Multiple sequence alignment - TraesCS4B01G266600

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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 TraesCS4B01G266600 chr4B 100.000 4858 0 0 1 4858 538680318 538675461 0.000000e+00 8972.0
1 TraesCS4B01G266600 chr4B 91.040 625 33 11 4254 4858 538267394 538268015 0.000000e+00 822.0
2 TraesCS4B01G266600 chr4B 85.056 629 62 12 4254 4854 538388193 538387569 3.210000e-171 612.0
3 TraesCS4B01G266600 chr4B 82.484 628 71 17 4254 4854 538373893 538373278 9.320000e-142 514.0
4 TraesCS4B01G266600 chr4B 93.966 232 14 0 1504 1735 538678740 538678509 7.740000e-93 351.0
5 TraesCS4B01G266600 chr4B 93.966 232 14 0 1579 1810 538678815 538678584 7.740000e-93 351.0
6 TraesCS4B01G266600 chr4B 76.677 656 97 32 1879 2503 567470447 567469817 3.650000e-81 313.0
7 TraesCS4B01G266600 chr4B 95.541 157 7 0 1504 1660 538678665 538678509 8.070000e-63 252.0
8 TraesCS4B01G266600 chr4B 95.541 157 7 0 1654 1810 538678815 538678659 8.070000e-63 252.0
9 TraesCS4B01G266600 chr4B 79.518 332 59 3 2875 3198 539293167 539293497 1.360000e-55 228.0
10 TraesCS4B01G266600 chr4B 81.185 287 39 6 1905 2178 537799118 537798834 2.940000e-52 217.0
11 TraesCS4B01G266600 chr4B 85.052 194 19 6 2758 2946 538374218 538374030 6.420000e-44 189.0
12 TraesCS4B01G266600 chr4B 88.235 136 12 1 2809 2944 538388491 538388360 5.030000e-35 159.0
13 TraesCS4B01G266600 chr4B 80.447 179 35 0 2544 2722 537798462 537798284 2.360000e-28 137.0
14 TraesCS4B01G266600 chr4B 91.011 89 4 1 824 908 538962862 538962774 3.070000e-22 117.0
15 TraesCS4B01G266600 chr4B 77.222 180 28 7 4680 4857 568412118 568411950 5.180000e-15 93.5
16 TraesCS4B01G266600 chr4B 92.000 50 4 0 1454 1503 538994411 538994362 2.430000e-08 71.3
17 TraesCS4B01G266600 chr4D 94.683 978 35 7 2879 3839 436876247 436875270 0.000000e+00 1502.0
18 TraesCS4B01G266600 chr4D 90.656 899 65 16 1654 2545 436877470 436876584 0.000000e+00 1177.0
19 TraesCS4B01G266600 chr4D 86.893 885 70 17 864 1740 436878080 436877234 0.000000e+00 950.0
20 TraesCS4B01G266600 chr4D 95.685 394 16 1 4254 4646 436376266 436376659 2.470000e-177 632.0
21 TraesCS4B01G266600 chr4D 84.385 634 64 18 4254 4858 436714322 436713695 1.510000e-164 590.0
22 TraesCS4B01G266600 chr4D 94.340 371 16 4 4254 4620 436874413 436874044 9.130000e-157 564.0
23 TraesCS4B01G266600 chr4D 87.654 405 33 8 2981 3375 436375524 436375921 5.730000e-124 455.0
24 TraesCS4B01G266600 chr4D 93.617 235 14 1 1579 1812 436877470 436877236 2.780000e-92 350.0
25 TraesCS4B01G266600 chr4D 78.755 546 90 16 240 766 494481278 494481816 4.660000e-90 342.0
26 TraesCS4B01G266600 chr4D 92.444 225 12 2 2544 2764 436876509 436876286 2.820000e-82 316.0
27 TraesCS4B01G266600 chr4D 84.036 332 44 3 2875 3198 437229976 437230306 1.310000e-80 311.0
28 TraesCS4B01G266600 chr4D 78.378 481 66 20 1930 2374 455017446 455016968 1.330000e-70 278.0
29 TraesCS4B01G266600 chr4D 86.434 258 17 10 4617 4858 436873019 436872764 2.880000e-67 267.0
30 TraesCS4B01G266600 chr4D 88.830 188 15 4 1504 1690 436877395 436877213 4.890000e-55 226.0
31 TraesCS4B01G266600 chr4D 87.179 195 19 4 2755 2949 436722615 436722427 2.940000e-52 217.0
32 TraesCS4B01G266600 chr4D 75.652 460 69 22 1961 2382 436957344 436956890 6.420000e-44 189.0
33 TraesCS4B01G266600 chr4D 97.222 108 3 0 763 870 436879466 436879359 2.990000e-42 183.0
34 TraesCS4B01G266600 chr4D 92.188 128 9 1 4732 4858 436376803 436376930 3.860000e-41 180.0
35 TraesCS4B01G266600 chr4D 88.148 135 15 1 4254 4387 436722267 436722133 5.030000e-35 159.0
36 TraesCS4B01G266600 chr4D 91.111 90 4 1 825 910 436952182 436952093 8.540000e-23 119.0
37 TraesCS4B01G266600 chr4D 93.750 48 3 0 1461 1508 436957547 436957500 6.740000e-09 73.1
38 TraesCS4B01G266600 chr4D 92.000 50 4 0 1454 1503 436982931 436982882 2.430000e-08 71.3
39 TraesCS4B01G266600 chr4A 93.807 985 37 12 2757 3728 31581658 31582631 0.000000e+00 1459.0
40 TraesCS4B01G266600 chr4A 90.182 988 57 18 765 1734 31579943 31580908 0.000000e+00 1251.0
41 TraesCS4B01G266600 chr4A 94.884 606 28 3 4254 4858 31593429 31594032 0.000000e+00 944.0
42 TraesCS4B01G266600 chr4A 87.828 723 66 17 1654 2370 31580678 31581384 0.000000e+00 828.0
43 TraesCS4B01G266600 chr4A 90.240 625 31 9 4254 4858 31624322 31623708 0.000000e+00 789.0
44 TraesCS4B01G266600 chr4A 92.717 357 17 4 3771 4118 31582627 31582983 1.560000e-139 507.0
45 TraesCS4B01G266600 chr4A 91.915 235 18 1 1579 1812 31580678 31580912 1.300000e-85 327.0
46 TraesCS4B01G266600 chr4A 96.154 182 7 0 2544 2725 31581476 31581657 1.020000e-76 298.0
47 TraesCS4B01G266600 chr4A 79.043 439 64 15 1957 2369 13266099 13266535 4.790000e-70 276.0
48 TraesCS4B01G266600 chr4A 88.830 188 15 4 1504 1690 31580753 31580935 4.890000e-55 226.0
49 TraesCS4B01G266600 chr4A 94.891 137 7 0 3238 3374 31624793 31624657 1.060000e-51 215.0
50 TraesCS4B01G266600 chr4A 86.842 76 10 0 2427 2502 13266540 13266615 8.660000e-13 86.1
51 TraesCS4B01G266600 chr3B 82.434 797 83 22 1 763 557106095 557105322 1.140000e-180 643.0
52 TraesCS4B01G266600 chr3B 96.429 56 2 0 680 735 239881371 239881426 5.180000e-15 93.5
53 TraesCS4B01G266600 chr7B 81.925 769 89 24 2 743 83989637 83990382 5.380000e-169 604.0
54 TraesCS4B01G266600 chr3D 80.982 815 100 26 2 766 474538005 474537196 3.240000e-166 595.0
55 TraesCS4B01G266600 chr3D 79.459 740 104 29 57 766 39991521 39992242 9.460000e-132 481.0
56 TraesCS4B01G266600 chr5B 82.079 731 79 24 63 763 575981241 575980533 1.170000e-160 577.0
57 TraesCS4B01G266600 chr2D 80.074 813 92 34 2 763 630677953 630677160 1.540000e-149 540.0
58 TraesCS4B01G266600 chr2D 79.061 788 95 30 2 766 159341681 159340941 1.220000e-130 477.0
59 TraesCS4B01G266600 chr2D 83.900 441 53 12 48 470 394534011 394534451 5.850000e-109 405.0
60 TraesCS4B01G266600 chr2D 83.784 444 50 15 48 476 87417338 87416902 7.570000e-108 401.0
61 TraesCS4B01G266600 chr7D 80.326 798 82 33 2 763 511987370 511988128 7.160000e-148 534.0
62 TraesCS4B01G266600 chr7D 81.329 557 65 25 240 763 538660051 538660601 2.700000e-112 416.0
63 TraesCS4B01G266600 chr7D 93.069 101 5 2 4158 4258 509611746 509611648 3.920000e-31 147.0
64 TraesCS4B01G266600 chr5D 86.270 488 54 7 2 483 260677213 260676733 7.210000e-143 518.0
65 TraesCS4B01G266600 chr5D 82.957 487 57 13 2 478 435666988 435667458 2.700000e-112 416.0
66 TraesCS4B01G266600 chr5D 95.789 95 4 0 4169 4263 225253184 225253278 2.340000e-33 154.0
67 TraesCS4B01G266600 chr3A 79.944 718 75 35 89 766 711097794 711097106 9.520000e-127 464.0
68 TraesCS4B01G266600 chr3A 94.949 99 4 1 4169 4266 55217079 55217177 2.340000e-33 154.0
69 TraesCS4B01G266600 chr1B 82.998 547 52 16 240 766 588760917 588761442 1.590000e-124 457.0
70 TraesCS4B01G266600 chr7A 81.342 477 72 10 2 471 677581615 677582081 5.940000e-99 372.0
71 TraesCS4B01G266600 chr7A 95.833 96 4 0 4164 4259 639594943 639595038 6.510000e-34 156.0
72 TraesCS4B01G266600 chr6D 78.732 489 61 20 2 473 444705127 444705589 2.210000e-73 287.0
73 TraesCS4B01G266600 chr6D 96.703 91 3 0 4167 4257 305158194 305158104 8.420000e-33 152.0
74 TraesCS4B01G266600 chr2B 98.901 91 1 0 4170 4260 230293602 230293512 3.890000e-36 163.0
75 TraesCS4B01G266600 chr2B 86.813 91 9 2 680 767 701196710 701196620 1.110000e-16 99.0
76 TraesCS4B01G266600 chr1A 97.849 93 2 0 4167 4259 560378110 560378202 1.400000e-35 161.0
77 TraesCS4B01G266600 chr1A 89.381 113 8 4 4145 4256 9546939 9547048 6.560000e-29 139.0
78 TraesCS4B01G266600 chr6A 95.604 91 4 0 4166 4256 616776282 616776372 3.920000e-31 147.0


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 TraesCS4B01G266600 chr4B 538675461 538680318 4857 True 2035.600000 8972 95.802800 1 4858 5 chr4B.!!$R8 4857
1 TraesCS4B01G266600 chr4B 538267394 538268015 621 False 822.000000 822 91.040000 4254 4858 1 chr4B.!!$F1 604
2 TraesCS4B01G266600 chr4B 538387569 538388491 922 True 385.500000 612 86.645500 2809 4854 2 chr4B.!!$R7 2045
3 TraesCS4B01G266600 chr4B 538373278 538374218 940 True 351.500000 514 83.768000 2758 4854 2 chr4B.!!$R6 2096
4 TraesCS4B01G266600 chr4B 567469817 567470447 630 True 313.000000 313 76.677000 1879 2503 1 chr4B.!!$R3 624
5 TraesCS4B01G266600 chr4D 436872764 436879466 6702 True 615.000000 1502 91.679889 763 4858 9 chr4D.!!$R6 4095
6 TraesCS4B01G266600 chr4D 436713695 436714322 627 True 590.000000 590 84.385000 4254 4858 1 chr4D.!!$R1 604
7 TraesCS4B01G266600 chr4D 436375524 436376930 1406 False 422.333333 632 91.842333 2981 4858 3 chr4D.!!$F3 1877
8 TraesCS4B01G266600 chr4D 494481278 494481816 538 False 342.000000 342 78.755000 240 766 1 chr4D.!!$F2 526
9 TraesCS4B01G266600 chr4A 31593429 31594032 603 False 944.000000 944 94.884000 4254 4858 1 chr4A.!!$F1 604
10 TraesCS4B01G266600 chr4A 31579943 31582983 3040 False 699.428571 1459 91.633286 765 4118 7 chr4A.!!$F3 3353
11 TraesCS4B01G266600 chr4A 31623708 31624793 1085 True 502.000000 789 92.565500 3238 4858 2 chr4A.!!$R1 1620
12 TraesCS4B01G266600 chr3B 557105322 557106095 773 True 643.000000 643 82.434000 1 763 1 chr3B.!!$R1 762
13 TraesCS4B01G266600 chr7B 83989637 83990382 745 False 604.000000 604 81.925000 2 743 1 chr7B.!!$F1 741
14 TraesCS4B01G266600 chr3D 474537196 474538005 809 True 595.000000 595 80.982000 2 766 1 chr3D.!!$R1 764
15 TraesCS4B01G266600 chr3D 39991521 39992242 721 False 481.000000 481 79.459000 57 766 1 chr3D.!!$F1 709
16 TraesCS4B01G266600 chr5B 575980533 575981241 708 True 577.000000 577 82.079000 63 763 1 chr5B.!!$R1 700
17 TraesCS4B01G266600 chr2D 630677160 630677953 793 True 540.000000 540 80.074000 2 763 1 chr2D.!!$R3 761
18 TraesCS4B01G266600 chr2D 159340941 159341681 740 True 477.000000 477 79.061000 2 766 1 chr2D.!!$R2 764
19 TraesCS4B01G266600 chr7D 511987370 511988128 758 False 534.000000 534 80.326000 2 763 1 chr7D.!!$F1 761
20 TraesCS4B01G266600 chr7D 538660051 538660601 550 False 416.000000 416 81.329000 240 763 1 chr7D.!!$F2 523
21 TraesCS4B01G266600 chr3A 711097106 711097794 688 True 464.000000 464 79.944000 89 766 1 chr3A.!!$R1 677
22 TraesCS4B01G266600 chr1B 588760917 588761442 525 False 457.000000 457 82.998000 240 766 1 chr1B.!!$F1 526

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
162 193 0.318762 GTCAAGCTGAAGACGGAGGT 59.681 55.0 0.0 0.0 0.00 3.85 F
1019 2522 0.178990 CTCCATTCCCCCGAAATCCC 60.179 60.0 0.0 0.0 0.00 3.85 F
1735 3286 0.179161 CAGTCGAGCTGTTCTACGGG 60.179 60.0 0.0 0.0 40.27 5.28 F
2106 3681 0.591741 GTTGACGAGGAGATACGCCG 60.592 60.0 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 3419 0.255033 TACCTCTGCTGCCTAGACGA 59.745 55.000 0.00 0.0 0.00 4.20 R
2984 4679 0.241213 CGAAGTCCTTGAGCTCGTCA 59.759 55.000 9.64 0.0 0.00 4.35 R
3672 5384 0.673644 CGGACTTCATCACCCGCTTT 60.674 55.000 0.00 0.0 35.29 3.51 R
4087 5976 1.001487 GCACCCTTTTGCATTTTTGGC 60.001 47.619 0.00 0.0 42.49 4.52 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
67 68 3.575351 GACCACTGAGACGCCGCTT 62.575 63.158 0.00 0.00 0.00 4.68
161 192 3.129792 GTCAAGCTGAAGACGGAGG 57.870 57.895 0.00 0.00 0.00 4.30
162 193 0.318762 GTCAAGCTGAAGACGGAGGT 59.681 55.000 0.00 0.00 0.00 3.85
270 358 4.660938 GGCGGCCTTGAAGTGGGT 62.661 66.667 12.87 0.00 0.00 4.51
330 418 1.498865 CGTGCCTTTGAGCAGTTCGT 61.499 55.000 0.00 0.00 45.14 3.85
440 580 2.426023 GGTCCAACAGTGGCGTCT 59.574 61.111 0.00 0.00 45.54 4.18
449 589 2.355837 GTGGCGTCTGCGTGAAGA 60.356 61.111 0.00 0.00 44.10 2.87
506 673 3.774959 CTCAGCGCGGTATTCGGCT 62.775 63.158 11.92 0.00 42.87 5.52
508 675 2.585247 AGCGCGGTATTCGGCTTC 60.585 61.111 10.12 0.00 40.60 3.86
522 691 0.458716 GGCTTCTAGTCACGGTCTGC 60.459 60.000 0.00 0.00 0.00 4.26
595 782 5.455849 CGAGATAATGTACTGTTTCACCGAG 59.544 44.000 0.00 0.00 0.00 4.63
599 786 9.128404 AGATAATGTACTGTTTCACCGAGTATA 57.872 33.333 0.00 0.00 0.00 1.47
604 791 5.916661 ACTGTTTCACCGAGTATATGTCT 57.083 39.130 0.00 0.00 0.00 3.41
768 984 3.051327 CGACTGCAGATGCTCTTAGATG 58.949 50.000 23.35 0.00 42.66 2.90
777 993 6.293298 GCAGATGCTCTTAGATGTTGGTAATG 60.293 42.308 0.00 0.00 38.21 1.90
924 2427 3.700350 CCTCCTCCTCCCACCCCT 61.700 72.222 0.00 0.00 0.00 4.79
925 2428 2.366167 CTCCTCCTCCCACCCCTG 60.366 72.222 0.00 0.00 0.00 4.45
928 2431 2.689034 CTCCTCCCACCCCTGGTC 60.689 72.222 0.00 0.00 35.46 4.02
929 2432 3.208592 TCCTCCCACCCCTGGTCT 61.209 66.667 0.00 0.00 35.46 3.85
930 2433 2.689034 CCTCCCACCCCTGGTCTC 60.689 72.222 0.00 0.00 35.46 3.36
931 2434 2.122729 CTCCCACCCCTGGTCTCA 59.877 66.667 0.00 0.00 35.46 3.27
932 2435 2.203938 TCCCACCCCTGGTCTCAC 60.204 66.667 0.00 0.00 35.46 3.51
933 2436 3.330720 CCCACCCCTGGTCTCACC 61.331 72.222 0.00 0.00 39.22 4.02
934 2437 3.706373 CCACCCCTGGTCTCACCG 61.706 72.222 0.00 0.00 42.58 4.94
935 2438 2.923035 CACCCCTGGTCTCACCGT 60.923 66.667 0.00 0.00 42.58 4.83
936 2439 2.603776 ACCCCTGGTCTCACCGTC 60.604 66.667 0.00 0.00 42.58 4.79
937 2440 2.603473 CCCCTGGTCTCACCGTCA 60.603 66.667 0.00 0.00 42.58 4.35
938 2441 2.657237 CCCTGGTCTCACCGTCAC 59.343 66.667 0.00 0.00 42.58 3.67
939 2442 2.258591 CCTGGTCTCACCGTCACG 59.741 66.667 0.00 0.00 42.58 4.35
940 2443 2.430921 CTGGTCTCACCGTCACGC 60.431 66.667 0.00 0.00 42.58 5.34
941 2444 3.916392 CTGGTCTCACCGTCACGCC 62.916 68.421 0.00 0.00 42.58 5.68
999 2502 1.066002 CGCTCGCCCAATTCATTCAAT 59.934 47.619 0.00 0.00 0.00 2.57
1012 2515 2.158623 TCATTCAATCTCCATTCCCCCG 60.159 50.000 0.00 0.00 0.00 5.73
1019 2522 0.178990 CTCCATTCCCCCGAAATCCC 60.179 60.000 0.00 0.00 0.00 3.85
1032 2535 0.890683 AAATCCCAGCAAGCCGAAAG 59.109 50.000 0.00 0.00 0.00 2.62
1055 2558 4.113354 CCCAGAGCAATCGAAACTAGTAC 58.887 47.826 0.00 0.00 0.00 2.73
1157 2678 4.517703 CCTCGTCCTCGTCGTCGC 62.518 72.222 0.00 0.00 38.33 5.19
1158 2679 3.488978 CTCGTCCTCGTCGTCGCT 61.489 66.667 0.00 0.00 38.33 4.93
1309 2860 2.482142 GGAGCTGTACTTGAGGGATTCG 60.482 54.545 0.00 0.00 0.00 3.34
1310 2861 1.134670 AGCTGTACTTGAGGGATTCGC 60.135 52.381 0.00 0.00 0.00 4.70
1311 2862 1.134670 GCTGTACTTGAGGGATTCGCT 60.135 52.381 2.42 2.42 0.00 4.93
1664 3215 4.452733 AGCTGTTCTACGGGCGGC 62.453 66.667 0.00 0.00 34.94 6.53
1683 3234 2.401592 CGAGACCTCGTCGAGCAG 59.598 66.667 17.02 6.84 46.99 4.24
1684 3235 2.101380 GAGACCTCGTCGAGCAGC 59.899 66.667 17.02 7.79 37.67 5.25
1685 3236 3.726631 GAGACCTCGTCGAGCAGCG 62.727 68.421 17.02 5.74 37.67 5.18
1727 3278 4.406173 CGTCCGCAGTCGAGCTGT 62.406 66.667 13.91 0.00 46.64 4.40
1728 3279 2.049063 GTCCGCAGTCGAGCTGTT 60.049 61.111 13.91 0.00 46.64 3.16
1729 3280 2.089349 GTCCGCAGTCGAGCTGTTC 61.089 63.158 13.91 1.63 46.64 3.18
1730 3281 2.259818 CCGCAGTCGAGCTGTTCT 59.740 61.111 13.91 0.00 46.64 3.01
1731 3282 0.958876 TCCGCAGTCGAGCTGTTCTA 60.959 55.000 13.91 0.00 46.64 2.10
1732 3283 0.798771 CCGCAGTCGAGCTGTTCTAC 60.799 60.000 13.91 0.00 46.64 2.59
1733 3284 1.128724 CGCAGTCGAGCTGTTCTACG 61.129 60.000 13.91 7.03 46.64 3.51
1734 3285 0.798771 GCAGTCGAGCTGTTCTACGG 60.799 60.000 13.91 0.00 46.64 4.02
1735 3286 0.179161 CAGTCGAGCTGTTCTACGGG 60.179 60.000 0.00 0.00 40.27 5.28
1736 3287 1.516603 GTCGAGCTGTTCTACGGGC 60.517 63.158 0.00 0.00 0.00 6.13
1737 3288 2.579787 CGAGCTGTTCTACGGGCG 60.580 66.667 0.00 0.00 0.00 6.13
1738 3289 2.202756 GAGCTGTTCTACGGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
1759 3310 3.844090 GGGACCTCCTCGAGCAGC 61.844 72.222 6.99 0.00 35.95 5.25
1805 3356 2.259818 CCGCAGTCGAGCTGTTCT 59.740 61.111 13.91 0.00 46.64 3.01
1806 3357 0.958876 TCCGCAGTCGAGCTGTTCTA 60.959 55.000 13.91 0.00 46.64 2.10
1807 3358 0.798771 CCGCAGTCGAGCTGTTCTAC 60.799 60.000 13.91 0.00 46.64 2.59
1808 3359 1.128724 CGCAGTCGAGCTGTTCTACG 61.129 60.000 13.91 7.03 46.64 3.51
1809 3360 0.798771 GCAGTCGAGCTGTTCTACGG 60.799 60.000 13.91 0.00 46.64 4.02
1815 3366 2.436115 GCTGTTCTACGGCCCACC 60.436 66.667 0.00 0.00 44.50 4.61
1816 3367 2.955881 GCTGTTCTACGGCCCACCT 61.956 63.158 0.00 0.00 44.50 4.00
1817 3368 1.218316 CTGTTCTACGGCCCACCTC 59.782 63.158 0.00 0.00 0.00 3.85
1818 3369 2.240162 CTGTTCTACGGCCCACCTCC 62.240 65.000 0.00 0.00 0.00 4.30
1819 3370 2.120940 TTCTACGGCCCACCTCCA 59.879 61.111 0.00 0.00 0.00 3.86
1820 3371 1.306654 TTCTACGGCCCACCTCCAT 60.307 57.895 0.00 0.00 0.00 3.41
1821 3372 1.335132 TTCTACGGCCCACCTCCATC 61.335 60.000 0.00 0.00 0.00 3.51
1822 3373 1.762460 CTACGGCCCACCTCCATCT 60.762 63.158 0.00 0.00 0.00 2.90
1823 3374 2.032860 CTACGGCCCACCTCCATCTG 62.033 65.000 0.00 0.00 0.00 2.90
1824 3375 2.523740 TACGGCCCACCTCCATCTGA 62.524 60.000 0.00 0.00 0.00 3.27
1825 3376 2.669133 CGGCCCACCTCCATCTGAA 61.669 63.158 0.00 0.00 0.00 3.02
1826 3377 1.225704 GGCCCACCTCCATCTGAAG 59.774 63.158 0.00 0.00 0.00 3.02
1827 3378 1.452833 GCCCACCTCCATCTGAAGC 60.453 63.158 0.00 0.00 0.00 3.86
1828 3379 1.225704 CCCACCTCCATCTGAAGCC 59.774 63.158 0.00 0.00 0.00 4.35
1829 3380 1.153289 CCACCTCCATCTGAAGCCG 60.153 63.158 0.00 0.00 0.00 5.52
1830 3381 1.817099 CACCTCCATCTGAAGCCGC 60.817 63.158 0.00 0.00 0.00 6.53
1831 3382 2.587194 CCTCCATCTGAAGCCGCG 60.587 66.667 0.00 0.00 0.00 6.46
1832 3383 3.267860 CTCCATCTGAAGCCGCGC 61.268 66.667 0.00 0.00 0.00 6.86
1833 3384 3.729965 CTCCATCTGAAGCCGCGCT 62.730 63.158 5.56 0.00 42.56 5.92
1834 3385 3.267860 CCATCTGAAGCCGCGCTC 61.268 66.667 5.56 0.00 38.25 5.03
1835 3386 3.624300 CATCTGAAGCCGCGCTCG 61.624 66.667 5.56 0.00 38.25 5.03
1853 3404 3.849951 CAGCGACCGCCCACCTAT 61.850 66.667 11.03 0.00 43.17 2.57
1854 3405 3.081409 AGCGACCGCCCACCTATT 61.081 61.111 11.03 0.00 43.17 1.73
1855 3406 2.895372 GCGACCGCCCACCTATTG 60.895 66.667 2.55 0.00 34.56 1.90
1856 3407 2.895372 CGACCGCCCACCTATTGC 60.895 66.667 0.00 0.00 0.00 3.56
1857 3408 2.516225 GACCGCCCACCTATTGCC 60.516 66.667 0.00 0.00 0.00 4.52
1858 3409 4.123545 ACCGCCCACCTATTGCCC 62.124 66.667 0.00 0.00 0.00 5.36
1859 3410 4.122149 CCGCCCACCTATTGCCCA 62.122 66.667 0.00 0.00 0.00 5.36
1860 3411 2.828549 CGCCCACCTATTGCCCAC 60.829 66.667 0.00 0.00 0.00 4.61
1861 3412 2.358619 GCCCACCTATTGCCCACA 59.641 61.111 0.00 0.00 0.00 4.17
1862 3413 1.754234 GCCCACCTATTGCCCACAG 60.754 63.158 0.00 0.00 0.00 3.66
1863 3414 1.754234 CCCACCTATTGCCCACAGC 60.754 63.158 0.00 0.00 44.14 4.40
1873 3424 4.039357 CCCACAGCGTCGTCGTCT 62.039 66.667 3.66 0.00 39.49 4.18
1874 3425 2.683859 CCCACAGCGTCGTCGTCTA 61.684 63.158 3.66 0.00 39.49 2.59
1875 3426 1.226046 CCACAGCGTCGTCGTCTAG 60.226 63.158 3.66 0.00 39.49 2.43
1876 3427 1.226046 CACAGCGTCGTCGTCTAGG 60.226 63.158 3.66 0.00 39.49 3.02
1877 3428 2.277373 CAGCGTCGTCGTCTAGGC 60.277 66.667 3.66 0.00 39.49 3.93
1940 3500 0.757188 CTATGCAGGGGACGAGACCT 60.757 60.000 0.00 0.00 37.66 3.85
1987 3547 1.276421 CCACCGATTCACCAAGACTCT 59.724 52.381 0.00 0.00 0.00 3.24
2106 3681 0.591741 GTTGACGAGGAGATACGCCG 60.592 60.000 0.00 0.00 0.00 6.46
2260 3835 2.915659 ACGCCCAACCTCGTCTCA 60.916 61.111 0.00 0.00 33.09 3.27
2291 3866 1.909376 CGGGTACGTTCACAGATCAG 58.091 55.000 0.00 0.00 34.81 2.90
2311 3886 5.087323 TCAGTGACTCCCTTCTATTTCAGT 58.913 41.667 0.00 0.00 0.00 3.41
2313 3888 5.872070 CAGTGACTCCCTTCTATTTCAGTTC 59.128 44.000 0.00 0.00 0.00 3.01
2351 3935 9.994432 CAGTTTGATCAGAAGTAATTTACCATC 57.006 33.333 2.92 3.01 0.00 3.51
2373 3957 3.124466 CGTGATTCGCATGTCCAAACTAA 59.876 43.478 0.00 0.00 0.00 2.24
2513 4118 4.157656 TCTGTGGCCAAATTATTACTGTGC 59.842 41.667 7.24 0.00 0.00 4.57
2515 4120 3.447229 GTGGCCAAATTATTACTGTGCCT 59.553 43.478 7.24 0.00 38.45 4.75
2516 4121 3.446873 TGGCCAAATTATTACTGTGCCTG 59.553 43.478 0.61 0.00 38.45 4.85
2517 4122 3.447229 GGCCAAATTATTACTGTGCCTGT 59.553 43.478 0.00 0.00 34.83 4.00
2518 4123 4.423732 GCCAAATTATTACTGTGCCTGTG 58.576 43.478 0.00 0.00 0.00 3.66
2523 4128 2.781681 ATTACTGTGCCTGTGGGTAC 57.218 50.000 0.00 0.00 46.34 3.34
2564 4245 0.892755 CAATGCAATGCAGGGTGACT 59.107 50.000 14.98 0.00 43.65 3.41
2585 4266 2.915349 TCTCTGAAGATGCTCATTGCC 58.085 47.619 0.00 0.00 42.00 4.52
2681 4362 1.339151 GGAGGGAACGAACTGATTGCT 60.339 52.381 0.00 0.00 0.00 3.91
2747 4432 2.353839 CGCAACAGCAGCAACCAC 60.354 61.111 0.00 0.00 0.00 4.16
2750 4435 1.361271 CAACAGCAGCAACCACTGG 59.639 57.895 0.00 0.00 38.16 4.00
2853 4543 6.208797 AGTGCACTACTACTTCTACATGACAA 59.791 38.462 20.16 0.00 38.04 3.18
2861 4551 8.988064 ACTACTTCTACATGACAAGTGTATTG 57.012 34.615 14.82 0.00 32.56 1.90
2862 4552 8.803235 ACTACTTCTACATGACAAGTGTATTGA 58.197 33.333 14.82 0.00 32.56 2.57
2863 4553 9.809096 CTACTTCTACATGACAAGTGTATTGAT 57.191 33.333 14.82 0.00 32.56 2.57
2864 4554 8.709386 ACTTCTACATGACAAGTGTATTGATC 57.291 34.615 0.00 0.00 32.13 2.92
3022 4717 1.535896 CGAGAAGGTCGTCTGTGAAGA 59.464 52.381 0.00 0.00 44.20 2.87
3139 4844 4.617995 CGCTCTGAACTCTGAAGTCTGAAT 60.618 45.833 0.00 0.00 33.48 2.57
3554 5266 3.676093 TGTCTGTCTGATAGTGACGACT 58.324 45.455 1.23 0.00 38.03 4.18
3672 5384 1.544691 GACCTGGAGAAGACTAACGCA 59.455 52.381 0.00 0.00 0.00 5.24
3714 5429 2.746375 CCGGATGGGGCTGTAGCTT 61.746 63.158 0.00 0.00 41.70 3.74
3739 5455 5.406780 TCGTTTCTGTGTTTTTGCATTGTTT 59.593 32.000 0.00 0.00 0.00 2.83
3742 5458 5.793026 TCTGTGTTTTTGCATTGTTTTCC 57.207 34.783 0.00 0.00 0.00 3.13
3757 5473 3.007506 TGTTTTCCATCTGACGGAAGCTA 59.992 43.478 5.27 0.00 43.29 3.32
3760 5476 1.964223 TCCATCTGACGGAAGCTATCC 59.036 52.381 0.00 0.00 45.57 2.59
3828 5547 3.738281 CGAGTACGAGCCTGATTTGGAAT 60.738 47.826 0.00 0.00 42.66 3.01
3833 5552 2.372264 GAGCCTGATTTGGAATGCTGA 58.628 47.619 0.00 0.00 0.00 4.26
3929 5799 0.734889 GGATGAAATGGCCGTCAGTG 59.265 55.000 0.00 0.00 0.00 3.66
3946 5823 1.134946 AGTGTTTTGTTCTGCTGGTGC 59.865 47.619 0.00 0.00 40.20 5.01
3955 5832 2.185004 TCTGCTGGTGCTTTAAGGAC 57.815 50.000 8.12 8.12 40.48 3.85
3974 5854 2.476619 GACTGCCGATGATATTTCACGG 59.523 50.000 16.72 16.72 43.42 4.94
3997 5886 5.027293 AGAAGGTTTCAGCTTGCAAATTT 57.973 34.783 0.00 0.00 35.86 1.82
4054 5943 6.211184 TCCAGAAATACAAGGGAGTAACGTTA 59.789 38.462 3.29 3.29 0.00 3.18
4087 5976 2.629617 ACAGGATTCACTTTTTGCTGGG 59.370 45.455 0.00 0.00 0.00 4.45
4144 6399 5.398169 TGGCAAATTATGTGTCGATGAAAC 58.602 37.500 0.00 0.00 0.00 2.78
4147 6402 6.033831 GGCAAATTATGTGTCGATGAAACTTG 59.966 38.462 0.00 0.00 0.00 3.16
4153 6408 2.744202 GTGTCGATGAAACTTGGATGCT 59.256 45.455 0.00 0.00 0.00 3.79
4154 6409 3.932710 GTGTCGATGAAACTTGGATGCTA 59.067 43.478 0.00 0.00 0.00 3.49
4155 6410 3.932710 TGTCGATGAAACTTGGATGCTAC 59.067 43.478 0.00 0.00 0.00 3.58
4177 6432 3.895232 CATGTGTGCTAACTACTCCCT 57.105 47.619 0.00 0.00 0.00 4.20
4178 6433 3.786635 CATGTGTGCTAACTACTCCCTC 58.213 50.000 0.00 0.00 0.00 4.30
4179 6434 2.176889 TGTGTGCTAACTACTCCCTCC 58.823 52.381 0.00 0.00 0.00 4.30
4180 6435 1.134560 GTGTGCTAACTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
4181 6436 1.272313 TGTGCTAACTACTCCCTCCGT 60.272 52.381 0.00 0.00 0.00 4.69
4182 6437 1.404748 GTGCTAACTACTCCCTCCGTC 59.595 57.143 0.00 0.00 0.00 4.79
4183 6438 1.031235 GCTAACTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
4184 6439 1.689984 CTAACTACTCCCTCCGTCCC 58.310 60.000 0.00 0.00 0.00 4.46
4185 6440 1.002069 TAACTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
4186 6441 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
4187 6442 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
4188 6443 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
4189 6444 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
4190 6445 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
4191 6446 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4192 6447 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4193 6448 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4194 6449 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4195 6450 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4196 6451 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
4197 6452 6.269194 TCCCTCCGTCCCATAATATAAGAAT 58.731 40.000 0.00 0.00 0.00 2.40
4198 6453 6.156256 TCCCTCCGTCCCATAATATAAGAATG 59.844 42.308 0.00 0.00 0.00 2.67
4199 6454 6.070194 CCCTCCGTCCCATAATATAAGAATGT 60.070 42.308 0.00 0.00 0.00 2.71
4200 6455 7.394816 CCTCCGTCCCATAATATAAGAATGTT 58.605 38.462 0.00 0.00 0.00 2.71
4201 6456 7.883311 CCTCCGTCCCATAATATAAGAATGTTT 59.117 37.037 0.00 0.00 0.00 2.83
4202 6457 9.284968 CTCCGTCCCATAATATAAGAATGTTTT 57.715 33.333 0.00 0.00 0.00 2.43
4203 6458 9.635404 TCCGTCCCATAATATAAGAATGTTTTT 57.365 29.630 0.00 0.00 0.00 1.94
4204 6459 9.677567 CCGTCCCATAATATAAGAATGTTTTTG 57.322 33.333 0.00 0.00 0.00 2.44
4217 6472 8.732746 AAGAATGTTTTTGACACTAGTGTAGT 57.267 30.769 27.98 10.32 45.05 2.73
4232 6487 8.707938 ACTAGTGTAGTGTTAAAAACGTTCTT 57.292 30.769 0.00 0.00 37.69 2.52
4233 6488 9.801873 ACTAGTGTAGTGTTAAAAACGTTCTTA 57.198 29.630 0.00 0.00 37.69 2.10
4247 6502 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
4248 6503 8.575649 AAACGTTCTTATATTTTGGGACAGAT 57.424 30.769 0.00 0.00 42.39 2.90
4249 6504 7.553881 ACGTTCTTATATTTTGGGACAGATG 57.446 36.000 0.00 0.00 42.39 2.90
4250 6505 6.542370 ACGTTCTTATATTTTGGGACAGATGG 59.458 38.462 0.00 0.00 42.39 3.51
4251 6506 6.765989 CGTTCTTATATTTTGGGACAGATGGA 59.234 38.462 0.00 0.00 42.39 3.41
4252 6507 7.041780 CGTTCTTATATTTTGGGACAGATGGAG 60.042 40.741 0.00 0.00 42.39 3.86
4382 6639 7.450014 TGAAACATTACACATTACAGACCCAAT 59.550 33.333 0.00 0.00 0.00 3.16
4521 6778 8.190326 TCCAAGATACTAGAAACTGAACAAGA 57.810 34.615 0.00 0.00 0.00 3.02
4564 6822 2.863153 CGGCACTACAAGCTGCAC 59.137 61.111 1.02 0.00 34.90 4.57
4637 7926 9.614792 CTAACCTAAAGAATAGTTATGCCAAGT 57.385 33.333 0.00 0.00 0.00 3.16
4742 8134 8.212317 GGCAATTTGGCATTATGATAAAAACT 57.788 30.769 17.26 0.00 43.14 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 120 0.923729 AGAGGAGCTGAGGAGGAGGA 60.924 60.000 0.00 0.00 0.00 3.71
150 154 3.319198 GCCCCACCTCCGTCTTCA 61.319 66.667 0.00 0.00 0.00 3.02
305 393 2.434185 CTCAAAGGCACGGCGCTA 60.434 61.111 6.90 0.00 41.91 4.26
429 567 3.439513 TTCACGCAGACGCCACTGT 62.440 57.895 6.65 0.00 45.53 3.55
440 580 1.000955 GTCCTTCTCCTTCTTCACGCA 59.999 52.381 0.00 0.00 0.00 5.24
449 589 0.604780 TCGTCGTCGTCCTTCTCCTT 60.605 55.000 1.33 0.00 38.33 3.36
497 664 2.098770 ACCGTGACTAGAAGCCGAATAC 59.901 50.000 0.00 0.00 0.00 1.89
506 673 1.961394 ACAAGCAGACCGTGACTAGAA 59.039 47.619 0.00 0.00 0.00 2.10
508 675 2.440539 AACAAGCAGACCGTGACTAG 57.559 50.000 0.00 0.00 0.00 2.57
568 755 6.097356 GGTGAAACAGTACATTATCTCGTCA 58.903 40.000 0.00 0.00 39.98 4.35
570 757 5.100259 CGGTGAAACAGTACATTATCTCGT 58.900 41.667 0.00 0.00 39.98 4.18
595 782 5.652744 AATTTGGCGAACGAGACATATAC 57.347 39.130 0.00 0.00 0.00 1.47
599 786 3.915437 AAAATTTGGCGAACGAGACAT 57.085 38.095 0.00 0.00 0.00 3.06
604 791 4.815040 TTGTCTAAAATTTGGCGAACGA 57.185 36.364 0.00 0.00 0.00 3.85
656 845 2.124403 CCCATGGTCAGCCTCAGC 60.124 66.667 11.73 0.00 40.32 4.26
716 928 2.403586 CTCGAAAAATCGCCGCCC 59.596 61.111 0.00 0.00 0.00 6.13
768 984 6.220930 TGGATCGCTCTATAACATTACCAAC 58.779 40.000 0.00 0.00 0.00 3.77
777 993 4.323553 AACACCTGGATCGCTCTATAAC 57.676 45.455 0.00 0.00 0.00 1.89
924 2427 3.986006 GGCGTGACGGTGAGACCA 61.986 66.667 7.25 0.00 38.47 4.02
925 2428 4.736896 GGGCGTGACGGTGAGACC 62.737 72.222 7.25 0.00 34.05 3.85
928 2431 3.680786 TGAGGGCGTGACGGTGAG 61.681 66.667 7.25 0.00 0.00 3.51
929 2432 3.986006 GTGAGGGCGTGACGGTGA 61.986 66.667 7.25 0.00 0.00 4.02
999 2502 0.843984 GGATTTCGGGGGAATGGAGA 59.156 55.000 0.00 0.00 0.00 3.71
1012 2515 0.887933 TTTCGGCTTGCTGGGATTTC 59.112 50.000 1.30 0.00 0.00 2.17
1019 2522 2.985282 TGGGCTTTCGGCTTGCTG 60.985 61.111 0.00 0.00 41.46 4.41
1032 2535 1.936547 CTAGTTTCGATTGCTCTGGGC 59.063 52.381 0.00 0.00 42.22 5.36
1055 2558 1.875576 GCTCGGATCCATGGCTTGTAG 60.876 57.143 13.41 2.87 0.00 2.74
1142 2663 3.785499 CAGCGACGACGAGGACGA 61.785 66.667 12.29 0.00 42.66 4.20
1217 2768 4.479993 ATCCACAGGCAGGCTCGC 62.480 66.667 0.00 0.00 0.00 5.03
1218 2769 2.202987 GATCCACAGGCAGGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
1219 2770 0.818445 CATGATCCACAGGCAGGCTC 60.818 60.000 0.00 0.00 0.00 4.70
1220 2771 1.226542 CATGATCCACAGGCAGGCT 59.773 57.895 0.00 0.00 0.00 4.58
1221 2772 1.826921 CCATGATCCACAGGCAGGC 60.827 63.158 0.00 0.00 0.00 4.85
1222 2773 1.152819 CCCATGATCCACAGGCAGG 60.153 63.158 0.00 0.00 0.00 4.85
1223 2774 1.152819 CCCCATGATCCACAGGCAG 60.153 63.158 0.00 0.00 0.00 4.85
1224 2775 3.009275 CCCCATGATCCACAGGCA 58.991 61.111 0.00 0.00 0.00 4.75
1225 2776 2.520260 GCCCCATGATCCACAGGC 60.520 66.667 0.00 0.00 31.90 4.85
1226 2777 2.203252 CGCCCCATGATCCACAGG 60.203 66.667 0.00 0.00 0.00 4.00
1227 2778 2.203252 CCGCCCCATGATCCACAG 60.203 66.667 0.00 0.00 0.00 3.66
1252 2803 2.124653 GACTCGAGCTCGGAGGGA 60.125 66.667 33.98 14.99 40.29 4.20
1667 3218 2.101380 GCTGCTCGACGAGGTCTC 59.899 66.667 25.31 9.84 0.00 3.36
1668 3219 3.805307 CGCTGCTCGACGAGGTCT 61.805 66.667 25.31 0.00 41.67 3.85
1717 3268 1.935327 GCCCGTAGAACAGCTCGACT 61.935 60.000 0.00 0.00 0.00 4.18
1718 3269 1.516603 GCCCGTAGAACAGCTCGAC 60.517 63.158 0.00 0.00 0.00 4.20
1719 3270 2.882876 GCCCGTAGAACAGCTCGA 59.117 61.111 0.00 0.00 0.00 4.04
1720 3271 2.579787 CGCCCGTAGAACAGCTCG 60.580 66.667 0.00 0.00 0.00 5.03
1721 3272 2.202756 CCGCCCGTAGAACAGCTC 60.203 66.667 0.00 0.00 0.00 4.09
1722 3273 4.452733 GCCGCCCGTAGAACAGCT 62.453 66.667 0.00 0.00 0.00 4.24
1797 3348 2.663196 GTGGGCCGTAGAACAGCT 59.337 61.111 0.00 0.00 0.00 4.24
1798 3349 2.436115 GGTGGGCCGTAGAACAGC 60.436 66.667 0.00 0.00 0.00 4.40
1805 3356 2.063979 CAGATGGAGGTGGGCCGTA 61.064 63.158 0.00 0.00 40.50 4.02
1806 3357 3.402681 CAGATGGAGGTGGGCCGT 61.403 66.667 0.00 0.00 40.50 5.68
1807 3358 2.599645 CTTCAGATGGAGGTGGGCCG 62.600 65.000 0.00 0.00 40.50 6.13
1808 3359 1.225704 CTTCAGATGGAGGTGGGCC 59.774 63.158 0.00 0.00 0.00 5.80
1809 3360 1.452833 GCTTCAGATGGAGGTGGGC 60.453 63.158 0.00 0.00 0.00 5.36
1810 3361 1.225704 GGCTTCAGATGGAGGTGGG 59.774 63.158 0.00 0.00 0.00 4.61
1811 3362 1.153289 CGGCTTCAGATGGAGGTGG 60.153 63.158 0.00 0.00 0.00 4.61
1812 3363 1.817099 GCGGCTTCAGATGGAGGTG 60.817 63.158 0.00 0.00 0.00 4.00
1813 3364 2.586792 GCGGCTTCAGATGGAGGT 59.413 61.111 0.00 0.00 0.00 3.85
1814 3365 2.587194 CGCGGCTTCAGATGGAGG 60.587 66.667 0.00 0.00 0.00 4.30
1815 3366 3.267860 GCGCGGCTTCAGATGGAG 61.268 66.667 8.83 0.00 0.00 3.86
1816 3367 3.723235 GAGCGCGGCTTCAGATGGA 62.723 63.158 8.83 0.00 39.88 3.41
1817 3368 3.267860 GAGCGCGGCTTCAGATGG 61.268 66.667 8.83 0.00 39.88 3.51
1818 3369 3.624300 CGAGCGCGGCTTCAGATG 61.624 66.667 8.83 0.00 39.88 2.90
1836 3387 3.385749 AATAGGTGGGCGGTCGCTG 62.386 63.158 15.04 0.00 41.60 5.18
1837 3388 3.081409 AATAGGTGGGCGGTCGCT 61.081 61.111 15.04 0.00 41.60 4.93
1838 3389 2.895372 CAATAGGTGGGCGGTCGC 60.895 66.667 6.83 6.83 41.06 5.19
1839 3390 2.895372 GCAATAGGTGGGCGGTCG 60.895 66.667 0.00 0.00 0.00 4.79
1840 3391 2.516225 GGCAATAGGTGGGCGGTC 60.516 66.667 0.00 0.00 0.00 4.79
1841 3392 4.123545 GGGCAATAGGTGGGCGGT 62.124 66.667 0.00 0.00 0.00 5.68
1842 3393 4.122149 TGGGCAATAGGTGGGCGG 62.122 66.667 0.00 0.00 0.00 6.13
1843 3394 2.828549 GTGGGCAATAGGTGGGCG 60.829 66.667 0.00 0.00 0.00 6.13
1844 3395 1.754234 CTGTGGGCAATAGGTGGGC 60.754 63.158 0.00 0.00 0.00 5.36
1845 3396 1.754234 GCTGTGGGCAATAGGTGGG 60.754 63.158 0.00 0.00 41.35 4.61
1846 3397 2.114670 CGCTGTGGGCAATAGGTGG 61.115 63.158 0.00 0.00 41.91 4.61
1847 3398 1.369091 GACGCTGTGGGCAATAGGTG 61.369 60.000 0.00 0.00 41.91 4.00
1848 3399 1.078426 GACGCTGTGGGCAATAGGT 60.078 57.895 0.00 0.00 41.91 3.08
1849 3400 2.173669 CGACGCTGTGGGCAATAGG 61.174 63.158 0.00 0.00 41.91 2.57
1850 3401 1.421410 GACGACGCTGTGGGCAATAG 61.421 60.000 0.00 0.00 41.91 1.73
1851 3402 1.447140 GACGACGCTGTGGGCAATA 60.447 57.895 0.00 0.00 41.91 1.90
1852 3403 2.742372 GACGACGCTGTGGGCAAT 60.742 61.111 0.00 0.00 41.91 3.56
1856 3407 2.579241 CTAGACGACGACGCTGTGGG 62.579 65.000 7.30 0.00 43.96 4.61
1857 3408 1.226046 CTAGACGACGACGCTGTGG 60.226 63.158 7.30 0.00 43.96 4.17
1858 3409 1.226046 CCTAGACGACGACGCTGTG 60.226 63.158 7.30 4.03 43.96 3.66
1859 3410 3.036783 GCCTAGACGACGACGCTGT 62.037 63.158 7.30 0.00 43.96 4.40
1860 3411 2.277373 GCCTAGACGACGACGCTG 60.277 66.667 7.30 0.00 43.96 5.18
1861 3412 2.745100 TGCCTAGACGACGACGCT 60.745 61.111 7.30 8.20 43.96 5.07
1862 3413 2.277373 CTGCCTAGACGACGACGC 60.277 66.667 7.30 0.27 43.96 5.19
1863 3414 2.277373 GCTGCCTAGACGACGACG 60.277 66.667 5.58 5.58 45.75 5.12
1864 3415 1.226435 CTGCTGCCTAGACGACGAC 60.226 63.158 0.00 0.00 0.00 4.34
1865 3416 1.369839 CTCTGCTGCCTAGACGACGA 61.370 60.000 0.00 0.00 0.00 4.20
1866 3417 1.063327 CTCTGCTGCCTAGACGACG 59.937 63.158 0.00 0.00 0.00 5.12
1867 3418 1.316706 ACCTCTGCTGCCTAGACGAC 61.317 60.000 0.00 0.00 0.00 4.34
1868 3419 0.255033 TACCTCTGCTGCCTAGACGA 59.745 55.000 0.00 0.00 0.00 4.20
1869 3420 0.382515 GTACCTCTGCTGCCTAGACG 59.617 60.000 0.00 0.00 0.00 4.18
1870 3421 0.382515 CGTACCTCTGCTGCCTAGAC 59.617 60.000 0.00 0.00 0.00 2.59
1871 3422 1.384989 GCGTACCTCTGCTGCCTAGA 61.385 60.000 0.00 0.00 0.00 2.43
1872 3423 1.066587 GCGTACCTCTGCTGCCTAG 59.933 63.158 0.00 0.00 0.00 3.02
1873 3424 2.771639 CGCGTACCTCTGCTGCCTA 61.772 63.158 0.00 0.00 0.00 3.93
1874 3425 4.135153 CGCGTACCTCTGCTGCCT 62.135 66.667 0.00 0.00 0.00 4.75
1922 3473 1.043116 CAGGTCTCGTCCCCTGCATA 61.043 60.000 0.00 0.00 41.65 3.14
1987 3547 2.520069 GATCGGATCTTCTCCAGCCTA 58.480 52.381 10.73 0.00 45.24 3.93
2065 3634 1.374758 CTCGAGCAGTTGGACCACC 60.375 63.158 0.00 0.00 0.00 4.61
2088 3657 1.725665 CGGCGTATCTCCTCGTCAA 59.274 57.895 0.00 0.00 0.00 3.18
2240 3815 2.227089 GAGACGAGGTTGGGCGTGAT 62.227 60.000 0.00 0.00 41.34 3.06
2260 3835 1.667722 GTACCCGTCGTTGGACCTT 59.332 57.895 0.00 0.00 40.17 3.50
2291 3866 6.043854 AGAACTGAAATAGAAGGGAGTCAC 57.956 41.667 0.00 0.00 0.00 3.67
2311 3886 1.677576 CAAACTGGCAGCACTGAAGAA 59.322 47.619 15.89 0.00 0.00 2.52
2313 3888 1.311859 TCAAACTGGCAGCACTGAAG 58.688 50.000 15.89 0.73 0.00 3.02
2351 3935 1.464608 AGTTTGGACATGCGAATCACG 59.535 47.619 0.00 0.00 45.66 4.35
2513 4118 4.340950 ACTTCATTTTGTTGTACCCACAGG 59.659 41.667 0.00 0.00 35.67 4.00
2515 4120 6.038825 CACTACTTCATTTTGTTGTACCCACA 59.961 38.462 0.00 0.00 0.00 4.17
2516 4121 6.038936 ACACTACTTCATTTTGTTGTACCCAC 59.961 38.462 0.00 0.00 0.00 4.61
2517 4122 6.123651 ACACTACTTCATTTTGTTGTACCCA 58.876 36.000 0.00 0.00 0.00 4.51
2518 4123 6.628919 ACACTACTTCATTTTGTTGTACCC 57.371 37.500 0.00 0.00 0.00 3.69
2523 4128 8.641155 CATTGCATACACTACTTCATTTTGTTG 58.359 33.333 0.00 0.00 0.00 3.33
2658 4339 1.614241 ATCAGTTCGTTCCCTCCGGG 61.614 60.000 0.00 0.00 46.11 5.73
2681 4362 1.225855 GCATCGTGGTGAAACAGTGA 58.774 50.000 0.00 0.00 39.98 3.41
2710 4391 1.988834 GCCGGCAATTACCTTGGTCG 61.989 60.000 24.80 0.00 35.25 4.79
2735 4416 1.303888 ATCCCAGTGGTTGCTGCTG 60.304 57.895 8.74 0.00 35.28 4.41
2747 4432 2.704464 TTCTGCATCACTGATCCCAG 57.296 50.000 8.84 8.84 45.76 4.45
2750 4435 5.571784 TGAAAATTCTGCATCACTGATCC 57.428 39.130 0.00 0.00 0.00 3.36
2842 4532 7.095695 TCGATCAATACACTTGTCATGTAGA 57.904 36.000 0.00 0.00 36.04 2.59
2853 4543 1.618837 CCCCCGATCGATCAATACACT 59.381 52.381 24.40 0.00 0.00 3.55
2861 4551 2.480845 CAAAGTAACCCCCGATCGATC 58.519 52.381 18.66 15.68 0.00 3.69
2862 4552 1.140252 CCAAAGTAACCCCCGATCGAT 59.860 52.381 18.66 0.00 0.00 3.59
2863 4553 0.538118 CCAAAGTAACCCCCGATCGA 59.462 55.000 18.66 0.00 0.00 3.59
2864 4554 0.251073 ACCAAAGTAACCCCCGATCG 59.749 55.000 8.51 8.51 0.00 3.69
2984 4679 0.241213 CGAAGTCCTTGAGCTCGTCA 59.759 55.000 9.64 0.00 0.00 4.35
3139 4844 4.340666 TGTCAGTTTTAGCTTGGCATTCAA 59.659 37.500 0.00 0.00 0.00 2.69
3554 5266 1.155889 CGCCATGCTCACAACAAGTA 58.844 50.000 0.00 0.00 0.00 2.24
3672 5384 0.673644 CGGACTTCATCACCCGCTTT 60.674 55.000 0.00 0.00 35.29 3.51
3714 5429 4.926238 ACAATGCAAAAACACAGAAACGAA 59.074 33.333 0.00 0.00 0.00 3.85
3739 5455 2.365617 GGATAGCTTCCGTCAGATGGAA 59.634 50.000 21.07 21.07 40.78 3.53
3757 5473 1.472662 CGAACTAGCCATCCCCGGAT 61.473 60.000 0.73 0.00 34.81 4.18
3760 5476 1.968050 AACCGAACTAGCCATCCCCG 61.968 60.000 0.00 0.00 0.00 5.73
3811 5530 1.098050 GCATTCCAAATCAGGCTCGT 58.902 50.000 0.00 0.00 0.00 4.18
3828 5547 9.461312 ACCTTAAGAATGTTATTTACATCAGCA 57.539 29.630 3.36 0.00 46.75 4.41
3929 5799 2.584492 AAGCACCAGCAGAACAAAAC 57.416 45.000 0.00 0.00 45.49 2.43
3946 5823 6.483307 TGAAATATCATCGGCAGTCCTTAAAG 59.517 38.462 0.00 0.00 0.00 1.85
3955 5832 2.733552 CTCCGTGAAATATCATCGGCAG 59.266 50.000 12.06 8.55 43.64 4.85
3974 5854 3.715628 TTTGCAAGCTGAAACCTTCTC 57.284 42.857 0.00 0.00 0.00 2.87
3997 5886 8.982723 AGAGTATAAGCTAGGTCTTGAAAATGA 58.017 33.333 0.00 0.00 0.00 2.57
4054 5943 8.617290 AAAGTGAATCCTGTTAAGACGTTTAT 57.383 30.769 0.00 0.00 0.00 1.40
4087 5976 1.001487 GCACCCTTTTGCATTTTTGGC 60.001 47.619 0.00 0.00 42.49 4.52
4170 6425 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4171 6426 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4172 6427 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4173 6428 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
4174 6429 6.070194 ACATTCTTATATTATGGGACGGAGGG 60.070 42.308 0.00 0.00 0.00 4.30
4175 6430 6.947464 ACATTCTTATATTATGGGACGGAGG 58.053 40.000 0.00 0.00 0.00 4.30
4176 6431 8.848474 AAACATTCTTATATTATGGGACGGAG 57.152 34.615 0.00 0.00 0.00 4.63
4177 6432 9.635404 AAAAACATTCTTATATTATGGGACGGA 57.365 29.630 0.00 0.00 0.00 4.69
4178 6433 9.677567 CAAAAACATTCTTATATTATGGGACGG 57.322 33.333 0.00 0.00 0.00 4.79
4191 6446 9.826574 ACTACACTAGTGTCAAAAACATTCTTA 57.173 29.630 31.11 8.36 43.74 2.10
4192 6447 8.732746 ACTACACTAGTGTCAAAAACATTCTT 57.267 30.769 31.11 4.99 43.74 2.52
4207 6462 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
4221 6476 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
4222 6477 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
4223 6478 7.989416 TCTGTCCCAAAATATAAGAACGTTT 57.011 32.000 0.46 0.00 0.00 3.60
4224 6479 7.067008 CCATCTGTCCCAAAATATAAGAACGTT 59.933 37.037 0.00 0.00 0.00 3.99
4225 6480 6.542370 CCATCTGTCCCAAAATATAAGAACGT 59.458 38.462 0.00 0.00 0.00 3.99
4226 6481 6.765989 TCCATCTGTCCCAAAATATAAGAACG 59.234 38.462 0.00 0.00 0.00 3.95
4227 6482 7.775561 ACTCCATCTGTCCCAAAATATAAGAAC 59.224 37.037 0.00 0.00 0.00 3.01
4228 6483 7.872138 ACTCCATCTGTCCCAAAATATAAGAA 58.128 34.615 0.00 0.00 0.00 2.52
4229 6484 7.451731 ACTCCATCTGTCCCAAAATATAAGA 57.548 36.000 0.00 0.00 0.00 2.10
4230 6485 8.651389 TCTACTCCATCTGTCCCAAAATATAAG 58.349 37.037 0.00 0.00 0.00 1.73
4231 6486 8.561536 TCTACTCCATCTGTCCCAAAATATAA 57.438 34.615 0.00 0.00 0.00 0.98
4232 6487 8.597167 CATCTACTCCATCTGTCCCAAAATATA 58.403 37.037 0.00 0.00 0.00 0.86
4233 6488 7.456725 CATCTACTCCATCTGTCCCAAAATAT 58.543 38.462 0.00 0.00 0.00 1.28
4234 6489 6.183361 CCATCTACTCCATCTGTCCCAAAATA 60.183 42.308 0.00 0.00 0.00 1.40
4235 6490 5.398353 CCATCTACTCCATCTGTCCCAAAAT 60.398 44.000 0.00 0.00 0.00 1.82
4236 6491 4.080356 CCATCTACTCCATCTGTCCCAAAA 60.080 45.833 0.00 0.00 0.00 2.44
4237 6492 3.455910 CCATCTACTCCATCTGTCCCAAA 59.544 47.826 0.00 0.00 0.00 3.28
4238 6493 3.041211 CCATCTACTCCATCTGTCCCAA 58.959 50.000 0.00 0.00 0.00 4.12
4239 6494 2.247372 TCCATCTACTCCATCTGTCCCA 59.753 50.000 0.00 0.00 0.00 4.37
4240 6495 2.964209 TCCATCTACTCCATCTGTCCC 58.036 52.381 0.00 0.00 0.00 4.46
4241 6496 4.407296 AGTTTCCATCTACTCCATCTGTCC 59.593 45.833 0.00 0.00 0.00 4.02
4242 6497 5.606348 AGTTTCCATCTACTCCATCTGTC 57.394 43.478 0.00 0.00 0.00 3.51
4243 6498 7.126421 ACATAAGTTTCCATCTACTCCATCTGT 59.874 37.037 0.00 0.00 0.00 3.41
4244 6499 7.440556 CACATAAGTTTCCATCTACTCCATCTG 59.559 40.741 0.00 0.00 0.00 2.90
4245 6500 7.126421 ACACATAAGTTTCCATCTACTCCATCT 59.874 37.037 0.00 0.00 0.00 2.90
4246 6501 7.275920 ACACATAAGTTTCCATCTACTCCATC 58.724 38.462 0.00 0.00 0.00 3.51
4247 6502 7.200434 ACACATAAGTTTCCATCTACTCCAT 57.800 36.000 0.00 0.00 0.00 3.41
4248 6503 6.620877 ACACATAAGTTTCCATCTACTCCA 57.379 37.500 0.00 0.00 0.00 3.86
4249 6504 5.749109 CGACACATAAGTTTCCATCTACTCC 59.251 44.000 0.00 0.00 0.00 3.85
4250 6505 6.561614 TCGACACATAAGTTTCCATCTACTC 58.438 40.000 0.00 0.00 0.00 2.59
4251 6506 6.525578 TCGACACATAAGTTTCCATCTACT 57.474 37.500 0.00 0.00 0.00 2.57
4252 6507 6.978659 TCATCGACACATAAGTTTCCATCTAC 59.021 38.462 0.00 0.00 0.00 2.59
4374 6631 1.963515 GAAGTTTGGTGCATTGGGTCT 59.036 47.619 0.00 0.00 0.00 3.85
4382 6639 1.153066 TGCTCGGAAGTTTGGTGCA 60.153 52.632 0.00 0.00 0.00 4.57
4564 6822 5.570344 TCATTGCATGTTTTTGTTGCTTTG 58.430 33.333 0.00 0.00 37.28 2.77
4637 7926 5.865085 ACTTGAACTAGCCAGTTGATGTTA 58.135 37.500 1.07 0.00 45.18 2.41
4674 7968 6.861065 TGAGTTGTTTCCTTGATAGTGTTC 57.139 37.500 0.00 0.00 0.00 3.18
4679 7973 7.337689 TCCATTGATGAGTTGTTTCCTTGATAG 59.662 37.037 0.00 0.00 0.00 2.08
4742 8134 5.195940 CCTTTTGGGAGAGATGCTCAATTA 58.804 41.667 0.00 0.00 45.81 1.40


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

AutoCloner maintained by Alex Coulton.