Multiple sequence alignment - TraesCS5A01G526700

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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 TraesCS5A01G526700 chr5A 100.000 2006 0 0 837 2842 687479723 687477718 0.000000e+00 3705.0
1 TraesCS5A01G526700 chr5A 89.399 981 88 6 1857 2833 150664036 150665004 0.000000e+00 1221.0
2 TraesCS5A01G526700 chr5A 100.000 423 0 0 1 423 687480559 687480137 0.000000e+00 782.0
3 TraesCS5A01G526700 chr5A 91.892 555 43 1 1857 2409 296719845 296719291 0.000000e+00 774.0
4 TraesCS5A01G526700 chr5A 91.758 546 42 2 1857 2400 154824652 154824108 0.000000e+00 756.0
5 TraesCS5A01G526700 chr5A 90.676 547 47 3 1857 2400 326921732 326921187 0.000000e+00 725.0
6 TraesCS5A01G526700 chr5A 94.349 407 22 1 2428 2834 446961340 446961745 8.650000e-175 623.0
7 TraesCS5A01G526700 chr5A 91.139 79 4 3 74 151 552157843 552157767 1.390000e-18 104.0
8 TraesCS5A01G526700 chr6A 96.086 1022 38 2 837 1858 581498121 581499140 0.000000e+00 1664.0
9 TraesCS5A01G526700 chr6A 93.333 555 34 3 1857 2409 242007884 242007331 0.000000e+00 817.0
10 TraesCS5A01G526700 chr6A 93.590 546 31 4 1857 2400 255041546 255042089 0.000000e+00 811.0
11 TraesCS5A01G526700 chr6A 92.432 555 33 4 1857 2409 201455902 201456449 0.000000e+00 784.0
12 TraesCS5A01G526700 chr6A 92.194 474 34 2 1929 2400 249837830 249837358 0.000000e+00 667.0
13 TraesCS5A01G526700 chr6A 90.667 75 5 2 73 146 208152075 208152148 6.480000e-17 99.0
14 TraesCS5A01G526700 chr6A 90.541 74 7 0 73 146 497935531 497935458 6.480000e-17 99.0
15 TraesCS5A01G526700 chr6A 89.333 75 8 0 73 147 329832392 329832466 8.380000e-16 95.3
16 TraesCS5A01G526700 chr6A 95.745 47 2 0 837 883 347321566 347321612 3.040000e-10 76.8
17 TraesCS5A01G526700 chr4A 95.303 1022 45 3 837 1858 440521861 440522879 0.000000e+00 1618.0
18 TraesCS5A01G526700 chr4A 93.407 546 32 3 1857 2400 505730843 505731386 0.000000e+00 806.0
19 TraesCS5A01G526700 chr4A 79.221 154 28 3 1 151 599019669 599019821 1.390000e-18 104.0
20 TraesCS5A01G526700 chr4A 89.474 76 8 0 73 148 479227269 479227194 2.330000e-16 97.1
21 TraesCS5A01G526700 chr2A 89.798 1039 70 19 837 1858 329629297 329630316 0.000000e+00 1299.0
22 TraesCS5A01G526700 chr2A 89.184 980 86 8 1862 2833 615854819 615855786 0.000000e+00 1205.0
23 TraesCS5A01G526700 chr2A 92.432 555 37 4 1857 2409 490884338 490883787 0.000000e+00 787.0
24 TraesCS5A01G526700 chr2A 92.072 555 41 2 1857 2409 380535510 380534957 0.000000e+00 778.0
25 TraesCS5A01G526700 chr2A 90.395 583 49 2 1857 2437 322679970 322679393 0.000000e+00 760.0
26 TraesCS5A01G526700 chr2A 82.270 141 21 3 10 147 628568157 628568018 4.970000e-23 119.0
27 TraesCS5A01G526700 chr7A 89.308 982 88 5 1857 2834 236633710 236632742 0.000000e+00 1216.0
28 TraesCS5A01G526700 chr7A 96.117 412 16 0 2425 2836 589074570 589074159 0.000000e+00 673.0
29 TraesCS5A01G526700 chr7A 95.355 409 19 0 2428 2836 325896715 325896307 0.000000e+00 651.0
30 TraesCS5A01G526700 chr7A 98.675 151 1 1 1 151 680374972 680375121 1.680000e-67 267.0
31 TraesCS5A01G526700 chr7A 89.744 78 6 2 70 146 586200034 586200110 6.480000e-17 99.0
32 TraesCS5A01G526700 chr3A 92.280 557 37 5 1857 2409 506522298 506521744 0.000000e+00 785.0
33 TraesCS5A01G526700 chr3A 89.964 548 46 5 1857 2400 335017509 335016967 0.000000e+00 699.0
34 TraesCS5A01G526700 chr3A 94.335 406 23 0 2428 2833 595673225 595673630 8.650000e-175 623.0
35 TraesCS5A01G526700 chr3A 94.132 409 24 0 2425 2833 641659324 641659732 8.650000e-175 623.0
36 TraesCS5A01G526700 chr3A 94.363 408 19 4 2428 2833 657521878 657522283 8.650000e-175 623.0
37 TraesCS5A01G526700 chr3A 82.000 150 24 3 2 151 7554536 7554390 1.070000e-24 124.0
38 TraesCS5A01G526700 chr3A 82.734 139 21 2 10 146 144466411 144466274 1.380000e-23 121.0
39 TraesCS5A01G526700 chr3A 92.188 64 5 0 139 202 53828695 53828632 1.080000e-14 91.6
40 TraesCS5A01G526700 chr1A 90.476 546 46 5 1857 2400 289174293 289173752 0.000000e+00 715.0
41 TraesCS5A01G526700 chr1A 89.744 78 8 0 73 150 228962972 228962895 1.800000e-17 100.0
42 TraesCS5A01G526700 chr1A 98.214 56 0 1 96 151 414782861 414782807 2.330000e-16 97.1
43 TraesCS5A01G526700 chr1A 89.333 75 8 0 69 143 465276151 465276225 8.380000e-16 95.3
44 TraesCS5A01G526700 chr1A 88.000 75 7 2 72 145 587058508 587058435 1.400000e-13 87.9
45 TraesCS5A01G526700 chr4B 98.611 144 2 0 1 144 260125472 260125615 3.630000e-64 255.0
46 TraesCS5A01G526700 chr4B 91.139 79 4 3 74 151 540473281 540473205 1.390000e-18 104.0
47 TraesCS5A01G526700 chr3B 82.895 152 24 2 1 151 66862571 66862721 4.940000e-28 135.0
48 TraesCS5A01G526700 chr6B 81.818 154 24 3 1 151 658720928 658720776 2.970000e-25 126.0
49 TraesCS5A01G526700 chr6B 92.857 70 4 1 70 138 34227409 34227340 1.800000e-17 100.0
50 TraesCS5A01G526700 chr6B 89.873 79 7 1 73 151 83588509 83588586 1.800000e-17 100.0
51 TraesCS5A01G526700 chr5B 82.143 140 22 2 5 141 188612066 188611927 1.790000e-22 117.0
52 TraesCS5A01G526700 chr5B 91.139 79 6 1 73 151 589366561 589366638 3.870000e-19 106.0
53 TraesCS5A01G526700 chr1B 90.361 83 7 1 69 151 458719417 458719498 1.080000e-19 108.0
54 TraesCS5A01G526700 chr1B 88.095 84 7 3 69 151 619576432 619576513 2.330000e-16 97.1
55 TraesCS5A01G526700 chr1B 91.429 70 5 1 70 138 498018382 498018313 8.380000e-16 95.3
56 TraesCS5A01G526700 chr7B 89.873 79 7 1 73 151 720134930 720134853 1.800000e-17 100.0
57 TraesCS5A01G526700 chr7B 88.889 63 4 3 149 210 937470 937530 1.090000e-09 75.0
58 TraesCS5A01G526700 chr1D 98.214 56 0 1 96 151 338693307 338693253 2.330000e-16 97.1
59 TraesCS5A01G526700 chr1D 88.312 77 7 2 73 147 87774856 87774932 1.080000e-14 91.6
60 TraesCS5A01G526700 chr1D 96.429 56 1 1 96 151 360266174 360266120 1.080000e-14 91.6
61 TraesCS5A01G526700 chr1D 87.671 73 7 2 73 144 400179348 400179277 1.810000e-12 84.2
62 TraesCS5A01G526700 chrUn 88.750 80 6 3 73 151 345390819 345390742 8.380000e-16 95.3
63 TraesCS5A01G526700 chrUn 87.500 80 7 3 73 151 68023136 68023213 3.900000e-14 89.8
64 TraesCS5A01G526700 chrUn 92.188 64 3 2 92 155 117165693 117165632 3.900000e-14 89.8
65 TraesCS5A01G526700 chrUn 96.154 52 2 0 96 147 17822509 17822458 5.040000e-13 86.1
66 TraesCS5A01G526700 chrUn 93.103 58 2 2 95 151 134952976 134953032 1.810000e-12 84.2
67 TraesCS5A01G526700 chrUn 93.103 58 2 2 95 151 134956476 134956532 1.810000e-12 84.2
68 TraesCS5A01G526700 chrUn 93.103 58 2 2 95 151 152545802 152545858 1.810000e-12 84.2
69 TraesCS5A01G526700 chrUn 93.103 58 2 2 95 151 152550340 152550396 1.810000e-12 84.2
70 TraesCS5A01G526700 chrUn 93.103 58 2 2 95 151 303760415 303760471 1.810000e-12 84.2
71 TraesCS5A01G526700 chr6D 88.608 79 8 1 73 151 315841781 315841858 8.380000e-16 95.3
72 TraesCS5A01G526700 chr5D 81.319 91 9 3 1756 1844 555648023 555647939 1.830000e-07 67.6
73 TraesCS5A01G526700 chr5D 100.000 30 0 0 1733 1762 555648075 555648046 3.960000e-04 56.5
74 TraesCS5A01G526700 chr5D 100.000 28 0 0 1756 1783 556053216 556053189 5.000000e-03 52.8


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 TraesCS5A01G526700 chr5A 687477718 687480559 2841 True 2243.5 3705 100.000 1 2842 2 chr5A.!!$R5 2841
1 TraesCS5A01G526700 chr5A 150664036 150665004 968 False 1221.0 1221 89.399 1857 2833 1 chr5A.!!$F1 976
2 TraesCS5A01G526700 chr5A 296719291 296719845 554 True 774.0 774 91.892 1857 2409 1 chr5A.!!$R2 552
3 TraesCS5A01G526700 chr5A 154824108 154824652 544 True 756.0 756 91.758 1857 2400 1 chr5A.!!$R1 543
4 TraesCS5A01G526700 chr5A 326921187 326921732 545 True 725.0 725 90.676 1857 2400 1 chr5A.!!$R3 543
5 TraesCS5A01G526700 chr6A 581498121 581499140 1019 False 1664.0 1664 96.086 837 1858 1 chr6A.!!$F6 1021
6 TraesCS5A01G526700 chr6A 242007331 242007884 553 True 817.0 817 93.333 1857 2409 1 chr6A.!!$R1 552
7 TraesCS5A01G526700 chr6A 255041546 255042089 543 False 811.0 811 93.590 1857 2400 1 chr6A.!!$F3 543
8 TraesCS5A01G526700 chr6A 201455902 201456449 547 False 784.0 784 92.432 1857 2409 1 chr6A.!!$F1 552
9 TraesCS5A01G526700 chr4A 440521861 440522879 1018 False 1618.0 1618 95.303 837 1858 1 chr4A.!!$F1 1021
10 TraesCS5A01G526700 chr4A 505730843 505731386 543 False 806.0 806 93.407 1857 2400 1 chr4A.!!$F2 543
11 TraesCS5A01G526700 chr2A 329629297 329630316 1019 False 1299.0 1299 89.798 837 1858 1 chr2A.!!$F1 1021
12 TraesCS5A01G526700 chr2A 615854819 615855786 967 False 1205.0 1205 89.184 1862 2833 1 chr2A.!!$F2 971
13 TraesCS5A01G526700 chr2A 490883787 490884338 551 True 787.0 787 92.432 1857 2409 1 chr2A.!!$R3 552
14 TraesCS5A01G526700 chr2A 380534957 380535510 553 True 778.0 778 92.072 1857 2409 1 chr2A.!!$R2 552
15 TraesCS5A01G526700 chr2A 322679393 322679970 577 True 760.0 760 90.395 1857 2437 1 chr2A.!!$R1 580
16 TraesCS5A01G526700 chr7A 236632742 236633710 968 True 1216.0 1216 89.308 1857 2834 1 chr7A.!!$R1 977
17 TraesCS5A01G526700 chr3A 506521744 506522298 554 True 785.0 785 92.280 1857 2409 1 chr3A.!!$R5 552
18 TraesCS5A01G526700 chr3A 335016967 335017509 542 True 699.0 699 89.964 1857 2400 1 chr3A.!!$R4 543
19 TraesCS5A01G526700 chr1A 289173752 289174293 541 True 715.0 715 90.476 1857 2400 1 chr1A.!!$R2 543

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
21 22 0.036306 CTGCTCACGGGTTAAAGGGT 59.964 55.0 0.00 0.0 0.00 4.34 F
252 253 0.106708 ACTGAACTGCGCCTGAAAGA 59.893 50.0 4.18 0.0 34.07 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 1070 1.289380 GTGAACGACGGAGGAGCTT 59.711 57.895 0.0 0.0 0.0 3.74 R
2042 2070 0.378257 CGTCGGAATGAGGCAAATGG 59.622 55.000 0.0 0.0 0.0 3.16 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
17 18 4.390048 GGCTGCTCACGGGTTAAA 57.610 55.556 0.00 0.00 0.00 1.52
18 19 2.171635 GGCTGCTCACGGGTTAAAG 58.828 57.895 0.00 0.00 0.00 1.85
19 20 1.305930 GGCTGCTCACGGGTTAAAGG 61.306 60.000 0.00 0.00 0.00 3.11
20 21 1.305930 GCTGCTCACGGGTTAAAGGG 61.306 60.000 0.00 0.00 0.00 3.95
21 22 0.036306 CTGCTCACGGGTTAAAGGGT 59.964 55.000 0.00 0.00 0.00 4.34
22 23 0.475044 TGCTCACGGGTTAAAGGGTT 59.525 50.000 0.00 0.00 0.00 4.11
23 24 1.162698 GCTCACGGGTTAAAGGGTTC 58.837 55.000 0.00 0.00 0.00 3.62
24 25 1.271217 GCTCACGGGTTAAAGGGTTCT 60.271 52.381 0.00 0.00 0.00 3.01
25 26 2.423577 CTCACGGGTTAAAGGGTTCTG 58.576 52.381 0.00 0.00 0.00 3.02
26 27 0.879090 CACGGGTTAAAGGGTTCTGC 59.121 55.000 0.00 0.00 0.00 4.26
27 28 0.251033 ACGGGTTAAAGGGTTCTGCC 60.251 55.000 0.00 0.00 0.00 4.85
36 37 2.029964 GGTTCTGCCCACGTTCGA 59.970 61.111 0.00 0.00 0.00 3.71
37 38 1.375523 GGTTCTGCCCACGTTCGAT 60.376 57.895 0.00 0.00 0.00 3.59
38 39 0.108520 GGTTCTGCCCACGTTCGATA 60.109 55.000 0.00 0.00 0.00 2.92
39 40 1.278238 GTTCTGCCCACGTTCGATAG 58.722 55.000 0.00 0.00 0.00 2.08
40 41 0.174845 TTCTGCCCACGTTCGATAGG 59.825 55.000 0.00 0.00 0.00 2.57
41 42 1.883084 CTGCCCACGTTCGATAGGC 60.883 63.158 14.11 14.11 44.13 3.93
42 43 2.588034 GCCCACGTTCGATAGGCC 60.588 66.667 0.00 0.00 37.66 5.19
43 44 2.897207 CCCACGTTCGATAGGCCA 59.103 61.111 5.01 0.00 0.00 5.36
44 45 1.227263 CCCACGTTCGATAGGCCAG 60.227 63.158 5.01 0.00 0.00 4.85
45 46 1.883084 CCACGTTCGATAGGCCAGC 60.883 63.158 5.01 0.00 0.00 4.85
46 47 1.153647 CACGTTCGATAGGCCAGCA 60.154 57.895 5.01 0.00 0.00 4.41
47 48 1.153628 ACGTTCGATAGGCCAGCAC 60.154 57.895 5.01 0.00 0.00 4.40
48 49 1.883084 CGTTCGATAGGCCAGCACC 60.883 63.158 5.01 0.00 0.00 5.01
49 50 1.522569 GTTCGATAGGCCAGCACCT 59.477 57.895 5.01 0.00 44.31 4.00
50 51 0.811616 GTTCGATAGGCCAGCACCTG 60.812 60.000 5.01 0.00 41.34 4.00
58 59 4.601794 CCAGCACCTGGTTGCCCA 62.602 66.667 14.77 0.00 45.82 5.36
67 68 2.150449 TGGTTGCCCAGCTTCTACA 58.850 52.632 0.00 0.00 35.17 2.74
68 69 0.698238 TGGTTGCCCAGCTTCTACAT 59.302 50.000 0.00 0.00 35.17 2.29
69 70 1.075374 TGGTTGCCCAGCTTCTACATT 59.925 47.619 0.00 0.00 35.17 2.71
70 71 2.171003 GGTTGCCCAGCTTCTACATTT 58.829 47.619 0.00 0.00 0.00 2.32
71 72 2.094545 GGTTGCCCAGCTTCTACATTTG 60.095 50.000 0.00 0.00 0.00 2.32
72 73 1.838112 TGCCCAGCTTCTACATTTGG 58.162 50.000 0.00 0.00 0.00 3.28
74 75 1.767759 CCCAGCTTCTACATTTGGGG 58.232 55.000 0.00 0.00 43.84 4.96
75 76 1.284785 CCCAGCTTCTACATTTGGGGA 59.715 52.381 0.00 0.00 43.84 4.81
76 77 2.369394 CCAGCTTCTACATTTGGGGAC 58.631 52.381 0.00 0.00 0.00 4.46
77 78 2.290896 CCAGCTTCTACATTTGGGGACA 60.291 50.000 0.00 0.00 39.83 4.02
78 79 2.749621 CAGCTTCTACATTTGGGGACAC 59.250 50.000 0.00 0.00 42.67 3.67
79 80 1.737793 GCTTCTACATTTGGGGACACG 59.262 52.381 0.00 0.00 42.67 4.49
80 81 2.874457 GCTTCTACATTTGGGGACACGT 60.874 50.000 0.00 0.00 42.67 4.49
81 82 2.465860 TCTACATTTGGGGACACGTG 57.534 50.000 15.48 15.48 42.67 4.49
82 83 1.972075 TCTACATTTGGGGACACGTGA 59.028 47.619 25.01 0.00 42.67 4.35
83 84 2.369203 TCTACATTTGGGGACACGTGAA 59.631 45.455 25.01 4.89 42.67 3.18
84 85 1.604604 ACATTTGGGGACACGTGAAG 58.395 50.000 25.01 0.00 42.67 3.02
85 86 1.142060 ACATTTGGGGACACGTGAAGA 59.858 47.619 25.01 0.79 42.67 2.87
86 87 1.535462 CATTTGGGGACACGTGAAGAC 59.465 52.381 25.01 10.17 42.67 3.01
87 88 0.179040 TTTGGGGACACGTGAAGACC 60.179 55.000 25.01 17.92 42.67 3.85
88 89 1.338890 TTGGGGACACGTGAAGACCA 61.339 55.000 25.01 20.22 42.67 4.02
89 90 1.125093 TGGGGACACGTGAAGACCAT 61.125 55.000 25.01 0.00 33.40 3.55
90 91 0.899720 GGGGACACGTGAAGACCATA 59.100 55.000 25.01 0.00 0.00 2.74
91 92 1.405121 GGGGACACGTGAAGACCATAC 60.405 57.143 25.01 0.00 0.00 2.39
92 93 1.274167 GGGACACGTGAAGACCATACA 59.726 52.381 25.01 0.00 0.00 2.29
93 94 2.289195 GGGACACGTGAAGACCATACAA 60.289 50.000 25.01 0.00 0.00 2.41
94 95 2.993899 GGACACGTGAAGACCATACAAG 59.006 50.000 25.01 0.00 0.00 3.16
95 96 3.554337 GGACACGTGAAGACCATACAAGT 60.554 47.826 25.01 0.00 0.00 3.16
96 97 4.321452 GGACACGTGAAGACCATACAAGTA 60.321 45.833 25.01 0.00 0.00 2.24
97 98 4.806330 ACACGTGAAGACCATACAAGTAG 58.194 43.478 25.01 0.00 0.00 2.57
98 99 4.174009 CACGTGAAGACCATACAAGTAGG 58.826 47.826 10.90 0.00 0.00 3.18
99 100 3.830755 ACGTGAAGACCATACAAGTAGGT 59.169 43.478 0.00 0.00 38.63 3.08
100 101 4.174009 CGTGAAGACCATACAAGTAGGTG 58.826 47.826 0.00 0.00 35.36 4.00
101 102 4.504858 GTGAAGACCATACAAGTAGGTGG 58.495 47.826 0.00 3.14 35.36 4.61
103 104 5.186409 GTGAAGACCATACAAGTAGGTGGTA 59.814 44.000 5.69 0.00 44.56 3.25
104 105 5.781306 TGAAGACCATACAAGTAGGTGGTAA 59.219 40.000 5.69 0.00 44.56 2.85
105 106 5.672421 AGACCATACAAGTAGGTGGTAAC 57.328 43.478 5.69 0.00 44.56 2.50
106 107 5.339477 AGACCATACAAGTAGGTGGTAACT 58.661 41.667 5.69 0.00 44.56 2.24
107 108 6.496743 AGACCATACAAGTAGGTGGTAACTA 58.503 40.000 5.69 0.00 44.56 2.24
108 109 6.379417 AGACCATACAAGTAGGTGGTAACTAC 59.621 42.308 5.69 0.00 44.56 2.73
109 110 5.423290 ACCATACAAGTAGGTGGTAACTACC 59.577 44.000 4.18 0.00 42.85 3.18
121 122 4.796038 GGTAACTACCACTGCTTGTAGA 57.204 45.455 0.80 0.00 45.73 2.59
122 123 5.340439 GGTAACTACCACTGCTTGTAGAT 57.660 43.478 0.80 0.00 45.73 1.98
123 124 6.461110 GGTAACTACCACTGCTTGTAGATA 57.539 41.667 0.80 0.00 45.73 1.98
124 125 6.870769 GGTAACTACCACTGCTTGTAGATAA 58.129 40.000 0.80 0.00 45.73 1.75
125 126 7.325694 GGTAACTACCACTGCTTGTAGATAAA 58.674 38.462 0.80 0.00 45.73 1.40
126 127 7.820872 GGTAACTACCACTGCTTGTAGATAAAA 59.179 37.037 0.80 0.00 45.73 1.52
127 128 9.379791 GTAACTACCACTGCTTGTAGATAAAAT 57.620 33.333 3.87 0.00 38.24 1.82
128 129 8.863872 AACTACCACTGCTTGTAGATAAAATT 57.136 30.769 3.87 0.00 38.24 1.82
129 130 8.863872 ACTACCACTGCTTGTAGATAAAATTT 57.136 30.769 3.87 0.00 38.24 1.82
130 131 8.730680 ACTACCACTGCTTGTAGATAAAATTTG 58.269 33.333 3.87 0.00 38.24 2.32
131 132 7.524717 ACCACTGCTTGTAGATAAAATTTGT 57.475 32.000 0.00 0.00 0.00 2.83
132 133 7.593825 ACCACTGCTTGTAGATAAAATTTGTC 58.406 34.615 0.00 0.00 0.00 3.18
133 134 7.230510 ACCACTGCTTGTAGATAAAATTTGTCA 59.769 33.333 5.32 0.00 0.00 3.58
134 135 8.246180 CCACTGCTTGTAGATAAAATTTGTCAT 58.754 33.333 5.32 0.00 0.00 3.06
186 187 8.713737 AAAGTCTTATTCTAATAACACCGACC 57.286 34.615 8.07 0.00 29.54 4.79
187 188 7.657023 AGTCTTATTCTAATAACACCGACCT 57.343 36.000 8.07 0.00 29.54 3.85
188 189 8.075761 AGTCTTATTCTAATAACACCGACCTT 57.924 34.615 8.07 0.00 29.54 3.50
189 190 9.193806 AGTCTTATTCTAATAACACCGACCTTA 57.806 33.333 8.07 0.00 29.54 2.69
190 191 9.978044 GTCTTATTCTAATAACACCGACCTTAT 57.022 33.333 0.00 0.00 0.00 1.73
201 202 7.781548 AACACCGACCTTATTATGATAACAC 57.218 36.000 0.00 0.00 0.00 3.32
202 203 6.285990 ACACCGACCTTATTATGATAACACC 58.714 40.000 0.00 0.00 0.00 4.16
203 204 6.099269 ACACCGACCTTATTATGATAACACCT 59.901 38.462 0.00 0.00 0.00 4.00
204 205 7.288389 ACACCGACCTTATTATGATAACACCTA 59.712 37.037 0.00 0.00 0.00 3.08
205 206 7.597743 CACCGACCTTATTATGATAACACCTAC 59.402 40.741 0.00 0.00 0.00 3.18
206 207 6.805271 CCGACCTTATTATGATAACACCTACG 59.195 42.308 0.00 0.00 0.00 3.51
207 208 7.308770 CCGACCTTATTATGATAACACCTACGA 60.309 40.741 0.00 0.00 0.00 3.43
208 209 7.536622 CGACCTTATTATGATAACACCTACGAC 59.463 40.741 0.00 0.00 0.00 4.34
209 210 7.664758 ACCTTATTATGATAACACCTACGACC 58.335 38.462 0.00 0.00 0.00 4.79
210 211 7.095270 CCTTATTATGATAACACCTACGACCC 58.905 42.308 0.00 0.00 0.00 4.46
211 212 7.256048 CCTTATTATGATAACACCTACGACCCA 60.256 40.741 0.00 0.00 0.00 4.51
212 213 3.814005 ATGATAACACCTACGACCCAC 57.186 47.619 0.00 0.00 0.00 4.61
213 214 2.527497 TGATAACACCTACGACCCACA 58.473 47.619 0.00 0.00 0.00 4.17
214 215 2.231964 TGATAACACCTACGACCCACAC 59.768 50.000 0.00 0.00 0.00 3.82
215 216 0.597568 TAACACCTACGACCCACACG 59.402 55.000 0.00 0.00 0.00 4.49
216 217 2.091102 AACACCTACGACCCACACGG 62.091 60.000 0.00 0.00 37.81 4.94
224 225 4.525467 ACCCACACGGTAGCTACA 57.475 55.556 24.75 0.00 45.97 2.74
225 226 2.749340 ACCCACACGGTAGCTACAA 58.251 52.632 24.75 0.00 45.97 2.41
226 227 1.050204 ACCCACACGGTAGCTACAAA 58.950 50.000 24.75 0.00 45.97 2.83
227 228 1.270465 ACCCACACGGTAGCTACAAAC 60.270 52.381 24.75 7.34 45.97 2.93
228 229 1.001633 CCCACACGGTAGCTACAAACT 59.998 52.381 24.75 2.09 0.00 2.66
229 230 2.231964 CCCACACGGTAGCTACAAACTA 59.768 50.000 24.75 0.00 0.00 2.24
230 231 3.306225 CCCACACGGTAGCTACAAACTAA 60.306 47.826 24.75 0.00 0.00 2.24
231 232 3.676646 CCACACGGTAGCTACAAACTAAC 59.323 47.826 24.75 5.19 0.00 2.34
232 233 3.676646 CACACGGTAGCTACAAACTAACC 59.323 47.826 24.75 7.09 0.00 2.85
233 234 3.321682 ACACGGTAGCTACAAACTAACCA 59.678 43.478 24.75 0.00 0.00 3.67
234 235 3.676646 CACGGTAGCTACAAACTAACCAC 59.323 47.826 24.75 3.07 0.00 4.16
235 236 3.575687 ACGGTAGCTACAAACTAACCACT 59.424 43.478 24.75 0.00 0.00 4.00
236 237 3.924686 CGGTAGCTACAAACTAACCACTG 59.075 47.826 24.75 0.00 0.00 3.66
237 238 4.321452 CGGTAGCTACAAACTAACCACTGA 60.321 45.833 24.75 0.00 0.00 3.41
238 239 5.544650 GGTAGCTACAAACTAACCACTGAA 58.455 41.667 24.75 0.00 0.00 3.02
239 240 5.407691 GGTAGCTACAAACTAACCACTGAAC 59.592 44.000 24.75 0.00 0.00 3.18
240 241 5.291905 AGCTACAAACTAACCACTGAACT 57.708 39.130 0.00 0.00 0.00 3.01
241 242 5.057149 AGCTACAAACTAACCACTGAACTG 58.943 41.667 0.00 0.00 0.00 3.16
242 243 4.319549 GCTACAAACTAACCACTGAACTGC 60.320 45.833 0.00 0.00 0.00 4.40
243 244 2.612212 ACAAACTAACCACTGAACTGCG 59.388 45.455 0.00 0.00 0.00 5.18
244 245 1.226746 AACTAACCACTGAACTGCGC 58.773 50.000 0.00 0.00 0.00 6.09
245 246 0.602905 ACTAACCACTGAACTGCGCC 60.603 55.000 4.18 0.00 0.00 6.53
246 247 0.320771 CTAACCACTGAACTGCGCCT 60.321 55.000 4.18 0.00 0.00 5.52
247 248 0.602638 TAACCACTGAACTGCGCCTG 60.603 55.000 4.18 0.00 0.00 4.85
248 249 2.031012 CCACTGAACTGCGCCTGA 59.969 61.111 4.18 0.00 0.00 3.86
249 250 1.597854 CCACTGAACTGCGCCTGAA 60.598 57.895 4.18 0.00 0.00 3.02
250 251 1.165907 CCACTGAACTGCGCCTGAAA 61.166 55.000 4.18 0.00 0.00 2.69
251 252 0.236711 CACTGAACTGCGCCTGAAAG 59.763 55.000 4.18 0.00 0.00 2.62
252 253 0.106708 ACTGAACTGCGCCTGAAAGA 59.893 50.000 4.18 0.00 34.07 2.52
253 254 1.229428 CTGAACTGCGCCTGAAAGAA 58.771 50.000 4.18 0.00 34.07 2.52
254 255 1.603802 CTGAACTGCGCCTGAAAGAAA 59.396 47.619 4.18 0.00 34.07 2.52
255 256 2.020720 TGAACTGCGCCTGAAAGAAAA 58.979 42.857 4.18 0.00 34.07 2.29
256 257 2.425312 TGAACTGCGCCTGAAAGAAAAA 59.575 40.909 4.18 0.00 34.07 1.94
275 276 2.762535 AACCACTCACCTTATCCACG 57.237 50.000 0.00 0.00 0.00 4.94
276 277 1.640917 ACCACTCACCTTATCCACGT 58.359 50.000 0.00 0.00 0.00 4.49
277 278 1.975680 ACCACTCACCTTATCCACGTT 59.024 47.619 0.00 0.00 0.00 3.99
278 279 2.289444 ACCACTCACCTTATCCACGTTG 60.289 50.000 0.00 0.00 0.00 4.10
279 280 2.346803 CACTCACCTTATCCACGTTGG 58.653 52.381 0.00 0.00 39.43 3.77
296 297 2.671682 GAGCACCAACTCCCCTCC 59.328 66.667 0.00 0.00 0.00 4.30
297 298 2.936032 AGCACCAACTCCCCTCCC 60.936 66.667 0.00 0.00 0.00 4.30
298 299 2.936032 GCACCAACTCCCCTCCCT 60.936 66.667 0.00 0.00 0.00 4.20
299 300 2.972819 GCACCAACTCCCCTCCCTC 61.973 68.421 0.00 0.00 0.00 4.30
300 301 1.229658 CACCAACTCCCCTCCCTCT 60.230 63.158 0.00 0.00 0.00 3.69
301 302 1.081277 ACCAACTCCCCTCCCTCTC 59.919 63.158 0.00 0.00 0.00 3.20
302 303 1.690985 CCAACTCCCCTCCCTCTCC 60.691 68.421 0.00 0.00 0.00 3.71
303 304 1.690985 CAACTCCCCTCCCTCTCCC 60.691 68.421 0.00 0.00 0.00 4.30
304 305 2.962138 AACTCCCCTCCCTCTCCCC 61.962 68.421 0.00 0.00 0.00 4.81
305 306 4.548513 CTCCCCTCCCTCTCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
325 326 4.715130 CCCCTCCACTCCCCACGA 62.715 72.222 0.00 0.00 0.00 4.35
326 327 3.391382 CCCTCCACTCCCCACGAC 61.391 72.222 0.00 0.00 0.00 4.34
327 328 3.391382 CCTCCACTCCCCACGACC 61.391 72.222 0.00 0.00 0.00 4.79
328 329 2.603473 CTCCACTCCCCACGACCA 60.603 66.667 0.00 0.00 0.00 4.02
329 330 2.920912 TCCACTCCCCACGACCAC 60.921 66.667 0.00 0.00 0.00 4.16
330 331 4.016706 CCACTCCCCACGACCACC 62.017 72.222 0.00 0.00 0.00 4.61
331 332 3.238497 CACTCCCCACGACCACCA 61.238 66.667 0.00 0.00 0.00 4.17
332 333 3.239253 ACTCCCCACGACCACCAC 61.239 66.667 0.00 0.00 0.00 4.16
333 334 4.016706 CTCCCCACGACCACCACC 62.017 72.222 0.00 0.00 0.00 4.61
334 335 4.567597 TCCCCACGACCACCACCT 62.568 66.667 0.00 0.00 0.00 4.00
335 336 4.016706 CCCCACGACCACCACCTC 62.017 72.222 0.00 0.00 0.00 3.85
336 337 4.016706 CCCACGACCACCACCTCC 62.017 72.222 0.00 0.00 0.00 4.30
337 338 2.923035 CCACGACCACCACCTCCT 60.923 66.667 0.00 0.00 0.00 3.69
338 339 1.608336 CCACGACCACCACCTCCTA 60.608 63.158 0.00 0.00 0.00 2.94
339 340 1.590147 CACGACCACCACCTCCTAC 59.410 63.158 0.00 0.00 0.00 3.18
340 341 1.608627 ACGACCACCACCTCCTACC 60.609 63.158 0.00 0.00 0.00 3.18
341 342 2.356780 CGACCACCACCTCCTACCC 61.357 68.421 0.00 0.00 0.00 3.69
342 343 1.993948 GACCACCACCTCCTACCCC 60.994 68.421 0.00 0.00 0.00 4.95
343 344 3.081409 CCACCACCTCCTACCCCG 61.081 72.222 0.00 0.00 0.00 5.73
344 345 3.782443 CACCACCTCCTACCCCGC 61.782 72.222 0.00 0.00 0.00 6.13
363 364 4.643387 GCCGCACAACCTCCACCT 62.643 66.667 0.00 0.00 0.00 4.00
364 365 2.358737 CCGCACAACCTCCACCTC 60.359 66.667 0.00 0.00 0.00 3.85
365 366 2.358737 CGCACAACCTCCACCTCC 60.359 66.667 0.00 0.00 0.00 4.30
366 367 2.034221 GCACAACCTCCACCTCCC 59.966 66.667 0.00 0.00 0.00 4.30
367 368 2.829384 GCACAACCTCCACCTCCCA 61.829 63.158 0.00 0.00 0.00 4.37
368 369 1.073199 CACAACCTCCACCTCCCAC 59.927 63.158 0.00 0.00 0.00 4.61
369 370 2.154074 ACAACCTCCACCTCCCACC 61.154 63.158 0.00 0.00 0.00 4.61
370 371 1.847968 CAACCTCCACCTCCCACCT 60.848 63.158 0.00 0.00 0.00 4.00
371 372 1.539124 AACCTCCACCTCCCACCTC 60.539 63.158 0.00 0.00 0.00 3.85
372 373 3.077556 CCTCCACCTCCCACCTCG 61.078 72.222 0.00 0.00 0.00 4.63
373 374 3.775654 CTCCACCTCCCACCTCGC 61.776 72.222 0.00 0.00 0.00 5.03
376 377 3.775654 CACCTCCCACCTCGCCTC 61.776 72.222 0.00 0.00 0.00 4.70
378 379 4.787280 CCTCCCACCTCGCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
379 380 3.151022 CTCCCACCTCGCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
380 381 4.779733 TCCCACCTCGCCTCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
381 382 4.787280 CCCACCTCGCCTCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
382 383 2.279073 CCACCTCGCCTCCTCCTA 59.721 66.667 0.00 0.00 0.00 2.94
383 384 2.128507 CCACCTCGCCTCCTCCTAC 61.129 68.421 0.00 0.00 0.00 3.18
384 385 2.128507 CACCTCGCCTCCTCCTACC 61.129 68.421 0.00 0.00 0.00 3.18
385 386 2.522193 CCTCGCCTCCTCCTACCC 60.522 72.222 0.00 0.00 0.00 3.69
386 387 2.522193 CTCGCCTCCTCCTACCCC 60.522 72.222 0.00 0.00 0.00 4.95
387 388 4.153330 TCGCCTCCTCCTACCCCC 62.153 72.222 0.00 0.00 0.00 5.40
388 389 4.475444 CGCCTCCTCCTACCCCCA 62.475 72.222 0.00 0.00 0.00 4.96
389 390 2.446802 GCCTCCTCCTACCCCCAG 60.447 72.222 0.00 0.00 0.00 4.45
390 391 2.446802 CCTCCTCCTACCCCCAGC 60.447 72.222 0.00 0.00 0.00 4.85
391 392 2.446802 CTCCTCCTACCCCCAGCC 60.447 72.222 0.00 0.00 0.00 4.85
392 393 4.475444 TCCTCCTACCCCCAGCCG 62.475 72.222 0.00 0.00 0.00 5.52
394 395 4.798682 CTCCTACCCCCAGCCGGT 62.799 72.222 1.90 0.00 37.40 5.28
975 976 4.962122 CGCAGTGCACGTGGTTGC 62.962 66.667 18.88 15.86 43.31 4.17
1253 1277 2.490148 CGATAGGAGACGGCTGCCA 61.490 63.158 20.29 0.00 32.04 4.92
1295 1319 2.043405 AACCACAACAGCACGTGCA 61.043 52.632 39.21 0.00 45.16 4.57
1654 1678 7.190920 AGCTAGTGTTTTGTAATTCTGTGTC 57.809 36.000 0.00 0.00 0.00 3.67
1850 1874 6.810888 CAAGTATTGTATTGAAAATGGCCG 57.189 37.500 0.00 0.00 42.34 6.13
1851 1875 6.559810 CAAGTATTGTATTGAAAATGGCCGA 58.440 36.000 0.00 0.00 42.34 5.54
1852 1876 6.959639 AGTATTGTATTGAAAATGGCCGAT 57.040 33.333 0.00 0.00 0.00 4.18
1853 1877 6.738114 AGTATTGTATTGAAAATGGCCGATG 58.262 36.000 0.00 0.00 0.00 3.84
1855 1879 4.630894 TGTATTGAAAATGGCCGATGAC 57.369 40.909 0.00 0.00 0.00 3.06
1949 1977 7.701809 TTGAAAAATAGAATTCCGCGTTTTT 57.298 28.000 4.92 8.76 33.11 1.94
1989 2017 5.393962 TCTTAAACCGTAACGAGTTAGAGC 58.606 41.667 0.00 0.00 0.00 4.09
2015 2043 8.586273 CAAACAATAGTTATGAAAAAGATGCGG 58.414 33.333 0.00 0.00 36.84 5.69
2042 2070 6.967135 TGACGATATCTATCCAACAGTGTAC 58.033 40.000 0.00 0.00 0.00 2.90
2476 2517 5.192923 ACCCAGGGTGCAGAATAAGTTATTA 59.807 40.000 11.70 0.00 32.98 0.98
2703 2744 6.360329 GGCGATTATGTATTTTCTTACGGTG 58.640 40.000 0.00 0.00 0.00 4.94
2773 2819 7.658525 ATGGTGCATTGATGGTAAAATAGAA 57.341 32.000 0.00 0.00 0.00 2.10
2774 2820 7.099266 TGGTGCATTGATGGTAAAATAGAAG 57.901 36.000 0.00 0.00 0.00 2.85
2776 2822 6.321181 GGTGCATTGATGGTAAAATAGAAGGA 59.679 38.462 0.00 0.00 0.00 3.36
2788 2834 9.549078 GGTAAAATAGAAGGAGGTGAAGAATAG 57.451 37.037 0.00 0.00 0.00 1.73
2794 2840 6.825610 AGAAGGAGGTGAAGAATAGCTATTG 58.174 40.000 23.51 0.00 0.00 1.90
2826 2872 0.659711 GACGAATAGCGCGACCCTAC 60.660 60.000 12.10 0.00 46.04 3.18
2834 2880 2.168496 AGCGCGACCCTACATATATGT 58.832 47.619 21.57 21.57 44.48 2.29
2835 2881 3.349927 AGCGCGACCCTACATATATGTA 58.650 45.455 21.50 21.50 41.97 2.29
2836 2882 3.128242 AGCGCGACCCTACATATATGTAC 59.872 47.826 19.51 10.37 41.97 2.90
2837 2883 3.128242 GCGCGACCCTACATATATGTACT 59.872 47.826 19.51 6.99 41.97 2.73
2838 2884 4.730035 GCGCGACCCTACATATATGTACTC 60.730 50.000 19.51 13.30 41.97 2.59
2839 2885 4.201891 CGCGACCCTACATATATGTACTCC 60.202 50.000 19.51 9.55 41.97 3.85
2840 2886 4.097589 GCGACCCTACATATATGTACTCCC 59.902 50.000 19.51 9.83 41.97 4.30
2841 2887 5.258841 CGACCCTACATATATGTACTCCCA 58.741 45.833 19.51 2.92 41.97 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.305930 CCTTTAACCCGTGAGCAGCC 61.306 60.000 0.00 0.00 0.00 4.85
1 2 1.305930 CCCTTTAACCCGTGAGCAGC 61.306 60.000 0.00 0.00 0.00 5.25
2 3 0.036306 ACCCTTTAACCCGTGAGCAG 59.964 55.000 0.00 0.00 0.00 4.24
3 4 0.475044 AACCCTTTAACCCGTGAGCA 59.525 50.000 0.00 0.00 0.00 4.26
4 5 1.162698 GAACCCTTTAACCCGTGAGC 58.837 55.000 0.00 0.00 0.00 4.26
5 6 2.423577 CAGAACCCTTTAACCCGTGAG 58.576 52.381 0.00 0.00 0.00 3.51
6 7 1.543871 GCAGAACCCTTTAACCCGTGA 60.544 52.381 0.00 0.00 0.00 4.35
7 8 0.879090 GCAGAACCCTTTAACCCGTG 59.121 55.000 0.00 0.00 0.00 4.94
8 9 0.251033 GGCAGAACCCTTTAACCCGT 60.251 55.000 0.00 0.00 0.00 5.28
9 10 2.563297 GGCAGAACCCTTTAACCCG 58.437 57.895 0.00 0.00 0.00 5.28
19 20 0.108520 TATCGAACGTGGGCAGAACC 60.109 55.000 0.00 0.00 37.93 3.62
20 21 1.278238 CTATCGAACGTGGGCAGAAC 58.722 55.000 0.00 0.00 0.00 3.01
21 22 0.174845 CCTATCGAACGTGGGCAGAA 59.825 55.000 0.00 0.00 0.00 3.02
22 23 1.813859 CCTATCGAACGTGGGCAGA 59.186 57.895 0.00 0.00 0.00 4.26
23 24 1.883084 GCCTATCGAACGTGGGCAG 60.883 63.158 6.98 0.00 42.08 4.85
24 25 2.185867 GCCTATCGAACGTGGGCA 59.814 61.111 6.98 0.00 42.08 5.36
25 26 2.588034 GGCCTATCGAACGTGGGC 60.588 66.667 3.43 3.43 41.80 5.36
26 27 1.227263 CTGGCCTATCGAACGTGGG 60.227 63.158 3.32 0.00 0.00 4.61
27 28 1.883084 GCTGGCCTATCGAACGTGG 60.883 63.158 3.32 0.00 0.00 4.94
28 29 1.153647 TGCTGGCCTATCGAACGTG 60.154 57.895 3.32 0.00 0.00 4.49
29 30 1.153628 GTGCTGGCCTATCGAACGT 60.154 57.895 3.32 0.00 0.00 3.99
30 31 1.883084 GGTGCTGGCCTATCGAACG 60.883 63.158 3.32 0.00 0.00 3.95
31 32 0.811616 CAGGTGCTGGCCTATCGAAC 60.812 60.000 3.32 0.00 37.04 3.95
32 33 1.522092 CAGGTGCTGGCCTATCGAA 59.478 57.895 3.32 0.00 37.04 3.71
33 34 2.434843 CCAGGTGCTGGCCTATCGA 61.435 63.158 3.32 0.00 45.13 3.59
34 35 2.109799 CCAGGTGCTGGCCTATCG 59.890 66.667 3.32 0.00 45.13 2.92
51 52 2.094545 CCAAATGTAGAAGCTGGGCAAC 60.095 50.000 0.00 0.00 0.00 4.17
52 53 2.170166 CCAAATGTAGAAGCTGGGCAA 58.830 47.619 0.00 0.00 0.00 4.52
53 54 1.616725 CCCAAATGTAGAAGCTGGGCA 60.617 52.381 0.00 0.00 40.37 5.36
54 55 1.106285 CCCAAATGTAGAAGCTGGGC 58.894 55.000 0.00 0.00 40.37 5.36
55 56 1.284785 TCCCCAAATGTAGAAGCTGGG 59.715 52.381 0.00 0.00 45.48 4.45
56 57 2.290896 TGTCCCCAAATGTAGAAGCTGG 60.291 50.000 0.00 0.00 0.00 4.85
57 58 2.749621 GTGTCCCCAAATGTAGAAGCTG 59.250 50.000 0.00 0.00 0.00 4.24
58 59 2.615493 CGTGTCCCCAAATGTAGAAGCT 60.615 50.000 0.00 0.00 0.00 3.74
59 60 1.737793 CGTGTCCCCAAATGTAGAAGC 59.262 52.381 0.00 0.00 0.00 3.86
60 61 2.742053 CACGTGTCCCCAAATGTAGAAG 59.258 50.000 7.58 0.00 0.00 2.85
61 62 2.369203 TCACGTGTCCCCAAATGTAGAA 59.631 45.455 16.51 0.00 0.00 2.10
62 63 1.972075 TCACGTGTCCCCAAATGTAGA 59.028 47.619 16.51 0.00 0.00 2.59
63 64 2.465860 TCACGTGTCCCCAAATGTAG 57.534 50.000 16.51 0.00 0.00 2.74
64 65 2.369203 TCTTCACGTGTCCCCAAATGTA 59.631 45.455 16.51 0.00 0.00 2.29
65 66 1.142060 TCTTCACGTGTCCCCAAATGT 59.858 47.619 16.51 0.00 0.00 2.71
66 67 1.535462 GTCTTCACGTGTCCCCAAATG 59.465 52.381 16.51 0.00 0.00 2.32
67 68 1.544759 GGTCTTCACGTGTCCCCAAAT 60.545 52.381 16.51 0.00 0.00 2.32
68 69 0.179040 GGTCTTCACGTGTCCCCAAA 60.179 55.000 16.51 0.00 0.00 3.28
69 70 1.338890 TGGTCTTCACGTGTCCCCAA 61.339 55.000 16.51 0.53 0.00 4.12
70 71 1.125093 ATGGTCTTCACGTGTCCCCA 61.125 55.000 16.51 16.71 0.00 4.96
71 72 0.899720 TATGGTCTTCACGTGTCCCC 59.100 55.000 16.51 11.74 0.00 4.81
72 73 1.274167 TGTATGGTCTTCACGTGTCCC 59.726 52.381 16.51 11.40 0.00 4.46
73 74 2.736144 TGTATGGTCTTCACGTGTCC 57.264 50.000 16.51 13.83 0.00 4.02
74 75 3.650139 ACTTGTATGGTCTTCACGTGTC 58.350 45.455 16.51 4.99 0.00 3.67
75 76 3.746045 ACTTGTATGGTCTTCACGTGT 57.254 42.857 16.51 0.00 0.00 4.49
76 77 4.174009 CCTACTTGTATGGTCTTCACGTG 58.826 47.826 9.94 9.94 0.00 4.49
77 78 3.830755 ACCTACTTGTATGGTCTTCACGT 59.169 43.478 0.00 0.00 0.00 4.49
78 79 4.174009 CACCTACTTGTATGGTCTTCACG 58.826 47.826 0.00 0.00 30.72 4.35
79 80 4.020485 ACCACCTACTTGTATGGTCTTCAC 60.020 45.833 1.44 0.00 41.76 3.18
80 81 4.164981 ACCACCTACTTGTATGGTCTTCA 58.835 43.478 1.44 0.00 41.76 3.02
81 82 4.820894 ACCACCTACTTGTATGGTCTTC 57.179 45.455 1.44 0.00 41.76 2.87
82 83 5.783875 AGTTACCACCTACTTGTATGGTCTT 59.216 40.000 8.75 0.00 44.40 3.01
83 84 5.339477 AGTTACCACCTACTTGTATGGTCT 58.661 41.667 8.75 1.11 44.40 3.85
84 85 5.672421 AGTTACCACCTACTTGTATGGTC 57.328 43.478 8.75 0.00 44.40 4.02
86 87 5.910614 GGTAGTTACCACCTACTTGTATGG 58.089 45.833 3.45 0.00 45.73 2.74
100 101 4.796038 TCTACAAGCAGTGGTAGTTACC 57.204 45.455 0.00 1.25 46.62 2.85
101 102 8.767478 TTTTATCTACAAGCAGTGGTAGTTAC 57.233 34.615 0.00 0.00 38.46 2.50
102 103 9.953565 AATTTTATCTACAAGCAGTGGTAGTTA 57.046 29.630 0.00 0.00 38.46 2.24
103 104 8.863872 AATTTTATCTACAAGCAGTGGTAGTT 57.136 30.769 0.00 0.00 38.46 2.24
104 105 8.730680 CAAATTTTATCTACAAGCAGTGGTAGT 58.269 33.333 0.00 0.00 38.46 2.73
105 106 8.730680 ACAAATTTTATCTACAAGCAGTGGTAG 58.269 33.333 0.00 0.00 38.63 3.18
106 107 8.630054 ACAAATTTTATCTACAAGCAGTGGTA 57.370 30.769 0.00 0.00 0.00 3.25
107 108 7.230510 TGACAAATTTTATCTACAAGCAGTGGT 59.769 33.333 0.00 0.00 0.00 4.16
108 109 7.592938 TGACAAATTTTATCTACAAGCAGTGG 58.407 34.615 0.00 0.00 0.00 4.00
160 161 9.159364 GGTCGGTGTTATTAGAATAAGACTTTT 57.841 33.333 17.10 0.00 41.94 2.27
161 162 8.537858 AGGTCGGTGTTATTAGAATAAGACTTT 58.462 33.333 17.10 4.40 41.94 2.66
162 163 8.075761 AGGTCGGTGTTATTAGAATAAGACTT 57.924 34.615 17.10 6.60 41.94 3.01
163 164 7.657023 AGGTCGGTGTTATTAGAATAAGACT 57.343 36.000 17.10 0.85 41.94 3.24
164 165 9.978044 ATAAGGTCGGTGTTATTAGAATAAGAC 57.022 33.333 11.84 11.84 41.69 3.01
175 176 9.485206 GTGTTATCATAATAAGGTCGGTGTTAT 57.515 33.333 0.00 0.00 0.00 1.89
176 177 7.927629 GGTGTTATCATAATAAGGTCGGTGTTA 59.072 37.037 0.00 0.00 0.00 2.41
177 178 6.764560 GGTGTTATCATAATAAGGTCGGTGTT 59.235 38.462 0.00 0.00 0.00 3.32
178 179 6.099269 AGGTGTTATCATAATAAGGTCGGTGT 59.901 38.462 0.00 0.00 0.00 4.16
179 180 6.522054 AGGTGTTATCATAATAAGGTCGGTG 58.478 40.000 0.00 0.00 0.00 4.94
180 181 6.742559 AGGTGTTATCATAATAAGGTCGGT 57.257 37.500 0.00 0.00 0.00 4.69
181 182 6.805271 CGTAGGTGTTATCATAATAAGGTCGG 59.195 42.308 0.00 0.00 0.00 4.79
182 183 7.536622 GTCGTAGGTGTTATCATAATAAGGTCG 59.463 40.741 0.00 0.00 0.00 4.79
183 184 7.811713 GGTCGTAGGTGTTATCATAATAAGGTC 59.188 40.741 0.00 0.00 0.00 3.85
184 185 7.256083 GGGTCGTAGGTGTTATCATAATAAGGT 60.256 40.741 0.00 0.00 0.00 3.50
185 186 7.095270 GGGTCGTAGGTGTTATCATAATAAGG 58.905 42.308 0.00 0.00 0.00 2.69
186 187 7.597743 GTGGGTCGTAGGTGTTATCATAATAAG 59.402 40.741 0.00 0.00 0.00 1.73
187 188 7.069702 TGTGGGTCGTAGGTGTTATCATAATAA 59.930 37.037 0.00 0.00 0.00 1.40
188 189 6.550481 TGTGGGTCGTAGGTGTTATCATAATA 59.450 38.462 0.00 0.00 0.00 0.98
189 190 5.364446 TGTGGGTCGTAGGTGTTATCATAAT 59.636 40.000 0.00 0.00 0.00 1.28
190 191 4.710865 TGTGGGTCGTAGGTGTTATCATAA 59.289 41.667 0.00 0.00 0.00 1.90
191 192 4.098349 GTGTGGGTCGTAGGTGTTATCATA 59.902 45.833 0.00 0.00 0.00 2.15
192 193 3.101437 TGTGGGTCGTAGGTGTTATCAT 58.899 45.455 0.00 0.00 0.00 2.45
193 194 2.231964 GTGTGGGTCGTAGGTGTTATCA 59.768 50.000 0.00 0.00 0.00 2.15
194 195 2.733227 CGTGTGGGTCGTAGGTGTTATC 60.733 54.545 0.00 0.00 0.00 1.75
195 196 1.203052 CGTGTGGGTCGTAGGTGTTAT 59.797 52.381 0.00 0.00 0.00 1.89
196 197 0.597568 CGTGTGGGTCGTAGGTGTTA 59.402 55.000 0.00 0.00 0.00 2.41
197 198 1.364901 CGTGTGGGTCGTAGGTGTT 59.635 57.895 0.00 0.00 0.00 3.32
198 199 2.567497 CCGTGTGGGTCGTAGGTGT 61.567 63.158 0.00 0.00 0.00 4.16
199 200 2.260434 CCGTGTGGGTCGTAGGTG 59.740 66.667 0.00 0.00 0.00 4.00
208 209 1.001633 AGTTTGTAGCTACCGTGTGGG 59.998 52.381 21.01 0.00 40.75 4.61
209 210 2.450609 AGTTTGTAGCTACCGTGTGG 57.549 50.000 21.01 0.00 42.84 4.17
210 211 3.676646 GGTTAGTTTGTAGCTACCGTGTG 59.323 47.826 21.01 0.00 0.00 3.82
211 212 3.321682 TGGTTAGTTTGTAGCTACCGTGT 59.678 43.478 21.01 6.31 0.00 4.49
212 213 3.676646 GTGGTTAGTTTGTAGCTACCGTG 59.323 47.826 21.01 0.00 0.00 4.94
213 214 3.575687 AGTGGTTAGTTTGTAGCTACCGT 59.424 43.478 21.01 5.62 0.00 4.83
214 215 3.924686 CAGTGGTTAGTTTGTAGCTACCG 59.075 47.826 21.01 0.00 0.00 4.02
215 216 5.143376 TCAGTGGTTAGTTTGTAGCTACC 57.857 43.478 21.01 6.25 0.00 3.18
216 217 6.145696 CAGTTCAGTGGTTAGTTTGTAGCTAC 59.854 42.308 17.30 17.30 0.00 3.58
217 218 6.220930 CAGTTCAGTGGTTAGTTTGTAGCTA 58.779 40.000 0.00 0.00 0.00 3.32
218 219 5.057149 CAGTTCAGTGGTTAGTTTGTAGCT 58.943 41.667 0.00 0.00 0.00 3.32
219 220 4.319549 GCAGTTCAGTGGTTAGTTTGTAGC 60.320 45.833 0.00 0.00 0.00 3.58
220 221 4.084537 CGCAGTTCAGTGGTTAGTTTGTAG 60.085 45.833 0.00 0.00 0.00 2.74
221 222 3.805422 CGCAGTTCAGTGGTTAGTTTGTA 59.195 43.478 0.00 0.00 0.00 2.41
222 223 2.612212 CGCAGTTCAGTGGTTAGTTTGT 59.388 45.455 0.00 0.00 0.00 2.83
223 224 2.602217 GCGCAGTTCAGTGGTTAGTTTG 60.602 50.000 0.30 0.00 0.00 2.93
224 225 1.602377 GCGCAGTTCAGTGGTTAGTTT 59.398 47.619 0.30 0.00 0.00 2.66
225 226 1.226746 GCGCAGTTCAGTGGTTAGTT 58.773 50.000 0.30 0.00 0.00 2.24
226 227 0.602905 GGCGCAGTTCAGTGGTTAGT 60.603 55.000 10.83 0.00 0.00 2.24
227 228 0.320771 AGGCGCAGTTCAGTGGTTAG 60.321 55.000 10.83 0.00 0.00 2.34
228 229 0.602638 CAGGCGCAGTTCAGTGGTTA 60.603 55.000 10.83 0.00 0.00 2.85
229 230 1.893808 CAGGCGCAGTTCAGTGGTT 60.894 57.895 10.83 0.00 0.00 3.67
230 231 2.281070 CAGGCGCAGTTCAGTGGT 60.281 61.111 10.83 0.00 0.00 4.16
231 232 1.165907 TTTCAGGCGCAGTTCAGTGG 61.166 55.000 10.83 0.00 0.00 4.00
232 233 0.236711 CTTTCAGGCGCAGTTCAGTG 59.763 55.000 10.83 0.00 0.00 3.66
233 234 0.106708 TCTTTCAGGCGCAGTTCAGT 59.893 50.000 10.83 0.00 0.00 3.41
234 235 1.229428 TTCTTTCAGGCGCAGTTCAG 58.771 50.000 10.83 0.00 0.00 3.02
235 236 1.674359 TTTCTTTCAGGCGCAGTTCA 58.326 45.000 10.83 0.00 0.00 3.18
236 237 2.774439 TTTTCTTTCAGGCGCAGTTC 57.226 45.000 10.83 0.00 0.00 3.01
253 254 3.818773 CGTGGATAAGGTGAGTGGTTTTT 59.181 43.478 0.00 0.00 0.00 1.94
254 255 3.181448 ACGTGGATAAGGTGAGTGGTTTT 60.181 43.478 0.00 0.00 0.00 2.43
255 256 2.370849 ACGTGGATAAGGTGAGTGGTTT 59.629 45.455 0.00 0.00 0.00 3.27
256 257 1.975680 ACGTGGATAAGGTGAGTGGTT 59.024 47.619 0.00 0.00 0.00 3.67
257 258 1.640917 ACGTGGATAAGGTGAGTGGT 58.359 50.000 0.00 0.00 0.00 4.16
258 259 2.346803 CAACGTGGATAAGGTGAGTGG 58.653 52.381 0.00 0.00 0.00 4.00
259 260 2.028476 TCCAACGTGGATAAGGTGAGTG 60.028 50.000 0.00 0.00 42.67 3.51
260 261 2.253610 TCCAACGTGGATAAGGTGAGT 58.746 47.619 0.00 0.00 42.67 3.41
279 280 2.671682 GGAGGGGAGTTGGTGCTC 59.328 66.667 0.00 0.00 34.89 4.26
280 281 2.936032 GGGAGGGGAGTTGGTGCT 60.936 66.667 0.00 0.00 0.00 4.40
281 282 2.936032 AGGGAGGGGAGTTGGTGC 60.936 66.667 0.00 0.00 0.00 5.01
282 283 1.229658 AGAGGGAGGGGAGTTGGTG 60.230 63.158 0.00 0.00 0.00 4.17
283 284 1.081277 GAGAGGGAGGGGAGTTGGT 59.919 63.158 0.00 0.00 0.00 3.67
284 285 1.690985 GGAGAGGGAGGGGAGTTGG 60.691 68.421 0.00 0.00 0.00 3.77
285 286 1.690985 GGGAGAGGGAGGGGAGTTG 60.691 68.421 0.00 0.00 0.00 3.16
286 287 2.788589 GGGAGAGGGAGGGGAGTT 59.211 66.667 0.00 0.00 0.00 3.01
287 288 3.369388 GGGGAGAGGGAGGGGAGT 61.369 72.222 0.00 0.00 0.00 3.85
288 289 4.548513 CGGGGAGAGGGAGGGGAG 62.549 77.778 0.00 0.00 0.00 4.30
308 309 4.715130 TCGTGGGGAGTGGAGGGG 62.715 72.222 0.00 0.00 0.00 4.79
309 310 3.391382 GTCGTGGGGAGTGGAGGG 61.391 72.222 0.00 0.00 0.00 4.30
310 311 3.391382 GGTCGTGGGGAGTGGAGG 61.391 72.222 0.00 0.00 0.00 4.30
311 312 2.603473 TGGTCGTGGGGAGTGGAG 60.603 66.667 0.00 0.00 0.00 3.86
312 313 2.920912 GTGGTCGTGGGGAGTGGA 60.921 66.667 0.00 0.00 0.00 4.02
313 314 4.016706 GGTGGTCGTGGGGAGTGG 62.017 72.222 0.00 0.00 0.00 4.00
314 315 3.238497 TGGTGGTCGTGGGGAGTG 61.238 66.667 0.00 0.00 0.00 3.51
315 316 3.239253 GTGGTGGTCGTGGGGAGT 61.239 66.667 0.00 0.00 0.00 3.85
316 317 4.016706 GGTGGTGGTCGTGGGGAG 62.017 72.222 0.00 0.00 0.00 4.30
317 318 4.567597 AGGTGGTGGTCGTGGGGA 62.568 66.667 0.00 0.00 0.00 4.81
318 319 4.016706 GAGGTGGTGGTCGTGGGG 62.017 72.222 0.00 0.00 0.00 4.96
319 320 4.016706 GGAGGTGGTGGTCGTGGG 62.017 72.222 0.00 0.00 0.00 4.61
320 321 1.608336 TAGGAGGTGGTGGTCGTGG 60.608 63.158 0.00 0.00 0.00 4.94
321 322 1.590147 GTAGGAGGTGGTGGTCGTG 59.410 63.158 0.00 0.00 0.00 4.35
322 323 1.608627 GGTAGGAGGTGGTGGTCGT 60.609 63.158 0.00 0.00 0.00 4.34
323 324 2.356780 GGGTAGGAGGTGGTGGTCG 61.357 68.421 0.00 0.00 0.00 4.79
324 325 1.993948 GGGGTAGGAGGTGGTGGTC 60.994 68.421 0.00 0.00 0.00 4.02
325 326 2.124312 GGGGTAGGAGGTGGTGGT 59.876 66.667 0.00 0.00 0.00 4.16
326 327 3.081409 CGGGGTAGGAGGTGGTGG 61.081 72.222 0.00 0.00 0.00 4.61
327 328 3.782443 GCGGGGTAGGAGGTGGTG 61.782 72.222 0.00 0.00 0.00 4.17
346 347 4.643387 AGGTGGAGGTTGTGCGGC 62.643 66.667 0.00 0.00 0.00 6.53
347 348 2.358737 GAGGTGGAGGTTGTGCGG 60.359 66.667 0.00 0.00 0.00 5.69
348 349 2.358737 GGAGGTGGAGGTTGTGCG 60.359 66.667 0.00 0.00 0.00 5.34
349 350 2.034221 GGGAGGTGGAGGTTGTGC 59.966 66.667 0.00 0.00 0.00 4.57
350 351 1.073199 GTGGGAGGTGGAGGTTGTG 59.927 63.158 0.00 0.00 0.00 3.33
351 352 2.154074 GGTGGGAGGTGGAGGTTGT 61.154 63.158 0.00 0.00 0.00 3.32
352 353 1.842381 GAGGTGGGAGGTGGAGGTTG 61.842 65.000 0.00 0.00 0.00 3.77
353 354 1.539124 GAGGTGGGAGGTGGAGGTT 60.539 63.158 0.00 0.00 0.00 3.50
354 355 2.122954 GAGGTGGGAGGTGGAGGT 59.877 66.667 0.00 0.00 0.00 3.85
355 356 3.077556 CGAGGTGGGAGGTGGAGG 61.078 72.222 0.00 0.00 0.00 4.30
356 357 3.775654 GCGAGGTGGGAGGTGGAG 61.776 72.222 0.00 0.00 0.00 3.86
359 360 3.775654 GAGGCGAGGTGGGAGGTG 61.776 72.222 0.00 0.00 0.00 4.00
361 362 4.787280 AGGAGGCGAGGTGGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
362 363 3.151022 GAGGAGGCGAGGTGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
363 364 4.779733 GGAGGAGGCGAGGTGGGA 62.780 72.222 0.00 0.00 0.00 4.37
364 365 3.375443 TAGGAGGAGGCGAGGTGGG 62.375 68.421 0.00 0.00 0.00 4.61
365 366 2.128507 GTAGGAGGAGGCGAGGTGG 61.129 68.421 0.00 0.00 0.00 4.61
366 367 2.128507 GGTAGGAGGAGGCGAGGTG 61.129 68.421 0.00 0.00 0.00 4.00
367 368 2.279408 GGTAGGAGGAGGCGAGGT 59.721 66.667 0.00 0.00 0.00 3.85
368 369 2.522193 GGGTAGGAGGAGGCGAGG 60.522 72.222 0.00 0.00 0.00 4.63
369 370 2.522193 GGGGTAGGAGGAGGCGAG 60.522 72.222 0.00 0.00 0.00 5.03
370 371 4.153330 GGGGGTAGGAGGAGGCGA 62.153 72.222 0.00 0.00 0.00 5.54
371 372 4.475444 TGGGGGTAGGAGGAGGCG 62.475 72.222 0.00 0.00 0.00 5.52
372 373 2.446802 CTGGGGGTAGGAGGAGGC 60.447 72.222 0.00 0.00 0.00 4.70
373 374 2.446802 GCTGGGGGTAGGAGGAGG 60.447 72.222 0.00 0.00 0.00 4.30
374 375 2.446802 GGCTGGGGGTAGGAGGAG 60.447 72.222 0.00 0.00 0.00 3.69
375 376 4.475444 CGGCTGGGGGTAGGAGGA 62.475 72.222 0.00 0.00 0.00 3.71
377 378 4.798682 ACCGGCTGGGGGTAGGAG 62.799 72.222 18.00 0.00 41.60 3.69
905 906 2.587247 GGCCTCCACTGCTCAGACA 61.587 63.158 3.60 0.00 0.00 3.41
1006 1007 2.014068 GCATTGCAGTAGGAGGTGGAC 61.014 57.143 3.15 0.00 0.00 4.02
1063 1070 1.289380 GTGAACGACGGAGGAGCTT 59.711 57.895 0.00 0.00 0.00 3.74
1654 1678 3.439476 AGACAGTAGGTTAGCAGTACACG 59.561 47.826 0.00 0.00 0.00 4.49
1824 1848 7.543868 CGGCCATTTTCAATACAATACTTGAAA 59.456 33.333 2.24 6.40 45.01 2.69
1843 1867 1.939934 CGTGTAATGTCATCGGCCATT 59.060 47.619 2.24 0.00 35.55 3.16
1850 1874 4.403453 GAAACAAGGCGTGTAATGTCATC 58.597 43.478 6.48 0.00 40.60 2.92
1851 1875 3.120338 CGAAACAAGGCGTGTAATGTCAT 60.120 43.478 6.48 0.00 40.60 3.06
1852 1876 2.222213 CGAAACAAGGCGTGTAATGTCA 59.778 45.455 6.48 0.00 40.60 3.58
1853 1877 2.477375 TCGAAACAAGGCGTGTAATGTC 59.523 45.455 6.48 1.94 40.60 3.06
1855 1879 2.222213 TGTCGAAACAAGGCGTGTAATG 59.778 45.455 6.48 0.00 40.60 1.90
1949 1977 7.646130 CGGTTTAAGAGCAGTTTCAAATTTACA 59.354 33.333 0.00 0.00 0.00 2.41
1989 2017 8.586273 CCGCATCTTTTTCATAACTATTGTTTG 58.414 33.333 0.00 0.00 37.59 2.93
2015 2043 5.403766 CACTGTTGGATAGATATCGTCAAGC 59.596 44.000 11.59 5.03 33.52 4.01
2042 2070 0.378257 CGTCGGAATGAGGCAAATGG 59.622 55.000 0.00 0.00 0.00 3.16
2114 2145 5.343307 AAGAGCAGTTTCAAAAATGGTGT 57.657 34.783 11.72 5.76 43.53 4.16
2688 2729 6.085849 CGCAAAAAGACACCGTAAGAAAATAC 59.914 38.462 0.00 0.00 43.02 1.89
2703 2744 4.844522 GTCTTATTTCCGACGCAAAAAGAC 59.155 41.667 16.31 16.31 0.00 3.01
2750 2791 6.096705 CCTTCTATTTTACCATCAATGCACCA 59.903 38.462 0.00 0.00 0.00 4.17
2773 2819 4.967036 GCAATAGCTATTCTTCACCTCCT 58.033 43.478 16.21 0.00 37.91 3.69
2788 2834 2.615912 GTCACCTTGGATGAGCAATAGC 59.384 50.000 0.00 0.00 42.56 2.97
2794 2840 2.029838 ATTCGTCACCTTGGATGAGC 57.970 50.000 0.00 0.00 34.50 4.26
2799 2845 0.459585 GCGCTATTCGTCACCTTGGA 60.460 55.000 0.00 0.00 41.07 3.53
2803 2849 1.226603 GTCGCGCTATTCGTCACCT 60.227 57.895 5.56 0.00 41.07 4.00


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

AutoCloner maintained by Alex Coulton.