Multiple sequence alignment - TraesCS7B01G331500

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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 TraesCS7B01G331500 chr7B 100.000 5111 0 0 1 5111 586714590 586719700 0.000000e+00 9439.0
1 TraesCS7B01G331500 chr7B 100.000 2459 0 0 5359 7817 586719948 586722406 0.000000e+00 4542.0
2 TraesCS7B01G331500 chr7B 92.275 2343 112 28 847 3133 621294194 621296523 0.000000e+00 3260.0
3 TraesCS7B01G331500 chr7B 96.334 1964 48 4 5877 7817 586844160 586846122 0.000000e+00 3206.0
4 TraesCS7B01G331500 chr7B 94.849 1029 29 6 3127 4138 621297071 621298092 0.000000e+00 1585.0
5 TraesCS7B01G331500 chr7B 94.659 880 44 3 4128 5006 621298141 621299018 0.000000e+00 1362.0
6 TraesCS7B01G331500 chr7B 95.103 776 28 5 4319 5088 586842696 586843467 0.000000e+00 1214.0
7 TraesCS7B01G331500 chr7B 96.269 536 17 1 5360 5892 621299314 621299849 0.000000e+00 876.0
8 TraesCS7B01G331500 chr7B 93.232 591 21 3 1039 1625 586703996 586704571 0.000000e+00 852.0
9 TraesCS7B01G331500 chr7B 95.536 448 19 1 5399 5845 586843716 586844163 0.000000e+00 715.0
10 TraesCS7B01G331500 chr7B 88.298 564 46 15 1078 1626 621404369 621403811 0.000000e+00 658.0
11 TraesCS7B01G331500 chr7B 93.075 361 16 2 6056 6407 621300225 621300585 3.230000e-143 520.0
12 TraesCS7B01G331500 chr7B 95.146 206 10 0 4128 4333 586759832 586760037 7.560000e-85 326.0
13 TraesCS7B01G331500 chr7B 94.660 206 11 0 4128 4333 586777782 586777987 3.520000e-83 320.0
14 TraesCS7B01G331500 chr7B 80.808 297 54 3 5664 5958 621455276 621455571 6.100000e-56 230.0
15 TraesCS7B01G331500 chr7B 88.701 177 17 2 3157 3330 586777539 586777715 6.140000e-51 213.0
16 TraesCS7B01G331500 chr7B 88.202 178 17 3 3157 3330 586759588 586759765 7.950000e-50 209.0
17 TraesCS7B01G331500 chr7B 78.723 329 54 10 2152 2472 212782879 212783199 1.030000e-48 206.0
18 TraesCS7B01G331500 chr7B 84.756 164 23 2 3591 3752 592706058 592706221 6.280000e-36 163.0
19 TraesCS7B01G331500 chr7B 89.474 133 7 4 847 972 586703764 586703896 2.260000e-35 161.0
20 TraesCS7B01G331500 chr7B 75.779 289 50 13 7240 7516 9816082 9816362 2.290000e-25 128.0
21 TraesCS7B01G331500 chr7D 90.521 1266 89 10 6574 7815 567470220 567471478 0.000000e+00 1644.0
22 TraesCS7B01G331500 chr7D 87.590 556 59 7 1078 1626 567515231 567514679 3.080000e-178 636.0
23 TraesCS7B01G331500 chr7D 76.682 446 71 18 347 790 528750401 528750815 4.750000e-52 217.0
24 TraesCS7B01G331500 chr7D 72.323 607 127 31 2345 2932 396100743 396101327 1.360000e-32 152.0
25 TraesCS7B01G331500 chr7D 82.286 175 27 3 3591 3763 429722898 429722726 1.760000e-31 148.0
26 TraesCS7B01G331500 chr7A 87.367 562 55 9 1078 1626 654110779 654110221 1.430000e-176 630.0
27 TraesCS7B01G331500 chr7A 87.500 168 9 7 872 1037 654006698 654006855 4.820000e-42 183.0
28 TraesCS7B01G331500 chr5D 80.706 793 121 13 2 790 61072844 61072080 8.740000e-164 588.0
29 TraesCS7B01G331500 chr5D 74.867 752 159 21 2367 3101 251939236 251938498 1.640000e-81 315.0
30 TraesCS7B01G331500 chr5D 79.439 321 56 9 3157 3473 255864639 255864953 1.320000e-52 219.0
31 TraesCS7B01G331500 chr5D 83.140 172 26 2 3591 3761 220212654 220212823 3.780000e-33 154.0
32 TraesCS7B01G331500 chr3B 86.372 521 52 11 1094 1597 572837710 572837192 1.150000e-152 551.0
33 TraesCS7B01G331500 chr3B 74.132 576 129 16 2155 2720 641622191 641622756 3.670000e-53 220.0
34 TraesCS7B01G331500 chr3D 84.991 533 49 20 1094 1597 437734964 437734434 5.410000e-141 512.0
35 TraesCS7B01G331500 chr3D 78.530 694 124 15 2 686 364658677 364658000 4.330000e-117 433.0
36 TraesCS7B01G331500 chr3D 83.537 164 23 4 3591 3752 339456130 339456291 4.890000e-32 150.0
37 TraesCS7B01G331500 chr3D 87.912 91 11 0 3157 3247 124644092 124644182 2.980000e-19 108.0
38 TraesCS7B01G331500 chr3D 85.075 67 4 3 2154 2215 154573889 154573954 6.550000e-06 63.9
39 TraesCS7B01G331500 chr3D 84.615 65 6 4 2154 2214 612983234 612983298 2.360000e-05 62.1
40 TraesCS7B01G331500 chr3A 84.962 532 51 17 1094 1597 575872144 575871614 5.410000e-141 512.0
41 TraesCS7B01G331500 chr3A 73.902 774 158 32 11 773 585025376 585026116 3.590000e-68 270.0
42 TraesCS7B01G331500 chr3A 75.714 350 69 11 3159 3496 399583290 399583635 2.260000e-35 161.0
43 TraesCS7B01G331500 chr2B 78.755 739 131 21 21 754 457334269 457333552 9.180000e-129 472.0
44 TraesCS7B01G331500 chr2B 76.471 748 142 22 11 752 583786973 583787692 7.410000e-100 375.0
45 TraesCS7B01G331500 chr2B 73.497 815 176 25 2154 2941 300435273 300436074 9.990000e-69 272.0
46 TraesCS7B01G331500 chr2B 74.688 640 125 24 103 736 798662852 798662244 4.680000e-62 250.0
47 TraesCS7B01G331500 chr2B 74.392 617 127 18 2155 2744 660112772 660112160 1.310000e-57 235.0
48 TraesCS7B01G331500 chr2B 87.273 165 17 4 3591 3752 45649353 45649516 1.340000e-42 185.0
49 TraesCS7B01G331500 chr2B 84.146 164 24 2 3591 3752 311489100 311489263 2.920000e-34 158.0
50 TraesCS7B01G331500 chr2B 84.049 163 24 2 3591 3751 65895087 65895249 1.050000e-33 156.0
51 TraesCS7B01G331500 chr2B 97.143 35 1 0 4787 4821 669650312 669650278 8.470000e-05 60.2
52 TraesCS7B01G331500 chr2A 78.289 760 135 21 19 769 21466766 21466028 5.530000e-126 462.0
53 TraesCS7B01G331500 chr2A 77.809 721 136 19 36 752 682516638 682515938 2.610000e-114 424.0
54 TraesCS7B01G331500 chr2A 80.350 514 90 9 11 516 642221063 642221573 5.720000e-101 379.0
55 TraesCS7B01G331500 chr2A 77.713 516 106 7 2 515 613070977 613071485 2.740000e-79 307.0
56 TraesCS7B01G331500 chr2A 77.665 394 66 14 409 800 591612588 591612215 3.670000e-53 220.0
57 TraesCS7B01G331500 chr2A 87.179 78 10 0 7441 7518 565750186 565750263 1.080000e-13 89.8
58 TraesCS7B01G331500 chr2A 73.460 211 41 11 3190 3398 70661987 70661790 1.820000e-06 65.8
59 TraesCS7B01G331500 chr4D 79.767 514 93 8 3 514 435662691 435662187 5.770000e-96 363.0
60 TraesCS7B01G331500 chr4D 75.067 750 147 25 2 749 312589159 312589870 5.890000e-81 313.0
61 TraesCS7B01G331500 chr1B 75.325 770 152 29 2199 2942 38233760 38233003 1.260000e-87 335.0
62 TraesCS7B01G331500 chr1D 76.479 676 107 28 98 752 47843819 47844463 3.520000e-83 320.0
63 TraesCS7B01G331500 chr1D 77.397 438 93 5 85 519 109820117 109819683 1.010000e-63 255.0
64 TraesCS7B01G331500 chr6A 77.381 504 101 10 19 519 483546189 483545696 3.570000e-73 287.0
65 TraesCS7B01G331500 chr6A 83.544 79 9 4 2157 2231 118861658 118861580 3.910000e-08 71.3
66 TraesCS7B01G331500 chr2D 77.393 491 97 11 2155 2635 14353991 14353505 5.970000e-71 279.0
67 TraesCS7B01G331500 chr2D 76.258 497 104 10 2199 2689 24225141 24224653 1.300000e-62 252.0
68 TraesCS7B01G331500 chr2D 80.345 290 40 7 7542 7817 591778103 591777817 3.700000e-48 204.0
69 TraesCS7B01G331500 chr2D 76.864 389 63 15 397 779 447212380 447212013 2.230000e-45 195.0
70 TraesCS7B01G331500 chr2D 80.370 270 36 10 7271 7529 368558460 368558197 1.040000e-43 189.0
71 TraesCS7B01G331500 chr2D 87.195 164 19 2 3591 3752 67547224 67547387 1.340000e-42 185.0
72 TraesCS7B01G331500 chr2D 78.358 134 23 6 4718 4848 560994570 560994440 1.810000e-11 82.4
73 TraesCS7B01G331500 chr1A 76.424 509 110 9 13 519 564350717 564350217 4.650000e-67 267.0
74 TraesCS7B01G331500 chr5A 72.443 929 205 36 2227 3133 678669125 678670024 4.680000e-62 250.0
75 TraesCS7B01G331500 chr5A 73.063 813 168 25 11 817 702238115 702237348 2.820000e-59 241.0
76 TraesCS7B01G331500 chr5A 80.000 290 40 12 7542 7817 669316325 669316610 1.720000e-46 198.0
77 TraesCS7B01G331500 chr5A 83.333 96 13 3 3157 3250 19345147 19345053 1.400000e-12 86.1
78 TraesCS7B01G331500 chr4A 78.818 203 32 9 3157 3354 675545997 675546193 8.230000e-25 126.0
79 TraesCS7B01G331500 chr4A 83.333 114 16 3 3156 3267 712137701 712137589 1.390000e-17 102.0
80 TraesCS7B01G331500 chr4A 85.000 60 5 4 2157 2212 121372590 121372531 3.050000e-04 58.4
81 TraesCS7B01G331500 chr5B 81.098 164 21 3 7366 7519 87655056 87655219 1.070000e-23 122.0
82 TraesCS7B01G331500 chr6B 82.031 128 19 4 3143 3267 362862769 362862643 1.070000e-18 106.0
83 TraesCS7B01G331500 chr6B 85.714 63 5 4 2157 2215 535244191 535244129 6.550000e-06 63.9
84 TraesCS7B01G331500 chr6B 81.013 79 11 4 2157 2231 151046191 151046113 8.470000e-05 60.2
85 TraesCS7B01G331500 chr6D 83.077 65 7 4 2154 2214 58500779 58500843 1.000000e-03 56.5


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 TraesCS7B01G331500 chr7B 586714590 586722406 7816 False 6990.500000 9439 100.000000 1 7817 2 chr7B.!!$F6 7816
1 TraesCS7B01G331500 chr7B 586842696 586846122 3426 False 1711.666667 3206 95.657667 4319 7817 3 chr7B.!!$F9 3498
2 TraesCS7B01G331500 chr7B 621294194 621300585 6391 False 1520.600000 3260 94.225400 847 6407 5 chr7B.!!$F10 5560
3 TraesCS7B01G331500 chr7B 621403811 621404369 558 True 658.000000 658 88.298000 1078 1626 1 chr7B.!!$R1 548
4 TraesCS7B01G331500 chr7B 586703764 586704571 807 False 506.500000 852 91.353000 847 1625 2 chr7B.!!$F5 778
5 TraesCS7B01G331500 chr7D 567470220 567471478 1258 False 1644.000000 1644 90.521000 6574 7815 1 chr7D.!!$F3 1241
6 TraesCS7B01G331500 chr7D 567514679 567515231 552 True 636.000000 636 87.590000 1078 1626 1 chr7D.!!$R2 548
7 TraesCS7B01G331500 chr7A 654110221 654110779 558 True 630.000000 630 87.367000 1078 1626 1 chr7A.!!$R1 548
8 TraesCS7B01G331500 chr5D 61072080 61072844 764 True 588.000000 588 80.706000 2 790 1 chr5D.!!$R1 788
9 TraesCS7B01G331500 chr5D 251938498 251939236 738 True 315.000000 315 74.867000 2367 3101 1 chr5D.!!$R2 734
10 TraesCS7B01G331500 chr3B 572837192 572837710 518 True 551.000000 551 86.372000 1094 1597 1 chr3B.!!$R1 503
11 TraesCS7B01G331500 chr3B 641622191 641622756 565 False 220.000000 220 74.132000 2155 2720 1 chr3B.!!$F1 565
12 TraesCS7B01G331500 chr3D 437734434 437734964 530 True 512.000000 512 84.991000 1094 1597 1 chr3D.!!$R2 503
13 TraesCS7B01G331500 chr3D 364658000 364658677 677 True 433.000000 433 78.530000 2 686 1 chr3D.!!$R1 684
14 TraesCS7B01G331500 chr3A 575871614 575872144 530 True 512.000000 512 84.962000 1094 1597 1 chr3A.!!$R1 503
15 TraesCS7B01G331500 chr3A 585025376 585026116 740 False 270.000000 270 73.902000 11 773 1 chr3A.!!$F2 762
16 TraesCS7B01G331500 chr2B 457333552 457334269 717 True 472.000000 472 78.755000 21 754 1 chr2B.!!$R1 733
17 TraesCS7B01G331500 chr2B 583786973 583787692 719 False 375.000000 375 76.471000 11 752 1 chr2B.!!$F5 741
18 TraesCS7B01G331500 chr2B 300435273 300436074 801 False 272.000000 272 73.497000 2154 2941 1 chr2B.!!$F3 787
19 TraesCS7B01G331500 chr2B 798662244 798662852 608 True 250.000000 250 74.688000 103 736 1 chr2B.!!$R4 633
20 TraesCS7B01G331500 chr2B 660112160 660112772 612 True 235.000000 235 74.392000 2155 2744 1 chr2B.!!$R2 589
21 TraesCS7B01G331500 chr2A 21466028 21466766 738 True 462.000000 462 78.289000 19 769 1 chr2A.!!$R1 750
22 TraesCS7B01G331500 chr2A 682515938 682516638 700 True 424.000000 424 77.809000 36 752 1 chr2A.!!$R4 716
23 TraesCS7B01G331500 chr2A 642221063 642221573 510 False 379.000000 379 80.350000 11 516 1 chr2A.!!$F3 505
24 TraesCS7B01G331500 chr2A 613070977 613071485 508 False 307.000000 307 77.713000 2 515 1 chr2A.!!$F2 513
25 TraesCS7B01G331500 chr4D 435662187 435662691 504 True 363.000000 363 79.767000 3 514 1 chr4D.!!$R1 511
26 TraesCS7B01G331500 chr4D 312589159 312589870 711 False 313.000000 313 75.067000 2 749 1 chr4D.!!$F1 747
27 TraesCS7B01G331500 chr1B 38233003 38233760 757 True 335.000000 335 75.325000 2199 2942 1 chr1B.!!$R1 743
28 TraesCS7B01G331500 chr1D 47843819 47844463 644 False 320.000000 320 76.479000 98 752 1 chr1D.!!$F1 654
29 TraesCS7B01G331500 chr1A 564350217 564350717 500 True 267.000000 267 76.424000 13 519 1 chr1A.!!$R1 506
30 TraesCS7B01G331500 chr5A 678669125 678670024 899 False 250.000000 250 72.443000 2227 3133 1 chr5A.!!$F2 906
31 TraesCS7B01G331500 chr5A 702237348 702238115 767 True 241.000000 241 73.063000 11 817 1 chr5A.!!$R2 806

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
844 893 0.252479 CAAGACCAGCTCCAGATGCT 59.748 55.0 0.00 0.00 42.06 3.79 F
846 895 0.325484 AGACCAGCTCCAGATGCTCT 60.325 55.0 0.00 0.00 38.92 4.09 F
2087 2242 0.534427 ATCTAGATCGTGCGGTCGGA 60.534 55.0 0.00 3.18 0.00 4.55 F
2948 3152 0.109689 GAGGACGAGGTCGACAACAG 60.110 60.0 18.91 7.89 43.02 3.16 F
3995 4778 0.252103 AGAGGGACGGTGGCTAGAAA 60.252 55.0 0.00 0.00 0.00 2.52 F
5106 5952 0.034059 CGTGTTCACTGAGAAGCCCT 59.966 55.0 1.53 0.00 36.78 5.19 F
5516 6362 0.381428 GCAAACGTTCGTGTGAGTCG 60.381 55.0 17.97 0.00 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2240 0.110373 GTGGATGTCAAAACGCGTCC 60.110 55.000 14.44 7.4 0.00 4.79 R
2089 2244 0.385473 CCACGTGGATGTCAAAACGC 60.385 55.000 31.31 0.0 39.58 4.84 R
3089 3301 0.738389 CAAGCGGTTAATCGGCCAAT 59.262 50.000 10.66 0.0 42.23 3.16 R
4359 5199 0.948623 TGCACGACATGGTGTACTGC 60.949 55.000 0.00 5.1 40.08 4.40 R
5968 6817 0.183971 AATGTCACGTGGTTGGGGAA 59.816 50.000 17.00 0.0 0.00 3.97 R
5969 6818 0.536233 CAATGTCACGTGGTTGGGGA 60.536 55.000 17.00 0.0 0.00 4.81 R
7089 8169 1.623811 GTACAAGCAAGGGGAGACTCA 59.376 52.381 4.53 0.0 0.00 3.41 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
190 192 1.852157 AAATGGCTCCTCGCTTGGGA 61.852 55.000 0.00 0.00 39.13 4.37
198 200 2.992689 TCGCTTGGGACTACCGCA 60.993 61.111 0.00 0.00 44.64 5.69
199 201 2.186903 CGCTTGGGACTACCGCAT 59.813 61.111 0.00 0.00 44.64 4.73
250 252 2.879907 CCTACGGCGGAAGAACGA 59.120 61.111 13.24 0.00 36.92 3.85
267 269 1.338200 ACGAGAAGGCGCTCTGATTTT 60.338 47.619 7.64 0.00 32.71 1.82
336 338 1.528309 CGGGTGGCCAAGTTGAAGT 60.528 57.895 7.24 0.00 0.00 3.01
343 345 1.283793 CCAAGTTGAAGTGGCAGCG 59.716 57.895 3.87 0.00 0.00 5.18
403 438 2.504244 CGACTCCTCGTCCAACGC 60.504 66.667 0.00 0.00 42.21 4.84
416 451 4.047059 AACGCCGACGACGACCAT 62.047 61.111 11.37 0.00 43.93 3.55
464 499 4.020617 CCTCCACCAGCCGCAGAA 62.021 66.667 0.00 0.00 0.00 3.02
473 508 0.671781 CAGCCGCAGAAGCTTACAGT 60.672 55.000 0.00 0.00 38.95 3.55
525 563 1.433534 GAGGAAGTGGCGAAGAAGTG 58.566 55.000 0.00 0.00 0.00 3.16
529 567 2.357034 GTGGCGAAGAAGTGGCGA 60.357 61.111 0.00 0.00 0.00 5.54
531 569 1.741401 TGGCGAAGAAGTGGCGATG 60.741 57.895 0.00 0.00 0.00 3.84
532 570 1.447838 GGCGAAGAAGTGGCGATGA 60.448 57.895 0.00 0.00 0.00 2.92
534 572 1.991430 CGAAGAAGTGGCGATGACG 59.009 57.895 0.00 0.00 42.93 4.35
544 582 4.719997 CGATGACGCTCCTCCTTC 57.280 61.111 0.00 0.00 0.00 3.46
545 583 1.066587 CGATGACGCTCCTCCTTCC 59.933 63.158 0.00 0.00 0.00 3.46
546 584 1.388065 CGATGACGCTCCTCCTTCCT 61.388 60.000 0.00 0.00 0.00 3.36
547 585 0.827368 GATGACGCTCCTCCTTCCTT 59.173 55.000 0.00 0.00 0.00 3.36
549 587 1.933021 TGACGCTCCTCCTTCCTTTA 58.067 50.000 0.00 0.00 0.00 1.85
553 591 4.142004 TGACGCTCCTCCTTCCTTTATTAC 60.142 45.833 0.00 0.00 0.00 1.89
555 593 3.494573 CGCTCCTCCTTCCTTTATTACCC 60.495 52.174 0.00 0.00 0.00 3.69
562 603 6.832384 CCTCCTTCCTTTATTACCCCTTTTAC 59.168 42.308 0.00 0.00 0.00 2.01
580 622 9.333724 CCCTTTTACTTGTCTAAGTTAAGAACA 57.666 33.333 12.39 0.00 44.57 3.18
607 649 2.323959 GCGATGAACTCCGATGATCTC 58.676 52.381 0.00 0.00 0.00 2.75
625 668 6.892485 TGATCTCTTGGATGATGTACAATGT 58.108 36.000 0.00 0.00 34.33 2.71
646 689 4.277174 TGTTTTATGTGCATTCGGTTGTCT 59.723 37.500 0.00 0.00 0.00 3.41
659 702 1.606668 GGTTGTCTGTTTGATGCCGAA 59.393 47.619 0.00 0.00 0.00 4.30
667 712 2.250188 GTTTGATGCCGAATTCGTTGG 58.750 47.619 25.10 12.10 37.74 3.77
712 757 3.100817 GTTCATCACGTTGCATGCATAC 58.899 45.455 23.37 19.80 0.00 2.39
725 774 7.043125 CGTTGCATGCATACTATGGATATAGAC 60.043 40.741 23.37 9.49 39.45 2.59
737 786 3.384789 TGGATATAGACTGCCGGATATGC 59.615 47.826 5.05 4.27 0.00 3.14
775 824 7.962918 GTGAAATGCATTATTTAAGACGTGACT 59.037 33.333 13.39 0.00 39.06 3.41
779 828 5.703592 TGCATTATTTAAGACGTGACTGGTT 59.296 36.000 0.00 0.00 0.00 3.67
781 830 7.064134 TGCATTATTTAAGACGTGACTGGTTAG 59.936 37.037 0.00 0.00 0.00 2.34
790 839 1.288127 GACTGGTTAGTGTCCGCGT 59.712 57.895 4.92 0.00 37.25 6.01
793 842 0.524862 CTGGTTAGTGTCCGCGTACT 59.475 55.000 4.92 9.22 0.00 2.73
798 847 0.390340 TAGTGTCCGCGTACTCGTCT 60.390 55.000 4.92 0.30 39.49 4.18
799 848 1.511464 GTGTCCGCGTACTCGTCTG 60.511 63.158 4.92 0.00 39.49 3.51
808 857 3.332493 TACTCGTCTGCGGGCGTTC 62.332 63.158 20.58 0.00 43.62 3.95
818 867 4.452733 GGGCGTTCGAGGGTCCAG 62.453 72.222 3.79 0.00 0.00 3.86
820 869 4.070552 GCGTTCGAGGGTCCAGCT 62.071 66.667 0.00 0.00 0.00 4.24
821 870 2.657237 CGTTCGAGGGTCCAGCTT 59.343 61.111 0.00 0.00 0.00 3.74
822 871 1.004918 CGTTCGAGGGTCCAGCTTT 60.005 57.895 0.00 0.00 0.00 3.51
823 872 1.291877 CGTTCGAGGGTCCAGCTTTG 61.292 60.000 0.00 0.00 0.00 2.77
824 873 1.302511 TTCGAGGGTCCAGCTTTGC 60.303 57.895 0.00 0.00 0.00 3.68
825 874 2.747855 CGAGGGTCCAGCTTTGCC 60.748 66.667 0.00 0.00 0.00 4.52
826 875 2.436109 GAGGGTCCAGCTTTGCCA 59.564 61.111 0.00 0.00 0.00 4.92
827 876 1.228552 GAGGGTCCAGCTTTGCCAA 60.229 57.895 0.00 0.00 0.00 4.52
828 877 1.228675 AGGGTCCAGCTTTGCCAAG 60.229 57.895 0.00 0.00 0.00 3.61
829 878 1.228552 GGGTCCAGCTTTGCCAAGA 60.229 57.895 0.86 0.00 30.57 3.02
830 879 1.527433 GGGTCCAGCTTTGCCAAGAC 61.527 60.000 0.86 0.00 30.57 3.01
831 880 1.527433 GGTCCAGCTTTGCCAAGACC 61.527 60.000 0.86 0.00 36.10 3.85
832 881 0.823356 GTCCAGCTTTGCCAAGACCA 60.823 55.000 0.86 0.00 30.57 4.02
833 882 0.538057 TCCAGCTTTGCCAAGACCAG 60.538 55.000 0.86 0.00 30.57 4.00
834 883 1.288127 CAGCTTTGCCAAGACCAGC 59.712 57.895 0.86 0.00 30.57 4.85
835 884 1.152368 AGCTTTGCCAAGACCAGCT 59.848 52.632 0.86 0.00 35.95 4.24
836 885 0.892814 AGCTTTGCCAAGACCAGCTC 60.893 55.000 0.86 0.00 35.95 4.09
837 886 1.871126 GCTTTGCCAAGACCAGCTCC 61.871 60.000 0.86 0.00 30.57 4.70
838 887 0.538057 CTTTGCCAAGACCAGCTCCA 60.538 55.000 0.00 0.00 30.57 3.86
839 888 0.538057 TTTGCCAAGACCAGCTCCAG 60.538 55.000 0.00 0.00 0.00 3.86
840 889 1.418097 TTGCCAAGACCAGCTCCAGA 61.418 55.000 0.00 0.00 0.00 3.86
841 890 1.203441 TGCCAAGACCAGCTCCAGAT 61.203 55.000 0.00 0.00 0.00 2.90
842 891 0.747283 GCCAAGACCAGCTCCAGATG 60.747 60.000 0.00 0.00 0.00 2.90
843 892 0.747283 CCAAGACCAGCTCCAGATGC 60.747 60.000 0.00 0.00 0.00 3.91
844 893 0.252479 CAAGACCAGCTCCAGATGCT 59.748 55.000 0.00 0.00 42.06 3.79
845 894 0.540923 AAGACCAGCTCCAGATGCTC 59.459 55.000 0.00 0.00 38.92 4.26
846 895 0.325484 AGACCAGCTCCAGATGCTCT 60.325 55.000 0.00 0.00 38.92 4.09
847 896 0.540923 GACCAGCTCCAGATGCTCTT 59.459 55.000 0.00 0.00 38.92 2.85
848 897 1.759445 GACCAGCTCCAGATGCTCTTA 59.241 52.381 0.00 0.00 38.92 2.10
849 898 1.761784 ACCAGCTCCAGATGCTCTTAG 59.238 52.381 0.00 0.00 38.92 2.18
850 899 1.540797 CCAGCTCCAGATGCTCTTAGC 60.541 57.143 0.00 8.21 42.82 3.09
954 1009 2.191908 GCACCACAGACCACACCA 59.808 61.111 0.00 0.00 0.00 4.17
955 1010 2.186826 GCACCACAGACCACACCAC 61.187 63.158 0.00 0.00 0.00 4.16
961 1016 3.249189 AGACCACACCACGGCCAT 61.249 61.111 2.24 0.00 0.00 4.40
982 1037 7.865707 GCCATGCCACTATATAATAATGTAGC 58.134 38.462 0.00 0.00 31.72 3.58
983 1038 7.307396 GCCATGCCACTATATAATAATGTAGCG 60.307 40.741 0.00 0.00 31.72 4.26
984 1039 7.307396 CCATGCCACTATATAATAATGTAGCGC 60.307 40.741 0.00 0.00 31.72 5.92
996 1051 0.729116 TGTAGCGCGTACTCCTACAC 59.271 55.000 16.33 0.00 37.21 2.90
1043 1150 7.956328 AAACACTATCACTGGTAGTATCTCA 57.044 36.000 1.45 0.00 31.46 3.27
1331 1443 2.049156 CCGACACGCTGCAGAAGA 60.049 61.111 20.43 0.00 0.00 2.87
1398 1510 4.880537 CTGCCGCGGCGAGAGATT 62.881 66.667 41.73 0.00 45.51 2.40
1406 1518 2.964389 GCGAGAGATTGAGCGGCC 60.964 66.667 0.00 0.00 0.00 6.13
1665 1816 3.807631 TTGCGGCAGTTGAGCGAGT 62.808 57.895 1.67 0.00 34.64 4.18
1787 1938 2.568509 TGTGCTGGTGAAGATGATGAGA 59.431 45.455 0.00 0.00 0.00 3.27
1881 2032 4.946478 AGGTTCTCAGGATTCCGAATAG 57.054 45.455 0.00 0.00 0.00 1.73
2060 2215 0.673644 CTCAACGCGGACCCTCAAAT 60.674 55.000 12.47 0.00 0.00 2.32
2072 2227 1.140852 CCCTCAAATCACCCGCATCTA 59.859 52.381 0.00 0.00 0.00 1.98
2076 2231 3.993081 CTCAAATCACCCGCATCTAGATC 59.007 47.826 1.03 0.00 0.00 2.75
2077 2232 2.732412 AATCACCCGCATCTAGATCG 57.268 50.000 1.03 9.56 0.00 3.69
2079 2234 0.668535 TCACCCGCATCTAGATCGTG 59.331 55.000 17.49 14.07 0.00 4.35
2080 2235 0.941463 CACCCGCATCTAGATCGTGC 60.941 60.000 17.49 13.00 35.59 5.34
2084 2239 2.802683 GCATCTAGATCGTGCGGTC 58.197 57.895 1.03 0.00 0.00 4.79
2085 2240 0.999228 GCATCTAGATCGTGCGGTCG 60.999 60.000 1.03 0.00 0.00 4.79
2087 2242 0.534427 ATCTAGATCGTGCGGTCGGA 60.534 55.000 0.00 3.18 0.00 4.55
2088 2243 1.009900 CTAGATCGTGCGGTCGGAC 60.010 63.158 4.95 4.95 0.00 4.79
2131 2292 0.594602 TGTATCGATTAGCCGACCGG 59.405 55.000 1.71 0.00 41.70 5.28
2192 2353 4.796231 CCGGTCGAGAACGCCCTG 62.796 72.222 4.84 0.00 40.82 4.45
2195 2356 2.357034 GTCGAGAACGCCCTGCAA 60.357 61.111 0.00 0.00 39.58 4.08
2246 2409 0.591170 CAAACGACAGCCCGTCATTT 59.409 50.000 4.88 0.00 45.70 2.32
2356 2523 1.829456 CCACATCTACCATCCGCCA 59.171 57.895 0.00 0.00 0.00 5.69
2485 2654 0.179145 CAACCTATCGTTCGAGCGGT 60.179 55.000 21.60 17.57 29.93 5.68
2493 2662 0.169672 CGTTCGAGCGGTAGAAGGAA 59.830 55.000 20.63 3.06 35.11 3.36
2507 2676 0.249398 AAGGAAATCGCCGCTAGTGT 59.751 50.000 1.99 0.00 0.00 3.55
2570 2771 1.511305 GAAGAGGCGACGGATGACA 59.489 57.895 0.00 0.00 0.00 3.58
2628 2829 2.665000 CATGGACGAGGCCTGTGT 59.335 61.111 12.00 8.90 0.00 3.72
2787 2991 1.521906 CGTGGACGTGGGTGAACAA 60.522 57.895 0.00 0.00 34.11 2.83
2876 3080 0.179134 CAGGCGGAGTTAGAAGACGG 60.179 60.000 0.00 0.00 0.00 4.79
2942 3146 2.435586 GGACGAGGACGAGGTCGA 60.436 66.667 6.35 0.00 43.02 4.20
2945 3149 1.572085 GACGAGGACGAGGTCGACAA 61.572 60.000 18.91 0.00 43.02 3.18
2948 3152 0.109689 GAGGACGAGGTCGACAACAG 60.110 60.000 18.91 7.89 43.02 3.16
2949 3153 0.822532 AGGACGAGGTCGACAACAGT 60.823 55.000 18.91 11.16 43.02 3.55
2954 3158 0.320771 GAGGTCGACAACAGTGCCAT 60.321 55.000 18.91 0.00 0.00 4.40
2956 3160 1.577328 GGTCGACAACAGTGCCATGG 61.577 60.000 18.91 7.63 0.00 3.66
2957 3161 1.965930 TCGACAACAGTGCCATGGC 60.966 57.895 30.54 30.54 42.35 4.40
2958 3162 2.964978 GACAACAGTGCCATGGCC 59.035 61.111 33.44 23.56 41.09 5.36
2959 3163 2.981560 GACAACAGTGCCATGGCCG 61.982 63.158 33.44 23.12 41.09 6.13
2960 3164 4.424566 CAACAGTGCCATGGCCGC 62.425 66.667 33.44 24.80 41.09 6.53
3019 3228 2.434185 GAAGCGCGTGGGATGTCA 60.434 61.111 8.43 0.00 0.00 3.58
3041 3250 3.081409 CACCCGGGTCCGAGGAAT 61.081 66.667 27.51 0.00 42.83 3.01
3042 3251 1.759299 CACCCGGGTCCGAGGAATA 60.759 63.158 27.51 0.00 42.83 1.75
3043 3252 1.457079 ACCCGGGTCCGAGGAATAG 60.457 63.158 24.16 0.00 42.83 1.73
3089 3301 1.371337 GCTTGGCACGCTCATCATCA 61.371 55.000 8.93 0.00 0.00 3.07
3115 3327 1.732259 CGATTAACCGCTTGCAGACTT 59.268 47.619 0.00 0.00 0.00 3.01
3170 3936 1.003580 CCATCCCTTACCCATCATCCG 59.996 57.143 0.00 0.00 0.00 4.18
3260 4026 5.099575 GCGGGTAAAAGTATTCACATTTGG 58.900 41.667 0.00 0.00 29.07 3.28
3276 4042 5.459762 CACATTTGGAACACACATTGACTTC 59.540 40.000 0.00 0.00 39.29 3.01
3376 4142 6.567959 TCATAAACATCAGCACAACACAAAA 58.432 32.000 0.00 0.00 0.00 2.44
3501 4267 6.749578 CACAGAGTATATAGCTAATTCGGCTG 59.250 42.308 13.85 5.10 40.52 4.85
3525 4291 4.733165 ACATAAGGCCACATCATAAGCAT 58.267 39.130 5.01 0.00 0.00 3.79
3533 4299 4.320421 GCCACATCATAAGCATCGCAATAA 60.320 41.667 0.00 0.00 0.00 1.40
3537 4303 8.022550 CCACATCATAAGCATCGCAATAAAATA 58.977 33.333 0.00 0.00 0.00 1.40
3579 4345 5.949952 ACAATAAATGAAGGGGAAGTACACC 59.050 40.000 0.00 0.00 43.70 4.16
3620 4386 5.221382 GGTACGCGGGTATGGATTATATGAT 60.221 44.000 15.92 0.00 0.00 2.45
3661 4427 6.092807 GCTCTACCGATGAGTTTGAGATTTTT 59.907 38.462 0.00 0.00 34.30 1.94
3731 4497 1.596203 GGCTTTATCCGCCGGGTAC 60.596 63.158 1.90 0.00 37.87 3.34
3764 4530 4.212716 GGTACCCATTTTACCATCCTTCC 58.787 47.826 0.00 0.00 39.17 3.46
3772 4538 4.927267 TTTACCATCCTTCCAGACATGT 57.073 40.909 0.00 0.00 0.00 3.21
3777 4543 3.370846 CCATCCTTCCAGACATGTGCTAA 60.371 47.826 1.15 0.00 0.00 3.09
3785 4551 2.160219 CAGACATGTGCTAAATGTGCGT 59.840 45.455 1.15 0.00 38.37 5.24
3788 4554 0.880441 ATGTGCTAAATGTGCGTGCA 59.120 45.000 0.00 0.00 0.00 4.57
3803 4569 5.100259 GTGCGTGCAAGAGAGTAGTAATAA 58.900 41.667 2.99 0.00 0.00 1.40
3806 4572 5.805994 GCGTGCAAGAGAGTAGTAATAAACT 59.194 40.000 2.99 0.00 42.62 2.66
3995 4778 0.252103 AGAGGGACGGTGGCTAGAAA 60.252 55.000 0.00 0.00 0.00 2.52
4134 4974 4.605183 TCTAACCTTCCTCTCTTCTCCTG 58.395 47.826 0.00 0.00 0.00 3.86
4139 4979 5.155905 ACCTTCCTCTCTTCTCCTGTTTTA 58.844 41.667 0.00 0.00 0.00 1.52
4178 5018 4.581077 TGCACATCTACATGTTTTTGCA 57.419 36.364 2.30 9.72 40.66 4.08
4213 5053 5.757850 AGATGCCAAAAATAATCCTCGAC 57.242 39.130 0.00 0.00 0.00 4.20
4222 5062 7.750903 CCAAAAATAATCCTCGACTCTTTGTTC 59.249 37.037 0.00 0.00 0.00 3.18
4277 5117 1.757118 TCTCATCAGGTCCGTCCATTC 59.243 52.381 0.00 0.00 39.02 2.67
4527 5367 4.373116 CACGGCACCCTGCTACGT 62.373 66.667 0.00 0.00 44.28 3.57
4563 5408 3.831715 GTGAGCACAACACCCTTATTC 57.168 47.619 0.00 0.00 32.84 1.75
4661 5506 6.597562 AGAGAGTTAGTTGAGATATCGAGGT 58.402 40.000 0.00 0.00 0.00 3.85
4746 5591 7.923344 TGTCTGCATATAAGTTCTCTCTTAAGC 59.077 37.037 0.00 0.00 34.28 3.09
4760 5605 6.987992 TCTCTCTTAAGCCAAACTTCGTAAAA 59.012 34.615 0.00 0.00 39.97 1.52
5038 5884 4.037446 TCAAGCACCTCAATTAACAACACC 59.963 41.667 0.00 0.00 0.00 4.16
5088 5934 1.436336 CCTACACGAAGGGCTACCG 59.564 63.158 0.00 0.00 43.47 4.02
5089 5935 1.318158 CCTACACGAAGGGCTACCGT 61.318 60.000 0.00 0.00 43.47 4.83
5091 5937 2.654877 CACGAAGGGCTACCGTGT 59.345 61.111 14.38 0.00 45.79 4.49
5092 5938 1.005394 CACGAAGGGCTACCGTGTT 60.005 57.895 14.38 0.00 45.79 3.32
5093 5939 1.012486 CACGAAGGGCTACCGTGTTC 61.012 60.000 14.38 0.00 45.79 3.18
5094 5940 1.290955 CGAAGGGCTACCGTGTTCA 59.709 57.895 0.00 0.00 43.47 3.18
5095 5941 1.012486 CGAAGGGCTACCGTGTTCAC 61.012 60.000 0.00 0.00 43.47 3.18
5096 5942 0.320697 GAAGGGCTACCGTGTTCACT 59.679 55.000 1.53 0.00 43.47 3.41
5097 5943 0.034896 AAGGGCTACCGTGTTCACTG 59.965 55.000 1.53 0.00 43.47 3.66
5098 5944 0.830444 AGGGCTACCGTGTTCACTGA 60.830 55.000 1.74 0.00 43.47 3.41
5099 5945 0.389948 GGGCTACCGTGTTCACTGAG 60.390 60.000 1.74 0.00 0.00 3.35
5100 5946 0.601558 GGCTACCGTGTTCACTGAGA 59.398 55.000 1.74 0.00 0.00 3.27
5101 5947 1.000506 GGCTACCGTGTTCACTGAGAA 59.999 52.381 1.74 0.00 0.00 2.87
5102 5948 2.329379 GCTACCGTGTTCACTGAGAAG 58.671 52.381 1.74 0.00 36.78 2.85
5103 5949 2.329379 CTACCGTGTTCACTGAGAAGC 58.671 52.381 1.74 0.00 36.78 3.86
5104 5950 0.249911 ACCGTGTTCACTGAGAAGCC 60.250 55.000 1.74 0.00 36.78 4.35
5105 5951 0.951040 CCGTGTTCACTGAGAAGCCC 60.951 60.000 1.53 0.00 36.78 5.19
5106 5952 0.034059 CGTGTTCACTGAGAAGCCCT 59.966 55.000 1.53 0.00 36.78 5.19
5107 5953 1.541233 CGTGTTCACTGAGAAGCCCTT 60.541 52.381 1.53 0.00 36.78 3.95
5108 5954 2.147150 GTGTTCACTGAGAAGCCCTTC 58.853 52.381 0.00 0.00 36.78 3.46
5109 5955 1.270305 TGTTCACTGAGAAGCCCTTCG 60.270 52.381 2.63 0.00 43.97 3.79
5110 5956 1.048601 TTCACTGAGAAGCCCTTCGT 58.951 50.000 2.63 0.00 43.97 3.85
5481 6327 2.299867 GGTTGCAGACAATCAAATGGGT 59.700 45.455 0.00 0.00 36.85 4.51
5516 6362 0.381428 GCAAACGTTCGTGTGAGTCG 60.381 55.000 17.97 0.00 0.00 4.18
5534 6380 3.583086 AGTCGAAAATGAGGAGAAGGGAA 59.417 43.478 0.00 0.00 0.00 3.97
5588 6437 4.381411 ACCTCTCTTTCTCTCCGTTTTTG 58.619 43.478 0.00 0.00 0.00 2.44
5702 6551 7.190871 TGAAAGACAAACGAAGTAATTTCCAC 58.809 34.615 0.00 0.00 45.00 4.02
5925 6774 2.044551 GGCTTGGCAAGGAGAGGG 60.045 66.667 27.25 2.65 0.00 4.30
6002 6851 2.230992 TGACATTGAAATGAAAGGCGGG 59.769 45.455 9.94 0.00 39.67 6.13
6003 6852 2.491693 GACATTGAAATGAAAGGCGGGA 59.508 45.455 9.94 0.00 39.67 5.14
6030 6896 0.881118 ACGCCATTTTGTGATTCGCT 59.119 45.000 0.00 0.00 0.00 4.93
6259 7323 1.522355 CATACAGGCAGCACTCCCG 60.522 63.158 0.00 0.00 0.00 5.14
6437 7507 2.237392 GGGATCCTTATCTCATTCCCCG 59.763 54.545 12.58 0.00 37.43 5.73
6582 7652 4.430137 AAATGTATCGCATGGCATGATC 57.570 40.909 30.69 12.98 37.96 2.92
6774 7850 1.470098 CTTGCGCAAGGCTAGTGAATT 59.530 47.619 36.86 0.00 44.05 2.17
6775 7851 0.804364 TGCGCAAGGCTAGTGAATTG 59.196 50.000 8.16 0.00 44.05 2.32
6809 7888 4.775236 AGTGACTCCCAATTAAGAGATGC 58.225 43.478 10.13 1.91 34.13 3.91
6987 8067 6.370166 TCTCAGATAGCACGACATACTCATAG 59.630 42.308 0.00 0.00 0.00 2.23
7072 8152 6.408548 CCTCTTGACTCCTTATATGCCAAGAA 60.409 42.308 0.00 0.00 38.29 2.52
7238 8323 0.040067 GTTGCACGCTTTGAGGGAAG 60.040 55.000 0.00 0.00 31.91 3.46
7268 8353 9.747898 TGTTGGGAAATGTATGTACTAGAAAAT 57.252 29.630 0.00 0.00 0.00 1.82
7297 8382 3.844640 TCCATCCTACGATCAAGATCCA 58.155 45.455 4.58 0.00 34.40 3.41
7409 8494 2.825861 GTTCCCCGAACTGTCTAACA 57.174 50.000 0.00 0.00 39.23 2.41
7698 8792 2.159824 TCGACTCACTGAGCTAAAGACG 59.840 50.000 5.92 0.00 32.04 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.470888 CCGCGTCCCTCTCCCATT 61.471 66.667 4.92 0.00 0.00 3.16
159 160 1.079405 GCCATTTGTCCTCGTCGGA 60.079 57.895 0.00 0.00 40.30 4.55
190 192 0.452184 CGTCAGAGACATGCGGTAGT 59.548 55.000 0.00 0.00 32.09 2.73
198 200 2.485582 CGCCGTCGTCAGAGACAT 59.514 61.111 0.00 0.00 40.98 3.06
199 201 3.733960 CCGCCGTCGTCAGAGACA 61.734 66.667 0.00 0.00 40.98 3.41
250 252 1.003580 TGGAAAATCAGAGCGCCTTCT 59.996 47.619 2.29 0.00 0.00 2.85
267 269 1.219124 GCTCCGACTGCTCAATGGA 59.781 57.895 0.00 0.00 0.00 3.41
296 298 3.640407 GCCTCCACCACTGCCTCA 61.640 66.667 0.00 0.00 0.00 3.86
403 438 1.009900 GAGCTATGGTCGTCGTCGG 60.010 63.158 1.55 0.00 37.69 4.79
416 451 1.076923 GTCGGAGGAGGTGGAGCTA 60.077 63.158 0.00 0.00 0.00 3.32
464 499 0.884704 CACCGGTGCAACTGTAAGCT 60.885 55.000 24.02 0.00 43.33 3.74
473 508 1.440938 CCTTTCGTTCACCGGTGCAA 61.441 55.000 30.25 20.59 37.11 4.08
529 567 1.280457 AAAGGAAGGAGGAGCGTCAT 58.720 50.000 0.00 0.00 0.00 3.06
531 569 3.545366 AATAAAGGAAGGAGGAGCGTC 57.455 47.619 0.00 0.00 0.00 5.19
532 570 3.134262 GGTAATAAAGGAAGGAGGAGCGT 59.866 47.826 0.00 0.00 0.00 5.07
534 572 3.181442 GGGGTAATAAAGGAAGGAGGAGC 60.181 52.174 0.00 0.00 0.00 4.70
537 575 5.467668 AAAGGGGTAATAAAGGAAGGAGG 57.532 43.478 0.00 0.00 0.00 4.30
540 578 7.672660 ACAAGTAAAAGGGGTAATAAAGGAAGG 59.327 37.037 0.00 0.00 0.00 3.46
542 580 8.450434 AGACAAGTAAAAGGGGTAATAAAGGAA 58.550 33.333 0.00 0.00 0.00 3.36
544 582 9.743581 TTAGACAAGTAAAAGGGGTAATAAAGG 57.256 33.333 0.00 0.00 0.00 3.11
553 591 8.781196 GTTCTTAACTTAGACAAGTAAAAGGGG 58.219 37.037 10.32 0.00 44.41 4.79
562 603 6.090898 CCGGACATGTTCTTAACTTAGACAAG 59.909 42.308 0.00 0.00 37.81 3.16
580 622 1.144057 GGAGTTCATCGCCGGACAT 59.856 57.895 5.05 0.00 0.00 3.06
607 649 9.292846 CACATAAAACATTGTACATCATCCAAG 57.707 33.333 0.00 0.00 0.00 3.61
625 668 4.277174 ACAGACAACCGAATGCACATAAAA 59.723 37.500 0.00 0.00 0.00 1.52
646 689 2.351253 CCAACGAATTCGGCATCAAACA 60.351 45.455 29.79 0.00 44.95 2.83
659 702 3.562141 TGATCAAACAACGACCAACGAAT 59.438 39.130 0.00 0.00 45.77 3.34
667 712 3.979495 ACTCTACGTGATCAAACAACGAC 59.021 43.478 9.36 0.00 0.00 4.34
712 757 6.571344 GCATATCCGGCAGTCTATATCCATAG 60.571 46.154 0.00 0.00 36.26 2.23
737 786 1.062002 GCATTTCACATCCGTGTACCG 59.938 52.381 0.00 0.00 44.02 4.02
775 824 0.523072 GAGTACGCGGACACTAACCA 59.477 55.000 25.94 0.00 0.00 3.67
779 828 0.390340 AGACGAGTACGCGGACACTA 60.390 55.000 25.94 0.00 43.96 2.74
781 830 1.511464 CAGACGAGTACGCGGACAC 60.511 63.158 25.94 17.49 43.96 3.67
790 839 3.332493 GAACGCCCGCAGACGAGTA 62.332 63.158 0.00 0.00 43.93 2.59
808 857 2.747855 GGCAAAGCTGGACCCTCG 60.748 66.667 0.00 0.00 0.00 4.63
814 863 0.538057 CTGGTCTTGGCAAAGCTGGA 60.538 55.000 0.00 0.00 33.06 3.86
817 866 0.892814 GAGCTGGTCTTGGCAAAGCT 60.893 55.000 20.79 20.79 46.53 3.74
818 867 1.583477 GAGCTGGTCTTGGCAAAGC 59.417 57.895 12.56 12.56 33.06 3.51
819 868 0.538057 TGGAGCTGGTCTTGGCAAAG 60.538 55.000 0.00 0.00 34.45 2.77
820 869 0.538057 CTGGAGCTGGTCTTGGCAAA 60.538 55.000 0.00 0.00 0.00 3.68
821 870 1.073722 CTGGAGCTGGTCTTGGCAA 59.926 57.895 6.83 0.00 0.00 4.52
822 871 1.203441 ATCTGGAGCTGGTCTTGGCA 61.203 55.000 6.83 0.00 0.00 4.92
823 872 0.747283 CATCTGGAGCTGGTCTTGGC 60.747 60.000 6.83 0.00 0.00 4.52
824 873 0.747283 GCATCTGGAGCTGGTCTTGG 60.747 60.000 6.83 0.00 0.00 3.61
825 874 0.252479 AGCATCTGGAGCTGGTCTTG 59.748 55.000 6.83 0.58 41.61 3.02
826 875 0.540923 GAGCATCTGGAGCTGGTCTT 59.459 55.000 6.83 0.00 43.58 3.01
827 876 2.210424 GAGCATCTGGAGCTGGTCT 58.790 57.895 6.83 0.00 43.58 3.85
828 877 4.852962 GAGCATCTGGAGCTGGTC 57.147 61.111 0.00 0.00 43.58 4.02
842 891 1.719600 CACCACAGAGTGCTAAGAGC 58.280 55.000 0.00 0.00 42.82 4.09
961 1016 5.746721 CGCGCTACATTATTATATAGTGGCA 59.253 40.000 5.56 0.00 36.63 4.92
972 1027 4.276678 TGTAGGAGTACGCGCTACATTATT 59.723 41.667 16.33 0.00 30.95 1.40
974 1029 3.002656 GTGTAGGAGTACGCGCTACATTA 59.997 47.826 21.04 8.76 33.83 1.90
975 1030 2.019249 TGTAGGAGTACGCGCTACATT 58.981 47.619 16.33 7.03 30.95 2.71
978 1033 1.012841 AGTGTAGGAGTACGCGCTAC 58.987 55.000 5.73 10.02 43.35 3.58
980 1035 1.801332 CAGTGTAGGAGTACGCGCT 59.199 57.895 5.73 0.00 43.35 5.92
981 1036 1.872679 GCAGTGTAGGAGTACGCGC 60.873 63.158 5.73 0.00 43.35 6.86
982 1037 0.109458 TTGCAGTGTAGGAGTACGCG 60.109 55.000 3.53 3.53 43.35 6.01
983 1038 1.927174 CATTGCAGTGTAGGAGTACGC 59.073 52.381 0.13 0.00 39.58 4.42
984 1039 3.119459 AGTCATTGCAGTGTAGGAGTACG 60.119 47.826 9.23 0.00 30.95 3.67
1043 1150 0.833287 AGCTTGATATGGCGACTGGT 59.167 50.000 0.00 0.00 0.00 4.00
1075 1186 0.888619 TGATCGATCGATGCCCTACC 59.111 55.000 33.86 17.92 34.60 3.18
1464 1615 1.526686 GGCACGCCCATGATGATGA 60.527 57.895 0.00 0.00 0.00 2.92
1665 1816 1.538634 CGTTCACGGTTACTTGGTGGA 60.539 52.381 0.00 0.00 35.37 4.02
1975 2129 3.155093 CTGTGCAGCTGTTGTTTTTCT 57.845 42.857 16.64 0.00 0.00 2.52
2060 2215 0.668535 CACGATCTAGATGCGGGTGA 59.331 55.000 10.74 0.00 0.00 4.02
2072 2227 4.175489 CGTCCGACCGCACGATCT 62.175 66.667 0.00 0.00 38.32 2.75
2080 2235 3.031457 TCAAAACGCGTCCGACCG 61.031 61.111 14.44 0.00 38.29 4.79
2084 2239 1.131826 GGATGTCAAAACGCGTCCG 59.868 57.895 14.44 3.86 41.14 4.79
2085 2240 0.110373 GTGGATGTCAAAACGCGTCC 60.110 55.000 14.44 7.40 0.00 4.79
2087 2242 1.155424 ACGTGGATGTCAAAACGCGT 61.155 50.000 5.58 5.58 44.05 6.01
2088 2243 0.721155 CACGTGGATGTCAAAACGCG 60.721 55.000 7.95 3.53 39.58 6.01
2089 2244 0.385473 CCACGTGGATGTCAAAACGC 60.385 55.000 31.31 0.00 39.58 4.84
2131 2292 1.405463 GAGGAAAAATCATGTCCCGGC 59.595 52.381 0.00 0.00 31.25 6.13
2179 2340 2.357034 GTTGCAGGGCGTTCTCGA 60.357 61.111 0.00 0.00 39.71 4.04
2185 2346 2.594592 GGAAGTGTTGCAGGGCGT 60.595 61.111 0.00 0.00 0.00 5.68
2190 2351 2.908073 GCACCGGGAAGTGTTGCAG 61.908 63.158 6.32 0.00 40.04 4.41
2191 2352 2.904866 GCACCGGGAAGTGTTGCA 60.905 61.111 6.32 0.00 40.04 4.08
2192 2353 2.904866 TGCACCGGGAAGTGTTGC 60.905 61.111 6.32 5.01 40.04 4.17
2246 2409 2.772077 TGTTTAATGTAGGCAGGCGA 57.228 45.000 0.00 0.00 0.00 5.54
2356 2523 1.139058 CGGGCTGGAGTGTAAATAGCT 59.861 52.381 0.00 0.00 34.89 3.32
2432 2601 1.519719 GAGCTCGAGGAAGCCATGT 59.480 57.895 15.58 0.00 43.56 3.21
2485 2654 2.029623 ACTAGCGGCGATTTCCTTCTA 58.970 47.619 12.98 0.00 0.00 2.10
2493 2662 2.106683 GGCAACACTAGCGGCGATT 61.107 57.895 12.98 0.00 0.00 3.34
2684 2887 3.190118 CGAAGGTTGTACTCTTAGTCCGT 59.810 47.826 0.00 0.00 0.00 4.69
2787 2991 1.620822 AGGATTCAAGCAACGCCTTT 58.379 45.000 0.00 0.00 0.00 3.11
2876 3080 3.063485 GCCTCATCGATCTCCTTAAAGC 58.937 50.000 0.00 0.00 0.00 3.51
2942 3146 2.985282 CGGCCATGGCACTGTTGT 60.985 61.111 36.56 0.00 44.11 3.32
3089 3301 0.738389 CAAGCGGTTAATCGGCCAAT 59.262 50.000 10.66 0.00 42.23 3.16
3170 3936 3.026694 ACCTACTGACGGGTATTGGTAC 58.973 50.000 0.00 0.00 33.59 3.34
3202 3968 3.463585 GTCGGGTGGCGGGTATGA 61.464 66.667 0.00 0.00 0.00 2.15
3204 3970 3.467226 CTGTCGGGTGGCGGGTAT 61.467 66.667 0.00 0.00 0.00 2.73
3239 4005 7.597369 GTGTTCCAAATGTGAATACTTTTACCC 59.403 37.037 0.00 0.00 33.81 3.69
3260 4026 3.313526 ACTGCTGAAGTCAATGTGTGTTC 59.686 43.478 0.00 0.00 31.64 3.18
3276 4042 2.935849 TGTTTATGACCGCATACTGCTG 59.064 45.455 0.00 0.00 42.25 4.41
3322 4088 9.230122 TGTTCTGTTGATATGATGTGTTGTTAT 57.770 29.630 0.00 0.00 0.00 1.89
3346 4112 6.654582 TGTTGTGCTGATGTTTATGAGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
3497 4263 2.222027 GATGTGGCCTTATGTACAGCC 58.778 52.381 15.18 15.18 45.96 4.85
3501 4267 5.063204 TGCTTATGATGTGGCCTTATGTAC 58.937 41.667 3.32 0.00 0.00 2.90
3525 4291 7.976175 TGTTATGTTGCCAATATTTTATTGCGA 59.024 29.630 0.00 0.00 0.00 5.10
3579 4345 5.288712 CGCGTACCCATATAAAATCTAGCAG 59.711 44.000 0.00 0.00 0.00 4.24
3620 4386 0.820891 GAGCGAGTACGGGTATGGGA 60.821 60.000 0.00 0.00 40.15 4.37
3692 4458 4.413760 CCCTATTAGGATCAGGGTACGAA 58.586 47.826 11.52 0.00 43.58 3.85
3704 4470 3.975168 GCGGATAAAGCCCTATTAGGA 57.025 47.619 11.52 0.00 37.67 2.94
3764 4530 2.160219 ACGCACATTTAGCACATGTCTG 59.840 45.455 0.00 0.00 32.25 3.51
3772 4538 1.197492 CTCTTGCACGCACATTTAGCA 59.803 47.619 0.00 0.00 0.00 3.49
3777 4543 2.289072 ACTACTCTCTTGCACGCACATT 60.289 45.455 0.00 0.00 0.00 2.71
3785 4551 7.241042 ACCAGTTTATTACTACTCTCTTGCA 57.759 36.000 0.00 0.00 34.56 4.08
3940 4706 8.881743 TGGCAATACAAATTTTGATTAGATTGC 58.118 29.630 23.25 23.25 43.61 3.56
3995 4778 1.986882 CTCAGCCCCAAAGAACTTGT 58.013 50.000 0.00 0.00 32.65 3.16
4134 4974 6.075780 GCATGTATTACGGCGACAAATAAAAC 60.076 38.462 16.62 6.40 0.00 2.43
4139 4979 2.939756 TGCATGTATTACGGCGACAAAT 59.060 40.909 16.62 12.63 0.00 2.32
4178 5018 1.915489 TGGCATCTTGATACCACACCT 59.085 47.619 0.00 0.00 0.00 4.00
4213 5053 7.490962 TGTAGTTTGTATGGTGAACAAAGAG 57.509 36.000 1.86 0.00 44.94 2.85
4222 5062 6.744112 ACCAATTGTTGTAGTTTGTATGGTG 58.256 36.000 4.43 0.00 36.19 4.17
4359 5199 0.948623 TGCACGACATGGTGTACTGC 60.949 55.000 0.00 5.10 40.08 4.40
4527 5367 3.244387 TGCTCACCTGTACAACAGCAATA 60.244 43.478 12.79 0.00 44.63 1.90
4714 5559 8.715191 AGAGAACTTATATGCAGACAAAAGAG 57.285 34.615 6.85 0.00 0.00 2.85
4716 5561 8.715191 AGAGAGAACTTATATGCAGACAAAAG 57.285 34.615 0.00 0.00 0.00 2.27
4720 5565 7.923344 GCTTAAGAGAGAACTTATATGCAGACA 59.077 37.037 6.67 0.00 33.29 3.41
4721 5566 7.383843 GGCTTAAGAGAGAACTTATATGCAGAC 59.616 40.741 6.67 0.00 33.29 3.51
5016 5862 4.037923 AGGTGTTGTTAATTGAGGTGCTTG 59.962 41.667 0.00 0.00 0.00 4.01
5038 5884 6.861065 TTGAACAGCCTTTCTTGTAGTAAG 57.139 37.500 0.00 0.00 0.00 2.34
5088 5934 2.147150 GAAGGGCTTCTCAGTGAACAC 58.853 52.381 0.00 0.00 36.69 3.32
5089 5935 1.270305 CGAAGGGCTTCTCAGTGAACA 60.270 52.381 0.00 0.00 37.44 3.18
5090 5936 1.270358 ACGAAGGGCTTCTCAGTGAAC 60.270 52.381 0.00 0.00 37.44 3.18
5091 5937 1.048601 ACGAAGGGCTTCTCAGTGAA 58.951 50.000 0.00 0.00 37.44 3.18
5092 5938 2.746697 ACGAAGGGCTTCTCAGTGA 58.253 52.632 0.00 0.00 37.44 3.41
5384 6230 7.975616 AGTTGTTGCACATATCCATAAAATGAC 59.024 33.333 0.00 0.00 0.00 3.06
5481 6327 4.694982 ACGTTTGCATCATCAATCACTACA 59.305 37.500 0.00 0.00 0.00 2.74
5516 6362 4.697828 GTGACTTCCCTTCTCCTCATTTTC 59.302 45.833 0.00 0.00 0.00 2.29
5534 6380 1.671742 CCACTACTTGGCGGTGACT 59.328 57.895 0.00 0.00 39.07 3.41
5588 6437 4.357918 TTGGAATCTATAGGCTCCTTGC 57.642 45.455 17.11 4.50 41.94 4.01
5671 6520 4.909894 ACTTCGTTTGTCTTTCAAAGAGC 58.090 39.130 0.00 0.00 45.15 4.09
5674 6523 8.743099 GGAAATTACTTCGTTTGTCTTTCAAAG 58.257 33.333 0.00 0.00 45.15 2.77
5702 6551 2.344142 GTGTTTGTTGTGAACCTTTGCG 59.656 45.455 0.00 0.00 0.00 4.85
5925 6774 0.371645 CGAGAGCAGCGAAAATGGAC 59.628 55.000 0.00 0.00 0.00 4.02
5968 6817 0.183971 AATGTCACGTGGTTGGGGAA 59.816 50.000 17.00 0.00 0.00 3.97
5969 6818 0.536233 CAATGTCACGTGGTTGGGGA 60.536 55.000 17.00 0.00 0.00 4.81
6030 6896 0.888736 CGTCCTTCCATGGTTGCACA 60.889 55.000 12.58 0.00 0.00 4.57
6100 7161 7.482169 ACTGGTGTTCTTACATTGATCTCTA 57.518 36.000 0.00 0.00 36.50 2.43
6101 7162 6.365970 ACTGGTGTTCTTACATTGATCTCT 57.634 37.500 0.00 0.00 36.50 3.10
6259 7323 0.729140 CAAATGAAGCGACGGCCAAC 60.729 55.000 2.24 0.00 41.24 3.77
6582 7652 6.501781 GTCATAATTTGCTTCCTTCTGGATG 58.498 40.000 0.00 0.00 42.81 3.51
6696 7772 7.816995 GCCAGTTAGAATTCCATCTCTGTATAG 59.183 40.741 0.65 0.00 0.00 1.31
6703 7779 4.133078 CAGGCCAGTTAGAATTCCATCTC 58.867 47.826 5.01 0.00 0.00 2.75
6858 7938 8.764558 ACACAACCCACTAATATTATGACACTA 58.235 33.333 0.00 0.00 0.00 2.74
6987 8067 1.734163 CCACGACATTGGTCCTAACC 58.266 55.000 0.00 0.00 46.66 2.85
7072 8152 3.065175 ACTCAGAGGTACCCTAGCCTAT 58.935 50.000 8.74 0.00 34.81 2.57
7089 8169 1.623811 GTACAAGCAAGGGGAGACTCA 59.376 52.381 4.53 0.00 0.00 3.41
7238 8323 9.826574 TCTAGTACATACATTTCCCAACAATAC 57.173 33.333 0.00 0.00 0.00 1.89
7277 8362 4.562347 CCTTGGATCTTGATCGTAGGATGG 60.562 50.000 17.43 5.84 31.51 3.51
7297 8382 4.785346 ATGCACCTTCATAGTGATCCTT 57.215 40.909 0.00 0.00 37.42 3.36
7409 8494 2.546789 GTGTTTGTTCGAGGGATCGTTT 59.453 45.455 0.00 0.00 0.00 3.60
7698 8792 0.317799 TGTTGCCATGGTTGATGTGC 59.682 50.000 14.67 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.