Multiple sequence alignment - TraesCS3A01G495500

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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 TraesCS3A01G495500 chr3A 100.000 6431 0 0 1 6431 721447403 721453833 0.000000e+00 11876.0
1 TraesCS3A01G495500 chr3A 92.818 1824 104 15 1092 2889 721260538 721258716 0.000000e+00 2617.0
2 TraesCS3A01G495500 chr3A 89.667 1742 139 27 4685 6413 721256677 721254964 0.000000e+00 2182.0
3 TraesCS3A01G495500 chr3A 93.486 1090 49 9 3605 4689 721257795 721256723 0.000000e+00 1600.0
4 TraesCS3A01G495500 chr3A 94.100 678 34 4 2945 3619 721258713 721258039 0.000000e+00 1026.0
5 TraesCS3A01G495500 chr3A 80.626 511 62 21 1 486 608829913 608829415 1.700000e-95 361.0
6 TraesCS3A01G495500 chr3A 88.835 206 16 1 3868 4073 484107137 484106939 4.980000e-61 246.0
7 TraesCS3A01G495500 chr3A 81.788 302 35 6 748 1049 721260913 721260632 1.080000e-57 235.0
8 TraesCS3A01G495500 chr3D 96.686 3772 75 13 2660 6413 590757805 590754066 0.000000e+00 6228.0
9 TraesCS3A01G495500 chr3D 94.760 1584 49 14 1092 2664 590764893 590763333 0.000000e+00 2435.0
10 TraesCS3A01G495500 chr3D 84.091 1144 145 24 2437 3558 591039399 591040527 0.000000e+00 1070.0
11 TraesCS3A01G495500 chr3D 88.889 288 25 5 1 285 89631856 89632139 1.330000e-91 348.0
12 TraesCS3A01G495500 chr3D 79.443 467 47 25 5983 6413 591042290 591042743 1.060000e-72 285.0
13 TraesCS3A01G495500 chr3D 81.449 345 30 11 748 1068 590766123 590765789 1.070000e-62 252.0
14 TraesCS3A01G495500 chr3D 90.909 99 9 0 2218 2316 591039050 591039148 4.050000e-27 134.0
15 TraesCS3A01G495500 chr3B 96.389 3240 87 12 1521 4751 790750577 790747359 0.000000e+00 5308.0
16 TraesCS3A01G495500 chr3B 96.468 1557 43 6 4745 6291 790745007 790743453 0.000000e+00 2560.0
17 TraesCS3A01G495500 chr3B 91.402 1826 118 19 1092 2889 791659597 791661411 0.000000e+00 2466.0
18 TraesCS3A01G495500 chr3B 89.265 1742 145 25 4685 6413 791663453 791665165 0.000000e+00 2143.0
19 TraesCS3A01G495500 chr3B 93.468 1087 49 10 3605 4686 791662335 791663404 0.000000e+00 1594.0
20 TraesCS3A01G495500 chr3B 83.403 1434 185 36 2444 3852 791281386 791282791 0.000000e+00 1280.0
21 TraesCS3A01G495500 chr3B 93.833 681 34 5 2945 3619 791661414 791662092 0.000000e+00 1018.0
22 TraesCS3A01G495500 chr3B 82.579 1016 122 21 2863 3864 792070287 792071261 0.000000e+00 845.0
23 TraesCS3A01G495500 chr3B 90.787 597 40 9 944 1529 790751792 790751200 0.000000e+00 784.0
24 TraesCS3A01G495500 chr3B 86.412 471 58 4 3051 3517 792115628 792116096 1.600000e-140 510.0
25 TraesCS3A01G495500 chr3B 86.047 473 58 4 3051 3517 792154976 792155446 9.630000e-138 501.0
26 TraesCS3A01G495500 chr3B 83.554 377 28 18 6086 6431 792142448 792142821 8.040000e-84 322.0
27 TraesCS3A01G495500 chr3B 83.554 377 28 18 6086 6431 792180511 792180884 8.040000e-84 322.0
28 TraesCS3A01G495500 chr3B 95.545 202 4 3 6232 6431 792253948 792254146 1.040000e-82 318.0
29 TraesCS3A01G495500 chr3B 95.050 202 5 3 6232 6431 792105354 792105552 4.840000e-81 313.0
30 TraesCS3A01G495500 chr3B 81.658 398 40 16 660 1057 791659147 791659511 3.770000e-77 300.0
31 TraesCS3A01G495500 chr3B 79.482 463 52 23 5983 6413 791285965 791286416 8.160000e-74 289.0
32 TraesCS3A01G495500 chr3B 83.072 319 47 4 4310 4628 791284289 791284600 3.800000e-72 283.0
33 TraesCS3A01G495500 chr3B 83.721 301 38 8 4330 4628 792243589 792243880 2.280000e-69 274.0
34 TraesCS3A01G495500 chr3B 81.931 321 47 8 4310 4628 792118035 792118346 1.780000e-65 261.0
35 TraesCS3A01G495500 chr3B 81.931 321 47 8 4310 4628 792157387 792157698 1.780000e-65 261.0
36 TraesCS3A01G495500 chr3B 80.534 262 41 7 2058 2316 791280872 791281126 6.580000e-45 193.0
37 TraesCS3A01G495500 chr3B 100.000 33 0 0 1055 1087 791659533 791659565 1.940000e-05 62.1
38 TraesCS3A01G495500 chr4D 82.385 545 56 20 1 512 101675703 101676240 7.650000e-119 438.0
39 TraesCS3A01G495500 chr4D 94.828 58 3 0 1701 1758 476868331 476868388 2.470000e-14 91.6
40 TraesCS3A01G495500 chr2A 81.569 548 57 24 1 512 721070999 721070460 4.640000e-111 412.0
41 TraesCS3A01G495500 chr2A 98.182 55 1 0 1704 1758 727238716 727238770 5.310000e-16 97.1
42 TraesCS3A01G495500 chr2A 92.593 54 4 0 4881 4934 562986624 562986571 1.920000e-10 78.7
43 TraesCS3A01G495500 chr2D 88.814 295 22 9 1 291 247789651 247789938 1.030000e-92 351.0
44 TraesCS3A01G495500 chr2D 89.947 189 16 2 324 511 565132419 565132233 2.320000e-59 241.0
45 TraesCS3A01G495500 chr2D 89.005 191 17 2 324 511 133248507 133248318 3.880000e-57 233.0
46 TraesCS3A01G495500 chr2D 93.548 62 3 1 1704 1765 351973406 351973346 2.470000e-14 91.6
47 TraesCS3A01G495500 chr5D 88.119 303 25 11 1 294 498930275 498929975 3.690000e-92 350.0
48 TraesCS3A01G495500 chr5D 88.980 245 19 3 3867 4109 385114395 385114157 4.880000e-76 296.0
49 TraesCS3A01G495500 chr5D 89.418 189 18 2 322 509 25282383 25282196 3.000000e-58 237.0
50 TraesCS3A01G495500 chr5D 88.601 193 20 2 322 513 101481886 101481695 3.880000e-57 233.0
51 TraesCS3A01G495500 chr5D 89.189 74 4 4 4613 4684 278274993 278275064 8.880000e-14 89.8
52 TraesCS3A01G495500 chr5D 97.297 37 1 0 4871 4907 416626690 416626654 5.380000e-06 63.9
53 TraesCS3A01G495500 chr5B 88.079 302 25 10 1 294 629081274 629080976 1.330000e-91 348.0
54 TraesCS3A01G495500 chr5B 90.688 247 18 3 3867 4109 316714640 316714395 2.240000e-84 324.0
55 TraesCS3A01G495500 chr4A 88.475 295 23 7 1 291 110877783 110878070 4.770000e-91 346.0
56 TraesCS3A01G495500 chr7D 86.322 329 28 12 1 319 637148979 637149300 6.170000e-90 342.0
57 TraesCS3A01G495500 chr7D 89.418 189 18 2 324 511 204444750 204444937 3.000000e-58 237.0
58 TraesCS3A01G495500 chr7D 88.542 192 18 3 324 512 612316533 612316343 5.020000e-56 230.0
59 TraesCS3A01G495500 chr7D 100.000 31 0 0 4879 4909 622102558 622102528 2.500000e-04 58.4
60 TraesCS3A01G495500 chr5A 86.018 329 31 12 1 319 296306501 296306178 7.990000e-89 339.0
61 TraesCS3A01G495500 chr5A 78.736 522 61 27 25 511 322134119 322134625 2.910000e-78 303.0
62 TraesCS3A01G495500 chr6B 91.429 245 13 3 3867 4109 551034130 551033892 4.810000e-86 329.0
63 TraesCS3A01G495500 chr2B 89.912 228 15 5 3867 4092 391143037 391143258 2.930000e-73 287.0
64 TraesCS3A01G495500 chr2B 90.306 196 14 4 322 514 27947870 27947677 1.070000e-62 252.0
65 TraesCS3A01G495500 chr2B 92.857 70 2 2 4042 4109 139349955 139349887 1.480000e-16 99.0
66 TraesCS3A01G495500 chr6D 98.182 55 1 0 1704 1758 391925929 391925983 5.310000e-16 97.1
67 TraesCS3A01G495500 chr6D 93.220 59 4 0 1704 1762 90111206 90111148 3.190000e-13 87.9
68 TraesCS3A01G495500 chr6D 94.545 55 3 0 1704 1758 467788014 467787960 1.150000e-12 86.1
69 TraesCS3A01G495500 chr6D 97.778 45 1 0 1714 1758 90111210 90111254 1.920000e-10 78.7
70 TraesCS3A01G495500 chr6D 97.778 45 1 0 1714 1758 302113704 302113748 1.920000e-10 78.7
71 TraesCS3A01G495500 chr1D 92.424 66 4 1 4869 4934 449466699 449466763 6.870000e-15 93.5
72 TraesCS3A01G495500 chr1D 91.111 45 4 0 1714 1758 383762048 383762004 1.940000e-05 62.1
73 TraesCS3A01G495500 chr1D 90.244 41 4 0 1718 1758 245970065 245970105 3.000000e-03 54.7
74 TraesCS3A01G495500 chr1A 92.424 66 4 1 4869 4934 544599651 544599715 6.870000e-15 93.5
75 TraesCS3A01G495500 chr1A 91.935 62 4 1 4867 4927 517515256 517515195 1.150000e-12 86.1
76 TraesCS3A01G495500 chr7B 94.828 58 3 0 1701 1758 34326123 34326180 2.470000e-14 91.6
77 TraesCS3A01G495500 chr6A 96.364 55 2 0 1704 1758 57731302 57731356 2.470000e-14 91.6
78 TraesCS3A01G495500 chr6A 96.364 55 2 0 1704 1758 454678025 454677971 2.470000e-14 91.6
79 TraesCS3A01G495500 chr4B 93.103 58 4 0 1701 1758 600920016 600920073 1.150000e-12 86.1
80 TraesCS3A01G495500 chrUn 95.556 45 2 0 1714 1758 19227878 19227922 8.940000e-09 73.1
81 TraesCS3A01G495500 chrUn 93.333 45 3 0 1714 1758 321894264 321894220 4.160000e-07 67.6


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 TraesCS3A01G495500 chr3A 721447403 721453833 6430 False 11876.000000 11876 100.000000 1 6431 1 chr3A.!!$F1 6430
1 TraesCS3A01G495500 chr3A 721254964 721260913 5949 True 1532.000000 2617 90.371800 748 6413 5 chr3A.!!$R3 5665
2 TraesCS3A01G495500 chr3D 590754066 590757805 3739 True 6228.000000 6228 96.686000 2660 6413 1 chr3D.!!$R1 3753
3 TraesCS3A01G495500 chr3D 590763333 590766123 2790 True 1343.500000 2435 88.104500 748 2664 2 chr3D.!!$R2 1916
4 TraesCS3A01G495500 chr3D 591039050 591042743 3693 False 496.333333 1070 84.814333 2218 6413 3 chr3D.!!$F2 4195
5 TraesCS3A01G495500 chr3B 790743453 790751792 8339 True 2884.000000 5308 94.548000 944 6291 3 chr3B.!!$R1 5347
6 TraesCS3A01G495500 chr3B 791659147 791665165 6018 False 1263.850000 2466 91.604333 660 6413 6 chr3B.!!$F8 5753
7 TraesCS3A01G495500 chr3B 792070287 792071261 974 False 845.000000 845 82.579000 2863 3864 1 chr3B.!!$F1 1001
8 TraesCS3A01G495500 chr3B 791280872 791286416 5544 False 511.250000 1280 81.622750 2058 6413 4 chr3B.!!$F7 4355
9 TraesCS3A01G495500 chr3B 792115628 792118346 2718 False 385.500000 510 84.171500 3051 4628 2 chr3B.!!$F9 1577
10 TraesCS3A01G495500 chr3B 792154976 792157698 2722 False 381.000000 501 83.989000 3051 4628 2 chr3B.!!$F10 1577
11 TraesCS3A01G495500 chr4D 101675703 101676240 537 False 438.000000 438 82.385000 1 512 1 chr4D.!!$F1 511
12 TraesCS3A01G495500 chr2A 721070460 721070999 539 True 412.000000 412 81.569000 1 512 1 chr2A.!!$R2 511
13 TraesCS3A01G495500 chr5A 322134119 322134625 506 False 303.000000 303 78.736000 25 511 1 chr5A.!!$F1 486

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
546 604 0.036388 GAATGACTCGGGGTTGCTGA 60.036 55.000 0.00 0.00 0.00 4.26 F
1140 2094 0.107361 CCCCCACGGTATCTTGTTCC 60.107 60.000 0.00 0.00 0.00 3.62 F
1426 2390 1.078143 GGGCTCATGGTGGTCTGTC 60.078 63.158 0.00 0.00 0.00 3.51 F
1470 2435 1.251251 GTGGAGATTGCTGCCTGTTT 58.749 50.000 0.00 0.00 0.00 2.83 F
1566 3163 1.750193 ATAAGGGGTCGTGTGCATTG 58.250 50.000 0.00 0.00 0.00 2.82 F
3473 5261 0.251077 AGCAGAAAGGACAAGGCCAG 60.251 55.000 5.01 0.00 0.00 4.85 F
4450 7893 2.905415 TTGGTGCCCAAGATGATCTT 57.095 45.000 0.97 0.97 38.75 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 2356 0.035881 ATGAGCCCTATGACGCCATG 59.964 55.000 0.00 0.0 34.31 3.66 R
2909 4686 2.135139 GCCGCTTTTTCTTTTCCAAGG 58.865 47.619 0.00 0.0 0.00 3.61 R
3323 5111 4.783055 TCTACTCTAGCAAGGAGGTACAG 58.217 47.826 0.00 0.0 35.34 2.74 R
3473 5261 7.377766 TCAATGCATACCTTTCTAGTTCAAC 57.622 36.000 0.00 0.0 0.00 3.18 R
3661 5708 7.923878 GTGGTGAAATTGTTACCAAAACTACAT 59.076 33.333 9.51 0.0 45.30 2.29 R
4909 10762 0.269477 TGGGTAGGGGGCAGCTTATA 59.731 55.000 0.00 0.0 0.00 0.98 R
6384 12426 1.017387 GGCAATACTGGTGCAGCTAC 58.983 55.000 18.08 0.0 44.07 3.58 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
63 64 1.947456 GGAAGCAAAACCGTGACTCTT 59.053 47.619 0.00 0.00 0.00 2.85
71 72 0.600255 ACCGTGACTCTTGCGAAAGG 60.600 55.000 2.54 0.00 0.00 3.11
72 73 0.319555 CCGTGACTCTTGCGAAAGGA 60.320 55.000 2.54 0.00 0.00 3.36
73 74 1.497991 CGTGACTCTTGCGAAAGGAA 58.502 50.000 2.54 0.00 39.89 3.36
74 75 2.069273 CGTGACTCTTGCGAAAGGAAT 58.931 47.619 2.54 0.00 41.82 3.01
120 127 1.039068 TCGTTTCCGAGGTACAACCA 58.961 50.000 0.00 0.00 41.95 3.67
176 183 0.104304 AGCAAAACCGTGACTCTCGT 59.896 50.000 0.24 0.00 0.00 4.18
245 253 1.372997 GGCTGTGACTCTCGCGAAA 60.373 57.895 11.33 0.00 0.00 3.46
248 256 1.487482 CTGTGACTCTCGCGAAACAA 58.513 50.000 11.33 0.00 0.00 2.83
257 265 1.298041 CGCGAAACAAAACCGTGCT 60.298 52.632 0.00 0.00 0.00 4.40
264 272 0.814010 ACAAAACCGTGCTTCTCGCT 60.814 50.000 0.00 0.00 40.11 4.93
285 293 2.210116 GAAGCAAAACCGTGACTCTCA 58.790 47.619 0.00 0.00 0.00 3.27
430 488 2.279851 CGCCCAGAACACGACACA 60.280 61.111 0.00 0.00 0.00 3.72
446 504 1.002430 ACACATGACGAATGGCTGAGT 59.998 47.619 0.00 0.00 40.94 3.41
512 570 3.309954 GCTCGTTAATTAGTTGCTCCCTG 59.690 47.826 0.00 0.00 0.00 4.45
513 571 4.755411 CTCGTTAATTAGTTGCTCCCTGA 58.245 43.478 0.00 0.00 0.00 3.86
514 572 5.155278 TCGTTAATTAGTTGCTCCCTGAA 57.845 39.130 0.00 0.00 0.00 3.02
515 573 5.741011 TCGTTAATTAGTTGCTCCCTGAAT 58.259 37.500 0.00 0.00 0.00 2.57
516 574 6.177610 TCGTTAATTAGTTGCTCCCTGAATT 58.822 36.000 0.00 0.00 0.00 2.17
517 575 6.657541 TCGTTAATTAGTTGCTCCCTGAATTT 59.342 34.615 0.00 0.00 0.00 1.82
518 576 6.967199 CGTTAATTAGTTGCTCCCTGAATTTC 59.033 38.462 0.00 0.00 0.00 2.17
519 577 7.361713 CGTTAATTAGTTGCTCCCTGAATTTCA 60.362 37.037 0.00 0.00 0.00 2.69
520 578 8.470002 GTTAATTAGTTGCTCCCTGAATTTCAT 58.530 33.333 0.00 0.00 0.00 2.57
521 579 6.705863 ATTAGTTGCTCCCTGAATTTCATC 57.294 37.500 0.00 0.00 0.00 2.92
522 580 4.313020 AGTTGCTCCCTGAATTTCATCT 57.687 40.909 0.00 0.00 0.00 2.90
523 581 4.670765 AGTTGCTCCCTGAATTTCATCTT 58.329 39.130 0.00 0.00 0.00 2.40
524 582 5.819991 AGTTGCTCCCTGAATTTCATCTTA 58.180 37.500 0.00 0.00 0.00 2.10
525 583 5.649831 AGTTGCTCCCTGAATTTCATCTTAC 59.350 40.000 0.00 0.00 0.00 2.34
526 584 4.526970 TGCTCCCTGAATTTCATCTTACC 58.473 43.478 0.00 0.00 0.00 2.85
527 585 3.561725 GCTCCCTGAATTTCATCTTACCG 59.438 47.826 0.00 0.00 0.00 4.02
528 586 4.683400 GCTCCCTGAATTTCATCTTACCGA 60.683 45.833 0.00 0.00 0.00 4.69
529 587 5.428253 CTCCCTGAATTTCATCTTACCGAA 58.572 41.667 0.00 0.00 0.00 4.30
530 588 6.001449 TCCCTGAATTTCATCTTACCGAAT 57.999 37.500 0.00 0.00 0.00 3.34
531 589 5.822519 TCCCTGAATTTCATCTTACCGAATG 59.177 40.000 0.00 0.00 0.00 2.67
532 590 5.822519 CCCTGAATTTCATCTTACCGAATGA 59.177 40.000 0.00 0.00 0.00 2.57
533 591 6.238484 CCCTGAATTTCATCTTACCGAATGAC 60.238 42.308 0.00 0.00 0.00 3.06
534 592 6.540189 CCTGAATTTCATCTTACCGAATGACT 59.460 38.462 0.00 0.00 0.00 3.41
535 593 7.254590 CCTGAATTTCATCTTACCGAATGACTC 60.255 40.741 0.00 0.00 0.00 3.36
543 601 3.486263 CGAATGACTCGGGGTTGC 58.514 61.111 0.00 0.00 44.20 4.17
544 602 1.079127 CGAATGACTCGGGGTTGCT 60.079 57.895 0.00 0.00 44.20 3.91
545 603 1.361668 CGAATGACTCGGGGTTGCTG 61.362 60.000 0.00 0.00 44.20 4.41
546 604 0.036388 GAATGACTCGGGGTTGCTGA 60.036 55.000 0.00 0.00 0.00 4.26
547 605 0.620556 AATGACTCGGGGTTGCTGAT 59.379 50.000 0.00 0.00 0.00 2.90
548 606 0.107508 ATGACTCGGGGTTGCTGATG 60.108 55.000 0.00 0.00 0.00 3.07
549 607 1.296715 GACTCGGGGTTGCTGATGT 59.703 57.895 0.00 0.00 0.00 3.06
550 608 1.003355 ACTCGGGGTTGCTGATGTG 60.003 57.895 0.00 0.00 0.00 3.21
551 609 1.003355 CTCGGGGTTGCTGATGTGT 60.003 57.895 0.00 0.00 0.00 3.72
552 610 1.003839 TCGGGGTTGCTGATGTGTC 60.004 57.895 0.00 0.00 0.00 3.67
553 611 1.003355 CGGGGTTGCTGATGTGTCT 60.003 57.895 0.00 0.00 0.00 3.41
554 612 1.021390 CGGGGTTGCTGATGTGTCTC 61.021 60.000 0.00 0.00 0.00 3.36
555 613 0.326264 GGGGTTGCTGATGTGTCTCT 59.674 55.000 0.00 0.00 0.00 3.10
556 614 1.677217 GGGGTTGCTGATGTGTCTCTC 60.677 57.143 0.00 0.00 0.00 3.20
557 615 1.002430 GGGTTGCTGATGTGTCTCTCA 59.998 52.381 0.00 0.00 0.00 3.27
558 616 2.355513 GGGTTGCTGATGTGTCTCTCAT 60.356 50.000 0.00 0.00 0.00 2.90
559 617 2.676839 GGTTGCTGATGTGTCTCTCATG 59.323 50.000 0.00 0.00 0.00 3.07
560 618 3.593096 GTTGCTGATGTGTCTCTCATGA 58.407 45.455 0.00 0.00 0.00 3.07
561 619 3.521947 TGCTGATGTGTCTCTCATGAG 57.478 47.619 17.07 17.07 41.51 2.90
562 620 2.830321 TGCTGATGTGTCTCTCATGAGT 59.170 45.455 21.92 0.71 40.98 3.41
563 621 3.188492 GCTGATGTGTCTCTCATGAGTG 58.812 50.000 21.92 19.32 40.98 3.51
564 622 3.188492 CTGATGTGTCTCTCATGAGTGC 58.812 50.000 21.92 15.15 40.98 4.40
565 623 2.830321 TGATGTGTCTCTCATGAGTGCT 59.170 45.455 21.92 3.56 40.98 4.40
566 624 3.260128 TGATGTGTCTCTCATGAGTGCTT 59.740 43.478 21.92 5.93 40.98 3.91
567 625 3.758755 TGTGTCTCTCATGAGTGCTTT 57.241 42.857 21.92 0.00 40.98 3.51
568 626 4.871933 TGTGTCTCTCATGAGTGCTTTA 57.128 40.909 21.92 0.94 40.98 1.85
569 627 5.213891 TGTGTCTCTCATGAGTGCTTTAA 57.786 39.130 21.92 1.03 40.98 1.52
570 628 5.233225 TGTGTCTCTCATGAGTGCTTTAAG 58.767 41.667 21.92 10.40 40.98 1.85
571 629 5.011023 TGTGTCTCTCATGAGTGCTTTAAGA 59.989 40.000 21.92 12.52 40.98 2.10
572 630 6.105333 GTGTCTCTCATGAGTGCTTTAAGAT 58.895 40.000 21.92 0.00 40.98 2.40
573 631 6.593382 GTGTCTCTCATGAGTGCTTTAAGATT 59.407 38.462 21.92 0.00 40.98 2.40
574 632 7.761704 GTGTCTCTCATGAGTGCTTTAAGATTA 59.238 37.037 21.92 6.83 40.98 1.75
575 633 7.978414 TGTCTCTCATGAGTGCTTTAAGATTAG 59.022 37.037 21.92 7.63 40.98 1.73
576 634 7.978975 GTCTCTCATGAGTGCTTTAAGATTAGT 59.021 37.037 21.92 0.00 40.98 2.24
577 635 7.978414 TCTCTCATGAGTGCTTTAAGATTAGTG 59.022 37.037 21.92 0.00 40.98 2.74
578 636 6.536582 TCTCATGAGTGCTTTAAGATTAGTGC 59.463 38.462 21.92 0.00 0.00 4.40
579 637 6.172630 TCATGAGTGCTTTAAGATTAGTGCA 58.827 36.000 0.00 0.00 0.00 4.57
580 638 6.314648 TCATGAGTGCTTTAAGATTAGTGCAG 59.685 38.462 0.00 0.00 0.00 4.41
581 639 4.393062 TGAGTGCTTTAAGATTAGTGCAGC 59.607 41.667 0.00 0.00 0.00 5.25
582 640 4.583871 AGTGCTTTAAGATTAGTGCAGCT 58.416 39.130 0.00 0.00 0.00 4.24
583 641 5.734720 AGTGCTTTAAGATTAGTGCAGCTA 58.265 37.500 0.00 0.00 0.00 3.32
584 642 6.173339 AGTGCTTTAAGATTAGTGCAGCTAA 58.827 36.000 10.01 10.01 43.13 3.09
592 650 2.309528 TAGTGCAGCTAATCCAACGG 57.690 50.000 0.00 0.00 0.00 4.44
593 651 1.026718 AGTGCAGCTAATCCAACGGC 61.027 55.000 0.00 0.00 0.00 5.68
594 652 1.748879 TGCAGCTAATCCAACGGCC 60.749 57.895 0.00 0.00 0.00 6.13
595 653 1.748879 GCAGCTAATCCAACGGCCA 60.749 57.895 2.24 0.00 0.00 5.36
596 654 1.718757 GCAGCTAATCCAACGGCCAG 61.719 60.000 2.24 0.00 0.00 4.85
597 655 0.107703 CAGCTAATCCAACGGCCAGA 60.108 55.000 2.24 0.00 0.00 3.86
598 656 0.618458 AGCTAATCCAACGGCCAGAA 59.382 50.000 2.24 0.00 0.00 3.02
599 657 1.017387 GCTAATCCAACGGCCAGAAG 58.983 55.000 2.24 0.00 0.00 2.85
600 658 1.668419 CTAATCCAACGGCCAGAAGG 58.332 55.000 2.24 0.00 38.23 3.46
601 659 1.209504 CTAATCCAACGGCCAGAAGGA 59.790 52.381 2.24 4.40 36.89 3.36
602 660 0.322546 AATCCAACGGCCAGAAGGAC 60.323 55.000 2.24 0.00 40.75 3.85
608 666 2.654877 GGCCAGAAGGACGTTCGA 59.345 61.111 0.00 0.00 40.49 3.71
609 667 1.218316 GGCCAGAAGGACGTTCGAT 59.782 57.895 0.00 0.00 40.49 3.59
610 668 1.084370 GGCCAGAAGGACGTTCGATG 61.084 60.000 0.00 0.00 40.49 3.84
611 669 1.084370 GCCAGAAGGACGTTCGATGG 61.084 60.000 9.85 9.85 40.49 3.51
612 670 0.460284 CCAGAAGGACGTTCGATGGG 60.460 60.000 7.03 3.56 40.49 4.00
613 671 0.530744 CAGAAGGACGTTCGATGGGA 59.469 55.000 0.00 0.00 40.49 4.37
614 672 1.067142 CAGAAGGACGTTCGATGGGAA 60.067 52.381 0.00 0.00 40.49 3.97
615 673 1.621814 AGAAGGACGTTCGATGGGAAA 59.378 47.619 0.00 0.00 40.49 3.13
616 674 2.038033 AGAAGGACGTTCGATGGGAAAA 59.962 45.455 0.00 0.00 40.49 2.29
617 675 2.094762 AGGACGTTCGATGGGAAAAG 57.905 50.000 0.00 0.00 36.14 2.27
618 676 1.346722 AGGACGTTCGATGGGAAAAGT 59.653 47.619 0.00 0.00 36.14 2.66
619 677 1.730612 GGACGTTCGATGGGAAAAGTC 59.269 52.381 0.00 0.00 40.73 3.01
620 678 2.612221 GGACGTTCGATGGGAAAAGTCT 60.612 50.000 0.00 0.00 40.99 3.24
621 679 2.666994 GACGTTCGATGGGAAAAGTCTC 59.333 50.000 0.00 0.00 39.50 3.36
622 680 2.299297 ACGTTCGATGGGAAAAGTCTCT 59.701 45.455 0.00 0.00 36.14 3.10
623 681 2.668457 CGTTCGATGGGAAAAGTCTCTG 59.332 50.000 0.00 0.00 36.14 3.35
624 682 3.003480 GTTCGATGGGAAAAGTCTCTGG 58.997 50.000 0.00 0.00 36.14 3.86
625 683 2.536066 TCGATGGGAAAAGTCTCTGGA 58.464 47.619 0.00 0.00 0.00 3.86
626 684 2.497675 TCGATGGGAAAAGTCTCTGGAG 59.502 50.000 0.00 0.00 0.00 3.86
627 685 2.419297 CGATGGGAAAAGTCTCTGGAGG 60.419 54.545 0.00 0.00 0.00 4.30
628 686 2.415983 TGGGAAAAGTCTCTGGAGGA 57.584 50.000 0.00 0.00 0.00 3.71
629 687 1.978580 TGGGAAAAGTCTCTGGAGGAC 59.021 52.381 0.00 0.00 0.00 3.85
630 688 1.279558 GGGAAAAGTCTCTGGAGGACC 59.720 57.143 0.00 0.00 34.56 4.46
631 689 1.279558 GGAAAAGTCTCTGGAGGACCC 59.720 57.143 0.00 0.00 34.56 4.46
632 690 1.279558 GAAAAGTCTCTGGAGGACCCC 59.720 57.143 0.00 0.00 34.56 4.95
633 691 0.193574 AAAGTCTCTGGAGGACCCCA 59.806 55.000 2.17 2.17 34.56 4.96
634 692 0.193574 AAGTCTCTGGAGGACCCCAA 59.806 55.000 3.62 0.00 35.47 4.12
635 693 0.193574 AGTCTCTGGAGGACCCCAAA 59.806 55.000 3.62 0.00 35.47 3.28
636 694 1.203492 AGTCTCTGGAGGACCCCAAAT 60.203 52.381 3.62 0.00 35.47 2.32
637 695 2.045885 AGTCTCTGGAGGACCCCAAATA 59.954 50.000 3.62 0.00 35.47 1.40
638 696 2.844348 GTCTCTGGAGGACCCCAAATAA 59.156 50.000 3.62 0.00 35.47 1.40
639 697 3.265995 GTCTCTGGAGGACCCCAAATAAA 59.734 47.826 3.62 0.00 35.47 1.40
640 698 3.920197 TCTCTGGAGGACCCCAAATAAAA 59.080 43.478 3.62 0.00 35.47 1.52
641 699 4.544152 TCTCTGGAGGACCCCAAATAAAAT 59.456 41.667 3.62 0.00 35.47 1.82
642 700 4.867086 TCTGGAGGACCCCAAATAAAATC 58.133 43.478 3.62 0.00 35.47 2.17
643 701 4.293634 TCTGGAGGACCCCAAATAAAATCA 59.706 41.667 3.62 0.00 35.47 2.57
644 702 5.017093 TGGAGGACCCCAAATAAAATCAA 57.983 39.130 0.00 0.00 32.31 2.57
645 703 5.407049 TGGAGGACCCCAAATAAAATCAAA 58.593 37.500 0.00 0.00 32.31 2.69
646 704 5.846714 TGGAGGACCCCAAATAAAATCAAAA 59.153 36.000 0.00 0.00 32.31 2.44
647 705 6.503570 TGGAGGACCCCAAATAAAATCAAAAT 59.496 34.615 0.00 0.00 32.31 1.82
648 706 7.047891 GGAGGACCCCAAATAAAATCAAAATC 58.952 38.462 0.00 0.00 0.00 2.17
649 707 6.957631 AGGACCCCAAATAAAATCAAAATCC 58.042 36.000 0.00 0.00 0.00 3.01
650 708 6.069673 AGGACCCCAAATAAAATCAAAATCCC 60.070 38.462 0.00 0.00 0.00 3.85
651 709 6.069673 GGACCCCAAATAAAATCAAAATCCCT 60.070 38.462 0.00 0.00 0.00 4.20
652 710 7.341885 ACCCCAAATAAAATCAAAATCCCTT 57.658 32.000 0.00 0.00 0.00 3.95
653 711 7.764617 ACCCCAAATAAAATCAAAATCCCTTT 58.235 30.769 0.00 0.00 0.00 3.11
654 712 8.231007 ACCCCAAATAAAATCAAAATCCCTTTT 58.769 29.630 0.00 0.00 34.90 2.27
655 713 8.739039 CCCCAAATAAAATCAAAATCCCTTTTC 58.261 33.333 0.00 0.00 32.21 2.29
656 714 8.450180 CCCAAATAAAATCAAAATCCCTTTTCG 58.550 33.333 0.00 0.00 32.21 3.46
657 715 9.213799 CCAAATAAAATCAAAATCCCTTTTCGA 57.786 29.630 0.00 0.00 32.21 3.71
675 733 4.452733 CTTCGACCTGGGACGGCC 62.453 72.222 0.00 0.00 34.42 6.13
710 768 2.181021 GGCACCTACCAGACGACG 59.819 66.667 0.00 0.00 0.00 5.12
740 798 1.112113 CTCGCTCCTAGGGTTAGCAA 58.888 55.000 18.29 2.06 35.98 3.91
817 875 1.064611 CCTCTCTTCCCTACTCGACCA 60.065 57.143 0.00 0.00 0.00 4.02
820 878 2.025226 TCTCTTCCCTACTCGACCACAT 60.025 50.000 0.00 0.00 0.00 3.21
824 882 1.063190 TCCCTACTCGACCACATCCAT 60.063 52.381 0.00 0.00 0.00 3.41
825 883 1.762957 CCCTACTCGACCACATCCATT 59.237 52.381 0.00 0.00 0.00 3.16
921 979 2.443016 CCCGACTCCCTCCTCTGG 60.443 72.222 0.00 0.00 0.00 3.86
1115 2069 3.637273 AGGGCCCACTGGACGTTC 61.637 66.667 27.56 0.00 42.67 3.95
1140 2094 0.107361 CCCCCACGGTATCTTGTTCC 60.107 60.000 0.00 0.00 0.00 3.62
1201 2155 3.606687 GCTCCTTTAGATTGGACGGAAA 58.393 45.455 0.00 0.00 0.00 3.13
1246 2200 3.802685 GGCGTATCACTGTTAATCCTGTC 59.197 47.826 0.00 0.00 0.00 3.51
1381 2340 5.468746 GGCAGTACATTTGTCTTGAGTGTTA 59.531 40.000 0.00 0.00 0.00 2.41
1396 2356 7.761704 TCTTGAGTGTTAGAGAATGCATAAGTC 59.238 37.037 0.00 0.00 0.00 3.01
1403 2367 2.874701 GAGAATGCATAAGTCATGGCGT 59.125 45.455 0.00 0.00 34.97 5.68
1426 2390 1.078143 GGGCTCATGGTGGTCTGTC 60.078 63.158 0.00 0.00 0.00 3.51
1470 2435 1.251251 GTGGAGATTGCTGCCTGTTT 58.749 50.000 0.00 0.00 0.00 2.83
1566 3163 1.750193 ATAAGGGGTCGTGTGCATTG 58.250 50.000 0.00 0.00 0.00 2.82
1935 3540 6.810911 ACTAACTTGCAGAGTAGTATCATGG 58.189 40.000 0.00 0.00 37.72 3.66
1968 3574 8.728337 TGAAATTCATATTCTCTTCAGGTGAG 57.272 34.615 0.00 0.00 0.00 3.51
2196 3817 3.724478 TGGATGTGGTGAGTAGGAAGAT 58.276 45.455 0.00 0.00 0.00 2.40
2200 3821 3.239449 TGTGGTGAGTAGGAAGATGTGT 58.761 45.455 0.00 0.00 0.00 3.72
2889 4666 5.793817 TGCGGTAGATATAACATTCAGCAT 58.206 37.500 0.00 0.00 0.00 3.79
2909 4686 9.571810 TCAGCATCATGTTTGTACATAAAATTC 57.428 29.630 0.00 0.00 43.07 2.17
3038 4816 2.034558 ACTTTCACATGTTTTGAGGCCG 59.965 45.455 0.00 0.00 0.00 6.13
3203 4984 5.123979 GTGATTCACCTCAATTTACTGGGTC 59.876 44.000 5.44 0.00 0.00 4.46
3252 5033 8.256356 AGACATGAACTTATGGTAGCTCTTAT 57.744 34.615 0.00 0.00 32.32 1.73
3473 5261 0.251077 AGCAGAAAGGACAAGGCCAG 60.251 55.000 5.01 0.00 0.00 4.85
3661 5708 7.231115 TCTGAATCTTTGTGGTTCATCATTCAA 59.769 33.333 0.00 0.00 31.48 2.69
4313 7756 7.013274 ACCATATGCAGTACATGTTTTATGTCC 59.987 37.037 2.30 0.00 40.06 4.02
4315 7758 8.623903 CATATGCAGTACATGTTTTATGTCCTT 58.376 33.333 2.30 0.00 40.06 3.36
4450 7893 2.905415 TTGGTGCCCAAGATGATCTT 57.095 45.000 0.97 0.97 38.75 2.40
4653 8096 4.895889 CCCTCTGATCCATAGTAAGTGTCA 59.104 45.833 0.00 0.00 0.00 3.58
4909 10762 1.044790 GCTTATGGGTGGCTGCCAAT 61.045 55.000 25.23 16.08 34.18 3.16
4996 10849 1.599071 GCGAAATCGGCATTCTGATGA 59.401 47.619 4.84 0.00 38.30 2.92
4997 10850 2.225019 GCGAAATCGGCATTCTGATGAT 59.775 45.455 4.84 0.00 38.30 2.45
5051 10907 3.779759 AGATCTCTGACGATCAAGCAAC 58.220 45.455 14.95 0.00 41.74 4.17
5052 10908 3.194329 AGATCTCTGACGATCAAGCAACA 59.806 43.478 14.95 0.00 41.74 3.33
5388 11247 6.887013 AGCTAAGATCATCACTGACATTCTT 58.113 36.000 0.00 0.00 34.33 2.52
5397 11256 4.392047 TCACTGACATTCTTGTGCAAGAT 58.608 39.130 14.43 1.36 45.78 2.40
5495 11354 3.888930 TCTTGGGTGTCATCAAAAGGTTC 59.111 43.478 0.00 0.00 0.00 3.62
5741 11623 8.059798 TGTAACTTACTTGGTACTAGATGGTC 57.940 38.462 0.00 0.00 0.00 4.02
5847 11729 4.129737 GGCAGCTCGCGTACAGGA 62.130 66.667 5.77 0.00 43.84 3.86
5971 11871 2.436109 GCTCAAGAACCCCTGGCA 59.564 61.111 0.00 0.00 0.00 4.92
6091 12097 7.928873 AGTAATCTTCCCTTCCTGTAAATCAA 58.071 34.615 0.00 0.00 0.00 2.57
6332 12372 5.359009 AGGACAATTCAAGCCATTAGATGTG 59.641 40.000 0.00 0.00 0.00 3.21
6413 12455 4.067896 CACCAGTATTGCCAGGATATGAC 58.932 47.826 0.00 0.00 0.00 3.06
6414 12456 3.976654 ACCAGTATTGCCAGGATATGACT 59.023 43.478 0.00 0.00 0.00 3.41
6415 12457 4.040952 ACCAGTATTGCCAGGATATGACTC 59.959 45.833 0.00 0.00 0.00 3.36
6416 12458 4.285517 CCAGTATTGCCAGGATATGACTCT 59.714 45.833 0.00 0.00 0.00 3.24
6417 12459 5.477510 CAGTATTGCCAGGATATGACTCTC 58.522 45.833 0.00 0.00 0.00 3.20
6418 12460 5.245751 CAGTATTGCCAGGATATGACTCTCT 59.754 44.000 0.00 0.00 0.00 3.10
6419 12461 6.435591 CAGTATTGCCAGGATATGACTCTCTA 59.564 42.308 0.00 0.00 0.00 2.43
6420 12462 7.013220 AGTATTGCCAGGATATGACTCTCTAA 58.987 38.462 0.00 0.00 0.00 2.10
6421 12463 5.798125 TTGCCAGGATATGACTCTCTAAG 57.202 43.478 0.00 0.00 0.00 2.18
6422 12464 4.809193 TGCCAGGATATGACTCTCTAAGT 58.191 43.478 0.00 0.00 42.42 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 1.730064 CATGGTTGTACCTCGGAAACG 59.270 52.381 0.00 0.00 46.51 3.60
103 105 2.740447 GTCATGGTTGTACCTCGGAAAC 59.260 50.000 0.00 0.00 39.58 2.78
104 106 2.635915 AGTCATGGTTGTACCTCGGAAA 59.364 45.455 0.00 0.00 39.58 3.13
105 107 2.232941 GAGTCATGGTTGTACCTCGGAA 59.767 50.000 0.00 0.00 39.58 4.30
107 109 1.825474 AGAGTCATGGTTGTACCTCGG 59.175 52.381 0.00 0.00 39.58 4.63
108 110 2.478031 CGAGAGTCATGGTTGTACCTCG 60.478 54.545 0.00 0.00 39.58 4.63
113 120 1.170442 TCGCGAGAGTCATGGTTGTA 58.830 50.000 3.71 0.00 34.84 2.41
116 123 1.714794 CTTTCGCGAGAGTCATGGTT 58.285 50.000 17.92 0.00 43.69 3.67
117 124 0.737715 GCTTTCGCGAGAGTCATGGT 60.738 55.000 25.34 0.00 43.69 3.55
120 127 2.743195 GTGCTTTCGCGAGAGTCAT 58.257 52.632 25.34 0.00 43.69 3.06
147 154 1.837538 CGGTTTTGCTTCCGCGAGAA 61.838 55.000 8.23 8.88 40.28 2.87
230 237 1.929230 TTTGTTTCGCGAGAGTCACA 58.071 45.000 9.59 6.00 43.69 3.58
257 265 0.586319 CGGTTTTGCTTCAGCGAGAA 59.414 50.000 0.00 0.00 45.83 2.87
264 272 2.210116 GAGAGTCACGGTTTTGCTTCA 58.790 47.619 0.00 0.00 0.00 3.02
369 420 2.150424 CACGCGTTTTCGGCTTTTTAAG 59.850 45.455 10.22 0.00 44.29 1.85
430 488 1.086067 CGCACTCAGCCATTCGTCAT 61.086 55.000 0.00 0.00 41.38 3.06
451 509 3.197790 CGATCAGCGCCACTTGGG 61.198 66.667 2.29 0.00 40.85 4.12
512 570 6.641062 CGAGTCATTCGGTAAGATGAAATTC 58.359 40.000 0.00 0.00 45.54 2.17
513 571 6.589830 CGAGTCATTCGGTAAGATGAAATT 57.410 37.500 0.00 0.00 45.54 1.82
527 585 0.036388 TCAGCAACCCCGAGTCATTC 60.036 55.000 0.00 0.00 0.00 2.67
528 586 0.620556 ATCAGCAACCCCGAGTCATT 59.379 50.000 0.00 0.00 0.00 2.57
529 587 0.107508 CATCAGCAACCCCGAGTCAT 60.108 55.000 0.00 0.00 0.00 3.06
530 588 1.296392 CATCAGCAACCCCGAGTCA 59.704 57.895 0.00 0.00 0.00 3.41
531 589 1.021390 CACATCAGCAACCCCGAGTC 61.021 60.000 0.00 0.00 0.00 3.36
532 590 1.003355 CACATCAGCAACCCCGAGT 60.003 57.895 0.00 0.00 0.00 4.18
533 591 1.003355 ACACATCAGCAACCCCGAG 60.003 57.895 0.00 0.00 0.00 4.63
534 592 1.003839 GACACATCAGCAACCCCGA 60.004 57.895 0.00 0.00 0.00 5.14
535 593 1.003355 AGACACATCAGCAACCCCG 60.003 57.895 0.00 0.00 0.00 5.73
536 594 0.326264 AGAGACACATCAGCAACCCC 59.674 55.000 0.00 0.00 0.00 4.95
537 595 1.002430 TGAGAGACACATCAGCAACCC 59.998 52.381 0.00 0.00 0.00 4.11
538 596 2.462456 TGAGAGACACATCAGCAACC 57.538 50.000 0.00 0.00 0.00 3.77
539 597 3.593096 TCATGAGAGACACATCAGCAAC 58.407 45.455 0.00 0.00 0.00 4.17
540 598 3.260128 ACTCATGAGAGACACATCAGCAA 59.740 43.478 29.27 0.00 44.98 3.91
541 599 2.830321 ACTCATGAGAGACACATCAGCA 59.170 45.455 29.27 0.00 44.98 4.41
542 600 3.188492 CACTCATGAGAGACACATCAGC 58.812 50.000 29.27 0.00 44.98 4.26
543 601 3.119065 AGCACTCATGAGAGACACATCAG 60.119 47.826 29.27 0.00 44.98 2.90
544 602 2.830321 AGCACTCATGAGAGACACATCA 59.170 45.455 29.27 0.00 44.98 3.07
545 603 3.523606 AGCACTCATGAGAGACACATC 57.476 47.619 29.27 7.34 44.98 3.06
546 604 3.977134 AAGCACTCATGAGAGACACAT 57.023 42.857 29.27 1.44 44.98 3.21
547 605 3.758755 AAAGCACTCATGAGAGACACA 57.241 42.857 29.27 0.00 44.98 3.72
548 606 5.473931 TCTTAAAGCACTCATGAGAGACAC 58.526 41.667 29.27 12.39 44.98 3.67
549 607 5.728637 TCTTAAAGCACTCATGAGAGACA 57.271 39.130 29.27 6.11 44.98 3.41
550 608 7.978975 ACTAATCTTAAAGCACTCATGAGAGAC 59.021 37.037 29.27 16.43 44.98 3.36
551 609 7.978414 CACTAATCTTAAAGCACTCATGAGAGA 59.022 37.037 29.27 18.38 44.98 3.10
553 611 6.536582 GCACTAATCTTAAAGCACTCATGAGA 59.463 38.462 29.27 2.25 0.00 3.27
554 612 6.314648 TGCACTAATCTTAAAGCACTCATGAG 59.685 38.462 21.37 21.37 0.00 2.90
555 613 6.172630 TGCACTAATCTTAAAGCACTCATGA 58.827 36.000 0.00 0.00 0.00 3.07
556 614 6.426980 TGCACTAATCTTAAAGCACTCATG 57.573 37.500 0.00 0.00 0.00 3.07
557 615 5.065731 GCTGCACTAATCTTAAAGCACTCAT 59.934 40.000 0.00 0.00 0.00 2.90
558 616 4.393062 GCTGCACTAATCTTAAAGCACTCA 59.607 41.667 0.00 0.00 0.00 3.41
559 617 4.633565 AGCTGCACTAATCTTAAAGCACTC 59.366 41.667 1.02 0.00 0.00 3.51
560 618 4.583871 AGCTGCACTAATCTTAAAGCACT 58.416 39.130 1.02 0.00 0.00 4.40
561 619 4.954092 AGCTGCACTAATCTTAAAGCAC 57.046 40.909 1.02 0.00 0.00 4.40
572 630 2.627945 CCGTTGGATTAGCTGCACTAA 58.372 47.619 1.02 10.01 44.87 2.24
573 631 1.742411 GCCGTTGGATTAGCTGCACTA 60.742 52.381 1.02 0.00 0.00 2.74
574 632 1.026718 GCCGTTGGATTAGCTGCACT 61.027 55.000 1.02 0.00 0.00 4.40
575 633 1.429423 GCCGTTGGATTAGCTGCAC 59.571 57.895 1.02 0.00 0.00 4.57
576 634 1.748879 GGCCGTTGGATTAGCTGCA 60.749 57.895 1.02 0.00 0.00 4.41
577 635 1.718757 CTGGCCGTTGGATTAGCTGC 61.719 60.000 0.00 0.00 0.00 5.25
578 636 0.107703 TCTGGCCGTTGGATTAGCTG 60.108 55.000 0.00 0.00 0.00 4.24
579 637 0.618458 TTCTGGCCGTTGGATTAGCT 59.382 50.000 0.00 0.00 0.00 3.32
580 638 1.017387 CTTCTGGCCGTTGGATTAGC 58.983 55.000 0.00 0.00 0.00 3.09
581 639 1.209504 TCCTTCTGGCCGTTGGATTAG 59.790 52.381 0.00 0.00 0.00 1.73
582 640 1.065709 GTCCTTCTGGCCGTTGGATTA 60.066 52.381 9.30 0.00 0.00 1.75
583 641 0.322546 GTCCTTCTGGCCGTTGGATT 60.323 55.000 9.30 0.00 0.00 3.01
584 642 1.299976 GTCCTTCTGGCCGTTGGAT 59.700 57.895 9.30 0.00 0.00 3.41
585 643 2.747686 GTCCTTCTGGCCGTTGGA 59.252 61.111 0.00 0.00 0.00 3.53
586 644 2.742372 CGTCCTTCTGGCCGTTGG 60.742 66.667 0.00 0.00 0.00 3.77
587 645 1.566018 GAACGTCCTTCTGGCCGTTG 61.566 60.000 8.58 0.00 0.00 4.10
588 646 1.301479 GAACGTCCTTCTGGCCGTT 60.301 57.895 3.56 3.56 0.00 4.44
589 647 2.342648 GAACGTCCTTCTGGCCGT 59.657 61.111 0.00 0.00 0.00 5.68
590 648 2.558554 ATCGAACGTCCTTCTGGCCG 62.559 60.000 0.00 0.00 0.00 6.13
591 649 1.084370 CATCGAACGTCCTTCTGGCC 61.084 60.000 0.00 0.00 0.00 5.36
592 650 1.084370 CCATCGAACGTCCTTCTGGC 61.084 60.000 0.00 0.00 0.00 4.85
593 651 0.460284 CCCATCGAACGTCCTTCTGG 60.460 60.000 0.00 0.00 0.00 3.86
594 652 0.530744 TCCCATCGAACGTCCTTCTG 59.469 55.000 0.00 0.00 0.00 3.02
595 653 1.263356 TTCCCATCGAACGTCCTTCT 58.737 50.000 0.00 0.00 0.00 2.85
596 654 2.088950 TTTCCCATCGAACGTCCTTC 57.911 50.000 0.00 0.00 0.00 3.46
597 655 2.224450 ACTTTTCCCATCGAACGTCCTT 60.224 45.455 0.00 0.00 0.00 3.36
598 656 1.346722 ACTTTTCCCATCGAACGTCCT 59.653 47.619 0.00 0.00 0.00 3.85
599 657 1.730612 GACTTTTCCCATCGAACGTCC 59.269 52.381 0.00 0.00 30.35 4.79
600 658 2.666994 GAGACTTTTCCCATCGAACGTC 59.333 50.000 0.00 0.00 33.99 4.34
601 659 2.299297 AGAGACTTTTCCCATCGAACGT 59.701 45.455 0.00 0.00 0.00 3.99
602 660 2.668457 CAGAGACTTTTCCCATCGAACG 59.332 50.000 0.00 0.00 0.00 3.95
603 661 3.003480 CCAGAGACTTTTCCCATCGAAC 58.997 50.000 0.00 0.00 0.00 3.95
604 662 2.903784 TCCAGAGACTTTTCCCATCGAA 59.096 45.455 0.00 0.00 0.00 3.71
605 663 2.497675 CTCCAGAGACTTTTCCCATCGA 59.502 50.000 0.00 0.00 0.00 3.59
606 664 2.419297 CCTCCAGAGACTTTTCCCATCG 60.419 54.545 0.00 0.00 0.00 3.84
607 665 2.840651 TCCTCCAGAGACTTTTCCCATC 59.159 50.000 0.00 0.00 0.00 3.51
608 666 2.573915 GTCCTCCAGAGACTTTTCCCAT 59.426 50.000 0.00 0.00 0.00 4.00
609 667 1.978580 GTCCTCCAGAGACTTTTCCCA 59.021 52.381 0.00 0.00 0.00 4.37
610 668 1.279558 GGTCCTCCAGAGACTTTTCCC 59.720 57.143 0.00 0.00 0.00 3.97
611 669 1.279558 GGGTCCTCCAGAGACTTTTCC 59.720 57.143 0.00 0.00 35.00 3.13
612 670 1.279558 GGGGTCCTCCAGAGACTTTTC 59.720 57.143 0.00 0.00 37.22 2.29
613 671 1.363246 GGGGTCCTCCAGAGACTTTT 58.637 55.000 0.00 0.00 37.22 2.27
614 672 0.193574 TGGGGTCCTCCAGAGACTTT 59.806 55.000 0.00 0.00 37.22 2.66
615 673 0.193574 TTGGGGTCCTCCAGAGACTT 59.806 55.000 0.00 0.00 38.17 3.01
616 674 0.193574 TTTGGGGTCCTCCAGAGACT 59.806 55.000 0.00 0.00 38.17 3.24
617 675 1.290134 ATTTGGGGTCCTCCAGAGAC 58.710 55.000 0.00 0.00 38.17 3.36
618 676 2.961536 TATTTGGGGTCCTCCAGAGA 57.038 50.000 0.00 0.00 38.17 3.10
619 677 4.316025 TTTTATTTGGGGTCCTCCAGAG 57.684 45.455 0.00 0.00 38.17 3.35
620 678 4.293634 TGATTTTATTTGGGGTCCTCCAGA 59.706 41.667 0.00 0.00 38.17 3.86
621 679 4.609301 TGATTTTATTTGGGGTCCTCCAG 58.391 43.478 0.00 0.00 38.17 3.86
622 680 4.683766 TGATTTTATTTGGGGTCCTCCA 57.316 40.909 0.00 0.00 37.22 3.86
623 681 6.367374 TTTTGATTTTATTTGGGGTCCTCC 57.633 37.500 0.00 0.00 0.00 4.30
624 682 7.047891 GGATTTTGATTTTATTTGGGGTCCTC 58.952 38.462 0.00 0.00 0.00 3.71
625 683 6.069673 GGGATTTTGATTTTATTTGGGGTCCT 60.070 38.462 0.00 0.00 0.00 3.85
626 684 6.069673 AGGGATTTTGATTTTATTTGGGGTCC 60.070 38.462 0.00 0.00 0.00 4.46
627 685 6.957631 AGGGATTTTGATTTTATTTGGGGTC 58.042 36.000 0.00 0.00 0.00 4.46
628 686 6.968400 AGGGATTTTGATTTTATTTGGGGT 57.032 33.333 0.00 0.00 0.00 4.95
629 687 8.648698 AAAAGGGATTTTGATTTTATTTGGGG 57.351 30.769 0.00 0.00 0.00 4.96
630 688 8.450180 CGAAAAGGGATTTTGATTTTATTTGGG 58.550 33.333 0.00 0.00 34.77 4.12
631 689 9.213799 TCGAAAAGGGATTTTGATTTTATTTGG 57.786 29.630 0.00 0.00 36.66 3.28
633 691 9.996554 AGTCGAAAAGGGATTTTGATTTTATTT 57.003 25.926 0.00 0.00 42.14 1.40
634 692 9.996554 AAGTCGAAAAGGGATTTTGATTTTATT 57.003 25.926 0.00 0.00 42.14 1.40
635 693 9.639601 GAAGTCGAAAAGGGATTTTGATTTTAT 57.360 29.630 0.00 0.00 42.14 1.40
636 694 7.806014 CGAAGTCGAAAAGGGATTTTGATTTTA 59.194 33.333 0.00 0.00 42.14 1.52
637 695 6.640907 CGAAGTCGAAAAGGGATTTTGATTTT 59.359 34.615 0.00 0.00 42.14 1.82
638 696 6.016610 TCGAAGTCGAAAAGGGATTTTGATTT 60.017 34.615 0.00 0.27 46.30 2.17
639 697 5.472137 TCGAAGTCGAAAAGGGATTTTGATT 59.528 36.000 0.00 0.00 46.30 2.57
640 698 5.001232 TCGAAGTCGAAAAGGGATTTTGAT 58.999 37.500 0.00 0.00 46.30 2.57
641 699 4.382291 TCGAAGTCGAAAAGGGATTTTGA 58.618 39.130 0.00 0.00 46.30 2.69
642 700 4.742438 TCGAAGTCGAAAAGGGATTTTG 57.258 40.909 0.00 0.00 46.30 2.44
655 713 2.178521 CGTCCCAGGTCGAAGTCG 59.821 66.667 0.00 0.00 41.45 4.18
656 714 2.572284 CCGTCCCAGGTCGAAGTC 59.428 66.667 4.87 0.00 0.00 3.01
657 715 3.692406 GCCGTCCCAGGTCGAAGT 61.692 66.667 4.87 0.00 0.00 3.01
658 716 4.452733 GGCCGTCCCAGGTCGAAG 62.453 72.222 4.87 0.00 0.00 3.79
675 733 1.443872 CGGTTCGGTCGAGACTTGG 60.444 63.158 3.09 0.00 0.00 3.61
710 768 2.028337 GAGCGAGGGGAATCGAGC 59.972 66.667 0.00 0.00 45.56 5.03
779 837 2.509336 AGTGTGTATCTGCGGCGC 60.509 61.111 27.44 27.44 0.00 6.53
789 847 3.592427 AGTAGGGAAGAGAGGAGTGTGTA 59.408 47.826 0.00 0.00 0.00 2.90
820 878 3.350909 CTGGGCGACGTCGAATGGA 62.351 63.158 39.74 17.12 43.02 3.41
900 958 3.273654 AGGAGGGAGTCGGGTGGA 61.274 66.667 0.00 0.00 0.00 4.02
950 1032 4.379243 CCGCGCTGGTGAGACCTT 62.379 66.667 5.56 0.00 39.58 3.50
1034 1116 3.267860 GAGATCGGCTGCCTTGCG 61.268 66.667 17.92 3.19 0.00 4.85
1049 1131 1.450312 GGCGTCATGGGGTCTTGAG 60.450 63.158 0.00 0.00 0.00 3.02
1115 2069 0.756903 AGATACCGTGGGGGATTTCG 59.243 55.000 0.00 0.00 36.82 3.46
1140 2094 7.499232 CAGTAAGGTAATTAATCCAGGGTCAAG 59.501 40.741 0.00 0.00 0.00 3.02
1381 2340 3.136763 CGCCATGACTTATGCATTCTCT 58.863 45.455 3.54 0.00 35.37 3.10
1396 2356 0.035881 ATGAGCCCTATGACGCCATG 59.964 55.000 0.00 0.00 34.31 3.66
1403 2367 1.131638 GACCACCATGAGCCCTATGA 58.868 55.000 0.00 0.00 0.00 2.15
1426 2390 6.587651 GCGTTTTACAGTCCAAAGTTACTAG 58.412 40.000 0.00 0.00 0.00 2.57
1470 2435 1.624312 TCCATGCCAAAGTACCGTACA 59.376 47.619 11.26 0.00 0.00 2.90
1968 3574 9.220767 AGTCTTCAGTTTCCATAACATAACTTC 57.779 33.333 0.00 0.00 0.00 3.01
2196 3817 8.474025 TGATTATGTCTGTATATGACACACACA 58.526 33.333 11.90 8.79 45.57 3.72
2889 4666 9.083422 TCCAAGGAATTTTATGTACAAACATGA 57.917 29.630 0.00 0.00 45.99 3.07
2909 4686 2.135139 GCCGCTTTTTCTTTTCCAAGG 58.865 47.619 0.00 0.00 0.00 3.61
3252 5033 9.679661 TTAGGTCATATTAGATTGCACTTTCAA 57.320 29.630 0.00 0.00 0.00 2.69
3323 5111 4.783055 TCTACTCTAGCAAGGAGGTACAG 58.217 47.826 0.00 0.00 35.34 2.74
3473 5261 7.377766 TCAATGCATACCTTTCTAGTTCAAC 57.622 36.000 0.00 0.00 0.00 3.18
3661 5708 7.923878 GTGGTGAAATTGTTACCAAAACTACAT 59.076 33.333 9.51 0.00 45.30 2.29
4653 8096 5.675538 AGTTCAGTCTTAGTTCAAAGCTGT 58.324 37.500 0.00 0.00 34.76 4.40
4909 10762 0.269477 TGGGTAGGGGGCAGCTTATA 59.731 55.000 0.00 0.00 0.00 0.98
4996 10849 1.072331 AGAACGAGCACCAAACTCCAT 59.928 47.619 0.00 0.00 0.00 3.41
4997 10850 0.468226 AGAACGAGCACCAAACTCCA 59.532 50.000 0.00 0.00 0.00 3.86
5051 10907 3.443681 AGCACGAATTGGGGTTTCTAATG 59.556 43.478 0.00 0.00 0.00 1.90
5052 10908 3.697166 AGCACGAATTGGGGTTTCTAAT 58.303 40.909 0.00 0.00 0.00 1.73
5406 11265 9.330063 CATCATAAAGGTTGTCTAATAGAAGCA 57.670 33.333 0.00 0.00 31.53 3.91
5423 11282 3.973973 TCTGGGTAGGGTCCATCATAAAG 59.026 47.826 0.00 0.00 33.29 1.85
5495 11354 3.772025 ACACCCTCTCTCCTTGATGTAAG 59.228 47.826 0.00 0.00 36.11 2.34
5741 11623 4.676951 AACCCACCACATGCCCGG 62.677 66.667 0.00 0.00 0.00 5.73
5835 11717 1.393539 CATGGTTTTCCTGTACGCGAG 59.606 52.381 15.93 0.00 41.38 5.03
5847 11729 4.148838 TGTCGAATTCTTCCCATGGTTTT 58.851 39.130 11.73 0.00 0.00 2.43
6091 12097 7.398024 ACTCTAATGCTAAACAAACTCTGGAT 58.602 34.615 0.00 0.00 0.00 3.41
6332 12372 6.844696 TCAGTTATGTGTTCTCAGTGTTTC 57.155 37.500 0.00 0.00 0.00 2.78
6384 12426 1.017387 GGCAATACTGGTGCAGCTAC 58.983 55.000 18.08 0.00 44.07 3.58


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

AutoCloner maintained by Alex Coulton.