Multiple sequence alignment - TraesCS3D01G537700

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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 TraesCS3D01G537700 chr3D 100.000 3105 0 0 456 3560 610799733 610802837 0.000000e+00 5734.0
1 TraesCS3D01G537700 chr3D 100.000 192 0 0 1 192 610799278 610799469 4.370000e-94 355.0
2 TraesCS3D01G537700 chr3D 96.552 116 4 0 39 154 380261334 380261219 3.630000e-45 193.0
3 TraesCS3D01G537700 chr3D 99.057 106 1 0 1 106 103817603 103817708 1.300000e-44 191.0
4 TraesCS3D01G537700 chr3D 99.057 106 1 0 1 106 141368358 141368253 1.300000e-44 191.0
5 TraesCS3D01G537700 chr3D 99.057 106 1 0 1 106 380261474 380261369 1.300000e-44 191.0
6 TraesCS3D01G537700 chr3D 94.915 59 2 1 107 164 103817732 103817790 1.360000e-14 91.6
7 TraesCS3D01G537700 chr3D 97.500 40 1 0 3236 3275 610802459 610802498 6.380000e-08 69.4
8 TraesCS3D01G537700 chr3D 97.500 40 1 0 3182 3221 610802513 610802552 6.380000e-08 69.4
9 TraesCS3D01G537700 chr3B 92.033 2749 137 39 531 3220 828416513 828419238 0.000000e+00 3788.0
10 TraesCS3D01G537700 chr3B 92.843 1970 101 25 1274 3220 828768063 828766111 0.000000e+00 2820.0
11 TraesCS3D01G537700 chr3B 88.727 275 22 6 667 940 828768391 828768125 9.530000e-86 327.0
12 TraesCS3D01G537700 chr3B 86.809 235 24 5 3241 3474 828766144 828765916 4.560000e-64 255.0
13 TraesCS3D01G537700 chr3B 86.383 235 25 5 3241 3474 828419205 828419433 2.120000e-62 250.0
14 TraesCS3D01G537700 chr3B 88.372 129 9 2 531 653 828768846 828768718 2.210000e-32 150.0
15 TraesCS3D01G537700 chr3B 97.101 69 1 1 43 111 28176278 28176345 8.080000e-22 115.0
16 TraesCS3D01G537700 chr3B 93.878 49 3 0 484 532 828416438 828416486 1.370000e-09 75.0
17 TraesCS3D01G537700 chr3A 89.633 1746 101 22 658 2361 745508471 745510178 0.000000e+00 2148.0
18 TraesCS3D01G537700 chr3A 88.095 126 12 2 531 653 745507975 745508100 2.860000e-31 147.0
19 TraesCS3D01G537700 chr5D 81.610 1354 210 29 1024 2362 289008155 289009484 0.000000e+00 1085.0
20 TraesCS3D01G537700 chr5D 81.784 1345 196 33 1033 2362 288818034 288819344 0.000000e+00 1081.0
21 TraesCS3D01G537700 chr5A 81.914 1327 197 32 1051 2362 382291614 382292912 0.000000e+00 1081.0
22 TraesCS3D01G537700 chr5B 81.236 1343 215 27 1033 2361 328233601 328234920 0.000000e+00 1050.0
23 TraesCS3D01G537700 chr5B 87.156 109 13 1 44 152 182441511 182441618 4.830000e-24 122.0
24 TraesCS3D01G537700 chr7D 99.351 154 1 0 1 154 545503719 545503872 2.710000e-71 279.0
25 TraesCS3D01G537700 chr7D 99.057 106 1 0 1 106 488055503 488055608 1.300000e-44 191.0
26 TraesCS3D01G537700 chrUn 99.057 106 1 0 1 106 94054864 94054759 1.300000e-44 191.0
27 TraesCS3D01G537700 chrUn 100.000 63 0 0 92 154 94054750 94054688 2.250000e-22 117.0
28 TraesCS3D01G537700 chrUn 86.000 100 14 0 2370 2469 99825666 99825567 1.350000e-19 108.0
29 TraesCS3D01G537700 chr4D 99.057 106 1 0 1 106 24101843 24101738 1.300000e-44 191.0
30 TraesCS3D01G537700 chr4D 93.333 75 5 0 92 166 102384794 102384868 1.040000e-20 111.0
31 TraesCS3D01G537700 chr1D 96.262 107 4 0 45 151 319557681 319557787 3.650000e-40 176.0
32 TraesCS3D01G537700 chr2A 96.040 101 4 0 43 143 720394104 720394004 7.910000e-37 165.0
33 TraesCS3D01G537700 chr2A 94.118 102 6 0 42 143 720394340 720394239 4.760000e-34 156.0
34 TraesCS3D01G537700 chr4A 89.831 118 6 2 1 112 673026555 673026672 2.860000e-31 147.0
35 TraesCS3D01G537700 chr1A 97.101 69 1 1 43 111 74737738 74737805 8.080000e-22 115.0


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 TraesCS3D01G537700 chr3D 610799278 610802837 3559 False 1556.95 5734 98.750000 1 3560 4 chr3D.!!$F2 3559
1 TraesCS3D01G537700 chr3B 828416438 828419433 2995 False 1371.00 3788 90.764667 484 3474 3 chr3B.!!$F2 2990
2 TraesCS3D01G537700 chr3B 828765916 828768846 2930 True 888.00 2820 89.187750 531 3474 4 chr3B.!!$R1 2943
3 TraesCS3D01G537700 chr3A 745507975 745510178 2203 False 1147.50 2148 88.864000 531 2361 2 chr3A.!!$F1 1830
4 TraesCS3D01G537700 chr5D 289008155 289009484 1329 False 1085.00 1085 81.610000 1024 2362 1 chr5D.!!$F2 1338
5 TraesCS3D01G537700 chr5D 288818034 288819344 1310 False 1081.00 1081 81.784000 1033 2362 1 chr5D.!!$F1 1329
6 TraesCS3D01G537700 chr5A 382291614 382292912 1298 False 1081.00 1081 81.914000 1051 2362 1 chr5A.!!$F1 1311
7 TraesCS3D01G537700 chr5B 328233601 328234920 1319 False 1050.00 1050 81.236000 1033 2361 1 chr5B.!!$F2 1328

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 0.165944 CCGACAAAGTCAATCCGTGC 59.834 55.0 0.00 0.0 32.09 5.34 F
527 528 0.326595 TTGGCGCTTCTGGTAATCCA 59.673 50.0 7.64 0.0 42.05 3.41 F
1042 1473 0.725117 AGTAAATTACACGGCGCTGC 59.275 50.0 18.15 0.0 0.00 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 2153 0.624500 TTCCCCCTCCATCCCTCTTG 60.625 60.000 0.0 0.0 0.0 3.02 R
2005 2483 1.338107 CAGTCGGGGCTATCATACCA 58.662 55.000 0.0 0.0 0.0 3.25 R
2872 3363 1.202817 GGTCGTCCTCTTCTCCTGAAC 59.797 57.143 0.0 0.0 0.0 3.18 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
26 27 9.760660 CTTTGGACTAAATTTTCTTAGACGATG 57.239 33.333 0.00 0.00 33.78 3.84
27 28 7.843490 TGGACTAAATTTTCTTAGACGATGG 57.157 36.000 0.00 0.00 33.78 3.51
28 29 7.617225 TGGACTAAATTTTCTTAGACGATGGA 58.383 34.615 0.00 0.00 33.78 3.41
29 30 8.265055 TGGACTAAATTTTCTTAGACGATGGAT 58.735 33.333 0.00 0.00 33.78 3.41
30 31 9.760077 GGACTAAATTTTCTTAGACGATGGATA 57.240 33.333 0.00 0.00 33.78 2.59
39 40 9.456147 TTTCTTAGACGATGGATAAAAATTCCA 57.544 29.630 0.00 0.00 46.86 3.53
58 59 8.446599 AATTCCATAAAATTAGTACCACCTCG 57.553 34.615 0.00 0.00 0.00 4.63
59 60 6.549433 TCCATAAAATTAGTACCACCTCGT 57.451 37.500 0.00 0.00 0.00 4.18
60 61 6.949715 TCCATAAAATTAGTACCACCTCGTT 58.050 36.000 0.00 0.00 0.00 3.85
61 62 7.396418 TCCATAAAATTAGTACCACCTCGTTT 58.604 34.615 0.00 0.00 0.00 3.60
62 63 8.538701 TCCATAAAATTAGTACCACCTCGTTTA 58.461 33.333 0.00 0.00 0.00 2.01
63 64 9.333724 CCATAAAATTAGTACCACCTCGTTTAT 57.666 33.333 0.00 0.00 0.00 1.40
69 70 9.683069 AATTAGTACCACCTCGTTTATATTACG 57.317 33.333 4.26 4.26 40.23 3.18
70 71 6.942532 AGTACCACCTCGTTTATATTACGA 57.057 37.500 10.95 10.95 44.88 3.43
71 72 7.516198 AGTACCACCTCGTTTATATTACGAT 57.484 36.000 11.61 2.35 45.76 3.73
72 73 7.945134 AGTACCACCTCGTTTATATTACGATT 58.055 34.615 11.61 2.44 45.76 3.34
73 74 8.416329 AGTACCACCTCGTTTATATTACGATTT 58.584 33.333 11.61 2.17 45.76 2.17
74 75 9.034544 GTACCACCTCGTTTATATTACGATTTT 57.965 33.333 11.61 0.27 45.76 1.82
75 76 7.912383 ACCACCTCGTTTATATTACGATTTTG 58.088 34.615 11.61 9.38 45.76 2.44
76 77 7.550196 ACCACCTCGTTTATATTACGATTTTGT 59.450 33.333 11.61 6.48 45.76 2.83
77 78 8.060090 CCACCTCGTTTATATTACGATTTTGTC 58.940 37.037 11.61 0.00 45.76 3.18
78 79 8.814235 CACCTCGTTTATATTACGATTTTGTCT 58.186 33.333 11.61 0.00 45.76 3.41
97 98 7.585286 TTGTCTATACAAATCGTAAAAGCGT 57.415 32.000 0.00 0.00 42.60 5.07
98 99 8.686397 TTGTCTATACAAATCGTAAAAGCGTA 57.314 30.769 0.00 0.00 42.60 4.42
99 100 8.861033 TGTCTATACAAATCGTAAAAGCGTAT 57.139 30.769 0.00 0.00 32.59 3.06
100 101 9.304731 TGTCTATACAAATCGTAAAAGCGTATT 57.695 29.630 0.00 0.00 32.59 1.89
106 107 7.114920 ACAAATCGTAAAAGCGTATTATGACG 58.885 34.615 4.08 0.00 45.70 4.35
107 108 5.817616 ATCGTAAAAGCGTATTATGACGG 57.182 39.130 0.00 0.00 43.13 4.79
114 115 1.862827 GCGTATTATGACGGTGAACCC 59.137 52.381 0.00 0.00 43.13 4.11
124 125 3.390003 GGTGAACCCGACAAAGTCA 57.610 52.632 0.00 0.00 32.09 3.41
125 126 1.670791 GGTGAACCCGACAAAGTCAA 58.329 50.000 0.00 0.00 32.09 3.18
126 127 2.227194 GGTGAACCCGACAAAGTCAAT 58.773 47.619 0.00 0.00 32.09 2.57
127 128 2.225727 GGTGAACCCGACAAAGTCAATC 59.774 50.000 0.00 0.00 32.09 2.67
128 129 2.225727 GTGAACCCGACAAAGTCAATCC 59.774 50.000 0.00 0.00 32.09 3.01
129 130 1.463444 GAACCCGACAAAGTCAATCCG 59.537 52.381 0.00 0.00 32.09 4.18
130 131 0.395312 ACCCGACAAAGTCAATCCGT 59.605 50.000 0.00 0.00 32.09 4.69
131 132 0.796312 CCCGACAAAGTCAATCCGTG 59.204 55.000 0.00 0.00 32.09 4.94
132 133 0.165944 CCGACAAAGTCAATCCGTGC 59.834 55.000 0.00 0.00 32.09 5.34
133 134 1.148310 CGACAAAGTCAATCCGTGCT 58.852 50.000 0.00 0.00 32.09 4.40
134 135 1.531149 CGACAAAGTCAATCCGTGCTT 59.469 47.619 0.00 0.00 32.09 3.91
135 136 2.032030 CGACAAAGTCAATCCGTGCTTT 60.032 45.455 0.00 0.00 35.37 3.51
136 137 3.185594 CGACAAAGTCAATCCGTGCTTTA 59.814 43.478 0.00 0.00 34.13 1.85
137 138 4.142902 CGACAAAGTCAATCCGTGCTTTAT 60.143 41.667 0.00 0.00 34.13 1.40
138 139 5.616866 CGACAAAGTCAATCCGTGCTTTATT 60.617 40.000 0.00 0.00 34.13 1.40
139 140 6.401688 CGACAAAGTCAATCCGTGCTTTATTA 60.402 38.462 0.00 0.00 34.13 0.98
140 141 7.391148 ACAAAGTCAATCCGTGCTTTATTAT 57.609 32.000 0.00 0.00 34.13 1.28
141 142 7.826690 ACAAAGTCAATCCGTGCTTTATTATT 58.173 30.769 0.00 0.00 34.13 1.40
142 143 8.952278 ACAAAGTCAATCCGTGCTTTATTATTA 58.048 29.630 0.00 0.00 34.13 0.98
143 144 9.438291 CAAAGTCAATCCGTGCTTTATTATTAG 57.562 33.333 0.00 0.00 34.13 1.73
144 145 7.730364 AGTCAATCCGTGCTTTATTATTAGG 57.270 36.000 0.00 0.00 0.00 2.69
145 146 6.710744 AGTCAATCCGTGCTTTATTATTAGGG 59.289 38.462 0.00 0.00 0.00 3.53
146 147 6.708949 GTCAATCCGTGCTTTATTATTAGGGA 59.291 38.462 0.00 0.00 0.00 4.20
147 148 7.390718 GTCAATCCGTGCTTTATTATTAGGGAT 59.609 37.037 0.00 0.00 37.56 3.85
148 149 8.598916 TCAATCCGTGCTTTATTATTAGGGATA 58.401 33.333 0.00 0.00 35.62 2.59
149 150 8.883731 CAATCCGTGCTTTATTATTAGGGATAG 58.116 37.037 0.00 0.00 35.62 2.08
150 151 7.786046 TCCGTGCTTTATTATTAGGGATAGA 57.214 36.000 0.00 0.00 0.00 1.98
151 152 8.375493 TCCGTGCTTTATTATTAGGGATAGAT 57.625 34.615 0.00 0.00 0.00 1.98
152 153 8.822805 TCCGTGCTTTATTATTAGGGATAGATT 58.177 33.333 0.00 0.00 0.00 2.40
185 186 6.512514 TTTTACCTTTGGTAAGTACCTGGA 57.487 37.500 16.20 0.39 46.91 3.86
186 187 5.750352 TTACCTTTGGTAAGTACCTGGAG 57.250 43.478 16.20 8.88 42.44 3.86
187 188 3.595021 ACCTTTGGTAAGTACCTGGAGT 58.405 45.455 16.20 5.41 46.58 3.85
188 189 4.755437 ACCTTTGGTAAGTACCTGGAGTA 58.245 43.478 16.20 0.00 46.58 2.59
189 190 4.529769 ACCTTTGGTAAGTACCTGGAGTAC 59.470 45.833 16.20 0.00 46.58 2.73
190 191 6.515707 ACCTTTGGTAAGTACCTGGAGTACC 61.516 48.000 16.20 6.80 42.80 3.34
191 192 8.869229 ACCTTTGGTAAGTACCTGGAGTACCA 62.869 46.154 16.20 9.29 42.80 3.25
480 481 8.068893 GCTATTGATTAATGGAGTTTGCATTG 57.931 34.615 6.13 0.00 38.84 2.82
481 482 7.922278 GCTATTGATTAATGGAGTTTGCATTGA 59.078 33.333 6.13 0.00 38.84 2.57
482 483 9.976511 CTATTGATTAATGGAGTTTGCATTGAT 57.023 29.630 6.13 3.65 38.84 2.57
512 513 2.185004 TGCCTAGAGTTGAAGTTGGC 57.815 50.000 0.00 0.00 39.33 4.52
518 519 1.202698 AGAGTTGAAGTTGGCGCTTCT 60.203 47.619 7.64 0.00 43.74 2.85
527 528 0.326595 TTGGCGCTTCTGGTAATCCA 59.673 50.000 7.64 0.00 42.05 3.41
548 577 4.091945 CCACATGTTTATCTGTCACTCACG 59.908 45.833 0.00 0.00 0.00 4.35
561 590 2.623416 TCACTCACGAAAAGAGAGCTGA 59.377 45.455 0.00 0.00 40.58 4.26
563 592 3.611986 CACTCACGAAAAGAGAGCTGATC 59.388 47.826 0.00 0.00 40.58 2.92
617 646 7.038154 TCTCAGAAAGGTTTTATTGTGGTTG 57.962 36.000 0.00 0.00 0.00 3.77
714 1126 2.083167 ATTCGCATGGCTTTGTTTGG 57.917 45.000 0.00 0.00 0.00 3.28
765 1177 6.593382 AGTTACGCGTATACCCAAAATACAAA 59.407 34.615 21.30 0.00 31.43 2.83
921 1336 2.980233 GACACGCCAAAGCCAGCT 60.980 61.111 0.00 0.00 34.57 4.24
1042 1473 0.725117 AGTAAATTACACGGCGCTGC 59.275 50.000 18.15 0.00 0.00 5.25
1229 1663 2.204448 TTCCAGCCCCCATCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
1239 1673 2.107204 CCCCCATCCCTTATCTCTTGTG 59.893 54.545 0.00 0.00 0.00 3.33
1247 1681 1.211457 CTTATCTCTTGTGGCAGGCCT 59.789 52.381 12.19 0.00 36.94 5.19
1259 1693 1.880027 GGCAGGCCTTTATCATAACCG 59.120 52.381 0.00 0.00 0.00 4.44
1938 2416 1.337071 TGGGCTCTCGATATCAACGAC 59.663 52.381 3.12 0.00 35.88 4.34
2005 2483 0.537143 TCGCATCTTTGTGGCAAGGT 60.537 50.000 0.00 0.00 34.03 3.50
2091 2569 2.173569 GGAAGGGCACAAGGATGAGTAT 59.826 50.000 0.00 0.00 0.00 2.12
2218 2696 6.021596 GTGGCGAAATACAAATACAAGACAG 58.978 40.000 0.00 0.00 0.00 3.51
2363 2854 8.102800 TGTCGAAGTCTCTAACTACATTTGTA 57.897 34.615 0.00 0.00 37.17 2.41
2396 2887 4.894784 TGTCCTCATGGAGTGAAAACTAC 58.105 43.478 0.00 0.00 44.16 2.73
2415 2906 2.477825 ACGGAGATTCATCTGAATGCG 58.522 47.619 10.04 7.81 44.14 4.73
2463 2954 3.248266 GCAGCTAAAGCAATTGGTTCAG 58.752 45.455 22.21 18.49 45.16 3.02
2483 2974 2.358898 AGGTATGCTTGGCGCTTTATTG 59.641 45.455 7.64 0.00 40.11 1.90
2484 2975 2.543653 GGTATGCTTGGCGCTTTATTGG 60.544 50.000 7.64 0.00 40.11 3.16
2508 2999 4.788840 GCTGCAACAGAATATCAGACATGC 60.789 45.833 0.00 0.00 32.44 4.06
2528 3019 8.967664 ACATGCATTTAAATTAGAATTGGCAT 57.032 26.923 10.79 10.79 0.00 4.40
2551 3042 7.859875 GCATTCTAAAGCTGTCCATAAATCTTC 59.140 37.037 0.00 0.00 0.00 2.87
2589 3080 1.915489 TGTTGGGAGCCATACAGTCAT 59.085 47.619 0.00 0.00 31.53 3.06
2591 3082 2.945668 GTTGGGAGCCATACAGTCATTC 59.054 50.000 0.00 0.00 31.53 2.67
2615 3106 3.820467 TCAAGGGCTCAATGTACACTTTG 59.180 43.478 0.00 0.00 33.75 2.77
2872 3363 5.183331 TGGAGTACTGTAGCTGTGTAGAAAG 59.817 44.000 0.00 0.00 0.00 2.62
2884 3375 5.509840 GCTGTGTAGAAAGTTCAGGAGAAGA 60.510 44.000 0.00 0.00 33.63 2.87
2909 3400 2.034879 CCAGCCAGGTTAGTGCGTG 61.035 63.158 0.00 0.00 0.00 5.34
2910 3401 2.358737 AGCCAGGTTAGTGCGTGC 60.359 61.111 0.00 0.00 0.00 5.34
2911 3402 2.668212 GCCAGGTTAGTGCGTGCA 60.668 61.111 0.00 0.00 0.00 4.57
2912 3403 2.966309 GCCAGGTTAGTGCGTGCAC 61.966 63.158 16.91 16.91 46.50 4.57
2962 3463 6.540189 ACTGATGCATTATTTGTCCTACACTC 59.460 38.462 0.00 0.00 0.00 3.51
2975 3476 7.418337 TGTCCTACACTCAAATGAGCTAATA 57.582 36.000 10.28 0.00 45.79 0.98
2977 3478 7.764443 TGTCCTACACTCAAATGAGCTAATAAC 59.236 37.037 10.28 4.06 45.79 1.89
2985 3486 9.944376 ACTCAAATGAGCTAATAACTTCACTTA 57.056 29.630 10.28 0.00 45.79 2.24
3019 3520 4.080129 TGATTTGAAGCTCCTTGCCTAGAT 60.080 41.667 0.00 0.00 44.23 1.98
3025 3526 7.136822 TGAAGCTCCTTGCCTAGATTAAATA 57.863 36.000 0.00 0.00 44.23 1.40
3026 3527 7.220030 TGAAGCTCCTTGCCTAGATTAAATAG 58.780 38.462 0.00 0.00 44.23 1.73
3030 3531 6.992715 GCTCCTTGCCTAGATTAAATAGAACA 59.007 38.462 0.00 0.00 35.15 3.18
3031 3532 7.172361 GCTCCTTGCCTAGATTAAATAGAACAG 59.828 40.741 0.00 0.00 35.15 3.16
3060 3573 7.913674 AAACCTTCAATGAACTAGCTCTTAG 57.086 36.000 0.00 0.00 35.39 2.18
3067 3580 6.437477 TCAATGAACTAGCTCTTAGTCTTGGA 59.563 38.462 0.00 0.00 41.80 3.53
3072 3585 6.702716 ACTAGCTCTTAGTCTTGGACATAC 57.297 41.667 0.00 0.00 38.20 2.39
3076 3589 4.865365 GCTCTTAGTCTTGGACATACACAC 59.135 45.833 0.52 0.00 34.60 3.82
3083 3596 2.183478 TGGACATACACACCAAGCTG 57.817 50.000 0.00 0.00 0.00 4.24
3084 3597 0.804989 GGACATACACACCAAGCTGC 59.195 55.000 0.00 0.00 0.00 5.25
3085 3598 1.522668 GACATACACACCAAGCTGCA 58.477 50.000 1.02 0.00 0.00 4.41
3087 3600 2.489329 GACATACACACCAAGCTGCAAT 59.511 45.455 1.02 0.00 0.00 3.56
3092 3605 2.366266 ACACACCAAGCTGCAATGATTT 59.634 40.909 1.02 0.00 0.00 2.17
3100 3613 1.203994 GCTGCAATGATTTGGTCAGCT 59.796 47.619 4.95 0.00 41.70 4.24
3107 3620 5.447818 GCAATGATTTGGTCAGCTACTGTAC 60.448 44.000 0.00 0.00 40.92 2.90
3111 3624 4.882842 TTTGGTCAGCTACTGTACATCA 57.117 40.909 0.00 0.00 32.61 3.07
3140 3653 2.048444 TCTGCGTCGGAGGTAATACT 57.952 50.000 14.16 0.00 0.00 2.12
3141 3654 1.674441 TCTGCGTCGGAGGTAATACTG 59.326 52.381 14.16 0.00 0.00 2.74
3149 3662 5.402568 CGTCGGAGGTAATACTGATTCAATG 59.597 44.000 0.00 0.00 0.00 2.82
3150 3663 5.177696 GTCGGAGGTAATACTGATTCAATGC 59.822 44.000 0.00 0.00 0.00 3.56
3151 3664 4.452455 CGGAGGTAATACTGATTCAATGCC 59.548 45.833 0.00 0.00 0.00 4.40
3152 3665 5.625150 GGAGGTAATACTGATTCAATGCCT 58.375 41.667 0.00 0.00 0.00 4.75
3158 3671 3.587797 ACTGATTCAATGCCTGCAAAG 57.412 42.857 0.00 0.00 0.00 2.77
3169 3682 4.935352 TGCCTGCAAAGATTTGTTTAGT 57.065 36.364 7.12 0.00 40.24 2.24
3198 3711 7.595819 ACCAAATTTCCATTACAAACTCAGA 57.404 32.000 0.00 0.00 0.00 3.27
3199 3712 8.017418 ACCAAATTTCCATTACAAACTCAGAA 57.983 30.769 0.00 0.00 0.00 3.02
3200 3713 7.926018 ACCAAATTTCCATTACAAACTCAGAAC 59.074 33.333 0.00 0.00 0.00 3.01
3201 3714 8.143835 CCAAATTTCCATTACAAACTCAGAACT 58.856 33.333 0.00 0.00 0.00 3.01
3202 3715 9.533253 CAAATTTCCATTACAAACTCAGAACTT 57.467 29.630 0.00 0.00 0.00 2.66
3204 3717 9.533253 AATTTCCATTACAAACTCAGAACTTTG 57.467 29.630 0.00 0.00 34.18 2.77
3205 3718 7.873719 TTCCATTACAAACTCAGAACTTTGA 57.126 32.000 7.09 0.00 32.63 2.69
3206 3719 7.873719 TCCATTACAAACTCAGAACTTTGAA 57.126 32.000 7.09 0.37 32.63 2.69
3207 3720 7.703328 TCCATTACAAACTCAGAACTTTGAAC 58.297 34.615 7.09 0.00 32.63 3.18
3208 3721 7.338196 TCCATTACAAACTCAGAACTTTGAACA 59.662 33.333 7.09 0.00 32.63 3.18
3209 3722 7.973388 CCATTACAAACTCAGAACTTTGAACAA 59.027 33.333 7.09 0.00 32.63 2.83
3210 3723 9.352784 CATTACAAACTCAGAACTTTGAACAAA 57.647 29.630 7.09 0.17 32.63 2.83
3212 3725 9.921637 TTACAAACTCAGAACTTTGAACAAATT 57.078 25.926 7.09 0.00 32.63 1.82
3249 3762 2.706890 TGCGGGTTCCATTAGAAACTC 58.293 47.619 0.00 0.00 42.30 3.01
3260 3773 8.621286 GTTCCATTAGAAACTCAGAACTTTGAA 58.379 33.333 0.00 0.00 35.85 2.69
3298 3811 9.856488 TCTAGATTCATAATAAACCGTATCAGC 57.144 33.333 0.00 0.00 0.00 4.26
3299 3812 7.907214 AGATTCATAATAAACCGTATCAGCC 57.093 36.000 0.00 0.00 0.00 4.85
3301 3814 7.936847 AGATTCATAATAAACCGTATCAGCCAA 59.063 33.333 0.00 0.00 0.00 4.52
3302 3815 7.867305 TTCATAATAAACCGTATCAGCCAAA 57.133 32.000 0.00 0.00 0.00 3.28
3303 3816 8.458573 TTCATAATAAACCGTATCAGCCAAAT 57.541 30.769 0.00 0.00 0.00 2.32
3304 3817 8.094798 TCATAATAAACCGTATCAGCCAAATC 57.905 34.615 0.00 0.00 0.00 2.17
3305 3818 7.936847 TCATAATAAACCGTATCAGCCAAATCT 59.063 33.333 0.00 0.00 0.00 2.40
3306 3819 9.214957 CATAATAAACCGTATCAGCCAAATCTA 57.785 33.333 0.00 0.00 0.00 1.98
3307 3820 9.787435 ATAATAAACCGTATCAGCCAAATCTAA 57.213 29.630 0.00 0.00 0.00 2.10
3359 3873 8.254508 TGTATTAGCACTTTTGACTTTTGGTTT 58.745 29.630 0.00 0.00 0.00 3.27
3362 3876 8.696410 TTAGCACTTTTGACTTTTGGTTTAAG 57.304 30.769 0.00 0.00 0.00 1.85
3365 3879 6.183360 GCACTTTTGACTTTTGGTTTAAGGTG 60.183 38.462 0.00 0.00 34.73 4.00
3369 3883 5.669164 TGACTTTTGGTTTAAGGTGCTTT 57.331 34.783 0.00 0.00 0.00 3.51
3374 3888 7.387643 ACTTTTGGTTTAAGGTGCTTTGTTTA 58.612 30.769 0.00 0.00 0.00 2.01
3387 3901 3.503748 GCTTTGTTTAGTCCATGAGTGCT 59.496 43.478 0.00 0.00 0.00 4.40
3392 3906 5.129634 TGTTTAGTCCATGAGTGCTCAAAA 58.870 37.500 5.95 0.00 43.58 2.44
3394 3908 3.213206 AGTCCATGAGTGCTCAAAACA 57.787 42.857 5.95 0.00 43.58 2.83
3401 3915 5.581874 CCATGAGTGCTCAAAACAAAACTTT 59.418 36.000 5.95 0.00 43.58 2.66
3443 3957 1.630878 GTTGGGATCTTCCTGGTCTGT 59.369 52.381 0.00 0.00 36.57 3.41
3452 3966 0.984230 TCCTGGTCTGTGGTGATTCC 59.016 55.000 0.00 0.00 0.00 3.01
3454 3968 1.003839 TGGTCTGTGGTGATTCCGC 60.004 57.895 0.00 0.00 46.12 5.54
3474 3988 3.553715 CGCAGGCTGATGTGTATCTACAT 60.554 47.826 20.86 0.00 43.61 2.29
3475 3989 3.744942 GCAGGCTGATGTGTATCTACATG 59.255 47.826 20.86 0.00 41.15 3.21
3476 3990 4.741837 GCAGGCTGATGTGTATCTACATGT 60.742 45.833 20.86 2.69 41.15 3.21
3477 3991 4.748600 CAGGCTGATGTGTATCTACATGTG 59.251 45.833 9.42 0.00 41.15 3.21
3478 3992 3.496130 GGCTGATGTGTATCTACATGTGC 59.504 47.826 9.11 0.00 41.15 4.57
3479 3993 3.496130 GCTGATGTGTATCTACATGTGCC 59.504 47.826 9.11 0.00 41.15 5.01
3480 3994 4.741837 GCTGATGTGTATCTACATGTGCCT 60.742 45.833 9.11 0.00 41.15 4.75
3481 3995 5.357742 TGATGTGTATCTACATGTGCCTT 57.642 39.130 9.11 0.00 41.15 4.35
3482 3996 5.118286 TGATGTGTATCTACATGTGCCTTG 58.882 41.667 9.11 0.00 41.15 3.61
3483 3997 4.551702 TGTGTATCTACATGTGCCTTGT 57.448 40.909 9.11 0.00 38.63 3.16
3484 3998 4.905429 TGTGTATCTACATGTGCCTTGTT 58.095 39.130 9.11 0.00 38.63 2.83
3485 3999 5.312895 TGTGTATCTACATGTGCCTTGTTT 58.687 37.500 9.11 0.00 38.63 2.83
3486 4000 5.767665 TGTGTATCTACATGTGCCTTGTTTT 59.232 36.000 9.11 0.00 38.63 2.43
3487 4001 6.264292 TGTGTATCTACATGTGCCTTGTTTTT 59.736 34.615 9.11 0.00 38.63 1.94
3488 4002 7.445707 TGTGTATCTACATGTGCCTTGTTTTTA 59.554 33.333 9.11 0.00 38.63 1.52
3489 4003 8.293867 GTGTATCTACATGTGCCTTGTTTTTAA 58.706 33.333 9.11 0.00 38.63 1.52
3490 4004 9.019656 TGTATCTACATGTGCCTTGTTTTTAAT 57.980 29.630 9.11 0.00 0.00 1.40
3491 4005 9.855021 GTATCTACATGTGCCTTGTTTTTAATT 57.145 29.630 9.11 0.00 0.00 1.40
3492 4006 8.761575 ATCTACATGTGCCTTGTTTTTAATTG 57.238 30.769 9.11 0.00 0.00 2.32
3493 4007 7.721402 TCTACATGTGCCTTGTTTTTAATTGT 58.279 30.769 9.11 0.00 0.00 2.71
3494 4008 8.200792 TCTACATGTGCCTTGTTTTTAATTGTT 58.799 29.630 9.11 0.00 0.00 2.83
3495 4009 7.622893 ACATGTGCCTTGTTTTTAATTGTTT 57.377 28.000 0.00 0.00 0.00 2.83
3496 4010 7.693020 ACATGTGCCTTGTTTTTAATTGTTTC 58.307 30.769 0.00 0.00 0.00 2.78
3497 4011 7.335422 ACATGTGCCTTGTTTTTAATTGTTTCA 59.665 29.630 0.00 0.00 0.00 2.69
3498 4012 7.066374 TGTGCCTTGTTTTTAATTGTTTCAC 57.934 32.000 0.00 0.00 0.00 3.18
3499 4013 6.876257 TGTGCCTTGTTTTTAATTGTTTCACT 59.124 30.769 0.00 0.00 0.00 3.41
3500 4014 7.064016 TGTGCCTTGTTTTTAATTGTTTCACTC 59.936 33.333 0.00 0.00 0.00 3.51
3501 4015 7.064016 GTGCCTTGTTTTTAATTGTTTCACTCA 59.936 33.333 0.00 0.00 0.00 3.41
3502 4016 7.768120 TGCCTTGTTTTTAATTGTTTCACTCAT 59.232 29.630 0.00 0.00 0.00 2.90
3503 4017 8.611757 GCCTTGTTTTTAATTGTTTCACTCATT 58.388 29.630 0.00 0.00 0.00 2.57
3510 4024 9.829507 TTTTAATTGTTTCACTCATTTCATGGT 57.170 25.926 0.00 0.00 0.00 3.55
3514 4028 7.815840 TTGTTTCACTCATTTCATGGTAAGA 57.184 32.000 0.00 0.00 0.00 2.10
3515 4029 7.202016 TGTTTCACTCATTTCATGGTAAGAC 57.798 36.000 0.00 0.00 0.00 3.01
3516 4030 6.770303 TGTTTCACTCATTTCATGGTAAGACA 59.230 34.615 0.00 0.00 0.00 3.41
3517 4031 7.041167 TGTTTCACTCATTTCATGGTAAGACAG 60.041 37.037 0.00 0.00 0.00 3.51
3518 4032 5.491070 TCACTCATTTCATGGTAAGACAGG 58.509 41.667 0.00 0.00 0.00 4.00
3519 4033 5.013079 TCACTCATTTCATGGTAAGACAGGT 59.987 40.000 0.00 0.00 0.00 4.00
3520 4034 5.122869 CACTCATTTCATGGTAAGACAGGTG 59.877 44.000 0.00 0.00 0.00 4.00
3521 4035 4.009675 TCATTTCATGGTAAGACAGGTGC 58.990 43.478 0.00 0.00 0.00 5.01
3522 4036 2.093306 TTCATGGTAAGACAGGTGCG 57.907 50.000 0.00 0.00 0.00 5.34
3523 4037 0.391130 TCATGGTAAGACAGGTGCGC 60.391 55.000 0.00 0.00 0.00 6.09
3524 4038 0.673333 CATGGTAAGACAGGTGCGCA 60.673 55.000 5.66 5.66 0.00 6.09
3525 4039 0.673644 ATGGTAAGACAGGTGCGCAC 60.674 55.000 32.15 32.15 0.00 5.34
3540 4054 3.566261 CACCAAGGTGCGCACTAG 58.434 61.111 36.84 25.69 39.39 2.57
3541 4055 2.034879 CACCAAGGTGCGCACTAGG 61.035 63.158 36.84 33.21 39.39 3.02
3542 4056 3.127533 CCAAGGTGCGCACTAGGC 61.128 66.667 36.84 21.92 39.90 3.93
3543 4057 2.358615 CAAGGTGCGCACTAGGCA 60.359 61.111 36.84 0.00 45.17 4.75
3559 4073 3.418684 AGGCACTAGTTTGGGTAGTTG 57.581 47.619 0.00 0.00 36.02 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.760660 CATCGTCTAAGAAAATTTAGTCCAAAG 57.239 33.333 0.00 0.00 33.38 2.77
1 2 8.726988 CCATCGTCTAAGAAAATTTAGTCCAAA 58.273 33.333 0.00 0.00 33.38 3.28
2 3 8.098286 TCCATCGTCTAAGAAAATTTAGTCCAA 58.902 33.333 0.00 0.00 33.38 3.53
3 4 7.617225 TCCATCGTCTAAGAAAATTTAGTCCA 58.383 34.615 0.00 0.00 33.38 4.02
4 5 8.664211 ATCCATCGTCTAAGAAAATTTAGTCC 57.336 34.615 0.00 0.00 33.38 3.85
13 14 9.456147 TGGAATTTTTATCCATCGTCTAAGAAA 57.544 29.630 0.00 0.00 41.98 2.52
32 33 8.899771 CGAGGTGGTACTAATTTTATGGAATTT 58.100 33.333 0.00 0.00 31.96 1.82
33 34 8.050930 ACGAGGTGGTACTAATTTTATGGAATT 58.949 33.333 0.00 0.00 33.95 2.17
34 35 7.571025 ACGAGGTGGTACTAATTTTATGGAAT 58.429 34.615 0.00 0.00 0.00 3.01
35 36 6.949715 ACGAGGTGGTACTAATTTTATGGAA 58.050 36.000 0.00 0.00 0.00 3.53
36 37 6.549433 ACGAGGTGGTACTAATTTTATGGA 57.451 37.500 0.00 0.00 0.00 3.41
37 38 7.619964 AAACGAGGTGGTACTAATTTTATGG 57.380 36.000 0.00 0.00 0.00 2.74
43 44 9.683069 CGTAATATAAACGAGGTGGTACTAATT 57.317 33.333 4.89 0.00 42.90 1.40
44 45 9.066892 TCGTAATATAAACGAGGTGGTACTAAT 57.933 33.333 8.67 0.00 43.90 1.73
45 46 8.445275 TCGTAATATAAACGAGGTGGTACTAA 57.555 34.615 8.67 0.00 43.90 2.24
47 48 6.942532 TCGTAATATAAACGAGGTGGTACT 57.057 37.500 8.67 0.00 43.90 2.73
71 72 8.497554 ACGCTTTTACGATTTGTATAGACAAAA 58.502 29.630 18.71 0.59 45.75 2.44
72 73 8.020861 ACGCTTTTACGATTTGTATAGACAAA 57.979 30.769 17.30 17.30 46.19 2.83
73 74 7.585286 ACGCTTTTACGATTTGTATAGACAA 57.415 32.000 0.00 0.00 39.11 3.18
74 75 8.861033 ATACGCTTTTACGATTTGTATAGACA 57.139 30.769 0.00 0.00 36.70 3.41
80 81 8.261229 CGTCATAATACGCTTTTACGATTTGTA 58.739 33.333 0.00 0.00 35.87 2.41
81 82 7.114920 CGTCATAATACGCTTTTACGATTTGT 58.885 34.615 0.00 0.00 35.87 2.83
82 83 6.568601 CCGTCATAATACGCTTTTACGATTTG 59.431 38.462 0.00 0.00 41.51 2.32
83 84 6.256321 ACCGTCATAATACGCTTTTACGATTT 59.744 34.615 0.00 0.00 41.51 2.17
84 85 5.750067 ACCGTCATAATACGCTTTTACGATT 59.250 36.000 0.00 0.00 41.51 3.34
85 86 5.174398 CACCGTCATAATACGCTTTTACGAT 59.826 40.000 0.00 0.00 41.51 3.73
86 87 4.500117 CACCGTCATAATACGCTTTTACGA 59.500 41.667 0.00 0.00 41.51 3.43
87 88 4.500117 TCACCGTCATAATACGCTTTTACG 59.500 41.667 0.00 0.00 41.51 3.18
88 89 5.954434 TCACCGTCATAATACGCTTTTAC 57.046 39.130 0.00 0.00 41.51 2.01
89 90 5.291614 GGTTCACCGTCATAATACGCTTTTA 59.708 40.000 0.00 0.00 41.51 1.52
90 91 4.093850 GGTTCACCGTCATAATACGCTTTT 59.906 41.667 0.00 0.00 41.51 2.27
91 92 3.619929 GGTTCACCGTCATAATACGCTTT 59.380 43.478 0.00 0.00 41.51 3.51
92 93 3.192466 GGTTCACCGTCATAATACGCTT 58.808 45.455 0.00 0.00 41.51 4.68
93 94 2.482490 GGGTTCACCGTCATAATACGCT 60.482 50.000 0.00 0.00 41.51 5.07
94 95 1.862827 GGGTTCACCGTCATAATACGC 59.137 52.381 0.00 0.00 41.51 4.42
106 107 1.670791 TTGACTTTGTCGGGTTCACC 58.329 50.000 0.00 0.00 34.95 4.02
107 108 2.225727 GGATTGACTTTGTCGGGTTCAC 59.774 50.000 0.00 0.00 34.95 3.18
108 109 2.500229 GGATTGACTTTGTCGGGTTCA 58.500 47.619 0.00 0.00 34.95 3.18
109 110 1.463444 CGGATTGACTTTGTCGGGTTC 59.537 52.381 0.00 0.00 34.95 3.62
110 111 1.202722 ACGGATTGACTTTGTCGGGTT 60.203 47.619 0.00 0.00 34.95 4.11
111 112 0.395312 ACGGATTGACTTTGTCGGGT 59.605 50.000 0.00 0.00 34.95 5.28
112 113 0.796312 CACGGATTGACTTTGTCGGG 59.204 55.000 0.00 0.00 34.95 5.14
113 114 0.165944 GCACGGATTGACTTTGTCGG 59.834 55.000 0.00 0.00 34.95 4.79
114 115 1.148310 AGCACGGATTGACTTTGTCG 58.852 50.000 0.00 0.00 34.95 4.35
115 116 3.626028 AAAGCACGGATTGACTTTGTC 57.374 42.857 0.00 0.00 33.18 3.18
116 117 5.705609 AATAAAGCACGGATTGACTTTGT 57.294 34.783 0.00 0.00 34.97 2.83
117 118 9.438291 CTAATAATAAAGCACGGATTGACTTTG 57.562 33.333 0.00 0.00 34.97 2.77
118 119 8.621286 CCTAATAATAAAGCACGGATTGACTTT 58.379 33.333 0.00 0.00 36.31 2.66
119 120 7.228706 CCCTAATAATAAAGCACGGATTGACTT 59.771 37.037 0.00 0.00 0.00 3.01
120 121 6.710744 CCCTAATAATAAAGCACGGATTGACT 59.289 38.462 0.00 0.00 0.00 3.41
121 122 6.708949 TCCCTAATAATAAAGCACGGATTGAC 59.291 38.462 0.00 0.00 0.00 3.18
122 123 6.833041 TCCCTAATAATAAAGCACGGATTGA 58.167 36.000 0.00 0.00 0.00 2.57
123 124 7.687941 ATCCCTAATAATAAAGCACGGATTG 57.312 36.000 0.00 0.00 0.00 2.67
124 125 8.822805 TCTATCCCTAATAATAAAGCACGGATT 58.177 33.333 0.00 0.00 0.00 3.01
125 126 8.375493 TCTATCCCTAATAATAAAGCACGGAT 57.625 34.615 0.00 0.00 0.00 4.18
126 127 7.786046 TCTATCCCTAATAATAAAGCACGGA 57.214 36.000 0.00 0.00 0.00 4.69
161 162 6.909076 TCCAGGTACTTACCAAAGGTAAAAA 58.091 36.000 9.67 0.00 45.92 1.94
162 163 6.101588 ACTCCAGGTACTTACCAAAGGTAAAA 59.898 38.462 9.67 0.00 45.92 1.52
163 164 5.608015 ACTCCAGGTACTTACCAAAGGTAAA 59.392 40.000 9.67 0.00 45.92 2.01
165 166 9.570379 TGGTACTCCAGGTACTTACCAAAGGTA 62.570 44.444 8.17 3.54 42.87 3.08
166 167 8.869229 TGGTACTCCAGGTACTTACCAAAGGT 62.869 46.154 8.17 0.00 42.87 3.50
167 168 6.515003 TGGTACTCCAGGTACTTACCAAAGG 61.515 48.000 8.17 6.71 42.87 3.11
168 169 4.529377 TGGTACTCCAGGTACTTACCAAAG 59.471 45.833 8.17 4.62 42.87 2.77
169 170 4.491675 TGGTACTCCAGGTACTTACCAAA 58.508 43.478 8.17 0.00 42.87 3.28
170 171 4.130719 TGGTACTCCAGGTACTTACCAA 57.869 45.455 8.17 0.00 42.87 3.67
455 456 7.922278 TCAATGCAAACTCCATTAATCAATAGC 59.078 33.333 0.00 0.00 32.03 2.97
456 457 9.976511 ATCAATGCAAACTCCATTAATCAATAG 57.023 29.630 0.00 0.00 32.03 1.73
457 458 9.970395 GATCAATGCAAACTCCATTAATCAATA 57.030 29.630 0.00 0.00 30.87 1.90
458 459 8.479689 TGATCAATGCAAACTCCATTAATCAAT 58.520 29.630 0.00 0.00 35.46 2.57
459 460 7.838884 TGATCAATGCAAACTCCATTAATCAA 58.161 30.769 0.00 0.00 35.46 2.57
460 461 7.407393 TGATCAATGCAAACTCCATTAATCA 57.593 32.000 0.00 0.00 35.83 2.57
461 462 8.761497 CAATGATCAATGCAAACTCCATTAATC 58.239 33.333 0.00 0.00 31.06 1.75
462 463 8.479689 TCAATGATCAATGCAAACTCCATTAAT 58.520 29.630 5.85 0.00 32.03 1.40
463 464 7.838884 TCAATGATCAATGCAAACTCCATTAA 58.161 30.769 5.85 0.00 32.03 1.40
464 465 7.407393 TCAATGATCAATGCAAACTCCATTA 57.593 32.000 5.85 0.00 32.03 1.90
465 466 6.288941 TCAATGATCAATGCAAACTCCATT 57.711 33.333 5.85 0.00 33.41 3.16
466 467 5.925506 TCAATGATCAATGCAAACTCCAT 57.074 34.783 5.85 0.00 0.00 3.41
467 468 5.186215 ACATCAATGATCAATGCAAACTCCA 59.814 36.000 5.85 0.00 0.00 3.86
468 469 5.657474 ACATCAATGATCAATGCAAACTCC 58.343 37.500 5.85 0.00 0.00 3.85
469 470 7.096189 GCATACATCAATGATCAATGCAAACTC 60.096 37.037 23.65 4.23 33.25 3.01
470 471 6.700081 GCATACATCAATGATCAATGCAAACT 59.300 34.615 23.65 0.00 33.25 2.66
471 472 6.073980 GGCATACATCAATGATCAATGCAAAC 60.074 38.462 26.91 14.68 34.54 2.93
472 473 5.986741 GGCATACATCAATGATCAATGCAAA 59.013 36.000 26.91 1.69 34.54 3.68
473 474 5.303333 AGGCATACATCAATGATCAATGCAA 59.697 36.000 26.91 6.37 34.54 4.08
474 475 4.830600 AGGCATACATCAATGATCAATGCA 59.169 37.500 26.91 5.24 34.54 3.96
475 476 5.386958 AGGCATACATCAATGATCAATGC 57.613 39.130 21.84 21.84 0.00 3.56
476 477 7.606839 ACTCTAGGCATACATCAATGATCAATG 59.393 37.037 4.26 4.26 0.00 2.82
477 478 7.687388 ACTCTAGGCATACATCAATGATCAAT 58.313 34.615 0.00 0.00 0.00 2.57
478 479 7.071069 ACTCTAGGCATACATCAATGATCAA 57.929 36.000 0.00 0.00 0.00 2.57
479 480 6.676990 ACTCTAGGCATACATCAATGATCA 57.323 37.500 0.00 0.00 0.00 2.92
480 481 7.157347 TCAACTCTAGGCATACATCAATGATC 58.843 38.462 0.00 0.00 0.00 2.92
481 482 7.071069 TCAACTCTAGGCATACATCAATGAT 57.929 36.000 0.00 0.00 0.00 2.45
482 483 6.484364 TCAACTCTAGGCATACATCAATGA 57.516 37.500 0.00 0.00 0.00 2.57
518 519 6.597672 GTGACAGATAAACATGTGGATTACCA 59.402 38.462 0.00 0.00 44.76 3.25
527 528 5.134202 TCGTGAGTGACAGATAAACATGT 57.866 39.130 0.00 0.00 0.00 3.21
561 590 1.478105 GCAAAATGGAAAGCCGGAGAT 59.522 47.619 5.05 0.00 36.79 2.75
563 592 0.108662 GGCAAAATGGAAAGCCGGAG 60.109 55.000 5.05 0.00 37.41 4.63
612 641 0.397187 TGGCGGCTAAACTACAACCA 59.603 50.000 11.43 0.00 0.00 3.67
617 646 1.022982 GGGTGTGGCGGCTAAACTAC 61.023 60.000 11.43 0.00 0.00 2.73
642 674 0.320771 TCAGGCAAGGTCTTCTTCGC 60.321 55.000 0.00 0.00 32.41 4.70
714 1126 4.558860 GTGCAGTTTGAACAAGACTTCAAC 59.441 41.667 0.00 0.00 39.37 3.18
1152 1586 2.280552 CCATTGCTTGCAGGTGGCT 61.281 57.895 13.39 0.00 45.15 4.75
1229 1663 1.289160 AAGGCCTGCCACAAGAGATA 58.711 50.000 5.69 0.00 38.92 1.98
1239 1673 1.880027 CGGTTATGATAAAGGCCTGCC 59.120 52.381 5.69 0.00 0.00 4.85
1247 1681 3.137544 AGGGGATGTGCGGTTATGATAAA 59.862 43.478 0.00 0.00 0.00 1.40
1259 1693 2.040544 CCGTCAACAGGGGATGTGC 61.041 63.158 0.00 0.00 43.00 4.57
1286 1720 1.884235 CGAGGAAGGAACAAAGCTGT 58.116 50.000 0.00 0.00 37.39 4.40
1684 2153 0.624500 TTCCCCCTCCATCCCTCTTG 60.625 60.000 0.00 0.00 0.00 3.02
1938 2416 1.772882 CACCATGTCGTCGTTGTCG 59.227 57.895 0.00 0.00 38.55 4.35
2005 2483 1.338107 CAGTCGGGGCTATCATACCA 58.662 55.000 0.00 0.00 0.00 3.25
2091 2569 7.054124 AGACAATCTTGGTAGACTGACAAAAA 58.946 34.615 0.00 0.00 32.14 1.94
2218 2696 6.808704 GGATAAGCCACAGTTTGAAAAGAATC 59.191 38.462 0.00 0.00 36.34 2.52
2227 2707 2.095768 CACACGGATAAGCCACAGTTTG 60.096 50.000 0.00 0.00 35.94 2.93
2363 2854 7.679881 TCACTCCATGAGGACATTATGGTATAT 59.320 37.037 10.33 0.00 41.61 0.86
2396 2887 2.730404 CTCGCATTCAGATGAATCTCCG 59.270 50.000 5.09 8.67 42.41 4.63
2415 2906 4.111375 TGAACTGAGCGATTAAGTCCTC 57.889 45.455 0.00 0.00 0.00 3.71
2483 2974 2.615912 GTCTGATATTCTGTTGCAGCCC 59.384 50.000 0.00 0.00 0.00 5.19
2484 2975 3.273434 TGTCTGATATTCTGTTGCAGCC 58.727 45.455 0.00 0.00 0.00 4.85
2528 3019 8.321353 TCAGAAGATTTATGGACAGCTTTAGAA 58.679 33.333 0.00 0.00 0.00 2.10
2534 3025 9.466497 TTTTAATCAGAAGATTTATGGACAGCT 57.534 29.630 0.00 0.00 41.64 4.24
2589 3080 4.072131 GTGTACATTGAGCCCTTGAAGAA 58.928 43.478 0.00 0.00 0.00 2.52
2591 3082 3.679389 AGTGTACATTGAGCCCTTGAAG 58.321 45.455 0.00 0.00 0.00 3.02
2615 3106 3.866327 GCCGAAGTTCAGAGGAAGATAAC 59.134 47.826 3.32 0.00 32.62 1.89
2654 3145 6.118852 AGATAAAGCCAAGAGGAATGTCTTC 58.881 40.000 0.00 0.00 34.38 2.87
2872 3363 1.202817 GGTCGTCCTCTTCTCCTGAAC 59.797 57.143 0.00 0.00 0.00 3.18
2924 3419 4.177165 TGCATCAGTCGCATCAAAAATT 57.823 36.364 0.00 0.00 33.55 1.82
2935 3430 5.523552 TGTAGGACAAATAATGCATCAGTCG 59.476 40.000 0.00 0.00 0.00 4.18
2945 3440 7.831193 AGCTCATTTGAGTGTAGGACAAATAAT 59.169 33.333 9.21 0.00 43.85 1.28
2946 3441 7.168219 AGCTCATTTGAGTGTAGGACAAATAA 58.832 34.615 9.21 0.00 43.85 1.40
2975 3476 9.651913 AAATCACACACAAAATTAAGTGAAGTT 57.348 25.926 14.88 0.00 39.17 2.66
2977 3478 9.299963 TCAAATCACACACAAAATTAAGTGAAG 57.700 29.630 14.88 9.99 39.17 3.02
2985 3486 5.754890 GGAGCTTCAAATCACACACAAAATT 59.245 36.000 0.00 0.00 0.00 1.82
3025 3526 7.775561 AGTTCATTGAAGGTTTTACTCTGTTCT 59.224 33.333 0.00 0.00 0.00 3.01
3026 3527 7.931275 AGTTCATTGAAGGTTTTACTCTGTTC 58.069 34.615 0.00 0.00 0.00 3.18
3030 3531 7.454225 AGCTAGTTCATTGAAGGTTTTACTCT 58.546 34.615 0.00 0.00 0.00 3.24
3031 3532 7.604545 AGAGCTAGTTCATTGAAGGTTTTACTC 59.395 37.037 9.43 1.86 0.00 2.59
3045 3546 5.717178 TGTCCAAGACTAAGAGCTAGTTCAT 59.283 40.000 9.43 0.00 41.17 2.57
3047 3548 5.646577 TGTCCAAGACTAAGAGCTAGTTC 57.353 43.478 0.00 0.00 41.17 3.01
3067 3580 1.979855 TTGCAGCTTGGTGTGTATGT 58.020 45.000 0.00 0.00 0.00 2.29
3072 3585 2.734606 CAAATCATTGCAGCTTGGTGTG 59.265 45.455 0.00 0.00 0.00 3.82
3076 3589 2.028839 TGACCAAATCATTGCAGCTTGG 60.029 45.455 7.19 7.19 41.91 3.61
3083 3596 3.441572 ACAGTAGCTGACCAAATCATTGC 59.558 43.478 0.00 0.00 36.48 3.56
3084 3597 5.643348 TGTACAGTAGCTGACCAAATCATTG 59.357 40.000 0.00 0.00 36.48 2.82
3085 3598 5.804639 TGTACAGTAGCTGACCAAATCATT 58.195 37.500 0.00 0.00 36.48 2.57
3087 3600 4.882842 TGTACAGTAGCTGACCAAATCA 57.117 40.909 0.00 0.00 35.18 2.57
3092 3605 5.420725 AAATGATGTACAGTAGCTGACCA 57.579 39.130 0.33 0.00 35.18 4.02
3119 3632 2.358267 AGTATTACCTCCGACGCAGAAG 59.642 50.000 0.00 0.00 0.00 2.85
3120 3633 2.098607 CAGTATTACCTCCGACGCAGAA 59.901 50.000 0.00 0.00 0.00 3.02
3121 3634 1.674441 CAGTATTACCTCCGACGCAGA 59.326 52.381 0.00 0.00 0.00 4.26
3122 3635 1.674441 TCAGTATTACCTCCGACGCAG 59.326 52.381 0.00 0.00 0.00 5.18
3126 3639 5.177696 GCATTGAATCAGTATTACCTCCGAC 59.822 44.000 0.00 0.00 0.00 4.79
3128 3641 4.452455 GGCATTGAATCAGTATTACCTCCG 59.548 45.833 0.00 0.00 0.00 4.63
3140 3653 4.811969 AATCTTTGCAGGCATTGAATCA 57.188 36.364 0.00 0.00 0.00 2.57
3141 3654 4.933400 ACAAATCTTTGCAGGCATTGAATC 59.067 37.500 10.50 0.00 41.79 2.52
3149 3662 7.889589 ATAAACTAAACAAATCTTTGCAGGC 57.110 32.000 2.63 0.00 41.79 4.85
3150 3663 9.353999 GGTATAAACTAAACAAATCTTTGCAGG 57.646 33.333 2.63 0.00 41.79 4.85
3151 3664 9.906660 TGGTATAAACTAAACAAATCTTTGCAG 57.093 29.630 2.63 1.42 41.79 4.41
3183 3696 7.479980 TGTTCAAAGTTCTGAGTTTGTAATGG 58.520 34.615 11.88 0.00 43.54 3.16
3184 3697 8.909708 TTGTTCAAAGTTCTGAGTTTGTAATG 57.090 30.769 11.88 0.00 43.54 1.90
3225 3738 4.342665 AGTTTCTAATGGAACCCGCAAAAA 59.657 37.500 0.00 0.00 33.13 1.94
3226 3739 3.892588 AGTTTCTAATGGAACCCGCAAAA 59.107 39.130 0.00 0.00 33.13 2.44
3227 3740 3.492337 AGTTTCTAATGGAACCCGCAAA 58.508 40.909 0.00 0.00 33.13 3.68
3228 3741 3.078837 GAGTTTCTAATGGAACCCGCAA 58.921 45.455 0.00 0.00 33.13 4.85
3229 3742 2.039216 TGAGTTTCTAATGGAACCCGCA 59.961 45.455 0.00 0.00 33.13 5.69
3230 3743 2.678336 CTGAGTTTCTAATGGAACCCGC 59.322 50.000 0.00 0.00 33.13 6.13
3231 3744 4.202245 TCTGAGTTTCTAATGGAACCCG 57.798 45.455 0.00 0.00 33.13 5.28
3232 3745 5.561679 AGTTCTGAGTTTCTAATGGAACCC 58.438 41.667 0.00 0.00 34.13 4.11
3233 3746 7.228706 TCAAAGTTCTGAGTTTCTAATGGAACC 59.771 37.037 0.00 0.00 34.13 3.62
3234 3747 8.154649 TCAAAGTTCTGAGTTTCTAATGGAAC 57.845 34.615 0.00 0.00 33.13 3.62
3235 3748 8.621286 GTTCAAAGTTCTGAGTTTCTAATGGAA 58.379 33.333 0.00 0.00 0.00 3.53
3236 3749 7.773224 TGTTCAAAGTTCTGAGTTTCTAATGGA 59.227 33.333 0.00 0.00 0.00 3.41
3237 3750 7.930217 TGTTCAAAGTTCTGAGTTTCTAATGG 58.070 34.615 0.00 0.00 0.00 3.16
3238 3751 9.787532 TTTGTTCAAAGTTCTGAGTTTCTAATG 57.212 29.630 0.00 0.00 0.00 1.90
3274 3787 8.590204 TGGCTGATACGGTTTATTATGAATCTA 58.410 33.333 0.00 0.00 0.00 1.98
3286 3799 5.123344 GTGTTAGATTTGGCTGATACGGTTT 59.877 40.000 0.00 0.00 0.00 3.27
3287 3800 4.634443 GTGTTAGATTTGGCTGATACGGTT 59.366 41.667 0.00 0.00 0.00 4.44
3289 3802 4.442706 AGTGTTAGATTTGGCTGATACGG 58.557 43.478 0.00 0.00 0.00 4.02
3295 3808 3.119708 GCAGGAAGTGTTAGATTTGGCTG 60.120 47.826 0.00 0.00 0.00 4.85
3296 3809 3.084786 GCAGGAAGTGTTAGATTTGGCT 58.915 45.455 0.00 0.00 0.00 4.75
3297 3810 2.819608 TGCAGGAAGTGTTAGATTTGGC 59.180 45.455 0.00 0.00 0.00 4.52
3298 3811 5.047802 ACAATGCAGGAAGTGTTAGATTTGG 60.048 40.000 0.00 0.00 0.00 3.28
3299 3812 6.017400 ACAATGCAGGAAGTGTTAGATTTG 57.983 37.500 0.00 0.00 0.00 2.32
3301 3814 7.759489 TTAACAATGCAGGAAGTGTTAGATT 57.241 32.000 1.15 0.00 37.65 2.40
3302 3815 7.309194 GGTTTAACAATGCAGGAAGTGTTAGAT 60.309 37.037 1.15 0.00 37.65 1.98
3303 3816 6.016610 GGTTTAACAATGCAGGAAGTGTTAGA 60.017 38.462 1.15 0.00 37.65 2.10
3304 3817 6.149633 GGTTTAACAATGCAGGAAGTGTTAG 58.850 40.000 1.15 0.00 37.65 2.34
3305 3818 5.010213 GGGTTTAACAATGCAGGAAGTGTTA 59.990 40.000 0.00 0.00 35.82 2.41
3306 3819 4.202212 GGGTTTAACAATGCAGGAAGTGTT 60.202 41.667 0.00 0.00 37.86 3.32
3307 3820 3.320826 GGGTTTAACAATGCAGGAAGTGT 59.679 43.478 0.00 0.00 0.00 3.55
3354 3868 5.068067 GGACTAAACAAAGCACCTTAAACCA 59.932 40.000 0.00 0.00 0.00 3.67
3356 3870 6.139048 TGGACTAAACAAAGCACCTTAAAC 57.861 37.500 0.00 0.00 0.00 2.01
3359 3873 5.626142 TCATGGACTAAACAAAGCACCTTA 58.374 37.500 0.00 0.00 0.00 2.69
3362 3876 3.821033 ACTCATGGACTAAACAAAGCACC 59.179 43.478 0.00 0.00 0.00 5.01
3365 3879 3.503748 AGCACTCATGGACTAAACAAAGC 59.496 43.478 0.00 0.00 0.00 3.51
3369 3883 4.350368 TTGAGCACTCATGGACTAAACA 57.650 40.909 0.31 0.00 39.64 2.83
3374 3888 3.213206 TGTTTTGAGCACTCATGGACT 57.787 42.857 0.31 0.00 39.64 3.85
3425 3939 1.279496 CACAGACCAGGAAGATCCCA 58.721 55.000 0.00 0.00 37.19 4.37
3426 3940 0.543749 CCACAGACCAGGAAGATCCC 59.456 60.000 0.00 0.00 37.19 3.85
3443 3957 1.913951 ATCAGCCTGCGGAATCACCA 61.914 55.000 0.00 0.00 38.90 4.17
3452 3966 2.223805 TGTAGATACACATCAGCCTGCG 60.224 50.000 0.00 0.00 33.21 5.18
3454 3968 4.748600 CACATGTAGATACACATCAGCCTG 59.251 45.833 0.00 0.00 39.30 4.85
3458 3972 4.953667 AGGCACATGTAGATACACATCAG 58.046 43.478 0.00 0.00 39.30 2.90
3465 3979 9.855021 AATTAAAAACAAGGCACATGTAGATAC 57.145 29.630 0.00 0.00 40.34 2.24
3474 3988 6.876257 AGTGAAACAATTAAAAACAAGGCACA 59.124 30.769 0.00 0.00 41.43 4.57
3475 3989 7.064016 TGAGTGAAACAATTAAAAACAAGGCAC 59.936 33.333 0.00 0.00 41.43 5.01
3476 3990 7.099764 TGAGTGAAACAATTAAAAACAAGGCA 58.900 30.769 0.00 0.00 41.43 4.75
3477 3991 7.532682 TGAGTGAAACAATTAAAAACAAGGC 57.467 32.000 0.00 0.00 41.43 4.35
3500 4014 3.181507 CGCACCTGTCTTACCATGAAATG 60.182 47.826 0.00 0.00 46.21 2.32
3501 4015 3.009723 CGCACCTGTCTTACCATGAAAT 58.990 45.455 0.00 0.00 0.00 2.17
3502 4016 2.422597 CGCACCTGTCTTACCATGAAA 58.577 47.619 0.00 0.00 0.00 2.69
3503 4017 1.943968 GCGCACCTGTCTTACCATGAA 60.944 52.381 0.30 0.00 0.00 2.57
3504 4018 0.391130 GCGCACCTGTCTTACCATGA 60.391 55.000 0.30 0.00 0.00 3.07
3505 4019 0.673333 TGCGCACCTGTCTTACCATG 60.673 55.000 5.66 0.00 0.00 3.66
3506 4020 0.673644 GTGCGCACCTGTCTTACCAT 60.674 55.000 30.12 0.00 0.00 3.55
3507 4021 1.301401 GTGCGCACCTGTCTTACCA 60.301 57.895 30.12 0.00 0.00 3.25
3508 4022 3.562635 GTGCGCACCTGTCTTACC 58.437 61.111 30.12 0.00 0.00 2.85
3522 4036 2.668212 TAGTGCGCACCTTGGTGC 60.668 61.111 35.51 29.03 46.06 5.01
3523 4037 2.034879 CCTAGTGCGCACCTTGGTG 61.035 63.158 35.51 18.49 0.00 4.17
3524 4038 2.347490 CCTAGTGCGCACCTTGGT 59.653 61.111 35.51 20.03 0.00 3.67
3525 4039 3.127533 GCCTAGTGCGCACCTTGG 61.128 66.667 35.51 31.37 0.00 3.61
3526 4040 2.358615 TGCCTAGTGCGCACCTTG 60.359 61.111 35.51 23.96 45.60 3.61
3532 4046 0.721718 CAAACTAGTGCCTAGTGCGC 59.278 55.000 13.52 0.00 45.28 6.09
3533 4047 1.359848 CCAAACTAGTGCCTAGTGCG 58.640 55.000 13.52 8.91 45.28 5.34
3534 4048 1.003233 ACCCAAACTAGTGCCTAGTGC 59.997 52.381 13.52 0.00 45.28 4.40
3535 4049 3.514309 ACTACCCAAACTAGTGCCTAGTG 59.486 47.826 13.52 6.01 45.28 2.74
3537 4051 4.504858 CAACTACCCAAACTAGTGCCTAG 58.495 47.826 0.00 7.46 39.72 3.02
3538 4052 4.546829 CAACTACCCAAACTAGTGCCTA 57.453 45.455 0.00 0.00 0.00 3.93
3539 4053 3.418684 CAACTACCCAAACTAGTGCCT 57.581 47.619 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.