Multiple sequence alignment - TraesCS1A01G105500

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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 TraesCS1A01G105500 chr1A 100.000 6523 0 0 1 6523 101383009 101376487 0.000000e+00 12046.0
1 TraesCS1A01G105500 chr1A 98.960 962 9 1 1 961 25577403 25576442 0.000000e+00 1720.0
2 TraesCS1A01G105500 chr1A 99.408 169 1 0 3731 3899 583789300 583789132 2.280000e-79 307.0
3 TraesCS1A01G105500 chr1A 84.775 289 26 6 2771 3041 101379965 101379677 2.320000e-69 274.0
4 TraesCS1A01G105500 chr1A 84.775 289 26 6 3045 3333 101380239 101379969 2.320000e-69 274.0
5 TraesCS1A01G105500 chr1A 72.396 797 165 34 5744 6515 547605249 547606015 1.110000e-47 202.0
6 TraesCS1A01G105500 chr1A 75.794 252 56 5 2120 2368 97961762 97961513 8.880000e-24 122.0
7 TraesCS1A01G105500 chr1A 82.258 124 21 1 2248 2370 556954508 556954631 8.950000e-19 106.0
8 TraesCS1A01G105500 chr1A 89.062 64 7 0 6339 6402 520920934 520920871 5.420000e-11 80.5
9 TraesCS1A01G105500 chr1B 94.052 2774 127 18 992 3736 162814882 162812118 0.000000e+00 4174.0
10 TraesCS1A01G105500 chr1B 95.993 1747 56 5 3899 5642 162812138 162810403 0.000000e+00 2826.0
11 TraesCS1A01G105500 chr1B 93.444 961 63 0 1 961 116971729 116972689 0.000000e+00 1426.0
12 TraesCS1A01G105500 chr1B 99.408 169 1 0 3731 3899 33923229 33923061 2.280000e-79 307.0
13 TraesCS1A01G105500 chr1B 99.408 169 1 0 3731 3899 110622983 110622815 2.280000e-79 307.0
14 TraesCS1A01G105500 chr1B 86.301 292 22 5 2771 3044 162812813 162812522 1.060000e-77 302.0
15 TraesCS1A01G105500 chr1B 83.986 281 26 6 3056 3333 162813081 162812817 1.090000e-62 252.0
16 TraesCS1A01G105500 chr1D 94.504 2256 84 18 964 3195 103406481 103408720 0.000000e+00 3443.0
17 TraesCS1A01G105500 chr1D 94.300 2070 89 9 3899 5963 103409406 103411451 0.000000e+00 3142.0
18 TraesCS1A01G105500 chr1D 90.305 722 54 4 5803 6523 103411454 103412160 0.000000e+00 931.0
19 TraesCS1A01G105500 chr1D 93.659 552 24 5 3193 3736 103408878 103409426 0.000000e+00 815.0
20 TraesCS1A01G105500 chr1D 83.871 279 28 5 3056 3333 103408305 103408567 3.910000e-62 250.0
21 TraesCS1A01G105500 chr1D 92.254 142 10 1 2901 3041 103408878 103409019 3.990000e-47 200.0
22 TraesCS1A01G105500 chr1D 82.171 129 21 2 2243 2370 464624108 464624235 6.920000e-20 110.0
23 TraesCS1A01G105500 chr2B 99.168 961 8 0 1 961 675361413 675360453 0.000000e+00 1731.0
24 TraesCS1A01G105500 chr2B 93.861 961 59 0 1 961 423825605 423824645 0.000000e+00 1448.0
25 TraesCS1A01G105500 chr2B 74.164 329 68 15 2051 2370 777832120 777832440 3.190000e-23 121.0
26 TraesCS1A01G105500 chr2B 76.923 130 25 5 2248 2372 272431298 272431169 1.170000e-07 69.4
27 TraesCS1A01G105500 chr3B 98.646 960 13 0 1 960 605009700 605010659 0.000000e+00 1701.0
28 TraesCS1A01G105500 chr3B 94.069 961 57 0 1 961 556437721 556438681 0.000000e+00 1459.0
29 TraesCS1A01G105500 chr3B 78.261 184 33 5 5948 6128 603632305 603632126 1.920000e-20 111.0
30 TraesCS1A01G105500 chr3B 88.172 93 9 2 2280 2370 581090377 581090285 6.920000e-20 110.0
31 TraesCS1A01G105500 chr3A 93.965 961 58 0 1 961 332226489 332227449 0.000000e+00 1454.0
32 TraesCS1A01G105500 chr5B 93.672 964 61 0 1 964 437765703 437764740 0.000000e+00 1443.0
33 TraesCS1A01G105500 chr4B 93.575 965 62 0 1 965 401108132 401107168 0.000000e+00 1439.0
34 TraesCS1A01G105500 chr4B 99.408 169 1 0 3731 3899 455621615 455621447 2.280000e-79 307.0
35 TraesCS1A01G105500 chr4B 78.286 175 31 3 6339 6510 520844041 520844211 8.950000e-19 106.0
36 TraesCS1A01G105500 chr3D 80.566 777 137 11 5750 6521 509208550 509209317 2.620000e-163 586.0
37 TraesCS1A01G105500 chr3D 71.354 768 168 41 5761 6517 515935046 515935772 1.130000e-32 152.0
38 TraesCS1A01G105500 chr3D 83.178 107 18 0 5948 6054 313121970 313121864 1.500000e-16 99.0
39 TraesCS1A01G105500 chr3D 75.275 182 41 3 6339 6519 562691988 562692166 4.190000e-12 84.2
40 TraesCS1A01G105500 chr2A 76.641 792 153 22 5743 6521 18830573 18829801 6.090000e-110 409.0
41 TraesCS1A01G105500 chr2A 76.375 491 102 11 5593 6072 408819974 408819487 1.090000e-62 252.0
42 TraesCS1A01G105500 chr6B 99.408 169 1 0 3731 3899 475722852 475722684 2.280000e-79 307.0
43 TraesCS1A01G105500 chr6A 99.408 169 1 0 3731 3899 7980459 7980291 2.280000e-79 307.0
44 TraesCS1A01G105500 chr6A 99.408 169 1 0 3731 3899 9365935 9366103 2.280000e-79 307.0
45 TraesCS1A01G105500 chr6A 80.426 235 34 11 2141 2369 96597772 96598000 1.120000e-37 169.0
46 TraesCS1A01G105500 chr4D 99.408 169 1 0 3731 3899 478512352 478512184 2.280000e-79 307.0
47 TraesCS1A01G105500 chr4D 74.716 704 138 23 5840 6515 47403505 47402814 1.790000e-70 278.0
48 TraesCS1A01G105500 chr4D 79.433 282 53 4 5808 6086 434960020 434959741 1.860000e-45 195.0
49 TraesCS1A01G105500 chr4D 76.923 182 36 4 6339 6517 470499542 470499364 1.500000e-16 99.0
50 TraesCS1A01G105500 chr4A 98.286 175 3 0 3731 3905 20234706 20234532 2.280000e-79 307.0
51 TraesCS1A01G105500 chr2D 82.267 344 54 7 5788 6128 645015857 645015518 2.300000e-74 291.0
52 TraesCS1A01G105500 chr6D 78.134 343 51 20 2041 2369 79867953 79868285 5.160000e-46 196.0
53 TraesCS1A01G105500 chr5D 75.216 347 73 10 6179 6516 452695558 452695216 1.130000e-32 152.0
54 TraesCS1A01G105500 chr7B 100.000 31 0 0 6339 6369 645517871 645517901 2.540000e-04 58.4


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 TraesCS1A01G105500 chr1A 101376487 101383009 6522 True 4198.0 12046 89.850000 1 6523 3 chr1A.!!$R5 6522
1 TraesCS1A01G105500 chr1A 25576442 25577403 961 True 1720.0 1720 98.960000 1 961 1 chr1A.!!$R1 960
2 TraesCS1A01G105500 chr1A 547605249 547606015 766 False 202.0 202 72.396000 5744 6515 1 chr1A.!!$F1 771
3 TraesCS1A01G105500 chr1B 162810403 162814882 4479 True 1888.5 4174 90.083000 992 5642 4 chr1B.!!$R3 4650
4 TraesCS1A01G105500 chr1B 116971729 116972689 960 False 1426.0 1426 93.444000 1 961 1 chr1B.!!$F1 960
5 TraesCS1A01G105500 chr1D 103406481 103412160 5679 False 1463.5 3443 91.482167 964 6523 6 chr1D.!!$F2 5559
6 TraesCS1A01G105500 chr2B 675360453 675361413 960 True 1731.0 1731 99.168000 1 961 1 chr2B.!!$R3 960
7 TraesCS1A01G105500 chr2B 423824645 423825605 960 True 1448.0 1448 93.861000 1 961 1 chr2B.!!$R2 960
8 TraesCS1A01G105500 chr3B 605009700 605010659 959 False 1701.0 1701 98.646000 1 960 1 chr3B.!!$F2 959
9 TraesCS1A01G105500 chr3B 556437721 556438681 960 False 1459.0 1459 94.069000 1 961 1 chr3B.!!$F1 960
10 TraesCS1A01G105500 chr3A 332226489 332227449 960 False 1454.0 1454 93.965000 1 961 1 chr3A.!!$F1 960
11 TraesCS1A01G105500 chr5B 437764740 437765703 963 True 1443.0 1443 93.672000 1 964 1 chr5B.!!$R1 963
12 TraesCS1A01G105500 chr4B 401107168 401108132 964 True 1439.0 1439 93.575000 1 965 1 chr4B.!!$R1 964
13 TraesCS1A01G105500 chr3D 509208550 509209317 767 False 586.0 586 80.566000 5750 6521 1 chr3D.!!$F1 771
14 TraesCS1A01G105500 chr2A 18829801 18830573 772 True 409.0 409 76.641000 5743 6521 1 chr2A.!!$R1 778
15 TraesCS1A01G105500 chr4D 47402814 47403505 691 True 278.0 278 74.716000 5840 6515 1 chr4D.!!$R1 675

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
286 287 0.175073 GAATGCGTCGGGGACTTACT 59.825 55.0 0.0 0.0 0.0 2.24 F
2151 2184 0.620556 TTGCACCATTCTCCCTCCTC 59.379 55.0 0.0 0.0 0.0 3.71 F
3726 3932 0.107703 TGATGATGTCTGCCGTTCCC 60.108 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2222 0.166814 GTCTGAAGACAATGCCACGC 59.833 55.0 5.58 0.0 44.18 5.34 R
3745 3951 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.0 0.00 0.0 44.78 4.85 R
5641 5852 0.456221 AGTCCGAACAGCTATGTCCG 59.544 55.0 0.00 0.0 39.29 4.79 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
286 287 0.175073 GAATGCGTCGGGGACTTACT 59.825 55.000 0.00 0.00 0.00 2.24
360 361 4.042809 TCCTTTGGAGCTATTTGGAAGTGA 59.957 41.667 0.00 0.00 0.00 3.41
793 794 2.606213 TGAGGATGTGGGCCACGA 60.606 61.111 30.14 19.86 37.14 4.35
859 860 3.249189 GGGTGGAGTGGTGGCTCA 61.249 66.667 0.00 0.00 37.24 4.26
894 895 2.253513 CCCAACCGGCACTTTGTAG 58.746 57.895 0.00 0.00 0.00 2.74
988 989 1.593265 CAGCAAATCCACAAGCCCC 59.407 57.895 0.00 0.00 0.00 5.80
1033 1044 2.031682 CACAACAAAGCGAGAGAAAGGG 60.032 50.000 0.00 0.00 0.00 3.95
1227 1244 2.028337 GCCGAGAAGGAGATCGCC 59.972 66.667 7.52 7.52 45.00 5.54
1404 1424 4.706476 CCCAATCATACTTGCCTCAGAAAA 59.294 41.667 0.00 0.00 0.00 2.29
1440 1460 3.931578 AGCTAATCAGTTCGTGCTTCTT 58.068 40.909 0.00 0.00 0.00 2.52
1565 1585 3.044305 GTGCAGAGGTGTCGTGCC 61.044 66.667 0.00 0.00 36.31 5.01
2151 2184 0.620556 TTGCACCATTCTCCCTCCTC 59.379 55.000 0.00 0.00 0.00 3.71
2170 2203 4.980805 GGGCGTTGTCGTGGAGCA 62.981 66.667 0.00 0.00 39.49 4.26
2188 2221 2.780010 AGCATAGGTGTTCTAGGGCATT 59.220 45.455 0.00 0.00 35.74 3.56
2189 2222 2.880890 GCATAGGTGTTCTAGGGCATTG 59.119 50.000 0.00 0.00 34.37 2.82
2238 2271 0.944311 TCTTTGTCGGCAGCGAAGTC 60.944 55.000 0.26 0.00 0.00 3.01
2260 2293 3.040099 GTGTGCGTTTTATGTTGTCCAC 58.960 45.455 0.00 0.00 0.00 4.02
2262 2295 3.002862 TGTGCGTTTTATGTTGTCCACTC 59.997 43.478 0.00 0.00 0.00 3.51
2267 2300 4.454161 CGTTTTATGTTGTCCACTCATCCA 59.546 41.667 0.00 0.00 0.00 3.41
2316 2349 5.491982 CTCACTACCTTCTATTGTTTGGCT 58.508 41.667 0.00 0.00 0.00 4.75
2442 2477 0.687757 AGCGTAGGGATTGCTCCTCA 60.688 55.000 0.00 0.00 41.74 3.86
2449 2484 4.703379 AGGGATTGCTCCTCAATTCTAG 57.297 45.455 0.00 0.00 44.95 2.43
2495 2530 5.626809 GCCCAAATAAAATTGAAGAGTCCCC 60.627 44.000 0.00 0.00 31.84 4.81
2497 2532 5.417580 CCAAATAAAATTGAAGAGTCCCCGA 59.582 40.000 0.00 0.00 31.84 5.14
2507 2542 0.685660 GAGTCCCCGAACCAACTTCT 59.314 55.000 0.00 0.00 0.00 2.85
2550 2585 5.148651 ACTGGTGGTGTTATTCTCTGTAC 57.851 43.478 0.00 0.00 0.00 2.90
2571 2606 1.077429 GGCTGGGGATCAAGTGTCC 60.077 63.158 0.00 0.00 34.92 4.02
2633 2668 4.720649 TCGTCTCCTGTGAGGAATTTAG 57.279 45.455 0.00 0.00 45.28 1.85
2640 2675 4.041567 TCCTGTGAGGAATTTAGTCTGCAA 59.958 41.667 0.00 0.00 42.51 4.08
2663 2698 8.125448 GCAAAGTGAATCATTTACTGGTATCTC 58.875 37.037 0.00 0.00 0.00 2.75
2669 2704 3.640029 TCATTTACTGGTATCTCGGTCCC 59.360 47.826 0.00 0.00 0.00 4.46
2724 2759 4.121317 CCTAGTAGGTCGAGTACTGTCTG 58.879 52.174 14.89 5.43 32.81 3.51
2781 2816 3.003480 CCCAGTCGAGTTTTGATCTTCC 58.997 50.000 0.00 0.00 0.00 3.46
2788 2823 3.821033 CGAGTTTTGATCTTCCAAGGGTT 59.179 43.478 0.00 0.00 0.00 4.11
2807 2842 2.908351 GTTCCACTAACCACCCTCCTAA 59.092 50.000 0.00 0.00 31.38 2.69
2838 2873 9.521503 GGAGATTTTATTGGTTTCTTATTGCTC 57.478 33.333 0.00 0.00 0.00 4.26
2875 2910 3.728845 CCTTTCTTCGAAGACAGTTGGA 58.271 45.455 29.88 13.43 34.32 3.53
2927 2964 2.061028 CGGTTTCTGCTTTCATTTGCC 58.939 47.619 0.00 0.00 0.00 4.52
3055 3093 3.934579 CTGCTTTGTGCTTTTGGTTTTCT 59.065 39.130 0.00 0.00 43.37 2.52
3056 3094 3.932089 TGCTTTGTGCTTTTGGTTTTCTC 59.068 39.130 0.00 0.00 43.37 2.87
3062 3100 4.953579 TGTGCTTTTGGTTTTCTCTAAGGT 59.046 37.500 0.00 0.00 0.00 3.50
3118 3156 6.913873 TTTATCGGTTCCTTATTGCACTAC 57.086 37.500 0.00 0.00 0.00 2.73
3232 3430 6.073602 GCTTTCATTTGCTTGGAAGGTTTTAG 60.074 38.462 5.45 0.00 33.50 1.85
3237 3435 5.514274 TTGCTTGGAAGGTTTTAGTCAAG 57.486 39.130 0.00 0.00 35.90 3.02
3334 3533 2.275134 TCCTGACATTCTGCTTTGCA 57.725 45.000 0.00 0.00 36.92 4.08
3439 3638 8.410673 TGTATTGGTTCTAAATGCCTTTTGTA 57.589 30.769 0.00 0.00 0.00 2.41
3544 3750 3.938963 TCTTCGGCATAACCATTCAACTC 59.061 43.478 0.00 0.00 39.03 3.01
3722 3928 4.707105 TCATTATTGATGATGTCTGCCGT 58.293 39.130 0.00 0.00 39.83 5.68
3723 3929 5.125356 TCATTATTGATGATGTCTGCCGTT 58.875 37.500 0.00 0.00 39.83 4.44
3724 3930 5.237127 TCATTATTGATGATGTCTGCCGTTC 59.763 40.000 0.00 0.00 39.83 3.95
3725 3931 1.737838 TTGATGATGTCTGCCGTTCC 58.262 50.000 0.00 0.00 0.00 3.62
3726 3932 0.107703 TGATGATGTCTGCCGTTCCC 60.108 55.000 0.00 0.00 0.00 3.97
3727 3933 0.107703 GATGATGTCTGCCGTTCCCA 60.108 55.000 0.00 0.00 0.00 4.37
3728 3934 0.548031 ATGATGTCTGCCGTTCCCAT 59.452 50.000 0.00 0.00 0.00 4.00
3729 3935 1.199615 TGATGTCTGCCGTTCCCATA 58.800 50.000 0.00 0.00 0.00 2.74
3730 3936 1.138859 TGATGTCTGCCGTTCCCATAG 59.861 52.381 0.00 0.00 0.00 2.23
3731 3937 0.179045 ATGTCTGCCGTTCCCATAGC 60.179 55.000 0.00 0.00 0.00 2.97
3732 3938 1.220749 GTCTGCCGTTCCCATAGCA 59.779 57.895 0.00 0.00 0.00 3.49
3733 3939 4.131376 CTGCCGTTCCCATAGCAG 57.869 61.111 0.00 0.00 45.92 4.24
3734 3940 1.221840 CTGCCGTTCCCATAGCAGT 59.778 57.895 2.75 0.00 46.00 4.40
3735 3941 1.078497 TGCCGTTCCCATAGCAGTG 60.078 57.895 0.00 0.00 0.00 3.66
3736 3942 1.819632 GCCGTTCCCATAGCAGTGG 60.820 63.158 0.63 0.63 39.05 4.00
3737 3943 1.602237 CCGTTCCCATAGCAGTGGT 59.398 57.895 0.00 0.00 37.57 4.16
3738 3944 0.828022 CCGTTCCCATAGCAGTGGTA 59.172 55.000 4.19 4.19 37.57 3.25
3739 3945 1.208535 CCGTTCCCATAGCAGTGGTAA 59.791 52.381 6.07 0.00 37.57 2.85
3740 3946 2.355310 CCGTTCCCATAGCAGTGGTAAA 60.355 50.000 6.07 0.00 37.57 2.01
3741 3947 2.936498 CGTTCCCATAGCAGTGGTAAAG 59.064 50.000 6.07 2.39 37.57 1.85
3742 3948 2.683362 GTTCCCATAGCAGTGGTAAAGC 59.317 50.000 6.07 0.00 37.57 3.51
3743 3949 2.196595 TCCCATAGCAGTGGTAAAGCT 58.803 47.619 6.07 0.00 42.14 3.74
3744 3950 2.092968 TCCCATAGCAGTGGTAAAGCTG 60.093 50.000 6.07 0.00 39.30 4.24
3749 3955 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
3750 3956 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
3751 3957 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
3752 3958 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
3753 3959 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
3754 3960 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
3755 3961 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
3756 3962 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
3757 3963 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
3758 3964 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
3759 3965 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
3760 3966 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
3761 3967 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
3762 3968 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
3763 3969 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
3773 3979 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
3774 3980 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
3775 3981 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
3776 3982 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
3777 3983 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
3778 3984 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
3779 3985 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
3780 3986 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
3781 3987 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
3782 3988 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
3783 3989 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
3784 3990 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
3785 3991 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
3786 3992 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
3787 3993 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
3798 4004 3.025924 TGGAAACAGCCTCTTGCAG 57.974 52.632 0.00 0.00 44.83 4.41
3799 4005 0.473755 TGGAAACAGCCTCTTGCAGA 59.526 50.000 0.00 0.00 44.83 4.26
3800 4006 1.133823 TGGAAACAGCCTCTTGCAGAA 60.134 47.619 0.00 0.00 44.83 3.02
3801 4007 1.956477 GGAAACAGCCTCTTGCAGAAA 59.044 47.619 0.00 0.00 44.83 2.52
3802 4008 2.560105 GGAAACAGCCTCTTGCAGAAAT 59.440 45.455 0.00 0.00 44.83 2.17
3803 4009 3.572584 GAAACAGCCTCTTGCAGAAATG 58.427 45.455 0.00 0.00 44.83 2.32
3804 4010 2.283145 ACAGCCTCTTGCAGAAATGT 57.717 45.000 0.00 0.00 44.83 2.71
3805 4011 3.423539 ACAGCCTCTTGCAGAAATGTA 57.576 42.857 0.00 0.00 44.83 2.29
3806 4012 3.341823 ACAGCCTCTTGCAGAAATGTAG 58.658 45.455 0.00 0.00 44.83 2.74
3807 4013 2.681848 CAGCCTCTTGCAGAAATGTAGG 59.318 50.000 0.00 0.00 44.83 3.18
3808 4014 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
3809 4015 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
3810 4016 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
3811 4017 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
3812 4018 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
3813 4019 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
3814 4020 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
3815 4021 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
3816 4022 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
3817 4023 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3818 4024 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3819 4025 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3820 4026 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3821 4027 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
3822 4028 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
3823 4029 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
3824 4030 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
3825 4031 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
3826 4032 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
3827 4033 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
3828 4034 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
3829 4035 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
3830 4036 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
3831 4037 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
3832 4038 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
3833 4039 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
3834 4040 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
3835 4041 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
3836 4042 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
3837 4043 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
3838 4044 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
3843 4049 2.671963 GACCCAAAGTGGTCGGGC 60.672 66.667 0.00 0.00 44.98 6.13
3844 4050 4.280019 ACCCAAAGTGGTCGGGCC 62.280 66.667 0.00 0.00 44.49 5.80
3846 4052 3.966543 CCAAAGTGGTCGGGCCCT 61.967 66.667 22.43 0.00 36.04 5.19
3847 4053 2.115266 CAAAGTGGTCGGGCCCTT 59.885 61.111 22.43 2.34 36.04 3.95
3848 4054 1.971695 CAAAGTGGTCGGGCCCTTC 60.972 63.158 22.43 12.49 36.04 3.46
3849 4055 3.205851 AAAGTGGTCGGGCCCTTCC 62.206 63.158 22.43 21.52 36.04 3.46
3859 4065 3.732849 GCCCTTCCCCAGACCCTG 61.733 72.222 0.00 0.00 0.00 4.45
3860 4066 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
3861 4067 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
3862 4068 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
3883 4089 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
3884 4090 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
3885 4091 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
3886 4092 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
3887 4093 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
3888 4094 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
3889 4095 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
3890 4096 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
3891 4097 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
3896 4102 2.203684 CACTGGGGCTGCCCTTTT 60.204 61.111 34.99 17.53 44.66 2.27
3897 4103 1.838396 CACTGGGGCTGCCCTTTTT 60.838 57.895 34.99 15.74 44.66 1.94
4114 4320 2.886862 TTGTGGCATGACTTTTGTGG 57.113 45.000 0.00 0.00 0.00 4.17
4120 4326 2.028748 GGCATGACTTTTGTGGAATGCT 60.029 45.455 0.00 0.00 38.92 3.79
4127 4333 1.327303 TTTGTGGAATGCTCGCCTTT 58.673 45.000 0.00 0.00 0.00 3.11
4145 4351 5.347907 CGCCTTTATATACTCCAAATCGGAC 59.652 44.000 0.00 0.00 39.64 4.79
4155 4361 2.761767 TCCAAATCGGACGATGAAGGTA 59.238 45.455 8.09 0.00 39.64 3.08
4205 4412 7.597288 ACATACAAGCCTAAAGAAAAAGGTT 57.403 32.000 0.00 0.00 35.16 3.50
4208 4415 9.974980 CATACAAGCCTAAAGAAAAAGGTTAAA 57.025 29.630 0.00 0.00 35.16 1.52
4241 4448 2.672961 TGCATGGTATATAGCCGAGC 57.327 50.000 9.38 10.47 0.00 5.03
4258 4465 1.198637 GAGCAAGGCATCAGTGTGTTC 59.801 52.381 0.00 0.00 0.00 3.18
4260 4467 1.901591 CAAGGCATCAGTGTGTTCCT 58.098 50.000 0.00 0.00 0.00 3.36
4261 4468 1.808945 CAAGGCATCAGTGTGTTCCTC 59.191 52.381 0.00 0.00 0.00 3.71
4262 4469 1.356124 AGGCATCAGTGTGTTCCTCT 58.644 50.000 0.00 0.00 0.00 3.69
4265 4472 3.327757 AGGCATCAGTGTGTTCCTCTTTA 59.672 43.478 0.00 0.00 0.00 1.85
4266 4473 3.437049 GGCATCAGTGTGTTCCTCTTTAC 59.563 47.826 0.00 0.00 0.00 2.01
4267 4474 4.065088 GCATCAGTGTGTTCCTCTTTACA 58.935 43.478 0.00 0.00 0.00 2.41
4415 4624 2.433868 AGCTCGAGTTTTTACTGCGA 57.566 45.000 15.13 0.00 0.00 5.10
4602 4811 1.863454 GCAGCATTGTCTATGTCCTCG 59.137 52.381 0.00 0.00 36.57 4.63
4653 4862 5.140454 TGATAGCAGCTGGACTAAGATGTA 58.860 41.667 17.12 0.00 35.97 2.29
4660 4869 3.491792 GCTGGACTAAGATGTAGGTGCTC 60.492 52.174 0.00 0.00 0.00 4.26
4704 4913 2.119495 CCTGGTACCTTGCTGATACCT 58.881 52.381 14.36 0.00 39.36 3.08
4713 4922 5.140454 ACCTTGCTGATACCTTCTGTTTTT 58.860 37.500 0.00 0.00 0.00 1.94
4920 5131 5.241728 GGTTACAAACTCCAAATCTGCTTCT 59.758 40.000 0.00 0.00 0.00 2.85
5160 5371 4.323477 AAGGTACGCGCCAAGCCA 62.323 61.111 5.73 0.00 44.76 4.75
5243 5454 3.806625 AATTTGCTGCTTGTGTTGTCT 57.193 38.095 0.00 0.00 0.00 3.41
5403 5614 0.541392 TCGTCTTGGGTGATGGATGG 59.459 55.000 0.00 0.00 0.00 3.51
5628 5839 0.893270 CAATGCCGACCCTCAAACCA 60.893 55.000 0.00 0.00 0.00 3.67
5631 5842 1.749258 GCCGACCCTCAAACCATCC 60.749 63.158 0.00 0.00 0.00 3.51
5641 5852 3.403038 CTCAAACCATCCGTATCCATCC 58.597 50.000 0.00 0.00 0.00 3.51
5651 5862 1.819288 CGTATCCATCCGGACATAGCT 59.181 52.381 6.12 0.00 46.79 3.32
5678 5889 1.298157 CTCCGCAAGCCATTCAACGA 61.298 55.000 0.00 0.00 0.00 3.85
5685 5896 2.380410 GCCATTCAACGACGACGCT 61.380 57.895 7.30 0.00 43.96 5.07
5696 5907 3.499737 CGACGCTCATTGGCCCAC 61.500 66.667 0.00 0.00 0.00 4.61
5714 5925 3.462678 GGAGCAGTCCGGACTCCC 61.463 72.222 34.28 27.90 43.54 4.30
5741 5952 1.278127 TCGAAAGAAACTAGGGGGCTG 59.722 52.381 0.00 0.00 37.03 4.85
5756 5967 1.147153 GCTGCCATGTAGGACTCCC 59.853 63.158 0.00 0.00 41.22 4.30
5786 5997 1.611491 GCCCACCAAAAATTGAGACGA 59.389 47.619 0.00 0.00 0.00 4.20
5791 6002 3.004734 CACCAAAAATTGAGACGAAGCCT 59.995 43.478 0.00 0.00 0.00 4.58
5821 6032 0.746659 AGCTGCCCGCATTATTTTCC 59.253 50.000 0.00 0.00 42.61 3.13
5856 6231 4.019321 TCTCATTCTCTTTTTCCATCCCGT 60.019 41.667 0.00 0.00 0.00 5.28
5876 6251 3.621268 CGTCGCTCTTCATTAAATTCCCA 59.379 43.478 0.00 0.00 0.00 4.37
5893 6269 1.425448 CCCACCCTTTTCCTCACTCTT 59.575 52.381 0.00 0.00 0.00 2.85
6415 6822 1.463444 GTACGACAACATGAACAGGGC 59.537 52.381 0.00 0.00 0.00 5.19
6447 6861 2.264480 TCCACAAGGGATGCGACG 59.736 61.111 0.00 0.00 42.15 5.12
6448 6862 2.264480 CCACAAGGGATGCGACGA 59.736 61.111 0.00 0.00 40.01 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
793 794 0.767375 TGCTCTCCAAAAGCTCCTGT 59.233 50.000 0.00 0.00 40.50 4.00
894 895 8.794335 AAGGGAGAAAAATATGTACAAGAGTC 57.206 34.615 0.00 0.00 0.00 3.36
961 962 5.532406 GCTTGTGGATTTGCTGGAGAATATA 59.468 40.000 0.00 0.00 0.00 0.86
1293 1310 1.229209 GAGGGAGGTGAGGTGGTCA 60.229 63.158 0.00 0.00 0.00 4.02
1404 1424 6.385467 ACTGATTAGCTAGAAAGTTGGGATCT 59.615 38.462 0.00 0.00 0.00 2.75
1440 1460 2.417586 CACGATCTTTGCAGCAGAATCA 59.582 45.455 0.00 0.00 0.00 2.57
1814 1834 3.261897 CAGGTTCTGTTCACCCTAGTCAT 59.738 47.826 0.00 0.00 34.44 3.06
1963 1986 3.726558 GATGCATCCAGGGCAGCCA 62.727 63.158 16.23 0.00 45.68 4.75
2127 2160 0.392461 GGGAGAATGGTGCAAGCGTA 60.392 55.000 0.00 0.00 36.92 4.42
2136 2169 3.331252 CCTGAGGAGGGAGAATGGT 57.669 57.895 0.00 0.00 35.40 3.55
2151 2184 2.738521 CTCCACGACAACGCCCTG 60.739 66.667 0.00 0.00 43.96 4.45
2170 2203 2.485479 CGCAATGCCCTAGAACACCTAT 60.485 50.000 0.00 0.00 0.00 2.57
2188 2221 0.250252 TCTGAAGACAATGCCACGCA 60.250 50.000 0.00 0.00 44.86 5.24
2189 2222 0.166814 GTCTGAAGACAATGCCACGC 59.833 55.000 5.58 0.00 44.18 5.34
2260 2293 0.467384 ACAGCCGATCCTTGGATGAG 59.533 55.000 9.93 1.31 45.67 2.90
2267 2300 1.482593 CCTCTTACACAGCCGATCCTT 59.517 52.381 0.00 0.00 0.00 3.36
2316 2349 4.792521 AAAGCACAAACCAAAGTACACA 57.207 36.364 0.00 0.00 0.00 3.72
2353 2386 4.529446 CGTCTACTCTCGAAATAGGCTTC 58.471 47.826 0.00 0.00 0.00 3.86
2421 2456 1.000052 GAGGAGCAATCCCTACGCTAC 60.000 57.143 0.00 0.00 36.83 3.58
2449 2484 7.284489 TGGGCTTTAACTGATATGTAATTCCAC 59.716 37.037 0.00 0.00 0.00 4.02
2495 2530 3.305335 CCCATGGAAAAGAAGTTGGTTCG 60.305 47.826 15.22 0.00 40.49 3.95
2497 2532 3.653164 ACCCATGGAAAAGAAGTTGGTT 58.347 40.909 15.22 0.00 0.00 3.67
2550 2585 0.038744 ACACTTGATCCCCAGCCAAG 59.961 55.000 0.00 0.00 42.04 3.61
2571 2606 1.379843 GCACCCCCACCAACATAGG 60.380 63.158 0.00 0.00 0.00 2.57
2621 2656 5.470098 TCACTTTGCAGACTAAATTCCTCAC 59.530 40.000 0.00 0.00 0.00 3.51
2633 2668 6.088824 CCAGTAAATGATTCACTTTGCAGAC 58.911 40.000 0.00 0.00 0.00 3.51
2640 2675 6.986817 CCGAGATACCAGTAAATGATTCACTT 59.013 38.462 0.00 0.00 0.00 3.16
2663 2698 0.902531 TGCTTAAAGAGGAGGGACCG 59.097 55.000 0.00 0.00 44.74 4.79
2669 2704 2.424956 GGTGGCATTGCTTAAAGAGGAG 59.575 50.000 8.82 0.00 0.00 3.69
2724 2759 6.401581 GCAGCTAGTCAAGACATCAGTAAAAC 60.402 42.308 2.72 0.00 0.00 2.43
2788 2823 3.278987 TTTAGGAGGGTGGTTAGTGGA 57.721 47.619 0.00 0.00 0.00 4.02
2823 2858 6.500589 AGCCTATAGAGCAATAAGAAACCA 57.499 37.500 13.52 0.00 0.00 3.67
2905 2942 3.305064 GGCAAATGAAAGCAGAAACCGTA 60.305 43.478 0.00 0.00 0.00 4.02
2907 2944 2.061028 GGCAAATGAAAGCAGAAACCG 58.939 47.619 0.00 0.00 0.00 4.44
2927 2964 8.134895 ACGCATAATTTGTATAAAACCATCCAG 58.865 33.333 0.00 0.00 0.00 3.86
3062 3100 2.929301 AGGAGGGAGGTTATGTGGAAA 58.071 47.619 0.00 0.00 0.00 3.13
3105 3143 4.002982 TGCAAGTCTGTAGTGCAATAAGG 58.997 43.478 0.00 0.00 44.88 2.69
3139 3177 2.028930 GTCTTCGACCAACTGTCCTCAT 60.029 50.000 0.00 0.00 41.18 2.90
3140 3178 1.340248 GTCTTCGACCAACTGTCCTCA 59.660 52.381 0.00 0.00 41.18 3.86
3141 3179 1.340248 TGTCTTCGACCAACTGTCCTC 59.660 52.381 0.00 0.00 41.18 3.71
3143 3181 1.340248 TCTGTCTTCGACCAACTGTCC 59.660 52.381 0.00 0.00 41.18 4.02
3232 3430 5.299279 CCATCCCCATTACACATAACTTGAC 59.701 44.000 0.00 0.00 0.00 3.18
3237 3435 3.832527 AGCCATCCCCATTACACATAAC 58.167 45.455 0.00 0.00 0.00 1.89
3334 3533 3.196901 TGGTCTACTGGCACATAAATCGT 59.803 43.478 0.00 0.00 38.20 3.73
3411 3610 7.961326 AAAGGCATTTAGAACCAATACAGAT 57.039 32.000 0.00 0.00 0.00 2.90
3419 3618 9.868277 CATAATTACAAAAGGCATTTAGAACCA 57.132 29.630 0.00 0.00 0.00 3.67
3451 3650 5.892119 TGATCCGGTAGATAACAACTCTCTT 59.108 40.000 0.00 0.00 34.42 2.85
3468 3667 6.202954 GGTTCTATCTTGTAAACATGATCCGG 59.797 42.308 13.06 0.00 40.08 5.14
3469 3668 6.986817 AGGTTCTATCTTGTAAACATGATCCG 59.013 38.462 13.06 7.79 40.08 4.18
3521 3720 4.331968 AGTTGAATGGTTATGCCGAAGAA 58.668 39.130 0.00 0.00 41.21 2.52
3544 3750 4.693283 TCAACGAGGTCCTGCATATAAAG 58.307 43.478 0.00 0.00 0.00 1.85
3712 3918 0.179045 GCTATGGGAACGGCAGACAT 60.179 55.000 0.00 0.00 0.00 3.06
3713 3919 1.220749 GCTATGGGAACGGCAGACA 59.779 57.895 0.00 0.00 0.00 3.41
3714 3920 0.811616 CTGCTATGGGAACGGCAGAC 60.812 60.000 7.89 0.00 46.53 3.51
3715 3921 1.264749 ACTGCTATGGGAACGGCAGA 61.265 55.000 18.52 0.00 46.53 4.26
3716 3922 4.131376 CTGCTATGGGAACGGCAG 57.869 61.111 0.00 0.00 41.75 4.85
3717 3923 1.078497 CACTGCTATGGGAACGGCA 60.078 57.895 0.00 0.00 0.00 5.69
3718 3924 1.819632 CCACTGCTATGGGAACGGC 60.820 63.158 0.00 0.00 35.95 5.68
3719 3925 0.828022 TACCACTGCTATGGGAACGG 59.172 55.000 11.00 0.00 44.81 4.44
3720 3926 2.684001 TTACCACTGCTATGGGAACG 57.316 50.000 11.00 0.00 44.81 3.95
3721 3927 2.683362 GCTTTACCACTGCTATGGGAAC 59.317 50.000 11.00 0.00 42.63 3.62
3722 3928 2.576191 AGCTTTACCACTGCTATGGGAA 59.424 45.455 11.00 6.12 44.81 3.97
3723 3929 2.092968 CAGCTTTACCACTGCTATGGGA 60.093 50.000 11.00 0.00 44.81 4.37
3724 3930 2.292267 CAGCTTTACCACTGCTATGGG 58.708 52.381 11.00 0.00 44.81 4.00
3731 3937 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
3732 3938 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
3733 3939 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
3734 3940 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
3735 3941 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
3736 3942 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
3737 3943 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
3738 3944 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
3739 3945 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
3740 3946 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
3741 3947 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
3742 3948 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3743 3949 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
3744 3950 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
3745 3951 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3746 3952 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
3757 3963 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
3758 3964 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
3759 3965 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
3760 3966 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
3761 3967 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
3762 3968 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
3763 3969 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
3764 3970 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
3765 3971 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
3766 3972 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
3767 3973 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
3768 3974 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
3769 3975 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3770 3976 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3771 3977 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3772 3978 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3773 3979 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3774 3980 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3775 3981 1.072965 CAAGAGGCTGTTTCCAGGACT 59.927 52.381 0.00 0.00 39.22 3.85
3776 3982 1.528129 CAAGAGGCTGTTTCCAGGAC 58.472 55.000 0.00 0.00 39.22 3.85
3777 3983 0.250901 GCAAGAGGCTGTTTCCAGGA 60.251 55.000 0.00 0.00 39.22 3.86
3778 3984 0.538057 TGCAAGAGGCTGTTTCCAGG 60.538 55.000 0.00 0.00 45.15 4.45
3779 3985 0.879765 CTGCAAGAGGCTGTTTCCAG 59.120 55.000 0.00 0.00 45.15 3.86
3780 3986 0.473755 TCTGCAAGAGGCTGTTTCCA 59.526 50.000 0.00 0.00 38.67 3.53
3781 3987 3.329300 TCTGCAAGAGGCTGTTTCC 57.671 52.632 0.00 0.00 38.67 3.13
3791 3997 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
3792 3998 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
3793 3999 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
3794 4000 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
3795 4001 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
3796 4002 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3797 4003 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3798 4004 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3799 4005 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3800 4006 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3801 4007 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
3802 4008 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
3803 4009 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
3804 4010 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
3805 4011 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
3806 4012 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
3807 4013 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
3808 4014 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
3809 4015 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
3810 4016 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
3811 4017 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
3812 4018 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
3813 4019 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
3814 4020 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
3815 4021 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
3816 4022 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
3817 4023 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
3829 4035 3.507377 AAGGGCCCGACCACTTTGG 62.507 63.158 18.44 0.00 45.02 3.28
3830 4036 1.971695 GAAGGGCCCGACCACTTTG 60.972 63.158 18.44 0.00 42.05 2.77
3831 4037 2.434774 GAAGGGCCCGACCACTTT 59.565 61.111 18.44 2.21 42.05 2.66
3832 4038 3.647771 GGAAGGGCCCGACCACTT 61.648 66.667 27.60 12.80 42.05 3.16
3842 4048 3.732849 CAGGGTCTGGGGAAGGGC 61.733 72.222 0.00 0.00 0.00 5.19
3843 4049 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
3844 4050 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
3845 4051 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
3857 4063 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
3860 4066 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
3861 4067 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
3862 4068 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
3863 4069 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
3865 4071 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
3866 4072 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
3867 4073 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
3868 4074 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
3869 4075 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
3870 4076 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
3871 4077 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
3872 4078 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
3873 4079 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
3894 4100 1.816224 GCTATGGGAACGGCAGAAAAA 59.184 47.619 0.00 0.00 0.00 1.94
3895 4101 1.271652 TGCTATGGGAACGGCAGAAAA 60.272 47.619 0.00 0.00 0.00 2.29
3896 4102 0.326595 TGCTATGGGAACGGCAGAAA 59.673 50.000 0.00 0.00 0.00 2.52
3897 4103 0.107703 CTGCTATGGGAACGGCAGAA 60.108 55.000 7.89 0.00 46.53 3.02
3913 4119 5.669477 AGATTCTTTACTCCATCTCACTGC 58.331 41.667 0.00 0.00 0.00 4.40
3944 4150 3.459227 TCCCATTCACCAATGCTCTATCA 59.541 43.478 0.00 0.00 38.53 2.15
3945 4151 4.090761 TCCCATTCACCAATGCTCTATC 57.909 45.455 0.00 0.00 38.53 2.08
3946 4152 4.404640 CATCCCATTCACCAATGCTCTAT 58.595 43.478 0.00 0.00 38.53 1.98
3947 4153 3.824133 CATCCCATTCACCAATGCTCTA 58.176 45.455 0.00 0.00 38.53 2.43
3948 4154 2.662866 CATCCCATTCACCAATGCTCT 58.337 47.619 0.00 0.00 38.53 4.09
3990 4196 5.996513 ACATGATTGATGAGCTATCAGAACC 59.003 40.000 0.00 0.00 46.01 3.62
4047 4253 6.879993 TGTACCCGCATAAAGTGATTAAGAAA 59.120 34.615 0.00 0.00 0.00 2.52
4114 4320 5.479306 TGGAGTATATAAAGGCGAGCATTC 58.521 41.667 0.00 0.00 0.00 2.67
4120 4326 5.244402 TCCGATTTGGAGTATATAAAGGCGA 59.756 40.000 0.00 0.00 43.74 5.54
4145 4351 6.737254 AGGTGTAACAAATTACCTTCATCG 57.263 37.500 0.00 0.00 40.51 3.84
4155 4361 2.614983 ACGCACGAAGGTGTAACAAATT 59.385 40.909 0.00 0.00 46.13 1.82
4171 4377 2.031157 AGGCTTGTATGTTTTCACGCAC 60.031 45.455 0.00 0.00 31.90 5.34
4205 4412 7.043300 ACCATGCATCCTCCCATAATATTTA 57.957 36.000 0.00 0.00 0.00 1.40
4208 4415 6.853669 ATACCATGCATCCTCCCATAATAT 57.146 37.500 0.00 0.00 0.00 1.28
4241 4448 1.808945 GAGGAACACACTGATGCCTTG 59.191 52.381 0.00 0.00 0.00 3.61
4265 4472 9.423061 GTTTTGCTCTATTTACATGGAAAATGT 57.577 29.630 7.30 0.00 32.48 2.71
4266 4473 8.872845 GGTTTTGCTCTATTTACATGGAAAATG 58.127 33.333 7.30 3.54 32.48 2.32
4267 4474 8.592809 TGGTTTTGCTCTATTTACATGGAAAAT 58.407 29.630 7.30 9.97 32.48 1.82
4366 4575 5.009210 TGCAGGGTAAACAATAACAAGACAC 59.991 40.000 0.00 0.00 0.00 3.67
4415 4624 3.933861 AGTTCCACAAACTCCTGAAGT 57.066 42.857 0.00 0.00 45.28 3.01
4602 4811 1.860326 GATGCAGGCACAACAAAACAC 59.140 47.619 0.00 0.00 0.00 3.32
4660 4869 3.872771 GCCCAATTTACCAATGATGCTTG 59.127 43.478 0.00 0.00 0.00 4.01
4704 4913 3.194005 AGACCTGCGAGAAAAACAGAA 57.806 42.857 0.00 0.00 33.10 3.02
4713 4922 2.233676 TGCTCAAATAAGACCTGCGAGA 59.766 45.455 0.00 0.00 0.00 4.04
4894 5105 4.892934 AGCAGATTTGGAGTTTGTAACCAA 59.107 37.500 0.00 0.00 41.12 3.67
5031 5242 3.336122 CTGCTTTGAGAAGGGCAGT 57.664 52.632 0.00 0.00 44.69 4.40
5155 5366 0.538287 GAGCAGAAGTGGGTTGGCTT 60.538 55.000 0.00 0.00 0.00 4.35
5160 5371 2.539081 GGGGGAGCAGAAGTGGGTT 61.539 63.158 0.00 0.00 0.00 4.11
5243 5454 1.470996 GCCTGGGATTTGCAACACCA 61.471 55.000 18.70 16.14 0.00 4.17
5403 5614 4.005650 TCAGACTGGCAATTCTCATCAAC 58.994 43.478 1.81 0.00 0.00 3.18
5602 5813 1.224592 GGGTCGGCATTGGAGATGT 59.775 57.895 0.00 0.00 0.00 3.06
5641 5852 0.456221 AGTCCGAACAGCTATGTCCG 59.544 55.000 0.00 0.00 39.29 4.79
5678 5889 4.015406 TGGGCCAATGAGCGTCGT 62.015 61.111 2.13 0.00 0.00 4.34
5685 5896 3.626996 CTGCTCCGTGGGCCAATGA 62.627 63.158 8.40 6.97 0.00 2.57
5714 5925 3.181520 CCCTAGTTTCTTTCGATGTTGCG 60.182 47.826 0.00 0.00 0.00 4.85
5739 5950 0.179000 GTGGGAGTCCTACATGGCAG 59.821 60.000 20.10 0.00 35.26 4.85
5741 5952 0.107654 GTGTGGGAGTCCTACATGGC 60.108 60.000 28.74 14.28 35.26 4.40
5821 6032 6.512342 AAGAGAATGAGAGATTTTTGCCAG 57.488 37.500 0.00 0.00 0.00 4.85
5856 6231 3.945285 GGTGGGAATTTAATGAAGAGCGA 59.055 43.478 0.00 0.00 0.00 4.93
5900 6276 2.534396 ATGGGTTGGTGGCGGAAGA 61.534 57.895 0.00 0.00 0.00 2.87
5935 6311 1.211212 CATCACCTCCATCTCTGGCAA 59.789 52.381 0.00 0.00 42.80 4.52
5986 6371 2.658707 GCTGTGTCGCCGAGTTGAC 61.659 63.158 0.00 0.00 35.67 3.18
6174 6566 1.988834 GCCTTGTAATGTTCCGCCCG 61.989 60.000 0.00 0.00 0.00 6.13
6402 6809 2.356135 GTACATCGCCCTGTTCATGTT 58.644 47.619 0.00 0.00 31.83 2.71
6415 6822 1.339929 TGTGGATCATCCCGTACATCG 59.660 52.381 0.00 0.00 35.03 3.84
6441 6851 0.609957 TAGGAACCTCCTTCGTCGCA 60.610 55.000 0.00 0.00 46.91 5.10
6446 6860 1.689273 CCCTCATAGGAACCTCCTTCG 59.311 57.143 0.00 0.00 46.91 3.79
6447 6861 1.418264 GCCCTCATAGGAACCTCCTTC 59.582 57.143 0.00 0.00 46.91 3.46
6448 6862 1.512735 GCCCTCATAGGAACCTCCTT 58.487 55.000 0.00 0.00 46.91 3.36
6466 6883 0.039074 CGAGTCATCCACCTATCCGC 60.039 60.000 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.