Multiple sequence alignment - TraesCS6D01G028600

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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 TraesCS6D01G028600 chr6D 100.000 4047 0 0 1 4047 11054390 11058436 0.000000e+00 7474.0
1 TraesCS6D01G028600 chr6D 87.054 1344 95 30 72 1381 10981770 10983068 0.000000e+00 1445.0
2 TraesCS6D01G028600 chr6D 85.809 1353 156 15 995 2318 11085331 11086676 0.000000e+00 1402.0
3 TraesCS6D01G028600 chr6D 85.609 1355 163 14 992 2317 11041880 11043231 0.000000e+00 1393.0
4 TraesCS6D01G028600 chr6D 88.363 1014 103 10 2364 3368 11110616 11111623 0.000000e+00 1205.0
5 TraesCS6D01G028600 chr6D 87.625 1002 106 13 1376 2365 11023870 11024865 0.000000e+00 1147.0
6 TraesCS6D01G028600 chr6D 84.152 997 141 14 2366 3355 10918453 10919439 0.000000e+00 950.0
7 TraesCS6D01G028600 chr6D 87.778 810 91 7 932 1734 10916544 10917352 0.000000e+00 941.0
8 TraesCS6D01G028600 chr6D 83.932 1002 136 19 2367 3357 11086803 11087790 0.000000e+00 935.0
9 TraesCS6D01G028600 chr6D 82.944 985 114 26 797 1738 10938146 10939119 0.000000e+00 839.0
10 TraesCS6D01G028600 chr6B 84.395 1743 143 45 72 1738 20755429 20757118 0.000000e+00 1592.0
11 TraesCS6D01G028600 chr6B 86.364 1408 154 12 992 2362 20821823 20823229 0.000000e+00 1502.0
12 TraesCS6D01G028600 chr6B 87.617 1171 114 15 994 2135 21039418 21040586 0.000000e+00 1330.0
13 TraesCS6D01G028600 chr6B 83.901 1410 177 21 999 2366 20999823 21001224 0.000000e+00 1301.0
14 TraesCS6D01G028600 chr6B 84.467 1352 175 20 995 2317 23173544 23172199 0.000000e+00 1301.0
15 TraesCS6D01G028600 chr6B 87.788 1130 113 13 2365 3485 21066471 21067584 0.000000e+00 1299.0
16 TraesCS6D01G028600 chr6B 85.904 1206 139 12 1140 2318 20919030 20920231 0.000000e+00 1256.0
17 TraesCS6D01G028600 chr6B 87.343 1114 110 15 2522 3618 20975147 20976246 0.000000e+00 1247.0
18 TraesCS6D01G028600 chr6B 87.351 1091 116 14 2402 3485 20823484 20824559 0.000000e+00 1230.0
19 TraesCS6D01G028600 chr6B 83.175 1052 151 21 2378 3419 20952428 20953463 0.000000e+00 939.0
20 TraesCS6D01G028600 chr6B 82.321 1103 168 18 2367 3462 23171962 23170880 0.000000e+00 931.0
21 TraesCS6D01G028600 chr6B 83.283 993 138 21 2365 3348 21001310 21002283 0.000000e+00 889.0
22 TraesCS6D01G028600 chr6B 83.973 886 102 18 888 1738 20689920 20690800 0.000000e+00 813.0
23 TraesCS6D01G028600 chr6B 86.505 741 92 4 1001 1734 20710606 20711345 0.000000e+00 808.0
24 TraesCS6D01G028600 chr6B 86.449 642 69 7 1740 2365 20974268 20974907 0.000000e+00 688.0
25 TraesCS6D01G028600 chr6B 80.042 471 72 18 2957 3419 20856519 20856975 3.020000e-86 329.0
26 TraesCS6D01G028600 chr6B 78.506 549 70 31 3484 4007 21068228 21068753 2.350000e-82 316.0
27 TraesCS6D01G028600 chr6A 84.672 1357 177 13 989 2318 12405816 12407168 0.000000e+00 1325.0
28 TraesCS6D01G028600 chr7B 100.000 28 0 0 624 651 481051805 481051778 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G028600 chr6D 11054390 11058436 4046 False 7474.0 7474 100.0000 1 4047 1 chr6D.!!$F5 4046
1 TraesCS6D01G028600 chr6D 10981770 10983068 1298 False 1445.0 1445 87.0540 72 1381 1 chr6D.!!$F2 1309
2 TraesCS6D01G028600 chr6D 11041880 11043231 1351 False 1393.0 1393 85.6090 992 2317 1 chr6D.!!$F4 1325
3 TraesCS6D01G028600 chr6D 11110616 11111623 1007 False 1205.0 1205 88.3630 2364 3368 1 chr6D.!!$F6 1004
4 TraesCS6D01G028600 chr6D 11085331 11087790 2459 False 1168.5 1402 84.8705 995 3357 2 chr6D.!!$F8 2362
5 TraesCS6D01G028600 chr6D 11023870 11024865 995 False 1147.0 1147 87.6250 1376 2365 1 chr6D.!!$F3 989
6 TraesCS6D01G028600 chr6D 10916544 10919439 2895 False 945.5 950 85.9650 932 3355 2 chr6D.!!$F7 2423
7 TraesCS6D01G028600 chr6D 10938146 10939119 973 False 839.0 839 82.9440 797 1738 1 chr6D.!!$F1 941
8 TraesCS6D01G028600 chr6B 20755429 20757118 1689 False 1592.0 1592 84.3950 72 1738 1 chr6B.!!$F3 1666
9 TraesCS6D01G028600 chr6B 20821823 20824559 2736 False 1366.0 1502 86.8575 992 3485 2 chr6B.!!$F8 2493
10 TraesCS6D01G028600 chr6B 21039418 21040586 1168 False 1330.0 1330 87.6170 994 2135 1 chr6B.!!$F7 1141
11 TraesCS6D01G028600 chr6B 20919030 20920231 1201 False 1256.0 1256 85.9040 1140 2318 1 chr6B.!!$F5 1178
12 TraesCS6D01G028600 chr6B 23170880 23173544 2664 True 1116.0 1301 83.3940 995 3462 2 chr6B.!!$R1 2467
13 TraesCS6D01G028600 chr6B 20999823 21002283 2460 False 1095.0 1301 83.5920 999 3348 2 chr6B.!!$F10 2349
14 TraesCS6D01G028600 chr6B 20974268 20976246 1978 False 967.5 1247 86.8960 1740 3618 2 chr6B.!!$F9 1878
15 TraesCS6D01G028600 chr6B 20952428 20953463 1035 False 939.0 939 83.1750 2378 3419 1 chr6B.!!$F6 1041
16 TraesCS6D01G028600 chr6B 20689920 20690800 880 False 813.0 813 83.9730 888 1738 1 chr6B.!!$F1 850
17 TraesCS6D01G028600 chr6B 20710606 20711345 739 False 808.0 808 86.5050 1001 1734 1 chr6B.!!$F2 733
18 TraesCS6D01G028600 chr6B 21066471 21068753 2282 False 807.5 1299 83.1470 2365 4007 2 chr6B.!!$F11 1642
19 TraesCS6D01G028600 chr6A 12405816 12407168 1352 False 1325.0 1325 84.6720 989 2318 1 chr6A.!!$F1 1329

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
82 83 0.095935 CGCGCTTCAGAGGTGAAATG 59.904 55.0 5.56 0.0 42.27 2.32 F
990 1063 0.107606 AGCAGAGCCAGAGCAATGAG 60.108 55.0 0.00 0.0 43.56 2.90 F
1734 1828 0.255890 ATTCCCGTGATGAGGTTGGG 59.744 55.0 0.00 0.0 41.43 4.12 F
2753 3690 0.111061 ACTGGCACTGGCTGATGAAA 59.889 50.0 15.27 0.0 40.87 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 1163 0.322816 TCAGACCCAATGCCAAGCTC 60.323 55.0 0.00 0.0 0.00 4.09 R
2231 2492 0.105964 CACACGACCACCTTCCAAGA 59.894 55.0 0.00 0.0 0.00 3.02 R
2966 3903 0.454600 AGCTGCAATGCCAAATCTCG 59.545 50.0 1.53 0.0 0.00 4.04 R
3838 5451 0.179076 TATGCACCGAGGAGCACATG 60.179 55.0 15.98 0.0 43.71 3.21 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 4.875536 ACTTGTTTCAAATTCCACCTTTGC 59.124 37.500 0.00 0.00 34.36 3.68
24 25 4.478206 TGTTTCAAATTCCACCTTTGCA 57.522 36.364 0.00 0.00 34.36 4.08
25 26 5.033589 TGTTTCAAATTCCACCTTTGCAT 57.966 34.783 0.00 0.00 34.36 3.96
26 27 5.435291 TGTTTCAAATTCCACCTTTGCATT 58.565 33.333 0.00 0.00 34.36 3.56
27 28 5.884792 TGTTTCAAATTCCACCTTTGCATTT 59.115 32.000 0.00 0.00 34.36 2.32
28 29 6.038050 TGTTTCAAATTCCACCTTTGCATTTC 59.962 34.615 0.00 0.00 34.36 2.17
29 30 4.305769 TCAAATTCCACCTTTGCATTTCG 58.694 39.130 0.00 0.00 34.36 3.46
30 31 4.057432 CAAATTCCACCTTTGCATTTCGT 58.943 39.130 0.00 0.00 0.00 3.85
31 32 5.010112 TCAAATTCCACCTTTGCATTTCGTA 59.990 36.000 0.00 0.00 34.36 3.43
32 33 5.659440 AATTCCACCTTTGCATTTCGTAT 57.341 34.783 0.00 0.00 0.00 3.06
33 34 5.659440 ATTCCACCTTTGCATTTCGTATT 57.341 34.783 0.00 0.00 0.00 1.89
34 35 6.767524 ATTCCACCTTTGCATTTCGTATTA 57.232 33.333 0.00 0.00 0.00 0.98
35 36 6.767524 TTCCACCTTTGCATTTCGTATTAT 57.232 33.333 0.00 0.00 0.00 1.28
36 37 6.130298 TCCACCTTTGCATTTCGTATTATG 57.870 37.500 0.00 0.00 0.00 1.90
37 38 5.650266 TCCACCTTTGCATTTCGTATTATGT 59.350 36.000 0.00 0.00 0.00 2.29
38 39 6.151985 TCCACCTTTGCATTTCGTATTATGTT 59.848 34.615 0.00 0.00 0.00 2.71
39 40 6.472163 CCACCTTTGCATTTCGTATTATGTTC 59.528 38.462 0.00 0.00 0.00 3.18
40 41 7.026562 CACCTTTGCATTTCGTATTATGTTCA 58.973 34.615 0.00 0.00 0.00 3.18
41 42 7.701924 CACCTTTGCATTTCGTATTATGTTCAT 59.298 33.333 0.00 0.00 0.00 2.57
42 43 8.898761 ACCTTTGCATTTCGTATTATGTTCATA 58.101 29.630 0.00 0.00 0.00 2.15
43 44 9.169468 CCTTTGCATTTCGTATTATGTTCATAC 57.831 33.333 0.00 0.00 0.00 2.39
44 45 9.715123 CTTTGCATTTCGTATTATGTTCATACA 57.285 29.630 0.00 0.00 38.95 2.29
52 53 9.878667 TTCGTATTATGTTCATACAAAAGGAGA 57.121 29.630 0.00 0.00 37.91 3.71
53 54 9.878667 TCGTATTATGTTCATACAAAAGGAGAA 57.121 29.630 0.00 0.00 37.91 2.87
57 58 9.807649 ATTATGTTCATACAAAAGGAGAAATGC 57.192 29.630 0.00 0.00 37.91 3.56
58 59 5.698832 TGTTCATACAAAAGGAGAAATGCG 58.301 37.500 0.00 0.00 0.00 4.73
59 60 4.355543 TCATACAAAAGGAGAAATGCGC 57.644 40.909 0.00 0.00 0.00 6.09
60 61 3.128589 TCATACAAAAGGAGAAATGCGCC 59.871 43.478 4.18 0.00 36.60 6.53
64 65 4.208632 AGGAGAAATGCGCCTTCG 57.791 55.556 4.18 0.00 45.36 3.79
76 77 2.262915 CCTTCGCGCTTCAGAGGT 59.737 61.111 5.56 0.00 0.00 3.85
82 83 0.095935 CGCGCTTCAGAGGTGAAATG 59.904 55.000 5.56 0.00 42.27 2.32
127 129 1.580059 ACGGTGTCCCCAGATAATGT 58.420 50.000 0.00 0.00 0.00 2.71
130 132 1.680338 GTGTCCCCAGATAATGTGCC 58.320 55.000 0.00 0.00 0.00 5.01
133 135 2.092429 TGTCCCCAGATAATGTGCCTTC 60.092 50.000 0.00 0.00 0.00 3.46
134 136 1.140852 TCCCCAGATAATGTGCCTTCG 59.859 52.381 0.00 0.00 0.00 3.79
135 137 0.947244 CCCAGATAATGTGCCTTCGC 59.053 55.000 0.00 0.00 0.00 4.70
136 138 0.947244 CCAGATAATGTGCCTTCGCC 59.053 55.000 0.00 0.00 0.00 5.54
137 139 1.667236 CAGATAATGTGCCTTCGCCA 58.333 50.000 0.00 0.00 0.00 5.69
138 140 1.331756 CAGATAATGTGCCTTCGCCAC 59.668 52.381 0.00 0.00 0.00 5.01
139 141 1.210478 AGATAATGTGCCTTCGCCACT 59.790 47.619 0.00 0.00 0.00 4.00
140 142 1.599542 GATAATGTGCCTTCGCCACTC 59.400 52.381 0.00 0.00 0.00 3.51
141 143 0.613260 TAATGTGCCTTCGCCACTCT 59.387 50.000 0.00 0.00 0.00 3.24
142 144 0.613260 AATGTGCCTTCGCCACTCTA 59.387 50.000 0.00 0.00 0.00 2.43
143 145 0.176680 ATGTGCCTTCGCCACTCTAG 59.823 55.000 0.00 0.00 0.00 2.43
156 158 0.485099 ACTCTAGGGGAGCATCGGAT 59.515 55.000 0.00 0.00 45.48 4.18
169 171 1.335182 CATCGGATCGGATAGCGCTAT 59.665 52.381 29.38 29.38 0.00 2.97
170 172 1.460504 TCGGATCGGATAGCGCTATT 58.539 50.000 29.53 14.93 0.00 1.73
172 174 1.135373 CGGATCGGATAGCGCTATTGT 60.135 52.381 29.53 16.07 0.00 2.71
174 176 3.696898 GGATCGGATAGCGCTATTGTAG 58.303 50.000 29.53 19.84 0.00 2.74
176 178 4.380655 GGATCGGATAGCGCTATTGTAGTT 60.381 45.833 29.53 15.71 0.00 2.24
179 181 4.083110 TCGGATAGCGCTATTGTAGTTACC 60.083 45.833 29.53 21.05 0.00 2.85
183 185 3.528532 AGCGCTATTGTAGTTACCCAAC 58.471 45.455 8.99 0.00 34.67 3.77
193 195 1.078159 AGTTACCCAACCCCCAAATCC 59.922 52.381 0.00 0.00 35.05 3.01
280 285 3.849951 CGGTGGGAGTCGGATGGG 61.850 72.222 0.00 0.00 0.00 4.00
298 303 3.084579 CAGCTGTGGCGATTCGTC 58.915 61.111 5.25 3.17 44.37 4.20
299 304 2.125512 AGCTGTGGCGATTCGTCC 60.126 61.111 8.38 10.02 44.37 4.79
300 305 3.554692 GCTGTGGCGATTCGTCCG 61.555 66.667 8.38 0.00 0.00 4.79
352 358 3.081133 CTGCGGTGGTTCGATTCG 58.919 61.111 0.00 0.00 0.00 3.34
375 381 3.502455 CGTCGTCGGTCCGATGGA 61.502 66.667 28.81 20.51 42.34 3.41
434 440 0.946221 CCGACAGACAAGACAGTGGC 60.946 60.000 0.00 0.00 0.00 5.01
478 484 2.626683 CCATTTTACCCCAGCCCAGATT 60.627 50.000 0.00 0.00 0.00 2.40
480 486 1.681229 TTTACCCCAGCCCAGATTCT 58.319 50.000 0.00 0.00 0.00 2.40
481 487 1.213296 TTACCCCAGCCCAGATTCTC 58.787 55.000 0.00 0.00 0.00 2.87
496 507 5.509498 CAGATTCTCTCCATTTTACCCCAA 58.491 41.667 0.00 0.00 0.00 4.12
524 544 2.226200 TGCAATGTCGGTCACTCATTTG 59.774 45.455 0.00 0.00 30.74 2.32
557 577 1.375140 ATCAGCTGCAGTGTCGGTG 60.375 57.895 16.64 5.63 0.00 4.94
561 581 3.046087 CTGCAGTGTCGGTGGCTG 61.046 66.667 5.25 0.00 0.00 4.85
563 583 4.314440 GCAGTGTCGGTGGCTGGA 62.314 66.667 0.00 0.00 0.00 3.86
564 584 2.665000 CAGTGTCGGTGGCTGGAT 59.335 61.111 0.00 0.00 0.00 3.41
565 585 1.897423 CAGTGTCGGTGGCTGGATA 59.103 57.895 0.00 0.00 0.00 2.59
566 586 0.179100 CAGTGTCGGTGGCTGGATAG 60.179 60.000 0.00 0.00 0.00 2.08
578 598 3.736530 GCTGGATAGCTATCGCAATTG 57.263 47.619 24.05 13.60 46.57 2.32
653 673 7.358770 ACTCATTACTCATTACTCATCAGCT 57.641 36.000 0.00 0.00 0.00 4.24
678 698 3.072211 GCCCAACCAACAAGAGTAGTAC 58.928 50.000 0.00 0.00 0.00 2.73
830 850 4.084287 ACTTCATCATGTGCAATGTCCTT 58.916 39.130 0.00 0.00 0.00 3.36
841 861 3.943381 TGCAATGTCCTTCATCACTCATC 59.057 43.478 0.00 0.00 35.48 2.92
909 938 0.180642 AGTCCATCAGCTGCTCCATG 59.819 55.000 9.47 7.51 0.00 3.66
911 940 1.226542 CCATCAGCTGCTCCATGGT 59.773 57.895 21.58 0.00 32.49 3.55
956 996 0.467290 TTTTGCTCCACCCACCAGAC 60.467 55.000 0.00 0.00 0.00 3.51
984 1057 2.187424 CTCCAGCAGAGCCAGAGC 59.813 66.667 0.00 0.00 35.31 4.09
985 1058 2.605601 TCCAGCAGAGCCAGAGCA 60.606 61.111 0.00 0.00 43.56 4.26
986 1059 2.181445 CTCCAGCAGAGCCAGAGCAA 62.181 60.000 0.00 0.00 43.56 3.91
987 1060 1.077644 CCAGCAGAGCCAGAGCAAT 60.078 57.895 0.00 0.00 43.56 3.56
990 1063 0.107606 AGCAGAGCCAGAGCAATGAG 60.108 55.000 0.00 0.00 43.56 2.90
992 1065 1.942677 CAGAGCCAGAGCAATGAGAG 58.057 55.000 0.00 0.00 43.56 3.20
1090 1163 2.203070 CGGAGGAAATCGGGCTGG 60.203 66.667 0.00 0.00 0.00 4.85
1103 1176 2.718073 GGCTGGAGCTTGGCATTGG 61.718 63.158 0.00 0.00 41.70 3.16
1335 1408 2.584970 CGCCGCATCGCTAAGGAA 60.585 61.111 0.00 0.00 0.00 3.36
1374 1447 1.194781 AGGTGGAGGACGTGAGCAAT 61.195 55.000 0.00 0.00 0.00 3.56
1425 1498 1.142748 CTCAGCCTCCAAGCCTACG 59.857 63.158 0.00 0.00 0.00 3.51
1690 1784 0.471211 TCCACAAGAGTTCCTCCGGT 60.471 55.000 0.00 0.00 0.00 5.28
1692 1786 0.951040 CACAAGAGTTCCTCCGGTGC 60.951 60.000 0.00 0.00 31.75 5.01
1729 1823 6.449635 TTTATGAAAATTCCCGTGATGAGG 57.550 37.500 0.00 0.00 0.00 3.86
1734 1828 0.255890 ATTCCCGTGATGAGGTTGGG 59.744 55.000 0.00 0.00 41.43 4.12
1766 1860 1.694150 CAGTCCACAAGAGTTCCTCCA 59.306 52.381 0.00 0.00 0.00 3.86
1835 2085 2.689983 AGCCAGAACAAGAAACAAGTGG 59.310 45.455 0.00 0.00 0.00 4.00
1996 2249 4.814771 AGTACTTTCCCGACAACAAGAAAG 59.185 41.667 9.22 9.22 46.78 2.62
2031 2287 0.654683 CCACGCAGCTAGCTGAAATC 59.345 55.000 41.87 25.33 46.30 2.17
2094 2350 3.749609 TGAAGCAGTTGTCATGTGATCAG 59.250 43.478 0.00 0.00 0.00 2.90
2137 2393 8.647143 CAAGAAGGTAAATCTTTTTCTTGCAA 57.353 30.769 11.01 0.00 44.16 4.08
2148 2404 6.165577 TCTTTTTCTTGCAAGTTTTCTGCTT 58.834 32.000 25.19 0.00 0.00 3.91
2231 2492 5.708697 TGCAGAATTCAGAACAACAGATCAT 59.291 36.000 8.44 0.00 0.00 2.45
2233 2494 6.093771 GCAGAATTCAGAACAACAGATCATCT 59.906 38.462 8.44 0.00 0.00 2.90
2238 2499 5.868454 TCAGAACAACAGATCATCTTGGAA 58.132 37.500 0.00 0.00 0.00 3.53
2243 2504 3.641434 ACAGATCATCTTGGAAGGTGG 57.359 47.619 0.00 0.00 37.73 4.61
2256 2517 0.398696 AAGGTGGTCGTGTGGCAATA 59.601 50.000 0.00 0.00 0.00 1.90
2284 2545 4.404073 ACACCAATGACAAAGCAAAGGTTA 59.596 37.500 0.00 0.00 29.85 2.85
2330 2604 4.262036 GGTGGGACTCCTCAAAATTCAAAC 60.262 45.833 0.00 0.00 39.21 2.93
2362 2637 8.797350 TGCATGTCTATGGATTATATTTGGAG 57.203 34.615 0.00 0.00 34.79 3.86
2397 3229 4.734398 TGTGCTTTCAAGTTGAACCAAT 57.266 36.364 17.85 0.00 35.89 3.16
2452 3383 4.408182 ACTGCTCTCACTAAAAGTGTGT 57.592 40.909 6.93 0.00 46.03 3.72
2455 3387 4.628074 TGCTCTCACTAAAAGTGTGTACC 58.372 43.478 6.93 0.31 46.03 3.34
2466 3398 8.434392 ACTAAAAGTGTGTACCTGAAAATCCTA 58.566 33.333 0.00 0.00 0.00 2.94
2515 3451 8.354711 AGTCTAGATGTGAAAATGTGTAGAGA 57.645 34.615 0.00 0.00 0.00 3.10
2598 3535 3.431725 GCCCGTTTCCGCCTCAAG 61.432 66.667 0.00 0.00 0.00 3.02
2657 3594 4.324563 CCACTGGTGAAATACAGGAGGAAT 60.325 45.833 1.93 0.00 39.00 3.01
2675 3612 7.628101 AGGAGGAATACCAAGAACCTAATAACT 59.372 37.037 0.00 0.00 38.94 2.24
2677 3614 7.803131 AGGAATACCAAGAACCTAATAACTCC 58.197 38.462 0.00 0.00 38.94 3.85
2753 3690 0.111061 ACTGGCACTGGCTGATGAAA 59.889 50.000 15.27 0.00 40.87 2.69
2757 3694 0.179119 GCACTGGCTGATGAAATGCC 60.179 55.000 0.00 0.00 46.26 4.40
2897 3834 0.815095 TCGAAGCATCTACCGAAGCA 59.185 50.000 0.00 0.00 36.37 3.91
2936 3873 3.982241 GTGCTTGGGCCACTGCAC 61.982 66.667 33.35 33.35 46.66 4.57
2962 3899 5.567423 GCGTCCTTTTAACCCTGAAGTACTA 60.567 44.000 0.00 0.00 0.00 1.82
2977 3914 5.401531 AAGTACTACTTCGAGATTTGGCA 57.598 39.130 0.00 0.00 31.77 4.92
3028 3966 2.624169 GCCGGAGCAACAACAACTA 58.376 52.632 5.05 0.00 39.53 2.24
3043 3981 7.100458 ACAACAACTAGAGTGCAAAAGAAAT 57.900 32.000 0.00 0.00 0.00 2.17
3044 3982 7.547227 ACAACAACTAGAGTGCAAAAGAAATT 58.453 30.769 0.00 0.00 0.00 1.82
3045 3983 8.682710 ACAACAACTAGAGTGCAAAAGAAATTA 58.317 29.630 0.00 0.00 0.00 1.40
3046 3984 9.515020 CAACAACTAGAGTGCAAAAGAAATTAA 57.485 29.630 0.00 0.00 0.00 1.40
3096 4037 1.253100 GAAGGAGCTAGCTCGGCTAT 58.747 55.000 32.78 19.08 43.59 2.97
3192 4133 5.462068 TGTTTAGATAATGCTGAACGGATCG 59.538 40.000 0.00 0.00 37.24 3.69
3244 4186 5.930837 AACATTGTTCAAGGGAAGACAAA 57.069 34.783 0.00 0.00 32.62 2.83
3290 4232 1.208052 AGTATGATGCGGCACTTGACT 59.792 47.619 4.03 4.15 0.00 3.41
3348 4290 9.620259 ATCCTTTCTTACCTTTCATATGAGTTC 57.380 33.333 5.39 0.00 0.00 3.01
3372 4314 5.695851 ACTTCACCTTGCATCAGTTTTAG 57.304 39.130 0.00 0.00 0.00 1.85
3387 4329 9.708222 CATCAGTTTTAGCTCATGTACAATTAC 57.292 33.333 0.00 0.00 0.00 1.89
3388 4330 8.840833 TCAGTTTTAGCTCATGTACAATTACA 57.159 30.769 0.00 0.00 42.53 2.41
3389 4331 9.278978 TCAGTTTTAGCTCATGTACAATTACAA 57.721 29.630 0.00 0.00 41.64 2.41
3422 4364 6.018669 CGTAAGCTTGAACTTTCTCTCAGTTT 60.019 38.462 9.86 0.00 34.49 2.66
3493 5081 0.035439 ACCCCAATAGTGGTTCAGCG 60.035 55.000 8.66 0.00 44.30 5.18
3495 5083 1.208535 CCCCAATAGTGGTTCAGCGTA 59.791 52.381 8.66 0.00 44.30 4.42
3499 5087 4.201910 CCCAATAGTGGTTCAGCGTATTTG 60.202 45.833 8.66 0.00 44.30 2.32
3588 5189 2.901839 TGCTACGTTAGGAGGGAGTTTT 59.098 45.455 0.00 0.00 0.00 2.43
3614 5215 9.522804 TTTTTGCTGGTATTGTTTGTAGTAAAG 57.477 29.630 0.00 0.00 0.00 1.85
3621 5222 7.013529 GGTATTGTTTGTAGTAAAGCTTGTCG 58.986 38.462 0.00 0.00 0.00 4.35
3622 5223 6.854496 ATTGTTTGTAGTAAAGCTTGTCGA 57.146 33.333 0.00 0.00 0.00 4.20
3623 5224 6.854496 TTGTTTGTAGTAAAGCTTGTCGAT 57.146 33.333 0.00 0.00 0.00 3.59
3626 5227 7.790000 TGTTTGTAGTAAAGCTTGTCGATAAC 58.210 34.615 0.00 0.93 0.00 1.89
3630 5231 8.624701 TGTAGTAAAGCTTGTCGATAACATAC 57.375 34.615 0.00 0.00 37.82 2.39
3633 5234 8.718102 AGTAAAGCTTGTCGATAACATACAAT 57.282 30.769 0.00 0.00 37.82 2.71
3636 5237 5.810525 AGCTTGTCGATAACATACAATTGC 58.189 37.500 5.05 0.00 37.82 3.56
3637 5238 5.586243 AGCTTGTCGATAACATACAATTGCT 59.414 36.000 5.05 0.00 37.82 3.91
3638 5239 6.761242 AGCTTGTCGATAACATACAATTGCTA 59.239 34.615 5.05 0.00 37.82 3.49
3639 5240 7.279981 AGCTTGTCGATAACATACAATTGCTAA 59.720 33.333 5.05 0.00 37.82 3.09
3641 5242 7.241663 TGTCGATAACATACAATTGCTAACC 57.758 36.000 5.05 0.00 31.20 2.85
3643 5244 7.011016 TGTCGATAACATACAATTGCTAACCTG 59.989 37.037 5.05 0.00 31.20 4.00
3644 5245 7.223971 GTCGATAACATACAATTGCTAACCTGA 59.776 37.037 5.05 0.00 0.00 3.86
3645 5246 7.223971 TCGATAACATACAATTGCTAACCTGAC 59.776 37.037 5.05 0.00 0.00 3.51
3647 5248 8.752005 ATAACATACAATTGCTAACCTGACAT 57.248 30.769 5.05 0.00 0.00 3.06
3649 5250 6.179756 ACATACAATTGCTAACCTGACATCA 58.820 36.000 5.05 0.00 0.00 3.07
3673 5283 5.167845 GGTTTGTTACCAAGGTTATGCATG 58.832 41.667 10.16 0.00 46.92 4.06
3690 5300 4.757594 TGCATGCAATTTTTAAGGGCTAG 58.242 39.130 20.30 0.00 0.00 3.42
3692 5302 5.129155 TGCATGCAATTTTTAAGGGCTAGAT 59.871 36.000 20.30 0.00 0.00 1.98
3712 5322 6.916360 AGATTAGCACCCATTTTTCTCAAA 57.084 33.333 0.00 0.00 0.00 2.69
3713 5323 7.486407 AGATTAGCACCCATTTTTCTCAAAT 57.514 32.000 0.00 0.00 0.00 2.32
3714 5324 7.910584 AGATTAGCACCCATTTTTCTCAAATT 58.089 30.769 0.00 0.00 0.00 1.82
3715 5325 8.377799 AGATTAGCACCCATTTTTCTCAAATTT 58.622 29.630 0.00 0.00 0.00 1.82
3716 5326 9.651913 GATTAGCACCCATTTTTCTCAAATTTA 57.348 29.630 0.00 0.00 0.00 1.40
3749 5359 7.953005 TTCACTGGAATAAATCTGCCAAATA 57.047 32.000 0.00 0.00 0.00 1.40
3788 5401 9.509855 GTAGTAATTGAAAATGTGTGTTTGTGA 57.490 29.630 0.00 0.00 0.00 3.58
3791 5404 9.848172 GTAATTGAAAATGTGTGTTTGTGATTC 57.152 29.630 0.00 0.00 0.00 2.52
3893 5507 1.332997 GCATGCTTCTAGGTGCACATC 59.667 52.381 20.43 1.46 42.26 3.06
3895 5509 2.391616 TGCTTCTAGGTGCACATCTG 57.608 50.000 20.43 8.61 33.94 2.90
3899 5513 3.944015 GCTTCTAGGTGCACATCTGAATT 59.056 43.478 20.43 0.00 0.00 2.17
3900 5514 4.201891 GCTTCTAGGTGCACATCTGAATTG 60.202 45.833 20.43 9.86 0.00 2.32
3903 5517 6.239217 TCTAGGTGCACATCTGAATTGTAT 57.761 37.500 20.43 0.00 0.00 2.29
3924 5539 8.581253 TGTATCAGTATCTAGGATACCATGTG 57.419 38.462 12.35 6.31 41.56 3.21
3930 5545 6.948886 AGTATCTAGGATACCATGTGTAGTGG 59.051 42.308 12.35 0.00 42.55 4.00
3944 5559 6.373186 TGTGTAGTGGATACTGAAGATACG 57.627 41.667 0.00 0.00 37.78 3.06
3949 5564 4.338682 AGTGGATACTGAAGATACGTGGAC 59.661 45.833 0.00 0.00 35.34 4.02
3955 5570 3.118738 ACTGAAGATACGTGGACATTCCC 60.119 47.826 0.00 0.00 35.03 3.97
3964 5579 1.678101 GTGGACATTCCCATGCTTAGC 59.322 52.381 0.00 0.00 38.66 3.09
3966 5581 1.475034 GGACATTCCCATGCTTAGCGA 60.475 52.381 0.00 0.00 33.05 4.93
3967 5582 1.599542 GACATTCCCATGCTTAGCGAC 59.400 52.381 0.00 0.00 33.05 5.19
3975 5590 2.484417 CCATGCTTAGCGACTTCTCCAT 60.484 50.000 0.00 0.00 0.00 3.41
3989 5604 6.690098 CGACTTCTCCATATGCAGAAAATTTG 59.310 38.462 10.28 1.46 0.00 2.32
3995 5610 8.587608 TCTCCATATGCAGAAAATTTGAAGTTT 58.412 29.630 0.00 0.00 0.00 2.66
3996 5611 8.537049 TCCATATGCAGAAAATTTGAAGTTTG 57.463 30.769 0.00 0.00 0.00 2.93
4000 5615 7.713764 ATGCAGAAAATTTGAAGTTTGTACC 57.286 32.000 0.00 0.00 0.00 3.34
4008 5623 9.981114 AAAATTTGAAGTTTGTACCCTTCTATG 57.019 29.630 14.41 0.00 38.30 2.23
4009 5624 8.706322 AATTTGAAGTTTGTACCCTTCTATGT 57.294 30.769 14.41 0.00 38.30 2.29
4010 5625 9.802039 AATTTGAAGTTTGTACCCTTCTATGTA 57.198 29.630 14.41 0.00 38.30 2.29
4011 5626 9.802039 ATTTGAAGTTTGTACCCTTCTATGTAA 57.198 29.630 14.41 2.61 38.30 2.41
4012 5627 9.802039 TTTGAAGTTTGTACCCTTCTATGTAAT 57.198 29.630 14.41 0.00 38.30 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.874966 TGCAAAGGTGGAATTTGAAACAAG 59.125 37.500 2.76 0.00 39.50 3.16
3 4 4.478206 TGCAAAGGTGGAATTTGAAACA 57.522 36.364 2.76 0.00 39.50 2.83
6 7 4.749099 CGAAATGCAAAGGTGGAATTTGAA 59.251 37.500 0.00 0.00 39.50 2.69
7 8 4.202202 ACGAAATGCAAAGGTGGAATTTGA 60.202 37.500 0.00 0.00 39.50 2.69
8 9 4.057432 ACGAAATGCAAAGGTGGAATTTG 58.943 39.130 0.00 0.00 39.99 2.32
9 10 4.335400 ACGAAATGCAAAGGTGGAATTT 57.665 36.364 0.00 0.00 0.00 1.82
10 11 5.659440 ATACGAAATGCAAAGGTGGAATT 57.341 34.783 0.00 0.00 0.00 2.17
11 12 5.659440 AATACGAAATGCAAAGGTGGAAT 57.341 34.783 0.00 0.00 0.00 3.01
12 13 6.151985 ACATAATACGAAATGCAAAGGTGGAA 59.848 34.615 0.00 0.00 0.00 3.53
13 14 5.650266 ACATAATACGAAATGCAAAGGTGGA 59.350 36.000 0.00 0.00 0.00 4.02
14 15 5.890334 ACATAATACGAAATGCAAAGGTGG 58.110 37.500 0.00 0.00 0.00 4.61
15 16 7.026562 TGAACATAATACGAAATGCAAAGGTG 58.973 34.615 0.00 0.00 0.00 4.00
16 17 7.151999 TGAACATAATACGAAATGCAAAGGT 57.848 32.000 0.00 0.00 0.00 3.50
17 18 9.169468 GTATGAACATAATACGAAATGCAAAGG 57.831 33.333 0.00 0.00 0.00 3.11
18 19 9.715123 TGTATGAACATAATACGAAATGCAAAG 57.285 29.630 0.00 0.00 33.93 2.77
26 27 9.878667 TCTCCTTTTGTATGAACATAATACGAA 57.121 29.630 0.00 0.00 34.97 3.85
27 28 9.878667 TTCTCCTTTTGTATGAACATAATACGA 57.121 29.630 0.00 0.00 34.97 3.43
31 32 9.807649 GCATTTCTCCTTTTGTATGAACATAAT 57.192 29.630 0.00 0.00 34.97 1.28
32 33 7.967854 CGCATTTCTCCTTTTGTATGAACATAA 59.032 33.333 0.00 0.00 34.97 1.90
33 34 7.471721 CGCATTTCTCCTTTTGTATGAACATA 58.528 34.615 0.00 0.00 34.97 2.29
34 35 6.324819 CGCATTTCTCCTTTTGTATGAACAT 58.675 36.000 0.00 0.00 34.97 2.71
35 36 5.698832 CGCATTTCTCCTTTTGTATGAACA 58.301 37.500 0.00 0.00 0.00 3.18
36 37 4.558860 GCGCATTTCTCCTTTTGTATGAAC 59.441 41.667 0.30 0.00 0.00 3.18
37 38 4.380444 GGCGCATTTCTCCTTTTGTATGAA 60.380 41.667 10.83 0.00 0.00 2.57
38 39 3.128589 GGCGCATTTCTCCTTTTGTATGA 59.871 43.478 10.83 0.00 0.00 2.15
39 40 3.129287 AGGCGCATTTCTCCTTTTGTATG 59.871 43.478 10.83 0.00 0.00 2.39
40 41 3.356290 AGGCGCATTTCTCCTTTTGTAT 58.644 40.909 10.83 0.00 0.00 2.29
41 42 2.790433 AGGCGCATTTCTCCTTTTGTA 58.210 42.857 10.83 0.00 0.00 2.41
42 43 1.620822 AGGCGCATTTCTCCTTTTGT 58.379 45.000 10.83 0.00 0.00 2.83
43 44 2.599659 GAAGGCGCATTTCTCCTTTTG 58.400 47.619 9.39 0.00 39.85 2.44
44 45 1.200020 CGAAGGCGCATTTCTCCTTTT 59.800 47.619 9.39 0.00 39.85 2.27
45 46 0.804989 CGAAGGCGCATTTCTCCTTT 59.195 50.000 9.39 0.00 39.85 3.11
46 47 2.471255 CGAAGGCGCATTTCTCCTT 58.529 52.632 9.39 0.00 42.31 3.36
47 48 4.208632 CGAAGGCGCATTTCTCCT 57.791 55.556 9.39 0.00 0.00 3.69
58 59 3.191539 CCTCTGAAGCGCGAAGGC 61.192 66.667 12.10 0.00 0.00 4.35
59 60 2.097038 CACCTCTGAAGCGCGAAGG 61.097 63.158 12.10 8.40 0.00 3.46
60 61 0.667487 TTCACCTCTGAAGCGCGAAG 60.667 55.000 12.10 0.48 32.33 3.79
61 62 0.249699 TTTCACCTCTGAAGCGCGAA 60.250 50.000 12.10 0.00 37.70 4.70
62 63 0.037326 ATTTCACCTCTGAAGCGCGA 60.037 50.000 12.10 0.00 37.70 5.87
63 64 0.095935 CATTTCACCTCTGAAGCGCG 59.904 55.000 0.00 0.00 37.70 6.86
64 65 0.179179 GCATTTCACCTCTGAAGCGC 60.179 55.000 0.00 0.00 37.70 5.92
65 66 0.095935 CGCATTTCACCTCTGAAGCG 59.904 55.000 0.00 0.00 41.69 4.68
66 67 0.179179 GCGCATTTCACCTCTGAAGC 60.179 55.000 0.30 0.00 37.70 3.86
67 68 0.449388 GGCGCATTTCACCTCTGAAG 59.551 55.000 10.83 0.00 37.70 3.02
68 69 0.036732 AGGCGCATTTCACCTCTGAA 59.963 50.000 10.83 0.00 34.39 3.02
69 70 0.036732 AAGGCGCATTTCACCTCTGA 59.963 50.000 10.83 0.00 31.86 3.27
70 71 0.449388 GAAGGCGCATTTCACCTCTG 59.551 55.000 9.39 0.00 31.86 3.35
93 94 3.429085 ACACCGTATTACGCTTACGAAG 58.571 45.455 10.72 7.73 43.88 3.79
114 115 1.140852 CGAAGGCACATTATCTGGGGA 59.859 52.381 0.00 0.00 0.00 4.81
130 132 2.022240 GCTCCCCTAGAGTGGCGAAG 62.022 65.000 0.00 0.00 45.21 3.79
133 135 2.093537 GATGCTCCCCTAGAGTGGCG 62.094 65.000 0.00 0.00 45.21 5.69
134 136 1.751563 GATGCTCCCCTAGAGTGGC 59.248 63.158 0.00 0.00 45.21 5.01
135 137 1.467678 CCGATGCTCCCCTAGAGTGG 61.468 65.000 0.00 0.00 45.21 4.00
136 138 0.468214 TCCGATGCTCCCCTAGAGTG 60.468 60.000 0.00 0.00 45.21 3.51
137 139 0.485099 ATCCGATGCTCCCCTAGAGT 59.515 55.000 0.00 0.00 45.21 3.24
138 140 1.181786 GATCCGATGCTCCCCTAGAG 58.818 60.000 0.00 0.00 46.29 2.43
139 141 0.609406 CGATCCGATGCTCCCCTAGA 60.609 60.000 0.00 0.00 0.00 2.43
140 142 1.599606 CCGATCCGATGCTCCCCTAG 61.600 65.000 0.00 0.00 0.00 3.02
141 143 1.606601 CCGATCCGATGCTCCCCTA 60.607 63.158 0.00 0.00 0.00 3.53
142 144 2.738510 ATCCGATCCGATGCTCCCCT 62.739 60.000 0.00 0.00 0.00 4.79
143 145 0.970937 TATCCGATCCGATGCTCCCC 60.971 60.000 6.79 0.00 0.00 4.81
156 158 4.083110 GGTAACTACAATAGCGCTATCCGA 60.083 45.833 29.11 15.86 40.02 4.55
169 171 1.830486 TGGGGGTTGGGTAACTACAA 58.170 50.000 0.00 0.00 36.99 2.41
170 172 1.830486 TTGGGGGTTGGGTAACTACA 58.170 50.000 0.00 0.00 36.99 2.74
172 174 2.312440 GGATTTGGGGGTTGGGTAACTA 59.688 50.000 0.00 0.00 36.99 2.24
174 176 1.563924 GGATTTGGGGGTTGGGTAAC 58.436 55.000 0.00 0.00 36.04 2.50
176 178 0.845543 TCGGATTTGGGGGTTGGGTA 60.846 55.000 0.00 0.00 0.00 3.69
179 181 1.343069 TTTTCGGATTTGGGGGTTGG 58.657 50.000 0.00 0.00 0.00 3.77
193 195 1.064060 GGATCAAGGCACCGATTTTCG 59.936 52.381 0.00 0.00 40.07 3.46
229 234 3.735029 AGGCTCCGTCGTCGACAC 61.735 66.667 24.13 11.68 39.71 3.67
280 285 3.088500 GACGAATCGCCACAGCTGC 62.089 63.158 15.27 0.00 36.60 5.25
420 426 2.743718 CCCGCCACTGTCTTGTCT 59.256 61.111 0.00 0.00 0.00 3.41
478 484 2.310647 GGGTTGGGGTAAAATGGAGAGA 59.689 50.000 0.00 0.00 0.00 3.10
480 486 2.042433 CTGGGTTGGGGTAAAATGGAGA 59.958 50.000 0.00 0.00 0.00 3.71
481 487 2.456577 CTGGGTTGGGGTAAAATGGAG 58.543 52.381 0.00 0.00 0.00 3.86
496 507 2.360350 CCGACATTGCAGCTGGGT 60.360 61.111 17.12 0.00 0.00 4.51
524 544 1.002033 GCTGATGGATTGAATGCGGAC 60.002 52.381 0.00 0.00 0.00 4.79
567 587 5.835257 ACCAAAATGATCCAATTGCGATAG 58.165 37.500 0.00 0.00 0.00 2.08
568 588 5.850557 ACCAAAATGATCCAATTGCGATA 57.149 34.783 0.00 0.00 0.00 2.92
569 589 4.741321 ACCAAAATGATCCAATTGCGAT 57.259 36.364 0.00 4.56 0.00 4.58
570 590 4.220382 AGAACCAAAATGATCCAATTGCGA 59.780 37.500 0.00 0.00 0.00 5.10
571 591 4.327898 CAGAACCAAAATGATCCAATTGCG 59.672 41.667 0.00 0.00 0.00 4.85
578 598 9.129532 AGATAGAAATCAGAACCAAAATGATCC 57.870 33.333 0.00 0.00 32.59 3.36
653 673 3.222855 CTTGTTGGTTGGGCCGCA 61.223 61.111 0.00 0.00 41.21 5.69
678 698 3.300857 CACTCACTCACTCACTTGTACG 58.699 50.000 0.00 0.00 0.00 3.67
830 850 3.638160 TGATGGACGATGATGAGTGATGA 59.362 43.478 0.00 0.00 0.00 2.92
841 861 2.216046 CTGGTGGATTGATGGACGATG 58.784 52.381 0.00 0.00 0.00 3.84
956 996 1.684386 CTGCTGGAGGAGGTGCTAGG 61.684 65.000 0.00 0.00 0.00 3.02
984 1057 1.767088 TCCATGCCTCTCCTCTCATTG 59.233 52.381 0.00 0.00 0.00 2.82
985 1058 2.048601 CTCCATGCCTCTCCTCTCATT 58.951 52.381 0.00 0.00 0.00 2.57
986 1059 1.719529 CTCCATGCCTCTCCTCTCAT 58.280 55.000 0.00 0.00 0.00 2.90
987 1060 0.398239 CCTCCATGCCTCTCCTCTCA 60.398 60.000 0.00 0.00 0.00 3.27
990 1063 2.828145 GCCTCCATGCCTCTCCTC 59.172 66.667 0.00 0.00 0.00 3.71
992 1065 3.157252 TCGCCTCCATGCCTCTCC 61.157 66.667 0.00 0.00 0.00 3.71
1090 1163 0.322816 TCAGACCCAATGCCAAGCTC 60.323 55.000 0.00 0.00 0.00 4.09
1103 1176 3.616956 TGATGAAGTCCACATCAGACC 57.383 47.619 0.00 0.00 45.71 3.85
1329 1402 2.027745 CCTCAGCTGCTTCACTTCCTTA 60.028 50.000 9.47 0.00 0.00 2.69
1335 1408 1.676384 GGTCCTCAGCTGCTTCACT 59.324 57.895 9.47 0.00 0.00 3.41
1453 1526 4.476361 GGTAAACATTGCCGCAGC 57.524 55.556 0.00 0.00 40.48 5.25
1690 1784 5.991933 TCATAAAATTGCCTTACCAAGCA 57.008 34.783 0.00 0.00 37.18 3.91
1729 1823 2.489722 GACTGAAAGATGGCTTCCCAAC 59.510 50.000 0.00 0.00 40.81 3.77
1734 1828 2.783135 TGTGGACTGAAAGATGGCTTC 58.217 47.619 0.00 0.00 37.43 3.86
1766 1860 5.951747 TCATAAAATTGCCTTACCAAGCTCT 59.048 36.000 0.00 0.00 0.00 4.09
1906 2159 9.909644 AATTACAACCAGATAGCTATTACTACG 57.090 33.333 7.87 0.00 0.00 3.51
1996 2249 2.159747 GCGTGGAAACAACGATTCTACC 60.160 50.000 2.77 0.00 46.06 3.18
2031 2287 1.082300 CTCTGTGCACAAGCTTGCG 60.082 57.895 26.27 18.30 46.20 4.85
2137 2393 9.435688 AAAGAAACAAATACAAAGCAGAAAACT 57.564 25.926 0.00 0.00 0.00 2.66
2231 2492 0.105964 CACACGACCACCTTCCAAGA 59.894 55.000 0.00 0.00 0.00 3.02
2233 2494 1.147376 CCACACGACCACCTTCCAA 59.853 57.895 0.00 0.00 0.00 3.53
2238 2499 0.618458 ATATTGCCACACGACCACCT 59.382 50.000 0.00 0.00 0.00 4.00
2243 2504 3.247648 GGTGTCATATATTGCCACACGAC 59.752 47.826 0.00 0.00 35.12 4.34
2256 2517 5.981088 TTGCTTTGTCATTGGTGTCATAT 57.019 34.783 0.00 0.00 0.00 1.78
2284 2545 1.071385 CAGTTTCTCCTCCACTGCAGT 59.929 52.381 15.25 15.25 31.99 4.40
2362 2637 8.603181 ACTTGAAAGCACAATGTATTTTTCAAC 58.397 29.630 18.90 2.13 38.72 3.18
2422 3351 5.939764 TTAGTGAGAGCAGTATGTCCAAT 57.060 39.130 0.00 0.00 39.31 3.16
2551 3488 1.886542 CATGATGCATGCATAGCCTGT 59.113 47.619 32.27 10.58 35.02 4.00
2592 3529 4.863131 CGGTAGTAGTAACTTTGCTTGAGG 59.137 45.833 0.00 0.00 37.15 3.86
2598 3535 7.412137 TTTTTCTCGGTAGTAGTAACTTTGC 57.588 36.000 0.00 0.00 37.15 3.68
2657 3594 5.025453 ACCGGAGTTATTAGGTTCTTGGTA 58.975 41.667 9.46 0.00 32.17 3.25
2690 3627 9.160496 CTTCTTTCTAGCAGTTGAGTTATGAAT 57.840 33.333 0.00 0.00 0.00 2.57
2757 3694 0.671781 CTCTGTTTCTCGCCCACAGG 60.672 60.000 0.00 0.00 38.80 4.00
2878 3815 0.815095 TGCTTCGGTAGATGCTTCGA 59.185 50.000 7.67 0.00 44.83 3.71
2907 3844 2.034687 AAGCACGCTTCCAGCCAT 59.965 55.556 0.00 0.00 38.18 4.40
2936 3873 2.178912 TCAGGGTTAAAAGGACGCAG 57.821 50.000 0.00 0.00 32.91 5.18
2962 3899 2.161855 TGCAATGCCAAATCTCGAAGT 58.838 42.857 1.53 0.00 0.00 3.01
2966 3903 0.454600 AGCTGCAATGCCAAATCTCG 59.545 50.000 1.53 0.00 0.00 4.04
2977 3914 7.278135 TCTTGAATAGTATTCTGAGCTGCAAT 58.722 34.615 20.80 0.00 0.00 3.56
3046 3984 9.442047 CCTGAAGATTCTTATCAGTTACACTTT 57.558 33.333 12.29 0.00 39.10 2.66
3047 3985 8.816894 TCCTGAAGATTCTTATCAGTTACACTT 58.183 33.333 12.29 0.00 39.10 3.16
3071 4009 2.478831 CGAGCTAGCTCCTTCAAATCC 58.521 52.381 33.57 10.48 39.77 3.01
3218 4160 4.099419 GTCTTCCCTTGAACAATGTTTGGT 59.901 41.667 0.00 0.00 34.12 3.67
3244 4186 7.500992 TCAGAACTTGAAGAGAGTACATGTTT 58.499 34.615 2.30 0.00 34.03 2.83
3348 4290 5.695851 AAAACTGATGCAAGGTGAAGTAG 57.304 39.130 0.00 0.00 0.00 2.57
3350 4292 4.022849 GCTAAAACTGATGCAAGGTGAAGT 60.023 41.667 0.00 0.00 0.00 3.01
3390 4332 9.871238 AGAGAAAGTTCAAGCTTACGAATATAA 57.129 29.630 0.00 0.00 0.00 0.98
3391 4333 9.517609 GAGAGAAAGTTCAAGCTTACGAATATA 57.482 33.333 0.00 0.00 0.00 0.86
3392 4334 8.035394 TGAGAGAAAGTTCAAGCTTACGAATAT 58.965 33.333 0.00 0.00 0.00 1.28
3422 4364 7.776030 TCAACTTTTATACTTCCACAAAGTCCA 59.224 33.333 0.00 0.00 45.28 4.02
3493 5081 1.812571 CCCTGTCCACAGTGCAAATAC 59.187 52.381 5.99 0.00 42.27 1.89
3495 5083 1.181098 GCCCTGTCCACAGTGCAAAT 61.181 55.000 9.06 0.00 44.90 2.32
3499 5087 3.909086 GAGGCCCTGTCCACAGTGC 62.909 68.421 0.00 5.67 44.83 4.40
3522 5110 0.747283 GGCAGGTCCAAGATGAGCAG 60.747 60.000 0.00 0.00 35.23 4.24
3549 5137 4.025040 AGCAATTCACACAATGAGGAGA 57.975 40.909 0.00 0.00 38.99 3.71
3588 5189 9.522804 CTTTACTACAAACAATACCAGCAAAAA 57.477 29.630 0.00 0.00 0.00 1.94
3607 5208 9.811995 ATTGTATGTTATCGACAAGCTTTACTA 57.188 29.630 0.00 0.00 42.62 1.82
3614 5215 5.810525 AGCAATTGTATGTTATCGACAAGC 58.189 37.500 7.40 0.00 42.62 4.01
3621 5222 8.208718 TGTCAGGTTAGCAATTGTATGTTATC 57.791 34.615 7.40 0.00 0.00 1.75
3622 5223 8.752005 ATGTCAGGTTAGCAATTGTATGTTAT 57.248 30.769 7.40 0.00 0.00 1.89
3623 5224 7.826744 TGATGTCAGGTTAGCAATTGTATGTTA 59.173 33.333 7.40 0.00 0.00 2.41
3626 5227 6.682423 TGATGTCAGGTTAGCAATTGTATG 57.318 37.500 7.40 0.00 0.00 2.39
3655 5256 4.448537 TTGCATGCATAACCTTGGTAAC 57.551 40.909 23.37 0.00 0.00 2.50
3658 5259 4.556592 AAATTGCATGCATAACCTTGGT 57.443 36.364 23.37 0.00 0.00 3.67
3659 5260 5.883503 AAAAATTGCATGCATAACCTTGG 57.116 34.783 23.37 0.00 0.00 3.61
3660 5261 7.414319 CCCTTAAAAATTGCATGCATAACCTTG 60.414 37.037 23.37 8.69 0.00 3.61
3662 5263 6.114767 CCCTTAAAAATTGCATGCATAACCT 58.885 36.000 23.37 9.17 0.00 3.50
3663 5264 5.220835 GCCCTTAAAAATTGCATGCATAACC 60.221 40.000 23.37 2.64 0.00 2.85
3665 5266 5.743117 AGCCCTTAAAAATTGCATGCATAA 58.257 33.333 23.37 15.19 0.00 1.90
3666 5267 5.356291 AGCCCTTAAAAATTGCATGCATA 57.644 34.783 23.37 12.94 0.00 3.14
3667 5268 4.224991 AGCCCTTAAAAATTGCATGCAT 57.775 36.364 23.37 8.77 0.00 3.96
3668 5269 3.699411 AGCCCTTAAAAATTGCATGCA 57.301 38.095 18.46 18.46 0.00 3.96
3669 5270 5.009854 TCTAGCCCTTAAAAATTGCATGC 57.990 39.130 11.82 11.82 0.00 4.06
3670 5271 7.383300 GCTAATCTAGCCCTTAAAAATTGCATG 59.617 37.037 0.00 0.00 45.95 4.06
3690 5300 8.552083 AAATTTGAGAAAAATGGGTGCTAATC 57.448 30.769 0.00 0.00 0.00 1.75
3722 5332 6.211587 TGGCAGATTTATTCCAGTGAAATG 57.788 37.500 0.00 0.00 33.32 2.32
3762 5375 9.509855 TCACAAACACACATTTTCAATTACTAC 57.490 29.630 0.00 0.00 0.00 2.73
3768 5381 8.721019 AAGAATCACAAACACACATTTTCAAT 57.279 26.923 0.00 0.00 0.00 2.57
3838 5451 0.179076 TATGCACCGAGGAGCACATG 60.179 55.000 15.98 0.00 43.71 3.21
3849 5462 4.782156 TGCGATAATTCAAATATGCACCG 58.218 39.130 0.00 0.00 0.00 4.94
3888 5502 9.636879 CCTAGATACTGATACAATTCAGATGTG 57.363 37.037 8.36 0.00 44.88 3.21
3899 5513 8.170730 ACACATGGTATCCTAGATACTGATACA 58.829 37.037 13.01 4.53 41.56 2.29
3900 5514 8.582657 ACACATGGTATCCTAGATACTGATAC 57.417 38.462 13.01 7.28 39.92 2.24
3903 5517 7.665974 CACTACACATGGTATCCTAGATACTGA 59.334 40.741 13.01 3.13 0.00 3.41
3924 5539 5.530171 TCCACGTATCTTCAGTATCCACTAC 59.470 44.000 0.00 0.00 32.21 2.73
3930 5545 5.921408 GGAATGTCCACGTATCTTCAGTATC 59.079 44.000 0.00 0.00 36.28 2.24
3944 5559 1.678101 GCTAAGCATGGGAATGTCCAC 59.322 52.381 0.00 0.00 39.97 4.02
3949 5564 1.959042 AGTCGCTAAGCATGGGAATG 58.041 50.000 0.00 0.00 0.00 2.67
3955 5570 2.299993 TGGAGAAGTCGCTAAGCATG 57.700 50.000 0.00 0.00 0.00 4.06
3975 5590 7.870445 GGGTACAAACTTCAAATTTTCTGCATA 59.130 33.333 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.