Multiple sequence alignment - TraesCS3B01G457500

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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 TraesCS3B01G457500 chr3B 100.000 4675 0 0 1 4675 699697649 699692975 0.000000e+00 8634.0
1 TraesCS3B01G457500 chr3B 89.744 858 85 3 1 858 181468262 181469116 0.000000e+00 1094.0
2 TraesCS3B01G457500 chr3B 92.076 631 43 4 3556 4185 699285542 699284918 0.000000e+00 881.0
3 TraesCS3B01G457500 chr3B 97.694 477 11 0 2701 3177 699287226 699286750 0.000000e+00 821.0
4 TraesCS3B01G457500 chr3B 96.452 310 3 3 4367 4675 699284921 699284619 5.400000e-139 505.0
5 TraesCS3B01G457500 chr3B 95.708 233 9 1 3326 3557 699285933 699285701 1.590000e-99 374.0
6 TraesCS3B01G457500 chr3B 95.395 152 7 0 2565 2716 699297060 699296909 4.670000e-60 243.0
7 TraesCS3B01G457500 chr3D 91.743 3064 186 22 906 3920 529141345 529138300 0.000000e+00 4194.0
8 TraesCS3B01G457500 chr3D 95.487 421 19 0 2627 3047 528799763 528800183 0.000000e+00 673.0
9 TraesCS3B01G457500 chr3D 84.804 408 46 14 3535 3927 528806132 528806538 3.390000e-106 396.0
10 TraesCS3B01G457500 chr3D 91.154 260 11 4 3914 4173 529136935 529136688 4.480000e-90 342.0
11 TraesCS3B01G457500 chr3D 90.800 250 11 6 3043 3292 528804735 528804972 1.620000e-84 324.0
12 TraesCS3B01G457500 chr3D 84.685 333 19 15 4367 4674 529136682 529136357 2.110000e-78 303.0
13 TraesCS3B01G457500 chr3D 90.583 223 21 0 3290 3512 528805925 528806147 3.540000e-76 296.0
14 TraesCS3B01G457500 chr3D 87.755 245 25 4 4432 4675 528807197 528807437 9.900000e-72 281.0
15 TraesCS3B01G457500 chr3D 92.265 181 4 2 4001 4181 528806937 528807107 1.000000e-61 248.0
16 TraesCS3B01G457500 chr3D 96.154 52 2 0 2564 2615 528794878 528794929 8.330000e-13 86.1
17 TraesCS3B01G457500 chr3A 87.392 2197 190 46 2022 4184 662813723 662815866 0.000000e+00 2442.0
18 TraesCS3B01G457500 chr3A 88.498 1478 115 36 2728 4184 663293691 663292248 0.000000e+00 1736.0
19 TraesCS3B01G457500 chr3A 91.322 968 50 6 1783 2734 663296593 663295644 0.000000e+00 1291.0
20 TraesCS3B01G457500 chr3A 90.677 901 61 16 906 1789 663297724 663296830 0.000000e+00 1177.0
21 TraesCS3B01G457500 chr3A 83.652 471 48 9 3251 3718 662820445 662820889 2.600000e-112 416.0
22 TraesCS3B01G457500 chr3A 94.068 118 1 2 4563 4674 663291766 663291649 1.730000e-39 174.0
23 TraesCS3B01G457500 chr3A 87.719 114 14 0 3138 3251 662820249 662820362 2.930000e-27 134.0
24 TraesCS3B01G457500 chr3A 94.048 84 3 1 4563 4644 662816002 662816085 4.910000e-25 126.0
25 TraesCS3B01G457500 chr2B 97.436 858 22 0 1 858 30102908 30102051 0.000000e+00 1463.0
26 TraesCS3B01G457500 chr2B 92.123 584 46 0 275 858 72595304 72594721 0.000000e+00 824.0
27 TraesCS3B01G457500 chr2B 82.168 858 149 4 2 858 38425218 38426072 0.000000e+00 734.0
28 TraesCS3B01G457500 chr2B 90.175 285 27 1 1 285 72598510 72598227 2.050000e-98 370.0
29 TraesCS3B01G457500 chr5A 90.793 858 79 0 1 858 504919457 504920314 0.000000e+00 1147.0
30 TraesCS3B01G457500 chr5A 90.793 858 79 0 1 858 510441640 510440783 0.000000e+00 1147.0
31 TraesCS3B01G457500 chr5A 93.782 193 12 0 4184 4376 471707271 471707079 1.650000e-74 291.0
32 TraesCS3B01G457500 chr6B 92.371 603 45 1 256 858 643533905 643533304 0.000000e+00 857.0
33 TraesCS3B01G457500 chr6B 94.709 189 10 0 4180 4368 33072777 33072965 1.270000e-75 294.0
34 TraesCS3B01G457500 chr7A 84.687 862 123 8 1 858 610215554 610216410 0.000000e+00 852.0
35 TraesCS3B01G457500 chr2A 81.787 862 150 6 1 858 684126936 684126078 0.000000e+00 715.0
36 TraesCS3B01G457500 chr1A 95.722 187 8 0 4181 4367 582559479 582559665 7.600000e-78 302.0
37 TraesCS3B01G457500 chr4D 94.792 192 10 0 4184 4375 503922207 503922016 2.730000e-77 300.0
38 TraesCS3B01G457500 chr2D 95.263 190 7 2 4184 4372 591983011 591983199 2.730000e-77 300.0
39 TraesCS3B01G457500 chr4B 95.187 187 9 0 4181 4367 625223526 625223712 3.540000e-76 296.0
40 TraesCS3B01G457500 chrUn 94.709 189 10 0 4184 4372 255618818 255618630 1.270000e-75 294.0
41 TraesCS3B01G457500 chr5B 93.878 196 11 1 4180 4375 588535270 588535464 1.270000e-75 294.0
42 TraesCS3B01G457500 chr4A 94.271 192 11 0 4176 4367 574198076 574197885 1.270000e-75 294.0


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 TraesCS3B01G457500 chr3B 699692975 699697649 4674 True 8634.00 8634 100.00000 1 4675 1 chr3B.!!$R2 4674
1 TraesCS3B01G457500 chr3B 181468262 181469116 854 False 1094.00 1094 89.74400 1 858 1 chr3B.!!$F1 857
2 TraesCS3B01G457500 chr3B 699284619 699287226 2607 True 645.25 881 95.48250 2701 4675 4 chr3B.!!$R3 1974
3 TraesCS3B01G457500 chr3D 529136357 529141345 4988 True 1613.00 4194 89.19400 906 4674 3 chr3D.!!$R1 3768
4 TraesCS3B01G457500 chr3D 528804735 528807437 2702 False 309.00 396 89.24140 3043 4675 5 chr3D.!!$F3 1632
5 TraesCS3B01G457500 chr3A 662813723 662816085 2362 False 1284.00 2442 90.72000 2022 4644 2 chr3A.!!$F1 2622
6 TraesCS3B01G457500 chr3A 663291649 663297724 6075 True 1094.50 1736 91.14125 906 4674 4 chr3A.!!$R1 3768
7 TraesCS3B01G457500 chr3A 662820249 662820889 640 False 275.00 416 85.68550 3138 3718 2 chr3A.!!$F2 580
8 TraesCS3B01G457500 chr2B 30102051 30102908 857 True 1463.00 1463 97.43600 1 858 1 chr2B.!!$R1 857
9 TraesCS3B01G457500 chr2B 38425218 38426072 854 False 734.00 734 82.16800 2 858 1 chr2B.!!$F1 856
10 TraesCS3B01G457500 chr2B 72594721 72598510 3789 True 597.00 824 91.14900 1 858 2 chr2B.!!$R2 857
11 TraesCS3B01G457500 chr5A 504919457 504920314 857 False 1147.00 1147 90.79300 1 858 1 chr5A.!!$F1 857
12 TraesCS3B01G457500 chr5A 510440783 510441640 857 True 1147.00 1147 90.79300 1 858 1 chr5A.!!$R2 857
13 TraesCS3B01G457500 chr6B 643533304 643533905 601 True 857.00 857 92.37100 256 858 1 chr6B.!!$R1 602
14 TraesCS3B01G457500 chr7A 610215554 610216410 856 False 852.00 852 84.68700 1 858 1 chr7A.!!$F1 857
15 TraesCS3B01G457500 chr2A 684126078 684126936 858 True 715.00 715 81.78700 1 858 1 chr2A.!!$R1 857

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
123 124 0.107214 CTGTACCAATGGACCGGCAT 60.107 55.000 6.16 0.0 0.00 4.40 F
187 188 0.538057 CAGGCTGCCAAACTCCTTGA 60.538 55.000 22.65 0.0 37.17 3.02 F
868 3803 2.285756 CGAGACCAAAACTAAACGTGCA 59.714 45.455 0.00 0.0 0.00 4.57 F
2138 5367 1.333791 GCGTTTGCAACACAGGAGTAC 60.334 52.381 0.00 0.0 42.15 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 4604 1.281867 TCTTGGCCAGTATTGGGACAG 59.718 52.381 5.11 0.0 46.14 3.51 R
1641 4608 1.479389 GGGATCTTGGCCAGTATTGGG 60.479 57.143 5.11 0.0 45.16 4.12 R
2217 5453 1.078143 CTGCCCTCCACAGTAAGGC 60.078 63.158 0.00 0.0 44.13 4.35 R
3903 11006 0.095245 CATTAACAGCCGCACAGTCG 59.905 55.000 0.00 0.0 0.00 4.18 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
69 70 1.635487 TGATGCAAGGCCTCCTTTAGT 59.365 47.619 5.23 0.00 41.69 2.24
83 84 5.278022 CCTCCTTTAGTTTCTTGACAACAGC 60.278 44.000 0.00 0.00 0.00 4.40
123 124 0.107214 CTGTACCAATGGACCGGCAT 60.107 55.000 6.16 0.00 0.00 4.40
187 188 0.538057 CAGGCTGCCAAACTCCTTGA 60.538 55.000 22.65 0.00 37.17 3.02
354 3289 3.445805 ACTGTTTCCGTTTTGGTGTTGAT 59.554 39.130 0.00 0.00 39.52 2.57
631 3566 4.371786 CGCTGATCTACTAAAATGCTCCA 58.628 43.478 0.00 0.00 0.00 3.86
699 3634 4.435518 GCATGTGGTAACGTATGAAGTGTG 60.436 45.833 0.00 0.00 42.51 3.82
858 3793 5.411781 ACAGATACATCTCGAGACCAAAAC 58.588 41.667 19.30 8.13 34.22 2.43
859 3794 5.186021 ACAGATACATCTCGAGACCAAAACT 59.814 40.000 19.30 10.28 34.22 2.66
860 3795 6.377429 ACAGATACATCTCGAGACCAAAACTA 59.623 38.462 19.30 0.00 34.22 2.24
861 3796 7.093902 ACAGATACATCTCGAGACCAAAACTAA 60.094 37.037 19.30 0.00 34.22 2.24
862 3797 7.759886 CAGATACATCTCGAGACCAAAACTAAA 59.240 37.037 19.30 0.00 34.22 1.85
863 3798 7.760340 AGATACATCTCGAGACCAAAACTAAAC 59.240 37.037 19.30 1.03 29.30 2.01
864 3799 4.684703 ACATCTCGAGACCAAAACTAAACG 59.315 41.667 19.30 0.00 0.00 3.60
865 3800 4.311816 TCTCGAGACCAAAACTAAACGT 57.688 40.909 12.08 0.00 0.00 3.99
866 3801 4.046462 TCTCGAGACCAAAACTAAACGTG 58.954 43.478 12.08 0.00 0.00 4.49
867 3802 2.540931 TCGAGACCAAAACTAAACGTGC 59.459 45.455 0.00 0.00 0.00 5.34
868 3803 2.285756 CGAGACCAAAACTAAACGTGCA 59.714 45.455 0.00 0.00 0.00 4.57
869 3804 3.242478 CGAGACCAAAACTAAACGTGCAA 60.242 43.478 0.00 0.00 0.00 4.08
870 3805 4.279659 GAGACCAAAACTAAACGTGCAAG 58.720 43.478 0.00 0.00 0.00 4.01
871 3806 3.692593 AGACCAAAACTAAACGTGCAAGT 59.307 39.130 0.00 0.00 0.00 3.16
872 3807 4.157105 AGACCAAAACTAAACGTGCAAGTT 59.843 37.500 12.50 12.50 35.01 2.66
873 3808 4.170256 ACCAAAACTAAACGTGCAAGTTG 58.830 39.130 18.80 9.76 33.85 3.16
874 3809 4.170256 CCAAAACTAAACGTGCAAGTTGT 58.830 39.130 18.80 10.41 33.85 3.32
875 3810 5.106237 ACCAAAACTAAACGTGCAAGTTGTA 60.106 36.000 18.80 11.64 33.85 2.41
876 3811 5.800941 CCAAAACTAAACGTGCAAGTTGTAA 59.199 36.000 18.80 6.99 33.85 2.41
877 3812 6.020995 CCAAAACTAAACGTGCAAGTTGTAAG 60.021 38.462 18.80 17.09 33.85 2.34
878 3813 6.425577 AAACTAAACGTGCAAGTTGTAAGA 57.574 33.333 18.80 2.15 33.85 2.10
879 3814 5.399604 ACTAAACGTGCAAGTTGTAAGAC 57.600 39.130 18.80 1.08 34.14 3.01
880 3815 5.114081 ACTAAACGTGCAAGTTGTAAGACT 58.886 37.500 18.80 3.96 34.14 3.24
881 3816 4.957759 AAACGTGCAAGTTGTAAGACTT 57.042 36.364 18.80 0.00 40.37 3.01
882 3817 6.757947 ACTAAACGTGCAAGTTGTAAGACTTA 59.242 34.615 18.80 4.23 37.76 2.24
883 3818 5.399604 AACGTGCAAGTTGTAAGACTTAC 57.600 39.130 17.44 16.97 37.76 2.34
884 3819 4.435425 ACGTGCAAGTTGTAAGACTTACA 58.565 39.130 21.54 21.54 43.92 2.41
885 3820 4.506654 ACGTGCAAGTTGTAAGACTTACAG 59.493 41.667 23.48 15.25 45.92 2.74
886 3821 4.506654 CGTGCAAGTTGTAAGACTTACAGT 59.493 41.667 23.48 14.75 45.92 3.55
887 3822 5.556382 CGTGCAAGTTGTAAGACTTACAGTG 60.556 44.000 23.48 21.83 45.92 3.66
888 3823 5.293569 GTGCAAGTTGTAAGACTTACAGTGT 59.706 40.000 23.48 12.38 45.92 3.55
889 3824 6.477688 GTGCAAGTTGTAAGACTTACAGTGTA 59.522 38.462 23.48 19.11 45.92 2.90
890 3825 7.170998 GTGCAAGTTGTAAGACTTACAGTGTAT 59.829 37.037 23.48 10.39 45.92 2.29
891 3826 7.713507 TGCAAGTTGTAAGACTTACAGTGTATT 59.286 33.333 23.48 14.06 45.92 1.89
892 3827 9.199982 GCAAGTTGTAAGACTTACAGTGTATTA 57.800 33.333 23.48 8.46 45.92 0.98
902 3837 9.476928 AGACTTACAGTGTATTATTACCTCTGT 57.523 33.333 3.28 17.98 41.24 3.41
1071 4006 4.070552 GCGGCCGTCCTTCTGACT 62.071 66.667 28.70 0.00 42.13 3.41
1381 4344 6.467677 GGATGATGCTAGATTGCTAGGTTTA 58.532 40.000 0.00 0.00 43.54 2.01
1382 4345 7.108847 GGATGATGCTAGATTGCTAGGTTTAT 58.891 38.462 0.00 0.00 43.54 1.40
1386 4349 6.731292 TGCTAGATTGCTAGGTTTATGAGA 57.269 37.500 0.00 0.00 43.54 3.27
1390 4353 8.716909 GCTAGATTGCTAGGTTTATGAGATTTC 58.283 37.037 0.00 0.00 43.54 2.17
1396 4359 6.994496 TGCTAGGTTTATGAGATTTCCAGATG 59.006 38.462 0.00 0.00 0.00 2.90
1397 4360 7.147497 TGCTAGGTTTATGAGATTTCCAGATGA 60.147 37.037 0.00 0.00 0.00 2.92
1398 4361 7.716998 GCTAGGTTTATGAGATTTCCAGATGAA 59.283 37.037 0.00 0.00 0.00 2.57
1399 4362 9.270640 CTAGGTTTATGAGATTTCCAGATGAAG 57.729 37.037 0.00 0.00 33.63 3.02
1400 4363 7.865820 AGGTTTATGAGATTTCCAGATGAAGA 58.134 34.615 0.00 0.00 33.63 2.87
1401 4364 8.501070 AGGTTTATGAGATTTCCAGATGAAGAT 58.499 33.333 0.00 0.00 33.63 2.40
1402 4365 8.782144 GGTTTATGAGATTTCCAGATGAAGATC 58.218 37.037 0.00 0.00 33.63 2.75
1410 4373 2.573009 TCCAGATGAAGATCCAAGTGCA 59.427 45.455 0.00 0.00 0.00 4.57
1416 4379 7.363181 CCAGATGAAGATCCAAGTGCAAAATAA 60.363 37.037 0.00 0.00 0.00 1.40
1420 4383 6.658816 TGAAGATCCAAGTGCAAAATAAGCTA 59.341 34.615 0.00 0.00 0.00 3.32
1436 4403 7.944729 AATAAGCTATTGTTCCTTCACACAT 57.055 32.000 0.00 0.00 0.00 3.21
1637 4604 5.904362 ACATTTGGTCTTCTAAGGAATGC 57.096 39.130 0.00 0.00 0.00 3.56
1641 4608 4.207891 TGGTCTTCTAAGGAATGCTGTC 57.792 45.455 0.00 0.00 0.00 3.51
1753 4728 6.463360 TGTTGTTGTGATACTTCTGCTATGA 58.537 36.000 0.00 0.00 0.00 2.15
1915 5133 4.034279 GCGGTAGTACTCTCTCAGTTGTAG 59.966 50.000 0.00 0.00 36.43 2.74
1929 5147 7.097192 TCTCAGTTGTAGTAGGCTGTATTTTG 58.903 38.462 0.00 0.00 0.00 2.44
1946 5165 5.733620 ATTTTGCCTGTCTGATGTTCAAT 57.266 34.783 0.00 0.00 0.00 2.57
1968 5187 7.814107 TCAATTTTGACAGCAAATTCCTGTATC 59.186 33.333 10.62 2.70 43.17 2.24
2015 5234 7.859325 AACTAGTCACAAGAAAGTGCTTTTA 57.141 32.000 0.00 0.00 39.35 1.52
2017 5236 7.920738 ACTAGTCACAAGAAAGTGCTTTTAAG 58.079 34.615 0.00 0.00 39.35 1.85
2068 5288 7.442656 ACTTATAGCATAACCCATGTACTGTC 58.557 38.462 0.00 0.00 36.95 3.51
2113 5341 3.199946 TGGATTTGGACAGTCAGGATACC 59.800 47.826 2.17 0.00 37.17 2.73
2114 5342 3.456277 GGATTTGGACAGTCAGGATACCT 59.544 47.826 2.17 0.00 37.17 3.08
2138 5367 1.333791 GCGTTTGCAACACAGGAGTAC 60.334 52.381 0.00 0.00 42.15 2.73
2185 5414 8.356657 AGATGCATACAAGATCTAGTTGTACTC 58.643 37.037 0.00 4.45 41.87 2.59
2549 5791 5.607477 TGACCGACACTTTTATCTGAAGTT 58.393 37.500 0.00 0.00 35.26 2.66
2556 5798 7.689812 CGACACTTTTATCTGAAGTTAGCAATG 59.310 37.037 0.00 0.00 35.26 2.82
2563 5805 6.874288 ATCTGAAGTTAGCAATGCTATTCC 57.126 37.500 16.35 7.31 41.01 3.01
2664 5906 0.538287 AAGCAAGGGCCACTGAGTTC 60.538 55.000 6.18 0.00 42.56 3.01
2694 5936 5.129815 ACTGTAACCTTCACACTGTTCCTTA 59.870 40.000 0.00 0.00 0.00 2.69
2856 8057 6.596309 AGTGAGAAACATCATGTCAGAGTA 57.404 37.500 0.00 0.00 0.00 2.59
2887 8089 7.200455 AGTAATTTATGGCCTTTATTGCGTTC 58.800 34.615 3.32 0.00 0.00 3.95
3156 8358 7.669089 TTATCTGTGGTCCATATTGTACTGA 57.331 36.000 0.00 0.00 0.00 3.41
3212 8451 1.849097 CGTGGAGAAACGGCCTATAC 58.151 55.000 0.00 0.00 39.89 1.47
3682 10768 4.363999 GACAGCGAGCTTTGATACATACT 58.636 43.478 0.00 0.00 0.00 2.12
3697 10784 9.996554 TTGATACATACTCGGATGTAATTTGAT 57.003 29.630 6.10 0.00 43.66 2.57
3778 10869 8.993121 CATCATGTTTAAAGTGTTACAGAGACT 58.007 33.333 0.00 0.00 32.32 3.24
3802 10894 5.007682 GGTTAGATTGCTGTACCAAAGGAA 58.992 41.667 0.00 0.00 33.08 3.36
3858 10954 3.350833 ACATCTTTTCACTCCTGATGGC 58.649 45.455 0.00 0.00 38.88 4.40
3862 10958 2.957402 TTTCACTCCTGATGGCTGTT 57.043 45.000 0.00 0.00 0.00 3.16
3864 10960 1.351076 TCACTCCTGATGGCTGTTCA 58.649 50.000 0.00 0.00 0.00 3.18
3868 10964 0.251354 TCCTGATGGCTGTTCAGCTC 59.749 55.000 21.46 13.88 39.42 4.09
3903 11006 7.920738 AGAACACAAGTATCTTCTGTTTGTTC 58.079 34.615 0.00 0.00 30.15 3.18
4002 12815 7.066645 GTGATCAGTGGAGAATGAATGAATGAA 59.933 37.037 0.00 0.00 0.00 2.57
4003 12816 7.778382 TGATCAGTGGAGAATGAATGAATGAAT 59.222 33.333 0.00 0.00 0.00 2.57
4095 12920 9.070179 TGGAATATATGTTCTTCATGTTCATGG 57.930 33.333 11.45 0.00 37.91 3.66
4096 12921 9.288576 GGAATATATGTTCTTCATGTTCATGGA 57.711 33.333 11.45 3.53 37.91 3.41
4188 13013 1.756430 GCTTCTAGCTTTTCAGGGGG 58.244 55.000 0.00 0.00 38.45 5.40
4189 13014 1.004862 GCTTCTAGCTTTTCAGGGGGT 59.995 52.381 0.00 0.00 38.45 4.95
4190 13015 2.716217 CTTCTAGCTTTTCAGGGGGTG 58.284 52.381 0.00 0.00 0.00 4.61
4193 13018 2.445525 TCTAGCTTTTCAGGGGGTGTTT 59.554 45.455 0.00 0.00 0.00 2.83
4194 13019 1.413118 AGCTTTTCAGGGGGTGTTTG 58.587 50.000 0.00 0.00 0.00 2.93
4197 13022 2.368548 GCTTTTCAGGGGGTGTTTGATT 59.631 45.455 0.00 0.00 0.00 2.57
4198 13023 3.554960 GCTTTTCAGGGGGTGTTTGATTC 60.555 47.826 0.00 0.00 0.00 2.52
4199 13024 3.320610 TTTCAGGGGGTGTTTGATTCA 57.679 42.857 0.00 0.00 0.00 2.57
4200 13025 2.584835 TCAGGGGGTGTTTGATTCAG 57.415 50.000 0.00 0.00 0.00 3.02
4201 13026 1.075374 TCAGGGGGTGTTTGATTCAGG 59.925 52.381 0.00 0.00 0.00 3.86
4202 13027 1.158007 AGGGGGTGTTTGATTCAGGT 58.842 50.000 0.00 0.00 0.00 4.00
4203 13028 2.041081 CAGGGGGTGTTTGATTCAGGTA 59.959 50.000 0.00 0.00 0.00 3.08
4209 13034 5.069914 GGGGTGTTTGATTCAGGTACTTTTT 59.930 40.000 0.00 0.00 34.60 1.94
4211 13036 7.368059 GGGTGTTTGATTCAGGTACTTTTTAG 58.632 38.462 0.00 0.00 34.60 1.85
4212 13037 7.013942 GGGTGTTTGATTCAGGTACTTTTTAGT 59.986 37.037 0.00 0.00 34.60 2.24
4213 13038 8.074370 GGTGTTTGATTCAGGTACTTTTTAGTC 58.926 37.037 0.00 0.00 34.60 2.59
4214 13039 8.074370 GTGTTTGATTCAGGTACTTTTTAGTCC 58.926 37.037 0.00 0.00 34.60 3.85
4215 13040 7.229907 TGTTTGATTCAGGTACTTTTTAGTCCC 59.770 37.037 0.00 0.00 34.60 4.46
4216 13041 6.442541 TGATTCAGGTACTTTTTAGTCCCA 57.557 37.500 0.00 0.00 34.60 4.37
4217 13042 6.472887 TGATTCAGGTACTTTTTAGTCCCAG 58.527 40.000 0.00 0.00 34.60 4.45
4218 13043 6.271391 TGATTCAGGTACTTTTTAGTCCCAGA 59.729 38.462 0.00 0.00 34.60 3.86
4219 13044 5.740290 TCAGGTACTTTTTAGTCCCAGAG 57.260 43.478 0.00 0.00 34.60 3.35
4220 13045 5.399991 TCAGGTACTTTTTAGTCCCAGAGA 58.600 41.667 0.00 0.00 34.60 3.10
4221 13046 6.023603 TCAGGTACTTTTTAGTCCCAGAGAT 58.976 40.000 0.00 0.00 34.60 2.75
4222 13047 6.500751 TCAGGTACTTTTTAGTCCCAGAGATT 59.499 38.462 0.00 0.00 34.60 2.40
4223 13048 7.676893 TCAGGTACTTTTTAGTCCCAGAGATTA 59.323 37.037 0.00 0.00 34.60 1.75
4224 13049 7.982354 CAGGTACTTTTTAGTCCCAGAGATTAG 59.018 40.741 0.00 0.00 34.60 1.73
4225 13050 7.899709 AGGTACTTTTTAGTCCCAGAGATTAGA 59.100 37.037 0.00 0.00 27.25 2.10
4226 13051 8.537858 GGTACTTTTTAGTCCCAGAGATTAGAA 58.462 37.037 0.00 0.00 0.00 2.10
4227 13052 9.939802 GTACTTTTTAGTCCCAGAGATTAGAAA 57.060 33.333 0.00 0.00 0.00 2.52
4229 13054 9.862149 ACTTTTTAGTCCCAGAGATTAGAAAAA 57.138 29.630 0.00 0.00 0.00 1.94
4231 13056 9.862149 TTTTTAGTCCCAGAGATTAGAAAAAGT 57.138 29.630 0.00 0.00 0.00 2.66
4232 13057 9.503399 TTTTAGTCCCAGAGATTAGAAAAAGTC 57.497 33.333 0.00 0.00 0.00 3.01
4233 13058 6.056090 AGTCCCAGAGATTAGAAAAAGTCC 57.944 41.667 0.00 0.00 0.00 3.85
4234 13059 5.045505 AGTCCCAGAGATTAGAAAAAGTCCC 60.046 44.000 0.00 0.00 0.00 4.46
4235 13060 5.045505 GTCCCAGAGATTAGAAAAAGTCCCT 60.046 44.000 0.00 0.00 0.00 4.20
4236 13061 6.156429 GTCCCAGAGATTAGAAAAAGTCCCTA 59.844 42.308 0.00 0.00 0.00 3.53
4237 13062 6.733807 TCCCAGAGATTAGAAAAAGTCCCTAA 59.266 38.462 0.00 0.00 0.00 2.69
4238 13063 7.051000 CCCAGAGATTAGAAAAAGTCCCTAAG 58.949 42.308 0.00 0.00 0.00 2.18
4239 13064 7.092846 CCCAGAGATTAGAAAAAGTCCCTAAGA 60.093 40.741 0.00 0.00 0.00 2.10
4240 13065 8.322091 CCAGAGATTAGAAAAAGTCCCTAAGAA 58.678 37.037 0.00 0.00 0.00 2.52
4241 13066 9.377312 CAGAGATTAGAAAAAGTCCCTAAGAAG 57.623 37.037 0.00 0.00 0.00 2.85
4242 13067 9.106977 AGAGATTAGAAAAAGTCCCTAAGAAGT 57.893 33.333 0.00 0.00 0.00 3.01
4243 13068 9.373603 GAGATTAGAAAAAGTCCCTAAGAAGTC 57.626 37.037 0.00 0.00 0.00 3.01
4244 13069 8.322828 AGATTAGAAAAAGTCCCTAAGAAGTCC 58.677 37.037 0.00 0.00 0.00 3.85
4245 13070 5.244189 AGAAAAAGTCCCTAAGAAGTCCC 57.756 43.478 0.00 0.00 0.00 4.46
4246 13071 4.914581 AGAAAAAGTCCCTAAGAAGTCCCT 59.085 41.667 0.00 0.00 0.00 4.20
4247 13072 6.089502 AGAAAAAGTCCCTAAGAAGTCCCTA 58.910 40.000 0.00 0.00 0.00 3.53
4248 13073 6.213802 AGAAAAAGTCCCTAAGAAGTCCCTAG 59.786 42.308 0.00 0.00 0.00 3.02
4249 13074 3.691698 AGTCCCTAAGAAGTCCCTAGG 57.308 52.381 0.06 0.06 0.00 3.02
4250 13075 3.208173 AGTCCCTAAGAAGTCCCTAGGA 58.792 50.000 11.48 0.00 0.00 2.94
4251 13076 3.601537 AGTCCCTAAGAAGTCCCTAGGAA 59.398 47.826 11.48 0.00 31.38 3.36
4252 13077 3.705579 GTCCCTAAGAAGTCCCTAGGAAC 59.294 52.174 11.48 0.00 31.38 3.62
4253 13078 3.039743 CCCTAAGAAGTCCCTAGGAACC 58.960 54.545 11.48 0.00 31.38 3.62
4254 13079 3.568109 CCCTAAGAAGTCCCTAGGAACCA 60.568 52.174 11.48 0.00 31.38 3.67
4255 13080 4.101856 CCTAAGAAGTCCCTAGGAACCAA 58.898 47.826 11.48 0.00 31.38 3.67
4256 13081 4.534897 CCTAAGAAGTCCCTAGGAACCAAA 59.465 45.833 11.48 0.00 31.38 3.28
4257 13082 4.368565 AAGAAGTCCCTAGGAACCAAAC 57.631 45.455 11.48 0.00 31.38 2.93
4258 13083 2.302157 AGAAGTCCCTAGGAACCAAACG 59.698 50.000 11.48 0.00 31.38 3.60
4259 13084 0.981943 AGTCCCTAGGAACCAAACGG 59.018 55.000 11.48 0.00 31.38 4.44
4260 13085 0.035725 GTCCCTAGGAACCAAACGGG 60.036 60.000 11.48 0.00 44.81 5.28
4261 13086 0.178897 TCCCTAGGAACCAAACGGGA 60.179 55.000 11.48 0.00 41.15 5.14
4262 13087 0.252197 CCCTAGGAACCAAACGGGAG 59.748 60.000 11.48 0.00 41.15 4.30
4263 13088 0.252197 CCTAGGAACCAAACGGGAGG 59.748 60.000 1.05 0.00 41.15 4.30
4264 13089 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
4265 13090 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
4266 13091 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
4268 13093 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
4269 13094 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
4270 13095 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
4271 13096 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
4272 13097 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
4273 13098 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
4274 13099 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
4275 13100 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
4276 13101 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
4277 13102 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
4278 13103 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
4279 13104 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
4280 13105 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
4281 13106 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
4282 13107 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
4283 13108 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
4284 13109 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
4285 13110 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
4286 13111 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
4287 13112 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
4288 13113 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
4292 13117 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
4293 13118 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
4294 13119 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
4295 13120 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
4296 13121 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
4297 13122 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
4298 13123 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
4299 13124 6.209788 ACAGGGACTAGAAAAAGACTCTACTG 59.790 42.308 0.00 0.00 36.02 2.74
4300 13125 6.434652 CAGGGACTAGAAAAAGACTCTACTGA 59.565 42.308 0.00 0.00 36.02 3.41
4301 13126 7.011382 AGGGACTAGAAAAAGACTCTACTGAA 58.989 38.462 0.00 0.00 36.02 3.02
4302 13127 7.177744 AGGGACTAGAAAAAGACTCTACTGAAG 59.822 40.741 0.00 0.00 36.02 3.02
4303 13128 7.177041 GGGACTAGAAAAAGACTCTACTGAAGA 59.823 40.741 0.00 0.00 0.00 2.87
4360 13185 5.861727 GTCCTAGGACTTCTAAACCAAACA 58.138 41.667 31.12 0.00 41.57 2.83
4361 13186 5.699915 GTCCTAGGACTTCTAAACCAAACAC 59.300 44.000 31.12 2.21 41.57 3.32
4362 13187 5.001874 CCTAGGACTTCTAAACCAAACACC 58.998 45.833 1.05 0.00 0.00 4.16
4363 13188 3.828921 AGGACTTCTAAACCAAACACCC 58.171 45.455 0.00 0.00 0.00 4.61
4364 13189 2.889045 GGACTTCTAAACCAAACACCCC 59.111 50.000 0.00 0.00 0.00 4.95
4365 13190 2.889045 GACTTCTAAACCAAACACCCCC 59.111 50.000 0.00 0.00 0.00 5.40
4515 13646 3.290710 GGCTTGAAGGAAGGAATGCATA 58.709 45.455 0.00 0.00 31.56 3.14
4516 13647 3.893813 GGCTTGAAGGAAGGAATGCATAT 59.106 43.478 0.00 0.00 31.56 1.78
4522 13653 4.662966 AGGAAGGAATGCATATGCCATA 57.337 40.909 24.54 6.97 41.18 2.74
4545 13676 1.913951 TACCATGCACCCTGCTCTGG 61.914 60.000 12.22 12.22 45.76 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.117888 AGGAGGAAGCTGTTGTCAAGAAA 60.118 43.478 0.00 0.00 0.00 2.52
83 84 2.711922 CCGACGGTGGAGGAGGAAG 61.712 68.421 5.48 0.00 0.00 3.46
288 3222 5.278512 GCAGACTCATACAGATTATGACCGA 60.279 44.000 0.00 0.00 31.39 4.69
354 3289 1.583556 TTAAGGAGAGCCTGCCATCA 58.416 50.000 0.00 0.00 46.28 3.07
631 3566 8.993424 AGATTACAATGAGACACTATACCCTTT 58.007 33.333 0.00 0.00 0.00 3.11
745 3680 2.031930 GGCGTTTCACTGGTTTTTACGA 59.968 45.455 0.00 0.00 0.00 3.43
858 3793 5.652744 AGTCTTACAACTTGCACGTTTAG 57.347 39.130 5.74 4.81 0.00 1.85
859 3794 6.534436 TGTAAGTCTTACAACTTGCACGTTTA 59.466 34.615 20.73 0.57 43.83 2.01
860 3795 4.957759 AAGTCTTACAACTTGCACGTTT 57.042 36.364 5.74 1.48 38.06 3.60
861 3796 4.871557 TGTAAGTCTTACAACTTGCACGTT 59.128 37.500 20.73 2.17 43.83 3.99
862 3797 4.435425 TGTAAGTCTTACAACTTGCACGT 58.565 39.130 20.73 0.00 43.83 4.49
863 3798 5.006649 CTGTAAGTCTTACAACTTGCACG 57.993 43.478 22.59 8.05 43.83 5.34
885 3820 9.971922 ACCGTTAATACAGAGGTAATAATACAC 57.028 33.333 0.00 0.00 29.99 2.90
889 3824 8.588472 GGGTACCGTTAATACAGAGGTAATAAT 58.412 37.037 5.65 0.00 40.86 1.28
890 3825 7.951591 GGGTACCGTTAATACAGAGGTAATAA 58.048 38.462 5.65 0.00 40.86 1.40
891 3826 7.524717 GGGTACCGTTAATACAGAGGTAATA 57.475 40.000 5.65 0.00 40.86 0.98
892 3827 6.410942 GGGTACCGTTAATACAGAGGTAAT 57.589 41.667 5.65 0.00 40.86 1.89
893 3828 5.852282 GGGTACCGTTAATACAGAGGTAA 57.148 43.478 5.65 0.00 40.86 2.85
1262 4203 3.252458 AGAGATTGCGGTTTGGTTACAAC 59.748 43.478 0.00 0.00 36.06 3.32
1381 4344 6.511017 TGGATCTTCATCTGGAAATCTCAT 57.489 37.500 0.00 0.00 34.44 2.90
1382 4345 5.963214 TGGATCTTCATCTGGAAATCTCA 57.037 39.130 0.00 0.00 34.44 3.27
1386 4349 4.643784 GCACTTGGATCTTCATCTGGAAAT 59.356 41.667 0.00 0.00 34.44 2.17
1390 4353 2.995283 TGCACTTGGATCTTCATCTGG 58.005 47.619 0.00 0.00 0.00 3.86
1396 4359 5.958955 AGCTTATTTTGCACTTGGATCTTC 58.041 37.500 0.00 0.00 0.00 2.87
1397 4360 5.990120 AGCTTATTTTGCACTTGGATCTT 57.010 34.783 0.00 0.00 0.00 2.40
1398 4361 7.123247 ACAATAGCTTATTTTGCACTTGGATCT 59.877 33.333 0.00 0.00 32.32 2.75
1399 4362 7.260603 ACAATAGCTTATTTTGCACTTGGATC 58.739 34.615 0.00 0.00 32.32 3.36
1400 4363 7.174107 ACAATAGCTTATTTTGCACTTGGAT 57.826 32.000 0.00 0.00 32.32 3.41
1401 4364 6.588719 ACAATAGCTTATTTTGCACTTGGA 57.411 33.333 0.00 0.00 32.32 3.53
1402 4365 6.311200 GGAACAATAGCTTATTTTGCACTTGG 59.689 38.462 0.00 0.00 32.32 3.61
1410 4373 8.177119 TGTGTGAAGGAACAATAGCTTATTTT 57.823 30.769 0.00 0.00 0.00 1.82
1416 4379 5.431765 CCTATGTGTGAAGGAACAATAGCT 58.568 41.667 0.00 0.00 34.58 3.32
1420 4383 3.356290 GCCCTATGTGTGAAGGAACAAT 58.644 45.455 0.00 0.00 34.58 2.71
1436 4403 1.751351 CAGTCTGAATCTCACGCCCTA 59.249 52.381 0.00 0.00 0.00 3.53
1484 4451 5.682234 AGCCTCCCCTCAATTTTTATTTG 57.318 39.130 0.00 0.00 0.00 2.32
1489 4456 5.363868 GCTAATTAGCCTCCCCTCAATTTTT 59.636 40.000 24.34 0.00 43.39 1.94
1589 4556 6.083383 ACTTCTGAGAGATATCCATCATGGT 58.917 40.000 2.79 0.00 39.03 3.55
1637 4604 1.281867 TCTTGGCCAGTATTGGGACAG 59.718 52.381 5.11 0.00 46.14 3.51
1641 4608 1.479389 GGGATCTTGGCCAGTATTGGG 60.479 57.143 5.11 0.00 45.16 4.12
1764 4739 8.243426 CCTTAGCAGCAAGTACATAATTTTTCA 58.757 33.333 0.00 0.00 0.00 2.69
1781 4756 9.884465 CTAAAATAATGTATGAACCTTAGCAGC 57.116 33.333 0.00 0.00 0.00 5.25
1812 5030 5.852282 TGTGATCGAATACTGGAGATTCA 57.148 39.130 0.00 0.00 33.66 2.57
1817 5035 4.503910 TGGTTTGTGATCGAATACTGGAG 58.496 43.478 0.00 0.00 0.00 3.86
1828 5046 2.154462 CCCACACTCTGGTTTGTGATC 58.846 52.381 3.30 0.00 45.03 2.92
1929 5147 4.919754 GTCAAAATTGAACATCAGACAGGC 59.080 41.667 0.00 0.00 39.21 4.85
1946 5165 6.265196 ACAGATACAGGAATTTGCTGTCAAAA 59.735 34.615 24.41 9.83 46.32 2.44
2015 5234 7.174107 AGCTCATACCATTAAATTTGCACTT 57.826 32.000 0.00 0.00 0.00 3.16
2050 5270 2.159014 TCCGACAGTACATGGGTTATGC 60.159 50.000 0.00 0.00 40.59 3.14
2089 5317 4.598036 ATCCTGACTGTCCAAATCCATT 57.402 40.909 5.17 0.00 0.00 3.16
2174 5403 7.065085 CCATTCAAACCATCTGAGTACAACTAG 59.935 40.741 0.00 0.00 0.00 2.57
2185 5414 5.350365 CAGCATTTTCCATTCAAACCATCTG 59.650 40.000 0.00 0.00 0.00 2.90
2217 5453 1.078143 CTGCCCTCCACAGTAAGGC 60.078 63.158 0.00 0.00 44.13 4.35
2267 5504 6.284459 AGCTAGGCATGTAGATACAGAAAAC 58.716 40.000 0.00 0.00 39.92 2.43
2343 5580 8.492415 ACCTGTATATGATTGCCTTAGAACTA 57.508 34.615 0.00 0.00 0.00 2.24
2412 5653 4.558538 AGAAAACAGTGTCATGTGAAGC 57.441 40.909 0.00 0.00 32.52 3.86
2524 5766 6.231211 ACTTCAGATAAAAGTGTCGGTCAAT 58.769 36.000 0.00 0.00 35.68 2.57
2549 5791 8.150827 AGTATCATAAGGGAATAGCATTGCTA 57.849 34.615 20.06 20.06 45.55 3.49
2664 5906 3.326880 AGTGTGAAGGTTACAGTAAGGGG 59.673 47.826 0.00 0.00 30.29 4.79
2694 5936 8.730680 GGACTATGTTGTTCATAAAGTCATTGT 58.269 33.333 10.72 0.00 40.84 2.71
2856 8057 9.143155 CAATAAAGGCCATAAATTACTAGGGTT 57.857 33.333 5.01 0.00 0.00 4.11
2887 8089 5.901552 ACATGACAAACAAACCAGGTAAAG 58.098 37.500 0.00 0.00 0.00 1.85
3110 8312 1.605232 CCAATAATCGCATGCTGCTCA 59.395 47.619 17.13 0.00 42.25 4.26
3212 8451 4.690748 TGCGAAGGTTTCTGATAAGAACAG 59.309 41.667 0.00 0.00 36.80 3.16
3324 9609 2.222027 CCCATCTTTGCGGGTATTCTC 58.778 52.381 0.00 0.00 37.70 2.87
3648 10734 2.049063 GCTGTCGTTGCTCTCCGT 60.049 61.111 0.00 0.00 0.00 4.69
3682 10768 8.759641 CAAAAACACAAATCAAATTACATCCGA 58.240 29.630 0.00 0.00 0.00 4.55
3697 10784 3.165124 GACGAACTCGCAAAAACACAAA 58.835 40.909 0.00 0.00 44.43 2.83
3722 10809 1.068417 GAAAACGGCGGCCCTTTTT 59.932 52.632 23.37 21.86 43.04 1.94
3743 10830 7.881142 ACACTTTAAACATGATGGAAAATCGA 58.119 30.769 0.00 0.00 0.00 3.59
3778 10869 4.042311 TCCTTTGGTACAGCAATCTAACCA 59.958 41.667 0.00 0.00 42.39 3.67
3858 10954 5.888691 TCTCACTACTAAGAGCTGAACAG 57.111 43.478 0.00 0.00 0.00 3.16
3862 10958 5.070685 TGTGTTCTCACTACTAAGAGCTGA 58.929 41.667 0.00 0.00 44.14 4.26
3864 10960 5.536916 ACTTGTGTTCTCACTACTAAGAGCT 59.463 40.000 0.00 0.00 44.14 4.09
3868 10964 9.562583 GAAGATACTTGTGTTCTCACTACTAAG 57.437 37.037 0.00 0.00 44.14 2.18
3903 11006 0.095245 CATTAACAGCCGCACAGTCG 59.905 55.000 0.00 0.00 0.00 4.18
4002 12815 2.237143 AGACCGGTGTTCACATGATCAT 59.763 45.455 14.63 1.18 0.00 2.45
4003 12816 1.623311 AGACCGGTGTTCACATGATCA 59.377 47.619 14.63 0.00 0.00 2.92
4095 12920 3.128938 ACTGCGAGTGTTGGATAGTACTC 59.871 47.826 0.00 0.00 36.95 2.59
4096 12921 3.090037 ACTGCGAGTGTTGGATAGTACT 58.910 45.455 0.00 0.00 0.00 2.73
4184 13009 2.041216 AGTACCTGAATCAAACACCCCC 59.959 50.000 0.00 0.00 0.00 5.40
4185 13010 3.434940 AGTACCTGAATCAAACACCCC 57.565 47.619 0.00 0.00 0.00 4.95
4186 13011 5.784578 AAAAGTACCTGAATCAAACACCC 57.215 39.130 0.00 0.00 0.00 4.61
4188 13013 8.074370 GGACTAAAAAGTACCTGAATCAAACAC 58.926 37.037 0.00 0.00 0.00 3.32
4189 13014 7.229907 GGGACTAAAAAGTACCTGAATCAAACA 59.770 37.037 0.00 0.00 39.69 2.83
4190 13015 7.229907 TGGGACTAAAAAGTACCTGAATCAAAC 59.770 37.037 8.24 0.00 43.24 2.93
4193 13018 6.271391 TCTGGGACTAAAAAGTACCTGAATCA 59.729 38.462 12.48 0.00 44.41 2.57
4194 13019 6.708285 TCTGGGACTAAAAAGTACCTGAATC 58.292 40.000 12.48 0.00 44.41 2.52
4197 13022 5.399991 TCTCTGGGACTAAAAAGTACCTGA 58.600 41.667 13.75 13.75 44.93 3.86
4198 13023 5.740290 TCTCTGGGACTAAAAAGTACCTG 57.260 43.478 8.24 7.70 43.24 4.00
4199 13024 6.954352 AATCTCTGGGACTAAAAAGTACCT 57.046 37.500 8.24 0.00 43.24 3.08
4200 13025 8.075761 TCTAATCTCTGGGACTAAAAAGTACC 57.924 38.462 0.00 0.00 43.13 3.34
4201 13026 9.939802 TTTCTAATCTCTGGGACTAAAAAGTAC 57.060 33.333 0.00 0.00 0.00 2.73
4203 13028 9.862149 TTTTTCTAATCTCTGGGACTAAAAAGT 57.138 29.630 0.00 0.00 0.00 2.66
4209 13034 6.156429 GGGACTTTTTCTAATCTCTGGGACTA 59.844 42.308 0.00 0.00 0.00 2.59
4211 13036 5.045505 AGGGACTTTTTCTAATCTCTGGGAC 60.046 44.000 0.00 0.00 27.25 4.46
4212 13037 5.101529 AGGGACTTTTTCTAATCTCTGGGA 58.898 41.667 0.00 0.00 27.25 4.37
4213 13038 5.443230 AGGGACTTTTTCTAATCTCTGGG 57.557 43.478 0.00 0.00 27.25 4.45
4214 13039 7.852263 TCTTAGGGACTTTTTCTAATCTCTGG 58.148 38.462 0.00 0.00 41.75 3.86
4215 13040 9.377312 CTTCTTAGGGACTTTTTCTAATCTCTG 57.623 37.037 0.00 0.00 41.75 3.35
4216 13041 9.106977 ACTTCTTAGGGACTTTTTCTAATCTCT 57.893 33.333 0.00 0.00 41.75 3.10
4217 13042 9.373603 GACTTCTTAGGGACTTTTTCTAATCTC 57.626 37.037 0.00 0.00 41.75 2.75
4218 13043 8.322828 GGACTTCTTAGGGACTTTTTCTAATCT 58.677 37.037 0.00 0.00 41.75 2.40
4219 13044 7.553402 GGGACTTCTTAGGGACTTTTTCTAATC 59.447 40.741 0.00 0.00 41.75 1.75
4220 13045 7.239984 AGGGACTTCTTAGGGACTTTTTCTAAT 59.760 37.037 0.00 0.00 34.75 1.73
4221 13046 6.561454 AGGGACTTCTTAGGGACTTTTTCTAA 59.439 38.462 0.00 0.00 34.75 2.10
4222 13047 6.089502 AGGGACTTCTTAGGGACTTTTTCTA 58.910 40.000 0.00 0.00 34.75 2.10
4223 13048 4.914581 AGGGACTTCTTAGGGACTTTTTCT 59.085 41.667 0.00 0.00 34.75 2.52
4224 13049 5.244189 AGGGACTTCTTAGGGACTTTTTC 57.756 43.478 0.00 0.00 34.75 2.29
4225 13050 5.251005 CCTAGGGACTTCTTAGGGACTTTTT 59.749 44.000 0.00 0.00 39.49 1.94
4226 13051 4.783763 CCTAGGGACTTCTTAGGGACTTTT 59.216 45.833 0.00 0.00 39.49 2.27
4227 13052 4.046876 TCCTAGGGACTTCTTAGGGACTTT 59.953 45.833 9.46 0.00 39.49 2.66
4228 13053 3.601537 TCCTAGGGACTTCTTAGGGACTT 59.398 47.826 9.46 0.00 39.49 3.01
4229 13054 3.208173 TCCTAGGGACTTCTTAGGGACT 58.792 50.000 9.46 0.00 41.75 3.85
4230 13055 3.684408 TCCTAGGGACTTCTTAGGGAC 57.316 52.381 9.46 0.00 41.75 4.46
4231 13056 3.310435 GGTTCCTAGGGACTTCTTAGGGA 60.310 52.174 20.08 0.00 41.75 4.20
4232 13057 3.039743 GGTTCCTAGGGACTTCTTAGGG 58.960 54.545 20.08 0.00 41.75 3.53
4233 13058 3.721021 TGGTTCCTAGGGACTTCTTAGG 58.279 50.000 20.08 0.00 41.75 2.69
4234 13059 5.489249 GTTTGGTTCCTAGGGACTTCTTAG 58.511 45.833 20.08 0.00 41.75 2.18
4235 13060 4.020839 CGTTTGGTTCCTAGGGACTTCTTA 60.021 45.833 20.08 0.00 41.75 2.10
4236 13061 3.244457 CGTTTGGTTCCTAGGGACTTCTT 60.244 47.826 20.08 0.00 41.75 2.52
4237 13062 2.302157 CGTTTGGTTCCTAGGGACTTCT 59.698 50.000 20.08 0.00 41.75 2.85
4238 13063 2.614734 CCGTTTGGTTCCTAGGGACTTC 60.615 54.545 20.08 4.83 41.75 3.01
4239 13064 1.350019 CCGTTTGGTTCCTAGGGACTT 59.650 52.381 20.08 0.00 41.75 3.01
4240 13065 0.981943 CCGTTTGGTTCCTAGGGACT 59.018 55.000 20.08 0.00 46.37 3.85
4241 13066 0.035725 CCCGTTTGGTTCCTAGGGAC 60.036 60.000 12.35 12.35 41.26 4.46
4242 13067 0.178897 TCCCGTTTGGTTCCTAGGGA 60.179 55.000 9.46 0.00 44.85 4.20
4243 13068 0.252197 CTCCCGTTTGGTTCCTAGGG 59.748 60.000 9.46 0.00 40.16 3.53
4244 13069 0.252197 CCTCCCGTTTGGTTCCTAGG 59.748 60.000 0.82 0.82 34.77 3.02
4245 13070 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
4246 13071 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
4247 13072 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
4248 13073 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
4249 13074 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
4250 13075 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
4251 13076 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
4252 13077 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
4253 13078 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
4254 13079 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
4255 13080 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
4256 13081 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
4257 13082 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
4258 13083 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
4259 13084 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
4260 13085 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
4261 13086 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
4262 13087 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
4263 13088 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
4269 13094 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
4270 13095 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
4271 13096 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
4272 13097 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
4273 13098 7.393796 CAGTAGAGTCTTTTTCTAGTCCCTGTA 59.606 40.741 0.00 0.00 30.30 2.74
4274 13099 6.209788 CAGTAGAGTCTTTTTCTAGTCCCTGT 59.790 42.308 0.00 0.00 30.30 4.00
4275 13100 6.434652 TCAGTAGAGTCTTTTTCTAGTCCCTG 59.565 42.308 0.00 0.00 30.30 4.45
4276 13101 6.553857 TCAGTAGAGTCTTTTTCTAGTCCCT 58.446 40.000 0.00 0.00 30.30 4.20
4277 13102 6.837471 TCAGTAGAGTCTTTTTCTAGTCCC 57.163 41.667 0.00 0.00 30.30 4.46
4278 13103 8.113173 TCTTCAGTAGAGTCTTTTTCTAGTCC 57.887 38.462 0.00 0.00 30.30 3.85
4337 13162 5.699915 GTGTTTGGTTTAGAAGTCCTAGGAC 59.300 44.000 31.29 31.29 44.86 3.85
4338 13163 5.221783 GGTGTTTGGTTTAGAAGTCCTAGGA 60.222 44.000 7.62 7.62 0.00 2.94
4339 13164 5.001874 GGTGTTTGGTTTAGAAGTCCTAGG 58.998 45.833 0.82 0.82 0.00 3.02
4340 13165 5.001874 GGGTGTTTGGTTTAGAAGTCCTAG 58.998 45.833 0.00 0.00 0.00 3.02
4341 13166 4.202493 GGGGTGTTTGGTTTAGAAGTCCTA 60.202 45.833 0.00 0.00 0.00 2.94
4342 13167 3.436035 GGGGTGTTTGGTTTAGAAGTCCT 60.436 47.826 0.00 0.00 0.00 3.85
4343 13168 2.889045 GGGGTGTTTGGTTTAGAAGTCC 59.111 50.000 0.00 0.00 0.00 3.85
4344 13169 2.889045 GGGGGTGTTTGGTTTAGAAGTC 59.111 50.000 0.00 0.00 0.00 3.01
4345 13170 2.516702 AGGGGGTGTTTGGTTTAGAAGT 59.483 45.455 0.00 0.00 0.00 3.01
4346 13171 3.154710 GAGGGGGTGTTTGGTTTAGAAG 58.845 50.000 0.00 0.00 0.00 2.85
4347 13172 2.514582 TGAGGGGGTGTTTGGTTTAGAA 59.485 45.455 0.00 0.00 0.00 2.10
4348 13173 2.107552 CTGAGGGGGTGTTTGGTTTAGA 59.892 50.000 0.00 0.00 0.00 2.10
4349 13174 2.158519 ACTGAGGGGGTGTTTGGTTTAG 60.159 50.000 0.00 0.00 0.00 1.85
4350 13175 1.854280 ACTGAGGGGGTGTTTGGTTTA 59.146 47.619 0.00 0.00 0.00 2.01
4351 13176 0.634465 ACTGAGGGGGTGTTTGGTTT 59.366 50.000 0.00 0.00 0.00 3.27
4352 13177 0.185175 GACTGAGGGGGTGTTTGGTT 59.815 55.000 0.00 0.00 0.00 3.67
4353 13178 0.697854 AGACTGAGGGGGTGTTTGGT 60.698 55.000 0.00 0.00 0.00 3.67
4354 13179 0.478507 AAGACTGAGGGGGTGTTTGG 59.521 55.000 0.00 0.00 0.00 3.28
4355 13180 1.142870 TGAAGACTGAGGGGGTGTTTG 59.857 52.381 0.00 0.00 0.00 2.93
4356 13181 1.518367 TGAAGACTGAGGGGGTGTTT 58.482 50.000 0.00 0.00 0.00 2.83
4357 13182 1.747444 ATGAAGACTGAGGGGGTGTT 58.253 50.000 0.00 0.00 0.00 3.32
4358 13183 1.630878 GAATGAAGACTGAGGGGGTGT 59.369 52.381 0.00 0.00 0.00 4.16
4359 13184 1.630369 TGAATGAAGACTGAGGGGGTG 59.370 52.381 0.00 0.00 0.00 4.61
4360 13185 2.044793 TGAATGAAGACTGAGGGGGT 57.955 50.000 0.00 0.00 0.00 4.95
4361 13186 2.943199 GCTTGAATGAAGACTGAGGGGG 60.943 54.545 0.00 0.00 32.82 5.40
4362 13187 2.363683 GCTTGAATGAAGACTGAGGGG 58.636 52.381 0.00 0.00 32.82 4.79
4363 13188 2.363683 GGCTTGAATGAAGACTGAGGG 58.636 52.381 0.00 0.00 36.65 4.30
4413 13519 4.994201 TGCGCGTCGGTCACAGAC 62.994 66.667 8.43 0.00 35.41 3.51
4515 13646 2.517959 GTGCATGGTATGGTATGGCAT 58.482 47.619 4.88 4.88 0.00 4.40
4516 13647 1.478471 GGTGCATGGTATGGTATGGCA 60.478 52.381 0.00 0.00 0.00 4.92
4522 13653 1.076777 GCAGGGTGCATGGTATGGT 60.077 57.895 0.00 0.00 44.26 3.55


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

AutoCloner maintained by Alex Coulton.