Multiple sequence alignment - TraesCS2D01G553300

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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 TraesCS2D01G553300 chr2D 100.000 4845 0 0 1 4845 628158162 628163006 0.000000e+00 8948.0
1 TraesCS2D01G553300 chr2D 85.329 593 65 8 2409 2988 627911962 627911379 1.160000e-165 593.0
2 TraesCS2D01G553300 chr2D 83.333 168 22 4 3815 3980 628618443 628618606 3.020000e-32 150.0
3 TraesCS2D01G553300 chr2A 89.211 3893 225 81 935 4736 758530123 758533911 0.000000e+00 4682.0
4 TraesCS2D01G553300 chr2A 87.947 531 61 3 2409 2937 758384732 758384203 1.480000e-174 623.0
5 TraesCS2D01G553300 chr2A 84.066 364 28 9 1607 1953 53326479 53326829 1.680000e-84 324.0
6 TraesCS2D01G553300 chr2A 84.834 211 26 4 676 884 692528064 692527858 1.770000e-49 207.0
7 TraesCS2D01G553300 chr2B 90.064 3573 193 69 819 4334 771184804 771188271 0.000000e+00 4482.0
8 TraesCS2D01G553300 chr2B 91.812 745 51 5 42 781 771184066 771184805 0.000000e+00 1029.0
9 TraesCS2D01G553300 chr2B 84.615 481 52 6 2568 3048 770663287 770662829 4.420000e-125 459.0
10 TraesCS2D01G553300 chr2B 77.536 690 62 48 3889 4548 770662736 770662110 3.620000e-86 329.0
11 TraesCS2D01G553300 chr2B 82.857 315 30 15 4386 4687 771188359 771188662 1.340000e-65 261.0
12 TraesCS2D01G553300 chr1B 84.870 575 44 17 1440 1993 65773934 65773382 1.530000e-149 540.0
13 TraesCS2D01G553300 chr1B 90.741 54 3 1 1138 1191 557401287 557401236 2.420000e-08 71.3
14 TraesCS2D01G553300 chr4D 79.022 777 119 27 61 823 337123339 337122593 4.360000e-135 492.0
15 TraesCS2D01G553300 chr4A 78.315 807 143 25 61 853 135623069 135623857 4.360000e-135 492.0
16 TraesCS2D01G553300 chr4A 81.735 219 24 6 2544 2761 420018032 420017829 8.340000e-38 169.0
17 TraesCS2D01G553300 chr4B 78.323 775 133 22 61 823 416251742 416250991 7.340000e-128 468.0
18 TraesCS2D01G553300 chr7B 84.573 363 27 9 1607 1953 580783654 580784003 2.790000e-87 333.0
19 TraesCS2D01G553300 chr7B 93.182 44 3 0 1138 1181 577295513 577295556 1.130000e-06 65.8
20 TraesCS2D01G553300 chr7A 82.192 219 23 6 2544 2761 299415205 299415002 1.790000e-39 174.0
21 TraesCS2D01G553300 chr1A 81.333 225 26 6 2538 2761 558015562 558015771 8.340000e-38 169.0
22 TraesCS2D01G553300 chr6D 80.804 224 25 3 2537 2757 169715950 169716158 5.020000e-35 159.0
23 TraesCS2D01G553300 chr5B 81.951 205 21 7 2558 2761 634119910 634119721 5.020000e-35 159.0
24 TraesCS2D01G553300 chr3D 80.263 228 26 8 2538 2761 30972871 30973083 2.340000e-33 154.0


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 TraesCS2D01G553300 chr2D 628158162 628163006 4844 False 8948 8948 100.000000 1 4845 1 chr2D.!!$F1 4844
1 TraesCS2D01G553300 chr2D 627911379 627911962 583 True 593 593 85.329000 2409 2988 1 chr2D.!!$R1 579
2 TraesCS2D01G553300 chr2A 758530123 758533911 3788 False 4682 4682 89.211000 935 4736 1 chr2A.!!$F2 3801
3 TraesCS2D01G553300 chr2A 758384203 758384732 529 True 623 623 87.947000 2409 2937 1 chr2A.!!$R2 528
4 TraesCS2D01G553300 chr2B 771184066 771188662 4596 False 1924 4482 88.244333 42 4687 3 chr2B.!!$F1 4645
5 TraesCS2D01G553300 chr2B 770662110 770663287 1177 True 394 459 81.075500 2568 4548 2 chr2B.!!$R1 1980
6 TraesCS2D01G553300 chr1B 65773382 65773934 552 True 540 540 84.870000 1440 1993 1 chr1B.!!$R1 553
7 TraesCS2D01G553300 chr4D 337122593 337123339 746 True 492 492 79.022000 61 823 1 chr4D.!!$R1 762
8 TraesCS2D01G553300 chr4A 135623069 135623857 788 False 492 492 78.315000 61 853 1 chr4A.!!$F1 792
9 TraesCS2D01G553300 chr4B 416250991 416251742 751 True 468 468 78.323000 61 823 1 chr4B.!!$R1 762

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
39 40 0.509929 AGTTCTAAAAACGCGTCGGC 59.490 50.0 14.44 0.0 0.00 5.54 F
1004 1062 0.109723 CAGAGTCGGAACCCCCAAAA 59.890 55.0 0.00 0.0 34.14 2.44 F
2203 2291 0.106708 ACATCACACCACAGAAGCGT 59.893 50.0 0.00 0.0 0.00 5.07 F
2232 2320 0.250640 CTGCTGAGTGCTGACCCTTT 60.251 55.0 0.00 0.0 42.27 3.11 F
3018 3126 0.833287 TGGCTTCCATCTACCAGAGC 59.167 55.0 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1499 0.392998 CTGGGAATGGCGCTTGTACT 60.393 55.000 7.64 0.0 0.00 2.73 R
2757 2863 1.134159 GGCAGAGTGCTGGATGAGATT 60.134 52.381 0.00 0.0 44.28 2.40 R
3576 3684 0.250467 GGCAGTTGCAGAACCTCTCA 60.250 55.000 6.43 0.0 44.36 3.27 R
3615 3723 0.739813 ACTCGTATGCTTTGCCGTCC 60.740 55.000 0.00 0.0 0.00 4.79 R
4813 5064 0.032267 GTAGGCGTCTAGGATGTGGC 59.968 60.000 0.00 0.0 0.00 5.01 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
38 39 2.936050 AAGTTCTAAAAACGCGTCGG 57.064 45.000 14.44 1.09 0.00 4.79
39 40 0.509929 AGTTCTAAAAACGCGTCGGC 59.490 50.000 14.44 0.00 0.00 5.54
40 41 0.509929 GTTCTAAAAACGCGTCGGCT 59.490 50.000 14.44 0.00 36.88 5.52
133 135 4.947388 AGGCAGTGTTGAAGAACTTTTACA 59.053 37.500 0.00 0.00 32.79 2.41
140 142 7.606456 AGTGTTGAAGAACTTTTACAACAGAGA 59.394 33.333 15.47 0.00 46.78 3.10
236 245 4.346787 GTCGCAGAAAAGGCTTTTGCAAT 61.347 43.478 28.54 5.31 44.22 3.56
314 323 2.356382 TGCCATTGTCGTCTTCGTTTTT 59.644 40.909 0.00 0.00 38.33 1.94
347 356 1.406898 TGTTGCCGAAATTTGTCAGCA 59.593 42.857 0.00 0.00 0.00 4.41
541 552 2.162008 GTGTCGTTCTCTCAGTCCCTAC 59.838 54.545 0.00 0.00 0.00 3.18
714 757 4.202151 GGTTTGCTTTCTGAAACAGGTGAT 60.202 41.667 0.00 0.00 34.36 3.06
724 767 2.936919 AACAGGTGATCAGTTGCAGA 57.063 45.000 0.00 0.00 0.00 4.26
730 773 2.165030 GGTGATCAGTTGCAGAAATGGG 59.835 50.000 0.00 0.00 0.00 4.00
805 849 4.722700 GATGTGGTGTGCGGGCCT 62.723 66.667 0.84 0.00 0.00 5.19
848 892 1.220817 GGACGCGGTGGACGTAAAAA 61.221 55.000 12.47 0.00 45.24 1.94
887 931 1.202245 TGCACACGAGCTTTTCCAAAC 60.202 47.619 0.00 0.00 34.99 2.93
891 935 3.923461 CACACGAGCTTTTCCAAACAAAA 59.077 39.130 0.00 0.00 0.00 2.44
984 1036 2.363147 GCTCCACCCGTCCTCTCT 60.363 66.667 0.00 0.00 0.00 3.10
993 1051 1.092921 CCGTCCTCTCTCAGAGTCGG 61.093 65.000 15.15 15.15 44.52 4.79
1004 1062 0.109723 CAGAGTCGGAACCCCCAAAA 59.890 55.000 0.00 0.00 34.14 2.44
1005 1063 0.400594 AGAGTCGGAACCCCCAAAAG 59.599 55.000 0.00 0.00 34.14 2.27
1006 1064 0.608308 GAGTCGGAACCCCCAAAAGG 60.608 60.000 0.00 0.00 34.14 3.11
1133 1191 0.435008 CCGCGAAGAACACGAAGAAG 59.565 55.000 8.23 0.00 0.00 2.85
1206 1264 4.521062 CGAAGGAGGCGGCAGAGG 62.521 72.222 13.08 0.00 0.00 3.69
1438 1499 1.529152 TACGTCAAGGAGCTCCGCAA 61.529 55.000 26.95 13.18 42.08 4.85
1500 1561 2.198304 ATCCCCCTCACCTTTGACGC 62.198 60.000 0.00 0.00 0.00 5.19
1665 1734 2.045131 GCTTTGCCTCCTCCAGCTG 61.045 63.158 6.78 6.78 0.00 4.24
1725 1809 5.451908 TCTTTGTGAAATCTTAGCTTTGCG 58.548 37.500 0.00 0.00 0.00 4.85
1780 1865 5.567037 TTCCGGATTCATGATGGAACTAT 57.433 39.130 4.15 0.00 33.95 2.12
1847 1932 2.456577 GGGTATGTTTGGTTGATGCCT 58.543 47.619 0.00 0.00 0.00 4.75
1862 1947 4.751060 TGATGCCTCAATGCAGATTTTTC 58.249 39.130 0.00 0.00 45.93 2.29
1868 1953 3.316283 TCAATGCAGATTTTTCGCCAAC 58.684 40.909 0.00 0.00 0.00 3.77
2047 2132 5.064707 CCAAACACAGCCTACATATGTACAC 59.935 44.000 11.62 6.85 0.00 2.90
2062 2147 9.487442 ACATATGTACACCCCAGAAATAATTTT 57.513 29.630 6.56 0.00 0.00 1.82
2074 2159 8.370182 CCCAGAAATAATTTTGCAGGCTATATT 58.630 33.333 0.00 0.00 0.00 1.28
2120 2208 7.562135 TGATAACCTCTTTTCTTAGCGGTAAT 58.438 34.615 7.64 0.00 32.20 1.89
2203 2291 0.106708 ACATCACACCACAGAAGCGT 59.893 50.000 0.00 0.00 0.00 5.07
2231 2319 1.123861 TCTGCTGAGTGCTGACCCTT 61.124 55.000 0.00 0.00 43.20 3.95
2232 2320 0.250640 CTGCTGAGTGCTGACCCTTT 60.251 55.000 0.00 0.00 42.27 3.11
2253 2344 5.581126 TTGAATGCTTGTTCTGTTTCAGT 57.419 34.783 0.00 0.00 32.61 3.41
2267 2358 5.647658 TCTGTTTCAGTGTTTTCTGATGTGT 59.352 36.000 0.00 0.00 42.84 3.72
2318 2409 7.234577 AGAGTAGGGAGGAGATTTGATATGTTC 59.765 40.741 0.00 0.00 0.00 3.18
2465 2557 3.477530 ACCTTCTGTTTGTACTTCTGCC 58.522 45.455 0.00 0.00 0.00 4.85
2481 2573 6.687604 ACTTCTGCCATTGGTGTTTAATTAC 58.312 36.000 4.26 0.00 0.00 1.89
2517 2609 7.869429 ACTTATGCAAGGATTTGTCTTTTCTTG 59.131 33.333 0.00 0.00 36.65 3.02
2757 2863 1.744798 CGCAAGATGGATGAGCTTGGA 60.745 52.381 0.00 0.00 46.40 3.53
3018 3126 0.833287 TGGCTTCCATCTACCAGAGC 59.167 55.000 0.00 0.00 0.00 4.09
3173 3281 2.148052 TGTGGGGCGTGGTTAAGGA 61.148 57.895 0.00 0.00 0.00 3.36
3240 3348 4.332268 CAGGCTCTTCTTAAGCTCAATGAC 59.668 45.833 0.00 0.00 39.75 3.06
3312 3420 3.731264 GCTACGACGTGAAGCTGACTAAT 60.731 47.826 11.56 0.00 33.40 1.73
3360 3468 1.252904 GCATGGCCAAGGAAGCAGAA 61.253 55.000 10.96 0.00 0.00 3.02
3418 3526 5.748592 GTTTTGACTCTAAAACATGCGAGT 58.251 37.500 8.70 0.00 45.35 4.18
3564 3672 5.753721 AGTACTTTGAAGAGCAGAAGGAT 57.246 39.130 0.00 0.00 0.00 3.24
3576 3684 2.034687 AAGGATGTGCAAGGCGCT 59.965 55.556 7.64 0.00 43.06 5.92
3705 3813 2.224079 GCAGCAGATCAAAGACGACAAA 59.776 45.455 0.00 0.00 0.00 2.83
3714 3822 7.691463 CAGATCAAAGACGACAAAATTGAGATC 59.309 37.037 0.00 0.00 33.91 2.75
3738 3846 0.957395 ACGACATTGGGAAGCTGCTG 60.957 55.000 1.35 0.00 0.00 4.41
3756 3870 2.203938 AAGAGGTTGGGCGAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
3793 3910 1.066358 GTTTCTGCCCCTAGCTTACGT 60.066 52.381 0.00 0.00 44.23 3.57
3807 3924 2.064014 CTTACGTCGGTGGTTTCTTCC 58.936 52.381 0.00 0.00 0.00 3.46
3829 3946 4.814234 CCGATTCCTTCCATGAACGAATAA 59.186 41.667 0.00 0.00 31.27 1.40
3845 3962 8.946085 TGAACGAATAACAGAAAGCAGATATTT 58.054 29.630 0.00 0.00 0.00 1.40
3852 3969 9.905713 ATAACAGAAAGCAGATATTTTAGGTGA 57.094 29.630 0.00 0.00 0.00 4.02
3857 3974 8.325046 AGAAAGCAGATATTTTAGGTGAGAAGT 58.675 33.333 0.00 0.00 0.00 3.01
3859 3976 6.951971 AGCAGATATTTTAGGTGAGAAGTGT 58.048 36.000 0.00 0.00 0.00 3.55
3860 3977 7.398024 AGCAGATATTTTAGGTGAGAAGTGTT 58.602 34.615 0.00 0.00 0.00 3.32
3863 3980 6.599638 AGATATTTTAGGTGAGAAGTGTTGCC 59.400 38.462 0.00 0.00 0.00 4.52
3864 3981 2.163818 TTAGGTGAGAAGTGTTGCCG 57.836 50.000 0.00 0.00 0.00 5.69
3923 4064 1.205893 AGAAGAAGCAGAACTAGGCCG 59.794 52.381 0.00 0.00 0.00 6.13
3925 4066 0.614979 AGAAGCAGAACTAGGCCGGA 60.615 55.000 5.05 0.00 0.00 5.14
3932 4073 0.249398 GAACTAGGCCGGAGCAAAGA 59.751 55.000 5.05 0.00 42.56 2.52
3965 4109 4.623932 AGCACAACTTGTAATCTGAGGA 57.376 40.909 0.00 0.00 0.00 3.71
3969 4113 3.910627 ACAACTTGTAATCTGAGGAGGGT 59.089 43.478 0.00 0.00 0.00 4.34
4146 4306 2.854963 TGTGAGCAGCAGATGAAAACT 58.145 42.857 0.00 0.00 0.00 2.66
4147 4307 2.551032 TGTGAGCAGCAGATGAAAACTG 59.449 45.455 0.00 0.00 40.09 3.16
4171 4337 5.458779 GCAAACAACAACCAGATAACAAGAC 59.541 40.000 0.00 0.00 0.00 3.01
4300 4495 4.020573 ACACATTGACTCCGGTTCTTCATA 60.021 41.667 0.00 0.00 0.00 2.15
4327 4522 5.875359 ACCCGATTCAGTTCTTATGTTCTTC 59.125 40.000 0.00 0.00 0.00 2.87
4343 4538 5.111989 TGTTCTTCTTATGCTCAAGATCGG 58.888 41.667 2.07 0.00 34.59 4.18
4345 4540 3.132824 TCTTCTTATGCTCAAGATCGGCA 59.867 43.478 7.80 7.80 40.32 5.69
4365 4560 4.035102 GGAGCGGCCAAGGGTCTT 62.035 66.667 2.24 0.00 36.34 3.01
4373 4573 0.540597 GCCAAGGGTCTTGCTTTCCT 60.541 55.000 2.38 0.00 0.00 3.36
4377 4577 0.251077 AGGGTCTTGCTTTCCTGCAG 60.251 55.000 6.78 6.78 44.27 4.41
4421 4653 7.201410 GCTTTTGCAATGTATGAGATGAAGTTG 60.201 37.037 0.00 0.00 46.58 3.16
4440 4672 1.134226 GGTGTTACTGTCGTCGGTTG 58.866 55.000 0.00 0.00 34.68 3.77
4472 4704 0.926720 AGGTCCAGCCCTCTCCTCTA 60.927 60.000 0.00 0.00 38.26 2.43
4476 4710 1.388065 CCAGCCCTCTCCTCTACGTG 61.388 65.000 0.00 0.00 0.00 4.49
4534 4782 7.811713 AGAGAGCAAATAATTCAGAAACAAAGC 59.188 33.333 0.00 0.00 0.00 3.51
4560 4808 3.244875 ACATCCATTACAGCCTGACAACA 60.245 43.478 0.00 0.00 0.00 3.33
4573 4821 0.372334 GACAACACAGACAAACGCGT 59.628 50.000 5.58 5.58 0.00 6.01
4599 4847 7.928167 TCAGATTGTGATCTTATACACACCATC 59.072 37.037 0.00 0.00 44.81 3.51
4681 4932 1.127951 CAAAATCGACAGTGCGGTACC 59.872 52.381 0.16 0.16 0.00 3.34
4690 4941 2.031919 TGCGGTACCTGTTGCCAG 59.968 61.111 10.90 0.00 38.50 4.85
4706 4957 2.625790 TGCCAGGTAACAATGGTGAAAC 59.374 45.455 0.00 0.00 38.91 2.78
4721 4972 0.315251 GAAACCTTTGCAGTCCCAGC 59.685 55.000 0.00 0.00 0.00 4.85
4736 4987 1.302271 CAGCTGCCACTCTTGCTCA 60.302 57.895 0.00 0.00 33.03 4.26
4737 4988 1.302351 AGCTGCCACTCTTGCTCAC 60.302 57.895 0.00 0.00 0.00 3.51
4738 4989 2.675056 GCTGCCACTCTTGCTCACG 61.675 63.158 0.00 0.00 0.00 4.35
4739 4990 2.031012 TGCCACTCTTGCTCACGG 59.969 61.111 0.00 0.00 0.00 4.94
4740 4991 3.426568 GCCACTCTTGCTCACGGC 61.427 66.667 0.00 0.00 42.22 5.68
4750 5001 3.863681 GCTCACGGCACAAATCAAA 57.136 47.368 0.00 0.00 41.35 2.69
4751 5002 1.408422 GCTCACGGCACAAATCAAAC 58.592 50.000 0.00 0.00 41.35 2.93
4752 5003 1.268999 GCTCACGGCACAAATCAAACA 60.269 47.619 0.00 0.00 41.35 2.83
4753 5004 2.797792 GCTCACGGCACAAATCAAACAA 60.798 45.455 0.00 0.00 41.35 2.83
4754 5005 3.044986 CTCACGGCACAAATCAAACAAG 58.955 45.455 0.00 0.00 0.00 3.16
4755 5006 1.522258 CACGGCACAAATCAAACAAGC 59.478 47.619 0.00 0.00 0.00 4.01
4756 5007 1.135915 ACGGCACAAATCAAACAAGCA 59.864 42.857 0.00 0.00 0.00 3.91
4757 5008 2.200067 CGGCACAAATCAAACAAGCAA 58.800 42.857 0.00 0.00 0.00 3.91
4758 5009 2.219216 CGGCACAAATCAAACAAGCAAG 59.781 45.455 0.00 0.00 0.00 4.01
4759 5010 2.032636 GGCACAAATCAAACAAGCAAGC 60.033 45.455 0.00 0.00 0.00 4.01
4760 5011 2.867975 GCACAAATCAAACAAGCAAGCT 59.132 40.909 0.00 0.00 0.00 3.74
4761 5012 3.310501 GCACAAATCAAACAAGCAAGCTT 59.689 39.130 0.59 0.59 36.60 3.74
4762 5013 4.551410 GCACAAATCAAACAAGCAAGCTTC 60.551 41.667 3.97 0.00 33.42 3.86
4763 5014 4.567558 CACAAATCAAACAAGCAAGCTTCA 59.432 37.500 3.97 0.00 33.42 3.02
4764 5015 4.567959 ACAAATCAAACAAGCAAGCTTCAC 59.432 37.500 3.97 0.00 33.42 3.18
4765 5016 4.389890 AATCAAACAAGCAAGCTTCACA 57.610 36.364 3.97 0.00 33.42 3.58
4766 5017 3.865011 TCAAACAAGCAAGCTTCACAA 57.135 38.095 3.97 0.00 33.42 3.33
4767 5018 4.185467 TCAAACAAGCAAGCTTCACAAA 57.815 36.364 3.97 0.00 33.42 2.83
4768 5019 4.564041 TCAAACAAGCAAGCTTCACAAAA 58.436 34.783 3.97 0.00 33.42 2.44
4769 5020 4.993584 TCAAACAAGCAAGCTTCACAAAAA 59.006 33.333 3.97 0.00 33.42 1.94
4770 5021 5.120519 TCAAACAAGCAAGCTTCACAAAAAG 59.879 36.000 3.97 0.00 33.42 2.27
4771 5022 3.524541 ACAAGCAAGCTTCACAAAAAGG 58.475 40.909 3.97 0.00 33.42 3.11
4772 5023 3.195396 ACAAGCAAGCTTCACAAAAAGGA 59.805 39.130 3.97 0.00 33.42 3.36
4773 5024 4.141869 ACAAGCAAGCTTCACAAAAAGGAT 60.142 37.500 3.97 0.00 33.42 3.24
4774 5025 4.248691 AGCAAGCTTCACAAAAAGGATC 57.751 40.909 0.00 0.00 0.00 3.36
4775 5026 3.638160 AGCAAGCTTCACAAAAAGGATCA 59.362 39.130 0.00 0.00 0.00 2.92
4776 5027 4.099881 AGCAAGCTTCACAAAAAGGATCAA 59.900 37.500 0.00 0.00 0.00 2.57
4777 5028 4.446719 GCAAGCTTCACAAAAAGGATCAAG 59.553 41.667 0.00 0.00 0.00 3.02
4778 5029 5.594926 CAAGCTTCACAAAAAGGATCAAGT 58.405 37.500 0.00 0.00 0.00 3.16
4779 5030 5.444663 AGCTTCACAAAAAGGATCAAGTC 57.555 39.130 0.00 0.00 0.00 3.01
4780 5031 4.889409 AGCTTCACAAAAAGGATCAAGTCA 59.111 37.500 0.00 0.00 0.00 3.41
4781 5032 4.978580 GCTTCACAAAAAGGATCAAGTCAC 59.021 41.667 0.00 0.00 0.00 3.67
4782 5033 5.221126 GCTTCACAAAAAGGATCAAGTCACT 60.221 40.000 0.00 0.00 0.00 3.41
4783 5034 6.377327 TTCACAAAAAGGATCAAGTCACTC 57.623 37.500 0.00 0.00 0.00 3.51
4784 5035 4.821805 TCACAAAAAGGATCAAGTCACTCC 59.178 41.667 0.00 0.00 0.00 3.85
4785 5036 4.022849 CACAAAAAGGATCAAGTCACTCCC 60.023 45.833 0.00 0.00 0.00 4.30
4786 5037 4.141158 ACAAAAAGGATCAAGTCACTCCCT 60.141 41.667 0.00 0.00 0.00 4.20
4787 5038 3.710209 AAAGGATCAAGTCACTCCCTG 57.290 47.619 0.00 0.00 0.00 4.45
4788 5039 2.334006 AGGATCAAGTCACTCCCTGT 57.666 50.000 0.00 0.00 0.00 4.00
4789 5040 2.183679 AGGATCAAGTCACTCCCTGTC 58.816 52.381 0.00 0.00 0.00 3.51
4790 5041 2.183679 GGATCAAGTCACTCCCTGTCT 58.816 52.381 0.00 0.00 0.00 3.41
4791 5042 2.167487 GGATCAAGTCACTCCCTGTCTC 59.833 54.545 0.00 0.00 0.00 3.36
4792 5043 1.633774 TCAAGTCACTCCCTGTCTCC 58.366 55.000 0.00 0.00 0.00 3.71
4793 5044 1.133167 TCAAGTCACTCCCTGTCTCCA 60.133 52.381 0.00 0.00 0.00 3.86
4794 5045 1.905215 CAAGTCACTCCCTGTCTCCAT 59.095 52.381 0.00 0.00 0.00 3.41
4795 5046 1.859302 AGTCACTCCCTGTCTCCATC 58.141 55.000 0.00 0.00 0.00 3.51
4796 5047 1.360852 AGTCACTCCCTGTCTCCATCT 59.639 52.381 0.00 0.00 0.00 2.90
4797 5048 2.583101 AGTCACTCCCTGTCTCCATCTA 59.417 50.000 0.00 0.00 0.00 1.98
4798 5049 2.955660 GTCACTCCCTGTCTCCATCTAG 59.044 54.545 0.00 0.00 0.00 2.43
4799 5050 2.583101 TCACTCCCTGTCTCCATCTAGT 59.417 50.000 0.00 0.00 0.00 2.57
4800 5051 3.011821 TCACTCCCTGTCTCCATCTAGTT 59.988 47.826 0.00 0.00 0.00 2.24
4801 5052 3.383185 CACTCCCTGTCTCCATCTAGTTC 59.617 52.174 0.00 0.00 0.00 3.01
4802 5053 2.621055 CTCCCTGTCTCCATCTAGTTCG 59.379 54.545 0.00 0.00 0.00 3.95
4803 5054 2.025226 TCCCTGTCTCCATCTAGTTCGT 60.025 50.000 0.00 0.00 0.00 3.85
4804 5055 3.201487 TCCCTGTCTCCATCTAGTTCGTA 59.799 47.826 0.00 0.00 0.00 3.43
4805 5056 3.952323 CCCTGTCTCCATCTAGTTCGTAA 59.048 47.826 0.00 0.00 0.00 3.18
4806 5057 4.202030 CCCTGTCTCCATCTAGTTCGTAAC 60.202 50.000 0.00 0.00 0.00 2.50
4807 5058 4.202030 CCTGTCTCCATCTAGTTCGTAACC 60.202 50.000 0.00 0.00 0.00 2.85
4808 5059 4.338012 TGTCTCCATCTAGTTCGTAACCA 58.662 43.478 0.00 0.00 0.00 3.67
4809 5060 4.398358 TGTCTCCATCTAGTTCGTAACCAG 59.602 45.833 0.00 0.00 0.00 4.00
4810 5061 3.380637 TCTCCATCTAGTTCGTAACCAGC 59.619 47.826 0.00 0.00 0.00 4.85
4811 5062 2.098607 TCCATCTAGTTCGTAACCAGCG 59.901 50.000 0.00 0.00 0.00 5.18
4812 5063 2.159282 CCATCTAGTTCGTAACCAGCGT 60.159 50.000 0.00 0.00 0.00 5.07
4813 5064 2.624316 TCTAGTTCGTAACCAGCGTG 57.376 50.000 0.00 0.00 0.00 5.34
4814 5065 0.989890 CTAGTTCGTAACCAGCGTGC 59.010 55.000 0.00 0.00 0.00 5.34
4815 5066 0.388907 TAGTTCGTAACCAGCGTGCC 60.389 55.000 0.00 0.00 0.00 5.01
4816 5067 1.957186 GTTCGTAACCAGCGTGCCA 60.957 57.895 0.00 0.00 0.00 4.92
4817 5068 1.957186 TTCGTAACCAGCGTGCCAC 60.957 57.895 0.00 0.00 0.00 5.01
4818 5069 2.646117 TTCGTAACCAGCGTGCCACA 62.646 55.000 0.00 0.00 0.00 4.17
4819 5070 2.032634 CGTAACCAGCGTGCCACAT 61.033 57.895 0.00 0.00 0.00 3.21
4820 5071 1.794222 GTAACCAGCGTGCCACATC 59.206 57.895 0.00 0.00 0.00 3.06
4821 5072 1.376683 TAACCAGCGTGCCACATCC 60.377 57.895 0.00 0.00 0.00 3.51
4822 5073 1.836999 TAACCAGCGTGCCACATCCT 61.837 55.000 0.00 0.00 0.00 3.24
4823 5074 1.836999 AACCAGCGTGCCACATCCTA 61.837 55.000 0.00 0.00 0.00 2.94
4824 5075 1.522355 CCAGCGTGCCACATCCTAG 60.522 63.158 0.00 0.00 0.00 3.02
4825 5076 1.517361 CAGCGTGCCACATCCTAGA 59.483 57.895 0.00 0.00 0.00 2.43
4826 5077 0.807667 CAGCGTGCCACATCCTAGAC 60.808 60.000 0.00 0.00 0.00 2.59
4827 5078 1.878522 GCGTGCCACATCCTAGACG 60.879 63.158 0.00 0.00 0.00 4.18
4828 5079 1.878522 CGTGCCACATCCTAGACGC 60.879 63.158 0.00 0.00 0.00 5.19
4829 5080 1.521681 GTGCCACATCCTAGACGCC 60.522 63.158 0.00 0.00 0.00 5.68
4830 5081 1.685765 TGCCACATCCTAGACGCCT 60.686 57.895 0.00 0.00 0.00 5.52
4831 5082 0.396556 TGCCACATCCTAGACGCCTA 60.397 55.000 0.00 0.00 0.00 3.93
4832 5083 0.032267 GCCACATCCTAGACGCCTAC 59.968 60.000 0.00 0.00 0.00 3.18
4833 5084 1.693627 CCACATCCTAGACGCCTACT 58.306 55.000 0.00 0.00 0.00 2.57
4834 5085 1.609555 CCACATCCTAGACGCCTACTC 59.390 57.143 0.00 0.00 0.00 2.59
4835 5086 2.577700 CACATCCTAGACGCCTACTCT 58.422 52.381 0.00 0.00 0.00 3.24
4836 5087 2.292016 CACATCCTAGACGCCTACTCTG 59.708 54.545 0.00 0.00 0.00 3.35
4837 5088 1.883275 CATCCTAGACGCCTACTCTGG 59.117 57.143 0.00 0.00 0.00 3.86
4838 5089 0.917533 TCCTAGACGCCTACTCTGGT 59.082 55.000 0.00 0.00 0.00 4.00
4839 5090 1.134159 TCCTAGACGCCTACTCTGGTC 60.134 57.143 0.00 0.00 0.00 4.02
4840 5091 1.310904 CTAGACGCCTACTCTGGTCC 58.689 60.000 0.00 0.00 0.00 4.46
4841 5092 0.106819 TAGACGCCTACTCTGGTCCC 60.107 60.000 0.00 0.00 0.00 4.46
4842 5093 1.380112 GACGCCTACTCTGGTCCCT 60.380 63.158 0.00 0.00 0.00 4.20
4843 5094 1.380112 ACGCCTACTCTGGTCCCTC 60.380 63.158 0.00 0.00 0.00 4.30
4844 5095 2.482333 CGCCTACTCTGGTCCCTCG 61.482 68.421 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.030366 CCGACGCGTTTTTAGAACTTTTT 58.970 39.130 15.53 0.00 0.00 1.94
17 18 3.610495 CCGACGCGTTTTTAGAACTTTT 58.390 40.909 15.53 0.00 0.00 2.27
18 19 2.600556 GCCGACGCGTTTTTAGAACTTT 60.601 45.455 15.53 0.00 0.00 2.66
19 20 1.070376 GCCGACGCGTTTTTAGAACTT 60.070 47.619 15.53 0.00 0.00 2.66
20 21 0.509929 GCCGACGCGTTTTTAGAACT 59.490 50.000 15.53 0.00 0.00 3.01
21 22 0.509929 AGCCGACGCGTTTTTAGAAC 59.490 50.000 15.53 0.00 41.18 3.01
22 23 2.063156 TAGCCGACGCGTTTTTAGAA 57.937 45.000 15.53 0.00 41.18 2.10
23 24 2.063156 TTAGCCGACGCGTTTTTAGA 57.937 45.000 15.53 0.00 41.18 2.10
24 25 2.859870 TTTAGCCGACGCGTTTTTAG 57.140 45.000 15.53 1.54 41.18 1.85
25 26 3.247173 TCTTTTTAGCCGACGCGTTTTTA 59.753 39.130 15.53 1.07 41.18 1.52
26 27 2.031930 TCTTTTTAGCCGACGCGTTTTT 59.968 40.909 15.53 2.16 41.18 1.94
27 28 1.598601 TCTTTTTAGCCGACGCGTTTT 59.401 42.857 15.53 1.76 41.18 2.43
28 29 1.219646 TCTTTTTAGCCGACGCGTTT 58.780 45.000 15.53 2.17 41.18 3.60
29 30 1.392510 GATCTTTTTAGCCGACGCGTT 59.607 47.619 15.53 0.00 41.18 4.84
30 31 0.997196 GATCTTTTTAGCCGACGCGT 59.003 50.000 13.85 13.85 41.18 6.01
31 32 0.300789 GGATCTTTTTAGCCGACGCG 59.699 55.000 3.53 3.53 41.18 6.01
37 38 1.355563 GCGGCGGATCTTTTTAGCC 59.644 57.895 9.78 0.00 44.00 3.93
38 39 1.355563 GGCGGCGGATCTTTTTAGC 59.644 57.895 9.78 0.00 0.00 3.09
39 40 1.641677 CGGCGGCGGATCTTTTTAG 59.358 57.895 25.36 0.00 0.00 1.85
40 41 2.466140 GCGGCGGCGGATCTTTTTA 61.466 57.895 33.02 0.00 0.00 1.52
236 245 5.850557 AAAAATCCGCAACATCATCCATA 57.149 34.783 0.00 0.00 0.00 2.74
263 272 4.439305 GCTGGTGCAACATCTTTCATTA 57.561 40.909 4.06 0.00 39.98 1.90
518 528 1.068194 GGGACTGAGAGAACGACACAG 60.068 57.143 0.00 0.00 35.14 3.66
521 531 2.040012 AGTAGGGACTGAGAGAACGACA 59.960 50.000 0.00 0.00 41.52 4.35
541 552 1.026718 GCCTCGTCCAATGAACCCAG 61.027 60.000 0.00 0.00 0.00 4.45
602 617 0.606604 GAGCAACTAGGGTGTCCGAA 59.393 55.000 0.00 0.00 38.33 4.30
603 618 1.255667 GGAGCAACTAGGGTGTCCGA 61.256 60.000 0.00 0.00 38.33 4.55
714 757 2.957402 ACTCCCATTTCTGCAACTGA 57.043 45.000 0.00 0.00 0.00 3.41
724 767 4.760204 GTGTTTGTGTAGCTACTCCCATTT 59.240 41.667 23.84 0.00 0.00 2.32
730 773 5.119279 CACTGATGTGTTTGTGTAGCTACTC 59.881 44.000 23.84 20.37 39.24 2.59
805 849 1.075542 CTTGCCACGCGTCTTGATTA 58.924 50.000 9.86 0.00 0.00 1.75
861 905 0.884704 AAAGCTCGTGTGCAACCGAT 60.885 50.000 9.14 0.00 38.47 4.18
869 913 2.842208 TGTTTGGAAAAGCTCGTGTG 57.158 45.000 0.00 0.00 0.00 3.82
891 935 3.306710 GGTCGCAAAAGAAATGGGGATTT 60.307 43.478 0.00 0.00 0.00 2.17
895 939 0.109319 CGGTCGCAAAAGAAATGGGG 60.109 55.000 0.00 0.00 0.00 4.96
896 940 0.732538 GCGGTCGCAAAAGAAATGGG 60.733 55.000 10.67 0.00 41.49 4.00
897 941 2.724403 GCGGTCGCAAAAGAAATGG 58.276 52.632 10.67 0.00 41.49 3.16
929 981 2.409651 GCGCCGGTTTGTTGTGAA 59.590 55.556 1.90 0.00 0.00 3.18
930 982 3.587933 GGCGCCGGTTTGTTGTGA 61.588 61.111 12.58 0.00 0.00 3.58
931 983 4.639171 GGGCGCCGGTTTGTTGTG 62.639 66.667 22.54 0.00 0.00 3.33
974 1026 2.389386 CGACTCTGAGAGAGGACGG 58.611 63.158 17.71 0.00 46.45 4.79
976 1028 1.741145 GTTCCGACTCTGAGAGAGGAC 59.259 57.143 23.30 16.81 46.45 3.85
980 1032 0.323542 GGGGTTCCGACTCTGAGAGA 60.324 60.000 17.71 2.32 33.32 3.10
984 1036 0.765135 TTTGGGGGTTCCGACTCTGA 60.765 55.000 0.00 0.00 38.76 3.27
993 1051 0.840617 TTTTGGCCTTTTGGGGGTTC 59.159 50.000 3.32 0.00 40.82 3.62
1004 1062 0.563672 TGGGTTTAGGGTTTTGGCCT 59.436 50.000 3.32 0.00 0.00 5.19
1005 1063 1.277842 CATGGGTTTAGGGTTTTGGCC 59.722 52.381 0.00 0.00 0.00 5.36
1006 1064 1.277842 CCATGGGTTTAGGGTTTTGGC 59.722 52.381 2.85 0.00 0.00 4.52
1227 1285 3.191539 CTCTGCCGCCTTCTTCGC 61.192 66.667 0.00 0.00 0.00 4.70
1228 1286 2.510238 CCTCTGCCGCCTTCTTCG 60.510 66.667 0.00 0.00 0.00 3.79
1229 1287 2.821810 GCCTCTGCCGCCTTCTTC 60.822 66.667 0.00 0.00 0.00 2.87
1230 1288 4.767255 CGCCTCTGCCGCCTTCTT 62.767 66.667 0.00 0.00 0.00 2.52
1438 1499 0.392998 CTGGGAATGGCGCTTGTACT 60.393 55.000 7.64 0.00 0.00 2.73
1519 1580 4.520492 ACCATTAACCAACAAGCAGAGAAG 59.480 41.667 0.00 0.00 0.00 2.85
1557 1626 3.206150 CCATCTTTCTGGTACCAATCCG 58.794 50.000 17.11 4.13 0.00 4.18
1589 1658 1.946081 TGAGCACATCGCAGAAAAACA 59.054 42.857 0.00 0.00 46.13 2.83
1593 1662 5.565592 ATTAATTGAGCACATCGCAGAAA 57.434 34.783 0.00 0.00 46.13 2.52
1600 1669 7.693952 TCCGTTCTAAATTAATTGAGCACATC 58.306 34.615 13.69 1.40 0.00 3.06
1665 1734 8.506437 TCCATTCGCACAATCTAATCATAAATC 58.494 33.333 0.00 0.00 0.00 2.17
1780 1865 8.154649 GAAAGTCAATTTCAGAGGAAACAGTA 57.845 34.615 0.00 0.00 45.22 2.74
1847 1932 3.316283 GTTGGCGAAAAATCTGCATTGA 58.684 40.909 0.00 0.00 0.00 2.57
1862 1947 2.480555 GCACAGGATTCGTTGGCG 59.519 61.111 0.00 0.00 39.92 5.69
1868 1953 4.208632 GTGAGGGCACAGGATTCG 57.791 61.111 0.00 0.00 44.51 3.34
2047 2132 3.198417 AGCCTGCAAAATTATTTCTGGGG 59.802 43.478 0.00 0.00 0.00 4.96
2086 2171 6.418101 AGAAAAGAGGTTATCAATGCTGCTA 58.582 36.000 0.00 0.00 0.00 3.49
2087 2172 5.259632 AGAAAAGAGGTTATCAATGCTGCT 58.740 37.500 0.00 0.00 0.00 4.24
2091 2176 6.195165 CGCTAAGAAAAGAGGTTATCAATGC 58.805 40.000 0.00 0.00 0.00 3.56
2147 2235 6.806249 GCTCATAGAATCTAGTTCGAAGGATG 59.194 42.308 0.00 0.00 41.84 3.51
2154 2242 7.359097 GCAGAAATGCTCATAGAATCTAGTTCG 60.359 40.741 0.00 0.00 41.84 3.95
2203 2291 1.811558 GCACTCAGCAGACTGGTTTGA 60.812 52.381 3.93 0.00 44.59 2.69
2231 2319 5.105797 ACACTGAAACAGAACAAGCATTCAA 60.106 36.000 5.76 0.00 35.18 2.69
2232 2320 4.398988 ACACTGAAACAGAACAAGCATTCA 59.601 37.500 5.76 0.00 35.18 2.57
2437 2529 8.499162 CAGAAGTACAAACAGAAGGTATGAAAG 58.501 37.037 0.00 0.00 0.00 2.62
2465 2557 7.136119 ACAACAGACGTAATTAAACACCAATG 58.864 34.615 0.00 0.00 0.00 2.82
2481 2573 4.242475 TCCTTGCATAAGTACAACAGACG 58.758 43.478 0.00 0.00 31.80 4.18
2517 2609 1.838112 TCCAATCCATCAACTGCCAC 58.162 50.000 0.00 0.00 0.00 5.01
2757 2863 1.134159 GGCAGAGTGCTGGATGAGATT 60.134 52.381 0.00 0.00 44.28 2.40
3018 3126 1.592543 GCTTTTTCAACCAAACCAGCG 59.407 47.619 0.00 0.00 0.00 5.18
3102 3210 5.523188 GGAAGCATACAGACTCATGAGAAAG 59.477 44.000 29.27 18.21 0.00 2.62
3105 3213 3.067320 CGGAAGCATACAGACTCATGAGA 59.933 47.826 29.27 6.62 0.00 3.27
3240 3348 0.583438 CCTGCTTCATGTAATCGGCG 59.417 55.000 0.00 0.00 0.00 6.46
3312 3420 1.591703 GTGGGCTCGAGTCATCACA 59.408 57.895 20.37 4.32 0.00 3.58
3360 3468 1.352622 TGGCCTTCTCCCACAACTGT 61.353 55.000 3.32 0.00 0.00 3.55
3418 3526 4.503910 CCCATGTAGTGATCGAGAAACAA 58.496 43.478 0.00 0.00 0.00 2.83
3576 3684 0.250467 GGCAGTTGCAGAACCTCTCA 60.250 55.000 6.43 0.00 44.36 3.27
3615 3723 0.739813 ACTCGTATGCTTTGCCGTCC 60.740 55.000 0.00 0.00 0.00 4.79
3705 3813 4.813161 CCAATGTCGTAGCAGATCTCAATT 59.187 41.667 0.00 0.00 0.00 2.32
3714 3822 1.009829 GCTTCCCAATGTCGTAGCAG 58.990 55.000 0.00 0.00 0.00 4.24
3738 3846 2.269241 CCCTCGCCCAACCTCTTC 59.731 66.667 0.00 0.00 0.00 2.87
3756 3870 4.695455 CAGAAACAGGTACCATTTCATCGT 59.305 41.667 29.26 15.19 35.26 3.73
3807 3924 5.293324 TGTTATTCGTTCATGGAAGGAATCG 59.707 40.000 22.58 5.25 46.92 3.34
3829 3946 7.624549 TCTCACCTAAAATATCTGCTTTCTGT 58.375 34.615 0.00 0.00 0.00 3.41
3845 3962 1.270625 CCGGCAACACTTCTCACCTAA 60.271 52.381 0.00 0.00 0.00 2.69
3848 3965 2.617274 GCCGGCAACACTTCTCACC 61.617 63.158 24.80 0.00 0.00 4.02
3850 3967 2.281484 GGCCGGCAACACTTCTCA 60.281 61.111 30.85 0.00 0.00 3.27
3851 3968 3.056328 GGGCCGGCAACACTTCTC 61.056 66.667 30.85 6.91 0.00 2.87
3852 3969 3.133365 AAGGGCCGGCAACACTTCT 62.133 57.895 30.85 10.18 0.00 2.85
3857 3974 2.909965 GAACAAGGGCCGGCAACA 60.910 61.111 30.85 0.00 0.00 3.33
3859 3976 2.597217 CAGAACAAGGGCCGGCAA 60.597 61.111 30.85 0.00 0.00 4.52
3860 3977 4.659172 CCAGAACAAGGGCCGGCA 62.659 66.667 30.85 0.00 0.00 5.69
3939 4080 6.346477 TCAGATTACAAGTTGTGCTAGAGT 57.654 37.500 18.90 0.00 0.00 3.24
3940 4081 5.809562 CCTCAGATTACAAGTTGTGCTAGAG 59.190 44.000 18.90 16.38 0.00 2.43
3942 4083 5.724328 TCCTCAGATTACAAGTTGTGCTAG 58.276 41.667 18.90 7.10 0.00 3.42
4002 4152 4.260784 GCCAATACATACAGAAGAAAGGCG 60.261 45.833 0.00 0.00 0.00 5.52
4036 4186 2.145397 TCCTTGCTCCAGTACTCGAT 57.855 50.000 0.00 0.00 0.00 3.59
4038 4188 1.804372 GCATCCTTGCTCCAGTACTCG 60.804 57.143 0.00 0.00 45.77 4.18
4065 4219 8.311836 AGAAACAGAATAAGAAACGATCCTGTA 58.688 33.333 0.00 0.00 33.80 2.74
4066 4220 7.118390 CAGAAACAGAATAAGAAACGATCCTGT 59.882 37.037 0.00 0.00 35.42 4.00
4067 4221 7.459486 CAGAAACAGAATAAGAAACGATCCTG 58.541 38.462 0.00 0.00 0.00 3.86
4146 4306 4.991153 TGTTATCTGGTTGTTGTTTGCA 57.009 36.364 0.00 0.00 0.00 4.08
4147 4307 5.458779 GTCTTGTTATCTGGTTGTTGTTTGC 59.541 40.000 0.00 0.00 0.00 3.68
4171 4337 8.654230 ACTATGAATGAACATTGCTAGTACAG 57.346 34.615 4.72 0.00 29.77 2.74
4233 4405 2.236395 ACCCAATGGAGGTCGAAGTAAG 59.764 50.000 0.00 0.00 28.99 2.34
4283 4478 4.100498 GGGTTATATGAAGAACCGGAGTCA 59.900 45.833 9.46 5.99 46.12 3.41
4284 4479 4.629092 GGGTTATATGAAGAACCGGAGTC 58.371 47.826 9.46 4.89 46.12 3.36
4288 4483 3.738830 TCGGGTTATATGAAGAACCGG 57.261 47.619 0.00 0.00 46.12 5.28
4300 4495 7.565680 AGAACATAAGAACTGAATCGGGTTAT 58.434 34.615 0.00 0.00 0.00 1.89
4327 4522 1.869767 GGTGCCGATCTTGAGCATAAG 59.130 52.381 0.00 0.00 39.04 1.73
4356 4551 0.600057 GCAGGAAAGCAAGACCCTTG 59.400 55.000 2.54 2.54 0.00 3.61
4357 4552 0.185901 TGCAGGAAAGCAAGACCCTT 59.814 50.000 0.00 0.00 42.46 3.95
4358 4553 0.251077 CTGCAGGAAAGCAAGACCCT 60.251 55.000 5.57 0.00 45.13 4.34
4361 4556 1.163554 CTCCTGCAGGAAAGCAAGAC 58.836 55.000 34.30 0.00 45.13 3.01
4377 4577 1.739562 CTCGACTGTTGCTGCCTCC 60.740 63.158 0.00 0.00 0.00 4.30
4421 4653 1.134226 CAACCGACGACAGTAACACC 58.866 55.000 0.00 0.00 0.00 4.16
4440 4672 1.452833 GGACCTGATGCTGGGAAGC 60.453 63.158 0.00 0.00 0.00 3.86
4472 4704 0.249911 GCAACTCTCAACCTCCACGT 60.250 55.000 0.00 0.00 0.00 4.49
4476 4710 1.967319 TTGTGCAACTCTCAACCTCC 58.033 50.000 0.00 0.00 38.04 4.30
4534 4782 1.674441 CAGGCTGTAATGGATGTGCTG 59.326 52.381 6.28 0.00 0.00 4.41
4560 4808 1.526887 CAATCTGACGCGTTTGTCTGT 59.473 47.619 15.53 0.00 39.64 3.41
4573 4821 7.181569 TGGTGTGTATAAGATCACAATCTGA 57.818 36.000 0.00 0.00 44.37 3.27
4614 4862 4.293648 CGTGGCTGTGGGTCGTGA 62.294 66.667 0.00 0.00 0.00 4.35
4634 4885 2.580867 CGACCTCGCTAGCTGCAC 60.581 66.667 13.93 0.00 43.06 4.57
4690 4941 4.055360 GCAAAGGTTTCACCATTGTTACC 58.945 43.478 11.45 0.00 45.77 2.85
4721 4972 2.031516 CCGTGAGCAAGAGTGGCAG 61.032 63.158 0.00 0.00 0.00 4.85
4736 4987 1.135915 TGCTTGTTTGATTTGTGCCGT 59.864 42.857 0.00 0.00 0.00 5.68
4737 4988 1.850377 TGCTTGTTTGATTTGTGCCG 58.150 45.000 0.00 0.00 0.00 5.69
4738 4989 2.032636 GCTTGCTTGTTTGATTTGTGCC 60.033 45.455 0.00 0.00 0.00 5.01
4739 4990 2.867975 AGCTTGCTTGTTTGATTTGTGC 59.132 40.909 0.00 0.00 0.00 4.57
4740 4991 4.567558 TGAAGCTTGCTTGTTTGATTTGTG 59.432 37.500 12.92 0.00 0.00 3.33
4741 4992 4.567959 GTGAAGCTTGCTTGTTTGATTTGT 59.432 37.500 12.92 0.00 0.00 2.83
4742 4993 4.567558 TGTGAAGCTTGCTTGTTTGATTTG 59.432 37.500 12.92 0.00 0.00 2.32
4743 4994 4.757594 TGTGAAGCTTGCTTGTTTGATTT 58.242 34.783 12.92 0.00 0.00 2.17
4744 4995 4.389890 TGTGAAGCTTGCTTGTTTGATT 57.610 36.364 12.92 0.00 0.00 2.57
4745 4996 4.389890 TTGTGAAGCTTGCTTGTTTGAT 57.610 36.364 12.92 0.00 0.00 2.57
4746 4997 3.865011 TTGTGAAGCTTGCTTGTTTGA 57.135 38.095 12.92 0.00 0.00 2.69
4747 4998 4.925061 TTTTGTGAAGCTTGCTTGTTTG 57.075 36.364 12.92 0.00 0.00 2.93
4748 4999 4.392754 CCTTTTTGTGAAGCTTGCTTGTTT 59.607 37.500 12.92 0.00 0.00 2.83
4749 5000 3.934579 CCTTTTTGTGAAGCTTGCTTGTT 59.065 39.130 12.92 0.00 0.00 2.83
4750 5001 3.195396 TCCTTTTTGTGAAGCTTGCTTGT 59.805 39.130 12.92 0.00 0.00 3.16
4751 5002 3.784338 TCCTTTTTGTGAAGCTTGCTTG 58.216 40.909 12.92 0.00 0.00 4.01
4752 5003 4.099881 TGATCCTTTTTGTGAAGCTTGCTT 59.900 37.500 2.10 7.65 0.00 3.91
4753 5004 3.638160 TGATCCTTTTTGTGAAGCTTGCT 59.362 39.130 2.10 0.00 0.00 3.91
4754 5005 3.981211 TGATCCTTTTTGTGAAGCTTGC 58.019 40.909 2.10 0.00 0.00 4.01
4755 5006 5.594926 ACTTGATCCTTTTTGTGAAGCTTG 58.405 37.500 2.10 0.00 0.00 4.01
4756 5007 5.360714 TGACTTGATCCTTTTTGTGAAGCTT 59.639 36.000 0.00 0.00 0.00 3.74
4757 5008 4.889409 TGACTTGATCCTTTTTGTGAAGCT 59.111 37.500 0.00 0.00 0.00 3.74
4758 5009 4.978580 GTGACTTGATCCTTTTTGTGAAGC 59.021 41.667 0.00 0.00 0.00 3.86
4759 5010 6.382869 AGTGACTTGATCCTTTTTGTGAAG 57.617 37.500 0.00 0.00 0.00 3.02
4760 5011 5.299279 GGAGTGACTTGATCCTTTTTGTGAA 59.701 40.000 0.00 0.00 0.00 3.18
4761 5012 4.821805 GGAGTGACTTGATCCTTTTTGTGA 59.178 41.667 0.00 0.00 0.00 3.58
4762 5013 4.022849 GGGAGTGACTTGATCCTTTTTGTG 60.023 45.833 0.00 0.00 33.40 3.33
4763 5014 4.141158 AGGGAGTGACTTGATCCTTTTTGT 60.141 41.667 0.00 0.00 33.40 2.83
4764 5015 4.217118 CAGGGAGTGACTTGATCCTTTTTG 59.783 45.833 0.00 0.00 33.40 2.44
4765 5016 4.141158 ACAGGGAGTGACTTGATCCTTTTT 60.141 41.667 0.00 0.00 33.40 1.94
4766 5017 3.395941 ACAGGGAGTGACTTGATCCTTTT 59.604 43.478 0.00 0.00 33.40 2.27
4767 5018 2.982488 ACAGGGAGTGACTTGATCCTTT 59.018 45.455 0.00 0.00 33.40 3.11
4768 5019 2.569404 GACAGGGAGTGACTTGATCCTT 59.431 50.000 0.00 0.00 33.40 3.36
4769 5020 2.183679 GACAGGGAGTGACTTGATCCT 58.816 52.381 0.00 0.00 33.40 3.24
4770 5021 2.167487 GAGACAGGGAGTGACTTGATCC 59.833 54.545 0.00 0.00 30.68 3.36
4771 5022 2.167487 GGAGACAGGGAGTGACTTGATC 59.833 54.545 0.00 0.00 30.68 2.92
4772 5023 2.183679 GGAGACAGGGAGTGACTTGAT 58.816 52.381 0.00 0.00 30.68 2.57
4773 5024 1.133167 TGGAGACAGGGAGTGACTTGA 60.133 52.381 0.00 0.00 30.68 3.02
4774 5025 1.342074 TGGAGACAGGGAGTGACTTG 58.658 55.000 0.00 0.00 30.68 3.16
4775 5026 3.871623 TGGAGACAGGGAGTGACTT 57.128 52.632 0.00 0.00 30.68 3.01
4784 5035 8.334966 CTGGTTACGAACTAGATGGAGACAGG 62.335 50.000 0.00 0.00 41.99 4.00
4785 5036 5.449314 CTGGTTACGAACTAGATGGAGACAG 60.449 48.000 0.00 0.00 41.99 3.51
4786 5037 4.398358 CTGGTTACGAACTAGATGGAGACA 59.602 45.833 0.00 0.00 41.99 3.41
4787 5038 4.734108 GCTGGTTACGAACTAGATGGAGAC 60.734 50.000 12.77 0.00 41.99 3.36
4788 5039 3.380637 GCTGGTTACGAACTAGATGGAGA 59.619 47.826 12.77 0.00 41.99 3.71
4789 5040 3.707793 GCTGGTTACGAACTAGATGGAG 58.292 50.000 12.77 0.00 41.99 3.86
4790 5041 2.098607 CGCTGGTTACGAACTAGATGGA 59.901 50.000 12.77 0.00 41.99 3.41
4791 5042 2.159282 ACGCTGGTTACGAACTAGATGG 60.159 50.000 12.77 0.00 41.99 3.51
4792 5043 2.852413 CACGCTGGTTACGAACTAGATG 59.148 50.000 12.77 7.74 41.99 2.90
4793 5044 2.734492 GCACGCTGGTTACGAACTAGAT 60.734 50.000 12.77 0.00 41.99 1.98
4794 5045 1.401931 GCACGCTGGTTACGAACTAGA 60.402 52.381 12.77 0.00 41.99 2.43
4795 5046 0.989890 GCACGCTGGTTACGAACTAG 59.010 55.000 0.00 0.00 42.28 2.57
4796 5047 0.388907 GGCACGCTGGTTACGAACTA 60.389 55.000 0.00 0.00 0.00 2.24
4797 5048 1.666872 GGCACGCTGGTTACGAACT 60.667 57.895 0.00 0.00 0.00 3.01
4798 5049 1.957186 TGGCACGCTGGTTACGAAC 60.957 57.895 0.00 0.00 0.00 3.95
4799 5050 1.957186 GTGGCACGCTGGTTACGAA 60.957 57.895 0.00 0.00 35.02 3.85
4800 5051 2.356553 GTGGCACGCTGGTTACGA 60.357 61.111 0.00 0.00 35.02 3.43
4801 5052 1.966493 GATGTGGCACGCTGGTTACG 61.966 60.000 13.77 0.00 40.97 3.18
4802 5053 1.644786 GGATGTGGCACGCTGGTTAC 61.645 60.000 13.77 0.00 40.97 2.50
4803 5054 1.376683 GGATGTGGCACGCTGGTTA 60.377 57.895 13.77 0.00 40.97 2.85
4804 5055 1.836999 TAGGATGTGGCACGCTGGTT 61.837 55.000 13.77 0.00 40.97 3.67
4805 5056 2.244117 CTAGGATGTGGCACGCTGGT 62.244 60.000 13.77 0.00 40.97 4.00
4806 5057 1.522355 CTAGGATGTGGCACGCTGG 60.522 63.158 13.77 0.00 40.97 4.85
4807 5058 0.807667 GTCTAGGATGTGGCACGCTG 60.808 60.000 13.77 0.15 40.97 5.18
4808 5059 1.517832 GTCTAGGATGTGGCACGCT 59.482 57.895 13.77 2.26 40.97 5.07
4809 5060 1.878522 CGTCTAGGATGTGGCACGC 60.879 63.158 13.77 7.46 40.62 5.34
4810 5061 1.878522 GCGTCTAGGATGTGGCACG 60.879 63.158 13.77 0.00 0.00 5.34
4811 5062 1.521681 GGCGTCTAGGATGTGGCAC 60.522 63.158 11.55 11.55 0.00 5.01
4812 5063 0.396556 TAGGCGTCTAGGATGTGGCA 60.397 55.000 0.00 0.00 0.00 4.92
4813 5064 0.032267 GTAGGCGTCTAGGATGTGGC 59.968 60.000 0.00 0.00 0.00 5.01
4814 5065 1.609555 GAGTAGGCGTCTAGGATGTGG 59.390 57.143 0.00 0.00 0.00 4.17
4815 5066 2.292016 CAGAGTAGGCGTCTAGGATGTG 59.708 54.545 0.00 0.00 0.00 3.21
4816 5067 2.577700 CAGAGTAGGCGTCTAGGATGT 58.422 52.381 0.00 0.00 0.00 3.06
4817 5068 1.883275 CCAGAGTAGGCGTCTAGGATG 59.117 57.143 0.00 0.00 0.00 3.51
4818 5069 1.495574 ACCAGAGTAGGCGTCTAGGAT 59.504 52.381 7.03 0.00 0.00 3.24
4819 5070 0.917533 ACCAGAGTAGGCGTCTAGGA 59.082 55.000 7.03 0.00 0.00 2.94
4820 5071 1.310904 GACCAGAGTAGGCGTCTAGG 58.689 60.000 0.00 0.00 0.00 3.02
4821 5072 1.310904 GGACCAGAGTAGGCGTCTAG 58.689 60.000 0.00 0.00 0.00 2.43
4822 5073 0.106819 GGGACCAGAGTAGGCGTCTA 60.107 60.000 0.00 0.00 0.00 2.59
4823 5074 1.380112 GGGACCAGAGTAGGCGTCT 60.380 63.158 0.00 0.00 0.00 4.18
4824 5075 1.380112 AGGGACCAGAGTAGGCGTC 60.380 63.158 0.00 0.00 0.00 5.19
4825 5076 1.380112 GAGGGACCAGAGTAGGCGT 60.380 63.158 0.00 0.00 0.00 5.68
4826 5077 2.482333 CGAGGGACCAGAGTAGGCG 61.482 68.421 0.00 0.00 0.00 5.52
4827 5078 3.527641 CGAGGGACCAGAGTAGGC 58.472 66.667 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.