Multiple sequence alignment - TraesCS5D01G388100

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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 TraesCS5D01G388100 chr5D 100.000 8237 0 0 1 8237 457670611 457678847 0.000000e+00 15211.0
1 TraesCS5D01G388100 chr5D 79.231 260 40 9 4058 4309 257509694 257509441 1.420000e-37 169.0
2 TraesCS5D01G388100 chr5D 82.955 88 13 2 4418 4503 545017883 545017970 2.460000e-10 78.7
3 TraesCS5D01G388100 chr5A 95.397 6474 177 45 840 7262 575603517 575609920 0.000000e+00 10192.0
4 TraesCS5D01G388100 chr5A 92.169 830 57 4 41 862 575602675 575603504 0.000000e+00 1166.0
5 TraesCS5D01G388100 chr5A 91.342 462 23 12 7724 8180 575611166 575611615 4.220000e-172 616.0
6 TraesCS5D01G388100 chr5A 89.744 195 10 4 7260 7444 575609947 575610141 2.970000e-59 241.0
7 TraesCS5D01G388100 chr5A 90.419 167 13 3 3725 3890 657269846 657270010 5.010000e-52 217.0
8 TraesCS5D01G388100 chr5A 90.441 136 13 0 7595 7730 575610760 575610895 6.570000e-41 180.0
9 TraesCS5D01G388100 chr5A 78.113 265 42 9 4058 4312 342236808 342236550 3.980000e-33 154.0
10 TraesCS5D01G388100 chr5A 88.660 97 9 2 7505 7599 575610458 575610554 5.220000e-22 117.0
11 TraesCS5D01G388100 chr5A 97.222 36 1 0 1 36 575602613 575602648 2.480000e-05 62.1
12 TraesCS5D01G388100 chr5B 89.202 1741 133 27 1699 3410 559771490 559773204 0.000000e+00 2122.0
13 TraesCS5D01G388100 chr5B 92.266 1280 68 18 273 1546 559769959 559771213 0.000000e+00 1786.0
14 TraesCS5D01G388100 chr5B 89.352 864 46 23 6432 7262 559775505 559776355 0.000000e+00 1044.0
15 TraesCS5D01G388100 chr5B 86.306 869 94 13 4562 5413 559773286 559774146 0.000000e+00 922.0
16 TraesCS5D01G388100 chr5B 83.352 895 76 26 5503 6368 559774159 559775009 0.000000e+00 760.0
17 TraesCS5D01G388100 chr5B 85.747 442 12 8 7826 8237 559776992 559777412 3.560000e-113 420.0
18 TraesCS5D01G388100 chr5B 88.382 241 22 5 7589 7824 559776723 559776962 1.350000e-72 285.0
19 TraesCS5D01G388100 chr5B 91.925 161 12 1 1541 1700 559771248 559771408 2.990000e-54 224.0
20 TraesCS5D01G388100 chr5B 79.231 260 41 8 4058 4309 291792190 291791936 1.420000e-37 169.0
21 TraesCS5D01G388100 chr5B 95.699 93 2 1 7260 7352 559776382 559776472 1.850000e-31 148.0
22 TraesCS5D01G388100 chr5B 94.186 86 4 1 5411 5496 364139417 364139501 6.710000e-26 130.0
23 TraesCS5D01G388100 chr5B 82.955 88 13 2 4418 4503 318646692 318646605 2.460000e-10 78.7
24 TraesCS5D01G388100 chrUn 100.000 400 0 0 2055 2454 478708249 478707850 0.000000e+00 739.0
25 TraesCS5D01G388100 chr6A 89.785 186 13 5 3536 3719 32531714 32531533 4.970000e-57 233.0
26 TraesCS5D01G388100 chr6A 89.247 186 14 5 3536 3719 32424119 32423938 2.310000e-55 228.0
27 TraesCS5D01G388100 chr6A 88.710 186 15 5 3536 3719 32557907 32557726 1.080000e-53 222.0
28 TraesCS5D01G388100 chr6A 80.000 275 42 9 4048 4311 617067260 617066988 3.030000e-44 191.0
29 TraesCS5D01G388100 chr6A 90.000 50 5 0 3422 3471 588444068 588444117 1.920000e-06 65.8
30 TraesCS5D01G388100 chr2B 91.071 168 15 0 3729 3896 31716187 31716020 2.310000e-55 228.0
31 TraesCS5D01G388100 chr2B 88.830 188 15 5 3534 3719 364848636 364848453 8.320000e-55 226.0
32 TraesCS5D01G388100 chr2B 85.906 149 21 0 3727 3875 90402927 90403075 8.560000e-35 159.0
33 TraesCS5D01G388100 chr3B 90.643 171 15 1 3726 3896 733573555 733573386 8.320000e-55 226.0
34 TraesCS5D01G388100 chr3B 83.810 210 25 5 4048 4252 508479099 508478894 3.030000e-44 191.0
35 TraesCS5D01G388100 chr6B 88.172 186 16 5 3536 3719 554799778 554799597 5.010000e-52 217.0
36 TraesCS5D01G388100 chr6B 80.365 219 28 8 4048 4251 717848477 717848695 1.430000e-32 152.0
37 TraesCS5D01G388100 chr6B 100.000 29 0 0 3422 3450 523759712 523759740 4.000000e-03 54.7
38 TraesCS5D01G388100 chr4D 88.172 186 16 5 3536 3719 69251497 69251316 5.010000e-52 217.0
39 TraesCS5D01G388100 chr4D 79.474 190 25 10 4320 4503 390207261 390207442 1.120000e-23 122.0
40 TraesCS5D01G388100 chr3A 86.275 204 21 5 3535 3734 550724957 550724757 1.800000e-51 215.0
41 TraesCS5D01G388100 chr2A 87.766 188 17 5 3534 3719 26936929 26936746 1.800000e-51 215.0
42 TraesCS5D01G388100 chr2A 92.308 91 4 3 5412 5502 79308144 79308231 8.680000e-25 126.0
43 TraesCS5D01G388100 chr2A 90.526 95 8 1 5412 5506 78845862 78845769 3.120000e-24 124.0
44 TraesCS5D01G388100 chr7B 89.024 164 18 0 3733 3896 268453083 268452920 3.900000e-48 204.0
45 TraesCS5D01G388100 chr3D 84.286 210 25 4 4048 4252 391261950 391261744 1.810000e-46 198.0
46 TraesCS5D01G388100 chr3D 93.478 92 4 2 5412 5503 381989158 381989069 1.440000e-27 135.0
47 TraesCS5D01G388100 chr3D 94.118 85 4 1 5412 5496 429306242 429306325 2.410000e-25 128.0
48 TraesCS5D01G388100 chr4B 87.059 170 20 2 3729 3896 99751545 99751714 3.030000e-44 191.0
49 TraesCS5D01G388100 chr7D 81.720 186 25 6 4056 4233 146866779 146866963 6.660000e-31 147.0
50 TraesCS5D01G388100 chr1D 94.565 92 4 1 5405 5496 120537708 120537618 3.100000e-29 141.0
51 TraesCS5D01G388100 chr7A 95.294 85 3 1 5412 5496 562274919 562275002 5.190000e-27 134.0
52 TraesCS5D01G388100 chr1A 89.796 98 9 1 5403 5499 589902811 589902714 3.120000e-24 124.0
53 TraesCS5D01G388100 chr4A 78.307 189 26 10 4320 4503 293778756 293778934 3.140000e-19 108.0
54 TraesCS5D01G388100 chr2D 77.128 188 30 7 4320 4503 169220362 169220184 6.800000e-16 97.1
55 TraesCS5D01G388100 chr6D 75.661 189 32 12 4320 4503 59923572 59923393 1.910000e-11 82.4
56 TraesCS5D01G388100 chr1B 82.955 88 13 2 4418 4503 318928590 318928503 2.460000e-10 78.7
57 TraesCS5D01G388100 chr1B 82.955 88 13 2 4418 4503 508054133 508054046 2.460000e-10 78.7


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 TraesCS5D01G388100 chr5D 457670611 457678847 8236 False 15211.000000 15211 100.000000 1 8237 1 chr5D.!!$F1 8236
1 TraesCS5D01G388100 chr5A 575602613 575611615 9002 False 1796.300000 10192 92.139286 1 8180 7 chr5A.!!$F2 8179
2 TraesCS5D01G388100 chr5B 559769959 559777412 7453 False 856.777778 2122 89.136778 273 8237 9 chr5B.!!$F2 7964

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
257 284 0.533755 AGAAGGTCTGCACTGCACAC 60.534 55.0 0.00 0.0 33.79 3.82 F
950 1016 0.615850 AGAGAAAGAAGAAGCGGGGG 59.384 55.0 0.00 0.0 0.00 5.40 F
1668 1776 0.537371 AGTCGGGGCAGGAAAAGTTG 60.537 55.0 0.00 0.0 0.00 3.16 F
3397 3620 0.796312 AGCGCAAAACATGGAGTACG 59.204 50.0 11.47 0.0 0.00 3.67 F
4429 4652 0.228742 CGTGAAGTGTGAACCGAACG 59.771 55.0 0.00 0.0 0.00 3.95 F
5042 5276 0.904649 ATGTTCCTCGATGTGGCTGA 59.095 50.0 0.00 0.0 0.00 4.26 F
6736 7459 0.477795 ATATGCCCCCTCCCCCTAAC 60.478 60.0 0.00 0.0 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1759 0.598065 CTTCAACTTTTCCTGCCCCG 59.402 55.000 0.00 0.0 0.00 5.73 R
2906 3127 4.226113 TGTTTCGAACCAAAAATACCCG 57.774 40.909 0.00 0.0 0.00 5.28 R
3566 3789 0.319297 GTCCCCGTATGCGTATCACC 60.319 60.000 1.69 0.0 36.15 4.02 R
4714 4939 0.036010 ATGCCCAGTCTTCTTGTCCG 60.036 55.000 0.00 0.0 0.00 4.79 R
5820 6080 0.671163 TAACGTGATCAACCACCGCC 60.671 55.000 0.00 0.0 33.67 6.13 R
6978 7701 0.044092 TTCCTCCCACCTATGGCAGA 59.956 55.000 0.00 0.0 45.76 4.26 R
8100 9653 0.866427 CATGTGCCGCTGATGAGATC 59.134 55.000 0.00 0.0 0.00 2.75 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
29 30 2.286950 TGTTCATGCTGTCGTTTGCTTC 60.287 45.455 0.00 0.00 0.00 3.86
36 37 2.046313 CTGTCGTTTGCTTCACAATGC 58.954 47.619 0.00 0.00 38.31 3.56
37 38 1.044725 GTCGTTTGCTTCACAATGCG 58.955 50.000 0.00 0.00 38.31 4.73
38 39 0.660488 TCGTTTGCTTCACAATGCGT 59.340 45.000 0.00 0.00 38.31 5.24
39 40 1.867865 TCGTTTGCTTCACAATGCGTA 59.132 42.857 0.00 0.00 38.31 4.42
42 65 2.261037 TTGCTTCACAATGCGTATGC 57.739 45.000 0.00 0.00 35.75 3.14
73 96 4.651503 TCCCATTCCTTTTAGTTTGTGCAA 59.348 37.500 0.00 0.00 0.00 4.08
151 178 1.133730 GGATCTGGGGTCGACTCTAGT 60.134 57.143 25.91 14.74 0.00 2.57
153 180 0.680280 TCTGGGGTCGACTCTAGTGC 60.680 60.000 25.91 5.21 0.00 4.40
160 187 1.649662 GTCGACTCTAGTGCGCTTTTC 59.350 52.381 9.73 0.00 0.00 2.29
169 196 1.372748 TGCGCTTTTCATTTGCCCG 60.373 52.632 9.73 0.00 0.00 6.13
188 215 1.881973 CGTGAAGCAATGGGGATATGG 59.118 52.381 0.00 0.00 0.00 2.74
191 218 2.108776 TGAAGCAATGGGGATATGGGAG 59.891 50.000 0.00 0.00 0.00 4.30
193 220 1.707427 AGCAATGGGGATATGGGAGAC 59.293 52.381 0.00 0.00 0.00 3.36
194 221 1.425066 GCAATGGGGATATGGGAGACA 59.575 52.381 0.00 0.00 0.00 3.41
211 238 7.075797 TGGGAGACATATTGGAGAGAAATAGA 58.924 38.462 0.00 0.00 0.00 1.98
257 284 0.533755 AGAAGGTCTGCACTGCACAC 60.534 55.000 0.00 0.00 33.79 3.82
271 298 4.275689 CACTGCACACACTTGATTTCCTTA 59.724 41.667 0.00 0.00 0.00 2.69
275 302 4.320494 GCACACACTTGATTTCCTTACCTG 60.320 45.833 0.00 0.00 0.00 4.00
282 309 6.246420 CTTGATTTCCTTACCTGTCAAGTG 57.754 41.667 0.00 0.00 38.33 3.16
333 360 5.402398 GCAGACCATTCAATTCCAGTTTAC 58.598 41.667 0.00 0.00 0.00 2.01
391 418 1.101331 CTCAGGCAGCCAAGGAATTC 58.899 55.000 15.80 0.00 0.00 2.17
415 442 5.294552 CGAAACAGAACTGAAGAAAGAACCT 59.705 40.000 8.87 0.00 0.00 3.50
454 481 4.614036 CCACCCACAACCCCCACC 62.614 72.222 0.00 0.00 0.00 4.61
529 556 1.649321 AAGAGAGCACATGAGGACCA 58.351 50.000 0.00 0.00 0.00 4.02
537 564 1.379044 CATGAGGACCAGGCCAACC 60.379 63.158 5.01 2.06 0.00 3.77
613 640 3.803778 CACATTGCTCCCTGTTTTTGTTC 59.196 43.478 0.00 0.00 0.00 3.18
639 666 2.148916 CAGGCCATGCAGCAATATTG 57.851 50.000 11.27 11.27 0.00 1.90
666 693 2.696759 CGGCGAAAATGTGTCCCCC 61.697 63.158 0.00 0.00 0.00 5.40
695 722 8.752005 AAATACCATGTTGCTAATGTATGAGT 57.248 30.769 0.00 0.00 0.00 3.41
699 726 8.574251 ACCATGTTGCTAATGTATGAGTTTAA 57.426 30.769 0.00 0.00 0.00 1.52
759 786 3.882888 TCTGCTGTTTTTCCTGTCGAAAT 59.117 39.130 0.00 0.00 40.18 2.17
761 788 5.529430 TCTGCTGTTTTTCCTGTCGAAATTA 59.471 36.000 0.00 0.00 40.18 1.40
762 789 6.206634 TCTGCTGTTTTTCCTGTCGAAATTAT 59.793 34.615 0.00 0.00 40.18 1.28
763 790 6.148948 TGCTGTTTTTCCTGTCGAAATTATG 58.851 36.000 0.00 0.00 40.18 1.90
764 791 5.572896 GCTGTTTTTCCTGTCGAAATTATGG 59.427 40.000 0.00 0.00 40.18 2.74
765 792 6.569610 GCTGTTTTTCCTGTCGAAATTATGGA 60.570 38.462 0.00 0.00 40.18 3.41
766 793 6.908825 TGTTTTTCCTGTCGAAATTATGGAG 58.091 36.000 0.00 0.00 40.18 3.86
767 794 6.488683 TGTTTTTCCTGTCGAAATTATGGAGT 59.511 34.615 0.00 0.00 40.18 3.85
768 795 7.662258 TGTTTTTCCTGTCGAAATTATGGAGTA 59.338 33.333 0.00 0.00 40.18 2.59
770 797 8.801882 TTTTCCTGTCGAAATTATGGAGTATT 57.198 30.769 0.00 0.00 40.18 1.89
771 798 7.786178 TTCCTGTCGAAATTATGGAGTATTG 57.214 36.000 0.00 0.00 0.00 1.90
794 825 5.189736 TGGTACATCAGTTTGGAATAGAGCT 59.810 40.000 0.00 0.00 0.00 4.09
823 854 0.677731 TGTGCCTGACATTGCTAGCC 60.678 55.000 13.29 0.00 0.00 3.93
837 868 1.474077 GCTAGCCCAGTTGGATTTGTG 59.526 52.381 2.29 0.00 37.39 3.33
856 887 1.195115 GGTAGTGAGGATGTGCCAGA 58.805 55.000 0.00 0.00 40.02 3.86
862 893 4.922206 AGTGAGGATGTGCCAGAATTTTA 58.078 39.130 0.00 0.00 40.02 1.52
863 894 4.946157 AGTGAGGATGTGCCAGAATTTTAG 59.054 41.667 0.00 0.00 40.02 1.85
864 895 4.702131 GTGAGGATGTGCCAGAATTTTAGT 59.298 41.667 0.00 0.00 40.02 2.24
865 896 4.943705 TGAGGATGTGCCAGAATTTTAGTC 59.056 41.667 0.00 0.00 40.02 2.59
877 943 7.577807 GCCAGAATTTTAGTCTGAGACACTAGA 60.578 40.741 15.86 0.00 44.44 2.43
898 964 3.645660 TGGGCCCGCATTGTCAGA 61.646 61.111 19.37 0.00 0.00 3.27
946 1012 1.128321 GCAGCAGAGAAAGAAGAAGCG 59.872 52.381 0.00 0.00 0.00 4.68
947 1013 1.731160 CAGCAGAGAAAGAAGAAGCGG 59.269 52.381 0.00 0.00 0.00 5.52
948 1014 1.082690 GCAGAGAAAGAAGAAGCGGG 58.917 55.000 0.00 0.00 0.00 6.13
949 1015 1.731720 CAGAGAAAGAAGAAGCGGGG 58.268 55.000 0.00 0.00 0.00 5.73
950 1016 0.615850 AGAGAAAGAAGAAGCGGGGG 59.384 55.000 0.00 0.00 0.00 5.40
951 1017 1.002011 AGAAAGAAGAAGCGGGGGC 60.002 57.895 0.00 0.00 0.00 5.80
952 1018 1.303317 GAAAGAAGAAGCGGGGGCA 60.303 57.895 0.00 0.00 0.00 5.36
953 1019 0.893727 GAAAGAAGAAGCGGGGGCAA 60.894 55.000 0.00 0.00 0.00 4.52
955 1021 2.034221 GAAGAAGCGGGGGCAACT 59.966 61.111 0.00 0.00 0.00 3.16
957 1023 1.152546 AAGAAGCGGGGGCAACTTT 60.153 52.632 0.00 0.00 0.00 2.66
1082 1149 1.212195 CCCTAAACCCTACCTTGAGCC 59.788 57.143 0.00 0.00 0.00 4.70
1083 1150 1.212195 CCTAAACCCTACCTTGAGCCC 59.788 57.143 0.00 0.00 0.00 5.19
1084 1151 1.212195 CTAAACCCTACCTTGAGCCCC 59.788 57.143 0.00 0.00 0.00 5.80
1085 1152 0.774491 AAACCCTACCTTGAGCCCCA 60.774 55.000 0.00 0.00 0.00 4.96
1086 1153 1.208165 AACCCTACCTTGAGCCCCAG 61.208 60.000 0.00 0.00 0.00 4.45
1087 1154 2.592308 CCTACCTTGAGCCCCAGC 59.408 66.667 0.00 0.00 40.32 4.85
1090 1157 3.881926 TACCTTGAGCCCCAGCCCA 62.882 63.158 0.00 0.00 41.25 5.36
1665 1772 2.084546 CTTTAGTCGGGGCAGGAAAAG 58.915 52.381 0.00 0.00 0.00 2.27
1668 1776 0.537371 AGTCGGGGCAGGAAAAGTTG 60.537 55.000 0.00 0.00 0.00 3.16
1930 2128 8.098286 AGTTTGCTAACCCAAAACTAAAGTTTT 58.902 29.630 13.70 13.70 44.61 2.43
2028 2226 8.656849 GTCTTCTCGTCACATGTTAAATAATGT 58.343 33.333 0.00 0.00 37.50 2.71
2550 2769 8.039603 TGTCTGTTTGCGATATTTACTTTCAT 57.960 30.769 0.00 0.00 0.00 2.57
2673 2892 5.985530 TCTGTAGTCTTCAAAGTCATGTGTG 59.014 40.000 0.00 0.00 0.00 3.82
2684 2903 1.212935 GTCATGTGTGATAGGCCCCTT 59.787 52.381 0.00 0.00 36.60 3.95
2876 3097 1.133253 CAGACATTTGCGCACCGAG 59.867 57.895 11.12 2.71 0.00 4.63
2897 3118 5.065090 CGAGTTGCATCAAGTTTCATGGATA 59.935 40.000 0.00 0.00 0.00 2.59
2906 3127 9.090692 CATCAAGTTTCATGGATATTTTCAACC 57.909 33.333 0.00 0.00 0.00 3.77
2910 3131 4.243793 TCATGGATATTTTCAACCGGGT 57.756 40.909 6.32 0.00 0.00 5.28
2922 3143 2.553172 TCAACCGGGTATTTTTGGTTCG 59.447 45.455 6.32 0.00 42.60 3.95
3257 3480 6.216456 AGGTGACATCTCCTTCTTTTATTCCT 59.784 38.462 0.00 0.00 36.53 3.36
3305 3528 8.338259 AGATGCATTGACGTATATTGTTTTCTC 58.662 33.333 0.00 0.00 0.00 2.87
3341 3564 7.117379 GTCTGTCTTTGTATGTAAACCACCTAC 59.883 40.741 0.00 0.00 0.00 3.18
3364 3587 9.226606 CTACACATTTTAGGAGTGTTTATCCAA 57.773 33.333 2.59 0.00 43.40 3.53
3397 3620 0.796312 AGCGCAAAACATGGAGTACG 59.204 50.000 11.47 0.00 0.00 3.67
3522 3745 8.630037 GGTTTACCAAATTACTATGGAATCCAG 58.370 37.037 8.40 0.00 39.12 3.86
3536 3759 4.077982 TGGAATCCAGTCCTATAACCTCCT 60.078 45.833 0.00 0.00 38.62 3.69
3554 3777 1.950909 CCTAAAAAGCACCAACACGGA 59.049 47.619 0.00 0.00 38.63 4.69
3557 3780 1.021968 AAAAGCACCAACACGGAGAC 58.978 50.000 0.00 0.00 38.63 3.36
3618 3841 4.516321 AGCATTTTCCAAAAACAGCCATTC 59.484 37.500 7.42 0.00 0.00 2.67
3726 3949 8.840200 TGAGATAATATCAGAATACTACCCCC 57.160 38.462 2.84 0.00 0.00 5.40
3780 4003 5.376653 AGAGGATTACAGGGGAATATCCT 57.623 43.478 0.00 0.00 45.86 3.24
3781 4004 5.742743 AGAGGATTACAGGGGAATATCCTT 58.257 41.667 0.00 0.00 43.83 3.36
3809 4032 2.619931 CCAAAATCCCCAGAAAACCCT 58.380 47.619 0.00 0.00 0.00 4.34
3827 4050 3.464833 ACCCTATCAGCCCATTTGATTCT 59.535 43.478 0.00 0.00 36.68 2.40
3871 4094 4.374584 CAATCCCCGCCAACCCCA 62.375 66.667 0.00 0.00 0.00 4.96
3909 4132 3.712218 TCAACAACCATATCGGGGATACA 59.288 43.478 0.00 0.00 40.22 2.29
3924 4147 3.400255 GGATACAGCGGGTATTTCCTTC 58.600 50.000 5.70 0.00 42.76 3.46
3956 4179 2.046292 TCGGAATCATGGGATACTGCA 58.954 47.619 0.00 0.00 32.09 4.41
3964 4187 2.082140 TGGGATACTGCAGGATACGT 57.918 50.000 19.93 0.00 46.39 3.57
3980 4203 4.720090 GATACGTGTATCCTGGTGTATCG 58.280 47.826 8.52 0.00 36.75 2.92
4103 4326 7.966812 AGCTCAAACCTCATTTTATTTTTCCT 58.033 30.769 0.00 0.00 0.00 3.36
4144 4367 3.306472 ACACCCTATCTCTCTCCACTC 57.694 52.381 0.00 0.00 0.00 3.51
4145 4368 2.856231 ACACCCTATCTCTCTCCACTCT 59.144 50.000 0.00 0.00 0.00 3.24
4167 4390 8.268605 ACTCTCTCCTAAATCCTGTAAAATTCC 58.731 37.037 0.00 0.00 0.00 3.01
4314 4537 0.883833 ACAATCCAAAGAAGCCTGCG 59.116 50.000 0.00 0.00 0.00 5.18
4318 4541 0.889186 TCCAAAGAAGCCTGCGAACC 60.889 55.000 0.00 0.00 0.00 3.62
4324 4547 1.079503 GAAGCCTGCGAACCTTAGTG 58.920 55.000 0.00 0.00 0.00 2.74
4367 4590 4.241590 ACATTGCATGTGATTTGACGTT 57.758 36.364 6.61 0.00 43.01 3.99
4373 4596 6.687653 TGCATGTGATTTGACGTTAATTTG 57.312 33.333 0.00 0.00 0.00 2.32
4411 4634 5.867174 GGAGTTTATGTTTTTCCAATTCCCG 59.133 40.000 0.00 0.00 0.00 5.14
4429 4652 0.228742 CGTGAAGTGTGAACCGAACG 59.771 55.000 0.00 0.00 0.00 3.95
4463 4686 7.942341 TGACATAATTTCTGTTTACCAGTCCTT 59.058 33.333 0.00 0.00 42.19 3.36
4527 4750 4.986708 TGCGAACCAAAGGGGCCC 62.987 66.667 17.12 17.12 42.05 5.80
4608 4831 3.572255 GGAGTGTAGCCAACATGGAAAAA 59.428 43.478 0.00 0.00 40.96 1.94
4865 5099 6.478344 TGCAATCGAATTTTAATGGGTTATGC 59.522 34.615 0.00 0.00 0.00 3.14
4891 5125 7.765819 CCTTATCACTTGTGTCAGTCATGATTA 59.234 37.037 0.00 0.00 37.87 1.75
4900 5134 5.237344 GTGTCAGTCATGATTATAAGGCACC 59.763 44.000 0.00 0.00 37.87 5.01
5042 5276 0.904649 ATGTTCCTCGATGTGGCTGA 59.095 50.000 0.00 0.00 0.00 4.26
5167 5403 5.181748 GCTGTTCTTGTGAGGATGAATAGT 58.818 41.667 0.00 0.00 0.00 2.12
5387 5624 5.163416 GCATAACTAAAGGGCCATTGTTCAT 60.163 40.000 1.95 0.00 0.00 2.57
5497 5735 1.497309 ATTTTGGGACGGAGGGAGCA 61.497 55.000 0.00 0.00 0.00 4.26
5562 5813 3.570550 TGCCACGCCTTAACTGTTTAAAT 59.429 39.130 0.00 0.00 0.00 1.40
5574 5827 6.724893 AACTGTTTAAATGTTAAGGCAGGT 57.275 33.333 7.48 8.22 0.00 4.00
5729 5989 6.496565 TCATCACCATCCATGTTTTTAAGGTT 59.503 34.615 0.00 0.00 0.00 3.50
5753 6013 3.119101 CCATAAGGCGACACTTAGACACT 60.119 47.826 0.00 0.00 36.47 3.55
5797 6057 2.898705 CAGCGTCCTAGCATTTCTTCT 58.101 47.619 0.00 0.00 40.15 2.85
5798 6058 2.606725 CAGCGTCCTAGCATTTCTTCTG 59.393 50.000 0.00 0.00 40.15 3.02
5814 6074 4.097418 TCTTCTGCCTTAGGAGCTTAAGT 58.903 43.478 0.69 0.00 31.46 2.24
5820 6080 3.274288 CCTTAGGAGCTTAAGTGGCAAG 58.726 50.000 4.02 2.39 0.00 4.01
5836 6097 1.671054 AAGGCGGTGGTTGATCACG 60.671 57.895 0.00 0.00 38.46 4.35
5891 6152 8.474831 TGCCATGATATGTATAGTACACCATAC 58.525 37.037 0.00 0.77 42.23 2.39
6051 6312 5.294306 CCATTGCTTTTCGTCTTAGCTATCA 59.706 40.000 0.00 0.00 35.93 2.15
6157 6425 2.100418 CTGATCGCTGGACATGAGAGAA 59.900 50.000 0.00 0.00 0.00 2.87
6276 6544 1.202114 CAAAATGATGTGACCCGGTGG 59.798 52.381 0.00 0.00 37.80 4.61
6323 6591 1.221840 CCACTCACTTGGATCCCCG 59.778 63.158 9.90 2.25 39.24 5.73
6326 6594 2.609299 TCACTTGGATCCCCGCCA 60.609 61.111 9.90 0.00 34.29 5.69
6582 7281 8.385111 GCAAAAATGATTCATCATGTTAGGTTG 58.615 33.333 5.75 2.79 46.22 3.77
6583 7282 9.426837 CAAAAATGATTCATCATGTTAGGTTGT 57.573 29.630 5.75 0.00 46.22 3.32
6585 7284 7.943079 AATGATTCATCATGTTAGGTTGTGA 57.057 32.000 2.98 0.00 46.22 3.58
6586 7285 7.943079 ATGATTCATCATGTTAGGTTGTGAA 57.057 32.000 1.28 0.00 45.27 3.18
6588 7287 8.352137 TGATTCATCATGTTAGGTTGTGAAAT 57.648 30.769 0.00 0.00 0.00 2.17
6591 7311 7.757941 TCATCATGTTAGGTTGTGAAATTCA 57.242 32.000 0.00 0.00 0.00 2.57
6613 7333 1.492599 GCCATCTTCCTTTCCTAGCCT 59.507 52.381 0.00 0.00 0.00 4.58
6614 7334 2.486370 GCCATCTTCCTTTCCTAGCCTC 60.486 54.545 0.00 0.00 0.00 4.70
6615 7335 2.105649 CCATCTTCCTTTCCTAGCCTCC 59.894 54.545 0.00 0.00 0.00 4.30
6616 7336 2.642171 TCTTCCTTTCCTAGCCTCCA 57.358 50.000 0.00 0.00 0.00 3.86
6636 7356 4.167892 TCCACCCCACAAGCTTTATCATAT 59.832 41.667 0.00 0.00 0.00 1.78
6637 7357 5.371176 TCCACCCCACAAGCTTTATCATATA 59.629 40.000 0.00 0.00 0.00 0.86
6642 7362 5.106396 CCCACAAGCTTTATCATATAGCAGC 60.106 44.000 9.49 0.00 35.55 5.25
6643 7363 5.704515 CCACAAGCTTTATCATATAGCAGCT 59.295 40.000 9.49 0.00 39.30 4.24
6660 7380 3.863400 GCAGCTGGTTGCATTTTCATTCT 60.863 43.478 17.12 0.00 45.94 2.40
6673 7395 8.444715 TGCATTTTCATTCTTGTATTCATTTGC 58.555 29.630 0.00 0.00 0.00 3.68
6702 7424 4.518590 CCAATGATTTGGCCATCATACGTA 59.481 41.667 19.78 0.00 45.71 3.57
6707 7429 5.700832 TGATTTGGCCATCATACGTATTCTC 59.299 40.000 6.09 0.00 0.00 2.87
6728 7450 5.249393 TCTCTGAAGAAATATATGCCCCCTC 59.751 44.000 0.00 0.00 0.00 4.30
6736 7459 0.477795 ATATGCCCCCTCCCCCTAAC 60.478 60.000 0.00 0.00 0.00 2.34
6963 7686 3.489908 CCGACGACTTCATGACATCTGAT 60.490 47.826 0.00 0.00 0.00 2.90
7074 7806 1.006086 TTAGTTGCGCCATGTCATCG 58.994 50.000 4.18 0.00 0.00 3.84
7139 7871 9.686683 AAGCTTTATTATTAGTCCATGTGTTCT 57.313 29.630 0.00 0.00 0.00 3.01
7173 7905 6.017109 GGTAGTGACAAATTGTGAACATGACT 60.017 38.462 2.20 0.00 0.00 3.41
7210 7942 0.246360 TCGTCCGCACATCAGTTGAT 59.754 50.000 0.00 0.00 34.56 2.57
7219 7951 2.819422 CATCAGTTGATGCGTTCCAG 57.181 50.000 9.00 0.00 44.44 3.86
7236 7973 0.173708 CAGCAGTAAGAGTCCCGTCC 59.826 60.000 0.00 0.00 0.00 4.79
7246 7983 0.833287 AGTCCCGTCCAATCAGATGG 59.167 55.000 0.00 0.00 41.85 3.51
7281 8047 2.550208 GCCGAATCTGTCCCCGAATATT 60.550 50.000 0.00 0.00 0.00 1.28
7363 8129 2.223363 ACACGTCGATACTCTGATGCTG 60.223 50.000 0.00 0.00 0.00 4.41
7373 8139 1.152943 CTGATGCTGCTGGCCAGAT 60.153 57.895 37.21 20.66 44.64 2.90
7374 8140 0.752009 CTGATGCTGCTGGCCAGATT 60.752 55.000 37.21 14.63 44.64 2.40
7375 8141 0.323999 TGATGCTGCTGGCCAGATTT 60.324 50.000 37.21 15.01 44.64 2.17
7376 8142 0.102481 GATGCTGCTGGCCAGATTTG 59.898 55.000 37.21 21.24 44.64 2.32
7377 8143 1.956629 ATGCTGCTGGCCAGATTTGC 61.957 55.000 37.21 28.85 44.64 3.68
7379 8145 1.214589 CTGCTGGCCAGATTTGCAC 59.785 57.895 37.21 16.86 44.64 4.57
7380 8146 2.221906 CTGCTGGCCAGATTTGCACC 62.222 60.000 37.21 16.08 44.64 5.01
7381 8147 2.879907 CTGGCCAGATTTGCACCG 59.120 61.111 29.88 0.00 0.00 4.94
7389 8165 4.432712 GCCAGATTTGCACCGAAAAATAT 58.567 39.130 0.00 0.00 0.00 1.28
7421 8197 3.317711 ACAGTGATGATTTGCACCGAAAA 59.682 39.130 0.00 0.00 35.67 2.29
7424 8200 5.406175 CAGTGATGATTTGCACCGAAAATTT 59.594 36.000 0.00 0.00 35.67 1.82
7444 8220 3.253416 GTCGACCAGACGGCTATTC 57.747 57.895 3.51 0.00 40.43 1.75
7448 8224 1.405821 CGACCAGACGGCTATTCTCTT 59.594 52.381 0.00 0.00 34.57 2.85
7466 8242 6.528537 TCTCTTCCTCTCTCTTTTCTGATG 57.471 41.667 0.00 0.00 0.00 3.07
7467 8243 6.252233 TCTCTTCCTCTCTCTTTTCTGATGA 58.748 40.000 0.00 0.00 0.00 2.92
7476 8252 3.149196 TCTTTTCTGATGAAGGGCACAC 58.851 45.455 0.00 0.00 33.28 3.82
7550 8582 2.036256 CCAGAAGGCACAAGGGGG 59.964 66.667 0.00 0.00 0.00 5.40
7572 8606 3.739810 GGTGTACTGACTTCGTTTTCTCC 59.260 47.826 0.00 0.00 0.00 3.71
7636 8880 0.918983 TGGGATGTGGATGAAGACCC 59.081 55.000 0.00 0.00 36.72 4.46
7639 8883 1.284785 GGATGTGGATGAAGACCCCAA 59.715 52.381 0.00 0.00 0.00 4.12
7718 8962 4.028993 AGGGTGGCTTCGATTTCTTTTA 57.971 40.909 0.00 0.00 0.00 1.52
7742 9262 4.336433 TGCTTCTATAAAGATGGTTGCAGC 59.664 41.667 0.00 0.00 0.00 5.25
7849 9401 6.980978 TGAAGACCTCACTCGATTTATTGATC 59.019 38.462 0.00 0.00 0.00 2.92
8000 9552 2.146342 CGCTTGACCAGTCTTGTGAAT 58.854 47.619 0.00 0.00 0.00 2.57
8001 9553 2.158449 CGCTTGACCAGTCTTGTGAATC 59.842 50.000 0.00 0.00 0.00 2.52
8002 9554 3.406764 GCTTGACCAGTCTTGTGAATCT 58.593 45.455 0.00 0.00 0.00 2.40
8003 9555 3.434984 GCTTGACCAGTCTTGTGAATCTC 59.565 47.826 0.00 0.00 0.00 2.75
8004 9556 4.802248 GCTTGACCAGTCTTGTGAATCTCT 60.802 45.833 0.00 0.00 0.00 3.10
8005 9557 4.527509 TGACCAGTCTTGTGAATCTCTC 57.472 45.455 0.00 0.00 0.00 3.20
8016 9568 5.698741 TGTGAATCTCTCTCTCTCTCTCT 57.301 43.478 0.00 0.00 0.00 3.10
8049 9601 3.763897 TGACTGAGCTGCTGTCTACAATA 59.236 43.478 7.01 0.00 43.53 1.90
8100 9653 0.316196 GAGGCCGCGATCGAATTTTG 60.316 55.000 21.57 0.43 38.10 2.44
8122 9675 1.434622 CTCATCAGCGGCACATGGTC 61.435 60.000 1.45 0.00 0.00 4.02
8146 9706 3.195661 GTTTCAAGTCAACGTCTCTGGT 58.804 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.167908 AACCACGCATACGCATTGTG 59.832 50.000 0.00 0.00 45.53 3.33
36 37 1.374885 TGGGACAACCACGCATACG 60.375 57.895 0.00 0.00 46.80 3.06
37 38 4.705746 TGGGACAACCACGCATAC 57.294 55.556 0.00 0.00 46.80 2.39
56 79 4.942852 CATGGTTGCACAAACTAAAAGGA 58.057 39.130 0.00 0.00 38.92 3.36
73 96 1.337447 GCAAGCACAAATCAGCATGGT 60.337 47.619 0.00 0.00 36.16 3.55
151 178 1.372748 CGGGCAAATGAAAAGCGCA 60.373 52.632 11.47 0.00 40.73 6.09
153 180 0.039617 TCACGGGCAAATGAAAAGCG 60.040 50.000 0.00 0.00 0.00 4.68
169 196 2.158475 TCCCATATCCCCATTGCTTCAC 60.158 50.000 0.00 0.00 0.00 3.18
188 215 8.415950 TCTCTATTTCTCTCCAATATGTCTCC 57.584 38.462 0.00 0.00 0.00 3.71
211 238 7.390027 CCTAGCCATGTATTTAGCATAACTCT 58.610 38.462 0.00 0.00 0.00 3.24
257 284 6.246420 CTTGACAGGTAAGGAAATCAAGTG 57.754 41.667 0.00 0.00 38.69 3.16
333 360 3.741344 CAGACAGGTAAGGAAACAAGTCG 59.259 47.826 0.00 0.00 32.90 4.18
391 418 5.294552 AGGTTCTTTCTTCAGTTCTGTTTCG 59.705 40.000 0.00 0.00 0.00 3.46
472 499 6.351711 CCTCTAGCTCCTTTTTCTCTTCATCA 60.352 42.308 0.00 0.00 0.00 3.07
529 556 1.895020 TAGTTCGCGATGGTTGGCCT 61.895 55.000 10.88 0.00 35.27 5.19
537 564 5.333513 ACTTTACTCTTCTAGTTCGCGATG 58.666 41.667 10.88 0.68 39.80 3.84
639 666 2.722116 CACATTTTCGCCGGTTACAAAC 59.278 45.455 1.90 0.00 0.00 2.93
666 693 6.455360 ACATTAGCAACATGGTATTTCAGG 57.545 37.500 0.00 0.00 29.73 3.86
699 726 9.109393 GTAACCTCATACATTGATGTACACAAT 57.891 33.333 14.20 14.20 45.11 2.71
728 755 5.239306 CAGGAAAAACAGCAGAGATGTACAA 59.761 40.000 0.00 0.00 29.75 2.41
759 786 7.773224 CCAAACTGATGTACCAATACTCCATAA 59.227 37.037 0.00 0.00 32.00 1.90
761 788 6.069673 TCCAAACTGATGTACCAATACTCCAT 60.070 38.462 0.00 0.00 32.00 3.41
762 789 5.249622 TCCAAACTGATGTACCAATACTCCA 59.750 40.000 0.00 0.00 32.00 3.86
763 790 5.741011 TCCAAACTGATGTACCAATACTCC 58.259 41.667 0.00 0.00 32.00 3.85
764 791 7.865706 ATTCCAAACTGATGTACCAATACTC 57.134 36.000 0.00 0.00 32.00 2.59
765 792 8.768397 TCTATTCCAAACTGATGTACCAATACT 58.232 33.333 0.00 0.00 32.00 2.12
766 793 8.958119 TCTATTCCAAACTGATGTACCAATAC 57.042 34.615 0.00 0.00 0.00 1.89
767 794 7.715249 GCTCTATTCCAAACTGATGTACCAATA 59.285 37.037 0.00 0.00 0.00 1.90
768 795 6.543831 GCTCTATTCCAAACTGATGTACCAAT 59.456 38.462 0.00 0.00 0.00 3.16
770 797 5.189736 AGCTCTATTCCAAACTGATGTACCA 59.810 40.000 0.00 0.00 0.00 3.25
771 798 5.525378 CAGCTCTATTCCAAACTGATGTACC 59.475 44.000 0.00 0.00 0.00 3.34
794 825 2.929641 TGTCAGGCACAATTCTTCACA 58.070 42.857 0.00 0.00 29.30 3.58
823 854 3.750371 TCACTACCACAAATCCAACTGG 58.250 45.455 0.00 0.00 0.00 4.00
837 868 1.195115 TCTGGCACATCCTCACTACC 58.805 55.000 0.00 0.00 38.20 3.18
856 887 6.726764 ACCCTCTAGTGTCTCAGACTAAAATT 59.273 38.462 6.33 0.00 33.15 1.82
862 893 2.291282 CCACCCTCTAGTGTCTCAGACT 60.291 54.545 6.33 0.00 35.93 3.24
863 894 2.096248 CCACCCTCTAGTGTCTCAGAC 58.904 57.143 0.00 0.00 35.93 3.51
864 895 1.006043 CCCACCCTCTAGTGTCTCAGA 59.994 57.143 0.00 0.00 35.93 3.27
865 896 1.479709 CCCACCCTCTAGTGTCTCAG 58.520 60.000 0.00 0.00 35.93 3.35
898 964 2.997986 CCAAAACGTTCGGCTATAGTGT 59.002 45.455 0.00 0.00 0.00 3.55
949 1015 4.986708 TGCCGGGGGAAAGTTGCC 62.987 66.667 2.18 0.00 38.05 4.52
950 1016 0.968393 TATTGCCGGGGGAAAGTTGC 60.968 55.000 2.18 0.00 0.00 4.17
951 1017 1.551452 TTATTGCCGGGGGAAAGTTG 58.449 50.000 2.18 0.00 0.00 3.16
952 1018 1.897133 GTTTATTGCCGGGGGAAAGTT 59.103 47.619 2.18 0.00 0.00 2.66
953 1019 1.076513 AGTTTATTGCCGGGGGAAAGT 59.923 47.619 2.18 0.00 0.00 2.66
955 1021 1.842052 GAGTTTATTGCCGGGGGAAA 58.158 50.000 2.18 0.00 0.00 3.13
957 1023 1.222387 CGAGTTTATTGCCGGGGGA 59.778 57.895 2.18 0.00 0.00 4.81
962 1028 1.636340 CCTCGCGAGTTTATTGCCG 59.364 57.895 32.41 11.77 34.44 5.69
998 1064 5.728637 ATTTCGGATTTTGCTTTCCTTCT 57.271 34.783 0.00 0.00 0.00 2.85
999 1065 7.044052 CGATAATTTCGGATTTTGCTTTCCTTC 60.044 37.037 0.00 0.00 44.28 3.46
1109 1176 2.835895 GGAGCCGAGGAGGAGACC 60.836 72.222 0.00 0.00 45.00 3.85
1121 1188 3.934962 GCGGAGATGGGAGGAGCC 61.935 72.222 0.00 0.00 0.00 4.70
1391 1458 2.035066 GCTCAGCCAATGCCGAAATTAT 59.965 45.455 0.00 0.00 38.69 1.28
1496 1563 0.897401 TTTGGCGGCATCCATGAACA 60.897 50.000 14.32 0.00 35.77 3.18
1605 1712 1.334869 CAATCTATGGCAAGGAACCGC 59.665 52.381 0.00 0.00 0.00 5.68
1652 1759 0.598065 CTTCAACTTTTCCTGCCCCG 59.402 55.000 0.00 0.00 0.00 5.73
1665 1772 6.836178 CCCCAAGGAAGAAGCATACTTCAAC 61.836 48.000 8.40 1.79 45.09 3.18
1668 1776 3.282885 CCCCAAGGAAGAAGCATACTTC 58.717 50.000 0.00 0.00 43.89 3.01
1938 2136 4.519540 TGGTTCCTAATTTTGCTTGAGC 57.480 40.909 0.00 0.00 42.50 4.26
2876 3097 8.483307 AAAATATCCATGAAACTTGATGCAAC 57.517 30.769 0.00 0.00 0.00 4.17
2897 3118 5.554437 ACCAAAAATACCCGGTTGAAAAT 57.446 34.783 0.00 0.00 0.00 1.82
2906 3127 4.226113 TGTTTCGAACCAAAAATACCCG 57.774 40.909 0.00 0.00 0.00 5.28
2910 3131 8.934507 AAAGATGTTGTTTCGAACCAAAAATA 57.065 26.923 9.89 0.00 0.00 1.40
3257 3480 9.447157 CATCTAAAATTCTAAATGCCCCAAAAA 57.553 29.630 0.00 0.00 0.00 1.94
3305 3528 8.087982 ACATACAAAGACAGACATTAACACAG 57.912 34.615 0.00 0.00 0.00 3.66
3364 3587 2.028420 TGCGCTCAGTCATTTGCTAT 57.972 45.000 9.73 0.00 0.00 2.97
3397 3620 5.127031 TCAATCAAAATAGGGCCTTAACAGC 59.873 40.000 13.45 0.00 0.00 4.40
3522 3745 5.821470 GGTGCTTTTTAGGAGGTTATAGGAC 59.179 44.000 0.00 0.00 0.00 3.85
3530 3753 2.956333 GTGTTGGTGCTTTTTAGGAGGT 59.044 45.455 0.00 0.00 0.00 3.85
3536 3759 2.614983 GTCTCCGTGTTGGTGCTTTTTA 59.385 45.455 0.00 0.00 39.52 1.52
3554 3777 0.389426 GTATCACCGTGTTGCCGTCT 60.389 55.000 0.00 0.00 0.00 4.18
3557 3780 3.077705 CGTATCACCGTGTTGCCG 58.922 61.111 0.00 0.00 0.00 5.69
3566 3789 0.319297 GTCCCCGTATGCGTATCACC 60.319 60.000 1.69 0.00 36.15 4.02
3596 3819 4.611130 CGAATGGCTGTTTTTGGAAAATGC 60.611 41.667 0.00 0.00 0.00 3.56
3600 3823 2.224161 CCCGAATGGCTGTTTTTGGAAA 60.224 45.455 0.00 0.00 0.00 3.13
3618 3841 1.386533 ATATACTCGCCGTATCCCCG 58.613 55.000 1.25 0.00 39.48 5.73
3709 3932 6.214819 GCCTTAATGGGGGTAGTATTCTGATA 59.785 42.308 0.00 0.00 36.00 2.15
3726 3949 3.278574 TCCATCAAACGAGGCCTTAATG 58.721 45.455 6.77 4.45 0.00 1.90
3780 4003 1.917787 GGGATTTTGGGCCCTGCAA 60.918 57.895 25.70 13.38 41.31 4.08
3781 4004 2.284552 GGGATTTTGGGCCCTGCA 60.285 61.111 25.70 6.58 41.31 4.41
3827 4050 3.161866 GTTTGGCCAGTTTAATCCCTGA 58.838 45.455 5.11 0.00 0.00 3.86
3936 4159 2.037641 CTGCAGTATCCCATGATTCCGA 59.962 50.000 5.25 0.00 32.18 4.55
3964 4187 1.411246 GCCACGATACACCAGGATACA 59.589 52.381 0.00 0.00 41.41 2.29
3972 4195 1.762222 GCGACATGCCACGATACACC 61.762 60.000 10.79 0.00 37.76 4.16
4034 4257 2.043227 GAGGGTATCTAGCAAGCACCT 58.957 52.381 0.00 0.00 31.54 4.00
4035 4258 1.070914 GGAGGGTATCTAGCAAGCACC 59.929 57.143 0.00 0.00 0.00 5.01
4103 4326 5.008613 GTGTAAGTGCATTGGACTTCTCAAA 59.991 40.000 24.41 6.60 35.30 2.69
4144 4367 8.049721 ACAGGAATTTTACAGGATTTAGGAGAG 58.950 37.037 0.00 0.00 0.00 3.20
4145 4368 7.829211 CACAGGAATTTTACAGGATTTAGGAGA 59.171 37.037 0.00 0.00 0.00 3.71
4167 4390 6.748333 ATGATGTACAGGAAATGAACACAG 57.252 37.500 0.33 0.00 0.00 3.66
4297 4520 1.541588 GTTCGCAGGCTTCTTTGGATT 59.458 47.619 0.00 0.00 0.00 3.01
4314 4537 7.048512 AGAATGTTACTATGCCACTAAGGTTC 58.951 38.462 0.00 0.00 40.61 3.62
4385 4608 6.873605 GGGAATTGGAAAAACATAAACTCCTG 59.126 38.462 0.00 0.00 0.00 3.86
4411 4634 0.042448 GCGTTCGGTTCACACTTCAC 60.042 55.000 0.00 0.00 0.00 3.18
4429 4652 9.118236 GTAAACAGAAATTATGTCAACTTGAGC 57.882 33.333 0.00 0.00 0.00 4.26
4527 4750 9.981114 ATTTCTTTGGTGGTTTAAGATGTTTAG 57.019 29.630 0.00 0.00 0.00 1.85
4714 4939 0.036010 ATGCCCAGTCTTCTTGTCCG 60.036 55.000 0.00 0.00 0.00 4.79
4865 5099 5.482006 TCATGACTGACACAAGTGATAAGG 58.518 41.667 7.28 0.00 0.00 2.69
4900 5134 1.195448 CACTGAAGCAACACTTAGGCG 59.805 52.381 0.00 0.00 39.29 5.52
4978 5212 0.807496 GCAGACACTTCAATGAGGCC 59.193 55.000 0.00 0.00 0.00 5.19
5042 5276 1.079073 CATTTCCAAGCCCCAGGGT 59.921 57.895 4.22 0.00 37.65 4.34
5167 5403 0.397941 CTTCTCCCTCACTGCAACCA 59.602 55.000 0.00 0.00 0.00 3.67
5464 5702 5.334569 CGTCCCAAAATAAGTGTCGTTGATT 60.335 40.000 0.00 0.00 0.00 2.57
5465 5703 4.153475 CGTCCCAAAATAAGTGTCGTTGAT 59.847 41.667 0.00 0.00 0.00 2.57
5466 5704 3.495377 CGTCCCAAAATAAGTGTCGTTGA 59.505 43.478 0.00 0.00 0.00 3.18
5497 5735 2.979678 AGGAACAGAACAGTGGGTACAT 59.020 45.455 0.00 0.00 0.00 2.29
5562 5813 1.913419 CCCCTAAGACCTGCCTTAACA 59.087 52.381 0.00 0.00 0.00 2.41
5574 5827 1.562672 GCAAGGTGAGGCCCCTAAGA 61.563 60.000 0.00 0.00 38.26 2.10
5729 5989 3.512329 TGTCTAAGTGTCGCCTTATGGAA 59.488 43.478 0.00 0.00 34.57 3.53
5753 6013 3.551259 GCACCTTACAGCCTAAGCA 57.449 52.632 0.00 0.00 43.56 3.91
5797 6057 1.065418 GCCACTTAAGCTCCTAAGGCA 60.065 52.381 12.82 0.00 33.85 4.75
5798 6058 1.065418 TGCCACTTAAGCTCCTAAGGC 60.065 52.381 1.29 10.38 33.85 4.35
5814 6074 3.505790 ATCAACCACCGCCTTGCCA 62.506 57.895 0.00 0.00 0.00 4.92
5820 6080 0.671163 TAACGTGATCAACCACCGCC 60.671 55.000 0.00 0.00 33.67 6.13
5891 6152 5.868801 ACAGTTTGACCACACATTTGAAAAG 59.131 36.000 0.00 0.00 0.00 2.27
6051 6312 1.526917 GAGGTGCAACAGCAGTGGT 60.527 57.895 3.64 0.00 39.30 4.16
6205 6473 2.627699 CCTCTCTCAGTCCAATAGCTCC 59.372 54.545 0.00 0.00 0.00 4.70
6276 6544 1.630878 ACAGGAGGAAGACAACCCATC 59.369 52.381 0.00 0.00 0.00 3.51
6323 6591 6.321181 CCAGTAGAGGAGAGAGAATATATGGC 59.679 46.154 0.00 0.00 0.00 4.40
6326 6594 7.038531 TGCCAGTAGAGGAGAGAGAATATAT 57.961 40.000 0.00 0.00 0.00 0.86
6582 7281 4.996788 AGGAAGATGGCATGAATTTCAC 57.003 40.909 3.81 0.00 0.00 3.18
6583 7282 5.105228 GGAAAGGAAGATGGCATGAATTTCA 60.105 40.000 3.81 0.75 0.00 2.69
6585 7284 5.028131 AGGAAAGGAAGATGGCATGAATTT 58.972 37.500 3.81 0.00 0.00 1.82
6586 7285 4.617593 AGGAAAGGAAGATGGCATGAATT 58.382 39.130 3.81 0.00 0.00 2.17
6588 7287 3.744940 AGGAAAGGAAGATGGCATGAA 57.255 42.857 3.81 0.00 0.00 2.57
6591 7311 2.158549 GGCTAGGAAAGGAAGATGGCAT 60.159 50.000 0.00 0.00 0.00 4.40
6613 7333 1.707989 TGATAAAGCTTGTGGGGTGGA 59.292 47.619 0.00 0.00 0.00 4.02
6614 7334 2.214376 TGATAAAGCTTGTGGGGTGG 57.786 50.000 0.00 0.00 0.00 4.61
6615 7335 5.182001 GCTATATGATAAAGCTTGTGGGGTG 59.818 44.000 0.00 0.00 33.40 4.61
6616 7336 5.163099 TGCTATATGATAAAGCTTGTGGGGT 60.163 40.000 0.00 0.00 37.16 4.95
6636 7356 2.237643 TGAAAATGCAACCAGCTGCTA 58.762 42.857 8.66 0.00 45.94 3.49
6637 7357 1.042229 TGAAAATGCAACCAGCTGCT 58.958 45.000 8.66 0.00 45.94 4.24
6642 7362 7.599621 TGAATACAAGAATGAAAATGCAACCAG 59.400 33.333 0.00 0.00 0.00 4.00
6643 7363 7.440198 TGAATACAAGAATGAAAATGCAACCA 58.560 30.769 0.00 0.00 0.00 3.67
6660 7380 4.597404 TGGTGCAAGCAAATGAATACAA 57.403 36.364 0.00 0.00 44.10 2.41
6702 7424 6.276568 AGGGGGCATATATTTCTTCAGAGAAT 59.723 38.462 0.00 0.00 41.35 2.40
6707 7429 4.568592 GGGAGGGGGCATATATTTCTTCAG 60.569 50.000 0.00 0.00 0.00 3.02
6728 7450 3.397618 TCATCATTGTATGGGTTAGGGGG 59.602 47.826 0.00 0.00 0.00 5.40
6766 7489 1.569479 GGGTTCTTCTGCTGACACGC 61.569 60.000 0.00 0.00 0.00 5.34
6834 7557 2.669240 GGGTTGTTCCTCCCCTCG 59.331 66.667 0.00 0.00 37.89 4.63
6877 7600 0.461961 CCCATCCTCGAGTCCAAGAC 59.538 60.000 12.31 0.00 0.00 3.01
6963 7686 1.216444 CAGAGCTTAGTCGCTGGCA 59.784 57.895 0.00 0.00 41.08 4.92
6978 7701 0.044092 TTCCTCCCACCTATGGCAGA 59.956 55.000 0.00 0.00 45.76 4.26
6983 7706 2.122768 AGAAGCTTCCTCCCACCTATG 58.877 52.381 22.81 0.00 0.00 2.23
7028 7757 6.363626 GCACCTTTCTAGTACATGATACGATG 59.636 42.308 0.00 0.00 0.00 3.84
7067 7799 4.829518 CGAGACGCGCCGATGACA 62.830 66.667 5.73 0.00 0.00 3.58
7074 7806 2.127383 CAAAAACCGAGACGCGCC 60.127 61.111 5.73 0.00 39.11 6.53
7139 7871 1.603456 TTGTCACTACCACCGACGTA 58.397 50.000 0.00 0.00 32.17 3.57
7189 7921 0.647410 CAACTGATGTGCGGACGATC 59.353 55.000 1.60 7.47 0.00 3.69
7210 7942 0.679505 ACTCTTACTGCTGGAACGCA 59.320 50.000 0.00 0.00 36.57 5.24
7219 7951 0.606604 TTGGACGGGACTCTTACTGC 59.393 55.000 0.00 0.00 0.00 4.40
7221 7953 2.761208 CTGATTGGACGGGACTCTTACT 59.239 50.000 0.00 0.00 0.00 2.24
7224 7956 1.938585 TCTGATTGGACGGGACTCTT 58.061 50.000 0.00 0.00 0.00 2.85
7225 7957 1.759445 CATCTGATTGGACGGGACTCT 59.241 52.381 0.00 0.00 0.00 3.24
7236 7973 6.320171 CAAACTCTTGTTAGCCATCTGATTG 58.680 40.000 0.00 0.00 34.96 2.67
7246 7983 3.437049 AGATTCGGCAAACTCTTGTTAGC 59.563 43.478 0.00 0.00 34.96 3.09
7363 8129 2.575461 GGTGCAAATCTGGCCAGC 59.425 61.111 28.91 17.55 0.00 4.85
7373 8139 4.468643 GTCGACATATTTTTCGGTGCAAA 58.531 39.130 11.55 0.00 35.89 3.68
7374 8140 3.120130 GGTCGACATATTTTTCGGTGCAA 60.120 43.478 18.91 0.00 35.89 4.08
7375 8141 2.417239 GGTCGACATATTTTTCGGTGCA 59.583 45.455 18.91 0.00 35.89 4.57
7376 8142 2.417239 TGGTCGACATATTTTTCGGTGC 59.583 45.455 18.91 0.00 35.89 5.01
7377 8143 3.930229 TCTGGTCGACATATTTTTCGGTG 59.070 43.478 18.91 0.00 35.89 4.94
7379 8145 4.516092 GTCTGGTCGACATATTTTTCGG 57.484 45.455 18.91 2.23 42.37 4.30
7402 8178 5.844301 AAATTTTCGGTGCAAATCATCAC 57.156 34.783 0.00 0.00 0.00 3.06
7421 8197 0.034896 AGCCGTCTGGTCGACAAAAT 59.965 50.000 18.91 0.00 42.98 1.82
7424 8200 0.892755 AATAGCCGTCTGGTCGACAA 59.107 50.000 18.91 4.84 42.98 3.18
7444 8220 6.528537 TCATCAGAAAAGAGAGAGGAAGAG 57.471 41.667 0.00 0.00 0.00 2.85
7448 8224 4.469227 CCCTTCATCAGAAAAGAGAGAGGA 59.531 45.833 0.00 0.00 32.35 3.71
7476 8252 0.736325 CTGGAGAAACGGTAGGCACG 60.736 60.000 0.00 0.00 37.36 5.34
7550 8582 3.739810 GGAGAAAACGAAGTCAGTACACC 59.260 47.826 0.00 0.00 45.00 4.16
7551 8583 4.444720 CAGGAGAAAACGAAGTCAGTACAC 59.555 45.833 0.00 0.00 45.00 2.90
7553 8585 4.618965 ACAGGAGAAAACGAAGTCAGTAC 58.381 43.478 0.00 0.00 45.00 2.73
7554 8586 4.931661 ACAGGAGAAAACGAAGTCAGTA 57.068 40.909 0.00 0.00 45.00 2.74
7555 8587 3.821421 ACAGGAGAAAACGAAGTCAGT 57.179 42.857 0.00 0.00 45.00 3.41
7556 8588 5.715070 AGATACAGGAGAAAACGAAGTCAG 58.285 41.667 0.00 0.00 45.00 3.51
7557 8589 5.723672 AGATACAGGAGAAAACGAAGTCA 57.276 39.130 0.00 0.00 45.00 3.41
7595 8629 6.324770 CCCAAGACCAAATTAGCCATCTTAAT 59.675 38.462 0.00 0.00 0.00 1.40
7656 8900 5.399152 GGTCTTTATGGCCTTTTCTCCCTAT 60.399 44.000 3.32 0.00 37.49 2.57
7662 8906 4.281657 GGATGGTCTTTATGGCCTTTTCT 58.718 43.478 3.32 0.00 42.07 2.52
7664 8908 3.245948 TGGGATGGTCTTTATGGCCTTTT 60.246 43.478 3.32 0.00 42.07 2.27
7668 8912 1.494721 TCTGGGATGGTCTTTATGGCC 59.505 52.381 0.00 0.00 41.87 5.36
7718 8962 5.009410 GCTGCAACCATCTTTATAGAAGCAT 59.991 40.000 0.00 0.00 33.20 3.79
7735 9255 6.868339 AGAAAATTACATAAACTGGCTGCAAC 59.132 34.615 0.50 0.00 0.00 4.17
7806 9327 7.877612 AGGTCTTCATCTTCTTCTTCTTCTTTC 59.122 37.037 0.00 0.00 0.00 2.62
7809 9330 6.496565 TGAGGTCTTCATCTTCTTCTTCTTCT 59.503 38.462 0.00 0.00 0.00 2.85
7818 9339 3.691575 TCGAGTGAGGTCTTCATCTTCT 58.308 45.455 0.00 0.00 38.29 2.85
8000 9552 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
8001 9553 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
8002 9554 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
8003 9555 3.634448 ACGAGAGAGAGAGAGAGAGAGAG 59.366 52.174 0.00 0.00 0.00 3.20
8004 9556 3.632333 ACGAGAGAGAGAGAGAGAGAGA 58.368 50.000 0.00 0.00 0.00 3.10
8005 9557 4.392921 AACGAGAGAGAGAGAGAGAGAG 57.607 50.000 0.00 0.00 0.00 3.20
8016 9568 2.227626 CAGCTCAGTCAAACGAGAGAGA 59.772 50.000 0.00 0.00 30.31 3.10
8100 9653 0.866427 CATGTGCCGCTGATGAGATC 59.134 55.000 0.00 0.00 0.00 2.75
8146 9706 5.063204 CCATCCGAATCTTTAGCCATGTTA 58.937 41.667 0.00 0.00 0.00 2.41
8198 9777 2.657237 CGAACCGTGGAGGCTCTT 59.343 61.111 15.23 0.00 46.52 2.85


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

AutoCloner maintained by Alex Coulton.