Multiple sequence alignment - TraesCS5A01G005000

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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 TraesCS5A01G005000 chr5A 100.000 3498 0 0 1 3498 3312623 3316120 0.000000e+00 6460.0
1 TraesCS5A01G005000 chr5A 79.944 1775 244 61 890 2610 3423038 3421322 0.000000e+00 1203.0
2 TraesCS5A01G005000 chr5A 79.950 1212 183 33 1398 2582 3303513 3304691 0.000000e+00 837.0
3 TraesCS5A01G005000 chr5A 81.503 1038 150 29 1746 2756 3159280 3160302 0.000000e+00 815.0
4 TraesCS5A01G005000 chr5A 89.899 99 10 0 677 775 3294673 3294771 1.020000e-25 128.0
5 TraesCS5A01G005000 chr5A 89.899 99 10 0 677 775 3295247 3295345 1.020000e-25 128.0
6 TraesCS5A01G005000 chr5A 89.899 99 10 0 677 775 3295822 3295920 1.020000e-25 128.0
7 TraesCS5A01G005000 chr5D 92.857 1442 77 7 900 2336 6355961 6354541 0.000000e+00 2069.0
8 TraesCS5A01G005000 chr5D 96.390 831 22 5 1 825 6356997 6356169 0.000000e+00 1362.0
9 TraesCS5A01G005000 chr5D 84.143 1318 168 27 904 2185 5793432 5794744 0.000000e+00 1238.0
10 TraesCS5A01G005000 chr5D 83.888 931 140 10 1008 1934 5567747 5568671 0.000000e+00 880.0
11 TraesCS5A01G005000 chr5D 80.749 1122 165 27 1489 2582 6373508 6372410 0.000000e+00 828.0
12 TraesCS5A01G005000 chr5D 77.687 1461 249 37 1014 2456 553626997 553625596 0.000000e+00 821.0
13 TraesCS5A01G005000 chr5D 81.310 1038 158 24 1746 2759 6492764 6491739 0.000000e+00 809.0
14 TraesCS5A01G005000 chr5D 91.412 524 35 7 2737 3257 6354535 6354019 0.000000e+00 710.0
15 TraesCS5A01G005000 chr5D 82.418 637 97 10 2051 2673 5568781 5569416 3.070000e-150 542.0
16 TraesCS5A01G005000 chr5D 77.199 557 98 19 2352 2893 5325357 5325899 7.340000e-77 298.0
17 TraesCS5A01G005000 chr5D 92.233 103 8 0 677 779 6375874 6375772 2.810000e-31 147.0
18 TraesCS5A01G005000 chr5D 97.260 73 2 0 834 906 6356074 6356002 1.320000e-24 124.0
19 TraesCS5A01G005000 chr5D 90.476 84 8 0 647 730 6369161 6369078 1.030000e-20 111.0
20 TraesCS5A01G005000 chr5B 79.490 1843 278 52 1008 2815 6603085 6601308 0.000000e+00 1218.0
21 TraesCS5A01G005000 chr5B 93.955 397 22 2 2198 2593 6514745 6514350 1.800000e-167 599.0
22 TraesCS5A01G005000 chr5B 81.806 720 69 25 2589 3257 6512117 6511409 6.600000e-152 547.0
23 TraesCS5A01G005000 chr5B 75.754 829 146 27 1747 2560 697173515 697174303 1.980000e-97 366.0
24 TraesCS5A01G005000 chr4A 77.230 1581 265 46 1014 2560 615099639 615101158 0.000000e+00 837.0
25 TraesCS5A01G005000 chr4A 75.877 1596 284 50 1014 2572 615058913 615060444 0.000000e+00 721.0
26 TraesCS5A01G005000 chr4A 76.725 855 136 33 1747 2571 614907673 614908494 5.400000e-113 418.0
27 TraesCS5A01G005000 chr4A 90.476 126 12 0 3134 3259 614873441 614873566 2.160000e-37 167.0
28 TraesCS5A01G005000 chrUn 79.070 860 156 15 1014 1867 31326931 31326090 1.410000e-158 569.0
29 TraesCS5A01G005000 chr7A 93.805 113 7 0 3386 3498 165003107 165002995 1.670000e-38 171.0
30 TraesCS5A01G005000 chr2B 75.430 407 69 16 2056 2460 781827470 781827093 6.000000e-38 169.0
31 TraesCS5A01G005000 chr7D 84.076 157 23 2 2050 2205 489902456 489902301 2.180000e-32 150.0
32 TraesCS5A01G005000 chr7D 97.222 36 0 1 3260 3295 84174582 84174548 3.770000e-05 60.2
33 TraesCS5A01G005000 chr7B 81.699 153 26 2 2054 2205 518394270 518394119 3.670000e-25 126.0
34 TraesCS5A01G005000 chr7B 81.699 153 26 2 2054 2205 518397579 518397428 3.670000e-25 126.0
35 TraesCS5A01G005000 chr7B 81.046 153 27 2 2054 2205 518413618 518413467 1.710000e-23 121.0
36 TraesCS5A01G005000 chr6A 84.426 122 9 7 3264 3380 37835430 37835546 1.030000e-20 111.0
37 TraesCS5A01G005000 chr2D 95.000 40 2 0 3264 3303 612941125 612941164 2.910000e-06 63.9
38 TraesCS5A01G005000 chr3A 94.872 39 2 0 3264 3302 702224719 702224757 1.050000e-05 62.1
39 TraesCS5A01G005000 chr3A 100.000 32 0 0 3264 3295 53322881 53322850 3.770000e-05 60.2
40 TraesCS5A01G005000 chr6B 96.970 33 1 0 3263 3295 96644830 96644862 4.880000e-04 56.5


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 TraesCS5A01G005000 chr5A 3312623 3316120 3497 False 6460.00 6460 100.000000 1 3498 1 chr5A.!!$F3 3497
1 TraesCS5A01G005000 chr5A 3421322 3423038 1716 True 1203.00 1203 79.944000 890 2610 1 chr5A.!!$R1 1720
2 TraesCS5A01G005000 chr5A 3303513 3304691 1178 False 837.00 837 79.950000 1398 2582 1 chr5A.!!$F2 1184
3 TraesCS5A01G005000 chr5A 3159280 3160302 1022 False 815.00 815 81.503000 1746 2756 1 chr5A.!!$F1 1010
4 TraesCS5A01G005000 chr5D 5793432 5794744 1312 False 1238.00 1238 84.143000 904 2185 1 chr5D.!!$F2 1281
5 TraesCS5A01G005000 chr5D 6354019 6356997 2978 True 1066.25 2069 94.479750 1 3257 4 chr5D.!!$R3 3256
6 TraesCS5A01G005000 chr5D 553625596 553626997 1401 True 821.00 821 77.687000 1014 2456 1 chr5D.!!$R2 1442
7 TraesCS5A01G005000 chr5D 6491739 6492764 1025 True 809.00 809 81.310000 1746 2759 1 chr5D.!!$R1 1013
8 TraesCS5A01G005000 chr5D 5567747 5569416 1669 False 711.00 880 83.153000 1008 2673 2 chr5D.!!$F3 1665
9 TraesCS5A01G005000 chr5D 6369078 6375874 6796 True 362.00 828 87.819333 647 2582 3 chr5D.!!$R4 1935
10 TraesCS5A01G005000 chr5D 5325357 5325899 542 False 298.00 298 77.199000 2352 2893 1 chr5D.!!$F1 541
11 TraesCS5A01G005000 chr5B 6601308 6603085 1777 True 1218.00 1218 79.490000 1008 2815 1 chr5B.!!$R1 1807
12 TraesCS5A01G005000 chr5B 6511409 6514745 3336 True 573.00 599 87.880500 2198 3257 2 chr5B.!!$R2 1059
13 TraesCS5A01G005000 chr5B 697173515 697174303 788 False 366.00 366 75.754000 1747 2560 1 chr5B.!!$F1 813
14 TraesCS5A01G005000 chr4A 615099639 615101158 1519 False 837.00 837 77.230000 1014 2560 1 chr4A.!!$F4 1546
15 TraesCS5A01G005000 chr4A 615058913 615060444 1531 False 721.00 721 75.877000 1014 2572 1 chr4A.!!$F3 1558
16 TraesCS5A01G005000 chr4A 614907673 614908494 821 False 418.00 418 76.725000 1747 2571 1 chr4A.!!$F2 824
17 TraesCS5A01G005000 chrUn 31326090 31326931 841 True 569.00 569 79.070000 1014 1867 1 chrUn.!!$R1 853

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
282 285 1.158007 ACCATCTCACCCCTTTTGGT 58.842 50.0 0.0 0.0 39.96 3.67 F
1266 3343 0.034337 GTGACGGTGCCACTTCCTTA 59.966 55.0 0.0 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 4176 0.03779 GCAAACCTCTCTCGAGTGCT 60.038 55.0 13.13 0.0 35.24 4.4 R
2943 7599 0.03601 CCGACACTGCCCTTGAAGAT 60.036 55.0 0.00 0.0 0.00 2.4 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
48 50 9.010029 TGTTGGGACTCACTTATAATTCTTTTC 57.990 33.333 0.00 0.00 0.00 2.29
121 123 4.631377 TGCGGTCTGTGATTTGATTTCTAG 59.369 41.667 0.00 0.00 0.00 2.43
282 285 1.158007 ACCATCTCACCCCTTTTGGT 58.842 50.000 0.00 0.00 39.96 3.67
298 301 5.121142 CCTTTTGGTAATCTCTTCGCGTTAA 59.879 40.000 5.77 0.00 34.07 2.01
309 312 2.806608 TCGCGTTAAAGACCAGACTT 57.193 45.000 5.77 0.00 0.00 3.01
334 337 6.098409 TGCCCCTCAGATCTAGTTTTACTAAG 59.902 42.308 0.00 0.00 29.00 2.18
335 338 6.463190 GCCCCTCAGATCTAGTTTTACTAAGG 60.463 46.154 0.00 0.00 29.00 2.69
336 339 6.612049 CCCCTCAGATCTAGTTTTACTAAGGT 59.388 42.308 0.00 0.00 29.00 3.50
356 363 6.215495 AGGTAGTTGAAGAAGAGATACTGC 57.785 41.667 0.00 0.00 0.00 4.40
387 394 1.555075 GGTGAACCAGTGCTAGGATCA 59.445 52.381 0.00 0.00 35.84 2.92
474 481 2.021457 CTGTTCGGTGTTGGGAACTTT 58.979 47.619 5.63 0.00 42.28 2.66
479 486 2.021457 CGGTGTTGGGAACTTTCAACT 58.979 47.619 0.00 0.00 42.48 3.16
480 487 2.425668 CGGTGTTGGGAACTTTCAACTT 59.574 45.455 0.00 0.00 42.48 2.66
516 523 3.994931 AACTTAACTGCCCTATCCGTT 57.005 42.857 0.00 0.00 0.00 4.44
554 561 5.680619 TCTGCTCACCGGTCATTATTATTT 58.319 37.500 2.59 0.00 0.00 1.40
597 604 5.053978 ACTGTCCTGAAATTGAAACCTCT 57.946 39.130 0.00 0.00 0.00 3.69
617 624 5.431420 TCTGACTAAAGCTCATCGATCTC 57.569 43.478 0.00 0.00 0.00 2.75
620 627 2.952978 ACTAAAGCTCATCGATCTCGGT 59.047 45.455 0.00 0.00 40.29 4.69
825 832 3.319137 TTCTAACTGCTGCGAGACAAT 57.681 42.857 6.18 0.00 0.00 2.71
862 955 9.503369 ACTGTAATAACTTATTAGAGGAACCCT 57.497 33.333 21.32 5.24 42.88 4.34
997 3056 1.746787 CATGCAGCCAGCTGTTTGATA 59.253 47.619 20.11 4.11 45.24 2.15
1257 3334 2.092882 GCTCTTACGTGACGGTGCC 61.093 63.158 10.66 0.00 0.00 5.01
1266 3343 0.034337 GTGACGGTGCCACTTCCTTA 59.966 55.000 0.00 0.00 0.00 2.69
1326 3403 2.949714 CAACGTGTTGTGAGTGGATC 57.050 50.000 4.58 0.00 35.92 3.36
1356 3433 3.485633 CATCATGCACAAAGTTCGTCTG 58.514 45.455 0.00 0.00 0.00 3.51
1432 3509 3.869912 GCACCTCAAAATAGTCAGGCTCA 60.870 47.826 0.00 0.00 0.00 4.26
1455 3532 8.231692 TCAAATCTAACTTGTTGAAACATGGA 57.768 30.769 12.15 0.35 38.95 3.41
1551 3634 1.600023 ACGAGATCTCATCGAGGTCC 58.400 55.000 22.31 0.00 40.39 4.46
1698 3782 3.832490 TGCCTTCTCTAGTAACAGCTTCA 59.168 43.478 0.00 0.00 0.00 3.02
1717 3801 4.601621 TCAGTTAGTCTGAGATTCGACG 57.398 45.455 0.00 0.00 46.77 5.12
1860 3947 5.029650 TGTGCATACAAGTTTCGATGAAC 57.970 39.130 0.00 0.00 32.88 3.18
2041 4157 5.181811 TCGCTGTCATCATTTTGATTTCACT 59.818 36.000 0.00 0.00 34.28 3.41
2138 4266 1.964552 GCATGGCTGCTGACTTCTAT 58.035 50.000 0.00 0.00 45.32 1.98
2359 4733 1.284111 TGCCATCATCAAGGGGAGCT 61.284 55.000 0.00 0.00 0.00 4.09
2479 4861 2.086869 CTGGTCAGTGATGCGGAAATT 58.913 47.619 0.00 0.00 0.00 1.82
2480 4862 1.811965 TGGTCAGTGATGCGGAAATTG 59.188 47.619 0.00 0.00 0.00 2.32
2498 4880 2.880879 GCATCGAGCGTCGCTGAA 60.881 61.111 27.16 12.70 38.15 3.02
2540 4930 0.324738 TTGTTTTGGGACCTGCCACA 60.325 50.000 0.00 0.00 38.95 4.17
2560 4950 5.106555 CCACAATTGGTCAGTGCTAAGTTAG 60.107 44.000 10.83 5.47 38.23 2.34
2564 4954 7.068226 ACAATTGGTCAGTGCTAAGTTAGTTTT 59.932 33.333 10.83 0.00 0.00 2.43
2586 4976 3.644966 TGAGACAAAGGTGTTTGGAGT 57.355 42.857 3.12 0.00 46.42 3.85
2599 7240 6.659242 AGGTGTTTGGAGTTCCTATGTTAATG 59.341 38.462 0.00 0.00 36.82 1.90
2607 7248 7.829211 TGGAGTTCCTATGTTAATGAGAAAAGG 59.171 37.037 0.00 0.00 36.82 3.11
2617 7258 0.110486 TGAGAAAAGGGCCACACTCC 59.890 55.000 6.18 0.00 0.00 3.85
2645 7286 3.482783 GCAGCGGCGAAGTGAGTC 61.483 66.667 12.98 0.00 0.00 3.36
2646 7287 2.811317 CAGCGGCGAAGTGAGTCC 60.811 66.667 12.98 0.00 0.00 3.85
2674 7317 5.172687 TCATGTTTTAGATAGTGGGTGCA 57.827 39.130 0.00 0.00 0.00 4.57
2696 7346 0.246757 CTCGTTGCGGTCGAATTTCG 60.247 55.000 12.54 12.54 42.10 3.46
2739 7390 5.738619 TGATCTTAGCTAGTTGGTCAACA 57.261 39.130 15.12 2.26 43.47 3.33
2751 7402 6.877611 AGTTGGTCAACATAAACTAGTTGG 57.122 37.500 9.34 4.83 43.91 3.77
2760 7411 5.313712 ACATAAACTAGTTGGGTGTTCAGG 58.686 41.667 9.34 0.00 0.00 3.86
2801 7452 5.338463 GGTTGCTGGGTATTCTAGTTCTTCT 60.338 44.000 0.00 0.00 0.00 2.85
2802 7453 5.344743 TGCTGGGTATTCTAGTTCTTCTG 57.655 43.478 0.00 0.00 0.00 3.02
2803 7454 5.023452 TGCTGGGTATTCTAGTTCTTCTGA 58.977 41.667 0.00 0.00 0.00 3.27
2835 7489 8.888579 ATATATGTAGTTGTGTTCTAGCCAAC 57.111 34.615 0.00 0.00 38.94 3.77
2877 7531 8.249638 CCTTATCTGTATGTATGATGAGGTCAG 58.750 40.741 0.00 0.00 40.92 3.51
2888 7542 0.551396 TGAGGTCAGAGGAGCCGATA 59.449 55.000 0.00 0.00 42.52 2.92
2902 7556 4.171754 GAGCCGATAAAAGTGTCGTTAGT 58.828 43.478 0.00 0.00 36.71 2.24
2903 7557 3.924686 AGCCGATAAAAGTGTCGTTAGTG 59.075 43.478 0.00 0.00 36.71 2.74
2927 7581 8.709646 GTGAAACTACCTTAATGTTGACACTAG 58.290 37.037 0.00 0.00 33.54 2.57
2928 7582 7.386848 TGAAACTACCTTAATGTTGACACTAGC 59.613 37.037 0.00 0.00 0.00 3.42
2939 7595 3.887621 TGACACTAGCAGGAATGTACC 57.112 47.619 0.00 0.00 0.00 3.34
2942 7598 0.464452 ACTAGCAGGAATGTACCGCC 59.536 55.000 0.00 0.00 32.85 6.13
2943 7599 0.464036 CTAGCAGGAATGTACCGCCA 59.536 55.000 0.00 0.00 32.85 5.69
2945 7601 0.179045 AGCAGGAATGTACCGCCATC 60.179 55.000 0.00 0.00 32.85 3.51
2946 7602 0.179045 GCAGGAATGTACCGCCATCT 60.179 55.000 0.00 0.00 34.73 2.90
2947 7603 1.747206 GCAGGAATGTACCGCCATCTT 60.747 52.381 0.00 0.00 34.73 2.40
2948 7604 2.213499 CAGGAATGTACCGCCATCTTC 58.787 52.381 0.00 0.00 34.73 2.87
2949 7605 1.837439 AGGAATGTACCGCCATCTTCA 59.163 47.619 0.00 0.00 34.73 3.02
2950 7606 2.238646 AGGAATGTACCGCCATCTTCAA 59.761 45.455 0.00 0.00 34.73 2.69
2951 7607 2.614057 GGAATGTACCGCCATCTTCAAG 59.386 50.000 0.00 0.00 0.00 3.02
2952 7608 2.332063 ATGTACCGCCATCTTCAAGG 57.668 50.000 0.00 0.00 0.00 3.61
2953 7609 0.251916 TGTACCGCCATCTTCAAGGG 59.748 55.000 0.00 0.00 0.00 3.95
2954 7610 1.095807 GTACCGCCATCTTCAAGGGC 61.096 60.000 0.00 0.00 44.27 5.19
2957 7613 4.751431 GCCATCTTCAAGGGCAGT 57.249 55.556 0.01 0.00 46.92 4.40
2959 7615 0.610232 GCCATCTTCAAGGGCAGTGT 60.610 55.000 0.01 0.00 46.92 3.55
2960 7616 1.457346 CCATCTTCAAGGGCAGTGTC 58.543 55.000 0.00 0.00 0.00 3.67
2962 7618 0.036010 ATCTTCAAGGGCAGTGTCGG 60.036 55.000 0.00 0.00 0.00 4.79
2968 7629 1.821061 AAGGGCAGTGTCGGACTCAG 61.821 60.000 9.88 4.03 29.75 3.35
2972 7633 1.080230 CAGTGTCGGACTCAGGCAG 60.080 63.158 9.88 0.00 29.75 4.85
2978 7639 1.109920 TCGGACTCAGGCAGCTATCC 61.110 60.000 0.00 0.00 0.00 2.59
2989 7650 2.569059 GCAGCTATCCTTGCATTGAGA 58.431 47.619 0.00 0.00 0.00 3.27
3007 7668 5.028549 TGAGAGGATCAAAATCTACTGCC 57.971 43.478 0.00 0.00 37.82 4.85
3010 7671 4.133078 GAGGATCAAAATCTACTGCCAGG 58.867 47.826 0.00 0.00 33.17 4.45
3011 7672 3.782523 AGGATCAAAATCTACTGCCAGGA 59.217 43.478 0.00 0.00 32.12 3.86
3012 7673 4.228210 AGGATCAAAATCTACTGCCAGGAA 59.772 41.667 0.00 0.00 32.12 3.36
3013 7674 4.578105 GGATCAAAATCTACTGCCAGGAAG 59.422 45.833 0.00 0.00 32.12 3.46
3015 7676 5.241403 TCAAAATCTACTGCCAGGAAGAA 57.759 39.130 0.00 0.00 0.00 2.52
3017 7678 5.707298 TCAAAATCTACTGCCAGGAAGAAAG 59.293 40.000 0.00 0.00 0.00 2.62
3018 7679 5.505181 AAATCTACTGCCAGGAAGAAAGA 57.495 39.130 0.00 4.03 0.00 2.52
3019 7680 5.707066 AATCTACTGCCAGGAAGAAAGAT 57.293 39.130 0.00 6.35 0.00 2.40
3020 7681 4.744795 TCTACTGCCAGGAAGAAAGATC 57.255 45.455 0.00 0.00 0.00 2.75
3021 7682 2.797177 ACTGCCAGGAAGAAAGATCC 57.203 50.000 0.00 0.00 37.22 3.36
3022 7683 1.988107 ACTGCCAGGAAGAAAGATCCA 59.012 47.619 0.00 0.00 39.55 3.41
3023 7684 2.376518 ACTGCCAGGAAGAAAGATCCAA 59.623 45.455 0.00 0.00 39.55 3.53
3024 7685 2.751806 CTGCCAGGAAGAAAGATCCAAC 59.248 50.000 0.00 0.00 39.55 3.77
3025 7686 1.740025 GCCAGGAAGAAAGATCCAACG 59.260 52.381 0.00 0.00 39.55 4.10
3026 7687 2.359900 CCAGGAAGAAAGATCCAACGG 58.640 52.381 0.00 0.00 39.55 4.44
3036 7720 1.134788 AGATCCAACGGACCGATTGTC 60.135 52.381 23.38 14.28 43.67 3.18
3071 7755 3.545703 TCAGCATCGACTGTCTCTGATA 58.454 45.455 6.21 0.00 38.84 2.15
3079 7763 6.852858 TCGACTGTCTCTGATATCTGTTAG 57.147 41.667 6.21 0.00 0.00 2.34
3083 7767 7.518211 CGACTGTCTCTGATATCTGTTAGTCAG 60.518 44.444 21.80 19.27 44.85 3.51
3086 7770 6.770303 TGTCTCTGATATCTGTTAGTCAGGAG 59.230 42.308 3.98 0.00 43.76 3.69
3095 7779 4.816385 TCTGTTAGTCAGGAGCTTGTTTTG 59.184 41.667 0.00 0.00 43.76 2.44
3186 7886 6.457934 GCCAAATGAGTAGTCATCATGTCTTG 60.458 42.308 13.46 12.10 43.04 3.02
3284 7985 6.849085 ATATCCAAAACAATAAGGTGTGCA 57.151 33.333 0.00 0.00 0.00 4.57
3285 7986 5.743636 ATCCAAAACAATAAGGTGTGCAT 57.256 34.783 0.00 0.00 0.00 3.96
3286 7987 5.132897 TCCAAAACAATAAGGTGTGCATC 57.867 39.130 0.00 0.00 0.00 3.91
3287 7988 4.586421 TCCAAAACAATAAGGTGTGCATCA 59.414 37.500 0.00 0.00 0.00 3.07
3288 7989 5.069648 TCCAAAACAATAAGGTGTGCATCAA 59.930 36.000 0.00 0.00 0.00 2.57
3290 7991 4.789012 AACAATAAGGTGTGCATCAAGG 57.211 40.909 0.00 0.00 0.00 3.61
3291 7992 4.032960 ACAATAAGGTGTGCATCAAGGA 57.967 40.909 0.00 0.00 0.00 3.36
3293 7994 2.787473 TAAGGTGTGCATCAAGGAGG 57.213 50.000 0.00 0.00 0.00 4.30
3294 7995 0.038744 AAGGTGTGCATCAAGGAGGG 59.961 55.000 0.00 0.00 0.00 4.30
3295 7996 0.842030 AGGTGTGCATCAAGGAGGGA 60.842 55.000 0.00 0.00 0.00 4.20
3296 7997 0.257039 GGTGTGCATCAAGGAGGGAT 59.743 55.000 0.00 0.00 0.00 3.85
3297 7998 1.341383 GGTGTGCATCAAGGAGGGATT 60.341 52.381 0.00 0.00 0.00 3.01
3298 7999 2.019984 GTGTGCATCAAGGAGGGATTC 58.980 52.381 0.00 0.00 0.00 2.52
3299 8000 1.918262 TGTGCATCAAGGAGGGATTCT 59.082 47.619 0.00 0.00 0.00 2.40
3300 8001 2.092753 TGTGCATCAAGGAGGGATTCTC 60.093 50.000 0.00 0.00 41.71 2.87
3301 8002 1.139654 TGCATCAAGGAGGGATTCTCG 59.860 52.381 0.00 0.00 43.34 4.04
3302 8003 1.876322 CATCAAGGAGGGATTCTCGC 58.124 55.000 0.00 0.00 43.34 5.03
3303 8004 1.139654 CATCAAGGAGGGATTCTCGCA 59.860 52.381 0.00 0.00 43.34 5.10
3304 8005 1.500474 TCAAGGAGGGATTCTCGCAT 58.500 50.000 0.00 0.00 43.34 4.73
3306 8007 0.179034 AAGGAGGGATTCTCGCATGC 60.179 55.000 7.91 7.91 43.34 4.06
3307 8008 1.146930 GGAGGGATTCTCGCATGCA 59.853 57.895 19.57 4.02 43.34 3.96
3308 8009 0.250640 GGAGGGATTCTCGCATGCAT 60.251 55.000 19.57 2.77 43.34 3.96
3309 8010 0.873054 GAGGGATTCTCGCATGCATG 59.127 55.000 22.70 22.70 32.18 4.06
3310 8011 0.182061 AGGGATTCTCGCATGCATGT 59.818 50.000 26.79 6.75 0.00 3.21
3311 8012 0.309922 GGGATTCTCGCATGCATGTG 59.690 55.000 30.15 30.15 39.55 3.21
3314 8015 1.033202 ATTCTCGCATGCATGTGCCA 61.033 50.000 30.95 18.60 42.06 4.92
3315 8016 1.033202 TTCTCGCATGCATGTGCCAT 61.033 50.000 30.95 0.00 42.06 4.40
3316 8017 1.299089 CTCGCATGCATGTGCCATG 60.299 57.895 30.95 18.00 42.06 3.66
3317 8018 2.000215 CTCGCATGCATGTGCCATGT 62.000 55.000 30.95 0.00 42.06 3.21
3319 8020 1.513622 GCATGCATGTGCCATGTCA 59.486 52.632 26.79 12.72 41.18 3.58
3320 8021 0.104120 GCATGCATGTGCCATGTCAT 59.896 50.000 26.79 13.93 41.18 3.06
3321 8022 1.868109 GCATGCATGTGCCATGTCATC 60.868 52.381 26.79 2.80 41.18 2.92
3322 8023 1.407258 CATGCATGTGCCATGTCATCA 59.593 47.619 18.91 6.43 41.18 3.07
3324 8025 0.812549 GCATGTGCCATGTCATCACA 59.187 50.000 14.21 9.16 43.72 3.58
3326 8027 1.404035 CATGTGCCATGTCATCACAGG 59.596 52.381 11.66 8.57 42.98 4.00
3327 8028 0.401356 TGTGCCATGTCATCACAGGT 59.599 50.000 3.78 0.00 35.99 4.00
3329 8030 2.239402 TGTGCCATGTCATCACAGGTAT 59.761 45.455 3.78 0.00 35.99 2.73
3330 8031 3.282021 GTGCCATGTCATCACAGGTATT 58.718 45.455 0.00 0.00 35.41 1.89
3331 8032 4.080638 TGTGCCATGTCATCACAGGTATTA 60.081 41.667 3.78 0.00 35.99 0.98
3332 8033 4.512944 GTGCCATGTCATCACAGGTATTAG 59.487 45.833 0.00 0.00 35.41 1.73
3333 8034 4.408596 TGCCATGTCATCACAGGTATTAGA 59.591 41.667 0.00 0.00 35.41 2.10
3334 8035 5.104569 TGCCATGTCATCACAGGTATTAGAA 60.105 40.000 0.00 0.00 35.41 2.10
3335 8036 5.822519 GCCATGTCATCACAGGTATTAGAAA 59.177 40.000 0.00 0.00 35.41 2.52
3336 8037 6.318648 GCCATGTCATCACAGGTATTAGAAAA 59.681 38.462 0.00 0.00 35.41 2.29
3337 8038 7.148086 GCCATGTCATCACAGGTATTAGAAAAA 60.148 37.037 0.00 0.00 35.41 1.94
3355 8056 2.273370 AAAACGAATCGAGCTAGCGA 57.727 45.000 10.55 1.38 45.22 4.93
3356 8057 2.273370 AAACGAATCGAGCTAGCGAA 57.727 45.000 10.55 0.00 44.22 4.70
3357 8058 2.493713 AACGAATCGAGCTAGCGAAT 57.506 45.000 10.55 1.23 44.22 3.34
3361 8062 1.000163 GAATCGAGCTAGCGAATGGGA 60.000 52.381 9.55 2.17 44.22 4.37
3362 8063 0.315568 ATCGAGCTAGCGAATGGGAC 59.684 55.000 9.55 0.00 44.22 4.46
3363 8064 1.300233 CGAGCTAGCGAATGGGACC 60.300 63.158 9.55 0.00 0.00 4.46
3364 8065 1.739338 CGAGCTAGCGAATGGGACCT 61.739 60.000 9.55 0.00 0.00 3.85
3366 8067 1.300233 GCTAGCGAATGGGACCTCG 60.300 63.158 0.00 0.00 36.05 4.63
3367 8068 2.017559 GCTAGCGAATGGGACCTCGT 62.018 60.000 0.00 0.00 35.51 4.18
3368 8069 0.460311 CTAGCGAATGGGACCTCGTT 59.540 55.000 3.84 0.58 35.51 3.85
3369 8070 0.899720 TAGCGAATGGGACCTCGTTT 59.100 50.000 3.84 0.00 35.51 3.60
3370 8071 0.036306 AGCGAATGGGACCTCGTTTT 59.964 50.000 3.84 0.00 35.51 2.43
3373 8074 1.804601 GAATGGGACCTCGTTTTCGT 58.195 50.000 0.00 0.00 44.46 3.85
3374 8075 1.730612 GAATGGGACCTCGTTTTCGTC 59.269 52.381 0.00 0.00 44.46 4.20
3375 8076 0.682852 ATGGGACCTCGTTTTCGTCA 59.317 50.000 0.00 0.00 44.46 4.35
3376 8077 0.032952 TGGGACCTCGTTTTCGTCAG 59.967 55.000 0.00 0.00 44.46 3.51
3377 8078 0.033090 GGGACCTCGTTTTCGTCAGT 59.967 55.000 0.00 0.00 44.46 3.41
3378 8079 1.539712 GGGACCTCGTTTTCGTCAGTT 60.540 52.381 0.00 0.00 44.46 3.16
3380 8081 2.466846 GACCTCGTTTTCGTCAGTTCA 58.533 47.619 0.00 0.00 44.46 3.18
3381 8082 2.470821 ACCTCGTTTTCGTCAGTTCAG 58.529 47.619 0.00 0.00 44.46 3.02
3382 8083 1.192534 CCTCGTTTTCGTCAGTTCAGC 59.807 52.381 0.00 0.00 44.46 4.26
3383 8084 1.858458 CTCGTTTTCGTCAGTTCAGCA 59.142 47.619 0.00 0.00 44.46 4.41
3384 8085 2.272678 TCGTTTTCGTCAGTTCAGCAA 58.727 42.857 0.00 0.00 44.46 3.91
3385 8086 2.673862 TCGTTTTCGTCAGTTCAGCAAA 59.326 40.909 0.00 0.00 44.46 3.68
3387 8088 3.485216 CGTTTTCGTCAGTTCAGCAAACT 60.485 43.478 0.00 0.00 42.71 2.66
3388 8089 4.412207 GTTTTCGTCAGTTCAGCAAACTT 58.588 39.130 2.04 0.00 46.26 2.66
3389 8090 3.944422 TTCGTCAGTTCAGCAAACTTC 57.056 42.857 2.04 0.00 46.26 3.01
3390 8091 3.179443 TCGTCAGTTCAGCAAACTTCT 57.821 42.857 2.04 0.00 46.26 2.85
3392 8093 3.309682 TCGTCAGTTCAGCAAACTTCTTG 59.690 43.478 2.04 0.00 46.26 3.02
3393 8094 3.063997 CGTCAGTTCAGCAAACTTCTTGT 59.936 43.478 2.04 0.00 46.26 3.16
3394 8095 4.437390 CGTCAGTTCAGCAAACTTCTTGTT 60.437 41.667 2.04 0.00 46.26 2.83
3396 8097 6.551736 GTCAGTTCAGCAAACTTCTTGTTTA 58.448 36.000 2.04 0.00 46.26 2.01
3397 8098 6.469275 GTCAGTTCAGCAAACTTCTTGTTTAC 59.531 38.462 2.04 0.00 46.26 2.01
3398 8099 6.150307 TCAGTTCAGCAAACTTCTTGTTTACA 59.850 34.615 2.04 0.00 46.26 2.41
3399 8100 6.806249 CAGTTCAGCAAACTTCTTGTTTACAA 59.194 34.615 2.04 0.00 46.26 2.41
3400 8101 7.328249 CAGTTCAGCAAACTTCTTGTTTACAAA 59.672 33.333 2.04 0.00 46.26 2.83
3402 8103 6.919721 TCAGCAAACTTCTTGTTTACAAACT 58.080 32.000 6.41 0.00 46.11 2.66
3403 8104 7.375053 TCAGCAAACTTCTTGTTTACAAACTT 58.625 30.769 6.41 0.00 46.11 2.66
3405 8106 8.495148 CAGCAAACTTCTTGTTTACAAACTTTT 58.505 29.630 6.41 0.00 46.11 2.27
3406 8107 8.495148 AGCAAACTTCTTGTTTACAAACTTTTG 58.505 29.630 6.41 0.00 46.11 2.44
3407 8108 7.268235 GCAAACTTCTTGTTTACAAACTTTTGC 59.732 33.333 17.93 17.93 46.11 3.68
3408 8109 8.495148 CAAACTTCTTGTTTACAAACTTTTGCT 58.505 29.630 6.41 0.00 46.11 3.91
3409 8110 7.812309 ACTTCTTGTTTACAAACTTTTGCTC 57.188 32.000 6.41 0.00 41.79 4.26
3410 8111 6.526674 ACTTCTTGTTTACAAACTTTTGCTCG 59.473 34.615 6.41 0.00 41.79 5.03
3411 8112 5.945155 TCTTGTTTACAAACTTTTGCTCGT 58.055 33.333 6.41 0.00 41.79 4.18
3412 8113 6.383415 TCTTGTTTACAAACTTTTGCTCGTT 58.617 32.000 6.41 0.00 41.79 3.85
3414 8115 5.945155 TGTTTACAAACTTTTGCTCGTTCT 58.055 33.333 6.41 0.00 41.79 3.01
3415 8116 7.074507 TGTTTACAAACTTTTGCTCGTTCTA 57.925 32.000 6.41 0.00 41.79 2.10
3416 8117 7.699566 TGTTTACAAACTTTTGCTCGTTCTAT 58.300 30.769 6.41 0.00 41.79 1.98
3417 8118 7.642194 TGTTTACAAACTTTTGCTCGTTCTATG 59.358 33.333 6.41 0.00 41.79 2.23
3420 8121 5.065988 ACAAACTTTTGCTCGTTCTATGTGT 59.934 36.000 1.49 0.00 41.79 3.72
3426 8127 1.673033 GCTCGTTCTATGTGTGGCAGT 60.673 52.381 0.00 0.00 0.00 4.40
3427 8128 2.688507 CTCGTTCTATGTGTGGCAGTT 58.311 47.619 0.00 0.00 0.00 3.16
3428 8129 2.668457 CTCGTTCTATGTGTGGCAGTTC 59.332 50.000 0.00 0.00 0.00 3.01
3429 8130 2.036604 TCGTTCTATGTGTGGCAGTTCA 59.963 45.455 0.00 0.00 0.00 3.18
3430 8131 2.413112 CGTTCTATGTGTGGCAGTTCAG 59.587 50.000 0.00 0.00 0.00 3.02
3431 8132 2.099141 TCTATGTGTGGCAGTTCAGC 57.901 50.000 0.00 0.00 0.00 4.26
3432 8133 1.347378 TCTATGTGTGGCAGTTCAGCA 59.653 47.619 0.00 0.00 35.83 4.41
3433 8134 2.153645 CTATGTGTGGCAGTTCAGCAA 58.846 47.619 0.00 0.00 35.83 3.91
3434 8135 1.401761 ATGTGTGGCAGTTCAGCAAA 58.598 45.000 0.00 0.00 35.83 3.68
3435 8136 1.401761 TGTGTGGCAGTTCAGCAAAT 58.598 45.000 0.00 0.00 35.83 2.32
3436 8137 1.755959 TGTGTGGCAGTTCAGCAAATT 59.244 42.857 0.00 0.00 35.83 1.82
3437 8138 2.954989 TGTGTGGCAGTTCAGCAAATTA 59.045 40.909 0.00 0.00 35.83 1.40
3439 8140 2.954989 TGTGGCAGTTCAGCAAATTACA 59.045 40.909 0.00 0.00 35.83 2.41
3440 8141 3.382865 TGTGGCAGTTCAGCAAATTACAA 59.617 39.130 0.00 0.00 35.83 2.41
3442 8143 3.005684 TGGCAGTTCAGCAAATTACAAGG 59.994 43.478 0.00 0.00 35.83 3.61
3443 8144 2.989166 GCAGTTCAGCAAATTACAAGGC 59.011 45.455 0.00 0.00 0.00 4.35
3444 8145 3.552684 GCAGTTCAGCAAATTACAAGGCA 60.553 43.478 0.00 0.00 0.00 4.75
3445 8146 4.232221 CAGTTCAGCAAATTACAAGGCAG 58.768 43.478 0.00 0.00 0.00 4.85
3446 8147 3.891366 AGTTCAGCAAATTACAAGGCAGT 59.109 39.130 0.00 0.00 0.00 4.40
3447 8148 3.921119 TCAGCAAATTACAAGGCAGTG 57.079 42.857 0.00 0.00 0.00 3.66
3448 8149 3.485394 TCAGCAAATTACAAGGCAGTGA 58.515 40.909 0.00 0.00 0.00 3.41
3450 8151 3.983344 CAGCAAATTACAAGGCAGTGAAC 59.017 43.478 0.00 0.00 0.00 3.18
3451 8152 3.891366 AGCAAATTACAAGGCAGTGAACT 59.109 39.130 0.00 0.00 0.00 3.01
3452 8153 4.022849 AGCAAATTACAAGGCAGTGAACTC 60.023 41.667 0.00 0.00 0.00 3.01
3454 8155 5.455392 CAAATTACAAGGCAGTGAACTCAG 58.545 41.667 0.00 0.00 0.00 3.35
3455 8156 3.838244 TTACAAGGCAGTGAACTCAGT 57.162 42.857 0.00 0.00 0.00 3.41
3456 8157 2.717639 ACAAGGCAGTGAACTCAGTT 57.282 45.000 0.00 0.00 0.00 3.16
3458 8159 2.945668 ACAAGGCAGTGAACTCAGTTTC 59.054 45.455 0.00 0.00 0.00 2.78
3459 8160 2.945008 CAAGGCAGTGAACTCAGTTTCA 59.055 45.455 0.00 0.00 32.94 2.69
3468 8169 5.592104 TGAACTCAGTTTCACTCTGTACA 57.408 39.130 0.00 0.00 34.86 2.90
3473 10179 6.170506 ACTCAGTTTCACTCTGTACACAAAA 58.829 36.000 0.00 0.00 34.86 2.44
3479 10185 9.337396 AGTTTCACTCTGTACACAAAATTATGA 57.663 29.630 0.00 0.00 0.00 2.15
3481 10187 9.554395 TTTCACTCTGTACACAAAATTATGAGA 57.446 29.630 9.25 0.00 0.00 3.27
3488 10194 8.492673 TGTACACAAAATTATGAGAGGACATC 57.507 34.615 0.00 0.00 0.00 3.06
3489 10195 7.552687 TGTACACAAAATTATGAGAGGACATCC 59.447 37.037 0.00 0.00 0.00 3.51
3491 10197 7.121382 ACACAAAATTATGAGAGGACATCCAT 58.879 34.615 0.00 0.00 38.89 3.41
3492 10198 7.284034 ACACAAAATTATGAGAGGACATCCATC 59.716 37.037 0.00 0.00 38.89 3.51
3493 10199 7.501559 CACAAAATTATGAGAGGACATCCATCT 59.498 37.037 0.00 0.48 38.89 2.90
3494 10200 8.057623 ACAAAATTATGAGAGGACATCCATCTT 58.942 33.333 0.00 0.00 38.89 2.40
3496 10202 2.996249 TGAGAGGACATCCATCTTGC 57.004 50.000 0.00 0.00 38.89 4.01
3497 10203 2.475155 TGAGAGGACATCCATCTTGCT 58.525 47.619 0.00 0.00 38.89 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 5.980116 AGACGCTGCAGTTCAGTAATATAAG 59.020 40.000 16.64 0.00 44.66 1.73
121 123 4.237724 GCAACAGCCATACCTTTTCTTTC 58.762 43.478 0.00 0.00 0.00 2.62
220 223 7.349412 AGATTTGTGTCTATCTACCTACCAC 57.651 40.000 0.00 0.00 29.56 4.16
282 285 5.063180 TGGTCTTTAACGCGAAGAGATTA 57.937 39.130 15.93 0.00 34.05 1.75
298 301 0.768221 TGAGGGGCAAGTCTGGTCTT 60.768 55.000 0.00 0.00 0.00 3.01
309 312 4.362677 AGTAAAACTAGATCTGAGGGGCA 58.637 43.478 5.18 0.00 0.00 5.36
334 337 5.038033 CGCAGTATCTCTTCTTCAACTACC 58.962 45.833 0.00 0.00 0.00 3.18
335 338 5.881447 TCGCAGTATCTCTTCTTCAACTAC 58.119 41.667 0.00 0.00 0.00 2.73
336 339 6.499172 CATCGCAGTATCTCTTCTTCAACTA 58.501 40.000 0.00 0.00 0.00 2.24
356 363 2.100631 GGTTCACCGGACTGCATCG 61.101 63.158 9.46 0.00 0.00 3.84
363 370 0.389948 CTAGCACTGGTTCACCGGAC 60.390 60.000 9.46 0.00 45.36 4.79
387 394 7.637511 ACCCTTGAATTCAGAATCTGAGTATT 58.362 34.615 13.11 10.98 41.75 1.89
486 493 9.315525 GATAGGGCAGTTAAGTTAAGTTAGAAG 57.684 37.037 0.00 0.00 0.00 2.85
491 498 5.046087 ACGGATAGGGCAGTTAAGTTAAGTT 60.046 40.000 0.00 0.37 0.00 2.66
516 523 4.943705 GTGAGCAGAAATTATCAGTTCCCA 59.056 41.667 0.00 0.00 0.00 4.37
554 561 8.375493 ACAGTATCCTTTCCAGTTATCAGTAA 57.625 34.615 0.00 0.00 0.00 2.24
597 604 3.003793 CCGAGATCGATGAGCTTTAGTCA 59.996 47.826 0.54 0.00 43.02 3.41
652 659 1.873591 CCACTTCACTAGTTGGCACAC 59.126 52.381 0.00 0.00 39.29 3.82
856 949 5.648092 ACATATCAGCAAACTTGTAGGGTTC 59.352 40.000 0.00 0.00 0.00 3.62
862 955 8.839343 CATTATCCACATATCAGCAAACTTGTA 58.161 33.333 0.00 0.00 0.00 2.41
986 3045 4.156008 GGGTCGACATTTTATCAAACAGCT 59.844 41.667 18.91 0.00 0.00 4.24
997 3056 0.872388 GAACTGCGGGTCGACATTTT 59.128 50.000 18.91 0.86 0.00 1.82
1257 3334 2.555199 CGGGCTTCATCTAAGGAAGTG 58.445 52.381 3.65 0.00 42.88 3.16
1266 3343 1.047002 CAGAGATCCGGGCTTCATCT 58.953 55.000 0.00 1.06 0.00 2.90
1356 3433 3.378339 GGCATATGCAGAAACATGAAGC 58.622 45.455 28.07 3.15 44.36 3.86
1432 3509 9.696917 GAATCCATGTTTCAACAAGTTAGATTT 57.303 29.630 0.00 0.00 43.03 2.17
1551 3634 5.406780 GCGAATGATATGTAGAACCTTGAGG 59.593 44.000 0.00 0.00 42.17 3.86
1698 3782 4.255301 ACTCGTCGAATCTCAGACTAACT 58.745 43.478 0.00 0.00 35.38 2.24
1712 3796 7.599621 TGTTTTCCTTATAATGAAACTCGTCGA 59.400 33.333 13.50 0.00 30.64 4.20
1713 3797 7.686938 GTGTTTTCCTTATAATGAAACTCGTCG 59.313 37.037 13.50 0.00 30.64 5.12
1743 3828 1.555075 TCAAGTAGACCATGACCCAGC 59.445 52.381 0.00 0.00 0.00 4.85
1860 3947 6.648725 AATCTAACTAAGCAAGCAAGTACG 57.351 37.500 0.00 0.00 0.00 3.67
1894 3985 6.763355 TCTGAATTTAAGTCAGAGAAGCAGT 58.237 36.000 19.23 0.00 45.11 4.40
1904 3996 7.911651 AGTGAAGATCCTCTGAATTTAAGTCA 58.088 34.615 0.00 0.00 0.00 3.41
2041 4157 4.333690 ACCTCTCTCGAGTGCTAACTTTA 58.666 43.478 13.13 0.00 36.52 1.85
2048 4176 0.037790 GCAAACCTCTCTCGAGTGCT 60.038 55.000 13.13 0.00 35.24 4.40
2138 4266 0.457853 GTAGAATGTGACGCAGCGGA 60.458 55.000 21.15 1.54 0.00 5.54
2498 4880 9.131791 ACAAAACAAGGTCTTGATTAACATAGT 57.868 29.630 16.55 3.41 42.93 2.12
2540 4930 7.582667 AAAACTAACTTAGCACTGACCAATT 57.417 32.000 0.00 0.00 0.00 2.32
2564 4954 4.340617 ACTCCAAACACCTTTGTCTCAAA 58.659 39.130 0.00 0.00 35.84 2.69
2586 4976 5.891551 GGCCCTTTTCTCATTAACATAGGAA 59.108 40.000 0.00 0.00 0.00 3.36
2599 7240 0.402121 AGGAGTGTGGCCCTTTTCTC 59.598 55.000 0.00 1.03 0.00 2.87
2607 7248 0.108585 TTCTGACAAGGAGTGTGGCC 59.891 55.000 0.00 0.00 41.96 5.36
2617 7258 1.208614 GCCGCTGCTTTCTGACAAG 59.791 57.895 0.00 0.00 33.53 3.16
2636 7277 4.592485 ACATGATATCGGGACTCACTTC 57.408 45.455 0.00 0.00 0.00 3.01
2645 7286 6.818644 CCCACTATCTAAAACATGATATCGGG 59.181 42.308 0.00 0.00 33.80 5.14
2646 7287 7.331934 CACCCACTATCTAAAACATGATATCGG 59.668 40.741 0.00 0.00 0.00 4.18
2674 7317 0.599204 AATTCGACCGCAACGAGTGT 60.599 50.000 0.00 0.00 40.72 3.55
2696 7346 9.236006 AGATCAAACCATCACCATTATATTAGC 57.764 33.333 0.00 0.00 0.00 3.09
2723 7374 8.130671 ACTAGTTTATGTTGACCAACTAGCTA 57.869 34.615 14.88 0.00 46.89 3.32
2739 7390 5.546499 TCTCCTGAACACCCAACTAGTTTAT 59.454 40.000 5.07 0.00 0.00 1.40
2751 7402 2.237143 TCCATCATGTCTCCTGAACACC 59.763 50.000 0.00 0.00 0.00 4.16
2760 7411 5.048921 CAGCAACCATAATCCATCATGTCTC 60.049 44.000 0.00 0.00 0.00 3.36
2852 7506 9.018582 TCTGACCTCATCATACATACAGATAAG 57.981 37.037 0.00 0.00 36.48 1.73
2853 7507 8.940397 TCTGACCTCATCATACATACAGATAA 57.060 34.615 0.00 0.00 36.48 1.75
2854 7508 7.613411 CCTCTGACCTCATCATACATACAGATA 59.387 40.741 0.00 0.00 36.48 1.98
2855 7509 6.436847 CCTCTGACCTCATCATACATACAGAT 59.563 42.308 0.00 0.00 36.48 2.90
2856 7510 5.772169 CCTCTGACCTCATCATACATACAGA 59.228 44.000 0.00 0.00 36.48 3.41
2857 7511 5.772169 TCCTCTGACCTCATCATACATACAG 59.228 44.000 0.00 0.00 36.48 2.74
2858 7512 5.705400 TCCTCTGACCTCATCATACATACA 58.295 41.667 0.00 0.00 36.48 2.29
2859 7513 5.336372 GCTCCTCTGACCTCATCATACATAC 60.336 48.000 0.00 0.00 36.48 2.39
2860 7514 4.769488 GCTCCTCTGACCTCATCATACATA 59.231 45.833 0.00 0.00 36.48 2.29
2861 7515 3.577848 GCTCCTCTGACCTCATCATACAT 59.422 47.826 0.00 0.00 36.48 2.29
2877 7531 2.194271 CGACACTTTTATCGGCTCCTC 58.806 52.381 0.00 0.00 34.67 3.71
2888 7542 6.343703 AGGTAGTTTCACTAACGACACTTTT 58.656 36.000 0.00 0.00 43.03 2.27
2902 7556 7.386848 GCTAGTGTCAACATTAAGGTAGTTTCA 59.613 37.037 0.00 0.00 0.00 2.69
2903 7557 7.386848 TGCTAGTGTCAACATTAAGGTAGTTTC 59.613 37.037 0.00 0.00 0.00 2.78
2927 7581 0.179045 AGATGGCGGTACATTCCTGC 60.179 55.000 0.00 0.00 0.00 4.85
2928 7582 2.213499 GAAGATGGCGGTACATTCCTG 58.787 52.381 0.00 0.00 0.00 3.86
2942 7598 1.081892 CGACACTGCCCTTGAAGATG 58.918 55.000 0.00 0.00 0.00 2.90
2943 7599 0.036010 CCGACACTGCCCTTGAAGAT 60.036 55.000 0.00 0.00 0.00 2.40
2945 7601 0.951040 GTCCGACACTGCCCTTGAAG 60.951 60.000 0.00 0.00 0.00 3.02
2946 7602 1.070786 GTCCGACACTGCCCTTGAA 59.929 57.895 0.00 0.00 0.00 2.69
2947 7603 1.816863 GAGTCCGACACTGCCCTTGA 61.817 60.000 0.40 0.00 34.41 3.02
2948 7604 1.374758 GAGTCCGACACTGCCCTTG 60.375 63.158 0.40 0.00 34.41 3.61
2949 7605 1.821061 CTGAGTCCGACACTGCCCTT 61.821 60.000 0.40 0.00 34.41 3.95
2950 7606 2.203640 TGAGTCCGACACTGCCCT 60.204 61.111 0.40 0.00 34.41 5.19
2951 7607 2.262915 CTGAGTCCGACACTGCCC 59.737 66.667 0.40 0.00 34.41 5.36
2952 7608 2.262915 CCTGAGTCCGACACTGCC 59.737 66.667 0.40 0.00 34.41 4.85
2953 7609 2.433318 GCCTGAGTCCGACACTGC 60.433 66.667 0.40 0.00 34.41 4.40
2954 7610 1.080230 CTGCCTGAGTCCGACACTG 60.080 63.158 0.40 0.00 34.41 3.66
2955 7611 2.936912 GCTGCCTGAGTCCGACACT 61.937 63.158 0.40 0.00 38.45 3.55
2957 7613 0.684479 ATAGCTGCCTGAGTCCGACA 60.684 55.000 0.00 0.00 0.00 4.35
2959 7615 1.109920 GGATAGCTGCCTGAGTCCGA 61.110 60.000 0.00 0.00 0.00 4.55
2960 7616 1.112315 AGGATAGCTGCCTGAGTCCG 61.112 60.000 8.97 0.00 33.59 4.79
2962 7618 1.809651 GCAAGGATAGCTGCCTGAGTC 60.810 57.143 10.35 0.00 35.50 3.36
2968 7629 1.607628 CTCAATGCAAGGATAGCTGCC 59.392 52.381 0.00 0.00 37.79 4.85
2972 7633 3.482156 TCCTCTCAATGCAAGGATAGC 57.518 47.619 0.00 0.00 34.26 2.97
2978 7639 6.452494 AGATTTTGATCCTCTCAATGCAAG 57.548 37.500 0.00 0.00 43.30 4.01
2989 7650 3.782523 TCCTGGCAGTAGATTTTGATCCT 59.217 43.478 14.43 0.00 0.00 3.24
3004 7665 2.795329 GTTGGATCTTTCTTCCTGGCA 58.205 47.619 0.00 0.00 34.17 4.92
3005 7666 1.740025 CGTTGGATCTTTCTTCCTGGC 59.260 52.381 0.00 0.00 34.17 4.85
3007 7668 3.003480 GTCCGTTGGATCTTTCTTCCTG 58.997 50.000 0.00 0.00 32.73 3.86
3010 7671 2.000447 CGGTCCGTTGGATCTTTCTTC 59.000 52.381 2.08 0.00 32.73 2.87
3011 7672 1.621814 TCGGTCCGTTGGATCTTTCTT 59.378 47.619 11.88 0.00 32.73 2.52
3012 7673 1.263356 TCGGTCCGTTGGATCTTTCT 58.737 50.000 11.88 0.00 32.73 2.52
3013 7674 2.311124 ATCGGTCCGTTGGATCTTTC 57.689 50.000 11.88 0.00 32.73 2.62
3015 7676 1.278127 ACAATCGGTCCGTTGGATCTT 59.722 47.619 22.21 6.32 32.73 2.40
3017 7678 1.287425 GACAATCGGTCCGTTGGATC 58.713 55.000 22.21 12.83 40.83 3.36
3018 7679 0.459585 CGACAATCGGTCCGTTGGAT 60.460 55.000 22.21 4.82 43.95 3.41
3019 7680 1.080366 CGACAATCGGTCCGTTGGA 60.080 57.895 22.21 2.77 43.95 3.53
3020 7681 3.470267 CGACAATCGGTCCGTTGG 58.530 61.111 22.21 11.94 43.95 3.77
3036 7720 1.652329 GCTGATTTTCGCATCGCCG 60.652 57.895 0.00 0.00 0.00 6.46
3045 7729 4.032672 CAGAGACAGTCGATGCTGATTTTC 59.967 45.833 9.80 0.00 39.62 2.29
3258 7959 9.634021 TGCACACCTTATTGTTTTGGATATATA 57.366 29.630 0.00 0.00 0.00 0.86
3259 7960 8.532186 TGCACACCTTATTGTTTTGGATATAT 57.468 30.769 0.00 0.00 0.00 0.86
3260 7961 7.946381 TGCACACCTTATTGTTTTGGATATA 57.054 32.000 0.00 0.00 0.00 0.86
3263 7964 5.245751 TGATGCACACCTTATTGTTTTGGAT 59.754 36.000 0.00 0.00 0.00 3.41
3265 7966 4.880759 TGATGCACACCTTATTGTTTTGG 58.119 39.130 0.00 0.00 0.00 3.28
3266 7967 5.406175 CCTTGATGCACACCTTATTGTTTTG 59.594 40.000 0.00 0.00 0.00 2.44
3267 7968 5.304101 TCCTTGATGCACACCTTATTGTTTT 59.696 36.000 0.00 0.00 0.00 2.43
3268 7969 4.832266 TCCTTGATGCACACCTTATTGTTT 59.168 37.500 0.00 0.00 0.00 2.83
3269 7970 4.406456 TCCTTGATGCACACCTTATTGTT 58.594 39.130 0.00 0.00 0.00 2.83
3272 7973 3.624777 CCTCCTTGATGCACACCTTATT 58.375 45.455 0.00 0.00 0.00 1.40
3273 7974 2.092212 CCCTCCTTGATGCACACCTTAT 60.092 50.000 0.00 0.00 0.00 1.73
3274 7975 1.281867 CCCTCCTTGATGCACACCTTA 59.718 52.381 0.00 0.00 0.00 2.69
3276 7977 0.842030 TCCCTCCTTGATGCACACCT 60.842 55.000 0.00 0.00 0.00 4.00
3277 7978 0.257039 ATCCCTCCTTGATGCACACC 59.743 55.000 0.00 0.00 0.00 4.16
3278 7979 2.019984 GAATCCCTCCTTGATGCACAC 58.980 52.381 0.00 0.00 0.00 3.82
3279 7980 1.918262 AGAATCCCTCCTTGATGCACA 59.082 47.619 0.00 0.00 0.00 4.57
3280 7981 2.570135 GAGAATCCCTCCTTGATGCAC 58.430 52.381 0.00 0.00 35.87 4.57
3281 7982 1.139654 CGAGAATCCCTCCTTGATGCA 59.860 52.381 0.00 0.00 38.71 3.96
3282 7983 1.876322 CGAGAATCCCTCCTTGATGC 58.124 55.000 0.00 0.00 38.71 3.91
3283 7984 1.139654 TGCGAGAATCCCTCCTTGATG 59.860 52.381 0.00 0.00 38.71 3.07
3284 7985 1.500474 TGCGAGAATCCCTCCTTGAT 58.500 50.000 0.00 0.00 38.71 2.57
3285 7986 1.139654 CATGCGAGAATCCCTCCTTGA 59.860 52.381 0.00 0.00 38.71 3.02
3286 7987 1.590932 CATGCGAGAATCCCTCCTTG 58.409 55.000 0.00 0.00 38.71 3.61
3287 7988 0.179034 GCATGCGAGAATCCCTCCTT 60.179 55.000 0.00 0.00 38.71 3.36
3288 7989 1.340399 TGCATGCGAGAATCCCTCCT 61.340 55.000 14.09 0.00 38.71 3.69
3290 7991 0.873054 CATGCATGCGAGAATCCCTC 59.127 55.000 14.93 0.00 38.55 4.30
3291 7992 0.182061 ACATGCATGCGAGAATCCCT 59.818 50.000 26.53 0.00 0.00 4.20
3293 7994 0.317603 GCACATGCATGCGAGAATCC 60.318 55.000 26.53 0.00 41.59 3.01
3294 7995 3.159446 GCACATGCATGCGAGAATC 57.841 52.632 26.53 0.00 41.59 2.52
3309 8010 2.401583 TACCTGTGATGACATGGCAC 57.598 50.000 1.45 3.24 0.00 5.01
3310 8011 3.650281 AATACCTGTGATGACATGGCA 57.350 42.857 2.18 2.18 0.00 4.92
3311 8012 4.960938 TCTAATACCTGTGATGACATGGC 58.039 43.478 0.00 0.00 0.00 4.40
3335 8036 2.602878 TCGCTAGCTCGATTCGTTTTT 58.397 42.857 13.93 0.00 33.02 1.94
3336 8037 2.273370 TCGCTAGCTCGATTCGTTTT 57.727 45.000 13.93 0.00 33.02 2.43
3337 8038 2.273370 TTCGCTAGCTCGATTCGTTT 57.727 45.000 13.93 0.00 38.37 3.60
3338 8039 2.120232 CATTCGCTAGCTCGATTCGTT 58.880 47.619 13.93 0.00 38.37 3.85
3339 8040 1.600663 CCATTCGCTAGCTCGATTCGT 60.601 52.381 13.93 0.00 38.37 3.85
3341 8042 1.000163 TCCCATTCGCTAGCTCGATTC 60.000 52.381 13.93 0.00 38.37 2.52
3342 8043 1.040646 TCCCATTCGCTAGCTCGATT 58.959 50.000 13.93 0.00 38.37 3.34
3343 8044 0.315568 GTCCCATTCGCTAGCTCGAT 59.684 55.000 13.93 0.77 38.37 3.59
3344 8045 1.734137 GTCCCATTCGCTAGCTCGA 59.266 57.895 13.93 0.00 36.60 4.04
3346 8047 0.032815 GAGGTCCCATTCGCTAGCTC 59.967 60.000 13.93 0.00 0.00 4.09
3347 8048 1.739338 CGAGGTCCCATTCGCTAGCT 61.739 60.000 13.93 0.00 0.00 3.32
3349 8050 0.460311 AACGAGGTCCCATTCGCTAG 59.540 55.000 0.00 0.00 40.32 3.42
3350 8051 0.899720 AAACGAGGTCCCATTCGCTA 59.100 50.000 0.00 0.00 40.32 4.26
3351 8052 0.036306 AAAACGAGGTCCCATTCGCT 59.964 50.000 0.00 0.00 40.32 4.93
3355 8056 1.071071 TGACGAAAACGAGGTCCCATT 59.929 47.619 0.00 0.00 0.00 3.16
3356 8057 0.682852 TGACGAAAACGAGGTCCCAT 59.317 50.000 0.00 0.00 0.00 4.00
3357 8058 0.032952 CTGACGAAAACGAGGTCCCA 59.967 55.000 0.00 0.00 0.00 4.37
3361 8062 2.470821 CTGAACTGACGAAAACGAGGT 58.529 47.619 0.00 0.00 0.00 3.85
3362 8063 1.192534 GCTGAACTGACGAAAACGAGG 59.807 52.381 0.00 0.00 0.00 4.63
3363 8064 1.858458 TGCTGAACTGACGAAAACGAG 59.142 47.619 0.00 0.00 0.00 4.18
3364 8065 1.929230 TGCTGAACTGACGAAAACGA 58.071 45.000 0.00 0.00 0.00 3.85
3366 8067 4.016113 AGTTTGCTGAACTGACGAAAAC 57.984 40.909 5.43 0.00 46.66 2.43
3382 8083 8.495148 AGCAAAAGTTTGTAAACAAGAAGTTTG 58.505 29.630 9.85 13.40 42.98 2.93
3383 8084 8.601845 AGCAAAAGTTTGTAAACAAGAAGTTT 57.398 26.923 9.85 0.00 43.98 2.66
3384 8085 7.061789 CGAGCAAAAGTTTGTAAACAAGAAGTT 59.938 33.333 9.85 0.00 41.30 2.66
3385 8086 6.526674 CGAGCAAAAGTTTGTAAACAAGAAGT 59.473 34.615 9.85 0.00 41.30 3.01
3387 8088 6.383415 ACGAGCAAAAGTTTGTAAACAAGAA 58.617 32.000 9.85 0.00 41.30 2.52
3388 8089 5.945155 ACGAGCAAAAGTTTGTAAACAAGA 58.055 33.333 9.85 0.00 41.30 3.02
3389 8090 6.526674 AGAACGAGCAAAAGTTTGTAAACAAG 59.473 34.615 9.85 0.00 41.30 3.16
3390 8091 6.383415 AGAACGAGCAAAAGTTTGTAAACAA 58.617 32.000 9.85 0.00 41.30 2.83
3392 8093 7.642586 ACATAGAACGAGCAAAAGTTTGTAAAC 59.357 33.333 5.71 0.00 40.24 2.01
3393 8094 7.642194 CACATAGAACGAGCAAAAGTTTGTAAA 59.358 33.333 5.71 0.00 40.24 2.01
3394 8095 7.129622 CACATAGAACGAGCAAAAGTTTGTAA 58.870 34.615 5.71 0.00 40.24 2.41
3396 8097 5.065988 ACACATAGAACGAGCAAAAGTTTGT 59.934 36.000 5.71 0.00 40.24 2.83
3397 8098 5.396362 CACACATAGAACGAGCAAAAGTTTG 59.604 40.000 0.00 0.00 41.03 2.93
3398 8099 5.505654 CCACACATAGAACGAGCAAAAGTTT 60.506 40.000 0.00 0.00 0.00 2.66
3399 8100 4.024048 CCACACATAGAACGAGCAAAAGTT 60.024 41.667 0.00 0.00 0.00 2.66
3400 8101 3.498397 CCACACATAGAACGAGCAAAAGT 59.502 43.478 0.00 0.00 0.00 2.66
3402 8103 2.225491 GCCACACATAGAACGAGCAAAA 59.775 45.455 0.00 0.00 0.00 2.44
3403 8104 1.804151 GCCACACATAGAACGAGCAAA 59.196 47.619 0.00 0.00 0.00 3.68
3405 8106 0.320050 TGCCACACATAGAACGAGCA 59.680 50.000 0.00 0.00 0.00 4.26
3406 8107 1.002366 CTGCCACACATAGAACGAGC 58.998 55.000 0.00 0.00 0.00 5.03
3407 8108 2.370281 ACTGCCACACATAGAACGAG 57.630 50.000 0.00 0.00 0.00 4.18
3408 8109 2.036604 TGAACTGCCACACATAGAACGA 59.963 45.455 0.00 0.00 0.00 3.85
3409 8110 2.412870 TGAACTGCCACACATAGAACG 58.587 47.619 0.00 0.00 0.00 3.95
3410 8111 2.160417 GCTGAACTGCCACACATAGAAC 59.840 50.000 0.00 0.00 0.00 3.01
3411 8112 2.224499 TGCTGAACTGCCACACATAGAA 60.224 45.455 0.00 0.00 0.00 2.10
3412 8113 1.347378 TGCTGAACTGCCACACATAGA 59.653 47.619 0.00 0.00 0.00 1.98
3414 8115 2.268762 TTGCTGAACTGCCACACATA 57.731 45.000 0.00 0.00 0.00 2.29
3415 8116 1.401761 TTTGCTGAACTGCCACACAT 58.598 45.000 0.00 0.00 0.00 3.21
3416 8117 1.401761 ATTTGCTGAACTGCCACACA 58.598 45.000 0.00 0.00 0.00 3.72
3417 8118 2.514205 AATTTGCTGAACTGCCACAC 57.486 45.000 0.00 0.00 0.00 3.82
3420 8121 3.005684 CCTTGTAATTTGCTGAACTGCCA 59.994 43.478 0.00 0.00 0.00 4.92
3426 8127 3.888323 TCACTGCCTTGTAATTTGCTGAA 59.112 39.130 0.00 0.00 0.00 3.02
3427 8128 3.485394 TCACTGCCTTGTAATTTGCTGA 58.515 40.909 0.00 0.00 0.00 4.26
3428 8129 3.921119 TCACTGCCTTGTAATTTGCTG 57.079 42.857 0.00 0.00 0.00 4.41
3429 8130 3.891366 AGTTCACTGCCTTGTAATTTGCT 59.109 39.130 0.00 0.00 0.00 3.91
3430 8131 4.229876 GAGTTCACTGCCTTGTAATTTGC 58.770 43.478 0.00 0.00 0.00 3.68
3431 8132 5.009010 ACTGAGTTCACTGCCTTGTAATTTG 59.991 40.000 0.00 0.00 0.00 2.32
3432 8133 5.133221 ACTGAGTTCACTGCCTTGTAATTT 58.867 37.500 0.00 0.00 0.00 1.82
3433 8134 4.718961 ACTGAGTTCACTGCCTTGTAATT 58.281 39.130 0.00 0.00 0.00 1.40
3434 8135 4.357918 ACTGAGTTCACTGCCTTGTAAT 57.642 40.909 0.00 0.00 0.00 1.89
3435 8136 3.838244 ACTGAGTTCACTGCCTTGTAA 57.162 42.857 0.00 0.00 0.00 2.41
3436 8137 3.838244 AACTGAGTTCACTGCCTTGTA 57.162 42.857 0.00 0.00 0.00 2.41
3437 8138 2.717639 AACTGAGTTCACTGCCTTGT 57.282 45.000 0.00 0.00 0.00 3.16
3439 8140 3.281727 TGAAACTGAGTTCACTGCCTT 57.718 42.857 0.00 0.00 32.56 4.35
3454 8155 9.599322 CTCATAATTTTGTGTACAGAGTGAAAC 57.401 33.333 0.00 0.00 0.00 2.78
3455 8156 9.554395 TCTCATAATTTTGTGTACAGAGTGAAA 57.446 29.630 0.00 0.00 0.00 2.69
3456 8157 9.208022 CTCTCATAATTTTGTGTACAGAGTGAA 57.792 33.333 0.00 0.00 0.00 3.18
3458 8159 7.819415 TCCTCTCATAATTTTGTGTACAGAGTG 59.181 37.037 0.00 0.00 0.00 3.51
3459 8160 7.819900 GTCCTCTCATAATTTTGTGTACAGAGT 59.180 37.037 0.00 0.00 0.00 3.24
3461 8162 7.676004 TGTCCTCTCATAATTTTGTGTACAGA 58.324 34.615 0.00 0.00 0.00 3.41
3462 8163 7.905604 TGTCCTCTCATAATTTTGTGTACAG 57.094 36.000 0.00 0.00 0.00 2.74
3463 8164 7.552687 GGATGTCCTCTCATAATTTTGTGTACA 59.447 37.037 0.00 0.00 0.00 2.90
3465 8166 7.629157 TGGATGTCCTCTCATAATTTTGTGTA 58.371 34.615 0.09 0.00 36.82 2.90
3466 8167 6.484288 TGGATGTCCTCTCATAATTTTGTGT 58.516 36.000 0.09 0.00 36.82 3.72
3467 8168 7.501559 AGATGGATGTCCTCTCATAATTTTGTG 59.498 37.037 0.09 0.00 36.82 3.33
3468 8169 7.580910 AGATGGATGTCCTCTCATAATTTTGT 58.419 34.615 0.09 0.00 36.82 2.83
3473 10179 5.310068 AGCAAGATGGATGTCCTCTCATAAT 59.690 40.000 0.09 0.00 36.82 1.28


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

AutoCloner maintained by Alex Coulton.