Multiple sequence alignment - TraesCS1B01G010600

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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 TraesCS1B01G010600 chr1B 100.000 2493 0 0 1 2493 5005923 5003431 0.000000e+00 4604
1 TraesCS1B01G010600 chr1B 100.000 428 0 0 2772 3199 5003152 5002725 0.000000e+00 791
2 TraesCS1B01G010600 chr1D 88.344 2282 190 27 151 2362 341791 339516 0.000000e+00 2671
3 TraesCS1B01G010600 chr1D 87.643 437 50 3 1386 1822 327550 327118 3.680000e-139 505
4 TraesCS1B01G010600 chr1D 84.848 363 36 7 1848 2209 327128 326784 6.570000e-92 348
5 TraesCS1B01G010600 chr1A 88.340 1072 84 9 1317 2362 3776501 3777557 0.000000e+00 1249
6 TraesCS1B01G010600 chr1A 88.150 1038 96 12 276 1289 3775487 3776521 0.000000e+00 1210
7 TraesCS1B01G010600 chr1A 84.580 869 87 17 1368 2216 3795257 3796098 0.000000e+00 819
8 TraesCS1B01G010600 chr1A 77.230 426 26 25 2773 3159 3777813 3778206 1.960000e-42 183


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 TraesCS1B01G010600 chr1B 5002725 5005923 3198 True 2697.500000 4604 100.000000 1 3199 2 chr1B.!!$R1 3198
1 TraesCS1B01G010600 chr1D 339516 341791 2275 True 2671.000000 2671 88.344000 151 2362 1 chr1D.!!$R1 2211
2 TraesCS1B01G010600 chr1D 326784 327550 766 True 426.500000 505 86.245500 1386 2209 2 chr1D.!!$R2 823
3 TraesCS1B01G010600 chr1A 3775487 3778206 2719 False 880.666667 1249 84.573333 276 3159 3 chr1A.!!$F2 2883
4 TraesCS1B01G010600 chr1A 3795257 3796098 841 False 819.000000 819 84.580000 1368 2216 1 chr1A.!!$F1 848

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
86 87 0.038251 TGGCTCGAGCTATTATGCGG 60.038 55.0 34.46 0.0 41.70 5.69 F
89 90 0.038251 CTCGAGCTATTATGCGGGCA 60.038 55.0 0.00 0.0 38.13 5.36 F
95 96 0.249699 CTATTATGCGGGCACACGGA 60.250 55.0 0.00 0.0 38.89 4.69 F
124 125 0.329596 AGAACTGGAGGTCATTGGCC 59.670 55.0 0.00 0.0 0.00 5.36 F
1726 1797 0.036010 ATAGCTGCCAGTTGAAGCGT 60.036 50.0 0.00 0.0 41.88 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1321 1353 0.396556 GTTGTTCCTGGGGTTGTGGT 60.397 55.000 0.00 0.00 0.00 4.16 R
1480 1530 0.943835 GTTGCGGGAATTGTGGTTGC 60.944 55.000 0.00 0.00 0.00 4.17 R
1661 1732 1.482593 GAACGGGATCACTGACTGGAT 59.517 52.381 0.00 0.00 0.00 3.41 R
2002 2092 1.714794 GTGCACTAGTGGTGTAGCAG 58.285 55.000 23.95 0.00 46.86 4.24 R
2824 3045 0.035317 AGGTCGCACAAATGAGCTCA 59.965 50.000 20.79 20.79 38.49 4.26 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
36 37 3.706373 CCTGGTGCTGCTACGGGT 61.706 66.667 12.06 0.00 0.00 5.28
37 38 2.125512 CTGGTGCTGCTACGGGTC 60.126 66.667 0.00 0.00 0.00 4.46
38 39 2.920384 TGGTGCTGCTACGGGTCA 60.920 61.111 0.00 0.00 0.00 4.02
39 40 2.434359 GGTGCTGCTACGGGTCAC 60.434 66.667 0.00 0.00 0.00 3.67
40 41 2.342279 GTGCTGCTACGGGTCACA 59.658 61.111 0.00 0.00 0.00 3.58
41 42 1.738099 GTGCTGCTACGGGTCACAG 60.738 63.158 0.00 0.00 0.00 3.66
42 43 2.125512 GCTGCTACGGGTCACAGG 60.126 66.667 0.00 0.00 0.00 4.00
43 44 2.646175 GCTGCTACGGGTCACAGGA 61.646 63.158 0.00 0.00 0.00 3.86
44 45 1.513158 CTGCTACGGGTCACAGGAG 59.487 63.158 0.00 0.00 0.00 3.69
45 46 1.949847 CTGCTACGGGTCACAGGAGG 61.950 65.000 0.00 0.00 0.00 4.30
46 47 1.681327 GCTACGGGTCACAGGAGGA 60.681 63.158 0.00 0.00 0.00 3.71
47 48 1.668101 GCTACGGGTCACAGGAGGAG 61.668 65.000 0.00 0.00 0.00 3.69
48 49 1.668101 CTACGGGTCACAGGAGGAGC 61.668 65.000 0.00 0.00 0.00 4.70
49 50 3.775654 CGGGTCACAGGAGGAGCC 61.776 72.222 0.00 0.00 46.78 4.70
51 52 3.483587 GGTCACAGGAGGAGCCAA 58.516 61.111 0.00 0.00 40.02 4.52
52 53 1.298014 GGTCACAGGAGGAGCCAAG 59.702 63.158 0.00 0.00 40.02 3.61
53 54 1.298014 GTCACAGGAGGAGCCAAGG 59.702 63.158 0.00 0.00 40.02 3.61
54 55 2.045536 CACAGGAGGAGCCAAGGC 60.046 66.667 2.02 2.02 40.02 4.35
79 80 3.227276 CCGGGTGGCTCGAGCTAT 61.227 66.667 34.46 0.00 41.70 2.97
80 81 2.797278 CCGGGTGGCTCGAGCTATT 61.797 63.158 34.46 0.00 41.70 1.73
81 82 1.461091 CCGGGTGGCTCGAGCTATTA 61.461 60.000 34.46 17.08 41.70 0.98
82 83 0.603569 CGGGTGGCTCGAGCTATTAT 59.396 55.000 34.46 0.00 41.70 1.28
83 84 1.670087 CGGGTGGCTCGAGCTATTATG 60.670 57.143 34.46 17.15 41.70 1.90
84 85 1.433534 GGTGGCTCGAGCTATTATGC 58.566 55.000 34.46 17.45 41.70 3.14
85 86 1.063806 GTGGCTCGAGCTATTATGCG 58.936 55.000 34.46 0.00 41.70 4.73
86 87 0.038251 TGGCTCGAGCTATTATGCGG 60.038 55.000 34.46 0.00 41.70 5.69
87 88 0.737715 GGCTCGAGCTATTATGCGGG 60.738 60.000 34.46 0.00 41.70 6.13
88 89 1.355066 GCTCGAGCTATTATGCGGGC 61.355 60.000 29.88 0.00 43.35 6.13
89 90 0.038251 CTCGAGCTATTATGCGGGCA 60.038 55.000 0.00 0.00 38.13 5.36
90 91 0.319555 TCGAGCTATTATGCGGGCAC 60.320 55.000 0.00 0.00 38.13 5.01
91 92 0.599991 CGAGCTATTATGCGGGCACA 60.600 55.000 0.00 0.00 38.13 4.57
92 93 0.868406 GAGCTATTATGCGGGCACAC 59.132 55.000 0.00 0.00 38.13 3.82
93 94 0.880278 AGCTATTATGCGGGCACACG 60.880 55.000 0.00 0.00 38.13 4.49
94 95 1.841663 GCTATTATGCGGGCACACGG 61.842 60.000 0.00 0.00 0.00 4.94
95 96 0.249699 CTATTATGCGGGCACACGGA 60.250 55.000 0.00 0.00 38.89 4.69
96 97 0.249699 TATTATGCGGGCACACGGAG 60.250 55.000 0.00 0.00 37.68 4.63
97 98 2.940890 ATTATGCGGGCACACGGAGG 62.941 60.000 0.00 0.00 37.68 4.30
112 113 0.531200 GGAGGTGTCCGTAGAACTGG 59.469 60.000 0.00 0.00 31.37 4.00
113 114 1.542492 GAGGTGTCCGTAGAACTGGA 58.458 55.000 0.00 0.00 0.00 3.86
114 115 1.473278 GAGGTGTCCGTAGAACTGGAG 59.527 57.143 0.00 0.00 34.21 3.86
115 116 0.531200 GGTGTCCGTAGAACTGGAGG 59.469 60.000 0.00 0.00 34.21 4.30
116 117 1.254954 GTGTCCGTAGAACTGGAGGT 58.745 55.000 0.00 0.00 34.21 3.85
117 118 1.201880 GTGTCCGTAGAACTGGAGGTC 59.798 57.143 0.00 0.00 34.21 3.85
118 119 1.202964 TGTCCGTAGAACTGGAGGTCA 60.203 52.381 0.00 0.00 34.21 4.02
119 120 2.100989 GTCCGTAGAACTGGAGGTCAT 58.899 52.381 0.00 0.00 34.21 3.06
120 121 2.496470 GTCCGTAGAACTGGAGGTCATT 59.504 50.000 0.00 0.00 34.21 2.57
121 122 2.496070 TCCGTAGAACTGGAGGTCATTG 59.504 50.000 0.00 0.00 0.00 2.82
122 123 2.418746 CCGTAGAACTGGAGGTCATTGG 60.419 54.545 0.00 0.00 0.00 3.16
123 124 2.633488 GTAGAACTGGAGGTCATTGGC 58.367 52.381 0.00 0.00 0.00 4.52
124 125 0.329596 AGAACTGGAGGTCATTGGCC 59.670 55.000 0.00 0.00 0.00 5.36
125 126 1.002134 AACTGGAGGTCATTGGCCG 60.002 57.895 0.70 0.00 0.00 6.13
126 127 2.124570 CTGGAGGTCATTGGCCGG 60.125 66.667 0.70 0.00 0.00 6.13
127 128 4.424711 TGGAGGTCATTGGCCGGC 62.425 66.667 21.18 21.18 0.00 6.13
145 146 3.195698 GCGGTGGCGTTGATCCTC 61.196 66.667 0.00 0.00 0.00 3.71
146 147 2.579201 CGGTGGCGTTGATCCTCT 59.421 61.111 0.00 0.00 0.00 3.69
147 148 1.519455 CGGTGGCGTTGATCCTCTC 60.519 63.158 0.00 0.00 0.00 3.20
148 149 1.519455 GGTGGCGTTGATCCTCTCG 60.519 63.158 0.00 0.00 0.00 4.04
149 150 1.511305 GTGGCGTTGATCCTCTCGA 59.489 57.895 0.00 0.00 0.00 4.04
150 151 0.802607 GTGGCGTTGATCCTCTCGAC 60.803 60.000 0.00 0.00 35.23 4.20
161 162 1.132844 CTCTCGACGAGTGACACCG 59.867 63.158 23.41 12.90 34.95 4.94
166 167 2.597805 ACGAGTGACACCGAGCCT 60.598 61.111 19.06 0.00 0.00 4.58
175 176 1.157870 ACACCGAGCCTTCAACAACG 61.158 55.000 0.00 0.00 0.00 4.10
182 183 1.098712 GCCTTCAACAACGGTGTCCA 61.099 55.000 6.54 0.00 36.80 4.02
201 207 2.958355 CCATTTCAGTTGGGTCTGTTGT 59.042 45.455 0.00 0.00 36.85 3.32
207 213 3.135712 TCAGTTGGGTCTGTTGTGTACAT 59.864 43.478 0.00 0.00 35.85 2.29
208 214 3.498397 CAGTTGGGTCTGTTGTGTACATC 59.502 47.826 0.00 0.00 35.85 3.06
225 231 2.593436 CGGTGGTGTCCGGCTTTT 60.593 61.111 0.00 0.00 45.88 2.27
237 243 2.470286 GCTTTTCGTCTGCGTCCG 59.530 61.111 0.00 0.00 39.49 4.79
244 250 2.028484 GTCTGCGTCCGTTGTCCA 59.972 61.111 0.00 0.00 0.00 4.02
252 258 0.671251 GTCCGTTGTCCATTTTGGCA 59.329 50.000 0.00 0.00 37.47 4.92
268 274 3.872459 TGGCAACCCAAATGGAAAAAT 57.128 38.095 0.00 0.00 38.46 1.82
269 275 3.484407 TGGCAACCCAAATGGAAAAATG 58.516 40.909 0.00 0.00 38.46 2.32
270 276 2.228582 GGCAACCCAAATGGAAAAATGC 59.771 45.455 0.00 4.08 37.39 3.56
271 277 2.883386 GCAACCCAAATGGAAAAATGCA 59.117 40.909 0.00 0.00 37.39 3.96
273 279 4.387598 CAACCCAAATGGAAAAATGCAGA 58.612 39.130 0.00 0.00 37.39 4.26
274 280 4.914177 ACCCAAATGGAAAAATGCAGAT 57.086 36.364 0.00 0.00 37.39 2.90
283 291 5.108517 TGGAAAAATGCAGATAAAATCCGC 58.891 37.500 0.00 0.00 33.35 5.54
289 297 2.652662 CAGATAAAATCCGCGTCTGC 57.347 50.000 4.92 0.00 37.91 4.26
300 308 1.292223 GCGTCTGCTTGGGTCACTA 59.708 57.895 0.00 0.00 38.39 2.74
306 314 2.086869 CTGCTTGGGTCACTACATTGG 58.913 52.381 0.00 0.00 0.00 3.16
315 323 1.086696 CACTACATTGGAGTTGGCCG 58.913 55.000 0.00 0.00 0.00 6.13
328 336 2.106511 AGTTGGCCGTATGCTATTCCAT 59.893 45.455 0.00 0.00 40.92 3.41
371 379 9.948964 TCTATAATTCACATAGCATGCTATTGT 57.051 29.630 32.84 28.13 37.16 2.71
379 387 2.826428 AGCATGCTATTGTAGGTGTCG 58.174 47.619 21.21 0.00 0.00 4.35
487 495 5.509501 GGGTTTAATATCATGTGCATGGTGG 60.510 44.000 11.68 0.00 39.24 4.61
491 499 0.627451 ATCATGTGCATGGTGGTCCT 59.373 50.000 11.68 0.00 39.24 3.85
494 502 2.282391 GTGCATGGTGGTCCTGCA 60.282 61.111 0.00 0.00 41.67 4.41
495 503 1.679977 GTGCATGGTGGTCCTGCAT 60.680 57.895 6.78 0.00 43.72 3.96
536 545 9.817809 CACCTAGTGTGTATTAACAACTCATAT 57.182 33.333 3.86 0.00 40.26 1.78
632 643 8.134905 ACACAAAACTACGAAGTTAGTTTAGG 57.865 34.615 8.74 7.48 45.37 2.69
639 650 7.600960 ACTACGAAGTTAGTTTAGGAAGAAGG 58.399 38.462 0.00 0.00 37.78 3.46
644 655 6.608539 AGTTAGTTTAGGAAGAAGGAGTCC 57.391 41.667 0.00 0.00 0.00 3.85
663 674 6.092807 GGAGTCCAGAACAATCTTCACATTAC 59.907 42.308 3.60 0.00 32.03 1.89
719 731 4.245251 ACAAACTTAGTTCCCCACAAGT 57.755 40.909 0.00 0.00 31.75 3.16
746 758 3.091545 CAACCTGGATGTGCCTAACAAT 58.908 45.455 0.00 0.00 43.61 2.71
747 759 2.726821 ACCTGGATGTGCCTAACAATG 58.273 47.619 0.00 0.00 43.61 2.82
755 767 5.414454 GGATGTGCCTAACAATGTGTAGAAA 59.586 40.000 0.00 0.00 43.61 2.52
803 816 6.990939 GGGGTGTAATCTAGATAAGTGTTTCC 59.009 42.308 5.46 1.40 0.00 3.13
804 817 6.700520 GGGTGTAATCTAGATAAGTGTTTCCG 59.299 42.308 5.46 0.00 0.00 4.30
893 906 3.181476 ACAAGAAAGCAACTTTGGCGATT 60.181 39.130 0.00 0.00 33.49 3.34
911 926 5.458779 GGCGATTAATCCAAATTACACTTGC 59.541 40.000 9.87 2.75 0.00 4.01
919 934 4.217550 TCCAAATTACACTTGCAAGTAGCC 59.782 41.667 30.67 0.00 44.83 3.93
921 936 3.721087 ATTACACTTGCAAGTAGCCCT 57.279 42.857 30.67 12.54 44.83 5.19
922 937 2.472695 TACACTTGCAAGTAGCCCTG 57.527 50.000 30.67 19.49 44.83 4.45
924 939 1.672356 ACTTGCAAGTAGCCCTGCG 60.672 57.895 30.25 1.60 44.83 5.18
925 940 1.375908 CTTGCAAGTAGCCCTGCGA 60.376 57.895 18.65 0.00 44.83 5.10
927 942 0.955428 TTGCAAGTAGCCCTGCGAAG 60.955 55.000 0.00 0.00 44.83 3.79
928 943 1.079127 GCAAGTAGCCCTGCGAAGA 60.079 57.895 0.00 0.00 37.23 2.87
929 944 0.462759 GCAAGTAGCCCTGCGAAGAT 60.463 55.000 0.00 0.00 37.23 2.40
945 977 8.085296 CCTGCGAAGATAGTTTGATAAGAGTAT 58.915 37.037 0.00 0.00 0.00 2.12
946 978 9.123709 CTGCGAAGATAGTTTGATAAGAGTATC 57.876 37.037 0.00 0.00 37.27 2.24
947 979 8.630037 TGCGAAGATAGTTTGATAAGAGTATCA 58.370 33.333 0.00 0.00 43.57 2.15
999 1031 6.400568 ACGAAAAGAAATCATTTCATGGCAT 58.599 32.000 12.74 0.00 42.10 4.40
1019 1051 5.523916 GGCATCTATAAATAGCCATACACCG 59.476 44.000 0.00 0.00 44.59 4.94
1045 1077 1.346885 ACCCCCTTCCATGATCCATCT 60.347 52.381 0.00 0.00 0.00 2.90
1057 1089 7.118060 TCCATGATCCATCTTTCACACATTTA 58.882 34.615 0.00 0.00 0.00 1.40
1073 1105 6.696583 CACACATTTAGAGCACAAACATTCAA 59.303 34.615 0.00 0.00 0.00 2.69
1084 1116 9.243637 GAGCACAAACATTCAAACTAAACAATA 57.756 29.630 0.00 0.00 0.00 1.90
1085 1117 9.030301 AGCACAAACATTCAAACTAAACAATAC 57.970 29.630 0.00 0.00 0.00 1.89
1104 1136 7.175104 ACAATACAGAGTAACCACAAATCCAT 58.825 34.615 0.00 0.00 0.00 3.41
1115 1147 4.891756 ACCACAAATCCATCATGAAGATCC 59.108 41.667 10.98 0.00 33.72 3.36
1164 1196 2.186903 GACCATCACCACCGCGAT 59.813 61.111 8.23 0.00 0.00 4.58
1167 1199 2.202743 CATCACCACCGCGATCGT 60.203 61.111 17.81 0.00 0.00 3.73
1183 1215 2.701780 CGTGCAGCTCGACCCTAGT 61.702 63.158 11.47 0.00 0.00 2.57
1184 1216 1.153745 GTGCAGCTCGACCCTAGTG 60.154 63.158 0.00 0.00 0.00 2.74
1213 1245 2.364970 CCAAGAAAGGCCACAACAATCA 59.635 45.455 5.01 0.00 0.00 2.57
1252 1284 2.627699 ACTTACCCAGCAACAACCATTG 59.372 45.455 0.00 0.00 0.00 2.82
1310 1342 4.486125 AAAGAGCCACAACAACCATTTT 57.514 36.364 0.00 0.00 0.00 1.82
1321 1353 0.388659 AACCATTTTCGCTGCAGCAA 59.611 45.000 36.03 25.38 42.21 3.91
1328 1360 2.335052 TTCGCTGCAGCAACCACAAC 62.335 55.000 36.03 5.81 42.21 3.32
1329 1361 2.028043 GCTGCAGCAACCACAACC 59.972 61.111 33.36 0.00 41.59 3.77
1334 1366 2.198426 AGCAACCACAACCCCAGG 59.802 61.111 0.00 0.00 0.00 4.45
1345 1377 0.336737 AACCCCAGGAACAACAACCA 59.663 50.000 0.00 0.00 0.00 3.67
1365 1397 3.614092 CATATCCACAACAGCCACTTCT 58.386 45.455 0.00 0.00 0.00 2.85
1396 1428 3.891049 ACTTCCCCAGCAACATCTATTC 58.109 45.455 0.00 0.00 0.00 1.75
1408 1440 1.699054 ATCTATTCCCGCAGCAGCCA 61.699 55.000 0.00 0.00 37.52 4.75
1426 1476 2.468831 CCACCACAACAACAATTTCCG 58.531 47.619 0.00 0.00 0.00 4.30
1444 1494 4.728409 CAGCAGATGCCACTTCCA 57.272 55.556 0.14 0.00 43.38 3.53
1445 1495 3.186345 CAGCAGATGCCACTTCCAT 57.814 52.632 0.14 0.00 43.38 3.41
1448 1498 2.552743 CAGCAGATGCCACTTCCATATG 59.447 50.000 0.14 0.00 43.38 1.78
1474 1524 2.126467 CAAACATTCCCGCAACAACAG 58.874 47.619 0.00 0.00 0.00 3.16
1480 1530 1.299316 CCCGCAACAACAGCAACAG 60.299 57.895 0.00 0.00 0.00 3.16
1511 1582 1.067821 TCCCGCAACAACAACCATTTC 59.932 47.619 0.00 0.00 0.00 2.17
1726 1797 0.036010 ATAGCTGCCAGTTGAAGCGT 60.036 50.000 0.00 0.00 41.88 5.07
2002 2092 0.391661 ACGTGCATGTCCCATCTGAC 60.392 55.000 5.51 0.00 35.77 3.51
2013 2103 1.406069 CCCATCTGACTGCTACACCAC 60.406 57.143 0.00 0.00 0.00 4.16
2056 2146 1.300971 CTGCCATGAACGGTGGACAG 61.301 60.000 0.00 0.13 39.12 3.51
2065 2155 2.631160 ACGGTGGACAGTGAAATGAA 57.369 45.000 0.00 0.00 0.00 2.57
2068 2158 3.066203 ACGGTGGACAGTGAAATGAAAAC 59.934 43.478 0.00 0.00 0.00 2.43
2135 2225 4.270084 GGACGATCGATGTAGCAATGAAAA 59.730 41.667 24.34 0.00 0.00 2.29
2210 2300 6.432403 TCAAACTTGGGAATAAAGGCAAAT 57.568 33.333 0.00 0.00 0.00 2.32
2216 2306 8.791327 ACTTGGGAATAAAGGCAAATAAAATG 57.209 30.769 0.00 0.00 0.00 2.32
2330 2441 5.413499 TCCTAGTCCGGAAAATTTAGTTCG 58.587 41.667 5.23 0.00 0.00 3.95
2332 2443 4.276058 AGTCCGGAAAATTTAGTTCGGA 57.724 40.909 5.23 8.02 0.00 4.55
2345 2456 1.680989 TTCGGAGATCTCGTGCCCA 60.681 57.895 16.46 0.00 35.04 5.36
2351 2462 2.600731 GAGATCTCGTGCCCATAATCG 58.399 52.381 7.04 0.00 0.00 3.34
2356 2467 2.515901 GTGCCCATAATCGCCCCT 59.484 61.111 0.00 0.00 0.00 4.79
2362 2473 0.620556 CCATAATCGCCCCTAGCCAT 59.379 55.000 0.00 0.00 38.78 4.40
2363 2474 1.004745 CCATAATCGCCCCTAGCCATT 59.995 52.381 0.00 0.00 38.78 3.16
2364 2475 2.086869 CATAATCGCCCCTAGCCATTG 58.913 52.381 0.00 0.00 32.91 2.82
2367 2478 0.550914 ATCGCCCCTAGCCATTGAAA 59.449 50.000 0.00 0.00 38.78 2.69
2368 2479 0.329931 TCGCCCCTAGCCATTGAAAA 59.670 50.000 0.00 0.00 38.78 2.29
2369 2480 1.181786 CGCCCCTAGCCATTGAAAAA 58.818 50.000 0.00 0.00 38.78 1.94
2391 2594 2.099141 ATGTCCGTGTGTGGATTCAG 57.901 50.000 0.00 0.00 40.91 3.02
2394 2597 0.602638 TCCGTGTGTGGATTCAGTGC 60.603 55.000 0.00 0.00 31.53 4.40
2406 2609 2.734755 TTCAGTGCATAGGAATGGGG 57.265 50.000 0.00 0.00 33.38 4.96
2442 2645 0.382515 TGCGCAAACGGCTTTAAAGT 59.617 45.000 8.16 0.00 41.67 2.66
2453 2656 2.755103 GGCTTTAAAGTCCAGGACCATG 59.245 50.000 16.72 2.49 32.18 3.66
2460 2663 0.326264 GTCCAGGACCATGTGCTTCT 59.674 55.000 8.65 0.00 30.21 2.85
2461 2664 1.067295 TCCAGGACCATGTGCTTCTT 58.933 50.000 0.00 0.00 30.21 2.52
2462 2665 1.003580 TCCAGGACCATGTGCTTCTTC 59.996 52.381 0.00 0.00 30.21 2.87
2465 2668 1.980765 AGGACCATGTGCTTCTTCAGA 59.019 47.619 0.00 0.00 27.37 3.27
2468 2689 3.760684 GGACCATGTGCTTCTTCAGATTT 59.239 43.478 0.00 0.00 0.00 2.17
2479 2700 6.040878 GCTTCTTCAGATTTTGAATCCCATG 58.959 40.000 0.00 0.00 44.48 3.66
2481 2702 6.764308 TCTTCAGATTTTGAATCCCATGTC 57.236 37.500 0.00 0.00 44.48 3.06
2482 2703 5.355071 TCTTCAGATTTTGAATCCCATGTCG 59.645 40.000 0.00 0.00 44.48 4.35
2483 2704 4.588899 TCAGATTTTGAATCCCATGTCGT 58.411 39.130 0.00 0.00 31.34 4.34
2484 2705 4.395854 TCAGATTTTGAATCCCATGTCGTG 59.604 41.667 0.00 0.00 31.34 4.35
2486 2707 4.766891 AGATTTTGAATCCCATGTCGTGTT 59.233 37.500 0.00 0.00 0.00 3.32
2487 2708 4.497473 TTTTGAATCCCATGTCGTGTTC 57.503 40.909 0.00 0.00 0.00 3.18
2490 2711 3.334691 TGAATCCCATGTCGTGTTCTTC 58.665 45.455 0.00 0.00 0.00 2.87
2491 2712 3.007940 TGAATCCCATGTCGTGTTCTTCT 59.992 43.478 0.00 0.00 0.00 2.85
2791 3012 1.635487 CCTCTGATTCCTCACCCCAAA 59.365 52.381 0.00 0.00 0.00 3.28
2793 3014 3.285484 CTCTGATTCCTCACCCCAAATG 58.715 50.000 0.00 0.00 0.00 2.32
2796 3017 2.291540 TGATTCCTCACCCCAAATGTCC 60.292 50.000 0.00 0.00 0.00 4.02
2818 3039 6.437477 GTCCCAAAATATCCCAAATCTATCCC 59.563 42.308 0.00 0.00 0.00 3.85
2841 3062 1.151668 ACTGAGCTCATTTGTGCGAC 58.848 50.000 18.63 0.00 39.31 5.19
2849 3070 0.652592 CATTTGTGCGACCTCGATCC 59.347 55.000 0.00 0.00 43.02 3.36
2851 3072 0.249120 TTTGTGCGACCTCGATCCAT 59.751 50.000 0.00 0.00 43.02 3.41
2852 3073 0.179111 TTGTGCGACCTCGATCCATC 60.179 55.000 0.00 0.00 43.02 3.51
2853 3074 1.300233 GTGCGACCTCGATCCATCC 60.300 63.158 0.00 0.00 43.02 3.51
2854 3075 1.756561 TGCGACCTCGATCCATCCA 60.757 57.895 0.00 0.00 43.02 3.41
2855 3076 1.326951 TGCGACCTCGATCCATCCAA 61.327 55.000 0.00 0.00 43.02 3.53
2856 3077 0.034059 GCGACCTCGATCCATCCAAT 59.966 55.000 0.00 0.00 43.02 3.16
2857 3078 1.541233 GCGACCTCGATCCATCCAATT 60.541 52.381 0.00 0.00 43.02 2.32
2858 3079 2.288825 GCGACCTCGATCCATCCAATTA 60.289 50.000 0.00 0.00 43.02 1.40
2859 3080 3.318017 CGACCTCGATCCATCCAATTAC 58.682 50.000 0.00 0.00 43.02 1.89
2860 3081 3.665190 GACCTCGATCCATCCAATTACC 58.335 50.000 0.00 0.00 0.00 2.85
2861 3082 2.037251 ACCTCGATCCATCCAATTACCG 59.963 50.000 0.00 0.00 0.00 4.02
2862 3083 2.612972 CCTCGATCCATCCAATTACCGG 60.613 54.545 0.00 0.00 0.00 5.28
2863 3084 1.346395 TCGATCCATCCAATTACCGGG 59.654 52.381 6.32 0.00 0.00 5.73
2864 3085 1.071699 CGATCCATCCAATTACCGGGT 59.928 52.381 6.32 4.46 0.00 5.28
2865 3086 2.779506 GATCCATCCAATTACCGGGTC 58.220 52.381 6.32 0.00 0.00 4.46
2866 3087 0.466543 TCCATCCAATTACCGGGTCG 59.533 55.000 6.32 0.00 0.00 4.79
2867 3088 0.466543 CCATCCAATTACCGGGTCGA 59.533 55.000 6.32 0.00 0.00 4.20
2897 3118 4.292178 GCGATGGAGCGGAGGGAG 62.292 72.222 0.00 0.00 0.00 4.30
2903 3124 2.438795 GAGCGGAGGGAGACGTCT 60.439 66.667 20.18 20.18 44.54 4.18
2904 3125 1.153208 GAGCGGAGGGAGACGTCTA 60.153 63.158 20.09 0.00 44.54 2.59
2905 3126 1.153127 AGCGGAGGGAGACGTCTAG 60.153 63.158 20.09 7.12 44.54 2.43
2915 3166 0.251653 AGACGTCTAGGGGCTCACAA 60.252 55.000 18.46 0.00 0.00 3.33
2922 3173 0.913934 TAGGGGCTCACAATGGCTCA 60.914 55.000 0.00 0.00 32.41 4.26
2943 3194 1.375396 CGCGGATTTGTGGTGGAGA 60.375 57.895 0.00 0.00 0.00 3.71
2957 3208 2.581354 GAGAGCGTGGTCATGGCT 59.419 61.111 0.00 0.00 40.29 4.75
2969 3220 2.027605 ATGGCTACGGCGTCATCG 59.972 61.111 19.21 4.89 39.81 3.84
2981 3232 0.524604 CGTCATCGTGTGCGTCCATA 60.525 55.000 0.00 0.00 39.49 2.74
2982 3233 1.635844 GTCATCGTGTGCGTCCATAA 58.364 50.000 0.00 0.00 39.49 1.90
2983 3234 1.323534 GTCATCGTGTGCGTCCATAAC 59.676 52.381 0.00 0.00 39.49 1.89
2984 3235 0.650512 CATCGTGTGCGTCCATAACC 59.349 55.000 0.00 0.00 39.49 2.85
2985 3236 0.461339 ATCGTGTGCGTCCATAACCC 60.461 55.000 0.00 0.00 39.49 4.11
2986 3237 1.374885 CGTGTGCGTCCATAACCCA 60.375 57.895 0.00 0.00 0.00 4.51
2987 3238 0.742990 CGTGTGCGTCCATAACCCAT 60.743 55.000 0.00 0.00 0.00 4.00
2989 3240 0.107410 TGTGCGTCCATAACCCATCC 60.107 55.000 0.00 0.00 0.00 3.51
2990 3241 0.180406 GTGCGTCCATAACCCATCCT 59.820 55.000 0.00 0.00 0.00 3.24
2991 3242 0.468226 TGCGTCCATAACCCATCCTC 59.532 55.000 0.00 0.00 0.00 3.71
2992 3243 0.600255 GCGTCCATAACCCATCCTCG 60.600 60.000 0.00 0.00 0.00 4.63
2993 3244 0.750850 CGTCCATAACCCATCCTCGT 59.249 55.000 0.00 0.00 0.00 4.18
2995 3246 1.485066 GTCCATAACCCATCCTCGTGT 59.515 52.381 0.00 0.00 0.00 4.49
2996 3247 1.484653 TCCATAACCCATCCTCGTGTG 59.515 52.381 0.00 0.00 0.00 3.82
2997 3248 1.299541 CATAACCCATCCTCGTGTGC 58.700 55.000 0.00 0.00 0.00 4.57
2998 3249 0.179084 ATAACCCATCCTCGTGTGCG 60.179 55.000 0.00 0.00 39.92 5.34
2999 3250 1.537814 TAACCCATCCTCGTGTGCGT 61.538 55.000 0.00 0.00 39.49 5.24
3000 3251 2.509336 CCCATCCTCGTGTGCGTC 60.509 66.667 0.00 0.00 39.49 5.19
3001 3252 2.261361 CCATCCTCGTGTGCGTCA 59.739 61.111 0.00 0.00 39.49 4.35
3002 3253 1.153568 CCATCCTCGTGTGCGTCAT 60.154 57.895 0.00 0.00 39.49 3.06
3003 3254 1.148157 CCATCCTCGTGTGCGTCATC 61.148 60.000 0.00 0.00 39.49 2.92
3004 3255 1.226688 ATCCTCGTGTGCGTCATCG 60.227 57.895 0.00 0.00 39.49 3.84
3005 3256 1.934220 ATCCTCGTGTGCGTCATCGT 61.934 55.000 0.00 0.00 39.49 3.73
3006 3257 2.436539 CCTCGTGTGCGTCATCGTG 61.437 63.158 0.00 0.00 39.49 4.35
3007 3258 1.729484 CTCGTGTGCGTCATCGTGT 60.729 57.895 0.00 0.00 39.49 4.49
3008 3259 0.453782 CTCGTGTGCGTCATCGTGTA 60.454 55.000 0.00 0.00 39.49 2.90
3009 3260 0.726787 TCGTGTGCGTCATCGTGTAC 60.727 55.000 0.00 0.00 39.49 2.90
3010 3261 1.694403 GTGTGCGTCATCGTGTACG 59.306 57.895 0.00 0.00 41.92 3.67
3011 3262 1.000233 GTGTGCGTCATCGTGTACGT 61.000 55.000 4.20 0.00 41.10 3.57
3012 3263 0.726787 TGTGCGTCATCGTGTACGTC 60.727 55.000 4.20 0.00 41.10 4.34
3013 3264 0.453950 GTGCGTCATCGTGTACGTCT 60.454 55.000 4.20 0.00 41.10 4.18
3014 3265 1.077915 TGCGTCATCGTGTACGTCTA 58.922 50.000 4.20 0.00 41.10 2.59
3015 3266 1.061566 TGCGTCATCGTGTACGTCTAG 59.938 52.381 4.20 0.00 41.10 2.43
3016 3267 1.061711 GCGTCATCGTGTACGTCTAGT 59.938 52.381 4.20 0.00 41.10 2.57
3017 3268 2.282555 GCGTCATCGTGTACGTCTAGTA 59.717 50.000 4.20 0.00 41.10 1.82
3027 3278 1.367659 ACGTCTAGTACTGAGCCGTC 58.632 55.000 5.39 0.00 0.00 4.79
3032 3283 0.463295 TAGTACTGAGCCGTCCCTCG 60.463 60.000 5.39 0.00 34.56 4.63
3046 3297 1.153745 CCTCGTCAGTACTGGCTGC 60.154 63.158 24.20 10.79 36.49 5.25
3048 3299 1.095600 CTCGTCAGTACTGGCTGCTA 58.904 55.000 24.20 7.13 36.49 3.49
3070 3321 0.830023 CTAGCCTAGGCACCTCCTCC 60.830 65.000 34.70 2.63 43.20 4.30
3072 3323 2.137528 GCCTAGGCACCTCCTCCTC 61.138 68.421 29.33 0.00 43.20 3.71
3101 3352 1.380785 CCTCACCCATGCAGCCATT 60.381 57.895 0.00 0.00 0.00 3.16
3159 3419 0.248539 GTCATGTCGTAGGGCGTCTC 60.249 60.000 0.00 0.00 42.13 3.36
3160 3420 1.065928 CATGTCGTAGGGCGTCTCC 59.934 63.158 0.00 0.00 42.13 3.71
3161 3421 1.076923 ATGTCGTAGGGCGTCTCCT 60.077 57.895 0.00 0.00 42.13 3.69
3162 3422 1.384989 ATGTCGTAGGGCGTCTCCTG 61.385 60.000 4.72 0.00 42.13 3.86
3163 3423 1.748122 GTCGTAGGGCGTCTCCTGA 60.748 63.158 4.72 0.00 42.13 3.86
3164 3424 1.102222 GTCGTAGGGCGTCTCCTGAT 61.102 60.000 4.72 0.00 42.13 2.90
3165 3425 0.395311 TCGTAGGGCGTCTCCTGATT 60.395 55.000 4.72 0.00 42.13 2.57
3166 3426 0.249073 CGTAGGGCGTCTCCTGATTG 60.249 60.000 4.72 0.00 37.75 2.67
3167 3427 1.112113 GTAGGGCGTCTCCTGATTGA 58.888 55.000 4.72 0.00 37.75 2.57
3168 3428 1.480954 GTAGGGCGTCTCCTGATTGAA 59.519 52.381 4.72 0.00 37.75 2.69
3169 3429 0.250513 AGGGCGTCTCCTGATTGAAC 59.749 55.000 0.00 0.00 35.47 3.18
3170 3430 0.744771 GGGCGTCTCCTGATTGAACC 60.745 60.000 0.00 0.00 34.39 3.62
3171 3431 0.036388 GGCGTCTCCTGATTGAACCA 60.036 55.000 0.00 0.00 0.00 3.67
3172 3432 1.079503 GCGTCTCCTGATTGAACCAC 58.920 55.000 0.00 0.00 0.00 4.16
3173 3433 1.726853 CGTCTCCTGATTGAACCACC 58.273 55.000 0.00 0.00 0.00 4.61
3174 3434 1.726853 GTCTCCTGATTGAACCACCG 58.273 55.000 0.00 0.00 0.00 4.94
3175 3435 1.002087 GTCTCCTGATTGAACCACCGT 59.998 52.381 0.00 0.00 0.00 4.83
3176 3436 1.001974 TCTCCTGATTGAACCACCGTG 59.998 52.381 0.00 0.00 0.00 4.94
3177 3437 0.605319 TCCTGATTGAACCACCGTGC 60.605 55.000 0.00 0.00 0.00 5.34
3178 3438 0.606401 CCTGATTGAACCACCGTGCT 60.606 55.000 0.00 0.00 0.00 4.40
3179 3439 0.518636 CTGATTGAACCACCGTGCTG 59.481 55.000 0.00 0.00 0.00 4.41
3180 3440 0.888736 TGATTGAACCACCGTGCTGG 60.889 55.000 0.00 0.00 46.41 4.85
3181 3441 2.200170 GATTGAACCACCGTGCTGGC 62.200 60.000 0.00 0.00 43.94 4.85
3182 3442 4.947147 TGAACCACCGTGCTGGCC 62.947 66.667 0.00 0.00 43.94 5.36
3192 3452 3.407083 TGCTGGCCGCCTCCAATA 61.407 61.111 11.61 0.00 38.05 1.90
3193 3453 2.902343 GCTGGCCGCCTCCAATAC 60.902 66.667 11.61 0.00 35.36 1.89
3194 3454 2.589540 CTGGCCGCCTCCAATACA 59.410 61.111 11.61 0.00 35.36 2.29
3195 3455 1.149174 CTGGCCGCCTCCAATACAT 59.851 57.895 11.61 0.00 35.36 2.29
3196 3456 0.466189 CTGGCCGCCTCCAATACATT 60.466 55.000 11.61 0.00 35.36 2.71
3197 3457 0.751277 TGGCCGCCTCCAATACATTG 60.751 55.000 11.61 0.00 37.52 2.82
3198 3458 1.360192 GCCGCCTCCAATACATTGC 59.640 57.895 0.00 0.00 36.48 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.665675 GACCCGTAGCAGCACCAGG 62.666 68.421 0.00 0.00 0.00 4.45
20 21 2.125512 GACCCGTAGCAGCACCAG 60.126 66.667 0.00 0.00 0.00 4.00
21 22 2.920384 TGACCCGTAGCAGCACCA 60.920 61.111 0.00 0.00 0.00 4.17
22 23 2.434359 GTGACCCGTAGCAGCACC 60.434 66.667 0.00 0.00 0.00 5.01
23 24 1.738099 CTGTGACCCGTAGCAGCAC 60.738 63.158 0.00 0.00 0.00 4.40
24 25 2.656646 CTGTGACCCGTAGCAGCA 59.343 61.111 0.00 0.00 0.00 4.41
25 26 2.125512 CCTGTGACCCGTAGCAGC 60.126 66.667 0.00 0.00 0.00 5.25
26 27 1.513158 CTCCTGTGACCCGTAGCAG 59.487 63.158 0.00 0.00 0.00 4.24
27 28 1.982395 CCTCCTGTGACCCGTAGCA 60.982 63.158 0.00 0.00 0.00 3.49
28 29 1.668101 CTCCTCCTGTGACCCGTAGC 61.668 65.000 0.00 0.00 0.00 3.58
29 30 1.668101 GCTCCTCCTGTGACCCGTAG 61.668 65.000 0.00 0.00 0.00 3.51
30 31 1.681327 GCTCCTCCTGTGACCCGTA 60.681 63.158 0.00 0.00 0.00 4.02
31 32 2.997897 GCTCCTCCTGTGACCCGT 60.998 66.667 0.00 0.00 0.00 5.28
32 33 3.775654 GGCTCCTCCTGTGACCCG 61.776 72.222 0.00 0.00 0.00 5.28
33 34 2.190488 CTTGGCTCCTCCTGTGACCC 62.190 65.000 0.00 0.00 35.26 4.46
34 35 1.298014 CTTGGCTCCTCCTGTGACC 59.702 63.158 0.00 0.00 35.26 4.02
35 36 1.298014 CCTTGGCTCCTCCTGTGAC 59.702 63.158 0.00 0.00 35.26 3.67
36 37 2.596851 GCCTTGGCTCCTCCTGTGA 61.597 63.158 4.11 0.00 35.26 3.58
37 38 2.045536 GCCTTGGCTCCTCCTGTG 60.046 66.667 4.11 0.00 35.26 3.66
38 39 3.710722 CGCCTTGGCTCCTCCTGT 61.711 66.667 10.12 0.00 35.26 4.00
39 40 4.479993 CCGCCTTGGCTCCTCCTG 62.480 72.222 10.12 0.00 35.26 3.86
62 63 1.461091 TAATAGCTCGAGCCACCCGG 61.461 60.000 32.94 0.00 43.38 5.73
63 64 0.603569 ATAATAGCTCGAGCCACCCG 59.396 55.000 32.94 0.00 43.38 5.28
64 65 1.941668 GCATAATAGCTCGAGCCACCC 60.942 57.143 32.94 11.91 43.38 4.61
65 66 1.433534 GCATAATAGCTCGAGCCACC 58.566 55.000 32.94 11.37 43.38 4.61
66 67 1.063806 CGCATAATAGCTCGAGCCAC 58.936 55.000 32.94 13.70 43.38 5.01
67 68 0.038251 CCGCATAATAGCTCGAGCCA 60.038 55.000 32.94 21.92 43.38 4.75
68 69 0.737715 CCCGCATAATAGCTCGAGCC 60.738 60.000 32.94 15.12 43.38 4.70
69 70 1.355066 GCCCGCATAATAGCTCGAGC 61.355 60.000 30.01 30.01 42.49 5.03
70 71 0.038251 TGCCCGCATAATAGCTCGAG 60.038 55.000 8.45 8.45 0.00 4.04
71 72 0.319555 GTGCCCGCATAATAGCTCGA 60.320 55.000 0.00 0.00 0.00 4.04
72 73 0.599991 TGTGCCCGCATAATAGCTCG 60.600 55.000 0.00 0.00 0.00 5.03
73 74 0.868406 GTGTGCCCGCATAATAGCTC 59.132 55.000 0.00 0.00 0.00 4.09
74 75 0.880278 CGTGTGCCCGCATAATAGCT 60.880 55.000 0.00 0.00 0.00 3.32
75 76 1.569493 CGTGTGCCCGCATAATAGC 59.431 57.895 0.00 0.00 0.00 2.97
76 77 0.249699 TCCGTGTGCCCGCATAATAG 60.250 55.000 0.00 0.00 0.00 1.73
77 78 0.249699 CTCCGTGTGCCCGCATAATA 60.250 55.000 0.00 0.00 0.00 0.98
78 79 1.523711 CTCCGTGTGCCCGCATAAT 60.524 57.895 0.00 0.00 0.00 1.28
79 80 2.125310 CTCCGTGTGCCCGCATAA 60.125 61.111 0.00 0.00 0.00 1.90
80 81 4.155733 CCTCCGTGTGCCCGCATA 62.156 66.667 0.00 0.00 0.00 3.14
93 94 0.531200 CCAGTTCTACGGACACCTCC 59.469 60.000 0.00 0.00 0.00 4.30
94 95 1.473278 CTCCAGTTCTACGGACACCTC 59.527 57.143 0.00 0.00 0.00 3.85
95 96 1.546961 CTCCAGTTCTACGGACACCT 58.453 55.000 0.00 0.00 0.00 4.00
96 97 0.531200 CCTCCAGTTCTACGGACACC 59.469 60.000 0.00 0.00 0.00 4.16
97 98 1.201880 GACCTCCAGTTCTACGGACAC 59.798 57.143 0.00 0.00 0.00 3.67
98 99 1.202964 TGACCTCCAGTTCTACGGACA 60.203 52.381 0.00 0.00 0.00 4.02
99 100 1.542492 TGACCTCCAGTTCTACGGAC 58.458 55.000 0.00 0.00 0.00 4.79
100 101 2.496070 CAATGACCTCCAGTTCTACGGA 59.504 50.000 0.00 0.00 0.00 4.69
101 102 2.418746 CCAATGACCTCCAGTTCTACGG 60.419 54.545 0.00 0.00 0.00 4.02
102 103 2.893637 CCAATGACCTCCAGTTCTACG 58.106 52.381 0.00 0.00 0.00 3.51
103 104 2.633488 GCCAATGACCTCCAGTTCTAC 58.367 52.381 0.00 0.00 0.00 2.59
104 105 1.559682 GGCCAATGACCTCCAGTTCTA 59.440 52.381 0.00 0.00 0.00 2.10
105 106 0.329596 GGCCAATGACCTCCAGTTCT 59.670 55.000 0.00 0.00 0.00 3.01
106 107 1.026718 CGGCCAATGACCTCCAGTTC 61.027 60.000 2.24 0.00 0.00 3.01
107 108 1.002134 CGGCCAATGACCTCCAGTT 60.002 57.895 2.24 0.00 0.00 3.16
108 109 2.671070 CGGCCAATGACCTCCAGT 59.329 61.111 2.24 0.00 0.00 4.00
109 110 2.124570 CCGGCCAATGACCTCCAG 60.125 66.667 2.24 0.00 0.00 3.86
110 111 4.424711 GCCGGCCAATGACCTCCA 62.425 66.667 18.11 0.00 0.00 3.86
128 129 3.195698 GAGGATCAACGCCACCGC 61.196 66.667 0.00 0.00 33.99 5.68
129 130 1.519455 GAGAGGATCAACGCCACCG 60.519 63.158 0.00 0.00 37.82 4.94
130 131 1.519455 CGAGAGGATCAACGCCACC 60.519 63.158 0.00 0.00 37.82 4.61
131 132 0.802607 GTCGAGAGGATCAACGCCAC 60.803 60.000 0.00 0.00 37.82 5.01
132 133 1.511305 GTCGAGAGGATCAACGCCA 59.489 57.895 0.00 0.00 37.82 5.69
133 134 1.586564 CGTCGAGAGGATCAACGCC 60.587 63.158 0.00 0.00 37.82 5.68
134 135 0.590230 CTCGTCGAGAGGATCAACGC 60.590 60.000 17.52 0.00 43.20 4.84
135 136 3.518017 CTCGTCGAGAGGATCAACG 57.482 57.895 17.52 0.00 43.20 4.10
144 145 1.289800 CTCGGTGTCACTCGTCGAGA 61.290 60.000 28.33 4.56 46.89 4.04
145 146 1.132844 CTCGGTGTCACTCGTCGAG 59.867 63.158 20.57 20.57 40.68 4.04
146 147 2.962827 GCTCGGTGTCACTCGTCGA 61.963 63.158 2.35 2.57 0.00 4.20
147 148 2.502080 GCTCGGTGTCACTCGTCG 60.502 66.667 2.35 0.00 0.00 5.12
148 149 2.126424 GGCTCGGTGTCACTCGTC 60.126 66.667 2.35 2.65 0.00 4.20
149 150 2.143594 GAAGGCTCGGTGTCACTCGT 62.144 60.000 2.35 0.00 0.00 4.18
150 151 1.444553 GAAGGCTCGGTGTCACTCG 60.445 63.158 2.35 5.30 0.00 4.18
151 152 0.033504 TTGAAGGCTCGGTGTCACTC 59.966 55.000 2.35 0.00 0.00 3.51
152 153 0.249911 GTTGAAGGCTCGGTGTCACT 60.250 55.000 2.35 0.00 0.00 3.41
153 154 0.531974 TGTTGAAGGCTCGGTGTCAC 60.532 55.000 0.00 0.00 0.00 3.67
154 155 0.179234 TTGTTGAAGGCTCGGTGTCA 59.821 50.000 0.00 0.00 0.00 3.58
161 162 0.586802 GACACCGTTGTTGAAGGCTC 59.413 55.000 0.00 0.00 35.47 4.70
166 167 3.017442 TGAAATGGACACCGTTGTTGAA 58.983 40.909 0.00 0.00 35.47 2.69
175 176 1.886542 GACCCAACTGAAATGGACACC 59.113 52.381 0.00 0.00 40.56 4.16
182 183 3.631250 ACACAACAGACCCAACTGAAAT 58.369 40.909 0.00 0.00 40.63 2.17
223 229 1.210545 GACAACGGACGCAGACGAAA 61.211 55.000 0.00 0.00 43.93 3.46
225 231 2.050714 GACAACGGACGCAGACGA 60.051 61.111 0.00 0.00 43.93 4.20
237 243 1.139853 TGGGTTGCCAAAATGGACAAC 59.860 47.619 19.43 19.43 45.31 3.32
244 250 3.872459 TTCCATTTGGGTTGCCAAAAT 57.128 38.095 0.00 0.00 41.96 1.82
252 258 4.703379 TCTGCATTTTTCCATTTGGGTT 57.297 36.364 0.00 0.00 38.11 4.11
270 276 2.205074 AGCAGACGCGGATTTTATCTG 58.795 47.619 12.47 13.59 45.49 2.90
271 277 2.604046 AGCAGACGCGGATTTTATCT 57.396 45.000 12.47 0.00 45.49 1.98
273 279 1.670811 CCAAGCAGACGCGGATTTTAT 59.329 47.619 12.47 0.00 45.49 1.40
274 280 1.083489 CCAAGCAGACGCGGATTTTA 58.917 50.000 12.47 0.00 45.49 1.52
283 291 0.317160 TGTAGTGACCCAAGCAGACG 59.683 55.000 0.00 0.00 0.00 4.18
289 297 3.703001 ACTCCAATGTAGTGACCCAAG 57.297 47.619 0.00 0.00 0.00 3.61
300 308 1.750193 CATACGGCCAACTCCAATGT 58.250 50.000 2.24 0.00 0.00 2.71
306 314 2.143925 GGAATAGCATACGGCCAACTC 58.856 52.381 2.24 0.00 46.50 3.01
370 378 6.986118 GTGTATCAAATACAACGACACCTAC 58.014 40.000 1.55 0.00 46.36 3.18
373 381 5.212589 GGTGTATCAAATACAACGACACC 57.787 43.478 5.60 5.60 46.36 4.16
379 387 4.083749 TGCACACGGTGTATCAAATACAAC 60.084 41.667 14.30 5.27 46.36 3.32
560 570 7.928103 AGCATACATGACTCATCAATTCTTTC 58.072 34.615 0.00 0.00 38.69 2.62
632 643 5.159273 AGATTGTTCTGGACTCCTTCTTC 57.841 43.478 0.00 0.00 0.00 2.87
639 650 6.876257 AGTAATGTGAAGATTGTTCTGGACTC 59.124 38.462 0.00 0.00 30.72 3.36
663 674 9.678941 TTGCGTTGTTAAGATAGATCATACTAG 57.321 33.333 0.00 0.00 0.00 2.57
719 731 1.473258 GCACATCCAGGTTGGCATAA 58.527 50.000 2.45 0.00 37.47 1.90
755 767 9.607988 CCCCTTTCAAAAACTAAGTTTGTAATT 57.392 29.630 0.00 0.00 35.80 1.40
773 785 7.402071 ACACTTATCTAGATTACACCCCTTTCA 59.598 37.037 11.25 0.00 0.00 2.69
893 906 7.362574 GGCTACTTGCAAGTGTAATTTGGATTA 60.363 37.037 36.50 14.74 45.15 1.75
911 926 2.101582 ACTATCTTCGCAGGGCTACTTG 59.898 50.000 0.00 0.00 0.00 3.16
919 934 6.276847 ACTCTTATCAAACTATCTTCGCAGG 58.723 40.000 0.00 0.00 0.00 4.85
921 936 8.630037 TGATACTCTTATCAAACTATCTTCGCA 58.370 33.333 0.00 0.00 41.03 5.10
922 937 9.123709 CTGATACTCTTATCAAACTATCTTCGC 57.876 37.037 0.00 0.00 42.93 4.70
999 1031 6.904463 TCACGGTGTATGGCTATTTATAGA 57.096 37.500 8.17 0.00 32.05 1.98
1037 1069 6.317140 TGCTCTAAATGTGTGAAAGATGGATC 59.683 38.462 0.00 0.00 0.00 3.36
1045 1077 6.201226 TGTTTGTGCTCTAAATGTGTGAAA 57.799 33.333 0.00 0.00 0.00 2.69
1057 1089 6.862209 TGTTTAGTTTGAATGTTTGTGCTCT 58.138 32.000 0.00 0.00 0.00 4.09
1073 1105 8.967664 TTGTGGTTACTCTGTATTGTTTAGTT 57.032 30.769 0.00 0.00 0.00 2.24
1084 1116 5.241403 TGATGGATTTGTGGTTACTCTGT 57.759 39.130 0.00 0.00 0.00 3.41
1085 1117 5.882000 TCATGATGGATTTGTGGTTACTCTG 59.118 40.000 0.00 0.00 0.00 3.35
1115 1147 0.695347 AGGAGGGCAAAGACCAAGAG 59.305 55.000 0.00 0.00 29.21 2.85
1164 1196 2.360726 TAGGGTCGAGCTGCACGA 60.361 61.111 17.83 17.83 37.43 4.35
1167 1199 1.595993 GACACTAGGGTCGAGCTGCA 61.596 60.000 9.90 0.00 0.00 4.41
1183 1215 1.547675 GGCCTTTCTTGGACATGGACA 60.548 52.381 0.00 0.00 34.56 4.02
1184 1216 1.177401 GGCCTTTCTTGGACATGGAC 58.823 55.000 0.00 0.00 34.56 4.02
1252 1284 2.844451 TTGTGGTTCTTGCAGCGGC 61.844 57.895 0.31 0.31 41.68 6.53
1264 1296 2.812613 CGGGAATAGTGGTTGTTGTGGT 60.813 50.000 0.00 0.00 0.00 4.16
1310 1342 2.515757 TTGTGGTTGCTGCAGCGA 60.516 55.556 32.11 28.81 45.83 4.93
1321 1353 0.396556 GTTGTTCCTGGGGTTGTGGT 60.397 55.000 0.00 0.00 0.00 4.16
1328 1360 2.595750 TATGGTTGTTGTTCCTGGGG 57.404 50.000 0.00 0.00 0.00 4.96
1329 1361 3.023832 GGATATGGTTGTTGTTCCTGGG 58.976 50.000 0.00 0.00 0.00 4.45
1334 1366 5.446143 TGTTGTGGATATGGTTGTTGTTC 57.554 39.130 0.00 0.00 0.00 3.18
1345 1377 3.370953 GGAGAAGTGGCTGTTGTGGATAT 60.371 47.826 0.00 0.00 0.00 1.63
1365 1397 2.026905 GCTGGGGAAGTTGTTGTTGGA 61.027 52.381 0.00 0.00 0.00 3.53
1408 1440 1.478510 TGCGGAAATTGTTGTTGTGGT 59.521 42.857 0.00 0.00 0.00 4.16
1444 1494 4.219507 TGCGGGAATGTTTGTTGTTCATAT 59.780 37.500 0.00 0.00 0.00 1.78
1445 1495 3.570125 TGCGGGAATGTTTGTTGTTCATA 59.430 39.130 0.00 0.00 0.00 2.15
1448 1498 2.500509 TGCGGGAATGTTTGTTGTTC 57.499 45.000 0.00 0.00 0.00 3.18
1474 1524 1.501169 GGAATTGTGGTTGCTGTTGC 58.499 50.000 0.00 0.00 40.20 4.17
1480 1530 0.943835 GTTGCGGGAATTGTGGTTGC 60.944 55.000 0.00 0.00 0.00 4.17
1511 1582 6.071108 TGTGTTAATGGTTGTTGATATTGGGG 60.071 38.462 0.00 0.00 0.00 4.96
1630 1701 2.847234 TCCTCCGGGTTGCACTGT 60.847 61.111 0.00 0.00 0.00 3.55
1661 1732 1.482593 GAACGGGATCACTGACTGGAT 59.517 52.381 0.00 0.00 0.00 3.41
2002 2092 1.714794 GTGCACTAGTGGTGTAGCAG 58.285 55.000 23.95 0.00 46.86 4.24
2042 2132 2.631160 TTTCACTGTCCACCGTTCAT 57.369 45.000 0.00 0.00 0.00 2.57
2043 2133 2.158885 TCATTTCACTGTCCACCGTTCA 60.159 45.455 0.00 0.00 0.00 3.18
2044 2134 2.489971 TCATTTCACTGTCCACCGTTC 58.510 47.619 0.00 0.00 0.00 3.95
2065 2155 9.696572 TCCATCTATCTAGTAGTACAACTGTTT 57.303 33.333 2.52 0.00 0.00 2.83
2068 2158 7.940137 AGGTCCATCTATCTAGTAGTACAACTG 59.060 40.741 2.52 0.00 0.00 3.16
2139 2229 9.299465 ACATATGATGGTGCATGACATTTTATA 57.701 29.630 10.38 0.09 33.60 0.98
2311 2422 4.020839 TCTCCGAACTAAATTTTCCGGACT 60.021 41.667 1.83 0.00 0.00 3.85
2312 2423 4.248058 TCTCCGAACTAAATTTTCCGGAC 58.752 43.478 1.83 0.00 0.00 4.79
2330 2441 2.672478 CGATTATGGGCACGAGATCTCC 60.672 54.545 17.13 3.30 0.00 3.71
2332 2443 1.337260 GCGATTATGGGCACGAGATCT 60.337 52.381 0.00 0.00 0.00 2.75
2345 2456 1.985159 TCAATGGCTAGGGGCGATTAT 59.015 47.619 0.00 0.00 45.25 1.28
2368 2479 3.634448 TGAATCCACACACGGACATTTTT 59.366 39.130 0.00 0.00 38.07 1.94
2369 2480 3.218453 TGAATCCACACACGGACATTTT 58.782 40.909 0.00 0.00 38.07 1.82
2370 2481 2.813754 CTGAATCCACACACGGACATTT 59.186 45.455 0.00 0.00 38.07 2.32
2372 2483 1.347707 ACTGAATCCACACACGGACAT 59.652 47.619 0.00 0.00 38.07 3.06
2386 2589 2.754186 GCCCCATTCCTATGCACTGAAT 60.754 50.000 0.00 0.00 0.00 2.57
2391 2594 1.531602 GGGCCCCATTCCTATGCAC 60.532 63.158 12.23 0.00 0.00 4.57
2394 2597 0.403271 CTCTGGGCCCCATTCCTATG 59.597 60.000 22.27 0.00 30.82 2.23
2428 2631 2.882761 GTCCTGGACTTTAAAGCCGTTT 59.117 45.455 19.53 0.00 0.00 3.60
2431 2634 1.271163 TGGTCCTGGACTTTAAAGCCG 60.271 52.381 25.01 12.17 32.47 5.52
2442 2645 1.003580 GAAGAAGCACATGGTCCTGGA 59.996 52.381 0.00 0.00 0.00 3.86
2461 2664 4.395854 CACGACATGGGATTCAAAATCTGA 59.604 41.667 0.00 0.00 0.00 3.27
2462 2665 4.156556 ACACGACATGGGATTCAAAATCTG 59.843 41.667 0.00 0.00 0.00 2.90
2465 2668 4.766891 AGAACACGACATGGGATTCAAAAT 59.233 37.500 0.00 0.00 0.00 1.82
2468 2689 3.417069 AGAACACGACATGGGATTCAA 57.583 42.857 0.00 0.00 0.00 2.69
2771 2992 1.289160 TTGGGGTGAGGAATCAGAGG 58.711 55.000 0.00 0.00 0.00 3.69
2786 3007 4.036518 TGGGATATTTTGGGACATTTGGG 58.963 43.478 0.00 0.00 39.30 4.12
2791 3012 7.675619 GGATAGATTTGGGATATTTTGGGACAT 59.324 37.037 0.00 0.00 39.30 3.06
2793 3014 6.437477 GGGATAGATTTGGGATATTTTGGGAC 59.563 42.308 0.00 0.00 0.00 4.46
2796 3017 7.854166 TTGGGATAGATTTGGGATATTTTGG 57.146 36.000 0.00 0.00 0.00 3.28
2818 3039 3.371898 TCGCACAAATGAGCTCAGTATTG 59.628 43.478 25.93 25.93 0.00 1.90
2824 3045 0.035317 AGGTCGCACAAATGAGCTCA 59.965 50.000 20.79 20.79 38.49 4.26
2841 3062 2.612972 CCGGTAATTGGATGGATCGAGG 60.613 54.545 0.00 0.00 0.00 4.63
2849 3070 2.413837 GATCGACCCGGTAATTGGATG 58.586 52.381 0.00 0.00 0.00 3.51
2851 3072 0.386476 CGATCGACCCGGTAATTGGA 59.614 55.000 10.26 0.00 0.00 3.53
2852 3073 0.103572 ACGATCGACCCGGTAATTGG 59.896 55.000 24.34 0.00 0.00 3.16
2853 3074 1.202325 TCACGATCGACCCGGTAATTG 60.202 52.381 24.34 5.36 0.00 2.32
2854 3075 1.105457 TCACGATCGACCCGGTAATT 58.895 50.000 24.34 0.00 0.00 1.40
2855 3076 0.383231 GTCACGATCGACCCGGTAAT 59.617 55.000 24.34 0.00 0.00 1.89
2856 3077 0.959867 TGTCACGATCGACCCGGTAA 60.960 55.000 24.34 0.00 34.88 2.85
2857 3078 1.377072 TGTCACGATCGACCCGGTA 60.377 57.895 24.34 0.00 34.88 4.02
2858 3079 2.674033 TGTCACGATCGACCCGGT 60.674 61.111 24.34 0.00 34.88 5.28
2859 3080 2.202570 GTGTCACGATCGACCCGG 60.203 66.667 24.34 0.00 34.88 5.73
2860 3081 1.226323 GAGTGTCACGATCGACCCG 60.226 63.158 24.34 7.18 34.88 5.28
2861 3082 0.179161 CTGAGTGTCACGATCGACCC 60.179 60.000 24.34 8.84 34.88 4.46
2862 3083 0.798771 GCTGAGTGTCACGATCGACC 60.799 60.000 24.34 9.21 34.88 4.79
2863 3084 1.128724 CGCTGAGTGTCACGATCGAC 61.129 60.000 24.34 11.27 36.40 4.20
2864 3085 1.134694 CGCTGAGTGTCACGATCGA 59.865 57.895 24.34 0.00 0.00 3.59
2865 3086 0.248255 ATCGCTGAGTGTCACGATCG 60.248 55.000 14.88 14.88 36.60 3.69
2866 3087 1.195347 CATCGCTGAGTGTCACGATC 58.805 55.000 0.00 0.00 37.99 3.69
2867 3088 0.179127 CCATCGCTGAGTGTCACGAT 60.179 55.000 0.00 7.92 39.40 3.73
2897 3118 0.824759 ATTGTGAGCCCCTAGACGTC 59.175 55.000 7.70 7.70 0.00 4.34
2903 3124 0.913934 TGAGCCATTGTGAGCCCCTA 60.914 55.000 0.00 0.00 0.00 3.53
2904 3125 1.792757 TTGAGCCATTGTGAGCCCCT 61.793 55.000 0.00 0.00 0.00 4.79
2905 3126 0.685458 ATTGAGCCATTGTGAGCCCC 60.685 55.000 0.00 0.00 0.00 5.80
2915 3166 0.664761 CAAATCCGCGATTGAGCCAT 59.335 50.000 8.23 0.00 32.14 4.40
2922 3173 0.322098 TCCACCACAAATCCGCGATT 60.322 50.000 8.23 2.39 33.25 3.34
2943 3194 2.184322 CGTAGCCATGACCACGCT 59.816 61.111 0.00 0.00 36.63 5.07
2957 3208 2.505337 GCACACGATGACGCCGTA 60.505 61.111 0.00 0.00 43.96 4.02
2969 3220 4.705746 TGGGTTATGGACGCACAC 57.294 55.556 0.00 0.00 45.15 3.82
2981 3232 2.047274 CGCACACGAGGATGGGTT 60.047 61.111 0.00 0.00 43.93 4.11
2982 3233 3.296709 GACGCACACGAGGATGGGT 62.297 63.158 0.00 0.00 43.90 4.51
2983 3234 2.509336 GACGCACACGAGGATGGG 60.509 66.667 0.00 0.00 43.93 4.00
2984 3235 1.148157 GATGACGCACACGAGGATGG 61.148 60.000 0.00 0.00 43.93 3.51
2985 3236 1.474648 CGATGACGCACACGAGGATG 61.475 60.000 0.00 0.00 43.93 3.51
2986 3237 1.226688 CGATGACGCACACGAGGAT 60.227 57.895 0.00 0.00 43.93 3.24
2987 3238 2.178273 CGATGACGCACACGAGGA 59.822 61.111 0.00 0.00 43.93 3.71
2989 3240 0.453782 TACACGATGACGCACACGAG 60.454 55.000 12.18 8.55 43.93 4.18
2990 3241 0.726787 GTACACGATGACGCACACGA 60.727 55.000 12.18 0.00 43.93 4.35
2991 3242 1.983268 CGTACACGATGACGCACACG 61.983 60.000 0.00 0.00 43.61 4.49
2992 3243 1.000233 ACGTACACGATGACGCACAC 61.000 55.000 9.04 0.00 42.81 3.82
2993 3244 0.726787 GACGTACACGATGACGCACA 60.727 55.000 9.04 0.00 42.81 4.57
2995 3246 1.061566 CTAGACGTACACGATGACGCA 59.938 52.381 9.04 0.00 42.81 5.24
2996 3247 1.061711 ACTAGACGTACACGATGACGC 59.938 52.381 9.04 2.38 42.81 5.19
2997 3248 3.843397 GTACTAGACGTACACGATGACG 58.157 50.000 9.04 0.00 46.21 4.35
3010 3261 1.023502 GGGACGGCTCAGTACTAGAC 58.976 60.000 0.00 0.00 0.00 2.59
3011 3262 0.917533 AGGGACGGCTCAGTACTAGA 59.082 55.000 0.00 0.00 0.00 2.43
3012 3263 1.310904 GAGGGACGGCTCAGTACTAG 58.689 60.000 0.00 0.00 0.00 2.57
3013 3264 0.463295 CGAGGGACGGCTCAGTACTA 60.463 60.000 0.00 0.00 38.46 1.82
3014 3265 1.749638 CGAGGGACGGCTCAGTACT 60.750 63.158 0.00 0.00 38.46 2.73
3015 3266 2.799371 CGAGGGACGGCTCAGTAC 59.201 66.667 0.00 0.00 38.46 2.73
3027 3278 1.513158 CAGCCAGTACTGACGAGGG 59.487 63.158 24.68 7.39 40.25 4.30
3032 3283 3.330766 CGTAGCAGCCAGTACTGAC 57.669 57.895 24.68 13.31 40.25 3.51
3046 3297 0.824182 AGGTGCCTAGGCTAGCGTAG 60.824 60.000 33.07 29.33 42.51 3.51
3048 3299 2.042843 AGGTGCCTAGGCTAGCGT 60.043 61.111 33.07 20.72 42.51 5.07
3070 3321 1.609783 GTGAGGATGGGTTGGGGAG 59.390 63.158 0.00 0.00 0.00 4.30
3072 3323 2.683475 GGTGAGGATGGGTTGGGG 59.317 66.667 0.00 0.00 0.00 4.96
3136 3396 3.103091 GCCCTACGACATGACCCCC 62.103 68.421 0.00 0.00 0.00 5.40
3159 3419 0.606401 AGCACGGTGGTTCAATCAGG 60.606 55.000 7.07 0.00 0.00 3.86
3160 3420 0.518636 CAGCACGGTGGTTCAATCAG 59.481 55.000 10.60 0.00 0.00 2.90
3161 3421 0.888736 CCAGCACGGTGGTTCAATCA 60.889 55.000 10.60 0.00 32.32 2.57
3162 3422 1.875963 CCAGCACGGTGGTTCAATC 59.124 57.895 10.60 0.00 32.32 2.67
3163 3423 2.268076 GCCAGCACGGTGGTTCAAT 61.268 57.895 16.17 0.00 40.09 2.57
3164 3424 2.904866 GCCAGCACGGTGGTTCAA 60.905 61.111 16.17 0.00 40.09 2.69
3165 3425 4.947147 GGCCAGCACGGTGGTTCA 62.947 66.667 16.17 0.00 40.09 3.18
3177 3437 0.466189 AATGTATTGGAGGCGGCCAG 60.466 55.000 23.09 0.00 39.52 4.85
3178 3438 0.751277 CAATGTATTGGAGGCGGCCA 60.751 55.000 23.09 0.00 34.22 5.36
3179 3439 2.032981 CAATGTATTGGAGGCGGCC 58.967 57.895 12.11 12.11 34.22 6.13
3180 3440 1.360192 GCAATGTATTGGAGGCGGC 59.640 57.895 0.00 0.00 38.21 6.53


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

AutoCloner maintained by Alex Coulton.