Multiple sequence alignment - TraesCS4A01G282600

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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 TraesCS4A01G282600 chr4A 100.000 7331 0 0 1 7331 590091917 590099247 0.000000e+00 13538.0
1 TraesCS4A01G282600 chr4A 90.323 93 9 0 5282 5374 725815511 725815419 9.990000e-24 122.0
2 TraesCS4A01G282600 chr4D 91.888 3168 193 29 710 3851 12543244 12540115 0.000000e+00 4368.0
3 TraesCS4A01G282600 chr4D 94.496 2689 133 7 1 2677 12535347 12532662 0.000000e+00 4132.0
4 TraesCS4A01G282600 chr4D 95.096 1937 73 6 5402 7331 12531724 12529803 0.000000e+00 3031.0
5 TraesCS4A01G282600 chr4D 90.376 1143 100 8 4146 5282 107700148 107699010 0.000000e+00 1493.0
6 TraesCS4A01G282600 chr4D 91.383 998 48 13 5402 6388 12539763 12538793 0.000000e+00 1332.0
7 TraesCS4A01G282600 chr4D 89.714 943 90 3 3198 4138 12532664 12531727 0.000000e+00 1197.0
8 TraesCS4A01G282600 chr4D 93.777 707 32 5 4 705 12544053 12543354 0.000000e+00 1051.0
9 TraesCS4A01G282600 chr4D 90.241 748 43 11 6386 7130 12538764 12538044 0.000000e+00 950.0
10 TraesCS4A01G282600 chr4D 84.765 361 27 12 3806 4139 12540124 12539765 3.280000e-88 337.0
11 TraesCS4A01G282600 chr4D 92.500 200 12 2 7134 7331 12538006 12537808 4.330000e-72 283.0
12 TraesCS4A01G282600 chr4D 79.798 99 16 2 2642 2737 465609792 465609695 1.320000e-07 69.4
13 TraesCS4A01G282600 chrUn 94.773 2028 97 4 205 2226 357650703 357652727 0.000000e+00 3149.0
14 TraesCS4A01G282600 chrUn 88.542 96 6 1 102 192 451988363 451988458 2.160000e-20 111.0
15 TraesCS4A01G282600 chr4B 93.818 1828 97 7 272 2089 22899046 22897225 0.000000e+00 2736.0
16 TraesCS4A01G282600 chr4B 92.661 1744 94 13 5402 7137 22894830 22893113 0.000000e+00 2481.0
17 TraesCS4A01G282600 chr4B 94.508 1311 56 4 5402 6705 22885220 22883919 0.000000e+00 2008.0
18 TraesCS4A01G282600 chr4B 89.449 1071 81 15 2403 3464 22896463 22895416 0.000000e+00 1323.0
19 TraesCS4A01G282600 chr4B 88.596 947 95 10 3198 4139 22886160 22885222 0.000000e+00 1138.0
20 TraesCS4A01G282600 chr4B 95.238 630 21 2 6702 7331 22881791 22881171 0.000000e+00 989.0
21 TraesCS4A01G282600 chr4B 88.945 597 63 3 3544 4139 22895426 22894832 0.000000e+00 734.0
22 TraesCS4A01G282600 chr4B 91.314 449 37 2 2230 2677 22886605 22886158 4.860000e-171 612.0
23 TraesCS4A01G282600 chr4B 90.221 317 29 2 2074 2389 22897036 22896721 5.290000e-111 412.0
24 TraesCS4A01G282600 chr4B 94.030 201 10 1 7133 7331 22893078 22892878 3.320000e-78 303.0
25 TraesCS4A01G282600 chr3D 90.451 1152 98 9 4137 5280 607539702 607538555 0.000000e+00 1507.0
26 TraesCS4A01G282600 chr3D 89.757 1152 99 11 4137 5282 511886142 511887280 0.000000e+00 1456.0
27 TraesCS4A01G282600 chr3D 82.178 101 11 5 2642 2737 26231091 26231189 6.100000e-11 80.5
28 TraesCS4A01G282600 chr1D 90.218 1145 98 11 4146 5282 118506256 118507394 0.000000e+00 1482.0
29 TraesCS4A01G282600 chr1D 87.736 106 10 2 5266 5371 391361561 391361663 3.590000e-23 121.0
30 TraesCS4A01G282600 chr5A 89.965 1156 102 10 4138 5287 9383409 9384556 0.000000e+00 1480.0
31 TraesCS4A01G282600 chr5A 90.323 93 8 1 5285 5377 9384581 9384672 3.590000e-23 121.0
32 TraesCS4A01G282600 chr1B 89.974 1157 98 11 4138 5282 334676650 334677800 0.000000e+00 1478.0
33 TraesCS4A01G282600 chr1B 89.301 1159 109 12 4138 5287 10381398 10380246 0.000000e+00 1439.0
34 TraesCS4A01G282600 chr1B 86.649 367 44 4 3761 4125 630752839 630752476 1.150000e-107 401.0
35 TraesCS4A01G282600 chr1B 85.302 381 40 5 3761 4126 45818308 45817929 5.370000e-101 379.0
36 TraesCS4A01G282600 chr1B 83.654 104 12 3 2638 2737 415385904 415386006 7.830000e-15 93.5
37 TraesCS4A01G282600 chr1B 83.871 93 14 1 3761 3853 58319454 58319363 3.640000e-13 87.9
38 TraesCS4A01G282600 chr5D 89.835 1151 106 9 4138 5282 517363413 517364558 0.000000e+00 1467.0
39 TraesCS4A01G282600 chr2D 89.283 1157 113 9 4138 5287 618689773 618688621 0.000000e+00 1439.0
40 TraesCS4A01G282600 chr2D 84.635 384 40 5 3758 4126 543823815 543823436 1.500000e-96 364.0
41 TraesCS4A01G282600 chr2D 85.870 92 13 0 5279 5370 70429044 70428953 1.680000e-16 99.0
42 TraesCS4A01G282600 chr7A 82.234 1137 130 42 3037 4125 625369947 625368835 0.000000e+00 915.0
43 TraesCS4A01G282600 chr7A 84.000 100 13 1 2656 2752 121928983 121928884 7.830000e-15 93.5
44 TraesCS4A01G282600 chr3A 86.567 536 56 10 3039 3570 608745475 608744952 1.770000e-160 577.0
45 TraesCS4A01G282600 chr3A 84.733 393 43 7 3761 4138 79392698 79393088 1.930000e-100 377.0
46 TraesCS4A01G282600 chr7D 88.702 416 36 8 3037 3448 543352434 543352026 1.420000e-136 497.0
47 TraesCS4A01G282600 chr7D 80.702 114 19 1 2642 2752 109304297 109304410 1.310000e-12 86.1
48 TraesCS4A01G282600 chr2A 83.523 528 60 13 3038 3555 4352829 4352319 1.110000e-127 468.0
49 TraesCS4A01G282600 chr5B 86.325 351 47 1 3780 4130 110129315 110128966 1.490000e-101 381.0
50 TraesCS4A01G282600 chr7B 85.714 364 35 8 3193 3556 689908050 689908396 1.160000e-97 368.0
51 TraesCS4A01G282600 chr6D 87.879 99 11 1 5279 5377 46898283 46898186 1.670000e-21 115.0
52 TraesCS4A01G282600 chr1A 87.234 94 10 2 5279 5371 88874799 88874891 1.010000e-18 106.0
53 TraesCS4A01G282600 chr1A 90.909 55 4 1 5321 5375 4206772 4206825 1.020000e-08 73.1
54 TraesCS4A01G282600 chr3B 81.707 82 12 1 2656 2734 811100608 811100689 1.710000e-06 65.8


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 TraesCS4A01G282600 chr4A 590091917 590099247 7330 False 13538.000000 13538 100.000000 1 7331 1 chr4A.!!$F1 7330
1 TraesCS4A01G282600 chr4D 12529803 12544053 14250 True 1853.444444 4368 91.540000 1 7331 9 chr4D.!!$R3 7330
2 TraesCS4A01G282600 chr4D 107699010 107700148 1138 True 1493.000000 1493 90.376000 4146 5282 1 chr4D.!!$R1 1136
3 TraesCS4A01G282600 chrUn 357650703 357652727 2024 False 3149.000000 3149 94.773000 205 2226 1 chrUn.!!$F1 2021
4 TraesCS4A01G282600 chr4B 22892878 22899046 6168 True 1331.500000 2736 91.520667 272 7331 6 chr4B.!!$R2 7059
5 TraesCS4A01G282600 chr4B 22881171 22886605 5434 True 1186.750000 2008 92.414000 2230 7331 4 chr4B.!!$R1 5101
6 TraesCS4A01G282600 chr3D 607538555 607539702 1147 True 1507.000000 1507 90.451000 4137 5280 1 chr3D.!!$R1 1143
7 TraesCS4A01G282600 chr3D 511886142 511887280 1138 False 1456.000000 1456 89.757000 4137 5282 1 chr3D.!!$F2 1145
8 TraesCS4A01G282600 chr1D 118506256 118507394 1138 False 1482.000000 1482 90.218000 4146 5282 1 chr1D.!!$F1 1136
9 TraesCS4A01G282600 chr5A 9383409 9384672 1263 False 800.500000 1480 90.144000 4138 5377 2 chr5A.!!$F1 1239
10 TraesCS4A01G282600 chr1B 334676650 334677800 1150 False 1478.000000 1478 89.974000 4138 5282 1 chr1B.!!$F1 1144
11 TraesCS4A01G282600 chr1B 10380246 10381398 1152 True 1439.000000 1439 89.301000 4138 5287 1 chr1B.!!$R1 1149
12 TraesCS4A01G282600 chr5D 517363413 517364558 1145 False 1467.000000 1467 89.835000 4138 5282 1 chr5D.!!$F1 1144
13 TraesCS4A01G282600 chr2D 618688621 618689773 1152 True 1439.000000 1439 89.283000 4138 5287 1 chr2D.!!$R3 1149
14 TraesCS4A01G282600 chr7A 625368835 625369947 1112 True 915.000000 915 82.234000 3037 4125 1 chr7A.!!$R2 1088
15 TraesCS4A01G282600 chr3A 608744952 608745475 523 True 577.000000 577 86.567000 3039 3570 1 chr3A.!!$R1 531
16 TraesCS4A01G282600 chr2A 4352319 4352829 510 True 468.000000 468 83.523000 3038 3555 1 chr2A.!!$R1 517

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
178 184 0.401356 TCACCATCTGCTTGCTTCCA 59.599 50.0 0.00 0.00 0.00 3.53 F
708 819 0.532862 ATGATCGTTGGCGGATGGAC 60.533 55.0 0.00 0.00 38.89 4.02 F
2182 2514 0.034896 TCGAAGGTCACTTTGGAGCC 59.965 55.0 0.00 0.00 38.43 4.70 F
2255 2587 0.179000 CATCTTCCACCTCCCTTCCG 59.821 60.0 0.00 0.00 0.00 4.30 F
3141 3732 0.042131 TCTGATAAGTGGGACCCGGT 59.958 55.0 5.91 0.00 0.00 5.28 F
3143 3734 0.042131 TGATAAGTGGGACCCGGTCT 59.958 55.0 17.27 1.27 32.47 3.85 F
3145 3736 0.042131 ATAAGTGGGACCCGGTCTCA 59.958 55.0 16.75 16.75 41.12 3.27 F
4350 13258 0.109723 ACCTCGCAGCCAAACCTAAA 59.890 50.0 0.00 0.00 0.00 1.85 F
4823 13739 0.601558 CCTCGAGAAGGGAACGACAA 59.398 55.0 15.71 0.00 42.03 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1679 0.391263 GTACTCGAGGCAAAGGGTGG 60.391 60.000 18.41 0.00 0.00 4.61 R
2271 2603 0.118346 TTAGGGCTCTGGGACAAGGA 59.882 55.000 0.00 0.00 38.70 3.36 R
3126 3717 0.042131 TGAGACCGGGTCCCACTTAT 59.958 55.000 23.21 2.86 32.18 1.73 R
3266 3857 0.122435 ACAGGGGGAGGGGTTGATTA 59.878 55.000 0.00 0.00 0.00 1.75 R
4800 13716 0.108138 CGTTCCCTTCTCGAGGCATT 60.108 55.000 13.56 0.00 44.85 3.56 R
4860 13776 1.130373 GCTTCCGATGAAAATCACGCA 59.870 47.619 0.00 0.00 0.00 5.24 R
4902 13818 4.473520 CCGCTCGGTTCCAGCCAT 62.474 66.667 0.00 0.00 32.83 4.40 R
5235 14153 1.327303 GGCGAGATCTCATCTGAGGT 58.673 55.000 22.31 0.00 42.30 3.85 R
6626 15581 0.171007 GCGTGCAACATGCCTAACAT 59.829 50.000 0.18 0.00 44.23 2.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.894782 TCACCACATGAAACATTGACG 57.105 42.857 0.00 0.00 33.02 4.35
28 29 2.551887 TCACCACATGAAACATTGACGG 59.448 45.455 0.00 0.00 33.02 4.79
37 38 6.313905 ACATGAAACATTGACGGTTAGATCTC 59.686 38.462 0.00 0.00 0.00 2.75
38 39 5.175859 TGAAACATTGACGGTTAGATCTCC 58.824 41.667 0.00 0.00 0.00 3.71
46 47 2.523412 TTAGATCTCCCCCGGCGG 60.523 66.667 21.46 21.46 0.00 6.13
67 68 1.130678 GCCTAGGGATCCCTTCCTGG 61.131 65.000 38.13 30.25 45.70 4.45
77 78 1.916181 TCCCTTCCTGGATCCAAACTC 59.084 52.381 17.00 0.00 38.35 3.01
134 135 2.292828 ATCAGGGTCAAGGTTTGTGG 57.707 50.000 0.00 0.00 0.00 4.17
136 137 1.780309 TCAGGGTCAAGGTTTGTGGAT 59.220 47.619 0.00 0.00 0.00 3.41
154 155 2.706190 GGATTATACTCCACCACTGCCT 59.294 50.000 4.29 0.00 35.24 4.75
178 184 0.401356 TCACCATCTGCTTGCTTCCA 59.599 50.000 0.00 0.00 0.00 3.53
240 246 7.147880 TGGATGATTTGAATGTTATCATGCACA 60.148 33.333 12.46 0.00 45.79 4.57
241 247 7.168637 GGATGATTTGAATGTTATCATGCACAC 59.831 37.037 9.85 0.00 42.87 3.82
328 334 7.792374 AACATTTACTACATGCATACTCCTG 57.208 36.000 0.00 0.00 0.00 3.86
361 367 8.114290 CACTTTGAAGATCAAAATATGCAATGC 58.886 33.333 0.00 0.00 44.69 3.56
367 373 6.798482 AGATCAAAATATGCAATGCTTTCGA 58.202 32.000 6.82 0.00 0.00 3.71
587 593 8.533569 ACCGGGACAATTATTCATCTTATTTT 57.466 30.769 6.32 0.00 0.00 1.82
644 650 3.292460 TCTTTCCCGGAAATTGTGTGTT 58.708 40.909 13.11 0.00 30.85 3.32
645 651 3.067461 TCTTTCCCGGAAATTGTGTGTTG 59.933 43.478 13.11 0.00 30.85 3.33
658 664 7.840342 AATTGTGTGTTGTATTGCAGAAAAA 57.160 28.000 0.00 0.00 0.00 1.94
705 711 5.801350 ATTATTATGATCGTTGGCGGATG 57.199 39.130 0.00 0.00 38.89 3.51
708 819 0.532862 ATGATCGTTGGCGGATGGAC 60.533 55.000 0.00 0.00 38.89 4.02
992 1106 0.835543 CCAGCCCACAAATCCCCAAA 60.836 55.000 0.00 0.00 0.00 3.28
1035 1149 3.553437 CTCCACGAGTCAACGGCGT 62.553 63.158 6.77 6.77 39.04 5.68
1102 1228 0.665835 GATGCTCGACGACATCCTCT 59.334 55.000 20.44 1.58 37.33 3.69
1391 1517 3.403057 GCACAAGCGCGTCGAGAA 61.403 61.111 8.43 0.00 0.00 2.87
1553 1679 1.301293 CAGGCTTCCCCAACCTCTC 59.699 63.158 0.00 0.00 35.39 3.20
1560 1686 1.852626 CCCCAACCTCTCCACCCTT 60.853 63.158 0.00 0.00 0.00 3.95
1595 1721 1.923395 TCCTCCCTTTCCATGGCGT 60.923 57.895 6.96 0.00 0.00 5.68
1654 1780 2.260844 CCTCACAAGGCTCTTGTTGA 57.739 50.000 15.32 14.36 35.37 3.18
1820 1946 5.582950 ATTTCCATTGATCCCCTATTCGA 57.417 39.130 0.00 0.00 0.00 3.71
1879 2005 8.603242 TTCTAGTGTTAAGAAGCTTTACTTGG 57.397 34.615 0.00 0.00 39.29 3.61
1901 2027 1.405821 CACCGACTCAGATCAGGTACC 59.594 57.143 2.73 2.73 33.30 3.34
1994 2121 4.098349 TGCATTGATGGCAATCTCTAAACC 59.902 41.667 2.00 0.00 42.66 3.27
2084 2212 1.204467 GCTGAGAGCAACTCTAGCAGT 59.796 52.381 19.27 0.00 41.35 4.40
2096 2428 0.904649 CTAGCAGTGTCACCATCCCA 59.095 55.000 0.00 0.00 0.00 4.37
2108 2440 0.251877 CCATCCCATGCCATGCCATA 60.252 55.000 0.00 0.00 0.00 2.74
2136 2468 1.963172 TGAAGCGCTCTCCGTATCTA 58.037 50.000 12.06 0.00 39.71 1.98
2182 2514 0.034896 TCGAAGGTCACTTTGGAGCC 59.965 55.000 0.00 0.00 38.43 4.70
2228 2560 1.059264 CGAAGGAAGTTTTAGCTCGCG 59.941 52.381 0.00 0.00 0.00 5.87
2255 2587 0.179000 CATCTTCCACCTCCCTTCCG 59.821 60.000 0.00 0.00 0.00 4.30
2320 2653 2.948720 GCACTGACCCCTCTTCGCT 61.949 63.158 0.00 0.00 0.00 4.93
2322 2655 2.286523 ACTGACCCCTCTTCGCTGG 61.287 63.158 0.00 0.00 0.00 4.85
2348 2681 7.582242 GCATAGCCCAAATCTAGGATTGATAGA 60.582 40.741 9.23 0.00 33.93 1.98
2384 2717 2.266055 GGGTTGGTGAGAGGCTCG 59.734 66.667 9.22 0.00 32.35 5.03
2417 2994 0.254178 GAGATTTCAGCTGGCCCTCA 59.746 55.000 15.13 0.00 0.00 3.86
2451 3028 1.296392 CCAGGCGACTCATTGTCCA 59.704 57.895 0.00 0.00 42.49 4.02
2454 3031 0.179000 AGGCGACTCATTGTCCATCC 59.821 55.000 0.00 0.00 42.49 3.51
2457 3034 1.656652 CGACTCATTGTCCATCCACC 58.343 55.000 0.00 0.00 42.49 4.61
2580 3158 7.040755 TGGGTCTCATGTGTAAAACAAATACTG 60.041 37.037 0.00 0.00 43.61 2.74
2633 3211 1.428869 CACATAGCCCTAGGAGCCTT 58.571 55.000 11.48 0.00 0.00 4.35
2634 3212 1.071385 CACATAGCCCTAGGAGCCTTG 59.929 57.143 11.48 13.81 0.00 3.61
2654 3232 2.771943 TGAAAATGCTCCCTCCGTCTAT 59.228 45.455 0.00 0.00 0.00 1.98
2665 3243 6.208204 GCTCCCTCCGTCTATAATTACTTGTA 59.792 42.308 0.00 0.00 0.00 2.41
2713 3291 9.610705 TGTATCTAGAACTAAACGTCTAGACAT 57.389 33.333 22.37 4.34 42.39 3.06
2752 3330 7.630924 ACAAGTATTTTCGAACAAAGAGAGTG 58.369 34.615 0.00 0.00 0.00 3.51
2796 3380 2.834638 ATGTAGGCTGCCCTTTTGAT 57.165 45.000 16.57 0.00 42.87 2.57
2834 3418 2.890945 CTCTGTTCCCGGGTTCAAAATT 59.109 45.455 22.86 0.00 0.00 1.82
3064 3652 7.277760 AGTTAAAAGCAGAAAACCACACATTTC 59.722 33.333 0.00 0.00 36.11 2.17
3126 3717 1.000385 CAAAAGCCACCGCATTTCTGA 60.000 47.619 0.00 0.00 33.80 3.27
3130 3721 2.292267 AGCCACCGCATTTCTGATAAG 58.708 47.619 0.00 0.00 37.52 1.73
3132 3723 2.223340 GCCACCGCATTTCTGATAAGTG 60.223 50.000 0.00 0.00 34.03 3.16
3133 3724 2.355756 CCACCGCATTTCTGATAAGTGG 59.644 50.000 2.15 2.15 37.76 4.00
3134 3725 2.355756 CACCGCATTTCTGATAAGTGGG 59.644 50.000 7.61 0.00 34.28 4.61
3135 3726 2.238646 ACCGCATTTCTGATAAGTGGGA 59.761 45.455 7.61 0.00 34.28 4.37
3136 3727 2.614057 CCGCATTTCTGATAAGTGGGAC 59.386 50.000 0.00 0.00 0.00 4.46
3137 3728 2.614057 CGCATTTCTGATAAGTGGGACC 59.386 50.000 0.00 0.00 0.00 4.46
3138 3729 2.952310 GCATTTCTGATAAGTGGGACCC 59.048 50.000 2.45 2.45 0.00 4.46
3139 3730 3.206150 CATTTCTGATAAGTGGGACCCG 58.794 50.000 5.91 0.00 0.00 5.28
3140 3731 1.200519 TTCTGATAAGTGGGACCCGG 58.799 55.000 5.91 0.00 0.00 5.73
3141 3732 0.042131 TCTGATAAGTGGGACCCGGT 59.958 55.000 5.91 0.00 0.00 5.28
3142 3733 0.464452 CTGATAAGTGGGACCCGGTC 59.536 60.000 9.30 9.30 0.00 4.79
3143 3734 0.042131 TGATAAGTGGGACCCGGTCT 59.958 55.000 17.27 1.27 32.47 3.85
3144 3735 0.751452 GATAAGTGGGACCCGGTCTC 59.249 60.000 17.27 14.27 32.92 3.36
3145 3736 0.042131 ATAAGTGGGACCCGGTCTCA 59.958 55.000 16.75 16.75 41.12 3.27
3146 3737 0.613853 TAAGTGGGACCCGGTCTCAG 60.614 60.000 21.15 0.00 44.23 3.35
3147 3738 2.283676 GTGGGACCCGGTCTCAGA 60.284 66.667 21.15 0.00 44.23 3.27
3189 3780 7.064609 CGATTTAGCCTGTTTGATCACTTTCTA 59.935 37.037 0.00 0.00 0.00 2.10
3190 3781 7.672983 TTTAGCCTGTTTGATCACTTTCTAG 57.327 36.000 0.00 0.00 0.00 2.43
3266 3857 8.170730 ACACCCCTATATCTGAAAAAGAAAAGT 58.829 33.333 0.00 0.00 38.79 2.66
3283 3874 0.426022 AGTAATCAACCCCTCCCCCT 59.574 55.000 0.00 0.00 0.00 4.79
3402 4004 3.023949 GCAGGGCGGACACAGAGAT 62.024 63.158 0.00 0.00 0.00 2.75
3441 4043 3.474570 GGAGATGGGCAGGAGCGT 61.475 66.667 0.00 0.00 43.41 5.07
3501 4193 2.335369 GCGGATAGCGACCACGAT 59.665 61.111 0.00 0.00 42.66 3.73
3543 4235 1.078848 GCATCACGACCTCCTGCTT 60.079 57.895 0.00 0.00 0.00 3.91
3872 4698 4.492303 GACGGGGATGGGAGGGGA 62.492 72.222 0.00 0.00 0.00 4.81
3966 4795 4.044065 ACCAAATCATCTCCTTACAACCCA 59.956 41.667 0.00 0.00 0.00 4.51
3973 12868 0.849094 TCCTTACAACCCAGCCCCAT 60.849 55.000 0.00 0.00 0.00 4.00
3976 12871 2.291930 CCTTACAACCCAGCCCCATTTA 60.292 50.000 0.00 0.00 0.00 1.40
3996 12891 7.861372 CCATTTATCAGAAAGTGATCAATCAGC 59.139 37.037 0.00 0.00 42.80 4.26
4023 12918 5.670792 ATCACCTGATCAATGCAATTTGT 57.329 34.783 0.00 0.00 31.22 2.83
4096 12991 2.395367 TTTTCCGCAAACGAAGCCCG 62.395 55.000 0.00 0.00 43.93 6.13
4108 13003 3.583882 AAGCCCGGAATGTGGTGGG 62.584 63.158 0.73 0.00 44.88 4.61
4125 13020 4.162320 TGGTGGGTTTTTGCAATTAACTCA 59.838 37.500 18.44 18.44 30.22 3.41
4162 13057 3.618858 AAAAAGGAGGAGGACCCCT 57.381 52.632 1.40 1.40 38.08 4.79
4230 13126 5.492895 TCACACAAGACCTTACAAAGTCAA 58.507 37.500 0.00 0.00 0.00 3.18
4231 13127 6.119536 TCACACAAGACCTTACAAAGTCAAT 58.880 36.000 0.00 0.00 0.00 2.57
4232 13128 7.276658 TCACACAAGACCTTACAAAGTCAATA 58.723 34.615 0.00 0.00 0.00 1.90
4261 13163 4.768968 AGTAAGACTAAAGCCACCGTCTAA 59.231 41.667 0.00 0.00 35.82 2.10
4269 13171 1.553248 AGCCACCGTCTAAGCAACATA 59.447 47.619 0.00 0.00 0.00 2.29
4301 13209 2.487986 CCTATCCAGTTGATGAAGGGGC 60.488 54.545 0.00 0.00 34.76 5.80
4350 13258 0.109723 ACCTCGCAGCCAAACCTAAA 59.890 50.000 0.00 0.00 0.00 1.85
4473 13382 2.283101 GCCACCTGCCACCAATCA 60.283 61.111 0.00 0.00 0.00 2.57
4484 13393 4.661222 TGCCACCAATCAATCTTTAGTGA 58.339 39.130 0.00 0.00 33.60 3.41
4507 13416 2.867109 ACTGTTGCATCTACCTTGCT 57.133 45.000 0.00 0.00 40.77 3.91
4508 13417 3.146104 ACTGTTGCATCTACCTTGCTT 57.854 42.857 0.00 0.00 40.77 3.91
4560 13469 1.302511 GACAACGCCACCATCCTGT 60.303 57.895 0.00 0.00 0.00 4.00
4721 13635 1.967235 GGAAAACGACATCGAAAACGC 59.033 47.619 8.54 0.00 43.02 4.84
4753 13667 1.889829 GATCCGGTAGACCCAGATCTG 59.110 57.143 16.24 16.24 38.40 2.90
4792 13708 1.471287 CGATCAGGTTGACGTGACCTA 59.529 52.381 17.30 8.76 45.58 3.08
4800 13716 1.023502 TGACGTGACCTACAACGACA 58.976 50.000 0.00 0.00 0.00 4.35
4822 13738 1.874345 GCCTCGAGAAGGGAACGACA 61.874 60.000 15.71 0.00 46.32 4.35
4823 13739 0.601558 CCTCGAGAAGGGAACGACAA 59.398 55.000 15.71 0.00 42.03 3.18
4831 13747 1.111116 AGGGAACGACAACCGAGACA 61.111 55.000 0.00 0.00 41.76 3.41
4845 13761 4.430765 GACACCGCCATCGTCCGT 62.431 66.667 0.00 0.00 0.00 4.69
4940 13856 0.811616 GCCTCGCCACGAAGATGAAT 60.812 55.000 0.00 0.00 34.74 2.57
4942 13858 1.645034 CTCGCCACGAAGATGAATGT 58.355 50.000 0.00 0.00 34.74 2.71
5222 14140 0.752009 CTTCGGATCCCACGAGAGGA 60.752 60.000 6.06 0.00 41.81 3.71
5307 14252 2.364317 CAGAAGGAGGGCGAGGGA 60.364 66.667 0.00 0.00 0.00 4.20
5319 14264 4.173924 GAGGGAGAGGCCTGCTGC 62.174 72.222 12.00 12.72 40.16 5.25
5329 14274 2.045926 CCTGCTGCGCTAGGGTTT 60.046 61.111 9.73 0.00 0.00 3.27
5330 14275 2.401766 CCTGCTGCGCTAGGGTTTG 61.402 63.158 9.73 0.65 0.00 2.93
5380 14325 2.689771 GCGAGGGGGAGGGGTTAA 60.690 66.667 0.00 0.00 0.00 2.01
5381 14326 2.303282 GCGAGGGGGAGGGGTTAAA 61.303 63.158 0.00 0.00 0.00 1.52
5382 14327 1.912971 CGAGGGGGAGGGGTTAAAG 59.087 63.158 0.00 0.00 0.00 1.85
5383 14328 0.619543 CGAGGGGGAGGGGTTAAAGA 60.620 60.000 0.00 0.00 0.00 2.52
5384 14329 1.677490 GAGGGGGAGGGGTTAAAGAA 58.323 55.000 0.00 0.00 0.00 2.52
5385 14330 1.997791 GAGGGGGAGGGGTTAAAGAAA 59.002 52.381 0.00 0.00 0.00 2.52
5386 14331 2.380932 GAGGGGGAGGGGTTAAAGAAAA 59.619 50.000 0.00 0.00 0.00 2.29
5387 14332 2.798972 AGGGGGAGGGGTTAAAGAAAAA 59.201 45.455 0.00 0.00 0.00 1.94
5388 14333 3.408237 AGGGGGAGGGGTTAAAGAAAAAT 59.592 43.478 0.00 0.00 0.00 1.82
5389 14334 3.517901 GGGGGAGGGGTTAAAGAAAAATG 59.482 47.826 0.00 0.00 0.00 2.32
5390 14335 3.517901 GGGGAGGGGTTAAAGAAAAATGG 59.482 47.826 0.00 0.00 0.00 3.16
5391 14336 4.164981 GGGAGGGGTTAAAGAAAAATGGT 58.835 43.478 0.00 0.00 0.00 3.55
5392 14337 4.222145 GGGAGGGGTTAAAGAAAAATGGTC 59.778 45.833 0.00 0.00 0.00 4.02
5393 14338 4.222145 GGAGGGGTTAAAGAAAAATGGTCC 59.778 45.833 0.00 0.00 0.00 4.46
5394 14339 5.084519 GAGGGGTTAAAGAAAAATGGTCCT 58.915 41.667 0.00 0.00 0.00 3.85
5395 14340 6.222227 AGGGGTTAAAGAAAAATGGTCCTA 57.778 37.500 0.00 0.00 0.00 2.94
5396 14341 6.626238 AGGGGTTAAAGAAAAATGGTCCTAA 58.374 36.000 0.00 0.00 0.00 2.69
5397 14342 6.724441 AGGGGTTAAAGAAAAATGGTCCTAAG 59.276 38.462 0.00 0.00 0.00 2.18
5398 14343 6.395629 GGGTTAAAGAAAAATGGTCCTAAGC 58.604 40.000 0.00 0.00 0.00 3.09
5399 14344 6.014925 GGGTTAAAGAAAAATGGTCCTAAGCA 60.015 38.462 0.00 0.00 37.29 3.91
5400 14345 7.310423 GGGTTAAAGAAAAATGGTCCTAAGCAT 60.310 37.037 0.00 0.00 45.33 3.79
5738 14692 4.816126 AGGACCATATGCTAGTCTAACCA 58.184 43.478 9.54 0.00 0.00 3.67
5981 14936 8.863049 CATTAATGGATTGAGTTGTTTAACTGC 58.137 33.333 7.62 0.00 46.79 4.40
6004 14959 3.571401 CACAGCAATCTTGGACTTCCTTT 59.429 43.478 0.00 0.00 36.82 3.11
6020 14975 2.232941 TCCTTTTGTAGGTAGTCAGGCG 59.767 50.000 0.00 0.00 45.03 5.52
6021 14976 2.232941 CCTTTTGTAGGTAGTCAGGCGA 59.767 50.000 0.00 0.00 39.39 5.54
6042 14997 5.435557 CGAGAAGTTGAAACTGACAATGAC 58.564 41.667 0.00 0.00 39.66 3.06
6090 15045 7.722949 TGATGCACTGATATATGATGACCTA 57.277 36.000 0.00 0.00 0.00 3.08
6121 15076 2.674852 CTCAAACATGTCTCGGTGGATG 59.325 50.000 0.00 0.00 0.00 3.51
6127 15082 3.458163 TCTCGGTGGATGGTCCGC 61.458 66.667 0.94 0.94 46.03 5.54
6300 15255 3.923461 CCGAAGCTATGCTCATACTAAGC 59.077 47.826 0.00 0.00 38.25 3.09
6351 15306 8.943594 TTTAAACCCCTAATCATGTTAGTTGT 57.056 30.769 11.58 7.22 0.00 3.32
6469 15424 7.148035 TGCTCATATGAACAATGCACAAGTAAT 60.148 33.333 11.39 0.00 0.00 1.89
6500 15455 2.600556 CGCAATGTTGTGGATCGCTATG 60.601 50.000 0.00 0.00 35.14 2.23
6586 15541 4.741321 ATTTATCTGTTGGGCCACATTG 57.259 40.909 5.23 0.00 0.00 2.82
6626 15581 0.407918 GAATTCCTTCCACCCACCCA 59.592 55.000 0.00 0.00 0.00 4.51
6712 17798 5.711976 GTGCCATGATTTATTAGCACCCTAT 59.288 40.000 7.87 0.00 39.16 2.57
6739 17825 8.704234 CCTGCTTATCGTACATAAGATTTCTTC 58.296 37.037 20.19 8.28 37.40 2.87
6798 17884 4.819630 CCCTACAAAAGTTGTGACTTGCTA 59.180 41.667 0.00 0.00 45.18 3.49
6808 17894 5.356751 AGTTGTGACTTGCTAACACATTTGA 59.643 36.000 0.00 0.00 42.65 2.69
6809 17895 6.039717 AGTTGTGACTTGCTAACACATTTGAT 59.960 34.615 0.00 0.00 42.65 2.57
6878 17964 4.402474 TCTGAAGTCTTGTGTTCTCTGTCA 59.598 41.667 0.00 0.00 0.00 3.58
6893 17979 6.231258 TCTCTGTCATCTTGATACTTGCAT 57.769 37.500 0.00 0.00 0.00 3.96
6996 18082 6.071108 GCATTCTCTAGCCATCTACATCCTTA 60.071 42.308 0.00 0.00 0.00 2.69
7043 18129 6.361433 TGGAAGTTTGTAGAAGATTGGAACA 58.639 36.000 0.00 0.00 0.00 3.18
7136 18262 6.651975 AATCCGTACTCTTGGTATCCTAAG 57.348 41.667 0.00 0.00 32.56 2.18
7288 18419 5.905331 TGGAGCCTCTCAAAATTATCCTAGA 59.095 40.000 0.00 0.00 31.08 2.43
7289 18420 6.386927 TGGAGCCTCTCAAAATTATCCTAGAA 59.613 38.462 0.00 0.00 31.08 2.10
7290 18421 6.934083 GGAGCCTCTCAAAATTATCCTAGAAG 59.066 42.308 0.00 0.00 31.08 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.921119 TGTTTCATGTGGTGATTGAGC 57.079 42.857 0.00 0.00 36.54 4.26
2 3 5.860182 GTCAATGTTTCATGTGGTGATTGAG 59.140 40.000 0.00 0.00 34.50 3.02
4 5 4.618067 CGTCAATGTTTCATGTGGTGATTG 59.382 41.667 0.00 0.00 36.54 2.67
5 6 4.321156 CCGTCAATGTTTCATGTGGTGATT 60.321 41.667 0.00 0.00 36.54 2.57
6 7 3.191162 CCGTCAATGTTTCATGTGGTGAT 59.809 43.478 0.00 0.00 36.54 3.06
7 8 2.551887 CCGTCAATGTTTCATGTGGTGA 59.448 45.455 0.00 0.00 34.25 4.02
27 28 2.868986 CGCCGGGGGAGATCTAACC 61.869 68.421 11.42 0.62 0.00 2.85
28 29 2.735237 CGCCGGGGGAGATCTAAC 59.265 66.667 11.42 0.00 0.00 2.34
67 68 2.414559 CGTGTGCAATGGAGTTTGGATC 60.415 50.000 0.00 0.00 29.37 3.36
77 78 1.028330 ATCCTGCTCGTGTGCAATGG 61.028 55.000 0.00 0.00 42.83 3.16
134 135 3.388024 TGAGGCAGTGGTGGAGTATAATC 59.612 47.826 0.00 0.00 0.00 1.75
136 137 2.827755 TGAGGCAGTGGTGGAGTATAA 58.172 47.619 0.00 0.00 0.00 0.98
154 155 1.558294 AGCAAGCAGATGGTGAGATGA 59.442 47.619 0.00 0.00 0.00 2.92
192 198 1.872388 TGAAACGTTGATCGGCTGAA 58.128 45.000 0.00 0.00 44.69 3.02
203 209 7.656948 ACATTCAAATCATCCAAATGAAACGTT 59.343 29.630 0.00 0.00 44.85 3.99
306 312 6.763135 ACACAGGAGTATGCATGTAGTAAATG 59.237 38.462 10.16 0.00 0.00 2.32
361 367 7.008440 TGAATGAAATAGCTGATGTCGAAAG 57.992 36.000 0.00 0.00 0.00 2.62
367 373 6.096001 GGGAAGTTGAATGAAATAGCTGATGT 59.904 38.462 0.00 0.00 0.00 3.06
587 593 8.220755 AGTTTAGAGACAAAACTATGCAACAA 57.779 30.769 0.00 0.00 43.54 2.83
658 664 6.788218 ACCTCTCAAGGAGAAAAATGATTCT 58.212 36.000 0.00 0.00 46.67 2.40
955 1069 1.841556 GTGTGGTGGGAGTGAGGGA 60.842 63.158 0.00 0.00 0.00 4.20
1102 1228 3.068691 CTCGAAGGGGAGCCGACA 61.069 66.667 0.00 0.00 0.00 4.35
1143 1269 4.659172 CGGTGCCAAGCAGGGGAA 62.659 66.667 0.00 0.00 40.08 3.97
1299 1425 1.001641 GGTGAAGCTGCAGATGGGT 60.002 57.895 20.43 0.00 0.00 4.51
1553 1679 0.391263 GTACTCGAGGCAAAGGGTGG 60.391 60.000 18.41 0.00 0.00 4.61
1654 1780 2.138320 GTCGCCGATCATGACATCATT 58.862 47.619 0.00 0.00 33.61 2.57
1820 1946 3.117512 AGTGTTGATGAAGTTTGGGGTCT 60.118 43.478 0.00 0.00 0.00 3.85
1879 2005 1.178276 ACCTGATCTGAGTCGGTGTC 58.822 55.000 0.38 0.00 0.00 3.67
1901 2027 4.616802 GGACATTTGACGCAATGTAGTTTG 59.383 41.667 7.90 0.00 0.00 2.93
1955 2082 4.157472 TCAATGCATGTCGCCTCAAATTAA 59.843 37.500 0.00 0.00 41.33 1.40
2034 2162 7.946207 TCAGTGCTTTGACCAATTAAATAACA 58.054 30.769 0.00 0.00 0.00 2.41
2096 2428 5.498393 TCAAAAATTGTTATGGCATGGCAT 58.502 33.333 33.85 33.85 0.00 4.40
2108 2440 3.642705 GGAGAGCGCTTCAAAAATTGTT 58.357 40.909 13.26 0.00 0.00 2.83
2136 2468 1.516110 AATATGCAGTCTGGGAGGCT 58.484 50.000 1.14 0.00 0.00 4.58
2228 2560 0.674895 AGGTGGAAGATGAGTTGCGC 60.675 55.000 0.00 0.00 0.00 6.09
2255 2587 3.412408 GAGGGGTGGAGGGGAAGC 61.412 72.222 0.00 0.00 0.00 3.86
2269 2601 2.674220 GGGCTCTGGGACAAGGAGG 61.674 68.421 0.00 0.00 38.70 4.30
2271 2603 0.118346 TTAGGGCTCTGGGACAAGGA 59.882 55.000 0.00 0.00 38.70 3.36
2322 2655 4.655963 TCAATCCTAGATTTGGGCTATGC 58.344 43.478 0.00 0.00 0.00 3.14
2332 2665 9.732453 ATCTGGATGATCTATCAATCCTAGATT 57.268 33.333 15.95 0.00 40.69 2.40
2348 2681 2.251818 CCCCTGTCGTATCTGGATGAT 58.748 52.381 0.00 0.00 39.11 2.45
2384 2717 3.772025 TGAAATCTCTCCCTCTGTTCTCC 59.228 47.826 0.00 0.00 0.00 3.71
2417 2994 1.558756 CCTGGCTCTGAAGATCCAAGT 59.441 52.381 4.56 0.00 39.54 3.16
2451 3028 2.797278 CGCCTTCGCCTAGGTGGAT 61.797 63.158 22.11 0.00 41.21 3.41
2457 3034 0.460284 AATGTCACGCCTTCGCCTAG 60.460 55.000 0.00 0.00 39.84 3.02
2532 3110 7.057894 CCCACCTATTGTTGGCTTACTATTTA 58.942 38.462 0.00 0.00 0.00 1.40
2580 3158 2.979813 CGCCAAACACAACTTTCATAGC 59.020 45.455 0.00 0.00 0.00 2.97
2588 3166 1.608590 CCAGATTCGCCAAACACAACT 59.391 47.619 0.00 0.00 0.00 3.16
2633 3211 0.984230 AGACGGAGGGAGCATTTTCA 59.016 50.000 0.00 0.00 0.00 2.69
2634 3212 2.981859 TAGACGGAGGGAGCATTTTC 57.018 50.000 0.00 0.00 0.00 2.29
2722 3300 7.763356 TCTTTGTTCGAAAATACTTGTTGGAA 58.237 30.769 0.00 0.00 0.00 3.53
2726 3304 8.122952 CACTCTCTTTGTTCGAAAATACTTGTT 58.877 33.333 0.00 0.00 0.00 2.83
2737 3315 3.320826 TCCATCACACTCTCTTTGTTCGA 59.679 43.478 0.00 0.00 0.00 3.71
2796 3380 0.805614 GAGCGACTCTAGCACAGTCA 59.194 55.000 9.90 0.00 40.42 3.41
2834 3418 1.686741 GGAGGGGACACAAAACACCAA 60.687 52.381 0.00 0.00 31.04 3.67
2932 3516 9.674068 GGTTAAGATGATCTTCTCTTAGGTTTT 57.326 33.333 11.53 0.00 37.89 2.43
3064 3652 4.155310 AGTTTTTCATAAACGAAGCCCG 57.845 40.909 0.00 0.00 45.44 6.13
3126 3717 0.042131 TGAGACCGGGTCCCACTTAT 59.958 55.000 23.21 2.86 32.18 1.73
3130 3721 1.477685 TTTCTGAGACCGGGTCCCAC 61.478 60.000 23.21 15.04 32.18 4.61
3132 3723 0.399075 TTTTTCTGAGACCGGGTCCC 59.601 55.000 23.21 12.96 32.18 4.46
3133 3724 1.202722 TGTTTTTCTGAGACCGGGTCC 60.203 52.381 23.21 14.91 32.18 4.46
3134 3725 1.871676 GTGTTTTTCTGAGACCGGGTC 59.128 52.381 19.61 19.61 0.00 4.46
3135 3726 1.476291 GGTGTTTTTCTGAGACCGGGT 60.476 52.381 6.32 0.00 0.00 5.28
3136 3727 1.235724 GGTGTTTTTCTGAGACCGGG 58.764 55.000 6.32 0.00 0.00 5.73
3137 3728 0.865769 CGGTGTTTTTCTGAGACCGG 59.134 55.000 0.00 0.00 46.56 5.28
3139 3730 3.058224 CCAATCGGTGTTTTTCTGAGACC 60.058 47.826 0.00 0.00 0.00 3.85
3140 3731 3.813166 TCCAATCGGTGTTTTTCTGAGAC 59.187 43.478 0.00 0.00 0.00 3.36
3141 3732 3.813166 GTCCAATCGGTGTTTTTCTGAGA 59.187 43.478 0.00 0.00 0.00 3.27
3142 3733 3.363970 CGTCCAATCGGTGTTTTTCTGAG 60.364 47.826 0.00 0.00 0.00 3.35
3143 3734 2.546368 CGTCCAATCGGTGTTTTTCTGA 59.454 45.455 0.00 0.00 0.00 3.27
3144 3735 2.546368 TCGTCCAATCGGTGTTTTTCTG 59.454 45.455 0.00 0.00 0.00 3.02
3145 3736 2.841215 TCGTCCAATCGGTGTTTTTCT 58.159 42.857 0.00 0.00 0.00 2.52
3146 3737 3.824414 ATCGTCCAATCGGTGTTTTTC 57.176 42.857 0.00 0.00 0.00 2.29
3147 3738 4.577834 AAATCGTCCAATCGGTGTTTTT 57.422 36.364 0.00 0.00 0.00 1.94
3189 3780 0.765519 ACAACCGGGTCCCACTTACT 60.766 55.000 9.12 0.00 0.00 2.24
3190 3781 0.975887 TACAACCGGGTCCCACTTAC 59.024 55.000 9.12 0.00 0.00 2.34
3266 3857 0.122435 ACAGGGGGAGGGGTTGATTA 59.878 55.000 0.00 0.00 0.00 1.75
3283 3874 2.262603 CAGTAGCGCTGCTCCACA 59.737 61.111 25.98 0.00 40.44 4.17
3402 4004 1.305633 CTGCTCCACCTCCTCCTCA 60.306 63.158 0.00 0.00 0.00 3.86
3489 4181 2.104267 GACCTGATCGTGGTCGCTA 58.896 57.895 18.02 0.00 43.55 4.26
3527 4219 1.599047 CCAAGCAGGAGGTCGTGAT 59.401 57.895 3.88 0.00 41.22 3.06
3557 4249 2.750237 TCCTCGTCGCTGCTGCTA 60.750 61.111 14.03 0.00 36.97 3.49
3561 4289 3.753434 CAGGTCCTCGTCGCTGCT 61.753 66.667 0.00 0.00 0.00 4.24
3586 4314 2.492773 GGTGTGGTTGCTGCTGCTT 61.493 57.895 17.00 0.00 40.48 3.91
3862 4687 2.004408 GCAATCAGCTCCCCTCCCAT 62.004 60.000 0.00 0.00 41.15 4.00
3911 4738 3.813443 CATACACCTCCCTGGATTTCAG 58.187 50.000 0.00 0.00 43.00 3.02
3963 4792 2.754012 TTCTGATAAATGGGGCTGGG 57.246 50.000 0.00 0.00 0.00 4.45
3966 4795 4.591321 TCACTTTCTGATAAATGGGGCT 57.409 40.909 0.00 0.00 0.00 5.19
3973 12868 7.114754 AGGCTGATTGATCACTTTCTGATAAA 58.885 34.615 0.00 0.00 39.96 1.40
3976 12871 5.113446 AGGCTGATTGATCACTTTCTGAT 57.887 39.130 0.00 0.00 42.84 2.90
3996 12891 5.840243 TTGCATTGATCAGGTGATTTAGG 57.160 39.130 12.75 0.00 34.37 2.69
4023 12918 9.410556 GTCACCACGTATCTAGTAAACTTTTTA 57.589 33.333 0.00 0.00 0.00 1.52
4096 12991 1.139853 TGCAAAAACCCACCACATTCC 59.860 47.619 0.00 0.00 0.00 3.01
4097 12992 2.611225 TGCAAAAACCCACCACATTC 57.389 45.000 0.00 0.00 0.00 2.67
4144 13039 1.076438 CAGGGGTCCTCCTCCTTTTT 58.924 55.000 0.00 0.00 33.94 1.94
4162 13057 4.119363 GCCCAGATGCAGAGGCCA 62.119 66.667 5.01 0.00 39.60 5.36
4230 13126 6.653740 GGTGGCTTTAGTCTTACTGTTGTTAT 59.346 38.462 0.00 0.00 0.00 1.89
4231 13127 5.993441 GGTGGCTTTAGTCTTACTGTTGTTA 59.007 40.000 0.00 0.00 0.00 2.41
4232 13128 4.820173 GGTGGCTTTAGTCTTACTGTTGTT 59.180 41.667 0.00 0.00 0.00 2.83
4269 13171 3.231207 ACTGGATAGGAGTAGCGACAT 57.769 47.619 0.00 0.00 0.00 3.06
4301 13209 3.858877 GCATTAGGTCCAGACTATCAGCG 60.859 52.174 0.00 0.00 0.00 5.18
4406 13314 3.390521 TTGAGGAGTGCGCCGGAT 61.391 61.111 5.05 0.00 0.00 4.18
4473 13382 7.826252 AGATGCAACAGTACATCACTAAAGATT 59.174 33.333 15.51 0.00 44.16 2.40
4484 13393 3.941483 GCAAGGTAGATGCAACAGTACAT 59.059 43.478 0.00 0.00 43.29 2.29
4507 13416 0.520404 GTCGACGACAGCTAGACCAA 59.480 55.000 22.66 0.00 32.09 3.67
4508 13417 1.632948 CGTCGACGACAGCTAGACCA 61.633 60.000 33.35 0.00 43.02 4.02
4541 13450 2.047274 AGGATGGTGGCGTTGTCG 60.047 61.111 0.00 0.00 40.37 4.35
4560 13469 0.458370 CGTGTGATGATGGACGAGCA 60.458 55.000 0.00 0.00 33.64 4.26
4610 13520 2.029964 GACAACGGCGGGTCTCAA 59.970 61.111 21.55 0.00 0.00 3.02
4673 13586 0.109132 GGCATCGTTTTGGAGCAAGG 60.109 55.000 0.00 0.00 0.00 3.61
4721 13635 2.051256 CGGATCGGACGATGACGG 60.051 66.667 12.40 0.00 44.46 4.79
4768 13684 1.341852 TCACGTCAACCTGATCGGAAA 59.658 47.619 2.08 0.00 36.31 3.13
4792 13708 0.317160 TCTCGAGGCATTGTCGTTGT 59.683 50.000 13.56 0.00 38.60 3.32
4800 13716 0.108138 CGTTCCCTTCTCGAGGCATT 60.108 55.000 13.56 0.00 44.85 3.56
4822 13738 2.264794 GATGGCGGTGTCTCGGTT 59.735 61.111 0.00 0.00 0.00 4.44
4823 13739 4.129737 CGATGGCGGTGTCTCGGT 62.130 66.667 0.00 0.00 0.00 4.69
4831 13747 3.458163 ATGACGGACGATGGCGGT 61.458 61.111 0.00 0.00 43.17 5.68
4860 13776 1.130373 GCTTCCGATGAAAATCACGCA 59.870 47.619 0.00 0.00 0.00 5.24
4902 13818 4.473520 CCGCTCGGTTCCAGCCAT 62.474 66.667 0.00 0.00 32.83 4.40
5235 14153 1.327303 GGCGAGATCTCATCTGAGGT 58.673 55.000 22.31 0.00 42.30 3.85
5301 14246 3.847602 CAGCAGGCCTCTCCCTCG 61.848 72.222 0.00 0.00 31.24 4.63
5317 14262 2.931105 TCCCCAAACCCTAGCGCA 60.931 61.111 11.47 0.00 0.00 6.09
5319 14264 2.271173 GGTCCCCAAACCCTAGCG 59.729 66.667 0.00 0.00 32.82 4.26
5365 14310 1.677490 TTCTTTAACCCCTCCCCCTC 58.323 55.000 0.00 0.00 0.00 4.30
5371 14316 5.084519 AGGACCATTTTTCTTTAACCCCTC 58.915 41.667 0.00 0.00 0.00 4.30
5372 14317 5.087923 AGGACCATTTTTCTTTAACCCCT 57.912 39.130 0.00 0.00 0.00 4.79
5376 14321 7.484959 CGATGCTTAGGACCATTTTTCTTTAAC 59.515 37.037 0.00 0.00 0.00 2.01
5377 14322 7.175990 ACGATGCTTAGGACCATTTTTCTTTAA 59.824 33.333 0.00 0.00 0.00 1.52
5378 14323 6.657541 ACGATGCTTAGGACCATTTTTCTTTA 59.342 34.615 0.00 0.00 0.00 1.85
5379 14324 5.476945 ACGATGCTTAGGACCATTTTTCTTT 59.523 36.000 0.00 0.00 0.00 2.52
5380 14325 5.010282 ACGATGCTTAGGACCATTTTTCTT 58.990 37.500 0.00 0.00 0.00 2.52
5381 14326 4.589908 ACGATGCTTAGGACCATTTTTCT 58.410 39.130 0.00 0.00 0.00 2.52
5382 14327 4.965119 ACGATGCTTAGGACCATTTTTC 57.035 40.909 0.00 0.00 0.00 2.29
5383 14328 5.944007 AGTAACGATGCTTAGGACCATTTTT 59.056 36.000 0.00 0.00 0.00 1.94
5384 14329 5.497474 AGTAACGATGCTTAGGACCATTTT 58.503 37.500 0.00 0.00 0.00 1.82
5385 14330 5.099042 AGTAACGATGCTTAGGACCATTT 57.901 39.130 0.00 0.00 0.00 2.32
5386 14331 4.755266 AGTAACGATGCTTAGGACCATT 57.245 40.909 0.00 0.00 0.00 3.16
5387 14332 4.647853 TGTAGTAACGATGCTTAGGACCAT 59.352 41.667 0.00 0.00 0.00 3.55
5388 14333 4.018490 TGTAGTAACGATGCTTAGGACCA 58.982 43.478 0.00 0.00 0.00 4.02
5389 14334 4.644103 TGTAGTAACGATGCTTAGGACC 57.356 45.455 0.00 0.00 0.00 4.46
5390 14335 5.828747 TCATGTAGTAACGATGCTTAGGAC 58.171 41.667 0.00 0.00 0.00 3.85
5391 14336 6.096423 ACTTCATGTAGTAACGATGCTTAGGA 59.904 38.462 2.74 0.00 0.00 2.94
5392 14337 6.273825 ACTTCATGTAGTAACGATGCTTAGG 58.726 40.000 2.74 0.00 0.00 2.69
5393 14338 9.464714 AATACTTCATGTAGTAACGATGCTTAG 57.535 33.333 15.14 0.00 34.50 2.18
5394 14339 9.459640 GAATACTTCATGTAGTAACGATGCTTA 57.540 33.333 15.14 0.00 34.50 3.09
5395 14340 7.979537 TGAATACTTCATGTAGTAACGATGCTT 59.020 33.333 15.14 4.53 34.50 3.91
5396 14341 7.489160 TGAATACTTCATGTAGTAACGATGCT 58.511 34.615 15.14 0.00 34.50 3.79
5397 14342 7.694388 TGAATACTTCATGTAGTAACGATGC 57.306 36.000 15.14 0.96 34.50 3.91
5398 14343 9.083080 TGTTGAATACTTCATGTAGTAACGATG 57.917 33.333 15.14 0.00 39.84 3.84
5399 14344 9.302345 CTGTTGAATACTTCATGTAGTAACGAT 57.698 33.333 15.14 3.89 39.84 3.73
5400 14345 8.301720 ACTGTTGAATACTTCATGTAGTAACGA 58.698 33.333 15.14 9.93 39.84 3.85
5491 14439 2.159627 CAGTATCCACGCACCAAAAGAC 59.840 50.000 0.00 0.00 0.00 3.01
5921 14876 3.576982 ACCGAGACATACAAGTTCAAGGA 59.423 43.478 0.00 0.00 0.00 3.36
5981 14936 1.815003 GGAAGTCCAAGATTGCTGTGG 59.185 52.381 0.00 0.00 35.64 4.17
6004 14959 2.502142 TCTCGCCTGACTACCTACAA 57.498 50.000 0.00 0.00 0.00 2.41
6020 14975 5.234329 TCGTCATTGTCAGTTTCAACTTCTC 59.766 40.000 0.00 0.00 37.08 2.87
6021 14976 5.116180 TCGTCATTGTCAGTTTCAACTTCT 58.884 37.500 0.00 0.00 37.08 2.85
6042 14997 6.308328 AAGAATATCTTGGTCGATGGCATCG 61.308 44.000 37.07 37.07 43.67 3.84
6090 15045 6.183360 CCGAGACATGTTTGAGATTAGCAAAT 60.183 38.462 0.00 0.00 37.54 2.32
6127 15082 4.478699 CACATGTCATTTGGCAAGTACTG 58.521 43.478 0.00 0.00 29.87 2.74
6193 15148 5.659463 TCCATGGTTGAAACTGACAAAAAG 58.341 37.500 12.58 0.00 0.00 2.27
6300 15255 1.415200 GGGTAGGCTTGTCTCTAGGG 58.585 60.000 0.00 0.00 0.00 3.53
6351 15306 6.964807 ATCATCTATGGTTTAAGCATGCAA 57.035 33.333 21.98 2.93 36.89 4.08
6469 15424 3.052455 ACAACATTGCGATGTGAGGTA 57.948 42.857 20.40 0.00 45.58 3.08
6586 15541 2.485814 CTGCAAGTTAAGAGCTGGTTCC 59.514 50.000 0.00 0.00 0.00 3.62
6626 15581 0.171007 GCGTGCAACATGCCTAACAT 59.829 50.000 0.18 0.00 44.23 2.71
6712 17798 7.952671 AGAAATCTTATGTACGATAAGCAGGA 58.047 34.615 14.94 4.78 33.00 3.86
6739 17825 1.420138 ACACCTGTGGTAAGACTTGGG 59.580 52.381 0.00 0.00 32.11 4.12
6798 17884 6.257630 GCCACACTTTTTGTATCAAATGTGTT 59.742 34.615 20.25 11.02 41.94 3.32
6808 17894 6.426633 GCCTAAATTTGCCACACTTTTTGTAT 59.573 34.615 0.00 0.00 35.67 2.29
6809 17895 5.755861 GCCTAAATTTGCCACACTTTTTGTA 59.244 36.000 0.00 0.00 35.67 2.41
6970 18056 3.650070 TGTAGATGGCTAGAGAATGCG 57.350 47.619 0.00 0.00 0.00 4.73
6996 18082 5.576447 AACACAAAGTCGAGGAAAAACAT 57.424 34.783 0.00 0.00 0.00 2.71
7288 18419 7.800300 AGATTCTACCAAGTAAAGACTCCTT 57.200 36.000 0.00 0.00 33.58 3.36
7289 18420 7.800300 AAGATTCTACCAAGTAAAGACTCCT 57.200 36.000 0.00 0.00 33.58 3.69
7290 18421 9.368674 GTTAAGATTCTACCAAGTAAAGACTCC 57.631 37.037 0.00 0.00 33.58 3.85


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

AutoCloner maintained by Alex Coulton.