Multiple sequence alignment - TraesCS1A01G180400

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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 TraesCS1A01G180400 chr1A 100.000 4357 0 0 1 4357 325781153 325785509 0.000000e+00 8046.0
1 TraesCS1A01G180400 chr1A 100.000 35 0 0 3980 4014 325785094 325785128 1.010000e-06 65.8
2 TraesCS1A01G180400 chr1A 100.000 35 0 0 3942 3976 325785132 325785166 1.010000e-06 65.8
3 TraesCS1A01G180400 chr1B 96.402 3252 91 15 738 3980 358838180 358841414 0.000000e+00 5334.0
4 TraesCS1A01G180400 chr1B 92.201 577 28 7 127 701 358837614 358838175 0.000000e+00 800.0
5 TraesCS1A01G180400 chr1B 89.226 297 24 5 4063 4357 358841457 358841747 8.900000e-97 364.0
6 TraesCS1A01G180400 chr1B 100.000 47 0 0 94 140 358837535 358837581 2.160000e-13 87.9
7 TraesCS1A01G180400 chr1D 95.413 3292 80 25 738 3983 253529132 253525866 0.000000e+00 5177.0
8 TraesCS1A01G180400 chr1D 91.939 459 23 7 244 701 253529582 253529137 7.950000e-177 630.0
9 TraesCS1A01G180400 chr1D 99.180 122 1 0 126 247 253529986 253529865 2.040000e-53 220.0
10 TraesCS1A01G180400 chr1D 100.000 45 0 0 96 140 253530052 253530008 2.790000e-12 84.2
11 TraesCS1A01G180400 chr1D 97.143 35 1 0 3980 4014 253525907 253525873 4.710000e-05 60.2
12 TraesCS1A01G180400 chr1D 94.595 37 2 0 4038 4074 253525877 253525841 1.690000e-04 58.4
13 TraesCS1A01G180400 chr3B 88.456 641 73 1 1229 1869 286217075 286217714 0.000000e+00 773.0
14 TraesCS1A01G180400 chr7B 88.300 641 59 2 1229 1869 305155527 305154903 0.000000e+00 754.0
15 TraesCS1A01G180400 chr6A 95.455 462 20 1 1229 1690 349933734 349934194 0.000000e+00 736.0
16 TraesCS1A01G180400 chr6A 95.804 143 6 0 1727 1869 349934194 349934336 9.420000e-57 231.0
17 TraesCS1A01G180400 chr2A 90.805 87 7 1 3821 3906 692757137 692757223 9.900000e-22 115.0
18 TraesCS1A01G180400 chr2A 88.235 85 10 0 3821 3905 753260807 753260891 7.710000e-18 102.0
19 TraesCS1A01G180400 chr2D 86.458 96 11 2 3821 3916 591380426 591380333 2.140000e-18 104.0
20 TraesCS1A01G180400 chr2D 87.209 86 11 0 3821 3906 190112160 190112245 9.970000e-17 99.0
21 TraesCS1A01G180400 chr7D 89.024 82 9 0 3821 3902 588088567 588088648 7.710000e-18 102.0
22 TraesCS1A01G180400 chr7D 90.667 75 7 0 3832 3906 625355910 625355836 2.770000e-17 100.0
23 TraesCS1A01G180400 chr4D 88.235 85 10 0 3821 3905 268071176 268071260 7.710000e-18 102.0


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 TraesCS1A01G180400 chr1A 325781153 325785509 4356 False 2725.866667 8046 100.000000 1 4357 3 chr1A.!!$F1 4356
1 TraesCS1A01G180400 chr1B 358837535 358841747 4212 False 1646.475000 5334 94.457250 94 4357 4 chr1B.!!$F1 4263
2 TraesCS1A01G180400 chr1D 253525841 253530052 4211 True 1038.300000 5177 96.378333 96 4074 6 chr1D.!!$R1 3978
3 TraesCS1A01G180400 chr3B 286217075 286217714 639 False 773.000000 773 88.456000 1229 1869 1 chr3B.!!$F1 640
4 TraesCS1A01G180400 chr7B 305154903 305155527 624 True 754.000000 754 88.300000 1229 1869 1 chr7B.!!$R1 640
5 TraesCS1A01G180400 chr6A 349933734 349934336 602 False 483.500000 736 95.629500 1229 1869 2 chr6A.!!$F1 640

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
46 47 0.036732 ACGGTTGCACCACATGAGAT 59.963 50.0 0.00 0.00 38.47 2.75 F
715 1049 0.394488 CGTCCTCAGGCTAGACTGGA 60.394 60.0 25.57 13.26 38.98 3.86 F
1854 2191 1.515521 CCCTTTCCCGCGAATATGGC 61.516 60.0 8.23 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 2215 0.321298 CCGACCAAAGGTTGACGGAT 60.321 55.000 15.89 0.0 45.60 4.18 R
2037 2375 0.331278 ATTCAAGCACGGAATGGGGA 59.669 50.000 0.00 0.0 33.88 4.81 R
3756 4110 1.935873 CAAGTACCAGGACATGCATCG 59.064 52.381 0.00 0.0 0.00 3.84 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
24 25 7.486407 AAAGAGAAAAATACATGGATGCCTT 57.514 32.000 0.00 0.00 0.00 4.35
25 26 6.461110 AGAGAAAAATACATGGATGCCTTG 57.539 37.500 0.00 0.00 35.21 3.61
26 27 5.014808 AGAAAAATACATGGATGCCTTGC 57.985 39.130 0.00 0.00 32.73 4.01
27 28 4.467082 AGAAAAATACATGGATGCCTTGCA 59.533 37.500 0.00 0.00 44.86 4.08
28 29 3.806625 AAATACATGGATGCCTTGCAC 57.193 42.857 0.00 0.00 43.04 4.57
29 30 1.311859 ATACATGGATGCCTTGCACG 58.688 50.000 0.00 0.00 43.04 5.34
30 31 0.747644 TACATGGATGCCTTGCACGG 60.748 55.000 4.51 4.51 43.04 4.94
31 32 2.048023 CATGGATGCCTTGCACGGT 61.048 57.895 11.38 0.00 43.04 4.83
32 33 1.304381 ATGGATGCCTTGCACGGTT 60.304 52.632 11.38 0.00 43.04 4.44
33 34 1.597797 ATGGATGCCTTGCACGGTTG 61.598 55.000 11.38 0.00 43.04 3.77
43 44 3.743208 CACGGTTGCACCACATGA 58.257 55.556 0.00 0.00 38.47 3.07
44 45 1.575922 CACGGTTGCACCACATGAG 59.424 57.895 0.00 0.00 38.47 2.90
45 46 0.884259 CACGGTTGCACCACATGAGA 60.884 55.000 0.00 0.00 38.47 3.27
46 47 0.036732 ACGGTTGCACCACATGAGAT 59.963 50.000 0.00 0.00 38.47 2.75
47 48 0.729116 CGGTTGCACCACATGAGATC 59.271 55.000 0.00 0.00 38.47 2.75
48 49 1.825090 GGTTGCACCACATGAGATCA 58.175 50.000 0.00 0.00 38.42 2.92
49 50 1.470098 GGTTGCACCACATGAGATCAC 59.530 52.381 0.00 0.00 38.42 3.06
50 51 2.430465 GTTGCACCACATGAGATCACT 58.570 47.619 0.00 0.00 0.00 3.41
51 52 2.391616 TGCACCACATGAGATCACTC 57.608 50.000 0.00 0.00 42.88 3.51
52 53 1.065926 TGCACCACATGAGATCACTCC 60.066 52.381 0.00 0.00 41.99 3.85
53 54 1.065926 GCACCACATGAGATCACTCCA 60.066 52.381 0.00 0.00 41.99 3.86
54 55 2.616256 GCACCACATGAGATCACTCCAA 60.616 50.000 0.00 0.00 41.99 3.53
55 56 3.005554 CACCACATGAGATCACTCCAAC 58.994 50.000 0.00 0.00 41.99 3.77
56 57 2.639347 ACCACATGAGATCACTCCAACA 59.361 45.455 0.00 0.00 41.99 3.33
57 58 3.265221 ACCACATGAGATCACTCCAACAT 59.735 43.478 0.00 0.00 41.99 2.71
58 59 3.875727 CCACATGAGATCACTCCAACATC 59.124 47.826 0.00 0.00 41.99 3.06
59 60 3.875727 CACATGAGATCACTCCAACATCC 59.124 47.826 0.00 0.00 41.99 3.51
60 61 3.520721 ACATGAGATCACTCCAACATCCA 59.479 43.478 0.00 0.00 41.99 3.41
61 62 3.616956 TGAGATCACTCCAACATCCAC 57.383 47.619 0.00 0.00 41.99 4.02
62 63 2.094026 TGAGATCACTCCAACATCCACG 60.094 50.000 0.00 0.00 41.99 4.94
63 64 1.208052 AGATCACTCCAACATCCACGG 59.792 52.381 0.00 0.00 0.00 4.94
64 65 0.984230 ATCACTCCAACATCCACGGT 59.016 50.000 0.00 0.00 0.00 4.83
65 66 0.762418 TCACTCCAACATCCACGGTT 59.238 50.000 0.00 0.00 0.00 4.44
66 67 1.142060 TCACTCCAACATCCACGGTTT 59.858 47.619 0.00 0.00 0.00 3.27
67 68 1.953686 CACTCCAACATCCACGGTTTT 59.046 47.619 0.00 0.00 0.00 2.43
68 69 2.360801 CACTCCAACATCCACGGTTTTT 59.639 45.455 0.00 0.00 0.00 1.94
89 90 4.527509 TTTTTGTTTGTGAGGAAGCACA 57.472 36.364 0.00 0.00 46.26 4.57
266 599 5.585047 CCTAATAAGGTTGCTTGACAGGTAC 59.415 44.000 0.00 0.00 38.19 3.34
267 600 4.910458 ATAAGGTTGCTTGACAGGTACT 57.090 40.909 0.00 0.00 43.88 2.73
324 657 2.519302 GCCAGCCACACACCTGTT 60.519 61.111 0.00 0.00 0.00 3.16
326 659 2.723746 CAGCCACACACCTGTTGC 59.276 61.111 0.00 0.00 38.97 4.17
338 671 3.838317 ACACCTGTTGCTCACTAGGATAA 59.162 43.478 0.00 0.00 34.42 1.75
385 718 3.895041 CCCATCCCCACAAATATTGGTAC 59.105 47.826 0.00 0.00 31.46 3.34
386 719 4.387437 CCCATCCCCACAAATATTGGTACT 60.387 45.833 0.00 0.00 31.46 2.73
387 720 5.163034 CCCATCCCCACAAATATTGGTACTA 60.163 44.000 0.00 0.00 31.46 1.82
388 721 6.003950 CCATCCCCACAAATATTGGTACTAG 58.996 44.000 0.00 0.00 31.46 2.57
389 722 6.410388 CCATCCCCACAAATATTGGTACTAGT 60.410 42.308 0.00 0.00 31.46 2.57
405 738 7.726216 TGGTACTAGTACAATCATTGATGAGG 58.274 38.462 29.38 0.00 37.74 3.86
428 761 3.384668 AGATCAGCGAATATGTTCCACG 58.615 45.455 0.00 0.00 0.00 4.94
445 778 2.357777 CCACGGGTCCCCTGAAAAATAT 60.358 50.000 8.40 0.00 33.36 1.28
448 781 5.221966 CCACGGGTCCCCTGAAAAATATATA 60.222 44.000 8.40 0.00 33.36 0.86
449 782 5.704053 CACGGGTCCCCTGAAAAATATATAC 59.296 44.000 1.00 0.00 33.36 1.47
450 783 5.609708 ACGGGTCCCCTGAAAAATATATACT 59.390 40.000 1.00 0.00 33.36 2.12
451 784 6.171213 CGGGTCCCCTGAAAAATATATACTC 58.829 44.000 1.00 0.00 29.82 2.59
471 804 5.460646 ACTCACATTTTATTTTGCGGAGTG 58.539 37.500 0.00 0.00 32.71 3.51
475 809 6.640499 TCACATTTTATTTTGCGGAGTGAAAG 59.360 34.615 0.00 0.00 31.36 2.62
477 811 6.863126 ACATTTTATTTTGCGGAGTGAAAGAG 59.137 34.615 0.00 0.00 0.00 2.85
520 854 2.573462 AGCACATTCCCTAGACACATGT 59.427 45.455 0.00 0.00 0.00 3.21
534 868 2.217750 CACATGTCACCCTTTCAACGA 58.782 47.619 0.00 0.00 0.00 3.85
537 871 0.542333 TGTCACCCTTTCAACGACCA 59.458 50.000 0.00 0.00 0.00 4.02
576 910 5.125578 TGCGCGGAGATATATTCTATTCTGT 59.874 40.000 8.83 0.00 33.74 3.41
580 914 7.642194 CGCGGAGATATATTCTATTCTGTTCTC 59.358 40.741 0.00 0.00 33.74 2.87
657 991 2.165641 CAGTCCACCACTAATCACGCTA 59.834 50.000 0.00 0.00 32.21 4.26
669 1003 4.171103 ACGCTAACCCATCGCCCC 62.171 66.667 0.00 0.00 0.00 5.80
701 1035 2.812983 GCTTCAAACCTTAACCCGTCCT 60.813 50.000 0.00 0.00 0.00 3.85
702 1036 2.845363 TCAAACCTTAACCCGTCCTC 57.155 50.000 0.00 0.00 0.00 3.71
703 1037 2.048601 TCAAACCTTAACCCGTCCTCA 58.951 47.619 0.00 0.00 0.00 3.86
704 1038 2.038033 TCAAACCTTAACCCGTCCTCAG 59.962 50.000 0.00 0.00 0.00 3.35
705 1039 0.981943 AACCTTAACCCGTCCTCAGG 59.018 55.000 0.00 0.00 0.00 3.86
706 1040 1.221021 CCTTAACCCGTCCTCAGGC 59.779 63.158 0.00 0.00 0.00 4.85
707 1041 1.265454 CCTTAACCCGTCCTCAGGCT 61.265 60.000 0.00 0.00 0.00 4.58
708 1042 1.481871 CTTAACCCGTCCTCAGGCTA 58.518 55.000 0.00 0.00 0.00 3.93
709 1043 1.409427 CTTAACCCGTCCTCAGGCTAG 59.591 57.143 0.00 0.00 0.00 3.42
710 1044 0.627451 TAACCCGTCCTCAGGCTAGA 59.373 55.000 0.00 0.00 0.00 2.43
711 1045 0.971447 AACCCGTCCTCAGGCTAGAC 60.971 60.000 0.00 0.00 0.00 2.59
712 1046 1.076632 CCCGTCCTCAGGCTAGACT 60.077 63.158 0.00 0.00 0.00 3.24
713 1047 1.388065 CCCGTCCTCAGGCTAGACTG 61.388 65.000 20.43 20.43 39.84 3.51
714 1048 1.388065 CCGTCCTCAGGCTAGACTGG 61.388 65.000 25.57 15.44 38.98 4.00
715 1049 0.394488 CGTCCTCAGGCTAGACTGGA 60.394 60.000 25.57 13.26 38.98 3.86
716 1050 1.853963 GTCCTCAGGCTAGACTGGAA 58.146 55.000 25.57 6.27 38.98 3.53
717 1051 2.393646 GTCCTCAGGCTAGACTGGAAT 58.606 52.381 25.57 0.00 38.98 3.01
718 1052 3.567397 GTCCTCAGGCTAGACTGGAATA 58.433 50.000 25.57 5.08 38.98 1.75
719 1053 3.961408 GTCCTCAGGCTAGACTGGAATAA 59.039 47.826 25.57 4.68 38.98 1.40
720 1054 4.406003 GTCCTCAGGCTAGACTGGAATAAA 59.594 45.833 25.57 3.90 38.98 1.40
721 1055 5.071115 GTCCTCAGGCTAGACTGGAATAAAT 59.929 44.000 25.57 0.00 38.98 1.40
722 1056 6.267928 GTCCTCAGGCTAGACTGGAATAAATA 59.732 42.308 25.57 2.33 38.98 1.40
723 1057 6.844388 TCCTCAGGCTAGACTGGAATAAATAA 59.156 38.462 25.57 1.56 38.98 1.40
724 1058 7.347222 TCCTCAGGCTAGACTGGAATAAATAAA 59.653 37.037 25.57 0.79 38.98 1.40
725 1059 8.160106 CCTCAGGCTAGACTGGAATAAATAAAT 58.840 37.037 25.57 0.00 38.98 1.40
726 1060 8.908786 TCAGGCTAGACTGGAATAAATAAATG 57.091 34.615 25.57 0.00 38.98 2.32
727 1061 8.713971 TCAGGCTAGACTGGAATAAATAAATGA 58.286 33.333 25.57 0.00 38.98 2.57
728 1062 8.778358 CAGGCTAGACTGGAATAAATAAATGAC 58.222 37.037 18.70 0.00 34.84 3.06
729 1063 8.494433 AGGCTAGACTGGAATAAATAAATGACA 58.506 33.333 0.00 0.00 0.00 3.58
730 1064 8.560374 GGCTAGACTGGAATAAATAAATGACAC 58.440 37.037 0.00 0.00 0.00 3.67
731 1065 8.560374 GCTAGACTGGAATAAATAAATGACACC 58.440 37.037 0.00 0.00 0.00 4.16
732 1066 7.553881 AGACTGGAATAAATAAATGACACCG 57.446 36.000 0.00 0.00 0.00 4.94
733 1067 6.038271 AGACTGGAATAAATAAATGACACCGC 59.962 38.462 0.00 0.00 0.00 5.68
734 1068 5.067283 ACTGGAATAAATAAATGACACCGCC 59.933 40.000 0.00 0.00 0.00 6.13
735 1069 4.339814 TGGAATAAATAAATGACACCGCCC 59.660 41.667 0.00 0.00 0.00 6.13
736 1070 4.583073 GGAATAAATAAATGACACCGCCCT 59.417 41.667 0.00 0.00 0.00 5.19
740 1074 2.570415 TAAATGACACCGCCCTTTCA 57.430 45.000 0.00 0.00 0.00 2.69
802 1138 8.657729 TCGTGCAAAGATTCGTAATGTTTTATA 58.342 29.630 0.00 0.00 32.68 0.98
803 1139 9.268255 CGTGCAAAGATTCGTAATGTTTTATAA 57.732 29.630 0.00 0.00 32.68 0.98
826 1163 9.893305 ATAAGTAAAATCCAGACGTTCTTTTTG 57.107 29.630 0.00 0.00 0.00 2.44
847 1184 3.192422 TGAAATACAAGGGGAAATGCACG 59.808 43.478 0.00 0.00 0.00 5.34
865 1202 3.054166 CACGGTTCGAATGTAGTGTGAA 58.946 45.455 0.00 0.00 0.00 3.18
1281 1618 1.661821 CATCGTCTTCGGGATCGCC 60.662 63.158 3.90 0.00 37.69 5.54
1854 2191 1.515521 CCCTTTCCCGCGAATATGGC 61.516 60.000 8.23 0.00 0.00 4.40
1988 2326 2.165030 CTCATCCCGAGCAAAGCAATTT 59.835 45.455 0.00 0.00 34.18 1.82
2031 2369 7.382759 GTGCTATGTAGATTCTGCTAGTAAACC 59.617 40.741 3.38 0.00 0.00 3.27
2037 2375 6.613153 AGATTCTGCTAGTAAACCAGTTCT 57.387 37.500 0.00 0.00 0.00 3.01
2047 2386 0.328258 AACCAGTTCTCCCCATTCCG 59.672 55.000 0.00 0.00 0.00 4.30
2072 2411 6.470235 GTGCTTGAATTAGTGCAATGTATCAC 59.530 38.462 0.00 0.00 37.17 3.06
2156 2495 3.507233 TGCTTTGGAAGTTTAGATGCTGG 59.493 43.478 0.00 0.00 0.00 4.85
2188 2527 9.005777 TGTTTTGAACTTTACTATGGGTATCAC 57.994 33.333 0.00 0.00 0.00 3.06
2264 2606 2.899900 AGCTGTGTCCTGTGTTATCTCA 59.100 45.455 0.00 0.00 0.00 3.27
2300 2642 1.467342 GTACAAAAGTAGGGCCTTGCG 59.533 52.381 13.45 0.00 0.00 4.85
2399 2741 5.333513 TGCTTGTTTACTTGTTTTACGGTG 58.666 37.500 0.00 0.00 0.00 4.94
2409 2751 4.413495 TGTTTTACGGTGCTATCTTTGC 57.587 40.909 0.00 0.00 0.00 3.68
2422 2764 5.474532 TGCTATCTTTGCACATCTCTTTGTT 59.525 36.000 0.00 0.00 35.31 2.83
2436 2778 4.631377 TCTCTTTGTTGGATAAGCACATCG 59.369 41.667 0.00 0.00 0.00 3.84
2593 2942 5.047660 CCCTGCTCTCCTAATGTATGTACTC 60.048 48.000 0.00 0.00 0.00 2.59
3210 3559 5.930837 ATCTCCTCTACTCTTTCAACCTG 57.069 43.478 0.00 0.00 0.00 4.00
3664 4015 2.283298 CCTTCTCGACCATGGTTGATG 58.717 52.381 31.06 23.90 37.82 3.07
3842 4197 5.941555 ACTCCCTCCGATCCATATTAATC 57.058 43.478 0.00 0.00 0.00 1.75
3896 4275 6.729391 TCAACGACAATTAAAATGGATCGA 57.271 33.333 9.90 0.00 32.63 3.59
3900 4279 5.878116 ACGACAATTAAAATGGATCGAAGGA 59.122 36.000 9.90 0.00 32.63 3.36
3905 4287 8.893727 ACAATTAAAATGGATCGAAGGAAGTAG 58.106 33.333 0.00 0.00 0.00 2.57
3907 4289 9.462606 AATTAAAATGGATCGAAGGAAGTAGTT 57.537 29.630 0.00 0.00 0.00 2.24
3970 4352 5.290386 ACCTGCAGTCTAATTAATACGAGC 58.710 41.667 13.81 9.31 0.00 5.03
3982 4364 9.370126 CTAATTAATACGAGCAACTTTATGTGC 57.630 33.333 0.00 0.00 0.00 4.57
3983 4365 6.978343 TTAATACGAGCAACTTTATGTGCT 57.022 33.333 0.00 0.00 36.35 4.40
3984 4366 5.880054 AATACGAGCAACTTTATGTGCTT 57.120 34.783 0.00 0.00 34.74 3.91
3985 4367 6.978343 AATACGAGCAACTTTATGTGCTTA 57.022 33.333 0.00 0.00 34.74 3.09
3986 4368 4.663636 ACGAGCAACTTTATGTGCTTAC 57.336 40.909 0.00 0.00 34.74 2.34
3987 4369 3.435671 ACGAGCAACTTTATGTGCTTACC 59.564 43.478 0.00 0.00 34.74 2.85
3988 4370 3.684788 CGAGCAACTTTATGTGCTTACCT 59.315 43.478 0.00 0.00 34.74 3.08
3989 4371 4.436050 CGAGCAACTTTATGTGCTTACCTG 60.436 45.833 0.00 0.00 34.74 4.00
3990 4372 3.191371 AGCAACTTTATGTGCTTACCTGC 59.809 43.478 0.00 0.00 32.11 4.85
3991 4373 3.057596 GCAACTTTATGTGCTTACCTGCA 60.058 43.478 0.00 0.00 41.05 4.41
3992 4374 4.726416 CAACTTTATGTGCTTACCTGCAG 58.274 43.478 6.78 6.78 44.20 4.41
3993 4375 4.021102 ACTTTATGTGCTTACCTGCAGT 57.979 40.909 13.81 3.45 44.20 4.40
3994 4376 4.003648 ACTTTATGTGCTTACCTGCAGTC 58.996 43.478 13.81 0.00 44.20 3.51
3995 4377 3.981071 TTATGTGCTTACCTGCAGTCT 57.019 42.857 13.81 0.00 44.20 3.24
3996 4378 5.046591 ACTTTATGTGCTTACCTGCAGTCTA 60.047 40.000 13.81 0.00 44.20 2.59
3997 4379 3.981071 ATGTGCTTACCTGCAGTCTAA 57.019 42.857 13.81 6.92 44.20 2.10
3998 4380 3.981071 TGTGCTTACCTGCAGTCTAAT 57.019 42.857 13.81 0.00 44.20 1.73
3999 4381 4.286297 TGTGCTTACCTGCAGTCTAATT 57.714 40.909 13.81 0.00 44.20 1.40
4000 4382 5.414789 TGTGCTTACCTGCAGTCTAATTA 57.585 39.130 13.81 0.00 44.20 1.40
4001 4383 5.800296 TGTGCTTACCTGCAGTCTAATTAA 58.200 37.500 13.81 0.00 44.20 1.40
4002 4384 6.414732 TGTGCTTACCTGCAGTCTAATTAAT 58.585 36.000 13.81 0.00 44.20 1.40
4003 4385 7.561251 TGTGCTTACCTGCAGTCTAATTAATA 58.439 34.615 13.81 0.00 44.20 0.98
4004 4386 7.494625 TGTGCTTACCTGCAGTCTAATTAATAC 59.505 37.037 13.81 0.23 44.20 1.89
4005 4387 6.700081 TGCTTACCTGCAGTCTAATTAATACG 59.300 38.462 13.81 0.00 38.12 3.06
4006 4388 6.921857 GCTTACCTGCAGTCTAATTAATACGA 59.078 38.462 13.81 0.00 0.00 3.43
4007 4389 7.115095 GCTTACCTGCAGTCTAATTAATACGAG 59.885 40.741 13.81 0.00 0.00 4.18
4008 4390 5.290386 ACCTGCAGTCTAATTAATACGAGC 58.710 41.667 13.81 9.31 0.00 5.03
4009 4391 5.163447 ACCTGCAGTCTAATTAATACGAGCA 60.163 40.000 13.81 14.33 0.00 4.26
4010 4392 5.753438 CCTGCAGTCTAATTAATACGAGCAA 59.247 40.000 13.81 6.37 31.85 3.91
4011 4393 6.292381 CCTGCAGTCTAATTAATACGAGCAAC 60.292 42.308 13.81 0.00 31.85 4.17
4012 4394 6.338146 TGCAGTCTAATTAATACGAGCAACT 58.662 36.000 13.44 0.00 0.00 3.16
4013 4395 6.816640 TGCAGTCTAATTAATACGAGCAACTT 59.183 34.615 13.44 0.00 0.00 2.66
4014 4396 7.119997 GCAGTCTAATTAATACGAGCAACTTG 58.880 38.462 0.00 0.00 0.00 3.16
4015 4397 7.010183 GCAGTCTAATTAATACGAGCAACTTGA 59.990 37.037 0.00 0.00 0.00 3.02
4016 4398 8.321716 CAGTCTAATTAATACGAGCAACTTGAC 58.678 37.037 0.00 0.00 0.00 3.18
4017 4399 7.491696 AGTCTAATTAATACGAGCAACTTGACC 59.508 37.037 0.00 0.00 0.00 4.02
4018 4400 5.813080 AATTAATACGAGCAACTTGACCC 57.187 39.130 0.00 0.00 0.00 4.46
4019 4401 4.546829 TTAATACGAGCAACTTGACCCT 57.453 40.909 0.00 0.00 0.00 4.34
4020 4402 2.674796 ATACGAGCAACTTGACCCTC 57.325 50.000 0.00 0.00 0.00 4.30
4021 4403 1.334160 TACGAGCAACTTGACCCTCA 58.666 50.000 0.00 0.00 0.00 3.86
4022 4404 0.468226 ACGAGCAACTTGACCCTCAA 59.532 50.000 0.00 0.00 34.79 3.02
4023 4405 1.134220 ACGAGCAACTTGACCCTCAAA 60.134 47.619 0.00 0.00 35.73 2.69
4024 4406 1.946768 CGAGCAACTTGACCCTCAAAA 59.053 47.619 0.00 0.00 35.73 2.44
4025 4407 2.357637 CGAGCAACTTGACCCTCAAAAA 59.642 45.455 0.00 0.00 35.73 1.94
4078 4486 9.507280 ACATTTTTATCATAGCATTCTTTGACG 57.493 29.630 0.00 0.00 34.04 4.35
4087 4495 3.120060 AGCATTCTTTGACGATTGCACTC 60.120 43.478 9.43 0.00 40.74 3.51
4088 4496 3.365264 GCATTCTTTGACGATTGCACTCA 60.365 43.478 4.82 0.00 39.09 3.41
4089 4497 4.400845 CATTCTTTGACGATTGCACTCAG 58.599 43.478 4.82 0.23 0.00 3.35
4090 4498 3.385193 TCTTTGACGATTGCACTCAGA 57.615 42.857 4.82 0.00 0.00 3.27
4099 4507 1.302366 TTGCACTCAGACAGTTGCAG 58.698 50.000 0.00 0.00 39.09 4.41
4101 4509 1.162181 GCACTCAGACAGTTGCAGCA 61.162 55.000 2.55 0.00 30.26 4.41
4104 4512 1.878088 ACTCAGACAGTTGCAGCATTG 59.122 47.619 2.55 0.34 26.56 2.82
4108 4516 3.130869 TCAGACAGTTGCAGCATTGTTTT 59.869 39.130 12.81 4.40 0.00 2.43
4119 4527 4.149396 GCAGCATTGTTTTCTGTTCATGTC 59.851 41.667 0.00 0.00 0.00 3.06
4126 4534 6.466308 TGTTTTCTGTTCATGTCGATACAG 57.534 37.500 0.00 0.00 39.49 2.74
4142 4550 4.024556 CGATACAGCAGGAATGGTTTCATC 60.025 45.833 0.00 0.00 33.23 2.92
4161 4569 8.299570 GTTTCATCCTTGTTCACTTATTCACAT 58.700 33.333 0.00 0.00 0.00 3.21
4163 4571 7.819644 TCATCCTTGTTCACTTATTCACATTG 58.180 34.615 0.00 0.00 0.00 2.82
4165 4573 6.068010 TCCTTGTTCACTTATTCACATTGGT 58.932 36.000 0.00 0.00 0.00 3.67
4167 4575 6.642131 CCTTGTTCACTTATTCACATTGGTTG 59.358 38.462 0.00 0.00 0.00 3.77
4170 4578 4.735369 TCACTTATTCACATTGGTTGGGT 58.265 39.130 0.00 0.00 0.00 4.51
4185 4593 4.347000 TGGTTGGGTAATAGGCAGATAGAC 59.653 45.833 0.00 0.00 0.00 2.59
4242 4650 5.700832 CAGTTATAGTGGACAAGTTGCTTGA 59.299 40.000 14.81 0.00 43.42 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.325694 CAAGGCATCCATGTATTTTTCTCTTT 58.674 34.615 0.00 0.00 0.00 2.52
1 2 6.628844 GCAAGGCATCCATGTATTTTTCTCTT 60.629 38.462 0.00 0.00 0.00 2.85
2 3 5.163478 GCAAGGCATCCATGTATTTTTCTCT 60.163 40.000 0.00 0.00 0.00 3.10
3 4 5.045872 GCAAGGCATCCATGTATTTTTCTC 58.954 41.667 0.00 0.00 0.00 2.87
4 5 4.467082 TGCAAGGCATCCATGTATTTTTCT 59.533 37.500 0.00 0.00 31.71 2.52
5 6 4.567959 GTGCAAGGCATCCATGTATTTTTC 59.432 41.667 0.00 0.00 41.91 2.29
6 7 4.506758 GTGCAAGGCATCCATGTATTTTT 58.493 39.130 0.00 0.00 41.91 1.94
7 8 3.429272 CGTGCAAGGCATCCATGTATTTT 60.429 43.478 0.00 0.00 41.91 1.82
8 9 2.099592 CGTGCAAGGCATCCATGTATTT 59.900 45.455 0.00 0.00 41.91 1.40
9 10 1.677576 CGTGCAAGGCATCCATGTATT 59.322 47.619 0.00 0.00 41.91 1.89
10 11 1.311859 CGTGCAAGGCATCCATGTAT 58.688 50.000 0.00 0.00 41.91 2.29
11 12 0.747644 CCGTGCAAGGCATCCATGTA 60.748 55.000 5.51 0.00 41.91 2.29
12 13 2.048023 CCGTGCAAGGCATCCATGT 61.048 57.895 5.51 0.00 41.91 3.21
13 14 1.597797 AACCGTGCAAGGCATCCATG 61.598 55.000 19.37 0.00 41.91 3.66
14 15 1.304381 AACCGTGCAAGGCATCCAT 60.304 52.632 19.37 0.00 41.91 3.41
15 16 2.115052 AACCGTGCAAGGCATCCA 59.885 55.556 19.37 0.00 41.91 3.41
16 17 2.568090 CAACCGTGCAAGGCATCC 59.432 61.111 19.37 0.00 41.91 3.51
30 31 2.417933 GAGTGATCTCATGTGGTGCAAC 59.582 50.000 0.00 0.00 40.18 4.17
31 32 2.616256 GGAGTGATCTCATGTGGTGCAA 60.616 50.000 0.00 0.00 42.05 4.08
32 33 1.065926 GGAGTGATCTCATGTGGTGCA 60.066 52.381 0.00 0.00 42.05 4.57
33 34 1.065926 TGGAGTGATCTCATGTGGTGC 60.066 52.381 0.00 0.00 42.05 5.01
34 35 3.005554 GTTGGAGTGATCTCATGTGGTG 58.994 50.000 0.00 0.00 42.05 4.17
35 36 2.639347 TGTTGGAGTGATCTCATGTGGT 59.361 45.455 0.00 0.00 42.05 4.16
36 37 3.339253 TGTTGGAGTGATCTCATGTGG 57.661 47.619 0.00 0.00 42.05 4.17
37 38 3.875727 GGATGTTGGAGTGATCTCATGTG 59.124 47.826 0.00 0.00 42.05 3.21
38 39 3.520721 TGGATGTTGGAGTGATCTCATGT 59.479 43.478 0.00 0.00 42.05 3.21
39 40 3.875727 GTGGATGTTGGAGTGATCTCATG 59.124 47.826 0.00 0.00 42.05 3.07
40 41 3.431346 CGTGGATGTTGGAGTGATCTCAT 60.431 47.826 0.00 0.00 42.05 2.90
41 42 2.094026 CGTGGATGTTGGAGTGATCTCA 60.094 50.000 0.00 0.00 42.05 3.27
42 43 2.544685 CGTGGATGTTGGAGTGATCTC 58.455 52.381 0.00 0.00 39.76 2.75
43 44 1.208052 CCGTGGATGTTGGAGTGATCT 59.792 52.381 0.00 0.00 0.00 2.75
44 45 1.066143 ACCGTGGATGTTGGAGTGATC 60.066 52.381 0.00 0.00 0.00 2.92
45 46 0.984230 ACCGTGGATGTTGGAGTGAT 59.016 50.000 0.00 0.00 0.00 3.06
46 47 0.762418 AACCGTGGATGTTGGAGTGA 59.238 50.000 0.00 0.00 0.00 3.41
47 48 1.604604 AAACCGTGGATGTTGGAGTG 58.395 50.000 0.00 0.00 0.00 3.51
48 49 2.358322 AAAACCGTGGATGTTGGAGT 57.642 45.000 0.00 0.00 0.00 3.85
68 69 4.219507 TCTGTGCTTCCTCACAAACAAAAA 59.780 37.500 0.00 0.00 45.22 1.94
69 70 3.761218 TCTGTGCTTCCTCACAAACAAAA 59.239 39.130 0.00 0.00 45.22 2.44
70 71 3.351740 TCTGTGCTTCCTCACAAACAAA 58.648 40.909 0.00 0.00 45.22 2.83
71 72 2.945008 CTCTGTGCTTCCTCACAAACAA 59.055 45.455 0.00 0.00 45.22 2.83
72 73 2.564771 CTCTGTGCTTCCTCACAAACA 58.435 47.619 0.00 0.00 45.22 2.83
73 74 1.265365 GCTCTGTGCTTCCTCACAAAC 59.735 52.381 0.00 0.00 45.22 2.93
74 75 1.597742 GCTCTGTGCTTCCTCACAAA 58.402 50.000 0.00 0.00 45.22 2.83
75 76 3.312404 GCTCTGTGCTTCCTCACAA 57.688 52.632 0.00 0.00 45.22 3.33
85 86 1.153588 GAGGCTGAGAGCTCTGTGC 60.154 63.158 23.91 22.95 41.99 4.57
86 87 0.825410 ATGAGGCTGAGAGCTCTGTG 59.175 55.000 23.91 14.34 41.99 3.66
87 88 2.450867 TATGAGGCTGAGAGCTCTGT 57.549 50.000 23.91 0.00 41.99 3.41
88 89 2.892215 TGATATGAGGCTGAGAGCTCTG 59.108 50.000 23.91 9.06 41.99 3.35
89 90 2.892852 GTGATATGAGGCTGAGAGCTCT 59.107 50.000 18.28 18.28 41.99 4.09
90 91 2.892852 AGTGATATGAGGCTGAGAGCTC 59.107 50.000 5.27 5.27 41.99 4.09
91 92 2.961510 AGTGATATGAGGCTGAGAGCT 58.038 47.619 0.00 0.00 41.99 4.09
92 93 4.462132 TGATAGTGATATGAGGCTGAGAGC 59.538 45.833 0.00 0.00 41.46 4.09
266 599 5.788450 AGTTGGAATCAGTGAGAGTTACAG 58.212 41.667 0.00 0.00 0.00 2.74
267 600 5.808366 AGTTGGAATCAGTGAGAGTTACA 57.192 39.130 0.00 0.00 0.00 2.41
268 601 6.926313 AGTAGTTGGAATCAGTGAGAGTTAC 58.074 40.000 0.00 0.00 0.00 2.50
269 602 7.378966 CAAGTAGTTGGAATCAGTGAGAGTTA 58.621 38.462 2.05 0.00 0.00 2.24
270 603 6.226787 CAAGTAGTTGGAATCAGTGAGAGTT 58.773 40.000 2.05 0.00 0.00 3.01
324 657 2.561419 GGCGGTATTATCCTAGTGAGCA 59.439 50.000 0.00 0.00 0.00 4.26
326 659 5.163540 GGTATGGCGGTATTATCCTAGTGAG 60.164 48.000 0.00 0.00 0.00 3.51
338 671 1.133945 TGCAATGTGGTATGGCGGTAT 60.134 47.619 0.00 0.00 0.00 2.73
385 718 9.853555 GATCTACCTCATCAATGATTGTACTAG 57.146 37.037 4.93 0.00 36.02 2.57
386 719 9.367160 TGATCTACCTCATCAATGATTGTACTA 57.633 33.333 4.93 0.00 36.02 1.82
387 720 8.255111 TGATCTACCTCATCAATGATTGTACT 57.745 34.615 4.93 0.00 36.02 2.73
388 721 7.117523 GCTGATCTACCTCATCAATGATTGTAC 59.882 40.741 4.93 0.00 36.02 2.90
389 722 7.157347 GCTGATCTACCTCATCAATGATTGTA 58.843 38.462 4.93 0.00 36.02 2.41
401 734 5.279006 GGAACATATTCGCTGATCTACCTCA 60.279 44.000 0.00 0.00 35.48 3.86
403 736 4.588951 TGGAACATATTCGCTGATCTACCT 59.411 41.667 0.00 0.00 35.48 3.08
405 738 4.383052 CGTGGAACATATTCGCTGATCTAC 59.617 45.833 0.00 0.00 44.52 2.59
445 778 8.394877 CACTCCGCAAAATAAAATGTGAGTATA 58.605 33.333 0.00 0.00 32.95 1.47
448 781 5.240623 TCACTCCGCAAAATAAAATGTGAGT 59.759 36.000 0.00 0.00 33.82 3.41
449 782 5.698832 TCACTCCGCAAAATAAAATGTGAG 58.301 37.500 0.00 0.00 0.00 3.51
450 783 5.697473 TCACTCCGCAAAATAAAATGTGA 57.303 34.783 0.00 0.00 0.00 3.58
451 784 6.640499 TCTTTCACTCCGCAAAATAAAATGTG 59.360 34.615 0.00 0.00 0.00 3.21
459 792 7.047891 TGTATATCTCTTTCACTCCGCAAAAT 58.952 34.615 0.00 0.00 0.00 1.82
520 854 1.961793 CTTGGTCGTTGAAAGGGTGA 58.038 50.000 0.00 0.00 0.00 4.02
553 887 5.583495 ACAGAATAGAATATATCTCCGCGC 58.417 41.667 0.00 0.00 39.71 6.86
576 910 2.093500 AGGCGACATGTATGCTTGAGAA 60.093 45.455 18.75 0.00 0.00 2.87
580 914 2.285220 GTGTAGGCGACATGTATGCTTG 59.715 50.000 18.75 0.00 41.14 4.01
669 1003 2.829206 TTTGAAGCGTGCACGTGGG 61.829 57.895 36.80 13.00 42.22 4.61
701 1035 8.713971 TCATTTATTTATTCCAGTCTAGCCTGA 58.286 33.333 1.43 0.00 34.23 3.86
702 1036 8.778358 GTCATTTATTTATTCCAGTCTAGCCTG 58.222 37.037 0.00 0.00 0.00 4.85
703 1037 8.494433 TGTCATTTATTTATTCCAGTCTAGCCT 58.506 33.333 0.00 0.00 0.00 4.58
704 1038 8.560374 GTGTCATTTATTTATTCCAGTCTAGCC 58.440 37.037 0.00 0.00 0.00 3.93
705 1039 8.560374 GGTGTCATTTATTTATTCCAGTCTAGC 58.440 37.037 0.00 0.00 0.00 3.42
706 1040 8.765219 CGGTGTCATTTATTTATTCCAGTCTAG 58.235 37.037 0.00 0.00 0.00 2.43
707 1041 7.225931 GCGGTGTCATTTATTTATTCCAGTCTA 59.774 37.037 0.00 0.00 0.00 2.59
708 1042 6.038271 GCGGTGTCATTTATTTATTCCAGTCT 59.962 38.462 0.00 0.00 0.00 3.24
709 1043 6.199393 GCGGTGTCATTTATTTATTCCAGTC 58.801 40.000 0.00 0.00 0.00 3.51
710 1044 5.067283 GGCGGTGTCATTTATTTATTCCAGT 59.933 40.000 0.00 0.00 0.00 4.00
711 1045 5.507315 GGGCGGTGTCATTTATTTATTCCAG 60.507 44.000 0.00 0.00 0.00 3.86
712 1046 4.339814 GGGCGGTGTCATTTATTTATTCCA 59.660 41.667 0.00 0.00 0.00 3.53
713 1047 4.583073 AGGGCGGTGTCATTTATTTATTCC 59.417 41.667 0.00 0.00 0.00 3.01
714 1048 5.767816 AGGGCGGTGTCATTTATTTATTC 57.232 39.130 0.00 0.00 0.00 1.75
715 1049 6.153680 TGAAAGGGCGGTGTCATTTATTTATT 59.846 34.615 0.00 0.00 0.00 1.40
716 1050 5.654650 TGAAAGGGCGGTGTCATTTATTTAT 59.345 36.000 0.00 0.00 0.00 1.40
717 1051 5.010933 TGAAAGGGCGGTGTCATTTATTTA 58.989 37.500 0.00 0.00 0.00 1.40
718 1052 3.829601 TGAAAGGGCGGTGTCATTTATTT 59.170 39.130 0.00 0.00 0.00 1.40
719 1053 3.426615 TGAAAGGGCGGTGTCATTTATT 58.573 40.909 0.00 0.00 0.00 1.40
720 1054 3.080300 TGAAAGGGCGGTGTCATTTAT 57.920 42.857 0.00 0.00 0.00 1.40
721 1055 2.570415 TGAAAGGGCGGTGTCATTTA 57.430 45.000 0.00 0.00 0.00 1.40
722 1056 1.698506 TTGAAAGGGCGGTGTCATTT 58.301 45.000 0.00 0.00 0.00 2.32
723 1057 1.698506 TTTGAAAGGGCGGTGTCATT 58.301 45.000 0.00 0.00 0.00 2.57
724 1058 1.923356 ATTTGAAAGGGCGGTGTCAT 58.077 45.000 0.00 0.00 0.00 3.06
725 1059 1.611491 GAATTTGAAAGGGCGGTGTCA 59.389 47.619 0.00 0.00 0.00 3.58
726 1060 1.611491 TGAATTTGAAAGGGCGGTGTC 59.389 47.619 0.00 0.00 0.00 3.67
727 1061 1.698506 TGAATTTGAAAGGGCGGTGT 58.301 45.000 0.00 0.00 0.00 4.16
728 1062 2.810439 TTGAATTTGAAAGGGCGGTG 57.190 45.000 0.00 0.00 0.00 4.94
729 1063 3.828875 TTTTGAATTTGAAAGGGCGGT 57.171 38.095 0.00 0.00 0.00 5.68
802 1138 7.992008 TCAAAAAGAACGTCTGGATTTTACTT 58.008 30.769 0.00 0.00 0.00 2.24
803 1139 7.562454 TCAAAAAGAACGTCTGGATTTTACT 57.438 32.000 0.00 0.00 0.00 2.24
804 1140 8.623310 TTTCAAAAAGAACGTCTGGATTTTAC 57.377 30.769 0.00 0.00 35.56 2.01
816 1152 6.079424 TCCCCTTGTATTTCAAAAAGAACG 57.921 37.500 0.00 0.00 35.56 3.95
826 1163 3.428862 CCGTGCATTTCCCCTTGTATTTC 60.429 47.826 0.00 0.00 0.00 2.17
847 1184 3.678548 GTCCTTCACACTACATTCGAACC 59.321 47.826 0.00 0.00 0.00 3.62
865 1202 2.910319 TGGTTGTAATAGCACAGGTCCT 59.090 45.455 0.00 0.00 0.00 3.85
919 1256 1.103398 GGCGATGTTTCAGGGATGGG 61.103 60.000 0.00 0.00 0.00 4.00
1251 1588 3.982372 GACGATGTGGGCGAGCGAA 62.982 63.158 0.00 0.00 0.00 4.70
1671 2008 0.906066 TGCCGTGGCTGAAATAGGTA 59.094 50.000 12.84 0.00 42.51 3.08
1877 2214 1.066716 CCGACCAAAGGTTGACGGATA 60.067 52.381 15.89 0.00 45.60 2.59
1878 2215 0.321298 CCGACCAAAGGTTGACGGAT 60.321 55.000 15.89 0.00 45.60 4.18
1879 2216 1.070105 CCGACCAAAGGTTGACGGA 59.930 57.895 15.89 0.00 45.60 4.69
1971 2309 0.602562 CCAAATTGCTTTGCTCGGGA 59.397 50.000 0.00 0.00 40.39 5.14
1974 2312 1.330306 CGACCAAATTGCTTTGCTCG 58.670 50.000 2.85 2.85 41.43 5.03
1988 2326 0.666274 CACGACAAGCTAAGCGACCA 60.666 55.000 8.70 0.00 0.00 4.02
2031 2369 1.026718 GCACGGAATGGGGAGAACTG 61.027 60.000 0.00 0.00 0.00 3.16
2037 2375 0.331278 ATTCAAGCACGGAATGGGGA 59.669 50.000 0.00 0.00 33.88 4.81
2047 2386 6.470235 GTGATACATTGCACTAATTCAAGCAC 59.530 38.462 0.00 0.00 36.62 4.40
2072 2411 1.728971 GTTCAGTCCACATCAAGAGCG 59.271 52.381 0.00 0.00 0.00 5.03
2156 2495 3.691498 AGTAAAGTTCAAAACAGCGCAC 58.309 40.909 11.47 0.00 0.00 5.34
2188 2527 4.840401 TTCTGTCATAACGAATCAAGCG 57.160 40.909 0.00 0.00 0.00 4.68
2264 2606 6.040391 ACTTTTGTACATGCATTACAACCAGT 59.960 34.615 22.77 22.28 38.79 4.00
2300 2642 7.834068 TGCTTTCACTATCATAAACACTCTC 57.166 36.000 0.00 0.00 0.00 3.20
2399 2741 5.557891 ACAAAGAGATGTGCAAAGATAGC 57.442 39.130 0.00 0.00 30.82 2.97
2409 2751 5.181811 TGTGCTTATCCAACAAAGAGATGTG 59.818 40.000 0.00 0.00 32.81 3.21
2418 2760 5.483811 TCTAACGATGTGCTTATCCAACAA 58.516 37.500 0.00 0.00 0.00 2.83
3210 3559 6.758886 AGCAGAATGATAGTTAGCAACTGTAC 59.241 38.462 10.59 0.00 39.88 2.90
3664 4015 2.797087 GCCTGCATTGCATACATGACAC 60.797 50.000 12.53 0.00 38.13 3.67
3756 4110 1.935873 CAAGTACCAGGACATGCATCG 59.064 52.381 0.00 0.00 0.00 3.84
3817 4172 4.625607 AATATGGATCGGAGGGAGTTTC 57.374 45.455 0.00 0.00 0.00 2.78
3818 4173 6.574465 CGATTAATATGGATCGGAGGGAGTTT 60.574 42.308 11.27 0.00 40.94 2.66
3819 4174 5.105310 CGATTAATATGGATCGGAGGGAGTT 60.105 44.000 11.27 0.00 40.94 3.01
3842 4197 6.304126 ACAACTTTGTATTAAATCAGCGACG 58.696 36.000 0.00 0.00 40.16 5.12
3876 4255 5.878116 TCCTTCGATCCATTTTAATTGTCGT 59.122 36.000 0.00 0.00 0.00 4.34
3887 4266 7.621796 AGTTTAACTACTTCCTTCGATCCATT 58.378 34.615 0.00 0.00 0.00 3.16
3970 4352 4.216257 ACTGCAGGTAAGCACATAAAGTTG 59.784 41.667 19.93 0.00 40.11 3.16
3982 4364 7.115095 GCTCGTATTAATTAGACTGCAGGTAAG 59.885 40.741 19.93 2.43 0.00 2.34
3983 4365 6.921857 GCTCGTATTAATTAGACTGCAGGTAA 59.078 38.462 19.93 15.22 0.00 2.85
3984 4366 6.040054 TGCTCGTATTAATTAGACTGCAGGTA 59.960 38.462 19.93 6.30 0.00 3.08
3985 4367 5.163447 TGCTCGTATTAATTAGACTGCAGGT 60.163 40.000 19.93 7.42 0.00 4.00
3986 4368 5.289595 TGCTCGTATTAATTAGACTGCAGG 58.710 41.667 19.93 0.00 0.00 4.85
3987 4369 6.477033 AGTTGCTCGTATTAATTAGACTGCAG 59.523 38.462 13.48 13.48 0.00 4.41
3988 4370 6.338146 AGTTGCTCGTATTAATTAGACTGCA 58.662 36.000 0.00 0.00 0.00 4.41
3989 4371 6.830114 AGTTGCTCGTATTAATTAGACTGC 57.170 37.500 0.00 0.00 0.00 4.40
3990 4372 8.321716 GTCAAGTTGCTCGTATTAATTAGACTG 58.678 37.037 0.00 0.00 0.00 3.51
3991 4373 7.491696 GGTCAAGTTGCTCGTATTAATTAGACT 59.508 37.037 0.00 0.00 0.00 3.24
3992 4374 7.254353 GGGTCAAGTTGCTCGTATTAATTAGAC 60.254 40.741 0.00 0.00 0.00 2.59
3993 4375 6.759827 GGGTCAAGTTGCTCGTATTAATTAGA 59.240 38.462 0.00 0.00 0.00 2.10
3994 4376 6.761714 AGGGTCAAGTTGCTCGTATTAATTAG 59.238 38.462 0.00 0.00 0.00 1.73
3995 4377 6.646267 AGGGTCAAGTTGCTCGTATTAATTA 58.354 36.000 0.00 0.00 0.00 1.40
3996 4378 5.497474 AGGGTCAAGTTGCTCGTATTAATT 58.503 37.500 0.00 0.00 0.00 1.40
3997 4379 5.099042 AGGGTCAAGTTGCTCGTATTAAT 57.901 39.130 0.00 0.00 0.00 1.40
3998 4380 4.020928 TGAGGGTCAAGTTGCTCGTATTAA 60.021 41.667 0.00 0.00 0.00 1.40
3999 4381 3.512329 TGAGGGTCAAGTTGCTCGTATTA 59.488 43.478 0.00 0.00 0.00 0.98
4000 4382 2.301870 TGAGGGTCAAGTTGCTCGTATT 59.698 45.455 0.00 0.00 0.00 1.89
4001 4383 1.899814 TGAGGGTCAAGTTGCTCGTAT 59.100 47.619 0.00 0.00 0.00 3.06
4002 4384 1.334160 TGAGGGTCAAGTTGCTCGTA 58.666 50.000 0.00 0.00 0.00 3.43
4003 4385 0.468226 TTGAGGGTCAAGTTGCTCGT 59.532 50.000 0.00 0.00 31.83 4.18
4004 4386 1.593196 TTTGAGGGTCAAGTTGCTCG 58.407 50.000 0.00 0.00 37.70 5.03
4027 4409 9.030301 GTAGTGCACATAAAGTTGTTCATTTTT 57.970 29.630 21.04 0.00 0.00 1.94
4028 4410 8.194104 TGTAGTGCACATAAAGTTGTTCATTTT 58.806 29.630 21.04 0.00 30.04 1.82
4029 4411 7.711846 TGTAGTGCACATAAAGTTGTTCATTT 58.288 30.769 21.04 0.00 30.04 2.32
4030 4412 7.270757 TGTAGTGCACATAAAGTTGTTCATT 57.729 32.000 21.04 0.00 30.04 2.57
4031 4413 6.875948 TGTAGTGCACATAAAGTTGTTCAT 57.124 33.333 21.04 0.00 30.04 2.57
4032 4414 6.875948 ATGTAGTGCACATAAAGTTGTTCA 57.124 33.333 21.04 0.00 46.34 3.18
4044 4426 7.622893 TGCTATGATAAAAATGTAGTGCACA 57.377 32.000 21.04 1.84 42.69 4.57
4045 4427 9.173939 GAATGCTATGATAAAAATGTAGTGCAC 57.826 33.333 9.40 9.40 0.00 4.57
4046 4428 9.123902 AGAATGCTATGATAAAAATGTAGTGCA 57.876 29.630 0.00 0.00 0.00 4.57
4047 4429 9.956720 AAGAATGCTATGATAAAAATGTAGTGC 57.043 29.630 0.00 0.00 0.00 4.40
4067 4449 4.152938 TCTGAGTGCAATCGTCAAAGAATG 59.847 41.667 9.92 0.00 0.00 2.67
4078 4486 1.875514 TGCAACTGTCTGAGTGCAATC 59.124 47.619 7.33 7.33 36.43 2.67
4087 4495 2.787601 AACAATGCTGCAACTGTCTG 57.212 45.000 17.66 7.23 0.00 3.51
4088 4496 3.382546 AGAAAACAATGCTGCAACTGTCT 59.617 39.130 17.66 10.22 0.00 3.41
4089 4497 3.488310 CAGAAAACAATGCTGCAACTGTC 59.512 43.478 17.66 8.53 0.00 3.51
4090 4498 3.119029 ACAGAAAACAATGCTGCAACTGT 60.119 39.130 6.36 10.67 33.03 3.55
4099 4507 4.536065 TCGACATGAACAGAAAACAATGC 58.464 39.130 0.00 0.00 0.00 3.56
4101 4509 7.433708 TGTATCGACATGAACAGAAAACAAT 57.566 32.000 0.00 0.00 0.00 2.71
4104 4512 5.107104 TGCTGTATCGACATGAACAGAAAAC 60.107 40.000 14.32 0.00 37.65 2.43
4108 4516 3.429410 CCTGCTGTATCGACATGAACAGA 60.429 47.826 14.32 0.00 37.65 3.41
4119 4527 3.270027 TGAAACCATTCCTGCTGTATCG 58.730 45.455 0.00 0.00 34.49 2.92
4126 4534 2.827921 ACAAGGATGAAACCATTCCTGC 59.172 45.455 0.00 0.00 34.49 4.85
4142 4550 6.331369 ACCAATGTGAATAAGTGAACAAGG 57.669 37.500 0.00 0.00 0.00 3.61
4161 4569 4.972568 TCTATCTGCCTATTACCCAACCAA 59.027 41.667 0.00 0.00 0.00 3.67
4163 4571 4.347000 TGTCTATCTGCCTATTACCCAACC 59.653 45.833 0.00 0.00 0.00 3.77
4165 4573 6.084738 AGATGTCTATCTGCCTATTACCCAA 58.915 40.000 0.00 0.00 42.04 4.12
4185 4593 7.809665 TGACTGTTTGATAATTGACACAGATG 58.190 34.615 4.19 0.00 0.00 2.90
4194 4602 9.764870 CTGATAACACTGACTGTTTGATAATTG 57.235 33.333 0.00 0.00 40.45 2.32
4195 4603 9.507329 ACTGATAACACTGACTGTTTGATAATT 57.493 29.630 0.00 0.00 40.45 1.40
4206 4614 7.396339 TGTCCACTATAACTGATAACACTGACT 59.604 37.037 0.00 0.00 0.00 3.41
4284 4692 6.723977 TGACAGAAATAACAGCCCCTATTTTT 59.276 34.615 0.00 0.00 29.84 1.94
4319 4727 8.410673 TTGGAATAAACAACCTGCTATACAAA 57.589 30.769 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.