Multiple sequence alignment - TraesCS7D01G439300

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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 TraesCS7D01G439300 chr7D 100.000 4372 0 0 1 4372 558973728 558969357 0.000000e+00 8074
1 TraesCS7D01G439300 chr7D 83.832 1336 173 31 2286 3591 557837682 557839004 0.000000e+00 1230
2 TraesCS7D01G439300 chr7D 86.761 710 77 9 2830 3534 557843136 557843833 0.000000e+00 774
3 TraesCS7D01G439300 chr7D 89.603 529 55 0 2210 2738 557842597 557843125 0.000000e+00 673
4 TraesCS7D01G439300 chr7D 81.567 689 109 17 1482 2157 557836721 557837404 1.780000e-153 553
5 TraesCS7D01G439300 chr7D 86.787 333 40 3 988 1316 557841218 557841550 6.910000e-98 368
6 TraesCS7D01G439300 chr7D 84.746 354 42 10 1387 1737 557841786 557842130 1.160000e-90 344
7 TraesCS7D01G439300 chr7D 84.722 288 43 1 1015 1301 557835809 557836096 1.990000e-73 287
8 TraesCS7D01G439300 chr7A 91.613 1407 67 26 1350 2738 643861909 643860536 0.000000e+00 1897
9 TraesCS7D01G439300 chr7A 92.251 1226 51 18 2744 3940 643860484 643859274 0.000000e+00 1698
10 TraesCS7D01G439300 chr7A 85.160 876 105 19 2739 3608 643422310 643423166 0.000000e+00 874
11 TraesCS7D01G439300 chr7A 89.299 542 56 2 2198 2738 643421719 643422259 0.000000e+00 678
12 TraesCS7D01G439300 chr7A 91.142 508 33 5 1 497 643863259 643862753 0.000000e+00 678
13 TraesCS7D01G439300 chr7A 82.337 736 114 16 2880 3604 643416541 643417271 3.710000e-175 625
14 TraesCS7D01G439300 chr7A 91.704 446 37 0 2286 2731 643416096 643416541 1.730000e-173 619
15 TraesCS7D01G439300 chr7A 92.857 406 18 8 947 1344 643862349 643861947 2.930000e-161 579
16 TraesCS7D01G439300 chr7A 89.589 365 17 5 481 840 643862737 643862389 1.120000e-120 444
17 TraesCS7D01G439300 chr7A 86.581 313 41 1 1002 1313 643420426 643420738 1.160000e-90 344
18 TraesCS7D01G439300 chr7A 84.211 361 41 10 1383 1736 643420840 643421191 1.950000e-88 337
19 TraesCS7D01G439300 chr7A 88.446 251 26 3 1492 1741 643415154 643415402 2.560000e-77 300
20 TraesCS7D01G439300 chr7A 96.089 179 5 2 4155 4333 643859211 643859035 1.540000e-74 291
21 TraesCS7D01G439300 chr7A 83.333 288 47 1 1015 1301 643414289 643414576 9.320000e-67 265
22 TraesCS7D01G439300 chr7B 90.669 718 51 7 2746 3448 606645015 606644299 0.000000e+00 941
23 TraesCS7D01G439300 chr7B 91.581 677 46 7 1490 2162 606646405 606645736 0.000000e+00 924
24 TraesCS7D01G439300 chr7B 95.882 510 18 3 2230 2738 606645575 606645068 0.000000e+00 822
25 TraesCS7D01G439300 chr7B 86.068 768 89 10 2812 3572 605956777 605957533 0.000000e+00 809
26 TraesCS7D01G439300 chr7B 92.549 510 25 9 850 1352 606646925 606646422 0.000000e+00 719
27 TraesCS7D01G439300 chr7B 88.489 556 60 2 2183 2738 605956195 605956746 0.000000e+00 669
28 TraesCS7D01G439300 chr7B 92.601 446 33 0 2286 2731 605908591 605909036 3.690000e-180 641
29 TraesCS7D01G439300 chr7B 86.678 578 76 1 2880 3456 605909036 605909613 1.330000e-179 640
30 TraesCS7D01G439300 chr7B 89.824 511 34 9 1 497 606795933 606795427 1.330000e-179 640
31 TraesCS7D01G439300 chr7B 89.071 366 26 6 481 840 606647266 606646909 4.010000e-120 442
32 TraesCS7D01G439300 chr7B 88.520 331 32 4 991 1316 605954835 605955164 3.170000e-106 396
33 TraesCS7D01G439300 chr7B 84.492 374 55 3 1785 2157 605907981 605908352 2.480000e-97 366
34 TraesCS7D01G439300 chr7B 93.117 247 15 2 1 247 606648066 606647822 1.160000e-95 361
35 TraesCS7D01G439300 chr7B 83.120 391 43 17 1349 1737 605955310 605955679 7.010000e-88 335
36 TraesCS7D01G439300 chr7B 87.912 273 25 7 850 1118 606779359 606779091 9.130000e-82 315
37 TraesCS7D01G439300 chr7B 85.764 288 40 1 1015 1301 605906822 605907109 1.980000e-78 303
38 TraesCS7D01G439300 chr7B 85.985 264 31 6 1475 1736 605907633 605907892 1.200000e-70 278
39 TraesCS7D01G439300 chr7B 88.128 219 18 2 287 497 606647497 606647279 2.020000e-63 254
40 TraesCS7D01G439300 chr7B 89.899 198 11 5 645 840 606779533 606779343 3.380000e-61 246
41 TraesCS7D01G439300 chr7B 89.011 182 18 1 3683 3862 606643908 606643727 1.580000e-54 224
42 TraesCS7D01G439300 chr7B 90.604 149 13 1 481 629 606795415 606795268 3.450000e-46 196


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 TraesCS7D01G439300 chr7D 558969357 558973728 4371 True 8074.000000 8074 100.000000 1 4372 1 chr7D.!!$R1 4371
1 TraesCS7D01G439300 chr7D 557835809 557843833 8024 False 604.142857 1230 85.431143 988 3591 7 chr7D.!!$F1 2603
2 TraesCS7D01G439300 chr7A 643859035 643863259 4224 True 931.166667 1897 92.256833 1 4333 6 chr7A.!!$R1 4332
3 TraesCS7D01G439300 chr7A 643414289 643423166 8877 False 505.250000 874 86.383875 1002 3608 8 chr7A.!!$F1 2606
4 TraesCS7D01G439300 chr7B 606643727 606648066 4339 True 585.875000 941 91.251000 1 3862 8 chr7B.!!$R1 3861
5 TraesCS7D01G439300 chr7B 605954835 605957533 2698 False 552.250000 809 86.549250 991 3572 4 chr7B.!!$F2 2581
6 TraesCS7D01G439300 chr7B 605906822 605909613 2791 False 445.600000 641 87.104000 1015 3456 5 chr7B.!!$F1 2441
7 TraesCS7D01G439300 chr7B 606795268 606795933 665 True 418.000000 640 90.214000 1 629 2 chr7B.!!$R3 628

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
673 1008 0.105039 CTAGGGCCACTTGATCGGTC 59.895 60.0 6.18 0.0 0.00 4.79 F
1408 12392 0.466739 TGGGCATGCATCTTGCTAGG 60.467 55.0 21.36 0.0 45.31 3.02 F
2168 13374 0.618458 TGGAGTAGAACACATGGCCC 59.382 55.0 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 12987 0.829333 ACTGGCAGCATCCTCTACAG 59.171 55.0 15.89 0.00 0.00 2.74 R
3215 14640 0.033781 GCAATGCAAAGTTCTGGCCA 59.966 50.0 4.71 4.71 0.00 5.36 R
3937 15529 0.034337 AGCGGTGCTAGTTCGGAAAA 59.966 50.0 0.00 0.00 36.99 2.29 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
21 22 2.499693 TCAGCACCTCGTATCATTTGGA 59.500 45.455 0.00 0.00 0.00 3.53
22 23 3.134623 TCAGCACCTCGTATCATTTGGAT 59.865 43.478 0.00 0.00 40.14 3.41
66 67 3.515104 GGGAAAAGCCTGATTCATGGAAA 59.485 43.478 0.00 0.00 36.66 3.13
261 262 6.267471 AGCAGGATATTTGTTGTTTCTGGAAA 59.733 34.615 0.00 0.00 0.00 3.13
291 577 2.649531 TGTGTTCTTTAGGTGGTGGG 57.350 50.000 0.00 0.00 0.00 4.61
392 687 6.868622 TCTGCAGAAAGAAGTATTACCTCTC 58.131 40.000 15.67 0.00 0.00 3.20
535 863 2.940158 TCGGAATGAAGGGAGTATCGA 58.060 47.619 0.00 0.00 34.37 3.59
593 922 1.210155 GCCTCGCATCCACACAAAC 59.790 57.895 0.00 0.00 0.00 2.93
673 1008 0.105039 CTAGGGCCACTTGATCGGTC 59.895 60.000 6.18 0.00 0.00 4.79
688 1023 1.878088 TCGGTCTATGTAGTCGCCATC 59.122 52.381 0.00 0.00 0.00 3.51
692 1027 2.294791 GTCTATGTAGTCGCCATCTGCT 59.705 50.000 0.00 0.00 38.05 4.24
694 1029 0.826715 ATGTAGTCGCCATCTGCTGT 59.173 50.000 0.00 0.00 38.05 4.40
732 1067 2.700897 TCTGGGTTTCTAGATGGCTAGC 59.299 50.000 6.04 6.04 43.13 3.42
735 1070 3.459598 TGGGTTTCTAGATGGCTAGCAAT 59.540 43.478 18.24 11.51 43.13 3.56
828 1164 2.102252 TCACACCAATTGAGCCAAAACC 59.898 45.455 7.12 0.00 0.00 3.27
829 1165 2.102925 CACACCAATTGAGCCAAAACCT 59.897 45.455 7.12 0.00 0.00 3.50
830 1166 2.365293 ACACCAATTGAGCCAAAACCTC 59.635 45.455 7.12 0.00 0.00 3.85
832 1168 1.885887 CCAATTGAGCCAAAACCTCGA 59.114 47.619 7.12 0.00 31.98 4.04
834 1170 3.568538 CAATTGAGCCAAAACCTCGAAG 58.431 45.455 0.00 0.00 31.98 3.79
835 1171 0.951558 TTGAGCCAAAACCTCGAAGC 59.048 50.000 0.00 0.00 31.98 3.86
837 1173 0.951558 GAGCCAAAACCTCGAAGCAA 59.048 50.000 0.00 0.00 0.00 3.91
839 1175 1.754226 AGCCAAAACCTCGAAGCAAAA 59.246 42.857 0.00 0.00 0.00 2.44
840 1176 2.365293 AGCCAAAACCTCGAAGCAAAAT 59.635 40.909 0.00 0.00 0.00 1.82
843 1179 4.367450 CCAAAACCTCGAAGCAAAATCAA 58.633 39.130 0.00 0.00 0.00 2.57
844 1180 4.808364 CCAAAACCTCGAAGCAAAATCAAA 59.192 37.500 0.00 0.00 0.00 2.69
845 1181 5.466393 CCAAAACCTCGAAGCAAAATCAAAT 59.534 36.000 0.00 0.00 0.00 2.32
846 1182 6.644592 CCAAAACCTCGAAGCAAAATCAAATA 59.355 34.615 0.00 0.00 0.00 1.40
847 1183 7.170658 CCAAAACCTCGAAGCAAAATCAAATAA 59.829 33.333 0.00 0.00 0.00 1.40
850 1186 8.655651 AACCTCGAAGCAAAATCAAATAAAAA 57.344 26.923 0.00 0.00 0.00 1.94
871 1207 3.715628 AAACTCGAAGCAAAACTGCAT 57.284 38.095 0.00 0.00 37.25 3.96
971 1307 2.011222 GTACGACTCCTGACTCCTGAG 58.989 57.143 0.00 0.00 0.00 3.35
987 1323 0.969917 TGAGCTCCTCCTCTGCACTC 60.970 60.000 12.15 0.00 33.02 3.51
988 1324 2.003658 GAGCTCCTCCTCTGCACTCG 62.004 65.000 0.87 0.00 0.00 4.18
989 1325 2.347322 GCTCCTCCTCTGCACTCGT 61.347 63.158 0.00 0.00 0.00 4.18
1221 11797 2.825836 CGATCACAGCCCTTGCCC 60.826 66.667 0.00 0.00 38.69 5.36
1303 11880 1.206371 ACGGTAATCTTTCAGTCCCCG 59.794 52.381 0.00 0.00 39.96 5.73
1345 12072 7.321153 TGAACTTTTTCTATTCTCCCTCGTAG 58.679 38.462 0.00 0.00 32.36 3.51
1408 12392 0.466739 TGGGCATGCATCTTGCTAGG 60.467 55.000 21.36 0.00 45.31 3.02
1428 12412 2.416431 GGCAGGAGCAGCTAACAAATTG 60.416 50.000 0.00 0.00 44.61 2.32
1429 12413 2.229784 GCAGGAGCAGCTAACAAATTGT 59.770 45.455 0.00 0.00 41.58 2.71
1430 12414 3.440173 GCAGGAGCAGCTAACAAATTGTA 59.560 43.478 0.00 0.00 41.58 2.41
1431 12415 4.082787 GCAGGAGCAGCTAACAAATTGTAA 60.083 41.667 0.00 0.00 41.58 2.41
1432 12416 5.393962 CAGGAGCAGCTAACAAATTGTAAC 58.606 41.667 0.00 0.00 0.00 2.50
1433 12417 5.048782 CAGGAGCAGCTAACAAATTGTAACA 60.049 40.000 0.00 0.00 0.00 2.41
1434 12418 5.711976 AGGAGCAGCTAACAAATTGTAACAT 59.288 36.000 0.00 0.00 0.00 2.71
1435 12419 6.030228 GGAGCAGCTAACAAATTGTAACATC 58.970 40.000 0.00 0.00 0.00 3.06
1456 12448 5.239359 TCTAACATGCATGCACTTTGATC 57.761 39.130 25.37 0.00 0.00 2.92
1477 12469 3.430556 TCACCGTACGATGTCACAAAATG 59.569 43.478 18.76 0.00 0.00 2.32
1490 12516 9.128107 GATGTCACAAAATGTCGATTTACAAAT 57.872 29.630 0.00 0.00 31.18 2.32
1522 12548 0.758685 TGCCCTTCACTTGGTTTGGG 60.759 55.000 0.00 0.00 37.76 4.12
1525 12551 1.659794 CTTCACTTGGTTTGGGCCG 59.340 57.895 0.00 0.00 0.00 6.13
1627 12653 1.133262 AGTAGCCGTATGGGGAAGCTA 60.133 52.381 2.41 0.00 35.03 3.32
1723 12749 3.217626 CCATGAGAAGATAAAGGTGCCC 58.782 50.000 0.00 0.00 0.00 5.36
1737 12763 1.000843 GGTGCCCTGTTCAATGGAAAC 59.999 52.381 0.00 0.00 34.13 2.78
1788 12966 5.311265 ACATGGGTATTGCATAGACTGATG 58.689 41.667 0.00 0.00 0.00 3.07
1789 12967 5.072193 ACATGGGTATTGCATAGACTGATGA 59.928 40.000 0.00 0.00 0.00 2.92
1801 12987 8.996271 TGCATAGACTGATGATAATGTTTCATC 58.004 33.333 6.70 6.70 46.30 2.92
1824 13010 1.831580 AGAGGATGCTGCCAGTTTTC 58.168 50.000 0.00 0.00 0.00 2.29
1918 13104 4.202503 ACACATGTCCTGAGTTCCAGAATT 60.203 41.667 0.00 0.00 45.78 2.17
2166 13372 3.428045 GCAAATGGAGTAGAACACATGGC 60.428 47.826 0.00 0.00 0.00 4.40
2168 13374 0.618458 TGGAGTAGAACACATGGCCC 59.382 55.000 0.00 0.00 0.00 5.80
2169 13375 0.912486 GGAGTAGAACACATGGCCCT 59.088 55.000 0.00 0.00 0.00 5.19
2192 13398 6.813152 CCTTGGTGTTTGATAAAAATAGCTGG 59.187 38.462 0.00 0.00 0.00 4.85
2193 13399 5.719173 TGGTGTTTGATAAAAATAGCTGGC 58.281 37.500 0.00 0.00 0.00 4.85
2640 13992 2.032528 CCGGAGTGGCAAGAGCAA 59.967 61.111 0.00 0.00 44.61 3.91
2731 14083 8.664798 TGAAGATTGTAAGTACGAAATTGATGG 58.335 33.333 0.00 0.00 0.00 3.51
2769 14171 5.977489 AAGAGTAGCCAACAATAAAACCC 57.023 39.130 0.00 0.00 0.00 4.11
2925 14350 3.323979 AGTGGTCGGAGTAATGTTCTTGT 59.676 43.478 0.00 0.00 0.00 3.16
2930 14355 5.120363 GGTCGGAGTAATGTTCTTGTTCTTC 59.880 44.000 0.00 0.00 0.00 2.87
3176 14601 3.430862 GCGGCAAAGCATCCGTCA 61.431 61.111 0.00 0.00 46.79 4.35
3215 14640 1.700042 GGGGTCCTCGGATCTGCATT 61.700 60.000 0.00 0.00 0.00 3.56
3230 14655 0.033781 GCATTGGCCAGAACTTTGCA 59.966 50.000 5.11 0.00 0.00 4.08
3278 14703 1.684386 CCATCCTCCAGCGCTTCTCT 61.684 60.000 7.50 0.00 0.00 3.10
3314 14739 1.069090 CTACACCCATGCGCCGTAT 59.931 57.895 4.18 0.00 0.00 3.06
3388 14814 3.742433 ATGATCACCCTTCTCATCGAC 57.258 47.619 0.00 0.00 0.00 4.20
3393 14819 1.276421 CACCCTTCTCATCGACCAGTT 59.724 52.381 0.00 0.00 0.00 3.16
3394 14820 1.276421 ACCCTTCTCATCGACCAGTTG 59.724 52.381 0.00 0.00 0.00 3.16
3403 14829 5.869344 TCTCATCGACCAGTTGATTTACTTG 59.131 40.000 0.00 0.00 31.51 3.16
3404 14830 5.547465 TCATCGACCAGTTGATTTACTTGT 58.453 37.500 0.00 0.00 31.51 3.16
3439 14873 6.139048 AGTTTAAAGTTTTAGCTTTCGGCA 57.861 33.333 0.00 0.00 44.79 5.69
3448 14882 4.593597 TTAGCTTTCGGCAGAATAAACG 57.406 40.909 0.00 0.00 44.79 3.60
3528 15074 5.182487 TGTAGTTTTCAGTTGAACTGCTCA 58.818 37.500 19.99 8.84 45.54 4.26
3538 15084 4.280174 AGTTGAACTGCTCATTTGCTTCAT 59.720 37.500 0.00 0.00 32.78 2.57
3648 15213 5.157940 TCTCTGCATCCTCCTTATATTGC 57.842 43.478 0.00 0.00 0.00 3.56
3831 15423 3.717294 AGATTCCGTGCGCCCCTT 61.717 61.111 4.18 0.00 0.00 3.95
3888 15480 7.132863 AGTGTCAATTCGCTCTAAAAGAAAAC 58.867 34.615 0.00 0.00 0.00 2.43
3900 15492 9.087424 GCTCTAAAAGAAAACAAGTTGAATTGT 57.913 29.630 10.54 0.00 45.18 2.71
3919 15511 3.659786 TGTCATCAGTGTAAAAGGACCG 58.340 45.455 0.00 0.00 0.00 4.79
3936 15528 3.366629 GACTGCAGGTCGGTGAGA 58.633 61.111 19.93 0.00 35.07 3.27
3937 15529 1.893786 GACTGCAGGTCGGTGAGAT 59.106 57.895 19.93 0.00 35.07 2.75
3938 15530 0.247736 GACTGCAGGTCGGTGAGATT 59.752 55.000 19.93 0.00 35.07 2.40
3939 15531 0.687354 ACTGCAGGTCGGTGAGATTT 59.313 50.000 19.93 0.00 31.81 2.17
3940 15532 1.072331 ACTGCAGGTCGGTGAGATTTT 59.928 47.619 19.93 0.00 31.81 1.82
3941 15533 1.734465 CTGCAGGTCGGTGAGATTTTC 59.266 52.381 5.57 0.00 0.00 2.29
3942 15534 1.087501 GCAGGTCGGTGAGATTTTCC 58.912 55.000 0.00 0.00 0.00 3.13
3943 15535 1.359848 CAGGTCGGTGAGATTTTCCG 58.640 55.000 0.00 0.00 44.76 4.30
3950 15542 2.603560 CGGTGAGATTTTCCGAACTAGC 59.396 50.000 0.00 0.00 46.05 3.42
3951 15543 3.596214 GGTGAGATTTTCCGAACTAGCA 58.404 45.455 0.00 0.00 0.00 3.49
3952 15544 3.371285 GGTGAGATTTTCCGAACTAGCAC 59.629 47.826 0.00 0.00 0.00 4.40
3953 15545 3.371285 GTGAGATTTTCCGAACTAGCACC 59.629 47.826 0.00 0.00 0.00 5.01
3954 15546 2.603560 GAGATTTTCCGAACTAGCACCG 59.396 50.000 0.00 0.00 0.00 4.94
3955 15547 1.062148 GATTTTCCGAACTAGCACCGC 59.938 52.381 0.00 0.00 0.00 5.68
3956 15548 0.034337 TTTTCCGAACTAGCACCGCT 59.966 50.000 0.00 0.00 43.41 5.52
3957 15549 0.034337 TTTCCGAACTAGCACCGCTT 59.966 50.000 0.00 0.00 40.44 4.68
3958 15550 0.389426 TTCCGAACTAGCACCGCTTC 60.389 55.000 0.00 0.00 40.44 3.86
3959 15551 2.158959 CCGAACTAGCACCGCTTCG 61.159 63.158 0.00 4.43 40.44 3.79
3960 15552 1.443872 CGAACTAGCACCGCTTCGT 60.444 57.895 0.00 0.00 40.44 3.85
3961 15553 1.007336 CGAACTAGCACCGCTTCGTT 61.007 55.000 0.00 0.00 40.44 3.85
3962 15554 1.145803 GAACTAGCACCGCTTCGTTT 58.854 50.000 0.00 0.00 40.44 3.60
3963 15555 1.529865 GAACTAGCACCGCTTCGTTTT 59.470 47.619 0.00 0.00 40.44 2.43
3964 15556 0.865769 ACTAGCACCGCTTCGTTTTG 59.134 50.000 0.00 0.00 40.44 2.44
3965 15557 0.452784 CTAGCACCGCTTCGTTTTGC 60.453 55.000 0.00 0.00 40.44 3.68
3966 15558 1.160946 TAGCACCGCTTCGTTTTGCA 61.161 50.000 0.00 0.00 40.44 4.08
3967 15559 2.292916 GCACCGCTTCGTTTTGCAC 61.293 57.895 0.00 0.00 0.00 4.57
3982 15574 5.254842 GTTTTGCACGAAATTTTCACAAGG 58.745 37.500 9.66 0.00 0.00 3.61
3983 15575 4.377839 TTGCACGAAATTTTCACAAGGA 57.622 36.364 9.66 0.00 0.00 3.36
3984 15576 3.701241 TGCACGAAATTTTCACAAGGAC 58.299 40.909 9.66 0.00 0.00 3.85
3985 15577 3.380004 TGCACGAAATTTTCACAAGGACT 59.620 39.130 9.66 0.00 0.00 3.85
3986 15578 3.975035 GCACGAAATTTTCACAAGGACTC 59.025 43.478 9.66 0.00 0.00 3.36
3987 15579 4.261197 GCACGAAATTTTCACAAGGACTCT 60.261 41.667 9.66 0.00 0.00 3.24
3988 15580 5.049680 GCACGAAATTTTCACAAGGACTCTA 60.050 40.000 9.66 0.00 0.00 2.43
3989 15581 6.593978 CACGAAATTTTCACAAGGACTCTAG 58.406 40.000 9.66 0.00 0.00 2.43
3990 15582 6.423905 CACGAAATTTTCACAAGGACTCTAGA 59.576 38.462 9.66 0.00 0.00 2.43
3991 15583 7.118390 CACGAAATTTTCACAAGGACTCTAGAT 59.882 37.037 9.66 0.00 0.00 1.98
3992 15584 7.332182 ACGAAATTTTCACAAGGACTCTAGATC 59.668 37.037 9.66 0.00 0.00 2.75
3993 15585 7.331934 CGAAATTTTCACAAGGACTCTAGATCA 59.668 37.037 9.66 0.00 0.00 2.92
3994 15586 9.171877 GAAATTTTCACAAGGACTCTAGATCAT 57.828 33.333 4.25 0.00 0.00 2.45
3995 15587 8.729805 AATTTTCACAAGGACTCTAGATCATC 57.270 34.615 0.00 0.00 0.00 2.92
3996 15588 6.857437 TTTCACAAGGACTCTAGATCATCA 57.143 37.500 0.00 0.00 0.00 3.07
3997 15589 6.462552 TTCACAAGGACTCTAGATCATCAG 57.537 41.667 0.00 0.00 0.00 2.90
3998 15590 5.514169 TCACAAGGACTCTAGATCATCAGT 58.486 41.667 0.00 0.00 0.00 3.41
3999 15591 5.954752 TCACAAGGACTCTAGATCATCAGTT 59.045 40.000 0.00 0.00 0.00 3.16
4000 15592 6.438741 TCACAAGGACTCTAGATCATCAGTTT 59.561 38.462 0.00 0.00 0.00 2.66
4001 15593 6.756074 CACAAGGACTCTAGATCATCAGTTTC 59.244 42.308 0.00 0.00 0.00 2.78
4002 15594 6.127196 ACAAGGACTCTAGATCATCAGTTTCC 60.127 42.308 0.00 0.54 0.00 3.13
4003 15595 5.523588 AGGACTCTAGATCATCAGTTTCCA 58.476 41.667 0.00 0.00 0.00 3.53
4004 15596 5.362430 AGGACTCTAGATCATCAGTTTCCAC 59.638 44.000 0.00 0.00 0.00 4.02
4005 15597 5.362430 GGACTCTAGATCATCAGTTTCCACT 59.638 44.000 0.00 0.00 0.00 4.00
4006 15598 6.547880 GGACTCTAGATCATCAGTTTCCACTA 59.452 42.308 0.00 0.00 0.00 2.74
4007 15599 7.255451 GGACTCTAGATCATCAGTTTCCACTAG 60.255 44.444 0.00 0.00 0.00 2.57
4008 15600 6.549364 ACTCTAGATCATCAGTTTCCACTAGG 59.451 42.308 0.00 0.00 0.00 3.02
4009 15601 4.414337 AGATCATCAGTTTCCACTAGGC 57.586 45.455 0.00 0.00 33.74 3.93
4010 15602 3.776969 AGATCATCAGTTTCCACTAGGCA 59.223 43.478 0.00 0.00 33.74 4.75
4011 15603 4.411540 AGATCATCAGTTTCCACTAGGCAT 59.588 41.667 0.00 0.00 33.74 4.40
4012 15604 4.574674 TCATCAGTTTCCACTAGGCATT 57.425 40.909 0.00 0.00 33.74 3.56
4013 15605 4.922206 TCATCAGTTTCCACTAGGCATTT 58.078 39.130 0.00 0.00 33.74 2.32
4014 15606 5.324409 TCATCAGTTTCCACTAGGCATTTT 58.676 37.500 0.00 0.00 33.74 1.82
4015 15607 5.774690 TCATCAGTTTCCACTAGGCATTTTT 59.225 36.000 0.00 0.00 33.74 1.94
4034 15626 4.933505 TTTTTGGTGTGATCATCAAGCA 57.066 36.364 0.00 1.09 44.10 3.91
4035 15627 4.508461 TTTTGGTGTGATCATCAAGCAG 57.492 40.909 0.00 0.00 44.10 4.24
4036 15628 3.421919 TTGGTGTGATCATCAAGCAGA 57.578 42.857 0.00 0.00 39.41 4.26
4037 15629 2.981898 TGGTGTGATCATCAAGCAGAG 58.018 47.619 0.00 0.00 31.11 3.35
4038 15630 2.286872 GGTGTGATCATCAAGCAGAGG 58.713 52.381 0.00 0.00 0.00 3.69
4039 15631 2.286872 GTGTGATCATCAAGCAGAGGG 58.713 52.381 0.00 0.00 0.00 4.30
4040 15632 1.307097 GTGATCATCAAGCAGAGGGC 58.693 55.000 0.00 0.00 45.30 5.19
4056 15648 3.567797 GCGATGGAGCCAAGCGAC 61.568 66.667 16.07 6.58 32.29 5.19
4057 15649 3.257561 CGATGGAGCCAAGCGACG 61.258 66.667 8.81 0.00 32.29 5.12
4058 15650 2.892425 GATGGAGCCAAGCGACGG 60.892 66.667 0.00 0.00 0.00 4.79
4059 15651 3.665675 GATGGAGCCAAGCGACGGT 62.666 63.158 0.00 0.00 0.00 4.83
4060 15652 3.254024 ATGGAGCCAAGCGACGGTT 62.254 57.895 6.44 6.44 0.00 4.44
4061 15653 2.668550 GGAGCCAAGCGACGGTTT 60.669 61.111 10.01 0.00 0.00 3.27
4062 15654 1.375013 GGAGCCAAGCGACGGTTTA 60.375 57.895 10.01 0.00 0.00 2.01
4063 15655 0.743345 GGAGCCAAGCGACGGTTTAT 60.743 55.000 10.01 0.00 0.00 1.40
4064 15656 0.373716 GAGCCAAGCGACGGTTTATG 59.626 55.000 10.01 0.00 0.00 1.90
4065 15657 1.226295 GCCAAGCGACGGTTTATGC 60.226 57.895 10.01 9.48 0.00 3.14
4066 15658 1.427819 CCAAGCGACGGTTTATGCC 59.572 57.895 10.01 0.00 0.00 4.40
4067 15659 1.302383 CCAAGCGACGGTTTATGCCA 61.302 55.000 10.01 0.00 0.00 4.92
4068 15660 0.096976 CAAGCGACGGTTTATGCCAG 59.903 55.000 10.01 0.00 0.00 4.85
4069 15661 1.644786 AAGCGACGGTTTATGCCAGC 61.645 55.000 6.44 0.00 0.00 4.85
4070 15662 2.395360 GCGACGGTTTATGCCAGCA 61.395 57.895 0.00 0.00 0.00 4.41
4071 15663 1.917782 GCGACGGTTTATGCCAGCAA 61.918 55.000 0.00 0.00 0.00 3.91
4072 15664 0.179200 CGACGGTTTATGCCAGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
4073 15665 0.179200 GACGGTTTATGCCAGCAACG 60.179 55.000 0.00 0.00 0.00 4.10
4074 15666 1.136565 CGGTTTATGCCAGCAACGG 59.863 57.895 0.00 0.00 0.00 4.44
4075 15667 1.510844 GGTTTATGCCAGCAACGGG 59.489 57.895 0.00 0.00 0.00 5.28
4076 15668 1.510844 GTTTATGCCAGCAACGGGG 59.489 57.895 0.00 0.00 0.00 5.73
4077 15669 1.075836 TTTATGCCAGCAACGGGGT 59.924 52.632 0.00 0.00 0.00 4.95
4078 15670 0.328592 TTTATGCCAGCAACGGGGTA 59.671 50.000 0.00 0.00 0.00 3.69
4079 15671 0.328592 TTATGCCAGCAACGGGGTAA 59.671 50.000 0.00 0.00 0.00 2.85
4080 15672 0.393267 TATGCCAGCAACGGGGTAAC 60.393 55.000 0.00 0.00 0.00 2.50
4081 15673 3.428282 GCCAGCAACGGGGTAACG 61.428 66.667 0.00 0.00 40.31 3.18
4088 15680 3.064324 ACGGGGTAACGTCGGAGG 61.064 66.667 0.00 0.00 45.08 4.30
4089 15681 4.503314 CGGGGTAACGTCGGAGGC 62.503 72.222 0.00 0.00 37.60 4.70
4090 15682 3.073101 GGGGTAACGTCGGAGGCT 61.073 66.667 0.00 0.00 37.60 4.58
4091 15683 2.183555 GGGTAACGTCGGAGGCTG 59.816 66.667 0.00 0.00 37.60 4.85
4092 15684 2.345760 GGGTAACGTCGGAGGCTGA 61.346 63.158 0.00 0.00 37.60 4.26
4093 15685 1.588082 GGTAACGTCGGAGGCTGAA 59.412 57.895 0.00 0.00 0.00 3.02
4094 15686 0.037975 GGTAACGTCGGAGGCTGAAA 60.038 55.000 0.00 0.00 0.00 2.69
4095 15687 1.606224 GGTAACGTCGGAGGCTGAAAA 60.606 52.381 0.00 0.00 0.00 2.29
4096 15688 2.137523 GTAACGTCGGAGGCTGAAAAA 58.862 47.619 0.00 0.00 0.00 1.94
4114 15706 3.356529 AAAAGTCCAGATGTGGCTAGG 57.643 47.619 3.40 0.00 44.60 3.02
4120 15712 5.216622 AGTCCAGATGTGGCTAGGTTTATA 58.783 41.667 3.40 0.00 44.60 0.98
4237 15853 5.739161 CGTTGGCAAAATATACTTGCTCTTC 59.261 40.000 17.42 6.15 46.74 2.87
4253 15869 3.670895 GCTCTTCTTCTTCGACGTCATCA 60.671 47.826 17.16 0.00 0.00 3.07
4288 15904 3.257561 CCTTGTCGATCGCTGCCG 61.258 66.667 11.09 0.00 0.00 5.69
4323 15939 1.105457 CCTCTCTGGTCTCTGCTCAG 58.895 60.000 0.00 0.00 0.00 3.35
4333 15949 1.202687 TCTCTGCTCAGTGGTTGTTGG 60.203 52.381 0.00 0.00 0.00 3.77
4334 15950 0.819259 TCTGCTCAGTGGTTGTTGGC 60.819 55.000 0.00 0.00 0.00 4.52
4335 15951 0.820891 CTGCTCAGTGGTTGTTGGCT 60.821 55.000 0.00 0.00 0.00 4.75
4336 15952 0.395586 TGCTCAGTGGTTGTTGGCTT 60.396 50.000 0.00 0.00 0.00 4.35
4337 15953 0.031178 GCTCAGTGGTTGTTGGCTTG 59.969 55.000 0.00 0.00 0.00 4.01
4338 15954 1.392589 CTCAGTGGTTGTTGGCTTGT 58.607 50.000 0.00 0.00 0.00 3.16
4339 15955 1.750778 CTCAGTGGTTGTTGGCTTGTT 59.249 47.619 0.00 0.00 0.00 2.83
4340 15956 1.476085 TCAGTGGTTGTTGGCTTGTTG 59.524 47.619 0.00 0.00 0.00 3.33
4341 15957 0.175531 AGTGGTTGTTGGCTTGTTGC 59.824 50.000 0.00 0.00 41.94 4.17
4350 15966 4.347453 GCTTGTTGCCCTGCCACG 62.347 66.667 0.00 0.00 35.15 4.94
4351 15967 3.673484 CTTGTTGCCCTGCCACGG 61.673 66.667 0.00 0.00 0.00 4.94
4352 15968 4.514585 TTGTTGCCCTGCCACGGT 62.515 61.111 0.00 0.00 0.00 4.83
4370 15986 4.388499 GCCGCCTCCGTCCAAGAA 62.388 66.667 0.00 0.00 0.00 2.52
4371 15987 2.434359 CCGCCTCCGTCCAAGAAC 60.434 66.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 7.563188 TCCCCATTTTGTATATAAAGCACACAT 59.437 33.333 0.00 0.00 0.00 3.21
22 23 6.892456 TCCCCATTTTGTATATAAAGCACACA 59.108 34.615 0.00 0.00 0.00 3.72
37 38 3.986996 ATCAGGCTTTTCCCCATTTTG 57.013 42.857 0.00 0.00 34.51 2.44
131 132 7.836842 TGACACACTCACATAGTTATACATGT 58.163 34.615 2.69 2.69 35.76 3.21
150 151 2.160615 CCAACTTCGTTGTTGTGACACA 59.839 45.455 3.56 3.56 44.01 3.72
203 204 7.003482 AGGGAAAACATTTGCACCATAAAAAT 58.997 30.769 0.00 0.00 0.00 1.82
349 644 3.665409 CAGAAAACAAACATGCTGTAGCG 59.335 43.478 1.70 0.00 45.83 4.26
350 645 3.426525 GCAGAAAACAAACATGCTGTAGC 59.573 43.478 1.70 0.00 42.50 3.58
353 648 3.130869 TCTGCAGAAAACAAACATGCTGT 59.869 39.130 15.67 0.00 37.76 4.40
433 728 5.634439 TGCATTTGTTCACTCATTTGTATGC 59.366 36.000 0.00 0.00 36.21 3.14
633 963 3.053842 AGTGATCACGTAGGGAGGAACTA 60.054 47.826 19.85 0.00 35.58 2.24
634 964 2.291670 AGTGATCACGTAGGGAGGAACT 60.292 50.000 19.85 0.00 37.78 3.01
688 1023 1.552337 AGTATGGGAGACACACAGCAG 59.448 52.381 0.00 0.00 34.42 4.24
692 1027 3.511540 CAGAGAAGTATGGGAGACACACA 59.488 47.826 0.00 0.00 35.88 3.72
694 1029 3.099905 CCAGAGAAGTATGGGAGACACA 58.900 50.000 0.00 0.00 30.62 3.72
871 1207 1.301087 CCGGTTGGCTTCACACGTA 60.301 57.895 0.00 0.00 0.00 3.57
894 1230 5.638234 GGTCTGAGTGGAGTTAAATACACAC 59.362 44.000 19.74 14.09 37.24 3.82
895 1231 5.279809 GGGTCTGAGTGGAGTTAAATACACA 60.280 44.000 19.74 0.00 36.35 3.72
896 1232 5.176592 GGGTCTGAGTGGAGTTAAATACAC 58.823 45.833 10.31 10.31 0.00 2.90
971 1307 1.032657 TACGAGTGCAGAGGAGGAGC 61.033 60.000 0.00 0.00 0.00 4.70
987 1323 3.955291 CAGCATCTGGAGACCTACG 57.045 57.895 0.00 0.00 0.00 3.51
1221 11797 3.432051 GATGTCGTGGGAGCCGAGG 62.432 68.421 0.00 0.00 34.56 4.63
1345 12072 3.934068 TGTCTTCTTTACCGAACATCCC 58.066 45.455 0.00 0.00 0.00 3.85
1347 12074 4.143179 CCGTTGTCTTCTTTACCGAACATC 60.143 45.833 0.00 0.00 0.00 3.06
1408 12392 2.229784 ACAATTTGTTAGCTGCTCCTGC 59.770 45.455 4.91 0.00 40.20 4.85
1428 12412 5.490139 AGTGCATGCATGTTAGATGTTAC 57.510 39.130 25.64 5.79 0.00 2.50
1429 12413 6.150809 TCAAAGTGCATGCATGTTAGATGTTA 59.849 34.615 25.64 4.16 0.00 2.41
1430 12414 5.047872 TCAAAGTGCATGCATGTTAGATGTT 60.048 36.000 25.64 10.15 0.00 2.71
1431 12415 4.460034 TCAAAGTGCATGCATGTTAGATGT 59.540 37.500 25.64 2.53 0.00 3.06
1432 12416 4.989044 TCAAAGTGCATGCATGTTAGATG 58.011 39.130 25.64 19.38 0.00 2.90
1433 12417 5.358725 TGATCAAAGTGCATGCATGTTAGAT 59.641 36.000 25.64 21.40 0.00 1.98
1434 12418 4.701171 TGATCAAAGTGCATGCATGTTAGA 59.299 37.500 25.64 17.84 0.00 2.10
1435 12419 4.796830 GTGATCAAAGTGCATGCATGTTAG 59.203 41.667 25.64 13.13 0.00 2.34
1456 12448 3.185594 ACATTTTGTGACATCGTACGGTG 59.814 43.478 26.33 26.33 0.00 4.94
1477 12469 6.371809 TTCCCTGCATATTTGTAAATCGAC 57.628 37.500 0.00 0.00 0.00 4.20
1525 12551 3.819877 AACCAACACCCTCGGCGTC 62.820 63.158 6.85 0.00 0.00 5.19
1541 12567 2.758979 TCACTAGATCCGGGTCAGAAAC 59.241 50.000 19.03 0.00 0.00 2.78
1788 12966 7.877097 AGCATCCTCTACAGATGAAACATTATC 59.123 37.037 4.98 0.00 43.15 1.75
1789 12967 7.660617 CAGCATCCTCTACAGATGAAACATTAT 59.339 37.037 4.98 0.00 43.15 1.28
1801 12987 0.829333 ACTGGCAGCATCCTCTACAG 59.171 55.000 15.89 0.00 0.00 2.74
1804 12990 2.573462 AGAAAACTGGCAGCATCCTCTA 59.427 45.455 15.89 0.00 0.00 2.43
1824 13010 3.372206 CCATTTCTTCGCAACAGGTAGAG 59.628 47.826 0.00 0.00 0.00 2.43
1918 13104 1.535226 CGCGATGACATCTCCGGTAAA 60.535 52.381 13.45 0.00 0.00 2.01
2105 13304 6.848470 CTTGCGTTATAAAGGTTTACAAGC 57.152 37.500 0.52 0.00 0.00 4.01
2141 13340 5.824624 CCATGTGTTCTACTCCATTTGCTAT 59.175 40.000 0.00 0.00 0.00 2.97
2166 13372 6.813152 CAGCTATTTTTATCAAACACCAAGGG 59.187 38.462 0.00 0.00 0.00 3.95
2168 13374 6.311200 GCCAGCTATTTTTATCAAACACCAAG 59.689 38.462 0.00 0.00 0.00 3.61
2169 13375 6.014669 AGCCAGCTATTTTTATCAAACACCAA 60.015 34.615 0.00 0.00 0.00 3.67
2322 13674 5.594725 TGTTGGTAAGAACCTGCAAATGTTA 59.405 36.000 0.00 0.00 46.91 2.41
2640 13992 1.141657 TGCAACACTTCCTCTCTTGCT 59.858 47.619 0.00 0.00 38.43 3.91
2731 14083 4.622701 ACTCTTTTGTTCACTCACAAGC 57.377 40.909 0.00 0.00 37.93 4.01
2769 14171 9.790344 AATGGAATGAAAATCTGATAGGAGTAG 57.210 33.333 0.00 0.00 0.00 2.57
2786 14188 9.368674 CATGCAGTACAATTTTTAATGGAATGA 57.631 29.630 0.00 0.00 26.89 2.57
2925 14350 7.067615 TGTTACCTGCAAAACAATACAGAAGAA 59.932 33.333 6.49 0.00 32.86 2.52
3215 14640 0.033781 GCAATGCAAAGTTCTGGCCA 59.966 50.000 4.71 4.71 0.00 5.36
3230 14655 2.305009 GCCATCTTAGCTTCCAGCAAT 58.695 47.619 0.00 0.00 45.56 3.56
3314 14739 1.327690 GCTGGAGGGTCATCACGGTA 61.328 60.000 0.00 0.00 0.00 4.02
3388 14814 4.739716 GCAACACACAAGTAAATCAACTGG 59.260 41.667 0.00 0.00 0.00 4.00
3393 14819 5.933187 ATACGCAACACACAAGTAAATCA 57.067 34.783 0.00 0.00 0.00 2.57
3394 14820 7.057149 ACTATACGCAACACACAAGTAAATC 57.943 36.000 0.00 0.00 0.00 2.17
3403 14829 8.551122 AAAACTTTAAACTATACGCAACACAC 57.449 30.769 0.00 0.00 0.00 3.82
3404 14830 9.866936 CTAAAACTTTAAACTATACGCAACACA 57.133 29.630 0.00 0.00 0.00 3.72
3439 14873 3.007635 GCCTGGTTGCTACGTTTATTCT 58.992 45.455 0.00 0.00 0.00 2.40
3448 14882 2.711542 ACATGTAAGCCTGGTTGCTAC 58.288 47.619 0.00 0.00 41.80 3.58
3490 14931 9.695526 CTGAAAACTACATTTCCATTCATTCAA 57.304 29.630 0.00 0.00 38.30 2.69
3554 15103 5.707298 CCATTGGATGACAGTTACAGACTTT 59.293 40.000 0.00 0.00 36.10 2.66
3648 15213 4.015406 TGCACGGCTACCCCAGTG 62.015 66.667 0.00 0.00 39.51 3.66
3831 15423 3.071479 GTTCAACCGTTGAGGCAAGATA 58.929 45.455 13.51 0.00 46.52 1.98
3888 15480 8.854979 TTTTACACTGATGACAATTCAACTTG 57.145 30.769 0.00 0.00 34.61 3.16
3900 15492 3.576982 AGTCGGTCCTTTTACACTGATGA 59.423 43.478 0.00 0.00 30.58 2.92
3901 15493 3.679980 CAGTCGGTCCTTTTACACTGATG 59.320 47.826 0.00 0.00 34.40 3.07
3902 15494 3.864921 GCAGTCGGTCCTTTTACACTGAT 60.865 47.826 1.09 0.00 34.40 2.90
3919 15511 0.247736 AATCTCACCGACCTGCAGTC 59.752 55.000 13.81 9.39 42.54 3.51
3936 15528 1.084289 GCGGTGCTAGTTCGGAAAAT 58.916 50.000 0.00 0.00 0.00 1.82
3937 15529 0.034337 AGCGGTGCTAGTTCGGAAAA 59.966 50.000 0.00 0.00 36.99 2.29
3938 15530 0.034337 AAGCGGTGCTAGTTCGGAAA 59.966 50.000 0.00 0.00 38.25 3.13
3939 15531 0.389426 GAAGCGGTGCTAGTTCGGAA 60.389 55.000 0.00 0.00 38.25 4.30
3940 15532 1.214589 GAAGCGGTGCTAGTTCGGA 59.785 57.895 0.00 0.00 38.25 4.55
3941 15533 2.158959 CGAAGCGGTGCTAGTTCGG 61.159 63.158 4.02 0.00 38.25 4.30
3942 15534 1.007336 AACGAAGCGGTGCTAGTTCG 61.007 55.000 9.16 9.16 40.70 3.95
3943 15535 1.145803 AAACGAAGCGGTGCTAGTTC 58.854 50.000 11.24 0.00 38.25 3.01
3944 15536 1.263217 CAAAACGAAGCGGTGCTAGTT 59.737 47.619 6.72 6.72 38.25 2.24
3945 15537 0.865769 CAAAACGAAGCGGTGCTAGT 59.134 50.000 0.00 0.00 38.25 2.57
3946 15538 0.452784 GCAAAACGAAGCGGTGCTAG 60.453 55.000 0.00 0.00 38.25 3.42
3947 15539 1.160946 TGCAAAACGAAGCGGTGCTA 61.161 50.000 11.58 0.26 38.25 3.49
3948 15540 2.331451 GCAAAACGAAGCGGTGCT 59.669 55.556 0.00 0.00 42.56 4.40
3949 15541 2.025441 TGCAAAACGAAGCGGTGC 59.975 55.556 0.00 0.00 35.16 5.01
3950 15542 3.902234 GTGCAAAACGAAGCGGTG 58.098 55.556 0.00 0.00 0.00 4.94
3959 15551 5.062809 TCCTTGTGAAAATTTCGTGCAAAAC 59.937 36.000 0.97 0.00 0.00 2.43
3960 15552 5.062809 GTCCTTGTGAAAATTTCGTGCAAAA 59.937 36.000 0.97 0.00 0.00 2.44
3961 15553 4.564769 GTCCTTGTGAAAATTTCGTGCAAA 59.435 37.500 0.97 0.00 0.00 3.68
3962 15554 4.109050 GTCCTTGTGAAAATTTCGTGCAA 58.891 39.130 0.97 5.81 0.00 4.08
3963 15555 3.380004 AGTCCTTGTGAAAATTTCGTGCA 59.620 39.130 0.97 0.00 0.00 4.57
3964 15556 3.964909 AGTCCTTGTGAAAATTTCGTGC 58.035 40.909 0.97 0.00 0.00 5.34
3965 15557 5.424121 AGAGTCCTTGTGAAAATTTCGTG 57.576 39.130 0.97 0.00 0.00 4.35
3966 15558 6.522054 TCTAGAGTCCTTGTGAAAATTTCGT 58.478 36.000 0.97 0.00 0.00 3.85
3967 15559 7.331934 TGATCTAGAGTCCTTGTGAAAATTTCG 59.668 37.037 0.00 0.00 0.00 3.46
3968 15560 8.553459 TGATCTAGAGTCCTTGTGAAAATTTC 57.447 34.615 0.00 0.00 0.00 2.17
3969 15561 9.171877 GATGATCTAGAGTCCTTGTGAAAATTT 57.828 33.333 0.00 0.00 0.00 1.82
3970 15562 8.324306 TGATGATCTAGAGTCCTTGTGAAAATT 58.676 33.333 0.00 0.00 0.00 1.82
3971 15563 7.855375 TGATGATCTAGAGTCCTTGTGAAAAT 58.145 34.615 0.00 0.00 0.00 1.82
3972 15564 7.038729 ACTGATGATCTAGAGTCCTTGTGAAAA 60.039 37.037 0.00 0.00 0.00 2.29
3973 15565 6.438741 ACTGATGATCTAGAGTCCTTGTGAAA 59.561 38.462 0.00 0.00 0.00 2.69
3974 15566 5.954752 ACTGATGATCTAGAGTCCTTGTGAA 59.045 40.000 0.00 0.00 0.00 3.18
3975 15567 5.514169 ACTGATGATCTAGAGTCCTTGTGA 58.486 41.667 0.00 0.00 0.00 3.58
3976 15568 5.850557 ACTGATGATCTAGAGTCCTTGTG 57.149 43.478 0.00 0.00 0.00 3.33
3977 15569 6.127196 GGAAACTGATGATCTAGAGTCCTTGT 60.127 42.308 0.00 0.00 0.00 3.16
3978 15570 6.127225 TGGAAACTGATGATCTAGAGTCCTTG 60.127 42.308 0.00 0.00 0.00 3.61
3979 15571 5.960811 TGGAAACTGATGATCTAGAGTCCTT 59.039 40.000 0.00 0.00 0.00 3.36
3980 15572 5.362430 GTGGAAACTGATGATCTAGAGTCCT 59.638 44.000 0.00 0.00 0.00 3.85
3981 15573 5.362430 AGTGGAAACTGATGATCTAGAGTCC 59.638 44.000 0.00 3.69 0.00 3.85
3982 15574 6.463995 AGTGGAAACTGATGATCTAGAGTC 57.536 41.667 0.00 0.00 0.00 3.36
3983 15575 6.549364 CCTAGTGGAAACTGATGATCTAGAGT 59.451 42.308 0.00 0.00 34.57 3.24
3984 15576 6.516527 GCCTAGTGGAAACTGATGATCTAGAG 60.517 46.154 0.00 0.00 34.57 2.43
3985 15577 5.303078 GCCTAGTGGAAACTGATGATCTAGA 59.697 44.000 0.00 0.00 34.57 2.43
3986 15578 5.069648 TGCCTAGTGGAAACTGATGATCTAG 59.930 44.000 0.00 0.00 34.57 2.43
3987 15579 4.962362 TGCCTAGTGGAAACTGATGATCTA 59.038 41.667 0.00 0.00 34.57 1.98
3988 15580 3.776969 TGCCTAGTGGAAACTGATGATCT 59.223 43.478 0.00 0.00 34.57 2.75
3989 15581 4.142609 TGCCTAGTGGAAACTGATGATC 57.857 45.455 0.00 0.00 34.57 2.92
3990 15582 4.785346 ATGCCTAGTGGAAACTGATGAT 57.215 40.909 0.00 0.00 34.57 2.45
3991 15583 4.574674 AATGCCTAGTGGAAACTGATGA 57.425 40.909 0.00 0.00 34.57 2.92
3992 15584 5.649782 AAAATGCCTAGTGGAAACTGATG 57.350 39.130 0.00 0.00 34.57 3.07
4013 15605 4.583907 TCTGCTTGATGATCACACCAAAAA 59.416 37.500 0.00 0.00 0.00 1.94
4014 15606 4.143543 TCTGCTTGATGATCACACCAAAA 58.856 39.130 0.00 0.00 0.00 2.44
4015 15607 3.753815 TCTGCTTGATGATCACACCAAA 58.246 40.909 0.00 0.00 0.00 3.28
4016 15608 3.340928 CTCTGCTTGATGATCACACCAA 58.659 45.455 0.00 2.21 0.00 3.67
4017 15609 2.355412 CCTCTGCTTGATGATCACACCA 60.355 50.000 0.00 0.00 0.00 4.17
4018 15610 2.286872 CCTCTGCTTGATGATCACACC 58.713 52.381 0.00 0.00 0.00 4.16
4019 15611 2.286872 CCCTCTGCTTGATGATCACAC 58.713 52.381 0.00 0.00 0.00 3.82
4020 15612 1.407851 GCCCTCTGCTTGATGATCACA 60.408 52.381 0.00 0.00 36.87 3.58
4021 15613 1.307097 GCCCTCTGCTTGATGATCAC 58.693 55.000 0.00 0.00 36.87 3.06
4022 15614 0.179065 CGCCCTCTGCTTGATGATCA 60.179 55.000 0.00 0.00 38.05 2.92
4023 15615 0.105593 TCGCCCTCTGCTTGATGATC 59.894 55.000 0.00 0.00 38.05 2.92
4024 15616 0.763652 ATCGCCCTCTGCTTGATGAT 59.236 50.000 0.00 0.00 38.05 2.45
4025 15617 0.179065 CATCGCCCTCTGCTTGATGA 60.179 55.000 0.00 0.00 39.05 2.92
4026 15618 1.164662 CCATCGCCCTCTGCTTGATG 61.165 60.000 0.00 0.00 37.49 3.07
4027 15619 1.147824 CCATCGCCCTCTGCTTGAT 59.852 57.895 0.00 0.00 38.05 2.57
4028 15620 1.964608 CTCCATCGCCCTCTGCTTGA 61.965 60.000 0.00 0.00 38.05 3.02
4029 15621 1.523258 CTCCATCGCCCTCTGCTTG 60.523 63.158 0.00 0.00 38.05 4.01
4030 15622 2.906458 CTCCATCGCCCTCTGCTT 59.094 61.111 0.00 0.00 38.05 3.91
4031 15623 3.859414 GCTCCATCGCCCTCTGCT 61.859 66.667 0.00 0.00 38.05 4.24
4032 15624 4.925861 GGCTCCATCGCCCTCTGC 62.926 72.222 0.00 0.00 44.41 4.26
4039 15631 3.567797 GTCGCTTGGCTCCATCGC 61.568 66.667 6.31 4.17 0.00 4.58
4040 15632 3.257561 CGTCGCTTGGCTCCATCG 61.258 66.667 5.19 5.19 0.00 3.84
4041 15633 2.892425 CCGTCGCTTGGCTCCATC 60.892 66.667 0.00 0.00 0.00 3.51
4042 15634 2.748058 AAACCGTCGCTTGGCTCCAT 62.748 55.000 0.00 0.00 0.00 3.41
4043 15635 2.102109 TAAACCGTCGCTTGGCTCCA 62.102 55.000 0.00 0.00 0.00 3.86
4044 15636 0.743345 ATAAACCGTCGCTTGGCTCC 60.743 55.000 0.00 0.00 0.00 4.70
4045 15637 0.373716 CATAAACCGTCGCTTGGCTC 59.626 55.000 0.00 0.00 0.00 4.70
4046 15638 1.644786 GCATAAACCGTCGCTTGGCT 61.645 55.000 0.00 0.00 0.00 4.75
4047 15639 1.226295 GCATAAACCGTCGCTTGGC 60.226 57.895 0.00 0.00 0.00 4.52
4048 15640 1.302383 TGGCATAAACCGTCGCTTGG 61.302 55.000 0.00 0.00 0.00 3.61
4049 15641 0.096976 CTGGCATAAACCGTCGCTTG 59.903 55.000 0.00 0.00 0.00 4.01
4050 15642 1.644786 GCTGGCATAAACCGTCGCTT 61.645 55.000 0.00 0.00 0.00 4.68
4051 15643 2.106683 GCTGGCATAAACCGTCGCT 61.107 57.895 0.00 0.00 0.00 4.93
4052 15644 1.917782 TTGCTGGCATAAACCGTCGC 61.918 55.000 0.00 0.00 0.00 5.19
4053 15645 0.179200 GTTGCTGGCATAAACCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
4054 15646 0.179200 CGTTGCTGGCATAAACCGTC 60.179 55.000 0.00 0.00 0.00 4.79
4055 15647 1.582610 CCGTTGCTGGCATAAACCGT 61.583 55.000 0.00 0.00 0.00 4.83
4056 15648 1.136565 CCGTTGCTGGCATAAACCG 59.863 57.895 0.00 3.41 0.00 4.44
4057 15649 1.510844 CCCGTTGCTGGCATAAACC 59.489 57.895 0.00 0.00 0.00 3.27
4058 15650 1.248101 ACCCCGTTGCTGGCATAAAC 61.248 55.000 0.00 0.00 0.00 2.01
4059 15651 0.328592 TACCCCGTTGCTGGCATAAA 59.671 50.000 0.00 0.00 0.00 1.40
4060 15652 0.328592 TTACCCCGTTGCTGGCATAA 59.671 50.000 0.00 0.00 0.00 1.90
4061 15653 0.393267 GTTACCCCGTTGCTGGCATA 60.393 55.000 0.00 0.00 0.00 3.14
4062 15654 1.677633 GTTACCCCGTTGCTGGCAT 60.678 57.895 0.00 0.00 0.00 4.40
4063 15655 2.281900 GTTACCCCGTTGCTGGCA 60.282 61.111 0.00 0.00 0.00 4.92
4064 15656 3.428282 CGTTACCCCGTTGCTGGC 61.428 66.667 0.00 0.00 0.00 4.85
4065 15657 2.030958 GACGTTACCCCGTTGCTGG 61.031 63.158 0.00 0.00 41.98 4.85
4066 15658 2.377310 CGACGTTACCCCGTTGCTG 61.377 63.158 0.00 0.00 41.98 4.41
4067 15659 2.048877 CGACGTTACCCCGTTGCT 60.049 61.111 0.00 0.00 41.98 3.91
4068 15660 3.113979 CCGACGTTACCCCGTTGC 61.114 66.667 0.00 0.00 41.98 4.17
4069 15661 1.444895 CTCCGACGTTACCCCGTTG 60.445 63.158 0.00 0.00 41.98 4.10
4070 15662 2.639327 CCTCCGACGTTACCCCGTT 61.639 63.158 0.00 0.00 41.98 4.44
4071 15663 3.064324 CCTCCGACGTTACCCCGT 61.064 66.667 0.00 0.00 45.18 5.28
4072 15664 4.503314 GCCTCCGACGTTACCCCG 62.503 72.222 0.00 0.00 0.00 5.73
4073 15665 3.073101 AGCCTCCGACGTTACCCC 61.073 66.667 0.00 0.00 0.00 4.95
4074 15666 1.880819 TTCAGCCTCCGACGTTACCC 61.881 60.000 0.00 0.00 0.00 3.69
4075 15667 0.037975 TTTCAGCCTCCGACGTTACC 60.038 55.000 0.00 0.00 0.00 2.85
4076 15668 1.787012 TTTTCAGCCTCCGACGTTAC 58.213 50.000 0.00 0.00 0.00 2.50
4077 15669 2.529780 TTTTTCAGCCTCCGACGTTA 57.470 45.000 0.00 0.00 0.00 3.18
4078 15670 3.390003 TTTTTCAGCCTCCGACGTT 57.610 47.368 0.00 0.00 0.00 3.99
4093 15685 3.074538 ACCTAGCCACATCTGGACTTTTT 59.925 43.478 0.00 0.00 40.55 1.94
4094 15686 2.644798 ACCTAGCCACATCTGGACTTTT 59.355 45.455 0.00 0.00 40.55 2.27
4095 15687 2.269940 ACCTAGCCACATCTGGACTTT 58.730 47.619 0.00 0.00 40.55 2.66
4096 15688 1.958288 ACCTAGCCACATCTGGACTT 58.042 50.000 0.00 0.00 40.55 3.01
4097 15689 1.958288 AACCTAGCCACATCTGGACT 58.042 50.000 0.00 0.00 40.55 3.85
4098 15690 2.789409 AAACCTAGCCACATCTGGAC 57.211 50.000 0.00 0.00 40.55 4.02
4099 15691 6.409234 CCTTTATAAACCTAGCCACATCTGGA 60.409 42.308 0.00 0.00 40.55 3.86
4100 15692 5.765182 CCTTTATAAACCTAGCCACATCTGG 59.235 44.000 0.00 0.00 41.13 3.86
4101 15693 6.591935 TCCTTTATAAACCTAGCCACATCTG 58.408 40.000 0.00 0.00 0.00 2.90
4102 15694 6.615726 TCTCCTTTATAAACCTAGCCACATCT 59.384 38.462 0.00 0.00 0.00 2.90
4103 15695 6.827727 TCTCCTTTATAAACCTAGCCACATC 58.172 40.000 0.00 0.00 0.00 3.06
4104 15696 6.824958 TCTCCTTTATAAACCTAGCCACAT 57.175 37.500 0.00 0.00 0.00 3.21
4105 15697 6.630203 TTCTCCTTTATAAACCTAGCCACA 57.370 37.500 0.00 0.00 0.00 4.17
4106 15698 7.148120 GGTTTTCTCCTTTATAAACCTAGCCAC 60.148 40.741 0.00 0.00 43.81 5.01
4107 15699 6.888088 GGTTTTCTCCTTTATAAACCTAGCCA 59.112 38.462 0.00 0.00 43.81 4.75
4108 15700 6.320672 GGGTTTTCTCCTTTATAAACCTAGCC 59.679 42.308 13.42 0.00 45.53 3.93
4109 15701 7.117397 AGGGTTTTCTCCTTTATAAACCTAGC 58.883 38.462 13.42 0.63 45.53 3.42
4237 15853 1.982612 TGCTGATGACGTCGAAGAAG 58.017 50.000 11.62 5.23 39.69 2.85
4253 15869 1.133792 AGGCCGCTGGTTAAATATGCT 60.134 47.619 0.00 0.00 0.00 3.79
4323 15939 2.676744 GCAACAAGCCAACAACCAC 58.323 52.632 0.00 0.00 37.23 4.16
4333 15949 4.347453 CGTGGCAGGGCAACAAGC 62.347 66.667 0.00 0.00 44.65 4.01
4334 15950 3.673484 CCGTGGCAGGGCAACAAG 61.673 66.667 14.01 0.00 30.74 3.16
4335 15951 4.514585 ACCGTGGCAGGGCAACAA 62.515 61.111 25.25 0.00 30.74 2.83
4353 15969 4.388499 TTCTTGGACGGAGGCGGC 62.388 66.667 0.00 0.00 0.00 6.53
4354 15970 2.434359 GTTCTTGGACGGAGGCGG 60.434 66.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.