Multiple sequence alignment - TraesCS2A01G169000

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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 TraesCS2A01G169000 chr2A 100.000 6555 0 0 1675 8229 123519983 123513429 0.000000e+00 12105.0
1 TraesCS2A01G169000 chr2A 100.000 1221 0 0 1 1221 123521657 123520437 0.000000e+00 2255.0
2 TraesCS2A01G169000 chr2A 98.000 50 1 0 3352 3401 123518258 123518209 4.090000e-13 87.9
3 TraesCS2A01G169000 chr2A 98.000 50 1 0 3400 3449 123518306 123518257 4.090000e-13 87.9
4 TraesCS2A01G169000 chr2B 95.447 5293 147 32 2131 7378 172895336 172890093 0.000000e+00 8353.0
5 TraesCS2A01G169000 chr2B 96.410 195 5 2 1934 2126 172895724 172895530 3.710000e-83 320.0
6 TraesCS2A01G169000 chr2B 90.196 153 3 6 1048 1197 172896557 172896414 1.090000e-43 189.0
7 TraesCS2A01G169000 chr2B 94.167 120 3 4 769 887 172897957 172897841 6.560000e-41 180.0
8 TraesCS2A01G169000 chr2B 98.000 50 1 0 3352 3401 172894057 172894008 4.090000e-13 87.9
9 TraesCS2A01G169000 chr2B 96.226 53 2 0 3397 3449 172894108 172894056 4.090000e-13 87.9
10 TraesCS2A01G169000 chr2B 100.000 28 0 0 7 34 172897984 172897957 1.500000e-02 52.8
11 TraesCS2A01G169000 chr2D 95.142 3561 122 30 4707 8229 120095255 120091708 0.000000e+00 5570.0
12 TraesCS2A01G169000 chr2D 97.968 2559 42 2 2131 4689 120097791 120095243 0.000000e+00 4429.0
13 TraesCS2A01G169000 chr2D 81.379 435 40 23 7744 8143 33361581 33362009 4.790000e-82 316.0
14 TraesCS2A01G169000 chr2D 75.816 674 88 33 7620 8225 494648082 494647416 1.050000e-68 272.0
15 TraesCS2A01G169000 chr2D 98.000 50 1 0 3352 3401 120096532 120096483 4.090000e-13 87.9
16 TraesCS2A01G169000 chr2D 94.231 52 2 1 4550 4601 120095422 120095372 2.460000e-10 78.7
17 TraesCS2A01G169000 chr1D 94.991 559 24 3 209 764 85938089 85938646 0.000000e+00 874.0
18 TraesCS2A01G169000 chr1D 97.714 175 4 0 36 210 85937592 85937766 1.340000e-77 302.0
19 TraesCS2A01G169000 chr1D 81.330 391 51 12 7753 8139 202354491 202354863 1.740000e-76 298.0
20 TraesCS2A01G169000 chr1D 91.818 110 9 0 7398 7507 99547572 99547681 3.980000e-33 154.0
21 TraesCS2A01G169000 chr5D 81.649 485 67 11 7672 8139 548018124 548017645 4.660000e-102 383.0
22 TraesCS2A01G169000 chr5D 84.642 293 32 10 7744 8034 466500648 466500929 6.290000e-71 279.0
23 TraesCS2A01G169000 chr5D 79.459 370 52 16 7674 8032 69985800 69986156 2.970000e-59 241.0
24 TraesCS2A01G169000 chr5D 87.500 56 7 0 8070 8125 451013115 451013170 1.920000e-06 65.8
25 TraesCS2A01G169000 chrUn 93.939 231 14 0 1896 2126 25868707 25868937 4.730000e-92 350.0
26 TraesCS2A01G169000 chrUn 95.270 148 4 3 1729 1873 25868508 25868655 1.790000e-56 231.0
27 TraesCS2A01G169000 chrUn 95.833 72 3 0 1150 1221 25868143 25868214 5.220000e-22 117.0
28 TraesCS2A01G169000 chr5B 78.230 565 93 18 7681 8222 692205869 692205312 1.320000e-87 335.0
29 TraesCS2A01G169000 chr5B 81.818 110 20 0 7398 7507 176234911 176234802 8.790000e-15 93.5
30 TraesCS2A01G169000 chr5B 90.000 70 7 0 8070 8139 332405153 332405084 3.160000e-14 91.6
31 TraesCS2A01G169000 chr3D 79.418 481 69 18 7677 8139 403674070 403673602 6.200000e-81 313.0
32 TraesCS2A01G169000 chr3D 77.801 473 74 18 7674 8124 578901260 578900797 6.330000e-66 263.0
33 TraesCS2A01G169000 chr1B 78.614 505 72 24 7746 8228 593481435 593480945 1.340000e-77 302.0
34 TraesCS2A01G169000 chr6D 78.337 517 68 16 7746 8224 349102534 349103044 2.250000e-75 294.0
35 TraesCS2A01G169000 chr6D 91.818 110 9 0 7398 7507 459701963 459701854 3.980000e-33 154.0
36 TraesCS2A01G169000 chr6D 90.909 110 10 0 7398 7507 440963327 440963436 1.850000e-31 148.0
37 TraesCS2A01G169000 chr3A 77.686 484 80 19 7674 8139 624960481 624960954 3.790000e-68 270.0
38 TraesCS2A01G169000 chr7A 81.962 316 49 6 7744 8057 118441090 118440781 2.280000e-65 261.0
39 TraesCS2A01G169000 chr7A 89.130 92 10 0 8137 8228 245826227 245826136 1.880000e-21 115.0
40 TraesCS2A01G169000 chr7A 100.000 46 0 0 8099 8144 679742135 679742090 1.470000e-12 86.1
41 TraesCS2A01G169000 chr7D 81.847 314 43 8 7701 8012 568768210 568768511 1.370000e-62 252.0
42 TraesCS2A01G169000 chr7D 80.233 344 53 10 7672 8005 368568101 368568439 2.290000e-60 244.0
43 TraesCS2A01G169000 chr7D 76.538 520 58 26 7767 8228 233065840 233066353 8.310000e-55 226.0
44 TraesCS2A01G169000 chr7D 91.818 110 9 0 7398 7507 618707246 618707137 3.980000e-33 154.0
45 TraesCS2A01G169000 chr4D 76.661 557 65 31 7725 8225 66772236 66771689 1.770000e-61 248.0
46 TraesCS2A01G169000 chr4D 80.175 343 56 8 7674 8015 69478045 69477714 6.380000e-61 246.0
47 TraesCS2A01G169000 chr4D 74.146 615 81 33 7674 8225 385519240 385519839 5.070000e-42 183.0
48 TraesCS2A01G169000 chr4D 78.344 157 26 7 7741 7895 23218790 23218940 2.450000e-15 95.3
49 TraesCS2A01G169000 chr1A 79.646 339 57 10 7686 8021 12780295 12780624 4.970000e-57 233.0
50 TraesCS2A01G169000 chr3B 76.074 489 86 20 7672 8139 403454358 403454836 8.310000e-55 226.0
51 TraesCS2A01G169000 chr3B 95.652 46 2 0 8099 8144 53890003 53889958 3.190000e-09 75.0
52 TraesCS2A01G169000 chr4A 97.500 40 1 0 8100 8139 604607752 604607713 1.480000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G169000 chr2A 123513429 123521657 8228 True 3633.950000 12105 99.00000 1 8229 4 chr2A.!!$R1 8228
1 TraesCS2A01G169000 chr2B 172890093 172897984 7891 True 1324.371429 8353 95.77800 7 7378 7 chr2B.!!$R1 7371
2 TraesCS2A01G169000 chr2D 120091708 120097791 6083 True 2541.400000 5570 96.33525 2131 8229 4 chr2D.!!$R2 6098
3 TraesCS2A01G169000 chr2D 494647416 494648082 666 True 272.000000 272 75.81600 7620 8225 1 chr2D.!!$R1 605
4 TraesCS2A01G169000 chr1D 85937592 85938646 1054 False 588.000000 874 96.35250 36 764 2 chr1D.!!$F3 728
5 TraesCS2A01G169000 chrUn 25868143 25868937 794 False 232.666667 350 95.01400 1150 2126 3 chrUn.!!$F1 976
6 TraesCS2A01G169000 chr5B 692205312 692205869 557 True 335.000000 335 78.23000 7681 8222 1 chr5B.!!$R3 541
7 TraesCS2A01G169000 chr6D 349102534 349103044 510 False 294.000000 294 78.33700 7746 8224 1 chr6D.!!$F1 478
8 TraesCS2A01G169000 chr7D 233065840 233066353 513 False 226.000000 226 76.53800 7767 8228 1 chr7D.!!$F1 461
9 TraesCS2A01G169000 chr4D 66771689 66772236 547 True 248.000000 248 76.66100 7725 8225 1 chr4D.!!$R1 500

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
138 139 0.109964 TTTGCTCCACGCGTATTTGC 60.110 50.000 13.44 14.75 43.27 3.68 F
1125 2619 0.105039 CCTCCACTCCATCGCTAACC 59.895 60.000 0.00 0.00 0.00 2.85 F
1720 3214 0.037590 CATTGGGAGTCGAAACCCCA 59.962 55.000 20.77 17.79 45.01 4.96 F
1721 3215 0.328258 ATTGGGAGTCGAAACCCCAG 59.672 55.000 20.77 0.00 42.94 4.45 F
3313 5212 0.468226 TGTTACCCGGATCAGGATGC 59.532 55.000 14.13 1.60 34.76 3.91 F
3903 5802 1.013596 TGTCAGTGTCGCCTTTTGTG 58.986 50.000 0.00 0.00 0.00 3.33 F
4212 6111 1.260544 AAAGCAGTCCCTTGAATGGC 58.739 50.000 0.00 0.00 37.08 4.40 F
5543 7466 1.968493 TCCACCCTGTTCAGTACTCAC 59.032 52.381 0.00 0.00 0.00 3.51 F
6435 8370 0.318762 ACAACGAGAAGAGCAGGTCC 59.681 55.000 0.00 0.00 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 3171 0.326618 AGTATCAGGGAGTGGGGGTG 60.327 60.000 0.00 0.0 0.00 4.61 R
2281 4168 2.867109 TTGCTCTCTTCTTTCCCCAG 57.133 50.000 0.00 0.0 0.00 4.45 R
3313 5212 0.661552 CTTCTGATCCATGCCTTGCG 59.338 55.000 0.00 0.0 0.00 4.85 R
3350 5249 3.508840 GATTGCGGAAGGGGTGCG 61.509 66.667 0.00 0.0 45.20 5.34 R
4212 6111 0.673333 TAGTGCATGGTGGCAGTTCG 60.673 55.000 0.38 0.0 44.78 3.95 R
5637 7560 1.470098 AGTTCCTGCAAACATGATCGC 59.530 47.619 0.00 0.0 0.00 4.58 R
6157 8080 2.570365 GCACATGCACAATCCCTGA 58.430 52.632 0.00 0.0 41.59 3.86 R
6512 8447 0.601046 CGACACAGCCTTCTTCTGCA 60.601 55.000 0.00 0.0 35.04 4.41 R
7705 9687 0.101399 CTGAGTCCGCTGACGCTAAT 59.899 55.000 12.72 0.0 46.51 1.73 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
138 139 0.109964 TTTGCTCCACGCGTATTTGC 60.110 50.000 13.44 14.75 43.27 3.68
185 186 2.439960 CGATCCACCCCGATTCCCA 61.440 63.158 0.00 0.00 0.00 4.37
244 569 1.513158 CCCGTCTGTCTCGCAATCT 59.487 57.895 0.00 0.00 0.00 2.40
285 610 2.916052 GCGTCACTCCACCTCACGA 61.916 63.158 0.00 0.00 32.08 4.35
298 623 0.798776 CTCACGAGGCCAACAACATC 59.201 55.000 5.01 0.00 0.00 3.06
299 624 0.605319 TCACGAGGCCAACAACATCC 60.605 55.000 5.01 0.00 0.00 3.51
304 629 0.779997 AGGCCAACAACATCCTCCTT 59.220 50.000 5.01 0.00 0.00 3.36
312 637 1.065126 CAACATCCTCCTTCACCTCCC 60.065 57.143 0.00 0.00 0.00 4.30
320 645 3.316573 CTTCACCTCCCAGGCCGTC 62.317 68.421 0.00 0.00 39.63 4.79
324 649 2.231380 ACCTCCCAGGCCGTCAAAT 61.231 57.895 0.00 0.00 39.63 2.32
330 655 1.671054 CAGGCCGTCAAATGGTCGT 60.671 57.895 0.00 0.00 33.08 4.34
381 706 2.202892 GCCGCCAGCTACCAGTAC 60.203 66.667 0.00 0.00 38.99 2.73
422 747 1.999071 CTCCAGCGAAGTCTCCTCCG 61.999 65.000 0.00 0.00 0.00 4.63
480 805 1.423921 GTTCCCTCCACCTTTCTTGGA 59.576 52.381 0.00 0.00 41.06 3.53
590 915 3.548770 CAGCCTAGATGGATTGCAAAGA 58.451 45.455 1.71 0.00 38.35 2.52
593 918 3.563390 GCCTAGATGGATTGCAAAGAGAC 59.437 47.826 1.71 0.00 38.35 3.36
595 920 5.188434 CCTAGATGGATTGCAAAGAGACAA 58.812 41.667 1.71 0.00 38.35 3.18
597 922 5.382618 AGATGGATTGCAAAGAGACAAAC 57.617 39.130 1.71 0.00 0.00 2.93
648 973 8.539856 AGATAAAATATTATCCCCCACTCCTT 57.460 34.615 5.25 0.00 45.71 3.36
649 974 9.643778 AGATAAAATATTATCCCCCACTCCTTA 57.356 33.333 5.25 0.00 45.71 2.69
727 1055 3.449227 GCCAGGGCGCCTTTTACC 61.449 66.667 28.56 8.41 0.00 2.85
728 1056 2.355115 CCAGGGCGCCTTTTACCT 59.645 61.111 28.56 11.02 0.00 3.08
729 1057 3.590824 CAGGGCGCCTTTTACCTG 58.409 61.111 28.56 19.63 43.87 4.00
730 1058 2.046285 CAGGGCGCCTTTTACCTGG 61.046 63.158 28.56 0.00 45.21 4.45
731 1059 2.228480 AGGGCGCCTTTTACCTGGA 61.228 57.895 28.56 0.00 30.71 3.86
732 1060 1.303806 GGGCGCCTTTTACCTGGAA 60.304 57.895 28.56 0.00 0.00 3.53
733 1061 0.683179 GGGCGCCTTTTACCTGGAAT 60.683 55.000 28.56 0.00 0.00 3.01
734 1062 1.182667 GGCGCCTTTTACCTGGAATT 58.817 50.000 22.15 0.00 0.00 2.17
735 1063 2.371306 GGCGCCTTTTACCTGGAATTA 58.629 47.619 22.15 0.00 0.00 1.40
736 1064 2.956333 GGCGCCTTTTACCTGGAATTAT 59.044 45.455 22.15 0.00 0.00 1.28
737 1065 3.004419 GGCGCCTTTTACCTGGAATTATC 59.996 47.826 22.15 0.00 0.00 1.75
738 1066 3.883489 GCGCCTTTTACCTGGAATTATCT 59.117 43.478 0.00 0.00 0.00 1.98
739 1067 4.023963 GCGCCTTTTACCTGGAATTATCTC 60.024 45.833 0.00 0.00 0.00 2.75
740 1068 4.515567 CGCCTTTTACCTGGAATTATCTCC 59.484 45.833 0.00 0.00 35.88 3.71
741 1069 4.827835 GCCTTTTACCTGGAATTATCTCCC 59.172 45.833 0.00 0.00 34.22 4.30
742 1070 5.399152 GCCTTTTACCTGGAATTATCTCCCT 60.399 44.000 0.00 0.00 34.22 4.20
743 1071 6.673583 CCTTTTACCTGGAATTATCTCCCTT 58.326 40.000 0.00 0.00 34.22 3.95
744 1072 7.639534 GCCTTTTACCTGGAATTATCTCCCTTA 60.640 40.741 0.00 0.00 34.22 2.69
745 1073 7.939588 CCTTTTACCTGGAATTATCTCCCTTAG 59.060 40.741 0.00 0.00 34.22 2.18
746 1074 4.984146 ACCTGGAATTATCTCCCTTAGC 57.016 45.455 0.00 0.00 34.22 3.09
747 1075 4.307259 ACCTGGAATTATCTCCCTTAGCA 58.693 43.478 0.00 0.00 34.22 3.49
748 1076 4.726825 ACCTGGAATTATCTCCCTTAGCAA 59.273 41.667 0.00 0.00 34.22 3.91
749 1077 5.066593 CCTGGAATTATCTCCCTTAGCAAC 58.933 45.833 0.00 0.00 34.22 4.17
750 1078 5.048846 TGGAATTATCTCCCTTAGCAACC 57.951 43.478 0.00 0.00 34.22 3.77
751 1079 4.476846 TGGAATTATCTCCCTTAGCAACCA 59.523 41.667 0.00 0.00 34.22 3.67
752 1080 5.044476 TGGAATTATCTCCCTTAGCAACCAA 60.044 40.000 0.00 0.00 34.22 3.67
753 1081 5.891551 GGAATTATCTCCCTTAGCAACCAAA 59.108 40.000 0.00 0.00 0.00 3.28
754 1082 6.183360 GGAATTATCTCCCTTAGCAACCAAAC 60.183 42.308 0.00 0.00 0.00 2.93
755 1083 3.806949 ATCTCCCTTAGCAACCAAACA 57.193 42.857 0.00 0.00 0.00 2.83
756 1084 3.586470 TCTCCCTTAGCAACCAAACAA 57.414 42.857 0.00 0.00 0.00 2.83
757 1085 3.486383 TCTCCCTTAGCAACCAAACAAG 58.514 45.455 0.00 0.00 0.00 3.16
758 1086 2.558359 CTCCCTTAGCAACCAAACAAGG 59.442 50.000 0.00 0.00 36.36 3.61
759 1087 1.000843 CCCTTAGCAACCAAACAAGGC 59.999 52.381 0.00 0.00 35.46 4.35
760 1088 1.000843 CCTTAGCAACCAAACAAGGCC 59.999 52.381 0.00 0.00 30.14 5.19
761 1089 1.963515 CTTAGCAACCAAACAAGGCCT 59.036 47.619 0.00 0.00 0.00 5.19
762 1090 2.080654 TAGCAACCAAACAAGGCCTT 57.919 45.000 13.78 13.78 0.00 4.35
763 1091 2.080654 AGCAACCAAACAAGGCCTTA 57.919 45.000 20.00 0.00 0.00 2.69
764 1092 1.963515 AGCAACCAAACAAGGCCTTAG 59.036 47.619 20.00 15.05 0.00 2.18
765 1093 1.960689 GCAACCAAACAAGGCCTTAGA 59.039 47.619 20.00 0.00 0.00 2.10
766 1094 2.029918 GCAACCAAACAAGGCCTTAGAG 60.030 50.000 20.00 8.91 0.00 2.43
767 1095 3.222603 CAACCAAACAAGGCCTTAGAGT 58.777 45.455 20.00 9.66 0.00 3.24
768 1096 3.595190 ACCAAACAAGGCCTTAGAGTT 57.405 42.857 20.00 15.66 0.00 3.01
807 1135 3.643792 AGTGAAAGGTCTGCTAGAGTTGT 59.356 43.478 0.00 0.00 0.00 3.32
926 2417 3.816994 TGAGAATACGAGGAATCGGAGA 58.183 45.455 2.46 0.00 45.75 3.71
944 2435 2.513026 GATGGGTCTGCGACAGTGCT 62.513 60.000 10.14 0.00 33.68 4.40
946 2437 2.807045 GGTCTGCGACAGTGCTCG 60.807 66.667 10.14 9.77 33.68 5.03
995 2486 3.250323 CGGCGCATCGAGTGTGAG 61.250 66.667 10.83 0.00 40.86 3.51
997 2488 1.875813 GGCGCATCGAGTGTGAGAG 60.876 63.158 10.83 0.00 40.86 3.20
1001 2492 1.793353 CGCATCGAGTGTGAGAGACAG 60.793 57.143 0.00 0.00 40.86 3.51
1002 2493 1.470494 GCATCGAGTGTGAGAGACAGA 59.530 52.381 0.00 0.00 34.28 3.41
1003 2494 2.477694 GCATCGAGTGTGAGAGACAGAG 60.478 54.545 0.00 0.00 34.28 3.35
1004 2495 1.160989 TCGAGTGTGAGAGACAGAGC 58.839 55.000 0.00 0.00 34.28 4.09
1005 2496 0.170116 CGAGTGTGAGAGACAGAGCC 59.830 60.000 0.00 0.00 34.28 4.70
1006 2497 0.530288 GAGTGTGAGAGACAGAGCCC 59.470 60.000 0.00 0.00 34.28 5.19
1007 2498 0.114168 AGTGTGAGAGACAGAGCCCT 59.886 55.000 0.00 0.00 34.28 5.19
1008 2499 0.530288 GTGTGAGAGACAGAGCCCTC 59.470 60.000 0.00 0.00 34.28 4.30
1009 2500 0.407528 TGTGAGAGACAGAGCCCTCT 59.592 55.000 0.00 0.00 42.01 3.69
1011 2502 2.807247 GAGAGACAGAGCCCTCTCC 58.193 63.158 0.00 0.00 45.89 3.71
1012 2503 0.755327 GAGAGACAGAGCCCTCTCCC 60.755 65.000 0.00 0.00 45.89 4.30
1013 2504 2.043450 AGACAGAGCCCTCTCCCG 60.043 66.667 0.00 0.00 40.22 5.14
1014 2505 2.363147 GACAGAGCCCTCTCCCGT 60.363 66.667 0.00 0.00 40.22 5.28
1015 2506 2.363147 ACAGAGCCCTCTCCCGTC 60.363 66.667 0.00 0.00 40.22 4.79
1016 2507 2.043450 CAGAGCCCTCTCCCGTCT 60.043 66.667 0.00 0.00 40.22 4.18
1017 2508 2.124693 CAGAGCCCTCTCCCGTCTC 61.125 68.421 0.00 0.00 40.22 3.36
1018 2509 2.835895 GAGCCCTCTCCCGTCTCC 60.836 72.222 0.00 0.00 33.19 3.71
1019 2510 3.663815 GAGCCCTCTCCCGTCTCCA 62.664 68.421 0.00 0.00 33.19 3.86
1020 2511 3.151022 GCCCTCTCCCGTCTCCAG 61.151 72.222 0.00 0.00 0.00 3.86
1021 2512 3.151022 CCCTCTCCCGTCTCCAGC 61.151 72.222 0.00 0.00 0.00 4.85
1022 2513 3.151022 CCTCTCCCGTCTCCAGCC 61.151 72.222 0.00 0.00 0.00 4.85
1023 2514 2.363018 CTCTCCCGTCTCCAGCCA 60.363 66.667 0.00 0.00 0.00 4.75
1024 2515 1.984570 CTCTCCCGTCTCCAGCCAA 60.985 63.158 0.00 0.00 0.00 4.52
1025 2516 1.954362 CTCTCCCGTCTCCAGCCAAG 61.954 65.000 0.00 0.00 0.00 3.61
1026 2517 3.672295 CTCCCGTCTCCAGCCAAGC 62.672 68.421 0.00 0.00 0.00 4.01
1027 2518 4.020617 CCCGTCTCCAGCCAAGCA 62.021 66.667 0.00 0.00 0.00 3.91
1028 2519 2.032528 CCGTCTCCAGCCAAGCAA 59.967 61.111 0.00 0.00 0.00 3.91
1029 2520 1.600636 CCGTCTCCAGCCAAGCAAA 60.601 57.895 0.00 0.00 0.00 3.68
1030 2521 1.580845 CCGTCTCCAGCCAAGCAAAG 61.581 60.000 0.00 0.00 0.00 2.77
1031 2522 1.583477 GTCTCCAGCCAAGCAAAGC 59.417 57.895 0.00 0.00 0.00 3.51
1032 2523 1.604593 TCTCCAGCCAAGCAAAGCC 60.605 57.895 0.00 0.00 0.00 4.35
1033 2524 2.601367 TCCAGCCAAGCAAAGCCC 60.601 61.111 0.00 0.00 0.00 5.19
1034 2525 2.602568 CCAGCCAAGCAAAGCCCT 60.603 61.111 0.00 0.00 0.00 5.19
1035 2526 2.643232 CCAGCCAAGCAAAGCCCTC 61.643 63.158 0.00 0.00 0.00 4.30
1036 2527 1.605738 CAGCCAAGCAAAGCCCTCT 60.606 57.895 0.00 0.00 0.00 3.69
1037 2528 1.303970 AGCCAAGCAAAGCCCTCTC 60.304 57.895 0.00 0.00 0.00 3.20
1038 2529 2.694760 GCCAAGCAAAGCCCTCTCG 61.695 63.158 0.00 0.00 0.00 4.04
1039 2530 2.694760 CCAAGCAAAGCCCTCTCGC 61.695 63.158 0.00 0.00 0.00 5.03
1040 2531 2.743928 AAGCAAAGCCCTCTCGCG 60.744 61.111 0.00 0.00 0.00 5.87
1041 2532 3.537206 AAGCAAAGCCCTCTCGCGT 62.537 57.895 5.77 0.00 0.00 6.01
1042 2533 3.491652 GCAAAGCCCTCTCGCGTC 61.492 66.667 5.77 0.00 0.00 5.19
1043 2534 2.048222 CAAAGCCCTCTCGCGTCA 60.048 61.111 5.77 0.00 0.00 4.35
1044 2535 2.097038 CAAAGCCCTCTCGCGTCAG 61.097 63.158 5.77 2.71 0.00 3.51
1045 2536 2.276116 AAAGCCCTCTCGCGTCAGA 61.276 57.895 5.77 0.79 0.00 3.27
1046 2537 2.493907 AAAGCCCTCTCGCGTCAGAC 62.494 60.000 5.77 0.00 0.00 3.51
1066 2557 3.431725 CGCGTGGCCTTTCTTCCC 61.432 66.667 3.32 0.00 0.00 3.97
1067 2558 2.034221 GCGTGGCCTTTCTTCCCT 59.966 61.111 3.32 0.00 0.00 4.20
1068 2559 2.041115 GCGTGGCCTTTCTTCCCTC 61.041 63.158 3.32 0.00 0.00 4.30
1069 2560 1.374947 CGTGGCCTTTCTTCCCTCA 59.625 57.895 3.32 0.00 0.00 3.86
1070 2561 0.955919 CGTGGCCTTTCTTCCCTCAC 60.956 60.000 3.32 0.00 0.00 3.51
1071 2562 0.609406 GTGGCCTTTCTTCCCTCACC 60.609 60.000 3.32 0.00 0.00 4.02
1098 2592 2.711922 CGCAGCCCTAGTTCGTCCT 61.712 63.158 0.00 0.00 0.00 3.85
1124 2618 0.824759 ACCTCCACTCCATCGCTAAC 59.175 55.000 0.00 0.00 0.00 2.34
1125 2619 0.105039 CCTCCACTCCATCGCTAACC 59.895 60.000 0.00 0.00 0.00 2.85
1126 2620 1.115467 CTCCACTCCATCGCTAACCT 58.885 55.000 0.00 0.00 0.00 3.50
1127 2621 1.067821 CTCCACTCCATCGCTAACCTC 59.932 57.143 0.00 0.00 0.00 3.85
1128 2622 0.105039 CCACTCCATCGCTAACCTCC 59.895 60.000 0.00 0.00 0.00 4.30
1129 2623 0.105039 CACTCCATCGCTAACCTCCC 59.895 60.000 0.00 0.00 0.00 4.30
1698 3192 0.326618 CCCCCACTCCCTGATACTGT 60.327 60.000 0.00 0.00 0.00 3.55
1702 3196 3.576861 CCCACTCCCTGATACTGTATCA 58.423 50.000 24.61 24.61 42.56 2.15
1715 3209 4.819105 ACTGTATCATTGGGAGTCGAAA 57.181 40.909 0.00 0.00 0.00 3.46
1717 3211 3.869065 TGTATCATTGGGAGTCGAAACC 58.131 45.455 0.00 0.00 0.00 3.27
1719 3213 0.326927 TCATTGGGAGTCGAAACCCC 59.673 55.000 20.77 15.74 45.01 4.95
1720 3214 0.037590 CATTGGGAGTCGAAACCCCA 59.962 55.000 20.77 17.79 45.01 4.96
1721 3215 0.328258 ATTGGGAGTCGAAACCCCAG 59.672 55.000 20.77 0.00 42.94 4.45
1722 3216 1.057851 TTGGGAGTCGAAACCCCAGT 61.058 55.000 20.77 0.00 42.94 4.00
1723 3217 1.057851 TGGGAGTCGAAACCCCAGTT 61.058 55.000 20.77 0.00 45.01 3.16
1724 3218 0.978907 GGGAGTCGAAACCCCAGTTA 59.021 55.000 14.97 0.00 40.19 2.24
1725 3219 1.558294 GGGAGTCGAAACCCCAGTTAT 59.442 52.381 14.97 0.00 40.19 1.89
1727 3221 2.419713 GGAGTCGAAACCCCAGTTATCC 60.420 54.545 0.00 0.00 34.19 2.59
1806 3473 3.308866 CGAGGTTTCTGTTTGTCTTCGTT 59.691 43.478 0.00 0.00 0.00 3.85
1809 3476 4.457949 AGGTTTCTGTTTGTCTTCGTTTGT 59.542 37.500 0.00 0.00 0.00 2.83
1862 3529 0.953003 GGGGACCGATCGAGTTAGAG 59.047 60.000 18.66 0.00 40.86 2.43
1869 3536 4.664392 ACCGATCGAGTTAGAGGGAATAT 58.336 43.478 18.66 0.00 0.00 1.28
1870 3537 4.459685 ACCGATCGAGTTAGAGGGAATATG 59.540 45.833 18.66 0.00 0.00 1.78
1871 3538 4.459685 CCGATCGAGTTAGAGGGAATATGT 59.540 45.833 18.66 0.00 0.00 2.29
1876 3543 6.942976 TCGAGTTAGAGGGAATATGTTTGTT 58.057 36.000 0.00 0.00 0.00 2.83
1878 3545 6.816640 CGAGTTAGAGGGAATATGTTTGTTCA 59.183 38.462 0.00 0.00 0.00 3.18
1879 3546 7.010552 CGAGTTAGAGGGAATATGTTTGTTCAG 59.989 40.741 0.00 0.00 0.00 3.02
1885 3552 7.175641 AGAGGGAATATGTTTGTTCAGTTTCTG 59.824 37.037 0.00 0.00 0.00 3.02
1886 3553 6.777580 AGGGAATATGTTTGTTCAGTTTCTGT 59.222 34.615 0.00 0.00 32.61 3.41
1887 3554 7.942341 AGGGAATATGTTTGTTCAGTTTCTGTA 59.058 33.333 0.00 0.00 32.61 2.74
1888 3555 8.573035 GGGAATATGTTTGTTCAGTTTCTGTAA 58.427 33.333 0.00 0.00 32.61 2.41
1889 3556 9.394477 GGAATATGTTTGTTCAGTTTCTGTAAC 57.606 33.333 0.00 0.00 36.99 2.50
1890 3557 9.394477 GAATATGTTTGTTCAGTTTCTGTAACC 57.606 33.333 0.00 0.00 37.46 2.85
1891 3558 5.570234 TGTTTGTTCAGTTTCTGTAACCC 57.430 39.130 0.00 0.00 37.46 4.11
1892 3559 5.258051 TGTTTGTTCAGTTTCTGTAACCCT 58.742 37.500 0.00 0.00 37.46 4.34
1893 3560 6.416415 TGTTTGTTCAGTTTCTGTAACCCTA 58.584 36.000 0.00 0.00 37.46 3.53
1894 3561 6.540914 TGTTTGTTCAGTTTCTGTAACCCTAG 59.459 38.462 0.00 0.00 37.46 3.02
1978 3675 3.003689 ACTCTGTAGTGTGCATTTTGTGC 59.996 43.478 0.00 0.00 43.94 4.57
2116 3814 1.071299 TGCGTGAGTGCCATTCTGT 59.929 52.632 0.00 0.00 0.00 3.41
2126 3824 5.412594 TGAGTGCCATTCTGTTTAGCTTAAG 59.587 40.000 0.00 0.00 0.00 1.85
2128 3826 6.183347 AGTGCCATTCTGTTTAGCTTAAGAT 58.817 36.000 6.67 1.53 0.00 2.40
2129 3827 6.317391 AGTGCCATTCTGTTTAGCTTAAGATC 59.683 38.462 6.67 0.00 0.00 2.75
2281 4168 7.845066 AAGTAACGAGAATATCCAGTTTTCC 57.155 36.000 0.00 0.00 0.00 3.13
2380 4267 5.378292 AGTACTCACTGTATGACTGTGTG 57.622 43.478 13.97 13.80 44.89 3.82
2601 4488 6.059484 CACTGGTAGTTTGTTCCTTCCTTAA 58.941 40.000 0.00 0.00 0.00 1.85
3169 5056 8.604640 ATGTCAATTTTGTTCATGCATTACAA 57.395 26.923 16.37 16.37 0.00 2.41
3313 5212 0.468226 TGTTACCCGGATCAGGATGC 59.532 55.000 14.13 1.60 34.76 3.91
3350 5249 2.032681 GTGGGTGCAGGTCTGGTC 59.967 66.667 0.00 0.00 0.00 4.02
3638 5537 7.397221 TCTCTGATAAGATGCCTTCAAAGAAA 58.603 34.615 0.00 0.00 33.94 2.52
3760 5659 3.312697 GTGAAAGTTCGCTCTGTTCCTTT 59.687 43.478 0.00 0.00 34.94 3.11
3903 5802 1.013596 TGTCAGTGTCGCCTTTTGTG 58.986 50.000 0.00 0.00 0.00 3.33
3956 5855 1.285641 GTTTGCCCGTGGACATGTG 59.714 57.895 1.15 0.00 0.00 3.21
4027 5926 9.621629 TCCAACTCCAACGTATCATAATTTAAT 57.378 29.630 0.00 0.00 0.00 1.40
4149 6048 3.009723 ACCAGACAATATGCCAAAGACG 58.990 45.455 0.00 0.00 0.00 4.18
4212 6111 1.260544 AAAGCAGTCCCTTGAATGGC 58.739 50.000 0.00 0.00 37.08 4.40
4387 6292 7.066781 AGTAAAGGGGTCTCAAATTTCTCAAA 58.933 34.615 0.00 0.00 0.00 2.69
4661 6566 7.020010 GTGAGTGATCTTTTCTTTGCTGTATG 58.980 38.462 0.00 0.00 0.00 2.39
4679 6584 6.590292 GCTGTATGGTCGCTTGTATATATGTT 59.410 38.462 0.00 0.00 0.00 2.71
4680 6585 7.411912 GCTGTATGGTCGCTTGTATATATGTTG 60.412 40.741 0.00 0.00 0.00 3.33
4681 6586 7.438564 TGTATGGTCGCTTGTATATATGTTGT 58.561 34.615 0.00 0.00 0.00 3.32
5156 7071 6.098552 TGTTTGGCATTGATGTGGATTATGAT 59.901 34.615 0.00 0.00 0.00 2.45
5221 7136 2.884639 GCTAAACCAACTCTTTCCTGCA 59.115 45.455 0.00 0.00 0.00 4.41
5222 7137 3.507622 GCTAAACCAACTCTTTCCTGCAT 59.492 43.478 0.00 0.00 0.00 3.96
5237 7152 8.055181 TCTTTCCTGCATCCATTACTATTTTCT 58.945 33.333 0.00 0.00 0.00 2.52
5238 7153 9.342308 CTTTCCTGCATCCATTACTATTTTCTA 57.658 33.333 0.00 0.00 0.00 2.10
5543 7466 1.968493 TCCACCCTGTTCAGTACTCAC 59.032 52.381 0.00 0.00 0.00 3.51
5844 7767 9.034544 GGAAAAGCATATGTTGTATTCAATTCC 57.965 33.333 4.29 2.52 35.92 3.01
5999 7922 9.515020 CATGTAATAAATTTCATACCAAGCGTT 57.485 29.630 0.00 0.00 0.00 4.84
6131 8054 6.365839 CGATGAGCACCAATATATGTGTTTC 58.634 40.000 5.40 4.82 34.94 2.78
6154 8077 7.817418 TCACTAGTTCTTTAGTTGGCAAATT 57.183 32.000 5.17 0.00 31.64 1.82
6157 8080 8.784043 CACTAGTTCTTTAGTTGGCAAATTAGT 58.216 33.333 5.17 2.85 31.64 2.24
6196 8119 3.316283 CAACGTTGCAATTGCTGGTTAT 58.684 40.909 29.37 10.17 42.66 1.89
6435 8370 0.318762 ACAACGAGAAGAGCAGGTCC 59.681 55.000 0.00 0.00 0.00 4.46
6436 8371 0.605589 CAACGAGAAGAGCAGGTCCT 59.394 55.000 0.00 0.00 0.00 3.85
6499 8434 9.961265 CTTTTCTGTACATGATATCAATGCAAT 57.039 29.630 9.99 0.00 0.00 3.56
6525 8460 4.655963 TGTTATTTCTGCAGAAGAAGGCT 58.344 39.130 27.02 12.44 45.64 4.58
6531 8466 0.601046 TGCAGAAGAAGGCTGTGTCG 60.601 55.000 0.00 0.00 35.81 4.35
6555 8490 4.037923 ACATCACATTGTTCTCAACCCAAC 59.962 41.667 0.00 0.00 36.33 3.77
6752 8687 1.270358 GGTGAGAGGAAGTCGTTTGCT 60.270 52.381 0.00 0.00 40.54 3.91
6762 8698 2.622436 AGTCGTTTGCTCTAAGATGGC 58.378 47.619 0.00 0.00 0.00 4.40
6764 8700 0.026803 CGTTTGCTCTAAGATGGCGC 59.973 55.000 0.00 0.00 0.00 6.53
6792 8728 2.966050 AGCTTCTTTGGAGTCGCTTAG 58.034 47.619 0.00 0.00 0.00 2.18
6890 8831 5.132897 AGCAACACTTCAAGTTTTTGTCA 57.867 34.783 9.48 0.00 35.73 3.58
6894 8835 5.059404 ACACTTCAAGTTTTTGTCACTGG 57.941 39.130 0.00 0.00 35.73 4.00
6895 8836 3.859386 CACTTCAAGTTTTTGTCACTGGC 59.141 43.478 0.00 0.00 35.73 4.85
6896 8837 3.509575 ACTTCAAGTTTTTGTCACTGGCA 59.490 39.130 0.00 0.00 35.73 4.92
6897 8838 4.021544 ACTTCAAGTTTTTGTCACTGGCAA 60.022 37.500 0.00 0.00 35.73 4.52
6898 8839 3.843999 TCAAGTTTTTGTCACTGGCAAC 58.156 40.909 0.00 0.00 35.73 4.17
6899 8840 2.929398 CAAGTTTTTGTCACTGGCAACC 59.071 45.455 0.00 0.00 0.00 3.77
6900 8841 2.456577 AGTTTTTGTCACTGGCAACCT 58.543 42.857 0.00 0.00 0.00 3.50
6946 8888 3.942829 TGGCTTCGACTGATTGAATTCT 58.057 40.909 7.05 0.00 0.00 2.40
6951 8893 3.525537 TCGACTGATTGAATTCTGAGGC 58.474 45.455 7.05 0.00 0.00 4.70
6994 8936 5.883115 GGATGTTCTTTCTTTAAGGAGGGAG 59.117 44.000 0.00 0.00 34.46 4.30
7021 8963 2.871796 AGGGGTGGGAATTATGAGGAA 58.128 47.619 0.00 0.00 0.00 3.36
7065 9007 5.940470 AGTAGTGGGAAATTTCTCATGACAC 59.060 40.000 23.16 16.85 40.32 3.67
7193 9135 1.208642 GCTGCTGCGTGTTTTTGGAC 61.209 55.000 0.00 0.00 0.00 4.02
7237 9179 7.974501 AGTATGTAGTATGTTCCGAAAGTTCAG 59.025 37.037 0.00 0.00 0.00 3.02
7408 9377 2.264794 GGAATCACTCCGCCACGT 59.735 61.111 0.00 0.00 33.37 4.49
7438 9407 3.587923 GGCATGCAGTTCAATTTTAGCA 58.412 40.909 21.36 0.00 36.34 3.49
7444 9413 3.857010 GCAGTTCAATTTTAGCAAGCGGT 60.857 43.478 0.00 0.00 0.00 5.68
7497 9466 1.207791 GAAGGAGCAGAGGATTCCCA 58.792 55.000 0.00 0.00 33.88 4.37
7528 9499 1.252215 TATGACGCACCCTCGGTTGA 61.252 55.000 0.00 0.00 31.02 3.18
7549 9520 1.128692 GTTGGACGTGTGCTAATCTGC 59.871 52.381 0.00 0.00 0.00 4.26
7575 9546 3.940852 TGTGACTATGCTGTAATGGCAAG 59.059 43.478 0.00 0.00 43.14 4.01
7603 9574 2.346803 CGGACGGACTCATCAAATGTT 58.653 47.619 0.00 0.00 0.00 2.71
7635 9606 0.842467 CTTCCCCAACAGGACCCTCT 60.842 60.000 0.00 0.00 38.24 3.69
7639 9610 1.554822 CCCCAACAGGACCCTCTAAGA 60.555 57.143 0.00 0.00 38.24 2.10
7642 9613 2.257207 CAACAGGACCCTCTAAGACCA 58.743 52.381 0.00 0.00 0.00 4.02
7689 9671 2.555227 GGTCTCAGGAGCCCAAATTTCA 60.555 50.000 0.00 0.00 34.23 2.69
7691 9673 2.376518 TCTCAGGAGCCCAAATTTCACT 59.623 45.455 0.00 0.00 0.00 3.41
7705 9687 0.766131 TTCACTGGTTAGGGCCGAAA 59.234 50.000 0.00 0.00 0.00 3.46
7714 9697 0.825410 TAGGGCCGAAATTAGCGTCA 59.175 50.000 0.00 0.00 0.00 4.35
8012 10020 4.980805 GGACGCACTCACCCGCAA 62.981 66.667 0.00 0.00 0.00 4.85
8026 10043 2.659610 GCAACCTCTCTCACCGCT 59.340 61.111 0.00 0.00 0.00 5.52
8030 10047 0.827925 AACCTCTCTCACCGCTGACA 60.828 55.000 0.00 0.00 0.00 3.58
8040 10057 2.671070 CGCTGACACCCCCATCTT 59.329 61.111 0.00 0.00 0.00 2.40
8082 10121 2.123251 ATCCGCCGATGGGAGAGT 60.123 61.111 0.00 0.00 36.91 3.24
8088 10127 1.743772 CGCCGATGGGAGAGTGATTTT 60.744 52.381 0.00 0.00 34.61 1.82
8097 10136 2.223971 GGAGAGTGATTTTCCGGCGATA 60.224 50.000 9.30 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.004277 CCTGCTACCAAACAAGGCCTA 59.996 52.381 5.16 0.00 0.00 3.93
138 139 0.993509 TATTCCCTCCCCCTTGCCAG 60.994 60.000 0.00 0.00 0.00 4.85
190 191 2.964464 TGTAAGGAGACGTGGGTTTGTA 59.036 45.455 0.00 0.00 0.00 2.41
199 200 3.583054 TCCCGATGTAAGGAGACGT 57.417 52.632 0.00 0.00 0.00 4.34
285 610 0.779997 AAGGAGGATGTTGTTGGCCT 59.220 50.000 3.32 0.00 0.00 5.19
298 623 2.674220 GCCTGGGAGGTGAAGGAGG 61.674 68.421 0.00 0.00 37.80 4.30
299 624 2.674220 GGCCTGGGAGGTGAAGGAG 61.674 68.421 0.00 0.00 37.80 3.69
304 629 4.631740 TGACGGCCTGGGAGGTGA 62.632 66.667 0.00 0.00 37.80 4.02
312 637 1.635663 GACGACCATTTGACGGCCTG 61.636 60.000 0.00 0.00 0.00 4.85
320 645 1.079127 AGGAGCCGACGACCATTTG 60.079 57.895 0.00 0.00 0.00 2.32
397 722 2.102252 GGAGACTTCGCTGGAGATTCAT 59.898 50.000 0.00 0.00 0.00 2.57
566 891 1.202734 TGCAATCCATCTAGGCTGCTC 60.203 52.381 0.00 0.00 42.92 4.26
574 899 6.240894 AGTTTGTCTCTTTGCAATCCATCTA 58.759 36.000 0.00 0.00 0.00 1.98
649 974 9.927081 ATATTCACTTCACTATTTGGGAGAAAT 57.073 29.630 0.00 0.00 0.00 2.17
721 1049 7.092174 TGCTAAGGGAGATAATTCCAGGTAAAA 60.092 37.037 0.00 0.00 39.09 1.52
722 1050 6.388689 TGCTAAGGGAGATAATTCCAGGTAAA 59.611 38.462 0.00 0.00 39.09 2.01
723 1051 5.908831 TGCTAAGGGAGATAATTCCAGGTAA 59.091 40.000 0.00 0.00 39.09 2.85
724 1052 5.473273 TGCTAAGGGAGATAATTCCAGGTA 58.527 41.667 0.00 0.00 39.09 3.08
725 1053 4.307259 TGCTAAGGGAGATAATTCCAGGT 58.693 43.478 0.00 0.00 39.09 4.00
726 1054 4.982241 TGCTAAGGGAGATAATTCCAGG 57.018 45.455 0.00 0.00 39.09 4.45
727 1055 5.066593 GGTTGCTAAGGGAGATAATTCCAG 58.933 45.833 0.00 0.00 39.09 3.86
728 1056 4.476846 TGGTTGCTAAGGGAGATAATTCCA 59.523 41.667 0.00 0.00 39.09 3.53
729 1057 5.048846 TGGTTGCTAAGGGAGATAATTCC 57.951 43.478 0.00 0.00 36.46 3.01
730 1058 6.377146 TGTTTGGTTGCTAAGGGAGATAATTC 59.623 38.462 0.00 0.00 0.00 2.17
731 1059 6.252995 TGTTTGGTTGCTAAGGGAGATAATT 58.747 36.000 0.00 0.00 0.00 1.40
732 1060 5.826643 TGTTTGGTTGCTAAGGGAGATAAT 58.173 37.500 0.00 0.00 0.00 1.28
733 1061 5.249780 TGTTTGGTTGCTAAGGGAGATAA 57.750 39.130 0.00 0.00 0.00 1.75
734 1062 4.919774 TGTTTGGTTGCTAAGGGAGATA 57.080 40.909 0.00 0.00 0.00 1.98
735 1063 3.806949 TGTTTGGTTGCTAAGGGAGAT 57.193 42.857 0.00 0.00 0.00 2.75
736 1064 3.486383 CTTGTTTGGTTGCTAAGGGAGA 58.514 45.455 0.00 0.00 0.00 3.71
737 1065 2.558359 CCTTGTTTGGTTGCTAAGGGAG 59.442 50.000 0.00 0.00 35.41 4.30
738 1066 2.593026 CCTTGTTTGGTTGCTAAGGGA 58.407 47.619 0.00 0.00 35.41 4.20
739 1067 1.000843 GCCTTGTTTGGTTGCTAAGGG 59.999 52.381 0.00 0.00 38.61 3.95
740 1068 1.000843 GGCCTTGTTTGGTTGCTAAGG 59.999 52.381 0.00 0.00 40.61 2.69
741 1069 1.963515 AGGCCTTGTTTGGTTGCTAAG 59.036 47.619 0.00 0.00 0.00 2.18
742 1070 2.080654 AGGCCTTGTTTGGTTGCTAA 57.919 45.000 0.00 0.00 0.00 3.09
743 1071 2.080654 AAGGCCTTGTTTGGTTGCTA 57.919 45.000 19.73 0.00 0.00 3.49
744 1072 1.963515 CTAAGGCCTTGTTTGGTTGCT 59.036 47.619 28.77 0.00 0.00 3.91
745 1073 1.960689 TCTAAGGCCTTGTTTGGTTGC 59.039 47.619 28.77 0.00 0.00 4.17
746 1074 3.222603 ACTCTAAGGCCTTGTTTGGTTG 58.777 45.455 28.77 11.05 0.00 3.77
747 1075 3.595190 ACTCTAAGGCCTTGTTTGGTT 57.405 42.857 28.77 0.57 0.00 3.67
748 1076 3.222603 CAACTCTAAGGCCTTGTTTGGT 58.777 45.455 28.77 15.39 0.00 3.67
749 1077 2.029918 GCAACTCTAAGGCCTTGTTTGG 60.030 50.000 28.77 13.00 0.00 3.28
750 1078 2.887152 AGCAACTCTAAGGCCTTGTTTG 59.113 45.455 28.77 22.53 0.00 2.93
751 1079 3.149981 GAGCAACTCTAAGGCCTTGTTT 58.850 45.455 28.77 12.05 0.00 2.83
752 1080 2.373502 AGAGCAACTCTAAGGCCTTGTT 59.626 45.455 28.77 19.90 39.28 2.83
753 1081 1.981495 AGAGCAACTCTAAGGCCTTGT 59.019 47.619 28.77 14.77 39.28 3.16
754 1082 2.777832 AGAGCAACTCTAAGGCCTTG 57.222 50.000 28.77 17.30 39.28 3.61
755 1083 4.226168 ACATAAGAGCAACTCTAAGGCCTT 59.774 41.667 24.18 24.18 40.28 4.35
756 1084 3.777522 ACATAAGAGCAACTCTAAGGCCT 59.222 43.478 0.00 0.00 40.28 5.19
757 1085 4.143986 ACATAAGAGCAACTCTAAGGCC 57.856 45.455 0.00 0.00 40.28 5.19
758 1086 6.502136 AAAACATAAGAGCAACTCTAAGGC 57.498 37.500 0.00 0.00 40.28 4.35
789 1117 4.965200 AGAACAACTCTAGCAGACCTTT 57.035 40.909 0.00 0.00 30.22 3.11
803 1131 9.134734 TCACTCAAAACAAAACATAAGAACAAC 57.865 29.630 0.00 0.00 0.00 3.32
807 1135 7.978975 CCCTTCACTCAAAACAAAACATAAGAA 59.021 33.333 0.00 0.00 0.00 2.52
901 2372 5.726397 TCCGATTCCTCGTATTCTCAAAAA 58.274 37.500 0.00 0.00 43.49 1.94
913 2404 0.315568 GACCCATCTCCGATTCCTCG 59.684 60.000 0.00 0.00 44.62 4.63
965 2456 0.593618 TGCGCCGCAGAAAAACAATA 59.406 45.000 8.16 0.00 33.32 1.90
991 2482 3.281332 AGAGGGCTCTGTCTCTCAC 57.719 57.895 0.00 0.00 38.75 3.51
994 2485 1.309688 GGGAGAGGGCTCTGTCTCT 59.690 63.158 11.05 2.59 42.44 3.10
995 2486 2.124693 CGGGAGAGGGCTCTGTCTC 61.125 68.421 11.05 5.46 40.61 3.36
997 2488 2.363147 ACGGGAGAGGGCTCTGTC 60.363 66.667 1.05 1.05 40.61 3.51
1001 2492 2.835895 GGAGACGGGAGAGGGCTC 60.836 72.222 0.00 0.00 40.54 4.70
1002 2493 3.670629 CTGGAGACGGGAGAGGGCT 62.671 68.421 0.00 0.00 0.00 5.19
1003 2494 3.151022 CTGGAGACGGGAGAGGGC 61.151 72.222 0.00 0.00 0.00 5.19
1004 2495 3.151022 GCTGGAGACGGGAGAGGG 61.151 72.222 0.00 0.00 37.13 4.30
1005 2496 3.151022 GGCTGGAGACGGGAGAGG 61.151 72.222 0.00 0.00 37.13 3.69
1006 2497 1.954362 CTTGGCTGGAGACGGGAGAG 61.954 65.000 0.00 0.00 37.13 3.20
1007 2498 1.984570 CTTGGCTGGAGACGGGAGA 60.985 63.158 0.00 0.00 37.13 3.71
1008 2499 2.581354 CTTGGCTGGAGACGGGAG 59.419 66.667 0.00 0.00 37.13 4.30
1009 2500 3.706373 GCTTGGCTGGAGACGGGA 61.706 66.667 0.00 0.00 37.13 5.14
1010 2501 3.551496 TTGCTTGGCTGGAGACGGG 62.551 63.158 0.00 0.00 37.13 5.28
1011 2502 1.580845 CTTTGCTTGGCTGGAGACGG 61.581 60.000 0.00 0.00 40.79 4.79
1012 2503 1.871772 CTTTGCTTGGCTGGAGACG 59.128 57.895 0.00 0.00 0.00 4.18
1013 2504 1.583477 GCTTTGCTTGGCTGGAGAC 59.417 57.895 0.00 0.00 0.00 3.36
1014 2505 1.604593 GGCTTTGCTTGGCTGGAGA 60.605 57.895 0.00 0.00 0.00 3.71
1015 2506 2.643232 GGGCTTTGCTTGGCTGGAG 61.643 63.158 0.00 0.00 0.00 3.86
1016 2507 2.601367 GGGCTTTGCTTGGCTGGA 60.601 61.111 0.00 0.00 0.00 3.86
1017 2508 2.602568 AGGGCTTTGCTTGGCTGG 60.603 61.111 0.00 0.00 0.00 4.85
1018 2509 1.593296 GAGAGGGCTTTGCTTGGCTG 61.593 60.000 0.00 0.00 0.00 4.85
1019 2510 1.303970 GAGAGGGCTTTGCTTGGCT 60.304 57.895 0.00 0.00 0.00 4.75
1020 2511 2.694760 CGAGAGGGCTTTGCTTGGC 61.695 63.158 0.00 0.00 0.00 4.52
1021 2512 2.694760 GCGAGAGGGCTTTGCTTGG 61.695 63.158 0.00 0.00 0.00 3.61
1022 2513 2.873288 GCGAGAGGGCTTTGCTTG 59.127 61.111 0.00 0.00 0.00 4.01
1023 2514 2.743928 CGCGAGAGGGCTTTGCTT 60.744 61.111 0.00 0.00 37.19 3.91
1083 2574 2.416432 GCGAGGACGAACTAGGGCT 61.416 63.158 0.00 0.00 42.66 5.19
1098 2592 3.371063 GGAGTGGAGGTGTCGCGA 61.371 66.667 3.71 3.71 0.00 5.87
1199 2693 1.221909 TGAGGTCCTAGGAGAGGCCA 61.222 60.000 13.15 3.49 46.25 5.36
1675 3169 2.561378 TATCAGGGAGTGGGGGTGGG 62.561 65.000 0.00 0.00 0.00 4.61
1676 3170 1.004230 TATCAGGGAGTGGGGGTGG 59.996 63.158 0.00 0.00 0.00 4.61
1677 3171 0.326618 AGTATCAGGGAGTGGGGGTG 60.327 60.000 0.00 0.00 0.00 4.61
1678 3172 0.326618 CAGTATCAGGGAGTGGGGGT 60.327 60.000 0.00 0.00 0.00 4.95
1681 3175 3.576861 TGATACAGTATCAGGGAGTGGG 58.423 50.000 17.93 0.00 40.09 4.61
1698 3192 2.171870 GGGGTTTCGACTCCCAATGATA 59.828 50.000 21.10 0.00 45.06 2.15
1702 3196 2.470311 TGGGGTTTCGACTCCCAAT 58.530 52.632 21.10 0.00 46.73 3.16
1715 3209 1.691689 GACGGGGGATAACTGGGGT 60.692 63.158 0.00 0.00 0.00 4.95
1717 3211 2.024590 GACGACGGGGGATAACTGGG 62.025 65.000 0.00 0.00 0.00 4.45
1719 3213 1.440476 GGACGACGGGGGATAACTG 59.560 63.158 0.00 0.00 0.00 3.16
1720 3214 2.123428 CGGACGACGGGGGATAACT 61.123 63.158 0.00 0.00 39.42 2.24
1721 3215 2.120909 TCGGACGACGGGGGATAAC 61.121 63.158 0.00 0.00 44.45 1.89
1722 3216 2.120909 GTCGGACGACGGGGGATAA 61.121 63.158 9.23 0.00 44.45 1.75
1723 3217 2.516930 GTCGGACGACGGGGGATA 60.517 66.667 9.23 0.00 44.45 2.59
1781 3447 2.484889 AGACAAACAGAAACCTCGAGC 58.515 47.619 6.99 0.00 0.00 5.03
1806 3473 6.059484 CCTAGGGTTACAGAAACTGAAACAA 58.941 40.000 0.00 0.00 38.23 2.83
1809 3476 5.899631 ACCTAGGGTTACAGAAACTGAAA 57.100 39.130 14.81 0.00 38.23 2.69
1862 3529 6.981722 ACAGAAACTGAACAAACATATTCCC 58.018 36.000 5.76 0.00 35.18 3.97
1869 3536 5.258051 AGGGTTACAGAAACTGAACAAACA 58.742 37.500 5.76 0.00 38.23 2.83
1870 3537 5.830000 AGGGTTACAGAAACTGAACAAAC 57.170 39.130 5.76 4.75 38.23 2.93
1871 3538 6.059484 CCTAGGGTTACAGAAACTGAACAAA 58.941 40.000 0.00 0.00 38.23 2.83
1876 3543 4.903049 TGAACCTAGGGTTACAGAAACTGA 59.097 41.667 14.81 0.00 46.95 3.41
1878 3545 5.546499 TCATGAACCTAGGGTTACAGAAACT 59.454 40.000 14.81 0.00 46.95 2.66
1879 3546 5.801380 TCATGAACCTAGGGTTACAGAAAC 58.199 41.667 14.81 0.00 46.95 2.78
1885 3552 6.127451 CCCAAAATTCATGAACCTAGGGTTAC 60.127 42.308 21.30 0.00 46.95 2.50
1886 3553 5.955355 CCCAAAATTCATGAACCTAGGGTTA 59.045 40.000 21.30 2.94 46.95 2.85
1888 3555 4.352893 CCCAAAATTCATGAACCTAGGGT 58.647 43.478 21.30 6.29 37.65 4.34
1889 3556 3.706086 CCCCAAAATTCATGAACCTAGGG 59.294 47.826 22.10 22.10 0.00 3.53
1890 3557 3.706086 CCCCCAAAATTCATGAACCTAGG 59.294 47.826 11.07 7.41 0.00 3.02
1891 3558 4.352893 ACCCCCAAAATTCATGAACCTAG 58.647 43.478 11.07 1.66 0.00 3.02
1892 3559 4.412060 ACCCCCAAAATTCATGAACCTA 57.588 40.909 11.07 0.00 0.00 3.08
1893 3560 3.274281 ACCCCCAAAATTCATGAACCT 57.726 42.857 11.07 0.00 0.00 3.50
1894 3561 3.072330 ACAACCCCCAAAATTCATGAACC 59.928 43.478 11.07 0.00 0.00 3.62
1978 3675 8.938906 CAAATACCAAAAGAATCATTCCCAAAG 58.061 33.333 0.00 0.00 0.00 2.77
2281 4168 2.867109 TTGCTCTCTTCTTTCCCCAG 57.133 50.000 0.00 0.00 0.00 4.45
3184 5071 8.714179 GTGTGTGTATAATGTACTGCTTAAACA 58.286 33.333 0.00 0.00 0.00 2.83
3230 5129 5.191722 TGCATCAGAAGGAGGGTAGTTAAAT 59.808 40.000 0.00 0.00 0.00 1.40
3313 5212 0.661552 CTTCTGATCCATGCCTTGCG 59.338 55.000 0.00 0.00 0.00 4.85
3350 5249 3.508840 GATTGCGGAAGGGGTGCG 61.509 66.667 0.00 0.00 45.20 5.34
3659 5558 6.876789 TCTTTGAAGGCATATTCTTCGTTGTA 59.123 34.615 9.65 0.00 42.43 2.41
3760 5659 1.169661 CCTTGTTGGTAGTTGCGCCA 61.170 55.000 4.18 0.00 0.00 5.69
3903 5802 5.413523 TGCTCGGGGTAAAGAATAAAAGAAC 59.586 40.000 0.00 0.00 0.00 3.01
3956 5855 1.400846 CACTGAGCATGCATCCAGTTC 59.599 52.381 26.86 13.75 37.74 3.01
4135 6034 2.819608 AGTGTTGCGTCTTTGGCATATT 59.180 40.909 0.00 0.00 40.62 1.28
4149 6048 1.550976 AGTAGAGTAGGCCAGTGTTGC 59.449 52.381 5.01 0.00 0.00 4.17
4212 6111 0.673333 TAGTGCATGGTGGCAGTTCG 60.673 55.000 0.38 0.00 44.78 3.95
4325 6230 5.751243 AAACGATTATATGTGCCCAAGAC 57.249 39.130 0.00 0.00 0.00 3.01
4661 6566 6.598753 ACAACAACATATATACAAGCGACC 57.401 37.500 0.00 0.00 0.00 4.79
4679 6584 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
4680 6585 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
4681 6586 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
4902 6816 3.921119 TGTGCTAGTTTTTCATGCCAG 57.079 42.857 0.00 0.00 0.00 4.85
5156 7071 3.149196 GTCAGTTGGAAAAGCTGGATCA 58.851 45.455 0.00 0.00 0.00 2.92
5237 7152 9.098355 GTGACTTGTTTATGATAATCTGCTGTA 57.902 33.333 0.00 0.00 0.00 2.74
5238 7153 7.066284 GGTGACTTGTTTATGATAATCTGCTGT 59.934 37.037 0.00 0.00 0.00 4.40
5543 7466 5.462405 AGACTAAACAAAGCACGAGTAGAG 58.538 41.667 0.00 0.00 0.00 2.43
5637 7560 1.470098 AGTTCCTGCAAACATGATCGC 59.530 47.619 0.00 0.00 0.00 4.58
5999 7922 6.935741 ACTGAAACATAACAAACAGTAGCA 57.064 33.333 0.00 0.00 36.94 3.49
6131 8054 8.784043 ACTAATTTGCCAACTAAAGAACTAGTG 58.216 33.333 0.00 0.00 32.35 2.74
6154 8077 2.940971 GCACATGCACAATCCCTGACTA 60.941 50.000 0.00 0.00 41.59 2.59
6157 8080 2.570365 GCACATGCACAATCCCTGA 58.430 52.632 0.00 0.00 41.59 3.86
6179 8102 5.059404 ACTGTATAACCAGCAATTGCAAC 57.941 39.130 30.89 16.30 45.16 4.17
6196 8119 4.062293 GTGGCAGTCACATACAAACTGTA 58.938 43.478 0.00 0.00 45.39 2.74
6435 8370 6.818644 CGGGATTAATTATAGGACACCATCAG 59.181 42.308 0.00 0.00 0.00 2.90
6436 8371 6.271391 ACGGGATTAATTATAGGACACCATCA 59.729 38.462 0.00 0.00 0.00 3.07
6499 8434 6.735694 GCCTTCTTCTGCAGAAATAACAACAA 60.736 38.462 28.16 10.74 41.25 2.83
6512 8447 0.601046 CGACACAGCCTTCTTCTGCA 60.601 55.000 0.00 0.00 35.04 4.41
6531 8466 3.820467 TGGGTTGAGAACAATGTGATGTC 59.180 43.478 0.00 0.00 38.32 3.06
6555 8490 4.978099 AGGCCAGGTCATATTCTATTGTG 58.022 43.478 5.01 0.00 0.00 3.33
6752 8687 3.243434 GCTACTTACTGCGCCATCTTAGA 60.243 47.826 4.18 0.00 0.00 2.10
6753 8688 3.053455 GCTACTTACTGCGCCATCTTAG 58.947 50.000 4.18 0.00 0.00 2.18
6754 8689 2.693591 AGCTACTTACTGCGCCATCTTA 59.306 45.455 4.18 0.00 0.00 2.10
6762 8698 3.585862 TCCAAAGAAGCTACTTACTGCG 58.414 45.455 0.00 0.00 0.00 5.18
6764 8700 4.859798 CGACTCCAAAGAAGCTACTTACTG 59.140 45.833 0.00 0.00 0.00 2.74
6792 8728 1.405391 CGGTTCCCATTCCATTTTGGC 60.405 52.381 0.00 0.00 37.47 4.52
6890 8831 3.696051 CAGCACATATAAAGGTTGCCAGT 59.304 43.478 0.00 0.00 0.00 4.00
6894 8835 4.339247 ACCATCAGCACATATAAAGGTTGC 59.661 41.667 0.00 0.00 0.00 4.17
6895 8836 6.455360 AACCATCAGCACATATAAAGGTTG 57.545 37.500 0.00 0.00 35.67 3.77
6896 8837 8.632679 CATAAACCATCAGCACATATAAAGGTT 58.367 33.333 0.00 0.00 38.38 3.50
6897 8838 7.779798 ACATAAACCATCAGCACATATAAAGGT 59.220 33.333 0.00 0.00 0.00 3.50
6898 8839 8.169977 ACATAAACCATCAGCACATATAAAGG 57.830 34.615 0.00 0.00 0.00 3.11
6900 8841 9.800433 CAAACATAAACCATCAGCACATATAAA 57.200 29.630 0.00 0.00 0.00 1.40
6946 8888 1.476845 TTGCAGTTAGTCCCGCCTCA 61.477 55.000 0.00 0.00 0.00 3.86
6951 8893 1.625616 CTACGTTGCAGTTAGTCCCG 58.374 55.000 0.00 0.00 0.00 5.14
6994 8936 6.353082 CCTCATAATTCCCACCCCTATACATC 60.353 46.154 0.00 0.00 0.00 3.06
7021 8963 5.690464 ACTCTGATTCCTGAAGCTAATGT 57.310 39.130 0.00 0.00 0.00 2.71
7065 9007 3.126171 CACTACTCTGACTCCTGAAGACG 59.874 52.174 0.00 0.00 0.00 4.18
7237 9179 1.406898 GCAGAAAAGATAGCCAAGCCC 59.593 52.381 0.00 0.00 0.00 5.19
7404 9360 2.885644 ATGCCGCTTCGCTACGTG 60.886 61.111 0.00 0.00 0.00 4.49
7405 9361 2.885644 CATGCCGCTTCGCTACGT 60.886 61.111 0.00 0.00 0.00 3.57
7408 9377 2.891936 CTGCATGCCGCTTCGCTA 60.892 61.111 16.68 0.00 43.06 4.26
7413 9382 0.604578 AATTGAACTGCATGCCGCTT 59.395 45.000 16.68 5.96 43.06 4.68
7421 9390 3.307674 CGCTTGCTAAAATTGAACTGCA 58.692 40.909 0.00 0.00 0.00 4.41
7422 9391 2.663119 CCGCTTGCTAAAATTGAACTGC 59.337 45.455 0.00 0.00 0.00 4.40
7438 9407 2.597510 GCACCCCTTTCACCGCTT 60.598 61.111 0.00 0.00 0.00 4.68
7479 9448 1.673767 TTGGGAATCCTCTGCTCCTT 58.326 50.000 0.00 0.00 0.00 3.36
7497 9466 1.156736 GCGTCATACTGGCTGTGTTT 58.843 50.000 7.34 0.00 0.00 2.83
7528 9499 2.688507 CAGATTAGCACACGTCCAACT 58.311 47.619 0.00 0.00 0.00 3.16
7569 9540 4.243008 TCCGCGTTGGACTTGCCA 62.243 61.111 4.92 0.00 43.74 4.92
7603 9574 2.832838 TGGGGAAGTGAAGATGCTCTA 58.167 47.619 0.00 0.00 0.00 2.43
7613 9584 1.423794 GGGTCCTGTTGGGGAAGTGA 61.424 60.000 0.00 0.00 37.10 3.41
7618 9589 0.494551 TTAGAGGGTCCTGTTGGGGA 59.505 55.000 0.00 0.00 35.33 4.81
7670 9652 2.376518 AGTGAAATTTGGGCTCCTGAGA 59.623 45.455 0.00 0.00 0.00 3.27
7672 9654 2.517959 CAGTGAAATTTGGGCTCCTGA 58.482 47.619 0.00 0.00 0.00 3.86
7689 9671 2.682858 GCTAATTTCGGCCCTAACCAGT 60.683 50.000 0.00 0.00 0.00 4.00
7691 9673 1.744456 CGCTAATTTCGGCCCTAACCA 60.744 52.381 0.00 0.00 0.00 3.67
7705 9687 0.101399 CTGAGTCCGCTGACGCTAAT 59.899 55.000 12.72 0.00 46.51 1.73
7714 9697 4.070552 GTTCGGCCTGAGTCCGCT 62.071 66.667 0.00 0.00 46.05 5.52
7809 9792 1.945354 GCGATGGGGAAGACGAGACA 61.945 60.000 0.00 0.00 0.00 3.41
7966 9970 1.410507 GGGAAGGGGCGGCTTTTATAA 60.411 52.381 9.56 0.00 0.00 0.98
8012 10020 1.228583 TGTCAGCGGTGAGAGAGGT 60.229 57.895 19.24 0.00 31.53 3.85
8026 10043 0.984230 GAGACAAGATGGGGGTGTCA 59.016 55.000 5.88 0.00 43.34 3.58
8030 10047 1.364328 AGAGAGAGACAAGATGGGGGT 59.636 52.381 0.00 0.00 0.00 4.95
8082 10121 1.865865 GCTCTATCGCCGGAAAATCA 58.134 50.000 5.05 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.