Multiple sequence alignment - TraesCS2A01G487600

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 TraesCS2A01G487600 chr2A 100.000 4873 0 0 1 4873 722211926 722207054 0.000000e+00 8999
1 TraesCS2A01G487600 chr2A 82.418 364 46 6 2892 3239 676339906 676339545 7.930000e-78 302
2 TraesCS2A01G487600 chr2A 94.792 96 5 0 3234 3329 769218691 769218596 3.040000e-32 150
3 TraesCS2A01G487600 chr2B 93.723 1832 80 18 1446 3246 709831917 709830090 0.000000e+00 2713
4 TraesCS2A01G487600 chr2B 80.308 1625 251 37 1661 3239 631449749 631448148 0.000000e+00 1164
5 TraesCS2A01G487600 chr2B 95.915 710 28 1 3324 4033 709830094 709829386 0.000000e+00 1149
6 TraesCS2A01G487600 chr2B 87.905 587 51 8 871 1449 709832528 709831954 0.000000e+00 673
7 TraesCS2A01G487600 chr2B 100.000 85 0 0 3241 3325 10214547 10214463 1.820000e-34 158
8 TraesCS2A01G487600 chr2B 96.809 94 2 1 3234 3326 383927933 383927840 6.530000e-34 156
9 TraesCS2A01G487600 chr2B 95.789 95 2 2 3241 3334 78868093 78868000 8.450000e-33 152
10 TraesCS2A01G487600 chr2B 95.652 46 2 0 4120 4165 509689053 509689098 1.880000e-09 75
11 TraesCS2A01G487600 chr2D 93.731 1627 62 5 1633 3242 587300040 587298437 0.000000e+00 2403
12 TraesCS2A01G487600 chr2D 94.118 1003 32 9 3324 4312 587298438 587297449 0.000000e+00 1500
13 TraesCS2A01G487600 chr2D 89.474 874 74 12 1 867 574952126 574952988 0.000000e+00 1088
14 TraesCS2A01G487600 chr2D 83.632 782 111 5 2473 3239 531685285 531684506 0.000000e+00 719
15 TraesCS2A01G487600 chr2D 97.455 275 6 1 4297 4571 587297435 587297162 7.390000e-128 468
16 TraesCS2A01G487600 chr2D 84.279 458 63 8 3404 3856 531684434 531683981 5.790000e-119 438
17 TraesCS2A01G487600 chr2D 93.665 221 12 2 4566 4784 587295308 587295088 3.640000e-86 329
18 TraesCS2A01G487600 chr2D 82.383 193 29 4 2115 2304 586309259 586309449 3.900000e-36 163
19 TraesCS2A01G487600 chr2D 88.542 96 11 0 1446 1541 587300137 587300042 3.080000e-22 117
20 TraesCS2A01G487600 chr6D 91.160 871 64 7 1 867 54849178 54850039 0.000000e+00 1170
21 TraesCS2A01G487600 chr6A 90.971 875 66 7 1 870 558580169 558579303 0.000000e+00 1166
22 TraesCS2A01G487600 chr6A 90.857 875 68 7 1 870 558194151 558193284 0.000000e+00 1162
23 TraesCS2A01G487600 chr6A 90.692 881 69 7 1 874 115724592 115723718 0.000000e+00 1160
24 TraesCS2A01G487600 chr6A 90.352 881 72 7 1 874 115755125 115754251 0.000000e+00 1144
25 TraesCS2A01G487600 chr6A 89.671 881 78 7 1 874 115790488 115789614 0.000000e+00 1110
26 TraesCS2A01G487600 chr3A 90.455 880 71 7 1 874 608334090 608334962 0.000000e+00 1147
27 TraesCS2A01G487600 chr3A 86.301 146 16 3 4639 4780 380921265 380921120 6.530000e-34 156
28 TraesCS2A01G487600 chr7A 90.011 871 81 5 1 867 625522924 625523792 0.000000e+00 1122
29 TraesCS2A01G487600 chr7A 90.909 110 6 3 3227 3335 114027069 114027175 1.410000e-30 145
30 TraesCS2A01G487600 chr7A 86.400 125 12 5 3231 3352 416496942 416496820 1.100000e-26 132
31 TraesCS2A01G487600 chr1D 71.940 1201 266 56 2057 3215 459521550 459522721 7.980000e-73 285
32 TraesCS2A01G487600 chr1D 88.000 100 8 4 3137 3234 459625430 459625333 1.110000e-21 115
33 TraesCS2A01G487600 chrUn 88.312 231 18 6 4556 4784 393624005 393624228 8.040000e-68 268
34 TraesCS2A01G487600 chr3B 88.312 231 18 6 4556 4784 815529905 815529682 8.040000e-68 268
35 TraesCS2A01G487600 chr3B 88.312 231 18 6 4556 4784 815563566 815563343 8.040000e-68 268
36 TraesCS2A01G487600 chr3B 88.312 231 18 6 4556 4784 815611010 815610787 8.040000e-68 268
37 TraesCS2A01G487600 chr3B 88.312 231 18 6 4556 4784 815659721 815659498 8.040000e-68 268
38 TraesCS2A01G487600 chr3D 87.069 232 21 5 4556 4784 606335390 606335615 2.250000e-63 254
39 TraesCS2A01G487600 chr7D 95.876 97 2 2 3235 3330 542092262 542092357 6.530000e-34 156
40 TraesCS2A01G487600 chr4D 92.523 107 6 2 3232 3336 136689529 136689423 8.450000e-33 152
41 TraesCS2A01G487600 chr5A 94.000 100 3 3 3234 3330 512022392 512022293 1.090000e-31 148
42 TraesCS2A01G487600 chr1A 78.037 214 34 7 3036 3244 551787013 551786808 6.620000e-24 122
43 TraesCS2A01G487600 chr1A 91.139 79 7 0 3137 3215 551532865 551532943 1.850000e-19 108


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 TraesCS2A01G487600 chr2A 722207054 722211926 4872 True 8999.000000 8999 100.000000 1 4873 1 chr2A.!!$R2 4872
1 TraesCS2A01G487600 chr2B 709829386 709832528 3142 True 1511.666667 2713 92.514333 871 4033 3 chr2B.!!$R5 3162
2 TraesCS2A01G487600 chr2B 631448148 631449749 1601 True 1164.000000 1164 80.308000 1661 3239 1 chr2B.!!$R4 1578
3 TraesCS2A01G487600 chr2D 574952126 574952988 862 False 1088.000000 1088 89.474000 1 867 1 chr2D.!!$F1 866
4 TraesCS2A01G487600 chr2D 587295088 587300137 5049 True 963.400000 2403 93.502200 1446 4784 5 chr2D.!!$R2 3338
5 TraesCS2A01G487600 chr2D 531683981 531685285 1304 True 578.500000 719 83.955500 2473 3856 2 chr2D.!!$R1 1383
6 TraesCS2A01G487600 chr6D 54849178 54850039 861 False 1170.000000 1170 91.160000 1 867 1 chr6D.!!$F1 866
7 TraesCS2A01G487600 chr6A 558579303 558580169 866 True 1166.000000 1166 90.971000 1 870 1 chr6A.!!$R5 869
8 TraesCS2A01G487600 chr6A 558193284 558194151 867 True 1162.000000 1162 90.857000 1 870 1 chr6A.!!$R4 869
9 TraesCS2A01G487600 chr6A 115723718 115724592 874 True 1160.000000 1160 90.692000 1 874 1 chr6A.!!$R1 873
10 TraesCS2A01G487600 chr6A 115754251 115755125 874 True 1144.000000 1144 90.352000 1 874 1 chr6A.!!$R2 873
11 TraesCS2A01G487600 chr6A 115789614 115790488 874 True 1110.000000 1110 89.671000 1 874 1 chr6A.!!$R3 873
12 TraesCS2A01G487600 chr3A 608334090 608334962 872 False 1147.000000 1147 90.455000 1 874 1 chr3A.!!$F1 873
13 TraesCS2A01G487600 chr7A 625522924 625523792 868 False 1122.000000 1122 90.011000 1 867 1 chr7A.!!$F2 866
14 TraesCS2A01G487600 chr1D 459521550 459522721 1171 False 285.000000 285 71.940000 2057 3215 1 chr1D.!!$F1 1158

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
259 260 0.171007 CATTGGGCGCATTTCTCGTT 59.829 50.0 10.83 0.00 0.00 3.85 F
493 494 0.732880 ACCAGACGAATTGAGACGCG 60.733 55.0 3.53 3.53 0.00 6.01 F
1292 1319 0.543277 CCTTAGCACCTGAGCATCCA 59.457 55.0 0.00 0.00 36.85 3.41 F
2501 2607 0.179108 GATGAGGCGGCTACGAGTTT 60.179 55.0 13.24 0.00 44.60 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1083 1110 0.344790 ACTGGGATGTGGAGAGGGAT 59.655 55.0 0.0 0.0 0.00 3.85 R
1299 1326 0.606604 GGACGGCTGAAACTGGTAGA 59.393 55.0 0.0 0.0 0.00 2.59 R
3238 3386 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.0 0.0 0.0 0.00 3.58 R
4336 4551 0.461548 GTCCATCAGGTCATCTCGCA 59.538 55.0 0.0 0.0 35.89 5.10 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
108 109 5.941555 AACCCTAGAAATCAGAATCGAGT 57.058 39.130 0.00 0.00 0.00 4.18
124 125 1.668101 GAGTCGTGTAGCAGAGGGGG 61.668 65.000 0.00 0.00 0.00 5.40
182 183 6.918626 TCGAAAATGGCAAATTAATCACTGA 58.081 32.000 0.00 0.00 0.00 3.41
259 260 0.171007 CATTGGGCGCATTTCTCGTT 59.829 50.000 10.83 0.00 0.00 3.85
489 490 2.673043 GCGGTTACCAGACGAATTGAGA 60.673 50.000 1.13 0.00 0.00 3.27
493 494 0.732880 ACCAGACGAATTGAGACGCG 60.733 55.000 3.53 3.53 0.00 6.01
506 512 1.298190 GACGCGCGAACTACTAGGG 60.298 63.158 39.36 2.23 0.00 3.53
507 513 1.986575 GACGCGCGAACTACTAGGGT 61.987 60.000 39.36 9.23 0.00 4.34
508 514 1.298190 CGCGCGAACTACTAGGGTC 60.298 63.158 28.94 0.00 0.00 4.46
509 515 1.298190 GCGCGAACTACTAGGGTCG 60.298 63.158 12.10 2.43 0.00 4.79
510 516 1.298190 CGCGAACTACTAGGGTCGC 60.298 63.158 18.13 18.13 42.25 5.19
513 519 1.599916 GCGAACTACTAGGGTCGCATC 60.600 57.143 21.73 3.06 44.60 3.91
660 669 4.499188 CGTGCCGTTATAGAGGAAATGAGA 60.499 45.833 0.30 0.00 0.00 3.27
668 681 2.808919 AGAGGAAATGAGACGAGTGGA 58.191 47.619 0.00 0.00 0.00 4.02
746 761 3.612247 GAGCGATGGCCCACACACT 62.612 63.158 0.00 0.00 41.24 3.55
747 762 3.434319 GCGATGGCCCACACACTG 61.434 66.667 0.00 0.00 0.00 3.66
779 794 5.767816 AAAACAAAACTACTCGCTGGAAT 57.232 34.783 0.00 0.00 0.00 3.01
784 799 5.351465 ACAAAACTACTCGCTGGAATATGTG 59.649 40.000 0.00 0.00 0.00 3.21
838 853 1.369321 GGGGTGGCGATTTTGCAAA 59.631 52.632 8.05 8.05 36.28 3.68
907 923 1.908066 GCCAAAAGTTCGACGCGGAT 61.908 55.000 12.47 0.00 0.00 4.18
913 929 0.732880 AGTTCGACGCGGATGACAAG 60.733 55.000 12.47 0.00 0.00 3.16
914 930 2.092291 TTCGACGCGGATGACAAGC 61.092 57.895 12.47 0.00 0.00 4.01
932 948 4.918201 GCGGATTCCCCTGCTCGG 62.918 72.222 0.00 0.00 33.62 4.63
933 949 4.918201 CGGATTCCCCTGCTCGGC 62.918 72.222 0.00 0.00 0.00 5.54
934 950 3.797353 GGATTCCCCTGCTCGGCA 61.797 66.667 0.00 0.00 36.92 5.69
935 951 2.514824 GATTCCCCTGCTCGGCAC 60.515 66.667 0.00 0.00 33.79 5.01
1018 1042 3.385384 TGGAGCTCCAGAGTGCCG 61.385 66.667 32.00 0.00 42.01 5.69
1019 1043 4.154347 GGAGCTCCAGAGTGCCGG 62.154 72.222 28.43 0.00 35.64 6.13
1060 1084 3.691342 CCCTGCCGGAACTCGACA 61.691 66.667 5.05 0.00 42.43 4.35
1080 1107 1.817447 ACTCCTCCTGCAAGTACGTAC 59.183 52.381 18.10 18.10 0.00 3.67
1081 1108 2.093106 CTCCTCCTGCAAGTACGTACT 58.907 52.381 22.45 22.45 38.39 2.73
1082 1109 2.492484 CTCCTCCTGCAAGTACGTACTT 59.508 50.000 30.57 30.57 46.76 2.24
1083 1110 3.689347 TCCTCCTGCAAGTACGTACTTA 58.311 45.455 34.03 21.82 44.19 2.24
1093 1120 4.785346 AGTACGTACTTATCCCTCTCCA 57.215 45.455 22.45 0.00 31.13 3.86
1096 1123 3.912248 ACGTACTTATCCCTCTCCACAT 58.088 45.455 0.00 0.00 0.00 3.21
1121 1148 4.760204 CCAGTTCCTCTGTTTTATTTCCGT 59.240 41.667 0.00 0.00 42.19 4.69
1122 1149 5.240844 CCAGTTCCTCTGTTTTATTTCCGTT 59.759 40.000 0.00 0.00 42.19 4.44
1124 1151 5.472478 AGTTCCTCTGTTTTATTTCCGTTCC 59.528 40.000 0.00 0.00 0.00 3.62
1125 1152 5.237236 TCCTCTGTTTTATTTCCGTTCCT 57.763 39.130 0.00 0.00 0.00 3.36
1126 1153 6.363167 TCCTCTGTTTTATTTCCGTTCCTA 57.637 37.500 0.00 0.00 0.00 2.94
1146 1173 2.853914 GCCGTCGAGCACTGTTTC 59.146 61.111 0.00 0.00 0.00 2.78
1150 1177 1.606350 CGTCGAGCACTGTTTCGTCC 61.606 60.000 10.19 3.84 37.99 4.79
1180 1207 2.605295 TTTCTTCCCCGCCTCCGA 60.605 61.111 0.00 0.00 36.29 4.55
1257 1284 2.902343 GCCGGGCTCCAGCAATAC 60.902 66.667 12.87 0.00 44.36 1.89
1261 1288 1.149401 GGGCTCCAGCAATACCTCC 59.851 63.158 0.03 0.00 44.36 4.30
1268 1295 1.492176 CCAGCAATACCTCCACCAGAT 59.508 52.381 0.00 0.00 0.00 2.90
1292 1319 0.543277 CCTTAGCACCTGAGCATCCA 59.457 55.000 0.00 0.00 36.85 3.41
1299 1326 0.622738 ACCTGAGCATCCATCCACCT 60.623 55.000 0.00 0.00 0.00 4.00
1326 1353 2.304761 AGTTTCAGCCGTCCTAAATCCA 59.695 45.455 0.00 0.00 0.00 3.41
1386 1413 3.117738 CCAATCCCTTCTGGCAGTTCTAT 60.118 47.826 15.27 0.63 0.00 1.98
1387 1414 3.853355 ATCCCTTCTGGCAGTTCTATG 57.147 47.619 15.27 0.00 0.00 2.23
1394 1421 5.163364 CCTTCTGGCAGTTCTATGTAGATGT 60.163 44.000 15.27 0.00 31.40 3.06
1397 1424 5.422012 TCTGGCAGTTCTATGTAGATGTGAA 59.578 40.000 15.27 0.00 31.40 3.18
1399 1426 7.287696 TCTGGCAGTTCTATGTAGATGTGAATA 59.712 37.037 15.27 0.00 31.40 1.75
1406 1433 7.544804 TCTATGTAGATGTGAATATGTGCCT 57.455 36.000 0.00 0.00 0.00 4.75
1408 1435 5.612725 TGTAGATGTGAATATGTGCCTCA 57.387 39.130 0.00 0.00 0.00 3.86
1410 1437 6.594744 TGTAGATGTGAATATGTGCCTCAAT 58.405 36.000 0.00 0.00 0.00 2.57
1443 1470 6.425114 GGTGTCGATGAACTGCAGAATATTAT 59.575 38.462 23.35 5.68 0.00 1.28
1462 1529 6.668541 ATTATTGGCTATCCGATCGATTTG 57.331 37.500 18.66 5.55 37.62 2.32
1494 1561 6.073657 GCAATGAACTGAGATAGATTCAGCTC 60.074 42.308 2.37 1.15 44.63 4.09
1507 1574 9.298774 GATAGATTCAGCTCAAAAATTTGGAAG 57.701 33.333 6.08 0.00 38.66 3.46
1541 1608 9.649167 AAAGTACATACGAGTTAGTGCTTTAAT 57.351 29.630 15.87 1.54 42.36 1.40
1546 1613 9.517609 ACATACGAGTTAGTGCTTTAATAAGAG 57.482 33.333 0.00 0.00 32.92 2.85
1547 1614 9.731819 CATACGAGTTAGTGCTTTAATAAGAGA 57.268 33.333 0.00 0.00 32.92 3.10
1596 1663 8.347771 TGCAGATTATCTTTTGTAATCATGCTC 58.652 33.333 19.03 5.09 39.72 4.26
1606 1673 8.795786 TTTTGTAATCATGCTCTGTGTTTTAC 57.204 30.769 0.00 0.00 0.00 2.01
1612 1679 5.376625 TCATGCTCTGTGTTTTACCTCTTT 58.623 37.500 0.00 0.00 0.00 2.52
1649 1720 3.199946 TCCCAAGATTTCCTAGCGTTCAT 59.800 43.478 0.00 0.00 0.00 2.57
1730 1801 2.364317 CAGAGAGGGGGCGGAGAA 60.364 66.667 0.00 0.00 0.00 2.87
1751 1822 5.824624 AGAACTTCATCAGCTGAAACAAAGA 59.175 36.000 22.50 9.13 43.20 2.52
1853 1924 1.663695 ATGGGTTGCGAATAACTCCG 58.336 50.000 0.00 0.00 29.81 4.63
1868 1943 7.254218 CGAATAACTCCGTGGTTATTAACTTCC 60.254 40.741 17.15 7.93 46.14 3.46
1873 1972 2.349590 GTGGTTATTAACTTCCGGCGT 58.650 47.619 6.01 0.00 0.00 5.68
1944 2043 9.009327 CATGGTAAATTCGCTAACAACAATTAG 57.991 33.333 0.00 0.00 35.59 1.73
2143 2249 2.024369 TCCCTCATGCCTGTACTAGACA 60.024 50.000 0.00 0.00 36.35 3.41
2179 2285 5.450688 GCCTGTGTATCTAGACGATTTCTGT 60.451 44.000 0.00 0.00 35.55 3.41
2231 2337 5.971202 CACTCAACATACAAACACTTTGGTC 59.029 40.000 0.12 0.00 44.81 4.02
2404 2510 2.294233 TGGCTCAGAATTGCTGTCAAAC 59.706 45.455 0.00 0.00 45.14 2.93
2501 2607 0.179108 GATGAGGCGGCTACGAGTTT 60.179 55.000 13.24 0.00 44.60 2.66
2538 2644 7.568349 TCTATATCTCCAACTGCACTTTTCAT 58.432 34.615 0.00 0.00 0.00 2.57
2546 2652 3.624777 ACTGCACTTTTCATCCCATAGG 58.375 45.455 0.00 0.00 0.00 2.57
2626 2752 0.531200 GGAGGGACTACGACAGTTGG 59.469 60.000 0.00 0.00 41.55 3.77
2741 2867 3.884853 TCCTCAAGGTTGGAAGGTGTCC 61.885 54.545 0.00 0.00 40.82 4.02
2890 3016 4.380655 CGTCCGGAATTCTCTCTTACAGTT 60.381 45.833 5.23 0.00 0.00 3.16
3057 3205 7.284034 AGACTTTGTTCTTCAGAATGTCAACAT 59.716 33.333 12.84 0.00 36.33 2.71
3242 3390 9.299963 CATGTCTTCTTGAGCTATATATGCTAC 57.700 37.037 8.92 4.39 41.30 3.58
3243 3391 8.642935 TGTCTTCTTGAGCTATATATGCTACT 57.357 34.615 8.92 0.00 41.30 2.57
3244 3392 8.735315 TGTCTTCTTGAGCTATATATGCTACTC 58.265 37.037 8.92 5.00 41.30 2.59
3245 3393 8.188139 GTCTTCTTGAGCTATATATGCTACTCC 58.812 40.741 8.92 0.56 41.30 3.85
3246 3394 7.340743 TCTTCTTGAGCTATATATGCTACTCCC 59.659 40.741 8.92 0.29 41.30 4.30
3247 3395 6.736581 TCTTGAGCTATATATGCTACTCCCT 58.263 40.000 8.92 0.00 41.30 4.20
3248 3396 6.831353 TCTTGAGCTATATATGCTACTCCCTC 59.169 42.308 8.92 0.00 41.30 4.30
3249 3397 5.450453 TGAGCTATATATGCTACTCCCTCC 58.550 45.833 8.92 0.00 41.30 4.30
3250 3398 4.465886 AGCTATATATGCTACTCCCTCCG 58.534 47.826 7.60 0.00 39.21 4.63
3251 3399 4.079672 AGCTATATATGCTACTCCCTCCGT 60.080 45.833 7.60 0.00 39.21 4.69
3252 3400 4.645588 GCTATATATGCTACTCCCTCCGTT 59.354 45.833 0.00 0.00 0.00 4.44
3253 3401 5.221087 GCTATATATGCTACTCCCTCCGTTC 60.221 48.000 0.00 0.00 0.00 3.95
3254 3402 1.700955 TATGCTACTCCCTCCGTTCC 58.299 55.000 0.00 0.00 0.00 3.62
3255 3403 0.325296 ATGCTACTCCCTCCGTTCCA 60.325 55.000 0.00 0.00 0.00 3.53
3256 3404 0.543410 TGCTACTCCCTCCGTTCCAA 60.543 55.000 0.00 0.00 0.00 3.53
3257 3405 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
3258 3406 1.002773 GCTACTCCCTCCGTTCCAAAA 59.997 52.381 0.00 0.00 0.00 2.44
3259 3407 2.355818 GCTACTCCCTCCGTTCCAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
3260 3408 3.118519 GCTACTCCCTCCGTTCCAAAATA 60.119 47.826 0.00 0.00 0.00 1.40
3261 3409 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3262 3410 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3263 3411 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3264 3412 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3265 3413 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3266 3414 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3267 3415 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
3268 3416 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
3269 3417 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3270 3418 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3271 3419 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
3272 3420 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
3273 3421 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
3274 3422 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
3275 3423 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
3276 3424 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3277 3425 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3278 3426 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3279 3427 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3286 3434 9.046296 AGATGACTCAACTTTGTACTAACTTTG 57.954 33.333 0.00 0.00 0.00 2.77
3287 3435 8.732746 ATGACTCAACTTTGTACTAACTTTGT 57.267 30.769 0.00 0.00 0.00 2.83
3288 3436 9.826574 ATGACTCAACTTTGTACTAACTTTGTA 57.173 29.630 0.00 0.00 0.00 2.41
3289 3437 9.090692 TGACTCAACTTTGTACTAACTTTGTAC 57.909 33.333 6.58 6.58 40.27 2.90
3290 3438 9.090692 GACTCAACTTTGTACTAACTTTGTACA 57.909 33.333 10.91 10.91 45.56 2.90
3310 3458 8.239681 TGTACAAAGTTGAGTCATCTATTTCG 57.760 34.615 4.14 0.00 0.00 3.46
3311 3459 6.727824 ACAAAGTTGAGTCATCTATTTCGG 57.272 37.500 4.14 0.00 0.00 4.30
3312 3460 6.464222 ACAAAGTTGAGTCATCTATTTCGGA 58.536 36.000 4.14 0.00 0.00 4.55
3313 3461 6.934645 ACAAAGTTGAGTCATCTATTTCGGAA 59.065 34.615 4.14 0.00 0.00 4.30
3314 3462 6.969828 AAGTTGAGTCATCTATTTCGGAAC 57.030 37.500 4.14 0.00 0.00 3.62
3542 3720 2.280524 CGCCTCAAACGGGTGACA 60.281 61.111 0.00 0.00 36.54 3.58
3638 3816 2.005960 GCCTCACGCTGGATACGACT 62.006 60.000 0.00 0.00 42.51 4.18
3663 3841 1.815840 GGCTGCGGTAGGAAGCTTC 60.816 63.158 18.54 18.54 0.00 3.86
3683 3861 1.920574 CGCGATACTAGCATATGCACC 59.079 52.381 28.62 9.99 45.16 5.01
3692 3870 1.298563 CATATGCACCGCCGCAAAG 60.299 57.895 0.87 0.00 46.87 2.77
3697 3875 2.899044 GCACCGCCGCAAAGTACAA 61.899 57.895 0.00 0.00 0.00 2.41
3717 3895 6.992063 ACAAGAGTAAATGCTGTTGGATAG 57.008 37.500 11.83 0.00 42.04 2.08
3783 3961 2.891580 GGTAGATACATCGCTGGGAGAA 59.108 50.000 0.00 0.00 0.00 2.87
3972 4150 1.864565 AGTTTCAAAACCAATGCGCC 58.135 45.000 4.18 0.00 39.71 6.53
4057 4236 3.633986 CCTTTCCTTGTCTTCTTGCTGTT 59.366 43.478 0.00 0.00 0.00 3.16
4069 4248 6.858478 GTCTTCTTGCTGTTGAGGAAAAATAC 59.142 38.462 0.00 0.00 0.00 1.89
4109 4288 5.996644 TGTACAGAGGGGGTATGTAATTTG 58.003 41.667 0.00 0.00 34.63 2.32
4113 4292 3.268334 AGAGGGGGTATGTAATTTGTGCA 59.732 43.478 0.00 0.00 0.00 4.57
4114 4293 3.631250 AGGGGGTATGTAATTTGTGCAG 58.369 45.455 0.00 0.00 0.00 4.41
4188 4367 5.359756 TGTTAAGATAGCTGTGCCACTATG 58.640 41.667 0.00 0.00 0.00 2.23
4215 4394 7.669427 TCTTGGTTCTAACTATACAACCGAAA 58.331 34.615 0.00 0.00 41.17 3.46
4235 4414 3.662247 ATCTTCGTTTCTCGTCAAGGT 57.338 42.857 0.00 0.00 40.80 3.50
4257 4436 9.988815 AAGGTGCTGTCATATTTATACTAAGAG 57.011 33.333 0.00 0.00 0.00 2.85
4281 4460 3.721087 AGGTGGATTTTACAGAGGTGG 57.279 47.619 0.00 0.00 0.00 4.61
4282 4461 2.986728 AGGTGGATTTTACAGAGGTGGT 59.013 45.455 0.00 0.00 0.00 4.16
4283 4462 4.172807 AGGTGGATTTTACAGAGGTGGTA 58.827 43.478 0.00 0.00 0.00 3.25
4284 4463 4.225267 AGGTGGATTTTACAGAGGTGGTAG 59.775 45.833 0.00 0.00 0.00 3.18
4285 4464 4.224370 GGTGGATTTTACAGAGGTGGTAGA 59.776 45.833 0.00 0.00 0.00 2.59
4286 4465 5.104485 GGTGGATTTTACAGAGGTGGTAGAT 60.104 44.000 0.00 0.00 0.00 1.98
4287 4466 6.049790 GTGGATTTTACAGAGGTGGTAGATC 58.950 44.000 0.00 0.00 0.00 2.75
4288 4467 5.964477 TGGATTTTACAGAGGTGGTAGATCT 59.036 40.000 0.00 0.00 0.00 2.75
4289 4468 6.443849 TGGATTTTACAGAGGTGGTAGATCTT 59.556 38.462 0.00 0.00 0.00 2.40
4291 4470 7.496263 GGATTTTACAGAGGTGGTAGATCTTTC 59.504 40.741 0.00 0.00 0.00 2.62
4292 4471 5.934402 TTACAGAGGTGGTAGATCTTTCC 57.066 43.478 0.00 5.09 0.00 3.13
4293 4472 3.108376 ACAGAGGTGGTAGATCTTTCCC 58.892 50.000 0.00 0.00 0.00 3.97
4295 4474 3.519510 CAGAGGTGGTAGATCTTTCCCAA 59.480 47.826 0.00 0.00 0.00 4.12
4336 4551 1.960689 AGTAATTGCACGGCCTGTTTT 59.039 42.857 0.00 0.00 0.00 2.43
4354 4569 1.194218 TTGCGAGATGACCTGATGGA 58.806 50.000 0.00 0.00 37.04 3.41
4434 4649 7.934120 AGTCTTTACAATAACTCAAGAGCTTGT 59.066 33.333 9.79 13.91 41.16 3.16
4497 4712 2.918712 AGGATCAATTCGGTAGCTGG 57.081 50.000 0.00 0.00 0.00 4.85
4504 4719 0.325296 ATTCGGTAGCTGGTGGGAGA 60.325 55.000 0.00 0.00 0.00 3.71
4660 6735 8.392372 ACAAACTCCTGTATAAAAGGTTTCTC 57.608 34.615 3.29 0.00 36.14 2.87
4709 6785 6.174720 ACTTTTGTCTCATGAGGAAGTGTA 57.825 37.500 22.42 0.00 0.00 2.90
4725 6801 7.263496 AGGAAGTGTAGCTATAAAGGTAAACG 58.737 38.462 0.00 0.00 45.05 3.60
4728 6804 6.261118 AGTGTAGCTATAAAGGTAAACGACG 58.739 40.000 0.00 0.00 45.05 5.12
4754 6830 7.063780 GTCGGACCTTATATTCAAACGAAGAAA 59.936 37.037 0.00 0.00 0.00 2.52
4785 6861 2.464582 GGTGATCCCCTATCCCCAC 58.535 63.158 0.00 0.00 32.64 4.61
4786 6862 0.401395 GGTGATCCCCTATCCCCACA 60.401 60.000 0.00 0.00 32.64 4.17
4787 6863 1.518367 GTGATCCCCTATCCCCACAA 58.482 55.000 0.00 0.00 33.22 3.33
4788 6864 1.421646 GTGATCCCCTATCCCCACAAG 59.578 57.143 0.00 0.00 33.22 3.16
4789 6865 0.402121 GATCCCCTATCCCCACAAGC 59.598 60.000 0.00 0.00 0.00 4.01
4790 6866 1.418908 ATCCCCTATCCCCACAAGCG 61.419 60.000 0.00 0.00 0.00 4.68
4791 6867 2.510906 CCCTATCCCCACAAGCGG 59.489 66.667 0.00 0.00 0.00 5.52
4792 6868 2.070039 CCCTATCCCCACAAGCGGA 61.070 63.158 0.00 0.00 0.00 5.54
4793 6869 1.632018 CCCTATCCCCACAAGCGGAA 61.632 60.000 0.00 0.00 0.00 4.30
4794 6870 0.179045 CCTATCCCCACAAGCGGAAG 60.179 60.000 0.00 0.00 0.00 3.46
4795 6871 0.830648 CTATCCCCACAAGCGGAAGA 59.169 55.000 0.00 0.00 0.00 2.87
4796 6872 0.539986 TATCCCCACAAGCGGAAGAC 59.460 55.000 0.00 0.00 0.00 3.01
4797 6873 1.201429 ATCCCCACAAGCGGAAGACT 61.201 55.000 0.00 0.00 0.00 3.24
4798 6874 1.376037 CCCCACAAGCGGAAGACTC 60.376 63.158 0.00 0.00 0.00 3.36
4799 6875 1.738099 CCCACAAGCGGAAGACTCG 60.738 63.158 0.00 0.00 0.00 4.18
4800 6876 1.738099 CCACAAGCGGAAGACTCGG 60.738 63.158 0.00 0.00 0.00 4.63
4801 6877 1.006102 CACAAGCGGAAGACTCGGT 60.006 57.895 0.00 0.00 40.18 4.69
4802 6878 0.242825 CACAAGCGGAAGACTCGGTA 59.757 55.000 0.00 0.00 37.36 4.02
4803 6879 0.526662 ACAAGCGGAAGACTCGGTAG 59.473 55.000 0.00 0.00 37.36 3.18
4804 6880 0.179134 CAAGCGGAAGACTCGGTAGG 60.179 60.000 0.00 0.00 37.36 3.18
4805 6881 1.321074 AAGCGGAAGACTCGGTAGGG 61.321 60.000 0.00 0.00 37.36 3.53
4806 6882 2.806237 CGGAAGACTCGGTAGGGC 59.194 66.667 0.00 0.00 0.00 5.19
4807 6883 2.806237 GGAAGACTCGGTAGGGCG 59.194 66.667 0.00 0.00 0.00 6.13
4808 6884 1.751927 GGAAGACTCGGTAGGGCGA 60.752 63.158 0.00 0.00 0.00 5.54
4809 6885 1.726533 GGAAGACTCGGTAGGGCGAG 61.727 65.000 0.00 0.00 38.14 5.03
4810 6886 1.726533 GAAGACTCGGTAGGGCGAGG 61.727 65.000 0.00 0.00 36.64 4.63
4811 6887 2.439883 GACTCGGTAGGGCGAGGT 60.440 66.667 0.00 0.00 36.64 3.85
4812 6888 2.754658 ACTCGGTAGGGCGAGGTG 60.755 66.667 0.00 0.00 36.64 4.00
4813 6889 2.439701 CTCGGTAGGGCGAGGTGA 60.440 66.667 0.00 0.00 0.00 4.02
4814 6890 2.439701 TCGGTAGGGCGAGGTGAG 60.440 66.667 0.00 0.00 0.00 3.51
4815 6891 3.528370 CGGTAGGGCGAGGTGAGG 61.528 72.222 0.00 0.00 0.00 3.86
4816 6892 3.851128 GGTAGGGCGAGGTGAGGC 61.851 72.222 0.00 0.00 0.00 4.70
4817 6893 4.208686 GTAGGGCGAGGTGAGGCG 62.209 72.222 0.00 0.00 34.74 5.52
4833 6909 3.861797 CGCCCGCCCTACCTTGAT 61.862 66.667 0.00 0.00 0.00 2.57
4834 6910 2.595655 GCCCGCCCTACCTTGATT 59.404 61.111 0.00 0.00 0.00 2.57
4835 6911 1.076995 GCCCGCCCTACCTTGATTT 60.077 57.895 0.00 0.00 0.00 2.17
4836 6912 0.181824 GCCCGCCCTACCTTGATTTA 59.818 55.000 0.00 0.00 0.00 1.40
4837 6913 1.814248 GCCCGCCCTACCTTGATTTAG 60.814 57.143 0.00 0.00 0.00 1.85
4838 6914 1.594331 CCGCCCTACCTTGATTTAGC 58.406 55.000 0.00 0.00 0.00 3.09
4839 6915 1.217882 CGCCCTACCTTGATTTAGCG 58.782 55.000 0.00 0.00 36.06 4.26
4840 6916 0.945099 GCCCTACCTTGATTTAGCGC 59.055 55.000 0.00 0.00 0.00 5.92
4841 6917 1.594331 CCCTACCTTGATTTAGCGCC 58.406 55.000 2.29 0.00 0.00 6.53
4842 6918 1.134220 CCCTACCTTGATTTAGCGCCA 60.134 52.381 2.29 0.00 0.00 5.69
4843 6919 2.213499 CCTACCTTGATTTAGCGCCAG 58.787 52.381 2.29 0.00 0.00 4.85
4844 6920 2.158957 CCTACCTTGATTTAGCGCCAGA 60.159 50.000 2.29 0.00 0.00 3.86
4845 6921 2.717639 ACCTTGATTTAGCGCCAGAT 57.282 45.000 2.29 0.00 0.00 2.90
4846 6922 3.004752 ACCTTGATTTAGCGCCAGATT 57.995 42.857 2.29 0.00 0.00 2.40
4847 6923 3.356290 ACCTTGATTTAGCGCCAGATTT 58.644 40.909 2.29 0.00 0.00 2.17
4848 6924 3.763897 ACCTTGATTTAGCGCCAGATTTT 59.236 39.130 2.29 0.00 0.00 1.82
4849 6925 4.947388 ACCTTGATTTAGCGCCAGATTTTA 59.053 37.500 2.29 0.00 0.00 1.52
4850 6926 5.594317 ACCTTGATTTAGCGCCAGATTTTAT 59.406 36.000 2.29 0.00 0.00 1.40
4851 6927 6.770785 ACCTTGATTTAGCGCCAGATTTTATA 59.229 34.615 2.29 0.00 0.00 0.98
4852 6928 7.448469 ACCTTGATTTAGCGCCAGATTTTATAT 59.552 33.333 2.29 0.00 0.00 0.86
4853 6929 8.946085 CCTTGATTTAGCGCCAGATTTTATATA 58.054 33.333 2.29 0.00 0.00 0.86
4854 6930 9.760660 CTTGATTTAGCGCCAGATTTTATATAC 57.239 33.333 2.29 0.00 0.00 1.47
4855 6931 8.263940 TGATTTAGCGCCAGATTTTATATACC 57.736 34.615 2.29 0.00 0.00 2.73
4856 6932 6.715344 TTTAGCGCCAGATTTTATATACCG 57.285 37.500 2.29 0.00 0.00 4.02
4857 6933 4.530710 AGCGCCAGATTTTATATACCGA 57.469 40.909 2.29 0.00 0.00 4.69
4858 6934 5.086104 AGCGCCAGATTTTATATACCGAT 57.914 39.130 2.29 0.00 0.00 4.18
4859 6935 6.216801 AGCGCCAGATTTTATATACCGATA 57.783 37.500 2.29 0.00 0.00 2.92
4860 6936 6.636705 AGCGCCAGATTTTATATACCGATAA 58.363 36.000 2.29 0.00 0.00 1.75
4861 6937 6.757010 AGCGCCAGATTTTATATACCGATAAG 59.243 38.462 2.29 0.00 0.00 1.73
4862 6938 6.509677 GCGCCAGATTTTATATACCGATAAGC 60.510 42.308 0.00 0.00 0.00 3.09
4863 6939 6.757010 CGCCAGATTTTATATACCGATAAGCT 59.243 38.462 0.00 0.00 0.00 3.74
4864 6940 7.254117 CGCCAGATTTTATATACCGATAAGCTG 60.254 40.741 0.00 0.00 0.00 4.24
4865 6941 7.466050 GCCAGATTTTATATACCGATAAGCTGC 60.466 40.741 0.00 0.00 0.00 5.25
4866 6942 7.254117 CCAGATTTTATATACCGATAAGCTGCG 60.254 40.741 0.00 0.00 0.00 5.18
4867 6943 5.773239 TTTTATATACCGATAAGCTGCGC 57.227 39.130 0.00 0.00 0.00 6.09
4868 6944 4.443913 TTATATACCGATAAGCTGCGCA 57.556 40.909 10.98 10.98 0.00 6.09
4869 6945 2.060326 TATACCGATAAGCTGCGCAC 57.940 50.000 5.66 3.54 0.00 5.34
4870 6946 0.104120 ATACCGATAAGCTGCGCACA 59.896 50.000 5.66 0.00 0.00 4.57
4871 6947 0.804544 TACCGATAAGCTGCGCACAC 60.805 55.000 5.66 0.59 0.00 3.82
4872 6948 2.100031 CCGATAAGCTGCGCACACA 61.100 57.895 5.66 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 1.681327 GACCCCCTCTGCTACACGA 60.681 63.158 0.00 0.00 0.00 4.35
124 125 5.278604 AGTTGCCGTAATTTTTGAACTGAC 58.721 37.500 0.00 0.00 0.00 3.51
182 183 1.001924 TGTTTCGCATGCACATCGTTT 60.002 42.857 19.57 0.00 0.00 3.60
259 260 4.331968 GGGATGGTCACATGTTAGAACAA 58.668 43.478 7.89 0.00 43.03 2.83
489 490 1.986575 GACCCTAGTAGTTCGCGCGT 61.987 60.000 30.98 13.76 0.00 6.01
493 494 0.384669 ATGCGACCCTAGTAGTTCGC 59.615 55.000 25.61 25.61 45.31 4.70
509 515 0.179062 ACTCAATCGCCCTCAGATGC 60.179 55.000 0.00 0.00 0.00 3.91
510 516 1.863267 GACTCAATCGCCCTCAGATG 58.137 55.000 0.00 0.00 0.00 2.90
513 519 4.409342 CGACTCAATCGCCCTCAG 57.591 61.111 0.00 0.00 45.52 3.35
541 547 1.079127 CGCCGGTCTTCTGTTCCAT 60.079 57.895 1.90 0.00 0.00 3.41
660 669 3.273654 TCCCCTCCCTCCACTCGT 61.274 66.667 0.00 0.00 0.00 4.18
668 681 1.342175 CGACTTAACTCTCCCCTCCCT 60.342 57.143 0.00 0.00 0.00 4.20
779 794 2.192664 AATCCAACGCACACCACATA 57.807 45.000 0.00 0.00 0.00 2.29
784 799 2.500509 TTTCAAATCCAACGCACACC 57.499 45.000 0.00 0.00 0.00 4.16
822 837 1.281566 CCGTTTGCAAAATCGCCACC 61.282 55.000 14.67 0.00 0.00 4.61
838 853 1.917872 ATTTGGTAACCATGTGCCGT 58.082 45.000 0.00 0.00 31.53 5.68
877 893 6.347888 CGTCGAACTTTTGGCCTTCTATAAAA 60.348 38.462 3.32 0.00 0.00 1.52
907 923 2.435938 GGGAATCCGCGCTTGTCA 60.436 61.111 5.56 0.00 0.00 3.58
938 954 4.477975 GGGTCTCGCCGTGTCTCG 62.478 72.222 0.00 0.00 38.44 4.04
939 955 4.131088 GGGGTCTCGCCGTGTCTC 62.131 72.222 0.00 0.00 38.44 3.36
940 956 4.680537 AGGGGTCTCGCCGTGTCT 62.681 66.667 0.00 0.00 41.60 3.41
941 957 4.131088 GAGGGGTCTCGCCGTGTC 62.131 72.222 0.00 0.00 41.60 3.67
959 983 4.487412 GGTGCCGACGACGTAGGG 62.487 72.222 25.59 18.78 37.88 3.53
994 1018 3.790437 CTGGAGCTCCATGGGCGT 61.790 66.667 35.11 4.60 46.46 5.68
995 1019 3.457625 CTCTGGAGCTCCATGGGCG 62.458 68.421 35.11 22.72 46.46 6.13
1060 1084 1.817447 GTACGTACTTGCAGGAGGAGT 59.183 52.381 18.47 0.00 0.00 3.85
1080 1107 2.636893 CTGGGATGTGGAGAGGGATAAG 59.363 54.545 0.00 0.00 0.00 1.73
1081 1108 2.022035 ACTGGGATGTGGAGAGGGATAA 60.022 50.000 0.00 0.00 0.00 1.75
1082 1109 1.580658 ACTGGGATGTGGAGAGGGATA 59.419 52.381 0.00 0.00 0.00 2.59
1083 1110 0.344790 ACTGGGATGTGGAGAGGGAT 59.655 55.000 0.00 0.00 0.00 3.85
1121 1148 4.189188 GCTCGACGGCGCTAGGAA 62.189 66.667 5.31 0.00 37.46 3.36
1139 1166 3.208747 AGATTTGGTGGACGAAACAGT 57.791 42.857 0.00 0.00 0.00 3.55
1140 1167 3.684788 CCTAGATTTGGTGGACGAAACAG 59.315 47.826 0.00 0.00 0.00 3.16
1143 1170 4.360951 AACCTAGATTTGGTGGACGAAA 57.639 40.909 0.00 0.00 37.93 3.46
1146 1173 3.939066 AGAAACCTAGATTTGGTGGACG 58.061 45.455 0.00 0.00 37.93 4.79
1150 1177 4.017126 GGGGAAGAAACCTAGATTTGGTG 58.983 47.826 0.00 0.00 37.93 4.17
1196 1223 3.710722 AGCGGAGGGGCAGTTCAG 61.711 66.667 0.00 0.00 34.64 3.02
1248 1275 0.911769 TCTGGTGGAGGTATTGCTGG 59.088 55.000 0.00 0.00 0.00 4.85
1253 1280 2.173569 GGAAGCATCTGGTGGAGGTATT 59.826 50.000 0.00 0.00 0.00 1.89
1254 1281 1.771255 GGAAGCATCTGGTGGAGGTAT 59.229 52.381 0.00 0.00 0.00 2.73
1257 1284 0.622665 AAGGAAGCATCTGGTGGAGG 59.377 55.000 0.00 0.00 0.00 4.30
1292 1319 2.237392 GCTGAAACTGGTAGAGGTGGAT 59.763 50.000 0.00 0.00 0.00 3.41
1299 1326 0.606604 GGACGGCTGAAACTGGTAGA 59.393 55.000 0.00 0.00 0.00 2.59
1326 1353 0.533032 GAAGCAACTCCCGAGTAGCT 59.467 55.000 0.00 0.00 41.58 3.32
1375 1402 5.675684 TTCACATCTACATAGAACTGCCA 57.324 39.130 0.00 0.00 35.69 4.92
1386 1413 5.612725 TGAGGCACATATTCACATCTACA 57.387 39.130 0.00 0.00 0.00 2.74
1387 1414 7.118390 GGTATTGAGGCACATATTCACATCTAC 59.882 40.741 0.00 0.00 0.00 2.59
1394 1421 3.389656 TCGGGTATTGAGGCACATATTCA 59.610 43.478 0.00 0.00 0.00 2.57
1397 1424 2.303022 CCTCGGGTATTGAGGCACATAT 59.697 50.000 0.00 0.00 45.99 1.78
1399 1426 0.469917 CCTCGGGTATTGAGGCACAT 59.530 55.000 0.00 0.00 45.99 3.21
1420 1447 7.041848 CCAATAATATTCTGCAGTTCATCGACA 60.042 37.037 14.67 0.00 0.00 4.35
1421 1448 7.293745 CCAATAATATTCTGCAGTTCATCGAC 58.706 38.462 14.67 0.00 0.00 4.20
1443 1470 2.367241 TCCAAATCGATCGGATAGCCAA 59.633 45.455 16.41 0.00 34.08 4.52
1462 1529 8.789825 ATCTATCTCAGTTCATTGCATAATCC 57.210 34.615 0.00 0.00 0.00 3.01
1494 1561 8.255394 ACTTTCAGTGTTCTTCCAAATTTTTG 57.745 30.769 0.00 0.00 37.90 2.44
1507 1574 7.806960 ACTAACTCGTATGTACTTTCAGTGTTC 59.193 37.037 0.00 0.00 0.00 3.18
1560 1627 8.242053 ACAAAAGATAATCTGCAATCTGTTGAG 58.758 33.333 25.65 9.25 44.83 3.02
1612 1679 9.651913 GAAATCTTGGGACATAATTGCTAAAAA 57.348 29.630 0.00 0.00 39.30 1.94
1617 1684 5.522641 AGGAAATCTTGGGACATAATTGCT 58.477 37.500 0.00 0.00 39.30 3.91
1618 1685 5.859205 AGGAAATCTTGGGACATAATTGC 57.141 39.130 0.00 0.00 39.30 3.56
1619 1686 6.293626 CGCTAGGAAATCTTGGGACATAATTG 60.294 42.308 0.00 0.00 39.30 2.32
1620 1687 5.765182 CGCTAGGAAATCTTGGGACATAATT 59.235 40.000 0.00 0.00 39.30 1.40
1631 1702 5.368145 TGCATATGAACGCTAGGAAATCTT 58.632 37.500 6.97 0.00 0.00 2.40
1649 1720 6.762187 CCATCATGCCATTAAAGTTTTGCATA 59.238 34.615 11.68 0.00 37.34 3.14
1853 1924 2.349590 ACGCCGGAAGTTAATAACCAC 58.650 47.619 5.05 0.00 0.00 4.16
1873 1972 4.368565 AGAGGTATACATCGGAGTGCTA 57.631 45.455 11.59 0.00 0.00 3.49
2143 2249 3.550431 ACAGGCAGCACGACCAGT 61.550 61.111 0.00 0.00 0.00 4.00
2179 2285 3.023832 TCGAGTAGCATCTCCATGAACA 58.976 45.455 0.00 0.00 30.57 3.18
2304 2410 2.401583 TCACCTTCATCCCATTGTCG 57.598 50.000 0.00 0.00 0.00 4.35
2404 2510 1.740025 GCGAAGTTCTTTGATCCCAGG 59.260 52.381 0.56 0.00 0.00 4.45
2538 2644 1.281867 CAGCCAAGTGTTCCTATGGGA 59.718 52.381 0.00 0.00 40.36 4.37
2546 2652 3.815401 TCTTCTAAAGCAGCCAAGTGTTC 59.185 43.478 0.00 0.00 0.00 3.18
2626 2752 7.967303 CCATTCTAAGCTGAAAGATTTTGAGAC 59.033 37.037 0.00 0.00 41.66 3.36
2741 2867 7.438757 CACTGATCTCTATCACCTGAATCTTTG 59.561 40.741 0.00 0.00 37.20 2.77
2890 3016 2.799562 CGATAGATGGAAGCTTCGCACA 60.800 50.000 19.91 12.79 30.71 4.57
3238 3386 0.611714 TTTGGAACGGAGGGAGTAGC 59.388 55.000 0.00 0.00 0.00 3.58
3242 3390 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3243 3391 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3244 3392 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3245 3393 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
3246 3394 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
3247 3395 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3248 3396 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
3249 3397 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
3250 3398 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3251 3399 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3252 3400 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3253 3401 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3260 3408 9.046296 CAAAGTTAGTACAAAGTTGAGTCATCT 57.954 33.333 0.00 0.00 0.00 2.90
3261 3409 8.827677 ACAAAGTTAGTACAAAGTTGAGTCATC 58.172 33.333 0.00 0.00 0.00 2.92
3262 3410 8.732746 ACAAAGTTAGTACAAAGTTGAGTCAT 57.267 30.769 0.00 0.00 0.00 3.06
3263 3411 9.090692 GTACAAAGTTAGTACAAAGTTGAGTCA 57.909 33.333 0.00 0.00 41.08 3.41
3264 3412 9.090692 TGTACAAAGTTAGTACAAAGTTGAGTC 57.909 33.333 3.90 0.00 46.22 3.36
3284 3432 8.708742 CGAAATAGATGACTCAACTTTGTACAA 58.291 33.333 3.59 3.59 0.00 2.41
3285 3433 7.330946 CCGAAATAGATGACTCAACTTTGTACA 59.669 37.037 0.00 0.00 0.00 2.90
3286 3434 7.544566 TCCGAAATAGATGACTCAACTTTGTAC 59.455 37.037 0.00 0.00 0.00 2.90
3287 3435 7.608153 TCCGAAATAGATGACTCAACTTTGTA 58.392 34.615 0.00 0.00 0.00 2.41
3288 3436 6.464222 TCCGAAATAGATGACTCAACTTTGT 58.536 36.000 0.00 0.00 0.00 2.83
3289 3437 6.968131 TCCGAAATAGATGACTCAACTTTG 57.032 37.500 0.00 0.00 0.00 2.77
3290 3438 6.090898 CGTTCCGAAATAGATGACTCAACTTT 59.909 38.462 0.00 0.00 0.00 2.66
3291 3439 5.577164 CGTTCCGAAATAGATGACTCAACTT 59.423 40.000 0.00 0.00 0.00 2.66
3292 3440 5.103000 CGTTCCGAAATAGATGACTCAACT 58.897 41.667 0.00 0.00 0.00 3.16
3293 3441 4.267928 CCGTTCCGAAATAGATGACTCAAC 59.732 45.833 0.00 0.00 0.00 3.18
3294 3442 4.158949 TCCGTTCCGAAATAGATGACTCAA 59.841 41.667 0.00 0.00 0.00 3.02
3295 3443 3.697542 TCCGTTCCGAAATAGATGACTCA 59.302 43.478 0.00 0.00 0.00 3.41
3296 3444 4.291783 CTCCGTTCCGAAATAGATGACTC 58.708 47.826 0.00 0.00 0.00 3.36
3297 3445 3.068307 CCTCCGTTCCGAAATAGATGACT 59.932 47.826 0.00 0.00 0.00 3.41
3298 3446 3.381949 CCTCCGTTCCGAAATAGATGAC 58.618 50.000 0.00 0.00 0.00 3.06
3299 3447 2.364324 CCCTCCGTTCCGAAATAGATGA 59.636 50.000 0.00 0.00 0.00 2.92
3300 3448 2.364324 TCCCTCCGTTCCGAAATAGATG 59.636 50.000 0.00 0.00 0.00 2.90
3301 3449 2.628657 CTCCCTCCGTTCCGAAATAGAT 59.371 50.000 0.00 0.00 0.00 1.98
3302 3450 2.029623 CTCCCTCCGTTCCGAAATAGA 58.970 52.381 0.00 0.00 0.00 1.98
3303 3451 1.755380 ACTCCCTCCGTTCCGAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
3304 3452 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3305 3453 1.856629 TACTCCCTCCGTTCCGAAAT 58.143 50.000 0.00 0.00 0.00 2.17
3306 3454 1.753073 GATACTCCCTCCGTTCCGAAA 59.247 52.381 0.00 0.00 0.00 3.46
3307 3455 1.064166 AGATACTCCCTCCGTTCCGAA 60.064 52.381 0.00 0.00 0.00 4.30
3308 3456 0.549950 AGATACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
3309 3457 2.267174 TAGATACTCCCTCCGTTCCG 57.733 55.000 0.00 0.00 0.00 4.30
3310 3458 2.826725 CCATAGATACTCCCTCCGTTCC 59.173 54.545 0.00 0.00 0.00 3.62
3311 3459 3.764218 TCCATAGATACTCCCTCCGTTC 58.236 50.000 0.00 0.00 0.00 3.95
3312 3460 3.897657 TCCATAGATACTCCCTCCGTT 57.102 47.619 0.00 0.00 0.00 4.44
3313 3461 3.897657 TTCCATAGATACTCCCTCCGT 57.102 47.619 0.00 0.00 0.00 4.69
3314 3462 4.262506 GGTTTTCCATAGATACTCCCTCCG 60.263 50.000 0.00 0.00 40.31 4.63
3315 3463 4.908481 AGGTTTTCCATAGATACTCCCTCC 59.092 45.833 0.00 0.00 43.73 4.30
3316 3464 5.221742 CCAGGTTTTCCATAGATACTCCCTC 60.222 48.000 0.00 0.00 43.73 4.30
3317 3465 4.660771 CCAGGTTTTCCATAGATACTCCCT 59.339 45.833 0.00 0.00 43.73 4.20
3318 3466 4.202472 CCCAGGTTTTCCATAGATACTCCC 60.202 50.000 0.00 0.00 43.73 4.30
3319 3467 4.658901 TCCCAGGTTTTCCATAGATACTCC 59.341 45.833 0.00 0.00 43.73 3.85
3320 3468 5.743422 GCTCCCAGGTTTTCCATAGATACTC 60.743 48.000 0.00 0.00 43.73 2.59
3321 3469 4.103311 GCTCCCAGGTTTTCCATAGATACT 59.897 45.833 0.00 0.00 43.73 2.12
3322 3470 4.141482 TGCTCCCAGGTTTTCCATAGATAC 60.141 45.833 0.00 0.00 43.73 2.24
3542 3720 1.813513 CTGAACAGAAGCCCGTGATT 58.186 50.000 0.00 0.00 0.00 2.57
3663 3841 1.920574 GGTGCATATGCTAGTATCGCG 59.079 52.381 27.13 0.00 42.66 5.87
3683 3861 1.705256 TACTCTTGTACTTTGCGGCG 58.295 50.000 0.51 0.51 0.00 6.46
3692 3870 6.743575 ATCCAACAGCATTTACTCTTGTAC 57.256 37.500 0.00 0.00 0.00 2.90
3697 3875 4.455606 GCCTATCCAACAGCATTTACTCT 58.544 43.478 0.00 0.00 0.00 3.24
3783 3961 3.763360 TCAAATTCAACAGCCGATGGAAT 59.237 39.130 0.00 0.00 0.00 3.01
3972 4150 1.210478 ACTGCACATAACCCAGGCTAG 59.790 52.381 0.00 0.00 0.00 3.42
4057 4236 1.074084 TGGTGGCCGTATTTTTCCTCA 59.926 47.619 0.00 0.00 0.00 3.86
4097 4276 4.035675 GCCTCTCTGCACAAATTACATACC 59.964 45.833 0.00 0.00 0.00 2.73
4109 4288 2.436292 CCAGCTGCCTCTCTGCAC 60.436 66.667 8.66 0.00 41.48 4.57
4113 4292 2.926779 TGCACCAGCTGCCTCTCT 60.927 61.111 8.66 0.00 46.51 3.10
4114 4293 2.745492 GTGCACCAGCTGCCTCTC 60.745 66.667 8.66 0.00 46.51 3.20
4188 4367 5.519206 CGGTTGTATAGTTAGAACCAAGAGC 59.481 44.000 11.26 0.00 46.96 4.09
4215 4394 3.318017 CACCTTGACGAGAAACGAAGAT 58.682 45.455 0.00 0.00 45.77 2.40
4226 4405 3.610040 AATATGACAGCACCTTGACGA 57.390 42.857 0.00 0.00 0.00 4.20
4228 4407 9.542462 TTAGTATAAATATGACAGCACCTTGAC 57.458 33.333 0.00 0.00 0.00 3.18
4257 4436 4.938226 CACCTCTGTAAAATCCACCTTCTC 59.062 45.833 0.00 0.00 0.00 2.87
4265 4444 6.487299 AGATCTACCACCTCTGTAAAATCC 57.513 41.667 0.00 0.00 0.00 3.01
4281 4460 7.657336 TGTTTGATTGTTTGGGAAAGATCTAC 58.343 34.615 0.00 0.00 0.00 2.59
4282 4461 7.831691 TGTTTGATTGTTTGGGAAAGATCTA 57.168 32.000 0.00 0.00 0.00 1.98
4283 4462 6.729690 TGTTTGATTGTTTGGGAAAGATCT 57.270 33.333 0.00 0.00 0.00 2.75
4284 4463 8.306761 ACTATGTTTGATTGTTTGGGAAAGATC 58.693 33.333 0.00 0.00 0.00 2.75
4285 4464 8.193953 ACTATGTTTGATTGTTTGGGAAAGAT 57.806 30.769 0.00 0.00 0.00 2.40
4286 4465 7.595819 ACTATGTTTGATTGTTTGGGAAAGA 57.404 32.000 0.00 0.00 0.00 2.52
4287 4466 7.710475 ACAACTATGTTTGATTGTTTGGGAAAG 59.290 33.333 0.00 0.00 35.91 2.62
4288 4467 7.560368 ACAACTATGTTTGATTGTTTGGGAAA 58.440 30.769 0.00 0.00 35.91 3.13
4289 4468 7.118496 ACAACTATGTTTGATTGTTTGGGAA 57.882 32.000 0.00 0.00 35.91 3.97
4291 4470 9.787532 CTATACAACTATGTTTGATTGTTTGGG 57.212 33.333 0.00 0.00 41.05 4.12
4336 4551 0.461548 GTCCATCAGGTCATCTCGCA 59.538 55.000 0.00 0.00 35.89 5.10
4354 4569 6.339587 TCTTCACAAACAAGGAAAAAGTGT 57.660 33.333 0.00 0.00 0.00 3.55
4404 4619 9.204570 GCTCTTGAGTTATTGTAAAGACTACAA 57.795 33.333 0.18 0.18 41.05 2.41
4422 4637 4.456911 TGGCTTTATTGACAAGCTCTTGAG 59.543 41.667 15.74 2.92 45.18 3.02
4434 4649 5.503927 AGATCTTGAAGCTGGCTTTATTGA 58.496 37.500 9.28 7.33 36.26 2.57
4497 4712 1.718280 AGGATATTCCGGTCTCCCAC 58.282 55.000 0.00 0.00 42.75 4.61
4504 4719 3.442076 GACCCATCTAGGATATTCCGGT 58.558 50.000 0.00 0.00 42.75 5.28
4643 6717 4.258543 TGGGCGAGAAACCTTTTATACAG 58.741 43.478 0.00 0.00 0.00 2.74
4649 6724 1.681264 CACTTGGGCGAGAAACCTTTT 59.319 47.619 0.00 0.00 0.00 2.27
4697 6772 8.548880 TTACCTTTATAGCTACACTTCCTCAT 57.451 34.615 0.00 0.00 0.00 2.90
4698 6773 7.966339 TTACCTTTATAGCTACACTTCCTCA 57.034 36.000 0.00 0.00 0.00 3.86
4709 6785 4.346129 CGACGTCGTTTACCTTTATAGCT 58.654 43.478 29.08 0.00 34.11 3.32
4725 6801 4.205792 CGTTTGAATATAAGGTCCGACGTC 59.794 45.833 5.18 5.18 0.00 4.34
4728 6804 6.038356 TCTTCGTTTGAATATAAGGTCCGAC 58.962 40.000 0.00 0.00 32.61 4.79
4784 6860 0.526662 CTACCGAGTCTTCCGCTTGT 59.473 55.000 0.00 0.00 0.00 3.16
4785 6861 0.179134 CCTACCGAGTCTTCCGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
4786 6862 1.321074 CCCTACCGAGTCTTCCGCTT 61.321 60.000 0.00 0.00 0.00 4.68
4787 6863 1.753463 CCCTACCGAGTCTTCCGCT 60.753 63.158 0.00 0.00 0.00 5.52
4788 6864 2.806237 CCCTACCGAGTCTTCCGC 59.194 66.667 0.00 0.00 0.00 5.54
4789 6865 2.806237 GCCCTACCGAGTCTTCCG 59.194 66.667 0.00 0.00 0.00 4.30
4790 6866 1.751927 TCGCCCTACCGAGTCTTCC 60.752 63.158 0.00 0.00 32.74 3.46
4791 6867 3.915575 TCGCCCTACCGAGTCTTC 58.084 61.111 0.00 0.00 32.74 2.87
4797 6873 2.439701 CTCACCTCGCCCTACCGA 60.440 66.667 0.00 0.00 35.68 4.69
4798 6874 3.528370 CCTCACCTCGCCCTACCG 61.528 72.222 0.00 0.00 0.00 4.02
4799 6875 3.851128 GCCTCACCTCGCCCTACC 61.851 72.222 0.00 0.00 0.00 3.18
4800 6876 4.208686 CGCCTCACCTCGCCCTAC 62.209 72.222 0.00 0.00 0.00 3.18
4816 6892 2.886730 AAATCAAGGTAGGGCGGGCG 62.887 60.000 0.00 0.00 0.00 6.13
4817 6893 0.181824 TAAATCAAGGTAGGGCGGGC 59.818 55.000 0.00 0.00 0.00 6.13
4818 6894 1.814248 GCTAAATCAAGGTAGGGCGGG 60.814 57.143 0.00 0.00 0.00 6.13
4819 6895 1.594331 GCTAAATCAAGGTAGGGCGG 58.406 55.000 0.00 0.00 0.00 6.13
4820 6896 1.217882 CGCTAAATCAAGGTAGGGCG 58.782 55.000 0.00 0.00 35.75 6.13
4821 6897 0.945099 GCGCTAAATCAAGGTAGGGC 59.055 55.000 0.00 4.32 45.34 5.19
4822 6898 1.134220 TGGCGCTAAATCAAGGTAGGG 60.134 52.381 7.64 0.00 34.35 3.53
4823 6899 2.158957 TCTGGCGCTAAATCAAGGTAGG 60.159 50.000 7.64 0.00 0.00 3.18
4824 6900 3.179443 TCTGGCGCTAAATCAAGGTAG 57.821 47.619 7.64 0.00 0.00 3.18
4825 6901 3.838244 ATCTGGCGCTAAATCAAGGTA 57.162 42.857 7.64 0.00 0.00 3.08
4826 6902 2.717639 ATCTGGCGCTAAATCAAGGT 57.282 45.000 7.64 0.00 0.00 3.50
4827 6903 4.376340 AAAATCTGGCGCTAAATCAAGG 57.624 40.909 7.64 0.00 0.00 3.61
4828 6904 9.760660 GTATATAAAATCTGGCGCTAAATCAAG 57.239 33.333 7.64 0.00 0.00 3.02
4829 6905 8.726988 GGTATATAAAATCTGGCGCTAAATCAA 58.273 33.333 7.64 0.00 0.00 2.57
4830 6906 7.064134 CGGTATATAAAATCTGGCGCTAAATCA 59.936 37.037 7.64 0.00 0.00 2.57
4831 6907 7.277098 TCGGTATATAAAATCTGGCGCTAAATC 59.723 37.037 7.64 0.00 0.00 2.17
4832 6908 7.101054 TCGGTATATAAAATCTGGCGCTAAAT 58.899 34.615 7.64 0.00 0.00 1.40
4833 6909 6.457355 TCGGTATATAAAATCTGGCGCTAAA 58.543 36.000 7.64 0.00 0.00 1.85
4834 6910 6.028146 TCGGTATATAAAATCTGGCGCTAA 57.972 37.500 7.64 0.00 0.00 3.09
4835 6911 5.648178 TCGGTATATAAAATCTGGCGCTA 57.352 39.130 7.64 0.00 0.00 4.26
4836 6912 4.530710 TCGGTATATAAAATCTGGCGCT 57.469 40.909 7.64 0.00 0.00 5.92
4837 6913 6.509677 GCTTATCGGTATATAAAATCTGGCGC 60.510 42.308 0.00 0.00 0.00 6.53
4838 6914 6.757010 AGCTTATCGGTATATAAAATCTGGCG 59.243 38.462 0.00 0.00 0.00 5.69
4839 6915 7.466050 GCAGCTTATCGGTATATAAAATCTGGC 60.466 40.741 0.00 0.00 0.00 4.85
4840 6916 7.254117 CGCAGCTTATCGGTATATAAAATCTGG 60.254 40.741 0.00 0.00 0.00 3.86
4841 6917 7.613146 CGCAGCTTATCGGTATATAAAATCTG 58.387 38.462 0.00 0.00 0.00 2.90
4842 6918 7.757097 CGCAGCTTATCGGTATATAAAATCT 57.243 36.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.