Multiple sequence alignment - TraesCS5B01G467000

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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 TraesCS5B01G467000 chr5B 100.000 3722 0 0 1 3722 641100834 641097113 0.000000e+00 6874.0
1 TraesCS5B01G467000 chr5B 95.455 44 2 0 3004 3047 641097785 641097742 1.850000e-08 71.3
2 TraesCS5B01G467000 chr5B 95.455 44 2 0 3050 3093 641097831 641097788 1.850000e-08 71.3
3 TraesCS5B01G467000 chr5D 92.326 2958 99 46 146 3052 510097784 510094904 0.000000e+00 4087.0
4 TraesCS5B01G467000 chr5D 89.851 335 15 4 3090 3423 510094602 510094286 2.670000e-111 412.0
5 TraesCS5B01G467000 chr5D 93.333 270 14 4 3456 3722 510094285 510094017 2.690000e-106 396.0
6 TraesCS5B01G467000 chr5D 95.745 47 2 0 3418 3464 480025183 480025229 3.990000e-10 76.8
7 TraesCS5B01G467000 chr5D 95.833 48 1 1 3418 3464 547276007 547276054 3.990000e-10 76.8
8 TraesCS5B01G467000 chr5D 94.118 51 0 2 3418 3467 450663334 450663286 1.430000e-09 75.0
9 TraesCS5B01G467000 chr5D 100.000 31 0 0 2504 2534 562835705 562835675 1.440000e-04 58.4
10 TraesCS5B01G467000 chr5D 100.000 31 0 0 2504 2534 562947281 562947251 1.440000e-04 58.4
11 TraesCS5B01G467000 chr5D 100.000 31 0 0 2504 2534 563001231 563001261 1.440000e-04 58.4
12 TraesCS5B01G467000 chr5A 94.498 2072 81 20 992 3052 638133908 638131859 0.000000e+00 3164.0
13 TraesCS5B01G467000 chr5A 88.323 805 45 21 193 988 638134746 638133982 0.000000e+00 920.0
14 TraesCS5B01G467000 chr5A 91.139 158 13 1 3565 3722 638131035 638130879 2.910000e-51 213.0
15 TraesCS5B01G467000 chr5A 83.824 204 10 10 3090 3291 638131560 638131378 4.940000e-39 172.0
16 TraesCS5B01G467000 chr5A 100.000 33 0 0 3054 3086 638131903 638131871 1.120000e-05 62.1
17 TraesCS5B01G467000 chr2B 95.833 48 2 0 3417 3464 40858780 40858827 1.110000e-10 78.7
18 TraesCS5B01G467000 chr4B 92.453 53 4 0 3412 3464 66801330 66801382 3.990000e-10 76.8
19 TraesCS5B01G467000 chr3B 95.745 47 2 0 3418 3464 829248449 829248495 3.990000e-10 76.8
20 TraesCS5B01G467000 chr4D 91.071 56 3 2 3414 3467 134127018 134127073 1.430000e-09 75.0
21 TraesCS5B01G467000 chr4D 89.831 59 2 2 3418 3473 121077002 121076945 5.160000e-09 73.1
22 TraesCS5B01G467000 chr7B 88.060 67 1 4 3418 3477 648760054 648759988 5.160000e-09 73.1


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 TraesCS5B01G467000 chr5B 641097113 641100834 3721 True 2338.866667 6874 96.970000 1 3722 3 chr5B.!!$R1 3721
1 TraesCS5B01G467000 chr5D 510094017 510097784 3767 True 1631.666667 4087 91.836667 146 3722 3 chr5D.!!$R4 3576
2 TraesCS5B01G467000 chr5A 638130879 638134746 3867 True 906.220000 3164 91.556800 193 3722 5 chr5A.!!$R1 3529

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
412 425 0.036732 GGATCCAACCACTGCACTCA 59.963 55.0 6.95 0.0 0.0 3.41 F
693 732 0.104120 CGGCGAGAGAGAGAGAGAGA 59.896 60.0 0.00 0.0 0.0 3.10 F
1749 1858 0.112606 TCGACCTCCTCCTTGTCAGT 59.887 55.0 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1855 0.600255 GGTCCTTGTGGTCGTCACTG 60.600 60.0 11.51 6.02 46.20 3.66 R
2512 2624 0.328592 TTGCCATTGCCATTGCCATT 59.671 45.0 0.00 0.00 36.33 3.16 R
3441 3964 0.033504 TCCCTCTGTCAACAACGCTC 59.966 55.0 0.00 0.00 0.00 5.03 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
22 23 5.947228 CAGAGCTTGTAGAAACATTTCCA 57.053 39.130 0.68 0.00 37.92 3.53
23 24 6.506500 CAGAGCTTGTAGAAACATTTCCAT 57.493 37.500 0.68 0.00 37.92 3.41
24 25 7.615582 CAGAGCTTGTAGAAACATTTCCATA 57.384 36.000 0.68 0.00 37.92 2.74
25 26 8.044060 CAGAGCTTGTAGAAACATTTCCATAA 57.956 34.615 0.68 0.00 37.92 1.90
26 27 8.514594 CAGAGCTTGTAGAAACATTTCCATAAA 58.485 33.333 0.68 0.00 37.92 1.40
27 28 9.077885 AGAGCTTGTAGAAACATTTCCATAAAA 57.922 29.630 0.68 0.00 37.92 1.52
28 29 9.691362 GAGCTTGTAGAAACATTTCCATAAAAA 57.309 29.630 0.68 0.00 37.92 1.94
29 30 9.696917 AGCTTGTAGAAACATTTCCATAAAAAG 57.303 29.630 0.68 0.00 37.92 2.27
30 31 9.476202 GCTTGTAGAAACATTTCCATAAAAAGT 57.524 29.630 0.68 0.00 37.92 2.66
66 67 8.205131 TCTAAATTAAATTCTTAGGGTGACGC 57.795 34.615 0.00 0.00 0.00 5.19
67 68 5.479716 AATTAAATTCTTAGGGTGACGCG 57.520 39.130 3.53 3.53 0.00 6.01
68 69 1.084289 AAATTCTTAGGGTGACGCGC 58.916 50.000 5.73 0.00 0.00 6.86
69 70 0.743345 AATTCTTAGGGTGACGCGCC 60.743 55.000 5.73 0.00 0.00 6.53
70 71 1.614241 ATTCTTAGGGTGACGCGCCT 61.614 55.000 5.73 7.21 33.98 5.52
71 72 2.501223 TTCTTAGGGTGACGCGCCTG 62.501 60.000 5.73 0.00 33.98 4.85
72 73 4.077184 TTAGGGTGACGCGCCTGG 62.077 66.667 5.73 0.00 33.98 4.45
84 85 4.096003 GCCTGGTTGCCGCCTCTA 62.096 66.667 0.00 0.00 0.00 2.43
85 86 2.668632 CCTGGTTGCCGCCTCTAA 59.331 61.111 0.00 0.00 0.00 2.10
86 87 1.450312 CCTGGTTGCCGCCTCTAAG 60.450 63.158 0.00 0.00 0.00 2.18
87 88 2.046314 TGGTTGCCGCCTCTAAGC 60.046 61.111 0.00 0.00 0.00 3.09
88 89 2.824489 GGTTGCCGCCTCTAAGCC 60.824 66.667 0.00 0.00 0.00 4.35
89 90 2.269241 GTTGCCGCCTCTAAGCCT 59.731 61.111 0.00 0.00 0.00 4.58
90 91 1.377333 GTTGCCGCCTCTAAGCCTT 60.377 57.895 0.00 0.00 0.00 4.35
91 92 1.078426 TTGCCGCCTCTAAGCCTTC 60.078 57.895 0.00 0.00 0.00 3.46
92 93 1.836999 TTGCCGCCTCTAAGCCTTCA 61.837 55.000 0.00 0.00 0.00 3.02
93 94 1.147153 GCCGCCTCTAAGCCTTCAT 59.853 57.895 0.00 0.00 0.00 2.57
94 95 0.882484 GCCGCCTCTAAGCCTTCATC 60.882 60.000 0.00 0.00 0.00 2.92
95 96 0.755686 CCGCCTCTAAGCCTTCATCT 59.244 55.000 0.00 0.00 0.00 2.90
96 97 1.270041 CCGCCTCTAAGCCTTCATCTC 60.270 57.143 0.00 0.00 0.00 2.75
97 98 1.410517 CGCCTCTAAGCCTTCATCTCA 59.589 52.381 0.00 0.00 0.00 3.27
98 99 2.545532 CGCCTCTAAGCCTTCATCTCAG 60.546 54.545 0.00 0.00 0.00 3.35
99 100 2.806382 GCCTCTAAGCCTTCATCTCAGC 60.806 54.545 0.00 0.00 0.00 4.26
100 101 2.433604 CCTCTAAGCCTTCATCTCAGCA 59.566 50.000 0.00 0.00 0.00 4.41
101 102 3.118482 CCTCTAAGCCTTCATCTCAGCAA 60.118 47.826 0.00 0.00 0.00 3.91
102 103 4.511527 CTCTAAGCCTTCATCTCAGCAAA 58.488 43.478 0.00 0.00 0.00 3.68
103 104 4.910195 TCTAAGCCTTCATCTCAGCAAAA 58.090 39.130 0.00 0.00 0.00 2.44
104 105 5.503927 TCTAAGCCTTCATCTCAGCAAAAT 58.496 37.500 0.00 0.00 0.00 1.82
105 106 4.715527 AAGCCTTCATCTCAGCAAAATC 57.284 40.909 0.00 0.00 0.00 2.17
106 107 3.693807 AGCCTTCATCTCAGCAAAATCA 58.306 40.909 0.00 0.00 0.00 2.57
107 108 4.084287 AGCCTTCATCTCAGCAAAATCAA 58.916 39.130 0.00 0.00 0.00 2.57
108 109 4.525487 AGCCTTCATCTCAGCAAAATCAAA 59.475 37.500 0.00 0.00 0.00 2.69
109 110 4.624452 GCCTTCATCTCAGCAAAATCAAAC 59.376 41.667 0.00 0.00 0.00 2.93
110 111 5.166398 CCTTCATCTCAGCAAAATCAAACC 58.834 41.667 0.00 0.00 0.00 3.27
111 112 5.047519 CCTTCATCTCAGCAAAATCAAACCT 60.048 40.000 0.00 0.00 0.00 3.50
112 113 5.381174 TCATCTCAGCAAAATCAAACCTG 57.619 39.130 0.00 0.00 0.00 4.00
113 114 4.828939 TCATCTCAGCAAAATCAAACCTGT 59.171 37.500 0.00 0.00 0.00 4.00
114 115 5.302568 TCATCTCAGCAAAATCAAACCTGTT 59.697 36.000 0.00 0.00 0.00 3.16
115 116 6.489700 TCATCTCAGCAAAATCAAACCTGTTA 59.510 34.615 0.00 0.00 0.00 2.41
116 117 6.707440 TCTCAGCAAAATCAAACCTGTTAA 57.293 33.333 0.00 0.00 0.00 2.01
117 118 7.106439 TCTCAGCAAAATCAAACCTGTTAAA 57.894 32.000 0.00 0.00 0.00 1.52
118 119 7.551585 TCTCAGCAAAATCAAACCTGTTAAAA 58.448 30.769 0.00 0.00 0.00 1.52
119 120 7.491048 TCTCAGCAAAATCAAACCTGTTAAAAC 59.509 33.333 0.00 0.00 0.00 2.43
120 121 6.536941 TCAGCAAAATCAAACCTGTTAAAACC 59.463 34.615 0.00 0.00 0.00 3.27
121 122 5.820423 AGCAAAATCAAACCTGTTAAAACCC 59.180 36.000 0.00 0.00 0.00 4.11
122 123 5.586643 GCAAAATCAAACCTGTTAAAACCCA 59.413 36.000 0.00 0.00 0.00 4.51
123 124 6.094186 GCAAAATCAAACCTGTTAAAACCCAA 59.906 34.615 0.00 0.00 0.00 4.12
124 125 7.362142 GCAAAATCAAACCTGTTAAAACCCAAA 60.362 33.333 0.00 0.00 0.00 3.28
125 126 8.681806 CAAAATCAAACCTGTTAAAACCCAAAT 58.318 29.630 0.00 0.00 0.00 2.32
126 127 7.800155 AATCAAACCTGTTAAAACCCAAATG 57.200 32.000 0.00 0.00 0.00 2.32
127 128 6.301169 TCAAACCTGTTAAAACCCAAATGT 57.699 33.333 0.00 0.00 0.00 2.71
128 129 6.712276 TCAAACCTGTTAAAACCCAAATGTT 58.288 32.000 0.00 0.00 0.00 2.71
129 130 7.168905 TCAAACCTGTTAAAACCCAAATGTTT 58.831 30.769 0.00 0.00 40.05 2.83
130 131 8.319146 TCAAACCTGTTAAAACCCAAATGTTTA 58.681 29.630 0.00 0.00 37.46 2.01
131 132 9.114952 CAAACCTGTTAAAACCCAAATGTTTAT 57.885 29.630 0.00 0.00 37.46 1.40
132 133 8.669946 AACCTGTTAAAACCCAAATGTTTATG 57.330 30.769 0.00 0.00 37.46 1.90
133 134 8.024145 ACCTGTTAAAACCCAAATGTTTATGA 57.976 30.769 0.00 0.00 37.46 2.15
134 135 8.487028 ACCTGTTAAAACCCAAATGTTTATGAA 58.513 29.630 0.00 0.00 37.46 2.57
135 136 9.331282 CCTGTTAAAACCCAAATGTTTATGAAA 57.669 29.630 0.00 0.00 37.46 2.69
159 160 1.798079 GCGACGATGTAGACCAAGACC 60.798 57.143 0.00 0.00 0.00 3.85
162 163 3.428999 CGACGATGTAGACCAAGACCAAT 60.429 47.826 0.00 0.00 0.00 3.16
178 179 1.311859 CAATAGATGCCCATGCGTGT 58.688 50.000 4.96 0.00 41.78 4.49
272 273 1.705745 AGGAAGAAAGGAAGTCCACCC 59.294 52.381 0.00 0.00 38.89 4.61
299 304 1.304617 CTGCCCTCCCTCCCTTTTC 59.695 63.158 0.00 0.00 0.00 2.29
325 330 3.277715 GCAACTACTACTACGACTCCCT 58.722 50.000 0.00 0.00 0.00 4.20
330 338 1.212441 ACTACTACGACTCCCTCCCAG 59.788 57.143 0.00 0.00 0.00 4.45
364 372 0.039074 CCTCGTCCTCACTGACACAC 60.039 60.000 0.00 0.00 34.88 3.82
389 402 4.660938 GAAACACAGGGCCCCGCT 62.661 66.667 21.43 0.00 0.00 5.52
390 403 4.660938 AAACACAGGGCCCCGCTC 62.661 66.667 21.43 0.00 0.00 5.03
411 424 1.021390 CGGATCCAACCACTGCACTC 61.021 60.000 13.41 0.00 0.00 3.51
412 425 0.036732 GGATCCAACCACTGCACTCA 59.963 55.000 6.95 0.00 0.00 3.41
413 426 1.340405 GGATCCAACCACTGCACTCAT 60.340 52.381 6.95 0.00 0.00 2.90
423 436 1.967597 CTGCACTCATCACTGCGCTG 61.968 60.000 13.23 13.23 36.08 5.18
536 553 2.536365 CAGTGTGCATCAATGGCATTC 58.464 47.619 10.36 0.00 44.11 2.67
584 601 0.618968 ACTCCCACATCCCCTGTCTC 60.619 60.000 0.00 0.00 35.29 3.36
587 604 1.341156 CCCACATCCCCTGTCTCCTC 61.341 65.000 0.00 0.00 35.29 3.71
593 610 1.231751 TCCCCTGTCTCCTCCATCCT 61.232 60.000 0.00 0.00 0.00 3.24
597 614 1.127343 CTGTCTCCTCCATCCTTCCC 58.873 60.000 0.00 0.00 0.00 3.97
598 615 0.687757 TGTCTCCTCCATCCTTCCCG 60.688 60.000 0.00 0.00 0.00 5.14
599 616 0.397254 GTCTCCTCCATCCTTCCCGA 60.397 60.000 0.00 0.00 0.00 5.14
607 629 1.002274 ATCCTTCCCGACCAGCTCT 59.998 57.895 0.00 0.00 0.00 4.09
618 640 1.153289 CCAGCTCTTCCACCCATCG 60.153 63.158 0.00 0.00 0.00 3.84
642 664 4.019681 TCTCCGCCATTTCTTTCTTTCCTA 60.020 41.667 0.00 0.00 0.00 2.94
643 665 4.658063 TCCGCCATTTCTTTCTTTCCTAA 58.342 39.130 0.00 0.00 0.00 2.69
644 666 5.261216 TCCGCCATTTCTTTCTTTCCTAAT 58.739 37.500 0.00 0.00 0.00 1.73
645 667 5.714806 TCCGCCATTTCTTTCTTTCCTAATT 59.285 36.000 0.00 0.00 0.00 1.40
646 668 6.036470 CCGCCATTTCTTTCTTTCCTAATTC 58.964 40.000 0.00 0.00 0.00 2.17
647 669 6.036470 CGCCATTTCTTTCTTTCCTAATTCC 58.964 40.000 0.00 0.00 0.00 3.01
648 670 6.127619 CGCCATTTCTTTCTTTCCTAATTCCT 60.128 38.462 0.00 0.00 0.00 3.36
649 671 7.038048 GCCATTTCTTTCTTTCCTAATTCCTG 58.962 38.462 0.00 0.00 0.00 3.86
650 672 7.550712 CCATTTCTTTCTTTCCTAATTCCTGG 58.449 38.462 0.00 0.00 0.00 4.45
651 673 7.179160 CCATTTCTTTCTTTCCTAATTCCTGGT 59.821 37.037 0.00 0.00 0.00 4.00
692 731 0.880278 CCGGCGAGAGAGAGAGAGAG 60.880 65.000 9.30 0.00 0.00 3.20
693 732 0.104120 CGGCGAGAGAGAGAGAGAGA 59.896 60.000 0.00 0.00 0.00 3.10
734 773 1.692749 TTCCTCCCCCATCTTCCCG 60.693 63.158 0.00 0.00 0.00 5.14
735 774 3.171388 CCTCCCCCATCTTCCCGG 61.171 72.222 0.00 0.00 0.00 5.73
739 778 4.195334 CCCCATCTTCCCGGCCAG 62.195 72.222 2.24 0.00 0.00 4.85
740 779 4.883354 CCCATCTTCCCGGCCAGC 62.883 72.222 2.24 0.00 0.00 4.85
742 781 2.203126 CATCTTCCCGGCCAGCTC 60.203 66.667 2.24 0.00 0.00 4.09
744 783 4.722535 TCTTCCCGGCCAGCTCCT 62.723 66.667 2.24 0.00 0.00 3.69
745 784 3.721706 CTTCCCGGCCAGCTCCTT 61.722 66.667 2.24 0.00 0.00 3.36
746 785 3.256960 TTCCCGGCCAGCTCCTTT 61.257 61.111 2.24 0.00 0.00 3.11
747 786 2.771328 CTTCCCGGCCAGCTCCTTTT 62.771 60.000 2.24 0.00 0.00 2.27
748 787 2.283173 CCCGGCCAGCTCCTTTTT 60.283 61.111 2.24 0.00 0.00 1.94
749 788 2.639327 CCCGGCCAGCTCCTTTTTG 61.639 63.158 2.24 0.00 0.00 2.44
750 789 2.639327 CCGGCCAGCTCCTTTTTGG 61.639 63.158 2.24 0.00 35.06 3.28
751 790 1.903404 CGGCCAGCTCCTTTTTGGT 60.903 57.895 2.24 0.00 37.07 3.67
752 791 1.866853 CGGCCAGCTCCTTTTTGGTC 61.867 60.000 2.24 0.00 37.07 4.02
753 792 0.540597 GGCCAGCTCCTTTTTGGTCT 60.541 55.000 0.00 0.00 33.83 3.85
754 793 0.600057 GCCAGCTCCTTTTTGGTCTG 59.400 55.000 0.00 0.00 37.30 3.51
755 794 1.986882 CCAGCTCCTTTTTGGTCTGT 58.013 50.000 0.00 0.00 36.51 3.41
756 795 1.882623 CCAGCTCCTTTTTGGTCTGTC 59.117 52.381 0.00 0.00 36.51 3.51
757 796 2.487986 CCAGCTCCTTTTTGGTCTGTCT 60.488 50.000 0.00 0.00 36.51 3.41
758 797 2.810852 CAGCTCCTTTTTGGTCTGTCTC 59.189 50.000 0.00 0.00 34.93 3.36
759 798 2.708325 AGCTCCTTTTTGGTCTGTCTCT 59.292 45.455 0.00 0.00 37.07 3.10
760 799 3.070748 GCTCCTTTTTGGTCTGTCTCTC 58.929 50.000 0.00 0.00 37.07 3.20
764 803 4.282195 TCCTTTTTGGTCTGTCTCTCTCTC 59.718 45.833 0.00 0.00 37.07 3.20
844 883 2.181021 CCAGTACTGTCCCGACGC 59.819 66.667 21.18 0.00 0.00 5.19
927 966 2.094234 GGGGTTCCAATTCAAATCCACG 60.094 50.000 1.99 0.00 0.00 4.94
950 989 0.440758 CGTCGCGTTGCTTGGATTTA 59.559 50.000 5.77 0.00 0.00 1.40
965 1004 5.437191 TGGATTTACTCCTTCCTTTCTCC 57.563 43.478 0.00 0.00 45.21 3.71
1085 1194 4.101448 CGGCAGGAAGGGGGACAG 62.101 72.222 0.00 0.00 0.00 3.51
1448 1557 3.749064 GTCTCAGTCCGAGGCGCA 61.749 66.667 10.83 0.00 42.55 6.09
1701 1810 1.511305 CGTCTACCACCGCATCTGT 59.489 57.895 0.00 0.00 0.00 3.41
1746 1855 1.950973 GCCTCGACCTCCTCCTTGTC 61.951 65.000 0.00 0.00 0.00 3.18
1747 1856 0.612174 CCTCGACCTCCTCCTTGTCA 60.612 60.000 0.00 0.00 0.00 3.58
1749 1858 0.112606 TCGACCTCCTCCTTGTCAGT 59.887 55.000 0.00 0.00 0.00 3.41
1750 1859 0.244994 CGACCTCCTCCTTGTCAGTG 59.755 60.000 0.00 0.00 0.00 3.66
1751 1860 1.633774 GACCTCCTCCTTGTCAGTGA 58.366 55.000 0.00 0.00 0.00 3.41
1772 1881 1.816863 GACCACAAGGACCGAGAGCA 61.817 60.000 0.00 0.00 38.69 4.26
1776 1885 1.079543 CAAGGACCGAGAGCACCAG 60.080 63.158 0.00 0.00 0.00 4.00
1864 1976 1.594331 GGGACCGATTATTGACAGGC 58.406 55.000 0.00 0.00 0.00 4.85
1871 1983 0.532862 ATTATTGACAGGCTCGCCGG 60.533 55.000 6.53 6.53 41.95 6.13
2325 2437 3.967335 CCGTCGAGCCTCCGATCC 61.967 72.222 0.00 0.00 40.91 3.36
2328 2440 2.203365 TCGAGCCTCCGATCCTCC 60.203 66.667 0.00 0.00 33.14 4.30
2334 2446 2.598985 CTCCGATCCTCCCTCCGG 60.599 72.222 0.00 0.00 43.02 5.14
2490 2602 2.516460 CAGCAGCAGATGGAGGCC 60.516 66.667 0.00 0.00 0.00 5.19
2493 2605 2.513204 CAGCAGATGGAGGCCGTG 60.513 66.667 0.00 0.00 0.00 4.94
2494 2606 4.479993 AGCAGATGGAGGCCGTGC 62.480 66.667 0.00 0.84 0.00 5.34
2495 2607 4.783621 GCAGATGGAGGCCGTGCA 62.784 66.667 0.00 0.00 34.18 4.57
2514 2626 4.809496 CAGCTCAGGGGCGGCAAT 62.809 66.667 12.47 0.00 37.29 3.56
2676 2788 2.381109 CTCCAGCAGCATCGACTTG 58.619 57.895 0.00 0.00 0.00 3.16
2718 2830 3.104766 CACGCCTCCATGCATCAC 58.895 61.111 0.00 0.00 0.00 3.06
2792 2906 7.981142 TCTTTTTGTTTGTAAGTAGTGTGAGG 58.019 34.615 0.00 0.00 0.00 3.86
2885 3018 1.843368 ATGCATGGGTTCAGGACTTG 58.157 50.000 0.00 0.00 0.00 3.16
2888 3021 1.003580 GCATGGGTTCAGGACTTGAGA 59.996 52.381 0.00 0.00 37.07 3.27
3004 3138 2.750141 ATCAGGCCTCAATGCAGAAT 57.250 45.000 0.00 0.00 0.00 2.40
3052 3191 7.186021 ACTGTTTGTTACTGCTTGTACATAC 57.814 36.000 0.00 0.00 0.00 2.39
3053 3192 6.764085 ACTGTTTGTTACTGCTTGTACATACA 59.236 34.615 0.00 0.00 31.34 2.29
3054 3193 7.042051 ACTGTTTGTTACTGCTTGTACATACAG 60.042 37.037 19.02 19.02 41.16 2.74
3055 3194 6.987404 TGTTTGTTACTGCTTGTACATACAGA 59.013 34.615 24.66 11.06 37.52 3.41
3056 3195 7.170828 TGTTTGTTACTGCTTGTACATACAGAG 59.829 37.037 24.66 9.36 37.52 3.35
3057 3196 5.720202 TGTTACTGCTTGTACATACAGAGG 58.280 41.667 24.66 7.90 37.52 3.69
3058 3197 5.479027 TGTTACTGCTTGTACATACAGAGGA 59.521 40.000 24.66 8.65 37.52 3.71
3059 3198 4.727507 ACTGCTTGTACATACAGAGGAG 57.272 45.455 24.66 18.03 38.00 3.69
3060 3199 3.449018 ACTGCTTGTACATACAGAGGAGG 59.551 47.826 24.66 6.73 37.24 4.30
3061 3200 3.441101 TGCTTGTACATACAGAGGAGGT 58.559 45.455 0.00 0.00 37.52 3.85
3062 3201 3.195610 TGCTTGTACATACAGAGGAGGTG 59.804 47.826 0.00 0.00 37.52 4.00
3063 3202 3.447586 GCTTGTACATACAGAGGAGGTGA 59.552 47.826 0.00 0.00 37.52 4.02
3064 3203 4.081642 GCTTGTACATACAGAGGAGGTGAA 60.082 45.833 0.00 0.00 37.52 3.18
3065 3204 5.395768 GCTTGTACATACAGAGGAGGTGAAT 60.396 44.000 0.00 0.00 37.52 2.57
3066 3205 6.620877 TTGTACATACAGAGGAGGTGAATT 57.379 37.500 0.00 0.00 37.52 2.17
3068 3207 7.727578 TGTACATACAGAGGAGGTGAATTTA 57.272 36.000 0.00 0.00 0.00 1.40
3069 3208 8.319057 TGTACATACAGAGGAGGTGAATTTAT 57.681 34.615 0.00 0.00 0.00 1.40
3071 3210 6.831976 ACATACAGAGGAGGTGAATTTATCC 58.168 40.000 0.00 0.00 0.00 2.59
3072 3211 6.386927 ACATACAGAGGAGGTGAATTTATCCA 59.613 38.462 0.00 0.00 34.08 3.41
3073 3212 5.779241 ACAGAGGAGGTGAATTTATCCAA 57.221 39.130 0.00 0.00 34.08 3.53
3075 3214 5.946377 ACAGAGGAGGTGAATTTATCCAAAC 59.054 40.000 0.00 0.00 34.08 2.93
3077 3216 6.094603 CAGAGGAGGTGAATTTATCCAAACTG 59.905 42.308 0.00 0.00 34.08 3.16
3079 3218 6.314917 AGGAGGTGAATTTATCCAAACTGTT 58.685 36.000 0.00 0.00 34.08 3.16
3080 3219 6.782494 AGGAGGTGAATTTATCCAAACTGTTT 59.218 34.615 0.00 0.00 34.08 2.83
3081 3220 6.868339 GGAGGTGAATTTATCCAAACTGTTTG 59.132 38.462 22.99 22.99 40.32 2.93
3082 3221 7.360113 AGGTGAATTTATCCAAACTGTTTGT 57.640 32.000 26.35 14.83 38.98 2.83
3083 3222 7.791029 AGGTGAATTTATCCAAACTGTTTGTT 58.209 30.769 26.35 17.73 41.29 2.83
3084 3223 8.919145 AGGTGAATTTATCCAAACTGTTTGTTA 58.081 29.630 26.35 16.98 38.03 2.41
3086 3225 8.687301 GTGAATTTATCCAAACTGTTTGTTACG 58.313 33.333 26.35 14.40 38.03 3.18
3088 3227 3.636282 ATCCAAACTGTTTGTTACGGC 57.364 42.857 26.35 0.00 38.03 5.68
3162 3668 1.207570 TGTTACTCCCGTGTGTGTGTT 59.792 47.619 0.00 0.00 0.00 3.32
3163 3669 2.429971 TGTTACTCCCGTGTGTGTGTTA 59.570 45.455 0.00 0.00 0.00 2.41
3165 3671 0.249741 ACTCCCGTGTGTGTGTTAGC 60.250 55.000 0.00 0.00 0.00 3.09
3168 3674 1.000060 TCCCGTGTGTGTGTTAGCTAC 60.000 52.381 0.00 0.00 0.00 3.58
3169 3675 1.000506 CCCGTGTGTGTGTTAGCTACT 59.999 52.381 0.00 0.00 0.00 2.57
3170 3676 2.229543 CCCGTGTGTGTGTTAGCTACTA 59.770 50.000 0.00 0.00 0.00 1.82
3171 3677 3.240069 CCGTGTGTGTGTTAGCTACTAC 58.760 50.000 0.00 0.00 0.00 2.73
3172 3678 3.057736 CCGTGTGTGTGTTAGCTACTACT 60.058 47.826 0.00 0.00 0.00 2.57
3308 3820 5.560953 GCGAAAATGTAGGATAATGCCTGTC 60.561 44.000 0.00 0.00 39.08 3.51
3309 3821 5.527214 CGAAAATGTAGGATAATGCCTGTCA 59.473 40.000 0.00 0.00 39.08 3.58
3310 3822 6.511767 CGAAAATGTAGGATAATGCCTGTCAC 60.512 42.308 0.00 0.00 39.08 3.67
3311 3823 5.372343 AATGTAGGATAATGCCTGTCACA 57.628 39.130 0.00 0.00 39.08 3.58
3342 3854 4.464597 AGGTAGAGTAGAACTTTGAGGCAG 59.535 45.833 0.00 0.00 0.00 4.85
3392 3915 2.289694 GGTCAGTAGCAGGTGTTGATGT 60.290 50.000 0.00 0.00 0.00 3.06
3403 3926 3.813166 AGGTGTTGATGTTTACCAACTCG 59.187 43.478 0.00 0.00 42.16 4.18
3423 3946 5.047448 ACTCGTCTTAAAAGGAAGTACTCCC 60.047 44.000 0.00 0.00 46.81 4.30
3424 3947 5.082425 TCGTCTTAAAAGGAAGTACTCCCT 58.918 41.667 0.00 0.00 46.81 4.20
3425 3948 5.184671 TCGTCTTAAAAGGAAGTACTCCCTC 59.815 44.000 0.00 0.00 46.81 4.30
3426 3949 5.624052 CGTCTTAAAAGGAAGTACTCCCTCC 60.624 48.000 0.00 2.10 46.81 4.30
3427 3950 4.465305 TCTTAAAAGGAAGTACTCCCTCCG 59.535 45.833 0.00 0.00 46.81 4.63
3428 3951 2.322339 AAAGGAAGTACTCCCTCCGT 57.678 50.000 0.00 0.00 46.81 4.69
3429 3952 1.849977 AAGGAAGTACTCCCTCCGTC 58.150 55.000 0.00 0.00 46.81 4.79
3430 3953 0.033306 AGGAAGTACTCCCTCCGTCC 60.033 60.000 0.00 0.00 46.81 4.79
3431 3954 1.042003 GGAAGTACTCCCTCCGTCCC 61.042 65.000 0.00 0.00 38.44 4.46
3432 3955 0.324091 GAAGTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
3433 3956 0.338814 AAGTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
3434 3957 1.229131 AGTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3435 3958 1.572415 AGTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3436 3959 2.179424 AGTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3437 3960 3.400322 AGTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3438 3961 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3439 3962 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3440 3963 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3441 3964 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3442 3965 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3443 3966 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3444 3967 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
3445 3968 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
3446 3969 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
3447 3970 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3448 3971 4.625742 CCGTCCCATAATATAAGAGCGTTG 59.374 45.833 0.00 0.00 0.00 4.10
3449 3972 5.227908 CGTCCCATAATATAAGAGCGTTGT 58.772 41.667 0.00 0.00 0.00 3.32
3450 3973 5.694910 CGTCCCATAATATAAGAGCGTTGTT 59.305 40.000 0.00 0.00 0.00 2.83
3451 3974 6.346598 CGTCCCATAATATAAGAGCGTTGTTG 60.347 42.308 0.00 0.00 0.00 3.33
3452 3975 6.704493 GTCCCATAATATAAGAGCGTTGTTGA 59.296 38.462 0.00 0.00 0.00 3.18
3453 3976 6.704493 TCCCATAATATAAGAGCGTTGTTGAC 59.296 38.462 0.00 0.00 0.00 3.18
3454 3977 6.481976 CCCATAATATAAGAGCGTTGTTGACA 59.518 38.462 0.00 0.00 0.00 3.58
3473 3996 7.233553 TGTTGACAGAGGGAGTAATATCCTATG 59.766 40.741 0.00 0.00 43.34 2.23
3508 4036 2.033194 AAGCCGCGACAGGTTTAGC 61.033 57.895 8.23 0.00 32.81 3.09
3566 4094 5.280419 CCTCCTTGTCTCAAGGATCTCTTTT 60.280 44.000 25.07 0.00 44.75 2.27
3568 4096 5.072329 TCCTTGTCTCAAGGATCTCTTTTGT 59.928 40.000 22.34 0.00 41.27 2.83
3569 4097 5.180868 CCTTGTCTCAAGGATCTCTTTTGTG 59.819 44.000 19.98 0.00 39.81 3.33
3611 4260 2.012673 CAGGCACCTTATCTGAACTGC 58.987 52.381 0.00 0.00 0.00 4.40
3637 4286 1.696063 CCGGGGATCATTTGCTCAAT 58.304 50.000 0.00 0.00 0.00 2.57
3644 4293 3.698040 GGATCATTTGCTCAATGGACAGT 59.302 43.478 8.73 0.00 42.52 3.55
3663 4312 5.435291 ACAGTTGCCCATTTTGAAATGAAA 58.565 33.333 16.00 6.57 46.72 2.69
3666 4315 5.993441 AGTTGCCCATTTTGAAATGAAAGAG 59.007 36.000 16.00 1.59 46.72 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.947228 TGGAAATGTTTCTACAAGCTCTG 57.053 39.130 5.56 0.00 37.91 3.35
2 3 9.691362 TTTTTATGGAAATGTTTCTACAAGCTC 57.309 29.630 5.56 0.00 37.91 4.09
40 41 8.837389 GCGTCACCCTAAGAATTTAATTTAGAT 58.163 33.333 0.00 0.00 0.00 1.98
41 42 7.010738 CGCGTCACCCTAAGAATTTAATTTAGA 59.989 37.037 0.00 0.00 0.00 2.10
42 43 7.123830 CGCGTCACCCTAAGAATTTAATTTAG 58.876 38.462 0.00 0.00 0.00 1.85
43 44 6.457257 GCGCGTCACCCTAAGAATTTAATTTA 60.457 38.462 8.43 0.00 0.00 1.40
44 45 5.675323 GCGCGTCACCCTAAGAATTTAATTT 60.675 40.000 8.43 0.00 0.00 1.82
45 46 4.201881 GCGCGTCACCCTAAGAATTTAATT 60.202 41.667 8.43 0.00 0.00 1.40
46 47 3.311596 GCGCGTCACCCTAAGAATTTAAT 59.688 43.478 8.43 0.00 0.00 1.40
47 48 2.674357 GCGCGTCACCCTAAGAATTTAA 59.326 45.455 8.43 0.00 0.00 1.52
48 49 2.273557 GCGCGTCACCCTAAGAATTTA 58.726 47.619 8.43 0.00 0.00 1.40
49 50 1.084289 GCGCGTCACCCTAAGAATTT 58.916 50.000 8.43 0.00 0.00 1.82
50 51 0.743345 GGCGCGTCACCCTAAGAATT 60.743 55.000 5.47 0.00 0.00 2.17
51 52 1.153429 GGCGCGTCACCCTAAGAAT 60.153 57.895 5.47 0.00 0.00 2.40
52 53 2.263540 GGCGCGTCACCCTAAGAA 59.736 61.111 5.47 0.00 0.00 2.52
53 54 2.678934 AGGCGCGTCACCCTAAGA 60.679 61.111 15.58 0.00 0.00 2.10
54 55 2.509336 CAGGCGCGTCACCCTAAG 60.509 66.667 15.58 0.00 0.00 2.18
55 56 4.077184 CCAGGCGCGTCACCCTAA 62.077 66.667 15.58 0.00 0.00 2.69
67 68 3.622060 TTAGAGGCGGCAACCAGGC 62.622 63.158 13.08 0.00 39.93 4.85
68 69 1.450312 CTTAGAGGCGGCAACCAGG 60.450 63.158 13.08 0.00 0.00 4.45
69 70 2.109126 GCTTAGAGGCGGCAACCAG 61.109 63.158 13.08 2.62 0.00 4.00
70 71 2.046314 GCTTAGAGGCGGCAACCA 60.046 61.111 13.08 0.00 0.00 3.67
71 72 2.821679 AAGGCTTAGAGGCGGCAACC 62.822 60.000 13.08 2.68 46.58 3.77
72 73 1.369839 GAAGGCTTAGAGGCGGCAAC 61.370 60.000 13.08 4.75 46.58 4.17
73 74 1.078426 GAAGGCTTAGAGGCGGCAA 60.078 57.895 13.08 0.00 46.58 4.52
74 75 1.626356 ATGAAGGCTTAGAGGCGGCA 61.626 55.000 13.08 0.00 46.58 5.69
75 76 0.882484 GATGAAGGCTTAGAGGCGGC 60.882 60.000 0.00 0.00 46.58 6.53
76 77 0.755686 AGATGAAGGCTTAGAGGCGG 59.244 55.000 0.00 0.00 46.58 6.13
77 78 1.410517 TGAGATGAAGGCTTAGAGGCG 59.589 52.381 0.00 0.00 46.58 5.52
78 79 2.806382 GCTGAGATGAAGGCTTAGAGGC 60.806 54.545 0.00 0.00 41.73 4.70
79 80 2.433604 TGCTGAGATGAAGGCTTAGAGG 59.566 50.000 0.00 0.00 0.00 3.69
80 81 3.815856 TGCTGAGATGAAGGCTTAGAG 57.184 47.619 0.00 0.00 0.00 2.43
81 82 4.558226 TTTGCTGAGATGAAGGCTTAGA 57.442 40.909 0.00 0.00 0.00 2.10
82 83 5.356190 TGATTTTGCTGAGATGAAGGCTTAG 59.644 40.000 0.00 0.00 0.00 2.18
83 84 5.255687 TGATTTTGCTGAGATGAAGGCTTA 58.744 37.500 0.00 0.00 0.00 3.09
84 85 4.084287 TGATTTTGCTGAGATGAAGGCTT 58.916 39.130 0.00 0.00 0.00 4.35
85 86 3.693807 TGATTTTGCTGAGATGAAGGCT 58.306 40.909 0.00 0.00 0.00 4.58
86 87 4.445452 TTGATTTTGCTGAGATGAAGGC 57.555 40.909 0.00 0.00 0.00 4.35
87 88 5.047519 AGGTTTGATTTTGCTGAGATGAAGG 60.048 40.000 0.00 0.00 0.00 3.46
88 89 5.862323 CAGGTTTGATTTTGCTGAGATGAAG 59.138 40.000 0.00 0.00 0.00 3.02
89 90 5.302568 ACAGGTTTGATTTTGCTGAGATGAA 59.697 36.000 0.00 0.00 0.00 2.57
90 91 4.828939 ACAGGTTTGATTTTGCTGAGATGA 59.171 37.500 0.00 0.00 0.00 2.92
91 92 5.130292 ACAGGTTTGATTTTGCTGAGATG 57.870 39.130 0.00 0.00 0.00 2.90
92 93 5.796424 AACAGGTTTGATTTTGCTGAGAT 57.204 34.783 0.00 0.00 0.00 2.75
93 94 6.707440 TTAACAGGTTTGATTTTGCTGAGA 57.293 33.333 0.00 0.00 0.00 3.27
94 95 7.254421 GGTTTTAACAGGTTTGATTTTGCTGAG 60.254 37.037 0.00 0.00 0.00 3.35
95 96 6.536941 GGTTTTAACAGGTTTGATTTTGCTGA 59.463 34.615 0.00 0.00 0.00 4.26
96 97 6.238347 GGGTTTTAACAGGTTTGATTTTGCTG 60.238 38.462 0.00 0.00 0.00 4.41
97 98 5.820423 GGGTTTTAACAGGTTTGATTTTGCT 59.180 36.000 0.00 0.00 0.00 3.91
98 99 5.586643 TGGGTTTTAACAGGTTTGATTTTGC 59.413 36.000 0.00 0.00 0.00 3.68
99 100 7.617041 TTGGGTTTTAACAGGTTTGATTTTG 57.383 32.000 0.00 0.00 0.00 2.44
100 101 8.681806 CATTTGGGTTTTAACAGGTTTGATTTT 58.318 29.630 0.00 0.00 0.00 1.82
101 102 7.831690 ACATTTGGGTTTTAACAGGTTTGATTT 59.168 29.630 0.00 0.00 0.00 2.17
102 103 7.342581 ACATTTGGGTTTTAACAGGTTTGATT 58.657 30.769 0.00 0.00 0.00 2.57
103 104 6.894682 ACATTTGGGTTTTAACAGGTTTGAT 58.105 32.000 0.00 0.00 0.00 2.57
104 105 6.301169 ACATTTGGGTTTTAACAGGTTTGA 57.699 33.333 0.00 0.00 0.00 2.69
105 106 6.993786 AACATTTGGGTTTTAACAGGTTTG 57.006 33.333 0.00 0.00 0.00 2.93
106 107 9.114952 CATAAACATTTGGGTTTTAACAGGTTT 57.885 29.630 0.00 0.00 41.07 3.27
107 108 8.487028 TCATAAACATTTGGGTTTTAACAGGTT 58.513 29.630 0.00 0.00 41.07 3.50
108 109 8.024145 TCATAAACATTTGGGTTTTAACAGGT 57.976 30.769 0.00 0.00 41.07 4.00
109 110 8.894768 TTCATAAACATTTGGGTTTTAACAGG 57.105 30.769 0.00 0.00 41.07 4.00
126 127 4.708601 ACATCGTCGCTGTTTTCATAAAC 58.291 39.130 0.00 0.00 43.17 2.01
127 128 5.865013 TCTACATCGTCGCTGTTTTCATAAA 59.135 36.000 7.08 0.00 0.00 1.40
128 129 5.287752 GTCTACATCGTCGCTGTTTTCATAA 59.712 40.000 7.08 0.00 0.00 1.90
129 130 4.796830 GTCTACATCGTCGCTGTTTTCATA 59.203 41.667 7.08 0.00 0.00 2.15
130 131 3.612860 GTCTACATCGTCGCTGTTTTCAT 59.387 43.478 7.08 0.00 0.00 2.57
131 132 2.984471 GTCTACATCGTCGCTGTTTTCA 59.016 45.455 7.08 0.00 0.00 2.69
132 133 2.344741 GGTCTACATCGTCGCTGTTTTC 59.655 50.000 7.08 0.00 0.00 2.29
133 134 2.288579 TGGTCTACATCGTCGCTGTTTT 60.289 45.455 7.08 0.00 0.00 2.43
134 135 1.271379 TGGTCTACATCGTCGCTGTTT 59.729 47.619 7.08 0.00 0.00 2.83
135 136 0.885879 TGGTCTACATCGTCGCTGTT 59.114 50.000 7.08 0.00 0.00 3.16
136 137 0.885879 TTGGTCTACATCGTCGCTGT 59.114 50.000 6.96 6.96 0.00 4.40
137 138 1.132453 TCTTGGTCTACATCGTCGCTG 59.868 52.381 0.00 0.00 0.00 5.18
138 139 1.132643 GTCTTGGTCTACATCGTCGCT 59.867 52.381 0.00 0.00 0.00 4.93
139 140 1.546834 GTCTTGGTCTACATCGTCGC 58.453 55.000 0.00 0.00 0.00 5.19
140 141 1.471287 TGGTCTTGGTCTACATCGTCG 59.529 52.381 0.00 0.00 0.00 5.12
141 142 3.587797 TTGGTCTTGGTCTACATCGTC 57.412 47.619 0.00 0.00 0.00 4.20
142 143 4.954202 TCTATTGGTCTTGGTCTACATCGT 59.046 41.667 0.00 0.00 0.00 3.73
143 144 5.515797 TCTATTGGTCTTGGTCTACATCG 57.484 43.478 0.00 0.00 0.00 3.84
144 145 5.698545 GCATCTATTGGTCTTGGTCTACATC 59.301 44.000 0.00 0.00 0.00 3.06
159 160 1.265095 GACACGCATGGGCATCTATTG 59.735 52.381 10.10 1.22 41.24 1.90
162 163 0.251634 TTGACACGCATGGGCATCTA 59.748 50.000 10.10 2.02 41.24 1.98
286 287 2.528564 TGCATTTGAAAAGGGAGGGAG 58.471 47.619 0.00 0.00 0.00 4.30
299 304 5.515626 GGAGTCGTAGTAGTAGTTGCATTTG 59.484 44.000 0.00 0.00 0.00 2.32
387 400 3.195698 GTGGTTGGATCCGCGAGC 61.196 66.667 8.23 6.07 0.00 5.03
389 402 2.264480 CAGTGGTTGGATCCGCGA 59.736 61.111 8.23 0.00 42.18 5.87
390 403 3.499737 GCAGTGGTTGGATCCGCG 61.500 66.667 7.39 0.00 42.18 6.46
513 530 0.179145 GCCATTGATGCACACTGCTC 60.179 55.000 0.00 0.00 45.31 4.26
584 601 1.689233 TGGTCGGGAAGGATGGAGG 60.689 63.158 0.00 0.00 0.00 4.30
587 604 2.190578 GCTGGTCGGGAAGGATGG 59.809 66.667 0.00 0.00 0.00 3.51
593 610 1.535444 TGGAAGAGCTGGTCGGGAA 60.535 57.895 0.00 0.00 0.00 3.97
597 614 1.903877 ATGGGTGGAAGAGCTGGTCG 61.904 60.000 0.00 0.00 0.00 4.79
598 615 0.107459 GATGGGTGGAAGAGCTGGTC 60.107 60.000 0.00 0.00 0.00 4.02
599 616 1.903877 CGATGGGTGGAAGAGCTGGT 61.904 60.000 0.00 0.00 0.00 4.00
618 640 3.119814 GGAAAGAAAGAAATGGCGGAGAC 60.120 47.826 0.00 0.00 0.00 3.36
645 667 1.573108 CTGCTTCCTTCCTACCAGGA 58.427 55.000 0.00 0.00 44.10 3.86
646 668 0.543749 CCTGCTTCCTTCCTACCAGG 59.456 60.000 0.00 0.00 36.46 4.45
647 669 0.543749 CCCTGCTTCCTTCCTACCAG 59.456 60.000 0.00 0.00 0.00 4.00
648 670 0.118346 TCCCTGCTTCCTTCCTACCA 59.882 55.000 0.00 0.00 0.00 3.25
649 671 0.542333 GTCCCTGCTTCCTTCCTACC 59.458 60.000 0.00 0.00 0.00 3.18
650 672 0.542333 GGTCCCTGCTTCCTTCCTAC 59.458 60.000 0.00 0.00 0.00 3.18
651 673 0.620700 GGGTCCCTGCTTCCTTCCTA 60.621 60.000 0.00 0.00 0.00 2.94
677 716 5.050769 CGAAAATCTCTCTCTCTCTCTCTCG 60.051 48.000 0.00 0.00 0.00 4.04
734 773 0.540597 AGACCAAAAAGGAGCTGGCC 60.541 55.000 0.00 0.00 41.22 5.36
735 774 0.600057 CAGACCAAAAAGGAGCTGGC 59.400 55.000 0.00 0.00 41.22 4.85
738 777 2.708325 AGAGACAGACCAAAAAGGAGCT 59.292 45.455 0.00 0.00 41.22 4.09
739 778 3.070748 GAGAGACAGACCAAAAAGGAGC 58.929 50.000 0.00 0.00 41.22 4.70
740 779 4.283212 AGAGAGAGACAGACCAAAAAGGAG 59.717 45.833 0.00 0.00 41.22 3.69
742 781 4.283212 AGAGAGAGAGACAGACCAAAAAGG 59.717 45.833 0.00 0.00 45.67 3.11
744 783 5.144100 AGAGAGAGAGAGACAGACCAAAAA 58.856 41.667 0.00 0.00 0.00 1.94
745 784 4.735369 AGAGAGAGAGAGACAGACCAAAA 58.265 43.478 0.00 0.00 0.00 2.44
746 785 4.042809 AGAGAGAGAGAGAGACAGACCAAA 59.957 45.833 0.00 0.00 0.00 3.28
747 786 3.587061 AGAGAGAGAGAGAGACAGACCAA 59.413 47.826 0.00 0.00 0.00 3.67
748 787 3.181329 AGAGAGAGAGAGAGACAGACCA 58.819 50.000 0.00 0.00 0.00 4.02
749 788 3.452627 AGAGAGAGAGAGAGAGACAGACC 59.547 52.174 0.00 0.00 0.00 3.85
750 789 4.404073 AGAGAGAGAGAGAGAGAGACAGAC 59.596 50.000 0.00 0.00 0.00 3.51
751 790 4.614475 AGAGAGAGAGAGAGAGAGACAGA 58.386 47.826 0.00 0.00 0.00 3.41
752 791 4.648762 AGAGAGAGAGAGAGAGAGAGACAG 59.351 50.000 0.00 0.00 0.00 3.51
753 792 4.614475 AGAGAGAGAGAGAGAGAGAGACA 58.386 47.826 0.00 0.00 0.00 3.41
754 793 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
755 794 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
756 795 4.039004 CCAGAGAGAGAGAGAGAGAGAGAG 59.961 54.167 0.00 0.00 0.00 3.20
757 796 3.963374 CCAGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
758 797 3.708631 ACCAGAGAGAGAGAGAGAGAGAG 59.291 52.174 0.00 0.00 0.00 3.20
759 798 3.724478 ACCAGAGAGAGAGAGAGAGAGA 58.276 50.000 0.00 0.00 0.00 3.10
760 799 4.494091 AACCAGAGAGAGAGAGAGAGAG 57.506 50.000 0.00 0.00 0.00 3.20
764 803 4.037923 GCCATTAACCAGAGAGAGAGAGAG 59.962 50.000 0.00 0.00 0.00 3.20
800 839 1.003355 TTACCAGACAGCAGCAGCC 60.003 57.895 0.00 0.00 43.56 4.85
838 877 1.081376 AGAGAAGTCAACGCGTCGG 60.081 57.895 14.44 8.61 0.00 4.79
844 883 2.730626 CGGAGCAGAGAAGTCAACG 58.269 57.895 0.00 0.00 0.00 4.10
909 948 2.250188 CGCGTGGATTTGAATTGGAAC 58.750 47.619 0.00 0.00 0.00 3.62
950 989 1.889530 CGGCGGAGAAAGGAAGGAGT 61.890 60.000 0.00 0.00 0.00 3.85
1044 1153 1.672356 CTTGTTGGAGAGGGTGGCG 60.672 63.158 0.00 0.00 0.00 5.69
1701 1810 3.437795 GGGTCGCCGAAGACGAGA 61.438 66.667 0.00 0.00 40.80 4.04
1746 1855 0.600255 GGTCCTTGTGGTCGTCACTG 60.600 60.000 11.51 6.02 46.20 3.66
1747 1856 1.746517 GGTCCTTGTGGTCGTCACT 59.253 57.895 11.51 0.00 46.20 3.41
1749 1858 1.802337 CTCGGTCCTTGTGGTCGTCA 61.802 60.000 0.00 0.00 34.64 4.35
1750 1859 1.080705 CTCGGTCCTTGTGGTCGTC 60.081 63.158 0.00 0.00 34.64 4.20
1751 1860 1.524863 CTCTCGGTCCTTGTGGTCGT 61.525 60.000 0.00 0.00 34.64 4.34
1772 1881 1.677966 CATTGGCTGCTCTGCTGGT 60.678 57.895 0.00 0.00 0.00 4.00
1848 1960 1.806623 GCGAGCCTGTCAATAATCGGT 60.807 52.381 0.00 0.00 0.00 4.69
1960 2072 1.211969 CGTCGTCGTCCTTCCATGT 59.788 57.895 0.00 0.00 0.00 3.21
2111 2223 0.709992 AGACCTCCTCCTTCTGCTCT 59.290 55.000 0.00 0.00 0.00 4.09
2467 2579 2.172372 CCATCTGCTGCTGCTCGAC 61.172 63.158 17.00 0.00 40.48 4.20
2512 2624 0.328592 TTGCCATTGCCATTGCCATT 59.671 45.000 0.00 0.00 36.33 3.16
2513 2625 0.548989 ATTGCCATTGCCATTGCCAT 59.451 45.000 0.00 0.00 36.33 4.40
2514 2626 0.393132 CATTGCCATTGCCATTGCCA 60.393 50.000 0.00 0.00 36.33 4.92
2601 2713 0.912486 AGATGTAGTTGAGCCCCACC 59.088 55.000 0.00 0.00 0.00 4.61
2668 2780 0.388649 GTGCAGTCGTCCAAGTCGAT 60.389 55.000 0.00 0.00 39.45 3.59
2676 2788 3.916392 CTCCACGGTGCAGTCGTCC 62.916 68.421 11.47 0.00 38.94 4.79
2792 2906 3.118542 CCTCTGTTTGCTTGCTTGTTTC 58.881 45.455 0.00 0.00 0.00 2.78
2864 2997 3.202818 TCAAGTCCTGAACCCATGCATAT 59.797 43.478 0.00 0.00 0.00 1.78
2866 2999 1.355381 TCAAGTCCTGAACCCATGCAT 59.645 47.619 0.00 0.00 0.00 3.96
2867 3000 0.770499 TCAAGTCCTGAACCCATGCA 59.230 50.000 0.00 0.00 0.00 3.96
2868 3001 1.003580 TCTCAAGTCCTGAACCCATGC 59.996 52.381 0.00 0.00 32.17 4.06
2880 3013 8.795513 TGATCTCATCTCATCTTATCTCAAGTC 58.204 37.037 0.00 0.00 0.00 3.01
3004 3138 6.884472 TTGGATAAATTCACCTCCTCTGTA 57.116 37.500 0.00 0.00 0.00 2.74
3052 3191 6.094603 CAGTTTGGATAAATTCACCTCCTCTG 59.905 42.308 0.00 0.00 0.00 3.35
3053 3192 6.183347 CAGTTTGGATAAATTCACCTCCTCT 58.817 40.000 0.00 0.00 0.00 3.69
3054 3193 5.946377 ACAGTTTGGATAAATTCACCTCCTC 59.054 40.000 0.00 0.00 0.00 3.71
3055 3194 5.892348 ACAGTTTGGATAAATTCACCTCCT 58.108 37.500 0.00 0.00 0.00 3.69
3056 3195 6.590234 AACAGTTTGGATAAATTCACCTCC 57.410 37.500 0.00 0.00 0.00 4.30
3057 3196 7.433680 ACAAACAGTTTGGATAAATTCACCTC 58.566 34.615 26.32 0.00 44.81 3.85
3058 3197 7.360113 ACAAACAGTTTGGATAAATTCACCT 57.640 32.000 26.32 1.65 44.81 4.00
3059 3198 8.974408 GTAACAAACAGTTTGGATAAATTCACC 58.026 33.333 26.32 5.74 44.81 4.02
3060 3199 8.687301 CGTAACAAACAGTTTGGATAAATTCAC 58.313 33.333 26.32 10.25 44.81 3.18
3061 3200 7.863375 CCGTAACAAACAGTTTGGATAAATTCA 59.137 33.333 26.32 0.68 44.81 2.57
3062 3201 7.148869 GCCGTAACAAACAGTTTGGATAAATTC 60.149 37.037 26.32 9.14 44.81 2.17
3063 3202 6.643360 GCCGTAACAAACAGTTTGGATAAATT 59.357 34.615 26.32 14.47 44.81 1.82
3064 3203 6.153756 GCCGTAACAAACAGTTTGGATAAAT 58.846 36.000 26.32 5.03 44.81 1.40
3065 3204 5.067413 TGCCGTAACAAACAGTTTGGATAAA 59.933 36.000 26.32 7.29 44.81 1.40
3066 3205 4.579340 TGCCGTAACAAACAGTTTGGATAA 59.421 37.500 26.32 8.85 44.81 1.75
3068 3207 2.952978 TGCCGTAACAAACAGTTTGGAT 59.047 40.909 26.32 17.95 44.81 3.41
3069 3208 2.366533 TGCCGTAACAAACAGTTTGGA 58.633 42.857 26.32 13.47 44.81 3.53
3071 3210 3.485378 CACATGCCGTAACAAACAGTTTG 59.515 43.478 22.26 22.26 45.95 2.93
3072 3211 3.129638 ACACATGCCGTAACAAACAGTTT 59.870 39.130 0.00 0.00 41.64 2.66
3073 3212 2.685897 ACACATGCCGTAACAAACAGTT 59.314 40.909 0.00 0.00 44.27 3.16
3075 3214 2.032799 ACACACATGCCGTAACAAACAG 59.967 45.455 0.00 0.00 0.00 3.16
3077 3216 2.032302 TGACACACATGCCGTAACAAAC 59.968 45.455 0.00 0.00 0.00 2.93
3079 3218 1.954927 TGACACACATGCCGTAACAA 58.045 45.000 0.00 0.00 0.00 2.83
3080 3219 2.073056 GATGACACACATGCCGTAACA 58.927 47.619 0.00 0.00 39.56 2.41
3081 3220 1.060553 CGATGACACACATGCCGTAAC 59.939 52.381 0.00 0.00 39.56 2.50
3082 3221 1.067495 TCGATGACACACATGCCGTAA 60.067 47.619 0.00 0.00 39.56 3.18
3083 3222 0.528470 TCGATGACACACATGCCGTA 59.472 50.000 0.00 0.00 39.56 4.02
3084 3223 0.320334 TTCGATGACACACATGCCGT 60.320 50.000 0.00 0.00 39.56 5.68
3086 3225 1.155889 TGTTCGATGACACACATGCC 58.844 50.000 0.00 0.00 39.56 4.40
3088 3227 4.472691 AGTTTGTTCGATGACACACATG 57.527 40.909 8.73 0.00 39.56 3.21
3162 3668 9.709495 GCTAGAATTCAGTAGTAGTAGTAGCTA 57.291 37.037 8.44 0.00 0.00 3.32
3163 3669 8.212312 TGCTAGAATTCAGTAGTAGTAGTAGCT 58.788 37.037 8.44 0.00 31.39 3.32
3170 3676 8.941995 TCCATATGCTAGAATTCAGTAGTAGT 57.058 34.615 8.44 0.00 0.00 2.73
3268 3779 1.350193 TCGCTTCTCGATGTGCTTTC 58.650 50.000 0.00 0.00 43.16 2.62
3291 3802 3.517500 TGTGTGACAGGCATTATCCTACA 59.482 43.478 0.00 0.00 33.95 2.74
3292 3803 3.871594 GTGTGTGACAGGCATTATCCTAC 59.128 47.826 0.00 0.00 33.95 3.18
3299 3811 1.761449 TTGTGTGTGTGACAGGCATT 58.239 45.000 0.00 0.00 34.28 3.56
3308 3820 5.196341 TCTACTCTACCTTTGTGTGTGTG 57.804 43.478 0.00 0.00 0.00 3.82
3309 3821 5.363005 AGTTCTACTCTACCTTTGTGTGTGT 59.637 40.000 0.00 0.00 0.00 3.72
3310 3822 5.844004 AGTTCTACTCTACCTTTGTGTGTG 58.156 41.667 0.00 0.00 0.00 3.82
3311 3823 6.481434 AAGTTCTACTCTACCTTTGTGTGT 57.519 37.500 0.00 0.00 0.00 3.72
3342 3854 0.938008 GCCGTGCTTAGACTAATGCC 59.062 55.000 11.63 5.39 0.00 4.40
3392 3915 7.049754 ACTTCCTTTTAAGACGAGTTGGTAAA 58.950 34.615 0.00 0.00 0.00 2.01
3403 3926 5.624052 CGGAGGGAGTACTTCCTTTTAAGAC 60.624 48.000 24.27 9.09 45.98 3.01
3423 3946 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
3424 3947 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3425 3948 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3426 3949 5.227908 ACAACGCTCTTATATTATGGGACG 58.772 41.667 0.00 0.00 0.00 4.79
3427 3950 6.704493 TCAACAACGCTCTTATATTATGGGAC 59.296 38.462 0.00 0.00 0.00 4.46
3428 3951 6.704493 GTCAACAACGCTCTTATATTATGGGA 59.296 38.462 0.00 0.00 0.00 4.37
3429 3952 6.481976 TGTCAACAACGCTCTTATATTATGGG 59.518 38.462 0.00 0.00 0.00 4.00
3430 3953 7.438160 TCTGTCAACAACGCTCTTATATTATGG 59.562 37.037 0.00 0.00 0.00 2.74
3431 3954 8.352752 TCTGTCAACAACGCTCTTATATTATG 57.647 34.615 0.00 0.00 0.00 1.90
3432 3955 7.653713 CCTCTGTCAACAACGCTCTTATATTAT 59.346 37.037 0.00 0.00 0.00 1.28
3433 3956 6.978659 CCTCTGTCAACAACGCTCTTATATTA 59.021 38.462 0.00 0.00 0.00 0.98
3434 3957 5.812642 CCTCTGTCAACAACGCTCTTATATT 59.187 40.000 0.00 0.00 0.00 1.28
3435 3958 5.352284 CCTCTGTCAACAACGCTCTTATAT 58.648 41.667 0.00 0.00 0.00 0.86
3436 3959 4.381612 CCCTCTGTCAACAACGCTCTTATA 60.382 45.833 0.00 0.00 0.00 0.98
3437 3960 3.589988 CCTCTGTCAACAACGCTCTTAT 58.410 45.455 0.00 0.00 0.00 1.73
3438 3961 2.288825 CCCTCTGTCAACAACGCTCTTA 60.289 50.000 0.00 0.00 0.00 2.10
3439 3962 1.541233 CCCTCTGTCAACAACGCTCTT 60.541 52.381 0.00 0.00 0.00 2.85
3440 3963 0.034059 CCCTCTGTCAACAACGCTCT 59.966 55.000 0.00 0.00 0.00 4.09
3441 3964 0.033504 TCCCTCTGTCAACAACGCTC 59.966 55.000 0.00 0.00 0.00 5.03
3442 3965 0.034059 CTCCCTCTGTCAACAACGCT 59.966 55.000 0.00 0.00 0.00 5.07
3443 3966 0.249911 ACTCCCTCTGTCAACAACGC 60.250 55.000 0.00 0.00 0.00 4.84
3444 3967 3.380479 TTACTCCCTCTGTCAACAACG 57.620 47.619 0.00 0.00 0.00 4.10
3445 3968 6.049790 GGATATTACTCCCTCTGTCAACAAC 58.950 44.000 0.00 0.00 0.00 3.32
3446 3969 5.964477 AGGATATTACTCCCTCTGTCAACAA 59.036 40.000 0.00 0.00 35.79 2.83
3447 3970 5.529289 AGGATATTACTCCCTCTGTCAACA 58.471 41.667 0.00 0.00 35.79 3.33
3448 3971 7.451877 TCATAGGATATTACTCCCTCTGTCAAC 59.548 40.741 0.00 0.00 35.79 3.18
3449 3972 7.535738 TCATAGGATATTACTCCCTCTGTCAA 58.464 38.462 0.00 0.00 35.79 3.18
3450 3973 7.103745 TCATAGGATATTACTCCCTCTGTCA 57.896 40.000 0.00 0.00 35.79 3.58
3451 3974 9.702253 TTATCATAGGATATTACTCCCTCTGTC 57.298 37.037 0.00 0.00 35.96 3.51
3473 3996 3.185797 CGGCTTGGCTTTACGGTATTATC 59.814 47.826 0.00 0.00 0.00 1.75
3508 4036 1.098050 GCTGCTAATTGACCCACCAG 58.902 55.000 0.00 0.00 0.00 4.00
3611 4260 1.338973 CAAATGATCCCCGGCAATCTG 59.661 52.381 13.51 2.95 0.00 2.90
3644 4293 6.172136 TCTCTTTCATTTCAAAATGGGCAA 57.828 33.333 13.88 5.85 44.51 4.52
3679 4328 4.219070 CAGGTTGTGGTGATGATTGATTGT 59.781 41.667 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.