Multiple sequence alignment - TraesCS3A01G324900

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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 TraesCS3A01G324900 chr3A 100.000 6793 0 0 1 6793 569430101 569423309 0.000000e+00 12545
1 TraesCS3A01G324900 chr3A 97.826 138 3 0 3545 3682 481651435 481651572 8.800000e-59 239
2 TraesCS3A01G324900 chr3A 96.429 140 4 1 3539 3678 383710080 383709942 5.300000e-56 230
3 TraesCS3A01G324900 chr3D 96.207 3111 70 18 3675 6751 432032324 432029228 0.000000e+00 5048
4 TraesCS3A01G324900 chr3D 94.581 3137 106 20 471 3553 432035447 432032321 0.000000e+00 4793
5 TraesCS3A01G324900 chr3D 94.719 303 12 2 119 417 432035835 432035533 1.030000e-127 468
6 TraesCS3A01G324900 chr3B 97.096 2996 64 5 3774 6753 564249936 564246948 0.000000e+00 5029
7 TraesCS3A01G324900 chr3B 94.471 2930 113 20 445 3341 564253434 564250521 0.000000e+00 4468
8 TraesCS3A01G324900 chr3B 88.957 326 5 7 129 425 564253829 564253506 2.310000e-99 374
9 TraesCS3A01G324900 chr3B 97.101 138 3 1 3542 3678 656597563 656597700 1.470000e-56 231
10 TraesCS3A01G324900 chr3B 90.850 153 11 1 3404 3553 564250445 564250293 1.160000e-47 202
11 TraesCS3A01G324900 chr3B 96.040 101 4 0 3675 3775 564250296 564250196 1.520000e-36 165
12 TraesCS3A01G324900 chr5A 98.540 137 1 1 3549 3684 645121663 645121799 2.450000e-59 241
13 TraesCS3A01G324900 chr5A 95.205 146 5 2 3542 3685 342456835 342456980 5.300000e-56 230
14 TraesCS3A01G324900 chr7A 99.237 131 1 0 3552 3682 77440541 77440671 3.170000e-58 237
15 TraesCS3A01G324900 chr2A 97.143 140 3 1 3546 3684 43500215 43500354 1.140000e-57 235
16 TraesCS3A01G324900 chr1A 97.122 139 3 1 3542 3679 311814222 311814084 4.100000e-57 233
17 TraesCS3A01G324900 chr1A 94.558 147 7 1 3532 3678 27289551 27289696 6.850000e-55 226


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 TraesCS3A01G324900 chr3A 569423309 569430101 6792 True 12545.000000 12545 100.0000 1 6793 1 chr3A.!!$R2 6792
1 TraesCS3A01G324900 chr3D 432029228 432035835 6607 True 3436.333333 5048 95.1690 119 6751 3 chr3D.!!$R1 6632
2 TraesCS3A01G324900 chr3B 564246948 564253829 6881 True 2047.600000 5029 93.4828 129 6753 5 chr3B.!!$R1 6624

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
104 105 0.034198 CCCACCACATGACACACGTA 59.966 55.000 0.00 0.0 0.00 3.57 F
932 1043 0.173481 TCCGTTTCGCATCTGAGGAG 59.827 55.000 0.00 0.0 0.00 3.69 F
1688 1835 1.612442 GGGCCAGGTCAGGACACTA 60.612 63.158 4.39 0.0 38.98 2.74 F
3568 3747 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.0 0.00 4.30 F
3569 3748 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.0 0.00 3.34 F
4390 4830 0.902984 TCAGAACGCAAGCCCCTCTA 60.903 55.000 0.00 0.0 45.62 2.43 F
4545 4985 3.629398 CCAGTCCAATTTCTGGTGCTATC 59.371 47.826 11.00 0.0 46.51 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 1457 0.609681 TGGGTTTGCATCGGTTACCC 60.610 55.000 0.00 0.0 46.98 3.69 R
2877 3024 0.110295 AGTATGCAACCACACTGCCA 59.890 50.000 0.00 0.0 39.13 4.92 R
3672 3851 0.759346 AACGCCCATCCATCTACTCC 59.241 55.000 0.00 0.0 0.00 3.85 R
4374 4814 0.178068 TCATAGAGGGGCTTGCGTTC 59.822 55.000 0.00 0.0 0.00 3.95 R
4545 4985 2.468777 GCAGTTGTGAAATGTTGAAGCG 59.531 45.455 0.00 0.0 0.00 4.68 R
5765 6208 1.267261 CATAAGTCCGGGAGTAGCTCG 59.733 57.143 4.46 0.0 41.20 5.03 R
6529 6992 1.673920 TCGTTCCTTGTTTGACTTGGC 59.326 47.619 0.00 0.0 0.00 4.52 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
45 46 7.648142 TCATTCTATTGTCAAATAAATCGGGC 58.352 34.615 0.00 0.00 0.00 6.13
46 47 5.666969 TCTATTGTCAAATAAATCGGGCG 57.333 39.130 0.00 0.00 0.00 6.13
47 48 3.708563 ATTGTCAAATAAATCGGGCGG 57.291 42.857 0.00 0.00 0.00 6.13
48 49 0.736053 TGTCAAATAAATCGGGCGGC 59.264 50.000 0.00 0.00 0.00 6.53
49 50 0.736053 GTCAAATAAATCGGGCGGCA 59.264 50.000 12.47 0.00 0.00 5.69
50 51 1.133407 GTCAAATAAATCGGGCGGCAA 59.867 47.619 12.47 0.00 0.00 4.52
51 52 1.819288 TCAAATAAATCGGGCGGCAAA 59.181 42.857 12.47 0.00 0.00 3.68
52 53 1.923864 CAAATAAATCGGGCGGCAAAC 59.076 47.619 12.47 0.00 0.00 2.93
62 63 2.580326 CGGCAAACGCATGGCATC 60.580 61.111 13.72 0.00 45.50 3.91
63 64 2.572812 GGCAAACGCATGGCATCA 59.427 55.556 0.00 0.00 44.66 3.07
64 65 1.079956 GGCAAACGCATGGCATCAA 60.080 52.632 0.00 0.00 44.66 2.57
65 66 1.353609 GGCAAACGCATGGCATCAAC 61.354 55.000 0.00 0.00 44.66 3.18
66 67 1.676438 GCAAACGCATGGCATCAACG 61.676 55.000 11.30 11.30 34.19 4.10
67 68 0.109827 CAAACGCATGGCATCAACGA 60.110 50.000 17.77 0.00 32.91 3.85
68 69 0.810648 AAACGCATGGCATCAACGAT 59.189 45.000 17.77 6.15 32.91 3.73
69 70 0.378257 AACGCATGGCATCAACGATC 59.622 50.000 17.77 0.00 32.91 3.69
70 71 1.280746 CGCATGGCATCAACGATCC 59.719 57.895 0.00 0.00 0.00 3.36
71 72 1.438562 CGCATGGCATCAACGATCCA 61.439 55.000 0.00 0.00 0.00 3.41
72 73 0.309922 GCATGGCATCAACGATCCAG 59.690 55.000 0.00 0.00 31.36 3.86
73 74 1.957668 CATGGCATCAACGATCCAGA 58.042 50.000 0.00 0.00 31.36 3.86
74 75 2.501261 CATGGCATCAACGATCCAGAT 58.499 47.619 0.00 0.00 31.36 2.90
75 76 1.957668 TGGCATCAACGATCCAGATG 58.042 50.000 10.67 10.67 41.50 2.90
80 81 4.658713 CATCAACGATCCAGATGCATAC 57.341 45.455 0.00 0.00 33.56 2.39
81 82 4.313282 CATCAACGATCCAGATGCATACT 58.687 43.478 0.00 0.00 33.56 2.12
82 83 3.982475 TCAACGATCCAGATGCATACTC 58.018 45.455 0.00 0.00 0.00 2.59
83 84 3.062763 CAACGATCCAGATGCATACTCC 58.937 50.000 0.00 0.00 0.00 3.85
84 85 1.620819 ACGATCCAGATGCATACTCCC 59.379 52.381 0.00 0.00 0.00 4.30
85 86 1.066573 CGATCCAGATGCATACTCCCC 60.067 57.143 0.00 0.00 0.00 4.81
86 87 1.280421 GATCCAGATGCATACTCCCCC 59.720 57.143 0.00 0.00 0.00 5.40
100 101 2.842801 CCCCCACCACATGACACA 59.157 61.111 0.00 0.00 0.00 3.72
101 102 1.603455 CCCCCACCACATGACACAC 60.603 63.158 0.00 0.00 0.00 3.82
102 103 1.965930 CCCCACCACATGACACACG 60.966 63.158 0.00 0.00 0.00 4.49
103 104 1.227823 CCCACCACATGACACACGT 60.228 57.895 0.00 0.00 0.00 4.49
104 105 0.034198 CCCACCACATGACACACGTA 59.966 55.000 0.00 0.00 0.00 3.57
105 106 1.428448 CCACCACATGACACACGTAG 58.572 55.000 0.00 0.00 0.00 3.51
107 108 2.029739 CCACCACATGACACACGTAGTA 60.030 50.000 0.00 0.00 41.61 1.82
108 109 3.553302 CCACCACATGACACACGTAGTAA 60.553 47.826 0.00 0.00 41.61 2.24
109 110 3.673338 CACCACATGACACACGTAGTAAG 59.327 47.826 0.00 0.00 41.61 2.34
110 111 2.666508 CCACATGACACACGTAGTAAGC 59.333 50.000 0.00 0.00 41.61 3.09
111 112 3.313690 CACATGACACACGTAGTAAGCA 58.686 45.455 0.00 0.00 41.61 3.91
112 113 3.738791 CACATGACACACGTAGTAAGCAA 59.261 43.478 0.00 0.00 41.61 3.91
113 114 4.388773 CACATGACACACGTAGTAAGCAAT 59.611 41.667 0.00 0.00 41.61 3.56
114 115 4.994852 ACATGACACACGTAGTAAGCAATT 59.005 37.500 0.00 0.00 41.61 2.32
115 116 5.120208 ACATGACACACGTAGTAAGCAATTC 59.880 40.000 0.00 0.00 41.61 2.17
116 117 4.623002 TGACACACGTAGTAAGCAATTCA 58.377 39.130 0.00 0.00 41.61 2.57
117 118 5.051153 TGACACACGTAGTAAGCAATTCAA 58.949 37.500 0.00 0.00 41.61 2.69
118 119 5.699001 TGACACACGTAGTAAGCAATTCAAT 59.301 36.000 0.00 0.00 41.61 2.57
119 120 6.128661 TGACACACGTAGTAAGCAATTCAATC 60.129 38.462 0.00 0.00 41.61 2.67
120 121 5.699001 ACACACGTAGTAAGCAATTCAATCA 59.301 36.000 0.00 0.00 41.61 2.57
121 122 6.203915 ACACACGTAGTAAGCAATTCAATCAA 59.796 34.615 0.00 0.00 41.61 2.57
122 123 7.075121 CACACGTAGTAAGCAATTCAATCAAA 58.925 34.615 0.00 0.00 41.61 2.69
123 124 7.059488 CACACGTAGTAAGCAATTCAATCAAAC 59.941 37.037 0.00 0.00 41.61 2.93
124 125 7.041372 ACACGTAGTAAGCAATTCAATCAAACT 60.041 33.333 0.00 0.00 41.61 2.66
125 126 8.440059 CACGTAGTAAGCAATTCAATCAAACTA 58.560 33.333 0.00 0.00 41.61 2.24
126 127 9.162764 ACGTAGTAAGCAATTCAATCAAACTAT 57.837 29.630 0.00 0.00 41.94 2.12
127 128 9.988350 CGTAGTAAGCAATTCAATCAAACTATT 57.012 29.630 0.00 0.00 0.00 1.73
175 176 1.609239 CCAATGAGCCCACCTAGCA 59.391 57.895 0.00 0.00 0.00 3.49
261 282 0.320858 ACGACACGAGAGAGAGAGCA 60.321 55.000 0.00 0.00 0.00 4.26
316 340 1.316651 AGTCGGGTAGGCGAGATAAC 58.683 55.000 0.00 0.00 0.00 1.89
352 381 0.686769 TCCTTAACCTCGGCTCCCTC 60.687 60.000 0.00 0.00 0.00 4.30
437 530 2.256461 CGGAAGCAAGGCAGCAAC 59.744 61.111 4.78 0.00 36.85 4.17
438 531 2.653115 GGAAGCAAGGCAGCAACC 59.347 61.111 4.78 3.77 36.85 3.77
439 532 2.256461 GAAGCAAGGCAGCAACCG 59.744 61.111 4.78 0.00 36.85 4.44
440 533 2.203337 AAGCAAGGCAGCAACCGA 60.203 55.556 4.78 0.00 36.85 4.69
441 534 1.589716 GAAGCAAGGCAGCAACCGAT 61.590 55.000 4.78 0.00 36.85 4.18
442 535 1.181098 AAGCAAGGCAGCAACCGATT 61.181 50.000 4.78 0.00 36.85 3.34
443 536 1.181098 AGCAAGGCAGCAACCGATTT 61.181 50.000 4.78 0.00 36.85 2.17
457 550 7.329226 CAGCAACCGATTTGATTTTTCAATACT 59.671 33.333 1.29 0.00 37.39 2.12
504 597 2.094494 CACCTAATCGATCCCATCTCCG 60.094 54.545 0.00 0.00 0.00 4.63
533 626 3.082055 GTCTCCGTCCCCTTCCCC 61.082 72.222 0.00 0.00 0.00 4.81
563 656 1.537990 CCACACGGCCAAAGGAAAAAG 60.538 52.381 2.24 0.00 0.00 2.27
582 675 2.587522 AGGAAAGAACAGGGCTCAAAC 58.412 47.619 0.00 0.00 0.00 2.93
748 851 2.900273 GGCCATGTCGCTCACCTA 59.100 61.111 0.00 0.00 0.00 3.08
795 898 3.608759 AAGAGCCTCCTCCGAGCCA 62.609 63.158 0.00 0.00 38.96 4.75
846 949 2.961721 GATTCGATCGCCGCAGCA 60.962 61.111 11.09 0.00 39.83 4.41
870 981 2.115910 CCCAGGTCAAGCCAAGCA 59.884 61.111 0.00 0.00 40.61 3.91
872 983 1.530013 CCCAGGTCAAGCCAAGCAAG 61.530 60.000 0.00 0.00 40.61 4.01
873 984 1.288127 CAGGTCAAGCCAAGCAAGC 59.712 57.895 0.00 0.00 40.61 4.01
903 1014 3.071479 TCTAGGTTTGGTTTAGCTTGCG 58.929 45.455 0.00 0.00 0.00 4.85
932 1043 0.173481 TCCGTTTCGCATCTGAGGAG 59.827 55.000 0.00 0.00 0.00 3.69
945 1056 4.851214 AGGAGGAGGAGGAGCGGC 62.851 72.222 0.00 0.00 0.00 6.53
1167 1291 4.796231 ATCGCCAGCCACGACGAC 62.796 66.667 0.00 0.00 43.23 4.34
1220 1346 3.942115 CCCTCTTTCGATCCTCTTTTTCC 59.058 47.826 0.00 0.00 0.00 3.13
1224 1350 6.128145 CCTCTTTCGATCCTCTTTTTCCTTTC 60.128 42.308 0.00 0.00 0.00 2.62
1228 1354 5.302360 TCGATCCTCTTTTTCCTTTCGAAA 58.698 37.500 10.71 10.71 38.74 3.46
1331 1457 3.687212 TGTCCCACGTGTGCATTAATAAG 59.313 43.478 15.65 0.00 0.00 1.73
1688 1835 1.612442 GGGCCAGGTCAGGACACTA 60.612 63.158 4.39 0.00 38.98 2.74
1706 1853 7.875041 AGGACACTATGACAATGCATATTCTAC 59.125 37.037 0.00 0.00 30.90 2.59
1719 1866 7.734924 TGCATATTCTACATCATTCCTTGTC 57.265 36.000 0.00 0.00 0.00 3.18
1733 1880 3.460103 TCCTTGTCCGTGTAAAGTTGTC 58.540 45.455 0.00 0.00 0.00 3.18
1734 1881 2.220133 CCTTGTCCGTGTAAAGTTGTCG 59.780 50.000 0.00 0.00 0.00 4.35
1755 1902 6.129393 GTCGTGATACATTCATTATGCACAC 58.871 40.000 0.00 0.00 37.81 3.82
1768 1915 8.648557 TCATTATGCACACTGAATCTACTAAC 57.351 34.615 0.00 0.00 0.00 2.34
1795 1942 4.974645 TGGGAGTGTGAGTTGTATTCTT 57.025 40.909 0.00 0.00 0.00 2.52
1831 1978 7.221838 CCTTTTGACATTGTAACACGACATTTT 59.778 33.333 0.00 0.00 0.00 1.82
1832 1979 8.467402 TTTTGACATTGTAACACGACATTTTT 57.533 26.923 0.00 0.00 0.00 1.94
1890 2037 6.315144 TGTGTCATTAACCTTGAATATCACCG 59.685 38.462 0.00 0.00 0.00 4.94
1953 2100 5.868454 TGTTCCTGATCTTGAAACTGATGA 58.132 37.500 0.00 0.00 0.00 2.92
1968 2115 8.321353 TGAAACTGATGATTAGTGGTTCATACT 58.679 33.333 1.69 0.00 32.84 2.12
2006 2153 8.953368 TGTGTTATAGTCAGTATCTTAGACGA 57.047 34.615 0.00 0.00 37.36 4.20
2245 2392 1.956477 GTGTGGGATGTTGAACAAGCT 59.044 47.619 0.62 0.00 0.00 3.74
2629 2776 6.684613 GCATACTTCCTGGTTCTAAATCGGTA 60.685 42.308 0.00 0.00 0.00 4.02
2877 3024 0.404040 TTCCGCCTCCTGGTTCAAAT 59.596 50.000 0.00 0.00 35.27 2.32
2984 3131 4.696479 AGCTGTCCAGGTATTATTCAGG 57.304 45.455 0.00 0.00 37.39 3.86
3123 3270 2.945008 ACACCGCATATGTTCTTCATGG 59.055 45.455 4.29 0.00 37.91 3.66
3213 3360 5.236263 TCCACATGCGAATCATACATACAAC 59.764 40.000 0.00 0.00 33.19 3.32
3250 3397 3.575687 CCGTTAGGGACCTAATAACCGAT 59.424 47.826 13.51 0.00 40.18 4.18
3287 3434 3.586470 ACCTGACAATGTGGTTGGTAA 57.414 42.857 0.00 0.00 42.28 2.85
3289 3436 4.479158 ACCTGACAATGTGGTTGGTAATT 58.521 39.130 0.00 0.00 42.28 1.40
3402 3577 5.462530 CCCCCGAAAAGATTTTGTTAGTT 57.537 39.130 0.00 0.00 0.00 2.24
3409 3584 7.845622 CCGAAAAGATTTTGTTAGTTTGCTTTG 59.154 33.333 0.00 0.00 0.00 2.77
3420 3595 8.445275 TGTTAGTTTGCTTTGTTCAGAAGATA 57.555 30.769 0.00 0.00 0.00 1.98
3453 3628 3.064207 TGTTTCCTTGTAGCGATGTGTC 58.936 45.455 0.00 0.00 0.00 3.67
3505 3684 1.565067 AGTTTAGTAGGACGGGTGGG 58.435 55.000 0.00 0.00 0.00 4.61
3534 3713 1.374947 CTCCTTCCTTTGGTCGGCA 59.625 57.895 0.00 0.00 0.00 5.69
3549 3728 3.476552 GTCGGCATGGGAATCAAAGATA 58.523 45.455 0.00 0.00 0.00 1.98
3550 3729 3.499918 GTCGGCATGGGAATCAAAGATAG 59.500 47.826 0.00 0.00 0.00 2.08
3551 3730 3.136443 TCGGCATGGGAATCAAAGATAGT 59.864 43.478 0.00 0.00 0.00 2.12
3552 3731 4.346709 TCGGCATGGGAATCAAAGATAGTA 59.653 41.667 0.00 0.00 0.00 1.82
3553 3732 4.452455 CGGCATGGGAATCAAAGATAGTAC 59.548 45.833 0.00 0.00 0.00 2.73
3554 3733 5.625150 GGCATGGGAATCAAAGATAGTACT 58.375 41.667 0.00 0.00 0.00 2.73
3555 3734 5.703130 GGCATGGGAATCAAAGATAGTACTC 59.297 44.000 0.00 0.00 0.00 2.59
3556 3735 5.703130 GCATGGGAATCAAAGATAGTACTCC 59.297 44.000 0.00 0.00 0.00 3.85
3557 3736 5.888982 TGGGAATCAAAGATAGTACTCCC 57.111 43.478 0.00 0.02 41.49 4.30
3558 3737 5.538877 TGGGAATCAAAGATAGTACTCCCT 58.461 41.667 0.00 0.00 41.64 4.20
3559 3738 5.602978 TGGGAATCAAAGATAGTACTCCCTC 59.397 44.000 0.00 0.00 41.64 4.30
3560 3739 5.012251 GGGAATCAAAGATAGTACTCCCTCC 59.988 48.000 0.00 0.00 38.61 4.30
3561 3740 5.279056 GGAATCAAAGATAGTACTCCCTCCG 60.279 48.000 0.00 0.00 0.00 4.63
3562 3741 4.246712 TCAAAGATAGTACTCCCTCCGT 57.753 45.455 0.00 0.00 0.00 4.69
3563 3742 4.607239 TCAAAGATAGTACTCCCTCCGTT 58.393 43.478 0.00 0.00 0.00 4.44
3564 3743 4.643784 TCAAAGATAGTACTCCCTCCGTTC 59.356 45.833 0.00 0.00 0.00 3.95
3565 3744 3.226682 AGATAGTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
3566 3745 1.878734 GATAGTACTCCCTCCGTTCCG 59.121 57.143 0.00 0.00 0.00 4.30
3567 3746 0.911769 TAGTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3568 3747 0.038744 AGTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3569 3748 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
3570 3749 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
3571 3750 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3572 3751 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3573 3752 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3574 3753 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
3575 3754 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3576 3755 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3577 3756 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3578 3757 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
3579 3758 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
3580 3759 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
3581 3760 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
3582 3761 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
3583 3762 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
3584 3763 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
3585 3764 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
3586 3765 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
3587 3766 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
3588 3767 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
3589 3768 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
3590 3769 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
3591 3770 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
3592 3771 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
3593 3772 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
3595 3774 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
3596 3775 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
3597 3776 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
3598 3777 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
3599 3778 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
3600 3779 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
3601 3780 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
3602 3781 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
3603 3782 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
3619 3798 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
3620 3799 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
3621 3800 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
3622 3801 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
3625 3804 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
3629 3808 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
3630 3809 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
3631 3810 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
3632 3811 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
3633 3812 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
3634 3813 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
3635 3814 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
3636 3815 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
3648 3827 7.690952 GATACCTCCGTATCTAGACAAATCT 57.309 40.000 0.00 0.00 45.11 2.40
3649 3828 8.789825 GATACCTCCGTATCTAGACAAATCTA 57.210 38.462 0.00 0.00 45.11 1.98
3650 3829 9.228949 GATACCTCCGTATCTAGACAAATCTAA 57.771 37.037 0.00 0.00 45.11 2.10
3651 3830 7.513371 ACCTCCGTATCTAGACAAATCTAAG 57.487 40.000 0.00 0.00 36.98 2.18
3652 3831 7.288560 ACCTCCGTATCTAGACAAATCTAAGA 58.711 38.462 0.00 0.00 36.98 2.10
3653 3832 7.229106 ACCTCCGTATCTAGACAAATCTAAGAC 59.771 40.741 0.00 0.00 36.98 3.01
3654 3833 7.228906 CCTCCGTATCTAGACAAATCTAAGACA 59.771 40.741 0.00 0.00 36.98 3.41
3655 3834 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3656 3835 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3657 3836 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
3668 3847 9.746711 CAAATCTAAGACAAGTAATTCAGAACG 57.253 33.333 0.00 0.00 0.00 3.95
3669 3848 8.480643 AATCTAAGACAAGTAATTCAGAACGG 57.519 34.615 0.00 0.00 0.00 4.44
3670 3849 7.223260 TCTAAGACAAGTAATTCAGAACGGA 57.777 36.000 0.00 0.00 0.00 4.69
3671 3850 7.313646 TCTAAGACAAGTAATTCAGAACGGAG 58.686 38.462 0.00 0.00 0.00 4.63
3672 3851 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
3673 3852 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
4137 4577 9.062524 TGGCTAAATGCATTCGTATTACTTAAT 57.937 29.630 13.38 0.00 45.15 1.40
4390 4830 0.902984 TCAGAACGCAAGCCCCTCTA 60.903 55.000 0.00 0.00 45.62 2.43
4545 4985 3.629398 CCAGTCCAATTTCTGGTGCTATC 59.371 47.826 11.00 0.00 46.51 2.08
4712 5155 5.371526 TGATTATCCTTCAGATGCCACTTC 58.628 41.667 0.00 0.00 36.33 3.01
4713 5156 5.131642 TGATTATCCTTCAGATGCCACTTCT 59.868 40.000 0.00 0.00 36.33 2.85
4714 5157 5.441718 TTATCCTTCAGATGCCACTTCTT 57.558 39.130 0.00 0.00 36.33 2.52
5368 5811 7.200434 AGTACATCCATCAGGTTGATAAAGT 57.800 36.000 0.00 0.00 34.28 2.66
5416 5859 6.885918 TGATGATGGTGTGTTGATGTTATTCT 59.114 34.615 0.00 0.00 0.00 2.40
5608 6051 7.770897 AGTCCCAAATAGTTCTGATGATAACAC 59.229 37.037 0.00 0.00 0.00 3.32
5765 6208 4.331168 AGCAAAGACGATTGTGAAGATAGC 59.669 41.667 0.00 0.00 32.80 2.97
5793 6236 2.695666 CTCCCGGACTTATGTCAGTGAT 59.304 50.000 0.73 0.00 44.61 3.06
5800 6243 6.071672 CCGGACTTATGTCAGTGATGATATCT 60.072 42.308 10.60 0.00 44.61 1.98
5871 6315 6.049790 AGTTGTTTGAACTTCTGAGGTAGTC 58.950 40.000 0.00 0.00 0.00 2.59
6040 6503 4.757657 TGTATGTTGCTGGTGTCGTTTTAT 59.242 37.500 0.00 0.00 0.00 1.40
6089 6552 5.046159 TCGTTTGGAAGTAATGGTCATAGGT 60.046 40.000 0.00 0.00 0.00 3.08
6131 6594 0.178906 TCACTGGTGATGGTCCTGGA 60.179 55.000 0.00 0.00 34.14 3.86
6168 6631 0.600255 CGCTGAAGTCTTTCCCGTGT 60.600 55.000 0.00 0.00 32.09 4.49
6296 6759 4.837093 TGAAAGGGAGGTCGAATTATGT 57.163 40.909 0.00 0.00 0.00 2.29
6311 6774 0.756294 TATGTCCCTGCGTGTATGGG 59.244 55.000 0.00 0.00 42.20 4.00
6445 6908 0.745845 GTCCATACTGGTGGCAGCTG 60.746 60.000 20.01 20.01 39.03 4.24
6502 6965 0.322187 AACTGGACCAATACCACCGC 60.322 55.000 0.00 0.00 33.57 5.68
6529 6992 1.977188 TGTTGTGCTGTCGATACTCG 58.023 50.000 0.00 0.00 42.10 4.18
6553 7016 5.335661 GCCAAGTCAAACAAGGAACGATTAT 60.336 40.000 0.00 0.00 0.00 1.28
6666 7142 4.315803 CTTTTCTAGGCCGAAAGAGTTCA 58.684 43.478 14.73 0.00 34.67 3.18
6699 7177 4.021192 GTGAGGATTTTTGGCTCAATGGAA 60.021 41.667 0.00 0.00 0.00 3.53
6703 7181 4.263025 GGATTTTTGGCTCAATGGAACCTT 60.263 41.667 0.00 0.00 30.27 3.50
6753 7232 8.293699 ACCTTGTAAGTTTCAAAAGATTCTGT 57.706 30.769 0.00 0.00 0.00 3.41
6754 7233 8.190784 ACCTTGTAAGTTTCAAAAGATTCTGTG 58.809 33.333 0.00 0.00 0.00 3.66
6755 7234 8.190784 CCTTGTAAGTTTCAAAAGATTCTGTGT 58.809 33.333 0.00 0.00 0.00 3.72
6757 7236 9.997482 TTGTAAGTTTCAAAAGATTCTGTGTAC 57.003 29.630 0.00 0.00 0.00 2.90
6758 7237 9.168451 TGTAAGTTTCAAAAGATTCTGTGTACA 57.832 29.630 0.00 0.00 0.00 2.90
6761 7240 8.225603 AGTTTCAAAAGATTCTGTGTACATGT 57.774 30.769 2.69 2.69 0.00 3.21
6762 7241 9.337396 AGTTTCAAAAGATTCTGTGTACATGTA 57.663 29.630 0.08 0.08 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 8.299570 GCCCGATTTATTTGACAATAGAATGAT 58.700 33.333 0.00 0.00 0.00 2.45
20 21 7.519809 CGCCCGATTTATTTGACAATAGAATGA 60.520 37.037 0.00 0.00 0.00 2.57
21 22 6.578545 CGCCCGATTTATTTGACAATAGAATG 59.421 38.462 0.00 0.00 0.00 2.67
22 23 6.293955 CCGCCCGATTTATTTGACAATAGAAT 60.294 38.462 0.00 0.00 0.00 2.40
23 24 5.008217 CCGCCCGATTTATTTGACAATAGAA 59.992 40.000 0.00 0.00 0.00 2.10
24 25 4.513692 CCGCCCGATTTATTTGACAATAGA 59.486 41.667 0.00 0.00 0.00 1.98
25 26 4.783242 CCGCCCGATTTATTTGACAATAG 58.217 43.478 0.00 0.00 0.00 1.73
26 27 3.003897 GCCGCCCGATTTATTTGACAATA 59.996 43.478 0.00 0.00 0.00 1.90
27 28 2.223711 GCCGCCCGATTTATTTGACAAT 60.224 45.455 0.00 0.00 0.00 2.71
28 29 1.133407 GCCGCCCGATTTATTTGACAA 59.867 47.619 0.00 0.00 0.00 3.18
29 30 0.736053 GCCGCCCGATTTATTTGACA 59.264 50.000 0.00 0.00 0.00 3.58
30 31 0.736053 TGCCGCCCGATTTATTTGAC 59.264 50.000 0.00 0.00 0.00 3.18
31 32 1.464734 TTGCCGCCCGATTTATTTGA 58.535 45.000 0.00 0.00 0.00 2.69
32 33 1.923864 GTTTGCCGCCCGATTTATTTG 59.076 47.619 0.00 0.00 0.00 2.32
33 34 1.468395 CGTTTGCCGCCCGATTTATTT 60.468 47.619 0.00 0.00 0.00 1.40
34 35 0.099791 CGTTTGCCGCCCGATTTATT 59.900 50.000 0.00 0.00 0.00 1.40
35 36 1.725066 CGTTTGCCGCCCGATTTAT 59.275 52.632 0.00 0.00 0.00 1.40
36 37 3.179481 CGTTTGCCGCCCGATTTA 58.821 55.556 0.00 0.00 0.00 1.40
45 46 2.580326 GATGCCATGCGTTTGCCG 60.580 61.111 0.00 0.00 41.78 5.69
46 47 1.079956 TTGATGCCATGCGTTTGCC 60.080 52.632 0.00 0.00 41.78 4.52
47 48 1.676438 CGTTGATGCCATGCGTTTGC 61.676 55.000 0.00 0.00 43.20 3.68
48 49 0.109827 TCGTTGATGCCATGCGTTTG 60.110 50.000 0.00 0.00 0.00 2.93
49 50 0.810648 ATCGTTGATGCCATGCGTTT 59.189 45.000 0.00 0.00 0.00 3.60
50 51 0.378257 GATCGTTGATGCCATGCGTT 59.622 50.000 0.00 0.00 0.00 4.84
51 52 1.439353 GGATCGTTGATGCCATGCGT 61.439 55.000 0.00 0.00 0.00 5.24
52 53 1.280746 GGATCGTTGATGCCATGCG 59.719 57.895 0.00 0.00 0.00 4.73
53 54 0.309922 CTGGATCGTTGATGCCATGC 59.690 55.000 0.00 0.00 29.18 4.06
54 55 1.957668 TCTGGATCGTTGATGCCATG 58.042 50.000 0.00 0.00 29.18 3.66
55 56 2.501261 CATCTGGATCGTTGATGCCAT 58.499 47.619 7.82 0.00 32.53 4.40
56 57 1.957668 CATCTGGATCGTTGATGCCA 58.042 50.000 7.82 0.00 32.53 4.92
59 60 4.313282 AGTATGCATCTGGATCGTTGATG 58.687 43.478 0.19 13.46 40.16 3.07
60 61 4.562347 GGAGTATGCATCTGGATCGTTGAT 60.562 45.833 0.19 0.00 0.00 2.57
61 62 3.243873 GGAGTATGCATCTGGATCGTTGA 60.244 47.826 0.19 0.00 0.00 3.18
62 63 3.062763 GGAGTATGCATCTGGATCGTTG 58.937 50.000 0.19 0.00 0.00 4.10
63 64 2.037772 GGGAGTATGCATCTGGATCGTT 59.962 50.000 0.19 0.00 0.00 3.85
64 65 1.620819 GGGAGTATGCATCTGGATCGT 59.379 52.381 0.19 0.00 0.00 3.73
65 66 1.066573 GGGGAGTATGCATCTGGATCG 60.067 57.143 0.19 0.00 0.00 3.69
66 67 1.280421 GGGGGAGTATGCATCTGGATC 59.720 57.143 0.19 0.00 0.00 3.36
67 68 1.366319 GGGGGAGTATGCATCTGGAT 58.634 55.000 0.19 0.00 0.00 3.41
68 69 2.854253 GGGGGAGTATGCATCTGGA 58.146 57.895 0.19 0.00 0.00 3.86
83 84 1.603455 GTGTGTCATGTGGTGGGGG 60.603 63.158 0.00 0.00 0.00 5.40
84 85 1.965930 CGTGTGTCATGTGGTGGGG 60.966 63.158 0.00 0.00 0.00 4.96
85 86 0.034198 TACGTGTGTCATGTGGTGGG 59.966 55.000 0.00 0.00 35.12 4.61
86 87 1.270094 ACTACGTGTGTCATGTGGTGG 60.270 52.381 9.58 0.00 42.03 4.61
87 88 2.148916 ACTACGTGTGTCATGTGGTG 57.851 50.000 9.58 1.89 42.03 4.17
88 89 3.859627 GCTTACTACGTGTGTCATGTGGT 60.860 47.826 13.65 13.65 44.78 4.16
89 90 2.666508 GCTTACTACGTGTGTCATGTGG 59.333 50.000 0.00 4.72 37.75 4.17
90 91 3.313690 TGCTTACTACGTGTGTCATGTG 58.686 45.455 0.00 0.00 35.12 3.21
91 92 3.653539 TGCTTACTACGTGTGTCATGT 57.346 42.857 0.00 0.45 37.38 3.21
92 93 5.120053 TGAATTGCTTACTACGTGTGTCATG 59.880 40.000 0.00 0.00 0.00 3.07
93 94 5.234752 TGAATTGCTTACTACGTGTGTCAT 58.765 37.500 0.00 0.00 0.00 3.06
94 95 4.623002 TGAATTGCTTACTACGTGTGTCA 58.377 39.130 0.00 0.00 0.00 3.58
95 96 5.585500 TTGAATTGCTTACTACGTGTGTC 57.415 39.130 0.00 0.00 0.00 3.67
96 97 5.699001 TGATTGAATTGCTTACTACGTGTGT 59.301 36.000 0.00 0.00 0.00 3.72
97 98 6.164408 TGATTGAATTGCTTACTACGTGTG 57.836 37.500 0.00 0.00 0.00 3.82
98 99 6.795098 TTGATTGAATTGCTTACTACGTGT 57.205 33.333 0.00 0.00 0.00 4.49
99 100 7.298122 AGTTTGATTGAATTGCTTACTACGTG 58.702 34.615 0.00 0.00 0.00 4.49
100 101 7.435068 AGTTTGATTGAATTGCTTACTACGT 57.565 32.000 0.00 0.00 0.00 3.57
101 102 9.988350 AATAGTTTGATTGAATTGCTTACTACG 57.012 29.630 0.00 0.00 0.00 3.51
125 126 9.399797 TCTGTCATGAGTATGCATCTTTTTAAT 57.600 29.630 0.19 0.00 34.21 1.40
126 127 8.668353 GTCTGTCATGAGTATGCATCTTTTTAA 58.332 33.333 0.19 0.00 34.21 1.52
127 128 7.280876 GGTCTGTCATGAGTATGCATCTTTTTA 59.719 37.037 0.19 0.00 34.21 1.52
261 282 4.446413 CGCCGGCTACGTTTCCCT 62.446 66.667 26.68 0.00 38.78 4.20
316 340 0.957362 GGAGTAGTAACGGGGATCGG 59.043 60.000 0.00 0.00 44.45 4.18
428 521 1.549203 AATCAAATCGGTTGCTGCCT 58.451 45.000 0.00 0.00 37.13 4.75
430 523 3.740321 TGAAAAATCAAATCGGTTGCTGC 59.260 39.130 0.00 0.00 37.13 5.25
431 524 5.903764 TTGAAAAATCAAATCGGTTGCTG 57.096 34.783 0.00 0.00 37.13 4.41
432 525 7.378181 AGTATTGAAAAATCAAATCGGTTGCT 58.622 30.769 0.00 0.00 37.13 3.91
433 526 7.201435 GGAGTATTGAAAAATCAAATCGGTTGC 60.201 37.037 0.00 0.00 37.13 4.17
434 527 8.028938 AGGAGTATTGAAAAATCAAATCGGTTG 58.971 33.333 0.00 0.00 38.71 3.77
435 528 8.122472 AGGAGTATTGAAAAATCAAATCGGTT 57.878 30.769 0.00 0.00 32.94 4.44
436 529 7.148069 GGAGGAGTATTGAAAAATCAAATCGGT 60.148 37.037 0.00 0.00 32.94 4.69
437 530 7.148086 TGGAGGAGTATTGAAAAATCAAATCGG 60.148 37.037 0.00 0.00 32.94 4.18
438 531 7.761409 TGGAGGAGTATTGAAAAATCAAATCG 58.239 34.615 0.00 0.00 32.94 3.34
441 534 8.531146 GGATTGGAGGAGTATTGAAAAATCAAA 58.469 33.333 0.00 0.00 32.94 2.69
442 535 7.673504 TGGATTGGAGGAGTATTGAAAAATCAA 59.326 33.333 0.00 0.00 0.00 2.57
443 536 7.181361 TGGATTGGAGGAGTATTGAAAAATCA 58.819 34.615 0.00 0.00 0.00 2.57
538 631 2.902846 TTTGGCCGTGTGGGAACG 60.903 61.111 0.00 0.00 43.20 3.95
539 632 2.561037 CCTTTGGCCGTGTGGGAAC 61.561 63.158 0.00 0.00 38.47 3.62
563 656 1.613925 GGTTTGAGCCCTGTTCTTTCC 59.386 52.381 0.00 0.00 0.00 3.13
582 675 2.978018 GAAAGCGAGGGTTTGCGGG 61.978 63.158 0.00 0.00 38.83 6.13
748 851 1.205460 AGCCCACCAACCGTATCCTT 61.205 55.000 0.00 0.00 0.00 3.36
795 898 1.073199 CCCGGGCTGTTTCTCTTGT 59.927 57.895 8.08 0.00 0.00 3.16
859 965 4.029186 CGCGCTTGCTTGGCTTGA 62.029 61.111 5.56 0.00 36.08 3.02
862 968 4.030452 GAACGCGCTTGCTTGGCT 62.030 61.111 5.73 0.00 36.08 4.75
903 1014 3.062466 GAAACGGAGCCTTGGCCC 61.062 66.667 8.17 8.36 0.00 5.80
981 1095 1.751927 CAAGCCAAGCCTAGCCCAG 60.752 63.158 0.00 0.00 0.00 4.45
988 1102 2.753043 CCGCATCAAGCCAAGCCT 60.753 61.111 0.00 0.00 41.38 4.58
1220 1346 3.234386 GACCAGCGGAAAATTTCGAAAG 58.766 45.455 16.80 2.53 0.00 2.62
1224 1350 0.793104 GCGACCAGCGGAAAATTTCG 60.793 55.000 0.00 0.00 41.29 3.46
1331 1457 0.609681 TGGGTTTGCATCGGTTACCC 60.610 55.000 0.00 0.00 46.98 3.69
1359 1486 2.025321 AGTTCCTTCCGGCCACAATTAT 60.025 45.455 2.24 0.00 0.00 1.28
1431 1558 6.563398 TGCGTCGACACTAACAATAAATAG 57.437 37.500 17.16 0.00 0.00 1.73
1465 1592 2.843730 TCAGCAGTTGGGTATATGGTGT 59.156 45.455 3.52 0.00 40.91 4.16
1688 1835 8.737175 GGAATGATGTAGAATATGCATTGTCAT 58.263 33.333 3.54 2.07 33.94 3.06
1706 1853 4.695455 ACTTTACACGGACAAGGAATGATG 59.305 41.667 0.00 0.00 0.00 3.07
1719 1866 3.982701 TGTATCACGACAACTTTACACGG 59.017 43.478 0.00 0.00 0.00 4.94
1733 1880 6.018832 TCAGTGTGCATAATGAATGTATCACG 60.019 38.462 11.32 0.00 41.93 4.35
1734 1881 7.250445 TCAGTGTGCATAATGAATGTATCAC 57.750 36.000 11.32 0.00 41.93 3.06
1755 1902 6.434652 ACTCCCATATCCGTTAGTAGATTCAG 59.565 42.308 0.00 0.00 0.00 3.02
1768 1915 2.168521 ACAACTCACACTCCCATATCCG 59.831 50.000 0.00 0.00 0.00 4.18
1831 1978 6.490721 TCCGATTTAGCCCTTTTTACAAGAAA 59.509 34.615 0.00 0.00 0.00 2.52
1832 1979 6.005198 TCCGATTTAGCCCTTTTTACAAGAA 58.995 36.000 0.00 0.00 0.00 2.52
1833 1980 5.562635 TCCGATTTAGCCCTTTTTACAAGA 58.437 37.500 0.00 0.00 0.00 3.02
1849 1996 4.942852 TGACACAGCAAAATTTCCGATTT 58.057 34.783 0.00 0.00 0.00 2.17
1968 2115 9.586435 CTGACTATAACACAATGATACTTGTCA 57.414 33.333 0.00 0.00 37.25 3.58
1998 2145 5.683859 GCATGGAAATGCTAATCGTCTAAG 58.316 41.667 3.47 0.00 43.79 2.18
2245 2392 9.978044 CTTGATTCTATCTGTCTTACATCATCA 57.022 33.333 0.00 0.00 0.00 3.07
2281 2428 3.908382 GCAGTTGTATGAAAGAAACAGCG 59.092 43.478 0.00 0.00 30.66 5.18
2877 3024 0.110295 AGTATGCAACCACACTGCCA 59.890 50.000 0.00 0.00 39.13 4.92
2984 3131 5.280654 ACCATTACCATTTGGAATCATGC 57.719 39.130 3.01 0.00 38.94 4.06
3105 3252 3.470709 AGTCCATGAAGAACATATGCGG 58.529 45.455 1.58 0.00 37.46 5.69
3107 3254 5.609423 AGAGAGTCCATGAAGAACATATGC 58.391 41.667 1.58 0.00 37.46 3.14
3123 3270 4.143986 CCACCTTTGGGATAAGAGAGTC 57.856 50.000 0.00 0.00 39.57 3.36
3152 3299 6.218315 AGAGTATCCCATATGCCATAACCAAT 59.782 38.462 0.00 0.00 33.66 3.16
3154 3301 5.100811 AGAGTATCCCATATGCCATAACCA 58.899 41.667 0.00 0.00 33.66 3.67
3213 3360 4.032104 CCCTAACGGTCTTAAAATTCGTCG 59.968 45.833 0.00 0.00 33.34 5.12
3250 3397 1.841277 AGGTTGTTACCCACAGTCACA 59.159 47.619 0.00 0.00 46.28 3.58
3384 3559 8.379902 ACAAAGCAAACTAACAAAATCTTTTCG 58.620 29.630 0.00 0.00 0.00 3.46
3400 3575 8.801715 TTCATTATCTTCTGAACAAAGCAAAC 57.198 30.769 0.00 0.00 0.00 2.93
3402 3577 9.467258 CTTTTCATTATCTTCTGAACAAAGCAA 57.533 29.630 0.00 0.00 31.41 3.91
3420 3595 7.203218 GCTACAAGGAAACAGAACTTTTCATT 58.797 34.615 0.00 0.00 37.43 2.57
3505 3684 4.950475 CCAAAGGAAGGAGGGATTTACTTC 59.050 45.833 0.00 0.00 38.80 3.01
3521 3700 1.784301 TTCCCATGCCGACCAAAGGA 61.784 55.000 0.00 0.00 0.00 3.36
3534 3713 6.153924 AGGGAGTACTATCTTTGATTCCCAT 58.846 40.000 13.55 0.00 44.37 4.00
3561 3740 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
3562 3741 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
3563 3742 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
3564 3743 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
3565 3744 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
3566 3745 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
3567 3746 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
3569 3748 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
3570 3749 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
3571 3750 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
3572 3751 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
3573 3752 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
3574 3753 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
3575 3754 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
3576 3755 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
3577 3756 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
3578 3757 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
3579 3758 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
3593 3772 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
3594 3773 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
3595 3774 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
3596 3775 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
3599 3778 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
3603 3782 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
3604 3783 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
3605 3784 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
3606 3785 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
3607 3786 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
3608 3787 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
3609 3788 6.153067 CGGAGGTATCTAGCACTAAAATGAG 58.847 44.000 0.00 0.00 0.00 2.90
3610 3789 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
3611 3790 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
3612 3791 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
3625 3804 9.233649 CTTAGATTTGTCTAGATACGGAGGTAT 57.766 37.037 0.00 0.00 42.01 2.73
3626 3805 8.435187 TCTTAGATTTGTCTAGATACGGAGGTA 58.565 37.037 0.00 0.00 0.00 3.08
3627 3806 7.229106 GTCTTAGATTTGTCTAGATACGGAGGT 59.771 40.741 0.00 0.00 0.00 3.85
3628 3807 7.228906 TGTCTTAGATTTGTCTAGATACGGAGG 59.771 40.741 0.00 0.00 0.00 4.30
3629 3808 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
3630 3809 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3631 3810 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
3642 3821 9.746711 CGTTCTGAATTACTTGTCTTAGATTTG 57.253 33.333 0.00 0.00 0.00 2.32
3643 3822 8.936864 CCGTTCTGAATTACTTGTCTTAGATTT 58.063 33.333 0.00 0.00 0.00 2.17
3644 3823 8.311836 TCCGTTCTGAATTACTTGTCTTAGATT 58.688 33.333 0.00 0.00 0.00 2.40
3645 3824 7.837863 TCCGTTCTGAATTACTTGTCTTAGAT 58.162 34.615 0.00 0.00 0.00 1.98
3646 3825 7.223260 TCCGTTCTGAATTACTTGTCTTAGA 57.777 36.000 0.00 0.00 0.00 2.10
3647 3826 6.531948 CCTCCGTTCTGAATTACTTGTCTTAG 59.468 42.308 0.00 0.00 0.00 2.18
3648 3827 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.00 0.00 2.10
3649 3828 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
3650 3829 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
3651 3830 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3652 3831 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3653 3832 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3654 3833 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
3655 3834 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
3656 3835 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
3657 3836 4.863548 TCTACTCCCTCCGTTCTGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
3658 3837 3.709587 TCTACTCCCTCCGTTCTGAATT 58.290 45.455 0.00 0.00 0.00 2.17
3659 3838 3.383698 TCTACTCCCTCCGTTCTGAAT 57.616 47.619 0.00 0.00 0.00 2.57
3660 3839 2.893215 TCTACTCCCTCCGTTCTGAA 57.107 50.000 0.00 0.00 0.00 3.02
3661 3840 2.656002 CATCTACTCCCTCCGTTCTGA 58.344 52.381 0.00 0.00 0.00 3.27
3662 3841 1.683917 CCATCTACTCCCTCCGTTCTG 59.316 57.143 0.00 0.00 0.00 3.02
3663 3842 1.569548 TCCATCTACTCCCTCCGTTCT 59.430 52.381 0.00 0.00 0.00 3.01
3664 3843 2.068834 TCCATCTACTCCCTCCGTTC 57.931 55.000 0.00 0.00 0.00 3.95
3665 3844 2.320781 CATCCATCTACTCCCTCCGTT 58.679 52.381 0.00 0.00 0.00 4.44
3666 3845 1.481428 CCATCCATCTACTCCCTCCGT 60.481 57.143 0.00 0.00 0.00 4.69
3667 3846 1.261480 CCATCCATCTACTCCCTCCG 58.739 60.000 0.00 0.00 0.00 4.63
3668 3847 1.650528 CCCATCCATCTACTCCCTCC 58.349 60.000 0.00 0.00 0.00 4.30
3669 3848 0.980423 GCCCATCCATCTACTCCCTC 59.020 60.000 0.00 0.00 0.00 4.30
3670 3849 0.833834 CGCCCATCCATCTACTCCCT 60.834 60.000 0.00 0.00 0.00 4.20
3671 3850 1.122019 ACGCCCATCCATCTACTCCC 61.122 60.000 0.00 0.00 0.00 4.30
3672 3851 0.759346 AACGCCCATCCATCTACTCC 59.241 55.000 0.00 0.00 0.00 3.85
3673 3852 1.541233 CCAACGCCCATCCATCTACTC 60.541 57.143 0.00 0.00 0.00 2.59
3745 3924 7.857734 TTGTAGAAAGACACATGTTTGAAGA 57.142 32.000 0.00 0.00 0.00 2.87
3784 4224 9.102757 CATGAAGTACATAAGACAAACATAGCT 57.897 33.333 0.00 0.00 37.46 3.32
4374 4814 0.178068 TCATAGAGGGGCTTGCGTTC 59.822 55.000 0.00 0.00 0.00 3.95
4390 4830 3.710677 AGCATCTTCTGACTAAGGCTCAT 59.289 43.478 0.00 0.00 0.00 2.90
4545 4985 2.468777 GCAGTTGTGAAATGTTGAAGCG 59.531 45.455 0.00 0.00 0.00 4.68
4712 5155 7.821359 TGTCAGTTTCTCTTTGAGATCCATAAG 59.179 37.037 0.00 0.00 38.56 1.73
4713 5156 7.604164 GTGTCAGTTTCTCTTTGAGATCCATAA 59.396 37.037 0.00 0.00 38.56 1.90
4714 5157 7.099764 GTGTCAGTTTCTCTTTGAGATCCATA 58.900 38.462 0.00 0.00 38.56 2.74
4866 5309 7.506261 GGATAGATACTAGTTCCTTTCCTGACA 59.494 40.741 18.05 0.00 0.00 3.58
5385 5828 8.158169 ACATCAACACACCATCATCATTATAC 57.842 34.615 0.00 0.00 0.00 1.47
5608 6051 8.682936 ATCTTCTACTAAATATTGGCCAACAG 57.317 34.615 23.27 14.83 0.00 3.16
5765 6208 1.267261 CATAAGTCCGGGAGTAGCTCG 59.733 57.143 4.46 0.00 41.20 5.03
5793 6236 6.070481 TGTTGTGGTGCTTACCTTAGATATCA 60.070 38.462 5.32 0.00 0.00 2.15
5800 6243 3.849563 AGTGTTGTGGTGCTTACCTTA 57.150 42.857 0.00 0.00 0.00 2.69
5822 6265 9.224267 CTTAATATGTATGCCTGTGCTTAGAAT 57.776 33.333 0.00 0.00 38.71 2.40
5871 6315 3.842732 TCTTCAGATGCAATGCAACAG 57.157 42.857 13.45 6.80 43.62 3.16
6029 6492 6.399564 GCAATTTTAGCACCATAAAACGACAC 60.400 38.462 0.00 0.00 37.43 3.67
6040 6503 3.386078 TGGTTCAAGCAATTTTAGCACCA 59.614 39.130 0.00 0.00 33.55 4.17
6311 6774 3.265791 CAACTTCACATCACTAGGGCTC 58.734 50.000 0.00 0.00 0.00 4.70
6445 6908 5.108517 CAGAACTGACAGGAAATCTCTAGC 58.891 45.833 7.51 0.00 0.00 3.42
6502 6965 8.131455 AGTATCGACAGCACAACATAATTAAG 57.869 34.615 0.00 0.00 0.00 1.85
6529 6992 1.673920 TCGTTCCTTGTTTGACTTGGC 59.326 47.619 0.00 0.00 0.00 4.52
6553 7016 4.056050 GCAACTTAGACTTCGTCAGGAAA 58.944 43.478 0.00 0.00 34.60 3.13
6650 7126 4.253685 CAAGAATGAACTCTTTCGGCCTA 58.746 43.478 0.00 0.00 33.25 3.93
6666 7142 4.774200 CCAAAAATCCTCACTCCCAAGAAT 59.226 41.667 0.00 0.00 0.00 2.40
6723 7201 9.811995 AATCTTTTGAAACTTACAAGGTTAACC 57.188 29.630 17.41 17.41 35.74 2.85


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

AutoCloner maintained by Alex Coulton.