Multiple sequence alignment - TraesCS2B01G178400

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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 TraesCS2B01G178400 chr2B 100.000 4279 0 0 1 4279 153584725 153589003 0.000000e+00 7902.0
1 TraesCS2B01G178400 chr2B 85.061 328 25 12 1526 1837 281527548 281527867 3.210000e-81 313.0
2 TraesCS2B01G178400 chr2B 85.356 239 15 8 945 1168 281527200 281527433 3.330000e-56 230.0
3 TraesCS2B01G178400 chr2A 88.421 2064 181 32 1479 3513 101377956 101379990 0.000000e+00 2435.0
4 TraesCS2B01G178400 chr2A 88.046 778 79 3 3516 4279 20898892 20898115 0.000000e+00 909.0
5 TraesCS2B01G178400 chr2A 87.879 693 70 8 3601 4279 20868651 20867959 0.000000e+00 802.0
6 TraesCS2B01G178400 chr2A 80.672 714 52 31 422 1110 101377008 101377660 3.870000e-130 475.0
7 TraesCS2B01G178400 chr2A 86.047 258 28 1 3592 3841 10489325 10489582 1.960000e-68 270.0
8 TraesCS2B01G178400 chr2A 89.437 142 6 5 82 223 101376634 101376766 2.050000e-38 171.0
9 TraesCS2B01G178400 chr2D 87.025 2158 174 46 1402 3516 102279694 102281788 0.000000e+00 2337.0
10 TraesCS2B01G178400 chr2D 85.772 745 37 21 389 1108 102278712 102279412 0.000000e+00 725.0
11 TraesCS2B01G178400 chr2D 85.043 234 18 6 3 223 102275849 102276078 5.570000e-54 222.0
12 TraesCS2B01G178400 chr2D 78.078 333 36 16 3034 3354 102282388 102282695 4.400000e-40 176.0
13 TraesCS2B01G178400 chr2D 96.610 59 2 0 232 290 102277300 102277358 9.790000e-17 99.0
14 TraesCS2B01G178400 chr6A 87.902 777 79 6 3516 4279 405890274 405889500 0.000000e+00 900.0
15 TraesCS2B01G178400 chr6A 83.990 406 48 12 1756 2156 555579211 555579604 1.450000e-99 374.0
16 TraesCS2B01G178400 chr6A 79.253 482 53 25 3843 4279 583024767 583024288 4.190000e-75 292.0
17 TraesCS2B01G178400 chr5A 87.500 776 76 9 3516 4279 444568789 444569555 0.000000e+00 876.0
18 TraesCS2B01G178400 chr5A 84.444 405 47 11 1756 2156 601236684 601237076 6.710000e-103 385.0
19 TraesCS2B01G178400 chr5B 87.347 490 48 7 3796 4279 360995536 360995055 2.250000e-152 549.0
20 TraesCS2B01G178400 chr5B 88.112 143 13 4 3844 3983 577939451 577939310 2.650000e-37 167.0
21 TraesCS2B01G178400 chr5B 89.333 75 8 0 3516 3590 41953987 41954061 1.270000e-15 95.3
22 TraesCS2B01G178400 chr1B 85.680 412 33 13 1526 1922 213407843 213407443 1.110000e-110 411.0
23 TraesCS2B01G178400 chr1B 84.841 409 47 10 1756 2159 338887256 338886858 8.620000e-107 398.0
24 TraesCS2B01G178400 chr1B 84.841 409 47 10 1756 2159 339079522 339079124 8.620000e-107 398.0
25 TraesCS2B01G178400 chr1B 80.907 419 54 16 1733 2141 427603368 427603770 1.490000e-79 307.0
26 TraesCS2B01G178400 chr1B 86.822 258 25 6 3592 3841 60344712 60344456 3.260000e-71 279.0
27 TraesCS2B01G178400 chr1B 92.810 153 3 4 945 1097 213408188 213408044 9.320000e-52 215.0
28 TraesCS2B01G178400 chr1B 91.549 71 6 0 3516 3586 100645517 100645447 9.790000e-17 99.0
29 TraesCS2B01G178400 chr3B 84.091 440 43 15 3843 4279 703847319 703846904 2.400000e-107 399.0
30 TraesCS2B01G178400 chr6B 84.597 409 48 10 1756 2159 42820674 42820276 4.010000e-105 392.0
31 TraesCS2B01G178400 chr6B 89.243 251 27 0 4022 4272 458013866 458014116 8.930000e-82 315.0
32 TraesCS2B01G178400 chr3A 89.535 258 25 2 4022 4279 667093863 667093608 4.130000e-85 326.0
33 TraesCS2B01G178400 chr6D 87.179 273 35 0 4007 4279 116915570 116915842 1.160000e-80 311.0
34 TraesCS2B01G178400 chr6D 85.659 258 29 5 3593 3842 42550324 42550067 9.120000e-67 265.0
35 TraesCS2B01G178400 chr7D 87.984 258 29 2 4022 4279 626045190 626044935 1.930000e-78 303.0
36 TraesCS2B01G178400 chr7D 85.000 260 28 7 3592 3841 161463672 161463930 1.970000e-63 254.0
37 TraesCS2B01G178400 chr7D 86.842 76 9 1 3516 3591 626046257 626046183 2.740000e-12 84.2
38 TraesCS2B01G178400 chr7A 85.441 261 29 7 3589 3841 183486741 183487000 3.280000e-66 263.0
39 TraesCS2B01G178400 chr7A 88.158 76 9 0 3516 3591 463290005 463290080 1.640000e-14 91.6
40 TraesCS2B01G178400 chr4B 87.324 142 15 3 3844 3983 40415274 40415134 4.430000e-35 159.0
41 TraesCS2B01G178400 chr4B 90.909 77 7 0 3514 3590 97382653 97382729 2.100000e-18 104.0
42 TraesCS2B01G178400 chr4B 96.552 58 2 0 2849 2906 444840878 444840821 3.520000e-16 97.1
43 TraesCS2B01G178400 chr4B 89.474 76 7 1 3515 3590 524858630 524858704 1.270000e-15 95.3
44 TraesCS2B01G178400 chr4A 85.443 158 18 4 3847 3999 400751842 400751999 4.430000e-35 159.0


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 TraesCS2B01G178400 chr2B 153584725 153589003 4278 False 7902.0 7902 100.000000 1 4279 1 chr2B.!!$F1 4278
1 TraesCS2B01G178400 chr2B 281527200 281527867 667 False 271.5 313 85.208500 945 1837 2 chr2B.!!$F2 892
2 TraesCS2B01G178400 chr2A 101376634 101379990 3356 False 1027.0 2435 86.176667 82 3513 3 chr2A.!!$F2 3431
3 TraesCS2B01G178400 chr2A 20898115 20898892 777 True 909.0 909 88.046000 3516 4279 1 chr2A.!!$R2 763
4 TraesCS2B01G178400 chr2A 20867959 20868651 692 True 802.0 802 87.879000 3601 4279 1 chr2A.!!$R1 678
5 TraesCS2B01G178400 chr2D 102275849 102282695 6846 False 711.8 2337 86.505600 3 3516 5 chr2D.!!$F1 3513
6 TraesCS2B01G178400 chr6A 405889500 405890274 774 True 900.0 900 87.902000 3516 4279 1 chr6A.!!$R1 763
7 TraesCS2B01G178400 chr5A 444568789 444569555 766 False 876.0 876 87.500000 3516 4279 1 chr5A.!!$F1 763
8 TraesCS2B01G178400 chr1B 213407443 213408188 745 True 313.0 411 89.245000 945 1922 2 chr1B.!!$R5 977

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
410 2893 0.384230 GAAATGCCACACACGTGTCG 60.384 55.0 20.49 16.54 42.83 4.35 F
1110 3632 0.324552 ATGCCATTGCCAGGTTGCTA 60.325 50.0 0.00 0.00 36.33 3.49 F
2336 4958 0.036388 TCACCAATTCTGACGAGGCC 60.036 55.0 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 3794 0.322456 TTTGTCCCGGCAGAGATTGG 60.322 55.000 0.0 0.0 0.00 3.16 R
3044 5685 0.320374 TGGATTCAGTCGTTCGCCTT 59.680 50.000 0.0 0.0 0.00 4.35 R
3943 6594 1.080093 CCAAGCGTAAGGAGCACGA 60.080 57.895 0.0 0.0 41.91 4.35 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
36 37 1.681264 CCAACGAAAAGGCAGGTTCTT 59.319 47.619 0.00 0.00 0.00 2.52
37 38 2.287608 CCAACGAAAAGGCAGGTTCTTC 60.288 50.000 0.00 0.00 0.00 2.87
38 39 2.618709 CAACGAAAAGGCAGGTTCTTCT 59.381 45.455 0.00 0.00 0.00 2.85
39 40 2.495084 ACGAAAAGGCAGGTTCTTCTC 58.505 47.619 0.00 0.00 0.00 2.87
40 41 2.104963 ACGAAAAGGCAGGTTCTTCTCT 59.895 45.455 0.00 0.00 0.00 3.10
41 42 2.739379 CGAAAAGGCAGGTTCTTCTCTC 59.261 50.000 0.00 0.00 0.00 3.20
42 43 2.869101 AAAGGCAGGTTCTTCTCTCC 57.131 50.000 0.00 0.00 0.00 3.71
43 44 1.734655 AAGGCAGGTTCTTCTCTCCA 58.265 50.000 0.00 0.00 0.00 3.86
44 45 1.274712 AGGCAGGTTCTTCTCTCCAG 58.725 55.000 0.00 0.00 0.00 3.86
45 46 1.203237 AGGCAGGTTCTTCTCTCCAGA 60.203 52.381 0.00 0.00 0.00 3.86
46 47 1.625818 GGCAGGTTCTTCTCTCCAGAA 59.374 52.381 0.00 0.00 37.11 3.02
47 48 2.039084 GGCAGGTTCTTCTCTCCAGAAA 59.961 50.000 0.00 0.00 38.23 2.52
49 50 4.137543 GCAGGTTCTTCTCTCCAGAAAAA 58.862 43.478 0.00 0.00 38.23 1.94
51 52 5.242615 GCAGGTTCTTCTCTCCAGAAAAATT 59.757 40.000 0.00 0.00 38.23 1.82
52 53 6.431234 GCAGGTTCTTCTCTCCAGAAAAATTA 59.569 38.462 0.00 0.00 38.23 1.40
53 54 7.121907 GCAGGTTCTTCTCTCCAGAAAAATTAT 59.878 37.037 0.00 0.00 38.23 1.28
55 56 9.898152 AGGTTCTTCTCTCCAGAAAAATTATAG 57.102 33.333 0.00 0.00 38.23 1.31
56 57 9.674068 GGTTCTTCTCTCCAGAAAAATTATAGT 57.326 33.333 0.00 0.00 38.23 2.12
145 158 0.592500 CTCCATCGTCCATCGTCACG 60.593 60.000 0.00 0.00 40.80 4.35
223 236 2.942804 TGACACTGAAAATGAAGGCCA 58.057 42.857 5.01 0.00 0.00 5.36
224 237 3.499338 TGACACTGAAAATGAAGGCCAT 58.501 40.909 5.01 0.00 36.99 4.40
228 1454 5.513233 ACACTGAAAATGAAGGCCATAGAT 58.487 37.500 5.01 0.00 34.45 1.98
230 1456 4.340381 ACTGAAAATGAAGGCCATAGATGC 59.660 41.667 5.01 0.00 34.45 3.91
237 1463 1.688772 AGGCCATAGATGCAGCTTTG 58.311 50.000 11.02 13.15 0.00 2.77
284 1510 1.009829 CTCACATAAACTCTGCGGCC 58.990 55.000 0.00 0.00 0.00 6.13
311 2105 1.811266 CGTTGCTCTCCCCATCACG 60.811 63.158 0.00 0.00 0.00 4.35
328 2124 1.068885 CACGCGCAAAAGGATAACCAA 60.069 47.619 5.73 0.00 38.94 3.67
344 2140 4.590850 AACCAAATCAAAACAGAGAGCC 57.409 40.909 0.00 0.00 0.00 4.70
348 2144 2.100605 ATCAAAACAGAGAGCCCGAC 57.899 50.000 0.00 0.00 0.00 4.79
397 2880 3.732721 GCGATGCCATCTTTAAGAAATGC 59.267 43.478 2.75 3.00 0.00 3.56
398 2881 4.293415 CGATGCCATCTTTAAGAAATGCC 58.707 43.478 2.75 0.00 0.00 4.40
410 2893 0.384230 GAAATGCCACACACGTGTCG 60.384 55.000 20.49 16.54 42.83 4.35
540 3026 0.901580 TCCTCCACACCGAACCCTAC 60.902 60.000 0.00 0.00 0.00 3.18
541 3027 1.189524 CCTCCACACCGAACCCTACA 61.190 60.000 0.00 0.00 0.00 2.74
542 3028 0.902531 CTCCACACCGAACCCTACAT 59.097 55.000 0.00 0.00 0.00 2.29
543 3029 1.278127 CTCCACACCGAACCCTACATT 59.722 52.381 0.00 0.00 0.00 2.71
546 3032 2.355716 CCACACCGAACCCTACATTCAT 60.356 50.000 0.00 0.00 0.00 2.57
562 3048 5.806286 ACATTCATTCATAGTTTAACGGCG 58.194 37.500 4.80 4.80 0.00 6.46
605 3091 1.737816 GCTACCCAATCGTCCGCTA 59.262 57.895 0.00 0.00 0.00 4.26
643 3129 3.552890 CCCAAGCTGAACTAAACCAAAGC 60.553 47.826 0.00 0.00 0.00 3.51
701 3188 1.433879 CCGATCCGATCCTATCCGC 59.566 63.158 2.69 0.00 0.00 5.54
801 3307 1.365368 GCCGAGCAGAGAAAGAAGCC 61.365 60.000 0.00 0.00 0.00 4.35
858 3372 4.803426 CTCGGCTCCGTGGTGCTC 62.803 72.222 12.22 2.89 40.74 4.26
943 3458 1.129251 CTCGTCATGTCATGTGTTGCC 59.871 52.381 12.54 0.00 0.00 4.52
1018 3540 2.543037 TGGCATCCACTACTCACCTA 57.457 50.000 0.00 0.00 0.00 3.08
1019 3541 2.388735 TGGCATCCACTACTCACCTAG 58.611 52.381 0.00 0.00 0.00 3.02
1020 3542 2.292257 TGGCATCCACTACTCACCTAGT 60.292 50.000 0.00 0.00 42.62 2.57
1110 3632 0.324552 ATGCCATTGCCAGGTTGCTA 60.325 50.000 0.00 0.00 36.33 3.49
1111 3633 0.966875 TGCCATTGCCAGGTTGCTAG 60.967 55.000 0.00 0.00 36.33 3.42
1135 3688 3.013219 GACCTTCCATCTCTTTCTTGCC 58.987 50.000 0.00 0.00 0.00 4.52
1141 3694 2.422832 CCATCTCTTTCTTGCCAGCTTC 59.577 50.000 0.00 0.00 0.00 3.86
1143 3696 3.051081 TCTCTTTCTTGCCAGCTTCTC 57.949 47.619 0.00 0.00 0.00 2.87
1174 3728 2.067013 CATGCTGATGCTAGTGATCCG 58.933 52.381 0.00 0.00 40.48 4.18
1176 3730 1.482182 TGCTGATGCTAGTGATCCGTT 59.518 47.619 0.00 0.00 40.48 4.44
1187 3741 2.693074 AGTGATCCGTTTGGTTTGCTTT 59.307 40.909 0.00 0.00 36.30 3.51
1192 3746 1.849829 CCGTTTGGTTTGCTTTCGTTC 59.150 47.619 0.00 0.00 0.00 3.95
1196 3750 4.259253 CGTTTGGTTTGCTTTCGTTCTTTC 60.259 41.667 0.00 0.00 0.00 2.62
1200 3754 3.981416 GGTTTGCTTTCGTTCTTTCATCC 59.019 43.478 0.00 0.00 0.00 3.51
1201 3755 3.915437 TTGCTTTCGTTCTTTCATCCC 57.085 42.857 0.00 0.00 0.00 3.85
1202 3756 2.857483 TGCTTTCGTTCTTTCATCCCA 58.143 42.857 0.00 0.00 0.00 4.37
1203 3757 2.813754 TGCTTTCGTTCTTTCATCCCAG 59.186 45.455 0.00 0.00 0.00 4.45
1204 3758 2.814336 GCTTTCGTTCTTTCATCCCAGT 59.186 45.455 0.00 0.00 0.00 4.00
1205 3759 3.253432 GCTTTCGTTCTTTCATCCCAGTT 59.747 43.478 0.00 0.00 0.00 3.16
1206 3760 4.613850 GCTTTCGTTCTTTCATCCCAGTTC 60.614 45.833 0.00 0.00 0.00 3.01
1207 3761 3.053831 TCGTTCTTTCATCCCAGTTCC 57.946 47.619 0.00 0.00 0.00 3.62
1208 3762 1.732259 CGTTCTTTCATCCCAGTTCCG 59.268 52.381 0.00 0.00 0.00 4.30
1209 3763 2.084546 GTTCTTTCATCCCAGTTCCGG 58.915 52.381 0.00 0.00 0.00 5.14
1210 3764 1.358152 TCTTTCATCCCAGTTCCGGT 58.642 50.000 0.00 0.00 0.00 5.28
1211 3765 1.003118 TCTTTCATCCCAGTTCCGGTG 59.997 52.381 0.00 0.00 0.00 4.94
1212 3766 1.003118 CTTTCATCCCAGTTCCGGTGA 59.997 52.381 0.00 0.00 0.00 4.02
1213 3767 0.613260 TTCATCCCAGTTCCGGTGAG 59.387 55.000 0.00 0.00 0.00 3.51
1214 3768 1.221840 CATCCCAGTTCCGGTGAGG 59.778 63.158 0.00 0.00 42.97 3.86
1215 3769 1.229529 ATCCCAGTTCCGGTGAGGT 60.230 57.895 0.00 0.00 41.99 3.85
1216 3770 0.840722 ATCCCAGTTCCGGTGAGGTT 60.841 55.000 0.00 0.00 41.99 3.50
1217 3771 1.057851 TCCCAGTTCCGGTGAGGTTT 61.058 55.000 0.00 0.00 41.99 3.27
1218 3772 0.688487 CCCAGTTCCGGTGAGGTTTA 59.312 55.000 0.00 0.00 41.99 2.01
1219 3773 1.280998 CCCAGTTCCGGTGAGGTTTAT 59.719 52.381 0.00 0.00 41.99 1.40
1220 3774 2.356135 CCAGTTCCGGTGAGGTTTATG 58.644 52.381 0.00 0.00 41.99 1.90
1231 3785 4.402155 GGTGAGGTTTATGGCATCATTTCA 59.598 41.667 1.65 0.31 34.96 2.69
1233 3787 5.126061 GTGAGGTTTATGGCATCATTTCACT 59.874 40.000 1.65 0.00 34.96 3.41
1234 3788 6.318648 GTGAGGTTTATGGCATCATTTCACTA 59.681 38.462 1.65 0.00 34.96 2.74
1239 3793 7.489113 GGTTTATGGCATCATTTCACTAAGTTG 59.511 37.037 1.65 0.00 34.96 3.16
1240 3794 4.439305 TGGCATCATTTCACTAAGTTGC 57.561 40.909 0.00 0.00 0.00 4.17
1241 3795 3.193267 TGGCATCATTTCACTAAGTTGCC 59.807 43.478 3.73 3.73 46.63 4.52
1244 3798 5.413499 GCATCATTTCACTAAGTTGCCAAT 58.587 37.500 0.00 0.00 0.00 3.16
1250 3804 3.338249 TCACTAAGTTGCCAATCTCTGC 58.662 45.455 0.00 0.00 0.00 4.26
1271 3825 2.143925 CGGGACAAACTCTGTTCTTCC 58.856 52.381 0.00 0.00 38.84 3.46
1273 3827 3.006537 CGGGACAAACTCTGTTCTTCCTA 59.993 47.826 8.97 0.00 38.84 2.94
1274 3828 4.316645 GGGACAAACTCTGTTCTTCCTAC 58.683 47.826 8.97 0.00 38.84 3.18
1275 3829 3.988517 GGACAAACTCTGTTCTTCCTACG 59.011 47.826 0.00 0.00 38.84 3.51
1276 3830 4.261909 GGACAAACTCTGTTCTTCCTACGA 60.262 45.833 0.00 0.00 38.84 3.43
1277 3831 5.470047 ACAAACTCTGTTCTTCCTACGAT 57.530 39.130 0.00 0.00 32.99 3.73
1278 3832 5.471257 ACAAACTCTGTTCTTCCTACGATC 58.529 41.667 0.00 0.00 32.99 3.69
1279 3833 5.010719 ACAAACTCTGTTCTTCCTACGATCA 59.989 40.000 0.00 0.00 32.99 2.92
1280 3834 5.923733 AACTCTGTTCTTCCTACGATCAT 57.076 39.130 0.00 0.00 0.00 2.45
1311 3877 8.621532 TTGAACTGATGCAAGTAGTAAGAAAT 57.378 30.769 0.00 0.00 0.00 2.17
1317 3883 9.760660 CTGATGCAAGTAGTAAGAAATAAACAC 57.239 33.333 0.00 0.00 0.00 3.32
1318 3884 9.502091 TGATGCAAGTAGTAAGAAATAAACACT 57.498 29.630 0.00 0.00 0.00 3.55
1333 3906 2.902705 ACACTGAACGGTTGCTAGAA 57.097 45.000 0.00 0.00 0.00 2.10
1334 3907 3.188159 ACACTGAACGGTTGCTAGAAA 57.812 42.857 0.00 0.00 0.00 2.52
1335 3908 2.870411 ACACTGAACGGTTGCTAGAAAC 59.130 45.455 4.85 4.85 0.00 2.78
1336 3909 2.869801 CACTGAACGGTTGCTAGAAACA 59.130 45.455 15.68 0.00 0.00 2.83
1337 3910 3.059597 CACTGAACGGTTGCTAGAAACAG 60.060 47.826 15.68 13.69 0.00 3.16
1338 3911 3.131396 CTGAACGGTTGCTAGAAACAGT 58.869 45.455 15.68 14.37 39.66 3.55
1339 3912 3.537580 TGAACGGTTGCTAGAAACAGTT 58.462 40.909 26.37 26.37 46.51 3.16
1340 3913 4.695396 TGAACGGTTGCTAGAAACAGTTA 58.305 39.130 26.19 14.85 44.76 2.24
1341 3914 5.302360 TGAACGGTTGCTAGAAACAGTTAT 58.698 37.500 26.19 10.71 44.76 1.89
1342 3915 5.178623 TGAACGGTTGCTAGAAACAGTTATG 59.821 40.000 26.19 7.59 44.76 1.90
1343 3916 4.890088 ACGGTTGCTAGAAACAGTTATGA 58.110 39.130 15.68 0.00 35.33 2.15
1344 3917 5.302360 ACGGTTGCTAGAAACAGTTATGAA 58.698 37.500 15.68 0.00 35.33 2.57
1345 3918 5.938125 ACGGTTGCTAGAAACAGTTATGAAT 59.062 36.000 15.68 0.00 35.33 2.57
1346 3919 7.101054 ACGGTTGCTAGAAACAGTTATGAATA 58.899 34.615 15.68 0.00 35.33 1.75
1347 3920 7.769044 ACGGTTGCTAGAAACAGTTATGAATAT 59.231 33.333 15.68 0.00 35.33 1.28
1348 3921 9.256477 CGGTTGCTAGAAACAGTTATGAATATA 57.744 33.333 15.68 0.00 0.00 0.86
1386 3959 3.270877 GCGGGTGACAGTTATGAAGAAT 58.729 45.455 0.00 0.00 0.00 2.40
1387 3960 3.689649 GCGGGTGACAGTTATGAAGAATT 59.310 43.478 0.00 0.00 0.00 2.17
1393 3966 7.255451 GGGTGACAGTTATGAAGAATTTGACAA 60.255 37.037 0.00 0.00 0.00 3.18
1394 3967 8.299570 GGTGACAGTTATGAAGAATTTGACAAT 58.700 33.333 0.00 0.00 0.00 2.71
1398 3971 8.450964 ACAGTTATGAAGAATTTGACAATACCG 58.549 33.333 0.00 0.00 0.00 4.02
1434 4007 4.988708 GCATCTAGCAAGATAAGAGTGC 57.011 45.455 0.00 0.00 40.65 4.40
1450 4026 3.533606 AGTGCATTAGTACTCAGCAGG 57.466 47.619 14.73 0.00 35.69 4.85
1458 4034 0.912486 GTACTCAGCAGGTCCCCAAT 59.088 55.000 0.00 0.00 0.00 3.16
1468 4044 3.613193 GCAGGTCCCCAATTTTAACGTTC 60.613 47.826 2.82 0.00 0.00 3.95
1472 4048 5.364446 AGGTCCCCAATTTTAACGTTCTTTT 59.636 36.000 2.82 0.00 0.00 2.27
1488 4068 6.533367 ACGTTCTTTTGCTAATTTCTTTTGCA 59.467 30.769 0.00 0.00 42.95 4.08
1495 4075 5.833082 TGCTAATTTCTTTTGCAACGGTTA 58.167 33.333 0.00 0.00 41.95 2.85
1515 4095 3.050275 GGCGCTGTCCAACCTGTC 61.050 66.667 7.64 0.00 0.00 3.51
1568 4154 3.921119 TGATTGCTTGCTGTTTGGTAG 57.079 42.857 0.00 0.00 0.00 3.18
1573 4159 1.537202 GCTTGCTGTTTGGTAGGTCTG 59.463 52.381 0.00 0.00 0.00 3.51
1579 4166 3.335579 CTGTTTGGTAGGTCTGCCTTAC 58.664 50.000 6.66 5.31 44.18 2.34
1585 4172 2.176889 GTAGGTCTGCCTTACCTGACA 58.823 52.381 11.01 0.00 46.90 3.58
1589 4176 2.224548 GGTCTGCCTTACCTGACAGTTT 60.225 50.000 0.93 0.00 35.96 2.66
1612 4201 7.993821 TTTTTCATCGCAACTGTATTTCAAA 57.006 28.000 0.00 0.00 0.00 2.69
1628 4217 2.783135 TCAAACATGGAGTTCTCTGCC 58.217 47.619 0.00 0.00 40.26 4.85
1632 4221 0.617413 CATGGAGTTCTCTGCCCAGT 59.383 55.000 0.00 0.00 31.48 4.00
1638 4227 3.514309 GGAGTTCTCTGCCCAGTACTTTA 59.486 47.826 0.00 0.00 0.00 1.85
1639 4228 4.496360 GAGTTCTCTGCCCAGTACTTTAC 58.504 47.826 0.00 0.00 0.00 2.01
1705 4298 1.078823 TGACACCCTCTACCCACTGAT 59.921 52.381 0.00 0.00 0.00 2.90
1707 4300 1.123928 CACCCTCTACCCACTGATCC 58.876 60.000 0.00 0.00 0.00 3.36
1733 4326 1.210155 CAACTTAGCCTGCCGCAAC 59.790 57.895 0.00 0.00 41.38 4.17
1763 4363 8.439964 TCCAAGGTAAGTGGTACTAATAAACT 57.560 34.615 0.00 0.00 37.43 2.66
1819 4421 7.596749 ATTTGTGTGCTCATACTACTTGTAC 57.403 36.000 0.00 0.00 33.45 2.90
1941 4548 1.338136 CGGTCTGAAGGTATGCCCCT 61.338 60.000 0.00 0.00 35.96 4.79
1955 4562 5.306160 GGTATGCCCCTGTACACTTAGATTA 59.694 44.000 0.00 0.00 0.00 1.75
1956 4563 5.552870 ATGCCCCTGTACACTTAGATTAG 57.447 43.478 0.00 0.00 0.00 1.73
1957 4564 4.359105 TGCCCCTGTACACTTAGATTAGT 58.641 43.478 0.00 0.00 0.00 2.24
1961 4568 7.153315 GCCCCTGTACACTTAGATTAGTATTC 58.847 42.308 0.00 0.00 0.00 1.75
2015 4633 8.276252 TCAAGCTACCCATTATGTTTCTAAAC 57.724 34.615 0.00 0.00 39.33 2.01
2017 4635 8.739972 CAAGCTACCCATTATGTTTCTAAACTT 58.260 33.333 7.09 3.65 39.59 2.66
2123 4741 1.142748 CGAGAAGCTGAAGCCGGAT 59.857 57.895 5.05 0.00 43.38 4.18
2182 4803 3.456277 AGGAAAATCGTAAGCTCATCCCT 59.544 43.478 0.00 0.00 37.18 4.20
2189 4810 2.225467 GTAAGCTCATCCCTTGCATCC 58.775 52.381 0.00 0.00 0.00 3.51
2192 4813 1.030457 GCTCATCCCTTGCATCCAAG 58.970 55.000 0.00 0.00 46.38 3.61
2195 4816 1.918262 TCATCCCTTGCATCCAAGTCT 59.082 47.619 0.00 0.00 45.57 3.24
2196 4817 2.092753 TCATCCCTTGCATCCAAGTCTC 60.093 50.000 0.00 0.00 45.57 3.36
2208 4829 5.700373 GCATCCAAGTCTCTCTGATATTTCC 59.300 44.000 0.00 0.00 0.00 3.13
2213 4834 6.041409 CCAAGTCTCTCTGATATTTCCTGCTA 59.959 42.308 0.00 0.00 0.00 3.49
2251 4873 5.470098 AGTCAACGACAGTTAATTGCTCATT 59.530 36.000 0.00 0.00 38.79 2.57
2259 4881 7.167302 CGACAGTTAATTGCTCATTTGTTTTCA 59.833 33.333 0.00 0.00 0.00 2.69
2266 4888 3.118847 TGCTCATTTGTTTTCAAGCACCA 60.119 39.130 0.00 0.00 41.09 4.17
2270 4892 6.175712 TCATTTGTTTTCAAGCACCAAAAC 57.824 33.333 9.17 9.17 41.13 2.43
2299 4921 2.415893 GCAGCAGTGACAGTTTGTTGTT 60.416 45.455 0.00 0.00 0.00 2.83
2302 4924 2.479560 GCAGTGACAGTTTGTTGTTCCC 60.480 50.000 0.00 0.00 0.00 3.97
2324 4946 4.458397 CTCCACTGCAGATATTCACCAAT 58.542 43.478 23.35 0.00 0.00 3.16
2336 4958 0.036388 TCACCAATTCTGACGAGGCC 60.036 55.000 0.00 0.00 0.00 5.19
2413 5035 1.079057 GCTTCGAGACCCTGAACCC 60.079 63.158 0.00 0.00 0.00 4.11
2414 5036 1.597461 CTTCGAGACCCTGAACCCC 59.403 63.158 0.00 0.00 0.00 4.95
2432 5054 1.073763 CCCAAGAATCCAGGTGACACA 59.926 52.381 8.08 0.00 0.00 3.72
2433 5055 2.430465 CCAAGAATCCAGGTGACACAG 58.570 52.381 8.08 0.00 0.00 3.66
2434 5056 2.038952 CCAAGAATCCAGGTGACACAGA 59.961 50.000 8.08 1.29 0.00 3.41
2438 5060 1.188219 ATCCAGGTGACACAGACGCT 61.188 55.000 8.08 0.00 0.00 5.07
2439 5061 0.538746 TCCAGGTGACACAGACGCTA 60.539 55.000 8.08 0.00 0.00 4.26
2442 5064 0.896019 AGGTGACACAGACGCTAGCT 60.896 55.000 13.93 0.00 0.00 3.32
2443 5065 0.456995 GGTGACACAGACGCTAGCTC 60.457 60.000 13.93 9.43 0.00 4.09
2459 5087 1.904032 CTCTGGCAAGAGGGTCCTC 59.096 63.158 10.61 8.91 45.45 3.71
2564 5192 2.028125 GCCATGGATTCCCTCGTCGA 62.028 60.000 18.40 0.00 0.00 4.20
2573 5201 4.225340 CCTCGTCGACTCTCCGCG 62.225 72.222 14.70 0.00 0.00 6.46
2631 5259 4.142966 CCGTTTAGTTTAGCAGCAGTAACC 60.143 45.833 0.00 0.00 0.00 2.85
2746 5374 1.978712 CTCTCACAGCCGCTGCATTG 61.979 60.000 20.56 11.38 41.13 2.82
2764 5392 1.077068 GATCCCCACGCCATTGGAA 60.077 57.895 6.95 0.00 39.24 3.53
2772 5400 2.091541 CACGCCATTGGAATACCTGTT 58.908 47.619 6.95 0.00 37.04 3.16
2782 5419 7.393234 CCATTGGAATACCTGTTAGAAACTGAA 59.607 37.037 0.00 0.00 37.04 3.02
2793 5430 3.047613 AGAAACTGAACGAACAAACGC 57.952 42.857 0.00 0.00 36.70 4.84
2805 5442 2.949714 ACAAACGCTCTGAAACGATG 57.050 45.000 6.74 7.44 0.00 3.84
3066 5707 0.108804 GCGAACGACTGAATCCAGGA 60.109 55.000 0.00 0.00 44.60 3.86
3081 5722 3.547746 TCCAGGAAAAACCCGTATATGC 58.452 45.455 0.00 0.00 40.05 3.14
3170 5811 5.702349 ACAGGTGTACTACTTGTGTACTC 57.298 43.478 10.75 0.00 46.50 2.59
3191 5832 3.676172 TCATGTGATCGAAACACCGTAAC 59.324 43.478 18.61 0.00 37.45 2.50
3235 5876 3.992643 AGATTCGCTCATTCAGATGGAG 58.007 45.455 0.00 0.00 33.93 3.86
3270 5911 7.633193 AATTGCAAATGCCATGTGATATTTT 57.367 28.000 1.71 0.00 41.18 1.82
3271 5912 8.734218 AATTGCAAATGCCATGTGATATTTTA 57.266 26.923 1.71 0.00 41.18 1.52
3272 5913 8.911918 ATTGCAAATGCCATGTGATATTTTAT 57.088 26.923 1.71 0.00 41.18 1.40
3273 5914 7.949903 TGCAAATGCCATGTGATATTTTATC 57.050 32.000 0.00 0.00 41.18 1.75
3274 5915 7.498443 TGCAAATGCCATGTGATATTTTATCA 58.502 30.769 0.00 0.00 41.18 2.15
3347 5988 8.373048 TGTACAAAGTACCTCAAACATAACAG 57.627 34.615 0.00 0.00 0.00 3.16
3350 5991 8.691661 ACAAAGTACCTCAAACATAACAGAAT 57.308 30.769 0.00 0.00 0.00 2.40
3391 6032 4.514577 GAGCAGCGGAGGCGCTAA 62.515 66.667 7.64 0.00 44.74 3.09
3490 6131 0.813184 AAATGGGCTGCTCATTGACG 59.187 50.000 27.03 0.00 35.31 4.35
3492 6133 0.541392 ATGGGCTGCTCATTGACGTA 59.459 50.000 9.72 0.00 0.00 3.57
3495 6136 0.740868 GGCTGCTCATTGACGTAGCA 60.741 55.000 19.44 9.46 43.66 3.49
3509 6150 5.981174 TGACGTAGCATGTTACTTTTCAAC 58.019 37.500 16.42 0.00 0.00 3.18
3530 6171 4.890088 ACAAAGAACTAGAACCATACGCA 58.110 39.130 0.00 0.00 0.00 5.24
3531 6172 5.488341 ACAAAGAACTAGAACCATACGCAT 58.512 37.500 0.00 0.00 0.00 4.73
3561 6202 2.673326 GCGCCGTTCTACTTTTCTACCT 60.673 50.000 0.00 0.00 0.00 3.08
3568 6209 9.154847 GCCGTTCTACTTTTCTACCTTTTATTA 57.845 33.333 0.00 0.00 0.00 0.98
3637 6278 5.234466 AGTGAGAAATACTTGGAAGCTGT 57.766 39.130 0.00 0.00 0.00 4.40
3658 6299 4.949238 TGTGGCACTGCATCAAAGTATATT 59.051 37.500 19.83 0.00 0.00 1.28
3758 6407 2.957680 TGATTTGCACTGCAGAAAAGGA 59.042 40.909 23.35 5.52 40.61 3.36
3806 6455 6.256819 TCTAAGAGGAAGAGACAGAAATGGA 58.743 40.000 0.00 0.00 0.00 3.41
3822 6471 7.772757 ACAGAAATGGAAGGATCAAGAGATAAC 59.227 37.037 0.00 0.00 33.72 1.89
3841 6490 9.593134 GAGATAACAGTACAAGTGATTGATCTT 57.407 33.333 0.00 0.00 0.00 2.40
3857 6506 4.109766 TGATCTTTGTACATAAGCGACCG 58.890 43.478 0.00 0.00 0.00 4.79
3858 6507 3.853831 TCTTTGTACATAAGCGACCGA 57.146 42.857 0.00 0.00 0.00 4.69
3878 6528 7.586300 CGACCGATGACAATTAACCAAATTATC 59.414 37.037 0.00 0.00 35.54 1.75
4103 7466 8.208224 TCTAGAAACTTGGTCAAACATAGACAA 58.792 33.333 0.00 0.00 37.74 3.18
4112 7475 6.260050 TGGTCAAACATAGACAACTTTGACTC 59.740 38.462 17.21 10.64 44.33 3.36
4116 7479 6.867662 AACATAGACAACTTTGACTCTTGG 57.132 37.500 0.00 0.00 35.06 3.61
4220 7583 0.172578 CGCGGACATGGTACTCAAGA 59.827 55.000 0.00 0.00 0.00 3.02
4235 7598 3.326006 ACTCAAGAAGTGAAGCATGAGGA 59.674 43.478 0.00 0.00 38.81 3.71
4259 7622 5.643379 TTCAGATTGAAACCTTACATGGC 57.357 39.130 0.00 0.00 32.71 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.033405 TTGGAAACGGGGGTGAAACA 60.033 50.000 0.00 0.00 39.98 2.83
1 2 0.386476 GTTGGAAACGGGGGTGAAAC 59.614 55.000 0.00 0.00 36.92 2.78
12 13 1.407618 ACCTGCCTTTTCGTTGGAAAC 59.592 47.619 0.00 0.00 41.66 2.78
14 15 1.679153 GAACCTGCCTTTTCGTTGGAA 59.321 47.619 0.00 0.00 0.00 3.53
36 37 9.672673 CCTTTCACTATAATTTTTCTGGAGAGA 57.327 33.333 0.00 0.00 0.00 3.10
37 38 8.401709 GCCTTTCACTATAATTTTTCTGGAGAG 58.598 37.037 0.00 0.00 0.00 3.20
38 39 7.888021 TGCCTTTCACTATAATTTTTCTGGAGA 59.112 33.333 0.00 0.00 0.00 3.71
39 40 8.055279 TGCCTTTCACTATAATTTTTCTGGAG 57.945 34.615 0.00 0.00 0.00 3.86
40 41 7.888021 TCTGCCTTTCACTATAATTTTTCTGGA 59.112 33.333 0.00 0.00 0.00 3.86
41 42 8.055279 TCTGCCTTTCACTATAATTTTTCTGG 57.945 34.615 0.00 0.00 0.00 3.86
46 47 8.907885 GGAGAATCTGCCTTTCACTATAATTTT 58.092 33.333 0.00 0.00 33.73 1.82
47 48 8.277918 AGGAGAATCTGCCTTTCACTATAATTT 58.722 33.333 0.00 0.00 33.73 1.82
49 50 7.385894 AGGAGAATCTGCCTTTCACTATAAT 57.614 36.000 0.00 0.00 33.73 1.28
51 52 6.814954 AAGGAGAATCTGCCTTTCACTATA 57.185 37.500 0.00 0.00 41.60 1.31
52 53 5.707066 AAGGAGAATCTGCCTTTCACTAT 57.293 39.130 0.00 0.00 41.60 2.12
97 98 1.001406 GATCCTCGGGCCATAGAACAG 59.999 57.143 4.39 0.00 0.00 3.16
145 158 4.767255 CCTGGCCACCGAGTGAGC 62.767 72.222 0.00 7.11 35.23 4.26
230 1456 1.860676 AGTTTGCATGCACAAAGCTG 58.139 45.000 22.58 0.00 45.94 4.24
237 1463 3.427528 CAGAATGACAAGTTTGCATGCAC 59.572 43.478 22.58 10.38 39.69 4.57
292 1518 2.109126 GTGATGGGGAGAGCAACGC 61.109 63.158 0.00 0.00 0.00 4.84
294 1520 2.109126 GCGTGATGGGGAGAGCAAC 61.109 63.158 0.00 0.00 0.00 4.17
295 1521 2.268920 GCGTGATGGGGAGAGCAA 59.731 61.111 0.00 0.00 0.00 3.91
296 1522 4.147449 CGCGTGATGGGGAGAGCA 62.147 66.667 0.00 0.00 0.00 4.26
298 1524 3.664025 TTGCGCGTGATGGGGAGAG 62.664 63.158 8.43 0.00 31.07 3.20
299 1525 2.739849 TTTTGCGCGTGATGGGGAGA 62.740 55.000 8.43 0.00 31.07 3.71
300 1526 2.257286 CTTTTGCGCGTGATGGGGAG 62.257 60.000 8.43 0.00 31.07 4.30
311 2105 3.843999 TGATTTGGTTATCCTTTTGCGC 58.156 40.909 0.00 0.00 34.23 6.09
328 2124 2.427506 GTCGGGCTCTCTGTTTTGATT 58.572 47.619 0.00 0.00 0.00 2.57
362 2158 2.165301 CATCGCTTTCGTCCCGTCC 61.165 63.158 0.00 0.00 36.96 4.79
363 2159 2.799540 GCATCGCTTTCGTCCCGTC 61.800 63.158 0.00 0.00 36.96 4.79
382 2186 4.853196 CGTGTGTGGCATTTCTTAAAGATG 59.147 41.667 0.00 0.00 0.00 2.90
419 2902 3.554692 GTGGAATCGCGAGCGTGG 61.555 66.667 16.66 0.00 40.74 4.94
483 2966 2.031069 CGTGCGTCACAGCCTATACTAT 60.031 50.000 9.95 0.00 33.40 2.12
485 2968 0.100682 CGTGCGTCACAGCCTATACT 59.899 55.000 9.95 0.00 33.40 2.12
486 2969 1.480219 GCGTGCGTCACAGCCTATAC 61.480 60.000 9.95 0.00 33.40 1.47
540 3026 6.043327 TCGCCGTTAAACTATGAATGAATG 57.957 37.500 0.00 0.00 0.00 2.67
541 3027 6.658831 CATCGCCGTTAAACTATGAATGAAT 58.341 36.000 0.00 0.00 0.00 2.57
542 3028 5.503357 GCATCGCCGTTAAACTATGAATGAA 60.503 40.000 0.00 0.00 0.00 2.57
543 3029 4.025229 GCATCGCCGTTAAACTATGAATGA 60.025 41.667 0.00 0.00 0.00 2.57
546 3032 2.610374 GGCATCGCCGTTAAACTATGAA 59.390 45.455 0.00 0.00 39.62 2.57
575 3061 1.131638 TGGGTAGCCATCAGACATCC 58.868 55.000 10.27 0.00 0.00 3.51
580 3066 1.412710 GACGATTGGGTAGCCATCAGA 59.587 52.381 15.77 0.00 0.00 3.27
581 3067 1.541233 GGACGATTGGGTAGCCATCAG 60.541 57.143 15.77 11.10 0.00 2.90
643 3129 7.148590 GCCAACTTTCCTTTAAAAGCACATATG 60.149 37.037 0.00 0.00 39.39 1.78
701 3188 3.047877 GTTCGGTGGAGTTGGCGG 61.048 66.667 0.00 0.00 0.00 6.13
858 3372 0.036010 GGGTGCTATCCGATGATGGG 60.036 60.000 0.00 0.00 30.58 4.00
887 3401 1.188219 TCTCTGGAGGGTGACACAGC 61.188 60.000 8.08 0.00 0.00 4.40
889 3403 0.832135 GGTCTCTGGAGGGTGACACA 60.832 60.000 8.08 0.00 0.00 3.72
898 3413 2.103941 GGGCTTTATCTGGTCTCTGGAG 59.896 54.545 0.00 0.00 0.00 3.86
943 3458 5.699915 ACAAAGATGATCAGAGTCACAACTG 59.300 40.000 0.09 0.00 35.28 3.16
1018 3540 1.089481 CACACACAACGCAGGTGACT 61.089 55.000 8.46 0.00 46.44 3.41
1019 3541 1.351707 CACACACAACGCAGGTGAC 59.648 57.895 8.46 0.00 39.53 3.67
1020 3542 1.078778 ACACACACAACGCAGGTGA 60.079 52.632 8.46 0.00 39.53 4.02
1110 3632 3.436243 AGAAAGAGATGGAAGGTCGACT 58.564 45.455 16.46 0.00 0.00 4.18
1111 3633 3.878160 AGAAAGAGATGGAAGGTCGAC 57.122 47.619 7.13 7.13 0.00 4.20
1135 3688 1.079543 CCGGTGACCAGAGAAGCTG 60.080 63.158 1.11 0.00 44.49 4.24
1141 3694 2.821366 GCATGCCGGTGACCAGAG 60.821 66.667 6.36 0.00 0.00 3.35
1143 3696 3.129502 CAGCATGCCGGTGACCAG 61.130 66.667 15.66 0.00 46.47 4.00
1169 3722 2.287368 ACGAAAGCAAACCAAACGGATC 60.287 45.455 0.00 0.00 0.00 3.36
1170 3723 1.679153 ACGAAAGCAAACCAAACGGAT 59.321 42.857 0.00 0.00 0.00 4.18
1171 3724 1.096416 ACGAAAGCAAACCAAACGGA 58.904 45.000 0.00 0.00 0.00 4.69
1172 3725 1.849829 GAACGAAAGCAAACCAAACGG 59.150 47.619 0.00 0.00 0.00 4.44
1174 3728 4.623595 TGAAAGAACGAAAGCAAACCAAAC 59.376 37.500 0.00 0.00 0.00 2.93
1176 3730 4.442375 TGAAAGAACGAAAGCAAACCAA 57.558 36.364 0.00 0.00 0.00 3.67
1187 3741 2.611971 CGGAACTGGGATGAAAGAACGA 60.612 50.000 0.00 0.00 0.00 3.85
1192 3746 1.003118 TCACCGGAACTGGGATGAAAG 59.997 52.381 9.46 0.00 0.00 2.62
1196 3750 1.221840 CCTCACCGGAACTGGGATG 59.778 63.158 9.46 0.00 33.16 3.51
1200 3754 2.356135 CATAAACCTCACCGGAACTGG 58.644 52.381 9.46 7.26 36.31 4.00
1201 3755 2.356135 CCATAAACCTCACCGGAACTG 58.644 52.381 9.46 0.00 36.31 3.16
1202 3756 1.339727 GCCATAAACCTCACCGGAACT 60.340 52.381 9.46 0.00 36.31 3.01
1203 3757 1.092348 GCCATAAACCTCACCGGAAC 58.908 55.000 9.46 0.00 36.31 3.62
1204 3758 0.693622 TGCCATAAACCTCACCGGAA 59.306 50.000 9.46 0.00 36.31 4.30
1205 3759 0.916086 ATGCCATAAACCTCACCGGA 59.084 50.000 9.46 0.00 36.31 5.14
1206 3760 1.308998 GATGCCATAAACCTCACCGG 58.691 55.000 0.00 0.00 39.35 5.28
1207 3761 2.036958 TGATGCCATAAACCTCACCG 57.963 50.000 0.00 0.00 0.00 4.94
1208 3762 4.402155 TGAAATGATGCCATAAACCTCACC 59.598 41.667 0.00 0.00 31.59 4.02
1209 3763 5.126061 AGTGAAATGATGCCATAAACCTCAC 59.874 40.000 0.00 0.00 31.59 3.51
1210 3764 5.263599 AGTGAAATGATGCCATAAACCTCA 58.736 37.500 0.00 0.00 31.59 3.86
1211 3765 5.841957 AGTGAAATGATGCCATAAACCTC 57.158 39.130 0.00 0.00 31.59 3.85
1212 3766 6.891908 ACTTAGTGAAATGATGCCATAAACCT 59.108 34.615 0.00 0.00 31.59 3.50
1213 3767 7.100458 ACTTAGTGAAATGATGCCATAAACC 57.900 36.000 0.00 0.00 31.59 3.27
1214 3768 7.009540 GCAACTTAGTGAAATGATGCCATAAAC 59.990 37.037 0.00 0.00 31.59 2.01
1215 3769 7.035004 GCAACTTAGTGAAATGATGCCATAAA 58.965 34.615 0.00 0.00 31.59 1.40
1216 3770 6.563422 GCAACTTAGTGAAATGATGCCATAA 58.437 36.000 0.00 0.00 31.59 1.90
1217 3771 6.135290 GCAACTTAGTGAAATGATGCCATA 57.865 37.500 0.00 0.00 31.59 2.74
1218 3772 5.002464 GCAACTTAGTGAAATGATGCCAT 57.998 39.130 0.00 0.00 33.66 4.40
1219 3773 4.439305 GCAACTTAGTGAAATGATGCCA 57.561 40.909 0.00 0.00 0.00 4.92
1220 3774 3.774066 GGCAACTTAGTGAAATGATGCC 58.226 45.455 6.27 6.27 44.44 4.40
1240 3794 0.322456 TTTGTCCCGGCAGAGATTGG 60.322 55.000 0.00 0.00 0.00 3.16
1241 3795 0.804989 GTTTGTCCCGGCAGAGATTG 59.195 55.000 0.00 0.00 0.00 2.67
1244 3798 0.832135 AGAGTTTGTCCCGGCAGAGA 60.832 55.000 0.00 0.00 0.00 3.10
1250 3804 2.143925 GAAGAACAGAGTTTGTCCCGG 58.856 52.381 0.00 0.00 39.73 5.73
1278 3832 3.775661 TGCATCAGTTCAATCAGCATG 57.224 42.857 0.00 0.00 37.54 4.06
1279 3833 3.762288 ACTTGCATCAGTTCAATCAGCAT 59.238 39.130 0.00 0.00 0.00 3.79
1280 3834 3.151554 ACTTGCATCAGTTCAATCAGCA 58.848 40.909 0.00 0.00 0.00 4.41
1311 3877 4.325028 TCTAGCAACCGTTCAGTGTTTA 57.675 40.909 0.00 0.00 0.00 2.01
1315 3881 2.869801 TGTTTCTAGCAACCGTTCAGTG 59.130 45.455 2.71 0.00 0.00 3.66
1317 3883 3.131396 ACTGTTTCTAGCAACCGTTCAG 58.869 45.455 2.71 0.00 0.00 3.02
1318 3884 3.188159 ACTGTTTCTAGCAACCGTTCA 57.812 42.857 2.71 0.00 0.00 3.18
1360 3933 3.215151 TCATAACTGTCACCCGCAAAAA 58.785 40.909 0.00 0.00 0.00 1.94
1361 3934 2.852449 TCATAACTGTCACCCGCAAAA 58.148 42.857 0.00 0.00 0.00 2.44
1362 3935 2.552599 TCATAACTGTCACCCGCAAA 57.447 45.000 0.00 0.00 0.00 3.68
1363 3936 2.037902 TCTTCATAACTGTCACCCGCAA 59.962 45.455 0.00 0.00 0.00 4.85
1364 3937 1.621317 TCTTCATAACTGTCACCCGCA 59.379 47.619 0.00 0.00 0.00 5.69
1365 3938 2.380084 TCTTCATAACTGTCACCCGC 57.620 50.000 0.00 0.00 0.00 6.13
1366 3939 5.411361 TCAAATTCTTCATAACTGTCACCCG 59.589 40.000 0.00 0.00 0.00 5.28
1367 3940 6.206634 TGTCAAATTCTTCATAACTGTCACCC 59.793 38.462 0.00 0.00 0.00 4.61
1368 3941 7.202016 TGTCAAATTCTTCATAACTGTCACC 57.798 36.000 0.00 0.00 0.00 4.02
1378 3951 8.792633 TCTTTTCGGTATTGTCAAATTCTTCAT 58.207 29.630 0.00 0.00 0.00 2.57
1386 3959 8.557864 TCGTATTTTCTTTTCGGTATTGTCAAA 58.442 29.630 0.00 0.00 0.00 2.69
1387 3960 8.085720 TCGTATTTTCTTTTCGGTATTGTCAA 57.914 30.769 0.00 0.00 0.00 3.18
1393 3966 6.761714 AGATGCTCGTATTTTCTTTTCGGTAT 59.238 34.615 0.00 0.00 0.00 2.73
1394 3967 6.103997 AGATGCTCGTATTTTCTTTTCGGTA 58.896 36.000 0.00 0.00 0.00 4.02
1395 3968 4.935808 AGATGCTCGTATTTTCTTTTCGGT 59.064 37.500 0.00 0.00 0.00 4.69
1396 3969 5.470845 AGATGCTCGTATTTTCTTTTCGG 57.529 39.130 0.00 0.00 0.00 4.30
1398 3971 7.005062 TGCTAGATGCTCGTATTTTCTTTTC 57.995 36.000 0.00 0.00 43.37 2.29
1426 3999 5.163509 CCTGCTGAGTACTAATGCACTCTTA 60.164 44.000 11.36 0.00 41.46 2.10
1434 4007 3.460857 GGGACCTGCTGAGTACTAATG 57.539 52.381 0.00 0.00 0.00 1.90
1450 4026 5.050634 GCAAAAGAACGTTAAAATTGGGGAC 60.051 40.000 0.00 0.00 0.00 4.46
1468 4044 6.128729 CCGTTGCAAAAGAAATTAGCAAAAG 58.871 36.000 0.00 0.00 45.46 2.27
1472 4048 4.314740 ACCGTTGCAAAAGAAATTAGCA 57.685 36.364 0.00 0.00 0.00 3.49
1485 4065 3.350612 GCGCCTGTAACCGTTGCA 61.351 61.111 0.00 1.89 0.00 4.08
1488 4068 1.666872 GACAGCGCCTGTAACCGTT 60.667 57.895 2.29 0.00 45.44 4.44
1515 4095 2.614057 GTTGGCGTAGGATTCCATCTTG 59.386 50.000 5.29 0.00 0.00 3.02
1568 4154 0.977395 ACTGTCAGGTAAGGCAGACC 59.023 55.000 4.53 0.00 37.22 3.85
1589 4176 6.975197 TGTTTGAAATACAGTTGCGATGAAAA 59.025 30.769 0.00 0.00 0.00 2.29
1596 4183 4.793071 TCCATGTTTGAAATACAGTTGCG 58.207 39.130 0.00 0.00 0.00 4.85
1603 4192 6.317857 GCAGAGAACTCCATGTTTGAAATAC 58.682 40.000 0.00 0.00 39.30 1.89
1610 4199 1.425066 TGGGCAGAGAACTCCATGTTT 59.575 47.619 0.00 0.00 39.30 2.83
1612 4201 0.617413 CTGGGCAGAGAACTCCATGT 59.383 55.000 0.00 0.00 0.00 3.21
1628 4217 4.286291 AGGGGTTCAGAAGTAAAGTACTGG 59.714 45.833 0.00 0.00 39.39 4.00
1632 4221 4.154942 ACGAGGGGTTCAGAAGTAAAGTA 58.845 43.478 0.00 0.00 0.00 2.24
1638 4227 1.420430 TCAACGAGGGGTTCAGAAGT 58.580 50.000 0.00 0.00 36.49 3.01
1639 4228 2.744202 CAATCAACGAGGGGTTCAGAAG 59.256 50.000 0.00 0.00 36.49 2.85
1705 4298 3.134804 GCAGGCTAAGTTGATTCCTAGGA 59.865 47.826 7.62 7.62 0.00 2.94
1707 4300 3.471680 GGCAGGCTAAGTTGATTCCTAG 58.528 50.000 0.00 0.00 0.00 3.02
1733 4326 4.906618 AGTACCACTTACCTTGGATGTTG 58.093 43.478 0.00 0.00 37.58 3.33
1763 4363 6.516527 GCATGAAAACAGAGGATTGGTGTAAA 60.517 38.462 0.00 0.00 0.00 2.01
1819 4421 3.520290 TGTAGTCTGCGATTTGGTAGG 57.480 47.619 0.00 0.00 0.00 3.18
1957 4564 9.273016 CCAACAGAAACTTGTAGAAGAAGAATA 57.727 33.333 6.63 0.00 32.98 1.75
1961 4568 6.927294 ACCAACAGAAACTTGTAGAAGAAG 57.073 37.500 6.63 0.00 32.98 2.85
1966 4573 6.726490 AGACTACCAACAGAAACTTGTAGA 57.274 37.500 0.00 0.00 0.00 2.59
2015 4633 7.707464 TGGCACATGAATAGCATTATGAAAAAG 59.293 33.333 0.00 0.00 34.15 2.27
2017 4635 7.110043 TGGCACATGAATAGCATTATGAAAA 57.890 32.000 0.00 0.00 34.15 2.29
2027 4645 3.057736 CCATAAGCTGGCACATGAATAGC 60.058 47.826 0.00 3.81 38.47 2.97
2051 4669 3.989705 TCGTCGTAGTCGAATTCGTAA 57.010 42.857 25.93 10.98 45.81 3.18
2123 4741 1.194781 GCAGGTTCCTCAGGACAGGA 61.195 60.000 0.00 0.00 41.16 3.86
2182 4803 5.883685 ATATCAGAGAGACTTGGATGCAA 57.116 39.130 0.00 0.00 0.00 4.08
2189 4810 5.916318 AGCAGGAAATATCAGAGAGACTTG 58.084 41.667 0.00 0.00 0.00 3.16
2192 4813 6.398234 TGTAGCAGGAAATATCAGAGAGAC 57.602 41.667 0.00 0.00 0.00 3.36
2195 4816 6.983906 TGATGTAGCAGGAAATATCAGAGA 57.016 37.500 0.00 0.00 0.00 3.10
2213 4834 2.549754 CGTTGACTCCTTTTGCTGATGT 59.450 45.455 0.00 0.00 0.00 3.06
2299 4921 2.435805 GTGAATATCTGCAGTGGAGGGA 59.564 50.000 14.67 0.26 0.00 4.20
2302 4924 3.548745 TGGTGAATATCTGCAGTGGAG 57.451 47.619 14.67 5.07 0.00 3.86
2324 4946 4.373116 GCGTGGGCCTCGTCAGAA 62.373 66.667 26.57 0.00 0.00 3.02
2413 5035 2.038952 TCTGTGTCACCTGGATTCTTGG 59.961 50.000 0.00 0.00 0.00 3.61
2414 5036 3.070018 GTCTGTGTCACCTGGATTCTTG 58.930 50.000 0.00 0.00 0.00 3.02
2432 5054 0.967887 TCTTGCCAGAGCTAGCGTCT 60.968 55.000 9.55 9.79 41.06 4.18
2433 5055 0.527385 CTCTTGCCAGAGCTAGCGTC 60.527 60.000 9.55 7.54 40.39 5.19
2434 5056 1.515020 CTCTTGCCAGAGCTAGCGT 59.485 57.895 9.55 0.00 40.39 5.07
2438 5060 0.978146 GGACCCTCTTGCCAGAGCTA 60.978 60.000 9.32 0.00 44.96 3.32
2439 5061 2.297129 GGACCCTCTTGCCAGAGCT 61.297 63.158 9.32 0.00 44.96 4.09
2442 5064 4.136978 GAGGACCCTCTTGCCAGA 57.863 61.111 8.76 0.00 39.80 3.86
2459 5087 3.965539 CTCCAGGGACGGCTTGCAG 62.966 68.421 0.00 0.00 0.00 4.41
2573 5201 1.577328 TAGCTTTGCAGTTCTGCGGC 61.577 55.000 17.95 19.25 38.79 6.53
2602 5230 0.367887 GCTAAACTAAACGGCGGTCG 59.632 55.000 13.24 0.00 45.88 4.79
2604 5232 1.435577 CTGCTAAACTAAACGGCGGT 58.564 50.000 13.24 0.00 0.00 5.68
2611 5239 4.687483 GTCGGTTACTGCTGCTAAACTAAA 59.313 41.667 0.00 0.00 0.00 1.85
2613 5241 3.671433 CGTCGGTTACTGCTGCTAAACTA 60.671 47.826 0.00 0.00 0.00 2.24
2631 5259 2.969443 AATCAAAGGCAGTTTCGTCG 57.031 45.000 0.00 0.00 0.00 5.12
2736 5364 2.124193 TGGGGATCAATGCAGCGG 60.124 61.111 0.00 0.00 0.00 5.52
2746 5374 0.468029 ATTCCAATGGCGTGGGGATC 60.468 55.000 0.00 0.00 39.34 3.36
2764 5392 6.518493 TGTTCGTTCAGTTTCTAACAGGTAT 58.482 36.000 0.00 0.00 0.00 2.73
2772 5400 3.866910 AGCGTTTGTTCGTTCAGTTTCTA 59.133 39.130 0.00 0.00 0.00 2.10
2782 5419 1.005347 CGTTTCAGAGCGTTTGTTCGT 60.005 47.619 0.00 0.00 0.00 3.85
2793 5430 1.081892 CCTGCACCATCGTTTCAGAG 58.918 55.000 0.00 0.00 0.00 3.35
2805 5442 2.904131 GAGCTCCCTACCTGCACC 59.096 66.667 0.87 0.00 0.00 5.01
3044 5685 0.320374 TGGATTCAGTCGTTCGCCTT 59.680 50.000 0.00 0.00 0.00 4.35
3054 5695 2.158519 ACGGGTTTTTCCTGGATTCAGT 60.159 45.455 0.00 0.00 46.44 3.41
3066 5707 7.776500 AGTAAACCATAGCATATACGGGTTTTT 59.224 33.333 11.32 0.00 43.88 1.94
3170 5811 3.430556 TGTTACGGTGTTTCGATCACATG 59.569 43.478 18.32 13.63 37.52 3.21
3191 5832 5.721876 TTACGGATTTACGGTGCTTATTG 57.278 39.130 0.00 0.00 38.39 1.90
3367 6008 1.597854 CCTCCGCTGCTCAACAACA 60.598 57.895 0.00 0.00 0.00 3.33
3456 6097 6.053005 CAGCCCATTTGATTTGCTTTGATAT 58.947 36.000 0.00 0.00 0.00 1.63
3466 6107 3.516300 TCAATGAGCAGCCCATTTGATTT 59.484 39.130 0.00 0.00 32.40 2.17
3490 6131 8.743099 GTTCTTTGTTGAAAAGTAACATGCTAC 58.257 33.333 0.00 0.00 37.81 3.58
3492 6133 7.547227 AGTTCTTTGTTGAAAAGTAACATGCT 58.453 30.769 0.00 0.00 37.81 3.79
3509 6150 5.727791 GCATGCGTATGGTTCTAGTTCTTTG 60.728 44.000 15.54 0.00 34.79 2.77
3590 6231 9.268268 CTTCCACTACACTTTTACTGTTATTGA 57.732 33.333 0.00 0.00 0.00 2.57
3598 6239 6.726490 TCTCACTTCCACTACACTTTTACT 57.274 37.500 0.00 0.00 0.00 2.24
3606 6247 6.269077 TCCAAGTATTTCTCACTTCCACTACA 59.731 38.462 0.00 0.00 33.99 2.74
3637 6278 4.202040 GCAATATACTTTGATGCAGTGCCA 60.202 41.667 13.72 0.54 37.00 4.92
3658 6299 6.855763 AATCAATATGGAAAACCAGAAGCA 57.144 33.333 0.00 0.00 0.00 3.91
3739 6380 4.405116 TTTCCTTTTCTGCAGTGCAAAT 57.595 36.364 20.22 0.00 38.41 2.32
3758 6407 4.499696 GGCCGCTATAAACATGCTTCATTT 60.500 41.667 0.00 0.00 0.00 2.32
3806 6455 8.037758 CACTTGTACTGTTATCTCTTGATCCTT 58.962 37.037 0.00 0.00 34.32 3.36
3822 6471 8.310406 TGTACAAAGATCAATCACTTGTACTG 57.690 34.615 27.13 7.95 45.89 2.74
3841 6490 3.119424 TGTCATCGGTCGCTTATGTACAA 60.119 43.478 0.00 0.00 0.00 2.41
3883 6533 9.672673 AAGCAAGATGATAGCTAAGTTTTTCTA 57.327 29.630 0.00 0.00 37.70 2.10
3896 6547 9.766277 GAACTAAACAAGAAAGCAAGATGATAG 57.234 33.333 0.00 0.00 0.00 2.08
3943 6594 1.080093 CCAAGCGTAAGGAGCACGA 60.080 57.895 0.00 0.00 41.91 4.35
4112 7475 7.830940 TGCAATGCATATTAGTTTTTCCAAG 57.169 32.000 2.72 0.00 31.71 3.61
4129 7492 2.602878 CTCTGTTCCACAATGCAATGC 58.397 47.619 0.46 0.00 0.00 3.56
4220 7583 4.914983 TCTGAAATCCTCATGCTTCACTT 58.085 39.130 0.00 0.00 32.14 3.16
4235 7598 6.625740 CGCCATGTAAGGTTTCAATCTGAAAT 60.626 38.462 5.20 0.00 46.55 2.17


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

AutoCloner maintained by Alex Coulton.