Multiple sequence alignment - TraesCS3B01G175400

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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 TraesCS3B01G175400 chr3B 100.000 4028 0 0 1 4028 177080352 177076325 0.000000e+00 7439.0
1 TraesCS3B01G175400 chr3B 75.372 942 202 23 2095 3017 177916935 177916005 1.030000e-115 427.0
2 TraesCS3B01G175400 chr3B 96.341 246 9 0 3783 4028 245527541 245527786 4.850000e-109 405.0
3 TraesCS3B01G175400 chr3B 89.855 69 7 0 2464 2532 673170487 673170419 5.540000e-14 89.8
4 TraesCS3B01G175400 chr3A 93.553 3645 198 19 1 3631 131347590 131351211 0.000000e+00 5395.0
5 TraesCS3B01G175400 chr3A 81.982 555 65 17 1 538 131346528 131347064 4.780000e-119 438.0
6 TraesCS3B01G175400 chr3A 89.873 158 10 2 3635 3786 131351188 131351345 8.830000e-47 198.0
7 TraesCS3B01G175400 chr3A 91.304 69 6 0 2464 2532 647613490 647613558 1.190000e-15 95.3
8 TraesCS3B01G175400 chr3D 94.643 2819 129 10 2 2810 123686628 123683822 0.000000e+00 4349.0
9 TraesCS3B01G175400 chr3D 89.700 1000 53 21 2806 3786 123678670 123677702 0.000000e+00 1230.0
10 TraesCS3B01G175400 chr3D 90.053 563 37 15 3013 3567 123664674 123664123 0.000000e+00 712.0
11 TraesCS3B01G175400 chr3D 82.627 472 54 17 79 538 123687605 123687150 3.770000e-105 392.0
12 TraesCS3B01G175400 chr3D 96.226 212 7 1 2810 3021 123665058 123664848 2.980000e-91 346.0
13 TraesCS3B01G175400 chr3D 89.610 154 14 1 3635 3786 123630367 123630214 1.140000e-45 195.0
14 TraesCS3B01G175400 chr3D 92.754 69 5 0 2464 2532 511535884 511535952 2.560000e-17 100.0
15 TraesCS3B01G175400 chr3D 96.552 58 2 0 3574 3631 123630401 123630344 3.310000e-16 97.1
16 TraesCS3B01G175400 chr2B 95.935 246 10 0 3783 4028 551493427 551493182 2.260000e-107 399.0
17 TraesCS3B01G175400 chr2B 93.676 253 14 2 3778 4028 739384320 739384068 1.060000e-100 377.0
18 TraesCS3B01G175400 chr2D 95.200 250 11 1 3779 4028 21615790 21616038 1.050000e-105 394.0
19 TraesCS3B01G175400 chr1B 95.436 241 11 0 3785 4025 425483420 425483660 6.320000e-103 385.0
20 TraesCS3B01G175400 chr1B 94.737 247 12 1 3783 4028 87970201 87969955 2.270000e-102 383.0
21 TraesCS3B01G175400 chr5B 94.715 246 13 0 3783 4028 478753100 478753345 2.270000e-102 383.0
22 TraesCS3B01G175400 chr5A 92.424 264 17 3 3767 4028 374886178 374885916 1.370000e-99 374.0
23 TraesCS3B01G175400 chr2A 90.614 277 21 5 3753 4028 15461080 15461352 2.960000e-96 363.0
24 TraesCS3B01G175400 chr7A 74.713 261 64 2 2450 2709 652339832 652340091 9.150000e-22 115.0


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 TraesCS3B01G175400 chr3B 177076325 177080352 4027 True 7439.000000 7439 100.000000 1 4028 1 chr3B.!!$R1 4027
1 TraesCS3B01G175400 chr3B 177916005 177916935 930 True 427.000000 427 75.372000 2095 3017 1 chr3B.!!$R2 922
2 TraesCS3B01G175400 chr3A 131346528 131351345 4817 False 2010.333333 5395 88.469333 1 3786 3 chr3A.!!$F2 3785
3 TraesCS3B01G175400 chr3D 123683822 123687605 3783 True 2370.500000 4349 88.635000 2 2810 2 chr3D.!!$R4 2808
4 TraesCS3B01G175400 chr3D 123677702 123678670 968 True 1230.000000 1230 89.700000 2806 3786 1 chr3D.!!$R1 980
5 TraesCS3B01G175400 chr3D 123664123 123665058 935 True 529.000000 712 93.139500 2810 3567 2 chr3D.!!$R3 757

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
495 1571 0.109342 ACCCTGCTTGGACTTGTCTG 59.891 55.0 0.61 0.0 38.35 3.51 F
1161 2239 0.035739 TGGCGGTTCTCCTTAACACC 59.964 55.0 0.00 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 3058 0.107508 ATGCTGTATGCGTCCTTGCT 60.108 50.0 0.00 0.0 46.63 3.91 R
3034 4310 0.249120 TACCCGTACGTCGAGGAGAA 59.751 55.0 15.21 0.0 42.86 2.87 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
29 1105 6.195700 TGGTCTATAGCTGAAGTACTCCTTT 58.804 40.000 0.00 0.00 32.03 3.11
39 1115 4.022589 TGAAGTACTCCTTTGTACAGGTCG 60.023 45.833 0.00 0.00 43.65 4.79
79 1155 9.658475 GTATATCTACTAGATCATCACATTCGC 57.342 37.037 1.56 0.00 36.20 4.70
109 1185 7.293402 TGCTTGCTTTTTCATGCAATATTAC 57.707 32.000 0.00 0.00 46.20 1.89
110 1186 6.034790 TGCTTGCTTTTTCATGCAATATTACG 59.965 34.615 0.00 0.00 46.20 3.18
112 1188 5.347342 TGCTTTTTCATGCAATATTACGGG 58.653 37.500 0.00 0.00 36.15 5.28
113 1189 5.105554 TGCTTTTTCATGCAATATTACGGGT 60.106 36.000 0.00 0.00 36.15 5.28
114 1190 5.458779 GCTTTTTCATGCAATATTACGGGTC 59.541 40.000 0.00 0.00 0.00 4.46
170 1246 3.250762 TCCTTGCACGAAAGAAGATTGTG 59.749 43.478 0.00 0.00 0.00 3.33
185 1261 1.116308 TTGTGTTCGACCAGGACAGA 58.884 50.000 0.00 0.00 0.00 3.41
198 1274 0.385751 GGACAGAGATGGCGATCGAA 59.614 55.000 21.57 6.31 33.34 3.71
205 1281 2.866156 GAGATGGCGATCGAATGAACAA 59.134 45.455 21.57 0.00 33.34 2.83
211 1287 3.498397 GGCGATCGAATGAACAATACCAT 59.502 43.478 21.57 0.00 0.00 3.55
217 1293 8.282592 CGATCGAATGAACAATACCATGTTTAT 58.717 33.333 10.26 0.00 43.31 1.40
231 1307 3.517296 TGTTTATGCCCTGAGGAAACA 57.483 42.857 10.97 10.97 35.89 2.83
235 1311 1.188863 ATGCCCTGAGGAAACAATGC 58.811 50.000 0.00 0.00 33.47 3.56
358 1434 2.835580 CATCTATGGAGCAGACTGGG 57.164 55.000 4.26 0.00 0.00 4.45
449 1525 4.094887 AGCACATCGTTACCATTTGTCATC 59.905 41.667 0.00 0.00 0.00 2.92
494 1570 0.398318 GACCCTGCTTGGACTTGTCT 59.602 55.000 0.61 0.00 38.35 3.41
495 1571 0.109342 ACCCTGCTTGGACTTGTCTG 59.891 55.000 0.61 0.00 38.35 3.51
497 1573 1.239968 CCTGCTTGGACTTGTCTGCC 61.240 60.000 0.61 0.00 38.35 4.85
538 1614 3.026630 TCAACTAACAGGTTGCTCTCG 57.973 47.619 0.00 0.00 44.19 4.04
539 1615 1.461127 CAACTAACAGGTTGCTCTCGC 59.539 52.381 0.00 0.00 39.76 5.03
540 1616 0.388649 ACTAACAGGTTGCTCTCGCG 60.389 55.000 0.00 0.00 39.65 5.87
542 1618 0.666274 TAACAGGTTGCTCTCGCGTG 60.666 55.000 5.77 3.13 39.65 5.34
544 1620 2.049063 AGGTTGCTCTCGCGTGTC 60.049 61.111 5.77 1.03 39.65 3.67
889 1966 1.000163 TCTATCTCGGGCAGCGAAATC 60.000 52.381 0.00 0.00 0.00 2.17
1043 2121 1.415659 CCCTATCACCAGCTTCCTCAG 59.584 57.143 0.00 0.00 0.00 3.35
1132 2210 3.006752 GGGTTCAGCAACAAATGGATCAA 59.993 43.478 0.00 0.00 33.70 2.57
1137 2215 8.399304 GTTCAGCAACAAATGGATCAACCAGA 62.399 42.308 0.00 0.00 41.19 3.86
1161 2239 0.035739 TGGCGGTTCTCCTTAACACC 59.964 55.000 0.00 0.00 0.00 4.16
1187 2265 6.376581 GGGAATTTTGTTGTGAGAGATCAGAT 59.623 38.462 0.00 0.00 0.00 2.90
1194 2272 4.462508 TGTGAGAGATCAGATCAACCAC 57.537 45.455 13.14 15.00 0.00 4.16
1204 2282 3.444034 TCAGATCAACCACTCTAAGGTCG 59.556 47.826 0.00 0.00 38.76 4.79
1267 2345 0.107456 AGCATGGCTAGGATTGGACG 59.893 55.000 0.00 0.00 36.99 4.79
1479 2561 6.495872 ACCCAAATGATATCCAATTCATGAGG 59.504 38.462 0.00 0.00 33.01 3.86
1762 2844 5.318349 ACTCGTTTGTTTTGTTAGACAACG 58.682 37.500 0.00 0.00 37.90 4.10
1797 2879 2.290896 TGCCAACCCTCAAGATACAAGG 60.291 50.000 0.00 0.00 0.00 3.61
1819 2901 5.011227 AGGGAAGAAACTAGTGAAGACTGTC 59.989 44.000 0.00 0.00 33.21 3.51
1823 2905 6.472686 AGAAACTAGTGAAGACTGTCAAGT 57.527 37.500 10.88 1.12 40.21 3.16
1824 2906 6.276847 AGAAACTAGTGAAGACTGTCAAGTG 58.723 40.000 10.88 0.00 36.52 3.16
1825 2907 4.592485 ACTAGTGAAGACTGTCAAGTGG 57.408 45.455 10.88 3.19 36.52 4.00
1835 2917 0.836606 TGTCAAGTGGCCTGTCTGAA 59.163 50.000 3.32 0.00 0.00 3.02
1891 2973 6.046290 TCTCTGGATGCAAGATATGGTATG 57.954 41.667 0.00 0.00 0.00 2.39
1899 2981 7.607607 GGATGCAAGATATGGTATGATGTGTTA 59.392 37.037 0.00 0.00 0.00 2.41
1936 3018 2.097466 GGAAATAGTGCCATTCACCACG 59.903 50.000 0.00 0.00 46.81 4.94
1973 3058 4.377021 CGTATAGCTCATGGTAAAAGGCA 58.623 43.478 0.00 0.00 0.00 4.75
1982 3067 0.521735 GGTAAAAGGCAGCAAGGACG 59.478 55.000 0.00 0.00 0.00 4.79
2090 3175 6.267699 TCTTCAAGACAGACTAAAGTGGATGA 59.732 38.462 0.00 0.00 0.00 2.92
2478 3563 5.055812 GGTCTTTCCTATCTGCATGAAGAG 58.944 45.833 9.83 0.00 0.00 2.85
2581 3666 4.007457 GCATGGCCAAGCTTCTCA 57.993 55.556 25.29 0.00 0.00 3.27
2693 3778 2.304180 AGGCAGATGTCTACAGCTTTGT 59.696 45.455 0.00 0.00 40.00 2.83
2713 3798 2.254546 TGTTGTGCTCCTCGAATTGT 57.745 45.000 0.00 0.00 0.00 2.71
2750 3844 3.747388 GCTACCGGGAATGGAAATCATCA 60.747 47.826 6.32 0.00 34.44 3.07
2993 4087 6.878923 ACTTCATTTCAGAACATTATGGACGA 59.121 34.615 0.00 0.00 0.00 4.20
3034 4310 2.896044 TCTGCAGAAGTGTGATCTGAGT 59.104 45.455 15.67 0.00 45.74 3.41
3130 4406 8.226819 TCCGGCTATAGTATTTATGATCAGAG 57.773 38.462 0.09 0.00 0.00 3.35
3224 4505 6.480320 CCTAGTTATATCTGGACAAACAGTGC 59.520 42.308 0.00 0.00 39.48 4.40
3275 4556 9.917887 AGATTCAGTTTGAGATATTTTGGATCT 57.082 29.630 0.00 0.00 36.33 2.75
3329 4612 7.616528 TCCCCTCTTTTCAAAAGAAATGATT 57.383 32.000 13.61 0.00 31.07 2.57
3336 4619 9.447157 TCTTTTCAAAAGAAATGATTGGTTTGT 57.553 25.926 10.29 0.00 0.00 2.83
3394 4691 3.482436 AGTTCTACGGTGCATTTTCCAA 58.518 40.909 0.00 0.00 0.00 3.53
3451 4749 5.556355 CAGATGAAAATCTGCAGCTAACA 57.444 39.130 9.47 5.91 41.18 2.41
3477 4776 7.497925 ACTCCAGTTTTCTAACATGAGAAAC 57.502 36.000 8.65 7.30 43.45 2.78
3481 4780 5.848036 CAGTTTTCTAACATGAGAAACAGCG 59.152 40.000 8.65 0.00 43.45 5.18
3533 4834 2.836372 TGCAATCCACTGACTGAGAGAT 59.164 45.455 0.00 0.00 0.00 2.75
3569 4871 3.500448 TGTCCTATGCTTGACCAACAA 57.500 42.857 0.00 0.00 36.97 2.83
3570 4872 3.826524 TGTCCTATGCTTGACCAACAAA 58.173 40.909 0.00 0.00 38.08 2.83
3608 4910 6.450545 GCCTATGCTTCCAAGATAAAATTCC 58.549 40.000 0.00 0.00 33.53 3.01
3609 4911 6.266330 GCCTATGCTTCCAAGATAAAATTCCT 59.734 38.462 0.00 0.00 33.53 3.36
3610 4912 7.448469 GCCTATGCTTCCAAGATAAAATTCCTA 59.552 37.037 0.00 0.00 33.53 2.94
3611 4913 9.007901 CCTATGCTTCCAAGATAAAATTCCTAG 57.992 37.037 0.00 0.00 0.00 3.02
3612 4914 9.566432 CTATGCTTCCAAGATAAAATTCCTAGT 57.434 33.333 0.00 0.00 0.00 2.57
3614 4916 8.732746 TGCTTCCAAGATAAAATTCCTAGTAC 57.267 34.615 0.00 0.00 0.00 2.73
3615 4917 8.548877 TGCTTCCAAGATAAAATTCCTAGTACT 58.451 33.333 0.00 0.00 0.00 2.73
3616 4918 9.047371 GCTTCCAAGATAAAATTCCTAGTACTC 57.953 37.037 0.00 0.00 0.00 2.59
3617 4919 9.549078 CTTCCAAGATAAAATTCCTAGTACTCC 57.451 37.037 0.00 0.00 0.00 3.85
3618 4920 8.618240 TCCAAGATAAAATTCCTAGTACTCCA 57.382 34.615 0.00 0.00 0.00 3.86
3619 4921 9.225682 TCCAAGATAAAATTCCTAGTACTCCAT 57.774 33.333 0.00 0.00 0.00 3.41
3620 4922 9.853177 CCAAGATAAAATTCCTAGTACTCCATT 57.147 33.333 0.00 0.00 0.00 3.16
3627 4929 9.807921 AAAATTCCTAGTACTCCATTTCTGAAA 57.192 29.630 5.15 5.15 0.00 2.69
3628 4930 9.807921 AAATTCCTAGTACTCCATTTCTGAAAA 57.192 29.630 6.95 0.00 0.00 2.29
3629 4931 9.981460 AATTCCTAGTACTCCATTTCTGAAAAT 57.019 29.630 6.95 0.00 35.43 1.82
3632 4934 9.886132 TCCTAGTACTCCATTTCTGAAAATAAC 57.114 33.333 6.95 1.13 33.27 1.89
3633 4935 9.110502 CCTAGTACTCCATTTCTGAAAATAACC 57.889 37.037 6.95 0.00 33.27 2.85
3643 4945 5.431179 TCTGAAAATAACCCCTGGTACTC 57.569 43.478 0.00 0.00 33.12 2.59
3673 4975 6.481313 TCTGAAAATATTTCCATCTCTCTGCG 59.519 38.462 0.10 0.00 0.00 5.18
3689 4991 1.154225 GCGTCCAAATGTTCCAGCG 60.154 57.895 0.00 0.00 0.00 5.18
3692 4994 1.976474 TCCAAATGTTCCAGCGGCC 60.976 57.895 0.00 0.00 0.00 6.13
3698 5000 3.134127 GTTCCAGCGGCCCATGAC 61.134 66.667 0.00 0.00 0.00 3.06
3710 5015 2.027745 GGCCCATGACGATGATGTCTAT 60.028 50.000 0.00 0.00 39.64 1.98
3719 5024 8.571336 CATGACGATGATGTCTATGGCTATATA 58.429 37.037 0.00 0.00 39.64 0.86
3786 5094 9.671279 AATGAAATTCCTTTTTGCCTATTTAGG 57.329 29.630 0.00 0.00 46.42 2.69
3787 5095 7.619965 TGAAATTCCTTTTTGCCTATTTAGGG 58.380 34.615 5.80 0.00 43.82 3.53
3799 5107 3.813166 CCTATTTAGGGCATGTACAACGG 59.187 47.826 0.00 0.00 39.86 4.44
3800 5108 2.863132 TTTAGGGCATGTACAACGGT 57.137 45.000 0.00 0.00 0.00 4.83
3801 5109 2.102070 TTAGGGCATGTACAACGGTG 57.898 50.000 0.00 0.00 0.00 4.94
3802 5110 0.250793 TAGGGCATGTACAACGGTGG 59.749 55.000 4.97 0.00 0.00 4.61
3803 5111 2.696759 GGGCATGTACAACGGTGGC 61.697 63.158 4.97 11.25 33.35 5.01
3804 5112 1.969064 GGCATGTACAACGGTGGCA 60.969 57.895 4.97 3.56 33.96 4.92
3805 5113 1.312371 GGCATGTACAACGGTGGCAT 61.312 55.000 4.97 6.15 33.96 4.40
3806 5114 1.374560 GCATGTACAACGGTGGCATA 58.625 50.000 4.97 0.00 0.00 3.14
3807 5115 1.946768 GCATGTACAACGGTGGCATAT 59.053 47.619 4.97 0.00 0.00 1.78
3808 5116 2.286950 GCATGTACAACGGTGGCATATG 60.287 50.000 4.97 7.52 0.00 1.78
3809 5117 2.031258 TGTACAACGGTGGCATATGG 57.969 50.000 4.97 0.00 0.00 2.74
3810 5118 1.555533 TGTACAACGGTGGCATATGGA 59.444 47.619 4.97 0.00 0.00 3.41
3811 5119 2.171659 TGTACAACGGTGGCATATGGAT 59.828 45.455 4.97 0.00 0.00 3.41
3812 5120 3.388350 TGTACAACGGTGGCATATGGATA 59.612 43.478 4.97 0.00 0.00 2.59
3813 5121 2.846193 ACAACGGTGGCATATGGATAC 58.154 47.619 4.97 0.00 0.00 2.24
3827 5135 3.719268 TGGATACATATGCCCCATGAC 57.281 47.619 1.58 0.00 46.17 3.06
3828 5136 2.985311 TGGATACATATGCCCCATGACA 59.015 45.455 1.58 0.00 46.17 3.58
3829 5137 3.397282 TGGATACATATGCCCCATGACAA 59.603 43.478 1.58 0.00 46.17 3.18
3830 5138 4.141065 TGGATACATATGCCCCATGACAAA 60.141 41.667 1.58 0.00 46.17 2.83
3831 5139 4.832266 GGATACATATGCCCCATGACAAAA 59.168 41.667 1.58 0.00 0.00 2.44
3832 5140 5.304101 GGATACATATGCCCCATGACAAAAA 59.696 40.000 1.58 0.00 0.00 1.94
3833 5141 4.741321 ACATATGCCCCATGACAAAAAG 57.259 40.909 1.58 0.00 0.00 2.27
3834 5142 4.095946 ACATATGCCCCATGACAAAAAGT 58.904 39.130 1.58 0.00 0.00 2.66
3835 5143 5.268387 ACATATGCCCCATGACAAAAAGTA 58.732 37.500 1.58 0.00 0.00 2.24
3836 5144 5.719085 ACATATGCCCCATGACAAAAAGTAA 59.281 36.000 1.58 0.00 0.00 2.24
3837 5145 6.383726 ACATATGCCCCATGACAAAAAGTAAT 59.616 34.615 1.58 0.00 0.00 1.89
3838 5146 5.760484 ATGCCCCATGACAAAAAGTAATT 57.240 34.783 0.00 0.00 0.00 1.40
3839 5147 5.559148 TGCCCCATGACAAAAAGTAATTT 57.441 34.783 0.00 0.00 0.00 1.82
3840 5148 5.303971 TGCCCCATGACAAAAAGTAATTTG 58.696 37.500 0.00 0.00 44.11 2.32
3841 5149 5.070981 TGCCCCATGACAAAAAGTAATTTGA 59.929 36.000 6.76 0.00 41.73 2.69
3842 5150 5.639082 GCCCCATGACAAAAAGTAATTTGAG 59.361 40.000 6.76 0.00 41.73 3.02
3843 5151 6.165577 CCCCATGACAAAAAGTAATTTGAGG 58.834 40.000 6.76 3.59 41.73 3.86
3844 5152 5.639082 CCCATGACAAAAAGTAATTTGAGGC 59.361 40.000 6.76 0.00 41.73 4.70
3845 5153 6.222389 CCATGACAAAAAGTAATTTGAGGCA 58.778 36.000 6.76 0.00 41.73 4.75
3846 5154 6.875195 CCATGACAAAAAGTAATTTGAGGCAT 59.125 34.615 6.76 3.81 41.73 4.40
3847 5155 7.063780 CCATGACAAAAAGTAATTTGAGGCATC 59.936 37.037 6.09 0.00 41.73 3.91
3848 5156 7.288810 TGACAAAAAGTAATTTGAGGCATCT 57.711 32.000 0.00 0.00 41.73 2.90
3849 5157 8.402798 TGACAAAAAGTAATTTGAGGCATCTA 57.597 30.769 0.00 0.00 41.73 1.98
3850 5158 9.023962 TGACAAAAAGTAATTTGAGGCATCTAT 57.976 29.630 0.00 0.00 41.73 1.98
3879 5187 4.519540 TTTTCTTCCCAATGCAAGCTAC 57.480 40.909 0.00 0.00 0.00 3.58
3880 5188 2.128771 TCTTCCCAATGCAAGCTACC 57.871 50.000 0.00 0.00 0.00 3.18
3881 5189 1.354031 TCTTCCCAATGCAAGCTACCA 59.646 47.619 0.00 0.00 0.00 3.25
3882 5190 2.025037 TCTTCCCAATGCAAGCTACCAT 60.025 45.455 0.00 0.00 0.00 3.55
3883 5191 2.530460 TCCCAATGCAAGCTACCATT 57.470 45.000 6.06 6.06 32.20 3.16
3884 5192 3.660970 TCCCAATGCAAGCTACCATTA 57.339 42.857 10.40 0.00 30.96 1.90
3885 5193 3.554934 TCCCAATGCAAGCTACCATTAG 58.445 45.455 10.40 5.05 30.96 1.73
3886 5194 3.053693 TCCCAATGCAAGCTACCATTAGT 60.054 43.478 10.40 0.00 30.96 2.24
3887 5195 3.067180 CCCAATGCAAGCTACCATTAGTG 59.933 47.826 10.40 2.05 30.96 2.74
3901 5209 5.930837 CCATTAGTGGGCCTCATTAAAAA 57.069 39.130 4.53 0.00 42.11 1.94
3931 5239 9.502091 AAAAATAAAGACTCTAGTACACATGCA 57.498 29.630 0.00 0.00 0.00 3.96
3932 5240 9.672673 AAAATAAAGACTCTAGTACACATGCAT 57.327 29.630 0.00 0.00 0.00 3.96
3933 5241 8.879342 AATAAAGACTCTAGTACACATGCATC 57.121 34.615 0.00 0.00 0.00 3.91
3934 5242 6.537453 AAAGACTCTAGTACACATGCATCT 57.463 37.500 0.00 0.00 0.00 2.90
3935 5243 5.766150 AGACTCTAGTACACATGCATCTC 57.234 43.478 0.00 0.00 0.00 2.75
3936 5244 5.445069 AGACTCTAGTACACATGCATCTCT 58.555 41.667 0.00 0.00 0.00 3.10
3937 5245 6.596621 AGACTCTAGTACACATGCATCTCTA 58.403 40.000 0.00 0.00 0.00 2.43
3938 5246 6.485313 AGACTCTAGTACACATGCATCTCTAC 59.515 42.308 0.00 0.00 0.00 2.59
3939 5247 6.361433 ACTCTAGTACACATGCATCTCTACT 58.639 40.000 0.00 4.19 0.00 2.57
3940 5248 6.831353 ACTCTAGTACACATGCATCTCTACTT 59.169 38.462 0.00 0.00 0.00 2.24
3941 5249 7.340743 ACTCTAGTACACATGCATCTCTACTTT 59.659 37.037 0.00 0.00 0.00 2.66
3942 5250 8.067751 TCTAGTACACATGCATCTCTACTTTT 57.932 34.615 0.00 0.00 0.00 2.27
3943 5251 8.191446 TCTAGTACACATGCATCTCTACTTTTC 58.809 37.037 0.00 0.00 0.00 2.29
3944 5252 6.701340 AGTACACATGCATCTCTACTTTTCA 58.299 36.000 0.00 0.00 0.00 2.69
3945 5253 5.869753 ACACATGCATCTCTACTTTTCAC 57.130 39.130 0.00 0.00 0.00 3.18
3946 5254 5.555017 ACACATGCATCTCTACTTTTCACT 58.445 37.500 0.00 0.00 0.00 3.41
3947 5255 5.641209 ACACATGCATCTCTACTTTTCACTC 59.359 40.000 0.00 0.00 0.00 3.51
3948 5256 5.064452 CACATGCATCTCTACTTTTCACTCC 59.936 44.000 0.00 0.00 0.00 3.85
3949 5257 4.890158 TGCATCTCTACTTTTCACTCCA 57.110 40.909 0.00 0.00 0.00 3.86
3950 5258 4.569943 TGCATCTCTACTTTTCACTCCAC 58.430 43.478 0.00 0.00 0.00 4.02
3951 5259 3.935828 GCATCTCTACTTTTCACTCCACC 59.064 47.826 0.00 0.00 0.00 4.61
3952 5260 4.323104 GCATCTCTACTTTTCACTCCACCT 60.323 45.833 0.00 0.00 0.00 4.00
3953 5261 5.799213 CATCTCTACTTTTCACTCCACCTT 58.201 41.667 0.00 0.00 0.00 3.50
3954 5262 5.888982 TCTCTACTTTTCACTCCACCTTT 57.111 39.130 0.00 0.00 0.00 3.11
3955 5263 6.248569 TCTCTACTTTTCACTCCACCTTTT 57.751 37.500 0.00 0.00 0.00 2.27
3956 5264 6.289064 TCTCTACTTTTCACTCCACCTTTTC 58.711 40.000 0.00 0.00 0.00 2.29
3957 5265 5.996644 TCTACTTTTCACTCCACCTTTTCA 58.003 37.500 0.00 0.00 0.00 2.69
3958 5266 6.055588 TCTACTTTTCACTCCACCTTTTCAG 58.944 40.000 0.00 0.00 0.00 3.02
3959 5267 3.381590 ACTTTTCACTCCACCTTTTCAGC 59.618 43.478 0.00 0.00 0.00 4.26
3960 5268 3.297134 TTTCACTCCACCTTTTCAGCT 57.703 42.857 0.00 0.00 0.00 4.24
3961 5269 3.297134 TTCACTCCACCTTTTCAGCTT 57.703 42.857 0.00 0.00 0.00 3.74
3962 5270 3.297134 TCACTCCACCTTTTCAGCTTT 57.703 42.857 0.00 0.00 0.00 3.51
3963 5271 3.631250 TCACTCCACCTTTTCAGCTTTT 58.369 40.909 0.00 0.00 0.00 2.27
3964 5272 3.381272 TCACTCCACCTTTTCAGCTTTTG 59.619 43.478 0.00 0.00 0.00 2.44
3965 5273 3.131046 CACTCCACCTTTTCAGCTTTTGT 59.869 43.478 0.00 0.00 0.00 2.83
3966 5274 3.381590 ACTCCACCTTTTCAGCTTTTGTC 59.618 43.478 0.00 0.00 0.00 3.18
3967 5275 3.360867 TCCACCTTTTCAGCTTTTGTCA 58.639 40.909 0.00 0.00 0.00 3.58
3968 5276 3.130340 TCCACCTTTTCAGCTTTTGTCAC 59.870 43.478 0.00 0.00 0.00 3.67
3969 5277 3.447742 CACCTTTTCAGCTTTTGTCACC 58.552 45.455 0.00 0.00 0.00 4.02
3970 5278 2.099098 ACCTTTTCAGCTTTTGTCACCG 59.901 45.455 0.00 0.00 0.00 4.94
3971 5279 2.543653 CCTTTTCAGCTTTTGTCACCGG 60.544 50.000 0.00 0.00 0.00 5.28
3972 5280 2.045561 TTTCAGCTTTTGTCACCGGA 57.954 45.000 9.46 0.00 0.00 5.14
3973 5281 1.305201 TTCAGCTTTTGTCACCGGAC 58.695 50.000 9.46 0.00 44.57 4.79
3974 5282 0.534203 TCAGCTTTTGTCACCGGACC 60.534 55.000 9.46 0.00 43.65 4.46
3975 5283 0.817634 CAGCTTTTGTCACCGGACCA 60.818 55.000 9.46 0.00 43.65 4.02
3976 5284 0.818040 AGCTTTTGTCACCGGACCAC 60.818 55.000 9.46 1.18 43.65 4.16
3977 5285 1.098712 GCTTTTGTCACCGGACCACA 61.099 55.000 9.46 4.37 43.65 4.17
3978 5286 0.661020 CTTTTGTCACCGGACCACAC 59.339 55.000 9.46 0.00 43.65 3.82
3979 5287 0.253610 TTTTGTCACCGGACCACACT 59.746 50.000 9.46 0.00 43.65 3.55
3980 5288 0.253610 TTTGTCACCGGACCACACTT 59.746 50.000 9.46 0.00 43.65 3.16
3981 5289 0.253610 TTGTCACCGGACCACACTTT 59.746 50.000 9.46 0.00 43.65 2.66
3982 5290 0.253610 TGTCACCGGACCACACTTTT 59.746 50.000 9.46 0.00 43.65 2.27
3983 5291 1.340211 TGTCACCGGACCACACTTTTT 60.340 47.619 9.46 0.00 43.65 1.94
3984 5292 1.332686 GTCACCGGACCACACTTTTTC 59.667 52.381 9.46 0.00 38.12 2.29
3985 5293 1.210967 TCACCGGACCACACTTTTTCT 59.789 47.619 9.46 0.00 0.00 2.52
3986 5294 1.602377 CACCGGACCACACTTTTTCTC 59.398 52.381 9.46 0.00 0.00 2.87
3987 5295 1.489230 ACCGGACCACACTTTTTCTCT 59.511 47.619 9.46 0.00 0.00 3.10
3988 5296 2.092592 ACCGGACCACACTTTTTCTCTT 60.093 45.455 9.46 0.00 0.00 2.85
3989 5297 2.949644 CCGGACCACACTTTTTCTCTTT 59.050 45.455 0.00 0.00 0.00 2.52
3990 5298 4.131596 CCGGACCACACTTTTTCTCTTTA 58.868 43.478 0.00 0.00 0.00 1.85
3991 5299 4.577283 CCGGACCACACTTTTTCTCTTTAA 59.423 41.667 0.00 0.00 0.00 1.52
3992 5300 5.277828 CCGGACCACACTTTTTCTCTTTAAG 60.278 44.000 0.00 0.00 0.00 1.85
3993 5301 5.520632 GGACCACACTTTTTCTCTTTAAGC 58.479 41.667 0.00 0.00 0.00 3.09
3994 5302 5.067283 GGACCACACTTTTTCTCTTTAAGCA 59.933 40.000 0.00 0.00 0.00 3.91
3995 5303 5.891451 ACCACACTTTTTCTCTTTAAGCAC 58.109 37.500 0.00 0.00 0.00 4.40
3996 5304 5.163550 ACCACACTTTTTCTCTTTAAGCACC 60.164 40.000 0.00 0.00 0.00 5.01
3997 5305 5.281727 CACACTTTTTCTCTTTAAGCACCC 58.718 41.667 0.00 0.00 0.00 4.61
3998 5306 4.036380 ACACTTTTTCTCTTTAAGCACCCG 59.964 41.667 0.00 0.00 0.00 5.28
3999 5307 3.004419 ACTTTTTCTCTTTAAGCACCCGC 59.996 43.478 0.00 0.00 38.99 6.13
4000 5308 1.530323 TTTCTCTTTAAGCACCCGCC 58.470 50.000 0.00 0.00 39.83 6.13
4001 5309 0.690762 TTCTCTTTAAGCACCCGCCT 59.309 50.000 0.00 0.00 39.83 5.52
4002 5310 0.690762 TCTCTTTAAGCACCCGCCTT 59.309 50.000 0.00 0.00 39.83 4.35
4003 5311 1.087501 CTCTTTAAGCACCCGCCTTC 58.912 55.000 0.00 0.00 39.83 3.46
4004 5312 0.690762 TCTTTAAGCACCCGCCTTCT 59.309 50.000 0.00 0.00 39.83 2.85
4005 5313 0.804989 CTTTAAGCACCCGCCTTCTG 59.195 55.000 0.00 0.00 39.83 3.02
4006 5314 0.608035 TTTAAGCACCCGCCTTCTGG 60.608 55.000 0.00 0.00 39.83 3.86
4007 5315 1.485294 TTAAGCACCCGCCTTCTGGA 61.485 55.000 0.00 0.00 39.83 3.86
4008 5316 1.899437 TAAGCACCCGCCTTCTGGAG 61.899 60.000 0.00 0.00 39.83 3.86
4009 5317 3.706373 GCACCCGCCTTCTGGAGA 61.706 66.667 0.00 0.00 34.95 3.71
4010 5318 2.581354 CACCCGCCTTCTGGAGAG 59.419 66.667 0.00 0.00 34.95 3.20
4011 5319 2.685380 ACCCGCCTTCTGGAGAGG 60.685 66.667 0.00 0.00 34.95 3.69
4012 5320 2.364317 CCCGCCTTCTGGAGAGGA 60.364 66.667 0.00 0.00 34.95 3.71
4013 5321 1.764054 CCCGCCTTCTGGAGAGGAT 60.764 63.158 0.00 0.00 34.95 3.24
4014 5322 1.745264 CCGCCTTCTGGAGAGGATC 59.255 63.158 0.00 0.00 34.95 3.36
4024 5332 1.506025 GGAGAGGATCCTGCTTTCCT 58.494 55.000 22.02 8.76 45.64 3.36
4025 5333 2.683768 GGAGAGGATCCTGCTTTCCTA 58.316 52.381 22.02 0.00 45.64 2.94
4026 5334 3.247162 GGAGAGGATCCTGCTTTCCTAT 58.753 50.000 22.02 0.00 45.64 2.57
4027 5335 3.260632 GGAGAGGATCCTGCTTTCCTATC 59.739 52.174 22.02 0.00 45.50 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 1090 4.246458 CCTGTACAAAGGAGTACTTCAGC 58.754 47.826 3.42 0.00 43.65 4.26
18 1094 3.893813 ACGACCTGTACAAAGGAGTACTT 59.106 43.478 8.09 0.00 43.65 2.24
29 1105 5.333299 AGCAACATTATACGACCTGTACA 57.667 39.130 0.00 0.00 35.44 2.90
68 1144 0.309922 GCATCCCTGCGAATGTGATG 59.690 55.000 0.00 0.00 38.92 3.07
79 1155 3.259064 CATGAAAAAGCAAGCATCCCTG 58.741 45.455 0.00 0.00 0.00 4.45
142 1218 2.210116 TCTTTCGTGCAAGGACAAGAC 58.790 47.619 0.00 0.00 29.61 3.01
170 1246 1.134965 CCATCTCTGTCCTGGTCGAAC 60.135 57.143 0.00 0.00 0.00 3.95
185 1261 2.602257 TGTTCATTCGATCGCCATCT 57.398 45.000 11.09 0.00 0.00 2.90
198 1274 5.898972 AGGGCATAAACATGGTATTGTTCAT 59.101 36.000 0.00 0.00 38.85 2.57
205 1281 3.721575 TCCTCAGGGCATAAACATGGTAT 59.278 43.478 0.00 0.00 0.00 2.73
211 1287 3.517296 TGTTTCCTCAGGGCATAAACA 57.483 42.857 4.64 4.64 35.71 2.83
217 1293 0.899717 GGCATTGTTTCCTCAGGGCA 60.900 55.000 0.00 0.00 0.00 5.36
235 1311 2.951642 CAGAGCCTCAGAGAGAAGTAGG 59.048 54.545 0.00 0.00 0.00 3.18
342 1418 0.692419 ACCCCCAGTCTGCTCCATAG 60.692 60.000 0.00 0.00 0.00 2.23
358 1434 2.360475 GTGCCTTGCTCCAGACCC 60.360 66.667 0.00 0.00 0.00 4.46
449 1525 9.079833 CAAGCAACCTATTTTGACTAATCAATG 57.920 33.333 0.00 0.00 44.36 2.82
538 1614 3.110358 GGTTGGTTTTGTTTAGACACGC 58.890 45.455 0.00 0.00 34.98 5.34
539 1615 4.099824 GTGGTTGGTTTTGTTTAGACACG 58.900 43.478 0.00 0.00 34.98 4.49
540 1616 4.082136 TGGTGGTTGGTTTTGTTTAGACAC 60.082 41.667 0.00 0.00 34.98 3.67
542 1618 4.158949 AGTGGTGGTTGGTTTTGTTTAGAC 59.841 41.667 0.00 0.00 0.00 2.59
544 1620 4.729227 AGTGGTGGTTGGTTTTGTTTAG 57.271 40.909 0.00 0.00 0.00 1.85
889 1966 2.504367 ACACCATTTTCGGAGACCAAG 58.496 47.619 0.00 0.00 34.32 3.61
1043 2121 0.317519 GGCAAGGTACAACGTTGTGC 60.318 55.000 37.43 35.22 43.57 4.57
1050 2128 3.263941 CCTGCGGCAAGGTACAAC 58.736 61.111 3.44 0.00 32.17 3.32
1132 2210 1.194781 AGAACCGCCACAGATCTGGT 61.195 55.000 26.08 11.58 33.30 4.00
1137 2215 1.568504 TAAGGAGAACCGCCACAGAT 58.431 50.000 0.00 0.00 41.83 2.90
1161 2239 4.455533 TGATCTCTCACAACAAAATTCCCG 59.544 41.667 0.00 0.00 0.00 5.14
1187 2265 3.446161 CCATACGACCTTAGAGTGGTTGA 59.554 47.826 7.11 0.00 40.54 3.18
1194 2272 2.287909 GCTCTGCCATACGACCTTAGAG 60.288 54.545 0.00 0.00 34.74 2.43
1204 2282 3.501445 GGATGATCAAAGCTCTGCCATAC 59.499 47.826 0.00 0.00 0.00 2.39
1465 2547 2.447408 TGCAGCCTCATGAATTGGAT 57.553 45.000 3.71 0.00 0.00 3.41
1479 2561 0.752743 TGACTTGCCCCATATGCAGC 60.753 55.000 7.95 7.95 40.35 5.25
1797 2879 5.844004 TGACAGTCTTCACTAGTTTCTTCC 58.156 41.667 1.31 0.00 0.00 3.46
1819 2901 0.179020 TGGTTCAGACAGGCCACTTG 60.179 55.000 5.01 0.00 0.00 3.16
1823 2905 0.895100 GCATTGGTTCAGACAGGCCA 60.895 55.000 5.01 0.00 0.00 5.36
1824 2906 0.610232 AGCATTGGTTCAGACAGGCC 60.610 55.000 0.00 0.00 0.00 5.19
1825 2907 2.113860 TAGCATTGGTTCAGACAGGC 57.886 50.000 0.00 0.00 0.00 4.85
1835 2917 1.024046 TGCGACGCAATAGCATTGGT 61.024 50.000 22.24 0.00 42.27 3.67
1891 2973 9.959749 TCCAAAAGTCAAATTAAGTAACACATC 57.040 29.630 0.00 0.00 0.00 3.06
1899 2981 9.476202 GCACTATTTCCAAAAGTCAAATTAAGT 57.524 29.630 0.00 0.00 0.00 2.24
1924 3006 1.315257 ATCTTGGCGTGGTGAATGGC 61.315 55.000 0.00 0.00 40.77 4.40
1936 3018 3.365364 GCTATACGCATGGAAATCTTGGC 60.365 47.826 0.00 0.00 38.92 4.52
1973 3058 0.107508 ATGCTGTATGCGTCCTTGCT 60.108 50.000 0.00 0.00 46.63 3.91
1982 3067 2.424601 ACCAACATGACATGCTGTATGC 59.575 45.455 15.49 0.12 40.59 3.14
2090 3175 9.893305 GTGTATAAGTGTAAACAGCAAGAAAAT 57.107 29.630 0.00 0.00 0.00 1.82
2581 3666 2.573869 CGTGCTCATGTCCCGTCT 59.426 61.111 0.00 0.00 0.00 4.18
2607 3692 1.100510 CGATGGTTCCACGGAGAGTA 58.899 55.000 0.00 0.00 0.00 2.59
2693 3778 2.571212 ACAATTCGAGGAGCACAACAA 58.429 42.857 0.00 0.00 0.00 2.83
2750 3844 2.092375 GCAGCATAAAGGGGGAAGTACT 60.092 50.000 0.00 0.00 0.00 2.73
2993 4087 1.789523 ATATGTACCACTGTCGCCCT 58.210 50.000 0.00 0.00 0.00 5.19
3034 4310 0.249120 TACCCGTACGTCGAGGAGAA 59.751 55.000 15.21 0.00 42.86 2.87
3130 4406 9.236691 CAATTGTATGACAAATACAAGTATGCC 57.763 33.333 14.27 0.00 44.56 4.40
3275 4556 3.904339 GGCTCTCTAAACCCATCTATCCA 59.096 47.826 0.00 0.00 0.00 3.41
3351 4636 6.838382 ACTATTGTTCTACAGTTTCAGGGTT 58.162 36.000 0.00 0.00 0.00 4.11
3477 4776 8.412608 TGATTAGTTTCTTTCTCTATTCGCTG 57.587 34.615 0.00 0.00 0.00 5.18
3558 4860 5.192327 AGCAAGATCTTTTGTTGGTCAAG 57.808 39.130 4.86 0.00 37.35 3.02
3569 4871 3.631227 GCATAGGCTCAAGCAAGATCTTT 59.369 43.478 4.86 0.00 44.36 2.52
3570 4872 3.212685 GCATAGGCTCAAGCAAGATCTT 58.787 45.455 0.88 0.88 44.36 2.40
3607 4909 9.110502 GGTTATTTTCAGAAATGGAGTACTAGG 57.889 37.037 0.00 0.00 36.22 3.02
3608 4910 9.110502 GGGTTATTTTCAGAAATGGAGTACTAG 57.889 37.037 0.00 0.00 36.22 2.57
3609 4911 8.050930 GGGGTTATTTTCAGAAATGGAGTACTA 58.949 37.037 0.00 0.00 36.22 1.82
3610 4912 6.890268 GGGGTTATTTTCAGAAATGGAGTACT 59.110 38.462 0.00 0.00 36.22 2.73
3611 4913 6.890268 AGGGGTTATTTTCAGAAATGGAGTAC 59.110 38.462 0.00 0.00 36.22 2.73
3612 4914 6.889722 CAGGGGTTATTTTCAGAAATGGAGTA 59.110 38.462 0.00 0.00 36.22 2.59
3613 4915 5.716703 CAGGGGTTATTTTCAGAAATGGAGT 59.283 40.000 0.00 0.00 36.22 3.85
3614 4916 5.127682 CCAGGGGTTATTTTCAGAAATGGAG 59.872 44.000 0.00 0.00 36.22 3.86
3615 4917 5.022787 CCAGGGGTTATTTTCAGAAATGGA 58.977 41.667 0.00 0.00 36.22 3.41
3616 4918 4.777366 ACCAGGGGTTATTTTCAGAAATGG 59.223 41.667 0.00 1.64 36.22 3.16
3617 4919 6.663523 AGTACCAGGGGTTATTTTCAGAAATG 59.336 38.462 0.00 0.00 37.09 2.32
3618 4920 6.800890 AGTACCAGGGGTTATTTTCAGAAAT 58.199 36.000 0.00 0.00 37.09 2.17
3619 4921 6.208840 AGTACCAGGGGTTATTTTCAGAAA 57.791 37.500 0.00 0.00 37.09 2.52
3620 4922 5.280830 GGAGTACCAGGGGTTATTTTCAGAA 60.281 44.000 0.00 0.00 37.09 3.02
3621 4923 4.226620 GGAGTACCAGGGGTTATTTTCAGA 59.773 45.833 0.00 0.00 37.09 3.27
3622 4924 4.018779 TGGAGTACCAGGGGTTATTTTCAG 60.019 45.833 0.00 0.00 41.77 3.02
3623 4925 3.917629 TGGAGTACCAGGGGTTATTTTCA 59.082 43.478 0.00 0.00 41.77 2.69
3624 4926 4.579647 TGGAGTACCAGGGGTTATTTTC 57.420 45.455 0.00 0.00 41.77 2.29
3643 4945 9.962783 GAGAGATGGAAATATTTTCAGAAATGG 57.037 33.333 14.43 0.00 36.22 3.16
3673 4975 1.212751 GCCGCTGGAACATTTGGAC 59.787 57.895 0.00 0.00 38.20 4.02
3689 4991 0.107456 AGACATCATCGTCATGGGCC 59.893 55.000 0.00 0.00 38.43 5.80
3692 4994 2.998670 GCCATAGACATCATCGTCATGG 59.001 50.000 13.54 13.54 41.95 3.66
3698 5000 9.201127 CCAAATATATAGCCATAGACATCATCG 57.799 37.037 0.00 0.00 0.00 3.84
3710 5015 6.331572 TCAGACCTTTCCCAAATATATAGCCA 59.668 38.462 0.00 0.00 0.00 4.75
3719 5024 6.547510 GCTATTACATCAGACCTTTCCCAAAT 59.452 38.462 0.00 0.00 0.00 2.32
3786 5094 1.312371 ATGCCACCGTTGTACATGCC 61.312 55.000 0.00 0.00 0.00 4.40
3787 5095 1.374560 TATGCCACCGTTGTACATGC 58.625 50.000 0.00 0.00 0.00 4.06
3788 5096 2.290367 CCATATGCCACCGTTGTACATG 59.710 50.000 0.00 0.00 0.00 3.21
3789 5097 2.171659 TCCATATGCCACCGTTGTACAT 59.828 45.455 0.00 0.00 0.00 2.29
3790 5098 1.555533 TCCATATGCCACCGTTGTACA 59.444 47.619 0.00 0.00 0.00 2.90
3791 5099 2.319136 TCCATATGCCACCGTTGTAC 57.681 50.000 0.00 0.00 0.00 2.90
3792 5100 3.388350 TGTATCCATATGCCACCGTTGTA 59.612 43.478 0.00 0.00 0.00 2.41
3793 5101 2.171659 TGTATCCATATGCCACCGTTGT 59.828 45.455 0.00 0.00 0.00 3.32
3794 5102 2.844946 TGTATCCATATGCCACCGTTG 58.155 47.619 0.00 0.00 0.00 4.10
3795 5103 3.788227 ATGTATCCATATGCCACCGTT 57.212 42.857 0.00 0.00 0.00 4.44
3804 5112 5.432720 TGTCATGGGGCATATGTATCCATAT 59.567 40.000 19.04 9.16 43.54 1.78
3805 5113 4.787534 TGTCATGGGGCATATGTATCCATA 59.212 41.667 19.04 7.91 36.55 2.74
3806 5114 3.592877 TGTCATGGGGCATATGTATCCAT 59.407 43.478 15.86 15.86 38.61 3.41
3807 5115 2.985311 TGTCATGGGGCATATGTATCCA 59.015 45.455 13.42 13.42 0.00 3.41
3808 5116 3.719268 TGTCATGGGGCATATGTATCC 57.281 47.619 4.29 4.59 0.00 2.59
3809 5117 6.040842 ACTTTTTGTCATGGGGCATATGTATC 59.959 38.462 4.29 0.00 0.00 2.24
3810 5118 5.898972 ACTTTTTGTCATGGGGCATATGTAT 59.101 36.000 4.29 0.00 0.00 2.29
3811 5119 5.268387 ACTTTTTGTCATGGGGCATATGTA 58.732 37.500 4.29 0.00 0.00 2.29
3812 5120 4.095946 ACTTTTTGTCATGGGGCATATGT 58.904 39.130 4.29 0.00 0.00 2.29
3813 5121 4.741321 ACTTTTTGTCATGGGGCATATG 57.259 40.909 0.00 0.00 0.00 1.78
3814 5122 7.436320 AATTACTTTTTGTCATGGGGCATAT 57.564 32.000 0.00 0.00 0.00 1.78
3815 5123 6.865834 AATTACTTTTTGTCATGGGGCATA 57.134 33.333 0.00 0.00 0.00 3.14
3816 5124 5.760484 AATTACTTTTTGTCATGGGGCAT 57.240 34.783 0.00 0.00 0.00 4.40
3817 5125 5.070981 TCAAATTACTTTTTGTCATGGGGCA 59.929 36.000 0.00 0.00 37.73 5.36
3818 5126 5.546526 TCAAATTACTTTTTGTCATGGGGC 58.453 37.500 0.00 0.00 37.73 5.80
3819 5127 6.165577 CCTCAAATTACTTTTTGTCATGGGG 58.834 40.000 0.00 0.00 37.73 4.96
3820 5128 5.639082 GCCTCAAATTACTTTTTGTCATGGG 59.361 40.000 0.00 0.00 37.73 4.00
3821 5129 6.222389 TGCCTCAAATTACTTTTTGTCATGG 58.778 36.000 0.00 0.00 37.73 3.66
3822 5130 7.816031 AGATGCCTCAAATTACTTTTTGTCATG 59.184 33.333 0.00 0.00 37.73 3.07
3823 5131 7.899973 AGATGCCTCAAATTACTTTTTGTCAT 58.100 30.769 0.00 0.00 37.73 3.06
3824 5132 7.288810 AGATGCCTCAAATTACTTTTTGTCA 57.711 32.000 0.00 0.00 37.73 3.58
3857 5165 4.262420 GGTAGCTTGCATTGGGAAGAAAAA 60.262 41.667 0.00 0.00 44.46 1.94
3858 5166 3.258123 GGTAGCTTGCATTGGGAAGAAAA 59.742 43.478 0.00 0.00 44.46 2.29
3859 5167 2.825532 GGTAGCTTGCATTGGGAAGAAA 59.174 45.455 0.00 0.00 44.46 2.52
3860 5168 2.224992 TGGTAGCTTGCATTGGGAAGAA 60.225 45.455 0.00 0.00 44.46 2.52
3861 5169 1.354031 TGGTAGCTTGCATTGGGAAGA 59.646 47.619 0.00 0.00 44.46 2.87
3862 5170 1.838112 TGGTAGCTTGCATTGGGAAG 58.162 50.000 0.00 0.00 44.50 3.46
3863 5171 2.530460 ATGGTAGCTTGCATTGGGAA 57.470 45.000 0.00 0.00 0.00 3.97
3864 5172 2.530460 AATGGTAGCTTGCATTGGGA 57.470 45.000 0.00 0.00 0.00 4.37
3865 5173 3.067180 CACTAATGGTAGCTTGCATTGGG 59.933 47.826 0.00 0.00 0.00 4.12
3866 5174 3.067180 CCACTAATGGTAGCTTGCATTGG 59.933 47.826 0.00 0.00 41.64 3.16
3867 5175 3.067180 CCCACTAATGGTAGCTTGCATTG 59.933 47.826 0.00 0.00 45.66 2.82
3868 5176 3.290710 CCCACTAATGGTAGCTTGCATT 58.709 45.455 0.00 0.00 45.66 3.56
3869 5177 2.936202 CCCACTAATGGTAGCTTGCAT 58.064 47.619 0.00 0.00 45.66 3.96
3870 5178 1.681780 GCCCACTAATGGTAGCTTGCA 60.682 52.381 0.00 0.00 45.66 4.08
3871 5179 1.025041 GCCCACTAATGGTAGCTTGC 58.975 55.000 0.00 0.00 45.66 4.01
3872 5180 1.212935 AGGCCCACTAATGGTAGCTTG 59.787 52.381 0.00 0.00 45.66 4.01
3873 5181 1.490910 GAGGCCCACTAATGGTAGCTT 59.509 52.381 0.00 0.00 45.66 3.74
3874 5182 1.132500 GAGGCCCACTAATGGTAGCT 58.868 55.000 0.00 0.00 45.66 3.32
3875 5183 0.837272 TGAGGCCCACTAATGGTAGC 59.163 55.000 0.00 0.00 45.66 3.58
3876 5184 3.864789 AATGAGGCCCACTAATGGTAG 57.135 47.619 0.00 0.00 45.66 3.18
3877 5185 5.718801 TTTAATGAGGCCCACTAATGGTA 57.281 39.130 0.00 0.00 45.66 3.25
3878 5186 4.601406 TTTAATGAGGCCCACTAATGGT 57.399 40.909 0.00 0.00 45.66 3.55
3879 5187 5.930837 TTTTTAATGAGGCCCACTAATGG 57.069 39.130 0.00 0.00 46.81 3.16
3905 5213 9.502091 TGCATGTGTACTAGAGTCTTTATTTTT 57.498 29.630 0.00 0.00 0.00 1.94
3906 5214 9.672673 ATGCATGTGTACTAGAGTCTTTATTTT 57.327 29.630 0.00 0.00 0.00 1.82
3907 5215 9.319143 GATGCATGTGTACTAGAGTCTTTATTT 57.681 33.333 2.46 0.00 0.00 1.40
3908 5216 8.700051 AGATGCATGTGTACTAGAGTCTTTATT 58.300 33.333 2.46 0.00 0.00 1.40
3909 5217 8.243961 AGATGCATGTGTACTAGAGTCTTTAT 57.756 34.615 2.46 0.00 0.00 1.40
3910 5218 7.558081 AGAGATGCATGTGTACTAGAGTCTTTA 59.442 37.037 2.46 0.00 0.00 1.85
3911 5219 6.379703 AGAGATGCATGTGTACTAGAGTCTTT 59.620 38.462 2.46 0.00 0.00 2.52
3912 5220 5.890985 AGAGATGCATGTGTACTAGAGTCTT 59.109 40.000 2.46 0.00 0.00 3.01
3913 5221 5.445069 AGAGATGCATGTGTACTAGAGTCT 58.555 41.667 2.46 0.00 0.00 3.24
3914 5222 5.766150 AGAGATGCATGTGTACTAGAGTC 57.234 43.478 2.46 0.00 0.00 3.36
3915 5223 6.361433 AGTAGAGATGCATGTGTACTAGAGT 58.639 40.000 26.28 7.72 30.07 3.24
3916 5224 6.875948 AGTAGAGATGCATGTGTACTAGAG 57.124 41.667 26.28 0.00 30.07 2.43
3917 5225 7.646548 AAAGTAGAGATGCATGTGTACTAGA 57.353 36.000 27.25 0.00 30.49 2.43
3918 5226 7.976175 TGAAAAGTAGAGATGCATGTGTACTAG 59.024 37.037 27.25 0.00 30.49 2.57
3919 5227 7.759886 GTGAAAAGTAGAGATGCATGTGTACTA 59.240 37.037 27.25 13.62 30.49 1.82
3920 5228 6.591834 GTGAAAAGTAGAGATGCATGTGTACT 59.408 38.462 23.22 23.22 32.62 2.73
3921 5229 6.591834 AGTGAAAAGTAGAGATGCATGTGTAC 59.408 38.462 19.88 19.88 0.00 2.90
3922 5230 6.701340 AGTGAAAAGTAGAGATGCATGTGTA 58.299 36.000 2.46 0.00 0.00 2.90
3923 5231 5.555017 AGTGAAAAGTAGAGATGCATGTGT 58.445 37.500 2.46 0.00 0.00 3.72
3924 5232 5.064452 GGAGTGAAAAGTAGAGATGCATGTG 59.936 44.000 2.46 0.00 0.00 3.21
3925 5233 5.181748 GGAGTGAAAAGTAGAGATGCATGT 58.818 41.667 2.46 0.00 0.00 3.21
3926 5234 5.064452 GTGGAGTGAAAAGTAGAGATGCATG 59.936 44.000 2.46 0.00 0.00 4.06
3927 5235 5.181748 GTGGAGTGAAAAGTAGAGATGCAT 58.818 41.667 0.00 0.00 0.00 3.96
3928 5236 4.563580 GGTGGAGTGAAAAGTAGAGATGCA 60.564 45.833 0.00 0.00 0.00 3.96
3929 5237 3.935828 GGTGGAGTGAAAAGTAGAGATGC 59.064 47.826 0.00 0.00 0.00 3.91
3930 5238 5.413309 AGGTGGAGTGAAAAGTAGAGATG 57.587 43.478 0.00 0.00 0.00 2.90
3931 5239 6.441088 AAAGGTGGAGTGAAAAGTAGAGAT 57.559 37.500 0.00 0.00 0.00 2.75
3932 5240 5.888982 AAAGGTGGAGTGAAAAGTAGAGA 57.111 39.130 0.00 0.00 0.00 3.10
3933 5241 6.055588 TGAAAAGGTGGAGTGAAAAGTAGAG 58.944 40.000 0.00 0.00 0.00 2.43
3934 5242 5.996644 TGAAAAGGTGGAGTGAAAAGTAGA 58.003 37.500 0.00 0.00 0.00 2.59
3935 5243 5.278022 GCTGAAAAGGTGGAGTGAAAAGTAG 60.278 44.000 0.00 0.00 0.00 2.57
3936 5244 4.578928 GCTGAAAAGGTGGAGTGAAAAGTA 59.421 41.667 0.00 0.00 0.00 2.24
3937 5245 3.381590 GCTGAAAAGGTGGAGTGAAAAGT 59.618 43.478 0.00 0.00 0.00 2.66
3938 5246 3.633986 AGCTGAAAAGGTGGAGTGAAAAG 59.366 43.478 0.00 0.00 0.00 2.27
3939 5247 3.631250 AGCTGAAAAGGTGGAGTGAAAA 58.369 40.909 0.00 0.00 0.00 2.29
3940 5248 3.297134 AGCTGAAAAGGTGGAGTGAAA 57.703 42.857 0.00 0.00 0.00 2.69
3941 5249 3.297134 AAGCTGAAAAGGTGGAGTGAA 57.703 42.857 0.00 0.00 0.00 3.18
3942 5250 3.297134 AAAGCTGAAAAGGTGGAGTGA 57.703 42.857 0.00 0.00 0.00 3.41
3943 5251 3.131046 ACAAAAGCTGAAAAGGTGGAGTG 59.869 43.478 0.00 0.00 0.00 3.51
3944 5252 3.365472 ACAAAAGCTGAAAAGGTGGAGT 58.635 40.909 0.00 0.00 0.00 3.85
3945 5253 3.381272 TGACAAAAGCTGAAAAGGTGGAG 59.619 43.478 0.00 0.00 0.00 3.86
3946 5254 3.130340 GTGACAAAAGCTGAAAAGGTGGA 59.870 43.478 0.00 0.00 0.00 4.02
3947 5255 3.447742 GTGACAAAAGCTGAAAAGGTGG 58.552 45.455 0.00 0.00 0.00 4.61
3948 5256 3.447742 GGTGACAAAAGCTGAAAAGGTG 58.552 45.455 0.00 0.00 0.00 4.00
3949 5257 2.099098 CGGTGACAAAAGCTGAAAAGGT 59.901 45.455 0.00 0.00 0.00 3.50
3950 5258 2.543653 CCGGTGACAAAAGCTGAAAAGG 60.544 50.000 0.00 0.00 0.00 3.11
3951 5259 2.357637 TCCGGTGACAAAAGCTGAAAAG 59.642 45.455 0.00 0.00 0.00 2.27
3952 5260 2.098443 GTCCGGTGACAAAAGCTGAAAA 59.902 45.455 0.00 0.00 41.37 2.29
3953 5261 1.673920 GTCCGGTGACAAAAGCTGAAA 59.326 47.619 0.00 0.00 41.37 2.69
3954 5262 1.305201 GTCCGGTGACAAAAGCTGAA 58.695 50.000 0.00 0.00 41.37 3.02
3955 5263 0.534203 GGTCCGGTGACAAAAGCTGA 60.534 55.000 0.00 0.00 43.65 4.26
3956 5264 0.817634 TGGTCCGGTGACAAAAGCTG 60.818 55.000 0.00 0.00 43.65 4.24
3957 5265 0.818040 GTGGTCCGGTGACAAAAGCT 60.818 55.000 0.00 0.00 43.65 3.74
3958 5266 1.098712 TGTGGTCCGGTGACAAAAGC 61.099 55.000 0.00 0.00 43.65 3.51
3959 5267 0.661020 GTGTGGTCCGGTGACAAAAG 59.339 55.000 0.00 0.00 43.65 2.27
3960 5268 0.253610 AGTGTGGTCCGGTGACAAAA 59.746 50.000 0.00 0.00 43.65 2.44
3961 5269 0.253610 AAGTGTGGTCCGGTGACAAA 59.746 50.000 0.00 0.00 43.65 2.83
3962 5270 0.253610 AAAGTGTGGTCCGGTGACAA 59.746 50.000 0.00 0.00 43.65 3.18
3963 5271 0.253610 AAAAGTGTGGTCCGGTGACA 59.746 50.000 0.00 0.00 43.65 3.58
3964 5272 1.332686 GAAAAAGTGTGGTCCGGTGAC 59.667 52.381 0.00 0.00 40.98 3.67
3965 5273 1.210967 AGAAAAAGTGTGGTCCGGTGA 59.789 47.619 0.00 0.00 0.00 4.02
3966 5274 1.602377 GAGAAAAAGTGTGGTCCGGTG 59.398 52.381 0.00 0.00 0.00 4.94
3967 5275 1.489230 AGAGAAAAAGTGTGGTCCGGT 59.511 47.619 0.00 0.00 0.00 5.28
3968 5276 2.256117 AGAGAAAAAGTGTGGTCCGG 57.744 50.000 0.00 0.00 0.00 5.14
3969 5277 5.744666 TTAAAGAGAAAAAGTGTGGTCCG 57.255 39.130 0.00 0.00 0.00 4.79
3970 5278 5.067283 TGCTTAAAGAGAAAAAGTGTGGTCC 59.933 40.000 0.00 0.00 0.00 4.46
3971 5279 5.971792 GTGCTTAAAGAGAAAAAGTGTGGTC 59.028 40.000 0.00 0.00 0.00 4.02
3972 5280 5.163550 GGTGCTTAAAGAGAAAAAGTGTGGT 60.164 40.000 0.00 0.00 0.00 4.16
3973 5281 5.281727 GGTGCTTAAAGAGAAAAAGTGTGG 58.718 41.667 0.00 0.00 0.00 4.17
3974 5282 5.281727 GGGTGCTTAAAGAGAAAAAGTGTG 58.718 41.667 0.00 0.00 0.00 3.82
3975 5283 4.036380 CGGGTGCTTAAAGAGAAAAAGTGT 59.964 41.667 0.00 0.00 0.00 3.55
3976 5284 4.537015 CGGGTGCTTAAAGAGAAAAAGTG 58.463 43.478 0.00 0.00 0.00 3.16
3977 5285 3.004419 GCGGGTGCTTAAAGAGAAAAAGT 59.996 43.478 0.00 0.00 38.39 2.66
3978 5286 3.565516 GCGGGTGCTTAAAGAGAAAAAG 58.434 45.455 0.00 0.00 38.39 2.27
3979 5287 2.295070 GGCGGGTGCTTAAAGAGAAAAA 59.705 45.455 0.00 0.00 42.25 1.94
3980 5288 1.883926 GGCGGGTGCTTAAAGAGAAAA 59.116 47.619 0.00 0.00 42.25 2.29
3981 5289 1.073284 AGGCGGGTGCTTAAAGAGAAA 59.927 47.619 0.00 0.00 42.25 2.52
3982 5290 0.690762 AGGCGGGTGCTTAAAGAGAA 59.309 50.000 0.00 0.00 42.25 2.87
3983 5291 0.690762 AAGGCGGGTGCTTAAAGAGA 59.309 50.000 0.00 0.00 42.25 3.10
3984 5292 1.087501 GAAGGCGGGTGCTTAAAGAG 58.912 55.000 0.00 0.00 42.25 2.85
3985 5293 0.690762 AGAAGGCGGGTGCTTAAAGA 59.309 50.000 0.00 0.00 42.25 2.52
3986 5294 0.804989 CAGAAGGCGGGTGCTTAAAG 59.195 55.000 0.00 0.00 42.25 1.85
3987 5295 0.608035 CCAGAAGGCGGGTGCTTAAA 60.608 55.000 0.00 0.00 42.25 1.52
3988 5296 1.002624 CCAGAAGGCGGGTGCTTAA 60.003 57.895 0.00 0.00 42.25 1.85
3989 5297 1.899437 CTCCAGAAGGCGGGTGCTTA 61.899 60.000 0.00 0.00 42.25 3.09
3990 5298 3.249189 TCCAGAAGGCGGGTGCTT 61.249 61.111 0.00 0.00 42.25 3.91
3991 5299 3.710722 CTCCAGAAGGCGGGTGCT 61.711 66.667 0.00 0.00 42.25 4.40
3992 5300 3.672295 CTCTCCAGAAGGCGGGTGC 62.672 68.421 0.00 0.00 41.71 5.01
3993 5301 2.581354 CTCTCCAGAAGGCGGGTG 59.419 66.667 0.00 0.00 33.74 4.61
3994 5302 2.537714 ATCCTCTCCAGAAGGCGGGT 62.538 60.000 0.00 0.00 33.74 5.28
3995 5303 1.753368 GATCCTCTCCAGAAGGCGGG 61.753 65.000 0.00 0.00 33.74 6.13
3996 5304 1.745264 GATCCTCTCCAGAAGGCGG 59.255 63.158 0.00 0.00 33.74 6.13
3997 5305 1.745264 GGATCCTCTCCAGAAGGCG 59.255 63.158 3.84 0.00 44.26 5.52
4005 5313 1.506025 AGGAAAGCAGGATCCTCTCC 58.494 55.000 12.69 15.00 42.44 3.71
4006 5314 4.535526 GATAGGAAAGCAGGATCCTCTC 57.464 50.000 12.69 6.88 42.44 3.20


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

AutoCloner maintained by Alex Coulton.