Multiple sequence alignment - TraesCS5D01G536500

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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 TraesCS5D01G536500 chr5D 100.000 4955 0 0 1 4955 549774672 549769718 0.000000e+00 9151.0
1 TraesCS5D01G536500 chr5D 91.066 347 23 5 3985 4326 549677231 549676888 3.490000e-126 462.0
2 TraesCS5D01G536500 chr5D 89.723 253 25 1 3544 3796 549770115 549769864 6.190000e-84 322.0
3 TraesCS5D01G536500 chr5D 89.723 253 25 1 4558 4809 549771129 549770877 6.190000e-84 322.0
4 TraesCS5D01G536500 chr5D 94.301 193 11 0 3462 3654 549758235 549758043 3.750000e-76 296.0
5 TraesCS5D01G536500 chr5D 91.150 113 10 0 4558 4670 549758153 549758041 2.390000e-33 154.0
6 TraesCS5D01G536500 chr5D 86.869 99 5 5 171 265 549792531 549792437 2.440000e-18 104.0
7 TraesCS5D01G536500 chr5D 95.122 41 1 1 455 494 549792295 549792255 4.140000e-06 63.9
8 TraesCS5D01G536500 chr5D 100.000 28 0 0 4479 4506 156602541 156602514 9.000000e-03 52.8
9 TraesCS5D01G536500 chr5B 89.968 3419 198 82 946 4290 701278412 701275065 0.000000e+00 4279.0
10 TraesCS5D01G536500 chr5B 88.750 400 22 15 34 423 701279252 701278866 7.510000e-128 468.0
11 TraesCS5D01G536500 chr5B 85.132 417 29 9 546 956 701278857 701278468 3.590000e-106 396.0
12 TraesCS5D01G536500 chr5B 88.933 253 27 1 4558 4809 701275809 701275557 1.340000e-80 311.0
13 TraesCS5D01G536500 chr5B 82.369 363 43 12 3971 4318 701273443 701273087 3.750000e-76 296.0
14 TraesCS5D01G536500 chr5B 98.113 53 1 0 4274 4326 701275050 701274998 5.280000e-15 93.5
15 TraesCS5D01G536500 chr5B 100.000 29 0 0 4476 4504 55521107 55521079 2.000000e-03 54.7
16 TraesCS5D01G536500 chr4A 90.639 1816 88 36 2324 4115 621291966 621290209 0.000000e+00 2337.0
17 TraesCS5D01G536500 chr4A 83.102 1515 102 57 857 2310 621293442 621292021 0.000000e+00 1238.0
18 TraesCS5D01G536500 chr4A 94.907 216 8 1 4114 4326 621290127 621289912 7.950000e-88 335.0
19 TraesCS5D01G536500 chr4A 90.119 253 24 1 4558 4809 621290768 621290516 1.330000e-85 327.0
20 TraesCS5D01G536500 chr4A 74.692 569 50 38 269 811 621293943 621293443 3.070000e-37 167.0
21 TraesCS5D01G536500 chr3A 93.333 150 7 3 4807 4955 476238420 476238567 8.350000e-53 219.0
22 TraesCS5D01G536500 chr3D 92.715 151 9 2 4807 4955 603247615 603247765 3.000000e-52 217.0
23 TraesCS5D01G536500 chr3D 75.676 333 59 17 2709 3027 536027821 536028145 4.000000e-31 147.0
24 TraesCS5D01G536500 chr1B 92.053 151 9 3 4807 4955 49089520 49089371 5.030000e-50 209.0
25 TraesCS5D01G536500 chr1B 90.000 150 12 3 4807 4954 49478557 49478409 1.820000e-44 191.0
26 TraesCS5D01G536500 chr1B 82.927 82 8 4 4473 4548 434081676 434081595 8.900000e-08 69.4
27 TraesCS5D01G536500 chr1D 90.667 150 13 1 4807 4955 48024586 48024437 1.090000e-46 198.0
28 TraesCS5D01G536500 chr2A 89.032 155 15 2 4803 4955 691177283 691177437 1.820000e-44 191.0
29 TraesCS5D01G536500 chr1A 92.537 134 9 1 4807 4939 47827259 47827126 1.820000e-44 191.0
30 TraesCS5D01G536500 chr2B 89.404 151 14 2 4805 4955 741470701 741470553 6.550000e-44 189.0
31 TraesCS5D01G536500 chr7D 87.662 154 16 3 4804 4955 576287577 576287729 5.100000e-40 176.0
32 TraesCS5D01G536500 chr6A 82.716 81 8 4 4473 4547 17099799 17099879 3.200000e-07 67.6
33 TraesCS5D01G536500 chr3B 86.538 52 7 0 4479 4530 201884556 201884505 1.930000e-04 58.4


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 TraesCS5D01G536500 chr5D 549769718 549774672 4954 True 9151.000000 9151 100.0000 1 4955 1 chr5D.!!$R3 4954
1 TraesCS5D01G536500 chr5D 549769864 549771129 1265 True 322.000000 322 89.7230 3544 4809 2 chr5D.!!$R5 1265
2 TraesCS5D01G536500 chr5B 701273087 701279252 6165 True 973.916667 4279 88.8775 34 4809 6 chr5B.!!$R2 4775
3 TraesCS5D01G536500 chr4A 621289912 621293943 4031 True 880.800000 2337 86.6918 269 4809 5 chr4A.!!$R1 4540

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
611 658 0.035152 TGTGGTAATCAGGCAGGCAG 60.035 55.0 0.00 0.00 0.00 4.85 F
887 935 0.181114 CTAGCCCCACAGCAAGCATA 59.819 55.0 0.00 0.00 34.23 3.14 F
1344 1478 0.235926 GCTGTTGAGTTTGAGCGTCC 59.764 55.0 0.00 0.00 0.00 4.79 F
1936 2107 0.036875 CAACCGCCCTCTCCTTTTCT 59.963 55.0 0.00 0.00 0.00 2.52 F
2413 2656 0.322456 TACAGGCTTGCATGTGACCC 60.322 55.0 20.83 0.00 0.00 4.46 F
2548 2797 0.379669 CGTCAGGCCTGCATTCATTC 59.620 55.0 28.91 8.96 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1957 0.096454 CGCCGCTTTTGGTTAGTAGC 59.904 55.000 0.00 0.00 0.00 3.58 R
1874 2045 0.106708 AAGCAGACGTCCACACACAT 59.893 50.000 13.01 0.00 0.00 3.21 R
3343 3636 0.306533 CAAACCACAAGTTCCGACCG 59.693 55.000 0.00 0.00 37.88 4.79 R
3369 3662 0.800012 TAAATGTTTCAGTCGGCCGC 59.200 50.000 23.51 16.31 0.00 6.53 R
3418 3711 4.520743 TTAGCGATCAAGATCAAAAGCG 57.479 40.909 10.39 0.00 37.69 4.68 R
4817 6095 2.108952 CCCCCTGATCCTTAATTCCTGG 59.891 54.545 0.00 0.00 0.00 4.45 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
17 18 3.781307 TTCATCGGGCGTGGGAGG 61.781 66.667 0.00 0.00 0.00 4.30
19 20 4.530857 CATCGGGCGTGGGAGGTC 62.531 72.222 0.00 0.00 0.00 3.85
30 31 4.754667 GGAGGTCGCCGGGTGTTC 62.755 72.222 2.18 4.49 0.00 3.18
31 32 3.998672 GAGGTCGCCGGGTGTTCA 61.999 66.667 2.18 0.00 0.00 3.18
32 33 3.310860 GAGGTCGCCGGGTGTTCAT 62.311 63.158 2.18 0.10 0.00 2.57
78 79 3.443037 GAACGAGTGGAGATGATCACAG 58.557 50.000 0.00 0.00 36.43 3.66
86 87 2.676839 GGAGATGATCACAGTTGCACAG 59.323 50.000 0.00 0.00 0.00 3.66
88 89 4.190001 GAGATGATCACAGTTGCACAGAT 58.810 43.478 0.00 0.00 0.00 2.90
89 90 3.939592 AGATGATCACAGTTGCACAGATG 59.060 43.478 0.00 0.00 0.00 2.90
90 91 3.405823 TGATCACAGTTGCACAGATGA 57.594 42.857 0.00 0.00 0.00 2.92
92 93 3.749609 TGATCACAGTTGCACAGATGAAG 59.250 43.478 0.00 0.00 0.00 3.02
93 94 3.198409 TCACAGTTGCACAGATGAAGT 57.802 42.857 0.00 0.00 0.00 3.01
96 97 5.122519 TCACAGTTGCACAGATGAAGTAAA 58.877 37.500 0.00 0.00 0.00 2.01
98 99 4.023707 ACAGTTGCACAGATGAAGTAAAGC 60.024 41.667 0.00 0.00 0.00 3.51
100 101 4.580167 AGTTGCACAGATGAAGTAAAGCAA 59.420 37.500 0.00 0.00 38.28 3.91
101 102 5.067674 AGTTGCACAGATGAAGTAAAGCAAA 59.932 36.000 0.00 0.00 41.64 3.68
102 103 5.112220 TGCACAGATGAAGTAAAGCAAAG 57.888 39.130 0.00 0.00 0.00 2.77
103 104 3.916776 GCACAGATGAAGTAAAGCAAAGC 59.083 43.478 0.00 0.00 0.00 3.51
104 105 4.479619 CACAGATGAAGTAAAGCAAAGCC 58.520 43.478 0.00 0.00 0.00 4.35
152 163 1.691434 GCAGGCTAGCTAGAGGACAAT 59.309 52.381 25.15 0.00 0.00 2.71
167 178 2.625737 GACAATAGCAGAGCAAGAGCA 58.374 47.619 0.00 0.00 45.49 4.26
168 179 2.608546 GACAATAGCAGAGCAAGAGCAG 59.391 50.000 0.00 0.00 45.49 4.24
169 180 1.941294 CAATAGCAGAGCAAGAGCAGG 59.059 52.381 0.00 0.00 45.49 4.85
170 181 0.469070 ATAGCAGAGCAAGAGCAGGG 59.531 55.000 0.00 0.00 45.49 4.45
171 182 2.249413 TAGCAGAGCAAGAGCAGGGC 62.249 60.000 0.00 0.00 45.49 5.19
191 202 0.112218 AGGGCAGTTGTTGGTATGCA 59.888 50.000 0.00 0.00 40.46 3.96
252 263 1.747898 CGGAGGAGGGTAGAGACAGAC 60.748 61.905 0.00 0.00 0.00 3.51
257 268 2.240160 GGAGGGTAGAGACAGACAGAGA 59.760 54.545 0.00 0.00 0.00 3.10
337 351 3.343421 GGTCGAACCGTGTGTGCC 61.343 66.667 0.00 0.00 0.00 5.01
367 381 3.451894 GCGATGGGGCCAAACAGG 61.452 66.667 4.39 0.00 41.84 4.00
368 382 2.035626 CGATGGGGCCAAACAGGT 59.964 61.111 4.39 0.00 40.61 4.00
369 383 2.342650 CGATGGGGCCAAACAGGTG 61.343 63.158 4.39 0.00 40.61 4.00
370 384 1.076549 GATGGGGCCAAACAGGTGA 59.923 57.895 4.39 0.00 40.61 4.02
371 385 0.967380 GATGGGGCCAAACAGGTGAG 60.967 60.000 4.39 0.00 40.61 3.51
382 396 1.073199 CAGGTGAGGTGGACCCAAC 59.927 63.158 0.00 0.00 36.42 3.77
411 425 2.617276 GCCAAGTACCACTACCTTTCCC 60.617 54.545 0.00 0.00 0.00 3.97
458 476 7.116736 AGTTTTTCCCTACTTTCTGTTGAGAA 58.883 34.615 0.00 0.00 36.36 2.87
474 514 7.466670 TGTTGAGAACAGCAAGAGGAGACTC 62.467 48.000 0.00 0.00 46.97 3.36
486 526 3.791973 AGGAGACTCGATCATCACAAC 57.208 47.619 0.00 0.00 32.90 3.32
490 530 1.840741 GACTCGATCATCACAACGACG 59.159 52.381 0.00 0.00 0.00 5.12
491 531 1.199327 ACTCGATCATCACAACGACGT 59.801 47.619 0.00 0.00 0.00 4.34
492 532 1.579361 CTCGATCATCACAACGACGTG 59.421 52.381 0.00 0.00 38.29 4.49
611 658 0.035152 TGTGGTAATCAGGCAGGCAG 60.035 55.000 0.00 0.00 0.00 4.85
612 659 0.749454 GTGGTAATCAGGCAGGCAGG 60.749 60.000 0.00 0.00 0.00 4.85
613 660 1.825622 GGTAATCAGGCAGGCAGGC 60.826 63.158 0.00 0.00 44.61 4.85
661 708 6.516739 AAGTTGATGATCTGTCGTCTCTAA 57.483 37.500 0.00 0.00 40.38 2.10
662 709 5.885881 AGTTGATGATCTGTCGTCTCTAAC 58.114 41.667 0.00 0.00 40.38 2.34
663 710 5.650266 AGTTGATGATCTGTCGTCTCTAACT 59.350 40.000 0.00 0.00 40.38 2.24
664 711 6.824196 AGTTGATGATCTGTCGTCTCTAACTA 59.176 38.462 0.00 0.00 40.38 2.24
665 712 7.500892 AGTTGATGATCTGTCGTCTCTAACTAT 59.499 37.037 0.00 0.00 40.38 2.12
666 713 8.775527 GTTGATGATCTGTCGTCTCTAACTATA 58.224 37.037 0.00 0.00 40.38 1.31
696 743 4.592192 CGACGCGCCATCCTCCAT 62.592 66.667 5.73 0.00 0.00 3.41
698 745 4.592192 ACGCGCCATCCTCCATCG 62.592 66.667 5.73 0.00 0.00 3.84
699 746 4.592192 CGCGCCATCCTCCATCGT 62.592 66.667 0.00 0.00 0.00 3.73
700 747 2.663188 GCGCCATCCTCCATCGTC 60.663 66.667 0.00 0.00 0.00 4.20
701 748 3.133014 CGCCATCCTCCATCGTCT 58.867 61.111 0.00 0.00 0.00 4.18
704 752 0.250081 GCCATCCTCCATCGTCTTCC 60.250 60.000 0.00 0.00 0.00 3.46
712 760 0.397816 CCATCGTCTTCCTCCTCCCT 60.398 60.000 0.00 0.00 0.00 4.20
774 822 0.404040 TCAACTTCAATTCCCCGCCT 59.596 50.000 0.00 0.00 0.00 5.52
811 859 1.551099 CCACCACCCAAGAGAGAGAGA 60.551 57.143 0.00 0.00 0.00 3.10
812 860 1.824230 CACCACCCAAGAGAGAGAGAG 59.176 57.143 0.00 0.00 0.00 3.20
813 861 1.713647 ACCACCCAAGAGAGAGAGAGA 59.286 52.381 0.00 0.00 0.00 3.10
814 862 2.291540 ACCACCCAAGAGAGAGAGAGAG 60.292 54.545 0.00 0.00 0.00 3.20
815 863 2.025416 CCACCCAAGAGAGAGAGAGAGA 60.025 54.545 0.00 0.00 0.00 3.10
816 864 3.282021 CACCCAAGAGAGAGAGAGAGAG 58.718 54.545 0.00 0.00 0.00 3.20
817 865 3.054434 CACCCAAGAGAGAGAGAGAGAGA 60.054 52.174 0.00 0.00 0.00 3.10
818 866 3.200825 ACCCAAGAGAGAGAGAGAGAGAG 59.799 52.174 0.00 0.00 0.00 3.20
842 890 3.650950 AGTCCCTGCCGTGCCAAT 61.651 61.111 0.00 0.00 0.00 3.16
843 891 3.134127 GTCCCTGCCGTGCCAATC 61.134 66.667 0.00 0.00 0.00 2.67
876 924 2.815963 CGCTCTCTAGATTCTAGCCCCA 60.816 54.545 14.75 0.00 0.00 4.96
887 935 0.181114 CTAGCCCCACAGCAAGCATA 59.819 55.000 0.00 0.00 34.23 3.14
908 958 9.381038 AGCATAGGATCAAACCTCTAGTATTAA 57.619 33.333 0.00 0.00 41.00 1.40
950 1000 1.901650 GCGCCGGAGTTGAAAGACAG 61.902 60.000 5.05 0.00 0.00 3.51
952 1002 1.433534 GCCGGAGTTGAAAGACAGAG 58.566 55.000 5.05 0.00 0.00 3.35
956 1006 3.306364 CCGGAGTTGAAAGACAGAGACAT 60.306 47.826 0.00 0.00 0.00 3.06
958 1008 5.394663 CCGGAGTTGAAAGACAGAGACATAT 60.395 44.000 0.00 0.00 0.00 1.78
960 1010 7.429633 CGGAGTTGAAAGACAGAGACATATAT 58.570 38.462 0.00 0.00 0.00 0.86
963 1079 9.405587 GAGTTGAAAGACAGAGACATATATAGC 57.594 37.037 0.00 0.00 0.00 2.97
974 1090 4.342378 AGACATATATAGCCGCCACATAGG 59.658 45.833 0.00 0.00 41.84 2.57
1314 1442 1.003003 TGATTGTTCTCGCACCCATCA 59.997 47.619 0.00 0.00 0.00 3.07
1344 1478 0.235926 GCTGTTGAGTTTGAGCGTCC 59.764 55.000 0.00 0.00 0.00 4.79
1372 1512 7.556275 TCTGCAGAAATTAACTCCGGATTAATT 59.444 33.333 24.11 24.11 41.70 1.40
1385 1525 9.901172 ACTCCGGATTAATTAATTAAGACTGTT 57.099 29.630 21.75 7.72 35.88 3.16
1432 1575 1.115467 ACAGCAGATACTTCTCCCCG 58.885 55.000 0.00 0.00 0.00 5.73
1437 1580 2.762459 ATACTTCTCCCCGCCGCA 60.762 61.111 0.00 0.00 0.00 5.69
1493 1641 5.061808 CGTTGGTCAAATGCACTAGTAGTAC 59.938 44.000 1.57 0.00 0.00 2.73
1538 1692 2.102578 CACACATGATTTTCCTCCCCC 58.897 52.381 0.00 0.00 0.00 5.40
1657 1811 5.422214 ACATATTCGGTGGAGGGATAATC 57.578 43.478 0.00 0.00 0.00 1.75
1679 1833 7.604657 ATCTCGGATACTAAAAACCAGAGAT 57.395 36.000 0.00 0.00 37.63 2.75
1695 1849 3.002042 CAGAGATGCCGTTTTCATGCTAG 59.998 47.826 0.00 0.00 0.00 3.42
1700 1854 2.230992 TGCCGTTTTCATGCTAGCAAAT 59.769 40.909 23.54 2.55 0.00 2.32
1802 1957 1.991264 CTGTGTTGATCGAGTCTGCTG 59.009 52.381 0.00 0.00 0.00 4.41
1803 1958 0.718343 GTGTTGATCGAGTCTGCTGC 59.282 55.000 0.00 0.00 0.00 5.25
1804 1959 0.605083 TGTTGATCGAGTCTGCTGCT 59.395 50.000 0.00 0.00 0.00 4.24
1823 1978 1.300266 TACTAACCAAAAGCGGCGGC 61.300 55.000 9.78 8.43 40.37 6.53
1824 1979 3.661025 CTAACCAAAAGCGGCGGCG 62.661 63.158 28.70 28.70 46.35 6.46
1868 2023 3.384014 CTCACGTCTCGAGGTCGGC 62.384 68.421 25.33 8.22 40.29 5.54
1878 2049 3.792053 GAGGTCGGCCGCCTATGTG 62.792 68.421 32.07 2.43 40.50 3.21
1926 2097 4.660938 GCCTCCAACAACCGCCCT 62.661 66.667 0.00 0.00 0.00 5.19
1936 2107 0.036875 CAACCGCCCTCTCCTTTTCT 59.963 55.000 0.00 0.00 0.00 2.52
1937 2108 0.771755 AACCGCCCTCTCCTTTTCTT 59.228 50.000 0.00 0.00 0.00 2.52
1938 2109 0.771755 ACCGCCCTCTCCTTTTCTTT 59.228 50.000 0.00 0.00 0.00 2.52
1939 2110 1.271434 ACCGCCCTCTCCTTTTCTTTC 60.271 52.381 0.00 0.00 0.00 2.62
1940 2111 1.454201 CGCCCTCTCCTTTTCTTTCC 58.546 55.000 0.00 0.00 0.00 3.13
1941 2112 1.003696 CGCCCTCTCCTTTTCTTTCCT 59.996 52.381 0.00 0.00 0.00 3.36
2009 2189 4.275810 TCTAGTAGGTGTCATTAGCCGTT 58.724 43.478 0.00 0.00 0.00 4.44
2044 2224 2.732412 AATGACTCACCACTCTCGTG 57.268 50.000 0.00 0.00 40.89 4.35
2053 2233 1.967535 CACTCTCGTGGCTTCTCCA 59.032 57.895 0.00 0.00 44.18 3.86
2085 2268 5.329493 ACAAAGAAAAGCTTGTTACACGAC 58.671 37.500 0.00 0.00 36.80 4.34
2087 2270 6.314400 ACAAAGAAAAGCTTGTTACACGACTA 59.686 34.615 0.00 0.00 36.80 2.59
2088 2271 6.526566 AAGAAAAGCTTGTTACACGACTAG 57.473 37.500 0.00 0.00 34.93 2.57
2090 2273 6.047231 AGAAAAGCTTGTTACACGACTAGTT 58.953 36.000 0.00 0.00 0.00 2.24
2092 2275 7.381678 AGAAAAGCTTGTTACACGACTAGTTAG 59.618 37.037 0.00 0.00 0.00 2.34
2093 2276 5.702349 AGCTTGTTACACGACTAGTTAGT 57.298 39.130 0.00 0.00 39.71 2.24
2094 2277 6.081872 AGCTTGTTACACGACTAGTTAGTT 57.918 37.500 0.00 0.00 36.50 2.24
2095 2278 6.148264 AGCTTGTTACACGACTAGTTAGTTC 58.852 40.000 0.00 0.00 36.50 3.01
2096 2279 5.916883 GCTTGTTACACGACTAGTTAGTTCA 59.083 40.000 0.00 0.00 36.50 3.18
2097 2280 6.585322 GCTTGTTACACGACTAGTTAGTTCAT 59.415 38.462 0.00 0.00 36.50 2.57
2099 2282 7.444629 TGTTACACGACTAGTTAGTTCATCT 57.555 36.000 0.00 0.00 36.50 2.90
2100 2283 7.879070 TGTTACACGACTAGTTAGTTCATCTT 58.121 34.615 0.00 0.00 36.50 2.40
2103 2286 6.844254 ACACGACTAGTTAGTTCATCTTCTC 58.156 40.000 0.00 0.00 36.50 2.87
2105 2288 5.944599 ACGACTAGTTAGTTCATCTTCTCCA 59.055 40.000 0.00 0.00 36.50 3.86
2107 2290 6.127980 CGACTAGTTAGTTCATCTTCTCCACA 60.128 42.308 0.00 0.00 36.50 4.17
2118 2304 5.188359 TCATCTTCTCCACATGATGACAAGA 59.812 40.000 0.00 4.70 39.91 3.02
2285 2485 2.762535 ACGGCTAGTTATGTTGCAGT 57.237 45.000 0.00 0.00 0.00 4.40
2287 2487 1.062587 CGGCTAGTTATGTTGCAGTGC 59.937 52.381 8.58 8.58 0.00 4.40
2304 2504 2.520982 CCTGATCGGACGGCCCTA 60.521 66.667 0.00 0.00 33.16 3.53
2320 2554 2.851195 CCCTACTTGCAGTGTTCTTGT 58.149 47.619 0.00 0.00 0.00 3.16
2321 2555 2.549754 CCCTACTTGCAGTGTTCTTGTG 59.450 50.000 0.00 0.00 0.00 3.33
2331 2572 2.106511 AGTGTTCTTGTGGTACAGGCAT 59.893 45.455 0.00 0.00 41.80 4.40
2343 2584 1.901948 CAGGCATAGCAGCATGGGG 60.902 63.158 0.00 0.00 42.15 4.96
2351 2592 2.836360 CAGCATGGGGGCATGTCC 60.836 66.667 8.19 8.19 35.16 4.02
2413 2656 0.322456 TACAGGCTTGCATGTGACCC 60.322 55.000 20.83 0.00 0.00 4.46
2548 2797 0.379669 CGTCAGGCCTGCATTCATTC 59.620 55.000 28.91 8.96 0.00 2.67
2549 2798 1.466856 GTCAGGCCTGCATTCATTCA 58.533 50.000 28.91 4.13 0.00 2.57
2586 2835 3.628942 TCTGTCCATGCAGCATAAATGTC 59.371 43.478 7.82 0.00 36.49 3.06
2601 2850 6.615088 CATAAATGTCCACAACTCTTCCAAG 58.385 40.000 0.00 0.00 0.00 3.61
2614 2863 5.010282 ACTCTTCCAAGCAATTAATCCGTT 58.990 37.500 0.00 0.00 0.00 4.44
2638 2896 2.670905 TCACTTACACGCCGATGAATTG 59.329 45.455 0.00 0.00 0.00 2.32
2639 2897 1.396996 ACTTACACGCCGATGAATTGC 59.603 47.619 0.00 0.00 0.00 3.56
2640 2898 1.665679 CTTACACGCCGATGAATTGCT 59.334 47.619 0.00 0.00 0.00 3.91
2644 2902 1.308069 ACGCCGATGAATTGCTTGCT 61.308 50.000 0.00 0.00 0.00 3.91
2786 3044 0.811915 TCTTCTTCGAGAGCTTCCGG 59.188 55.000 0.00 0.00 0.00 5.14
2891 3149 2.391389 GCACCCGCACTGCTACTTC 61.391 63.158 0.00 0.00 38.36 3.01
3098 3361 3.958147 TCGATGGCAGTTAGTTAGGATGA 59.042 43.478 0.00 0.00 0.00 2.92
3106 3369 6.992715 GGCAGTTAGTTAGGATGAACATACAT 59.007 38.462 0.00 0.00 0.00 2.29
3146 3409 5.648572 AGCTAGATTGGTTACGTGTTAGTC 58.351 41.667 0.00 0.00 0.00 2.59
3155 3418 2.298411 ACGTGTTAGTCGGTGTGTTT 57.702 45.000 0.00 0.00 0.00 2.83
3176 3447 2.390599 CGTTGGATCGGTGGCTGTG 61.391 63.158 0.00 0.00 0.00 3.66
3276 3548 2.420022 GGACTTTGACAATGGTGATCGG 59.580 50.000 6.09 0.00 0.00 4.18
3334 3627 2.096980 GCATATGCATCGATCATGTGGG 59.903 50.000 22.84 5.04 41.59 4.61
3335 3628 1.812235 TATGCATCGATCATGTGGGC 58.188 50.000 0.19 7.43 34.56 5.36
3336 3629 0.892358 ATGCATCGATCATGTGGGCC 60.892 55.000 0.00 0.00 34.56 5.80
3337 3630 2.263741 GCATCGATCATGTGGGCCC 61.264 63.158 17.59 17.59 34.56 5.80
3338 3631 1.962822 CATCGATCATGTGGGCCCG 60.963 63.158 19.37 1.86 0.00 6.13
3339 3632 3.832237 ATCGATCATGTGGGCCCGC 62.832 63.158 29.34 29.34 0.00 6.13
3368 3661 1.002792 GGAACTTGTGGTTTGTCTCGC 60.003 52.381 0.00 0.00 38.41 5.03
3369 3662 0.655733 AACTTGTGGTTTGTCTCGCG 59.344 50.000 0.00 0.00 33.90 5.87
3462 3757 2.621055 ACTAATGTTCAAAACGCTGGCA 59.379 40.909 0.00 0.00 0.00 4.92
4809 6087 3.971702 GCAGGGGCCTCAACCAGT 61.972 66.667 4.79 0.00 0.00 4.00
4810 6088 2.034687 CAGGGGCCTCAACCAGTG 59.965 66.667 4.79 0.00 0.00 3.66
4816 6094 4.709840 CCTCAACCAGTGGCAGAG 57.290 61.111 19.64 19.64 0.00 3.35
4817 6095 1.673665 CCTCAACCAGTGGCAGAGC 60.674 63.158 20.69 0.00 0.00 4.09
4830 6108 2.717639 GCAGAGCCAGGAATTAAGGA 57.282 50.000 0.00 0.00 0.00 3.36
4832 6110 3.145286 GCAGAGCCAGGAATTAAGGATC 58.855 50.000 0.00 0.00 38.09 3.36
4833 6111 3.434167 GCAGAGCCAGGAATTAAGGATCA 60.434 47.826 10.13 0.00 40.19 2.92
4835 6113 3.393941 AGAGCCAGGAATTAAGGATCAGG 59.606 47.826 10.13 0.00 40.19 3.86
4836 6114 2.444766 AGCCAGGAATTAAGGATCAGGG 59.555 50.000 0.00 0.00 0.00 4.45
4838 6116 2.108952 CCAGGAATTAAGGATCAGGGGG 59.891 54.545 0.00 0.00 0.00 5.40
4839 6117 3.056080 CAGGAATTAAGGATCAGGGGGA 58.944 50.000 0.00 0.00 0.00 4.81
4840 6118 3.056832 AGGAATTAAGGATCAGGGGGAC 58.943 50.000 0.00 0.00 0.00 4.46
4855 6133 2.640316 GGGACCAAGTCACTCAAACT 57.360 50.000 0.00 0.00 32.50 2.66
4856 6134 2.932261 GGGACCAAGTCACTCAAACTT 58.068 47.619 0.00 0.00 37.44 2.66
4857 6135 3.288092 GGGACCAAGTCACTCAAACTTT 58.712 45.455 0.00 0.00 34.79 2.66
4858 6136 3.699538 GGGACCAAGTCACTCAAACTTTT 59.300 43.478 0.00 0.00 34.79 2.27
4860 6138 4.398044 GGACCAAGTCACTCAAACTTTTGA 59.602 41.667 4.39 4.39 38.32 2.69
4862 6140 6.262273 GGACCAAGTCACTCAAACTTTTGATA 59.738 38.462 4.89 0.00 39.13 2.15
4863 6141 7.201785 GGACCAAGTCACTCAAACTTTTGATAA 60.202 37.037 4.89 0.00 39.13 1.75
4865 6143 7.122055 ACCAAGTCACTCAAACTTTTGATAACA 59.878 33.333 4.89 0.00 45.26 2.41
4866 6144 7.645340 CCAAGTCACTCAAACTTTTGATAACAG 59.355 37.037 4.89 0.00 45.26 3.16
4867 6145 7.264373 AGTCACTCAAACTTTTGATAACAGG 57.736 36.000 4.89 0.00 45.26 4.00
4868 6146 6.263168 AGTCACTCAAACTTTTGATAACAGGG 59.737 38.462 4.89 0.00 45.26 4.45
4869 6147 5.534654 TCACTCAAACTTTTGATAACAGGGG 59.465 40.000 4.89 0.00 45.26 4.79
4870 6148 4.280929 ACTCAAACTTTTGATAACAGGGGC 59.719 41.667 4.89 0.00 45.26 5.80
4871 6149 3.576550 TCAAACTTTTGATAACAGGGGCC 59.423 43.478 0.00 0.00 41.88 5.80
4872 6150 2.990740 ACTTTTGATAACAGGGGCCA 57.009 45.000 4.39 0.00 0.00 5.36
4873 6151 3.252554 ACTTTTGATAACAGGGGCCAA 57.747 42.857 4.39 0.00 0.00 4.52
4874 6152 3.582164 ACTTTTGATAACAGGGGCCAAA 58.418 40.909 4.39 0.00 0.00 3.28
4875 6153 3.323691 ACTTTTGATAACAGGGGCCAAAC 59.676 43.478 4.39 0.00 0.00 2.93
4876 6154 2.685106 TTGATAACAGGGGCCAAACA 57.315 45.000 4.39 0.00 0.00 2.83
4878 6156 3.182887 TGATAACAGGGGCCAAACAAT 57.817 42.857 4.39 0.00 0.00 2.71
4881 6159 2.694616 AACAGGGGCCAAACAATACT 57.305 45.000 4.39 0.00 0.00 2.12
4882 6160 3.818295 AACAGGGGCCAAACAATACTA 57.182 42.857 4.39 0.00 0.00 1.82
4885 6163 5.459982 ACAGGGGCCAAACAATACTAATA 57.540 39.130 4.39 0.00 0.00 0.98
4886 6164 5.198207 ACAGGGGCCAAACAATACTAATAC 58.802 41.667 4.39 0.00 0.00 1.89
4918 6293 9.624697 TTTTGTCTAAATTATGCACTGTTCATC 57.375 29.630 0.00 0.00 0.00 2.92
4919 6294 8.565896 TTGTCTAAATTATGCACTGTTCATCT 57.434 30.769 0.00 0.00 0.00 2.90
4921 6296 9.098355 TGTCTAAATTATGCACTGTTCATCTAC 57.902 33.333 0.00 0.00 0.00 2.59
4926 6301 9.672673 AAATTATGCACTGTTCATCTACTAACT 57.327 29.630 0.00 0.00 0.00 2.24
4928 6303 9.973450 ATTATGCACTGTTCATCTACTAACTAG 57.027 33.333 0.00 0.00 0.00 2.57
4929 6304 5.651530 TGCACTGTTCATCTACTAACTAGC 58.348 41.667 0.00 0.00 0.00 3.42
4930 6305 5.185056 TGCACTGTTCATCTACTAACTAGCA 59.815 40.000 0.00 0.00 0.00 3.49
4932 6307 6.035112 GCACTGTTCATCTACTAACTAGCAAC 59.965 42.308 0.00 0.00 0.00 4.17
4933 6308 7.090808 CACTGTTCATCTACTAACTAGCAACA 58.909 38.462 0.00 0.00 0.00 3.33
4935 6310 8.148351 ACTGTTCATCTACTAACTAGCAACAAA 58.852 33.333 0.00 0.00 0.00 2.83
4937 6312 9.151471 TGTTCATCTACTAACTAGCAACAAATC 57.849 33.333 0.00 0.00 0.00 2.17
4938 6313 9.151471 GTTCATCTACTAACTAGCAACAAATCA 57.849 33.333 0.00 0.00 0.00 2.57
4939 6314 9.719355 TTCATCTACTAACTAGCAACAAATCAA 57.281 29.630 0.00 0.00 0.00 2.57
4941 6316 9.926751 CATCTACTAACTAGCAACAAATCAATG 57.073 33.333 0.00 0.00 0.00 2.82
4942 6317 9.890629 ATCTACTAACTAGCAACAAATCAATGA 57.109 29.630 0.00 0.00 0.00 2.57
4943 6318 9.890629 TCTACTAACTAGCAACAAATCAATGAT 57.109 29.630 0.00 0.00 0.00 2.45
4946 6321 9.236006 ACTAACTAGCAACAAATCAATGATCTT 57.764 29.630 0.00 0.00 0.00 2.40
4950 6325 6.461110 AGCAACAAATCAATGATCTTAGGG 57.539 37.500 0.00 0.00 0.00 3.53
4952 6327 5.452356 GCAACAAATCAATGATCTTAGGGGG 60.452 44.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.781307 CCTCCCACGCCCGATGAA 61.781 66.667 0.00 0.00 0.00 2.57
2 3 4.530857 GACCTCCCACGCCCGATG 62.531 72.222 0.00 0.00 0.00 3.84
13 14 4.754667 GAACACCCGGCGACCTCC 62.755 72.222 9.30 0.00 0.00 4.30
14 15 3.310860 ATGAACACCCGGCGACCTC 62.311 63.158 9.30 0.00 0.00 3.85
15 16 3.310860 GATGAACACCCGGCGACCT 62.311 63.158 9.30 0.00 0.00 3.85
16 17 2.818274 GATGAACACCCGGCGACC 60.818 66.667 9.30 0.00 0.00 4.79
17 18 3.186047 CGATGAACACCCGGCGAC 61.186 66.667 9.30 0.00 0.00 5.19
18 19 3.687102 ACGATGAACACCCGGCGA 61.687 61.111 9.30 0.00 0.00 5.54
19 20 3.487202 CACGATGAACACCCGGCG 61.487 66.667 0.00 0.00 0.00 6.46
20 21 3.799755 GCACGATGAACACCCGGC 61.800 66.667 0.00 0.00 0.00 6.13
21 22 3.487202 CGCACGATGAACACCCGG 61.487 66.667 0.00 0.00 0.00 5.73
22 23 2.726691 GACGCACGATGAACACCCG 61.727 63.158 0.00 0.00 0.00 5.28
23 24 2.726691 CGACGCACGATGAACACCC 61.727 63.158 0.00 0.00 45.77 4.61
24 25 2.769617 CGACGCACGATGAACACC 59.230 61.111 0.00 0.00 45.77 4.16
25 26 2.093983 GCGACGCACGATGAACAC 59.906 61.111 16.42 0.00 45.77 3.32
26 27 3.466260 CGCGACGCACGATGAACA 61.466 61.111 21.35 0.00 45.77 3.18
27 28 4.191485 CCGCGACGCACGATGAAC 62.191 66.667 21.35 0.00 45.77 3.18
28 29 4.710695 ACCGCGACGCACGATGAA 62.711 61.111 21.35 0.00 45.77 2.57
78 79 4.488126 TGCTTTACTTCATCTGTGCAAC 57.512 40.909 0.00 0.00 37.35 4.17
86 87 3.426292 GGACGGCTTTGCTTTACTTCATC 60.426 47.826 0.00 0.00 0.00 2.92
88 89 1.877443 GGACGGCTTTGCTTTACTTCA 59.123 47.619 0.00 0.00 0.00 3.02
89 90 1.877443 TGGACGGCTTTGCTTTACTTC 59.123 47.619 0.00 0.00 0.00 3.01
90 91 1.880027 CTGGACGGCTTTGCTTTACTT 59.120 47.619 0.00 0.00 0.00 2.24
92 93 1.464997 CTCTGGACGGCTTTGCTTTAC 59.535 52.381 0.00 0.00 0.00 2.01
93 94 1.346395 TCTCTGGACGGCTTTGCTTTA 59.654 47.619 0.00 0.00 0.00 1.85
96 97 1.004440 GTCTCTGGACGGCTTTGCT 60.004 57.895 0.00 0.00 32.47 3.91
152 163 1.903294 CCCTGCTCTTGCTCTGCTA 59.097 57.895 0.00 0.00 40.48 3.49
167 178 2.203538 CAACAACTGCCCTGCCCT 60.204 61.111 0.00 0.00 0.00 5.19
168 179 2.706952 TACCAACAACTGCCCTGCCC 62.707 60.000 0.00 0.00 0.00 5.36
169 180 0.611896 ATACCAACAACTGCCCTGCC 60.612 55.000 0.00 0.00 0.00 4.85
170 181 0.527565 CATACCAACAACTGCCCTGC 59.472 55.000 0.00 0.00 0.00 4.85
171 182 0.527565 GCATACCAACAACTGCCCTG 59.472 55.000 0.00 0.00 0.00 4.45
222 233 2.711922 CCTCCTCCGCGTTACTGCT 61.712 63.158 4.92 0.00 0.00 4.24
252 263 4.463879 CCTGCCCGTGCCTCTCTG 62.464 72.222 0.00 0.00 36.33 3.35
337 351 2.095059 CCCCATCGCTTTGAAAGTCTTG 60.095 50.000 6.81 2.13 0.00 3.02
367 381 2.002018 TTGGGTTGGGTCCACCTCAC 62.002 60.000 0.00 0.00 41.11 3.51
368 382 1.698116 TTGGGTTGGGTCCACCTCA 60.698 57.895 0.00 0.00 41.11 3.86
369 383 1.228459 GTTGGGTTGGGTCCACCTC 60.228 63.158 0.00 0.00 41.11 3.85
370 384 2.931921 GTTGGGTTGGGTCCACCT 59.068 61.111 0.00 0.00 41.11 4.00
371 385 2.596338 CGTTGGGTTGGGTCCACC 60.596 66.667 0.00 0.00 40.81 4.61
382 396 0.953960 GTGGTACTTGGCTCGTTGGG 60.954 60.000 0.00 0.00 0.00 4.12
430 444 6.887545 TCAACAGAAAGTAGGGAAAAACTTCA 59.112 34.615 0.00 0.00 34.91 3.02
431 445 7.282450 TCTCAACAGAAAGTAGGGAAAAACTTC 59.718 37.037 0.00 0.00 34.91 3.01
432 446 7.116736 TCTCAACAGAAAGTAGGGAAAAACTT 58.883 34.615 0.00 0.00 37.54 2.66
433 447 6.659824 TCTCAACAGAAAGTAGGGAAAAACT 58.340 36.000 0.00 0.00 0.00 2.66
435 449 6.887545 TGTTCTCAACAGAAAGTAGGGAAAAA 59.112 34.615 0.00 0.00 40.49 1.94
436 450 6.419791 TGTTCTCAACAGAAAGTAGGGAAAA 58.580 36.000 0.00 0.00 40.49 2.29
437 451 5.996644 TGTTCTCAACAGAAAGTAGGGAAA 58.003 37.500 0.00 0.00 40.49 3.13
438 452 5.623956 TGTTCTCAACAGAAAGTAGGGAA 57.376 39.130 0.00 0.00 40.49 3.97
458 476 1.748493 GATCGAGTCTCCTCTTGCTGT 59.252 52.381 0.00 0.00 35.43 4.40
461 479 2.360483 TGATGATCGAGTCTCCTCTTGC 59.640 50.000 0.00 0.00 35.43 4.01
462 480 3.379688 TGTGATGATCGAGTCTCCTCTTG 59.620 47.826 0.00 0.00 35.43 3.02
466 506 2.098280 CGTTGTGATGATCGAGTCTCCT 59.902 50.000 0.00 0.00 0.00 3.69
474 514 1.613270 TCACGTCGTTGTGATGATCG 58.387 50.000 8.11 0.00 43.62 3.69
490 530 2.668550 GGGTGGGCTCACGTTCAC 60.669 66.667 11.38 0.00 44.50 3.18
491 531 2.272230 TTTGGGTGGGCTCACGTTCA 62.272 55.000 11.38 6.28 44.50 3.18
492 532 1.515521 CTTTGGGTGGGCTCACGTTC 61.516 60.000 11.38 3.45 44.50 3.95
493 533 1.528309 CTTTGGGTGGGCTCACGTT 60.528 57.895 11.38 0.00 44.50 3.99
494 534 2.113139 CTTTGGGTGGGCTCACGT 59.887 61.111 11.38 0.00 44.50 4.49
495 535 3.365265 GCTTTGGGTGGGCTCACG 61.365 66.667 11.38 0.00 44.50 4.35
496 536 2.991540 GGCTTTGGGTGGGCTCAC 60.992 66.667 8.68 8.68 42.91 3.51
505 545 1.966451 GACTGGTCACGGCTTTGGG 60.966 63.158 0.00 0.00 0.00 4.12
611 658 2.832201 GATTGAGCCTGCCCTGCC 60.832 66.667 0.00 0.00 0.00 4.85
612 659 2.044650 TGATTGAGCCTGCCCTGC 60.045 61.111 0.00 0.00 0.00 4.85
613 660 1.030488 CACTGATTGAGCCTGCCCTG 61.030 60.000 0.00 0.00 0.00 4.45
614 661 1.302285 CACTGATTGAGCCTGCCCT 59.698 57.895 0.00 0.00 0.00 5.19
615 662 1.751927 CCACTGATTGAGCCTGCCC 60.752 63.158 0.00 0.00 0.00 5.36
616 663 1.751927 CCCACTGATTGAGCCTGCC 60.752 63.158 0.00 0.00 0.00 4.85
617 664 0.322816 TTCCCACTGATTGAGCCTGC 60.323 55.000 0.00 0.00 0.00 4.85
618 665 2.431954 ATTCCCACTGATTGAGCCTG 57.568 50.000 0.00 0.00 0.00 4.85
661 708 3.158648 TGGCGGGCGGCTTATAGT 61.159 61.111 16.89 0.00 42.94 2.12
662 709 2.665185 GTGGCGGGCGGCTTATAG 60.665 66.667 16.89 0.00 42.94 1.31
663 710 4.595538 CGTGGCGGGCGGCTTATA 62.596 66.667 16.89 0.00 42.94 0.98
696 743 1.306970 GGAGGGAGGAGGAAGACGA 59.693 63.158 0.00 0.00 0.00 4.20
698 745 0.397957 GAGGGAGGGAGGAGGAAGAC 60.398 65.000 0.00 0.00 0.00 3.01
699 746 1.595058 GGAGGGAGGGAGGAGGAAGA 61.595 65.000 0.00 0.00 0.00 2.87
700 747 1.074850 GGAGGGAGGGAGGAGGAAG 60.075 68.421 0.00 0.00 0.00 3.46
701 748 2.647949 GGGAGGGAGGGAGGAGGAA 61.648 68.421 0.00 0.00 0.00 3.36
704 752 1.598856 AAGAGGGAGGGAGGGAGGAG 61.599 65.000 0.00 0.00 0.00 3.69
712 760 1.296002 GGGCTTTTAAGAGGGAGGGA 58.704 55.000 0.00 0.00 0.00 4.20
774 822 3.936203 GTGGTGGTGGACGGAGCA 61.936 66.667 0.00 0.00 0.00 4.26
811 859 0.398381 GGGACTGGATGCCTCTCTCT 60.398 60.000 0.00 0.00 35.42 3.10
812 860 2.132300 GGGACTGGATGCCTCTCTC 58.868 63.158 0.00 0.00 35.42 3.20
813 861 4.390341 GGGACTGGATGCCTCTCT 57.610 61.111 0.00 0.00 35.42 3.10
851 899 3.128589 GGCTAGAATCTAGAGAGCGATGG 59.871 52.174 20.58 0.00 33.85 3.51
876 924 3.019564 GGTTTGATCCTATGCTTGCTGT 58.980 45.455 0.00 0.00 0.00 4.40
908 958 0.177604 CGAGCAGAGCCCTCTTGAAT 59.822 55.000 0.00 0.00 37.98 2.57
937 987 9.405587 GCTATATATGTCTCTGTCTTTCAACTC 57.594 37.037 0.00 0.00 0.00 3.01
950 1000 3.868757 TGTGGCGGCTATATATGTCTC 57.131 47.619 11.43 0.00 0.00 3.36
952 1002 4.621991 CCTATGTGGCGGCTATATATGTC 58.378 47.826 11.43 0.00 0.00 3.06
974 1090 2.757099 CCCCCAACATCTGGCTGC 60.757 66.667 0.00 0.00 44.90 5.25
1140 1262 3.343972 CCGTTGTTGTGGCTCCAG 58.656 61.111 0.00 0.00 0.00 3.86
1314 1442 7.520614 GCTCAAACTCAACAGCAATACTAGTTT 60.521 37.037 0.00 0.00 35.00 2.66
1344 1478 4.253685 TCCGGAGTTAATTTCTGCAGAAG 58.746 43.478 27.02 13.31 35.21 2.85
1385 1525 7.504574 TGATCCTACAGTGATAATCCTCGTAAA 59.495 37.037 0.00 0.00 0.00 2.01
1417 1557 1.364171 CGGCGGGGAGAAGTATCTG 59.636 63.158 0.00 0.00 35.54 2.90
1437 1580 1.217244 GGGAACGCCACAGACGTAT 59.783 57.895 0.00 0.00 44.30 3.06
1463 1606 1.083489 GCATTTGACCAACGATCGGA 58.917 50.000 20.98 0.00 0.00 4.55
1493 1641 6.475596 AAATGGAAAATATCTTGAGCCTGG 57.524 37.500 0.00 0.00 0.00 4.45
1657 1811 5.463724 GCATCTCTGGTTTTTAGTATCCGAG 59.536 44.000 0.00 0.00 0.00 4.63
1679 1833 1.242989 TTGCTAGCATGAAAACGGCA 58.757 45.000 20.13 0.00 0.00 5.69
1802 1957 0.096454 CGCCGCTTTTGGTTAGTAGC 59.904 55.000 0.00 0.00 0.00 3.58
1803 1958 0.725117 CCGCCGCTTTTGGTTAGTAG 59.275 55.000 0.00 0.00 0.00 2.57
1804 1959 1.300266 GCCGCCGCTTTTGGTTAGTA 61.300 55.000 0.00 0.00 0.00 1.82
1868 2023 1.809619 CGTCCACACACATAGGCGG 60.810 63.158 0.00 0.00 0.00 6.13
1871 2026 1.996292 CAGACGTCCACACACATAGG 58.004 55.000 13.01 0.00 0.00 2.57
1874 2045 0.106708 AAGCAGACGTCCACACACAT 59.893 50.000 13.01 0.00 0.00 3.21
1878 2049 1.140816 GAGAAAGCAGACGTCCACAC 58.859 55.000 13.01 0.00 0.00 3.82
1926 2097 5.075067 AGGATGGAAAGGAAAGAAAAGGAGA 59.925 40.000 0.00 0.00 0.00 3.71
1936 2107 1.766951 TGGGGAGGATGGAAAGGAAA 58.233 50.000 0.00 0.00 0.00 3.13
1937 2108 1.570501 CATGGGGAGGATGGAAAGGAA 59.429 52.381 0.00 0.00 0.00 3.36
1938 2109 1.225373 CATGGGGAGGATGGAAAGGA 58.775 55.000 0.00 0.00 0.00 3.36
1939 2110 0.929244 ACATGGGGAGGATGGAAAGG 59.071 55.000 0.00 0.00 0.00 3.11
1940 2111 1.849039 AGACATGGGGAGGATGGAAAG 59.151 52.381 0.00 0.00 0.00 2.62
1941 2112 1.985622 AGACATGGGGAGGATGGAAA 58.014 50.000 0.00 0.00 0.00 3.13
1979 2159 7.386848 GCTAATGACACCTACTAGAGTCTAGAG 59.613 44.444 29.87 21.19 32.41 2.43
1980 2160 7.218614 GCTAATGACACCTACTAGAGTCTAGA 58.781 42.308 29.87 14.50 32.41 2.43
1984 2164 4.023878 CGGCTAATGACACCTACTAGAGTC 60.024 50.000 0.00 0.00 0.00 3.36
1986 2166 3.884091 ACGGCTAATGACACCTACTAGAG 59.116 47.826 0.00 0.00 0.00 2.43
1988 2168 4.360563 CAACGGCTAATGACACCTACTAG 58.639 47.826 0.00 0.00 0.00 2.57
2009 2189 5.104151 TGAGTCATTAGGGTTGATAATGGCA 60.104 40.000 11.55 0.00 44.15 4.92
2044 2224 1.134699 TGTCGATCATGTGGAGAAGCC 60.135 52.381 0.00 0.00 37.10 4.35
2053 2233 5.009010 ACAAGCTTTTCTTTGTCGATCATGT 59.991 36.000 0.00 0.00 31.27 3.21
2060 2240 4.433304 CGTGTAACAAGCTTTTCTTTGTCG 59.567 41.667 0.00 0.00 35.74 4.35
2085 2268 7.776107 TCATGTGGAGAAGATGAACTAACTAG 58.224 38.462 0.00 0.00 35.72 2.57
2087 2270 6.611613 TCATGTGGAGAAGATGAACTAACT 57.388 37.500 0.00 0.00 35.72 2.24
2088 2271 7.010923 GTCATCATGTGGAGAAGATGAACTAAC 59.989 40.741 5.62 0.00 45.78 2.34
2090 2273 6.155049 TGTCATCATGTGGAGAAGATGAACTA 59.845 38.462 5.62 0.00 45.78 2.24
2092 2275 5.181009 TGTCATCATGTGGAGAAGATGAAC 58.819 41.667 5.62 2.51 45.78 3.18
2093 2276 5.425196 TGTCATCATGTGGAGAAGATGAA 57.575 39.130 5.62 0.00 45.78 2.57
2094 2277 5.188359 TCTTGTCATCATGTGGAGAAGATGA 59.812 40.000 18.08 0.00 42.34 2.92
2095 2278 5.425630 TCTTGTCATCATGTGGAGAAGATG 58.574 41.667 18.08 0.00 38.17 2.90
2096 2279 5.688814 TCTTGTCATCATGTGGAGAAGAT 57.311 39.130 18.08 0.00 38.17 2.40
2097 2280 5.488262 TTCTTGTCATCATGTGGAGAAGA 57.512 39.130 18.08 18.08 40.39 2.87
2099 2282 5.005740 CCTTTCTTGTCATCATGTGGAGAA 58.994 41.667 0.00 0.00 0.00 2.87
2100 2283 4.042062 ACCTTTCTTGTCATCATGTGGAGA 59.958 41.667 0.00 0.00 0.00 3.71
2103 2286 4.074259 TGACCTTTCTTGTCATCATGTGG 58.926 43.478 0.00 0.00 37.80 4.17
2287 2487 2.520982 TAGGGCCGTCCGATCAGG 60.521 66.667 0.00 0.00 41.52 3.86
2320 2554 0.839277 ATGCTGCTATGCCTGTACCA 59.161 50.000 0.00 0.00 0.00 3.25
2321 2555 1.233019 CATGCTGCTATGCCTGTACC 58.767 55.000 0.00 0.00 0.00 3.34
2331 2572 2.196502 CATGCCCCCATGCTGCTA 59.803 61.111 0.00 0.00 42.08 3.49
2343 2584 1.039856 GAGAGAGAGAGGGACATGCC 58.960 60.000 0.00 0.00 0.00 4.40
2351 2592 6.522625 TTTTGTATGTCAGAGAGAGAGAGG 57.477 41.667 0.00 0.00 0.00 3.69
2413 2656 2.492019 TGTGCGACCTAATGATCGAG 57.508 50.000 0.00 0.00 40.86 4.04
2478 2721 9.191995 AGCAGCAAATTAATTTTGTAGTTGTAC 57.808 29.630 10.77 0.00 45.41 2.90
2481 2724 8.375465 GCTAGCAGCAAATTAATTTTGTAGTTG 58.625 33.333 10.63 9.02 45.41 3.16
2482 2731 8.306761 AGCTAGCAGCAAATTAATTTTGTAGTT 58.693 29.630 18.83 7.73 45.56 2.24
2484 2733 8.693542 AAGCTAGCAGCAAATTAATTTTGTAG 57.306 30.769 18.83 11.77 45.56 2.74
2548 2797 4.160635 GATTTGGACGCGCGGGTG 62.161 66.667 34.38 11.92 0.00 4.61
2549 2798 4.388499 AGATTTGGACGCGCGGGT 62.388 61.111 35.22 29.93 0.00 5.28
2586 2835 5.452078 TTAATTGCTTGGAAGAGTTGTGG 57.548 39.130 0.00 0.00 0.00 4.17
2601 2850 6.304683 GTGTAAGTGACAAACGGATTAATTGC 59.695 38.462 0.00 0.00 40.66 3.56
2614 2863 1.000052 TCATCGGCGTGTAAGTGACAA 60.000 47.619 6.85 0.00 40.66 3.18
2639 2897 4.099170 GACGCAGCCTGCAGCAAG 62.099 66.667 18.21 1.96 45.36 4.01
3039 3297 7.815398 TGCATGAAGTTGTTGCATAATAAAG 57.185 32.000 0.00 0.00 41.18 1.85
3098 3361 4.037446 ACCAACTTGTCGCAAATGTATGTT 59.963 37.500 0.00 0.00 0.00 2.71
3106 3369 2.294074 AGCTAACCAACTTGTCGCAAA 58.706 42.857 0.00 0.00 0.00 3.68
3146 3409 0.941542 ATCCAACGTGAAACACACCG 59.058 50.000 0.00 0.00 45.73 4.94
3155 3418 2.047655 GCCACCGATCCAACGTGA 60.048 61.111 0.00 0.00 0.00 4.35
3188 3459 1.594293 AGTTCAACTGGGCACGACG 60.594 57.895 0.00 0.00 0.00 5.12
3291 3563 3.406764 GGCAGAATCTAATGGCTACCTG 58.593 50.000 0.00 0.00 38.83 4.00
3339 3632 4.675029 ACAAGTTCCGACCGGCCG 62.675 66.667 21.04 21.04 34.68 6.13
3340 3633 3.047877 CACAAGTTCCGACCGGCC 61.048 66.667 0.00 0.00 34.68 6.13
3341 3634 3.047877 CCACAAGTTCCGACCGGC 61.048 66.667 0.00 0.00 34.68 6.13
3342 3635 0.816421 AAACCACAAGTTCCGACCGG 60.816 55.000 0.00 0.00 37.88 5.28
3343 3636 0.306533 CAAACCACAAGTTCCGACCG 59.693 55.000 0.00 0.00 37.88 4.79
3344 3637 1.332686 GACAAACCACAAGTTCCGACC 59.667 52.381 0.00 0.00 37.88 4.79
3345 3638 2.285977 AGACAAACCACAAGTTCCGAC 58.714 47.619 0.00 0.00 37.88 4.79
3346 3639 2.557317 GAGACAAACCACAAGTTCCGA 58.443 47.619 0.00 0.00 37.88 4.55
3347 3640 1.260561 CGAGACAAACCACAAGTTCCG 59.739 52.381 0.00 0.00 37.88 4.30
3348 3641 1.002792 GCGAGACAAACCACAAGTTCC 60.003 52.381 0.00 0.00 37.88 3.62
3349 3642 1.332904 CGCGAGACAAACCACAAGTTC 60.333 52.381 0.00 0.00 37.88 3.01
3368 3661 2.182614 AAATGTTTCAGTCGGCCGCG 62.183 55.000 23.51 11.80 0.00 6.46
3369 3662 0.800012 TAAATGTTTCAGTCGGCCGC 59.200 50.000 23.51 16.31 0.00 6.53
3418 3711 4.520743 TTAGCGATCAAGATCAAAAGCG 57.479 40.909 10.39 0.00 37.69 4.68
4812 6090 4.387598 CTGATCCTTAATTCCTGGCTCTG 58.612 47.826 0.00 0.00 0.00 3.35
4813 6091 3.393941 CCTGATCCTTAATTCCTGGCTCT 59.606 47.826 0.00 0.00 0.00 4.09
4814 6092 3.497584 CCCTGATCCTTAATTCCTGGCTC 60.498 52.174 0.00 0.00 0.00 4.70
4815 6093 2.444766 CCCTGATCCTTAATTCCTGGCT 59.555 50.000 0.00 0.00 0.00 4.75
4816 6094 2.489802 CCCCTGATCCTTAATTCCTGGC 60.490 54.545 0.00 0.00 0.00 4.85
4817 6095 2.108952 CCCCCTGATCCTTAATTCCTGG 59.891 54.545 0.00 0.00 0.00 4.45
4820 6098 2.108425 GGTCCCCCTGATCCTTAATTCC 59.892 54.545 0.00 0.00 0.00 3.01
4822 6100 2.871796 TGGTCCCCCTGATCCTTAATT 58.128 47.619 0.00 0.00 0.00 1.40
4823 6101 2.605825 TGGTCCCCCTGATCCTTAAT 57.394 50.000 0.00 0.00 0.00 1.40
4824 6102 2.205342 CTTGGTCCCCCTGATCCTTAA 58.795 52.381 0.00 0.00 0.00 1.85
4826 6104 0.178831 ACTTGGTCCCCCTGATCCTT 60.179 55.000 0.00 0.00 0.00 3.36
4827 6105 0.621862 GACTTGGTCCCCCTGATCCT 60.622 60.000 0.00 0.00 0.00 3.24
4828 6106 0.914417 TGACTTGGTCCCCCTGATCC 60.914 60.000 0.00 0.00 0.00 3.36
4829 6107 0.253327 GTGACTTGGTCCCCCTGATC 59.747 60.000 0.00 0.00 0.00 2.92
4830 6108 0.178861 AGTGACTTGGTCCCCCTGAT 60.179 55.000 0.00 0.00 0.00 2.90
4832 6110 1.127567 TGAGTGACTTGGTCCCCCTG 61.128 60.000 0.00 0.00 0.00 4.45
4833 6111 0.401395 TTGAGTGACTTGGTCCCCCT 60.401 55.000 0.00 0.00 0.00 4.79
4835 6113 1.143073 AGTTTGAGTGACTTGGTCCCC 59.857 52.381 0.00 0.00 0.00 4.81
4836 6114 2.640316 AGTTTGAGTGACTTGGTCCC 57.360 50.000 0.00 0.00 0.00 4.46
4838 6116 5.560966 TCAAAAGTTTGAGTGACTTGGTC 57.439 39.130 2.32 0.00 41.88 4.02
4850 6128 3.323403 TGGCCCCTGTTATCAAAAGTTTG 59.677 43.478 0.00 0.00 39.48 2.93
4851 6129 3.582164 TGGCCCCTGTTATCAAAAGTTT 58.418 40.909 0.00 0.00 0.00 2.66
4852 6130 3.252554 TGGCCCCTGTTATCAAAAGTT 57.747 42.857 0.00 0.00 0.00 2.66
4853 6131 2.990740 TGGCCCCTGTTATCAAAAGT 57.009 45.000 0.00 0.00 0.00 2.66
4855 6133 3.309296 TGTTTGGCCCCTGTTATCAAAA 58.691 40.909 0.00 0.00 0.00 2.44
4856 6134 2.964209 TGTTTGGCCCCTGTTATCAAA 58.036 42.857 0.00 0.00 0.00 2.69
4857 6135 2.685106 TGTTTGGCCCCTGTTATCAA 57.315 45.000 0.00 0.00 0.00 2.57
4858 6136 2.685106 TTGTTTGGCCCCTGTTATCA 57.315 45.000 0.00 0.00 0.00 2.15
4860 6138 4.331159 AGTATTGTTTGGCCCCTGTTAT 57.669 40.909 0.00 0.00 0.00 1.89
4862 6140 2.694616 AGTATTGTTTGGCCCCTGTT 57.305 45.000 0.00 0.00 0.00 3.16
4863 6141 3.818295 TTAGTATTGTTTGGCCCCTGT 57.182 42.857 0.00 0.00 0.00 4.00
4865 6143 5.459982 TGTATTAGTATTGTTTGGCCCCT 57.540 39.130 0.00 0.00 0.00 4.79
4866 6144 5.596772 ACATGTATTAGTATTGTTTGGCCCC 59.403 40.000 0.00 0.00 0.00 5.80
4867 6145 6.709018 ACATGTATTAGTATTGTTTGGCCC 57.291 37.500 0.00 0.00 0.00 5.80
4900 6275 9.672673 AGTTAGTAGATGAACAGTGCATAATTT 57.327 29.630 0.00 0.00 0.00 1.82
4902 6277 9.973450 CTAGTTAGTAGATGAACAGTGCATAAT 57.027 33.333 0.00 0.00 0.00 1.28
4903 6278 7.921214 GCTAGTTAGTAGATGAACAGTGCATAA 59.079 37.037 0.00 0.00 0.00 1.90
4904 6279 7.068226 TGCTAGTTAGTAGATGAACAGTGCATA 59.932 37.037 0.00 0.00 0.00 3.14
4905 6280 6.127338 TGCTAGTTAGTAGATGAACAGTGCAT 60.127 38.462 0.00 0.00 0.00 3.96
4906 6281 5.185056 TGCTAGTTAGTAGATGAACAGTGCA 59.815 40.000 0.00 0.00 0.00 4.57
4907 6282 5.651530 TGCTAGTTAGTAGATGAACAGTGC 58.348 41.667 0.00 0.00 0.00 4.40
4908 6283 7.090808 TGTTGCTAGTTAGTAGATGAACAGTG 58.909 38.462 0.00 0.00 0.00 3.66
4910 6285 8.534333 TTTGTTGCTAGTTAGTAGATGAACAG 57.466 34.615 0.00 0.00 31.09 3.16
4913 6288 9.719355 TTGATTTGTTGCTAGTTAGTAGATGAA 57.281 29.630 0.00 0.00 0.00 2.57
4914 6289 9.890629 ATTGATTTGTTGCTAGTTAGTAGATGA 57.109 29.630 0.00 0.00 0.00 2.92
4915 6290 9.926751 CATTGATTTGTTGCTAGTTAGTAGATG 57.073 33.333 0.00 0.00 0.00 2.90
4916 6291 9.890629 TCATTGATTTGTTGCTAGTTAGTAGAT 57.109 29.630 0.00 0.00 0.00 1.98
4917 6292 9.890629 ATCATTGATTTGTTGCTAGTTAGTAGA 57.109 29.630 0.00 0.00 0.00 2.59
4919 6294 9.890629 AGATCATTGATTTGTTGCTAGTTAGTA 57.109 29.630 0.00 0.00 0.00 1.82
4923 6298 8.680903 CCTAAGATCATTGATTTGTTGCTAGTT 58.319 33.333 0.00 0.00 0.00 2.24
4924 6299 7.284034 CCCTAAGATCATTGATTTGTTGCTAGT 59.716 37.037 0.00 0.00 0.00 2.57
4925 6300 7.255381 CCCCTAAGATCATTGATTTGTTGCTAG 60.255 40.741 0.00 0.00 0.00 3.42
4926 6301 6.547141 CCCCTAAGATCATTGATTTGTTGCTA 59.453 38.462 0.00 0.00 0.00 3.49
4927 6302 5.361857 CCCCTAAGATCATTGATTTGTTGCT 59.638 40.000 0.00 0.00 0.00 3.91
4928 6303 5.452356 CCCCCTAAGATCATTGATTTGTTGC 60.452 44.000 0.00 0.00 0.00 4.17
4929 6304 6.152932 CCCCCTAAGATCATTGATTTGTTG 57.847 41.667 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.