Multiple sequence alignment - TraesCS3B01G509300

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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 TraesCS3B01G509300 chr3B 100.000 2873 0 0 1 2873 753560008 753562880 0.000000e+00 5306.0
1 TraesCS3B01G509300 chr3B 77.535 1558 261 47 987 2496 753672733 753674249 0.000000e+00 856.0
2 TraesCS3B01G509300 chr3B 77.114 603 112 17 1556 2151 752172792 752172209 2.760000e-85 326.0
3 TraesCS3B01G509300 chr3B 98.601 143 2 0 2731 2873 753577288 753577430 1.320000e-63 254.0
4 TraesCS3B01G509300 chr3B 84.314 204 30 2 990 1192 753867299 753867501 6.280000e-47 198.0
5 TraesCS3B01G509300 chr3B 83.978 181 19 9 1322 1495 752972964 752972787 6.370000e-37 165.0
6 TraesCS3B01G509300 chr3D 92.604 1271 65 9 902 2157 565535424 565536680 0.000000e+00 1799.0
7 TraesCS3B01G509300 chr3D 77.713 1548 273 43 987 2495 565604190 565605704 0.000000e+00 881.0
8 TraesCS3B01G509300 chr3D 92.021 376 25 5 49 422 565531429 565531801 9.120000e-145 523.0
9 TraesCS3B01G509300 chr3D 91.054 313 5 8 2154 2466 565536782 565537071 4.460000e-108 401.0
10 TraesCS3B01G509300 chr3D 75.000 860 175 28 1658 2495 565326275 565327116 7.570000e-96 361.0
11 TraesCS3B01G509300 chr3D 76.355 609 111 22 1556 2151 564392609 564392021 2.160000e-76 296.0
12 TraesCS3B01G509300 chr3D 93.125 160 7 3 49 204 565462183 565462342 6.190000e-57 231.0
13 TraesCS3B01G509300 chr3D 90.588 170 7 7 2561 2730 565558830 565558990 1.730000e-52 217.0
14 TraesCS3B01G509300 chr3D 83.902 205 31 2 990 1193 565641908 565642111 8.120000e-46 195.0
15 TraesCS3B01G509300 chr3D 82.174 230 35 5 984 1208 567664811 567664583 2.920000e-45 193.0
16 TraesCS3B01G509300 chr3D 83.750 80 1 6 870 949 565462338 565462405 6.640000e-07 65.8
17 TraesCS3B01G509300 chr3D 92.857 42 1 2 2455 2495 565558782 565558822 3.090000e-05 60.2
18 TraesCS3B01G509300 chr3A 94.782 939 46 1 1560 2495 699750894 699751832 0.000000e+00 1459.0
19 TraesCS3B01G509300 chr3A 90.642 919 60 10 438 1345 699748797 699749700 0.000000e+00 1197.0
20 TraesCS3B01G509300 chr3A 77.950 1551 259 44 987 2495 699762936 699764445 0.000000e+00 893.0
21 TraesCS3B01G509300 chr3A 94.702 453 24 0 1273 1725 699749772 699750224 0.000000e+00 704.0
22 TraesCS3B01G509300 chr3A 94.578 166 9 0 1560 1725 699750724 699750889 1.020000e-64 257.0
23 TraesCS3B01G509300 chr3A 75.085 586 117 17 1561 2141 699190377 699189816 2.210000e-61 246.0
24 TraesCS3B01G509300 chr3A 95.139 144 7 0 1560 1703 699750229 699750372 8.010000e-56 228.0
25 TraesCS3B01G509300 chr3A 89.412 170 9 7 2561 2730 699751840 699752000 3.750000e-49 206.0
26 TraesCS3B01G509300 chr3A 84.390 205 30 2 990 1193 699975129 699975332 1.750000e-47 200.0
27 TraesCS3B01G509300 chr3A 83.173 208 33 2 992 1198 697596990 697596784 3.780000e-44 189.0
28 TraesCS3B01G509300 chr3A 94.521 73 4 0 1273 1345 699749700 699749772 2.340000e-21 113.0
29 TraesCS3B01G509300 chr3A 96.078 51 2 0 372 422 699748749 699748799 1.830000e-12 84.2
30 TraesCS3B01G509300 chr7D 84.058 690 75 15 210 872 638157397 638156716 1.450000e-177 632.0
31 TraesCS3B01G509300 chr6D 77.206 952 183 20 1561 2493 380452258 380451322 2.540000e-145 525.0
32 TraesCS3B01G509300 chr6D 81.550 542 75 18 987 1510 380452944 380452410 9.520000e-115 424.0
33 TraesCS3B01G509300 chr6B 81.919 542 73 17 987 1510 565398514 565399048 4.400000e-118 435.0
34 TraesCS3B01G509300 chrUn 95.726 117 5 0 2744 2860 62947578 62947694 3.780000e-44 189.0
35 TraesCS3B01G509300 chrUn 86.154 130 6 1 2731 2860 62942491 62942608 2.320000e-26 130.0
36 TraesCS3B01G509300 chr7A 80.208 96 10 5 1321 1416 41048399 41048313 2.390000e-06 63.9
37 TraesCS3B01G509300 chr7A 100.000 28 0 0 32 59 202995245 202995218 5.000000e-03 52.8
38 TraesCS3B01G509300 chr4A 80.208 96 10 7 1321 1416 648794939 648794853 2.390000e-06 63.9
39 TraesCS3B01G509300 chr4D 100.000 29 0 0 32 60 234179238 234179266 1.000000e-03 54.7
40 TraesCS3B01G509300 chr2B 94.444 36 0 2 27 62 147492735 147492702 1.000000e-03 54.7


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 TraesCS3B01G509300 chr3B 753560008 753562880 2872 False 5306.000000 5306 100.00000 1 2873 1 chr3B.!!$F1 2872
1 TraesCS3B01G509300 chr3B 753672733 753674249 1516 False 856.000000 856 77.53500 987 2496 1 chr3B.!!$F3 1509
2 TraesCS3B01G509300 chr3B 752172209 752172792 583 True 326.000000 326 77.11400 1556 2151 1 chr3B.!!$R1 595
3 TraesCS3B01G509300 chr3D 565531429 565537071 5642 False 907.666667 1799 91.89300 49 2466 3 chr3D.!!$F5 2417
4 TraesCS3B01G509300 chr3D 565604190 565605704 1514 False 881.000000 881 77.71300 987 2495 1 chr3D.!!$F2 1508
5 TraesCS3B01G509300 chr3D 565326275 565327116 841 False 361.000000 361 75.00000 1658 2495 1 chr3D.!!$F1 837
6 TraesCS3B01G509300 chr3D 564392021 564392609 588 True 296.000000 296 76.35500 1556 2151 1 chr3D.!!$R1 595
7 TraesCS3B01G509300 chr3A 699762936 699764445 1509 False 893.000000 893 77.95000 987 2495 1 chr3A.!!$F1 1508
8 TraesCS3B01G509300 chr3A 699748749 699752000 3251 False 531.025000 1459 93.73175 372 2730 8 chr3A.!!$F3 2358
9 TraesCS3B01G509300 chr3A 699189816 699190377 561 True 246.000000 246 75.08500 1561 2141 1 chr3A.!!$R2 580
10 TraesCS3B01G509300 chr7D 638156716 638157397 681 True 632.000000 632 84.05800 210 872 1 chr7D.!!$R1 662
11 TraesCS3B01G509300 chr6D 380451322 380452944 1622 True 474.500000 525 79.37800 987 2493 2 chr6D.!!$R1 1506
12 TraesCS3B01G509300 chr6B 565398514 565399048 534 False 435.000000 435 81.91900 987 1510 1 chr6B.!!$F1 523

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
50 51 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.0 13.64 0.0 46.06 3.85 F
51 52 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 F
135 136 0.400213 TCCCAAGCGTTCTGTTCCAT 59.600 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 4881 1.064906 AGGGCATCATGAGGTCACAAG 60.065 52.381 14.65 0.0 0.00 3.16 R
1823 6267 1.133253 CAACTGAACATGCCGAGCG 59.867 57.895 0.00 0.0 0.00 5.03 R
2095 6547 0.599558 TGCTTCAGCTGCAATTGACC 59.400 50.000 9.47 0.0 42.66 4.02 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
26 27 9.271921 TCATATAAGGTATGCATCCAGATTACT 57.728 33.333 0.19 0.00 0.00 2.24
38 39 9.599866 TGCATCCAGATTACTAATATATTTCCG 57.400 33.333 2.68 0.00 0.00 4.30
39 40 9.046296 GCATCCAGATTACTAATATATTTCCGG 57.954 37.037 2.68 0.00 0.00 5.14
42 43 8.464404 TCCAGATTACTAATATATTTCCGGACG 58.536 37.037 1.83 0.00 0.00 4.79
43 44 7.705325 CCAGATTACTAATATATTTCCGGACGG 59.295 40.741 1.83 3.96 0.00 4.79
44 45 8.464404 CAGATTACTAATATATTTCCGGACGGA 58.536 37.037 1.83 9.76 43.52 4.69
45 46 8.684520 AGATTACTAATATATTTCCGGACGGAG 58.315 37.037 13.64 1.72 46.06 4.63
46 47 5.656213 ACTAATATATTTCCGGACGGAGG 57.344 43.478 13.64 0.00 46.06 4.30
47 48 3.975168 AATATATTTCCGGACGGAGGG 57.025 47.619 13.64 0.00 46.06 4.30
48 49 2.681319 TATATTTCCGGACGGAGGGA 57.319 50.000 13.64 4.95 46.06 4.20
49 50 1.339097 ATATTTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
50 51 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
51 52 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
52 53 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
53 54 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
54 55 1.379576 CCGGACGGAGGGAGTACTT 60.380 63.158 4.40 0.00 37.50 2.24
65 66 3.087781 AGGGAGTACTTCGTTGTAGGTC 58.912 50.000 0.00 0.00 0.00 3.85
72 73 7.928706 GGAGTACTTCGTTGTAGGTCTATAGTA 59.071 40.741 0.00 0.00 0.00 1.82
85 86 9.896263 GTAGGTCTATAGTAAGAAACTACATGC 57.104 37.037 8.14 0.00 43.47 4.06
98 99 3.540617 ACTACATGCACATGCGGATAAA 58.459 40.909 10.50 0.00 45.83 1.40
99 100 3.944650 ACTACATGCACATGCGGATAAAA 59.055 39.130 10.50 0.00 45.83 1.52
132 133 2.095212 GGAATTCCCAAGCGTTCTGTTC 60.095 50.000 14.03 0.00 34.14 3.18
135 136 0.400213 TCCCAAGCGTTCTGTTCCAT 59.600 50.000 0.00 0.00 0.00 3.41
177 178 5.521735 ACTGAATCTCTATTTTAGCGTGCTG 59.478 40.000 4.25 0.00 0.00 4.41
192 194 1.662044 GCTGGTTGCAAAGACCTGG 59.338 57.895 0.00 0.00 42.31 4.45
208 210 1.920351 CCTGGGCTAAAGGTAGGGAAA 59.080 52.381 0.00 0.00 0.00 3.13
292 295 2.808543 GGATCCGCGAATCTTAAAGCAT 59.191 45.455 8.23 0.00 0.00 3.79
310 313 2.747799 GCATCCACTCCATCTTCTTCCC 60.748 54.545 0.00 0.00 0.00 3.97
322 325 4.387026 TCTTCTTCCCCAAATCATGTGT 57.613 40.909 0.00 0.00 0.00 3.72
323 326 4.739793 TCTTCTTCCCCAAATCATGTGTT 58.260 39.130 0.00 0.00 0.00 3.32
486 489 1.472878 CAGCCGCAACAGTACTCTCTA 59.527 52.381 0.00 0.00 0.00 2.43
490 493 2.747989 CCGCAACAGTACTCTCTACTGA 59.252 50.000 13.23 0.00 45.69 3.41
616 633 1.377202 GAGCGGCAGGAATTGACCA 60.377 57.895 1.45 0.00 0.00 4.02
618 635 1.212751 GCGGCAGGAATTGACCAAC 59.787 57.895 0.00 0.00 0.00 3.77
664 684 2.500098 AGAAGGCAGCACGAAATAGGTA 59.500 45.455 0.00 0.00 0.00 3.08
793 932 1.649321 AGAAGATGTGGAGTGGCTGA 58.351 50.000 0.00 0.00 0.00 4.26
810 949 1.256376 CTGATTTGAGATTCGCGGACG 59.744 52.381 6.13 0.00 42.01 4.79
830 1129 0.729116 CACGTGTCATTGGATGGAGC 59.271 55.000 7.58 0.00 0.00 4.70
879 1367 2.030717 CGGTCGGATTGGATAGAGTCAG 60.031 54.545 0.00 0.00 0.00 3.51
886 1374 4.407296 GGATTGGATAGAGTCAGGTCAAGT 59.593 45.833 0.00 0.00 0.00 3.16
894 1382 2.557490 GAGTCAGGTCAAGTCCGTTAGT 59.443 50.000 0.00 0.00 0.00 2.24
900 1388 2.298163 GGTCAAGTCCGTTAGTTCCTGA 59.702 50.000 0.00 0.00 0.00 3.86
912 4190 6.459848 CCGTTAGTTCCTGATTACTAGGACTG 60.460 46.154 0.00 0.00 43.75 3.51
913 4191 6.095160 CGTTAGTTCCTGATTACTAGGACTGT 59.905 42.308 0.00 0.00 43.75 3.55
914 4192 7.482474 GTTAGTTCCTGATTACTAGGACTGTC 58.518 42.308 0.00 0.00 43.75 3.51
915 4193 4.957327 AGTTCCTGATTACTAGGACTGTCC 59.043 45.833 19.20 19.20 43.75 4.02
916 4194 4.603094 TCCTGATTACTAGGACTGTCCA 57.397 45.455 27.48 13.11 39.36 4.02
917 4195 5.144159 TCCTGATTACTAGGACTGTCCAT 57.856 43.478 27.48 12.52 39.36 3.41
918 4196 5.141182 TCCTGATTACTAGGACTGTCCATC 58.859 45.833 27.48 19.99 39.36 3.51
919 4197 4.895889 CCTGATTACTAGGACTGTCCATCA 59.104 45.833 27.48 22.91 39.61 3.07
920 4198 7.142512 TCCTGATTACTAGGACTGTCCATCAG 61.143 46.154 29.43 29.43 39.36 2.90
1053 4341 2.122813 CTACCTGGCCTCCCGGAT 60.123 66.667 0.73 0.00 40.14 4.18
1108 4397 2.034066 CCAAAGCCCTTCTCCGCA 59.966 61.111 0.00 0.00 0.00 5.69
1213 4517 3.822192 TCGCCTCCGGTCACGATG 61.822 66.667 0.00 0.00 44.60 3.84
1359 4816 3.238597 CCTCCTCCTCCTTTCCTATGAG 58.761 54.545 0.00 0.00 0.00 2.90
1432 4889 4.947147 TGCCGGTGCCTTGTGACC 62.947 66.667 1.90 0.00 36.33 4.02
1489 4958 0.820891 GGGCGAGTACCGGATACTGA 60.821 60.000 9.46 0.00 44.64 3.41
1494 4963 3.364764 GCGAGTACCGGATACTGATGTAC 60.365 52.174 9.46 0.00 44.64 2.90
1515 5002 8.314143 TGTACGATAAAAACGAGGAAGAAATT 57.686 30.769 0.00 0.00 34.70 1.82
1518 5005 7.519002 ACGATAAAAACGAGGAAGAAATTGAG 58.481 34.615 0.00 0.00 34.70 3.02
1522 5009 3.059352 ACGAGGAAGAAATTGAGGGTG 57.941 47.619 0.00 0.00 0.00 4.61
1524 5014 3.072476 ACGAGGAAGAAATTGAGGGTGAA 59.928 43.478 0.00 0.00 0.00 3.18
1525 5015 4.072131 CGAGGAAGAAATTGAGGGTGAAA 58.928 43.478 0.00 0.00 0.00 2.69
1604 5199 1.134220 GCCATCAAGGAACATCGGGTA 60.134 52.381 0.00 0.00 41.22 3.69
1641 6071 2.050985 GTGCTTTCACGCTGTGGC 60.051 61.111 8.46 5.51 33.87 5.01
1705 6140 2.376808 AGAGCAACGTGAGAATGGAG 57.623 50.000 0.00 0.00 0.00 3.86
1732 6167 3.703286 TGGTACTGGTATTCGACATCG 57.297 47.619 0.00 0.00 41.45 3.84
1768 6203 1.510480 GCATATGCAGGCTCCGGTTC 61.510 60.000 22.84 0.00 41.59 3.62
1787 6222 3.117491 TCTTCAAGTTGCTCCAGACTG 57.883 47.619 0.00 0.00 0.00 3.51
1823 6267 0.665835 TTGTTTGACATGGACGGCAC 59.334 50.000 0.00 0.00 0.00 5.01
1842 6286 1.154150 GCTCGGCATGTTCAGTTGC 60.154 57.895 0.00 0.00 38.14 4.17
1861 6305 3.118807 GCAATGATGATGCAGCTATCG 57.881 47.619 2.53 0.00 43.29 2.92
1871 6315 4.876107 TGATGCAGCTATCGTCGATATCTA 59.124 41.667 16.08 5.02 0.00 1.98
1935 6381 4.044426 GCAAGATTGAATTGCCGGTTATC 58.956 43.478 1.90 0.00 45.79 1.75
1960 6406 6.019237 CGAGATCAAGTTATTGTGTGGAGATG 60.019 42.308 0.00 0.00 37.68 2.90
2055 6507 2.553028 GCTTCAGGTTGACATGGAAGGA 60.553 50.000 0.00 0.00 0.00 3.36
2095 6547 3.187022 TCATCACGACAAAGTCATTGCTG 59.813 43.478 0.00 0.00 43.13 4.41
2248 6809 4.953667 TGTATTCCTCTAGAGCTGCAATG 58.046 43.478 14.73 0.00 0.00 2.82
2249 6810 2.322355 TTCCTCTAGAGCTGCAATGC 57.678 50.000 14.73 0.00 0.00 3.56
2379 6941 2.441375 TGACACCCTTCCATGTTGAAGA 59.559 45.455 11.91 0.00 43.60 2.87
2514 7085 9.513727 GCTCTTTACAGTATACTTAGTACAACC 57.486 37.037 1.56 0.00 0.00 3.77
2519 7090 9.643693 TTACAGTATACTTAGTACAACCTTTGC 57.356 33.333 1.56 0.00 0.00 3.68
2520 7091 7.101700 ACAGTATACTTAGTACAACCTTTGCC 58.898 38.462 1.56 0.00 0.00 4.52
2521 7092 7.038516 ACAGTATACTTAGTACAACCTTTGCCT 60.039 37.037 1.56 0.00 0.00 4.75
2522 7093 7.491696 CAGTATACTTAGTACAACCTTTGCCTC 59.508 40.741 1.56 0.00 0.00 4.70
2523 7094 4.976540 ACTTAGTACAACCTTTGCCTCT 57.023 40.909 0.00 0.00 0.00 3.69
2524 7095 5.306114 ACTTAGTACAACCTTTGCCTCTT 57.694 39.130 0.00 0.00 0.00 2.85
2525 7096 5.306394 ACTTAGTACAACCTTTGCCTCTTC 58.694 41.667 0.00 0.00 0.00 2.87
2526 7097 3.141767 AGTACAACCTTTGCCTCTTCC 57.858 47.619 0.00 0.00 0.00 3.46
2527 7098 2.441750 AGTACAACCTTTGCCTCTTCCA 59.558 45.455 0.00 0.00 0.00 3.53
2528 7099 2.683211 ACAACCTTTGCCTCTTCCAT 57.317 45.000 0.00 0.00 0.00 3.41
2529 7100 3.806949 ACAACCTTTGCCTCTTCCATA 57.193 42.857 0.00 0.00 0.00 2.74
2530 7101 4.112634 ACAACCTTTGCCTCTTCCATAA 57.887 40.909 0.00 0.00 0.00 1.90
2531 7102 4.082125 ACAACCTTTGCCTCTTCCATAAG 58.918 43.478 0.00 0.00 0.00 1.73
2532 7103 4.082125 CAACCTTTGCCTCTTCCATAAGT 58.918 43.478 0.00 0.00 34.13 2.24
2533 7104 4.388577 ACCTTTGCCTCTTCCATAAGTT 57.611 40.909 0.00 0.00 34.13 2.66
2534 7105 4.336280 ACCTTTGCCTCTTCCATAAGTTC 58.664 43.478 0.00 0.00 34.13 3.01
2535 7106 4.043435 ACCTTTGCCTCTTCCATAAGTTCT 59.957 41.667 0.00 0.00 34.13 3.01
2536 7107 5.012893 CCTTTGCCTCTTCCATAAGTTCTT 58.987 41.667 0.00 0.00 34.13 2.52
2537 7108 5.478332 CCTTTGCCTCTTCCATAAGTTCTTT 59.522 40.000 0.00 0.00 34.13 2.52
2538 7109 6.015095 CCTTTGCCTCTTCCATAAGTTCTTTT 60.015 38.462 0.00 0.00 34.13 2.27
2539 7110 6.976934 TTGCCTCTTCCATAAGTTCTTTTT 57.023 33.333 0.00 0.00 34.13 1.94
2559 7130 4.370364 TTTGTTCAACCTTTGAGTGAGC 57.630 40.909 0.00 0.00 41.38 4.26
2560 7131 3.281727 TGTTCAACCTTTGAGTGAGCT 57.718 42.857 0.00 0.00 41.38 4.09
2561 7132 2.945008 TGTTCAACCTTTGAGTGAGCTG 59.055 45.455 0.00 0.00 41.38 4.24
2562 7133 2.260844 TCAACCTTTGAGTGAGCTGG 57.739 50.000 0.00 0.00 34.08 4.85
2563 7134 1.490490 TCAACCTTTGAGTGAGCTGGT 59.510 47.619 0.00 0.00 34.08 4.00
2564 7135 1.876156 CAACCTTTGAGTGAGCTGGTC 59.124 52.381 0.00 0.00 0.00 4.02
2565 7136 1.428869 ACCTTTGAGTGAGCTGGTCT 58.571 50.000 8.47 0.00 0.00 3.85
2566 7137 1.771255 ACCTTTGAGTGAGCTGGTCTT 59.229 47.619 8.47 0.00 0.00 3.01
2567 7138 2.224402 ACCTTTGAGTGAGCTGGTCTTC 60.224 50.000 8.47 6.69 0.00 2.87
2568 7139 2.224378 CCTTTGAGTGAGCTGGTCTTCA 60.224 50.000 8.47 9.05 0.00 3.02
2569 7140 2.533266 TTGAGTGAGCTGGTCTTCAC 57.467 50.000 8.47 0.00 0.00 3.18
2570 7141 1.413118 TGAGTGAGCTGGTCTTCACA 58.587 50.000 8.47 4.03 35.73 3.58
2571 7142 1.342496 TGAGTGAGCTGGTCTTCACAG 59.658 52.381 8.47 0.00 38.95 3.66
2607 7178 7.266400 ACTACTTACTAATCTGCTTGCCTTAC 58.734 38.462 0.00 0.00 0.00 2.34
2608 7179 6.301169 ACTTACTAATCTGCTTGCCTTACT 57.699 37.500 0.00 0.00 0.00 2.24
2609 7180 7.419711 ACTTACTAATCTGCTTGCCTTACTA 57.580 36.000 0.00 0.00 0.00 1.82
2610 7181 7.848128 ACTTACTAATCTGCTTGCCTTACTAA 58.152 34.615 0.00 0.00 0.00 2.24
2612 7183 8.888579 TTACTAATCTGCTTGCCTTACTAATC 57.111 34.615 0.00 0.00 0.00 1.75
2614 7185 8.251383 ACTAATCTGCTTGCCTTACTAATCTA 57.749 34.615 0.00 0.00 0.00 1.98
2615 7186 8.145122 ACTAATCTGCTTGCCTTACTAATCTAC 58.855 37.037 0.00 0.00 0.00 2.59
2616 7187 6.739331 ATCTGCTTGCCTTACTAATCTACT 57.261 37.500 0.00 0.00 0.00 2.57
2617 7188 5.907207 TCTGCTTGCCTTACTAATCTACTG 58.093 41.667 0.00 0.00 0.00 2.74
2618 7189 5.656859 TCTGCTTGCCTTACTAATCTACTGA 59.343 40.000 0.00 0.00 0.00 3.41
2619 7190 5.907207 TGCTTGCCTTACTAATCTACTGAG 58.093 41.667 0.00 0.00 0.00 3.35
2638 7209 7.736447 ACTGAGTAATTTCTTGAACTGAAGG 57.264 36.000 0.00 0.00 0.00 3.46
2692 7263 2.094286 CCCGAGAGATCATCTATGGTGC 60.094 54.545 0.00 0.00 38.84 5.01
2716 7287 8.409371 TGCTCTCAATACTGACTTACTTCATAG 58.591 37.037 0.00 0.00 0.00 2.23
2717 7288 8.410141 GCTCTCAATACTGACTTACTTCATAGT 58.590 37.037 0.00 0.00 38.44 2.12
2744 7315 8.718102 TTTAGCAATATTGTTAGACAGGAGAC 57.282 34.615 16.61 0.00 0.00 3.36
2745 7316 6.552445 AGCAATATTGTTAGACAGGAGACT 57.448 37.500 16.61 0.00 46.44 3.24
2746 7317 6.578023 AGCAATATTGTTAGACAGGAGACTC 58.422 40.000 16.61 0.00 40.21 3.36
2747 7318 5.460419 GCAATATTGTTAGACAGGAGACTCG 59.540 44.000 16.61 0.00 40.21 4.18
2748 7319 5.776173 ATATTGTTAGACAGGAGACTCGG 57.224 43.478 0.00 0.00 40.21 4.63
2749 7320 2.581216 TGTTAGACAGGAGACTCGGT 57.419 50.000 0.00 0.00 40.21 4.69
2750 7321 2.434428 TGTTAGACAGGAGACTCGGTC 58.566 52.381 14.73 14.73 40.21 4.79
2751 7322 1.744522 GTTAGACAGGAGACTCGGTCC 59.255 57.143 17.49 4.47 40.21 4.46
2752 7323 0.989602 TAGACAGGAGACTCGGTCCA 59.010 55.000 17.49 6.22 40.21 4.02
2753 7324 0.609681 AGACAGGAGACTCGGTCCAC 60.610 60.000 17.49 0.60 40.21 4.02
2754 7325 1.596895 GACAGGAGACTCGGTCCACC 61.597 65.000 12.53 5.48 40.21 4.61
2755 7326 1.606601 CAGGAGACTCGGTCCACCA 60.607 63.158 14.82 0.00 40.21 4.17
2756 7327 1.155390 AGGAGACTCGGTCCACCAA 59.845 57.895 14.82 0.00 36.43 3.67
2757 7328 0.900647 AGGAGACTCGGTCCACCAAG 60.901 60.000 14.82 0.00 36.43 3.61
2758 7329 1.186267 GGAGACTCGGTCCACCAAGT 61.186 60.000 0.00 0.00 33.84 3.16
2759 7330 0.244178 GAGACTCGGTCCACCAAGTC 59.756 60.000 8.59 8.59 35.14 3.01
2760 7331 0.178958 AGACTCGGTCCACCAAGTCT 60.179 55.000 12.84 12.84 35.14 3.24
2761 7332 0.244178 GACTCGGTCCACCAAGTCTC 59.756 60.000 9.28 0.00 35.14 3.36
2762 7333 1.186267 ACTCGGTCCACCAAGTCTCC 61.186 60.000 0.00 0.00 35.14 3.71
2763 7334 1.889530 CTCGGTCCACCAAGTCTCCC 61.890 65.000 0.00 0.00 35.14 4.30
2764 7335 2.955881 CGGTCCACCAAGTCTCCCC 61.956 68.421 0.00 0.00 35.14 4.81
2765 7336 1.846124 GGTCCACCAAGTCTCCCCA 60.846 63.158 0.00 0.00 35.64 4.96
2766 7337 1.375326 GTCCACCAAGTCTCCCCAC 59.625 63.158 0.00 0.00 0.00 4.61
2767 7338 2.214216 TCCACCAAGTCTCCCCACG 61.214 63.158 0.00 0.00 0.00 4.94
2768 7339 2.214216 CCACCAAGTCTCCCCACGA 61.214 63.158 0.00 0.00 0.00 4.35
2769 7340 1.553690 CCACCAAGTCTCCCCACGAT 61.554 60.000 0.00 0.00 0.00 3.73
2770 7341 0.108138 CACCAAGTCTCCCCACGATC 60.108 60.000 0.00 0.00 0.00 3.69
2771 7342 0.252284 ACCAAGTCTCCCCACGATCT 60.252 55.000 0.00 0.00 0.00 2.75
2772 7343 0.176680 CCAAGTCTCCCCACGATCTG 59.823 60.000 0.00 0.00 0.00 2.90
2773 7344 0.460987 CAAGTCTCCCCACGATCTGC 60.461 60.000 0.00 0.00 0.00 4.26
2775 7346 3.838271 TCTCCCCACGATCTGCGC 61.838 66.667 0.00 0.00 46.04 6.09
2776 7347 4.147449 CTCCCCACGATCTGCGCA 62.147 66.667 10.98 10.98 46.04 6.09
2777 7348 4.451150 TCCCCACGATCTGCGCAC 62.451 66.667 5.66 0.00 46.04 5.34
2779 7350 4.794439 CCCACGATCTGCGCACGA 62.794 66.667 23.36 17.11 46.04 4.35
2780 7351 3.545481 CCACGATCTGCGCACGAC 61.545 66.667 23.36 9.05 46.04 4.34
2781 7352 2.504899 CACGATCTGCGCACGACT 60.505 61.111 23.36 8.22 46.04 4.18
2782 7353 1.226295 CACGATCTGCGCACGACTA 60.226 57.895 23.36 0.25 46.04 2.59
2783 7354 1.062685 ACGATCTGCGCACGACTAG 59.937 57.895 23.36 13.52 46.04 2.57
2784 7355 1.655654 CGATCTGCGCACGACTAGG 60.656 63.158 5.66 0.00 0.00 3.02
2785 7356 1.946650 GATCTGCGCACGACTAGGC 60.947 63.158 5.66 0.00 0.00 3.93
2792 7363 2.430244 CACGACTAGGCGCACGTT 60.430 61.111 20.33 0.00 36.86 3.99
2793 7364 2.126580 ACGACTAGGCGCACGTTC 60.127 61.111 20.33 0.00 35.47 3.95
2794 7365 2.178521 CGACTAGGCGCACGTTCT 59.821 61.111 4.31 0.00 0.00 3.01
2795 7366 1.868251 CGACTAGGCGCACGTTCTC 60.868 63.158 4.31 0.00 0.00 2.87
2796 7367 1.516603 GACTAGGCGCACGTTCTCC 60.517 63.158 10.83 0.00 0.00 3.71
2797 7368 2.579787 CTAGGCGCACGTTCTCCG 60.580 66.667 10.83 0.00 44.03 4.63
2807 7378 2.437850 CGTTCTCCGTTACGTTGGG 58.562 57.895 3.52 0.00 33.33 4.12
2808 7379 1.620413 CGTTCTCCGTTACGTTGGGC 61.620 60.000 3.52 0.00 33.33 5.36
2823 7394 3.807368 GGCGTGGCCCTCCTATAT 58.193 61.111 0.00 0.00 44.06 0.86
2824 7395 1.296715 GGCGTGGCCCTCCTATATG 59.703 63.158 0.00 0.00 44.06 1.78
2825 7396 1.481056 GGCGTGGCCCTCCTATATGT 61.481 60.000 0.00 0.00 44.06 2.29
2826 7397 1.263356 GCGTGGCCCTCCTATATGTA 58.737 55.000 0.00 0.00 0.00 2.29
2827 7398 1.067071 GCGTGGCCCTCCTATATGTAC 60.067 57.143 0.00 0.00 0.00 2.90
2828 7399 1.549170 CGTGGCCCTCCTATATGTACC 59.451 57.143 0.00 0.00 0.00 3.34
2829 7400 1.907255 GTGGCCCTCCTATATGTACCC 59.093 57.143 0.00 0.00 0.00 3.69
2830 7401 1.799575 TGGCCCTCCTATATGTACCCT 59.200 52.381 0.00 0.00 0.00 4.34
2831 7402 2.188817 GGCCCTCCTATATGTACCCTG 58.811 57.143 0.00 0.00 0.00 4.45
2832 7403 1.555533 GCCCTCCTATATGTACCCTGC 59.444 57.143 0.00 0.00 0.00 4.85
2833 7404 2.188817 CCCTCCTATATGTACCCTGCC 58.811 57.143 0.00 0.00 0.00 4.85
2834 7405 2.225650 CCCTCCTATATGTACCCTGCCT 60.226 54.545 0.00 0.00 0.00 4.75
2835 7406 3.521727 CCTCCTATATGTACCCTGCCTT 58.478 50.000 0.00 0.00 0.00 4.35
2836 7407 3.261897 CCTCCTATATGTACCCTGCCTTG 59.738 52.174 0.00 0.00 0.00 3.61
2837 7408 3.904339 CTCCTATATGTACCCTGCCTTGT 59.096 47.826 0.00 0.00 0.00 3.16
2838 7409 5.082633 TCCTATATGTACCCTGCCTTGTA 57.917 43.478 0.00 0.00 0.00 2.41
2839 7410 4.836736 TCCTATATGTACCCTGCCTTGTAC 59.163 45.833 0.00 0.00 38.22 2.90
2840 7411 4.838986 CCTATATGTACCCTGCCTTGTACT 59.161 45.833 0.00 0.00 38.48 2.73
2841 7412 4.957684 ATATGTACCCTGCCTTGTACTC 57.042 45.455 0.00 0.00 38.48 2.59
2842 7413 2.320681 TGTACCCTGCCTTGTACTCT 57.679 50.000 0.00 0.00 38.48 3.24
2843 7414 1.899814 TGTACCCTGCCTTGTACTCTG 59.100 52.381 0.00 0.00 38.48 3.35
2844 7415 2.176889 GTACCCTGCCTTGTACTCTGA 58.823 52.381 0.00 0.00 35.55 3.27
2845 7416 1.729586 ACCCTGCCTTGTACTCTGAA 58.270 50.000 0.00 0.00 0.00 3.02
2846 7417 2.269940 ACCCTGCCTTGTACTCTGAAT 58.730 47.619 0.00 0.00 0.00 2.57
2847 7418 2.026822 ACCCTGCCTTGTACTCTGAATG 60.027 50.000 0.00 0.00 0.00 2.67
2848 7419 2.237143 CCCTGCCTTGTACTCTGAATGA 59.763 50.000 0.00 0.00 0.00 2.57
2849 7420 3.307691 CCCTGCCTTGTACTCTGAATGAA 60.308 47.826 0.00 0.00 0.00 2.57
2850 7421 4.521146 CCTGCCTTGTACTCTGAATGAAT 58.479 43.478 0.00 0.00 0.00 2.57
2851 7422 4.946157 CCTGCCTTGTACTCTGAATGAATT 59.054 41.667 0.00 0.00 0.00 2.17
2852 7423 6.115446 CCTGCCTTGTACTCTGAATGAATTA 58.885 40.000 0.00 0.00 0.00 1.40
2853 7424 6.599244 CCTGCCTTGTACTCTGAATGAATTAA 59.401 38.462 0.00 0.00 0.00 1.40
2854 7425 7.201679 CCTGCCTTGTACTCTGAATGAATTAAG 60.202 40.741 0.00 0.00 0.00 1.85
2855 7426 6.599244 TGCCTTGTACTCTGAATGAATTAAGG 59.401 38.462 0.00 0.00 35.31 2.69
2856 7427 6.823689 GCCTTGTACTCTGAATGAATTAAGGA 59.176 38.462 0.00 0.00 34.38 3.36
2857 7428 7.336931 GCCTTGTACTCTGAATGAATTAAGGAA 59.663 37.037 0.00 0.00 34.38 3.36
2858 7429 9.231297 CCTTGTACTCTGAATGAATTAAGGAAA 57.769 33.333 0.00 0.00 34.38 3.13
2860 7431 9.793259 TTGTACTCTGAATGAATTAAGGAAAGT 57.207 29.630 0.00 0.00 0.00 2.66
2864 7435 9.660180 ACTCTGAATGAATTAAGGAAAGTACTC 57.340 33.333 0.00 0.00 0.00 2.59
2865 7436 9.883142 CTCTGAATGAATTAAGGAAAGTACTCT 57.117 33.333 0.00 0.00 0.00 3.24
2866 7437 9.658799 TCTGAATGAATTAAGGAAAGTACTCTG 57.341 33.333 0.00 0.00 0.00 3.35
2867 7438 9.442047 CTGAATGAATTAAGGAAAGTACTCTGT 57.558 33.333 0.00 0.00 0.00 3.41
2868 7439 9.793259 TGAATGAATTAAGGAAAGTACTCTGTT 57.207 29.630 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.271921 AGTAATCTGGATGCATACCTTATATGA 57.728 33.333 6.42 0.00 0.00 2.15
12 13 9.599866 CGGAAATATATTAGTAATCTGGATGCA 57.400 33.333 0.00 0.00 0.00 3.96
13 14 9.046296 CCGGAAATATATTAGTAATCTGGATGC 57.954 37.037 13.51 0.00 34.47 3.91
16 17 8.464404 CGTCCGGAAATATATTAGTAATCTGGA 58.536 37.037 5.23 16.03 38.27 3.86
17 18 7.705325 CCGTCCGGAAATATATTAGTAATCTGG 59.295 40.741 5.23 12.88 37.50 3.86
18 19 8.464404 TCCGTCCGGAAATATATTAGTAATCTG 58.536 37.037 5.23 0.00 42.05 2.90
19 20 8.585471 TCCGTCCGGAAATATATTAGTAATCT 57.415 34.615 5.23 0.00 42.05 2.40
20 21 7.919621 CCTCCGTCCGGAAATATATTAGTAATC 59.080 40.741 5.23 0.00 44.66 1.75
21 22 7.147776 CCCTCCGTCCGGAAATATATTAGTAAT 60.148 40.741 5.23 0.17 44.66 1.89
22 23 6.153340 CCCTCCGTCCGGAAATATATTAGTAA 59.847 42.308 5.23 0.00 44.66 2.24
23 24 5.653769 CCCTCCGTCCGGAAATATATTAGTA 59.346 44.000 5.23 0.00 44.66 1.82
24 25 4.465305 CCCTCCGTCCGGAAATATATTAGT 59.535 45.833 5.23 0.00 44.66 2.24
25 26 4.708421 TCCCTCCGTCCGGAAATATATTAG 59.292 45.833 5.23 0.00 44.66 1.73
26 27 4.676109 TCCCTCCGTCCGGAAATATATTA 58.324 43.478 5.23 0.00 44.66 0.98
27 28 3.513517 TCCCTCCGTCCGGAAATATATT 58.486 45.455 5.23 0.00 44.66 1.28
28 29 3.097614 CTCCCTCCGTCCGGAAATATAT 58.902 50.000 5.23 0.00 44.66 0.86
29 30 2.158415 ACTCCCTCCGTCCGGAAATATA 60.158 50.000 5.23 0.00 44.66 0.86
30 31 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
31 32 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
32 33 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
33 34 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
34 35 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
35 36 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
36 37 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
37 38 1.712977 CGAAGTACTCCCTCCGTCCG 61.713 65.000 0.00 0.00 0.00 4.79
38 39 0.679321 ACGAAGTACTCCCTCCGTCC 60.679 60.000 0.00 0.00 41.94 4.79
39 40 1.135460 CAACGAAGTACTCCCTCCGTC 60.135 57.143 0.00 0.00 45.00 4.79
40 41 0.886563 CAACGAAGTACTCCCTCCGT 59.113 55.000 0.00 0.00 45.00 4.69
41 42 0.886563 ACAACGAAGTACTCCCTCCG 59.113 55.000 0.00 0.00 45.00 4.63
42 43 2.426381 CCTACAACGAAGTACTCCCTCC 59.574 54.545 0.00 0.00 45.00 4.30
43 44 3.087781 ACCTACAACGAAGTACTCCCTC 58.912 50.000 0.00 0.00 45.00 4.30
44 45 3.087781 GACCTACAACGAAGTACTCCCT 58.912 50.000 0.00 0.00 45.00 4.20
45 46 3.087781 AGACCTACAACGAAGTACTCCC 58.912 50.000 0.00 0.00 45.00 4.30
46 47 6.765512 ACTATAGACCTACAACGAAGTACTCC 59.234 42.308 6.78 0.00 45.00 3.85
47 48 7.784633 ACTATAGACCTACAACGAAGTACTC 57.215 40.000 6.78 0.00 45.00 2.59
48 49 9.323985 CTTACTATAGACCTACAACGAAGTACT 57.676 37.037 6.78 0.00 45.00 2.73
49 50 9.319143 TCTTACTATAGACCTACAACGAAGTAC 57.681 37.037 6.78 0.00 45.00 2.73
50 51 9.890629 TTCTTACTATAGACCTACAACGAAGTA 57.109 33.333 6.78 0.00 45.00 2.24
52 53 9.500864 GTTTCTTACTATAGACCTACAACGAAG 57.499 37.037 6.78 0.00 0.00 3.79
53 54 9.236006 AGTTTCTTACTATAGACCTACAACGAA 57.764 33.333 6.78 0.00 34.56 3.85
54 55 8.798859 AGTTTCTTACTATAGACCTACAACGA 57.201 34.615 6.78 0.00 34.56 3.85
65 66 8.491152 GCATGTGCATGTAGTTTCTTACTATAG 58.509 37.037 12.96 0.00 40.08 1.31
72 73 2.162208 CCGCATGTGCATGTAGTTTCTT 59.838 45.455 12.96 0.00 42.21 2.52
149 150 7.515998 GCACGCTAAAATAGAGATTCAGTTCTC 60.516 40.741 0.00 0.00 42.08 2.87
150 151 6.256757 GCACGCTAAAATAGAGATTCAGTTCT 59.743 38.462 0.00 0.00 0.00 3.01
151 152 6.256757 AGCACGCTAAAATAGAGATTCAGTTC 59.743 38.462 0.00 0.00 0.00 3.01
177 178 0.251165 TAGCCCAGGTCTTTGCAACC 60.251 55.000 0.00 0.00 37.03 3.77
208 210 6.803366 ACTACCAGGTCGTATAGGATTTTT 57.197 37.500 0.00 0.00 0.00 1.94
225 227 1.180456 TCGTTCGCTCCCAACTACCA 61.180 55.000 0.00 0.00 0.00 3.25
292 295 1.203428 TGGGGAAGAAGATGGAGTGGA 60.203 52.381 0.00 0.00 0.00 4.02
310 313 2.518949 GCGCTACAACACATGATTTGG 58.481 47.619 0.00 0.00 0.00 3.28
322 325 0.747852 TCGATATGGTGGCGCTACAA 59.252 50.000 25.79 15.84 0.00 2.41
323 326 0.966179 ATCGATATGGTGGCGCTACA 59.034 50.000 25.79 13.56 0.00 2.74
486 489 1.439353 CTGGCACTGCGTTGTTCAGT 61.439 55.000 0.00 0.00 44.87 3.41
540 557 3.501548 TAAATGAACGCGGGCGGC 61.502 61.111 18.03 7.01 44.69 6.53
544 561 2.401990 GCCGTAAATGAACGCGGG 59.598 61.111 12.47 0.00 43.90 6.13
551 568 1.640428 CTTGCTCTCGCCGTAAATGA 58.360 50.000 0.00 0.00 34.43 2.57
616 633 1.613437 CGGCAAGTCCATGGAAAAGTT 59.387 47.619 18.20 5.03 34.01 2.66
618 635 1.470098 CTCGGCAAGTCCATGGAAAAG 59.530 52.381 18.20 10.08 34.01 2.27
664 684 2.350522 GACATCGTGGAGTTGATGCTT 58.649 47.619 2.33 0.00 44.57 3.91
793 932 0.739462 TGCGTCCGCGAATCTCAAAT 60.739 50.000 8.23 0.00 45.51 2.32
810 949 0.729116 CTCCATCCAATGACACGTGC 59.271 55.000 17.22 9.30 0.00 5.34
864 1163 5.452636 GGACTTGACCTGACTCTATCCAATC 60.453 48.000 0.00 0.00 0.00 2.67
879 1367 2.298163 TCAGGAACTAACGGACTTGACC 59.702 50.000 0.00 0.00 36.02 4.02
886 1374 5.591877 GTCCTAGTAATCAGGAACTAACGGA 59.408 44.000 0.00 0.00 43.78 4.69
894 1382 4.942944 TGGACAGTCCTAGTAATCAGGAA 58.057 43.478 20.82 0.00 43.78 3.36
912 4190 3.034635 AGTAGGTGATGGACTGATGGAC 58.965 50.000 0.00 0.00 0.00 4.02
913 4191 3.300388 GAGTAGGTGATGGACTGATGGA 58.700 50.000 0.00 0.00 0.00 3.41
914 4192 2.366916 GGAGTAGGTGATGGACTGATGG 59.633 54.545 0.00 0.00 0.00 3.51
915 4193 2.035193 CGGAGTAGGTGATGGACTGATG 59.965 54.545 0.00 0.00 0.00 3.07
916 4194 2.311463 CGGAGTAGGTGATGGACTGAT 58.689 52.381 0.00 0.00 0.00 2.90
917 4195 1.005569 ACGGAGTAGGTGATGGACTGA 59.994 52.381 0.00 0.00 41.94 3.41
918 4196 1.475403 ACGGAGTAGGTGATGGACTG 58.525 55.000 0.00 0.00 41.94 3.51
1053 4341 2.143876 TCTCCCAGATGACGATGTCA 57.856 50.000 1.65 1.65 46.90 3.58
1089 4377 2.751837 CGGAGAAGGGCTTTGGGC 60.752 66.667 0.00 0.00 40.90 5.36
1213 4517 2.672908 TAGTATTCGCCGCTGCCGTC 62.673 60.000 0.00 0.00 0.00 4.79
1282 4589 1.967319 TCAAGCTGGGTGAAGTGTTC 58.033 50.000 0.00 0.00 0.00 3.18
1424 4881 1.064906 AGGGCATCATGAGGTCACAAG 60.065 52.381 14.65 0.00 0.00 3.16
1432 4889 1.961394 CATTCCCAAGGGCATCATGAG 59.039 52.381 0.09 0.00 34.68 2.90
1489 4958 7.894376 TTTCTTCCTCGTTTTTATCGTACAT 57.106 32.000 0.00 0.00 0.00 2.29
1494 4963 6.961554 CCTCAATTTCTTCCTCGTTTTTATCG 59.038 38.462 0.00 0.00 0.00 2.92
1515 5002 8.281531 ACATATATTTCCTCATTTTCACCCTCA 58.718 33.333 0.00 0.00 0.00 3.86
1518 5005 7.308589 CGGACATATATTTCCTCATTTTCACCC 60.309 40.741 14.56 0.00 0.00 4.61
1522 5009 8.378172 TCACGGACATATATTTCCTCATTTTC 57.622 34.615 14.56 0.00 0.00 2.29
1524 5014 7.391554 CCATCACGGACATATATTTCCTCATTT 59.608 37.037 14.56 0.00 36.56 2.32
1525 5015 6.881065 CCATCACGGACATATATTTCCTCATT 59.119 38.462 14.56 0.00 36.56 2.57
1641 6071 1.746615 CAAGACGACTGCCCCATGG 60.747 63.158 4.14 4.14 0.00 3.66
1705 6140 2.480845 GAATACCAGTACCATGTCGCC 58.519 52.381 0.00 0.00 0.00 5.54
1768 6203 2.805099 GACAGTCTGGAGCAACTTGAAG 59.195 50.000 4.53 0.00 0.00 3.02
1823 6267 1.133253 CAACTGAACATGCCGAGCG 59.867 57.895 0.00 0.00 0.00 5.03
1842 6286 3.181533 CGACGATAGCTGCATCATCATTG 60.182 47.826 1.02 0.00 42.67 2.82
1861 6305 5.299782 AGTCCTTCAACACCTAGATATCGAC 59.700 44.000 0.00 0.00 0.00 4.20
1871 6315 6.542821 TCATTTTCATAGTCCTTCAACACCT 58.457 36.000 0.00 0.00 0.00 4.00
1935 6381 5.410924 TCTCCACACAATAACTTGATCTCG 58.589 41.667 0.00 0.00 36.20 4.04
1960 6406 4.526970 ACCACCACATACAAGGAATCATC 58.473 43.478 0.00 0.00 0.00 2.92
2034 6486 1.815003 CCTTCCATGTCAACCTGAAGC 59.185 52.381 0.00 0.00 0.00 3.86
2055 6507 2.096248 TGAAAACTGCCGACCAACTTT 58.904 42.857 0.00 0.00 0.00 2.66
2095 6547 0.599558 TGCTTCAGCTGCAATTGACC 59.400 50.000 9.47 0.00 42.66 4.02
2248 6809 0.104304 ACTGGATCCCATTCGTACGC 59.896 55.000 11.24 0.00 30.82 4.42
2249 6810 3.254903 TCATACTGGATCCCATTCGTACG 59.745 47.826 9.53 9.53 30.82 3.67
2379 6941 4.269183 TCAACATGGACAACAGTCACTTT 58.731 39.130 0.00 0.00 33.90 2.66
2495 7066 7.038516 AGGCAAAGGTTGTACTAAGTATACTGT 60.039 37.037 6.06 3.61 0.00 3.55
2496 7067 7.328737 AGGCAAAGGTTGTACTAAGTATACTG 58.671 38.462 6.06 0.00 0.00 2.74
2498 7069 7.554211 AGAGGCAAAGGTTGTACTAAGTATAC 58.446 38.462 0.00 0.00 0.00 1.47
2501 7072 6.429521 AAGAGGCAAAGGTTGTACTAAGTA 57.570 37.500 0.00 0.00 0.00 2.24
2502 7073 4.976540 AGAGGCAAAGGTTGTACTAAGT 57.023 40.909 0.00 0.00 0.00 2.24
2503 7074 4.695928 GGAAGAGGCAAAGGTTGTACTAAG 59.304 45.833 0.00 0.00 0.00 2.18
2506 7077 2.441750 TGGAAGAGGCAAAGGTTGTACT 59.558 45.455 0.00 0.00 0.00 2.73
2507 7078 2.858745 TGGAAGAGGCAAAGGTTGTAC 58.141 47.619 0.00 0.00 0.00 2.90
2509 7080 2.683211 ATGGAAGAGGCAAAGGTTGT 57.317 45.000 0.00 0.00 0.00 3.32
2510 7081 4.082125 ACTTATGGAAGAGGCAAAGGTTG 58.918 43.478 0.00 0.00 36.45 3.77
2511 7082 4.388577 ACTTATGGAAGAGGCAAAGGTT 57.611 40.909 0.00 0.00 36.45 3.50
2514 7085 6.581171 AAAGAACTTATGGAAGAGGCAAAG 57.419 37.500 0.00 0.00 36.45 2.77
2515 7086 6.976934 AAAAGAACTTATGGAAGAGGCAAA 57.023 33.333 0.00 0.00 36.45 3.68
2516 7087 6.976934 AAAAAGAACTTATGGAAGAGGCAA 57.023 33.333 0.00 0.00 36.45 4.52
2536 7107 5.047377 AGCTCACTCAAAGGTTGAACAAAAA 60.047 36.000 0.00 0.00 39.58 1.94
2537 7108 4.462483 AGCTCACTCAAAGGTTGAACAAAA 59.538 37.500 0.00 0.00 39.58 2.44
2538 7109 4.016444 AGCTCACTCAAAGGTTGAACAAA 58.984 39.130 0.00 0.00 39.58 2.83
2539 7110 3.378112 CAGCTCACTCAAAGGTTGAACAA 59.622 43.478 0.00 0.00 39.58 2.83
2540 7111 2.945008 CAGCTCACTCAAAGGTTGAACA 59.055 45.455 0.00 0.00 39.58 3.18
2541 7112 2.291741 CCAGCTCACTCAAAGGTTGAAC 59.708 50.000 0.00 0.00 39.58 3.18
2542 7113 2.092429 ACCAGCTCACTCAAAGGTTGAA 60.092 45.455 0.00 0.00 39.58 2.69
2543 7114 1.490490 ACCAGCTCACTCAAAGGTTGA 59.510 47.619 0.00 0.00 38.17 3.18
2544 7115 1.876156 GACCAGCTCACTCAAAGGTTG 59.124 52.381 0.00 0.00 0.00 3.77
2545 7116 1.771255 AGACCAGCTCACTCAAAGGTT 59.229 47.619 0.00 0.00 0.00 3.50
2546 7117 1.428869 AGACCAGCTCACTCAAAGGT 58.571 50.000 0.00 0.00 0.00 3.50
2547 7118 2.224378 TGAAGACCAGCTCACTCAAAGG 60.224 50.000 0.00 0.00 0.00 3.11
2548 7119 2.805099 GTGAAGACCAGCTCACTCAAAG 59.195 50.000 0.00 0.00 0.00 2.77
2549 7120 2.170397 TGTGAAGACCAGCTCACTCAAA 59.830 45.455 4.07 0.00 34.51 2.69
2550 7121 1.762370 TGTGAAGACCAGCTCACTCAA 59.238 47.619 4.07 0.00 34.51 3.02
2551 7122 1.342496 CTGTGAAGACCAGCTCACTCA 59.658 52.381 4.07 0.00 34.51 3.41
2552 7123 1.342819 ACTGTGAAGACCAGCTCACTC 59.657 52.381 4.07 0.00 34.51 3.51
2553 7124 1.418334 ACTGTGAAGACCAGCTCACT 58.582 50.000 4.07 0.00 34.51 3.41
2554 7125 3.601443 ATACTGTGAAGACCAGCTCAC 57.399 47.619 0.00 0.00 33.09 3.51
2555 7126 4.344978 AGTATACTGTGAAGACCAGCTCA 58.655 43.478 4.10 0.00 33.09 4.26
2556 7127 4.993029 AGTATACTGTGAAGACCAGCTC 57.007 45.455 4.10 0.00 33.09 4.09
2557 7128 5.952947 ACTAAGTATACTGTGAAGACCAGCT 59.047 40.000 6.06 0.00 33.09 4.24
2558 7129 6.210287 ACTAAGTATACTGTGAAGACCAGC 57.790 41.667 6.06 0.00 33.09 4.85
2559 7130 8.508883 AGTACTAAGTATACTGTGAAGACCAG 57.491 38.462 6.06 0.00 31.54 4.00
2560 7131 9.388506 GTAGTACTAAGTATACTGTGAAGACCA 57.611 37.037 6.06 0.00 34.66 4.02
2561 7132 9.612066 AGTAGTACTAAGTATACTGTGAAGACC 57.388 37.037 6.06 0.00 34.66 3.85
2597 7168 5.908341 ACTCAGTAGATTAGTAAGGCAAGC 58.092 41.667 0.00 0.00 0.00 4.01
2612 7183 8.930760 CCTTCAGTTCAAGAAATTACTCAGTAG 58.069 37.037 0.00 0.00 0.00 2.57
2614 7185 7.442666 GTCCTTCAGTTCAAGAAATTACTCAGT 59.557 37.037 0.00 0.00 0.00 3.41
2615 7186 7.659390 AGTCCTTCAGTTCAAGAAATTACTCAG 59.341 37.037 0.00 0.00 0.00 3.35
2616 7187 7.442364 CAGTCCTTCAGTTCAAGAAATTACTCA 59.558 37.037 0.00 0.00 0.00 3.41
2617 7188 7.657761 TCAGTCCTTCAGTTCAAGAAATTACTC 59.342 37.037 0.00 0.00 0.00 2.59
2618 7189 7.509546 TCAGTCCTTCAGTTCAAGAAATTACT 58.490 34.615 0.00 0.00 0.00 2.24
2619 7190 7.730364 TCAGTCCTTCAGTTCAAGAAATTAC 57.270 36.000 0.00 0.00 0.00 1.89
2635 7206 7.301868 TGATAAAAAGGCAAAATCAGTCCTT 57.698 32.000 0.00 0.00 40.39 3.36
2638 7209 7.586714 CCTTGATAAAAAGGCAAAATCAGTC 57.413 36.000 0.00 0.00 40.37 3.51
2677 7248 6.725369 AGTATTGAGAGCACCATAGATGATCT 59.275 38.462 0.00 0.00 45.22 2.75
2718 7289 9.331282 GTCTCCTGTCTAACAATATTGCTAAAT 57.669 33.333 15.48 0.16 0.00 1.40
2730 7301 2.434428 GACCGAGTCTCCTGTCTAACA 58.566 52.381 9.05 0.00 0.00 2.41
2731 7302 1.744522 GGACCGAGTCTCCTGTCTAAC 59.255 57.143 13.87 0.00 32.47 2.34
2732 7303 1.353358 TGGACCGAGTCTCCTGTCTAA 59.647 52.381 13.87 4.19 32.47 2.10
2733 7304 0.989602 TGGACCGAGTCTCCTGTCTA 59.010 55.000 13.87 7.73 32.47 2.59
2734 7305 0.609681 GTGGACCGAGTCTCCTGTCT 60.610 60.000 13.87 0.00 32.47 3.41
2735 7306 1.596895 GGTGGACCGAGTCTCCTGTC 61.597 65.000 8.14 8.14 32.47 3.51
2736 7307 1.606889 GGTGGACCGAGTCTCCTGT 60.607 63.158 0.54 0.00 32.47 4.00
2737 7308 1.185618 TTGGTGGACCGAGTCTCCTG 61.186 60.000 0.54 0.00 39.43 3.86
2738 7309 0.900647 CTTGGTGGACCGAGTCTCCT 60.901 60.000 5.01 0.00 41.66 3.69
2739 7310 1.592223 CTTGGTGGACCGAGTCTCC 59.408 63.158 5.01 7.52 41.66 3.71
2745 7316 1.911766 GGGAGACTTGGTGGACCGA 60.912 63.158 0.00 0.00 39.43 4.69
2746 7317 2.663196 GGGAGACTTGGTGGACCG 59.337 66.667 0.00 0.00 39.43 4.79
2747 7318 1.846124 TGGGGAGACTTGGTGGACC 60.846 63.158 0.00 0.00 0.00 4.46
2748 7319 1.375326 GTGGGGAGACTTGGTGGAC 59.625 63.158 0.00 0.00 0.00 4.02
2749 7320 2.214216 CGTGGGGAGACTTGGTGGA 61.214 63.158 0.00 0.00 0.00 4.02
2750 7321 1.553690 ATCGTGGGGAGACTTGGTGG 61.554 60.000 0.00 0.00 0.00 4.61
2751 7322 0.108138 GATCGTGGGGAGACTTGGTG 60.108 60.000 0.00 0.00 0.00 4.17
2752 7323 0.252284 AGATCGTGGGGAGACTTGGT 60.252 55.000 0.00 0.00 0.00 3.67
2753 7324 0.176680 CAGATCGTGGGGAGACTTGG 59.823 60.000 0.00 0.00 0.00 3.61
2754 7325 0.460987 GCAGATCGTGGGGAGACTTG 60.461 60.000 0.00 0.00 0.00 3.16
2755 7326 1.901085 GCAGATCGTGGGGAGACTT 59.099 57.895 0.00 0.00 0.00 3.01
2756 7327 2.418910 CGCAGATCGTGGGGAGACT 61.419 63.158 0.00 0.00 35.43 3.24
2757 7328 2.105128 CGCAGATCGTGGGGAGAC 59.895 66.667 0.00 0.00 35.43 3.36
2758 7329 3.838271 GCGCAGATCGTGGGGAGA 61.838 66.667 0.30 0.00 39.54 3.71
2759 7330 4.147449 TGCGCAGATCGTGGGGAG 62.147 66.667 5.66 0.00 39.54 4.30
2760 7331 4.451150 GTGCGCAGATCGTGGGGA 62.451 66.667 12.22 5.67 39.54 4.81
2762 7333 4.794439 TCGTGCGCAGATCGTGGG 62.794 66.667 12.22 5.30 42.10 4.61
2763 7334 2.592623 TAGTCGTGCGCAGATCGTGG 62.593 60.000 12.22 0.00 41.07 4.94
2764 7335 1.196749 CTAGTCGTGCGCAGATCGTG 61.197 60.000 12.22 0.00 41.07 4.35
2765 7336 1.062685 CTAGTCGTGCGCAGATCGT 59.937 57.895 12.22 0.00 41.07 3.73
2766 7337 1.655654 CCTAGTCGTGCGCAGATCG 60.656 63.158 12.22 12.20 42.12 3.69
2767 7338 1.946650 GCCTAGTCGTGCGCAGATC 60.947 63.158 12.22 3.60 0.00 2.75
2768 7339 2.105128 GCCTAGTCGTGCGCAGAT 59.895 61.111 12.22 0.00 0.00 2.90
2769 7340 4.476410 CGCCTAGTCGTGCGCAGA 62.476 66.667 12.22 8.04 44.64 4.26
2775 7346 2.430244 AACGTGCGCCTAGTCGTG 60.430 61.111 4.18 0.00 36.65 4.35
2776 7347 2.126580 GAACGTGCGCCTAGTCGT 60.127 61.111 4.18 5.38 38.15 4.34
2777 7348 1.868251 GAGAACGTGCGCCTAGTCG 60.868 63.158 4.18 4.70 0.00 4.18
2778 7349 1.516603 GGAGAACGTGCGCCTAGTC 60.517 63.158 9.43 0.00 0.00 2.59
2779 7350 2.572284 GGAGAACGTGCGCCTAGT 59.428 61.111 9.43 0.00 0.00 2.57
2780 7351 2.579787 CGGAGAACGTGCGCCTAG 60.580 66.667 14.99 0.00 37.93 3.02
2790 7361 1.620413 CGCCCAACGTAACGGAGAAC 61.620 60.000 0.00 0.00 36.87 3.01
2791 7362 1.373246 CGCCCAACGTAACGGAGAA 60.373 57.895 0.00 0.00 36.87 2.87
2792 7363 2.259204 CGCCCAACGTAACGGAGA 59.741 61.111 0.00 0.00 36.87 3.71
2807 7378 1.067071 GTACATATAGGAGGGCCACGC 60.067 57.143 6.18 0.00 36.29 5.34
2808 7379 1.549170 GGTACATATAGGAGGGCCACG 59.451 57.143 6.18 0.00 36.29 4.94
2809 7380 1.907255 GGGTACATATAGGAGGGCCAC 59.093 57.143 6.18 0.00 36.29 5.01
2810 7381 1.799575 AGGGTACATATAGGAGGGCCA 59.200 52.381 6.18 0.00 36.29 5.36
2811 7382 2.188817 CAGGGTACATATAGGAGGGCC 58.811 57.143 0.00 0.00 0.00 5.80
2812 7383 1.555533 GCAGGGTACATATAGGAGGGC 59.444 57.143 0.00 0.00 0.00 5.19
2813 7384 2.188817 GGCAGGGTACATATAGGAGGG 58.811 57.143 0.00 0.00 0.00 4.30
2814 7385 3.191888 AGGCAGGGTACATATAGGAGG 57.808 52.381 0.00 0.00 0.00 4.30
2815 7386 3.904339 ACAAGGCAGGGTACATATAGGAG 59.096 47.826 0.00 0.00 0.00 3.69
2816 7387 3.936461 ACAAGGCAGGGTACATATAGGA 58.064 45.455 0.00 0.00 0.00 2.94
2817 7388 4.838986 AGTACAAGGCAGGGTACATATAGG 59.161 45.833 13.36 0.00 41.74 2.57
2818 7389 5.775701 AGAGTACAAGGCAGGGTACATATAG 59.224 44.000 13.36 0.00 41.74 1.31
2819 7390 5.538813 CAGAGTACAAGGCAGGGTACATATA 59.461 44.000 13.36 0.00 41.74 0.86
2820 7391 4.345257 CAGAGTACAAGGCAGGGTACATAT 59.655 45.833 13.36 0.00 41.74 1.78
2821 7392 3.704566 CAGAGTACAAGGCAGGGTACATA 59.295 47.826 13.36 0.00 41.74 2.29
2822 7393 2.501723 CAGAGTACAAGGCAGGGTACAT 59.498 50.000 13.36 2.37 41.74 2.29
2823 7394 1.899814 CAGAGTACAAGGCAGGGTACA 59.100 52.381 13.36 0.00 41.74 2.90
2824 7395 2.176889 TCAGAGTACAAGGCAGGGTAC 58.823 52.381 0.00 5.55 40.06 3.34
2825 7396 2.615986 TCAGAGTACAAGGCAGGGTA 57.384 50.000 0.00 0.00 0.00 3.69
2826 7397 1.729586 TTCAGAGTACAAGGCAGGGT 58.270 50.000 0.00 0.00 0.00 4.34
2827 7398 2.237143 TCATTCAGAGTACAAGGCAGGG 59.763 50.000 0.00 0.00 0.00 4.45
2828 7399 3.616956 TCATTCAGAGTACAAGGCAGG 57.383 47.619 0.00 0.00 0.00 4.85
2829 7400 7.201679 CCTTAATTCATTCAGAGTACAAGGCAG 60.202 40.741 0.00 0.00 28.38 4.85
2830 7401 6.599244 CCTTAATTCATTCAGAGTACAAGGCA 59.401 38.462 0.00 0.00 28.38 4.75
2831 7402 6.823689 TCCTTAATTCATTCAGAGTACAAGGC 59.176 38.462 0.00 0.00 32.63 4.35
2832 7403 8.792830 TTCCTTAATTCATTCAGAGTACAAGG 57.207 34.615 0.00 0.00 33.28 3.61
2834 7405 9.793259 ACTTTCCTTAATTCATTCAGAGTACAA 57.207 29.630 0.00 0.00 0.00 2.41
2838 7409 9.660180 GAGTACTTTCCTTAATTCATTCAGAGT 57.340 33.333 0.00 0.00 0.00 3.24
2839 7410 9.883142 AGAGTACTTTCCTTAATTCATTCAGAG 57.117 33.333 0.00 0.00 0.00 3.35
2840 7411 9.658799 CAGAGTACTTTCCTTAATTCATTCAGA 57.341 33.333 0.00 0.00 0.00 3.27
2841 7412 9.442047 ACAGAGTACTTTCCTTAATTCATTCAG 57.558 33.333 0.00 0.00 0.00 3.02
2842 7413 9.793259 AACAGAGTACTTTCCTTAATTCATTCA 57.207 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.