Multiple sequence alignment - TraesCS1A01G257400

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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 TraesCS1A01G257400 chr1A 100.000 4623 0 0 1 4623 449622222 449626844 0.000000e+00 8538.0
1 TraesCS1A01G257400 chr1A 83.377 770 116 11 2768 3534 449813119 449813879 0.000000e+00 702.0
2 TraesCS1A01G257400 chr1A 77.778 837 159 24 2709 3530 449821484 449820660 1.490000e-134 490.0
3 TraesCS1A01G257400 chr1A 82.783 424 58 12 1603 2014 449812151 449812571 9.450000e-97 364.0
4 TraesCS1A01G257400 chr1A 84.507 355 49 6 2090 2441 449812602 449812953 3.420000e-91 346.0
5 TraesCS1A01G257400 chr1A 80.288 416 76 6 1603 2015 449822382 449821970 4.490000e-80 309.0
6 TraesCS1A01G257400 chr1A 81.061 132 20 2 4118 4244 486340642 486340773 2.940000e-17 100.0
7 TraesCS1A01G257400 chr1A 79.104 134 20 4 4118 4244 555517741 555517609 8.240000e-13 86.1
8 TraesCS1A01G257400 chr1B 91.273 1650 85 24 937 2581 470910834 470912429 0.000000e+00 2194.0
9 TraesCS1A01G257400 chr1B 95.737 1079 44 1 2619 3697 470912517 470913593 0.000000e+00 1736.0
10 TraesCS1A01G257400 chr1B 91.265 664 52 4 1 663 583419096 583418438 0.000000e+00 900.0
11 TraesCS1A01G257400 chr1B 83.773 758 109 11 2768 3521 471025654 471026401 0.000000e+00 706.0
12 TraesCS1A01G257400 chr1B 87.346 324 20 7 3688 3992 470913617 470913938 7.360000e-93 351.0
13 TraesCS1A01G257400 chr1B 82.160 426 57 17 1603 2014 471024692 471025112 9.520000e-92 348.0
14 TraesCS1A01G257400 chr1B 84.639 332 47 4 2103 2432 471025156 471025485 1.240000e-85 327.0
15 TraesCS1A01G257400 chr1B 88.889 261 21 5 4345 4604 470924121 470924374 9.660000e-82 315.0
16 TraesCS1A01G257400 chr1B 87.259 259 20 5 665 915 470910492 470910745 2.720000e-72 283.0
17 TraesCS1A01G257400 chr1B 79.087 416 81 6 1603 2015 471175417 471175005 9.790000e-72 281.0
18 TraesCS1A01G257400 chr1B 92.857 70 4 1 4045 4114 470913934 470914002 2.940000e-17 100.0
19 TraesCS1A01G257400 chr1B 96.226 53 2 0 3994 4046 519277354 519277302 2.290000e-13 87.9
20 TraesCS1A01G257400 chr1B 94.643 56 2 1 3991 4046 491705686 491705740 8.240000e-13 86.1
21 TraesCS1A01G257400 chr1B 93.103 58 3 1 3989 4046 495844051 495844107 2.960000e-12 84.2
22 TraesCS1A01G257400 chr1B 97.561 41 1 0 2575 2615 470912437 470912477 2.310000e-08 71.3
23 TraesCS1A01G257400 chr1D 95.052 1354 43 10 2619 3955 349254879 349256225 0.000000e+00 2108.0
24 TraesCS1A01G257400 chr1D 95.538 1031 34 6 1552 2581 349253773 349254792 0.000000e+00 1639.0
25 TraesCS1A01G257400 chr1D 95.324 663 29 2 1 663 25415842 25416502 0.000000e+00 1051.0
26 TraesCS1A01G257400 chr1D 82.403 824 128 12 2705 3521 349478943 349479756 0.000000e+00 702.0
27 TraesCS1A01G257400 chr1D 77.907 774 144 24 2772 3530 349538288 349537527 1.520000e-124 457.0
28 TraesCS1A01G257400 chr1D 89.415 359 34 3 4259 4614 349256608 349256965 2.540000e-122 449.0
29 TraesCS1A01G257400 chr1D 81.991 422 65 10 1603 2014 349478047 349478467 9.520000e-92 348.0
30 TraesCS1A01G257400 chr1D 83.662 355 52 6 2090 2441 349478498 349478849 3.450000e-86 329.0
31 TraesCS1A01G257400 chr1D 82.020 406 30 15 948 1345 349253009 349253379 5.810000e-79 305.0
32 TraesCS1A01G257400 chr1D 87.645 259 24 5 664 919 349252694 349252947 1.260000e-75 294.0
33 TraesCS1A01G257400 chr1D 79.567 416 79 6 1603 2015 349539258 349538846 4.520000e-75 292.0
34 TraesCS1A01G257400 chr1D 85.202 223 21 4 4044 4256 349256343 349256563 7.790000e-53 219.0
35 TraesCS1A01G257400 chr1D 93.056 72 5 0 4447 4518 12203866 12203795 6.330000e-19 106.0
36 TraesCS1A01G257400 chr1D 93.056 72 5 0 1457 1528 349253484 349253555 6.330000e-19 106.0
37 TraesCS1A01G257400 chr1D 81.061 132 20 2 4118 4244 386431977 386432108 2.940000e-17 100.0
38 TraesCS1A01G257400 chr4D 94.419 663 34 3 1 663 408584943 408585602 0.000000e+00 1016.0
39 TraesCS1A01G257400 chr2A 94.127 664 38 1 1 664 16968148 16967486 0.000000e+00 1009.0
40 TraesCS1A01G257400 chr2A 93.103 58 3 1 3989 4046 412471537 412471593 2.960000e-12 84.2
41 TraesCS1A01G257400 chr2A 79.130 115 19 2 4135 4246 335631280 335631392 1.780000e-09 75.0
42 TraesCS1A01G257400 chr7D 93.373 664 42 2 1 664 514914473 514913812 0.000000e+00 981.0
43 TraesCS1A01G257400 chr7D 74.017 712 149 28 2767 3457 167529827 167530523 1.650000e-64 257.0
44 TraesCS1A01G257400 chr7D 77.451 306 67 2 2139 2443 167528242 167528546 1.020000e-41 182.0
45 TraesCS1A01G257400 chr7D 81.513 119 16 2 4132 4244 488610745 488610627 4.930000e-15 93.5
46 TraesCS1A01G257400 chr3B 94.543 623 30 2 1 623 737761199 737761817 0.000000e+00 959.0
47 TraesCS1A01G257400 chr3B 91.679 661 54 1 3 663 823838463 823839122 0.000000e+00 915.0
48 TraesCS1A01G257400 chr3B 89.189 74 8 0 4117 4190 137608296 137608223 4.930000e-15 93.5
49 TraesCS1A01G257400 chr5B 91.867 664 50 4 1 663 247436024 247436684 0.000000e+00 924.0
50 TraesCS1A01G257400 chr5B 96.226 53 2 0 3994 4046 134582453 134582505 2.290000e-13 87.9
51 TraesCS1A01G257400 chr4A 91.541 662 53 3 1 662 659941517 659942175 0.000000e+00 909.0
52 TraesCS1A01G257400 chr4A 82.273 220 32 6 4407 4621 32405327 32405544 2.840000e-42 183.0
53 TraesCS1A01G257400 chr4A 91.667 60 5 0 3987 4046 644026595 644026536 2.960000e-12 84.2
54 TraesCS1A01G257400 chr7A 75.649 616 116 27 2767 3365 169024360 169024958 4.560000e-70 276.0
55 TraesCS1A01G257400 chr7B 75.684 621 107 36 2767 3365 131945854 131946452 2.120000e-68 270.0
56 TraesCS1A01G257400 chrUn 81.061 132 20 2 4118 4244 480163339 480163470 2.940000e-17 100.0
57 TraesCS1A01G257400 chrUn 94.643 56 2 1 3991 4046 8133934 8133880 8.240000e-13 86.1
58 TraesCS1A01G257400 chr6A 80.000 135 20 5 4118 4245 187733538 187733672 4.930000e-15 93.5
59 TraesCS1A01G257400 chr6A 91.803 61 3 2 3987 4046 587781952 587782011 2.960000e-12 84.2
60 TraesCS1A01G257400 chr2B 94.643 56 3 0 3991 4046 131290897 131290842 2.290000e-13 87.9
61 TraesCS1A01G257400 chr5D 78.986 138 19 4 4118 4246 363123418 363123554 8.240000e-13 86.1
62 TraesCS1A01G257400 chr6B 82.000 100 13 4 4141 4235 261146282 261146183 3.830000e-11 80.5


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 TraesCS1A01G257400 chr1A 449622222 449626844 4622 False 8538.000000 8538 100.000000 1 4623 1 chr1A.!!$F1 4622
1 TraesCS1A01G257400 chr1A 449812151 449813879 1728 False 470.666667 702 83.555667 1603 3534 3 chr1A.!!$F3 1931
2 TraesCS1A01G257400 chr1A 449820660 449822382 1722 True 399.500000 490 79.033000 1603 3530 2 chr1A.!!$R2 1927
3 TraesCS1A01G257400 chr1B 583418438 583419096 658 True 900.000000 900 91.265000 1 663 1 chr1B.!!$R3 662
4 TraesCS1A01G257400 chr1B 470910492 470914002 3510 False 789.216667 2194 92.005500 665 4114 6 chr1B.!!$F4 3449
5 TraesCS1A01G257400 chr1B 471024692 471026401 1709 False 460.333333 706 83.524000 1603 3521 3 chr1B.!!$F5 1918
6 TraesCS1A01G257400 chr1D 25415842 25416502 660 False 1051.000000 1051 95.324000 1 663 1 chr1D.!!$F1 662
7 TraesCS1A01G257400 chr1D 349252694 349256965 4271 False 731.428571 2108 89.704000 664 4614 7 chr1D.!!$F3 3950
8 TraesCS1A01G257400 chr1D 349478047 349479756 1709 False 459.666667 702 82.685333 1603 3521 3 chr1D.!!$F4 1918
9 TraesCS1A01G257400 chr1D 349537527 349539258 1731 True 374.500000 457 78.737000 1603 3530 2 chr1D.!!$R2 1927
10 TraesCS1A01G257400 chr4D 408584943 408585602 659 False 1016.000000 1016 94.419000 1 663 1 chr4D.!!$F1 662
11 TraesCS1A01G257400 chr2A 16967486 16968148 662 True 1009.000000 1009 94.127000 1 664 1 chr2A.!!$R1 663
12 TraesCS1A01G257400 chr7D 514913812 514914473 661 True 981.000000 981 93.373000 1 664 1 chr7D.!!$R2 663
13 TraesCS1A01G257400 chr7D 167528242 167530523 2281 False 219.500000 257 75.734000 2139 3457 2 chr7D.!!$F1 1318
14 TraesCS1A01G257400 chr3B 737761199 737761817 618 False 959.000000 959 94.543000 1 623 1 chr3B.!!$F1 622
15 TraesCS1A01G257400 chr3B 823838463 823839122 659 False 915.000000 915 91.679000 3 663 1 chr3B.!!$F2 660
16 TraesCS1A01G257400 chr5B 247436024 247436684 660 False 924.000000 924 91.867000 1 663 1 chr5B.!!$F2 662
17 TraesCS1A01G257400 chr4A 659941517 659942175 658 False 909.000000 909 91.541000 1 662 1 chr4A.!!$F2 661
18 TraesCS1A01G257400 chr7A 169024360 169024958 598 False 276.000000 276 75.649000 2767 3365 1 chr7A.!!$F1 598
19 TraesCS1A01G257400 chr7B 131945854 131946452 598 False 270.000000 270 75.684000 2767 3365 1 chr7B.!!$F1 598

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
990 1073 0.314302 ATCACATAGCCGTCCGTAGC 59.686 55.0 0.00 0.0 0.0 3.58 F
1586 1902 0.025001 CATCGCTTTTGCTACGTCGG 59.975 55.0 0.00 0.0 44.8 4.79 F
2615 3655 0.321021 TAGTTTAAACCGCGCCTCCA 59.679 50.0 14.72 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2573 3046 0.093705 CAGTACGCGCTCTTGCTTTC 59.906 55.0 5.73 0.0 36.97 2.62 R
2669 3749 0.376152 CATGCAAGCGTCCATCAGAC 59.624 55.0 0.00 0.0 42.54 3.51 R
3918 5311 0.250901 TGGCCTGAACAAGAGAAGCC 60.251 55.0 3.32 0.0 39.41 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
134 135 4.082523 CATCCGGCGGTGTGAGGT 62.083 66.667 27.32 1.55 0.00 3.85
343 344 3.493303 GATGAGGTGGAGGCCCCC 61.493 72.222 0.00 0.00 0.00 5.40
364 365 1.478916 GAGTGTAGAGGAAGTGGAGGC 59.521 57.143 0.00 0.00 0.00 4.70
365 366 1.203187 AGTGTAGAGGAAGTGGAGGCA 60.203 52.381 0.00 0.00 0.00 4.75
408 409 1.992277 GGAGGAGGAAGGAGCTGCA 60.992 63.158 8.35 0.00 0.00 4.41
435 436 4.779733 AGGGAGGATGACGGCGGT 62.780 66.667 13.24 0.00 0.00 5.68
523 525 0.759346 ACAGTTTGAGGGAAGACGCT 59.241 50.000 0.00 0.00 41.94 5.07
717 719 1.401905 CGTTTCATTTCCTAGCCAGCC 59.598 52.381 0.00 0.00 0.00 4.85
718 720 2.446435 GTTTCATTTCCTAGCCAGCCA 58.554 47.619 0.00 0.00 0.00 4.75
719 721 2.424956 GTTTCATTTCCTAGCCAGCCAG 59.575 50.000 0.00 0.00 0.00 4.85
722 724 1.574526 ATTTCCTAGCCAGCCAGCCA 61.575 55.000 0.00 0.00 0.00 4.75
723 725 2.202236 TTTCCTAGCCAGCCAGCCAG 62.202 60.000 0.00 0.00 0.00 4.85
724 726 4.871910 CCTAGCCAGCCAGCCAGC 62.872 72.222 0.00 0.00 0.00 4.85
725 727 4.105553 CTAGCCAGCCAGCCAGCA 62.106 66.667 4.54 0.00 34.23 4.41
728 730 2.898920 TAGCCAGCCAGCCAGCATTC 62.899 60.000 4.54 0.00 34.23 2.67
773 777 2.285220 CAGCAAAATCCCAGATCGTACG 59.715 50.000 9.53 9.53 0.00 3.67
882 895 4.333649 GTCGCACCTATATATACGTGGCTA 59.666 45.833 17.99 5.73 0.00 3.93
888 901 5.832060 ACCTATATATACGTGGCTACATCCC 59.168 44.000 0.00 0.00 0.00 3.85
922 935 4.085876 GCATGTGAAGGCCACTGT 57.914 55.556 5.01 0.00 45.86 3.55
924 937 1.915614 GCATGTGAAGGCCACTGTCG 61.916 60.000 5.01 0.00 45.86 4.35
926 939 2.280797 GTGAAGGCCACTGTCGCA 60.281 61.111 5.01 0.00 42.44 5.10
927 940 1.672356 GTGAAGGCCACTGTCGCAT 60.672 57.895 5.01 0.00 42.44 4.73
930 943 2.527951 GAAGGCCACTGTCGCATCCT 62.528 60.000 5.01 0.00 0.00 3.24
932 945 2.581354 GCCACTGTCGCATCCTCT 59.419 61.111 0.00 0.00 0.00 3.69
933 946 1.812922 GCCACTGTCGCATCCTCTG 60.813 63.158 0.00 0.00 0.00 3.35
942 955 2.716814 GCATCCTCTGCCTCCATTG 58.283 57.895 0.00 0.00 45.66 2.82
944 957 1.684248 GCATCCTCTGCCTCCATTGTT 60.684 52.381 0.00 0.00 45.66 2.83
945 958 2.731572 CATCCTCTGCCTCCATTGTTT 58.268 47.619 0.00 0.00 0.00 2.83
946 959 2.205022 TCCTCTGCCTCCATTGTTTG 57.795 50.000 0.00 0.00 0.00 2.93
981 1064 0.855349 CGAGCGTTCATCACATAGCC 59.145 55.000 0.00 0.00 0.00 3.93
986 1069 1.209128 GTTCATCACATAGCCGTCCG 58.791 55.000 0.00 0.00 0.00 4.79
990 1073 0.314302 ATCACATAGCCGTCCGTAGC 59.686 55.000 0.00 0.00 0.00 3.58
1107 1192 1.405105 CTAGGTGAGTGAGAGCTGCTC 59.595 57.143 21.72 21.72 44.21 4.26
1142 1227 3.976339 GCATCTGCTGTCGGTAGAT 57.024 52.632 6.45 6.45 45.88 1.98
1144 1229 3.976339 ATCTGCTGTCGGTAGATGC 57.024 52.632 11.12 0.00 43.87 3.91
1145 1230 1.114627 ATCTGCTGTCGGTAGATGCA 58.885 50.000 11.12 0.00 43.87 3.96
1146 1231 1.114627 TCTGCTGTCGGTAGATGCAT 58.885 50.000 0.00 0.00 37.78 3.96
1147 1232 1.067669 TCTGCTGTCGGTAGATGCATC 59.932 52.381 19.37 19.37 37.78 3.91
1148 1233 0.104855 TGCTGTCGGTAGATGCATCC 59.895 55.000 23.06 7.98 35.15 3.51
1149 1234 0.390860 GCTGTCGGTAGATGCATCCT 59.609 55.000 23.06 12.70 0.00 3.24
1150 1235 1.202580 GCTGTCGGTAGATGCATCCTT 60.203 52.381 23.06 8.39 0.00 3.36
1151 1236 2.748605 CTGTCGGTAGATGCATCCTTC 58.251 52.381 23.06 12.99 0.00 3.46
1153 1238 1.689273 GTCGGTAGATGCATCCTTCCT 59.311 52.381 23.06 6.85 0.00 3.36
1154 1239 1.688735 TCGGTAGATGCATCCTTCCTG 59.311 52.381 23.06 16.46 0.00 3.86
1155 1240 1.688735 CGGTAGATGCATCCTTCCTGA 59.311 52.381 23.06 0.00 0.00 3.86
1156 1241 2.103094 CGGTAGATGCATCCTTCCTGAA 59.897 50.000 23.06 0.00 0.00 3.02
1181 1266 7.482654 TGAATATAATCTGAGGAAACAAGCG 57.517 36.000 0.00 0.00 0.00 4.68
1203 1288 4.557695 CGAGCATTGTAGAGTCCATCCTAC 60.558 50.000 0.00 0.00 36.64 3.18
1243 1336 3.777925 CGGCAACTCAAGGTCGCG 61.778 66.667 0.00 0.00 0.00 5.87
1259 1352 2.298593 GCGTCCAGCGAAGATTACC 58.701 57.895 0.00 0.00 44.77 2.85
1300 1393 9.502145 TGACGACTTGCATTTTATATGATTTTC 57.498 29.630 0.00 0.00 0.00 2.29
1328 1421 1.062206 CGAAGACGTACGCCTCTCC 59.938 63.158 16.72 0.00 34.56 3.71
1356 1477 5.913137 TGGATATTTGGCCAGTAACTTTG 57.087 39.130 5.11 0.00 0.00 2.77
1357 1478 5.329399 TGGATATTTGGCCAGTAACTTTGT 58.671 37.500 5.11 0.00 0.00 2.83
1360 1481 6.811665 GGATATTTGGCCAGTAACTTTGTTTC 59.188 38.462 5.11 0.00 0.00 2.78
1361 1482 3.701532 TTGGCCAGTAACTTTGTTTCG 57.298 42.857 5.11 0.00 0.00 3.46
1362 1483 2.645802 TGGCCAGTAACTTTGTTTCGT 58.354 42.857 0.00 0.00 0.00 3.85
1364 1485 3.065648 TGGCCAGTAACTTTGTTTCGTTC 59.934 43.478 0.00 0.00 0.00 3.95
1365 1486 3.314357 GGCCAGTAACTTTGTTTCGTTCT 59.686 43.478 0.00 0.00 0.00 3.01
1366 1487 4.512571 GGCCAGTAACTTTGTTTCGTTCTA 59.487 41.667 0.00 0.00 0.00 2.10
1367 1488 5.333875 GGCCAGTAACTTTGTTTCGTTCTAG 60.334 44.000 0.00 0.00 0.00 2.43
1368 1489 5.464389 GCCAGTAACTTTGTTTCGTTCTAGA 59.536 40.000 0.00 0.00 0.00 2.43
1369 1490 6.346678 GCCAGTAACTTTGTTTCGTTCTAGAG 60.347 42.308 0.00 0.00 0.00 2.43
1370 1491 6.700520 CCAGTAACTTTGTTTCGTTCTAGAGT 59.299 38.462 0.00 0.00 0.00 3.24
1371 1492 7.864379 CCAGTAACTTTGTTTCGTTCTAGAGTA 59.136 37.037 0.00 0.00 0.00 2.59
1372 1493 8.903723 CAGTAACTTTGTTTCGTTCTAGAGTAG 58.096 37.037 0.00 0.00 0.00 2.57
1373 1494 8.844244 AGTAACTTTGTTTCGTTCTAGAGTAGA 58.156 33.333 0.00 0.00 0.00 2.59
1392 1513 6.224584 AGTAGAGTAGTTGGTTTCTTGCTTC 58.775 40.000 0.00 0.00 0.00 3.86
1394 1515 5.301555 AGAGTAGTTGGTTTCTTGCTTCTC 58.698 41.667 0.00 0.00 0.00 2.87
1402 1523 3.304996 GGTTTCTTGCTTCTCCTTTCTGC 60.305 47.826 0.00 0.00 0.00 4.26
1421 1542 1.888215 CTGGCAGTTGAGCTTCTTGA 58.112 50.000 6.28 0.00 34.17 3.02
1422 1543 1.534595 CTGGCAGTTGAGCTTCTTGAC 59.465 52.381 6.28 0.00 34.17 3.18
1425 1546 1.193426 GCAGTTGAGCTTCTTGACGAC 59.807 52.381 0.00 0.00 0.00 4.34
1430 1551 4.212214 AGTTGAGCTTCTTGACGACAATTC 59.788 41.667 0.00 0.00 35.37 2.17
1437 1558 0.533085 TTGACGACAATTCCGCACCA 60.533 50.000 0.00 0.00 0.00 4.17
1438 1559 0.533085 TGACGACAATTCCGCACCAA 60.533 50.000 0.00 0.00 0.00 3.67
1445 1566 2.288763 ACAATTCCGCACCAATTTCCAC 60.289 45.455 0.00 0.00 0.00 4.02
1462 1583 1.153168 ACTGCCAGTTTGTCGCACT 60.153 52.632 0.00 0.00 0.00 4.40
1464 1585 0.317269 CTGCCAGTTTGTCGCACTTG 60.317 55.000 0.00 0.00 0.00 3.16
1478 1599 6.983910 TGTCGCACTTGAAACAAAATTTAAC 58.016 32.000 0.00 0.00 0.00 2.01
1509 1630 2.489971 TGGCAAAAACTGGAGTAGACG 58.510 47.619 0.00 0.00 0.00 4.18
1528 1649 4.860907 AGACGAACAATTGGACATACGTAC 59.139 41.667 10.83 6.55 33.10 3.67
1529 1650 4.813027 ACGAACAATTGGACATACGTACT 58.187 39.130 10.83 0.00 0.00 2.73
1530 1651 5.232463 ACGAACAATTGGACATACGTACTT 58.768 37.500 10.83 0.00 0.00 2.24
1551 1867 6.270815 ACTTCAATTCAATACATGCATGAGC 58.729 36.000 32.75 0.00 42.57 4.26
1556 1872 7.276878 TCAATTCAATACATGCATGAGCTTTTG 59.723 33.333 32.75 23.15 42.74 2.44
1571 1887 5.579904 TGAGCTTTTGATTCTCTTCTCATCG 59.420 40.000 0.00 0.00 0.00 3.84
1584 1900 2.259618 TCTCATCGCTTTTGCTACGTC 58.740 47.619 0.00 0.00 44.80 4.34
1585 1901 0.989164 TCATCGCTTTTGCTACGTCG 59.011 50.000 0.00 0.00 44.80 5.12
1586 1902 0.025001 CATCGCTTTTGCTACGTCGG 59.975 55.000 0.00 0.00 44.80 4.79
1587 1903 0.389426 ATCGCTTTTGCTACGTCGGT 60.389 50.000 0.00 0.00 44.80 4.69
1600 1916 0.386731 CGTCGGTCCAAAATTGTGCC 60.387 55.000 0.00 0.00 0.00 5.01
2047 2372 4.200283 GCAGGACGAGGAGGAGCG 62.200 72.222 0.00 0.00 0.00 5.03
2573 3046 8.292448 AGTTACATTATCAGTGCACAAAGAAAG 58.708 33.333 21.04 9.29 0.00 2.62
2606 3646 4.388790 CGCGTACTGCTTTAGTTTAAACC 58.611 43.478 14.72 0.00 43.27 3.27
2615 3655 0.321021 TAGTTTAAACCGCGCCTCCA 59.679 50.000 14.72 0.00 0.00 3.86
2616 3656 1.208358 GTTTAAACCGCGCCTCCAC 59.792 57.895 7.12 0.00 0.00 4.02
2617 3657 2.319096 TTTAAACCGCGCCTCCACG 61.319 57.895 0.00 0.00 0.00 4.94
3523 4866 2.002586 CACTTCTACACCATGAAGCCG 58.997 52.381 0.00 0.00 42.27 5.52
3562 4905 2.654877 GGCGACCACGAGAAGGAA 59.345 61.111 0.00 0.00 42.66 3.36
3635 4978 4.519730 GGCTGGTATAAGATCGTGTAGAGT 59.480 45.833 0.00 0.00 0.00 3.24
3647 4990 4.449131 TCGTGTAGAGTGAGGGTATAGTG 58.551 47.826 0.00 0.00 0.00 2.74
3668 5011 2.994186 TTACGGGGAATCTGGTTAGC 57.006 50.000 0.00 0.00 0.00 3.09
3673 5016 1.017387 GGGAATCTGGTTAGCAAGCG 58.983 55.000 0.00 0.00 0.00 4.68
3790 5169 3.260884 AGTTGTGGAGATAATGGTCGTGT 59.739 43.478 0.00 0.00 0.00 4.49
3791 5170 3.520290 TGTGGAGATAATGGTCGTGTC 57.480 47.619 0.00 0.00 0.00 3.67
3792 5171 2.159296 TGTGGAGATAATGGTCGTGTCG 60.159 50.000 0.00 0.00 0.00 4.35
3793 5172 1.202371 TGGAGATAATGGTCGTGTCGC 60.202 52.381 0.00 0.00 0.00 5.19
3794 5173 1.202371 GGAGATAATGGTCGTGTCGCA 60.202 52.381 0.00 0.00 0.00 5.10
3808 5192 4.791163 TCGTGTCGCAAAAAGAAAGAAAAG 59.209 37.500 0.00 0.00 0.00 2.27
3820 5204 5.911378 AGAAAGAAAAGGAAGATCATGCC 57.089 39.130 0.00 0.00 0.00 4.40
3837 5221 1.664873 CCGCAAAAGGCAACCATGA 59.335 52.632 0.00 0.00 45.17 3.07
3838 5222 0.247185 CCGCAAAAGGCAACCATGAT 59.753 50.000 0.00 0.00 45.17 2.45
3879 5272 9.045223 TCTTGTTAATATGGATCATCTTGTTCG 57.955 33.333 0.00 0.00 0.00 3.95
3901 5294 8.662141 GTTCGCTTTAATAATTGGAGTAAGACA 58.338 33.333 0.00 0.00 0.00 3.41
3935 5328 1.301677 CCGGCTTCTCTTGTTCAGGC 61.302 60.000 0.00 0.00 0.00 4.85
3942 5335 0.524862 CTCTTGTTCAGGCCACATGC 59.475 55.000 5.01 0.00 40.16 4.06
3983 5376 3.823873 TGCGTGAGGTTGAACCATTAAAT 59.176 39.130 17.83 0.00 41.95 1.40
3992 5491 8.959705 AGGTTGAACCATTAAATAGCTAGTAC 57.040 34.615 17.83 0.00 41.95 2.73
3993 5492 7.709613 AGGTTGAACCATTAAATAGCTAGTACG 59.290 37.037 17.83 0.00 41.95 3.67
3994 5493 7.493645 GGTTGAACCATTAAATAGCTAGTACGT 59.506 37.037 9.98 0.00 38.42 3.57
3995 5494 9.520204 GTTGAACCATTAAATAGCTAGTACGTA 57.480 33.333 0.00 0.00 0.00 3.57
3999 5498 9.702494 AACCATTAAATAGCTAGTACGTAATCC 57.298 33.333 0.00 0.00 0.00 3.01
4000 5499 8.309656 ACCATTAAATAGCTAGTACGTAATCCC 58.690 37.037 0.00 0.00 0.00 3.85
4001 5500 8.529476 CCATTAAATAGCTAGTACGTAATCCCT 58.471 37.037 0.00 0.00 0.00 4.20
4002 5501 9.570488 CATTAAATAGCTAGTACGTAATCCCTC 57.430 37.037 0.00 0.00 0.00 4.30
4003 5502 6.587206 AAATAGCTAGTACGTAATCCCTCC 57.413 41.667 0.00 0.00 0.00 4.30
4004 5503 2.502295 AGCTAGTACGTAATCCCTCCG 58.498 52.381 0.00 0.00 0.00 4.63
4005 5504 2.158696 AGCTAGTACGTAATCCCTCCGT 60.159 50.000 0.00 0.00 38.53 4.69
4006 5505 2.620585 GCTAGTACGTAATCCCTCCGTT 59.379 50.000 0.00 0.00 36.12 4.44
4007 5506 3.304324 GCTAGTACGTAATCCCTCCGTTC 60.304 52.174 0.00 0.00 36.12 3.95
4008 5507 1.672881 AGTACGTAATCCCTCCGTTCG 59.327 52.381 0.00 0.00 36.12 3.95
4009 5508 1.024271 TACGTAATCCCTCCGTTCGG 58.976 55.000 4.74 4.74 36.12 4.30
4010 5509 0.680921 ACGTAATCCCTCCGTTCGGA 60.681 55.000 13.34 13.34 0.00 4.55
4011 5510 0.457035 CGTAATCCCTCCGTTCGGAA 59.543 55.000 14.79 1.17 33.41 4.30
4012 5511 1.068127 CGTAATCCCTCCGTTCGGAAT 59.932 52.381 14.79 3.52 33.41 3.01
4013 5512 2.482490 CGTAATCCCTCCGTTCGGAATT 60.482 50.000 14.79 13.32 33.41 2.17
4014 5513 3.243501 CGTAATCCCTCCGTTCGGAATTA 60.244 47.826 14.79 12.45 33.41 1.40
4015 5514 2.904697 ATCCCTCCGTTCGGAATTAC 57.095 50.000 14.79 0.00 33.41 1.89
4016 5515 1.856629 TCCCTCCGTTCGGAATTACT 58.143 50.000 14.79 0.00 33.41 2.24
4017 5516 2.181975 TCCCTCCGTTCGGAATTACTT 58.818 47.619 14.79 0.00 33.41 2.24
4018 5517 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
4019 5518 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
4020 5519 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
4021 5520 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
4022 5521 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
4023 5522 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
4024 5523 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
4025 5524 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
4026 5525 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
4027 5526 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
4028 5527 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
4029 5528 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
4030 5529 6.623486 TCGGAATTACTTGTCGTAGAAATGA 58.377 36.000 0.00 0.00 39.69 2.57
4031 5530 7.092079 TCGGAATTACTTGTCGTAGAAATGAA 58.908 34.615 0.00 0.00 39.69 2.57
4032 5531 7.762615 TCGGAATTACTTGTCGTAGAAATGAAT 59.237 33.333 0.00 0.00 39.69 2.57
4033 5532 9.027129 CGGAATTACTTGTCGTAGAAATGAATA 57.973 33.333 0.00 0.00 39.69 1.75
4093 5592 2.287644 TCGCATGCAATGGATTTACTCG 59.712 45.455 19.57 0.00 46.86 4.18
4096 5595 3.624900 CATGCAATGGATTTACTCGCTG 58.375 45.455 0.00 0.00 41.79 5.18
4113 5612 3.741856 TCGCTGCGTTCACAAATAAAGTA 59.258 39.130 22.48 0.00 0.00 2.24
4115 5614 4.491942 CGCTGCGTTCACAAATAAAGTATG 59.508 41.667 14.93 0.00 0.00 2.39
4116 5615 4.262976 GCTGCGTTCACAAATAAAGTATGC 59.737 41.667 0.00 0.00 0.00 3.14
4122 5621 9.710979 GCGTTCACAAATAAAGTATGCTATAAA 57.289 29.630 0.00 0.00 0.00 1.40
4191 5691 9.789029 GAGTAAACAAATAGACTAAAACGTGTC 57.211 33.333 0.00 0.00 0.00 3.67
4196 5696 9.444600 AACAAATAGACTAAAACGTGTCCATAT 57.555 29.630 0.00 0.00 34.02 1.78
4210 5717 5.514279 GTGTCCATATACATGCAAGAAAGC 58.486 41.667 0.00 0.00 0.00 3.51
4219 5726 5.557891 ACATGCAAGAAAGCTAGAACATC 57.442 39.130 0.00 0.00 34.99 3.06
4256 5763 3.310501 GGAGAGAGTACTCGTCAAGTAGC 59.689 52.174 22.41 7.17 46.64 3.58
4257 5764 3.272581 AGAGAGTACTCGTCAAGTAGCC 58.727 50.000 17.07 0.00 46.64 3.93
4270 5819 6.016527 TCGTCAAGTAGCCGATCAATTACTAT 60.017 38.462 0.00 0.00 0.00 2.12
4271 5820 6.088217 CGTCAAGTAGCCGATCAATTACTATG 59.912 42.308 0.00 0.25 0.00 2.23
4272 5821 5.926542 TCAAGTAGCCGATCAATTACTATGC 59.073 40.000 0.00 0.00 0.00 3.14
4287 5836 8.648097 CAATTACTATGCATAGTATTCACCGAC 58.352 37.037 35.59 0.00 43.26 4.79
4300 5849 3.728076 TCACCGACAGTAATCCTATGC 57.272 47.619 0.00 0.00 0.00 3.14
4317 5866 3.788333 ATGCATTGTTTCCATCTTCCG 57.212 42.857 0.00 0.00 0.00 4.30
4328 5877 0.371301 CATCTTCCGTGTGTGCATCG 59.629 55.000 0.00 0.00 0.00 3.84
4335 5884 2.670905 TCCGTGTGTGCATCGAAATTAG 59.329 45.455 0.00 0.00 0.00 1.73
4382 5932 2.296752 CTGTTTGTGATTGTGCATCCCA 59.703 45.455 0.00 0.00 0.00 4.37
4396 5946 2.158475 GCATCCCATCCCATCAACCTAA 60.158 50.000 0.00 0.00 0.00 2.69
4409 5959 6.172630 CCATCAACCTAAAATTTCTTTGGGG 58.827 40.000 4.87 0.00 0.00 4.96
4411 5961 4.904853 TCAACCTAAAATTTCTTTGGGGCT 59.095 37.500 4.87 0.00 0.00 5.19
4412 5962 6.078664 TCAACCTAAAATTTCTTTGGGGCTA 58.921 36.000 4.87 0.00 0.00 3.93
4450 6000 5.654497 GCCTGATTTTAAGAATTGGGTCAG 58.346 41.667 0.00 0.00 33.46 3.51
4453 6003 6.403636 CCTGATTTTAAGAATTGGGTCAGTCG 60.404 42.308 0.00 0.00 32.16 4.18
4457 6007 7.519032 TTTTAAGAATTGGGTCAGTCGATTT 57.481 32.000 0.00 0.00 0.00 2.17
4462 6012 5.875359 AGAATTGGGTCAGTCGATTTCTAAC 59.125 40.000 0.00 0.00 0.00 2.34
4467 6017 4.941873 GGGTCAGTCGATTTCTAACCAATT 59.058 41.667 0.00 0.00 0.00 2.32
4471 6021 6.369065 GTCAGTCGATTTCTAACCAATTGAGT 59.631 38.462 7.12 0.00 30.55 3.41
4551 6101 5.173854 GCATACAAAAACAACAGAAGCTCAC 59.826 40.000 0.00 0.00 0.00 3.51
4572 6122 1.075601 AGACTTCTTGGGCCCAATGA 58.924 50.000 37.10 29.69 35.20 2.57
4584 6134 1.811965 GCCCAATGAAAAACAATGGCC 59.188 47.619 0.00 0.00 45.40 5.36
4585 6135 2.435422 CCCAATGAAAAACAATGGCCC 58.565 47.619 0.00 0.00 45.40 5.80
4592 6142 2.453983 AAAACAATGGCCCGTTGATG 57.546 45.000 22.31 0.00 34.77 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
317 318 2.951745 CACCTCATCGACGCTCGC 60.952 66.667 0.00 0.00 40.21 5.03
343 344 1.746220 CCTCCACTTCCTCTACACTCG 59.254 57.143 0.00 0.00 0.00 4.18
364 365 2.202797 CCGCCATGTCGACCTCTG 60.203 66.667 14.12 7.93 0.00 3.35
365 366 4.148825 GCCGCCATGTCGACCTCT 62.149 66.667 14.12 0.00 0.00 3.69
435 436 1.152567 CCACCAAAACCCTCAGCCA 60.153 57.895 0.00 0.00 0.00 4.75
440 441 3.680786 GCCGCCACCAAAACCCTC 61.681 66.667 0.00 0.00 0.00 4.30
523 525 2.900273 CCGATCGCCCCTTGAGAA 59.100 61.111 10.32 0.00 0.00 2.87
717 719 3.672767 AAAAGAAAGGAATGCTGGCTG 57.327 42.857 0.00 0.00 0.00 4.85
754 758 1.003866 GCGTACGATCTGGGATTTTGC 60.004 52.381 21.65 0.00 0.00 3.68
756 760 2.550978 CAGCGTACGATCTGGGATTTT 58.449 47.619 21.65 0.00 0.00 1.82
773 777 1.745653 GCTCAGACCAATTAACCCAGC 59.254 52.381 0.00 0.00 0.00 4.85
864 877 5.832060 GGGATGTAGCCACGTATATATAGGT 59.168 44.000 11.44 11.44 32.13 3.08
882 895 3.565764 CTACATGTGATGTGGGGATGT 57.434 47.619 9.11 0.00 44.60 3.06
888 901 0.255604 TGCCCCTACATGTGATGTGG 59.744 55.000 9.11 3.09 44.60 4.17
926 939 2.731572 CAAACAATGGAGGCAGAGGAT 58.268 47.619 0.00 0.00 0.00 3.24
927 940 1.887956 GCAAACAATGGAGGCAGAGGA 60.888 52.381 0.00 0.00 0.00 3.71
930 943 3.435846 TGCAAACAATGGAGGCAGA 57.564 47.368 0.00 0.00 0.00 4.26
932 945 1.114119 TGCTGCAAACAATGGAGGCA 61.114 50.000 0.00 0.00 46.76 4.75
933 946 0.033781 TTGCTGCAAACAATGGAGGC 59.966 50.000 13.51 0.00 46.76 4.70
934 947 1.938016 GCTTGCTGCAAACAATGGAGG 60.938 52.381 16.74 2.48 46.76 4.30
975 1058 2.729862 GCGCTACGGACGGCTATG 60.730 66.667 0.00 0.00 0.00 2.23
1124 1209 1.495878 CATCTACCGACAGCAGATGC 58.504 55.000 0.00 0.00 39.29 3.91
1140 1225 8.571461 TTATATTCATTCAGGAAGGATGCATC 57.429 34.615 18.81 18.81 30.79 3.91
1142 1227 8.388589 AGATTATATTCATTCAGGAAGGATGCA 58.611 33.333 0.00 0.00 30.79 3.96
1143 1228 8.675504 CAGATTATATTCATTCAGGAAGGATGC 58.324 37.037 0.00 0.00 30.79 3.91
1144 1229 9.955102 TCAGATTATATTCATTCAGGAAGGATG 57.045 33.333 0.00 0.00 30.79 3.51
1146 1231 8.600668 CCTCAGATTATATTCATTCAGGAAGGA 58.399 37.037 0.00 0.00 0.00 3.36
1147 1232 8.600668 TCCTCAGATTATATTCATTCAGGAAGG 58.399 37.037 0.00 0.00 0.00 3.46
1150 1235 9.784531 GTTTCCTCAGATTATATTCATTCAGGA 57.215 33.333 0.00 0.00 0.00 3.86
1151 1236 9.565090 TGTTTCCTCAGATTATATTCATTCAGG 57.435 33.333 0.00 0.00 0.00 3.86
1154 1239 9.890352 GCTTGTTTCCTCAGATTATATTCATTC 57.110 33.333 0.00 0.00 0.00 2.67
1155 1240 8.562892 CGCTTGTTTCCTCAGATTATATTCATT 58.437 33.333 0.00 0.00 0.00 2.57
1156 1241 7.933577 TCGCTTGTTTCCTCAGATTATATTCAT 59.066 33.333 0.00 0.00 0.00 2.57
1181 1266 4.262249 GGTAGGATGGACTCTACAATGCTC 60.262 50.000 0.00 0.00 38.00 4.26
1203 1288 4.434713 CCAAATCGGGAACTTTACAAGG 57.565 45.455 0.00 0.00 0.00 3.61
1243 1336 2.973945 AGTTGGTAATCTTCGCTGGAC 58.026 47.619 0.00 0.00 0.00 4.02
1259 1352 0.710567 CGTCACAAGCGCTCTAGTTG 59.289 55.000 12.06 7.58 0.00 3.16
1328 1421 3.016736 ACTGGCCAAATATCCAAAGACG 58.983 45.455 7.01 0.00 30.98 4.18
1356 1477 7.094848 ACCAACTACTCTACTCTAGAACGAAAC 60.095 40.741 0.00 0.00 33.75 2.78
1357 1478 6.939163 ACCAACTACTCTACTCTAGAACGAAA 59.061 38.462 0.00 0.00 33.75 3.46
1360 1481 6.740411 AACCAACTACTCTACTCTAGAACG 57.260 41.667 0.00 0.00 33.75 3.95
1361 1482 8.339344 AGAAACCAACTACTCTACTCTAGAAC 57.661 38.462 0.00 0.00 33.75 3.01
1362 1483 8.794553 CAAGAAACCAACTACTCTACTCTAGAA 58.205 37.037 0.00 0.00 33.75 2.10
1364 1485 7.030768 GCAAGAAACCAACTACTCTACTCTAG 58.969 42.308 0.00 0.00 0.00 2.43
1365 1486 6.720288 AGCAAGAAACCAACTACTCTACTCTA 59.280 38.462 0.00 0.00 0.00 2.43
1366 1487 5.540719 AGCAAGAAACCAACTACTCTACTCT 59.459 40.000 0.00 0.00 0.00 3.24
1367 1488 5.785243 AGCAAGAAACCAACTACTCTACTC 58.215 41.667 0.00 0.00 0.00 2.59
1368 1489 5.810080 AGCAAGAAACCAACTACTCTACT 57.190 39.130 0.00 0.00 0.00 2.57
1369 1490 6.224584 AGAAGCAAGAAACCAACTACTCTAC 58.775 40.000 0.00 0.00 0.00 2.59
1370 1491 6.420913 AGAAGCAAGAAACCAACTACTCTA 57.579 37.500 0.00 0.00 0.00 2.43
1371 1492 5.297569 AGAAGCAAGAAACCAACTACTCT 57.702 39.130 0.00 0.00 0.00 3.24
1372 1493 4.452795 GGAGAAGCAAGAAACCAACTACTC 59.547 45.833 0.00 0.00 0.00 2.59
1373 1494 4.103311 AGGAGAAGCAAGAAACCAACTACT 59.897 41.667 0.00 0.00 0.00 2.57
1392 1513 0.879765 CAACTGCCAGCAGAAAGGAG 59.120 55.000 25.66 5.26 46.30 3.69
1394 1515 0.879765 CTCAACTGCCAGCAGAAAGG 59.120 55.000 25.66 11.42 46.30 3.11
1402 1523 1.534595 GTCAAGAAGCTCAACTGCCAG 59.465 52.381 0.00 0.00 0.00 4.85
1421 1542 1.243902 AATTGGTGCGGAATTGTCGT 58.756 45.000 0.00 0.00 0.00 4.34
1422 1543 2.250188 GAAATTGGTGCGGAATTGTCG 58.750 47.619 0.00 0.00 0.00 4.35
1425 1546 2.029110 AGTGGAAATTGGTGCGGAATTG 60.029 45.455 0.00 0.00 0.00 2.32
1430 1551 1.080569 GCAGTGGAAATTGGTGCGG 60.081 57.895 0.00 0.00 0.00 5.69
1437 1558 2.034558 CGACAAACTGGCAGTGGAAATT 59.965 45.455 22.83 8.40 0.00 1.82
1438 1559 1.608590 CGACAAACTGGCAGTGGAAAT 59.391 47.619 22.83 1.09 0.00 2.17
1445 1566 0.317269 CAAGTGCGACAAACTGGCAG 60.317 55.000 14.16 14.16 37.36 4.85
1462 1583 7.278868 ACTTGCCATCGTTAAATTTTGTTTCAA 59.721 29.630 0.00 0.00 0.00 2.69
1464 1585 7.172654 ACTTGCCATCGTTAAATTTTGTTTC 57.827 32.000 0.00 0.00 0.00 2.78
1478 1599 1.526464 GTTTTTGCCAACTTGCCATCG 59.474 47.619 0.00 0.00 0.00 3.84
1509 1630 6.715344 TGAAGTACGTATGTCCAATTGTTC 57.285 37.500 4.43 0.00 0.00 3.18
1528 1649 6.504398 AGCTCATGCATGTATTGAATTGAAG 58.496 36.000 25.43 12.12 42.74 3.02
1529 1650 6.459670 AGCTCATGCATGTATTGAATTGAA 57.540 33.333 25.43 1.46 42.74 2.69
1530 1651 6.459670 AAGCTCATGCATGTATTGAATTGA 57.540 33.333 25.43 2.85 42.74 2.57
1551 1867 6.419980 AAGCGATGAGAAGAGAATCAAAAG 57.580 37.500 0.00 0.00 37.82 2.27
1556 1872 4.332268 AGCAAAAGCGATGAGAAGAGAATC 59.668 41.667 0.00 0.00 0.00 2.52
1571 1887 0.947180 TGGACCGACGTAGCAAAAGC 60.947 55.000 0.00 0.00 0.00 3.51
1584 1900 1.080839 CCGGCACAATTTTGGACCG 60.081 57.895 15.32 15.32 44.92 4.79
1585 1901 1.374125 GCCGGCACAATTTTGGACC 60.374 57.895 24.80 0.00 0.00 4.46
1586 1902 0.667184 CTGCCGGCACAATTTTGGAC 60.667 55.000 29.03 0.00 0.00 4.02
1587 1903 1.112315 ACTGCCGGCACAATTTTGGA 61.112 50.000 29.03 0.00 0.00 3.53
1600 1916 2.029073 ACACCTCGTTCACTGCCG 59.971 61.111 0.00 0.00 0.00 5.69
2017 2342 4.834453 CCTGCTCCTGCTCCTGCG 62.834 72.222 0.00 0.00 43.34 5.18
2031 2356 4.200283 GCGCTCCTCCTCGTCCTG 62.200 72.222 0.00 0.00 0.00 3.86
2084 2409 1.810030 GTACTGCCGCTTCTTCCCG 60.810 63.158 0.00 0.00 0.00 5.14
2513 2854 1.349627 CGACATGGCGAGCACAATC 59.650 57.895 18.41 0.00 0.00 2.67
2573 3046 0.093705 CAGTACGCGCTCTTGCTTTC 59.906 55.000 5.73 0.00 36.97 2.62
2615 3655 1.720301 GTCTCCATCGACGCTACGT 59.280 57.895 0.00 0.00 45.10 3.57
2616 3656 4.591852 GTCTCCATCGACGCTACG 57.408 61.111 0.00 0.00 0.00 3.51
2648 3724 1.584742 GCTCCGAAGCCGTACGTAC 60.585 63.158 15.90 15.90 43.10 3.67
2669 3749 0.376152 CATGCAAGCGTCCATCAGAC 59.624 55.000 0.00 0.00 42.54 3.51
2761 4072 2.358737 CGCCACAGGTCCACCTTC 60.359 66.667 0.00 0.00 46.09 3.46
3184 4521 2.740714 GAACACGCTCATCGGCACC 61.741 63.158 0.00 0.00 43.86 5.01
3523 4866 3.706373 TCTTCCGCCACCTCCAGC 61.706 66.667 0.00 0.00 0.00 4.85
3562 4905 3.069980 GACGGAGGACAGCTCGCAT 62.070 63.158 0.00 0.00 0.00 4.73
3635 4978 3.140707 TCCCCGTAATCACTATACCCTCA 59.859 47.826 0.00 0.00 0.00 3.86
3647 4990 3.181458 TGCTAACCAGATTCCCCGTAATC 60.181 47.826 0.00 0.00 36.33 1.75
3668 5011 3.858040 CGCAACTAGTTAGCGCTTG 57.142 52.632 27.17 6.99 45.14 4.01
3673 5016 2.950433 TGTGTACCGCAACTAGTTAGC 58.050 47.619 8.04 12.94 0.00 3.09
3787 5166 5.099575 TCCTTTTCTTTCTTTTTGCGACAC 58.900 37.500 0.00 0.00 0.00 3.67
3790 5169 6.202516 TCTTCCTTTTCTTTCTTTTTGCGA 57.797 33.333 0.00 0.00 0.00 5.10
3791 5170 6.697019 TGATCTTCCTTTTCTTTCTTTTTGCG 59.303 34.615 0.00 0.00 0.00 4.85
3792 5171 8.493547 CATGATCTTCCTTTTCTTTCTTTTTGC 58.506 33.333 0.00 0.00 0.00 3.68
3793 5172 8.493547 GCATGATCTTCCTTTTCTTTCTTTTTG 58.506 33.333 0.00 0.00 0.00 2.44
3794 5173 7.658982 GGCATGATCTTCCTTTTCTTTCTTTTT 59.341 33.333 0.00 0.00 0.00 1.94
3808 5192 1.202336 CCTTTTGCGGCATGATCTTCC 60.202 52.381 2.28 0.00 0.00 3.46
3820 5204 2.937469 TATCATGGTTGCCTTTTGCG 57.063 45.000 0.00 0.00 45.60 4.85
3879 5272 8.662141 TCGTTGTCTTACTCCAATTATTAAAGC 58.338 33.333 0.00 0.00 0.00 3.51
3915 5308 1.301677 CCTGAACAAGAGAAGCCGGC 61.302 60.000 21.89 21.89 0.00 6.13
3918 5311 0.250901 TGGCCTGAACAAGAGAAGCC 60.251 55.000 3.32 0.00 39.41 4.35
3919 5312 0.877743 GTGGCCTGAACAAGAGAAGC 59.122 55.000 3.32 0.00 0.00 3.86
3920 5313 2.260844 TGTGGCCTGAACAAGAGAAG 57.739 50.000 3.32 0.00 0.00 2.85
3956 5349 1.815840 TTCAACCTCACGCACGCAA 60.816 52.632 0.00 0.00 0.00 4.85
3966 5359 9.043079 GTACTAGCTATTTAATGGTTCAACCTC 57.957 37.037 8.40 0.00 39.58 3.85
3967 5360 7.709613 CGTACTAGCTATTTAATGGTTCAACCT 59.290 37.037 8.40 0.00 39.58 3.50
3983 5376 3.071602 ACGGAGGGATTACGTACTAGCTA 59.928 47.826 0.00 0.00 46.85 3.32
3992 5491 0.457035 TTCCGAACGGAGGGATTACG 59.543 55.000 15.34 0.00 46.06 3.18
3993 5492 2.904697 ATTCCGAACGGAGGGATTAC 57.095 50.000 15.34 0.00 46.06 1.89
3994 5493 3.962718 AGTAATTCCGAACGGAGGGATTA 59.037 43.478 15.34 13.43 46.06 1.75
3995 5494 2.770232 AGTAATTCCGAACGGAGGGATT 59.230 45.455 15.34 14.30 46.06 3.01
3996 5495 2.395619 AGTAATTCCGAACGGAGGGAT 58.604 47.619 15.34 4.75 46.06 3.85
3997 5496 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3998 5497 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3999 5498 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
4000 5499 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
4001 5500 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
4002 5501 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
4003 5502 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
4004 5503 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
4005 5504 7.092079 TCATTTCTACGACAAGTAATTCCGAA 58.908 34.615 0.00 0.00 34.45 4.30
4006 5505 6.623486 TCATTTCTACGACAAGTAATTCCGA 58.377 36.000 0.00 0.00 34.45 4.55
4007 5506 6.880822 TCATTTCTACGACAAGTAATTCCG 57.119 37.500 0.00 0.00 34.45 4.30
4035 5534 9.944376 TTGCTCTTGTTTTTACTACATCTAGAT 57.056 29.630 0.00 0.00 0.00 1.98
4036 5535 9.772973 TTTGCTCTTGTTTTTACTACATCTAGA 57.227 29.630 0.00 0.00 0.00 2.43
4039 5538 9.899226 GATTTTGCTCTTGTTTTTACTACATCT 57.101 29.630 0.00 0.00 0.00 2.90
4040 5539 9.129209 GGATTTTGCTCTTGTTTTTACTACATC 57.871 33.333 0.00 0.00 0.00 3.06
4041 5540 8.637986 TGGATTTTGCTCTTGTTTTTACTACAT 58.362 29.630 0.00 0.00 0.00 2.29
4042 5541 8.001881 TGGATTTTGCTCTTGTTTTTACTACA 57.998 30.769 0.00 0.00 0.00 2.74
4043 5542 8.135529 ACTGGATTTTGCTCTTGTTTTTACTAC 58.864 33.333 0.00 0.00 0.00 2.73
4044 5543 8.134895 CACTGGATTTTGCTCTTGTTTTTACTA 58.865 33.333 0.00 0.00 0.00 1.82
4045 5544 6.980397 CACTGGATTTTGCTCTTGTTTTTACT 59.020 34.615 0.00 0.00 0.00 2.24
4046 5545 6.978080 TCACTGGATTTTGCTCTTGTTTTTAC 59.022 34.615 0.00 0.00 0.00 2.01
4047 5546 7.106439 TCACTGGATTTTGCTCTTGTTTTTA 57.894 32.000 0.00 0.00 0.00 1.52
4048 5547 5.976458 TCACTGGATTTTGCTCTTGTTTTT 58.024 33.333 0.00 0.00 0.00 1.94
4049 5548 5.596836 TCACTGGATTTTGCTCTTGTTTT 57.403 34.783 0.00 0.00 0.00 2.43
4093 5592 4.262976 GCATACTTTATTTGTGAACGCAGC 59.737 41.667 0.00 0.00 0.00 5.25
4096 5595 9.710979 TTTATAGCATACTTTATTTGTGAACGC 57.289 29.630 0.00 0.00 0.00 4.84
4145 5644 9.979578 TTTACTCATTTCAATTTGCATGTAGTT 57.020 25.926 0.00 0.00 0.00 2.24
4149 5648 8.659925 TTGTTTACTCATTTCAATTTGCATGT 57.340 26.923 0.00 0.00 0.00 3.21
4169 5668 7.556733 TGGACACGTTTTAGTCTATTTGTTT 57.443 32.000 4.05 0.00 35.18 2.83
4183 5683 5.182487 TCTTGCATGTATATGGACACGTTT 58.818 37.500 1.33 0.00 34.12 3.60
4184 5684 4.765273 TCTTGCATGTATATGGACACGTT 58.235 39.130 1.33 0.00 34.12 3.99
4186 5686 5.733226 TTTCTTGCATGTATATGGACACG 57.267 39.130 1.33 0.00 34.12 4.49
4191 5691 7.227314 TGTTCTAGCTTTCTTGCATGTATATGG 59.773 37.037 0.00 0.00 34.79 2.74
4196 5696 6.409704 AGATGTTCTAGCTTTCTTGCATGTA 58.590 36.000 0.00 0.00 34.99 2.29
4210 5717 9.529325 TCCGTTCACAAATATAAGATGTTCTAG 57.471 33.333 0.00 0.00 0.00 2.43
4219 5726 8.407064 AGTACTCTCTCCGTTCACAAATATAAG 58.593 37.037 0.00 0.00 0.00 1.73
4228 5735 2.075338 ACGAGTACTCTCTCCGTTCAC 58.925 52.381 20.34 0.00 38.45 3.18
4256 5763 9.586435 TGAATACTATGCATAGTAATTGATCGG 57.414 33.333 37.50 13.49 45.79 4.18
4270 5819 5.585820 TTACTGTCGGTGAATACTATGCA 57.414 39.130 0.00 0.00 0.00 3.96
4271 5820 5.634020 GGATTACTGTCGGTGAATACTATGC 59.366 44.000 0.00 0.00 0.00 3.14
4272 5821 6.982852 AGGATTACTGTCGGTGAATACTATG 58.017 40.000 0.00 0.00 0.00 2.23
4287 5836 6.698008 TGGAAACAATGCATAGGATTACTG 57.302 37.500 0.00 0.00 37.44 2.74
4317 5866 6.589830 ACTATCTAATTTCGATGCACACAC 57.410 37.500 0.00 0.00 0.00 3.82
4353 5902 8.915871 ATGCACAATCACAAACAGAATTATAC 57.084 30.769 0.00 0.00 0.00 1.47
4367 5916 1.035139 GGGATGGGATGCACAATCAC 58.965 55.000 0.00 0.00 39.39 3.06
4368 5917 0.630134 TGGGATGGGATGCACAATCA 59.370 50.000 0.00 0.00 36.98 2.57
4382 5932 7.311234 CCCAAAGAAATTTTAGGTTGATGGGAT 60.311 37.037 0.00 0.00 44.24 3.85
4396 5946 3.694566 CGTAGCTAGCCCCAAAGAAATTT 59.305 43.478 12.13 0.00 0.00 1.82
4409 5959 1.355916 CGACTGACCCGTAGCTAGC 59.644 63.158 6.62 6.62 0.00 3.42
4411 5961 2.117156 GGCGACTGACCCGTAGCTA 61.117 63.158 0.00 0.00 36.07 3.32
4412 5962 3.450115 GGCGACTGACCCGTAGCT 61.450 66.667 0.00 0.00 36.07 3.32
4435 5985 6.472887 AGAAATCGACTGACCCAATTCTTAA 58.527 36.000 0.00 0.00 0.00 1.85
4436 5986 6.049955 AGAAATCGACTGACCCAATTCTTA 57.950 37.500 0.00 0.00 0.00 2.10
4438 5988 4.559862 AGAAATCGACTGACCCAATTCT 57.440 40.909 0.00 0.00 0.00 2.40
4442 5992 3.325425 TGGTTAGAAATCGACTGACCCAA 59.675 43.478 11.47 0.00 41.37 4.12
4450 6000 6.721571 TCACTCAATTGGTTAGAAATCGAC 57.278 37.500 5.42 0.00 0.00 4.20
4453 6003 7.214467 TGGTTCACTCAATTGGTTAGAAATC 57.786 36.000 5.42 0.00 0.00 2.17
4457 6007 7.595819 ATTTTGGTTCACTCAATTGGTTAGA 57.404 32.000 5.42 0.00 0.00 2.10
4462 6012 5.236911 CCACAATTTTGGTTCACTCAATTGG 59.763 40.000 5.42 0.00 38.58 3.16
4487 6037 6.934083 TGTGCTATAACACTGAAATTGACTGA 59.066 34.615 7.73 0.00 41.30 3.41
4490 6040 7.584987 AGTTGTGCTATAACACTGAAATTGAC 58.415 34.615 7.73 0.00 41.30 3.18
4494 6044 9.284968 ACTTAAGTTGTGCTATAACACTGAAAT 57.715 29.630 1.12 0.00 41.30 2.17
4537 6087 3.550437 AGTCTTGTGAGCTTCTGTTGT 57.450 42.857 0.00 0.00 0.00 3.32
4572 6122 2.366916 TCATCAACGGGCCATTGTTTTT 59.633 40.909 12.63 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.