Multiple sequence alignment - TraesCS1B01G393200

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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 TraesCS1B01G393200 chr1B 100.000 3760 0 0 1 3760 626106609 626102850 0.000000e+00 6944.0
1 TraesCS1B01G393200 chr1B 97.917 48 1 0 156 203 626136210 626136163 2.410000e-12 84.2
2 TraesCS1B01G393200 chr1B 97.619 42 1 0 13 54 626136561 626136520 5.210000e-09 73.1
3 TraesCS1B01G393200 chr1D 88.577 3738 224 98 56 3702 455768231 455764606 0.000000e+00 4349.0
4 TraesCS1B01G393200 chr1A 88.801 2402 169 57 168 2538 549315387 549313055 0.000000e+00 2854.0
5 TraesCS1B01G393200 chr1A 91.058 1040 63 13 2542 3569 549312922 549311901 0.000000e+00 1378.0
6 TraesCS1B01G393200 chr1A 92.179 179 11 3 3583 3760 549306669 549306493 2.240000e-62 250.0
7 TraesCS1B01G393200 chr5B 93.023 86 6 0 873 958 108496592 108496507 3.940000e-25 126.0
8 TraesCS1B01G393200 chr5B 92.453 53 4 0 2380 2432 130516930 130516982 4.030000e-10 76.8
9 TraesCS1B01G393200 chr4B 95.522 67 3 0 892 958 669567783 669567717 1.430000e-19 108.0
10 TraesCS1B01G393200 chr4B 94.030 67 4 0 889 955 98597818 98597884 6.640000e-18 102.0
11 TraesCS1B01G393200 chr7D 95.652 46 2 0 2383 2428 577219679 577219724 1.450000e-09 75.0
12 TraesCS1B01G393200 chr7B 91.071 56 3 2 2375 2429 631056904 631056958 1.450000e-09 75.0
13 TraesCS1B01G393200 chr7B 90.566 53 5 0 2384 2436 700180671 700180723 1.870000e-08 71.3
14 TraesCS1B01G393200 chr5D 92.157 51 3 1 2380 2430 6376276 6376325 1.870000e-08 71.3
15 TraesCS1B01G393200 chr3D 86.364 66 7 2 2383 2446 571052705 571052770 1.870000e-08 71.3
16 TraesCS1B01G393200 chr6D 86.441 59 8 0 2383 2441 28289944 28289886 8.720000e-07 65.8


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 TraesCS1B01G393200 chr1B 626102850 626106609 3759 True 6944 6944 100.0000 1 3760 1 chr1B.!!$R1 3759
1 TraesCS1B01G393200 chr1D 455764606 455768231 3625 True 4349 4349 88.5770 56 3702 1 chr1D.!!$R1 3646
2 TraesCS1B01G393200 chr1A 549311901 549315387 3486 True 2116 2854 89.9295 168 3569 2 chr1A.!!$R2 3401

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
132 133 0.037447 TGTTGATCATTCACCGGCCA 59.963 50.0 0.0 0.0 0.00 5.36 F
147 148 0.037975 GGCCAAACCTGTCATGCTTG 60.038 55.0 0.0 0.0 34.51 4.01 F
1188 1260 0.103026 TCGCCGAGTTCATGATGGAG 59.897 55.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 1401 0.030235 CGTTCGTCCACAGTCAGACA 59.970 55.0 2.66 0.0 33.08 3.41 R
1333 1405 0.038618 CATCCGTTCGTCCACAGTCA 60.039 55.0 0.00 0.0 0.00 3.41 R
3082 3308 0.037232 CTCTTCGTTCCCTTTCGCCT 60.037 55.0 0.00 0.0 0.00 5.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.791355 GTCAAAACAATTAGGTTGACGTATTT 57.209 30.769 10.00 0.00 40.16 1.40
26 27 9.240159 GTCAAAACAATTAGGTTGACGTATTTT 57.760 29.630 10.00 0.00 40.16 1.82
27 28 9.453325 TCAAAACAATTAGGTTGACGTATTTTC 57.547 29.630 0.00 0.00 40.37 2.29
28 29 9.239002 CAAAACAATTAGGTTGACGTATTTTCA 57.761 29.630 0.00 0.00 40.37 2.69
29 30 9.804758 AAAACAATTAGGTTGACGTATTTTCAA 57.195 25.926 0.00 0.00 40.37 2.69
38 39 6.438259 TTGACGTATTTTCAACACTTTGGA 57.562 33.333 0.00 0.00 33.06 3.53
39 40 6.627395 TGACGTATTTTCAACACTTTGGAT 57.373 33.333 0.00 0.00 33.06 3.41
40 41 7.033530 TGACGTATTTTCAACACTTTGGATT 57.966 32.000 0.00 0.00 33.06 3.01
41 42 8.155821 TGACGTATTTTCAACACTTTGGATTA 57.844 30.769 0.00 0.00 33.06 1.75
42 43 8.788806 TGACGTATTTTCAACACTTTGGATTAT 58.211 29.630 0.00 0.00 33.06 1.28
79 80 9.866655 AAATATGGCATTTTATACTCTCTTGGA 57.133 29.630 4.78 0.00 0.00 3.53
80 81 9.866655 AATATGGCATTTTATACTCTCTTGGAA 57.133 29.630 4.78 0.00 0.00 3.53
107 108 4.052229 CGGCGTGTCGACCCTCTT 62.052 66.667 14.12 0.00 0.00 2.85
108 109 2.432628 GGCGTGTCGACCCTCTTG 60.433 66.667 14.12 0.00 0.00 3.02
125 126 4.216902 CCTCTTGCTTGTGTTGATCATTCA 59.783 41.667 0.00 0.00 0.00 2.57
132 133 0.037447 TGTTGATCATTCACCGGCCA 59.963 50.000 0.00 0.00 0.00 5.36
133 134 1.173043 GTTGATCATTCACCGGCCAA 58.827 50.000 0.00 0.00 0.00 4.52
134 135 1.543802 GTTGATCATTCACCGGCCAAA 59.456 47.619 0.00 0.00 0.00 3.28
135 136 1.173043 TGATCATTCACCGGCCAAAC 58.827 50.000 0.00 0.00 0.00 2.93
136 137 0.455815 GATCATTCACCGGCCAAACC 59.544 55.000 0.00 0.00 0.00 3.27
137 138 0.039618 ATCATTCACCGGCCAAACCT 59.960 50.000 0.00 0.00 35.61 3.50
138 139 0.893270 TCATTCACCGGCCAAACCTG 60.893 55.000 0.00 0.00 35.61 4.00
139 140 1.152830 ATTCACCGGCCAAACCTGT 59.847 52.632 0.00 0.00 36.06 4.00
140 141 0.893727 ATTCACCGGCCAAACCTGTC 60.894 55.000 0.00 0.00 32.76 3.51
141 142 2.203280 CACCGGCCAAACCTGTCA 60.203 61.111 0.00 0.00 32.76 3.58
142 143 1.603455 CACCGGCCAAACCTGTCAT 60.603 57.895 0.00 0.00 32.76 3.06
143 144 1.603455 ACCGGCCAAACCTGTCATG 60.603 57.895 0.00 0.00 27.81 3.07
144 145 2.568090 CGGCCAAACCTGTCATGC 59.432 61.111 2.24 0.00 35.61 4.06
145 146 1.973281 CGGCCAAACCTGTCATGCT 60.973 57.895 2.24 0.00 35.61 3.79
146 147 1.526575 CGGCCAAACCTGTCATGCTT 61.527 55.000 2.24 0.00 35.61 3.91
147 148 0.037975 GGCCAAACCTGTCATGCTTG 60.038 55.000 0.00 0.00 34.51 4.01
148 149 0.668401 GCCAAACCTGTCATGCTTGC 60.668 55.000 0.00 0.00 0.00 4.01
149 150 0.963962 CCAAACCTGTCATGCTTGCT 59.036 50.000 0.00 0.00 0.00 3.91
150 151 2.161855 CCAAACCTGTCATGCTTGCTA 58.838 47.619 0.00 0.00 0.00 3.49
151 152 2.756760 CCAAACCTGTCATGCTTGCTAT 59.243 45.455 0.00 0.00 0.00 2.97
152 153 3.194116 CCAAACCTGTCATGCTTGCTATT 59.806 43.478 0.00 0.00 0.00 1.73
153 154 4.398988 CCAAACCTGTCATGCTTGCTATTA 59.601 41.667 0.00 0.00 0.00 0.98
154 155 5.335127 CAAACCTGTCATGCTTGCTATTAC 58.665 41.667 0.00 0.00 0.00 1.89
196 197 4.982916 GTCTGTCGACGCATAATAAATCCT 59.017 41.667 11.62 0.00 0.00 3.24
206 207 5.120208 CGCATAATAAATCCTAGACAACGGG 59.880 44.000 0.00 0.00 0.00 5.28
223 227 1.958205 GGAGCATTGATCTCCGGCG 60.958 63.158 0.00 0.00 40.51 6.46
237 241 2.943033 CTCCGGCGGAAGATATTGTTTT 59.057 45.455 30.59 0.00 0.00 2.43
303 307 2.430921 CCGTCGTCACAGCTCACC 60.431 66.667 0.00 0.00 0.00 4.02
305 309 1.080501 CGTCGTCACAGCTCACCAT 60.081 57.895 0.00 0.00 0.00 3.55
324 328 4.410743 GGCGCAAGTCAAGGCAGC 62.411 66.667 10.83 0.00 45.31 5.25
325 329 3.663176 GCGCAAGTCAAGGCAGCA 61.663 61.111 0.30 0.00 41.68 4.41
326 330 3.033184 CGCAAGTCAAGGCAGCAA 58.967 55.556 0.00 0.00 0.00 3.91
327 331 1.081641 CGCAAGTCAAGGCAGCAAG 60.082 57.895 0.00 0.00 0.00 4.01
328 332 1.509644 CGCAAGTCAAGGCAGCAAGA 61.510 55.000 0.00 0.00 0.00 3.02
329 333 0.886563 GCAAGTCAAGGCAGCAAGAT 59.113 50.000 0.00 0.00 0.00 2.40
330 334 1.271656 GCAAGTCAAGGCAGCAAGATT 59.728 47.619 0.00 0.00 0.00 2.40
455 461 4.704833 TCAGCCGCTCCCAGTTGC 62.705 66.667 0.00 0.00 0.00 4.17
459 465 4.431131 CCGCTCCCAGTTGCCCAT 62.431 66.667 0.00 0.00 0.00 4.00
462 468 2.988839 GCTCCCAGTTGCCCATCCT 61.989 63.158 0.00 0.00 0.00 3.24
463 469 1.225704 CTCCCAGTTGCCCATCCTC 59.774 63.158 0.00 0.00 0.00 3.71
464 470 1.229951 TCCCAGTTGCCCATCCTCT 60.230 57.895 0.00 0.00 0.00 3.69
465 471 1.225704 CCCAGTTGCCCATCCTCTC 59.774 63.158 0.00 0.00 0.00 3.20
474 480 1.120795 CCCATCCTCTCTCTCAGGCC 61.121 65.000 0.00 0.00 0.00 5.19
520 527 2.221981 GGGAGCATCGTCGAAATCAATC 59.778 50.000 0.00 0.00 34.37 2.67
522 529 1.860950 AGCATCGTCGAAATCAATCCG 59.139 47.619 0.00 0.00 0.00 4.18
529 536 3.539592 CGTCGAAATCAATCCGAGAAACG 60.540 47.826 0.00 0.00 42.18 3.60
544 552 2.333701 AAACGGACCGGCTCCAACTT 62.334 55.000 20.00 0.00 39.39 2.66
553 561 1.032114 GGCTCCAACTTCCCAATCGG 61.032 60.000 0.00 0.00 0.00 4.18
645 692 3.512516 GGCAGGACATTGAGCCGC 61.513 66.667 0.00 0.61 37.41 6.53
646 693 3.512516 GCAGGACATTGAGCCGCC 61.513 66.667 0.00 0.00 0.00 6.13
715 772 1.380650 GCGAAGGAGGAGGAGGAGT 60.381 63.158 0.00 0.00 0.00 3.85
734 793 2.725127 TAGGAGGTGGTGGTGCTCGT 62.725 60.000 0.00 0.00 0.00 4.18
757 816 2.668550 AAGCCGCCGTTGACTTCC 60.669 61.111 0.00 0.00 0.00 3.46
786 845 1.311403 TCCGGCAGGAGGAATCTCT 59.689 57.895 0.00 0.00 42.75 3.10
796 855 0.463620 AGGAATCTCTGCTCTTCGCC 59.536 55.000 0.00 0.00 38.05 5.54
836 898 2.733542 CGTCACTGCACCTGTCATCTAG 60.734 54.545 0.00 0.00 0.00 2.43
837 899 2.493675 GTCACTGCACCTGTCATCTAGA 59.506 50.000 0.00 0.00 0.00 2.43
838 900 2.757314 TCACTGCACCTGTCATCTAGAG 59.243 50.000 0.00 0.00 0.00 2.43
839 901 2.495270 CACTGCACCTGTCATCTAGAGT 59.505 50.000 0.00 0.00 0.00 3.24
840 902 3.696548 CACTGCACCTGTCATCTAGAGTA 59.303 47.826 0.00 0.00 0.00 2.59
869 931 0.464916 GGTCTCCGTCTCTCTCCTCC 60.465 65.000 0.00 0.00 0.00 4.30
908 970 4.516326 ATTCCCCTCCCCTCCCCG 62.516 72.222 0.00 0.00 0.00 5.73
937 1000 2.125952 GCATGGAAAACGCAGGCC 60.126 61.111 0.00 0.00 0.00 5.19
1188 1260 0.103026 TCGCCGAGTTCATGATGGAG 59.897 55.000 0.00 0.00 0.00 3.86
1266 1338 3.743017 CCCATCCACCCCCACCTG 61.743 72.222 0.00 0.00 0.00 4.00
1280 1352 2.227036 ACCTGCCCTCCTGACCTTG 61.227 63.158 0.00 0.00 0.00 3.61
1308 1380 6.697019 TCTGCAAAATTTCTTCTTTTTCCTCG 59.303 34.615 0.00 0.00 0.00 4.63
1329 1401 0.179067 TTGACCGAACCTTGCTCGTT 60.179 50.000 0.00 0.00 34.46 3.85
1333 1405 0.600255 CCGAACCTTGCTCGTTGTCT 60.600 55.000 0.00 0.00 34.46 3.41
1335 1407 1.865865 GAACCTTGCTCGTTGTCTGA 58.134 50.000 0.00 0.00 0.00 3.27
1336 1408 1.527311 GAACCTTGCTCGTTGTCTGAC 59.473 52.381 0.00 0.00 0.00 3.51
1337 1409 0.753262 ACCTTGCTCGTTGTCTGACT 59.247 50.000 9.51 0.00 0.00 3.41
1338 1410 1.143305 CCTTGCTCGTTGTCTGACTG 58.857 55.000 9.51 0.00 0.00 3.51
1339 1411 1.539065 CCTTGCTCGTTGTCTGACTGT 60.539 52.381 9.51 0.00 0.00 3.55
1341 1413 0.249447 TGCTCGTTGTCTGACTGTGG 60.249 55.000 9.51 0.00 0.00 4.17
1342 1414 0.032130 GCTCGTTGTCTGACTGTGGA 59.968 55.000 9.51 1.02 0.00 4.02
1343 1415 1.772182 CTCGTTGTCTGACTGTGGAC 58.228 55.000 9.51 0.00 0.00 4.02
1344 1416 0.030235 TCGTTGTCTGACTGTGGACG 59.970 55.000 9.51 10.92 35.45 4.79
1345 1417 0.030235 CGTTGTCTGACTGTGGACGA 59.970 55.000 9.51 0.00 35.45 4.20
1478 1550 2.584791 CGGTGCTGCTGTTAATTGTTC 58.415 47.619 0.00 0.00 0.00 3.18
1526 1598 5.698089 TCAGTTTATTCAGAACACTGCTCTG 59.302 40.000 11.75 3.37 41.47 3.35
1527 1599 4.453819 AGTTTATTCAGAACACTGCTCTGC 59.546 41.667 4.76 0.00 40.18 4.26
1531 1603 1.413812 TCAGAACACTGCTCTGCTCAA 59.586 47.619 4.76 0.00 40.18 3.02
1532 1604 2.038164 TCAGAACACTGCTCTGCTCAAT 59.962 45.455 4.76 0.00 40.18 2.57
1533 1605 2.812591 CAGAACACTGCTCTGCTCAATT 59.187 45.455 0.00 0.00 34.32 2.32
1534 1606 3.072944 AGAACACTGCTCTGCTCAATTC 58.927 45.455 0.00 0.00 0.00 2.17
1537 1609 1.659601 CACTGCTCTGCTCAATTCTCG 59.340 52.381 0.00 0.00 0.00 4.04
1547 1619 3.498397 TGCTCAATTCTCGGTTCTGAAAC 59.502 43.478 0.00 0.00 34.46 2.78
1551 1623 5.304778 TCAATTCTCGGTTCTGAAACATGA 58.695 37.500 6.23 0.00 37.10 3.07
1552 1624 5.762711 TCAATTCTCGGTTCTGAAACATGAA 59.237 36.000 6.23 9.01 37.10 2.57
1553 1625 6.262049 TCAATTCTCGGTTCTGAAACATGAAA 59.738 34.615 6.23 0.00 37.10 2.69
1554 1626 6.633500 ATTCTCGGTTCTGAAACATGAAAA 57.367 33.333 6.23 0.00 37.10 2.29
1555 1627 6.443934 TTCTCGGTTCTGAAACATGAAAAA 57.556 33.333 6.23 0.00 37.10 1.94
1668 1743 0.824109 ATCGATGCTTTCCTGACGGA 59.176 50.000 0.00 0.00 37.60 4.69
1691 1766 2.202676 GGTGAGCTCTCTTCCGCG 60.203 66.667 16.19 0.00 0.00 6.46
1761 1836 4.985538 TCCAGTTGCCTTTTCAGAACTAT 58.014 39.130 0.00 0.00 0.00 2.12
1881 1956 2.426024 CCACCATCTGCAATTCTGAAGG 59.574 50.000 0.00 0.00 37.47 3.46
1942 2017 8.602472 ACTGGTTATCTTTCTAGATCACTTCT 57.398 34.615 0.00 0.00 41.38 2.85
2098 2176 1.242076 GACACATTGCCAAGCTCTGT 58.758 50.000 0.00 0.00 0.00 3.41
2099 2177 0.956633 ACACATTGCCAAGCTCTGTG 59.043 50.000 15.66 15.66 42.59 3.66
2113 2191 1.184970 TCTGTGTCGTGATCCTGCCA 61.185 55.000 0.00 0.00 0.00 4.92
2191 2269 3.656045 GACGTGTTTGCCGGTGGG 61.656 66.667 1.90 0.00 0.00 4.61
2197 2275 1.749258 GTTTGCCGGTGGGATCCTC 60.749 63.158 12.58 5.33 34.06 3.71
2373 2454 7.797123 GCTAGCAAACACGGTACATTTATAATC 59.203 37.037 10.63 0.00 0.00 1.75
2375 2456 7.693952 AGCAAACACGGTACATTTATAATCTG 58.306 34.615 0.00 0.00 0.00 2.90
2521 2604 7.414873 CCATTGTCAGATGTACAGAAATGAAGG 60.415 40.741 0.33 0.87 0.00 3.46
2530 2613 4.607293 ACAGAAATGAAGGCCTTTTTCC 57.393 40.909 27.78 14.86 0.00 3.13
2538 2621 2.215942 AGGCCTTTTTCCGCAACTAT 57.784 45.000 0.00 0.00 0.00 2.12
2543 2758 4.272748 GGCCTTTTTCCGCAACTATAGTAG 59.727 45.833 5.65 1.08 0.00 2.57
2544 2759 4.874396 GCCTTTTTCCGCAACTATAGTAGT 59.126 41.667 5.65 0.00 41.73 2.73
2545 2760 6.044682 GCCTTTTTCCGCAACTATAGTAGTA 58.955 40.000 5.65 0.00 38.26 1.82
2546 2761 6.704937 GCCTTTTTCCGCAACTATAGTAGTAT 59.295 38.462 5.65 0.00 38.26 2.12
2547 2762 7.869429 GCCTTTTTCCGCAACTATAGTAGTATA 59.131 37.037 5.65 0.00 38.26 1.47
2572 2787 6.867662 ACTGAAGTGAAATGTTACCTCTTG 57.132 37.500 0.00 0.00 0.00 3.02
2649 2864 4.389374 TGAGAACCAAGGAACAACAGATC 58.611 43.478 0.00 0.00 0.00 2.75
2787 3011 4.545076 CCACCATGGGGATGGGGC 62.545 72.222 18.14 0.00 43.73 5.80
2852 3077 8.169393 AGGTAGGTACTAGTAGAACTCTTGTTT 58.831 37.037 1.87 0.00 44.14 2.83
2854 3079 9.623350 GTAGGTACTAGTAGAACTCTTGTTTTG 57.377 37.037 1.87 0.00 44.14 2.44
2855 3080 8.247666 AGGTACTAGTAGAACTCTTGTTTTGT 57.752 34.615 1.87 0.00 36.02 2.83
2856 3081 9.359653 AGGTACTAGTAGAACTCTTGTTTTGTA 57.640 33.333 1.87 0.00 36.02 2.41
2904 3129 0.239879 ATTGCGCGATTTGGTTCGTT 59.760 45.000 12.10 0.00 41.16 3.85
2950 3175 5.412594 TCCTTGAGTTTTCAGAATCAATCCG 59.587 40.000 0.00 0.00 34.15 4.18
3075 3301 8.978472 ACCTAACATGTTAGAATTGACTAGCTA 58.022 33.333 36.37 6.76 43.90 3.32
3079 3305 5.258456 TGTTAGAATTGACTAGCTACCCG 57.742 43.478 0.00 0.00 0.00 5.28
3081 3307 5.419788 TGTTAGAATTGACTAGCTACCCGAA 59.580 40.000 0.00 0.00 0.00 4.30
3082 3308 6.071221 TGTTAGAATTGACTAGCTACCCGAAA 60.071 38.462 0.00 0.00 0.00 3.46
3083 3309 5.012328 AGAATTGACTAGCTACCCGAAAG 57.988 43.478 0.00 0.00 0.00 2.62
3116 3342 2.416162 CGAAGAGGGAGTCAACTAGTGC 60.416 54.545 0.00 0.00 0.00 4.40
3119 3345 1.133407 GAGGGAGTCAACTAGTGCTCG 59.867 57.143 0.00 0.00 33.62 5.03
3133 3359 4.905412 AGTGCTCGTATCTTTTCGAAAC 57.095 40.909 10.79 0.00 35.69 2.78
3161 3387 2.922955 TGGAACCAATTGAGGGGATACA 59.077 45.455 7.12 0.00 39.74 2.29
3280 3508 3.686016 ACACGTCTGATTTAAGGGCATT 58.314 40.909 0.00 0.00 0.00 3.56
3281 3509 4.079253 ACACGTCTGATTTAAGGGCATTT 58.921 39.130 0.00 0.00 0.00 2.32
3349 3577 3.411446 CACATGTTTGAGCTAAGGTGGA 58.589 45.455 0.00 0.00 0.00 4.02
3364 3592 4.450082 AGGTGGACAAAGTTTGACAAAC 57.550 40.909 22.23 21.09 41.69 2.93
3365 3593 3.829601 AGGTGGACAAAGTTTGACAAACA 59.170 39.130 28.07 6.96 43.79 2.83
3467 3696 7.012421 AGGCATTACTGTAAAAATCCTCGAATC 59.988 37.037 4.11 0.00 0.00 2.52
3502 3731 8.286191 AGATTAAATAAAGCCCTCTTTGAGTG 57.714 34.615 0.95 0.00 42.17 3.51
3534 3763 5.074929 TCCTGGGTATCTTCATAATTGGCAT 59.925 40.000 0.00 0.00 0.00 4.40
3574 3803 5.948162 AGAACAAAGGACTGATATGCACATT 59.052 36.000 0.00 0.00 0.00 2.71
3576 3805 6.932356 ACAAAGGACTGATATGCACATTAG 57.068 37.500 0.00 0.00 0.00 1.73
3577 3806 5.297776 ACAAAGGACTGATATGCACATTAGC 59.702 40.000 0.00 0.00 0.00 3.09
3588 3817 3.951306 TGCACATTAGCATACGAAATGC 58.049 40.909 16.33 16.33 44.85 3.56
3620 3850 5.585047 GGGCAGTAGTTATTTACAGACTTGG 59.415 44.000 0.00 0.00 0.00 3.61
3634 3864 5.308825 ACAGACTTGGAAGTTGAGTAATGG 58.691 41.667 0.00 0.00 39.88 3.16
3636 3866 4.072131 GACTTGGAAGTTGAGTAATGGCA 58.928 43.478 0.00 0.00 39.88 4.92
3655 3885 3.249559 GGCAACTCTTTTCTCAGACAGTG 59.750 47.826 0.00 0.00 0.00 3.66
3664 3894 1.069204 TCTCAGACAGTGGCAAGTCAC 59.931 52.381 19.53 0.00 37.23 3.67
3665 3895 0.249447 TCAGACAGTGGCAAGTCACG 60.249 55.000 19.53 12.05 42.10 4.35
3666 3896 1.069765 AGACAGTGGCAAGTCACGG 59.930 57.895 19.53 3.46 42.10 4.94
3667 3897 1.069090 GACAGTGGCAAGTCACGGA 59.931 57.895 11.70 0.00 42.10 4.69
3668 3898 0.320771 GACAGTGGCAAGTCACGGAT 60.321 55.000 11.70 0.00 42.10 4.18
3669 3899 0.320771 ACAGTGGCAAGTCACGGATC 60.321 55.000 11.70 0.00 42.10 3.36
3711 3941 3.996825 CGGAGCAAAAAGAATCGGG 57.003 52.632 0.00 0.00 0.00 5.14
3712 3942 0.179163 CGGAGCAAAAAGAATCGGGC 60.179 55.000 0.00 0.00 0.00 6.13
3713 3943 0.173481 GGAGCAAAAAGAATCGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
3714 3944 1.177401 GAGCAAAAAGAATCGGGCCT 58.823 50.000 0.84 0.00 0.00 5.19
3715 3945 1.546029 GAGCAAAAAGAATCGGGCCTT 59.454 47.619 0.84 0.00 0.00 4.35
3716 3946 1.546029 AGCAAAAAGAATCGGGCCTTC 59.454 47.619 0.84 0.00 0.00 3.46
3717 3947 1.732405 GCAAAAAGAATCGGGCCTTCG 60.732 52.381 0.84 0.00 0.00 3.79
3718 3948 1.135402 CAAAAAGAATCGGGCCTTCGG 60.135 52.381 0.84 0.00 0.00 4.30
3719 3949 0.326927 AAAAGAATCGGGCCTTCGGA 59.673 50.000 0.84 0.00 0.00 4.55
3720 3950 0.107654 AAAGAATCGGGCCTTCGGAG 60.108 55.000 0.84 0.00 0.00 4.63
3721 3951 0.976073 AAGAATCGGGCCTTCGGAGA 60.976 55.000 0.84 0.00 0.00 3.71
3722 3952 0.976073 AGAATCGGGCCTTCGGAGAA 60.976 55.000 0.84 0.00 45.90 2.87
3723 3953 0.530870 GAATCGGGCCTTCGGAGAAG 60.531 60.000 0.84 2.99 45.90 2.85
3724 3954 1.265454 AATCGGGCCTTCGGAGAAGT 61.265 55.000 0.84 0.00 45.90 3.01
3725 3955 1.265454 ATCGGGCCTTCGGAGAAGTT 61.265 55.000 0.84 0.00 45.90 2.66
3726 3956 1.448013 CGGGCCTTCGGAGAAGTTC 60.448 63.158 0.84 0.00 45.90 3.01
3727 3957 1.677552 GGGCCTTCGGAGAAGTTCA 59.322 57.895 0.84 0.00 45.90 3.18
3728 3958 0.391793 GGGCCTTCGGAGAAGTTCAG 60.392 60.000 0.84 0.00 45.90 3.02
3729 3959 0.608640 GGCCTTCGGAGAAGTTCAGA 59.391 55.000 5.50 0.00 45.90 3.27
3730 3960 1.208293 GGCCTTCGGAGAAGTTCAGAT 59.792 52.381 5.50 0.00 45.90 2.90
3731 3961 2.545731 GCCTTCGGAGAAGTTCAGATC 58.454 52.381 5.50 0.00 45.90 2.75
3732 3962 2.803451 CCTTCGGAGAAGTTCAGATCG 58.197 52.381 5.50 3.57 45.90 3.69
3733 3963 2.189342 CTTCGGAGAAGTTCAGATCGC 58.811 52.381 5.50 0.00 45.90 4.58
3734 3964 1.173913 TCGGAGAAGTTCAGATCGCA 58.826 50.000 5.50 0.00 0.00 5.10
3735 3965 1.135373 TCGGAGAAGTTCAGATCGCAC 60.135 52.381 5.50 0.00 0.00 5.34
3736 3966 1.402852 CGGAGAAGTTCAGATCGCACA 60.403 52.381 5.50 0.00 0.00 4.57
3737 3967 2.266554 GGAGAAGTTCAGATCGCACAG 58.733 52.381 5.50 0.00 0.00 3.66
3738 3968 2.094494 GGAGAAGTTCAGATCGCACAGA 60.094 50.000 5.50 0.00 0.00 3.41
3739 3969 3.178267 GAGAAGTTCAGATCGCACAGAG 58.822 50.000 5.50 0.00 0.00 3.35
3740 3970 2.094286 AGAAGTTCAGATCGCACAGAGG 60.094 50.000 5.50 0.00 0.00 3.69
3741 3971 0.108424 AGTTCAGATCGCACAGAGGC 60.108 55.000 0.00 0.00 0.00 4.70
3742 3972 0.108424 GTTCAGATCGCACAGAGGCT 60.108 55.000 0.00 0.00 0.00 4.58
3743 3973 0.610174 TTCAGATCGCACAGAGGCTT 59.390 50.000 0.00 0.00 0.00 4.35
3744 3974 0.610174 TCAGATCGCACAGAGGCTTT 59.390 50.000 0.00 0.00 0.00 3.51
3745 3975 0.725686 CAGATCGCACAGAGGCTTTG 59.274 55.000 3.08 3.08 0.00 2.77
3746 3976 0.392193 AGATCGCACAGAGGCTTTGG 60.392 55.000 10.06 0.00 0.00 3.28
3747 3977 0.674895 GATCGCACAGAGGCTTTGGT 60.675 55.000 10.06 0.00 0.00 3.67
3748 3978 0.674895 ATCGCACAGAGGCTTTGGTC 60.675 55.000 10.06 0.00 0.00 4.02
3749 3979 1.302033 CGCACAGAGGCTTTGGTCT 60.302 57.895 10.06 0.00 0.00 3.85
3750 3980 0.037326 CGCACAGAGGCTTTGGTCTA 60.037 55.000 10.06 0.00 0.00 2.59
3751 3981 1.443802 GCACAGAGGCTTTGGTCTAC 58.556 55.000 10.06 0.00 0.00 2.59
3752 3982 1.946283 GCACAGAGGCTTTGGTCTACC 60.946 57.143 10.06 0.00 0.00 3.18
3753 3983 1.625818 CACAGAGGCTTTGGTCTACCT 59.374 52.381 10.06 0.00 36.82 3.08
3754 3984 2.039084 CACAGAGGCTTTGGTCTACCTT 59.961 50.000 10.06 0.00 36.82 3.50
3755 3985 2.039084 ACAGAGGCTTTGGTCTACCTTG 59.961 50.000 10.06 0.00 36.82 3.61
3756 3986 2.303022 CAGAGGCTTTGGTCTACCTTGA 59.697 50.000 0.00 0.00 36.82 3.02
3757 3987 2.569404 AGAGGCTTTGGTCTACCTTGAG 59.431 50.000 0.02 0.00 36.82 3.02
3758 3988 2.303311 GAGGCTTTGGTCTACCTTGAGT 59.697 50.000 0.02 0.00 36.82 3.41
3759 3989 3.514309 GAGGCTTTGGTCTACCTTGAGTA 59.486 47.826 0.02 0.00 36.82 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.791355 AAATACGTCAACCTAATTGTTTTGAC 57.209 30.769 13.74 13.74 42.88 3.18
1 2 9.453325 GAAAATACGTCAACCTAATTGTTTTGA 57.547 29.630 0.00 0.00 39.54 2.69
2 3 9.239002 TGAAAATACGTCAACCTAATTGTTTTG 57.761 29.630 0.00 0.00 39.54 2.44
3 4 9.804758 TTGAAAATACGTCAACCTAATTGTTTT 57.195 25.926 0.00 0.00 39.54 2.43
4 5 9.240159 GTTGAAAATACGTCAACCTAATTGTTT 57.760 29.630 5.92 0.00 45.99 2.83
5 6 8.791355 GTTGAAAATACGTCAACCTAATTGTT 57.209 30.769 5.92 0.00 45.99 2.83
15 16 6.438259 TCCAAAGTGTTGAAAATACGTCAA 57.562 33.333 0.00 0.00 43.29 3.18
16 17 6.627395 ATCCAAAGTGTTGAAAATACGTCA 57.373 33.333 0.00 0.00 43.29 4.35
53 54 9.866655 TCCAAGAGAGTATAAAATGCCATATTT 57.133 29.630 0.00 0.00 0.00 1.40
54 55 9.866655 TTCCAAGAGAGTATAAAATGCCATATT 57.133 29.630 0.00 0.00 0.00 1.28
70 71 3.873952 CCGCCTAGAAAATTCCAAGAGAG 59.126 47.826 0.00 0.00 0.00 3.20
72 73 2.356069 GCCGCCTAGAAAATTCCAAGAG 59.644 50.000 0.00 0.00 0.00 2.85
79 80 1.084289 GACACGCCGCCTAGAAAATT 58.916 50.000 0.00 0.00 0.00 1.82
80 81 1.082117 CGACACGCCGCCTAGAAAAT 61.082 55.000 0.00 0.00 0.00 1.82
107 108 2.226200 CGGTGAATGATCAACACAAGCA 59.774 45.455 26.17 6.93 43.85 3.91
108 109 2.414559 CCGGTGAATGATCAACACAAGC 60.415 50.000 26.17 14.81 43.85 4.01
132 133 5.009631 TGTAATAGCAAGCATGACAGGTTT 58.990 37.500 0.00 0.00 0.00 3.27
133 134 4.588899 TGTAATAGCAAGCATGACAGGTT 58.411 39.130 0.00 0.00 0.00 3.50
134 135 4.194640 CTGTAATAGCAAGCATGACAGGT 58.805 43.478 0.00 0.00 31.34 4.00
135 136 4.194640 ACTGTAATAGCAAGCATGACAGG 58.805 43.478 18.08 0.00 37.68 4.00
136 137 6.045318 AGTACTGTAATAGCAAGCATGACAG 58.955 40.000 14.85 14.85 38.96 3.51
137 138 5.977635 AGTACTGTAATAGCAAGCATGACA 58.022 37.500 0.00 0.00 0.00 3.58
138 139 6.238211 CCAAGTACTGTAATAGCAAGCATGAC 60.238 42.308 0.00 0.00 0.00 3.06
139 140 5.817296 CCAAGTACTGTAATAGCAAGCATGA 59.183 40.000 0.00 0.00 0.00 3.07
140 141 5.504665 GCCAAGTACTGTAATAGCAAGCATG 60.505 44.000 0.00 0.00 0.00 4.06
141 142 4.576463 GCCAAGTACTGTAATAGCAAGCAT 59.424 41.667 0.00 0.00 0.00 3.79
142 143 3.938963 GCCAAGTACTGTAATAGCAAGCA 59.061 43.478 0.00 0.00 0.00 3.91
143 144 4.192317 AGCCAAGTACTGTAATAGCAAGC 58.808 43.478 0.00 1.59 0.00 4.01
144 145 6.371548 TCAAAGCCAAGTACTGTAATAGCAAG 59.628 38.462 0.00 3.20 0.00 4.01
145 146 6.234920 TCAAAGCCAAGTACTGTAATAGCAA 58.765 36.000 0.00 0.00 0.00 3.91
146 147 5.800296 TCAAAGCCAAGTACTGTAATAGCA 58.200 37.500 0.00 0.00 0.00 3.49
147 148 6.675728 GCTTCAAAGCCAAGTACTGTAATAGC 60.676 42.308 0.00 2.98 46.20 2.97
148 149 6.776094 GCTTCAAAGCCAAGTACTGTAATAG 58.224 40.000 0.00 0.00 46.20 1.73
149 150 6.737254 GCTTCAAAGCCAAGTACTGTAATA 57.263 37.500 0.00 0.00 46.20 0.98
150 151 5.629079 GCTTCAAAGCCAAGTACTGTAAT 57.371 39.130 0.00 0.00 46.20 1.89
196 197 2.766263 AGATCAATGCTCCCGTTGTCTA 59.234 45.455 0.00 0.00 38.73 2.59
206 207 1.958205 CCGCCGGAGATCAATGCTC 60.958 63.158 5.05 0.00 0.00 4.26
220 223 5.963586 CGTAAAGAAAACAATATCTTCCGCC 59.036 40.000 0.00 0.00 34.90 6.13
223 227 9.326339 GTCAACGTAAAGAAAACAATATCTTCC 57.674 33.333 0.00 0.00 34.90 3.46
237 241 0.664166 GCGACCCGTCAACGTAAAGA 60.664 55.000 1.48 0.00 37.74 2.52
303 307 2.879907 CCTTGACTTGCGCCCATG 59.120 61.111 4.18 0.20 0.00 3.66
305 309 4.577677 TGCCTTGACTTGCGCCCA 62.578 61.111 4.18 0.00 0.00 5.36
311 315 2.352421 CCAATCTTGCTGCCTTGACTTG 60.352 50.000 0.00 0.00 0.00 3.16
321 325 2.409870 GGACCGGCCAATCTTGCTG 61.410 63.158 0.00 0.00 36.34 4.41
322 326 2.044946 GGACCGGCCAATCTTGCT 60.045 61.111 0.00 0.00 36.34 3.91
323 327 3.140814 GGGACCGGCCAATCTTGC 61.141 66.667 15.49 0.00 38.95 4.01
324 328 2.440247 GGGGACCGGCCAATCTTG 60.440 66.667 15.49 0.00 40.86 3.02
348 352 0.250124 TGGTTGTTGGAATCGAGCGT 60.250 50.000 0.00 0.00 0.00 5.07
455 461 1.120795 GGCCTGAGAGAGAGGATGGG 61.121 65.000 0.00 0.00 31.48 4.00
459 465 0.707024 TTCTGGCCTGAGAGAGAGGA 59.293 55.000 12.54 0.00 31.48 3.71
462 468 1.277557 GCTTTTCTGGCCTGAGAGAGA 59.722 52.381 21.54 6.69 0.00 3.10
463 469 1.002888 TGCTTTTCTGGCCTGAGAGAG 59.997 52.381 21.54 16.75 0.00 3.20
464 470 1.059098 TGCTTTTCTGGCCTGAGAGA 58.941 50.000 21.54 7.67 0.00 3.10
465 471 1.163554 GTGCTTTTCTGGCCTGAGAG 58.836 55.000 12.54 14.69 0.00 3.20
474 480 1.070309 GTCTCTGCGTGTGCTTTTCTG 60.070 52.381 0.00 0.00 43.34 3.02
497 504 1.212616 GATTTCGACGATGCTCCCTG 58.787 55.000 0.00 0.00 0.00 4.45
501 508 2.097202 CGGATTGATTTCGACGATGCTC 60.097 50.000 0.00 0.00 0.00 4.26
522 529 2.125633 GGAGCCGGTCCGTTTCTC 60.126 66.667 11.06 12.75 34.84 2.87
534 541 1.032114 CCGATTGGGAAGTTGGAGCC 61.032 60.000 0.00 0.00 38.47 4.70
535 542 1.657751 GCCGATTGGGAAGTTGGAGC 61.658 60.000 0.00 0.00 38.47 4.70
536 543 1.369091 CGCCGATTGGGAAGTTGGAG 61.369 60.000 0.00 0.00 38.47 3.86
638 685 4.927782 GGTGTGTGTGGCGGCTCA 62.928 66.667 11.43 10.62 0.00 4.26
715 772 1.982395 CGAGCACCACCACCTCCTA 60.982 63.158 0.00 0.00 0.00 2.94
734 793 4.697756 CAACGGCGGCTTCAGGGA 62.698 66.667 13.24 0.00 0.00 4.20
796 855 0.531200 GACAGGTACTCACGGGAAGG 59.469 60.000 0.00 0.00 34.60 3.46
836 898 1.202121 GGAGACCGCAAGTACGTACTC 60.202 57.143 27.51 15.46 34.99 2.59
837 899 0.807496 GGAGACCGCAAGTACGTACT 59.193 55.000 22.45 22.45 38.39 2.73
838 900 0.522076 CGGAGACCGCAAGTACGTAC 60.522 60.000 18.10 18.10 41.17 3.67
839 901 1.796151 CGGAGACCGCAAGTACGTA 59.204 57.895 0.00 0.00 41.17 3.57
840 902 2.564975 CGGAGACCGCAAGTACGT 59.435 61.111 0.00 0.00 41.17 3.57
861 923 2.503061 CATGTGCGGGGAGGAGAG 59.497 66.667 0.00 0.00 0.00 3.20
916 978 4.397090 TGCGTTTTCCATGCGGCG 62.397 61.111 0.51 0.51 40.80 6.46
1083 1155 1.809619 CCAGTCGTACATGTGCCGG 60.810 63.158 9.11 0.00 0.00 6.13
1136 1208 2.456119 GGCGTGATGAGGTTGAGCG 61.456 63.158 0.00 0.00 0.00 5.03
1188 1260 2.446036 ATGGGGTAGCGGAGGTCC 60.446 66.667 0.00 0.00 40.68 4.46
1245 1317 2.286578 TGGGGGTGGATGGGGTAC 60.287 66.667 0.00 0.00 0.00 3.34
1266 1338 0.907230 AGAGACAAGGTCAGGAGGGC 60.907 60.000 0.00 0.00 34.60 5.19
1271 1343 2.260844 TTTGCAGAGACAAGGTCAGG 57.739 50.000 0.00 0.00 34.60 3.86
1272 1344 4.843220 AATTTTGCAGAGACAAGGTCAG 57.157 40.909 0.00 0.00 34.60 3.51
1273 1345 4.889409 AGAAATTTTGCAGAGACAAGGTCA 59.111 37.500 0.00 0.00 34.60 4.02
1274 1346 5.444663 AGAAATTTTGCAGAGACAAGGTC 57.555 39.130 0.00 0.00 0.00 3.85
1275 1347 5.595952 AGAAGAAATTTTGCAGAGACAAGGT 59.404 36.000 0.00 0.00 0.00 3.50
1280 1352 7.708322 AGGAAAAAGAAGAAATTTTGCAGAGAC 59.292 33.333 0.00 0.00 38.74 3.36
1308 1380 0.721718 CGAGCAAGGTTCGGTCAATC 59.278 55.000 0.00 0.00 34.56 2.67
1329 1401 0.030235 CGTTCGTCCACAGTCAGACA 59.970 55.000 2.66 0.00 33.08 3.41
1333 1405 0.038618 CATCCGTTCGTCCACAGTCA 60.039 55.000 0.00 0.00 0.00 3.41
1335 1407 1.374252 GCATCCGTTCGTCCACAGT 60.374 57.895 0.00 0.00 0.00 3.55
1336 1408 1.354337 CTGCATCCGTTCGTCCACAG 61.354 60.000 0.00 0.00 0.00 3.66
1337 1409 1.374125 CTGCATCCGTTCGTCCACA 60.374 57.895 0.00 0.00 0.00 4.17
1338 1410 0.460284 ATCTGCATCCGTTCGTCCAC 60.460 55.000 0.00 0.00 0.00 4.02
1339 1411 1.107945 TATCTGCATCCGTTCGTCCA 58.892 50.000 0.00 0.00 0.00 4.02
1341 1413 2.909244 CGTATATCTGCATCCGTTCGTC 59.091 50.000 0.00 0.00 0.00 4.20
1342 1414 2.921069 GCGTATATCTGCATCCGTTCGT 60.921 50.000 0.00 0.00 0.00 3.85
1343 1415 1.649171 GCGTATATCTGCATCCGTTCG 59.351 52.381 0.00 0.00 0.00 3.95
1344 1416 1.993370 GGCGTATATCTGCATCCGTTC 59.007 52.381 0.00 0.00 0.00 3.95
1345 1417 1.668919 CGGCGTATATCTGCATCCGTT 60.669 52.381 0.00 0.00 0.00 4.44
1526 1598 3.498397 TGTTTCAGAACCGAGAATTGAGC 59.502 43.478 0.00 0.00 34.80 4.26
1527 1599 5.409520 TCATGTTTCAGAACCGAGAATTGAG 59.590 40.000 0.00 0.00 34.80 3.02
1531 1603 6.633500 TTTTCATGTTTCAGAACCGAGAAT 57.367 33.333 0.00 0.00 34.80 2.40
1532 1604 6.443934 TTTTTCATGTTTCAGAACCGAGAA 57.556 33.333 0.00 0.00 34.80 2.87
1552 1624 3.116079 CAGCAGGCCTGTCAAATTTTT 57.884 42.857 32.81 5.90 36.79 1.94
1553 1625 2.825861 CAGCAGGCCTGTCAAATTTT 57.174 45.000 32.81 6.58 36.79 1.82
1605 1680 3.982372 GACGCCGTCCTTGATCGCA 62.982 63.158 5.81 0.00 0.00 5.10
1668 1743 1.882989 GAAGAGAGCTCACCGGCACT 61.883 60.000 17.77 0.00 35.97 4.40
1691 1766 3.755378 TGGAAAGCTCTGAAGAAGCAATC 59.245 43.478 0.00 0.00 0.00 2.67
1761 1836 2.142357 CTTGTCGAGTGACCGCCTCA 62.142 60.000 0.00 0.00 44.86 3.86
1881 1956 4.293415 CAACTCAAACAAGTTCAGATGGC 58.707 43.478 0.00 0.00 37.38 4.40
2098 2176 1.293179 CAGTGGCAGGATCACGACA 59.707 57.895 0.00 0.00 39.86 4.35
2099 2177 2.103042 GCAGTGGCAGGATCACGAC 61.103 63.158 0.00 0.00 39.86 4.34
2191 2269 1.475682 AGTTGGAACGTACCGAGGATC 59.524 52.381 0.00 0.00 0.00 3.36
2197 2275 1.286880 ACGGAGTTGGAACGTACCG 59.713 57.895 17.40 17.40 37.78 4.02
2214 2292 4.745649 ACTGAACTTATAACGGCTCTGAC 58.254 43.478 0.00 0.00 0.00 3.51
2373 2454 7.611213 AACCTATTTCGTTAATCCAGAACAG 57.389 36.000 0.00 0.00 0.00 3.16
2375 2456 7.691050 CGAAAACCTATTTCGTTAATCCAGAAC 59.309 37.037 13.50 0.00 44.25 3.01
2521 2604 4.874396 ACTACTATAGTTGCGGAAAAAGGC 59.126 41.667 11.40 0.00 34.86 4.35
2530 2613 9.947669 ACTTCAGTTTATACTACTATAGTTGCG 57.052 33.333 11.40 3.05 40.14 4.85
2545 2760 9.574516 AAGAGGTAACATTTCACTTCAGTTTAT 57.425 29.630 0.00 0.00 41.41 1.40
2546 2761 8.836413 CAAGAGGTAACATTTCACTTCAGTTTA 58.164 33.333 0.00 0.00 41.41 2.01
2547 2762 7.339466 ACAAGAGGTAACATTTCACTTCAGTTT 59.661 33.333 0.00 0.00 41.41 2.66
2569 2784 0.670162 CCACAGCCCTGAAACACAAG 59.330 55.000 1.69 0.00 0.00 3.16
2572 2787 3.042560 GCCACAGCCCTGAAACAC 58.957 61.111 1.69 0.00 0.00 3.32
2609 2824 1.835531 TCAGTTTCCGGGTTAGGATCC 59.164 52.381 2.48 2.48 40.48 3.36
2610 2825 2.764572 TCTCAGTTTCCGGGTTAGGATC 59.235 50.000 0.00 0.00 40.48 3.36
2649 2864 2.124983 CAGCACCGACTGATGGGG 60.125 66.667 0.00 0.00 40.25 4.96
2682 2906 1.954382 CATCTCCATGGAGGCAACATG 59.046 52.381 35.95 27.37 44.03 3.21
2796 3020 2.625737 GTGATGTCTCTCATGGTGGTG 58.374 52.381 0.00 0.00 36.83 4.17
2797 3021 1.556911 GGTGATGTCTCTCATGGTGGT 59.443 52.381 0.00 0.00 36.83 4.16
2798 3022 1.836166 AGGTGATGTCTCTCATGGTGG 59.164 52.381 0.00 0.00 36.83 4.61
2882 3107 1.317319 CGAACCAAATCGCGCAATTTC 59.683 47.619 8.75 0.00 35.85 2.17
2904 3129 4.597004 ACTAGATCTACTTCGGTCCAACA 58.403 43.478 0.00 0.00 0.00 3.33
2950 3175 5.932303 TGCACTTGTTTAGGACTAGATCAAC 59.068 40.000 0.00 0.00 35.45 3.18
3051 3276 9.250624 GGTAGCTAGTCAATTCTAACATGTTAG 57.749 37.037 31.44 31.44 42.86 2.34
3075 3301 2.033602 CCCTTTCGCCTTTCGGGT 59.966 61.111 0.00 0.00 39.05 5.28
3079 3305 1.197036 CTTCGTTCCCTTTCGCCTTTC 59.803 52.381 0.00 0.00 0.00 2.62
3081 3307 0.395312 TCTTCGTTCCCTTTCGCCTT 59.605 50.000 0.00 0.00 0.00 4.35
3082 3308 0.037232 CTCTTCGTTCCCTTTCGCCT 60.037 55.000 0.00 0.00 0.00 5.52
3083 3309 1.019805 CCTCTTCGTTCCCTTTCGCC 61.020 60.000 0.00 0.00 0.00 5.54
3084 3310 1.019805 CCCTCTTCGTTCCCTTTCGC 61.020 60.000 0.00 0.00 0.00 4.70
3085 3311 0.606604 TCCCTCTTCGTTCCCTTTCG 59.393 55.000 0.00 0.00 0.00 3.46
3086 3312 1.624312 ACTCCCTCTTCGTTCCCTTTC 59.376 52.381 0.00 0.00 0.00 2.62
3116 3342 5.517037 AAGCTGTTTCGAAAAGATACGAG 57.483 39.130 13.10 2.71 39.59 4.18
3119 3345 7.303634 TCCATAAGCTGTTTCGAAAAGATAC 57.696 36.000 13.10 0.55 0.00 2.24
3133 3359 3.382546 CCCTCAATTGGTTCCATAAGCTG 59.617 47.826 5.42 0.00 34.13 4.24
3179 3405 7.009568 TGTGTTGTATTTTCCACAAAAATGC 57.990 32.000 6.11 5.48 45.15 3.56
3258 3486 2.695359 TGCCCTTAAATCAGACGTGTC 58.305 47.619 0.00 0.00 0.00 3.67
3259 3487 2.851263 TGCCCTTAAATCAGACGTGT 57.149 45.000 0.00 0.00 0.00 4.49
3261 3489 5.010282 AGAAAATGCCCTTAAATCAGACGT 58.990 37.500 0.00 0.00 0.00 4.34
3264 3492 6.891361 TGATCAGAAAATGCCCTTAAATCAGA 59.109 34.615 0.00 0.00 0.00 3.27
3273 3501 2.097825 GCAGTGATCAGAAAATGCCCT 58.902 47.619 0.00 0.00 0.00 5.19
3280 3508 0.602638 AACGCGGCAGTGATCAGAAA 60.603 50.000 12.47 0.00 0.00 2.52
3281 3509 0.602638 AAACGCGGCAGTGATCAGAA 60.603 50.000 12.47 0.00 0.00 3.02
3349 3577 9.296400 GTACATGTATTGTTTGTCAAACTTTGT 57.704 29.630 24.94 19.35 41.90 2.83
3364 3592 9.955208 AATGCTCAAATATGTGTACATGTATTG 57.045 29.630 9.18 7.71 37.15 1.90
3467 3696 7.013369 AGGGCTTTATTTAATCTTTTCGCCTAG 59.987 37.037 0.00 0.00 34.42 3.02
3470 3699 5.902681 AGGGCTTTATTTAATCTTTTCGCC 58.097 37.500 0.00 0.00 0.00 5.54
3502 3731 4.918588 TGAAGATACCCAGGAGAAAAACC 58.081 43.478 0.00 0.00 0.00 3.27
3534 3763 4.350368 TGTTCTGTCTGCATCAGGTTAA 57.650 40.909 15.70 4.26 34.15 2.01
3574 3803 6.093495 GCCCTATATTTGCATTTCGTATGCTA 59.907 38.462 20.22 13.32 44.79 3.49
3576 3805 5.095490 GCCCTATATTTGCATTTCGTATGC 58.905 41.667 15.23 15.23 44.76 3.14
3577 3806 6.072508 ACTGCCCTATATTTGCATTTCGTATG 60.073 38.462 0.00 0.00 33.97 2.39
3579 3808 5.373222 ACTGCCCTATATTTGCATTTCGTA 58.627 37.500 0.00 0.00 33.97 3.43
3581 3810 4.836125 ACTGCCCTATATTTGCATTTCG 57.164 40.909 0.00 0.00 33.97 3.46
3634 3864 3.249559 CCACTGTCTGAGAAAAGAGTTGC 59.750 47.826 0.86 0.00 0.00 4.17
3636 3866 3.118261 TGCCACTGTCTGAGAAAAGAGTT 60.118 43.478 0.86 0.00 0.00 3.01
3655 3885 2.415893 CCATTTTGATCCGTGACTTGCC 60.416 50.000 0.00 0.00 0.00 4.52
3664 3894 5.685511 CGCTTTATAAACCCATTTTGATCCG 59.314 40.000 0.00 0.00 0.00 4.18
3665 3895 5.983118 CCGCTTTATAAACCCATTTTGATCC 59.017 40.000 0.00 0.00 0.00 3.36
3666 3896 6.569780 ACCGCTTTATAAACCCATTTTGATC 58.430 36.000 0.00 0.00 0.00 2.92
3667 3897 6.538945 ACCGCTTTATAAACCCATTTTGAT 57.461 33.333 0.00 0.00 0.00 2.57
3668 3898 5.986501 ACCGCTTTATAAACCCATTTTGA 57.013 34.783 0.00 0.00 0.00 2.69
3669 3899 5.163903 GCAACCGCTTTATAAACCCATTTTG 60.164 40.000 0.00 0.00 34.30 2.44
3694 3924 0.173481 GGCCCGATTCTTTTTGCTCC 59.827 55.000 0.00 0.00 0.00 4.70
3697 3927 1.732405 CGAAGGCCCGATTCTTTTTGC 60.732 52.381 0.00 0.00 0.00 3.68
3713 3943 2.189342 GCGATCTGAACTTCTCCGAAG 58.811 52.381 2.26 2.26 0.00 3.79
3714 3944 1.544246 TGCGATCTGAACTTCTCCGAA 59.456 47.619 0.00 0.00 0.00 4.30
3715 3945 1.135373 GTGCGATCTGAACTTCTCCGA 60.135 52.381 0.00 0.00 0.00 4.55
3716 3946 1.272781 GTGCGATCTGAACTTCTCCG 58.727 55.000 0.00 0.00 0.00 4.63
3717 3947 2.094494 TCTGTGCGATCTGAACTTCTCC 60.094 50.000 0.00 0.00 0.00 3.71
3718 3948 3.178267 CTCTGTGCGATCTGAACTTCTC 58.822 50.000 0.00 0.00 0.00 2.87
3719 3949 2.094286 CCTCTGTGCGATCTGAACTTCT 60.094 50.000 0.00 0.00 0.00 2.85
3720 3950 2.266554 CCTCTGTGCGATCTGAACTTC 58.733 52.381 0.00 0.00 0.00 3.01
3721 3951 1.674221 GCCTCTGTGCGATCTGAACTT 60.674 52.381 0.00 0.00 0.00 2.66
3722 3952 0.108424 GCCTCTGTGCGATCTGAACT 60.108 55.000 0.00 0.00 0.00 3.01
3723 3953 0.108424 AGCCTCTGTGCGATCTGAAC 60.108 55.000 0.00 0.00 36.02 3.18
3724 3954 0.610174 AAGCCTCTGTGCGATCTGAA 59.390 50.000 0.00 0.00 36.02 3.02
3725 3955 0.610174 AAAGCCTCTGTGCGATCTGA 59.390 50.000 0.00 0.00 36.02 3.27
3726 3956 0.725686 CAAAGCCTCTGTGCGATCTG 59.274 55.000 0.00 0.00 36.02 2.90
3727 3957 0.392193 CCAAAGCCTCTGTGCGATCT 60.392 55.000 0.00 0.00 36.02 2.75
3728 3958 0.674895 ACCAAAGCCTCTGTGCGATC 60.675 55.000 0.00 0.00 36.02 3.69
3729 3959 0.674895 GACCAAAGCCTCTGTGCGAT 60.675 55.000 0.00 0.00 36.02 4.58
3730 3960 1.301716 GACCAAAGCCTCTGTGCGA 60.302 57.895 0.00 0.00 36.02 5.10
3731 3961 0.037326 TAGACCAAAGCCTCTGTGCG 60.037 55.000 0.00 0.00 36.02 5.34
3732 3962 1.443802 GTAGACCAAAGCCTCTGTGC 58.556 55.000 0.00 0.00 0.00 4.57
3733 3963 1.625818 AGGTAGACCAAAGCCTCTGTG 59.374 52.381 0.66 0.00 38.89 3.66
3734 3964 2.031495 AGGTAGACCAAAGCCTCTGT 57.969 50.000 0.66 0.00 38.89 3.41
3735 3965 2.303022 TCAAGGTAGACCAAAGCCTCTG 59.697 50.000 0.66 0.00 38.89 3.35
3736 3966 2.569404 CTCAAGGTAGACCAAAGCCTCT 59.431 50.000 0.66 0.00 38.89 3.69
3737 3967 2.303311 ACTCAAGGTAGACCAAAGCCTC 59.697 50.000 0.66 0.00 38.89 4.70
3738 3968 2.339769 ACTCAAGGTAGACCAAAGCCT 58.660 47.619 0.66 0.00 38.89 4.58
3739 3969 2.861147 ACTCAAGGTAGACCAAAGCC 57.139 50.000 0.66 0.00 38.89 4.35


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

AutoCloner maintained by Alex Coulton.