Multiple sequence alignment - TraesCS3A01G174500

Loading Multiple Alignment...

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 TraesCS3A01G174500 chr3A 100.000 7284 0 0 1 7284 193604234 193596951 0.000000e+00 13452.0
1 TraesCS3A01G174500 chr3A 97.306 5085 108 13 182 5240 33428294 33423213 0.000000e+00 8604.0
2 TraesCS3A01G174500 chr3A 92.460 1114 49 15 5239 6319 33423268 33422157 0.000000e+00 1559.0
3 TraesCS3A01G174500 chr3A 86.747 415 25 12 5983 6397 33422492 33422108 1.120000e-117 435.0
4 TraesCS3A01G174500 chr3A 83.278 299 23 9 5983 6280 33422172 33421900 4.360000e-62 250.0
5 TraesCS3A01G174500 chr3A 92.523 107 8 0 6218 6324 193591577 193591471 3.520000e-33 154.0
6 TraesCS3A01G174500 chr3A 91.667 96 7 1 5779 5873 33422822 33422727 1.650000e-26 132.0
7 TraesCS3A01G174500 chr3A 88.158 76 4 2 112 182 599583663 599583738 1.300000e-12 86.1
8 TraesCS3A01G174500 chr3A 92.857 56 4 0 5185 5240 193598996 193598941 1.680000e-11 82.4
9 TraesCS3A01G174500 chr3A 92.857 56 4 0 5239 5294 193599050 193598995 1.680000e-11 82.4
10 TraesCS3A01G174500 chr3B 94.807 4294 163 23 989 5240 41251238 41255513 0.000000e+00 6639.0
11 TraesCS3A01G174500 chr3B 93.625 753 38 7 5239 5981 41255458 41256210 0.000000e+00 1116.0
12 TraesCS3A01G174500 chr3B 88.224 518 51 5 461 968 41249432 41249949 1.740000e-170 610.0
13 TraesCS3A01G174500 chr3B 93.275 342 22 1 5983 6324 41256241 41256581 3.030000e-138 503.0
14 TraesCS3A01G174500 chr3B 89.298 299 30 2 5983 6280 41256561 41256858 2.480000e-99 374.0
15 TraesCS3A01G174500 chr3B 72.587 1233 259 55 1240 2432 49675443 49674250 1.510000e-86 331.0
16 TraesCS3A01G174500 chr3B 84.135 208 29 4 1266 1471 49721049 49721254 1.600000e-46 198.0
17 TraesCS3A01G174500 chr3B 84.884 172 23 3 1247 1416 41356595 41356425 3.490000e-38 171.0
18 TraesCS3A01G174500 chr3B 92.857 84 6 0 6316 6399 41256544 41256627 9.920000e-24 122.0
19 TraesCS3A01G174500 chr3B 89.474 76 2 4 112 182 127293070 127292996 2.800000e-14 91.6
20 TraesCS3A01G174500 chr3D 94.007 4005 172 25 1057 5015 24055661 24059643 0.000000e+00 6006.0
21 TraesCS3A01G174500 chr3D 94.400 3250 131 21 1798 5015 24051704 24048474 0.000000e+00 4946.0
22 TraesCS3A01G174500 chr3D 89.198 898 82 10 6395 7284 474535618 474534728 0.000000e+00 1107.0
23 TraesCS3A01G174500 chr3D 97.861 187 4 0 5412 5598 24048411 24048225 2.530000e-84 324.0
24 TraesCS3A01G174500 chr3D 97.861 187 4 0 5412 5598 24059706 24059892 2.530000e-84 324.0
25 TraesCS3A01G174500 chr3D 83.817 241 27 8 616 852 24053019 24052787 1.230000e-52 219.0
26 TraesCS3A01G174500 chr3D 83.401 247 29 8 610 852 24054335 24054573 1.230000e-52 219.0
27 TraesCS3A01G174500 chr3D 84.545 220 29 5 1254 1470 29161886 29161669 5.720000e-51 213.0
28 TraesCS3A01G174500 chr3D 81.858 226 35 5 1257 1482 24095207 24094988 1.250000e-42 185.0
29 TraesCS3A01G174500 chr3D 79.412 272 44 11 1250 1515 28977955 28977690 1.610000e-41 182.0
30 TraesCS3A01G174500 chr3D 97.531 81 2 0 2314 2394 24062961 24063041 9.850000e-29 139.0
31 TraesCS3A01G174500 chr3D 87.059 85 7 2 112 192 12275316 12275232 7.780000e-15 93.5
32 TraesCS3A01G174500 chr3D 87.931 58 6 1 5721 5778 394142773 394142829 4.720000e-07 67.6
33 TraesCS3A01G174500 chr3D 100.000 35 0 0 5460 5494 24048439 24048405 1.700000e-06 65.8
34 TraesCS3A01G174500 chr3D 100.000 35 0 0 5460 5494 24059678 24059712 1.700000e-06 65.8
35 TraesCS3A01G174500 chr1D 92.360 890 62 6 6399 7284 127200300 127201187 0.000000e+00 1262.0
36 TraesCS3A01G174500 chr1D 90.101 889 81 6 6402 7284 288458557 288459444 0.000000e+00 1147.0
37 TraesCS3A01G174500 chr1D 89.027 884 90 6 6407 7284 288534546 288535428 0.000000e+00 1088.0
38 TraesCS3A01G174500 chr7B 91.610 882 68 5 6408 7284 462250332 462251212 0.000000e+00 1214.0
39 TraesCS3A01G174500 chr7B 89.474 76 4 2 121 192 26643011 26642936 7.780000e-15 93.5
40 TraesCS3A01G174500 chr6D 89.253 884 86 8 6408 7284 451816615 451815734 0.000000e+00 1098.0
41 TraesCS3A01G174500 chr6D 70.709 536 133 19 1775 2301 411492478 411491958 1.670000e-16 99.0
42 TraesCS3A01G174500 chr6D 82.653 98 11 2 111 207 309955300 309955208 1.680000e-11 82.4
43 TraesCS3A01G174500 chr6D 88.462 52 4 2 5443 5494 105556608 105556559 2.190000e-05 62.1
44 TraesCS3A01G174500 chr2D 89.619 867 81 8 6425 7284 156815908 156816772 0.000000e+00 1094.0
45 TraesCS3A01G174500 chr4D 89.492 866 76 11 6426 7284 399500944 399500087 0.000000e+00 1081.0
46 TraesCS3A01G174500 chr4D 88.690 893 90 10 6400 7284 381090241 381091130 0.000000e+00 1079.0
47 TraesCS3A01G174500 chrUn 100.000 402 0 0 3292 3693 478553503 478553904 0.000000e+00 743.0
48 TraesCS3A01G174500 chr2B 88.514 148 14 3 6117 6263 12947186 12947041 7.510000e-40 176.0
49 TraesCS3A01G174500 chr4B 84.571 175 26 1 176 349 634412858 634412684 9.720000e-39 172.0
50 TraesCS3A01G174500 chr4B 88.372 86 6 2 111 192 532633434 532633349 4.650000e-17 100.0
51 TraesCS3A01G174500 chr4B 95.918 49 2 0 6277 6325 447455401 447455449 6.060000e-11 80.5
52 TraesCS3A01G174500 chr5A 92.233 103 8 0 1 103 338226229 338226127 5.890000e-31 147.0
53 TraesCS3A01G174500 chr1B 88.571 105 11 1 1 104 20569454 20569350 7.670000e-25 126.0
54 TraesCS3A01G174500 chr5B 89.109 101 8 2 1 101 508775374 508775277 9.920000e-24 122.0
55 TraesCS3A01G174500 chr6A 70.896 536 132 19 1775 2301 556093778 556093258 3.590000e-18 104.0
56 TraesCS3A01G174500 chr7D 88.372 86 6 2 112 193 127287393 127287308 4.650000e-17 100.0
57 TraesCS3A01G174500 chr7D 87.059 85 7 2 112 192 616456122 616456206 7.780000e-15 93.5
58 TraesCS3A01G174500 chr4A 87.209 86 5 3 112 193 683881250 683881167 7.780000e-15 93.5
59 TraesCS3A01G174500 chr4A 80.460 87 17 0 537 623 666152953 666153039 4.720000e-07 67.6


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 TraesCS3A01G174500 chr3A 193596951 193604234 7283 True 13452.000000 13452 100.000000 1 7284 1 chr3A.!!$R2 7283
1 TraesCS3A01G174500 chr3A 33421900 33428294 6394 True 2196.000000 8604 90.291600 182 6397 5 chr3A.!!$R3 6215
2 TraesCS3A01G174500 chr3B 41249432 41256858 7426 False 1560.666667 6639 92.014333 461 6399 6 chr3B.!!$F2 5938
3 TraesCS3A01G174500 chr3B 49674250 49675443 1193 True 331.000000 331 72.587000 1240 2432 1 chr3B.!!$R2 1192
4 TraesCS3A01G174500 chr3D 24048225 24053019 4794 True 1388.700000 4946 94.019500 616 5598 4 chr3D.!!$R6 4982
5 TraesCS3A01G174500 chr3D 24054335 24063041 8706 False 1350.760000 6006 94.560000 610 5598 5 chr3D.!!$F2 4988
6 TraesCS3A01G174500 chr3D 474534728 474535618 890 True 1107.000000 1107 89.198000 6395 7284 1 chr3D.!!$R5 889
7 TraesCS3A01G174500 chr1D 127200300 127201187 887 False 1262.000000 1262 92.360000 6399 7284 1 chr1D.!!$F1 885
8 TraesCS3A01G174500 chr1D 288458557 288459444 887 False 1147.000000 1147 90.101000 6402 7284 1 chr1D.!!$F2 882
9 TraesCS3A01G174500 chr1D 288534546 288535428 882 False 1088.000000 1088 89.027000 6407 7284 1 chr1D.!!$F3 877
10 TraesCS3A01G174500 chr7B 462250332 462251212 880 False 1214.000000 1214 91.610000 6408 7284 1 chr7B.!!$F1 876
11 TraesCS3A01G174500 chr6D 451815734 451816615 881 True 1098.000000 1098 89.253000 6408 7284 1 chr6D.!!$R4 876
12 TraesCS3A01G174500 chr2D 156815908 156816772 864 False 1094.000000 1094 89.619000 6425 7284 1 chr2D.!!$F1 859
13 TraesCS3A01G174500 chr4D 399500087 399500944 857 True 1081.000000 1081 89.492000 6426 7284 1 chr4D.!!$R1 858
14 TraesCS3A01G174500 chr4D 381090241 381091130 889 False 1079.000000 1079 88.690000 6400 7284 1 chr4D.!!$F1 884

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
73 74 0.041135 GACATCGTCCGGATCTCGTC 60.041 60.0 7.81 9.35 37.11 4.20 F
83 84 0.176680 GGATCTCGTCCATGCACTGT 59.823 55.0 0.00 0.00 46.96 3.55 F
85 86 0.179127 ATCTCGTCCATGCACTGTCG 60.179 55.0 0.00 0.00 0.00 4.35 F
102 103 0.240145 TCGTGTGCAGAGTACTTCCG 59.760 55.0 0.00 0.00 0.00 4.30 F
103 104 0.240145 CGTGTGCAGAGTACTTCCGA 59.760 55.0 0.00 0.00 0.00 4.55 F
361 366 0.714439 GCTCTAACGAAAGCGACACC 59.286 55.0 0.00 0.00 41.64 4.16 F
535 540 1.189524 TGTGGGACGACCTTTCCGAT 61.190 55.0 3.44 0.00 41.11 4.18 F
2963 5120 1.027357 CCGGCTCATTCCATTCCTTG 58.973 55.0 0.00 0.00 0.00 3.61 F
4952 7167 1.412453 AACCGCTGGTGGTACTTGGA 61.412 55.0 6.24 0.00 42.89 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 3840 2.176546 CGTCCATGCCTGCGTTTG 59.823 61.111 0.00 0.0 0.00 2.93 R
1723 3871 2.540383 TGTCAGCAGGGTCTGATAAGT 58.460 47.619 0.00 0.0 44.04 2.24 R
1866 4020 6.483640 GTCACTGGTAATGGGATTATCTTGAC 59.516 42.308 0.00 0.0 34.98 3.18 R
2133 4290 1.404391 CAGCTCAGGCAATTTAGCAGG 59.596 52.381 0.00 0.0 41.70 4.85 R
2513 4670 4.873259 TCAAAACTGAGACGTTCACATGAA 59.127 37.500 0.00 0.0 0.00 2.57 R
2936 5093 5.476945 GGAATGGAATGAGCCGGTTAATTAT 59.523 40.000 1.90 0.0 0.00 1.28 R
3066 5229 4.787260 TGTGCTTCGGTATTGTGTAGTA 57.213 40.909 0.00 0.0 0.00 1.82 R
5192 7429 0.245266 TACGATGCACCGAAAGAGCA 59.755 50.000 7.92 0.0 43.80 4.26 R
6657 10431 0.175760 GCTGCACGATGTTCCTCCTA 59.824 55.000 0.00 0.0 0.00 2.94 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
23 24 5.916318 GGATCAAATTATTGTTGGATGGCA 58.084 37.500 0.00 0.00 37.79 4.92
24 25 6.527423 GGATCAAATTATTGTTGGATGGCAT 58.473 36.000 0.00 0.00 37.79 4.40
25 26 6.647895 GGATCAAATTATTGTTGGATGGCATC 59.352 38.462 19.23 19.23 37.79 3.91
26 27 6.795144 TCAAATTATTGTTGGATGGCATCT 57.205 33.333 25.48 8.53 37.79 2.90
27 28 7.185318 TCAAATTATTGTTGGATGGCATCTT 57.815 32.000 25.48 7.17 37.79 2.40
28 29 7.622713 TCAAATTATTGTTGGATGGCATCTTT 58.377 30.769 25.48 12.48 37.79 2.52
29 30 7.765360 TCAAATTATTGTTGGATGGCATCTTTC 59.235 33.333 25.48 15.80 37.79 2.62
30 31 6.795144 ATTATTGTTGGATGGCATCTTTCA 57.205 33.333 25.48 17.86 0.00 2.69
31 32 4.730949 ATTGTTGGATGGCATCTTTCAG 57.269 40.909 25.48 0.00 0.00 3.02
32 33 1.820519 TGTTGGATGGCATCTTTCAGC 59.179 47.619 25.48 17.16 0.00 4.26
33 34 1.820519 GTTGGATGGCATCTTTCAGCA 59.179 47.619 25.48 11.99 0.00 4.41
34 35 2.219080 TGGATGGCATCTTTCAGCAA 57.781 45.000 25.48 0.95 0.00 3.91
35 36 2.527497 TGGATGGCATCTTTCAGCAAA 58.473 42.857 25.48 0.00 0.00 3.68
36 37 3.101437 TGGATGGCATCTTTCAGCAAAT 58.899 40.909 25.48 0.00 0.00 2.32
37 38 3.131577 TGGATGGCATCTTTCAGCAAATC 59.868 43.478 25.48 6.27 0.00 2.17
38 39 3.131577 GGATGGCATCTTTCAGCAAATCA 59.868 43.478 25.48 0.00 31.06 2.57
39 40 3.861276 TGGCATCTTTCAGCAAATCAG 57.139 42.857 0.00 0.00 0.00 2.90
40 41 2.094390 TGGCATCTTTCAGCAAATCAGC 60.094 45.455 0.00 0.00 0.00 4.26
41 42 2.094390 GGCATCTTTCAGCAAATCAGCA 60.094 45.455 0.00 0.00 36.85 4.41
42 43 2.921754 GCATCTTTCAGCAAATCAGCAC 59.078 45.455 0.00 0.00 36.85 4.40
43 44 3.508762 CATCTTTCAGCAAATCAGCACC 58.491 45.455 0.00 0.00 36.85 5.01
44 45 1.536766 TCTTTCAGCAAATCAGCACCG 59.463 47.619 0.00 0.00 36.85 4.94
45 46 1.267806 CTTTCAGCAAATCAGCACCGT 59.732 47.619 0.00 0.00 36.85 4.83
46 47 1.317613 TTCAGCAAATCAGCACCGTT 58.682 45.000 0.00 0.00 36.85 4.44
47 48 1.317613 TCAGCAAATCAGCACCGTTT 58.682 45.000 0.00 0.00 36.85 3.60
48 49 2.499197 TCAGCAAATCAGCACCGTTTA 58.501 42.857 0.00 0.00 36.85 2.01
49 50 2.881513 TCAGCAAATCAGCACCGTTTAA 59.118 40.909 0.00 0.00 36.85 1.52
50 51 3.058293 TCAGCAAATCAGCACCGTTTAAG 60.058 43.478 0.00 0.00 36.85 1.85
51 52 3.058293 CAGCAAATCAGCACCGTTTAAGA 60.058 43.478 0.00 0.00 36.85 2.10
52 53 3.758554 AGCAAATCAGCACCGTTTAAGAT 59.241 39.130 0.00 0.00 36.85 2.40
53 54 3.853671 GCAAATCAGCACCGTTTAAGATG 59.146 43.478 0.00 0.00 0.00 2.90
54 55 4.414852 CAAATCAGCACCGTTTAAGATGG 58.585 43.478 0.00 0.00 40.53 3.51
55 56 3.627395 ATCAGCACCGTTTAAGATGGA 57.373 42.857 0.00 0.00 37.88 3.41
56 57 2.695359 TCAGCACCGTTTAAGATGGAC 58.305 47.619 0.00 0.00 37.88 4.02
57 58 2.037902 TCAGCACCGTTTAAGATGGACA 59.962 45.455 0.00 0.00 37.88 4.02
58 59 3.009723 CAGCACCGTTTAAGATGGACAT 58.990 45.455 0.00 0.00 37.88 3.06
59 60 3.063997 CAGCACCGTTTAAGATGGACATC 59.936 47.826 4.15 4.15 37.88 3.06
60 61 2.030457 GCACCGTTTAAGATGGACATCG 59.970 50.000 6.65 0.00 42.48 3.84
61 62 3.259064 CACCGTTTAAGATGGACATCGT 58.741 45.455 6.65 6.34 42.48 3.73
62 63 3.306166 CACCGTTTAAGATGGACATCGTC 59.694 47.826 4.06 0.00 42.48 4.20
71 72 1.283181 GGACATCGTCCGGATCTCG 59.717 63.158 7.81 7.09 43.14 4.04
72 73 1.445716 GGACATCGTCCGGATCTCGT 61.446 60.000 7.81 2.91 43.14 4.18
73 74 0.041135 GACATCGTCCGGATCTCGTC 60.041 60.000 7.81 9.35 37.11 4.20
74 75 1.283181 CATCGTCCGGATCTCGTCC 59.717 63.158 7.81 0.00 44.10 4.79
82 83 2.983433 GGATCTCGTCCATGCACTG 58.017 57.895 0.00 0.00 46.96 3.66
83 84 0.176680 GGATCTCGTCCATGCACTGT 59.823 55.000 0.00 0.00 46.96 3.55
84 85 1.565305 GATCTCGTCCATGCACTGTC 58.435 55.000 0.00 0.00 0.00 3.51
85 86 0.179127 ATCTCGTCCATGCACTGTCG 60.179 55.000 0.00 0.00 0.00 4.35
86 87 1.080501 CTCGTCCATGCACTGTCGT 60.081 57.895 0.00 0.00 0.00 4.34
87 88 1.347097 CTCGTCCATGCACTGTCGTG 61.347 60.000 0.00 0.00 44.07 4.35
88 89 1.664649 CGTCCATGCACTGTCGTGT 60.665 57.895 0.00 0.00 43.16 4.49
89 90 1.862123 GTCCATGCACTGTCGTGTG 59.138 57.895 0.00 0.00 43.16 3.82
95 96 4.738198 CACTGTCGTGTGCAGAGT 57.262 55.556 0.00 0.00 37.40 3.24
96 97 3.865700 CACTGTCGTGTGCAGAGTA 57.134 52.632 0.00 0.00 37.40 2.59
97 98 1.409412 CACTGTCGTGTGCAGAGTAC 58.591 55.000 0.00 0.00 37.40 2.73
98 99 1.001268 CACTGTCGTGTGCAGAGTACT 60.001 52.381 0.00 0.00 37.40 2.73
99 100 1.681793 ACTGTCGTGTGCAGAGTACTT 59.318 47.619 0.00 0.00 37.40 2.24
100 101 2.287668 ACTGTCGTGTGCAGAGTACTTC 60.288 50.000 0.00 0.00 37.40 3.01
101 102 1.000607 TGTCGTGTGCAGAGTACTTCC 60.001 52.381 0.00 0.00 0.00 3.46
102 103 0.240145 TCGTGTGCAGAGTACTTCCG 59.760 55.000 0.00 0.00 0.00 4.30
103 104 0.240145 CGTGTGCAGAGTACTTCCGA 59.760 55.000 0.00 0.00 0.00 4.55
104 105 1.135373 CGTGTGCAGAGTACTTCCGAT 60.135 52.381 0.00 0.00 0.00 4.18
105 106 2.263077 GTGTGCAGAGTACTTCCGATG 58.737 52.381 0.00 0.00 0.00 3.84
106 107 1.281899 GTGCAGAGTACTTCCGATGC 58.718 55.000 0.00 4.10 0.00 3.91
107 108 1.134965 GTGCAGAGTACTTCCGATGCT 60.135 52.381 0.00 0.00 34.80 3.79
108 109 2.099263 GTGCAGAGTACTTCCGATGCTA 59.901 50.000 0.00 0.00 34.80 3.49
109 110 2.359214 TGCAGAGTACTTCCGATGCTAG 59.641 50.000 0.00 0.00 34.80 3.42
110 111 2.359531 GCAGAGTACTTCCGATGCTAGT 59.640 50.000 0.00 0.00 0.00 2.57
111 112 3.181485 GCAGAGTACTTCCGATGCTAGTT 60.181 47.826 0.00 0.00 0.00 2.24
112 113 4.036498 GCAGAGTACTTCCGATGCTAGTTA 59.964 45.833 0.00 0.00 0.00 2.24
113 114 5.512473 CAGAGTACTTCCGATGCTAGTTAC 58.488 45.833 0.00 0.00 0.00 2.50
114 115 5.297278 CAGAGTACTTCCGATGCTAGTTACT 59.703 44.000 0.00 0.00 0.00 2.24
115 116 5.528320 AGAGTACTTCCGATGCTAGTTACTC 59.472 44.000 0.00 0.00 0.00 2.59
116 117 4.579753 AGTACTTCCGATGCTAGTTACTCC 59.420 45.833 0.00 0.00 0.00 3.85
117 118 2.694109 ACTTCCGATGCTAGTTACTCCC 59.306 50.000 0.00 0.00 0.00 4.30
118 119 2.750141 TCCGATGCTAGTTACTCCCT 57.250 50.000 0.00 0.00 0.00 4.20
119 120 3.028094 TCCGATGCTAGTTACTCCCTT 57.972 47.619 0.00 0.00 0.00 3.95
120 121 2.957006 TCCGATGCTAGTTACTCCCTTC 59.043 50.000 0.00 0.00 0.00 3.46
121 122 2.287668 CCGATGCTAGTTACTCCCTTCG 60.288 54.545 10.95 10.95 0.00 3.79
122 123 2.358267 CGATGCTAGTTACTCCCTTCGT 59.642 50.000 0.00 0.00 0.00 3.85
123 124 3.562973 CGATGCTAGTTACTCCCTTCGTA 59.437 47.826 0.00 0.00 0.00 3.43
124 125 4.215827 CGATGCTAGTTACTCCCTTCGTAT 59.784 45.833 0.00 0.00 0.00 3.06
125 126 5.410746 CGATGCTAGTTACTCCCTTCGTATA 59.589 44.000 0.00 0.00 0.00 1.47
126 127 6.572167 ATGCTAGTTACTCCCTTCGTATAC 57.428 41.667 0.00 0.00 0.00 1.47
127 128 5.688807 TGCTAGTTACTCCCTTCGTATACT 58.311 41.667 0.56 0.00 0.00 2.12
128 129 6.830912 TGCTAGTTACTCCCTTCGTATACTA 58.169 40.000 0.56 0.00 0.00 1.82
129 130 7.282585 TGCTAGTTACTCCCTTCGTATACTAA 58.717 38.462 0.56 0.00 0.00 2.24
130 131 7.941238 TGCTAGTTACTCCCTTCGTATACTAAT 59.059 37.037 0.56 0.00 0.00 1.73
131 132 9.442047 GCTAGTTACTCCCTTCGTATACTAATA 57.558 37.037 0.56 0.00 0.00 0.98
138 139 9.176460 ACTCCCTTCGTATACTAATATAAGAGC 57.824 37.037 0.56 0.00 34.52 4.09
139 140 8.206325 TCCCTTCGTATACTAATATAAGAGCG 57.794 38.462 0.56 0.00 34.52 5.03
140 141 7.826252 TCCCTTCGTATACTAATATAAGAGCGT 59.174 37.037 0.56 0.00 34.52 5.07
141 142 8.457261 CCCTTCGTATACTAATATAAGAGCGTT 58.543 37.037 0.56 0.00 34.52 4.84
142 143 9.837525 CCTTCGTATACTAATATAAGAGCGTTT 57.162 33.333 0.56 0.00 34.52 3.60
160 161 9.509956 AGAGCGTTTAGAATACTATAGTGATCT 57.490 33.333 15.90 18.33 0.00 2.75
258 259 5.051891 ACATAGACATTCTGCTGCAAAAC 57.948 39.130 3.02 0.00 0.00 2.43
261 262 6.600822 ACATAGACATTCTGCTGCAAAACTAT 59.399 34.615 3.02 0.00 0.00 2.12
264 265 5.939883 AGACATTCTGCTGCAAAACTATACA 59.060 36.000 3.02 0.00 0.00 2.29
266 267 7.770433 AGACATTCTGCTGCAAAACTATACATA 59.230 33.333 3.02 0.00 0.00 2.29
359 364 2.094700 AGATGCTCTAACGAAAGCGACA 60.095 45.455 0.00 0.00 41.51 4.35
360 365 1.415374 TGCTCTAACGAAAGCGACAC 58.585 50.000 0.00 0.00 41.51 3.67
361 366 0.714439 GCTCTAACGAAAGCGACACC 59.286 55.000 0.00 0.00 41.64 4.16
362 367 1.933500 GCTCTAACGAAAGCGACACCA 60.934 52.381 0.00 0.00 41.64 4.17
363 368 2.607187 CTCTAACGAAAGCGACACCAT 58.393 47.619 0.00 0.00 41.64 3.55
364 369 3.766151 CTCTAACGAAAGCGACACCATA 58.234 45.455 0.00 0.00 41.64 2.74
365 370 4.360563 CTCTAACGAAAGCGACACCATAT 58.639 43.478 0.00 0.00 41.64 1.78
366 371 4.357142 TCTAACGAAAGCGACACCATATC 58.643 43.478 0.00 0.00 41.64 1.63
367 372 2.961526 ACGAAAGCGACACCATATCT 57.038 45.000 0.00 0.00 41.64 1.98
368 373 3.247006 ACGAAAGCGACACCATATCTT 57.753 42.857 0.00 0.00 41.64 2.40
369 374 2.930040 ACGAAAGCGACACCATATCTTG 59.070 45.455 0.00 0.00 41.64 3.02
399 404 4.380233 CCAGATGAAGAGTTGATTTGCCAC 60.380 45.833 0.00 0.00 0.00 5.01
529 534 1.705997 AAGCCTTGTGGGACGACCTT 61.706 55.000 3.44 0.00 41.11 3.50
534 539 1.401318 TTGTGGGACGACCTTTCCGA 61.401 55.000 3.44 0.00 41.11 4.55
535 540 1.189524 TGTGGGACGACCTTTCCGAT 61.190 55.000 3.44 0.00 41.11 4.18
547 552 4.714632 ACCTTTCCGATGAACAGAAGAAA 58.285 39.130 0.00 0.00 0.00 2.52
555 560 6.936900 TCCGATGAACAGAAGAAAGATCTTTT 59.063 34.615 21.33 7.12 45.91 2.27
567 572 9.852091 GAAGAAAGATCTTTTTGATATTGCAGT 57.148 29.630 21.33 0.00 45.91 4.40
574 579 5.931724 TCTTTTTGATATTGCAGTCGACTGA 59.068 36.000 42.03 26.45 46.59 3.41
731 739 2.710096 ATATGCAGGCTACCAAACGT 57.290 45.000 0.00 0.00 0.00 3.99
749 757 8.956426 ACCAAACGTCTGAATGAATTATATTGT 58.044 29.630 0.00 0.00 0.00 2.71
1667 3815 1.309950 TCCAAAACGATGTTTGCCGA 58.690 45.000 0.00 0.00 37.20 5.54
1692 3840 3.316588 TGATGCCTATGTCTTCTCGTCTC 59.683 47.826 0.00 0.00 0.00 3.36
1723 3871 3.319198 GACGACCAGGAAGGCCCA 61.319 66.667 0.00 0.00 43.14 5.36
2133 4290 3.963383 TCTCGGTTGACAAAAGCTTTC 57.037 42.857 13.10 0.29 0.00 2.62
2936 5093 9.573166 AGCATAATGTTATGTTAATTGAGGCTA 57.427 29.630 12.80 0.00 41.92 3.93
2963 5120 1.027357 CCGGCTCATTCCATTCCTTG 58.973 55.000 0.00 0.00 0.00 3.61
3066 5229 5.365619 AGTTTATCCTCAAGTGTCGTTTGT 58.634 37.500 0.00 0.00 0.00 2.83
3732 5905 2.693069 CAGCAGACTCGAGAATGGTTT 58.307 47.619 21.68 0.00 0.00 3.27
4293 6491 2.750948 TCTCTTTGAACTACGCACACC 58.249 47.619 0.00 0.00 0.00 4.16
4563 6776 5.463724 GCTAACCGAGTCATTTAATGAGGAG 59.536 44.000 15.64 7.16 40.53 3.69
4942 7157 2.193536 GTGGCTTTGAACCGCTGGT 61.194 57.895 0.00 0.00 37.65 4.00
4952 7167 1.412453 AACCGCTGGTGGTACTTGGA 61.412 55.000 6.24 0.00 42.89 3.53
5140 7377 2.359975 CCAGGTTTCGGGGTGAGC 60.360 66.667 0.00 0.00 0.00 4.26
5194 7431 6.994221 ACAGTATATTACCATAGTCACCTGC 58.006 40.000 0.00 0.00 0.00 4.85
5195 7432 6.782988 ACAGTATATTACCATAGTCACCTGCT 59.217 38.462 0.00 0.00 0.00 4.24
5196 7433 7.039644 ACAGTATATTACCATAGTCACCTGCTC 60.040 40.741 0.00 0.00 0.00 4.26
5197 7434 7.177568 CAGTATATTACCATAGTCACCTGCTCT 59.822 40.741 0.00 0.00 0.00 4.09
5198 7435 7.730784 AGTATATTACCATAGTCACCTGCTCTT 59.269 37.037 0.00 0.00 0.00 2.85
5199 7436 5.700402 ATTACCATAGTCACCTGCTCTTT 57.300 39.130 0.00 0.00 0.00 2.52
5200 7437 3.618690 ACCATAGTCACCTGCTCTTTC 57.381 47.619 0.00 0.00 0.00 2.62
5201 7438 2.093973 ACCATAGTCACCTGCTCTTTCG 60.094 50.000 0.00 0.00 0.00 3.46
5202 7439 2.544685 CATAGTCACCTGCTCTTTCGG 58.455 52.381 0.00 0.00 0.00 4.30
5203 7440 1.629043 TAGTCACCTGCTCTTTCGGT 58.371 50.000 0.00 0.00 0.00 4.69
5205 7442 1.301716 TCACCTGCTCTTTCGGTGC 60.302 57.895 2.91 0.00 45.99 5.01
5206 7443 1.597854 CACCTGCTCTTTCGGTGCA 60.598 57.895 0.00 0.00 41.39 4.57
5207 7444 0.957395 CACCTGCTCTTTCGGTGCAT 60.957 55.000 0.00 0.00 42.42 3.96
5208 7445 0.674895 ACCTGCTCTTTCGGTGCATC 60.675 55.000 0.00 0.00 42.42 3.91
5209 7446 1.699656 CCTGCTCTTTCGGTGCATCG 61.700 60.000 14.66 14.66 42.42 3.84
5210 7447 1.005037 TGCTCTTTCGGTGCATCGT 60.005 52.632 20.53 0.00 39.16 3.73
5211 7448 0.245266 TGCTCTTTCGGTGCATCGTA 59.755 50.000 20.53 6.99 39.16 3.43
5212 7449 1.134818 TGCTCTTTCGGTGCATCGTAT 60.135 47.619 20.53 0.00 39.16 3.06
5213 7450 1.523095 GCTCTTTCGGTGCATCGTATC 59.477 52.381 20.53 0.38 34.88 2.24
5214 7451 2.799917 GCTCTTTCGGTGCATCGTATCT 60.800 50.000 20.53 0.00 34.88 1.98
5215 7452 3.448686 CTCTTTCGGTGCATCGTATCTT 58.551 45.455 20.53 0.00 0.00 2.40
5216 7453 3.186909 TCTTTCGGTGCATCGTATCTTG 58.813 45.455 20.53 5.36 0.00 3.02
5217 7454 2.951457 TTCGGTGCATCGTATCTTGA 57.049 45.000 20.53 0.00 0.00 3.02
5218 7455 2.951457 TCGGTGCATCGTATCTTGAA 57.049 45.000 20.53 0.00 0.00 2.69
5219 7456 2.536365 TCGGTGCATCGTATCTTGAAC 58.464 47.619 20.53 0.00 0.00 3.18
5220 7457 1.255342 CGGTGCATCGTATCTTGAACG 59.745 52.381 12.24 0.00 41.64 3.95
5241 7478 5.502153 CGATAGTTCTGGCAGTAGTTAGT 57.498 43.478 15.27 2.27 0.00 2.24
5242 7479 5.512473 CGATAGTTCTGGCAGTAGTTAGTC 58.488 45.833 15.27 6.53 0.00 2.59
5390 7627 2.185310 AACTGCGTCAGGGGTGGATC 62.185 60.000 10.80 0.00 35.51 3.36
5446 7684 1.669779 GCCAGTTTCATGAGCTAGCTG 59.330 52.381 24.99 9.28 0.00 4.24
5582 7820 5.517299 GGGCAGGGTTGGAGATGAATATATT 60.517 44.000 0.00 0.00 0.00 1.28
5655 7897 7.823635 ACTACTAAAGGGAGAGATGTGGTATA 58.176 38.462 0.00 0.00 0.00 1.47
5740 7986 2.512056 TGACCCCATAAATCCCGAACAT 59.488 45.455 0.00 0.00 0.00 2.71
5837 8084 4.358214 ACCCCAATAAATCCCGAACATTT 58.642 39.130 0.00 0.00 0.00 2.32
5867 8114 8.555166 TTTAAACATGTCATCTTGAACGTTTC 57.445 30.769 0.46 0.00 31.30 2.78
5891 8138 2.251642 GGCAAGTTGACGCGAGGTT 61.252 57.895 15.93 0.00 0.00 3.50
5892 8139 1.647084 GCAAGTTGACGCGAGGTTT 59.353 52.632 15.93 0.00 0.00 3.27
5896 8143 1.878953 AGTTGACGCGAGGTTTCAAT 58.121 45.000 15.93 0.00 32.10 2.57
5933 9087 2.323599 TGGCAATGTTGTCCCAATTCA 58.676 42.857 0.00 0.00 30.03 2.57
6000 9183 8.962884 AACTGAAGCTTAAAATCCAAATGTTT 57.037 26.923 0.00 0.00 0.00 2.83
6072 9255 2.203252 CACGCAGCTATGGGCCAT 60.203 61.111 24.69 24.69 42.93 4.40
6163 9927 7.231317 GCAGGAATTCACAGGGAAATTATATCA 59.769 37.037 7.93 0.00 39.39 2.15
6215 9979 1.541588 GGATCCAACCACACTTGAAGC 59.458 52.381 6.95 0.00 0.00 3.86
6235 9999 1.004560 CCTCGCAGTCCAAGAAGCA 60.005 57.895 0.00 0.00 0.00 3.91
6254 10018 5.220710 AGCACTATCTTTAGCGGATGATT 57.779 39.130 0.00 0.00 0.00 2.57
6266 10030 4.330250 AGCGGATGATTTCTATGAATGGG 58.670 43.478 0.00 0.00 0.00 4.00
6267 10031 4.042062 AGCGGATGATTTCTATGAATGGGA 59.958 41.667 0.00 0.00 0.00 4.37
6295 10059 0.312416 TGCCATGAAAAACGTTCGGG 59.688 50.000 0.00 0.00 0.00 5.14
6296 10060 1.006825 GCCATGAAAAACGTTCGGGC 61.007 55.000 0.00 3.35 35.43 6.13
6297 10061 0.596082 CCATGAAAAACGTTCGGGCT 59.404 50.000 0.00 0.00 0.00 5.19
6298 10062 1.665735 CCATGAAAAACGTTCGGGCTG 60.666 52.381 0.00 0.00 0.00 4.85
6299 10063 1.001815 CATGAAAAACGTTCGGGCTGT 60.002 47.619 0.00 0.00 0.00 4.40
6300 10064 0.658897 TGAAAAACGTTCGGGCTGTC 59.341 50.000 0.00 0.00 0.00 3.51
6301 10065 0.658897 GAAAAACGTTCGGGCTGTCA 59.341 50.000 0.00 0.00 0.00 3.58
6302 10066 1.265905 GAAAAACGTTCGGGCTGTCAT 59.734 47.619 0.00 0.00 0.00 3.06
6303 10067 0.591170 AAAACGTTCGGGCTGTCATG 59.409 50.000 0.00 0.00 0.00 3.07
6304 10068 1.852067 AAACGTTCGGGCTGTCATGC 61.852 55.000 0.00 0.00 0.00 4.06
6305 10069 2.434884 CGTTCGGGCTGTCATGCT 60.435 61.111 0.00 0.00 0.00 3.79
6306 10070 2.034879 CGTTCGGGCTGTCATGCTT 61.035 57.895 0.00 0.00 0.00 3.91
6307 10071 0.739462 CGTTCGGGCTGTCATGCTTA 60.739 55.000 0.00 0.00 0.00 3.09
6308 10072 1.448985 GTTCGGGCTGTCATGCTTAA 58.551 50.000 0.00 0.00 0.00 1.85
6309 10073 1.810151 GTTCGGGCTGTCATGCTTAAA 59.190 47.619 0.00 0.00 0.00 1.52
6310 10074 2.192664 TCGGGCTGTCATGCTTAAAA 57.807 45.000 0.00 0.00 0.00 1.52
6311 10075 2.722094 TCGGGCTGTCATGCTTAAAAT 58.278 42.857 0.00 0.00 0.00 1.82
6312 10076 2.682856 TCGGGCTGTCATGCTTAAAATC 59.317 45.455 0.00 0.00 0.00 2.17
6313 10077 2.223572 CGGGCTGTCATGCTTAAAATCC 60.224 50.000 0.00 0.00 0.00 3.01
6314 10078 2.223572 GGGCTGTCATGCTTAAAATCCG 60.224 50.000 0.00 0.00 0.00 4.18
6315 10079 2.682856 GGCTGTCATGCTTAAAATCCGA 59.317 45.455 0.00 0.00 0.00 4.55
6316 10080 3.128589 GGCTGTCATGCTTAAAATCCGAA 59.871 43.478 0.00 0.00 0.00 4.30
6317 10081 4.098416 GCTGTCATGCTTAAAATCCGAAC 58.902 43.478 0.00 0.00 0.00 3.95
6318 10082 4.334443 CTGTCATGCTTAAAATCCGAACG 58.666 43.478 0.00 0.00 0.00 3.95
6319 10083 3.749088 TGTCATGCTTAAAATCCGAACGT 59.251 39.130 0.00 0.00 0.00 3.99
6320 10084 4.214545 TGTCATGCTTAAAATCCGAACGTT 59.785 37.500 0.00 0.00 0.00 3.99
6321 10085 4.786575 GTCATGCTTAAAATCCGAACGTTC 59.213 41.667 18.47 18.47 0.00 3.95
6386 10150 4.891992 TTGATCTCGAAAAGAGGTTCCT 57.108 40.909 0.00 0.00 46.82 3.36
6390 10154 4.957684 TCTCGAAAAGAGGTTCCTTCTT 57.042 40.909 0.00 0.00 46.82 2.52
6405 10169 3.920197 TCCTTCTTGGTTTCCCTATTGGA 59.080 43.478 0.00 0.00 38.11 3.53
6448 10214 8.761575 TCGACTACAAATAAAAATTCCTACGT 57.238 30.769 0.00 0.00 0.00 3.57
6475 10241 3.472652 ACAACCAAGAACATGCTACGAA 58.527 40.909 0.00 0.00 0.00 3.85
6496 10263 5.520288 CGAAAATGGATCACAGATCGTTACT 59.480 40.000 0.00 0.00 31.67 2.24
6509 10276 5.043903 AGATCGTTACTACTAGACGCGTAA 58.956 41.667 13.97 1.85 36.77 3.18
6514 10285 5.175856 CGTTACTACTAGACGCGTAATACCT 59.824 44.000 13.97 7.27 0.00 3.08
6519 10290 2.373540 AGACGCGTAATACCTTGCAA 57.626 45.000 13.97 0.00 0.00 4.08
6657 10431 2.224066 GCCTCTAACAGTATCCGCATGT 60.224 50.000 0.00 0.00 0.00 3.21
6728 10502 1.948145 CGAGTGGAGGTAGCTATTCGT 59.052 52.381 0.00 0.00 0.00 3.85
6806 10583 4.263506 GCACCCCACTTTATATAGGCATCT 60.264 45.833 0.00 0.00 0.00 2.90
6825 10602 2.110213 TCGCGGGCTCAACACTTT 59.890 55.556 6.13 0.00 0.00 2.66
6862 10639 3.137544 TCCTAAAGCCCAAAGTCTGTTCA 59.862 43.478 0.00 0.00 0.00 3.18
6899 10676 2.820787 CGAGTAGGACCACTTCTGACTT 59.179 50.000 0.00 0.00 0.00 3.01
6915 10692 2.522436 TTGTGGAGTCGGACCGGT 60.522 61.111 6.92 6.92 0.00 5.28
7043 10829 2.151202 CGTGCCAACCACAAAGTAGAT 58.849 47.619 0.00 0.00 44.91 1.98
7183 11315 0.327924 ATTCCAGTGATGCCGACCAA 59.672 50.000 0.00 0.00 0.00 3.67
7248 11380 2.202756 GTCGGATCACACGAGGGC 60.203 66.667 0.00 0.00 41.50 5.19
7251 11383 4.530857 GGATCACACGAGGGCCCG 62.531 72.222 18.44 8.21 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.916318 TGCCATCCAACAATAATTTGATCC 58.084 37.500 0.00 0.00 36.64 3.36
1 2 7.439381 AGATGCCATCCAACAATAATTTGATC 58.561 34.615 0.00 0.00 36.64 2.92
4 5 7.549842 TGAAAGATGCCATCCAACAATAATTTG 59.450 33.333 0.00 0.00 38.86 2.32
5 6 7.622713 TGAAAGATGCCATCCAACAATAATTT 58.377 30.769 0.00 0.00 0.00 1.82
6 7 7.185318 TGAAAGATGCCATCCAACAATAATT 57.815 32.000 0.00 0.00 0.00 1.40
8 9 5.394443 GCTGAAAGATGCCATCCAACAATAA 60.394 40.000 0.00 0.00 34.07 1.40
10 11 3.118884 GCTGAAAGATGCCATCCAACAAT 60.119 43.478 0.00 0.00 34.07 2.71
11 12 2.231964 GCTGAAAGATGCCATCCAACAA 59.768 45.455 0.00 0.00 34.07 2.83
12 13 1.820519 GCTGAAAGATGCCATCCAACA 59.179 47.619 0.00 0.00 34.07 3.33
13 14 1.820519 TGCTGAAAGATGCCATCCAAC 59.179 47.619 0.00 0.00 34.07 3.77
14 15 2.219080 TGCTGAAAGATGCCATCCAA 57.781 45.000 0.00 0.00 34.07 3.53
15 16 2.219080 TTGCTGAAAGATGCCATCCA 57.781 45.000 0.00 0.00 34.07 3.41
16 17 3.131577 TGATTTGCTGAAAGATGCCATCC 59.868 43.478 0.00 0.00 34.07 3.51
17 18 4.360563 CTGATTTGCTGAAAGATGCCATC 58.639 43.478 0.00 0.00 34.07 3.51
18 19 3.430374 GCTGATTTGCTGAAAGATGCCAT 60.430 43.478 0.00 0.00 34.07 4.40
19 20 2.094390 GCTGATTTGCTGAAAGATGCCA 60.094 45.455 0.00 0.00 34.07 4.92
20 21 2.094390 TGCTGATTTGCTGAAAGATGCC 60.094 45.455 0.00 0.00 34.07 4.40
21 22 2.921754 GTGCTGATTTGCTGAAAGATGC 59.078 45.455 0.00 0.00 34.07 3.91
22 23 3.508762 GGTGCTGATTTGCTGAAAGATG 58.491 45.455 0.00 0.00 34.07 2.90
23 24 2.163010 CGGTGCTGATTTGCTGAAAGAT 59.837 45.455 0.00 0.00 34.07 2.40
24 25 1.536766 CGGTGCTGATTTGCTGAAAGA 59.463 47.619 0.00 0.00 34.07 2.52
25 26 1.267806 ACGGTGCTGATTTGCTGAAAG 59.732 47.619 0.00 0.00 0.00 2.62
26 27 1.317613 ACGGTGCTGATTTGCTGAAA 58.682 45.000 0.00 0.00 0.00 2.69
27 28 1.317613 AACGGTGCTGATTTGCTGAA 58.682 45.000 0.00 0.00 0.00 3.02
28 29 1.317613 AAACGGTGCTGATTTGCTGA 58.682 45.000 0.00 0.00 0.00 4.26
29 30 2.987413 TAAACGGTGCTGATTTGCTG 57.013 45.000 0.00 0.00 0.00 4.41
30 31 3.146066 TCTTAAACGGTGCTGATTTGCT 58.854 40.909 0.00 0.00 0.00 3.91
31 32 3.552604 TCTTAAACGGTGCTGATTTGC 57.447 42.857 0.00 0.00 0.00 3.68
32 33 4.155826 TCCATCTTAAACGGTGCTGATTTG 59.844 41.667 0.00 0.00 0.00 2.32
33 34 4.156008 GTCCATCTTAAACGGTGCTGATTT 59.844 41.667 0.00 0.00 0.00 2.17
34 35 3.689649 GTCCATCTTAAACGGTGCTGATT 59.310 43.478 0.00 0.00 0.00 2.57
35 36 3.270877 GTCCATCTTAAACGGTGCTGAT 58.729 45.455 0.00 0.00 0.00 2.90
36 37 2.037902 TGTCCATCTTAAACGGTGCTGA 59.962 45.455 0.00 0.00 0.00 4.26
37 38 2.422597 TGTCCATCTTAAACGGTGCTG 58.577 47.619 0.00 0.00 0.00 4.41
38 39 2.851263 TGTCCATCTTAAACGGTGCT 57.149 45.000 0.00 0.00 0.00 4.40
39 40 2.030457 CGATGTCCATCTTAAACGGTGC 59.970 50.000 5.79 0.00 35.72 5.01
40 41 3.259064 ACGATGTCCATCTTAAACGGTG 58.741 45.455 5.79 0.00 35.72 4.94
41 42 3.518590 GACGATGTCCATCTTAAACGGT 58.481 45.455 5.79 0.00 35.72 4.83
54 55 0.041135 GACGAGATCCGGACGATGTC 60.041 60.000 18.64 14.80 43.93 3.06
55 56 1.445716 GGACGAGATCCGGACGATGT 61.446 60.000 18.64 10.15 43.93 3.06
56 57 1.283181 GGACGAGATCCGGACGATG 59.717 63.158 18.64 6.97 43.93 3.84
57 58 3.747266 GGACGAGATCCGGACGAT 58.253 61.111 18.64 2.13 43.93 3.73
65 66 1.565305 GACAGTGCATGGACGAGATC 58.435 55.000 12.02 4.77 0.00 2.75
66 67 0.179127 CGACAGTGCATGGACGAGAT 60.179 55.000 12.02 0.00 35.75 2.75
67 68 1.212751 CGACAGTGCATGGACGAGA 59.787 57.895 12.02 0.00 35.75 4.04
68 69 1.080501 ACGACAGTGCATGGACGAG 60.081 57.895 12.02 11.10 36.88 4.18
69 70 1.372872 CACGACAGTGCATGGACGA 60.373 57.895 12.02 0.00 41.94 4.20
70 71 3.159070 CACGACAGTGCATGGACG 58.841 61.111 12.02 9.40 41.94 4.79
79 80 1.319541 AGTACTCTGCACACGACAGT 58.680 50.000 0.00 0.00 36.50 3.55
80 81 2.320367 GAAGTACTCTGCACACGACAG 58.680 52.381 0.00 0.00 36.44 3.51
81 82 1.000607 GGAAGTACTCTGCACACGACA 60.001 52.381 0.00 0.00 0.00 4.35
82 83 1.699343 GGAAGTACTCTGCACACGAC 58.301 55.000 0.00 0.00 0.00 4.34
83 84 0.240145 CGGAAGTACTCTGCACACGA 59.760 55.000 0.00 0.00 0.00 4.35
84 85 0.240145 TCGGAAGTACTCTGCACACG 59.760 55.000 0.00 0.00 0.00 4.49
85 86 2.263077 CATCGGAAGTACTCTGCACAC 58.737 52.381 0.00 0.00 0.00 3.82
86 87 1.404181 GCATCGGAAGTACTCTGCACA 60.404 52.381 0.00 0.00 0.00 4.57
87 88 1.134965 AGCATCGGAAGTACTCTGCAC 60.135 52.381 0.00 0.00 32.18 4.57
88 89 1.186200 AGCATCGGAAGTACTCTGCA 58.814 50.000 0.00 0.00 32.18 4.41
89 90 2.359531 ACTAGCATCGGAAGTACTCTGC 59.640 50.000 0.00 1.21 0.00 4.26
90 91 4.640789 AACTAGCATCGGAAGTACTCTG 57.359 45.455 0.00 0.00 0.00 3.35
91 92 5.438833 AGTAACTAGCATCGGAAGTACTCT 58.561 41.667 0.00 0.00 0.00 3.24
92 93 5.277925 GGAGTAACTAGCATCGGAAGTACTC 60.278 48.000 0.00 0.00 0.00 2.59
93 94 4.579753 GGAGTAACTAGCATCGGAAGTACT 59.420 45.833 0.00 0.00 0.00 2.73
94 95 4.261530 GGGAGTAACTAGCATCGGAAGTAC 60.262 50.000 0.00 0.00 0.00 2.73
95 96 3.887716 GGGAGTAACTAGCATCGGAAGTA 59.112 47.826 0.00 0.00 0.00 2.24
96 97 2.694109 GGGAGTAACTAGCATCGGAAGT 59.306 50.000 0.00 0.00 0.00 3.01
97 98 2.959707 AGGGAGTAACTAGCATCGGAAG 59.040 50.000 0.00 0.00 0.00 3.46
98 99 3.028094 AGGGAGTAACTAGCATCGGAA 57.972 47.619 0.00 0.00 0.00 4.30
99 100 2.750141 AGGGAGTAACTAGCATCGGA 57.250 50.000 0.00 0.00 0.00 4.55
100 101 2.287668 CGAAGGGAGTAACTAGCATCGG 60.288 54.545 0.00 0.00 0.00 4.18
101 102 2.358267 ACGAAGGGAGTAACTAGCATCG 59.642 50.000 0.00 0.00 0.00 3.84
102 103 5.708877 ATACGAAGGGAGTAACTAGCATC 57.291 43.478 0.00 0.00 0.00 3.91
103 104 6.305411 AGTATACGAAGGGAGTAACTAGCAT 58.695 40.000 0.00 0.00 0.00 3.79
104 105 5.688807 AGTATACGAAGGGAGTAACTAGCA 58.311 41.667 0.00 0.00 0.00 3.49
105 106 7.736447 TTAGTATACGAAGGGAGTAACTAGC 57.264 40.000 0.00 0.00 0.00 3.42
112 113 9.176460 GCTCTTATATTAGTATACGAAGGGAGT 57.824 37.037 4.70 0.00 0.00 3.85
113 114 8.336806 CGCTCTTATATTAGTATACGAAGGGAG 58.663 40.741 4.70 7.71 0.00 4.30
114 115 7.826252 ACGCTCTTATATTAGTATACGAAGGGA 59.174 37.037 4.70 0.00 0.00 4.20
115 116 7.983307 ACGCTCTTATATTAGTATACGAAGGG 58.017 38.462 4.70 0.59 0.00 3.95
116 117 9.837525 AAACGCTCTTATATTAGTATACGAAGG 57.162 33.333 4.70 0.00 0.00 3.46
134 135 9.509956 AGATCACTATAGTATTCTAAACGCTCT 57.490 33.333 4.74 0.00 0.00 4.09
229 230 7.047271 TGCAGCAGAATGTCTATGTACATAAA 58.953 34.615 16.17 0.47 39.16 1.40
232 233 5.027293 TGCAGCAGAATGTCTATGTACAT 57.973 39.130 13.93 13.93 41.87 2.29
236 237 4.763793 AGTTTTGCAGCAGAATGTCTATGT 59.236 37.500 0.99 0.00 39.31 2.29
351 356 2.420022 GCACAAGATATGGTGTCGCTTT 59.580 45.455 0.00 0.00 37.35 3.51
359 364 4.508551 TCTGGATTGCACAAGATATGGT 57.491 40.909 0.00 0.00 0.00 3.55
360 365 5.067954 TCATCTGGATTGCACAAGATATGG 58.932 41.667 0.00 0.00 0.00 2.74
361 366 6.485648 TCTTCATCTGGATTGCACAAGATATG 59.514 38.462 0.00 0.00 0.00 1.78
362 367 6.598503 TCTTCATCTGGATTGCACAAGATAT 58.401 36.000 0.00 0.00 0.00 1.63
363 368 5.993055 TCTTCATCTGGATTGCACAAGATA 58.007 37.500 0.00 0.00 0.00 1.98
364 369 4.851843 TCTTCATCTGGATTGCACAAGAT 58.148 39.130 0.00 0.00 0.00 2.40
365 370 4.259356 CTCTTCATCTGGATTGCACAAGA 58.741 43.478 0.00 0.00 0.00 3.02
366 371 4.008330 ACTCTTCATCTGGATTGCACAAG 58.992 43.478 0.00 0.00 0.00 3.16
367 372 4.025040 ACTCTTCATCTGGATTGCACAA 57.975 40.909 0.00 0.00 0.00 3.33
368 373 3.708403 ACTCTTCATCTGGATTGCACA 57.292 42.857 0.00 0.00 0.00 4.57
369 374 4.005650 TCAACTCTTCATCTGGATTGCAC 58.994 43.478 0.00 0.00 0.00 4.57
450 455 0.955428 TGGAGTGCGAAGTTCCATGC 60.955 55.000 0.00 0.00 36.13 4.06
455 460 1.205893 AGGAGATGGAGTGCGAAGTTC 59.794 52.381 0.00 0.00 0.00 3.01
458 463 1.110442 AGAGGAGATGGAGTGCGAAG 58.890 55.000 0.00 0.00 0.00 3.79
529 534 6.042638 AGATCTTTCTTCTGTTCATCGGAA 57.957 37.500 0.00 0.00 38.90 4.30
547 552 6.820656 AGTCGACTGCAATATCAAAAAGATCT 59.179 34.615 19.30 0.00 38.19 2.75
553 558 5.120674 CACTCAGTCGACTGCAATATCAAAA 59.879 40.000 35.48 16.58 43.46 2.44
555 560 4.176271 CACTCAGTCGACTGCAATATCAA 58.824 43.478 35.48 17.93 43.46 2.57
567 572 3.371063 GTCGGGCCACTCAGTCGA 61.371 66.667 4.39 0.00 0.00 4.20
613 618 1.884235 CCGACTCCAAAGAGCTTGTT 58.116 50.000 0.00 0.00 44.65 2.83
654 662 3.679824 TTGAATGTTTGGCATGCATGA 57.320 38.095 30.64 7.50 42.45 3.07
705 713 5.897851 TTGGTAGCCTGCATATACCTTAA 57.102 39.130 17.94 7.05 39.78 1.85
749 757 2.223618 GCCGGTTCACTTTGCAGTTTTA 60.224 45.455 1.90 0.00 0.00 1.52
1615 3763 4.697756 CGAGGAAGGCCACGGCAA 62.698 66.667 10.83 0.00 43.37 4.52
1667 3815 5.028549 ACGAGAAGACATAGGCATCAAAT 57.971 39.130 0.00 0.00 0.00 2.32
1692 3840 2.176546 CGTCCATGCCTGCGTTTG 59.823 61.111 0.00 0.00 0.00 2.93
1723 3871 2.540383 TGTCAGCAGGGTCTGATAAGT 58.460 47.619 0.00 0.00 44.04 2.24
1866 4020 6.483640 GTCACTGGTAATGGGATTATCTTGAC 59.516 42.308 0.00 0.00 34.98 3.18
2133 4290 1.404391 CAGCTCAGGCAATTTAGCAGG 59.596 52.381 0.00 0.00 41.70 4.85
2513 4670 4.873259 TCAAAACTGAGACGTTCACATGAA 59.127 37.500 0.00 0.00 0.00 2.57
2936 5093 5.476945 GGAATGGAATGAGCCGGTTAATTAT 59.523 40.000 1.90 0.00 0.00 1.28
2963 5120 9.076596 GCATCAACAATTCCTTTCTGTTTATAC 57.923 33.333 0.00 0.00 30.99 1.47
3066 5229 4.787260 TGTGCTTCGGTATTGTGTAGTA 57.213 40.909 0.00 0.00 0.00 1.82
3732 5905 3.385755 GCGGACTAATACCAAGTTCCCTA 59.614 47.826 0.00 0.00 0.00 3.53
4563 6776 0.615331 TCAGGGTCTCATCACTTGCC 59.385 55.000 0.00 0.00 0.00 4.52
4942 7157 1.836999 ATGCAGCCGTCCAAGTACCA 61.837 55.000 0.00 0.00 0.00 3.25
5140 7377 1.663702 GCAAGCTGCAGCCAACTTG 60.664 57.895 34.39 29.45 44.24 3.16
5189 7426 0.674895 GATGCACCGAAAGAGCAGGT 60.675 55.000 0.00 0.00 43.15 4.00
5190 7427 1.699656 CGATGCACCGAAAGAGCAGG 61.700 60.000 0.00 0.00 43.15 4.85
5191 7428 1.016130 ACGATGCACCGAAAGAGCAG 61.016 55.000 7.92 0.00 43.15 4.24
5192 7429 0.245266 TACGATGCACCGAAAGAGCA 59.755 50.000 7.92 0.00 43.80 4.26
5193 7430 1.523095 GATACGATGCACCGAAAGAGC 59.477 52.381 7.92 0.00 0.00 4.09
5194 7431 3.085443 AGATACGATGCACCGAAAGAG 57.915 47.619 7.92 0.00 0.00 2.85
5195 7432 3.119280 TCAAGATACGATGCACCGAAAGA 60.119 43.478 7.92 0.00 0.00 2.52
5196 7433 3.186909 TCAAGATACGATGCACCGAAAG 58.813 45.455 7.92 0.00 0.00 2.62
5197 7434 3.239587 TCAAGATACGATGCACCGAAA 57.760 42.857 7.92 0.00 0.00 3.46
5198 7435 2.927477 GTTCAAGATACGATGCACCGAA 59.073 45.455 7.92 0.00 0.00 4.30
5199 7436 2.536365 GTTCAAGATACGATGCACCGA 58.464 47.619 7.92 0.00 0.00 4.69
5200 7437 1.255342 CGTTCAAGATACGATGCACCG 59.745 52.381 0.00 0.00 41.33 4.94
5201 7438 2.536365 TCGTTCAAGATACGATGCACC 58.464 47.619 0.00 0.00 42.51 5.01
5217 7454 4.803098 AACTACTGCCAGAACTATCGTT 57.197 40.909 0.00 0.00 35.68 3.85
5218 7455 4.948621 ACTAACTACTGCCAGAACTATCGT 59.051 41.667 0.00 0.00 0.00 3.73
5219 7456 5.066117 TGACTAACTACTGCCAGAACTATCG 59.934 44.000 0.00 0.00 0.00 2.92
5220 7457 6.267070 GTGACTAACTACTGCCAGAACTATC 58.733 44.000 0.00 0.00 0.00 2.08
5221 7458 5.127356 GGTGACTAACTACTGCCAGAACTAT 59.873 44.000 0.00 0.00 0.00 2.12
5222 7459 4.461781 GGTGACTAACTACTGCCAGAACTA 59.538 45.833 0.00 0.00 0.00 2.24
5223 7460 3.258622 GGTGACTAACTACTGCCAGAACT 59.741 47.826 0.00 0.00 0.00 3.01
5224 7461 3.258622 AGGTGACTAACTACTGCCAGAAC 59.741 47.826 0.00 0.00 40.61 3.01
5225 7462 3.258372 CAGGTGACTAACTACTGCCAGAA 59.742 47.826 0.00 0.00 40.21 3.02
5226 7463 2.826128 CAGGTGACTAACTACTGCCAGA 59.174 50.000 0.00 0.00 40.21 3.86
5227 7464 2.675317 GCAGGTGACTAACTACTGCCAG 60.675 54.545 0.00 0.00 46.47 4.85
5228 7465 1.275291 GCAGGTGACTAACTACTGCCA 59.725 52.381 0.00 0.00 46.47 4.92
5229 7466 2.011540 GCAGGTGACTAACTACTGCC 57.988 55.000 0.00 0.00 46.47 4.85
5231 7468 4.792521 AAGAGCAGGTGACTAACTACTG 57.207 45.455 0.00 0.00 40.21 2.74
5232 7469 4.082679 CGAAAGAGCAGGTGACTAACTACT 60.083 45.833 0.00 0.00 40.21 2.57
5233 7470 4.167268 CGAAAGAGCAGGTGACTAACTAC 58.833 47.826 0.00 0.00 40.21 2.73
5234 7471 3.192844 CCGAAAGAGCAGGTGACTAACTA 59.807 47.826 0.00 0.00 40.21 2.24
5235 7472 2.028930 CCGAAAGAGCAGGTGACTAACT 60.029 50.000 0.00 0.00 40.21 2.24
5236 7473 2.288886 ACCGAAAGAGCAGGTGACTAAC 60.289 50.000 0.00 0.00 40.21 2.34
5237 7474 1.968493 ACCGAAAGAGCAGGTGACTAA 59.032 47.619 0.00 0.00 40.21 2.24
5238 7475 1.629043 ACCGAAAGAGCAGGTGACTA 58.371 50.000 0.00 0.00 40.21 2.59
5239 7476 2.442056 ACCGAAAGAGCAGGTGACT 58.558 52.632 0.00 0.00 46.44 3.41
5446 7684 9.364989 GATCATTGTAATAGAGAGTAATCAGGC 57.635 37.037 0.00 0.00 0.00 4.85
5655 7897 6.597672 TGTTAAAGATGCATGACGGATTAAGT 59.402 34.615 2.46 0.00 0.00 2.24
5837 8084 7.807433 CGTTCAAGATGACATGTTTAAAATCCA 59.193 33.333 0.00 0.00 0.00 3.41
5867 8114 0.453282 CGCGTCAACTTGCCATGAAG 60.453 55.000 0.00 0.00 0.00 3.02
5891 8138 7.981789 TGCCATGTTGTAACAACTAAAATTGAA 59.018 29.630 6.96 0.00 43.03 2.69
5892 8139 7.492524 TGCCATGTTGTAACAACTAAAATTGA 58.507 30.769 6.96 0.00 43.03 2.57
5896 8143 7.268586 ACATTGCCATGTTGTAACAACTAAAA 58.731 30.769 6.96 0.31 41.16 1.52
6051 9234 3.204827 CCCATAGCTGCGTGCCAC 61.205 66.667 0.00 0.00 44.23 5.01
6104 9287 0.712222 GCTCCTACAAACACGTACGC 59.288 55.000 16.72 0.00 0.00 4.42
6163 9927 0.681564 AAGGTGATCGTCGAGGCTCT 60.682 55.000 13.50 0.00 0.00 4.09
6215 9979 1.078848 CTTCTTGGACTGCGAGGGG 60.079 63.158 0.00 0.00 0.00 4.79
6235 9999 8.807118 TCATAGAAATCATCCGCTAAAGATAGT 58.193 33.333 0.00 0.00 0.00 2.12
6254 10018 8.613923 TGGCATATAGATTTCCCATTCATAGAA 58.386 33.333 0.00 0.00 0.00 2.10
6266 10030 8.856490 AACGTTTTTCATGGCATATAGATTTC 57.144 30.769 0.00 0.00 0.00 2.17
6267 10031 7.643764 CGAACGTTTTTCATGGCATATAGATTT 59.356 33.333 0.46 0.00 0.00 2.17
6295 10059 4.098416 GTTCGGATTTTAAGCATGACAGC 58.902 43.478 0.00 0.00 0.00 4.40
6296 10060 4.142902 ACGTTCGGATTTTAAGCATGACAG 60.143 41.667 0.00 0.00 0.00 3.51
6297 10061 3.749088 ACGTTCGGATTTTAAGCATGACA 59.251 39.130 0.00 0.00 0.00 3.58
6298 10062 4.336532 ACGTTCGGATTTTAAGCATGAC 57.663 40.909 0.00 0.00 0.00 3.06
6299 10063 4.434989 CGAACGTTCGGATTTTAAGCATGA 60.435 41.667 36.53 0.00 46.30 3.07
6300 10064 3.778718 CGAACGTTCGGATTTTAAGCATG 59.221 43.478 36.53 8.97 46.30 4.06
6301 10065 3.998522 CGAACGTTCGGATTTTAAGCAT 58.001 40.909 36.53 0.00 46.30 3.79
6302 10066 3.443054 CGAACGTTCGGATTTTAAGCA 57.557 42.857 36.53 0.00 46.30 3.91
6314 10078 1.787847 CATGACAGCCCGAACGTTC 59.212 57.895 18.47 18.47 0.00 3.95
6315 10079 2.325082 GCATGACAGCCCGAACGTT 61.325 57.895 0.00 0.00 0.00 3.99
6316 10080 2.731691 AAGCATGACAGCCCGAACGT 62.732 55.000 0.00 0.00 34.23 3.99
6317 10081 0.739462 TAAGCATGACAGCCCGAACG 60.739 55.000 0.00 0.00 34.23 3.95
6318 10082 1.448985 TTAAGCATGACAGCCCGAAC 58.551 50.000 0.00 0.00 34.23 3.95
6319 10083 2.192664 TTTAAGCATGACAGCCCGAA 57.807 45.000 0.00 0.00 34.23 4.30
6320 10084 2.192664 TTTTAAGCATGACAGCCCGA 57.807 45.000 0.00 0.00 34.23 5.14
6321 10085 2.223572 GGATTTTAAGCATGACAGCCCG 60.224 50.000 0.00 0.00 34.23 6.13
6322 10086 2.223572 CGGATTTTAAGCATGACAGCCC 60.224 50.000 0.00 0.00 34.23 5.19
6323 10087 2.682856 TCGGATTTTAAGCATGACAGCC 59.317 45.455 0.00 0.00 34.23 4.85
6328 10092 4.434989 CGAACGTTCGGATTTTAAGCATGA 60.435 41.667 36.53 0.00 46.30 3.07
6405 10169 4.702612 AGTCGATGCATCCTATCGTAGATT 59.297 41.667 20.87 3.89 45.55 2.40
6448 10214 2.223782 GCATGTTCTTGGTTGTTCTGCA 60.224 45.455 0.00 0.00 0.00 4.41
6475 10241 7.113658 AGTAGTAACGATCTGTGATCCATTT 57.886 36.000 0.00 0.00 0.00 2.32
6496 10263 3.627123 TGCAAGGTATTACGCGTCTAGTA 59.373 43.478 18.63 0.00 0.00 1.82
6509 10276 3.008049 ACTCTTCTTCCGTTGCAAGGTAT 59.992 43.478 17.23 0.00 0.00 2.73
6514 10285 1.946768 CCAACTCTTCTTCCGTTGCAA 59.053 47.619 0.00 0.00 37.34 4.08
6519 10290 1.375326 GCCCCAACTCTTCTTCCGT 59.625 57.895 0.00 0.00 0.00 4.69
6657 10431 0.175760 GCTGCACGATGTTCCTCCTA 59.824 55.000 0.00 0.00 0.00 2.94
6728 10502 4.069304 GTCACTAGGGTTTGCATGTGTTA 58.931 43.478 0.00 0.00 0.00 2.41
6806 10583 2.933878 AAAGTGTTGAGCCCGCGACA 62.934 55.000 8.23 0.00 0.00 4.35
6862 10639 1.379977 TCGGACTCGGATTCAGGCT 60.380 57.895 0.00 0.00 36.95 4.58
6899 10676 2.987547 GACCGGTCCGACTCCACA 60.988 66.667 24.75 0.00 0.00 4.17
6948 10725 1.739067 AAGCCGACTTGAACCTATGC 58.261 50.000 0.00 0.00 33.84 3.14
7043 10829 4.127171 GGTTCGCCTAATCAGCTTCATAA 58.873 43.478 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.