Multiple sequence alignment - TraesCS4A01G013500

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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 TraesCS4A01G013500 chr4A 100.000 4911 0 0 1 4911 7744402 7749312 0.000000e+00 9070
1 TraesCS4A01G013500 chr4A 94.624 93 4 1 45 136 707022185 707022277 5.120000e-30 143
2 TraesCS4A01G013500 chr4D 95.279 2796 100 22 2139 4911 460483193 460480407 0.000000e+00 4403
3 TraesCS4A01G013500 chr4D 89.244 1125 87 24 730 1842 460484689 460483587 0.000000e+00 1376
4 TraesCS4A01G013500 chr4D 89.149 599 54 8 128 724 460485640 460485051 0.000000e+00 736
5 TraesCS4A01G013500 chr4B 93.110 2627 117 30 1947 4544 574952475 574949884 0.000000e+00 3790
6 TraesCS4A01G013500 chr4B 87.959 1578 136 30 394 1950 574954050 574952506 0.000000e+00 1812
7 TraesCS4A01G013500 chr4B 88.629 299 16 4 4619 4911 574949849 574949563 1.010000e-91 348
8 TraesCS4A01G013500 chr5D 94.286 105 5 1 45 148 418294205 418294309 5.090000e-35 159
9 TraesCS4A01G013500 chr2A 96.875 96 2 1 45 139 497997508 497997413 5.090000e-35 159
10 TraesCS4A01G013500 chr2A 94.681 94 4 1 45 137 169355649 169355556 1.420000e-30 145
11 TraesCS4A01G013500 chr7D 95.652 92 3 1 45 135 208291262 208291171 3.960000e-31 147
12 TraesCS4A01G013500 chr7D 94.624 93 4 1 45 136 369463367 369463275 5.120000e-30 143
13 TraesCS4A01G013500 chr6B 93.750 96 5 1 45 139 347227234 347227139 5.120000e-30 143
14 TraesCS4A01G013500 chr1D 94.624 93 4 1 45 136 420948091 420947999 5.120000e-30 143
15 TraesCS4A01G013500 chr3D 92.857 98 5 2 45 140 563449022 563448925 1.840000e-29 141


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 TraesCS4A01G013500 chr4A 7744402 7749312 4910 False 9070.000000 9070 100.000000 1 4911 1 chr4A.!!$F1 4910
1 TraesCS4A01G013500 chr4D 460480407 460485640 5233 True 2171.666667 4403 91.224000 128 4911 3 chr4D.!!$R1 4783
2 TraesCS4A01G013500 chr4B 574949563 574954050 4487 True 1983.333333 3790 89.899333 394 4911 3 chr4B.!!$R1 4517

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
58 59 0.032017 AGGCCTCTAGGTCGTTGGAT 60.032 55.0 0.0 0.0 46.49 3.41 F
226 227 0.106708 TGCCATCTTGTCTATCCCGC 59.893 55.0 0.0 0.0 0.00 6.13 F
1332 1710 0.464036 TCGTGTGCTCTGGTTTGAGT 59.536 50.0 0.0 0.0 36.51 3.41 F
1560 1939 0.527565 GTACCGAAGCCCGTACAAGA 59.472 55.0 0.0 0.0 36.31 3.02 F
3231 3740 0.961753 GCCCTTTCCCAACTGAACTG 59.038 55.0 0.0 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 2117 0.331278 TACCAGCCCAATGTTCCAGG 59.669 55.000 0.00 0.00 0.0 4.45 R
1884 2318 0.892755 TTTACGGCCAGATGTCGAGT 59.107 50.000 2.24 0.00 0.0 4.18 R
3231 3740 1.280421 ACATCACCTTCCTCTCCAAGC 59.720 52.381 0.00 0.00 0.0 4.01 R
3264 3773 2.747446 AGTCGTTCCAAATTCCATTCCG 59.253 45.455 0.00 0.00 0.0 4.30 R
4502 5038 1.202568 TCATGTAGCTCGGCATGAAGG 60.203 52.381 19.61 2.08 45.6 3.46 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
38 39 4.948576 CGGTTAAACCAAACGCCC 57.051 55.556 0.00 0.00 41.13 6.13
39 40 2.031360 CGGTTAAACCAAACGCCCA 58.969 52.632 0.00 0.00 41.13 5.36
40 41 0.039888 CGGTTAAACCAAACGCCCAG 60.040 55.000 0.00 0.00 41.13 4.45
41 42 0.315886 GGTTAAACCAAACGCCCAGG 59.684 55.000 0.00 0.00 38.42 4.45
42 43 0.319211 GTTAAACCAAACGCCCAGGC 60.319 55.000 0.00 0.00 37.85 4.85
43 44 1.465200 TTAAACCAAACGCCCAGGCC 61.465 55.000 2.37 0.00 37.98 5.19
44 45 2.360439 TAAACCAAACGCCCAGGCCT 62.360 55.000 0.00 0.00 37.98 5.19
45 46 4.660938 ACCAAACGCCCAGGCCTC 62.661 66.667 0.00 0.00 37.98 4.70
46 47 4.351054 CCAAACGCCCAGGCCTCT 62.351 66.667 0.00 0.00 37.98 3.69
47 48 2.668632 CAAACGCCCAGGCCTCTA 59.331 61.111 0.00 0.00 37.98 2.43
48 49 1.450312 CAAACGCCCAGGCCTCTAG 60.450 63.158 0.00 0.00 37.98 2.43
49 50 2.670148 AAACGCCCAGGCCTCTAGG 61.670 63.158 0.00 5.27 37.98 3.02
50 51 3.925914 AACGCCCAGGCCTCTAGGT 62.926 63.158 0.00 0.00 37.98 3.08
51 52 3.541713 CGCCCAGGCCTCTAGGTC 61.542 72.222 0.00 0.00 40.99 3.85
52 53 3.541713 GCCCAGGCCTCTAGGTCG 61.542 72.222 0.00 0.00 46.49 4.79
53 54 2.042843 CCCAGGCCTCTAGGTCGT 60.043 66.667 0.00 0.00 46.49 4.34
54 55 1.686110 CCCAGGCCTCTAGGTCGTT 60.686 63.158 0.00 0.00 46.49 3.85
55 56 1.517832 CCAGGCCTCTAGGTCGTTG 59.482 63.158 0.00 0.00 46.49 4.10
56 57 1.517832 CAGGCCTCTAGGTCGTTGG 59.482 63.158 0.00 0.00 46.49 3.77
57 58 0.970937 CAGGCCTCTAGGTCGTTGGA 60.971 60.000 0.00 0.00 46.49 3.53
58 59 0.032017 AGGCCTCTAGGTCGTTGGAT 60.032 55.000 0.00 0.00 46.49 3.41
59 60 0.831307 GGCCTCTAGGTCGTTGGATT 59.169 55.000 0.00 0.00 37.57 3.01
60 61 1.473434 GGCCTCTAGGTCGTTGGATTG 60.473 57.143 0.00 0.00 37.57 2.67
61 62 1.480954 GCCTCTAGGTCGTTGGATTGA 59.519 52.381 0.00 0.00 37.57 2.57
62 63 2.738964 GCCTCTAGGTCGTTGGATTGAC 60.739 54.545 0.00 0.00 37.57 3.18
63 64 2.496070 CCTCTAGGTCGTTGGATTGACA 59.504 50.000 0.00 0.00 36.83 3.58
64 65 3.133003 CCTCTAGGTCGTTGGATTGACAT 59.867 47.826 0.00 0.00 36.83 3.06
65 66 4.115516 CTCTAGGTCGTTGGATTGACATG 58.884 47.826 0.00 0.00 36.83 3.21
66 67 3.767131 TCTAGGTCGTTGGATTGACATGA 59.233 43.478 0.00 0.00 36.83 3.07
67 68 3.634397 AGGTCGTTGGATTGACATGAT 57.366 42.857 0.00 0.00 36.83 2.45
68 69 3.955471 AGGTCGTTGGATTGACATGATT 58.045 40.909 0.00 0.00 36.83 2.57
69 70 4.335416 AGGTCGTTGGATTGACATGATTT 58.665 39.130 0.00 0.00 36.83 2.17
70 71 4.156556 AGGTCGTTGGATTGACATGATTTG 59.843 41.667 0.00 0.00 36.83 2.32
71 72 4.155826 GGTCGTTGGATTGACATGATTTGA 59.844 41.667 0.00 0.00 36.83 2.69
72 73 5.163622 GGTCGTTGGATTGACATGATTTGAT 60.164 40.000 0.00 0.00 36.83 2.57
73 74 5.740569 GTCGTTGGATTGACATGATTTGATG 59.259 40.000 0.00 0.00 35.20 3.07
74 75 5.038683 CGTTGGATTGACATGATTTGATGG 58.961 41.667 0.00 0.00 0.00 3.51
75 76 4.659111 TGGATTGACATGATTTGATGGC 57.341 40.909 0.00 0.00 0.00 4.40
76 77 3.385433 TGGATTGACATGATTTGATGGCC 59.615 43.478 0.00 0.00 29.16 5.36
77 78 3.551454 GGATTGACATGATTTGATGGCCG 60.551 47.826 0.00 0.00 29.16 6.13
78 79 2.416680 TGACATGATTTGATGGCCGA 57.583 45.000 0.00 0.00 29.16 5.54
79 80 2.291365 TGACATGATTTGATGGCCGAG 58.709 47.619 0.00 0.00 29.16 4.63
80 81 2.093021 TGACATGATTTGATGGCCGAGA 60.093 45.455 0.00 0.00 29.16 4.04
81 82 3.144506 GACATGATTTGATGGCCGAGAT 58.855 45.455 0.00 0.00 0.00 2.75
82 83 3.559069 ACATGATTTGATGGCCGAGATT 58.441 40.909 0.00 0.00 0.00 2.40
83 84 4.717877 ACATGATTTGATGGCCGAGATTA 58.282 39.130 0.00 0.00 0.00 1.75
84 85 5.132502 ACATGATTTGATGGCCGAGATTAA 58.867 37.500 0.00 0.00 0.00 1.40
85 86 5.771666 ACATGATTTGATGGCCGAGATTAAT 59.228 36.000 0.00 0.00 0.00 1.40
86 87 6.266103 ACATGATTTGATGGCCGAGATTAATT 59.734 34.615 0.00 0.00 0.00 1.40
87 88 6.075762 TGATTTGATGGCCGAGATTAATTG 57.924 37.500 0.00 0.00 0.00 2.32
88 89 5.827267 TGATTTGATGGCCGAGATTAATTGA 59.173 36.000 0.00 0.00 0.00 2.57
89 90 6.320926 TGATTTGATGGCCGAGATTAATTGAA 59.679 34.615 0.00 0.00 0.00 2.69
90 91 6.713762 TTTGATGGCCGAGATTAATTGAAT 57.286 33.333 0.00 0.00 0.00 2.57
91 92 5.947228 TGATGGCCGAGATTAATTGAATC 57.053 39.130 0.00 0.00 43.89 2.52
92 93 4.761739 TGATGGCCGAGATTAATTGAATCC 59.238 41.667 0.00 0.00 44.54 3.01
93 94 3.138304 TGGCCGAGATTAATTGAATCCG 58.862 45.455 0.00 1.33 44.54 4.18
94 95 2.095718 GGCCGAGATTAATTGAATCCGC 60.096 50.000 0.00 0.00 44.54 5.54
95 96 2.095718 GCCGAGATTAATTGAATCCGCC 60.096 50.000 0.00 0.00 44.54 6.13
96 97 2.484264 CCGAGATTAATTGAATCCGCCC 59.516 50.000 0.00 0.00 44.54 6.13
97 98 3.403038 CGAGATTAATTGAATCCGCCCT 58.597 45.455 0.00 0.00 44.54 5.19
98 99 3.815401 CGAGATTAATTGAATCCGCCCTT 59.185 43.478 0.00 0.00 44.54 3.95
99 100 4.275936 CGAGATTAATTGAATCCGCCCTTT 59.724 41.667 0.00 0.00 44.54 3.11
100 101 5.520376 AGATTAATTGAATCCGCCCTTTG 57.480 39.130 0.00 0.00 44.54 2.77
101 102 4.342092 AGATTAATTGAATCCGCCCTTTGG 59.658 41.667 0.00 0.00 44.54 3.28
102 103 2.230130 AATTGAATCCGCCCTTTGGA 57.770 45.000 0.00 0.00 40.46 3.53
104 105 1.762708 TTGAATCCGCCCTTTGGATC 58.237 50.000 0.00 0.00 45.46 3.36
105 106 0.918983 TGAATCCGCCCTTTGGATCT 59.081 50.000 0.00 0.00 45.46 2.75
106 107 1.284785 TGAATCCGCCCTTTGGATCTT 59.715 47.619 0.00 0.00 45.46 2.40
107 108 2.291540 TGAATCCGCCCTTTGGATCTTT 60.292 45.455 0.00 0.00 45.46 2.52
108 109 2.532250 ATCCGCCCTTTGGATCTTTT 57.468 45.000 0.00 0.00 42.62 2.27
109 110 2.302587 TCCGCCCTTTGGATCTTTTT 57.697 45.000 0.00 0.00 0.00 1.94
110 111 3.443145 TCCGCCCTTTGGATCTTTTTA 57.557 42.857 0.00 0.00 0.00 1.52
111 112 3.976015 TCCGCCCTTTGGATCTTTTTAT 58.024 40.909 0.00 0.00 0.00 1.40
112 113 5.118729 TCCGCCCTTTGGATCTTTTTATA 57.881 39.130 0.00 0.00 0.00 0.98
113 114 5.701224 TCCGCCCTTTGGATCTTTTTATAT 58.299 37.500 0.00 0.00 0.00 0.86
114 115 6.133356 TCCGCCCTTTGGATCTTTTTATATT 58.867 36.000 0.00 0.00 0.00 1.28
115 116 6.040391 TCCGCCCTTTGGATCTTTTTATATTG 59.960 38.462 0.00 0.00 0.00 1.90
116 117 6.215845 CGCCCTTTGGATCTTTTTATATTGG 58.784 40.000 0.00 0.00 0.00 3.16
117 118 6.183360 CGCCCTTTGGATCTTTTTATATTGGT 60.183 38.462 0.00 0.00 0.00 3.67
118 119 7.013846 CGCCCTTTGGATCTTTTTATATTGGTA 59.986 37.037 0.00 0.00 0.00 3.25
119 120 8.870116 GCCCTTTGGATCTTTTTATATTGGTAT 58.130 33.333 0.00 0.00 0.00 2.73
195 196 8.659527 TGACATAATGATATAAGAGGCAAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
214 215 2.627515 ACATCACGCTAATGCCATCT 57.372 45.000 0.00 0.00 35.36 2.90
226 227 0.106708 TGCCATCTTGTCTATCCCGC 59.893 55.000 0.00 0.00 0.00 6.13
231 232 3.545703 CATCTTGTCTATCCCGCCTTTT 58.454 45.455 0.00 0.00 0.00 2.27
273 274 3.004734 CCTTTGTTGTTAGGCTCTTGTGG 59.995 47.826 0.00 0.00 0.00 4.17
283 284 1.815421 CTCTTGTGGCCGCGCTATT 60.815 57.895 12.58 0.00 0.00 1.73
284 285 2.040213 CTCTTGTGGCCGCGCTATTG 62.040 60.000 12.58 0.00 0.00 1.90
286 287 3.910914 TTGTGGCCGCGCTATTGGT 62.911 57.895 12.58 0.00 0.00 3.67
303 304 0.804989 GGTTGTTCTTCCTCGCATGG 59.195 55.000 0.00 0.00 0.00 3.66
310 311 3.203086 TTCCTCGCATGGGGCACAA 62.203 57.895 10.21 0.00 45.17 3.33
311 312 2.440796 CCTCGCATGGGGCACAAT 60.441 61.111 10.21 0.00 45.17 2.71
319 320 2.415893 GCATGGGGCACAATATATTCGC 60.416 50.000 0.00 7.56 43.97 4.70
322 323 3.146066 TGGGGCACAATATATTCGCTTC 58.854 45.455 13.47 8.43 0.00 3.86
323 324 2.488153 GGGGCACAATATATTCGCTTCC 59.512 50.000 13.47 11.84 0.00 3.46
329 330 4.821805 CACAATATATTCGCTTCCCAACCT 59.178 41.667 0.00 0.00 0.00 3.50
341 342 1.957877 TCCCAACCTTTTTGTTAGCGG 59.042 47.619 0.00 0.00 0.00 5.52
342 343 1.684450 CCCAACCTTTTTGTTAGCGGT 59.316 47.619 0.00 0.00 0.00 5.68
344 345 2.544903 CCAACCTTTTTGTTAGCGGTGG 60.545 50.000 0.00 0.00 0.00 4.61
362 363 5.739358 GCGGTGGAGCTAGTACTTCAAATAT 60.739 44.000 0.00 0.00 0.00 1.28
365 366 6.702282 GGTGGAGCTAGTACTTCAAATATCAC 59.298 42.308 0.00 0.77 0.00 3.06
368 369 6.418226 GGAGCTAGTACTTCAAATATCACACG 59.582 42.308 0.00 0.00 0.00 4.49
389 390 6.431852 ACACGTATTAAAATGGCCAAGTACTT 59.568 34.615 10.96 1.12 0.00 2.24
398 399 7.803279 AAATGGCCAAGTACTTAACTATAGC 57.197 36.000 10.96 3.15 37.50 2.97
403 404 6.346896 GCCAAGTACTTAACTATAGCCTGTT 58.653 40.000 8.04 0.00 37.50 3.16
526 529 5.372343 TGATGCATCACCTACATAACCTT 57.628 39.130 25.42 0.00 0.00 3.50
537 540 8.682710 TCACCTACATAACCTTAAAATTCATGC 58.317 33.333 0.00 0.00 0.00 4.06
569 572 1.004610 CAAGGCATAACGTCGCTCATG 60.005 52.381 0.00 0.00 0.00 3.07
603 606 4.396790 TCCACAGCAAATAATTAACCCGAC 59.603 41.667 0.00 0.00 0.00 4.79
635 638 9.853555 GAATCACACATGTAAATGTCCATAAAA 57.146 29.630 0.00 0.00 31.37 1.52
672 675 6.506500 ACAAGAGGCAGAATAACAAATGAG 57.493 37.500 0.00 0.00 0.00 2.90
676 679 4.592942 AGGCAGAATAACAAATGAGCAGA 58.407 39.130 0.00 0.00 0.00 4.26
677 680 4.397417 AGGCAGAATAACAAATGAGCAGAC 59.603 41.667 0.00 0.00 0.00 3.51
680 683 6.327934 GCAGAATAACAAATGAGCAGACAAT 58.672 36.000 0.00 0.00 0.00 2.71
682 685 6.685828 CAGAATAACAAATGAGCAGACAATCG 59.314 38.462 0.00 0.00 0.00 3.34
683 686 6.595326 AGAATAACAAATGAGCAGACAATCGA 59.405 34.615 0.00 0.00 0.00 3.59
684 687 6.932356 ATAACAAATGAGCAGACAATCGAT 57.068 33.333 0.00 0.00 0.00 3.59
688 691 6.546395 ACAAATGAGCAGACAATCGATTTAC 58.454 36.000 8.21 5.60 0.00 2.01
698 701 7.304735 CAGACAATCGATTTACCATGTGAAAA 58.695 34.615 8.21 0.00 0.00 2.29
699 702 7.271223 CAGACAATCGATTTACCATGTGAAAAC 59.729 37.037 8.21 0.00 0.00 2.43
706 709 2.264005 ACCATGTGAAAACGTAGCCA 57.736 45.000 0.00 0.00 0.00 4.75
708 711 2.747446 ACCATGTGAAAACGTAGCCATC 59.253 45.455 0.00 0.00 0.00 3.51
710 713 2.442212 TGTGAAAACGTAGCCATCGA 57.558 45.000 0.00 0.00 0.00 3.59
725 728 2.033801 CCATCGAAAGGACATCAATGGC 59.966 50.000 1.18 0.00 34.16 4.40
738 1097 6.357579 ACATCAATGGCTGTAAAAATTCCA 57.642 33.333 0.00 0.00 0.00 3.53
802 1170 1.580942 CCAAGATTGGTGCACGGTG 59.419 57.895 11.45 3.15 43.43 4.94
825 1193 1.328279 TCTCTCTTTGGTCGACAGCA 58.672 50.000 18.91 3.92 0.00 4.41
828 1196 2.210116 TCTCTTTGGTCGACAGCAAAC 58.790 47.619 18.91 0.00 43.50 2.93
832 1200 0.878523 TTGGTCGACAGCAAACGAGG 60.879 55.000 18.91 0.00 37.07 4.63
834 1202 2.357034 TCGACAGCAAACGAGGCC 60.357 61.111 0.00 0.00 34.49 5.19
845 1213 0.909610 AACGAGGCCAAGAGGATCCA 60.910 55.000 15.82 0.00 36.89 3.41
860 1229 6.266857 AGAGGATCCAATTCCCTTTGAAAAT 58.733 36.000 15.82 0.00 36.35 1.82
898 1267 3.327757 TCCCCATCATTTTCTATCCCTCG 59.672 47.826 0.00 0.00 0.00 4.63
902 1275 6.006449 CCCATCATTTTCTATCCCTCGAAAT 58.994 40.000 0.00 0.00 0.00 2.17
904 1277 7.665559 CCCATCATTTTCTATCCCTCGAAATAA 59.334 37.037 0.00 0.00 0.00 1.40
961 1335 0.872388 ACTTAAACGGAAAGCAGCGG 59.128 50.000 0.00 0.00 0.00 5.52
1022 1397 2.583441 CGCTCTCCACCCTCAACCA 61.583 63.158 0.00 0.00 0.00 3.67
1023 1398 1.003233 GCTCTCCACCCTCAACCAC 60.003 63.158 0.00 0.00 0.00 4.16
1024 1399 1.679898 CTCTCCACCCTCAACCACC 59.320 63.158 0.00 0.00 0.00 4.61
1206 1584 4.803426 CAGGTCTCCGGCGTGCTC 62.803 72.222 6.01 0.00 0.00 4.26
1331 1709 0.861837 GTCGTGTGCTCTGGTTTGAG 59.138 55.000 0.00 0.00 37.16 3.02
1332 1710 0.464036 TCGTGTGCTCTGGTTTGAGT 59.536 50.000 0.00 0.00 36.51 3.41
1364 1743 2.674852 TCATTGTCGATTGAAGCTGCTC 59.325 45.455 1.00 0.00 0.00 4.26
1389 1768 2.972505 CCACTGCGCGTTCCAGTT 60.973 61.111 14.09 0.00 41.34 3.16
1392 1771 1.522806 ACTGCGCGTTCCAGTTGAA 60.523 52.632 8.43 0.00 40.45 2.69
1393 1772 1.092921 ACTGCGCGTTCCAGTTGAAA 61.093 50.000 8.43 0.00 40.45 2.69
1399 1778 3.601360 GCGCGTTCCAGTTGAAATTTTTG 60.601 43.478 8.43 0.00 33.94 2.44
1400 1779 3.794028 CGCGTTCCAGTTGAAATTTTTGA 59.206 39.130 0.00 0.00 33.94 2.69
1401 1780 4.444056 CGCGTTCCAGTTGAAATTTTTGAT 59.556 37.500 0.00 0.00 33.94 2.57
1402 1781 5.627367 CGCGTTCCAGTTGAAATTTTTGATA 59.373 36.000 0.00 0.00 33.94 2.15
1403 1782 6.307800 CGCGTTCCAGTTGAAATTTTTGATAT 59.692 34.615 0.00 0.00 33.94 1.63
1404 1783 7.461416 CGCGTTCCAGTTGAAATTTTTGATATC 60.461 37.037 0.00 0.00 33.94 1.63
1406 1785 7.537306 CGTTCCAGTTGAAATTTTTGATATCGT 59.463 33.333 0.00 0.00 33.94 3.73
1407 1786 9.834628 GTTCCAGTTGAAATTTTTGATATCGTA 57.165 29.630 0.00 0.00 33.94 3.43
1424 1803 2.030540 TCGTATACGCTTGTAGGATGGC 60.031 50.000 20.42 0.00 39.60 4.40
1427 1806 3.398920 CGCTTGTAGGATGGCGTG 58.601 61.111 0.00 0.00 42.23 5.34
1432 1811 2.550978 CTTGTAGGATGGCGTGGTAAG 58.449 52.381 0.00 0.00 0.00 2.34
1449 1828 5.068591 GTGGTAAGAGTTGTTTTGGTGGATT 59.931 40.000 0.00 0.00 0.00 3.01
1454 1833 3.989817 GAGTTGTTTTGGTGGATTGATGC 59.010 43.478 0.00 0.00 0.00 3.91
1480 1859 4.585955 TCCGGATGTTAGAGTAATCTGC 57.414 45.455 0.00 0.00 0.00 4.26
1492 1871 5.593010 AGAGTAATCTGCGTGTAGAATTCC 58.407 41.667 0.65 0.00 0.00 3.01
1528 1907 3.945285 TGTTTGGAAGAGGTGTGTTTCTC 59.055 43.478 0.00 0.00 0.00 2.87
1560 1939 0.527565 GTACCGAAGCCCGTACAAGA 59.472 55.000 0.00 0.00 36.31 3.02
1561 1940 1.067635 GTACCGAAGCCCGTACAAGAA 60.068 52.381 0.00 0.00 36.31 2.52
1599 1978 5.302823 CCCCAAAGATGTTAATTCTGGGATC 59.697 44.000 10.21 0.00 31.15 3.36
1635 2014 7.678947 AAAATATGTATAGTGGAGCTCATGC 57.321 36.000 17.19 4.49 40.05 4.06
1692 2071 7.607250 TCGATTTTGTTTAATATTGGGTTGCT 58.393 30.769 0.00 0.00 0.00 3.91
1732 2115 7.666623 TCTTCTTTTTACATTTTGTGGATCCC 58.333 34.615 9.90 0.85 0.00 3.85
1734 2117 3.859411 TTTACATTTTGTGGATCCCGC 57.141 42.857 9.90 2.62 34.12 6.13
1754 2137 1.683011 CCTGGAACATTGGGCTGGTAG 60.683 57.143 0.00 0.00 38.20 3.18
1759 2142 3.560453 GGAACATTGGGCTGGTAGTTACA 60.560 47.826 0.00 0.00 0.00 2.41
1791 2175 5.809001 TGGATATTTGATCCTGATAGCCAC 58.191 41.667 11.01 0.00 37.02 5.01
1843 2227 5.559148 ATCTGGTAGGATGAAAGATGGAC 57.441 43.478 0.00 0.00 0.00 4.02
1864 2298 3.190535 ACGTTAATTTCATGTCCAGTGGC 59.809 43.478 3.51 0.00 0.00 5.01
1866 2300 4.437390 CGTTAATTTCATGTCCAGTGGCTC 60.437 45.833 3.51 0.43 0.00 4.70
1884 2318 6.664816 AGTGGCTCCTAAATGAAATGAATTGA 59.335 34.615 0.00 0.00 0.00 2.57
1885 2319 6.753744 GTGGCTCCTAAATGAAATGAATTGAC 59.246 38.462 0.00 0.00 0.00 3.18
1888 2322 6.909357 GCTCCTAAATGAAATGAATTGACTCG 59.091 38.462 0.00 0.00 0.00 4.18
1897 2331 2.621338 TGAATTGACTCGACATCTGGC 58.379 47.619 0.00 0.00 0.00 4.85
1977 2452 6.362283 GGTTGGTAAACAATCTGATTTGTTCG 59.638 38.462 14.26 2.28 46.33 3.95
1996 2471 1.134965 CGACTCACTTAGGCTTGAGGG 60.135 57.143 16.74 6.57 43.12 4.30
2013 2489 5.387113 TGAGGGTTTACCATAATCTGCAT 57.613 39.130 0.69 0.00 43.89 3.96
2017 2493 5.132648 AGGGTTTACCATAATCTGCATCAGA 59.867 40.000 0.69 0.00 42.96 3.27
2041 2520 4.142271 CCTCTGTACTTTGGTTGTTTTGCA 60.142 41.667 0.00 0.00 0.00 4.08
2059 2538 7.704472 TGTTTTGCATACTCTTTCGATTTTTGT 59.296 29.630 0.00 0.00 0.00 2.83
2062 2541 6.837992 TGCATACTCTTTCGATTTTTGTACC 58.162 36.000 0.00 0.00 0.00 3.34
2066 2545 9.146984 CATACTCTTTCGATTTTTGTACCAGTA 57.853 33.333 0.00 0.00 0.00 2.74
2076 2555 5.395682 TTTTGTACCAGTAGTGTATCGCT 57.604 39.130 0.00 0.00 0.00 4.93
2077 2556 5.395682 TTTGTACCAGTAGTGTATCGCTT 57.604 39.130 0.00 0.00 0.00 4.68
2078 2557 4.365899 TGTACCAGTAGTGTATCGCTTG 57.634 45.455 0.00 0.00 0.00 4.01
2079 2558 3.760151 TGTACCAGTAGTGTATCGCTTGT 59.240 43.478 0.00 0.00 0.00 3.16
2080 2559 4.943093 TGTACCAGTAGTGTATCGCTTGTA 59.057 41.667 0.00 0.00 0.00 2.41
2083 2562 5.348986 ACCAGTAGTGTATCGCTTGTATTG 58.651 41.667 0.00 0.00 0.00 1.90
2095 2574 6.494893 TCGCTTGTATTGTAGCAATCTTTT 57.505 33.333 0.00 0.00 37.23 2.27
2100 2579 9.626045 GCTTGTATTGTAGCAATCTTTTAACTT 57.374 29.630 0.00 0.00 37.35 2.66
2156 2663 5.763876 ACTACTGCTCCTAAAAGGTCATT 57.236 39.130 0.00 0.00 36.53 2.57
2188 2695 9.869757 ATTTTTGTGAGTTTAATATGGTTAGCC 57.130 29.630 0.00 0.00 0.00 3.93
2227 2734 8.807948 TGATTAGTTTAGATTTCCCTTTCCTG 57.192 34.615 0.00 0.00 0.00 3.86
2343 2850 5.071250 TGGGATGTAGCATCGGTACTTAATT 59.929 40.000 5.10 0.00 37.41 1.40
2344 2851 5.995897 GGGATGTAGCATCGGTACTTAATTT 59.004 40.000 5.10 0.00 37.41 1.82
2346 2853 6.073222 GGATGTAGCATCGGTACTTAATTTGG 60.073 42.308 5.10 0.00 37.41 3.28
2347 2854 5.736813 TGTAGCATCGGTACTTAATTTGGT 58.263 37.500 5.10 0.00 37.41 3.67
2372 2879 1.242076 CCAGTTGGCCACTTCTCTTG 58.758 55.000 3.88 0.00 30.92 3.02
2579 3086 4.142403 GGCGAAATTGATGGTCTTCAATCA 60.142 41.667 10.98 0.00 43.73 2.57
2619 3126 3.901222 TGGAAGAATACTGGTGTCTGACA 59.099 43.478 6.36 6.36 0.00 3.58
2810 3317 7.346751 TGGGGATAAGCTTGATGTTTTATTC 57.653 36.000 9.86 0.00 0.00 1.75
3062 3569 1.526575 CCGCTGGTGGAATTTGCACT 61.527 55.000 18.73 0.00 38.83 4.40
3231 3740 0.961753 GCCCTTTCCCAACTGAACTG 59.038 55.000 0.00 0.00 0.00 3.16
3264 3773 2.239907 AGGTGATGTTCTTAGGAAGGCC 59.760 50.000 0.00 0.00 31.46 5.19
3539 4050 7.279750 TGTGTTTACATGTCTGAGTAGTACA 57.720 36.000 0.00 0.00 0.00 2.90
3602 4113 6.591935 TGTTCTTTCTCTGGTTGTAAGATGT 58.408 36.000 0.00 0.00 0.00 3.06
3649 4160 7.303261 GCTTTAGTTCTGTGGTATTGTAAACC 58.697 38.462 0.00 0.00 37.53 3.27
3778 4289 1.275666 CTGGGTGGGACAGTGACATA 58.724 55.000 0.00 0.00 41.80 2.29
3849 4360 1.539827 GGAGAGGATAGAAGAGCTCGC 59.460 57.143 8.37 4.71 0.00 5.03
3971 4482 4.820894 AATTCAGTCTTAACTAGGCCGT 57.179 40.909 0.00 0.00 33.25 5.68
3974 4485 2.895404 TCAGTCTTAACTAGGCCGTTGT 59.105 45.455 6.30 0.00 33.25 3.32
4026 4537 2.322161 CCAATCGTAGCGGGTAATACG 58.678 52.381 0.00 0.00 44.66 3.06
4231 4743 1.615392 GCTGAATGCTTTCTTGTGGGT 59.385 47.619 12.96 0.00 38.95 4.51
4378 4914 4.613925 ATGACGTTGATGCTATCTGGAT 57.386 40.909 0.00 0.00 0.00 3.41
4379 4915 5.728637 ATGACGTTGATGCTATCTGGATA 57.271 39.130 0.00 0.00 0.00 2.59
4380 4916 5.529581 TGACGTTGATGCTATCTGGATAA 57.470 39.130 0.00 0.00 0.00 1.75
4381 4917 5.532557 TGACGTTGATGCTATCTGGATAAG 58.467 41.667 0.00 0.00 0.00 1.73
4382 4918 5.301805 TGACGTTGATGCTATCTGGATAAGA 59.698 40.000 0.00 0.00 39.94 2.10
4385 4921 7.220030 ACGTTGATGCTATCTGGATAAGATTT 58.780 34.615 0.00 0.00 43.52 2.17
4427 4963 5.055265 TGTTGGTCTCATTTTCCTGGTTA 57.945 39.130 0.00 0.00 0.00 2.85
4512 5048 3.535561 ACAGATCTAAACCTTCATGCCG 58.464 45.455 0.00 0.00 0.00 5.69
4514 5050 3.806521 CAGATCTAAACCTTCATGCCGAG 59.193 47.826 0.00 0.00 0.00 4.63
4532 5068 2.739932 CGAGCTACATGAAGAACCTGGG 60.740 54.545 0.00 0.00 0.00 4.45
4549 5085 2.959707 CTGGGAGCTAAACCTCGTAGAT 59.040 50.000 0.00 0.00 33.89 1.98
4580 5116 7.825331 TCAGAGATCGAAGGTAGTAAATCAT 57.175 36.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.396854 CGATCGGTTCGGTTCCTC 57.603 61.111 7.38 0.00 44.28 3.71
19 20 0.667453 GGGCGTTTGGTTTAACCGAA 59.333 50.000 12.47 12.47 42.58 4.30
20 21 0.465097 TGGGCGTTTGGTTTAACCGA 60.465 50.000 9.77 4.62 42.58 4.69
21 22 0.039888 CTGGGCGTTTGGTTTAACCG 60.040 55.000 9.77 0.00 42.58 4.44
22 23 0.315886 CCTGGGCGTTTGGTTTAACC 59.684 55.000 7.27 7.27 39.22 2.85
23 24 0.319211 GCCTGGGCGTTTGGTTTAAC 60.319 55.000 0.00 0.00 0.00 2.01
24 25 1.465200 GGCCTGGGCGTTTGGTTTAA 61.465 55.000 3.84 0.00 43.06 1.52
25 26 1.904378 GGCCTGGGCGTTTGGTTTA 60.904 57.895 3.84 0.00 43.06 2.01
26 27 3.230990 GGCCTGGGCGTTTGGTTT 61.231 61.111 3.84 0.00 43.06 3.27
27 28 4.218686 AGGCCTGGGCGTTTGGTT 62.219 61.111 15.17 0.00 43.06 3.67
28 29 4.660938 GAGGCCTGGGCGTTTGGT 62.661 66.667 12.00 0.00 43.06 3.67
29 30 2.876368 CTAGAGGCCTGGGCGTTTGG 62.876 65.000 12.00 2.85 43.06 3.28
30 31 1.450312 CTAGAGGCCTGGGCGTTTG 60.450 63.158 12.00 4.52 43.06 2.93
31 32 2.670148 CCTAGAGGCCTGGGCGTTT 61.670 63.158 12.00 6.99 43.06 3.60
32 33 3.083997 CCTAGAGGCCTGGGCGTT 61.084 66.667 12.00 9.53 43.06 4.84
33 34 4.400251 ACCTAGAGGCCTGGGCGT 62.400 66.667 12.00 6.52 44.15 5.68
34 35 3.541713 GACCTAGAGGCCTGGGCG 61.542 72.222 12.00 2.45 44.15 6.13
35 36 3.541713 CGACCTAGAGGCCTGGGC 61.542 72.222 12.00 13.15 44.15 5.36
36 37 1.686110 AACGACCTAGAGGCCTGGG 60.686 63.158 12.00 12.56 45.62 4.45
37 38 1.517832 CAACGACCTAGAGGCCTGG 59.482 63.158 12.00 8.36 39.32 4.45
38 39 0.970937 TCCAACGACCTAGAGGCCTG 60.971 60.000 12.00 0.00 39.32 4.85
39 40 0.032017 ATCCAACGACCTAGAGGCCT 60.032 55.000 3.86 3.86 39.32 5.19
40 41 0.831307 AATCCAACGACCTAGAGGCC 59.169 55.000 0.00 0.00 39.32 5.19
41 42 1.480954 TCAATCCAACGACCTAGAGGC 59.519 52.381 0.00 0.00 39.32 4.70
42 43 2.496070 TGTCAATCCAACGACCTAGAGG 59.504 50.000 0.00 0.00 42.17 3.69
43 44 3.868757 TGTCAATCCAACGACCTAGAG 57.131 47.619 0.00 0.00 0.00 2.43
44 45 3.767131 TCATGTCAATCCAACGACCTAGA 59.233 43.478 0.00 0.00 0.00 2.43
45 46 4.123497 TCATGTCAATCCAACGACCTAG 57.877 45.455 0.00 0.00 0.00 3.02
46 47 4.753516 ATCATGTCAATCCAACGACCTA 57.246 40.909 0.00 0.00 0.00 3.08
47 48 3.634397 ATCATGTCAATCCAACGACCT 57.366 42.857 0.00 0.00 0.00 3.85
48 49 4.155826 TCAAATCATGTCAATCCAACGACC 59.844 41.667 0.00 0.00 0.00 4.79
49 50 5.295431 TCAAATCATGTCAATCCAACGAC 57.705 39.130 0.00 0.00 0.00 4.34
50 51 5.163632 CCATCAAATCATGTCAATCCAACGA 60.164 40.000 0.00 0.00 0.00 3.85
51 52 5.038683 CCATCAAATCATGTCAATCCAACG 58.961 41.667 0.00 0.00 0.00 4.10
52 53 4.807304 GCCATCAAATCATGTCAATCCAAC 59.193 41.667 0.00 0.00 0.00 3.77
53 54 4.141892 GGCCATCAAATCATGTCAATCCAA 60.142 41.667 0.00 0.00 0.00 3.53
54 55 3.385433 GGCCATCAAATCATGTCAATCCA 59.615 43.478 0.00 0.00 0.00 3.41
55 56 3.551454 CGGCCATCAAATCATGTCAATCC 60.551 47.826 2.24 0.00 0.00 3.01
56 57 3.316029 TCGGCCATCAAATCATGTCAATC 59.684 43.478 2.24 0.00 0.00 2.67
57 58 3.289836 TCGGCCATCAAATCATGTCAAT 58.710 40.909 2.24 0.00 0.00 2.57
58 59 2.684374 CTCGGCCATCAAATCATGTCAA 59.316 45.455 2.24 0.00 0.00 3.18
59 60 2.093021 TCTCGGCCATCAAATCATGTCA 60.093 45.455 2.24 0.00 0.00 3.58
60 61 2.564771 TCTCGGCCATCAAATCATGTC 58.435 47.619 2.24 0.00 0.00 3.06
61 62 2.715749 TCTCGGCCATCAAATCATGT 57.284 45.000 2.24 0.00 0.00 3.21
62 63 5.694231 TTAATCTCGGCCATCAAATCATG 57.306 39.130 2.24 0.00 0.00 3.07
63 64 6.491062 TCAATTAATCTCGGCCATCAAATCAT 59.509 34.615 2.24 0.00 0.00 2.45
64 65 5.827267 TCAATTAATCTCGGCCATCAAATCA 59.173 36.000 2.24 0.00 0.00 2.57
65 66 6.317789 TCAATTAATCTCGGCCATCAAATC 57.682 37.500 2.24 0.00 0.00 2.17
66 67 6.713762 TTCAATTAATCTCGGCCATCAAAT 57.286 33.333 2.24 0.00 0.00 2.32
67 68 6.239008 GGATTCAATTAATCTCGGCCATCAAA 60.239 38.462 2.24 0.00 43.14 2.69
68 69 5.241506 GGATTCAATTAATCTCGGCCATCAA 59.758 40.000 2.24 0.00 43.14 2.57
69 70 4.761739 GGATTCAATTAATCTCGGCCATCA 59.238 41.667 2.24 0.00 43.14 3.07
70 71 4.142816 CGGATTCAATTAATCTCGGCCATC 60.143 45.833 2.24 0.00 43.14 3.51
71 72 3.753272 CGGATTCAATTAATCTCGGCCAT 59.247 43.478 2.24 0.00 43.14 4.40
72 73 3.138304 CGGATTCAATTAATCTCGGCCA 58.862 45.455 2.24 0.00 43.14 5.36
73 74 2.095718 GCGGATTCAATTAATCTCGGCC 60.096 50.000 0.00 0.00 43.14 6.13
74 75 2.095718 GGCGGATTCAATTAATCTCGGC 60.096 50.000 14.33 14.33 46.11 5.54
75 76 2.484264 GGGCGGATTCAATTAATCTCGG 59.516 50.000 0.00 0.00 43.14 4.63
76 77 3.403038 AGGGCGGATTCAATTAATCTCG 58.597 45.455 0.00 0.00 43.14 4.04
77 78 5.507985 CCAAAGGGCGGATTCAATTAATCTC 60.508 44.000 0.00 0.00 43.14 2.75
78 79 4.342092 CCAAAGGGCGGATTCAATTAATCT 59.658 41.667 0.00 0.00 43.14 2.40
79 80 4.340950 TCCAAAGGGCGGATTCAATTAATC 59.659 41.667 0.00 0.00 42.90 1.75
80 81 4.285863 TCCAAAGGGCGGATTCAATTAAT 58.714 39.130 0.00 0.00 0.00 1.40
81 82 3.702792 TCCAAAGGGCGGATTCAATTAA 58.297 40.909 0.00 0.00 0.00 1.40
82 83 3.374042 TCCAAAGGGCGGATTCAATTA 57.626 42.857 0.00 0.00 0.00 1.40
83 84 2.230130 TCCAAAGGGCGGATTCAATT 57.770 45.000 0.00 0.00 0.00 2.32
84 85 2.091665 AGATCCAAAGGGCGGATTCAAT 60.092 45.455 0.00 0.00 43.49 2.57
85 86 1.284785 AGATCCAAAGGGCGGATTCAA 59.715 47.619 0.00 0.00 43.49 2.69
86 87 0.918983 AGATCCAAAGGGCGGATTCA 59.081 50.000 0.00 0.00 43.49 2.57
87 88 2.058593 AAGATCCAAAGGGCGGATTC 57.941 50.000 0.00 0.00 43.49 2.52
88 89 2.532250 AAAGATCCAAAGGGCGGATT 57.468 45.000 0.00 0.00 43.49 3.01
89 90 2.532250 AAAAGATCCAAAGGGCGGAT 57.468 45.000 0.00 0.00 46.20 4.18
90 91 2.302587 AAAAAGATCCAAAGGGCGGA 57.697 45.000 0.00 0.00 36.84 5.54
91 92 6.215845 CAATATAAAAAGATCCAAAGGGCGG 58.784 40.000 0.00 0.00 0.00 6.13
92 93 6.183360 ACCAATATAAAAAGATCCAAAGGGCG 60.183 38.462 0.00 0.00 0.00 6.13
93 94 7.124573 ACCAATATAAAAAGATCCAAAGGGC 57.875 36.000 0.00 0.00 0.00 5.19
147 148 6.533723 GTCATGTATCGGTCACTTTGATGTTA 59.466 38.462 0.00 0.00 0.00 2.41
154 155 7.272244 TCATTATGTCATGTATCGGTCACTTT 58.728 34.615 0.00 0.00 0.00 2.66
195 196 2.615447 CAAGATGGCATTAGCGTGATGT 59.385 45.455 0.00 0.00 43.41 3.06
214 215 4.563140 ACTAAAAAGGCGGGATAGACAA 57.437 40.909 0.00 0.00 0.00 3.18
226 227 6.677187 GCTTAACGAAGGCCATACTAAAAAGG 60.677 42.308 5.01 0.00 32.84 3.11
269 270 3.910914 AACCAATAGCGCGGCCACA 62.911 57.895 8.83 0.00 0.00 4.17
273 274 1.226295 GAACAACCAATAGCGCGGC 60.226 57.895 8.83 0.00 0.00 6.53
276 277 2.084546 AGGAAGAACAACCAATAGCGC 58.915 47.619 0.00 0.00 0.00 5.92
278 279 2.096013 GCGAGGAAGAACAACCAATAGC 59.904 50.000 0.00 0.00 0.00 2.97
283 284 1.522668 CATGCGAGGAAGAACAACCA 58.477 50.000 0.00 0.00 0.00 3.67
284 285 0.804989 CCATGCGAGGAAGAACAACC 59.195 55.000 0.00 0.00 0.00 3.77
286 287 0.322456 CCCCATGCGAGGAAGAACAA 60.322 55.000 0.00 0.00 0.00 2.83
303 304 2.488153 GGGAAGCGAATATATTGTGCCC 59.512 50.000 1.78 1.28 0.00 5.36
310 311 6.379988 ACAAAAAGGTTGGGAAGCGAATATAT 59.620 34.615 0.00 0.00 0.00 0.86
311 312 5.712917 ACAAAAAGGTTGGGAAGCGAATATA 59.287 36.000 0.00 0.00 0.00 0.86
319 320 3.552068 CCGCTAACAAAAAGGTTGGGAAG 60.552 47.826 0.00 0.00 30.77 3.46
322 323 1.684450 ACCGCTAACAAAAAGGTTGGG 59.316 47.619 0.00 0.00 30.77 4.12
323 324 2.544903 CCACCGCTAACAAAAAGGTTGG 60.545 50.000 0.00 0.00 32.04 3.77
329 330 1.975660 AGCTCCACCGCTAACAAAAA 58.024 45.000 0.00 0.00 38.76 1.94
341 342 7.222999 GTGTGATATTTGAAGTACTAGCTCCAC 59.777 40.741 0.00 0.00 0.00 4.02
342 343 7.265673 GTGTGATATTTGAAGTACTAGCTCCA 58.734 38.462 0.00 0.00 0.00 3.86
344 345 6.973474 ACGTGTGATATTTGAAGTACTAGCTC 59.027 38.462 0.00 0.00 0.00 4.09
362 363 4.762765 ACTTGGCCATTTTAATACGTGTGA 59.237 37.500 6.09 0.00 0.00 3.58
365 366 6.431198 AGTACTTGGCCATTTTAATACGTG 57.569 37.500 6.09 0.00 0.00 4.49
377 378 4.966805 AGGCTATAGTTAAGTACTTGGCCA 59.033 41.667 18.56 0.00 40.54 5.36
398 399 9.906660 TTATGTGCTTTTGTAATTCTTAACAGG 57.093 29.630 0.00 0.00 0.00 4.00
415 416 5.940192 TTGTTTCGAGATGTTATGTGCTT 57.060 34.783 0.00 0.00 0.00 3.91
416 417 5.940192 TTTGTTTCGAGATGTTATGTGCT 57.060 34.783 0.00 0.00 0.00 4.40
497 500 5.156608 TGTAGGTGATGCATCATATCTGG 57.843 43.478 30.89 0.00 39.30 3.86
537 540 9.365311 CGACGTTATGCCTTGTTAATTAATTAG 57.635 33.333 7.91 2.40 0.00 1.73
569 572 4.883026 CTGTGGATTTGCAGCTGC 57.117 55.556 31.89 31.89 42.50 5.25
587 590 8.925161 ATTCATTGTGTCGGGTTAATTATTTG 57.075 30.769 0.00 0.00 0.00 2.32
603 606 7.274033 GGACATTTACATGTGTGATTCATTGTG 59.726 37.037 9.11 0.00 44.22 3.33
635 638 9.515226 TTCTGCCTCTTGTACTTTTATTTACAT 57.485 29.630 0.00 0.00 0.00 2.29
647 650 7.377766 TCATTTGTTATTCTGCCTCTTGTAC 57.622 36.000 0.00 0.00 0.00 2.90
648 651 6.094048 GCTCATTTGTTATTCTGCCTCTTGTA 59.906 38.462 0.00 0.00 0.00 2.41
652 655 4.592942 TGCTCATTTGTTATTCTGCCTCT 58.407 39.130 0.00 0.00 0.00 3.69
656 659 5.300969 TGTCTGCTCATTTGTTATTCTGC 57.699 39.130 0.00 0.00 0.00 4.26
657 660 6.685828 CGATTGTCTGCTCATTTGTTATTCTG 59.314 38.462 0.00 0.00 0.00 3.02
672 675 4.332543 TCACATGGTAAATCGATTGTCTGC 59.667 41.667 12.25 0.00 0.00 4.26
676 679 6.083630 CGTTTTCACATGGTAAATCGATTGT 58.916 36.000 12.25 1.46 32.32 2.71
677 680 6.083630 ACGTTTTCACATGGTAAATCGATTG 58.916 36.000 21.95 0.74 33.93 2.67
680 683 5.163933 GCTACGTTTTCACATGGTAAATCGA 60.164 40.000 21.95 0.00 33.93 3.59
682 685 5.106475 TGGCTACGTTTTCACATGGTAAATC 60.106 40.000 0.00 0.00 0.00 2.17
683 686 4.762765 TGGCTACGTTTTCACATGGTAAAT 59.237 37.500 0.00 0.00 0.00 1.40
684 687 4.135306 TGGCTACGTTTTCACATGGTAAA 58.865 39.130 0.00 0.00 0.00 2.01
688 691 2.223021 CGATGGCTACGTTTTCACATGG 60.223 50.000 0.00 0.00 0.00 3.66
698 701 0.892755 TGTCCTTTCGATGGCTACGT 59.107 50.000 0.00 0.00 0.00 3.57
699 702 2.128035 GATGTCCTTTCGATGGCTACG 58.872 52.381 0.00 0.00 0.00 3.51
706 709 2.947652 CAGCCATTGATGTCCTTTCGAT 59.052 45.455 0.00 0.00 0.00 3.59
708 711 2.086869 ACAGCCATTGATGTCCTTTCG 58.913 47.619 0.00 0.00 35.98 3.46
710 713 6.418057 TTTTTACAGCCATTGATGTCCTTT 57.582 33.333 0.00 0.00 40.99 3.11
794 1162 2.807967 CAAAGAGAGATTTCACCGTGCA 59.192 45.455 0.00 0.00 0.00 4.57
795 1163 2.160417 CCAAAGAGAGATTTCACCGTGC 59.840 50.000 0.00 0.00 0.00 5.34
796 1164 3.403038 ACCAAAGAGAGATTTCACCGTG 58.597 45.455 0.00 0.00 0.00 4.94
802 1170 3.369451 GCTGTCGACCAAAGAGAGATTTC 59.631 47.826 14.12 0.00 31.48 2.17
825 1193 0.253327 GGATCCTCTTGGCCTCGTTT 59.747 55.000 3.84 0.00 0.00 3.60
828 1196 0.471617 ATTGGATCCTCTTGGCCTCG 59.528 55.000 14.23 0.00 0.00 4.63
832 1200 1.216427 AGGGAATTGGATCCTCTTGGC 59.784 52.381 14.23 0.00 39.57 4.52
834 1202 4.603131 TCAAAGGGAATTGGATCCTCTTG 58.397 43.478 14.23 3.81 39.57 3.02
845 1213 8.670521 ATCCTCTTGTATTTTCAAAGGGAATT 57.329 30.769 0.00 0.00 34.91 2.17
860 1229 3.469859 TGGGGAATTGGATCCTCTTGTA 58.530 45.455 14.23 0.00 40.90 2.41
910 1283 1.347378 ACGTGTAATAAACGGTGGGGT 59.653 47.619 7.96 0.00 45.20 4.95
1180 1558 3.071206 GGAGACCTGGCTCAGCGA 61.071 66.667 16.37 0.00 36.62 4.93
1331 1709 1.131126 CGACAATGATTGGCACAGGAC 59.869 52.381 12.11 0.00 42.39 3.85
1332 1710 1.003003 TCGACAATGATTGGCACAGGA 59.997 47.619 12.11 0.00 42.39 3.86
1380 1759 7.537306 ACGATATCAAAAATTTCAACTGGAACG 59.463 33.333 3.12 0.00 34.56 3.95
1381 1760 8.742554 ACGATATCAAAAATTTCAACTGGAAC 57.257 30.769 3.12 0.00 34.56 3.62
1389 1768 9.644993 CAAGCGTATACGATATCAAAAATTTCA 57.355 29.630 28.66 0.00 43.02 2.69
1393 1772 8.922676 CCTACAAGCGTATACGATATCAAAAAT 58.077 33.333 28.66 1.59 43.02 1.82
1399 1778 6.200100 CCATCCTACAAGCGTATACGATATC 58.800 44.000 28.66 10.78 43.02 1.63
1400 1779 5.450137 GCCATCCTACAAGCGTATACGATAT 60.450 44.000 28.66 16.24 43.02 1.63
1401 1780 4.142534 GCCATCCTACAAGCGTATACGATA 60.143 45.833 28.66 12.82 43.02 2.92
1402 1781 3.367087 GCCATCCTACAAGCGTATACGAT 60.367 47.826 28.66 20.56 43.02 3.73
1403 1782 2.030540 GCCATCCTACAAGCGTATACGA 60.031 50.000 28.66 6.45 43.02 3.43
1404 1783 2.325761 GCCATCCTACAAGCGTATACG 58.674 52.381 20.87 20.87 43.27 3.06
1406 1785 2.717580 CGCCATCCTACAAGCGTATA 57.282 50.000 0.00 0.00 43.45 1.47
1407 1786 3.588277 CGCCATCCTACAAGCGTAT 57.412 52.632 0.00 0.00 43.45 3.06
1414 1793 1.754803 CTCTTACCACGCCATCCTACA 59.245 52.381 0.00 0.00 0.00 2.74
1424 1803 3.242936 CCACCAAAACAACTCTTACCACG 60.243 47.826 0.00 0.00 0.00 4.94
1425 1804 3.949113 TCCACCAAAACAACTCTTACCAC 59.051 43.478 0.00 0.00 0.00 4.16
1427 1806 5.300792 TCAATCCACCAAAACAACTCTTACC 59.699 40.000 0.00 0.00 0.00 2.85
1432 1811 3.989817 GCATCAATCCACCAAAACAACTC 59.010 43.478 0.00 0.00 0.00 3.01
1449 1828 0.839277 AACATCCGGATCAGGCATCA 59.161 50.000 15.88 0.00 32.33 3.07
1454 1833 5.478679 AGATTACTCTAACATCCGGATCAGG 59.521 44.000 15.88 6.32 0.00 3.86
1480 1859 1.557832 TGGGAAGGGGAATTCTACACG 59.442 52.381 5.23 0.00 0.00 4.49
1528 1907 3.678548 GCTTCGGTACCAAAACTCTACTG 59.321 47.826 13.54 0.00 0.00 2.74
1561 1940 3.079843 TCTTTGGGGATGGGGGTATTTTT 59.920 43.478 0.00 0.00 0.00 1.94
1635 2014 9.942850 AAGATTTACAATTTTATCCCCTTTGTG 57.057 29.630 0.00 0.00 33.03 3.33
1667 2046 7.607250 AGCAACCCAATATTAAACAAAATCGA 58.393 30.769 0.00 0.00 0.00 3.59
1683 2062 9.812347 AGAAATATCATCATATAAGCAACCCAA 57.188 29.630 0.00 0.00 0.00 4.12
1684 2063 9.812347 AAGAAATATCATCATATAAGCAACCCA 57.188 29.630 0.00 0.00 0.00 4.51
1730 2113 2.755469 CCCAATGTTCCAGGCGGG 60.755 66.667 0.00 0.00 38.37 6.13
1734 2117 0.331278 TACCAGCCCAATGTTCCAGG 59.669 55.000 0.00 0.00 0.00 4.45
1843 2227 3.440173 AGCCACTGGACATGAAATTAACG 59.560 43.478 0.00 0.00 0.00 3.18
1864 2298 8.119226 GTCGAGTCAATTCATTTCATTTAGGAG 58.881 37.037 0.00 0.00 0.00 3.69
1866 2300 7.751732 TGTCGAGTCAATTCATTTCATTTAGG 58.248 34.615 0.00 0.00 0.00 2.69
1884 2318 0.892755 TTTACGGCCAGATGTCGAGT 59.107 50.000 2.24 0.00 0.00 4.18
1885 2319 1.278238 GTTTACGGCCAGATGTCGAG 58.722 55.000 2.24 0.00 0.00 4.04
1977 2452 1.903183 ACCCTCAAGCCTAAGTGAGTC 59.097 52.381 0.00 0.00 39.76 3.36
1996 2471 6.058183 AGGTCTGATGCAGATTATGGTAAAC 58.942 40.000 0.00 0.00 42.73 2.01
2013 2489 3.709653 ACAACCAAAGTACAGAGGTCTGA 59.290 43.478 13.99 0.00 46.59 3.27
2017 2493 4.142249 GCAAAACAACCAAAGTACAGAGGT 60.142 41.667 0.00 0.00 35.47 3.85
2041 2520 9.367444 CTACTGGTACAAAAATCGAAAGAGTAT 57.633 33.333 0.00 0.00 41.44 2.12
2059 2538 6.095860 ACAATACAAGCGATACACTACTGGTA 59.904 38.462 0.00 0.00 0.00 3.25
2062 2541 6.142480 GCTACAATACAAGCGATACACTACTG 59.858 42.308 0.00 0.00 0.00 2.74
2066 2545 5.006153 TGCTACAATACAAGCGATACACT 57.994 39.130 0.00 0.00 41.77 3.55
2076 2555 9.405587 GCAAGTTAAAAGATTGCTACAATACAA 57.594 29.630 2.07 0.00 44.57 2.41
2077 2556 8.964420 GCAAGTTAAAAGATTGCTACAATACA 57.036 30.769 2.07 0.00 44.57 2.29
2126 2605 7.071321 ACCTTTTAGGAGCAGTAGTAATAGCAT 59.929 37.037 0.00 0.00 37.67 3.79
2127 2606 6.383147 ACCTTTTAGGAGCAGTAGTAATAGCA 59.617 38.462 0.00 0.00 37.67 3.49
2128 2607 6.818233 ACCTTTTAGGAGCAGTAGTAATAGC 58.182 40.000 0.00 0.00 37.67 2.97
2137 2644 5.006386 CAGAAATGACCTTTTAGGAGCAGT 58.994 41.667 0.00 0.00 37.67 4.40
2156 2663 9.421806 CCATATTAAACTCACAAAAATGCAGAA 57.578 29.630 0.00 0.00 0.00 3.02
2217 2724 5.463154 TCAAAGAAAATTCCAGGAAAGGGA 58.537 37.500 5.81 0.00 0.00 4.20
2258 2765 8.402798 TGCAGATACAAAAGGTTAATCTTCAA 57.597 30.769 0.38 0.00 0.00 2.69
2260 2767 9.860898 AATTGCAGATACAAAAGGTTAATCTTC 57.139 29.630 0.38 0.00 32.27 2.87
2311 2818 5.063204 CCGATGCTACATCCCAAGAATTTA 58.937 41.667 2.15 0.00 0.00 1.40
2346 2853 2.200373 AGTGGCCAACTGGTAATGAC 57.800 50.000 7.24 0.00 37.88 3.06
2347 2854 2.375174 AGAAGTGGCCAACTGGTAATGA 59.625 45.455 7.24 0.00 39.81 2.57
2372 2879 8.989653 ACTCAGATAAACAAGCTACTAAACTC 57.010 34.615 0.00 0.00 0.00 3.01
2579 3086 4.371624 TCCATCACAACTGACTCCATTT 57.628 40.909 0.00 0.00 0.00 2.32
2619 3126 2.592102 TCAAAGAGCAAATGAGCCCT 57.408 45.000 0.00 0.00 34.23 5.19
2810 3317 2.523507 CCTCGCAGCAGCATCTTCG 61.524 63.158 0.82 0.00 42.27 3.79
3231 3740 1.280421 ACATCACCTTCCTCTCCAAGC 59.720 52.381 0.00 0.00 0.00 4.01
3264 3773 2.747446 AGTCGTTCCAAATTCCATTCCG 59.253 45.455 0.00 0.00 0.00 4.30
3602 4113 6.414732 AGCCAGTACATTAGCAACTAAATCA 58.585 36.000 0.00 0.00 29.35 2.57
3849 4360 0.037605 GTAGTGGACTGGAACACCGG 60.038 60.000 0.00 0.00 38.34 5.28
3971 4482 1.605232 CTGACACAGCAATGCTCACAA 59.395 47.619 4.03 0.00 36.40 3.33
4026 4537 0.872021 CCGCCAGTAGCTTGTCGATC 60.872 60.000 0.00 0.00 40.39 3.69
4029 4540 2.509336 CCCGCCAGTAGCTTGTCG 60.509 66.667 0.00 0.00 40.39 4.35
4173 4684 6.035843 GCAAAATATGACGGTGAATTGTGAT 58.964 36.000 0.00 0.00 0.00 3.06
4231 4743 6.422701 CGTGGTGAAAACTTACATCAGACTTA 59.577 38.462 0.00 0.00 0.00 2.24
4406 4942 5.105756 CCATAACCAGGAAAATGAGACCAAC 60.106 44.000 0.00 0.00 0.00 3.77
4427 4963 1.848932 CGCGCATGAGCTATTGCCAT 61.849 55.000 19.47 0.00 40.80 4.40
4502 5038 1.202568 TCATGTAGCTCGGCATGAAGG 60.203 52.381 19.61 2.08 45.60 3.46
4512 5048 2.501723 TCCCAGGTTCTTCATGTAGCTC 59.498 50.000 0.00 0.00 0.00 4.09
4514 5050 2.911484 CTCCCAGGTTCTTCATGTAGC 58.089 52.381 0.00 0.00 0.00 3.58
4532 5068 6.328641 TGGATTATCTACGAGGTTTAGCTC 57.671 41.667 0.00 0.00 0.00 4.09
4549 5085 6.307776 ACTACCTTCGATCTCTGATGGATTA 58.692 40.000 7.67 0.00 35.31 1.75


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

AutoCloner maintained by Alex Coulton.