Multiple sequence alignment - TraesCS1B01G269200

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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 TraesCS1B01G269200 chr1B 100.000 3642 0 0 1 3642 473551686 473555327 0.000000e+00 6726.0
1 TraesCS1B01G269200 chr1D 94.019 2558 112 20 111 2663 350944654 350947175 0.000000e+00 3838.0
2 TraesCS1B01G269200 chr1D 93.840 487 14 4 3158 3642 350947745 350948217 0.000000e+00 719.0
3 TraesCS1B01G269200 chr1D 96.501 343 10 2 2661 3002 350947408 350947749 1.900000e-157 566.0
4 TraesCS1B01G269200 chr1D 76.216 370 67 12 339 692 409018992 409018628 3.740000e-40 176.0
5 TraesCS1B01G269200 chr1A 96.641 1965 56 9 1042 3002 451849875 451851833 0.000000e+00 3254.0
6 TraesCS1B01G269200 chr1A 90.467 493 20 6 3158 3642 451851829 451852302 3.090000e-175 625.0
7 TraesCS1B01G269200 chr5D 85.371 499 65 8 339 834 482288326 482288819 9.020000e-141 510.0
8 TraesCS1B01G269200 chr5D 93.562 233 13 2 107 339 215135087 215135317 2.690000e-91 346.0
9 TraesCS1B01G269200 chr5D 95.935 123 3 2 1 122 412437526 412437405 7.980000e-47 198.0
10 TraesCS1B01G269200 chr4B 83.366 511 61 12 339 834 417407479 417407980 5.550000e-123 451.0
11 TraesCS1B01G269200 chr4B 96.386 166 6 0 2999 3164 407061336 407061171 1.290000e-69 274.0
12 TraesCS1B01G269200 chr3D 82.677 508 69 9 339 834 16268225 16267725 2.010000e-117 433.0
13 TraesCS1B01G269200 chr3D 81.087 497 86 6 339 832 37967529 37968020 1.230000e-104 390.0
14 TraesCS1B01G269200 chr3D 95.322 171 8 0 2994 3164 181652446 181652616 4.630000e-69 272.0
15 TraesCS1B01G269200 chr3D 97.436 117 3 0 1 117 71787218 71787102 2.220000e-47 200.0
16 TraesCS1B01G269200 chr3D 87.209 86 10 1 2857 2942 247881573 247881657 2.990000e-16 97.1
17 TraesCS1B01G269200 chr3D 91.837 49 2 2 2857 2905 291230749 291230703 2.350000e-07 67.6
18 TraesCS1B01G269200 chr5B 87.755 343 33 8 1 339 567928474 567928811 3.410000e-105 392.0
19 TraesCS1B01G269200 chr7A 80.315 508 72 12 339 834 681732024 681732515 3.460000e-95 359.0
20 TraesCS1B01G269200 chr7A 83.607 366 43 8 339 692 207031090 207030730 9.750000e-86 327.0
21 TraesCS1B01G269200 chr7A 95.556 45 1 1 2856 2900 26030897 26030854 1.810000e-08 71.3
22 TraesCS1B01G269200 chr7A 93.333 45 2 1 2857 2901 634386524 634386481 8.440000e-07 65.8
23 TraesCS1B01G269200 chr3B 85.549 346 38 7 1 339 81919512 81919852 5.790000e-93 351.0
24 TraesCS1B01G269200 chr3B 98.148 162 3 0 3000 3161 444965495 444965656 2.140000e-72 283.0
25 TraesCS1B01G269200 chr5A 84.770 348 40 10 1 339 244878752 244879095 1.620000e-88 337.0
26 TraesCS1B01G269200 chr5A 85.714 84 9 3 2861 2943 279115739 279115820 6.480000e-13 86.1
27 TraesCS1B01G269200 chr2A 84.211 361 40 12 1 351 585012264 585012617 5.830000e-88 335.0
28 TraesCS1B01G269200 chr7D 92.340 235 14 4 107 340 462272391 462272160 7.540000e-87 331.0
29 TraesCS1B01G269200 chr7D 92.609 230 16 1 111 340 136024221 136023993 2.710000e-86 329.0
30 TraesCS1B01G269200 chr7D 99.115 113 1 0 1 113 518496515 518496627 1.710000e-48 204.0
31 TraesCS1B01G269200 chr4D 92.576 229 16 1 111 339 90314760 90314987 9.750000e-86 327.0
32 TraesCS1B01G269200 chr7B 97.531 162 4 0 3000 3161 677027611 677027450 9.960000e-71 278.0
33 TraesCS1B01G269200 chr6B 94.915 177 9 0 2989 3165 699977438 699977614 9.960000e-71 278.0
34 TraesCS1B01G269200 chr6B 95.294 170 8 0 2992 3161 591255378 591255547 1.670000e-68 270.0
35 TraesCS1B01G269200 chr6B 95.868 121 5 0 1 121 612368799 612368679 2.870000e-46 196.0
36 TraesCS1B01G269200 chr2B 96.364 165 6 0 2997 3161 237581407 237581571 4.630000e-69 272.0
37 TraesCS1B01G269200 chr2B 93.750 128 6 2 1 127 679108876 679108750 1.330000e-44 191.0
38 TraesCS1B01G269200 chr4A 95.808 167 7 0 2996 3162 696729855 696730021 1.670000e-68 270.0
39 TraesCS1B01G269200 chr4A 90.476 63 6 0 2865 2927 614099450 614099512 2.330000e-12 84.2
40 TraesCS1B01G269200 chr6D 95.294 170 7 1 2995 3164 15801275 15801107 5.990000e-68 268.0
41 TraesCS1B01G269200 chr2D 76.648 364 66 11 343 692 481450239 481449881 2.230000e-42 183.0
42 TraesCS1B01G269200 chr3A 87.209 86 10 1 2857 2942 256236276 256236360 2.990000e-16 97.1


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 TraesCS1B01G269200 chr1B 473551686 473555327 3641 False 6726.000000 6726 100.000000 1 3642 1 chr1B.!!$F1 3641
1 TraesCS1B01G269200 chr1D 350944654 350948217 3563 False 1707.666667 3838 94.786667 111 3642 3 chr1D.!!$F1 3531
2 TraesCS1B01G269200 chr1A 451849875 451852302 2427 False 1939.500000 3254 93.554000 1042 3642 2 chr1A.!!$F1 2600
3 TraesCS1B01G269200 chr4B 417407479 417407980 501 False 451.000000 451 83.366000 339 834 1 chr4B.!!$F1 495
4 TraesCS1B01G269200 chr3D 16267725 16268225 500 True 433.000000 433 82.677000 339 834 1 chr3D.!!$R1 495

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
79 80 0.038166 TTGGAGGCCCAACATGAGTC 59.962 55.0 0.0 0.0 46.94 3.36 F
1169 1188 0.539518 GTCTCTGCCTCTTCCCCTTC 59.460 60.0 0.0 0.0 0.00 3.46 F
1170 1189 0.618968 TCTCTGCCTCTTCCCCTTCC 60.619 60.0 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1191 1.219393 GAAGTGGCGGAGAGGGAAG 59.781 63.158 0.0 0.0 0.0 3.46 R
2106 2128 0.689623 CCTTCCTTCCTCAGCAGTGT 59.310 55.000 0.0 0.0 0.0 3.55 R
3146 3406 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.000 0.0 0.0 0.0 3.62 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.636454 TGATAAACCTTAGGTCATCCACTT 57.364 37.500 17.80 5.73 33.12 3.16
24 25 6.414732 TGATAAACCTTAGGTCATCCACTTG 58.585 40.000 17.80 0.00 33.12 3.16
25 26 4.993705 AAACCTTAGGTCATCCACTTGA 57.006 40.909 3.62 0.00 33.12 3.02
26 27 4.559862 AACCTTAGGTCATCCACTTGAG 57.440 45.455 3.62 0.00 33.12 3.02
27 28 3.791320 ACCTTAGGTCATCCACTTGAGA 58.209 45.455 0.00 0.00 35.89 3.27
28 29 3.772025 ACCTTAGGTCATCCACTTGAGAG 59.228 47.826 0.00 0.00 35.89 3.20
29 30 4.026744 CCTTAGGTCATCCACTTGAGAGA 58.973 47.826 0.00 0.00 35.89 3.10
30 31 4.467795 CCTTAGGTCATCCACTTGAGAGAA 59.532 45.833 0.00 0.00 35.89 2.87
31 32 5.046304 CCTTAGGTCATCCACTTGAGAGAAA 60.046 44.000 0.00 0.00 35.89 2.52
32 33 4.982241 AGGTCATCCACTTGAGAGAAAA 57.018 40.909 0.00 0.00 35.89 2.29
33 34 5.511386 AGGTCATCCACTTGAGAGAAAAT 57.489 39.130 0.00 0.00 35.89 1.82
34 35 5.885465 AGGTCATCCACTTGAGAGAAAATT 58.115 37.500 0.00 0.00 35.89 1.82
35 36 5.709164 AGGTCATCCACTTGAGAGAAAATTG 59.291 40.000 0.00 0.00 35.89 2.32
36 37 5.397326 GTCATCCACTTGAGAGAAAATTGC 58.603 41.667 0.00 0.00 0.00 3.56
37 38 5.182760 GTCATCCACTTGAGAGAAAATTGCT 59.817 40.000 0.00 0.00 0.00 3.91
38 39 6.372659 GTCATCCACTTGAGAGAAAATTGCTA 59.627 38.462 0.00 0.00 0.00 3.49
39 40 6.372659 TCATCCACTTGAGAGAAAATTGCTAC 59.627 38.462 0.00 0.00 0.00 3.58
40 41 5.869579 TCCACTTGAGAGAAAATTGCTACT 58.130 37.500 0.00 0.00 0.00 2.57
41 42 5.702670 TCCACTTGAGAGAAAATTGCTACTG 59.297 40.000 0.00 0.00 0.00 2.74
42 43 5.471456 CCACTTGAGAGAAAATTGCTACTGT 59.529 40.000 0.00 0.00 0.00 3.55
43 44 6.348050 CCACTTGAGAGAAAATTGCTACTGTC 60.348 42.308 0.00 0.00 0.00 3.51
44 45 5.703130 ACTTGAGAGAAAATTGCTACTGTCC 59.297 40.000 0.00 0.00 0.00 4.02
45 46 5.489792 TGAGAGAAAATTGCTACTGTCCT 57.510 39.130 0.00 0.00 0.00 3.85
46 47 6.605471 TGAGAGAAAATTGCTACTGTCCTA 57.395 37.500 0.00 0.00 0.00 2.94
47 48 6.398918 TGAGAGAAAATTGCTACTGTCCTAC 58.601 40.000 0.00 0.00 0.00 3.18
48 49 6.014584 TGAGAGAAAATTGCTACTGTCCTACA 60.015 38.462 0.00 0.00 0.00 2.74
49 50 6.769512 AGAGAAAATTGCTACTGTCCTACAA 58.230 36.000 0.00 0.00 0.00 2.41
50 51 7.224297 AGAGAAAATTGCTACTGTCCTACAAA 58.776 34.615 0.00 0.00 0.00 2.83
51 52 7.719633 AGAGAAAATTGCTACTGTCCTACAAAA 59.280 33.333 0.00 0.00 0.00 2.44
52 53 7.649057 AGAAAATTGCTACTGTCCTACAAAAC 58.351 34.615 0.00 0.00 0.00 2.43
53 54 7.502561 AGAAAATTGCTACTGTCCTACAAAACT 59.497 33.333 0.00 0.00 0.00 2.66
54 55 6.803154 AATTGCTACTGTCCTACAAAACTC 57.197 37.500 0.00 0.00 0.00 3.01
55 56 5.546621 TTGCTACTGTCCTACAAAACTCT 57.453 39.130 0.00 0.00 0.00 3.24
56 57 4.883083 TGCTACTGTCCTACAAAACTCTG 58.117 43.478 0.00 0.00 0.00 3.35
57 58 3.680458 GCTACTGTCCTACAAAACTCTGC 59.320 47.826 0.00 0.00 0.00 4.26
58 59 2.755650 ACTGTCCTACAAAACTCTGCG 58.244 47.619 0.00 0.00 0.00 5.18
59 60 1.461127 CTGTCCTACAAAACTCTGCGC 59.539 52.381 0.00 0.00 0.00 6.09
60 61 1.070134 TGTCCTACAAAACTCTGCGCT 59.930 47.619 9.73 0.00 0.00 5.92
61 62 2.143925 GTCCTACAAAACTCTGCGCTT 58.856 47.619 9.73 0.00 0.00 4.68
62 63 2.096218 GTCCTACAAAACTCTGCGCTTG 60.096 50.000 9.73 6.07 0.00 4.01
63 64 1.197721 CCTACAAAACTCTGCGCTTGG 59.802 52.381 9.73 0.20 0.00 3.61
64 65 2.143122 CTACAAAACTCTGCGCTTGGA 58.857 47.619 9.73 0.00 0.00 3.53
65 66 0.947244 ACAAAACTCTGCGCTTGGAG 59.053 50.000 9.73 15.60 35.86 3.86
66 67 0.239347 CAAAACTCTGCGCTTGGAGG 59.761 55.000 22.09 10.10 34.22 4.30
67 68 1.518903 AAAACTCTGCGCTTGGAGGC 61.519 55.000 22.09 0.00 34.22 4.70
68 69 3.909086 AACTCTGCGCTTGGAGGCC 62.909 63.158 22.09 0.00 34.22 5.19
74 75 2.361610 CGCTTGGAGGCCCAACAT 60.362 61.111 0.00 0.00 46.94 2.71
75 76 2.703798 CGCTTGGAGGCCCAACATG 61.704 63.158 0.00 0.00 46.94 3.21
76 77 1.304381 GCTTGGAGGCCCAACATGA 60.304 57.895 0.00 0.00 46.94 3.07
77 78 1.318158 GCTTGGAGGCCCAACATGAG 61.318 60.000 0.00 0.00 46.94 2.90
78 79 0.038744 CTTGGAGGCCCAACATGAGT 59.961 55.000 0.00 0.00 46.94 3.41
79 80 0.038166 TTGGAGGCCCAACATGAGTC 59.962 55.000 0.00 0.00 46.94 3.36
80 81 0.842030 TGGAGGCCCAACATGAGTCT 60.842 55.000 0.00 0.00 40.09 3.24
81 82 1.204146 GGAGGCCCAACATGAGTCTA 58.796 55.000 0.00 0.00 0.00 2.59
82 83 1.134371 GGAGGCCCAACATGAGTCTAC 60.134 57.143 0.00 0.00 0.00 2.59
83 84 1.555075 GAGGCCCAACATGAGTCTACA 59.445 52.381 0.00 0.00 0.00 2.74
84 85 1.985159 AGGCCCAACATGAGTCTACAA 59.015 47.619 0.00 0.00 0.00 2.41
85 86 2.026822 AGGCCCAACATGAGTCTACAAG 60.027 50.000 0.00 0.00 0.00 3.16
86 87 2.027192 GGCCCAACATGAGTCTACAAGA 60.027 50.000 0.00 0.00 0.00 3.02
87 88 3.559171 GGCCCAACATGAGTCTACAAGAA 60.559 47.826 0.00 0.00 0.00 2.52
88 89 4.265073 GCCCAACATGAGTCTACAAGAAT 58.735 43.478 0.00 0.00 0.00 2.40
89 90 5.428253 GCCCAACATGAGTCTACAAGAATA 58.572 41.667 0.00 0.00 0.00 1.75
90 91 5.880332 GCCCAACATGAGTCTACAAGAATAA 59.120 40.000 0.00 0.00 0.00 1.40
91 92 6.374333 GCCCAACATGAGTCTACAAGAATAAA 59.626 38.462 0.00 0.00 0.00 1.40
92 93 7.414540 GCCCAACATGAGTCTACAAGAATAAAG 60.415 40.741 0.00 0.00 0.00 1.85
93 94 7.607991 CCCAACATGAGTCTACAAGAATAAAGT 59.392 37.037 0.00 0.00 0.00 2.66
94 95 9.003658 CCAACATGAGTCTACAAGAATAAAGTT 57.996 33.333 0.00 0.00 0.00 2.66
95 96 9.817365 CAACATGAGTCTACAAGAATAAAGTTG 57.183 33.333 0.00 0.00 0.00 3.16
96 97 8.034058 ACATGAGTCTACAAGAATAAAGTTGC 57.966 34.615 0.00 0.00 0.00 4.17
97 98 6.706055 TGAGTCTACAAGAATAAAGTTGCG 57.294 37.500 0.00 0.00 0.00 4.85
98 99 6.220930 TGAGTCTACAAGAATAAAGTTGCGT 58.779 36.000 0.00 0.00 0.00 5.24
99 100 7.372714 TGAGTCTACAAGAATAAAGTTGCGTA 58.627 34.615 0.00 0.00 0.00 4.42
100 101 7.541091 TGAGTCTACAAGAATAAAGTTGCGTAG 59.459 37.037 0.00 0.00 0.00 3.51
101 102 7.376615 AGTCTACAAGAATAAAGTTGCGTAGT 58.623 34.615 0.00 0.00 0.00 2.73
102 103 8.517878 AGTCTACAAGAATAAAGTTGCGTAGTA 58.482 33.333 0.00 0.00 0.00 1.82
103 104 8.796278 GTCTACAAGAATAAAGTTGCGTAGTAG 58.204 37.037 0.00 0.00 0.00 2.57
104 105 8.733458 TCTACAAGAATAAAGTTGCGTAGTAGA 58.267 33.333 0.00 0.00 33.00 2.59
105 106 7.578169 ACAAGAATAAAGTTGCGTAGTAGAC 57.422 36.000 0.00 0.00 0.00 2.59
106 107 7.149973 ACAAGAATAAAGTTGCGTAGTAGACA 58.850 34.615 0.00 0.00 0.00 3.41
107 108 7.817962 ACAAGAATAAAGTTGCGTAGTAGACAT 59.182 33.333 0.00 0.00 0.00 3.06
108 109 7.988904 AGAATAAAGTTGCGTAGTAGACATC 57.011 36.000 0.00 0.00 0.00 3.06
109 110 7.544622 AGAATAAAGTTGCGTAGTAGACATCA 58.455 34.615 0.00 0.00 0.00 3.07
155 156 5.394553 GGCTTCCTTGCTGCACTTTATTTAT 60.395 40.000 0.00 0.00 0.00 1.40
173 174 9.638239 TTTATTTATCGTTACCGTTACTTGTCT 57.362 29.630 0.00 0.00 35.01 3.41
174 175 6.932901 TTTATCGTTACCGTTACTTGTCTG 57.067 37.500 0.00 0.00 35.01 3.51
175 176 3.988379 TCGTTACCGTTACTTGTCTGT 57.012 42.857 0.00 0.00 35.01 3.41
214 215 6.460781 TCATGAAACTACTTGTTACCGACAT 58.539 36.000 0.00 0.00 38.26 3.06
223 224 3.889196 TGTTACCGACATTTTCAGTGC 57.111 42.857 0.00 0.00 32.00 4.40
236 237 6.421801 ACATTTTCAGTGCTTGCAGAAATTAC 59.578 34.615 9.67 0.00 30.92 1.89
250 251 5.738783 GCAGAAATTACCTTGCTGAAAACCA 60.739 40.000 0.00 0.00 0.00 3.67
251 252 6.458210 CAGAAATTACCTTGCTGAAAACCAT 58.542 36.000 0.00 0.00 0.00 3.55
307 308 6.636044 CGACACTATTACTTATCGAAAGGACC 59.364 42.308 10.65 0.00 0.00 4.46
357 358 2.343758 CTCACACCACCCTGACCG 59.656 66.667 0.00 0.00 0.00 4.79
495 498 2.184167 CCAAAACAGACCACCGCGT 61.184 57.895 4.92 0.00 0.00 6.01
584 597 0.847373 TGTTGGGTCTGGTTTGCCTA 59.153 50.000 0.00 0.00 35.27 3.93
684 697 3.650950 AACCTCAGCCGGCACCAT 61.651 61.111 31.54 4.11 0.00 3.55
686 699 4.100084 CCTCAGCCGGCACCATCA 62.100 66.667 31.54 3.89 0.00 3.07
715 728 3.771160 ACCATCCAGACGCCGTCC 61.771 66.667 14.60 0.00 32.18 4.79
716 729 3.770040 CCATCCAGACGCCGTCCA 61.770 66.667 14.60 0.00 32.18 4.02
732 745 2.357517 CAGCGGCGAGAAACTGGT 60.358 61.111 12.98 0.00 0.00 4.00
771 784 2.933287 ATCGGGCCCAACCACTGA 60.933 61.111 24.92 9.43 42.05 3.41
787 800 0.614415 CTGAGAGTCCCTCACAGCCT 60.614 60.000 5.89 0.00 46.38 4.58
842 855 3.090532 GACCTCCTGCCCCCGATT 61.091 66.667 0.00 0.00 0.00 3.34
850 863 1.550976 CCTGCCCCCGATTCTAGATAC 59.449 57.143 0.00 0.00 0.00 2.24
855 868 3.015327 CCCCCGATTCTAGATACCTACG 58.985 54.545 0.00 0.00 0.00 3.51
859 872 5.526846 CCCCGATTCTAGATACCTACGATAC 59.473 48.000 0.00 0.00 0.00 2.24
867 880 7.482474 TCTAGATACCTACGATACGAGAGATG 58.518 42.308 0.00 0.00 0.00 2.90
911 924 3.066291 TCACAGGACAATTGCGGTATT 57.934 42.857 5.05 0.00 0.00 1.89
918 931 6.377146 ACAGGACAATTGCGGTATTTAAGATT 59.623 34.615 5.05 0.00 0.00 2.40
920 933 5.977129 GGACAATTGCGGTATTTAAGATTGG 59.023 40.000 5.05 0.00 0.00 3.16
933 946 6.859420 TTTAAGATTGGCTTTTCTTTTGGC 57.141 33.333 3.24 0.00 38.05 4.52
942 955 4.873259 GGCTTTTCTTTTGGCTGTAAAACA 59.127 37.500 0.00 0.00 0.00 2.83
973 986 4.017808 GCGGGATGTGGTAGAGTATAGAT 58.982 47.826 0.00 0.00 0.00 1.98
977 990 5.020132 GGATGTGGTAGAGTATAGATGGCT 58.980 45.833 0.00 0.00 0.00 4.75
978 991 6.188407 GGATGTGGTAGAGTATAGATGGCTA 58.812 44.000 0.00 0.00 0.00 3.93
1000 1013 6.381707 GCTATTTATAAACCCCAAAACCTCCA 59.618 38.462 0.00 0.00 0.00 3.86
1028 1041 5.147032 ACCACCATCCAAAAAGAAATCTCA 58.853 37.500 0.00 0.00 0.00 3.27
1029 1042 5.602145 ACCACCATCCAAAAAGAAATCTCAA 59.398 36.000 0.00 0.00 0.00 3.02
1030 1043 6.270695 ACCACCATCCAAAAAGAAATCTCAAT 59.729 34.615 0.00 0.00 0.00 2.57
1031 1044 6.815142 CCACCATCCAAAAAGAAATCTCAATC 59.185 38.462 0.00 0.00 0.00 2.67
1032 1045 6.815142 CACCATCCAAAAAGAAATCTCAATCC 59.185 38.462 0.00 0.00 0.00 3.01
1033 1046 6.727697 ACCATCCAAAAAGAAATCTCAATCCT 59.272 34.615 0.00 0.00 0.00 3.24
1034 1047 7.093596 ACCATCCAAAAAGAAATCTCAATCCTC 60.094 37.037 0.00 0.00 0.00 3.71
1035 1048 7.093640 CCATCCAAAAAGAAATCTCAATCCTCA 60.094 37.037 0.00 0.00 0.00 3.86
1036 1049 7.838079 TCCAAAAAGAAATCTCAATCCTCAA 57.162 32.000 0.00 0.00 0.00 3.02
1037 1050 8.248904 TCCAAAAAGAAATCTCAATCCTCAAA 57.751 30.769 0.00 0.00 0.00 2.69
1038 1051 8.703743 TCCAAAAAGAAATCTCAATCCTCAAAA 58.296 29.630 0.00 0.00 0.00 2.44
1039 1052 9.328845 CCAAAAAGAAATCTCAATCCTCAAAAA 57.671 29.630 0.00 0.00 0.00 1.94
1087 1100 2.368311 AAGAAAAACCCTAACCGGCA 57.632 45.000 0.00 0.00 0.00 5.69
1167 1186 1.684049 CGTCTCTGCCTCTTCCCCT 60.684 63.158 0.00 0.00 0.00 4.79
1168 1187 1.261238 CGTCTCTGCCTCTTCCCCTT 61.261 60.000 0.00 0.00 0.00 3.95
1169 1188 0.539518 GTCTCTGCCTCTTCCCCTTC 59.460 60.000 0.00 0.00 0.00 3.46
1170 1189 0.618968 TCTCTGCCTCTTCCCCTTCC 60.619 60.000 0.00 0.00 0.00 3.46
1171 1190 1.616628 TCTGCCTCTTCCCCTTCCC 60.617 63.158 0.00 0.00 0.00 3.97
1172 1191 2.614013 TGCCTCTTCCCCTTCCCC 60.614 66.667 0.00 0.00 0.00 4.81
1262 1284 1.275573 GACCCCACTGTGTTCTACCTC 59.724 57.143 7.08 0.00 0.00 3.85
1547 1569 4.388499 CCCGTTGTCCTCCACCGG 62.388 72.222 0.00 0.00 38.39 5.28
1795 1817 2.278857 CTTGGCCGAGATCGTCCG 60.279 66.667 15.76 0.00 40.77 4.79
2049 2071 0.758734 CCTGGAAGATATCGTGGCCA 59.241 55.000 0.00 0.00 34.07 5.36
2106 2128 4.314440 GGAGGTGTGCGGTGCTCA 62.314 66.667 0.00 0.00 0.00 4.26
2279 2301 0.550914 AGGGCTTCAGTGTGTTGGAA 59.449 50.000 0.00 0.00 0.00 3.53
2330 2352 1.140652 TGATGTCATCGGCCTATGCAA 59.859 47.619 12.38 3.52 40.13 4.08
2643 2665 3.770263 ATGAACAGTCATTTGGATGCG 57.230 42.857 0.00 0.00 42.03 4.73
2657 2679 0.463654 GATGCGGTGAGGCCATAACA 60.464 55.000 5.01 0.00 36.97 2.41
2670 2927 8.736244 GTGAGGCCATAACATTTTACTCTTTTA 58.264 33.333 5.01 0.00 0.00 1.52
2699 2956 6.330004 TGACATATTTGCACAACACTCATT 57.670 33.333 0.00 0.00 0.00 2.57
2716 2973 5.632347 CACTCATTGAAATCTTGTTCTTGCC 59.368 40.000 0.00 0.00 0.00 4.52
2724 2981 1.133823 TCTTGTTCTTGCCTGGCTGAA 60.134 47.619 21.03 19.57 0.00 3.02
2741 2998 3.686726 GCTGAATTTGATCTCGAGTGGTT 59.313 43.478 13.13 0.51 0.00 3.67
2771 3028 9.451963 GTGGAACATGAGGATGAAATCAAAGGG 62.452 44.444 0.00 0.00 44.43 3.95
2997 3257 6.308015 AGTTGGTATCCAGCAAATAGTGTA 57.692 37.500 5.53 0.00 43.39 2.90
2998 3258 6.349300 AGTTGGTATCCAGCAAATAGTGTAG 58.651 40.000 5.53 0.00 43.39 2.74
2999 3259 5.950544 TGGTATCCAGCAAATAGTGTAGT 57.049 39.130 0.00 0.00 0.00 2.73
3000 3260 7.125204 AGTTGGTATCCAGCAAATAGTGTAGTA 59.875 37.037 5.53 0.00 43.39 1.82
3001 3261 6.812998 TGGTATCCAGCAAATAGTGTAGTAC 58.187 40.000 0.00 0.00 0.00 2.73
3002 3262 6.610020 TGGTATCCAGCAAATAGTGTAGTACT 59.390 38.462 0.00 0.00 43.56 2.73
3003 3263 7.146648 GGTATCCAGCAAATAGTGTAGTACTC 58.853 42.308 0.00 0.00 40.89 2.59
3004 3264 5.593679 TCCAGCAAATAGTGTAGTACTCC 57.406 43.478 0.00 0.00 40.89 3.85
3005 3265 4.404715 TCCAGCAAATAGTGTAGTACTCCC 59.595 45.833 0.00 0.00 40.89 4.30
3006 3266 4.406003 CCAGCAAATAGTGTAGTACTCCCT 59.594 45.833 0.00 0.00 40.89 4.20
3007 3267 5.452077 CCAGCAAATAGTGTAGTACTCCCTC 60.452 48.000 0.00 0.00 40.89 4.30
3008 3268 4.650131 AGCAAATAGTGTAGTACTCCCTCC 59.350 45.833 0.00 0.00 40.89 4.30
3009 3269 4.499357 GCAAATAGTGTAGTACTCCCTCCG 60.499 50.000 0.00 0.00 40.89 4.63
3010 3270 4.516652 AATAGTGTAGTACTCCCTCCGT 57.483 45.455 0.00 0.00 40.89 4.69
3011 3271 2.895242 AGTGTAGTACTCCCTCCGTT 57.105 50.000 0.00 0.00 33.17 4.44
3012 3272 2.720915 AGTGTAGTACTCCCTCCGTTC 58.279 52.381 0.00 0.00 33.17 3.95
3013 3273 1.747924 GTGTAGTACTCCCTCCGTTCC 59.252 57.143 0.00 0.00 0.00 3.62
3014 3274 1.637553 TGTAGTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
3015 3275 2.846206 TGTAGTACTCCCTCCGTTCCTA 59.154 50.000 0.00 0.00 0.00 2.94
3016 3276 3.266772 TGTAGTACTCCCTCCGTTCCTAA 59.733 47.826 0.00 0.00 0.00 2.69
3017 3277 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3018 3278 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3019 3279 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3020 3280 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3021 3281 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
3022 3282 6.947158 AGTACTCCCTCCGTTCCTAAATATAG 59.053 42.308 0.00 0.00 0.00 1.31
3038 3298 9.936759 CCTAAATATAGGTCTTTGGAGAGATTC 57.063 37.037 0.00 0.00 43.32 2.52
3039 3299 9.936759 CTAAATATAGGTCTTTGGAGAGATTCC 57.063 37.037 0.00 0.00 46.98 3.01
3051 3311 4.698575 GGAGAGATTCCACTATGAACCAC 58.301 47.826 0.00 0.00 46.01 4.16
3052 3312 4.162320 GGAGAGATTCCACTATGAACCACA 59.838 45.833 0.00 0.00 46.01 4.17
3053 3313 5.163258 GGAGAGATTCCACTATGAACCACAT 60.163 44.000 0.00 0.00 46.01 3.21
3054 3314 6.042093 GGAGAGATTCCACTATGAACCACATA 59.958 42.308 0.00 0.00 46.01 2.29
3055 3315 6.821388 AGAGATTCCACTATGAACCACATAC 58.179 40.000 0.00 0.00 40.07 2.39
3056 3316 5.601662 AGATTCCACTATGAACCACATACG 58.398 41.667 0.00 0.00 40.07 3.06
3057 3317 3.812156 TCCACTATGAACCACATACGG 57.188 47.619 0.00 0.00 40.07 4.02
3058 3318 3.367321 TCCACTATGAACCACATACGGA 58.633 45.455 0.00 0.00 40.07 4.69
3059 3319 3.964688 TCCACTATGAACCACATACGGAT 59.035 43.478 0.00 0.00 40.07 4.18
3060 3320 4.058124 CCACTATGAACCACATACGGATG 58.942 47.826 5.94 5.94 40.07 3.51
3062 3322 5.221362 CCACTATGAACCACATACGGATGTA 60.221 44.000 14.23 0.00 44.82 2.29
3063 3323 6.455647 CACTATGAACCACATACGGATGTAT 58.544 40.000 14.23 5.54 44.82 2.29
3077 3337 6.304356 ACGGATGTATGTAGATGCATTTTG 57.696 37.500 0.00 1.79 35.26 2.44
3078 3338 5.239306 ACGGATGTATGTAGATGCATTTTGG 59.761 40.000 0.00 0.00 35.26 3.28
3079 3339 5.469760 CGGATGTATGTAGATGCATTTTGGA 59.530 40.000 0.00 0.00 35.26 3.53
3080 3340 6.347969 CGGATGTATGTAGATGCATTTTGGAG 60.348 42.308 0.00 0.00 35.26 3.86
3081 3341 6.488006 GGATGTATGTAGATGCATTTTGGAGT 59.512 38.462 0.00 0.00 35.26 3.85
3082 3342 6.682423 TGTATGTAGATGCATTTTGGAGTG 57.318 37.500 0.00 0.00 0.00 3.51
3083 3343 6.179756 TGTATGTAGATGCATTTTGGAGTGT 58.820 36.000 0.00 0.00 0.00 3.55
3084 3344 7.334858 TGTATGTAGATGCATTTTGGAGTGTA 58.665 34.615 0.00 0.00 0.00 2.90
3085 3345 6.932356 ATGTAGATGCATTTTGGAGTGTAG 57.068 37.500 0.00 0.00 0.00 2.74
3086 3346 6.048732 TGTAGATGCATTTTGGAGTGTAGA 57.951 37.500 0.00 0.00 0.00 2.59
3087 3347 6.653020 TGTAGATGCATTTTGGAGTGTAGAT 58.347 36.000 0.00 0.00 0.00 1.98
3088 3348 7.112122 TGTAGATGCATTTTGGAGTGTAGATT 58.888 34.615 0.00 0.00 0.00 2.40
3089 3349 6.690194 AGATGCATTTTGGAGTGTAGATTC 57.310 37.500 0.00 0.00 0.00 2.52
3090 3350 6.182627 AGATGCATTTTGGAGTGTAGATTCA 58.817 36.000 0.00 0.00 0.00 2.57
3091 3351 5.627499 TGCATTTTGGAGTGTAGATTCAC 57.373 39.130 0.00 0.00 38.46 3.18
3103 3363 7.602517 AGTGTAGATTCACTCATTTTGCTAC 57.397 36.000 0.00 0.00 44.07 3.58
3104 3364 6.311445 AGTGTAGATTCACTCATTTTGCTACG 59.689 38.462 0.00 0.00 44.07 3.51
3105 3365 6.090898 GTGTAGATTCACTCATTTTGCTACGT 59.909 38.462 0.00 0.00 35.68 3.57
3106 3366 7.274904 GTGTAGATTCACTCATTTTGCTACGTA 59.725 37.037 0.00 0.00 35.68 3.57
3107 3367 7.979537 TGTAGATTCACTCATTTTGCTACGTAT 59.020 33.333 0.00 0.00 31.97 3.06
3108 3368 7.239166 AGATTCACTCATTTTGCTACGTATG 57.761 36.000 0.00 0.00 0.00 2.39
3109 3369 6.818644 AGATTCACTCATTTTGCTACGTATGT 59.181 34.615 0.00 0.00 0.00 2.29
3110 3370 7.979537 AGATTCACTCATTTTGCTACGTATGTA 59.020 33.333 0.00 0.00 0.00 2.29
3128 3388 9.352191 ACGTATGTAGTCCATAGTAAAATCTCT 57.648 33.333 0.00 0.00 36.71 3.10
3154 3414 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3155 3415 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
3156 3416 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3166 3426 1.553704 GGAACGGAGGGAGTACATGTT 59.446 52.381 2.30 0.00 0.00 2.71
3219 3479 3.132111 AGCAATTTTGTTTCTTGACCGGT 59.868 39.130 6.92 6.92 0.00 5.28
3378 3644 5.480073 TGCACTAAACTGGAATTTGCCTTAT 59.520 36.000 0.00 0.00 0.00 1.73
3379 3645 6.014669 TGCACTAAACTGGAATTTGCCTTATT 60.015 34.615 0.00 0.00 0.00 1.40
3380 3646 7.177568 TGCACTAAACTGGAATTTGCCTTATTA 59.822 33.333 0.00 0.00 0.00 0.98
3381 3647 8.032451 GCACTAAACTGGAATTTGCCTTATTAA 58.968 33.333 0.00 0.00 0.00 1.40
3384 3650 7.848223 AAACTGGAATTTGCCTTATTAATGC 57.152 32.000 0.00 0.00 0.00 3.56
3385 3651 5.917462 ACTGGAATTTGCCTTATTAATGCC 58.083 37.500 0.00 0.00 0.00 4.40
3386 3652 5.662657 ACTGGAATTTGCCTTATTAATGCCT 59.337 36.000 0.00 0.00 29.69 4.75
3387 3653 6.156775 ACTGGAATTTGCCTTATTAATGCCTT 59.843 34.615 0.00 0.00 29.69 4.35
3388 3654 7.344352 ACTGGAATTTGCCTTATTAATGCCTTA 59.656 33.333 0.00 0.00 29.69 2.69
3561 3827 0.675083 TTAGTGCGGTGGAGAAACGA 59.325 50.000 0.00 0.00 0.00 3.85
3604 3870 3.146828 AAACCTCCACCACCTGGGC 62.147 63.158 0.00 0.00 41.06 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.214615 TCAAGTGGATGACCTAAGGTTTATCA 59.785 38.462 0.00 0.00 35.25 2.15
1 2 6.650120 TCAAGTGGATGACCTAAGGTTTATC 58.350 40.000 0.00 0.00 35.25 1.75
3 4 5.783360 TCTCAAGTGGATGACCTAAGGTTTA 59.217 40.000 0.00 0.00 35.25 2.01
4 5 4.597507 TCTCAAGTGGATGACCTAAGGTTT 59.402 41.667 0.00 0.00 35.25 3.27
7 8 4.026744 TCTCTCAAGTGGATGACCTAAGG 58.973 47.826 0.00 0.00 37.04 2.69
8 9 5.667539 TTCTCTCAAGTGGATGACCTAAG 57.332 43.478 0.00 0.00 37.04 2.18
11 12 4.982241 TTTTCTCTCAAGTGGATGACCT 57.018 40.909 0.00 0.00 37.04 3.85
12 13 5.620879 GCAATTTTCTCTCAAGTGGATGACC 60.621 44.000 0.00 0.00 0.00 4.02
13 14 5.182760 AGCAATTTTCTCTCAAGTGGATGAC 59.817 40.000 0.00 0.00 0.00 3.06
14 15 5.319453 AGCAATTTTCTCTCAAGTGGATGA 58.681 37.500 0.00 0.00 0.00 2.92
15 16 5.640189 AGCAATTTTCTCTCAAGTGGATG 57.360 39.130 0.00 0.00 0.00 3.51
16 17 6.373774 CAGTAGCAATTTTCTCTCAAGTGGAT 59.626 38.462 0.00 0.00 0.00 3.41
17 18 5.702670 CAGTAGCAATTTTCTCTCAAGTGGA 59.297 40.000 0.00 0.00 0.00 4.02
18 19 5.471456 ACAGTAGCAATTTTCTCTCAAGTGG 59.529 40.000 0.00 0.00 0.00 4.00
19 20 6.348050 GGACAGTAGCAATTTTCTCTCAAGTG 60.348 42.308 0.00 0.00 0.00 3.16
20 21 5.703130 GGACAGTAGCAATTTTCTCTCAAGT 59.297 40.000 0.00 0.00 0.00 3.16
21 22 5.936956 AGGACAGTAGCAATTTTCTCTCAAG 59.063 40.000 0.00 0.00 0.00 3.02
22 23 5.869579 AGGACAGTAGCAATTTTCTCTCAA 58.130 37.500 0.00 0.00 0.00 3.02
23 24 5.489792 AGGACAGTAGCAATTTTCTCTCA 57.510 39.130 0.00 0.00 0.00 3.27
24 25 6.398918 TGTAGGACAGTAGCAATTTTCTCTC 58.601 40.000 0.00 0.00 0.00 3.20
25 26 6.360370 TGTAGGACAGTAGCAATTTTCTCT 57.640 37.500 0.00 0.00 0.00 3.10
26 27 7.435068 TTTGTAGGACAGTAGCAATTTTCTC 57.565 36.000 0.00 0.00 0.00 2.87
27 28 7.502561 AGTTTTGTAGGACAGTAGCAATTTTCT 59.497 33.333 0.00 0.00 0.00 2.52
28 29 7.649057 AGTTTTGTAGGACAGTAGCAATTTTC 58.351 34.615 0.00 0.00 0.00 2.29
29 30 7.502561 AGAGTTTTGTAGGACAGTAGCAATTTT 59.497 33.333 0.00 0.00 0.00 1.82
30 31 6.998673 AGAGTTTTGTAGGACAGTAGCAATTT 59.001 34.615 0.00 0.00 0.00 1.82
31 32 6.428159 CAGAGTTTTGTAGGACAGTAGCAATT 59.572 38.462 0.00 0.00 0.00 2.32
32 33 5.934625 CAGAGTTTTGTAGGACAGTAGCAAT 59.065 40.000 0.00 0.00 0.00 3.56
33 34 5.297547 CAGAGTTTTGTAGGACAGTAGCAA 58.702 41.667 0.00 0.00 0.00 3.91
34 35 4.799586 GCAGAGTTTTGTAGGACAGTAGCA 60.800 45.833 0.00 0.00 0.00 3.49
35 36 3.680458 GCAGAGTTTTGTAGGACAGTAGC 59.320 47.826 0.00 0.00 0.00 3.58
36 37 3.921021 CGCAGAGTTTTGTAGGACAGTAG 59.079 47.826 0.00 0.00 0.00 2.57
37 38 3.859627 GCGCAGAGTTTTGTAGGACAGTA 60.860 47.826 0.30 0.00 0.00 2.74
38 39 2.755650 CGCAGAGTTTTGTAGGACAGT 58.244 47.619 0.00 0.00 0.00 3.55
39 40 1.461127 GCGCAGAGTTTTGTAGGACAG 59.539 52.381 0.30 0.00 0.00 3.51
40 41 1.070134 AGCGCAGAGTTTTGTAGGACA 59.930 47.619 11.47 0.00 0.00 4.02
41 42 1.797025 AGCGCAGAGTTTTGTAGGAC 58.203 50.000 11.47 0.00 0.00 3.85
42 43 2.143122 CAAGCGCAGAGTTTTGTAGGA 58.857 47.619 11.47 0.00 0.00 2.94
43 44 1.197721 CCAAGCGCAGAGTTTTGTAGG 59.802 52.381 11.47 0.00 0.00 3.18
44 45 2.143122 TCCAAGCGCAGAGTTTTGTAG 58.857 47.619 11.47 0.00 0.00 2.74
45 46 2.143122 CTCCAAGCGCAGAGTTTTGTA 58.857 47.619 11.47 0.00 0.00 2.41
46 47 0.947244 CTCCAAGCGCAGAGTTTTGT 59.053 50.000 11.47 0.00 0.00 2.83
47 48 0.239347 CCTCCAAGCGCAGAGTTTTG 59.761 55.000 11.47 3.68 0.00 2.44
48 49 1.518903 GCCTCCAAGCGCAGAGTTTT 61.519 55.000 11.47 0.00 0.00 2.43
49 50 1.968540 GCCTCCAAGCGCAGAGTTT 60.969 57.895 11.47 0.00 0.00 2.66
50 51 2.359230 GCCTCCAAGCGCAGAGTT 60.359 61.111 11.47 0.00 0.00 3.01
51 52 4.400961 GGCCTCCAAGCGCAGAGT 62.401 66.667 11.47 0.00 0.00 3.24
61 62 0.842030 AGACTCATGTTGGGCCTCCA 60.842 55.000 4.53 0.88 42.25 3.86
62 63 1.134371 GTAGACTCATGTTGGGCCTCC 60.134 57.143 4.53 0.00 0.00 4.30
63 64 1.555075 TGTAGACTCATGTTGGGCCTC 59.445 52.381 4.53 0.00 0.00 4.70
64 65 1.656587 TGTAGACTCATGTTGGGCCT 58.343 50.000 4.53 0.00 0.00 5.19
65 66 2.027192 TCTTGTAGACTCATGTTGGGCC 60.027 50.000 0.00 0.00 0.00 5.80
66 67 3.334583 TCTTGTAGACTCATGTTGGGC 57.665 47.619 0.00 0.00 0.00 5.36
67 68 7.607991 ACTTTATTCTTGTAGACTCATGTTGGG 59.392 37.037 0.00 0.00 0.00 4.12
68 69 8.553459 ACTTTATTCTTGTAGACTCATGTTGG 57.447 34.615 0.00 0.00 0.00 3.77
69 70 9.817365 CAACTTTATTCTTGTAGACTCATGTTG 57.183 33.333 0.00 0.00 0.00 3.33
70 71 8.507249 GCAACTTTATTCTTGTAGACTCATGTT 58.493 33.333 0.00 0.00 0.00 2.71
71 72 7.148573 CGCAACTTTATTCTTGTAGACTCATGT 60.149 37.037 0.00 0.00 0.00 3.21
72 73 7.148573 ACGCAACTTTATTCTTGTAGACTCATG 60.149 37.037 0.00 0.00 0.00 3.07
73 74 6.874134 ACGCAACTTTATTCTTGTAGACTCAT 59.126 34.615 0.00 0.00 0.00 2.90
74 75 6.220930 ACGCAACTTTATTCTTGTAGACTCA 58.779 36.000 0.00 0.00 0.00 3.41
75 76 6.707599 ACGCAACTTTATTCTTGTAGACTC 57.292 37.500 0.00 0.00 0.00 3.36
76 77 7.376615 ACTACGCAACTTTATTCTTGTAGACT 58.623 34.615 3.35 0.00 33.91 3.24
77 78 7.578169 ACTACGCAACTTTATTCTTGTAGAC 57.422 36.000 3.35 0.00 33.91 2.59
78 79 8.733458 TCTACTACGCAACTTTATTCTTGTAGA 58.267 33.333 3.35 0.00 33.91 2.59
79 80 8.796278 GTCTACTACGCAACTTTATTCTTGTAG 58.204 37.037 0.00 0.00 35.40 2.74
80 81 8.298854 TGTCTACTACGCAACTTTATTCTTGTA 58.701 33.333 0.00 0.00 0.00 2.41
81 82 7.149973 TGTCTACTACGCAACTTTATTCTTGT 58.850 34.615 0.00 0.00 0.00 3.16
82 83 7.576750 TGTCTACTACGCAACTTTATTCTTG 57.423 36.000 0.00 0.00 0.00 3.02
83 84 8.033038 TGATGTCTACTACGCAACTTTATTCTT 58.967 33.333 0.00 0.00 0.00 2.52
84 85 7.488471 GTGATGTCTACTACGCAACTTTATTCT 59.512 37.037 0.00 0.00 0.00 2.40
85 86 7.488471 AGTGATGTCTACTACGCAACTTTATTC 59.512 37.037 0.00 0.00 0.00 1.75
86 87 7.321153 AGTGATGTCTACTACGCAACTTTATT 58.679 34.615 0.00 0.00 0.00 1.40
87 88 6.864342 AGTGATGTCTACTACGCAACTTTAT 58.136 36.000 0.00 0.00 0.00 1.40
88 89 6.263516 AGTGATGTCTACTACGCAACTTTA 57.736 37.500 0.00 0.00 0.00 1.85
89 90 5.135508 AGTGATGTCTACTACGCAACTTT 57.864 39.130 0.00 0.00 0.00 2.66
90 91 4.785511 AGTGATGTCTACTACGCAACTT 57.214 40.909 0.00 0.00 0.00 2.66
91 92 4.785511 AAGTGATGTCTACTACGCAACT 57.214 40.909 0.00 0.00 0.00 3.16
92 93 4.434330 GCAAAGTGATGTCTACTACGCAAC 60.434 45.833 0.00 0.00 0.00 4.17
93 94 3.678072 GCAAAGTGATGTCTACTACGCAA 59.322 43.478 0.00 0.00 0.00 4.85
94 95 3.056821 AGCAAAGTGATGTCTACTACGCA 60.057 43.478 0.00 0.00 31.49 5.24
95 96 3.512680 AGCAAAGTGATGTCTACTACGC 58.487 45.455 0.00 0.00 0.00 4.42
96 97 5.637809 TGTAGCAAAGTGATGTCTACTACG 58.362 41.667 0.00 0.00 34.20 3.51
97 98 7.884816 TTTGTAGCAAAGTGATGTCTACTAC 57.115 36.000 0.00 0.00 34.20 2.73
98 99 8.896320 TTTTTGTAGCAAAGTGATGTCTACTA 57.104 30.769 0.00 0.00 34.20 1.82
99 100 7.801716 TTTTTGTAGCAAAGTGATGTCTACT 57.198 32.000 0.00 0.00 34.20 2.57
126 127 1.252904 TGCAGCAAGGAAGCCCAATC 61.253 55.000 0.00 0.00 34.23 2.67
127 128 1.228956 TGCAGCAAGGAAGCCCAAT 60.229 52.632 0.00 0.00 34.23 3.16
129 130 2.598394 GTGCAGCAAGGAAGCCCA 60.598 61.111 0.00 0.00 34.23 5.36
131 132 1.247567 TAAAGTGCAGCAAGGAAGCC 58.752 50.000 0.00 0.00 34.23 4.35
132 133 3.582714 AATAAAGTGCAGCAAGGAAGC 57.417 42.857 0.00 0.00 0.00 3.86
135 136 4.941263 ACGATAAATAAAGTGCAGCAAGGA 59.059 37.500 0.00 0.00 0.00 3.36
194 195 7.632721 TGAAAATGTCGGTAACAAGTAGTTTC 58.367 34.615 0.00 0.00 42.37 2.78
205 206 3.304391 GCAAGCACTGAAAATGTCGGTAA 60.304 43.478 0.00 0.00 44.55 2.85
214 215 5.068987 AGGTAATTTCTGCAAGCACTGAAAA 59.931 36.000 11.75 2.86 39.78 2.29
223 224 4.771590 TCAGCAAGGTAATTTCTGCAAG 57.228 40.909 0.00 0.00 0.00 4.01
236 237 4.057406 TGACAAATGGTTTTCAGCAAGG 57.943 40.909 0.00 0.00 33.01 3.61
250 251 4.670765 AGGAGCAGAAGGAAATGACAAAT 58.329 39.130 0.00 0.00 0.00 2.32
251 252 4.074970 GAGGAGCAGAAGGAAATGACAAA 58.925 43.478 0.00 0.00 0.00 2.83
307 308 4.991056 CACAAGTATAGGGGATCAATCGTG 59.009 45.833 0.00 0.00 0.00 4.35
380 381 2.030562 CGACTTGGTTCGCCCAGT 59.969 61.111 0.00 0.00 46.31 4.00
418 419 2.203112 GCCCAGATCTGCGCATGA 60.203 61.111 24.22 11.53 34.70 3.07
449 450 0.802494 CTGTTTTCCCGTTGCGCTAT 59.198 50.000 9.73 0.00 0.00 2.97
450 451 0.249953 TCTGTTTTCCCGTTGCGCTA 60.250 50.000 9.73 0.00 0.00 4.26
459 460 2.661718 TGGTTTCACCTCTGTTTTCCC 58.338 47.619 0.00 0.00 39.58 3.97
495 498 1.598685 GGTTTTCGCCCAGTTCCGA 60.599 57.895 0.00 0.00 0.00 4.55
571 584 2.288886 ACGAGACTTAGGCAAACCAGAC 60.289 50.000 0.00 0.00 39.06 3.51
584 597 1.202639 TGTTGGTGCATGACGAGACTT 60.203 47.619 0.00 0.00 0.00 3.01
684 697 2.463589 GATGGTGAAGGCGGTGGTGA 62.464 60.000 0.00 0.00 0.00 4.02
686 699 2.351276 GATGGTGAAGGCGGTGGT 59.649 61.111 0.00 0.00 0.00 4.16
715 728 2.357517 ACCAGTTTCTCGCCGCTG 60.358 61.111 0.00 0.00 0.00 5.18
716 729 2.048127 GACCAGTTTCTCGCCGCT 60.048 61.111 0.00 0.00 0.00 5.52
787 800 1.952133 CGTGAAGGTTTGGCGTCGA 60.952 57.895 0.00 0.00 0.00 4.20
814 827 2.281276 GGAGGTCGCGGTGGTTTT 60.281 61.111 6.13 0.00 0.00 2.43
838 851 6.971756 TCTCGTATCGTAGGTATCTAGAATCG 59.028 42.308 0.00 0.00 0.00 3.34
842 855 7.122501 ACATCTCTCGTATCGTAGGTATCTAGA 59.877 40.741 0.00 0.00 0.00 2.43
884 897 4.621034 CCGCAATTGTCCTGTGAAAATTAC 59.379 41.667 7.40 0.00 36.47 1.89
896 909 5.977129 CCAATCTTAAATACCGCAATTGTCC 59.023 40.000 7.40 0.00 0.00 4.02
911 924 5.990996 CAGCCAAAAGAAAAGCCAATCTTAA 59.009 36.000 0.00 0.00 34.90 1.85
918 931 4.744795 TTTACAGCCAAAAGAAAAGCCA 57.255 36.364 0.00 0.00 0.00 4.75
920 933 6.036246 CTGTTTTACAGCCAAAAGAAAAGC 57.964 37.500 0.00 0.00 39.62 3.51
942 955 0.107214 CCACATCCCGCATAACCACT 60.107 55.000 0.00 0.00 0.00 4.00
944 957 1.140052 CTACCACATCCCGCATAACCA 59.860 52.381 0.00 0.00 0.00 3.67
952 965 4.399618 CCATCTATACTCTACCACATCCCG 59.600 50.000 0.00 0.00 0.00 5.14
973 986 6.265304 AGGTTTTGGGGTTTATAAATAGCCA 58.735 36.000 0.31 0.00 33.60 4.75
977 990 8.737601 TTTGGAGGTTTTGGGGTTTATAAATA 57.262 30.769 0.31 0.00 0.00 1.40
978 991 7.634526 TTTGGAGGTTTTGGGGTTTATAAAT 57.365 32.000 0.31 0.00 0.00 1.40
1167 1186 2.687566 GCGGAGAGGGAAGGGGAA 60.688 66.667 0.00 0.00 0.00 3.97
1168 1187 4.798682 GGCGGAGAGGGAAGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
1170 1189 3.787001 GTGGCGGAGAGGGAAGGG 61.787 72.222 0.00 0.00 0.00 3.95
1171 1190 2.245438 GAAGTGGCGGAGAGGGAAGG 62.245 65.000 0.00 0.00 0.00 3.46
1172 1191 1.219393 GAAGTGGCGGAGAGGGAAG 59.781 63.158 0.00 0.00 0.00 3.46
1253 1275 2.738964 GCAGGTGGATTCGAGGTAGAAC 60.739 54.545 0.00 0.00 32.39 3.01
1547 1569 1.524482 GAGGTGGTCCTGGATGCTC 59.476 63.158 0.00 0.00 45.24 4.26
1751 1773 2.124612 CCCTGCATGATGACGCCA 60.125 61.111 0.00 0.00 0.00 5.69
2049 2071 2.117156 GCACCAGCATGCTCGGATT 61.117 57.895 30.67 14.89 42.62 3.01
2106 2128 0.689623 CCTTCCTTCCTCAGCAGTGT 59.310 55.000 0.00 0.00 0.00 3.55
2279 2301 4.181010 CTGGGCGGCTGTGGCTAT 62.181 66.667 9.56 0.00 38.73 2.97
2330 2352 3.117738 CCTAAGCAGATCCCACCAAGAAT 60.118 47.826 0.00 0.00 0.00 2.40
2369 2391 2.158784 ACAAACATTGGCCAAGCAACAT 60.159 40.909 24.94 2.19 34.12 2.71
2605 2627 7.067859 ACTGTTCATTAATGAGGAACATCCATG 59.932 37.037 17.28 9.76 46.75 3.66
2643 2665 5.193679 AGAGTAAAATGTTATGGCCTCACC 58.806 41.667 3.32 0.00 39.84 4.02
2692 2949 5.632347 GGCAAGAACAAGATTTCAATGAGTG 59.368 40.000 0.00 0.00 0.00 3.51
2699 2956 2.297033 GCCAGGCAAGAACAAGATTTCA 59.703 45.455 6.55 0.00 0.00 2.69
2716 2973 3.309138 CACTCGAGATCAAATTCAGCCAG 59.691 47.826 21.68 0.00 0.00 4.85
2724 2981 4.633126 CACATCAACCACTCGAGATCAAAT 59.367 41.667 21.68 2.38 0.00 2.32
2741 2998 4.573021 TTCATCCTCATGTTCCACATCA 57.427 40.909 0.00 0.00 36.53 3.07
2753 3010 4.324563 GGACTCCCTTTGATTTCATCCTCA 60.325 45.833 0.00 0.00 0.00 3.86
2771 3028 1.200948 GCAGGCTGAAAATGTGGACTC 59.799 52.381 20.86 0.00 0.00 3.36
2997 3257 3.463048 TTTAGGAACGGAGGGAGTACT 57.537 47.619 0.00 0.00 0.00 2.73
2998 3258 7.155655 CTATATTTAGGAACGGAGGGAGTAC 57.844 44.000 0.00 0.00 0.00 2.73
3013 3273 9.936759 GGAATCTCTCCAAAGACCTATATTTAG 57.063 37.037 0.00 0.00 44.67 1.85
3027 3287 8.954344 ATGTGGTTCATAGTGGAATCTCTCCAA 61.954 40.741 0.00 0.00 44.66 3.53
3028 3288 7.548782 ATGTGGTTCATAGTGGAATCTCTCCA 61.549 42.308 0.00 0.00 42.66 3.86
3029 3289 4.162320 TGTGGTTCATAGTGGAATCTCTCC 59.838 45.833 0.00 0.00 45.64 3.71
3030 3290 5.344743 TGTGGTTCATAGTGGAATCTCTC 57.655 43.478 0.00 0.00 0.00 3.20
3031 3291 5.965033 ATGTGGTTCATAGTGGAATCTCT 57.035 39.130 0.00 0.00 34.67 3.10
3032 3292 5.692204 CGTATGTGGTTCATAGTGGAATCTC 59.308 44.000 0.00 0.00 39.36 2.75
3033 3293 5.453339 CCGTATGTGGTTCATAGTGGAATCT 60.453 44.000 0.00 0.00 39.36 2.40
3034 3294 4.750098 CCGTATGTGGTTCATAGTGGAATC 59.250 45.833 0.00 0.00 39.36 2.52
3035 3295 4.407621 TCCGTATGTGGTTCATAGTGGAAT 59.592 41.667 0.00 0.00 39.60 3.01
3036 3296 3.770388 TCCGTATGTGGTTCATAGTGGAA 59.230 43.478 0.00 0.00 39.60 3.53
3037 3297 3.367321 TCCGTATGTGGTTCATAGTGGA 58.633 45.455 0.00 0.00 39.94 4.02
3038 3298 3.812156 TCCGTATGTGGTTCATAGTGG 57.188 47.619 0.00 0.00 39.36 4.00
3039 3299 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
3040 3300 6.455647 CATACATCCGTATGTGGTTCATAGT 58.544 40.000 3.56 0.00 46.70 2.12
3041 3301 6.951256 CATACATCCGTATGTGGTTCATAG 57.049 41.667 3.56 0.00 46.70 2.23
3052 3312 7.119699 CCAAAATGCATCTACATACATCCGTAT 59.880 37.037 0.00 0.00 38.96 3.06
3053 3313 6.426633 CCAAAATGCATCTACATACATCCGTA 59.573 38.462 0.00 0.00 0.00 4.02
3054 3314 5.239306 CCAAAATGCATCTACATACATCCGT 59.761 40.000 0.00 0.00 0.00 4.69
3055 3315 5.469760 TCCAAAATGCATCTACATACATCCG 59.530 40.000 0.00 0.00 0.00 4.18
3056 3316 6.488006 ACTCCAAAATGCATCTACATACATCC 59.512 38.462 0.00 0.00 0.00 3.51
3057 3317 7.012704 ACACTCCAAAATGCATCTACATACATC 59.987 37.037 0.00 0.00 0.00 3.06
3058 3318 6.830324 ACACTCCAAAATGCATCTACATACAT 59.170 34.615 0.00 0.00 0.00 2.29
3059 3319 6.179756 ACACTCCAAAATGCATCTACATACA 58.820 36.000 0.00 0.00 0.00 2.29
3060 3320 6.683974 ACACTCCAAAATGCATCTACATAC 57.316 37.500 0.00 0.00 0.00 2.39
3061 3321 7.791029 TCTACACTCCAAAATGCATCTACATA 58.209 34.615 0.00 0.00 0.00 2.29
3062 3322 6.653020 TCTACACTCCAAAATGCATCTACAT 58.347 36.000 0.00 0.00 0.00 2.29
3063 3323 6.048732 TCTACACTCCAAAATGCATCTACA 57.951 37.500 0.00 0.00 0.00 2.74
3064 3324 7.280876 TGAATCTACACTCCAAAATGCATCTAC 59.719 37.037 0.00 0.00 0.00 2.59
3065 3325 7.280876 GTGAATCTACACTCCAAAATGCATCTA 59.719 37.037 0.00 0.00 37.73 1.98
3066 3326 6.094603 GTGAATCTACACTCCAAAATGCATCT 59.905 38.462 0.00 0.00 37.73 2.90
3067 3327 6.094603 AGTGAATCTACACTCCAAAATGCATC 59.905 38.462 0.00 0.00 46.36 3.91
3068 3328 5.948162 AGTGAATCTACACTCCAAAATGCAT 59.052 36.000 0.00 0.00 46.36 3.96
3069 3329 5.316167 AGTGAATCTACACTCCAAAATGCA 58.684 37.500 0.00 0.00 46.36 3.96
3070 3330 5.886960 AGTGAATCTACACTCCAAAATGC 57.113 39.130 0.00 0.00 46.36 3.56
3080 3340 6.090898 ACGTAGCAAAATGAGTGAATCTACAC 59.909 38.462 0.00 0.00 40.60 2.90
3081 3341 6.163476 ACGTAGCAAAATGAGTGAATCTACA 58.837 36.000 0.00 0.00 0.00 2.74
3082 3342 6.648725 ACGTAGCAAAATGAGTGAATCTAC 57.351 37.500 0.00 0.00 0.00 2.59
3083 3343 7.979537 ACATACGTAGCAAAATGAGTGAATCTA 59.020 33.333 0.08 0.00 0.00 1.98
3084 3344 6.818644 ACATACGTAGCAAAATGAGTGAATCT 59.181 34.615 0.08 0.00 0.00 2.40
3085 3345 7.005062 ACATACGTAGCAAAATGAGTGAATC 57.995 36.000 0.08 0.00 0.00 2.52
3086 3346 6.985188 ACATACGTAGCAAAATGAGTGAAT 57.015 33.333 0.08 0.00 0.00 2.57
3087 3347 7.520119 CTACATACGTAGCAAAATGAGTGAA 57.480 36.000 0.08 0.00 38.84 3.18
3102 3362 9.352191 AGAGATTTTACTATGGACTACATACGT 57.648 33.333 0.00 0.00 41.03 3.57
3129 3389 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3130 3390 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3131 3391 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3132 3392 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3133 3393 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3134 3394 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3135 3395 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3136 3396 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3137 3397 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3138 3398 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
3139 3399 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3140 3400 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3141 3401 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3142 3402 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3143 3403 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3144 3404 2.024655 ACATGTACTCCCTCCGTTCCTA 60.025 50.000 0.00 0.00 0.00 2.94
3145 3405 1.273098 ACATGTACTCCCTCCGTTCCT 60.273 52.381 0.00 0.00 0.00 3.36
3146 3406 1.192428 ACATGTACTCCCTCCGTTCC 58.808 55.000 0.00 0.00 0.00 3.62
3147 3407 3.000727 CAAACATGTACTCCCTCCGTTC 58.999 50.000 0.00 0.00 0.00 3.95
3148 3408 2.370849 ACAAACATGTACTCCCTCCGTT 59.629 45.455 0.00 0.00 0.00 4.44
3149 3409 1.975680 ACAAACATGTACTCCCTCCGT 59.024 47.619 0.00 0.00 0.00 4.69
3150 3410 2.233922 AGACAAACATGTACTCCCTCCG 59.766 50.000 0.00 0.00 0.00 4.63
3151 3411 3.600388 CAGACAAACATGTACTCCCTCC 58.400 50.000 0.00 0.00 0.00 4.30
3152 3412 3.003480 GCAGACAAACATGTACTCCCTC 58.997 50.000 0.00 0.00 0.00 4.30
3153 3413 2.639839 AGCAGACAAACATGTACTCCCT 59.360 45.455 0.00 0.00 0.00 4.20
3154 3414 3.059352 AGCAGACAAACATGTACTCCC 57.941 47.619 0.00 0.00 0.00 4.30
3155 3415 4.153117 CAGAAGCAGACAAACATGTACTCC 59.847 45.833 0.00 0.00 0.00 3.85
3156 3416 4.377841 GCAGAAGCAGACAAACATGTACTC 60.378 45.833 0.00 0.00 41.58 2.59
3219 3479 8.362639 ACACTAGGATCTTTTCGTACTTTGTTA 58.637 33.333 0.00 0.00 0.00 2.41
3378 3644 4.545678 ACTGGGCATTGATAAGGCATTAA 58.454 39.130 0.00 0.00 40.56 1.40
3379 3645 4.183223 ACTGGGCATTGATAAGGCATTA 57.817 40.909 0.00 0.00 40.56 1.90
3380 3646 3.036452 ACTGGGCATTGATAAGGCATT 57.964 42.857 0.60 0.00 40.56 3.56
3381 3647 2.696707 CAACTGGGCATTGATAAGGCAT 59.303 45.455 0.60 0.00 40.56 4.40
3382 3648 2.101783 CAACTGGGCATTGATAAGGCA 58.898 47.619 0.60 0.00 40.56 4.75
3383 3649 2.102578 ACAACTGGGCATTGATAAGGC 58.897 47.619 2.83 0.00 37.49 4.35
3384 3650 2.159198 GCACAACTGGGCATTGATAAGG 60.159 50.000 0.00 0.00 45.57 2.69
3385 3651 3.155093 GCACAACTGGGCATTGATAAG 57.845 47.619 0.00 0.00 45.57 1.73
3561 3827 0.768221 TCCACCACAAGAGGAAGCCT 60.768 55.000 0.00 0.00 36.03 4.58
3573 3839 1.545841 GAGGTTTCCCATTCCACCAC 58.454 55.000 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.