Multiple sequence alignment - TraesCS7A01G242600

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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 TraesCS7A01G242600 chr7A 100.000 5271 0 0 1 5271 218025794 218031064 0.000000e+00 9734.0
1 TraesCS7A01G242600 chr7A 90.834 2891 183 36 1678 4532 213818720 213815876 0.000000e+00 3795.0
2 TraesCS7A01G242600 chr7A 93.602 422 25 2 948 1368 213820335 213819915 3.460000e-176 628.0
3 TraesCS7A01G242600 chr7A 94.198 293 17 0 1357 1649 213819012 213818720 1.040000e-121 448.0
4 TraesCS7A01G242600 chr7A 85.714 336 34 7 623 952 213831711 213831384 5.050000e-90 342.0
5 TraesCS7A01G242600 chr7A 81.579 76 6 6 2 69 57751216 57751291 7.370000e-04 56.5
6 TraesCS7A01G242600 chr7D 93.766 4347 194 37 159 4462 205722717 205727029 0.000000e+00 6455.0
7 TraesCS7A01G242600 chr7B 93.165 3950 184 30 143 4059 196660958 196657062 0.000000e+00 5720.0
8 TraesCS7A01G242600 chr7B 89.450 1308 113 16 3230 4532 197475737 197474450 0.000000e+00 1628.0
9 TraesCS7A01G242600 chr7B 92.265 1073 63 9 2045 3103 197476804 197475738 0.000000e+00 1504.0
10 TraesCS7A01G242600 chr7B 92.065 1046 61 17 618 1648 197486791 197485753 0.000000e+00 1452.0
11 TraesCS7A01G242600 chr7B 97.921 433 6 2 4058 4489 196656788 196656358 0.000000e+00 747.0
12 TraesCS7A01G242600 chr7B 86.482 614 52 16 322 905 172568528 172569140 0.000000e+00 645.0
13 TraesCS7A01G242600 chr7B 84.526 517 52 10 4768 5268 196656019 196655515 2.210000e-133 486.0
14 TraesCS7A01G242600 chr7B 94.677 263 13 1 1766 2028 197484954 197484693 1.770000e-109 407.0
15 TraesCS7A01G242600 chr7B 93.182 264 17 1 1125 1387 197487202 197486939 2.300000e-103 387.0
16 TraesCS7A01G242600 chr7B 92.268 194 14 1 944 1137 197490386 197490194 1.870000e-69 274.0
17 TraesCS7A01G242600 chr7B 86.243 189 12 7 4538 4719 196656360 196656179 5.390000e-45 193.0
18 TraesCS7A01G242600 chr7B 93.478 46 0 2 2 44 426782437 426782482 1.230000e-06 65.8
19 TraesCS7A01G242600 chr3D 80.952 315 51 8 4955 5264 116330522 116330832 1.900000e-59 241.0
20 TraesCS7A01G242600 chr3D 82.143 196 22 8 4586 4769 108980207 108980401 7.070000e-34 156.0
21 TraesCS7A01G242600 chr3D 76.842 285 51 13 4955 5231 523398302 523398025 4.250000e-31 147.0
22 TraesCS7A01G242600 chr3B 88.587 184 17 2 4765 4944 160398135 160398318 2.470000e-53 220.0
23 TraesCS7A01G242600 chr3B 78.730 315 57 9 4955 5264 169902936 169903245 8.950000e-48 202.0
24 TraesCS7A01G242600 chr3B 79.237 236 47 2 4955 5189 146202713 146202479 4.220000e-36 163.0
25 TraesCS7A01G242600 chr3B 93.617 47 0 1 1 44 61905331 61905377 3.410000e-07 67.6
26 TraesCS7A01G242600 chr5B 84.177 158 23 2 4955 5111 322281335 322281491 9.140000e-33 152.0
27 TraesCS7A01G242600 chr4D 78.205 234 46 5 4958 5189 236943309 236943079 1.530000e-30 145.0
28 TraesCS7A01G242600 chr6D 79.558 181 33 4 4950 5129 470518284 470518461 5.540000e-25 126.0
29 TraesCS7A01G242600 chr5A 78.199 211 36 9 4952 5157 291268716 291268921 5.540000e-25 126.0
30 TraesCS7A01G242600 chr5D 76.316 228 51 3 4955 5180 24965449 24965223 9.270000e-23 119.0
31 TraesCS7A01G242600 chr5D 93.478 46 0 2 2 44 391361469 391361514 1.230000e-06 65.8
32 TraesCS7A01G242600 chr5D 87.719 57 2 2 2 53 469793493 469793549 1.580000e-05 62.1
33 TraesCS7A01G242600 chr5D 86.207 58 3 3 2 54 441860051 441859994 2.050000e-04 58.4
34 TraesCS7A01G242600 chr2B 93.478 46 0 2 2 44 59324814 59324859 1.230000e-06 65.8
35 TraesCS7A01G242600 chr4B 91.489 47 3 1 52 98 578072177 578072132 4.410000e-06 63.9
36 TraesCS7A01G242600 chrUn 86.441 59 2 6 56 114 303635946 303635894 5.700000e-05 60.2
37 TraesCS7A01G242600 chrUn 86.441 59 2 6 56 114 383713942 383713890 5.700000e-05 60.2
38 TraesCS7A01G242600 chr3A 97.143 35 1 0 53 87 707699423 707699457 5.700000e-05 60.2
39 TraesCS7A01G242600 chr3A 97.143 35 1 0 53 87 707733505 707733539 5.700000e-05 60.2
40 TraesCS7A01G242600 chr3A 97.143 35 1 0 53 87 707762520 707762554 5.700000e-05 60.2
41 TraesCS7A01G242600 chr3A 97.143 35 1 0 53 87 707794360 707794394 5.700000e-05 60.2
42 TraesCS7A01G242600 chr3A 97.143 35 1 0 53 87 707822913 707822947 5.700000e-05 60.2
43 TraesCS7A01G242600 chr1A 86.441 59 2 6 56 114 315264707 315264655 5.700000e-05 60.2
44 TraesCS7A01G242600 chr1D 86.207 58 3 3 2 54 40282423 40282366 2.050000e-04 58.4
45 TraesCS7A01G242600 chr1D 86.207 58 3 3 2 54 40417866 40417809 2.050000e-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 TraesCS7A01G242600 chr7A 218025794 218031064 5270 False 9734.000000 9734 100.00000 1 5271 1 chr7A.!!$F2 5270
1 TraesCS7A01G242600 chr7A 213815876 213820335 4459 True 1623.666667 3795 92.87800 948 4532 3 chr7A.!!$R2 3584
2 TraesCS7A01G242600 chr7D 205722717 205727029 4312 False 6455.000000 6455 93.76600 159 4462 1 chr7D.!!$F1 4303
3 TraesCS7A01G242600 chr7B 196655515 196660958 5443 True 1786.500000 5720 90.46375 143 5268 4 chr7B.!!$R1 5125
4 TraesCS7A01G242600 chr7B 197474450 197476804 2354 True 1566.000000 1628 90.85750 2045 4532 2 chr7B.!!$R2 2487
5 TraesCS7A01G242600 chr7B 172568528 172569140 612 False 645.000000 645 86.48200 322 905 1 chr7B.!!$F1 583
6 TraesCS7A01G242600 chr7B 197484693 197490386 5693 True 630.000000 1452 93.04800 618 2028 4 chr7B.!!$R3 1410

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
315 326 1.502640 CTCTCGAACGTTCCGCTCT 59.497 57.895 22.07 0.0 0.00 4.09 F
1500 5417 1.672356 CAGGCCCCGAGTTTCACTG 60.672 63.158 0.00 0.0 0.00 3.66 F
1661 5578 1.070134 GTTTGCTCTTTTTGGACCCCC 59.930 52.381 0.00 0.0 0.00 5.40 F
3145 7803 0.839277 ATCCGGATGATGCTGGTCAA 59.161 50.000 18.33 0.0 35.72 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 5456 1.269012 CCCCGGGTAAGTGAAGTGTA 58.731 55.0 21.85 0.0 0.0 2.90 R
2962 7620 0.252742 AACTCGATCCTCCCCCAAGT 60.253 55.0 0.00 0.0 0.0 3.16 R
3170 7828 0.544357 TCATCTGGGTCTGGTTCCGT 60.544 55.0 0.00 0.0 0.0 4.69 R
4939 10036 0.034896 TGGCCGAAGACTCCTCAAAC 59.965 55.0 0.00 0.0 0.0 2.93 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 3.090210 TGATGAGGTGGATTTGCATGT 57.910 42.857 0.00 0.00 0.00 3.21
24 25 4.598022 TGATGAGGTGGATTTGCATGTTA 58.402 39.130 0.00 0.00 0.00 2.41
26 27 5.125900 TGATGAGGTGGATTTGCATGTTAAG 59.874 40.000 0.00 0.00 0.00 1.85
29 30 4.922206 AGGTGGATTTGCATGTTAAGAGA 58.078 39.130 0.00 0.00 0.00 3.10
31 32 5.774690 AGGTGGATTTGCATGTTAAGAGAAA 59.225 36.000 0.00 0.00 0.00 2.52
32 33 6.438425 AGGTGGATTTGCATGTTAAGAGAAAT 59.562 34.615 0.00 0.00 0.00 2.17
37 38 8.470002 GGATTTGCATGTTAAGAGAAATAGGTT 58.530 33.333 0.00 0.00 0.00 3.50
41 42 8.492673 TGCATGTTAAGAGAAATAGGTTAGTG 57.507 34.615 0.00 0.00 0.00 2.74
42 43 7.552687 TGCATGTTAAGAGAAATAGGTTAGTGG 59.447 37.037 0.00 0.00 0.00 4.00
43 44 7.012421 GCATGTTAAGAGAAATAGGTTAGTGGG 59.988 40.741 0.00 0.00 0.00 4.61
44 45 6.412214 TGTTAAGAGAAATAGGTTAGTGGGC 58.588 40.000 0.00 0.00 0.00 5.36
46 47 7.400915 TGTTAAGAGAAATAGGTTAGTGGGCTA 59.599 37.037 0.00 0.00 0.00 3.93
47 48 5.873146 AGAGAAATAGGTTAGTGGGCTAC 57.127 43.478 0.00 0.00 0.00 3.58
48 49 5.530243 AGAGAAATAGGTTAGTGGGCTACT 58.470 41.667 9.01 9.01 43.56 2.57
49 50 5.965091 AGAGAAATAGGTTAGTGGGCTACTT 59.035 40.000 9.37 0.00 40.89 2.24
50 51 6.444171 AGAGAAATAGGTTAGTGGGCTACTTT 59.556 38.462 9.37 0.00 40.89 2.66
51 52 7.029053 AGAAATAGGTTAGTGGGCTACTTTT 57.971 36.000 9.37 2.12 40.89 2.27
52 53 7.467650 AGAAATAGGTTAGTGGGCTACTTTTT 58.532 34.615 9.37 0.80 40.89 1.94
83 84 9.696917 ACAAAGTTGAATCATCTATTTTGGAAC 57.303 29.630 10.86 0.00 40.04 3.62
86 87 6.884295 AGTTGAATCATCTATTTTGGAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
87 88 7.393234 AGTTGAATCATCTATTTTGGAACGGAA 59.607 33.333 0.00 0.00 0.00 4.30
88 89 7.320443 TGAATCATCTATTTTGGAACGGAAG 57.680 36.000 0.00 0.00 0.00 3.46
106 107 7.401955 ACGGAAGTAGTTAGTAGTAGCATTT 57.598 36.000 0.00 0.00 46.88 2.32
107 108 7.256286 ACGGAAGTAGTTAGTAGTAGCATTTG 58.744 38.462 0.00 0.00 46.88 2.32
108 109 6.696148 CGGAAGTAGTTAGTAGTAGCATTTGG 59.304 42.308 0.00 0.00 0.00 3.28
109 110 7.415989 CGGAAGTAGTTAGTAGTAGCATTTGGA 60.416 40.741 0.00 0.00 0.00 3.53
110 111 8.422566 GGAAGTAGTTAGTAGTAGCATTTGGAT 58.577 37.037 0.00 0.00 0.00 3.41
133 134 7.864379 GGATACAGAAGATATGCACAAATTTGG 59.136 37.037 21.74 11.81 0.00 3.28
135 136 7.414222 ACAGAAGATATGCACAAATTTGGAT 57.586 32.000 21.74 12.58 0.00 3.41
136 137 8.523915 ACAGAAGATATGCACAAATTTGGATA 57.476 30.769 21.74 14.13 34.67 2.59
137 138 9.139734 ACAGAAGATATGCACAAATTTGGATAT 57.860 29.630 21.74 17.51 41.67 1.63
138 139 9.406828 CAGAAGATATGCACAAATTTGGATATG 57.593 33.333 21.74 11.86 39.75 1.78
139 140 8.086522 AGAAGATATGCACAAATTTGGATATGC 58.913 33.333 21.74 20.36 39.75 3.14
141 142 7.375834 AGATATGCACAAATTTGGATATGCAG 58.624 34.615 27.53 9.61 45.42 4.41
154 155 4.155826 TGGATATGCAGCAAGTTACACAAC 59.844 41.667 0.00 0.00 34.67 3.32
170 171 1.600916 AACCAGGTTCAGAAGGCGC 60.601 57.895 0.00 0.00 0.00 6.53
315 326 1.502640 CTCTCGAACGTTCCGCTCT 59.497 57.895 22.07 0.00 0.00 4.09
598 617 2.132089 TTTCGGTCGAATTGGGGGCT 62.132 55.000 6.63 0.00 33.79 5.19
625 3604 7.654116 GTCTTAGGATTCCAGTAAGTATTCAGC 59.346 40.741 5.29 0.00 0.00 4.26
686 3666 3.531538 TCGGTAAAGATCACATGGAAGC 58.468 45.455 0.00 0.00 0.00 3.86
690 3670 5.527214 CGGTAAAGATCACATGGAAGCATTA 59.473 40.000 0.00 0.00 0.00 1.90
691 3671 6.511767 CGGTAAAGATCACATGGAAGCATTAC 60.512 42.308 0.00 1.45 0.00 1.89
809 3791 6.571605 GGAAATTAGGAGTAGTGTACAGGAC 58.428 44.000 0.00 0.00 0.00 3.85
856 3839 2.813754 CCCATGGTATTAACAGGATGCG 59.186 50.000 11.73 0.00 42.53 4.73
884 3871 7.981225 TGAGCTTATTTTCATGGCTAATTTTCC 59.019 33.333 0.00 0.00 33.13 3.13
895 3885 5.579047 TGGCTAATTTTCCATCTTCCTTCA 58.421 37.500 0.00 0.00 0.00 3.02
905 3895 6.566079 TCCATCTTCCTTCACACTGATAAT 57.434 37.500 0.00 0.00 0.00 1.28
907 3897 7.500992 TCCATCTTCCTTCACACTGATAATAC 58.499 38.462 0.00 0.00 0.00 1.89
932 3922 4.521130 TGAGATGACACTCTGGTTGTAC 57.479 45.455 0.00 0.00 37.73 2.90
933 3923 4.152647 TGAGATGACACTCTGGTTGTACT 58.847 43.478 0.00 0.00 37.73 2.73
934 3924 5.321927 TGAGATGACACTCTGGTTGTACTA 58.678 41.667 0.00 0.00 37.73 1.82
939 3929 6.754702 TGACACTCTGGTTGTACTAGATAC 57.245 41.667 0.00 0.00 35.13 2.24
1074 4074 2.224843 TGATGTTGATGCAGACCCAAGT 60.225 45.455 0.00 0.00 0.00 3.16
1160 4160 2.169352 AGCTCATAGTTCCGCAATCTGT 59.831 45.455 0.00 0.00 0.00 3.41
1288 4288 4.782019 TTGAACATGCTGTTGGGTAATC 57.218 40.909 6.31 0.00 41.28 1.75
1307 4307 3.696281 TCGCTAATGCAATGGTGAATG 57.304 42.857 0.00 0.00 39.64 2.67
1426 5343 4.701651 CAGACAATGGCAAAAGACCAGATA 59.298 41.667 0.00 0.00 41.46 1.98
1500 5417 1.672356 CAGGCCCCGAGTTTCACTG 60.672 63.158 0.00 0.00 0.00 3.66
1515 5432 1.843851 TCACTGAAACTTCCACAGGGT 59.156 47.619 0.00 0.00 36.57 4.34
1539 5456 7.148407 GGTCAATACATCTTCTGTGATTTTCGT 60.148 37.037 0.00 0.00 38.92 3.85
1577 5494 4.279922 CGGGGTTGAGGTTAGTCAATTTTT 59.720 41.667 0.00 0.00 38.68 1.94
1633 5550 6.996879 AGACAGATCCATTGGATAACAATCAG 59.003 38.462 18.20 5.51 46.67 2.90
1653 5570 3.131046 CAGGACACCAGTTTGCTCTTTTT 59.869 43.478 0.00 0.00 0.00 1.94
1661 5578 1.070134 GTTTGCTCTTTTTGGACCCCC 59.930 52.381 0.00 0.00 0.00 5.40
1676 5593 3.581770 GGACCCCCTATATGTCAACCTAC 59.418 52.174 0.00 0.00 0.00 3.18
1735 5652 5.452078 TTACATTTTTGGTCTTCCTGCTG 57.548 39.130 0.00 0.00 34.23 4.41
1794 6421 7.068716 AGTCAGCAGTGTGTATGTCATAGATAA 59.931 37.037 0.00 0.00 0.00 1.75
1891 6518 8.034215 CCCAAAATCATGTTGTCTGCTAATTTA 58.966 33.333 0.00 0.00 0.00 1.40
1978 6605 9.731819 CTTTCTAGAATGATGAAATCCATGTTG 57.268 33.333 11.96 0.00 44.73 3.33
2072 6713 3.748568 GCTAGTAGCAGCAACTTTCTGTT 59.251 43.478 17.47 0.00 41.89 3.16
2095 6736 9.051679 TGTTTGATTTGTATAATCGTGGATAGG 57.948 33.333 0.00 0.00 0.00 2.57
2096 6737 7.667043 TTGATTTGTATAATCGTGGATAGGC 57.333 36.000 0.00 0.00 0.00 3.93
2272 6914 2.159254 TGGCAAGTCTGTTTCTTTGTGC 60.159 45.455 0.00 0.00 0.00 4.57
2274 6916 2.854185 GCAAGTCTGTTTCTTTGTGCAC 59.146 45.455 10.75 10.75 0.00 4.57
2288 6930 9.462174 TTTCTTTGTGCACTTTCATATTTACAG 57.538 29.630 19.41 0.00 0.00 2.74
2289 6931 8.165239 TCTTTGTGCACTTTCATATTTACAGT 57.835 30.769 19.41 0.00 0.00 3.55
2290 6932 8.629158 TCTTTGTGCACTTTCATATTTACAGTT 58.371 29.630 19.41 0.00 0.00 3.16
2291 6933 9.891828 CTTTGTGCACTTTCATATTTACAGTTA 57.108 29.630 19.41 0.00 0.00 2.24
2292 6934 9.891828 TTTGTGCACTTTCATATTTACAGTTAG 57.108 29.630 19.41 0.00 0.00 2.34
2634 7284 5.651172 TTTGTATTTCGTATGCGGATCAG 57.349 39.130 2.62 0.00 38.89 2.90
2751 7403 4.465632 TCGCTCTTAATAAGCAGGTTCA 57.534 40.909 9.80 0.00 39.81 3.18
2851 7509 2.156917 CAGTTGAATGAGGAAGCTGCA 58.843 47.619 1.02 0.00 0.00 4.41
2962 7620 1.601903 GCTCATGTTGTCGGTCACAAA 59.398 47.619 0.00 0.00 46.90 2.83
3053 7711 5.981174 TCTTGAGTGCATCATCAACAGATA 58.019 37.500 7.61 0.00 37.89 1.98
3091 7749 7.870954 CACAGTAGTGTTACTAAATCTGTGGAA 59.129 37.037 19.82 0.00 42.91 3.53
3093 7751 9.436957 CAGTAGTGTTACTAAATCTGTGGAAAT 57.563 33.333 0.00 0.00 38.05 2.17
3145 7803 0.839277 ATCCGGATGATGCTGGTCAA 59.161 50.000 18.33 0.00 35.72 3.18
3146 7804 0.839277 TCCGGATGATGCTGGTCAAT 59.161 50.000 0.00 0.00 35.72 2.57
3152 7810 5.217393 CGGATGATGCTGGTCAATATTTTG 58.783 41.667 0.00 0.00 0.00 2.44
3206 7864 4.017126 AGATGATAATGATGCCATGCCTG 58.983 43.478 0.00 0.00 32.36 4.85
3217 7875 1.818060 GCCATGCCTGTTGATGTAACA 59.182 47.619 0.00 0.00 46.62 2.41
3233 7891 5.940192 TGTAACAATTGTGACATCAGGAC 57.060 39.130 22.65 6.36 34.57 3.85
3291 7949 5.163258 CCATAGGTTATTCTGAGCCTGTTCT 60.163 44.000 0.00 0.00 32.90 3.01
3324 7982 3.317993 GCCAAGAAAAGCTCTGTTGGTTA 59.682 43.478 19.79 0.00 35.29 2.85
3376 8034 4.829064 TGTTGACATGCTTAACAAGGAC 57.171 40.909 7.34 0.00 31.95 3.85
3415 8073 6.528321 TGATAATGAACCTGATCCTGATGAC 58.472 40.000 0.00 0.00 0.00 3.06
3418 8076 0.179000 AACCTGATCCTGATGACGGC 59.821 55.000 0.00 0.00 0.00 5.68
3436 8094 3.259876 ACGGCACTAGTGAATTTGTCCTA 59.740 43.478 27.08 0.00 0.00 2.94
3537 8195 6.458232 TGACTCCTCTAGCTCTATTCAAAC 57.542 41.667 0.00 0.00 0.00 2.93
3570 8228 1.117150 ATTGATGGGAAGCACATGGC 58.883 50.000 0.00 0.00 45.30 4.40
3598 8256 2.298446 TGATCCAGATGCTAGTAGCTGC 59.702 50.000 22.34 13.91 42.97 5.25
3682 8340 4.103153 TCAGTTTTGGAGTCTGAACCTGAT 59.897 41.667 3.45 0.00 35.65 2.90
3691 8349 1.819288 TCTGAACCTGATCCTGACGAC 59.181 52.381 0.00 0.00 0.00 4.34
3706 8364 4.082274 TGACGACAATGCTGCTAATTTG 57.918 40.909 0.00 2.75 0.00 2.32
3766 8424 2.341543 CTATGCTCGCGCCTCCAT 59.658 61.111 0.00 4.09 34.43 3.41
3972 8630 9.688592 CAAATTATTGCTAATCCTCATCCTTTC 57.311 33.333 0.00 0.00 0.00 2.62
4049 8707 4.038162 GGTACATCTCTTACCTCTGCGAAT 59.962 45.833 0.00 0.00 36.75 3.34
4189 9125 0.745486 CAGATGAGATTGGGCGTGCA 60.745 55.000 0.00 0.00 0.00 4.57
4337 9273 4.142425 CCTTTGTGCTGCAAAAATGGTTTT 60.142 37.500 17.68 0.00 45.35 2.43
4387 9324 7.584987 AGAACATTAAACTATGTGTTGTCTGC 58.415 34.615 0.00 0.00 38.69 4.26
4462 9399 2.843730 TCTTGTCTGGGGCTTATGCTAA 59.156 45.455 0.13 0.00 39.59 3.09
4496 9435 6.955987 GTTTGGAGAAACATTGAGCATCACAA 60.956 38.462 0.00 0.00 42.63 3.33
4532 9471 0.315251 GCAGTGCTCCCTTTTTGGAC 59.685 55.000 8.18 0.00 38.35 4.02
4533 9472 1.986882 CAGTGCTCCCTTTTTGGACT 58.013 50.000 0.00 0.00 38.35 3.85
4534 9473 2.310538 CAGTGCTCCCTTTTTGGACTT 58.689 47.619 0.00 0.00 38.35 3.01
4535 9474 2.695147 CAGTGCTCCCTTTTTGGACTTT 59.305 45.455 0.00 0.00 38.35 2.66
4536 9475 2.695147 AGTGCTCCCTTTTTGGACTTTG 59.305 45.455 0.00 0.00 38.35 2.77
4537 9476 2.038659 TGCTCCCTTTTTGGACTTTGG 58.961 47.619 0.00 0.00 38.35 3.28
4538 9477 2.316108 GCTCCCTTTTTGGACTTTGGA 58.684 47.619 0.00 0.00 38.35 3.53
4539 9478 2.297315 GCTCCCTTTTTGGACTTTGGAG 59.703 50.000 0.00 0.00 40.65 3.86
4541 9480 3.823304 CTCCCTTTTTGGACTTTGGAGAG 59.177 47.826 0.00 0.00 40.23 3.20
4547 9486 1.448717 GGACTTTGGAGAGAGCGCC 60.449 63.158 2.29 0.00 34.13 6.53
4558 9497 0.663153 GAGAGCGCCACACAACTTTT 59.337 50.000 2.29 0.00 0.00 2.27
4559 9498 1.065551 GAGAGCGCCACACAACTTTTT 59.934 47.619 2.29 0.00 0.00 1.94
4585 9524 1.808390 GCGTGGATACCGTGACACC 60.808 63.158 0.00 0.00 33.54 4.16
4586 9525 1.888018 CGTGGATACCGTGACACCT 59.112 57.895 0.00 0.00 0.00 4.00
4615 9554 5.188988 AGGGGTAAACCAAGTTCTTATCC 57.811 43.478 0.81 0.00 42.91 2.59
4616 9555 4.604490 AGGGGTAAACCAAGTTCTTATCCA 59.396 41.667 0.81 0.00 42.91 3.41
4617 9556 5.255443 AGGGGTAAACCAAGTTCTTATCCAT 59.745 40.000 0.81 0.00 42.91 3.41
4618 9557 6.449041 AGGGGTAAACCAAGTTCTTATCCATA 59.551 38.462 0.81 0.00 42.91 2.74
4640 9579 2.348411 AAACCACACTTCAGGTCAGG 57.652 50.000 0.00 0.00 37.07 3.86
4646 9585 2.037641 CACACTTCAGGTCAGGTCATGA 59.962 50.000 0.00 0.00 34.79 3.07
4675 9621 2.461110 GCCAGACATAACGCCGGTG 61.461 63.158 14.93 14.93 0.00 4.94
4682 9628 0.249322 CATAACGCCGGTGACCTAGG 60.249 60.000 24.59 7.41 0.00 3.02
4692 9638 2.424246 CGGTGACCTAGGAAGAGAGAAC 59.576 54.545 17.98 1.46 0.00 3.01
4693 9639 2.761767 GGTGACCTAGGAAGAGAGAACC 59.238 54.545 17.98 6.95 0.00 3.62
4713 9659 3.200825 ACCTGGCTAAACTATGTGCATCT 59.799 43.478 0.00 0.00 0.00 2.90
4715 9661 4.445453 CTGGCTAAACTATGTGCATCTGA 58.555 43.478 0.00 0.00 0.00 3.27
4719 9665 7.053498 TGGCTAAACTATGTGCATCTGAATTA 58.947 34.615 0.00 0.00 0.00 1.40
4733 9822 6.563753 GCATCTGAATTAGAAGCACGATCTTC 60.564 42.308 11.54 11.54 46.59 2.87
4734 9823 5.037385 TCTGAATTAGAAGCACGATCTTCG 58.963 41.667 12.94 0.00 45.28 3.79
4748 9837 6.404342 GCACGATCTTCGAAAGTAAAATTACG 59.596 38.462 0.00 0.00 43.74 3.18
4771 9860 8.419076 ACGTTGAAATAAAATTGCTTGAAAGT 57.581 26.923 0.00 0.00 0.00 2.66
4772 9861 9.522804 ACGTTGAAATAAAATTGCTTGAAAGTA 57.477 25.926 0.00 0.00 0.00 2.24
4836 9925 4.989875 ATGATAGCTCCATAGTTGCCTT 57.010 40.909 0.00 0.00 0.00 4.35
4889 9986 3.835779 TGCGATGACAAAATGTTGGATG 58.164 40.909 0.00 0.00 39.22 3.51
4919 10016 0.745845 CGGCTAGTGCAATTGCCTCT 60.746 55.000 30.93 24.24 42.90 3.69
4920 10017 1.020437 GGCTAGTGCAATTGCCTCTC 58.980 55.000 28.22 16.25 41.92 3.20
4921 10018 0.654683 GCTAGTGCAATTGCCTCTCG 59.345 55.000 26.94 19.81 41.18 4.04
4922 10019 1.293924 CTAGTGCAATTGCCTCTCGG 58.706 55.000 26.94 16.00 41.18 4.63
4939 10036 1.563435 CGGCATGCAATCGCCTCTAG 61.563 60.000 21.36 4.15 46.62 2.43
4944 10041 2.760634 TGCAATCGCCTCTAGTTTGA 57.239 45.000 0.00 0.00 37.32 2.69
4956 10053 2.492484 TCTAGTTTGAGGAGTCTTCGGC 59.508 50.000 0.00 0.00 0.00 5.54
4962 10059 0.108567 GAGGAGTCTTCGGCCAACTC 60.109 60.000 2.24 9.68 38.94 3.01
4965 10062 0.034896 GAGTCTTCGGCCAACTCCAA 59.965 55.000 2.24 0.00 34.63 3.53
4970 10067 4.025401 CGGCCAACTCCAACGCAC 62.025 66.667 2.24 0.00 0.00 5.34
5003 10100 3.068064 GGCCATGTCCGTTTGGGG 61.068 66.667 0.00 0.00 36.01 4.96
5007 10104 1.459450 CCATGTCCGTTTGGGGTAAG 58.541 55.000 0.00 0.00 36.01 2.34
5029 10126 2.126502 CACAAATCGCGGCCCAAC 60.127 61.111 6.13 0.00 0.00 3.77
5089 10186 2.034999 TGGACGCATTCCCAACCC 59.965 61.111 0.00 0.00 45.17 4.11
5096 10193 2.900546 ACGCATTCCCAACCCAAATTTA 59.099 40.909 0.00 0.00 0.00 1.40
5122 10219 2.902484 GCGTTTGCGTCAAAATAGACAG 59.098 45.455 6.59 0.00 38.43 3.51
5124 10221 2.873170 TTGCGTCAAAATAGACAGCG 57.127 45.000 0.00 0.00 39.30 5.18
5126 10223 0.584054 GCGTCAAAATAGACAGCGCG 60.584 55.000 0.00 0.00 38.43 6.86
5131 10228 1.693083 AAAATAGACAGCGCGCGGAC 61.693 55.000 36.82 29.91 0.00 4.79
5161 10259 1.261480 GCTCTCTTGTCCTCCACTGA 58.739 55.000 0.00 0.00 0.00 3.41
5165 10263 0.105194 TCTTGTCCTCCACTGACCCA 60.105 55.000 0.00 0.00 31.60 4.51
5166 10264 0.035458 CTTGTCCTCCACTGACCCAC 59.965 60.000 0.00 0.00 31.60 4.61
5167 10265 0.399949 TTGTCCTCCACTGACCCACT 60.400 55.000 0.00 0.00 31.60 4.00
5168 10266 0.399949 TGTCCTCCACTGACCCACTT 60.400 55.000 0.00 0.00 31.60 3.16
5182 10280 1.164041 CCACTTGTCGGGGACACAAC 61.164 60.000 0.00 0.00 42.60 3.32
5183 10281 1.227438 ACTTGTCGGGGACACAACG 60.227 57.895 0.00 0.00 42.60 4.10
5184 10282 2.589442 TTGTCGGGGACACAACGC 60.589 61.111 0.00 0.00 42.60 4.84
5185 10283 4.953868 TGTCGGGGACACAACGCG 62.954 66.667 3.53 3.53 44.34 6.01
5192 10290 3.712881 GACACAACGCGCCCACTC 61.713 66.667 5.73 0.00 0.00 3.51
5220 10318 0.541998 CTTTCCCCAAACCCTCCCAC 60.542 60.000 0.00 0.00 0.00 4.61
5268 10371 2.114411 GTGCCCCGAAGAAACCCA 59.886 61.111 0.00 0.00 0.00 4.51
5269 10372 1.971695 GTGCCCCGAAGAAACCCAG 60.972 63.158 0.00 0.00 0.00 4.45
5270 10373 3.062466 GCCCCGAAGAAACCCAGC 61.062 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.795469 ACATGCAAATCCACCTCATCATA 58.205 39.130 0.00 0.00 0.00 2.15
3 4 5.357878 TCTTAACATGCAAATCCACCTCATC 59.642 40.000 0.00 0.00 0.00 2.92
6 7 4.943705 TCTCTTAACATGCAAATCCACCTC 59.056 41.667 0.00 0.00 0.00 3.85
7 8 4.922206 TCTCTTAACATGCAAATCCACCT 58.078 39.130 0.00 0.00 0.00 4.00
8 9 5.643379 TTCTCTTAACATGCAAATCCACC 57.357 39.130 0.00 0.00 0.00 4.61
9 10 7.917505 CCTATTTCTCTTAACATGCAAATCCAC 59.082 37.037 0.00 0.00 0.00 4.02
10 11 7.615365 ACCTATTTCTCTTAACATGCAAATCCA 59.385 33.333 0.00 0.00 0.00 3.41
11 12 8.000780 ACCTATTTCTCTTAACATGCAAATCC 57.999 34.615 0.00 0.00 0.00 3.01
14 15 9.515226 ACTAACCTATTTCTCTTAACATGCAAA 57.485 29.630 0.00 0.00 0.00 3.68
15 16 8.946085 CACTAACCTATTTCTCTTAACATGCAA 58.054 33.333 0.00 0.00 0.00 4.08
16 17 7.552687 CCACTAACCTATTTCTCTTAACATGCA 59.447 37.037 0.00 0.00 0.00 3.96
17 18 7.012421 CCCACTAACCTATTTCTCTTAACATGC 59.988 40.741 0.00 0.00 0.00 4.06
18 19 7.012421 GCCCACTAACCTATTTCTCTTAACATG 59.988 40.741 0.00 0.00 0.00 3.21
20 21 6.214819 AGCCCACTAACCTATTTCTCTTAACA 59.785 38.462 0.00 0.00 0.00 2.41
21 22 6.651086 AGCCCACTAACCTATTTCTCTTAAC 58.349 40.000 0.00 0.00 0.00 2.01
22 23 6.886178 AGCCCACTAACCTATTTCTCTTAA 57.114 37.500 0.00 0.00 0.00 1.85
24 25 5.965091 AGTAGCCCACTAACCTATTTCTCTT 59.035 40.000 0.00 0.00 34.98 2.85
26 27 5.873146 AGTAGCCCACTAACCTATTTCTC 57.127 43.478 0.00 0.00 34.98 2.87
57 58 9.696917 GTTCCAAAATAGATGATTCAACTTTGT 57.303 29.630 1.47 0.00 0.00 2.83
58 59 8.853345 CGTTCCAAAATAGATGATTCAACTTTG 58.147 33.333 1.47 1.65 0.00 2.77
59 60 8.028938 CCGTTCCAAAATAGATGATTCAACTTT 58.971 33.333 1.47 0.00 0.00 2.66
63 64 7.393234 ACTTCCGTTCCAAAATAGATGATTCAA 59.607 33.333 0.00 0.00 0.00 2.69
64 65 6.884295 ACTTCCGTTCCAAAATAGATGATTCA 59.116 34.615 0.00 0.00 0.00 2.57
65 66 7.321745 ACTTCCGTTCCAAAATAGATGATTC 57.678 36.000 0.00 0.00 0.00 2.52
67 68 7.565680 ACTACTTCCGTTCCAAAATAGATGAT 58.434 34.615 0.00 0.00 0.00 2.45
68 69 6.942976 ACTACTTCCGTTCCAAAATAGATGA 58.057 36.000 0.00 0.00 0.00 2.92
69 70 7.611213 AACTACTTCCGTTCCAAAATAGATG 57.389 36.000 0.00 0.00 0.00 2.90
71 72 7.899973 ACTAACTACTTCCGTTCCAAAATAGA 58.100 34.615 0.00 0.00 0.00 1.98
72 73 9.298774 CTACTAACTACTTCCGTTCCAAAATAG 57.701 37.037 0.00 0.00 0.00 1.73
73 74 8.806146 ACTACTAACTACTTCCGTTCCAAAATA 58.194 33.333 0.00 0.00 0.00 1.40
74 75 7.674120 ACTACTAACTACTTCCGTTCCAAAAT 58.326 34.615 0.00 0.00 0.00 1.82
75 76 7.054491 ACTACTAACTACTTCCGTTCCAAAA 57.946 36.000 0.00 0.00 0.00 2.44
77 78 6.127897 GCTACTACTAACTACTTCCGTTCCAA 60.128 42.308 0.00 0.00 0.00 3.53
78 79 5.355350 GCTACTACTAACTACTTCCGTTCCA 59.645 44.000 0.00 0.00 0.00 3.53
79 80 5.355350 TGCTACTACTAACTACTTCCGTTCC 59.645 44.000 0.00 0.00 0.00 3.62
80 81 6.428385 TGCTACTACTAACTACTTCCGTTC 57.572 41.667 0.00 0.00 0.00 3.95
81 82 7.401955 AATGCTACTACTAACTACTTCCGTT 57.598 36.000 0.00 0.00 0.00 4.44
82 83 7.256286 CAAATGCTACTACTAACTACTTCCGT 58.744 38.462 0.00 0.00 0.00 4.69
83 84 6.696148 CCAAATGCTACTACTAACTACTTCCG 59.304 42.308 0.00 0.00 0.00 4.30
87 88 9.417561 TGTATCCAAATGCTACTACTAACTACT 57.582 33.333 0.00 0.00 0.00 2.57
88 89 9.680315 CTGTATCCAAATGCTACTACTAACTAC 57.320 37.037 0.00 0.00 0.00 2.73
89 90 9.636789 TCTGTATCCAAATGCTACTACTAACTA 57.363 33.333 0.00 0.00 0.00 2.24
90 91 8.534954 TCTGTATCCAAATGCTACTACTAACT 57.465 34.615 0.00 0.00 0.00 2.24
91 92 9.250624 CTTCTGTATCCAAATGCTACTACTAAC 57.749 37.037 0.00 0.00 0.00 2.34
93 94 8.762481 TCTTCTGTATCCAAATGCTACTACTA 57.238 34.615 0.00 0.00 0.00 1.82
94 95 7.661536 TCTTCTGTATCCAAATGCTACTACT 57.338 36.000 0.00 0.00 0.00 2.57
99 100 7.388776 GTGCATATCTTCTGTATCCAAATGCTA 59.611 37.037 0.00 0.00 38.36 3.49
100 101 6.206243 GTGCATATCTTCTGTATCCAAATGCT 59.794 38.462 0.00 0.00 38.36 3.79
101 102 6.016860 TGTGCATATCTTCTGTATCCAAATGC 60.017 38.462 0.00 0.00 38.10 3.56
102 103 7.500720 TGTGCATATCTTCTGTATCCAAATG 57.499 36.000 0.00 0.00 0.00 2.32
103 104 8.523915 TTTGTGCATATCTTCTGTATCCAAAT 57.476 30.769 0.00 0.00 0.00 2.32
104 105 7.936496 TTTGTGCATATCTTCTGTATCCAAA 57.064 32.000 0.00 0.00 0.00 3.28
105 106 8.523915 AATTTGTGCATATCTTCTGTATCCAA 57.476 30.769 0.00 0.00 0.00 3.53
106 107 8.407832 CAAATTTGTGCATATCTTCTGTATCCA 58.592 33.333 10.15 0.00 0.00 3.41
107 108 7.864379 CCAAATTTGTGCATATCTTCTGTATCC 59.136 37.037 16.73 0.00 0.00 2.59
108 109 8.623903 TCCAAATTTGTGCATATCTTCTGTATC 58.376 33.333 16.73 0.00 0.00 2.24
109 110 8.523915 TCCAAATTTGTGCATATCTTCTGTAT 57.476 30.769 16.73 0.00 0.00 2.29
110 111 7.936496 TCCAAATTTGTGCATATCTTCTGTA 57.064 32.000 16.73 0.00 0.00 2.74
111 112 6.839124 TCCAAATTTGTGCATATCTTCTGT 57.161 33.333 16.73 0.00 0.00 3.41
113 114 8.086522 GCATATCCAAATTTGTGCATATCTTCT 58.913 33.333 20.54 0.00 33.09 2.85
114 115 7.868922 TGCATATCCAAATTTGTGCATATCTTC 59.131 33.333 22.96 11.14 37.63 2.87
115 116 7.728148 TGCATATCCAAATTTGTGCATATCTT 58.272 30.769 22.96 1.07 37.63 2.40
116 117 7.292713 TGCATATCCAAATTTGTGCATATCT 57.707 32.000 22.96 1.61 37.63 1.98
117 118 6.090358 GCTGCATATCCAAATTTGTGCATATC 59.910 38.462 25.43 17.06 41.17 1.63
118 119 5.929992 GCTGCATATCCAAATTTGTGCATAT 59.070 36.000 25.43 16.57 41.17 1.78
119 120 5.163437 TGCTGCATATCCAAATTTGTGCATA 60.163 36.000 25.43 17.94 41.17 3.14
120 121 4.124238 GCTGCATATCCAAATTTGTGCAT 58.876 39.130 25.43 14.10 41.17 3.96
121 122 3.056035 TGCTGCATATCCAAATTTGTGCA 60.056 39.130 24.33 24.33 39.94 4.57
123 124 5.172934 ACTTGCTGCATATCCAAATTTGTG 58.827 37.500 16.73 9.41 0.00 3.33
124 125 5.410355 ACTTGCTGCATATCCAAATTTGT 57.590 34.783 16.73 2.12 0.00 2.83
125 126 6.812656 TGTAACTTGCTGCATATCCAAATTTG 59.187 34.615 11.40 11.40 0.00 2.32
126 127 6.813152 GTGTAACTTGCTGCATATCCAAATTT 59.187 34.615 1.84 0.00 0.00 1.82
129 130 4.764308 TGTGTAACTTGCTGCATATCCAAA 59.236 37.500 1.84 0.00 38.04 3.28
130 131 4.331108 TGTGTAACTTGCTGCATATCCAA 58.669 39.130 1.84 0.00 38.04 3.53
133 134 4.155826 TGGTTGTGTAACTTGCTGCATATC 59.844 41.667 1.84 0.00 38.04 1.63
135 136 3.481453 TGGTTGTGTAACTTGCTGCATA 58.519 40.909 1.84 0.00 38.04 3.14
136 137 2.294233 CTGGTTGTGTAACTTGCTGCAT 59.706 45.455 1.84 0.00 38.04 3.96
137 138 1.675483 CTGGTTGTGTAACTTGCTGCA 59.325 47.619 0.00 0.00 38.04 4.41
138 139 1.001378 CCTGGTTGTGTAACTTGCTGC 60.001 52.381 0.00 0.00 38.04 5.25
139 140 2.297701 ACCTGGTTGTGTAACTTGCTG 58.702 47.619 0.00 0.00 38.04 4.41
141 142 2.685897 TGAACCTGGTTGTGTAACTTGC 59.314 45.455 18.42 0.00 38.04 4.01
154 155 3.121030 CGCGCCTTCTGAACCTGG 61.121 66.667 0.00 0.00 0.00 4.45
170 171 1.322338 CGCCTCCGTATGTACAAAACG 59.678 52.381 21.04 21.04 36.42 3.60
198 200 2.107750 ATCGCTGACGGGCTGATG 59.892 61.111 0.00 0.00 40.63 3.07
274 285 2.744307 AAAGACGACGAGGACCACGC 62.744 60.000 11.51 3.70 0.00 5.34
278 289 2.087009 CGCAAAGACGACGAGGACC 61.087 63.158 0.00 0.00 34.06 4.46
315 326 1.356398 GGGTGTGGGTTATTTGGAGGA 59.644 52.381 0.00 0.00 0.00 3.71
566 585 2.274437 GACCGAAATTCCCGACCTAAC 58.726 52.381 2.26 0.00 0.00 2.34
598 617 8.603898 TGAATACTTACTGGAATCCTAAGACA 57.396 34.615 13.29 6.69 0.00 3.41
809 3791 1.202687 TCCTGAGCCCAATTGCTATCG 60.203 52.381 0.00 0.00 42.95 2.92
843 3825 2.991250 AGCTCAACGCATCCTGTTAAT 58.009 42.857 0.00 0.00 42.61 1.40
856 3839 8.707938 AAATTAGCCATGAAAATAAGCTCAAC 57.292 30.769 0.00 0.00 35.03 3.18
884 3871 8.200120 TCAGTATTATCAGTGTGAAGGAAGATG 58.800 37.037 0.00 0.00 0.00 2.90
895 3885 8.140628 GTGTCATCTCATCAGTATTATCAGTGT 58.859 37.037 0.00 0.00 0.00 3.55
905 3895 4.604156 ACCAGAGTGTCATCTCATCAGTA 58.396 43.478 5.57 0.00 36.97 2.74
907 3897 4.182339 CAACCAGAGTGTCATCTCATCAG 58.818 47.826 5.57 0.00 36.97 2.90
961 3961 4.324267 ACCACCTTATGCTGTCAGTTTAC 58.676 43.478 0.93 0.00 0.00 2.01
1074 4074 3.150767 CCCAAATTCCTTCACCGTACAA 58.849 45.455 0.00 0.00 0.00 2.41
1160 4160 7.175104 ACTGATCAGCTTGGAACCTTTATTTA 58.825 34.615 22.83 0.00 0.00 1.40
1288 4288 3.181498 TGTCATTCACCATTGCATTAGCG 60.181 43.478 0.00 0.00 46.23 4.26
1307 4307 7.066766 AGAGAAAAGGTGCATAGAAATGATGTC 59.933 37.037 0.00 0.00 34.84 3.06
1426 5343 5.242393 CCTCTTCAAATCCAATTATCCGCAT 59.758 40.000 0.00 0.00 0.00 4.73
1500 5417 4.394729 TGTATTGACCCTGTGGAAGTTTC 58.605 43.478 0.00 0.00 34.81 2.78
1515 5432 7.905604 ACGAAAATCACAGAAGATGTATTGA 57.094 32.000 0.00 0.00 41.41 2.57
1539 5456 1.269012 CCCCGGGTAAGTGAAGTGTA 58.731 55.000 21.85 0.00 0.00 2.90
1577 5494 7.614583 TGAACCGAAAAACATATATGGGGTTAA 59.385 33.333 16.96 9.76 35.54 2.01
1579 5496 5.952947 TGAACCGAAAAACATATATGGGGTT 59.047 36.000 16.96 16.63 37.91 4.11
1633 5550 3.447742 CAAAAAGAGCAAACTGGTGTCC 58.552 45.455 0.00 0.00 0.00 4.02
1653 5570 2.021441 AGGTTGACATATAGGGGGTCCA 60.021 50.000 0.00 0.00 34.83 4.02
1676 5593 5.180868 GCATGAGCAGGAGTAAGATTTATGG 59.819 44.000 0.00 0.00 41.58 2.74
1690 5607 2.939103 GGTACAAAGTAGCATGAGCAGG 59.061 50.000 0.00 0.00 45.49 4.85
1735 5652 8.469309 TGATCCAATGGAAAGAGAATTATTCC 57.531 34.615 5.89 0.00 42.39 3.01
1863 6490 3.642848 AGCAGACAACATGATTTTGGGTT 59.357 39.130 0.00 0.00 0.00 4.11
1933 6560 6.109359 AGAAAGTTAGTGGTATGAGATGCAC 58.891 40.000 0.00 0.00 0.00 4.57
1935 6562 7.717568 TCTAGAAAGTTAGTGGTATGAGATGC 58.282 38.462 0.00 0.00 0.00 3.91
1978 6605 2.492484 ACCTGACACGATCAAGGAGTAC 59.508 50.000 12.84 0.00 36.69 2.73
2058 6699 7.935338 ATACAAATCAAACAGAAAGTTGCTG 57.065 32.000 9.51 9.51 41.19 4.41
2072 6713 6.367695 CGCCTATCCACGATTATACAAATCAA 59.632 38.462 0.00 0.00 0.00 2.57
2223 6865 8.408043 TGAAGATTGTTACCTTGTTCATGATT 57.592 30.769 0.00 0.00 0.00 2.57
2422 7068 8.098220 TGCTGCGTGATGAATATTAATTGTAT 57.902 30.769 0.00 0.00 0.00 2.29
2634 7284 5.556355 AACCCGTAACTATAGCAAAAAGC 57.444 39.130 0.00 0.00 46.19 3.51
2751 7403 4.893524 GGTAACAGGGGCAGCTAAAATAAT 59.106 41.667 0.00 0.00 0.00 1.28
2851 7509 2.649312 TGATTTGGTCCAGTCCAAGGAT 59.351 45.455 0.00 0.00 46.27 3.24
2962 7620 0.252742 AACTCGATCCTCCCCCAAGT 60.253 55.000 0.00 0.00 0.00 3.16
3091 7749 8.567948 GCTTGTGTACCTTGCACATTATATATT 58.432 33.333 0.00 0.00 44.91 1.28
3093 7751 7.226523 CAGCTTGTGTACCTTGCACATTATATA 59.773 37.037 0.00 0.00 44.91 0.86
3145 7803 9.696917 GTCTTCACATTTTCCTGAACAAAATAT 57.303 29.630 0.00 0.00 32.74 1.28
3146 7804 7.860373 CGTCTTCACATTTTCCTGAACAAAATA 59.140 33.333 0.00 0.00 32.74 1.40
3152 7810 3.813166 TCCGTCTTCACATTTTCCTGAAC 59.187 43.478 0.00 0.00 0.00 3.18
3170 7828 0.544357 TCATCTGGGTCTGGTTCCGT 60.544 55.000 0.00 0.00 0.00 4.69
3217 7875 2.224843 TGCTGGTCCTGATGTCACAATT 60.225 45.455 0.00 0.00 0.00 2.32
3233 7891 2.440409 AGATGCTACAAAACCTGCTGG 58.560 47.619 8.29 8.29 39.83 4.85
3324 7982 4.271807 TCATCAGGATCAGGTTCTAGGT 57.728 45.455 0.00 0.00 0.00 3.08
3376 8034 6.569179 TCATTATCATGCTCACCATTGATG 57.431 37.500 0.00 0.00 29.71 3.07
3415 8073 2.699954 AGGACAAATTCACTAGTGCCG 58.300 47.619 18.45 6.64 0.00 5.69
3418 8076 7.493971 CCAGATTCTAGGACAAATTCACTAGTG 59.506 40.741 17.17 17.17 35.56 2.74
3436 8094 5.709164 CACTTCCATCTTGTTTCCAGATTCT 59.291 40.000 0.00 0.00 0.00 2.40
3508 8166 2.158475 AGAGCTAGAGGAGTCATCAGGG 60.158 54.545 7.65 0.00 0.00 4.45
3537 8195 2.022195 CATCAATGCTCACCTTCTGGG 58.978 52.381 0.00 0.00 41.89 4.45
3570 8228 3.387374 ACTAGCATCTGGATCAGGTTCTG 59.613 47.826 0.00 0.00 31.51 3.02
3612 8270 5.528690 TCCGCTTGAATCTTATTTCCAGATG 59.471 40.000 0.00 0.00 31.00 2.90
3682 8340 0.894835 TAGCAGCATTGTCGTCAGGA 59.105 50.000 0.00 0.00 0.00 3.86
3691 8349 3.789756 CGCTCTTCAAATTAGCAGCATTG 59.210 43.478 0.00 0.00 35.98 2.82
3766 8424 3.118038 ACCGGAGCATTTCAATAGCCTTA 60.118 43.478 9.46 0.00 0.00 2.69
3972 8630 4.226168 AGGATTGGTCTAGAAGTTTGGAGG 59.774 45.833 0.00 0.00 0.00 4.30
4049 8707 7.014230 AGCAGAATTTTAAGACTTAAGTGGCAA 59.986 33.333 14.14 0.58 0.00 4.52
4168 9104 2.013563 GCACGCCCAATCTCATCTGAA 61.014 52.381 0.00 0.00 0.00 3.02
4171 9107 0.463295 CTGCACGCCCAATCTCATCT 60.463 55.000 0.00 0.00 0.00 2.90
4337 9273 1.072173 CTCATCCCACAAGACCACACA 59.928 52.381 0.00 0.00 0.00 3.72
4387 9324 7.798596 ATTTGATATACAGTTGAGAAGCTGG 57.201 36.000 0.00 0.00 37.07 4.85
4496 9435 2.974489 GCGCAGTGAGCACAGCATT 61.974 57.895 14.47 0.00 46.13 3.56
4508 9447 2.965716 AAAAGGGAGCACTGCGCAGT 62.966 55.000 36.44 36.44 46.13 4.40
4509 9448 1.799258 AAAAAGGGAGCACTGCGCAG 61.799 55.000 34.89 34.89 46.13 5.18
4513 9452 0.315251 GTCCAAAAAGGGAGCACTGC 59.685 55.000 0.00 0.00 37.71 4.40
4524 9463 2.878406 CGCTCTCTCCAAAGTCCAAAAA 59.122 45.455 0.00 0.00 0.00 1.94
4532 9471 1.004560 TGTGGCGCTCTCTCCAAAG 60.005 57.895 7.64 0.00 33.57 2.77
4533 9472 1.301716 GTGTGGCGCTCTCTCCAAA 60.302 57.895 7.64 0.00 33.57 3.28
4534 9473 2.038814 TTGTGTGGCGCTCTCTCCAA 62.039 55.000 7.64 0.35 33.57 3.53
4535 9474 2.506957 TTGTGTGGCGCTCTCTCCA 61.507 57.895 7.64 0.00 0.00 3.86
4536 9475 2.029844 GTTGTGTGGCGCTCTCTCC 61.030 63.158 7.64 0.00 0.00 3.71
4537 9476 0.601311 AAGTTGTGTGGCGCTCTCTC 60.601 55.000 7.64 0.39 0.00 3.20
4538 9477 0.179045 AAAGTTGTGTGGCGCTCTCT 60.179 50.000 7.64 0.00 0.00 3.10
4539 9478 0.663153 AAAAGTTGTGTGGCGCTCTC 59.337 50.000 7.64 2.81 0.00 3.20
4541 9480 3.641031 AAAAAGTTGTGTGGCGCTC 57.359 47.368 7.64 1.21 0.00 5.03
4666 9605 1.885163 CTTCCTAGGTCACCGGCGTT 61.885 60.000 9.08 0.00 0.00 4.84
4675 9621 3.028130 CCAGGTTCTCTCTTCCTAGGTC 58.972 54.545 9.08 0.00 0.00 3.85
4682 9628 4.545208 AGTTTAGCCAGGTTCTCTCTTC 57.455 45.455 0.00 0.00 0.00 2.87
4692 9638 3.562973 CAGATGCACATAGTTTAGCCAGG 59.437 47.826 0.00 0.00 0.00 4.45
4693 9639 4.445453 TCAGATGCACATAGTTTAGCCAG 58.555 43.478 0.00 0.00 0.00 4.85
4713 9659 4.993905 TCGAAGATCGTGCTTCTAATTCA 58.006 39.130 14.66 0.00 41.60 2.57
4715 9661 5.869888 ACTTTCGAAGATCGTGCTTCTAATT 59.130 36.000 14.66 0.00 41.60 1.40
4719 9665 3.305398 ACTTTCGAAGATCGTGCTTCT 57.695 42.857 14.66 0.00 41.60 2.85
4777 9866 9.677567 GACTTCAAGCAGTTTTATTTCAACATA 57.322 29.630 0.00 0.00 0.00 2.29
4778 9867 8.416329 AGACTTCAAGCAGTTTTATTTCAACAT 58.584 29.630 0.00 0.00 0.00 2.71
4779 9868 7.771183 AGACTTCAAGCAGTTTTATTTCAACA 58.229 30.769 0.00 0.00 0.00 3.33
4780 9869 9.730420 TTAGACTTCAAGCAGTTTTATTTCAAC 57.270 29.630 0.00 0.00 0.00 3.18
4785 9874 9.612620 CGAAATTAGACTTCAAGCAGTTTTATT 57.387 29.630 0.00 0.00 0.00 1.40
4786 9875 7.750903 GCGAAATTAGACTTCAAGCAGTTTTAT 59.249 33.333 0.00 0.00 0.00 1.40
4787 9876 7.041372 AGCGAAATTAGACTTCAAGCAGTTTTA 60.041 33.333 0.00 0.00 0.00 1.52
4788 9877 5.915196 GCGAAATTAGACTTCAAGCAGTTTT 59.085 36.000 0.00 0.00 0.00 2.43
4789 9878 5.239525 AGCGAAATTAGACTTCAAGCAGTTT 59.760 36.000 0.00 0.00 0.00 2.66
4790 9879 4.757149 AGCGAAATTAGACTTCAAGCAGTT 59.243 37.500 0.00 0.00 0.00 3.16
4791 9880 4.319177 AGCGAAATTAGACTTCAAGCAGT 58.681 39.130 0.00 0.00 0.00 4.40
4792 9881 4.935885 AGCGAAATTAGACTTCAAGCAG 57.064 40.909 0.00 0.00 0.00 4.24
4836 9925 1.284491 TGATATCAACAAGGGCAGCCA 59.716 47.619 15.19 0.00 0.00 4.75
4889 9986 2.197577 GCACTAGCCGAAGATCTCAAC 58.802 52.381 0.00 0.00 33.58 3.18
4922 10019 1.303309 AACTAGAGGCGATTGCATGC 58.697 50.000 11.82 11.82 45.35 4.06
4923 10020 2.938451 TCAAACTAGAGGCGATTGCATG 59.062 45.455 7.38 0.00 45.35 4.06
4924 10021 3.201290 CTCAAACTAGAGGCGATTGCAT 58.799 45.455 7.38 0.00 45.35 3.96
4925 10022 2.621338 CTCAAACTAGAGGCGATTGCA 58.379 47.619 7.38 0.00 45.35 4.08
4939 10036 0.034896 TGGCCGAAGACTCCTCAAAC 59.965 55.000 0.00 0.00 0.00 2.93
4944 10041 1.976112 GAGTTGGCCGAAGACTCCT 59.024 57.895 14.16 0.00 35.02 3.69
4953 10050 4.025401 GTGCGTTGGAGTTGGCCG 62.025 66.667 0.00 0.00 0.00 6.13
4956 10053 2.604174 GGTCGTGCGTTGGAGTTGG 61.604 63.158 0.00 0.00 0.00 3.77
4962 10059 2.265182 ATTTGGGGTCGTGCGTTGG 61.265 57.895 0.00 0.00 0.00 3.77
4965 10062 2.671619 CCATTTGGGGTCGTGCGT 60.672 61.111 0.00 0.00 0.00 5.24
4986 10083 2.487274 TACCCCAAACGGACATGGCC 62.487 60.000 7.86 7.86 35.28 5.36
4991 10088 1.301874 CGCTTACCCCAAACGGACA 60.302 57.895 0.00 0.00 0.00 4.02
4992 10089 2.036571 CCGCTTACCCCAAACGGAC 61.037 63.158 0.00 0.00 46.71 4.79
4998 10095 0.183014 TTTGTGTCCGCTTACCCCAA 59.817 50.000 0.00 0.00 0.00 4.12
5003 10100 0.247145 CGCGATTTGTGTCCGCTTAC 60.247 55.000 0.00 0.00 45.91 2.34
5007 10104 4.811761 GCCGCGATTTGTGTCCGC 62.812 66.667 8.23 0.00 44.81 5.54
5033 10130 1.078426 ATTTGTCCGCTTCCTCCCG 60.078 57.895 0.00 0.00 0.00 5.14
5039 10136 2.681152 AACGAACATTTGTCCGCTTC 57.319 45.000 0.00 0.00 0.00 3.86
5089 10186 0.713329 GCAAACGCGGCCTAAATTTG 59.287 50.000 12.47 11.32 34.17 2.32
5109 10206 0.584054 CGCGCGCTGTCTATTTTGAC 60.584 55.000 30.48 0.00 37.47 3.18
5134 10231 3.612371 GACAAGAGAGCGCGTCCGT 62.612 63.158 8.43 3.45 36.67 4.69
5138 10235 2.569134 GAGGACAAGAGAGCGCGT 59.431 61.111 8.43 0.00 0.00 6.01
5139 10236 2.202676 GGAGGACAAGAGAGCGCG 60.203 66.667 0.00 0.00 0.00 6.86
5140 10237 1.446966 GTGGAGGACAAGAGAGCGC 60.447 63.158 0.00 0.00 0.00 5.92
5141 10238 0.108898 CAGTGGAGGACAAGAGAGCG 60.109 60.000 0.00 0.00 0.00 5.03
5142 10239 1.067213 GTCAGTGGAGGACAAGAGAGC 60.067 57.143 0.00 0.00 35.36 4.09
5143 10240 1.548269 GGTCAGTGGAGGACAAGAGAG 59.452 57.143 0.00 0.00 37.00 3.20
5144 10241 1.633774 GGTCAGTGGAGGACAAGAGA 58.366 55.000 0.00 0.00 37.00 3.10
5145 10242 0.610687 GGGTCAGTGGAGGACAAGAG 59.389 60.000 0.00 0.00 37.00 2.85
5146 10243 0.105194 TGGGTCAGTGGAGGACAAGA 60.105 55.000 0.00 0.00 37.00 3.02
5161 10259 2.446994 TGTCCCCGACAAGTGGGT 60.447 61.111 0.58 0.00 45.86 4.51
5165 10263 1.227438 CGTTGTGTCCCCGACAAGT 60.227 57.895 0.00 0.00 44.49 3.16
5166 10264 2.604174 GCGTTGTGTCCCCGACAAG 61.604 63.158 0.00 0.00 44.49 3.16
5167 10265 2.589442 GCGTTGTGTCCCCGACAA 60.589 61.111 0.00 0.00 44.49 3.18
5168 10266 4.953868 CGCGTTGTGTCCCCGACA 62.954 66.667 0.00 0.00 40.50 4.35
5198 10296 1.078528 GAGGGTTTGGGGAAAGGGG 59.921 63.158 0.00 0.00 0.00 4.79
5201 10299 0.541998 GTGGGAGGGTTTGGGGAAAG 60.542 60.000 0.00 0.00 0.00 2.62
5232 10330 1.228063 CGGCAATGGAGGAGGGATG 60.228 63.158 0.00 0.00 0.00 3.51
5233 10331 2.455565 CCGGCAATGGAGGAGGGAT 61.456 63.158 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.