Multiple sequence alignment - TraesCS5D01G116300

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 TraesCS5D01G116300 chr5D 100.000 4617 0 0 1 4617 136348153 136352769 0.000000e+00 8527.0
1 TraesCS5D01G116300 chr5D 100.000 739 0 0 4871 5609 136353023 136353761 0.000000e+00 1365.0
2 TraesCS5D01G116300 chr5D 88.180 846 99 1 9 854 356832218 356833062 0.000000e+00 1007.0
3 TraesCS5D01G116300 chr5D 87.746 865 103 3 1 865 433195995 433196856 0.000000e+00 1007.0
4 TraesCS5D01G116300 chr5D 97.674 43 1 0 4137 4179 464690683 464690725 2.170000e-09 75.0
5 TraesCS5D01G116300 chr5B 91.829 2570 101 31 1237 3741 149331572 149329047 0.000000e+00 3482.0
6 TraesCS5D01G116300 chr5B 95.100 551 18 5 4873 5423 149328180 149327639 0.000000e+00 859.0
7 TraesCS5D01G116300 chr5B 87.316 749 73 17 3891 4617 149328937 149328189 0.000000e+00 837.0
8 TraesCS5D01G116300 chr5B 91.437 327 11 2 864 1185 149331887 149331573 3.100000e-117 433.0
9 TraesCS5D01G116300 chr5B 95.364 151 6 1 5460 5609 149327642 149327492 7.260000e-59 239.0
10 TraesCS5D01G116300 chr5B 97.674 43 1 0 4137 4179 571616770 571616728 2.170000e-09 75.0
11 TraesCS5D01G116300 chr5A 87.746 1779 122 42 1315 3043 168865248 168863516 0.000000e+00 1989.0
12 TraesCS5D01G116300 chr5A 88.005 867 101 3 1 865 299057909 299058774 0.000000e+00 1022.0
13 TraesCS5D01G116300 chr5A 93.496 615 32 5 3173 3782 168849222 168848611 0.000000e+00 907.0
14 TraesCS5D01G116300 chr5A 86.945 743 61 11 4875 5608 168848225 168847510 0.000000e+00 802.0
15 TraesCS5D01G116300 chr5A 86.962 744 59 16 452 1185 168866068 168865353 0.000000e+00 802.0
16 TraesCS5D01G116300 chr5A 91.343 335 28 1 4176 4509 168848568 168848234 1.840000e-124 457.0
17 TraesCS5D01G116300 chr5A 74.271 583 118 25 4871 5432 30083572 30084143 3.400000e-52 217.0
18 TraesCS5D01G116300 chr1D 89.940 835 77 6 36 868 341233474 341232645 0.000000e+00 1070.0
19 TraesCS5D01G116300 chr1D 88.222 866 99 2 1 864 102828006 102828870 0.000000e+00 1031.0
20 TraesCS5D01G116300 chr1D 95.098 306 15 0 3785 4090 433461624 433461929 3.040000e-132 483.0
21 TraesCS5D01G116300 chr1D 75.000 584 112 27 4871 5432 114151254 114150683 7.260000e-59 239.0
22 TraesCS5D01G116300 chr1D 100.000 54 0 0 1184 1237 275787132 275787079 3.580000e-17 100.0
23 TraesCS5D01G116300 chr7D 88.773 864 96 1 1 864 104667628 104668490 0.000000e+00 1057.0
24 TraesCS5D01G116300 chr7D 100.000 54 0 0 1184 1237 307033195 307033142 3.580000e-17 100.0
25 TraesCS5D01G116300 chr7D 100.000 54 0 0 1184 1237 606840029 606840082 3.580000e-17 100.0
26 TraesCS5D01G116300 chr7D 100.000 54 0 0 1184 1237 626711741 626711688 3.580000e-17 100.0
27 TraesCS5D01G116300 chr3A 88.337 866 96 3 1 864 696473492 696474354 0.000000e+00 1035.0
28 TraesCS5D01G116300 chr3A 86.885 61 5 2 4121 4178 414817175 414817115 1.300000e-06 65.8
29 TraesCS5D01G116300 chr3A 86.667 60 7 1 4142 4200 477794502 477794561 1.300000e-06 65.8
30 TraesCS5D01G116300 chr3B 88.005 867 99 5 1 864 471466235 471465371 0.000000e+00 1020.0
31 TraesCS5D01G116300 chr3B 94.754 305 14 2 3785 4089 452109301 452109603 1.830000e-129 473.0
32 TraesCS5D01G116300 chr1B 87.903 868 98 4 1 864 8617301 8616437 0.000000e+00 1014.0
33 TraesCS5D01G116300 chr6B 95.050 303 15 0 3785 4087 375363238 375363540 1.410000e-130 477.0
34 TraesCS5D01G116300 chr6B 100.000 54 0 0 1184 1237 307027266 307027319 3.580000e-17 100.0
35 TraesCS5D01G116300 chr4A 95.050 303 15 0 3785 4087 47646379 47646681 1.410000e-130 477.0
36 TraesCS5D01G116300 chr4A 95.050 303 15 0 3785 4087 219188142 219187840 1.410000e-130 477.0
37 TraesCS5D01G116300 chr4A 95.050 303 15 0 3784 4086 396762234 396762536 1.410000e-130 477.0
38 TraesCS5D01G116300 chr4A 94.516 310 14 3 3785 4093 439012922 439013229 5.080000e-130 475.0
39 TraesCS5D01G116300 chr4A 74.486 584 115 27 4871 5432 36299341 36299912 7.310000e-54 222.0
40 TraesCS5D01G116300 chr4A 95.652 46 2 0 4132 4177 486122084 486122129 2.170000e-09 75.0
41 TraesCS5D01G116300 chr2A 95.050 303 15 0 3785 4087 482409814 482410116 1.410000e-130 477.0
42 TraesCS5D01G116300 chr7A 94.444 306 17 0 3785 4090 452751143 452751448 6.580000e-129 472.0
43 TraesCS5D01G116300 chr6A 75.000 584 112 27 4871 5432 616712008 616711437 7.260000e-59 239.0
44 TraesCS5D01G116300 chr6A 73.552 518 113 18 4871 5371 570514217 570514727 5.780000e-40 176.0
45 TraesCS5D01G116300 chr3D 75.000 584 112 27 4871 5432 425139506 425140077 7.260000e-59 239.0
46 TraesCS5D01G116300 chr3D 100.000 54 0 0 1184 1237 501885457 501885510 3.580000e-17 100.0
47 TraesCS5D01G116300 chr3D 93.750 48 1 2 4138 4184 315481467 315481421 2.800000e-08 71.3
48 TraesCS5D01G116300 chr2D 75.000 584 112 27 4871 5432 651160425 651159854 7.260000e-59 239.0
49 TraesCS5D01G116300 chr2D 74.829 584 113 27 4871 5432 348978180 348978751 3.380000e-57 233.0
50 TraesCS5D01G116300 chrUn 100.000 54 0 0 1184 1237 171007740 171007793 3.580000e-17 100.0
51 TraesCS5D01G116300 chrUn 100.000 54 0 0 1184 1237 432741807 432741860 3.580000e-17 100.0
52 TraesCS5D01G116300 chr1A 100.000 54 0 0 1184 1237 94580349 94580402 3.580000e-17 100.0
53 TraesCS5D01G116300 chr2B 95.556 45 1 1 4137 4181 645479734 645479691 2.800000e-08 71.3
54 TraesCS5D01G116300 chr7B 90.566 53 2 1 4137 4189 392853857 392853906 3.630000e-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 TraesCS5D01G116300 chr5D 136348153 136353761 5608 False 4946.0 8527 100.000000 1 5609 2 chr5D.!!$F4 5608
1 TraesCS5D01G116300 chr5D 356832218 356833062 844 False 1007.0 1007 88.180000 9 854 1 chr5D.!!$F1 845
2 TraesCS5D01G116300 chr5D 433195995 433196856 861 False 1007.0 1007 87.746000 1 865 1 chr5D.!!$F2 864
3 TraesCS5D01G116300 chr5B 149327492 149331887 4395 True 1170.0 3482 92.209200 864 5609 5 chr5B.!!$R2 4745
4 TraesCS5D01G116300 chr5A 168863516 168866068 2552 True 1395.5 1989 87.354000 452 3043 2 chr5A.!!$R2 2591
5 TraesCS5D01G116300 chr5A 299057909 299058774 865 False 1022.0 1022 88.005000 1 865 1 chr5A.!!$F2 864
6 TraesCS5D01G116300 chr5A 168847510 168849222 1712 True 722.0 907 90.594667 3173 5608 3 chr5A.!!$R1 2435
7 TraesCS5D01G116300 chr5A 30083572 30084143 571 False 217.0 217 74.271000 4871 5432 1 chr5A.!!$F1 561
8 TraesCS5D01G116300 chr1D 341232645 341233474 829 True 1070.0 1070 89.940000 36 868 1 chr1D.!!$R3 832
9 TraesCS5D01G116300 chr1D 102828006 102828870 864 False 1031.0 1031 88.222000 1 864 1 chr1D.!!$F1 863
10 TraesCS5D01G116300 chr1D 114150683 114151254 571 True 239.0 239 75.000000 4871 5432 1 chr1D.!!$R1 561
11 TraesCS5D01G116300 chr7D 104667628 104668490 862 False 1057.0 1057 88.773000 1 864 1 chr7D.!!$F1 863
12 TraesCS5D01G116300 chr3A 696473492 696474354 862 False 1035.0 1035 88.337000 1 864 1 chr3A.!!$F2 863
13 TraesCS5D01G116300 chr3B 471465371 471466235 864 True 1020.0 1020 88.005000 1 864 1 chr3B.!!$R1 863
14 TraesCS5D01G116300 chr1B 8616437 8617301 864 True 1014.0 1014 87.903000 1 864 1 chr1B.!!$R1 863
15 TraesCS5D01G116300 chr4A 36299341 36299912 571 False 222.0 222 74.486000 4871 5432 1 chr4A.!!$F1 561
16 TraesCS5D01G116300 chr6A 616711437 616712008 571 True 239.0 239 75.000000 4871 5432 1 chr6A.!!$R1 561
17 TraesCS5D01G116300 chr3D 425139506 425140077 571 False 239.0 239 75.000000 4871 5432 1 chr3D.!!$F1 561
18 TraesCS5D01G116300 chr2D 651159854 651160425 571 True 239.0 239 75.000000 4871 5432 1 chr2D.!!$R1 561
19 TraesCS5D01G116300 chr2D 348978180 348978751 571 False 233.0 233 74.829000 4871 5432 1 chr2D.!!$F1 561

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
653 657 0.183492 GGGTGGCAGCATAATCTCCA 59.817 55.0 19.48 0.00 0.00 3.86 F
1201 1220 0.105658 TATTCCGGTCCTGGGAGAGG 60.106 60.0 0.00 4.54 44.45 3.69 F
2363 2491 0.036010 CCCGACCAAGAAGAGCATGT 60.036 55.0 0.00 0.00 0.00 3.21 F
3204 3372 0.400213 AACCAAATCTCGGCAGGTCA 59.600 50.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1757 0.040058 TTGCAGTCATGGCCTCCATT 59.960 50.0 3.32 0.00 42.23 3.16 R
3197 3365 0.804989 GGTATTGCACTGTGACCTGC 59.195 55.0 12.86 0.00 0.00 4.85 R
3841 4019 0.174162 GATTCAAGTGGGCATGCCAC 59.826 55.0 36.56 29.23 37.98 5.01 R
5161 5399 0.955428 AAGCGACCACATGCGATGTT 60.955 50.0 0.00 0.00 42.70 2.71 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.513912 TGGAGTCGATTAACCTGACACAT 59.486 43.478 0.00 0.00 35.09 3.21
63 64 3.099905 CTGGAACCTCACTACATCTGGA 58.900 50.000 0.00 0.00 0.00 3.86
84 85 8.448816 TCTGGATCCTTCATAGTTGACTCTATA 58.551 37.037 14.23 0.00 0.00 1.31
99 100 3.826729 ACTCTATATACCATGCGCTCACA 59.173 43.478 9.73 0.00 0.00 3.58
147 148 5.238006 ACAAGAAAATTTGGACGTCGAAA 57.762 34.783 24.86 24.86 32.32 3.46
160 161 6.961576 TGGACGTCGAAAATTTCACTAAAAT 58.038 32.000 9.92 0.00 39.30 1.82
210 212 2.504367 GGAGTTGTGCTAGCCAAAGAA 58.496 47.619 13.29 0.00 0.00 2.52
214 216 5.183140 GGAGTTGTGCTAGCCAAAGAAAATA 59.817 40.000 13.29 0.00 0.00 1.40
263 265 7.074502 AGTAAGAAGTGTAGTTTTCGTACTCG 58.925 38.462 6.90 0.00 41.49 4.18
283 285 2.538037 CGTGACGAGACAATCAAACACA 59.462 45.455 0.00 0.00 0.00 3.72
335 337 3.003689 GCGTGGTCAATCATCCAAATAGG 59.996 47.826 0.00 0.00 35.38 2.57
341 343 4.823989 GTCAATCATCCAAATAGGGTCCAG 59.176 45.833 0.00 0.00 38.24 3.86
380 382 7.867403 CACAAGTGTTGCTAATATTTTTGGTCT 59.133 33.333 0.00 0.00 0.00 3.85
494 496 4.599047 TGATTTTCGAGGGCAAAAACAT 57.401 36.364 0.00 0.00 0.00 2.71
499 501 3.973206 TCGAGGGCAAAAACATCTCTA 57.027 42.857 0.00 0.00 0.00 2.43
504 506 5.642063 CGAGGGCAAAAACATCTCTACTTTA 59.358 40.000 0.00 0.00 0.00 1.85
553 555 4.643334 TGCTTCGTACATGGTCTACACTAT 59.357 41.667 0.00 0.00 0.00 2.12
555 557 6.017357 TGCTTCGTACATGGTCTACACTATAG 60.017 42.308 0.00 0.00 0.00 1.31
556 558 6.017275 GCTTCGTACATGGTCTACACTATAGT 60.017 42.308 0.00 0.00 0.00 2.12
623 627 1.002011 GGGTGGCCAGAAAGGTCTC 60.002 63.158 5.11 0.00 44.59 3.36
653 657 0.183492 GGGTGGCAGCATAATCTCCA 59.817 55.000 19.48 0.00 0.00 3.86
664 668 3.825014 GCATAATCTCCAGATTGGTGCAT 59.175 43.478 23.20 6.30 45.78 3.96
686 690 0.390860 CCTCCTTCGACCTAGGCATG 59.609 60.000 9.30 0.00 32.59 4.06
712 716 4.096682 GTCGGTCCTATATGATCCTACTGC 59.903 50.000 0.00 0.00 0.00 4.40
765 774 8.516811 TTTTAGTTTGTTTTTGTTTCGCTGTA 57.483 26.923 0.00 0.00 0.00 2.74
823 833 6.765512 TCATCATGTTTTGTATCCGCTTGATA 59.234 34.615 0.00 0.00 34.76 2.15
824 834 7.445096 TCATCATGTTTTGTATCCGCTTGATAT 59.555 33.333 0.00 0.00 38.21 1.63
855 865 9.838339 TTTTGAGTCAATAAAAATGGCCTTTTA 57.162 25.926 16.35 13.57 36.01 1.52
871 881 6.128007 TGGCCTTTTATCGAAAAATGAGACTC 60.128 38.462 3.32 0.00 34.16 3.36
930 940 1.275573 GTGTGGGGTCCTGAAGACTAC 59.724 57.143 0.00 0.00 45.54 2.73
962 977 2.578786 CACCTAACCTTTTCCCACGTT 58.421 47.619 0.00 0.00 0.00 3.99
1021 1036 1.915078 ATTTGACCGCCTCCTCCCTG 61.915 60.000 0.00 0.00 0.00 4.45
1145 1164 5.014544 TCAATTCATCTCCTTTCCTTGACCT 59.985 40.000 0.00 0.00 0.00 3.85
1166 1185 1.337384 ATCGCCTCCTACCACATGCA 61.337 55.000 0.00 0.00 0.00 3.96
1170 1189 1.683011 GCCTCCTACCACATGCACATT 60.683 52.381 0.00 0.00 0.00 2.71
1185 1204 7.227314 CACATGCACATTGTAGACCTACATATT 59.773 37.037 10.32 0.00 44.54 1.28
1186 1205 7.442364 ACATGCACATTGTAGACCTACATATTC 59.558 37.037 10.32 1.90 44.54 1.75
1187 1206 6.288294 TGCACATTGTAGACCTACATATTCC 58.712 40.000 10.32 2.10 44.54 3.01
1188 1207 5.405571 GCACATTGTAGACCTACATATTCCG 59.594 44.000 10.32 0.82 44.54 4.30
1189 1208 5.926542 CACATTGTAGACCTACATATTCCGG 59.073 44.000 10.32 0.00 44.54 5.14
1190 1209 5.601313 ACATTGTAGACCTACATATTCCGGT 59.399 40.000 10.32 0.00 44.54 5.28
1191 1210 5.779529 TTGTAGACCTACATATTCCGGTC 57.220 43.478 10.32 0.00 44.54 4.79
1192 1211 4.147321 TGTAGACCTACATATTCCGGTCC 58.853 47.826 0.00 0.00 45.45 4.46
1193 1212 3.614568 AGACCTACATATTCCGGTCCT 57.385 47.619 0.00 0.00 45.45 3.85
1194 1213 3.231818 AGACCTACATATTCCGGTCCTG 58.768 50.000 0.00 0.00 45.45 3.86
1195 1214 2.299297 GACCTACATATTCCGGTCCTGG 59.701 54.545 0.00 0.00 39.96 4.45
1196 1215 1.623811 CCTACATATTCCGGTCCTGGG 59.376 57.143 0.00 0.00 0.00 4.45
1197 1216 2.605257 CTACATATTCCGGTCCTGGGA 58.395 52.381 0.00 0.00 0.00 4.37
1198 1217 1.424638 ACATATTCCGGTCCTGGGAG 58.575 55.000 0.00 0.00 34.45 4.30
1199 1218 1.062428 ACATATTCCGGTCCTGGGAGA 60.062 52.381 0.00 0.00 34.45 3.71
1200 1219 1.620819 CATATTCCGGTCCTGGGAGAG 59.379 57.143 0.00 0.00 34.45 3.20
1201 1220 0.105658 TATTCCGGTCCTGGGAGAGG 60.106 60.000 0.00 4.54 44.45 3.69
1202 1221 2.182858 ATTCCGGTCCTGGGAGAGGT 62.183 60.000 0.00 0.00 43.37 3.85
1203 1222 3.077556 CCGGTCCTGGGAGAGGTG 61.078 72.222 0.00 0.00 43.37 4.00
1204 1223 3.077556 CGGTCCTGGGAGAGGTGG 61.078 72.222 0.00 0.00 43.37 4.61
1205 1224 3.403558 GGTCCTGGGAGAGGTGGC 61.404 72.222 0.00 0.00 43.37 5.01
1206 1225 3.775654 GTCCTGGGAGAGGTGGCG 61.776 72.222 0.00 0.00 43.37 5.69
1207 1226 3.992641 TCCTGGGAGAGGTGGCGA 61.993 66.667 0.00 0.00 43.37 5.54
1208 1227 3.775654 CCTGGGAGAGGTGGCGAC 61.776 72.222 0.00 0.00 37.02 5.19
1209 1228 2.997315 CTGGGAGAGGTGGCGACA 60.997 66.667 0.00 0.00 38.70 4.35
1219 1238 3.051210 TGGCGACACCAGTCTGAG 58.949 61.111 0.00 0.00 46.36 3.35
1220 1239 2.433318 GGCGACACCAGTCTGAGC 60.433 66.667 0.00 0.00 42.73 4.26
1221 1240 2.653702 GCGACACCAGTCTGAGCT 59.346 61.111 0.00 0.00 42.73 4.09
1222 1241 1.735920 GCGACACCAGTCTGAGCTG 60.736 63.158 0.00 0.00 42.73 4.24
1223 1242 1.959848 CGACACCAGTCTGAGCTGA 59.040 57.895 0.00 0.00 42.73 4.26
1224 1243 0.109365 CGACACCAGTCTGAGCTGAG 60.109 60.000 0.00 0.00 42.73 3.35
1225 1244 0.246086 GACACCAGTCTGAGCTGAGG 59.754 60.000 0.00 0.00 41.64 3.86
1226 1245 1.190833 ACACCAGTCTGAGCTGAGGG 61.191 60.000 0.00 0.00 38.70 4.30
1227 1246 0.902048 CACCAGTCTGAGCTGAGGGA 60.902 60.000 0.00 0.00 38.70 4.20
1228 1247 0.178921 ACCAGTCTGAGCTGAGGGAA 60.179 55.000 0.00 0.00 38.70 3.97
1229 1248 0.536260 CCAGTCTGAGCTGAGGGAAG 59.464 60.000 0.00 0.00 38.70 3.46
1230 1249 0.108233 CAGTCTGAGCTGAGGGAAGC 60.108 60.000 0.00 0.00 43.88 3.86
1231 1250 1.220477 GTCTGAGCTGAGGGAAGCC 59.780 63.158 0.00 0.00 44.68 4.35
1232 1251 1.229304 TCTGAGCTGAGGGAAGCCA 60.229 57.895 0.00 0.00 44.68 4.75
1233 1252 1.221293 CTGAGCTGAGGGAAGCCAG 59.779 63.158 0.00 0.00 44.68 4.85
1287 1310 2.046892 CCAGGCTTGACCAGTCCG 60.047 66.667 0.00 0.00 43.14 4.79
1289 1312 2.925170 AGGCTTGACCAGTCCGCT 60.925 61.111 8.46 0.00 43.14 5.52
1290 1313 2.435059 GGCTTGACCAGTCCGCTC 60.435 66.667 8.46 0.00 38.86 5.03
1321 1366 3.391296 ACAAGAACAGCCTACCTTCTTCA 59.609 43.478 0.00 0.00 32.96 3.02
1392 1440 1.821332 CCAGAAGAATGGAGCGGGC 60.821 63.158 0.00 0.00 43.57 6.13
1448 1496 4.440880 CTGTCCTCTGCTTGATTTCTAGG 58.559 47.826 0.00 0.00 0.00 3.02
1464 1515 5.796424 TTCTAGGTTCTTTCGGTTACACT 57.204 39.130 0.00 0.00 0.00 3.55
1466 1517 3.121738 AGGTTCTTTCGGTTACACTGG 57.878 47.619 0.00 0.00 0.00 4.00
1531 1592 3.978759 CAGTCGTGCTTGTATTTTCTCG 58.021 45.455 0.00 0.00 0.00 4.04
1647 1736 1.428869 CTGGATCGAGGGAGGGAATT 58.571 55.000 0.00 0.00 0.00 2.17
1668 1757 3.281727 AAGAGCTTCAACTTGTCACCA 57.718 42.857 0.00 0.00 0.00 4.17
1830 1922 3.494336 CGGAAGAAGCAGCAGCCG 61.494 66.667 0.00 0.00 43.56 5.52
1845 1937 3.143675 GCCGTCAGCTTCAGATGAA 57.856 52.632 0.00 0.00 42.53 2.57
1953 2051 1.079503 GTGGGAGCGAGATTGTTGTC 58.920 55.000 0.00 0.00 0.00 3.18
2011 2109 2.435586 CAGTTCCAGCTCCAGCCG 60.436 66.667 0.00 0.00 43.38 5.52
2052 2156 2.225753 ACCTGATGGGAGGAAGAAGAGT 60.226 50.000 0.00 0.00 36.51 3.24
2170 2277 2.596338 TCAGGTCGACGCTCACCA 60.596 61.111 9.92 0.00 34.80 4.17
2341 2469 1.939980 ACAGGGGAAGTCACTCTACC 58.060 55.000 0.00 0.00 0.00 3.18
2360 2488 1.544825 CCTCCCGACCAAGAAGAGCA 61.545 60.000 0.00 0.00 0.00 4.26
2363 2491 0.036010 CCCGACCAAGAAGAGCATGT 60.036 55.000 0.00 0.00 0.00 3.21
2364 2492 1.081892 CCGACCAAGAAGAGCATGTG 58.918 55.000 0.00 0.00 0.00 3.21
2365 2493 1.609061 CCGACCAAGAAGAGCATGTGT 60.609 52.381 0.00 0.00 0.00 3.72
2369 2497 2.158623 ACCAAGAAGAGCATGTGTCCAA 60.159 45.455 0.00 0.00 0.00 3.53
2412 2546 2.124151 GCACATCGGAGGGCCAAT 60.124 61.111 6.18 0.00 0.00 3.16
2421 2555 0.475906 GGAGGGCCAATAGCATGAGT 59.524 55.000 6.18 0.00 46.50 3.41
2445 2579 4.760047 AGCCGATCGGTGCGCTTT 62.760 61.111 33.33 9.46 37.65 3.51
2453 2587 2.556287 GGTGCGCTTTCCGTTCAG 59.444 61.111 9.73 0.00 39.71 3.02
2511 2645 2.359107 TCCAAGAGCAGCAAGGCG 60.359 61.111 0.00 0.00 39.27 5.52
2643 2777 3.531207 CGAGGGAGCGGCATCTCA 61.531 66.667 1.45 0.00 34.84 3.27
2814 2951 3.103742 TGTTGGGGCTTTTGAAACTCTT 58.896 40.909 0.00 0.00 0.00 2.85
2860 2997 2.431260 CAGCCGCATTGCACCAAC 60.431 61.111 9.69 0.00 0.00 3.77
3090 3248 5.308825 TGCTTTTCAAGGGAAAACAACAAA 58.691 33.333 0.00 0.00 45.51 2.83
3197 3365 3.435671 GTCCAGTGTTAACCAAATCTCGG 59.564 47.826 2.48 0.00 0.00 4.63
3203 3371 2.396590 TAACCAAATCTCGGCAGGTC 57.603 50.000 0.00 0.00 0.00 3.85
3204 3372 0.400213 AACCAAATCTCGGCAGGTCA 59.600 50.000 0.00 0.00 0.00 4.02
3326 3504 4.211794 GGAACGAATGAACCGTCTTGTTTA 59.788 41.667 0.00 0.00 39.57 2.01
3383 3561 5.163854 CGGTTCCTCATGTTAAGTGTTCATC 60.164 44.000 0.00 0.00 0.00 2.92
3481 3659 1.109323 GCCAGGCACCAGTTTCAGTT 61.109 55.000 6.55 0.00 0.00 3.16
3600 3778 5.838531 AGTCCTAGTTTCTACCAGATTCG 57.161 43.478 0.00 0.00 0.00 3.34
3608 3786 1.609072 TCTACCAGATTCGCATCCTCG 59.391 52.381 0.00 0.00 0.00 4.63
3623 3801 5.573282 CGCATCCTCGTCAATAAATAGTAGG 59.427 44.000 0.00 0.00 0.00 3.18
3716 3894 1.369625 CGTGGAAGTGGCAGATAACC 58.630 55.000 0.00 0.00 0.00 2.85
3737 3915 4.121317 CCAAGCTTGAACAAATGCTGAAA 58.879 39.130 28.05 0.00 35.79 2.69
3741 3919 7.118680 CCAAGCTTGAACAAATGCTGAAATAAT 59.881 33.333 28.05 0.00 35.79 1.28
3742 3920 9.142515 CAAGCTTGAACAAATGCTGAAATAATA 57.857 29.630 22.31 0.00 35.79 0.98
3743 3921 9.709495 AAGCTTGAACAAATGCTGAAATAATAA 57.291 25.926 0.00 0.00 35.79 1.40
3744 3922 9.362539 AGCTTGAACAAATGCTGAAATAATAAG 57.637 29.630 1.54 0.00 34.19 1.73
3745 3923 9.143631 GCTTGAACAAATGCTGAAATAATAAGT 57.856 29.630 0.00 0.00 0.00 2.24
3768 3946 8.435931 AGTATATCACAAACCTAGGATATGCA 57.564 34.615 17.98 0.00 37.62 3.96
3769 3947 8.535335 AGTATATCACAAACCTAGGATATGCAG 58.465 37.037 17.98 7.66 37.62 4.41
3770 3948 3.808728 TCACAAACCTAGGATATGCAGC 58.191 45.455 17.98 0.00 0.00 5.25
3771 3949 3.199727 TCACAAACCTAGGATATGCAGCA 59.800 43.478 17.98 0.00 0.00 4.41
3772 3950 3.313526 CACAAACCTAGGATATGCAGCAC 59.686 47.826 17.98 0.00 0.00 4.40
3773 3951 3.054434 ACAAACCTAGGATATGCAGCACA 60.054 43.478 17.98 0.00 0.00 4.57
3774 3952 3.931907 AACCTAGGATATGCAGCACAA 57.068 42.857 17.98 0.00 0.00 3.33
3775 3953 3.199880 ACCTAGGATATGCAGCACAAC 57.800 47.619 17.98 0.00 0.00 3.32
3776 3954 2.774234 ACCTAGGATATGCAGCACAACT 59.226 45.455 17.98 0.00 0.00 3.16
3798 3976 4.394729 TGGTAAAAGCCTCTTTGATTCGT 58.605 39.130 0.00 0.00 0.00 3.85
3800 3978 6.177610 TGGTAAAAGCCTCTTTGATTCGTAT 58.822 36.000 0.00 0.00 0.00 3.06
3804 3982 7.396540 AAAAGCCTCTTTGATTCGTATGATT 57.603 32.000 0.00 0.00 0.00 2.57
3805 3983 7.396540 AAAGCCTCTTTGATTCGTATGATTT 57.603 32.000 0.00 0.00 0.00 2.17
3807 3985 6.789262 AGCCTCTTTGATTCGTATGATTTTG 58.211 36.000 0.00 0.00 0.00 2.44
3841 4019 7.072581 AGGAATAGAAAAGGTATAGGGTTGGAG 59.927 40.741 0.00 0.00 0.00 3.86
3844 4022 4.227527 AGAAAAGGTATAGGGTTGGAGTGG 59.772 45.833 0.00 0.00 0.00 4.00
3849 4027 0.106519 ATAGGGTTGGAGTGGCATGC 60.107 55.000 9.90 9.90 0.00 4.06
3852 4030 2.283101 GTTGGAGTGGCATGCCCA 60.283 61.111 33.44 20.96 42.79 5.36
3859 4037 4.870069 TGGCATGCCCACTTGAAT 57.130 50.000 33.44 0.00 39.18 2.57
3860 4038 2.582272 TGGCATGCCCACTTGAATC 58.418 52.632 33.44 5.25 39.18 2.52
3861 4039 0.971959 TGGCATGCCCACTTGAATCC 60.972 55.000 33.44 4.70 39.18 3.01
3863 4041 1.410083 GGCATGCCCACTTGAATCCTA 60.410 52.381 27.24 0.00 0.00 2.94
3864 4042 2.590821 GCATGCCCACTTGAATCCTAT 58.409 47.619 6.36 0.00 0.00 2.57
3865 4043 3.498481 GGCATGCCCACTTGAATCCTATA 60.498 47.826 27.24 0.00 0.00 1.31
3867 4045 4.330250 CATGCCCACTTGAATCCTATAGG 58.670 47.826 13.07 13.07 0.00 2.57
3883 4061 7.618019 TCCTATAGGATTAGCAATGAGTGTT 57.382 36.000 18.00 0.00 39.78 3.32
3884 4062 8.034313 TCCTATAGGATTAGCAATGAGTGTTT 57.966 34.615 18.00 0.00 39.78 2.83
3885 4063 7.933577 TCCTATAGGATTAGCAATGAGTGTTTG 59.066 37.037 18.00 0.00 39.78 2.93
3886 4064 7.933577 CCTATAGGATTAGCAATGAGTGTTTGA 59.066 37.037 14.11 0.00 37.39 2.69
3908 4088 2.834549 TGCCACAGGAAAAACAAAGGAA 59.165 40.909 0.00 0.00 0.00 3.36
3910 4090 4.080638 TGCCACAGGAAAAACAAAGGAATT 60.081 37.500 0.00 0.00 0.00 2.17
3911 4091 4.273235 GCCACAGGAAAAACAAAGGAATTG 59.727 41.667 0.00 0.00 44.95 2.32
3934 4114 3.884037 AAAAGAGGTTGGAGTGGATGT 57.116 42.857 0.00 0.00 0.00 3.06
3937 4117 4.559862 AAGAGGTTGGAGTGGATGTTAG 57.440 45.455 0.00 0.00 0.00 2.34
3939 4119 4.366267 AGAGGTTGGAGTGGATGTTAGAT 58.634 43.478 0.00 0.00 0.00 1.98
3940 4120 4.785376 AGAGGTTGGAGTGGATGTTAGATT 59.215 41.667 0.00 0.00 0.00 2.40
3942 4122 5.501156 AGGTTGGAGTGGATGTTAGATTTC 58.499 41.667 0.00 0.00 0.00 2.17
3948 4128 6.615316 TGGAGTGGATGTTAGATTTCCTATGA 59.385 38.462 0.00 0.00 0.00 2.15
3951 4131 8.503428 AGTGGATGTTAGATTTCCTATGAGAT 57.497 34.615 0.00 0.00 0.00 2.75
4018 4198 8.418662 CAATCCTATGAATCAAATGACCAACAT 58.581 33.333 0.00 0.00 41.45 2.71
4126 4349 6.727824 AAAAGGATCATGAAGTGTAAGACG 57.272 37.500 0.00 0.00 0.00 4.18
4127 4350 5.407407 AAGGATCATGAAGTGTAAGACGT 57.593 39.130 0.00 0.00 0.00 4.34
4129 4352 5.794894 AGGATCATGAAGTGTAAGACGTTT 58.205 37.500 0.00 0.00 0.00 3.60
4130 4353 6.231211 AGGATCATGAAGTGTAAGACGTTTT 58.769 36.000 0.00 0.00 0.00 2.43
4131 4354 7.383687 AGGATCATGAAGTGTAAGACGTTTTA 58.616 34.615 0.00 0.00 0.00 1.52
4132 4355 7.331193 AGGATCATGAAGTGTAAGACGTTTTAC 59.669 37.037 19.19 19.19 34.78 2.01
4171 4394 9.874215 AAAACGTCTTATAAAAGTTTACAGAGC 57.126 29.630 10.86 0.00 34.42 4.09
4316 4539 3.640407 ATGCACCAGACGGGCACT 61.640 61.111 0.00 0.00 40.07 4.40
4495 4719 2.098607 CAGTTGCACAATATCTGGCAGG 59.901 50.000 15.73 0.00 34.18 4.85
4579 4803 1.344763 ACAGTACAACACTCCAGAGGC 59.655 52.381 0.00 0.00 34.26 4.70
5024 5261 6.824958 AGGATTAATAGTGGAGGTTTAGCA 57.175 37.500 0.00 0.00 0.00 3.49
5115 5353 3.774528 CTGCTGCGGGAGTGCCTA 61.775 66.667 5.78 0.00 0.00 3.93
5285 5523 0.894184 TTCAAGACTCCTCGCTCGGT 60.894 55.000 0.00 0.00 0.00 4.69
5367 5605 4.901197 TTCAGGTCTGCCATACACTTAA 57.099 40.909 0.00 0.00 37.19 1.85
5372 5610 5.237996 CAGGTCTGCCATACACTTAATGATG 59.762 44.000 0.00 0.00 37.19 3.07
5444 5682 2.224257 ACAAACAACCAATGGCATGACC 60.224 45.455 11.92 0.00 39.84 4.02
5447 5685 1.259609 CAACCAATGGCATGACCTGT 58.740 50.000 0.00 0.00 40.22 4.00
5457 5695 1.271597 GCATGACCTGTTCTTGGAGGT 60.272 52.381 0.00 0.00 45.73 3.85
5458 5696 2.430465 CATGACCTGTTCTTGGAGGTG 58.570 52.381 0.00 0.00 42.95 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.593209 GCGAAACACGTCCTGTCCA 60.593 57.895 0.00 0.00 44.60 4.02
84 85 1.942657 GAATGTGTGAGCGCATGGTAT 59.057 47.619 11.47 0.00 44.23 2.73
99 100 0.987294 CCACTGGGACCTCTGAATGT 59.013 55.000 0.00 0.00 35.59 2.71
160 161 9.443323 TCGAAGATACCACATGAAGATTTTAAA 57.557 29.630 0.00 0.00 0.00 1.52
210 212 1.002900 CAATTGCGACGGGCGATATTT 60.003 47.619 7.81 0.00 45.30 1.40
263 265 4.449068 AGATGTGTTTGATTGTCTCGTCAC 59.551 41.667 0.00 0.00 0.00 3.67
322 324 5.203528 CAAACTGGACCCTATTTGGATGAT 58.796 41.667 4.89 0.00 38.35 2.45
335 337 0.746923 GGGCGGATACAAACTGGACC 60.747 60.000 0.00 0.00 0.00 4.46
341 343 1.199097 CACTTGTGGGCGGATACAAAC 59.801 52.381 0.00 0.00 36.47 2.93
380 382 4.737855 TTTGAAATTCCGTCCAACCAAA 57.262 36.364 0.00 0.00 0.00 3.28
494 496 7.899973 ACGGAAAATAACCTGTAAAGTAGAGA 58.100 34.615 0.00 0.00 0.00 3.10
499 501 6.947644 ACAACGGAAAATAACCTGTAAAGT 57.052 33.333 0.00 0.00 0.00 2.66
504 506 5.007921 GTGTGTACAACGGAAAATAACCTGT 59.992 40.000 0.00 0.00 0.00 4.00
553 555 1.541147 CGGTTGGTACTCCGTTCACTA 59.459 52.381 13.47 0.00 40.23 2.74
555 557 1.287041 GCGGTTGGTACTCCGTTCAC 61.287 60.000 19.36 5.81 44.68 3.18
556 558 1.005867 GCGGTTGGTACTCCGTTCA 60.006 57.895 19.36 0.00 44.68 3.18
615 619 0.038744 CATGCTGGGTGGAGACCTTT 59.961 55.000 0.00 0.00 42.66 3.11
616 620 1.687612 CATGCTGGGTGGAGACCTT 59.312 57.895 0.00 0.00 42.66 3.50
664 668 0.683504 GCCTAGGTCGAAGGAGGTGA 60.684 60.000 11.31 0.00 36.08 4.02
686 690 3.432378 AGGATCATATAGGACCGACACC 58.568 50.000 0.00 0.00 0.00 4.16
824 834 9.213799 GGCCATTTTTATTGACTCAAAATGTAA 57.786 29.630 0.00 0.00 42.54 2.41
855 865 2.932614 CTGCCGAGTCTCATTTTTCGAT 59.067 45.455 0.00 0.00 35.19 3.59
871 881 1.596954 CCACGTTTGAAAACTCTGCCG 60.597 52.381 4.54 0.00 36.77 5.69
930 940 3.442076 AGGTTAGGTGGGTTCTGACTAG 58.558 50.000 0.00 0.00 0.00 2.57
962 977 8.579006 GTGCTTGATTGGATCCATTTGAATATA 58.421 33.333 17.06 0.00 0.00 0.86
1021 1036 4.920828 TTCAACCAGAACCAGGCC 57.079 55.556 0.00 0.00 0.00 5.19
1145 1164 0.752658 CATGTGGTAGGAGGCGATCA 59.247 55.000 0.00 0.00 0.00 2.92
1192 1211 2.997315 TGTCGCCACCTCTCCCAG 60.997 66.667 0.00 0.00 0.00 4.45
1193 1212 3.311110 GTGTCGCCACCTCTCCCA 61.311 66.667 0.00 0.00 35.44 4.37
1206 1225 0.246086 CCTCAGCTCAGACTGGTGTC 59.754 60.000 1.81 0.00 43.22 3.67
1207 1226 1.190833 CCCTCAGCTCAGACTGGTGT 61.191 60.000 1.81 0.00 38.26 4.16
1208 1227 0.902048 TCCCTCAGCTCAGACTGGTG 60.902 60.000 1.81 0.00 38.26 4.17
1209 1228 0.178921 TTCCCTCAGCTCAGACTGGT 60.179 55.000 1.81 0.00 38.26 4.00
1210 1229 0.536260 CTTCCCTCAGCTCAGACTGG 59.464 60.000 1.81 0.00 38.26 4.00
1211 1230 0.108233 GCTTCCCTCAGCTCAGACTG 60.108 60.000 0.00 0.00 36.79 3.51
1212 1231 1.264045 GGCTTCCCTCAGCTCAGACT 61.264 60.000 0.00 0.00 39.97 3.24
1213 1232 1.220477 GGCTTCCCTCAGCTCAGAC 59.780 63.158 0.00 0.00 39.97 3.51
1214 1233 1.229304 TGGCTTCCCTCAGCTCAGA 60.229 57.895 0.00 0.00 39.97 3.27
1215 1234 1.221293 CTGGCTTCCCTCAGCTCAG 59.779 63.158 0.00 0.00 39.97 3.35
1216 1235 3.396767 CTGGCTTCCCTCAGCTCA 58.603 61.111 0.00 0.00 39.97 4.26
1220 1239 2.045536 GTGGCTGGCTTCCCTCAG 60.046 66.667 2.00 0.00 0.00 3.35
1221 1240 4.020617 CGTGGCTGGCTTCCCTCA 62.021 66.667 2.00 0.00 0.00 3.86
1226 1245 4.704833 TGAGGCGTGGCTGGCTTC 62.705 66.667 0.00 6.67 45.90 3.86
1287 1310 4.225208 GCTGTTCTTGTTGATTTCTGAGC 58.775 43.478 0.00 0.00 0.00 4.26
1289 1312 4.464008 AGGCTGTTCTTGTTGATTTCTGA 58.536 39.130 0.00 0.00 0.00 3.27
1290 1313 4.843220 AGGCTGTTCTTGTTGATTTCTG 57.157 40.909 0.00 0.00 0.00 3.02
1321 1366 7.180051 TCCTGCTAAGAAGAAGAAGAAGAAGAT 59.820 37.037 0.00 0.00 28.15 2.40
1392 1440 2.892425 GATGCCCGCTTCACTCGG 60.892 66.667 0.00 0.00 46.05 4.63
1448 1496 1.193874 CGCCAGTGTAACCGAAAGAAC 59.806 52.381 0.00 0.00 37.80 3.01
1464 1515 0.871722 CAATTTCCGTGAACTCGCCA 59.128 50.000 0.00 0.00 0.00 5.69
1466 1517 0.168128 CCCAATTTCCGTGAACTCGC 59.832 55.000 0.00 0.00 0.00 5.03
1647 1736 4.415881 TGGTGACAAGTTGAAGCTCTTA 57.584 40.909 10.54 0.00 37.44 2.10
1668 1757 0.040058 TTGCAGTCATGGCCTCCATT 59.960 50.000 3.32 0.00 42.23 3.16
1830 1922 4.564041 TCTTCTGTTCATCTGAAGCTGAC 58.436 43.478 0.00 0.00 45.46 3.51
1839 1931 3.055240 CCAGCCTTCTCTTCTGTTCATCT 60.055 47.826 0.00 0.00 0.00 2.90
1845 1937 1.722034 TGACCAGCCTTCTCTTCTGT 58.278 50.000 0.00 0.00 0.00 3.41
1953 2051 0.458543 CCACGATGTCCTTCCACTCG 60.459 60.000 0.00 0.00 35.56 4.18
2011 2109 3.629398 GGTTGTTGATGAGATGGTCCATC 59.371 47.826 22.47 22.47 40.80 3.51
2052 2156 3.826157 GTGTTTTCCCCTTCATCACATCA 59.174 43.478 0.00 0.00 0.00 3.07
2101 2208 1.239347 GTTGGGTTCTTGACAGGAGC 58.761 55.000 0.00 0.00 0.00 4.70
2170 2277 1.563410 CTTCTTGATGGAGGCCTTCCT 59.437 52.381 9.13 0.00 46.92 3.36
2303 2428 4.793216 CCTGTTTAACATCATTAGTTGCGC 59.207 41.667 0.00 0.00 0.00 6.09
2341 2469 1.219393 GCTCTTCTTGGTCGGGAGG 59.781 63.158 0.00 0.00 0.00 4.30
2360 2488 3.119245 GCTTGATTCAGCATTGGACACAT 60.119 43.478 0.00 0.00 39.83 3.21
2363 2491 2.516906 TGCTTGATTCAGCATTGGACA 58.483 42.857 6.68 0.00 45.14 4.02
2412 2546 1.000171 CGGCTGCTGATACTCATGCTA 60.000 52.381 1.17 0.00 0.00 3.49
2421 2555 1.363807 CACCGATCGGCTGCTGATA 59.636 57.895 33.62 0.00 39.32 2.15
2445 2579 2.029964 GGTTGTCGGCTGAACGGA 59.970 61.111 0.00 0.00 0.00 4.69
2453 2587 2.539338 TTGTTGCTCGGTTGTCGGC 61.539 57.895 0.00 0.00 39.77 5.54
2511 2645 2.452064 TTCGGATGGGAGGATGGGC 61.452 63.158 0.00 0.00 0.00 5.36
2553 2687 1.064832 GCTGCTCTCCCCTTTCTGAAT 60.065 52.381 0.00 0.00 0.00 2.57
2640 2774 3.429141 CCTGTTGCGCTGCCTGAG 61.429 66.667 9.73 0.00 0.00 3.35
2814 2951 4.081087 CCCTACTTTCCGATCTTGGAGAAA 60.081 45.833 0.00 0.00 39.72 2.52
2851 2988 3.131396 ACAAAACAAAACGTTGGTGCAA 58.869 36.364 0.00 0.00 39.22 4.08
2860 2997 4.201763 CCCATGGACAAACAAAACAAAACG 60.202 41.667 15.22 0.00 0.00 3.60
3106 3264 5.914898 TTTGAGATGTGAGATTCTCCGTA 57.085 39.130 11.12 0.00 38.05 4.02
3197 3365 0.804989 GGTATTGCACTGTGACCTGC 59.195 55.000 12.86 0.00 0.00 4.85
3203 3371 2.050691 GCGTTTTGGTATTGCACTGTG 58.949 47.619 2.76 2.76 0.00 3.66
3204 3372 1.678627 TGCGTTTTGGTATTGCACTGT 59.321 42.857 0.00 0.00 0.00 3.55
3309 3487 8.630037 AGAAATTCTTAAACAAGACGGTTCATT 58.370 29.630 0.00 0.00 0.00 2.57
3310 3488 8.076178 CAGAAATTCTTAAACAAGACGGTTCAT 58.924 33.333 0.00 0.00 0.00 2.57
3311 3489 7.414436 CAGAAATTCTTAAACAAGACGGTTCA 58.586 34.615 0.00 0.00 0.00 3.18
3312 3490 6.856426 CCAGAAATTCTTAAACAAGACGGTTC 59.144 38.462 0.00 0.00 0.00 3.62
3313 3491 6.544564 TCCAGAAATTCTTAAACAAGACGGTT 59.455 34.615 0.00 0.00 0.00 4.44
3314 3492 6.059484 TCCAGAAATTCTTAAACAAGACGGT 58.941 36.000 0.00 0.00 0.00 4.83
3315 3493 6.554334 TCCAGAAATTCTTAAACAAGACGG 57.446 37.500 0.00 0.00 0.00 4.79
3316 3494 7.798982 GTCTTCCAGAAATTCTTAAACAAGACG 59.201 37.037 0.00 0.00 30.04 4.18
3317 3495 8.841300 AGTCTTCCAGAAATTCTTAAACAAGAC 58.159 33.333 14.87 14.87 37.40 3.01
3326 3504 6.310149 ACATTCCAGTCTTCCAGAAATTCTT 58.690 36.000 0.00 0.00 0.00 2.52
3383 3561 1.338105 TGTTTCGACATCTGGCTCCTG 60.338 52.381 0.00 0.00 0.00 3.86
3410 3588 4.203226 TGATGCAGTTGGTTAACTTGTCA 58.797 39.130 5.42 0.00 44.57 3.58
3600 3778 6.586844 GTCCTACTATTTATTGACGAGGATGC 59.413 42.308 0.00 0.00 34.50 3.91
3608 3786 5.598769 ACGGCTGTCCTACTATTTATTGAC 58.401 41.667 0.00 0.00 0.00 3.18
3623 3801 1.639298 GGCTTGTCATGACGGCTGTC 61.639 60.000 29.41 19.20 45.71 3.51
3662 3840 6.656314 TGTTGCCTAATATAACTGTTCGTG 57.344 37.500 0.00 0.00 0.00 4.35
3716 3894 5.917541 ATTTCAGCATTTGTTCAAGCTTG 57.082 34.783 20.81 20.81 34.61 4.01
3742 3920 8.880244 TGCATATCCTAGGTTTGTGATATACTT 58.120 33.333 9.08 0.00 31.10 2.24
3743 3921 8.435931 TGCATATCCTAGGTTTGTGATATACT 57.564 34.615 9.08 0.00 31.10 2.12
3744 3922 7.278868 GCTGCATATCCTAGGTTTGTGATATAC 59.721 40.741 9.08 0.00 31.10 1.47
3745 3923 7.038373 TGCTGCATATCCTAGGTTTGTGATATA 60.038 37.037 9.08 0.00 31.10 0.86
3746 3924 6.176183 GCTGCATATCCTAGGTTTGTGATAT 58.824 40.000 9.08 0.59 32.13 1.63
3747 3925 5.071653 TGCTGCATATCCTAGGTTTGTGATA 59.928 40.000 9.08 0.00 0.00 2.15
3748 3926 4.141413 TGCTGCATATCCTAGGTTTGTGAT 60.141 41.667 9.08 0.00 0.00 3.06
3749 3927 3.199727 TGCTGCATATCCTAGGTTTGTGA 59.800 43.478 9.08 0.00 0.00 3.58
3750 3928 3.313526 GTGCTGCATATCCTAGGTTTGTG 59.686 47.826 9.08 7.66 0.00 3.33
3751 3929 3.054434 TGTGCTGCATATCCTAGGTTTGT 60.054 43.478 9.08 0.00 0.00 2.83
3752 3930 3.544684 TGTGCTGCATATCCTAGGTTTG 58.455 45.455 9.08 6.35 0.00 2.93
3753 3931 3.931907 TGTGCTGCATATCCTAGGTTT 57.068 42.857 9.08 0.14 0.00 3.27
3754 3932 3.200825 AGTTGTGCTGCATATCCTAGGTT 59.799 43.478 9.08 2.60 0.00 3.50
3755 3933 2.774234 AGTTGTGCTGCATATCCTAGGT 59.226 45.455 9.08 0.00 0.00 3.08
3756 3934 3.136763 CAGTTGTGCTGCATATCCTAGG 58.863 50.000 5.27 0.82 38.52 3.02
3757 3935 3.136763 CCAGTTGTGCTGCATATCCTAG 58.863 50.000 5.27 0.00 43.71 3.02
3758 3936 2.505407 ACCAGTTGTGCTGCATATCCTA 59.495 45.455 5.27 0.00 43.71 2.94
3759 3937 1.283029 ACCAGTTGTGCTGCATATCCT 59.717 47.619 5.27 0.00 43.71 3.24
3760 3938 1.755179 ACCAGTTGTGCTGCATATCC 58.245 50.000 5.27 0.00 43.71 2.59
3761 3939 4.963276 TTTACCAGTTGTGCTGCATATC 57.037 40.909 5.27 2.06 43.71 1.63
3762 3940 4.380867 GCTTTTACCAGTTGTGCTGCATAT 60.381 41.667 5.27 0.00 43.71 1.78
3763 3941 3.057596 GCTTTTACCAGTTGTGCTGCATA 60.058 43.478 5.27 0.00 43.71 3.14
3764 3942 2.288395 GCTTTTACCAGTTGTGCTGCAT 60.288 45.455 5.27 0.00 43.71 3.96
3765 3943 1.066908 GCTTTTACCAGTTGTGCTGCA 59.933 47.619 0.00 0.00 43.71 4.41
3766 3944 1.602920 GGCTTTTACCAGTTGTGCTGC 60.603 52.381 0.00 0.00 43.71 5.25
3767 3945 1.956477 AGGCTTTTACCAGTTGTGCTG 59.044 47.619 0.00 0.00 44.63 4.41
3768 3946 2.158608 AGAGGCTTTTACCAGTTGTGCT 60.159 45.455 0.00 0.00 0.00 4.40
3769 3947 2.230660 AGAGGCTTTTACCAGTTGTGC 58.769 47.619 0.00 0.00 0.00 4.57
3770 3948 4.338118 TCAAAGAGGCTTTTACCAGTTGTG 59.662 41.667 0.00 0.00 0.00 3.33
3771 3949 4.532834 TCAAAGAGGCTTTTACCAGTTGT 58.467 39.130 0.00 0.00 0.00 3.32
3772 3950 5.712152 ATCAAAGAGGCTTTTACCAGTTG 57.288 39.130 0.00 0.00 0.00 3.16
3773 3951 5.048713 CGAATCAAAGAGGCTTTTACCAGTT 60.049 40.000 0.00 0.00 0.00 3.16
3774 3952 4.455877 CGAATCAAAGAGGCTTTTACCAGT 59.544 41.667 0.00 0.00 0.00 4.00
3775 3953 4.455877 ACGAATCAAAGAGGCTTTTACCAG 59.544 41.667 0.00 0.00 0.00 4.00
3776 3954 4.394729 ACGAATCAAAGAGGCTTTTACCA 58.605 39.130 0.00 0.00 0.00 3.25
3777 3955 6.315393 TCATACGAATCAAAGAGGCTTTTACC 59.685 38.462 0.00 0.00 0.00 2.85
3778 3956 7.303634 TCATACGAATCAAAGAGGCTTTTAC 57.696 36.000 0.00 0.00 0.00 2.01
3779 3957 8.506168 AATCATACGAATCAAAGAGGCTTTTA 57.494 30.769 0.00 0.00 0.00 1.52
3780 3958 7.396540 AATCATACGAATCAAAGAGGCTTTT 57.603 32.000 0.00 0.00 0.00 2.27
3781 3959 7.396540 AAATCATACGAATCAAAGAGGCTTT 57.603 32.000 0.00 0.00 0.00 3.51
3782 3960 7.121168 TCAAAATCATACGAATCAAAGAGGCTT 59.879 33.333 0.00 0.00 0.00 4.35
3783 3961 6.599244 TCAAAATCATACGAATCAAAGAGGCT 59.401 34.615 0.00 0.00 0.00 4.58
3815 3993 6.912561 TCCAACCCTATACCTTTTCTATTCCT 59.087 38.462 0.00 0.00 0.00 3.36
3821 3999 4.227527 CCACTCCAACCCTATACCTTTTCT 59.772 45.833 0.00 0.00 0.00 2.52
3827 4005 1.209621 TGCCACTCCAACCCTATACC 58.790 55.000 0.00 0.00 0.00 2.73
3828 4006 2.851195 CATGCCACTCCAACCCTATAC 58.149 52.381 0.00 0.00 0.00 1.47
3829 4007 1.142870 GCATGCCACTCCAACCCTATA 59.857 52.381 6.36 0.00 0.00 1.31
3835 4013 2.283101 TGGGCATGCCACTCCAAC 60.283 61.111 36.56 18.56 37.98 3.77
3841 4019 0.174162 GATTCAAGTGGGCATGCCAC 59.826 55.000 36.56 29.23 37.98 5.01
3844 4022 2.057137 TAGGATTCAAGTGGGCATGC 57.943 50.000 9.90 9.90 0.00 4.06
3860 4038 7.933577 TCAAACACTCATTGCTAATCCTATAGG 59.066 37.037 13.07 13.07 0.00 2.57
3861 4039 8.893219 TCAAACACTCATTGCTAATCCTATAG 57.107 34.615 0.00 0.00 0.00 1.31
3863 4041 7.255381 GCATCAAACACTCATTGCTAATCCTAT 60.255 37.037 0.00 0.00 0.00 2.57
3864 4042 6.038603 GCATCAAACACTCATTGCTAATCCTA 59.961 38.462 0.00 0.00 0.00 2.94
3865 4043 5.163581 GCATCAAACACTCATTGCTAATCCT 60.164 40.000 0.00 0.00 0.00 3.24
3867 4045 5.039333 GGCATCAAACACTCATTGCTAATC 58.961 41.667 0.00 0.00 0.00 1.75
3869 4047 3.825585 TGGCATCAAACACTCATTGCTAA 59.174 39.130 0.00 0.00 0.00 3.09
3870 4048 3.191162 GTGGCATCAAACACTCATTGCTA 59.809 43.478 0.00 0.00 34.84 3.49
3871 4049 2.029649 GTGGCATCAAACACTCATTGCT 60.030 45.455 0.00 0.00 34.84 3.91
3872 4050 2.288334 TGTGGCATCAAACACTCATTGC 60.288 45.455 0.00 0.00 38.39 3.56
3873 4051 3.571571 CTGTGGCATCAAACACTCATTG 58.428 45.455 0.00 0.00 38.39 2.82
3874 4052 2.559668 CCTGTGGCATCAAACACTCATT 59.440 45.455 0.00 0.00 38.39 2.57
3875 4053 2.165167 CCTGTGGCATCAAACACTCAT 58.835 47.619 0.00 0.00 38.39 2.90
3876 4054 1.142667 TCCTGTGGCATCAAACACTCA 59.857 47.619 0.00 0.00 38.39 3.41
3878 4056 2.363306 TTCCTGTGGCATCAAACACT 57.637 45.000 0.00 0.00 38.39 3.55
3879 4057 3.451141 TTTTCCTGTGGCATCAAACAC 57.549 42.857 0.00 0.00 38.08 3.32
3880 4058 3.196469 TGTTTTTCCTGTGGCATCAAACA 59.804 39.130 0.00 0.00 31.84 2.83
3881 4059 3.791245 TGTTTTTCCTGTGGCATCAAAC 58.209 40.909 0.00 0.00 0.00 2.93
3883 4061 4.440880 CTTTGTTTTTCCTGTGGCATCAA 58.559 39.130 0.00 0.00 0.00 2.57
3884 4062 3.181467 CCTTTGTTTTTCCTGTGGCATCA 60.181 43.478 0.00 0.00 0.00 3.07
3885 4063 3.069443 TCCTTTGTTTTTCCTGTGGCATC 59.931 43.478 0.00 0.00 0.00 3.91
3886 4064 3.037549 TCCTTTGTTTTTCCTGTGGCAT 58.962 40.909 0.00 0.00 0.00 4.40
3908 4088 5.701224 TCCACTCCAACCTCTTTTTACAAT 58.299 37.500 0.00 0.00 0.00 2.71
3910 4090 4.781775 TCCACTCCAACCTCTTTTTACA 57.218 40.909 0.00 0.00 0.00 2.41
3911 4091 5.070685 ACATCCACTCCAACCTCTTTTTAC 58.929 41.667 0.00 0.00 0.00 2.01
3913 4093 4.184649 ACATCCACTCCAACCTCTTTTT 57.815 40.909 0.00 0.00 0.00 1.94
3914 4094 3.884037 ACATCCACTCCAACCTCTTTT 57.116 42.857 0.00 0.00 0.00 2.27
3915 4095 3.884037 AACATCCACTCCAACCTCTTT 57.116 42.857 0.00 0.00 0.00 2.52
3924 4104 7.015682 TCTCATAGGAAATCTAACATCCACTCC 59.984 40.741 0.00 0.00 35.62 3.85
3942 4122 9.482627 GGAATCTTTTGTACTACATCTCATAGG 57.517 37.037 0.00 0.00 0.00 2.57
3948 4128 9.213777 TCCTATGGAATCTTTTGTACTACATCT 57.786 33.333 0.00 0.00 0.00 2.90
3991 4171 6.964807 TGGTCATTTGATTCATAGGATTGG 57.035 37.500 0.00 0.00 0.00 3.16
3992 4172 7.774134 TGTTGGTCATTTGATTCATAGGATTG 58.226 34.615 0.00 0.00 0.00 2.67
4084 4264 4.664150 TTTTTCCTTGTTGCCACTTAGG 57.336 40.909 4.06 4.06 41.84 2.69
4130 4353 4.997395 AGACGTTTTAGGTCACTAGACGTA 59.003 41.667 14.07 0.00 45.37 3.57
4131 4354 3.817647 AGACGTTTTAGGTCACTAGACGT 59.182 43.478 14.01 14.01 46.66 4.34
4132 4355 4.416505 AGACGTTTTAGGTCACTAGACG 57.583 45.455 0.00 0.00 45.92 4.18
4133 4356 9.846248 TTTATAAGACGTTTTAGGTCACTAGAC 57.154 33.333 4.75 0.00 44.21 2.59
4137 4360 9.551734 AACTTTTATAAGACGTTTTAGGTCACT 57.448 29.630 4.75 0.00 35.60 3.41
4316 4539 1.243902 GGTTTGATTTGGCTCGGACA 58.756 50.000 0.00 0.00 0.00 4.02
4495 4719 3.068165 CCCAAACAGGTTCTGGAACTTTC 59.932 47.826 12.34 0.00 40.94 2.62
4870 5094 3.119316 ACAAGATCGCTAACTGTCCAGAG 60.119 47.826 0.40 0.00 0.00 3.35
4871 5095 2.826128 ACAAGATCGCTAACTGTCCAGA 59.174 45.455 0.40 0.00 0.00 3.86
4993 5217 8.625467 ACCTCCACTATTAATCCTTCTAAACT 57.375 34.615 0.00 0.00 0.00 2.66
4998 5222 7.127339 TGCTAAACCTCCACTATTAATCCTTCT 59.873 37.037 0.00 0.00 0.00 2.85
5024 5261 4.730949 CATGGATTCATGCCAGAAAAGT 57.269 40.909 0.00 0.00 43.44 2.66
5115 5353 4.021925 GCGGGTGAGCCTCCAAGT 62.022 66.667 0.00 0.00 34.45 3.16
5161 5399 0.955428 AAGCGACCACATGCGATGTT 60.955 50.000 0.00 0.00 42.70 2.71
5423 5661 2.224257 GGTCATGCCATTGGTTGTTTGT 60.224 45.455 4.26 0.00 37.17 2.83
5444 5682 0.474184 ACACCCACCTCCAAGAACAG 59.526 55.000 0.00 0.00 0.00 3.16
5447 5685 2.488347 GCTTAACACCCACCTCCAAGAA 60.488 50.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.