Multiple sequence alignment - TraesCS2A01G119200

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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 TraesCS2A01G119200 chr2A 100.000 4367 0 0 1 4367 69321392 69325758 0.000000e+00 8065
1 TraesCS2A01G119200 chr2A 92.000 100 6 2 3592 3690 69324950 69325048 5.890000e-29 139
2 TraesCS2A01G119200 chr2A 92.000 100 6 2 3559 3657 69324983 69325081 5.890000e-29 139
3 TraesCS2A01G119200 chr2B 90.381 2339 136 45 721 3019 105905994 105908283 0.000000e+00 2990
4 TraesCS2A01G119200 chr2B 95.244 757 25 10 3613 4367 105908841 105909588 0.000000e+00 1188
5 TraesCS2A01G119200 chr2B 90.803 598 39 11 3030 3623 105908330 105908915 0.000000e+00 785
6 TraesCS2A01G119200 chr2B 84.114 491 34 21 235 691 105905331 105905811 6.710000e-118 435
7 TraesCS2A01G119200 chr2D 91.530 1523 77 25 815 2308 69501890 69503389 0.000000e+00 2050
8 TraesCS2A01G119200 chr2D 90.798 1228 82 20 2401 3623 69503385 69504586 0.000000e+00 1613
9 TraesCS2A01G119200 chr2D 94.422 753 27 7 3614 4363 69504509 69505249 0.000000e+00 1144
10 TraesCS2A01G119200 chr2D 80.682 352 31 21 56 371 69501168 69501518 5.640000e-59 239
11 TraesCS2A01G119200 chr5A 81.756 1321 135 40 561 1810 274972954 274974239 0.000000e+00 1007
12 TraesCS2A01G119200 chr5A 89.796 196 20 0 2400 2595 423175592 423175397 7.250000e-63 252
13 TraesCS2A01G119200 chr7B 80.775 1316 146 49 578 1822 257239135 257237856 0.000000e+00 929
14 TraesCS2A01G119200 chr4B 80.862 1322 125 45 561 1822 527926364 527925111 0.000000e+00 922
15 TraesCS2A01G119200 chr5B 89.286 196 21 0 2400 2595 377535832 377535637 3.370000e-61 246
16 TraesCS2A01G119200 chr5B 71.751 531 141 8 1589 2115 377536775 377536250 1.640000e-29 141
17 TraesCS2A01G119200 chr5B 79.793 193 38 1 2403 2595 694256822 694256631 5.890000e-29 139
18 TraesCS2A01G119200 chr5D 88.265 196 23 0 2400 2595 325086147 325085952 7.300000e-58 235
19 TraesCS2A01G119200 chr5D 72.505 531 137 8 1589 2115 325087082 325086557 3.490000e-36 163


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 TraesCS2A01G119200 chr2A 69321392 69325758 4366 False 2781.0 8065 94.666667 1 4367 3 chr2A.!!$F1 4366
1 TraesCS2A01G119200 chr2B 105905331 105909588 4257 False 1349.5 2990 90.135500 235 4367 4 chr2B.!!$F1 4132
2 TraesCS2A01G119200 chr2D 69501168 69505249 4081 False 1261.5 2050 89.358000 56 4363 4 chr2D.!!$F1 4307
3 TraesCS2A01G119200 chr5A 274972954 274974239 1285 False 1007.0 1007 81.756000 561 1810 1 chr5A.!!$F1 1249
4 TraesCS2A01G119200 chr7B 257237856 257239135 1279 True 929.0 929 80.775000 578 1822 1 chr7B.!!$R1 1244
5 TraesCS2A01G119200 chr4B 527925111 527926364 1253 True 922.0 922 80.862000 561 1822 1 chr4B.!!$R1 1261

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
367 411 0.235144 GCATGATCGTGATGCAGAGC 59.765 55.0 19.3 0.0 44.74 4.09 F
1036 1378 0.250295 TCCTCTTCTTGTTGCGGTGG 60.250 55.0 0.0 0.0 0.00 4.61 F
2332 2718 0.041833 TTCTCCCTCCTCTGGTCTGG 59.958 60.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 2699 0.041833 CCAGACCAGAGGAGGGAGAA 59.958 60.0 0.00 0.00 0.0 2.87 R
2395 2781 0.035725 CTGAACTCCTCCTGCATGCA 60.036 55.0 21.29 21.29 0.0 3.96 R
4123 4657 1.119574 ACAAGACCACCGTGCCTACT 61.120 55.0 0.00 0.00 0.0 2.57 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
17 18 2.809601 CGTCCTGGGAAGCGAACG 60.810 66.667 0.00 0.00 0.00 3.95
18 19 2.434359 GTCCTGGGAAGCGAACGG 60.434 66.667 0.00 0.00 0.00 4.44
19 20 4.388499 TCCTGGGAAGCGAACGGC 62.388 66.667 0.00 0.00 44.05 5.68
28 29 3.619054 GCGAACGGCTAGAGATGC 58.381 61.111 0.00 0.00 39.11 3.91
29 30 1.066587 GCGAACGGCTAGAGATGCT 59.933 57.895 0.00 0.00 39.11 3.79
30 31 0.937231 GCGAACGGCTAGAGATGCTC 60.937 60.000 0.00 0.00 39.11 4.26
31 32 0.665835 CGAACGGCTAGAGATGCTCT 59.334 55.000 0.00 2.22 43.83 4.09
32 33 1.066303 CGAACGGCTAGAGATGCTCTT 59.934 52.381 1.88 0.00 41.50 2.85
33 34 2.290916 CGAACGGCTAGAGATGCTCTTA 59.709 50.000 1.88 0.00 41.50 2.10
34 35 3.634283 GAACGGCTAGAGATGCTCTTAC 58.366 50.000 1.88 0.00 41.50 2.34
35 36 2.656002 ACGGCTAGAGATGCTCTTACA 58.344 47.619 1.88 0.00 41.50 2.41
36 37 3.226777 ACGGCTAGAGATGCTCTTACAT 58.773 45.455 1.88 0.00 41.50 2.29
37 38 3.005261 ACGGCTAGAGATGCTCTTACATG 59.995 47.826 1.88 0.00 41.50 3.21
38 39 3.005261 CGGCTAGAGATGCTCTTACATGT 59.995 47.826 2.69 2.69 41.50 3.21
39 40 4.305769 GGCTAGAGATGCTCTTACATGTG 58.694 47.826 9.11 0.00 41.50 3.21
40 41 4.202202 GGCTAGAGATGCTCTTACATGTGT 60.202 45.833 9.11 0.00 41.50 3.72
41 42 4.744137 GCTAGAGATGCTCTTACATGTGTG 59.256 45.833 9.11 0.77 41.50 3.82
42 43 5.451103 GCTAGAGATGCTCTTACATGTGTGA 60.451 44.000 9.11 5.55 41.50 3.58
43 44 5.411831 AGAGATGCTCTTACATGTGTGAA 57.588 39.130 9.11 0.00 37.60 3.18
44 45 5.798132 AGAGATGCTCTTACATGTGTGAAA 58.202 37.500 9.11 0.00 37.60 2.69
45 46 6.233434 AGAGATGCTCTTACATGTGTGAAAA 58.767 36.000 9.11 0.00 37.60 2.29
46 47 6.883217 AGAGATGCTCTTACATGTGTGAAAAT 59.117 34.615 9.11 3.19 37.60 1.82
47 48 7.392673 AGAGATGCTCTTACATGTGTGAAAATT 59.607 33.333 9.11 0.00 37.60 1.82
48 49 7.533426 AGATGCTCTTACATGTGTGAAAATTC 58.467 34.615 9.11 0.00 0.00 2.17
49 50 6.631971 TGCTCTTACATGTGTGAAAATTCA 57.368 33.333 9.11 0.00 34.20 2.57
50 51 7.036996 TGCTCTTACATGTGTGAAAATTCAA 57.963 32.000 9.11 0.00 39.21 2.69
51 52 7.487484 TGCTCTTACATGTGTGAAAATTCAAA 58.513 30.769 9.11 0.00 39.21 2.69
52 53 7.648908 TGCTCTTACATGTGTGAAAATTCAAAG 59.351 33.333 9.11 0.00 39.21 2.77
53 54 7.649306 GCTCTTACATGTGTGAAAATTCAAAGT 59.351 33.333 9.11 0.00 39.21 2.66
54 55 9.173939 CTCTTACATGTGTGAAAATTCAAAGTC 57.826 33.333 9.11 0.00 39.21 3.01
55 56 8.681806 TCTTACATGTGTGAAAATTCAAAGTCA 58.318 29.630 9.11 0.00 39.21 3.41
56 57 9.299963 CTTACATGTGTGAAAATTCAAAGTCAA 57.700 29.630 9.11 0.00 39.21 3.18
57 58 7.760131 ACATGTGTGAAAATTCAAAGTCAAG 57.240 32.000 0.00 0.00 39.21 3.02
58 59 7.546358 ACATGTGTGAAAATTCAAAGTCAAGA 58.454 30.769 0.00 0.00 39.21 3.02
59 60 8.034215 ACATGTGTGAAAATTCAAAGTCAAGAA 58.966 29.630 0.00 0.00 39.21 2.52
60 61 8.871862 CATGTGTGAAAATTCAAAGTCAAGAAA 58.128 29.630 0.00 0.00 39.21 2.52
61 62 8.824159 TGTGTGAAAATTCAAAGTCAAGAAAA 57.176 26.923 0.00 0.00 39.21 2.29
97 101 1.004440 ACTCGCCTTCCTGTCTTGC 60.004 57.895 0.00 0.00 0.00 4.01
114 118 2.722731 GCCGCGAACGAAACGATCA 61.723 57.895 8.23 0.00 43.93 2.92
146 150 4.962836 CCATCGGCCAGGGCATCC 62.963 72.222 14.59 0.00 44.11 3.51
180 184 1.741770 GGCTGACGGCTCATTCGTT 60.742 57.895 6.16 0.00 41.22 3.85
187 191 1.654023 CGGCTCATTCGTTTTCCCCC 61.654 60.000 0.00 0.00 0.00 5.40
197 205 0.251209 GTTTTCCCCCTCGCCTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
199 207 0.840722 TTTCCCCCTCGCCTTCTTCT 60.841 55.000 0.00 0.00 0.00 2.85
201 209 1.222113 CCCCCTCGCCTTCTTCTTC 59.778 63.158 0.00 0.00 0.00 2.87
204 212 0.615850 CCCTCGCCTTCTTCTTCCTT 59.384 55.000 0.00 0.00 0.00 3.36
207 215 0.389948 TCGCCTTCTTCTTCCTTCGC 60.390 55.000 0.00 0.00 0.00 4.70
234 242 2.415010 CCGCCCACTCTCATCTCG 59.585 66.667 0.00 0.00 0.00 4.04
235 243 2.121538 CCGCCCACTCTCATCTCGA 61.122 63.158 0.00 0.00 0.00 4.04
236 244 1.064946 CGCCCACTCTCATCTCGAC 59.935 63.158 0.00 0.00 0.00 4.20
238 246 1.730487 CCCACTCTCATCTCGACGG 59.270 63.158 0.00 0.00 0.00 4.79
239 247 1.032657 CCCACTCTCATCTCGACGGT 61.033 60.000 0.00 0.00 0.00 4.83
240 248 0.811915 CCACTCTCATCTCGACGGTT 59.188 55.000 0.00 0.00 0.00 4.44
241 249 1.202200 CCACTCTCATCTCGACGGTTC 60.202 57.143 0.00 0.00 0.00 3.62
345 389 3.205784 ACTGCTCTGTTTCTTGCTTCT 57.794 42.857 0.00 0.00 0.00 2.85
367 411 0.235144 GCATGATCGTGATGCAGAGC 59.765 55.000 19.30 0.00 44.74 4.09
368 412 1.578583 CATGATCGTGATGCAGAGCA 58.421 50.000 9.46 0.00 44.86 4.26
369 413 1.527311 CATGATCGTGATGCAGAGCAG 59.473 52.381 9.46 0.00 43.65 4.24
370 414 0.808847 TGATCGTGATGCAGAGCAGC 60.809 55.000 0.00 0.00 45.81 5.25
394 438 0.315382 GAGCCATGAATCGCGAAACG 60.315 55.000 15.24 0.00 45.62 3.60
442 486 0.881118 TTTCTGAGCCCGCAAATCAC 59.119 50.000 0.00 0.00 0.00 3.06
444 488 3.386867 CTGAGCCCGCAAATCACGC 62.387 63.158 0.00 0.00 0.00 5.34
480 537 4.436998 GACTGGTCGGACGGGCAG 62.437 72.222 10.21 10.21 0.00 4.85
521 578 8.147704 GGAGAAGAAGAAGAAGAAGAAGAAGAA 58.852 37.037 0.00 0.00 0.00 2.52
522 579 9.196552 GAGAAGAAGAAGAAGAAGAAGAAGAAG 57.803 37.037 0.00 0.00 0.00 2.85
523 580 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
524 581 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
525 582 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
526 583 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
527 584 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
528 585 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
534 591 5.760484 AGAAGAAGAAGAAGAAGCTGGAT 57.240 39.130 0.00 0.00 0.00 3.41
553 610 1.018840 TCTGGGAGAAGGGATCAGGA 58.981 55.000 0.00 0.00 0.00 3.86
565 649 1.098050 GATCAGGAGCACCGCAAAAT 58.902 50.000 0.00 0.00 41.83 1.82
661 765 6.831769 TCAAGCAAGATTTACATCTTTCGAC 58.168 36.000 1.22 0.00 46.07 4.20
680 784 0.462759 CGCATCAGTTCCTTCCCCTC 60.463 60.000 0.00 0.00 0.00 4.30
708 812 3.496130 AGTTGATTCGTTTGCTCTGTGAG 59.504 43.478 0.00 0.00 0.00 3.51
732 836 1.920051 CATGCGACGGAGATGAACG 59.080 57.895 0.00 0.00 0.00 3.95
737 1006 4.861883 ACGGAGATGAACGTCACG 57.138 55.556 0.00 0.00 39.40 4.35
864 1179 2.854185 GCAAATGCAGCTCCGTTTAATC 59.146 45.455 0.00 0.00 41.59 1.75
876 1191 6.073222 AGCTCCGTTTAATCACAAGTTTACAG 60.073 38.462 0.00 0.00 0.00 2.74
973 1305 5.006386 ACACTCCCAAAATCATTCAGAGTC 58.994 41.667 0.00 0.00 30.99 3.36
974 1306 5.005740 CACTCCCAAAATCATTCAGAGTCA 58.994 41.667 0.00 0.00 30.99 3.41
975 1307 5.651139 CACTCCCAAAATCATTCAGAGTCAT 59.349 40.000 0.00 0.00 30.99 3.06
976 1308 5.884792 ACTCCCAAAATCATTCAGAGTCATC 59.115 40.000 0.00 0.00 0.00 2.92
977 1309 5.195940 TCCCAAAATCATTCAGAGTCATCC 58.804 41.667 0.00 0.00 0.00 3.51
978 1310 4.951715 CCCAAAATCATTCAGAGTCATCCA 59.048 41.667 0.00 0.00 0.00 3.41
989 1326 2.114616 GAGTCATCCATCCAGACTGGT 58.885 52.381 21.06 6.10 42.29 4.00
990 1327 3.052566 AGAGTCATCCATCCAGACTGGTA 60.053 47.826 21.06 8.59 42.29 3.25
991 1328 3.034635 AGTCATCCATCCAGACTGGTAC 58.965 50.000 21.06 9.01 40.83 3.34
997 1339 3.118775 TCCATCCAGACTGGTACATTTCG 60.119 47.826 21.06 2.29 39.03 3.46
1013 1355 3.667497 TTTCGAGATGAGAAGCACAGT 57.333 42.857 0.00 0.00 0.00 3.55
1019 1361 2.170187 AGATGAGAAGCACAGTCCATCC 59.830 50.000 0.00 0.00 33.00 3.51
1032 1374 1.734465 GTCCATCCTCTTCTTGTTGCG 59.266 52.381 0.00 0.00 0.00 4.85
1033 1375 1.089920 CCATCCTCTTCTTGTTGCGG 58.910 55.000 0.00 0.00 0.00 5.69
1034 1376 1.611673 CCATCCTCTTCTTGTTGCGGT 60.612 52.381 0.00 0.00 0.00 5.68
1035 1377 1.466167 CATCCTCTTCTTGTTGCGGTG 59.534 52.381 0.00 0.00 0.00 4.94
1036 1378 0.250295 TCCTCTTCTTGTTGCGGTGG 60.250 55.000 0.00 0.00 0.00 4.61
1037 1379 1.576421 CTCTTCTTGTTGCGGTGGC 59.424 57.895 0.00 0.00 40.52 5.01
1038 1380 2.175184 CTCTTCTTGTTGCGGTGGCG 62.175 60.000 0.00 0.00 44.10 5.69
1108 1450 1.414866 GGGCATCTTCTCCTCCTCCC 61.415 65.000 0.00 0.00 0.00 4.30
1120 1468 1.614226 TCCTCCCCTAAACCCACGG 60.614 63.158 0.00 0.00 0.00 4.94
1344 1692 2.811317 GACAAGGAGCGCCAGTCG 60.811 66.667 9.88 0.00 42.12 4.18
1529 1879 1.473965 CCAGCTCCAGTACGCAATCAT 60.474 52.381 0.00 0.00 0.00 2.45
1531 1881 3.555795 CCAGCTCCAGTACGCAATCATAT 60.556 47.826 0.00 0.00 0.00 1.78
1534 1884 3.554960 GCTCCAGTACGCAATCATATCCA 60.555 47.826 0.00 0.00 0.00 3.41
1554 1904 1.043816 ATCCGCCATGATCGTCTTCT 58.956 50.000 0.00 0.00 0.00 2.85
1557 1907 1.212616 CGCCATGATCGTCTTCTTCC 58.787 55.000 0.00 0.00 0.00 3.46
1560 1910 2.102252 GCCATGATCGTCTTCTTCCTCT 59.898 50.000 0.00 0.00 0.00 3.69
1563 1913 4.099266 CCATGATCGTCTTCTTCCTCTTCT 59.901 45.833 0.00 0.00 0.00 2.85
1570 1938 5.478679 TCGTCTTCTTCCTCTTCTTCTTGAT 59.521 40.000 0.00 0.00 0.00 2.57
1573 1941 7.158021 GTCTTCTTCCTCTTCTTCTTGATTGA 58.842 38.462 0.00 0.00 0.00 2.57
1581 1954 7.720957 TCCTCTTCTTCTTGATTGATTTGTGAA 59.279 33.333 0.00 0.00 0.00 3.18
1583 1956 9.557338 CTCTTCTTCTTGATTGATTTGTGAATC 57.443 33.333 0.00 0.00 41.67 2.52
1587 1960 5.393124 TCTTGATTGATTTGTGAATCGTGC 58.607 37.500 0.00 0.00 43.75 5.34
1724 2110 1.153667 GGAGTCGAGCAAGCTCCAG 60.154 63.158 15.81 3.78 45.93 3.86
2157 2543 2.604686 AGCTCCACGGCTTCCTGA 60.605 61.111 0.00 0.00 39.86 3.86
2158 2544 2.125350 GCTCCACGGCTTCCTGAG 60.125 66.667 0.00 0.00 0.00 3.35
2278 2664 2.202797 CCACGACCTCCTCATGCG 60.203 66.667 0.00 0.00 0.00 4.73
2303 2689 3.133946 GAGTCGATCCTCCAGGCC 58.866 66.667 0.00 0.00 34.44 5.19
2304 2690 2.444895 AGTCGATCCTCCAGGCCC 60.445 66.667 0.00 0.00 34.44 5.80
2305 2691 2.764128 GTCGATCCTCCAGGCCCA 60.764 66.667 0.00 0.00 34.44 5.36
2306 2692 2.444706 TCGATCCTCCAGGCCCAG 60.445 66.667 0.00 0.00 34.44 4.45
2307 2693 3.554342 CGATCCTCCAGGCCCAGG 61.554 72.222 0.00 1.14 34.44 4.45
2308 2694 2.367512 GATCCTCCAGGCCCAGGT 60.368 66.667 11.36 0.74 34.44 4.00
2309 2695 2.367512 ATCCTCCAGGCCCAGGTC 60.368 66.667 11.36 0.00 34.44 3.85
2310 2696 2.905676 GATCCTCCAGGCCCAGGTCT 62.906 65.000 11.36 1.98 34.44 3.85
2311 2697 2.498820 ATCCTCCAGGCCCAGGTCTT 62.499 60.000 11.36 0.00 34.44 3.01
2312 2698 2.674220 CCTCCAGGCCCAGGTCTTC 61.674 68.421 11.36 0.00 0.00 2.87
2313 2699 1.614824 CTCCAGGCCCAGGTCTTCT 60.615 63.158 11.36 0.00 0.00 2.85
2314 2700 1.151810 TCCAGGCCCAGGTCTTCTT 60.152 57.895 11.36 0.00 0.00 2.52
2315 2701 1.201429 TCCAGGCCCAGGTCTTCTTC 61.201 60.000 11.36 0.00 0.00 2.87
2316 2702 1.204113 CCAGGCCCAGGTCTTCTTCT 61.204 60.000 0.00 0.00 0.00 2.85
2317 2703 0.251634 CAGGCCCAGGTCTTCTTCTC 59.748 60.000 0.00 0.00 0.00 2.87
2318 2704 0.912006 AGGCCCAGGTCTTCTTCTCC 60.912 60.000 0.00 0.00 0.00 3.71
2319 2705 1.604915 GCCCAGGTCTTCTTCTCCC 59.395 63.158 0.00 0.00 0.00 4.30
2320 2706 0.912006 GCCCAGGTCTTCTTCTCCCT 60.912 60.000 0.00 0.00 0.00 4.20
2321 2707 1.199615 CCCAGGTCTTCTTCTCCCTC 58.800 60.000 0.00 0.00 0.00 4.30
2322 2708 1.199615 CCAGGTCTTCTTCTCCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
2323 2709 1.273552 CCAGGTCTTCTTCTCCCTCCT 60.274 57.143 0.00 0.00 0.00 3.69
2324 2710 2.107366 CAGGTCTTCTTCTCCCTCCTC 58.893 57.143 0.00 0.00 0.00 3.71
2325 2711 2.007636 AGGTCTTCTTCTCCCTCCTCT 58.992 52.381 0.00 0.00 0.00 3.69
2326 2712 2.107366 GGTCTTCTTCTCCCTCCTCTG 58.893 57.143 0.00 0.00 0.00 3.35
2327 2713 2.107366 GTCTTCTTCTCCCTCCTCTGG 58.893 57.143 0.00 0.00 0.00 3.86
2328 2714 1.719378 TCTTCTTCTCCCTCCTCTGGT 59.281 52.381 0.00 0.00 0.00 4.00
2329 2715 2.107366 CTTCTTCTCCCTCCTCTGGTC 58.893 57.143 0.00 0.00 0.00 4.02
2330 2716 1.388174 TCTTCTCCCTCCTCTGGTCT 58.612 55.000 0.00 0.00 0.00 3.85
2331 2717 1.006519 TCTTCTCCCTCCTCTGGTCTG 59.993 57.143 0.00 0.00 0.00 3.51
2332 2718 0.041833 TTCTCCCTCCTCTGGTCTGG 59.958 60.000 0.00 0.00 0.00 3.86
2333 2719 1.149782 TCTCCCTCCTCTGGTCTGGT 61.150 60.000 0.00 0.00 0.00 4.00
2334 2720 0.631753 CTCCCTCCTCTGGTCTGGTA 59.368 60.000 0.00 0.00 0.00 3.25
2335 2721 0.335361 TCCCTCCTCTGGTCTGGTAC 59.665 60.000 0.00 0.00 0.00 3.34
2336 2722 0.336737 CCCTCCTCTGGTCTGGTACT 59.663 60.000 0.00 0.00 0.00 2.73
2337 2723 1.686741 CCCTCCTCTGGTCTGGTACTC 60.687 61.905 0.00 0.00 0.00 2.59
2338 2724 1.286553 CCTCCTCTGGTCTGGTACTCT 59.713 57.143 0.00 0.00 0.00 3.24
2339 2725 2.374184 CTCCTCTGGTCTGGTACTCTG 58.626 57.143 0.00 0.00 0.00 3.35
2340 2726 1.006043 TCCTCTGGTCTGGTACTCTGG 59.994 57.143 0.00 0.00 0.00 3.86
2341 2727 1.272760 CCTCTGGTCTGGTACTCTGGT 60.273 57.143 0.00 0.00 0.00 4.00
2342 2728 2.530701 CTCTGGTCTGGTACTCTGGTT 58.469 52.381 0.00 0.00 0.00 3.67
2343 2729 2.900546 CTCTGGTCTGGTACTCTGGTTT 59.099 50.000 0.00 0.00 0.00 3.27
2344 2730 2.632996 TCTGGTCTGGTACTCTGGTTTG 59.367 50.000 0.00 0.00 0.00 2.93
2345 2731 1.071699 TGGTCTGGTACTCTGGTTTGC 59.928 52.381 0.00 0.00 0.00 3.68
2346 2732 1.071699 GGTCTGGTACTCTGGTTTGCA 59.928 52.381 0.00 0.00 0.00 4.08
2347 2733 2.486548 GGTCTGGTACTCTGGTTTGCAA 60.487 50.000 0.00 0.00 0.00 4.08
2348 2734 2.808543 GTCTGGTACTCTGGTTTGCAAG 59.191 50.000 0.00 0.00 0.00 4.01
2349 2735 2.703536 TCTGGTACTCTGGTTTGCAAGA 59.296 45.455 0.00 0.00 0.00 3.02
2350 2736 2.808543 CTGGTACTCTGGTTTGCAAGAC 59.191 50.000 0.00 1.22 0.00 3.01
2351 2737 1.798813 GGTACTCTGGTTTGCAAGACG 59.201 52.381 0.00 0.00 0.00 4.18
2352 2738 2.480845 GTACTCTGGTTTGCAAGACGT 58.519 47.619 0.00 0.00 0.00 4.34
2353 2739 1.299541 ACTCTGGTTTGCAAGACGTG 58.700 50.000 0.00 0.00 0.00 4.49
2362 2748 2.551270 CAAGACGTGCTGAACCGC 59.449 61.111 0.00 0.00 0.00 5.68
2363 2749 2.665185 AAGACGTGCTGAACCGCC 60.665 61.111 0.00 0.00 0.00 6.13
2364 2750 3.454587 AAGACGTGCTGAACCGCCA 62.455 57.895 0.00 0.00 0.00 5.69
2365 2751 2.731691 AAGACGTGCTGAACCGCCAT 62.732 55.000 0.00 0.00 0.00 4.40
2366 2752 2.281484 ACGTGCTGAACCGCCATT 60.281 55.556 0.00 0.00 0.00 3.16
2367 2753 2.176546 CGTGCTGAACCGCCATTG 59.823 61.111 0.00 0.00 0.00 2.82
2368 2754 2.324330 CGTGCTGAACCGCCATTGA 61.324 57.895 0.00 0.00 0.00 2.57
2369 2755 1.647545 CGTGCTGAACCGCCATTGAT 61.648 55.000 0.00 0.00 0.00 2.57
2370 2756 0.099436 GTGCTGAACCGCCATTGATC 59.901 55.000 0.00 0.00 0.00 2.92
2371 2757 1.031571 TGCTGAACCGCCATTGATCC 61.032 55.000 0.00 0.00 0.00 3.36
2372 2758 2.016961 CTGAACCGCCATTGATCCG 58.983 57.895 0.00 0.00 0.00 4.18
2373 2759 1.439353 CTGAACCGCCATTGATCCGG 61.439 60.000 0.00 0.00 46.97 5.14
2374 2760 1.153249 GAACCGCCATTGATCCGGA 60.153 57.895 6.61 6.61 44.55 5.14
2375 2761 1.153168 AACCGCCATTGATCCGGAG 60.153 57.895 11.34 0.00 44.55 4.63
2376 2762 2.974698 CCGCCATTGATCCGGAGC 60.975 66.667 14.17 14.17 44.55 4.70
2377 2763 2.109799 CGCCATTGATCCGGAGCT 59.890 61.111 22.18 0.00 0.00 4.09
2378 2764 1.958205 CGCCATTGATCCGGAGCTC 60.958 63.158 22.18 9.88 0.00 4.09
2379 2765 1.958205 GCCATTGATCCGGAGCTCG 60.958 63.158 22.18 8.87 38.88 5.03
2380 2766 1.742146 CCATTGATCCGGAGCTCGA 59.258 57.895 22.18 9.47 42.43 4.04
2381 2767 0.319728 CCATTGATCCGGAGCTCGAT 59.680 55.000 22.18 11.53 42.43 3.59
2382 2768 1.671261 CCATTGATCCGGAGCTCGATC 60.671 57.143 22.18 19.24 42.43 3.69
2383 2769 0.242286 ATTGATCCGGAGCTCGATCG 59.758 55.000 22.18 9.36 42.43 3.69
2384 2770 1.796190 TTGATCCGGAGCTCGATCGG 61.796 60.000 22.18 20.13 44.59 4.18
2385 2771 2.203365 ATCCGGAGCTCGATCGGT 60.203 61.111 23.59 12.28 43.75 4.69
2386 2772 2.190101 GATCCGGAGCTCGATCGGTC 62.190 65.000 23.59 17.62 43.75 4.79
2396 2782 2.849007 GATCGGTCGATGCGCATG 59.151 61.111 30.76 19.56 34.60 4.06
2397 2783 3.287121 GATCGGTCGATGCGCATGC 62.287 63.158 30.76 17.81 43.20 4.06
2463 2941 0.243907 TGGACAAGCTCTACGTGCTC 59.756 55.000 0.00 0.00 40.22 4.26
2478 2956 2.109126 GCTCCACAACGCCATCCTC 61.109 63.158 0.00 0.00 0.00 3.71
2487 2965 2.105128 GCCATCCTCGTGGAGTCG 59.895 66.667 12.42 3.21 46.91 4.18
2506 2984 1.717937 CGCTTCATCAAGGCCTTCG 59.282 57.895 17.29 10.76 0.00 3.79
2571 3049 0.962356 CCAAGCAGACCTTCGCCATT 60.962 55.000 0.00 0.00 0.00 3.16
2596 3074 1.203994 GCCAGCTCTACTTCGGTAACA 59.796 52.381 0.00 0.00 0.00 2.41
2599 3077 3.243336 CAGCTCTACTTCGGTAACACAC 58.757 50.000 0.00 0.00 0.00 3.82
2600 3078 2.889045 AGCTCTACTTCGGTAACACACA 59.111 45.455 0.00 0.00 0.00 3.72
2602 3080 3.858238 GCTCTACTTCGGTAACACACATC 59.142 47.826 0.00 0.00 0.00 3.06
2603 3081 4.380655 GCTCTACTTCGGTAACACACATCT 60.381 45.833 0.00 0.00 0.00 2.90
2604 3082 5.710984 CTCTACTTCGGTAACACACATCTT 58.289 41.667 0.00 0.00 0.00 2.40
2606 3084 4.602340 ACTTCGGTAACACACATCTTCT 57.398 40.909 0.00 0.00 0.00 2.85
2608 3086 2.683968 TCGGTAACACACATCTTCTGC 58.316 47.619 0.00 0.00 0.00 4.26
2609 3087 2.036604 TCGGTAACACACATCTTCTGCA 59.963 45.455 0.00 0.00 0.00 4.41
2610 3088 2.413112 CGGTAACACACATCTTCTGCAG 59.587 50.000 7.63 7.63 0.00 4.41
2632 3115 2.120232 CTCCGATCATCGTTTCCTTCG 58.880 52.381 6.25 0.00 38.40 3.79
2639 3122 1.594862 CATCGTTTCCTTCGCTCCATC 59.405 52.381 0.00 0.00 0.00 3.51
2641 3124 1.421410 CGTTTCCTTCGCTCCATCGG 61.421 60.000 0.00 0.00 0.00 4.18
2642 3125 0.108329 GTTTCCTTCGCTCCATCGGA 60.108 55.000 0.00 0.00 0.00 4.55
2656 3139 3.817084 TCCATCGGATCATTTCTTCATGC 59.183 43.478 0.00 0.00 0.00 4.06
2658 3141 2.905075 TCGGATCATTTCTTCATGCGT 58.095 42.857 0.00 0.00 33.54 5.24
2659 3142 3.270027 TCGGATCATTTCTTCATGCGTT 58.730 40.909 0.00 0.00 33.54 4.84
2660 3143 3.689161 TCGGATCATTTCTTCATGCGTTT 59.311 39.130 0.00 0.00 33.54 3.60
2661 3144 4.031028 CGGATCATTTCTTCATGCGTTTC 58.969 43.478 0.00 0.00 0.00 2.78
2662 3145 4.201851 CGGATCATTTCTTCATGCGTTTCT 60.202 41.667 0.00 0.00 0.00 2.52
2664 3147 5.514204 GGATCATTTCTTCATGCGTTTCTTG 59.486 40.000 0.00 0.00 0.00 3.02
2665 3148 4.797471 TCATTTCTTCATGCGTTTCTTGG 58.203 39.130 0.00 0.00 0.00 3.61
2666 3149 4.518590 TCATTTCTTCATGCGTTTCTTGGA 59.481 37.500 0.00 0.00 0.00 3.53
2668 3151 5.452078 TTTCTTCATGCGTTTCTTGGATT 57.548 34.783 0.00 0.00 0.00 3.01
2669 3152 5.452078 TTCTTCATGCGTTTCTTGGATTT 57.548 34.783 0.00 0.00 0.00 2.17
2670 3153 4.797471 TCTTCATGCGTTTCTTGGATTTG 58.203 39.130 0.00 0.00 0.00 2.32
2671 3154 4.518590 TCTTCATGCGTTTCTTGGATTTGA 59.481 37.500 0.00 0.00 0.00 2.69
2672 3155 4.159377 TCATGCGTTTCTTGGATTTGAC 57.841 40.909 0.00 0.00 0.00 3.18
2747 3237 4.813526 CGCCGACGACGACCTCAG 62.814 72.222 9.28 0.00 43.93 3.35
2875 3365 1.933853 CGTGGAATCCCGATCTTGAAC 59.066 52.381 0.00 0.00 34.29 3.18
2879 3369 0.810031 AATCCCGATCTTGAACCGCG 60.810 55.000 0.00 0.00 0.00 6.46
2880 3370 2.644555 ATCCCGATCTTGAACCGCGG 62.645 60.000 26.86 26.86 41.53 6.46
2881 3371 3.564027 CCGATCTTGAACCGCGGC 61.564 66.667 28.58 11.02 35.17 6.53
2882 3372 3.913573 CGATCTTGAACCGCGGCG 61.914 66.667 28.58 16.78 0.00 6.46
2883 3373 2.813908 GATCTTGAACCGCGGCGT 60.814 61.111 28.58 14.60 0.00 5.68
2885 3375 3.583276 ATCTTGAACCGCGGCGTCA 62.583 57.895 28.58 25.91 0.00 4.35
2886 3376 4.072088 CTTGAACCGCGGCGTCAC 62.072 66.667 28.58 12.70 0.00 3.67
2887 3377 4.893601 TTGAACCGCGGCGTCACA 62.894 61.111 28.58 15.30 0.00 3.58
2890 3380 3.902162 GAACCGCGGCGTCACAGTA 62.902 63.158 28.58 0.00 0.00 2.74
2891 3381 4.712425 ACCGCGGCGTCACAGTAC 62.712 66.667 28.58 0.00 0.00 2.73
3055 3582 2.727544 CCGCCAACTGGTGTTTGG 59.272 61.111 8.44 0.00 43.97 3.28
3064 3591 5.181748 CCAACTGGTGTTTGGATTTTGAAA 58.818 37.500 0.00 0.00 33.52 2.69
3076 3603 3.612423 GGATTTTGAAACGTAATGCTGGC 59.388 43.478 0.00 0.00 0.00 4.85
3077 3604 2.323939 TTTGAAACGTAATGCTGGCG 57.676 45.000 0.00 0.00 0.00 5.69
3096 3623 2.223525 GCGCCGAATCTGAACTACTAGT 60.224 50.000 0.00 0.00 0.00 2.57
3097 3624 3.003068 GCGCCGAATCTGAACTACTAGTA 59.997 47.826 1.89 1.89 0.00 1.82
3316 3843 0.436531 CGAAAACTCACTCTCAGCGC 59.563 55.000 0.00 0.00 0.00 5.92
3357 3884 2.469516 CCTTCGGGCACGCATTACC 61.470 63.158 1.67 0.00 40.69 2.85
3368 3895 1.003112 GCATTACCCCACGGTGACA 60.003 57.895 10.28 0.00 44.40 3.58
3407 3934 7.161773 ACATATATGTGCAGAAATATTGCCC 57.838 36.000 17.60 0.00 40.03 5.36
3418 3945 6.332630 CAGAAATATTGCCCGAAGTTGAAAT 58.667 36.000 0.00 0.00 0.00 2.17
3461 3989 2.807967 TGAAGAACTGAAGGACAATGCG 59.192 45.455 0.00 0.00 0.00 4.73
3531 4064 7.123547 ACTTGTGAAGTCATAAAGGGAAAACAA 59.876 33.333 9.96 0.00 37.02 2.83
3538 4071 7.564793 AGTCATAAAGGGAAAACAAAAAGCTT 58.435 30.769 0.00 0.00 0.00 3.74
3540 4073 6.765512 TCATAAAGGGAAAACAAAAAGCTTGG 59.234 34.615 0.00 0.00 0.00 3.61
3541 4074 4.835284 AAGGGAAAACAAAAAGCTTGGA 57.165 36.364 0.00 0.00 0.00 3.53
3546 4079 5.182190 GGGAAAACAAAAAGCTTGGACAAAA 59.818 36.000 0.00 0.00 0.00 2.44
3556 4089 6.899393 AAGCTTGGACAAAACATCAGATTA 57.101 33.333 0.00 0.00 0.00 1.75
3591 4124 8.996024 TCAATCTAACATGAAACATAACTCGA 57.004 30.769 0.00 0.00 0.00 4.04
3592 4125 9.087424 TCAATCTAACATGAAACATAACTCGAG 57.913 33.333 11.84 11.84 0.00 4.04
3593 4126 9.087424 CAATCTAACATGAAACATAACTCGAGA 57.913 33.333 21.68 0.00 0.00 4.04
3594 4127 9.653287 AATCTAACATGAAACATAACTCGAGAA 57.347 29.630 21.68 7.10 0.00 2.87
3595 4128 9.653287 ATCTAACATGAAACATAACTCGAGAAA 57.347 29.630 21.68 6.69 0.00 2.52
3596 4129 9.653287 TCTAACATGAAACATAACTCGAGAAAT 57.347 29.630 21.68 8.95 0.00 2.17
3790 4324 6.851222 ACATGACATATAGCTGCTTGTAAC 57.149 37.500 7.79 0.00 0.00 2.50
3841 4375 1.752683 TCGACTAACTGAGCTCCCTC 58.247 55.000 12.15 0.00 38.62 4.30
3842 4376 1.282447 TCGACTAACTGAGCTCCCTCT 59.718 52.381 12.15 0.00 38.93 3.69
4111 4645 3.721706 CCAGGAGGGTCCACCAGC 61.722 72.222 6.27 0.00 43.89 4.85
4134 4668 1.671742 CAGACCAAGTAGGCACGGT 59.328 57.895 0.00 0.00 43.14 4.83
4147 4681 1.280206 GCACGGTGGTCTTGTCGTAC 61.280 60.000 10.60 0.00 34.31 3.67
4165 4699 4.335315 TCGTACGGAAATACGGTACTGAAT 59.665 41.667 16.52 0.00 46.32 2.57
4313 4847 8.019094 GCGTTATTAGCCTTCTTTTCTGTAAAA 58.981 33.333 0.00 0.00 33.58 1.52
4338 4872 5.488341 GGTAAAGTTGAGTCCAGATTAGCA 58.512 41.667 0.00 0.00 0.00 3.49
4350 4884 2.850060 CAGATTAGCATTTGCAACAGCG 59.150 45.455 14.52 0.00 45.16 5.18
4363 4897 3.057548 CAGCGGACATGGCAAGCA 61.058 61.111 18.60 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.809601 CGTTCGCTTCCCAGGACG 60.810 66.667 0.00 0.00 0.00 4.79
1 2 2.434359 CCGTTCGCTTCCCAGGAC 60.434 66.667 0.00 0.00 0.00 3.85
2 3 4.388499 GCCGTTCGCTTCCCAGGA 62.388 66.667 0.00 0.00 0.00 3.86
11 12 0.937231 GAGCATCTCTAGCCGTTCGC 60.937 60.000 0.00 0.00 37.98 4.70
12 13 3.171705 GAGCATCTCTAGCCGTTCG 57.828 57.895 0.00 0.00 0.00 3.95
23 24 7.175467 TGAATTTTCACACATGTAAGAGCATCT 59.825 33.333 0.00 0.00 38.92 2.90
24 25 7.307694 TGAATTTTCACACATGTAAGAGCATC 58.692 34.615 0.00 0.00 31.01 3.91
25 26 7.218228 TGAATTTTCACACATGTAAGAGCAT 57.782 32.000 0.00 0.00 31.01 3.79
26 27 6.631971 TGAATTTTCACACATGTAAGAGCA 57.368 33.333 0.00 0.00 31.01 4.26
27 28 7.649306 ACTTTGAATTTTCACACATGTAAGAGC 59.351 33.333 0.00 0.00 36.83 4.09
28 29 9.173939 GACTTTGAATTTTCACACATGTAAGAG 57.826 33.333 0.00 0.00 36.83 2.85
29 30 8.681806 TGACTTTGAATTTTCACACATGTAAGA 58.318 29.630 0.00 0.00 36.83 2.10
30 31 8.854979 TGACTTTGAATTTTCACACATGTAAG 57.145 30.769 0.00 0.00 36.83 2.34
31 32 9.299963 CTTGACTTTGAATTTTCACACATGTAA 57.700 29.630 0.00 0.00 36.83 2.41
32 33 8.681806 TCTTGACTTTGAATTTTCACACATGTA 58.318 29.630 0.00 0.00 36.83 2.29
33 34 7.546358 TCTTGACTTTGAATTTTCACACATGT 58.454 30.769 0.00 0.00 36.83 3.21
34 35 7.990541 TCTTGACTTTGAATTTTCACACATG 57.009 32.000 0.00 0.00 36.83 3.21
35 36 9.434420 TTTTCTTGACTTTGAATTTTCACACAT 57.566 25.926 0.00 0.00 36.83 3.21
36 37 8.824159 TTTTCTTGACTTTGAATTTTCACACA 57.176 26.923 0.00 0.00 36.83 3.72
59 60 1.935199 TCGGTTCGAGCGTTTCTTTTT 59.065 42.857 6.40 0.00 40.41 1.94
60 61 1.259770 GTCGGTTCGAGCGTTTCTTTT 59.740 47.619 6.40 0.00 40.41 2.27
61 62 0.857287 GTCGGTTCGAGCGTTTCTTT 59.143 50.000 6.40 0.00 40.41 2.52
64 65 1.662845 CGAGTCGGTTCGAGCGTTTC 61.663 60.000 4.10 5.27 43.03 2.78
67 68 4.755614 GCGAGTCGGTTCGAGCGT 62.756 66.667 15.52 0.00 43.03 5.07
97 101 0.246757 CTTGATCGTTTCGTTCGCGG 60.247 55.000 6.13 0.00 41.70 6.46
146 150 1.969589 GCCCCGGGCCGTATTTATG 60.970 63.158 26.32 7.19 44.06 1.90
180 184 0.840722 AGAAGAAGGCGAGGGGGAAA 60.841 55.000 0.00 0.00 0.00 3.13
187 191 1.634702 CGAAGGAAGAAGAAGGCGAG 58.365 55.000 0.00 0.00 0.00 5.03
197 205 1.725557 CGGATCGGAGCGAAGGAAGA 61.726 60.000 0.00 0.00 39.99 2.87
199 207 2.805546 CGGATCGGAGCGAAGGAA 59.194 61.111 0.00 0.00 39.99 3.36
201 209 4.951963 GGCGGATCGGAGCGAAGG 62.952 72.222 4.16 0.00 39.99 3.46
220 228 1.032657 ACCGTCGAGATGAGAGTGGG 61.033 60.000 0.00 0.00 0.00 4.61
229 237 1.162698 TCGAACTGAACCGTCGAGAT 58.837 50.000 0.00 0.00 0.00 2.75
234 242 1.066114 CGAGCTCGAACTGAACCGTC 61.066 60.000 32.06 0.00 43.02 4.79
235 243 1.081376 CGAGCTCGAACTGAACCGT 60.081 57.895 32.06 0.00 43.02 4.83
236 244 1.209383 TCGAGCTCGAACTGAACCG 59.791 57.895 35.16 7.09 46.30 4.44
367 411 1.595466 GATTCATGGCTCCTCTGCTG 58.405 55.000 0.00 0.00 0.00 4.41
368 412 0.106335 CGATTCATGGCTCCTCTGCT 59.894 55.000 0.00 0.00 0.00 4.24
369 413 1.505477 GCGATTCATGGCTCCTCTGC 61.505 60.000 0.00 0.00 0.00 4.26
370 414 1.220169 CGCGATTCATGGCTCCTCTG 61.220 60.000 0.00 0.00 0.00 3.35
371 415 1.068753 CGCGATTCATGGCTCCTCT 59.931 57.895 0.00 0.00 0.00 3.69
465 522 4.135153 CTCTGCCCGTCCGACCAG 62.135 72.222 0.00 0.00 0.00 4.00
466 523 4.671590 TCTCTGCCCGTCCGACCA 62.672 66.667 0.00 0.00 0.00 4.02
469 526 2.035155 TTCTCTCTGCCCGTCCGA 59.965 61.111 0.00 0.00 0.00 4.55
477 534 2.817396 GGCGGTGCTTCTCTCTGC 60.817 66.667 0.00 0.00 39.26 4.26
478 535 2.507992 CGGCGGTGCTTCTCTCTG 60.508 66.667 0.00 0.00 0.00 3.35
479 536 3.764466 CCGGCGGTGCTTCTCTCT 61.764 66.667 19.97 0.00 0.00 3.10
480 537 3.708220 CTCCGGCGGTGCTTCTCTC 62.708 68.421 27.32 0.00 0.00 3.20
521 578 2.117865 CTCCCAGATCCAGCTTCTTCT 58.882 52.381 0.00 0.00 0.00 2.85
522 579 2.114616 TCTCCCAGATCCAGCTTCTTC 58.885 52.381 0.00 0.00 0.00 2.87
523 580 2.260639 TCTCCCAGATCCAGCTTCTT 57.739 50.000 0.00 0.00 0.00 2.52
524 581 2.117865 CTTCTCCCAGATCCAGCTTCT 58.882 52.381 0.00 0.00 0.00 2.85
525 582 1.140652 CCTTCTCCCAGATCCAGCTTC 59.859 57.143 0.00 0.00 0.00 3.86
526 583 1.211456 CCTTCTCCCAGATCCAGCTT 58.789 55.000 0.00 0.00 0.00 3.74
527 584 0.693767 CCCTTCTCCCAGATCCAGCT 60.694 60.000 0.00 0.00 0.00 4.24
528 585 0.692419 TCCCTTCTCCCAGATCCAGC 60.692 60.000 0.00 0.00 0.00 4.85
534 591 1.018840 TCCTGATCCCTTCTCCCAGA 58.981 55.000 0.00 0.00 0.00 3.86
553 610 2.036992 TGGAATTTCATTTTGCGGTGCT 59.963 40.909 0.00 0.00 0.00 4.40
565 649 7.057894 AGGTTATAATTAGCGGTGGAATTTCA 58.942 34.615 0.00 0.00 0.00 2.69
661 765 0.462759 GAGGGGAAGGAACTGATGCG 60.463 60.000 0.00 0.00 40.86 4.73
680 784 3.374745 AGCAAACGAATCAACTGCAAAG 58.625 40.909 0.00 0.00 35.44 2.77
708 812 1.193203 CATCTCCGTCGCATGCATTAC 59.807 52.381 19.57 11.35 0.00 1.89
732 836 4.243270 AGTAAGCAGTAATTGGTCGTGAC 58.757 43.478 0.00 0.00 36.24 3.67
737 1006 5.292101 CAGCAGTAGTAAGCAGTAATTGGTC 59.708 44.000 0.00 0.00 36.24 4.02
864 1179 0.859232 AGACGCGCTGTAAACTTGTG 59.141 50.000 5.73 0.00 0.00 3.33
876 1191 1.553185 GCAAACAAAACAGACGCGC 59.447 52.632 5.73 0.00 0.00 6.86
973 1305 4.428294 AATGTACCAGTCTGGATGGATG 57.572 45.455 26.18 0.00 40.96 3.51
974 1306 4.443457 CGAAATGTACCAGTCTGGATGGAT 60.443 45.833 26.18 4.98 40.96 3.41
975 1307 3.118775 CGAAATGTACCAGTCTGGATGGA 60.119 47.826 26.18 6.50 40.96 3.41
976 1308 3.118775 TCGAAATGTACCAGTCTGGATGG 60.119 47.826 26.18 0.00 40.96 3.51
977 1309 4.115516 CTCGAAATGTACCAGTCTGGATG 58.884 47.826 26.18 0.00 40.96 3.51
978 1310 4.023980 TCTCGAAATGTACCAGTCTGGAT 58.976 43.478 26.18 11.99 40.96 3.41
989 1326 5.072040 TGTGCTTCTCATCTCGAAATGTA 57.928 39.130 0.00 0.00 0.00 2.29
990 1327 3.930336 TGTGCTTCTCATCTCGAAATGT 58.070 40.909 0.00 0.00 0.00 2.71
991 1328 3.931468 ACTGTGCTTCTCATCTCGAAATG 59.069 43.478 0.00 0.00 0.00 2.32
997 1339 3.456280 GATGGACTGTGCTTCTCATCTC 58.544 50.000 7.75 0.00 0.00 2.75
1013 1355 1.339055 CCGCAACAAGAAGAGGATGGA 60.339 52.381 0.00 0.00 0.00 3.41
1019 1361 1.576421 GCCACCGCAACAAGAAGAG 59.424 57.895 0.00 0.00 34.03 2.85
1035 1377 4.856801 ATCATCACCGCCACCGCC 62.857 66.667 0.00 0.00 0.00 6.13
1036 1378 3.272334 GATCATCACCGCCACCGC 61.272 66.667 0.00 0.00 0.00 5.68
1037 1379 2.588877 GGATCATCACCGCCACCG 60.589 66.667 0.00 0.00 0.00 4.94
1038 1380 1.524621 CAGGATCATCACCGCCACC 60.525 63.158 0.00 0.00 0.00 4.61
1048 1390 2.413351 CGACGGCGACAGGATCAT 59.587 61.111 16.62 0.00 40.82 2.45
1108 1450 2.045340 CTGGCCCGTGGGTTTAGG 60.045 66.667 6.82 0.00 37.65 2.69
1529 1879 1.623311 ACGATCATGGCGGATTGGATA 59.377 47.619 12.30 0.00 33.70 2.59
1531 1881 0.249868 GACGATCATGGCGGATTGGA 60.250 55.000 12.30 0.00 33.70 3.53
1534 1884 1.414181 AGAAGACGATCATGGCGGATT 59.586 47.619 12.30 7.04 0.00 3.01
1554 1904 7.720957 TCACAAATCAATCAAGAAGAAGAGGAA 59.279 33.333 0.00 0.00 0.00 3.36
1557 1907 9.557338 GATTCACAAATCAATCAAGAAGAAGAG 57.443 33.333 0.00 0.00 40.90 2.85
1560 1910 7.804600 CACGATTCACAAATCAATCAAGAAGAA 59.195 33.333 0.00 0.00 41.22 2.52
1563 1913 5.858049 GCACGATTCACAAATCAATCAAGAA 59.142 36.000 0.00 0.00 41.22 2.52
1570 1938 1.265365 TGCGCACGATTCACAAATCAA 59.735 42.857 5.66 0.00 41.22 2.57
1573 1941 0.168788 CCTGCGCACGATTCACAAAT 59.831 50.000 5.66 0.00 0.00 2.32
1598 1981 2.313172 CGTGCTCTGCTTGAACGCT 61.313 57.895 0.00 0.00 0.00 5.07
1724 2110 1.300233 GATCGACGACATGGAGCCC 60.300 63.158 0.00 0.00 0.00 5.19
1829 2215 1.299014 GATCTGCCTCGACTGCTCG 60.299 63.158 4.04 0.00 41.65 5.03
2075 2461 2.343758 TGGTTCTCCAGCGACTGC 59.656 61.111 0.00 0.00 39.03 4.40
2168 2554 3.160748 GCCTCCCTGCTCTCCTCC 61.161 72.222 0.00 0.00 0.00 4.30
2269 2655 2.125552 CCGAGTTGCGCATGAGGA 60.126 61.111 12.75 0.00 39.11 3.71
2303 2689 1.199615 GGAGGGAGAAGAAGACCTGG 58.800 60.000 0.00 0.00 32.42 4.45
2304 2690 2.107366 GAGGAGGGAGAAGAAGACCTG 58.893 57.143 0.00 0.00 32.42 4.00
2305 2691 2.007636 AGAGGAGGGAGAAGAAGACCT 58.992 52.381 0.00 0.00 35.67 3.85
2306 2692 2.107366 CAGAGGAGGGAGAAGAAGACC 58.893 57.143 0.00 0.00 0.00 3.85
2307 2693 2.107366 CCAGAGGAGGGAGAAGAAGAC 58.893 57.143 0.00 0.00 0.00 3.01
2308 2694 1.719378 ACCAGAGGAGGGAGAAGAAGA 59.281 52.381 0.00 0.00 0.00 2.87
2309 2695 2.107366 GACCAGAGGAGGGAGAAGAAG 58.893 57.143 0.00 0.00 0.00 2.85
2310 2696 1.719378 AGACCAGAGGAGGGAGAAGAA 59.281 52.381 0.00 0.00 0.00 2.52
2311 2697 1.006519 CAGACCAGAGGAGGGAGAAGA 59.993 57.143 0.00 0.00 0.00 2.87
2312 2698 1.484038 CAGACCAGAGGAGGGAGAAG 58.516 60.000 0.00 0.00 0.00 2.85
2313 2699 0.041833 CCAGACCAGAGGAGGGAGAA 59.958 60.000 0.00 0.00 0.00 2.87
2314 2700 1.149782 ACCAGACCAGAGGAGGGAGA 61.150 60.000 0.00 0.00 0.00 3.71
2315 2701 0.631753 TACCAGACCAGAGGAGGGAG 59.368 60.000 0.00 0.00 0.00 4.30
2316 2702 0.335361 GTACCAGACCAGAGGAGGGA 59.665 60.000 0.00 0.00 0.00 4.20
2317 2703 0.336737 AGTACCAGACCAGAGGAGGG 59.663 60.000 0.00 0.00 0.00 4.30
2318 2704 1.286553 AGAGTACCAGACCAGAGGAGG 59.713 57.143 0.00 0.00 0.00 4.30
2319 2705 2.374184 CAGAGTACCAGACCAGAGGAG 58.626 57.143 0.00 0.00 0.00 3.69
2320 2706 1.006043 CCAGAGTACCAGACCAGAGGA 59.994 57.143 0.00 0.00 0.00 3.71
2321 2707 1.272760 ACCAGAGTACCAGACCAGAGG 60.273 57.143 0.00 0.00 0.00 3.69
2322 2708 2.223803 ACCAGAGTACCAGACCAGAG 57.776 55.000 0.00 0.00 0.00 3.35
2323 2709 2.632996 CAAACCAGAGTACCAGACCAGA 59.367 50.000 0.00 0.00 0.00 3.86
2324 2710 2.872038 GCAAACCAGAGTACCAGACCAG 60.872 54.545 0.00 0.00 0.00 4.00
2325 2711 1.071699 GCAAACCAGAGTACCAGACCA 59.928 52.381 0.00 0.00 0.00 4.02
2326 2712 1.071699 TGCAAACCAGAGTACCAGACC 59.928 52.381 0.00 0.00 0.00 3.85
2327 2713 2.543777 TGCAAACCAGAGTACCAGAC 57.456 50.000 0.00 0.00 0.00 3.51
2328 2714 2.703536 TCTTGCAAACCAGAGTACCAGA 59.296 45.455 0.00 0.00 0.00 3.86
2329 2715 2.808543 GTCTTGCAAACCAGAGTACCAG 59.191 50.000 0.00 0.00 0.00 4.00
2330 2716 2.805295 CGTCTTGCAAACCAGAGTACCA 60.805 50.000 0.00 0.00 0.00 3.25
2331 2717 1.798813 CGTCTTGCAAACCAGAGTACC 59.201 52.381 0.00 0.00 0.00 3.34
2332 2718 2.221055 CACGTCTTGCAAACCAGAGTAC 59.779 50.000 0.00 0.00 0.00 2.73
2333 2719 2.479837 CACGTCTTGCAAACCAGAGTA 58.520 47.619 0.00 0.00 0.00 2.59
2334 2720 1.299541 CACGTCTTGCAAACCAGAGT 58.700 50.000 0.00 0.00 0.00 3.24
2345 2731 2.551270 GCGGTTCAGCACGTCTTG 59.449 61.111 0.00 0.00 37.05 3.02
2346 2732 2.665185 GGCGGTTCAGCACGTCTT 60.665 61.111 0.00 0.00 39.27 3.01
2347 2733 2.731691 AATGGCGGTTCAGCACGTCT 62.732 55.000 0.00 0.00 39.27 4.18
2348 2734 2.325082 AATGGCGGTTCAGCACGTC 61.325 57.895 0.00 0.00 39.27 4.34
2349 2735 2.281484 AATGGCGGTTCAGCACGT 60.281 55.556 0.00 0.00 39.27 4.49
2350 2736 1.647545 ATCAATGGCGGTTCAGCACG 61.648 55.000 0.00 0.00 39.27 5.34
2351 2737 0.099436 GATCAATGGCGGTTCAGCAC 59.901 55.000 0.00 0.00 39.27 4.40
2352 2738 1.031571 GGATCAATGGCGGTTCAGCA 61.032 55.000 0.00 0.00 39.27 4.41
2353 2739 1.729881 GGATCAATGGCGGTTCAGC 59.270 57.895 0.00 0.00 0.00 4.26
2354 2740 1.439353 CCGGATCAATGGCGGTTCAG 61.439 60.000 0.00 0.00 0.00 3.02
2355 2741 1.451207 CCGGATCAATGGCGGTTCA 60.451 57.895 0.00 0.00 0.00 3.18
2356 2742 1.153249 TCCGGATCAATGGCGGTTC 60.153 57.895 0.00 0.00 0.00 3.62
2357 2743 1.153168 CTCCGGATCAATGGCGGTT 60.153 57.895 3.57 0.00 0.00 4.44
2358 2744 2.505982 CTCCGGATCAATGGCGGT 59.494 61.111 3.57 0.00 0.00 5.68
2359 2745 2.974698 GCTCCGGATCAATGGCGG 60.975 66.667 3.57 1.32 0.00 6.13
2360 2746 1.958205 GAGCTCCGGATCAATGGCG 60.958 63.158 3.57 0.00 0.00 5.69
2361 2747 1.958205 CGAGCTCCGGATCAATGGC 60.958 63.158 3.57 3.24 33.91 4.40
2362 2748 0.319728 ATCGAGCTCCGGATCAATGG 59.680 55.000 3.57 0.00 39.14 3.16
2363 2749 1.707632 GATCGAGCTCCGGATCAATG 58.292 55.000 20.47 0.00 39.14 2.82
2364 2750 0.242286 CGATCGAGCTCCGGATCAAT 59.758 55.000 23.23 0.00 39.14 2.57
2365 2751 1.654774 CGATCGAGCTCCGGATCAA 59.345 57.895 23.23 0.00 39.14 2.57
2366 2752 2.261586 CCGATCGAGCTCCGGATCA 61.262 63.158 21.21 0.00 45.58 2.92
2367 2753 2.190101 GACCGATCGAGCTCCGGATC 62.190 65.000 29.22 23.04 45.58 3.36
2368 2754 2.203365 ACCGATCGAGCTCCGGAT 60.203 61.111 29.22 18.01 45.58 4.18
2369 2755 2.900838 GACCGATCGAGCTCCGGA 60.901 66.667 29.22 14.25 45.58 5.14
2379 2765 2.849007 CATGCGCATCGACCGATC 59.151 61.111 22.51 0.00 31.62 3.69
2380 2766 3.341043 GCATGCGCATCGACCGAT 61.341 61.111 22.51 0.00 38.36 4.18
2381 2767 4.810661 TGCATGCGCATCGACCGA 62.811 61.111 22.51 0.00 45.36 4.69
2393 2779 1.022735 GAACTCCTCCTGCATGCATG 58.977 55.000 22.97 22.70 0.00 4.06
2394 2780 0.622136 TGAACTCCTCCTGCATGCAT 59.378 50.000 22.97 2.77 0.00 3.96
2395 2781 0.035725 CTGAACTCCTCCTGCATGCA 60.036 55.000 21.29 21.29 0.00 3.96
2396 2782 1.375098 GCTGAACTCCTCCTGCATGC 61.375 60.000 11.82 11.82 0.00 4.06
2397 2783 1.088340 CGCTGAACTCCTCCTGCATG 61.088 60.000 0.00 0.00 0.00 4.06
2398 2784 1.220206 CGCTGAACTCCTCCTGCAT 59.780 57.895 0.00 0.00 0.00 3.96
2399 2785 2.659016 CGCTGAACTCCTCCTGCA 59.341 61.111 0.00 0.00 0.00 4.41
2463 2941 2.047274 ACGAGGATGGCGTTGTGG 60.047 61.111 0.00 0.00 39.18 4.17
2478 2956 2.507102 ATGAAGCGCGACTCCACG 60.507 61.111 12.10 0.00 0.00 4.94
2487 2965 1.431036 GAAGGCCTTGATGAAGCGC 59.569 57.895 26.25 0.00 0.00 5.92
2506 2984 0.109689 ACGACGCAGCTGTAGAAGAC 60.110 55.000 16.64 0.00 0.00 3.01
2596 3074 1.067283 CGGAGTCTGCAGAAGATGTGT 60.067 52.381 20.19 0.00 37.23 3.72
2599 3077 2.100418 TGATCGGAGTCTGCAGAAGATG 59.900 50.000 20.19 9.41 37.23 2.90
2600 3078 2.382882 TGATCGGAGTCTGCAGAAGAT 58.617 47.619 20.19 19.35 37.23 2.40
2602 3080 2.741612 GATGATCGGAGTCTGCAGAAG 58.258 52.381 20.19 10.51 0.00 2.85
2603 3081 1.066152 CGATGATCGGAGTCTGCAGAA 59.934 52.381 20.19 2.01 36.00 3.02
2604 3082 0.665298 CGATGATCGGAGTCTGCAGA 59.335 55.000 13.74 13.74 36.00 4.26
2606 3084 0.817654 AACGATGATCGGAGTCTGCA 59.182 50.000 19.82 0.00 45.59 4.41
2608 3086 2.099921 AGGAAACGATGATCGGAGTCTG 59.900 50.000 19.82 0.00 45.59 3.51
2609 3087 2.379972 AGGAAACGATGATCGGAGTCT 58.620 47.619 19.82 8.29 45.59 3.24
2610 3088 2.873133 AGGAAACGATGATCGGAGTC 57.127 50.000 19.82 12.13 45.59 3.36
2632 3115 3.470709 TGAAGAAATGATCCGATGGAGC 58.529 45.455 0.00 0.00 38.78 4.70
2639 3122 3.680642 AACGCATGAAGAAATGATCCG 57.319 42.857 0.00 0.00 0.00 4.18
2641 3124 5.514204 CCAAGAAACGCATGAAGAAATGATC 59.486 40.000 0.00 0.00 0.00 2.92
2642 3125 5.183713 TCCAAGAAACGCATGAAGAAATGAT 59.816 36.000 0.00 0.00 0.00 2.45
2656 3139 4.048504 GGTTTGGTCAAATCCAAGAAACG 58.951 43.478 0.00 0.00 46.27 3.60
2658 3141 4.100808 CCTGGTTTGGTCAAATCCAAGAAA 59.899 41.667 14.07 0.00 46.27 2.52
2659 3142 3.640967 CCTGGTTTGGTCAAATCCAAGAA 59.359 43.478 14.07 0.00 46.27 2.52
2660 3143 3.230134 CCTGGTTTGGTCAAATCCAAGA 58.770 45.455 14.07 0.00 46.27 3.02
2661 3144 2.965147 ACCTGGTTTGGTCAAATCCAAG 59.035 45.455 14.07 11.89 46.27 3.61
2662 3145 3.039252 ACCTGGTTTGGTCAAATCCAA 57.961 42.857 14.07 0.00 44.48 3.53
2671 3154 0.185901 ATGCACAGACCTGGTTTGGT 59.814 50.000 20.10 7.60 44.10 3.67
2672 3155 0.883833 GATGCACAGACCTGGTTTGG 59.116 55.000 20.10 10.86 34.19 3.28
2864 3354 3.564027 GCCGCGGTTCAAGATCGG 61.564 66.667 28.70 0.00 42.68 4.18
2879 3369 0.455633 CGTACTGGTACTGTGACGCC 60.456 60.000 8.89 0.00 41.61 5.68
2880 3370 0.239347 ACGTACTGGTACTGTGACGC 59.761 55.000 8.89 0.00 41.61 5.19
2881 3371 2.031769 TCAACGTACTGGTACTGTGACG 60.032 50.000 8.89 8.62 41.61 4.35
2882 3372 3.631145 TCAACGTACTGGTACTGTGAC 57.369 47.619 8.89 0.00 41.61 3.67
2883 3373 4.077108 AGATCAACGTACTGGTACTGTGA 58.923 43.478 8.89 10.90 41.61 3.58
2885 3375 4.077108 TGAGATCAACGTACTGGTACTGT 58.923 43.478 8.89 6.11 44.39 3.55
2886 3376 4.696899 TGAGATCAACGTACTGGTACTG 57.303 45.455 8.89 5.59 34.04 2.74
2887 3377 5.066634 CAGATGAGATCAACGTACTGGTACT 59.933 44.000 8.89 0.00 34.04 2.73
2888 3378 5.066117 TCAGATGAGATCAACGTACTGGTAC 59.934 44.000 0.00 1.18 0.00 3.34
2889 3379 5.190677 TCAGATGAGATCAACGTACTGGTA 58.809 41.667 0.00 0.00 0.00 3.25
2890 3380 4.017126 TCAGATGAGATCAACGTACTGGT 58.983 43.478 0.00 0.00 0.00 4.00
2891 3381 4.639135 TCAGATGAGATCAACGTACTGG 57.361 45.455 0.00 0.00 0.00 4.00
2991 3481 2.695646 GCGGCGTTGTCTTCGATC 59.304 61.111 9.37 0.00 0.00 3.69
3017 3507 0.958382 CAAGGGACGGCGGATGAAAA 60.958 55.000 13.24 0.00 0.00 2.29
3055 3582 3.300590 CGCCAGCATTACGTTTCAAAATC 59.699 43.478 0.00 0.00 0.00 2.17
3076 3603 3.694535 ACTAGTAGTTCAGATTCGGCG 57.305 47.619 0.00 0.00 0.00 6.46
3077 3604 6.134040 ACTTACTAGTAGTTCAGATTCGGC 57.866 41.667 8.40 0.00 31.21 5.54
3096 3623 6.923670 ACCAGAGGAGGATGATAAGTACTTA 58.076 40.000 17.41 17.41 0.00 2.24
3097 3624 5.782925 ACCAGAGGAGGATGATAAGTACTT 58.217 41.667 13.68 13.68 0.00 2.24
3226 3753 2.126580 CACGAAGTCCGGGTCGAC 60.127 66.667 23.77 7.13 41.61 4.20
3316 3843 1.135257 GTATCTCCTCATGGCGATCGG 60.135 57.143 18.30 0.00 38.58 4.18
3368 3895 5.304614 ACATATATGTTCTACTTCCGTGCCT 59.695 40.000 12.75 0.00 37.90 4.75
3391 3918 2.423538 ACTTCGGGCAATATTTCTGCAC 59.576 45.455 0.59 0.00 41.78 4.57
3407 3934 7.167302 TGCTGACATTTAACAATTTCAACTTCG 59.833 33.333 0.00 0.00 30.34 3.79
3531 4064 5.596836 TCTGATGTTTTGTCCAAGCTTTT 57.403 34.783 0.00 0.00 0.00 2.27
3642 4175 9.612620 GGACACTTCTTAAGTTATGTTTCATTG 57.387 33.333 1.63 0.00 40.46 2.82
3643 4176 9.349713 TGGACACTTCTTAAGTTATGTTTCATT 57.650 29.630 1.63 0.00 40.46 2.57
3644 4177 8.918202 TGGACACTTCTTAAGTTATGTTTCAT 57.082 30.769 1.63 0.00 40.46 2.57
3645 4178 8.740123 TTGGACACTTCTTAAGTTATGTTTCA 57.260 30.769 1.63 5.79 40.46 2.69
3646 4179 9.827411 GATTGGACACTTCTTAAGTTATGTTTC 57.173 33.333 1.63 1.15 40.46 2.78
3647 4180 9.574516 AGATTGGACACTTCTTAAGTTATGTTT 57.425 29.630 1.63 0.00 40.46 2.83
3653 4186 9.003658 CATGTTAGATTGGACACTTCTTAAGTT 57.996 33.333 1.63 0.00 40.46 2.66
3654 4187 8.375506 TCATGTTAGATTGGACACTTCTTAAGT 58.624 33.333 1.63 0.00 44.06 2.24
3665 4198 9.884465 GCAGTTATATTTCATGTTAGATTGGAC 57.116 33.333 0.00 0.00 0.00 4.02
3790 4324 9.191995 GTACATTAGGTTGTCCTTTTTCATTTG 57.808 33.333 0.00 0.00 42.12 2.32
3841 4375 2.230025 CCGCAGTGTATAGATGGGAGAG 59.770 54.545 0.00 0.00 0.00 3.20
3842 4376 2.239400 CCGCAGTGTATAGATGGGAGA 58.761 52.381 0.00 0.00 0.00 3.71
3924 4458 5.336849 GGGAGATCTGATTATACGACCAAGG 60.337 48.000 0.00 0.00 0.00 3.61
3969 4503 8.786826 ATTCTTCAATACGGACAATTTACTCA 57.213 30.769 0.00 0.00 0.00 3.41
4123 4657 1.119574 ACAAGACCACCGTGCCTACT 61.120 55.000 0.00 0.00 0.00 2.57
4134 4668 3.836949 GTATTTCCGTACGACAAGACCA 58.163 45.455 18.76 0.00 0.00 4.02
4147 4681 5.231568 GTCTTCATTCAGTACCGTATTTCCG 59.768 44.000 0.00 0.00 0.00 4.30
4165 4699 2.606519 CCCCCAGACCCGTCTTCA 60.607 66.667 0.00 0.00 37.98 3.02
4313 4847 5.338463 GCTAATCTGGACTCAACTTTACCCT 60.338 44.000 0.00 0.00 0.00 4.34
4338 4872 0.244450 CCATGTCCGCTGTTGCAAAT 59.756 50.000 0.00 0.00 39.64 2.32


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

AutoCloner maintained by Alex Coulton.