Multiple sequence alignment - TraesCS1D01G379800

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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 TraesCS1D01G379800 chr1D 100.000 3841 0 0 1 3841 455768361 455764521 0.000000e+00 7094.0
1 TraesCS1D01G379800 chr1D 88.073 109 13 0 2616 2724 455751306 455751198 3.110000e-26 130.0
2 TraesCS1D01G379800 chr1B 88.156 3850 226 110 131 3841 626106554 626102796 0.000000e+00 4372.0
3 TraesCS1D01G379800 chr1B 89.796 196 16 2 65 256 626136358 626136163 8.240000e-62 248.0
4 TraesCS1D01G379800 chr1B 91.818 110 8 1 2616 2724 626087153 626087044 6.650000e-33 152.0
5 TraesCS1D01G379800 chr1A 87.824 2431 163 82 221 2615 549315387 549313054 0.000000e+00 2726.0
6 TraesCS1D01G379800 chr1A 92.398 1026 55 10 2616 3623 549312921 549311901 0.000000e+00 1441.0
7 TraesCS1D01G379800 chr1A 92.086 139 9 2 3619 3756 549306687 549306550 1.090000e-45 195.0
8 TraesCS1D01G379800 chr1A 94.545 55 3 0 3754 3808 549306530 549306476 6.840000e-13 86.1
9 TraesCS1D01G379800 chr7A 81.538 195 36 0 2092 2286 483966414 483966608 1.100000e-35 161.0
10 TraesCS1D01G379800 chr7D 79.188 197 38 3 2092 2286 433070993 433071188 2.410000e-27 134.0
11 TraesCS1D01G379800 chr7B 77.487 191 43 0 2092 2282 449547422 449547232 8.720000e-22 115.0
12 TraesCS1D01G379800 chr5B 90.566 53 5 0 2456 2508 130516930 130516982 1.910000e-08 71.3
13 TraesCS1D01G379800 chr5B 87.719 57 5 2 2453 2508 64727160 64727105 8.910000e-07 65.8
14 TraesCS1D01G379800 chrUn 89.091 55 5 1 2455 2508 362849379 362849433 2.480000e-07 67.6
15 TraesCS1D01G379800 chr3B 89.091 55 5 1 2455 2508 700864744 700864690 2.480000e-07 67.6
16 TraesCS1D01G379800 chr3B 89.091 55 5 1 2455 2508 700867941 700867887 2.480000e-07 67.6
17 TraesCS1D01G379800 chr3B 89.091 55 5 1 2455 2508 700893166 700893112 2.480000e-07 67.6
18 TraesCS1D01G379800 chr3D 84.848 66 8 2 2459 2522 571052705 571052770 8.910000e-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 TraesCS1D01G379800 chr1D 455764521 455768361 3840 True 7094.0 7094 100.000 1 3841 1 chr1D.!!$R2 3840
1 TraesCS1D01G379800 chr1B 626102796 626106554 3758 True 4372.0 4372 88.156 131 3841 1 chr1B.!!$R2 3710
2 TraesCS1D01G379800 chr1A 549311901 549315387 3486 True 2083.5 2726 90.111 221 3623 2 chr1A.!!$R2 3402

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
485 517 0.104934 CCTAGCATACACCTCCCCCT 60.105 60.0 0.0 0.0 0.0 4.79 F
923 981 0.108615 ACTGCACCTGTCATCTACGC 60.109 55.0 0.0 0.0 0.0 4.42 F
1350 1418 0.253327 GTTCCCCATCCACCTGACTC 59.747 60.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1924 0.301687 CGTGGCATATGACTTGTCGC 59.698 55.000 10.60 0.0 0.00 5.19 R
2006 2084 0.486879 TTGCCAAGGGGGAAGTGATT 59.513 50.000 0.00 0.0 39.90 2.57 R
2846 3065 1.153168 CATCCCCATGGTGGTCGTC 60.153 63.158 11.73 0.0 35.17 4.20 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
27 28 5.970140 TGACGTATTTTCAACACTTTCGA 57.030 34.783 0.00 0.00 0.00 3.71
28 29 6.533819 TGACGTATTTTCAACACTTTCGAT 57.466 33.333 0.00 0.00 0.00 3.59
29 30 6.950545 TGACGTATTTTCAACACTTTCGATT 58.049 32.000 0.00 0.00 0.00 3.34
30 31 8.074474 TGACGTATTTTCAACACTTTCGATTA 57.926 30.769 0.00 0.00 0.00 1.75
31 32 8.714179 TGACGTATTTTCAACACTTTCGATTAT 58.286 29.630 0.00 0.00 0.00 1.28
60 61 9.699410 ATAAATTTATTCCCTCTCAATCACACA 57.301 29.630 4.81 0.00 0.00 3.72
61 62 7.636150 AATTTATTCCCTCTCAATCACACAG 57.364 36.000 0.00 0.00 0.00 3.66
62 63 5.762179 TTATTCCCTCTCAATCACACAGT 57.238 39.130 0.00 0.00 0.00 3.55
63 64 6.867519 TTATTCCCTCTCAATCACACAGTA 57.132 37.500 0.00 0.00 0.00 2.74
64 65 5.965033 ATTCCCTCTCAATCACACAGTAT 57.035 39.130 0.00 0.00 0.00 2.12
65 66 8.547481 TTATTCCCTCTCAATCACACAGTATA 57.453 34.615 0.00 0.00 0.00 1.47
66 67 6.867519 TTCCCTCTCAATCACACAGTATAA 57.132 37.500 0.00 0.00 0.00 0.98
67 68 6.471233 TCCCTCTCAATCACACAGTATAAG 57.529 41.667 0.00 0.00 0.00 1.73
68 69 5.958380 TCCCTCTCAATCACACAGTATAAGT 59.042 40.000 0.00 0.00 0.00 2.24
69 70 6.045318 CCCTCTCAATCACACAGTATAAGTG 58.955 44.000 5.31 5.31 42.56 3.16
71 72 6.754209 CCTCTCAATCACACAGTATAAGTGTC 59.246 42.308 8.77 0.00 46.57 3.67
72 73 7.363355 CCTCTCAATCACACAGTATAAGTGTCT 60.363 40.741 8.77 0.00 46.57 3.41
73 74 7.539436 TCTCAATCACACAGTATAAGTGTCTC 58.461 38.462 8.77 0.00 46.57 3.36
74 75 7.176690 TCTCAATCACACAGTATAAGTGTCTCA 59.823 37.037 8.77 0.00 46.57 3.27
75 76 7.666623 TCAATCACACAGTATAAGTGTCTCAA 58.333 34.615 8.77 0.00 46.57 3.02
76 77 7.598869 TCAATCACACAGTATAAGTGTCTCAAC 59.401 37.037 8.77 0.00 46.57 3.18
77 78 6.650427 TCACACAGTATAAGTGTCTCAACT 57.350 37.500 8.77 0.00 46.57 3.16
78 79 7.050970 TCACACAGTATAAGTGTCTCAACTT 57.949 36.000 8.77 0.00 46.57 2.66
79 80 7.497595 TCACACAGTATAAGTGTCTCAACTTT 58.502 34.615 8.77 0.00 46.57 2.66
80 81 8.635328 TCACACAGTATAAGTGTCTCAACTTTA 58.365 33.333 8.77 0.00 46.57 1.85
81 82 9.424319 CACACAGTATAAGTGTCTCAACTTTAT 57.576 33.333 8.77 0.00 46.57 1.40
89 90 6.435292 AGTGTCTCAACTTTATACCAAGGT 57.565 37.500 0.00 0.00 0.00 3.50
90 91 6.838382 AGTGTCTCAACTTTATACCAAGGTT 58.162 36.000 0.00 0.00 0.00 3.50
91 92 7.970102 AGTGTCTCAACTTTATACCAAGGTTA 58.030 34.615 0.00 0.00 0.00 2.85
92 93 8.095169 AGTGTCTCAACTTTATACCAAGGTTAG 58.905 37.037 0.00 0.00 0.00 2.34
93 94 7.876582 GTGTCTCAACTTTATACCAAGGTTAGT 59.123 37.037 0.00 0.00 0.00 2.24
94 95 9.092338 TGTCTCAACTTTATACCAAGGTTAGTA 57.908 33.333 0.00 0.00 0.00 1.82
107 108 8.488651 ACCAAGGTTAGTATAAAATTGAGACG 57.511 34.615 0.00 0.00 0.00 4.18
108 109 8.098912 ACCAAGGTTAGTATAAAATTGAGACGT 58.901 33.333 0.00 0.00 0.00 4.34
109 110 8.943002 CCAAGGTTAGTATAAAATTGAGACGTT 58.057 33.333 0.00 0.00 0.00 3.99
119 120 8.996024 ATAAAATTGAGACGTTTATTTTGGGG 57.004 30.769 15.18 0.00 33.59 4.96
120 121 3.926821 TTGAGACGTTTATTTTGGGGC 57.073 42.857 0.00 0.00 0.00 5.80
121 122 1.807742 TGAGACGTTTATTTTGGGGCG 59.192 47.619 0.00 0.00 0.00 6.13
122 123 1.131693 GAGACGTTTATTTTGGGGCGG 59.868 52.381 0.00 0.00 0.00 6.13
123 124 1.166989 GACGTTTATTTTGGGGCGGA 58.833 50.000 0.00 0.00 0.00 5.54
124 125 1.131693 GACGTTTATTTTGGGGCGGAG 59.868 52.381 0.00 0.00 0.00 4.63
125 126 0.454196 CGTTTATTTTGGGGCGGAGG 59.546 55.000 0.00 0.00 0.00 4.30
126 127 0.821517 GTTTATTTTGGGGCGGAGGG 59.178 55.000 0.00 0.00 0.00 4.30
127 128 0.705253 TTTATTTTGGGGCGGAGGGA 59.295 50.000 0.00 0.00 0.00 4.20
128 129 0.257616 TTATTTTGGGGCGGAGGGAG 59.742 55.000 0.00 0.00 0.00 4.30
129 130 0.917333 TATTTTGGGGCGGAGGGAGT 60.917 55.000 0.00 0.00 0.00 3.85
136 137 0.544595 GGGCGGAGGGAGTATATGGT 60.545 60.000 0.00 0.00 0.00 3.55
145 146 8.648693 GCGGAGGGAGTATATGGTATTTTATAT 58.351 37.037 0.00 0.00 0.00 0.86
182 183 3.129502 CGGCGTGTCGACCCTCTA 61.130 66.667 14.12 0.00 0.00 2.43
199 201 4.568359 CCCTCTACTTGTGTTGATCATTCG 59.432 45.833 0.00 0.00 0.00 3.34
206 208 2.894879 TTGATCATTCGCCGGCCG 60.895 61.111 23.46 21.04 38.61 6.13
207 209 4.908687 TGATCATTCGCCGGCCGG 62.909 66.667 40.26 40.26 37.59 6.13
273 298 2.290260 ACAACGGAAGCATTGATCTCCA 60.290 45.455 0.00 0.00 0.00 3.86
276 301 1.744798 CGGAAGCATTGATCTCCAGCA 60.745 52.381 0.00 0.00 0.00 4.41
289 314 7.365497 TGATCTCCAGCAAGAAGATATTGTA 57.635 36.000 0.00 0.00 0.00 2.41
291 316 8.093307 TGATCTCCAGCAAGAAGATATTGTATC 58.907 37.037 0.00 0.00 0.00 2.24
311 336 0.940519 CTTTACGTTGACGGGTCGCA 60.941 55.000 8.52 0.00 44.95 5.10
359 384 2.807045 GTCGCCACAGCTCACGAG 60.807 66.667 0.00 0.00 34.83 4.18
375 400 2.529389 AGGGGCGGAAGTCAAGGT 60.529 61.111 0.00 0.00 37.54 3.50
376 401 2.359975 GGGGCGGAAGTCAAGGTG 60.360 66.667 0.00 0.00 37.54 4.00
377 402 3.056328 GGGCGGAAGTCAAGGTGC 61.056 66.667 0.00 0.00 37.54 5.01
419 446 2.334946 GCGCTCCATTCCAGCAACA 61.335 57.895 0.00 0.00 36.61 3.33
434 463 3.068590 CAGCAACAACCTGAACCATTCTT 59.931 43.478 0.00 0.00 32.03 2.52
485 517 0.104934 CCTAGCATACACCTCCCCCT 60.105 60.000 0.00 0.00 0.00 4.79
515 547 3.953775 CCAGTTGGCCACCCGTCT 61.954 66.667 3.88 0.00 0.00 4.18
516 548 2.358737 CAGTTGGCCACCCGTCTC 60.359 66.667 3.88 0.00 0.00 3.36
538 582 2.081212 CACACGGAGAAGACGCGAC 61.081 63.158 15.93 6.86 34.00 5.19
545 589 1.666446 GAGAAGACGCGACGAAGCAC 61.666 60.000 15.93 0.00 36.85 4.40
559 603 1.737793 GAAGCACCGTCGGAATCAATT 59.262 47.619 20.51 3.54 0.00 2.32
573 617 5.316327 GAATCAATTCCAGAAACAGACCC 57.684 43.478 0.00 0.00 0.00 4.46
574 618 3.154827 TCAATTCCAGAAACAGACCCC 57.845 47.619 0.00 0.00 0.00 4.95
575 619 2.716424 TCAATTCCAGAAACAGACCCCT 59.284 45.455 0.00 0.00 0.00 4.79
576 620 3.140144 TCAATTCCAGAAACAGACCCCTT 59.860 43.478 0.00 0.00 0.00 3.95
584 628 2.658807 AACAGACCCCTTTCCAACTC 57.341 50.000 0.00 0.00 0.00 3.01
593 637 1.004277 CCTTTCCAACTCCCCAATCGA 59.996 52.381 0.00 0.00 0.00 3.59
674 722 1.617947 GGGCGGAGGAACACAGAGAT 61.618 60.000 0.00 0.00 0.00 2.75
677 725 1.066858 GCGGAGGAACACAGAGATTCA 60.067 52.381 0.00 0.00 0.00 2.57
684 732 6.432472 GGAGGAACACAGAGATTCAAAGAAAT 59.568 38.462 0.00 0.00 0.00 2.17
686 734 8.558973 AGGAACACAGAGATTCAAAGAAATAG 57.441 34.615 0.00 0.00 0.00 1.73
687 735 8.378565 AGGAACACAGAGATTCAAAGAAATAGA 58.621 33.333 0.00 0.00 0.00 1.98
688 736 8.663911 GGAACACAGAGATTCAAAGAAATAGAG 58.336 37.037 0.00 0.00 0.00 2.43
713 761 2.202987 CGAGGCAGGCAGGACATC 60.203 66.667 0.00 0.00 0.00 3.06
722 770 3.303189 CAGGACATCGAGCCTGGT 58.697 61.111 18.90 0.96 46.24 4.00
723 771 1.153489 CAGGACATCGAGCCTGGTG 60.153 63.158 18.90 2.35 46.24 4.17
724 772 2.512515 GGACATCGAGCCTGGTGC 60.513 66.667 0.00 0.00 41.71 5.01
728 776 4.101448 ATCGAGCCTGGTGCCACC 62.101 66.667 7.01 7.01 42.71 4.61
780 831 4.399395 CCCTGCAGCGAAGGAGCA 62.399 66.667 8.66 0.00 40.15 4.26
784 835 3.497932 GCAGCGAAGGAGCAGCAG 61.498 66.667 0.00 0.00 46.77 4.24
785 836 3.497932 CAGCGAAGGAGCAGCAGC 61.498 66.667 0.00 0.00 40.15 5.25
786 837 4.012811 AGCGAAGGAGCAGCAGCA 62.013 61.111 3.17 0.00 45.49 4.41
787 838 3.497932 GCGAAGGAGCAGCAGCAG 61.498 66.667 3.17 0.00 45.49 4.24
801 852 3.160748 GCAGGAGGAGGAGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
877 930 4.736896 GGAACCTCCGCGCTTCGT 62.737 66.667 5.56 0.00 36.19 3.85
923 981 0.108615 ACTGCACCTGTCATCTACGC 60.109 55.000 0.00 0.00 0.00 4.42
946 1004 2.785921 CGGTCTCCGTCTGTCTCG 59.214 66.667 0.00 0.00 42.73 4.04
947 1005 2.486042 GGTCTCCGTCTGTCTCGC 59.514 66.667 0.00 0.00 0.00 5.03
948 1006 2.041686 GGTCTCCGTCTGTCTCGCT 61.042 63.158 0.00 0.00 0.00 4.93
970 1031 0.392998 ACATGCCCTGTCCACGAATC 60.393 55.000 0.00 0.00 29.94 2.52
972 1033 1.561769 ATGCCCTGTCCACGAATCCA 61.562 55.000 0.00 0.00 0.00 3.41
973 1034 1.002624 GCCCTGTCCACGAATCCAA 60.003 57.895 0.00 0.00 0.00 3.53
974 1035 0.394352 GCCCTGTCCACGAATCCAAT 60.394 55.000 0.00 0.00 0.00 3.16
975 1036 1.668419 CCCTGTCCACGAATCCAATC 58.332 55.000 0.00 0.00 0.00 2.67
978 1039 0.988063 TGTCCACGAATCCAATCCCA 59.012 50.000 0.00 0.00 0.00 4.37
986 1047 2.418669 GAATCCAATCCCACTCCCCTA 58.581 52.381 0.00 0.00 0.00 3.53
987 1048 2.124560 ATCCAATCCCACTCCCCTAG 57.875 55.000 0.00 0.00 0.00 3.02
988 1049 0.694444 TCCAATCCCACTCCCCTAGC 60.694 60.000 0.00 0.00 0.00 3.42
989 1050 1.447643 CAATCCCACTCCCCTAGCG 59.552 63.158 0.00 0.00 0.00 4.26
991 1052 2.898472 AATCCCACTCCCCTAGCGCT 62.898 60.000 17.26 17.26 0.00 5.92
992 1053 2.020100 ATCCCACTCCCCTAGCGCTA 62.020 60.000 17.75 17.75 0.00 4.26
993 1054 1.760875 CCCACTCCCCTAGCGCTAA 60.761 63.158 19.37 2.13 0.00 3.09
994 1055 1.122019 CCCACTCCCCTAGCGCTAAT 61.122 60.000 19.37 0.00 0.00 1.73
996 1057 1.333177 CACTCCCCTAGCGCTAATCT 58.667 55.000 19.37 0.00 0.00 2.40
997 1058 1.689273 CACTCCCCTAGCGCTAATCTT 59.311 52.381 19.37 0.00 0.00 2.40
998 1059 1.689273 ACTCCCCTAGCGCTAATCTTG 59.311 52.381 19.37 11.10 0.00 3.02
999 1060 1.001406 CTCCCCTAGCGCTAATCTTGG 59.999 57.143 19.37 15.07 0.00 3.61
1005 1066 2.246719 AGCGCTAATCTTGGATGGAC 57.753 50.000 8.99 0.00 0.00 4.02
1338 1399 2.284847 GTCCCGGTAGGTTCCCCA 60.285 66.667 0.00 0.00 36.75 4.96
1339 1400 1.691689 GTCCCGGTAGGTTCCCCAT 60.692 63.158 0.00 0.00 36.75 4.00
1347 1415 0.419865 TAGGTTCCCCATCCACCTGA 59.580 55.000 0.11 0.00 41.28 3.86
1349 1417 1.208165 GGTTCCCCATCCACCTGACT 61.208 60.000 0.00 0.00 0.00 3.41
1350 1418 0.253327 GTTCCCCATCCACCTGACTC 59.747 60.000 0.00 0.00 0.00 3.36
1355 1423 1.222936 CATCCACCTGACTCCCTGC 59.777 63.158 0.00 0.00 0.00 4.85
1357 1425 2.483329 ATCCACCTGACTCCCTGCCT 62.483 60.000 0.00 0.00 0.00 4.75
1359 1427 0.909610 CCACCTGACTCCCTGCCTTA 60.910 60.000 0.00 0.00 0.00 2.69
1394 1465 2.790433 TCTTTTTCCTCCATTGACCGG 58.210 47.619 0.00 0.00 0.00 5.28
1405 1476 3.876589 TTGACCGGACCTTGCTCGC 62.877 63.158 9.46 0.00 0.00 5.03
1540 1613 1.134521 CAGGTTATCCTTGCGGTGCTA 60.135 52.381 0.00 0.00 43.07 3.49
1542 1615 1.296727 GTTATCCTTGCGGTGCTACC 58.703 55.000 0.00 0.00 34.05 3.18
1595 1668 3.496884 TGCGTCAGTTTATTCAGAACACC 59.503 43.478 0.00 0.00 0.00 4.16
1727 1804 1.867166 GCCCCAACTTCTACTATCGC 58.133 55.000 0.00 0.00 0.00 4.58
1763 1840 2.355193 GCCGGTGAGCTCTCTTCCT 61.355 63.158 16.19 0.00 0.00 3.36
1800 1878 6.927381 CAGAGCTTTCCATTTCTTCAACATTT 59.073 34.615 0.00 0.00 0.00 2.32
1816 1894 2.568062 ACATTTGCCATGCTGAATCCAA 59.432 40.909 0.00 0.00 0.00 3.53
1846 1924 1.513586 GAACTACGAGGCGGTCACG 60.514 63.158 0.00 0.00 44.63 4.35
1977 2055 4.949856 ACCATCTGAACTTGTTTGAGTTGT 59.050 37.500 0.00 0.00 39.84 3.32
1987 2065 5.293569 ACTTGTTTGAGTTGTACTGTAGCAC 59.706 40.000 0.00 0.00 0.00 4.40
2006 2084 5.790593 AGCACGAACTGGTTATCTTTCTAA 58.209 37.500 0.00 0.00 0.00 2.10
2023 2101 2.025321 TCTAAATCACTTCCCCCTTGGC 60.025 50.000 0.00 0.00 0.00 4.52
2024 2102 0.486879 AAATCACTTCCCCCTTGGCA 59.513 50.000 0.00 0.00 0.00 4.92
2025 2103 0.486879 AATCACTTCCCCCTTGGCAA 59.513 50.000 0.00 0.00 0.00 4.52
2026 2104 0.486879 ATCACTTCCCCCTTGGCAAA 59.513 50.000 0.00 0.00 0.00 3.68
2066 2144 6.673154 TCGATCTGATAGTTTTCTCGTGTA 57.327 37.500 0.00 0.00 0.00 2.90
2281 2359 1.734163 GGTGGAATCCTTGGTACGTG 58.266 55.000 0.00 0.00 0.00 4.49
2293 2371 1.082117 GGTACGTGCCAACTCCATCG 61.082 60.000 18.66 0.00 0.00 3.84
2348 2429 1.067565 TGAAGATCGCACTGACAGACC 60.068 52.381 10.08 0.00 0.00 3.85
2445 2526 4.436451 GGCTAGCAAACACGGTACATTTAC 60.436 45.833 18.24 0.00 0.00 2.01
2453 2534 8.580431 GCAAACACGGTACATTTACAATTTATC 58.420 33.333 0.00 0.00 0.00 1.75
2568 2649 4.281688 ACATAATGCCACTGCTCTTTGTTT 59.718 37.500 0.00 0.00 38.71 2.83
2580 2661 1.265635 TCTTTGTTTCCGCCATTGTCG 59.734 47.619 0.00 0.00 0.00 4.35
2589 2671 1.581934 CGCCATTGTCGGATGTACAT 58.418 50.000 8.43 8.43 0.00 2.29
2598 2680 5.984233 TGTCGGATGTACATAAATGAAGC 57.016 39.130 8.71 0.00 0.00 3.86
2687 2906 1.748879 ATTCCGGCACCACAATCCG 60.749 57.895 0.00 0.00 42.58 4.18
2721 2940 5.071788 ACTGAGAACCAAGGAACAACAGATA 59.928 40.000 0.00 0.00 0.00 1.98
2737 2956 0.249911 GATACCCATCAGTCGGTGCC 60.250 60.000 0.00 0.00 33.36 5.01
2846 3065 1.677217 GGCAGAGCCTGGTAACTGAAG 60.677 57.143 16.46 0.00 46.69 3.02
2973 3198 6.317910 AGACAAATAAAATTGCGCGATTTC 57.682 33.333 30.67 18.78 33.52 2.17
2992 3217 0.947180 CGTTCGTGGTTGGACCGAAT 60.947 55.000 0.00 0.00 42.58 3.34
2996 3221 1.619827 TCGTGGTTGGACCGAATTAGT 59.380 47.619 0.00 0.00 42.58 2.24
3097 3322 9.046296 AGTATATACTTTTGCTATCACTTGCAC 57.954 33.333 9.71 0.00 34.14 4.57
3147 3372 8.661257 CATAACGTAACATGTTAGGAATTGACA 58.339 33.333 33.60 16.16 34.37 3.58
3181 3412 1.346722 GGGAACGAAGAGGGAGTCAAA 59.653 52.381 0.00 0.00 0.00 2.69
3187 3418 3.195825 ACGAAGAGGGAGTCAAATAGTGG 59.804 47.826 0.00 0.00 0.00 4.00
3231 3462 6.544327 TTATGGAACCAATTGAGGGGATAT 57.456 37.500 7.12 0.00 0.00 1.63
3354 3590 1.215173 TGATTTAGGGGCATGGTCTGG 59.785 52.381 0.00 0.00 0.00 3.86
3362 3598 1.002868 GCATGGTCTGGTCACTGCT 60.003 57.895 0.00 0.00 0.00 4.24
3375 3611 2.252260 CTGCTGCGTTTTGACGGG 59.748 61.111 0.93 0.00 0.00 5.28
3411 3647 2.357154 GGGGTCCACATGTTTGAGCTAT 60.357 50.000 18.62 0.00 0.00 2.97
3415 3651 3.758554 GTCCACATGTTTGAGCTATGGTT 59.241 43.478 0.00 0.00 0.00 3.67
3596 3847 5.815581 TCTTCATAATTGGCAGTAACCTGT 58.184 37.500 0.00 0.00 41.02 4.00
3628 3879 6.539826 CAGAACAAAGGACTGATATGCACATA 59.460 38.462 0.00 0.00 34.07 2.29
3630 3881 7.611467 AGAACAAAGGACTGATATGCACATAAA 59.389 33.333 0.00 0.00 0.00 1.40
3631 3882 7.325660 ACAAAGGACTGATATGCACATAAAG 57.674 36.000 0.00 0.00 0.00 1.85
3633 3884 7.281774 ACAAAGGACTGATATGCACATAAAGAG 59.718 37.037 0.00 3.03 0.00 2.85
3635 3886 7.129457 AGGACTGATATGCACATAAAGAGAA 57.871 36.000 0.00 0.00 0.00 2.87
3642 3893 9.399797 TGATATGCACATAAAGAGAAGAAATGT 57.600 29.630 0.00 0.00 0.00 2.71
3660 3911 9.561069 AAGAAATGTAAATATAGGGCAGTAGTG 57.439 33.333 0.00 0.00 0.00 2.74
3688 3940 9.778741 ATTTACAGACTTGAAGTTGAGTAATGA 57.221 29.630 14.42 6.03 0.00 2.57
3690 3942 5.992217 ACAGACTTGAAGTTGAGTAATGACC 59.008 40.000 0.00 0.00 0.00 4.02
3709 3961 4.893524 TGACCACTCTTTTCTCAGACAGTA 59.106 41.667 0.00 0.00 0.00 2.74
3718 3970 4.511617 TTCTCAGACAGTAGCAAGTCAG 57.488 45.455 0.00 0.00 37.23 3.51
3719 3971 3.756117 TCTCAGACAGTAGCAAGTCAGA 58.244 45.455 0.00 0.00 37.23 3.27
3720 3972 4.145052 TCTCAGACAGTAGCAAGTCAGAA 58.855 43.478 0.00 0.00 37.23 3.02
3721 3973 4.769488 TCTCAGACAGTAGCAAGTCAGAAT 59.231 41.667 0.00 0.00 37.23 2.40
3722 3974 5.065704 TCAGACAGTAGCAAGTCAGAATC 57.934 43.478 0.00 0.00 37.23 2.52
3723 3975 4.524328 TCAGACAGTAGCAAGTCAGAATCA 59.476 41.667 0.00 0.00 37.23 2.57
3748 4000 2.515854 TGGGTTTATAAAGCGGTTGCA 58.484 42.857 18.46 9.49 46.23 4.08
3751 4003 3.191791 GGGTTTATAAAGCGGTTGCAGAA 59.808 43.478 18.46 0.00 46.23 3.02
3758 4032 2.888834 AGCGGTTGCAGAACAAATTT 57.111 40.000 0.00 0.00 46.23 1.82
3764 4038 5.619981 GCGGTTGCAGAACAAATTTAGATCT 60.620 40.000 0.00 0.00 40.82 2.75
3822 4101 3.048337 TCACAAATAGGGTGACGGAAC 57.952 47.619 0.00 0.00 40.16 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.347270 TCGAAAGTGTTGAAAATACGTCAA 57.653 33.333 0.00 0.00 43.29 3.18
5 6 5.970140 TCGAAAGTGTTGAAAATACGTCA 57.030 34.783 0.00 0.00 43.29 4.35
34 35 9.699410 TGTGTGATTGAGAGGGAATAAATTTAT 57.301 29.630 4.81 4.81 0.00 1.40
35 36 9.177608 CTGTGTGATTGAGAGGGAATAAATTTA 57.822 33.333 0.00 0.00 0.00 1.40
36 37 7.671398 ACTGTGTGATTGAGAGGGAATAAATTT 59.329 33.333 0.00 0.00 0.00 1.82
37 38 7.177878 ACTGTGTGATTGAGAGGGAATAAATT 58.822 34.615 0.00 0.00 0.00 1.82
38 39 6.725364 ACTGTGTGATTGAGAGGGAATAAAT 58.275 36.000 0.00 0.00 0.00 1.40
39 40 6.126863 ACTGTGTGATTGAGAGGGAATAAA 57.873 37.500 0.00 0.00 0.00 1.40
40 41 5.762179 ACTGTGTGATTGAGAGGGAATAA 57.238 39.130 0.00 0.00 0.00 1.40
41 42 8.547481 TTATACTGTGTGATTGAGAGGGAATA 57.453 34.615 0.00 0.00 0.00 1.75
42 43 5.965033 ATACTGTGTGATTGAGAGGGAAT 57.035 39.130 0.00 0.00 0.00 3.01
43 44 6.440647 ACTTATACTGTGTGATTGAGAGGGAA 59.559 38.462 0.00 0.00 0.00 3.97
44 45 5.958380 ACTTATACTGTGTGATTGAGAGGGA 59.042 40.000 0.00 0.00 0.00 4.20
45 46 6.045318 CACTTATACTGTGTGATTGAGAGGG 58.955 44.000 0.00 0.00 33.95 4.30
46 47 6.634805 ACACTTATACTGTGTGATTGAGAGG 58.365 40.000 9.20 0.00 45.57 3.69
63 64 8.603304 ACCTTGGTATAAAGTTGAGACACTTAT 58.397 33.333 0.00 0.00 35.87 1.73
64 65 7.970102 ACCTTGGTATAAAGTTGAGACACTTA 58.030 34.615 0.00 0.00 35.87 2.24
65 66 6.838382 ACCTTGGTATAAAGTTGAGACACTT 58.162 36.000 0.00 0.00 38.74 3.16
66 67 6.435292 ACCTTGGTATAAAGTTGAGACACT 57.565 37.500 0.00 0.00 0.00 3.55
67 68 7.876582 ACTAACCTTGGTATAAAGTTGAGACAC 59.123 37.037 0.00 0.00 0.00 3.67
68 69 7.970102 ACTAACCTTGGTATAAAGTTGAGACA 58.030 34.615 0.00 0.00 0.00 3.41
81 82 9.590451 CGTCTCAATTTTATACTAACCTTGGTA 57.410 33.333 0.00 0.00 0.00 3.25
82 83 8.098912 ACGTCTCAATTTTATACTAACCTTGGT 58.901 33.333 0.00 0.00 0.00 3.67
83 84 8.488651 ACGTCTCAATTTTATACTAACCTTGG 57.511 34.615 0.00 0.00 0.00 3.61
94 95 7.547722 GCCCCAAAATAAACGTCTCAATTTTAT 59.452 33.333 0.00 0.00 31.97 1.40
95 96 6.869388 GCCCCAAAATAAACGTCTCAATTTTA 59.131 34.615 0.00 0.00 31.97 1.52
96 97 5.699001 GCCCCAAAATAAACGTCTCAATTTT 59.301 36.000 0.00 0.00 33.07 1.82
97 98 5.234752 GCCCCAAAATAAACGTCTCAATTT 58.765 37.500 0.00 0.00 0.00 1.82
98 99 4.617298 CGCCCCAAAATAAACGTCTCAATT 60.617 41.667 0.00 0.00 0.00 2.32
99 100 3.119637 CGCCCCAAAATAAACGTCTCAAT 60.120 43.478 0.00 0.00 0.00 2.57
100 101 2.226912 CGCCCCAAAATAAACGTCTCAA 59.773 45.455 0.00 0.00 0.00 3.02
101 102 1.807742 CGCCCCAAAATAAACGTCTCA 59.192 47.619 0.00 0.00 0.00 3.27
102 103 1.131693 CCGCCCCAAAATAAACGTCTC 59.868 52.381 0.00 0.00 0.00 3.36
103 104 1.170442 CCGCCCCAAAATAAACGTCT 58.830 50.000 0.00 0.00 0.00 4.18
104 105 1.131693 CTCCGCCCCAAAATAAACGTC 59.868 52.381 0.00 0.00 0.00 4.34
105 106 1.170442 CTCCGCCCCAAAATAAACGT 58.830 50.000 0.00 0.00 0.00 3.99
106 107 0.454196 CCTCCGCCCCAAAATAAACG 59.546 55.000 0.00 0.00 0.00 3.60
107 108 0.821517 CCCTCCGCCCCAAAATAAAC 59.178 55.000 0.00 0.00 0.00 2.01
108 109 0.705253 TCCCTCCGCCCCAAAATAAA 59.295 50.000 0.00 0.00 0.00 1.40
109 110 0.257616 CTCCCTCCGCCCCAAAATAA 59.742 55.000 0.00 0.00 0.00 1.40
110 111 0.917333 ACTCCCTCCGCCCCAAAATA 60.917 55.000 0.00 0.00 0.00 1.40
111 112 0.917333 TACTCCCTCCGCCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
112 113 0.917333 ATACTCCCTCCGCCCCAAAA 60.917 55.000 0.00 0.00 0.00 2.44
113 114 0.030909 TATACTCCCTCCGCCCCAAA 60.031 55.000 0.00 0.00 0.00 3.28
114 115 0.192566 ATATACTCCCTCCGCCCCAA 59.807 55.000 0.00 0.00 0.00 4.12
115 116 0.544357 CATATACTCCCTCCGCCCCA 60.544 60.000 0.00 0.00 0.00 4.96
116 117 1.265454 CCATATACTCCCTCCGCCCC 61.265 65.000 0.00 0.00 0.00 5.80
117 118 0.544595 ACCATATACTCCCTCCGCCC 60.545 60.000 0.00 0.00 0.00 6.13
118 119 2.226962 TACCATATACTCCCTCCGCC 57.773 55.000 0.00 0.00 0.00 6.13
119 120 4.820894 AAATACCATATACTCCCTCCGC 57.179 45.455 0.00 0.00 0.00 5.54
145 146 2.552315 CGCCTAGAAAAAGCCAAGACAA 59.448 45.455 0.00 0.00 0.00 3.18
147 148 1.468914 CCGCCTAGAAAAAGCCAAGAC 59.531 52.381 0.00 0.00 0.00 3.01
154 155 0.442699 GACACGCCGCCTAGAAAAAG 59.557 55.000 0.00 0.00 0.00 2.27
155 156 1.286354 CGACACGCCGCCTAGAAAAA 61.286 55.000 0.00 0.00 0.00 1.94
182 183 1.464608 CGGCGAATGATCAACACAAGT 59.535 47.619 0.00 0.00 0.00 3.16
199 201 4.832608 CCAAGTACTCCGGCCGGC 62.833 72.222 39.89 25.10 34.68 6.13
273 298 8.204836 ACGTAAAGGATACAATATCTTCTTGCT 58.795 33.333 0.00 0.00 41.41 3.91
289 314 1.403249 CGACCCGTCAACGTAAAGGAT 60.403 52.381 1.48 0.00 37.74 3.24
291 316 1.620413 GCGACCCGTCAACGTAAAGG 61.620 60.000 1.48 0.00 37.74 3.11
346 371 4.767255 GCCCCTCGTGAGCTGTGG 62.767 72.222 0.00 0.00 0.00 4.17
359 384 2.359975 CACCTTGACTTCCGCCCC 60.360 66.667 0.00 0.00 0.00 5.80
365 390 1.578423 GCTGCTGCACCTTGACTTC 59.422 57.895 11.11 0.00 39.41 3.01
407 434 2.288395 GGTTCAGGTTGTTGCTGGAATG 60.288 50.000 0.00 0.00 0.00 2.67
414 441 3.068024 TGAAGAATGGTTCAGGTTGTTGC 59.932 43.478 0.00 0.00 32.54 4.17
419 446 2.504367 CCGTGAAGAATGGTTCAGGTT 58.496 47.619 8.42 0.00 39.58 3.50
469 498 0.550147 ACAAGGGGGAGGTGTATGCT 60.550 55.000 0.00 0.00 0.00 3.79
472 501 1.584724 CTGACAAGGGGGAGGTGTAT 58.415 55.000 0.00 0.00 0.00 2.29
485 517 2.818169 AACTGGGAGCGGCTGACAA 61.818 57.895 7.50 0.00 0.00 3.18
518 550 3.112709 GCGTCTTCTCCGTGTGCC 61.113 66.667 0.00 0.00 0.00 5.01
526 570 1.442184 TGCTTCGTCGCGTCTTCTC 60.442 57.895 5.77 0.00 0.00 2.87
528 572 2.717809 GGTGCTTCGTCGCGTCTTC 61.718 63.158 5.77 0.00 0.00 2.87
529 573 2.733593 GGTGCTTCGTCGCGTCTT 60.734 61.111 5.77 0.00 0.00 3.01
538 582 1.011968 TTGATTCCGACGGTGCTTCG 61.012 55.000 14.79 0.00 36.20 3.79
551 595 4.158579 GGGGTCTGTTTCTGGAATTGATTC 59.841 45.833 0.00 0.00 36.08 2.52
559 603 1.423921 GGAAAGGGGTCTGTTTCTGGA 59.576 52.381 0.00 0.00 33.85 3.86
561 605 2.623416 GTTGGAAAGGGGTCTGTTTCTG 59.377 50.000 0.00 0.00 33.85 3.02
568 612 1.140772 GGGGAGTTGGAAAGGGGTCT 61.141 60.000 0.00 0.00 0.00 3.85
573 617 1.004277 TCGATTGGGGAGTTGGAAAGG 59.996 52.381 0.00 0.00 0.00 3.11
574 618 2.084546 GTCGATTGGGGAGTTGGAAAG 58.915 52.381 0.00 0.00 0.00 2.62
575 619 1.609580 CGTCGATTGGGGAGTTGGAAA 60.610 52.381 0.00 0.00 0.00 3.13
576 620 0.036765 CGTCGATTGGGGAGTTGGAA 60.037 55.000 0.00 0.00 0.00 3.53
654 702 3.649277 CTCTGTGTTCCTCCGCCCG 62.649 68.421 0.00 0.00 0.00 6.13
663 711 8.663911 CCTCTATTTCTTTGAATCTCTGTGTTC 58.336 37.037 0.00 0.00 0.00 3.18
667 715 7.563906 CCTCCTCTATTTCTTTGAATCTCTGT 58.436 38.462 0.00 0.00 0.00 3.41
674 722 4.589908 GGTGCCTCCTCTATTTCTTTGAA 58.410 43.478 0.00 0.00 0.00 2.69
677 725 2.838202 TCGGTGCCTCCTCTATTTCTTT 59.162 45.455 0.00 0.00 0.00 2.52
684 732 2.442272 GCCTCGGTGCCTCCTCTA 60.442 66.667 0.00 0.00 0.00 2.43
686 734 4.154347 CTGCCTCGGTGCCTCCTC 62.154 72.222 0.00 0.00 0.00 3.71
779 830 2.733669 CCTCCTCCTCCTGCTGCTG 61.734 68.421 0.00 0.00 0.00 4.41
780 831 2.365370 CCTCCTCCTCCTGCTGCT 60.365 66.667 0.00 0.00 0.00 4.24
781 832 2.364842 TCCTCCTCCTCCTGCTGC 60.365 66.667 0.00 0.00 0.00 5.25
782 833 1.761667 CCTCCTCCTCCTCCTGCTG 60.762 68.421 0.00 0.00 0.00 4.41
783 834 2.695597 CCTCCTCCTCCTCCTGCT 59.304 66.667 0.00 0.00 0.00 4.24
784 835 3.160748 GCCTCCTCCTCCTCCTGC 61.161 72.222 0.00 0.00 0.00 4.85
785 836 2.837291 CGCCTCCTCCTCCTCCTG 60.837 72.222 0.00 0.00 0.00 3.86
786 837 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
787 838 4.467107 ACCGCCTCCTCCTCCTCC 62.467 72.222 0.00 0.00 0.00 4.30
877 930 2.036098 TACTCACGGGAGGGCGAA 59.964 61.111 20.91 0.00 45.81 4.70
880 933 2.363925 AGGTACTCACGGGAGGGC 60.364 66.667 20.91 10.89 45.81 5.19
881 934 1.305046 ACAGGTACTCACGGGAGGG 60.305 63.158 20.91 5.36 45.81 4.30
882 935 1.654954 CGACAGGTACTCACGGGAGG 61.655 65.000 20.91 2.63 45.81 4.30
883 936 0.959372 ACGACAGGTACTCACGGGAG 60.959 60.000 14.61 14.61 46.96 4.30
970 1031 1.839894 GCTAGGGGAGTGGGATTGG 59.160 63.158 0.00 0.00 0.00 3.16
972 1033 2.444256 GCGCTAGGGGAGTGGGATT 61.444 63.158 9.09 0.00 36.08 3.01
973 1034 2.020100 TAGCGCTAGGGGAGTGGGAT 62.020 60.000 14.45 0.00 36.08 3.85
974 1035 2.232892 TTAGCGCTAGGGGAGTGGGA 62.233 60.000 17.98 0.00 36.08 4.37
975 1036 1.122019 ATTAGCGCTAGGGGAGTGGG 61.122 60.000 17.98 0.00 36.08 4.61
978 1039 1.689273 CAAGATTAGCGCTAGGGGAGT 59.311 52.381 17.98 0.00 0.00 3.85
986 1047 1.486310 TGTCCATCCAAGATTAGCGCT 59.514 47.619 17.26 17.26 0.00 5.92
987 1048 1.953559 TGTCCATCCAAGATTAGCGC 58.046 50.000 0.00 0.00 0.00 5.92
988 1049 2.285220 CGTTGTCCATCCAAGATTAGCG 59.715 50.000 0.00 0.00 0.00 4.26
989 1050 2.032178 GCGTTGTCCATCCAAGATTAGC 59.968 50.000 0.00 0.00 0.00 3.09
991 1052 3.270027 CTGCGTTGTCCATCCAAGATTA 58.730 45.455 0.00 0.00 0.00 1.75
992 1053 2.086869 CTGCGTTGTCCATCCAAGATT 58.913 47.619 0.00 0.00 0.00 2.40
993 1054 1.679944 CCTGCGTTGTCCATCCAAGAT 60.680 52.381 0.00 0.00 0.00 2.40
994 1055 0.321564 CCTGCGTTGTCCATCCAAGA 60.322 55.000 0.00 0.00 0.00 3.02
996 1057 1.971167 GCCTGCGTTGTCCATCCAA 60.971 57.895 0.00 0.00 0.00 3.53
997 1058 2.359850 GCCTGCGTTGTCCATCCA 60.360 61.111 0.00 0.00 0.00 3.41
998 1059 2.045926 AGCCTGCGTTGTCCATCC 60.046 61.111 0.00 0.00 0.00 3.51
999 1060 2.456119 CGAGCCTGCGTTGTCCATC 61.456 63.158 0.00 0.00 0.00 3.51
1338 1399 1.997874 GGCAGGGAGTCAGGTGGAT 60.998 63.158 0.00 0.00 0.00 3.41
1339 1400 2.607750 GGCAGGGAGTCAGGTGGA 60.608 66.667 0.00 0.00 0.00 4.02
1347 1415 1.289160 TTGCAGATAAGGCAGGGAGT 58.711 50.000 0.00 0.00 43.05 3.85
1349 1417 2.897271 TTTTGCAGATAAGGCAGGGA 57.103 45.000 0.00 0.00 43.05 4.20
1350 1418 4.161001 AGAAATTTTGCAGATAAGGCAGGG 59.839 41.667 0.00 0.00 43.05 4.45
1359 1427 7.658982 GGAGGAAAAAGAAGAAATTTTGCAGAT 59.341 33.333 0.00 0.00 38.74 2.90
1414 1485 2.363711 TATCTGCATCCGTCCACCGC 62.364 60.000 0.00 0.00 34.38 5.68
1540 1613 3.861886 GCTGCAGCACAACAATTAATGGT 60.862 43.478 33.36 0.00 41.59 3.55
1542 1615 3.984018 GCTGCAGCACAACAATTAATG 57.016 42.857 33.36 0.00 41.59 1.90
1595 1668 2.951726 TCAGAACTGATGACAAGAGCG 58.048 47.619 0.00 0.00 34.14 5.03
1682 1759 2.885644 CCGACGCCGTCCTTGATG 60.886 66.667 12.26 0.00 0.00 3.07
1727 1804 1.672356 CACCCCGTCAGGAAAGCAG 60.672 63.158 0.00 0.00 41.02 4.24
1763 1840 5.316167 TGGAAAGCTCTGAAGAAGCAATTA 58.684 37.500 0.00 0.00 0.00 1.40
1800 1878 1.134640 GCAATTGGATTCAGCATGGCA 60.135 47.619 7.72 0.00 36.16 4.92
1816 1894 4.003648 CCTCGTAGTTCTGAAAAGGCAAT 58.996 43.478 0.00 0.00 0.00 3.56
1846 1924 0.301687 CGTGGCATATGACTTGTCGC 59.698 55.000 10.60 0.00 0.00 5.19
1977 2055 4.703575 AGATAACCAGTTCGTGCTACAGTA 59.296 41.667 0.00 0.00 0.00 2.74
1987 2065 8.480643 AGTGATTTAGAAAGATAACCAGTTCG 57.519 34.615 0.00 0.00 0.00 3.95
2006 2084 0.486879 TTGCCAAGGGGGAAGTGATT 59.513 50.000 0.00 0.00 39.90 2.57
2038 2116 5.457148 CGAGAAAACTATCAGATCGAACTGG 59.543 44.000 20.95 9.00 38.31 4.00
2045 2123 8.132362 AGATGTACACGAGAAAACTATCAGATC 58.868 37.037 0.00 0.00 0.00 2.75
2046 2124 7.918033 CAGATGTACACGAGAAAACTATCAGAT 59.082 37.037 0.00 0.00 0.00 2.90
2066 2144 2.158564 CCCTGCATTCCATACCAGATGT 60.159 50.000 0.00 0.00 0.00 3.06
2219 2297 2.341101 CCAGTAGTCTGCGACCCGT 61.341 63.158 5.29 0.00 40.09 5.28
2252 2330 1.175983 GGATTCCACCGGCAAACACA 61.176 55.000 0.00 0.00 0.00 3.72
2293 2371 5.041940 CACTACTGAACTTATAACGGCTCC 58.958 45.833 0.00 0.00 0.00 4.70
2348 2429 2.138320 GATACACCCACATGATCAGCG 58.862 52.381 0.00 0.00 0.00 5.18
2471 2552 7.690952 TTTATATATAAAGCGGGGCGAAAAT 57.309 32.000 12.90 0.00 0.00 1.82
2580 2661 6.715347 AAAGGGCTTCATTTATGTACATCC 57.285 37.500 12.68 4.51 0.00 3.51
2589 2671 4.038642 AGTTGCGAAAAAGGGCTTCATTTA 59.961 37.500 0.00 0.00 0.00 1.40
2598 2680 6.370718 AGTTATACTGTAGTTGCGAAAAAGGG 59.629 38.462 0.00 0.00 0.00 3.95
2630 2849 6.002062 CCTGAAACAGAACAGGTAACATTC 57.998 41.667 0.00 0.00 45.82 2.67
2687 2906 1.202722 TGGTTCTCAGTTTCCGGGTTC 60.203 52.381 0.00 0.00 0.00 3.62
2721 2940 4.082523 CGGCACCGACTGATGGGT 62.083 66.667 2.01 0.00 42.83 4.51
2737 2956 1.596203 ATGGACAGATCATGCGGCG 60.596 57.895 0.51 0.51 0.00 6.46
2846 3065 1.153168 CATCCCCATGGTGGTCGTC 60.153 63.158 11.73 0.00 35.17 4.20
2973 3198 1.592131 TTCGGTCCAACCACGAACG 60.592 57.895 0.00 0.00 41.12 3.95
2992 3217 8.246430 TCTGAAAACTCAAGGACTAGAACTAA 57.754 34.615 0.00 0.00 0.00 2.24
2996 3221 7.735917 TGATTCTGAAAACTCAAGGACTAGAA 58.264 34.615 0.00 0.00 0.00 2.10
3120 3345 7.638683 GTCAATTCCTAACATGTTACGTTATGC 59.361 37.037 14.35 5.01 0.00 3.14
3181 3412 8.398665 GCTTTTTCGAAAAGATATGACCACTAT 58.601 33.333 21.53 0.00 0.00 2.12
3187 3418 9.226345 CCATAAGCTTTTTCGAAAAGATATGAC 57.774 33.333 27.05 15.37 34.30 3.06
3258 3491 4.438200 GGTGGCTATGTGTTGTATTTTCCG 60.438 45.833 0.00 0.00 0.00 4.30
3290 3524 4.883585 CACAATACCAGTGGCTATGTGATT 59.116 41.667 26.06 7.75 33.43 2.57
3354 3590 0.654472 CGTCAAAACGCAGCAGTGAC 60.654 55.000 0.00 0.00 42.82 3.67
3375 3611 2.092323 GACCCCACCAGTCATAAAAGC 58.908 52.381 0.00 0.00 34.27 3.51
3596 3847 2.945008 CAGTCCTTTGTTCTGTCTGCAA 59.055 45.455 0.00 0.00 0.00 4.08
3628 3879 9.920946 TGCCCTATATTTACATTTCTTCTCTTT 57.079 29.630 0.00 0.00 0.00 2.52
3630 3881 8.718656 ACTGCCCTATATTTACATTTCTTCTCT 58.281 33.333 0.00 0.00 0.00 3.10
3631 3882 8.910351 ACTGCCCTATATTTACATTTCTTCTC 57.090 34.615 0.00 0.00 0.00 2.87
3633 3884 9.780186 ACTACTGCCCTATATTTACATTTCTTC 57.220 33.333 0.00 0.00 0.00 2.87
3635 3886 8.714906 ACACTACTGCCCTATATTTACATTTCT 58.285 33.333 0.00 0.00 0.00 2.52
3688 3940 4.262249 GCTACTGTCTGAGAAAAGAGTGGT 60.262 45.833 0.86 0.00 0.00 4.16
3690 3942 4.876125 TGCTACTGTCTGAGAAAAGAGTG 58.124 43.478 0.86 0.00 0.00 3.51
3709 3961 4.590222 ACCCATTTTTGATTCTGACTTGCT 59.410 37.500 0.00 0.00 0.00 3.91
3718 3970 7.547722 ACCGCTTTATAAACCCATTTTTGATTC 59.452 33.333 0.00 0.00 0.00 2.52
3719 3971 7.390823 ACCGCTTTATAAACCCATTTTTGATT 58.609 30.769 0.00 0.00 0.00 2.57
3720 3972 6.941857 ACCGCTTTATAAACCCATTTTTGAT 58.058 32.000 0.00 0.00 0.00 2.57
3721 3973 6.347859 ACCGCTTTATAAACCCATTTTTGA 57.652 33.333 0.00 0.00 0.00 2.69
3722 3974 6.619660 GCAACCGCTTTATAAACCCATTTTTG 60.620 38.462 0.00 0.00 34.30 2.44
3723 3975 5.410132 GCAACCGCTTTATAAACCCATTTTT 59.590 36.000 0.00 0.00 34.30 1.94
3748 4000 6.597280 GCCTCTGTGAGATCTAAATTTGTTCT 59.403 38.462 0.00 0.17 0.00 3.01
3751 4003 6.059787 AGCCTCTGTGAGATCTAAATTTGT 57.940 37.500 0.00 0.00 0.00 2.83
3758 4032 3.027412 GACCAAGCCTCTGTGAGATCTA 58.973 50.000 0.00 0.00 0.00 1.98
3764 4038 1.203187 AGGTAGACCAAGCCTCTGTGA 60.203 52.381 0.66 0.00 38.89 3.58
3810 4085 1.002773 GGTGTAATGTTCCGTCACCCT 59.997 52.381 0.00 0.00 41.58 4.34
3815 4094 3.857052 TCTGATGGTGTAATGTTCCGTC 58.143 45.455 0.00 0.00 37.66 4.79


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

AutoCloner maintained by Alex Coulton.