Multiple sequence alignment - TraesCS2B01G584000

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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 TraesCS2B01G584000 chr2B 100.000 4697 0 0 1 4697 771183999 771188695 0.000000e+00 8674.0
1 TraesCS2B01G584000 chr2B 82.536 481 62 6 2499 2979 770663287 770662829 2.040000e-108 403.0
2 TraesCS2B01G584000 chr2B 80.000 515 81 17 254 753 221485111 221485618 1.240000e-95 361.0
3 TraesCS2B01G584000 chr2B 93.846 65 4 0 4280 4344 571714465 571714529 1.080000e-16 99.0
4 TraesCS2B01G584000 chr2D 90.064 3573 193 69 806 4273 628158980 628162495 0.000000e+00 4482.0
5 TraesCS2B01G584000 chr2D 90.765 823 54 9 1 807 628158126 628158942 0.000000e+00 1079.0
6 TraesCS2B01G584000 chr2D 83.811 593 74 7 2340 2919 627911962 627911379 1.150000e-150 544.0
7 TraesCS2B01G584000 chr2D 82.857 315 30 15 4361 4664 628162547 628162848 1.300000e-65 261.0
8 TraesCS2B01G584000 chr2D 77.698 278 35 19 3981 4245 627911002 627910739 1.360000e-30 145.0
9 TraesCS2B01G584000 chr2A 92.594 2876 168 18 941 3788 758530149 758533007 0.000000e+00 4089.0
10 TraesCS2B01G584000 chr2A 86.654 532 66 4 2340 2868 758384732 758384203 6.770000e-163 584.0
11 TraesCS2B01G584000 chr2A 82.435 501 48 21 3788 4273 758533046 758533521 7.320000e-108 401.0
12 TraesCS2B01G584000 chr2A 85.586 222 21 4 4369 4588 758533560 758533772 6.120000e-54 222.0
13 TraesCS2B01G584000 chr2A 87.037 108 12 2 702 807 692528064 692527957 2.300000e-23 121.0
14 TraesCS2B01G584000 chr4A 78.455 738 123 24 87 807 135623069 135623787 2.580000e-122 449.0
15 TraesCS2B01G584000 chr4A 79.909 219 28 4 2475 2692 420018032 420017829 3.790000e-31 147.0
16 TraesCS2B01G584000 chr4A 93.651 63 4 0 4280 4342 647942169 647942107 1.390000e-15 95.3
17 TraesCS2B01G584000 chr3B 81.778 225 26 6 2468 2692 726178949 726178740 1.740000e-39 174.0
18 TraesCS2B01G584000 chr1A 79.556 225 30 4 2469 2692 558015562 558015771 3.790000e-31 147.0
19 TraesCS2B01G584000 chr3D 90.476 105 10 0 2588 2692 30972979 30973083 6.340000e-29 139.0
20 TraesCS2B01G584000 chr3D 91.176 68 4 2 4283 4349 264427664 264427598 1.800000e-14 91.6
21 TraesCS2B01G584000 chrUn 93.056 72 3 2 4280 4350 27374842 27374772 2.310000e-18 104.0
22 TraesCS2B01G584000 chrUn 89.855 69 3 4 4286 4351 323134059 323134126 8.370000e-13 86.1
23 TraesCS2B01G584000 chrUn 89.855 69 3 4 4286 4351 333082398 333082331 8.370000e-13 86.1
24 TraesCS2B01G584000 chr1B 93.056 72 2 3 4278 4348 16953317 16953386 8.320000e-18 102.0
25 TraesCS2B01G584000 chr1B 90.741 54 3 1 1115 1168 557401287 557401236 2.340000e-08 71.3
26 TraesCS2B01G584000 chr5D 91.667 72 4 2 4279 4349 390273845 390273915 1.080000e-16 99.0
27 TraesCS2B01G584000 chr5A 89.333 75 2 4 4279 4349 493473946 493474018 6.470000e-14 89.8
28 TraesCS2B01G584000 chr7B 84.932 73 8 1 1086 1158 577295487 577295556 2.340000e-08 71.3


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 TraesCS2B01G584000 chr2B 771183999 771188695 4696 False 8674.000000 8674 100.000000 1 4697 1 chr2B.!!$F3 4696
1 TraesCS2B01G584000 chr2B 221485111 221485618 507 False 361.000000 361 80.000000 254 753 1 chr2B.!!$F1 499
2 TraesCS2B01G584000 chr2D 628158126 628162848 4722 False 1940.666667 4482 87.895333 1 4664 3 chr2D.!!$F1 4663
3 TraesCS2B01G584000 chr2D 627910739 627911962 1223 True 344.500000 544 80.754500 2340 4245 2 chr2D.!!$R1 1905
4 TraesCS2B01G584000 chr2A 758530149 758533772 3623 False 1570.666667 4089 86.871667 941 4588 3 chr2A.!!$F1 3647
5 TraesCS2B01G584000 chr2A 758384203 758384732 529 True 584.000000 584 86.654000 2340 2868 1 chr2A.!!$R2 528
6 TraesCS2B01G584000 chr4A 135623069 135623787 718 False 449.000000 449 78.455000 87 807 1 chr4A.!!$F1 720

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
794 851 0.456628 TCAGTGACCGACGTTTCACA 59.543 50.0 22.02 6.31 43.94 3.58 F
1461 1609 0.773644 ACCTTTGACATCCCAGCACT 59.226 50.0 0.00 0.00 0.00 4.40 F
1858 2046 0.774096 TGTGAGGGGAATTGGTGGGA 60.774 55.0 0.00 0.00 0.00 4.37 F
2134 2325 1.230635 ACATCACACCACAGAAGCGC 61.231 55.0 0.00 0.00 0.00 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 2098 0.037590 AAACGTCTGGCAGCCCATTA 59.962 50.0 9.64 0.00 41.21 1.90 R
2583 2785 0.322456 TTCGATGGTTCTTGGCTGGG 60.322 55.0 0.00 0.00 0.00 4.45 R
3272 3482 0.323178 CTCTGCTTCCTTGGCCATGT 60.323 55.0 6.09 0.00 0.00 3.21 R
4034 4423 0.439985 CACAAAGTCTGGCACGATCG 59.560 55.0 14.88 14.88 0.00 3.69 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
31 32 6.909550 TTGGGCTACACTATCAACATTTTT 57.090 33.333 0.00 0.00 0.00 1.94
95 106 4.899239 CCGCCGCCAGATCTGACC 62.899 72.222 24.62 13.04 0.00 4.02
115 126 3.272020 ACCATATCCAATGACCCAACCTT 59.728 43.478 0.00 0.00 0.00 3.50
159 170 4.035208 AGGCAGTGTTGAAGAACTTTTACG 59.965 41.667 0.00 0.00 32.79 3.18
166 177 5.006358 TGTTGAAGAACTTTTACGACAGAGC 59.994 40.000 0.00 0.00 32.79 4.09
208 252 3.469564 AACAGAGGTTGTGTCGCAA 57.530 47.368 0.00 0.00 40.74 4.85
329 379 3.067106 CACTAGTGCCATTGTCGTCTTT 58.933 45.455 10.54 0.00 0.00 2.52
353 403 2.830285 GCAACTCCGCCGTTGTTGT 61.830 57.895 16.61 0.00 44.61 3.32
371 421 1.937223 TGTCGAAATTTGTCAGCGTGT 59.063 42.857 0.00 0.00 0.00 4.49
373 423 1.937223 TCGAAATTTGTCAGCGTGTGT 59.063 42.857 0.00 0.00 0.00 3.72
453 504 4.988598 CGCTGGTCCTGCAACCGT 62.989 66.667 19.58 0.00 42.62 4.83
521 573 0.815615 GACGACAAGGGGGATGCATC 60.816 60.000 18.81 18.81 0.00 3.91
554 606 0.663568 AAGGTTGCGTCGTTCTCTCG 60.664 55.000 0.00 0.00 0.00 4.04
562 614 1.677942 GTCGTTCTCTCGGTCCCTAT 58.322 55.000 0.00 0.00 0.00 2.57
615 667 4.592192 CCTCGGCGGCATCGATGT 62.592 66.667 25.47 0.00 39.00 3.06
769 825 4.437239 CAGGAATGGAAGTAGCTACACAG 58.563 47.826 25.28 5.99 0.00 3.66
794 851 0.456628 TCAGTGACCGACGTTTCACA 59.543 50.000 22.02 6.31 43.94 3.58
832 928 2.108514 TAGGACGCGGTGGACGTAG 61.109 63.158 12.47 0.00 45.24 3.51
835 931 1.513586 GACGCGGTGGACGTAGAAG 60.514 63.158 12.47 0.00 45.24 2.85
845 944 3.858238 GTGGACGTAGAAGAAAAGATCGG 59.142 47.826 0.00 0.00 0.00 4.18
853 952 3.006537 AGAAGAAAAGATCGGTCGGTTGA 59.993 43.478 0.00 0.00 0.00 3.18
871 970 4.170256 GTTGAACACGAGCTTTTCCAAAA 58.830 39.130 0.00 0.00 0.00 2.44
931 1030 2.263153 GGCACGGGCATTTTACAGT 58.737 52.632 13.89 0.00 43.71 3.55
932 1031 1.455248 GGCACGGGCATTTTACAGTA 58.545 50.000 13.89 0.00 43.71 2.74
933 1032 1.400494 GGCACGGGCATTTTACAGTAG 59.600 52.381 13.89 0.00 43.71 2.57
934 1033 1.202143 GCACGGGCATTTTACAGTAGC 60.202 52.381 3.77 0.00 40.72 3.58
936 1035 1.066716 ACGGGCATTTTACAGTAGCGA 60.067 47.619 0.00 0.00 0.00 4.93
937 1036 1.326548 CGGGCATTTTACAGTAGCGAC 59.673 52.381 0.00 0.00 0.00 5.19
939 1038 1.326548 GGCATTTTACAGTAGCGACCG 59.673 52.381 0.00 0.00 0.00 4.79
984 1104 1.477923 CCAGAGTCGAAACCCCCAAAA 60.478 52.381 0.00 0.00 0.00 2.44
1371 1518 3.187699 CTCCGTGGATCTCGAGCGG 62.188 68.421 18.79 18.79 43.32 5.52
1410 1557 1.654023 GGTACAAGCGCCATTCCCAC 61.654 60.000 2.29 0.00 0.00 4.61
1440 1588 4.981812 AGGTACGAATGATTTTATCCCCC 58.018 43.478 0.00 0.00 0.00 5.40
1461 1609 0.773644 ACCTTTGACATCCCAGCACT 59.226 50.000 0.00 0.00 0.00 4.40
1462 1610 1.985159 ACCTTTGACATCCCAGCACTA 59.015 47.619 0.00 0.00 0.00 2.74
1540 1716 5.228635 CGTTATTCTGCAATGTGCTCAATTC 59.771 40.000 1.43 0.00 45.31 2.17
1634 1822 5.758296 TGTGCGAATGGAATAGAAGTAATCC 59.242 40.000 0.00 0.00 0.00 3.01
1652 1840 8.499403 AGTAATCCTTGTGAAATCTTAGCTTC 57.501 34.615 0.00 0.00 0.00 3.86
1655 1843 3.181506 CCTTGTGAAATCTTAGCTTCGCC 60.182 47.826 0.00 0.00 32.28 5.54
1728 1916 7.228706 TGGAACTAAACTGTTTCCTCTGAAATC 59.771 37.037 9.38 0.00 42.20 2.17
1810 1998 1.000396 GGCCAAGGAATCCTGTGCT 60.000 57.895 18.76 0.00 32.13 4.40
1851 2039 7.071824 TGTTTTTAGGAAATTGTGAGGGGAATT 59.928 33.333 0.00 0.00 0.00 2.17
1858 2046 0.774096 TGTGAGGGGAATTGGTGGGA 60.774 55.000 0.00 0.00 0.00 4.37
1887 2075 5.033589 AGACATCCCAAAAATTTGCAACA 57.966 34.783 0.00 0.00 36.86 3.33
1897 2085 1.873698 ATTTGCAACAAGCCAAGCAG 58.126 45.000 0.00 0.00 44.83 4.24
1910 2098 5.945144 AGCCAAGCAGGAATTGAAATATT 57.055 34.783 0.00 0.00 41.22 1.28
1925 2113 4.584325 TGAAATATTAATGGGCTGCCAGAC 59.416 41.667 22.05 3.49 0.00 3.51
1996 2184 4.023291 ACAACCCAGAAATAATTCCGCAT 58.977 39.130 0.00 0.00 36.12 4.73
1998 2186 3.631250 ACCCAGAAATAATTCCGCATGT 58.369 40.909 0.00 0.00 36.12 3.21
2003 2191 7.040686 ACCCAGAAATAATTCCGCATGTTATAC 60.041 37.037 0.00 0.00 36.12 1.47
2032 2220 3.772387 TGCTTGGGGAACATTGATAACA 58.228 40.909 0.00 0.00 0.00 2.41
2037 2225 6.351286 GCTTGGGGAACATTGATAACATCTTT 60.351 38.462 0.00 0.00 0.00 2.52
2047 2238 8.946085 ACATTGATAACATCTTTTTCTTAGCGA 58.054 29.630 0.00 0.00 0.00 4.93
2095 2286 9.286170 ACTTTTAAAGACCCTTTGAACTAGATC 57.714 33.333 12.02 0.00 0.00 2.75
2108 2299 8.442632 TTTGAACTAGATCCTATGAGCATTTG 57.557 34.615 0.00 0.00 0.00 2.32
2134 2325 1.230635 ACATCACACCACAGAAGCGC 61.231 55.000 0.00 0.00 0.00 5.92
2325 2519 1.242076 CAGTTGTCTTCAAGGCCAGG 58.758 55.000 5.01 0.00 33.97 4.45
2394 2589 8.837389 GTTTCATACCTTCTGTTTGTACTTCTT 58.163 33.333 0.00 0.00 0.00 2.52
2508 2710 7.064253 GGTATGAACATGTCTTACACTAACCAC 59.936 40.741 0.00 0.00 38.20 4.16
2529 2731 4.536364 CGCAATACGTTTGGATCTCATT 57.464 40.909 0.00 0.00 36.87 2.57
2544 2746 2.811431 TCTCATTTACAAAGTGCGTGGG 59.189 45.455 0.00 0.00 0.00 4.61
2583 2785 2.044123 ATTTCGATGGCCTTCCTGAC 57.956 50.000 12.77 0.00 0.00 3.51
2658 2866 3.120854 CGAAGAAGGAAGAGAAAGCAACG 60.121 47.826 0.00 0.00 0.00 4.10
2814 3022 2.568062 TGTTAAGCCGGATAACCTGACA 59.432 45.455 21.09 5.57 33.32 3.58
2826 3036 3.354948 AACCTGACATGCTGCATTCTA 57.645 42.857 13.38 0.94 0.00 2.10
2859 3069 2.677836 TGCGGCATTGAACAAGATAGAC 59.322 45.455 0.00 0.00 0.00 2.59
2916 3126 1.611261 TGGGGTTCTAGGGTGGTCG 60.611 63.158 0.00 0.00 0.00 4.79
3078 3288 2.736719 CGTAGGCAATCTGAGTGAGGTG 60.737 54.545 9.58 0.00 0.00 4.00
3093 3303 2.154074 GGTGAAGAGGGTGTGGGGT 61.154 63.158 0.00 0.00 0.00 4.95
3159 3369 2.119655 CATGCTGCAGGCCCTTCTC 61.120 63.158 17.12 0.00 40.92 2.87
3252 3462 2.656560 AGCTGACTAACGTGATGACC 57.343 50.000 0.00 0.00 0.00 4.02
3266 3476 3.775654 GACCCGAGCCCACCTGAG 61.776 72.222 0.00 0.00 0.00 3.35
3272 3482 1.617018 CGAGCCCACCTGAGGAATGA 61.617 60.000 4.99 0.00 0.00 2.57
3324 3534 2.573340 GCCAAGGAAATGGGTGCG 59.427 61.111 0.00 0.00 41.01 5.34
3330 3540 0.958822 AGGAAATGGGTGCGTGTTTC 59.041 50.000 0.00 0.00 0.00 2.78
3457 3667 2.039613 GGGAAGCTGGATCCTGATAAGG 59.960 54.545 21.91 0.00 37.14 2.69
3558 3768 3.430862 TGCATCGACGGCAAAGCC 61.431 61.111 10.85 0.00 46.75 4.35
3637 3847 2.414481 CAGCAGATCAAAGACGACAAGG 59.586 50.000 0.00 0.00 0.00 3.61
3639 3849 2.413453 GCAGATCAAAGACGACAAGGTC 59.587 50.000 0.00 0.00 37.19 3.85
3676 3886 1.748500 GGGAAGCTGCTCAAGAGGC 60.749 63.158 1.00 0.00 0.00 4.70
3684 3897 2.125350 CTCAAGAGGCTGGGCGAC 60.125 66.667 0.00 0.00 0.00 5.19
3685 3898 2.922503 TCAAGAGGCTGGGCGACA 60.923 61.111 0.00 0.00 0.00 4.35
3686 3899 2.032528 CAAGAGGCTGGGCGACAA 59.967 61.111 0.00 0.00 0.00 3.18
3702 3915 0.039618 ACAAGGGGCGATGAAATGGT 59.960 50.000 0.00 0.00 0.00 3.55
3703 3916 1.283613 ACAAGGGGCGATGAAATGGTA 59.716 47.619 0.00 0.00 0.00 3.25
3704 3917 1.676006 CAAGGGGCGATGAAATGGTAC 59.324 52.381 0.00 0.00 0.00 3.34
3763 4082 2.496070 TCTGATTCCTTCCGTGAACGAT 59.504 45.455 4.03 0.00 43.02 3.73
3764 4083 3.697542 TCTGATTCCTTCCGTGAACGATA 59.302 43.478 4.03 0.00 43.02 2.92
3769 4088 1.659098 CCTTCCGTGAACGATAAGCAC 59.341 52.381 4.03 0.00 43.02 4.40
3805 4163 2.187073 GCCCTTGTTCTGGCTCATG 58.813 57.895 0.00 0.00 44.46 3.07
3820 4178 1.080569 CATGGGCGTTTGGTGCTTC 60.081 57.895 0.00 0.00 0.00 3.86
3956 4329 3.935203 CTGTATGTACTGGCTGTTTCAGG 59.065 47.826 1.31 0.00 36.62 3.86
3978 4354 2.859165 TTTGAGTACTGGAGCAAGGG 57.141 50.000 0.00 0.00 0.00 3.95
3979 4355 0.324943 TTGAGTACTGGAGCAAGGGC 59.675 55.000 0.00 0.00 41.61 5.19
4034 4423 1.198637 GTGCAGTCAGTTTCCATGCTC 59.801 52.381 0.00 0.00 37.76 4.26
4035 4424 0.445436 GCAGTCAGTTTCCATGCTCG 59.555 55.000 0.00 0.00 34.10 5.03
4036 4425 1.941209 GCAGTCAGTTTCCATGCTCGA 60.941 52.381 0.00 0.00 34.10 4.04
4037 4426 2.625737 CAGTCAGTTTCCATGCTCGAT 58.374 47.619 0.00 0.00 0.00 3.59
4057 4446 1.159713 CGTGCCAGACTTTGTGAGCA 61.160 55.000 0.00 0.00 0.00 4.26
4058 4447 0.590195 GTGCCAGACTTTGTGAGCAG 59.410 55.000 0.00 0.00 0.00 4.24
4059 4448 1.168407 TGCCAGACTTTGTGAGCAGC 61.168 55.000 0.00 0.00 0.00 5.25
4075 4464 1.268899 GCAGCAGCAGATGAAAACTGT 59.731 47.619 0.00 0.00 39.19 3.55
4088 4477 7.543868 CAGATGAAAACTGTAAACAACAACCAA 59.456 33.333 0.00 0.00 37.74 3.67
4089 4478 7.544217 AGATGAAAACTGTAAACAACAACCAAC 59.456 33.333 0.00 0.00 37.74 3.77
4090 4479 6.513180 TGAAAACTGTAAACAACAACCAACA 58.487 32.000 0.00 0.00 37.74 3.33
4091 4480 7.155328 TGAAAACTGTAAACAACAACCAACAT 58.845 30.769 0.00 0.00 37.74 2.71
4105 4494 8.914654 CAACAACCAACATATAACAAGATTGTG 58.085 33.333 0.00 0.00 41.31 3.33
4145 4537 8.776470 TCCTAGTAAAAACATGTCTAAAAACCG 58.224 33.333 0.00 0.00 0.00 4.44
4148 4540 8.217131 AGTAAAAACATGTCTAAAAACCGAGT 57.783 30.769 0.00 0.00 0.00 4.18
4154 4546 7.360575 ACATGTCTAAAAACCGAGTGAATAC 57.639 36.000 0.00 0.00 0.00 1.89
4179 4575 3.118223 CCTCCTTTACTTGGACCTCCATC 60.118 52.174 0.00 0.00 46.97 3.51
4187 4596 2.187946 GACCTCCATCGGGTGCAG 59.812 66.667 0.00 0.00 37.17 4.41
4188 4597 2.284625 ACCTCCATCGGGTGCAGA 60.285 61.111 0.00 0.00 35.51 4.26
4189 4598 2.303549 GACCTCCATCGGGTGCAGAG 62.304 65.000 0.00 0.00 37.17 3.35
4190 4599 2.503061 CTCCATCGGGTGCAGAGG 59.497 66.667 0.00 0.00 34.93 3.69
4191 4600 3.746949 CTCCATCGGGTGCAGAGGC 62.747 68.421 0.00 0.00 41.68 4.70
4192 4601 4.864334 CCATCGGGTGCAGAGGCC 62.864 72.222 0.00 0.00 40.13 5.19
4196 4605 4.020617 CGGGTGCAGAGGCCTGAA 62.021 66.667 12.00 0.00 43.02 3.02
4197 4606 2.045536 GGGTGCAGAGGCCTGAAG 60.046 66.667 12.00 0.00 43.02 3.02
4216 4625 8.522653 GCCTGAAGCAATGAAATCTGAAAGAAG 61.523 40.741 0.00 0.00 45.21 2.85
4256 4665 3.581755 TCAGTTAACCCGATTCAGTTCG 58.418 45.455 0.88 0.00 38.83 3.95
4259 4668 4.325472 CAGTTAACCCGATTCAGTTCGTAC 59.675 45.833 0.88 0.00 37.42 3.67
4263 4672 1.652124 CCCGATTCAGTTCGTACGTTG 59.348 52.381 16.05 12.24 37.42 4.10
4273 4682 5.862860 TCAGTTCGTACGTTGTTATTATGCA 59.137 36.000 16.05 0.00 0.00 3.96
4274 4683 6.532302 TCAGTTCGTACGTTGTTATTATGCAT 59.468 34.615 16.05 3.79 0.00 3.96
4275 4684 6.623353 CAGTTCGTACGTTGTTATTATGCATG 59.377 38.462 16.05 0.00 0.00 4.06
4276 4685 6.311935 AGTTCGTACGTTGTTATTATGCATGT 59.688 34.615 16.05 0.04 0.00 3.21
4277 4686 6.650239 TCGTACGTTGTTATTATGCATGTT 57.350 33.333 16.05 0.00 0.00 2.71
4278 4687 7.062906 TCGTACGTTGTTATTATGCATGTTT 57.937 32.000 16.05 0.00 0.00 2.83
4280 4689 7.478978 TCGTACGTTGTTATTATGCATGTTTTG 59.521 33.333 16.05 0.00 0.00 2.44
4281 4690 7.478978 CGTACGTTGTTATTATGCATGTTTTGA 59.521 33.333 10.16 0.00 0.00 2.69
4282 4691 9.119329 GTACGTTGTTATTATGCATGTTTTGAA 57.881 29.630 10.16 0.00 0.00 2.69
4284 4693 7.865385 ACGTTGTTATTATGCATGTTTTGAACT 59.135 29.630 10.16 0.00 0.00 3.01
4285 4694 8.698854 CGTTGTTATTATGCATGTTTTGAACTT 58.301 29.630 10.16 0.00 0.00 2.66
4286 4695 9.796062 GTTGTTATTATGCATGTTTTGAACTTG 57.204 29.630 10.16 3.21 38.98 3.16
4288 4697 8.363390 TGTTATTATGCATGTTTTGAACTTGGA 58.637 29.630 10.16 6.22 40.21 3.53
4289 4698 9.369904 GTTATTATGCATGTTTTGAACTTGGAT 57.630 29.630 10.16 14.61 45.15 3.41
4290 4699 9.941325 TTATTATGCATGTTTTGAACTTGGATT 57.059 25.926 10.16 5.40 42.22 3.01
4291 4700 8.851541 ATTATGCATGTTTTGAACTTGGATTT 57.148 26.923 10.16 5.40 42.22 2.17
4295 4704 4.751767 TGTTTTGAACTTGGATTTGGCT 57.248 36.364 0.00 0.00 0.00 4.75
4297 4706 4.081198 TGTTTTGAACTTGGATTTGGCTGT 60.081 37.500 0.00 0.00 0.00 4.40
4298 4707 5.127845 TGTTTTGAACTTGGATTTGGCTGTA 59.872 36.000 0.00 0.00 0.00 2.74
4299 4708 6.183360 TGTTTTGAACTTGGATTTGGCTGTAT 60.183 34.615 0.00 0.00 0.00 2.29
4303 4712 3.891049 ACTTGGATTTGGCTGTATCTCC 58.109 45.455 0.00 0.00 0.00 3.71
4305 4714 1.837439 TGGATTTGGCTGTATCTCCGT 59.163 47.619 0.00 0.00 0.00 4.69
4306 4715 2.238646 TGGATTTGGCTGTATCTCCGTT 59.761 45.455 0.00 0.00 0.00 4.44
4307 4716 3.452990 TGGATTTGGCTGTATCTCCGTTA 59.547 43.478 0.00 0.00 0.00 3.18
4311 4720 4.746535 TTGGCTGTATCTCCGTTATTCA 57.253 40.909 0.00 0.00 0.00 2.57
4313 4722 5.290493 TGGCTGTATCTCCGTTATTCATT 57.710 39.130 0.00 0.00 0.00 2.57
4314 4723 6.413783 TGGCTGTATCTCCGTTATTCATTA 57.586 37.500 0.00 0.00 0.00 1.90
4316 4725 7.450074 TGGCTGTATCTCCGTTATTCATTAAT 58.550 34.615 0.00 0.00 0.00 1.40
4318 4727 7.148407 GGCTGTATCTCCGTTATTCATTAATGG 60.148 40.741 15.36 0.00 45.09 3.16
4325 4734 6.084326 CCGTTATTCATTAATGGAAAGGGG 57.916 41.667 15.36 7.22 46.17 4.79
4326 4735 5.830991 CCGTTATTCATTAATGGAAAGGGGA 59.169 40.000 15.36 0.00 46.17 4.81
4327 4736 6.493458 CCGTTATTCATTAATGGAAAGGGGAT 59.507 38.462 15.36 0.00 46.17 3.85
4328 4737 7.015195 CCGTTATTCATTAATGGAAAGGGGATT 59.985 37.037 15.36 0.00 46.17 3.01
4329 4738 9.073475 CGTTATTCATTAATGGAAAGGGGATTA 57.927 33.333 15.36 0.00 0.00 1.75
4331 4740 6.976934 TTCATTAATGGAAAGGGGATTAGC 57.023 37.500 15.36 0.00 0.00 3.09
4332 4741 5.393866 TCATTAATGGAAAGGGGATTAGCC 58.606 41.667 15.36 0.00 0.00 3.93
4346 4755 5.585820 GGATTAGCCCGGTTCAAAAATAA 57.414 39.130 0.00 0.00 0.00 1.40
4347 4756 5.968254 GGATTAGCCCGGTTCAAAAATAAA 58.032 37.500 0.00 0.00 0.00 1.40
4348 4757 6.399743 GGATTAGCCCGGTTCAAAAATAAAA 58.600 36.000 0.00 0.00 0.00 1.52
4349 4758 7.045416 GGATTAGCCCGGTTCAAAAATAAAAT 58.955 34.615 0.00 0.00 0.00 1.82
4350 4759 8.198778 GGATTAGCCCGGTTCAAAAATAAAATA 58.801 33.333 0.00 0.00 0.00 1.40
4351 4760 9.589111 GATTAGCCCGGTTCAAAAATAAAATAA 57.411 29.630 0.00 0.00 0.00 1.40
4352 4761 9.945904 ATTAGCCCGGTTCAAAAATAAAATAAA 57.054 25.926 0.00 0.00 0.00 1.40
4353 4762 9.774413 TTAGCCCGGTTCAAAAATAAAATAAAA 57.226 25.926 0.00 0.00 0.00 1.52
4354 4763 8.856153 AGCCCGGTTCAAAAATAAAATAAAAT 57.144 26.923 0.00 0.00 0.00 1.82
4355 4764 9.290988 AGCCCGGTTCAAAAATAAAATAAAATT 57.709 25.926 0.00 0.00 0.00 1.82
4411 4820 3.772932 TGAAGTTCGTGTTACTGTCGTT 58.227 40.909 0.00 0.00 0.00 3.85
4439 4848 2.672908 CAGCATCAGGTCCAGCCA 59.327 61.111 0.00 0.00 40.61 4.75
4489 4900 6.175471 TGCACAATGTATGAACTGAAGAGAT 58.825 36.000 0.00 0.00 0.00 2.75
4490 4901 6.656270 TGCACAATGTATGAACTGAAGAGATT 59.344 34.615 0.00 0.00 0.00 2.40
4491 4902 6.965500 GCACAATGTATGAACTGAAGAGATTG 59.035 38.462 0.00 0.00 0.00 2.67
4494 4905 8.725148 ACAATGTATGAACTGAAGAGATTGAAC 58.275 33.333 0.00 0.00 0.00 3.18
4503 4914 7.991084 ACTGAAGAGATTGAACAATTCATCA 57.009 32.000 1.56 8.54 39.84 3.07
4504 4915 8.041829 ACTGAAGAGATTGAACAATTCATCAG 57.958 34.615 23.08 23.08 39.84 2.90
4505 4916 7.120873 ACTGAAGAGATTGAACAATTCATCAGG 59.879 37.037 25.20 17.21 39.84 3.86
4506 4917 7.170277 TGAAGAGATTGAACAATTCATCAGGA 58.830 34.615 1.56 0.00 39.84 3.86
4507 4918 7.666804 TGAAGAGATTGAACAATTCATCAGGAA 59.333 33.333 1.56 0.00 39.84 3.36
4508 4919 7.627298 AGAGATTGAACAATTCATCAGGAAG 57.373 36.000 1.56 0.00 39.84 3.46
4509 4920 7.400439 AGAGATTGAACAATTCATCAGGAAGA 58.600 34.615 1.56 0.00 39.84 2.87
4510 4921 7.886970 AGAGATTGAACAATTCATCAGGAAGAA 59.113 33.333 1.56 0.00 39.84 2.52
4520 4931 8.758715 CAATTCATCAGGAAGAAAGAAACAAAC 58.241 33.333 0.00 0.00 39.30 2.93
4535 4946 6.996509 AGAAACAAACAAGCACATCCATTAT 58.003 32.000 0.00 0.00 0.00 1.28
4543 4954 4.923516 AGCACATCCATTATAGCCTGAT 57.076 40.909 0.00 0.00 0.00 2.90
4582 4993 5.698089 CGCCAGATTGTGATCTTATACACAT 59.302 40.000 0.00 0.00 44.56 3.21
4584 4995 6.148480 GCCAGATTGTGATCTTATACACATCC 59.852 42.308 0.00 0.00 44.56 3.51
4585 4996 7.219322 CCAGATTGTGATCTTATACACATCCA 58.781 38.462 0.00 0.00 44.56 3.41
4587 4998 9.281371 CAGATTGTGATCTTATACACATCCATT 57.719 33.333 0.00 0.00 44.56 3.16
4592 5003 9.875691 TGTGATCTTATACACATCCATTATAGC 57.124 33.333 0.00 0.00 41.19 2.97
4594 5005 9.271921 TGATCTTATACACATCCATTATAGCCT 57.728 33.333 0.00 0.00 0.00 4.58
4595 5006 9.539825 GATCTTATACACATCCATTATAGCCTG 57.460 37.037 0.00 0.00 0.00 4.85
4596 5007 8.664669 TCTTATACACATCCATTATAGCCTGA 57.335 34.615 0.00 0.00 0.00 3.86
4597 5008 8.753133 TCTTATACACATCCATTATAGCCTGAG 58.247 37.037 0.00 0.00 0.00 3.35
4598 5009 8.664669 TTATACACATCCATTATAGCCTGAGA 57.335 34.615 0.00 0.00 0.00 3.27
4599 5010 5.894298 ACACATCCATTATAGCCTGAGAA 57.106 39.130 0.00 0.00 0.00 2.87
4601 5012 5.221803 ACACATCCATTATAGCCTGAGAAGG 60.222 44.000 0.00 0.00 0.00 3.46
4608 5029 0.252239 TAGCCTGAGAAGGAGCCACA 60.252 55.000 0.00 0.00 0.00 4.17
4611 5032 0.397941 CCTGAGAAGGAGCCACACAA 59.602 55.000 0.00 0.00 0.00 3.33
4620 5041 1.167851 GAGCCACACAATGCAGCTAA 58.832 50.000 0.00 0.00 30.42 3.09
4621 5042 1.747355 GAGCCACACAATGCAGCTAAT 59.253 47.619 0.00 0.00 30.42 1.73
4629 5050 1.600957 CAATGCAGCTAATGAGGTCGG 59.399 52.381 0.00 0.00 0.00 4.79
4656 5077 1.127951 GACGAAATCGACAATGCGGTT 59.872 47.619 10.16 0.00 43.02 4.44
4658 5079 1.393539 CGAAATCGACAATGCGGTTCT 59.606 47.619 0.00 0.00 43.02 3.01
4664 5085 1.662876 CGACAATGCGGTTCTTGTTGG 60.663 52.381 0.00 0.00 35.80 3.77
4665 5086 1.336755 GACAATGCGGTTCTTGTTGGT 59.663 47.619 0.00 0.00 35.80 3.67
4666 5087 1.754226 ACAATGCGGTTCTTGTTGGTT 59.246 42.857 0.00 0.00 31.74 3.67
4667 5088 2.126467 CAATGCGGTTCTTGTTGGTTG 58.874 47.619 0.00 0.00 0.00 3.77
4668 5089 1.398692 ATGCGGTTCTTGTTGGTTGT 58.601 45.000 0.00 0.00 0.00 3.32
4669 5090 2.039818 TGCGGTTCTTGTTGGTTGTA 57.960 45.000 0.00 0.00 0.00 2.41
4670 5091 2.366533 TGCGGTTCTTGTTGGTTGTAA 58.633 42.857 0.00 0.00 0.00 2.41
4671 5092 2.097791 TGCGGTTCTTGTTGGTTGTAAC 59.902 45.455 0.00 0.00 0.00 2.50
4684 5105 3.113260 GTTGTAACCAGCTGACACTCT 57.887 47.619 17.39 0.00 0.00 3.24
4685 5106 3.467803 GTTGTAACCAGCTGACACTCTT 58.532 45.455 17.39 0.00 0.00 2.85
4686 5107 4.628074 GTTGTAACCAGCTGACACTCTTA 58.372 43.478 17.39 0.00 0.00 2.10
4687 5108 4.252971 TGTAACCAGCTGACACTCTTAC 57.747 45.455 17.39 10.47 0.00 2.34
4688 5109 2.841442 AACCAGCTGACACTCTTACC 57.159 50.000 17.39 0.00 0.00 2.85
4689 5110 2.016905 ACCAGCTGACACTCTTACCT 57.983 50.000 17.39 0.00 0.00 3.08
4690 5111 1.896465 ACCAGCTGACACTCTTACCTC 59.104 52.381 17.39 0.00 0.00 3.85
4691 5112 1.895798 CCAGCTGACACTCTTACCTCA 59.104 52.381 17.39 0.00 0.00 3.86
4692 5113 2.300152 CCAGCTGACACTCTTACCTCAA 59.700 50.000 17.39 0.00 0.00 3.02
4693 5114 3.055530 CCAGCTGACACTCTTACCTCAAT 60.056 47.826 17.39 0.00 0.00 2.57
4694 5115 4.180057 CAGCTGACACTCTTACCTCAATC 58.820 47.826 8.42 0.00 0.00 2.67
4695 5116 3.119316 AGCTGACACTCTTACCTCAATCG 60.119 47.826 0.00 0.00 0.00 3.34
4696 5117 3.367498 GCTGACACTCTTACCTCAATCGT 60.367 47.826 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 106 4.280819 ACAAGGTTGGGTCATTGGATATG 58.719 43.478 0.00 0.00 34.11 1.78
115 126 4.278170 CCTTTTGTTGCAATAGTGAGGACA 59.722 41.667 0.59 0.00 0.00 4.02
159 170 2.977914 TCCTGCAACATAAGCTCTGTC 58.022 47.619 2.65 0.00 0.00 3.51
244 289 2.549329 CCATGTTGCAAAAGCCTTTTCC 59.451 45.455 0.00 0.00 0.00 3.13
299 349 0.465278 TGGCACTAGTGTTGCTGCAA 60.465 50.000 23.44 11.69 0.00 4.08
329 379 1.658686 AACGGCGGAGTTGCAAAACA 61.659 50.000 13.24 0.00 36.28 2.83
353 403 1.937223 ACACACGCTGACAAATTTCGA 59.063 42.857 3.55 0.00 0.00 3.71
496 548 4.796231 CCCCTTGTCGTCTCCGCG 62.796 72.222 0.00 0.00 0.00 6.46
506 558 1.274703 ACGAGATGCATCCCCCTTGT 61.275 55.000 23.06 11.48 0.00 3.16
521 573 1.831652 AACCTTCCCTGGCAGACGAG 61.832 60.000 17.94 9.80 0.00 4.18
562 614 1.904287 CCTCGACCAATGAACCCAAA 58.096 50.000 0.00 0.00 0.00 3.28
576 628 0.753479 CTAGCAGGGAAGAGCCTCGA 60.753 60.000 0.00 0.00 36.66 4.04
769 825 0.039437 ACGTCGGTCACTGATGTGTC 60.039 55.000 10.92 0.00 44.14 3.67
784 841 5.673818 GCCATCCTTATCTTTGTGAAACGTC 60.674 44.000 0.00 0.00 42.39 4.34
794 851 3.004752 ACGCTTGCCATCCTTATCTTT 57.995 42.857 0.00 0.00 0.00 2.52
832 928 3.323243 TCAACCGACCGATCTTTTCTTC 58.677 45.455 0.00 0.00 0.00 2.87
835 931 2.803956 TGTTCAACCGACCGATCTTTTC 59.196 45.455 0.00 0.00 0.00 2.29
845 944 0.935196 AAAGCTCGTGTTCAACCGAC 59.065 50.000 0.00 0.00 0.00 4.79
881 980 5.163804 GGTCGCAAAAGAAAATGGTGTTTTT 60.164 36.000 0.00 0.00 0.00 1.94
882 981 4.331443 GGTCGCAAAAGAAAATGGTGTTTT 59.669 37.500 0.00 0.00 0.00 2.43
884 983 3.453424 GGTCGCAAAAGAAAATGGTGTT 58.547 40.909 0.00 0.00 0.00 3.32
885 984 2.542824 CGGTCGCAAAAGAAAATGGTGT 60.543 45.455 0.00 0.00 0.00 4.16
886 985 2.050691 CGGTCGCAAAAGAAAATGGTG 58.949 47.619 0.00 0.00 0.00 4.17
887 986 1.601914 GCGGTCGCAAAAGAAAATGGT 60.602 47.619 10.67 0.00 41.49 3.55
888 987 1.059942 GCGGTCGCAAAAGAAAATGG 58.940 50.000 10.67 0.00 41.49 3.16
921 1020 2.601763 GACCGGTCGCTACTGTAAAATG 59.398 50.000 20.85 0.00 0.00 2.32
922 1021 2.733227 CGACCGGTCGCTACTGTAAAAT 60.733 50.000 40.78 0.00 46.50 1.82
923 1022 1.401409 CGACCGGTCGCTACTGTAAAA 60.401 52.381 40.78 0.00 46.50 1.52
924 1023 0.168788 CGACCGGTCGCTACTGTAAA 59.831 55.000 40.78 0.00 46.50 2.01
925 1024 1.796151 CGACCGGTCGCTACTGTAA 59.204 57.895 40.78 0.00 46.50 2.41
926 1025 3.489731 CGACCGGTCGCTACTGTA 58.510 61.111 40.78 0.00 46.50 2.74
984 1104 1.974957 GCCATGGGTTTAGGGTTTTGT 59.025 47.619 15.13 0.00 0.00 2.83
1294 1441 4.467107 GGAGACGCTCCCCTCCCT 62.467 72.222 13.12 0.00 44.36 4.20
1318 1465 2.620112 CCCGCAGCCACTTGTTGAG 61.620 63.158 0.00 0.00 0.00 3.02
1320 1467 2.594303 TCCCGCAGCCACTTGTTG 60.594 61.111 0.00 0.00 0.00 3.33
1371 1518 4.787999 CGGAGCTCCTTGACGTAC 57.212 61.111 29.73 0.81 0.00 3.67
1440 1588 0.251297 TGCTGGGATGTCAAAGGTGG 60.251 55.000 0.00 0.00 0.00 4.61
1461 1609 4.262036 CGTCCTAAGCAGAGCACCATTATA 60.262 45.833 0.00 0.00 0.00 0.98
1462 1610 3.493350 CGTCCTAAGCAGAGCACCATTAT 60.493 47.826 0.00 0.00 0.00 1.28
1540 1716 6.796426 TCATCTACTCACTCCGTTCTAAATG 58.204 40.000 0.00 0.00 0.00 2.32
1728 1916 2.805099 AGAGCTCTGCTTTTGAAAGTCG 59.195 45.455 17.42 0.00 39.88 4.18
1810 1998 6.831353 TCCTAAAAACAATTGACCAAGTGAGA 59.169 34.615 13.59 0.00 38.53 3.27
1851 2039 2.771943 GGATGTCTATGAGTTCCCACCA 59.228 50.000 0.00 0.00 0.00 4.17
1858 2046 7.099120 GCAAATTTTTGGGATGTCTATGAGTT 58.901 34.615 5.28 0.00 38.57 3.01
1877 2065 2.215196 CTGCTTGGCTTGTTGCAAATT 58.785 42.857 0.00 0.00 45.15 1.82
1878 2066 1.541670 CCTGCTTGGCTTGTTGCAAAT 60.542 47.619 0.00 0.00 45.15 2.32
1887 2075 5.945144 ATATTTCAATTCCTGCTTGGCTT 57.055 34.783 0.00 0.00 35.26 4.35
1897 2085 5.934043 GGCAGCCCATTAATATTTCAATTCC 59.066 40.000 0.00 0.00 0.00 3.01
1910 2098 0.037590 AAACGTCTGGCAGCCCATTA 59.962 50.000 9.64 0.00 41.21 1.90
1925 2113 0.794229 CACATTAGCGCTGCCAAACG 60.794 55.000 22.90 0.17 0.00 3.60
1991 2179 3.631144 CATTTGCTGGTATAACATGCGG 58.369 45.455 0.00 0.00 0.00 5.69
2062 2253 8.319143 TCAAAGGGTCTTTAAAAGTTCTATCG 57.681 34.615 0.00 0.00 0.00 2.92
2069 2260 9.286170 GATCTAGTTCAAAGGGTCTTTAAAAGT 57.714 33.333 0.00 0.00 0.00 2.66
2080 2271 5.070981 TGCTCATAGGATCTAGTTCAAAGGG 59.929 44.000 3.30 0.00 0.00 3.95
2108 2299 1.283793 GTGGTGTGATGTGCTGCAC 59.716 57.895 25.15 25.15 35.63 4.57
2134 2325 1.233019 CACTCAGCAGACTGGTTTGG 58.767 55.000 3.93 0.91 44.59 3.28
2325 2519 8.736244 TCCAGCCATACTACAAGTAAATTTTTC 58.264 33.333 0.00 0.00 33.89 2.29
2394 2589 7.066163 CAGCAGACATGATTAAACACCAATAGA 59.934 37.037 0.00 0.00 0.00 1.98
2529 2731 1.001068 TCGATCCCACGCACTTTGTAA 59.999 47.619 0.00 0.00 0.00 2.41
2544 2746 5.429957 AATATTTTTCAGCTGCCTCGATC 57.570 39.130 9.47 0.00 0.00 3.69
2583 2785 0.322456 TTCGATGGTTCTTGGCTGGG 60.322 55.000 0.00 0.00 0.00 4.45
2658 2866 1.065709 TCCATCTTGCGGTAAAGGTCC 60.066 52.381 0.00 0.00 0.00 4.46
2814 3022 2.621998 GCTGGTCATTAGAATGCAGCAT 59.378 45.455 20.71 0.52 44.66 3.79
2826 3036 3.058160 GCCGCACAGCTGGTCATT 61.058 61.111 19.93 0.00 0.00 2.57
2859 3069 6.028040 TCTTTTAGAACTTGTTCAACGTCG 57.972 37.500 14.80 0.00 0.00 5.12
2916 3126 3.880846 GCCAGCGTGCTGTATGCC 61.881 66.667 19.58 0.53 42.47 4.40
2928 3138 0.833287 TCTGGTAGATGGAAGCCAGC 59.167 55.000 4.69 0.00 45.86 4.85
2956 3166 4.220533 CAGACTCTGCTTTTTCAACCAG 57.779 45.455 0.00 0.00 0.00 4.00
3072 3282 1.127567 CCCACACCCTCTTCACCTCA 61.128 60.000 0.00 0.00 0.00 3.86
3078 3288 1.073199 CACACCCCACACCCTCTTC 59.927 63.158 0.00 0.00 0.00 2.87
3093 3303 1.479757 GGGAAAGTGCCCTTAACCACA 60.480 52.381 7.21 0.00 45.12 4.17
3153 3363 2.358267 GGCATCATTGAGCTTGAGAAGG 59.642 50.000 0.00 0.00 0.00 3.46
3159 3369 3.313249 TGTAATCGGCATCATTGAGCTTG 59.687 43.478 0.00 0.00 0.00 4.01
3252 3462 2.370445 ATTCCTCAGGTGGGCTCGG 61.370 63.158 0.00 0.00 0.00 4.63
3266 3476 1.753073 CTTCCTTGGCCATGTCATTCC 59.247 52.381 6.09 0.00 0.00 3.01
3272 3482 0.323178 CTCTGCTTCCTTGGCCATGT 60.323 55.000 6.09 0.00 0.00 3.21
3324 3534 4.084745 TCGCATGTTTTAGAGTCGAAACAC 60.085 41.667 21.96 13.63 45.33 3.32
3330 3540 2.028523 CAGCTCGCATGTTTTAGAGTCG 59.971 50.000 0.00 0.00 33.57 4.18
3457 3667 2.561858 AGTACTTGGAGAACTTCGGGAC 59.438 50.000 0.00 0.00 0.00 4.46
3511 3721 3.060615 CAGGCAGCAGCAGAACCC 61.061 66.667 2.65 0.00 44.61 4.11
3639 3849 1.781429 CCGATGTCGTAGCAAATCTCG 59.219 52.381 1.44 0.00 37.74 4.04
3657 3867 1.449246 CCTCTTGAGCAGCTTCCCG 60.449 63.158 0.00 0.00 0.00 5.14
3684 3897 1.676006 GTACCATTTCATCGCCCCTTG 59.324 52.381 0.00 0.00 0.00 3.61
3685 3898 1.564348 AGTACCATTTCATCGCCCCTT 59.436 47.619 0.00 0.00 0.00 3.95
3686 3899 1.213296 AGTACCATTTCATCGCCCCT 58.787 50.000 0.00 0.00 0.00 4.79
3702 3915 2.337359 AGGGGCAGAAACAGGTAGTA 57.663 50.000 0.00 0.00 0.00 1.82
3703 3916 2.188817 CTAGGGGCAGAAACAGGTAGT 58.811 52.381 0.00 0.00 0.00 2.73
3704 3917 1.134371 GCTAGGGGCAGAAACAGGTAG 60.134 57.143 0.00 0.00 41.35 3.18
3763 4082 9.383519 GGCTATATAATATCTGCTTTGTGCTTA 57.616 33.333 0.00 0.00 43.37 3.09
3764 4083 7.337942 GGGCTATATAATATCTGCTTTGTGCTT 59.662 37.037 0.00 0.00 43.37 3.91
3769 4088 8.798859 ACAAGGGCTATATAATATCTGCTTTG 57.201 34.615 0.00 0.00 0.00 2.77
3805 4163 2.644992 CAGAAGCACCAAACGCCC 59.355 61.111 0.00 0.00 0.00 6.13
3867 4240 5.451354 AGAAAGATCCCCTCAGACTACTAC 58.549 45.833 0.00 0.00 0.00 2.73
3868 4241 5.399267 GGAGAAAGATCCCCTCAGACTACTA 60.399 48.000 8.32 0.00 32.79 1.82
3869 4242 4.542697 GAGAAAGATCCCCTCAGACTACT 58.457 47.826 0.00 0.00 0.00 2.57
3943 4316 1.682854 TCAAAAGCCTGAAACAGCCAG 59.317 47.619 0.00 0.00 0.00 4.85
3956 4329 2.485814 CCTTGCTCCAGTACTCAAAAGC 59.514 50.000 0.00 0.32 0.00 3.51
3978 4354 2.117910 GAAACGATCCTGTAGTAGCGC 58.882 52.381 0.00 0.00 0.00 5.92
3979 4355 3.694535 AGAAACGATCCTGTAGTAGCG 57.305 47.619 0.00 0.00 0.00 4.26
4034 4423 0.439985 CACAAAGTCTGGCACGATCG 59.560 55.000 14.88 14.88 0.00 3.69
4035 4424 1.728971 CTCACAAAGTCTGGCACGATC 59.271 52.381 0.00 0.00 0.00 3.69
4036 4425 1.800805 CTCACAAAGTCTGGCACGAT 58.199 50.000 0.00 0.00 0.00 3.73
4037 4426 0.880278 GCTCACAAAGTCTGGCACGA 60.880 55.000 0.00 0.00 0.00 4.35
4057 4446 4.580167 TGTTTACAGTTTTCATCTGCTGCT 59.420 37.500 0.00 0.00 36.50 4.24
4058 4447 4.858935 TGTTTACAGTTTTCATCTGCTGC 58.141 39.130 0.00 0.00 36.50 5.25
4059 4448 6.264832 TGTTGTTTACAGTTTTCATCTGCTG 58.735 36.000 0.00 0.00 36.50 4.41
4088 4477 8.594881 GCTAGTAGCACAATCTTGTTATATGT 57.405 34.615 17.47 0.00 41.89 2.29
4145 4537 5.678955 AGTAAAGGAGGGTGTATTCACTC 57.321 43.478 2.29 0.00 44.73 3.51
4148 4540 4.847512 TCCAAGTAAAGGAGGGTGTATTCA 59.152 41.667 0.00 0.00 0.00 2.57
4154 4546 1.985895 AGGTCCAAGTAAAGGAGGGTG 59.014 52.381 0.00 0.00 35.42 4.61
4179 4575 3.965539 CTTCAGGCCTCTGCACCCG 62.966 68.421 0.00 0.00 40.69 5.28
4187 4596 3.022406 AGATTTCATTGCTTCAGGCCTC 58.978 45.455 0.00 0.00 40.92 4.70
4188 4597 2.758979 CAGATTTCATTGCTTCAGGCCT 59.241 45.455 0.00 0.00 40.92 5.19
4189 4598 2.756760 TCAGATTTCATTGCTTCAGGCC 59.243 45.455 0.00 0.00 40.92 5.19
4190 4599 4.445452 TTCAGATTTCATTGCTTCAGGC 57.555 40.909 0.00 0.00 42.22 4.85
4191 4600 6.263516 TCTTTCAGATTTCATTGCTTCAGG 57.736 37.500 0.00 0.00 0.00 3.86
4192 4601 6.308282 GCTTCTTTCAGATTTCATTGCTTCAG 59.692 38.462 0.00 0.00 0.00 3.02
4195 4604 5.924825 GTGCTTCTTTCAGATTTCATTGCTT 59.075 36.000 0.00 0.00 0.00 3.91
4196 4605 5.010314 TGTGCTTCTTTCAGATTTCATTGCT 59.990 36.000 0.00 0.00 0.00 3.91
4197 4606 5.224888 TGTGCTTCTTTCAGATTTCATTGC 58.775 37.500 0.00 0.00 0.00 3.56
4216 4625 2.548057 TGAAGAACCGAAGTTGATGTGC 59.452 45.455 0.00 0.00 35.94 4.57
4256 4665 8.662369 TCAAAACATGCATAATAACAACGTAC 57.338 30.769 0.00 0.00 0.00 3.67
4259 4668 8.226543 AGTTCAAAACATGCATAATAACAACG 57.773 30.769 0.00 0.00 0.00 4.10
4263 4672 8.755696 TCCAAGTTCAAAACATGCATAATAAC 57.244 30.769 0.00 0.00 0.00 1.89
4273 4682 5.058490 CAGCCAAATCCAAGTTCAAAACAT 58.942 37.500 0.00 0.00 0.00 2.71
4274 4683 4.081198 ACAGCCAAATCCAAGTTCAAAACA 60.081 37.500 0.00 0.00 0.00 2.83
4275 4684 4.441792 ACAGCCAAATCCAAGTTCAAAAC 58.558 39.130 0.00 0.00 0.00 2.43
4276 4685 4.751767 ACAGCCAAATCCAAGTTCAAAA 57.248 36.364 0.00 0.00 0.00 2.44
4277 4686 5.774690 AGATACAGCCAAATCCAAGTTCAAA 59.225 36.000 0.00 0.00 0.00 2.69
4278 4687 5.324409 AGATACAGCCAAATCCAAGTTCAA 58.676 37.500 0.00 0.00 0.00 2.69
4280 4689 4.336713 GGAGATACAGCCAAATCCAAGTTC 59.663 45.833 0.00 0.00 0.00 3.01
4281 4690 4.273318 GGAGATACAGCCAAATCCAAGTT 58.727 43.478 0.00 0.00 0.00 2.66
4282 4691 3.682718 CGGAGATACAGCCAAATCCAAGT 60.683 47.826 0.00 0.00 0.00 3.16
4284 4693 2.238646 ACGGAGATACAGCCAAATCCAA 59.761 45.455 0.00 0.00 0.00 3.53
4285 4694 1.837439 ACGGAGATACAGCCAAATCCA 59.163 47.619 0.00 0.00 0.00 3.41
4286 4695 2.622064 ACGGAGATACAGCCAAATCC 57.378 50.000 0.00 0.00 0.00 3.01
4288 4697 5.680619 TGAATAACGGAGATACAGCCAAAT 58.319 37.500 0.00 0.00 0.00 2.32
4289 4698 5.092554 TGAATAACGGAGATACAGCCAAA 57.907 39.130 0.00 0.00 0.00 3.28
4290 4699 4.746535 TGAATAACGGAGATACAGCCAA 57.253 40.909 0.00 0.00 0.00 4.52
4291 4700 4.955811 ATGAATAACGGAGATACAGCCA 57.044 40.909 0.00 0.00 0.00 4.75
4295 4704 9.839817 TTTCCATTAATGAATAACGGAGATACA 57.160 29.630 17.23 0.00 37.19 2.29
4297 4706 9.502091 CCTTTCCATTAATGAATAACGGAGATA 57.498 33.333 17.23 0.00 37.19 1.98
4298 4707 7.448469 CCCTTTCCATTAATGAATAACGGAGAT 59.552 37.037 17.23 0.00 37.19 2.75
4299 4708 6.770785 CCCTTTCCATTAATGAATAACGGAGA 59.229 38.462 17.23 0.00 37.19 3.71
4303 4712 6.952773 TCCCCTTTCCATTAATGAATAACG 57.047 37.500 17.23 5.99 0.00 3.18
4305 4714 9.088987 GCTAATCCCCTTTCCATTAATGAATAA 57.911 33.333 17.23 5.52 0.00 1.40
4306 4715 7.673926 GGCTAATCCCCTTTCCATTAATGAATA 59.326 37.037 17.23 0.00 0.00 1.75
4307 4716 6.498303 GGCTAATCCCCTTTCCATTAATGAAT 59.502 38.462 17.23 0.00 0.00 2.57
4324 4733 5.585820 TTATTTTTGAACCGGGCTAATCC 57.414 39.130 6.32 0.00 0.00 3.01
4325 4734 9.589111 TTATTTTATTTTTGAACCGGGCTAATC 57.411 29.630 6.32 0.00 0.00 1.75
4326 4735 9.945904 TTTATTTTATTTTTGAACCGGGCTAAT 57.054 25.926 6.32 0.00 0.00 1.73
4327 4736 9.774413 TTTTATTTTATTTTTGAACCGGGCTAA 57.226 25.926 6.32 0.00 0.00 3.09
4328 4737 9.945904 ATTTTATTTTATTTTTGAACCGGGCTA 57.054 25.926 6.32 0.00 0.00 3.93
4329 4738 8.856153 ATTTTATTTTATTTTTGAACCGGGCT 57.144 26.923 6.32 0.00 0.00 5.19
4345 4754 8.964150 GCTCGACTGTTGTGTTAATTTTATTTT 58.036 29.630 0.00 0.00 0.00 1.82
4346 4755 8.349983 AGCTCGACTGTTGTGTTAATTTTATTT 58.650 29.630 0.00 0.00 0.00 1.40
4347 4756 7.871853 AGCTCGACTGTTGTGTTAATTTTATT 58.128 30.769 0.00 0.00 0.00 1.40
4348 4757 7.435068 AGCTCGACTGTTGTGTTAATTTTAT 57.565 32.000 0.00 0.00 0.00 1.40
4349 4758 6.854496 AGCTCGACTGTTGTGTTAATTTTA 57.146 33.333 0.00 0.00 0.00 1.52
4350 4759 5.751243 AGCTCGACTGTTGTGTTAATTTT 57.249 34.783 0.00 0.00 0.00 1.82
4351 4760 5.751243 AAGCTCGACTGTTGTGTTAATTT 57.249 34.783 0.00 0.00 0.00 1.82
4352 4761 5.751243 AAAGCTCGACTGTTGTGTTAATT 57.249 34.783 0.00 0.00 0.00 1.40
4353 4762 5.510671 CAAAAGCTCGACTGTTGTGTTAAT 58.489 37.500 8.79 0.00 38.61 1.40
4354 4763 4.729458 GCAAAAGCTCGACTGTTGTGTTAA 60.729 41.667 15.05 0.00 44.42 2.01
4355 4764 3.242608 GCAAAAGCTCGACTGTTGTGTTA 60.243 43.478 15.05 0.00 44.42 2.41
4356 4765 2.477863 GCAAAAGCTCGACTGTTGTGTT 60.478 45.455 15.05 0.00 44.42 3.32
4357 4766 1.064060 GCAAAAGCTCGACTGTTGTGT 59.936 47.619 15.05 0.00 44.42 3.72
4358 4767 1.063912 TGCAAAAGCTCGACTGTTGTG 59.936 47.619 15.05 2.50 44.42 3.33
4359 4768 1.378531 TGCAAAAGCTCGACTGTTGT 58.621 45.000 15.05 0.00 44.42 3.32
4411 4820 1.281867 CCTGATGCTGGGAAGTAACCA 59.718 52.381 0.00 0.00 36.38 3.67
4489 4900 7.822161 TCTTTCTTCCTGATGAATTGTTCAA 57.178 32.000 0.00 0.00 43.95 2.69
4490 4901 7.822161 TTCTTTCTTCCTGATGAATTGTTCA 57.178 32.000 0.00 0.00 45.01 3.18
4491 4902 8.137437 TGTTTCTTTCTTCCTGATGAATTGTTC 58.863 33.333 0.00 0.00 31.06 3.18
4494 4905 8.758715 GTTTGTTTCTTTCTTCCTGATGAATTG 58.241 33.333 0.00 0.00 31.06 2.32
4503 4914 5.047377 TGTGCTTGTTTGTTTCTTTCTTCCT 60.047 36.000 0.00 0.00 0.00 3.36
4504 4915 5.167845 TGTGCTTGTTTGTTTCTTTCTTCC 58.832 37.500 0.00 0.00 0.00 3.46
4505 4916 6.019559 GGATGTGCTTGTTTGTTTCTTTCTTC 60.020 38.462 0.00 0.00 0.00 2.87
4506 4917 5.812127 GGATGTGCTTGTTTGTTTCTTTCTT 59.188 36.000 0.00 0.00 0.00 2.52
4507 4918 5.105392 TGGATGTGCTTGTTTGTTTCTTTCT 60.105 36.000 0.00 0.00 0.00 2.52
4508 4919 5.108517 TGGATGTGCTTGTTTGTTTCTTTC 58.891 37.500 0.00 0.00 0.00 2.62
4509 4920 5.083533 TGGATGTGCTTGTTTGTTTCTTT 57.916 34.783 0.00 0.00 0.00 2.52
4510 4921 4.734398 TGGATGTGCTTGTTTGTTTCTT 57.266 36.364 0.00 0.00 0.00 2.52
4520 4931 4.392047 TCAGGCTATAATGGATGTGCTTG 58.608 43.478 0.00 0.00 31.39 4.01
4543 4954 0.249531 TGGCGCGTTTGTCTGAGTTA 60.250 50.000 8.43 0.00 0.00 2.24
4582 4993 3.580458 GCTCCTTCTCAGGCTATAATGGA 59.420 47.826 0.00 0.00 40.58 3.41
4584 4995 3.326006 TGGCTCCTTCTCAGGCTATAATG 59.674 47.826 0.00 0.00 40.58 1.90
4585 4996 3.326297 GTGGCTCCTTCTCAGGCTATAAT 59.674 47.826 0.00 0.00 40.58 1.28
4587 4998 2.320781 GTGGCTCCTTCTCAGGCTATA 58.679 52.381 0.00 0.00 40.58 1.31
4588 4999 1.127343 GTGGCTCCTTCTCAGGCTAT 58.873 55.000 0.00 0.00 40.58 2.97
4589 5000 0.252239 TGTGGCTCCTTCTCAGGCTA 60.252 55.000 0.00 0.00 40.58 3.93
4590 5001 1.537397 TGTGGCTCCTTCTCAGGCT 60.537 57.895 0.00 0.00 40.58 4.58
4591 5002 1.376553 GTGTGGCTCCTTCTCAGGC 60.377 63.158 0.00 0.00 40.58 4.85
4592 5003 0.397941 TTGTGTGGCTCCTTCTCAGG 59.602 55.000 0.00 0.00 42.50 3.86
4594 5005 1.883638 GCATTGTGTGGCTCCTTCTCA 60.884 52.381 0.00 0.00 0.00 3.27
4595 5006 0.807496 GCATTGTGTGGCTCCTTCTC 59.193 55.000 0.00 0.00 0.00 2.87
4596 5007 0.111061 TGCATTGTGTGGCTCCTTCT 59.889 50.000 0.00 0.00 0.00 2.85
4597 5008 0.524862 CTGCATTGTGTGGCTCCTTC 59.475 55.000 0.00 0.00 0.00 3.46
4598 5009 1.530013 GCTGCATTGTGTGGCTCCTT 61.530 55.000 0.00 0.00 0.00 3.36
4599 5010 1.975407 GCTGCATTGTGTGGCTCCT 60.975 57.895 0.00 0.00 0.00 3.69
4601 5012 1.167851 TTAGCTGCATTGTGTGGCTC 58.832 50.000 1.02 0.00 34.88 4.70
4608 5029 2.283298 CGACCTCATTAGCTGCATTGT 58.717 47.619 1.02 0.00 0.00 2.71
4611 5032 0.107456 CCCGACCTCATTAGCTGCAT 59.893 55.000 1.02 0.00 0.00 3.96
4636 5057 0.719465 ACCGCATTGTCGATTTCGTC 59.281 50.000 0.00 0.00 40.80 4.20
4639 5060 3.163594 CAAGAACCGCATTGTCGATTTC 58.836 45.455 0.00 5.07 0.00 2.17
4649 5070 1.398692 ACAACCAACAAGAACCGCAT 58.601 45.000 0.00 0.00 0.00 4.73
4664 5085 3.113260 AGAGTGTCAGCTGGTTACAAC 57.887 47.619 15.13 3.77 0.00 3.32
4665 5086 3.838244 AAGAGTGTCAGCTGGTTACAA 57.162 42.857 15.13 0.00 0.00 2.41
4666 5087 3.006537 GGTAAGAGTGTCAGCTGGTTACA 59.993 47.826 15.13 8.35 0.00 2.41
4667 5088 3.258622 AGGTAAGAGTGTCAGCTGGTTAC 59.741 47.826 15.13 10.56 0.00 2.50
4668 5089 3.507411 AGGTAAGAGTGTCAGCTGGTTA 58.493 45.455 15.13 0.00 0.00 2.85
4669 5090 2.300437 GAGGTAAGAGTGTCAGCTGGTT 59.700 50.000 15.13 0.00 0.00 3.67
4670 5091 1.896465 GAGGTAAGAGTGTCAGCTGGT 59.104 52.381 15.13 0.00 0.00 4.00
4671 5092 1.895798 TGAGGTAAGAGTGTCAGCTGG 59.104 52.381 15.13 0.00 0.00 4.85
4672 5093 3.667497 TTGAGGTAAGAGTGTCAGCTG 57.333 47.619 7.63 7.63 0.00 4.24
4673 5094 3.119316 CGATTGAGGTAAGAGTGTCAGCT 60.119 47.826 0.00 0.00 0.00 4.24
4674 5095 3.182967 CGATTGAGGTAAGAGTGTCAGC 58.817 50.000 0.00 0.00 0.00 4.26
4675 5096 4.442375 ACGATTGAGGTAAGAGTGTCAG 57.558 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.