Multiple sequence alignment - TraesCS3D01G195000

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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 TraesCS3D01G195000 chr3D 100.000 4890 0 0 1 4890 188353501 188358390 0.000000e+00 9031.0
1 TraesCS3D01G195000 chr3D 86.082 661 69 18 13 663 575932088 575932735 0.000000e+00 689.0
2 TraesCS3D01G195000 chr3D 100.000 36 0 0 4781 4816 300930565 300930600 3.160000e-07 67.6
3 TraesCS3D01G195000 chr3A 95.158 4110 144 25 678 4752 241927635 241923546 0.000000e+00 6436.0
4 TraesCS3D01G195000 chr3B 95.780 3199 84 21 1268 4443 270887254 270890424 0.000000e+00 5112.0
5 TraesCS3D01G195000 chr3B 94.877 527 22 4 725 1250 270886745 270887267 0.000000e+00 819.0
6 TraesCS3D01G195000 chr3B 85.542 664 72 14 15 667 792855588 792854938 0.000000e+00 673.0
7 TraesCS3D01G195000 chr3B 93.182 44 3 0 4780 4823 452492904 452492861 1.140000e-06 65.8
8 TraesCS3D01G195000 chr7D 88.823 671 67 6 2 669 419771574 419772239 0.000000e+00 817.0
9 TraesCS3D01G195000 chr7D 85.976 656 73 15 15 655 603159610 603160261 0.000000e+00 684.0
10 TraesCS3D01G195000 chr7D 85.457 667 77 14 9 664 575003931 575004588 0.000000e+00 676.0
11 TraesCS3D01G195000 chr4D 89.552 603 54 8 9 609 386367861 386368456 0.000000e+00 756.0
12 TraesCS3D01G195000 chr4D 87.576 660 62 15 14 667 34131612 34130967 0.000000e+00 747.0
13 TraesCS3D01G195000 chr4D 86.145 166 16 6 4400 4563 98888342 98888182 6.510000e-39 172.0
14 TraesCS3D01G195000 chr5D 87.192 609 62 12 2 603 391216491 391215892 0.000000e+00 678.0
15 TraesCS3D01G195000 chr1D 85.871 637 77 8 36 667 79830419 79829791 0.000000e+00 665.0
16 TraesCS3D01G195000 chr1D 83.929 168 19 7 4400 4563 80020496 80020659 2.360000e-33 154.0
17 TraesCS3D01G195000 chr4B 80.543 221 27 8 4356 4563 140706925 140706708 6.550000e-34 156.0
18 TraesCS3D01G195000 chr4B 82.317 164 21 7 4400 4561 438599205 438599362 8.540000e-28 135.0
19 TraesCS3D01G195000 chr4B 93.182 44 3 0 4780 4823 648544187 648544230 1.140000e-06 65.8
20 TraesCS3D01G195000 chr4A 83.735 166 22 4 4400 4563 477060604 477060766 8.480000e-33 152.0
21 TraesCS3D01G195000 chr1B 83.735 166 21 5 4400 4563 132059090 132059251 8.480000e-33 152.0
22 TraesCS3D01G195000 chr1B 87.097 62 4 4 4784 4845 684346501 684346444 3.160000e-07 67.6
23 TraesCS3D01G195000 chr7B 84.000 150 19 4 4414 4562 263110096 263109951 6.600000e-29 139.0
24 TraesCS3D01G195000 chr6D 83.444 151 18 4 4414 4563 423771427 423771283 3.070000e-27 134.0
25 TraesCS3D01G195000 chr5A 81.595 163 25 5 4397 4558 589246747 589246905 3.970000e-26 130.0
26 TraesCS3D01G195000 chr5A 86.154 65 5 4 4781 4845 53231707 53231767 3.160000e-07 67.6
27 TraesCS3D01G195000 chr6A 97.727 44 1 0 4780 4823 91866661 91866704 5.250000e-10 76.8
28 TraesCS3D01G195000 chr6A 93.182 44 3 0 4780 4823 571646157 571646200 1.140000e-06 65.8
29 TraesCS3D01G195000 chr1A 95.455 44 2 0 4780 4823 209362066 209362109 2.440000e-08 71.3
30 TraesCS3D01G195000 chr2B 95.238 42 2 0 4782 4823 632380913 632380954 3.160000e-07 67.6


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 TraesCS3D01G195000 chr3D 188353501 188358390 4889 False 9031.0 9031 100.0000 1 4890 1 chr3D.!!$F1 4889
1 TraesCS3D01G195000 chr3D 575932088 575932735 647 False 689.0 689 86.0820 13 663 1 chr3D.!!$F3 650
2 TraesCS3D01G195000 chr3A 241923546 241927635 4089 True 6436.0 6436 95.1580 678 4752 1 chr3A.!!$R1 4074
3 TraesCS3D01G195000 chr3B 270886745 270890424 3679 False 2965.5 5112 95.3285 725 4443 2 chr3B.!!$F1 3718
4 TraesCS3D01G195000 chr3B 792854938 792855588 650 True 673.0 673 85.5420 15 667 1 chr3B.!!$R2 652
5 TraesCS3D01G195000 chr7D 419771574 419772239 665 False 817.0 817 88.8230 2 669 1 chr7D.!!$F1 667
6 TraesCS3D01G195000 chr7D 603159610 603160261 651 False 684.0 684 85.9760 15 655 1 chr7D.!!$F3 640
7 TraesCS3D01G195000 chr7D 575003931 575004588 657 False 676.0 676 85.4570 9 664 1 chr7D.!!$F2 655
8 TraesCS3D01G195000 chr4D 386367861 386368456 595 False 756.0 756 89.5520 9 609 1 chr4D.!!$F1 600
9 TraesCS3D01G195000 chr4D 34130967 34131612 645 True 747.0 747 87.5760 14 667 1 chr4D.!!$R1 653
10 TraesCS3D01G195000 chr5D 391215892 391216491 599 True 678.0 678 87.1920 2 603 1 chr5D.!!$R1 601
11 TraesCS3D01G195000 chr1D 79829791 79830419 628 True 665.0 665 85.8710 36 667 1 chr1D.!!$R1 631

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
678 718 1.045407 TGCTCCAAGAACCGTACTGT 58.955 50.000 0.00 0.0 0.0 3.55 F
1903 1950 0.323087 TCGATGACTTGGAGGACGGA 60.323 55.000 0.00 0.0 0.0 4.69 F
2060 2107 1.283029 CAATGAAGAAGGCCTCCCAGA 59.717 52.381 5.23 0.0 0.0 3.86 F
2583 2638 2.594654 GACTGTTCTCATTGTAGTCGCG 59.405 50.000 0.00 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 2545 0.871722 CGATTGACACGGCAAAAGGA 59.128 50.000 0.00 0.00 0.00 3.36 R
3070 3130 1.228245 TGGCTCAACACCTTCTGCC 60.228 57.895 0.00 0.00 40.62 4.85 R
3262 3322 1.526575 CCTCGCAAACCTGCCACATT 61.527 55.000 0.00 0.00 46.56 2.71 R
4060 4120 0.032678 AGGGCAGCAACTCGATATCG 59.967 55.000 19.14 19.14 41.45 2.92 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
75 76 1.074405 AGTAGTACACGAGTGGGTCCA 59.926 52.381 8.19 0.00 34.19 4.02
310 330 2.338620 CTCTGGACACGGCGTTCA 59.661 61.111 11.19 8.60 0.00 3.18
476 503 1.067516 CTTCATGGCCGGCTTTAATGG 59.932 52.381 28.56 9.30 0.00 3.16
597 637 1.374252 GGACATCGTGTTCGCCTGT 60.374 57.895 0.00 0.00 36.16 4.00
619 659 5.536916 TGTCCGACCCAAATGAATAAAAAGT 59.463 36.000 0.00 0.00 0.00 2.66
673 713 3.307379 GAGTTGCTCCAAGAACCGT 57.693 52.632 0.00 0.00 0.00 4.83
674 714 2.450609 GAGTTGCTCCAAGAACCGTA 57.549 50.000 0.00 0.00 0.00 4.02
675 715 2.067013 GAGTTGCTCCAAGAACCGTAC 58.933 52.381 0.00 0.00 0.00 3.67
676 716 1.692519 AGTTGCTCCAAGAACCGTACT 59.307 47.619 0.00 0.00 0.00 2.73
677 717 1.798813 GTTGCTCCAAGAACCGTACTG 59.201 52.381 0.00 0.00 0.00 2.74
678 718 1.045407 TGCTCCAAGAACCGTACTGT 58.955 50.000 0.00 0.00 0.00 3.55
679 719 2.241160 TGCTCCAAGAACCGTACTGTA 58.759 47.619 0.00 0.00 0.00 2.74
680 720 2.829720 TGCTCCAAGAACCGTACTGTAT 59.170 45.455 0.00 0.00 0.00 2.29
685 725 6.018994 GCTCCAAGAACCGTACTGTATTATTG 60.019 42.308 0.00 0.00 0.00 1.90
904 946 3.935456 TTTAGCCGCCTCCCTCCCA 62.935 63.158 0.00 0.00 0.00 4.37
926 968 4.351054 CCCCTTGCTGCGTTCCCT 62.351 66.667 0.00 0.00 0.00 4.20
928 970 2.335712 CCCTTGCTGCGTTCCCTTC 61.336 63.158 0.00 0.00 0.00 3.46
929 971 1.600636 CCTTGCTGCGTTCCCTTCA 60.601 57.895 0.00 0.00 0.00 3.02
1079 1122 2.345124 AGGGATTCAGATGCTCTTGC 57.655 50.000 0.00 0.00 40.20 4.01
1089 1132 1.002430 GATGCTCTTGCCCGGATGATA 59.998 52.381 0.73 0.00 38.71 2.15
1090 1133 1.059098 TGCTCTTGCCCGGATGATAT 58.941 50.000 0.73 0.00 38.71 1.63
1091 1134 2.256306 TGCTCTTGCCCGGATGATATA 58.744 47.619 0.73 0.00 38.71 0.86
1092 1135 2.234661 TGCTCTTGCCCGGATGATATAG 59.765 50.000 0.73 0.00 38.71 1.31
1093 1136 2.419297 GCTCTTGCCCGGATGATATAGG 60.419 54.545 0.73 0.00 0.00 2.57
1094 1137 2.834549 CTCTTGCCCGGATGATATAGGT 59.165 50.000 0.73 0.00 0.00 3.08
1095 1138 2.832129 TCTTGCCCGGATGATATAGGTC 59.168 50.000 0.73 0.00 0.00 3.85
1096 1139 2.319025 TGCCCGGATGATATAGGTCA 57.681 50.000 0.73 0.00 0.00 4.02
1097 1140 2.179427 TGCCCGGATGATATAGGTCAG 58.821 52.381 0.73 0.00 0.00 3.51
1098 1141 2.180276 GCCCGGATGATATAGGTCAGT 58.820 52.381 0.73 0.00 0.00 3.41
1102 1145 3.578716 CCGGATGATATAGGTCAGTTGGT 59.421 47.826 0.00 0.00 0.00 3.67
1406 1450 0.809636 CCGCACGATGCTGTTGGATA 60.810 55.000 8.07 0.00 42.25 2.59
1470 1516 6.889301 TTCTTTCTGATGCTTGATTGAAGT 57.111 33.333 0.00 0.00 33.73 3.01
1609 1656 7.252708 CAACATGTATCTTGTGTTGCATACAT 58.747 34.615 0.00 2.87 44.00 2.29
1749 1796 4.214119 TGCTAAGAATGCAGAACAACACTC 59.786 41.667 0.00 0.00 35.31 3.51
1873 1920 3.490439 TCTCAGACTGGTGCAAATTCA 57.510 42.857 1.81 0.00 0.00 2.57
1903 1950 0.323087 TCGATGACTTGGAGGACGGA 60.323 55.000 0.00 0.00 0.00 4.69
2004 2051 3.841643 CTGTTGATGGAATTGGCTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
2060 2107 1.283029 CAATGAAGAAGGCCTCCCAGA 59.717 52.381 5.23 0.00 0.00 3.86
2229 2276 4.647399 AGCCTTGCAGGTGTTTAACTTTTA 59.353 37.500 0.00 0.00 37.80 1.52
2234 2281 4.957327 TGCAGGTGTTTAACTTTTACCCTT 59.043 37.500 0.00 0.00 31.80 3.95
2238 2285 8.145767 GCAGGTGTTTAACTTTTACCCTTTATT 58.854 33.333 0.00 0.00 31.80 1.40
2266 2313 6.949352 TTCTCTCTATTTTCCCATGATTGC 57.051 37.500 0.00 0.00 0.00 3.56
2462 2517 8.332996 AGCTATACAATGGAATTAGCATTCTG 57.667 34.615 1.43 0.00 36.80 3.02
2514 2569 3.047280 GCCGTGTCAATCGCCACA 61.047 61.111 0.00 0.00 0.00 4.17
2521 2576 3.181511 CGTGTCAATCGCCACATGTTTAT 60.182 43.478 0.00 0.00 0.00 1.40
2583 2638 2.594654 GACTGTTCTCATTGTAGTCGCG 59.405 50.000 0.00 0.00 0.00 5.87
2588 2643 4.142556 TGTTCTCATTGTAGTCGCGTATCA 60.143 41.667 5.77 0.00 0.00 2.15
3070 3130 3.885484 AAAGTTGTTGAGTCGATGCAG 57.115 42.857 0.00 0.00 0.00 4.41
3262 3322 3.616956 AAGAAGGATGATGTTGAGCGA 57.383 42.857 0.00 0.00 0.00 4.93
3391 3451 2.112475 TGTTTGCGACATGGAAAACG 57.888 45.000 0.00 0.00 39.78 3.60
3449 3509 6.446318 GTGTATGCTGATCAAAACCTTTTCA 58.554 36.000 0.00 0.00 0.00 2.69
3520 3580 6.182627 ACTAGGCATCTCAACAATTGATTCA 58.817 36.000 13.59 0.00 39.30 2.57
3841 3901 1.132640 CGCGTCTTTACTTGCTGCC 59.867 57.895 0.00 0.00 0.00 4.85
4060 4120 3.416156 ACTGAACTTTCTGCCAGGAATC 58.584 45.455 0.00 0.00 0.00 2.52
4181 4241 4.387026 TTTTGAAGGACTGATGGGTGAT 57.613 40.909 0.00 0.00 0.00 3.06
4212 4272 4.335400 TTGCTTTTTGTGGGAATTCTCC 57.665 40.909 2.04 4.49 41.59 3.71
4262 4322 6.888105 ACATTGAAGTTTGTTCCTGGAATTT 58.112 32.000 13.07 3.02 0.00 1.82
4263 4323 6.986231 ACATTGAAGTTTGTTCCTGGAATTTC 59.014 34.615 13.07 11.57 0.00 2.17
4264 4324 6.790232 TTGAAGTTTGTTCCTGGAATTTCT 57.210 33.333 13.07 6.50 0.00 2.52
4303 4363 5.171339 AGTGGTCTTGTCTATTCTGCAAT 57.829 39.130 0.00 0.00 0.00 3.56
4357 4417 3.380393 AGGCCAACTTTACTTGGGTTTT 58.620 40.909 5.01 0.00 41.12 2.43
4374 4434 5.013704 TGGGTTTTAGAGCAATTCTGTAGGA 59.986 40.000 0.00 0.00 36.61 2.94
4391 4451 9.676129 TTCTGTAGGAATTCTAAAGGATAGGAT 57.324 33.333 5.23 0.00 34.68 3.24
4421 4492 4.829064 TTGCAGCACTTAAGTTTGTAGG 57.171 40.909 5.07 0.00 0.00 3.18
4423 4494 4.456535 TGCAGCACTTAAGTTTGTAGGAA 58.543 39.130 5.07 0.00 0.00 3.36
4424 4495 5.070001 TGCAGCACTTAAGTTTGTAGGAAT 58.930 37.500 5.07 0.00 0.00 3.01
4500 4571 8.990163 AAAAAGGACAATAGTCTAGAACCAAA 57.010 30.769 0.00 0.00 44.36 3.28
4501 4572 9.588096 AAAAAGGACAATAGTCTAGAACCAAAT 57.412 29.630 0.00 0.00 44.36 2.32
4532 4603 8.837788 ATTCATATCTTATGAATCAAGCGACA 57.162 30.769 14.16 0.00 43.07 4.35
4540 4611 8.197439 TCTTATGAATCAAGCGACATCTCTTTA 58.803 33.333 0.00 0.00 0.00 1.85
4544 4633 8.131455 TGAATCAAGCGACATCTCTTTAATAC 57.869 34.615 0.00 0.00 0.00 1.89
4545 4634 7.981789 TGAATCAAGCGACATCTCTTTAATACT 59.018 33.333 0.00 0.00 0.00 2.12
4550 4639 9.347934 CAAGCGACATCTCTTTAATACTATAGG 57.652 37.037 4.43 0.00 0.00 2.57
4566 4655 6.274157 ACTATAGGCAATTGAGATACTCCG 57.726 41.667 10.34 0.00 0.00 4.63
4567 4656 6.010850 ACTATAGGCAATTGAGATACTCCGA 58.989 40.000 10.34 0.00 0.00 4.55
4568 4657 3.742433 AGGCAATTGAGATACTCCGAG 57.258 47.619 10.34 0.00 0.00 4.63
4569 4658 3.300388 AGGCAATTGAGATACTCCGAGA 58.700 45.455 10.34 0.00 0.00 4.04
4571 4660 3.804873 GGCAATTGAGATACTCCGAGAAC 59.195 47.826 10.34 0.00 0.00 3.01
4572 4661 4.442192 GGCAATTGAGATACTCCGAGAACT 60.442 45.833 10.34 0.00 0.00 3.01
4574 4663 6.273825 GCAATTGAGATACTCCGAGAACTAA 58.726 40.000 10.34 0.00 0.00 2.24
4575 4664 6.757010 GCAATTGAGATACTCCGAGAACTAAA 59.243 38.462 10.34 0.00 0.00 1.85
4576 4665 7.043059 GCAATTGAGATACTCCGAGAACTAAAG 60.043 40.741 10.34 0.00 0.00 1.85
4577 4666 7.648039 ATTGAGATACTCCGAGAACTAAAGT 57.352 36.000 1.33 0.00 0.00 2.66
4578 4667 6.438259 TGAGATACTCCGAGAACTAAAGTG 57.562 41.667 1.33 0.00 0.00 3.16
4580 4669 6.829298 TGAGATACTCCGAGAACTAAAGTGAT 59.171 38.462 1.33 0.00 0.00 3.06
4581 4670 7.012515 TGAGATACTCCGAGAACTAAAGTGATC 59.987 40.741 1.33 0.00 0.00 2.92
4582 4671 7.057894 AGATACTCCGAGAACTAAAGTGATCT 58.942 38.462 1.33 0.00 0.00 2.75
4583 4672 5.570234 ACTCCGAGAACTAAAGTGATCTC 57.430 43.478 1.33 2.88 35.95 2.75
4584 4673 5.010933 ACTCCGAGAACTAAAGTGATCTCA 58.989 41.667 1.33 0.00 38.55 3.27
4585 4674 5.106078 ACTCCGAGAACTAAAGTGATCTCAC 60.106 44.000 1.33 2.01 46.77 3.51
4643 4732 2.288273 ACAGAAGTGTAGGACTCGCAAC 60.288 50.000 0.00 0.00 34.05 4.17
4654 4743 2.032178 GGACTCGCAACATTTGGCTATC 59.968 50.000 0.00 0.00 0.00 2.08
4671 4760 2.282701 ATCGCATTGTCATTTGTGCC 57.717 45.000 0.00 0.00 34.20 5.01
4679 4768 3.448093 TGTCATTTGTGCCCCTCATTA 57.552 42.857 0.00 0.00 0.00 1.90
4716 4805 3.775316 GGTCTTGAGAGATAAACCCTCCA 59.225 47.826 0.00 0.00 33.70 3.86
4752 4841 7.819900 AGTTGAAAGTCTTATCACGAGCTTAAT 59.180 33.333 0.00 0.00 0.00 1.40
4753 4842 7.757097 TGAAAGTCTTATCACGAGCTTAATC 57.243 36.000 0.00 0.00 0.00 1.75
4754 4843 6.757010 TGAAAGTCTTATCACGAGCTTAATCC 59.243 38.462 0.00 0.00 0.00 3.01
4755 4844 6.472686 AAGTCTTATCACGAGCTTAATCCT 57.527 37.500 0.00 0.00 0.00 3.24
4756 4845 7.584122 AAGTCTTATCACGAGCTTAATCCTA 57.416 36.000 0.00 0.00 0.00 2.94
4757 4846 6.972722 AGTCTTATCACGAGCTTAATCCTAC 58.027 40.000 0.00 0.00 0.00 3.18
4758 4847 5.852229 GTCTTATCACGAGCTTAATCCTACG 59.148 44.000 0.00 0.00 0.00 3.51
4759 4848 5.761726 TCTTATCACGAGCTTAATCCTACGA 59.238 40.000 0.00 0.00 0.00 3.43
4760 4849 4.913335 ATCACGAGCTTAATCCTACGAA 57.087 40.909 0.00 0.00 0.00 3.85
4761 4850 4.288670 TCACGAGCTTAATCCTACGAAG 57.711 45.455 0.00 0.00 0.00 3.79
4762 4851 3.943381 TCACGAGCTTAATCCTACGAAGA 59.057 43.478 0.00 0.00 0.00 2.87
4763 4852 4.397103 TCACGAGCTTAATCCTACGAAGAA 59.603 41.667 0.00 0.00 0.00 2.52
4764 4853 4.735822 CACGAGCTTAATCCTACGAAGAAG 59.264 45.833 0.00 0.00 0.00 2.85
4765 4854 3.731717 CGAGCTTAATCCTACGAAGAAGC 59.268 47.826 0.00 0.00 38.86 3.86
4766 4855 4.498345 CGAGCTTAATCCTACGAAGAAGCT 60.498 45.833 6.64 6.64 45.65 3.74
4767 4856 5.277876 CGAGCTTAATCCTACGAAGAAGCTA 60.278 44.000 6.90 0.00 44.24 3.32
4768 4857 6.568844 CGAGCTTAATCCTACGAAGAAGCTAT 60.569 42.308 6.90 0.00 44.24 2.97
4769 4858 6.683715 AGCTTAATCCTACGAAGAAGCTATC 58.316 40.000 5.19 0.00 43.26 2.08
4770 4859 5.865013 GCTTAATCCTACGAAGAAGCTATCC 59.135 44.000 0.00 0.00 37.06 2.59
4771 4860 6.516860 GCTTAATCCTACGAAGAAGCTATCCA 60.517 42.308 0.00 0.00 37.06 3.41
4772 4861 5.461032 AATCCTACGAAGAAGCTATCCAG 57.539 43.478 0.00 0.00 0.00 3.86
4773 4862 4.166246 TCCTACGAAGAAGCTATCCAGA 57.834 45.455 0.00 0.00 0.00 3.86
4774 4863 4.730966 TCCTACGAAGAAGCTATCCAGAT 58.269 43.478 0.00 0.00 0.00 2.90
4775 4864 5.141182 TCCTACGAAGAAGCTATCCAGATT 58.859 41.667 0.00 0.00 31.65 2.40
4776 4865 5.010112 TCCTACGAAGAAGCTATCCAGATTG 59.990 44.000 0.00 0.00 28.29 2.67
4777 4866 4.065321 ACGAAGAAGCTATCCAGATTGG 57.935 45.455 0.00 0.00 39.43 3.16
4778 4867 2.805099 CGAAGAAGCTATCCAGATTGGC 59.195 50.000 0.00 0.00 37.47 4.52
4779 4868 2.540265 AGAAGCTATCCAGATTGGCG 57.460 50.000 0.00 0.00 37.47 5.69
4780 4869 2.042464 AGAAGCTATCCAGATTGGCGA 58.958 47.619 0.00 0.00 37.47 5.54
4781 4870 2.435805 AGAAGCTATCCAGATTGGCGAA 59.564 45.455 0.00 0.00 37.47 4.70
4782 4871 2.540265 AGCTATCCAGATTGGCGAAG 57.460 50.000 0.00 0.00 37.47 3.79
4783 4872 1.765314 AGCTATCCAGATTGGCGAAGT 59.235 47.619 0.00 0.00 37.47 3.01
4784 4873 2.965831 AGCTATCCAGATTGGCGAAGTA 59.034 45.455 0.00 0.00 37.47 2.24
4785 4874 3.060602 GCTATCCAGATTGGCGAAGTAC 58.939 50.000 0.00 0.00 37.47 2.73
4786 4875 3.243907 GCTATCCAGATTGGCGAAGTACT 60.244 47.826 0.00 0.00 37.47 2.73
4787 4876 2.961526 TCCAGATTGGCGAAGTACTC 57.038 50.000 0.00 0.00 37.47 2.59
4788 4877 1.480954 TCCAGATTGGCGAAGTACTCC 59.519 52.381 0.00 0.00 37.47 3.85
4789 4878 1.473434 CCAGATTGGCGAAGTACTCCC 60.473 57.143 0.00 0.00 0.00 4.30
4790 4879 1.482593 CAGATTGGCGAAGTACTCCCT 59.517 52.381 0.00 0.00 0.00 4.20
4791 4880 1.757699 AGATTGGCGAAGTACTCCCTC 59.242 52.381 0.00 0.00 0.00 4.30
4792 4881 0.831307 ATTGGCGAAGTACTCCCTCC 59.169 55.000 0.00 0.00 0.00 4.30
4793 4882 1.601419 TTGGCGAAGTACTCCCTCCG 61.601 60.000 0.00 0.00 0.00 4.63
4794 4883 2.050934 GGCGAAGTACTCCCTCCGT 61.051 63.158 0.00 0.00 0.00 4.69
4795 4884 0.749454 GGCGAAGTACTCCCTCCGTA 60.749 60.000 0.00 0.00 0.00 4.02
4796 4885 1.098050 GCGAAGTACTCCCTCCGTAA 58.902 55.000 0.00 0.00 0.00 3.18
4797 4886 1.474077 GCGAAGTACTCCCTCCGTAAA 59.526 52.381 0.00 0.00 0.00 2.01
4798 4887 2.733542 GCGAAGTACTCCCTCCGTAAAC 60.734 54.545 0.00 0.00 0.00 2.01
4799 4888 2.489329 CGAAGTACTCCCTCCGTAAACA 59.511 50.000 0.00 0.00 0.00 2.83
4800 4889 3.057315 CGAAGTACTCCCTCCGTAAACAA 60.057 47.826 0.00 0.00 0.00 2.83
4801 4890 4.559300 CGAAGTACTCCCTCCGTAAACAAA 60.559 45.833 0.00 0.00 0.00 2.83
4802 4891 5.485620 GAAGTACTCCCTCCGTAAACAAAT 58.514 41.667 0.00 0.00 0.00 2.32
4803 4892 6.610075 AAGTACTCCCTCCGTAAACAAATA 57.390 37.500 0.00 0.00 0.00 1.40
4804 4893 6.803366 AGTACTCCCTCCGTAAACAAATAT 57.197 37.500 0.00 0.00 0.00 1.28
4805 4894 7.902920 AGTACTCCCTCCGTAAACAAATATA 57.097 36.000 0.00 0.00 0.00 0.86
4806 4895 8.310122 AGTACTCCCTCCGTAAACAAATATAA 57.690 34.615 0.00 0.00 0.00 0.98
4807 4896 8.761689 AGTACTCCCTCCGTAAACAAATATAAA 58.238 33.333 0.00 0.00 0.00 1.40
4808 4897 9.382275 GTACTCCCTCCGTAAACAAATATAAAA 57.618 33.333 0.00 0.00 0.00 1.52
4809 4898 8.502105 ACTCCCTCCGTAAACAAATATAAAAG 57.498 34.615 0.00 0.00 0.00 2.27
4810 4899 7.066645 ACTCCCTCCGTAAACAAATATAAAAGC 59.933 37.037 0.00 0.00 0.00 3.51
4811 4900 6.037391 TCCCTCCGTAAACAAATATAAAAGCG 59.963 38.462 0.00 0.00 0.00 4.68
4812 4901 6.183360 CCCTCCGTAAACAAATATAAAAGCGT 60.183 38.462 0.00 0.00 0.00 5.07
4813 4902 7.245604 CCTCCGTAAACAAATATAAAAGCGTT 58.754 34.615 0.00 0.00 0.00 4.84
4814 4903 7.751793 CCTCCGTAAACAAATATAAAAGCGTTT 59.248 33.333 2.53 2.53 0.00 3.60
4815 4904 9.757859 CTCCGTAAACAAATATAAAAGCGTTTA 57.242 29.630 7.30 7.30 33.76 2.01
4816 4905 9.540431 TCCGTAAACAAATATAAAAGCGTTTAC 57.460 29.630 7.00 11.17 42.32 2.01
4817 4906 9.327529 CCGTAAACAAATATAAAAGCGTTTACA 57.672 29.630 17.91 0.00 44.31 2.41
4829 4918 9.738832 ATAAAAGCGTTTACATTACTTGTTTGT 57.261 25.926 7.00 0.00 39.87 2.83
4830 4919 8.468720 AAAAGCGTTTACATTACTTGTTTGTT 57.531 26.923 0.00 0.00 39.87 2.83
4831 4920 8.468720 AAAGCGTTTACATTACTTGTTTGTTT 57.531 26.923 0.00 0.00 39.87 2.83
4832 4921 9.570488 AAAGCGTTTACATTACTTGTTTGTTTA 57.430 25.926 0.00 0.00 39.87 2.01
4833 4922 8.551122 AGCGTTTACATTACTTGTTTGTTTAC 57.449 30.769 0.00 0.00 39.87 2.01
4834 4923 7.373966 AGCGTTTACATTACTTGTTTGTTTACG 59.626 33.333 0.00 0.00 39.87 3.18
4835 4924 7.356638 GCGTTTACATTACTTGTTTGTTTACGG 60.357 37.037 0.00 0.00 39.87 4.02
4836 4925 7.850003 CGTTTACATTACTTGTTTGTTTACGGA 59.150 33.333 0.00 0.00 39.87 4.69
4837 4926 9.161684 GTTTACATTACTTGTTTGTTTACGGAG 57.838 33.333 0.00 0.00 39.87 4.63
4838 4927 6.308371 ACATTACTTGTTTGTTTACGGAGG 57.692 37.500 0.00 0.00 33.74 4.30
4839 4928 5.239963 ACATTACTTGTTTGTTTACGGAGGG 59.760 40.000 0.00 0.00 33.74 4.30
4840 4929 3.564053 ACTTGTTTGTTTACGGAGGGA 57.436 42.857 0.00 0.00 0.00 4.20
4841 4930 3.473625 ACTTGTTTGTTTACGGAGGGAG 58.526 45.455 0.00 0.00 0.00 4.30
4842 4931 3.118149 ACTTGTTTGTTTACGGAGGGAGT 60.118 43.478 0.00 0.00 0.00 3.85
4843 4932 4.101430 ACTTGTTTGTTTACGGAGGGAGTA 59.899 41.667 0.00 0.00 0.00 2.59
4844 4933 3.993920 TGTTTGTTTACGGAGGGAGTAC 58.006 45.455 0.00 0.00 0.00 2.73
4845 4934 3.642848 TGTTTGTTTACGGAGGGAGTACT 59.357 43.478 0.00 0.00 0.00 2.73
4846 4935 4.832266 TGTTTGTTTACGGAGGGAGTACTA 59.168 41.667 0.00 0.00 0.00 1.82
4847 4936 5.047802 TGTTTGTTTACGGAGGGAGTACTAG 60.048 44.000 0.00 0.00 0.00 2.57
4848 4937 4.307032 TGTTTACGGAGGGAGTACTAGT 57.693 45.455 0.00 0.00 0.00 2.57
4849 4938 4.666512 TGTTTACGGAGGGAGTACTAGTT 58.333 43.478 0.00 0.00 0.00 2.24
4850 4939 4.460382 TGTTTACGGAGGGAGTACTAGTTG 59.540 45.833 0.00 0.00 0.00 3.16
4851 4940 4.574674 TTACGGAGGGAGTACTAGTTGA 57.425 45.455 0.00 0.00 0.00 3.18
4852 4941 3.002038 ACGGAGGGAGTACTAGTTGAG 57.998 52.381 0.00 0.00 0.00 3.02
4853 4942 2.575279 ACGGAGGGAGTACTAGTTGAGA 59.425 50.000 0.00 0.00 0.00 3.27
4854 4943 3.009916 ACGGAGGGAGTACTAGTTGAGAA 59.990 47.826 0.00 0.00 0.00 2.87
4855 4944 4.208746 CGGAGGGAGTACTAGTTGAGAAT 58.791 47.826 0.00 0.00 0.00 2.40
4856 4945 5.104193 ACGGAGGGAGTACTAGTTGAGAATA 60.104 44.000 0.00 0.00 0.00 1.75
4857 4946 6.005198 CGGAGGGAGTACTAGTTGAGAATAT 58.995 44.000 0.00 0.00 0.00 1.28
4858 4947 6.490721 CGGAGGGAGTACTAGTTGAGAATATT 59.509 42.308 0.00 0.00 0.00 1.28
4859 4948 7.014422 CGGAGGGAGTACTAGTTGAGAATATTT 59.986 40.741 0.00 0.00 0.00 1.40
4860 4949 8.361889 GGAGGGAGTACTAGTTGAGAATATTTC 58.638 40.741 0.00 0.00 0.00 2.17
4861 4950 8.840200 AGGGAGTACTAGTTGAGAATATTTCA 57.160 34.615 0.00 0.00 0.00 2.69
4862 4951 9.440761 AGGGAGTACTAGTTGAGAATATTTCAT 57.559 33.333 0.00 0.00 0.00 2.57
4863 4952 9.482627 GGGAGTACTAGTTGAGAATATTTCATG 57.517 37.037 0.00 0.00 0.00 3.07
4872 4961 8.849168 AGTTGAGAATATTTCATGACAAACACA 58.151 29.630 0.00 0.00 0.00 3.72
4873 4962 9.121517 GTTGAGAATATTTCATGACAAACACAG 57.878 33.333 0.00 0.00 0.00 3.66
4874 4963 8.620116 TGAGAATATTTCATGACAAACACAGA 57.380 30.769 0.00 0.00 0.00 3.41
4875 4964 9.234827 TGAGAATATTTCATGACAAACACAGAT 57.765 29.630 0.00 0.00 0.00 2.90
4880 4969 5.611796 TTCATGACAAACACAGATACAGC 57.388 39.130 0.00 0.00 0.00 4.40
4881 4970 4.640364 TCATGACAAACACAGATACAGCA 58.360 39.130 0.00 0.00 0.00 4.41
4882 4971 5.062528 TCATGACAAACACAGATACAGCAA 58.937 37.500 0.00 0.00 0.00 3.91
4883 4972 5.179929 TCATGACAAACACAGATACAGCAAG 59.820 40.000 0.00 0.00 0.00 4.01
4884 4973 3.814842 TGACAAACACAGATACAGCAAGG 59.185 43.478 0.00 0.00 0.00 3.61
4885 4974 3.149196 ACAAACACAGATACAGCAAGGG 58.851 45.455 0.00 0.00 0.00 3.95
4886 4975 3.181445 ACAAACACAGATACAGCAAGGGA 60.181 43.478 0.00 0.00 0.00 4.20
4887 4976 3.788227 AACACAGATACAGCAAGGGAA 57.212 42.857 0.00 0.00 0.00 3.97
4888 4977 3.340814 ACACAGATACAGCAAGGGAAG 57.659 47.619 0.00 0.00 0.00 3.46
4889 4978 2.026822 ACACAGATACAGCAAGGGAAGG 60.027 50.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.992834 TAGCGCTTGATGGGGGACA 60.993 57.895 18.68 0.00 0.00 4.02
61 62 4.295119 GCGTGGACCCACTCGTGT 62.295 66.667 16.25 0.00 44.16 4.49
292 311 2.338984 GAACGCCGTGTCCAGAGT 59.661 61.111 0.00 0.00 0.00 3.24
424 451 1.009108 CACGCGTCCACATTTGCAA 60.009 52.632 9.86 0.00 0.00 4.08
516 555 1.444212 CCATTTTGACGGCGCTTGG 60.444 57.895 6.90 1.12 0.00 3.61
518 557 1.862602 GACCCATTTTGACGGCGCTT 61.863 55.000 6.90 0.00 0.00 4.68
559 598 2.950172 CTTCCGCGTTTGTGTCGGG 61.950 63.158 4.92 0.00 43.10 5.14
597 637 5.770663 TCACTTTTTATTCATTTGGGTCGGA 59.229 36.000 0.00 0.00 0.00 4.55
619 659 1.025812 ACGGACGGCAATTTTGTTCA 58.974 45.000 0.00 0.00 0.00 3.18
664 704 7.591006 ACACAATAATACAGTACGGTTCTTG 57.409 36.000 3.39 6.15 0.00 3.02
669 709 9.709495 TTTAGAAACACAATAATACAGTACGGT 57.291 29.630 3.62 3.62 0.00 4.83
674 714 9.893305 GCAACTTTAGAAACACAATAATACAGT 57.107 29.630 0.00 0.00 0.00 3.55
675 715 9.891828 TGCAACTTTAGAAACACAATAATACAG 57.108 29.630 0.00 0.00 0.00 2.74
676 716 9.891828 CTGCAACTTTAGAAACACAATAATACA 57.108 29.630 0.00 0.00 0.00 2.29
677 717 9.893305 ACTGCAACTTTAGAAACACAATAATAC 57.107 29.630 0.00 0.00 0.00 1.89
679 719 9.893305 GTACTGCAACTTTAGAAACACAATAAT 57.107 29.630 0.00 0.00 0.00 1.28
680 720 8.347035 GGTACTGCAACTTTAGAAACACAATAA 58.653 33.333 0.00 0.00 0.00 1.40
685 725 5.744666 TGGTACTGCAACTTTAGAAACAC 57.255 39.130 0.00 0.00 0.00 3.32
719 759 7.414436 CGGAGAAATTACACTTTTCTGTTCAA 58.586 34.615 3.58 0.00 42.08 2.69
1079 1122 3.055819 CCAACTGACCTATATCATCCGGG 60.056 52.174 0.00 0.00 0.00 5.73
1089 1132 2.615493 CCGCTGAAACCAACTGACCTAT 60.615 50.000 0.00 0.00 0.00 2.57
1090 1133 1.270625 CCGCTGAAACCAACTGACCTA 60.271 52.381 0.00 0.00 0.00 3.08
1091 1134 0.535102 CCGCTGAAACCAACTGACCT 60.535 55.000 0.00 0.00 0.00 3.85
1092 1135 0.534203 TCCGCTGAAACCAACTGACC 60.534 55.000 0.00 0.00 0.00 4.02
1093 1136 0.586802 GTCCGCTGAAACCAACTGAC 59.413 55.000 0.00 0.00 0.00 3.51
1094 1137 0.179234 TGTCCGCTGAAACCAACTGA 59.821 50.000 0.00 0.00 0.00 3.41
1095 1138 0.588252 CTGTCCGCTGAAACCAACTG 59.412 55.000 0.00 0.00 0.00 3.16
1096 1139 0.180406 ACTGTCCGCTGAAACCAACT 59.820 50.000 0.00 0.00 0.00 3.16
1097 1140 0.586802 GACTGTCCGCTGAAACCAAC 59.413 55.000 0.00 0.00 0.00 3.77
1098 1141 0.468226 AGACTGTCCGCTGAAACCAA 59.532 50.000 3.76 0.00 0.00 3.67
1102 1145 0.318699 CGTCAGACTGTCCGCTGAAA 60.319 55.000 3.76 0.00 42.27 2.69
1199 1242 2.028567 GGCACGGGGAATCAAATCAAAA 60.029 45.455 0.00 0.00 0.00 2.44
1299 1342 1.959226 GACGGTGCGAGCTTTCCAA 60.959 57.895 0.00 0.00 0.00 3.53
1406 1450 1.066143 CAAGGCTTCAGGTACGTGGAT 60.066 52.381 15.15 0.00 0.00 3.41
1470 1516 9.280174 CAAGTAAAAGAAAGGACAAGTATGGTA 57.720 33.333 0.00 0.00 0.00 3.25
1873 1920 1.633774 AGTCATCGACCTTGTCACCT 58.366 50.000 0.00 0.00 32.18 4.00
1903 1950 4.934797 TGGAACCTCCAGATCAGAAAAT 57.065 40.909 0.00 0.00 42.67 1.82
2004 2051 2.541288 GCATCAGCATCATCTCCCG 58.459 57.895 0.00 0.00 41.58 5.14
2209 2256 5.068591 AGGGTAAAAGTTAAACACCTGCAAG 59.931 40.000 0.00 0.00 0.00 4.01
2240 2287 8.253113 GCAATCATGGGAAAATAGAGAGAAAAA 58.747 33.333 0.00 0.00 0.00 1.94
2301 2350 4.190001 CAGAGATTGCTTGCATGTCTACT 58.810 43.478 9.81 7.38 0.00 2.57
2302 2351 3.311871 CCAGAGATTGCTTGCATGTCTAC 59.688 47.826 9.81 5.87 0.00 2.59
2455 2510 7.642071 ACATGTTTTATTGTTCACAGAATGC 57.358 32.000 0.00 0.00 42.53 3.56
2484 2539 6.293407 CGATTGACACGGCAAAAGGATATATT 60.293 38.462 0.00 0.00 0.00 1.28
2490 2545 0.871722 CGATTGACACGGCAAAAGGA 59.128 50.000 0.00 0.00 0.00 3.36
2583 2638 8.664798 TGTAATAAGACAAACATGCTGTGATAC 58.335 33.333 5.80 3.57 0.00 2.24
2588 2643 7.686438 TCATGTAATAAGACAAACATGCTGT 57.314 32.000 8.96 0.79 45.59 4.40
3070 3130 1.228245 TGGCTCAACACCTTCTGCC 60.228 57.895 0.00 0.00 40.62 4.85
3262 3322 1.526575 CCTCGCAAACCTGCCACATT 61.527 55.000 0.00 0.00 46.56 2.71
3391 3451 4.036144 GCATTGTAGAATTTGGAGGAGAGC 59.964 45.833 0.00 0.00 0.00 4.09
3449 3509 2.834113 TGCTAGCTCCTTACCCTTCTT 58.166 47.619 17.23 0.00 0.00 2.52
3520 3580 1.556911 CCCACATAGAGCTTCACCAGT 59.443 52.381 0.00 0.00 0.00 4.00
3841 3901 4.002982 TCTTCTTGTTGAATGGATCGGTG 58.997 43.478 0.00 0.00 33.71 4.94
4060 4120 0.032678 AGGGCAGCAACTCGATATCG 59.967 55.000 19.14 19.14 41.45 2.92
4070 4130 7.290061 ACATAAATAAGAATCTAGGGCAGCAA 58.710 34.615 0.00 0.00 0.00 3.91
4181 4241 3.006752 CCACAAAAAGCAATCTAAGGCCA 59.993 43.478 5.01 0.00 0.00 5.36
4212 4272 3.375782 TCCATCATACGAGCATCAGTG 57.624 47.619 0.00 0.00 33.17 3.66
4332 4392 4.548669 ACCCAAGTAAAGTTGGCCTAAAA 58.451 39.130 3.32 0.00 45.08 1.52
4398 4469 5.358442 TCCTACAAACTTAAGTGCTGCAAAA 59.642 36.000 9.34 0.00 0.00 2.44
4449 4520 9.927668 TTCCTTTGAAATATGAAGGATTTGTTC 57.072 29.630 5.03 0.00 45.99 3.18
4511 4582 8.530311 AGAGATGTCGCTTGATTCATAAGATAT 58.470 33.333 0.00 0.00 0.00 1.63
4528 4599 9.862371 ATTGCCTATAGTATTAAAGAGATGTCG 57.138 33.333 0.00 0.00 0.00 4.35
4540 4611 8.470805 CGGAGTATCTCAATTGCCTATAGTATT 58.529 37.037 0.00 0.00 33.73 1.89
4544 4633 6.375736 TCTCGGAGTATCTCAATTGCCTATAG 59.624 42.308 4.69 0.00 33.73 1.31
4545 4634 6.246163 TCTCGGAGTATCTCAATTGCCTATA 58.754 40.000 4.69 0.00 33.73 1.31
4548 4637 3.300388 TCTCGGAGTATCTCAATTGCCT 58.700 45.455 4.69 0.00 33.73 4.75
4550 4639 4.688021 AGTTCTCGGAGTATCTCAATTGC 58.312 43.478 4.69 0.00 33.73 3.56
4561 4650 5.010933 TGAGATCACTTTAGTTCTCGGAGT 58.989 41.667 4.69 0.00 35.65 3.85
4563 4652 5.312120 GTGAGATCACTTTAGTTCTCGGA 57.688 43.478 5.72 0.00 43.25 4.55
4576 4665 6.052360 GGAGGAATAGGAAAAGTGAGATCAC 58.948 44.000 4.77 4.77 46.77 3.06
4577 4666 5.726308 TGGAGGAATAGGAAAAGTGAGATCA 59.274 40.000 0.00 0.00 0.00 2.92
4578 4667 6.240549 TGGAGGAATAGGAAAAGTGAGATC 57.759 41.667 0.00 0.00 0.00 2.75
4580 4669 6.272324 TCTTTGGAGGAATAGGAAAAGTGAGA 59.728 38.462 0.00 0.00 0.00 3.27
4581 4670 6.476378 TCTTTGGAGGAATAGGAAAAGTGAG 58.524 40.000 0.00 0.00 0.00 3.51
4582 4671 6.448369 TCTTTGGAGGAATAGGAAAAGTGA 57.552 37.500 0.00 0.00 0.00 3.41
4583 4672 6.749923 CTCTTTGGAGGAATAGGAAAAGTG 57.250 41.667 0.00 0.00 36.03 3.16
4608 4697 8.352942 CCTACACTTCTGTTTTTCAGCTTAATT 58.647 33.333 0.00 0.00 43.32 1.40
4609 4698 7.719633 TCCTACACTTCTGTTTTTCAGCTTAAT 59.280 33.333 0.00 0.00 43.32 1.40
4612 4701 5.297029 GTCCTACACTTCTGTTTTTCAGCTT 59.703 40.000 0.00 0.00 43.32 3.74
4628 4717 2.159627 CCAAATGTTGCGAGTCCTACAC 59.840 50.000 0.00 0.00 0.00 2.90
4654 4743 0.737019 GGGGCACAAATGACAATGCG 60.737 55.000 0.00 0.00 39.02 4.73
4671 4760 8.980481 ACCTGAGTTATAAACAATAATGAGGG 57.020 34.615 0.00 0.00 32.70 4.30
4700 4789 2.403561 AGGCTGGAGGGTTTATCTCTC 58.596 52.381 0.00 0.00 42.62 3.20
4727 4816 5.847670 AAGCTCGTGATAAGACTTTCAAC 57.152 39.130 0.00 0.00 0.00 3.18
4752 4841 4.166246 TCTGGATAGCTTCTTCGTAGGA 57.834 45.455 0.00 0.00 0.00 2.94
4753 4842 5.226396 CAATCTGGATAGCTTCTTCGTAGG 58.774 45.833 0.00 0.00 0.00 3.18
4754 4843 5.226396 CCAATCTGGATAGCTTCTTCGTAG 58.774 45.833 0.00 0.00 40.96 3.51
4755 4844 4.501571 GCCAATCTGGATAGCTTCTTCGTA 60.502 45.833 0.00 0.00 40.96 3.43
4756 4845 3.742640 GCCAATCTGGATAGCTTCTTCGT 60.743 47.826 0.00 0.00 40.96 3.85
4757 4846 2.805099 GCCAATCTGGATAGCTTCTTCG 59.195 50.000 0.00 0.00 40.96 3.79
4758 4847 2.805099 CGCCAATCTGGATAGCTTCTTC 59.195 50.000 0.00 0.00 40.96 2.87
4759 4848 2.435805 TCGCCAATCTGGATAGCTTCTT 59.564 45.455 0.00 0.00 40.96 2.52
4760 4849 2.042464 TCGCCAATCTGGATAGCTTCT 58.958 47.619 0.00 0.00 40.96 2.85
4761 4850 2.533266 TCGCCAATCTGGATAGCTTC 57.467 50.000 0.00 0.00 40.96 3.86
4762 4851 2.171448 ACTTCGCCAATCTGGATAGCTT 59.829 45.455 0.00 0.00 40.96 3.74
4763 4852 1.765314 ACTTCGCCAATCTGGATAGCT 59.235 47.619 0.00 0.00 40.96 3.32
4764 4853 2.246719 ACTTCGCCAATCTGGATAGC 57.753 50.000 0.00 0.00 40.96 2.97
4765 4854 4.551388 GAGTACTTCGCCAATCTGGATAG 58.449 47.826 0.00 0.00 40.96 2.08
4766 4855 3.321111 GGAGTACTTCGCCAATCTGGATA 59.679 47.826 0.00 0.00 40.96 2.59
4767 4856 2.103263 GGAGTACTTCGCCAATCTGGAT 59.897 50.000 0.00 0.00 40.96 3.41
4768 4857 1.480954 GGAGTACTTCGCCAATCTGGA 59.519 52.381 0.00 0.00 40.96 3.86
4769 4858 1.473434 GGGAGTACTTCGCCAATCTGG 60.473 57.143 0.00 0.00 41.55 3.86
4770 4859 1.482593 AGGGAGTACTTCGCCAATCTG 59.517 52.381 0.00 0.00 39.46 2.90
4771 4860 1.757699 GAGGGAGTACTTCGCCAATCT 59.242 52.381 0.00 0.00 39.46 2.40
4772 4861 1.202545 GGAGGGAGTACTTCGCCAATC 60.203 57.143 12.62 5.48 39.46 2.67
4773 4862 0.831307 GGAGGGAGTACTTCGCCAAT 59.169 55.000 12.62 0.00 39.46 3.16
4774 4863 1.601419 CGGAGGGAGTACTTCGCCAA 61.601 60.000 15.98 0.00 39.46 4.52
4775 4864 2.050350 CGGAGGGAGTACTTCGCCA 61.050 63.158 15.98 0.00 39.46 5.69
4776 4865 0.749454 TACGGAGGGAGTACTTCGCC 60.749 60.000 0.00 3.42 43.24 5.54
4777 4866 1.098050 TTACGGAGGGAGTACTTCGC 58.902 55.000 0.00 0.00 43.24 4.70
4778 4867 2.489329 TGTTTACGGAGGGAGTACTTCG 59.511 50.000 0.00 0.00 44.95 3.79
4779 4868 4.525912 TTGTTTACGGAGGGAGTACTTC 57.474 45.455 0.00 0.00 0.00 3.01
4780 4869 4.961438 TTTGTTTACGGAGGGAGTACTT 57.039 40.909 0.00 0.00 0.00 2.24
4781 4870 6.803366 ATATTTGTTTACGGAGGGAGTACT 57.197 37.500 0.00 0.00 0.00 2.73
4782 4871 8.947055 TTTATATTTGTTTACGGAGGGAGTAC 57.053 34.615 0.00 0.00 0.00 2.73
4783 4872 9.603921 CTTTTATATTTGTTTACGGAGGGAGTA 57.396 33.333 0.00 0.00 0.00 2.59
4784 4873 7.066645 GCTTTTATATTTGTTTACGGAGGGAGT 59.933 37.037 0.00 0.00 0.00 3.85
4785 4874 7.415229 GCTTTTATATTTGTTTACGGAGGGAG 58.585 38.462 0.00 0.00 0.00 4.30
4786 4875 6.037391 CGCTTTTATATTTGTTTACGGAGGGA 59.963 38.462 0.00 0.00 0.00 4.20
4787 4876 6.183360 ACGCTTTTATATTTGTTTACGGAGGG 60.183 38.462 0.00 0.00 0.00 4.30
4788 4877 6.778108 ACGCTTTTATATTTGTTTACGGAGG 58.222 36.000 0.00 0.00 0.00 4.30
4789 4878 8.663771 AAACGCTTTTATATTTGTTTACGGAG 57.336 30.769 0.00 0.00 0.00 4.63
4790 4879 9.540431 GTAAACGCTTTTATATTTGTTTACGGA 57.460 29.630 9.24 0.00 40.64 4.69
4803 4892 9.738832 ACAAACAAGTAATGTAAACGCTTTTAT 57.261 25.926 0.00 0.00 42.99 1.40
4804 4893 9.570488 AACAAACAAGTAATGTAAACGCTTTTA 57.430 25.926 0.00 0.00 42.99 1.52
4805 4894 8.468720 AACAAACAAGTAATGTAAACGCTTTT 57.531 26.923 0.00 0.00 42.99 2.27
4806 4895 8.468720 AAACAAACAAGTAATGTAAACGCTTT 57.531 26.923 0.00 0.00 42.99 3.51
4807 4896 9.012448 GTAAACAAACAAGTAATGTAAACGCTT 57.988 29.630 0.00 0.00 42.99 4.68
4808 4897 7.373966 CGTAAACAAACAAGTAATGTAAACGCT 59.626 33.333 10.31 0.00 42.99 5.07
4809 4898 7.356638 CCGTAAACAAACAAGTAATGTAAACGC 60.357 37.037 14.04 0.00 42.99 4.84
4810 4899 7.850003 TCCGTAAACAAACAAGTAATGTAAACG 59.150 33.333 13.27 13.27 42.99 3.60
4811 4900 9.161684 CTCCGTAAACAAACAAGTAATGTAAAC 57.838 33.333 0.00 0.00 42.99 2.01
4812 4901 8.344098 CCTCCGTAAACAAACAAGTAATGTAAA 58.656 33.333 0.00 0.00 42.99 2.01
4813 4902 7.041235 CCCTCCGTAAACAAACAAGTAATGTAA 60.041 37.037 0.00 0.00 42.99 2.41
4814 4903 6.427547 CCCTCCGTAAACAAACAAGTAATGTA 59.572 38.462 0.00 0.00 42.99 2.29
4815 4904 5.239963 CCCTCCGTAAACAAACAAGTAATGT 59.760 40.000 0.00 0.00 46.82 2.71
4816 4905 5.470777 TCCCTCCGTAAACAAACAAGTAATG 59.529 40.000 0.00 0.00 0.00 1.90
4817 4906 5.623169 TCCCTCCGTAAACAAACAAGTAAT 58.377 37.500 0.00 0.00 0.00 1.89
4818 4907 5.033589 TCCCTCCGTAAACAAACAAGTAA 57.966 39.130 0.00 0.00 0.00 2.24
4819 4908 4.101430 ACTCCCTCCGTAAACAAACAAGTA 59.899 41.667 0.00 0.00 0.00 2.24
4820 4909 3.118149 ACTCCCTCCGTAAACAAACAAGT 60.118 43.478 0.00 0.00 0.00 3.16
4821 4910 3.473625 ACTCCCTCCGTAAACAAACAAG 58.526 45.455 0.00 0.00 0.00 3.16
4822 4911 3.564053 ACTCCCTCCGTAAACAAACAA 57.436 42.857 0.00 0.00 0.00 2.83
4823 4912 3.642848 AGTACTCCCTCCGTAAACAAACA 59.357 43.478 0.00 0.00 0.00 2.83
4824 4913 4.263018 AGTACTCCCTCCGTAAACAAAC 57.737 45.455 0.00 0.00 0.00 2.93
4825 4914 5.079643 ACTAGTACTCCCTCCGTAAACAAA 58.920 41.667 0.00 0.00 0.00 2.83
4826 4915 4.666512 ACTAGTACTCCCTCCGTAAACAA 58.333 43.478 0.00 0.00 0.00 2.83
4827 4916 4.307032 ACTAGTACTCCCTCCGTAAACA 57.693 45.455 0.00 0.00 0.00 2.83
4828 4917 4.702131 TCAACTAGTACTCCCTCCGTAAAC 59.298 45.833 0.00 0.00 0.00 2.01
4829 4918 4.922206 TCAACTAGTACTCCCTCCGTAAA 58.078 43.478 0.00 0.00 0.00 2.01
4830 4919 4.225942 TCTCAACTAGTACTCCCTCCGTAA 59.774 45.833 0.00 0.00 0.00 3.18
4831 4920 3.776969 TCTCAACTAGTACTCCCTCCGTA 59.223 47.826 0.00 0.00 0.00 4.02
4832 4921 2.575279 TCTCAACTAGTACTCCCTCCGT 59.425 50.000 0.00 0.00 0.00 4.69
4833 4922 3.278668 TCTCAACTAGTACTCCCTCCG 57.721 52.381 0.00 0.00 0.00 4.63
4834 4923 7.842887 AATATTCTCAACTAGTACTCCCTCC 57.157 40.000 0.00 0.00 0.00 4.30
4835 4924 8.915036 TGAAATATTCTCAACTAGTACTCCCTC 58.085 37.037 0.00 0.00 0.00 4.30
4836 4925 8.840200 TGAAATATTCTCAACTAGTACTCCCT 57.160 34.615 0.00 0.00 0.00 4.20
4837 4926 9.482627 CATGAAATATTCTCAACTAGTACTCCC 57.517 37.037 0.00 0.00 0.00 4.30
4846 4935 8.849168 TGTGTTTGTCATGAAATATTCTCAACT 58.151 29.630 0.00 0.00 0.00 3.16
4847 4936 9.121517 CTGTGTTTGTCATGAAATATTCTCAAC 57.878 33.333 0.00 0.00 0.00 3.18
4848 4937 9.065798 TCTGTGTTTGTCATGAAATATTCTCAA 57.934 29.630 0.00 0.00 0.00 3.02
4849 4938 8.620116 TCTGTGTTTGTCATGAAATATTCTCA 57.380 30.769 0.00 0.00 0.00 3.27
4854 4943 8.400947 GCTGTATCTGTGTTTGTCATGAAATAT 58.599 33.333 0.00 0.00 0.00 1.28
4855 4944 7.390162 TGCTGTATCTGTGTTTGTCATGAAATA 59.610 33.333 0.00 0.00 0.00 1.40
4856 4945 6.207221 TGCTGTATCTGTGTTTGTCATGAAAT 59.793 34.615 0.00 0.00 0.00 2.17
4857 4946 5.530543 TGCTGTATCTGTGTTTGTCATGAAA 59.469 36.000 0.00 0.00 0.00 2.69
4858 4947 5.062528 TGCTGTATCTGTGTTTGTCATGAA 58.937 37.500 0.00 0.00 0.00 2.57
4859 4948 4.640364 TGCTGTATCTGTGTTTGTCATGA 58.360 39.130 0.00 0.00 0.00 3.07
4860 4949 5.361135 TTGCTGTATCTGTGTTTGTCATG 57.639 39.130 0.00 0.00 0.00 3.07
4861 4950 4.456911 CCTTGCTGTATCTGTGTTTGTCAT 59.543 41.667 0.00 0.00 0.00 3.06
4862 4951 3.814842 CCTTGCTGTATCTGTGTTTGTCA 59.185 43.478 0.00 0.00 0.00 3.58
4863 4952 3.189287 CCCTTGCTGTATCTGTGTTTGTC 59.811 47.826 0.00 0.00 0.00 3.18
4864 4953 3.149196 CCCTTGCTGTATCTGTGTTTGT 58.851 45.455 0.00 0.00 0.00 2.83
4865 4954 3.411446 TCCCTTGCTGTATCTGTGTTTG 58.589 45.455 0.00 0.00 0.00 2.93
4866 4955 3.788227 TCCCTTGCTGTATCTGTGTTT 57.212 42.857 0.00 0.00 0.00 2.83
4867 4956 3.560025 CCTTCCCTTGCTGTATCTGTGTT 60.560 47.826 0.00 0.00 0.00 3.32
4868 4957 2.026822 CCTTCCCTTGCTGTATCTGTGT 60.027 50.000 0.00 0.00 0.00 3.72
4869 4958 2.636830 CCTTCCCTTGCTGTATCTGTG 58.363 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.