Multiple sequence alignment - TraesCS4D01G234000

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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 TraesCS4D01G234000 chr4D 100.000 3770 0 0 1 3770 394360547 394364316 0.000000e+00 6962.0
1 TraesCS4D01G234000 chr4D 83.333 198 29 4 1343 1538 394379102 394378907 2.990000e-41 180.0
2 TraesCS4D01G234000 chr4A 92.220 2275 94 35 736 2977 75465418 75467642 0.000000e+00 3144.0
3 TraesCS4D01G234000 chr4A 93.172 454 25 5 3319 3769 75826113 75826563 0.000000e+00 662.0
4 TraesCS4D01G234000 chr4A 88.473 347 32 3 1 346 75464452 75464791 2.710000e-111 412.0
5 TraesCS4D01G234000 chr4A 82.828 198 30 4 1343 1538 75843038 75842843 1.390000e-39 174.0
6 TraesCS4D01G234000 chr4A 84.507 71 2 3 647 708 75465351 75465421 1.130000e-05 62.1
7 TraesCS4D01G234000 chr4A 90.698 43 4 0 378 420 75465128 75465170 1.460000e-04 58.4
8 TraesCS4D01G234000 chr4B 93.196 1411 62 14 1589 2977 483951502 483952900 0.000000e+00 2043.0
9 TraesCS4D01G234000 chr4B 91.996 912 44 8 647 1550 483950610 483951500 0.000000e+00 1253.0
10 TraesCS4D01G234000 chr4B 91.994 687 46 6 3088 3770 484081478 484082159 0.000000e+00 955.0
11 TraesCS4D01G234000 chr4B 90.028 361 32 4 1 358 483949691 483950050 7.380000e-127 464.0
12 TraesCS4D01G234000 chr4B 81.818 209 34 4 1332 1538 484105651 484105445 5.010000e-39 172.0
13 TraesCS4D01G234000 chr7B 77.778 360 63 10 2354 2703 578439703 578440055 4.940000e-49 206.0
14 TraesCS4D01G234000 chr7B 81.944 216 36 3 1343 1557 578438826 578439039 2.990000e-41 180.0
15 TraesCS4D01G234000 chr7B 98.810 84 1 0 438 521 337929757 337929674 2.350000e-32 150.0
16 TraesCS4D01G234000 chr7D 81.860 215 36 3 1343 1556 535967329 535967541 1.080000e-40 178.0
17 TraesCS4D01G234000 chr7D 100.000 31 0 0 2988 3018 90636473 90636443 1.460000e-04 58.4
18 TraesCS4D01G234000 chr7A 82.266 203 32 4 1343 1543 617385972 617385772 5.010000e-39 172.0
19 TraesCS4D01G234000 chr7A 90.476 42 3 1 2976 3017 595072546 595072506 2.000000e-03 54.7
20 TraesCS4D01G234000 chr1D 79.208 202 40 2 1343 1543 467611811 467611611 5.080000e-29 139.0
21 TraesCS4D01G234000 chr6B 95.000 60 1 2 459 518 502300350 502300407 4.010000e-15 93.5
22 TraesCS4D01G234000 chr6B 92.500 40 1 2 2979 3017 679623392 679623430 5.260000e-04 56.5
23 TraesCS4D01G234000 chr6B 90.698 43 1 3 2975 3017 149018470 149018509 2.000000e-03 54.7
24 TraesCS4D01G234000 chr2A 96.154 52 2 0 467 518 21422234 21422285 6.710000e-13 86.1
25 TraesCS4D01G234000 chr6A 94.444 54 2 1 469 522 36987839 36987891 8.680000e-12 82.4
26 TraesCS4D01G234000 chr3A 94.231 52 2 1 467 517 710103909 710103960 1.120000e-10 78.7
27 TraesCS4D01G234000 chr3A 94.595 37 0 2 2981 3017 12239987 12239953 5.260000e-04 56.5
28 TraesCS4D01G234000 chr1B 86.111 72 8 2 3092 3162 4784527 4784597 4.040000e-10 76.8
29 TraesCS4D01G234000 chr1B 84.722 72 9 2 3092 3162 4091565 4091495 1.880000e-08 71.3
30 TraesCS4D01G234000 chr2D 100.000 36 0 0 2983 3018 176105378 176105413 2.430000e-07 67.6
31 TraesCS4D01G234000 chr2B 100.000 36 0 0 2983 3018 233169822 233169857 2.430000e-07 67.6
32 TraesCS4D01G234000 chrUn 86.441 59 8 0 1175 1233 195649503 195649445 8.740000e-07 65.8
33 TraesCS4D01G234000 chrUn 86.441 59 8 0 1175 1233 195664734 195664676 8.740000e-07 65.8
34 TraesCS4D01G234000 chrUn 86.441 59 8 0 1175 1233 226785666 226785608 8.740000e-07 65.8
35 TraesCS4D01G234000 chrUn 86.441 59 8 0 1175 1233 269606498 269606556 8.740000e-07 65.8
36 TraesCS4D01G234000 chrUn 86.441 59 8 0 1175 1233 287107940 287107998 8.740000e-07 65.8
37 TraesCS4D01G234000 chrUn 86.441 59 8 0 1175 1233 347578031 347578089 8.740000e-07 65.8
38 TraesCS4D01G234000 chr3B 86.441 59 8 0 1175 1233 807440697 807440639 8.740000e-07 65.8
39 TraesCS4D01G234000 chr1A 97.222 36 0 1 2983 3018 249057553 249057519 4.070000e-05 60.2
40 TraesCS4D01G234000 chr5B 100.000 31 0 0 2988 3018 611335964 611335934 1.460000e-04 58.4


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 TraesCS4D01G234000 chr4D 394360547 394364316 3769 False 6962.000000 6962 100.0000 1 3770 1 chr4D.!!$F1 3769
1 TraesCS4D01G234000 chr4A 75464452 75467642 3190 False 919.125000 3144 88.9745 1 2977 4 chr4A.!!$F2 2976
2 TraesCS4D01G234000 chr4B 483949691 483952900 3209 False 1253.333333 2043 91.7400 1 2977 3 chr4B.!!$F2 2976
3 TraesCS4D01G234000 chr4B 484081478 484082159 681 False 955.000000 955 91.9940 3088 3770 1 chr4B.!!$F1 682

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
433 987 0.036010 CGGCCAGATGAAGAACAGGT 60.036 55.0 2.24 0.0 0.00 4.00 F
492 1046 0.036306 AAGGTTCAGGCCGGTGTAAG 59.964 55.0 1.90 0.0 0.00 2.34 F
676 1280 0.176219 CGTGGATAGTAAACCGGGCA 59.824 55.0 6.32 0.0 0.00 5.36 F
1742 2377 0.250234 TCATATATGCCAGAGCCCGC 59.750 55.0 7.92 0.0 38.69 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2306 2957 0.179045 GATCCTGGATCAACCACGGG 60.179 60.000 27.72 0.0 44.64 5.28 R
2320 2971 1.271379 CCACGACCCAAACAAGATCCT 60.271 52.381 0.00 0.0 0.00 3.24 R
2499 3150 1.162181 TCGTGTCGAGGTCGTTGAGT 61.162 55.000 0.00 0.0 40.80 3.41 R
2987 3644 0.038744 TTCGGACGGAGGGAGTAGTT 59.961 55.000 0.00 0.0 0.00 2.24 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
44 45 3.689224 GCTGTACTAGCGACGACAA 57.311 52.632 0.00 0.00 43.63 3.18
45 46 1.257539 GCTGTACTAGCGACGACAAC 58.742 55.000 0.00 0.00 43.63 3.32
123 124 5.881923 TTCACCTACCACCAACTATATCC 57.118 43.478 0.00 0.00 0.00 2.59
141 142 3.828023 AGGGCCCGGTTTGTTGGT 61.828 61.111 18.44 0.00 0.00 3.67
183 185 2.791868 GGCCGGCAAGTTTGTTGGT 61.792 57.895 30.85 0.00 0.00 3.67
185 187 1.008995 CCGGCAAGTTTGTTGGTCG 60.009 57.895 0.00 0.00 0.00 4.79
187 189 1.720694 CGGCAAGTTTGTTGGTCGGT 61.721 55.000 0.00 0.00 0.00 4.69
224 226 7.537306 CGTAAGTCACCTGAATTTACAATTTGG 59.463 37.037 0.78 0.00 34.03 3.28
226 228 4.929211 GTCACCTGAATTTACAATTTGGGC 59.071 41.667 0.78 0.00 0.00 5.36
232 235 4.590647 TGAATTTACAATTTGGGCCAGTCA 59.409 37.500 6.23 0.00 0.00 3.41
243 246 0.804989 GGCCAGTCAATTCGGTTGAG 59.195 55.000 0.00 0.00 46.99 3.02
253 256 2.859165 TTCGGTTGAGAAGGAAGCAT 57.141 45.000 0.00 0.00 0.00 3.79
276 279 2.886124 GTAGAGCACCGAAGCCGC 60.886 66.667 0.00 0.00 34.23 6.53
305 308 1.271102 GGCAGGATGGATCTCGTCTAC 59.729 57.143 0.00 0.00 35.86 2.59
325 329 3.154827 CCTTAGGTGCAAGGGAAGAAA 57.845 47.619 0.00 0.00 41.30 2.52
340 344 4.506802 GGGAAGAAAAAGGCTCCTTGTCTA 60.507 45.833 12.76 0.00 36.26 2.59
346 350 7.334858 AGAAAAAGGCTCCTTGTCTATCTTAG 58.665 38.462 11.39 0.00 36.26 2.18
347 351 5.622346 AAAGGCTCCTTGTCTATCTTAGG 57.378 43.478 1.33 0.00 36.26 2.69
348 352 3.582164 AGGCTCCTTGTCTATCTTAGGG 58.418 50.000 0.00 0.00 0.00 3.53
349 353 3.051727 AGGCTCCTTGTCTATCTTAGGGT 60.052 47.826 0.00 0.00 0.00 4.34
352 608 4.547671 CTCCTTGTCTATCTTAGGGTCCA 58.452 47.826 0.00 0.00 0.00 4.02
354 610 3.643792 CCTTGTCTATCTTAGGGTCCAGG 59.356 52.174 0.00 0.00 0.00 4.45
357 613 1.508185 TCTATCTTAGGGTCCAGGGGG 59.492 57.143 0.00 0.00 0.00 5.40
358 614 1.508185 CTATCTTAGGGTCCAGGGGGA 59.492 57.143 0.00 0.00 42.29 4.81
369 625 3.342477 AGGGGGAAGAAGCCTGGC 61.342 66.667 11.65 11.65 0.00 4.85
371 627 3.717294 GGGGAAGAAGCCTGGCGA 61.717 66.667 13.96 0.00 0.00 5.54
372 628 2.124942 GGGAAGAAGCCTGGCGAG 60.125 66.667 13.96 0.00 0.00 5.03
425 979 3.797353 GGAGGGCGGCCAGATGAA 61.797 66.667 31.59 0.00 0.00 2.57
429 983 2.115291 GGGCGGCCAGATGAAGAAC 61.115 63.158 25.33 0.00 0.00 3.01
431 985 1.372087 GGCGGCCAGATGAAGAACAG 61.372 60.000 15.62 0.00 0.00 3.16
432 986 1.372087 GCGGCCAGATGAAGAACAGG 61.372 60.000 2.24 0.00 0.00 4.00
433 987 0.036010 CGGCCAGATGAAGAACAGGT 60.036 55.000 2.24 0.00 0.00 4.00
434 988 1.611673 CGGCCAGATGAAGAACAGGTT 60.612 52.381 2.24 0.00 0.00 3.50
435 989 2.519013 GGCCAGATGAAGAACAGGTTT 58.481 47.619 0.00 0.00 0.00 3.27
436 990 3.686016 GGCCAGATGAAGAACAGGTTTA 58.314 45.455 0.00 0.00 0.00 2.01
437 991 3.691609 GGCCAGATGAAGAACAGGTTTAG 59.308 47.826 0.00 0.00 0.00 1.85
438 992 4.565652 GGCCAGATGAAGAACAGGTTTAGA 60.566 45.833 0.00 0.00 0.00 2.10
439 993 5.189180 GCCAGATGAAGAACAGGTTTAGAT 58.811 41.667 0.00 0.00 0.00 1.98
440 994 5.295540 GCCAGATGAAGAACAGGTTTAGATC 59.704 44.000 0.00 0.00 0.00 2.75
441 995 6.648192 CCAGATGAAGAACAGGTTTAGATCT 58.352 40.000 0.00 0.00 0.00 2.75
442 996 6.538021 CCAGATGAAGAACAGGTTTAGATCTG 59.462 42.308 5.18 0.00 37.07 2.90
443 997 6.036953 CAGATGAAGAACAGGTTTAGATCTGC 59.963 42.308 5.18 0.00 34.57 4.26
444 998 4.579869 TGAAGAACAGGTTTAGATCTGCC 58.420 43.478 5.18 5.12 34.57 4.85
445 999 3.636153 AGAACAGGTTTAGATCTGCCC 57.364 47.619 5.18 2.19 34.57 5.36
446 1000 2.239907 AGAACAGGTTTAGATCTGCCCC 59.760 50.000 5.18 1.80 34.57 5.80
447 1001 1.972588 ACAGGTTTAGATCTGCCCCT 58.027 50.000 5.18 4.29 34.57 4.79
448 1002 1.561542 ACAGGTTTAGATCTGCCCCTG 59.438 52.381 23.98 23.98 43.98 4.45
449 1003 1.561542 CAGGTTTAGATCTGCCCCTGT 59.438 52.381 20.19 0.00 35.77 4.00
450 1004 2.771943 CAGGTTTAGATCTGCCCCTGTA 59.228 50.000 20.19 0.00 35.77 2.74
451 1005 2.772515 AGGTTTAGATCTGCCCCTGTAC 59.227 50.000 5.18 0.00 0.00 2.90
452 1006 2.772515 GGTTTAGATCTGCCCCTGTACT 59.227 50.000 5.18 0.00 0.00 2.73
453 1007 3.200165 GGTTTAGATCTGCCCCTGTACTT 59.800 47.826 5.18 0.00 0.00 2.24
454 1008 4.324331 GGTTTAGATCTGCCCCTGTACTTT 60.324 45.833 5.18 0.00 0.00 2.66
455 1009 4.487714 TTAGATCTGCCCCTGTACTTTG 57.512 45.455 5.18 0.00 0.00 2.77
456 1010 2.269940 AGATCTGCCCCTGTACTTTGT 58.730 47.619 0.00 0.00 0.00 2.83
457 1011 2.644798 AGATCTGCCCCTGTACTTTGTT 59.355 45.455 0.00 0.00 0.00 2.83
458 1012 3.844211 AGATCTGCCCCTGTACTTTGTTA 59.156 43.478 0.00 0.00 0.00 2.41
459 1013 4.475016 AGATCTGCCCCTGTACTTTGTTAT 59.525 41.667 0.00 0.00 0.00 1.89
460 1014 3.950397 TCTGCCCCTGTACTTTGTTATG 58.050 45.455 0.00 0.00 0.00 1.90
461 1015 3.329520 TCTGCCCCTGTACTTTGTTATGT 59.670 43.478 0.00 0.00 0.00 2.29
462 1016 4.079253 CTGCCCCTGTACTTTGTTATGTT 58.921 43.478 0.00 0.00 0.00 2.71
463 1017 4.475345 TGCCCCTGTACTTTGTTATGTTT 58.525 39.130 0.00 0.00 0.00 2.83
464 1018 4.521256 TGCCCCTGTACTTTGTTATGTTTC 59.479 41.667 0.00 0.00 0.00 2.78
465 1019 4.082408 GCCCCTGTACTTTGTTATGTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
466 1020 4.155280 CCCCTGTACTTTGTTATGTTTCCG 59.845 45.833 0.00 0.00 0.00 4.30
467 1021 4.758165 CCCTGTACTTTGTTATGTTTCCGT 59.242 41.667 0.00 0.00 0.00 4.69
468 1022 5.933463 CCCTGTACTTTGTTATGTTTCCGTA 59.067 40.000 0.00 0.00 0.00 4.02
469 1023 6.427547 CCCTGTACTTTGTTATGTTTCCGTAA 59.572 38.462 0.00 0.00 0.00 3.18
470 1024 7.120138 CCCTGTACTTTGTTATGTTTCCGTAAT 59.880 37.037 0.00 0.00 0.00 1.89
471 1025 9.153721 CCTGTACTTTGTTATGTTTCCGTAATA 57.846 33.333 0.00 0.00 0.00 0.98
480 1034 9.887629 TGTTATGTTTCCGTAATATAAGGTTCA 57.112 29.630 0.00 0.00 32.54 3.18
482 1036 9.550406 TTATGTTTCCGTAATATAAGGTTCAGG 57.450 33.333 0.00 0.00 29.64 3.86
483 1037 5.818857 TGTTTCCGTAATATAAGGTTCAGGC 59.181 40.000 0.00 0.00 0.00 4.85
484 1038 4.612264 TCCGTAATATAAGGTTCAGGCC 57.388 45.455 0.00 0.00 0.00 5.19
485 1039 3.006110 TCCGTAATATAAGGTTCAGGCCG 59.994 47.826 0.00 0.00 0.00 6.13
486 1040 3.323243 CGTAATATAAGGTTCAGGCCGG 58.677 50.000 0.00 0.00 0.00 6.13
487 1041 3.243975 CGTAATATAAGGTTCAGGCCGGT 60.244 47.826 1.90 0.00 0.00 5.28
488 1042 2.930826 ATATAAGGTTCAGGCCGGTG 57.069 50.000 1.90 0.00 0.00 4.94
489 1043 1.575419 TATAAGGTTCAGGCCGGTGT 58.425 50.000 1.90 0.00 0.00 4.16
490 1044 1.575419 ATAAGGTTCAGGCCGGTGTA 58.425 50.000 1.90 0.00 0.00 2.90
491 1045 1.350071 TAAGGTTCAGGCCGGTGTAA 58.650 50.000 1.90 0.00 0.00 2.41
492 1046 0.036306 AAGGTTCAGGCCGGTGTAAG 59.964 55.000 1.90 0.00 0.00 2.34
493 1047 2.038837 GGTTCAGGCCGGTGTAAGC 61.039 63.158 1.90 0.00 0.00 3.09
502 1056 3.428282 GGTGTAAGCCCGCCGTTG 61.428 66.667 0.00 0.00 0.00 4.10
503 1057 2.357760 GTGTAAGCCCGCCGTTGA 60.358 61.111 0.00 0.00 0.00 3.18
504 1058 2.357760 TGTAAGCCCGCCGTTGAC 60.358 61.111 0.00 0.00 0.00 3.18
505 1059 3.484547 GTAAGCCCGCCGTTGACG 61.485 66.667 0.00 0.00 39.44 4.35
562 1116 4.397417 GGGAGGAAGATGATGAACAGTTTG 59.603 45.833 0.00 0.00 0.00 2.93
593 1147 5.208121 AGGGAAGTAGAAGAAGGAGATCTG 58.792 45.833 0.00 0.00 0.00 2.90
642 1198 3.005791 GGACCAATTTGACTGACCCAAAG 59.994 47.826 0.00 0.00 37.00 2.77
649 1253 5.730296 TTTGACTGACCCAAAGAACAAAA 57.270 34.783 0.00 0.00 0.00 2.44
656 1260 3.037549 ACCCAAAGAACAAAATCAGGCA 58.962 40.909 0.00 0.00 0.00 4.75
660 1264 3.354089 AAGAACAAAATCAGGCACGTG 57.646 42.857 12.28 12.28 0.00 4.49
676 1280 0.176219 CGTGGATAGTAAACCGGGCA 59.824 55.000 6.32 0.00 0.00 5.36
709 1321 1.941975 GCAAAGTGCTTTTGTTGGCAT 59.058 42.857 13.33 0.00 46.35 4.40
713 1325 5.163963 GCAAAGTGCTTTTGTTGGCATATAC 60.164 40.000 13.33 0.00 46.35 1.47
765 1377 3.129502 CGACGCCCTGACGGACTA 61.130 66.667 0.00 0.00 37.37 2.59
834 1447 2.567049 CCTCTCCGTGTCCGTGAC 59.433 66.667 0.00 0.00 0.00 3.67
906 1519 3.697747 CCGGCCGTGAACCACCTA 61.698 66.667 26.12 0.00 0.00 3.08
982 1600 2.085262 CGTGCTCGCAGACAGAGTG 61.085 63.158 0.00 0.00 37.99 3.51
1012 1630 1.523154 GGCAAAGATGGTTCGTGGCA 61.523 55.000 0.00 0.00 37.32 4.92
1252 1874 3.045142 GCAACCAGCTGCATGTGT 58.955 55.556 8.66 0.00 42.17 3.72
1253 1875 1.372499 GCAACCAGCTGCATGTGTG 60.372 57.895 8.66 4.21 42.17 3.82
1279 1901 1.154543 CAAACCTTACGGCGTTCGC 60.155 57.895 21.24 8.75 43.89 4.70
1280 1902 1.301165 AAACCTTACGGCGTTCGCT 60.301 52.632 21.24 0.00 43.89 4.93
1289 1911 2.431260 GCGTTCGCTTGGGTCGTA 60.431 61.111 9.99 0.00 0.00 3.43
1290 1912 2.723719 GCGTTCGCTTGGGTCGTAC 61.724 63.158 9.99 0.00 0.00 3.67
1291 1913 2.430942 CGTTCGCTTGGGTCGTACG 61.431 63.158 9.53 9.53 42.22 3.67
1292 1914 1.372128 GTTCGCTTGGGTCGTACGT 60.372 57.895 16.05 0.00 0.00 3.57
1734 2369 5.540337 GGTATAGCCTAGCTCATATATGCCA 59.460 44.000 7.92 0.00 40.44 4.92
1740 2375 2.035530 GCTCATATATGCCAGAGCCC 57.964 55.000 7.92 0.00 45.79 5.19
1742 2377 0.250234 TCATATATGCCAGAGCCCGC 59.750 55.000 7.92 0.00 38.69 6.13
1801 2436 0.388778 TGCATGCAAACGATGGCTTG 60.389 50.000 20.30 3.83 37.99 4.01
1880 2525 4.098654 ACGTGGTTCCATGTCAATCAAAAA 59.901 37.500 10.51 0.00 31.29 1.94
1921 2566 2.492484 GCTAGTACGAGGTGGGGATATG 59.508 54.545 5.08 0.00 0.00 1.78
2001 2647 4.158394 TCTCTTTAATCCAACAAGCATGGC 59.842 41.667 0.00 0.00 37.88 4.40
2002 2648 3.831333 TCTTTAATCCAACAAGCATGGCA 59.169 39.130 0.00 0.00 37.88 4.92
2003 2649 4.467082 TCTTTAATCCAACAAGCATGGCAT 59.533 37.500 0.00 0.00 37.88 4.40
2004 2650 2.684001 AATCCAACAAGCATGGCATG 57.316 45.000 22.99 22.99 37.88 4.06
2005 2651 0.828022 ATCCAACAAGCATGGCATGG 59.172 50.000 27.48 14.27 37.88 3.66
2032 2678 2.202703 CGACGAACGTCCCCATCC 60.203 66.667 19.15 0.00 41.76 3.51
2154 2802 2.361737 GCCAACAGCCTCCTTCCC 60.362 66.667 0.00 0.00 34.35 3.97
2288 2939 4.297768 TCAGTTCATCACCATCCTATCCA 58.702 43.478 0.00 0.00 0.00 3.41
2306 2957 4.047059 TCGAACTCGACGTGCCCC 62.047 66.667 0.00 0.00 44.22 5.80
2424 3075 4.349503 AGCAAGACGGGCATGCCA 62.350 61.111 36.56 0.00 41.96 4.92
2499 3150 4.308458 CACGGGAACAGGTCGGCA 62.308 66.667 0.00 0.00 0.00 5.69
2515 3166 1.007734 GCACTCAACGACCTCGACA 60.008 57.895 0.78 0.00 43.02 4.35
2715 3366 0.179020 TGGGGAATATCAAGCCGCTG 60.179 55.000 0.00 0.00 35.82 5.18
2812 3465 4.998672 GTGGTTTAGCTTGTACCATGTACA 59.001 41.667 14.84 0.00 43.33 2.90
2815 3468 6.717540 TGGTTTAGCTTGTACCATGTACAATT 59.282 34.615 17.36 12.35 37.04 2.32
2999 3656 9.703677 ATAGAATTATAGCTAACTACTCCCTCC 57.296 37.037 0.00 0.00 0.00 4.30
3000 3657 6.660094 AGAATTATAGCTAACTACTCCCTCCG 59.340 42.308 0.00 0.00 0.00 4.63
3001 3658 3.880168 ATAGCTAACTACTCCCTCCGT 57.120 47.619 0.00 0.00 0.00 4.69
3002 3659 2.055684 AGCTAACTACTCCCTCCGTC 57.944 55.000 0.00 0.00 0.00 4.79
3003 3660 1.031235 GCTAACTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
3004 3661 1.307097 CTAACTACTCCCTCCGTCCG 58.693 60.000 0.00 0.00 0.00 4.79
3005 3662 0.911769 TAACTACTCCCTCCGTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
3006 3663 0.038744 AACTACTCCCTCCGTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3007 3664 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
3008 3665 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
3009 3666 1.547372 CTACTCCCTCCGTCCGAAAAA 59.453 52.381 0.00 0.00 0.00 1.94
3035 3692 4.569761 GTCTATATGAGACGTGGCAAGA 57.430 45.455 7.60 0.00 45.16 3.02
3036 3693 4.541779 GTCTATATGAGACGTGGCAAGAG 58.458 47.826 7.60 0.00 45.16 2.85
3037 3694 4.276183 GTCTATATGAGACGTGGCAAGAGA 59.724 45.833 7.60 0.00 45.16 3.10
3038 3695 4.887655 TCTATATGAGACGTGGCAAGAGAA 59.112 41.667 7.60 0.00 0.00 2.87
3039 3696 2.086054 ATGAGACGTGGCAAGAGAAC 57.914 50.000 7.60 0.00 0.00 3.01
3040 3697 0.750249 TGAGACGTGGCAAGAGAACA 59.250 50.000 7.60 0.00 0.00 3.18
3041 3698 1.138069 TGAGACGTGGCAAGAGAACAA 59.862 47.619 7.60 0.00 0.00 2.83
3042 3699 1.795286 GAGACGTGGCAAGAGAACAAG 59.205 52.381 7.60 0.00 0.00 3.16
3043 3700 1.139058 AGACGTGGCAAGAGAACAAGT 59.861 47.619 7.60 0.00 0.00 3.16
3044 3701 1.940613 GACGTGGCAAGAGAACAAGTT 59.059 47.619 7.60 0.00 0.00 2.66
3045 3702 2.354821 GACGTGGCAAGAGAACAAGTTT 59.645 45.455 7.60 0.00 0.00 2.66
3046 3703 2.097466 ACGTGGCAAGAGAACAAGTTTG 59.903 45.455 7.60 0.00 0.00 2.93
3047 3704 2.541588 CGTGGCAAGAGAACAAGTTTGG 60.542 50.000 0.00 0.00 0.00 3.28
3048 3705 2.031120 TGGCAAGAGAACAAGTTTGGG 58.969 47.619 0.00 0.00 0.00 4.12
3049 3706 2.306847 GGCAAGAGAACAAGTTTGGGA 58.693 47.619 0.00 0.00 0.00 4.37
3050 3707 2.893489 GGCAAGAGAACAAGTTTGGGAT 59.107 45.455 0.00 0.00 0.00 3.85
3051 3708 4.079253 GGCAAGAGAACAAGTTTGGGATA 58.921 43.478 0.00 0.00 0.00 2.59
3052 3709 4.522789 GGCAAGAGAACAAGTTTGGGATAA 59.477 41.667 0.00 0.00 0.00 1.75
3053 3710 5.010617 GGCAAGAGAACAAGTTTGGGATAAA 59.989 40.000 0.00 0.00 0.00 1.40
3054 3711 5.920840 GCAAGAGAACAAGTTTGGGATAAAC 59.079 40.000 0.00 0.00 0.00 2.01
3055 3712 6.239036 GCAAGAGAACAAGTTTGGGATAAACT 60.239 38.462 0.00 0.00 41.82 2.66
3057 3714 7.898014 AGAGAACAAGTTTGGGATAAACTTT 57.102 32.000 13.37 2.96 45.20 2.66
3058 3715 8.306313 AGAGAACAAGTTTGGGATAAACTTTT 57.694 30.769 13.37 11.36 45.20 2.27
3059 3716 8.758829 AGAGAACAAGTTTGGGATAAACTTTTT 58.241 29.630 13.37 13.37 45.20 1.94
3060 3717 8.942338 AGAACAAGTTTGGGATAAACTTTTTC 57.058 30.769 23.28 23.28 46.58 2.29
3061 3718 7.764695 AACAAGTTTGGGATAAACTTTTTCG 57.235 32.000 13.37 6.83 45.20 3.46
3062 3719 6.277605 ACAAGTTTGGGATAAACTTTTTCGG 58.722 36.000 13.37 6.54 45.20 4.30
3063 3720 6.097129 ACAAGTTTGGGATAAACTTTTTCGGA 59.903 34.615 13.37 0.00 45.20 4.55
3064 3721 6.080648 AGTTTGGGATAAACTTTTTCGGAC 57.919 37.500 0.00 0.00 37.18 4.79
3065 3722 5.595133 AGTTTGGGATAAACTTTTTCGGACA 59.405 36.000 0.00 0.00 37.18 4.02
3066 3723 6.097129 AGTTTGGGATAAACTTTTTCGGACAA 59.903 34.615 0.00 0.00 37.18 3.18
3067 3724 6.466885 TTGGGATAAACTTTTTCGGACAAA 57.533 33.333 0.00 0.00 0.00 2.83
3068 3725 6.079424 TGGGATAAACTTTTTCGGACAAAG 57.921 37.500 13.57 13.57 37.29 2.77
3069 3726 5.010213 TGGGATAAACTTTTTCGGACAAAGG 59.990 40.000 18.02 7.20 35.82 3.11
3070 3727 5.466819 GGATAAACTTTTTCGGACAAAGGG 58.533 41.667 18.02 0.00 35.82 3.95
3071 3728 5.242171 GGATAAACTTTTTCGGACAAAGGGA 59.758 40.000 18.02 5.94 35.82 4.20
3072 3729 4.649088 AAACTTTTTCGGACAAAGGGAG 57.351 40.909 18.02 0.00 35.82 4.30
3073 3730 3.292492 ACTTTTTCGGACAAAGGGAGT 57.708 42.857 18.02 0.00 35.82 3.85
3074 3731 4.426736 ACTTTTTCGGACAAAGGGAGTA 57.573 40.909 18.02 0.00 35.82 2.59
3075 3732 4.132336 ACTTTTTCGGACAAAGGGAGTAC 58.868 43.478 18.02 0.00 35.82 2.73
3076 3733 4.141551 ACTTTTTCGGACAAAGGGAGTACT 60.142 41.667 18.02 0.00 35.82 2.73
3077 3734 5.070847 ACTTTTTCGGACAAAGGGAGTACTA 59.929 40.000 18.02 0.00 35.82 1.82
3078 3735 5.750352 TTTTCGGACAAAGGGAGTACTAT 57.250 39.130 0.00 0.00 0.00 2.12
3079 3736 4.730949 TTCGGACAAAGGGAGTACTATG 57.269 45.455 0.00 0.00 0.00 2.23
3080 3737 2.429610 TCGGACAAAGGGAGTACTATGC 59.570 50.000 0.00 0.00 0.00 3.14
3081 3738 2.167693 CGGACAAAGGGAGTACTATGCA 59.832 50.000 0.00 0.00 0.00 3.96
3082 3739 3.369052 CGGACAAAGGGAGTACTATGCAA 60.369 47.826 0.00 0.00 0.00 4.08
3083 3740 4.192317 GGACAAAGGGAGTACTATGCAAG 58.808 47.826 0.00 0.00 0.00 4.01
3084 3741 3.610911 ACAAAGGGAGTACTATGCAAGC 58.389 45.455 0.00 0.00 0.00 4.01
3085 3742 3.264450 ACAAAGGGAGTACTATGCAAGCT 59.736 43.478 0.00 0.00 0.00 3.74
3086 3743 4.469945 ACAAAGGGAGTACTATGCAAGCTA 59.530 41.667 0.00 0.00 0.00 3.32
3087 3744 4.674281 AAGGGAGTACTATGCAAGCTAC 57.326 45.455 0.00 0.00 0.00 3.58
3088 3745 3.917300 AGGGAGTACTATGCAAGCTACT 58.083 45.455 0.00 0.00 0.00 2.57
3089 3746 5.063017 AGGGAGTACTATGCAAGCTACTA 57.937 43.478 0.00 0.00 0.00 1.82
3090 3747 5.074115 AGGGAGTACTATGCAAGCTACTAG 58.926 45.833 0.00 0.00 0.00 2.57
3101 3758 9.579768 CTATGCAAGCTACTAGTATTAGATTGG 57.420 37.037 20.53 6.46 41.31 3.16
3130 3787 5.348986 TGAGACGTGGCAAGAAGATATAAC 58.651 41.667 7.60 0.00 0.00 1.89
3131 3788 5.105513 TGAGACGTGGCAAGAAGATATAACA 60.106 40.000 7.60 0.00 0.00 2.41
3255 3912 4.323569 AGTCTAACTCTGGAGATGACCA 57.676 45.455 4.49 0.00 38.33 4.02
3258 3915 4.026744 TCTAACTCTGGAGATGACCAAGG 58.973 47.826 4.49 0.00 39.59 3.61
3267 3924 1.137872 AGATGACCAAGGATCTCGCAC 59.862 52.381 0.00 0.00 0.00 5.34
3280 3937 0.179127 CTCGCACGACTCATGACCAT 60.179 55.000 0.00 0.00 0.00 3.55
3306 3963 7.883311 TGAGAATGTAGCTTTTAGCCTAGTTTT 59.117 33.333 0.00 0.00 43.77 2.43
3309 3966 6.123045 TGTAGCTTTTAGCCTAGTTTTCCT 57.877 37.500 0.00 0.00 43.77 3.36
3319 3976 6.755542 AGCCTAGTTTTCCTCTATTGCTAT 57.244 37.500 0.00 0.00 0.00 2.97
3320 3977 7.142995 AGCCTAGTTTTCCTCTATTGCTATT 57.857 36.000 0.00 0.00 0.00 1.73
3321 3978 6.995091 AGCCTAGTTTTCCTCTATTGCTATTG 59.005 38.462 0.00 0.00 0.00 1.90
3323 3980 7.254932 GCCTAGTTTTCCTCTATTGCTATTGTG 60.255 40.741 0.00 0.00 0.00 3.33
3346 4003 1.377333 GCTAGTTGAGCCCACCCAC 60.377 63.158 0.00 0.00 46.41 4.61
3347 4004 1.842381 GCTAGTTGAGCCCACCCACT 61.842 60.000 0.00 0.00 46.41 4.00
3368 4025 2.110188 TCCCGGGCTAGAGAATGTATCT 59.890 50.000 18.49 0.00 42.61 1.98
3377 4034 9.430623 GGGCTAGAGAATGTATCTTAGAAATTC 57.569 37.037 0.00 7.26 38.96 2.17
3378 4035 9.430623 GGCTAGAGAATGTATCTTAGAAATTCC 57.569 37.037 0.00 5.03 38.96 3.01
3404 4063 4.338682 AGTGTAATCCATGTACTCGAGGTC 59.661 45.833 18.41 9.65 0.00 3.85
3419 4078 5.812642 ACTCGAGGTCAAATACATTGCTAAG 59.187 40.000 18.41 0.00 38.98 2.18
3487 4147 2.113860 ATGTCACATCCAAGAACCCG 57.886 50.000 0.00 0.00 0.00 5.28
3496 4156 4.022329 ACATCCAAGAACCCGATTTCAAAC 60.022 41.667 0.00 0.00 0.00 2.93
3516 4176 6.875195 TCAAACTATAACACGGGGAGTTTTAG 59.125 38.462 6.55 7.14 38.06 1.85
3531 4191 7.614583 GGGGAGTTTTAGAAAAACTTATAGCCT 59.385 37.037 16.48 0.00 40.27 4.58
3669 4330 8.562892 CATGTACTCAGATGTTTTCAGAGTTTT 58.437 33.333 6.06 0.00 45.87 2.43
3670 4331 8.506168 TGTACTCAGATGTTTTCAGAGTTTTT 57.494 30.769 6.06 0.00 45.87 1.94
3718 4379 1.451927 GGGTGCTCCGATTGCATCA 60.452 57.895 9.08 0.00 42.81 3.07
3740 4401 2.465860 TGGTTGGTCCACAAGATACG 57.534 50.000 0.00 0.00 41.93 3.06
3741 4402 1.002659 TGGTTGGTCCACAAGATACGG 59.997 52.381 0.00 0.00 41.93 4.02
3753 4414 3.443329 ACAAGATACGGCATGCATCAAAA 59.557 39.130 21.36 0.00 0.00 2.44
3754 4415 4.098349 ACAAGATACGGCATGCATCAAAAT 59.902 37.500 21.36 3.49 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.940470 CCTGGAGAAATGCTACACTTTAGTT 59.060 40.000 0.00 0.00 32.72 2.24
44 45 5.248477 TCCTGGAGAAATGCTACACTTTAGT 59.752 40.000 0.00 0.00 32.72 2.24
45 46 5.734720 TCCTGGAGAAATGCTACACTTTAG 58.265 41.667 0.00 0.00 32.72 1.85
123 124 2.700407 TACCAACAAACCGGGCCCTG 62.700 60.000 22.43 17.38 0.00 4.45
141 142 7.531716 CCTTTGCACTTTTGAATAATACGGTA 58.468 34.615 0.00 0.00 0.00 4.02
183 185 1.868498 CTTACGTCCAGCAAAAACCGA 59.132 47.619 0.00 0.00 0.00 4.69
185 187 2.614983 TGACTTACGTCCAGCAAAAACC 59.385 45.455 0.00 0.00 39.47 3.27
187 189 2.614983 GGTGACTTACGTCCAGCAAAAA 59.385 45.455 0.00 0.00 39.47 1.94
206 208 3.906846 TGGCCCAAATTGTAAATTCAGGT 59.093 39.130 0.00 0.00 0.00 4.00
224 226 0.804989 CTCAACCGAATTGACTGGCC 59.195 55.000 0.00 0.00 42.62 5.36
226 228 2.744202 CCTTCTCAACCGAATTGACTGG 59.256 50.000 0.00 0.00 42.62 4.00
232 235 3.140325 TGCTTCCTTCTCAACCGAATT 57.860 42.857 0.00 0.00 0.00 2.17
243 246 3.620821 GCTCTACAGTTGATGCTTCCTTC 59.379 47.826 0.00 0.00 0.00 3.46
253 256 1.336887 GCTTCGGTGCTCTACAGTTGA 60.337 52.381 0.00 0.00 0.00 3.18
281 284 3.543536 GAGATCCATCCTGCCGCCC 62.544 68.421 0.00 0.00 0.00 6.13
285 288 1.271102 GTAGACGAGATCCATCCTGCC 59.729 57.143 0.00 0.00 0.00 4.85
293 296 2.293955 GCACCTAAGGTAGACGAGATCC 59.706 54.545 0.00 0.00 32.11 3.36
305 308 2.879103 TTCTTCCCTTGCACCTAAGG 57.121 50.000 0.00 0.00 45.51 2.69
325 329 4.410555 CCCTAAGATAGACAAGGAGCCTTT 59.589 45.833 0.00 0.00 33.42 3.11
340 344 0.728843 TTCCCCCTGGACCCTAAGAT 59.271 55.000 0.00 0.00 41.57 2.40
346 350 2.985116 GCTTCTTCCCCCTGGACCC 61.985 68.421 0.00 0.00 41.57 4.46
347 351 2.677848 GCTTCTTCCCCCTGGACC 59.322 66.667 0.00 0.00 41.57 4.46
348 352 1.925972 AGGCTTCTTCCCCCTGGAC 60.926 63.158 0.00 0.00 41.57 4.02
349 353 1.925455 CAGGCTTCTTCCCCCTGGA 60.925 63.158 0.00 0.00 41.87 3.86
352 608 3.342477 GCCAGGCTTCTTCCCCCT 61.342 66.667 3.29 0.00 0.00 4.79
354 610 3.689002 CTCGCCAGGCTTCTTCCCC 62.689 68.421 10.54 0.00 0.00 4.81
357 613 2.124942 CCCTCGCCAGGCTTCTTC 60.125 66.667 10.54 0.00 38.72 2.87
358 614 3.721706 CCCCTCGCCAGGCTTCTT 61.722 66.667 10.54 0.00 38.72 2.52
420 974 5.295540 GGCAGATCTAAACCTGTTCTTCATC 59.704 44.000 0.00 0.00 33.19 2.92
422 976 4.565652 GGGCAGATCTAAACCTGTTCTTCA 60.566 45.833 0.00 0.00 33.19 3.02
425 979 2.239907 GGGGCAGATCTAAACCTGTTCT 59.760 50.000 0.00 0.00 33.19 3.01
429 983 2.338577 CAGGGGCAGATCTAAACCTG 57.661 55.000 18.67 18.67 39.45 4.00
431 985 2.772515 AGTACAGGGGCAGATCTAAACC 59.227 50.000 0.00 0.00 0.00 3.27
432 986 4.489306 AAGTACAGGGGCAGATCTAAAC 57.511 45.455 0.00 0.00 0.00 2.01
433 987 4.288626 ACAAAGTACAGGGGCAGATCTAAA 59.711 41.667 0.00 0.00 0.00 1.85
434 988 3.844211 ACAAAGTACAGGGGCAGATCTAA 59.156 43.478 0.00 0.00 0.00 2.10
435 989 3.450904 ACAAAGTACAGGGGCAGATCTA 58.549 45.455 0.00 0.00 0.00 1.98
436 990 2.269940 ACAAAGTACAGGGGCAGATCT 58.730 47.619 0.00 0.00 0.00 2.75
437 991 2.789409 ACAAAGTACAGGGGCAGATC 57.211 50.000 0.00 0.00 0.00 2.75
438 992 4.018415 ACATAACAAAGTACAGGGGCAGAT 60.018 41.667 0.00 0.00 0.00 2.90
439 993 3.329520 ACATAACAAAGTACAGGGGCAGA 59.670 43.478 0.00 0.00 0.00 4.26
440 994 3.686016 ACATAACAAAGTACAGGGGCAG 58.314 45.455 0.00 0.00 0.00 4.85
441 995 3.799432 ACATAACAAAGTACAGGGGCA 57.201 42.857 0.00 0.00 0.00 5.36
442 996 4.082408 GGAAACATAACAAAGTACAGGGGC 60.082 45.833 0.00 0.00 0.00 5.80
443 997 4.155280 CGGAAACATAACAAAGTACAGGGG 59.845 45.833 0.00 0.00 0.00 4.79
444 998 4.758165 ACGGAAACATAACAAAGTACAGGG 59.242 41.667 0.00 0.00 0.00 4.45
445 999 5.934935 ACGGAAACATAACAAAGTACAGG 57.065 39.130 0.00 0.00 0.00 4.00
454 1008 9.887629 TGAACCTTATATTACGGAAACATAACA 57.112 29.630 0.00 0.00 0.00 2.41
456 1010 9.550406 CCTGAACCTTATATTACGGAAACATAA 57.450 33.333 0.00 0.00 0.00 1.90
457 1011 7.658575 GCCTGAACCTTATATTACGGAAACATA 59.341 37.037 0.00 0.00 0.00 2.29
458 1012 6.485648 GCCTGAACCTTATATTACGGAAACAT 59.514 38.462 0.00 0.00 0.00 2.71
459 1013 5.818857 GCCTGAACCTTATATTACGGAAACA 59.181 40.000 0.00 0.00 0.00 2.83
460 1014 5.237996 GGCCTGAACCTTATATTACGGAAAC 59.762 44.000 0.00 0.00 0.00 2.78
461 1015 5.370679 GGCCTGAACCTTATATTACGGAAA 58.629 41.667 0.00 0.00 0.00 3.13
462 1016 4.501915 CGGCCTGAACCTTATATTACGGAA 60.502 45.833 0.00 0.00 0.00 4.30
463 1017 3.006110 CGGCCTGAACCTTATATTACGGA 59.994 47.826 0.00 0.00 0.00 4.69
464 1018 3.323243 CGGCCTGAACCTTATATTACGG 58.677 50.000 0.00 0.00 0.00 4.02
465 1019 3.243975 ACCGGCCTGAACCTTATATTACG 60.244 47.826 0.00 0.00 0.00 3.18
466 1020 4.062991 CACCGGCCTGAACCTTATATTAC 58.937 47.826 0.00 0.00 0.00 1.89
467 1021 3.712733 ACACCGGCCTGAACCTTATATTA 59.287 43.478 0.00 0.00 0.00 0.98
468 1022 2.508300 ACACCGGCCTGAACCTTATATT 59.492 45.455 0.00 0.00 0.00 1.28
469 1023 2.124411 ACACCGGCCTGAACCTTATAT 58.876 47.619 0.00 0.00 0.00 0.86
470 1024 1.575419 ACACCGGCCTGAACCTTATA 58.425 50.000 0.00 0.00 0.00 0.98
471 1025 1.575419 TACACCGGCCTGAACCTTAT 58.425 50.000 0.00 0.00 0.00 1.73
472 1026 1.276989 CTTACACCGGCCTGAACCTTA 59.723 52.381 0.00 0.00 0.00 2.69
473 1027 0.036306 CTTACACCGGCCTGAACCTT 59.964 55.000 0.00 0.00 0.00 3.50
474 1028 1.677552 CTTACACCGGCCTGAACCT 59.322 57.895 0.00 0.00 0.00 3.50
475 1029 2.038837 GCTTACACCGGCCTGAACC 61.039 63.158 0.00 0.00 0.00 3.62
476 1030 2.038837 GGCTTACACCGGCCTGAAC 61.039 63.158 0.00 0.00 44.48 3.18
477 1031 2.349755 GGCTTACACCGGCCTGAA 59.650 61.111 0.00 0.00 44.48 3.02
478 1032 3.712907 GGGCTTACACCGGCCTGA 61.713 66.667 0.00 0.00 46.80 3.86
485 1039 3.428282 CAACGGCGGGCTTACACC 61.428 66.667 13.24 0.00 0.00 4.16
486 1040 2.357760 TCAACGGCGGGCTTACAC 60.358 61.111 13.24 0.00 0.00 2.90
487 1041 2.357760 GTCAACGGCGGGCTTACA 60.358 61.111 13.24 0.00 0.00 2.41
488 1042 3.484547 CGTCAACGGCGGGCTTAC 61.485 66.667 13.24 0.77 35.37 2.34
516 1070 5.163416 CCCACCATCTGAACTTGTTCTTTTT 60.163 40.000 13.65 0.00 0.00 1.94
517 1071 4.342092 CCCACCATCTGAACTTGTTCTTTT 59.658 41.667 13.65 0.00 0.00 2.27
518 1072 3.891366 CCCACCATCTGAACTTGTTCTTT 59.109 43.478 13.65 0.00 0.00 2.52
519 1073 3.490348 CCCACCATCTGAACTTGTTCTT 58.510 45.455 13.65 0.00 0.00 2.52
520 1074 2.224867 CCCCACCATCTGAACTTGTTCT 60.225 50.000 13.65 0.00 0.00 3.01
521 1075 2.162681 CCCCACCATCTGAACTTGTTC 58.837 52.381 6.56 6.56 0.00 3.18
522 1076 1.780309 TCCCCACCATCTGAACTTGTT 59.220 47.619 0.00 0.00 0.00 2.83
523 1077 1.352352 CTCCCCACCATCTGAACTTGT 59.648 52.381 0.00 0.00 0.00 3.16
524 1078 1.340405 CCTCCCCACCATCTGAACTTG 60.340 57.143 0.00 0.00 0.00 3.16
525 1079 0.995024 CCTCCCCACCATCTGAACTT 59.005 55.000 0.00 0.00 0.00 2.66
526 1080 0.119155 TCCTCCCCACCATCTGAACT 59.881 55.000 0.00 0.00 0.00 3.01
535 1089 1.511613 TCATCATCTTCCTCCCCACC 58.488 55.000 0.00 0.00 0.00 4.61
562 1116 3.100671 TCTTCTACTTCCCTCCTGAAGC 58.899 50.000 0.90 0.00 44.50 3.86
593 1147 4.460505 CGTTGGATGAAAAAGTAACGGTC 58.539 43.478 0.00 0.00 37.73 4.79
623 1179 4.099266 TGTTCTTTGGGTCAGTCAAATTGG 59.901 41.667 0.00 0.00 34.19 3.16
642 1198 1.606668 TCCACGTGCCTGATTTTGTTC 59.393 47.619 10.91 0.00 0.00 3.18
649 1253 3.431766 GGTTTACTATCCACGTGCCTGAT 60.432 47.826 10.91 10.42 0.00 2.90
656 1260 0.176449 GCCCGGTTTACTATCCACGT 59.824 55.000 0.00 0.00 0.00 4.49
660 1264 1.202770 AGCATGCCCGGTTTACTATCC 60.203 52.381 15.66 0.00 0.00 2.59
709 1321 0.682852 GCAGGTGGGGTATGCGTATA 59.317 55.000 0.00 0.00 0.00 1.47
713 1325 2.188829 CATGCAGGTGGGGTATGCG 61.189 63.158 0.00 0.00 42.92 4.73
765 1377 5.670792 ATCAATCATTTGCTGTTCATGGT 57.329 34.783 0.00 0.00 32.61 3.55
862 1475 1.446966 GTCCCACGAGCTGAAGAGC 60.447 63.158 0.00 0.00 46.64 4.09
906 1519 1.525765 TGTGTGCATGTGCCGACTT 60.526 52.632 2.07 0.00 41.18 3.01
982 1600 1.474077 CATCTTTGCCTGCCTTGGTAC 59.526 52.381 0.00 0.00 0.00 3.34
1012 1630 2.587753 CGCACCGCCGTAATGGAT 60.588 61.111 0.00 0.00 42.00 3.41
1089 1707 0.034059 AGAACTTGTCGTCCAGCTGG 59.966 55.000 27.87 27.87 0.00 4.85
1253 1875 3.996825 CGTAAGGTTTGCATGGAGC 57.003 52.632 0.00 0.00 45.96 4.70
1279 1901 1.342082 CGAAGCACGTACGACCCAAG 61.342 60.000 24.41 5.23 37.22 3.61
1280 1902 1.372004 CGAAGCACGTACGACCCAA 60.372 57.895 24.41 0.00 37.22 4.12
1291 1913 2.098443 TCAAAAACCTTGGACGAAGCAC 59.902 45.455 0.00 0.00 0.00 4.40
1292 1914 2.098443 GTCAAAAACCTTGGACGAAGCA 59.902 45.455 0.00 0.00 0.00 3.91
1677 2312 1.521681 GCTAGTACCTTGCCAGCCG 60.522 63.158 0.00 0.00 0.00 5.52
1740 2375 2.450160 GGTTTCTGAATTATTGCCGCG 58.550 47.619 0.00 0.00 0.00 6.46
1742 2377 3.680789 GACGGTTTCTGAATTATTGCCG 58.319 45.455 0.00 0.00 43.05 5.69
1801 2436 1.262151 GTCGATCTCTCCAGTCTACGC 59.738 57.143 0.00 0.00 0.00 4.42
1892 2537 2.617774 CACCTCGTACTAGCTAGGTTCC 59.382 54.545 24.35 8.18 40.39 3.62
1895 2540 1.133853 CCCACCTCGTACTAGCTAGGT 60.134 57.143 24.35 11.69 43.15 3.08
1921 2566 1.210155 GTGCGATGTGGACTTTGCC 59.790 57.895 0.00 0.00 35.76 4.52
2002 2648 0.320334 TTCGTCGTGCATGTGACCAT 60.320 50.000 5.68 0.00 0.00 3.55
2003 2649 1.068250 TTCGTCGTGCATGTGACCA 59.932 52.632 5.68 0.00 0.00 4.02
2004 2650 1.491563 GTTCGTCGTGCATGTGACC 59.508 57.895 5.68 0.00 0.00 4.02
2005 2651 1.127817 CGTTCGTCGTGCATGTGAC 59.872 57.895 5.68 6.24 34.52 3.67
2154 2802 4.974721 AGGTTGTTGCGGGGGCTG 62.975 66.667 0.00 0.00 0.00 4.85
2304 2955 2.272146 CTGGATCAACCACGGGGG 59.728 66.667 9.50 0.00 44.64 5.40
2305 2956 1.635817 ATCCTGGATCAACCACGGGG 61.636 60.000 0.00 0.00 44.64 5.73
2306 2957 0.179045 GATCCTGGATCAACCACGGG 60.179 60.000 27.72 0.00 44.64 5.28
2315 2966 3.282885 GACCCAAACAAGATCCTGGATC 58.717 50.000 25.90 25.90 39.17 3.36
2320 2971 1.271379 CCACGACCCAAACAAGATCCT 60.271 52.381 0.00 0.00 0.00 3.24
2499 3150 1.162181 TCGTGTCGAGGTCGTTGAGT 61.162 55.000 0.00 0.00 40.80 3.41
2812 3465 3.945981 TGCATGCATGACACAGAAATT 57.054 38.095 30.64 0.00 0.00 1.82
2815 3468 1.068125 GCTTGCATGCATGACACAGAA 60.068 47.619 31.38 9.95 0.00 3.02
2926 3583 3.042059 ACCCATGTTAGTATCTCGGGT 57.958 47.619 0.00 0.00 40.65 5.28
2977 3634 6.313324 ACGGAGGGAGTAGTTAGCTATAATT 58.687 40.000 0.00 0.00 0.00 1.40
2978 3635 5.890049 ACGGAGGGAGTAGTTAGCTATAAT 58.110 41.667 0.00 0.00 0.00 1.28
2979 3636 5.312079 GACGGAGGGAGTAGTTAGCTATAA 58.688 45.833 0.00 0.00 0.00 0.98
2980 3637 4.263243 GGACGGAGGGAGTAGTTAGCTATA 60.263 50.000 0.00 0.00 0.00 1.31
2981 3638 3.498301 GGACGGAGGGAGTAGTTAGCTAT 60.498 52.174 0.00 0.00 0.00 2.97
2982 3639 2.158696 GGACGGAGGGAGTAGTTAGCTA 60.159 54.545 0.00 0.00 0.00 3.32
2983 3640 1.409942 GGACGGAGGGAGTAGTTAGCT 60.410 57.143 0.00 0.00 0.00 3.32
2984 3641 1.031235 GGACGGAGGGAGTAGTTAGC 58.969 60.000 0.00 0.00 0.00 3.09
2985 3642 1.134280 TCGGACGGAGGGAGTAGTTAG 60.134 57.143 0.00 0.00 0.00 2.34
2986 3643 0.911769 TCGGACGGAGGGAGTAGTTA 59.088 55.000 0.00 0.00 0.00 2.24
2987 3644 0.038744 TTCGGACGGAGGGAGTAGTT 59.961 55.000 0.00 0.00 0.00 2.24
2988 3645 0.038744 TTTCGGACGGAGGGAGTAGT 59.961 55.000 0.00 0.00 0.00 2.73
2989 3646 1.180029 TTTTCGGACGGAGGGAGTAG 58.820 55.000 0.00 0.00 0.00 2.57
2990 3647 1.631405 TTTTTCGGACGGAGGGAGTA 58.369 50.000 0.00 0.00 0.00 2.59
2991 3648 2.444281 TTTTTCGGACGGAGGGAGT 58.556 52.632 0.00 0.00 0.00 3.85
3015 3672 4.461198 TCTCTTGCCACGTCTCATATAGA 58.539 43.478 0.00 0.00 0.00 1.98
3016 3673 4.837896 TCTCTTGCCACGTCTCATATAG 57.162 45.455 0.00 0.00 0.00 1.31
3017 3674 4.401202 TGTTCTCTTGCCACGTCTCATATA 59.599 41.667 0.00 0.00 0.00 0.86
3018 3675 3.195610 TGTTCTCTTGCCACGTCTCATAT 59.804 43.478 0.00 0.00 0.00 1.78
3019 3676 2.560981 TGTTCTCTTGCCACGTCTCATA 59.439 45.455 0.00 0.00 0.00 2.15
3020 3677 1.344438 TGTTCTCTTGCCACGTCTCAT 59.656 47.619 0.00 0.00 0.00 2.90
3021 3678 0.750249 TGTTCTCTTGCCACGTCTCA 59.250 50.000 0.00 0.00 0.00 3.27
3022 3679 1.795286 CTTGTTCTCTTGCCACGTCTC 59.205 52.381 0.00 0.00 0.00 3.36
3023 3680 1.139058 ACTTGTTCTCTTGCCACGTCT 59.861 47.619 0.00 0.00 0.00 4.18
3024 3681 1.583054 ACTTGTTCTCTTGCCACGTC 58.417 50.000 0.00 0.00 0.00 4.34
3025 3682 2.038387 AACTTGTTCTCTTGCCACGT 57.962 45.000 0.00 0.00 0.00 4.49
3026 3683 2.541588 CCAAACTTGTTCTCTTGCCACG 60.542 50.000 0.00 0.00 0.00 4.94
3027 3684 2.223805 CCCAAACTTGTTCTCTTGCCAC 60.224 50.000 0.00 0.00 0.00 5.01
3028 3685 2.031120 CCCAAACTTGTTCTCTTGCCA 58.969 47.619 0.00 0.00 0.00 4.92
3029 3686 2.306847 TCCCAAACTTGTTCTCTTGCC 58.693 47.619 0.00 0.00 0.00 4.52
3030 3687 5.705609 TTATCCCAAACTTGTTCTCTTGC 57.294 39.130 0.00 0.00 0.00 4.01
3031 3688 7.277174 AGTTTATCCCAAACTTGTTCTCTTG 57.723 36.000 0.00 0.00 37.18 3.02
3032 3689 7.898014 AAGTTTATCCCAAACTTGTTCTCTT 57.102 32.000 12.88 0.00 45.58 2.85
3033 3690 7.898014 AAAGTTTATCCCAAACTTGTTCTCT 57.102 32.000 14.04 0.00 46.33 3.10
3034 3691 8.942338 AAAAAGTTTATCCCAAACTTGTTCTC 57.058 30.769 14.04 0.00 46.33 2.87
3037 3694 6.759356 CCGAAAAAGTTTATCCCAAACTTGTT 59.241 34.615 14.74 14.74 46.33 2.83
3038 3695 6.097129 TCCGAAAAAGTTTATCCCAAACTTGT 59.903 34.615 14.04 7.50 46.33 3.16
3039 3696 6.419710 GTCCGAAAAAGTTTATCCCAAACTTG 59.580 38.462 14.04 4.04 46.33 3.16
3041 3698 5.595133 TGTCCGAAAAAGTTTATCCCAAACT 59.405 36.000 0.00 0.00 41.82 2.66
3042 3699 5.834169 TGTCCGAAAAAGTTTATCCCAAAC 58.166 37.500 0.00 0.00 0.00 2.93
3043 3700 6.466885 TTGTCCGAAAAAGTTTATCCCAAA 57.533 33.333 0.00 0.00 0.00 3.28
3044 3701 6.461788 CCTTTGTCCGAAAAAGTTTATCCCAA 60.462 38.462 9.72 0.00 33.61 4.12
3045 3702 5.010213 CCTTTGTCCGAAAAAGTTTATCCCA 59.990 40.000 9.72 0.00 33.61 4.37
3046 3703 5.466819 CCTTTGTCCGAAAAAGTTTATCCC 58.533 41.667 9.72 0.00 33.61 3.85
3047 3704 5.242171 TCCCTTTGTCCGAAAAAGTTTATCC 59.758 40.000 9.72 0.00 33.61 2.59
3048 3705 6.016527 ACTCCCTTTGTCCGAAAAAGTTTATC 60.017 38.462 9.72 0.00 33.61 1.75
3049 3706 5.831525 ACTCCCTTTGTCCGAAAAAGTTTAT 59.168 36.000 9.72 0.00 33.61 1.40
3050 3707 5.195185 ACTCCCTTTGTCCGAAAAAGTTTA 58.805 37.500 9.72 0.00 33.61 2.01
3051 3708 4.021229 ACTCCCTTTGTCCGAAAAAGTTT 58.979 39.130 9.72 0.00 33.61 2.66
3052 3709 3.628008 ACTCCCTTTGTCCGAAAAAGTT 58.372 40.909 9.72 0.00 33.61 2.66
3053 3710 3.292492 ACTCCCTTTGTCCGAAAAAGT 57.708 42.857 9.72 0.00 33.61 2.66
3054 3711 4.386711 AGTACTCCCTTTGTCCGAAAAAG 58.613 43.478 4.25 4.25 34.94 2.27
3055 3712 4.426736 AGTACTCCCTTTGTCCGAAAAA 57.573 40.909 0.00 0.00 0.00 1.94
3056 3713 5.484715 CATAGTACTCCCTTTGTCCGAAAA 58.515 41.667 0.00 0.00 0.00 2.29
3057 3714 4.622220 GCATAGTACTCCCTTTGTCCGAAA 60.622 45.833 0.00 0.00 0.00 3.46
3058 3715 3.118884 GCATAGTACTCCCTTTGTCCGAA 60.119 47.826 0.00 0.00 0.00 4.30
3059 3716 2.429610 GCATAGTACTCCCTTTGTCCGA 59.570 50.000 0.00 0.00 0.00 4.55
3060 3717 2.167693 TGCATAGTACTCCCTTTGTCCG 59.832 50.000 0.00 0.00 0.00 4.79
3061 3718 3.906720 TGCATAGTACTCCCTTTGTCC 57.093 47.619 0.00 0.00 0.00 4.02
3062 3719 3.623510 GCTTGCATAGTACTCCCTTTGTC 59.376 47.826 0.00 0.00 0.00 3.18
3063 3720 3.264450 AGCTTGCATAGTACTCCCTTTGT 59.736 43.478 0.00 0.00 0.00 2.83
3064 3721 3.878778 AGCTTGCATAGTACTCCCTTTG 58.121 45.455 0.00 0.00 0.00 2.77
3065 3722 4.717280 AGTAGCTTGCATAGTACTCCCTTT 59.283 41.667 0.00 0.00 0.00 3.11
3066 3723 4.290942 AGTAGCTTGCATAGTACTCCCTT 58.709 43.478 0.00 0.00 0.00 3.95
3067 3724 3.917300 AGTAGCTTGCATAGTACTCCCT 58.083 45.455 0.00 0.00 0.00 4.20
3068 3725 4.828387 ACTAGTAGCTTGCATAGTACTCCC 59.172 45.833 0.00 0.00 0.00 4.30
3069 3726 7.690952 ATACTAGTAGCTTGCATAGTACTCC 57.309 40.000 8.85 0.00 34.49 3.85
3075 3732 9.579768 CCAATCTAATACTAGTAGCTTGCATAG 57.420 37.037 8.85 3.09 0.00 2.23
3076 3733 8.035394 GCCAATCTAATACTAGTAGCTTGCATA 58.965 37.037 8.85 0.00 0.00 3.14
3077 3734 6.876257 GCCAATCTAATACTAGTAGCTTGCAT 59.124 38.462 8.85 0.00 0.00 3.96
3078 3735 6.042093 AGCCAATCTAATACTAGTAGCTTGCA 59.958 38.462 8.85 0.00 0.00 4.08
3079 3736 6.459923 AGCCAATCTAATACTAGTAGCTTGC 58.540 40.000 8.85 3.44 0.00 4.01
3088 3745 9.682465 ACGTCTCATATAGCCAATCTAATACTA 57.318 33.333 0.00 0.00 0.00 1.82
3089 3746 8.462811 CACGTCTCATATAGCCAATCTAATACT 58.537 37.037 0.00 0.00 0.00 2.12
3090 3747 7.702772 CCACGTCTCATATAGCCAATCTAATAC 59.297 40.741 0.00 0.00 0.00 1.89
3101 3758 3.371102 TCTTGCCACGTCTCATATAGC 57.629 47.619 0.00 0.00 0.00 2.97
3112 3769 6.176975 TGTTTGTTATATCTTCTTGCCACG 57.823 37.500 0.00 0.00 0.00 4.94
3227 3884 9.344772 GTCATCTCCAGAGTTAGACTTAATAGA 57.655 37.037 0.00 0.00 0.00 1.98
3236 3893 4.026744 CCTTGGTCATCTCCAGAGTTAGA 58.973 47.826 0.00 0.00 38.80 2.10
3246 3903 1.410517 TGCGAGATCCTTGGTCATCTC 59.589 52.381 7.79 7.79 41.15 2.75
3255 3912 1.107114 ATGAGTCGTGCGAGATCCTT 58.893 50.000 0.00 0.00 0.00 3.36
3258 3915 1.471964 GTCATGAGTCGTGCGAGATC 58.528 55.000 7.52 0.00 0.00 2.75
3280 3937 6.546428 ACTAGGCTAAAAGCTACATTCTCA 57.454 37.500 0.00 0.00 41.99 3.27
3343 4000 0.760945 ATTCTCTAGCCCGGGAGTGG 60.761 60.000 29.31 13.03 0.00 4.00
3346 4003 1.996798 TACATTCTCTAGCCCGGGAG 58.003 55.000 29.31 14.83 0.00 4.30
3347 4004 2.110188 AGATACATTCTCTAGCCCGGGA 59.890 50.000 29.31 2.11 0.00 5.14
3377 4034 6.387041 TCGAGTACATGGATTACACTTAGG 57.613 41.667 0.00 0.00 0.00 2.69
3378 4035 6.039493 ACCTCGAGTACATGGATTACACTTAG 59.961 42.308 12.31 0.00 0.00 2.18
3404 4063 5.197451 TGGTACCCCTTAGCAATGTATTTG 58.803 41.667 10.07 0.00 35.19 2.32
3471 4130 3.244735 TGAAATCGGGTTCTTGGATGTGA 60.245 43.478 1.57 0.00 0.00 3.58
3479 4138 7.360607 CGTGTTATAGTTTGAAATCGGGTTCTT 60.361 37.037 1.57 0.00 0.00 2.52
3487 4147 5.878669 ACTCCCCGTGTTATAGTTTGAAATC 59.121 40.000 0.00 0.00 0.00 2.17
3496 4156 7.910441 TTTTCTAAAACTCCCCGTGTTATAG 57.090 36.000 0.00 0.00 0.00 1.31
3671 4332 8.682710 GGTCCACATTCTTTGCTATATGTAAAA 58.317 33.333 0.00 0.00 30.25 1.52
3683 4344 1.271379 ACCCGAGGTCCACATTCTTTG 60.271 52.381 0.00 0.00 0.00 2.77
3686 4347 1.983224 CACCCGAGGTCCACATTCT 59.017 57.895 0.00 0.00 31.02 2.40


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

AutoCloner maintained by Alex Coulton.