Multiple sequence alignment - TraesCS2D01G276900

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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 TraesCS2D01G276900 chr2D 100.000 4843 0 0 1 4843 346573770 346578612 0.000000e+00 8944.0
1 TraesCS2D01G276900 chr2D 93.173 249 17 0 4001 4249 428658583 428658335 2.750000e-97 366.0
2 TraesCS2D01G276900 chr2D 89.831 59 2 4 4000 4055 34269653 34269710 6.720000e-09 73.1
3 TraesCS2D01G276900 chr2A 90.743 2031 76 33 461 2453 460899135 460901091 0.000000e+00 2606.0
4 TraesCS2D01G276900 chr2A 94.258 1550 50 26 2473 4004 460901073 460902601 0.000000e+00 2333.0
5 TraesCS2D01G276900 chr2A 91.528 602 13 14 4244 4843 460902603 460903168 0.000000e+00 795.0
6 TraesCS2D01G276900 chr2B 92.000 1700 80 11 789 2443 412399377 412401065 0.000000e+00 2335.0
7 TraesCS2D01G276900 chr2B 93.357 1385 54 21 2515 3882 412401083 412402446 0.000000e+00 2013.0
8 TraesCS2D01G276900 chr2B 88.636 792 31 28 3 764 412398616 412399378 0.000000e+00 909.0
9 TraesCS2D01G276900 chr2B 95.954 346 13 1 4498 4843 412402667 412403011 1.180000e-155 560.0
10 TraesCS2D01G276900 chr2B 91.667 60 2 3 4002 4060 510793525 510793582 4.020000e-11 80.5
11 TraesCS2D01G276900 chr7D 89.710 1069 96 7 2538 3603 91679571 91678514 0.000000e+00 1352.0
12 TraesCS2D01G276900 chr7D 90.909 330 30 0 2019 2348 91681370 91681041 1.240000e-120 444.0
13 TraesCS2D01G276900 chr7D 97.826 46 1 0 4002 4047 21942015 21942060 4.020000e-11 80.5
14 TraesCS2D01G276900 chr7B 86.223 1263 138 19 2346 3603 43248915 43250146 0.000000e+00 1336.0
15 TraesCS2D01G276900 chr7B 87.216 485 52 3 1801 2283 43247525 43248001 1.190000e-150 544.0
16 TraesCS2D01G276900 chr7B 91.228 57 2 3 4002 4055 674298804 674298748 1.870000e-09 75.0
17 TraesCS2D01G276900 chr7A 88.920 1074 98 15 2538 3605 93252345 93251287 0.000000e+00 1304.0
18 TraesCS2D01G276900 chr7A 86.562 320 30 5 1815 2130 93253161 93252851 1.670000e-89 340.0
19 TraesCS2D01G276900 chr5D 86.093 755 88 9 2783 3521 543586796 543586043 0.000000e+00 797.0
20 TraesCS2D01G276900 chr5D 92.105 152 12 0 2057 2208 543587234 543587083 1.060000e-51 215.0
21 TraesCS2D01G276900 chr5A 90.000 470 45 2 2750 3219 9593671 9593204 1.490000e-169 606.0
22 TraesCS2D01G276900 chr5A 88.342 386 39 6 1969 2348 9595523 9595138 4.420000e-125 459.0
23 TraesCS2D01G276900 chr5A 87.080 387 41 5 3223 3603 9590239 9589856 3.460000e-116 429.0
24 TraesCS2D01G276900 chr5A 91.071 56 3 2 4000 4053 296178096 296178151 1.870000e-09 75.0
25 TraesCS2D01G276900 chr1A 90.040 251 24 1 4000 4249 297743668 297743918 1.680000e-84 324.0
26 TraesCS2D01G276900 chr3A 82.727 110 18 1 4485 4594 455780142 455780250 3.990000e-16 97.1
27 TraesCS2D01G276900 chr3A 92.593 54 4 0 3994 4047 623194963 623195016 1.450000e-10 78.7
28 TraesCS2D01G276900 chr3B 92.308 52 2 2 4005 4055 236036773 236036723 6.720000e-09 73.1


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 TraesCS2D01G276900 chr2D 346573770 346578612 4842 False 8944.000000 8944 100.000000 1 4843 1 chr2D.!!$F2 4842
1 TraesCS2D01G276900 chr2A 460899135 460903168 4033 False 1911.333333 2606 92.176333 461 4843 3 chr2A.!!$F1 4382
2 TraesCS2D01G276900 chr2B 412398616 412403011 4395 False 1454.250000 2335 92.486750 3 4843 4 chr2B.!!$F2 4840
3 TraesCS2D01G276900 chr7D 91678514 91681370 2856 True 898.000000 1352 90.309500 2019 3603 2 chr7D.!!$R1 1584
4 TraesCS2D01G276900 chr7B 43247525 43250146 2621 False 940.000000 1336 86.719500 1801 3603 2 chr7B.!!$F1 1802
5 TraesCS2D01G276900 chr7A 93251287 93253161 1874 True 822.000000 1304 87.741000 1815 3605 2 chr7A.!!$R1 1790
6 TraesCS2D01G276900 chr5D 543586043 543587234 1191 True 506.000000 797 89.099000 2057 3521 2 chr5D.!!$R1 1464
7 TraesCS2D01G276900 chr5A 9589856 9595523 5667 True 498.000000 606 88.474000 1969 3603 3 chr5A.!!$R1 1634

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
820 862 0.613777 CGGGCCTTCTAGAACCAACT 59.386 55.0 12.77 0.00 0.00 3.16 F
1857 1948 0.109919 TGTGAGTCAATCGGTCGACG 60.110 55.0 9.92 5.26 46.11 5.12 F
2490 3533 0.239613 TTGTGTGTGTGTGTGTGTGC 59.760 50.0 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 3514 0.239613 GCACACACACACACACACAA 59.760 50.000 0.00 0.00 0.00 3.33 R
3834 9135 2.838736 TGTTCTTCTGCAGAGGTCAAC 58.161 47.619 23.56 20.52 31.12 3.18 R
4215 9517 0.104855 CGGAGATTTGGATGGAGCGA 59.895 55.000 0.00 0.00 0.00 4.93 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
297 316 2.303022 TGATCTGAACAGAAGGGACCAC 59.697 50.000 8.59 0.00 41.36 4.16
348 367 2.674796 AGACCAACCGCTACATCTTC 57.325 50.000 0.00 0.00 0.00 2.87
358 377 6.222038 ACCGCTACATCTTCTCTCATTTTA 57.778 37.500 0.00 0.00 0.00 1.52
453 472 8.279970 TGCTAATACACAGCAAAATACAGAAT 57.720 30.769 0.00 0.00 45.71 2.40
454 473 8.739039 TGCTAATACACAGCAAAATACAGAATT 58.261 29.630 0.00 0.00 45.71 2.17
455 474 9.226345 GCTAATACACAGCAAAATACAGAATTC 57.774 33.333 0.00 0.00 38.93 2.17
506 535 2.689034 AGTACCTGGGCTGGAGGC 60.689 66.667 0.00 0.00 40.90 4.70
527 556 1.314581 CGTTTCGAATTTGCCGACAC 58.685 50.000 0.00 0.00 35.61 3.67
531 560 3.733024 TTCGAATTTGCCGACACATAC 57.267 42.857 0.00 0.00 35.61 2.39
541 572 2.601804 CCGACACATACACACGATCAA 58.398 47.619 0.00 0.00 0.00 2.57
597 628 2.113986 AGCCTGGCACCAGACAAC 59.886 61.111 22.65 4.78 46.30 3.32
607 638 2.316867 CCAGACAACGACGCATGCA 61.317 57.895 19.57 0.00 0.00 3.96
699 740 0.808125 TTTTCACACACTGCTGCGTT 59.192 45.000 0.00 0.00 0.00 4.84
742 783 2.591715 GGCCACGGCGCTATGAAT 60.592 61.111 6.90 0.00 43.06 2.57
762 803 1.373497 GTGTCAGCCCAGTCACGAG 60.373 63.158 0.00 0.00 0.00 4.18
820 862 0.613777 CGGGCCTTCTAGAACCAACT 59.386 55.000 12.77 0.00 0.00 3.16
886 929 2.202932 CCCAGGATTCCTCGCGTG 60.203 66.667 5.77 2.75 0.00 5.34
921 971 1.682854 GATCTCAGCCCAGAGAGACAG 59.317 57.143 7.14 0.00 46.90 3.51
988 1038 4.241555 ATCTCCGGCCACGCATCC 62.242 66.667 2.24 0.00 39.22 3.51
1056 1106 2.202676 CCTCCGTGCGCTCTCTTC 60.203 66.667 9.73 0.00 0.00 2.87
1065 1115 1.153549 CGCTCTCTTCTTTCCCCCG 60.154 63.158 0.00 0.00 0.00 5.73
1156 1206 1.017701 CCGTCGGCCTCAAGGTAAAC 61.018 60.000 0.00 0.00 37.57 2.01
1164 1214 3.751698 GGCCTCAAGGTAAACAGTTACTG 59.248 47.826 11.21 11.21 39.73 2.74
1230 1283 2.658707 GGCGCGCGAGATTGGTATC 61.659 63.158 37.18 11.43 0.00 2.24
1231 1284 2.658707 GCGCGCGAGATTGGTATCC 61.659 63.158 37.18 6.98 0.00 2.59
1239 1292 2.576615 GAGATTGGTATCCTTGGTGCC 58.423 52.381 0.00 0.00 0.00 5.01
1253 1306 0.826062 GGTGCCAAGGATGATTTGGG 59.174 55.000 6.19 0.00 44.21 4.12
1278 1331 5.005779 CGATTCACTGGCTAATTGACTACAC 59.994 44.000 0.00 0.00 0.00 2.90
1340 1423 1.203523 GGAGATCGCAGTCAGTTCACT 59.796 52.381 0.00 0.00 0.00 3.41
1468 1551 2.436646 GTGATGGGCACTCGGTGG 60.437 66.667 6.23 0.00 44.27 4.61
1488 1571 7.068962 TCGGTGGTTGTATGATCTATTGAGTAA 59.931 37.037 0.00 0.00 0.00 2.24
1510 1593 7.827729 AGTAATTTAGTGGTTTCTATGGTGGTC 59.172 37.037 0.00 0.00 0.00 4.02
1511 1594 2.762535 AGTGGTTTCTATGGTGGTCG 57.237 50.000 0.00 0.00 0.00 4.79
1774 1861 5.048083 GTGTTAGATGATTGGAAAAGCACCA 60.048 40.000 0.00 0.00 35.47 4.17
1779 1866 3.149196 TGATTGGAAAAGCACCAGAGAC 58.851 45.455 0.00 0.00 38.70 3.36
1780 1867 2.727123 TTGGAAAAGCACCAGAGACA 57.273 45.000 0.00 0.00 38.70 3.41
1785 1872 4.134563 GGAAAAGCACCAGAGACAACTTA 58.865 43.478 0.00 0.00 0.00 2.24
1834 1925 1.869767 CAAGTCAGTTGTGTGAGCTCC 59.130 52.381 12.15 3.09 0.00 4.70
1835 1926 0.394565 AGTCAGTTGTGTGAGCTCCC 59.605 55.000 12.15 0.00 0.00 4.30
1857 1948 0.109919 TGTGAGTCAATCGGTCGACG 60.110 55.000 9.92 5.26 46.11 5.12
1905 1996 1.112113 TAGCCTAGAGAGGTTTGCCG 58.888 55.000 0.00 0.00 45.78 5.69
2166 2266 2.225779 TGGAAGATACAGAAGGGGGACA 60.226 50.000 0.00 0.00 0.00 4.02
2295 2709 6.271391 TGTTTGGAGGTTTCCTATGTAGAGAA 59.729 38.462 0.00 0.00 44.36 2.87
2333 2747 7.447243 AGCGTAGTTATGAGAACGTTATTTC 57.553 36.000 0.00 0.04 37.64 2.17
2454 3497 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2455 3498 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2457 3500 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2459 3502 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2461 3504 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2462 3505 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2465 3508 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2466 3509 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2467 3510 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2468 3511 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2471 3514 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
2472 3515 1.950216 TGTGTGTGTGTGTGTGTGTTT 59.050 42.857 0.00 0.00 0.00 2.83
2474 3517 1.950216 TGTGTGTGTGTGTGTGTTTGT 59.050 42.857 0.00 0.00 0.00 2.83
2475 3518 2.287248 TGTGTGTGTGTGTGTGTTTGTG 60.287 45.455 0.00 0.00 0.00 3.33
2476 3519 1.950216 TGTGTGTGTGTGTGTTTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
2477 3520 2.287248 TGTGTGTGTGTGTGTTTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
2478 3521 1.950216 TGTGTGTGTGTGTTTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
2479 3522 2.287248 TGTGTGTGTGTGTTTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
2480 3523 1.950216 TGTGTGTGTGTTTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
2481 3524 2.287248 TGTGTGTGTGTTTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
2485 3528 2.287248 TGTGTGTTTGTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
2486 3529 1.950216 TGTGTTTGTGTGTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
2489 3532 2.287248 TGTTTGTGTGTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
2490 3533 0.239613 TTGTGTGTGTGTGTGTGTGC 59.760 50.000 0.00 0.00 0.00 4.57
2493 3536 0.450983 TGTGTGTGTGTGTGTGCATG 59.549 50.000 0.00 0.00 0.00 4.06
2494 3537 0.731994 GTGTGTGTGTGTGTGCATGA 59.268 50.000 0.00 0.00 0.00 3.07
2495 3538 1.132073 GTGTGTGTGTGTGTGCATGAA 59.868 47.619 0.00 0.00 0.00 2.57
2496 3539 1.815003 TGTGTGTGTGTGTGCATGAAA 59.185 42.857 0.00 0.00 0.00 2.69
2497 3540 2.184448 GTGTGTGTGTGTGCATGAAAC 58.816 47.619 0.00 0.00 0.00 2.78
2498 3541 1.815003 TGTGTGTGTGTGCATGAAACA 59.185 42.857 0.00 0.00 0.00 2.83
2499 3542 2.229784 TGTGTGTGTGTGCATGAAACAA 59.770 40.909 0.00 0.00 0.00 2.83
2500 3543 2.598192 GTGTGTGTGTGCATGAAACAAC 59.402 45.455 0.00 2.76 0.00 3.32
2504 4266 2.282290 GTGTGTGCATGAAACAACTTGC 59.718 45.455 0.00 0.00 40.00 4.01
2506 4268 2.536803 GTGTGCATGAAACAACTTGCTG 59.463 45.455 0.00 0.00 40.16 4.41
2509 4271 4.277921 TGTGCATGAAACAACTTGCTGATA 59.722 37.500 0.00 0.00 40.16 2.15
2512 4274 5.416639 TGCATGAAACAACTTGCTGATAGAT 59.583 36.000 0.00 0.00 40.16 1.98
2513 4275 5.742453 GCATGAAACAACTTGCTGATAGATG 59.258 40.000 0.00 0.00 37.75 2.90
2641 4403 1.083806 TGATCAAGTCGTCGCCATGC 61.084 55.000 0.00 0.00 0.00 4.06
2662 4424 4.333649 TGCTGAACTCTTTTGTGAGTGAAG 59.666 41.667 0.00 0.00 45.49 3.02
2788 5079 9.647797 TGTAAACTCGTTAATGTGATAATGTCT 57.352 29.630 3.82 0.00 0.00 3.41
2897 5188 3.334054 GAGGGTGCTGGGCTTCCT 61.334 66.667 4.56 4.56 35.32 3.36
3475 8742 1.406539 CCATGCCACTGGTAAGATTGC 59.593 52.381 0.00 0.00 0.00 3.56
3521 8794 3.688272 GTCGACGCTTGCTAGTATTACA 58.312 45.455 0.00 0.00 0.00 2.41
3674 8964 6.203723 GGGTATTGAGAGATATGAGTTGCAAC 59.796 42.308 22.17 22.17 0.00 4.17
3808 9109 5.738909 CCAGAATTCAGTATCACCTTCAGT 58.261 41.667 8.44 0.00 0.00 3.41
3834 9135 3.064207 TCTCGATCCAAACAAAGAACCG 58.936 45.455 0.00 0.00 0.00 4.44
3837 9138 3.002862 TCGATCCAAACAAAGAACCGTTG 59.997 43.478 0.00 0.00 0.00 4.10
3859 9160 3.070018 ACCTCTGCAGAAGAACAAATCG 58.930 45.455 19.22 2.40 33.37 3.34
3898 9199 0.333993 AGAACAGTAGGGGCGTAGGA 59.666 55.000 0.00 0.00 0.00 2.94
3984 9286 5.699839 CCATTTAGTCGTTCCAGAAAAAGG 58.300 41.667 0.00 0.00 0.00 3.11
4004 9306 3.714280 AGGGGTTTGGTGCACTAATTTTT 59.286 39.130 16.93 0.00 0.00 1.94
4028 9330 5.898630 TTAAAACGAGGCAAAAGATTTGC 57.101 34.783 17.18 17.18 44.22 3.68
4042 9344 9.628746 GCAAAAGATTTGCCATTTTTATTGAAT 57.371 25.926 15.12 0.00 39.38 2.57
4050 9352 9.874205 TTTGCCATTTTTATTGAATAAGAGAGG 57.126 29.630 0.00 1.91 0.00 3.69
4051 9353 8.821686 TGCCATTTTTATTGAATAAGAGAGGA 57.178 30.769 10.40 0.00 0.00 3.71
4052 9354 8.906867 TGCCATTTTTATTGAATAAGAGAGGAG 58.093 33.333 10.40 0.00 0.00 3.69
4053 9355 8.907885 GCCATTTTTATTGAATAAGAGAGGAGT 58.092 33.333 10.40 0.00 0.00 3.85
4062 9364 9.883142 ATTGAATAAGAGAGGAGTTTAGAGTTG 57.117 33.333 0.00 0.00 0.00 3.16
4063 9365 8.651589 TGAATAAGAGAGGAGTTTAGAGTTGA 57.348 34.615 0.00 0.00 0.00 3.18
4064 9366 9.261035 TGAATAAGAGAGGAGTTTAGAGTTGAT 57.739 33.333 0.00 0.00 0.00 2.57
4065 9367 9.528018 GAATAAGAGAGGAGTTTAGAGTTGATG 57.472 37.037 0.00 0.00 0.00 3.07
4066 9368 5.930837 AGAGAGGAGTTTAGAGTTGATGG 57.069 43.478 0.00 0.00 0.00 3.51
4067 9369 4.161377 AGAGAGGAGTTTAGAGTTGATGGC 59.839 45.833 0.00 0.00 0.00 4.40
4068 9370 3.198853 AGAGGAGTTTAGAGTTGATGGCC 59.801 47.826 0.00 0.00 0.00 5.36
4069 9371 2.912956 AGGAGTTTAGAGTTGATGGCCA 59.087 45.455 8.56 8.56 0.00 5.36
4070 9372 3.330701 AGGAGTTTAGAGTTGATGGCCAA 59.669 43.478 10.96 0.00 0.00 4.52
4071 9373 4.079253 GGAGTTTAGAGTTGATGGCCAAA 58.921 43.478 10.96 0.00 36.36 3.28
4072 9374 4.156739 GGAGTTTAGAGTTGATGGCCAAAG 59.843 45.833 10.96 0.00 36.36 2.77
4073 9375 4.082125 AGTTTAGAGTTGATGGCCAAAGG 58.918 43.478 10.96 0.00 36.36 3.11
4099 9401 4.383861 CAGGCCACTGCTCTCGCA 62.384 66.667 5.01 0.00 45.60 5.10
4115 9417 6.769608 CTCTCGCAGCATAATATTACACAA 57.230 37.500 0.00 0.00 0.00 3.33
4116 9418 7.177498 CTCTCGCAGCATAATATTACACAAA 57.823 36.000 0.00 0.00 0.00 2.83
4117 9419 7.728847 TCTCGCAGCATAATATTACACAAAT 57.271 32.000 0.00 0.00 0.00 2.32
4118 9420 7.575365 TCTCGCAGCATAATATTACACAAATG 58.425 34.615 0.00 0.00 0.00 2.32
4119 9421 6.142139 TCGCAGCATAATATTACACAAATGC 58.858 36.000 9.61 9.61 39.93 3.56
4121 9423 6.638063 CGCAGCATAATATTACACAAATGCTT 59.362 34.615 15.34 3.02 45.70 3.91
4122 9424 7.167968 CGCAGCATAATATTACACAAATGCTTT 59.832 33.333 15.34 0.00 45.70 3.51
4123 9425 8.270799 GCAGCATAATATTACACAAATGCTTTG 58.729 33.333 15.34 9.59 45.70 2.77
4124 9426 8.270799 CAGCATAATATTACACAAATGCTTTGC 58.729 33.333 15.34 8.97 45.70 3.68
4125 9427 7.167968 AGCATAATATTACACAAATGCTTTGCG 59.832 33.333 13.10 2.96 45.70 4.85
4126 9428 5.701029 AATATTACACAAATGCTTTGCGC 57.299 34.783 0.00 0.00 44.39 6.09
4127 9429 1.777101 TTACACAAATGCTTTGCGCC 58.223 45.000 4.18 0.00 44.39 6.53
4128 9430 0.038709 TACACAAATGCTTTGCGCCC 60.039 50.000 4.18 0.00 44.39 6.13
4129 9431 2.049248 ACAAATGCTTTGCGCCCG 60.049 55.556 4.18 0.00 44.39 6.13
4130 9432 3.481024 CAAATGCTTTGCGCCCGC 61.481 61.111 4.18 5.60 42.35 6.13
4153 9455 2.556534 GCTTCAAAGCGAGCATTCAT 57.443 45.000 0.00 0.00 42.88 2.57
4154 9456 2.448219 GCTTCAAAGCGAGCATTCATC 58.552 47.619 0.00 0.00 42.88 2.92
4155 9457 2.097142 GCTTCAAAGCGAGCATTCATCT 59.903 45.455 0.00 0.00 42.88 2.90
4156 9458 3.427233 GCTTCAAAGCGAGCATTCATCTT 60.427 43.478 0.00 0.00 42.88 2.40
4157 9459 4.730657 CTTCAAAGCGAGCATTCATCTTT 58.269 39.130 0.00 0.00 0.00 2.52
4158 9460 5.674569 GCTTCAAAGCGAGCATTCATCTTTA 60.675 40.000 0.00 0.00 42.88 1.85
4159 9461 5.878332 TCAAAGCGAGCATTCATCTTTAA 57.122 34.783 0.00 0.00 29.87 1.52
4160 9462 6.441093 TCAAAGCGAGCATTCATCTTTAAT 57.559 33.333 0.00 0.00 29.87 1.40
4161 9463 6.489675 TCAAAGCGAGCATTCATCTTTAATC 58.510 36.000 0.00 0.00 29.87 1.75
4162 9464 6.317140 TCAAAGCGAGCATTCATCTTTAATCT 59.683 34.615 0.00 0.00 29.87 2.40
4163 9465 6.690194 AAGCGAGCATTCATCTTTAATCTT 57.310 33.333 0.00 0.00 0.00 2.40
4164 9466 6.057627 AGCGAGCATTCATCTTTAATCTTG 57.942 37.500 0.00 0.00 0.00 3.02
4165 9467 5.819379 AGCGAGCATTCATCTTTAATCTTGA 59.181 36.000 0.00 0.00 0.00 3.02
4166 9468 5.906285 GCGAGCATTCATCTTTAATCTTGAC 59.094 40.000 0.00 0.00 0.00 3.18
4167 9469 6.125419 CGAGCATTCATCTTTAATCTTGACG 58.875 40.000 0.00 0.00 0.00 4.35
4168 9470 6.019559 CGAGCATTCATCTTTAATCTTGACGA 60.020 38.462 0.00 0.00 0.00 4.20
4169 9471 7.009568 AGCATTCATCTTTAATCTTGACGAC 57.990 36.000 0.00 0.00 0.00 4.34
4170 9472 6.820656 AGCATTCATCTTTAATCTTGACGACT 59.179 34.615 0.00 0.00 0.00 4.18
4171 9473 7.981789 AGCATTCATCTTTAATCTTGACGACTA 59.018 33.333 0.00 0.00 0.00 2.59
4172 9474 8.604035 GCATTCATCTTTAATCTTGACGACTAA 58.396 33.333 0.00 0.00 0.00 2.24
4173 9475 9.907576 CATTCATCTTTAATCTTGACGACTAAC 57.092 33.333 0.00 0.00 0.00 2.34
4174 9476 9.653287 ATTCATCTTTAATCTTGACGACTAACA 57.347 29.630 0.00 0.00 0.00 2.41
4175 9477 8.462143 TCATCTTTAATCTTGACGACTAACAC 57.538 34.615 0.00 0.00 0.00 3.32
4176 9478 8.304596 TCATCTTTAATCTTGACGACTAACACT 58.695 33.333 0.00 0.00 0.00 3.55
4177 9479 8.587950 CATCTTTAATCTTGACGACTAACACTC 58.412 37.037 0.00 0.00 0.00 3.51
4178 9480 7.088905 TCTTTAATCTTGACGACTAACACTCC 58.911 38.462 0.00 0.00 0.00 3.85
4179 9481 6.585695 TTAATCTTGACGACTAACACTCCT 57.414 37.500 0.00 0.00 0.00 3.69
4180 9482 7.692460 TTAATCTTGACGACTAACACTCCTA 57.308 36.000 0.00 0.00 0.00 2.94
4181 9483 5.564048 ATCTTGACGACTAACACTCCTAC 57.436 43.478 0.00 0.00 0.00 3.18
4182 9484 3.755378 TCTTGACGACTAACACTCCTACC 59.245 47.826 0.00 0.00 0.00 3.18
4183 9485 3.144657 TGACGACTAACACTCCTACCA 57.855 47.619 0.00 0.00 0.00 3.25
4184 9486 3.079578 TGACGACTAACACTCCTACCAG 58.920 50.000 0.00 0.00 0.00 4.00
4185 9487 2.422832 GACGACTAACACTCCTACCAGG 59.577 54.545 0.00 0.00 36.46 4.45
4186 9488 2.040813 ACGACTAACACTCCTACCAGGA 59.959 50.000 0.00 0.00 43.43 3.86
4187 9489 2.422832 CGACTAACACTCCTACCAGGAC 59.577 54.545 0.00 0.00 40.06 3.85
4188 9490 2.759535 GACTAACACTCCTACCAGGACC 59.240 54.545 0.00 0.00 40.06 4.46
4189 9491 1.749634 CTAACACTCCTACCAGGACCG 59.250 57.143 0.00 0.00 40.06 4.79
4190 9492 1.542187 AACACTCCTACCAGGACCGC 61.542 60.000 0.00 0.00 40.06 5.68
4191 9493 2.754658 ACTCCTACCAGGACCGCG 60.755 66.667 0.00 0.00 40.06 6.46
4192 9494 3.528370 CTCCTACCAGGACCGCGG 61.528 72.222 26.86 26.86 40.06 6.46
4193 9495 4.371417 TCCTACCAGGACCGCGGT 62.371 66.667 34.89 34.89 40.06 5.68
4194 9496 2.440796 CCTACCAGGACCGCGGTA 60.441 66.667 34.36 14.16 37.67 4.02
4195 9497 1.831286 CCTACCAGGACCGCGGTAT 60.831 63.158 34.36 20.99 37.67 2.73
4196 9498 1.397390 CCTACCAGGACCGCGGTATT 61.397 60.000 34.36 20.02 37.67 1.89
4197 9499 1.321474 CTACCAGGACCGCGGTATTA 58.679 55.000 34.36 16.20 37.15 0.98
4198 9500 1.000938 CTACCAGGACCGCGGTATTAC 60.001 57.143 34.36 21.32 37.15 1.89
4199 9501 1.299620 CCAGGACCGCGGTATTACG 60.300 63.158 34.36 17.62 0.00 3.18
4207 9509 0.652071 CGCGGTATTACGGAAAACCC 59.348 55.000 0.00 0.00 0.00 4.11
4208 9510 1.736612 GCGGTATTACGGAAAACCCA 58.263 50.000 5.64 0.00 34.14 4.51
4209 9511 2.083002 GCGGTATTACGGAAAACCCAA 58.917 47.619 5.64 0.00 34.14 4.12
4210 9512 2.096335 GCGGTATTACGGAAAACCCAAG 59.904 50.000 5.64 0.00 34.14 3.61
4211 9513 2.096335 CGGTATTACGGAAAACCCAAGC 59.904 50.000 0.00 0.00 34.14 4.01
4212 9514 2.096335 GGTATTACGGAAAACCCAAGCG 59.904 50.000 0.00 0.00 34.14 4.68
4213 9515 1.900245 ATTACGGAAAACCCAAGCGT 58.100 45.000 0.00 0.00 34.14 5.07
4214 9516 1.677942 TTACGGAAAACCCAAGCGTT 58.322 45.000 0.00 0.00 34.14 4.84
4215 9517 1.677942 TACGGAAAACCCAAGCGTTT 58.322 45.000 0.00 0.00 37.56 3.60
4216 9518 0.382873 ACGGAAAACCCAAGCGTTTC 59.617 50.000 0.00 0.00 34.89 2.78
4217 9519 0.659123 CGGAAAACCCAAGCGTTTCG 60.659 55.000 0.00 0.00 34.89 3.46
4218 9520 0.937699 GGAAAACCCAAGCGTTTCGC 60.938 55.000 6.00 6.00 43.69 4.70
4230 9532 2.458592 CGTTTCGCTCCATCCAAATC 57.541 50.000 0.00 0.00 0.00 2.17
4231 9533 2.009774 CGTTTCGCTCCATCCAAATCT 58.990 47.619 0.00 0.00 0.00 2.40
4232 9534 2.030946 CGTTTCGCTCCATCCAAATCTC 59.969 50.000 0.00 0.00 0.00 2.75
4233 9535 2.332063 TTCGCTCCATCCAAATCTCC 57.668 50.000 0.00 0.00 0.00 3.71
4234 9536 0.104855 TCGCTCCATCCAAATCTCCG 59.895 55.000 0.00 0.00 0.00 4.63
4235 9537 0.104855 CGCTCCATCCAAATCTCCGA 59.895 55.000 0.00 0.00 0.00 4.55
4236 9538 1.473257 CGCTCCATCCAAATCTCCGAA 60.473 52.381 0.00 0.00 0.00 4.30
4237 9539 2.216898 GCTCCATCCAAATCTCCGAAG 58.783 52.381 0.00 0.00 0.00 3.79
4238 9540 2.158900 GCTCCATCCAAATCTCCGAAGA 60.159 50.000 0.00 0.00 35.54 2.87
4239 9541 3.726607 CTCCATCCAAATCTCCGAAGAG 58.273 50.000 0.00 0.00 41.93 2.85
4265 9567 5.959618 AGCAACTCTAAACAATTACCCAC 57.040 39.130 0.00 0.00 0.00 4.61
4316 9618 1.532868 ACAGCAAATCAAGCTCGTGAC 59.467 47.619 0.00 0.00 41.14 3.67
4324 9626 1.226603 AAGCTCGTGACGATACGGC 60.227 57.895 8.60 8.61 43.85 5.68
4338 9640 3.239026 CGATACGGCGTAAACTACTTGTG 59.761 47.826 24.81 3.47 0.00 3.33
4459 9769 5.008118 TCAAGTTATGTTGTGCGATGACAAA 59.992 36.000 0.00 0.00 37.58 2.83
4464 9774 5.827568 ATGTTGTGCGATGACAAATTTTC 57.172 34.783 0.00 0.00 37.58 2.29
4475 9785 6.509837 CGATGACAAATTTTCAAAGCAAGCAA 60.510 34.615 7.01 0.00 0.00 3.91
4478 9788 6.093771 TGACAAATTTTCAAAGCAAGCAATGT 59.906 30.769 0.00 0.00 0.00 2.71
4479 9789 6.854778 ACAAATTTTCAAAGCAAGCAATGTT 58.145 28.000 0.00 0.00 0.00 2.71
4481 9791 7.813627 ACAAATTTTCAAAGCAAGCAATGTTTT 59.186 25.926 0.00 0.00 42.39 2.43
4482 9792 9.286946 CAAATTTTCAAAGCAAGCAATGTTTTA 57.713 25.926 4.49 0.00 40.04 1.52
4483 9793 9.852091 AAATTTTCAAAGCAAGCAATGTTTTAA 57.148 22.222 4.49 0.00 40.04 1.52
4484 9794 9.505995 AATTTTCAAAGCAAGCAATGTTTTAAG 57.494 25.926 4.49 0.00 40.04 1.85
4485 9795 5.655893 TCAAAGCAAGCAATGTTTTAAGC 57.344 34.783 4.49 0.00 40.04 3.09
4486 9796 5.114780 TCAAAGCAAGCAATGTTTTAAGCA 58.885 33.333 4.49 0.00 40.04 3.91
4487 9797 5.583854 TCAAAGCAAGCAATGTTTTAAGCAA 59.416 32.000 4.49 0.00 40.04 3.91
4488 9798 5.662211 AAGCAAGCAATGTTTTAAGCAAG 57.338 34.783 0.00 0.00 0.00 4.01
4489 9799 3.495753 AGCAAGCAATGTTTTAAGCAAGC 59.504 39.130 0.00 2.49 0.00 4.01
4490 9800 3.248125 GCAAGCAATGTTTTAAGCAAGCA 59.752 39.130 10.78 0.00 0.00 3.91
4491 9801 4.083696 GCAAGCAATGTTTTAAGCAAGCAT 60.084 37.500 10.78 0.00 37.90 3.79
4492 9802 5.561339 GCAAGCAATGTTTTAAGCAAGCATT 60.561 36.000 10.78 0.00 44.67 3.56
4509 9819 2.273557 CATTGCCCATGCTTGCTTTAC 58.726 47.619 0.00 0.00 38.71 2.01
4526 9836 4.754114 GCTTTACAAAATTGCCATCCACAA 59.246 37.500 0.00 0.00 0.00 3.33
4546 9856 6.427547 CCACAAAACAACATAATTTGCCATCT 59.572 34.615 0.00 0.00 37.52 2.90
4555 9865 5.126061 ACATAATTTGCCATCTCAGGTGTTC 59.874 40.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.426292 GCTATTCGTGAGGACCTTTTTGC 60.426 47.826 0.00 0.00 0.00 3.68
75 76 4.961438 TCTGTGGCTATAGCATGATTGA 57.039 40.909 25.53 12.39 44.36 2.57
208 209 6.935167 TCATATGAGTAGCAGTTTCAAGACA 58.065 36.000 0.00 0.00 0.00 3.41
211 212 5.814188 TGCTCATATGAGTAGCAGTTTCAAG 59.186 40.000 28.92 4.79 41.15 3.02
297 316 5.049680 AGCTGTTTACGTACAAGTCCATTTG 60.050 40.000 0.00 0.00 0.00 2.32
348 367 5.449999 GGGCCGGTGTATTTTAAAATGAGAG 60.450 44.000 21.19 9.87 0.00 3.20
358 377 0.745486 GCGTAGGGCCGGTGTATTTT 60.745 55.000 1.90 0.00 34.80 1.82
393 412 7.137426 GCTTCATAATCAGAATTGGCTAACTG 58.863 38.462 0.00 0.00 0.00 3.16
450 469 3.841643 CCAACCTTGCACATCAGAATTC 58.158 45.455 0.00 0.00 0.00 2.17
453 472 0.961019 GCCAACCTTGCACATCAGAA 59.039 50.000 0.00 0.00 0.00 3.02
454 473 0.111061 AGCCAACCTTGCACATCAGA 59.889 50.000 0.00 0.00 0.00 3.27
455 474 0.242825 CAGCCAACCTTGCACATCAG 59.757 55.000 0.00 0.00 0.00 2.90
506 535 0.453782 GTCGGCAAATTCGAAACGGG 60.454 55.000 0.00 0.00 38.42 5.28
527 556 1.267038 GCGTGCTTGATCGTGTGTATG 60.267 52.381 0.00 0.00 0.00 2.39
531 560 0.041400 TTTGCGTGCTTGATCGTGTG 60.041 50.000 0.00 0.00 0.00 3.82
597 628 4.214383 CGAAGGCTGCATGCGTCG 62.214 66.667 14.09 12.42 44.05 5.12
675 716 1.008538 GCAGTGTGTGAAAAGCGGG 60.009 57.895 0.00 0.00 0.00 6.13
699 740 2.809307 TTGGCTCGTTTGGTCCCGA 61.809 57.895 0.00 0.00 0.00 5.14
742 783 2.734591 GTGACTGGGCTGACACGA 59.265 61.111 0.00 0.00 0.00 4.35
784 825 4.107051 GCTGATGTGTGTGCGGCC 62.107 66.667 0.00 0.00 0.00 6.13
820 862 1.884579 GAGTCTGGGCCGTAATATCGA 59.115 52.381 0.00 0.00 0.00 3.59
886 929 2.422479 TGAGATCTATATACGCACGCCC 59.578 50.000 0.00 0.00 0.00 6.13
921 971 0.971386 TTCTTGGGGTACACGTCCTC 59.029 55.000 0.00 0.00 0.00 3.71
988 1038 0.722469 CTGTTTGCGTGTGCTTAGCG 60.722 55.000 0.00 0.00 43.34 4.26
1056 1106 2.275418 CCATGGGACGGGGGAAAG 59.725 66.667 2.85 0.00 0.00 2.62
1065 1115 4.447342 CTGGGGTGGCCATGGGAC 62.447 72.222 9.72 0.00 0.00 4.46
1140 1190 1.053424 ACTGTTTACCTTGAGGCCGA 58.947 50.000 0.00 0.00 39.32 5.54
1156 1206 2.460918 CGCTATCCCGAACAGTAACTG 58.539 52.381 0.00 0.00 37.52 3.16
1164 1214 2.008268 TTCGACCCGCTATCCCGAAC 62.008 60.000 0.00 0.00 34.83 3.95
1171 1224 0.249398 AACAAGCTTCGACCCGCTAT 59.751 50.000 0.00 0.00 34.96 2.97
1239 1292 2.689471 TGAATCGCCCAAATCATCCTTG 59.311 45.455 0.00 0.00 0.00 3.61
1253 1306 2.939103 AGTCAATTAGCCAGTGAATCGC 59.061 45.455 0.00 0.00 0.00 4.58
1380 1463 3.257127 GCTACAGCTAGCTACTTGGCTAT 59.743 47.826 18.86 0.00 42.84 2.97
1417 1500 1.897560 AAGCCGCTAGAGCAAAGTTT 58.102 45.000 7.80 0.00 42.21 2.66
1488 1571 5.183228 CGACCACCATAGAAACCACTAAAT 58.817 41.667 0.00 0.00 0.00 1.40
1511 1594 8.085296 AGAATATATCTAGCTAGTGCAACACAC 58.915 37.037 20.10 6.36 42.78 3.82
1794 1881 9.958180 TGACTTGGTCATCTCAATCTTATTAAA 57.042 29.630 0.00 0.00 37.67 1.52
1795 1882 9.605275 CTGACTTGGTCATCTCAATCTTATTAA 57.395 33.333 0.71 0.00 41.94 1.40
1857 1948 3.258372 GGTTCTTGTGAAAAGAATCCCCC 59.742 47.826 0.46 0.00 38.39 5.40
2295 2709 3.408634 ACTACGCTTGGTGCTATTTTGT 58.591 40.909 0.00 0.00 40.11 2.83
2333 2747 7.725818 ATAACATAGCAAGACTGACATGATG 57.274 36.000 0.00 0.00 0.00 3.07
2454 3497 1.950216 ACAAACACACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
2455 3498 2.287308 ACACAAACACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
2457 3500 2.287308 ACACACAAACACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
2459 3502 2.287308 ACACACACAAACACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
2461 3504 2.287308 ACACACACACAAACACACACAC 60.287 45.455 0.00 0.00 0.00 3.82
2462 3505 1.950216 ACACACACACAAACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
2465 3508 2.287308 ACACACACACACACAAACACAC 60.287 45.455 0.00 0.00 0.00 3.82
2466 3509 1.950216 ACACACACACACACAAACACA 59.050 42.857 0.00 0.00 0.00 3.72
2467 3510 2.287308 ACACACACACACACACAAACAC 60.287 45.455 0.00 0.00 0.00 3.32
2468 3511 1.950216 ACACACACACACACACAAACA 59.050 42.857 0.00 0.00 0.00 2.83
2471 3514 0.239613 GCACACACACACACACACAA 59.760 50.000 0.00 0.00 0.00 3.33
2472 3515 0.886490 TGCACACACACACACACACA 60.886 50.000 0.00 0.00 0.00 3.72
2474 3517 0.450983 CATGCACACACACACACACA 59.549 50.000 0.00 0.00 0.00 3.72
2475 3518 0.731994 TCATGCACACACACACACAC 59.268 50.000 0.00 0.00 0.00 3.82
2476 3519 1.457346 TTCATGCACACACACACACA 58.543 45.000 0.00 0.00 0.00 3.72
2477 3520 2.184448 GTTTCATGCACACACACACAC 58.816 47.619 0.00 0.00 0.00 3.82
2478 3521 1.815003 TGTTTCATGCACACACACACA 59.185 42.857 0.00 0.00 0.00 3.72
2479 3522 2.558265 TGTTTCATGCACACACACAC 57.442 45.000 0.00 0.00 0.00 3.82
2480 3523 2.491298 AGTTGTTTCATGCACACACACA 59.509 40.909 0.00 0.00 0.00 3.72
2481 3524 3.149436 AGTTGTTTCATGCACACACAC 57.851 42.857 0.00 0.00 0.00 3.82
2485 3528 2.536803 CAGCAAGTTGTTTCATGCACAC 59.463 45.455 4.48 0.00 41.18 3.82
2486 3529 2.426381 TCAGCAAGTTGTTTCATGCACA 59.574 40.909 4.48 0.00 41.18 4.57
2489 3532 5.300969 TCTATCAGCAAGTTGTTTCATGC 57.699 39.130 4.48 0.00 39.06 4.06
2490 3533 7.080353 TCATCTATCAGCAAGTTGTTTCATG 57.920 36.000 4.48 0.00 0.00 3.07
2493 3536 7.138692 AGTTCATCTATCAGCAAGTTGTTTC 57.861 36.000 4.48 0.00 0.00 2.78
2494 3537 7.365741 CAAGTTCATCTATCAGCAAGTTGTTT 58.634 34.615 4.48 0.00 0.00 2.83
2495 3538 6.569226 GCAAGTTCATCTATCAGCAAGTTGTT 60.569 38.462 4.48 0.00 32.32 2.83
2496 3539 5.106396 GCAAGTTCATCTATCAGCAAGTTGT 60.106 40.000 4.48 0.00 32.32 3.32
2497 3540 5.123502 AGCAAGTTCATCTATCAGCAAGTTG 59.876 40.000 0.00 0.00 32.70 3.16
2498 3541 5.123502 CAGCAAGTTCATCTATCAGCAAGTT 59.876 40.000 0.00 0.00 0.00 2.66
2499 3542 4.634883 CAGCAAGTTCATCTATCAGCAAGT 59.365 41.667 0.00 0.00 0.00 3.16
2500 3543 4.874396 TCAGCAAGTTCATCTATCAGCAAG 59.126 41.667 0.00 0.00 0.00 4.01
2504 4266 7.063662 GCATCTATCAGCAAGTTCATCTATCAG 59.936 40.741 0.00 0.00 0.00 2.90
2506 4268 6.872547 TGCATCTATCAGCAAGTTCATCTATC 59.127 38.462 0.00 0.00 37.90 2.08
2509 4271 5.032327 TGCATCTATCAGCAAGTTCATCT 57.968 39.130 0.00 0.00 37.90 2.90
2512 4274 5.032327 AGATGCATCTATCAGCAAGTTCA 57.968 39.130 27.73 0.00 44.88 3.18
2513 4275 5.299148 AGAGATGCATCTATCAGCAAGTTC 58.701 41.667 28.78 12.03 44.88 3.01
2641 4403 6.092670 TGAACTTCACTCACAAAAGAGTTCAG 59.907 38.462 10.84 0.00 46.26 3.02
2662 4424 5.215160 GGAAATGTGTTGTCATGAGTGAAC 58.785 41.667 0.00 0.26 35.80 3.18
2788 5079 2.875933 CCTCCGTTCTGTAACAGCAAAA 59.124 45.455 0.00 0.00 35.16 2.44
3475 8742 3.364864 CGATCAGCTCTCTATCTCAACGG 60.365 52.174 0.00 0.00 0.00 4.44
3505 8772 5.581085 AGTCCTTTTGTAATACTAGCAAGCG 59.419 40.000 0.00 0.00 0.00 4.68
3521 8794 4.516698 CACTGTCTGTATGCAAGTCCTTTT 59.483 41.667 0.00 0.00 0.00 2.27
3674 8964 8.360325 TGTTTACGATAGCCATATACAGTTTG 57.640 34.615 0.00 0.00 42.67 2.93
3834 9135 2.838736 TGTTCTTCTGCAGAGGTCAAC 58.161 47.619 23.56 20.52 31.12 3.18
3837 9138 3.124297 CGATTTGTTCTTCTGCAGAGGTC 59.876 47.826 23.56 17.77 31.12 3.85
3859 9160 3.133003 TCTGCTTTGGGCTCTCAGTATAC 59.867 47.826 0.00 0.00 42.39 1.47
3898 9199 4.645136 TGGTCTGCTATATTCAAGAGACGT 59.355 41.667 0.00 0.00 32.32 4.34
4004 9306 6.710611 GCAAATCTTTTGCCTCGTTTTAAAA 58.289 32.000 12.74 0.00 39.38 1.52
4005 9307 6.280537 GCAAATCTTTTGCCTCGTTTTAAA 57.719 33.333 12.74 0.00 39.38 1.52
4006 9308 5.898630 GCAAATCTTTTGCCTCGTTTTAA 57.101 34.783 12.74 0.00 39.38 1.52
4016 9318 9.628746 ATTCAATAAAAATGGCAAATCTTTTGC 57.371 25.926 14.88 14.88 44.22 3.68
4024 9326 9.874205 CCTCTCTTATTCAATAAAAATGGCAAA 57.126 29.630 0.00 0.00 0.00 3.68
4025 9327 9.253832 TCCTCTCTTATTCAATAAAAATGGCAA 57.746 29.630 0.00 0.00 0.00 4.52
4026 9328 8.821686 TCCTCTCTTATTCAATAAAAATGGCA 57.178 30.769 0.00 0.00 0.00 4.92
4027 9329 8.907885 ACTCCTCTCTTATTCAATAAAAATGGC 58.092 33.333 0.00 0.00 0.00 4.40
4036 9338 9.883142 CAACTCTAAACTCCTCTCTTATTCAAT 57.117 33.333 0.00 0.00 0.00 2.57
4037 9339 9.090103 TCAACTCTAAACTCCTCTCTTATTCAA 57.910 33.333 0.00 0.00 0.00 2.69
4038 9340 8.651589 TCAACTCTAAACTCCTCTCTTATTCA 57.348 34.615 0.00 0.00 0.00 2.57
4039 9341 9.528018 CATCAACTCTAAACTCCTCTCTTATTC 57.472 37.037 0.00 0.00 0.00 1.75
4040 9342 8.482128 CCATCAACTCTAAACTCCTCTCTTATT 58.518 37.037 0.00 0.00 0.00 1.40
4041 9343 7.418483 GCCATCAACTCTAAACTCCTCTCTTAT 60.418 40.741 0.00 0.00 0.00 1.73
4042 9344 6.127310 GCCATCAACTCTAAACTCCTCTCTTA 60.127 42.308 0.00 0.00 0.00 2.10
4043 9345 5.337975 GCCATCAACTCTAAACTCCTCTCTT 60.338 44.000 0.00 0.00 0.00 2.85
4044 9346 4.161377 GCCATCAACTCTAAACTCCTCTCT 59.839 45.833 0.00 0.00 0.00 3.10
4045 9347 4.438148 GCCATCAACTCTAAACTCCTCTC 58.562 47.826 0.00 0.00 0.00 3.20
4046 9348 3.198853 GGCCATCAACTCTAAACTCCTCT 59.801 47.826 0.00 0.00 0.00 3.69
4047 9349 3.055094 TGGCCATCAACTCTAAACTCCTC 60.055 47.826 0.00 0.00 0.00 3.71
4048 9350 2.912956 TGGCCATCAACTCTAAACTCCT 59.087 45.455 0.00 0.00 0.00 3.69
4049 9351 3.350219 TGGCCATCAACTCTAAACTCC 57.650 47.619 0.00 0.00 0.00 3.85
4050 9352 4.156739 CCTTTGGCCATCAACTCTAAACTC 59.843 45.833 6.09 0.00 34.67 3.01
4051 9353 4.082125 CCTTTGGCCATCAACTCTAAACT 58.918 43.478 6.09 0.00 34.67 2.66
4052 9354 3.367395 GCCTTTGGCCATCAACTCTAAAC 60.367 47.826 6.09 0.00 44.06 2.01
4053 9355 2.825532 GCCTTTGGCCATCAACTCTAAA 59.174 45.455 6.09 0.00 44.06 1.85
4054 9356 2.446435 GCCTTTGGCCATCAACTCTAA 58.554 47.619 6.09 0.00 44.06 2.10
4055 9357 2.128771 GCCTTTGGCCATCAACTCTA 57.871 50.000 6.09 0.00 44.06 2.43
4056 9358 2.967270 GCCTTTGGCCATCAACTCT 58.033 52.632 6.09 0.00 44.06 3.24
4075 9377 1.209019 AGAGCAGTGGCCTGTAATCAG 59.791 52.381 3.32 0.00 42.56 2.90
4076 9378 1.208052 GAGAGCAGTGGCCTGTAATCA 59.792 52.381 3.32 0.00 42.56 2.57
4077 9379 1.804372 CGAGAGCAGTGGCCTGTAATC 60.804 57.143 3.32 0.00 42.56 1.75
4078 9380 0.176680 CGAGAGCAGTGGCCTGTAAT 59.823 55.000 3.32 0.00 42.56 1.89
4079 9381 1.591703 CGAGAGCAGTGGCCTGTAA 59.408 57.895 3.32 0.00 42.56 2.41
4080 9382 3.288484 CGAGAGCAGTGGCCTGTA 58.712 61.111 3.32 0.00 42.56 2.74
4092 9394 6.769608 TTGTGTAATATTATGCTGCGAGAG 57.230 37.500 0.00 0.00 0.00 3.20
4093 9395 7.575365 CATTTGTGTAATATTATGCTGCGAGA 58.425 34.615 0.00 0.00 0.00 4.04
4094 9396 6.303970 GCATTTGTGTAATATTATGCTGCGAG 59.696 38.462 10.15 0.00 36.39 5.03
4095 9397 6.017192 AGCATTTGTGTAATATTATGCTGCGA 60.017 34.615 16.62 0.00 44.88 5.10
4096 9398 6.144854 AGCATTTGTGTAATATTATGCTGCG 58.855 36.000 16.62 0.00 44.88 5.18
4097 9399 7.935338 AAGCATTTGTGTAATATTATGCTGC 57.065 32.000 17.61 11.92 45.59 5.25
4126 9428 2.259511 GCTTTGAAGCCTTGCGGG 59.740 61.111 4.38 0.00 46.20 6.13
4135 9437 4.352600 AAGATGAATGCTCGCTTTGAAG 57.647 40.909 0.00 0.00 0.00 3.02
4136 9438 4.771590 AAAGATGAATGCTCGCTTTGAA 57.228 36.364 0.00 0.00 31.42 2.69
4137 9439 5.878332 TTAAAGATGAATGCTCGCTTTGA 57.122 34.783 0.00 0.00 33.45 2.69
4138 9440 6.493116 AGATTAAAGATGAATGCTCGCTTTG 58.507 36.000 0.00 0.00 33.45 2.77
4139 9441 6.690194 AGATTAAAGATGAATGCTCGCTTT 57.310 33.333 0.00 0.00 34.81 3.51
4140 9442 6.317140 TCAAGATTAAAGATGAATGCTCGCTT 59.683 34.615 0.00 0.00 0.00 4.68
4141 9443 5.819379 TCAAGATTAAAGATGAATGCTCGCT 59.181 36.000 0.00 0.00 0.00 4.93
4142 9444 5.906285 GTCAAGATTAAAGATGAATGCTCGC 59.094 40.000 0.00 0.00 0.00 5.03
4143 9445 6.019559 TCGTCAAGATTAAAGATGAATGCTCG 60.020 38.462 0.00 0.00 0.00 5.03
4144 9446 7.010923 AGTCGTCAAGATTAAAGATGAATGCTC 59.989 37.037 0.00 0.00 0.00 4.26
4145 9447 6.820656 AGTCGTCAAGATTAAAGATGAATGCT 59.179 34.615 0.00 0.00 0.00 3.79
4146 9448 7.009568 AGTCGTCAAGATTAAAGATGAATGC 57.990 36.000 0.00 0.00 0.00 3.56
4147 9449 9.907576 GTTAGTCGTCAAGATTAAAGATGAATG 57.092 33.333 0.00 0.00 33.68 2.67
4148 9450 9.653287 TGTTAGTCGTCAAGATTAAAGATGAAT 57.347 29.630 0.00 0.00 33.68 2.57
4149 9451 8.922676 GTGTTAGTCGTCAAGATTAAAGATGAA 58.077 33.333 0.00 0.00 33.68 2.57
4150 9452 8.304596 AGTGTTAGTCGTCAAGATTAAAGATGA 58.695 33.333 0.00 0.00 33.68 2.92
4151 9453 8.467402 AGTGTTAGTCGTCAAGATTAAAGATG 57.533 34.615 0.00 0.00 33.68 2.90
4152 9454 7.760340 GGAGTGTTAGTCGTCAAGATTAAAGAT 59.240 37.037 0.00 0.00 33.68 2.40
4153 9455 7.039923 AGGAGTGTTAGTCGTCAAGATTAAAGA 60.040 37.037 0.00 0.00 33.68 2.52
4154 9456 7.091443 AGGAGTGTTAGTCGTCAAGATTAAAG 58.909 38.462 0.00 0.00 33.68 1.85
4155 9457 6.989659 AGGAGTGTTAGTCGTCAAGATTAAA 58.010 36.000 0.00 0.00 33.68 1.52
4156 9458 6.585695 AGGAGTGTTAGTCGTCAAGATTAA 57.414 37.500 0.00 0.00 0.00 1.40
4157 9459 6.094603 GGTAGGAGTGTTAGTCGTCAAGATTA 59.905 42.308 0.00 0.00 0.00 1.75
4158 9460 5.105837 GGTAGGAGTGTTAGTCGTCAAGATT 60.106 44.000 0.00 0.00 0.00 2.40
4159 9461 4.398673 GGTAGGAGTGTTAGTCGTCAAGAT 59.601 45.833 0.00 0.00 0.00 2.40
4160 9462 3.755378 GGTAGGAGTGTTAGTCGTCAAGA 59.245 47.826 0.00 0.00 0.00 3.02
4161 9463 3.504906 TGGTAGGAGTGTTAGTCGTCAAG 59.495 47.826 0.00 0.00 0.00 3.02
4162 9464 3.489355 TGGTAGGAGTGTTAGTCGTCAA 58.511 45.455 0.00 0.00 0.00 3.18
4163 9465 3.079578 CTGGTAGGAGTGTTAGTCGTCA 58.920 50.000 0.00 0.00 0.00 4.35
4164 9466 2.422832 CCTGGTAGGAGTGTTAGTCGTC 59.577 54.545 0.00 0.00 37.67 4.20
4165 9467 2.040813 TCCTGGTAGGAGTGTTAGTCGT 59.959 50.000 0.00 0.00 40.06 4.34
4166 9468 2.422832 GTCCTGGTAGGAGTGTTAGTCG 59.577 54.545 0.00 0.00 46.90 4.18
4167 9469 2.759535 GGTCCTGGTAGGAGTGTTAGTC 59.240 54.545 0.00 0.00 46.90 2.59
4168 9470 2.817665 GGTCCTGGTAGGAGTGTTAGT 58.182 52.381 0.00 0.00 46.90 2.24
4169 9471 1.749634 CGGTCCTGGTAGGAGTGTTAG 59.250 57.143 0.00 0.00 46.90 2.34
4170 9472 1.843368 CGGTCCTGGTAGGAGTGTTA 58.157 55.000 0.00 0.00 46.90 2.41
4171 9473 1.542187 GCGGTCCTGGTAGGAGTGTT 61.542 60.000 0.00 0.00 46.90 3.32
4172 9474 1.982938 GCGGTCCTGGTAGGAGTGT 60.983 63.158 0.00 0.00 46.90 3.55
4173 9475 2.893398 GCGGTCCTGGTAGGAGTG 59.107 66.667 0.00 0.00 46.90 3.51
4174 9476 2.754658 CGCGGTCCTGGTAGGAGT 60.755 66.667 0.00 0.00 46.90 3.85
4175 9477 2.898920 TACCGCGGTCCTGGTAGGAG 62.899 65.000 38.01 0.28 46.90 3.69
4176 9478 2.288642 ATACCGCGGTCCTGGTAGGA 62.289 60.000 38.01 15.03 43.58 2.94
4177 9479 1.397390 AATACCGCGGTCCTGGTAGG 61.397 60.000 38.01 1.18 43.58 3.18
4178 9480 1.000938 GTAATACCGCGGTCCTGGTAG 60.001 57.143 38.01 2.09 43.58 3.18
4179 9481 1.032014 GTAATACCGCGGTCCTGGTA 58.968 55.000 38.01 17.72 44.40 3.25
4180 9482 1.818555 GTAATACCGCGGTCCTGGT 59.181 57.895 38.01 18.48 42.34 4.00
4181 9483 1.299620 CGTAATACCGCGGTCCTGG 60.300 63.158 38.01 17.72 0.00 4.45
4182 9484 1.299620 CCGTAATACCGCGGTCCTG 60.300 63.158 38.01 20.44 42.73 3.86
4183 9485 3.122850 CCGTAATACCGCGGTCCT 58.877 61.111 38.01 25.06 42.73 3.85
4188 9490 0.652071 GGGTTTTCCGTAATACCGCG 59.348 55.000 0.00 0.00 37.52 6.46
4189 9491 1.736612 TGGGTTTTCCGTAATACCGC 58.263 50.000 0.00 0.00 37.52 5.68
4190 9492 2.096335 GCTTGGGTTTTCCGTAATACCG 59.904 50.000 0.00 0.00 37.52 4.02
4191 9493 2.096335 CGCTTGGGTTTTCCGTAATACC 59.904 50.000 0.00 0.00 41.82 2.73
4192 9494 2.743664 ACGCTTGGGTTTTCCGTAATAC 59.256 45.455 0.00 0.00 41.82 1.89
4193 9495 3.056588 ACGCTTGGGTTTTCCGTAATA 57.943 42.857 0.00 0.00 41.82 0.98
4194 9496 1.900245 ACGCTTGGGTTTTCCGTAAT 58.100 45.000 0.00 0.00 41.82 1.89
4195 9497 1.677942 AACGCTTGGGTTTTCCGTAA 58.322 45.000 0.00 0.00 41.82 3.18
4196 9498 1.603326 GAAACGCTTGGGTTTTCCGTA 59.397 47.619 15.13 0.00 40.05 4.02
4197 9499 0.382873 GAAACGCTTGGGTTTTCCGT 59.617 50.000 15.13 0.00 40.05 4.69
4198 9500 0.659123 CGAAACGCTTGGGTTTTCCG 60.659 55.000 15.13 11.74 40.05 4.30
4199 9501 3.173247 CGAAACGCTTGGGTTTTCC 57.827 52.632 15.13 5.05 40.05 3.13
4211 9513 2.009774 AGATTTGGATGGAGCGAAACG 58.990 47.619 0.00 0.00 0.00 3.60
4212 9514 2.356069 GGAGATTTGGATGGAGCGAAAC 59.644 50.000 0.00 0.00 0.00 2.78
4213 9515 2.643551 GGAGATTTGGATGGAGCGAAA 58.356 47.619 0.00 0.00 0.00 3.46
4214 9516 1.473257 CGGAGATTTGGATGGAGCGAA 60.473 52.381 0.00 0.00 0.00 4.70
4215 9517 0.104855 CGGAGATTTGGATGGAGCGA 59.895 55.000 0.00 0.00 0.00 4.93
4216 9518 0.104855 TCGGAGATTTGGATGGAGCG 59.895 55.000 0.00 0.00 0.00 5.03
4217 9519 2.158900 TCTTCGGAGATTTGGATGGAGC 60.159 50.000 0.00 0.00 35.04 4.70
4218 9520 3.386078 TCTCTTCGGAGATTTGGATGGAG 59.614 47.826 0.00 0.00 45.16 3.86
4219 9521 3.374764 TCTCTTCGGAGATTTGGATGGA 58.625 45.455 0.00 0.00 45.16 3.41
4220 9522 3.827008 TCTCTTCGGAGATTTGGATGG 57.173 47.619 0.00 0.00 45.16 3.51
4230 9532 2.029470 AGAGTTGCTTGTCTCTTCGGAG 60.029 50.000 0.00 0.00 43.09 4.63
4231 9533 1.964223 AGAGTTGCTTGTCTCTTCGGA 59.036 47.619 0.00 0.00 37.72 4.55
4232 9534 2.447244 AGAGTTGCTTGTCTCTTCGG 57.553 50.000 0.00 0.00 37.72 4.30
4233 9535 4.745125 TGTTTAGAGTTGCTTGTCTCTTCG 59.255 41.667 0.00 0.00 40.78 3.79
4234 9536 6.604735 TTGTTTAGAGTTGCTTGTCTCTTC 57.395 37.500 0.00 0.00 40.78 2.87
4235 9537 7.573968 AATTGTTTAGAGTTGCTTGTCTCTT 57.426 32.000 0.00 0.00 40.78 2.85
4236 9538 7.173390 GGTAATTGTTTAGAGTTGCTTGTCTCT 59.827 37.037 0.00 0.00 42.62 3.10
4237 9539 7.298854 GGTAATTGTTTAGAGTTGCTTGTCTC 58.701 38.462 0.00 0.00 0.00 3.36
4238 9540 6.206829 GGGTAATTGTTTAGAGTTGCTTGTCT 59.793 38.462 0.00 0.00 0.00 3.41
4239 9541 6.016610 TGGGTAATTGTTTAGAGTTGCTTGTC 60.017 38.462 0.00 0.00 0.00 3.18
4240 9542 5.830991 TGGGTAATTGTTTAGAGTTGCTTGT 59.169 36.000 0.00 0.00 0.00 3.16
4241 9543 6.149633 GTGGGTAATTGTTTAGAGTTGCTTG 58.850 40.000 0.00 0.00 0.00 4.01
4242 9544 5.830991 TGTGGGTAATTGTTTAGAGTTGCTT 59.169 36.000 0.00 0.00 0.00 3.91
4316 9618 3.239026 CACAAGTAGTTTACGCCGTATCG 59.761 47.826 0.00 0.00 0.00 2.92
4324 9626 2.660236 GACGGAGCACAAGTAGTTTACG 59.340 50.000 0.00 0.00 0.00 3.18
4338 9640 1.014044 TGATTCGCACAAGACGGAGC 61.014 55.000 0.00 0.00 0.00 4.70
4446 9756 4.208873 GCTTTGAAAATTTGTCATCGCACA 59.791 37.500 0.00 0.00 0.00 4.57
4450 9760 5.050904 TGCTTGCTTTGAAAATTTGTCATCG 60.051 36.000 0.00 0.00 0.00 3.84
4459 9769 7.644945 GCTTAAAACATTGCTTGCTTTGAAAAT 59.355 29.630 0.00 0.00 0.00 1.82
4464 9774 5.406767 TGCTTAAAACATTGCTTGCTTTG 57.593 34.783 0.00 0.00 0.00 2.77
4489 9799 2.273557 GTAAAGCAAGCATGGGCAATG 58.726 47.619 0.00 0.00 44.61 2.82
4490 9800 1.901159 TGTAAAGCAAGCATGGGCAAT 59.099 42.857 0.00 0.00 44.61 3.56
4491 9801 1.336131 TGTAAAGCAAGCATGGGCAA 58.664 45.000 0.00 0.00 44.61 4.52
4492 9802 1.336131 TTGTAAAGCAAGCATGGGCA 58.664 45.000 0.00 0.00 44.61 5.36
4493 9803 2.453983 TTTGTAAAGCAAGCATGGGC 57.546 45.000 0.00 0.00 38.47 5.36
4494 9804 4.378666 GCAATTTTGTAAAGCAAGCATGGG 60.379 41.667 0.00 0.00 38.47 4.00
4509 9819 5.163683 TGTTGTTTTGTGGATGGCAATTTTG 60.164 36.000 0.00 0.00 0.00 2.44
4526 9836 6.014327 ACCTGAGATGGCAAATTATGTTGTTT 60.014 34.615 0.00 0.00 0.00 2.83
4546 9856 1.811965 CATGGCAAATCGAACACCTGA 59.188 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.