Multiple sequence alignment - TraesCS4B01G348600

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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 TraesCS4B01G348600 chr4B 100.000 5649 0 0 1 5649 642096962 642102610 0.000000e+00 10432.0
1 TraesCS4B01G348600 chr4B 86.711 602 46 22 5071 5649 534344986 534344396 6.170000e-179 638.0
2 TraesCS4B01G348600 chr5A 94.604 2020 82 17 2735 4734 680086958 680088970 0.000000e+00 3101.0
3 TraesCS4B01G348600 chr5A 89.006 855 49 20 578 1423 680084815 680085633 0.000000e+00 1016.0
4 TraesCS4B01G348600 chr5A 90.089 787 54 7 1890 2655 680086124 680086907 0.000000e+00 1000.0
5 TraesCS4B01G348600 chr5A 93.023 301 19 2 4770 5068 680088975 680089275 6.720000e-119 438.0
6 TraesCS4B01G348600 chr5A 83.621 232 24 10 201 421 680083989 680084217 7.420000e-49 206.0
7 TraesCS4B01G348600 chr5A 86.986 146 17 2 1499 1643 680085640 680085784 4.530000e-36 163.0
8 TraesCS4B01G348600 chr4D 95.079 1260 46 7 2744 3992 499303889 499305143 0.000000e+00 1969.0
9 TraesCS4B01G348600 chr4D 95.338 1094 46 5 3977 5068 499305228 499306318 0.000000e+00 1733.0
10 TraesCS4B01G348600 chr4D 87.403 770 52 17 1962 2700 499303116 499303871 0.000000e+00 843.0
11 TraesCS4B01G348600 chr4D 90.955 597 26 15 661 1237 499302184 499302772 0.000000e+00 778.0
12 TraesCS4B01G348600 chr4D 88.556 367 23 8 1512 1864 499302756 499303117 1.450000e-115 427.0
13 TraesCS4B01G348600 chr4D 88.793 348 34 5 43 387 499300619 499300964 6.770000e-114 422.0
14 TraesCS4B01G348600 chr7A 85.179 1201 126 31 3488 4644 251839177 251840369 0.000000e+00 1184.0
15 TraesCS4B01G348600 chr7A 90.947 243 16 1 2741 2977 251838342 251838584 7.060000e-84 322.0
16 TraesCS4B01G348600 chr7A 77.281 537 80 28 2120 2632 62825024 62825542 1.550000e-70 278.0
17 TraesCS4B01G348600 chr7A 85.484 248 21 5 2740 2972 62825637 62825884 1.570000e-60 244.0
18 TraesCS4B01G348600 chr7A 91.026 156 12 1 2485 2638 251838117 251838272 5.740000e-50 209.0
19 TraesCS4B01G348600 chr7A 91.333 150 13 0 3259 3408 251838914 251839063 7.420000e-49 206.0
20 TraesCS4B01G348600 chr7A 77.397 292 52 10 2154 2436 251836819 251837105 1.630000e-35 161.0
21 TraesCS4B01G348600 chr7A 92.079 101 5 1 3062 3162 251838693 251838790 7.630000e-29 139.0
22 TraesCS4B01G348600 chr7A 84.828 145 10 2 984 1125 62824431 62824566 9.870000e-28 135.0
23 TraesCS4B01G348600 chr7D 85.441 941 106 19 3797 4715 236688937 236689868 0.000000e+00 950.0
24 TraesCS4B01G348600 chr7D 84.983 879 114 14 3805 4669 58483003 58483877 0.000000e+00 876.0
25 TraesCS4B01G348600 chr7D 80.876 502 61 24 2496 2972 58482094 58482585 4.160000e-96 363.0
26 TraesCS4B01G348600 chr7D 82.483 451 44 18 2741 3162 236687745 236688189 4.160000e-96 363.0
27 TraesCS4B01G348600 chr7D 81.235 421 52 17 892 1301 236686317 236686721 1.180000e-81 315.0
28 TraesCS4B01G348600 chr7D 91.503 153 10 2 3259 3408 236688317 236688469 2.060000e-49 207.0
29 TraesCS4B01G348600 chr7D 92.199 141 11 0 2496 2636 236687527 236687667 3.450000e-47 200.0
30 TraesCS4B01G348600 chr7D 84.459 148 8 8 984 1125 58480883 58481021 1.280000e-26 132.0
31 TraesCS4B01G348600 chr7D 87.755 98 12 0 2345 2442 58481679 58481776 1.290000e-21 115.0
32 TraesCS4B01G348600 chr7D 88.506 87 10 0 3074 3160 58482584 58482670 7.740000e-19 106.0
33 TraesCS4B01G348600 chr7D 80.597 134 22 2 2124 2257 58481475 58481604 3.600000e-17 100.0
34 TraesCS4B01G348600 chr4A 86.427 862 96 15 3805 4652 674909032 674909886 0.000000e+00 924.0
35 TraesCS4B01G348600 chr4A 84.642 853 111 15 3803 4649 674925036 674925874 0.000000e+00 832.0
36 TraesCS4B01G348600 chr4A 81.994 311 41 13 2336 2632 674918446 674918755 3.380000e-62 250.0
37 TraesCS4B01G348600 chr4A 86.449 214 14 7 2781 2979 674918891 674919104 2.650000e-53 220.0
38 TraesCS4B01G348600 chr4A 88.356 146 17 0 3270 3415 674919312 674919457 5.820000e-40 176.0
39 TraesCS4B01G348600 chr4A 82.609 138 22 1 2120 2257 674907772 674907907 2.760000e-23 121.0
40 TraesCS4B01G348600 chr4A 89.655 87 9 0 3074 3160 674908613 674908699 1.660000e-20 111.0
41 TraesCS4B01G348600 chr4A 80.272 147 20 5 980 1123 674917848 674917988 1.000000e-17 102.0
42 TraesCS4B01G348600 chr4A 79.048 105 22 0 2153 2257 674918236 674918340 7.850000e-09 73.1
43 TraesCS4B01G348600 chr7B 85.320 906 107 17 3787 4669 213417573 213418475 0.000000e+00 913.0
44 TraesCS4B01G348600 chr7B 79.215 688 70 40 2346 2982 213394184 213394849 1.460000e-110 411.0
45 TraesCS4B01G348600 chr7B 89.610 231 20 4 3488 3715 213417163 213417392 1.990000e-74 291.0
46 TraesCS4B01G348600 chr7B 92.157 153 9 2 3259 3408 213416901 213417053 4.430000e-51 213.0
47 TraesCS4B01G348600 chr7B 89.744 117 11 1 2144 2259 213393976 213394092 1.270000e-31 148.0
48 TraesCS4B01G348600 chr7B 93.333 90 6 0 3073 3162 213416672 213416761 3.550000e-27 134.0
49 TraesCS4B01G348600 chr1D 89.748 634 62 3 4026 4658 467519435 467518804 0.000000e+00 808.0
50 TraesCS4B01G348600 chr1D 81.798 445 67 13 3501 3941 467519936 467519502 1.500000e-95 361.0
51 TraesCS4B01G348600 chr1D 80.137 438 53 17 2740 3159 467520688 467520267 4.280000e-76 296.0
52 TraesCS4B01G348600 chr1D 84.239 184 17 5 1012 1192 467521752 467521578 9.730000e-38 169.0
53 TraesCS4B01G348600 chr1B 89.715 632 63 2 4031 4661 645347796 645347166 0.000000e+00 806.0
54 TraesCS4B01G348600 chr1B 87.755 588 56 11 5067 5649 113646057 113645481 0.000000e+00 673.0
55 TraesCS4B01G348600 chr1B 87.895 190 14 4 1006 1195 645350230 645350050 1.230000e-51 215.0
56 TraesCS4B01G348600 chr1B 90.476 147 9 5 2494 2638 645349358 645349215 7.470000e-44 189.0
57 TraesCS4B01G348600 chr1B 91.241 137 12 0 3800 3936 645348037 645347901 2.690000e-43 187.0
58 TraesCS4B01G348600 chr3B 90.395 583 39 9 5064 5638 666846311 666846884 0.000000e+00 750.0
59 TraesCS4B01G348600 chr3B 88.406 552 40 17 5110 5649 143069077 143069616 1.330000e-180 643.0
60 TraesCS4B01G348600 chr5B 89.376 593 44 11 5066 5649 680391839 680391257 0.000000e+00 728.0
61 TraesCS4B01G348600 chr5B 89.402 585 41 9 5068 5649 680371070 680370504 0.000000e+00 717.0
62 TraesCS4B01G348600 chr5B 86.733 603 46 20 5066 5649 153543226 153542639 1.720000e-179 640.0
63 TraesCS4B01G348600 chr5B 86.418 589 66 9 5066 5649 677625262 677625841 2.870000e-177 632.0
64 TraesCS4B01G348600 chr2B 86.409 596 62 11 5066 5649 404217571 404216983 7.980000e-178 634.0
65 TraesCS4B01G348600 chr2B 97.500 40 1 0 1 40 160728143 160728182 1.020000e-07 69.4
66 TraesCS4B01G348600 chr1A 81.124 445 68 11 3501 3941 560468762 560469194 5.420000e-90 342.0
67 TraesCS4B01G348600 chr1A 80.543 442 52 18 2737 3159 560467999 560468425 5.500000e-80 309.0
68 TraesCS4B01G348600 chr1A 75.728 515 82 28 2149 2638 560467438 560467934 9.530000e-53 219.0
69 TraesCS4B01G348600 chr1A 87.766 188 14 4 1005 1192 560466263 560466441 1.590000e-50 211.0
70 TraesCS4B01G348600 chr1A 88.435 147 17 0 3259 3405 560468493 560468639 1.620000e-40 178.0


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 TraesCS4B01G348600 chr4B 642096962 642102610 5648 False 10432.000000 10432 100.000000 1 5649 1 chr4B.!!$F1 5648
1 TraesCS4B01G348600 chr4B 534344396 534344986 590 True 638.000000 638 86.711000 5071 5649 1 chr4B.!!$R1 578
2 TraesCS4B01G348600 chr5A 680083989 680089275 5286 False 987.333333 3101 89.554833 201 5068 6 chr5A.!!$F1 4867
3 TraesCS4B01G348600 chr4D 499300619 499306318 5699 False 1028.666667 1969 91.020667 43 5068 6 chr4D.!!$F1 5025
4 TraesCS4B01G348600 chr7A 251836819 251840369 3550 False 370.166667 1184 87.993500 2154 4644 6 chr7A.!!$F2 2490
5 TraesCS4B01G348600 chr7A 62824431 62825884 1453 False 219.000000 278 82.531000 984 2972 3 chr7A.!!$F1 1988
6 TraesCS4B01G348600 chr7D 236686317 236689868 3551 False 407.000000 950 86.572200 892 4715 5 chr7D.!!$F2 3823
7 TraesCS4B01G348600 chr7D 58480883 58483877 2994 False 282.000000 876 84.529333 984 4669 6 chr7D.!!$F1 3685
8 TraesCS4B01G348600 chr4A 674925036 674925874 838 False 832.000000 832 84.642000 3803 4649 1 chr4A.!!$F1 846
9 TraesCS4B01G348600 chr4A 674907772 674909886 2114 False 385.333333 924 86.230333 2120 4652 3 chr4A.!!$F2 2532
10 TraesCS4B01G348600 chr7B 213416672 213418475 1803 False 387.750000 913 90.105000 3073 4669 4 chr7B.!!$F2 1596
11 TraesCS4B01G348600 chr7B 213393976 213394849 873 False 279.500000 411 84.479500 2144 2982 2 chr7B.!!$F1 838
12 TraesCS4B01G348600 chr1D 467518804 467521752 2948 True 408.500000 808 83.980500 1012 4658 4 chr1D.!!$R1 3646
13 TraesCS4B01G348600 chr1B 113645481 113646057 576 True 673.000000 673 87.755000 5067 5649 1 chr1B.!!$R1 582
14 TraesCS4B01G348600 chr1B 645347166 645350230 3064 True 349.250000 806 89.831750 1006 4661 4 chr1B.!!$R2 3655
15 TraesCS4B01G348600 chr3B 666846311 666846884 573 False 750.000000 750 90.395000 5064 5638 1 chr3B.!!$F2 574
16 TraesCS4B01G348600 chr3B 143069077 143069616 539 False 643.000000 643 88.406000 5110 5649 1 chr3B.!!$F1 539
17 TraesCS4B01G348600 chr5B 680391257 680391839 582 True 728.000000 728 89.376000 5066 5649 1 chr5B.!!$R3 583
18 TraesCS4B01G348600 chr5B 680370504 680371070 566 True 717.000000 717 89.402000 5068 5649 1 chr5B.!!$R2 581
19 TraesCS4B01G348600 chr5B 153542639 153543226 587 True 640.000000 640 86.733000 5066 5649 1 chr5B.!!$R1 583
20 TraesCS4B01G348600 chr5B 677625262 677625841 579 False 632.000000 632 86.418000 5066 5649 1 chr5B.!!$F1 583
21 TraesCS4B01G348600 chr2B 404216983 404217571 588 True 634.000000 634 86.409000 5066 5649 1 chr2B.!!$R1 583
22 TraesCS4B01G348600 chr1A 560466263 560469194 2931 False 251.800000 342 82.719200 1005 3941 5 chr1A.!!$F1 2936

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
326 335 0.107703 ATGGCACGTGTTGATCGGAT 60.108 50.000 18.38 0.00 0.00 4.18 F
640 1909 1.069227 TGTCACGTCAGTCGATGTCAG 60.069 52.381 0.00 0.00 39.45 3.51 F
1463 2802 0.107897 TGGTAACCACATAGCGCTGG 60.108 55.000 22.90 16.55 0.00 4.85 F
1483 2822 0.319211 CGCTACTCACACGTTGGGAA 60.319 55.000 4.88 0.00 0.00 3.97 F
1970 3553 0.676466 TCATAGTTGCACCGGCTTGG 60.676 55.000 0.00 0.00 46.41 3.61 F
2720 6496 0.729140 GAAATTGTGAGCGCCCGTTG 60.729 55.000 2.29 0.00 0.00 4.10 F
3695 7763 1.216178 CCCATCAGCGCCAAAAAGG 59.784 57.895 2.29 0.00 41.84 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 2783 0.107897 CCAGCGCTATGTGGTTACCA 60.108 55.0 10.99 0.0 0.00 3.25 R
2311 4741 0.252881 AGCCAGAGGATCCAACAGGA 60.253 55.0 15.82 0.0 33.66 3.86 R
3063 7003 0.320374 CCGGCTCGCCTGGATAATAA 59.680 55.0 11.67 0.0 33.64 1.40 R
3428 7447 0.718904 TTGTCATGCGTGCGATACAC 59.281 50.0 0.00 0.0 46.45 2.90 R
3631 7699 0.322816 ACTGCGAGAGGTACCCGTTA 60.323 55.0 8.74 0.0 0.00 3.18 R
4333 8731 1.599606 CGCACTGGCTCTGGTAGAGT 61.600 60.0 7.59 0.0 44.12 3.24 R
5594 10036 0.105709 CCCTCTCCCTCTCCTTCCTC 60.106 65.0 0.00 0.0 0.00 3.71 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
18 19 3.625314 AGTTTGCCCCCAGTCAAAA 57.375 47.368 0.00 0.00 34.44 2.44
19 20 2.101640 AGTTTGCCCCCAGTCAAAAT 57.898 45.000 0.00 0.00 34.44 1.82
20 21 3.252554 AGTTTGCCCCCAGTCAAAATA 57.747 42.857 0.00 0.00 34.44 1.40
21 22 2.897326 AGTTTGCCCCCAGTCAAAATAC 59.103 45.455 0.00 0.00 34.44 1.89
22 23 2.897326 GTTTGCCCCCAGTCAAAATACT 59.103 45.455 0.00 0.00 34.44 2.12
23 24 2.507407 TGCCCCCAGTCAAAATACTC 57.493 50.000 0.00 0.00 0.00 2.59
24 25 1.005450 TGCCCCCAGTCAAAATACTCC 59.995 52.381 0.00 0.00 0.00 3.85
25 26 1.685180 GCCCCCAGTCAAAATACTCCC 60.685 57.143 0.00 0.00 0.00 4.30
26 27 1.923148 CCCCCAGTCAAAATACTCCCT 59.077 52.381 0.00 0.00 0.00 4.20
27 28 3.120108 CCCCCAGTCAAAATACTCCCTA 58.880 50.000 0.00 0.00 0.00 3.53
28 29 3.136626 CCCCCAGTCAAAATACTCCCTAG 59.863 52.174 0.00 0.00 0.00 3.02
29 30 3.136626 CCCCAGTCAAAATACTCCCTAGG 59.863 52.174 0.06 0.06 0.00 3.02
30 31 3.780850 CCCAGTCAAAATACTCCCTAGGT 59.219 47.826 8.29 0.00 0.00 3.08
31 32 4.141688 CCCAGTCAAAATACTCCCTAGGTC 60.142 50.000 8.29 0.00 0.00 3.85
32 33 4.141688 CCAGTCAAAATACTCCCTAGGTCC 60.142 50.000 8.29 0.00 0.00 4.46
33 34 3.705072 AGTCAAAATACTCCCTAGGTCCG 59.295 47.826 8.29 0.00 0.00 4.79
34 35 2.433239 TCAAAATACTCCCTAGGTCCGC 59.567 50.000 8.29 0.00 0.00 5.54
35 36 1.421480 AAATACTCCCTAGGTCCGCC 58.579 55.000 8.29 0.00 0.00 6.13
36 37 0.263765 AATACTCCCTAGGTCCGCCA 59.736 55.000 8.29 0.00 37.19 5.69
37 38 0.469518 ATACTCCCTAGGTCCGCCAC 60.470 60.000 8.29 0.00 37.19 5.01
38 39 1.578215 TACTCCCTAGGTCCGCCACT 61.578 60.000 8.29 0.00 37.19 4.00
39 40 2.363795 TCCCTAGGTCCGCCACTG 60.364 66.667 8.29 0.00 37.19 3.66
40 41 2.363795 CCCTAGGTCCGCCACTGA 60.364 66.667 8.29 0.00 37.19 3.41
41 42 1.762460 CCCTAGGTCCGCCACTGAT 60.762 63.158 8.29 0.00 37.19 2.90
42 43 1.443407 CCTAGGTCCGCCACTGATG 59.557 63.158 0.00 0.00 37.19 3.07
94 95 2.877691 GGAAGCGATGTTGCCACC 59.122 61.111 0.00 0.00 34.65 4.61
95 96 1.675641 GGAAGCGATGTTGCCACCT 60.676 57.895 0.00 0.00 34.65 4.00
113 114 4.202503 CCACCTGGATTGGAGTAGCATATT 60.203 45.833 0.00 0.00 36.02 1.28
114 115 5.380043 CACCTGGATTGGAGTAGCATATTT 58.620 41.667 0.00 0.00 0.00 1.40
143 144 2.183300 GTCGGTGCCACGATGCTA 59.817 61.111 3.12 0.00 45.47 3.49
147 148 1.220749 GGTGCCACGATGCTAGGAA 59.779 57.895 0.00 0.00 0.00 3.36
160 161 2.105806 CTAGGAATGGAGGAGGGCGC 62.106 65.000 0.00 0.00 0.00 6.53
161 162 2.605535 TAGGAATGGAGGAGGGCGCT 62.606 60.000 7.64 1.38 0.00 5.92
189 190 3.051581 AGCAGTGTATGAAGGATGGGAT 58.948 45.455 0.00 0.00 0.00 3.85
192 193 4.139786 CAGTGTATGAAGGATGGGATTGG 58.860 47.826 0.00 0.00 0.00 3.16
208 209 3.838271 GGCGATGGTGGAGCGAGA 61.838 66.667 0.00 0.00 34.57 4.04
254 256 2.838202 GAGGTGTGTGGGGAGAAGAATA 59.162 50.000 0.00 0.00 0.00 1.75
257 259 3.054361 GGTGTGTGGGGAGAAGAATACAT 60.054 47.826 0.00 0.00 0.00 2.29
258 260 3.941483 GTGTGTGGGGAGAAGAATACATG 59.059 47.826 0.00 0.00 0.00 3.21
270 272 8.041323 GGAGAAGAATACATGTGGTCTAGAAAA 58.959 37.037 9.11 0.00 0.00 2.29
271 273 8.779354 AGAAGAATACATGTGGTCTAGAAAAC 57.221 34.615 9.11 0.00 0.00 2.43
280 285 5.996644 TGTGGTCTAGAAAACTTTGGAGAA 58.003 37.500 0.00 0.00 0.00 2.87
301 306 1.673626 GGATAACGTTGCTTCGGTGGA 60.674 52.381 11.99 0.00 34.94 4.02
311 316 1.372087 CTTCGGTGGAGCTCAATGGC 61.372 60.000 17.19 0.00 0.00 4.40
317 326 1.672356 GGAGCTCAATGGCACGTGT 60.672 57.895 18.38 0.00 34.17 4.49
323 332 0.795698 TCAATGGCACGTGTTGATCG 59.204 50.000 18.38 2.13 0.00 3.69
326 335 0.107703 ATGGCACGTGTTGATCGGAT 60.108 50.000 18.38 0.00 0.00 4.18
408 449 7.589954 ACTTTACGAGTTGAACATAATTTGTGC 59.410 33.333 0.00 0.00 34.94 4.57
409 450 5.431420 ACGAGTTGAACATAATTTGTGCA 57.569 34.783 0.00 0.00 42.48 4.57
410 451 6.012658 ACGAGTTGAACATAATTTGTGCAT 57.987 33.333 0.00 0.00 43.67 3.96
411 452 5.858049 ACGAGTTGAACATAATTTGTGCATG 59.142 36.000 0.00 0.00 43.67 4.06
412 453 6.085573 CGAGTTGAACATAATTTGTGCATGA 58.914 36.000 0.00 0.00 43.67 3.07
413 454 6.249893 CGAGTTGAACATAATTTGTGCATGAG 59.750 38.462 0.00 0.00 43.67 2.90
414 455 5.865552 AGTTGAACATAATTTGTGCATGAGC 59.134 36.000 0.00 0.00 43.67 4.26
467 508 8.877808 TGAGCATCACTACTTTGAGTATAATG 57.122 34.615 0.00 0.00 42.56 1.90
468 509 8.478066 TGAGCATCACTACTTTGAGTATAATGT 58.522 33.333 0.00 0.00 42.56 2.71
469 510 8.654230 AGCATCACTACTTTGAGTATAATGTG 57.346 34.615 0.00 0.00 29.08 3.21
470 511 8.478066 AGCATCACTACTTTGAGTATAATGTGA 58.522 33.333 9.09 9.09 36.92 3.58
491 532 6.236017 TGAACTAAGTTCAGTATTTTGGCG 57.764 37.500 0.00 0.00 45.88 5.69
640 1909 1.069227 TGTCACGTCAGTCGATGTCAG 60.069 52.381 0.00 0.00 39.45 3.51
649 1918 7.379797 CACGTCAGTCGATGTCAGATAATAAAT 59.620 37.037 0.00 0.00 39.45 1.40
658 1927 8.611757 CGATGTCAGATAATAAATGTTGTCCAA 58.388 33.333 0.00 0.00 0.00 3.53
701 1970 5.163301 ACAAATAGATAATGGAGCACGAGGT 60.163 40.000 0.00 0.00 0.00 3.85
762 2031 3.195698 GGGATGACGTGCTTCGCC 61.196 66.667 0.00 0.00 44.19 5.54
821 2091 2.034305 CCGCTACCACATGGAGTAGTAC 59.966 54.545 19.63 0.00 38.57 2.73
824 2094 4.760715 CGCTACCACATGGAGTAGTACTAT 59.239 45.833 19.63 0.00 38.57 2.12
825 2095 5.334957 CGCTACCACATGGAGTAGTACTATG 60.335 48.000 19.63 7.12 38.57 2.23
826 2096 5.535406 GCTACCACATGGAGTAGTACTATGT 59.465 44.000 19.63 11.41 39.36 2.29
827 2097 6.713903 GCTACCACATGGAGTAGTACTATGTA 59.286 42.308 15.29 3.75 37.35 2.29
869 2149 4.802051 CACTGTGATGGCCCCGGG 62.802 72.222 15.80 15.80 0.00 5.73
952 2233 4.275508 CACCAGCCTGGGCACAGT 62.276 66.667 16.38 0.00 43.37 3.55
965 2246 2.925170 ACAGTGGAAGGAGCGGCT 60.925 61.111 0.00 0.00 0.00 5.52
1224 2547 9.823098 GCTAATTGATCAGCTACTTTATCAATG 57.177 33.333 15.37 9.15 44.33 2.82
1245 2568 4.693283 TGTTTATCTGCCTAATCTGACCG 58.307 43.478 0.00 0.00 0.00 4.79
1256 2579 1.475403 ATCTGACCGACGGAACAGAT 58.525 50.000 33.03 33.03 41.21 2.90
1266 2592 3.182967 GACGGAACAGATAACAGCTCTG 58.817 50.000 0.00 0.00 44.60 3.35
1340 2673 3.257393 CACAGTGTGCTAGTTGGATCTC 58.743 50.000 10.97 0.00 0.00 2.75
1341 2674 2.899900 ACAGTGTGCTAGTTGGATCTCA 59.100 45.455 0.00 0.00 0.00 3.27
1342 2675 3.257393 CAGTGTGCTAGTTGGATCTCAC 58.743 50.000 0.00 0.00 0.00 3.51
1354 2693 3.994317 TGGATCTCACTACATCCAAGGA 58.006 45.455 0.00 0.00 44.68 3.36
1361 2700 4.160329 TCACTACATCCAAGGACAGAACT 58.840 43.478 0.00 0.00 0.00 3.01
1369 2708 4.134563 TCCAAGGACAGAACTAGCAAAAC 58.865 43.478 0.00 0.00 0.00 2.43
1371 2710 4.023707 CCAAGGACAGAACTAGCAAAACAG 60.024 45.833 0.00 0.00 0.00 3.16
1373 2712 5.546621 AGGACAGAACTAGCAAAACAGTA 57.453 39.130 0.00 0.00 0.00 2.74
1375 2714 5.070580 AGGACAGAACTAGCAAAACAGTACT 59.929 40.000 0.00 0.00 0.00 2.73
1415 2754 8.925161 ATAACACGGAAATTTGATGTATTTGG 57.075 30.769 0.00 0.00 0.00 3.28
1416 2755 6.582677 ACACGGAAATTTGATGTATTTGGA 57.417 33.333 0.00 0.00 0.00 3.53
1417 2756 6.386654 ACACGGAAATTTGATGTATTTGGAC 58.613 36.000 0.00 0.00 0.00 4.02
1418 2757 6.208599 ACACGGAAATTTGATGTATTTGGACT 59.791 34.615 0.00 0.00 0.00 3.85
1420 2759 8.405531 CACGGAAATTTGATGTATTTGGACTAT 58.594 33.333 0.00 0.00 0.00 2.12
1421 2760 9.621629 ACGGAAATTTGATGTATTTGGACTATA 57.378 29.630 0.00 0.00 0.00 1.31
1438 2777 9.725019 TTGGACTATAAATCTATAATGGTGCTG 57.275 33.333 0.00 0.00 0.00 4.41
1439 2778 7.824289 TGGACTATAAATCTATAATGGTGCTGC 59.176 37.037 0.00 0.00 0.00 5.25
1440 2779 8.043710 GGACTATAAATCTATAATGGTGCTGCT 58.956 37.037 0.00 0.00 0.00 4.24
1445 2784 7.502120 AAATCTATAATGGTGCTGCTAAGTG 57.498 36.000 0.00 0.00 0.00 3.16
1446 2785 4.960938 TCTATAATGGTGCTGCTAAGTGG 58.039 43.478 0.00 0.00 0.00 4.00
1447 2786 3.652057 ATAATGGTGCTGCTAAGTGGT 57.348 42.857 0.00 0.00 0.00 4.16
1448 2787 4.771114 ATAATGGTGCTGCTAAGTGGTA 57.229 40.909 0.00 0.00 0.00 3.25
1449 2788 3.433306 AATGGTGCTGCTAAGTGGTAA 57.567 42.857 0.00 0.00 0.00 2.85
1450 2789 2.178912 TGGTGCTGCTAAGTGGTAAC 57.821 50.000 0.00 0.00 0.00 2.50
1451 2790 1.271163 TGGTGCTGCTAAGTGGTAACC 60.271 52.381 0.00 0.00 0.00 2.85
1452 2791 1.271163 GGTGCTGCTAAGTGGTAACCA 60.271 52.381 0.00 0.00 0.00 3.67
1462 2801 3.451793 TGGTAACCACATAGCGCTG 57.548 52.632 22.90 7.81 0.00 5.18
1463 2802 0.107897 TGGTAACCACATAGCGCTGG 60.108 55.000 22.90 16.55 0.00 4.85
1464 2803 1.436983 GGTAACCACATAGCGCTGGC 61.437 60.000 22.90 0.35 40.37 4.85
1465 2804 1.520564 TAACCACATAGCGCTGGCG 60.521 57.895 22.90 10.73 46.35 5.69
1475 2814 3.181967 CGCTGGCGCTACTCACAC 61.182 66.667 7.64 0.00 0.00 3.82
1476 2815 3.181967 GCTGGCGCTACTCACACG 61.182 66.667 7.64 0.00 0.00 4.49
1477 2816 2.258591 CTGGCGCTACTCACACGT 59.741 61.111 7.64 0.00 0.00 4.49
1478 2817 1.372997 CTGGCGCTACTCACACGTT 60.373 57.895 7.64 0.00 0.00 3.99
1479 2818 1.617755 CTGGCGCTACTCACACGTTG 61.618 60.000 7.64 0.00 0.00 4.10
1480 2819 2.380410 GGCGCTACTCACACGTTGG 61.380 63.158 7.64 0.00 0.00 3.77
1481 2820 2.380410 GCGCTACTCACACGTTGGG 61.380 63.158 0.00 0.00 0.00 4.12
1482 2821 1.287815 CGCTACTCACACGTTGGGA 59.712 57.895 4.88 0.00 0.00 4.37
1483 2822 0.319211 CGCTACTCACACGTTGGGAA 60.319 55.000 4.88 0.00 0.00 3.97
1484 2823 1.671850 CGCTACTCACACGTTGGGAAT 60.672 52.381 4.88 0.00 0.00 3.01
1485 2824 2.423577 GCTACTCACACGTTGGGAATT 58.576 47.619 4.88 0.00 0.00 2.17
1486 2825 2.812011 GCTACTCACACGTTGGGAATTT 59.188 45.455 4.88 0.00 0.00 1.82
1487 2826 3.252458 GCTACTCACACGTTGGGAATTTT 59.748 43.478 4.88 0.00 0.00 1.82
1488 2827 3.708563 ACTCACACGTTGGGAATTTTG 57.291 42.857 4.88 0.00 0.00 2.44
1489 2828 3.283751 ACTCACACGTTGGGAATTTTGA 58.716 40.909 4.88 0.00 0.00 2.69
1490 2829 3.315191 ACTCACACGTTGGGAATTTTGAG 59.685 43.478 4.88 0.00 36.20 3.02
1491 2830 3.546724 TCACACGTTGGGAATTTTGAGA 58.453 40.909 0.00 0.00 0.00 3.27
1492 2831 3.563808 TCACACGTTGGGAATTTTGAGAG 59.436 43.478 0.00 0.00 0.00 3.20
1493 2832 2.293399 ACACGTTGGGAATTTTGAGAGC 59.707 45.455 0.00 0.00 0.00 4.09
1494 2833 2.293122 CACGTTGGGAATTTTGAGAGCA 59.707 45.455 0.00 0.00 0.00 4.26
1495 2834 2.554032 ACGTTGGGAATTTTGAGAGCAG 59.446 45.455 0.00 0.00 0.00 4.24
1496 2835 2.813754 CGTTGGGAATTTTGAGAGCAGA 59.186 45.455 0.00 0.00 0.00 4.26
1497 2836 3.365364 CGTTGGGAATTTTGAGAGCAGAC 60.365 47.826 0.00 0.00 0.00 3.51
1541 2881 4.579869 TCTGTCCTAGTTCATTTGCTTCC 58.420 43.478 0.00 0.00 0.00 3.46
1621 3017 3.959535 ATTGAATGGCCGACACAAAAT 57.040 38.095 0.00 0.00 0.00 1.82
1634 3030 5.448438 CGACACAAAATTGCTAAGCTTACA 58.552 37.500 0.86 3.49 0.00 2.41
1704 3246 8.298140 AGTAATCTTATCCGTCTGTAGCATTAC 58.702 37.037 0.00 0.00 0.00 1.89
1708 3250 1.136305 TCCGTCTGTAGCATTACTGGC 59.864 52.381 0.00 0.00 32.04 4.85
1773 3315 4.074970 GCCACTTGTCCATTAGATATGGG 58.925 47.826 4.10 0.00 39.60 4.00
1797 3339 1.254026 CTCCCCTCACTACGTGACAA 58.746 55.000 0.00 0.00 37.67 3.18
1865 3407 3.496884 TGCTTGTTTACGAATCAGGACAC 59.503 43.478 0.00 0.00 0.00 3.67
1872 3414 1.000955 ACGAATCAGGACACTGTCACC 59.999 52.381 11.34 0.00 45.14 4.02
1873 3415 1.000843 CGAATCAGGACACTGTCACCA 59.999 52.381 11.34 0.00 45.14 4.17
1885 3427 1.594293 GTCACCATGGATACGCCGG 60.594 63.158 21.47 0.00 40.66 6.13
1921 3504 3.875727 GCTGATTCTGTGCATGTGTAGAT 59.124 43.478 0.00 0.00 0.00 1.98
1937 3520 7.144722 TGTGTAGATAACAAAAGGCATCTTG 57.855 36.000 0.00 0.00 40.63 3.02
1969 3552 0.729116 CTCATAGTTGCACCGGCTTG 59.271 55.000 0.00 0.00 41.91 4.01
1970 3553 0.676466 TCATAGTTGCACCGGCTTGG 60.676 55.000 0.00 0.00 46.41 3.61
2015 3910 5.523552 ACATAAAAGCCAAAAGAAAGTGCAC 59.476 36.000 9.40 9.40 0.00 4.57
2020 3915 3.684305 AGCCAAAAGAAAGTGCACAAAAC 59.316 39.130 21.04 7.39 0.00 2.43
2094 4318 8.824159 ATCATCTACTACATGACATAAACAGC 57.176 34.615 0.00 0.00 33.04 4.40
2103 4327 6.051717 ACATGACATAAACAGCAGGTAGATC 58.948 40.000 0.00 0.00 0.00 2.75
2104 4328 4.682787 TGACATAAACAGCAGGTAGATCG 58.317 43.478 0.00 0.00 0.00 3.69
2105 4329 4.401202 TGACATAAACAGCAGGTAGATCGA 59.599 41.667 0.00 0.00 0.00 3.59
2106 4330 4.938080 ACATAAACAGCAGGTAGATCGAG 58.062 43.478 0.00 0.00 0.00 4.04
2110 4533 5.599999 AAACAGCAGGTAGATCGAGTAAT 57.400 39.130 0.00 0.00 0.00 1.89
2114 4537 6.505272 ACAGCAGGTAGATCGAGTAATAAAC 58.495 40.000 0.00 0.00 0.00 2.01
2117 4540 7.653713 CAGCAGGTAGATCGAGTAATAAACAAT 59.346 37.037 0.00 0.00 0.00 2.71
2118 4541 7.653713 AGCAGGTAGATCGAGTAATAAACAATG 59.346 37.037 0.00 0.00 0.00 2.82
2144 4567 7.784633 ATCTAAGCAACTCAGAATTTAGAGC 57.215 36.000 7.71 0.00 35.28 4.09
2147 4570 5.157940 AGCAACTCAGAATTTAGAGCTGA 57.842 39.130 12.80 5.09 37.17 4.26
2166 4591 2.200067 GAATGCATCTGACAGGACGAG 58.800 52.381 0.00 0.00 0.00 4.18
2259 4684 2.285083 CCCGCCGATTTCATGTAAGAA 58.715 47.619 0.00 0.00 0.00 2.52
2292 4718 6.602410 TGACATTCCAAATTTCCAAGCATA 57.398 33.333 0.00 0.00 0.00 3.14
2675 6451 4.763793 ACTGTTCTAGCATGTGCAATTTCT 59.236 37.500 7.83 0.00 45.16 2.52
2676 6452 5.939883 ACTGTTCTAGCATGTGCAATTTCTA 59.060 36.000 7.83 0.00 45.16 2.10
2677 6453 6.128172 ACTGTTCTAGCATGTGCAATTTCTAC 60.128 38.462 7.83 0.00 45.16 2.59
2678 6454 5.163864 TGTTCTAGCATGTGCAATTTCTACG 60.164 40.000 7.83 0.00 45.16 3.51
2679 6455 4.503910 TCTAGCATGTGCAATTTCTACGT 58.496 39.130 7.83 0.00 45.16 3.57
2711 6487 5.450137 GCCAATGAGGATCTGAAATTGTGAG 60.450 44.000 0.00 0.00 41.22 3.51
2715 6491 1.064654 GGATCTGAAATTGTGAGCGCC 59.935 52.381 2.29 0.00 0.00 6.53
2716 6492 1.064654 GATCTGAAATTGTGAGCGCCC 59.935 52.381 2.29 0.00 0.00 6.13
2717 6493 1.135315 CTGAAATTGTGAGCGCCCG 59.865 57.895 2.29 0.00 0.00 6.13
2719 6495 1.169661 TGAAATTGTGAGCGCCCGTT 61.170 50.000 2.29 0.00 0.00 4.44
2720 6496 0.729140 GAAATTGTGAGCGCCCGTTG 60.729 55.000 2.29 0.00 0.00 4.10
2732 6508 2.983592 CCGTTGGCTGTGGGTTCC 60.984 66.667 0.00 0.00 0.00 3.62
2733 6509 2.983592 CGTTGGCTGTGGGTTCCC 60.984 66.667 0.12 0.12 0.00 3.97
3012 6934 5.560375 GCATCAACTCAGATCATACATGCAC 60.560 44.000 0.00 0.00 35.31 4.57
3063 7003 7.805542 GTGCTATTTTGTTTTGTTTTGGTTGTT 59.194 29.630 0.00 0.00 0.00 2.83
3064 7004 8.352942 TGCTATTTTGTTTTGTTTTGGTTGTTT 58.647 25.926 0.00 0.00 0.00 2.83
3065 7005 9.827411 GCTATTTTGTTTTGTTTTGGTTGTTTA 57.173 25.926 0.00 0.00 0.00 2.01
3193 7158 5.833667 AGATGTGTTACCGAGGAGAATGATA 59.166 40.000 0.00 0.00 0.00 2.15
3196 7161 5.299531 TGTGTTACCGAGGAGAATGATAGAG 59.700 44.000 0.00 0.00 0.00 2.43
3221 7186 4.320421 CGTCCTTGACAAATGCTCAAATGA 60.320 41.667 0.00 0.00 32.09 2.57
3428 7447 9.979270 GTACAATTGAATGTGTCTCTCTTAATG 57.021 33.333 13.59 0.00 34.75 1.90
3695 7763 1.216178 CCCATCAGCGCCAAAAAGG 59.784 57.895 2.29 0.00 41.84 3.11
4014 8405 7.870445 GGTTAATTTCAAGTGACAAAATGGCTA 59.130 33.333 0.00 0.00 0.00 3.93
4126 8524 4.866508 ACAGTACAAGTTCATCGAGGAA 57.133 40.909 8.70 8.70 0.00 3.36
4181 8579 1.737735 CTCATCTTCACGGCGCACA 60.738 57.895 10.83 0.00 0.00 4.57
4333 8731 1.317431 ACTACGAGCGTACATGCCCA 61.317 55.000 0.00 0.00 34.65 5.36
4661 9059 1.264749 TAGCTGATGGTCTGGCCGTT 61.265 55.000 0.00 0.00 41.21 4.44
4709 9111 6.056236 TGGTAAGCCGCACAATTTATATGTA 58.944 36.000 0.00 0.00 37.67 2.29
4760 9162 1.373435 GGTGTCCAACCGTCATGGA 59.627 57.895 0.00 0.00 44.58 3.41
4766 9168 1.407618 TCCAACCGTCATGGAGTATCG 59.592 52.381 0.00 0.00 41.98 2.92
4969 9371 6.895204 AGAGCTACCTTCTTCTGTAGAATTCT 59.105 38.462 13.56 13.56 41.89 2.40
5044 9447 0.667487 CTGATCGCGTGTTGTGACCT 60.667 55.000 5.77 0.00 40.56 3.85
5046 9449 0.438830 GATCGCGTGTTGTGACCTTC 59.561 55.000 5.77 0.00 40.56 3.46
5116 9519 7.534085 AAAAATTCTACGATCACGCAAGATA 57.466 32.000 0.00 0.00 43.96 1.98
5133 9536 6.200475 CGCAAGATATATCTAGGTGATGCATG 59.800 42.308 24.27 13.93 34.51 4.06
5150 9553 0.909610 ATGGCAACGAGAGGGGAGAA 60.910 55.000 0.00 0.00 42.51 2.87
5238 9643 1.215655 CTTCGCGATCCAACCGATCC 61.216 60.000 10.88 0.00 44.07 3.36
5250 9655 1.259609 ACCGATCCAAGTACCGAACA 58.740 50.000 0.00 0.00 0.00 3.18
5315 9720 3.490078 CCCTCGTGCTCTTGATCTAGTTC 60.490 52.174 4.06 0.00 0.00 3.01
5398 9823 3.321111 ACCTAAGCACTACGATGGTATGG 59.679 47.826 0.00 0.00 0.00 2.74
5418 9843 0.677288 TCGAGGTGTGTAACTGTGGG 59.323 55.000 0.00 0.00 38.04 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.101640 ATTTTGACTGGGGGCAAACT 57.898 45.000 0.00 0.00 34.09 2.66
2 3 3.161866 GAGTATTTTGACTGGGGGCAAA 58.838 45.455 0.00 0.00 32.63 3.68
3 4 2.556559 GGAGTATTTTGACTGGGGGCAA 60.557 50.000 0.00 0.00 0.00 4.52
4 5 1.005450 GGAGTATTTTGACTGGGGGCA 59.995 52.381 0.00 0.00 0.00 5.36
6 7 1.923148 AGGGAGTATTTTGACTGGGGG 59.077 52.381 0.00 0.00 0.00 5.40
7 8 3.136626 CCTAGGGAGTATTTTGACTGGGG 59.863 52.174 0.00 0.00 0.00 4.96
8 9 3.780850 ACCTAGGGAGTATTTTGACTGGG 59.219 47.826 14.81 0.00 33.42 4.45
9 10 4.141688 GGACCTAGGGAGTATTTTGACTGG 60.142 50.000 14.81 0.00 0.00 4.00
10 11 4.441634 CGGACCTAGGGAGTATTTTGACTG 60.442 50.000 14.81 0.00 0.00 3.51
11 12 3.705072 CGGACCTAGGGAGTATTTTGACT 59.295 47.826 14.81 0.00 0.00 3.41
12 13 3.740452 GCGGACCTAGGGAGTATTTTGAC 60.740 52.174 14.81 0.00 0.00 3.18
13 14 2.433239 GCGGACCTAGGGAGTATTTTGA 59.567 50.000 14.81 0.00 0.00 2.69
14 15 2.484947 GGCGGACCTAGGGAGTATTTTG 60.485 54.545 14.81 0.00 0.00 2.44
15 16 1.767088 GGCGGACCTAGGGAGTATTTT 59.233 52.381 14.81 0.00 0.00 1.82
16 17 1.343681 TGGCGGACCTAGGGAGTATTT 60.344 52.381 14.81 0.00 36.63 1.40
17 18 0.263765 TGGCGGACCTAGGGAGTATT 59.736 55.000 14.81 0.00 36.63 1.89
18 19 0.469518 GTGGCGGACCTAGGGAGTAT 60.470 60.000 14.81 0.00 36.63 2.12
19 20 1.076485 GTGGCGGACCTAGGGAGTA 60.076 63.158 14.81 0.00 36.63 2.59
20 21 2.363925 GTGGCGGACCTAGGGAGT 60.364 66.667 14.81 0.00 36.63 3.85
21 22 2.042843 AGTGGCGGACCTAGGGAG 60.043 66.667 14.81 4.85 36.63 4.30
22 23 2.238319 ATCAGTGGCGGACCTAGGGA 62.238 60.000 14.81 0.00 36.63 4.20
23 24 1.762460 ATCAGTGGCGGACCTAGGG 60.762 63.158 14.81 0.00 36.63 3.53
24 25 1.443407 CATCAGTGGCGGACCTAGG 59.557 63.158 7.41 7.41 36.63 3.02
25 26 1.443407 CCATCAGTGGCGGACCTAG 59.557 63.158 0.00 0.00 39.01 3.02
26 27 3.628989 CCATCAGTGGCGGACCTA 58.371 61.111 0.00 0.00 39.01 3.08
35 36 0.524862 GAAGCTGGTTGCCATCAGTG 59.475 55.000 0.00 0.00 44.23 3.66
36 37 0.957395 CGAAGCTGGTTGCCATCAGT 60.957 55.000 0.00 0.00 44.23 3.41
37 38 1.798735 CGAAGCTGGTTGCCATCAG 59.201 57.895 0.00 0.00 44.23 2.90
38 39 3.985877 CGAAGCTGGTTGCCATCA 58.014 55.556 0.00 0.00 44.23 3.07
122 123 4.082523 ATCGTGGCACCGACCCAG 62.083 66.667 12.86 0.00 40.08 4.45
137 138 1.627834 CCCTCCTCCATTCCTAGCATC 59.372 57.143 0.00 0.00 0.00 3.91
138 139 1.739750 CCCTCCTCCATTCCTAGCAT 58.260 55.000 0.00 0.00 0.00 3.79
143 144 3.483869 GCGCCCTCCTCCATTCCT 61.484 66.667 0.00 0.00 0.00 3.36
147 148 3.474570 GACAGCGCCCTCCTCCAT 61.475 66.667 2.29 0.00 0.00 3.41
160 161 3.931468 CCTTCATACACTGCTTCTGACAG 59.069 47.826 0.00 0.00 41.08 3.51
161 162 3.578282 TCCTTCATACACTGCTTCTGACA 59.422 43.478 0.00 0.00 0.00 3.58
189 190 3.664025 CTCGCTCCACCATCGCCAA 62.664 63.158 0.00 0.00 0.00 4.52
192 193 1.953138 CATCTCGCTCCACCATCGC 60.953 63.158 0.00 0.00 0.00 4.58
208 209 9.320295 TCCCAAATTCTTCTACCAAATAAACAT 57.680 29.630 0.00 0.00 0.00 2.71
254 256 5.690865 TCCAAAGTTTTCTAGACCACATGT 58.309 37.500 0.00 0.00 0.00 3.21
257 259 5.623956 TCTCCAAAGTTTTCTAGACCACA 57.376 39.130 0.00 0.00 0.00 4.17
258 260 5.470437 CCTTCTCCAAAGTTTTCTAGACCAC 59.530 44.000 0.00 0.00 0.00 4.16
270 272 3.751698 GCAACGTTATCCTTCTCCAAAGT 59.248 43.478 0.00 0.00 0.00 2.66
271 273 4.003648 AGCAACGTTATCCTTCTCCAAAG 58.996 43.478 0.00 0.00 0.00 2.77
280 285 1.674817 CCACCGAAGCAACGTTATCCT 60.675 52.381 0.00 0.00 0.00 3.24
301 306 0.534877 TCAACACGTGCCATTGAGCT 60.535 50.000 17.22 0.00 0.00 4.09
311 316 1.089481 CCCCATCCGATCAACACGTG 61.089 60.000 15.48 15.48 0.00 4.49
317 326 1.912220 GGTCACCCCATCCGATCAA 59.088 57.895 0.00 0.00 0.00 2.57
323 332 0.393077 CTGTATCGGTCACCCCATCC 59.607 60.000 0.00 0.00 0.00 3.51
326 335 1.687840 CCCTGTATCGGTCACCCCA 60.688 63.158 0.00 0.00 0.00 4.96
386 427 6.546972 TGCACAAATTATGTTCAACTCGTA 57.453 33.333 0.00 0.00 41.46 3.43
442 483 8.478066 ACATTATACTCAAAGTAGTGATGCTCA 58.522 33.333 0.00 0.00 33.66 4.26
466 507 6.293190 CGCCAAAATACTGAACTTAGTTCACA 60.293 38.462 22.16 13.89 45.88 3.58
467 508 6.077838 CGCCAAAATACTGAACTTAGTTCAC 58.922 40.000 22.16 9.50 45.88 3.18
469 510 5.180680 ACCGCCAAAATACTGAACTTAGTTC 59.819 40.000 17.34 17.34 42.26 3.01
470 511 5.067954 ACCGCCAAAATACTGAACTTAGTT 58.932 37.500 0.00 0.00 32.19 2.24
472 513 6.592607 TCTTACCGCCAAAATACTGAACTTAG 59.407 38.462 0.00 0.00 0.00 2.18
473 514 6.465948 TCTTACCGCCAAAATACTGAACTTA 58.534 36.000 0.00 0.00 0.00 2.24
476 517 4.694037 ACTCTTACCGCCAAAATACTGAAC 59.306 41.667 0.00 0.00 0.00 3.18
477 518 4.901868 ACTCTTACCGCCAAAATACTGAA 58.098 39.130 0.00 0.00 0.00 3.02
478 519 4.546829 ACTCTTACCGCCAAAATACTGA 57.453 40.909 0.00 0.00 0.00 3.41
481 522 6.970613 CCAATAAACTCTTACCGCCAAAATAC 59.029 38.462 0.00 0.00 0.00 1.89
482 523 6.660094 ACCAATAAACTCTTACCGCCAAAATA 59.340 34.615 0.00 0.00 0.00 1.40
483 524 5.479027 ACCAATAAACTCTTACCGCCAAAAT 59.521 36.000 0.00 0.00 0.00 1.82
484 525 4.828387 ACCAATAAACTCTTACCGCCAAAA 59.172 37.500 0.00 0.00 0.00 2.44
488 529 3.602483 TGACCAATAAACTCTTACCGCC 58.398 45.455 0.00 0.00 0.00 6.13
489 530 5.813080 AATGACCAATAAACTCTTACCGC 57.187 39.130 0.00 0.00 0.00 5.68
528 597 1.533625 TTTGAGATTGGAAGCCGTGG 58.466 50.000 0.00 0.00 0.00 4.94
570 1835 2.873133 TTCGCGTGGGTTTGATTTTT 57.127 40.000 5.77 0.00 0.00 1.94
573 1838 2.286833 CGATATTCGCGTGGGTTTGATT 59.713 45.455 5.77 0.00 31.14 2.57
576 1841 3.798506 CGATATTCGCGTGGGTTTG 57.201 52.632 5.77 0.00 31.14 2.93
587 1852 1.156736 CCAATCGGGGTGCGATATTC 58.843 55.000 0.00 0.00 0.00 1.75
743 2012 4.521075 CGAAGCACGTCATCCCAT 57.479 55.556 0.00 0.00 37.22 4.00
762 2031 4.295141 TGGTTATTCCAAGTGGTACCTG 57.705 45.455 14.36 2.79 44.12 4.00
1224 2547 4.745620 GTCGGTCAGATTAGGCAGATAAAC 59.254 45.833 0.00 0.00 0.00 2.01
1245 2568 3.182967 CAGAGCTGTTATCTGTTCCGTC 58.817 50.000 0.00 0.00 39.48 4.79
1256 2579 1.264749 ATGGCCCGACAGAGCTGTTA 61.265 55.000 0.00 0.00 45.05 2.41
1284 2615 1.782044 CATTCCAAACTGCAAACCCG 58.218 50.000 0.00 0.00 0.00 5.28
1319 2650 3.257393 GAGATCCAACTAGCACACTGTG 58.743 50.000 6.19 6.19 36.51 3.66
1321 2654 3.056250 AGTGAGATCCAACTAGCACACTG 60.056 47.826 0.00 0.00 36.29 3.66
1340 2673 4.543590 AGTTCTGTCCTTGGATGTAGTG 57.456 45.455 0.00 0.00 0.00 2.74
1341 2674 4.160626 GCTAGTTCTGTCCTTGGATGTAGT 59.839 45.833 0.00 0.00 0.00 2.73
1342 2675 4.160439 TGCTAGTTCTGTCCTTGGATGTAG 59.840 45.833 0.00 0.00 0.00 2.74
1354 2693 5.671493 ACAGTACTGTTTTGCTAGTTCTGT 58.329 37.500 22.95 9.78 44.99 3.41
1361 2700 9.211485 GTTCCTAAATACAGTACTGTTTTGCTA 57.789 33.333 32.15 18.47 41.83 3.49
1373 2712 8.752187 TCCGTGTTATTAGTTCCTAAATACAGT 58.248 33.333 0.00 0.00 30.14 3.55
1375 2714 9.941325 TTTCCGTGTTATTAGTTCCTAAATACA 57.059 29.630 0.00 0.00 29.35 2.29
1394 2733 6.620678 AGTCCAAATACATCAAATTTCCGTG 58.379 36.000 0.00 0.00 0.00 4.94
1413 2752 7.824289 GCAGCACCATTATAGATTTATAGTCCA 59.176 37.037 0.00 0.00 0.00 4.02
1414 2753 8.043710 AGCAGCACCATTATAGATTTATAGTCC 58.956 37.037 0.00 0.00 0.00 3.85
1420 2759 7.661437 CCACTTAGCAGCACCATTATAGATTTA 59.339 37.037 0.00 0.00 0.00 1.40
1421 2760 6.488006 CCACTTAGCAGCACCATTATAGATTT 59.512 38.462 0.00 0.00 0.00 2.17
1422 2761 6.000219 CCACTTAGCAGCACCATTATAGATT 59.000 40.000 0.00 0.00 0.00 2.40
1423 2762 5.072329 ACCACTTAGCAGCACCATTATAGAT 59.928 40.000 0.00 0.00 0.00 1.98
1424 2763 4.408921 ACCACTTAGCAGCACCATTATAGA 59.591 41.667 0.00 0.00 0.00 1.98
1425 2764 4.708177 ACCACTTAGCAGCACCATTATAG 58.292 43.478 0.00 0.00 0.00 1.31
1444 2783 0.107897 CCAGCGCTATGTGGTTACCA 60.108 55.000 10.99 0.00 0.00 3.25
1445 2784 1.436983 GCCAGCGCTATGTGGTTACC 61.437 60.000 10.99 0.00 36.10 2.85
1446 2785 1.762222 CGCCAGCGCTATGTGGTTAC 61.762 60.000 10.99 0.00 36.10 2.50
1447 2786 1.520564 CGCCAGCGCTATGTGGTTA 60.521 57.895 10.99 0.00 36.10 2.85
1448 2787 2.819595 CGCCAGCGCTATGTGGTT 60.820 61.111 10.99 0.00 36.10 3.67
1459 2798 3.181967 CGTGTGAGTAGCGCCAGC 61.182 66.667 2.29 0.00 45.58 4.85
1460 2799 1.372997 AACGTGTGAGTAGCGCCAG 60.373 57.895 2.29 0.00 0.00 4.85
1461 2800 1.663388 CAACGTGTGAGTAGCGCCA 60.663 57.895 2.29 0.00 0.00 5.69
1462 2801 2.380410 CCAACGTGTGAGTAGCGCC 61.380 63.158 2.29 0.00 0.00 6.53
1463 2802 2.380410 CCCAACGTGTGAGTAGCGC 61.380 63.158 0.00 0.00 0.00 5.92
1464 2803 0.319211 TTCCCAACGTGTGAGTAGCG 60.319 55.000 0.00 0.00 0.00 4.26
1465 2804 2.094762 ATTCCCAACGTGTGAGTAGC 57.905 50.000 0.00 0.00 0.00 3.58
1466 2805 4.513692 TCAAAATTCCCAACGTGTGAGTAG 59.486 41.667 0.00 0.00 0.00 2.57
1467 2806 4.452825 TCAAAATTCCCAACGTGTGAGTA 58.547 39.130 0.00 0.00 0.00 2.59
1468 2807 3.283751 TCAAAATTCCCAACGTGTGAGT 58.716 40.909 0.00 0.00 0.00 3.41
1469 2808 3.563808 TCTCAAAATTCCCAACGTGTGAG 59.436 43.478 0.00 0.00 34.01 3.51
1470 2809 3.546724 TCTCAAAATTCCCAACGTGTGA 58.453 40.909 0.00 0.00 0.00 3.58
1471 2810 3.853307 GCTCTCAAAATTCCCAACGTGTG 60.853 47.826 0.00 0.00 0.00 3.82
1472 2811 2.293399 GCTCTCAAAATTCCCAACGTGT 59.707 45.455 0.00 0.00 0.00 4.49
1473 2812 2.293122 TGCTCTCAAAATTCCCAACGTG 59.707 45.455 0.00 0.00 0.00 4.49
1474 2813 2.554032 CTGCTCTCAAAATTCCCAACGT 59.446 45.455 0.00 0.00 0.00 3.99
1475 2814 2.813754 TCTGCTCTCAAAATTCCCAACG 59.186 45.455 0.00 0.00 0.00 4.10
1476 2815 3.569701 TGTCTGCTCTCAAAATTCCCAAC 59.430 43.478 0.00 0.00 0.00 3.77
1477 2816 3.822735 CTGTCTGCTCTCAAAATTCCCAA 59.177 43.478 0.00 0.00 0.00 4.12
1478 2817 3.415212 CTGTCTGCTCTCAAAATTCCCA 58.585 45.455 0.00 0.00 0.00 4.37
1479 2818 2.163211 GCTGTCTGCTCTCAAAATTCCC 59.837 50.000 0.00 0.00 38.95 3.97
1480 2819 2.163211 GGCTGTCTGCTCTCAAAATTCC 59.837 50.000 1.44 0.00 42.39 3.01
1481 2820 2.159599 CGGCTGTCTGCTCTCAAAATTC 60.160 50.000 1.44 0.00 42.39 2.17
1482 2821 1.808945 CGGCTGTCTGCTCTCAAAATT 59.191 47.619 1.44 0.00 42.39 1.82
1483 2822 1.002430 TCGGCTGTCTGCTCTCAAAAT 59.998 47.619 1.44 0.00 42.39 1.82
1484 2823 0.392706 TCGGCTGTCTGCTCTCAAAA 59.607 50.000 1.44 0.00 42.39 2.44
1485 2824 0.319900 GTCGGCTGTCTGCTCTCAAA 60.320 55.000 1.44 0.00 42.39 2.69
1486 2825 1.290324 GTCGGCTGTCTGCTCTCAA 59.710 57.895 1.44 0.00 42.39 3.02
1487 2826 2.640302 GGTCGGCTGTCTGCTCTCA 61.640 63.158 1.44 0.00 42.39 3.27
1488 2827 2.183046 GGTCGGCTGTCTGCTCTC 59.817 66.667 1.44 0.00 42.39 3.20
1489 2828 3.386237 GGGTCGGCTGTCTGCTCT 61.386 66.667 1.44 0.00 42.39 4.09
1490 2829 2.527951 AATGGGTCGGCTGTCTGCTC 62.528 60.000 1.44 0.00 42.39 4.26
1491 2830 2.596851 AATGGGTCGGCTGTCTGCT 61.597 57.895 1.44 0.00 42.39 4.24
1492 2831 2.045926 AATGGGTCGGCTGTCTGC 60.046 61.111 0.00 0.00 41.94 4.26
1493 2832 1.003355 ACAATGGGTCGGCTGTCTG 60.003 57.895 0.00 0.00 0.00 3.51
1494 2833 1.296715 GACAATGGGTCGGCTGTCT 59.703 57.895 0.30 0.00 36.65 3.41
1495 2834 3.890674 GACAATGGGTCGGCTGTC 58.109 61.111 0.00 0.00 36.65 3.51
1541 2881 3.091633 AGATGTCCCCTGAACATTTGG 57.908 47.619 0.00 0.00 37.47 3.28
1634 3030 3.502211 CACGTGATTGGAAGCTTAAACCT 59.498 43.478 10.90 0.00 0.00 3.50
1704 3246 2.107041 TTGGTACTGTGGGTCGCCAG 62.107 60.000 0.00 4.53 35.58 4.85
1708 3250 2.465860 TCATTTGGTACTGTGGGTCG 57.534 50.000 0.00 0.00 0.00 4.79
1773 3315 1.757340 CGTAGTGAGGGGAGGGGTC 60.757 68.421 0.00 0.00 0.00 4.46
1872 3414 0.318441 AGTCATCCGGCGTATCCATG 59.682 55.000 6.01 0.00 34.01 3.66
1873 3415 1.048601 AAGTCATCCGGCGTATCCAT 58.951 50.000 6.01 0.00 34.01 3.41
1885 3427 4.094590 CAGAATCAGCAGGACAAAGTCATC 59.905 45.833 0.00 0.00 33.68 2.92
1921 3504 6.648879 AAGCTAACAAGATGCCTTTTGTTA 57.351 33.333 14.29 14.29 43.54 2.41
1937 3520 5.755375 TGCAACTATGAGATGCTAAGCTAAC 59.245 40.000 9.69 0.00 43.40 2.34
1969 3552 8.608844 ATGTGTAGCTAGTTTAATAATCAGCC 57.391 34.615 0.00 0.00 0.00 4.85
2015 3910 0.315544 CGTCACGGTCCGTTGTTTTG 60.316 55.000 15.97 2.14 38.32 2.44
2020 3915 1.545614 CTTCACGTCACGGTCCGTTG 61.546 60.000 15.97 10.98 38.32 4.10
2094 4318 9.529325 TTCATTGTTTATTACTCGATCTACCTG 57.471 33.333 0.00 0.00 0.00 4.00
2110 4533 8.846943 TCTGAGTTGCTTAGATTCATTGTTTA 57.153 30.769 0.00 0.00 0.00 2.01
2117 4540 9.376075 CTCTAAATTCTGAGTTGCTTAGATTCA 57.624 33.333 0.00 0.00 0.00 2.57
2118 4541 8.334632 GCTCTAAATTCTGAGTTGCTTAGATTC 58.665 37.037 8.73 0.00 33.22 2.52
2140 4563 2.420269 CCTGTCAGATGCATTCAGCTCT 60.420 50.000 0.00 0.00 45.94 4.09
2144 4567 1.931841 CGTCCTGTCAGATGCATTCAG 59.068 52.381 0.00 7.77 0.00 3.02
2147 4570 1.134580 CCTCGTCCTGTCAGATGCATT 60.135 52.381 0.00 0.00 0.00 3.56
2311 4741 0.252881 AGCCAGAGGATCCAACAGGA 60.253 55.000 15.82 0.00 33.66 3.86
2658 6434 4.864916 ACGTAGAAATTGCACATGCTAG 57.135 40.909 5.31 0.00 42.66 3.42
2675 6451 2.167693 CCTCATTGGCTCCACTTACGTA 59.832 50.000 0.00 0.00 0.00 3.57
2676 6452 1.066143 CCTCATTGGCTCCACTTACGT 60.066 52.381 0.00 0.00 0.00 3.57
2677 6453 1.207089 TCCTCATTGGCTCCACTTACG 59.793 52.381 0.00 0.00 35.26 3.18
2678 6454 3.135530 AGATCCTCATTGGCTCCACTTAC 59.864 47.826 0.00 0.00 31.55 2.34
2679 6455 3.135348 CAGATCCTCATTGGCTCCACTTA 59.865 47.826 0.00 0.00 31.55 2.24
2687 6463 4.400251 TCACAATTTCAGATCCTCATTGGC 59.600 41.667 8.55 0.00 35.26 4.52
2692 6468 3.264947 CGCTCACAATTTCAGATCCTCA 58.735 45.455 0.00 0.00 0.00 3.86
2715 6491 2.983592 GGAACCCACAGCCAACGG 60.984 66.667 0.00 0.00 0.00 4.44
2729 6505 2.035321 CGGCTGCAAAAAGTAAAGGGAA 59.965 45.455 0.50 0.00 0.00 3.97
2732 6508 3.308530 CTTCGGCTGCAAAAAGTAAAGG 58.691 45.455 0.50 0.00 0.00 3.11
2733 6509 2.726241 GCTTCGGCTGCAAAAAGTAAAG 59.274 45.455 0.50 0.00 38.08 1.85
3012 6934 2.990066 ACCTTCTATCTTCTTGCCCG 57.010 50.000 0.00 0.00 0.00 6.13
3063 7003 0.320374 CCGGCTCGCCTGGATAATAA 59.680 55.000 11.67 0.00 33.64 1.40
3064 7004 1.972198 CCGGCTCGCCTGGATAATA 59.028 57.895 11.67 0.00 33.64 0.98
3065 7005 2.743718 CCGGCTCGCCTGGATAAT 59.256 61.111 11.67 0.00 33.64 1.28
3193 7158 2.037772 AGCATTTGTCAAGGACGACTCT 59.962 45.455 0.00 0.00 36.82 3.24
3196 7161 2.143122 TGAGCATTTGTCAAGGACGAC 58.857 47.619 0.00 0.00 34.95 4.34
3221 7186 7.060421 ACCGATGTTGGATAAATTAACCTGAT 58.940 34.615 1.08 0.00 0.00 2.90
3240 7252 3.735240 CACAATTCACAAACCAACCGATG 59.265 43.478 0.00 0.00 0.00 3.84
3428 7447 0.718904 TTGTCATGCGTGCGATACAC 59.281 50.000 0.00 0.00 46.45 2.90
3438 7463 6.456447 AAAATGAAGTGAAATTGTCATGCG 57.544 33.333 0.00 0.00 38.90 4.73
3631 7699 0.322816 ACTGCGAGAGGTACCCGTTA 60.323 55.000 8.74 0.00 0.00 3.18
3691 7759 1.895131 CTTGCAACCATGTAGGCCTTT 59.105 47.619 12.58 0.00 43.14 3.11
3695 7763 1.743394 GTACCTTGCAACCATGTAGGC 59.257 52.381 0.00 0.00 43.14 3.93
4014 8405 7.875041 CCTTGTACCTTTAGATTCATCGATGAT 59.125 37.037 27.75 17.53 36.56 2.45
4104 8502 4.866508 TCCTCGATGAACTTGTACTGTT 57.133 40.909 4.88 4.88 0.00 3.16
4126 8524 2.284625 TCCACCGTGGAGAGGCAT 60.285 61.111 16.73 0.00 42.67 4.40
4181 8579 2.760385 GGAGTAGCCGAGCACCCT 60.760 66.667 0.00 0.00 0.00 4.34
4333 8731 1.599606 CGCACTGGCTCTGGTAGAGT 61.600 60.000 7.59 0.00 44.12 3.24
4661 9059 3.949586 TTATTGCATGACCCTCCATGA 57.050 42.857 7.94 0.00 44.98 3.07
4709 9111 4.331717 CGCCCACGAGATTTGTTTATTAGT 59.668 41.667 0.00 0.00 43.93 2.24
4760 9162 6.238484 GCTGACCAATTTTATTGCTCGATACT 60.238 38.462 0.00 0.00 0.00 2.12
4763 9165 4.641989 AGCTGACCAATTTTATTGCTCGAT 59.358 37.500 0.00 0.00 0.00 3.59
4766 9168 3.861689 GCAGCTGACCAATTTTATTGCTC 59.138 43.478 20.43 0.00 0.00 4.26
4818 9220 2.178912 AACACCAACTCATACCCACG 57.821 50.000 0.00 0.00 0.00 4.94
4931 9333 9.886132 AAGAAGGTAGCTCTATTTTTCGATAAA 57.114 29.630 3.47 3.47 0.00 1.40
5019 9422 1.067565 ACAACACGCGATCAGACTGAT 60.068 47.619 17.98 17.98 40.34 2.90
5044 9447 6.182507 ACAACATACACAAAGTAGGAGGAA 57.817 37.500 0.00 0.00 36.63 3.36
5046 9449 5.181245 CCAACAACATACACAAAGTAGGAGG 59.819 44.000 0.00 0.00 36.63 4.30
5116 9519 4.330250 GTTGCCATGCATCACCTAGATAT 58.670 43.478 0.00 0.00 38.76 1.63
5133 9536 0.462759 CATTCTCCCCTCTCGTTGCC 60.463 60.000 0.00 0.00 0.00 4.52
5150 9553 1.568504 ACGAGGGTACATGGACACAT 58.431 50.000 14.19 0.00 37.99 3.21
5315 9720 0.176680 CGGAACTCACCCTCATCCTG 59.823 60.000 0.00 0.00 0.00 3.86
5398 9823 1.604693 CCCACAGTTACACACCTCGAC 60.605 57.143 0.00 0.00 0.00 4.20
5441 9866 3.456277 AGAACACACAAGTTTCTCTCCCT 59.544 43.478 0.00 0.00 0.00 4.20
5561 9996 3.585732 CCCTCTTGGTGGAAACCTACTAA 59.414 47.826 0.00 0.00 0.00 2.24
5594 10036 0.105709 CCCTCTCCCTCTCCTTCCTC 60.106 65.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.