Multiple sequence alignment - TraesCS4B01G177100

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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 TraesCS4B01G177100 chr4B 100.000 3429 0 0 1 3429 387512660 387509232 0.000000e+00 6333
1 TraesCS4B01G177100 chr4B 89.444 360 22 9 1279 1635 307579998 307579652 1.130000e-119 440
2 TraesCS4B01G177100 chr4D 87.931 2668 138 79 431 2991 310112073 310109483 0.000000e+00 2974
3 TraesCS4B01G177100 chr4D 86.867 731 41 28 2731 3428 310108771 310108063 0.000000e+00 767
4 TraesCS4B01G177100 chr4D 83.871 465 32 25 2569 3016 384967751 384968189 1.480000e-108 403
5 TraesCS4B01G177100 chr4D 92.000 225 18 0 1 225 310112802 310112578 1.990000e-82 316
6 TraesCS4B01G177100 chr4D 80.788 203 4 10 2474 2673 310108941 310108771 3.590000e-25 126
7 TraesCS4B01G177100 chr4A 89.818 1758 75 42 742 2446 164625558 164627264 0.000000e+00 2159
8 TraesCS4B01G177100 chr4A 84.458 489 33 15 2872 3338 164627555 164628022 3.140000e-120 442
9 TraesCS4B01G177100 chr4A 85.556 270 37 2 1 269 463827936 463827668 7.250000e-72 281
10 TraesCS4B01G177100 chr4A 90.000 90 5 2 2731 2820 164627447 164627532 2.800000e-21 113
11 TraesCS4B01G177100 chr3A 75.070 1075 190 55 1151 2198 583926764 583927787 2.450000e-116 429
12 TraesCS4B01G177100 chr5D 82.759 464 38 25 2569 3014 152779803 152780242 3.230000e-100 375
13 TraesCS4B01G177100 chr3D 73.538 1077 209 57 1151 2205 442754804 442755826 1.180000e-89 340
14 TraesCS4B01G177100 chr3B 81.197 351 56 9 1 349 744081059 744081401 1.210000e-69 274
15 TraesCS4B01G177100 chr7A 83.813 278 40 4 1 276 464272928 464272654 3.390000e-65 259
16 TraesCS4B01G177100 chr7A 93.939 165 10 0 1135 1299 733838447 733838611 2.040000e-62 250
17 TraesCS4B01G177100 chr7A 93.939 165 10 0 1135 1299 733850948 733851112 2.040000e-62 250
18 TraesCS4B01G177100 chr7A 88.268 179 13 3 2846 3016 638526520 638526698 1.250000e-49 207
19 TraesCS4B01G177100 chr7B 86.547 223 30 0 1 223 417872690 417872468 2.640000e-61 246
20 TraesCS4B01G177100 chr7B 81.298 262 44 4 10 269 524713686 524713428 1.250000e-49 207
21 TraesCS4B01G177100 chr6A 82.772 267 42 4 11 276 175559190 175558927 5.720000e-58 235
22 TraesCS4B01G177100 chr2D 82.397 267 47 0 1 267 46206739 46207005 2.060000e-57 233
23 TraesCS4B01G177100 chr1A 84.454 238 33 4 17 253 96315100 96315334 7.400000e-57 231


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 TraesCS4B01G177100 chr4B 387509232 387512660 3428 True 6333.000000 6333 100.0000 1 3429 1 chr4B.!!$R2 3428
1 TraesCS4B01G177100 chr4D 310108063 310112802 4739 True 1045.750000 2974 86.8965 1 3428 4 chr4D.!!$R1 3427
2 TraesCS4B01G177100 chr4A 164625558 164628022 2464 False 904.666667 2159 88.0920 742 3338 3 chr4A.!!$F1 2596
3 TraesCS4B01G177100 chr3A 583926764 583927787 1023 False 429.000000 429 75.0700 1151 2198 1 chr3A.!!$F1 1047
4 TraesCS4B01G177100 chr3D 442754804 442755826 1022 False 340.000000 340 73.5380 1151 2205 1 chr3D.!!$F1 1054

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
231 232 0.035458 ACCCCGTCTTGCTCTTTGAG 59.965 55.0 0.0 0.0 0.0 3.02 F
902 1295 0.108585 CGGAGAGGAGAGGAGAGGAG 59.891 65.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1487 0.325933 TGGACTGCATTCTGGACTGG 59.674 55.0 3.88 0.0 0.00 4.00 R
2721 3219 0.034477 AAATTCGGGGCAGACGGATT 60.034 50.0 0.00 0.0 41.03 3.01 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 1.258445 CCACCGGCACTAGGAACTCT 61.258 60.000 0.00 0.00 41.75 3.24
25 26 0.108615 CACCGGCACTAGGAACTCTG 60.109 60.000 0.00 0.00 41.75 3.35
36 37 1.817099 GAACTCTGCATCCGCCTGG 60.817 63.158 0.00 0.00 37.32 4.45
62 63 1.137282 GATCTCCGGGAAGTTGAGGTC 59.863 57.143 0.00 0.00 0.00 3.85
79 80 4.778143 CCGTCTTTGGCCTCCCGG 62.778 72.222 3.32 4.85 0.00 5.73
135 136 2.035469 TCGGCGGTGGTGTAGGTA 59.965 61.111 7.21 0.00 0.00 3.08
148 149 1.278127 TGTAGGTACCAAGCCAGAAGC 59.722 52.381 15.94 0.00 44.25 3.86
197 198 2.006888 GAAATTGTCGGATGGCTTCGA 58.993 47.619 0.00 0.00 0.00 3.71
200 201 2.582498 GTCGGATGGCTTCGACCG 60.582 66.667 13.71 3.66 46.79 4.79
205 206 4.373116 ATGGCTTCGACCGCACGT 62.373 61.111 8.02 0.00 34.70 4.49
225 226 1.014564 CGAAGAACCCCGTCTTGCTC 61.015 60.000 0.00 0.00 37.98 4.26
226 227 0.321996 GAAGAACCCCGTCTTGCTCT 59.678 55.000 0.00 0.00 37.98 4.09
227 228 0.765510 AAGAACCCCGTCTTGCTCTT 59.234 50.000 0.00 0.00 36.48 2.85
228 229 0.765510 AGAACCCCGTCTTGCTCTTT 59.234 50.000 0.00 0.00 0.00 2.52
229 230 0.875059 GAACCCCGTCTTGCTCTTTG 59.125 55.000 0.00 0.00 0.00 2.77
230 231 0.472471 AACCCCGTCTTGCTCTTTGA 59.528 50.000 0.00 0.00 0.00 2.69
231 232 0.035458 ACCCCGTCTTGCTCTTTGAG 59.965 55.000 0.00 0.00 0.00 3.02
232 233 0.321671 CCCCGTCTTGCTCTTTGAGA 59.678 55.000 0.00 0.00 0.00 3.27
233 234 1.065854 CCCCGTCTTGCTCTTTGAGAT 60.066 52.381 0.00 0.00 0.00 2.75
234 235 2.275318 CCCGTCTTGCTCTTTGAGATC 58.725 52.381 0.00 0.00 0.00 2.75
235 236 2.093764 CCCGTCTTGCTCTTTGAGATCT 60.094 50.000 0.00 0.00 0.00 2.75
236 237 3.594134 CCGTCTTGCTCTTTGAGATCTT 58.406 45.455 0.00 0.00 0.00 2.40
237 238 3.616379 CCGTCTTGCTCTTTGAGATCTTC 59.384 47.826 0.00 0.00 0.00 2.87
238 239 4.493547 CGTCTTGCTCTTTGAGATCTTCT 58.506 43.478 0.00 0.00 0.00 2.85
239 240 4.928615 CGTCTTGCTCTTTGAGATCTTCTT 59.071 41.667 0.00 0.00 0.00 2.52
240 241 5.062058 CGTCTTGCTCTTTGAGATCTTCTTC 59.938 44.000 0.00 0.00 0.00 2.87
241 242 5.062058 GTCTTGCTCTTTGAGATCTTCTTCG 59.938 44.000 0.00 0.00 0.00 3.79
242 243 3.854666 TGCTCTTTGAGATCTTCTTCGG 58.145 45.455 0.00 0.00 0.00 4.30
243 244 2.607180 GCTCTTTGAGATCTTCTTCGGC 59.393 50.000 0.00 0.00 0.00 5.54
244 245 2.857152 CTCTTTGAGATCTTCTTCGGCG 59.143 50.000 0.00 0.00 0.00 6.46
245 246 2.492088 TCTTTGAGATCTTCTTCGGCGA 59.508 45.455 4.99 4.99 0.00 5.54
246 247 2.279582 TTGAGATCTTCTTCGGCGAC 57.720 50.000 10.16 0.00 0.00 5.19
247 248 1.173913 TGAGATCTTCTTCGGCGACA 58.826 50.000 10.16 0.00 0.00 4.35
248 249 1.751351 TGAGATCTTCTTCGGCGACAT 59.249 47.619 10.16 0.00 0.00 3.06
249 250 2.123342 GAGATCTTCTTCGGCGACATG 58.877 52.381 10.16 2.90 0.00 3.21
250 251 1.202463 AGATCTTCTTCGGCGACATGG 60.202 52.381 10.16 0.46 0.00 3.66
251 252 0.811616 ATCTTCTTCGGCGACATGGC 60.812 55.000 10.16 0.00 40.44 4.40
284 285 4.440127 GCAATGGGCAAGGTGGCG 62.440 66.667 0.00 0.00 44.78 5.69
285 286 3.762247 CAATGGGCAAGGTGGCGG 61.762 66.667 0.00 0.00 44.78 6.13
286 287 4.299796 AATGGGCAAGGTGGCGGT 62.300 61.111 0.00 0.00 44.78 5.68
425 779 2.124736 CGGCGATGGTGGTGGAAT 60.125 61.111 0.00 0.00 0.00 3.01
426 780 2.180204 CGGCGATGGTGGTGGAATC 61.180 63.158 0.00 0.00 0.00 2.52
427 781 2.180204 GGCGATGGTGGTGGAATCG 61.180 63.158 0.00 0.00 44.59 3.34
428 782 1.153449 GCGATGGTGGTGGAATCGA 60.153 57.895 8.35 0.00 44.57 3.59
429 783 0.742990 GCGATGGTGGTGGAATCGAA 60.743 55.000 8.35 0.00 44.57 3.71
436 790 3.861263 GTGGAATCGAACGGCGGC 61.861 66.667 13.24 0.00 41.33 6.53
437 791 4.380781 TGGAATCGAACGGCGGCA 62.381 61.111 13.24 0.00 41.33 5.69
454 808 2.024918 CAGCTGGCTGTCAAAACGT 58.975 52.632 13.76 0.00 39.10 3.99
465 819 3.281395 AAAACGTGGCGGAACCGG 61.281 61.111 15.01 0.00 43.94 5.28
487 850 4.626081 GGAGTGTGGCGGCAGTGT 62.626 66.667 13.91 0.00 0.00 3.55
498 861 2.281484 GCAGTGTGGCGGGAAGAA 60.281 61.111 0.00 0.00 0.00 2.52
512 877 2.095461 GGAAGAAGAAGATGGGGTTGC 58.905 52.381 0.00 0.00 0.00 4.17
524 889 2.052104 GGGTTGCGGGAGGAAATGG 61.052 63.158 0.00 0.00 43.46 3.16
529 894 2.112815 GCGGGAGGAAATGGAACGG 61.113 63.158 0.00 0.00 0.00 4.44
568 933 1.199097 CGGCTGGCGTTTTTACATCTT 59.801 47.619 16.07 0.00 0.00 2.40
574 939 3.185594 TGGCGTTTTTACATCTTCAGTCG 59.814 43.478 0.00 0.00 0.00 4.18
587 952 2.542020 TCAGTCGGTGAAGATGCAAA 57.458 45.000 0.00 0.00 29.64 3.68
588 953 3.057969 TCAGTCGGTGAAGATGCAAAT 57.942 42.857 0.00 0.00 29.64 2.32
589 954 3.411446 TCAGTCGGTGAAGATGCAAATT 58.589 40.909 0.00 0.00 29.64 1.82
590 955 3.820467 TCAGTCGGTGAAGATGCAAATTT 59.180 39.130 0.00 0.00 29.64 1.82
591 956 5.000591 TCAGTCGGTGAAGATGCAAATTTA 58.999 37.500 0.00 0.00 29.64 1.40
594 959 5.415701 AGTCGGTGAAGATGCAAATTTACAT 59.584 36.000 3.46 3.46 0.00 2.29
595 960 5.739161 GTCGGTGAAGATGCAAATTTACATC 59.261 40.000 19.65 19.65 42.45 3.06
597 962 5.512788 CGGTGAAGATGCAAATTTACATCAC 59.487 40.000 26.03 19.06 44.16 3.06
602 973 4.943705 AGATGCAAATTTACATCACGACCT 59.056 37.500 26.03 8.03 44.16 3.85
614 985 5.734720 ACATCACGACCTGAAGATGTAAAT 58.265 37.500 5.21 0.00 46.54 1.40
615 986 6.173339 ACATCACGACCTGAAGATGTAAATT 58.827 36.000 5.21 0.00 46.54 1.82
616 987 6.655003 ACATCACGACCTGAAGATGTAAATTT 59.345 34.615 5.21 0.00 46.54 1.82
617 988 6.721571 TCACGACCTGAAGATGTAAATTTC 57.278 37.500 0.00 0.00 0.00 2.17
618 989 6.464222 TCACGACCTGAAGATGTAAATTTCT 58.536 36.000 0.00 0.00 0.00 2.52
641 1012 4.880886 TTTTGCATCTACATCATCCGTG 57.119 40.909 0.00 0.00 0.00 4.94
643 1014 1.070601 TGCATCTACATCATCCGTGGG 59.929 52.381 0.00 0.00 0.00 4.61
644 1015 1.609061 GCATCTACATCATCCGTGGGG 60.609 57.143 0.00 0.00 0.00 4.96
645 1016 1.694150 CATCTACATCATCCGTGGGGT 59.306 52.381 0.00 0.00 33.83 4.95
646 1017 1.874129 TCTACATCATCCGTGGGGTT 58.126 50.000 0.00 0.00 33.83 4.11
647 1018 2.193127 TCTACATCATCCGTGGGGTTT 58.807 47.619 0.00 0.00 33.83 3.27
648 1019 2.574369 TCTACATCATCCGTGGGGTTTT 59.426 45.455 0.00 0.00 33.83 2.43
651 1022 0.701731 ATCATCCGTGGGGTTTTGGA 59.298 50.000 0.00 0.00 34.45 3.53
652 1023 0.250989 TCATCCGTGGGGTTTTGGAC 60.251 55.000 0.00 0.00 32.33 4.02
670 1041 3.465990 CCTCGATGGTGTTGCATCT 57.534 52.632 0.00 0.00 0.00 2.90
671 1042 2.602257 CCTCGATGGTGTTGCATCTA 57.398 50.000 0.00 0.00 0.00 1.98
672 1043 2.205074 CCTCGATGGTGTTGCATCTAC 58.795 52.381 0.00 0.00 0.00 2.59
673 1044 1.854743 CTCGATGGTGTTGCATCTACG 59.145 52.381 0.00 0.00 0.00 3.51
674 1045 1.203758 TCGATGGTGTTGCATCTACGT 59.796 47.619 0.00 0.00 0.00 3.57
675 1046 1.588404 CGATGGTGTTGCATCTACGTC 59.412 52.381 0.00 0.00 0.00 4.34
678 1049 2.412870 TGGTGTTGCATCTACGTCTTG 58.587 47.619 0.00 0.00 0.00 3.02
680 1051 2.157668 GGTGTTGCATCTACGTCTTGTG 59.842 50.000 0.00 0.00 0.00 3.33
703 1083 6.250951 GTGTAAGTAGTGCTAAGAAACGCTAG 59.749 42.308 0.00 0.00 29.96 3.42
719 1099 1.065701 GCTAGAGGCGACGAAGATGAA 59.934 52.381 0.00 0.00 0.00 2.57
723 1103 4.592485 AGAGGCGACGAAGATGAATAAT 57.408 40.909 0.00 0.00 0.00 1.28
724 1104 5.707242 AGAGGCGACGAAGATGAATAATA 57.293 39.130 0.00 0.00 0.00 0.98
725 1105 6.085555 AGAGGCGACGAAGATGAATAATAA 57.914 37.500 0.00 0.00 0.00 1.40
726 1106 6.513180 AGAGGCGACGAAGATGAATAATAAA 58.487 36.000 0.00 0.00 0.00 1.40
727 1107 7.155328 AGAGGCGACGAAGATGAATAATAAAT 58.845 34.615 0.00 0.00 0.00 1.40
728 1108 8.304596 AGAGGCGACGAAGATGAATAATAAATA 58.695 33.333 0.00 0.00 0.00 1.40
729 1109 8.827177 AGGCGACGAAGATGAATAATAAATAA 57.173 30.769 0.00 0.00 0.00 1.40
730 1110 9.268268 AGGCGACGAAGATGAATAATAAATAAA 57.732 29.630 0.00 0.00 0.00 1.40
731 1111 9.314501 GGCGACGAAGATGAATAATAAATAAAC 57.685 33.333 0.00 0.00 0.00 2.01
802 1187 8.353684 GGGAGGTAAAGAAAAGAAGAAGAAAAG 58.646 37.037 0.00 0.00 0.00 2.27
883 1276 3.424962 GCGAGTCATGGAGTTAAACAAGC 60.425 47.826 0.00 0.00 0.00 4.01
891 1284 2.028385 GGAGTTAAACAAGCGGAGAGGA 60.028 50.000 0.00 0.00 0.00 3.71
892 1285 3.254892 GAGTTAAACAAGCGGAGAGGAG 58.745 50.000 0.00 0.00 0.00 3.69
893 1286 2.897969 AGTTAAACAAGCGGAGAGGAGA 59.102 45.455 0.00 0.00 0.00 3.71
895 1288 0.610687 AAACAAGCGGAGAGGAGAGG 59.389 55.000 0.00 0.00 0.00 3.69
896 1289 0.251832 AACAAGCGGAGAGGAGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
897 1290 0.682855 ACAAGCGGAGAGGAGAGGAG 60.683 60.000 0.00 0.00 0.00 3.69
898 1291 0.395036 CAAGCGGAGAGGAGAGGAGA 60.395 60.000 0.00 0.00 0.00 3.71
900 1293 1.528309 GCGGAGAGGAGAGGAGAGG 60.528 68.421 0.00 0.00 0.00 3.69
901 1294 1.990160 GCGGAGAGGAGAGGAGAGGA 61.990 65.000 0.00 0.00 0.00 3.71
902 1295 0.108585 CGGAGAGGAGAGGAGAGGAG 59.891 65.000 0.00 0.00 0.00 3.69
903 1296 1.518367 GGAGAGGAGAGGAGAGGAGA 58.482 60.000 0.00 0.00 0.00 3.71
904 1297 1.421646 GGAGAGGAGAGGAGAGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
905 1298 1.421646 GAGAGGAGAGGAGAGGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
906 1299 0.478507 GAGGAGAGGAGAGGAGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
907 1300 0.254107 AGGAGAGGAGAGGAGAGGGT 60.254 60.000 0.00 0.00 0.00 4.34
908 1301 0.185175 GGAGAGGAGAGGAGAGGGTC 59.815 65.000 0.00 0.00 0.00 4.46
974 1370 0.539051 CTCACCATCACCACCCTCTC 59.461 60.000 0.00 0.00 0.00 3.20
987 1383 1.007842 ACCCTCTCCTTCCTCTTCCTC 59.992 57.143 0.00 0.00 0.00 3.71
1004 1403 1.196012 CTCCAACCTCACCTACTCCC 58.804 60.000 0.00 0.00 0.00 4.30
1005 1404 0.790993 TCCAACCTCACCTACTCCCT 59.209 55.000 0.00 0.00 0.00 4.20
1006 1405 0.905357 CCAACCTCACCTACTCCCTG 59.095 60.000 0.00 0.00 0.00 4.45
1073 1487 2.125350 CGGAGCAGAGCAACCCTC 60.125 66.667 0.00 0.00 41.07 4.30
1074 1488 2.270527 GGAGCAGAGCAACCCTCC 59.729 66.667 0.00 0.00 41.74 4.30
1075 1489 2.596851 GGAGCAGAGCAACCCTCCA 61.597 63.158 8.17 0.00 42.66 3.86
1076 1490 1.078567 GAGCAGAGCAACCCTCCAG 60.079 63.158 0.00 0.00 41.74 3.86
1681 2125 4.773117 GGACGACCACGACGCCTC 62.773 72.222 0.00 0.00 42.66 4.70
1730 2174 1.464376 ATGGGAGCATACCGGAGTCG 61.464 60.000 9.46 0.00 0.00 4.18
2210 2660 2.739932 CGGCTTCTAATCCTGTGACCTG 60.740 54.545 0.00 0.00 0.00 4.00
2211 2661 2.501723 GGCTTCTAATCCTGTGACCTGA 59.498 50.000 0.00 0.00 0.00 3.86
2213 2663 3.680196 GCTTCTAATCCTGTGACCTGACC 60.680 52.174 0.00 0.00 0.00 4.02
2215 2665 3.791320 TCTAATCCTGTGACCTGACCTT 58.209 45.455 0.00 0.00 0.00 3.50
2334 2805 2.967599 AACAGCAGCGATCATGTCTA 57.032 45.000 0.00 0.00 0.00 2.59
2335 2806 2.505628 ACAGCAGCGATCATGTCTAG 57.494 50.000 0.00 0.00 0.00 2.43
2337 2808 2.223688 ACAGCAGCGATCATGTCTAGTC 60.224 50.000 0.00 0.00 0.00 2.59
2338 2809 2.027385 AGCAGCGATCATGTCTAGTCA 58.973 47.619 0.00 0.00 0.00 3.41
2341 2819 3.917380 GCAGCGATCATGTCTAGTCATAC 59.083 47.826 2.02 0.00 0.00 2.39
2350 2828 6.739112 TCATGTCTAGTCATACCTCATTTCG 58.261 40.000 2.02 0.00 0.00 3.46
2364 2842 1.732259 CATTTCGTCGCTACTGCCTTT 59.268 47.619 0.00 0.00 35.36 3.11
2392 2890 0.530288 TCGTTGCGGTGATCTCATCA 59.470 50.000 0.00 0.00 36.84 3.07
2446 2944 8.777413 GTGATACGACATTACCACATACTACTA 58.223 37.037 0.00 0.00 0.00 1.82
2447 2945 8.777413 TGATACGACATTACCACATACTACTAC 58.223 37.037 0.00 0.00 0.00 2.73
2448 2946 8.681486 ATACGACATTACCACATACTACTACA 57.319 34.615 0.00 0.00 0.00 2.74
2449 2947 7.024340 ACGACATTACCACATACTACTACAG 57.976 40.000 0.00 0.00 0.00 2.74
2450 2948 6.600822 ACGACATTACCACATACTACTACAGT 59.399 38.462 0.00 0.00 41.62 3.55
2451 2949 7.770433 ACGACATTACCACATACTACTACAGTA 59.230 37.037 0.00 0.00 43.89 2.74
2452 2950 8.066595 CGACATTACCACATACTACTACAGTAC 58.933 40.741 0.00 0.00 42.56 2.73
2453 2951 8.812513 ACATTACCACATACTACTACAGTACA 57.187 34.615 0.00 0.00 42.56 2.90
2454 2952 9.417561 ACATTACCACATACTACTACAGTACAT 57.582 33.333 0.00 0.00 42.56 2.29
2455 2953 9.894783 CATTACCACATACTACTACAGTACATC 57.105 37.037 0.00 0.00 42.56 3.06
2456 2954 9.636789 ATTACCACATACTACTACAGTACATCA 57.363 33.333 0.00 0.00 42.56 3.07
2457 2955 9.636789 TTACCACATACTACTACAGTACATCAT 57.363 33.333 0.00 0.00 42.56 2.45
2458 2956 8.167605 ACCACATACTACTACAGTACATCATC 57.832 38.462 0.00 0.00 42.56 2.92
2566 3064 4.895297 AGCTTTCCTCCTCAACATGAAAAA 59.105 37.500 0.00 0.00 0.00 1.94
2570 3068 5.310409 TCCTCCTCAACATGAAAAAGAGT 57.690 39.130 0.00 0.00 0.00 3.24
2601 3099 8.251026 TGCATAGATAGATATTAAACCGAGGTG 58.749 37.037 0.00 0.00 0.00 4.00
2612 3110 2.616969 CCGAGGTGGTGTGAGTTTG 58.383 57.895 0.00 0.00 0.00 2.93
2616 3114 2.213499 GAGGTGGTGTGAGTTTGTGAG 58.787 52.381 0.00 0.00 0.00 3.51
2625 3123 2.945668 GTGAGTTTGTGAGCAGGAAACT 59.054 45.455 0.00 0.00 41.51 2.66
2635 3133 5.061179 GTGAGCAGGAAACTTTAACCACTA 58.939 41.667 0.00 0.00 40.21 2.74
2646 3144 2.762535 TAACCACTAGTGCTTCAGGC 57.237 50.000 17.86 0.00 42.22 4.85
2647 3145 0.320771 AACCACTAGTGCTTCAGGCG 60.321 55.000 17.86 3.74 45.43 5.52
2648 3146 1.448540 CCACTAGTGCTTCAGGCGG 60.449 63.158 17.86 0.00 45.43 6.13
2649 3147 1.591703 CACTAGTGCTTCAGGCGGA 59.408 57.895 10.54 0.00 45.43 5.54
2650 3148 0.176680 CACTAGTGCTTCAGGCGGAT 59.823 55.000 10.54 0.00 45.43 4.18
2651 3149 1.409064 CACTAGTGCTTCAGGCGGATA 59.591 52.381 10.54 0.00 45.43 2.59
2655 3153 4.528596 ACTAGTGCTTCAGGCGGATAATAT 59.471 41.667 0.00 0.00 45.43 1.28
2685 3183 2.676748 TGGTGTGGGAATGCTTTCTTT 58.323 42.857 11.68 0.00 32.16 2.52
2686 3184 2.627699 TGGTGTGGGAATGCTTTCTTTC 59.372 45.455 11.68 3.87 32.16 2.62
2687 3185 2.893489 GGTGTGGGAATGCTTTCTTTCT 59.107 45.455 11.68 0.00 32.16 2.52
2688 3186 3.321968 GGTGTGGGAATGCTTTCTTTCTT 59.678 43.478 11.68 0.00 32.16 2.52
2689 3187 4.550422 GTGTGGGAATGCTTTCTTTCTTC 58.450 43.478 11.68 0.00 32.16 2.87
2690 3188 4.279420 GTGTGGGAATGCTTTCTTTCTTCT 59.721 41.667 11.68 0.00 32.16 2.85
2691 3189 4.895297 TGTGGGAATGCTTTCTTTCTTCTT 59.105 37.500 11.68 0.00 32.16 2.52
2721 3219 7.333323 TGAAATGAGAGATTTAGCTCACATCA 58.667 34.615 8.07 0.00 42.68 3.07
2764 3264 5.547666 TGCATTTGCTCCTATCCTAATCCTA 59.452 40.000 3.94 0.00 42.66 2.94
2765 3265 6.216251 TGCATTTGCTCCTATCCTAATCCTAT 59.784 38.462 3.94 0.00 42.66 2.57
2785 3285 9.927081 ATCCTATTTGTCAAGAATGTTAATCCT 57.073 29.630 0.00 0.00 0.00 3.24
2837 4358 3.887716 CCTTGCTTGATTCAATCCCCTAG 59.112 47.826 0.00 0.00 0.00 3.02
2838 4359 4.530875 CTTGCTTGATTCAATCCCCTAGT 58.469 43.478 0.00 0.00 0.00 2.57
2839 4360 5.397899 CCTTGCTTGATTCAATCCCCTAGTA 60.398 44.000 0.00 0.00 0.00 1.82
2840 4361 5.912149 TGCTTGATTCAATCCCCTAGTAT 57.088 39.130 0.00 0.00 0.00 2.12
2841 4362 6.266131 TGCTTGATTCAATCCCCTAGTATT 57.734 37.500 0.00 0.00 0.00 1.89
2842 4363 6.064060 TGCTTGATTCAATCCCCTAGTATTG 58.936 40.000 0.00 4.22 34.96 1.90
2853 4374 8.768397 CAATCCCCTAGTATTGCTACCATATAA 58.232 37.037 0.00 0.00 0.00 0.98
2856 4377 6.992715 CCCCTAGTATTGCTACCATATAATGC 59.007 42.308 0.00 0.00 0.00 3.56
2885 4406 5.221048 CCAGCTTTGCAGTTACTTAGTGTTT 60.221 40.000 0.00 0.00 0.00 2.83
2901 4422 2.817844 GTGTTTGGGATAAGCTTTCCGT 59.182 45.455 3.20 0.00 33.82 4.69
2908 4429 2.032178 GGATAAGCTTTCCGTGATGCAC 59.968 50.000 3.20 0.00 0.00 4.57
2909 4430 2.472695 TAAGCTTTCCGTGATGCACT 57.527 45.000 3.20 0.00 31.34 4.40
2944 4475 5.068198 ACAGTATTTCGGATCGGCTTACTTA 59.932 40.000 0.00 0.00 0.00 2.24
2991 4522 0.790814 GCACGCCAGACTAGACAAAC 59.209 55.000 0.00 0.00 0.00 2.93
3018 4555 3.999001 TCCGGAGTGCATATACTACTACG 59.001 47.826 0.00 9.41 45.77 3.51
3028 4565 7.844653 GTGCATATACTACTACGTTTTCTTTGC 59.155 37.037 0.00 0.00 0.00 3.68
3035 4572 5.074430 ACTACGTTTTCTTTGCGTTGTAG 57.926 39.130 0.00 0.00 41.11 2.74
3038 4575 4.825400 ACGTTTTCTTTGCGTTGTAGTAC 58.175 39.130 0.00 0.00 35.11 2.73
3039 4576 3.890246 CGTTTTCTTTGCGTTGTAGTACG 59.110 43.478 0.00 0.00 44.09 3.67
3040 4577 4.317278 CGTTTTCTTTGCGTTGTAGTACGA 60.317 41.667 0.00 0.00 43.99 3.43
3041 4578 4.697300 TTTCTTTGCGTTGTAGTACGAC 57.303 40.909 10.28 10.28 43.99 4.34
3061 4598 5.220381 CGACTAGTAATGTAATCCACGCAT 58.780 41.667 0.00 0.00 0.00 4.73
3113 4650 3.132925 ACATTGTCAAAATGCTTGGTGC 58.867 40.909 0.00 0.00 43.25 5.01
3138 4675 3.915575 GCAGTTGAGATGCCCTGG 58.084 61.111 0.00 0.00 37.73 4.45
3154 4697 5.132502 TGCCCTGGTCTTTATGTGATAATG 58.867 41.667 0.00 0.00 0.00 1.90
3155 4698 4.022849 GCCCTGGTCTTTATGTGATAATGC 60.023 45.833 0.00 0.00 0.00 3.56
3212 4758 7.281841 TGTGTAAAGATGGAGATAATGCATGA 58.718 34.615 0.00 0.00 40.55 3.07
3228 4775 2.980568 CATGATTTGCTGGGTTTGCAT 58.019 42.857 0.00 0.00 40.34 3.96
3281 4828 0.885879 TGTGTCGCGATTACAGAGGT 59.114 50.000 20.61 0.00 0.00 3.85
3350 4898 2.485659 TCCATGAGGGAGAGCTTGAAT 58.514 47.619 0.00 0.00 42.15 2.57
3393 4941 2.371841 ACCAGTGCTAGTGATTGTTGGA 59.628 45.455 0.00 0.00 0.00 3.53
3395 4943 3.624861 CCAGTGCTAGTGATTGTTGGATC 59.375 47.826 0.00 0.00 0.00 3.36
3396 4944 4.256110 CAGTGCTAGTGATTGTTGGATCA 58.744 43.478 0.00 0.00 33.81 2.92
3407 4963 1.887854 TGTTGGATCAGCATTGTGGTG 59.112 47.619 2.91 2.91 46.40 4.17
3415 4973 6.262944 TGGATCAGCATTGTGGTGTATATTTC 59.737 38.462 8.74 0.19 45.34 2.17
3428 4986 5.403466 GGTGTATATTTCGCGTTAGGTTAGG 59.597 44.000 5.77 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.889530 GCAGAGTTCCTAGTGCCGGT 61.890 60.000 1.90 0.00 0.00 5.28
24 25 3.785859 GAGACCCAGGCGGATGCA 61.786 66.667 0.00 0.00 45.35 3.96
25 26 4.899239 CGAGACCCAGGCGGATGC 62.899 72.222 0.00 0.00 41.71 3.91
36 37 0.752376 ACTTCCCGGAGATCGAGACC 60.752 60.000 0.73 0.00 42.43 3.85
85 86 2.754648 CCTATGACGTGGCAGTGTG 58.245 57.895 0.00 0.00 0.00 3.82
135 136 2.281761 CACCGCTTCTGGCTTGGT 60.282 61.111 0.00 0.00 39.13 3.67
138 139 2.357517 CGTCACCGCTTCTGGCTT 60.358 61.111 0.00 0.00 39.13 4.35
148 149 1.929806 TTCTCCGATGTCCGTCACCG 61.930 60.000 0.00 0.00 36.31 4.94
151 152 0.809385 GAGTTCTCCGATGTCCGTCA 59.191 55.000 0.00 0.00 36.31 4.35
156 157 1.936547 GGCATTGAGTTCTCCGATGTC 59.063 52.381 11.80 7.92 0.00 3.06
157 158 1.740380 CGGCATTGAGTTCTCCGATGT 60.740 52.381 11.80 0.00 42.43 3.06
159 160 0.824109 TCGGCATTGAGTTCTCCGAT 59.176 50.000 0.00 0.00 43.42 4.18
186 187 3.195698 GTGCGGTCGAAGCCATCC 61.196 66.667 11.01 0.00 0.00 3.51
197 198 2.355481 GGTTCTTCGACGTGCGGT 60.355 61.111 0.00 0.00 41.33 5.68
200 201 3.110178 CGGGGTTCTTCGACGTGC 61.110 66.667 0.00 0.00 0.00 5.34
205 206 1.005394 GCAAGACGGGGTTCTTCGA 60.005 57.895 0.00 0.00 33.31 3.71
225 226 2.600867 GTCGCCGAAGAAGATCTCAAAG 59.399 50.000 0.00 0.00 0.00 2.77
226 227 2.029380 TGTCGCCGAAGAAGATCTCAAA 60.029 45.455 0.00 0.00 0.00 2.69
227 228 1.544246 TGTCGCCGAAGAAGATCTCAA 59.456 47.619 0.00 0.00 0.00 3.02
228 229 1.173913 TGTCGCCGAAGAAGATCTCA 58.826 50.000 0.00 0.00 0.00 3.27
229 230 2.123342 CATGTCGCCGAAGAAGATCTC 58.877 52.381 0.00 0.00 0.00 2.75
230 231 1.202463 CCATGTCGCCGAAGAAGATCT 60.202 52.381 0.00 0.00 0.00 2.75
231 232 1.212616 CCATGTCGCCGAAGAAGATC 58.787 55.000 0.00 0.00 0.00 2.75
232 233 0.811616 GCCATGTCGCCGAAGAAGAT 60.812 55.000 0.00 0.00 0.00 2.40
233 234 1.447838 GCCATGTCGCCGAAGAAGA 60.448 57.895 0.00 0.00 0.00 2.87
234 235 2.802667 CGCCATGTCGCCGAAGAAG 61.803 63.158 0.00 0.00 0.00 2.85
235 236 2.813474 CGCCATGTCGCCGAAGAA 60.813 61.111 0.00 0.00 0.00 2.52
236 237 4.812476 CCGCCATGTCGCCGAAGA 62.812 66.667 0.00 0.00 0.00 2.87
261 262 4.440127 CTTGCCCATTGCCGCCAC 62.440 66.667 0.00 0.00 40.16 5.01
264 265 4.440127 CACCTTGCCCATTGCCGC 62.440 66.667 0.00 0.00 40.16 6.53
265 266 3.762247 CCACCTTGCCCATTGCCG 61.762 66.667 0.00 0.00 40.16 5.69
266 267 4.086547 GCCACCTTGCCCATTGCC 62.087 66.667 0.00 0.00 40.16 4.52
267 268 4.440127 CGCCACCTTGCCCATTGC 62.440 66.667 0.00 0.00 41.77 3.56
268 269 3.762247 CCGCCACCTTGCCCATTG 61.762 66.667 0.00 0.00 0.00 2.82
269 270 4.299796 ACCGCCACCTTGCCCATT 62.300 61.111 0.00 0.00 0.00 3.16
367 721 2.823829 GATTCCACCATCGCACCGC 61.824 63.158 0.00 0.00 0.00 5.68
368 722 2.525248 CGATTCCACCATCGCACCG 61.525 63.158 0.00 0.00 39.69 4.94
369 723 1.153449 TCGATTCCACCATCGCACC 60.153 57.895 0.00 0.00 44.80 5.01
370 724 1.766143 GCTCGATTCCACCATCGCAC 61.766 60.000 0.00 0.00 44.80 5.34
371 725 1.521457 GCTCGATTCCACCATCGCA 60.521 57.895 0.00 0.00 44.80 5.10
375 729 2.203070 GCCGCTCGATTCCACCAT 60.203 61.111 0.00 0.00 0.00 3.55
408 762 2.124736 ATTCCACCACCATCGCCG 60.125 61.111 0.00 0.00 0.00 6.46
409 763 2.180204 CGATTCCACCACCATCGCC 61.180 63.158 0.00 0.00 33.94 5.54
410 764 0.742990 TTCGATTCCACCACCATCGC 60.743 55.000 0.00 0.00 39.73 4.58
411 765 1.006832 GTTCGATTCCACCACCATCG 58.993 55.000 0.00 0.00 40.98 3.84
412 766 1.006832 CGTTCGATTCCACCACCATC 58.993 55.000 0.00 0.00 0.00 3.51
413 767 0.392461 CCGTTCGATTCCACCACCAT 60.392 55.000 0.00 0.00 0.00 3.55
414 768 1.004320 CCGTTCGATTCCACCACCA 60.004 57.895 0.00 0.00 0.00 4.17
415 769 2.396157 GCCGTTCGATTCCACCACC 61.396 63.158 0.00 0.00 0.00 4.61
416 770 2.736682 CGCCGTTCGATTCCACCAC 61.737 63.158 0.00 0.00 41.67 4.16
417 771 2.433491 CGCCGTTCGATTCCACCA 60.433 61.111 0.00 0.00 41.67 4.17
418 772 3.192922 CCGCCGTTCGATTCCACC 61.193 66.667 0.00 0.00 41.67 4.61
419 773 3.861263 GCCGCCGTTCGATTCCAC 61.861 66.667 0.00 0.00 41.67 4.02
420 774 4.380781 TGCCGCCGTTCGATTCCA 62.381 61.111 0.00 0.00 41.67 3.53
421 775 3.564027 CTGCCGCCGTTCGATTCC 61.564 66.667 0.00 0.00 41.67 3.01
422 776 4.223964 GCTGCCGCCGTTCGATTC 62.224 66.667 0.00 0.00 41.67 2.52
423 777 4.760047 AGCTGCCGCCGTTCGATT 62.760 61.111 0.00 0.00 41.67 3.34
437 791 1.447317 CCACGTTTTGACAGCCAGCT 61.447 55.000 0.00 0.00 0.00 4.24
444 798 1.716826 GGTTCCGCCACGTTTTGACA 61.717 55.000 0.00 0.00 37.17 3.58
448 802 3.281395 CCGGTTCCGCCACGTTTT 61.281 61.111 5.66 0.00 36.97 2.43
483 846 0.035458 CTTCTTCTTCCCGCCACACT 59.965 55.000 0.00 0.00 0.00 3.55
484 847 0.034896 TCTTCTTCTTCCCGCCACAC 59.965 55.000 0.00 0.00 0.00 3.82
487 850 0.253044 CCATCTTCTTCTTCCCGCCA 59.747 55.000 0.00 0.00 0.00 5.69
493 856 1.740025 CGCAACCCCATCTTCTTCTTC 59.260 52.381 0.00 0.00 0.00 2.87
494 857 1.614317 CCGCAACCCCATCTTCTTCTT 60.614 52.381 0.00 0.00 0.00 2.52
495 858 0.035056 CCGCAACCCCATCTTCTTCT 60.035 55.000 0.00 0.00 0.00 2.85
498 861 1.915078 CTCCCGCAACCCCATCTTCT 61.915 60.000 0.00 0.00 0.00 2.85
512 877 2.112815 GCCGTTCCATTTCCTCCCG 61.113 63.158 0.00 0.00 0.00 5.14
548 913 0.802494 AGATGTAAAAACGCCAGCCG 59.198 50.000 0.00 0.00 44.21 5.52
556 921 5.917541 TCACCGACTGAAGATGTAAAAAC 57.082 39.130 0.00 0.00 0.00 2.43
568 933 2.542020 TTTGCATCTTCACCGACTGA 57.458 45.000 0.00 0.00 0.00 3.41
574 939 5.512788 CGTGATGTAAATTTGCATCTTCACC 59.487 40.000 34.37 21.56 46.32 4.02
582 947 4.068599 TCAGGTCGTGATGTAAATTTGCA 58.931 39.130 11.51 11.51 0.00 4.08
587 952 5.734720 ACATCTTCAGGTCGTGATGTAAAT 58.265 37.500 5.77 0.00 44.97 1.40
588 953 5.147330 ACATCTTCAGGTCGTGATGTAAA 57.853 39.130 5.77 0.00 44.97 2.01
589 954 4.801330 ACATCTTCAGGTCGTGATGTAA 57.199 40.909 5.77 0.00 44.97 2.41
590 955 5.907866 TTACATCTTCAGGTCGTGATGTA 57.092 39.130 9.67 9.67 44.97 2.29
594 959 6.464222 AGAAATTTACATCTTCAGGTCGTGA 58.536 36.000 0.00 0.00 0.00 4.35
595 960 6.727824 AGAAATTTACATCTTCAGGTCGTG 57.272 37.500 0.00 0.00 0.00 4.35
634 1005 1.248101 GGTCCAAAACCCCACGGATG 61.248 60.000 0.00 0.00 42.85 3.51
652 1023 2.205074 GTAGATGCAACACCATCGAGG 58.795 52.381 0.00 0.00 44.86 4.63
653 1024 1.854743 CGTAGATGCAACACCATCGAG 59.145 52.381 0.00 0.00 44.86 4.04
655 1026 1.588404 GACGTAGATGCAACACCATCG 59.412 52.381 0.00 0.00 44.86 3.84
657 1028 3.002791 CAAGACGTAGATGCAACACCAT 58.997 45.455 0.00 0.00 0.00 3.55
658 1029 2.224185 ACAAGACGTAGATGCAACACCA 60.224 45.455 0.00 0.00 0.00 4.17
659 1030 2.157668 CACAAGACGTAGATGCAACACC 59.842 50.000 0.00 0.00 0.00 4.16
660 1031 2.800544 ACACAAGACGTAGATGCAACAC 59.199 45.455 0.00 0.00 0.00 3.32
661 1032 3.106242 ACACAAGACGTAGATGCAACA 57.894 42.857 0.00 0.00 0.00 3.33
662 1033 4.684703 ACTTACACAAGACGTAGATGCAAC 59.315 41.667 0.00 0.00 35.60 4.17
663 1034 4.878439 ACTTACACAAGACGTAGATGCAA 58.122 39.130 0.00 0.00 35.60 4.08
664 1035 4.514781 ACTTACACAAGACGTAGATGCA 57.485 40.909 0.00 0.00 35.60 3.96
665 1036 5.512082 CACTACTTACACAAGACGTAGATGC 59.488 44.000 0.00 0.00 35.60 3.91
666 1037 5.512082 GCACTACTTACACAAGACGTAGATG 59.488 44.000 0.00 0.00 35.60 2.90
667 1038 5.415077 AGCACTACTTACACAAGACGTAGAT 59.585 40.000 0.00 0.00 35.60 1.98
669 1040 5.044428 AGCACTACTTACACAAGACGTAG 57.956 43.478 0.00 0.00 35.60 3.51
670 1041 6.427853 TCTTAGCACTACTTACACAAGACGTA 59.572 38.462 0.00 0.00 35.60 3.57
671 1042 5.240183 TCTTAGCACTACTTACACAAGACGT 59.760 40.000 0.00 0.00 35.60 4.34
672 1043 5.696822 TCTTAGCACTACTTACACAAGACG 58.303 41.667 0.00 0.00 35.60 4.18
673 1044 7.358187 CGTTTCTTAGCACTACTTACACAAGAC 60.358 40.741 0.00 0.00 35.60 3.01
674 1045 6.639686 CGTTTCTTAGCACTACTTACACAAGA 59.360 38.462 0.00 0.00 35.60 3.02
675 1046 6.615839 GCGTTTCTTAGCACTACTTACACAAG 60.616 42.308 0.00 0.00 37.81 3.16
678 1049 4.922103 AGCGTTTCTTAGCACTACTTACAC 59.078 41.667 0.00 0.00 35.48 2.90
680 1051 6.549952 TCTAGCGTTTCTTAGCACTACTTAC 58.450 40.000 0.00 0.00 35.48 2.34
703 1083 6.764877 TTTATTATTCATCTTCGTCGCCTC 57.235 37.500 0.00 0.00 0.00 4.70
740 1120 2.347731 GTGCTTCTTACCAGTAGCCAC 58.652 52.381 0.00 0.00 41.60 5.01
802 1187 2.997897 AGGGAGCAGGACGACCAC 60.998 66.667 6.71 0.00 38.94 4.16
883 1276 0.108585 CTCCTCTCCTCTCCTCTCCG 59.891 65.000 0.00 0.00 0.00 4.63
891 1284 1.293683 GGGACCCTCTCCTCTCCTCT 61.294 65.000 2.09 0.00 39.39 3.69
892 1285 1.231928 GGGACCCTCTCCTCTCCTC 59.768 68.421 2.09 0.00 39.39 3.71
893 1286 1.230819 AGGGACCCTCTCCTCTCCT 60.231 63.158 7.44 0.00 39.39 3.69
915 1308 0.874607 AGAGTTATAAAGGCGCGCGG 60.875 55.000 33.06 13.66 0.00 6.46
974 1370 1.557371 GAGGTTGGAGGAAGAGGAAGG 59.443 57.143 0.00 0.00 0.00 3.46
987 1383 0.905357 CAGGGAGTAGGTGAGGTTGG 59.095 60.000 0.00 0.00 0.00 3.77
1004 1403 3.400928 AGCAGCAGGAGGAGGCAG 61.401 66.667 0.00 0.00 0.00 4.85
1005 1404 3.714001 CAGCAGCAGGAGGAGGCA 61.714 66.667 0.00 0.00 0.00 4.75
1060 1474 1.376553 GACTGGAGGGTTGCTCTGC 60.377 63.158 0.00 0.00 0.00 4.26
1061 1475 1.298014 GGACTGGAGGGTTGCTCTG 59.702 63.158 0.00 0.00 0.00 3.35
1062 1476 1.152030 TGGACTGGAGGGTTGCTCT 60.152 57.895 0.00 0.00 0.00 4.09
1063 1477 1.194781 TCTGGACTGGAGGGTTGCTC 61.195 60.000 0.00 0.00 0.00 4.26
1064 1478 0.768221 TTCTGGACTGGAGGGTTGCT 60.768 55.000 0.00 0.00 0.00 3.91
1065 1479 0.329596 ATTCTGGACTGGAGGGTTGC 59.670 55.000 0.00 0.00 0.00 4.17
1066 1480 1.952367 GCATTCTGGACTGGAGGGTTG 60.952 57.143 0.00 0.00 0.00 3.77
1068 1482 0.842030 TGCATTCTGGACTGGAGGGT 60.842 55.000 0.00 0.00 0.00 4.34
1070 1484 0.617413 ACTGCATTCTGGACTGGAGG 59.383 55.000 12.31 0.00 35.38 4.30
1073 1487 0.325933 TGGACTGCATTCTGGACTGG 59.674 55.000 3.88 0.00 0.00 4.00
1074 1488 1.678123 CCTGGACTGCATTCTGGACTG 60.678 57.143 3.88 0.00 0.00 3.51
1075 1489 0.617413 CCTGGACTGCATTCTGGACT 59.383 55.000 3.88 0.00 0.00 3.85
1076 1490 1.028868 GCCTGGACTGCATTCTGGAC 61.029 60.000 16.34 7.56 0.00 4.02
1132 1546 2.804828 GAAGTGGTCCTCCCCTTGCG 62.805 65.000 0.00 0.00 0.00 4.85
1730 2174 2.030958 CCCGCCGTTGGTGTAGAAC 61.031 63.158 0.00 0.00 0.00 3.01
2120 2570 2.584608 CTGAAGGGCCCGTCGAAT 59.415 61.111 29.40 2.77 0.00 3.34
2211 2661 4.742201 ATCTCGCGCGCACAAGGT 62.742 61.111 32.61 18.21 0.00 3.50
2213 2663 4.214383 CCATCTCGCGCGCACAAG 62.214 66.667 32.61 23.57 0.00 3.16
2291 2753 1.000955 ACAAGGAACACCTCGCTAGTG 59.999 52.381 0.00 0.00 41.15 2.74
2292 2754 1.339097 ACAAGGAACACCTCGCTAGT 58.661 50.000 0.00 0.00 32.98 2.57
2294 2756 1.414919 ACAACAAGGAACACCTCGCTA 59.585 47.619 0.00 0.00 32.98 4.26
2295 2757 0.180406 ACAACAAGGAACACCTCGCT 59.820 50.000 0.00 0.00 32.98 4.93
2334 2805 2.427453 AGCGACGAAATGAGGTATGACT 59.573 45.455 0.00 0.00 0.00 3.41
2335 2806 2.810650 AGCGACGAAATGAGGTATGAC 58.189 47.619 0.00 0.00 0.00 3.06
2337 2808 3.731216 CAGTAGCGACGAAATGAGGTATG 59.269 47.826 0.00 0.00 0.00 2.39
2338 2809 3.795826 GCAGTAGCGACGAAATGAGGTAT 60.796 47.826 0.00 0.00 0.00 2.73
2341 2819 0.924090 GCAGTAGCGACGAAATGAGG 59.076 55.000 0.00 0.00 0.00 3.86
2364 2842 0.109827 CACCGCAACGAAATGATGCA 60.110 50.000 0.00 0.00 45.93 3.96
2392 2890 9.511272 TCATTTCATTCATCCATTAATCGATCT 57.489 29.630 0.00 0.00 0.00 2.75
2446 2944 5.809001 ACACTTCATTGGATGATGTACTGT 58.191 37.500 8.54 2.56 43.30 3.55
2447 2945 6.149973 ACAACACTTCATTGGATGATGTACTG 59.850 38.462 8.54 10.35 43.30 2.74
2448 2946 6.240894 ACAACACTTCATTGGATGATGTACT 58.759 36.000 8.54 0.00 43.30 2.73
2449 2947 6.500684 ACAACACTTCATTGGATGATGTAC 57.499 37.500 8.54 0.00 43.30 2.90
2450 2948 7.523293 AAACAACACTTCATTGGATGATGTA 57.477 32.000 8.54 0.00 43.30 2.29
2451 2949 6.409524 AAACAACACTTCATTGGATGATGT 57.590 33.333 4.25 4.25 45.21 3.06
2454 2952 9.460019 TGATATAAACAACACTTCATTGGATGA 57.540 29.630 0.00 0.00 37.55 2.92
2458 2956 9.859427 ACAATGATATAAACAACACTTCATTGG 57.141 29.630 20.44 8.28 46.60 3.16
2522 3020 7.203255 AGCTCAACTTTTTATTCAGTGGTAC 57.797 36.000 0.00 0.00 0.00 3.34
2523 3021 7.817418 AAGCTCAACTTTTTATTCAGTGGTA 57.183 32.000 0.00 0.00 33.71 3.25
2601 3099 0.947244 CCTGCTCACAAACTCACACC 59.053 55.000 0.00 0.00 0.00 4.16
2611 3109 3.630312 GTGGTTAAAGTTTCCTGCTCACA 59.370 43.478 0.00 0.00 0.00 3.58
2612 3110 3.883489 AGTGGTTAAAGTTTCCTGCTCAC 59.117 43.478 0.00 0.00 0.00 3.51
2616 3114 4.320275 GCACTAGTGGTTAAAGTTTCCTGC 60.320 45.833 23.95 0.05 0.00 4.85
2635 3133 3.668447 CATATTATCCGCCTGAAGCACT 58.332 45.455 0.00 0.00 44.04 4.40
2646 3144 2.736721 CCAACGTGGAGCATATTATCCG 59.263 50.000 0.00 0.00 40.96 4.18
2647 3145 3.498397 CACCAACGTGGAGCATATTATCC 59.502 47.826 10.46 0.00 40.96 2.59
2648 3146 4.024893 CACACCAACGTGGAGCATATTATC 60.025 45.833 10.46 0.00 44.86 1.75
2649 3147 3.876914 CACACCAACGTGGAGCATATTAT 59.123 43.478 10.46 0.00 44.86 1.28
2650 3148 3.266636 CACACCAACGTGGAGCATATTA 58.733 45.455 10.46 0.00 44.86 0.98
2651 3149 2.083774 CACACCAACGTGGAGCATATT 58.916 47.619 10.46 0.00 44.86 1.28
2685 3183 8.859236 AAATCTCTCATTTCATGACAAGAAGA 57.141 30.769 0.00 0.00 35.06 2.87
2687 3185 8.671921 GCTAAATCTCTCATTTCATGACAAGAA 58.328 33.333 0.00 0.00 35.06 2.52
2688 3186 8.045507 AGCTAAATCTCTCATTTCATGACAAGA 58.954 33.333 0.00 0.00 35.06 3.02
2689 3187 8.211116 AGCTAAATCTCTCATTTCATGACAAG 57.789 34.615 0.00 0.00 35.06 3.16
2690 3188 7.825761 TGAGCTAAATCTCTCATTTCATGACAA 59.174 33.333 0.00 0.00 34.69 3.18
2691 3189 7.279536 GTGAGCTAAATCTCTCATTTCATGACA 59.720 37.037 0.00 0.00 40.89 3.58
2721 3219 0.034477 AAATTCGGGGCAGACGGATT 60.034 50.000 0.00 0.00 41.03 3.01
2778 3278 7.497249 GCAAGAGAGAAGCAATAAGAGGATTAA 59.503 37.037 0.00 0.00 0.00 1.40
2785 3285 2.932614 GCGCAAGAGAGAAGCAATAAGA 59.067 45.455 0.30 0.00 43.02 2.10
2837 4358 6.460123 GGCATGGCATTATATGGTAGCAATAC 60.460 42.308 15.47 0.00 0.00 1.89
2838 4359 5.593909 GGCATGGCATTATATGGTAGCAATA 59.406 40.000 15.47 0.00 0.00 1.90
2839 4360 4.403432 GGCATGGCATTATATGGTAGCAAT 59.597 41.667 15.47 0.00 0.00 3.56
2840 4361 3.763360 GGCATGGCATTATATGGTAGCAA 59.237 43.478 15.47 0.00 0.00 3.91
2841 4362 3.245193 TGGCATGGCATTATATGGTAGCA 60.245 43.478 19.43 0.00 0.00 3.49
2842 4363 3.355378 TGGCATGGCATTATATGGTAGC 58.645 45.455 19.43 0.00 0.00 3.58
2853 4374 2.238847 CTGCAAAGCTGGCATGGCAT 62.239 55.000 23.59 5.90 41.06 4.40
2856 4377 0.889994 TAACTGCAAAGCTGGCATGG 59.110 50.000 13.10 6.14 41.06 3.66
2885 4406 2.917933 CATCACGGAAAGCTTATCCCA 58.082 47.619 16.96 6.60 33.13 4.37
2901 4422 6.178607 ACTGTATGGATATTGAGTGCATCA 57.821 37.500 0.00 0.00 35.62 3.07
2908 4429 9.307121 GATCCGAAATACTGTATGGATATTGAG 57.693 37.037 14.65 0.00 36.40 3.02
2909 4430 7.973944 CGATCCGAAATACTGTATGGATATTGA 59.026 37.037 14.65 2.67 36.40 2.57
2968 4499 0.456995 GTCTAGTCTGGCGTGCAGAC 60.457 60.000 12.21 12.21 46.82 3.51
2991 4522 5.652891 AGTAGTATATGCACTCCGGAATAGG 59.347 44.000 5.23 0.00 0.00 2.57
3018 4555 4.894556 GTCGTACTACAACGCAAAGAAAAC 59.105 41.667 0.00 0.00 42.56 2.43
3028 4565 9.362911 GATTACATTACTAGTCGTACTACAACG 57.637 37.037 0.00 0.00 44.19 4.10
3035 4572 5.622856 GCGTGGATTACATTACTAGTCGTAC 59.377 44.000 0.00 0.00 0.00 3.67
3038 4575 4.603985 TGCGTGGATTACATTACTAGTCG 58.396 43.478 0.00 0.00 0.00 4.18
3039 4576 5.107453 GCATGCGTGGATTACATTACTAGTC 60.107 44.000 8.27 0.00 0.00 2.59
3040 4577 4.750098 GCATGCGTGGATTACATTACTAGT 59.250 41.667 8.27 0.00 0.00 2.57
3041 4578 4.749598 TGCATGCGTGGATTACATTACTAG 59.250 41.667 14.09 0.00 0.00 2.57
3061 4598 4.299586 TCAGTTCCCAGTCAATAATGCA 57.700 40.909 0.00 0.00 0.00 3.96
3113 4650 0.742281 CATCTCAACTGCCTCCCACG 60.742 60.000 0.00 0.00 0.00 4.94
3135 4672 5.380043 AGGGCATTATCACATAAAGACCAG 58.620 41.667 6.23 0.00 42.63 4.00
3138 4675 6.543831 AGTCAAGGGCATTATCACATAAAGAC 59.456 38.462 0.00 0.00 0.00 3.01
3154 4697 1.303643 CCTCCCACAAGTCAAGGGC 60.304 63.158 0.00 0.00 42.52 5.19
3155 4698 0.771127 TTCCTCCCACAAGTCAAGGG 59.229 55.000 0.00 0.00 44.22 3.95
3212 4758 1.202782 TGCAATGCAAACCCAGCAAAT 60.203 42.857 5.01 0.00 46.27 2.32
3228 4775 1.201414 CAGCAGCTCACAATGATGCAA 59.799 47.619 6.74 0.00 35.46 4.08
3281 4828 4.694760 ACATGCATGTCTAGCCTAATCA 57.305 40.909 26.61 0.00 35.87 2.57
3375 4923 4.511527 CTGATCCAACAATCACTAGCACT 58.488 43.478 0.00 0.00 32.36 4.40
3393 4941 5.277974 GCGAAATATACACCACAATGCTGAT 60.278 40.000 0.00 0.00 0.00 2.90
3395 4943 4.282068 GCGAAATATACACCACAATGCTG 58.718 43.478 0.00 0.00 0.00 4.41
3396 4944 3.002246 CGCGAAATATACACCACAATGCT 59.998 43.478 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.