Multiple sequence alignment - TraesCS6A01G384100

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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 TraesCS6A01G384100 chr6A 100.000 3557 0 0 1 3557 602741569 602738013 0.000000e+00 6569.0
1 TraesCS6A01G384100 chr6A 91.994 712 38 4 2854 3557 410336772 410336072 0.000000e+00 981.0
2 TraesCS6A01G384100 chr6A 85.731 876 68 27 999 1867 602727030 602726205 0.000000e+00 872.0
3 TraesCS6A01G384100 chr6A 96.436 505 18 0 1001 1505 602717637 602717133 0.000000e+00 833.0
4 TraesCS6A01G384100 chr6A 79.112 608 101 15 2041 2628 602715937 602715336 2.570000e-106 396.0
5 TraesCS6A01G384100 chr6A 98.544 206 1 1 1 206 562702126 562702329 2.610000e-96 363.0
6 TraesCS6A01G384100 chr6A 96.226 212 7 1 1 212 59329722 59329932 2.630000e-91 346.0
7 TraesCS6A01G384100 chr6A 88.213 263 27 3 2369 2630 602725523 602725264 9.590000e-81 311.0
8 TraesCS6A01G384100 chr6A 87.898 157 15 3 1867 2023 602726169 602726017 7.840000e-42 182.0
9 TraesCS6A01G384100 chr6D 91.869 1648 69 24 997 2630 455970012 455968416 0.000000e+00 2241.0
10 TraesCS6A01G384100 chr6D 86.154 1040 85 30 999 2016 455935640 455934638 0.000000e+00 1068.0
11 TraesCS6A01G384100 chr6D 84.552 725 72 28 997 1711 455899723 455899029 0.000000e+00 682.0
12 TraesCS6A01G384100 chr6D 88.732 497 43 7 1001 1494 455907727 455907241 2.360000e-166 595.0
13 TraesCS6A01G384100 chr6D 82.665 623 76 22 2023 2630 455934496 455933891 1.130000e-144 523.0
14 TraesCS6A01G384100 chr6D 79.672 610 94 21 2041 2628 455906365 455905764 2.560000e-111 412.0
15 TraesCS6A01G384100 chr6D 87.072 263 31 3 2369 2628 455897780 455897518 9.660000e-76 294.0
16 TraesCS6A01G384100 chr6D 93.333 135 5 3 827 957 455970267 455970133 2.800000e-46 196.0
17 TraesCS6A01G384100 chr6D 100.000 33 0 0 958 990 455970114 455970082 1.070000e-05 62.1
18 TraesCS6A01G384100 chr3A 95.532 940 19 3 2631 3557 32005852 32004923 0.000000e+00 1482.0
19 TraesCS6A01G384100 chr3A 92.867 715 34 3 2850 3557 711147567 711148271 0.000000e+00 1022.0
20 TraesCS6A01G384100 chr3A 91.031 223 19 1 2631 2852 711147383 711147605 2.080000e-77 300.0
21 TraesCS6A01G384100 chr2D 88.710 992 45 21 2630 3557 103471295 103470307 0.000000e+00 1149.0
22 TraesCS6A01G384100 chr2D 93.233 399 22 3 2632 3026 619424036 619424433 1.840000e-162 582.0
23 TraesCS6A01G384100 chr2D 80.728 467 78 6 202 657 55609341 55608876 1.570000e-93 353.0
24 TraesCS6A01G384100 chr2D 79.853 407 76 5 217 620 310724051 310723648 3.470000e-75 292.0
25 TraesCS6A01G384100 chr7A 92.727 715 35 3 2850 3557 114984033 114984737 0.000000e+00 1016.0
26 TraesCS6A01G384100 chr7A 92.168 715 39 3 2850 3557 98090847 98091551 0.000000e+00 994.0
27 TraesCS6A01G384100 chr7A 90.330 455 29 3 2854 3301 665948054 665947608 1.840000e-162 582.0
28 TraesCS6A01G384100 chr7A 98.529 204 2 1 1 204 690772693 690772491 3.380000e-95 359.0
29 TraesCS6A01G384100 chr7A 97.573 206 4 1 1 206 178022187 178021983 5.650000e-93 351.0
30 TraesCS6A01G384100 chr7A 97.115 208 4 2 1 208 5357873 5358078 2.030000e-92 350.0
31 TraesCS6A01G384100 chr7A 92.241 232 10 3 2628 2851 98090653 98090884 4.430000e-84 322.0
32 TraesCS6A01G384100 chr1A 92.373 708 36 4 2850 3550 572732196 572731500 0.000000e+00 992.0
33 TraesCS6A01G384100 chr1A 91.436 724 43 4 2841 3557 328124056 328123345 0.000000e+00 976.0
34 TraesCS6A01G384100 chr1A 92.174 230 10 3 2631 2852 572732387 572732158 5.730000e-83 318.0
35 TraesCS6A01G384100 chr1A 79.319 411 76 8 202 608 374281222 374281627 2.700000e-71 279.0
36 TraesCS6A01G384100 chr5A 91.329 715 46 3 2850 3557 18521599 18520894 0.000000e+00 963.0
37 TraesCS6A01G384100 chr5A 98.058 206 3 1 1 206 294024897 294025101 1.210000e-94 357.0
38 TraesCS6A01G384100 chr5A 98.058 206 3 1 1 206 461619606 461619810 1.210000e-94 357.0
39 TraesCS6A01G384100 chr2B 88.089 764 43 7 2630 3345 768100721 768101484 0.000000e+00 863.0
40 TraesCS6A01G384100 chr2B 76.190 420 89 8 207 616 75688535 75688117 1.000000e-50 211.0
41 TraesCS6A01G384100 chr2B 83.505 97 14 2 539 634 732863717 732863622 4.890000e-14 89.8
42 TraesCS6A01G384100 chr6B 87.197 742 62 15 999 1733 693324355 693323640 0.000000e+00 813.0
43 TraesCS6A01G384100 chr6B 91.585 511 29 10 997 1494 693133130 693132621 0.000000e+00 693.0
44 TraesCS6A01G384100 chr6B 89.600 500 39 6 1001 1494 693302744 693302252 1.080000e-174 623.0
45 TraesCS6A01G384100 chr6B 87.450 502 47 3 202 690 693325452 693324954 6.670000e-157 564.0
46 TraesCS6A01G384100 chr6B 82.581 620 82 18 2023 2630 693323119 693322514 1.130000e-144 523.0
47 TraesCS6A01G384100 chr6B 78.548 606 110 15 2041 2628 693300293 693299690 7.210000e-102 381.0
48 TraesCS6A01G384100 chr6B 78.748 607 100 19 2047 2628 693131581 693130979 2.590000e-101 379.0
49 TraesCS6A01G384100 chr6B 80.132 302 57 2 335 634 532268641 532268941 4.620000e-54 222.0
50 TraesCS6A01G384100 chr6B 88.623 167 13 5 1867 2031 693323421 693323259 7.790000e-47 198.0
51 TraesCS6A01G384100 chr6B 93.162 117 3 2 814 925 693324648 693324532 2.200000e-37 167.0
52 TraesCS6A01G384100 chr2A 88.403 595 37 15 2887 3449 714341512 714340918 0.000000e+00 688.0
53 TraesCS6A01G384100 chr2A 98.529 204 2 1 1 204 744534063 744533861 3.380000e-95 359.0
54 TraesCS6A01G384100 chr2A 97.573 206 4 1 1 206 5173380 5173584 5.650000e-93 351.0
55 TraesCS6A01G384100 chr2A 79.213 356 63 10 229 577 676978748 676978397 1.650000e-58 237.0
56 TraesCS6A01G384100 chrUn 88.798 491 30 5 2631 3105 314913371 314912890 2.380000e-161 579.0
57 TraesCS6A01G384100 chrUn 88.664 494 31 5 2628 3105 350108096 350108580 2.380000e-161 579.0
58 TraesCS6A01G384100 chr4B 85.686 503 27 12 2630 3087 661718385 661718887 4.130000e-134 488.0
59 TraesCS6A01G384100 chr3B 86.605 433 37 15 2631 3048 687574347 687574773 3.240000e-125 459.0
60 TraesCS6A01G384100 chr3D 78.805 519 78 21 2037 2548 457057243 457057736 1.590000e-83 320.0
61 TraesCS6A01G384100 chr3D 91.111 135 12 0 1357 1491 457047667 457047801 2.180000e-42 183.0
62 TraesCS6A01G384100 chr5B 81.701 388 66 3 207 592 270760900 270760516 5.730000e-83 318.0
63 TraesCS6A01G384100 chr7D 78.132 439 86 9 202 634 64492048 64492482 1.630000e-68 270.0


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 TraesCS6A01G384100 chr6A 602738013 602741569 3556 True 6569.000000 6569 100.000000 1 3557 1 chr6A.!!$R2 3556
1 TraesCS6A01G384100 chr6A 410336072 410336772 700 True 981.000000 981 91.994000 2854 3557 1 chr6A.!!$R1 703
2 TraesCS6A01G384100 chr6A 602715336 602717637 2301 True 614.500000 833 87.774000 1001 2628 2 chr6A.!!$R3 1627
3 TraesCS6A01G384100 chr6A 602725264 602727030 1766 True 455.000000 872 87.280667 999 2630 3 chr6A.!!$R4 1631
4 TraesCS6A01G384100 chr6D 455968416 455970267 1851 True 833.033333 2241 95.067333 827 2630 3 chr6D.!!$R4 1803
5 TraesCS6A01G384100 chr6D 455933891 455935640 1749 True 795.500000 1068 84.409500 999 2630 2 chr6D.!!$R3 1631
6 TraesCS6A01G384100 chr6D 455905764 455907727 1963 True 503.500000 595 84.202000 1001 2628 2 chr6D.!!$R2 1627
7 TraesCS6A01G384100 chr6D 455897518 455899723 2205 True 488.000000 682 85.812000 997 2628 2 chr6D.!!$R1 1631
8 TraesCS6A01G384100 chr3A 32004923 32005852 929 True 1482.000000 1482 95.532000 2631 3557 1 chr3A.!!$R1 926
9 TraesCS6A01G384100 chr3A 711147383 711148271 888 False 661.000000 1022 91.949000 2631 3557 2 chr3A.!!$F1 926
10 TraesCS6A01G384100 chr2D 103470307 103471295 988 True 1149.000000 1149 88.710000 2630 3557 1 chr2D.!!$R2 927
11 TraesCS6A01G384100 chr7A 114984033 114984737 704 False 1016.000000 1016 92.727000 2850 3557 1 chr7A.!!$F2 707
12 TraesCS6A01G384100 chr7A 98090653 98091551 898 False 658.000000 994 92.204500 2628 3557 2 chr7A.!!$F3 929
13 TraesCS6A01G384100 chr1A 328123345 328124056 711 True 976.000000 976 91.436000 2841 3557 1 chr1A.!!$R1 716
14 TraesCS6A01G384100 chr1A 572731500 572732387 887 True 655.000000 992 92.273500 2631 3550 2 chr1A.!!$R2 919
15 TraesCS6A01G384100 chr5A 18520894 18521599 705 True 963.000000 963 91.329000 2850 3557 1 chr5A.!!$R1 707
16 TraesCS6A01G384100 chr2B 768100721 768101484 763 False 863.000000 863 88.089000 2630 3345 1 chr2B.!!$F1 715
17 TraesCS6A01G384100 chr6B 693130979 693133130 2151 True 536.000000 693 85.166500 997 2628 2 chr6B.!!$R1 1631
18 TraesCS6A01G384100 chr6B 693299690 693302744 3054 True 502.000000 623 84.074000 1001 2628 2 chr6B.!!$R2 1627
19 TraesCS6A01G384100 chr6B 693322514 693325452 2938 True 453.000000 813 87.802600 202 2630 5 chr6B.!!$R3 2428
20 TraesCS6A01G384100 chr2A 714340918 714341512 594 True 688.000000 688 88.403000 2887 3449 1 chr2A.!!$R2 562
21 TraesCS6A01G384100 chr4B 661718385 661718887 502 False 488.000000 488 85.686000 2630 3087 1 chr4B.!!$F1 457

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
411 412 0.026803 GATTCGCGGATGCAGTCAAC 59.973 55.0 3.53 0.00 42.97 3.18 F
695 709 0.035458 CAGCGTTGGAGGAGAAGGTT 59.965 55.0 0.00 0.00 0.00 3.50 F
2287 5253 0.230515 CAATGATGATGACGACGGCG 59.769 55.0 10.39 10.39 44.79 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 5101 0.538118 GGCGGTATAGGTTGTGTCCA 59.462 55.000 0.0 0.0 0.00 4.02 R
2485 5574 0.469144 TTCCAGTTCCCACCTTTGGC 60.469 55.000 0.0 0.0 42.35 4.52 R
3459 6765 3.805971 GGTCGTGTAGCAAACTAGTGTTT 59.194 43.478 0.0 0.0 46.20 2.83 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
21 22 2.596862 GCCGAAATTTATCGTGTTTGGC 59.403 45.455 0.00 0.00 41.16 4.52
22 23 3.175929 CCGAAATTTATCGTGTTTGGCC 58.824 45.455 0.00 0.00 41.16 5.36
23 24 2.843643 CGAAATTTATCGTGTTTGGCCG 59.156 45.455 0.00 0.00 38.01 6.13
24 25 3.425094 CGAAATTTATCGTGTTTGGCCGA 60.425 43.478 0.00 0.00 38.01 5.54
25 26 4.477780 GAAATTTATCGTGTTTGGCCGAA 58.522 39.130 0.00 0.00 36.57 4.30
26 27 4.712122 AATTTATCGTGTTTGGCCGAAT 57.288 36.364 9.15 0.00 36.57 3.34
27 28 4.712122 ATTTATCGTGTTTGGCCGAATT 57.288 36.364 9.15 0.00 36.57 2.17
28 29 4.506886 TTTATCGTGTTTGGCCGAATTT 57.493 36.364 9.15 0.00 36.57 1.82
29 30 4.506886 TTATCGTGTTTGGCCGAATTTT 57.493 36.364 9.15 0.00 36.57 1.82
30 31 5.624344 TTATCGTGTTTGGCCGAATTTTA 57.376 34.783 9.15 0.00 36.57 1.52
31 32 4.712122 ATCGTGTTTGGCCGAATTTTAT 57.288 36.364 9.15 0.00 36.57 1.40
32 33 4.086199 TCGTGTTTGGCCGAATTTTATC 57.914 40.909 9.15 0.00 0.00 1.75
33 34 2.843643 CGTGTTTGGCCGAATTTTATCG 59.156 45.455 9.15 4.53 42.37 2.92
34 35 3.668491 CGTGTTTGGCCGAATTTTATCGT 60.668 43.478 9.15 0.00 41.16 3.73
35 36 3.606346 GTGTTTGGCCGAATTTTATCGTG 59.394 43.478 9.15 0.00 41.16 4.35
36 37 3.253677 TGTTTGGCCGAATTTTATCGTGT 59.746 39.130 9.15 0.00 41.16 4.49
37 38 4.231439 GTTTGGCCGAATTTTATCGTGTT 58.769 39.130 9.15 0.00 41.16 3.32
38 39 4.506886 TTGGCCGAATTTTATCGTGTTT 57.493 36.364 0.00 0.00 41.16 2.83
39 40 5.624344 TTGGCCGAATTTTATCGTGTTTA 57.376 34.783 0.00 0.00 41.16 2.01
40 41 5.624344 TGGCCGAATTTTATCGTGTTTAA 57.376 34.783 0.00 0.00 41.16 1.52
41 42 5.632959 TGGCCGAATTTTATCGTGTTTAAG 58.367 37.500 0.00 0.00 41.16 1.85
42 43 4.497966 GGCCGAATTTTATCGTGTTTAAGC 59.502 41.667 0.00 0.00 41.16 3.09
43 44 4.497966 GCCGAATTTTATCGTGTTTAAGCC 59.502 41.667 0.00 0.00 41.16 4.35
44 45 4.726704 CCGAATTTTATCGTGTTTAAGCCG 59.273 41.667 0.00 0.00 41.16 5.52
45 46 5.446206 CCGAATTTTATCGTGTTTAAGCCGA 60.446 40.000 5.63 5.63 41.16 5.54
46 47 6.016718 CGAATTTTATCGTGTTTAAGCCGAA 58.983 36.000 6.90 0.00 38.01 4.30
47 48 6.022794 CGAATTTTATCGTGTTTAAGCCGAAC 60.023 38.462 6.90 0.00 38.01 3.95
48 49 5.927954 TTTTATCGTGTTTAAGCCGAACT 57.072 34.783 6.90 0.00 33.89 3.01
49 50 5.927954 TTTATCGTGTTTAAGCCGAACTT 57.072 34.783 6.90 0.00 42.76 2.66
50 51 5.520022 TTATCGTGTTTAAGCCGAACTTC 57.480 39.130 6.90 0.00 39.97 3.01
51 52 1.788308 TCGTGTTTAAGCCGAACTTCG 59.212 47.619 4.07 4.07 39.97 3.79
61 62 2.810486 CGAACTTCGGCGAACTTCT 58.190 52.632 27.33 12.14 36.00 2.85
62 63 1.137513 CGAACTTCGGCGAACTTCTT 58.862 50.000 27.33 14.99 36.00 2.52
63 64 1.525619 CGAACTTCGGCGAACTTCTTT 59.474 47.619 27.33 14.42 36.00 2.52
64 65 2.033151 CGAACTTCGGCGAACTTCTTTT 60.033 45.455 27.33 13.07 36.00 2.27
65 66 3.182972 CGAACTTCGGCGAACTTCTTTTA 59.817 43.478 27.33 6.28 36.00 1.52
66 67 4.143179 CGAACTTCGGCGAACTTCTTTTAT 60.143 41.667 27.33 7.42 36.00 1.40
67 68 5.614013 CGAACTTCGGCGAACTTCTTTTATT 60.614 40.000 27.33 10.76 36.00 1.40
68 69 5.684550 ACTTCGGCGAACTTCTTTTATTT 57.315 34.783 19.83 0.00 0.00 1.40
69 70 6.068473 ACTTCGGCGAACTTCTTTTATTTT 57.932 33.333 19.83 0.00 0.00 1.82
70 71 7.193377 ACTTCGGCGAACTTCTTTTATTTTA 57.807 32.000 19.83 0.00 0.00 1.52
71 72 7.641760 ACTTCGGCGAACTTCTTTTATTTTAA 58.358 30.769 19.83 0.00 0.00 1.52
72 73 8.130469 ACTTCGGCGAACTTCTTTTATTTTAAA 58.870 29.630 19.83 0.00 0.00 1.52
73 74 8.853469 TTCGGCGAACTTCTTTTATTTTAAAA 57.147 26.923 19.83 2.51 0.00 1.52
74 75 8.272436 TCGGCGAACTTCTTTTATTTTAAAAC 57.728 30.769 7.35 0.00 0.00 2.43
75 76 7.111870 TCGGCGAACTTCTTTTATTTTAAAACG 59.888 33.333 7.35 0.00 0.00 3.60
76 77 7.096925 CGGCGAACTTCTTTTATTTTAAAACGT 60.097 33.333 0.00 0.00 0.00 3.99
77 78 7.994343 GGCGAACTTCTTTTATTTTAAAACGTG 59.006 33.333 1.97 0.00 0.00 4.49
78 79 7.521571 GCGAACTTCTTTTATTTTAAAACGTGC 59.478 33.333 1.97 0.00 0.00 5.34
79 80 7.994343 CGAACTTCTTTTATTTTAAAACGTGCC 59.006 33.333 1.97 0.00 0.00 5.01
80 81 8.936070 AACTTCTTTTATTTTAAAACGTGCCT 57.064 26.923 1.97 0.00 0.00 4.75
81 82 8.347729 ACTTCTTTTATTTTAAAACGTGCCTG 57.652 30.769 1.97 0.00 0.00 4.85
82 83 7.436970 ACTTCTTTTATTTTAAAACGTGCCTGG 59.563 33.333 1.97 0.00 0.00 4.45
83 84 6.217294 TCTTTTATTTTAAAACGTGCCTGGG 58.783 36.000 1.97 0.00 0.00 4.45
84 85 4.522722 TTATTTTAAAACGTGCCTGGGG 57.477 40.909 1.97 0.00 0.00 4.96
85 86 1.041437 TTTTAAAACGTGCCTGGGGG 58.959 50.000 0.00 0.00 0.00 5.40
86 87 0.185416 TTTAAAACGTGCCTGGGGGA 59.815 50.000 0.00 0.00 33.58 4.81
87 88 0.537828 TTAAAACGTGCCTGGGGGAC 60.538 55.000 0.00 0.00 40.73 4.46
126 127 4.410400 GGACCAACTCGCCCCCAG 62.410 72.222 0.00 0.00 0.00 4.45
127 128 4.410400 GACCAACTCGCCCCCAGG 62.410 72.222 0.00 0.00 0.00 4.45
137 138 4.248908 CCCCCAGGCCCAATTTTT 57.751 55.556 0.00 0.00 0.00 1.94
138 139 1.684629 CCCCCAGGCCCAATTTTTG 59.315 57.895 0.00 0.00 0.00 2.44
139 140 1.002257 CCCCAGGCCCAATTTTTGC 60.002 57.895 0.00 0.00 0.00 3.68
140 141 1.375780 CCCAGGCCCAATTTTTGCG 60.376 57.895 0.00 0.00 0.00 4.85
141 142 2.034317 CCAGGCCCAATTTTTGCGC 61.034 57.895 0.00 0.00 33.80 6.09
143 144 3.117812 GGCCCAATTTTTGCGCCG 61.118 61.111 4.18 0.00 43.89 6.46
144 145 3.117812 GCCCAATTTTTGCGCCGG 61.118 61.111 4.18 0.00 0.00 6.13
145 146 3.117812 CCCAATTTTTGCGCCGGC 61.118 61.111 19.07 19.07 40.52 6.13
146 147 2.048316 CCAATTTTTGCGCCGGCT 60.048 55.556 26.68 0.00 40.82 5.52
147 148 2.094066 CCAATTTTTGCGCCGGCTC 61.094 57.895 26.68 18.89 40.82 4.70
148 149 1.372748 CAATTTTTGCGCCGGCTCA 60.373 52.632 26.68 21.91 40.82 4.26
149 150 1.372872 AATTTTTGCGCCGGCTCAC 60.373 52.632 26.68 14.53 40.82 3.51
150 151 2.763627 AATTTTTGCGCCGGCTCACC 62.764 55.000 26.68 10.54 40.82 4.02
167 168 2.124487 CCCCAGGCGGCGATTTTA 60.124 61.111 12.98 0.00 0.00 1.52
168 169 2.186826 CCCCAGGCGGCGATTTTAG 61.187 63.158 12.98 0.00 0.00 1.85
169 170 2.186826 CCCAGGCGGCGATTTTAGG 61.187 63.158 12.98 2.42 0.00 2.69
170 171 2.715624 CAGGCGGCGATTTTAGGC 59.284 61.111 12.98 0.00 0.00 3.93
176 177 3.592814 GCGATTTTAGGCGCCCCC 61.593 66.667 26.15 5.00 46.93 5.40
178 179 2.186826 CGATTTTAGGCGCCCCCTG 61.187 63.158 26.15 2.62 45.91 4.45
179 180 1.828224 GATTTTAGGCGCCCCCTGG 60.828 63.158 26.15 0.00 45.91 4.45
180 181 3.373932 ATTTTAGGCGCCCCCTGGG 62.374 63.158 26.15 5.50 45.91 4.45
230 231 2.468670 GCATATCAACCGCGCCACA 61.469 57.895 0.00 0.00 0.00 4.17
239 240 3.029735 CGCGCCACAAAACTTGCC 61.030 61.111 0.00 0.00 0.00 4.52
247 248 1.008995 CAAAACTTGCCGACGGTGG 60.009 57.895 16.73 8.42 0.00 4.61
260 261 2.159212 CGACGGTGGTATGAATGGTGTA 60.159 50.000 0.00 0.00 0.00 2.90
284 285 4.383052 CCATCGATATGCTAACGACTTCAC 59.617 45.833 0.00 0.00 38.79 3.18
290 291 1.459209 TGCTAACGACTTCACATTGCG 59.541 47.619 0.00 0.00 0.00 4.85
293 294 3.606153 GCTAACGACTTCACATTGCGTTT 60.606 43.478 0.00 0.00 41.74 3.60
311 312 4.734402 GCGTTTATGGATGATGTGCATGTT 60.734 41.667 0.00 0.00 39.44 2.71
312 313 4.736307 CGTTTATGGATGATGTGCATGTTG 59.264 41.667 0.00 0.00 39.44 3.33
313 314 2.882927 ATGGATGATGTGCATGTTGC 57.117 45.000 0.00 0.00 45.29 4.17
342 343 5.829681 GCAATATACTATCGTGCGTGTAAC 58.170 41.667 0.00 0.00 0.00 2.50
399 400 2.852748 CTTCTATCTACGGGATTCGCG 58.147 52.381 20.03 20.03 45.13 5.87
403 404 0.243907 ATCTACGGGATTCGCGGATG 59.756 55.000 24.34 14.50 43.94 3.51
411 412 0.026803 GATTCGCGGATGCAGTCAAC 59.973 55.000 3.53 0.00 42.97 3.18
428 429 1.719725 AACCACGCATCGCACAACAA 61.720 50.000 0.00 0.00 0.00 2.83
434 435 1.400113 CGCATCGCACAACAACTCATT 60.400 47.619 0.00 0.00 0.00 2.57
441 442 3.684305 CGCACAACAACTCATTCTCCATA 59.316 43.478 0.00 0.00 0.00 2.74
459 460 1.688772 TACTCGAGTACCCTGCCATC 58.311 55.000 21.25 0.00 0.00 3.51
531 532 1.444119 GAACGAACACCTGCCAAGCA 61.444 55.000 0.00 0.00 36.92 3.91
564 567 3.986006 GTCGTCGACAGTGGGGCA 61.986 66.667 20.28 0.00 32.09 5.36
568 571 2.997315 TCGACAGTGGGGCAGAGG 60.997 66.667 0.00 0.00 0.00 3.69
586 589 3.755628 GTACCTGGCTGCGGACGA 61.756 66.667 0.00 0.00 0.00 4.20
592 595 2.016393 CTGGCTGCGGACGAATCCTA 62.016 60.000 0.00 0.00 43.73 2.94
594 597 1.734137 GCTGCGGACGAATCCTAGA 59.266 57.895 0.00 0.00 43.73 2.43
620 623 4.895854 GCCGTACTACAAGGCGAA 57.104 55.556 0.00 0.00 42.15 4.70
622 625 0.388907 GCCGTACTACAAGGCGAACA 60.389 55.000 0.00 0.00 42.15 3.18
623 626 1.738030 GCCGTACTACAAGGCGAACAT 60.738 52.381 0.00 0.00 42.15 2.71
657 671 2.341875 CGACAATGCATGGGTGGCA 61.342 57.895 5.94 0.00 46.66 4.92
674 688 0.106708 GCAGCCGGGAAGATACATCA 59.893 55.000 2.18 0.00 0.00 3.07
680 694 1.860950 CGGGAAGATACATCAACAGCG 59.139 52.381 0.00 0.00 0.00 5.18
681 695 2.738643 CGGGAAGATACATCAACAGCGT 60.739 50.000 0.00 0.00 0.00 5.07
682 696 3.270877 GGGAAGATACATCAACAGCGTT 58.729 45.455 0.00 0.00 0.00 4.84
685 699 3.610040 AGATACATCAACAGCGTTGGA 57.390 42.857 17.28 8.11 0.00 3.53
690 704 0.976641 ATCAACAGCGTTGGAGGAGA 59.023 50.000 17.28 0.00 0.00 3.71
695 709 0.035458 CAGCGTTGGAGGAGAAGGTT 59.965 55.000 0.00 0.00 0.00 3.50
699 713 0.955919 GTTGGAGGAGAAGGTTGCGG 60.956 60.000 0.00 0.00 0.00 5.69
702 716 1.120530 GGAGGAGAAGGTTGCGGATA 58.879 55.000 0.00 0.00 0.00 2.59
705 719 1.482593 AGGAGAAGGTTGCGGATACAG 59.517 52.381 0.00 0.00 0.00 2.74
710 724 3.961408 AGAAGGTTGCGGATACAGAGTAT 59.039 43.478 0.00 0.00 0.00 2.12
714 728 2.364324 GTTGCGGATACAGAGTATGGGA 59.636 50.000 0.00 0.00 0.00 4.37
715 729 2.673258 TGCGGATACAGAGTATGGGAA 58.327 47.619 0.00 0.00 0.00 3.97
716 730 3.035363 TGCGGATACAGAGTATGGGAAA 58.965 45.455 0.00 0.00 0.00 3.13
717 731 3.069586 TGCGGATACAGAGTATGGGAAAG 59.930 47.826 0.00 0.00 0.00 2.62
718 732 3.654414 CGGATACAGAGTATGGGAAAGC 58.346 50.000 0.00 0.00 0.00 3.51
720 734 4.262635 CGGATACAGAGTATGGGAAAGCAT 60.263 45.833 0.00 0.00 0.00 3.79
721 735 4.999950 GGATACAGAGTATGGGAAAGCATG 59.000 45.833 0.00 0.00 0.00 4.06
722 736 5.455326 GGATACAGAGTATGGGAAAGCATGT 60.455 44.000 0.00 0.00 0.00 3.21
724 898 5.636903 ACAGAGTATGGGAAAGCATGTAT 57.363 39.130 0.00 0.00 0.00 2.29
727 901 7.749666 ACAGAGTATGGGAAAGCATGTATATT 58.250 34.615 0.00 0.00 0.00 1.28
750 924 5.543507 TTTTATGGCAAAACACATCCAGT 57.456 34.783 0.00 0.00 31.36 4.00
755 929 2.102252 GGCAAAACACATCCAGTCCAAA 59.898 45.455 0.00 0.00 0.00 3.28
758 932 1.604604 AACACATCCAGTCCAAACGG 58.395 50.000 0.00 0.00 0.00 4.44
759 933 0.762418 ACACATCCAGTCCAAACGGA 59.238 50.000 0.00 0.00 34.26 4.69
772 950 1.241315 AAACGGATGCGGTTTGAGGG 61.241 55.000 12.44 0.00 35.99 4.30
773 951 3.508840 CGGATGCGGTTTGAGGGC 61.509 66.667 0.00 0.00 0.00 5.19
784 962 0.757188 TTTGAGGGCCCGCTTTGAAA 60.757 50.000 27.03 15.32 0.00 2.69
785 963 0.541764 TTGAGGGCCCGCTTTGAAAT 60.542 50.000 27.03 0.00 0.00 2.17
786 964 1.250154 TGAGGGCCCGCTTTGAAATG 61.250 55.000 27.03 0.00 0.00 2.32
787 965 2.125552 GGGCCCGCTTTGAAATGC 60.126 61.111 5.69 0.00 0.00 3.56
789 967 2.506881 GCCCGCTTTGAAATGCCG 60.507 61.111 0.00 0.00 0.00 5.69
797 983 2.287909 GCTTTGAAATGCCGTTACCACA 60.288 45.455 0.00 0.00 0.00 4.17
798 984 3.613910 GCTTTGAAATGCCGTTACCACAT 60.614 43.478 0.00 0.00 0.00 3.21
820 1019 1.603455 CACAACCGGCCTGGATTGT 60.603 57.895 18.74 18.80 42.00 2.71
990 1241 0.250901 AACCAGTTGCCAATCTCGCT 60.251 50.000 0.00 0.00 0.00 4.93
992 1243 1.699656 CCAGTTGCCAATCTCGCTCG 61.700 60.000 0.00 0.00 0.00 5.03
993 1244 0.737367 CAGTTGCCAATCTCGCTCGA 60.737 55.000 0.00 0.00 0.00 4.04
1510 1850 0.889638 TCGTCGCACTCTCCTGTTCT 60.890 55.000 0.00 0.00 0.00 3.01
1511 1851 0.730834 CGTCGCACTCTCCTGTTCTG 60.731 60.000 0.00 0.00 0.00 3.02
1512 1852 0.389166 GTCGCACTCTCCTGTTCTGG 60.389 60.000 0.00 0.00 0.00 3.86
1513 1853 0.827925 TCGCACTCTCCTGTTCTGGT 60.828 55.000 0.00 0.00 0.00 4.00
1515 1855 0.952984 GCACTCTCCTGTTCTGGTGC 60.953 60.000 0.00 0.00 42.04 5.01
1516 1856 0.394192 CACTCTCCTGTTCTGGTGCA 59.606 55.000 0.00 0.00 0.00 4.57
1517 1857 0.683973 ACTCTCCTGTTCTGGTGCAG 59.316 55.000 0.00 0.00 0.00 4.41
1518 1858 0.972134 CTCTCCTGTTCTGGTGCAGA 59.028 55.000 0.00 0.00 38.87 4.26
1634 3584 1.014352 GTTGCTTTGTGGTCTCACGT 58.986 50.000 0.00 0.00 46.42 4.49
1754 3747 7.177392 CCAAAAACTCAGAATAGGGATTTCAGT 59.823 37.037 0.00 0.00 0.00 3.41
1815 3819 6.860023 CACTTGAAATCAGTTGTTGAAGATCC 59.140 38.462 0.00 0.00 39.77 3.36
1860 3864 6.849588 AAGTTGAAGTCAATTTCATTTGGC 57.150 33.333 0.00 0.00 36.97 4.52
2033 4999 3.498397 ACAGTCGGCAATCTTTGTTACAG 59.502 43.478 0.00 0.00 0.00 2.74
2149 5115 3.054655 GCTTTCCCTGGACACAACCTATA 60.055 47.826 0.00 0.00 0.00 1.31
2281 5247 6.362210 TCCAACATAACAATGATGATGACG 57.638 37.500 0.00 0.00 30.79 4.35
2282 5248 6.112058 TCCAACATAACAATGATGATGACGA 58.888 36.000 0.00 0.00 30.79 4.20
2283 5249 6.037062 TCCAACATAACAATGATGATGACGAC 59.963 38.462 0.00 0.00 30.79 4.34
2284 5250 5.641777 ACATAACAATGATGATGACGACG 57.358 39.130 0.00 0.00 0.00 5.12
2285 5251 4.507756 ACATAACAATGATGATGACGACGG 59.492 41.667 0.00 0.00 0.00 4.79
2286 5252 1.290203 ACAATGATGATGACGACGGC 58.710 50.000 0.00 0.00 0.00 5.68
2287 5253 0.230515 CAATGATGATGACGACGGCG 59.769 55.000 10.39 10.39 44.79 6.46
2485 5574 2.060383 TCCATCAGCCTGACGGAGG 61.060 63.158 5.19 1.82 46.13 4.30
2609 5707 4.038162 CCCGGGTCAAAGTAAATGAACAAA 59.962 41.667 14.18 0.00 36.19 2.83
2621 5719 9.559958 AAGTAAATGAACAAAGAAAGCATATCG 57.440 29.630 0.00 0.00 0.00 2.92
3170 6425 7.934120 AGTTCTATTATCTGTAGGTGGATTTGC 59.066 37.037 0.00 0.00 0.00 3.68
3179 6434 0.675633 GGTGGATTTGCAGTGCAGTT 59.324 50.000 18.81 9.77 40.61 3.16
3459 6765 9.389755 TCATATTCATTTGTTTAGAACGATCCA 57.610 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.086199 TCGGCCAAACACGATAAATTTC 57.914 40.909 2.24 0.00 33.69 2.17
4 5 4.506886 TTCGGCCAAACACGATAAATTT 57.493 36.364 2.24 0.00 39.06 1.82
5 6 4.712122 ATTCGGCCAAACACGATAAATT 57.288 36.364 2.24 0.00 39.06 1.82
6 7 4.712122 AATTCGGCCAAACACGATAAAT 57.288 36.364 2.24 0.00 39.06 1.40
7 8 4.506886 AAATTCGGCCAAACACGATAAA 57.493 36.364 2.24 0.00 39.06 1.40
8 9 4.506886 AAAATTCGGCCAAACACGATAA 57.493 36.364 2.24 0.00 39.06 1.75
9 10 5.502706 CGATAAAATTCGGCCAAACACGATA 60.503 40.000 2.24 0.00 39.06 2.92
10 11 4.668289 GATAAAATTCGGCCAAACACGAT 58.332 39.130 2.24 0.00 39.06 3.73
11 12 3.425094 CGATAAAATTCGGCCAAACACGA 60.425 43.478 2.24 0.00 35.50 4.35
12 13 2.843643 CGATAAAATTCGGCCAAACACG 59.156 45.455 2.24 0.00 35.50 4.49
13 14 3.606346 CACGATAAAATTCGGCCAAACAC 59.394 43.478 2.24 0.00 43.33 3.32
14 15 3.253677 ACACGATAAAATTCGGCCAAACA 59.746 39.130 2.24 0.00 43.33 2.83
15 16 3.828786 ACACGATAAAATTCGGCCAAAC 58.171 40.909 2.24 0.00 43.33 2.93
16 17 4.506886 AACACGATAAAATTCGGCCAAA 57.493 36.364 2.24 0.00 43.33 3.28
17 18 4.506886 AAACACGATAAAATTCGGCCAA 57.493 36.364 2.24 0.00 43.33 4.52
18 19 5.624344 TTAAACACGATAAAATTCGGCCA 57.376 34.783 2.24 0.00 43.33 5.36
19 20 4.497966 GCTTAAACACGATAAAATTCGGCC 59.502 41.667 0.00 0.00 43.33 6.13
20 21 4.497966 GGCTTAAACACGATAAAATTCGGC 59.502 41.667 0.00 0.00 43.33 5.54
21 22 4.726704 CGGCTTAAACACGATAAAATTCGG 59.273 41.667 0.00 0.00 43.33 4.30
22 23 5.552807 TCGGCTTAAACACGATAAAATTCG 58.447 37.500 0.00 0.00 44.56 3.34
23 24 7.019418 AGTTCGGCTTAAACACGATAAAATTC 58.981 34.615 0.00 0.00 36.43 2.17
24 25 6.905578 AGTTCGGCTTAAACACGATAAAATT 58.094 32.000 0.00 0.00 36.43 1.82
25 26 6.490566 AGTTCGGCTTAAACACGATAAAAT 57.509 33.333 0.00 0.00 36.43 1.82
26 27 5.927954 AGTTCGGCTTAAACACGATAAAA 57.072 34.783 0.00 0.00 36.43 1.52
27 28 5.388682 CGAAGTTCGGCTTAAACACGATAAA 60.389 40.000 17.61 0.00 37.59 1.40
28 29 4.090354 CGAAGTTCGGCTTAAACACGATAA 59.910 41.667 17.61 0.00 37.59 1.75
29 30 3.609373 CGAAGTTCGGCTTAAACACGATA 59.391 43.478 17.61 0.00 37.59 2.92
30 31 2.410730 CGAAGTTCGGCTTAAACACGAT 59.589 45.455 17.61 0.00 37.59 3.73
31 32 1.788308 CGAAGTTCGGCTTAAACACGA 59.212 47.619 17.61 0.00 37.59 4.35
32 33 2.207041 CGAAGTTCGGCTTAAACACG 57.793 50.000 17.61 0.00 37.59 4.49
44 45 3.604065 AAAAGAAGTTCGCCGAAGTTC 57.396 42.857 30.52 30.52 46.41 3.01
45 46 5.684550 AATAAAAGAAGTTCGCCGAAGTT 57.315 34.783 19.08 19.08 37.82 2.66
46 47 5.684550 AAATAAAAGAAGTTCGCCGAAGT 57.315 34.783 0.00 0.00 0.00 3.01
47 48 8.496872 TTTAAAATAAAAGAAGTTCGCCGAAG 57.503 30.769 0.00 0.00 0.00 3.79
48 49 8.744923 GTTTTAAAATAAAAGAAGTTCGCCGAA 58.255 29.630 3.52 0.00 0.00 4.30
49 50 7.111870 CGTTTTAAAATAAAAGAAGTTCGCCGA 59.888 33.333 3.52 0.00 0.00 5.54
50 51 7.096925 ACGTTTTAAAATAAAAGAAGTTCGCCG 60.097 33.333 3.52 0.01 0.00 6.46
51 52 7.994343 CACGTTTTAAAATAAAAGAAGTTCGCC 59.006 33.333 3.52 0.00 0.00 5.54
52 53 7.521571 GCACGTTTTAAAATAAAAGAAGTTCGC 59.478 33.333 3.52 0.00 0.00 4.70
53 54 7.994343 GGCACGTTTTAAAATAAAAGAAGTTCG 59.006 33.333 3.52 1.24 0.00 3.95
54 55 9.027129 AGGCACGTTTTAAAATAAAAGAAGTTC 57.973 29.630 3.52 0.00 0.00 3.01
55 56 8.813282 CAGGCACGTTTTAAAATAAAAGAAGTT 58.187 29.630 3.52 0.00 0.00 2.66
56 57 7.436970 CCAGGCACGTTTTAAAATAAAAGAAGT 59.563 33.333 3.52 0.00 0.00 3.01
57 58 7.095816 CCCAGGCACGTTTTAAAATAAAAGAAG 60.096 37.037 3.52 0.00 0.00 2.85
58 59 6.702282 CCCAGGCACGTTTTAAAATAAAAGAA 59.298 34.615 3.52 0.00 0.00 2.52
59 60 6.217294 CCCAGGCACGTTTTAAAATAAAAGA 58.783 36.000 3.52 0.00 0.00 2.52
60 61 5.407084 CCCCAGGCACGTTTTAAAATAAAAG 59.593 40.000 3.52 0.00 0.00 2.27
61 62 5.298347 CCCCAGGCACGTTTTAAAATAAAA 58.702 37.500 3.52 0.00 0.00 1.52
62 63 4.262506 CCCCCAGGCACGTTTTAAAATAAA 60.263 41.667 3.52 0.00 0.00 1.40
63 64 3.258622 CCCCCAGGCACGTTTTAAAATAA 59.741 43.478 3.52 0.00 0.00 1.40
64 65 2.826725 CCCCCAGGCACGTTTTAAAATA 59.173 45.455 3.52 0.00 0.00 1.40
65 66 1.621317 CCCCCAGGCACGTTTTAAAAT 59.379 47.619 3.52 0.00 0.00 1.82
66 67 1.041437 CCCCCAGGCACGTTTTAAAA 58.959 50.000 0.00 0.00 0.00 1.52
67 68 0.185416 TCCCCCAGGCACGTTTTAAA 59.815 50.000 0.00 0.00 0.00 1.52
68 69 0.537828 GTCCCCCAGGCACGTTTTAA 60.538 55.000 0.00 0.00 0.00 1.52
69 70 1.073548 GTCCCCCAGGCACGTTTTA 59.926 57.895 0.00 0.00 0.00 1.52
70 71 2.203437 GTCCCCCAGGCACGTTTT 60.203 61.111 0.00 0.00 0.00 2.43
71 72 4.636435 CGTCCCCCAGGCACGTTT 62.636 66.667 0.00 0.00 34.19 3.60
102 103 4.760047 CGAGTTGGTCCCCAGCCG 62.760 72.222 0.00 0.00 35.27 5.52
105 106 4.410400 GGGCGAGTTGGTCCCCAG 62.410 72.222 0.00 0.00 36.26 4.45
109 110 4.410400 CTGGGGGCGAGTTGGTCC 62.410 72.222 0.00 0.00 0.00 4.46
110 111 4.410400 CCTGGGGGCGAGTTGGTC 62.410 72.222 0.00 0.00 0.00 4.02
120 121 1.684629 CAAAAATTGGGCCTGGGGG 59.315 57.895 4.53 0.00 0.00 5.40
121 122 1.002257 GCAAAAATTGGGCCTGGGG 60.002 57.895 4.53 0.00 0.00 4.96
122 123 1.375780 CGCAAAAATTGGGCCTGGG 60.376 57.895 4.53 0.00 36.79 4.45
123 124 4.282399 CGCAAAAATTGGGCCTGG 57.718 55.556 4.53 0.00 36.79 4.45
128 129 3.117812 GCCGGCGCAAAAATTGGG 61.118 61.111 12.58 3.09 45.41 4.12
129 130 2.048316 AGCCGGCGCAAAAATTGG 60.048 55.556 23.20 0.00 37.52 3.16
130 131 1.372748 TGAGCCGGCGCAAAAATTG 60.373 52.632 31.47 0.00 37.52 2.32
131 132 1.372872 GTGAGCCGGCGCAAAAATT 60.373 52.632 34.87 7.50 37.52 1.82
132 133 2.258286 GTGAGCCGGCGCAAAAAT 59.742 55.556 34.87 8.42 37.52 1.82
133 134 3.972276 GGTGAGCCGGCGCAAAAA 61.972 61.111 34.87 9.47 37.52 1.94
151 152 2.186826 CCTAAAATCGCCGCCTGGG 61.187 63.158 0.00 0.00 39.58 4.45
152 153 2.834618 GCCTAAAATCGCCGCCTGG 61.835 63.158 0.00 0.00 38.77 4.45
153 154 2.715624 GCCTAAAATCGCCGCCTG 59.284 61.111 0.00 0.00 0.00 4.85
154 155 2.895372 CGCCTAAAATCGCCGCCT 60.895 61.111 0.00 0.00 0.00 5.52
155 156 4.607606 GCGCCTAAAATCGCCGCC 62.608 66.667 0.00 0.00 45.01 6.13
160 161 2.186826 CAGGGGGCGCCTAAAATCG 61.187 63.158 28.56 5.85 0.00 3.34
161 162 1.828224 CCAGGGGGCGCCTAAAATC 60.828 63.158 28.56 8.16 0.00 2.17
162 163 2.278738 CCAGGGGGCGCCTAAAAT 59.721 61.111 28.56 5.30 0.00 1.82
163 164 4.055227 CCCAGGGGGCGCCTAAAA 62.055 66.667 28.56 0.00 35.35 1.52
190 191 0.107643 GAGGTAAGGGCATCTCCAGC 59.892 60.000 0.00 0.00 36.21 4.85
191 192 0.761802 GGAGGTAAGGGCATCTCCAG 59.238 60.000 0.00 0.00 43.78 3.86
192 193 2.930935 GGAGGTAAGGGCATCTCCA 58.069 57.895 0.00 0.00 43.78 3.86
193 194 0.761802 CTGGAGGTAAGGGCATCTCC 59.238 60.000 0.00 0.00 44.39 3.71
194 195 0.107643 GCTGGAGGTAAGGGCATCTC 59.892 60.000 0.00 0.00 0.00 2.75
195 196 0.621571 TGCTGGAGGTAAGGGCATCT 60.622 55.000 0.00 0.00 0.00 2.90
196 197 0.475906 ATGCTGGAGGTAAGGGCATC 59.524 55.000 0.00 0.00 39.02 3.91
197 198 1.819753 TATGCTGGAGGTAAGGGCAT 58.180 50.000 0.00 0.00 44.31 4.40
198 199 1.699634 GATATGCTGGAGGTAAGGGCA 59.300 52.381 0.00 0.00 37.32 5.36
199 200 1.699634 TGATATGCTGGAGGTAAGGGC 59.300 52.381 0.00 0.00 0.00 5.19
200 201 3.496870 GGTTGATATGCTGGAGGTAAGGG 60.497 52.174 0.00 0.00 0.00 3.95
230 231 0.179051 TACCACCGTCGGCAAGTTTT 60.179 50.000 12.28 0.00 0.00 2.43
239 240 1.286501 CACCATTCATACCACCGTCG 58.713 55.000 0.00 0.00 0.00 5.12
260 261 4.037565 TGAAGTCGTTAGCATATCGATGGT 59.962 41.667 8.54 1.54 43.62 3.55
284 285 3.732219 GCACATCATCCATAAACGCAATG 59.268 43.478 0.00 0.00 0.00 2.82
290 291 4.505191 GCAACATGCACATCATCCATAAAC 59.495 41.667 0.00 0.00 44.26 2.01
293 294 3.994204 GCAACATGCACATCATCCATA 57.006 42.857 0.00 0.00 44.26 2.74
312 313 1.927174 CGATAGTATATTGCGCCCTGC 59.073 52.381 4.18 0.00 46.70 4.85
329 330 1.985334 TGATTCGTTACACGCACGAT 58.015 45.000 0.00 0.00 45.67 3.73
339 340 1.926510 CAGAGCGTGCATGATTCGTTA 59.073 47.619 10.93 0.00 0.00 3.18
399 400 1.308069 ATGCGTGGTTGACTGCATCC 61.308 55.000 0.00 0.00 39.20 3.51
403 404 2.476051 CGATGCGTGGTTGACTGC 59.524 61.111 0.00 0.00 0.00 4.40
411 412 1.725625 GTTGTTGTGCGATGCGTGG 60.726 57.895 0.00 0.00 0.00 4.94
428 429 4.822896 GGTACTCGAGTATGGAGAATGAGT 59.177 45.833 27.02 0.00 44.45 3.41
434 435 2.748798 GCAGGGTACTCGAGTATGGAGA 60.749 54.545 27.02 3.78 44.45 3.71
441 442 1.043673 GGATGGCAGGGTACTCGAGT 61.044 60.000 23.66 23.66 0.00 4.18
489 490 6.938507 TCAAATGCCATTGAGCTAAATTTCT 58.061 32.000 0.00 0.00 34.50 2.52
501 502 2.730928 GGTGTTCGTTCAAATGCCATTG 59.269 45.455 0.00 0.00 0.00 2.82
502 503 2.627699 AGGTGTTCGTTCAAATGCCATT 59.372 40.909 0.00 0.00 0.00 3.16
503 504 2.030007 CAGGTGTTCGTTCAAATGCCAT 60.030 45.455 0.00 0.00 0.00 4.40
538 539 1.392853 ACTGTCGACGACGTCTATGAC 59.607 52.381 24.36 22.28 40.69 3.06
564 567 3.077556 CGCAGCCAGGTACCCTCT 61.078 66.667 8.74 0.00 0.00 3.69
568 571 4.814294 CGTCCGCAGCCAGGTACC 62.814 72.222 2.73 2.73 0.00 3.34
603 606 0.388907 TGTTCGCCTTGTAGTACGGC 60.389 55.000 8.69 8.69 40.40 5.68
604 607 1.924524 CATGTTCGCCTTGTAGTACGG 59.075 52.381 0.00 0.00 0.00 4.02
657 671 1.837439 TGTTGATGTATCTTCCCGGCT 59.163 47.619 0.00 0.00 0.00 5.52
663 677 3.932710 TCCAACGCTGTTGATGTATCTTC 59.067 43.478 18.69 0.00 0.00 2.87
664 678 3.935203 CTCCAACGCTGTTGATGTATCTT 59.065 43.478 18.69 0.00 0.00 2.40
667 681 2.236146 TCCTCCAACGCTGTTGATGTAT 59.764 45.455 18.69 0.00 0.00 2.29
674 688 0.035458 CCTTCTCCTCCAACGCTGTT 59.965 55.000 0.00 0.00 0.00 3.16
680 694 0.955919 CCGCAACCTTCTCCTCCAAC 60.956 60.000 0.00 0.00 0.00 3.77
681 695 1.125093 TCCGCAACCTTCTCCTCCAA 61.125 55.000 0.00 0.00 0.00 3.53
682 696 0.909610 ATCCGCAACCTTCTCCTCCA 60.910 55.000 0.00 0.00 0.00 3.86
685 699 1.482593 CTGTATCCGCAACCTTCTCCT 59.517 52.381 0.00 0.00 0.00 3.69
690 704 3.181465 CCATACTCTGTATCCGCAACCTT 60.181 47.826 0.00 0.00 0.00 3.50
695 709 2.375014 TCCCATACTCTGTATCCGCA 57.625 50.000 0.00 0.00 0.00 5.69
699 713 5.615289 ACATGCTTTCCCATACTCTGTATC 58.385 41.667 0.00 0.00 0.00 2.24
702 716 5.636903 ATACATGCTTTCCCATACTCTGT 57.363 39.130 0.00 0.00 0.00 3.41
727 901 5.923204 ACTGGATGTGTTTTGCCATAAAAA 58.077 33.333 0.00 0.00 0.00 1.94
731 905 3.088532 GGACTGGATGTGTTTTGCCATA 58.911 45.455 0.00 0.00 0.00 2.74
755 929 2.046314 CCCTCAAACCGCATCCGT 60.046 61.111 0.00 0.00 0.00 4.69
758 932 3.140814 GGGCCCTCAAACCGCATC 61.141 66.667 17.04 0.00 0.00 3.91
772 950 2.506881 CGGCATTTCAAAGCGGGC 60.507 61.111 0.00 0.00 0.00 6.13
773 951 0.523966 TAACGGCATTTCAAAGCGGG 59.476 50.000 0.00 0.00 35.65 6.13
776 954 2.287909 TGTGGTAACGGCATTTCAAAGC 60.288 45.455 0.00 0.00 42.51 3.51
777 955 3.634568 TGTGGTAACGGCATTTCAAAG 57.365 42.857 0.00 0.00 42.51 2.77
784 962 0.326595 TGGACATGTGGTAACGGCAT 59.673 50.000 1.15 0.00 42.51 4.40
785 963 0.604243 GTGGACATGTGGTAACGGCA 60.604 55.000 1.15 0.00 42.51 5.69
786 964 0.604243 TGTGGACATGTGGTAACGGC 60.604 55.000 1.15 0.00 42.51 5.68
787 965 1.533731 GTTGTGGACATGTGGTAACGG 59.466 52.381 1.15 0.00 42.51 4.44
789 967 1.533731 CGGTTGTGGACATGTGGTAAC 59.466 52.381 1.15 3.26 0.00 2.50
797 983 2.034066 CAGGCCGGTTGTGGACAT 59.966 61.111 1.90 0.00 40.67 3.06
798 984 4.263572 CCAGGCCGGTTGTGGACA 62.264 66.667 12.18 0.00 40.67 4.02
941 1167 6.036844 GGTGTGAGGAACGGATATTCTTTTAC 59.963 42.308 0.00 0.00 0.00 2.01
992 1243 1.369321 GCCTCCTCCATCGGTGATC 59.631 63.158 0.00 0.00 0.00 2.92
993 1244 2.143419 GGCCTCCTCCATCGGTGAT 61.143 63.158 0.00 0.00 0.00 3.06
1515 1855 7.756395 ATAATTTGGATAATCTGCACCTCTG 57.244 36.000 0.00 0.00 0.00 3.35
1516 1856 9.678260 GATATAATTTGGATAATCTGCACCTCT 57.322 33.333 0.00 0.00 0.00 3.69
1517 1857 9.678260 AGATATAATTTGGATAATCTGCACCTC 57.322 33.333 0.00 0.00 0.00 3.85
1538 1886 5.367937 ACATTCAGGAACACAGGCTAGATAT 59.632 40.000 0.00 0.00 0.00 1.63
1634 3584 6.581919 CACGTCAAATTAATTGCAATCAGACA 59.418 34.615 13.38 0.00 38.98 3.41
1754 3747 9.679661 TCATAAAATTTGCTAGTCAGAACCATA 57.320 29.630 0.00 0.00 0.00 2.74
1787 3791 8.675705 TCTTCAACAACTGATTTCAAGTGATA 57.324 30.769 0.00 0.00 32.78 2.15
1790 3794 6.860023 GGATCTTCAACAACTGATTTCAAGTG 59.140 38.462 0.00 0.00 32.78 3.16
2033 4999 2.271800 CGCAAACATAGGGTCAGAGTC 58.728 52.381 0.00 0.00 0.00 3.36
2095 5061 1.323412 ATCTTCCCACGGATCTCGAG 58.677 55.000 5.93 5.93 42.43 4.04
2135 5101 0.538118 GGCGGTATAGGTTGTGTCCA 59.462 55.000 0.00 0.00 0.00 4.02
2149 5115 0.981183 TTGAAGACCATGTAGGCGGT 59.019 50.000 0.00 0.00 43.14 5.68
2284 5250 2.890474 ATCATTGTCGCCGTCGCC 60.890 61.111 0.00 0.00 35.26 5.54
2285 5251 2.164663 TCATCATTGTCGCCGTCGC 61.165 57.895 0.00 0.00 35.26 5.19
2286 5252 1.631072 GTCATCATTGTCGCCGTCG 59.369 57.895 0.00 0.00 0.00 5.12
2287 5253 0.800683 TCGTCATCATTGTCGCCGTC 60.801 55.000 0.00 0.00 34.92 4.79
2291 5257 1.071894 CGTCATCGTCATCATTGTCGC 60.072 52.381 0.00 0.00 34.92 5.19
2454 5543 2.680352 ATGGACACCTCGCCGTCT 60.680 61.111 0.00 0.00 32.57 4.18
2485 5574 0.469144 TTCCAGTTCCCACCTTTGGC 60.469 55.000 0.00 0.00 42.35 4.52
2609 5707 5.836821 TGACTACAGACGATATGCTTTCT 57.163 39.130 0.00 0.00 0.00 2.52
2621 5719 1.589196 GCCGCCGATGACTACAGAC 60.589 63.158 0.00 0.00 0.00 3.51
2961 6198 4.338795 AGAGGAGAATAGAACCTGGTCA 57.661 45.455 0.00 0.00 33.89 4.02
3033 6274 1.135199 CAGGCGCTGCTTCAATTTGAT 60.135 47.619 7.64 0.00 0.00 2.57
3170 6425 6.564499 GCAATTTGTCCAATTTAACTGCACTG 60.564 38.462 0.00 0.00 32.24 3.66
3179 6434 6.015519 ACACTAGCAGCAATTTGTCCAATTTA 60.016 34.615 0.00 0.00 32.24 1.40
3459 6765 3.805971 GGTCGTGTAGCAAACTAGTGTTT 59.194 43.478 0.00 0.00 46.20 2.83


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

AutoCloner maintained by Alex Coulton.