Multiple sequence alignment - TraesCS2A01G409200

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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 TraesCS2A01G409200 chr2A 100.000 7936 0 0 1 7936 666567384 666559449 0.000000e+00 14656.0
1 TraesCS2A01G409200 chr2A 87.164 335 29 7 1505 1826 23546996 23546663 1.260000e-97 368.0
2 TraesCS2A01G409200 chr2A 80.247 486 45 26 940 1423 23547463 23547027 1.290000e-82 318.0
3 TraesCS2A01G409200 chr2A 98.039 51 1 0 6767 6817 666560567 666560517 1.100000e-13 89.8
4 TraesCS2A01G409200 chr2A 98.039 51 1 0 6818 6868 666560618 666560568 1.100000e-13 89.8
5 TraesCS2A01G409200 chr2A 88.889 54 4 2 7373 7426 52016957 52016906 1.850000e-06 65.8
6 TraesCS2A01G409200 chr2D 92.909 3596 162 31 336 3877 520642654 520646210 0.000000e+00 5142.0
7 TraesCS2A01G409200 chr2D 94.020 2960 96 19 3878 6817 520646237 520649135 0.000000e+00 4410.0
8 TraesCS2A01G409200 chr2D 87.629 388 25 3 6818 7205 520649085 520649449 5.690000e-116 429.0
9 TraesCS2A01G409200 chr2D 82.370 346 46 12 1 333 520640756 520641099 3.620000e-73 287.0
10 TraesCS2A01G409200 chr2D 95.238 63 3 0 5632 5694 179827518 179827456 5.070000e-17 100.0
11 TraesCS2A01G409200 chr2B 94.903 1864 55 11 1539 3383 614919058 614917216 0.000000e+00 2880.0
12 TraesCS2A01G409200 chr2B 94.867 1773 64 9 5578 7337 614909214 614907456 0.000000e+00 2745.0
13 TraesCS2A01G409200 chr2B 94.977 1712 57 12 3881 5581 614916615 614914922 0.000000e+00 2658.0
14 TraesCS2A01G409200 chr2B 87.934 1036 44 27 558 1540 614920225 614919218 0.000000e+00 1146.0
15 TraesCS2A01G409200 chr2B 96.494 542 19 0 7395 7936 614907460 614906919 0.000000e+00 896.0
16 TraesCS2A01G409200 chr2B 95.181 498 23 1 3382 3878 614917142 614916645 0.000000e+00 785.0
17 TraesCS2A01G409200 chr2B 92.683 41 3 0 6714 6754 786213347 786213387 8.600000e-05 60.2
18 TraesCS2A01G409200 chr1A 89.124 331 24 6 1509 1828 77161262 77161591 1.240000e-107 401.0
19 TraesCS2A01G409200 chr1A 81.490 443 48 19 983 1423 77160818 77161228 4.590000e-87 333.0
20 TraesCS2A01G409200 chr1A 93.750 64 4 0 5632 5695 17268521 17268458 6.560000e-16 97.1
21 TraesCS2A01G409200 chr6B 81.070 486 49 23 940 1423 80463955 80463511 1.640000e-91 348.0
22 TraesCS2A01G409200 chr6B 87.719 57 5 2 6718 6773 44546346 44546291 1.850000e-06 65.8
23 TraesCS2A01G409200 chr6A 91.339 127 10 1 2651 2777 150465715 150465590 1.060000e-38 172.0
24 TraesCS2A01G409200 chr6A 92.857 42 3 0 7373 7414 181913722 181913681 2.390000e-05 62.1
25 TraesCS2A01G409200 chr5B 92.000 75 6 0 5620 5694 508368004 508368078 1.090000e-18 106.0
26 TraesCS2A01G409200 chr5B 89.189 74 6 2 2 74 466647921 466647849 3.050000e-14 91.6
27 TraesCS2A01G409200 chr4B 95.238 63 3 0 5632 5694 547578723 547578661 5.070000e-17 100.0
28 TraesCS2A01G409200 chrUn 93.846 65 4 0 5632 5696 49493984 49493920 1.820000e-16 99.0
29 TraesCS2A01G409200 chr3A 87.356 87 9 1 5609 5695 560633996 560633912 1.820000e-16 99.0
30 TraesCS2A01G409200 chr3A 86.364 66 7 2 1 65 40159815 40159879 3.970000e-08 71.3
31 TraesCS2A01G409200 chr3A 88.462 52 4 2 7375 7426 198177657 198177608 2.390000e-05 62.1
32 TraesCS2A01G409200 chr6D 93.750 64 4 0 5632 5695 458133741 458133678 6.560000e-16 97.1
33 TraesCS2A01G409200 chr5A 87.838 74 7 2 1 73 491235068 491234996 1.420000e-12 86.1
34 TraesCS2A01G409200 chr5A 88.889 54 4 2 7373 7426 35085205 35085256 1.850000e-06 65.8
35 TraesCS2A01G409200 chr5A 88.679 53 4 2 7374 7426 616867627 616867677 6.650000e-06 63.9
36 TraesCS2A01G409200 chr7D 85.915 71 8 2 1 70 163196045 163195976 3.070000e-09 75.0
37 TraesCS2A01G409200 chr7B 80.612 98 17 1 463 560 603203540 603203445 3.070000e-09 75.0
38 TraesCS2A01G409200 chr7B 93.023 43 3 0 7372 7414 558895067 558895025 6.650000e-06 63.9
39 TraesCS2A01G409200 chr7B 88.000 50 4 2 7376 7425 133487897 133487850 3.090000e-04 58.4
40 TraesCS2A01G409200 chr3D 88.525 61 5 2 7366 7426 505946228 505946286 1.100000e-08 73.1
41 TraesCS2A01G409200 chr7A 88.462 52 3 2 7374 7425 139633894 139633942 8.600000e-05 60.2
42 TraesCS2A01G409200 chr1B 90.698 43 4 0 6727 6769 5949337 5949379 3.090000e-04 58.4


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 TraesCS2A01G409200 chr2A 666559449 666567384 7935 True 14656.00 14656 100.00000 1 7936 1 chr2A.!!$R2 7935
1 TraesCS2A01G409200 chr2A 23546663 23547463 800 True 343.00 368 83.70550 940 1826 2 chr2A.!!$R3 886
2 TraesCS2A01G409200 chr2D 520640756 520649449 8693 False 2567.00 5142 89.23200 1 7205 4 chr2D.!!$F1 7204
3 TraesCS2A01G409200 chr2B 614914922 614920225 5303 True 1867.25 2880 93.24875 558 5581 4 chr2B.!!$R2 5023
4 TraesCS2A01G409200 chr2B 614906919 614909214 2295 True 1820.50 2745 95.68050 5578 7936 2 chr2B.!!$R1 2358
5 TraesCS2A01G409200 chr1A 77160818 77161591 773 False 367.00 401 85.30700 983 1828 2 chr1A.!!$F1 845

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
102 113 0.034896 GAGAAACCAACTCCGGCAGA 59.965 55.000 0.00 0.00 0.00 4.26 F
516 2082 0.106569 TAGTCCCCTATCCGCGAACA 60.107 55.000 8.23 0.00 0.00 3.18 F
1886 3730 0.187117 TGAATGGGTTGGGTGCTTCA 59.813 50.000 0.00 0.00 0.00 3.02 F
2583 4429 3.191371 AGCTTTAGGATTTCCGTTTGCAG 59.809 43.478 0.00 0.00 42.08 4.41 F
3194 5047 4.636169 ACAATTGATTGGGCAGGCATGC 62.636 50.000 16.47 16.47 44.96 4.06 F
4724 6698 2.291043 CCAGGGGAAGCGTGTACCT 61.291 63.158 0.00 0.00 0.00 3.08 F
5183 7161 1.141858 GGAGGATCAGCCCCACTAAAG 59.858 57.143 0.00 0.00 36.25 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 3719 0.316841 GCCGAAAATGAAGCACCCAA 59.683 50.000 0.00 0.0 0.00 4.12 R
2229 4074 3.944015 ACTTCAGCCTGCAAGATAATGAC 59.056 43.478 9.81 0.0 34.07 3.06 R
3234 5087 1.094785 GGCGGTCAAATACATGCAGT 58.905 50.000 0.00 0.0 33.84 4.40 R
3898 5854 2.158986 AGTGAGCTGATGTATGGACTGC 60.159 50.000 0.00 0.0 0.00 4.40 R
4747 6723 4.034048 ACAAAACTGTCGTTTGAGCTACTG 59.966 41.667 10.92 0.0 42.28 2.74 R
5666 7647 1.136500 GGGTTTCACCTCTAGCCTACG 59.864 57.143 0.00 0.0 38.64 3.51 R
7155 9153 0.387112 CATTCATGTGCGGCGTGTTT 60.387 50.000 9.37 0.0 35.64 2.83 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
19 20 2.202783 GCGGCCAACATTGATGCC 60.203 61.111 2.24 2.70 40.54 4.40
20 21 2.495866 CGGCCAACATTGATGCCC 59.504 61.111 2.24 0.00 40.87 5.36
22 23 2.350458 GGCCAACATTGATGCCCGT 61.350 57.895 0.00 0.00 37.94 5.28
31 32 1.024046 TTGATGCCCGTGATTGACCG 61.024 55.000 0.00 0.00 0.00 4.79
75 86 2.110967 CGACCTCTCGGGCTTCGTA 61.111 63.158 0.60 0.00 35.52 3.43
100 111 0.250295 CTGAGAAACCAACTCCGGCA 60.250 55.000 0.00 0.00 33.95 5.69
102 113 0.034896 GAGAAACCAACTCCGGCAGA 59.965 55.000 0.00 0.00 0.00 4.26
106 117 2.124570 CCAACTCCGGCAGATGGG 60.125 66.667 17.09 8.25 40.69 4.00
107 118 2.825836 CAACTCCGGCAGATGGGC 60.826 66.667 0.00 0.00 39.06 5.36
186 197 2.256764 CGAGCGTCAGACAGCTGT 59.743 61.111 21.88 21.88 44.69 4.40
196 207 1.862806 GACAGCTGTCGAACAAGGC 59.137 57.895 29.84 5.86 35.12 4.35
198 209 0.679505 ACAGCTGTCGAACAAGGCTA 59.320 50.000 15.25 0.00 29.89 3.93
200 211 2.289694 ACAGCTGTCGAACAAGGCTATT 60.290 45.455 15.25 0.00 29.89 1.73
211 222 2.807622 GGCTATTGCGGCCCTTTG 59.192 61.111 0.00 0.00 43.49 2.77
212 223 2.785425 GGCTATTGCGGCCCTTTGG 61.785 63.158 0.00 0.00 43.49 3.28
224 235 0.394352 CCCTTTGGCATCCTTACGCT 60.394 55.000 0.00 0.00 0.00 5.07
225 236 1.134220 CCCTTTGGCATCCTTACGCTA 60.134 52.381 0.00 0.00 0.00 4.26
226 237 1.940613 CCTTTGGCATCCTTACGCTAC 59.059 52.381 0.00 0.00 0.00 3.58
235 246 0.745468 CCTTACGCTACTGGAGGGAC 59.255 60.000 11.35 0.00 40.59 4.46
241 252 0.824759 GCTACTGGAGGGACGACAAT 59.175 55.000 0.00 0.00 0.00 2.71
243 254 1.137086 CTACTGGAGGGACGACAATGG 59.863 57.143 0.00 0.00 0.00 3.16
245 256 2.184020 CTGGAGGGACGACAATGGCA 62.184 60.000 0.00 0.00 0.00 4.92
246 257 1.450312 GGAGGGACGACAATGGCAG 60.450 63.158 0.00 0.00 0.00 4.85
280 294 3.941188 CGTGTGGCAGGACAGGGT 61.941 66.667 0.00 0.00 0.00 4.34
286 300 2.606587 GGCAGGACAGGGTGGTCAT 61.607 63.158 0.00 0.00 39.59 3.06
299 313 1.067142 GTGGTCATGCTTACGAGGTGA 60.067 52.381 0.00 0.00 0.00 4.02
319 333 9.400638 GAGGTGATCGTTCAATATAGAGTTTAG 57.599 37.037 0.00 0.00 32.48 1.85
359 1924 9.715121 AGTTTTAGTAGAACGGTCAAAATATCA 57.285 29.630 1.87 0.00 32.38 2.15
371 1936 8.397906 ACGGTCAAAATATCATCTGTTTATGTG 58.602 33.333 0.00 0.00 0.00 3.21
421 1986 9.956720 ATCTATCCAATTTGAATGAATTTCGTC 57.043 29.630 0.00 0.00 37.13 4.20
422 1987 9.177608 TCTATCCAATTTGAATGAATTTCGTCT 57.822 29.630 0.00 0.00 37.13 4.18
423 1988 9.229784 CTATCCAATTTGAATGAATTTCGTCTG 57.770 33.333 0.00 0.00 37.13 3.51
424 1989 6.389091 TCCAATTTGAATGAATTTCGTCTGG 58.611 36.000 0.00 0.00 37.13 3.86
425 1990 5.577945 CCAATTTGAATGAATTTCGTCTGGG 59.422 40.000 0.00 0.00 37.13 4.45
427 1992 5.782893 TTTGAATGAATTTCGTCTGGGTT 57.217 34.783 0.00 0.00 37.13 4.11
429 1994 5.782893 TGAATGAATTTCGTCTGGGTTTT 57.217 34.783 0.00 0.00 37.13 2.43
430 1995 6.155475 TGAATGAATTTCGTCTGGGTTTTT 57.845 33.333 0.00 0.00 37.13 1.94
431 1996 6.212955 TGAATGAATTTCGTCTGGGTTTTTC 58.787 36.000 0.00 0.00 37.13 2.29
432 1997 4.217754 TGAATTTCGTCTGGGTTTTTCG 57.782 40.909 0.00 0.00 0.00 3.46
433 1998 3.628487 TGAATTTCGTCTGGGTTTTTCGT 59.372 39.130 0.00 0.00 0.00 3.85
434 1999 4.815308 TGAATTTCGTCTGGGTTTTTCGTA 59.185 37.500 0.00 0.00 0.00 3.43
448 2013 7.146648 GGGTTTTTCGTATTGTTGTCCAAATA 58.853 34.615 0.00 0.00 36.44 1.40
478 2043 2.341846 TTATTGGATGACGGCCTTCC 57.658 50.000 6.80 5.43 39.03 3.46
498 2063 2.562738 CCGCATCTGTATCCATGGACTA 59.437 50.000 18.99 8.15 0.00 2.59
499 2064 3.367806 CCGCATCTGTATCCATGGACTAG 60.368 52.174 18.99 15.30 0.00 2.57
516 2082 0.106569 TAGTCCCCTATCCGCGAACA 60.107 55.000 8.23 0.00 0.00 3.18
528 2094 1.556564 CGCGAACAGATACGGATTGT 58.443 50.000 0.00 0.00 0.00 2.71
529 2095 1.924524 CGCGAACAGATACGGATTGTT 59.075 47.619 0.00 7.60 37.72 2.83
530 2096 2.347452 CGCGAACAGATACGGATTGTTT 59.653 45.455 0.00 0.00 35.35 2.83
553 2119 6.838198 TTTTACGGATTATCGTTGGAGATG 57.162 37.500 0.00 0.00 43.59 2.90
554 2120 5.524971 TTACGGATTATCGTTGGAGATGT 57.475 39.130 0.00 0.00 43.59 3.06
555 2121 3.978687 ACGGATTATCGTTGGAGATGTC 58.021 45.455 0.00 0.00 40.85 3.06
556 2122 3.243771 ACGGATTATCGTTGGAGATGTCC 60.244 47.826 0.83 0.83 40.85 4.02
608 2174 0.248702 GAAGAGATGCCCGACGAGAC 60.249 60.000 0.00 0.00 0.00 3.36
634 2201 0.605050 TCCAGTAAAGCGCACATGCA 60.605 50.000 11.47 0.00 42.21 3.96
715 2292 4.647611 TCGGCTACCCCACATATATTTTG 58.352 43.478 0.00 0.00 0.00 2.44
745 2322 2.203082 ACACGCCACTGAGAGAGCA 61.203 57.895 0.00 0.00 0.00 4.26
781 2358 4.640855 CGTCACGCGTCCACACCT 62.641 66.667 9.86 0.00 35.54 4.00
782 2359 2.733593 GTCACGCGTCCACACCTC 60.734 66.667 9.86 0.00 0.00 3.85
783 2360 2.910479 TCACGCGTCCACACCTCT 60.910 61.111 9.86 0.00 0.00 3.69
887 2481 3.616821 GCCAAATCCCAATCGCTTTTAAC 59.383 43.478 0.00 0.00 0.00 2.01
899 2493 7.326063 CCAATCGCTTTTAACTTCGAGATTTTT 59.674 33.333 0.00 0.00 34.30 1.94
900 2494 9.325150 CAATCGCTTTTAACTTCGAGATTTTTA 57.675 29.630 0.00 0.00 34.30 1.52
903 2497 9.887406 TCGCTTTTAACTTCGAGATTTTTATTT 57.113 25.926 0.00 0.00 0.00 1.40
919 2515 1.675552 ATTTATTGTCCGCCTTCCCG 58.324 50.000 0.00 0.00 0.00 5.14
936 2532 4.400961 GGAACCGCAGCTGCCTCT 62.401 66.667 32.07 16.57 37.91 3.69
1221 2824 1.079127 CCCCGTCCTTGTGCTGTAG 60.079 63.158 0.00 0.00 0.00 2.74
1222 2825 1.741770 CCCGTCCTTGTGCTGTAGC 60.742 63.158 0.00 0.00 42.50 3.58
1237 2842 1.602888 TAGCGCCCCCTAGATCGAC 60.603 63.158 2.29 0.00 0.00 4.20
1372 3019 6.005066 TGATGTGACTCCCATGATTTGTAT 57.995 37.500 0.00 0.00 0.00 2.29
1428 3096 4.995487 TCTGTATGCATCTCATGATTCTGC 59.005 41.667 0.19 14.19 36.63 4.26
1633 3473 4.402155 TGGGGTCAAGTTGATTTATGCATC 59.598 41.667 9.18 0.00 0.00 3.91
1675 3517 3.609853 TGCAGAACCTGGTGATTATGTC 58.390 45.455 0.00 0.00 31.21 3.06
1696 3538 1.959226 CCGTGAAGGTGAACCCGTG 60.959 63.158 0.00 0.00 38.74 4.94
1838 3680 7.760607 TCACTATGAGAGGTCCTGATTACTAT 58.239 38.462 0.00 0.00 0.00 2.12
1846 3688 8.380742 AGAGGTCCTGATTACTATCTGAAAAA 57.619 34.615 0.00 0.00 33.00 1.94
1847 3689 8.261522 AGAGGTCCTGATTACTATCTGAAAAAC 58.738 37.037 0.00 0.00 33.00 2.43
1848 3690 7.918076 AGGTCCTGATTACTATCTGAAAAACA 58.082 34.615 0.00 0.00 33.00 2.83
1850 3692 9.178758 GGTCCTGATTACTATCTGAAAAACAAT 57.821 33.333 0.00 0.00 33.00 2.71
1875 3719 7.902920 ACTATATCAGCAAATTTGAATGGGT 57.097 32.000 22.31 12.85 0.00 4.51
1886 3730 0.187117 TGAATGGGTTGGGTGCTTCA 59.813 50.000 0.00 0.00 0.00 3.02
1973 3817 7.500720 TTCTATTTGTCATCAATGCATCGAT 57.499 32.000 0.00 0.00 33.32 3.59
2177 4022 8.826765 ACCTTCAGAGTAAAATTCCTATCTCAA 58.173 33.333 0.00 0.00 0.00 3.02
2185 4030 6.521151 AAAATTCCTATCTCAACAGCCAAG 57.479 37.500 0.00 0.00 0.00 3.61
2205 4050 7.066766 AGCCAAGAAAGTATTGCTCTATCAAAG 59.933 37.037 0.00 0.00 0.00 2.77
2583 4429 3.191371 AGCTTTAGGATTTCCGTTTGCAG 59.809 43.478 0.00 0.00 42.08 4.41
2799 4645 8.746052 AGAGGTATGTCTAGATAGATGTATGC 57.254 38.462 0.00 0.00 34.39 3.14
2950 4803 6.707440 TTTAATATCATCGTTGGCCATTGT 57.293 33.333 6.09 0.00 0.00 2.71
2961 4814 6.326375 TCGTTGGCCATTGTATTTTATTGAC 58.674 36.000 6.09 0.00 0.00 3.18
3194 5047 4.636169 ACAATTGATTGGGCAGGCATGC 62.636 50.000 16.47 16.47 44.96 4.06
3234 5087 4.961438 TGCTGTCATCTATATCTGCCAA 57.039 40.909 0.00 0.00 0.00 4.52
3691 5620 9.703892 CTCACTTGGTGATTATAGATTTCTAGG 57.296 37.037 0.71 0.00 41.94 3.02
3728 5657 6.554334 TTTATTTGAAGTTCTGAACTCGGG 57.446 37.500 22.24 0.00 41.91 5.14
3741 5670 5.186992 TCTGAACTCGGGACAAGATCAAATA 59.813 40.000 0.00 0.00 0.00 1.40
3835 5764 9.346725 GTCTCAGCTTTTCTGTTATTTAAATGG 57.653 33.333 11.05 0.00 43.32 3.16
3863 5792 7.630242 TCACTCAAGATATCAAATGGAAACC 57.370 36.000 5.32 0.00 0.00 3.27
3903 5859 6.855836 TCATTATCAAATGAAACCAGCAGTC 58.144 36.000 0.00 0.00 46.64 3.51
3943 5910 2.498167 GGAGCAGTTCAGCAGAAAGAA 58.502 47.619 0.00 0.00 35.08 2.52
3944 5911 2.880890 GGAGCAGTTCAGCAGAAAGAAA 59.119 45.455 0.00 0.00 35.08 2.52
3945 5912 3.316308 GGAGCAGTTCAGCAGAAAGAAAA 59.684 43.478 0.00 0.00 35.08 2.29
3946 5913 4.202050 GGAGCAGTTCAGCAGAAAGAAAAA 60.202 41.667 0.00 0.00 35.08 1.94
3947 5914 5.508657 GGAGCAGTTCAGCAGAAAGAAAAAT 60.509 40.000 0.00 0.00 35.08 1.82
3948 5915 6.294176 GGAGCAGTTCAGCAGAAAGAAAAATA 60.294 38.462 0.00 0.00 35.08 1.40
3949 5916 6.675987 AGCAGTTCAGCAGAAAGAAAAATAG 58.324 36.000 0.00 0.00 35.08 1.73
3950 5917 5.344396 GCAGTTCAGCAGAAAGAAAAATAGC 59.656 40.000 0.00 0.00 35.08 2.97
3951 5918 6.675987 CAGTTCAGCAGAAAGAAAAATAGCT 58.324 36.000 0.00 0.00 35.08 3.32
3952 5919 7.573843 GCAGTTCAGCAGAAAGAAAAATAGCTA 60.574 37.037 0.00 0.00 35.08 3.32
3953 5920 7.961827 CAGTTCAGCAGAAAGAAAAATAGCTAG 59.038 37.037 0.00 0.00 35.08 3.42
3954 5921 7.880195 AGTTCAGCAGAAAGAAAAATAGCTAGA 59.120 33.333 0.00 0.00 35.08 2.43
4031 5998 8.824781 CACTGTATGAACCTTATTCTGATTCAG 58.175 37.037 7.38 7.38 33.09 3.02
4107 6081 3.271225 TCCCTACACTCCCATACAAGAGA 59.729 47.826 0.00 0.00 34.13 3.10
4421 6395 7.817418 TTAATGCCCTGTTCTGTAATTATCC 57.183 36.000 0.00 0.00 0.00 2.59
4502 6476 4.284490 TCTGTCTTTGTTATGTCCTCTGCT 59.716 41.667 0.00 0.00 0.00 4.24
4503 6477 5.480422 TCTGTCTTTGTTATGTCCTCTGCTA 59.520 40.000 0.00 0.00 0.00 3.49
4724 6698 2.291043 CCAGGGGAAGCGTGTACCT 61.291 63.158 0.00 0.00 0.00 3.08
4747 6723 9.167311 ACCTTGTTCATGTTGAGAATATTAGAC 57.833 33.333 0.00 0.00 0.00 2.59
4813 6790 7.867305 TGTTGTGTCAAATAGTTGTTCCTTA 57.133 32.000 2.43 0.00 36.07 2.69
4950 6928 7.604657 ACTAGGTTCATATGTTCCTAAGAGG 57.395 40.000 20.32 14.58 36.46 3.69
4979 6957 8.866093 TCCATGATAATCAAATCAAGCATGAAT 58.134 29.630 0.00 0.00 39.25 2.57
5065 7043 6.294120 CCGCTGCCAATAGATCAATTCAATTA 60.294 38.462 0.00 0.00 0.00 1.40
5079 7057 9.790344 ATCAATTCAATTATTTGTCCCAAACAA 57.210 25.926 0.00 0.00 46.11 2.83
5090 7068 4.148079 TGTCCCAAACAACAATCAGCATA 58.852 39.130 0.00 0.00 34.03 3.14
5094 7072 6.919662 GTCCCAAACAACAATCAGCATATATG 59.080 38.462 8.45 8.45 0.00 1.78
5137 7115 4.948341 TTGTCCAAGAGTACAACTAGCA 57.052 40.909 0.00 0.00 30.88 3.49
5183 7161 1.141858 GGAGGATCAGCCCCACTAAAG 59.858 57.143 0.00 0.00 36.25 1.85
5194 7172 7.073854 TCAGCCCCACTAAAGTAATCTACTAT 58.926 38.462 0.00 0.00 38.26 2.12
5315 7293 3.321682 TCCAGAACAGGCAAGGATTTTTG 59.678 43.478 0.00 0.00 0.00 2.44
5455 7433 9.409949 GATGTAAATTTTCTTGACTACGAATCG 57.590 33.333 0.00 0.00 0.00 3.34
5468 7446 6.471198 TGACTACGAATCGTATGTTTTGCTAG 59.529 38.462 16.23 4.74 41.53 3.42
5522 7500 8.757982 AATATTCACCTTAAGATGCAACATCT 57.242 30.769 3.36 4.26 0.00 2.90
5523 7501 8.757982 ATATTCACCTTAAGATGCAACATCTT 57.242 30.769 22.39 22.39 40.95 2.40
5524 7502 6.500684 TTCACCTTAAGATGCAACATCTTC 57.499 37.500 22.42 0.00 39.01 2.87
5525 7503 5.809001 TCACCTTAAGATGCAACATCTTCT 58.191 37.500 22.42 6.56 39.01 2.85
5526 7504 5.645067 TCACCTTAAGATGCAACATCTTCTG 59.355 40.000 22.42 16.44 39.01 3.02
5527 7505 5.645067 CACCTTAAGATGCAACATCTTCTGA 59.355 40.000 22.42 11.51 39.01 3.27
5528 7506 6.149973 CACCTTAAGATGCAACATCTTCTGAA 59.850 38.462 22.42 12.80 39.01 3.02
5529 7507 6.150140 ACCTTAAGATGCAACATCTTCTGAAC 59.850 38.462 22.42 0.00 39.01 3.18
5530 7508 6.373774 CCTTAAGATGCAACATCTTCTGAACT 59.626 38.462 22.42 4.01 39.01 3.01
5531 7509 5.624344 AAGATGCAACATCTTCTGAACTG 57.376 39.130 15.35 0.00 33.43 3.16
5607 7585 3.704566 TCTGGTAATGGCACTAGTTCGAT 59.295 43.478 0.00 0.00 0.00 3.59
5627 7605 5.937540 TCGATGACACATTTGGAATAACAGT 59.062 36.000 0.00 0.00 0.00 3.55
5658 7639 6.987403 ACAATTAAGCCTTTAGTCCCAAAA 57.013 33.333 0.00 0.00 0.00 2.44
5744 7725 8.097038 ACTTCTTAAGCTTCAGTTGTCATATGA 58.903 33.333 0.00 0.00 0.00 2.15
6182 8165 6.838198 TTTATCGCTGTACATTGGTCATAC 57.162 37.500 0.00 0.00 0.00 2.39
6186 8169 4.629634 TCGCTGTACATTGGTCATACTTTG 59.370 41.667 0.00 0.00 0.00 2.77
6196 8179 3.674997 GGTCATACTTTGAACAGCTGGA 58.325 45.455 19.93 0.00 42.03 3.86
6356 8346 4.513442 TGTTTCAAGAGTCATTATCGGGG 58.487 43.478 0.00 0.00 0.00 5.73
6361 8351 5.566469 TCAAGAGTCATTATCGGGGTTTTT 58.434 37.500 0.00 0.00 0.00 1.94
6487 8477 6.001460 TGTTATATGTGGTAAGCTATTGGCC 58.999 40.000 0.00 0.00 43.05 5.36
6500 8490 5.312079 AGCTATTGGCCTGTATCTTCAATC 58.688 41.667 3.32 0.00 43.05 2.67
6679 8669 1.532868 CTTTCAAAGCTCCGACTGTGG 59.467 52.381 0.00 0.00 0.00 4.17
6754 8751 2.325583 AGCCACGACACTCTTTTTGA 57.674 45.000 0.00 0.00 0.00 2.69
6755 8752 2.851195 AGCCACGACACTCTTTTTGAT 58.149 42.857 0.00 0.00 0.00 2.57
6759 8756 3.247648 CCACGACACTCTTTTTGATTCGT 59.752 43.478 0.00 0.00 35.99 3.85
6767 8764 6.014840 ACACTCTTTTTGATTCGTAGGGAGTA 60.015 38.462 0.00 0.00 31.55 2.59
6779 8777 7.707624 TTCGTAGGGAGTACTATTTTTCTCA 57.292 36.000 0.00 0.00 0.00 3.27
6781 8779 8.985315 TCGTAGGGAGTACTATTTTTCTCATA 57.015 34.615 0.00 0.00 0.00 2.15
6988 8986 5.921962 ATATTTTCTTTCCCCTTGCTGTC 57.078 39.130 0.00 0.00 0.00 3.51
7037 9035 3.319122 GGGGACAATGGTGAGATTTATGC 59.681 47.826 0.00 0.00 0.00 3.14
7163 9161 1.070038 CAATTGCCATCAAACACGCC 58.930 50.000 0.00 0.00 35.56 5.68
7197 9195 6.330278 TGTAGACAGATGTACCTCAAATTCG 58.670 40.000 0.81 0.00 0.00 3.34
7206 9204 6.687081 TGTACCTCAAATTCGAAGTTTTGT 57.313 33.333 18.77 13.68 34.88 2.83
7258 9256 7.335673 TCAAATATCTGTTCCACGCTCAATTTA 59.664 33.333 0.00 0.00 0.00 1.40
7307 9305 8.040716 AGTTAAATATATTGCGCCTATTCCAC 57.959 34.615 4.18 4.28 0.00 4.02
7337 9335 7.967854 TCTGTTAAATTGGCGAAACTATTGATG 59.032 33.333 0.00 0.00 0.00 3.07
7338 9336 7.821652 TGTTAAATTGGCGAAACTATTGATGA 58.178 30.769 0.00 0.00 0.00 2.92
7339 9337 8.465999 TGTTAAATTGGCGAAACTATTGATGAT 58.534 29.630 0.00 0.00 0.00 2.45
7340 9338 8.745837 GTTAAATTGGCGAAACTATTGATGATG 58.254 33.333 0.00 0.00 0.00 3.07
7341 9339 6.455360 AATTGGCGAAACTATTGATGATGT 57.545 33.333 0.00 0.00 0.00 3.06
7342 9340 4.880886 TGGCGAAACTATTGATGATGTG 57.119 40.909 0.00 0.00 0.00 3.21
7343 9341 4.512484 TGGCGAAACTATTGATGATGTGA 58.488 39.130 0.00 0.00 0.00 3.58
7344 9342 5.125356 TGGCGAAACTATTGATGATGTGAT 58.875 37.500 0.00 0.00 0.00 3.06
7345 9343 5.007921 TGGCGAAACTATTGATGATGTGATG 59.992 40.000 0.00 0.00 0.00 3.07
7346 9344 4.908156 GCGAAACTATTGATGATGTGATGC 59.092 41.667 0.00 0.00 0.00 3.91
7347 9345 5.277683 GCGAAACTATTGATGATGTGATGCT 60.278 40.000 0.00 0.00 0.00 3.79
7348 9346 6.073602 GCGAAACTATTGATGATGTGATGCTA 60.074 38.462 0.00 0.00 0.00 3.49
7349 9347 7.360691 GCGAAACTATTGATGATGTGATGCTAT 60.361 37.037 0.00 0.00 0.00 2.97
7350 9348 8.167345 CGAAACTATTGATGATGTGATGCTATC 58.833 37.037 0.00 0.00 0.00 2.08
7351 9349 7.918536 AACTATTGATGATGTGATGCTATCC 57.081 36.000 0.00 0.00 0.00 2.59
7352 9350 7.255199 ACTATTGATGATGTGATGCTATCCT 57.745 36.000 0.00 0.00 0.00 3.24
7353 9351 8.371571 ACTATTGATGATGTGATGCTATCCTA 57.628 34.615 0.00 0.00 0.00 2.94
7354 9352 8.990203 ACTATTGATGATGTGATGCTATCCTAT 58.010 33.333 0.00 0.00 0.00 2.57
7357 9355 7.968014 TGATGATGTGATGCTATCCTATACT 57.032 36.000 0.00 0.00 0.00 2.12
7358 9356 8.371571 TGATGATGTGATGCTATCCTATACTT 57.628 34.615 0.00 0.00 0.00 2.24
7359 9357 8.255905 TGATGATGTGATGCTATCCTATACTTG 58.744 37.037 0.00 0.00 0.00 3.16
7360 9358 7.544804 TGATGTGATGCTATCCTATACTTGT 57.455 36.000 0.00 0.00 0.00 3.16
7361 9359 7.381323 TGATGTGATGCTATCCTATACTTGTG 58.619 38.462 0.00 0.00 0.00 3.33
7362 9360 6.976934 TGTGATGCTATCCTATACTTGTGA 57.023 37.500 0.00 0.00 0.00 3.58
7363 9361 6.749139 TGTGATGCTATCCTATACTTGTGAC 58.251 40.000 0.00 0.00 0.00 3.67
7364 9362 6.323739 TGTGATGCTATCCTATACTTGTGACA 59.676 38.462 0.00 0.00 0.00 3.58
7365 9363 6.642950 GTGATGCTATCCTATACTTGTGACAC 59.357 42.308 0.00 0.00 0.00 3.67
7366 9364 6.551227 TGATGCTATCCTATACTTGTGACACT 59.449 38.462 7.20 0.00 0.00 3.55
7367 9365 7.724061 TGATGCTATCCTATACTTGTGACACTA 59.276 37.037 7.20 0.00 0.00 2.74
7368 9366 8.657387 ATGCTATCCTATACTTGTGACACTAT 57.343 34.615 7.20 0.00 0.00 2.12
7369 9367 8.112016 TGCTATCCTATACTTGTGACACTATC 57.888 38.462 7.20 0.00 0.00 2.08
7370 9368 7.176865 TGCTATCCTATACTTGTGACACTATCC 59.823 40.741 7.20 0.00 0.00 2.59
7371 9369 7.394923 GCTATCCTATACTTGTGACACTATCCT 59.605 40.741 7.20 0.00 0.00 3.24
7372 9370 9.961264 CTATCCTATACTTGTGACACTATCCTA 57.039 37.037 7.20 0.00 0.00 2.94
7375 9373 9.736414 TCCTATACTTGTGACACTATCCTATAC 57.264 37.037 7.20 0.00 0.00 1.47
7376 9374 9.742144 CCTATACTTGTGACACTATCCTATACT 57.258 37.037 7.20 0.00 0.00 2.12
7387 9385 9.857957 GACACTATCCTATACTAGTTAAATGCC 57.142 37.037 0.00 0.00 0.00 4.40
7388 9386 8.813951 ACACTATCCTATACTAGTTAAATGCCC 58.186 37.037 0.00 0.00 0.00 5.36
7389 9387 7.974501 CACTATCCTATACTAGTTAAATGCCCG 59.025 40.741 0.00 0.00 0.00 6.13
7390 9388 6.930068 ATCCTATACTAGTTAAATGCCCGT 57.070 37.500 0.00 0.00 0.00 5.28
7391 9389 6.092955 TCCTATACTAGTTAAATGCCCGTG 57.907 41.667 0.00 0.00 0.00 4.94
7392 9390 4.689345 CCTATACTAGTTAAATGCCCGTGC 59.311 45.833 0.00 0.00 38.26 5.34
7393 9391 1.365699 ACTAGTTAAATGCCCGTGCG 58.634 50.000 0.00 0.00 41.78 5.34
7394 9392 1.338389 ACTAGTTAAATGCCCGTGCGT 60.338 47.619 0.00 0.00 41.78 5.24
7396 9394 0.239879 AGTTAAATGCCCGTGCGTTG 59.760 50.000 0.00 0.00 45.88 4.10
7397 9395 1.081108 TTAAATGCCCGTGCGTTGC 60.081 52.632 0.00 0.00 45.88 4.17
7398 9396 1.519751 TTAAATGCCCGTGCGTTGCT 61.520 50.000 0.00 0.00 45.88 3.91
7505 9503 3.861113 CCGCATTTCTCATTTCACATTGG 59.139 43.478 0.00 0.00 0.00 3.16
7554 9552 9.119418 TCTCACAATGTTGTAATTTCTTCTTCA 57.881 29.630 0.00 0.00 39.91 3.02
7590 9588 5.132648 ACAGAAATAATAGCCATGGTCTCCA 59.867 40.000 14.67 0.00 38.19 3.86
7646 9644 1.821088 AGGGGTCAAGAGGAAGTTGT 58.179 50.000 0.00 0.00 0.00 3.32
7718 9716 7.876068 TGTGAACTATAATTCAAAGGAAGACGT 59.124 33.333 0.00 0.00 40.22 4.34
7749 9747 2.877786 TGCATGTTGACTGTCGTTCATT 59.122 40.909 2.98 0.00 0.00 2.57
7819 9817 5.441718 TCCAATTCTGATGCTTCTTAGGT 57.558 39.130 0.88 0.00 0.00 3.08
7902 9900 9.875691 CAAGTCATGCTATATAGGCAATAGTAA 57.124 33.333 11.72 0.00 43.14 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.164219 GTCAATCACGGGCATCAATGTT 59.836 45.455 0.00 0.00 0.00 2.71
20 21 2.495366 TTCCCGTCCGGTCAATCACG 62.495 60.000 0.00 2.12 0.00 4.35
22 23 1.594833 CTTCCCGTCCGGTCAATCA 59.405 57.895 0.00 0.00 0.00 2.57
69 70 2.251893 GTTTCTCAGGACGCTACGAAG 58.748 52.381 0.00 0.00 0.00 3.79
70 71 1.068055 GGTTTCTCAGGACGCTACGAA 60.068 52.381 0.00 0.00 0.00 3.85
75 86 0.759346 AGTTGGTTTCTCAGGACGCT 59.241 50.000 0.00 0.00 0.00 5.07
81 92 0.250295 TGCCGGAGTTGGTTTCTCAG 60.250 55.000 5.05 0.00 34.04 3.35
82 93 0.250295 CTGCCGGAGTTGGTTTCTCA 60.250 55.000 5.05 0.00 34.04 3.27
100 111 2.123428 GCTTCAATGCGGCCCATCT 61.123 57.895 7.12 0.00 31.43 2.90
143 154 3.883997 CTTAAAAAGCCGCAGCCAA 57.116 47.368 0.00 0.00 41.25 4.52
155 166 1.079875 CGCTCGCGTAGGGCTTAAAA 61.080 55.000 5.77 0.00 46.47 1.52
169 180 1.799519 GACAGCTGTCTGACGCTCG 60.800 63.158 34.54 16.78 42.95 5.03
184 195 1.075542 CGCAATAGCCTTGTTCGACA 58.924 50.000 0.00 0.00 37.52 4.35
186 197 1.366111 GCCGCAATAGCCTTGTTCGA 61.366 55.000 0.00 0.00 37.52 3.71
210 221 0.464036 CCAGTAGCGTAAGGATGCCA 59.536 55.000 0.00 0.00 38.47 4.92
211 222 0.750850 TCCAGTAGCGTAAGGATGCC 59.249 55.000 0.00 0.00 38.47 4.40
212 223 1.269831 CCTCCAGTAGCGTAAGGATGC 60.270 57.143 0.00 0.00 37.92 3.91
220 231 2.045131 GTCGTCCCTCCAGTAGCGT 61.045 63.158 0.00 0.00 0.00 5.07
224 235 1.191535 CCATTGTCGTCCCTCCAGTA 58.808 55.000 0.00 0.00 0.00 2.74
225 236 1.983224 CCATTGTCGTCCCTCCAGT 59.017 57.895 0.00 0.00 0.00 4.00
226 237 1.450312 GCCATTGTCGTCCCTCCAG 60.450 63.158 0.00 0.00 0.00 3.86
235 246 1.430632 GTCCATGCTGCCATTGTCG 59.569 57.895 0.00 0.00 0.00 4.35
243 254 4.465512 CGTTGGCGTCCATGCTGC 62.466 66.667 0.00 0.00 31.53 5.25
264 278 2.281761 CACCCTGTCCTGCCACAC 60.282 66.667 0.00 0.00 0.00 3.82
267 281 3.249189 GACCACCCTGTCCTGCCA 61.249 66.667 0.00 0.00 0.00 4.92
278 292 0.249398 ACCTCGTAAGCATGACCACC 59.751 55.000 0.00 0.00 37.18 4.61
280 294 1.262417 TCACCTCGTAAGCATGACCA 58.738 50.000 0.00 0.00 37.18 4.02
333 347 9.715121 TGATATTTTGACCGTTCTACTAAAACT 57.285 29.630 0.00 0.00 0.00 2.66
337 351 9.529325 CAGATGATATTTTGACCGTTCTACTAA 57.471 33.333 0.00 0.00 0.00 2.24
338 352 8.692710 ACAGATGATATTTTGACCGTTCTACTA 58.307 33.333 0.00 0.00 0.00 1.82
339 353 7.556844 ACAGATGATATTTTGACCGTTCTACT 58.443 34.615 0.00 0.00 0.00 2.57
340 354 7.772332 ACAGATGATATTTTGACCGTTCTAC 57.228 36.000 0.00 0.00 0.00 2.59
342 356 7.687941 AAACAGATGATATTTTGACCGTTCT 57.312 32.000 0.00 0.00 0.00 3.01
343 357 9.438291 CATAAACAGATGATATTTTGACCGTTC 57.562 33.333 0.00 0.00 0.00 3.95
398 1963 8.190122 CCAGACGAAATTCATTCAAATTGGATA 58.810 33.333 0.00 0.00 37.96 2.59
401 1966 5.577945 CCCAGACGAAATTCATTCAAATTGG 59.422 40.000 0.00 0.00 37.96 3.16
403 1968 6.345096 ACCCAGACGAAATTCATTCAAATT 57.655 33.333 0.00 0.00 37.96 1.82
404 1969 5.982890 ACCCAGACGAAATTCATTCAAAT 57.017 34.783 0.00 0.00 37.96 2.32
411 1976 3.628487 ACGAAAAACCCAGACGAAATTCA 59.372 39.130 0.00 0.00 0.00 2.57
413 1978 5.952526 ATACGAAAAACCCAGACGAAATT 57.047 34.783 0.00 0.00 0.00 1.82
421 1986 4.036971 TGGACAACAATACGAAAAACCCAG 59.963 41.667 0.00 0.00 0.00 4.45
422 1987 3.952323 TGGACAACAATACGAAAAACCCA 59.048 39.130 0.00 0.00 0.00 4.51
423 1988 4.571372 TGGACAACAATACGAAAAACCC 57.429 40.909 0.00 0.00 0.00 4.11
424 1989 8.751302 ATATTTGGACAACAATACGAAAAACC 57.249 30.769 0.00 0.00 39.21 3.27
448 2013 8.103305 GGCCGTCATCCAATAATATCCATATAT 58.897 37.037 0.00 0.00 0.00 0.86
453 2018 3.587061 AGGCCGTCATCCAATAATATCCA 59.413 43.478 0.00 0.00 0.00 3.41
454 2019 4.222124 AGGCCGTCATCCAATAATATCC 57.778 45.455 0.00 0.00 0.00 2.59
457 2022 4.015872 GGAAGGCCGTCATCCAATAATA 57.984 45.455 20.72 0.00 33.30 0.98
459 2024 2.341846 GGAAGGCCGTCATCCAATAA 57.658 50.000 20.72 0.00 33.30 1.40
498 2063 1.380785 TGTTCGCGGATAGGGGACT 60.381 57.895 6.13 0.00 41.50 3.85
499 2064 1.067582 CTGTTCGCGGATAGGGGAC 59.932 63.158 6.13 0.00 41.33 4.46
502 2067 1.401148 CGTATCTGTTCGCGGATAGGG 60.401 57.143 11.60 0.04 43.82 3.53
508 2074 0.852777 CAATCCGTATCTGTTCGCGG 59.147 55.000 6.13 0.00 44.95 6.46
529 2095 6.819649 ACATCTCCAACGATAATCCGTAAAAA 59.180 34.615 0.00 0.00 42.54 1.94
530 2096 6.342906 ACATCTCCAACGATAATCCGTAAAA 58.657 36.000 0.00 0.00 42.54 1.52
535 2101 3.005897 AGGACATCTCCAACGATAATCCG 59.994 47.826 0.00 0.00 39.39 4.18
537 2103 8.524487 ACTATTAGGACATCTCCAACGATAATC 58.476 37.037 0.00 0.00 39.39 1.75
538 2104 8.307483 CACTATTAGGACATCTCCAACGATAAT 58.693 37.037 0.00 0.00 39.39 1.28
540 2106 6.776116 ACACTATTAGGACATCTCCAACGATA 59.224 38.462 0.00 0.00 39.39 2.92
541 2107 5.598830 ACACTATTAGGACATCTCCAACGAT 59.401 40.000 0.00 0.00 39.39 3.73
542 2108 4.954202 ACACTATTAGGACATCTCCAACGA 59.046 41.667 0.00 0.00 39.39 3.85
543 2109 5.043903 CACACTATTAGGACATCTCCAACG 58.956 45.833 0.00 0.00 39.39 4.10
544 2110 6.222038 TCACACTATTAGGACATCTCCAAC 57.778 41.667 0.00 0.00 39.39 3.77
546 2112 8.727100 ATAATCACACTATTAGGACATCTCCA 57.273 34.615 0.00 0.00 39.39 3.86
548 2114 9.776158 CGTATAATCACACTATTAGGACATCTC 57.224 37.037 0.00 0.00 0.00 2.75
549 2115 9.516546 TCGTATAATCACACTATTAGGACATCT 57.483 33.333 0.00 0.00 0.00 2.90
550 2116 9.776158 CTCGTATAATCACACTATTAGGACATC 57.224 37.037 0.00 0.00 0.00 3.06
551 2117 8.244802 GCTCGTATAATCACACTATTAGGACAT 58.755 37.037 0.00 0.00 0.00 3.06
552 2118 7.229907 TGCTCGTATAATCACACTATTAGGACA 59.770 37.037 0.00 0.00 0.00 4.02
553 2119 7.591165 TGCTCGTATAATCACACTATTAGGAC 58.409 38.462 0.00 0.00 0.00 3.85
554 2120 7.754851 TGCTCGTATAATCACACTATTAGGA 57.245 36.000 0.00 0.00 0.00 2.94
555 2121 8.244113 TGATGCTCGTATAATCACACTATTAGG 58.756 37.037 0.00 0.00 0.00 2.69
556 2122 9.626045 TTGATGCTCGTATAATCACACTATTAG 57.374 33.333 0.00 0.00 30.26 1.73
608 2174 1.199789 TGCGCTTTACTGGAATGCTTG 59.800 47.619 9.73 0.00 36.33 4.01
634 2201 4.722526 TTGATGATGGGGGAATCGTTAT 57.277 40.909 0.00 0.00 0.00 1.89
745 2322 3.386237 GGCTGGAGTCGCTGGAGT 61.386 66.667 0.00 0.00 0.00 3.85
773 2350 4.270482 ACACGTGAGAGGTGTGGA 57.730 55.556 25.01 0.00 44.42 4.02
776 2353 0.828022 TTTCCACACGTGAGAGGTGT 59.172 50.000 25.01 0.00 46.71 4.16
777 2354 1.948104 TTTTCCACACGTGAGAGGTG 58.052 50.000 25.01 9.49 39.65 4.00
778 2355 2.702592 TTTTTCCACACGTGAGAGGT 57.297 45.000 25.01 0.00 0.00 3.85
887 2481 7.376072 GGCGGACAATAAATAAAAATCTCGAAG 59.624 37.037 0.00 0.00 0.00 3.79
899 2493 2.485835 CCGGGAAGGCGGACAATAAATA 60.486 50.000 0.00 0.00 0.00 1.40
900 2494 1.675552 CGGGAAGGCGGACAATAAAT 58.324 50.000 0.00 0.00 0.00 1.40
901 2495 0.393267 CCGGGAAGGCGGACAATAAA 60.393 55.000 0.00 0.00 0.00 1.40
902 2496 1.222387 CCGGGAAGGCGGACAATAA 59.778 57.895 0.00 0.00 0.00 1.40
903 2497 1.266160 TTCCGGGAAGGCGGACAATA 61.266 55.000 5.09 0.00 40.77 1.90
919 2515 4.400961 AGAGGCAGCTGCGGTTCC 62.401 66.667 31.19 17.57 43.26 3.62
922 2518 4.079850 CAGAGAGGCAGCTGCGGT 62.080 66.667 31.19 21.58 43.26 5.68
1221 2824 3.992317 GGTCGATCTAGGGGGCGC 61.992 72.222 0.00 0.00 0.00 6.53
1222 2825 3.671411 CGGTCGATCTAGGGGGCG 61.671 72.222 0.00 0.00 0.00 6.13
1225 2828 3.760917 GACCGGTCGATCTAGGGG 58.239 66.667 20.85 0.00 0.00 4.79
1372 3019 4.508861 GCGGTTTGAAGTACAGTGAACTAA 59.491 41.667 0.00 0.00 0.00 2.24
1392 3042 1.070376 CATACAGAATCATGTGCGCGG 60.070 52.381 8.83 0.00 34.56 6.46
1428 3096 2.780643 CAGATCGCAACGCCAGTG 59.219 61.111 0.00 0.00 0.00 3.66
1633 3473 5.757320 TGCAAAATACCACCATGAAAACAAG 59.243 36.000 0.00 0.00 0.00 3.16
1675 3517 3.047877 GGTTCACCTTCACGGGCG 61.048 66.667 0.00 0.00 36.97 6.13
1696 3538 3.306502 CCAATATGATGCAAAGGCCATCC 60.307 47.826 5.01 0.00 40.13 3.51
1850 3692 8.995027 ACCCATTCAAATTTGCTGATATAGTA 57.005 30.769 13.54 0.00 0.00 1.82
1851 3693 7.902920 ACCCATTCAAATTTGCTGATATAGT 57.097 32.000 13.54 1.01 0.00 2.12
1852 3694 7.654520 CCAACCCATTCAAATTTGCTGATATAG 59.345 37.037 13.54 1.15 0.00 1.31
1869 3713 2.028561 AATGAAGCACCCAACCCATT 57.971 45.000 0.00 0.00 0.00 3.16
1875 3719 0.316841 GCCGAAAATGAAGCACCCAA 59.683 50.000 0.00 0.00 0.00 4.12
1886 3730 7.933577 TGATCTTCTATCTGTAATGCCGAAAAT 59.066 33.333 0.00 0.00 0.00 1.82
2177 4022 4.026356 AGAGCAATACTTTCTTGGCTGT 57.974 40.909 0.00 0.00 0.00 4.40
2229 4074 3.944015 ACTTCAGCCTGCAAGATAATGAC 59.056 43.478 9.81 0.00 34.07 3.06
2781 4627 9.746457 AGATACAAGCATACATCTATCTAGACA 57.254 33.333 0.00 0.00 34.72 3.41
2895 4748 6.530913 AGCAGACATAGCATAAATGTTACG 57.469 37.500 0.00 0.00 37.69 3.18
3073 4926 7.872113 AAGAATTAAGGTAAGCAAGATCAGG 57.128 36.000 0.00 0.00 0.00 3.86
3194 5047 4.450419 CAGCAACTAAGAGAGTGGTTGAAG 59.550 45.833 8.55 0.00 41.69 3.02
3234 5087 1.094785 GGCGGTCAAATACATGCAGT 58.905 50.000 0.00 0.00 33.84 4.40
3471 5399 3.004629 CCAACAACAATGCAACAGAGCTA 59.995 43.478 0.00 0.00 34.99 3.32
3582 5510 9.829507 ATTCAAAAGGAACATTTATGTGAACAA 57.170 25.926 0.00 0.00 41.61 2.83
3583 5511 9.258826 CATTCAAAAGGAACATTTATGTGAACA 57.741 29.630 0.00 0.00 41.61 3.18
3595 5523 3.252215 CGTACAGGCATTCAAAAGGAACA 59.748 43.478 0.00 0.00 38.60 3.18
3718 5647 3.319137 TTGATCTTGTCCCGAGTTCAG 57.681 47.619 0.00 0.00 28.94 3.02
3741 5670 5.537674 AGCAACCATGACAAAGAAGATTTCT 59.462 36.000 0.00 0.00 43.15 2.52
3835 5764 7.615582 TCCATTTGATATCTTGAGTGAACAC 57.384 36.000 3.98 0.00 0.00 3.32
3879 5835 6.127647 GGACTGCTGGTTTCATTTGATAATGA 60.128 38.462 0.00 0.00 46.38 2.57
3898 5854 2.158986 AGTGAGCTGATGTATGGACTGC 60.159 50.000 0.00 0.00 0.00 4.40
3903 5859 3.643320 TCCCTAAGTGAGCTGATGTATGG 59.357 47.826 0.00 0.00 0.00 2.74
3945 5912 9.438228 GTTCTAAAACCTTTCTGTCTAGCTATT 57.562 33.333 0.00 0.00 0.00 1.73
3946 5913 8.594550 TGTTCTAAAACCTTTCTGTCTAGCTAT 58.405 33.333 0.00 0.00 34.28 2.97
3947 5914 7.959175 TGTTCTAAAACCTTTCTGTCTAGCTA 58.041 34.615 0.00 0.00 34.28 3.32
3948 5915 6.827727 TGTTCTAAAACCTTTCTGTCTAGCT 58.172 36.000 0.00 0.00 34.28 3.32
3949 5916 7.674471 ATGTTCTAAAACCTTTCTGTCTAGC 57.326 36.000 0.00 0.00 34.28 3.42
3952 5919 8.837389 GTGTTATGTTCTAAAACCTTTCTGTCT 58.163 33.333 0.00 0.00 34.28 3.41
3953 5920 8.617809 TGTGTTATGTTCTAAAACCTTTCTGTC 58.382 33.333 0.00 0.00 34.28 3.51
3954 5921 8.514330 TGTGTTATGTTCTAAAACCTTTCTGT 57.486 30.769 0.00 0.00 34.28 3.41
4031 5998 8.661257 AGTGCTTTTTAACCAAACACAAATAAC 58.339 29.630 0.00 0.00 0.00 1.89
4316 6290 8.878769 GTTATGGACAAAATGAACACAAAGTTT 58.121 29.630 0.00 0.00 41.51 2.66
4724 6698 9.725019 ACTGTCTAATATTCTCAACATGAACAA 57.275 29.630 0.00 0.00 0.00 2.83
4747 6723 4.034048 ACAAAACTGTCGTTTGAGCTACTG 59.966 41.667 10.92 0.00 42.28 2.74
4772 6748 4.330074 CACAACATTTCGGAAGCTACTAGG 59.670 45.833 0.00 0.00 0.00 3.02
4813 6790 9.880254 TTTAGGGGGTTTAAACACTAATAAACT 57.120 29.630 19.63 9.32 40.30 2.66
4821 6798 8.838741 TGATATAGTTTAGGGGGTTTAAACACT 58.161 33.333 19.63 15.35 41.31 3.55
4822 6799 9.636789 ATGATATAGTTTAGGGGGTTTAAACAC 57.363 33.333 19.57 16.22 41.31 3.32
4823 6800 9.856162 GATGATATAGTTTAGGGGGTTTAAACA 57.144 33.333 19.57 0.00 41.31 2.83
4826 6803 9.232882 ACAGATGATATAGTTTAGGGGGTTTAA 57.767 33.333 0.00 0.00 0.00 1.52
4828 6805 7.202195 GGACAGATGATATAGTTTAGGGGGTTT 60.202 40.741 0.00 0.00 0.00 3.27
4950 6928 8.761497 CATGCTTGATTTGATTATCATGGAAAC 58.239 33.333 0.00 0.00 35.03 2.78
5079 7057 9.783081 TCACTTTGATACATATATGCTGATTGT 57.217 29.630 12.79 1.98 0.00 2.71
5123 7101 9.804758 GTAGTATCATTTTGCTAGTTGTACTCT 57.195 33.333 0.00 0.00 0.00 3.24
5137 7115 9.424319 CAATGTATCGCCTAGTAGTATCATTTT 57.576 33.333 0.00 0.00 0.00 1.82
5194 7172 7.133133 AGTTAGACACCCTTTCTTCTTTGTA 57.867 36.000 0.00 0.00 0.00 2.41
5315 7293 1.280421 AGGGCATCAGAGGAAAGTGAC 59.720 52.381 0.00 0.00 0.00 3.67
5455 7433 6.909909 AGTTTAGCCAACTAGCAAAACATAC 58.090 36.000 0.00 0.00 44.56 2.39
5513 7491 5.610398 TCTAACAGTTCAGAAGATGTTGCA 58.390 37.500 18.15 6.78 36.59 4.08
5522 7500 7.750229 ATCATGCTTTTCTAACAGTTCAGAA 57.250 32.000 0.00 0.00 0.00 3.02
5523 7501 7.229306 ACAATCATGCTTTTCTAACAGTTCAGA 59.771 33.333 0.00 0.00 0.00 3.27
5524 7502 7.365741 ACAATCATGCTTTTCTAACAGTTCAG 58.634 34.615 0.00 0.00 0.00 3.02
5525 7503 7.275888 ACAATCATGCTTTTCTAACAGTTCA 57.724 32.000 0.00 0.00 0.00 3.18
5526 7504 8.579682 AAACAATCATGCTTTTCTAACAGTTC 57.420 30.769 0.00 0.00 0.00 3.01
5528 7506 9.630098 CATAAACAATCATGCTTTTCTAACAGT 57.370 29.630 0.00 0.00 0.00 3.55
5529 7507 9.630098 ACATAAACAATCATGCTTTTCTAACAG 57.370 29.630 0.00 0.00 0.00 3.16
5530 7508 9.409312 CACATAAACAATCATGCTTTTCTAACA 57.591 29.630 0.00 0.00 0.00 2.41
5531 7509 9.410556 ACACATAAACAATCATGCTTTTCTAAC 57.589 29.630 0.00 0.00 0.00 2.34
5658 7639 1.207329 CCTCTAGCCTACGCCAACTTT 59.793 52.381 0.00 0.00 34.57 2.66
5666 7647 1.136500 GGGTTTCACCTCTAGCCTACG 59.864 57.143 0.00 0.00 38.64 3.51
6356 8346 5.107259 GGGACGAATGTGGCAAATTAAAAAC 60.107 40.000 2.11 0.00 0.00 2.43
6361 8351 2.490115 GTGGGACGAATGTGGCAAATTA 59.510 45.455 2.11 0.00 0.00 1.40
6487 8477 9.852091 TTCTATCATGATCGATTGAAGATACAG 57.148 33.333 12.53 0.00 33.92 2.74
6679 8669 1.153549 CGGAGGGAGTAAGCAGCAC 60.154 63.158 0.00 0.00 0.00 4.40
6717 8712 6.018507 TCGTGGCTTTAGTTCAGTTTTAGTTC 60.019 38.462 0.00 0.00 0.00 3.01
6754 8751 8.302515 TGAGAAAAATAGTACTCCCTACGAAT 57.697 34.615 0.00 0.00 0.00 3.34
6755 8752 7.707624 TGAGAAAAATAGTACTCCCTACGAA 57.292 36.000 0.00 0.00 0.00 3.85
6795 8793 6.818644 AGTAACACGATGAGCTGACAATTTAT 59.181 34.615 0.00 0.00 0.00 1.40
6799 8797 4.193826 AGTAACACGATGAGCTGACAAT 57.806 40.909 0.00 0.00 0.00 2.71
7017 9015 5.779529 ATGCATAAATCTCACCATTGTCC 57.220 39.130 0.00 0.00 0.00 4.02
7080 9078 2.927477 GCGAGGATACAATCGTTCACAA 59.073 45.455 0.00 0.00 40.97 3.33
7155 9153 0.387112 CATTCATGTGCGGCGTGTTT 60.387 50.000 9.37 0.00 35.64 2.83
7163 9161 3.867493 ACATCTGTCTACATTCATGTGCG 59.133 43.478 2.50 0.00 41.89 5.34
7197 9195 6.431234 ACATGACCTCAGGATTACAAAACTTC 59.569 38.462 0.00 0.00 0.00 3.01
7206 9204 5.773091 TGGTACTACATGACCTCAGGATTA 58.227 41.667 0.00 0.00 36.62 1.75
7258 9256 1.078143 GCATGAGGCCCGAGACTTT 60.078 57.895 0.00 0.00 36.11 2.66
7307 9305 2.823196 TCGCCAATTTAACAGATGCG 57.177 45.000 0.00 0.00 41.68 4.73
7312 9310 7.967854 TCATCAATAGTTTCGCCAATTTAACAG 59.032 33.333 0.00 0.00 0.00 3.16
7337 9335 7.543868 GTCACAAGTATAGGATAGCATCACATC 59.456 40.741 0.00 0.00 0.00 3.06
7338 9336 7.015584 TGTCACAAGTATAGGATAGCATCACAT 59.984 37.037 0.00 0.00 0.00 3.21
7339 9337 6.323739 TGTCACAAGTATAGGATAGCATCACA 59.676 38.462 0.00 0.00 0.00 3.58
7340 9338 6.642950 GTGTCACAAGTATAGGATAGCATCAC 59.357 42.308 0.00 0.00 0.00 3.06
7341 9339 6.551227 AGTGTCACAAGTATAGGATAGCATCA 59.449 38.462 5.62 0.00 0.00 3.07
7342 9340 6.987386 AGTGTCACAAGTATAGGATAGCATC 58.013 40.000 5.62 0.00 0.00 3.91
7343 9341 6.985653 AGTGTCACAAGTATAGGATAGCAT 57.014 37.500 5.62 0.00 0.00 3.79
7344 9342 7.176865 GGATAGTGTCACAAGTATAGGATAGCA 59.823 40.741 5.62 0.00 0.00 3.49
7345 9343 7.394923 AGGATAGTGTCACAAGTATAGGATAGC 59.605 40.741 5.62 0.00 0.00 2.97
7346 9344 8.871629 AGGATAGTGTCACAAGTATAGGATAG 57.128 38.462 5.62 0.00 0.00 2.08
7349 9347 9.736414 GTATAGGATAGTGTCACAAGTATAGGA 57.264 37.037 5.62 0.00 0.00 2.94
7350 9348 9.742144 AGTATAGGATAGTGTCACAAGTATAGG 57.258 37.037 5.62 0.00 0.00 2.57
7361 9359 9.857957 GGCATTTAACTAGTATAGGATAGTGTC 57.142 37.037 0.00 0.00 44.97 3.67
7362 9360 8.813951 GGGCATTTAACTAGTATAGGATAGTGT 58.186 37.037 0.00 0.00 44.97 3.55
7363 9361 7.974501 CGGGCATTTAACTAGTATAGGATAGTG 59.025 40.741 0.00 0.00 44.97 2.74
7364 9362 7.673082 ACGGGCATTTAACTAGTATAGGATAGT 59.327 37.037 0.00 0.00 44.97 2.12
7365 9363 7.974501 CACGGGCATTTAACTAGTATAGGATAG 59.025 40.741 0.00 0.00 44.97 2.08
7366 9364 7.578189 GCACGGGCATTTAACTAGTATAGGATA 60.578 40.741 3.77 0.00 41.08 2.59
7367 9365 6.698380 CACGGGCATTTAACTAGTATAGGAT 58.302 40.000 0.00 0.00 44.97 3.24
7368 9366 5.510179 GCACGGGCATTTAACTAGTATAGGA 60.510 44.000 3.77 0.00 41.08 2.94
7369 9367 4.689345 GCACGGGCATTTAACTAGTATAGG 59.311 45.833 3.77 0.00 41.08 2.57
7370 9368 4.384846 CGCACGGGCATTTAACTAGTATAG 59.615 45.833 11.77 0.00 42.35 1.31
7371 9369 4.202141 ACGCACGGGCATTTAACTAGTATA 60.202 41.667 11.77 0.00 41.24 1.47
7372 9370 3.128349 CGCACGGGCATTTAACTAGTAT 58.872 45.455 11.77 0.00 41.24 2.12
7373 9371 2.094078 ACGCACGGGCATTTAACTAGTA 60.094 45.455 11.77 0.00 41.24 1.82
7374 9372 1.338389 ACGCACGGGCATTTAACTAGT 60.338 47.619 11.77 0.00 41.24 2.57
7375 9373 1.365699 ACGCACGGGCATTTAACTAG 58.634 50.000 11.77 0.00 41.24 2.57
7376 9374 1.465387 CAACGCACGGGCATTTAACTA 59.535 47.619 11.77 0.00 41.24 2.24
7377 9375 0.239879 CAACGCACGGGCATTTAACT 59.760 50.000 11.77 0.00 41.24 2.24
7378 9376 1.341369 GCAACGCACGGGCATTTAAC 61.341 55.000 11.77 0.00 41.24 2.01
7379 9377 1.081108 GCAACGCACGGGCATTTAA 60.081 52.632 11.77 0.00 41.24 1.52
7380 9378 0.673956 TAGCAACGCACGGGCATTTA 60.674 50.000 11.77 0.00 41.24 1.40
7381 9379 1.969064 TAGCAACGCACGGGCATTT 60.969 52.632 11.77 0.00 41.24 2.32
7382 9380 2.359354 TAGCAACGCACGGGCATT 60.359 55.556 11.77 0.00 41.24 3.56
7383 9381 3.124921 GTAGCAACGCACGGGCAT 61.125 61.111 11.77 0.00 41.24 4.40
7396 9394 1.601759 ATGCATCATGCCCCGTAGC 60.602 57.895 7.30 0.00 44.23 3.58
7397 9395 0.535780 ACATGCATCATGCCCCGTAG 60.536 55.000 7.30 0.00 44.80 3.51
7398 9396 0.761802 TACATGCATCATGCCCCGTA 59.238 50.000 7.30 2.99 44.80 4.02
7404 9402 7.652300 ATCAATTCATTTACATGCATCATGC 57.348 32.000 1.35 1.35 44.80 4.06
7469 9467 2.755469 GCGGCCCATGACACCATT 60.755 61.111 0.00 0.00 0.00 3.16
7527 9525 9.950680 GAAGAAGAAATTACAACATTGTGAGAA 57.049 29.630 7.53 0.00 42.31 2.87
7529 9527 9.173939 GTGAAGAAGAAATTACAACATTGTGAG 57.826 33.333 7.53 0.00 42.31 3.51
7536 9534 7.873719 TTCAGGTGAAGAAGAAATTACAACA 57.126 32.000 0.00 0.00 0.00 3.33
7621 9619 1.553706 TCCTCTTGACCCCTACGAAC 58.446 55.000 0.00 0.00 0.00 3.95
7625 9623 2.638363 ACAACTTCCTCTTGACCCCTAC 59.362 50.000 0.00 0.00 0.00 3.18
7646 9644 2.299582 CAAATTCAGTGTCCCCATGCAA 59.700 45.455 0.00 0.00 0.00 4.08
7695 9693 8.932791 TGAACGTCTTCCTTTGAATTATAGTTC 58.067 33.333 1.17 1.17 34.24 3.01
7718 9716 1.264020 GTCAACATGCAGCGAAGTGAA 59.736 47.619 0.00 0.00 0.00 3.18
7749 9747 7.147983 GGGTCACACTTATATTGCCAACATAAA 60.148 37.037 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.