Multiple sequence alignment - TraesCS7B01G168900

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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 TraesCS7B01G168900 chr7B 100.000 2165 0 0 1 2165 237747937 237745773 0.000000e+00 3999.0
1 TraesCS7B01G168900 chr7B 96.292 836 29 2 159 993 16988543 16989377 0.000000e+00 1371.0
2 TraesCS7B01G168900 chr7B 96.897 290 9 0 1180 1469 115178023 115178312 8.980000e-134 486.0
3 TraesCS7B01G168900 chr7B 96.296 162 6 0 1 162 334093293 334093132 1.270000e-67 267.0
4 TraesCS7B01G168900 chr7B 96.296 162 6 0 1 162 527590625 527590786 1.270000e-67 267.0
5 TraesCS7B01G168900 chr3B 96.766 835 25 2 159 993 325725268 325726100 0.000000e+00 1391.0
6 TraesCS7B01G168900 chr3B 96.407 835 29 1 159 993 472389042 472388209 0.000000e+00 1375.0
7 TraesCS7B01G168900 chr3B 98.396 187 3 0 994 1180 201554240 201554426 1.600000e-86 329.0
8 TraesCS7B01G168900 chr5B 96.647 835 27 1 159 993 167274900 167274067 0.000000e+00 1386.0
9 TraesCS7B01G168900 chr5B 96.527 835 27 2 159 993 256577721 256576889 0.000000e+00 1380.0
10 TraesCS7B01G168900 chr5B 96.407 835 29 1 159 993 245869353 245868520 0.000000e+00 1375.0
11 TraesCS7B01G168900 chr5B 97.861 187 4 0 994 1180 429064459 429064273 7.450000e-85 324.0
12 TraesCS7B01G168900 chr5B 96.296 162 6 0 1 162 611504887 611504726 1.270000e-67 267.0
13 TraesCS7B01G168900 chr1B 96.527 835 28 1 159 993 329918337 329919170 0.000000e+00 1380.0
14 TraesCS7B01G168900 chr1B 97.241 290 8 0 1180 1469 633712961 633712672 1.930000e-135 492.0
15 TraesCS7B01G168900 chr1B 96.296 162 6 0 1 162 75016245 75016084 1.270000e-67 267.0
16 TraesCS7B01G168900 chr1B 96.296 162 6 0 1 162 596027767 596027606 1.270000e-67 267.0
17 TraesCS7B01G168900 chr3D 96.168 835 31 1 159 993 28666391 28665558 0.000000e+00 1363.0
18 TraesCS7B01G168900 chr3D 97.326 187 5 0 994 1180 158938169 158937983 3.470000e-83 318.0
19 TraesCS7B01G168900 chr3D 97.326 187 5 0 994 1180 589249397 589249211 3.470000e-83 318.0
20 TraesCS7B01G168900 chr2B 90.854 995 87 4 1 993 635297699 635296707 0.000000e+00 1330.0
21 TraesCS7B01G168900 chr2B 96.296 162 6 0 1 162 398227417 398227256 1.270000e-67 267.0
22 TraesCS7B01G168900 chr2D 92.635 706 51 1 1461 2165 41829017 41828312 0.000000e+00 1014.0
23 TraesCS7B01G168900 chr2D 92.243 709 51 3 1461 2165 352922374 352923082 0.000000e+00 1002.0
24 TraesCS7B01G168900 chr2D 92.429 700 53 0 1466 2165 463963672 463964371 0.000000e+00 1000.0
25 TraesCS7B01G168900 chr2D 92.102 709 52 3 1461 2165 404568684 404569392 0.000000e+00 996.0
26 TraesCS7B01G168900 chr4D 92.493 706 52 1 1461 2165 24018764 24019469 0.000000e+00 1009.0
27 TraesCS7B01G168900 chr4D 97.959 49 1 0 994 1042 130665697 130665649 3.830000e-13 86.1
28 TraesCS7B01G168900 chr6D 92.243 709 51 3 1461 2165 265087896 265087188 0.000000e+00 1002.0
29 TraesCS7B01G168900 chr6D 92.232 708 51 3 1462 2165 101479289 101478582 0.000000e+00 1000.0
30 TraesCS7B01G168900 chr6D 92.232 708 52 2 1461 2165 452291352 452290645 0.000000e+00 1000.0
31 TraesCS7B01G168900 chr6D 92.102 709 51 4 1461 2165 126210886 126210179 0.000000e+00 994.0
32 TraesCS7B01G168900 chr6D 95.745 47 1 1 994 1040 1689862 1689817 8.290000e-10 75.0
33 TraesCS7B01G168900 chr5D 97.586 290 7 0 1180 1469 503332282 503331993 4.150000e-137 497.0
34 TraesCS7B01G168900 chr5D 96.897 290 9 0 1180 1469 503309666 503309377 8.980000e-134 486.0
35 TraesCS7B01G168900 chr5D 96.552 290 10 0 1180 1469 6257109 6257398 4.180000e-132 481.0
36 TraesCS7B01G168900 chr5D 97.173 283 7 1 1180 1462 403458465 403458184 5.410000e-131 477.0
37 TraesCS7B01G168900 chr5D 97.861 187 4 0 994 1180 503253967 503253781 7.450000e-85 324.0
38 TraesCS7B01G168900 chr5D 97.861 187 4 0 994 1180 523037345 523037159 7.450000e-85 324.0
39 TraesCS7B01G168900 chr1A 97.241 290 8 0 1180 1469 554478233 554477944 1.930000e-135 492.0
40 TraesCS7B01G168900 chr1D 96.552 290 8 1 1180 1469 51835966 51836253 1.500000e-131 479.0
41 TraesCS7B01G168900 chr1D 96.552 290 9 1 1180 1469 254452796 254452508 1.500000e-131 479.0
42 TraesCS7B01G168900 chr1D 98.000 50 1 0 994 1043 492056491 492056442 1.060000e-13 87.9
43 TraesCS7B01G168900 chr5A 98.396 187 3 0 994 1180 482022831 482023017 1.600000e-86 329.0
44 TraesCS7B01G168900 chrUn 97.861 187 4 0 994 1180 371791601 371791415 7.450000e-85 324.0
45 TraesCS7B01G168900 chrUn 97.326 187 5 0 994 1180 418304939 418304753 3.470000e-83 318.0
46 TraesCS7B01G168900 chr4B 90.278 216 18 2 1 214 288215326 288215540 1.640000e-71 279.0
47 TraesCS7B01G168900 chr6B 96.296 162 6 0 1 162 175962352 175962513 1.270000e-67 267.0


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 TraesCS7B01G168900 chr7B 237745773 237747937 2164 True 3999 3999 100.000 1 2165 1 chr7B.!!$R1 2164
1 TraesCS7B01G168900 chr7B 16988543 16989377 834 False 1371 1371 96.292 159 993 1 chr7B.!!$F1 834
2 TraesCS7B01G168900 chr3B 325725268 325726100 832 False 1391 1391 96.766 159 993 1 chr3B.!!$F2 834
3 TraesCS7B01G168900 chr3B 472388209 472389042 833 True 1375 1375 96.407 159 993 1 chr3B.!!$R1 834
4 TraesCS7B01G168900 chr5B 167274067 167274900 833 True 1386 1386 96.647 159 993 1 chr5B.!!$R1 834
5 TraesCS7B01G168900 chr5B 256576889 256577721 832 True 1380 1380 96.527 159 993 1 chr5B.!!$R3 834
6 TraesCS7B01G168900 chr5B 245868520 245869353 833 True 1375 1375 96.407 159 993 1 chr5B.!!$R2 834
7 TraesCS7B01G168900 chr1B 329918337 329919170 833 False 1380 1380 96.527 159 993 1 chr1B.!!$F1 834
8 TraesCS7B01G168900 chr3D 28665558 28666391 833 True 1363 1363 96.168 159 993 1 chr3D.!!$R1 834
9 TraesCS7B01G168900 chr2B 635296707 635297699 992 True 1330 1330 90.854 1 993 1 chr2B.!!$R2 992
10 TraesCS7B01G168900 chr2D 41828312 41829017 705 True 1014 1014 92.635 1461 2165 1 chr2D.!!$R1 704
11 TraesCS7B01G168900 chr2D 352922374 352923082 708 False 1002 1002 92.243 1461 2165 1 chr2D.!!$F1 704
12 TraesCS7B01G168900 chr2D 463963672 463964371 699 False 1000 1000 92.429 1466 2165 1 chr2D.!!$F3 699
13 TraesCS7B01G168900 chr2D 404568684 404569392 708 False 996 996 92.102 1461 2165 1 chr2D.!!$F2 704
14 TraesCS7B01G168900 chr4D 24018764 24019469 705 False 1009 1009 92.493 1461 2165 1 chr4D.!!$F1 704
15 TraesCS7B01G168900 chr6D 265087188 265087896 708 True 1002 1002 92.243 1461 2165 1 chr6D.!!$R4 704
16 TraesCS7B01G168900 chr6D 101478582 101479289 707 True 1000 1000 92.232 1462 2165 1 chr6D.!!$R2 703
17 TraesCS7B01G168900 chr6D 452290645 452291352 707 True 1000 1000 92.232 1461 2165 1 chr6D.!!$R5 704
18 TraesCS7B01G168900 chr6D 126210179 126210886 707 True 994 994 92.102 1461 2165 1 chr6D.!!$R3 704

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
355 357 0.396974 TATGCCCCAAGACAATGCCC 60.397 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1648 0.817654 TGTATGTGGAGAGGCTGACG 59.182 55.0 0.0 0.0 0.0 4.35 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 7.778470 AGTATCAAGAGTTTTACTAGCATGC 57.222 36.000 10.51 10.51 0.00 4.06
27 28 4.937620 TCAAGAGTTTTACTAGCATGCTGG 59.062 41.667 30.42 28.93 0.00 4.85
36 37 7.496529 TTTACTAGCATGCTGGATAACATTC 57.503 36.000 34.54 0.00 0.00 2.67
38 39 5.439721 ACTAGCATGCTGGATAACATTCAA 58.560 37.500 34.54 7.90 0.00 2.69
63 64 6.620877 TTCTTATCAACTCTTTGCCCTAGA 57.379 37.500 0.00 0.00 32.17 2.43
65 66 6.407202 TCTTATCAACTCTTTGCCCTAGAAC 58.593 40.000 0.00 0.00 32.17 3.01
67 68 4.431416 TCAACTCTTTGCCCTAGAACAA 57.569 40.909 0.00 0.00 32.17 2.83
72 73 2.173782 TCTTTGCCCTAGAACAACACCA 59.826 45.455 0.00 0.00 0.00 4.17
113 114 7.342799 AGCATCACACATAATTTCAAAGGGTAT 59.657 33.333 0.00 0.00 0.00 2.73
156 157 2.857186 TAGGTGCAGTGATCAAAGCA 57.143 45.000 16.77 16.77 34.10 3.91
285 287 2.568509 CCTTGGGACATGGCATCTTTTT 59.431 45.455 0.00 0.00 46.55 1.94
355 357 0.396974 TATGCCCCAAGACAATGCCC 60.397 55.000 0.00 0.00 0.00 5.36
403 405 6.540438 TCCCAATTCAAGACGATACTAGTT 57.460 37.500 0.00 0.00 0.00 2.24
462 464 9.023649 GCTCAAGCAATCATCAAAAGAGGATCT 62.024 40.741 0.00 0.00 45.28 2.75
506 508 8.472413 CCATGAATACCTCACAAATCTTTTCAT 58.528 33.333 0.00 0.00 36.69 2.57
638 641 3.020984 GTTTTTGATTGATCCCCCGCTA 58.979 45.455 0.00 0.00 0.00 4.26
735 738 8.707938 AGCATTTGATCAATAAAAGGTAAAGC 57.292 30.769 9.40 0.00 0.00 3.51
969 972 9.284968 CCTTTCTAACCACTTCTTTCATCTTAA 57.715 33.333 0.00 0.00 0.00 1.85
993 996 3.868757 TCAATCGTCGTTGAGGATCTT 57.131 42.857 2.84 0.00 36.36 2.40
994 997 4.976224 TCAATCGTCGTTGAGGATCTTA 57.024 40.909 2.84 0.00 36.36 2.10
995 998 4.669318 TCAATCGTCGTTGAGGATCTTAC 58.331 43.478 2.84 0.00 36.36 2.34
996 999 4.398358 TCAATCGTCGTTGAGGATCTTACT 59.602 41.667 2.84 0.00 36.36 2.24
997 1000 4.985538 ATCGTCGTTGAGGATCTTACTT 57.014 40.909 0.00 0.00 32.69 2.24
998 1001 4.352600 TCGTCGTTGAGGATCTTACTTC 57.647 45.455 0.00 0.00 34.92 3.01
999 1002 3.754850 TCGTCGTTGAGGATCTTACTTCA 59.245 43.478 0.00 0.00 34.92 3.02
1000 1003 4.216902 TCGTCGTTGAGGATCTTACTTCAA 59.783 41.667 0.00 0.00 34.43 2.69
1001 1004 5.103000 CGTCGTTGAGGATCTTACTTCAAT 58.897 41.667 0.00 0.00 37.95 2.57
1002 1005 5.004821 CGTCGTTGAGGATCTTACTTCAATG 59.995 44.000 0.00 0.00 41.20 2.82
1003 1006 5.869888 GTCGTTGAGGATCTTACTTCAATGT 59.130 40.000 0.00 0.00 40.89 2.71
1004 1007 6.035112 GTCGTTGAGGATCTTACTTCAATGTC 59.965 42.308 0.00 0.00 40.89 3.06
1005 1008 5.869344 CGTTGAGGATCTTACTTCAATGTCA 59.131 40.000 0.00 0.00 37.95 3.58
1006 1009 6.368791 CGTTGAGGATCTTACTTCAATGTCAA 59.631 38.462 0.00 0.00 37.95 3.18
1007 1010 7.095229 CGTTGAGGATCTTACTTCAATGTCAAA 60.095 37.037 0.00 0.00 37.95 2.69
1008 1011 8.567948 GTTGAGGATCTTACTTCAATGTCAAAA 58.432 33.333 0.00 0.00 37.95 2.44
1009 1012 8.690203 TGAGGATCTTACTTCAATGTCAAAAA 57.310 30.769 0.00 0.00 34.92 1.94
1032 1035 7.734538 AAAGCGTATTCGTGAAAATATTTGG 57.265 32.000 0.39 0.00 39.49 3.28
1033 1036 6.671614 AGCGTATTCGTGAAAATATTTGGA 57.328 33.333 0.39 0.00 39.49 3.53
1034 1037 7.079182 AGCGTATTCGTGAAAATATTTGGAA 57.921 32.000 0.39 4.43 39.49 3.53
1035 1038 7.186804 AGCGTATTCGTGAAAATATTTGGAAG 58.813 34.615 0.39 0.00 39.49 3.46
1036 1039 7.065324 AGCGTATTCGTGAAAATATTTGGAAGA 59.935 33.333 0.39 0.00 39.49 2.87
1037 1040 7.694784 GCGTATTCGTGAAAATATTTGGAAGAA 59.305 33.333 0.39 6.09 39.49 2.52
1038 1041 9.549509 CGTATTCGTGAAAATATTTGGAAGAAA 57.450 29.630 0.39 0.00 0.00 2.52
1043 1046 9.458374 TCGTGAAAATATTTGGAAGAAAAAGAC 57.542 29.630 0.39 0.00 0.00 3.01
1044 1047 9.463443 CGTGAAAATATTTGGAAGAAAAAGACT 57.537 29.630 0.39 0.00 0.00 3.24
1098 1101 9.988350 TTAGTAAAATCAAGATCATTTTCGAGC 57.012 29.630 5.72 0.00 35.52 5.03
1099 1102 7.182761 AGTAAAATCAAGATCATTTTCGAGCG 58.817 34.615 5.72 0.00 35.52 5.03
1100 1103 5.801350 AAATCAAGATCATTTTCGAGCGA 57.199 34.783 0.00 0.00 0.00 4.93
1101 1104 5.998454 AATCAAGATCATTTTCGAGCGAT 57.002 34.783 0.00 0.00 0.00 4.58
1102 1105 7.482654 AAATCAAGATCATTTTCGAGCGATA 57.517 32.000 0.00 0.00 0.00 2.92
1103 1106 7.482654 AATCAAGATCATTTTCGAGCGATAA 57.517 32.000 0.00 0.00 0.00 1.75
1104 1107 7.664082 ATCAAGATCATTTTCGAGCGATAAT 57.336 32.000 0.00 3.32 0.00 1.28
1105 1108 6.881017 TCAAGATCATTTTCGAGCGATAATG 58.119 36.000 21.76 21.76 41.56 1.90
1107 1110 6.702972 AGATCATTTTCGAGCGATAATGAG 57.297 37.500 28.56 12.66 46.96 2.90
1108 1111 4.715520 TCATTTTCGAGCGATAATGAGC 57.284 40.909 24.49 0.00 42.87 4.26
1109 1112 4.119136 TCATTTTCGAGCGATAATGAGCA 58.881 39.130 24.49 11.07 42.87 4.26
1110 1113 3.925688 TTTTCGAGCGATAATGAGCAC 57.074 42.857 0.00 0.00 35.48 4.40
1111 1114 1.852942 TTCGAGCGATAATGAGCACC 58.147 50.000 0.00 0.00 35.48 5.01
1112 1115 0.032130 TCGAGCGATAATGAGCACCC 59.968 55.000 0.00 0.00 35.48 4.61
1113 1116 0.249447 CGAGCGATAATGAGCACCCA 60.249 55.000 0.00 0.00 35.48 4.51
1114 1117 1.806247 CGAGCGATAATGAGCACCCAA 60.806 52.381 0.00 0.00 35.48 4.12
1115 1118 2.288666 GAGCGATAATGAGCACCCAAA 58.711 47.619 0.00 0.00 35.48 3.28
1116 1119 2.682856 GAGCGATAATGAGCACCCAAAA 59.317 45.455 0.00 0.00 35.48 2.44
1117 1120 2.423538 AGCGATAATGAGCACCCAAAAC 59.576 45.455 0.00 0.00 35.48 2.43
1118 1121 2.479560 GCGATAATGAGCACCCAAAACC 60.480 50.000 0.00 0.00 0.00 3.27
1119 1122 2.752354 CGATAATGAGCACCCAAAACCA 59.248 45.455 0.00 0.00 0.00 3.67
1120 1123 3.192422 CGATAATGAGCACCCAAAACCAA 59.808 43.478 0.00 0.00 0.00 3.67
1121 1124 4.321601 CGATAATGAGCACCCAAAACCAAA 60.322 41.667 0.00 0.00 0.00 3.28
1122 1125 3.473923 AATGAGCACCCAAAACCAAAG 57.526 42.857 0.00 0.00 0.00 2.77
1123 1126 1.118838 TGAGCACCCAAAACCAAAGG 58.881 50.000 0.00 0.00 0.00 3.11
1136 1139 1.127343 CCAAAGGGTTTTTCTGGGCA 58.873 50.000 0.00 0.00 0.00 5.36
1137 1140 1.488393 CCAAAGGGTTTTTCTGGGCAA 59.512 47.619 0.00 0.00 0.00 4.52
1138 1141 2.560504 CAAAGGGTTTTTCTGGGCAAC 58.439 47.619 0.00 0.00 0.00 4.17
1139 1142 1.872773 AAGGGTTTTTCTGGGCAACA 58.127 45.000 0.00 0.00 39.74 3.33
1140 1143 1.872773 AGGGTTTTTCTGGGCAACAA 58.127 45.000 0.00 0.00 39.74 2.83
1141 1144 2.192263 AGGGTTTTTCTGGGCAACAAA 58.808 42.857 0.00 0.00 39.74 2.83
1142 1145 2.093181 AGGGTTTTTCTGGGCAACAAAC 60.093 45.455 0.00 0.00 39.74 2.93
1143 1146 2.355209 GGGTTTTTCTGGGCAACAAACA 60.355 45.455 0.00 0.00 39.74 2.83
1144 1147 3.339141 GGTTTTTCTGGGCAACAAACAA 58.661 40.909 0.00 0.00 39.74 2.83
1145 1148 3.753797 GGTTTTTCTGGGCAACAAACAAA 59.246 39.130 0.00 0.00 39.74 2.83
1146 1149 4.397730 GGTTTTTCTGGGCAACAAACAAAT 59.602 37.500 0.00 0.00 39.74 2.32
1147 1150 5.586643 GGTTTTTCTGGGCAACAAACAAATA 59.413 36.000 0.00 0.00 39.74 1.40
1148 1151 6.094186 GGTTTTTCTGGGCAACAAACAAATAA 59.906 34.615 0.00 0.00 39.74 1.40
1149 1152 7.201776 GGTTTTTCTGGGCAACAAACAAATAAT 60.202 33.333 0.00 0.00 39.74 1.28
1150 1153 8.831550 GTTTTTCTGGGCAACAAACAAATAATA 58.168 29.630 0.00 0.00 39.74 0.98
1151 1154 8.964476 TTTTCTGGGCAACAAACAAATAATAA 57.036 26.923 0.00 0.00 39.74 1.40
1152 1155 8.600449 TTTCTGGGCAACAAACAAATAATAAG 57.400 30.769 0.00 0.00 39.74 1.73
1153 1156 7.531857 TCTGGGCAACAAACAAATAATAAGA 57.468 32.000 0.00 0.00 39.74 2.10
1154 1157 8.133024 TCTGGGCAACAAACAAATAATAAGAT 57.867 30.769 0.00 0.00 39.74 2.40
1155 1158 8.592809 TCTGGGCAACAAACAAATAATAAGATT 58.407 29.630 0.00 0.00 39.74 2.40
1156 1159 9.218440 CTGGGCAACAAACAAATAATAAGATTT 57.782 29.630 0.00 0.00 39.74 2.17
1157 1160 9.566432 TGGGCAACAAACAAATAATAAGATTTT 57.434 25.926 0.00 0.00 39.74 1.82
1198 1201 9.706691 TGACTTATAAGTTCTTGAAGTACTTGG 57.293 33.333 22.28 13.66 36.66 3.61
1199 1202 9.924650 GACTTATAAGTTCTTGAAGTACTTGGA 57.075 33.333 22.28 10.51 36.66 3.53
1202 1205 9.720769 TTATAAGTTCTTGAAGTACTTGGAAGG 57.279 33.333 22.28 0.00 36.66 3.46
1203 1206 5.632034 AGTTCTTGAAGTACTTGGAAGGT 57.368 39.130 14.14 2.99 0.00 3.50
1204 1207 6.002653 AGTTCTTGAAGTACTTGGAAGGTT 57.997 37.500 14.14 2.40 0.00 3.50
1205 1208 6.424032 AGTTCTTGAAGTACTTGGAAGGTTT 58.576 36.000 14.14 2.09 0.00 3.27
1206 1209 6.318900 AGTTCTTGAAGTACTTGGAAGGTTTG 59.681 38.462 14.14 0.00 0.00 2.93
1207 1210 5.751586 TCTTGAAGTACTTGGAAGGTTTGT 58.248 37.500 14.14 0.00 0.00 2.83
1208 1211 6.184789 TCTTGAAGTACTTGGAAGGTTTGTT 58.815 36.000 14.14 0.00 0.00 2.83
1209 1212 6.661805 TCTTGAAGTACTTGGAAGGTTTGTTT 59.338 34.615 14.14 0.00 0.00 2.83
1210 1213 6.844097 TGAAGTACTTGGAAGGTTTGTTTT 57.156 33.333 14.14 0.00 0.00 2.43
1211 1214 7.941431 TGAAGTACTTGGAAGGTTTGTTTTA 57.059 32.000 14.14 0.00 0.00 1.52
1212 1215 8.350852 TGAAGTACTTGGAAGGTTTGTTTTAA 57.649 30.769 14.14 0.00 0.00 1.52
1213 1216 8.804204 TGAAGTACTTGGAAGGTTTGTTTTAAA 58.196 29.630 14.14 0.00 0.00 1.52
1214 1217 9.811995 GAAGTACTTGGAAGGTTTGTTTTAAAT 57.188 29.630 14.14 0.00 0.00 1.40
1216 1219 9.594478 AGTACTTGGAAGGTTTGTTTTAAATTG 57.406 29.630 0.00 0.00 0.00 2.32
1217 1220 9.373603 GTACTTGGAAGGTTTGTTTTAAATTGT 57.626 29.630 0.00 0.00 0.00 2.71
1218 1221 8.487313 ACTTGGAAGGTTTGTTTTAAATTGTC 57.513 30.769 0.00 0.00 0.00 3.18
1219 1222 8.097662 ACTTGGAAGGTTTGTTTTAAATTGTCA 58.902 29.630 0.00 0.00 0.00 3.58
1220 1223 8.848474 TTGGAAGGTTTGTTTTAAATTGTCAA 57.152 26.923 0.00 0.00 0.00 3.18
1221 1224 9.454859 TTGGAAGGTTTGTTTTAAATTGTCAAT 57.545 25.926 0.00 0.00 0.00 2.57
1222 1225 8.887717 TGGAAGGTTTGTTTTAAATTGTCAATG 58.112 29.630 0.00 0.00 0.00 2.82
1223 1226 8.341903 GGAAGGTTTGTTTTAAATTGTCAATGG 58.658 33.333 0.00 0.00 0.00 3.16
1224 1227 9.103861 GAAGGTTTGTTTTAAATTGTCAATGGA 57.896 29.630 0.00 0.00 0.00 3.41
1225 1228 8.432110 AGGTTTGTTTTAAATTGTCAATGGAC 57.568 30.769 0.00 0.00 44.57 4.02
1314 1317 1.797025 GCTACAATAGCGCCTAAGGG 58.203 55.000 2.29 0.00 42.62 3.95
1328 1331 4.471904 CCTAAGGGCCCAAAAATTTCTC 57.528 45.455 27.56 0.00 0.00 2.87
1329 1332 3.119137 CCTAAGGGCCCAAAAATTTCTCG 60.119 47.826 27.56 0.60 0.00 4.04
1330 1333 2.302587 AGGGCCCAAAAATTTCTCGA 57.697 45.000 27.56 0.00 0.00 4.04
1331 1334 2.604139 AGGGCCCAAAAATTTCTCGAA 58.396 42.857 27.56 0.00 0.00 3.71
1332 1335 3.173151 AGGGCCCAAAAATTTCTCGAAT 58.827 40.909 27.56 0.00 0.00 3.34
1333 1336 4.349365 AGGGCCCAAAAATTTCTCGAATA 58.651 39.130 27.56 0.00 0.00 1.75
1334 1337 4.402474 AGGGCCCAAAAATTTCTCGAATAG 59.598 41.667 27.56 0.00 0.00 1.73
1335 1338 4.441495 GGGCCCAAAAATTTCTCGAATAGG 60.441 45.833 19.95 0.00 0.00 2.57
1336 1339 4.401202 GGCCCAAAAATTTCTCGAATAGGA 59.599 41.667 0.00 0.00 0.00 2.94
1337 1340 5.105513 GGCCCAAAAATTTCTCGAATAGGAA 60.106 40.000 0.00 0.00 0.00 3.36
1338 1341 6.406961 GGCCCAAAAATTTCTCGAATAGGAAT 60.407 38.462 0.00 0.00 34.60 3.01
1339 1342 7.041721 GCCCAAAAATTTCTCGAATAGGAATT 58.958 34.615 0.00 0.00 44.07 2.17
1340 1343 7.222805 GCCCAAAAATTTCTCGAATAGGAATTC 59.777 37.037 0.00 0.00 41.77 2.17
1341 1344 8.470002 CCCAAAAATTTCTCGAATAGGAATTCT 58.530 33.333 5.23 0.00 41.77 2.40
1348 1351 9.936759 ATTTCTCGAATAGGAATTCTAGGATTC 57.063 33.333 14.61 14.61 39.56 2.52
1367 1370 8.015185 AGGATTCCATTCTTTTATCACATTGG 57.985 34.615 5.29 0.00 0.00 3.16
1368 1371 7.070322 AGGATTCCATTCTTTTATCACATTGGG 59.930 37.037 5.29 0.00 0.00 4.12
1369 1372 7.069826 GGATTCCATTCTTTTATCACATTGGGA 59.930 37.037 0.00 0.00 0.00 4.37
1370 1373 7.976414 TTCCATTCTTTTATCACATTGGGAT 57.024 32.000 6.64 6.64 0.00 3.85
1371 1374 7.350744 TCCATTCTTTTATCACATTGGGATG 57.649 36.000 11.76 0.00 39.25 3.51
1373 1376 7.399765 TCCATTCTTTTATCACATTGGGATGTT 59.600 33.333 11.76 0.00 43.92 2.71
1374 1377 8.042515 CCATTCTTTTATCACATTGGGATGTTT 58.957 33.333 11.76 0.00 43.92 2.83
1375 1378 9.439500 CATTCTTTTATCACATTGGGATGTTTT 57.561 29.630 11.76 0.00 43.92 2.43
1376 1379 8.830201 TTCTTTTATCACATTGGGATGTTTTG 57.170 30.769 11.76 0.00 43.92 2.44
1377 1380 8.187913 TCTTTTATCACATTGGGATGTTTTGA 57.812 30.769 11.76 1.38 43.92 2.69
1378 1381 8.646004 TCTTTTATCACATTGGGATGTTTTGAA 58.354 29.630 11.76 0.00 43.92 2.69
1379 1382 9.439500 CTTTTATCACATTGGGATGTTTTGAAT 57.561 29.630 11.76 0.00 43.92 2.57
1380 1383 9.790344 TTTTATCACATTGGGATGTTTTGAATT 57.210 25.926 11.76 0.00 43.92 2.17
1381 1384 9.434420 TTTATCACATTGGGATGTTTTGAATTC 57.566 29.630 11.76 0.00 43.92 2.17
1382 1385 6.669125 TCACATTGGGATGTTTTGAATTCT 57.331 33.333 7.05 0.00 43.92 2.40
1383 1386 7.065120 TCACATTGGGATGTTTTGAATTCTT 57.935 32.000 7.05 0.00 43.92 2.52
1384 1387 6.930164 TCACATTGGGATGTTTTGAATTCTTG 59.070 34.615 7.05 0.00 43.92 3.02
1385 1388 6.930164 CACATTGGGATGTTTTGAATTCTTGA 59.070 34.615 7.05 0.00 43.92 3.02
1386 1389 7.441760 CACATTGGGATGTTTTGAATTCTTGAA 59.558 33.333 7.05 0.00 43.92 2.69
1387 1390 8.158789 ACATTGGGATGTTTTGAATTCTTGAAT 58.841 29.630 7.05 0.00 43.92 2.57
1388 1391 9.656040 CATTGGGATGTTTTGAATTCTTGAATA 57.344 29.630 7.05 0.00 0.00 1.75
1391 1394 9.487790 TGGGATGTTTTGAATTCTTGAATAAAC 57.512 29.630 7.05 10.74 0.00 2.01
1392 1395 8.935844 GGGATGTTTTGAATTCTTGAATAAACC 58.064 33.333 7.05 5.76 0.00 3.27
1393 1396 9.487790 GGATGTTTTGAATTCTTGAATAAACCA 57.512 29.630 7.05 0.00 0.00 3.67
1399 1402 9.973450 TTTGAATTCTTGAATAAACCAATTCGA 57.027 25.926 7.05 0.00 38.47 3.71
1400 1403 9.624697 TTGAATTCTTGAATAAACCAATTCGAG 57.375 29.630 7.05 7.29 44.07 4.04
1404 1407 7.737972 TCTTGAATAAACCAATTCGAGAACA 57.262 32.000 12.14 0.00 46.41 3.18
1405 1408 7.806690 TCTTGAATAAACCAATTCGAGAACAG 58.193 34.615 12.14 0.00 46.41 3.16
1406 1409 7.444183 TCTTGAATAAACCAATTCGAGAACAGT 59.556 33.333 12.14 0.00 46.41 3.55
1407 1410 7.504924 TGAATAAACCAATTCGAGAACAGTT 57.495 32.000 0.00 0.00 38.47 3.16
1408 1411 7.359595 TGAATAAACCAATTCGAGAACAGTTG 58.640 34.615 0.00 0.00 38.47 3.16
1409 1412 4.568152 AAACCAATTCGAGAACAGTTGG 57.432 40.909 12.57 12.57 43.75 3.77
1410 1413 3.485463 ACCAATTCGAGAACAGTTGGA 57.515 42.857 18.27 0.00 41.36 3.53
1411 1414 4.021102 ACCAATTCGAGAACAGTTGGAT 57.979 40.909 18.27 5.42 41.36 3.41
1412 1415 3.753272 ACCAATTCGAGAACAGTTGGATG 59.247 43.478 18.27 0.00 41.36 3.51
1413 1416 3.426695 CCAATTCGAGAACAGTTGGATGC 60.427 47.826 9.82 0.00 41.36 3.91
1414 1417 2.839486 TTCGAGAACAGTTGGATGCT 57.161 45.000 0.00 0.00 0.00 3.79
1415 1418 2.084610 TCGAGAACAGTTGGATGCTG 57.915 50.000 0.00 0.00 39.67 4.41
1416 1419 1.618343 TCGAGAACAGTTGGATGCTGA 59.382 47.619 0.00 0.00 37.40 4.26
1417 1420 1.728971 CGAGAACAGTTGGATGCTGAC 59.271 52.381 0.00 0.00 37.40 3.51
1418 1421 2.771089 GAGAACAGTTGGATGCTGACA 58.229 47.619 0.00 0.00 37.40 3.58
1419 1422 3.141398 GAGAACAGTTGGATGCTGACAA 58.859 45.455 0.00 0.00 37.40 3.18
1420 1423 3.554934 AGAACAGTTGGATGCTGACAAA 58.445 40.909 0.00 0.00 37.40 2.83
1421 1424 3.953612 AGAACAGTTGGATGCTGACAAAA 59.046 39.130 0.00 0.00 37.40 2.44
1422 1425 4.586001 AGAACAGTTGGATGCTGACAAAAT 59.414 37.500 0.00 0.00 37.40 1.82
1423 1426 4.510038 ACAGTTGGATGCTGACAAAATC 57.490 40.909 0.00 0.00 37.40 2.17
1424 1427 3.890756 ACAGTTGGATGCTGACAAAATCA 59.109 39.130 0.00 0.00 37.40 2.57
1425 1428 4.525487 ACAGTTGGATGCTGACAAAATCAT 59.475 37.500 0.00 0.00 36.48 2.45
1426 1429 5.100259 CAGTTGGATGCTGACAAAATCATC 58.900 41.667 0.00 0.00 36.48 2.92
1427 1430 4.768448 AGTTGGATGCTGACAAAATCATCA 59.232 37.500 0.00 0.00 37.83 3.07
1428 1431 5.244402 AGTTGGATGCTGACAAAATCATCAA 59.756 36.000 0.00 0.00 37.03 2.57
1429 1432 5.725325 TGGATGCTGACAAAATCATCAAA 57.275 34.783 0.00 0.00 37.03 2.69
1430 1433 5.716094 TGGATGCTGACAAAATCATCAAAG 58.284 37.500 0.00 0.00 37.03 2.77
1431 1434 5.477637 TGGATGCTGACAAAATCATCAAAGA 59.522 36.000 0.00 0.00 37.03 2.52
1432 1435 6.034591 GGATGCTGACAAAATCATCAAAGAG 58.965 40.000 0.00 0.00 37.03 2.85
1433 1436 6.349944 GGATGCTGACAAAATCATCAAAGAGT 60.350 38.462 0.00 0.00 37.03 3.24
1434 1437 5.765176 TGCTGACAAAATCATCAAAGAGTG 58.235 37.500 0.00 0.00 36.48 3.51
1435 1438 5.159209 GCTGACAAAATCATCAAAGAGTGG 58.841 41.667 0.00 0.00 36.48 4.00
1436 1439 5.278660 GCTGACAAAATCATCAAAGAGTGGT 60.279 40.000 0.00 0.00 36.48 4.16
1437 1440 6.072508 GCTGACAAAATCATCAAAGAGTGGTA 60.073 38.462 0.00 0.00 36.48 3.25
1438 1441 7.362401 GCTGACAAAATCATCAAAGAGTGGTAT 60.362 37.037 0.00 0.00 36.48 2.73
1439 1442 8.408043 TGACAAAATCATCAAAGAGTGGTATT 57.592 30.769 0.00 0.00 29.99 1.89
1440 1443 8.514594 TGACAAAATCATCAAAGAGTGGTATTC 58.485 33.333 0.00 0.00 29.99 1.75
1441 1444 8.641498 ACAAAATCATCAAAGAGTGGTATTCT 57.359 30.769 0.00 0.00 0.00 2.40
1442 1445 9.082313 ACAAAATCATCAAAGAGTGGTATTCTT 57.918 29.630 0.00 0.00 36.49 2.52
1449 1452 9.708222 CATCAAAGAGTGGTATTCTTAATTTCG 57.292 33.333 0.00 0.00 33.92 3.46
1450 1453 9.667107 ATCAAAGAGTGGTATTCTTAATTTCGA 57.333 29.630 0.00 0.00 33.92 3.71
1451 1454 9.667107 TCAAAGAGTGGTATTCTTAATTTCGAT 57.333 29.630 0.00 0.00 33.92 3.59
1454 1457 9.667107 AAGAGTGGTATTCTTAATTTCGATTCA 57.333 29.630 0.00 0.00 33.30 2.57
1455 1458 9.667107 AGAGTGGTATTCTTAATTTCGATTCAA 57.333 29.630 0.00 0.00 0.00 2.69
1456 1459 9.704098 GAGTGGTATTCTTAATTTCGATTCAAC 57.296 33.333 0.00 0.00 0.00 3.18
1457 1460 9.226606 AGTGGTATTCTTAATTTCGATTCAACA 57.773 29.630 0.00 0.00 0.00 3.33
1458 1461 9.834628 GTGGTATTCTTAATTTCGATTCAACAA 57.165 29.630 0.00 0.00 0.00 2.83
1463 1466 7.851822 TCTTAATTTCGATTCAACAAAGTGC 57.148 32.000 0.00 0.00 0.00 4.40
1464 1467 6.861055 TCTTAATTTCGATTCAACAAAGTGCC 59.139 34.615 0.00 0.00 0.00 5.01
1496 1499 2.158449 CACTTCCTTGCGTGTGAAGATC 59.842 50.000 10.77 0.00 39.01 2.75
1559 1563 2.093447 CACGAAATACAGAGGCCCTTCT 60.093 50.000 0.00 0.00 0.00 2.85
1589 1593 3.041211 CCAGATGTCAGGTGGAGGAATA 58.959 50.000 0.00 0.00 32.60 1.75
1632 1636 1.659233 CATTTCCTTGTGTGCGGCA 59.341 52.632 0.00 0.00 0.00 5.69
1659 1663 1.837051 AACCGTCAGCCTCTCCACA 60.837 57.895 0.00 0.00 0.00 4.17
1694 1698 4.081476 TCTGATGGATGTCGTTCATTGACT 60.081 41.667 0.00 0.00 36.83 3.41
1764 1768 0.599558 CCTACGAAGGGAACGACACA 59.400 55.000 0.00 0.00 39.48 3.72
1805 1809 2.672996 GCTGCCCACACGGTTGAT 60.673 61.111 0.00 0.00 0.00 2.57
1820 1824 4.468510 ACGGTTGATAGTATGAGGGTTGAA 59.531 41.667 0.00 0.00 0.00 2.69
1850 1854 2.612212 CTGCCATCGCCGTAAAATAACT 59.388 45.455 0.00 0.00 0.00 2.24
1860 1864 4.571919 CCGTAAAATAACTGGAGGTGTGA 58.428 43.478 0.00 0.00 0.00 3.58
1888 1892 0.029681 AGGGATAGACATGCCAGGGT 60.030 55.000 0.00 0.00 44.90 4.34
1968 1974 1.667830 CACGCGGTTCTGATGGTGT 60.668 57.895 12.47 0.00 0.00 4.16
1998 2004 0.625849 GGCTGGGGAAGGAAGATCAA 59.374 55.000 0.00 0.00 0.00 2.57
2010 2016 6.883756 GGAAGGAAGATCAAAGACTGAAGAAT 59.116 38.462 0.00 0.00 37.67 2.40
2136 2142 2.965147 CCCACAAGTCAACCTCCAAATT 59.035 45.455 0.00 0.00 0.00 1.82
2152 2158 3.742369 CCAAATTTGTGGCAGACAACATC 59.258 43.478 16.73 0.00 44.53 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.587844 CCAGCATGCTAGTAAAACTCTTGAT 59.412 40.000 22.19 0.00 31.97 2.57
36 37 6.928520 AGGGCAAAGAGTTGATAAGAAATTG 58.071 36.000 0.00 0.00 36.83 2.32
38 39 7.633789 TCTAGGGCAAAGAGTTGATAAGAAAT 58.366 34.615 0.00 0.00 36.83 2.17
52 53 2.582052 TGGTGTTGTTCTAGGGCAAAG 58.418 47.619 0.00 0.00 0.00 2.77
63 64 4.584325 AGTGATTATGCTGTTGGTGTTGTT 59.416 37.500 0.00 0.00 0.00 2.83
65 66 4.771590 AGTGATTATGCTGTTGGTGTTG 57.228 40.909 0.00 0.00 0.00 3.33
67 68 3.941483 GCTAGTGATTATGCTGTTGGTGT 59.059 43.478 0.00 0.00 0.00 4.16
72 73 5.295292 GTGTGATGCTAGTGATTATGCTGTT 59.705 40.000 0.00 0.00 0.00 3.16
113 114 3.585289 TGTTCAGCCACCTAGTTGGAATA 59.415 43.478 11.09 0.00 39.24 1.75
121 122 3.535561 CACCTATTGTTCAGCCACCTAG 58.464 50.000 0.00 0.00 0.00 3.02
122 123 2.355716 GCACCTATTGTTCAGCCACCTA 60.356 50.000 0.00 0.00 0.00 3.08
146 147 8.604640 TTATTGCAAAAAGAATGCTTTGATCA 57.395 26.923 1.71 0.00 43.32 2.92
180 182 6.153510 GGACTTTTCCAAAATCTCTAGGCATT 59.846 38.462 0.00 0.00 42.30 3.56
182 184 5.010282 GGACTTTTCCAAAATCTCTAGGCA 58.990 41.667 0.00 0.00 42.30 4.75
403 405 3.141398 AGTTTTGCAGAGATGCGAAGAA 58.859 40.909 3.35 0.00 39.13 2.52
462 464 8.812513 ATTCATGGATGATTTCTCTGTTTACA 57.187 30.769 0.00 0.00 36.56 2.41
469 471 7.147426 TGTGAGGTATTCATGGATGATTTCTCT 60.147 37.037 0.00 0.00 38.29 3.10
506 508 9.716531 CATGATGGCTATATTCTCTGACTTTTA 57.283 33.333 0.00 0.00 0.00 1.52
638 641 5.690865 TGGTTTCTCTCAAATACCTGTGTT 58.309 37.500 0.00 0.00 0.00 3.32
950 953 8.924511 TGAATCTTAAGATGAAAGAAGTGGTT 57.075 30.769 18.61 0.00 36.60 3.67
969 972 3.868757 TCCTCAACGACGATTGAATCT 57.131 42.857 0.00 0.00 38.12 2.40
1006 1009 8.643752 CCAAATATTTTCACGAATACGCTTTTT 58.356 29.630 0.00 0.00 43.96 1.94
1007 1010 8.024285 TCCAAATATTTTCACGAATACGCTTTT 58.976 29.630 0.00 0.00 43.96 2.27
1008 1011 7.531716 TCCAAATATTTTCACGAATACGCTTT 58.468 30.769 0.00 0.00 43.96 3.51
1009 1012 7.079182 TCCAAATATTTTCACGAATACGCTT 57.921 32.000 0.00 0.00 43.96 4.68
1010 1013 6.671614 TCCAAATATTTTCACGAATACGCT 57.328 33.333 0.00 0.00 43.96 5.07
1011 1014 7.184106 TCTTCCAAATATTTTCACGAATACGC 58.816 34.615 0.00 0.00 43.96 4.42
1012 1015 9.549509 TTTCTTCCAAATATTTTCACGAATACG 57.450 29.630 0.00 0.00 45.75 3.06
1017 1020 9.458374 GTCTTTTTCTTCCAAATATTTTCACGA 57.542 29.630 0.00 0.00 0.00 4.35
1018 1021 9.463443 AGTCTTTTTCTTCCAAATATTTTCACG 57.537 29.630 0.00 0.00 0.00 4.35
1072 1075 9.988350 GCTCGAAAATGATCTTGATTTTACTAA 57.012 29.630 3.05 0.00 34.00 2.24
1073 1076 8.328146 CGCTCGAAAATGATCTTGATTTTACTA 58.672 33.333 3.05 0.00 34.00 1.82
1074 1077 7.064609 TCGCTCGAAAATGATCTTGATTTTACT 59.935 33.333 3.05 0.00 34.00 2.24
1075 1078 7.180079 TCGCTCGAAAATGATCTTGATTTTAC 58.820 34.615 3.05 0.00 34.00 2.01
1076 1079 7.302350 TCGCTCGAAAATGATCTTGATTTTA 57.698 32.000 3.05 0.00 34.00 1.52
1077 1080 6.182039 TCGCTCGAAAATGATCTTGATTTT 57.818 33.333 2.74 2.74 36.04 1.82
1078 1081 5.801350 TCGCTCGAAAATGATCTTGATTT 57.199 34.783 0.00 0.00 0.00 2.17
1079 1082 5.998454 ATCGCTCGAAAATGATCTTGATT 57.002 34.783 0.00 0.00 0.00 2.57
1080 1083 7.386025 TCATTATCGCTCGAAAATGATCTTGAT 59.614 33.333 0.00 0.00 34.34 2.57
1081 1084 6.701400 TCATTATCGCTCGAAAATGATCTTGA 59.299 34.615 0.00 0.00 34.34 3.02
1082 1085 6.881017 TCATTATCGCTCGAAAATGATCTTG 58.119 36.000 0.00 0.00 34.34 3.02
1083 1086 6.347240 GCTCATTATCGCTCGAAAATGATCTT 60.347 38.462 0.00 0.00 37.62 2.40
1084 1087 5.119898 GCTCATTATCGCTCGAAAATGATCT 59.880 40.000 0.00 0.00 37.62 2.75
1085 1088 5.107337 TGCTCATTATCGCTCGAAAATGATC 60.107 40.000 0.00 0.00 37.62 2.92
1086 1089 4.751600 TGCTCATTATCGCTCGAAAATGAT 59.248 37.500 0.00 2.06 37.62 2.45
1087 1090 4.025730 GTGCTCATTATCGCTCGAAAATGA 60.026 41.667 0.00 0.00 36.32 2.57
1088 1091 4.206843 GTGCTCATTATCGCTCGAAAATG 58.793 43.478 0.00 0.00 0.00 2.32
1089 1092 3.248602 GGTGCTCATTATCGCTCGAAAAT 59.751 43.478 0.00 0.00 0.00 1.82
1090 1093 2.607635 GGTGCTCATTATCGCTCGAAAA 59.392 45.455 0.00 0.00 0.00 2.29
1091 1094 2.201732 GGTGCTCATTATCGCTCGAAA 58.798 47.619 0.00 0.00 0.00 3.46
1092 1095 1.538204 GGGTGCTCATTATCGCTCGAA 60.538 52.381 0.00 0.00 0.00 3.71
1093 1096 0.032130 GGGTGCTCATTATCGCTCGA 59.968 55.000 0.00 0.00 0.00 4.04
1094 1097 0.249447 TGGGTGCTCATTATCGCTCG 60.249 55.000 0.00 0.00 0.00 5.03
1095 1098 1.953559 TTGGGTGCTCATTATCGCTC 58.046 50.000 0.00 0.00 0.00 5.03
1096 1099 2.418368 TTTGGGTGCTCATTATCGCT 57.582 45.000 0.00 0.00 0.00 4.93
1097 1100 2.479560 GGTTTTGGGTGCTCATTATCGC 60.480 50.000 0.00 0.00 0.00 4.58
1098 1101 2.752354 TGGTTTTGGGTGCTCATTATCG 59.248 45.455 0.00 0.00 0.00 2.92
1099 1102 4.799564 TTGGTTTTGGGTGCTCATTATC 57.200 40.909 0.00 0.00 0.00 1.75
1100 1103 4.020307 CCTTTGGTTTTGGGTGCTCATTAT 60.020 41.667 0.00 0.00 0.00 1.28
1101 1104 3.323403 CCTTTGGTTTTGGGTGCTCATTA 59.677 43.478 0.00 0.00 0.00 1.90
1102 1105 2.104622 CCTTTGGTTTTGGGTGCTCATT 59.895 45.455 0.00 0.00 0.00 2.57
1103 1106 1.693606 CCTTTGGTTTTGGGTGCTCAT 59.306 47.619 0.00 0.00 0.00 2.90
1104 1107 1.118838 CCTTTGGTTTTGGGTGCTCA 58.881 50.000 0.00 0.00 0.00 4.26
1105 1108 0.392706 CCCTTTGGTTTTGGGTGCTC 59.607 55.000 0.00 0.00 36.32 4.26
1106 1109 2.526958 CCCTTTGGTTTTGGGTGCT 58.473 52.632 0.00 0.00 36.32 4.40
1117 1120 1.127343 TGCCCAGAAAAACCCTTTGG 58.873 50.000 0.00 0.00 37.80 3.28
1118 1121 2.093235 TGTTGCCCAGAAAAACCCTTTG 60.093 45.455 0.00 0.00 0.00 2.77
1119 1122 2.192263 TGTTGCCCAGAAAAACCCTTT 58.808 42.857 0.00 0.00 0.00 3.11
1120 1123 1.872773 TGTTGCCCAGAAAAACCCTT 58.127 45.000 0.00 0.00 0.00 3.95
1121 1124 1.872773 TTGTTGCCCAGAAAAACCCT 58.127 45.000 0.00 0.00 0.00 4.34
1122 1125 2.285083 GTTTGTTGCCCAGAAAAACCC 58.715 47.619 0.00 0.00 0.00 4.11
1123 1126 2.979240 TGTTTGTTGCCCAGAAAAACC 58.021 42.857 0.00 0.00 31.28 3.27
1124 1127 5.559427 ATTTGTTTGTTGCCCAGAAAAAC 57.441 34.783 0.00 0.00 0.00 2.43
1125 1128 7.872113 ATTATTTGTTTGTTGCCCAGAAAAA 57.128 28.000 0.00 0.00 0.00 1.94
1126 1129 8.964476 TTATTATTTGTTTGTTGCCCAGAAAA 57.036 26.923 0.00 0.00 0.00 2.29
1127 1130 8.424918 TCTTATTATTTGTTTGTTGCCCAGAAA 58.575 29.630 0.00 0.00 0.00 2.52
1128 1131 7.957002 TCTTATTATTTGTTTGTTGCCCAGAA 58.043 30.769 0.00 0.00 0.00 3.02
1129 1132 7.531857 TCTTATTATTTGTTTGTTGCCCAGA 57.468 32.000 0.00 0.00 0.00 3.86
1130 1133 8.776376 AATCTTATTATTTGTTTGTTGCCCAG 57.224 30.769 0.00 0.00 0.00 4.45
1131 1134 9.566432 AAAATCTTATTATTTGTTTGTTGCCCA 57.434 25.926 0.00 0.00 0.00 5.36
1172 1175 9.706691 CCAAGTACTTCAAGAACTTATAAGTCA 57.293 33.333 18.28 0.00 38.57 3.41
1173 1176 9.924650 TCCAAGTACTTCAAGAACTTATAAGTC 57.075 33.333 18.28 11.66 38.57 3.01
1176 1179 9.720769 CCTTCCAAGTACTTCAAGAACTTATAA 57.279 33.333 19.28 0.00 32.35 0.98
1177 1180 8.877195 ACCTTCCAAGTACTTCAAGAACTTATA 58.123 33.333 19.28 0.00 32.35 0.98
1178 1181 7.746703 ACCTTCCAAGTACTTCAAGAACTTAT 58.253 34.615 19.28 2.12 32.35 1.73
1179 1182 7.133133 ACCTTCCAAGTACTTCAAGAACTTA 57.867 36.000 19.28 0.00 32.35 2.24
1180 1183 6.002653 ACCTTCCAAGTACTTCAAGAACTT 57.997 37.500 19.28 4.76 33.82 2.66
1181 1184 5.632034 ACCTTCCAAGTACTTCAAGAACT 57.368 39.130 19.28 4.95 0.00 3.01
1182 1185 6.095021 ACAAACCTTCCAAGTACTTCAAGAAC 59.905 38.462 19.28 0.00 0.00 3.01
1183 1186 6.184789 ACAAACCTTCCAAGTACTTCAAGAA 58.815 36.000 19.28 14.84 0.00 2.52
1184 1187 5.751586 ACAAACCTTCCAAGTACTTCAAGA 58.248 37.500 19.28 9.49 0.00 3.02
1185 1188 6.451064 AACAAACCTTCCAAGTACTTCAAG 57.549 37.500 4.77 10.52 0.00 3.02
1186 1189 6.844097 AAACAAACCTTCCAAGTACTTCAA 57.156 33.333 4.77 0.77 0.00 2.69
1187 1190 6.844097 AAAACAAACCTTCCAAGTACTTCA 57.156 33.333 4.77 0.00 0.00 3.02
1188 1191 9.811995 ATTTAAAACAAACCTTCCAAGTACTTC 57.188 29.630 4.77 0.00 0.00 3.01
1190 1193 9.594478 CAATTTAAAACAAACCTTCCAAGTACT 57.406 29.630 0.00 0.00 0.00 2.73
1191 1194 9.373603 ACAATTTAAAACAAACCTTCCAAGTAC 57.626 29.630 0.00 0.00 0.00 2.73
1192 1195 9.589111 GACAATTTAAAACAAACCTTCCAAGTA 57.411 29.630 0.00 0.00 0.00 2.24
1193 1196 8.097662 TGACAATTTAAAACAAACCTTCCAAGT 58.902 29.630 0.00 0.00 0.00 3.16
1194 1197 8.485976 TGACAATTTAAAACAAACCTTCCAAG 57.514 30.769 0.00 0.00 0.00 3.61
1195 1198 8.848474 TTGACAATTTAAAACAAACCTTCCAA 57.152 26.923 0.00 0.00 0.00 3.53
1196 1199 8.887717 CATTGACAATTTAAAACAAACCTTCCA 58.112 29.630 0.00 0.00 0.00 3.53
1197 1200 8.341903 CCATTGACAATTTAAAACAAACCTTCC 58.658 33.333 0.00 0.00 0.00 3.46
1198 1201 9.103861 TCCATTGACAATTTAAAACAAACCTTC 57.896 29.630 0.00 0.00 0.00 3.46
1199 1202 8.888716 GTCCATTGACAATTTAAAACAAACCTT 58.111 29.630 0.00 0.00 41.37 3.50
1200 1203 8.432110 GTCCATTGACAATTTAAAACAAACCT 57.568 30.769 0.00 0.00 41.37 3.50
1307 1310 3.119137 CGAGAAATTTTTGGGCCCTTAGG 60.119 47.826 25.70 0.00 0.00 2.69
1308 1311 3.761752 TCGAGAAATTTTTGGGCCCTTAG 59.238 43.478 25.70 3.12 0.00 2.18
1309 1312 3.768878 TCGAGAAATTTTTGGGCCCTTA 58.231 40.909 25.70 8.41 0.00 2.69
1310 1313 2.604139 TCGAGAAATTTTTGGGCCCTT 58.396 42.857 25.70 7.51 0.00 3.95
1311 1314 2.302587 TCGAGAAATTTTTGGGCCCT 57.697 45.000 25.70 0.00 0.00 5.19
1312 1315 3.610040 ATTCGAGAAATTTTTGGGCCC 57.390 42.857 17.59 17.59 0.00 5.80
1313 1316 4.401202 TCCTATTCGAGAAATTTTTGGGCC 59.599 41.667 0.00 0.00 0.00 5.80
1314 1317 5.576447 TCCTATTCGAGAAATTTTTGGGC 57.424 39.130 0.00 0.00 0.00 5.36
1315 1318 8.470002 AGAATTCCTATTCGAGAAATTTTTGGG 58.530 33.333 0.65 0.00 43.99 4.12
1322 1325 9.936759 GAATCCTAGAATTCCTATTCGAGAAAT 57.063 33.333 0.65 1.92 42.66 2.17
1341 1344 9.135189 CCAATGTGATAAAAGAATGGAATCCTA 57.865 33.333 0.00 0.00 0.00 2.94
1342 1345 7.070322 CCCAATGTGATAAAAGAATGGAATCCT 59.930 37.037 0.00 0.00 0.00 3.24
1343 1346 7.069826 TCCCAATGTGATAAAAGAATGGAATCC 59.930 37.037 0.00 0.00 0.00 3.01
1344 1347 8.010733 TCCCAATGTGATAAAAGAATGGAATC 57.989 34.615 0.00 0.00 0.00 2.52
1345 1348 7.976414 TCCCAATGTGATAAAAGAATGGAAT 57.024 32.000 0.00 0.00 0.00 3.01
1346 1349 7.399765 ACATCCCAATGTGATAAAAGAATGGAA 59.600 33.333 0.00 0.00 44.51 3.53
1347 1350 6.896860 ACATCCCAATGTGATAAAAGAATGGA 59.103 34.615 0.00 0.00 44.51 3.41
1348 1351 7.116075 ACATCCCAATGTGATAAAAGAATGG 57.884 36.000 0.00 0.00 44.51 3.16
1349 1352 9.439500 AAAACATCCCAATGTGATAAAAGAATG 57.561 29.630 0.00 0.00 45.48 2.67
1350 1353 9.439500 CAAAACATCCCAATGTGATAAAAGAAT 57.561 29.630 0.00 0.00 45.48 2.40
1351 1354 8.646004 TCAAAACATCCCAATGTGATAAAAGAA 58.354 29.630 0.00 0.00 45.48 2.52
1352 1355 8.187913 TCAAAACATCCCAATGTGATAAAAGA 57.812 30.769 0.00 0.00 45.48 2.52
1353 1356 8.830201 TTCAAAACATCCCAATGTGATAAAAG 57.170 30.769 0.00 0.00 45.48 2.27
1354 1357 9.790344 AATTCAAAACATCCCAATGTGATAAAA 57.210 25.926 0.00 0.00 45.48 1.52
1355 1358 9.434420 GAATTCAAAACATCCCAATGTGATAAA 57.566 29.630 0.00 0.00 45.48 1.40
1356 1359 8.814931 AGAATTCAAAACATCCCAATGTGATAA 58.185 29.630 8.44 0.00 45.48 1.75
1357 1360 8.365060 AGAATTCAAAACATCCCAATGTGATA 57.635 30.769 8.44 0.00 45.48 2.15
1358 1361 7.248743 AGAATTCAAAACATCCCAATGTGAT 57.751 32.000 8.44 0.00 45.48 3.06
1359 1362 6.669125 AGAATTCAAAACATCCCAATGTGA 57.331 33.333 8.44 0.00 45.48 3.58
1360 1363 6.930164 TCAAGAATTCAAAACATCCCAATGTG 59.070 34.615 8.44 0.00 45.48 3.21
1362 1365 7.966246 TTCAAGAATTCAAAACATCCCAATG 57.034 32.000 8.44 0.00 38.93 2.82
1365 1368 9.487790 GTTTATTCAAGAATTCAAAACATCCCA 57.512 29.630 8.44 0.00 32.50 4.37
1366 1369 8.935844 GGTTTATTCAAGAATTCAAAACATCCC 58.064 33.333 8.44 0.00 32.50 3.85
1367 1370 9.487790 TGGTTTATTCAAGAATTCAAAACATCC 57.512 29.630 8.44 0.93 32.50 3.51
1373 1376 9.973450 TCGAATTGGTTTATTCAAGAATTCAAA 57.027 25.926 8.44 0.00 34.83 2.69
1374 1377 9.624697 CTCGAATTGGTTTATTCAAGAATTCAA 57.375 29.630 8.44 0.00 34.83 2.69
1375 1378 9.008965 TCTCGAATTGGTTTATTCAAGAATTCA 57.991 29.630 8.44 0.00 34.83 2.57
1376 1379 9.840427 TTCTCGAATTGGTTTATTCAAGAATTC 57.160 29.630 0.00 0.00 34.36 2.17
1377 1380 9.626045 GTTCTCGAATTGGTTTATTCAAGAATT 57.374 29.630 0.02 0.00 38.87 2.17
1378 1381 8.792633 TGTTCTCGAATTGGTTTATTCAAGAAT 58.207 29.630 0.00 0.52 38.87 2.40
1379 1382 8.160521 TGTTCTCGAATTGGTTTATTCAAGAA 57.839 30.769 0.00 0.00 36.00 2.52
1380 1383 7.444183 ACTGTTCTCGAATTGGTTTATTCAAGA 59.556 33.333 0.00 0.00 34.83 3.02
1381 1384 7.584987 ACTGTTCTCGAATTGGTTTATTCAAG 58.415 34.615 0.00 0.00 34.83 3.02
1382 1385 7.504924 ACTGTTCTCGAATTGGTTTATTCAA 57.495 32.000 0.00 0.00 34.83 2.69
1383 1386 7.359595 CAACTGTTCTCGAATTGGTTTATTCA 58.640 34.615 0.00 0.00 34.83 2.57
1384 1387 6.801862 CCAACTGTTCTCGAATTGGTTTATTC 59.198 38.462 0.00 0.00 35.98 1.75
1385 1388 6.488683 TCCAACTGTTCTCGAATTGGTTTATT 59.511 34.615 9.23 0.00 40.61 1.40
1386 1389 6.001460 TCCAACTGTTCTCGAATTGGTTTAT 58.999 36.000 9.23 0.00 40.61 1.40
1387 1390 5.369833 TCCAACTGTTCTCGAATTGGTTTA 58.630 37.500 9.23 0.00 40.61 2.01
1388 1391 4.204012 TCCAACTGTTCTCGAATTGGTTT 58.796 39.130 9.23 0.00 40.61 3.27
1389 1392 3.815809 TCCAACTGTTCTCGAATTGGTT 58.184 40.909 9.23 1.77 40.61 3.67
1390 1393 3.485463 TCCAACTGTTCTCGAATTGGT 57.515 42.857 9.23 0.00 40.61 3.67
1391 1394 3.426695 GCATCCAACTGTTCTCGAATTGG 60.427 47.826 4.79 4.79 41.04 3.16
1392 1395 3.438087 AGCATCCAACTGTTCTCGAATTG 59.562 43.478 0.00 0.00 0.00 2.32
1393 1396 3.438087 CAGCATCCAACTGTTCTCGAATT 59.562 43.478 0.00 0.00 0.00 2.17
1394 1397 3.005554 CAGCATCCAACTGTTCTCGAAT 58.994 45.455 0.00 0.00 0.00 3.34
1395 1398 2.037121 TCAGCATCCAACTGTTCTCGAA 59.963 45.455 0.00 0.00 36.50 3.71
1396 1399 1.618343 TCAGCATCCAACTGTTCTCGA 59.382 47.619 0.00 0.00 36.50 4.04
1397 1400 1.728971 GTCAGCATCCAACTGTTCTCG 59.271 52.381 0.00 0.00 36.50 4.04
1398 1401 2.771089 TGTCAGCATCCAACTGTTCTC 58.229 47.619 0.00 0.00 36.50 2.87
1399 1402 2.936919 TGTCAGCATCCAACTGTTCT 57.063 45.000 0.00 0.00 36.50 3.01
1400 1403 3.988379 TTTGTCAGCATCCAACTGTTC 57.012 42.857 0.00 0.00 36.50 3.18
1401 1404 4.341806 TGATTTTGTCAGCATCCAACTGTT 59.658 37.500 0.00 0.00 36.50 3.16
1402 1405 3.890756 TGATTTTGTCAGCATCCAACTGT 59.109 39.130 0.00 0.00 36.50 3.55
1403 1406 4.508461 TGATTTTGTCAGCATCCAACTG 57.492 40.909 0.00 0.00 36.44 3.16
1404 1407 5.320549 GATGATTTTGTCAGCATCCAACT 57.679 39.130 0.00 0.00 42.75 3.16
1412 1415 5.159209 CCACTCTTTGATGATTTTGTCAGC 58.841 41.667 0.00 0.00 43.51 4.26
1413 1416 6.323203 ACCACTCTTTGATGATTTTGTCAG 57.677 37.500 0.00 0.00 40.92 3.51
1414 1417 8.408043 AATACCACTCTTTGATGATTTTGTCA 57.592 30.769 0.00 0.00 42.06 3.58
1415 1418 8.734386 AGAATACCACTCTTTGATGATTTTGTC 58.266 33.333 0.00 0.00 0.00 3.18
1416 1419 8.641498 AGAATACCACTCTTTGATGATTTTGT 57.359 30.769 0.00 0.00 0.00 2.83
1423 1426 9.708222 CGAAATTAAGAATACCACTCTTTGATG 57.292 33.333 0.00 0.00 34.90 3.07
1424 1427 9.667107 TCGAAATTAAGAATACCACTCTTTGAT 57.333 29.630 0.00 0.00 34.90 2.57
1425 1428 9.667107 ATCGAAATTAAGAATACCACTCTTTGA 57.333 29.630 0.00 0.00 34.90 2.69
1428 1431 9.667107 TGAATCGAAATTAAGAATACCACTCTT 57.333 29.630 0.00 0.00 37.00 2.85
1429 1432 9.667107 TTGAATCGAAATTAAGAATACCACTCT 57.333 29.630 0.00 0.00 0.00 3.24
1430 1433 9.704098 GTTGAATCGAAATTAAGAATACCACTC 57.296 33.333 0.00 0.00 0.00 3.51
1431 1434 9.226606 TGTTGAATCGAAATTAAGAATACCACT 57.773 29.630 0.00 0.00 0.00 4.00
1432 1435 9.834628 TTGTTGAATCGAAATTAAGAATACCAC 57.165 29.630 0.00 0.00 0.00 4.16
1437 1440 8.915654 GCACTTTGTTGAATCGAAATTAAGAAT 58.084 29.630 0.00 0.00 0.00 2.40
1438 1441 7.381139 GGCACTTTGTTGAATCGAAATTAAGAA 59.619 33.333 0.00 0.00 0.00 2.52
1439 1442 6.861055 GGCACTTTGTTGAATCGAAATTAAGA 59.139 34.615 0.00 0.00 0.00 2.10
1440 1443 6.640499 TGGCACTTTGTTGAATCGAAATTAAG 59.360 34.615 0.00 0.00 0.00 1.85
1441 1444 6.507900 TGGCACTTTGTTGAATCGAAATTAA 58.492 32.000 0.00 0.00 0.00 1.40
1442 1445 6.078202 TGGCACTTTGTTGAATCGAAATTA 57.922 33.333 0.00 0.00 0.00 1.40
1443 1446 4.942852 TGGCACTTTGTTGAATCGAAATT 58.057 34.783 0.00 0.00 0.00 1.82
1444 1447 4.582701 TGGCACTTTGTTGAATCGAAAT 57.417 36.364 0.00 0.00 0.00 2.17
1445 1448 4.377839 TTGGCACTTTGTTGAATCGAAA 57.622 36.364 0.00 0.00 0.00 3.46
1446 1449 4.582701 ATTGGCACTTTGTTGAATCGAA 57.417 36.364 0.00 0.00 0.00 3.71
1447 1450 5.471797 TCTTATTGGCACTTTGTTGAATCGA 59.528 36.000 0.00 0.00 0.00 3.59
1448 1451 5.698832 TCTTATTGGCACTTTGTTGAATCG 58.301 37.500 0.00 0.00 0.00 3.34
1449 1452 6.587608 CCTTCTTATTGGCACTTTGTTGAATC 59.412 38.462 0.00 0.00 0.00 2.52
1450 1453 6.458210 CCTTCTTATTGGCACTTTGTTGAAT 58.542 36.000 0.00 0.00 0.00 2.57
1451 1454 5.841810 CCTTCTTATTGGCACTTTGTTGAA 58.158 37.500 0.00 0.00 0.00 2.69
1452 1455 5.452078 CCTTCTTATTGGCACTTTGTTGA 57.548 39.130 0.00 0.00 0.00 3.18
1496 1499 0.903454 AGGTCGGACCCACCAACTAG 60.903 60.000 23.21 0.00 39.75 2.57
1565 1569 1.279496 CTCCACCTGACATCTGGGAA 58.721 55.000 9.36 0.00 39.04 3.97
1589 1593 7.147983 TGCCTCCTTATTACACGCAAAATAATT 60.148 33.333 0.00 0.00 29.65 1.40
1632 1636 3.148084 CTGACGGTTGGGTCCACT 58.852 61.111 0.00 0.00 36.07 4.00
1644 1648 0.817654 TGTATGTGGAGAGGCTGACG 59.182 55.000 0.00 0.00 0.00 4.35
1694 1698 2.735478 CGCGGCGTGGTCAACTTA 60.735 61.111 15.36 0.00 0.00 2.24
1764 1768 3.382832 CGTGTCTTCCCCGGCTCT 61.383 66.667 0.00 0.00 0.00 4.09
1802 1806 6.575244 AACCATTCAACCCTCATACTATCA 57.425 37.500 0.00 0.00 0.00 2.15
1805 1809 4.141801 CCGAACCATTCAACCCTCATACTA 60.142 45.833 0.00 0.00 0.00 1.82
1841 1845 6.042781 ACTCACTCACACCTCCAGTTATTTTA 59.957 38.462 0.00 0.00 0.00 1.52
1850 1854 2.555448 CCTCTACTCACTCACACCTCCA 60.555 54.545 0.00 0.00 0.00 3.86
1860 1864 4.148838 GCATGTCTATCCCTCTACTCACT 58.851 47.826 0.00 0.00 0.00 3.41
1888 1892 1.148273 GGCCCCATCATACTCGCAA 59.852 57.895 0.00 0.00 0.00 4.85
1952 1958 1.497278 CAACACCATCAGAACCGCG 59.503 57.895 0.00 0.00 0.00 6.46
1998 2004 3.686726 GGCAATCGTGATTCTTCAGTCTT 59.313 43.478 0.00 0.00 30.85 3.01
2010 2016 8.779758 AGATGTCAATCTAACGGCAATCGTGA 62.780 42.308 0.00 0.00 45.18 4.35
2044 2050 1.544691 ACAATCGACTCTACCAGCGTT 59.455 47.619 0.00 0.00 0.00 4.84
2136 2142 1.337703 GCTTGATGTTGTCTGCCACAA 59.662 47.619 0.00 0.00 43.12 3.33


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

AutoCloner maintained by Alex Coulton.