Multiple sequence alignment - TraesCS3D01G246300

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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 TraesCS3D01G246300 chr3D 100.000 7057 0 0 1 7057 343494901 343487845 0.000000e+00 13032.0
1 TraesCS3D01G246300 chr3D 85.340 191 15 11 6086 6274 343488752 343488573 1.210000e-42 185.0
2 TraesCS3D01G246300 chr3D 85.340 191 15 11 6150 6329 343488816 343488628 1.210000e-42 185.0
3 TraesCS3D01G246300 chr3D 82.911 158 25 2 4041 4197 405309894 405309738 2.650000e-29 141.0
4 TraesCS3D01G246300 chr3B 91.187 2621 116 56 3671 6263 443354249 443356782 0.000000e+00 3454.0
5 TraesCS3D01G246300 chr3B 92.303 1689 58 27 1 1675 443347169 443348799 0.000000e+00 2333.0
6 TraesCS3D01G246300 chr3B 83.134 1085 126 28 1674 2719 443348950 443350016 0.000000e+00 937.0
7 TraesCS3D01G246300 chr3B 88.797 607 33 16 6151 6743 443356621 443357206 0.000000e+00 712.0
8 TraesCS3D01G246300 chr3B 89.031 547 43 8 3136 3676 443353674 443354209 0.000000e+00 662.0
9 TraesCS3D01G246300 chr3B 85.143 350 18 9 6736 7057 443357666 443358009 1.900000e-85 327.0
10 TraesCS3D01G246300 chr3B 82.911 158 25 2 4041 4197 531212193 531212037 2.650000e-29 141.0
11 TraesCS3D01G246300 chr3B 77.340 203 32 8 2039 2228 31999001 31999202 2.690000e-19 108.0
12 TraesCS3D01G246300 chr3A 94.253 2001 68 23 3707 5683 458939289 458941266 0.000000e+00 3014.0
13 TraesCS3D01G246300 chr3A 90.395 2124 120 43 60 2142 458934739 458936819 0.000000e+00 2715.0
14 TraesCS3D01G246300 chr3A 90.360 778 53 13 2729 3498 458938064 458938827 0.000000e+00 1002.0
15 TraesCS3D01G246300 chr3A 89.404 604 52 11 6180 6778 458985591 458986187 0.000000e+00 750.0
16 TraesCS3D01G246300 chr3A 78.674 347 35 21 5940 6281 458985437 458985749 2.010000e-45 195.0
17 TraesCS3D01G246300 chr3A 84.146 164 21 3 2146 2305 458936890 458937052 3.410000e-33 154.0
18 TraesCS3D01G246300 chr3A 82.911 158 25 2 4041 4197 527839881 527839725 2.650000e-29 141.0
19 TraesCS3D01G246300 chr5D 83.562 365 50 9 2805 3163 114371230 114371590 4.080000e-87 333.0
20 TraesCS3D01G246300 chr5A 80.051 396 71 7 2630 3024 119553210 119553598 3.220000e-73 287.0
21 TraesCS3D01G246300 chr2D 84.937 239 35 1 1987 2225 440325014 440324777 2.540000e-59 241.0
22 TraesCS3D01G246300 chr2A 84.519 239 31 2 1987 2225 583841342 583841110 1.530000e-56 231.0
23 TraesCS3D01G246300 chr2A 86.441 59 8 0 2496 2554 624366242 624366184 1.640000e-06 65.8
24 TraesCS3D01G246300 chr4B 79.051 253 33 13 1982 2232 448534142 448534376 9.480000e-34 156.0
25 TraesCS3D01G246300 chr1D 83.974 156 25 0 4041 4196 363725547 363725392 4.410000e-32 150.0
26 TraesCS3D01G246300 chr1A 83.974 156 25 0 4041 4196 462796126 462795971 4.410000e-32 150.0
27 TraesCS3D01G246300 chrUn 82.390 159 28 0 4039 4197 276463061 276462903 9.550000e-29 139.0
28 TraesCS3D01G246300 chrUn 82.390 159 28 0 4039 4197 276527445 276527603 9.550000e-29 139.0
29 TraesCS3D01G246300 chr7A 75.862 261 47 7 1976 2223 68738659 68738402 1.240000e-22 119.0
30 TraesCS3D01G246300 chr2B 76.596 141 24 8 6128 6263 74197462 74197598 1.270000e-07 69.4
31 TraesCS3D01G246300 chr2B 95.000 40 2 0 2493 2532 165110236 165110197 5.910000e-06 63.9
32 TraesCS3D01G246300 chr2B 97.143 35 1 0 2493 2527 13061437 13061403 7.640000e-05 60.2
33 TraesCS3D01G246300 chr6A 95.238 42 2 0 3579 3620 22295881 22295922 4.570000e-07 67.6
34 TraesCS3D01G246300 chr6A 90.385 52 4 1 2495 2545 48522575 48522626 4.570000e-07 67.6
35 TraesCS3D01G246300 chr6A 85.965 57 8 0 2493 2549 115337520 115337464 2.130000e-05 62.1
36 TraesCS3D01G246300 chr7D 93.182 44 3 0 2493 2536 601689979 601689936 1.640000e-06 65.8
37 TraesCS3D01G246300 chr1B 93.023 43 3 0 2490 2532 4995169 4995127 5.910000e-06 63.9
38 TraesCS3D01G246300 chr7B 100.000 30 0 0 2493 2522 550533838 550533867 1.000000e-03 56.5
39 TraesCS3D01G246300 chr7B 78.095 105 10 9 3575 3677 73301451 73301544 4.000000e-03 54.7
40 TraesCS3D01G246300 chr4D 100.000 29 0 0 5760 5788 74265788 74265760 4.000000e-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 TraesCS3D01G246300 chr3D 343487845 343494901 7056 True 13032.000000 13032 100.000000 1 7057 1 chr3D.!!$R1 7056
1 TraesCS3D01G246300 chr3B 443347169 443358009 10840 False 1404.166667 3454 88.265833 1 7057 6 chr3B.!!$F2 7056
2 TraesCS3D01G246300 chr3A 458934739 458941266 6527 False 1721.250000 3014 89.788500 60 5683 4 chr3A.!!$F1 5623
3 TraesCS3D01G246300 chr3A 458985437 458986187 750 False 472.500000 750 84.039000 5940 6778 2 chr3A.!!$F2 838

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
54 55 0.256752 TCTGGAAGGGACGATACCGA 59.743 55.000 0.00 0.00 39.50 4.69 F
57 58 0.317479 GGAAGGGACGATACCGATGG 59.683 60.000 0.00 0.00 39.50 3.51 F
818 837 0.325390 AGGCCGGAGCTTAAGGTAGT 60.325 55.000 5.05 0.00 39.73 2.73 F
2103 2311 0.107410 ACACACGGCAAGGTTCTGAA 60.107 50.000 0.00 0.00 0.00 3.02 F
2594 2878 0.036765 ATACGGCGTCATGTTGGTGT 60.037 50.000 19.21 0.00 0.00 4.16 F
2650 2935 0.038526 AAGTGCGTCGACGAGGAATT 60.039 50.000 39.74 23.56 43.02 2.17 F
2731 3638 0.192566 TTCTATAGGCCGGGGGTGAT 59.807 55.000 2.18 0.00 0.00 3.06 F
3691 8164 0.771127 TTTTGGGACCAGAGGGAGTG 59.229 55.000 0.00 0.00 38.05 3.51 F
4698 9191 0.790814 CGACCTGTTTTCTTCGAGCC 59.209 55.000 0.00 0.00 33.20 4.70 F
4970 9471 0.611618 TCAACATCCCGCAGCCATTT 60.612 50.000 0.00 0.00 0.00 2.32 F
5739 10248 1.123576 CGACATACACACGTTTGGTCG 59.876 52.381 14.44 14.44 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1559 0.380733 ATTCGCAGCGATGAGTACGA 59.619 50.000 20.32 0.0 35.23 3.43 R
1516 1560 1.200483 AATTCGCAGCGATGAGTACG 58.800 50.000 20.32 0.0 35.23 3.67 R
2575 2859 0.036765 ACACCAACATGACGCCGTAT 60.037 50.000 0.00 0.0 0.00 3.06 R
3299 7446 0.037046 GCCCTGTTGCCAAAGGATTG 60.037 55.000 0.00 0.0 35.40 2.67 R
3549 7970 0.459237 CTGCTAGCCTCTGTTCACCG 60.459 60.000 13.29 0.0 0.00 4.94 R
3743 8222 1.522668 TCTCCAACCTGCAATGTTCG 58.477 50.000 0.00 0.0 0.00 3.95 R
4681 9174 1.141053 ACTGGCTCGAAGAAAACAGGT 59.859 47.619 0.00 0.0 36.39 4.00 R
4970 9471 1.335132 GGGTTCTGCTCCGGATGGTA 61.335 60.000 3.57 0.0 36.30 3.25 R
5830 10344 0.111639 TGGGCCTGACAAACCCTAAC 59.888 55.000 4.53 0.0 44.56 2.34 R
5831 10345 0.404040 CTGGGCCTGACAAACCCTAA 59.596 55.000 4.53 0.0 44.56 2.69 R
6759 11766 0.527565 CATGCCCAACAGGTTAGTGC 59.472 55.000 0.00 0.0 38.26 4.40 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
54 55 0.256752 TCTGGAAGGGACGATACCGA 59.743 55.000 0.00 0.00 39.50 4.69
57 58 0.317479 GGAAGGGACGATACCGATGG 59.683 60.000 0.00 0.00 39.50 3.51
93 94 1.890876 CAAATCCGAGTTGTCACCCA 58.109 50.000 0.30 0.00 0.00 4.51
162 164 9.869757 TCCTTTTTCTCCTTTAAGTTTTCTTTG 57.130 29.630 0.00 0.00 40.91 2.77
667 683 2.304751 ACGAATTTAGTAGGCCGTGG 57.695 50.000 0.00 0.00 0.00 4.94
818 837 0.325390 AGGCCGGAGCTTAAGGTAGT 60.325 55.000 5.05 0.00 39.73 2.73
820 839 1.340568 GGCCGGAGCTTAAGGTAGTAG 59.659 57.143 5.05 0.00 39.73 2.57
823 842 3.294214 CCGGAGCTTAAGGTAGTAGGAA 58.706 50.000 7.26 0.00 0.00 3.36
824 843 3.318557 CCGGAGCTTAAGGTAGTAGGAAG 59.681 52.174 7.26 0.00 0.00 3.46
829 848 7.177041 CGGAGCTTAAGGTAGTAGGAAGATTAT 59.823 40.741 7.26 0.00 0.00 1.28
830 849 8.872134 GGAGCTTAAGGTAGTAGGAAGATTATT 58.128 37.037 7.26 0.00 0.00 1.40
874 893 6.037610 GTCATAGACAAAAAGGTAGGCTGATG 59.962 42.308 0.00 0.00 32.09 3.07
893 916 7.175119 GGCTGATGATAATTAAGGGGAAGTTAC 59.825 40.741 0.00 0.00 0.00 2.50
930 953 3.568007 TCCACTGTTTCTTTTGGATTCGG 59.432 43.478 0.00 0.00 33.02 4.30
933 956 3.004734 ACTGTTTCTTTTGGATTCGGCTG 59.995 43.478 0.00 0.00 0.00 4.85
959 982 7.615582 TTGGATAGCACTAAACTTTCTCATG 57.384 36.000 0.00 0.00 0.00 3.07
981 1004 4.345547 TGCAATACCCTACATCACCGATTA 59.654 41.667 0.00 0.00 0.00 1.75
1267 1311 2.087009 CGAGGTTGAACGACGGAGC 61.087 63.158 0.00 0.00 0.00 4.70
1482 1526 3.364249 CTCCTCGTCGACGACCGTG 62.364 68.421 34.97 24.47 44.22 4.94
1514 1558 4.256140 CGTGAGGTACTAACTCGTACAG 57.744 50.000 0.00 0.00 41.55 2.74
1515 1559 3.681897 CGTGAGGTACTAACTCGTACAGT 59.318 47.826 0.00 0.00 41.55 3.55
1516 1560 4.201666 CGTGAGGTACTAACTCGTACAGTC 60.202 50.000 0.00 0.00 41.55 3.51
1517 1561 3.928992 TGAGGTACTAACTCGTACAGTCG 59.071 47.826 0.00 0.00 41.55 4.18
1518 1562 3.929610 GAGGTACTAACTCGTACAGTCGT 59.070 47.826 0.00 0.83 41.55 4.34
1519 1563 5.073311 AGGTACTAACTCGTACAGTCGTA 57.927 43.478 0.00 0.00 41.12 3.43
1520 1564 4.865365 AGGTACTAACTCGTACAGTCGTAC 59.135 45.833 17.64 17.64 41.12 3.67
1569 1613 5.477291 CCTTTAGGACTCTTGGCGATATCTA 59.523 44.000 0.34 0.00 37.39 1.98
1571 1615 6.761099 TTAGGACTCTTGGCGATATCTATC 57.239 41.667 0.34 0.00 0.00 2.08
1572 1616 4.929479 AGGACTCTTGGCGATATCTATCT 58.071 43.478 0.34 0.00 0.00 1.98
1577 1621 5.068460 ACTCTTGGCGATATCTATCTATGCC 59.932 44.000 8.19 8.19 37.30 4.40
1836 2041 5.731599 ACTTTGTCCTAGTACGTATCTCG 57.268 43.478 0.00 0.00 46.00 4.04
1876 2081 6.696441 TCTCTAACCGATCCTCTAAAAGAC 57.304 41.667 0.00 0.00 0.00 3.01
1880 2085 4.107363 ACCGATCCTCTAAAAGACGTTC 57.893 45.455 0.00 0.00 0.00 3.95
1944 2151 9.319143 CCTAACTGATCTCATAAAACTGTTAGG 57.681 37.037 18.84 18.84 46.04 2.69
1946 2153 6.653989 ACTGATCTCATAAAACTGTTAGGGG 58.346 40.000 0.00 0.00 0.00 4.79
1949 2156 6.672218 TGATCTCATAAAACTGTTAGGGGAGA 59.328 38.462 13.53 13.53 33.88 3.71
2011 2219 4.698304 CCCAAATGATAAGTACCACACGTT 59.302 41.667 0.00 0.00 0.00 3.99
2014 2222 6.036735 CCAAATGATAAGTACCACACGTTAGG 59.963 42.308 1.56 1.56 0.00 2.69
2070 2278 3.256631 GCAGTTCCAATCACACAAGGATT 59.743 43.478 0.00 0.00 35.43 3.01
2102 2310 0.531974 GACACACGGCAAGGTTCTGA 60.532 55.000 0.00 0.00 0.00 3.27
2103 2311 0.107410 ACACACGGCAAGGTTCTGAA 60.107 50.000 0.00 0.00 0.00 3.02
2134 2342 4.060205 ACTGAAGCACAAAATTTGCCATC 58.940 39.130 5.52 1.10 41.18 3.51
2142 2352 4.998672 CACAAAATTTGCCATCCTTGACAT 59.001 37.500 5.52 0.00 0.00 3.06
2144 2354 4.476628 AAATTTGCCATCCTTGACATCC 57.523 40.909 0.00 0.00 0.00 3.51
2145 2355 1.851304 TTTGCCATCCTTGACATCCC 58.149 50.000 0.00 0.00 0.00 3.85
2147 2357 0.920763 TGCCATCCTTGACATCCCCT 60.921 55.000 0.00 0.00 0.00 4.79
2148 2358 0.259938 GCCATCCTTGACATCCCCTT 59.740 55.000 0.00 0.00 0.00 3.95
2159 2436 4.015872 GACATCCCCTTGTCACTAAACA 57.984 45.455 0.00 0.00 44.38 2.83
2164 2441 2.555227 CCCCTTGTCACTAAACATGCCT 60.555 50.000 0.00 0.00 0.00 4.75
2174 2451 4.048504 ACTAAACATGCCTTCAAAAACGC 58.951 39.130 0.00 0.00 0.00 4.84
2178 2455 0.240945 ATGCCTTCAAAAACGCTCGG 59.759 50.000 0.00 0.00 0.00 4.63
2193 2470 0.957395 CTCGGAGTTGCCATGTGCTT 60.957 55.000 7.54 0.00 42.00 3.91
2261 2541 3.512219 ACGTTGGGGTAAAAATCTCCA 57.488 42.857 0.00 0.00 0.00 3.86
2271 2552 1.392407 AAAATCTCCATCCCCCACCA 58.608 50.000 0.00 0.00 0.00 4.17
2283 2564 1.064685 CCCCCACCACTTGACCTTATC 60.065 57.143 0.00 0.00 0.00 1.75
2289 2570 2.572104 ACCACTTGACCTTATCCACTCC 59.428 50.000 0.00 0.00 0.00 3.85
2290 2571 2.418746 CCACTTGACCTTATCCACTCCG 60.419 54.545 0.00 0.00 0.00 4.63
2296 2577 4.215742 TTATCCACTCCGCCGCCG 62.216 66.667 0.00 0.00 0.00 6.46
2313 2594 0.536687 CCGATGATGCCTCCATGCTT 60.537 55.000 0.00 0.00 0.00 3.91
2331 2612 0.334676 TTCCCAAAATGGCCGGATCT 59.665 50.000 5.05 0.00 35.79 2.75
2335 2616 1.477558 CCAAAATGGCCGGATCTAGCT 60.478 52.381 5.05 0.00 0.00 3.32
2364 2648 2.892425 CCACCGATCAGAAGCGCC 60.892 66.667 2.29 0.00 31.57 6.53
2394 2678 1.597854 CAAGAGCCTGTGGTCGCAA 60.598 57.895 0.00 0.00 43.79 4.85
2469 2753 1.007271 CGGCGCCATAGAGTAGGTG 60.007 63.158 28.98 0.37 38.43 4.00
2549 2833 3.064079 CGTCAGCGGATTTGGATCA 57.936 52.632 0.00 0.00 33.77 2.92
2566 2850 2.502142 TCAGTTCCTACTAGTCGGCA 57.498 50.000 8.58 0.00 31.96 5.69
2567 2851 3.014304 TCAGTTCCTACTAGTCGGCAT 57.986 47.619 8.58 0.00 31.96 4.40
2575 2859 3.469754 CTAGTCGGCATCGCGAGCA 62.470 63.158 24.72 8.94 36.13 4.26
2580 2864 3.406361 GGCATCGCGAGCATACGG 61.406 66.667 24.72 7.44 0.00 4.02
2594 2878 0.036765 ATACGGCGTCATGTTGGTGT 60.037 50.000 19.21 0.00 0.00 4.16
2602 2886 0.405198 TCATGTTGGTGTGCCTCCAT 59.595 50.000 0.00 0.00 34.75 3.41
2628 2912 1.738474 AACCCCCGACTAAACTTCCT 58.262 50.000 0.00 0.00 0.00 3.36
2632 2916 1.547372 CCCCGACTAAACTTCCTCGAA 59.453 52.381 0.00 0.00 0.00 3.71
2633 2917 2.416972 CCCCGACTAAACTTCCTCGAAG 60.417 54.545 0.00 0.00 44.37 3.79
2650 2935 0.038526 AAGTGCGTCGACGAGGAATT 60.039 50.000 39.74 23.56 43.02 2.17
2674 2959 4.767255 GGAGCTCCGCCACCTGTG 62.767 72.222 19.06 0.00 0.00 3.66
2705 2990 3.234390 CACGAACAGTGTCGGCAG 58.766 61.111 16.00 0.00 45.40 4.85
2731 3638 0.192566 TTCTATAGGCCGGGGGTGAT 59.807 55.000 2.18 0.00 0.00 3.06
2756 3663 1.537202 GTCATCGACCTTTGCTTGCTT 59.463 47.619 0.00 0.00 0.00 3.91
2757 3664 1.806542 TCATCGACCTTTGCTTGCTTC 59.193 47.619 0.00 0.00 0.00 3.86
2779 3686 2.771639 TTCGACGGAGATGGCGAGG 61.772 63.158 0.00 0.00 34.01 4.63
2882 3789 2.171237 AGATGATTGCCGAGGTCAATGA 59.829 45.455 13.62 8.11 34.59 2.57
2885 3792 3.732212 TGATTGCCGAGGTCAATGATAG 58.268 45.455 13.62 0.00 34.59 2.08
2895 3805 6.218746 CGAGGTCAATGATAGTGATGATGAA 58.781 40.000 0.00 0.00 0.00 2.57
2983 3893 3.093057 ACTAGTGGCTGAATCGAGTTCT 58.907 45.455 0.00 0.00 37.72 3.01
2994 3904 6.752351 GCTGAATCGAGTTCTAATCAAGTACA 59.248 38.462 0.00 0.00 37.72 2.90
3000 3910 7.033791 TCGAGTTCTAATCAAGTACAATGGAC 58.966 38.462 0.00 0.00 0.00 4.02
3033 3943 8.994429 ATCAAATTTGCACCGAATTTATGTTA 57.006 26.923 13.54 0.00 35.87 2.41
3034 3944 8.994429 TCAAATTTGCACCGAATTTATGTTAT 57.006 26.923 13.54 0.00 35.87 1.89
3155 7302 5.693769 AAATTAGAAGGGATCGGTCAGAA 57.306 39.130 0.00 0.00 0.00 3.02
3183 7330 9.237187 TGCTCTAACACCAATATACAAAAATCA 57.763 29.630 0.00 0.00 0.00 2.57
3208 7355 4.402474 GGCCCAATAAAAGTAGCATGTCTT 59.598 41.667 0.00 0.00 0.00 3.01
3270 7417 2.386864 TCCATCTGGGGTGGAACAG 58.613 57.895 0.00 0.00 42.56 3.16
3299 7446 4.928615 CAGATCTTTGAGTCACTTCAGTCC 59.071 45.833 0.00 0.00 0.00 3.85
3411 7558 5.287226 AGATACGTTTTATAGAGTTGGGCG 58.713 41.667 0.00 0.00 0.00 6.13
3412 7559 2.624636 ACGTTTTATAGAGTTGGGCGG 58.375 47.619 0.00 0.00 0.00 6.13
3443 7590 6.096846 GGCATTCTTTCTTTGGCCTTATCTTA 59.903 38.462 3.32 0.00 38.37 2.10
3494 7641 2.752354 CGACCTTGATCTGAGACTGAGT 59.248 50.000 0.00 0.00 0.00 3.41
3498 7645 3.763360 CCTTGATCTGAGACTGAGTCTGT 59.237 47.826 21.45 1.78 43.53 3.41
3506 7927 3.256879 TGAGACTGAGTCTGTCCATGTTC 59.743 47.826 21.45 14.94 43.53 3.18
3509 7930 2.037772 ACTGAGTCTGTCCATGTTCCAC 59.962 50.000 0.00 0.00 0.00 4.02
3526 7947 6.166279 TGTTCCACTGATCTGAGTATTTCAC 58.834 40.000 6.60 0.00 0.00 3.18
3532 7953 8.200120 CCACTGATCTGAGTATTTCACTAATGA 58.800 37.037 6.60 0.00 37.72 2.57
3549 7970 7.767659 TCACTAATGATTCATATAGAGCATGGC 59.232 37.037 16.21 0.00 0.00 4.40
3587 8008 2.834549 CAGATGTGTTGGTACTCCCTCT 59.165 50.000 0.00 0.00 0.00 3.69
3602 8023 9.761504 GGTACTCCCTCTGTTTCTAAATATAAC 57.238 37.037 0.00 0.00 0.00 1.89
3606 8027 9.535878 CTCCCTCTGTTTCTAAATATAACACTC 57.464 37.037 0.00 0.00 0.00 3.51
3640 8061 6.413783 TCATTCAATAAGGGCTACATACGA 57.586 37.500 0.00 0.00 0.00 3.43
3646 8067 7.600065 TCAATAAGGGCTACATACGAATCTAC 58.400 38.462 0.00 0.00 0.00 2.59
3652 8079 7.773149 AGGGCTACATACGAATCTACATATTC 58.227 38.462 0.00 0.00 33.37 1.75
3680 8153 8.207545 AGAGTGTAGATTCATCTATTTTGGGAC 58.792 37.037 0.00 0.00 41.09 4.46
3691 8164 0.771127 TTTTGGGACCAGAGGGAGTG 59.229 55.000 0.00 0.00 38.05 3.51
3700 8173 2.578021 ACCAGAGGGAGTGCATGTTTAT 59.422 45.455 0.00 0.00 38.05 1.40
3715 8188 9.158364 GTGCATGTTTATTCATGACTAATAACG 57.842 33.333 6.37 0.00 45.41 3.18
3743 8222 8.580431 GGTAAAATCGCACACATTTATTTGTAC 58.420 33.333 0.00 0.00 0.00 2.90
3773 8252 1.056660 GGTTGGAGAAGGACACCAGA 58.943 55.000 0.00 0.00 40.10 3.86
3874 8353 3.871006 CGAATTACTAGTTGGCTCATGCA 59.129 43.478 0.00 0.00 41.91 3.96
4036 8515 2.202336 TTCGCCTACACGTACGCG 60.202 61.111 16.72 8.78 40.29 6.01
4236 8715 1.064017 ACCTTCCTCACCAGCAAACAA 60.064 47.619 0.00 0.00 0.00 2.83
4261 8751 3.597324 CATAGTAAAAGCATCACACGCG 58.403 45.455 3.53 3.53 0.00 6.01
4617 9110 2.632996 ACATTGTCCTGGAGAACGAGAA 59.367 45.455 8.62 0.00 0.00 2.87
4675 9168 7.088589 AGTGGTAAATTCACTGCACATATTC 57.911 36.000 0.00 0.00 43.07 1.75
4681 9174 3.866883 TCACTGCACATATTCTCACGA 57.133 42.857 0.00 0.00 0.00 4.35
4694 9187 2.739292 TCTCACGACCTGTTTTCTTCG 58.261 47.619 0.00 0.00 37.50 3.79
4697 9190 1.192534 CACGACCTGTTTTCTTCGAGC 59.807 52.381 0.00 0.00 35.45 5.03
4698 9191 0.790814 CGACCTGTTTTCTTCGAGCC 59.209 55.000 0.00 0.00 33.20 4.70
4702 9195 2.222027 CCTGTTTTCTTCGAGCCAGTT 58.778 47.619 0.00 0.00 0.00 3.16
4815 9308 3.561120 ATTTGCCGGAACCCGCTGA 62.561 57.895 5.05 0.00 46.86 4.26
4970 9471 0.611618 TCAACATCCCGCAGCCATTT 60.612 50.000 0.00 0.00 0.00 2.32
5006 9507 1.273438 ACCCTAACCCAGGTCATACGT 60.273 52.381 0.00 0.00 43.80 3.57
5063 9564 2.227089 CTACTGCAGACGGGGACACC 62.227 65.000 23.35 0.00 0.00 4.16
5119 9620 4.022589 ACATATGCTGCATTATTCAGGTGC 60.023 41.667 21.56 0.00 39.26 5.01
5188 9696 8.647796 TCTTTTACTAGATTGTCTGAACTTGGA 58.352 33.333 0.00 0.00 0.00 3.53
5340 9848 4.794439 GGGCAAATTCCGCACGGC 62.794 66.667 3.66 0.00 34.68 5.68
5555 10063 8.556213 ACTGTACTCTAAAGTCTCTAACTCAG 57.444 38.462 0.00 0.00 37.17 3.35
5557 10065 8.325421 TGTACTCTAAAGTCTCTAACTCAGTG 57.675 38.462 0.00 0.00 37.17 3.66
5558 10066 6.262193 ACTCTAAAGTCTCTAACTCAGTGC 57.738 41.667 0.00 0.00 37.17 4.40
5559 10067 5.770663 ACTCTAAAGTCTCTAACTCAGTGCA 59.229 40.000 0.00 0.00 37.17 4.57
5561 10069 6.625362 TCTAAAGTCTCTAACTCAGTGCATG 58.375 40.000 0.00 0.00 37.17 4.06
5683 10192 1.468224 CGAGGATGAGGACAGACAACG 60.468 57.143 0.00 0.00 0.00 4.10
5725 10234 3.494924 CCCTTCCTGCATGATTCGACATA 60.495 47.826 0.00 0.00 0.00 2.29
5731 10240 2.602660 TGCATGATTCGACATACACACG 59.397 45.455 0.00 0.00 0.00 4.49
5739 10248 1.123576 CGACATACACACGTTTGGTCG 59.876 52.381 14.44 14.44 0.00 4.79
5757 10271 3.119955 GGTCGAAATCACAAGTTAAGGGC 60.120 47.826 0.00 0.00 0.00 5.19
5780 10294 1.840635 GGGTTTGTCTAGGCCTCATCT 59.159 52.381 9.68 0.00 0.00 2.90
5782 10296 3.070302 GGGTTTGTCTAGGCCTCATCTAG 59.930 52.174 9.68 0.00 36.46 2.43
5783 10297 3.961408 GGTTTGTCTAGGCCTCATCTAGA 59.039 47.826 9.68 2.39 40.38 2.43
5784 10298 4.591072 GGTTTGTCTAGGCCTCATCTAGAT 59.409 45.833 9.68 0.00 43.25 1.98
5785 10299 5.510520 GGTTTGTCTAGGCCTCATCTAGATG 60.511 48.000 24.32 24.32 43.25 2.90
5786 10300 4.461450 TGTCTAGGCCTCATCTAGATGT 57.539 45.455 27.80 13.87 43.25 3.06
5810 10324 1.663643 GCGATCGCTTACAACCATTCA 59.336 47.619 31.94 0.00 38.26 2.57
5815 10329 5.635280 CGATCGCTTACAACCATTCAGATAT 59.365 40.000 0.26 0.00 0.00 1.63
5816 10330 6.400409 CGATCGCTTACAACCATTCAGATATG 60.400 42.308 0.26 0.00 0.00 1.78
5825 10339 4.563337 CCATTCAGATATGGTGCACAAG 57.437 45.455 20.43 0.00 40.20 3.16
5826 10340 3.949754 CCATTCAGATATGGTGCACAAGT 59.050 43.478 20.43 6.13 40.20 3.16
5827 10341 4.400251 CCATTCAGATATGGTGCACAAGTT 59.600 41.667 20.43 0.00 40.20 2.66
5828 10342 5.589855 CCATTCAGATATGGTGCACAAGTTA 59.410 40.000 20.43 4.52 40.20 2.24
5829 10343 6.095300 CCATTCAGATATGGTGCACAAGTTAA 59.905 38.462 20.43 2.55 40.20 2.01
5830 10344 6.741992 TTCAGATATGGTGCACAAGTTAAG 57.258 37.500 20.43 3.42 0.00 1.85
5831 10345 5.804639 TCAGATATGGTGCACAAGTTAAGT 58.195 37.500 20.43 0.00 0.00 2.24
5832 10346 6.237901 TCAGATATGGTGCACAAGTTAAGTT 58.762 36.000 20.43 0.00 0.00 2.66
5833 10347 7.390823 TCAGATATGGTGCACAAGTTAAGTTA 58.609 34.615 20.43 0.00 0.00 2.24
5834 10348 7.549134 TCAGATATGGTGCACAAGTTAAGTTAG 59.451 37.037 20.43 0.00 0.00 2.34
5835 10349 6.823689 AGATATGGTGCACAAGTTAAGTTAGG 59.176 38.462 20.43 0.00 0.00 2.69
5836 10350 3.482436 TGGTGCACAAGTTAAGTTAGGG 58.518 45.455 20.43 0.00 0.00 3.53
5837 10351 3.117813 TGGTGCACAAGTTAAGTTAGGGT 60.118 43.478 20.43 0.00 0.00 4.34
5838 10352 3.887110 GGTGCACAAGTTAAGTTAGGGTT 59.113 43.478 20.43 0.00 0.00 4.11
5839 10353 4.340097 GGTGCACAAGTTAAGTTAGGGTTT 59.660 41.667 20.43 0.00 0.00 3.27
5891 10409 8.437274 TCTCTTCTAGGTATTCTTTTTCTGGT 57.563 34.615 0.00 0.00 0.00 4.00
5979 10498 7.327275 GCACAAATTTCAAATACACACCGAATA 59.673 33.333 0.00 0.00 0.00 1.75
6013 10533 4.125703 TGGTGAACATTTTCCAAATGCAC 58.874 39.130 8.77 9.27 0.00 4.57
6014 10534 4.125703 GGTGAACATTTTCCAAATGCACA 58.874 39.130 15.70 10.91 0.00 4.57
6015 10535 4.211794 GGTGAACATTTTCCAAATGCACAG 59.788 41.667 15.70 0.00 0.00 3.66
6115 10635 9.629878 TTTAACTGTAGGGTGAACTATTTTTCA 57.370 29.630 0.00 0.00 32.94 2.69
6116 10636 9.802039 TTAACTGTAGGGTGAACTATTTTTCAT 57.198 29.630 0.00 0.00 37.80 2.57
6117 10637 7.687941 ACTGTAGGGTGAACTATTTTTCATG 57.312 36.000 0.00 0.00 37.80 3.07
6118 10638 7.231467 ACTGTAGGGTGAACTATTTTTCATGT 58.769 34.615 0.00 0.00 37.80 3.21
6119 10639 8.380099 ACTGTAGGGTGAACTATTTTTCATGTA 58.620 33.333 0.00 0.00 37.80 2.29
6120 10640 9.396022 CTGTAGGGTGAACTATTTTTCATGTAT 57.604 33.333 0.00 0.00 37.80 2.29
6121 10641 9.173021 TGTAGGGTGAACTATTTTTCATGTATG 57.827 33.333 0.00 0.00 37.80 2.39
6122 10642 9.391006 GTAGGGTGAACTATTTTTCATGTATGA 57.609 33.333 0.00 0.00 37.80 2.15
6124 10644 9.125026 AGGGTGAACTATTTTTCATGTATGATC 57.875 33.333 0.00 0.00 37.80 2.92
6125 10645 8.902806 GGGTGAACTATTTTTCATGTATGATCA 58.097 33.333 0.00 0.00 37.80 2.92
6126 10646 9.722056 GGTGAACTATTTTTCATGTATGATCAC 57.278 33.333 0.00 10.33 37.80 3.06
6127 10647 9.722056 GTGAACTATTTTTCATGTATGATCACC 57.278 33.333 0.00 0.00 37.80 4.02
6128 10648 9.460019 TGAACTATTTTTCATGTATGATCACCA 57.540 29.630 0.00 0.00 36.56 4.17
6187 10707 9.125026 AGGGTGAACTATTTTTCATGTATGATC 57.875 33.333 0.00 0.00 37.80 2.92
6348 10876 9.908152 AAACTGAACTTATTTAAATGTAGGTGC 57.092 29.630 11.05 0.00 0.00 5.01
6546 11083 3.399330 CGCTCAAAACTAGAGAAACCCA 58.601 45.455 0.00 0.00 35.09 4.51
6600 11137 3.004752 GGAAGCTTCCTGAAATAGGCA 57.995 47.619 33.98 0.00 46.87 4.75
6648 11185 0.512518 TTGCTCACGAAACGATGCTG 59.487 50.000 0.00 0.00 0.00 4.41
6751 11758 3.102204 TGGGTAGCCTAAGTACAACCTC 58.898 50.000 13.11 0.00 0.00 3.85
6752 11759 3.245875 TGGGTAGCCTAAGTACAACCTCT 60.246 47.826 13.11 0.00 0.00 3.69
6753 11760 4.017222 TGGGTAGCCTAAGTACAACCTCTA 60.017 45.833 13.11 0.00 0.00 2.43
6759 11766 4.678309 GCCTAAGTACAACCTCTACTGCAG 60.678 50.000 13.48 13.48 0.00 4.41
6809 11816 4.510038 AGTTATTGTTGGTACTCGACGT 57.490 40.909 0.00 0.00 32.34 4.34
6812 11819 5.754890 AGTTATTGTTGGTACTCGACGTTTT 59.245 36.000 0.00 0.00 32.34 2.43
6813 11820 6.258507 AGTTATTGTTGGTACTCGACGTTTTT 59.741 34.615 0.00 0.00 32.34 1.94
6814 11821 7.437862 AGTTATTGTTGGTACTCGACGTTTTTA 59.562 33.333 0.00 0.00 32.34 1.52
6817 11824 6.601741 TGTTGGTACTCGACGTTTTTATTT 57.398 33.333 0.00 0.00 32.34 1.40
6830 11837 5.293079 ACGTTTTTATTTGTTGTTGCTGCAT 59.707 32.000 1.84 0.00 0.00 3.96
6875 11883 0.470766 ACAAGCCTACAACGGGTCAA 59.529 50.000 0.00 0.00 32.66 3.18
6879 11887 1.628846 AGCCTACAACGGGTCAAATCT 59.371 47.619 0.00 0.00 0.00 2.40
6891 11899 4.589908 GGGTCAAATCTTGGCTTCTAGAA 58.410 43.478 4.81 4.81 35.12 2.10
6893 11901 5.476945 GGGTCAAATCTTGGCTTCTAGAAAA 59.523 40.000 6.63 0.00 35.12 2.29
6987 12021 1.074889 GCCTTCCTACCCCTTGTTTCA 59.925 52.381 0.00 0.00 0.00 2.69
7007 12041 2.742053 CAGGGTGTTATTGGTCACGAAG 59.258 50.000 0.00 0.00 35.67 3.79
7020 12054 6.438259 TGGTCACGAAGAAACAAAACATTA 57.562 33.333 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.141688 GGTATCGTCCCTTCCAGAAATTCT 60.142 45.833 0.00 0.00 0.00 2.40
54 55 2.382993 TGCCATCTATATTTGCCCCCAT 59.617 45.455 0.00 0.00 0.00 4.00
57 58 4.081476 GGATTTGCCATCTATATTTGCCCC 60.081 45.833 0.00 0.00 36.34 5.80
93 94 2.129555 AAACGCTGATGGGCTCACCT 62.130 55.000 0.00 0.00 41.11 4.00
162 164 9.663904 GGGAAGAAAATGAAATAAAAGCAAAAC 57.336 29.630 0.00 0.00 0.00 2.43
164 166 9.625747 AAGGGAAGAAAATGAAATAAAAGCAAA 57.374 25.926 0.00 0.00 0.00 3.68
165 167 9.625747 AAAGGGAAGAAAATGAAATAAAAGCAA 57.374 25.926 0.00 0.00 0.00 3.91
644 660 4.436451 CCACGGCCTACTAAATTCGTTTTC 60.436 45.833 0.00 0.00 0.00 2.29
667 683 1.463674 CTTACATGGGTTGGCCAGAC 58.536 55.000 5.11 7.55 36.17 3.51
874 893 9.822185 TTACTTCGTAACTTCCCCTTAATTATC 57.178 33.333 0.00 0.00 0.00 1.75
893 916 8.504005 AGAAACAGTGGAATTGTATTTACTTCG 58.496 33.333 0.00 0.00 34.84 3.79
930 953 6.317391 AGAAAGTTTAGTGCTATCCAATCAGC 59.683 38.462 0.00 0.00 38.31 4.26
933 956 7.849804 TGAGAAAGTTTAGTGCTATCCAATC 57.150 36.000 0.00 0.00 0.00 2.67
959 982 2.902705 TCGGTGATGTAGGGTATTGC 57.097 50.000 0.00 0.00 0.00 3.56
981 1004 3.199289 CAGGGTTAACCGGGAAAGTATCT 59.801 47.826 18.39 2.91 46.96 1.98
1227 1254 2.309528 TAGCACGTGGATTCATGGAC 57.690 50.000 18.88 0.00 34.31 4.02
1267 1311 1.876799 AGTACCTGCGATCGAGATCAG 59.123 52.381 21.57 15.81 37.69 2.90
1513 1557 1.062685 CGCAGCGATGAGTACGACT 59.937 57.895 9.98 0.00 0.00 4.18
1514 1558 0.522705 TTCGCAGCGATGAGTACGAC 60.523 55.000 20.32 0.00 35.23 4.34
1515 1559 0.380733 ATTCGCAGCGATGAGTACGA 59.619 50.000 20.32 0.00 35.23 3.43
1516 1560 1.200483 AATTCGCAGCGATGAGTACG 58.800 50.000 20.32 0.00 35.23 3.67
1517 1561 4.974103 ATTAATTCGCAGCGATGAGTAC 57.026 40.909 20.32 0.00 35.23 2.73
1518 1562 5.293324 ACAAATTAATTCGCAGCGATGAGTA 59.707 36.000 20.32 5.35 35.23 2.59
1519 1563 4.094887 ACAAATTAATTCGCAGCGATGAGT 59.905 37.500 20.32 6.50 35.23 3.41
1520 1564 4.591202 ACAAATTAATTCGCAGCGATGAG 58.409 39.130 20.32 0.00 35.23 2.90
1569 1613 5.046304 ACGCATGGTCTTATTAGGCATAGAT 60.046 40.000 0.00 0.00 0.00 1.98
1571 1615 4.569943 ACGCATGGTCTTATTAGGCATAG 58.430 43.478 0.00 0.00 0.00 2.23
1572 1616 4.617253 ACGCATGGTCTTATTAGGCATA 57.383 40.909 0.00 0.00 0.00 3.14
1577 1621 5.845953 CGCAAAATACGCATGGTCTTATTAG 59.154 40.000 0.00 0.00 0.00 1.73
1836 2041 4.981806 AGAGATGCTCTTAGTGAGACAC 57.018 45.455 0.00 0.00 45.39 3.67
1838 2043 5.504994 CGGTTAGAGATGCTCTTAGTGAGAC 60.505 48.000 1.88 0.00 45.39 3.36
1843 2048 4.521256 GGATCGGTTAGAGATGCTCTTAGT 59.479 45.833 1.88 0.00 41.50 2.24
1844 2049 4.764823 AGGATCGGTTAGAGATGCTCTTAG 59.235 45.833 1.88 0.00 41.89 2.18
1917 2124 7.617041 AACAGTTTTATGAGATCAGTTAGGC 57.383 36.000 0.00 0.00 0.00 3.93
2057 2265 4.925054 CGAAAATTGCAATCCTTGTGTGAT 59.075 37.500 13.38 0.00 0.00 3.06
2070 2278 1.268285 CGTGTGTCACCGAAAATTGCA 60.268 47.619 0.00 0.00 0.00 4.08
2126 2334 1.619432 GGGGATGTCAAGGATGGCAAA 60.619 52.381 0.00 0.00 45.86 3.68
2142 2352 2.554344 GGCATGTTTAGTGACAAGGGGA 60.554 50.000 0.00 0.00 32.47 4.81
2144 2354 2.795329 AGGCATGTTTAGTGACAAGGG 58.205 47.619 0.00 0.00 32.47 3.95
2145 2355 3.820467 TGAAGGCATGTTTAGTGACAAGG 59.180 43.478 0.00 0.00 32.47 3.61
2147 2357 5.843673 TTTGAAGGCATGTTTAGTGACAA 57.156 34.783 0.00 0.00 32.47 3.18
2148 2358 5.843673 TTTTGAAGGCATGTTTAGTGACA 57.156 34.783 0.00 0.00 0.00 3.58
2159 2436 0.240945 CCGAGCGTTTTTGAAGGCAT 59.759 50.000 6.60 0.00 36.14 4.40
2164 2441 1.268335 GCAACTCCGAGCGTTTTTGAA 60.268 47.619 0.00 0.00 0.00 2.69
2174 2451 3.181367 GCACATGGCAACTCCGAG 58.819 61.111 0.00 0.00 43.97 4.63
2241 2521 3.512219 TGGAGATTTTTACCCCAACGT 57.488 42.857 0.00 0.00 0.00 3.99
2248 2528 3.296854 GTGGGGGATGGAGATTTTTACC 58.703 50.000 0.00 0.00 0.00 2.85
2261 2541 0.776080 AAGGTCAAGTGGTGGGGGAT 60.776 55.000 0.00 0.00 0.00 3.85
2271 2552 1.207329 GCGGAGTGGATAAGGTCAAGT 59.793 52.381 0.00 0.00 0.00 3.16
2296 2577 1.245732 GGAAGCATGGAGGCATCATC 58.754 55.000 0.00 0.00 33.39 2.92
2297 2578 0.178970 GGGAAGCATGGAGGCATCAT 60.179 55.000 0.00 0.00 33.39 2.45
2298 2579 1.228228 GGGAAGCATGGAGGCATCA 59.772 57.895 0.00 0.00 33.39 3.07
2300 2581 0.041535 TTTGGGAAGCATGGAGGCAT 59.958 50.000 0.00 0.00 35.83 4.40
2305 2586 0.903942 GCCATTTTGGGAAGCATGGA 59.096 50.000 1.07 0.00 38.88 3.41
2313 2594 1.142870 CTAGATCCGGCCATTTTGGGA 59.857 52.381 2.24 0.00 38.19 4.37
2377 2661 1.598130 GTTGCGACCACAGGCTCTT 60.598 57.895 0.00 0.00 0.00 2.85
2384 2668 1.697772 GACACAACGTTGCGACCACA 61.698 55.000 27.61 0.00 0.00 4.17
2394 2678 2.050269 CAGGAGGAGGACACAACGT 58.950 57.895 0.00 0.00 0.00 3.99
2447 2731 2.755542 CTACTCTATGGCGCCGGCAG 62.756 65.000 28.98 20.12 42.43 4.85
2448 2732 2.835895 TACTCTATGGCGCCGGCA 60.836 61.111 28.98 17.86 43.52 5.69
2499 2783 3.770040 TGATCTCCGCCACCCACG 61.770 66.667 0.00 0.00 0.00 4.94
2533 2817 2.632377 GAACTGATCCAAATCCGCTGA 58.368 47.619 0.00 0.00 0.00 4.26
2549 2833 1.948145 CGATGCCGACTAGTAGGAACT 59.052 52.381 24.64 8.44 39.80 3.01
2566 2850 4.266070 ACGCCGTATGCTCGCGAT 62.266 61.111 10.36 0.00 38.05 4.58
2567 2851 4.899687 GACGCCGTATGCTCGCGA 62.900 66.667 9.26 9.26 38.05 5.87
2575 2859 0.036765 ACACCAACATGACGCCGTAT 60.037 50.000 0.00 0.00 0.00 3.06
2580 2864 2.187599 GAGGCACACCAACATGACGC 62.188 60.000 0.00 0.00 39.06 5.19
2582 2866 2.257353 GGAGGCACACCAACATGAC 58.743 57.895 0.00 0.00 39.49 3.06
2594 2878 1.907807 GGTTTGCACCATGGAGGCA 60.908 57.895 25.04 25.04 43.61 4.75
2602 2886 1.706995 TTAGTCGGGGGTTTGCACCA 61.707 55.000 0.00 0.00 46.43 4.17
2628 2912 2.172659 CTCGTCGACGCACTTCGA 59.827 61.111 32.19 12.91 45.62 3.71
2632 2916 0.456312 GAATTCCTCGTCGACGCACT 60.456 55.000 32.19 13.08 39.60 4.40
2633 2917 0.731514 TGAATTCCTCGTCGACGCAC 60.732 55.000 32.19 16.67 39.60 5.34
2638 2923 0.527600 CGCCATGAATTCCTCGTCGA 60.528 55.000 2.27 0.00 0.00 4.20
2690 2975 0.318360 TGTACTGCCGACACTGTTCG 60.318 55.000 0.00 5.72 38.80 3.95
2694 2979 1.792949 GAACTTGTACTGCCGACACTG 59.207 52.381 0.00 0.00 0.00 3.66
2697 2982 4.097437 CCTATAGAACTTGTACTGCCGACA 59.903 45.833 0.00 0.00 0.00 4.35
2699 2984 3.067742 GCCTATAGAACTTGTACTGCCGA 59.932 47.826 0.00 0.00 0.00 5.54
2705 2990 2.036862 CCCCGGCCTATAGAACTTGTAC 59.963 54.545 0.00 0.00 0.00 2.90
2756 3663 2.412323 CCATCTCCGTCGAACCCGA 61.412 63.158 0.00 0.00 43.35 5.14
2757 3664 2.104331 CCATCTCCGTCGAACCCG 59.896 66.667 0.00 0.00 37.07 5.28
2835 3742 0.686441 ATTCCTCGTCGGTCATGGGA 60.686 55.000 0.00 0.00 0.00 4.37
2837 3744 0.530650 CCATTCCTCGTCGGTCATGG 60.531 60.000 0.00 10.46 37.93 3.66
2950 3860 5.381757 TCAGCCACTAGTGTAAACCATTTT 58.618 37.500 21.18 0.00 0.00 1.82
2955 3865 3.617263 CGATTCAGCCACTAGTGTAAACC 59.383 47.826 21.18 4.67 0.00 3.27
2957 3867 4.219944 ACTCGATTCAGCCACTAGTGTAAA 59.780 41.667 21.18 9.90 0.00 2.01
2962 3872 3.093057 AGAACTCGATTCAGCCACTAGT 58.907 45.455 9.31 0.00 40.09 2.57
2963 3873 3.791973 AGAACTCGATTCAGCCACTAG 57.208 47.619 9.31 0.00 40.09 2.57
2994 3904 7.599998 GTGCAAATTTGATCAAACTAGTCCATT 59.400 33.333 22.71 8.15 32.51 3.16
3000 3910 5.698832 TCGGTGCAAATTTGATCAAACTAG 58.301 37.500 22.71 15.25 32.51 2.57
3056 3967 7.640597 AAAGTGCAGTTTCTAACTAAAACCT 57.359 32.000 13.86 0.00 40.46 3.50
3129 4044 6.610020 TCTGACCGATCCCTTCTAATTTAGAA 59.390 38.462 16.09 16.09 42.19 2.10
3151 7298 8.437360 TGTATATTGGTGTTAGAGCATTTCTG 57.563 34.615 0.00 0.00 36.61 3.02
3183 7330 4.289245 ACATGCTACTTTTATTGGGCCAT 58.711 39.130 7.26 0.00 0.00 4.40
3208 7355 8.492748 GTGTTACTTGTTTCATTCTATGTCGAA 58.507 33.333 0.00 0.00 0.00 3.71
3220 7367 3.623960 CCGAACAGGTGTTACTTGTTTCA 59.376 43.478 10.18 0.00 46.38 2.69
3270 7417 6.648310 TGAAGTGACTCAAAGATCTGACATTC 59.352 38.462 0.00 0.00 0.00 2.67
3284 7431 3.242867 AGGATTGGACTGAAGTGACTCA 58.757 45.455 0.00 0.00 0.00 3.41
3299 7446 0.037046 GCCCTGTTGCCAAAGGATTG 60.037 55.000 0.00 0.00 35.40 2.67
3411 7558 1.250840 AAGAAAGAATGCCACGCCCC 61.251 55.000 0.00 0.00 0.00 5.80
3412 7559 0.603065 AAAGAAAGAATGCCACGCCC 59.397 50.000 0.00 0.00 0.00 6.13
3443 7590 1.001268 CGACTGCACTATACAGCCGAT 60.001 52.381 0.00 0.00 42.69 4.18
3469 7616 2.165437 AGTCTCAGATCAAGGTCGCTTC 59.835 50.000 0.00 0.00 0.00 3.86
3494 7641 3.055602 CAGATCAGTGGAACATGGACAGA 60.056 47.826 0.00 0.00 44.52 3.41
3498 7645 3.176411 ACTCAGATCAGTGGAACATGGA 58.824 45.455 0.00 0.00 44.52 3.41
3506 7927 8.200120 TCATTAGTGAAATACTCAGATCAGTGG 58.800 37.037 0.00 0.00 40.89 4.00
3526 7947 6.202379 CCGCCATGCTCTATATGAATCATTAG 59.798 42.308 0.00 3.93 0.00 1.73
3532 7953 3.261643 TCACCGCCATGCTCTATATGAAT 59.738 43.478 0.00 0.00 0.00 2.57
3549 7970 0.459237 CTGCTAGCCTCTGTTCACCG 60.459 60.000 13.29 0.00 0.00 4.94
3615 8036 7.276658 TCGTATGTAGCCCTTATTGAATGAAA 58.723 34.615 0.00 0.00 0.00 2.69
3618 8039 7.604164 AGATTCGTATGTAGCCCTTATTGAATG 59.396 37.037 0.00 0.00 0.00 2.67
3627 8048 7.616150 AGAATATGTAGATTCGTATGTAGCCCT 59.384 37.037 0.00 0.00 40.20 5.19
3652 8079 9.703892 CCCAAAATAGATGAATCTACACTCTAG 57.296 37.037 2.15 0.00 41.77 2.43
3657 8084 7.054124 TGGTCCCAAAATAGATGAATCTACAC 58.946 38.462 2.15 0.00 41.77 2.90
3669 8096 2.846827 ACTCCCTCTGGTCCCAAAATAG 59.153 50.000 0.00 0.00 0.00 1.73
3670 8097 2.576191 CACTCCCTCTGGTCCCAAAATA 59.424 50.000 0.00 0.00 0.00 1.40
3676 8103 1.997874 ATGCACTCCCTCTGGTCCC 60.998 63.158 0.00 0.00 0.00 4.46
3680 8153 2.787473 TAAACATGCACTCCCTCTGG 57.213 50.000 0.00 0.00 0.00 3.86
3691 8164 9.586150 CTCGTTATTAGTCATGAATAAACATGC 57.414 33.333 18.53 7.65 44.79 4.06
3700 8173 9.027129 CGATTTTACCTCGTTATTAGTCATGAA 57.973 33.333 0.00 0.00 0.00 2.57
3715 8188 7.540745 ACAAATAAATGTGTGCGATTTTACCTC 59.459 33.333 0.00 0.00 30.82 3.85
3743 8222 1.522668 TCTCCAACCTGCAATGTTCG 58.477 50.000 0.00 0.00 0.00 3.95
3773 8252 3.010808 ACCTAGTCCAGAAGTAGCTCAGT 59.989 47.826 0.00 0.00 30.55 3.41
3874 8353 4.012374 CCTGCATCACCAACTTCTGTTAT 58.988 43.478 0.00 0.00 34.60 1.89
4236 8715 4.435518 CGTGTGATGCTTTTACTATGCGTT 60.436 41.667 0.00 0.00 0.00 4.84
4365 8858 3.451556 ATCTGCTCCCGCATCCACG 62.452 63.158 0.00 0.00 46.74 4.94
4617 9110 1.664321 GATGTAGCAGTCGGTCGGGT 61.664 60.000 0.00 0.00 0.00 5.28
4675 9168 2.726760 CTCGAAGAAAACAGGTCGTGAG 59.273 50.000 0.00 0.00 34.09 3.51
4681 9174 1.141053 ACTGGCTCGAAGAAAACAGGT 59.859 47.619 0.00 0.00 36.39 4.00
4694 9187 3.321111 TCAGGGAATATACGAACTGGCTC 59.679 47.826 0.00 0.00 0.00 4.70
4697 9190 4.341235 TCAGTCAGGGAATATACGAACTGG 59.659 45.833 0.00 0.00 0.00 4.00
4698 9191 5.163550 TGTCAGTCAGGGAATATACGAACTG 60.164 44.000 0.00 0.00 0.00 3.16
4702 9195 5.137551 TGATGTCAGTCAGGGAATATACGA 58.862 41.667 0.00 0.00 0.00 3.43
4853 9354 5.539048 GCAGGTTATATAGTCGTTGTCCAT 58.461 41.667 0.00 0.00 0.00 3.41
4970 9471 1.335132 GGGTTCTGCTCCGGATGGTA 61.335 60.000 3.57 0.00 36.30 3.25
5006 9507 1.483004 TGCAAGTGGCTACGGCTTATA 59.517 47.619 17.72 0.00 45.15 0.98
5063 9564 8.960591 AGTACCTGAACAAAATTGGAGAATATG 58.039 33.333 0.00 0.00 0.00 1.78
5119 9620 5.649395 TCAGGATATTTTTGCTTCTGGACAG 59.351 40.000 0.00 0.00 0.00 3.51
5163 9664 8.833231 TCCAAGTTCAGACAATCTAGTAAAAG 57.167 34.615 0.00 0.00 0.00 2.27
5325 9833 2.504681 CTGCCGTGCGGAATTTGC 60.505 61.111 15.45 0.00 37.02 3.68
5555 10063 4.202161 CGATCCCCCTATCTATACATGCAC 60.202 50.000 0.00 0.00 0.00 4.57
5557 10065 4.038162 GTCGATCCCCCTATCTATACATGC 59.962 50.000 0.00 0.00 0.00 4.06
5558 10066 5.450453 AGTCGATCCCCCTATCTATACATG 58.550 45.833 0.00 0.00 0.00 3.21
5559 10067 5.735733 AGTCGATCCCCCTATCTATACAT 57.264 43.478 0.00 0.00 0.00 2.29
5561 10069 5.055812 CGTAGTCGATCCCCCTATCTATAC 58.944 50.000 0.00 0.00 39.71 1.47
5725 10234 2.031191 GTGATTTCGACCAAACGTGTGT 59.969 45.455 4.73 0.00 34.70 3.72
5731 10240 5.912955 CCTTAACTTGTGATTTCGACCAAAC 59.087 40.000 0.00 0.00 0.00 2.93
5739 10248 4.640647 CCCTAGCCCTTAACTTGTGATTTC 59.359 45.833 0.00 0.00 0.00 2.17
5757 10271 2.467880 TGAGGCCTAGACAAACCCTAG 58.532 52.381 4.42 0.00 34.77 3.02
5790 10304 1.663643 TGAATGGTTGTAAGCGATCGC 59.336 47.619 32.15 32.15 42.33 4.58
5808 10322 5.804639 ACTTAACTTGTGCACCATATCTGA 58.195 37.500 15.69 0.00 0.00 3.27
5810 10324 6.823689 CCTAACTTAACTTGTGCACCATATCT 59.176 38.462 15.69 0.00 0.00 1.98
5815 10329 3.117813 ACCCTAACTTAACTTGTGCACCA 60.118 43.478 15.69 1.44 0.00 4.17
5816 10330 3.483421 ACCCTAACTTAACTTGTGCACC 58.517 45.455 15.69 0.00 0.00 5.01
5818 10332 4.951094 ACAAACCCTAACTTAACTTGTGCA 59.049 37.500 0.00 0.00 0.00 4.57
5819 10333 5.066764 TGACAAACCCTAACTTAACTTGTGC 59.933 40.000 0.00 0.00 0.00 4.57
5820 10334 6.238648 CCTGACAAACCCTAACTTAACTTGTG 60.239 42.308 0.00 0.00 0.00 3.33
5821 10335 5.826208 CCTGACAAACCCTAACTTAACTTGT 59.174 40.000 0.00 0.00 0.00 3.16
5822 10336 5.278315 GCCTGACAAACCCTAACTTAACTTG 60.278 44.000 0.00 0.00 0.00 3.16
5823 10337 4.825634 GCCTGACAAACCCTAACTTAACTT 59.174 41.667 0.00 0.00 0.00 2.66
5824 10338 4.395625 GCCTGACAAACCCTAACTTAACT 58.604 43.478 0.00 0.00 0.00 2.24
5825 10339 3.504906 GGCCTGACAAACCCTAACTTAAC 59.495 47.826 0.00 0.00 0.00 2.01
5826 10340 3.499021 GGGCCTGACAAACCCTAACTTAA 60.499 47.826 0.84 0.00 40.75 1.85
5827 10341 2.040679 GGGCCTGACAAACCCTAACTTA 59.959 50.000 0.84 0.00 40.75 2.24
5828 10342 1.203013 GGGCCTGACAAACCCTAACTT 60.203 52.381 0.84 0.00 40.75 2.66
5829 10343 0.404426 GGGCCTGACAAACCCTAACT 59.596 55.000 0.84 0.00 40.75 2.24
5830 10344 0.111639 TGGGCCTGACAAACCCTAAC 59.888 55.000 4.53 0.00 44.56 2.34
5831 10345 0.404040 CTGGGCCTGACAAACCCTAA 59.596 55.000 4.53 0.00 44.56 2.69
5832 10346 1.497309 CCTGGGCCTGACAAACCCTA 61.497 60.000 12.58 0.95 44.56 3.53
5833 10347 2.845345 CCTGGGCCTGACAAACCCT 61.845 63.158 12.58 0.00 44.56 4.34
5834 10348 2.283173 CCTGGGCCTGACAAACCC 60.283 66.667 12.58 5.62 44.52 4.11
5835 10349 1.603739 GACCTGGGCCTGACAAACC 60.604 63.158 12.58 0.00 0.00 3.27
5836 10350 1.603739 GGACCTGGGCCTGACAAAC 60.604 63.158 12.69 0.00 0.00 2.93
5837 10351 1.360393 AAGGACCTGGGCCTGACAAA 61.360 55.000 25.12 0.00 35.50 2.83
5838 10352 1.774217 AAGGACCTGGGCCTGACAA 60.774 57.895 25.12 0.00 35.50 3.18
5839 10353 2.121963 AAGGACCTGGGCCTGACA 60.122 61.111 25.12 0.00 35.50 3.58
5865 10379 8.881262 ACCAGAAAAAGAATACCTAGAAGAGAA 58.119 33.333 0.00 0.00 0.00 2.87
5870 10388 9.862149 AGAAAACCAGAAAAAGAATACCTAGAA 57.138 29.630 0.00 0.00 0.00 2.10
5986 10505 8.316946 TGCATTTGGAAAATGTTCACCATATTA 58.683 29.630 12.82 0.00 35.25 0.98
6094 10614 7.687941 ACATGAAAAATAGTTCACCCTACAG 57.312 36.000 0.00 0.00 40.22 2.74
6095 10615 9.173021 CATACATGAAAAATAGTTCACCCTACA 57.827 33.333 0.00 0.00 40.22 2.74
6096 10616 9.391006 TCATACATGAAAAATAGTTCACCCTAC 57.609 33.333 0.00 0.00 40.22 3.18
6098 10618 9.125026 GATCATACATGAAAAATAGTTCACCCT 57.875 33.333 0.00 0.00 40.22 4.34
6099 10619 8.902806 TGATCATACATGAAAAATAGTTCACCC 58.097 33.333 0.00 0.00 40.22 4.61
6100 10620 9.722056 GTGATCATACATGAAAAATAGTTCACC 57.278 33.333 0.00 0.00 40.22 4.02
6101 10621 9.722056 GGTGATCATACATGAAAAATAGTTCAC 57.278 33.333 0.00 8.68 40.22 3.18
6102 10622 9.460019 TGGTGATCATACATGAAAAATAGTTCA 57.540 29.630 0.00 0.00 40.69 3.18
6152 10672 9.629878 TGAAAAATAGTTCACCCTACACTAAAA 57.370 29.630 0.00 0.00 32.56 1.52
6153 10673 9.802039 ATGAAAAATAGTTCACCCTACACTAAA 57.198 29.630 0.00 0.00 40.22 1.85
6154 10674 9.226606 CATGAAAAATAGTTCACCCTACACTAA 57.773 33.333 0.00 0.00 40.22 2.24
6319 10847 9.906660 CCTACATTTAAATAAGTTCAGTTTGCA 57.093 29.630 0.00 0.00 0.00 4.08
6320 10848 9.908152 ACCTACATTTAAATAAGTTCAGTTTGC 57.092 29.630 0.00 0.00 0.00 3.68
6324 10852 8.512138 GTGCACCTACATTTAAATAAGTTCAGT 58.488 33.333 5.22 0.00 0.00 3.41
6325 10853 8.730680 AGTGCACCTACATTTAAATAAGTTCAG 58.269 33.333 14.63 0.00 0.00 3.02
6348 10876 7.778470 TTGTATTAAAACCAGCCAAAAAGTG 57.222 32.000 0.00 0.00 0.00 3.16
6389 10922 9.225436 TCTTACCTTTTCAAATTTGCAAAGTTT 57.775 25.926 29.15 21.69 38.96 2.66
6390 10923 8.785329 TCTTACCTTTTCAAATTTGCAAAGTT 57.215 26.923 29.15 22.73 38.96 2.66
6391 10924 8.785329 TTCTTACCTTTTCAAATTTGCAAAGT 57.215 26.923 29.15 22.25 38.96 2.66
6392 10925 9.654417 CATTCTTACCTTTTCAAATTTGCAAAG 57.346 29.630 26.64 26.64 39.86 2.77
6393 10926 9.388506 TCATTCTTACCTTTTCAAATTTGCAAA 57.611 25.926 15.44 15.44 0.00 3.68
6394 10927 8.954950 TCATTCTTACCTTTTCAAATTTGCAA 57.045 26.923 13.54 6.22 0.00 4.08
6395 10928 8.954950 TTCATTCTTACCTTTTCAAATTTGCA 57.045 26.923 13.54 0.00 0.00 4.08
6484 11018 8.512138 TCATTTCTCCTTTTCCTTTTCGTTATC 58.488 33.333 0.00 0.00 0.00 1.75
6596 11133 1.324005 GGTTCCTACGAGCTCTGCCT 61.324 60.000 12.85 0.00 0.00 4.75
6600 11137 1.476477 GGAAGGTTCCTACGAGCTCT 58.524 55.000 12.85 1.42 44.11 4.09
6648 11185 2.750888 GCCGACCCATTCACGAAGC 61.751 63.158 0.00 0.00 0.00 3.86
6673 11210 9.565625 AGGTACTTCTTGCTAAATAGCGATCCC 62.566 44.444 7.84 0.87 45.75 3.85
6751 11758 2.738846 CAACAGGTTAGTGCTGCAGTAG 59.261 50.000 16.64 8.28 0.00 2.57
6752 11759 2.549992 CCAACAGGTTAGTGCTGCAGTA 60.550 50.000 16.64 12.98 0.00 2.74
6753 11760 1.597742 CAACAGGTTAGTGCTGCAGT 58.402 50.000 16.64 15.20 0.00 4.40
6759 11766 0.527565 CATGCCCAACAGGTTAGTGC 59.472 55.000 0.00 0.00 38.26 4.40
6809 11816 6.760298 TCTCATGCAGCAACAACAAATAAAAA 59.240 30.769 0.00 0.00 0.00 1.94
6812 11819 5.450592 TCTCATGCAGCAACAACAAATAA 57.549 34.783 0.00 0.00 0.00 1.40
6813 11820 5.648178 ATCTCATGCAGCAACAACAAATA 57.352 34.783 0.00 0.00 0.00 1.40
6814 11821 4.530710 ATCTCATGCAGCAACAACAAAT 57.469 36.364 0.00 0.00 0.00 2.32
6817 11824 5.450592 TTTTATCTCATGCAGCAACAACA 57.549 34.783 0.00 0.00 0.00 3.33
6843 11850 2.587522 AGGCTTGTCTGTTTTTCCCTC 58.412 47.619 0.00 0.00 0.00 4.30
6844 11851 2.755952 AGGCTTGTCTGTTTTTCCCT 57.244 45.000 0.00 0.00 0.00 4.20
6846 11853 4.607955 GTTGTAGGCTTGTCTGTTTTTCC 58.392 43.478 0.00 0.00 0.00 3.13
6847 11854 4.279659 CGTTGTAGGCTTGTCTGTTTTTC 58.720 43.478 0.00 0.00 0.00 2.29
6893 11901 6.998673 ACTCTCATGTGTAGGCTTAAGTTTTT 59.001 34.615 4.02 0.00 0.00 1.94
6895 11903 6.115448 ACTCTCATGTGTAGGCTTAAGTTT 57.885 37.500 4.02 0.00 0.00 2.66
6898 11906 5.105146 AGGAACTCTCATGTGTAGGCTTAAG 60.105 44.000 0.00 0.00 0.00 1.85
6987 12021 2.635915 TCTTCGTGACCAATAACACCCT 59.364 45.455 0.00 0.00 34.05 4.34
6998 12032 6.413818 CACTAATGTTTTGTTTCTTCGTGACC 59.586 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.