1.002868 GGAGGCAGTGCAGTGTGAT 60.003 57.895 22.22 8.97 0.00 3.06
1105 1683 1.303799 GGAGGCAGTGCAGTGTGATG 61.304 60.000 22.22 0.00 0.00 3.07
1106 1684 1.919956 GAGGCAGTGCAGTGTGATGC 61.920 60.000 22.22 7.79 46.68 3.91
1116 1694 3.961182 GCAGTGTGATGCAATAAGATGG 58.039 45.455 0.00 0.00 45.77 3.51
1117 1695 3.794475 GCAGTGTGATGCAATAAGATGGC 60.794 47.826 0.00 0.00 45.77 4.40
1118 1696 3.630769 CAGTGTGATGCAATAAGATGGCT 59.369 43.478 0.00 0.00 0.00 4.75
1119 1697 3.630769 AGTGTGATGCAATAAGATGGCTG 59.369 43.478 0.00 0.00 0.00 4.85
1120 1698 2.953648 TGTGATGCAATAAGATGGCTGG 59.046 45.455 0.00 0.00 0.00 4.85
1121 1699 3.216800 GTGATGCAATAAGATGGCTGGA 58.783 45.455 0.00 0.00 0.00 3.86
1122 1700 3.633525 GTGATGCAATAAGATGGCTGGAA 59.366 43.478 0.00 0.00 0.00 3.53
1123 1701 3.887110 TGATGCAATAAGATGGCTGGAAG 59.113 43.478 0.00 0.00 0.00 3.46
1124 1702 3.370840 TGCAATAAGATGGCTGGAAGT 57.629 42.857 0.00 0.00 35.30 3.01
1125 1703 3.700538 TGCAATAAGATGGCTGGAAGTT 58.299 40.909 0.00 0.00 35.30 2.66
1126 1704 4.088634 TGCAATAAGATGGCTGGAAGTTT 58.911 39.130 0.00 0.00 35.30 2.66
1127 1705 4.527816 TGCAATAAGATGGCTGGAAGTTTT 59.472 37.500 0.00 0.00 35.30 2.43
1128 1706 5.011943 TGCAATAAGATGGCTGGAAGTTTTT 59.988 36.000 0.00 0.00 35.30 1.94
1129 1707 6.210385 TGCAATAAGATGGCTGGAAGTTTTTA 59.790 34.615 0.00 0.00 35.30 1.52
1130 1708 7.093377 TGCAATAAGATGGCTGGAAGTTTTTAT 60.093 33.333 0.00 0.00 35.30 1.40
1131 1709 7.765819 GCAATAAGATGGCTGGAAGTTTTTATT 59.234 33.333 0.00 0.00 35.30 1.40
1132 1710 9.657419 CAATAAGATGGCTGGAAGTTTTTATTT 57.343 29.630 0.00 0.00 35.30 1.40
1134 1712 9.875691 ATAAGATGGCTGGAAGTTTTTATTTTC 57.124 29.630 0.00 0.00 35.30 2.29
1135 1713 7.544804 AGATGGCTGGAAGTTTTTATTTTCT 57.455 32.000 0.00 0.00 35.30 2.52
1136 1714 8.650143 AGATGGCTGGAAGTTTTTATTTTCTA 57.350 30.769 0.00 0.00 35.30 2.10
1137 1715 8.743714 AGATGGCTGGAAGTTTTTATTTTCTAG 58.256 33.333 0.00 0.00 35.30 2.43
1138 1716 7.227049 TGGCTGGAAGTTTTTATTTTCTAGG 57.773 36.000 0.00 0.00 35.30 3.02
1139 1717 6.100004 GGCTGGAAGTTTTTATTTTCTAGGC 58.900 40.000 7.41 7.41 43.68 3.93
1140 1718 6.071334 GGCTGGAAGTTTTTATTTTCTAGGCT 60.071 38.462 13.45 0.00 45.28 4.58
1141 1719 7.122204 GGCTGGAAGTTTTTATTTTCTAGGCTA 59.878 37.037 13.45 0.00 45.28 3.93
1142 1720 8.184848 GCTGGAAGTTTTTATTTTCTAGGCTAG 58.815 37.037 15.56 15.56 35.30 3.42
1143 1721 8.575649 TGGAAGTTTTTATTTTCTAGGCTAGG 57.424 34.615 20.92 3.37 0.00 3.02
1144 1722 7.122204 TGGAAGTTTTTATTTTCTAGGCTAGGC 59.878 37.037 20.92 8.55 0.00 3.93
1155 1733 3.991242 GGCTAGGCCTAACTAGTGC 57.009 57.895 14.85 12.23 46.69 4.40
1156 1734 0.032267 GGCTAGGCCTAACTAGTGCG 59.968 60.000 14.85 0.12 46.69 5.34
1157 1735 0.597898 GCTAGGCCTAACTAGTGCGC 60.598 60.000 14.85 7.28 41.93 6.09
1158 1736 1.033574 CTAGGCCTAACTAGTGCGCT 58.966 55.000 14.85 4.58 36.53 5.92
1159 1737 1.409427 CTAGGCCTAACTAGTGCGCTT 59.591 52.381 14.85 0.00 36.53 4.68
1160 1738 1.481871 AGGCCTAACTAGTGCGCTTA 58.518 50.000 1.29 0.00 0.00 3.09
1161 1739 1.409427 AGGCCTAACTAGTGCGCTTAG 59.591 52.381 1.29 13.16 0.00 2.18
1162 1740 1.136500 GGCCTAACTAGTGCGCTTAGT 59.864 52.381 9.73 13.84 0.00 2.24
1163 1741 2.360165 GGCCTAACTAGTGCGCTTAGTA 59.640 50.000 20.30 4.24 0.00 1.82
1164 1742 3.550436 GGCCTAACTAGTGCGCTTAGTAG 60.550 52.174 20.30 14.46 0.00 2.57
1165 1743 3.066481 GCCTAACTAGTGCGCTTAGTAGT 59.934 47.826 20.30 15.01 38.20 2.73
1166 1744 4.274459 GCCTAACTAGTGCGCTTAGTAGTA 59.726 45.833 20.30 12.06 36.14 1.82
1167 1745 5.220931 GCCTAACTAGTGCGCTTAGTAGTAA 60.221 44.000 20.30 9.58 36.14 2.24
1168 1746 6.514705 GCCTAACTAGTGCGCTTAGTAGTAAT 60.515 42.308 20.30 10.58 36.14 1.89
1169 1747 7.424001 CCTAACTAGTGCGCTTAGTAGTAATT 58.576 38.462 20.30 10.05 36.14 1.40
1170 1748 7.919621 CCTAACTAGTGCGCTTAGTAGTAATTT 59.080 37.037 20.30 9.52 36.14 1.82
1171 1749 9.298774 CTAACTAGTGCGCTTAGTAGTAATTTT 57.701 33.333 20.30 7.15 36.14 1.82
1172 1750 8.543862 AACTAGTGCGCTTAGTAGTAATTTTT 57.456 30.769 20.30 2.31 36.14 1.94
1209 1787 1.831580 AGGATTGAGCCTGTTCAAGC 58.168 50.000 3.75 3.75 41.47 4.01
1211 1789 1.831580 GATTGAGCCTGTTCAAGCCT 58.168 50.000 1.16 0.00 40.16 4.58
1212 1790 1.471684 GATTGAGCCTGTTCAAGCCTG 59.528 52.381 1.16 0.00 40.16 4.85
1213 1791 0.183492 TTGAGCCTGTTCAAGCCTGT 59.817 50.000 0.00 0.00 32.39 4.00
1214 1792 0.183492 TGAGCCTGTTCAAGCCTGTT 59.817 50.000 0.00 0.00 0.00 3.16
1215 1793 0.595095 GAGCCTGTTCAAGCCTGTTG 59.405 55.000 0.00 0.00 0.00 3.33
1216 1794 0.183492 AGCCTGTTCAAGCCTGTTGA 59.817 50.000 0.00 0.00 0.00 3.18
1217 1795 0.595095 GCCTGTTCAAGCCTGTTGAG 59.405 55.000 0.00 0.00 0.00 3.02
1218 1796 1.972872 CCTGTTCAAGCCTGTTGAGT 58.027 50.000 0.00 0.00 0.00 3.41
1219 1797 2.810400 GCCTGTTCAAGCCTGTTGAGTA 60.810 50.000 0.00 0.00 0.00 2.59
1220 1798 3.070018 CCTGTTCAAGCCTGTTGAGTAG 58.930 50.000 0.00 0.00 0.00 2.57
1221 1799 3.244215 CCTGTTCAAGCCTGTTGAGTAGA 60.244 47.826 0.00 0.00 0.00 2.59
1222 1800 4.380531 CTGTTCAAGCCTGTTGAGTAGAA 58.619 43.478 0.00 0.00 0.00 2.10
1223 1801 4.973168 TGTTCAAGCCTGTTGAGTAGAAT 58.027 39.130 0.00 0.00 0.00 2.40
1224 1802 4.997395 TGTTCAAGCCTGTTGAGTAGAATC 59.003 41.667 0.00 0.00 0.00 2.52
1225 1803 3.849911 TCAAGCCTGTTGAGTAGAATCG 58.150 45.455 0.00 0.00 0.00 3.34
1226 1804 2.932614 CAAGCCTGTTGAGTAGAATCGG 59.067 50.000 0.00 0.00 0.00 4.18
1227 1805 1.134670 AGCCTGTTGAGTAGAATCGGC 60.135 52.381 0.00 0.00 36.58 5.54
1228 1806 1.405526 GCCTGTTGAGTAGAATCGGCA 60.406 52.381 0.00 0.00 36.37 5.69
1229 1807 2.271800 CCTGTTGAGTAGAATCGGCAC 58.728 52.381 0.00 0.00 0.00 5.01
1230 1808 2.093973 CCTGTTGAGTAGAATCGGCACT 60.094 50.000 0.00 0.00 0.00 4.40
1231 1809 2.926200 CTGTTGAGTAGAATCGGCACTG 59.074 50.000 0.00 0.00 0.00 3.66
1232 1810 1.661112 GTTGAGTAGAATCGGCACTGC 59.339 52.381 0.00 0.00 0.00 4.40
1233 1811 1.186200 TGAGTAGAATCGGCACTGCT 58.814 50.000 0.00 0.00 0.00 4.24
1234 1812 1.550524 TGAGTAGAATCGGCACTGCTT 59.449 47.619 0.00 0.00 0.00 3.91
1235 1813 2.197577 GAGTAGAATCGGCACTGCTTC 58.802 52.381 0.00 0.00 0.00 3.86
1236 1814 1.550524 AGTAGAATCGGCACTGCTTCA 59.449 47.619 0.00 0.00 0.00 3.02
1237 1815 2.169352 AGTAGAATCGGCACTGCTTCAT 59.831 45.455 0.00 0.00 0.00 2.57
1238 1816 1.376543 AGAATCGGCACTGCTTCATG 58.623 50.000 0.00 0.00 0.00 3.07
1239 1817 0.379669 GAATCGGCACTGCTTCATGG 59.620 55.000 0.00 0.00 0.00 3.66
1854 2463 4.039730 ACATTTGATAGAGACCGATGGAGG 59.960 45.833 0.00 0.00 37.30 4.30
1880 2489 0.191064 TAGGGAGCGGAGGATTCCAT 59.809 55.000 5.29 0.00 44.26 3.41
1947 2556 1.868498 CGAAGGGCACGTCAAAAACTA 59.132 47.619 2.03 0.00 0.00 2.24
2533 3144 1.732809 GCTAAAGTTCTTCGGTCAGCC 59.267 52.381 0.00 0.00 0.00 4.85
2726 3337 2.413796 GCCGTGTTACGAAATCACATCA 59.586 45.455 2.52 0.00 46.05 3.07
4427 5062 4.686972 TGAGAGCTGAATGGAATAACTCG 58.313 43.478 0.00 0.00 0.00 4.18
5115 5754 6.051717 CCATATTCTGAAAGTGACCGATTCT 58.948 40.000 0.00 0.00 33.76 2.40
5406 6050 7.611467 GGTTATGCACATAGGGATTTCATATGA 59.389 37.037 0.00 0.00 32.44 2.15
5419 6063 5.375283 TTTCATATGAACGGGGAATGGTA 57.625 39.130 17.76 0.00 33.13 3.25
5511 6155 1.335597 GGCAACCGAACAAAGCCTTAC 60.336 52.381 0.00 0.00 42.01 2.34
5515 6159 3.418684 ACCGAACAAAGCCTTACTGAT 57.581 42.857 0.00 0.00 0.00 2.90
5533 6177 4.021916 CTGATCTTGAGCCAAAAGGGATT 58.978 43.478 0.00 0.00 40.01 3.01
5661 6306 2.223688 GCTCGATGCACTCACTACAGAT 60.224 50.000 0.00 0.00 42.31 2.90
5666 6311 4.498682 CGATGCACTCACTACAGATCATGA 60.499 45.833 0.00 0.00 0.00 3.07
5672 6317 6.335777 CACTCACTACAGATCATGACATGAA 58.664 40.000 21.52 4.52 43.50 2.57
5773 6418 1.737838 TAGCAACATCCTCGGCAAAG 58.262 50.000 0.00 0.00 0.00 2.77
5814 6460 8.034313 ACAATCTGCCAGGATTACTTTATAGA 57.966 34.615 0.00 0.00 34.59 1.98
5831 6477 9.738832 ACTTTATAGAAAAAGTAGAGCTCGATC 57.261 33.333 8.37 2.93 45.53 3.69
5842 6488 0.100325 AGCTCGATCGACTCAAGCTG 59.900 55.000 23.13 9.64 0.00 4.24
6094 6748 3.878778 ACAAGGCAAGCACCTCTATAAG 58.121 45.455 0.00 0.00 39.93 1.73
6131 6785 7.801716 TTTAACAAAACACATGTAGAGCTCT 57.198 32.000 22.17 22.17 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.005791 GCTTTGCCATGTTAAGTTCCTGT 59.994 43.478 0.00 0.00 0.00 4.00
6 7 3.989817 CCTTGCTTTGCCATGTTAAGTTC 59.010 43.478 0.00 0.00 0.00 3.01
7 8 3.803368 GCCTTGCTTTGCCATGTTAAGTT 60.803 43.478 0.00 0.00 0.00 2.66
8 9 2.289010 GCCTTGCTTTGCCATGTTAAGT 60.289 45.455 0.00 0.00 0.00 2.24
10 11 2.453983 GCCTTGCTTTGCCATGTTAA 57.546 45.000 0.00 0.00 0.00 2.01
18 19 2.094675 TCATTCTAGGCCTTGCTTTGC 58.905 47.619 12.58 0.00 0.00 3.68
19 20 3.428589 GCTTCATTCTAGGCCTTGCTTTG 60.429 47.826 12.58 7.53 0.00 2.77
20 21 2.757314 GCTTCATTCTAGGCCTTGCTTT 59.243 45.455 12.58 0.00 0.00 3.51
21 22 2.025510 AGCTTCATTCTAGGCCTTGCTT 60.026 45.455 12.58 0.00 0.00 3.91
22 23 1.563410 AGCTTCATTCTAGGCCTTGCT 59.437 47.619 12.58 5.51 0.00 3.91
23 24 2.049888 AGCTTCATTCTAGGCCTTGC 57.950 50.000 12.58 3.11 0.00 4.01
24 25 4.141846 TGAGTAGCTTCATTCTAGGCCTTG 60.142 45.833 12.58 9.98 0.00 3.61
25 26 4.033709 TGAGTAGCTTCATTCTAGGCCTT 58.966 43.478 12.58 0.00 0.00 4.35
26 27 3.647636 TGAGTAGCTTCATTCTAGGCCT 58.352 45.455 11.78 11.78 0.00 5.19
27 28 4.408182 TTGAGTAGCTTCATTCTAGGCC 57.592 45.455 0.00 0.00 0.00 5.19
28 29 4.272261 GCTTTGAGTAGCTTCATTCTAGGC 59.728 45.833 0.00 0.00 38.15 3.93
29 30 5.293079 GTGCTTTGAGTAGCTTCATTCTAGG 59.707 44.000 0.00 0.00 41.76 3.02
30 31 6.105333 AGTGCTTTGAGTAGCTTCATTCTAG 58.895 40.000 0.00 0.00 41.76 2.43
31 32 6.042638 AGTGCTTTGAGTAGCTTCATTCTA 57.957 37.500 0.00 0.00 41.76 2.10
32 33 4.904241 AGTGCTTTGAGTAGCTTCATTCT 58.096 39.130 0.00 0.00 41.76 2.40
33 34 5.619625 AAGTGCTTTGAGTAGCTTCATTC 57.380 39.130 0.00 0.00 41.76 2.67
34 35 6.486657 TGTTAAGTGCTTTGAGTAGCTTCATT 59.513 34.615 0.00 0.00 41.76 2.57
35 36 5.997746 TGTTAAGTGCTTTGAGTAGCTTCAT 59.002 36.000 0.00 0.00 41.76 2.57
36 37 5.364778 TGTTAAGTGCTTTGAGTAGCTTCA 58.635 37.500 0.00 0.00 41.76 3.02
37 38 5.924475 TGTTAAGTGCTTTGAGTAGCTTC 57.076 39.130 0.00 0.00 41.76 3.86
38 39 6.693315 TTTGTTAAGTGCTTTGAGTAGCTT 57.307 33.333 0.00 0.00 41.76 3.74
39 40 6.318900 ACTTTTGTTAAGTGCTTTGAGTAGCT 59.681 34.615 0.00 0.00 41.76 3.32
40 41 6.495706 ACTTTTGTTAAGTGCTTTGAGTAGC 58.504 36.000 0.00 0.00 41.59 3.58
41 42 7.132863 GGACTTTTGTTAAGTGCTTTGAGTAG 58.867 38.462 0.00 0.00 35.97 2.57
42 43 6.038936 GGGACTTTTGTTAAGTGCTTTGAGTA 59.961 38.462 8.66 0.00 38.45 2.59
43 44 5.163550 GGGACTTTTGTTAAGTGCTTTGAGT 60.164 40.000 8.66 0.00 38.45 3.41
44 45 5.067805 AGGGACTTTTGTTAAGTGCTTTGAG 59.932 40.000 8.66 0.00 38.45 3.02
45 46 4.953579 AGGGACTTTTGTTAAGTGCTTTGA 59.046 37.500 8.66 0.00 38.45 2.69
46 47 5.262588 AGGGACTTTTGTTAAGTGCTTTG 57.737 39.130 8.66 0.00 38.45 2.77
63 64 1.141234 CGAACGAGGCCTAAGGGAC 59.859 63.158 4.42 0.00 42.21 4.46
144 147 2.684735 GGCCGGGTTTATTCCCCA 59.315 61.111 2.18 0.00 44.32 4.96
240 245 3.402681 CGGGGTGCCAGGAGATGT 61.403 66.667 0.00 0.00 0.00 3.06
544 579 2.355756 CTGCTAGAGAGAGAGACAGTGC 59.644 54.545 0.00 0.00 0.00 4.40
665 743 7.645340 CACTGCATTGCCTATCTAAATAACAAC 59.355 37.037 6.12 0.00 0.00 3.32
856 1191 9.459640 GAACAACAACATATACGATCTTAGCTA 57.540 33.333 0.00 0.00 0.00 3.32
1024 1602 0.872021 GCGTCCTAGATTCGCCACTG 60.872 60.000 12.59 0.00 43.41 3.66
1025 1603 1.437986 GCGTCCTAGATTCGCCACT 59.562 57.895 12.59 0.00 43.41 4.00
1026 1604 4.014065 GCGTCCTAGATTCGCCAC 57.986 61.111 12.59 0.00 43.41 5.01
1030 1608 2.797156 CTCCATTTGCGTCCTAGATTCG 59.203 50.000 0.00 0.00 0.00 3.34
1031 1609 3.134458 CCTCCATTTGCGTCCTAGATTC 58.866 50.000 0.00 0.00 0.00 2.52
1032 1610 2.158755 CCCTCCATTTGCGTCCTAGATT 60.159 50.000 0.00 0.00 0.00 2.40
1033 1611 1.417890 CCCTCCATTTGCGTCCTAGAT 59.582 52.381 0.00 0.00 0.00 1.98
1034 1612 0.830648 CCCTCCATTTGCGTCCTAGA 59.169 55.000 0.00 0.00 0.00 2.43
1035 1613 0.541863 ACCCTCCATTTGCGTCCTAG 59.458 55.000 0.00 0.00 0.00 3.02
1036 1614 1.760613 CTACCCTCCATTTGCGTCCTA 59.239 52.381 0.00 0.00 0.00 2.94
1037 1615 0.541863 CTACCCTCCATTTGCGTCCT 59.458 55.000 0.00 0.00 0.00 3.85
1038 1616 0.463833 CCTACCCTCCATTTGCGTCC 60.464 60.000 0.00 0.00 0.00 4.79
1039 1617 1.095807 GCCTACCCTCCATTTGCGTC 61.096 60.000 0.00 0.00 0.00 5.19
1040 1618 1.077716 GCCTACCCTCCATTTGCGT 60.078 57.895 0.00 0.00 0.00 5.24
1041 1619 1.097547 CAGCCTACCCTCCATTTGCG 61.098 60.000 0.00 0.00 0.00 4.85
1042 1620 0.255890 TCAGCCTACCCTCCATTTGC 59.744 55.000 0.00 0.00 0.00 3.68
1043 1621 2.025887 AGTTCAGCCTACCCTCCATTTG 60.026 50.000 0.00 0.00 0.00 2.32
1044 1622 2.279173 AGTTCAGCCTACCCTCCATTT 58.721 47.619 0.00 0.00 0.00 2.32
1045 1623 1.972588 AGTTCAGCCTACCCTCCATT 58.027 50.000 0.00 0.00 0.00 3.16
1046 1624 1.561542 CAAGTTCAGCCTACCCTCCAT 59.438 52.381 0.00 0.00 0.00 3.41
1047 1625 0.984230 CAAGTTCAGCCTACCCTCCA 59.016 55.000 0.00 0.00 0.00 3.86
1048 1626 1.276622 TCAAGTTCAGCCTACCCTCC 58.723 55.000 0.00 0.00 0.00 4.30
1049 1627 3.418684 TTTCAAGTTCAGCCTACCCTC 57.581 47.619 0.00 0.00 0.00 4.30
1050 1628 4.623171 CGTATTTCAAGTTCAGCCTACCCT 60.623 45.833 0.00 0.00 0.00 4.34
1051 1629 3.621715 CGTATTTCAAGTTCAGCCTACCC 59.378 47.826 0.00 0.00 0.00 3.69
1052 1630 4.251268 ACGTATTTCAAGTTCAGCCTACC 58.749 43.478 0.00 0.00 0.00 3.18
1053 1631 5.857822 AACGTATTTCAAGTTCAGCCTAC 57.142 39.130 0.00 0.00 0.00 3.18
1054 1632 8.556213 AATTAACGTATTTCAAGTTCAGCCTA 57.444 30.769 0.00 0.00 30.98 3.93
1055 1633 7.448748 AATTAACGTATTTCAAGTTCAGCCT 57.551 32.000 0.00 0.00 30.98 4.58
1056 1634 8.515473 AAAATTAACGTATTTCAAGTTCAGCC 57.485 30.769 0.00 0.00 30.98 4.85
1057 1635 9.777843 CAAAAATTAACGTATTTCAAGTTCAGC 57.222 29.630 0.00 0.00 30.98 4.26
1062 1640 9.804758 TCCAACAAAAATTAACGTATTTCAAGT 57.195 25.926 0.00 0.00 0.00 3.16
1064 1642 9.250624 CCTCCAACAAAAATTAACGTATTTCAA 57.749 29.630 0.00 0.00 0.00 2.69
1065 1643 7.382759 GCCTCCAACAAAAATTAACGTATTTCA 59.617 33.333 0.00 0.00 0.00 2.69
1066 1644 7.382759 TGCCTCCAACAAAAATTAACGTATTTC 59.617 33.333 0.00 0.00 0.00 2.17
1067 1645 7.210873 TGCCTCCAACAAAAATTAACGTATTT 58.789 30.769 0.00 0.00 0.00 1.40
1068 1646 6.750148 TGCCTCCAACAAAAATTAACGTATT 58.250 32.000 0.00 0.00 0.00 1.89
1069 1647 6.015772 ACTGCCTCCAACAAAAATTAACGTAT 60.016 34.615 0.00 0.00 0.00 3.06
1070 1648 5.299782 ACTGCCTCCAACAAAAATTAACGTA 59.700 36.000 0.00 0.00 0.00 3.57
1071 1649 4.098807 ACTGCCTCCAACAAAAATTAACGT 59.901 37.500 0.00 0.00 0.00 3.99
1072 1650 4.444056 CACTGCCTCCAACAAAAATTAACG 59.556 41.667 0.00 0.00 0.00 3.18
1073 1651 4.211164 GCACTGCCTCCAACAAAAATTAAC 59.789 41.667 0.00 0.00 0.00 2.01
1074 1652 4.141846 TGCACTGCCTCCAACAAAAATTAA 60.142 37.500 0.00 0.00 0.00 1.40
1075 1653 3.386078 TGCACTGCCTCCAACAAAAATTA 59.614 39.130 0.00 0.00 0.00 1.40
1076 1654 2.170187 TGCACTGCCTCCAACAAAAATT 59.830 40.909 0.00 0.00 0.00 1.82
1077 1655 1.761784 TGCACTGCCTCCAACAAAAAT 59.238 42.857 0.00 0.00 0.00 1.82
1078 1656 1.136695 CTGCACTGCCTCCAACAAAAA 59.863 47.619 0.00 0.00 0.00 1.94
1079 1657 0.746063 CTGCACTGCCTCCAACAAAA 59.254 50.000 0.00 0.00 0.00 2.44
1080 1658 0.395586 ACTGCACTGCCTCCAACAAA 60.396 50.000 0.00 0.00 0.00 2.83
1081 1659 1.102809 CACTGCACTGCCTCCAACAA 61.103 55.000 0.00 0.00 0.00 2.83
1082 1660 1.526686 CACTGCACTGCCTCCAACA 60.527 57.895 0.00 0.00 0.00 3.33
1083 1661 1.526917 ACACTGCACTGCCTCCAAC 60.527 57.895 0.00 0.00 0.00 3.77
1084 1662 1.526686 CACACTGCACTGCCTCCAA 60.527 57.895 0.00 0.00 0.00 3.53
1085 1663 1.771783 ATCACACTGCACTGCCTCCA 61.772 55.000 0.00 0.00 0.00 3.86
1086 1664 1.002868 ATCACACTGCACTGCCTCC 60.003 57.895 0.00 0.00 0.00 4.30
1087 1665 1.919956 GCATCACACTGCACTGCCTC 61.920 60.000 0.00 0.00 41.87 4.70
1088 1666 1.970114 GCATCACACTGCACTGCCT 60.970 57.895 0.00 0.00 41.87 4.75
1089 1667 2.263021 TGCATCACACTGCACTGCC 61.263 57.895 0.00 0.00 46.76 4.85
1090 1668 3.347168 TGCATCACACTGCACTGC 58.653 55.556 0.00 0.00 46.76 4.40
1095 1673 3.794475 GCCATCTTATTGCATCACACTGC 60.794 47.826 0.00 0.00 42.62 4.40
1096 1674 3.630769 AGCCATCTTATTGCATCACACTG 59.369 43.478 0.00 0.00 0.00 3.66
1097 1675 3.630769 CAGCCATCTTATTGCATCACACT 59.369 43.478 0.00 0.00 0.00 3.55
1098 1676 3.243301 CCAGCCATCTTATTGCATCACAC 60.243 47.826 0.00 0.00 0.00 3.82
1099 1677 2.953648 CCAGCCATCTTATTGCATCACA 59.046 45.455 0.00 0.00 0.00 3.58
1100 1678 3.216800 TCCAGCCATCTTATTGCATCAC 58.783 45.455 0.00 0.00 0.00 3.06
1101 1679 3.581265 TCCAGCCATCTTATTGCATCA 57.419 42.857 0.00 0.00 0.00 3.07
1102 1680 3.887716 ACTTCCAGCCATCTTATTGCATC 59.112 43.478 0.00 0.00 0.00 3.91
1103 1681 3.907221 ACTTCCAGCCATCTTATTGCAT 58.093 40.909 0.00 0.00 0.00 3.96
1104 1682 3.370840 ACTTCCAGCCATCTTATTGCA 57.629 42.857 0.00 0.00 0.00 4.08
1105 1683 4.725790 AAACTTCCAGCCATCTTATTGC 57.274 40.909 0.00 0.00 0.00 3.56
1106 1684 9.657419 AAATAAAAACTTCCAGCCATCTTATTG 57.343 29.630 0.00 0.00 0.00 1.90
1108 1686 9.875691 GAAAATAAAAACTTCCAGCCATCTTAT 57.124 29.630 0.00 0.00 0.00 1.73
1109 1687 9.088987 AGAAAATAAAAACTTCCAGCCATCTTA 57.911 29.630 0.00 0.00 0.00 2.10
1110 1688 7.966812 AGAAAATAAAAACTTCCAGCCATCTT 58.033 30.769 0.00 0.00 0.00 2.40
1111 1689 7.544804 AGAAAATAAAAACTTCCAGCCATCT 57.455 32.000 0.00 0.00 0.00 2.90
1112 1690 7.976175 CCTAGAAAATAAAAACTTCCAGCCATC 59.024 37.037 0.00 0.00 0.00 3.51
1113 1691 7.579531 GCCTAGAAAATAAAAACTTCCAGCCAT 60.580 37.037 0.00 0.00 0.00 4.40
1114 1692 6.295067 GCCTAGAAAATAAAAACTTCCAGCCA 60.295 38.462 0.00 0.00 0.00 4.75
1115 1693 6.071334 AGCCTAGAAAATAAAAACTTCCAGCC 60.071 38.462 0.00 0.00 0.00 4.85
1116 1694 6.925211 AGCCTAGAAAATAAAAACTTCCAGC 58.075 36.000 0.00 0.00 0.00 4.85
1117 1695 8.678199 CCTAGCCTAGAAAATAAAAACTTCCAG 58.322 37.037 0.00 0.00 0.00 3.86
1118 1696 7.122204 GCCTAGCCTAGAAAATAAAAACTTCCA 59.878 37.037 0.00 0.00 0.00 3.53
1119 1697 7.416438 GGCCTAGCCTAGAAAATAAAAACTTCC 60.416 40.741 0.00 0.00 46.69 3.46
1120 1698 7.481642 GGCCTAGCCTAGAAAATAAAAACTTC 58.518 38.462 0.00 0.00 46.69 3.01
1121 1699 7.406031 GGCCTAGCCTAGAAAATAAAAACTT 57.594 36.000 0.00 0.00 46.69 2.66
1138 1716 0.597898 GCGCACTAGTTAGGCCTAGC 60.598 60.000 18.35 18.35 38.39 3.42
1139 1717 1.033574 AGCGCACTAGTTAGGCCTAG 58.966 55.000 13.36 5.56 40.26 3.02
1140 1718 1.481871 AAGCGCACTAGTTAGGCCTA 58.518 50.000 8.91 8.91 0.00 3.93
1141 1719 1.409427 CTAAGCGCACTAGTTAGGCCT 59.591 52.381 11.78 11.78 0.00 5.19
1142 1720 1.136500 ACTAAGCGCACTAGTTAGGCC 59.864 52.381 11.47 0.00 0.00 5.19
1143 1721 2.580966 ACTAAGCGCACTAGTTAGGC 57.419 50.000 11.47 0.00 0.00 3.93
1144 1722 4.897025 ACTACTAAGCGCACTAGTTAGG 57.103 45.455 22.42 16.14 0.00 2.69
1145 1723 8.853469 AAATTACTACTAAGCGCACTAGTTAG 57.147 34.615 22.42 16.75 0.00 2.34
1146 1724 9.643693 AAAAATTACTACTAAGCGCACTAGTTA 57.356 29.630 22.42 10.76 0.00 2.24
1147 1725 8.543862 AAAAATTACTACTAAGCGCACTAGTT 57.456 30.769 22.42 11.57 0.00 2.24
1180 1758 2.456577 GGCTCAATCCTGCCCTAAAAA 58.543 47.619 0.00 0.00 43.11 1.94
1181 1759 2.143876 GGCTCAATCCTGCCCTAAAA 57.856 50.000 0.00 0.00 43.11 1.52
1182 1760 3.903208 GGCTCAATCCTGCCCTAAA 57.097 52.632 0.00 0.00 43.11 1.85
1190 1768 1.615384 GGCTTGAACAGGCTCAATCCT 60.615 52.381 8.63 0.00 45.03 3.24
1191 1769 0.813821 GGCTTGAACAGGCTCAATCC 59.186 55.000 8.63 0.00 45.03 3.01
1199 1777 1.972872 ACTCAACAGGCTTGAACAGG 58.027 50.000 1.40 0.00 0.00 4.00
1200 1778 3.995199 TCTACTCAACAGGCTTGAACAG 58.005 45.455 1.40 0.00 0.00 3.16
1201 1779 4.415881 TTCTACTCAACAGGCTTGAACA 57.584 40.909 1.40 0.00 0.00 3.18
1202 1780 4.092091 CGATTCTACTCAACAGGCTTGAAC 59.908 45.833 1.40 0.00 0.00 3.18
1203 1781 4.245660 CGATTCTACTCAACAGGCTTGAA 58.754 43.478 1.40 0.00 0.00 2.69
1204 1782 3.368427 CCGATTCTACTCAACAGGCTTGA 60.368 47.826 1.40 0.00 0.00 3.02
1205 1783 2.932614 CCGATTCTACTCAACAGGCTTG 59.067 50.000 0.00 0.00 0.00 4.01
1206 1784 2.678190 GCCGATTCTACTCAACAGGCTT 60.678 50.000 0.00 0.00 40.12 4.35
1207 1785 1.134670 GCCGATTCTACTCAACAGGCT 60.135 52.381 0.00 0.00 40.12 4.58
1208 1786 1.291132 GCCGATTCTACTCAACAGGC 58.709 55.000 0.00 0.00 36.32 4.85
1209 1787 2.093973 AGTGCCGATTCTACTCAACAGG 60.094 50.000 0.00 0.00 0.00 4.00
1210 1788 2.926200 CAGTGCCGATTCTACTCAACAG 59.074 50.000 0.00 0.00 0.00 3.16
1211 1789 2.930887 GCAGTGCCGATTCTACTCAACA 60.931 50.000 2.85 0.00 0.00 3.33
1212 1790 1.661112 GCAGTGCCGATTCTACTCAAC 59.339 52.381 2.85 0.00 0.00 3.18
1213 1791 1.550524 AGCAGTGCCGATTCTACTCAA 59.449 47.619 12.58 0.00 0.00 3.02
1214 1792 1.186200 AGCAGTGCCGATTCTACTCA 58.814 50.000 12.58 0.00 0.00 3.41
1215 1793 2.197577 GAAGCAGTGCCGATTCTACTC 58.802 52.381 12.58 0.00 0.00 2.59
1216 1794 1.550524 TGAAGCAGTGCCGATTCTACT 59.449 47.619 12.58 0.00 0.00 2.57
1217 1795 2.010145 TGAAGCAGTGCCGATTCTAC 57.990 50.000 12.58 0.00 0.00 2.59
1218 1796 2.554142 CATGAAGCAGTGCCGATTCTA 58.446 47.619 12.58 1.41 0.00 2.10
1219 1797 1.376543 CATGAAGCAGTGCCGATTCT 58.623 50.000 12.58 0.00 0.00 2.40
1220 1798 0.379669 CCATGAAGCAGTGCCGATTC 59.620 55.000 12.58 10.02 0.00 2.52
1221 1799 0.322816 ACCATGAAGCAGTGCCGATT 60.323 50.000 12.58 0.00 0.00 3.34
1222 1800 1.028330 CACCATGAAGCAGTGCCGAT 61.028 55.000 12.58 0.00 0.00 4.18
1223 1801 1.672030 CACCATGAAGCAGTGCCGA 60.672 57.895 12.58 0.00 0.00 5.54
1224 1802 2.872557 CACCATGAAGCAGTGCCG 59.127 61.111 12.58 0.00 0.00 5.69
1227 1805 1.155889 TTACGCACCATGAAGCAGTG 58.844 50.000 9.49 2.96 34.58 3.66
1228 1806 2.009774 GATTACGCACCATGAAGCAGT 58.990 47.619 9.49 9.74 0.00 4.40
1229 1807 2.009051 TGATTACGCACCATGAAGCAG 58.991 47.619 9.49 5.34 0.00 4.24
1230 1808 2.106477 TGATTACGCACCATGAAGCA 57.894 45.000 9.49 0.00 0.00 3.91
1231 1809 2.613595 TGATGATTACGCACCATGAAGC 59.386 45.455 0.00 0.00 0.00 3.86
1232 1810 4.753610 AGATGATGATTACGCACCATGAAG 59.246 41.667 0.00 0.00 0.00 3.02
1233 1811 4.512571 CAGATGATGATTACGCACCATGAA 59.487 41.667 0.00 0.00 0.00 2.57
1234 1812 4.060205 CAGATGATGATTACGCACCATGA 58.940 43.478 0.00 0.00 0.00 3.07
1235 1813 3.811497 ACAGATGATGATTACGCACCATG 59.189 43.478 0.00 0.00 0.00 3.66
1236 1814 4.077300 ACAGATGATGATTACGCACCAT 57.923 40.909 0.00 0.00 0.00 3.55
1237 1815 3.541996 ACAGATGATGATTACGCACCA 57.458 42.857 0.00 0.00 0.00 4.17
1238 1816 4.122776 AGAACAGATGATGATTACGCACC 58.877 43.478 0.00 0.00 0.00 5.01
1239 1817 5.291858 TCAAGAACAGATGATGATTACGCAC 59.708 40.000 0.00 0.00 0.00 5.34
1242 1820 8.362860 AGAATCAAGAACAGATGATGATTACG 57.637 34.615 0.00 0.00 39.95 3.18
1822 2431 5.163405 GGTCTCTATCAAATGTAGTGCAGGA 60.163 44.000 0.00 0.00 0.00 3.86
1880 2489 3.392882 CTGTTAGCGATGATGTATGGCA 58.607 45.455 0.00 0.00 42.34 4.92
1947 2556 3.248024 TCCATCCTAAATGCTACCCGAT 58.752 45.455 0.00 0.00 0.00 4.18
2533 3144 2.159382 ACATGAAACCCGCTGTTAAGG 58.841 47.619 0.00 0.00 35.67 2.69
2726 3337 4.855298 TCAAGATTCCTAATCCCCGTTT 57.145 40.909 0.00 0.00 38.71 3.60
2972 3583 1.589803 TGATGAGCAATGGCATCTCG 58.410 50.000 0.00 0.00 44.61 4.04
3332 3957 1.002430 TCCATTGCGCTCTGTCTTCTT 59.998 47.619 9.73 0.00 0.00 2.52
4427 5062 7.631717 AAATAGAAGCAGAATTTGAGTACCC 57.368 36.000 0.00 0.00 0.00 3.69
4892 5531 5.989551 ACTTTTGGCAATCAACAATCAAC 57.010 34.783 0.00 0.00 34.67 3.18
5080 5719 8.680903 CACTTTCAGAATATGGTTTAGCATCTT 58.319 33.333 0.00 0.00 0.00 2.40
5115 5754 7.340743 TCAAAAATTCTCAGTTGTCCCAAACTA 59.659 33.333 0.00 0.00 38.34 2.24
5293 5933 1.470098 CCACACAGCCTACATGCTTTC 59.530 52.381 0.00 0.00 40.32 2.62
5391 6035 4.236195 TCCCCGTTCATATGAAATCCCTA 58.764 43.478 19.55 2.15 35.58 3.53
5406 6050 1.230050 ACCCCTACCATTCCCCGTT 60.230 57.895 0.00 0.00 0.00 4.44
5419 6063 2.203182 TCTTGTCACCCGACCCCT 59.797 61.111 0.00 0.00 41.85 4.79
5511 6155 3.077484 TCCCTTTTGGCTCAAGATCAG 57.923 47.619 0.00 0.00 38.58 2.90
5515 6159 4.927267 TCTAATCCCTTTTGGCTCAAGA 57.073 40.909 0.00 0.00 38.58 3.02
5533 6177 7.600960 TCACATGCTTGCAATTGTATTTTCTA 58.399 30.769 7.40 0.00 0.00 2.10
5661 6306 8.236586 GTGTATGCTTAGTTTTTCATGTCATGA 58.763 33.333 11.62 11.62 37.55 3.07
5666 6311 5.772672 TGGGTGTATGCTTAGTTTTTCATGT 59.227 36.000 0.00 0.00 0.00 3.21
5672 6317 6.245408 TCTTGATGGGTGTATGCTTAGTTTT 58.755 36.000 0.00 0.00 0.00 2.43
5773 6418 5.082059 CAGATTGTTGACATGTTTAGCGAC 58.918 41.667 0.00 0.00 0.00 5.19
5814 6460 4.156190 TGAGTCGATCGAGCTCTACTTTTT 59.844 41.667 30.10 5.74 0.00 1.94
5831 6477 0.809241 GAGCATCCCAGCTTGAGTCG 60.809 60.000 0.00 0.00 46.75 4.18
5842 6488 5.857540 TTTGTTTGCAATTATGGAGCATCCC 60.858 40.000 0.00 0.00 44.53 3.85
6076 6730 2.764269 TCCTTATAGAGGTGCTTGCCT 58.236 47.619 0.00 0.00 46.39 4.75
6094 6748 3.540314 TTGTTAAATGCCATGCCATCC 57.460 42.857 0.00 0.00 0.00 3.51
6131 6785 2.713863 TGTGTGCATGCTATGATCCA 57.286 45.000 20.33 3.16 0.00 3.41


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

AutoCloner maintained by Alex Coulton.