Multiple sequence alignment - TraesCS7B01G355300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G355300 chr7B 100.000 3592 0 0 1 3592 614222899 614219308 0.000000e+00 6634
1 TraesCS7B01G355300 chr7B 77.250 611 89 31 3013 3590 20045770 20045177 2.690000e-81 313
2 TraesCS7B01G355300 chr7D 90.356 1431 99 22 1585 2984 563824663 563826085 0.000000e+00 1842
3 TraesCS7B01G355300 chr7D 90.909 869 74 5 1944 2811 66073778 66074642 0.000000e+00 1162
4 TraesCS7B01G355300 chr7D 82.011 706 96 21 661 1359 563823746 563824427 4.020000e-159 571
5 TraesCS7B01G355300 chr7D 89.125 377 34 5 269 640 563823303 563823677 2.530000e-126 462
6 TraesCS7B01G355300 chr7D 93.359 256 16 1 1 256 563823063 563823317 9.410000e-101 377
7 TraesCS7B01G355300 chr7A 89.866 898 64 15 1585 2478 649425971 649425097 0.000000e+00 1129
8 TraesCS7B01G355300 chr7A 88.294 504 48 6 660 1157 649426869 649426371 8.590000e-166 593
9 TraesCS7B01G355300 chr7A 96.000 325 13 0 2487 2811 649424787 649424463 2.460000e-146 529
10 TraesCS7B01G355300 chr7A 82.772 267 32 12 840 1101 649479176 649478919 3.610000e-55 226
11 TraesCS7B01G355300 chr2D 92.530 656 45 4 2157 2811 558943846 558943194 0.000000e+00 937
12 TraesCS7B01G355300 chr1D 92.343 653 44 6 2161 2811 421493874 421494522 0.000000e+00 924
13 TraesCS7B01G355300 chr3D 92.037 653 46 6 2161 2811 577441570 577442218 0.000000e+00 913
14 TraesCS7B01G355300 chr2A 84.176 613 63 20 2992 3590 615286360 615285768 6.730000e-157 564
15 TraesCS7B01G355300 chr6B 82.708 613 75 18 2992 3590 575545146 575544551 1.910000e-142 516
16 TraesCS7B01G355300 chr6B 91.018 167 15 0 1947 2113 7342068 7341902 3.610000e-55 226
17 TraesCS7B01G355300 chr6B 91.018 167 15 0 1947 2113 7383488 7383322 3.610000e-55 226
18 TraesCS7B01G355300 chr6B 89.286 140 15 0 2288 2427 172325508 172325369 3.690000e-40 176
19 TraesCS7B01G355300 chr5B 82.537 607 71 21 2992 3582 460969530 460968943 5.350000e-138 501
20 TraesCS7B01G355300 chr5B 89.614 337 33 2 1957 2293 20983779 20983445 9.220000e-116 427
21 TraesCS7B01G355300 chr5B 79.906 637 76 25 2992 3590 535474538 535475160 1.540000e-113 420
22 TraesCS7B01G355300 chr5B 88.298 188 20 2 2106 2293 6247205 6247020 1.300000e-54 224
23 TraesCS7B01G355300 chr6D 89.286 140 15 0 2288 2427 89824005 89823866 3.690000e-40 176
24 TraesCS7B01G355300 chr6A 89.286 140 15 0 2288 2427 108202845 108202706 3.690000e-40 176


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 TraesCS7B01G355300 chr7B 614219308 614222899 3591 True 6634.000000 6634 100.000000 1 3592 1 chr7B.!!$R2 3591
1 TraesCS7B01G355300 chr7B 20045177 20045770 593 True 313.000000 313 77.250000 3013 3590 1 chr7B.!!$R1 577
2 TraesCS7B01G355300 chr7D 66073778 66074642 864 False 1162.000000 1162 90.909000 1944 2811 1 chr7D.!!$F1 867
3 TraesCS7B01G355300 chr7D 563823063 563826085 3022 False 813.000000 1842 88.712750 1 2984 4 chr7D.!!$F2 2983
4 TraesCS7B01G355300 chr7A 649424463 649426869 2406 True 750.333333 1129 91.386667 660 2811 3 chr7A.!!$R2 2151
5 TraesCS7B01G355300 chr2D 558943194 558943846 652 True 937.000000 937 92.530000 2157 2811 1 chr2D.!!$R1 654
6 TraesCS7B01G355300 chr1D 421493874 421494522 648 False 924.000000 924 92.343000 2161 2811 1 chr1D.!!$F1 650
7 TraesCS7B01G355300 chr3D 577441570 577442218 648 False 913.000000 913 92.037000 2161 2811 1 chr3D.!!$F1 650
8 TraesCS7B01G355300 chr2A 615285768 615286360 592 True 564.000000 564 84.176000 2992 3590 1 chr2A.!!$R1 598
9 TraesCS7B01G355300 chr6B 575544551 575545146 595 True 516.000000 516 82.708000 2992 3590 1 chr6B.!!$R4 598
10 TraesCS7B01G355300 chr5B 460968943 460969530 587 True 501.000000 501 82.537000 2992 3582 1 chr5B.!!$R3 590
11 TraesCS7B01G355300 chr5B 535474538 535475160 622 False 420.000000 420 79.906000 2992 3590 1 chr5B.!!$F1 598

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
713 767 0.100503 AACTTTTGCTGTCACGTGGC 59.899 50.0 14.58 14.58 0.00 5.01 F
817 871 0.173255 AGGGCAAAATCGGCATTTCG 59.827 50.0 0.00 0.00 30.37 3.46 F
1038 1095 0.176680 CTGACTAGGTGGCTGCGATT 59.823 55.0 0.00 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1753 0.240145 CTGTTCTGTGCAGCACATGG 59.760 55.0 28.37 17.72 43.71 3.66 R
2508 2960 0.601046 TCCTCTGCAGCACAAGAACG 60.601 55.0 9.47 0.00 0.00 3.95 R
2946 3427 0.116342 TCAAGGGGAGTACAGAGGCA 59.884 55.0 0.00 0.00 0.00 4.75 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
28 29 5.552766 ACCTCACCCTACCCTAATTTTACAA 59.447 40.000 0.00 0.00 0.00 2.41
64 65 4.222336 TCACATTGGTCCCAAAACATCTT 58.778 39.130 2.32 0.00 39.55 2.40
182 183 5.494632 TTTTCTTTCGGTTCTCTGGTTTC 57.505 39.130 0.00 0.00 0.00 2.78
183 184 2.750948 TCTTTCGGTTCTCTGGTTTCG 58.249 47.619 0.00 0.00 0.00 3.46
188 189 1.375326 GTTCTCTGGTTTCGCCCCT 59.625 57.895 0.00 0.00 36.04 4.79
203 204 1.155889 CCCCTTTTTGCGCCAATTTC 58.844 50.000 4.18 0.00 0.00 2.17
204 205 1.155889 CCCTTTTTGCGCCAATTTCC 58.844 50.000 4.18 0.00 0.00 3.13
212 213 1.344226 GCGCCAATTTCCGCTTTCAC 61.344 55.000 11.15 0.00 46.14 3.18
220 221 1.698506 TTCCGCTTTCACCCATTTGT 58.301 45.000 0.00 0.00 0.00 2.83
224 225 3.118592 TCCGCTTTCACCCATTTGTTTTT 60.119 39.130 0.00 0.00 0.00 1.94
274 275 2.785357 TTTTTGTGGGGGATTCCTGT 57.215 45.000 2.01 0.00 35.33 4.00
275 276 2.008242 TTTTGTGGGGGATTCCTGTG 57.992 50.000 2.01 0.00 35.33 3.66
276 277 0.856982 TTTGTGGGGGATTCCTGTGT 59.143 50.000 2.01 0.00 35.33 3.72
277 278 0.112218 TTGTGGGGGATTCCTGTGTG 59.888 55.000 2.01 0.00 35.33 3.82
278 279 1.065410 TGTGGGGGATTCCTGTGTGT 61.065 55.000 2.01 0.00 35.33 3.72
279 280 0.988832 GTGGGGGATTCCTGTGTGTA 59.011 55.000 2.01 0.00 35.33 2.90
280 281 0.988832 TGGGGGATTCCTGTGTGTAC 59.011 55.000 2.01 0.00 35.33 2.90
281 282 1.286248 GGGGGATTCCTGTGTGTACT 58.714 55.000 2.01 0.00 35.33 2.73
282 283 1.633945 GGGGGATTCCTGTGTGTACTT 59.366 52.381 2.01 0.00 35.33 2.24
394 397 5.775195 ACATAGGGAAAAGAAAAAGGGAGTG 59.225 40.000 0.00 0.00 0.00 3.51
419 422 2.679930 GCTCTAAACACCGGCCAATACT 60.680 50.000 0.00 0.00 0.00 2.12
431 434 1.134729 GCCAATACTGCCCAAACATGG 60.135 52.381 0.00 0.00 0.00 3.66
433 436 2.166254 CCAATACTGCCCAAACATGGAC 59.834 50.000 0.00 0.00 0.00 4.02
434 437 2.824936 CAATACTGCCCAAACATGGACA 59.175 45.455 0.00 0.00 0.00 4.02
435 438 2.897271 TACTGCCCAAACATGGACAT 57.103 45.000 0.00 0.00 0.00 3.06
436 439 1.259609 ACTGCCCAAACATGGACATG 58.740 50.000 10.57 10.57 44.15 3.21
437 440 0.533491 CTGCCCAAACATGGACATGG 59.467 55.000 15.94 0.00 42.91 3.66
438 441 0.178938 TGCCCAAACATGGACATGGT 60.179 50.000 15.94 7.14 41.22 3.55
439 442 0.247185 GCCCAAACATGGACATGGTG 59.753 55.000 15.94 12.54 37.86 4.17
440 443 0.896923 CCCAAACATGGACATGGTGG 59.103 55.000 21.28 21.28 42.77 4.61
441 444 0.247185 CCAAACATGGACATGGTGGC 59.753 55.000 18.37 0.00 37.86 5.01
442 445 1.259609 CAAACATGGACATGGTGGCT 58.740 50.000 15.94 0.00 37.86 4.75
443 446 1.619827 CAAACATGGACATGGTGGCTT 59.380 47.619 15.94 0.00 37.86 4.35
444 447 2.824936 CAAACATGGACATGGTGGCTTA 59.175 45.455 15.94 0.00 37.86 3.09
493 498 9.729281 ATAGAGTTTCATAGTTTCGGGTAAAAA 57.271 29.630 0.00 0.00 0.00 1.94
553 558 4.530161 TGGGATGATTTTAAGGGTGGTTTG 59.470 41.667 0.00 0.00 0.00 2.93
614 620 3.849911 TCAGAGCATCGACGAAGAAATT 58.150 40.909 0.00 0.00 42.67 1.82
628 634 2.753247 AGAAATTAGAGGAGGCCGACT 58.247 47.619 0.00 0.00 0.00 4.18
640 646 1.811679 GCCGACTCACCTAGCAAGC 60.812 63.158 0.00 0.00 0.00 4.01
642 648 0.737715 CCGACTCACCTAGCAAGCAC 60.738 60.000 0.00 0.00 0.00 4.40
644 650 0.391793 GACTCACCTAGCAAGCACCC 60.392 60.000 0.00 0.00 0.00 4.61
645 651 1.448540 CTCACCTAGCAAGCACCCG 60.449 63.158 0.00 0.00 0.00 5.28
646 652 3.127533 CACCTAGCAAGCACCCGC 61.128 66.667 0.00 0.00 38.99 6.13
649 655 4.101448 CTAGCAAGCACCCGCCCT 62.101 66.667 0.00 0.00 39.83 5.19
650 656 4.096003 TAGCAAGCACCCGCCCTC 62.096 66.667 0.00 0.00 39.83 4.30
675 729 2.223112 CCATTCAGAGACGAAAATGCCG 60.223 50.000 0.00 0.00 0.00 5.69
695 749 3.196040 GCATCCAGCCCATTCAGAA 57.804 52.632 0.00 0.00 37.23 3.02
702 756 2.611224 CCAGCCCATTCAGAACTTTTGC 60.611 50.000 0.00 0.00 0.00 3.68
709 763 3.673746 TTCAGAACTTTTGCTGTCACG 57.326 42.857 0.00 0.00 33.90 4.35
713 767 0.100503 AACTTTTGCTGTCACGTGGC 59.899 50.000 14.58 14.58 0.00 5.01
816 870 1.204467 TGAGGGCAAAATCGGCATTTC 59.796 47.619 0.00 0.00 30.37 2.17
817 871 0.173255 AGGGCAAAATCGGCATTTCG 59.827 50.000 0.00 0.00 30.37 3.46
820 874 0.458370 GCAAAATCGGCATTTCGGCT 60.458 50.000 0.00 0.00 38.27 5.52
903 957 2.363018 CCTCCGACCCTCTGAGCA 60.363 66.667 0.00 0.00 0.00 4.26
948 1005 4.927782 TCAACCAGGCGCGCACTT 62.928 61.111 34.42 15.17 0.00 3.16
959 1016 2.896443 CGCACTTCTCCCCCTCTC 59.104 66.667 0.00 0.00 0.00 3.20
960 1017 2.726351 CGCACTTCTCCCCCTCTCC 61.726 68.421 0.00 0.00 0.00 3.71
1005 1062 4.201679 CTCCGCGCGACCATGGTA 62.202 66.667 34.63 0.00 0.00 3.25
1010 1067 2.795389 GCGCGACCATGGTACGTTC 61.795 63.158 29.95 19.94 32.57 3.95
1013 1070 1.153509 CGACCATGGTACGTTCCCC 60.154 63.158 19.80 1.08 0.00 4.81
1023 1080 0.906282 TACGTTCCCCTTCCCCTGAC 60.906 60.000 0.00 0.00 0.00 3.51
1029 1086 0.983378 CCCCTTCCCCTGACTAGGTG 60.983 65.000 0.00 0.00 42.96 4.00
1030 1087 0.983378 CCCTTCCCCTGACTAGGTGG 60.983 65.000 0.00 0.00 42.96 4.61
1031 1088 1.627297 CCTTCCCCTGACTAGGTGGC 61.627 65.000 0.00 0.00 42.96 5.01
1032 1089 0.618968 CTTCCCCTGACTAGGTGGCT 60.619 60.000 0.00 0.00 42.96 4.75
1033 1090 0.909610 TTCCCCTGACTAGGTGGCTG 60.910 60.000 0.00 0.00 42.96 4.85
1034 1091 2.586792 CCCTGACTAGGTGGCTGC 59.413 66.667 0.00 0.00 42.96 5.25
1035 1092 2.185350 CCTGACTAGGTGGCTGCG 59.815 66.667 0.00 0.00 39.39 5.18
1036 1093 2.351244 CCTGACTAGGTGGCTGCGA 61.351 63.158 0.00 0.00 39.39 5.10
1037 1094 1.680522 CCTGACTAGGTGGCTGCGAT 61.681 60.000 0.00 0.00 39.39 4.58
1038 1095 0.176680 CTGACTAGGTGGCTGCGATT 59.823 55.000 0.00 0.00 0.00 3.34
1039 1096 0.613260 TGACTAGGTGGCTGCGATTT 59.387 50.000 0.00 0.00 0.00 2.17
1040 1097 1.009829 GACTAGGTGGCTGCGATTTG 58.990 55.000 0.00 0.00 0.00 2.32
1041 1098 1.026718 ACTAGGTGGCTGCGATTTGC 61.027 55.000 0.00 0.00 46.70 3.68
1093 1166 2.791560 CGCAGATTCGGTAGATTCACAG 59.208 50.000 0.00 0.00 31.18 3.66
1131 1204 1.203389 TGGTTGAGGCTAGGTAGGGTT 60.203 52.381 0.00 0.00 0.00 4.11
1137 1210 5.349738 TGAGGCTAGGTAGGGTTATATGT 57.650 43.478 0.00 0.00 0.00 2.29
1156 1229 3.427573 TGTTAGGACAGAGGTGATTCGA 58.572 45.455 0.00 0.00 0.00 3.71
1163 1236 3.426615 ACAGAGGTGATTCGAGTTCTCT 58.573 45.455 4.44 4.44 32.51 3.10
1164 1237 3.829601 ACAGAGGTGATTCGAGTTCTCTT 59.170 43.478 6.65 0.00 30.20 2.85
1170 1243 5.712917 AGGTGATTCGAGTTCTCTTAGAGTT 59.287 40.000 9.25 0.00 0.00 3.01
1171 1244 5.802956 GGTGATTCGAGTTCTCTTAGAGTTG 59.197 44.000 9.25 0.00 0.00 3.16
1172 1245 5.802956 GTGATTCGAGTTCTCTTAGAGTTGG 59.197 44.000 9.25 0.00 0.00 3.77
1177 1250 4.261656 CGAGTTCTCTTAGAGTTGGTGTGT 60.262 45.833 9.25 0.00 0.00 3.72
1180 1255 5.010213 AGTTCTCTTAGAGTTGGTGTGTCTC 59.990 44.000 9.25 0.00 0.00 3.36
1182 1257 3.220110 TCTTAGAGTTGGTGTGTCTCGT 58.780 45.455 0.00 0.00 33.96 4.18
1186 1261 3.220110 AGAGTTGGTGTGTCTCGTTAGA 58.780 45.455 0.00 0.00 33.96 2.10
1187 1262 3.827302 AGAGTTGGTGTGTCTCGTTAGAT 59.173 43.478 0.00 0.00 33.30 1.98
1188 1263 4.281182 AGAGTTGGTGTGTCTCGTTAGATT 59.719 41.667 0.00 0.00 33.30 2.40
1189 1264 4.557205 AGTTGGTGTGTCTCGTTAGATTC 58.443 43.478 0.00 0.00 33.30 2.52
1190 1265 4.281182 AGTTGGTGTGTCTCGTTAGATTCT 59.719 41.667 0.00 0.00 33.30 2.40
1193 1268 4.462834 TGGTGTGTCTCGTTAGATTCTCAT 59.537 41.667 0.00 0.00 33.30 2.90
1202 1277 8.963130 GTCTCGTTAGATTCTCATGATTTGTAG 58.037 37.037 0.00 0.00 33.30 2.74
1204 1279 8.634475 TCGTTAGATTCTCATGATTTGTAGTG 57.366 34.615 0.00 0.00 0.00 2.74
1207 1282 8.607459 GTTAGATTCTCATGATTTGTAGTGTGG 58.393 37.037 0.00 0.00 0.00 4.17
1208 1283 5.587844 AGATTCTCATGATTTGTAGTGTGGC 59.412 40.000 0.00 0.00 0.00 5.01
1211 1286 1.739466 CATGATTTGTAGTGTGGCGCT 59.261 47.619 7.64 0.00 0.00 5.92
1213 1288 1.156736 GATTTGTAGTGTGGCGCTGT 58.843 50.000 7.64 0.00 0.00 4.40
1216 1291 2.242047 TTGTAGTGTGGCGCTGTTAA 57.758 45.000 7.64 0.00 0.00 2.01
1222 1297 0.600557 TGTGGCGCTGTTAAATTGGG 59.399 50.000 7.64 0.00 0.00 4.12
1233 1308 1.173043 TAAATTGGGTGAAGCTGCGG 58.827 50.000 0.00 0.00 0.00 5.69
1255 1331 6.732154 CGGTAGGATTACGTATTTCTCTTCA 58.268 40.000 1.53 0.00 0.00 3.02
1256 1332 7.198390 CGGTAGGATTACGTATTTCTCTTCAA 58.802 38.462 1.53 0.00 0.00 2.69
1257 1333 7.703621 CGGTAGGATTACGTATTTCTCTTCAAA 59.296 37.037 1.53 0.00 0.00 2.69
1292 1368 5.864474 GGATGCTAGTAAATGTCGAGTATGG 59.136 44.000 0.00 0.00 0.00 2.74
1295 1371 4.444720 GCTAGTAAATGTCGAGTATGGCAC 59.555 45.833 0.00 0.00 0.00 5.01
1296 1372 4.737855 AGTAAATGTCGAGTATGGCACT 57.262 40.909 0.00 0.00 41.47 4.40
1297 1373 4.433615 AGTAAATGTCGAGTATGGCACTG 58.566 43.478 0.00 0.00 37.72 3.66
1299 1375 3.827008 AATGTCGAGTATGGCACTGAT 57.173 42.857 0.00 0.00 37.72 2.90
1300 1376 4.937201 AATGTCGAGTATGGCACTGATA 57.063 40.909 0.00 0.00 37.72 2.15
1301 1377 3.990318 TGTCGAGTATGGCACTGATAG 57.010 47.619 0.00 0.00 37.72 2.08
1302 1378 3.551846 TGTCGAGTATGGCACTGATAGA 58.448 45.455 0.00 0.00 37.72 1.98
1305 1381 4.068599 TCGAGTATGGCACTGATAGAGAG 58.931 47.826 0.00 0.00 37.72 3.20
1307 1383 4.517075 CGAGTATGGCACTGATAGAGAGAA 59.483 45.833 0.00 0.00 37.72 2.87
1309 1385 6.294453 CGAGTATGGCACTGATAGAGAGAATT 60.294 42.308 0.00 0.00 37.72 2.17
1310 1386 7.094592 CGAGTATGGCACTGATAGAGAGAATTA 60.095 40.741 0.00 0.00 37.72 1.40
1322 1398 5.543507 AGAGAGAATTACATTCGGCATCT 57.456 39.130 0.00 0.00 43.92 2.90
1324 1400 4.636249 AGAGAATTACATTCGGCATCTCC 58.364 43.478 0.00 0.00 43.92 3.71
1342 1418 1.570857 CCTGGTGGAATGGGGTAGCA 61.571 60.000 0.00 0.00 34.57 3.49
1353 1429 3.788227 TGGGGTAGCATGGATGAATAC 57.212 47.619 0.00 0.00 0.00 1.89
1360 1436 6.942576 GGGTAGCATGGATGAATACAGTTAAT 59.057 38.462 0.00 0.00 0.00 1.40
1364 1440 8.297470 AGCATGGATGAATACAGTTAATTTGT 57.703 30.769 0.00 1.87 0.00 2.83
1366 1442 9.023967 GCATGGATGAATACAGTTAATTTGTTC 57.976 33.333 0.00 0.00 0.00 3.18
1368 1444 8.330466 TGGATGAATACAGTTAATTTGTTCGT 57.670 30.769 1.57 0.00 0.00 3.85
1377 1453 7.375053 ACAGTTAATTTGTTCGTATGGCAAAT 58.625 30.769 0.00 10.52 42.46 2.32
1386 1462 0.829990 GTATGGCAAATGGGTTGGGG 59.170 55.000 0.00 0.00 37.73 4.96
1388 1464 2.203922 GGCAAATGGGTTGGGGGT 60.204 61.111 0.00 0.00 37.73 4.95
1396 1472 3.639625 ATGGGTTGGGGGTTTTTAGAA 57.360 42.857 0.00 0.00 0.00 2.10
1403 1510 5.452776 GGTTGGGGGTTTTTAGAAAACTGAG 60.453 44.000 13.91 0.00 32.91 3.35
1419 1526 7.609532 AGAAAACTGAGTTAATCTCCATCCTTG 59.390 37.037 0.00 0.00 42.12 3.61
1422 1529 7.496346 ACTGAGTTAATCTCCATCCTTGTTA 57.504 36.000 3.59 0.00 42.12 2.41
1435 1542 6.262273 TCCATCCTTGTTAGTTGAGTTTTCAC 59.738 38.462 0.00 0.00 31.71 3.18
1436 1543 6.438763 CATCCTTGTTAGTTGAGTTTTCACC 58.561 40.000 0.00 0.00 31.71 4.02
1440 1547 7.123547 TCCTTGTTAGTTGAGTTTTCACCATTT 59.876 33.333 0.00 0.00 31.71 2.32
1441 1548 8.410141 CCTTGTTAGTTGAGTTTTCACCATTTA 58.590 33.333 0.00 0.00 31.71 1.40
1455 1564 3.755378 CACCATTTATCCCAGCATCTAGC 59.245 47.826 0.00 0.00 46.19 3.42
1471 1580 5.836347 CATCTAGCTATGCTGTTAGTGTCA 58.164 41.667 1.96 0.00 40.10 3.58
1476 1585 3.733224 GCTATGCTGTTAGTGTCAGATCG 59.267 47.826 0.00 0.00 35.20 3.69
1490 1599 4.279922 TGTCAGATCGTCTCCAAACAGTTA 59.720 41.667 0.00 0.00 0.00 2.24
1491 1600 5.221362 TGTCAGATCGTCTCCAAACAGTTAA 60.221 40.000 0.00 0.00 0.00 2.01
1504 1613 9.853555 CTCCAAACAGTTAATTTGCACAATATA 57.146 29.630 0.00 0.00 36.01 0.86
1508 1617 8.687824 AACAGTTAATTTGCACAATATACTGC 57.312 30.769 20.50 0.00 0.00 4.40
1534 1643 2.880890 CAGTAACTCTGCTGCCAGTTTT 59.119 45.455 16.43 6.12 40.09 2.43
1538 1647 1.678101 ACTCTGCTGCCAGTTTTTCAC 59.322 47.619 0.00 0.00 40.09 3.18
1547 1656 3.882888 TGCCAGTTTTTCACCTTCTACTG 59.117 43.478 0.00 0.00 34.32 2.74
1553 1664 8.567285 CAGTTTTTCACCTTCTACTGGAATAT 57.433 34.615 0.00 0.00 33.01 1.28
1560 1671 7.685481 TCACCTTCTACTGGAATATTGAAACA 58.315 34.615 0.00 0.00 33.01 2.83
1561 1672 8.328758 TCACCTTCTACTGGAATATTGAAACAT 58.671 33.333 0.00 0.00 33.01 2.71
1605 1750 8.579850 TGACTTTGTATCAAATTTAGGCTGAT 57.420 30.769 0.00 0.00 34.29 2.90
1660 1806 7.175467 TCTGAAAATGCTGTCATTCATGTTAGT 59.825 33.333 0.00 0.00 41.77 2.24
1661 1807 7.660112 TGAAAATGCTGTCATTCATGTTAGTT 58.340 30.769 0.00 0.00 41.77 2.24
1664 1810 7.400599 AATGCTGTCATTCATGTTAGTTGAT 57.599 32.000 0.00 0.00 38.47 2.57
1667 1813 6.207221 TGCTGTCATTCATGTTAGTTGATTGT 59.793 34.615 0.00 0.00 0.00 2.71
1668 1814 6.525628 GCTGTCATTCATGTTAGTTGATTGTG 59.474 38.462 0.00 0.00 0.00 3.33
1683 1829 7.538575 AGTTGATTGTGTTTATCTAATGCCAC 58.461 34.615 0.00 0.00 0.00 5.01
1689 1835 6.941857 TGTGTTTATCTAATGCCACTAGTGA 58.058 36.000 24.68 5.51 0.00 3.41
1828 1974 3.753272 CCTTCAATGACACCTTCATCGTT 59.247 43.478 0.00 0.00 44.86 3.85
1848 1994 6.452242 TCGTTAGTATTTTCTTCTCAGCACA 58.548 36.000 0.00 0.00 0.00 4.57
1885 2031 5.698089 ACTGTTGTCTCATGTGTATTGACTG 59.302 40.000 0.00 0.00 0.00 3.51
1886 2032 5.610398 TGTTGTCTCATGTGTATTGACTGT 58.390 37.500 0.00 0.00 0.00 3.55
2067 2213 2.621338 GTCAAGGCTGATCGTGATGAA 58.379 47.619 0.00 0.00 33.05 2.57
2070 2216 2.145958 AGGCTGATCGTGATGAATCG 57.854 50.000 0.00 0.00 0.00 3.34
2127 2273 1.338389 GCTACCCGTTGCAAGGTAAGA 60.338 52.381 17.23 0.00 38.15 2.10
2128 2274 2.679930 GCTACCCGTTGCAAGGTAAGAT 60.680 50.000 17.23 1.64 38.15 2.40
2140 2286 8.470002 GTTGCAAGGTAAGATTCCTGAAATATT 58.530 33.333 0.00 0.00 35.27 1.28
2173 2319 7.044181 CACTTTCAGCTGTTCCTATTATCAGA 58.956 38.462 14.67 0.00 0.00 3.27
2258 2404 0.833287 TAGTCCTGCATTGCTCTCCC 59.167 55.000 10.49 0.00 0.00 4.30
2269 2418 3.973206 TTGCTCTCCCGAGATGTTTTA 57.027 42.857 0.00 0.00 39.74 1.52
2371 2521 2.930562 ACACCTGGACCTGGAGCC 60.931 66.667 23.36 1.64 0.00 4.70
2440 2590 3.836949 CATTGGTACGCAATGCTTCTTT 58.163 40.909 18.15 0.00 33.95 2.52
2441 2591 2.987413 TGGTACGCAATGCTTCTTTG 57.013 45.000 2.94 0.00 0.00 2.77
2455 2605 8.589629 CAATGCTTCTTTGAATATAGTGTTTGC 58.410 33.333 0.00 0.00 0.00 3.68
2485 2937 7.012704 AGCACATATGTCCATGTTATTGTCTTC 59.987 37.037 5.07 0.00 37.02 2.87
2497 2949 6.230472 TGTTATTGTCTTCGCATATGCCTAT 58.770 36.000 21.77 11.56 37.91 2.57
2508 2960 5.817296 TCGCATATGCCTATCCATAATGTTC 59.183 40.000 21.77 0.00 37.91 3.18
2642 3095 1.627834 AGAAACTTGCTCCTCTCTGGG 59.372 52.381 0.00 0.00 36.20 4.45
2715 3168 4.517285 TGAGGATCATTTGCTGTTAGTCC 58.483 43.478 0.00 0.00 42.56 3.85
2730 3183 7.042335 GCTGTTAGTCCTACTATGAATGTTGT 58.958 38.462 0.00 0.00 29.64 3.32
2731 3184 7.010552 GCTGTTAGTCCTACTATGAATGTTGTG 59.989 40.741 0.00 0.00 29.64 3.33
2833 3310 4.612264 TGTTACTTACTCCCACTTGTCC 57.388 45.455 0.00 0.00 0.00 4.02
2836 3313 5.131475 TGTTACTTACTCCCACTTGTCCTTT 59.869 40.000 0.00 0.00 0.00 3.11
2837 3314 4.790718 ACTTACTCCCACTTGTCCTTTT 57.209 40.909 0.00 0.00 0.00 2.27
2838 3315 5.125367 ACTTACTCCCACTTGTCCTTTTT 57.875 39.130 0.00 0.00 0.00 1.94
2859 3336 2.507484 TGGTGCTGTGATCCTTCTTTG 58.493 47.619 0.00 0.00 0.00 2.77
2860 3337 2.106338 TGGTGCTGTGATCCTTCTTTGA 59.894 45.455 0.00 0.00 0.00 2.69
2886 3363 1.453155 ACATCCTTCATGTTCCACGC 58.547 50.000 0.00 0.00 43.89 5.34
2891 3368 2.154462 CCTTCATGTTCCACGCTTCTT 58.846 47.619 0.00 0.00 0.00 2.52
2892 3369 2.160417 CCTTCATGTTCCACGCTTCTTC 59.840 50.000 0.00 0.00 0.00 2.87
2895 3372 2.154462 CATGTTCCACGCTTCTTCCTT 58.846 47.619 0.00 0.00 0.00 3.36
2901 3378 3.777478 TCCACGCTTCTTCCTTATAACG 58.223 45.455 0.00 0.00 0.00 3.18
2907 3384 4.181578 GCTTCTTCCTTATAACGAGTGCA 58.818 43.478 0.00 0.00 0.00 4.57
2915 3392 9.438291 CTTCCTTATAACGAGTGCATTTTATTG 57.562 33.333 0.00 0.00 0.00 1.90
2946 3427 2.025321 ACCCAAGAAAGTGTGGTGAGTT 60.025 45.455 0.00 0.00 32.60 3.01
2969 3450 0.617820 TCTGTACTCCCCTTGAGGCC 60.618 60.000 0.00 0.00 46.01 5.19
2970 3451 0.618968 CTGTACTCCCCTTGAGGCCT 60.619 60.000 3.86 3.86 46.01 5.19
2984 3465 1.821136 GAGGCCTCATTTGGTTCCAAG 59.179 52.381 28.43 0.00 0.00 3.61
2985 3466 1.147817 AGGCCTCATTTGGTTCCAAGT 59.852 47.619 0.00 0.00 0.00 3.16
2986 3467 1.273327 GGCCTCATTTGGTTCCAAGTG 59.727 52.381 17.21 17.21 35.77 3.16
2987 3468 1.337167 GCCTCATTTGGTTCCAAGTGC 60.337 52.381 18.11 7.03 34.88 4.40
2988 3469 1.068333 CCTCATTTGGTTCCAAGTGCG 60.068 52.381 18.11 13.63 34.88 5.34
2989 3470 0.313672 TCATTTGGTTCCAAGTGCGC 59.686 50.000 18.11 0.00 34.88 6.09
2990 3471 0.314935 CATTTGGTTCCAAGTGCGCT 59.685 50.000 9.73 0.00 29.59 5.92
2996 3477 1.073025 TTCCAAGTGCGCTGATGGT 59.927 52.632 20.15 0.00 34.50 3.55
2998 3479 2.693762 CCAAGTGCGCTGATGGTGG 61.694 63.158 9.73 5.29 0.00 4.61
3006 3487 1.805120 GCGCTGATGGTGGTAATACGT 60.805 52.381 0.00 0.00 0.00 3.57
3104 3592 5.291858 TGCAGCTTTAAGAACATGACTATCG 59.708 40.000 0.00 0.00 0.00 2.92
3130 3618 3.381983 ACATCAGGCGACGGCTCA 61.382 61.111 22.39 9.86 35.88 4.26
3153 3642 2.806244 CCGAATTTGGTTCTCGTCAGTT 59.194 45.455 3.21 0.00 34.56 3.16
3154 3643 3.363970 CCGAATTTGGTTCTCGTCAGTTG 60.364 47.826 3.21 0.00 34.56 3.16
3174 3667 1.522668 CATGCCGGAGACAACAAGAA 58.477 50.000 5.05 0.00 0.00 2.52
3175 3668 1.879380 CATGCCGGAGACAACAAGAAA 59.121 47.619 5.05 0.00 0.00 2.52
3176 3669 1.593196 TGCCGGAGACAACAAGAAAG 58.407 50.000 5.05 0.00 0.00 2.62
3177 3670 1.140052 TGCCGGAGACAACAAGAAAGA 59.860 47.619 5.05 0.00 0.00 2.52
3178 3671 2.224523 TGCCGGAGACAACAAGAAAGAT 60.225 45.455 5.05 0.00 0.00 2.40
3179 3672 2.416893 GCCGGAGACAACAAGAAAGATC 59.583 50.000 5.05 0.00 0.00 2.75
3180 3673 3.866449 GCCGGAGACAACAAGAAAGATCT 60.866 47.826 5.05 0.00 37.57 2.75
3208 3703 3.933155 GTGACTTCACCGCAGATAATG 57.067 47.619 0.00 0.00 40.85 1.90
3213 3708 1.496060 TCACCGCAGATAATGGGAGT 58.504 50.000 0.00 0.00 44.43 3.85
3217 3712 1.224069 CGCAGATAATGGGAGTGGCG 61.224 60.000 0.00 0.00 44.43 5.69
3218 3713 1.510480 GCAGATAATGGGAGTGGCGC 61.510 60.000 0.00 0.00 0.00 6.53
3219 3714 0.179048 CAGATAATGGGAGTGGCGCA 60.179 55.000 10.83 0.00 44.12 6.09
3220 3715 0.179045 AGATAATGGGAGTGGCGCAC 60.179 55.000 10.83 5.73 42.69 5.34
3221 3716 1.498865 GATAATGGGAGTGGCGCACG 61.499 60.000 10.83 0.00 42.69 5.34
3222 3717 2.940890 ATAATGGGAGTGGCGCACGG 62.941 60.000 10.83 0.00 42.69 4.94
3247 3742 2.039084 ACCTGCTTTTCTCCTTGACGAT 59.961 45.455 0.00 0.00 0.00 3.73
3248 3743 3.260884 ACCTGCTTTTCTCCTTGACGATA 59.739 43.478 0.00 0.00 0.00 2.92
3250 3745 4.499183 CTGCTTTTCTCCTTGACGATACT 58.501 43.478 0.00 0.00 0.00 2.12
3261 3759 2.028190 CGATACTGGGCTGGCGAG 59.972 66.667 11.59 11.59 0.00 5.03
3289 3787 0.546267 ACACAGGTCAGATCAGGCCT 60.546 55.000 5.25 5.25 0.00 5.19
3290 3788 0.177604 CACAGGTCAGATCAGGCCTC 59.822 60.000 8.55 0.00 0.00 4.70
3298 3796 2.750637 ATCAGGCCTCGACGTCGT 60.751 61.111 34.40 14.92 40.80 4.34
3316 3814 1.453197 TAGCTCGACGAGGGATGCA 60.453 57.895 25.31 0.00 0.00 3.96
3318 3816 2.167861 GCTCGACGAGGGATGCAAC 61.168 63.158 25.31 3.18 0.00 4.17
3319 3817 1.215382 CTCGACGAGGGATGCAACA 59.785 57.895 17.27 0.00 0.00 3.33
3320 3818 0.179100 CTCGACGAGGGATGCAACAT 60.179 55.000 17.27 0.00 0.00 2.71
3330 3831 0.740737 GATGCAACATACCAGGTGGC 59.259 55.000 0.76 0.00 39.32 5.01
3340 3841 3.322466 CAGGTGGCGGAGGGACTT 61.322 66.667 0.00 0.00 41.55 3.01
3373 3912 1.639635 GGATGGAGGTGGGACATGCT 61.640 60.000 0.00 0.00 44.52 3.79
3374 3913 0.257039 GATGGAGGTGGGACATGCTT 59.743 55.000 0.00 0.00 44.52 3.91
3390 3940 3.726595 CTTTGGCGGGCCGTCGATA 62.727 63.158 27.04 11.08 39.42 2.92
3433 3985 2.746277 GGGCATTGCTTCGGTCGT 60.746 61.111 8.82 0.00 0.00 4.34
3436 3988 1.154225 GCATTGCTTCGGTCGTTGG 60.154 57.895 0.16 0.00 0.00 3.77
3498 4054 2.041922 AGGCGGGTGCTGGATCTA 60.042 61.111 0.00 0.00 42.25 1.98
3508 4065 1.240256 GCTGGATCTAGGTCGACGAT 58.760 55.000 9.92 6.81 0.00 3.73
3513 4070 1.609555 GATCTAGGTCGACGATGCCTT 59.390 52.381 11.81 0.00 34.07 4.35
3536 4094 3.579685 CTCGTCTCACTCGAGCCA 58.420 61.111 13.61 0.00 45.77 4.75
3551 4110 2.683465 GCCATGGCTTCTCTCCCCA 61.683 63.158 29.98 0.00 38.26 4.96
3586 4145 1.545841 GCTTTTCTCCCCGTGGAAAT 58.454 50.000 0.00 0.00 41.17 2.17
3590 4149 1.358152 TTCTCCCCGTGGAAATGACT 58.642 50.000 0.00 0.00 41.17 3.41
3591 4150 0.613260 TCTCCCCGTGGAAATGACTG 59.387 55.000 0.00 0.00 41.17 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.328505 GCAAGATGTTTTGGGACCAATG 58.671 45.455 4.36 0.00 35.70 2.82
147 148 5.128008 ACCGAAAGAAAATGAAGGAAAACCA 59.872 36.000 0.00 0.00 0.00 3.67
160 161 4.034742 CGAAACCAGAGAACCGAAAGAAAA 59.965 41.667 0.00 0.00 0.00 2.29
167 168 1.005394 GGCGAAACCAGAGAACCGA 60.005 57.895 0.00 0.00 38.86 4.69
188 189 0.249657 AGCGGAAATTGGCGCAAAAA 60.250 45.000 10.83 0.00 0.00 1.94
195 196 0.389817 GGGTGAAAGCGGAAATTGGC 60.390 55.000 0.00 0.00 33.03 4.52
203 204 2.524569 AAACAAATGGGTGAAAGCGG 57.475 45.000 0.00 0.00 33.03 5.52
256 257 1.219213 ACACAGGAATCCCCCACAAAA 59.781 47.619 0.00 0.00 34.66 2.44
257 258 0.856982 ACACAGGAATCCCCCACAAA 59.143 50.000 0.00 0.00 34.66 2.83
258 259 0.112218 CACACAGGAATCCCCCACAA 59.888 55.000 0.00 0.00 34.66 3.33
259 260 1.065410 ACACACAGGAATCCCCCACA 61.065 55.000 0.00 0.00 34.66 4.17
260 261 0.988832 TACACACAGGAATCCCCCAC 59.011 55.000 0.00 0.00 34.66 4.61
261 262 0.988832 GTACACACAGGAATCCCCCA 59.011 55.000 0.00 0.00 34.66 4.96
262 263 1.286248 AGTACACACAGGAATCCCCC 58.714 55.000 0.00 0.00 34.66 5.40
263 264 2.304761 TCAAGTACACACAGGAATCCCC 59.695 50.000 0.00 0.00 0.00 4.81
264 265 3.695830 TCAAGTACACACAGGAATCCC 57.304 47.619 0.00 0.00 0.00 3.85
265 266 7.770897 AGAATATTCAAGTACACACAGGAATCC 59.229 37.037 17.56 0.00 33.97 3.01
266 267 8.723942 AGAATATTCAAGTACACACAGGAATC 57.276 34.615 17.56 0.00 33.97 2.52
267 268 9.520515 AAAGAATATTCAAGTACACACAGGAAT 57.479 29.630 17.56 0.00 35.32 3.01
268 269 8.918202 AAAGAATATTCAAGTACACACAGGAA 57.082 30.769 17.56 0.00 0.00 3.36
269 270 8.918202 AAAAGAATATTCAAGTACACACAGGA 57.082 30.769 17.56 0.00 0.00 3.86
369 372 6.946009 CACTCCCTTTTTCTTTTCCCTATGTA 59.054 38.462 0.00 0.00 0.00 2.29
377 380 4.342378 AGCCTTCACTCCCTTTTTCTTTTC 59.658 41.667 0.00 0.00 0.00 2.29
394 397 1.025113 GGCCGGTGTTTAGAGCCTTC 61.025 60.000 1.90 0.00 40.57 3.46
438 441 4.464597 AACACTTCAGTGGTTTTTAAGCCA 59.535 37.500 11.62 0.00 44.92 4.75
439 442 5.006153 AACACTTCAGTGGTTTTTAAGCC 57.994 39.130 11.62 0.00 44.92 4.35
440 443 8.642908 AATTAACACTTCAGTGGTTTTTAAGC 57.357 30.769 11.62 0.00 44.92 3.09
500 505 9.317936 GGACCATATCCTTGAATTCAATTTTTC 57.682 33.333 20.76 9.41 45.22 2.29
509 514 8.084173 TCCCAATGGGACCATATCCTTGAATT 62.084 42.308 18.77 0.00 46.17 2.17
510 515 6.662015 TCCCAATGGGACCATATCCTTGAAT 61.662 44.000 18.77 0.00 46.17 2.57
525 530 4.101430 CACCCTTAAAATCATCCCAATGGG 59.899 45.833 13.28 13.28 46.11 4.00
543 548 7.849322 AACAAAGATTTATACAAACCACCCT 57.151 32.000 0.00 0.00 0.00 4.34
578 584 2.680221 GCTCTGAGCACTCATGGACAAT 60.680 50.000 24.02 0.00 41.89 2.71
591 597 0.099613 TCTTCGTCGATGCTCTGAGC 59.900 55.000 22.38 22.38 42.82 4.26
602 608 3.117046 GCCTCCTCTAATTTCTTCGTCG 58.883 50.000 0.00 0.00 0.00 5.12
614 620 1.076923 GGTGAGTCGGCCTCCTCTA 60.077 63.158 16.67 4.16 39.65 2.43
628 634 2.662596 CGGGTGCTTGCTAGGTGA 59.337 61.111 0.00 0.00 0.00 4.02
645 651 3.764160 CTCTGAATGGGCGGAGGGC 62.764 68.421 0.00 0.00 37.58 5.19
646 652 2.066393 TCTCTGAATGGGCGGAGGG 61.066 63.158 0.00 0.00 40.82 4.30
648 654 1.227089 CGTCTCTGAATGGGCGGAG 60.227 63.158 0.00 0.00 41.62 4.63
649 655 1.254975 TTCGTCTCTGAATGGGCGGA 61.255 55.000 0.00 0.00 0.00 5.54
650 656 0.391130 TTTCGTCTCTGAATGGGCGG 60.391 55.000 0.00 0.00 0.00 6.13
651 657 1.438651 TTTTCGTCTCTGAATGGGCG 58.561 50.000 0.00 0.00 0.00 6.13
652 658 2.478539 GCATTTTCGTCTCTGAATGGGC 60.479 50.000 0.00 0.00 31.78 5.36
655 661 2.672874 TCGGCATTTTCGTCTCTGAATG 59.327 45.455 0.00 0.00 33.71 2.67
656 662 2.932614 CTCGGCATTTTCGTCTCTGAAT 59.067 45.455 0.00 0.00 0.00 2.57
657 663 2.337583 CTCGGCATTTTCGTCTCTGAA 58.662 47.619 0.00 0.00 0.00 3.02
658 664 1.996292 CTCGGCATTTTCGTCTCTGA 58.004 50.000 0.00 0.00 0.00 3.27
675 729 0.182061 TCTGAATGGGCTGGATGCTC 59.818 55.000 0.00 0.00 44.01 4.26
693 747 1.859998 GCCACGTGACAGCAAAAGTTC 60.860 52.381 19.30 0.00 0.00 3.01
695 749 1.724582 GGCCACGTGACAGCAAAAGT 61.725 55.000 19.30 0.00 0.00 2.66
702 756 4.308458 TTCGGGGCCACGTGACAG 62.308 66.667 29.71 7.84 34.94 3.51
709 763 2.781431 AATGGTTCCTTCGGGGCCAC 62.781 60.000 4.39 0.00 40.92 5.01
713 767 2.143876 ATGAAATGGTTCCTTCGGGG 57.856 50.000 0.00 0.00 35.37 5.73
721 775 1.181786 TGGGCCGAATGAAATGGTTC 58.818 50.000 0.00 0.00 0.00 3.62
755 809 1.318576 GTCCAAGGGATTATTGGCGG 58.681 55.000 0.00 0.00 45.69 6.13
1005 1062 2.206036 TCAGGGGAAGGGGAACGT 59.794 61.111 0.00 0.00 0.00 3.99
1010 1067 4.401657 CCTAGTCAGGGGAAGGGG 57.598 66.667 0.00 0.00 38.41 4.79
1023 1080 1.723870 GCAAATCGCAGCCACCTAG 59.276 57.895 0.00 0.00 41.79 3.02
1030 1087 2.023320 GCTACGGCAAATCGCAGC 59.977 61.111 0.00 0.00 45.17 5.25
1031 1088 3.485110 TGCTACGGCAAATCGCAG 58.515 55.556 0.00 0.00 46.36 5.18
1040 1097 0.179258 CGACGAAAAACTGCTACGGC 60.179 55.000 0.00 0.00 39.26 5.68
1041 1098 0.437295 CCGACGAAAAACTGCTACGG 59.563 55.000 0.00 0.00 0.00 4.02
1070 1143 1.140816 GAATCTACCGAATCTGCGCC 58.859 55.000 4.18 0.00 0.00 6.53
1131 1204 7.002276 TCGAATCACCTCTGTCCTAACATATA 58.998 38.462 0.00 0.00 34.13 0.86
1137 1210 3.698289 ACTCGAATCACCTCTGTCCTAA 58.302 45.455 0.00 0.00 0.00 2.69
1156 1229 4.896482 AGACACACCAACTCTAAGAGAACT 59.104 41.667 0.00 0.00 33.32 3.01
1163 1236 4.823442 TCTAACGAGACACACCAACTCTAA 59.177 41.667 0.00 0.00 0.00 2.10
1164 1237 4.392047 TCTAACGAGACACACCAACTCTA 58.608 43.478 0.00 0.00 0.00 2.43
1170 1243 3.824443 TGAGAATCTAACGAGACACACCA 59.176 43.478 0.00 0.00 33.41 4.17
1171 1244 4.436242 TGAGAATCTAACGAGACACACC 57.564 45.455 0.00 0.00 33.41 4.16
1172 1245 5.641709 TCATGAGAATCTAACGAGACACAC 58.358 41.667 0.00 0.00 33.41 3.82
1177 1250 8.687242 ACTACAAATCATGAGAATCTAACGAGA 58.313 33.333 0.09 0.00 34.92 4.04
1180 1255 8.323854 CACACTACAAATCATGAGAATCTAACG 58.676 37.037 0.09 0.00 34.92 3.18
1182 1257 7.280876 GCCACACTACAAATCATGAGAATCTAA 59.719 37.037 0.09 0.00 34.92 2.10
1186 1261 4.333649 CGCCACACTACAAATCATGAGAAT 59.666 41.667 0.09 0.00 0.00 2.40
1187 1262 3.684305 CGCCACACTACAAATCATGAGAA 59.316 43.478 0.09 0.00 0.00 2.87
1188 1263 3.261580 CGCCACACTACAAATCATGAGA 58.738 45.455 0.09 0.00 0.00 3.27
1189 1264 2.223112 GCGCCACACTACAAATCATGAG 60.223 50.000 0.09 0.00 0.00 2.90
1190 1265 1.737236 GCGCCACACTACAAATCATGA 59.263 47.619 0.00 0.00 0.00 3.07
1193 1268 1.155889 CAGCGCCACACTACAAATCA 58.844 50.000 2.29 0.00 0.00 2.57
1202 1277 1.668628 CCCAATTTAACAGCGCCACAC 60.669 52.381 2.29 0.00 0.00 3.82
1204 1279 0.601057 ACCCAATTTAACAGCGCCAC 59.399 50.000 2.29 0.00 0.00 5.01
1207 1282 2.595386 CTTCACCCAATTTAACAGCGC 58.405 47.619 0.00 0.00 0.00 5.92
1208 1283 2.228822 AGCTTCACCCAATTTAACAGCG 59.771 45.455 0.00 0.00 0.00 5.18
1211 1286 2.030363 CGCAGCTTCACCCAATTTAACA 60.030 45.455 0.00 0.00 0.00 2.41
1213 1288 1.543802 CCGCAGCTTCACCCAATTTAA 59.456 47.619 0.00 0.00 0.00 1.52
1216 1291 0.037590 TACCGCAGCTTCACCCAATT 59.962 50.000 0.00 0.00 0.00 2.32
1222 1297 2.202566 GTAATCCTACCGCAGCTTCAC 58.797 52.381 0.00 0.00 0.00 3.18
1255 1331 8.644374 TTTACTAGCATCCACAAGGTAAATTT 57.356 30.769 0.00 0.00 35.89 1.82
1256 1332 8.686334 CATTTACTAGCATCCACAAGGTAAATT 58.314 33.333 0.00 0.00 36.73 1.82
1257 1333 7.834181 ACATTTACTAGCATCCACAAGGTAAAT 59.166 33.333 0.00 0.00 38.24 1.40
1259 1335 6.717289 ACATTTACTAGCATCCACAAGGTAA 58.283 36.000 0.00 0.00 35.89 2.85
1264 1340 5.079689 TCGACATTTACTAGCATCCACAA 57.920 39.130 0.00 0.00 0.00 3.33
1307 1383 2.439507 ACCAGGAGATGCCGAATGTAAT 59.560 45.455 0.00 0.00 43.43 1.89
1309 1385 1.138859 CACCAGGAGATGCCGAATGTA 59.861 52.381 0.00 0.00 43.43 2.29
1310 1386 0.107508 CACCAGGAGATGCCGAATGT 60.108 55.000 0.00 0.00 43.43 2.71
1322 1398 1.279025 GCTACCCCATTCCACCAGGA 61.279 60.000 0.00 0.00 43.93 3.86
1324 1400 0.552848 ATGCTACCCCATTCCACCAG 59.447 55.000 0.00 0.00 0.00 4.00
1342 1418 8.956426 ACGAACAAATTAACTGTATTCATCCAT 58.044 29.630 0.00 0.00 0.00 3.41
1353 1429 7.201427 CCATTTGCCATACGAACAAATTAACTG 60.201 37.037 0.00 0.00 40.94 3.16
1360 1436 2.894126 ACCCATTTGCCATACGAACAAA 59.106 40.909 0.00 0.00 37.66 2.83
1364 1440 1.821753 CCAACCCATTTGCCATACGAA 59.178 47.619 0.00 0.00 33.34 3.85
1366 1442 0.459489 CCCAACCCATTTGCCATACG 59.541 55.000 0.00 0.00 33.34 3.06
1368 1444 0.326048 CCCCCAACCCATTTGCCATA 60.326 55.000 0.00 0.00 33.34 2.74
1372 1448 0.476338 AAAACCCCCAACCCATTTGC 59.524 50.000 0.00 0.00 33.34 3.68
1377 1453 3.416414 TTTCTAAAAACCCCCAACCCA 57.584 42.857 0.00 0.00 0.00 4.51
1386 1462 9.894783 GGAGATTAACTCAGTTTTCTAAAAACC 57.105 33.333 10.75 0.00 46.54 3.27
1396 1472 6.784031 ACAAGGATGGAGATTAACTCAGTTT 58.216 36.000 0.00 0.00 46.54 2.66
1403 1510 7.824779 ACTCAACTAACAAGGATGGAGATTAAC 59.175 37.037 0.00 0.00 0.00 2.01
1419 1526 8.027189 GGGATAAATGGTGAAAACTCAACTAAC 58.973 37.037 0.00 0.00 0.00 2.34
1422 1529 6.074648 TGGGATAAATGGTGAAAACTCAACT 58.925 36.000 0.00 0.00 0.00 3.16
1455 1564 4.926244 ACGATCTGACACTAACAGCATAG 58.074 43.478 0.00 0.00 35.61 2.23
1471 1580 6.348540 GCAAATTAACTGTTTGGAGACGATCT 60.349 38.462 0.00 0.00 37.12 2.75
1476 1585 5.587289 TGTGCAAATTAACTGTTTGGAGAC 58.413 37.500 0.00 0.00 37.53 3.36
1519 1628 1.000938 GGTGAAAAACTGGCAGCAGAG 60.001 52.381 15.89 0.00 0.00 3.35
1534 1643 8.160765 TGTTTCAATATTCCAGTAGAAGGTGAA 58.839 33.333 0.00 0.00 38.07 3.18
1579 1690 8.579850 TCAGCCTAAATTTGATACAAAGTCAT 57.420 30.769 0.00 0.00 0.00 3.06
1584 1696 9.249053 TGGTAATCAGCCTAAATTTGATACAAA 57.751 29.630 0.00 0.00 31.64 2.83
1586 1698 8.849168 CATGGTAATCAGCCTAAATTTGATACA 58.151 33.333 0.00 0.00 31.64 2.29
1587 1699 8.850156 ACATGGTAATCAGCCTAAATTTGATAC 58.150 33.333 0.00 0.00 31.64 2.24
1589 1701 7.685155 GCACATGGTAATCAGCCTAAATTTGAT 60.685 37.037 0.00 0.00 33.18 2.57
1591 1703 5.750067 GCACATGGTAATCAGCCTAAATTTG 59.250 40.000 0.00 0.00 0.00 2.32
1592 1704 5.658190 AGCACATGGTAATCAGCCTAAATTT 59.342 36.000 0.00 0.00 0.00 1.82
1595 1740 3.947196 CAGCACATGGTAATCAGCCTAAA 59.053 43.478 0.00 0.00 0.00 1.85
1605 1750 1.879380 GTTCTGTGCAGCACATGGTAA 59.121 47.619 28.37 16.60 43.71 2.85
1608 1753 0.240145 CTGTTCTGTGCAGCACATGG 59.760 55.000 28.37 17.72 43.71 3.66
1638 1784 7.660112 TCAACTAACATGAATGACAGCATTTT 58.340 30.769 0.00 0.00 44.47 1.82
1660 1806 7.701539 AGTGGCATTAGATAAACACAATCAA 57.298 32.000 0.00 0.00 0.00 2.57
1661 1807 8.046708 ACTAGTGGCATTAGATAAACACAATCA 58.953 33.333 22.06 0.00 0.00 2.57
1664 1810 7.390823 TCACTAGTGGCATTAGATAAACACAA 58.609 34.615 22.48 0.00 0.00 3.33
1667 1813 8.892723 CAAATCACTAGTGGCATTAGATAAACA 58.107 33.333 22.48 0.00 0.00 2.83
1668 1814 8.893727 ACAAATCACTAGTGGCATTAGATAAAC 58.106 33.333 22.48 0.00 0.00 2.01
1680 1826 4.036734 ACTGCAACAACAAATCACTAGTGG 59.963 41.667 22.48 9.03 0.00 4.00
1683 1829 4.024893 ACGACTGCAACAACAAATCACTAG 60.025 41.667 0.00 0.00 0.00 2.57
1689 1835 1.937223 TCGACGACTGCAACAACAAAT 59.063 42.857 0.00 0.00 0.00 2.32
1848 1994 4.566004 AGACAACAGTGTACGTTGCATAT 58.434 39.130 10.81 0.00 46.14 1.78
1856 2002 3.381045 ACACATGAGACAACAGTGTACG 58.619 45.455 0.00 0.00 41.21 3.67
1858 2004 6.645003 GTCAATACACATGAGACAACAGTGTA 59.355 38.462 0.00 0.00 46.03 2.90
1885 2031 6.854892 GTCACATGCTGCATAATGAGATTAAC 59.145 38.462 22.19 11.12 0.00 2.01
1886 2032 6.769341 AGTCACATGCTGCATAATGAGATTAA 59.231 34.615 22.19 4.60 0.00 1.40
2067 2213 1.704641 TAGCAGCATAGGGTGACGAT 58.295 50.000 11.30 0.00 45.29 3.73
2070 2216 1.071385 AGCATAGCAGCATAGGGTGAC 59.929 52.381 11.30 1.89 45.29 3.67
2127 2273 9.547279 AAAGTGGAACCTAAATATTTCAGGAAT 57.453 29.630 21.06 13.51 37.80 3.01
2128 2274 8.950007 AAAGTGGAACCTAAATATTTCAGGAA 57.050 30.769 21.06 0.66 37.80 3.36
2140 2286 3.857157 ACAGCTGAAAGTGGAACCTAA 57.143 42.857 23.35 0.00 37.80 2.69
2147 2293 6.115446 TGATAATAGGAACAGCTGAAAGTGG 58.885 40.000 23.35 0.00 35.30 4.00
2173 2319 3.453717 TCAGCCTAATGAGCAGAAGACAT 59.546 43.478 0.00 0.00 0.00 3.06
2191 2337 2.359848 TCATAGCATGGCAAACATCAGC 59.640 45.455 0.00 0.00 37.84 4.26
2205 2351 5.109500 TGTACCAACATTCCATCATAGCA 57.891 39.130 0.00 0.00 0.00 3.49
2258 2404 7.954248 CAGAAACAACTCTGATAAAACATCTCG 59.046 37.037 0.00 0.00 44.82 4.04
2269 2418 6.261826 CCTGAAAGAACAGAAACAACTCTGAT 59.738 38.462 7.57 0.00 40.35 2.90
2371 2521 1.958902 GAGCCCTGAGAGCAGACTGG 61.959 65.000 4.26 0.00 45.17 4.00
2440 2590 4.257731 TGCTTCCGCAAACACTATATTCA 58.742 39.130 0.00 0.00 44.62 2.57
2441 2591 4.875544 TGCTTCCGCAAACACTATATTC 57.124 40.909 0.00 0.00 44.62 1.75
2455 2605 2.564771 ACATGGACATATGTGCTTCCG 58.435 47.619 25.27 14.24 39.68 4.30
2485 2937 5.277011 CGAACATTATGGATAGGCATATGCG 60.277 44.000 21.04 5.53 43.26 4.73
2497 2949 4.154015 CAGCACAAGAACGAACATTATGGA 59.846 41.667 0.00 0.00 0.00 3.41
2508 2960 0.601046 TCCTCTGCAGCACAAGAACG 60.601 55.000 9.47 0.00 0.00 3.95
2642 3095 6.109359 ACATTCATAGAAACAGCAGGACTAC 58.891 40.000 0.00 0.00 0.00 2.73
2715 3168 6.586344 AGGATCCACACAACATTCATAGTAG 58.414 40.000 15.82 0.00 0.00 2.57
2730 3183 5.886609 TCTGAACCAAAAATAGGATCCACA 58.113 37.500 15.82 0.77 0.00 4.17
2731 3184 6.834168 TTCTGAACCAAAAATAGGATCCAC 57.166 37.500 15.82 0.00 0.00 4.02
2836 3313 3.228188 AGAAGGATCACAGCACCAAAA 57.772 42.857 0.00 0.00 0.00 2.44
2837 3314 2.957402 AGAAGGATCACAGCACCAAA 57.043 45.000 0.00 0.00 0.00 3.28
2838 3315 2.886523 CAAAGAAGGATCACAGCACCAA 59.113 45.455 0.00 0.00 0.00 3.67
2854 3331 7.453393 ACATGAAGGATGTTACTTCTCAAAGA 58.547 34.615 0.00 0.00 43.20 2.52
2881 3358 3.777478 TCGTTATAAGGAAGAAGCGTGG 58.223 45.455 5.41 0.00 0.00 4.94
2886 3363 6.910536 AATGCACTCGTTATAAGGAAGAAG 57.089 37.500 9.04 0.96 0.00 2.85
2891 3368 7.414436 GCAATAAAATGCACTCGTTATAAGGA 58.586 34.615 7.59 7.59 45.70 3.36
2892 3369 7.608974 GCAATAAAATGCACTCGTTATAAGG 57.391 36.000 0.00 0.00 45.70 2.69
2915 3392 6.206498 CACACTTTCTTGGGTAGTTTAAAGC 58.794 40.000 0.00 0.00 0.00 3.51
2946 3427 0.116342 TCAAGGGGAGTACAGAGGCA 59.884 55.000 0.00 0.00 0.00 4.75
2969 3450 1.666888 GCGCACTTGGAACCAAATGAG 60.667 52.381 17.30 14.94 35.47 2.90
2970 3451 0.313672 GCGCACTTGGAACCAAATGA 59.686 50.000 17.30 0.00 35.47 2.57
2984 3465 1.597663 GTATTACCACCATCAGCGCAC 59.402 52.381 11.47 0.00 0.00 5.34
2985 3466 1.804746 CGTATTACCACCATCAGCGCA 60.805 52.381 11.47 0.00 0.00 6.09
2986 3467 0.859232 CGTATTACCACCATCAGCGC 59.141 55.000 0.00 0.00 0.00 5.92
2987 3468 2.124903 GACGTATTACCACCATCAGCG 58.875 52.381 0.00 0.00 0.00 5.18
2988 3469 2.102588 AGGACGTATTACCACCATCAGC 59.897 50.000 0.00 0.00 0.00 4.26
2989 3470 4.099573 AGAAGGACGTATTACCACCATCAG 59.900 45.833 0.00 0.00 0.00 2.90
2990 3471 4.028131 AGAAGGACGTATTACCACCATCA 58.972 43.478 0.00 0.00 0.00 3.07
2998 3479 5.813672 TGCATTGGTAAGAAGGACGTATTAC 59.186 40.000 0.00 0.00 0.00 1.89
3006 3487 7.615365 ACTGAATAATTGCATTGGTAAGAAGGA 59.385 33.333 0.00 0.00 0.00 3.36
3087 3573 4.142337 TGCGGTCGATAGTCATGTTCTTAA 60.142 41.667 0.00 0.00 37.40 1.85
3104 3592 2.528743 CGCCTGATGTGATGCGGTC 61.529 63.158 0.00 0.00 43.08 4.79
3142 3630 2.543578 GGCATGCAACTGACGAGAA 58.456 52.632 21.36 0.00 0.00 2.87
3153 3642 1.228094 TTGTTGTCTCCGGCATGCA 60.228 52.632 21.36 0.00 0.00 3.96
3154 3643 0.955428 TCTTGTTGTCTCCGGCATGC 60.955 55.000 9.90 9.90 0.00 4.06
3174 3667 6.459923 GGTGAAGTCACTAAACTCAGATCTT 58.540 40.000 11.07 0.00 45.73 2.40
3175 3668 5.336055 CGGTGAAGTCACTAAACTCAGATCT 60.336 44.000 11.07 0.00 45.73 2.75
3176 3669 4.859798 CGGTGAAGTCACTAAACTCAGATC 59.140 45.833 11.07 0.00 45.73 2.75
3177 3670 4.810790 CGGTGAAGTCACTAAACTCAGAT 58.189 43.478 11.07 0.00 45.73 2.90
3178 3671 3.552273 GCGGTGAAGTCACTAAACTCAGA 60.552 47.826 11.07 0.00 45.73 3.27
3179 3672 2.731976 GCGGTGAAGTCACTAAACTCAG 59.268 50.000 11.07 0.00 45.73 3.35
3180 3673 2.101750 TGCGGTGAAGTCACTAAACTCA 59.898 45.455 11.07 0.00 45.73 3.41
3247 3742 1.605058 GACTTCTCGCCAGCCCAGTA 61.605 60.000 0.00 0.00 0.00 2.74
3248 3743 2.925170 ACTTCTCGCCAGCCCAGT 60.925 61.111 0.00 0.00 0.00 4.00
3250 3745 4.069232 CGACTTCTCGCCAGCCCA 62.069 66.667 0.00 0.00 31.91 5.36
3261 3759 0.946221 CTGACCTGTGTGGCGACTTC 60.946 60.000 0.00 0.00 40.22 3.01
3298 3796 1.035385 TTGCATCCCTCGTCGAGCTA 61.035 55.000 17.02 6.96 0.00 3.32
3316 3814 1.602237 CTCCGCCACCTGGTATGTT 59.398 57.895 0.00 0.00 37.57 2.71
3318 3816 2.505982 CCTCCGCCACCTGGTATG 59.494 66.667 0.00 0.00 37.57 2.39
3319 3817 2.768344 CCCTCCGCCACCTGGTAT 60.768 66.667 0.00 0.00 37.57 2.73
3320 3818 4.000620 TCCCTCCGCCACCTGGTA 62.001 66.667 0.00 0.00 37.57 3.25
3330 3831 4.796231 CGACGGCAAGTCCCTCCG 62.796 72.222 6.06 0.00 46.92 4.63
3363 3872 2.676121 CCGCCAAAGCATGTCCCA 60.676 61.111 0.00 0.00 39.83 4.37
3373 3912 3.772281 TATCGACGGCCCGCCAAA 61.772 61.111 1.23 0.00 35.37 3.28
3374 3913 4.517815 GTATCGACGGCCCGCCAA 62.518 66.667 1.23 0.00 35.37 4.52
3400 3950 2.641746 CCCCTGACCCTCTCCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
3444 3996 1.807886 GACACCTACGCATCGGACT 59.192 57.895 0.00 0.00 0.00 3.85
3498 4054 1.153823 CGAAAGGCATCGTCGACCT 60.154 57.895 10.58 0.00 38.01 3.85
3508 4065 4.357947 AGACGAGCGCGAAAGGCA 62.358 61.111 19.05 0.00 43.84 4.75
3513 4070 2.176055 GAGTGAGACGAGCGCGAA 59.824 61.111 19.05 0.00 41.64 4.70
3536 4094 0.551131 AGGTTGGGGAGAGAAGCCAT 60.551 55.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.