Multiple sequence alignment - TraesCS2D01G381000

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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 TraesCS2D01G381000 chr2D 100.000 6039 0 0 1 6039 484975797 484981835 0.000000e+00 11153.0
1 TraesCS2D01G381000 chr2D 84.924 723 96 9 3715 4430 485088794 485089510 0.000000e+00 719.0
2 TraesCS2D01G381000 chr2D 79.863 730 110 16 3707 4420 13885508 13886216 3.250000e-137 499.0
3 TraesCS2D01G381000 chr2D 85.859 297 39 3 2897 3191 485084135 485084430 4.540000e-81 313.0
4 TraesCS2D01G381000 chr2D 87.452 263 31 1 4813 5075 485089798 485090058 9.840000e-78 302.0
5 TraesCS2D01G381000 chr2D 91.964 112 9 0 1232 1343 485078476 485078587 2.250000e-34 158.0
6 TraesCS2D01G381000 chr2D 91.892 111 9 0 2642 2752 485083993 485084103 8.100000e-34 156.0
7 TraesCS2D01G381000 chr2D 85.000 140 13 4 997 1129 13863048 13863186 1.060000e-27 135.0
8 TraesCS2D01G381000 chr2D 87.179 78 9 1 4666 4742 489051448 489051525 3.000000e-13 87.9
9 TraesCS2D01G381000 chr2B 89.843 2540 112 60 763 3204 569975978 569978469 0.000000e+00 3127.0
10 TraesCS2D01G381000 chr2B 91.745 957 72 2 3712 4667 569980134 569981084 0.000000e+00 1323.0
11 TraesCS2D01G381000 chr2B 92.764 539 26 8 243 769 569975414 569975951 0.000000e+00 767.0
12 TraesCS2D01G381000 chr2B 90.289 484 31 10 4776 5255 569981077 569981548 2.390000e-173 619.0
13 TraesCS2D01G381000 chr2B 80.191 732 112 19 3707 4420 25250104 25250820 8.970000e-143 518.0
14 TraesCS2D01G381000 chr2B 89.640 222 17 4 3216 3436 569979852 569980068 1.660000e-70 278.0
15 TraesCS2D01G381000 chr2B 85.641 195 11 4 69 248 569975185 569975377 7.990000e-44 189.0
16 TraesCS2D01G381000 chr2B 97.468 79 2 0 1256 1334 25246924 25247002 1.060000e-27 135.0
17 TraesCS2D01G381000 chr2A 90.568 1919 126 27 1559 3436 629105460 629107364 0.000000e+00 2490.0
18 TraesCS2D01G381000 chr2A 93.625 1004 54 8 3707 4702 629107427 629108428 0.000000e+00 1491.0
19 TraesCS2D01G381000 chr2A 87.747 759 79 10 3707 4456 630067945 630068698 0.000000e+00 874.0
20 TraesCS2D01G381000 chr2A 91.738 581 30 7 4685 5255 629108606 629109178 0.000000e+00 791.0
21 TraesCS2D01G381000 chr2A 81.489 967 84 56 271 1195 629999159 630000072 0.000000e+00 706.0
22 TraesCS2D01G381000 chr2A 83.757 708 80 17 3715 4416 629641331 629642009 6.600000e-179 638.0
23 TraesCS2D01G381000 chr2A 85.290 639 46 19 763 1366 629104663 629105288 3.090000e-172 616.0
24 TraesCS2D01G381000 chr2A 87.732 538 47 11 2901 3425 630067317 630067848 1.440000e-170 610.0
25 TraesCS2D01G381000 chr2A 83.562 584 71 15 2897 3460 629639807 629640385 1.930000e-144 523.0
26 TraesCS2D01G381000 chr2A 84.444 540 53 17 239 769 629104121 629104638 2.510000e-138 503.0
27 TraesCS2D01G381000 chr2A 85.746 456 43 16 1464 1897 630002401 630002856 4.260000e-126 462.0
28 TraesCS2D01G381000 chr2A 87.317 410 32 8 4790 5179 630075952 630076361 9.230000e-123 451.0
29 TraesCS2D01G381000 chr2A 85.882 425 36 7 2033 2436 630002913 630003334 1.200000e-116 431.0
30 TraesCS2D01G381000 chr2A 97.561 123 3 0 2643 2765 630009182 630009304 1.710000e-50 211.0
31 TraesCS2D01G381000 chr2A 91.892 111 9 0 2642 2752 629639665 629639775 8.100000e-34 156.0
32 TraesCS2D01G381000 chr2A 91.964 112 6 1 1232 1343 629634334 629634442 2.910000e-33 154.0
33 TraesCS2D01G381000 chr2A 87.050 139 12 2 997 1129 16095186 16095324 1.050000e-32 152.0
34 TraesCS2D01G381000 chr2A 87.050 139 12 2 997 1129 16097928 16098066 1.050000e-32 152.0
35 TraesCS2D01G381000 chr2A 98.701 77 1 0 1257 1333 630000092 630000168 2.940000e-28 137.0
36 TraesCS2D01G381000 chr2A 84.892 139 15 2 997 1129 16083843 16083981 1.060000e-27 135.0
37 TraesCS2D01G381000 chr2A 84.173 139 16 2 997 1129 16065659 16065797 4.910000e-26 130.0
38 TraesCS2D01G381000 chr2A 96.154 78 3 0 1256 1333 16065892 16065969 1.770000e-25 128.0
39 TraesCS2D01G381000 chr2A 93.827 81 5 0 1253 1333 16084082 16084162 8.220000e-24 122.0
40 TraesCS2D01G381000 chr2A 93.827 81 5 0 1253 1333 16095425 16095505 8.220000e-24 122.0
41 TraesCS2D01G381000 chr2A 90.278 72 0 5 763 828 629999667 629999737 3.000000e-13 87.9
42 TraesCS2D01G381000 chr2A 83.333 78 8 5 3496 3569 74364384 74364460 3.910000e-07 67.6
43 TraesCS2D01G381000 chr5D 91.741 787 64 1 5254 6039 304886973 304887759 0.000000e+00 1092.0
44 TraesCS2D01G381000 chr6A 91.720 785 64 1 5256 6039 346380267 346379483 0.000000e+00 1088.0
45 TraesCS2D01G381000 chr6A 91.774 778 60 3 5256 6030 487048253 487049029 0.000000e+00 1079.0
46 TraesCS2D01G381000 chr3A 91.371 788 66 2 5254 6039 517270173 517269386 0.000000e+00 1077.0
47 TraesCS2D01G381000 chr3A 89.247 93 7 3 4666 4756 728351725 728351634 4.950000e-21 113.0
48 TraesCS2D01G381000 chr6D 90.724 787 68 4 5255 6039 100871414 100870631 0.000000e+00 1044.0
49 TraesCS2D01G381000 chr1B 90.816 784 67 4 5256 6037 368899884 368900664 0.000000e+00 1044.0
50 TraesCS2D01G381000 chr1B 90.862 777 66 4 5256 6030 339125772 339126545 0.000000e+00 1037.0
51 TraesCS2D01G381000 chr1B 94.545 55 2 1 4705 4758 439840291 439840345 3.880000e-12 84.2
52 TraesCS2D01G381000 chr1D 90.306 784 72 3 5258 6039 447056013 447055232 0.000000e+00 1024.0
53 TraesCS2D01G381000 chr7D 89.975 788 72 6 5256 6039 416805306 416804522 0.000000e+00 1011.0
54 TraesCS2D01G381000 chrUn 76.349 482 63 34 2098 2556 363203572 363203119 1.710000e-50 211.0
55 TraesCS2D01G381000 chrUn 76.349 482 63 34 2098 2556 413748189 413747736 1.710000e-50 211.0
56 TraesCS2D01G381000 chrUn 86.735 98 11 2 4666 4761 42093529 42093626 2.300000e-19 108.0
57 TraesCS2D01G381000 chr1A 92.308 91 5 2 4666 4755 552373371 552373460 1.770000e-25 128.0
58 TraesCS2D01G381000 chr3D 88.298 94 10 1 4666 4758 598188915 598188822 1.780000e-20 111.0
59 TraesCS2D01G381000 chr3D 87.805 82 8 2 4685 4765 598183831 598183751 1.790000e-15 95.3
60 TraesCS2D01G381000 chr3D 83.333 72 8 3 3502 3569 585231954 585231883 5.050000e-06 63.9
61 TraesCS2D01G381000 chr7B 84.416 77 8 3 4671 4744 12714861 12714786 8.400000e-09 73.1


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 TraesCS2D01G381000 chr2D 484975797 484981835 6038 False 11153.00 11153 100.000000 1 6039 1 chr2D.!!$F3 6038
1 TraesCS2D01G381000 chr2D 485088794 485090058 1264 False 510.50 719 86.188000 3715 5075 2 chr2D.!!$F7 1360
2 TraesCS2D01G381000 chr2D 13885508 13886216 708 False 499.00 499 79.863000 3707 4420 1 chr2D.!!$F2 713
3 TraesCS2D01G381000 chr2B 569975185 569981548 6363 False 1050.50 3127 89.987000 69 5255 6 chr2B.!!$F2 5186
4 TraesCS2D01G381000 chr2B 25246924 25250820 3896 False 326.50 518 88.829500 1256 4420 2 chr2B.!!$F1 3164
5 TraesCS2D01G381000 chr2A 629104121 629109178 5057 False 1178.20 2490 89.133000 239 5255 5 chr2A.!!$F8 5016
6 TraesCS2D01G381000 chr2A 630067317 630068698 1381 False 742.00 874 87.739500 2901 4456 2 chr2A.!!$F11 1555
7 TraesCS2D01G381000 chr2A 629639665 629642009 2344 False 439.00 638 86.403667 2642 4416 3 chr2A.!!$F9 1774
8 TraesCS2D01G381000 chr2A 629999159 630003334 4175 False 364.78 706 88.419200 271 2436 5 chr2A.!!$F10 2165
9 TraesCS2D01G381000 chr5D 304886973 304887759 786 False 1092.00 1092 91.741000 5254 6039 1 chr5D.!!$F1 785
10 TraesCS2D01G381000 chr6A 346379483 346380267 784 True 1088.00 1088 91.720000 5256 6039 1 chr6A.!!$R1 783
11 TraesCS2D01G381000 chr6A 487048253 487049029 776 False 1079.00 1079 91.774000 5256 6030 1 chr6A.!!$F1 774
12 TraesCS2D01G381000 chr3A 517269386 517270173 787 True 1077.00 1077 91.371000 5254 6039 1 chr3A.!!$R1 785
13 TraesCS2D01G381000 chr6D 100870631 100871414 783 True 1044.00 1044 90.724000 5255 6039 1 chr6D.!!$R1 784
14 TraesCS2D01G381000 chr1B 368899884 368900664 780 False 1044.00 1044 90.816000 5256 6037 1 chr1B.!!$F2 781
15 TraesCS2D01G381000 chr1B 339125772 339126545 773 False 1037.00 1037 90.862000 5256 6030 1 chr1B.!!$F1 774
16 TraesCS2D01G381000 chr1D 447055232 447056013 781 True 1024.00 1024 90.306000 5258 6039 1 chr1D.!!$R1 781
17 TraesCS2D01G381000 chr7D 416804522 416805306 784 True 1011.00 1011 89.975000 5256 6039 1 chr7D.!!$R1 783

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
171 172 0.036388 TGTTGCCCGTCCTGAGATTC 60.036 55.0 0.00 0.0 0.00 2.52 F
197 198 0.038251 CTCGCCTCTGCTGTTGTACA 60.038 55.0 0.00 0.0 34.43 2.90 F
198 199 0.319555 TCGCCTCTGCTGTTGTACAC 60.320 55.0 0.00 0.0 34.43 2.90 F
898 1032 0.460284 GTGACAGGGACATGGCGTAG 60.460 60.0 0.00 0.0 0.00 3.51 F
2289 5976 0.258774 GCCCATGTAACCCTGGACAT 59.741 55.0 0.00 0.0 36.73 3.06 F
3616 9453 0.320771 AGTACAGCTGGCAAACGGAG 60.321 55.0 19.93 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1251 1422 1.153349 GCCCTCGATCTGGAACCAC 60.153 63.158 3.53 0.00 0.00 4.16 R
1981 5583 3.559655 TCACGACAGCAATTGCCATATAC 59.440 43.478 26.45 11.27 43.38 1.47 R
2084 5752 5.316167 TGAGAGCAAAGAAGCTATTTGGAA 58.684 37.500 20.10 0.00 46.75 3.53 R
2864 6582 0.105593 CCAGTAGGAGTCGCATGCAT 59.894 55.000 19.57 2.11 36.89 3.96 R
3642 9479 0.035439 AGTTATCCTGCCGGTTGTGG 60.035 55.000 1.90 0.11 0.00 4.17 R
5380 11522 0.175073 AAGCCTTTACCTCGCTACGG 59.825 55.000 0.00 0.00 31.12 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.214980 GATGTAATCAATGGTCCTTGCG 57.785 45.455 0.00 0.00 44.70 4.85
35 36 2.364632 TGTAATCAATGGTCCTTGCGG 58.635 47.619 0.00 0.00 0.00 5.69
36 37 2.290641 TGTAATCAATGGTCCTTGCGGT 60.291 45.455 0.00 0.00 0.00 5.68
37 38 2.799126 AATCAATGGTCCTTGCGGTA 57.201 45.000 0.00 0.00 0.00 4.02
38 39 2.038387 ATCAATGGTCCTTGCGGTAC 57.962 50.000 0.00 0.00 0.00 3.34
39 40 0.981183 TCAATGGTCCTTGCGGTACT 59.019 50.000 0.00 0.00 0.00 2.73
40 41 1.066430 TCAATGGTCCTTGCGGTACTC 60.066 52.381 0.00 0.00 0.00 2.59
41 42 0.252197 AATGGTCCTTGCGGTACTCC 59.748 55.000 0.00 0.00 0.00 3.85
42 43 0.907704 ATGGTCCTTGCGGTACTCCA 60.908 55.000 0.00 0.00 0.00 3.86
43 44 1.218316 GGTCCTTGCGGTACTCCAG 59.782 63.158 0.00 0.00 0.00 3.86
44 45 1.218316 GTCCTTGCGGTACTCCAGG 59.782 63.158 0.00 0.00 0.00 4.45
45 46 1.229082 TCCTTGCGGTACTCCAGGT 60.229 57.895 0.00 0.00 0.00 4.00
46 47 1.218316 CCTTGCGGTACTCCAGGTC 59.782 63.158 0.00 0.00 0.00 3.85
47 48 1.258445 CCTTGCGGTACTCCAGGTCT 61.258 60.000 0.00 0.00 0.00 3.85
48 49 1.471119 CTTGCGGTACTCCAGGTCTA 58.529 55.000 0.00 0.00 0.00 2.59
49 50 2.032620 CTTGCGGTACTCCAGGTCTAT 58.967 52.381 0.00 0.00 0.00 1.98
50 51 1.688772 TGCGGTACTCCAGGTCTATC 58.311 55.000 0.00 0.00 0.00 2.08
51 52 1.214673 TGCGGTACTCCAGGTCTATCT 59.785 52.381 0.00 0.00 0.00 1.98
52 53 1.881324 GCGGTACTCCAGGTCTATCTC 59.119 57.143 0.00 0.00 0.00 2.75
53 54 2.506444 CGGTACTCCAGGTCTATCTCC 58.494 57.143 0.00 0.00 0.00 3.71
54 55 2.158652 CGGTACTCCAGGTCTATCTCCA 60.159 54.545 0.00 0.00 0.00 3.86
55 56 3.492337 GGTACTCCAGGTCTATCTCCAG 58.508 54.545 0.00 0.00 0.00 3.86
56 57 3.117436 GGTACTCCAGGTCTATCTCCAGT 60.117 52.174 0.00 0.00 0.00 4.00
57 58 3.767309 ACTCCAGGTCTATCTCCAGTT 57.233 47.619 0.00 0.00 0.00 3.16
58 59 4.067944 ACTCCAGGTCTATCTCCAGTTT 57.932 45.455 0.00 0.00 0.00 2.66
59 60 4.430441 ACTCCAGGTCTATCTCCAGTTTT 58.570 43.478 0.00 0.00 0.00 2.43
60 61 4.846940 ACTCCAGGTCTATCTCCAGTTTTT 59.153 41.667 0.00 0.00 0.00 1.94
61 62 5.165961 TCCAGGTCTATCTCCAGTTTTTG 57.834 43.478 0.00 0.00 0.00 2.44
62 63 3.691609 CCAGGTCTATCTCCAGTTTTTGC 59.308 47.826 0.00 0.00 0.00 3.68
63 64 4.566488 CCAGGTCTATCTCCAGTTTTTGCT 60.566 45.833 0.00 0.00 0.00 3.91
64 65 4.394300 CAGGTCTATCTCCAGTTTTTGCTG 59.606 45.833 0.00 0.00 36.31 4.41
65 66 3.127721 GGTCTATCTCCAGTTTTTGCTGC 59.872 47.826 0.00 0.00 35.28 5.25
66 67 3.753272 GTCTATCTCCAGTTTTTGCTGCA 59.247 43.478 0.00 0.00 35.28 4.41
67 68 3.753272 TCTATCTCCAGTTTTTGCTGCAC 59.247 43.478 0.00 0.00 35.28 4.57
75 76 0.532573 TTTTTGCTGCACCCACGAAA 59.467 45.000 0.00 0.00 0.00 3.46
81 82 0.813610 CTGCACCCACGAAACACTGA 60.814 55.000 0.00 0.00 0.00 3.41
82 83 0.179032 TGCACCCACGAAACACTGAT 60.179 50.000 0.00 0.00 0.00 2.90
83 84 0.517316 GCACCCACGAAACACTGATC 59.483 55.000 0.00 0.00 0.00 2.92
89 90 1.136252 CACGAAACACTGATCGGCTTG 60.136 52.381 0.00 0.00 43.11 4.01
140 141 7.067372 CACACATGGTAATATTTGGTCTGACAT 59.933 37.037 10.38 0.00 0.00 3.06
146 147 4.753516 ATATTTGGTCTGACATGGTCGA 57.246 40.909 10.38 0.00 34.95 4.20
165 166 1.101049 AACAAGTGTTGCCCGTCCTG 61.101 55.000 0.00 0.00 36.80 3.86
170 171 0.321653 GTGTTGCCCGTCCTGAGATT 60.322 55.000 0.00 0.00 0.00 2.40
171 172 0.036388 TGTTGCCCGTCCTGAGATTC 60.036 55.000 0.00 0.00 0.00 2.52
196 197 0.243907 TCTCGCCTCTGCTGTTGTAC 59.756 55.000 0.00 0.00 34.43 2.90
197 198 0.038251 CTCGCCTCTGCTGTTGTACA 60.038 55.000 0.00 0.00 34.43 2.90
198 199 0.319555 TCGCCTCTGCTGTTGTACAC 60.320 55.000 0.00 0.00 34.43 2.90
223 239 2.808543 CGGAACTTGTTCCCAGAGAAAG 59.191 50.000 22.34 6.27 37.84 2.62
476 548 1.214589 CGTGCCGTGCTTACCTACT 59.785 57.895 0.00 0.00 0.00 2.57
498 574 3.311110 GAGGCCACGACCCTGTCA 61.311 66.667 5.01 0.00 31.41 3.58
609 688 3.122971 GACCCGGCGCTTTGGTAC 61.123 66.667 7.64 2.78 30.97 3.34
743 824 2.774234 CCATGTGGATCTCAGTTACCCT 59.226 50.000 0.00 0.00 37.39 4.34
753 834 4.964593 TCTCAGTTACCCTAACCAACAAC 58.035 43.478 0.00 0.00 39.47 3.32
862 989 7.261829 CCGTAGGCAGGACTAGATATAATAC 57.738 44.000 0.00 0.00 46.14 1.89
864 991 7.012515 CCGTAGGCAGGACTAGATATAATACTG 59.987 44.444 0.00 0.00 46.14 2.74
871 1002 8.616942 CAGGACTAGATATAATACTGATCGGTG 58.383 40.741 17.78 0.00 0.00 4.94
898 1032 0.460284 GTGACAGGGACATGGCGTAG 60.460 60.000 0.00 0.00 0.00 3.51
919 1054 3.005791 AGCTTCGCTGTTGCCTTTAAATT 59.994 39.130 0.00 0.00 37.57 1.82
925 1060 4.558860 CGCTGTTGCCTTTAAATTAGCTTC 59.441 41.667 0.00 2.04 35.36 3.86
1101 1267 2.352805 CCGCCTGGCTTCCTCTTT 59.647 61.111 17.92 0.00 0.00 2.52
1251 1422 4.260497 CCACAACGCATGAACTATGATCTG 60.260 45.833 0.00 0.00 39.21 2.90
1398 3867 2.557924 TGTGATCCATGTTGCCTTTGTC 59.442 45.455 0.00 0.00 0.00 3.18
1399 3868 2.821969 GTGATCCATGTTGCCTTTGTCT 59.178 45.455 0.00 0.00 0.00 3.41
1400 3869 2.821378 TGATCCATGTTGCCTTTGTCTG 59.179 45.455 0.00 0.00 0.00 3.51
1436 3905 8.752005 ATGCTTAGCTTATGATAAGGTTGAAA 57.248 30.769 20.37 9.42 41.12 2.69
1438 3907 8.623903 TGCTTAGCTTATGATAAGGTTGAAATG 58.376 33.333 20.37 7.55 41.12 2.32
1439 3908 8.078596 GCTTAGCTTATGATAAGGTTGAAATGG 58.921 37.037 20.37 6.44 41.12 3.16
1555 4035 4.647853 TGTTAGTACTAATCATGAGGCCGT 59.352 41.667 18.03 0.00 0.00 5.68
1622 4122 7.819900 AGTACTGCTAGACTCCAAAAATGTTAG 59.180 37.037 0.00 0.00 0.00 2.34
1955 5556 4.894784 ACCATAATAATACGAGTGGCCAG 58.105 43.478 5.11 0.00 0.00 4.85
1981 5583 2.323939 TTTGCGCTTTATCCGTGTTG 57.676 45.000 9.73 0.00 0.00 3.33
2003 5605 2.106477 TATGGCAATTGCTGTCGTGA 57.894 45.000 28.42 6.07 41.70 4.35
2007 5627 1.089920 GCAATTGCTGTCGTGAGGAT 58.910 50.000 23.21 0.00 38.21 3.24
2022 5642 4.698201 TGAGGATCAACTAACACCACAA 57.302 40.909 0.00 0.00 45.97 3.33
2023 5643 5.042463 TGAGGATCAACTAACACCACAAA 57.958 39.130 0.00 0.00 45.97 2.83
2024 5644 5.441500 TGAGGATCAACTAACACCACAAAA 58.558 37.500 0.00 0.00 45.97 2.44
2025 5645 5.888724 TGAGGATCAACTAACACCACAAAAA 59.111 36.000 0.00 0.00 45.97 1.94
2026 5646 6.549364 TGAGGATCAACTAACACCACAAAAAT 59.451 34.615 0.00 0.00 45.97 1.82
2027 5647 7.069331 TGAGGATCAACTAACACCACAAAAATT 59.931 33.333 0.00 0.00 45.97 1.82
2028 5648 7.791029 AGGATCAACTAACACCACAAAAATTT 58.209 30.769 0.00 0.00 0.00 1.82
2029 5649 8.264347 AGGATCAACTAACACCACAAAAATTTT 58.736 29.630 0.00 0.00 0.00 1.82
2030 5650 8.547894 GGATCAACTAACACCACAAAAATTTTC 58.452 33.333 3.41 0.00 0.00 2.29
2031 5651 7.835634 TCAACTAACACCACAAAAATTTTCC 57.164 32.000 3.41 0.00 0.00 3.13
2037 5680 5.912892 ACACCACAAAAATTTTCCGATCTT 58.087 33.333 3.41 0.00 0.00 2.40
2079 5735 2.931969 CAGCTAACGCATGTGATCTTCA 59.068 45.455 14.43 0.00 39.10 3.02
2080 5736 3.558829 CAGCTAACGCATGTGATCTTCAT 59.441 43.478 14.43 0.00 39.10 2.57
2081 5737 4.746611 CAGCTAACGCATGTGATCTTCATA 59.253 41.667 14.43 0.00 39.10 2.15
2084 5752 7.277319 CAGCTAACGCATGTGATCTTCATATAT 59.723 37.037 14.43 0.00 39.10 0.86
2086 5754 8.113062 GCTAACGCATGTGATCTTCATATATTC 58.887 37.037 14.43 0.00 35.78 1.75
2091 5759 8.456471 CGCATGTGATCTTCATATATTCCAAAT 58.544 33.333 0.00 0.00 0.00 2.32
2223 5891 5.754782 TGATTAGCCCAACATACAATCACT 58.245 37.500 0.00 0.00 29.84 3.41
2284 5971 0.611618 TGCTTGCCCATGTAACCCTG 60.612 55.000 0.00 0.00 0.00 4.45
2289 5976 0.258774 GCCCATGTAACCCTGGACAT 59.741 55.000 0.00 0.00 36.73 3.06
2290 5977 1.750682 GCCCATGTAACCCTGGACATC 60.751 57.143 0.00 0.00 34.01 3.06
2471 6170 2.038426 ACTGTCGTTGAATCATGGTCCA 59.962 45.455 0.00 0.00 0.00 4.02
2511 6210 1.466855 GCGTTAATTCGGCTGCAATC 58.533 50.000 0.50 0.00 0.00 2.67
2525 6224 1.337354 TGCAATCGCTTTCTACGACCA 60.337 47.619 0.00 0.00 43.23 4.02
2586 6285 1.965930 GCCACGCCACACATCTGAA 60.966 57.895 0.00 0.00 0.00 3.02
2620 6323 6.556212 TCAACTCTAGCTAATCTTCAACGAG 58.444 40.000 0.00 0.00 0.00 4.18
2621 6324 6.374613 TCAACTCTAGCTAATCTTCAACGAGA 59.625 38.462 7.59 0.00 0.00 4.04
2634 6337 5.607119 TTCAACGAGAAGCAATCCTAAAC 57.393 39.130 0.00 0.00 0.00 2.01
2635 6338 3.678072 TCAACGAGAAGCAATCCTAAACG 59.322 43.478 0.00 0.00 0.00 3.60
2636 6339 3.314541 ACGAGAAGCAATCCTAAACGT 57.685 42.857 0.00 0.00 0.00 3.99
2637 6340 4.445452 ACGAGAAGCAATCCTAAACGTA 57.555 40.909 0.00 0.00 0.00 3.57
2638 6341 5.007385 ACGAGAAGCAATCCTAAACGTAT 57.993 39.130 0.00 0.00 0.00 3.06
2786 6503 0.322456 TACTGGTTGCACATGCCCTC 60.322 55.000 0.49 0.00 41.18 4.30
2797 6514 0.679002 CATGCCCTCCCTGTGACTTG 60.679 60.000 0.00 0.00 0.00 3.16
2798 6515 0.842030 ATGCCCTCCCTGTGACTTGA 60.842 55.000 0.00 0.00 0.00 3.02
2800 6517 1.484444 GCCCTCCCTGTGACTTGACT 61.484 60.000 0.00 0.00 0.00 3.41
2804 6521 3.072476 CCCTCCCTGTGACTTGACTTTTA 59.928 47.826 0.00 0.00 0.00 1.52
2805 6522 4.065789 CCTCCCTGTGACTTGACTTTTAC 58.934 47.826 0.00 0.00 0.00 2.01
2863 6581 3.705043 CTGGCTAAATCAGGAATGTGC 57.295 47.619 0.00 0.00 0.00 4.57
2864 6582 3.018856 CTGGCTAAATCAGGAATGTGCA 58.981 45.455 0.00 0.00 0.00 4.57
2936 6656 0.898789 TCACAGGGAGGAGTTCGACC 60.899 60.000 0.00 0.00 0.00 4.79
3098 6818 1.146041 AACAGCGGCAACTCTCACA 59.854 52.632 1.45 0.00 0.00 3.58
3184 6908 1.831736 AGGAACTATCAGGTGAACCCG 59.168 52.381 0.00 0.00 36.02 5.28
3227 8327 2.887152 GGAGCTTCCTTCTCAAAAGCAA 59.113 45.455 8.80 0.00 46.11 3.91
3229 8329 4.021632 GGAGCTTCCTTCTCAAAAGCAAAT 60.022 41.667 8.80 0.00 46.11 2.32
3240 8340 4.047822 TCAAAAGCAAATACGCCTTTGTG 58.952 39.130 10.78 3.42 41.79 3.33
3252 8353 2.419667 GCCTTTGTGTTAGCCGTTCTA 58.580 47.619 0.00 0.00 0.00 2.10
3415 8523 5.644206 GGTATGTCCTTTCTTCTTTCACCTC 59.356 44.000 0.00 0.00 0.00 3.85
3425 8533 0.588252 CTTTCACCTCCTGTGCAACG 59.412 55.000 0.00 0.00 45.03 4.10
3438 8579 4.033358 CCTGTGCAACGAGAAATATGAGAC 59.967 45.833 0.00 0.00 42.39 3.36
3461 9297 1.518325 TCACAGCAACATTACCCACG 58.482 50.000 0.00 0.00 0.00 4.94
3466 9302 3.004315 ACAGCAACATTACCCACGAAAAG 59.996 43.478 0.00 0.00 0.00 2.27
3470 9306 4.621034 GCAACATTACCCACGAAAAGAATG 59.379 41.667 0.00 0.00 0.00 2.67
3477 9314 5.331876 ACCCACGAAAAGAATGTGAAAAA 57.668 34.783 0.00 0.00 35.66 1.94
3479 9316 5.105513 ACCCACGAAAAGAATGTGAAAAACT 60.106 36.000 0.00 0.00 35.66 2.66
3480 9317 5.231991 CCCACGAAAAGAATGTGAAAAACTG 59.768 40.000 0.00 0.00 35.66 3.16
3481 9318 5.804979 CCACGAAAAGAATGTGAAAAACTGT 59.195 36.000 0.00 0.00 35.66 3.55
3482 9319 6.310224 CCACGAAAAGAATGTGAAAAACTGTT 59.690 34.615 0.00 0.00 35.66 3.16
3484 9321 8.523464 CACGAAAAGAATGTGAAAAACTGTTAG 58.477 33.333 0.00 0.00 35.66 2.34
3486 9323 8.523464 CGAAAAGAATGTGAAAAACTGTTAGTG 58.477 33.333 0.00 0.00 0.00 2.74
3487 9324 9.353999 GAAAAGAATGTGAAAAACTGTTAGTGT 57.646 29.630 0.00 0.00 0.00 3.55
3488 9325 9.705290 AAAAGAATGTGAAAAACTGTTAGTGTT 57.295 25.926 0.00 0.00 0.00 3.32
3491 9328 9.950680 AGAATGTGAAAAACTGTTAGTGTTATG 57.049 29.630 0.00 0.00 0.00 1.90
3494 9331 9.897744 ATGTGAAAAACTGTTAGTGTTATGATG 57.102 29.630 0.00 0.00 0.00 3.07
3496 9333 9.730420 GTGAAAAACTGTTAGTGTTATGATGTT 57.270 29.630 0.00 0.00 0.00 2.71
3526 9363 4.948341 TTTTTGGAAAAGGAGGCTTACC 57.052 40.909 0.00 0.00 0.00 2.85
3527 9364 2.194201 TTGGAAAAGGAGGCTTACCG 57.806 50.000 0.00 0.00 42.76 4.02
3528 9365 0.322187 TGGAAAAGGAGGCTTACCGC 60.322 55.000 0.00 0.00 42.76 5.68
3544 9381 1.745115 CGCCTCGGCATCCAAAAGA 60.745 57.895 8.87 0.00 42.06 2.52
3545 9382 1.097547 CGCCTCGGCATCCAAAAGAT 61.098 55.000 8.87 0.00 42.06 2.40
3555 9392 3.973657 CATCCAAAAGATGCATGTAGCC 58.026 45.455 2.46 0.00 45.76 3.93
3556 9393 3.084536 TCCAAAAGATGCATGTAGCCA 57.915 42.857 2.46 0.00 44.83 4.75
3557 9394 3.634504 TCCAAAAGATGCATGTAGCCAT 58.365 40.909 2.46 0.00 44.83 4.40
3558 9395 4.790937 TCCAAAAGATGCATGTAGCCATA 58.209 39.130 2.46 0.00 44.83 2.74
3559 9396 5.387788 TCCAAAAGATGCATGTAGCCATAT 58.612 37.500 2.46 0.00 44.83 1.78
3560 9397 5.834742 TCCAAAAGATGCATGTAGCCATATT 59.165 36.000 2.46 0.00 44.83 1.28
3561 9398 7.003482 TCCAAAAGATGCATGTAGCCATATTA 58.997 34.615 2.46 0.00 44.83 0.98
3563 9400 8.308931 CCAAAAGATGCATGTAGCCATATTATT 58.691 33.333 2.46 0.00 44.83 1.40
3596 9433 9.871238 TGTGAACTAAAACATAGTCTTAGATCC 57.129 33.333 0.00 0.00 0.00 3.36
3597 9434 9.871238 GTGAACTAAAACATAGTCTTAGATCCA 57.129 33.333 0.00 0.00 0.00 3.41
3604 9441 6.642707 ACATAGTCTTAGATCCAGTACAGC 57.357 41.667 0.00 0.00 0.00 4.40
3605 9442 6.369629 ACATAGTCTTAGATCCAGTACAGCT 58.630 40.000 0.00 0.00 0.00 4.24
3606 9443 6.264292 ACATAGTCTTAGATCCAGTACAGCTG 59.736 42.308 13.48 13.48 44.63 4.24
3614 9451 1.868997 CAGTACAGCTGGCAAACGG 59.131 57.895 19.93 7.51 41.42 4.44
3615 9452 0.602638 CAGTACAGCTGGCAAACGGA 60.603 55.000 19.93 0.00 41.42 4.69
3616 9453 0.320771 AGTACAGCTGGCAAACGGAG 60.321 55.000 19.93 0.00 0.00 4.63
3617 9454 1.671054 TACAGCTGGCAAACGGAGC 60.671 57.895 19.93 0.00 0.00 4.70
3618 9455 2.390306 TACAGCTGGCAAACGGAGCA 62.390 55.000 19.93 0.00 35.03 4.26
3619 9456 2.203337 AGCTGGCAAACGGAGCAA 60.203 55.556 0.00 0.00 35.03 3.91
3620 9457 1.827789 AGCTGGCAAACGGAGCAAA 60.828 52.632 0.00 0.00 35.03 3.68
3622 9459 0.529555 GCTGGCAAACGGAGCAAAAA 60.530 50.000 0.00 0.00 32.70 1.94
3646 9483 8.729805 AAAAGAAATAAAAACTCATTGCCACA 57.270 26.923 0.00 0.00 0.00 4.17
3647 9484 8.729805 AAAGAAATAAAAACTCATTGCCACAA 57.270 26.923 0.00 0.00 0.00 3.33
3648 9485 7.713764 AGAAATAAAAACTCATTGCCACAAC 57.286 32.000 0.00 0.00 0.00 3.32
3649 9486 6.705825 AGAAATAAAAACTCATTGCCACAACC 59.294 34.615 0.00 0.00 0.00 3.77
3650 9487 2.507339 AAAACTCATTGCCACAACCG 57.493 45.000 0.00 0.00 0.00 4.44
3651 9488 0.673437 AAACTCATTGCCACAACCGG 59.327 50.000 0.00 0.00 0.00 5.28
3660 9497 2.477880 CCACAACCGGCAGGATAAC 58.522 57.895 10.86 0.00 41.02 1.89
3661 9498 0.035439 CCACAACCGGCAGGATAACT 60.035 55.000 10.86 0.00 41.02 2.24
3675 9512 5.738909 CAGGATAACTGGACAAGATCACTT 58.261 41.667 0.00 0.00 43.70 3.16
3678 9515 6.670027 AGGATAACTGGACAAGATCACTTAGT 59.330 38.462 0.00 0.00 34.70 2.24
3679 9516 6.758886 GGATAACTGGACAAGATCACTTAGTG 59.241 42.308 5.94 5.94 34.70 2.74
3680 9517 5.552870 AACTGGACAAGATCACTTAGTGT 57.447 39.130 12.41 0.00 34.70 3.55
3681 9518 5.552870 ACTGGACAAGATCACTTAGTGTT 57.447 39.130 12.41 3.76 34.70 3.32
3683 9520 7.246171 ACTGGACAAGATCACTTAGTGTTAT 57.754 36.000 12.41 0.00 34.70 1.89
3685 9522 7.039011 ACTGGACAAGATCACTTAGTGTTATGA 60.039 37.037 12.41 0.00 34.70 2.15
3686 9523 7.851228 TGGACAAGATCACTTAGTGTTATGAT 58.149 34.615 12.41 0.00 34.70 2.45
3687 9524 7.765819 TGGACAAGATCACTTAGTGTTATGATG 59.234 37.037 12.41 7.87 34.70 3.07
3688 9525 7.766278 GGACAAGATCACTTAGTGTTATGATGT 59.234 37.037 12.41 10.63 34.70 3.06
3689 9526 9.155975 GACAAGATCACTTAGTGTTATGATGTT 57.844 33.333 12.41 0.38 35.96 2.71
3690 9527 9.507329 ACAAGATCACTTAGTGTTATGATGTTT 57.493 29.630 12.41 0.00 34.01 2.83
3691 9528 9.979270 CAAGATCACTTAGTGTTATGATGTTTC 57.021 33.333 12.41 0.00 34.01 2.78
3756 9612 4.008074 TCTGGATCCGATATTCTTTGGC 57.992 45.455 7.39 0.00 0.00 4.52
3966 9834 3.179939 GGCGAAAGAGACGGCGTC 61.180 66.667 31.33 31.33 45.03 5.19
4020 9893 6.410942 TCTGTCACCATCCTATACATTCTG 57.589 41.667 0.00 0.00 0.00 3.02
4022 9895 6.384015 TCTGTCACCATCCTATACATTCTGTT 59.616 38.462 0.00 0.00 0.00 3.16
4023 9896 6.582636 TGTCACCATCCTATACATTCTGTTC 58.417 40.000 0.00 0.00 0.00 3.18
4036 9922 4.155826 ACATTCTGTTCTCTCTCTCTGACG 59.844 45.833 0.00 0.00 0.00 4.35
4096 9982 6.575244 TTCCATGGTTACTATGATGTTCCT 57.425 37.500 12.58 0.00 0.00 3.36
4119 10005 1.959985 AGGTATGGAGCTGATCGTCAG 59.040 52.381 0.00 9.73 46.90 3.51
4133 10019 3.165058 TCGTCAGGTATGTCAATCAGC 57.835 47.619 0.00 0.00 0.00 4.26
4176 10062 7.602644 TGTCTACATTACTGAAAATGGTGAGTC 59.397 37.037 10.58 0.00 40.48 3.36
4260 10149 5.651530 TCTAGTGTCTCCTAATTTGCTTCG 58.348 41.667 0.00 0.00 0.00 3.79
4454 10366 7.992608 TCATCATGCACATTACACTATTTACCT 59.007 33.333 0.00 0.00 0.00 3.08
4667 10604 2.350522 ACTCTGCATTCCGAATGTGTC 58.649 47.619 19.86 6.62 41.01 3.67
4691 10628 8.880750 GTCTACTGACCTGGATGTAAATTTAAC 58.119 37.037 0.00 0.00 37.24 2.01
4844 10974 3.149981 GCTTACAGGAAAGGAGCAAACT 58.850 45.455 0.00 0.00 33.68 2.66
4939 11069 7.087639 GGATTTATCACGTGGATTTTGAAACA 58.912 34.615 17.00 0.00 37.44 2.83
5086 11216 3.913799 TCCAGTTACCCCTGAAATGAGAA 59.086 43.478 0.00 0.00 34.23 2.87
5089 11219 5.823045 CCAGTTACCCCTGAAATGAGAATAC 59.177 44.000 0.00 0.00 34.23 1.89
5182 11315 5.793030 ATAGCGTCTTTGCCTAGTAGAAT 57.207 39.130 0.00 0.00 34.65 2.40
5247 11389 5.016831 GGAGGTTTTCATCACTTTGGGTAT 58.983 41.667 0.00 0.00 31.64 2.73
5271 11413 1.764134 AGGGTGTCGTGGACTTAACAA 59.236 47.619 0.00 0.00 33.15 2.83
5276 11418 2.215196 GTCGTGGACTTAACAAGGCAA 58.785 47.619 0.00 0.00 38.70 4.52
5352 11494 2.640184 GGGTTAATCGGGACAAAGGAG 58.360 52.381 0.00 0.00 0.00 3.69
5380 11522 0.547553 TTTATACTGGTTCGGCCCCC 59.452 55.000 0.00 0.00 36.04 5.40
5495 11641 1.868498 TGTTTCTTGAGTTAACCCGCG 59.132 47.619 0.00 0.00 0.00 6.46
5523 11669 4.657039 GGTCACCCCTTTATATACACAGGA 59.343 45.833 4.08 0.00 0.00 3.86
5553 11699 1.002502 GGCTTACAAAGTCCCGGCT 60.003 57.895 0.00 0.00 0.00 5.52
5611 11757 5.648092 ACTAAGCTTGCCTTACAATACAAGG 59.352 40.000 9.86 0.00 44.61 3.61
5734 11881 3.094498 GGTATGACCCGGCCCCTT 61.094 66.667 0.00 0.00 30.04 3.95
5811 11958 9.252962 GATTTGAACTTGTTCACATCAATCTTT 57.747 29.630 25.34 3.85 37.80 2.52
5877 12024 0.672401 CTGTAACCCGCCATGACGTT 60.672 55.000 0.00 0.00 0.00 3.99
5942 12089 0.036010 ATTTCACACGAGGCCCAGAG 60.036 55.000 0.00 0.00 0.00 3.35
5945 12092 1.215647 CACACGAGGCCCAGAGTAC 59.784 63.158 0.00 0.00 0.00 2.73
5997 12145 2.230992 CCGAAAATCAAGGCATCCACAA 59.769 45.455 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.277783 GACCATTGATTACATCTAGCAAATAGT 57.722 33.333 0.00 0.00 32.85 2.12
3 4 8.725148 GGACCATTGATTACATCTAGCAAATAG 58.275 37.037 0.00 0.00 0.00 1.73
4 5 8.439971 AGGACCATTGATTACATCTAGCAAATA 58.560 33.333 0.00 0.00 0.00 1.40
6 7 6.662755 AGGACCATTGATTACATCTAGCAAA 58.337 36.000 0.00 0.00 0.00 3.68
9 10 5.049129 GCAAGGACCATTGATTACATCTAGC 60.049 44.000 7.59 0.00 31.55 3.42
10 11 5.178252 CGCAAGGACCATTGATTACATCTAG 59.822 44.000 7.59 0.00 31.55 2.43
11 12 5.056480 CGCAAGGACCATTGATTACATCTA 58.944 41.667 7.59 0.00 31.55 1.98
12 13 3.879295 CGCAAGGACCATTGATTACATCT 59.121 43.478 7.59 0.00 31.55 2.90
13 14 4.214980 CGCAAGGACCATTGATTACATC 57.785 45.455 7.59 0.00 31.55 3.06
29 30 1.471119 TAGACCTGGAGTACCGCAAG 58.529 55.000 0.00 0.00 39.42 4.01
30 31 2.029623 GATAGACCTGGAGTACCGCAA 58.970 52.381 0.00 0.00 39.42 4.85
31 32 1.214673 AGATAGACCTGGAGTACCGCA 59.785 52.381 0.00 0.00 39.42 5.69
32 33 1.881324 GAGATAGACCTGGAGTACCGC 59.119 57.143 0.00 0.00 39.42 5.68
33 34 2.158652 TGGAGATAGACCTGGAGTACCG 60.159 54.545 0.00 0.00 39.42 4.02
34 35 3.117436 ACTGGAGATAGACCTGGAGTACC 60.117 52.174 0.00 0.00 0.00 3.34
35 36 4.173290 ACTGGAGATAGACCTGGAGTAC 57.827 50.000 0.00 0.00 0.00 2.73
36 37 4.883021 AACTGGAGATAGACCTGGAGTA 57.117 45.455 0.00 0.00 0.00 2.59
37 38 3.767309 AACTGGAGATAGACCTGGAGT 57.233 47.619 0.00 0.00 0.00 3.85
38 39 5.181748 CAAAAACTGGAGATAGACCTGGAG 58.818 45.833 0.00 0.00 0.00 3.86
39 40 4.565652 GCAAAAACTGGAGATAGACCTGGA 60.566 45.833 0.00 0.00 0.00 3.86
40 41 3.691609 GCAAAAACTGGAGATAGACCTGG 59.308 47.826 0.00 0.00 0.00 4.45
41 42 4.394300 CAGCAAAAACTGGAGATAGACCTG 59.606 45.833 0.00 0.00 33.85 4.00
42 43 4.583871 CAGCAAAAACTGGAGATAGACCT 58.416 43.478 0.00 0.00 33.85 3.85
43 44 3.127721 GCAGCAAAAACTGGAGATAGACC 59.872 47.826 0.00 0.00 38.16 3.85
44 45 3.753272 TGCAGCAAAAACTGGAGATAGAC 59.247 43.478 0.00 0.00 38.16 2.59
45 46 3.753272 GTGCAGCAAAAACTGGAGATAGA 59.247 43.478 0.00 0.00 38.81 1.98
46 47 3.119708 GGTGCAGCAAAAACTGGAGATAG 60.120 47.826 11.86 0.00 38.81 2.08
47 48 2.819608 GGTGCAGCAAAAACTGGAGATA 59.180 45.455 11.86 0.00 38.81 1.98
48 49 1.615392 GGTGCAGCAAAAACTGGAGAT 59.385 47.619 11.86 0.00 38.81 2.75
49 50 1.032014 GGTGCAGCAAAAACTGGAGA 58.968 50.000 11.86 0.00 38.81 3.71
50 51 0.032540 GGGTGCAGCAAAAACTGGAG 59.967 55.000 19.06 0.00 38.81 3.86
51 52 0.685785 TGGGTGCAGCAAAAACTGGA 60.686 50.000 19.06 0.00 38.16 3.86
52 53 0.530431 GTGGGTGCAGCAAAAACTGG 60.530 55.000 19.06 0.00 38.16 4.00
53 54 0.871163 CGTGGGTGCAGCAAAAACTG 60.871 55.000 19.06 3.64 40.80 3.16
54 55 1.034838 TCGTGGGTGCAGCAAAAACT 61.035 50.000 19.06 0.00 0.00 2.66
55 56 0.179124 TTCGTGGGTGCAGCAAAAAC 60.179 50.000 19.06 8.98 0.00 2.43
56 57 0.532573 TTTCGTGGGTGCAGCAAAAA 59.467 45.000 19.06 8.90 0.00 1.94
57 58 0.179124 GTTTCGTGGGTGCAGCAAAA 60.179 50.000 19.06 9.24 0.00 2.44
58 59 1.315981 TGTTTCGTGGGTGCAGCAAA 61.316 50.000 19.06 6.63 0.00 3.68
59 60 1.750780 TGTTTCGTGGGTGCAGCAA 60.751 52.632 19.06 2.65 0.00 3.91
60 61 2.124529 TGTTTCGTGGGTGCAGCA 60.125 55.556 19.06 0.00 0.00 4.41
61 62 2.186826 AGTGTTTCGTGGGTGCAGC 61.187 57.895 7.55 7.55 0.00 5.25
62 63 0.813610 TCAGTGTTTCGTGGGTGCAG 60.814 55.000 0.00 0.00 0.00 4.41
63 64 0.179032 ATCAGTGTTTCGTGGGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
64 65 0.517316 GATCAGTGTTTCGTGGGTGC 59.483 55.000 0.00 0.00 0.00 5.01
65 66 0.790207 CGATCAGTGTTTCGTGGGTG 59.210 55.000 9.20 0.00 0.00 4.61
66 67 0.320421 CCGATCAGTGTTTCGTGGGT 60.320 55.000 14.15 0.00 33.60 4.51
67 68 1.635663 GCCGATCAGTGTTTCGTGGG 61.636 60.000 14.15 4.13 33.60 4.61
75 76 0.108585 AACACCAAGCCGATCAGTGT 59.891 50.000 0.00 0.00 43.21 3.55
81 82 1.002134 CAGGGAACACCAAGCCGAT 60.002 57.895 0.00 0.00 43.89 4.18
82 83 2.429930 CAGGGAACACCAAGCCGA 59.570 61.111 0.00 0.00 43.89 5.54
83 84 2.672996 CCAGGGAACACCAAGCCG 60.673 66.667 0.00 0.00 43.89 5.52
89 90 3.070576 GCATGGCCAGGGAACACC 61.071 66.667 20.75 0.00 40.67 4.16
135 136 2.611751 CAACACTTGTTCGACCATGTCA 59.388 45.455 0.00 0.00 35.83 3.58
140 141 1.098712 GGGCAACACTTGTTCGACCA 61.099 55.000 10.04 0.00 35.83 4.02
146 147 1.101049 CAGGACGGGCAACACTTGTT 61.101 55.000 0.00 0.00 39.12 2.83
170 171 1.886585 GCAGAGGCGAGAACAGAGA 59.113 57.895 0.00 0.00 0.00 3.10
171 172 4.492955 GCAGAGGCGAGAACAGAG 57.507 61.111 0.00 0.00 0.00 3.35
223 239 3.240861 CGATAAGTTGTCGCTAGTTCTGC 59.759 47.826 9.15 0.00 31.85 4.26
258 316 6.428159 GGTTCATTATCTTATCGCCAGTGATT 59.572 38.462 0.00 0.00 0.00 2.57
262 320 4.038763 TCGGTTCATTATCTTATCGCCAGT 59.961 41.667 0.00 0.00 0.00 4.00
265 323 5.063564 GGAATCGGTTCATTATCTTATCGCC 59.936 44.000 11.19 0.00 36.01 5.54
476 548 3.311110 GGGTCGTGGCCTCACAGA 61.311 66.667 3.32 0.00 43.79 3.41
498 574 0.798776 CGAAAGCAACTTCGGCAGAT 59.201 50.000 7.49 0.00 43.51 2.90
609 688 1.493950 GATGCCCGTCGAATCAGCTG 61.494 60.000 7.63 7.63 0.00 4.24
743 824 3.810310 CCAAGCTTTGGTTGTTGGTTA 57.190 42.857 0.00 0.00 45.93 2.85
855 982 5.243060 CCTGTCACCACCGATCAGTATTATA 59.757 44.000 0.00 0.00 0.00 0.98
859 986 1.757118 CCTGTCACCACCGATCAGTAT 59.243 52.381 0.00 0.00 0.00 2.12
860 987 1.182667 CCTGTCACCACCGATCAGTA 58.817 55.000 0.00 0.00 0.00 2.74
862 989 0.390340 CACCTGTCACCACCGATCAG 60.390 60.000 0.00 0.00 0.00 2.90
864 991 0.389948 GTCACCTGTCACCACCGATC 60.390 60.000 0.00 0.00 0.00 3.69
871 1002 1.371558 GTCCCTGTCACCTGTCACC 59.628 63.158 0.00 0.00 0.00 4.02
934 1069 0.253327 CTGGTTCTTGTCTAGCCCCC 59.747 60.000 0.00 0.00 0.00 5.40
945 1080 1.831652 CGCCCTGGAGTCTGGTTCTT 61.832 60.000 0.00 0.00 0.00 2.52
975 1134 5.118286 TCCTCAAGGTAGCTAAGCTTAGCA 61.118 45.833 43.84 31.80 44.06 3.49
1089 1255 2.672996 GCGCCAAAGAGGAAGCCA 60.673 61.111 0.00 0.00 41.22 4.75
1092 1258 3.804193 GCGGCGCCAAAGAGGAAG 61.804 66.667 28.98 7.61 41.22 3.46
1251 1422 1.153349 GCCCTCGATCTGGAACCAC 60.153 63.158 3.53 0.00 0.00 4.16
1398 3867 4.580868 AGCTAAGCATCATGGATCATCAG 58.419 43.478 0.00 0.00 0.00 2.90
1399 3868 4.635699 AGCTAAGCATCATGGATCATCA 57.364 40.909 0.00 0.00 0.00 3.07
1400 3869 6.822170 TCATAAGCTAAGCATCATGGATCATC 59.178 38.462 0.00 0.00 0.00 2.92
1549 4029 3.877508 GTCTTGCTGATAATTTACGGCCT 59.122 43.478 0.00 0.00 37.57 5.19
1622 4122 4.279420 ACTCAAACCTGAATCTTTCAAGGC 59.721 41.667 0.00 0.00 39.58 4.35
1731 4235 7.672122 AGTTATATAAACTCGAGGGAAAGGT 57.328 36.000 18.41 0.00 0.00 3.50
1737 4241 8.202137 TCTTTCCAAGTTATATAAACTCGAGGG 58.798 37.037 18.41 3.25 0.00 4.30
1955 5556 4.262976 CACGGATAAAGCGCAAAAATTCTC 59.737 41.667 11.47 0.00 0.00 2.87
1981 5583 3.559655 TCACGACAGCAATTGCCATATAC 59.440 43.478 26.45 11.27 43.38 1.47
2003 5605 6.976934 ATTTTTGTGGTGTTAGTTGATCCT 57.023 33.333 0.00 0.00 0.00 3.24
2007 5627 6.531948 CGGAAAATTTTTGTGGTGTTAGTTGA 59.468 34.615 4.63 0.00 0.00 3.18
2017 5637 8.931385 ATATGAAGATCGGAAAATTTTTGTGG 57.069 30.769 4.63 0.00 0.00 4.17
2029 5649 9.920133 CTTCTTTCAGAATATATGAAGATCGGA 57.080 33.333 0.00 0.00 37.91 4.55
2030 5650 9.920133 TCTTCTTTCAGAATATATGAAGATCGG 57.080 33.333 0.00 0.00 37.91 4.18
2079 5735 9.804977 AGAGCAAAGAAGCTATTTGGAATATAT 57.195 29.630 20.10 0.00 46.75 0.86
2080 5736 9.277783 GAGAGCAAAGAAGCTATTTGGAATATA 57.722 33.333 20.10 0.00 46.75 0.86
2081 5737 7.776969 TGAGAGCAAAGAAGCTATTTGGAATAT 59.223 33.333 20.10 0.00 46.75 1.28
2084 5752 5.316167 TGAGAGCAAAGAAGCTATTTGGAA 58.684 37.500 20.10 0.00 46.75 3.53
2086 5754 5.633830 TTGAGAGCAAAGAAGCTATTTGG 57.366 39.130 20.10 3.90 46.75 3.28
2091 5759 6.639632 AACATTTTGAGAGCAAAGAAGCTA 57.360 33.333 0.00 0.00 46.75 3.32
2223 5891 8.691797 TGCATAATCACATGACAAGTACTAGTA 58.308 33.333 0.00 0.00 0.00 1.82
2284 5971 2.030805 GCTCAACAACAAGGTGATGTCC 60.031 50.000 0.00 0.00 44.51 4.02
2289 5976 1.211703 TCCTGCTCAACAACAAGGTGA 59.788 47.619 0.00 0.00 43.06 4.02
2290 5977 1.679139 TCCTGCTCAACAACAAGGTG 58.321 50.000 0.00 0.00 35.78 4.00
2471 6170 3.771160 CAAGCCGGCCTCCTACGT 61.771 66.667 26.15 0.00 0.00 3.57
2511 6210 0.242825 TCAGGTGGTCGTAGAAAGCG 59.757 55.000 0.00 0.00 39.69 4.68
2586 6285 2.757868 AGCTAGAGTTGAATCTGCTCGT 59.242 45.455 0.00 0.00 32.05 4.18
2634 6337 3.573598 TGACATTTTTGGCAGCAATACG 58.426 40.909 0.00 0.00 0.00 3.06
2635 6338 4.143052 GCTTGACATTTTTGGCAGCAATAC 60.143 41.667 0.00 0.00 0.00 1.89
2636 6339 3.995705 GCTTGACATTTTTGGCAGCAATA 59.004 39.130 0.00 0.00 0.00 1.90
2637 6340 2.809696 GCTTGACATTTTTGGCAGCAAT 59.190 40.909 0.00 0.00 0.00 3.56
2638 6341 2.211806 GCTTGACATTTTTGGCAGCAA 58.788 42.857 0.00 0.00 0.00 3.91
2786 6503 7.064728 GCTAATAGTAAAAGTCAAGTCACAGGG 59.935 40.741 0.00 0.00 0.00 4.45
2797 6514 5.292834 GGGAACGTGGCTAATAGTAAAAGTC 59.707 44.000 0.00 0.00 0.00 3.01
2798 6515 5.181009 GGGAACGTGGCTAATAGTAAAAGT 58.819 41.667 0.00 0.00 0.00 2.66
2846 6564 3.181484 TGCATGCACATTCCTGATTTAGC 60.181 43.478 18.46 0.00 0.00 3.09
2863 6581 1.215244 CAGTAGGAGTCGCATGCATG 58.785 55.000 22.70 22.70 0.00 4.06
2864 6582 0.105593 CCAGTAGGAGTCGCATGCAT 59.894 55.000 19.57 2.11 36.89 3.96
3240 8340 1.997606 ACACGCATTAGAACGGCTAAC 59.002 47.619 2.65 0.00 41.64 2.34
3268 8369 0.456653 GCCTTGCGTTGCCTAACATG 60.457 55.000 0.00 0.00 36.58 3.21
3270 8371 3.350377 GCCTTGCGTTGCCTAACA 58.650 55.556 0.00 0.00 36.58 2.41
3415 8523 4.033358 GTCTCATATTTCTCGTTGCACAGG 59.967 45.833 0.00 0.00 0.00 4.00
3425 8533 5.871524 TGCTGTGAACAGTCTCATATTTCTC 59.128 40.000 11.87 0.00 45.45 2.87
3438 8579 2.884012 TGGGTAATGTTGCTGTGAACAG 59.116 45.455 6.08 6.08 46.40 3.16
3447 8588 3.907894 TCTTTTCGTGGGTAATGTTGC 57.092 42.857 0.00 0.00 0.00 4.17
3452 8593 6.642707 TTTCACATTCTTTTCGTGGGTAAT 57.357 33.333 0.00 0.00 0.00 1.89
3461 9297 9.353999 ACACTAACAGTTTTTCACATTCTTTTC 57.646 29.630 0.00 0.00 0.00 2.29
3466 9302 9.944663 TCATAACACTAACAGTTTTTCACATTC 57.055 29.630 0.00 0.00 0.00 2.67
3470 9306 9.730420 AACATCATAACACTAACAGTTTTTCAC 57.270 29.630 0.00 0.00 0.00 3.18
3505 9342 3.319689 CGGTAAGCCTCCTTTTCCAAAAA 59.680 43.478 0.00 0.00 32.47 1.94
3506 9343 2.888414 CGGTAAGCCTCCTTTTCCAAAA 59.112 45.455 0.00 0.00 32.47 2.44
3508 9345 1.884928 GCGGTAAGCCTCCTTTTCCAA 60.885 52.381 0.00 0.00 40.81 3.53
3510 9347 2.478989 GCGGTAAGCCTCCTTTTCC 58.521 57.895 0.00 0.00 40.81 3.13
3526 9363 1.097547 ATCTTTTGGATGCCGAGGCG 61.098 55.000 9.78 0.00 45.51 5.52
3527 9364 0.383231 CATCTTTTGGATGCCGAGGC 59.617 55.000 7.26 7.26 44.21 4.70
3545 9382 9.964303 CACTTTTTAATAATATGGCTACATGCA 57.036 29.630 0.00 0.00 45.15 3.96
3546 9383 9.965824 ACACTTTTTAATAATATGGCTACATGC 57.034 29.630 0.00 0.00 37.97 4.06
3570 9407 9.871238 GGATCTAAGACTATGTTTTAGTTCACA 57.129 33.333 14.93 0.00 33.98 3.58
3578 9415 7.982354 GCTGTACTGGATCTAAGACTATGTTTT 59.018 37.037 1.65 0.00 0.00 2.43
3579 9416 7.343316 AGCTGTACTGGATCTAAGACTATGTTT 59.657 37.037 1.65 0.00 0.00 2.83
3580 9417 6.836527 AGCTGTACTGGATCTAAGACTATGTT 59.163 38.462 1.65 0.00 0.00 2.71
3581 9418 6.264292 CAGCTGTACTGGATCTAAGACTATGT 59.736 42.308 5.25 0.00 43.19 2.29
3583 9420 6.892658 CAGCTGTACTGGATCTAAGACTAT 57.107 41.667 5.25 0.00 43.19 2.12
3596 9433 0.602638 TCCGTTTGCCAGCTGTACTG 60.603 55.000 13.81 0.00 46.77 2.74
3597 9434 0.320771 CTCCGTTTGCCAGCTGTACT 60.321 55.000 13.81 0.00 0.00 2.73
3598 9435 1.912371 GCTCCGTTTGCCAGCTGTAC 61.912 60.000 13.81 4.91 0.00 2.90
3599 9436 1.671054 GCTCCGTTTGCCAGCTGTA 60.671 57.895 13.81 0.00 0.00 2.74
3603 9440 0.529555 TTTTTGCTCCGTTTGCCAGC 60.530 50.000 0.00 0.00 0.00 4.85
3604 9441 3.657956 TTTTTGCTCCGTTTGCCAG 57.342 47.368 0.00 0.00 0.00 4.85
3620 9457 9.171877 TGTGGCAATGAGTTTTTATTTCTTTTT 57.828 25.926 0.00 0.00 0.00 1.94
3622 9459 8.611757 GTTGTGGCAATGAGTTTTTATTTCTTT 58.388 29.630 0.00 0.00 0.00 2.52
3624 9461 6.705825 GGTTGTGGCAATGAGTTTTTATTTCT 59.294 34.615 0.00 0.00 0.00 2.52
3625 9462 6.346518 CGGTTGTGGCAATGAGTTTTTATTTC 60.347 38.462 0.00 0.00 0.00 2.17
3626 9463 5.465056 CGGTTGTGGCAATGAGTTTTTATTT 59.535 36.000 0.00 0.00 0.00 1.40
3627 9464 4.987912 CGGTTGTGGCAATGAGTTTTTATT 59.012 37.500 0.00 0.00 0.00 1.40
3628 9465 4.555262 CGGTTGTGGCAATGAGTTTTTAT 58.445 39.130 0.00 0.00 0.00 1.40
3630 9467 2.482839 CCGGTTGTGGCAATGAGTTTTT 60.483 45.455 0.00 0.00 0.00 1.94
3631 9468 1.068434 CCGGTTGTGGCAATGAGTTTT 59.932 47.619 0.00 0.00 0.00 2.43
3633 9470 2.340427 CCGGTTGTGGCAATGAGTT 58.660 52.632 0.00 0.00 0.00 3.01
3642 9479 0.035439 AGTTATCCTGCCGGTTGTGG 60.035 55.000 1.90 0.11 0.00 4.17
3643 9480 1.086696 CAGTTATCCTGCCGGTTGTG 58.913 55.000 1.90 0.00 33.59 3.33
3644 9481 0.035439 CCAGTTATCCTGCCGGTTGT 60.035 55.000 1.90 0.00 40.06 3.32
3645 9482 0.251916 TCCAGTTATCCTGCCGGTTG 59.748 55.000 1.90 0.00 40.06 3.77
3646 9483 0.252197 GTCCAGTTATCCTGCCGGTT 59.748 55.000 1.90 0.00 40.06 4.44
3647 9484 0.907704 TGTCCAGTTATCCTGCCGGT 60.908 55.000 1.90 0.00 40.06 5.28
3648 9485 0.251916 TTGTCCAGTTATCCTGCCGG 59.748 55.000 0.00 0.00 40.06 6.13
3649 9486 1.207089 TCTTGTCCAGTTATCCTGCCG 59.793 52.381 0.00 0.00 40.06 5.69
3650 9487 3.118261 TGATCTTGTCCAGTTATCCTGCC 60.118 47.826 0.00 0.00 40.06 4.85
3651 9488 3.873952 GTGATCTTGTCCAGTTATCCTGC 59.126 47.826 0.00 0.00 40.06 4.85
3652 9489 5.350504 AGTGATCTTGTCCAGTTATCCTG 57.649 43.478 0.00 0.00 41.15 3.86
3654 9491 6.758886 CACTAAGTGATCTTGTCCAGTTATCC 59.241 42.308 0.00 0.00 35.23 2.59
3656 9493 7.246171 ACACTAAGTGATCTTGTCCAGTTAT 57.754 36.000 0.00 0.00 36.96 1.89
3658 9495 5.552870 ACACTAAGTGATCTTGTCCAGTT 57.447 39.130 0.00 0.00 36.96 3.16
3659 9496 5.552870 AACACTAAGTGATCTTGTCCAGT 57.447 39.130 0.00 0.00 36.96 4.00
3660 9497 7.323420 TCATAACACTAAGTGATCTTGTCCAG 58.677 38.462 0.00 0.00 36.96 3.86
3661 9498 7.239763 TCATAACACTAAGTGATCTTGTCCA 57.760 36.000 0.00 0.00 36.96 4.02
3662 9499 7.766278 ACATCATAACACTAAGTGATCTTGTCC 59.234 37.037 0.00 0.00 36.96 4.02
3663 9500 8.709386 ACATCATAACACTAAGTGATCTTGTC 57.291 34.615 0.00 0.00 36.96 3.18
3664 9501 9.507329 AAACATCATAACACTAAGTGATCTTGT 57.493 29.630 0.00 0.00 36.96 3.16
3665 9502 9.979270 GAAACATCATAACACTAAGTGATCTTG 57.021 33.333 0.00 0.00 36.96 3.02
3683 9520 9.399797 AGAATCAGCATAACATTAGAAACATCA 57.600 29.630 0.00 0.00 0.00 3.07
3756 9612 2.223829 ACGCATTTCTCTGGGATAGTCG 60.224 50.000 0.00 0.00 33.60 4.18
3810 9666 2.725637 AGTAACCTCTTCTCCTCCGAC 58.274 52.381 0.00 0.00 0.00 4.79
3813 9669 4.857679 TCTGTAGTAACCTCTTCTCCTCC 58.142 47.826 0.00 0.00 0.00 4.30
3966 9834 3.334691 TCTTACTGGTCTTCCAATTGCG 58.665 45.455 0.00 0.00 43.81 4.85
4020 9893 3.665848 CGAACACGTCAGAGAGAGAGAAC 60.666 52.174 0.00 0.00 0.00 3.01
4022 9895 2.070028 CGAACACGTCAGAGAGAGAGA 58.930 52.381 0.00 0.00 0.00 3.10
4023 9896 1.801771 ACGAACACGTCAGAGAGAGAG 59.198 52.381 0.00 0.00 35.22 3.20
4036 9922 7.347508 GGTTGATCACCATATATACGAACAC 57.652 40.000 0.00 0.00 46.42 3.32
4096 9982 2.362397 GACGATCAGCTCCATACCTTCA 59.638 50.000 0.00 0.00 0.00 3.02
4119 10005 5.289595 TCTTGTATCGCTGATTGACATACC 58.710 41.667 0.00 0.00 0.00 2.73
4133 10019 1.654105 GACAGGCGTGTTCTTGTATCG 59.346 52.381 14.12 0.00 36.88 2.92
4176 10062 2.125912 CCTGACGACCCTCTTGCG 60.126 66.667 0.00 0.00 0.00 4.85
4188 10074 3.503363 TGAATGCACTGTGAATTCCTGAC 59.497 43.478 29.70 12.79 30.75 3.51
4260 10149 6.515272 ACACATGGTCATTGAAAACCTATC 57.485 37.500 0.00 0.00 36.47 2.08
4598 10534 9.809096 TTCAATTTTCATTTTTACTAGTGCACA 57.191 25.926 21.04 4.13 0.00 4.57
4667 10604 9.099454 GAGTTAAATTTACATCCAGGTCAGTAG 57.901 37.037 0.00 0.00 0.00 2.57
4786 10916 6.034256 CCGGTATACGTTGTGTTAGAAAAGAG 59.966 42.308 0.00 0.00 42.24 2.85
4844 10974 1.155889 CACACGAAGTAGCCATGCAA 58.844 50.000 0.00 0.00 41.61 4.08
4939 11069 3.906846 ACATCTTTGGAGTCCTCTCTTGT 59.093 43.478 11.33 6.30 40.29 3.16
5115 11245 8.648557 TGTTTAGCAAACTAGCAGTATCTATG 57.351 34.615 11.34 0.00 41.90 2.23
5182 11315 6.177610 CCTTTACAGCACCCTAGATTTACAA 58.822 40.000 0.00 0.00 0.00 2.41
5222 11355 3.005791 CCCAAAGTGATGAAAACCTCCAC 59.994 47.826 0.00 0.00 0.00 4.02
5231 11372 4.569653 CCCTCCAATACCCAAAGTGATGAA 60.570 45.833 0.00 0.00 0.00 2.57
5247 11389 1.052124 AAGTCCACGACACCCTCCAA 61.052 55.000 0.00 0.00 34.60 3.53
5271 11413 2.359900 CTTTCGCTAGGACATTTGCCT 58.640 47.619 0.00 0.00 39.56 4.75
5352 11494 5.163884 GCCGAACCAGTATAAACTTTCTGTC 60.164 44.000 0.00 0.00 31.97 3.51
5380 11522 0.175073 AAGCCTTTACCTCGCTACGG 59.825 55.000 0.00 0.00 31.12 4.02
5543 11689 1.689233 TATGAGCCAGCCGGGACTT 60.689 57.895 2.18 0.00 40.01 3.01
5611 11757 2.806244 GGATGAACCGCCATATGTGTAC 59.194 50.000 1.24 0.00 0.00 2.90
5877 12024 6.455647 CGGGTTAATATGATTCTGTGAGCTA 58.544 40.000 0.00 0.00 0.00 3.32
5997 12145 1.406539 GCCGAAATCATCATGTGGCTT 59.593 47.619 0.00 0.00 38.00 4.35


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

AutoCloner maintained by Alex Coulton.