Multiple sequence alignment - TraesCS5B01G170700

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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 TraesCS5B01G170700 chr5B 100.000 5848 0 0 1 5848 315618918 315613071 0.000000e+00 10800.0
1 TraesCS5B01G170700 chr5B 84.158 101 15 1 3038 3137 505213156 505213056 4.820000e-16 97.1
2 TraesCS5B01G170700 chr5B 93.333 60 3 1 1708 1766 332408561 332408620 2.900000e-13 87.9
3 TraesCS5B01G170700 chr5B 85.915 71 8 2 3193 3262 710654471 710654540 2.260000e-09 75.0
4 TraesCS5B01G170700 chr5B 86.441 59 7 1 3192 3249 263518835 263518893 4.890000e-06 63.9
5 TraesCS5B01G170700 chr5D 95.607 2572 82 7 3296 5848 277561502 277558943 0.000000e+00 4095.0
6 TraesCS5B01G170700 chr5D 93.846 1560 61 12 158 1710 277564665 277563134 0.000000e+00 2316.0
7 TraesCS5B01G170700 chr5D 94.094 1507 51 14 1763 3265 277563116 277561644 0.000000e+00 2255.0
8 TraesCS5B01G170700 chr5D 95.652 46 0 2 1722 1766 39032971 39033015 8.130000e-09 73.1
9 TraesCS5B01G170700 chr5D 85.938 64 7 2 3188 3249 240088125 240088062 3.780000e-07 67.6
10 TraesCS5B01G170700 chr5D 73.391 233 41 16 3022 3249 286187759 286187543 3.780000e-07 67.6
11 TraesCS5B01G170700 chr5A 95.451 2572 85 7 3296 5848 366635376 366632818 0.000000e+00 4072.0
12 TraesCS5B01G170700 chr5A 96.426 1511 40 8 1763 3265 366637022 366635518 0.000000e+00 2479.0
13 TraesCS5B01G170700 chr5A 93.577 1557 63 16 158 1710 366638563 366637040 0.000000e+00 2287.0
14 TraesCS5B01G170700 chr5A 85.938 64 7 2 3188 3249 313876828 313876891 3.780000e-07 67.6
15 TraesCS5B01G170700 chr2B 94.444 72 2 1 18 87 583409644 583409715 6.200000e-20 110.0
16 TraesCS5B01G170700 chr2B 93.878 49 2 1 1726 1773 157060997 157061045 8.130000e-09 73.1
17 TraesCS5B01G170700 chr7B 100.000 49 0 0 3296 3344 567998967 567999015 2.240000e-14 91.6
18 TraesCS5B01G170700 chr7A 100.000 49 0 0 3296 3344 462978691 462978739 2.240000e-14 91.6
19 TraesCS5B01G170700 chr3D 91.304 69 2 2 1702 1766 549065875 549065943 2.240000e-14 91.6
20 TraesCS5B01G170700 chr1B 98.113 53 0 1 3293 3344 442177215 442177267 2.240000e-14 91.6
21 TraesCS5B01G170700 chrUn 98.000 50 1 0 3296 3345 27074501 27074550 2.900000e-13 87.9
22 TraesCS5B01G170700 chrUn 100.000 29 0 0 3174 3202 32248345 32248317 3.000000e-03 54.7
23 TraesCS5B01G170700 chr6D 98.000 50 1 0 3296 3345 12492341 12492390 2.900000e-13 87.9
24 TraesCS5B01G170700 chr2A 94.545 55 3 0 1708 1762 18654487 18654541 1.040000e-12 86.1
25 TraesCS5B01G170700 chr2A 80.952 105 17 3 3026 3128 677046776 677046879 4.860000e-11 80.5
26 TraesCS5B01G170700 chr2A 95.745 47 2 0 3086 3132 707078236 707078282 6.280000e-10 76.8
27 TraesCS5B01G170700 chr1D 98.000 50 0 1 3293 3341 328098881 328098930 1.040000e-12 86.1
28 TraesCS5B01G170700 chr1A 96.226 53 1 1 3293 3344 407324698 407324750 1.040000e-12 86.1
29 TraesCS5B01G170700 chr1A 88.333 60 5 1 1708 1765 504258335 504258276 2.920000e-08 71.3
30 TraesCS5B01G170700 chr7D 100.000 40 0 0 1726 1765 101477172 101477211 2.260000e-09 75.0
31 TraesCS5B01G170700 chr4B 91.837 49 4 0 1708 1756 578043794 578043842 1.050000e-07 69.4
32 TraesCS5B01G170700 chr3B 89.286 56 2 2 1708 1763 242876363 242876312 3.780000e-07 67.6
33 TraesCS5B01G170700 chr3B 94.595 37 2 0 3094 3130 788164154 788164118 2.280000e-04 58.4


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 TraesCS5B01G170700 chr5B 315613071 315618918 5847 True 10800.000000 10800 100.000000 1 5848 1 chr5B.!!$R1 5847
1 TraesCS5B01G170700 chr5D 277558943 277564665 5722 True 2888.666667 4095 94.515667 158 5848 3 chr5D.!!$R3 5690
2 TraesCS5B01G170700 chr5A 366632818 366638563 5745 True 2946.000000 4072 95.151333 158 5848 3 chr5A.!!$R1 5690

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
387 393 0.179000 CCCTACGAGCAAGCAATCCT 59.821 55.000 0.0 0.0 0.00 3.24 F
1171 1181 0.178992 CCTGACCAACCCAGCAAAGA 60.179 55.000 0.0 0.0 0.00 2.52 F
1443 1453 0.737019 GGGATGTTTGCAATGCGGTG 60.737 55.000 0.0 0.0 0.00 4.94 F
2037 2047 1.378646 GTGCAGGGACCTAAAGGCC 60.379 63.158 0.0 0.0 39.32 5.19 F
3348 3478 0.406750 TGAACGGAGGGAGTAGGACA 59.593 55.000 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1591 0.108804 TCCGACGAAGCAATGGAGTC 60.109 55.000 0.0 0.0 0.0 3.36 R
2037 2047 2.053627 GCACCAAGAAGCACATTTTCG 58.946 47.619 0.0 0.0 0.0 3.46 R
3348 3478 2.378547 TGCTTTTCCCTGGTATCCTTGT 59.621 45.455 0.0 0.0 0.0 3.16 R
3715 3846 0.104671 TTTGCCTGAGGTTGCTTTGC 59.895 50.000 0.0 0.0 0.0 3.68 R
4948 5084 0.764369 TGCTCCCTCTCAACACCACT 60.764 55.000 0.0 0.0 0.0 4.00 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
23 24 1.958288 AGGCAGGACTATGACTTGGT 58.042 50.000 0.00 0.00 33.61 3.67
24 25 2.269940 AGGCAGGACTATGACTTGGTT 58.730 47.619 0.00 0.00 33.61 3.67
25 26 2.026822 AGGCAGGACTATGACTTGGTTG 60.027 50.000 0.00 0.00 33.61 3.77
26 27 2.359900 GCAGGACTATGACTTGGTTGG 58.640 52.381 0.00 0.00 0.00 3.77
27 28 2.941415 GCAGGACTATGACTTGGTTGGG 60.941 54.545 0.00 0.00 0.00 4.12
28 29 2.305927 CAGGACTATGACTTGGTTGGGT 59.694 50.000 0.00 0.00 0.00 4.51
29 30 2.986728 AGGACTATGACTTGGTTGGGTT 59.013 45.455 0.00 0.00 0.00 4.11
30 31 3.009143 AGGACTATGACTTGGTTGGGTTC 59.991 47.826 0.00 0.00 0.00 3.62
31 32 3.244770 GGACTATGACTTGGTTGGGTTCA 60.245 47.826 0.00 0.00 0.00 3.18
32 33 4.003648 GACTATGACTTGGTTGGGTTCAG 58.996 47.826 0.00 0.00 0.00 3.02
33 34 2.292828 ATGACTTGGTTGGGTTCAGG 57.707 50.000 0.00 0.00 0.00 3.86
34 35 0.467290 TGACTTGGTTGGGTTCAGGC 60.467 55.000 0.00 0.00 0.00 4.85
35 36 1.152546 ACTTGGTTGGGTTCAGGCC 60.153 57.895 0.00 0.00 0.00 5.19
42 43 3.415186 GGGTTCAGGCCCTGATGA 58.585 61.111 15.62 0.00 45.22 2.92
43 44 1.691219 GGGTTCAGGCCCTGATGAA 59.309 57.895 15.62 0.00 45.22 2.57
44 45 0.394899 GGGTTCAGGCCCTGATGAAG 60.395 60.000 15.62 0.00 45.22 3.02
45 46 0.329596 GGTTCAGGCCCTGATGAAGT 59.670 55.000 15.62 0.00 40.39 3.01
46 47 1.272147 GGTTCAGGCCCTGATGAAGTT 60.272 52.381 15.62 0.00 40.39 2.66
47 48 2.087646 GTTCAGGCCCTGATGAAGTTC 58.912 52.381 15.62 0.00 40.39 3.01
48 49 1.661463 TCAGGCCCTGATGAAGTTCT 58.339 50.000 10.05 0.00 35.39 3.01
49 50 1.556911 TCAGGCCCTGATGAAGTTCTC 59.443 52.381 10.05 0.36 35.39 2.87
50 51 0.539051 AGGCCCTGATGAAGTTCTCG 59.461 55.000 0.00 0.00 0.00 4.04
51 52 0.250513 GGCCCTGATGAAGTTCTCGT 59.749 55.000 4.17 0.00 0.00 4.18
52 53 1.480954 GGCCCTGATGAAGTTCTCGTA 59.519 52.381 4.17 0.00 0.00 3.43
53 54 2.482142 GGCCCTGATGAAGTTCTCGTAG 60.482 54.545 4.17 0.00 0.00 3.51
54 55 2.427453 GCCCTGATGAAGTTCTCGTAGA 59.573 50.000 4.17 0.00 0.00 2.59
55 56 3.119101 GCCCTGATGAAGTTCTCGTAGAA 60.119 47.826 4.17 0.00 34.09 2.10
56 57 4.677584 CCCTGATGAAGTTCTCGTAGAAG 58.322 47.826 4.17 0.00 34.42 2.85
57 58 4.158764 CCCTGATGAAGTTCTCGTAGAAGT 59.841 45.833 4.17 0.00 39.44 3.01
66 67 6.492007 AGTTCTCGTAGAAGTTCGTAATGA 57.508 37.500 0.00 0.00 34.37 2.57
67 68 7.086230 AGTTCTCGTAGAAGTTCGTAATGAT 57.914 36.000 0.00 0.00 34.37 2.45
68 69 7.536855 AGTTCTCGTAGAAGTTCGTAATGATT 58.463 34.615 0.00 0.00 34.37 2.57
69 70 7.485277 AGTTCTCGTAGAAGTTCGTAATGATTG 59.515 37.037 0.00 0.00 34.37 2.67
70 71 6.849502 TCTCGTAGAAGTTCGTAATGATTGT 58.150 36.000 0.00 0.00 34.09 2.71
71 72 7.977904 TCTCGTAGAAGTTCGTAATGATTGTA 58.022 34.615 0.00 0.00 34.09 2.41
72 73 8.121086 TCTCGTAGAAGTTCGTAATGATTGTAG 58.879 37.037 0.00 0.00 34.09 2.74
73 74 7.977904 TCGTAGAAGTTCGTAATGATTGTAGA 58.022 34.615 0.00 0.00 0.00 2.59
74 75 7.907045 TCGTAGAAGTTCGTAATGATTGTAGAC 59.093 37.037 0.00 0.00 0.00 2.59
75 76 7.695201 CGTAGAAGTTCGTAATGATTGTAGACA 59.305 37.037 0.00 0.00 0.00 3.41
76 77 9.517609 GTAGAAGTTCGTAATGATTGTAGACAT 57.482 33.333 0.00 0.00 0.00 3.06
78 79 8.873830 AGAAGTTCGTAATGATTGTAGACATTG 58.126 33.333 0.00 0.00 37.32 2.82
79 80 8.547967 AAGTTCGTAATGATTGTAGACATTGT 57.452 30.769 0.00 0.00 37.32 2.71
80 81 7.963981 AGTTCGTAATGATTGTAGACATTGTG 58.036 34.615 0.00 0.00 37.32 3.33
81 82 7.817478 AGTTCGTAATGATTGTAGACATTGTGA 59.183 33.333 0.00 0.00 37.32 3.58
82 83 8.604035 GTTCGTAATGATTGTAGACATTGTGAT 58.396 33.333 0.00 0.00 37.32 3.06
83 84 9.810545 TTCGTAATGATTGTAGACATTGTGATA 57.189 29.630 0.00 0.00 37.32 2.15
84 85 9.463443 TCGTAATGATTGTAGACATTGTGATAG 57.537 33.333 0.00 0.00 37.32 2.08
85 86 9.463443 CGTAATGATTGTAGACATTGTGATAGA 57.537 33.333 0.00 0.00 37.32 1.98
104 105 9.708092 GTGATAGAGTAATACAAGTATTTCCCC 57.292 37.037 10.41 2.41 37.07 4.81
105 106 8.582437 TGATAGAGTAATACAAGTATTTCCCCG 58.418 37.037 10.41 0.00 37.07 5.73
106 107 8.716674 ATAGAGTAATACAAGTATTTCCCCGA 57.283 34.615 10.41 0.00 37.07 5.14
107 108 7.427989 AGAGTAATACAAGTATTTCCCCGAA 57.572 36.000 10.41 0.00 37.07 4.30
108 109 7.854337 AGAGTAATACAAGTATTTCCCCGAAA 58.146 34.615 10.41 0.00 37.07 3.46
109 110 8.323567 AGAGTAATACAAGTATTTCCCCGAAAA 58.676 33.333 10.41 0.00 37.07 2.29
110 111 8.866970 AGTAATACAAGTATTTCCCCGAAAAA 57.133 30.769 10.41 0.00 37.07 1.94
133 134 8.759481 AAAAAGAGAGAAGGAAGAAAGTGATT 57.241 30.769 0.00 0.00 0.00 2.57
134 135 7.742556 AAAGAGAGAAGGAAGAAAGTGATTG 57.257 36.000 0.00 0.00 0.00 2.67
135 136 6.432403 AGAGAGAAGGAAGAAAGTGATTGT 57.568 37.500 0.00 0.00 0.00 2.71
136 137 6.229733 AGAGAGAAGGAAGAAAGTGATTGTG 58.770 40.000 0.00 0.00 0.00 3.33
137 138 4.759183 AGAGAAGGAAGAAAGTGATTGTGC 59.241 41.667 0.00 0.00 0.00 4.57
138 139 4.723309 AGAAGGAAGAAAGTGATTGTGCT 58.277 39.130 0.00 0.00 0.00 4.40
139 140 5.869579 AGAAGGAAGAAAGTGATTGTGCTA 58.130 37.500 0.00 0.00 0.00 3.49
140 141 6.299141 AGAAGGAAGAAAGTGATTGTGCTAA 58.701 36.000 0.00 0.00 0.00 3.09
141 142 6.429385 AGAAGGAAGAAAGTGATTGTGCTAAG 59.571 38.462 0.00 0.00 0.00 2.18
142 143 4.457257 AGGAAGAAAGTGATTGTGCTAAGC 59.543 41.667 0.00 0.00 0.00 3.09
143 144 4.216257 GGAAGAAAGTGATTGTGCTAAGCA 59.784 41.667 0.00 0.00 35.60 3.91
144 145 5.278463 GGAAGAAAGTGATTGTGCTAAGCAA 60.278 40.000 0.00 0.00 41.47 3.91
145 146 5.368256 AGAAAGTGATTGTGCTAAGCAAG 57.632 39.130 0.00 0.00 41.47 4.01
202 205 1.071314 TCCCTTCCTTTTCCCCAGCA 61.071 55.000 0.00 0.00 0.00 4.41
229 232 4.934989 GGAACGTGCTAGGGAAGG 57.065 61.111 0.00 0.00 0.00 3.46
231 234 1.262640 GGAACGTGCTAGGGAAGGGA 61.263 60.000 0.00 0.00 0.00 4.20
232 235 0.611714 GAACGTGCTAGGGAAGGGAA 59.388 55.000 0.00 0.00 0.00 3.97
233 236 0.323957 AACGTGCTAGGGAAGGGAAC 59.676 55.000 0.00 0.00 0.00 3.62
277 283 2.165301 CGCGACGGAAATCCCACTC 61.165 63.158 0.00 0.00 34.14 3.51
302 308 4.124351 CTCGCCTCGCCACCGTAA 62.124 66.667 0.00 0.00 35.54 3.18
303 309 4.124351 TCGCCTCGCCACCGTAAG 62.124 66.667 0.00 0.00 35.54 2.34
387 393 0.179000 CCCTACGAGCAAGCAATCCT 59.821 55.000 0.00 0.00 0.00 3.24
398 404 2.757099 CAATCCTGCCTGCCCCAC 60.757 66.667 0.00 0.00 0.00 4.61
455 461 2.274760 CGAGTCCCGGACCCTACT 59.725 66.667 14.32 0.00 32.18 2.57
469 475 1.479709 CCTACTACACCTGCTGCTCT 58.520 55.000 0.00 0.00 0.00 4.09
508 514 2.430367 GGTTGGTCGCTTCCTGGT 59.570 61.111 0.00 0.00 0.00 4.00
655 665 4.349503 TCGGCTGGCCATTGCAGT 62.350 61.111 17.88 0.00 40.13 4.40
656 666 3.376078 CGGCTGGCCATTGCAGTT 61.376 61.111 17.88 0.00 40.13 3.16
657 667 2.263540 GGCTGGCCATTGCAGTTG 59.736 61.111 17.88 0.00 40.13 3.16
658 668 2.433664 GCTGGCCATTGCAGTTGC 60.434 61.111 5.51 0.00 40.13 4.17
681 691 1.142965 AAGGTGTTTGTTTGGCGGC 59.857 52.632 0.00 0.00 0.00 6.53
682 692 1.608717 AAGGTGTTTGTTTGGCGGCA 61.609 50.000 7.97 7.97 0.00 5.69
683 693 1.591327 GGTGTTTGTTTGGCGGCAG 60.591 57.895 12.87 0.00 0.00 4.85
684 694 1.591327 GTGTTTGTTTGGCGGCAGG 60.591 57.895 12.87 0.00 0.00 4.85
685 695 2.028925 GTTTGTTTGGCGGCAGGG 59.971 61.111 12.87 0.00 0.00 4.45
686 696 3.922640 TTTGTTTGGCGGCAGGGC 61.923 61.111 12.87 7.15 42.69 5.19
729 739 2.029288 TTGCTCGCTGGCTTCTTCG 61.029 57.895 0.00 0.00 0.00 3.79
738 748 2.489971 CTGGCTTCTTCGTTGGTGTTA 58.510 47.619 0.00 0.00 0.00 2.41
739 749 2.875933 CTGGCTTCTTCGTTGGTGTTAA 59.124 45.455 0.00 0.00 0.00 2.01
746 756 2.747396 TCGTTGGTGTTAAGCGGTAT 57.253 45.000 0.00 0.00 0.00 2.73
805 815 3.424039 CGACAGTTGCTGTATCAAAGCTG 60.424 47.826 1.43 0.00 45.44 4.24
1164 1174 3.246112 CGGGACCTGACCAACCCA 61.246 66.667 0.00 0.00 42.16 4.51
1167 1177 2.829384 GGACCTGACCAACCCAGCA 61.829 63.158 0.00 0.00 0.00 4.41
1171 1181 0.178992 CCTGACCAACCCAGCAAAGA 60.179 55.000 0.00 0.00 0.00 2.52
1196 1206 1.510623 CGCTCAAGCACGTCATTGC 60.511 57.895 2.50 0.00 43.34 3.56
1443 1453 0.737019 GGGATGTTTGCAATGCGGTG 60.737 55.000 0.00 0.00 0.00 4.94
1531 1541 5.048782 GGAATTGCTGTGTGAAATGTCTACA 60.049 40.000 0.00 0.00 0.00 2.74
1548 1558 2.338577 ACAGCAAGCAGTTCTCTGTT 57.661 45.000 0.00 0.00 43.05 3.16
1581 1591 3.158103 GCAATGAACGTTTTGCATGTG 57.842 42.857 25.38 14.93 45.83 3.21
1594 1604 1.814394 TGCATGTGACTCCATTGCTTC 59.186 47.619 0.00 0.00 36.13 3.86
1644 1654 3.693085 CAGCAGGAAATCATGTGCTAGTT 59.307 43.478 5.98 0.00 44.45 2.24
1710 1720 7.831691 ATACTGTATTGCTCTCTGATGTACT 57.168 36.000 0.00 0.00 0.00 2.73
1711 1721 6.142818 ACTGTATTGCTCTCTGATGTACTC 57.857 41.667 0.00 0.00 0.00 2.59
1713 1723 4.342378 TGTATTGCTCTCTGATGTACTCCC 59.658 45.833 0.00 0.00 0.00 4.30
1715 1725 2.660572 TGCTCTCTGATGTACTCCCTC 58.339 52.381 0.00 0.00 0.00 4.30
1716 1726 1.960689 GCTCTCTGATGTACTCCCTCC 59.039 57.143 0.00 0.00 0.00 4.30
1717 1727 2.226330 CTCTCTGATGTACTCCCTCCG 58.774 57.143 0.00 0.00 0.00 4.63
1718 1728 1.564818 TCTCTGATGTACTCCCTCCGT 59.435 52.381 0.00 0.00 0.00 4.69
1720 1730 3.201487 TCTCTGATGTACTCCCTCCGTAA 59.799 47.826 0.00 0.00 0.00 3.18
1721 1731 3.952323 CTCTGATGTACTCCCTCCGTAAA 59.048 47.826 0.00 0.00 0.00 2.01
1722 1732 3.698040 TCTGATGTACTCCCTCCGTAAAC 59.302 47.826 0.00 0.00 0.00 2.01
1723 1733 3.700038 CTGATGTACTCCCTCCGTAAACT 59.300 47.826 0.00 0.00 0.00 2.66
1725 1735 4.885907 TGATGTACTCCCTCCGTAAACTAG 59.114 45.833 0.00 0.00 0.00 2.57
1727 1737 5.435686 TGTACTCCCTCCGTAAACTAGTA 57.564 43.478 0.00 0.00 0.00 1.82
1728 1738 5.815581 TGTACTCCCTCCGTAAACTAGTAA 58.184 41.667 0.00 0.00 0.00 2.24
1729 1739 6.245408 TGTACTCCCTCCGTAAACTAGTAAA 58.755 40.000 0.00 0.00 0.00 2.01
1730 1740 5.651387 ACTCCCTCCGTAAACTAGTAAAC 57.349 43.478 0.00 0.00 0.00 2.01
1731 1741 5.328565 ACTCCCTCCGTAAACTAGTAAACT 58.671 41.667 0.00 0.00 0.00 2.66
1732 1742 6.485171 ACTCCCTCCGTAAACTAGTAAACTA 58.515 40.000 0.00 0.00 0.00 2.24
1733 1743 6.948309 ACTCCCTCCGTAAACTAGTAAACTAA 59.052 38.462 0.00 0.00 0.00 2.24
1734 1744 7.617329 ACTCCCTCCGTAAACTAGTAAACTAAT 59.383 37.037 0.00 0.00 0.00 1.73
1735 1745 9.125026 CTCCCTCCGTAAACTAGTAAACTAATA 57.875 37.037 0.00 0.00 0.00 0.98
1736 1746 9.646522 TCCCTCCGTAAACTAGTAAACTAATAT 57.353 33.333 0.00 0.00 0.00 1.28
1825 1835 7.922811 GGCAGCTTTAGTTTTGCATAATTCTAT 59.077 33.333 0.00 0.00 38.27 1.98
1865 1875 2.479837 CACTCAGTCTTGGTTGCGTTA 58.520 47.619 0.00 0.00 0.00 3.18
1913 1923 3.194116 AGTTGGCTGTAGATTGCAATTGG 59.806 43.478 14.33 3.87 0.00 3.16
1980 1990 3.678072 TCCTTCAAGAAATTGCTACGTCG 59.322 43.478 0.00 0.00 0.00 5.12
1990 2000 5.643339 AATTGCTACGTCGATCTTCATTC 57.357 39.130 0.00 0.00 0.00 2.67
2037 2047 1.378646 GTGCAGGGACCTAAAGGCC 60.379 63.158 0.00 0.00 39.32 5.19
2519 2532 6.913170 TCTGCTACTTAAAATCAGCTTTTGG 58.087 36.000 0.00 0.00 37.61 3.28
2521 2534 7.014230 TCTGCTACTTAAAATCAGCTTTTGGTT 59.986 33.333 0.00 0.00 37.61 3.67
2522 2535 7.496747 TGCTACTTAAAATCAGCTTTTGGTTT 58.503 30.769 0.00 0.00 41.87 3.27
2749 2762 9.785982 AATTAGCCTTCCAGTTCTCTAATATTC 57.214 33.333 0.00 0.00 0.00 1.75
2885 2898 3.181429 TGAGGATGAAGGTTTGGCTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
2886 2899 3.829026 GAGGATGAAGGTTTGGCTTCTTT 59.171 43.478 0.00 0.00 0.00 2.52
2899 2912 3.244181 TGGCTTCTTTGATTTTGCCCTTC 60.244 43.478 0.00 0.00 39.60 3.46
2941 2954 5.473039 GCTGTGAGCATGGTTTCTTATTTT 58.527 37.500 0.00 0.00 41.89 1.82
3054 3067 9.523168 TGGATGCAATATATTTCATGAGATTCA 57.477 29.630 14.25 0.00 0.00 2.57
3275 3294 9.786105 CATGTTTGCATGTGAATATAAGTGTAA 57.214 29.630 0.00 0.00 45.48 2.41
3277 3296 9.008965 TGTTTGCATGTGAATATAAGTGTAAGT 57.991 29.630 0.00 0.00 0.00 2.24
3348 3478 0.406750 TGAACGGAGGGAGTAGGACA 59.593 55.000 0.00 0.00 0.00 4.02
3367 3497 4.010349 GACACAAGGATACCAGGGAAAAG 58.990 47.826 0.00 0.00 37.17 2.27
3476 3607 7.542130 GTGATTTTGGTTCCATATGAGAACAAC 59.458 37.037 25.40 16.02 44.40 3.32
3525 3656 6.636454 TGAAAACTATGTATTCCAGGACCT 57.364 37.500 0.00 0.00 0.00 3.85
3535 3666 3.703001 TTCCAGGACCTTCTTCATCAC 57.297 47.619 0.00 0.00 0.00 3.06
3602 3733 1.967319 TTGAGGTCACAAGTTCCTGC 58.033 50.000 0.00 0.00 0.00 4.85
3703 3834 5.303078 TCAGTTCTAGATCAAGAGCCCATAC 59.697 44.000 3.70 0.00 0.00 2.39
3747 3878 2.023673 CAGGCAAAGAACCAGAACACA 58.976 47.619 0.00 0.00 0.00 3.72
3960 4091 1.599047 CTCAGAGGACAATGCCGGT 59.401 57.895 1.90 0.00 0.00 5.28
3970 4101 3.425227 GGACAATGCCGGTAGTTTAAACG 60.425 47.826 12.54 1.00 0.00 3.60
3973 4104 1.290491 TGCCGGTAGTTTAAACGCGG 61.290 55.000 12.47 12.72 35.26 6.46
3989 4120 2.250188 CGCGGCAAGTAAATTGAAAGG 58.750 47.619 0.00 0.00 41.83 3.11
4047 4178 6.886459 AGGAGCAATTGAAGATAGCAAACTTA 59.114 34.615 10.34 0.00 0.00 2.24
4062 4193 7.680442 AGCAAACTTAGAGAAGGAAGAAATC 57.320 36.000 0.00 0.00 36.95 2.17
4134 4265 5.063564 GGAGATACAGGAACTTAAACAAGCG 59.936 44.000 0.00 0.00 34.60 4.68
4144 4275 1.885560 TAAACAAGCGCTAGCCACAA 58.114 45.000 12.05 0.00 46.67 3.33
4157 4288 1.103398 GCCACAACTTCTGCACCAGT 61.103 55.000 0.00 0.00 32.61 4.00
4239 4370 5.301045 CCTTGACACTCCGGTATGATTACTA 59.699 44.000 13.58 1.18 0.00 1.82
4241 4372 5.195185 TGACACTCCGGTATGATTACTACA 58.805 41.667 13.58 0.00 0.00 2.74
4242 4373 5.831525 TGACACTCCGGTATGATTACTACAT 59.168 40.000 13.58 0.00 0.00 2.29
4243 4374 6.085555 ACACTCCGGTATGATTACTACATG 57.914 41.667 13.58 0.00 0.00 3.21
4296 4431 6.773976 ATATCTAGATTGACTGGCTAGAGC 57.226 41.667 11.25 0.00 42.56 4.09
4298 4433 0.749649 AGATTGACTGGCTAGAGCGG 59.250 55.000 3.17 0.00 43.26 5.52
4389 4524 2.167662 CTAGCCCGGTGTTTCCAATTT 58.832 47.619 0.00 0.00 35.57 1.82
4402 4538 9.736023 GGTGTTTCCAATTTCATAGCTAATTAG 57.264 33.333 8.20 8.20 35.97 1.73
4530 4666 3.981071 TTACATCAAGTCCAGGGACAG 57.019 47.619 19.92 11.98 46.76 3.51
4562 4698 1.508088 CAAGCCATGGTCCGCTTTC 59.492 57.895 14.67 0.00 42.61 2.62
4603 4739 0.673437 GCAGCTGTAAAAAGTGCCCA 59.327 50.000 16.64 0.00 0.00 5.36
4790 4926 2.964209 TCTCAGTCCCTCAACACTCTT 58.036 47.619 0.00 0.00 0.00 2.85
4982 5118 0.247460 GAGCAAAATGAGCCCAACCC 59.753 55.000 0.00 0.00 0.00 4.11
5008 5144 3.451178 AGTGCCAGAATTGACGTAGGTAT 59.549 43.478 0.00 0.00 0.00 2.73
5037 5173 6.251376 CGCCAATGCTTTTGTATAAGTTTCTC 59.749 38.462 0.00 0.00 34.43 2.87
5200 5350 3.449377 TGGACACACGTGACATGGTATAT 59.551 43.478 25.01 0.00 0.00 0.86
5201 5351 4.645588 TGGACACACGTGACATGGTATATA 59.354 41.667 25.01 0.00 0.00 0.86
5202 5352 5.303333 TGGACACACGTGACATGGTATATAT 59.697 40.000 25.01 0.00 0.00 0.86
5203 5353 5.862323 GGACACACGTGACATGGTATATATC 59.138 44.000 25.01 1.87 0.00 1.63
5204 5354 6.294564 GGACACACGTGACATGGTATATATCT 60.295 42.308 25.01 0.00 0.00 1.98
5205 5355 7.050970 ACACACGTGACATGGTATATATCTT 57.949 36.000 25.01 0.00 0.00 2.40
5206 5356 7.145985 ACACACGTGACATGGTATATATCTTC 58.854 38.462 25.01 0.00 0.00 2.87
5207 5357 7.145323 CACACGTGACATGGTATATATCTTCA 58.855 38.462 25.01 0.00 0.00 3.02
5208 5358 7.651704 CACACGTGACATGGTATATATCTTCAA 59.348 37.037 25.01 0.00 0.00 2.69
5209 5359 7.867909 ACACGTGACATGGTATATATCTTCAAG 59.132 37.037 25.01 0.70 0.00 3.02
5269 5419 7.859325 ACACATACCAAGGTAATACATTGTC 57.141 36.000 15.30 0.00 38.12 3.18
5344 5494 7.112779 AGAATACTGTTCTATTTTGGGGTCAG 58.887 38.462 0.00 0.00 0.00 3.51
5378 5528 3.380320 TGCAAGCATGAGAATCCATCTTG 59.620 43.478 0.00 0.00 38.96 3.02
5524 5674 4.381398 CCAGGAGGCTCATATGATTAGACG 60.381 50.000 17.69 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.431486 CCAAGTCATAGTCCTGCCTTCTC 60.431 52.174 0.00 0.00 0.00 2.87
1 2 2.503356 CCAAGTCATAGTCCTGCCTTCT 59.497 50.000 0.00 0.00 0.00 2.85
2 3 2.237392 ACCAAGTCATAGTCCTGCCTTC 59.763 50.000 0.00 0.00 0.00 3.46
3 4 2.269940 ACCAAGTCATAGTCCTGCCTT 58.730 47.619 0.00 0.00 0.00 4.35
4 5 1.958288 ACCAAGTCATAGTCCTGCCT 58.042 50.000 0.00 0.00 0.00 4.75
5 6 2.359900 CAACCAAGTCATAGTCCTGCC 58.640 52.381 0.00 0.00 0.00 4.85
6 7 2.359900 CCAACCAAGTCATAGTCCTGC 58.640 52.381 0.00 0.00 0.00 4.85
7 8 2.305927 ACCCAACCAAGTCATAGTCCTG 59.694 50.000 0.00 0.00 0.00 3.86
8 9 2.632537 ACCCAACCAAGTCATAGTCCT 58.367 47.619 0.00 0.00 0.00 3.85
9 10 3.244770 TGAACCCAACCAAGTCATAGTCC 60.245 47.826 0.00 0.00 0.00 3.85
10 11 4.003648 CTGAACCCAACCAAGTCATAGTC 58.996 47.826 0.00 0.00 0.00 2.59
11 12 3.244911 CCTGAACCCAACCAAGTCATAGT 60.245 47.826 0.00 0.00 0.00 2.12
12 13 3.347216 CCTGAACCCAACCAAGTCATAG 58.653 50.000 0.00 0.00 0.00 2.23
13 14 2.554344 GCCTGAACCCAACCAAGTCATA 60.554 50.000 0.00 0.00 0.00 2.15
14 15 1.823250 GCCTGAACCCAACCAAGTCAT 60.823 52.381 0.00 0.00 0.00 3.06
15 16 0.467290 GCCTGAACCCAACCAAGTCA 60.467 55.000 0.00 0.00 0.00 3.41
16 17 1.179174 GGCCTGAACCCAACCAAGTC 61.179 60.000 0.00 0.00 0.00 3.01
17 18 1.152546 GGCCTGAACCCAACCAAGT 60.153 57.895 0.00 0.00 0.00 3.16
18 19 3.777556 GGCCTGAACCCAACCAAG 58.222 61.111 0.00 0.00 0.00 3.61
26 27 0.329596 ACTTCATCAGGGCCTGAACC 59.670 55.000 37.86 0.00 44.04 3.62
27 28 2.087646 GAACTTCATCAGGGCCTGAAC 58.912 52.381 37.86 18.89 44.04 3.18
28 29 1.988107 AGAACTTCATCAGGGCCTGAA 59.012 47.619 37.86 21.69 44.04 3.02
29 30 1.556911 GAGAACTTCATCAGGGCCTGA 59.443 52.381 36.61 36.61 44.99 3.86
30 31 1.741732 CGAGAACTTCATCAGGGCCTG 60.742 57.143 28.01 28.01 0.00 4.85
31 32 0.539051 CGAGAACTTCATCAGGGCCT 59.461 55.000 0.00 0.00 0.00 5.19
32 33 0.250513 ACGAGAACTTCATCAGGGCC 59.749 55.000 0.00 0.00 0.00 5.80
33 34 2.427453 TCTACGAGAACTTCATCAGGGC 59.573 50.000 0.00 0.00 0.00 5.19
34 35 4.158764 ACTTCTACGAGAACTTCATCAGGG 59.841 45.833 0.00 0.00 29.89 4.45
35 36 5.317733 ACTTCTACGAGAACTTCATCAGG 57.682 43.478 0.00 0.00 29.89 3.86
36 37 5.509972 CGAACTTCTACGAGAACTTCATCAG 59.490 44.000 0.00 0.00 31.05 2.90
37 38 5.048921 ACGAACTTCTACGAGAACTTCATCA 60.049 40.000 0.00 0.00 31.05 3.07
38 39 5.392286 ACGAACTTCTACGAGAACTTCATC 58.608 41.667 0.00 0.00 31.05 2.92
39 40 5.373981 ACGAACTTCTACGAGAACTTCAT 57.626 39.130 0.00 0.00 31.05 2.57
40 41 4.825546 ACGAACTTCTACGAGAACTTCA 57.174 40.909 0.00 0.00 31.05 3.02
41 42 7.020010 TCATTACGAACTTCTACGAGAACTTC 58.980 38.462 0.00 0.00 29.89 3.01
42 43 6.906659 TCATTACGAACTTCTACGAGAACTT 58.093 36.000 0.00 0.00 29.89 2.66
43 44 6.492007 TCATTACGAACTTCTACGAGAACT 57.508 37.500 0.00 0.00 29.89 3.01
44 45 7.272948 ACAATCATTACGAACTTCTACGAGAAC 59.727 37.037 0.00 0.00 29.89 3.01
45 46 7.310664 ACAATCATTACGAACTTCTACGAGAA 58.689 34.615 0.00 0.00 32.50 2.87
46 47 6.849502 ACAATCATTACGAACTTCTACGAGA 58.150 36.000 0.00 0.00 0.00 4.04
47 48 8.121086 TCTACAATCATTACGAACTTCTACGAG 58.879 37.037 0.00 0.00 0.00 4.18
48 49 7.907045 GTCTACAATCATTACGAACTTCTACGA 59.093 37.037 0.00 0.00 0.00 3.43
49 50 7.695201 TGTCTACAATCATTACGAACTTCTACG 59.305 37.037 0.00 0.00 0.00 3.51
50 51 8.906636 TGTCTACAATCATTACGAACTTCTAC 57.093 34.615 0.00 0.00 0.00 2.59
52 53 8.873830 CAATGTCTACAATCATTACGAACTTCT 58.126 33.333 0.00 0.00 33.69 2.85
53 54 8.656849 ACAATGTCTACAATCATTACGAACTTC 58.343 33.333 0.00 0.00 33.69 3.01
54 55 8.443160 CACAATGTCTACAATCATTACGAACTT 58.557 33.333 0.00 0.00 33.69 2.66
55 56 7.817478 TCACAATGTCTACAATCATTACGAACT 59.183 33.333 0.00 0.00 33.69 3.01
56 57 7.959733 TCACAATGTCTACAATCATTACGAAC 58.040 34.615 0.00 0.00 33.69 3.95
57 58 8.716646 ATCACAATGTCTACAATCATTACGAA 57.283 30.769 0.00 0.00 33.69 3.85
58 59 9.463443 CTATCACAATGTCTACAATCATTACGA 57.537 33.333 0.00 0.00 33.69 3.43
59 60 9.463443 TCTATCACAATGTCTACAATCATTACG 57.537 33.333 0.00 0.00 33.69 3.18
78 79 9.708092 GGGGAAATACTTGTATTACTCTATCAC 57.292 37.037 6.46 1.66 0.00 3.06
79 80 8.582437 CGGGGAAATACTTGTATTACTCTATCA 58.418 37.037 6.46 0.00 0.00 2.15
80 81 8.800332 TCGGGGAAATACTTGTATTACTCTATC 58.200 37.037 6.46 0.77 0.00 2.08
81 82 8.716674 TCGGGGAAATACTTGTATTACTCTAT 57.283 34.615 6.46 0.00 0.00 1.98
82 83 8.537728 TTCGGGGAAATACTTGTATTACTCTA 57.462 34.615 6.46 0.00 0.00 2.43
83 84 7.427989 TTCGGGGAAATACTTGTATTACTCT 57.572 36.000 6.46 0.00 0.00 3.24
84 85 8.496707 TTTTCGGGGAAATACTTGTATTACTC 57.503 34.615 6.46 2.56 31.34 2.59
85 86 8.866970 TTTTTCGGGGAAATACTTGTATTACT 57.133 30.769 6.46 0.00 31.34 2.24
108 109 8.628280 CAATCACTTTCTTCCTTCTCTCTTTTT 58.372 33.333 0.00 0.00 0.00 1.94
109 110 7.777440 ACAATCACTTTCTTCCTTCTCTCTTTT 59.223 33.333 0.00 0.00 0.00 2.27
110 111 7.228308 CACAATCACTTTCTTCCTTCTCTCTTT 59.772 37.037 0.00 0.00 0.00 2.52
111 112 6.709846 CACAATCACTTTCTTCCTTCTCTCTT 59.290 38.462 0.00 0.00 0.00 2.85
112 113 6.229733 CACAATCACTTTCTTCCTTCTCTCT 58.770 40.000 0.00 0.00 0.00 3.10
113 114 5.106752 GCACAATCACTTTCTTCCTTCTCTC 60.107 44.000 0.00 0.00 0.00 3.20
114 115 4.759183 GCACAATCACTTTCTTCCTTCTCT 59.241 41.667 0.00 0.00 0.00 3.10
115 116 4.759183 AGCACAATCACTTTCTTCCTTCTC 59.241 41.667 0.00 0.00 0.00 2.87
116 117 4.723309 AGCACAATCACTTTCTTCCTTCT 58.277 39.130 0.00 0.00 0.00 2.85
117 118 6.560253 TTAGCACAATCACTTTCTTCCTTC 57.440 37.500 0.00 0.00 0.00 3.46
118 119 5.048434 GCTTAGCACAATCACTTTCTTCCTT 60.048 40.000 0.00 0.00 0.00 3.36
119 120 4.457257 GCTTAGCACAATCACTTTCTTCCT 59.543 41.667 0.00 0.00 0.00 3.36
120 121 4.216257 TGCTTAGCACAATCACTTTCTTCC 59.784 41.667 1.39 0.00 31.71 3.46
121 122 5.362556 TGCTTAGCACAATCACTTTCTTC 57.637 39.130 1.39 0.00 31.71 2.87
122 123 5.766222 CTTGCTTAGCACAATCACTTTCTT 58.234 37.500 6.34 0.00 38.71 2.52
123 124 5.368256 CTTGCTTAGCACAATCACTTTCT 57.632 39.130 6.34 0.00 38.71 2.52
146 147 0.025898 CTGTCGCATTCGCATCTGTG 59.974 55.000 0.00 0.00 38.40 3.66
147 148 0.390340 ACTGTCGCATTCGCATCTGT 60.390 50.000 0.00 0.00 38.40 3.41
148 149 0.025898 CACTGTCGCATTCGCATCTG 59.974 55.000 0.00 0.00 38.40 2.90
149 150 1.699656 GCACTGTCGCATTCGCATCT 61.700 55.000 0.00 0.00 38.40 2.90
150 151 1.297158 GCACTGTCGCATTCGCATC 60.297 57.895 0.00 0.00 38.40 3.91
151 152 1.576451 TTGCACTGTCGCATTCGCAT 61.576 50.000 5.90 0.00 42.62 4.73
152 153 2.250237 TTGCACTGTCGCATTCGCA 61.250 52.632 5.90 0.00 42.62 5.10
153 154 1.793613 GTTGCACTGTCGCATTCGC 60.794 57.895 5.90 0.00 42.62 4.70
154 155 1.154413 GGTTGCACTGTCGCATTCG 60.154 57.895 5.90 0.00 42.62 3.34
155 156 0.310543 TTGGTTGCACTGTCGCATTC 59.689 50.000 5.90 3.80 42.62 2.67
156 157 0.030638 GTTGGTTGCACTGTCGCATT 59.969 50.000 5.90 0.00 42.62 3.56
172 173 1.303643 GGAAGGGACAGGCTGGTTG 60.304 63.158 20.34 0.00 0.00 3.77
222 225 1.151877 AAGACCGGTTCCCTTCCCT 60.152 57.895 9.42 0.00 0.00 4.20
228 231 2.047560 CGTGGAAGACCGGTTCCC 60.048 66.667 20.37 16.18 44.93 3.97
229 232 2.741211 GCGTGGAAGACCGGTTCC 60.741 66.667 17.13 17.13 45.63 3.62
231 234 3.552384 TGGCGTGGAAGACCGGTT 61.552 61.111 9.42 0.00 39.42 4.44
232 235 4.309950 GTGGCGTGGAAGACCGGT 62.310 66.667 6.92 6.92 39.42 5.28
292 298 3.646023 TTACGGGCTTACGGTGGCG 62.646 63.158 0.00 0.00 38.39 5.69
293 299 2.102438 GTTACGGGCTTACGGTGGC 61.102 63.158 0.00 0.00 38.39 5.01
294 300 0.320596 TTGTTACGGGCTTACGGTGG 60.321 55.000 0.00 0.00 38.39 4.61
295 301 1.195222 GTTTGTTACGGGCTTACGGTG 59.805 52.381 0.00 0.00 38.39 4.94
296 302 1.202627 TGTTTGTTACGGGCTTACGGT 60.203 47.619 0.00 0.00 38.39 4.83
297 303 1.510776 TGTTTGTTACGGGCTTACGG 58.489 50.000 0.00 0.00 38.39 4.02
298 304 3.605743 TTTGTTTGTTACGGGCTTACG 57.394 42.857 0.00 0.00 40.31 3.18
299 305 5.366829 AGATTTGTTTGTTACGGGCTTAC 57.633 39.130 0.00 0.00 0.00 2.34
300 306 6.394025 AAAGATTTGTTTGTTACGGGCTTA 57.606 33.333 0.00 0.00 0.00 3.09
301 307 4.929819 AAGATTTGTTTGTTACGGGCTT 57.070 36.364 0.00 0.00 0.00 4.35
302 308 4.261867 GGAAAGATTTGTTTGTTACGGGCT 60.262 41.667 0.00 0.00 0.00 5.19
303 309 3.985279 GGAAAGATTTGTTTGTTACGGGC 59.015 43.478 0.00 0.00 0.00 6.13
304 310 5.240844 AGAGGAAAGATTTGTTTGTTACGGG 59.759 40.000 0.00 0.00 0.00 5.28
455 461 0.605083 CACTCAGAGCAGCAGGTGTA 59.395 55.000 0.66 0.00 0.00 2.90
729 739 1.131693 GGCATACCGCTTAACACCAAC 59.868 52.381 0.00 0.00 41.91 3.77
738 748 0.981277 ACCTACCTGGCATACCGCTT 60.981 55.000 0.00 0.00 41.91 4.68
739 749 0.105862 TACCTACCTGGCATACCGCT 60.106 55.000 0.00 0.00 41.91 5.52
746 756 1.062886 AGCAGATCTACCTACCTGGCA 60.063 52.381 0.00 0.00 40.22 4.92
805 815 3.894427 TCTCAAGATCTGCCTGTCTATCC 59.106 47.826 0.00 0.00 0.00 2.59
1116 1126 2.879233 GCACGAGAACCCACCCTCA 61.879 63.158 0.00 0.00 0.00 3.86
1164 1174 0.319555 TGAGCGCGTACTTCTTTGCT 60.320 50.000 8.43 0.00 34.96 3.91
1167 1177 0.790814 GCTTGAGCGCGTACTTCTTT 59.209 50.000 8.43 0.00 0.00 2.52
1171 1181 3.550656 GTGCTTGAGCGCGTACTT 58.449 55.556 8.43 0.00 45.83 2.24
1196 1206 2.266055 GCGACTCCTTGTCCTGGG 59.734 66.667 0.00 0.00 42.49 4.45
1297 1307 1.463214 TCCCACGGCCCATATCCAT 60.463 57.895 0.00 0.00 0.00 3.41
1323 1333 2.008329 CAGAACTCCATCAGCAGAAGC 58.992 52.381 0.00 0.00 42.56 3.86
1443 1453 3.372676 CTGGCAGTGCATCGCGAAC 62.373 63.158 15.24 7.19 0.00 3.95
1531 1541 2.338577 ACAACAGAGAACTGCTTGCT 57.661 45.000 0.00 0.00 46.95 3.91
1548 1558 2.935201 GTTCATTGCAAAAGCACCAACA 59.065 40.909 1.71 0.00 0.00 3.33
1581 1591 0.108804 TCCGACGAAGCAATGGAGTC 60.109 55.000 0.00 0.00 0.00 3.36
1594 1604 2.569059 TGGGACTAACTCTATCCGACG 58.431 52.381 0.00 0.00 32.90 5.12
1644 1654 8.874156 ACAATATGCTCAAGATAAGATGGAGTA 58.126 33.333 0.00 0.00 0.00 2.59
1710 1720 7.961326 ATTAGTTTACTAGTTTACGGAGGGA 57.039 36.000 0.00 0.00 0.00 4.20
1747 1757 9.201989 TGTGTCCTGATACTATTTTAGTGATCT 57.798 33.333 0.00 0.00 39.81 2.75
1748 1758 9.817809 TTGTGTCCTGATACTATTTTAGTGATC 57.182 33.333 0.00 0.00 39.81 2.92
1749 1759 9.823647 CTTGTGTCCTGATACTATTTTAGTGAT 57.176 33.333 0.00 0.00 39.81 3.06
1750 1760 8.812972 ACTTGTGTCCTGATACTATTTTAGTGA 58.187 33.333 0.00 0.00 39.81 3.41
1755 1765 9.601217 GACATACTTGTGTCCTGATACTATTTT 57.399 33.333 0.00 0.00 42.04 1.82
1756 1766 8.758829 TGACATACTTGTGTCCTGATACTATTT 58.241 33.333 3.93 0.00 46.17 1.40
1757 1767 8.198109 GTGACATACTTGTGTCCTGATACTATT 58.802 37.037 3.93 0.00 46.17 1.73
1758 1768 7.561722 AGTGACATACTTGTGTCCTGATACTAT 59.438 37.037 3.93 0.00 46.17 2.12
1759 1769 6.890268 AGTGACATACTTGTGTCCTGATACTA 59.110 38.462 3.93 0.00 46.17 1.82
1760 1770 5.717178 AGTGACATACTTGTGTCCTGATACT 59.283 40.000 3.93 0.00 46.17 2.12
1761 1771 5.967088 AGTGACATACTTGTGTCCTGATAC 58.033 41.667 3.93 0.00 46.17 2.24
1783 1793 2.222678 GCTGCCACATGATCGATGTAAG 59.777 50.000 0.54 9.01 43.96 2.34
1785 1795 1.413812 AGCTGCCACATGATCGATGTA 59.586 47.619 0.54 0.00 43.96 2.29
1825 1835 5.500234 AGTGGAAAGCTATATGAAACAGCA 58.500 37.500 0.00 0.00 37.78 4.41
1844 1854 0.532862 ACGCAACCAAGACTGAGTGG 60.533 55.000 0.00 0.00 41.00 4.00
1865 1875 8.486210 TGGAGTTTATAATGCACTAGATGAAGT 58.514 33.333 0.00 0.00 0.00 3.01
1956 1966 5.163854 CGACGTAGCAATTTCTTGAAGGATT 60.164 40.000 0.00 0.00 34.04 3.01
1980 1990 5.851720 TGTGATGCCTCTAGAATGAAGATC 58.148 41.667 0.00 0.00 0.00 2.75
1990 2000 3.806380 AGATTTGCTGTGATGCCTCTAG 58.194 45.455 0.00 0.00 0.00 2.43
2037 2047 2.053627 GCACCAAGAAGCACATTTTCG 58.946 47.619 0.00 0.00 0.00 3.46
2519 2532 7.335422 TGAGGATCTGAAGCTTTGATTCTAAAC 59.665 37.037 18.42 10.71 34.92 2.01
2521 2534 6.950842 TGAGGATCTGAAGCTTTGATTCTAA 58.049 36.000 18.42 12.04 34.92 2.10
2522 2535 6.550938 TGAGGATCTGAAGCTTTGATTCTA 57.449 37.500 18.42 9.00 34.92 2.10
2668 2681 2.761767 TCATGGAAGTGAATGGCCAATG 59.238 45.455 10.96 5.63 33.51 2.82
2749 2762 7.161404 ACCATACCTATAACAGTACATGCATG 58.839 38.462 25.09 25.09 0.00 4.06
2866 2879 3.573967 TCAAAGAAGCCAAACCTTCATCC 59.426 43.478 4.92 0.00 42.84 3.51
2885 2898 7.961351 TCAATTCTTAAGAAGGGCAAAATCAA 58.039 30.769 21.75 0.00 37.48 2.57
2886 2899 7.537596 TCAATTCTTAAGAAGGGCAAAATCA 57.462 32.000 21.75 0.00 37.48 2.57
2899 2912 2.790387 GCAGCGGCTTCAATTCTTAAG 58.210 47.619 0.00 0.00 36.96 1.85
3021 3034 6.157904 TGAAATATATTGCATCCAATTGCCG 58.842 36.000 1.62 0.00 41.68 5.69
3054 3067 7.288810 ACAAATGTTCATGTTCCATACAACT 57.711 32.000 0.00 0.00 40.89 3.16
3348 3478 2.378547 TGCTTTTCCCTGGTATCCTTGT 59.621 45.455 0.00 0.00 0.00 3.16
3431 3562 7.546250 AATCACTGAGACCTAGAGAAGAAAA 57.454 36.000 0.00 0.00 0.00 2.29
3509 3640 6.615316 TGATGAAGAAGGTCCTGGAATACATA 59.385 38.462 0.00 0.00 0.00 2.29
3517 3648 1.406069 CCGTGATGAAGAAGGTCCTGG 60.406 57.143 0.00 0.00 0.00 4.45
3525 3656 3.320826 TGTCTCTTGACCGTGATGAAGAA 59.679 43.478 0.00 0.00 42.28 2.52
3535 3666 3.303881 TCTCACATTGTCTCTTGACCG 57.696 47.619 0.00 0.00 42.28 4.79
3581 3712 2.687935 GCAGGAACTTGTGACCTCAAAA 59.312 45.455 0.00 0.00 34.60 2.44
3602 3733 2.093764 CCTGCAGAACCCTTACTCTCAG 60.094 54.545 17.39 0.00 0.00 3.35
3703 3834 3.120792 GTTGCTTTGCTATGCCATCATG 58.879 45.455 3.74 0.00 34.22 3.07
3715 3846 0.104671 TTTGCCTGAGGTTGCTTTGC 59.895 50.000 0.00 0.00 0.00 3.68
3747 3878 3.002791 CTGTCTGTATGCATTCCGTGTT 58.997 45.455 3.54 0.00 0.00 3.32
3960 4091 5.610235 ATTTACTTGCCGCGTTTAAACTA 57.390 34.783 16.01 0.00 0.00 2.24
3970 4101 3.242518 GTCCTTTCAATTTACTTGCCGC 58.757 45.455 0.00 0.00 34.66 6.53
3973 4104 5.175673 GCTGTTGTCCTTTCAATTTACTTGC 59.824 40.000 0.00 0.00 34.66 4.01
3989 4120 2.743928 CGGCCTCCAGCTGTTGTC 60.744 66.667 13.81 0.72 43.46 3.18
4047 4178 6.269769 ACTTCAGTGAGATTTCTTCCTTCTCT 59.730 38.462 0.00 0.00 37.40 3.10
4062 4193 7.412781 GCTGACAATCTATCAAACTTCAGTGAG 60.413 40.741 0.00 0.00 33.30 3.51
4134 4265 0.519077 GTGCAGAAGTTGTGGCTAGC 59.481 55.000 6.04 6.04 0.00 3.42
4157 4288 4.431416 TCTTTCAACTCCTTAACTGGCA 57.569 40.909 0.00 0.00 0.00 4.92
4284 4419 2.317530 ATTTTCCGCTCTAGCCAGTC 57.682 50.000 0.00 0.00 37.91 3.51
4351 4486 9.784531 CCGGGCTAGATCATTAATTCATTATAT 57.215 33.333 0.00 0.00 0.00 0.86
4353 4488 7.554118 CACCGGGCTAGATCATTAATTCATTAT 59.446 37.037 6.32 0.00 0.00 1.28
4402 4538 2.749076 TCAGATTGTGTGCAGTAATGGC 59.251 45.455 0.00 0.00 0.00 4.40
4414 4550 3.942829 TCAGCTAAGGGTTCAGATTGTG 58.057 45.455 0.00 0.00 0.00 3.33
4530 4666 2.421399 GCTTGGGATCTGGGCTTGC 61.421 63.158 0.00 0.00 0.00 4.01
4562 4698 3.896479 GCTTTCGGCTCTTCAGGG 58.104 61.111 0.00 0.00 38.06 4.45
4660 4796 5.679638 GCACCAGAGTTTGTTTTTGACTGAT 60.680 40.000 0.00 0.00 0.00 2.90
4790 4926 4.836825 CATCTTTCTCCACTTCAGCCTTA 58.163 43.478 0.00 0.00 0.00 2.69
4948 5084 0.764369 TGCTCCCTCTCAACACCACT 60.764 55.000 0.00 0.00 0.00 4.00
4982 5118 1.081892 CGTCAATTCTGGCACTCCTG 58.918 55.000 0.00 0.00 0.00 3.86
5037 5173 6.149308 TGCATGTCACTAAATTTCAGTACCAG 59.851 38.462 0.00 0.00 0.00 4.00
5186 5336 6.813649 CCCTTGAAGATATATACCATGTCACG 59.186 42.308 0.00 0.00 0.00 4.35
5200 5350 6.782494 TGATAGTGCTACATCCCTTGAAGATA 59.218 38.462 0.00 0.00 0.00 1.98
5201 5351 5.604231 TGATAGTGCTACATCCCTTGAAGAT 59.396 40.000 0.00 0.00 0.00 2.40
5202 5352 4.962362 TGATAGTGCTACATCCCTTGAAGA 59.038 41.667 0.00 0.00 0.00 2.87
5203 5353 5.282055 TGATAGTGCTACATCCCTTGAAG 57.718 43.478 0.00 0.00 0.00 3.02
5204 5354 5.692115 TTGATAGTGCTACATCCCTTGAA 57.308 39.130 0.00 0.00 0.00 2.69
5205 5355 5.130975 ACATTGATAGTGCTACATCCCTTGA 59.869 40.000 0.00 0.00 0.00 3.02
5206 5356 5.371526 ACATTGATAGTGCTACATCCCTTG 58.628 41.667 0.00 0.00 0.00 3.61
5207 5357 5.636903 ACATTGATAGTGCTACATCCCTT 57.363 39.130 0.00 0.00 0.00 3.95
5208 5358 5.636903 AACATTGATAGTGCTACATCCCT 57.363 39.130 0.00 0.00 0.00 4.20
5209 5359 5.009010 CCAAACATTGATAGTGCTACATCCC 59.991 44.000 0.00 0.00 0.00 3.85
5317 5467 7.027874 ACCCCAAAATAGAACAGTATTCTCA 57.972 36.000 0.00 0.00 0.00 3.27
5344 5494 2.925578 TGCTTGCAAGATGTATGTGC 57.074 45.000 30.39 12.39 38.78 4.57
5378 5528 1.002792 GTGCAAGGAAACCTGACGAAC 60.003 52.381 0.00 0.00 32.13 3.95
5524 5674 3.386768 TCTGTGGACAGTAAGCACTTC 57.613 47.619 6.68 0.00 44.12 3.01


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

AutoCloner maintained by Alex Coulton.