Multiple sequence alignment - TraesCS1D01G412600

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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 TraesCS1D01G412600 chr1D 100.000 5641 0 0 1 5641 473863449 473857809 0.000000e+00 10418
1 TraesCS1D01G412600 chr1D 91.400 500 42 1 245 744 451140231 451140729 0.000000e+00 684
2 TraesCS1D01G412600 chr1D 92.908 141 10 0 249 389 451243741 451243881 7.410000e-49 206
3 TraesCS1D01G412600 chr1D 93.578 109 6 1 3061 3168 354519021 354518913 1.630000e-35 161
4 TraesCS1D01G412600 chr1B 93.324 4164 155 35 1545 5641 658914350 658910243 0.000000e+00 6035
5 TraesCS1D01G412600 chr1B 90.015 1372 73 24 20 1372 658915851 658914525 0.000000e+00 1716
6 TraesCS1D01G412600 chr1B 87.352 506 51 4 245 741 619528830 619529331 8.200000e-158 568
7 TraesCS1D01G412600 chr1B 87.968 374 35 6 1001 1370 637286336 637285969 3.120000e-117 433
8 TraesCS1D01G412600 chr1B 84.491 432 67 0 263 694 619535200 619535631 1.450000e-115 427
9 TraesCS1D01G412600 chr1B 82.533 229 26 5 245 473 619544057 619544271 7.460000e-44 189
10 TraesCS1D01G412600 chr1A 93.416 1458 67 9 1381 2830 568107920 568106484 0.000000e+00 2134
11 TraesCS1D01G412600 chr1A 89.782 1145 62 34 245 1373 568109064 568107959 0.000000e+00 1415
12 TraesCS1D01G412600 chr1A 91.200 500 43 1 245 744 545896228 545896726 0.000000e+00 678
13 TraesCS1D01G412600 chr1A 89.394 132 11 2 31 161 568109229 568109100 4.520000e-36 163
14 TraesCS1D01G412600 chrUn 89.742 1277 72 27 3415 4659 1490509 1491758 0.000000e+00 1578
15 TraesCS1D01G412600 chrUn 93.200 1000 41 10 4658 5641 1491786 1492774 0.000000e+00 1445
16 TraesCS1D01G412600 chrUn 96.350 411 15 0 2825 3235 477580889 477580479 0.000000e+00 676
17 TraesCS1D01G412600 chr4B 88.418 354 33 4 1019 1370 11349862 11349515 2.430000e-113 420
18 TraesCS1D01G412600 chr5B 88.258 264 30 1 337 600 710757894 710757632 1.180000e-81 315
19 TraesCS1D01G412600 chr5B 87.879 264 30 2 337 600 673112696 673112435 5.490000e-80 309
20 TraesCS1D01G412600 chr5B 92.105 114 6 2 3051 3164 693583791 693583901 2.100000e-34 158
21 TraesCS1D01G412600 chr6D 88.845 251 28 0 470 720 318999482 318999232 5.490000e-80 309
22 TraesCS1D01G412600 chr7B 95.192 104 4 1 3065 3167 589348319 589348422 4.520000e-36 163
23 TraesCS1D01G412600 chr7B 94.286 105 6 0 3059 3163 194667990 194668094 1.630000e-35 161
24 TraesCS1D01G412600 chr7B 91.150 113 9 1 3050 3161 134634105 134634217 9.790000e-33 152
25 TraesCS1D01G412600 chr4D 93.519 108 6 1 3058 3164 490940037 490940144 5.850000e-35 159
26 TraesCS1D01G412600 chr3B 87.692 130 12 4 3056 3183 791257953 791257826 1.270000e-31 148


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 TraesCS1D01G412600 chr1D 473857809 473863449 5640 True 10418.000000 10418 100.0000 1 5641 1 chr1D.!!$R2 5640
1 TraesCS1D01G412600 chr1B 658910243 658915851 5608 True 3875.500000 6035 91.6695 20 5641 2 chr1B.!!$R2 5621
2 TraesCS1D01G412600 chr1B 619528830 619529331 501 False 568.000000 568 87.3520 245 741 1 chr1B.!!$F1 496
3 TraesCS1D01G412600 chr1A 568106484 568109229 2745 True 1237.333333 2134 90.8640 31 2830 3 chr1A.!!$R1 2799
4 TraesCS1D01G412600 chrUn 1490509 1492774 2265 False 1511.500000 1578 91.4710 3415 5641 2 chrUn.!!$F1 2226

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
240 241 0.108585 ATTCGGTGGCAGACTGTGTT 59.891 50.0 3.99 0.0 32.09 3.32 F
920 955 0.322187 GGTTATGGGCCGCCGATTAT 60.322 55.0 12.63 2.6 0.00 1.28 F
1671 1757 0.105760 ATGTGGCTGTGTTGGGGAAA 60.106 50.0 0.00 0.0 0.00 3.13 F
1764 1850 1.503818 AAACCACACGTCACCGCATC 61.504 55.0 0.00 0.0 37.70 3.91 F
3080 3175 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.0 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1711 0.601311 GGAGACACACAGCACAGACC 60.601 60.000 0.00 0.00 0.00 3.85 R
1999 2089 1.064621 GTCCGCGTTACCGATAGCA 59.935 57.895 4.92 0.00 35.63 3.49 R
3059 3154 0.822944 GGGACGGAGGGAGTAGTAGC 60.823 65.000 0.00 0.00 0.00 3.58 R
3457 3574 1.410882 GGACTTGCTCCCTGTAGCTAG 59.589 57.143 0.00 5.89 46.56 3.42 R
4651 4798 0.108329 ACCCGATAAGGCGAAGTGTG 60.108 55.000 0.00 0.00 39.21 3.82 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
42 43 2.854805 GCACTTGAAGAAAACCTGCGTC 60.855 50.000 0.00 0.00 0.00 5.19
56 57 0.394938 TGCGTCCAATACACACCTGT 59.605 50.000 0.00 0.00 0.00 4.00
77 78 6.647212 TGTTTAAGACAGAACATGATAGCG 57.353 37.500 0.00 0.00 33.40 4.26
147 148 5.515270 CAGCTGATTTTGATATGTGCACTTG 59.485 40.000 19.41 0.00 0.00 3.16
161 162 1.597742 CACTTGACACAGGGGAACAG 58.402 55.000 0.00 0.00 0.00 3.16
167 168 0.250901 ACACAGGGGAACAGCATCAC 60.251 55.000 0.00 0.00 0.00 3.06
178 179 3.141002 ACAGCATCACGAATCATTTGC 57.859 42.857 0.00 0.00 0.00 3.68
183 184 3.348309 CATCACGAATCATTTGCAGTCG 58.652 45.455 0.00 0.00 37.71 4.18
191 192 3.198409 TCATTTGCAGTCGATGGCTAT 57.802 42.857 11.74 4.02 0.00 2.97
192 193 3.544684 TCATTTGCAGTCGATGGCTATT 58.455 40.909 11.74 0.06 0.00 1.73
216 217 1.671054 CACAACGGATTCAGCGGGT 60.671 57.895 0.00 0.00 0.00 5.28
226 227 3.197790 CAGCGGGTCAGCATTCGG 61.198 66.667 0.00 0.00 40.15 4.30
227 228 3.706373 AGCGGGTCAGCATTCGGT 61.706 61.111 0.00 0.00 40.15 4.69
235 236 1.376424 CAGCATTCGGTGGCAGACT 60.376 57.895 0.00 0.00 36.97 3.24
237 238 1.672356 GCATTCGGTGGCAGACTGT 60.672 57.895 3.99 0.00 32.09 3.55
240 241 0.108585 ATTCGGTGGCAGACTGTGTT 59.891 50.000 3.99 0.00 32.09 3.32
504 508 3.718210 GATGGGCACGAGGTCGACC 62.718 68.421 27.67 27.67 43.02 4.79
774 799 2.328589 TGGAGGAGGAGGAGGAGGG 61.329 68.421 0.00 0.00 0.00 4.30
817 847 1.600511 GGTTTATGCCGGGTGGGTTG 61.601 60.000 2.18 0.00 38.44 3.77
818 848 1.304547 TTTATGCCGGGTGGGTTGG 60.305 57.895 2.18 0.00 38.44 3.77
823 853 3.576259 CCGGGTGGGTTGGGTTCT 61.576 66.667 0.00 0.00 0.00 3.01
825 855 2.600470 GGGTGGGTTGGGTTCTGC 60.600 66.667 0.00 0.00 0.00 4.26
826 856 2.520968 GGTGGGTTGGGTTCTGCT 59.479 61.111 0.00 0.00 0.00 4.24
896 931 2.755469 CCCGATGGGCCTGTTTGG 60.755 66.667 4.53 2.99 35.35 3.28
898 933 2.035626 CGATGGGCCTGTTTGGGT 59.964 61.111 4.53 0.00 36.00 4.51
900 935 1.228862 GATGGGCCTGTTTGGGTGT 60.229 57.895 4.53 0.00 36.00 4.16
901 936 1.533753 ATGGGCCTGTTTGGGTGTG 60.534 57.895 4.53 0.00 36.00 3.82
902 937 2.917227 GGGCCTGTTTGGGTGTGG 60.917 66.667 0.84 0.00 36.00 4.17
903 938 2.123468 GGCCTGTTTGGGTGTGGT 60.123 61.111 0.00 0.00 36.00 4.16
905 940 0.468400 GGCCTGTTTGGGTGTGGTTA 60.468 55.000 0.00 0.00 36.00 2.85
910 945 0.606096 GTTTGGGTGTGGTTATGGGC 59.394 55.000 0.00 0.00 0.00 5.36
912 947 2.439519 GGGTGTGGTTATGGGCCG 60.440 66.667 0.00 0.00 0.00 6.13
913 948 3.138128 GGTGTGGTTATGGGCCGC 61.138 66.667 0.00 0.00 37.06 6.53
914 949 3.138128 GTGTGGTTATGGGCCGCC 61.138 66.667 0.00 0.00 35.76 6.13
916 951 4.476752 GTGGTTATGGGCCGCCGA 62.477 66.667 2.55 0.00 0.00 5.54
917 952 3.484806 TGGTTATGGGCCGCCGAT 61.485 61.111 12.03 12.03 0.00 4.18
919 954 1.071814 GGTTATGGGCCGCCGATTA 59.928 57.895 12.63 0.02 0.00 1.75
920 955 0.322187 GGTTATGGGCCGCCGATTAT 60.322 55.000 12.63 2.60 0.00 1.28
942 979 2.666098 GCCCTGGGCCGTAAAGAGA 61.666 63.158 27.77 0.00 44.06 3.10
943 980 1.988015 CCCTGGGCCGTAAAGAGAA 59.012 57.895 0.00 0.00 0.00 2.87
944 981 0.326927 CCCTGGGCCGTAAAGAGAAA 59.673 55.000 0.00 0.00 0.00 2.52
945 982 1.064685 CCCTGGGCCGTAAAGAGAAAT 60.065 52.381 0.00 0.00 0.00 2.17
946 983 2.620627 CCCTGGGCCGTAAAGAGAAATT 60.621 50.000 0.00 0.00 0.00 1.82
947 984 3.371166 CCCTGGGCCGTAAAGAGAAATTA 60.371 47.826 0.00 0.00 0.00 1.40
948 985 4.266714 CCTGGGCCGTAAAGAGAAATTAA 58.733 43.478 0.00 0.00 0.00 1.40
949 986 4.703093 CCTGGGCCGTAAAGAGAAATTAAA 59.297 41.667 0.00 0.00 0.00 1.52
950 987 5.359860 CCTGGGCCGTAAAGAGAAATTAAAT 59.640 40.000 0.00 0.00 0.00 1.40
951 988 6.202516 TGGGCCGTAAAGAGAAATTAAATG 57.797 37.500 0.00 0.00 0.00 2.32
952 989 5.946972 TGGGCCGTAAAGAGAAATTAAATGA 59.053 36.000 0.00 0.00 0.00 2.57
998 1036 5.966935 TCTTCTCTTCCACTCTTATCCCATT 59.033 40.000 0.00 0.00 0.00 3.16
999 1037 6.445139 TCTTCTCTTCCACTCTTATCCCATTT 59.555 38.462 0.00 0.00 0.00 2.32
1000 1038 5.994250 TCTCTTCCACTCTTATCCCATTTG 58.006 41.667 0.00 0.00 0.00 2.32
1003 1041 2.580322 TCCACTCTTATCCCATTTGCCA 59.420 45.455 0.00 0.00 0.00 4.92
1010 1048 2.149973 ATCCCATTTGCCACTTCTCC 57.850 50.000 0.00 0.00 0.00 3.71
1097 1143 3.510633 TCCTCCCCCGCCGGTATA 61.511 66.667 1.90 0.00 0.00 1.47
1100 1146 1.295423 CTCCCCCGCCGGTATATTG 59.705 63.158 1.90 0.00 0.00 1.90
1188 1237 4.736896 GTCGACGAGTGGGGGTGC 62.737 72.222 0.00 0.00 0.00 5.01
1233 1282 4.825679 GGTGGAGGAGGGGGAGGG 62.826 77.778 0.00 0.00 0.00 4.30
1234 1283 4.825679 GTGGAGGAGGGGGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
1237 1286 4.179599 GAGGAGGGGGAGGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1244 1293 2.727071 GGGGAGGGGGAGGAGATGA 61.727 68.421 0.00 0.00 0.00 2.92
1324 1373 2.043852 GAGTCGGAGGAGCTGGGA 60.044 66.667 0.00 0.00 0.00 4.37
1373 1422 2.564947 GGTGAGCCTTCTTCTTCTCTCA 59.435 50.000 0.00 0.00 0.00 3.27
1375 1424 3.258123 GTGAGCCTTCTTCTTCTCTCAGT 59.742 47.826 0.00 0.00 32.08 3.41
1376 1425 4.461081 GTGAGCCTTCTTCTTCTCTCAGTA 59.539 45.833 0.00 0.00 32.08 2.74
1387 1471 5.561679 TCTTCTCTCAGTACTTAGCACTCA 58.438 41.667 0.00 0.00 0.00 3.41
1396 1480 1.142870 ACTTAGCACTCACTGGCCAAA 59.857 47.619 7.01 0.00 0.00 3.28
1397 1481 2.229792 CTTAGCACTCACTGGCCAAAA 58.770 47.619 7.01 0.00 0.00 2.44
1399 1483 1.708341 AGCACTCACTGGCCAAAAAT 58.292 45.000 7.01 0.00 0.00 1.82
1408 1492 7.492344 CACTCACTGGCCAAAAATATTATTTCC 59.508 37.037 7.01 0.95 0.00 3.13
1409 1493 7.400052 ACTCACTGGCCAAAAATATTATTTCCT 59.600 33.333 7.01 0.00 0.00 3.36
1463 1548 5.473504 ACCAGTAGCATTTTTGGTTCAGTAG 59.526 40.000 0.00 0.00 40.94 2.57
1494 1579 5.290158 GGAATTTGTCATTGTGCAGCATAAG 59.710 40.000 10.62 3.38 0.00 1.73
1502 1587 6.470235 GTCATTGTGCAGCATAAGTAAATGAC 59.530 38.462 15.55 15.55 42.87 3.06
1505 1590 6.513806 TGTGCAGCATAAGTAAATGACAAT 57.486 33.333 0.00 0.00 0.00 2.71
1506 1591 6.923012 TGTGCAGCATAAGTAAATGACAATT 58.077 32.000 0.00 0.00 0.00 2.32
1508 1593 8.518702 TGTGCAGCATAAGTAAATGACAATTAA 58.481 29.630 0.00 0.00 0.00 1.40
1510 1595 8.955388 TGCAGCATAAGTAAATGACAATTAAGA 58.045 29.630 0.00 0.00 0.00 2.10
1524 1609 2.597578 TTAAGAGGGGGAAAAGTGCC 57.402 50.000 0.00 0.00 33.53 5.01
1585 1671 6.223852 TCAGAGGAAACAACTTATCTGACAC 58.776 40.000 0.00 0.00 36.07 3.67
1625 1711 1.545136 TGCCATGTTGTAATGCTGTGG 59.455 47.619 0.00 0.00 0.00 4.17
1671 1757 0.105760 ATGTGGCTGTGTTGGGGAAA 60.106 50.000 0.00 0.00 0.00 3.13
1695 1781 2.435059 GTCGGCAAGAGCACCCTC 60.435 66.667 0.00 0.00 44.61 4.30
1764 1850 1.503818 AAACCACACGTCACCGCATC 61.504 55.000 0.00 0.00 37.70 3.91
1767 1853 2.094659 CACACGTCACCGCATCCTC 61.095 63.158 0.00 0.00 37.70 3.71
1776 1862 3.050703 CCGCATCCTCGGTATATGC 57.949 57.895 0.00 0.00 44.18 3.14
1999 2089 5.688814 TGATGATGAAGAATGTCCAGAGT 57.311 39.130 0.00 0.00 0.00 3.24
2105 2195 3.244353 ACCAGGTGAATGTCTTGAGTCTG 60.244 47.826 0.00 0.00 0.00 3.51
2120 2210 3.244526 TGAGTCTGCCTTGCTTGACATTA 60.245 43.478 12.49 0.70 36.11 1.90
2121 2211 3.341823 AGTCTGCCTTGCTTGACATTAG 58.658 45.455 12.49 0.00 36.11 1.73
2234 2324 8.996651 AAGATATGATAAAACCCGGAGAAATT 57.003 30.769 0.73 0.00 0.00 1.82
2264 2354 5.532664 AACTCGAGGTAAGAAACTGAACT 57.467 39.130 18.41 0.00 0.00 3.01
2486 2579 8.537728 AGGTATCATTATGGAAGATGCAAAAA 57.462 30.769 0.00 0.00 0.00 1.94
2513 2608 7.661536 TCTGAAGCAGTTAGTACTATGGATT 57.338 36.000 2.79 1.58 31.96 3.01
2530 2625 5.138125 TGGATTGACAGCCATTTTCTTTC 57.862 39.130 0.00 0.00 0.00 2.62
2645 2740 6.583806 GCAAGAATCAACACCTTTTGATAGTG 59.416 38.462 0.00 0.00 43.95 2.74
2695 2790 5.324409 TGGTTAAGAATGTCTGCCTGATTT 58.676 37.500 0.00 0.00 0.00 2.17
2696 2791 5.183713 TGGTTAAGAATGTCTGCCTGATTTG 59.816 40.000 0.00 0.00 0.00 2.32
2697 2792 3.863142 AAGAATGTCTGCCTGATTTGC 57.137 42.857 0.00 0.00 0.00 3.68
2698 2793 3.083122 AGAATGTCTGCCTGATTTGCT 57.917 42.857 0.00 0.00 0.00 3.91
2699 2794 4.226427 AGAATGTCTGCCTGATTTGCTA 57.774 40.909 0.00 0.00 0.00 3.49
2700 2795 4.197750 AGAATGTCTGCCTGATTTGCTAG 58.802 43.478 0.00 0.00 0.00 3.42
2701 2796 2.408271 TGTCTGCCTGATTTGCTAGG 57.592 50.000 0.00 0.00 37.14 3.02
2702 2797 1.908619 TGTCTGCCTGATTTGCTAGGA 59.091 47.619 0.00 0.00 36.11 2.94
2703 2798 2.507058 TGTCTGCCTGATTTGCTAGGAT 59.493 45.455 0.00 0.00 36.11 3.24
2704 2799 3.137533 GTCTGCCTGATTTGCTAGGATC 58.862 50.000 0.00 0.00 36.11 3.36
2705 2800 2.773661 TCTGCCTGATTTGCTAGGATCA 59.226 45.455 0.00 0.00 36.11 2.92
2706 2801 3.393609 TCTGCCTGATTTGCTAGGATCAT 59.606 43.478 0.00 0.00 36.11 2.45
2707 2802 3.748083 TGCCTGATTTGCTAGGATCATC 58.252 45.455 0.00 0.00 36.11 2.92
2708 2803 3.393609 TGCCTGATTTGCTAGGATCATCT 59.606 43.478 0.00 0.00 36.11 2.90
2709 2804 4.141321 TGCCTGATTTGCTAGGATCATCTT 60.141 41.667 0.00 0.00 36.11 2.40
2710 2805 5.072193 TGCCTGATTTGCTAGGATCATCTTA 59.928 40.000 0.00 0.00 36.11 2.10
2711 2806 6.179040 GCCTGATTTGCTAGGATCATCTTAT 58.821 40.000 0.00 0.00 36.11 1.73
2712 2807 7.038088 TGCCTGATTTGCTAGGATCATCTTATA 60.038 37.037 0.00 0.00 36.11 0.98
2713 2808 7.826252 GCCTGATTTGCTAGGATCATCTTATAA 59.174 37.037 0.00 0.00 36.11 0.98
2714 2809 9.381033 CCTGATTTGCTAGGATCATCTTATAAG 57.619 37.037 6.11 6.11 36.11 1.73
2902 2997 6.712095 ACTGTTCTATGAGTTCAATTGCTTCA 59.288 34.615 0.00 4.82 0.00 3.02
2985 3080 6.240894 ACCATCATTGTAACACAGTTCTGAT 58.759 36.000 6.83 0.00 0.00 2.90
3040 3135 5.758296 GTGAACTCGGAGGCATGATAATTTA 59.242 40.000 10.23 0.00 0.00 1.40
3043 3138 7.338196 TGAACTCGGAGGCATGATAATTTAAAA 59.662 33.333 10.23 0.00 0.00 1.52
3073 3168 3.860968 TGACTAGCTACTACTCCCTCC 57.139 52.381 0.00 0.00 0.00 4.30
3080 3175 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3112 3207 8.351461 GTGTCTCAACTTTGTACTAACTCTAGT 58.649 37.037 0.00 0.00 41.43 2.57
3150 3245 4.459337 GGGTTGAGACACTTATTTTGGGAG 59.541 45.833 0.00 0.00 0.00 4.30
3151 3246 4.459337 GGTTGAGACACTTATTTTGGGAGG 59.541 45.833 0.00 0.00 0.00 4.30
3157 3252 2.580783 CACTTATTTTGGGAGGGAGGGA 59.419 50.000 0.00 0.00 0.00 4.20
3158 3253 2.853077 ACTTATTTTGGGAGGGAGGGAG 59.147 50.000 0.00 0.00 0.00 4.30
3159 3254 2.680439 TATTTTGGGAGGGAGGGAGT 57.320 50.000 0.00 0.00 0.00 3.85
3160 3255 2.680439 ATTTTGGGAGGGAGGGAGTA 57.320 50.000 0.00 0.00 0.00 2.59
3161 3256 2.680439 TTTTGGGAGGGAGGGAGTAT 57.320 50.000 0.00 0.00 0.00 2.12
3162 3257 2.680439 TTTGGGAGGGAGGGAGTATT 57.320 50.000 0.00 0.00 0.00 1.89
3163 3258 3.807288 TTTGGGAGGGAGGGAGTATTA 57.193 47.619 0.00 0.00 0.00 0.98
3285 3380 6.747280 CCACAGCTTTAAACTTTATTCCATCG 59.253 38.462 0.00 0.00 0.00 3.84
3325 3420 9.378597 CTTGAAGTCATTATGATGCTAAAATCG 57.621 33.333 0.00 0.00 33.14 3.34
3326 3421 8.661352 TGAAGTCATTATGATGCTAAAATCGA 57.339 30.769 0.00 0.00 33.14 3.59
3327 3422 8.768019 TGAAGTCATTATGATGCTAAAATCGAG 58.232 33.333 0.00 0.00 33.14 4.04
3375 3492 7.553044 GGCATATCTGTTAAAGGTAGTTTCAGT 59.447 37.037 0.00 0.00 0.00 3.41
3382 3499 6.256321 TGTTAAAGGTAGTTTCAGTTCGACAC 59.744 38.462 0.00 0.00 0.00 3.67
3412 3529 7.990886 TCTGTTAAAGGTAGTCTCATGTTTGTT 59.009 33.333 0.00 0.00 0.00 2.83
3457 3574 3.334691 TCCAGGTGTTCATTTCGATGTC 58.665 45.455 0.00 0.00 0.00 3.06
3547 3664 1.927487 TAGCTAGTGAACACCCCGAA 58.073 50.000 1.11 0.00 0.00 4.30
3647 3764 7.348274 AGGTATATCTTCTGGTGATTTCCTCAA 59.652 37.037 0.00 0.00 35.07 3.02
3687 3804 2.223711 CCGTTTTGCTAGCCTGTTTGTT 60.224 45.455 13.29 0.00 0.00 2.83
3820 3937 7.208064 AGCATTATACTTGGGAAGGTAAAGA 57.792 36.000 0.00 0.00 0.00 2.52
3843 3965 7.590279 AGAAGTTTAAAATATTCGTGTGTGGG 58.410 34.615 0.00 0.00 0.00 4.61
3862 3984 5.127519 TGTGGGCTTGAATATTTCAGGATTG 59.872 40.000 3.82 0.00 41.38 2.67
3874 3996 8.712285 ATATTTCAGGATTGCAAATTCAGTTG 57.288 30.769 1.71 0.00 0.00 3.16
4000 4144 6.133356 TGAAACAGAAGTAAGGAATTGGGTT 58.867 36.000 0.00 0.00 0.00 4.11
4048 4192 7.039993 GGGAATGAAACAGTTCCTAGCTTAAAA 60.040 37.037 0.00 0.00 42.76 1.52
4193 4337 5.422214 TGAGGTCATAACTTCTTCCTTCC 57.578 43.478 0.00 0.00 32.89 3.46
4199 4343 6.154706 GGTCATAACTTCTTCCTTCCTCTGTA 59.845 42.308 0.00 0.00 0.00 2.74
4201 4345 4.545208 AACTTCTTCCTTCCTCTGTAGC 57.455 45.455 0.00 0.00 0.00 3.58
4213 4357 2.045524 CTCTGTAGCCATGATCACCCT 58.954 52.381 0.00 0.00 0.00 4.34
4216 4360 3.117131 TCTGTAGCCATGATCACCCTCTA 60.117 47.826 0.00 0.00 0.00 2.43
4219 4363 1.983691 AGCCATGATCACCCTCTATGG 59.016 52.381 0.00 0.52 40.91 2.74
4220 4364 1.980765 GCCATGATCACCCTCTATGGA 59.019 52.381 12.44 0.00 40.52 3.41
4221 4365 2.373169 GCCATGATCACCCTCTATGGAA 59.627 50.000 12.44 0.00 40.52 3.53
4222 4366 3.009916 GCCATGATCACCCTCTATGGAAT 59.990 47.826 12.44 0.00 40.52 3.01
4223 4367 4.586884 CCATGATCACCCTCTATGGAATG 58.413 47.826 0.00 0.00 40.52 2.67
4224 4368 4.287845 CCATGATCACCCTCTATGGAATGA 59.712 45.833 0.00 0.00 40.52 2.57
4225 4369 5.045066 CCATGATCACCCTCTATGGAATGAT 60.045 44.000 0.00 1.24 41.28 2.45
4226 4370 5.494390 TGATCACCCTCTATGGAATGATG 57.506 43.478 0.00 0.00 39.79 3.07
4227 4371 5.157395 TGATCACCCTCTATGGAATGATGA 58.843 41.667 0.00 0.00 39.79 2.92
4230 4374 6.119240 TCACCCTCTATGGAATGATGAATC 57.881 41.667 0.00 0.00 38.35 2.52
4237 4381 7.116948 CCTCTATGGAATGATGAATCGTTGTAC 59.883 40.741 2.51 0.00 36.24 2.90
4250 4394 5.840940 ATCGTTGTACAGCAGTTTCTAAC 57.159 39.130 10.49 0.00 0.00 2.34
4251 4395 3.732219 TCGTTGTACAGCAGTTTCTAACG 59.268 43.478 10.49 6.77 40.44 3.18
4264 4408 5.173312 CAGTTTCTAACGACCGCATACTATG 59.827 44.000 0.00 0.00 36.23 2.23
4266 4410 4.478843 TCTAACGACCGCATACTATGTC 57.521 45.455 0.00 0.00 0.00 3.06
4268 4412 0.672342 ACGACCGCATACTATGTCCC 59.328 55.000 0.00 0.00 0.00 4.46
4378 4523 6.236357 CGCTATAAATACAAGCATGACATCG 58.764 40.000 0.00 0.00 35.98 3.84
4385 4530 0.723414 AAGCATGACATCGTCGCTTG 59.277 50.000 9.30 0.00 37.66 4.01
4389 4534 2.809181 TGACATCGTCGCTTGTCAC 58.191 52.632 20.17 4.24 45.35 3.67
4396 4541 1.001745 CGTCGCTTGTCACGTCATGA 61.002 55.000 0.00 0.00 33.79 3.07
4407 4552 4.279922 TGTCACGTCATGAGAGTAGGAAAA 59.720 41.667 0.00 0.00 38.28 2.29
4408 4553 5.047306 TGTCACGTCATGAGAGTAGGAAAAT 60.047 40.000 0.00 0.00 38.28 1.82
4409 4554 6.152154 TGTCACGTCATGAGAGTAGGAAAATA 59.848 38.462 0.00 0.00 38.28 1.40
4410 4555 6.693545 GTCACGTCATGAGAGTAGGAAAATAG 59.306 42.308 0.00 0.00 38.28 1.73
4411 4556 6.377429 TCACGTCATGAGAGTAGGAAAATAGT 59.623 38.462 0.00 0.00 31.91 2.12
4414 4559 6.458478 CGTCATGAGAGTAGGAAAATAGTCGT 60.458 42.308 0.00 0.00 31.55 4.34
4418 4563 6.989659 TGAGAGTAGGAAAATAGTCGTGTTT 58.010 36.000 0.00 0.00 31.55 2.83
4419 4564 7.088905 TGAGAGTAGGAAAATAGTCGTGTTTC 58.911 38.462 0.00 0.00 31.55 2.78
4607 4754 2.522836 CTGTAGATAGCCTGCAGTGG 57.477 55.000 13.81 0.00 46.44 4.00
4630 4777 4.933400 GTGCAATGCAAATTCAATCCTCTT 59.067 37.500 10.44 0.00 41.47 2.85
4651 4798 3.698029 TTTGTCTGCTGAAGTTGCTTC 57.302 42.857 0.00 2.22 40.54 3.86
4664 4840 1.871039 GTTGCTTCACACTTCGCCTTA 59.129 47.619 0.00 0.00 0.00 2.69
4674 4850 1.287425 CTTCGCCTTATCGGGTTGTC 58.713 55.000 0.00 0.00 0.00 3.18
4727 4903 4.678509 AAGCTGCGTCGAAATGAAAATA 57.321 36.364 0.00 0.00 0.00 1.40
4771 4949 0.615331 GTCTGGGATCACAGGAGCAA 59.385 55.000 24.64 1.80 38.98 3.91
4811 4989 8.585189 TTTCATCTTCGAGATAATCATCAGTG 57.415 34.615 0.00 0.00 32.12 3.66
4838 5016 9.559958 AAAACAGTTTATCTTGATTGAATAGCG 57.440 29.630 0.00 0.00 0.00 4.26
4842 5020 8.272176 CAGTTTATCTTGATTGAATAGCGTCTC 58.728 37.037 0.00 0.00 0.00 3.36
4874 5052 3.686726 GTCTGAACTAAAGCCACCTCATG 59.313 47.826 0.00 0.00 0.00 3.07
4899 5077 9.513906 TGTATTCTCATCAATCTACCACAAAAA 57.486 29.630 0.00 0.00 0.00 1.94
4996 5187 0.536006 CATCTCCTCCAATTCCGGCC 60.536 60.000 0.00 0.00 0.00 6.13
5126 5317 0.384353 GAAGCGAGCAAACGACCAAC 60.384 55.000 0.00 0.00 35.09 3.77
5247 5438 4.767255 GCTCCACCTCCGGCACTG 62.767 72.222 0.00 0.00 0.00 3.66
5248 5439 4.767255 CTCCACCTCCGGCACTGC 62.767 72.222 0.00 0.00 0.00 4.40
5460 5651 2.047465 AACAGCTGCGGCAGAGAG 60.047 61.111 32.72 21.60 41.70 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.496873 AAGTGCTTGTGTTGTTACTTATATGTA 57.503 29.630 0.00 0.00 0.00 2.29
2 3 8.503196 TCAAGTGCTTGTGTTGTTACTTATATG 58.497 33.333 11.17 0.00 41.16 1.78
3 4 8.615878 TCAAGTGCTTGTGTTGTTACTTATAT 57.384 30.769 11.17 0.00 41.16 0.86
4 5 8.439993 TTCAAGTGCTTGTGTTGTTACTTATA 57.560 30.769 11.17 0.00 41.16 0.98
5 6 6.935741 TCAAGTGCTTGTGTTGTTACTTAT 57.064 33.333 11.17 0.00 41.16 1.73
6 7 6.596106 TCTTCAAGTGCTTGTGTTGTTACTTA 59.404 34.615 11.17 0.00 41.16 2.24
7 8 5.414454 TCTTCAAGTGCTTGTGTTGTTACTT 59.586 36.000 11.17 0.00 41.16 2.24
8 9 4.941263 TCTTCAAGTGCTTGTGTTGTTACT 59.059 37.500 11.17 0.00 41.16 2.24
9 10 5.229921 TCTTCAAGTGCTTGTGTTGTTAC 57.770 39.130 11.17 0.00 41.16 2.50
10 11 5.888691 TTCTTCAAGTGCTTGTGTTGTTA 57.111 34.783 11.17 0.00 41.16 2.41
11 12 4.782019 TTCTTCAAGTGCTTGTGTTGTT 57.218 36.364 11.17 0.00 41.16 2.83
12 13 4.782019 TTTCTTCAAGTGCTTGTGTTGT 57.218 36.364 11.17 0.00 41.16 3.32
13 14 4.327087 GGTTTTCTTCAAGTGCTTGTGTTG 59.673 41.667 11.17 2.26 41.16 3.33
14 15 4.220602 AGGTTTTCTTCAAGTGCTTGTGTT 59.779 37.500 11.17 0.00 41.16 3.32
15 16 3.763897 AGGTTTTCTTCAAGTGCTTGTGT 59.236 39.130 11.17 0.00 41.16 3.72
16 17 4.107622 CAGGTTTTCTTCAAGTGCTTGTG 58.892 43.478 11.17 6.60 41.16 3.33
17 18 3.429410 GCAGGTTTTCTTCAAGTGCTTGT 60.429 43.478 11.17 0.00 41.16 3.16
18 19 3.118542 GCAGGTTTTCTTCAAGTGCTTG 58.881 45.455 5.63 5.63 41.71 4.01
22 23 2.287009 GGACGCAGGTTTTCTTCAAGTG 60.287 50.000 0.00 0.00 0.00 3.16
56 57 6.649141 ACAACGCTATCATGTTCTGTCTTAAA 59.351 34.615 0.00 0.00 0.00 1.52
77 78 3.263425 TCTTCAGGTCCCAGGATTACAAC 59.737 47.826 0.00 0.00 0.00 3.32
147 148 0.036732 TGATGCTGTTCCCCTGTGTC 59.963 55.000 0.00 0.00 0.00 3.67
161 162 3.103738 GACTGCAAATGATTCGTGATGC 58.896 45.455 9.03 9.03 0.00 3.91
167 168 2.852143 GCCATCGACTGCAAATGATTCG 60.852 50.000 3.27 0.00 0.00 3.34
200 201 1.361668 CTGACCCGCTGAATCCGTTG 61.362 60.000 0.00 0.00 0.00 4.10
216 217 1.375908 GTCTGCCACCGAATGCTGA 60.376 57.895 0.00 0.00 33.76 4.26
226 227 2.076863 GGTATCAACACAGTCTGCCAC 58.923 52.381 0.00 0.00 0.00 5.01
227 228 1.977854 AGGTATCAACACAGTCTGCCA 59.022 47.619 0.00 0.00 0.00 4.92
231 232 3.646162 TCACCAAGGTATCAACACAGTCT 59.354 43.478 0.00 0.00 0.00 3.24
235 236 4.632327 TCATCACCAAGGTATCAACACA 57.368 40.909 0.00 0.00 0.00 3.72
237 238 4.588899 CCTTCATCACCAAGGTATCAACA 58.411 43.478 0.00 0.00 36.40 3.33
240 241 2.419990 CGCCTTCATCACCAAGGTATCA 60.420 50.000 0.00 0.00 42.35 2.15
753 776 0.041833 CTCCTCCTCCTCCTCCACAA 59.958 60.000 0.00 0.00 0.00 3.33
774 799 3.115017 TAGGCTCCATCCCCTCCCC 62.115 68.421 0.00 0.00 32.65 4.81
895 930 2.439519 CGGCCCATAACCACACCC 60.440 66.667 0.00 0.00 0.00 4.61
896 931 3.138128 GCGGCCCATAACCACACC 61.138 66.667 0.00 0.00 0.00 4.16
898 933 4.787286 CGGCGGCCCATAACCACA 62.787 66.667 14.55 0.00 0.00 4.17
900 935 1.697082 TAATCGGCGGCCCATAACCA 61.697 55.000 14.55 0.00 0.00 3.67
901 936 0.322187 ATAATCGGCGGCCCATAACC 60.322 55.000 14.55 0.00 0.00 2.85
902 937 1.199097 CAATAATCGGCGGCCCATAAC 59.801 52.381 14.55 0.00 0.00 1.89
903 938 1.529226 CAATAATCGGCGGCCCATAA 58.471 50.000 14.55 0.00 0.00 1.90
905 940 1.603455 CCAATAATCGGCGGCCCAT 60.603 57.895 14.55 2.57 0.00 4.00
910 945 2.983592 GGGCCCAATAATCGGCGG 60.984 66.667 19.95 0.00 46.73 6.13
912 947 1.903404 CCAGGGCCCAATAATCGGC 60.903 63.158 27.56 0.00 44.92 5.54
913 948 1.228552 CCCAGGGCCCAATAATCGG 60.229 63.158 27.56 11.82 0.00 4.18
914 949 1.903404 GCCCAGGGCCCAATAATCG 60.903 63.158 27.56 4.51 44.06 3.34
947 984 8.998377 CGACCCAAAAGGATTTAATTTTCATTT 58.002 29.630 0.00 0.00 37.28 2.32
948 985 8.154203 ACGACCCAAAAGGATTTAATTTTCATT 58.846 29.630 0.00 0.00 37.28 2.57
949 986 7.676004 ACGACCCAAAAGGATTTAATTTTCAT 58.324 30.769 0.00 0.00 37.28 2.57
950 987 7.014808 AGACGACCCAAAAGGATTTAATTTTCA 59.985 33.333 0.00 0.00 37.28 2.69
951 988 7.375834 AGACGACCCAAAAGGATTTAATTTTC 58.624 34.615 0.00 0.00 37.28 2.29
952 989 7.297936 AGACGACCCAAAAGGATTTAATTTT 57.702 32.000 0.00 0.00 37.28 1.82
963 1000 3.067833 GGAAGAGAAGACGACCCAAAAG 58.932 50.000 0.00 0.00 0.00 2.27
1010 1048 2.586792 CAGAGGAAGCGAAGGGGG 59.413 66.667 0.00 0.00 0.00 5.40
1014 1052 1.083242 GCAGAGCAGAGGAAGCGAAG 61.083 60.000 0.00 0.00 37.01 3.79
1080 1126 2.390777 AATATACCGGCGGGGGAGGA 62.391 60.000 31.78 9.29 41.60 3.71
1094 1140 3.342627 GCACGGCGGCGCAATATA 61.343 61.111 34.36 0.00 0.00 0.86
1188 1237 0.739462 TTCAACCACCGCATAGCTCG 60.739 55.000 0.00 0.00 0.00 5.03
1233 1282 2.503382 GGCCTCGTCATCTCCTCCC 61.503 68.421 0.00 0.00 0.00 4.30
1234 1283 2.851071 CGGCCTCGTCATCTCCTCC 61.851 68.421 0.00 0.00 0.00 4.30
1235 1284 2.725008 CGGCCTCGTCATCTCCTC 59.275 66.667 0.00 0.00 0.00 3.71
1236 1285 3.532155 GCGGCCTCGTCATCTCCT 61.532 66.667 0.00 0.00 38.89 3.69
1237 1286 4.933064 CGCGGCCTCGTCATCTCC 62.933 72.222 7.05 0.00 38.89 3.71
1238 1287 4.933064 CCGCGGCCTCGTCATCTC 62.933 72.222 14.67 0.00 38.89 2.75
1373 1422 1.550976 GGCCAGTGAGTGCTAAGTACT 59.449 52.381 0.00 0.00 0.00 2.73
1375 1424 1.639722 TGGCCAGTGAGTGCTAAGTA 58.360 50.000 0.00 0.00 0.00 2.24
1376 1425 0.764890 TTGGCCAGTGAGTGCTAAGT 59.235 50.000 5.11 0.00 0.00 2.24
1387 1471 7.917003 ACAAGGAAATAATATTTTTGGCCAGT 58.083 30.769 5.11 0.00 0.00 4.00
1408 1492 6.614160 TGATGCATCATGAACACTAAACAAG 58.386 36.000 25.42 0.00 0.00 3.16
1409 1493 6.572167 TGATGCATCATGAACACTAAACAA 57.428 33.333 25.42 0.00 0.00 2.83
1463 1548 5.927689 TGCACAATGACAAATTCCTGAATTC 59.072 36.000 5.64 0.00 39.88 2.17
1494 1579 7.712204 TTTCCCCCTCTTAATTGTCATTTAC 57.288 36.000 0.00 0.00 0.00 2.01
1502 1587 3.195610 GGCACTTTTCCCCCTCTTAATTG 59.804 47.826 0.00 0.00 0.00 2.32
1505 1590 2.041216 GAGGCACTTTTCCCCCTCTTAA 59.959 50.000 0.00 0.00 41.55 1.85
1506 1591 1.633945 GAGGCACTTTTCCCCCTCTTA 59.366 52.381 0.00 0.00 41.55 2.10
1508 1593 1.501654 GGAGGCACTTTTCCCCCTCT 61.502 60.000 5.61 0.00 41.55 3.69
1510 1595 1.466186 AGGAGGCACTTTTCCCCCT 60.466 57.895 0.00 0.00 41.55 4.79
1543 1628 2.615912 CTGAATTCTCCCGGAATCTTGC 59.384 50.000 0.73 0.00 43.17 4.01
1625 1711 0.601311 GGAGACACACAGCACAGACC 60.601 60.000 0.00 0.00 0.00 3.85
1656 1742 2.561037 CGGTTTCCCCAACACAGCC 61.561 63.158 0.00 0.00 37.07 4.85
1695 1781 4.006989 TCTGACCCACGATTTGGTTTATG 58.993 43.478 0.00 0.00 45.25 1.90
1764 1850 1.067776 GGTTCCGAGCATATACCGAGG 60.068 57.143 0.00 0.00 0.00 4.63
1767 1853 1.611977 TCTGGTTCCGAGCATATACCG 59.388 52.381 0.00 0.00 31.96 4.02
1776 1862 1.831736 ACCTGGTATTCTGGTTCCGAG 59.168 52.381 0.00 0.00 43.99 4.63
1871 1961 2.668457 AGCATTCAGAAATCGTCGTGAC 59.332 45.455 0.00 0.00 0.00 3.67
1875 1965 3.060003 GGATCAGCATTCAGAAATCGTCG 60.060 47.826 0.00 0.00 0.00 5.12
1999 2089 1.064621 GTCCGCGTTACCGATAGCA 59.935 57.895 4.92 0.00 35.63 3.49
2105 2195 2.354199 GAGAGCTAATGTCAAGCAAGGC 59.646 50.000 0.00 0.00 42.62 4.35
2120 2210 7.854166 ATCATCTATCTAAAACCAGAGAGCT 57.146 36.000 0.00 0.00 34.53 4.09
2121 2211 9.585099 CATATCATCTATCTAAAACCAGAGAGC 57.415 37.037 0.00 0.00 34.53 4.09
2234 2324 4.330944 TCTTACCTCGAGTTTCTTTGCA 57.669 40.909 12.31 0.00 0.00 4.08
2486 2579 8.079211 TCCATAGTACTAACTGCTTCAGAAAT 57.921 34.615 6.70 0.00 36.36 2.17
2513 2608 4.828939 ACATGAGAAAGAAAATGGCTGTCA 59.171 37.500 0.00 0.00 0.00 3.58
2530 2625 9.409312 CTACTTGATTTGCTAGATCTACATGAG 57.591 37.037 0.00 0.00 0.00 2.90
2700 2795 9.881649 TGAGCACATTATCTTATAAGATGATCC 57.118 33.333 30.14 19.20 45.01 3.36
2703 2798 9.159364 GCATGAGCACATTATCTTATAAGATGA 57.841 33.333 30.14 24.73 42.30 2.92
2704 2799 8.396390 GGCATGAGCACATTATCTTATAAGATG 58.604 37.037 30.14 20.78 43.46 2.90
2705 2800 8.105197 TGGCATGAGCACATTATCTTATAAGAT 58.895 33.333 26.87 26.87 44.73 2.40
2706 2801 7.452562 TGGCATGAGCACATTATCTTATAAGA 58.547 34.615 17.32 17.32 44.61 2.10
2707 2802 7.677454 TGGCATGAGCACATTATCTTATAAG 57.323 36.000 6.11 6.11 44.61 1.73
2708 2803 8.462589 TTTGGCATGAGCACATTATCTTATAA 57.537 30.769 0.00 0.00 44.61 0.98
2709 2804 8.640063 ATTTGGCATGAGCACATTATCTTATA 57.360 30.769 0.00 0.00 44.61 0.98
2710 2805 6.964807 TTTGGCATGAGCACATTATCTTAT 57.035 33.333 0.00 0.00 44.61 1.73
2711 2806 6.964807 ATTTGGCATGAGCACATTATCTTA 57.035 33.333 0.00 0.00 44.61 2.10
2712 2807 5.864418 ATTTGGCATGAGCACATTATCTT 57.136 34.783 0.00 0.00 44.61 2.40
2713 2808 5.864418 AATTTGGCATGAGCACATTATCT 57.136 34.783 0.00 0.00 44.61 1.98
2714 2809 6.044046 TCAAATTTGGCATGAGCACATTATC 58.956 36.000 17.90 0.00 44.61 1.75
2715 2810 5.979993 TCAAATTTGGCATGAGCACATTAT 58.020 33.333 17.90 0.00 44.61 1.28
2716 2811 5.402997 TCAAATTTGGCATGAGCACATTA 57.597 34.783 17.90 0.00 44.61 1.90
2717 2812 4.274602 TCAAATTTGGCATGAGCACATT 57.725 36.364 17.90 0.00 44.61 2.71
2902 2997 4.343526 TGTGGTATTGGTTTGCAACTGATT 59.656 37.500 0.00 0.00 0.00 2.57
2951 3046 8.100164 TGTGTTACAATGATGGTAAGATTCTCA 58.900 33.333 0.00 0.00 31.82 3.27
2985 3080 5.539048 GCTTATATAAAGCTGTCTCGGGAA 58.461 41.667 2.55 0.00 40.01 3.97
3040 3135 5.765182 AGTAGCTAGTCAAATGTGCTGTTTT 59.235 36.000 0.00 0.00 35.47 2.43
3043 3138 4.543590 AGTAGCTAGTCAAATGTGCTGT 57.456 40.909 0.00 0.00 35.47 4.40
3059 3154 0.822944 GGGACGGAGGGAGTAGTAGC 60.823 65.000 0.00 0.00 0.00 3.58
3073 3168 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
3112 3207 4.101898 TCTCAACCCTAGTACAACTTTGCA 59.898 41.667 0.00 0.00 0.00 4.08
3127 3222 4.403734 TCCCAAAATAAGTGTCTCAACCC 58.596 43.478 0.00 0.00 0.00 4.11
3150 3245 7.661847 CACAACTGATTTATAATACTCCCTCCC 59.338 40.741 0.00 0.00 0.00 4.30
3151 3246 7.173390 GCACAACTGATTTATAATACTCCCTCC 59.827 40.741 0.00 0.00 0.00 4.30
3235 3330 7.427214 GGATGATTACTCTACAGTAACAGGTC 58.573 42.308 0.00 0.00 45.90 3.85
3375 3492 7.833786 ACTACCTTTAACAGATATGTGTCGAA 58.166 34.615 5.89 1.43 0.00 3.71
3382 3499 9.823647 AACATGAGACTACCTTTAACAGATATG 57.176 33.333 0.00 0.00 0.00 1.78
3412 3529 8.097038 GGAATGCAGTAATAGACCATCTAATGA 58.903 37.037 0.00 0.00 31.96 2.57
3457 3574 1.410882 GGACTTGCTCCCTGTAGCTAG 59.589 57.143 0.00 5.89 46.56 3.42
3820 3937 6.015772 AGCCCACACACGAATATTTTAAACTT 60.016 34.615 0.00 0.00 0.00 2.66
3825 3942 5.004448 TCAAGCCCACACACGAATATTTTA 58.996 37.500 0.00 0.00 0.00 1.52
3840 3962 4.099881 GCAATCCTGAAATATTCAAGCCCA 59.900 41.667 0.00 0.00 39.58 5.36
3841 3963 4.099881 TGCAATCCTGAAATATTCAAGCCC 59.900 41.667 0.00 0.00 39.58 5.19
3843 3965 7.781548 ATTTGCAATCCTGAAATATTCAAGC 57.218 32.000 0.00 0.00 39.58 4.01
3862 3984 7.594758 TGTTATGCTTAACTCAACTGAATTTGC 59.405 33.333 19.69 0.00 38.81 3.68
3874 3996 9.346725 CCTTCAATTTCTTGTTATGCTTAACTC 57.653 33.333 19.69 0.00 38.81 3.01
4016 4160 4.284234 AGGAACTGTTTCATTCCCCAAATG 59.716 41.667 0.98 0.00 44.78 2.32
4048 4192 6.183359 GCATGATCGTTTTGCTCGTTAAATTT 60.183 34.615 0.00 0.00 33.61 1.82
4050 4194 4.793216 GCATGATCGTTTTGCTCGTTAAAT 59.207 37.500 0.00 0.00 33.61 1.40
4156 4300 8.884726 GTTATGACCTCAAGATAAACCTTCTTC 58.115 37.037 0.00 0.00 31.11 2.87
4193 4337 2.036992 GAGGGTGATCATGGCTACAGAG 59.963 54.545 0.00 0.00 0.00 3.35
4199 4343 1.983691 CCATAGAGGGTGATCATGGCT 59.016 52.381 0.00 0.00 30.49 4.75
4201 4345 4.287845 TCATTCCATAGAGGGTGATCATGG 59.712 45.833 0.00 0.13 37.98 3.66
4213 4357 7.496747 TGTACAACGATTCATCATTCCATAGA 58.503 34.615 0.00 0.00 0.00 1.98
4216 4360 5.008019 GCTGTACAACGATTCATCATTCCAT 59.992 40.000 0.00 0.00 0.00 3.41
4219 4363 5.063944 ACTGCTGTACAACGATTCATCATTC 59.936 40.000 0.00 0.00 0.00 2.67
4220 4364 4.937620 ACTGCTGTACAACGATTCATCATT 59.062 37.500 0.00 0.00 0.00 2.57
4221 4365 4.507710 ACTGCTGTACAACGATTCATCAT 58.492 39.130 0.00 0.00 0.00 2.45
4222 4366 3.925379 ACTGCTGTACAACGATTCATCA 58.075 40.909 0.00 0.00 0.00 3.07
4223 4367 4.928661 AACTGCTGTACAACGATTCATC 57.071 40.909 0.00 0.00 0.00 2.92
4224 4368 4.997395 AGAAACTGCTGTACAACGATTCAT 59.003 37.500 0.00 0.00 0.00 2.57
4225 4369 4.377021 AGAAACTGCTGTACAACGATTCA 58.623 39.130 0.00 0.00 0.00 2.57
4226 4370 4.992381 AGAAACTGCTGTACAACGATTC 57.008 40.909 0.00 0.00 0.00 2.52
4227 4371 5.107607 CGTTAGAAACTGCTGTACAACGATT 60.108 40.000 18.45 1.62 39.73 3.34
4230 4374 3.732219 TCGTTAGAAACTGCTGTACAACG 59.268 43.478 17.75 17.75 38.96 4.10
4237 4381 0.438830 GCGGTCGTTAGAAACTGCTG 59.561 55.000 0.00 0.00 43.07 4.41
4250 4394 0.386858 CGGGACATAGTATGCGGTCG 60.387 60.000 10.16 5.85 0.00 4.79
4251 4395 0.956633 TCGGGACATAGTATGCGGTC 59.043 55.000 10.16 0.70 0.00 4.79
4264 4408 1.957177 TCACATCTATCTGCTCGGGAC 59.043 52.381 0.00 0.00 0.00 4.46
4266 4410 2.288702 CCTTCACATCTATCTGCTCGGG 60.289 54.545 0.00 0.00 0.00 5.14
4268 4412 3.067320 TCACCTTCACATCTATCTGCTCG 59.933 47.826 0.00 0.00 0.00 5.03
4378 4523 0.710567 CTCATGACGTGACAAGCGAC 59.289 55.000 0.00 0.00 32.22 5.19
4385 4530 4.436242 TTTCCTACTCTCATGACGTGAC 57.564 45.455 0.00 0.00 32.22 3.67
4389 4534 5.910166 CGACTATTTTCCTACTCTCATGACG 59.090 44.000 0.00 0.00 0.00 4.35
4396 4541 7.229581 AGAAACACGACTATTTTCCTACTCT 57.770 36.000 0.00 0.00 30.82 3.24
4407 4552 8.664211 AAGAAAAGAAGAAGAAACACGACTAT 57.336 30.769 0.00 0.00 0.00 2.12
4408 4553 8.488651 AAAGAAAAGAAGAAGAAACACGACTA 57.511 30.769 0.00 0.00 0.00 2.59
4409 4554 6.986904 AAGAAAAGAAGAAGAAACACGACT 57.013 33.333 0.00 0.00 0.00 4.18
4410 4555 7.963465 AGAAAAGAAAAGAAGAAGAAACACGAC 59.037 33.333 0.00 0.00 0.00 4.34
4411 4556 8.040716 AGAAAAGAAAAGAAGAAGAAACACGA 57.959 30.769 0.00 0.00 0.00 4.35
4418 4563 7.283354 GGGTGAGAAGAAAAGAAAAGAAGAAGA 59.717 37.037 0.00 0.00 0.00 2.87
4419 4564 7.284261 AGGGTGAGAAGAAAAGAAAAGAAGAAG 59.716 37.037 0.00 0.00 0.00 2.85
4607 4754 4.501071 AGAGGATTGAATTTGCATTGCAC 58.499 39.130 11.66 0.00 38.71 4.57
4616 4763 6.927381 CAGCAGACAAAAAGAGGATTGAATTT 59.073 34.615 0.00 0.00 0.00 1.82
4630 4777 3.443329 TGAAGCAACTTCAGCAGACAAAA 59.557 39.130 5.94 0.00 44.27 2.44
4651 4798 0.108329 ACCCGATAAGGCGAAGTGTG 60.108 55.000 0.00 0.00 39.21 3.82
4664 4840 1.274703 ATGGAGCCAGACAACCCGAT 61.275 55.000 0.00 0.00 0.00 4.18
4727 4903 2.863704 GCCTGAATTTTGCAAAGCGTCT 60.864 45.455 12.41 0.00 0.00 4.18
4771 4949 6.128172 CGAAGATGAAATTAACCTCAGCACTT 60.128 38.462 6.64 6.16 30.32 3.16
4838 5016 4.561105 AGTTCAGACCTTCAAATCGAGAC 58.439 43.478 0.00 0.00 0.00 3.36
4842 5020 5.390991 GGCTTTAGTTCAGACCTTCAAATCG 60.391 44.000 0.00 0.00 0.00 3.34
4899 5077 3.305608 GCAGCAGCTTTGGAGTAACAAAT 60.306 43.478 0.00 0.00 39.39 2.32
5126 5317 3.493877 CGGCTAGCTTGATCAAGAAGATG 59.506 47.826 34.43 21.01 40.79 2.90


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

AutoCloner maintained by Alex Coulton.