Multiple sequence alignment - TraesCS5B01G029200

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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 TraesCS5B01G029200 chr5B 100.000 2013 0 0 1 2013 28224562 28226574 0.000000e+00 3718.0
1 TraesCS5B01G029200 chr5B 100.000 302 0 0 2335 2636 28226896 28227197 2.290000e-155 558.0
2 TraesCS5B01G029200 chr5D 82.198 1028 102 28 263 1239 39014244 39013247 0.000000e+00 809.0
3 TraesCS5B01G029200 chr5D 84.494 316 28 14 2335 2631 38990895 38990582 2.570000e-75 292.0
4 TraesCS5B01G029200 chr5D 85.069 288 27 10 2353 2626 38990613 38990328 2.000000e-71 279.0
5 TraesCS5B01G029200 chr5D 84.138 290 25 10 2353 2631 38990354 38990075 7.240000e-66 261.0
6 TraesCS5B01G029200 chr5D 93.506 77 4 1 202 277 39014337 39014261 2.140000e-21 113.0
7 TraesCS5B01G029200 chr5D 96.970 66 0 1 138 203 39014459 39014396 2.770000e-20 110.0
8 TraesCS5B01G029200 chr5D 80.612 98 9 3 56 147 39014565 39014472 1.690000e-07 67.6
9 TraesCS5B01G029200 chr5A 80.160 1003 117 29 308 1258 27700475 27699503 0.000000e+00 675.0
10 TraesCS5B01G029200 chr5A 85.399 363 50 3 1639 1999 99534720 99535081 8.910000e-100 374.0
11 TraesCS5B01G029200 chr5A 87.781 311 24 5 2335 2631 27636513 27636203 4.170000e-93 351.0
12 TraesCS5B01G029200 chr5A 83.758 314 26 14 2335 2631 27635753 27635448 9.300000e-70 274.0
13 TraesCS5B01G029200 chr5A 82.484 314 30 12 2335 2631 27636005 27635700 4.360000e-63 252.0
14 TraesCS5B01G029200 chr5A 83.219 292 27 14 2353 2631 27636234 27635952 5.630000e-62 248.0
15 TraesCS5B01G029200 chr5A 85.526 76 3 5 128 203 27716509 27716442 3.640000e-09 73.1
16 TraesCS5B01G029200 chr7B 91.842 380 31 0 1264 1643 517097488 517097867 5.000000e-147 531.0
17 TraesCS5B01G029200 chr7B 87.268 377 38 5 1639 2013 517097715 517098083 3.140000e-114 422.0
18 TraesCS5B01G029200 chr3D 88.251 366 43 0 1278 1643 351131567 351131932 3.110000e-119 438.0
19 TraesCS5B01G029200 chr3D 85.600 375 52 2 1639 2013 351131780 351132152 2.460000e-105 392.0
20 TraesCS5B01G029200 chr3B 88.011 367 44 0 1272 1638 528419316 528419682 4.030000e-118 435.0
21 TraesCS5B01G029200 chr3B 87.467 375 44 1 1267 1641 342860574 342860945 1.870000e-116 429.0
22 TraesCS5B01G029200 chr6B 87.845 362 40 4 1640 1999 523889449 523889090 3.140000e-114 422.0
23 TraesCS5B01G029200 chr6B 82.633 357 55 7 1657 2009 3805769 3806122 2.550000e-80 309.0
24 TraesCS5B01G029200 chr1D 86.472 377 51 0 1265 1641 261091074 261090698 5.250000e-112 414.0
25 TraesCS5B01G029200 chr4A 87.123 365 45 2 1278 1641 591291678 591291315 1.890000e-111 412.0
26 TraesCS5B01G029200 chr4A 86.575 365 47 2 1278 1641 591672938 591672575 4.090000e-108 401.0
27 TraesCS5B01G029200 chr4A 85.753 365 50 2 1278 1641 592639948 592640311 4.120000e-103 385.0
28 TraesCS5B01G029200 chr2D 85.989 364 48 1 1278 1641 55240409 55240049 1.140000e-103 387.0
29 TraesCS5B01G029200 chrUn 89.803 304 18 2 2336 2631 65582234 65581936 6.890000e-101 377.0
30 TraesCS5B01G029200 chrUn 83.221 298 30 9 2353 2631 65581967 65581671 3.370000e-64 255.0
31 TraesCS5B01G029200 chr7D 84.881 377 53 3 1639 2013 116342463 116342837 6.890000e-101 377.0
32 TraesCS5B01G029200 chr7D 83.106 367 53 8 1644 2009 326743922 326744280 2.530000e-85 326.0
33 TraesCS5B01G029200 chr1A 84.973 366 47 5 1640 1999 402275593 402275956 5.360000e-97 364.0
34 TraesCS5B01G029200 chr7A 84.953 319 40 4 1639 1956 412913039 412912728 1.520000e-82 316.0


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 TraesCS5B01G029200 chr5B 28224562 28227197 2635 False 2138.000000 3718 100.0000 1 2636 2 chr5B.!!$F1 2635
1 TraesCS5B01G029200 chr5D 38990075 38990895 820 True 277.333333 292 84.5670 2335 2631 3 chr5D.!!$R1 296
2 TraesCS5B01G029200 chr5D 39013247 39014565 1318 True 274.900000 809 88.3215 56 1239 4 chr5D.!!$R2 1183
3 TraesCS5B01G029200 chr5A 27699503 27700475 972 True 675.000000 675 80.1600 308 1258 1 chr5A.!!$R1 950
4 TraesCS5B01G029200 chr5A 27635448 27636513 1065 True 281.250000 351 84.3105 2335 2631 4 chr5A.!!$R3 296
5 TraesCS5B01G029200 chr7B 517097488 517098083 595 False 476.500000 531 89.5550 1264 2013 2 chr7B.!!$F1 749
6 TraesCS5B01G029200 chr3D 351131567 351132152 585 False 415.000000 438 86.9255 1278 2013 2 chr3D.!!$F1 735
7 TraesCS5B01G029200 chrUn 65581671 65582234 563 True 316.000000 377 86.5120 2336 2631 2 chrUn.!!$R1 295

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
776 924 0.033504 ACGCTTGACCGACACTTCAT 59.966 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1909 0.034896 ACGCCGTCATTGTCCTTCTT 59.965 50.0 0.0 0.0 0.0 2.52 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
22 23 5.471556 TTTGATGTAAACTGTCCGGTAGA 57.528 39.130 14.00 0.00 0.00 2.59
23 24 5.670792 TTGATGTAAACTGTCCGGTAGAT 57.329 39.130 14.00 1.12 0.00 1.98
24 25 5.670792 TGATGTAAACTGTCCGGTAGATT 57.329 39.130 14.00 11.02 0.00 2.40
25 26 6.778834 TGATGTAAACTGTCCGGTAGATTA 57.221 37.500 14.00 10.19 0.00 1.75
26 27 7.172868 TGATGTAAACTGTCCGGTAGATTAA 57.827 36.000 14.00 5.98 0.00 1.40
27 28 7.788026 TGATGTAAACTGTCCGGTAGATTAAT 58.212 34.615 14.00 0.00 0.00 1.40
28 29 8.262227 TGATGTAAACTGTCCGGTAGATTAATT 58.738 33.333 14.00 5.34 0.00 1.40
29 30 9.106070 GATGTAAACTGTCCGGTAGATTAATTT 57.894 33.333 14.00 7.16 0.00 1.82
30 31 8.259049 TGTAAACTGTCCGGTAGATTAATTTG 57.741 34.615 14.00 0.00 0.00 2.32
31 32 7.879160 TGTAAACTGTCCGGTAGATTAATTTGT 59.121 33.333 14.00 0.00 0.00 2.83
32 33 7.754851 AAACTGTCCGGTAGATTAATTTGTT 57.245 32.000 14.00 0.00 0.00 2.83
33 34 8.851541 AAACTGTCCGGTAGATTAATTTGTTA 57.148 30.769 14.00 0.00 0.00 2.41
34 35 8.488651 AACTGTCCGGTAGATTAATTTGTTAG 57.511 34.615 14.00 0.00 0.00 2.34
35 36 7.618137 ACTGTCCGGTAGATTAATTTGTTAGT 58.382 34.615 14.00 0.00 0.00 2.24
36 37 8.752187 ACTGTCCGGTAGATTAATTTGTTAGTA 58.248 33.333 14.00 0.00 0.00 1.82
37 38 9.245962 CTGTCCGGTAGATTAATTTGTTAGTAG 57.754 37.037 0.00 0.00 0.00 2.57
38 39 8.199449 TGTCCGGTAGATTAATTTGTTAGTAGG 58.801 37.037 0.00 0.00 0.00 3.18
39 40 7.170489 GTCCGGTAGATTAATTTGTTAGTAGGC 59.830 40.741 0.00 0.00 0.00 3.93
40 41 6.987992 CCGGTAGATTAATTTGTTAGTAGGCA 59.012 38.462 0.00 0.00 0.00 4.75
41 42 7.170998 CCGGTAGATTAATTTGTTAGTAGGCAG 59.829 40.741 0.00 0.00 0.00 4.85
42 43 7.307219 CGGTAGATTAATTTGTTAGTAGGCAGC 60.307 40.741 0.00 0.00 0.00 5.25
43 44 7.715686 GGTAGATTAATTTGTTAGTAGGCAGCT 59.284 37.037 0.00 0.00 0.00 4.24
44 45 7.559590 AGATTAATTTGTTAGTAGGCAGCTG 57.440 36.000 10.11 10.11 0.00 4.24
45 46 7.338710 AGATTAATTTGTTAGTAGGCAGCTGA 58.661 34.615 20.43 0.00 0.00 4.26
46 47 6.985188 TTAATTTGTTAGTAGGCAGCTGAG 57.015 37.500 20.43 0.00 0.00 3.35
47 48 2.386661 TTGTTAGTAGGCAGCTGAGC 57.613 50.000 20.43 1.76 0.00 4.26
67 68 2.941064 GCCAGGTCGATAAAAAGTACCC 59.059 50.000 0.00 0.00 0.00 3.69
68 69 3.620472 GCCAGGTCGATAAAAAGTACCCA 60.620 47.826 0.00 0.00 0.00 4.51
70 71 4.574828 CCAGGTCGATAAAAAGTACCCATG 59.425 45.833 0.00 0.00 0.00 3.66
71 72 4.035208 CAGGTCGATAAAAAGTACCCATGC 59.965 45.833 0.00 0.00 0.00 4.06
72 73 3.001939 GGTCGATAAAAAGTACCCATGCG 59.998 47.826 0.00 0.00 0.00 4.73
73 74 3.001939 GTCGATAAAAAGTACCCATGCGG 59.998 47.826 0.00 0.00 37.81 5.69
107 108 9.283768 TGTTTATTTGCTCTTAAGATTCAGTCA 57.716 29.630 5.44 0.00 0.00 3.41
110 111 6.545504 TTTGCTCTTAAGATTCAGTCACAC 57.454 37.500 5.44 0.00 0.00 3.82
117 118 2.838736 AGATTCAGTCACACGTTGCTT 58.161 42.857 0.00 0.00 0.00 3.91
120 121 1.083401 CAGTCACACGTTGCTTCGC 60.083 57.895 0.00 0.00 0.00 4.70
123 124 0.942410 GTCACACGTTGCTTCGCCTA 60.942 55.000 0.00 0.00 0.00 3.93
126 127 0.249741 ACACGTTGCTTCGCCTAACT 60.250 50.000 0.00 0.00 0.00 2.24
127 128 1.000060 ACACGTTGCTTCGCCTAACTA 60.000 47.619 0.00 0.00 0.00 2.24
128 129 2.268298 CACGTTGCTTCGCCTAACTAT 58.732 47.619 0.00 0.00 0.00 2.12
129 130 3.119388 ACACGTTGCTTCGCCTAACTATA 60.119 43.478 0.00 0.00 0.00 1.31
131 132 4.049186 ACGTTGCTTCGCCTAACTATATG 58.951 43.478 1.49 0.00 0.00 1.78
132 133 3.428870 CGTTGCTTCGCCTAACTATATGG 59.571 47.826 0.00 0.00 0.00 2.74
133 134 4.377897 GTTGCTTCGCCTAACTATATGGT 58.622 43.478 0.00 0.00 0.00 3.55
134 135 5.535333 GTTGCTTCGCCTAACTATATGGTA 58.465 41.667 0.00 0.00 0.00 3.25
135 136 5.995565 TGCTTCGCCTAACTATATGGTAT 57.004 39.130 0.00 0.00 0.00 2.73
136 137 7.318141 GTTGCTTCGCCTAACTATATGGTATA 58.682 38.462 0.00 0.00 0.00 1.47
173 202 7.055667 ACCCATACATACTCTAGTCATTGTG 57.944 40.000 0.00 0.00 0.00 3.33
174 203 6.611642 ACCCATACATACTCTAGTCATTGTGT 59.388 38.462 0.00 0.00 0.00 3.72
240 330 5.239306 TCACAGCTTGTCAGTTTGGATTAAG 59.761 40.000 0.00 0.00 0.00 1.85
242 332 3.507622 AGCTTGTCAGTTTGGATTAAGGC 59.492 43.478 0.00 0.00 0.00 4.35
246 336 2.418976 GTCAGTTTGGATTAAGGCGACC 59.581 50.000 0.00 0.00 0.00 4.79
261 351 1.472026 GCGACCGGCCTGTTAATTAGA 60.472 52.381 0.00 0.00 34.80 2.10
313 435 5.094569 AGCTTATCCTAGTGGAGGGTATT 57.905 43.478 0.00 0.00 46.91 1.89
395 526 5.675538 ACTCTCAGTCCCAATAAAGCATAC 58.324 41.667 0.00 0.00 0.00 2.39
396 527 5.036117 TCTCAGTCCCAATAAAGCATACC 57.964 43.478 0.00 0.00 0.00 2.73
397 528 3.804036 TCAGTCCCAATAAAGCATACCG 58.196 45.455 0.00 0.00 0.00 4.02
398 529 3.199071 TCAGTCCCAATAAAGCATACCGT 59.801 43.478 0.00 0.00 0.00 4.83
399 530 3.945285 CAGTCCCAATAAAGCATACCGTT 59.055 43.478 0.00 0.00 0.00 4.44
400 531 5.104859 TCAGTCCCAATAAAGCATACCGTTA 60.105 40.000 0.00 0.00 0.00 3.18
401 532 5.007332 CAGTCCCAATAAAGCATACCGTTAC 59.993 44.000 0.00 0.00 0.00 2.50
402 533 4.877251 GTCCCAATAAAGCATACCGTTACA 59.123 41.667 0.00 0.00 0.00 2.41
403 534 5.354792 GTCCCAATAAAGCATACCGTTACAA 59.645 40.000 0.00 0.00 0.00 2.41
404 535 5.944599 TCCCAATAAAGCATACCGTTACAAA 59.055 36.000 0.00 0.00 0.00 2.83
405 536 6.433404 TCCCAATAAAGCATACCGTTACAAAA 59.567 34.615 0.00 0.00 0.00 2.44
406 537 7.039923 TCCCAATAAAGCATACCGTTACAAAAA 60.040 33.333 0.00 0.00 0.00 1.94
448 579 6.587608 GCTGGGTGCATATAATTTATTCAAGC 59.412 38.462 0.00 0.00 42.31 4.01
506 637 2.158534 ACACATTGTTAGGGCAACTCCA 60.159 45.455 0.00 0.00 38.05 3.86
512 643 2.107378 TGTTAGGGCAACTCCAATGTGA 59.893 45.455 0.00 0.00 38.05 3.58
525 656 5.067413 ACTCCAATGTGATGCATCAAATCTC 59.933 40.000 28.57 17.82 38.75 2.75
547 679 3.701241 GACACTTTTTGGCATTCAACGA 58.299 40.909 0.00 0.00 34.67 3.85
554 686 0.533085 TGGCATTCAACGACGTGGAA 60.533 50.000 19.61 19.61 29.45 3.53
560 692 0.646381 TCAACGACGTGGAACAAACG 59.354 50.000 1.61 0.00 44.16 3.60
588 720 1.266718 ACGCGTCTGCATGTTTGAATT 59.733 42.857 5.58 0.00 42.97 2.17
597 729 4.880759 TGCATGTTTGAATTCCGACAAAT 58.119 34.783 13.04 0.00 38.09 2.32
624 756 1.840198 AACCCGAGGGAGGTTTCGT 60.840 57.895 16.26 0.00 45.46 3.85
625 757 1.413256 AACCCGAGGGAGGTTTCGTT 61.413 55.000 16.26 0.00 45.46 3.85
695 843 1.308069 ACTCGCCACACATTCATGCC 61.308 55.000 0.00 0.00 0.00 4.40
701 849 1.002257 ACACATTCATGCCGCTCCA 60.002 52.632 0.00 0.00 0.00 3.86
734 882 0.107831 GGCCGCCTACCACATTCATA 59.892 55.000 0.71 0.00 0.00 2.15
760 908 0.248825 AGATCGATGTGAGCAGACGC 60.249 55.000 0.54 0.00 34.70 5.19
770 918 2.355837 GCAGACGCTTGACCGACA 60.356 61.111 0.00 0.00 34.30 4.35
776 924 0.033504 ACGCTTGACCGACACTTCAT 59.966 50.000 0.00 0.00 0.00 2.57
781 929 1.960417 TGACCGACACTTCATTGCAA 58.040 45.000 0.00 0.00 0.00 4.08
782 930 1.872952 TGACCGACACTTCATTGCAAG 59.127 47.619 4.94 0.00 0.00 4.01
800 948 2.253758 GCGTGGCAACTGAGAAGCA 61.254 57.895 0.00 0.00 37.61 3.91
827 975 2.473378 CGCTCTGCACGCTTTGAG 59.527 61.111 2.19 0.00 0.00 3.02
884 1032 1.228552 ATGGCTTGCCGACAAACCT 60.229 52.632 5.48 0.00 41.73 3.50
901 1049 1.854280 ACCTTATCTCCTCTCCTCCGT 59.146 52.381 0.00 0.00 0.00 4.69
908 1056 1.489649 CTCCTCTCCTCCGTACACCTA 59.510 57.143 0.00 0.00 0.00 3.08
924 1072 3.726859 ACACCTATCCTCTCCTCTCATCT 59.273 47.826 0.00 0.00 0.00 2.90
925 1073 4.081406 CACCTATCCTCTCCTCTCATCTG 58.919 52.174 0.00 0.00 0.00 2.90
932 1080 1.953231 CTCCTCTCATCTGCACGCCA 61.953 60.000 0.00 0.00 0.00 5.69
933 1081 1.145598 CCTCTCATCTGCACGCCAT 59.854 57.895 0.00 0.00 0.00 4.40
970 1118 1.591327 CAGTTGGTTTTGGCACCGC 60.591 57.895 0.00 0.00 40.09 5.68
1043 1191 2.106332 GCCCGTCTACATCCACCG 59.894 66.667 0.00 0.00 0.00 4.94
1049 1197 2.125326 TCTACATCCACCGCTCCCG 61.125 63.158 0.00 0.00 0.00 5.14
1100 1274 0.260230 AGGAGGAGCAGTAGCAGCTA 59.740 55.000 0.00 0.00 43.58 3.32
1112 1286 0.252012 AGCAGCTACCACTCCTCACT 60.252 55.000 0.00 0.00 0.00 3.41
1113 1287 0.108424 GCAGCTACCACTCCTCACTG 60.108 60.000 0.00 0.00 0.00 3.66
1126 1300 3.807538 CACTGAGGCCGCATGCAC 61.808 66.667 19.57 8.95 43.89 4.57
1128 1302 2.827190 CTGAGGCCGCATGCACAT 60.827 61.111 19.57 6.53 43.89 3.21
1130 1304 1.779025 CTGAGGCCGCATGCACATAC 61.779 60.000 19.57 6.38 43.89 2.39
1158 1332 0.661187 CGCCACACACATCAAGTTGC 60.661 55.000 0.00 0.00 0.00 4.17
1159 1333 0.670162 GCCACACACATCAAGTTGCT 59.330 50.000 0.00 0.00 0.00 3.91
1205 1379 1.594331 GTCGGCATCCTACCAAATCC 58.406 55.000 0.00 0.00 0.00 3.01
1210 1384 2.427095 GGCATCCTACCAAATCCAACAC 59.573 50.000 0.00 0.00 0.00 3.32
1211 1385 3.088532 GCATCCTACCAAATCCAACACA 58.911 45.455 0.00 0.00 0.00 3.72
1228 1410 1.079543 CAGTGTCAAGGAGGAGCCG 60.080 63.158 0.00 0.00 43.43 5.52
1240 1422 4.101448 GAGCCGCCCTCACCACAT 62.101 66.667 0.00 0.00 40.45 3.21
1245 1427 2.048023 CGCCCTCACCACATGCAAT 61.048 57.895 0.00 0.00 0.00 3.56
1266 1448 2.824041 ATCGTCCAATGCCACGGC 60.824 61.111 0.00 0.00 42.35 5.68
1293 1475 1.076727 TTCCTCCTGCCTCGTCAGA 59.923 57.895 4.22 0.00 36.19 3.27
1296 1478 1.979155 CTCCTGCCTCGTCAGACCA 60.979 63.158 0.00 0.00 36.19 4.02
1300 1482 0.671781 CTGCCTCGTCAGACCAAAGG 60.672 60.000 6.85 6.85 36.19 3.11
1402 1584 3.000819 AGGATTGGGCGTGGACGA 61.001 61.111 2.73 0.00 43.02 4.20
1588 1770 1.132527 TGAAGGGGGAGAAGAAGGACA 60.133 52.381 0.00 0.00 0.00 4.02
1589 1771 2.200955 GAAGGGGGAGAAGAAGGACAT 58.799 52.381 0.00 0.00 0.00 3.06
1598 1780 1.874345 AAGAAGGACATCGACGGCGT 61.874 55.000 14.65 14.65 38.98 5.68
1627 1809 1.487482 CGTGTTCAGCGAGTTCTTCA 58.513 50.000 0.00 0.00 0.00 3.02
1647 1829 4.156622 CTGTAGGCGCGACGACGA 62.157 66.667 20.46 8.74 41.28 4.20
1648 1830 4.156622 TGTAGGCGCGACGACGAG 62.157 66.667 20.46 9.33 41.28 4.18
1649 1831 4.883300 GTAGGCGCGACGACGAGG 62.883 72.222 10.11 2.85 41.28 4.63
1671 1853 3.370231 GTCGCCGGCCAAACCAAT 61.370 61.111 23.46 0.00 39.03 3.16
1672 1854 3.059386 TCGCCGGCCAAACCAATC 61.059 61.111 23.46 0.00 39.03 2.67
1673 1855 4.128388 CGCCGGCCAAACCAATCC 62.128 66.667 23.46 0.00 39.03 3.01
1674 1856 4.128388 GCCGGCCAAACCAATCCG 62.128 66.667 18.11 0.00 39.03 4.18
1675 1857 4.128388 CCGGCCAAACCAATCCGC 62.128 66.667 2.24 0.00 40.49 5.54
1676 1858 3.061848 CGGCCAAACCAATCCGCT 61.062 61.111 2.24 0.00 39.03 5.52
1677 1859 1.747367 CGGCCAAACCAATCCGCTA 60.747 57.895 2.24 0.00 39.03 4.26
1678 1860 1.714899 CGGCCAAACCAATCCGCTAG 61.715 60.000 2.24 0.00 39.03 3.42
1679 1861 1.384222 GGCCAAACCAATCCGCTAGG 61.384 60.000 0.00 0.00 38.86 3.02
1680 1862 1.384222 GCCAAACCAATCCGCTAGGG 61.384 60.000 0.00 0.00 38.33 3.53
1681 1863 0.751643 CCAAACCAATCCGCTAGGGG 60.752 60.000 19.63 19.63 38.33 4.79
1682 1864 0.751643 CAAACCAATCCGCTAGGGGG 60.752 60.000 24.48 11.59 38.33 5.40
1704 1886 3.528370 CGGGCAGGGGTCGACTAG 61.528 72.222 16.46 4.23 0.00 2.57
1705 1887 3.155167 GGGCAGGGGTCGACTAGG 61.155 72.222 16.46 4.21 0.00 3.02
1706 1888 3.155167 GGCAGGGGTCGACTAGGG 61.155 72.222 16.46 4.58 0.00 3.53
1707 1889 2.043248 GCAGGGGTCGACTAGGGA 60.043 66.667 16.46 0.00 0.00 4.20
1708 1890 2.424733 GCAGGGGTCGACTAGGGAC 61.425 68.421 16.46 7.47 0.00 4.46
1709 1891 2.119655 CAGGGGTCGACTAGGGACG 61.120 68.421 16.46 5.33 35.24 4.79
1710 1892 2.832201 GGGGTCGACTAGGGACGG 60.832 72.222 16.46 0.00 35.24 4.79
1711 1893 2.044551 GGGTCGACTAGGGACGGT 60.045 66.667 16.46 0.00 35.24 4.83
1712 1894 1.680314 GGGTCGACTAGGGACGGTT 60.680 63.158 16.46 0.00 35.24 4.44
1713 1895 1.509923 GGTCGACTAGGGACGGTTG 59.490 63.158 16.46 0.00 35.24 3.77
1714 1896 1.153881 GTCGACTAGGGACGGTTGC 60.154 63.158 8.70 0.00 0.00 4.17
1715 1897 2.202570 CGACTAGGGACGGTTGCG 60.203 66.667 0.00 0.00 0.00 4.85
1716 1898 2.968206 GACTAGGGACGGTTGCGT 59.032 61.111 0.00 0.00 0.00 5.24
1717 1899 1.445582 GACTAGGGACGGTTGCGTG 60.446 63.158 0.00 0.00 0.00 5.34
1718 1900 1.870055 GACTAGGGACGGTTGCGTGA 61.870 60.000 0.00 0.00 0.00 4.35
1719 1901 1.290955 CTAGGGACGGTTGCGTGAA 59.709 57.895 0.00 0.00 0.00 3.18
1720 1902 0.736325 CTAGGGACGGTTGCGTGAAG 60.736 60.000 0.00 0.00 0.00 3.02
1721 1903 2.162338 TAGGGACGGTTGCGTGAAGG 62.162 60.000 0.00 0.00 0.00 3.46
1722 1904 3.047877 GGACGGTTGCGTGAAGGG 61.048 66.667 0.00 0.00 0.00 3.95
1723 1905 3.047877 GACGGTTGCGTGAAGGGG 61.048 66.667 0.00 0.00 0.00 4.79
1724 1906 4.636435 ACGGTTGCGTGAAGGGGG 62.636 66.667 0.00 0.00 0.00 5.40
1725 1907 4.323477 CGGTTGCGTGAAGGGGGA 62.323 66.667 0.00 0.00 0.00 4.81
1726 1908 2.359975 GGTTGCGTGAAGGGGGAG 60.360 66.667 0.00 0.00 0.00 4.30
1727 1909 2.747686 GTTGCGTGAAGGGGGAGA 59.252 61.111 0.00 0.00 0.00 3.71
1728 1910 1.072505 GTTGCGTGAAGGGGGAGAA 59.927 57.895 0.00 0.00 0.00 2.87
1729 1911 0.955919 GTTGCGTGAAGGGGGAGAAG 60.956 60.000 0.00 0.00 0.00 2.85
1730 1912 1.125093 TTGCGTGAAGGGGGAGAAGA 61.125 55.000 0.00 0.00 0.00 2.87
1731 1913 1.125093 TGCGTGAAGGGGGAGAAGAA 61.125 55.000 0.00 0.00 0.00 2.52
1732 1914 0.391793 GCGTGAAGGGGGAGAAGAAG 60.392 60.000 0.00 0.00 0.00 2.85
1733 1915 0.250513 CGTGAAGGGGGAGAAGAAGG 59.749 60.000 0.00 0.00 0.00 3.46
1734 1916 1.657804 GTGAAGGGGGAGAAGAAGGA 58.342 55.000 0.00 0.00 0.00 3.36
1735 1917 1.279558 GTGAAGGGGGAGAAGAAGGAC 59.720 57.143 0.00 0.00 0.00 3.85
1736 1918 1.132527 TGAAGGGGGAGAAGAAGGACA 60.133 52.381 0.00 0.00 0.00 4.02
1737 1919 1.985895 GAAGGGGGAGAAGAAGGACAA 59.014 52.381 0.00 0.00 0.00 3.18
1738 1920 2.367947 AGGGGGAGAAGAAGGACAAT 57.632 50.000 0.00 0.00 0.00 2.71
1739 1921 1.918957 AGGGGGAGAAGAAGGACAATG 59.081 52.381 0.00 0.00 0.00 2.82
1740 1922 1.916181 GGGGGAGAAGAAGGACAATGA 59.084 52.381 0.00 0.00 0.00 2.57
1741 1923 2.356227 GGGGGAGAAGAAGGACAATGAC 60.356 54.545 0.00 0.00 0.00 3.06
1742 1924 2.622436 GGGAGAAGAAGGACAATGACG 58.378 52.381 0.00 0.00 0.00 4.35
1743 1925 2.622436 GGAGAAGAAGGACAATGACGG 58.378 52.381 0.00 0.00 0.00 4.79
1744 1926 2.003301 GAGAAGAAGGACAATGACGGC 58.997 52.381 0.00 0.00 0.00 5.68
1745 1927 0.721718 GAAGAAGGACAATGACGGCG 59.278 55.000 4.80 4.80 0.00 6.46
1746 1928 0.034896 AAGAAGGACAATGACGGCGT 59.965 50.000 14.65 14.65 0.00 5.68
1747 1929 0.389948 AGAAGGACAATGACGGCGTC 60.390 55.000 31.68 31.68 0.00 5.19
1748 1930 1.683790 GAAGGACAATGACGGCGTCG 61.684 60.000 31.90 21.36 43.02 5.12
1749 1931 2.126228 GGACAATGACGGCGTCGA 60.126 61.111 31.90 22.03 40.11 4.20
1750 1932 2.442188 GGACAATGACGGCGTCGAC 61.442 63.158 31.90 18.78 40.11 4.20
1751 1933 1.443872 GACAATGACGGCGTCGACT 60.444 57.895 31.90 18.07 40.11 4.18
1752 1934 1.006571 ACAATGACGGCGTCGACTT 60.007 52.632 31.90 22.33 40.11 3.01
1753 1935 0.599204 ACAATGACGGCGTCGACTTT 60.599 50.000 31.90 20.20 40.11 2.66
1754 1936 0.179250 CAATGACGGCGTCGACTTTG 60.179 55.000 31.90 25.82 38.71 2.77
1755 1937 1.289109 AATGACGGCGTCGACTTTGG 61.289 55.000 31.90 2.71 40.11 3.28
1756 1938 3.774702 GACGGCGTCGACTTTGGC 61.775 66.667 25.42 9.31 40.11 4.52
1759 1941 4.072088 GGCGTCGACTTTGGCGTG 62.072 66.667 14.70 0.00 0.00 5.34
1760 1942 3.335534 GCGTCGACTTTGGCGTGT 61.336 61.111 14.70 0.00 0.00 4.49
1761 1943 2.877974 GCGTCGACTTTGGCGTGTT 61.878 57.895 14.70 0.00 0.00 3.32
1762 1944 1.200839 CGTCGACTTTGGCGTGTTC 59.799 57.895 14.70 0.00 0.00 3.18
1763 1945 1.484227 CGTCGACTTTGGCGTGTTCA 61.484 55.000 14.70 0.00 0.00 3.18
1764 1946 0.865769 GTCGACTTTGGCGTGTTCAT 59.134 50.000 8.70 0.00 0.00 2.57
1765 1947 1.136336 GTCGACTTTGGCGTGTTCATC 60.136 52.381 8.70 0.00 0.00 2.92
1766 1948 0.179250 CGACTTTGGCGTGTTCATCG 60.179 55.000 0.00 0.00 0.00 3.84
1767 1949 1.144969 GACTTTGGCGTGTTCATCGA 58.855 50.000 0.00 0.00 0.00 3.59
1768 1950 1.126846 GACTTTGGCGTGTTCATCGAG 59.873 52.381 0.00 0.00 0.00 4.04
1769 1951 1.148310 CTTTGGCGTGTTCATCGAGT 58.852 50.000 0.00 0.00 0.00 4.18
1770 1952 1.531149 CTTTGGCGTGTTCATCGAGTT 59.469 47.619 0.00 0.00 0.00 3.01
1771 1953 1.144969 TTGGCGTGTTCATCGAGTTC 58.855 50.000 0.00 0.00 0.00 3.01
1772 1954 0.317160 TGGCGTGTTCATCGAGTTCT 59.683 50.000 0.00 0.00 0.00 3.01
1773 1955 1.270094 TGGCGTGTTCATCGAGTTCTT 60.270 47.619 0.00 0.00 0.00 2.52
1774 1956 1.390463 GGCGTGTTCATCGAGTTCTTC 59.610 52.381 0.00 0.00 0.00 2.87
1775 1957 2.058798 GCGTGTTCATCGAGTTCTTCA 58.941 47.619 0.00 0.00 0.00 3.02
1776 1958 2.091277 GCGTGTTCATCGAGTTCTTCAG 59.909 50.000 0.00 0.00 0.00 3.02
1777 1959 2.091277 CGTGTTCATCGAGTTCTTCAGC 59.909 50.000 0.00 0.00 0.00 4.26
1778 1960 2.413453 GTGTTCATCGAGTTCTTCAGCC 59.587 50.000 0.00 0.00 0.00 4.85
1779 1961 2.300152 TGTTCATCGAGTTCTTCAGCCT 59.700 45.455 0.00 0.00 0.00 4.58
1780 1962 2.662006 TCATCGAGTTCTTCAGCCTG 57.338 50.000 0.00 0.00 0.00 4.85
1781 1963 1.895798 TCATCGAGTTCTTCAGCCTGT 59.104 47.619 0.00 0.00 0.00 4.00
1782 1964 3.089284 TCATCGAGTTCTTCAGCCTGTA 58.911 45.455 0.00 0.00 0.00 2.74
1783 1965 3.129462 TCATCGAGTTCTTCAGCCTGTAG 59.871 47.826 0.00 0.00 0.00 2.74
1784 1966 1.819288 TCGAGTTCTTCAGCCTGTAGG 59.181 52.381 0.00 0.00 38.53 3.18
1861 2044 2.616842 ACAAAACTGTGAACCGCCTAAG 59.383 45.455 0.00 0.00 0.00 2.18
1877 2060 4.437794 CGCCTAAGTATCGCCGAATGTATA 60.438 45.833 0.00 0.00 0.00 1.47
1886 2070 4.114073 TCGCCGAATGTATATCGTGTTTT 58.886 39.130 0.00 0.00 38.60 2.43
1899 2083 3.404899 TCGTGTTTTCCGAAATTAGCCT 58.595 40.909 0.00 0.00 0.00 4.58
1939 2123 8.454570 AAAACTTATAAAAGACCGTTTGGAGA 57.545 30.769 0.61 0.00 35.94 3.71
1947 2131 1.111116 ACCGTTTGGAGACGACCTGA 61.111 55.000 0.00 0.00 45.47 3.86
1965 2149 3.637273 GGGTGGCGACTGGGAAGT 61.637 66.667 0.00 0.00 0.00 3.01
1978 2162 1.345715 GGGAAGTCGATCACCCCCAT 61.346 60.000 11.15 0.00 37.99 4.00
2009 2193 2.203422 CCGGTTCAACCCCAAGCA 60.203 61.111 0.00 0.00 33.75 3.91
2457 3424 9.613428 TGTTCCTAGATATTTACAAGACATTGG 57.387 33.333 0.00 0.00 40.97 3.16
2471 3447 3.849911 GACATTGGTCTCTCGATTGACA 58.150 45.455 16.29 1.84 40.99 3.58
2485 3461 4.211164 TCGATTGACAAGACAACATGTGAC 59.789 41.667 0.00 0.00 32.50 3.67
2489 3465 3.118445 TGACAAGACAACATGTGACAGGA 60.118 43.478 3.52 0.00 0.00 3.86
2514 3490 1.028330 AGCTCATGCATGACCAACCG 61.028 55.000 25.42 15.25 42.74 4.44
2518 3494 2.228582 CTCATGCATGACCAACCGAAAA 59.771 45.455 25.42 0.62 32.50 2.29
2520 3496 6.680294 CTCATGCATGACCAACCGAAAAGG 62.680 50.000 25.42 7.28 38.16 3.11
2525 3501 4.082463 GCATGACCAACCGAAAAGGAAATA 60.082 41.667 0.00 0.00 45.00 1.40
2631 3611 9.063615 ACCGTAAGATTCTATTCAAACTGTTTT 57.936 29.630 2.41 0.00 43.02 2.43
2632 3612 9.893305 CCGTAAGATTCTATTCAAACTGTTTTT 57.107 29.630 2.41 0.00 43.02 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.471556 TCTACCGGACAGTTTACATCAAA 57.528 39.130 9.46 0.00 0.00 2.69
1 2 5.670792 ATCTACCGGACAGTTTACATCAA 57.329 39.130 9.46 0.00 0.00 2.57
2 3 5.670792 AATCTACCGGACAGTTTACATCA 57.329 39.130 9.46 0.00 0.00 3.07
3 4 8.658499 AATTAATCTACCGGACAGTTTACATC 57.342 34.615 9.46 0.00 0.00 3.06
6 7 8.260270 ACAAATTAATCTACCGGACAGTTTAC 57.740 34.615 9.46 0.00 0.00 2.01
7 8 8.851541 AACAAATTAATCTACCGGACAGTTTA 57.148 30.769 9.46 7.78 0.00 2.01
8 9 7.754851 AACAAATTAATCTACCGGACAGTTT 57.245 32.000 9.46 8.79 0.00 2.66
9 10 8.098912 ACTAACAAATTAATCTACCGGACAGTT 58.901 33.333 9.46 0.00 0.00 3.16
10 11 7.618137 ACTAACAAATTAATCTACCGGACAGT 58.382 34.615 9.46 0.00 0.00 3.55
11 12 9.245962 CTACTAACAAATTAATCTACCGGACAG 57.754 37.037 9.46 4.73 0.00 3.51
12 13 8.199449 CCTACTAACAAATTAATCTACCGGACA 58.801 37.037 9.46 0.00 0.00 4.02
13 14 7.170489 GCCTACTAACAAATTAATCTACCGGAC 59.830 40.741 9.46 0.00 0.00 4.79
14 15 7.147689 TGCCTACTAACAAATTAATCTACCGGA 60.148 37.037 9.46 0.00 0.00 5.14
15 16 6.987992 TGCCTACTAACAAATTAATCTACCGG 59.012 38.462 0.00 0.00 0.00 5.28
16 17 7.307219 GCTGCCTACTAACAAATTAATCTACCG 60.307 40.741 0.00 0.00 0.00 4.02
17 18 7.715686 AGCTGCCTACTAACAAATTAATCTACC 59.284 37.037 0.00 0.00 0.00 3.18
18 19 8.552034 CAGCTGCCTACTAACAAATTAATCTAC 58.448 37.037 0.00 0.00 0.00 2.59
19 20 8.482943 TCAGCTGCCTACTAACAAATTAATCTA 58.517 33.333 9.47 0.00 0.00 1.98
20 21 7.338710 TCAGCTGCCTACTAACAAATTAATCT 58.661 34.615 9.47 0.00 0.00 2.40
21 22 7.553881 TCAGCTGCCTACTAACAAATTAATC 57.446 36.000 9.47 0.00 0.00 1.75
22 23 6.038714 GCTCAGCTGCCTACTAACAAATTAAT 59.961 38.462 9.47 0.00 0.00 1.40
23 24 5.354234 GCTCAGCTGCCTACTAACAAATTAA 59.646 40.000 9.47 0.00 0.00 1.40
24 25 4.876107 GCTCAGCTGCCTACTAACAAATTA 59.124 41.667 9.47 0.00 0.00 1.40
25 26 3.691609 GCTCAGCTGCCTACTAACAAATT 59.308 43.478 9.47 0.00 0.00 1.82
26 27 3.274288 GCTCAGCTGCCTACTAACAAAT 58.726 45.455 9.47 0.00 0.00 2.32
27 28 2.699954 GCTCAGCTGCCTACTAACAAA 58.300 47.619 9.47 0.00 0.00 2.83
28 29 2.386661 GCTCAGCTGCCTACTAACAA 57.613 50.000 9.47 0.00 0.00 2.83
38 39 2.021068 TATCGACCTGGCTCAGCTGC 62.021 60.000 9.47 0.00 0.00 5.25
39 40 0.461548 TTATCGACCTGGCTCAGCTG 59.538 55.000 7.63 7.63 0.00 4.24
40 41 1.195115 TTTATCGACCTGGCTCAGCT 58.805 50.000 0.00 0.00 0.00 4.24
41 42 2.024176 TTTTATCGACCTGGCTCAGC 57.976 50.000 0.00 0.00 0.00 4.26
42 43 3.600388 ACTTTTTATCGACCTGGCTCAG 58.400 45.455 0.00 0.00 0.00 3.35
43 44 3.695830 ACTTTTTATCGACCTGGCTCA 57.304 42.857 0.00 0.00 0.00 4.26
44 45 3.869832 GGTACTTTTTATCGACCTGGCTC 59.130 47.826 0.00 0.00 0.00 4.70
45 46 3.370209 GGGTACTTTTTATCGACCTGGCT 60.370 47.826 0.00 0.00 0.00 4.75
46 47 2.941064 GGGTACTTTTTATCGACCTGGC 59.059 50.000 0.00 0.00 0.00 4.85
47 48 4.210724 TGGGTACTTTTTATCGACCTGG 57.789 45.455 0.00 0.00 0.00 4.45
48 49 4.035208 GCATGGGTACTTTTTATCGACCTG 59.965 45.833 0.00 0.00 0.00 4.00
49 50 4.196971 GCATGGGTACTTTTTATCGACCT 58.803 43.478 0.00 0.00 0.00 3.85
50 51 3.001939 CGCATGGGTACTTTTTATCGACC 59.998 47.826 0.68 0.00 0.00 4.79
51 52 3.001939 CCGCATGGGTACTTTTTATCGAC 59.998 47.826 9.14 0.00 0.00 4.20
52 53 3.199677 CCGCATGGGTACTTTTTATCGA 58.800 45.455 9.14 0.00 0.00 3.59
53 54 3.602390 CCGCATGGGTACTTTTTATCG 57.398 47.619 9.14 0.00 0.00 2.92
67 68 1.585267 TAAACAGCAGCCACCGCATG 61.585 55.000 0.00 0.00 37.52 4.06
68 69 0.680921 ATAAACAGCAGCCACCGCAT 60.681 50.000 0.00 0.00 37.52 4.73
70 71 0.243636 AAATAAACAGCAGCCACCGC 59.756 50.000 0.00 0.00 0.00 5.68
71 72 1.981254 CAAATAAACAGCAGCCACCG 58.019 50.000 0.00 0.00 0.00 4.94
72 73 1.273327 AGCAAATAAACAGCAGCCACC 59.727 47.619 0.00 0.00 0.00 4.61
73 74 2.229784 AGAGCAAATAAACAGCAGCCAC 59.770 45.455 0.00 0.00 0.00 5.01
74 75 2.517959 AGAGCAAATAAACAGCAGCCA 58.482 42.857 0.00 0.00 0.00 4.75
75 76 3.582714 AAGAGCAAATAAACAGCAGCC 57.417 42.857 0.00 0.00 0.00 4.85
76 77 5.942872 TCTTAAGAGCAAATAAACAGCAGC 58.057 37.500 0.00 0.00 0.00 5.25
77 78 8.239314 TGAATCTTAAGAGCAAATAAACAGCAG 58.761 33.333 11.53 0.00 0.00 4.24
78 79 8.109705 TGAATCTTAAGAGCAAATAAACAGCA 57.890 30.769 11.53 0.00 0.00 4.41
117 118 5.947566 TGCACTATACCATATAGTTAGGCGA 59.052 40.000 5.89 0.00 32.93 5.54
120 121 6.697455 CGCATGCACTATACCATATAGTTAGG 59.303 42.308 19.57 2.89 32.93 2.69
123 124 4.870426 GCGCATGCACTATACCATATAGTT 59.130 41.667 19.57 0.00 42.15 2.24
126 127 4.159506 TCAGCGCATGCACTATACCATATA 59.840 41.667 19.57 0.00 46.23 0.86
127 128 3.055891 TCAGCGCATGCACTATACCATAT 60.056 43.478 19.57 0.00 46.23 1.78
128 129 2.298729 TCAGCGCATGCACTATACCATA 59.701 45.455 19.57 0.00 46.23 2.74
129 130 1.070601 TCAGCGCATGCACTATACCAT 59.929 47.619 19.57 0.00 46.23 3.55
131 132 0.861837 GTCAGCGCATGCACTATACC 59.138 55.000 19.57 0.00 46.23 2.73
132 133 0.861837 GGTCAGCGCATGCACTATAC 59.138 55.000 19.57 14.13 46.23 1.47
133 134 0.249868 GGGTCAGCGCATGCACTATA 60.250 55.000 19.57 2.01 46.23 1.31
134 135 1.524621 GGGTCAGCGCATGCACTAT 60.525 57.895 19.57 0.00 46.23 2.12
135 136 2.125147 GGGTCAGCGCATGCACTA 60.125 61.111 19.57 0.00 46.23 2.74
136 137 2.256072 TATGGGTCAGCGCATGCACT 62.256 55.000 19.57 11.06 45.95 4.40
173 202 0.689055 AGGGGGAAACGGTTGACTAC 59.311 55.000 0.00 0.00 0.00 2.73
174 203 2.181975 CTAGGGGGAAACGGTTGACTA 58.818 52.381 0.00 0.00 0.00 2.59
242 332 2.589798 TCTAATTAACAGGCCGGTCG 57.410 50.000 9.62 0.00 0.00 4.79
282 404 7.820578 TCCACTAGGATAAGCTTAACTACTC 57.179 40.000 10.85 2.82 39.61 2.59
306 428 1.907240 ATGTAGTGCCCCAATACCCT 58.093 50.000 1.11 0.00 34.57 4.34
313 435 4.947883 AGCTCTATATATGTAGTGCCCCA 58.052 43.478 22.37 0.00 40.34 4.96
376 507 3.199071 ACGGTATGCTTTATTGGGACTGA 59.801 43.478 0.00 0.00 0.00 3.41
447 578 0.729116 CACATCCACCTCATGAACGC 59.271 55.000 0.00 0.00 0.00 4.84
448 579 1.066215 TCCACATCCACCTCATGAACG 60.066 52.381 0.00 0.00 0.00 3.95
506 637 4.637091 TGTCGAGATTTGATGCATCACATT 59.363 37.500 28.72 16.99 39.84 2.71
512 643 5.633830 AAAAGTGTCGAGATTTGATGCAT 57.366 34.783 0.00 0.00 0.00 3.96
525 656 2.467305 CGTTGAATGCCAAAAAGTGTCG 59.533 45.455 0.00 0.00 36.36 4.35
579 711 6.384258 TTCAGATTTGTCGGAATTCAAACA 57.616 33.333 7.93 7.84 36.58 2.83
588 720 2.552315 GGTTTGCTTCAGATTTGTCGGA 59.448 45.455 0.00 0.00 0.00 4.55
597 729 1.125093 TCCCTCGGGTTTGCTTCAGA 61.125 55.000 1.18 0.00 36.47 3.27
638 785 2.747686 GCGAGGACTTTGGGTGGA 59.252 61.111 0.00 0.00 0.00 4.02
666 814 0.179234 TGTGGCGAGTGTTCTGGAAA 59.821 50.000 0.00 0.00 0.00 3.13
718 866 2.288825 ACCGATATGAATGTGGTAGGCG 60.289 50.000 0.00 0.00 0.00 5.52
723 871 4.559502 CGATCTGACCGATATGAATGTGGT 60.560 45.833 0.00 0.00 35.14 4.16
726 874 5.047731 ACATCGATCTGACCGATATGAATGT 60.048 40.000 6.60 0.00 43.93 2.71
734 882 1.000827 GCTCACATCGATCTGACCGAT 60.001 52.381 0.00 0.00 46.32 4.18
760 908 1.872952 TGCAATGAAGTGTCGGTCAAG 59.127 47.619 0.00 0.00 0.00 3.02
761 909 1.960417 TGCAATGAAGTGTCGGTCAA 58.040 45.000 0.00 0.00 0.00 3.18
770 918 1.286880 GCCACGCTTGCAATGAAGT 59.713 52.632 0.00 0.00 0.00 3.01
776 924 2.062361 CTCAGTTGCCACGCTTGCAA 62.062 55.000 0.00 0.00 45.83 4.08
781 929 1.963338 GCTTCTCAGTTGCCACGCT 60.963 57.895 0.00 0.00 0.00 5.07
782 930 1.580845 ATGCTTCTCAGTTGCCACGC 61.581 55.000 0.00 0.00 0.00 5.34
800 948 2.060383 TGCAGAGCGGCCAGAGTAT 61.060 57.895 2.24 0.00 0.00 2.12
884 1032 3.434739 GGTGTACGGAGGAGAGGAGATAA 60.435 52.174 0.00 0.00 0.00 1.75
901 1049 4.917040 AGATGAGAGGAGAGGATAGGTGTA 59.083 45.833 0.00 0.00 0.00 2.90
908 1056 2.318908 GTGCAGATGAGAGGAGAGGAT 58.681 52.381 0.00 0.00 0.00 3.24
924 1072 4.538233 CCATCACTATGGCGTGCA 57.462 55.556 0.00 0.00 46.17 4.57
943 1091 1.950909 CAAAACCAACTGCGGGACTTA 59.049 47.619 0.00 0.00 0.00 2.24
950 1098 1.591327 GGTGCCAAAACCAACTGCG 60.591 57.895 0.00 0.00 40.22 5.18
951 1099 1.591327 CGGTGCCAAAACCAACTGC 60.591 57.895 0.00 0.00 40.53 4.40
1049 1197 0.603975 AGAGCAACCTCTTTGACCGC 60.604 55.000 0.00 0.00 46.16 5.68
1078 1252 1.484038 CTGCTACTGCTCCTCCTCTT 58.516 55.000 0.00 0.00 40.48 2.85
1079 1253 1.042559 GCTGCTACTGCTCCTCCTCT 61.043 60.000 0.00 0.00 40.48 3.69
1080 1254 1.042559 AGCTGCTACTGCTCCTCCTC 61.043 60.000 0.00 0.00 40.48 3.71
1112 1286 1.819208 GTATGTGCATGCGGCCTCA 60.819 57.895 14.09 0.00 43.89 3.86
1113 1287 2.885676 CGTATGTGCATGCGGCCTC 61.886 63.158 14.09 0.00 41.99 4.70
1121 1295 1.545759 CGAACTCGTCGTATGTGCAT 58.454 50.000 0.00 0.00 45.09 3.96
1142 1316 1.335810 AGCAGCAACTTGATGTGTGTG 59.664 47.619 8.74 0.00 35.94 3.82
1145 1319 0.870393 CGAGCAGCAACTTGATGTGT 59.130 50.000 8.74 0.00 35.94 3.72
1192 1366 4.202567 ACACTGTGTTGGATTTGGTAGGAT 60.203 41.667 7.80 0.00 0.00 3.24
1205 1379 2.487934 CTCCTCCTTGACACTGTGTTG 58.512 52.381 15.54 8.46 0.00 3.33
1210 1384 1.079543 CGGCTCCTCCTTGACACTG 60.080 63.158 0.00 0.00 0.00 3.66
1211 1385 2.948720 GCGGCTCCTCCTTGACACT 61.949 63.158 0.00 0.00 0.00 3.55
1228 1410 0.108520 CAATTGCATGTGGTGAGGGC 60.109 55.000 0.00 0.00 0.00 5.19
1249 1431 2.824041 GCCGTGGCATTGGACGAT 60.824 61.111 12.37 0.00 41.49 3.73
1282 1464 1.371183 CCTTTGGTCTGACGAGGCA 59.629 57.895 9.55 0.00 0.00 4.75
1381 1563 3.727258 CCACGCCCAATCCTCCCA 61.727 66.667 0.00 0.00 0.00 4.37
1402 1584 2.437359 GTGCTGGCGCTCCATCTT 60.437 61.111 7.64 0.00 42.51 2.40
1429 1611 2.829003 TCGAGCGGCGATCTCCTT 60.829 61.111 23.49 0.00 45.59 3.36
1472 1654 2.654912 CTGTCGTCGGGAACAACGC 61.655 63.158 0.00 0.00 0.00 4.84
1476 1658 4.351938 CCGCTGTCGTCGGGAACA 62.352 66.667 0.00 0.00 42.99 3.18
1507 1689 3.059386 GATTGGTTTGGCCGGCGA 61.059 61.111 22.54 15.52 41.21 5.54
1562 1744 2.837371 CTTCTCCCCCTTCACGCGAC 62.837 65.000 15.93 0.00 0.00 5.19
1563 1745 2.602267 TTCTCCCCCTTCACGCGA 60.602 61.111 15.93 0.00 0.00 5.87
1574 1756 1.202313 CGTCGATGTCCTTCTTCTCCC 60.202 57.143 0.00 0.00 0.00 4.30
1598 1780 1.495584 GCTGAACACGCCAAAGTCGA 61.496 55.000 0.00 0.00 0.00 4.20
1605 1787 1.954146 GAACTCGCTGAACACGCCA 60.954 57.895 0.00 0.00 0.00 5.69
1654 1836 3.336715 GATTGGTTTGGCCGGCGAC 62.337 63.158 22.54 18.33 41.21 5.19
1655 1837 3.059386 GATTGGTTTGGCCGGCGA 61.059 61.111 22.54 15.52 41.21 5.54
1656 1838 4.128388 GGATTGGTTTGGCCGGCG 62.128 66.667 22.54 0.00 41.21 6.46
1657 1839 4.128388 CGGATTGGTTTGGCCGGC 62.128 66.667 21.18 21.18 40.08 6.13
1658 1840 4.128388 GCGGATTGGTTTGGCCGG 62.128 66.667 0.00 0.00 43.73 6.13
1659 1841 1.714899 CTAGCGGATTGGTTTGGCCG 61.715 60.000 0.00 0.00 46.14 6.13
1660 1842 1.384222 CCTAGCGGATTGGTTTGGCC 61.384 60.000 0.00 0.00 37.90 5.36
1661 1843 1.384222 CCCTAGCGGATTGGTTTGGC 61.384 60.000 0.00 0.00 0.00 4.52
1662 1844 0.751643 CCCCTAGCGGATTGGTTTGG 60.752 60.000 0.00 0.00 0.00 3.28
1663 1845 0.751643 CCCCCTAGCGGATTGGTTTG 60.752 60.000 0.00 0.00 0.00 2.93
1664 1846 0.917333 TCCCCCTAGCGGATTGGTTT 60.917 55.000 0.00 0.00 0.00 3.27
1665 1847 1.307517 TCCCCCTAGCGGATTGGTT 60.308 57.895 0.00 0.00 0.00 3.67
1666 1848 2.070650 GTCCCCCTAGCGGATTGGT 61.071 63.158 0.00 0.00 0.00 3.67
1667 1849 2.819284 GGTCCCCCTAGCGGATTGG 61.819 68.421 0.00 0.00 0.00 3.16
1668 1850 2.819284 GGGTCCCCCTAGCGGATTG 61.819 68.421 0.00 0.00 41.34 2.67
1669 1851 2.447959 GGGTCCCCCTAGCGGATT 60.448 66.667 0.00 0.00 41.34 3.01
1687 1869 3.528370 CTAGTCGACCCCTGCCCG 61.528 72.222 13.01 0.00 0.00 6.13
1688 1870 3.155167 CCTAGTCGACCCCTGCCC 61.155 72.222 13.01 0.00 0.00 5.36
1689 1871 3.155167 CCCTAGTCGACCCCTGCC 61.155 72.222 13.01 0.00 0.00 4.85
1690 1872 2.043248 TCCCTAGTCGACCCCTGC 60.043 66.667 13.01 0.00 0.00 4.85
1691 1873 2.119655 CGTCCCTAGTCGACCCCTG 61.120 68.421 13.01 0.00 0.00 4.45
1692 1874 2.274760 CGTCCCTAGTCGACCCCT 59.725 66.667 13.01 0.00 0.00 4.79
1693 1875 2.832201 CCGTCCCTAGTCGACCCC 60.832 72.222 13.01 0.00 0.00 4.95
1694 1876 1.680314 AACCGTCCCTAGTCGACCC 60.680 63.158 13.01 0.00 0.00 4.46
1695 1877 1.509923 CAACCGTCCCTAGTCGACC 59.490 63.158 13.01 0.00 0.00 4.79
1696 1878 1.153881 GCAACCGTCCCTAGTCGAC 60.154 63.158 7.70 7.70 0.00 4.20
1697 1879 2.693762 CGCAACCGTCCCTAGTCGA 61.694 63.158 0.00 0.00 0.00 4.20
1698 1880 2.202570 CGCAACCGTCCCTAGTCG 60.203 66.667 0.00 0.00 0.00 4.18
1699 1881 1.445582 CACGCAACCGTCCCTAGTC 60.446 63.158 0.00 0.00 46.39 2.59
1700 1882 1.466025 TTCACGCAACCGTCCCTAGT 61.466 55.000 0.00 0.00 46.39 2.57
1701 1883 0.736325 CTTCACGCAACCGTCCCTAG 60.736 60.000 0.00 0.00 46.39 3.02
1702 1884 1.290955 CTTCACGCAACCGTCCCTA 59.709 57.895 0.00 0.00 46.39 3.53
1703 1885 2.030562 CTTCACGCAACCGTCCCT 59.969 61.111 0.00 0.00 46.39 4.20
1704 1886 3.047877 CCTTCACGCAACCGTCCC 61.048 66.667 0.00 0.00 46.39 4.46
1705 1887 3.047877 CCCTTCACGCAACCGTCC 61.048 66.667 0.00 0.00 46.39 4.79
1706 1888 3.047877 CCCCTTCACGCAACCGTC 61.048 66.667 0.00 0.00 46.39 4.79
1708 1890 4.323477 TCCCCCTTCACGCAACCG 62.323 66.667 0.00 0.00 41.14 4.44
1709 1891 2.359975 CTCCCCCTTCACGCAACC 60.360 66.667 0.00 0.00 0.00 3.77
1710 1892 0.955919 CTTCTCCCCCTTCACGCAAC 60.956 60.000 0.00 0.00 0.00 4.17
1711 1893 1.125093 TCTTCTCCCCCTTCACGCAA 61.125 55.000 0.00 0.00 0.00 4.85
1712 1894 1.125093 TTCTTCTCCCCCTTCACGCA 61.125 55.000 0.00 0.00 0.00 5.24
1713 1895 0.391793 CTTCTTCTCCCCCTTCACGC 60.392 60.000 0.00 0.00 0.00 5.34
1714 1896 0.250513 CCTTCTTCTCCCCCTTCACG 59.749 60.000 0.00 0.00 0.00 4.35
1715 1897 1.279558 GTCCTTCTTCTCCCCCTTCAC 59.720 57.143 0.00 0.00 0.00 3.18
1716 1898 1.132527 TGTCCTTCTTCTCCCCCTTCA 60.133 52.381 0.00 0.00 0.00 3.02
1717 1899 1.657804 TGTCCTTCTTCTCCCCCTTC 58.342 55.000 0.00 0.00 0.00 3.46
1718 1900 2.133858 TTGTCCTTCTTCTCCCCCTT 57.866 50.000 0.00 0.00 0.00 3.95
1719 1901 1.918957 CATTGTCCTTCTTCTCCCCCT 59.081 52.381 0.00 0.00 0.00 4.79
1720 1902 1.916181 TCATTGTCCTTCTTCTCCCCC 59.084 52.381 0.00 0.00 0.00 5.40
1721 1903 2.678190 CGTCATTGTCCTTCTTCTCCCC 60.678 54.545 0.00 0.00 0.00 4.81
1722 1904 2.622436 CGTCATTGTCCTTCTTCTCCC 58.378 52.381 0.00 0.00 0.00 4.30
1723 1905 2.622436 CCGTCATTGTCCTTCTTCTCC 58.378 52.381 0.00 0.00 0.00 3.71
1724 1906 2.003301 GCCGTCATTGTCCTTCTTCTC 58.997 52.381 0.00 0.00 0.00 2.87
1725 1907 1.673033 CGCCGTCATTGTCCTTCTTCT 60.673 52.381 0.00 0.00 0.00 2.85
1726 1908 0.721718 CGCCGTCATTGTCCTTCTTC 59.278 55.000 0.00 0.00 0.00 2.87
1727 1909 0.034896 ACGCCGTCATTGTCCTTCTT 59.965 50.000 0.00 0.00 0.00 2.52
1728 1910 0.389948 GACGCCGTCATTGTCCTTCT 60.390 55.000 13.23 0.00 32.09 2.85
1729 1911 1.683790 CGACGCCGTCATTGTCCTTC 61.684 60.000 18.40 0.00 32.09 3.46
1730 1912 1.736645 CGACGCCGTCATTGTCCTT 60.737 57.895 18.40 0.00 32.09 3.36
1731 1913 2.126071 CGACGCCGTCATTGTCCT 60.126 61.111 18.40 0.00 32.09 3.85
1732 1914 2.126228 TCGACGCCGTCATTGTCC 60.126 61.111 18.40 0.00 37.05 4.02
1733 1915 1.007336 AAGTCGACGCCGTCATTGTC 61.007 55.000 18.40 2.40 37.05 3.18
1734 1916 0.599204 AAAGTCGACGCCGTCATTGT 60.599 50.000 18.40 0.00 37.05 2.71
1735 1917 0.179250 CAAAGTCGACGCCGTCATTG 60.179 55.000 18.40 11.93 37.05 2.82
1736 1918 1.289109 CCAAAGTCGACGCCGTCATT 61.289 55.000 18.40 5.81 37.05 2.57
1737 1919 1.736645 CCAAAGTCGACGCCGTCAT 60.737 57.895 18.40 0.00 37.05 3.06
1738 1920 2.355363 CCAAAGTCGACGCCGTCA 60.355 61.111 18.40 1.54 37.05 4.35
1739 1921 3.774702 GCCAAAGTCGACGCCGTC 61.775 66.667 10.46 7.29 37.05 4.79
1742 1924 4.072088 CACGCCAAAGTCGACGCC 62.072 66.667 10.46 0.00 0.00 5.68
1743 1925 2.743871 GAACACGCCAAAGTCGACGC 62.744 60.000 10.46 6.50 0.00 5.19
1744 1926 1.200839 GAACACGCCAAAGTCGACG 59.799 57.895 10.46 0.00 0.00 5.12
1745 1927 0.865769 ATGAACACGCCAAAGTCGAC 59.134 50.000 7.70 7.70 0.00 4.20
1746 1928 1.144969 GATGAACACGCCAAAGTCGA 58.855 50.000 0.00 0.00 0.00 4.20
1747 1929 0.179250 CGATGAACACGCCAAAGTCG 60.179 55.000 0.00 0.00 0.00 4.18
1748 1930 1.126846 CTCGATGAACACGCCAAAGTC 59.873 52.381 0.00 0.00 0.00 3.01
1749 1931 1.148310 CTCGATGAACACGCCAAAGT 58.852 50.000 0.00 0.00 0.00 2.66
1750 1932 1.148310 ACTCGATGAACACGCCAAAG 58.852 50.000 0.00 0.00 0.00 2.77
1751 1933 1.529438 GAACTCGATGAACACGCCAAA 59.471 47.619 0.00 0.00 0.00 3.28
1752 1934 1.144969 GAACTCGATGAACACGCCAA 58.855 50.000 0.00 0.00 0.00 4.52
1753 1935 0.317160 AGAACTCGATGAACACGCCA 59.683 50.000 0.00 0.00 0.00 5.69
1754 1936 1.390463 GAAGAACTCGATGAACACGCC 59.610 52.381 0.00 0.00 0.00 5.68
1755 1937 2.058798 TGAAGAACTCGATGAACACGC 58.941 47.619 0.00 0.00 0.00 5.34
1756 1938 2.091277 GCTGAAGAACTCGATGAACACG 59.909 50.000 0.00 0.00 0.00 4.49
1757 1939 2.413453 GGCTGAAGAACTCGATGAACAC 59.587 50.000 0.00 0.00 0.00 3.32
1758 1940 2.300152 AGGCTGAAGAACTCGATGAACA 59.700 45.455 0.00 0.00 0.00 3.18
1759 1941 2.670414 CAGGCTGAAGAACTCGATGAAC 59.330 50.000 9.42 0.00 0.00 3.18
1760 1942 2.300152 ACAGGCTGAAGAACTCGATGAA 59.700 45.455 23.66 0.00 0.00 2.57
1761 1943 1.895798 ACAGGCTGAAGAACTCGATGA 59.104 47.619 23.66 0.00 0.00 2.92
1762 1944 2.376808 ACAGGCTGAAGAACTCGATG 57.623 50.000 23.66 0.00 0.00 3.84
1763 1945 2.428890 CCTACAGGCTGAAGAACTCGAT 59.571 50.000 23.66 0.00 0.00 3.59
1764 1946 1.819288 CCTACAGGCTGAAGAACTCGA 59.181 52.381 23.66 0.00 0.00 4.04
1765 1947 2.285827 CCTACAGGCTGAAGAACTCG 57.714 55.000 23.66 0.00 0.00 4.18
1783 1965 4.337060 AAGAAAAACGGCCGCGCC 62.337 61.111 28.58 10.38 46.75 6.53
1784 1966 2.726850 AAGAAGAAAAACGGCCGCGC 62.727 55.000 28.58 10.26 0.00 6.86
1785 1967 0.724785 GAAGAAGAAAAACGGCCGCG 60.725 55.000 28.58 1.99 0.00 6.46
1786 1968 0.591659 AGAAGAAGAAAAACGGCCGC 59.408 50.000 28.58 8.62 0.00 6.53
1787 1969 3.349488 AAAGAAGAAGAAAAACGGCCG 57.651 42.857 26.86 26.86 0.00 6.13
1788 1970 6.270815 ACTAAAAAGAAGAAGAAAAACGGCC 58.729 36.000 0.00 0.00 0.00 6.13
1789 1971 8.340443 TCTACTAAAAAGAAGAAGAAAAACGGC 58.660 33.333 0.00 0.00 0.00 5.68
1790 1972 9.647679 GTCTACTAAAAAGAAGAAGAAAAACGG 57.352 33.333 0.00 0.00 0.00 4.44
1841 2023 2.616842 ACTTAGGCGGTTCACAGTTTTG 59.383 45.455 0.00 0.00 0.00 2.44
1861 2044 4.409570 ACACGATATACATTCGGCGATAC 58.590 43.478 11.76 0.00 40.83 2.24
1877 2060 4.007659 AGGCTAATTTCGGAAAACACGAT 58.992 39.130 7.33 0.00 40.38 3.73
1914 2098 8.347771 GTCTCCAAACGGTCTTTTATAAGTTTT 58.652 33.333 0.00 0.00 32.98 2.43
1915 2099 7.307573 CGTCTCCAAACGGTCTTTTATAAGTTT 60.308 37.037 0.00 0.00 38.96 2.66
1916 2100 6.146673 CGTCTCCAAACGGTCTTTTATAAGTT 59.853 38.462 0.00 0.00 38.96 2.66
1917 2101 5.636543 CGTCTCCAAACGGTCTTTTATAAGT 59.363 40.000 0.00 0.00 38.96 2.24
1918 2102 5.865552 TCGTCTCCAAACGGTCTTTTATAAG 59.134 40.000 0.00 0.00 42.80 1.73
1921 2105 3.992427 GTCGTCTCCAAACGGTCTTTTAT 59.008 43.478 0.00 0.00 42.80 1.40
1933 2117 1.155390 ACCCTCAGGTCGTCTCCAA 59.845 57.895 0.00 0.00 46.45 3.53
1937 2121 2.997897 GCCACCCTCAGGTCGTCT 60.998 66.667 0.00 0.00 46.45 4.18
1939 2123 4.988716 TCGCCACCCTCAGGTCGT 62.989 66.667 0.00 0.00 46.45 4.34
1947 2131 3.322466 CTTCCCAGTCGCCACCCT 61.322 66.667 0.00 0.00 0.00 4.34
1956 2140 1.265454 GGGGTGATCGACTTCCCAGT 61.265 60.000 18.23 0.00 41.51 4.00
1965 2149 3.860605 CGGCATGGGGGTGATCGA 61.861 66.667 0.00 0.00 0.00 3.59
1971 2155 1.817740 CGATATTTTCGGCATGGGGGT 60.818 52.381 0.00 0.00 44.28 4.95
2451 3414 3.961480 TGTCAATCGAGAGACCAATGT 57.039 42.857 15.02 0.00 46.97 2.71
2457 3424 4.299155 TGTTGTCTTGTCAATCGAGAGAC 58.701 43.478 11.83 11.83 46.97 3.36
2460 3427 4.448732 CACATGTTGTCTTGTCAATCGAGA 59.551 41.667 0.00 0.00 34.47 4.04
2464 3432 5.422666 TGTCACATGTTGTCTTGTCAATC 57.577 39.130 0.00 0.00 31.09 2.67
2471 3447 3.879295 CACTTCCTGTCACATGTTGTCTT 59.121 43.478 0.00 0.00 0.00 3.01
2485 3461 1.817357 TGCATGAGCTTCACTTCCTG 58.183 50.000 0.00 0.00 42.74 3.86
2525 3501 9.499479 CTGCTAGGTCAGTTTTATATGATTGAT 57.501 33.333 0.00 0.00 0.00 2.57
2540 3516 7.278461 TCTTAATTAGTAGCTGCTAGGTCAG 57.722 40.000 10.13 7.52 37.15 3.51


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

AutoCloner maintained by Alex Coulton.