Multiple sequence alignment - TraesCS6A01G139800

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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 TraesCS6A01G139800 chr6A 100.000 3534 0 0 1 3534 114994494 114990961 0.000000e+00 6527.0
1 TraesCS6A01G139800 chr6A 90.323 279 26 1 2914 3191 559205441 559205719 7.210000e-97 364.0
2 TraesCS6A01G139800 chr6A 89.825 285 27 2 2914 3196 599844027 599843743 7.210000e-97 364.0
3 TraesCS6A01G139800 chr6D 93.528 1746 77 19 925 2643 93809882 93811618 0.000000e+00 2566.0
4 TraesCS6A01G139800 chr6D 81.757 296 27 16 612 904 93809630 93809901 4.590000e-54 222.0
5 TraesCS6A01G139800 chr6D 97.436 39 1 0 450 488 18958799 18958837 2.280000e-07 67.6
6 TraesCS6A01G139800 chr6B 92.967 1166 43 16 925 2080 179340295 179339159 0.000000e+00 1663.0
7 TraesCS6A01G139800 chr6B 91.309 909 40 14 1 904 179341150 179340276 0.000000e+00 1205.0
8 TraesCS6A01G139800 chr6B 87.900 719 55 17 2077 2765 179337856 179337140 0.000000e+00 817.0
9 TraesCS6A01G139800 chr6B 87.246 345 11 15 3188 3531 171414384 171414696 2.590000e-96 363.0
10 TraesCS6A01G139800 chr6B 94.521 146 6 1 2773 2916 171414241 171414386 1.280000e-54 224.0
11 TraesCS6A01G139800 chr4B 93.103 348 18 4 3188 3534 8104703 8104361 4.070000e-139 505.0
12 TraesCS6A01G139800 chr4B 92.222 270 11 5 3266 3534 575755265 575755005 1.200000e-99 374.0
13 TraesCS6A01G139800 chr4B 90.179 224 20 2 3312 3534 129006800 129006578 1.240000e-74 291.0
14 TraesCS6A01G139800 chr4B 94.068 118 5 1 2805 2920 575755431 575755314 1.010000e-40 178.0
15 TraesCS6A01G139800 chr4B 100.000 56 0 0 3188 3243 575755320 575755265 1.740000e-18 104.0
16 TraesCS6A01G139800 chr4B 100.000 48 0 0 2773 2820 575756906 575756859 4.860000e-14 89.8
17 TraesCS6A01G139800 chr2D 90.828 338 25 4 3188 3524 127515541 127515209 6.960000e-122 448.0
18 TraesCS6A01G139800 chr2D 92.537 134 10 0 2773 2906 127515744 127515611 3.600000e-45 193.0
19 TraesCS6A01G139800 chr2D 92.593 54 2 2 393 444 134302362 134302309 3.780000e-10 76.8
20 TraesCS6A01G139800 chr2B 90.145 345 10 6 3188 3531 485996755 485997076 9.070000e-116 427.0
21 TraesCS6A01G139800 chr2B 91.391 151 11 1 2772 2920 485996611 485996761 4.620000e-49 206.0
22 TraesCS6A01G139800 chr2B 100.000 29 0 0 462 490 42955562 42955534 2.000000e-03 54.7
23 TraesCS6A01G139800 chr5A 93.007 286 16 2 3247 3531 84162180 84162462 7.060000e-112 414.0
24 TraesCS6A01G139800 chr5A 90.614 277 26 0 2914 3190 131405015 131404739 5.570000e-98 368.0
25 TraesCS6A01G139800 chr5A 81.915 94 14 2 355 446 399461802 399461894 3.780000e-10 76.8
26 TraesCS6A01G139800 chr1B 88.657 335 14 10 3188 3521 630604548 630604237 1.540000e-103 387.0
27 TraesCS6A01G139800 chr1B 90.253 277 27 0 2914 3190 317200780 317201056 2.590000e-96 363.0
28 TraesCS6A01G139800 chr1B 88.927 289 30 2 2911 3197 13966397 13966685 4.340000e-94 355.0
29 TraesCS6A01G139800 chr1B 93.377 151 8 1 2772 2920 630604692 630604542 4.590000e-54 222.0
30 TraesCS6A01G139800 chr4D 91.367 278 23 1 2914 3190 437030448 437030171 2.570000e-101 379.0
31 TraesCS6A01G139800 chr1A 91.111 270 24 0 2921 3190 263624680 263624411 2.000000e-97 366.0
32 TraesCS6A01G139800 chr1A 90.288 278 26 1 2914 3190 53022266 53021989 2.590000e-96 363.0
33 TraesCS6A01G139800 chr1A 88.667 150 17 0 2771 2920 72496925 72497074 2.170000e-42 183.0
34 TraesCS6A01G139800 chr1A 87.805 123 12 2 2646 2765 544814456 544814578 1.320000e-29 141.0
35 TraesCS6A01G139800 chr1A 91.489 47 4 0 450 496 520337710 520337756 8.190000e-07 65.8
36 TraesCS6A01G139800 chr1A 94.872 39 2 0 450 488 27312659 27312697 1.060000e-05 62.1
37 TraesCS6A01G139800 chr5B 90.000 280 27 1 2911 3190 320410908 320411186 9.330000e-96 361.0
38 TraesCS6A01G139800 chr5B 85.920 348 16 11 3188 3534 96973858 96973543 1.210000e-89 340.0
39 TraesCS6A01G139800 chr5B 95.890 146 4 1 2773 2916 96974001 96973856 5.900000e-58 235.0
40 TraesCS6A01G139800 chr5B 79.487 117 20 3 326 442 537924593 537924705 2.920000e-11 80.5
41 TraesCS6A01G139800 chr3A 92.754 207 11 2 3188 3394 212037154 212037356 2.670000e-76 296.0
42 TraesCS6A01G139800 chr3A 92.105 152 8 2 3384 3534 212037514 212037662 9.940000e-51 211.0
43 TraesCS6A01G139800 chr3A 88.667 150 17 0 2771 2920 212037011 212037160 2.170000e-42 183.0
44 TraesCS6A01G139800 chr3A 87.778 90 10 1 356 444 112333417 112333506 1.740000e-18 104.0
45 TraesCS6A01G139800 chr3A 91.935 62 5 0 383 444 88852992 88853053 1.750000e-13 87.9
46 TraesCS6A01G139800 chr4A 87.838 148 16 1 2773 2920 531368789 531368644 4.690000e-39 172.0
47 TraesCS6A01G139800 chr5D 87.395 119 12 3 326 444 456746838 456746723 2.210000e-27 134.0
48 TraesCS6A01G139800 chr3D 87.234 94 8 3 351 444 67650192 67650103 1.740000e-18 104.0
49 TraesCS6A01G139800 chr3B 81.818 110 15 5 336 444 10573589 10573694 1.750000e-13 87.9
50 TraesCS6A01G139800 chr2A 97.727 44 1 0 450 493 415064240 415064197 3.780000e-10 76.8
51 TraesCS6A01G139800 chr1D 94.872 39 2 0 450 488 71038175 71038137 1.060000e-05 62.1


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 TraesCS6A01G139800 chr6A 114990961 114994494 3533 True 6527.000000 6527 100.000000 1 3534 1 chr6A.!!$R1 3533
1 TraesCS6A01G139800 chr6D 93809630 93811618 1988 False 1394.000000 2566 87.642500 612 2643 2 chr6D.!!$F2 2031
2 TraesCS6A01G139800 chr6B 179337140 179341150 4010 True 1228.333333 1663 90.725333 1 2765 3 chr6B.!!$R1 2764
3 TraesCS6A01G139800 chr2D 127515209 127515744 535 True 320.500000 448 91.682500 2773 3524 2 chr2D.!!$R2 751
4 TraesCS6A01G139800 chr3A 212037011 212037662 651 False 230.000000 296 91.175333 2771 3534 3 chr3A.!!$F3 763

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
52 53 0.456221 CTCGACCTGTCCGTTGCTAT 59.544 55.000 0.00 0.00 0.0 2.97 F
1385 1400 1.663388 TAACATATCAGCGCGCCGG 60.663 57.895 30.33 21.21 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1982 0.385390 CCTTGTTGTGGTTGGTCAGC 59.615 55.0 0.00 0.0 0.00 4.26 R
3364 4790 0.104855 TTGCGCCAGGCTAGATGTAG 59.895 55.0 10.54 0.0 44.05 2.74 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
41 42 5.918576 GGTAAACAAAAATTTCCTCGACCTG 59.081 40.000 0.00 0.00 0.00 4.00
49 50 2.430382 TTCCTCGACCTGTCCGTTGC 62.430 60.000 0.00 0.00 0.00 4.17
52 53 0.456221 CTCGACCTGTCCGTTGCTAT 59.544 55.000 0.00 0.00 0.00 2.97
183 184 4.016706 CACCACGTCCCTCCACCC 62.017 72.222 0.00 0.00 0.00 4.61
210 211 6.127507 CCCATTCGCTTATCTCTCATCATCTA 60.128 42.308 0.00 0.00 0.00 1.98
212 213 7.362834 CCATTCGCTTATCTCTCATCATCTACT 60.363 40.741 0.00 0.00 0.00 2.57
216 217 6.371271 CGCTTATCTCTCATCATCTACTCTCA 59.629 42.308 0.00 0.00 0.00 3.27
224 225 6.775142 TCTCATCATCTACTCTCAAACCCTAG 59.225 42.308 0.00 0.00 0.00 3.02
226 227 7.583625 TCATCATCTACTCTCAAACCCTAGTA 58.416 38.462 0.00 0.00 0.00 1.82
234 235 6.231211 ACTCTCAAACCCTAGTATGTTGTTG 58.769 40.000 0.00 0.00 0.00 3.33
307 308 5.824624 TCTCTTCTTCTCACAATTGCACTTT 59.175 36.000 5.05 0.00 0.00 2.66
308 309 6.319658 TCTCTTCTTCTCACAATTGCACTTTT 59.680 34.615 5.05 0.00 0.00 2.27
309 310 6.866480 TCTTCTTCTCACAATTGCACTTTTT 58.134 32.000 5.05 0.00 0.00 1.94
380 385 6.925610 AAAAAGGACAAAAGGAAATGCTTC 57.074 33.333 0.00 0.00 0.00 3.86
412 417 8.710835 TTTTAGCGTACAATCAATGACATAGA 57.289 30.769 0.00 0.00 0.00 1.98
424 429 9.896645 AATCAATGACATAGAACTTAGATGTGT 57.103 29.630 0.00 0.00 33.99 3.72
538 543 4.277672 TCACGTGTAATATGCTACCTCCTC 59.722 45.833 16.51 0.00 0.00 3.71
540 545 3.827302 CGTGTAATATGCTACCTCCTCCT 59.173 47.826 0.00 0.00 0.00 3.69
541 546 4.321304 CGTGTAATATGCTACCTCCTCCTG 60.321 50.000 0.00 0.00 0.00 3.86
542 547 4.589374 GTGTAATATGCTACCTCCTCCTGT 59.411 45.833 0.00 0.00 0.00 4.00
615 620 4.926140 TGTTGTCAAATTGTGGCATGTA 57.074 36.364 0.00 0.00 42.79 2.29
651 656 8.603304 AGGGACAACATAACTAAAACTATCTGT 58.397 33.333 0.00 0.00 0.00 3.41
747 752 6.816640 CGTAATGGGTCATTCTAGTGAAAAGA 59.183 38.462 0.00 0.00 35.54 2.52
764 769 6.861055 GTGAAAAGAAACGGATGAATTGCTTA 59.139 34.615 0.00 0.00 0.00 3.09
769 774 6.963796 AGAAACGGATGAATTGCTTATGATC 58.036 36.000 0.00 0.00 0.00 2.92
771 776 4.631131 ACGGATGAATTGCTTATGATCGA 58.369 39.130 0.00 0.00 0.00 3.59
904 913 8.930846 TCTCTCAATTCTTCTTCTTCCATTTT 57.069 30.769 0.00 0.00 0.00 1.82
905 914 9.359653 TCTCTCAATTCTTCTTCTTCCATTTTT 57.640 29.630 0.00 0.00 0.00 1.94
935 944 9.927081 AGAACCATGGATATACAATTTTCTTCT 57.073 29.630 21.47 8.66 0.00 2.85
938 947 9.136323 ACCATGGATATACAATTTTCTTCTTCC 57.864 33.333 21.47 0.00 0.00 3.46
939 948 9.135189 CCATGGATATACAATTTTCTTCTTCCA 57.865 33.333 5.56 0.00 34.33 3.53
1041 1053 8.854979 TGTGTTGTTTAAAATCAATCAGTCAG 57.145 30.769 0.00 0.00 0.00 3.51
1145 1160 7.778853 GGAGATTTCCATGATCTATTGCCATAT 59.221 37.037 0.00 0.00 43.45 1.78
1146 1161 9.842775 GAGATTTCCATGATCTATTGCCATATA 57.157 33.333 0.00 0.00 34.13 0.86
1147 1162 9.624373 AGATTTCCATGATCTATTGCCATATAC 57.376 33.333 0.00 0.00 32.27 1.47
1167 1182 4.107363 ACTACTAGCTGTTTCGCTTACC 57.893 45.455 0.00 0.00 41.30 2.85
1171 1186 2.674796 AGCTGTTTCGCTTACCCTAG 57.325 50.000 0.00 0.00 36.74 3.02
1261 1276 9.255304 GTACTGATCTTCTATCTGTTCAAATCC 57.745 37.037 0.00 0.00 33.34 3.01
1276 1291 6.825213 TGTTCAAATCCTCACAAGATATCTGG 59.175 38.462 5.86 5.67 0.00 3.86
1385 1400 1.663388 TAACATATCAGCGCGCCGG 60.663 57.895 30.33 21.21 0.00 6.13
1529 1553 2.890474 GGCGGCAGGACATACGTG 60.890 66.667 3.07 0.00 37.43 4.49
1876 1903 4.675029 GGACGTGTGGGTGGACCG 62.675 72.222 0.00 0.00 44.64 4.79
1955 1982 1.374758 GACCGTCTCCAACTGCCTG 60.375 63.158 0.00 0.00 0.00 4.85
2144 3477 3.340789 GGGAAATACGCCATCGGC 58.659 61.111 0.00 0.00 46.75 5.54
2231 3564 1.236616 TGCTCCTGTGTTTCATGGCG 61.237 55.000 0.00 0.00 0.00 5.69
2233 3566 1.943968 GCTCCTGTGTTTCATGGCGTA 60.944 52.381 0.00 0.00 0.00 4.42
2234 3567 1.732259 CTCCTGTGTTTCATGGCGTAC 59.268 52.381 0.00 0.00 0.00 3.67
2269 3607 4.740695 GTCTTATGATGAAGCTGACCGTAC 59.259 45.833 0.00 0.00 0.00 3.67
2499 3837 0.037326 CGTGCAGCAAGGGTTCTCTA 60.037 55.000 0.00 0.00 0.00 2.43
2508 3846 2.941720 CAAGGGTTCTCTATGCTGAAGC 59.058 50.000 0.00 0.00 39.21 3.86
2511 3849 1.472376 GGTTCTCTATGCTGAAGCGCT 60.472 52.381 2.64 2.64 45.83 5.92
2512 3850 1.857837 GTTCTCTATGCTGAAGCGCTC 59.142 52.381 12.06 4.99 45.83 5.03
2513 3851 1.397672 TCTCTATGCTGAAGCGCTCT 58.602 50.000 12.06 0.00 45.83 4.09
2514 3852 2.576615 TCTCTATGCTGAAGCGCTCTA 58.423 47.619 12.06 1.01 45.83 2.43
2517 3876 0.032678 TATGCTGAAGCGCTCTAGGC 59.967 55.000 12.06 13.77 45.83 3.93
2520 3879 0.318614 GCTGAAGCGCTCTAGGCTAG 60.319 60.000 12.06 15.56 40.53 3.42
2522 3881 1.001815 CTGAAGCGCTCTAGGCTAGAC 60.002 57.143 20.11 15.10 40.53 2.59
2525 3884 0.106918 AGCGCTCTAGGCTAGACAGT 60.107 55.000 20.11 2.94 39.39 3.55
2539 3898 6.321690 AGGCTAGACAGTCACGTAGAATAAAT 59.678 38.462 0.00 0.00 0.00 1.40
2551 3910 3.637911 AGAATAAATGGCCACCACGTA 57.362 42.857 8.16 0.00 35.80 3.57
2566 3925 6.551736 CCACCACGTAGGATTCTTTTATTTG 58.448 40.000 10.46 0.00 41.22 2.32
2596 3955 4.399934 GCACCAGTAGAGCCTATATAGTCC 59.600 50.000 8.92 0.00 0.00 3.85
2598 3957 5.650266 CACCAGTAGAGCCTATATAGTCCTG 59.350 48.000 8.92 4.89 0.00 3.86
2599 3958 5.197451 CCAGTAGAGCCTATATAGTCCTGG 58.803 50.000 8.92 9.21 0.00 4.45
2643 4002 8.548025 TGATTTGTTATCAATTCCTCCTCTGTA 58.452 33.333 6.15 0.00 34.79 2.74
2644 4003 9.396022 GATTTGTTATCAATTCCTCCTCTGTAA 57.604 33.333 0.00 0.00 33.32 2.41
2659 4020 5.929992 TCCTCTGTAACGTCCTACAAATTTG 59.070 40.000 16.67 16.67 31.51 2.32
2669 4030 4.342665 GTCCTACAAATTTGGGTGGTTTGA 59.657 41.667 21.74 4.64 36.58 2.69
2670 4031 4.586841 TCCTACAAATTTGGGTGGTTTGAG 59.413 41.667 21.74 5.16 36.58 3.02
2675 4036 5.366477 ACAAATTTGGGTGGTTTGAGAATCT 59.634 36.000 21.74 0.00 36.58 2.40
2678 4039 3.874383 TGGGTGGTTTGAGAATCTTGA 57.126 42.857 0.00 0.00 34.92 3.02
2698 4059 4.793071 TGAATATTGACAAGTTTGCACGG 58.207 39.130 0.00 0.00 0.00 4.94
2706 4067 2.223711 ACAAGTTTGCACGGGCTTTAAG 60.224 45.455 12.74 0.00 41.91 1.85
2707 4068 1.687563 AGTTTGCACGGGCTTTAAGT 58.312 45.000 12.74 2.52 41.91 2.24
2711 4072 1.234615 TGCACGGGCTTTAAGTCTGC 61.235 55.000 12.74 4.63 41.91 4.26
2715 4076 1.479323 ACGGGCTTTAAGTCTGCGATA 59.521 47.619 5.18 0.00 26.44 2.92
2726 4087 5.339008 AAGTCTGCGATAGTTATGGTTCA 57.661 39.130 0.00 0.00 39.35 3.18
2732 4093 3.181469 GCGATAGTTATGGTTCACCTGGA 60.181 47.826 0.00 0.00 35.92 3.86
2739 4100 1.078426 GGTTCACCTGGATGGACCG 60.078 63.158 0.00 0.00 38.51 4.79
2765 4129 4.202151 GGGCATGGATTGGTCTTGAAATAC 60.202 45.833 0.00 0.00 0.00 1.89
2766 4130 4.646492 GGCATGGATTGGTCTTGAAATACT 59.354 41.667 0.00 0.00 0.00 2.12
2767 4131 5.827797 GGCATGGATTGGTCTTGAAATACTA 59.172 40.000 0.00 0.00 0.00 1.82
2768 4132 6.238759 GGCATGGATTGGTCTTGAAATACTAC 60.239 42.308 0.00 0.00 0.00 2.73
2769 4133 6.238759 GCATGGATTGGTCTTGAAATACTACC 60.239 42.308 0.00 0.00 0.00 3.18
2834 4198 2.239124 TTTTGACGTCCGTGACCGC 61.239 57.895 14.12 0.00 0.00 5.68
2866 4230 1.258445 ATCGGTTGTCCTCGAGCCTT 61.258 55.000 6.99 0.00 38.83 4.35
2869 4233 1.301716 GTTGTCCTCGAGCCTTGCA 60.302 57.895 6.99 0.00 0.00 4.08
2875 4239 2.046023 TCGAGCCTTGCATGGTGG 60.046 61.111 19.05 9.34 0.00 4.61
2895 4321 3.554342 CTAGGGCCGCTGCTCCAT 61.554 66.667 0.00 5.41 39.53 3.41
2913 4339 4.368067 TCCATAAACTTACCTAGGCCTGT 58.632 43.478 17.99 8.47 0.00 4.00
2914 4340 4.786454 TCCATAAACTTACCTAGGCCTGTT 59.214 41.667 17.99 6.82 0.00 3.16
2915 4341 5.965705 TCCATAAACTTACCTAGGCCTGTTA 59.034 40.000 17.99 0.00 0.00 2.41
2916 4342 6.099269 TCCATAAACTTACCTAGGCCTGTTAG 59.901 42.308 17.99 11.59 0.00 2.34
2917 4343 4.838904 AAACTTACCTAGGCCTGTTAGG 57.161 45.455 17.99 17.56 42.78 2.69
2918 4344 2.760581 ACTTACCTAGGCCTGTTAGGG 58.239 52.381 21.79 14.67 41.66 3.53
2919 4345 2.045465 ACTTACCTAGGCCTGTTAGGGT 59.955 50.000 21.79 18.73 41.66 4.34
2920 4346 3.273084 ACTTACCTAGGCCTGTTAGGGTA 59.727 47.826 21.79 17.89 41.66 3.69
2921 4347 4.078160 ACTTACCTAGGCCTGTTAGGGTAT 60.078 45.833 21.79 6.04 41.66 2.73
2922 4348 2.690840 ACCTAGGCCTGTTAGGGTATG 58.309 52.381 21.79 0.00 41.66 2.39
2923 4349 2.022330 ACCTAGGCCTGTTAGGGTATGT 60.022 50.000 21.79 0.18 41.66 2.29
2924 4350 3.208234 ACCTAGGCCTGTTAGGGTATGTA 59.792 47.826 21.79 0.00 41.66 2.29
2925 4351 3.577415 CCTAGGCCTGTTAGGGTATGTAC 59.423 52.174 17.99 0.00 35.37 2.90
2926 4352 3.124856 AGGCCTGTTAGGGTATGTACA 57.875 47.619 3.11 0.00 35.37 2.90
2927 4353 3.456842 AGGCCTGTTAGGGTATGTACAA 58.543 45.455 3.11 0.00 35.37 2.41
2928 4354 4.045022 AGGCCTGTTAGGGTATGTACAAT 58.955 43.478 3.11 0.00 35.37 2.71
2929 4355 4.134563 GGCCTGTTAGGGTATGTACAATG 58.865 47.826 0.00 0.00 35.37 2.82
2930 4356 4.134563 GCCTGTTAGGGTATGTACAATGG 58.865 47.826 0.00 0.00 35.37 3.16
2931 4357 4.384868 GCCTGTTAGGGTATGTACAATGGT 60.385 45.833 0.00 0.00 35.37 3.55
2932 4358 5.751586 CCTGTTAGGGTATGTACAATGGTT 58.248 41.667 0.00 0.00 0.00 3.67
2933 4359 5.588648 CCTGTTAGGGTATGTACAATGGTTG 59.411 44.000 0.00 0.00 0.00 3.77
2934 4360 6.375830 TGTTAGGGTATGTACAATGGTTGA 57.624 37.500 0.00 0.00 0.00 3.18
2935 4361 6.964464 TGTTAGGGTATGTACAATGGTTGAT 58.036 36.000 0.00 0.00 0.00 2.57
2936 4362 8.091952 TGTTAGGGTATGTACAATGGTTGATA 57.908 34.615 0.00 0.00 0.00 2.15
2937 4363 8.549731 TGTTAGGGTATGTACAATGGTTGATAA 58.450 33.333 0.00 0.00 0.00 1.75
2938 4364 9.052759 GTTAGGGTATGTACAATGGTTGATAAG 57.947 37.037 0.00 0.00 0.00 1.73
2939 4365 7.446106 AGGGTATGTACAATGGTTGATAAGA 57.554 36.000 0.00 0.00 0.00 2.10
2940 4366 7.280356 AGGGTATGTACAATGGTTGATAAGAC 58.720 38.462 0.00 0.00 0.00 3.01
2941 4367 7.051623 GGGTATGTACAATGGTTGATAAGACA 58.948 38.462 0.00 0.00 0.00 3.41
2942 4368 7.226720 GGGTATGTACAATGGTTGATAAGACAG 59.773 40.741 0.00 0.00 0.00 3.51
2943 4369 7.769044 GGTATGTACAATGGTTGATAAGACAGT 59.231 37.037 0.00 0.00 0.00 3.55
2944 4370 9.811995 GTATGTACAATGGTTGATAAGACAGTA 57.188 33.333 0.00 0.00 0.00 2.74
2946 4372 9.905713 ATGTACAATGGTTGATAAGACAGTATT 57.094 29.630 0.00 0.00 0.00 1.89
2977 4403 8.780846 AAATCTTGCATGCAATTTAAAGATGA 57.219 26.923 31.96 21.68 35.22 2.92
2978 4404 7.766219 ATCTTGCATGCAATTTAAAGATGAC 57.234 32.000 31.96 0.00 34.09 3.06
2979 4405 6.689554 TCTTGCATGCAATTTAAAGATGACA 58.310 32.000 31.96 6.17 35.20 3.58
2980 4406 7.153315 TCTTGCATGCAATTTAAAGATGACAA 58.847 30.769 31.96 5.49 35.20 3.18
2981 4407 7.656542 TCTTGCATGCAATTTAAAGATGACAAA 59.343 29.630 31.96 5.09 35.20 2.83
2982 4408 7.725818 TGCATGCAATTTAAAGATGACAAAA 57.274 28.000 20.30 0.00 0.00 2.44
2983 4409 8.151141 TGCATGCAATTTAAAGATGACAAAAA 57.849 26.923 20.30 0.00 0.00 1.94
3004 4430 5.418310 AAAACCGTCTACAACAAGTCATG 57.582 39.130 0.00 0.00 0.00 3.07
3005 4431 3.746045 ACCGTCTACAACAAGTCATGT 57.254 42.857 0.00 0.00 46.82 3.21
3006 4432 3.650139 ACCGTCTACAACAAGTCATGTC 58.350 45.455 0.00 0.00 42.99 3.06
3007 4433 3.321111 ACCGTCTACAACAAGTCATGTCT 59.679 43.478 0.00 0.00 42.99 3.41
3008 4434 4.202223 ACCGTCTACAACAAGTCATGTCTT 60.202 41.667 0.00 0.00 42.99 3.01
3009 4435 5.010314 ACCGTCTACAACAAGTCATGTCTTA 59.990 40.000 4.85 0.00 42.99 2.10
3010 4436 5.573282 CCGTCTACAACAAGTCATGTCTTAG 59.427 44.000 4.85 0.00 42.99 2.18
3011 4437 6.150318 CGTCTACAACAAGTCATGTCTTAGT 58.850 40.000 4.85 7.21 42.99 2.24
3012 4438 6.305877 CGTCTACAACAAGTCATGTCTTAGTC 59.694 42.308 4.85 0.00 42.99 2.59
3013 4439 7.371936 GTCTACAACAAGTCATGTCTTAGTCT 58.628 38.462 4.85 0.18 42.99 3.24
3014 4440 7.868415 GTCTACAACAAGTCATGTCTTAGTCTT 59.132 37.037 4.85 1.36 42.99 3.01
3015 4441 9.074576 TCTACAACAAGTCATGTCTTAGTCTTA 57.925 33.333 4.85 2.21 42.99 2.10
3016 4442 9.862371 CTACAACAAGTCATGTCTTAGTCTTAT 57.138 33.333 4.85 0.00 42.99 1.73
3018 4444 9.561069 ACAACAAGTCATGTCTTAGTCTTATTT 57.439 29.630 4.85 0.00 42.99 1.40
3053 4479 8.910351 AGCTATTCCTAAAAATATGGTGAGAC 57.090 34.615 0.00 0.00 0.00 3.36
3054 4480 8.494433 AGCTATTCCTAAAAATATGGTGAGACA 58.506 33.333 0.00 0.00 0.00 3.41
3055 4481 9.289782 GCTATTCCTAAAAATATGGTGAGACAT 57.710 33.333 0.00 0.00 34.90 3.06
3066 4492 8.613060 AATATGGTGAGACATATTGTGCTAAG 57.387 34.615 9.82 0.00 46.68 2.18
3067 4493 5.675684 TGGTGAGACATATTGTGCTAAGA 57.324 39.130 0.00 0.00 0.00 2.10
3068 4494 5.664457 TGGTGAGACATATTGTGCTAAGAG 58.336 41.667 0.00 0.00 0.00 2.85
3069 4495 5.422012 TGGTGAGACATATTGTGCTAAGAGA 59.578 40.000 0.00 0.00 0.00 3.10
3070 4496 6.098838 TGGTGAGACATATTGTGCTAAGAGAT 59.901 38.462 0.00 0.00 0.00 2.75
3071 4497 6.644592 GGTGAGACATATTGTGCTAAGAGATC 59.355 42.308 0.00 0.00 0.00 2.75
3072 4498 7.205992 GTGAGACATATTGTGCTAAGAGATCA 58.794 38.462 0.00 0.00 0.00 2.92
3073 4499 7.871973 GTGAGACATATTGTGCTAAGAGATCAT 59.128 37.037 0.00 0.00 0.00 2.45
3074 4500 8.087136 TGAGACATATTGTGCTAAGAGATCATC 58.913 37.037 0.00 0.00 0.00 2.92
3075 4501 8.192743 AGACATATTGTGCTAAGAGATCATCT 57.807 34.615 0.00 0.00 41.27 2.90
3076 4502 8.306038 AGACATATTGTGCTAAGAGATCATCTC 58.694 37.037 6.55 6.55 43.70 2.75
3120 4546 8.300495 GAGAAGACAAATCTTTTCTTACGAGT 57.700 34.615 0.00 0.00 45.60 4.18
3121 4547 8.664211 AGAAGACAAATCTTTTCTTACGAGTT 57.336 30.769 0.00 0.00 45.60 3.01
3122 4548 9.110502 AGAAGACAAATCTTTTCTTACGAGTTT 57.889 29.630 0.00 0.00 45.60 2.66
3123 4549 9.717892 GAAGACAAATCTTTTCTTACGAGTTTT 57.282 29.630 0.00 0.00 45.60 2.43
3124 4550 9.717892 AAGACAAATCTTTTCTTACGAGTTTTC 57.282 29.630 0.00 0.00 42.91 2.29
3125 4551 9.110502 AGACAAATCTTTTCTTACGAGTTTTCT 57.889 29.630 0.00 0.00 0.00 2.52
3126 4552 9.371333 GACAAATCTTTTCTTACGAGTTTTCTC 57.629 33.333 0.00 0.00 43.01 2.87
3127 4553 9.110502 ACAAATCTTTTCTTACGAGTTTTCTCT 57.889 29.630 0.00 0.00 44.16 3.10
3128 4554 9.587461 CAAATCTTTTCTTACGAGTTTTCTCTC 57.413 33.333 0.00 0.00 44.16 3.20
3129 4555 7.892778 ATCTTTTCTTACGAGTTTTCTCTCC 57.107 36.000 0.00 0.00 44.16 3.71
3130 4556 7.052142 TCTTTTCTTACGAGTTTTCTCTCCT 57.948 36.000 0.00 0.00 44.16 3.69
3131 4557 7.146648 TCTTTTCTTACGAGTTTTCTCTCCTC 58.853 38.462 0.00 0.00 44.16 3.71
3132 4558 5.388408 TTCTTACGAGTTTTCTCTCCTCC 57.612 43.478 0.00 0.00 44.16 4.30
3133 4559 4.404640 TCTTACGAGTTTTCTCTCCTCCA 58.595 43.478 0.00 0.00 44.16 3.86
3134 4560 4.217983 TCTTACGAGTTTTCTCTCCTCCAC 59.782 45.833 0.00 0.00 44.16 4.02
3135 4561 1.619332 ACGAGTTTTCTCTCCTCCACC 59.381 52.381 0.00 0.00 44.16 4.61
3136 4562 1.896465 CGAGTTTTCTCTCCTCCACCT 59.104 52.381 0.00 0.00 44.16 4.00
3137 4563 2.094442 CGAGTTTTCTCTCCTCCACCTC 60.094 54.545 0.00 0.00 44.16 3.85
3138 4564 2.900546 GAGTTTTCTCTCCTCCACCTCA 59.099 50.000 0.00 0.00 43.12 3.86
3139 4565 3.517500 GAGTTTTCTCTCCTCCACCTCAT 59.482 47.826 0.00 0.00 43.12 2.90
3140 4566 3.517500 AGTTTTCTCTCCTCCACCTCATC 59.482 47.826 0.00 0.00 0.00 2.92
3141 4567 2.928036 TTCTCTCCTCCACCTCATCA 57.072 50.000 0.00 0.00 0.00 3.07
3142 4568 3.411454 TTCTCTCCTCCACCTCATCAT 57.589 47.619 0.00 0.00 0.00 2.45
3143 4569 3.411454 TCTCTCCTCCACCTCATCATT 57.589 47.619 0.00 0.00 0.00 2.57
3144 4570 3.729108 TCTCTCCTCCACCTCATCATTT 58.271 45.455 0.00 0.00 0.00 2.32
3145 4571 4.883759 TCTCTCCTCCACCTCATCATTTA 58.116 43.478 0.00 0.00 0.00 1.40
3146 4572 5.471424 TCTCTCCTCCACCTCATCATTTAT 58.529 41.667 0.00 0.00 0.00 1.40
3147 4573 5.907662 TCTCTCCTCCACCTCATCATTTATT 59.092 40.000 0.00 0.00 0.00 1.40
3148 4574 6.042552 TCTCTCCTCCACCTCATCATTTATTC 59.957 42.308 0.00 0.00 0.00 1.75
3149 4575 5.907662 TCTCCTCCACCTCATCATTTATTCT 59.092 40.000 0.00 0.00 0.00 2.40
3150 4576 7.075797 TCTCCTCCACCTCATCATTTATTCTA 58.924 38.462 0.00 0.00 0.00 2.10
3151 4577 7.015682 TCTCCTCCACCTCATCATTTATTCTAC 59.984 40.741 0.00 0.00 0.00 2.59
3152 4578 5.928839 CCTCCACCTCATCATTTATTCTACG 59.071 44.000 0.00 0.00 0.00 3.51
3153 4579 6.463049 CCTCCACCTCATCATTTATTCTACGT 60.463 42.308 0.00 0.00 0.00 3.57
3154 4580 6.280643 TCCACCTCATCATTTATTCTACGTG 58.719 40.000 0.00 0.00 0.00 4.49
3155 4581 5.466728 CCACCTCATCATTTATTCTACGTGG 59.533 44.000 0.00 0.00 0.00 4.94
3156 4582 5.050091 CACCTCATCATTTATTCTACGTGGC 60.050 44.000 0.00 0.00 0.00 5.01
3157 4583 5.056480 CCTCATCATTTATTCTACGTGGCA 58.944 41.667 0.00 0.00 0.00 4.92
3158 4584 5.050091 CCTCATCATTTATTCTACGTGGCAC 60.050 44.000 7.79 7.79 0.00 5.01
3159 4585 5.670485 TCATCATTTATTCTACGTGGCACT 58.330 37.500 16.72 5.47 0.00 4.40
3160 4586 5.753438 TCATCATTTATTCTACGTGGCACTC 59.247 40.000 16.72 0.00 0.00 3.51
3161 4587 4.439057 TCATTTATTCTACGTGGCACTCC 58.561 43.478 16.72 0.00 0.00 3.85
3162 4588 4.161565 TCATTTATTCTACGTGGCACTCCT 59.838 41.667 16.72 0.21 0.00 3.69
3163 4589 5.361571 TCATTTATTCTACGTGGCACTCCTA 59.638 40.000 16.72 1.46 0.00 2.94
3164 4590 5.664294 TTTATTCTACGTGGCACTCCTAA 57.336 39.130 16.72 5.50 0.00 2.69
3165 4591 3.802948 ATTCTACGTGGCACTCCTAAG 57.197 47.619 16.72 5.74 0.00 2.18
3166 4592 2.502142 TCTACGTGGCACTCCTAAGA 57.498 50.000 16.72 7.94 0.00 2.10
3167 4593 3.014304 TCTACGTGGCACTCCTAAGAT 57.986 47.619 16.72 0.00 0.00 2.40
3168 4594 4.160642 TCTACGTGGCACTCCTAAGATA 57.839 45.455 16.72 0.00 0.00 1.98
3169 4595 4.135306 TCTACGTGGCACTCCTAAGATAG 58.865 47.826 16.72 4.78 0.00 2.08
3170 4596 1.409427 ACGTGGCACTCCTAAGATAGC 59.591 52.381 16.72 0.00 0.00 2.97
3171 4597 1.409064 CGTGGCACTCCTAAGATAGCA 59.591 52.381 16.72 0.00 0.00 3.49
3172 4598 2.036475 CGTGGCACTCCTAAGATAGCAT 59.964 50.000 16.72 0.00 0.00 3.79
3173 4599 3.493350 CGTGGCACTCCTAAGATAGCATT 60.493 47.826 16.72 0.00 0.00 3.56
3174 4600 4.262036 CGTGGCACTCCTAAGATAGCATTA 60.262 45.833 16.72 0.00 0.00 1.90
3175 4601 5.567623 CGTGGCACTCCTAAGATAGCATTAT 60.568 44.000 16.72 0.00 0.00 1.28
3176 4602 6.234177 GTGGCACTCCTAAGATAGCATTATT 58.766 40.000 11.13 0.00 0.00 1.40
3177 4603 6.148480 GTGGCACTCCTAAGATAGCATTATTG 59.852 42.308 11.13 0.00 0.00 1.90
3178 4604 6.183361 TGGCACTCCTAAGATAGCATTATTGT 60.183 38.462 0.00 0.00 0.00 2.71
3179 4605 7.016170 TGGCACTCCTAAGATAGCATTATTGTA 59.984 37.037 0.00 0.00 0.00 2.41
3180 4606 7.332182 GGCACTCCTAAGATAGCATTATTGTAC 59.668 40.741 0.00 0.00 0.00 2.90
3181 4607 7.872993 GCACTCCTAAGATAGCATTATTGTACA 59.127 37.037 0.00 0.00 0.00 2.90
3182 4608 9.935241 CACTCCTAAGATAGCATTATTGTACAT 57.065 33.333 0.00 0.00 0.00 2.29
3183 4609 9.935241 ACTCCTAAGATAGCATTATTGTACATG 57.065 33.333 0.00 0.00 0.00 3.21
3184 4610 8.777865 TCCTAAGATAGCATTATTGTACATGC 57.222 34.615 10.53 10.53 45.30 4.06
3185 4611 7.824289 TCCTAAGATAGCATTATTGTACATGCC 59.176 37.037 14.08 1.71 45.99 4.40
3186 4612 6.824305 AAGATAGCATTATTGTACATGCCC 57.176 37.500 14.08 5.86 45.99 5.36
3249 4675 1.295423 CTGGTGGTACTCAACGGGG 59.705 63.158 0.00 0.00 35.82 5.73
3277 4703 2.439104 ATCTCCCTTGCGAGCCTCC 61.439 63.158 0.00 0.00 0.00 4.30
3278 4704 2.887738 ATCTCCCTTGCGAGCCTCCT 62.888 60.000 0.00 0.00 0.00 3.69
3279 4705 3.077556 TCCCTTGCGAGCCTCCTC 61.078 66.667 0.00 0.00 34.66 3.71
3294 4720 1.210204 TCCTCTTTCTGGCCCTGCAT 61.210 55.000 0.00 0.00 0.00 3.96
3301 4727 0.686441 TCTGGCCCTGCATACGTACT 60.686 55.000 0.00 0.00 0.00 2.73
3394 4820 1.002366 CTGGCGCAAGTACTCATGTC 58.998 55.000 10.83 0.00 41.68 3.06
3416 5011 2.476619 CTCTCACATTTCACACGTCACC 59.523 50.000 0.00 0.00 0.00 4.02
3430 5025 3.059257 CACGTCACCAGAGAGATCTATCG 60.059 52.174 11.56 6.91 0.00 2.92
3431 5026 3.135225 CGTCACCAGAGAGATCTATCGT 58.865 50.000 11.56 2.13 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.668469 AGGTCGAGGAAATTTTTGTTTACCTAT 59.332 33.333 9.15 0.00 28.32 2.57
35 36 2.394708 CATATAGCAACGGACAGGTCG 58.605 52.381 0.00 0.00 0.00 4.79
41 42 0.784778 GCTCGCATATAGCAACGGAC 59.215 55.000 0.00 0.00 46.13 4.79
49 50 1.723542 CCGCTTTGAGCTCGCATATAG 59.276 52.381 9.64 1.12 39.60 1.31
52 53 1.083806 CACCGCTTTGAGCTCGCATA 61.084 55.000 9.64 0.00 39.60 3.14
71 72 2.751259 GGGATTGGTCGTTAGGGTTTTC 59.249 50.000 0.00 0.00 0.00 2.29
74 75 0.622136 GGGGATTGGTCGTTAGGGTT 59.378 55.000 0.00 0.00 0.00 4.11
183 184 1.694150 TGAGAGATAAGCGAATGGGGG 59.306 52.381 0.00 0.00 0.00 5.40
188 189 7.611467 AGAGTAGATGATGAGAGATAAGCGAAT 59.389 37.037 0.00 0.00 0.00 3.34
195 196 7.450014 GGGTTTGAGAGTAGATGATGAGAGATA 59.550 40.741 0.00 0.00 0.00 1.98
210 211 6.183361 ACAACAACATACTAGGGTTTGAGAGT 60.183 38.462 0.00 0.00 0.00 3.24
212 213 6.182507 ACAACAACATACTAGGGTTTGAGA 57.817 37.500 0.00 0.00 0.00 3.27
216 217 5.240121 CGGTACAACAACATACTAGGGTTT 58.760 41.667 0.00 0.00 0.00 3.27
224 225 2.928116 GAGAGGCGGTACAACAACATAC 59.072 50.000 0.00 0.00 0.00 2.39
226 227 1.338769 GGAGAGGCGGTACAACAACAT 60.339 52.381 0.00 0.00 0.00 2.71
234 235 3.217743 CGGGAGGAGAGGCGGTAC 61.218 72.222 0.00 0.00 0.00 3.34
265 266 2.956333 GAGAGGAAGAAGCCTAGAGACC 59.044 54.545 0.00 0.00 38.73 3.85
309 310 7.094162 TGGGTCACTTATGCGATAATTGAAAAA 60.094 33.333 9.09 0.36 36.56 1.94
323 324 8.737168 TTTCTAGATTCATTGGGTCACTTATG 57.263 34.615 0.00 0.00 0.00 1.90
371 376 5.807011 ACGCTAAAATTCATGGAAGCATTTC 59.193 36.000 0.00 0.00 0.00 2.17
380 385 7.914871 TCATTGATTGTACGCTAAAATTCATGG 59.085 33.333 0.00 0.00 0.00 3.66
383 388 7.811653 TGTCATTGATTGTACGCTAAAATTCA 58.188 30.769 0.00 0.00 0.00 2.57
412 417 9.804758 GTGCTCTAAGTATTACACATCTAAGTT 57.195 33.333 0.00 0.00 28.84 2.66
457 462 9.830975 TTTGCTAAAACATATCTAGATGTGCTA 57.169 29.630 24.68 14.58 39.99 3.49
458 463 8.737168 TTTGCTAAAACATATCTAGATGTGCT 57.263 30.769 24.68 13.40 39.99 4.40
528 533 1.137872 CACATGACAGGAGGAGGTAGC 59.862 57.143 0.00 0.00 0.00 3.58
664 669 8.130307 AGTTATTTGCATGTCACAACTTTTTC 57.870 30.769 0.00 0.00 0.00 2.29
747 752 5.527214 TCGATCATAAGCAATTCATCCGTTT 59.473 36.000 0.00 0.00 0.00 3.60
764 769 4.274214 ACATTTGCGATGTTCATCGATCAT 59.726 37.500 30.58 18.13 46.12 2.45
769 774 2.841907 CACACATTTGCGATGTTCATCG 59.158 45.455 24.77 24.77 45.99 3.84
771 776 2.094597 CCCACACATTTGCGATGTTCAT 60.095 45.455 3.03 0.00 0.00 2.57
909 918 9.927081 AGAAGAAAATTGTATATCCATGGTTCT 57.073 29.630 12.58 6.37 0.00 3.01
912 921 9.136323 GGAAGAAGAAAATTGTATATCCATGGT 57.864 33.333 12.58 1.59 0.00 3.55
913 922 9.135189 TGGAAGAAGAAAATTGTATATCCATGG 57.865 33.333 4.97 4.97 0.00 3.66
1021 1033 8.344831 CACTGACTGACTGATTGATTTTAAACA 58.655 33.333 0.00 0.00 0.00 2.83
1167 1182 5.351465 CACAAGGCCGCATAATAATACTAGG 59.649 44.000 0.00 0.00 0.00 3.02
1171 1186 3.252215 TGCACAAGGCCGCATAATAATAC 59.748 43.478 0.00 0.00 43.89 1.89
1233 1248 7.625828 TTGAACAGATAGAAGATCAGTACGA 57.374 36.000 0.00 0.00 0.00 3.43
1234 1249 8.864069 ATTTGAACAGATAGAAGATCAGTACG 57.136 34.615 0.00 0.00 0.00 3.67
1261 1276 6.183360 TGTTCCTGATCCAGATATCTTGTGAG 60.183 42.308 1.33 0.00 32.44 3.51
1276 1291 3.294214 AGAATGGCCATTGTTCCTGATC 58.706 45.455 35.31 17.26 0.00 2.92
1910 1937 3.330853 GATGCCGCGATCACGTCC 61.331 66.667 8.23 0.00 41.98 4.79
1955 1982 0.385390 CCTTGTTGTGGTTGGTCAGC 59.615 55.000 0.00 0.00 0.00 4.26
1999 2026 2.799371 CCCTGTCGTCCTCGTAGC 59.201 66.667 0.00 0.00 38.33 3.58
2150 3483 0.318360 TAAGTATGGTCGGCGATGCG 60.318 55.000 14.79 0.00 0.00 4.73
2231 3564 2.192608 AAGACGAGGGCACGACGTAC 62.193 60.000 13.42 0.00 40.29 3.67
2233 3566 1.310933 ATAAGACGAGGGCACGACGT 61.311 55.000 13.33 13.33 42.84 4.34
2234 3567 0.866061 CATAAGACGAGGGCACGACG 60.866 60.000 9.99 7.02 37.03 5.12
2269 3607 0.108472 TGCAGAGATGGCAGAGTTCG 60.108 55.000 0.00 0.00 36.11 3.95
2316 3654 0.320247 ACTTCTGCCACTCGCTCTTG 60.320 55.000 0.00 0.00 38.78 3.02
2499 3837 1.227497 GCCTAGAGCGCTTCAGCAT 60.227 57.895 13.26 0.00 42.21 3.79
2511 3849 2.783609 ACGTGACTGTCTAGCCTAGA 57.216 50.000 9.51 0.00 0.00 2.43
2512 3850 3.794717 TCTACGTGACTGTCTAGCCTAG 58.205 50.000 9.51 0.00 0.00 3.02
2513 3851 3.900966 TCTACGTGACTGTCTAGCCTA 57.099 47.619 9.51 0.00 0.00 3.93
2514 3852 2.783609 TCTACGTGACTGTCTAGCCT 57.216 50.000 9.51 0.00 0.00 4.58
2517 3876 6.418226 GCCATTTATTCTACGTGACTGTCTAG 59.582 42.308 9.51 5.54 0.00 2.43
2520 3879 4.270325 GGCCATTTATTCTACGTGACTGTC 59.730 45.833 0.00 0.00 0.00 3.51
2522 3881 4.034048 GTGGCCATTTATTCTACGTGACTG 59.966 45.833 9.72 0.00 0.00 3.51
2525 3884 3.055021 TGGTGGCCATTTATTCTACGTGA 60.055 43.478 9.72 0.00 0.00 4.35
2539 3898 0.907704 AGAATCCTACGTGGTGGCCA 60.908 55.000 0.00 0.00 37.07 5.36
2551 3910 5.774690 TGCAGTGGACAAATAAAAGAATCCT 59.225 36.000 0.00 0.00 0.00 3.24
2566 3925 0.390472 GCTCTACTGGTGCAGTGGAC 60.390 60.000 6.17 6.17 44.71 4.02
2596 3955 9.462606 AAATCAAGTATAACCTACTTTTCCCAG 57.537 33.333 0.00 0.00 35.76 4.45
2598 3957 9.239551 ACAAATCAAGTATAACCTACTTTTCCC 57.760 33.333 0.00 0.00 35.76 3.97
2628 3987 3.195825 AGGACGTTACAGAGGAGGAATTG 59.804 47.826 0.00 0.00 0.00 2.32
2643 4002 2.888414 CCACCCAAATTTGTAGGACGTT 59.112 45.455 16.73 0.00 0.00 3.99
2644 4003 2.158579 ACCACCCAAATTTGTAGGACGT 60.159 45.455 20.88 12.78 0.00 4.34
2659 4020 7.122650 TCAATATTCAAGATTCTCAAACCACCC 59.877 37.037 0.00 0.00 0.00 4.61
2669 4030 8.579006 TGCAAACTTGTCAATATTCAAGATTCT 58.421 29.630 18.76 0.02 42.22 2.40
2670 4031 8.642020 GTGCAAACTTGTCAATATTCAAGATTC 58.358 33.333 18.76 10.51 42.22 2.52
2675 4036 5.218885 CCGTGCAAACTTGTCAATATTCAA 58.781 37.500 0.00 0.00 0.00 2.69
2678 4039 3.613910 GCCCGTGCAAACTTGTCAATATT 60.614 43.478 0.00 0.00 37.47 1.28
2698 4059 5.177696 CCATAACTATCGCAGACTTAAAGCC 59.822 44.000 0.00 0.00 42.51 4.35
2706 4067 3.802685 GGTGAACCATAACTATCGCAGAC 59.197 47.826 0.00 0.00 35.72 3.51
2707 4068 3.704566 AGGTGAACCATAACTATCGCAGA 59.295 43.478 1.62 0.00 39.18 4.26
2711 4072 4.665833 TCCAGGTGAACCATAACTATCG 57.334 45.455 1.62 0.00 38.89 2.92
2715 4076 3.054361 GTCCATCCAGGTGAACCATAACT 60.054 47.826 1.62 0.00 38.89 2.24
2739 4100 3.219198 GACCAATCCATGCCCGCC 61.219 66.667 0.00 0.00 0.00 6.13
2834 4198 4.681942 GGACAACCGATCGATCTAATCAAG 59.318 45.833 22.43 5.62 0.00 3.02
2866 4230 1.302949 GCCCTAGAACCACCATGCA 59.697 57.895 0.00 0.00 0.00 3.96
2869 4233 3.043999 GCGGCCCTAGAACCACCAT 62.044 63.158 0.00 0.00 0.00 3.55
2875 4239 2.202946 GAGCAGCGGCCCTAGAAC 60.203 66.667 4.82 0.00 42.56 3.01
2895 4321 4.718276 CCCTAACAGGCCTAGGTAAGTTTA 59.282 45.833 17.28 1.76 35.10 2.01
2913 4339 8.994500 TCTTATCAACCATTGTACATACCCTAA 58.006 33.333 0.00 0.00 0.00 2.69
2914 4340 8.426489 GTCTTATCAACCATTGTACATACCCTA 58.574 37.037 0.00 0.00 0.00 3.53
2915 4341 7.092623 TGTCTTATCAACCATTGTACATACCCT 60.093 37.037 0.00 0.00 0.00 4.34
2916 4342 7.051623 TGTCTTATCAACCATTGTACATACCC 58.948 38.462 0.00 0.00 0.00 3.69
2917 4343 7.769044 ACTGTCTTATCAACCATTGTACATACC 59.231 37.037 0.00 0.00 0.00 2.73
2918 4344 8.718102 ACTGTCTTATCAACCATTGTACATAC 57.282 34.615 0.00 0.00 0.00 2.39
2920 4346 9.905713 AATACTGTCTTATCAACCATTGTACAT 57.094 29.630 0.00 0.00 0.00 2.29
2951 4377 9.872721 TCATCTTTAAATTGCATGCAAGATTTA 57.127 25.926 34.15 28.96 39.47 1.40
2952 4378 8.662141 GTCATCTTTAAATTGCATGCAAGATTT 58.338 29.630 34.15 29.87 39.47 2.17
2953 4379 7.820386 TGTCATCTTTAAATTGCATGCAAGATT 59.180 29.630 34.15 30.21 39.47 2.40
2954 4380 7.324935 TGTCATCTTTAAATTGCATGCAAGAT 58.675 30.769 34.15 26.49 39.47 2.40
2955 4381 6.689554 TGTCATCTTTAAATTGCATGCAAGA 58.310 32.000 34.15 25.56 39.47 3.02
2956 4382 6.954616 TGTCATCTTTAAATTGCATGCAAG 57.045 33.333 34.15 21.48 39.47 4.01
2957 4383 7.725818 TTTGTCATCTTTAAATTGCATGCAA 57.274 28.000 33.57 33.57 40.47 4.08
2958 4384 7.725818 TTTTGTCATCTTTAAATTGCATGCA 57.274 28.000 18.46 18.46 0.00 3.96
2981 4407 5.355910 ACATGACTTGTTGTAGACGGTTTTT 59.644 36.000 0.00 0.00 33.74 1.94
2982 4408 4.879545 ACATGACTTGTTGTAGACGGTTTT 59.120 37.500 0.00 0.00 33.74 2.43
2983 4409 4.448210 ACATGACTTGTTGTAGACGGTTT 58.552 39.130 0.00 0.00 33.74 3.27
2984 4410 4.056050 GACATGACTTGTTGTAGACGGTT 58.944 43.478 0.00 0.00 39.18 4.44
2985 4411 3.321111 AGACATGACTTGTTGTAGACGGT 59.679 43.478 0.00 0.00 39.18 4.83
2986 4412 3.914312 AGACATGACTTGTTGTAGACGG 58.086 45.455 0.00 0.00 39.18 4.79
2987 4413 6.150318 ACTAAGACATGACTTGTTGTAGACG 58.850 40.000 18.80 0.00 39.18 4.18
2988 4414 7.371936 AGACTAAGACATGACTTGTTGTAGAC 58.628 38.462 18.80 9.11 39.18 2.59
2989 4415 7.526142 AGACTAAGACATGACTTGTTGTAGA 57.474 36.000 18.80 0.00 39.18 2.59
2990 4416 9.862371 ATAAGACTAAGACATGACTTGTTGTAG 57.138 33.333 18.80 10.88 39.18 2.74
2992 4418 9.561069 AAATAAGACTAAGACATGACTTGTTGT 57.439 29.630 18.80 14.18 39.18 3.32
3027 4453 9.998106 GTCTCACCATATTTTTAGGAATAGCTA 57.002 33.333 0.00 0.00 0.00 3.32
3028 4454 8.494433 TGTCTCACCATATTTTTAGGAATAGCT 58.506 33.333 0.00 0.00 0.00 3.32
3029 4455 8.677148 TGTCTCACCATATTTTTAGGAATAGC 57.323 34.615 0.00 0.00 0.00 2.97
3036 4462 9.669353 GCACAATATGTCTCACCATATTTTTAG 57.331 33.333 4.17 0.00 42.54 1.85
3037 4463 9.407380 AGCACAATATGTCTCACCATATTTTTA 57.593 29.630 4.17 0.00 42.54 1.52
3038 4464 8.297470 AGCACAATATGTCTCACCATATTTTT 57.703 30.769 4.17 0.00 42.54 1.94
3039 4465 7.886629 AGCACAATATGTCTCACCATATTTT 57.113 32.000 4.17 0.00 42.54 1.82
3040 4466 8.978874 TTAGCACAATATGTCTCACCATATTT 57.021 30.769 4.17 0.00 42.54 1.40
3041 4467 8.432013 TCTTAGCACAATATGTCTCACCATATT 58.568 33.333 0.00 0.00 44.78 1.28
3042 4468 7.966812 TCTTAGCACAATATGTCTCACCATAT 58.033 34.615 0.00 0.00 39.20 1.78
3043 4469 7.287696 TCTCTTAGCACAATATGTCTCACCATA 59.712 37.037 0.00 0.00 0.00 2.74
3044 4470 6.098838 TCTCTTAGCACAATATGTCTCACCAT 59.901 38.462 0.00 0.00 0.00 3.55
3045 4471 5.422012 TCTCTTAGCACAATATGTCTCACCA 59.578 40.000 0.00 0.00 0.00 4.17
3046 4472 5.907207 TCTCTTAGCACAATATGTCTCACC 58.093 41.667 0.00 0.00 0.00 4.02
3047 4473 7.205992 TGATCTCTTAGCACAATATGTCTCAC 58.794 38.462 0.00 0.00 0.00 3.51
3048 4474 7.352079 TGATCTCTTAGCACAATATGTCTCA 57.648 36.000 0.00 0.00 0.00 3.27
3049 4475 8.306038 AGATGATCTCTTAGCACAATATGTCTC 58.694 37.037 0.00 0.00 0.00 3.36
3050 4476 8.192743 AGATGATCTCTTAGCACAATATGTCT 57.807 34.615 0.00 0.00 0.00 3.41
3051 4477 8.464770 GAGATGATCTCTTAGCACAATATGTC 57.535 38.462 14.98 0.00 40.30 3.06
3112 4538 4.487019 GTGGAGGAGAGAAAACTCGTAAG 58.513 47.826 0.00 0.00 37.74 2.34
3113 4539 3.257624 GGTGGAGGAGAGAAAACTCGTAA 59.742 47.826 0.00 0.00 37.74 3.18
3114 4540 2.824341 GGTGGAGGAGAGAAAACTCGTA 59.176 50.000 0.00 0.00 37.74 3.43
3115 4541 1.619332 GGTGGAGGAGAGAAAACTCGT 59.381 52.381 0.00 0.00 37.74 4.18
3116 4542 1.896465 AGGTGGAGGAGAGAAAACTCG 59.104 52.381 0.00 0.00 37.74 4.18
3117 4543 2.900546 TGAGGTGGAGGAGAGAAAACTC 59.099 50.000 0.00 0.00 36.31 3.01
3118 4544 2.977808 TGAGGTGGAGGAGAGAAAACT 58.022 47.619 0.00 0.00 0.00 2.66
3119 4545 3.261897 TGATGAGGTGGAGGAGAGAAAAC 59.738 47.826 0.00 0.00 0.00 2.43
3120 4546 3.520696 TGATGAGGTGGAGGAGAGAAAA 58.479 45.455 0.00 0.00 0.00 2.29
3121 4547 3.190383 TGATGAGGTGGAGGAGAGAAA 57.810 47.619 0.00 0.00 0.00 2.52
3122 4548 2.928036 TGATGAGGTGGAGGAGAGAA 57.072 50.000 0.00 0.00 0.00 2.87
3123 4549 3.411454 AATGATGAGGTGGAGGAGAGA 57.589 47.619 0.00 0.00 0.00 3.10
3124 4550 5.822132 ATAAATGATGAGGTGGAGGAGAG 57.178 43.478 0.00 0.00 0.00 3.20
3125 4551 5.907662 AGAATAAATGATGAGGTGGAGGAGA 59.092 40.000 0.00 0.00 0.00 3.71
3126 4552 6.185114 AGAATAAATGATGAGGTGGAGGAG 57.815 41.667 0.00 0.00 0.00 3.69
3127 4553 6.239317 CGTAGAATAAATGATGAGGTGGAGGA 60.239 42.308 0.00 0.00 0.00 3.71
3128 4554 5.928839 CGTAGAATAAATGATGAGGTGGAGG 59.071 44.000 0.00 0.00 0.00 4.30
3129 4555 6.422100 CACGTAGAATAAATGATGAGGTGGAG 59.578 42.308 0.00 0.00 0.00 3.86
3130 4556 6.280643 CACGTAGAATAAATGATGAGGTGGA 58.719 40.000 0.00 0.00 0.00 4.02
3131 4557 5.466728 CCACGTAGAATAAATGATGAGGTGG 59.533 44.000 0.00 0.00 34.75 4.61
3132 4558 5.050091 GCCACGTAGAATAAATGATGAGGTG 60.050 44.000 0.00 0.00 0.00 4.00
3133 4559 5.057149 GCCACGTAGAATAAATGATGAGGT 58.943 41.667 0.00 0.00 0.00 3.85
3134 4560 5.050091 GTGCCACGTAGAATAAATGATGAGG 60.050 44.000 0.00 0.00 0.00 3.86
3135 4561 5.755375 AGTGCCACGTAGAATAAATGATGAG 59.245 40.000 0.00 0.00 0.00 2.90
3136 4562 5.670485 AGTGCCACGTAGAATAAATGATGA 58.330 37.500 0.00 0.00 0.00 2.92
3137 4563 5.050091 GGAGTGCCACGTAGAATAAATGATG 60.050 44.000 0.00 0.00 0.00 3.07
3138 4564 5.057149 GGAGTGCCACGTAGAATAAATGAT 58.943 41.667 0.00 0.00 0.00 2.45
3139 4565 4.161565 AGGAGTGCCACGTAGAATAAATGA 59.838 41.667 0.00 0.00 36.29 2.57
3140 4566 4.442706 AGGAGTGCCACGTAGAATAAATG 58.557 43.478 0.00 0.00 36.29 2.32
3141 4567 4.755266 AGGAGTGCCACGTAGAATAAAT 57.245 40.909 0.00 0.00 36.29 1.40
3142 4568 5.419788 TCTTAGGAGTGCCACGTAGAATAAA 59.580 40.000 0.00 0.00 36.29 1.40
3143 4569 4.951715 TCTTAGGAGTGCCACGTAGAATAA 59.048 41.667 0.00 0.00 36.29 1.40
3144 4570 4.529897 TCTTAGGAGTGCCACGTAGAATA 58.470 43.478 0.00 0.00 36.29 1.75
3145 4571 3.362706 TCTTAGGAGTGCCACGTAGAAT 58.637 45.455 0.00 0.00 36.29 2.40
3146 4572 2.799017 TCTTAGGAGTGCCACGTAGAA 58.201 47.619 0.00 0.00 36.29 2.10
3147 4573 2.502142 TCTTAGGAGTGCCACGTAGA 57.498 50.000 0.00 0.00 36.29 2.59
3148 4574 3.304794 GCTATCTTAGGAGTGCCACGTAG 60.305 52.174 0.00 0.00 36.29 3.51
3149 4575 2.621998 GCTATCTTAGGAGTGCCACGTA 59.378 50.000 0.00 0.00 36.29 3.57
3150 4576 1.409427 GCTATCTTAGGAGTGCCACGT 59.591 52.381 0.00 0.00 36.29 4.49
3151 4577 1.409064 TGCTATCTTAGGAGTGCCACG 59.591 52.381 0.00 0.00 36.29 4.94
3152 4578 3.760580 ATGCTATCTTAGGAGTGCCAC 57.239 47.619 0.00 0.00 36.29 5.01
3153 4579 6.183361 ACAATAATGCTATCTTAGGAGTGCCA 60.183 38.462 0.00 0.00 36.29 4.92
3154 4580 6.234177 ACAATAATGCTATCTTAGGAGTGCC 58.766 40.000 0.70 0.00 0.00 5.01
3155 4581 7.872993 TGTACAATAATGCTATCTTAGGAGTGC 59.127 37.037 0.00 0.00 0.00 4.40
3156 4582 9.935241 ATGTACAATAATGCTATCTTAGGAGTG 57.065 33.333 0.00 0.00 0.00 3.51
3157 4583 9.935241 CATGTACAATAATGCTATCTTAGGAGT 57.065 33.333 0.00 0.00 0.00 3.85
3158 4584 8.877779 GCATGTACAATAATGCTATCTTAGGAG 58.122 37.037 11.12 0.00 44.64 3.69
3159 4585 7.824289 GGCATGTACAATAATGCTATCTTAGGA 59.176 37.037 16.47 0.00 46.72 2.94
3160 4586 7.066284 GGGCATGTACAATAATGCTATCTTAGG 59.934 40.741 16.47 0.00 46.72 2.69
3161 4587 7.826252 AGGGCATGTACAATAATGCTATCTTAG 59.174 37.037 16.47 0.00 46.72 2.18
3162 4588 7.689299 AGGGCATGTACAATAATGCTATCTTA 58.311 34.615 16.47 0.00 46.72 2.10
3163 4589 6.546484 AGGGCATGTACAATAATGCTATCTT 58.454 36.000 16.47 0.00 46.72 2.40
3164 4590 6.131972 AGGGCATGTACAATAATGCTATCT 57.868 37.500 16.47 10.22 46.72 1.98
3165 4591 6.824305 AAGGGCATGTACAATAATGCTATC 57.176 37.500 16.47 8.57 46.72 2.08
3166 4592 7.340232 CCATAAGGGCATGTACAATAATGCTAT 59.660 37.037 16.47 6.42 46.72 2.97
3167 4593 6.658816 CCATAAGGGCATGTACAATAATGCTA 59.341 38.462 16.47 4.64 46.72 3.49
3168 4594 5.477984 CCATAAGGGCATGTACAATAATGCT 59.522 40.000 16.47 2.77 46.72 3.79
3169 4595 5.243730 ACCATAAGGGCATGTACAATAATGC 59.756 40.000 10.12 10.12 46.80 3.56
3170 4596 6.348458 CGACCATAAGGGCATGTACAATAATG 60.348 42.308 0.00 0.00 46.60 1.90
3171 4597 5.705441 CGACCATAAGGGCATGTACAATAAT 59.295 40.000 0.00 0.00 46.60 1.28
3172 4598 5.060506 CGACCATAAGGGCATGTACAATAA 58.939 41.667 0.00 0.00 46.60 1.40
3173 4599 4.345547 TCGACCATAAGGGCATGTACAATA 59.654 41.667 0.00 0.00 46.60 1.90
3174 4600 3.135712 TCGACCATAAGGGCATGTACAAT 59.864 43.478 0.00 0.00 46.60 2.71
3175 4601 2.502130 TCGACCATAAGGGCATGTACAA 59.498 45.455 0.00 0.00 46.60 2.41
3176 4602 2.112190 TCGACCATAAGGGCATGTACA 58.888 47.619 0.00 0.00 46.60 2.90
3177 4603 2.902705 TCGACCATAAGGGCATGTAC 57.097 50.000 0.00 0.00 46.60 2.90
3178 4604 2.029380 CGATCGACCATAAGGGCATGTA 60.029 50.000 10.26 0.00 46.60 2.29
3179 4605 1.270305 CGATCGACCATAAGGGCATGT 60.270 52.381 10.26 0.00 46.60 3.21
3180 4606 1.432514 CGATCGACCATAAGGGCATG 58.567 55.000 10.26 0.00 46.60 4.06
3181 4607 0.321671 CCGATCGACCATAAGGGCAT 59.678 55.000 18.66 0.00 46.60 4.40
3182 4608 1.745890 CCGATCGACCATAAGGGCA 59.254 57.895 18.66 0.00 46.60 5.36
3183 4609 1.004918 CCCGATCGACCATAAGGGC 60.005 63.158 18.66 0.00 42.05 5.19
3184 4610 1.004918 GCCCGATCGACCATAAGGG 60.005 63.158 18.66 7.58 44.81 3.95
3185 4611 0.319900 CAGCCCGATCGACCATAAGG 60.320 60.000 18.66 8.38 42.21 2.69
3186 4612 0.319900 CCAGCCCGATCGACCATAAG 60.320 60.000 18.66 0.00 0.00 1.73
3263 4689 2.190488 AAAGAGGAGGCTCGCAAGGG 62.190 60.000 8.69 0.00 44.72 3.95
3277 4703 1.673168 GTATGCAGGGCCAGAAAGAG 58.327 55.000 6.18 0.00 0.00 2.85
3278 4704 0.107703 CGTATGCAGGGCCAGAAAGA 60.108 55.000 6.18 0.00 0.00 2.52
3279 4705 0.392998 ACGTATGCAGGGCCAGAAAG 60.393 55.000 6.18 0.00 0.00 2.62
3294 4720 4.626042 GACCGAGGAATCTCTAGTACGTA 58.374 47.826 0.00 0.00 37.86 3.57
3301 4727 0.183014 AGCCGACCGAGGAATCTCTA 59.817 55.000 0.00 0.00 37.86 2.43
3364 4790 0.104855 TTGCGCCAGGCTAGATGTAG 59.895 55.000 10.54 0.00 44.05 2.74
3378 4804 1.134965 AGAGGACATGAGTACTTGCGC 60.135 52.381 0.00 0.00 39.69 6.09
3394 4820 2.476619 GTGACGTGTGAAATGTGAGAGG 59.523 50.000 0.00 0.00 0.00 3.69
3416 5011 8.989653 TGTAGTATACACGATAGATCTCTCTG 57.010 38.462 0.00 2.57 46.14 3.35


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

AutoCloner maintained by Alex Coulton.