Multiple sequence alignment - TraesCS5D01G034000

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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 TraesCS5D01G034000 chr5D 100.000 3375 0 0 1 3375 32809296 32812670 0.000000e+00 6233.0
1 TraesCS5D01G034000 chr5D 86.439 848 95 7 1517 2354 32699373 32698536 0.000000e+00 911.0
2 TraesCS5D01G034000 chr5D 90.596 436 35 4 983 1417 239492848 239493278 1.050000e-159 573.0
3 TraesCS5D01G034000 chr5D 80.741 675 84 21 657 1315 32709819 32709175 5.060000e-133 484.0
4 TraesCS5D01G034000 chr5D 92.116 241 14 3 1178 1417 423368694 423368458 5.400000e-88 335.0
5 TraesCS5D01G034000 chr5D 93.491 169 10 1 983 1151 423368855 423368688 2.010000e-62 250.0
6 TraesCS5D01G034000 chr5D 95.385 130 6 0 3 132 62071611 62071482 1.230000e-49 207.0
7 TraesCS5D01G034000 chr5D 94.595 37 0 1 3314 3350 170680298 170680264 4.700000e-04 56.5
8 TraesCS5D01G034000 chr5A 92.297 2142 109 35 663 2773 21418460 21420576 0.000000e+00 2990.0
9 TraesCS5D01G034000 chr5A 86.879 1570 149 31 833 2390 21415076 21413552 0.000000e+00 1705.0
10 TraesCS5D01G034000 chr5A 91.150 565 27 6 2773 3318 21420608 21421168 0.000000e+00 745.0
11 TraesCS5D01G034000 chr5A 86.580 462 38 10 233 680 21417997 21418448 3.910000e-134 488.0
12 TraesCS5D01G034000 chr5A 95.385 130 5 1 1 130 631788815 631788943 4.410000e-49 206.0
13 TraesCS5D01G034000 chr5A 92.727 110 8 0 3205 3314 337050782 337050891 3.490000e-35 159.0
14 TraesCS5D01G034000 chr5A 94.872 39 2 0 138 176 21416895 21416933 1.010000e-05 62.1
15 TraesCS5D01G034000 chr2A 87.235 1888 113 41 637 2467 38614891 38613075 0.000000e+00 2034.0
16 TraesCS5D01G034000 chr2A 94.118 136 8 0 1 136 311191559 311191424 1.230000e-49 207.0
17 TraesCS5D01G034000 chr6B 89.968 1585 97 22 834 2399 683371500 683373041 0.000000e+00 1989.0
18 TraesCS5D01G034000 chr6B 87.925 588 43 13 1892 2471 683317379 683317946 0.000000e+00 667.0
19 TraesCS5D01G034000 chr6B 89.849 463 29 12 834 1283 683316888 683317345 2.260000e-161 579.0
20 TraesCS5D01G034000 chr6B 90.930 430 31 4 983 1412 705881148 705880727 3.780000e-159 571.0
21 TraesCS5D01G034000 chr6B 87.209 430 25 11 983 1412 683411606 683411207 2.370000e-126 462.0
22 TraesCS5D01G034000 chr6B 82.353 221 13 11 640 840 683316638 683316852 5.790000e-38 169.0
23 TraesCS5D01G034000 chr2D 89.014 974 63 18 1506 2470 605386712 605385774 0.000000e+00 1166.0
24 TraesCS5D01G034000 chr2D 91.241 685 40 12 834 1510 605387620 605386948 0.000000e+00 915.0
25 TraesCS5D01G034000 chr2D 90.099 101 8 1 637 735 605387827 605387727 2.730000e-26 130.0
26 TraesCS5D01G034000 chr7D 93.836 438 20 5 983 1417 500956170 500956603 0.000000e+00 652.0
27 TraesCS5D01G034000 chr3D 76.361 1341 244 53 1066 2374 50425054 50426353 0.000000e+00 652.0
28 TraesCS5D01G034000 chr3D 75.477 1362 252 59 1038 2358 80568959 80567639 1.040000e-164 590.0
29 TraesCS5D01G034000 chr3D 83.309 677 55 17 2566 3201 491175054 491174395 3.780000e-159 571.0
30 TraesCS5D01G034000 chr3B 76.318 1347 236 53 1069 2374 79979184 79980488 0.000000e+00 643.0
31 TraesCS5D01G034000 chr3B 76.194 1319 248 45 1069 2358 126310679 126309398 1.320000e-178 636.0
32 TraesCS5D01G034000 chr3B 75.746 1340 267 47 1066 2374 126302784 126301472 3.700000e-174 621.0
33 TraesCS5D01G034000 chr3A 76.318 1347 232 50 1066 2374 63485406 63486703 1.020000e-179 640.0
34 TraesCS5D01G034000 chr3A 76.779 1124 203 41 1263 2360 94107021 94108112 8.120000e-161 577.0
35 TraesCS5D01G034000 chr3A 76.947 642 115 22 1391 2010 94102326 94102956 5.400000e-88 335.0
36 TraesCS5D01G034000 chr3A 83.929 112 16 2 3200 3309 343808677 343808566 4.610000e-19 106.0
37 TraesCS5D01G034000 chr3A 92.500 40 1 1 3311 3350 409802518 409802555 4.700000e-04 56.5
38 TraesCS5D01G034000 chr4A 90.995 422 33 3 989 1410 275447605 275448021 6.320000e-157 564.0
39 TraesCS5D01G034000 chr4A 79.769 692 81 24 2543 3201 174726257 174725592 6.640000e-122 448.0
40 TraesCS5D01G034000 chr4A 71.084 996 211 55 1073 2030 665438936 665439892 4.480000e-39 172.0
41 TraesCS5D01G034000 chr4A 96.774 62 2 0 1 62 177524371 177524310 1.660000e-18 104.0
42 TraesCS5D01G034000 chr4A 97.143 35 1 0 3314 3348 99001523 99001557 3.640000e-05 60.2
43 TraesCS5D01G034000 chr6A 84.668 587 53 22 2566 3120 553938284 553938865 4.920000e-153 551.0
44 TraesCS5D01G034000 chr6A 97.143 35 1 0 3314 3348 389564051 389564085 3.640000e-05 60.2
45 TraesCS5D01G034000 chr2B 82.570 677 60 21 2566 3201 690932394 690933053 8.240000e-151 544.0
46 TraesCS5D01G034000 chr2B 93.805 113 5 2 3199 3310 765197871 765197982 5.790000e-38 169.0
47 TraesCS5D01G034000 chr5B 88.276 435 44 6 1542 1973 24104702 24104272 6.460000e-142 514.0
48 TraesCS5D01G034000 chr5B 89.474 342 33 1 1154 1495 24105037 24104699 2.410000e-116 429.0
49 TraesCS5D01G034000 chr5B 91.279 172 15 0 2183 2354 24104276 24104105 5.630000e-58 235.0
50 TraesCS5D01G034000 chr5B 81.046 153 21 8 3161 3309 650159612 650159760 7.650000e-22 115.0
51 TraesCS5D01G034000 chr5B 92.683 41 3 0 735 775 24106702 24106662 3.640000e-05 60.2
52 TraesCS5D01G034000 chr6D 92.308 130 8 1 1 130 111430599 111430726 2.070000e-42 183.0
53 TraesCS5D01G034000 chr6D 94.595 37 0 1 3314 3350 353052028 353052062 4.700000e-04 56.5
54 TraesCS5D01G034000 chr1D 90.000 130 10 3 3186 3314 455801637 455801764 7.490000e-37 165.0
55 TraesCS5D01G034000 chr7B 92.174 115 7 2 3197 3310 424980078 424979965 9.690000e-36 161.0
56 TraesCS5D01G034000 chr1B 92.174 115 7 2 3197 3310 543806106 543805993 9.690000e-36 161.0
57 TraesCS5D01G034000 chr1A 89.431 123 13 0 3195 3317 494894231 494894109 4.510000e-34 156.0
58 TraesCS5D01G034000 chr7A 90.517 116 10 1 3198 3312 206711956 206712071 5.830000e-33 152.0
59 TraesCS5D01G034000 chr7A 94.737 38 2 0 3314 3351 31002729 31002692 3.640000e-05 60.2
60 TraesCS5D01G034000 chr7A 88.235 51 4 2 3314 3363 37349571 37349522 3.640000e-05 60.2
61 TraesCS5D01G034000 chrUn 84.667 150 15 6 3200 3348 121742705 121742563 3.510000e-30 143.0
62 TraesCS5D01G034000 chr4B 81.579 114 18 3 489 600 6064860 6064748 1.290000e-14 91.6


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 TraesCS5D01G034000 chr5D 32809296 32812670 3374 False 6233.000000 6233 100.00000 1 3375 1 chr5D.!!$F1 3374
1 TraesCS5D01G034000 chr5D 32698536 32699373 837 True 911.000000 911 86.43900 1517 2354 1 chr5D.!!$R1 837
2 TraesCS5D01G034000 chr5D 32709175 32709819 644 True 484.000000 484 80.74100 657 1315 1 chr5D.!!$R2 658
3 TraesCS5D01G034000 chr5A 21413552 21415076 1524 True 1705.000000 1705 86.87900 833 2390 1 chr5A.!!$R1 1557
4 TraesCS5D01G034000 chr5A 21416895 21421168 4273 False 1071.275000 2990 91.22475 138 3318 4 chr5A.!!$F3 3180
5 TraesCS5D01G034000 chr2A 38613075 38614891 1816 True 2034.000000 2034 87.23500 637 2467 1 chr2A.!!$R1 1830
6 TraesCS5D01G034000 chr6B 683371500 683373041 1541 False 1989.000000 1989 89.96800 834 2399 1 chr6B.!!$F1 1565
7 TraesCS5D01G034000 chr6B 683316638 683317946 1308 False 471.666667 667 86.70900 640 2471 3 chr6B.!!$F2 1831
8 TraesCS5D01G034000 chr2D 605385774 605387827 2053 True 737.000000 1166 90.11800 637 2470 3 chr2D.!!$R1 1833
9 TraesCS5D01G034000 chr3D 50425054 50426353 1299 False 652.000000 652 76.36100 1066 2374 1 chr3D.!!$F1 1308
10 TraesCS5D01G034000 chr3D 80567639 80568959 1320 True 590.000000 590 75.47700 1038 2358 1 chr3D.!!$R1 1320
11 TraesCS5D01G034000 chr3D 491174395 491175054 659 True 571.000000 571 83.30900 2566 3201 1 chr3D.!!$R2 635
12 TraesCS5D01G034000 chr3B 79979184 79980488 1304 False 643.000000 643 76.31800 1069 2374 1 chr3B.!!$F1 1305
13 TraesCS5D01G034000 chr3B 126309398 126310679 1281 True 636.000000 636 76.19400 1069 2358 1 chr3B.!!$R2 1289
14 TraesCS5D01G034000 chr3B 126301472 126302784 1312 True 621.000000 621 75.74600 1066 2374 1 chr3B.!!$R1 1308
15 TraesCS5D01G034000 chr3A 63485406 63486703 1297 False 640.000000 640 76.31800 1066 2374 1 chr3A.!!$F1 1308
16 TraesCS5D01G034000 chr3A 94107021 94108112 1091 False 577.000000 577 76.77900 1263 2360 1 chr3A.!!$F3 1097
17 TraesCS5D01G034000 chr3A 94102326 94102956 630 False 335.000000 335 76.94700 1391 2010 1 chr3A.!!$F2 619
18 TraesCS5D01G034000 chr4A 174725592 174726257 665 True 448.000000 448 79.76900 2543 3201 1 chr4A.!!$R1 658
19 TraesCS5D01G034000 chr6A 553938284 553938865 581 False 551.000000 551 84.66800 2566 3120 1 chr6A.!!$F2 554
20 TraesCS5D01G034000 chr2B 690932394 690933053 659 False 544.000000 544 82.57000 2566 3201 1 chr2B.!!$F1 635
21 TraesCS5D01G034000 chr5B 24104105 24106702 2597 True 309.550000 514 90.42800 735 2354 4 chr5B.!!$R1 1619

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
268 1276 0.098376 CGACAGGCTAGGTACACGAC 59.902 60.0 0.0 0.0 0.0 4.34 F
519 1541 0.238553 GGTCTCTTTTCGCCTTGTGC 59.761 55.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 3656 0.315568 GCCGTCAGTGTCAGAAGAGT 59.684 55.000 0.00 0.00 0.00 3.24 R
2477 5390 1.460743 CCAGACACATGTGCGTACAAG 59.539 52.381 25.68 9.11 40.84 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
26 27 6.693761 AACAGTACAAACGGTTTTCAAAAC 57.306 33.333 4.25 4.25 40.51 2.43
31 32 2.827152 CGGTTTTCAAAACGCGCG 59.173 55.556 30.96 30.96 42.60 6.86
32 33 2.537578 GGTTTTCAAAACGCGCGC 59.462 55.556 32.58 23.91 0.00 6.86
33 34 2.537578 GTTTTCAAAACGCGCGCC 59.462 55.556 32.58 8.11 0.00 6.53
34 35 2.655685 TTTTCAAAACGCGCGCCC 60.656 55.556 32.58 0.00 0.00 6.13
35 36 3.411418 TTTTCAAAACGCGCGCCCA 62.411 52.632 32.58 6.56 0.00 5.36
36 37 2.884087 TTTTCAAAACGCGCGCCCAA 62.884 50.000 32.58 12.96 0.00 4.12
37 38 4.615834 TCAAAACGCGCGCCCAAC 62.616 61.111 32.58 0.00 0.00 3.77
38 39 4.914420 CAAAACGCGCGCCCAACA 62.914 61.111 32.58 0.00 0.00 3.33
39 40 4.194720 AAAACGCGCGCCCAACAA 62.195 55.556 32.58 0.00 0.00 2.83
40 41 3.701604 AAAACGCGCGCCCAACAAA 62.702 52.632 32.58 0.00 0.00 2.83
41 42 4.622456 AACGCGCGCCCAACAAAG 62.622 61.111 32.58 11.44 0.00 2.77
43 44 4.320928 CGCGCGCCCAACAAAGAA 62.321 61.111 27.72 0.00 0.00 2.52
44 45 2.026879 GCGCGCCCAACAAAGAAA 59.973 55.556 23.24 0.00 0.00 2.52
45 46 2.300066 GCGCGCCCAACAAAGAAAC 61.300 57.895 23.24 0.00 0.00 2.78
46 47 1.064946 CGCGCCCAACAAAGAAACA 59.935 52.632 0.00 0.00 0.00 2.83
47 48 0.934436 CGCGCCCAACAAAGAAACAG 60.934 55.000 0.00 0.00 0.00 3.16
48 49 0.383949 GCGCCCAACAAAGAAACAGA 59.616 50.000 0.00 0.00 0.00 3.41
49 50 1.600413 GCGCCCAACAAAGAAACAGAG 60.600 52.381 0.00 0.00 0.00 3.35
50 51 1.946768 CGCCCAACAAAGAAACAGAGA 59.053 47.619 0.00 0.00 0.00 3.10
51 52 2.357637 CGCCCAACAAAGAAACAGAGAA 59.642 45.455 0.00 0.00 0.00 2.87
52 53 3.181491 CGCCCAACAAAGAAACAGAGAAA 60.181 43.478 0.00 0.00 0.00 2.52
53 54 4.112634 GCCCAACAAAGAAACAGAGAAAC 58.887 43.478 0.00 0.00 0.00 2.78
54 55 4.351192 CCCAACAAAGAAACAGAGAAACG 58.649 43.478 0.00 0.00 0.00 3.60
55 56 3.791353 CCAACAAAGAAACAGAGAAACGC 59.209 43.478 0.00 0.00 0.00 4.84
56 57 3.319238 ACAAAGAAACAGAGAAACGCG 57.681 42.857 3.53 3.53 0.00 6.01
57 58 2.031683 ACAAAGAAACAGAGAAACGCGG 59.968 45.455 12.47 0.00 0.00 6.46
58 59 0.586802 AAGAAACAGAGAAACGCGGC 59.413 50.000 12.47 0.00 0.00 6.53
59 60 1.206831 GAAACAGAGAAACGCGGCC 59.793 57.895 12.47 0.00 0.00 6.13
60 61 2.183858 GAAACAGAGAAACGCGGCCC 62.184 60.000 12.47 0.00 0.00 5.80
61 62 2.951475 AAACAGAGAAACGCGGCCCA 62.951 55.000 12.47 0.00 0.00 5.36
62 63 2.668212 CAGAGAAACGCGGCCCAA 60.668 61.111 12.47 0.00 0.00 4.12
63 64 2.112297 AGAGAAACGCGGCCCAAA 59.888 55.556 12.47 0.00 0.00 3.28
64 65 2.254350 GAGAAACGCGGCCCAAAC 59.746 61.111 12.47 0.00 0.00 2.93
65 66 2.517402 AGAAACGCGGCCCAAACA 60.517 55.556 12.47 0.00 0.00 2.83
66 67 2.050442 GAAACGCGGCCCAAACAG 60.050 61.111 12.47 0.00 0.00 3.16
67 68 4.279043 AAACGCGGCCCAAACAGC 62.279 61.111 12.47 0.00 0.00 4.40
73 74 2.438795 GGCCCAAACAGCCCACTA 59.561 61.111 0.00 0.00 45.16 2.74
74 75 1.678970 GGCCCAAACAGCCCACTAG 60.679 63.158 0.00 0.00 45.16 2.57
75 76 2.343426 GCCCAAACAGCCCACTAGC 61.343 63.158 0.00 0.00 0.00 3.42
76 77 2.040544 CCCAAACAGCCCACTAGCG 61.041 63.158 0.00 0.00 38.01 4.26
77 78 1.003839 CCAAACAGCCCACTAGCGA 60.004 57.895 0.00 0.00 38.01 4.93
78 79 0.605319 CCAAACAGCCCACTAGCGAA 60.605 55.000 0.00 0.00 38.01 4.70
79 80 1.453155 CAAACAGCCCACTAGCGAAT 58.547 50.000 0.00 0.00 38.01 3.34
80 81 1.398390 CAAACAGCCCACTAGCGAATC 59.602 52.381 0.00 0.00 38.01 2.52
81 82 0.107654 AACAGCCCACTAGCGAATCC 60.108 55.000 0.00 0.00 38.01 3.01
82 83 1.227674 CAGCCCACTAGCGAATCCC 60.228 63.158 0.00 0.00 38.01 3.85
83 84 2.111251 GCCCACTAGCGAATCCCC 59.889 66.667 0.00 0.00 0.00 4.81
84 85 2.829592 CCCACTAGCGAATCCCCC 59.170 66.667 0.00 0.00 0.00 5.40
105 106 4.595538 TGCGAACGCCCGACACTT 62.596 61.111 16.27 0.00 41.09 3.16
106 107 3.343421 GCGAACGCCCGACACTTT 61.343 61.111 8.03 0.00 34.56 2.66
107 108 2.549282 CGAACGCCCGACACTTTG 59.451 61.111 0.00 0.00 0.00 2.77
108 109 1.952133 CGAACGCCCGACACTTTGA 60.952 57.895 0.00 0.00 0.00 2.69
109 110 1.568025 GAACGCCCGACACTTTGAC 59.432 57.895 0.00 0.00 0.00 3.18
110 111 1.153329 AACGCCCGACACTTTGACA 60.153 52.632 0.00 0.00 0.00 3.58
111 112 1.433837 AACGCCCGACACTTTGACAC 61.434 55.000 0.00 0.00 0.00 3.67
112 113 1.885388 CGCCCGACACTTTGACACA 60.885 57.895 0.00 0.00 0.00 3.72
113 114 1.831389 CGCCCGACACTTTGACACAG 61.831 60.000 0.00 0.00 0.00 3.66
114 115 0.531974 GCCCGACACTTTGACACAGA 60.532 55.000 0.00 0.00 0.00 3.41
115 116 1.948104 CCCGACACTTTGACACAGAA 58.052 50.000 0.00 0.00 0.00 3.02
116 117 2.494059 CCCGACACTTTGACACAGAAT 58.506 47.619 0.00 0.00 0.00 2.40
117 118 2.224079 CCCGACACTTTGACACAGAATG 59.776 50.000 0.00 0.00 46.00 2.67
118 119 2.349817 CCGACACTTTGACACAGAATGC 60.350 50.000 0.00 0.00 42.53 3.56
119 120 2.660094 CGACACTTTGACACAGAATGCG 60.660 50.000 0.00 0.00 42.53 4.73
120 121 2.287915 GACACTTTGACACAGAATGCGT 59.712 45.455 0.00 0.00 42.53 5.24
128 129 3.043586 GACACAGAATGCGTCGTATAGG 58.956 50.000 0.00 0.00 38.50 2.57
129 130 2.686405 ACACAGAATGCGTCGTATAGGA 59.314 45.455 0.00 0.00 42.53 2.94
130 131 3.043586 CACAGAATGCGTCGTATAGGAC 58.956 50.000 14.29 14.29 42.53 3.85
131 132 2.034305 ACAGAATGCGTCGTATAGGACC 59.966 50.000 17.57 11.79 42.53 4.46
132 133 1.266175 AGAATGCGTCGTATAGGACCG 59.734 52.381 17.57 13.84 33.30 4.79
133 134 0.318445 AATGCGTCGTATAGGACCGC 60.318 55.000 23.26 23.26 37.15 5.68
134 135 2.050623 GCGTCGTATAGGACCGCC 60.051 66.667 21.22 9.18 33.47 6.13
135 136 2.641559 CGTCGTATAGGACCGCCC 59.358 66.667 17.57 0.00 33.30 6.13
141 142 1.460689 TATAGGACCGCCCTTGGGG 60.461 63.158 7.91 1.39 44.85 4.96
176 177 4.811555 TGCTTACATCGATGTTTATGCC 57.188 40.909 34.06 17.23 41.97 4.40
177 178 3.563808 TGCTTACATCGATGTTTATGCCC 59.436 43.478 34.06 16.31 41.97 5.36
178 179 3.815401 GCTTACATCGATGTTTATGCCCT 59.185 43.478 34.06 10.27 41.97 5.19
182 183 1.934589 TCGATGTTTATGCCCTGACG 58.065 50.000 0.00 0.00 0.00 4.35
183 184 0.304705 CGATGTTTATGCCCTGACGC 59.695 55.000 0.00 0.00 0.00 5.19
184 185 1.378531 GATGTTTATGCCCTGACGCA 58.621 50.000 0.00 0.00 44.35 5.24
186 187 1.295357 TGTTTATGCCCTGACGCACG 61.295 55.000 0.00 0.00 42.70 5.34
187 188 1.743623 TTTATGCCCTGACGCACGG 60.744 57.895 0.00 0.00 42.70 4.94
188 189 3.673956 TTATGCCCTGACGCACGGG 62.674 63.158 0.00 1.60 42.70 5.28
194 195 4.988598 CTGACGCACGGGGCACTT 62.989 66.667 1.92 0.00 45.17 3.16
195 196 3.583276 CTGACGCACGGGGCACTTA 62.583 63.158 1.92 0.00 45.17 2.24
196 197 2.813908 GACGCACGGGGCACTTAG 60.814 66.667 1.92 0.00 45.17 2.18
199 200 2.032071 GCACGGGGCACTTAGTGT 59.968 61.111 14.23 0.00 43.97 3.55
208 209 1.669115 CACTTAGTGTGCGGCTGCT 60.669 57.895 20.27 0.00 43.34 4.24
209 210 1.071471 ACTTAGTGTGCGGCTGCTT 59.929 52.632 20.27 4.41 43.34 3.91
212 213 0.950555 TTAGTGTGCGGCTGCTTCTG 60.951 55.000 20.27 0.00 43.34 3.02
214 215 4.254709 TGTGCGGCTGCTTCTGGT 62.255 61.111 20.27 0.00 43.34 4.00
215 216 3.730761 GTGCGGCTGCTTCTGGTG 61.731 66.667 20.27 0.00 43.34 4.17
216 217 4.254709 TGCGGCTGCTTCTGGTGT 62.255 61.111 20.27 0.00 43.34 4.16
217 218 3.426568 GCGGCTGCTTCTGGTGTC 61.427 66.667 11.21 0.00 38.39 3.67
218 219 2.345244 CGGCTGCTTCTGGTGTCT 59.655 61.111 0.00 0.00 0.00 3.41
220 221 1.572085 CGGCTGCTTCTGGTGTCTTG 61.572 60.000 0.00 0.00 0.00 3.02
222 223 0.871057 GCTGCTTCTGGTGTCTTGAC 59.129 55.000 0.00 0.00 0.00 3.18
223 224 1.517242 CTGCTTCTGGTGTCTTGACC 58.483 55.000 0.00 0.00 36.43 4.02
225 226 0.108585 GCTTCTGGTGTCTTGACCCA 59.891 55.000 9.46 9.46 34.79 4.51
228 229 0.757561 TCTGGTGTCTTGACCCACGA 60.758 55.000 0.00 6.61 34.79 4.35
229 230 0.600255 CTGGTGTCTTGACCCACGAC 60.600 60.000 0.00 0.00 34.79 4.34
230 231 1.301479 GGTGTCTTGACCCACGACC 60.301 63.158 0.00 0.00 32.71 4.79
232 233 2.346365 GTCTTGACCCACGACCCC 59.654 66.667 0.00 0.00 28.30 4.95
233 234 2.926242 TCTTGACCCACGACCCCC 60.926 66.667 0.00 0.00 0.00 5.40
235 236 4.938074 TTGACCCACGACCCCCGA 62.938 66.667 0.00 0.00 41.76 5.14
242 1250 2.043248 ACGACCCCCGACTAGCAT 60.043 61.111 0.00 0.00 41.76 3.79
268 1276 0.098376 CGACAGGCTAGGTACACGAC 59.902 60.000 0.00 0.00 0.00 4.34
277 1285 1.514553 GGTACACGACCCAGGTAGC 59.485 63.158 0.00 0.00 43.25 3.58
281 1289 1.125711 ACACGACCCAGGTAGCCTTT 61.126 55.000 0.00 0.00 0.00 3.11
282 1290 0.673644 CACGACCCAGGTAGCCTTTG 60.674 60.000 0.00 0.00 0.00 2.77
294 1302 0.397941 AGCCTTTGAGCACTGTAGCA 59.602 50.000 5.32 0.00 36.85 3.49
298 1320 2.289320 CCTTTGAGCACTGTAGCAGACT 60.289 50.000 2.91 0.23 35.18 3.24
328 1350 1.002857 AGCAAGGAAACTAGGCCCAT 58.997 50.000 0.00 0.00 42.68 4.00
329 1351 1.106285 GCAAGGAAACTAGGCCCATG 58.894 55.000 0.00 0.00 42.68 3.66
405 1427 8.379457 AGTTTCTATTCTTTAAACTGTTCGCT 57.621 30.769 0.00 0.00 40.85 4.93
462 1484 0.251209 TAGCCTCTCTGTGTGGACGT 60.251 55.000 0.00 0.00 0.00 4.34
484 1506 3.838271 GGGCGCGAGATCCAGTCA 61.838 66.667 12.10 0.00 0.00 3.41
488 1510 1.227089 CGCGAGATCCAGTCAAGGG 60.227 63.158 0.00 0.00 0.00 3.95
517 1539 1.228657 GCGGTCTCTTTTCGCCTTGT 61.229 55.000 0.00 0.00 43.17 3.16
519 1541 0.238553 GGTCTCTTTTCGCCTTGTGC 59.761 55.000 0.00 0.00 0.00 4.57
568 1590 3.440415 GGGCGCCAGTTACCTTGC 61.440 66.667 30.85 1.84 0.00 4.01
569 1591 3.440415 GGCGCCAGTTACCTTGCC 61.440 66.667 24.80 0.00 35.04 4.52
573 1595 2.750237 CCAGTTACCTTGCCCGCC 60.750 66.667 0.00 0.00 0.00 6.13
574 1596 3.124921 CAGTTACCTTGCCCGCCG 61.125 66.667 0.00 0.00 0.00 6.46
577 1599 3.392243 TTACCTTGCCCGCCGCTA 61.392 61.111 0.00 0.00 38.78 4.26
578 1600 2.957080 TTACCTTGCCCGCCGCTAA 61.957 57.895 0.00 0.00 38.78 3.09
579 1601 2.466523 TTACCTTGCCCGCCGCTAAA 62.467 55.000 0.00 0.00 38.78 1.85
580 1602 2.862674 TACCTTGCCCGCCGCTAAAG 62.863 60.000 0.00 0.00 38.78 1.85
581 1603 3.508840 CTTGCCCGCCGCTAAAGG 61.509 66.667 0.00 0.00 38.78 3.11
598 1620 2.967615 GCGCGCAATAGGAGGTCC 60.968 66.667 29.10 0.00 0.00 4.46
599 1621 2.280186 CGCGCAATAGGAGGTCCC 60.280 66.667 8.75 0.00 36.42 4.46
623 1645 5.870978 CCTAAAACATGGCCAGATGAAAAAG 59.129 40.000 13.05 1.67 0.00 2.27
625 1647 4.796038 AACATGGCCAGATGAAAAAGAG 57.204 40.909 13.05 0.00 0.00 2.85
746 1826 5.420104 AGAATCAATTGATTGTCTTCCCACC 59.580 40.000 32.89 16.77 44.14 4.61
837 1923 7.723172 ACTTATACCGCCTTCAAGTATAGTAGT 59.277 37.037 0.00 0.00 32.21 2.73
838 1924 9.224267 CTTATACCGCCTTCAAGTATAGTAGTA 57.776 37.037 0.00 0.00 32.21 1.82
919 2048 1.134175 CTTTTGAAACACACTGCCCGT 59.866 47.619 0.00 0.00 0.00 5.28
960 2089 8.407064 TGAGAAGAAGATCGAGTTAGGAATTAC 58.593 37.037 0.00 0.00 0.00 1.89
961 2090 8.528044 AGAAGAAGATCGAGTTAGGAATTACT 57.472 34.615 0.00 0.00 0.00 2.24
962 2091 9.629878 AGAAGAAGATCGAGTTAGGAATTACTA 57.370 33.333 0.00 0.00 0.00 1.82
1083 2237 4.424566 GACGGCGGGTTCAGCGTA 62.425 66.667 13.24 0.00 35.00 4.42
1128 2282 2.203523 TCTCCGTTCCACGACCCA 60.204 61.111 0.00 0.00 46.05 4.51
1132 2286 2.048503 CGTTCCACGACCCAGTCC 60.049 66.667 0.00 0.00 46.05 3.85
1188 3656 3.506096 CTCGTACGCCGGCTCAGA 61.506 66.667 26.68 16.73 37.11 3.27
1352 3869 1.302511 GGTTCTGCTTCTCCGGCAA 60.303 57.895 0.00 0.00 39.30 4.52
1353 3870 1.578206 GGTTCTGCTTCTCCGGCAAC 61.578 60.000 0.00 0.00 39.30 4.17
1414 3943 0.252197 TCGACATCTCCTCCTCGTCA 59.748 55.000 0.00 0.00 0.00 4.35
1510 4039 2.619177 CTGCCAGTACAGCTACTCGTAT 59.381 50.000 9.06 0.00 30.03 3.06
1522 4291 4.246206 TCGTATGTCGGCGGCTCG 62.246 66.667 14.51 14.86 40.32 5.03
1570 4339 2.049802 TTCACCTTCGACGACGCC 60.050 61.111 1.48 0.00 39.58 5.68
2370 5260 1.137086 CGCCCTCTGTTGTGTAGCTAT 59.863 52.381 0.00 0.00 0.00 2.97
2400 5290 2.686915 AGCTAATCGCCACGTAAGTAGT 59.313 45.455 0.00 0.00 46.34 2.73
2438 5328 9.645059 CCATGTCTTCTATGGTGTTATATACAG 57.355 37.037 0.00 0.00 40.15 2.74
2477 5390 3.057456 TCTTCAACGAAGTAGTCCAGCTC 60.057 47.826 3.81 0.00 45.00 4.09
2494 5407 1.126846 GCTCTTGTACGCACATGTGTC 59.873 52.381 26.01 17.03 39.74 3.67
2514 5427 3.570125 GTCTGGAAGGGAAAAGAACCAAG 59.430 47.826 0.00 0.00 0.00 3.61
2519 5432 0.969149 GGGAAAAGAACCAAGCCAGG 59.031 55.000 0.00 0.00 0.00 4.45
2533 5446 4.082245 CCAAGCCAGGGTAATAACAAACAG 60.082 45.833 0.00 0.00 0.00 3.16
2535 5448 4.993028 AGCCAGGGTAATAACAAACAGAA 58.007 39.130 0.00 0.00 0.00 3.02
2536 5449 5.580022 AGCCAGGGTAATAACAAACAGAAT 58.420 37.500 0.00 0.00 0.00 2.40
2538 5451 5.417580 GCCAGGGTAATAACAAACAGAATCA 59.582 40.000 0.00 0.00 0.00 2.57
2539 5452 6.404734 GCCAGGGTAATAACAAACAGAATCAG 60.405 42.308 0.00 0.00 0.00 2.90
2540 5453 6.095440 CCAGGGTAATAACAAACAGAATCAGG 59.905 42.308 0.00 0.00 0.00 3.86
2541 5454 6.884295 CAGGGTAATAACAAACAGAATCAGGA 59.116 38.462 0.00 0.00 0.00 3.86
2552 5465 3.011821 ACAGAATCAGGAGGGACTGTCTA 59.988 47.826 7.85 0.00 41.55 2.59
2558 5471 7.570607 AGAATCAGGAGGGACTGTCTATTTTAT 59.429 37.037 7.85 0.00 41.55 1.40
2563 5476 8.097662 CAGGAGGGACTGTCTATTTTATATTCC 58.902 40.741 7.85 0.00 41.55 3.01
2601 5514 4.676924 CGTTTTCAGTCAGATTTTTCAGCC 59.323 41.667 0.00 0.00 0.00 4.85
2603 5516 5.850557 TTTCAGTCAGATTTTTCAGCCAA 57.149 34.783 0.00 0.00 0.00 4.52
2634 5547 1.768275 ACAAGTGTCACATGTCCTCCA 59.232 47.619 8.01 0.00 0.00 3.86
2793 5742 3.837399 ACAGTTCCCTCTCCTACTTCT 57.163 47.619 0.00 0.00 0.00 2.85
2794 5743 4.134933 ACAGTTCCCTCTCCTACTTCTT 57.865 45.455 0.00 0.00 0.00 2.52
2900 5853 2.039613 GGAGAATGAGGTCATGGGATCC 59.960 54.545 1.92 1.92 36.56 3.36
2947 5900 6.027482 TCAAACTCCCCCTTTACATAGTACT 58.973 40.000 0.00 0.00 0.00 2.73
3015 5970 6.071784 TGTGAGCAGTGATCATTTTAGCAAAT 60.072 34.615 15.17 0.00 32.36 2.32
3042 5997 7.859325 ACAGTGACTTTTACAGTACAATTGT 57.141 32.000 16.68 16.68 35.01 2.71
3278 6263 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3310 6295 7.639113 TGCATCTATATACATCCGTATGTGA 57.361 36.000 3.56 0.00 45.99 3.58
3324 6309 9.534565 CATCCGTATGTGATCCTTATATTTAGG 57.465 37.037 0.00 0.00 0.00 2.69
3325 6310 8.888836 TCCGTATGTGATCCTTATATTTAGGA 57.111 34.615 8.29 8.29 45.45 2.94
3326 6311 9.316594 TCCGTATGTGATCCTTATATTTAGGAA 57.683 33.333 9.57 0.00 44.59 3.36
3332 6317 8.605947 TGTGATCCTTATATTTAGGAATGGAGG 58.394 37.037 9.57 0.00 44.59 4.30
3333 6318 8.049721 GTGATCCTTATATTTAGGAATGGAGGG 58.950 40.741 9.57 0.00 44.59 4.30
3334 6319 7.967170 TGATCCTTATATTTAGGAATGGAGGGA 59.033 37.037 9.57 0.00 44.59 4.20
3335 6320 7.814693 TCCTTATATTTAGGAATGGAGGGAG 57.185 40.000 4.28 0.00 38.83 4.30
3336 6321 7.321530 TCCTTATATTTAGGAATGGAGGGAGT 58.678 38.462 4.28 0.00 38.83 3.85
3337 6322 8.470109 TCCTTATATTTAGGAATGGAGGGAGTA 58.530 37.037 4.28 0.00 38.83 2.59
3338 6323 8.763601 CCTTATATTTAGGAATGGAGGGAGTAG 58.236 40.741 0.00 0.00 34.56 2.57
3339 6324 9.327731 CTTATATTTAGGAATGGAGGGAGTAGT 57.672 37.037 0.00 0.00 0.00 2.73
3341 6326 8.903059 ATATTTAGGAATGGAGGGAGTAGTAG 57.097 38.462 0.00 0.00 0.00 2.57
3342 6327 6.351317 TTTAGGAATGGAGGGAGTAGTAGA 57.649 41.667 0.00 0.00 0.00 2.59
3343 6328 6.547396 TTAGGAATGGAGGGAGTAGTAGAT 57.453 41.667 0.00 0.00 0.00 1.98
3344 6329 5.426325 AGGAATGGAGGGAGTAGTAGATT 57.574 43.478 0.00 0.00 0.00 2.40
3345 6330 5.793967 AGGAATGGAGGGAGTAGTAGATTT 58.206 41.667 0.00 0.00 0.00 2.17
3346 6331 6.935036 AGGAATGGAGGGAGTAGTAGATTTA 58.065 40.000 0.00 0.00 0.00 1.40
3347 6332 7.549141 AGGAATGGAGGGAGTAGTAGATTTAT 58.451 38.462 0.00 0.00 0.00 1.40
3348 6333 8.689054 AGGAATGGAGGGAGTAGTAGATTTATA 58.311 37.037 0.00 0.00 0.00 0.98
3349 6334 9.495382 GGAATGGAGGGAGTAGTAGATTTATAT 57.505 37.037 0.00 0.00 0.00 0.86
3352 6337 9.845214 ATGGAGGGAGTAGTAGATTTATATTGT 57.155 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.649977 TGAAAACCGTTTGTACTGTTTCG 58.350 39.130 0.00 0.00 39.71 3.46
1 2 6.931243 TTTGAAAACCGTTTGTACTGTTTC 57.069 33.333 0.00 0.00 39.71 2.78
2 3 6.129141 CGTTTTGAAAACCGTTTGTACTGTTT 60.129 34.615 14.50 0.00 41.55 2.83
3 4 5.342791 CGTTTTGAAAACCGTTTGTACTGTT 59.657 36.000 14.50 0.00 33.77 3.16
4 5 4.852650 CGTTTTGAAAACCGTTTGTACTGT 59.147 37.500 14.50 0.00 0.00 3.55
5 6 4.259095 GCGTTTTGAAAACCGTTTGTACTG 60.259 41.667 14.50 0.00 0.00 2.74
6 7 3.853103 GCGTTTTGAAAACCGTTTGTACT 59.147 39.130 14.50 0.00 0.00 2.73
7 8 3.300440 CGCGTTTTGAAAACCGTTTGTAC 60.300 43.478 14.50 0.00 0.00 2.90
8 9 2.844804 CGCGTTTTGAAAACCGTTTGTA 59.155 40.909 14.50 0.00 0.00 2.41
9 10 1.649662 CGCGTTTTGAAAACCGTTTGT 59.350 42.857 14.50 0.00 0.00 2.83
10 11 1.587847 GCGCGTTTTGAAAACCGTTTG 60.588 47.619 22.68 9.66 0.00 2.93
11 12 0.641275 GCGCGTTTTGAAAACCGTTT 59.359 45.000 22.68 0.00 0.00 3.60
12 13 1.465209 CGCGCGTTTTGAAAACCGTT 61.465 50.000 24.19 0.00 0.00 4.44
13 14 1.935436 CGCGCGTTTTGAAAACCGT 60.935 52.632 24.19 0.00 0.00 4.83
14 15 2.827152 CGCGCGTTTTGAAAACCG 59.173 55.556 24.19 19.84 0.00 4.44
15 16 2.537578 GCGCGCGTTTTGAAAACC 59.462 55.556 32.35 6.30 0.00 3.27
16 17 2.537578 GGCGCGCGTTTTGAAAAC 59.462 55.556 32.35 10.62 0.00 2.43
17 18 2.655685 GGGCGCGCGTTTTGAAAA 60.656 55.556 32.35 0.00 0.00 2.29
18 19 3.411418 TTGGGCGCGCGTTTTGAAA 62.411 52.632 32.35 14.25 0.00 2.69
19 20 3.889044 TTGGGCGCGCGTTTTGAA 61.889 55.556 32.35 14.10 0.00 2.69
20 21 4.615834 GTTGGGCGCGCGTTTTGA 62.616 61.111 32.35 11.23 0.00 2.69
21 22 4.914420 TGTTGGGCGCGCGTTTTG 62.914 61.111 32.35 2.67 0.00 2.44
22 23 3.701604 TTTGTTGGGCGCGCGTTTT 62.702 52.632 32.35 0.00 0.00 2.43
23 24 4.194720 TTTGTTGGGCGCGCGTTT 62.195 55.556 32.35 0.00 0.00 3.60
24 25 4.622456 CTTTGTTGGGCGCGCGTT 62.622 61.111 32.35 0.00 0.00 4.84
26 27 3.815569 TTTCTTTGTTGGGCGCGCG 62.816 57.895 28.44 28.44 0.00 6.86
27 28 2.026879 TTTCTTTGTTGGGCGCGC 59.973 55.556 25.94 25.94 0.00 6.86
28 29 0.934436 CTGTTTCTTTGTTGGGCGCG 60.934 55.000 0.00 0.00 0.00 6.86
29 30 0.383949 TCTGTTTCTTTGTTGGGCGC 59.616 50.000 0.00 0.00 0.00 6.53
30 31 1.946768 TCTCTGTTTCTTTGTTGGGCG 59.053 47.619 0.00 0.00 0.00 6.13
31 32 4.112634 GTTTCTCTGTTTCTTTGTTGGGC 58.887 43.478 0.00 0.00 0.00 5.36
32 33 4.351192 CGTTTCTCTGTTTCTTTGTTGGG 58.649 43.478 0.00 0.00 0.00 4.12
33 34 3.791353 GCGTTTCTCTGTTTCTTTGTTGG 59.209 43.478 0.00 0.00 0.00 3.77
34 35 3.478516 CGCGTTTCTCTGTTTCTTTGTTG 59.521 43.478 0.00 0.00 0.00 3.33
35 36 3.486875 CCGCGTTTCTCTGTTTCTTTGTT 60.487 43.478 4.92 0.00 0.00 2.83
36 37 2.031683 CCGCGTTTCTCTGTTTCTTTGT 59.968 45.455 4.92 0.00 0.00 2.83
37 38 2.639751 CCGCGTTTCTCTGTTTCTTTG 58.360 47.619 4.92 0.00 0.00 2.77
38 39 1.002792 GCCGCGTTTCTCTGTTTCTTT 60.003 47.619 4.92 0.00 0.00 2.52
39 40 0.586802 GCCGCGTTTCTCTGTTTCTT 59.413 50.000 4.92 0.00 0.00 2.52
40 41 1.228657 GGCCGCGTTTCTCTGTTTCT 61.229 55.000 4.92 0.00 0.00 2.52
41 42 1.206831 GGCCGCGTTTCTCTGTTTC 59.793 57.895 4.92 0.00 0.00 2.78
42 43 2.258726 GGGCCGCGTTTCTCTGTTT 61.259 57.895 4.92 0.00 0.00 2.83
43 44 2.668550 GGGCCGCGTTTCTCTGTT 60.669 61.111 4.92 0.00 0.00 3.16
44 45 2.951475 TTTGGGCCGCGTTTCTCTGT 62.951 55.000 4.92 0.00 0.00 3.41
45 46 2.258013 TTTGGGCCGCGTTTCTCTG 61.258 57.895 4.92 0.00 0.00 3.35
46 47 2.112297 TTTGGGCCGCGTTTCTCT 59.888 55.556 4.92 0.00 0.00 3.10
47 48 2.254350 GTTTGGGCCGCGTTTCTC 59.746 61.111 4.92 0.00 0.00 2.87
48 49 2.517402 TGTTTGGGCCGCGTTTCT 60.517 55.556 4.92 0.00 0.00 2.52
49 50 2.050442 CTGTTTGGGCCGCGTTTC 60.050 61.111 4.92 0.00 0.00 2.78
50 51 4.279043 GCTGTTTGGGCCGCGTTT 62.279 61.111 4.92 0.00 0.00 3.60
57 58 2.343426 GCTAGTGGGCTGTTTGGGC 61.343 63.158 0.00 0.00 0.00 5.36
58 59 2.040544 CGCTAGTGGGCTGTTTGGG 61.041 63.158 0.00 0.00 0.00 4.12
59 60 0.605319 TTCGCTAGTGGGCTGTTTGG 60.605 55.000 2.90 0.00 0.00 3.28
60 61 1.398390 GATTCGCTAGTGGGCTGTTTG 59.602 52.381 2.90 0.00 0.00 2.93
61 62 1.679032 GGATTCGCTAGTGGGCTGTTT 60.679 52.381 2.90 0.00 0.00 2.83
62 63 0.107654 GGATTCGCTAGTGGGCTGTT 60.108 55.000 2.90 0.00 0.00 3.16
63 64 1.522569 GGATTCGCTAGTGGGCTGT 59.477 57.895 2.90 0.00 0.00 4.40
64 65 1.227674 GGGATTCGCTAGTGGGCTG 60.228 63.158 2.90 0.00 0.00 4.85
65 66 2.444256 GGGGATTCGCTAGTGGGCT 61.444 63.158 2.90 0.00 0.00 5.19
66 67 2.111251 GGGGATTCGCTAGTGGGC 59.889 66.667 2.90 0.00 0.00 5.36
67 68 2.829592 GGGGGATTCGCTAGTGGG 59.170 66.667 2.90 0.00 0.00 4.61
88 89 4.595538 AAGTGTCGGGCGTTCGCA 62.596 61.111 18.46 0.00 0.00 5.10
89 90 3.343421 AAAGTGTCGGGCGTTCGC 61.343 61.111 8.75 8.75 0.00 4.70
90 91 1.952133 TCAAAGTGTCGGGCGTTCG 60.952 57.895 0.00 0.00 0.00 3.95
91 92 1.155424 TGTCAAAGTGTCGGGCGTTC 61.155 55.000 0.00 0.00 0.00 3.95
92 93 1.153329 TGTCAAAGTGTCGGGCGTT 60.153 52.632 0.00 0.00 0.00 4.84
93 94 1.885850 GTGTCAAAGTGTCGGGCGT 60.886 57.895 0.00 0.00 0.00 5.68
94 95 1.831389 CTGTGTCAAAGTGTCGGGCG 61.831 60.000 0.00 0.00 0.00 6.13
95 96 0.531974 TCTGTGTCAAAGTGTCGGGC 60.532 55.000 0.00 0.00 0.00 6.13
96 97 1.948104 TTCTGTGTCAAAGTGTCGGG 58.052 50.000 0.00 0.00 0.00 5.14
97 98 2.349817 GCATTCTGTGTCAAAGTGTCGG 60.350 50.000 0.00 0.00 0.00 4.79
98 99 2.660094 CGCATTCTGTGTCAAAGTGTCG 60.660 50.000 0.00 0.00 0.00 4.35
99 100 2.287915 ACGCATTCTGTGTCAAAGTGTC 59.712 45.455 0.00 0.00 36.11 3.67
100 101 2.288666 ACGCATTCTGTGTCAAAGTGT 58.711 42.857 0.00 0.00 36.11 3.55
108 109 2.686405 TCCTATACGACGCATTCTGTGT 59.314 45.455 0.00 0.00 44.78 3.72
109 110 3.043586 GTCCTATACGACGCATTCTGTG 58.956 50.000 0.00 0.00 0.00 3.66
110 111 2.034305 GGTCCTATACGACGCATTCTGT 59.966 50.000 0.00 0.00 33.30 3.41
111 112 2.662700 GGTCCTATACGACGCATTCTG 58.337 52.381 0.00 0.00 33.30 3.02
112 113 1.266175 CGGTCCTATACGACGCATTCT 59.734 52.381 0.00 0.00 33.30 2.40
113 114 1.682982 CGGTCCTATACGACGCATTC 58.317 55.000 0.00 0.00 33.30 2.67
114 115 0.318445 GCGGTCCTATACGACGCATT 60.318 55.000 0.00 0.00 34.56 3.56
115 116 1.285023 GCGGTCCTATACGACGCAT 59.715 57.895 0.00 0.00 34.56 4.73
116 117 2.717485 GCGGTCCTATACGACGCA 59.283 61.111 0.00 0.00 34.56 5.24
117 118 2.050623 GGCGGTCCTATACGACGC 60.051 66.667 0.00 0.00 33.30 5.19
118 119 1.895707 AGGGCGGTCCTATACGACG 60.896 63.158 0.00 0.00 45.98 5.12
119 120 4.170947 AGGGCGGTCCTATACGAC 57.829 61.111 0.00 0.00 45.98 4.34
134 135 1.895020 TATATAGGCGCGCCCCAAGG 61.895 60.000 44.47 0.00 36.58 3.61
135 136 0.178068 ATATATAGGCGCGCCCCAAG 59.822 55.000 44.47 0.00 36.58 3.61
136 137 0.616371 AATATATAGGCGCGCCCCAA 59.384 50.000 44.47 30.89 36.58 4.12
141 142 2.927477 TGTAAGCAATATATAGGCGCGC 59.073 45.455 25.94 25.94 0.00 6.86
177 178 3.583276 TAAGTGCCCCGTGCGTCAG 62.583 63.158 0.00 0.00 45.60 3.51
178 179 3.583276 CTAAGTGCCCCGTGCGTCA 62.583 63.158 0.00 0.00 45.60 4.35
182 183 2.032071 ACACTAAGTGCCCCGTGC 59.968 61.111 0.00 0.00 36.98 5.34
183 184 3.966215 CACACTAAGTGCCCCGTG 58.034 61.111 0.00 0.00 42.15 4.94
192 193 0.671781 AGAAGCAGCCGCACACTAAG 60.672 55.000 0.00 0.00 42.27 2.18
193 194 0.950555 CAGAAGCAGCCGCACACTAA 60.951 55.000 0.00 0.00 42.27 2.24
194 195 1.374631 CAGAAGCAGCCGCACACTA 60.375 57.895 0.00 0.00 42.27 2.74
195 196 2.667536 CAGAAGCAGCCGCACACT 60.668 61.111 0.00 0.00 42.27 3.55
196 197 3.730761 CCAGAAGCAGCCGCACAC 61.731 66.667 0.00 0.00 42.27 3.82
199 200 4.254709 ACACCAGAAGCAGCCGCA 62.255 61.111 0.00 0.00 42.27 5.69
201 202 1.302033 AAGACACCAGAAGCAGCCG 60.302 57.895 0.00 0.00 0.00 5.52
202 203 0.250467 TCAAGACACCAGAAGCAGCC 60.250 55.000 0.00 0.00 0.00 4.85
203 204 0.871057 GTCAAGACACCAGAAGCAGC 59.129 55.000 0.00 0.00 0.00 5.25
205 206 0.108585 GGGTCAAGACACCAGAAGCA 59.891 55.000 2.29 0.00 38.32 3.91
206 207 0.108585 TGGGTCAAGACACCAGAAGC 59.891 55.000 0.00 0.00 38.32 3.86
208 209 0.105964 CGTGGGTCAAGACACCAGAA 59.894 55.000 9.67 0.00 38.32 3.02
209 210 0.757561 TCGTGGGTCAAGACACCAGA 60.758 55.000 9.67 2.69 38.32 3.86
212 213 1.301479 GGTCGTGGGTCAAGACACC 60.301 63.158 13.90 0.88 42.81 4.16
214 215 2.513259 GGGGTCGTGGGTCAAGACA 61.513 63.158 13.90 0.00 42.81 3.41
215 216 2.346365 GGGGTCGTGGGTCAAGAC 59.654 66.667 5.62 5.62 40.94 3.01
216 217 2.926242 GGGGGTCGTGGGTCAAGA 60.926 66.667 0.00 0.00 0.00 3.02
217 218 4.388499 CGGGGGTCGTGGGTCAAG 62.388 72.222 0.00 0.00 0.00 3.02
218 219 4.938074 TCGGGGGTCGTGGGTCAA 62.938 66.667 0.00 0.00 40.32 3.18
220 221 3.944250 TAGTCGGGGGTCGTGGGTC 62.944 68.421 0.00 0.00 40.32 4.46
222 223 3.145551 CTAGTCGGGGGTCGTGGG 61.146 72.222 0.00 0.00 40.32 4.61
223 224 3.834799 GCTAGTCGGGGGTCGTGG 61.835 72.222 0.00 0.00 40.32 4.94
225 226 0.396139 TAATGCTAGTCGGGGGTCGT 60.396 55.000 0.00 0.00 40.32 4.34
228 229 2.134092 GCTAATGCTAGTCGGGGGT 58.866 57.895 0.00 0.00 36.03 4.95
242 1250 2.431954 ACCTAGCCTGTCGTAGCTAA 57.568 50.000 0.00 0.00 40.89 3.09
268 1276 0.678048 GTGCTCAAAGGCTACCTGGG 60.678 60.000 0.00 0.00 32.13 4.45
277 1285 2.072298 GTCTGCTACAGTGCTCAAAGG 58.928 52.381 0.00 0.00 32.61 3.11
281 1289 0.037882 GCAGTCTGCTACAGTGCTCA 60.038 55.000 17.89 0.00 40.96 4.26
282 1290 2.748268 GCAGTCTGCTACAGTGCTC 58.252 57.895 17.89 0.00 40.96 4.26
298 1320 4.144297 AGTTTCCTTGCTTCATTGTAGCA 58.856 39.130 13.25 13.25 46.26 3.49
305 1327 2.621668 GGGCCTAGTTTCCTTGCTTCAT 60.622 50.000 0.84 0.00 0.00 2.57
306 1328 1.271926 GGGCCTAGTTTCCTTGCTTCA 60.272 52.381 0.84 0.00 0.00 3.02
307 1329 1.271926 TGGGCCTAGTTTCCTTGCTTC 60.272 52.381 4.53 0.00 0.00 3.86
373 1395 9.742552 CAGTTTAAAGAATAGAAACTTAGACGC 57.257 33.333 0.00 0.00 40.54 5.19
405 1427 6.018751 GCTAATTGCTCGTGAATATTCACAGA 60.019 38.462 35.71 30.66 46.62 3.41
425 1447 3.555966 GCTAACCATTGGACCAGCTAAT 58.444 45.455 10.37 0.00 0.00 1.73
429 1451 0.034089 AGGCTAACCATTGGACCAGC 60.034 55.000 10.37 13.46 39.06 4.85
434 1456 2.237143 CACAGAGAGGCTAACCATTGGA 59.763 50.000 10.37 0.00 39.06 3.53
484 1506 1.182667 GACCGCCAAAAATAGCCCTT 58.817 50.000 0.00 0.00 0.00 3.95
488 1510 3.850122 AAAGAGACCGCCAAAAATAGC 57.150 42.857 0.00 0.00 0.00 2.97
513 1535 3.499737 GGCCCACGATCGCACAAG 61.500 66.667 16.60 0.71 0.00 3.16
545 1567 1.816259 GTAACTGGCGCCCGCAATA 60.816 57.895 26.77 9.23 44.11 1.90
574 1596 1.157870 TCCTATTGCGCGCCTTTAGC 61.158 55.000 30.77 0.00 38.52 3.09
575 1597 0.861837 CTCCTATTGCGCGCCTTTAG 59.138 55.000 30.77 23.72 0.00 1.85
576 1598 0.531974 CCTCCTATTGCGCGCCTTTA 60.532 55.000 30.77 16.00 0.00 1.85
577 1599 1.819632 CCTCCTATTGCGCGCCTTT 60.820 57.895 30.77 15.69 0.00 3.11
578 1600 2.203070 CCTCCTATTGCGCGCCTT 60.203 61.111 30.77 18.48 0.00 4.35
579 1601 3.447025 GACCTCCTATTGCGCGCCT 62.447 63.158 30.77 18.71 0.00 5.52
580 1602 2.967615 GACCTCCTATTGCGCGCC 60.968 66.667 30.77 11.42 0.00 6.53
581 1603 2.967615 GGACCTCCTATTGCGCGC 60.968 66.667 27.26 27.26 0.00 6.86
598 1620 3.017048 TCATCTGGCCATGTTTTAGGG 57.983 47.619 5.51 0.00 0.00 3.53
599 1621 5.404466 TTTTCATCTGGCCATGTTTTAGG 57.596 39.130 5.51 0.00 0.00 2.69
623 1645 7.761038 TCTTCTTTGTTATTTTCTTCCCCTC 57.239 36.000 0.00 0.00 0.00 4.30
673 1724 8.677300 GCATCAACATTAGACCTTTCAGAAATA 58.323 33.333 0.00 0.00 0.00 1.40
780 1860 8.600625 GCAACAAATGATTAGTGATTACGAGTA 58.399 33.333 0.00 0.00 0.00 2.59
782 1862 6.624917 CGCAACAAATGATTAGTGATTACGAG 59.375 38.462 0.00 0.00 0.00 4.18
785 1865 7.240674 TGACGCAACAAATGATTAGTGATTAC 58.759 34.615 0.00 0.00 0.00 1.89
786 1866 7.371126 TGACGCAACAAATGATTAGTGATTA 57.629 32.000 0.00 0.00 0.00 1.75
787 1867 6.252967 TGACGCAACAAATGATTAGTGATT 57.747 33.333 0.00 0.00 0.00 2.57
789 1869 5.238432 AGTTGACGCAACAAATGATTAGTGA 59.762 36.000 19.82 0.00 45.66 3.41
837 1923 1.963172 TTAGCGAGAGATCAGCGGTA 58.037 50.000 8.89 8.89 37.02 4.02
838 1924 1.268352 GATTAGCGAGAGATCAGCGGT 59.732 52.381 10.51 10.51 39.26 5.68
897 2026 2.416701 CGGGCAGTGTGTTTCAAAAGTT 60.417 45.455 0.00 0.00 0.00 2.66
919 2048 8.319057 TCTTCTTCTCAGGGCAGTATTAATAA 57.681 34.615 0.00 0.00 0.00 1.40
960 2089 9.742552 GCTTTTGATAGTTTCGTAAGTTCTTAG 57.257 33.333 0.00 0.00 39.48 2.18
961 2090 9.263538 TGCTTTTGATAGTTTCGTAAGTTCTTA 57.736 29.630 0.00 0.00 39.48 2.10
962 2091 8.149973 TGCTTTTGATAGTTTCGTAAGTTCTT 57.850 30.769 0.00 0.00 39.48 2.52
963 2092 7.724305 TGCTTTTGATAGTTTCGTAAGTTCT 57.276 32.000 0.00 0.00 39.48 3.01
971 2105 3.543494 CGCCATTGCTTTTGATAGTTTCG 59.457 43.478 0.00 0.00 34.43 3.46
1083 2237 2.060980 GTCCCGGTGGATGAGCTCT 61.061 63.158 16.19 0.00 44.28 4.09
1188 3656 0.315568 GCCGTCAGTGTCAGAAGAGT 59.684 55.000 0.00 0.00 0.00 3.24
1216 3702 0.613292 ACGTGCCTGAGATCACCTCT 60.613 55.000 0.00 0.00 42.44 3.69
1510 4039 4.717629 CTGTTCGAGCCGCCGACA 62.718 66.667 0.00 5.41 38.39 4.35
2436 5326 7.076842 TGAAGAGTGTGTTTCTTTTTCTCTG 57.923 36.000 0.00 0.00 35.14 3.35
2438 5328 6.466097 CGTTGAAGAGTGTGTTTCTTTTTCTC 59.534 38.462 0.00 0.00 35.14 2.87
2452 5365 4.230657 CTGGACTACTTCGTTGAAGAGTG 58.769 47.826 13.13 5.43 41.71 3.51
2477 5390 1.460743 CCAGACACATGTGCGTACAAG 59.539 52.381 25.68 9.11 40.84 3.16
2494 5407 2.297315 GCTTGGTTCTTTTCCCTTCCAG 59.703 50.000 0.00 0.00 0.00 3.86
2514 5427 5.417580 TGATTCTGTTTGTTATTACCCTGGC 59.582 40.000 0.00 0.00 0.00 4.85
2519 5432 6.318900 CCCTCCTGATTCTGTTTGTTATTACC 59.681 42.308 0.00 0.00 0.00 2.85
2533 5446 5.622346 AAATAGACAGTCCCTCCTGATTC 57.378 43.478 0.00 0.00 36.30 2.52
2535 5448 8.980832 ATATAAAATAGACAGTCCCTCCTGAT 57.019 34.615 0.00 0.00 36.30 2.90
2536 5449 8.798975 AATATAAAATAGACAGTCCCTCCTGA 57.201 34.615 0.00 0.00 36.30 3.86
2538 5451 7.794683 TGGAATATAAAATAGACAGTCCCTCCT 59.205 37.037 0.00 0.00 0.00 3.69
2539 5452 7.878644 GTGGAATATAAAATAGACAGTCCCTCC 59.121 40.741 0.00 0.00 0.00 4.30
2540 5453 8.652290 AGTGGAATATAAAATAGACAGTCCCTC 58.348 37.037 0.00 0.00 0.00 4.30
2541 5454 8.432805 CAGTGGAATATAAAATAGACAGTCCCT 58.567 37.037 0.00 0.00 0.00 4.20
2558 5471 7.461182 AAACGAATTGGATTTCAGTGGAATA 57.539 32.000 0.00 0.00 31.93 1.75
2563 5476 6.680055 CTGAAAACGAATTGGATTTCAGTG 57.320 37.500 29.04 16.07 46.89 3.66
2601 5514 6.607689 TGTGACACTTGTTAAACTCTGTTTG 58.392 36.000 7.20 0.00 0.00 2.93
2603 5516 6.374333 ACATGTGACACTTGTTAAACTCTGTT 59.626 34.615 18.62 0.00 33.38 3.16
2634 5547 3.611025 TTCAGGGGACAGGAACAAAAT 57.389 42.857 0.00 0.00 0.00 1.82
2793 5742 6.480651 TGTGCACTTTTCGTGTAGATTCTAAA 59.519 34.615 19.41 0.00 45.57 1.85
2794 5743 5.986741 TGTGCACTTTTCGTGTAGATTCTAA 59.013 36.000 19.41 0.00 45.57 2.10
2947 5900 7.514721 AGTAGAGTTCCTGTTTTATGTTTCCA 58.485 34.615 0.00 0.00 0.00 3.53
3100 6070 1.247567 ACTGGAACAATGGCCTTTCG 58.752 50.000 3.32 1.87 38.70 3.46
3105 6075 3.763897 AGACAATTACTGGAACAATGGCC 59.236 43.478 0.00 0.00 38.70 5.36
3170 6154 8.773404 AATGTCACTGTAACCTGTAGTAATTC 57.227 34.615 0.00 0.00 0.00 2.17
3250 6235 6.582636 AGATTCACTCATTTTGCTCCGTATA 58.417 36.000 0.00 0.00 0.00 1.47
3255 6240 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3256 6241 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3278 6263 9.809096 ACGGATGTATATAGATGCATTTTAGAG 57.191 33.333 11.19 0.00 38.38 2.43
3310 6295 7.970061 ACTCCCTCCATTCCTAAATATAAGGAT 59.030 37.037 7.40 0.00 42.69 3.24
3318 6303 6.935036 TCTACTACTCCCTCCATTCCTAAAT 58.065 40.000 0.00 0.00 0.00 1.40
3319 6304 6.351317 TCTACTACTCCCTCCATTCCTAAA 57.649 41.667 0.00 0.00 0.00 1.85
3320 6305 6.547396 ATCTACTACTCCCTCCATTCCTAA 57.453 41.667 0.00 0.00 0.00 2.69
3321 6306 6.547396 AATCTACTACTCCCTCCATTCCTA 57.453 41.667 0.00 0.00 0.00 2.94
3322 6307 5.426325 AATCTACTACTCCCTCCATTCCT 57.574 43.478 0.00 0.00 0.00 3.36
3323 6308 7.800300 ATAAATCTACTACTCCCTCCATTCC 57.200 40.000 0.00 0.00 0.00 3.01
3326 6311 9.845214 ACAATATAAATCTACTACTCCCTCCAT 57.155 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.