Multiple sequence alignment - TraesCS2D01G148300

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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 TraesCS2D01G148300 chr2D 100.000 8302 0 0 1 8302 89420143 89428444 0.000000e+00 15332.0
1 TraesCS2D01G148300 chr2A 92.557 6194 242 101 115 6165 89159396 89165513 0.000000e+00 8682.0
2 TraesCS2D01G148300 chr2A 96.179 1073 41 0 6410 7482 89165510 89166582 0.000000e+00 1755.0
3 TraesCS2D01G148300 chr2A 88.889 153 12 5 7542 7691 89167366 89167516 5.120000e-42 183.0
4 TraesCS2D01G148300 chr2A 93.151 73 5 0 1 73 89159316 89159388 3.170000e-19 108.0
5 TraesCS2D01G148300 chr2B 95.637 2544 75 19 3552 6065 142241678 142244215 0.000000e+00 4050.0
6 TraesCS2D01G148300 chr2B 91.111 2970 144 50 647 3552 142238684 142241597 0.000000e+00 3912.0
7 TraesCS2D01G148300 chr2B 94.033 1391 61 13 6094 7479 142244206 142245579 0.000000e+00 2089.0
8 TraesCS2D01G148300 chr2B 83.741 572 28 27 79 608 142237790 142238338 1.620000e-131 481.0
9 TraesCS2D01G148300 chr2B 88.352 352 30 11 7854 8197 142246568 142246916 6.000000e-111 412.0
10 TraesCS2D01G148300 chr2B 91.892 74 5 1 1 73 142237737 142237810 1.470000e-17 102.0
11 TraesCS2D01G148300 chrUn 88.608 79 5 3 6106 6183 261570662 261570587 8.870000e-15 93.5
12 TraesCS2D01G148300 chrUn 87.805 82 6 3 6103 6183 388894202 388894280 8.870000e-15 93.5
13 TraesCS2D01G148300 chr7D 88.462 78 8 1 8210 8286 182608425 182608348 8.870000e-15 93.5
14 TraesCS2D01G148300 chr5D 88.608 79 5 3 6106 6183 329128792 329128717 8.870000e-15 93.5
15 TraesCS2D01G148300 chr4B 88.608 79 5 3 6106 6183 70583075 70583000 8.870000e-15 93.5
16 TraesCS2D01G148300 chr3D 87.805 82 6 3 6103 6183 22479585 22479663 8.870000e-15 93.5
17 TraesCS2D01G148300 chr1A 87.805 82 6 3 6103 6183 393046685 393046763 8.870000e-15 93.5
18 TraesCS2D01G148300 chr1A 87.805 82 6 3 6103 6183 554479347 554479425 8.870000e-15 93.5
19 TraesCS2D01G148300 chr1A 82.524 103 14 3 8202 8300 442478014 442477912 4.130000e-13 87.9


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 TraesCS2D01G148300 chr2D 89420143 89428444 8301 False 15332 15332 100.000000 1 8302 1 chr2D.!!$F1 8301
1 TraesCS2D01G148300 chr2A 89159316 89167516 8200 False 2682 8682 92.694000 1 7691 4 chr2A.!!$F1 7690
2 TraesCS2D01G148300 chr2B 142237737 142246916 9179 False 1841 4050 90.794333 1 8197 6 chr2B.!!$F1 8196

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
50 51 0.106335 CCCTGGCAGATCAGTAGCAG 59.894 60.0 17.94 0.00 33.14 4.24 F
292 312 0.175760 CACCCATACCTCTGGTCGTG 59.824 60.0 0.00 0.00 37.09 4.35 F
661 1027 0.249405 CCGGAAGCAAGCAAGCAAAA 60.249 50.0 0.00 0.00 36.85 2.44 F
1172 1599 0.467659 CACCTACCTACCCCTCCTCG 60.468 65.0 0.00 0.00 0.00 4.63 F
2165 2627 0.677731 CCACGATGCAAGGGATGTGT 60.678 55.0 0.00 0.00 0.00 3.72 F
2166 2628 1.167851 CACGATGCAAGGGATGTGTT 58.832 50.0 0.00 0.00 0.00 3.32 F
3104 3581 1.746727 GCACACTATGCGACGCTCAG 61.747 60.0 22.08 18.77 46.55 3.35 F
4185 4754 0.526211 TCAGGGTCGTCAGTCAATCG 59.474 55.0 0.00 0.00 0.00 3.34 F
5157 5728 0.524862 CAGAATGCCACAGAACAGCC 59.475 55.0 0.00 0.00 0.00 4.85 F
6635 7234 0.043334 AGGCTGGAGTCTGGGTACAT 59.957 55.0 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1747 0.916358 CCCCCAGGAACCAGATGACT 60.916 60.000 0.00 0.00 33.47 3.41 R
1782 2241 1.073923 CCTTGGCTTGTAACCCAGTCT 59.926 52.381 0.00 0.00 31.73 3.24 R
2136 2598 2.491152 CATCGTGGGCCATGTTGC 59.509 61.111 24.48 3.13 0.00 4.17 R
2228 2690 2.634982 TGCTTTGATTAAGGCTTGCG 57.365 45.000 10.69 0.00 39.43 4.85 R
3270 3748 1.068333 GCACTTGGTTCAATGCGACAT 60.068 47.619 0.00 0.00 0.00 3.06 R
3900 4469 2.048601 TGCAACCCTTTCCATGCAC 58.951 52.632 0.00 0.00 43.32 4.57 R
4354 4923 2.027100 ACCAAACCCGAATCTCTTCCTC 60.027 50.000 0.00 0.00 0.00 3.71 R
6072 6670 1.651240 CCGTGAGCATTTCAGCCTGG 61.651 60.000 0.00 0.00 36.21 4.45 R
6902 7501 0.942410 TTTCGCACGGAGAGGTTTCG 60.942 55.000 0.00 0.00 0.00 3.46 R
7827 9414 0.741221 CTCTAGAACAAGCCGGCACC 60.741 60.000 31.54 12.22 0.00 5.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.270205 CAGTAGGCACCCTGGCAG 59.730 66.667 7.75 7.75 46.46 4.85
50 51 0.106335 CCCTGGCAGATCAGTAGCAG 59.894 60.000 17.94 0.00 33.14 4.24
73 74 7.470563 GCAGAGGCTAAATATGGCATAAAAGTT 60.471 37.037 11.86 6.35 34.13 2.66
75 76 7.231519 AGAGGCTAAATATGGCATAAAAGTTCC 59.768 37.037 11.86 8.74 34.13 3.62
76 77 6.267699 AGGCTAAATATGGCATAAAAGTTCCC 59.732 38.462 11.86 6.59 34.13 3.97
77 78 6.455647 GCTAAATATGGCATAAAAGTTCCCC 58.544 40.000 11.86 0.00 32.44 4.81
78 79 5.529581 AAATATGGCATAAAAGTTCCCCG 57.470 39.130 11.86 0.00 0.00 5.73
79 80 1.111277 ATGGCATAAAAGTTCCCCGC 58.889 50.000 0.00 0.00 0.00 6.13
81 82 0.892063 GGCATAAAAGTTCCCCGCAA 59.108 50.000 0.00 0.00 0.00 4.85
82 83 1.273886 GGCATAAAAGTTCCCCGCAAA 59.726 47.619 0.00 0.00 0.00 3.68
84 85 3.394719 GCATAAAAGTTCCCCGCAAAAA 58.605 40.909 0.00 0.00 0.00 1.94
104 105 4.687901 AAAAAGGCATAAAAGTGCAGGT 57.312 36.364 1.06 0.00 46.81 4.00
134 135 4.543590 AAGCATGTTAGCAGTACTCACT 57.456 40.909 0.00 0.00 36.85 3.41
207 210 2.226437 GTCGAGGATGATCAGAGAGCTC 59.774 54.545 5.27 5.27 0.00 4.09
210 213 2.821969 GAGGATGATCAGAGAGCTCCTC 59.178 54.545 19.88 19.88 42.28 3.71
217 220 3.290948 TCAGAGAGCTCCTCCTACTTC 57.709 52.381 10.93 0.00 42.97 3.01
222 225 3.037549 AGAGCTCCTCCTACTTCCATTG 58.962 50.000 10.93 0.00 0.00 2.82
265 285 2.133281 TGGATCAAATGCCAGTGGAG 57.867 50.000 15.20 0.00 0.00 3.86
280 300 2.138179 GGAGCTACCCGCACCCATA 61.138 63.158 0.00 0.00 42.80 2.74
286 306 1.046472 TACCCGCACCCATACCTCTG 61.046 60.000 0.00 0.00 0.00 3.35
287 307 2.505982 CCGCACCCATACCTCTGG 59.494 66.667 0.00 0.00 35.95 3.86
289 309 1.144057 CGCACCCATACCTCTGGTC 59.856 63.158 0.00 0.00 37.09 4.02
290 310 1.144057 GCACCCATACCTCTGGTCG 59.856 63.158 0.00 0.00 37.09 4.79
292 312 0.175760 CACCCATACCTCTGGTCGTG 59.824 60.000 0.00 0.00 37.09 4.35
296 340 1.182667 CATACCTCTGGTCGTGGTCA 58.817 55.000 0.00 0.00 39.97 4.02
307 351 0.676736 TCGTGGTCATACTGCACACA 59.323 50.000 2.79 0.00 32.58 3.72
324 368 0.827507 ACATTGGCGGCTCCTTTTGT 60.828 50.000 11.43 2.06 35.26 2.83
441 488 4.135153 CTGCTACTCGGTGCGGCT 62.135 66.667 0.00 0.00 0.00 5.52
485 532 1.120147 CATGCTACGCGCGTTGAAAC 61.120 55.000 40.36 25.84 43.27 2.78
491 538 4.736631 GCGCGTTGAAACTCGGCC 62.737 66.667 8.43 0.00 37.58 6.13
496 543 1.658114 GTTGAAACTCGGCCCCAAC 59.342 57.895 0.00 0.00 0.00 3.77
660 1026 1.363443 CCGGAAGCAAGCAAGCAAA 59.637 52.632 0.00 0.00 36.85 3.68
661 1027 0.249405 CCGGAAGCAAGCAAGCAAAA 60.249 50.000 0.00 0.00 36.85 2.44
662 1028 1.606224 CCGGAAGCAAGCAAGCAAAAT 60.606 47.619 0.00 0.00 36.85 1.82
663 1029 2.137523 CGGAAGCAAGCAAGCAAAATT 58.862 42.857 3.19 0.00 36.85 1.82
664 1030 2.096614 CGGAAGCAAGCAAGCAAAATTG 60.097 45.455 3.19 0.00 36.85 2.32
665 1031 3.132925 GGAAGCAAGCAAGCAAAATTGA 58.867 40.909 3.19 0.00 36.85 2.57
666 1032 3.560896 GGAAGCAAGCAAGCAAAATTGAA 59.439 39.130 3.19 0.00 36.85 2.69
667 1033 4.035441 GGAAGCAAGCAAGCAAAATTGAAA 59.965 37.500 3.19 0.00 36.85 2.69
828 1204 4.519437 CATCCGCTGCGCCAGAGA 62.519 66.667 18.00 8.53 33.20 3.10
886 1265 3.959478 GCTTTATTTTAGCCCCCGC 57.041 52.632 0.00 0.00 32.45 6.13
986 1389 1.862602 GCACGCCGAGGTTTCCATTT 61.863 55.000 0.00 0.00 0.00 2.32
990 1393 1.305930 GCCGAGGTTTCCATTTCGCT 61.306 55.000 0.00 0.00 0.00 4.93
994 1397 1.136774 GGTTTCCATTTCGCTCGCC 59.863 57.895 0.00 0.00 0.00 5.54
995 1398 1.226018 GTTTCCATTTCGCTCGCCG 60.226 57.895 0.00 0.00 38.61 6.46
1168 1595 2.132352 CCGCACCTACCTACCCCTC 61.132 68.421 0.00 0.00 0.00 4.30
1169 1596 2.132352 CGCACCTACCTACCCCTCC 61.132 68.421 0.00 0.00 0.00 4.30
1170 1597 1.313822 GCACCTACCTACCCCTCCT 59.686 63.158 0.00 0.00 0.00 3.69
1171 1598 0.759812 GCACCTACCTACCCCTCCTC 60.760 65.000 0.00 0.00 0.00 3.71
1172 1599 0.467659 CACCTACCTACCCCTCCTCG 60.468 65.000 0.00 0.00 0.00 4.63
1173 1600 1.153292 CCTACCTACCCCTCCTCGG 59.847 68.421 0.00 0.00 0.00 4.63
1174 1601 1.531128 CTACCTACCCCTCCTCGGC 60.531 68.421 0.00 0.00 0.00 5.54
1175 1602 2.998301 CTACCTACCCCTCCTCGGCC 62.998 70.000 0.00 0.00 0.00 6.13
1219 1646 2.721274 TCCGTTGCATTGATTGGTTG 57.279 45.000 0.00 0.00 0.00 3.77
1245 1678 1.666209 GGCGCCATGGTTGCTATTGT 61.666 55.000 24.80 0.00 0.00 2.71
1256 1689 4.873827 TGGTTGCTATTGTCTAAATCGACC 59.126 41.667 0.00 0.00 32.97 4.79
1258 1691 3.713288 TGCTATTGTCTAAATCGACCCG 58.287 45.455 0.00 0.00 32.97 5.28
1312 1747 2.889522 ATTAACTCCTAGGGGCTCCA 57.110 50.000 9.18 0.00 34.83 3.86
1380 1821 2.556287 CTGCGCGAGTTTGGTTCC 59.444 61.111 12.10 0.00 0.00 3.62
1395 1836 3.410508 TGGTTCCGCGGTAGTAATTTTT 58.589 40.909 27.15 0.00 0.00 1.94
1397 1838 4.391523 TGGTTCCGCGGTAGTAATTTTTAC 59.608 41.667 27.15 0.00 0.00 2.01
1406 1847 7.441864 GCGGTAGTAATTTTTACACAAATTGC 58.558 34.615 0.00 1.30 38.39 3.56
1414 1855 1.993956 TACACAAATTGCCTGGTGCT 58.006 45.000 0.00 0.00 42.00 4.40
1433 1874 2.226674 GCTCGGCTGCTAATAATTTCCC 59.773 50.000 0.00 0.00 0.00 3.97
1702 2161 0.935196 ACCGTGCTCAAGTCGTTTTC 59.065 50.000 0.00 0.00 0.00 2.29
1777 2236 2.437281 TGTGCATTGAATGGGGTTTGTT 59.563 40.909 7.35 0.00 0.00 2.83
1782 2241 1.500474 TGAATGGGGTTTGTTTGGCA 58.500 45.000 0.00 0.00 0.00 4.92
2114 2576 5.716228 GGGCATTGATCATTGGACCATATTA 59.284 40.000 17.03 0.00 0.00 0.98
2157 2619 1.597797 AACATGGCCCACGATGCAAG 61.598 55.000 0.00 0.00 0.00 4.01
2158 2620 2.440796 ATGGCCCACGATGCAAGG 60.441 61.111 0.00 0.00 0.00 3.61
2159 2621 4.738998 TGGCCCACGATGCAAGGG 62.739 66.667 0.00 11.36 45.68 3.95
2160 2622 4.424711 GGCCCACGATGCAAGGGA 62.425 66.667 17.93 0.00 45.80 4.20
2161 2623 2.124151 GCCCACGATGCAAGGGAT 60.124 61.111 17.93 0.00 45.80 3.85
2162 2624 2.484062 GCCCACGATGCAAGGGATG 61.484 63.158 17.93 1.29 45.80 3.51
2163 2625 1.077501 CCCACGATGCAAGGGATGT 60.078 57.895 10.44 0.00 45.80 3.06
2164 2626 1.378882 CCCACGATGCAAGGGATGTG 61.379 60.000 10.44 4.24 45.80 3.21
2165 2627 0.677731 CCACGATGCAAGGGATGTGT 60.678 55.000 0.00 0.00 0.00 3.72
2166 2628 1.167851 CACGATGCAAGGGATGTGTT 58.832 50.000 0.00 0.00 0.00 3.32
2202 2664 9.634021 ACACATGTCTAACTGAAGATAGAGATA 57.366 33.333 0.00 0.00 33.68 1.98
2228 2690 2.034558 AGTGGTTAGCACATGCACAAAC 59.965 45.455 17.00 7.31 45.16 2.93
2355 2817 8.389779 TCAAGTAACTTGAACAATATCTTGCA 57.610 30.769 0.00 0.00 45.84 4.08
2446 2908 5.621634 CGCAGACACGTCTCTTATATACTTG 59.378 44.000 0.00 0.00 37.98 3.16
2628 3097 8.708378 TCATTCAGGATATGACTACTTCATGTT 58.292 33.333 0.00 0.00 45.22 2.71
2768 3245 8.328758 AGTCCCATGAAACTTCATATTCAGTAA 58.671 33.333 4.66 0.00 45.62 2.24
2826 3303 7.028962 TCTATATTTGTGCTGTGCAAATGTTC 58.971 34.615 16.14 0.00 43.70 3.18
2943 3420 6.907206 ATGTTTGAAACAGTTGAACCATTG 57.093 33.333 16.43 0.00 45.95 2.82
3013 3490 3.677121 CAGCTGCGCTTACCATCTAATAG 59.323 47.826 9.73 0.00 36.40 1.73
3104 3581 1.746727 GCACACTATGCGACGCTCAG 61.747 60.000 22.08 18.77 46.55 3.35
3217 3695 2.607635 CGACATTCCCGAACTTGTATGG 59.392 50.000 0.00 0.00 0.00 2.74
3218 3696 3.677700 CGACATTCCCGAACTTGTATGGA 60.678 47.826 0.00 0.00 0.00 3.41
3406 3888 2.962421 TGTTCTTGTCATTTTCACCCCC 59.038 45.455 0.00 0.00 0.00 5.40
3544 4028 8.168790 TCACATGGTATACTGTAACGCTATAA 57.831 34.615 2.25 0.00 0.00 0.98
3545 4029 8.799367 TCACATGGTATACTGTAACGCTATAAT 58.201 33.333 2.25 0.00 0.00 1.28
3734 4303 3.777106 TCATGCAGTGATATCTTCCCC 57.223 47.619 3.98 0.00 0.00 4.81
3900 4469 1.808945 GTTGAGAAGATGTGGCCAGTG 59.191 52.381 5.11 0.00 0.00 3.66
4116 4685 7.282585 ACTTATTATATGTGCAGAGGAAAGCA 58.717 34.615 0.00 0.00 38.65 3.91
4185 4754 0.526211 TCAGGGTCGTCAGTCAATCG 59.474 55.000 0.00 0.00 0.00 3.34
4238 4807 7.896811 TGCGATACCTTTCATATAGATGTCTT 58.103 34.615 0.00 0.00 34.41 3.01
4354 4923 1.470098 GCAAGGATGGCTGTACAACTG 59.530 52.381 0.00 0.00 26.77 3.16
4366 4935 4.867608 GCTGTACAACTGAGGAAGAGATTC 59.132 45.833 0.00 0.00 0.00 2.52
4594 5164 3.069729 GGGTCTAGACTAAATGCGTGGAT 59.930 47.826 21.88 0.00 0.00 3.41
4739 5310 2.681848 CTCACCAGGCATGTCTGAATTC 59.318 50.000 28.72 0.00 36.93 2.17
4804 5375 3.429272 CCTTTATTGGGCGTGTACGAGTA 60.429 47.826 8.82 0.00 43.02 2.59
5031 5602 1.073284 GTTGCCTTTGGACAGACCCTA 59.927 52.381 0.00 0.00 38.00 3.53
5068 5639 9.195411 GATTACAGAAGTCATGCATTTTCAAAA 57.805 29.630 14.41 0.00 0.00 2.44
5156 5727 1.242076 ACAGAATGCCACAGAACAGC 58.758 50.000 0.00 0.00 42.53 4.40
5157 5728 0.524862 CAGAATGCCACAGAACAGCC 59.475 55.000 0.00 0.00 0.00 4.85
5173 5769 3.471680 ACAGCCAGTTTCTTGTTCTCTC 58.528 45.455 0.00 0.00 0.00 3.20
5202 5798 8.865978 TGTATACACGATAAACAATGTTCTGTC 58.134 33.333 0.08 0.00 0.00 3.51
5256 5852 3.797039 TGATATGGAGAAGTTTGCCTCG 58.203 45.455 0.00 0.00 0.00 4.63
5305 5901 7.436118 ACATGAACTAATTGTTGTGCTTCAAT 58.564 30.769 0.00 0.00 39.30 2.57
5353 5949 3.181503 CCTCTGTCTGGAATTGATTTGCG 60.182 47.826 0.00 0.00 0.00 4.85
5457 6053 2.485814 GGCTGACATGAAACCTTCTGAC 59.514 50.000 0.00 0.00 0.00 3.51
5514 6110 6.580788 TCAACATTTCTTTCAGGAAAATGCA 58.419 32.000 6.90 0.00 38.46 3.96
5560 6158 4.218852 TGAAATGCTCATTGAACTGATGCA 59.781 37.500 0.00 0.00 35.39 3.96
5595 6193 1.009829 CGTATGTGAAAGGCCAGCTC 58.990 55.000 5.01 0.00 0.00 4.09
5691 6289 6.676558 ACCAATTACTTCATGGGAATCATCT 58.323 36.000 0.00 0.00 38.58 2.90
5797 6395 8.475331 AACATCTCTTGCAATCATTCAAATTC 57.525 30.769 0.00 0.00 0.00 2.17
5805 6403 6.092092 TGCAATCATTCAAATTCTTGTACGG 58.908 36.000 0.00 0.00 33.94 4.02
5883 6481 3.848019 CGCAGCAATTGTTCAATCAGTAC 59.152 43.478 7.40 0.00 0.00 2.73
6090 6688 0.957395 ACCAGGCTGAAATGCTCACG 60.957 55.000 17.94 0.00 0.00 4.35
6093 6691 2.486966 GCTGAAATGCTCACGGCC 59.513 61.111 0.00 0.00 40.92 6.13
6116 6714 3.058501 CCGCTGGGTTGTTTACTTTACTG 60.059 47.826 0.00 0.00 0.00 2.74
6119 6717 4.581409 GCTGGGTTGTTTACTTTACTGGAA 59.419 41.667 0.00 0.00 0.00 3.53
6138 6736 7.054124 ACTGGAATTTTGAACTCAGAACACTA 58.946 34.615 0.00 0.00 0.00 2.74
6191 6789 9.397280 GAATCTATATTTAATAAGGCCCAGTCC 57.603 37.037 0.00 0.00 0.00 3.85
6195 6793 1.702022 TAATAAGGCCCAGTCCCCGC 61.702 60.000 0.00 0.00 0.00 6.13
6213 6811 3.056328 GGTGGTGCTCGCCTTTCC 61.056 66.667 0.86 0.00 42.62 3.13
6215 6813 2.035442 GTGGTGCTCGCCTTTCCTC 61.035 63.158 0.86 0.00 0.00 3.71
6261 6859 3.248024 AGTCATGGTTGGTAGAGTTCCA 58.752 45.455 0.00 0.00 0.00 3.53
6262 6860 3.846588 AGTCATGGTTGGTAGAGTTCCAT 59.153 43.478 0.00 0.00 39.14 3.41
6267 6865 6.208599 TCATGGTTGGTAGAGTTCCATTTTTC 59.791 38.462 0.00 0.00 36.86 2.29
6268 6866 4.517453 TGGTTGGTAGAGTTCCATTTTTCG 59.483 41.667 0.00 0.00 34.75 3.46
6292 6891 2.299867 CTGGTTGCCAGCCAGTTTTTAT 59.700 45.455 18.57 0.00 45.13 1.40
6314 6913 2.906691 ACTGATGGAGATGCAGTAGC 57.093 50.000 0.00 0.00 40.79 3.58
6364 6963 4.529377 AGAAACCGGTAAGGATCACAGTTA 59.471 41.667 8.00 0.00 45.00 2.24
6367 6966 6.549433 AACCGGTAAGGATCACAGTTATTA 57.451 37.500 8.00 0.00 45.00 0.98
6370 6969 8.253867 ACCGGTAAGGATCACAGTTATTATTA 57.746 34.615 4.49 0.00 45.00 0.98
6400 6999 6.039605 TGAACCATGCATGAATTGTACCATAG 59.960 38.462 28.31 8.60 0.00 2.23
6405 7004 7.175467 CCATGCATGAATTGTACCATAGTATGT 59.825 37.037 28.31 0.75 0.00 2.29
6464 7063 2.187958 TGCTTGCAGGTACCTAGTGAT 58.812 47.619 15.80 0.00 0.00 3.06
6635 7234 0.043334 AGGCTGGAGTCTGGGTACAT 59.957 55.000 0.00 0.00 0.00 2.29
6997 7596 3.376078 CGACGAAGACCCCGGGAA 61.376 66.667 26.32 0.00 0.00 3.97
7157 7756 0.964358 GCATGCTCAGCAGGAAAGGT 60.964 55.000 17.29 0.00 43.36 3.50
7242 7841 0.516877 TGATTCTTTTCCTGCACGCG 59.483 50.000 3.53 3.53 0.00 6.01
7293 7892 1.188863 GGCTGATGGCAAGGACAAAT 58.811 50.000 0.00 0.00 44.01 2.32
7294 7893 1.551883 GGCTGATGGCAAGGACAAATT 59.448 47.619 0.00 0.00 44.01 1.82
7313 7913 3.543680 TTGCTGTAGAATCTGGGTAGC 57.456 47.619 0.00 0.00 0.00 3.58
7475 8075 1.418097 TTTGGCTGGCACCTGAGAGA 61.418 55.000 2.29 0.00 0.00 3.10
7520 8867 4.763073 CTGGCACATCAGAGAGAAATGTA 58.237 43.478 0.00 0.00 38.20 2.29
7531 9114 6.708502 TCAGAGAGAAATGTAGTATCTCCGAG 59.291 42.308 0.00 0.00 40.34 4.63
7533 9116 5.942961 AGAGAAATGTAGTATCTCCGAGGA 58.057 41.667 0.00 0.00 40.34 3.71
7639 9222 2.455674 TGAGTGTTTATCAGCGTGCT 57.544 45.000 0.00 0.00 0.00 4.40
7640 9223 2.068519 TGAGTGTTTATCAGCGTGCTG 58.931 47.619 15.59 15.59 44.86 4.41
7670 9253 4.919754 GTGATGAAAAACATTCAGTGCTCC 59.080 41.667 0.00 0.00 39.56 4.70
7707 9290 1.251251 AAACATTCAGTGCTCCAGGC 58.749 50.000 0.00 0.00 42.22 4.85
7708 9291 0.403271 AACATTCAGTGCTCCAGGCT 59.597 50.000 0.00 0.00 42.39 4.58
7709 9292 1.279496 ACATTCAGTGCTCCAGGCTA 58.721 50.000 0.00 0.00 42.39 3.93
7710 9293 1.630369 ACATTCAGTGCTCCAGGCTAA 59.370 47.619 0.00 0.00 42.39 3.09
7711 9294 2.040278 ACATTCAGTGCTCCAGGCTAAA 59.960 45.455 0.00 0.00 42.39 1.85
7712 9295 2.479566 TTCAGTGCTCCAGGCTAAAG 57.520 50.000 0.00 0.00 42.39 1.85
7713 9296 1.352083 TCAGTGCTCCAGGCTAAAGT 58.648 50.000 0.00 0.00 42.39 2.66
7714 9297 1.276421 TCAGTGCTCCAGGCTAAAGTC 59.724 52.381 0.00 0.00 42.39 3.01
7715 9298 1.277557 CAGTGCTCCAGGCTAAAGTCT 59.722 52.381 0.00 0.00 42.39 3.24
7716 9299 2.497675 CAGTGCTCCAGGCTAAAGTCTA 59.502 50.000 0.00 0.00 42.39 2.59
7717 9300 3.055819 CAGTGCTCCAGGCTAAAGTCTAA 60.056 47.826 0.00 0.00 42.39 2.10
7718 9301 3.583086 AGTGCTCCAGGCTAAAGTCTAAA 59.417 43.478 0.00 0.00 42.39 1.85
7719 9302 4.041691 AGTGCTCCAGGCTAAAGTCTAAAA 59.958 41.667 0.00 0.00 42.39 1.52
7771 9358 5.163468 TGGAGCATTCTTGTTTTTGTTGCTA 60.163 36.000 0.00 0.00 38.93 3.49
7799 9386 3.728076 TGTCATTCTATACGCTGGTCC 57.272 47.619 0.00 0.00 0.00 4.46
7800 9387 3.028130 TGTCATTCTATACGCTGGTCCA 58.972 45.455 0.00 0.00 0.00 4.02
7801 9388 3.641436 TGTCATTCTATACGCTGGTCCAT 59.359 43.478 0.00 0.00 0.00 3.41
7802 9389 4.830600 TGTCATTCTATACGCTGGTCCATA 59.169 41.667 0.00 0.00 0.00 2.74
7803 9390 5.162075 GTCATTCTATACGCTGGTCCATAC 58.838 45.833 0.00 0.00 0.00 2.39
7804 9391 3.909776 TTCTATACGCTGGTCCATACG 57.090 47.619 11.76 11.76 0.00 3.06
7805 9392 2.156917 TCTATACGCTGGTCCATACGG 58.843 52.381 16.33 0.00 0.00 4.02
7806 9393 2.156917 CTATACGCTGGTCCATACGGA 58.843 52.381 16.33 9.98 39.79 4.69
7822 9409 2.631418 CGGACACGTGTATGAAGACT 57.369 50.000 23.44 0.00 34.81 3.24
7824 9411 3.314553 CGGACACGTGTATGAAGACTTT 58.685 45.455 23.44 0.00 34.81 2.66
7825 9412 3.739300 CGGACACGTGTATGAAGACTTTT 59.261 43.478 23.44 0.00 34.81 2.27
7826 9413 4.376008 CGGACACGTGTATGAAGACTTTTG 60.376 45.833 23.44 0.00 34.81 2.44
7827 9414 4.084013 GGACACGTGTATGAAGACTTTTGG 60.084 45.833 23.44 0.00 0.00 3.28
7831 9418 3.364964 CGTGTATGAAGACTTTTGGGTGC 60.365 47.826 0.00 0.00 0.00 5.01
7832 9419 3.057526 GTGTATGAAGACTTTTGGGTGCC 60.058 47.826 0.00 0.00 0.00 5.01
7833 9420 1.247567 ATGAAGACTTTTGGGTGCCG 58.752 50.000 0.00 0.00 0.00 5.69
7834 9421 0.821711 TGAAGACTTTTGGGTGCCGG 60.822 55.000 0.00 0.00 0.00 6.13
7835 9422 2.142357 GAAGACTTTTGGGTGCCGGC 62.142 60.000 22.73 22.73 0.00 6.13
7837 9424 2.123468 ACTTTTGGGTGCCGGCTT 60.123 55.556 29.70 0.00 0.00 4.35
7839 9426 2.443016 TTTTGGGTGCCGGCTTGT 60.443 55.556 29.70 0.00 0.00 3.16
7841 9428 2.022240 TTTTGGGTGCCGGCTTGTTC 62.022 55.000 29.70 12.95 0.00 3.18
7842 9429 2.920076 TTTGGGTGCCGGCTTGTTCT 62.920 55.000 29.70 0.00 0.00 3.01
7843 9430 2.058125 TTGGGTGCCGGCTTGTTCTA 62.058 55.000 29.70 1.01 0.00 2.10
7846 9433 0.741221 GGTGCCGGCTTGTTCTAGAG 60.741 60.000 29.70 0.00 0.00 2.43
7847 9434 1.079127 TGCCGGCTTGTTCTAGAGC 60.079 57.895 29.70 0.00 38.17 4.09
7848 9435 1.079127 GCCGGCTTGTTCTAGAGCA 60.079 57.895 22.15 5.01 40.63 4.26
7849 9436 0.462759 GCCGGCTTGTTCTAGAGCAT 60.463 55.000 22.15 0.00 40.63 3.79
7851 9438 2.359900 CCGGCTTGTTCTAGAGCATTT 58.640 47.619 10.32 0.00 40.63 2.32
7852 9439 2.749621 CCGGCTTGTTCTAGAGCATTTT 59.250 45.455 10.32 0.00 40.63 1.82
7853 9440 3.181506 CCGGCTTGTTCTAGAGCATTTTC 60.182 47.826 10.32 0.62 40.63 2.29
7854 9441 3.484229 CGGCTTGTTCTAGAGCATTTTCG 60.484 47.826 10.32 8.49 40.63 3.46
7855 9442 3.437049 GGCTTGTTCTAGAGCATTTTCGT 59.563 43.478 10.32 0.00 40.63 3.85
7856 9443 4.398247 GCTTGTTCTAGAGCATTTTCGTG 58.602 43.478 10.32 0.00 38.73 4.35
7869 9780 9.559958 AGAGCATTTTCGTGAACTTTTATAATG 57.440 29.630 0.00 0.00 0.00 1.90
7870 9781 9.554724 GAGCATTTTCGTGAACTTTTATAATGA 57.445 29.630 0.00 0.00 0.00 2.57
7912 9828 7.722795 AACTAACCATATTGTTGCCAAAAAC 57.277 32.000 2.51 0.00 33.44 2.43
7915 9831 6.557291 AACCATATTGTTGCCAAAAACATG 57.443 33.333 0.00 0.00 39.68 3.21
7921 9837 3.930336 TGTTGCCAAAAACATGTGTTCA 58.070 36.364 0.63 0.00 37.25 3.18
7929 9845 9.330063 TGCCAAAAACATGTGTTCATTATAAAA 57.670 25.926 0.63 0.00 37.25 1.52
7962 9878 0.238289 CGTTGTTCATGCTGGTCACC 59.762 55.000 0.00 0.00 0.00 4.02
8011 9927 6.204688 TGCAAAGTATGTAGAAAACTGACCAG 59.795 38.462 0.00 0.00 0.00 4.00
8017 9933 3.625764 TGTAGAAAACTGACCAGTGTTGC 59.374 43.478 10.08 3.45 38.90 4.17
8155 10072 2.498167 GCTCCTCAGCACTTCTTTCAA 58.502 47.619 0.00 0.00 46.06 2.69
8156 10073 2.225255 GCTCCTCAGCACTTCTTTCAAC 59.775 50.000 0.00 0.00 46.06 3.18
8176 10093 4.875544 ACATATACACATGCGAACCAAC 57.124 40.909 0.00 0.00 0.00 3.77
8177 10094 4.513442 ACATATACACATGCGAACCAACT 58.487 39.130 0.00 0.00 0.00 3.16
8179 10096 5.414454 ACATATACACATGCGAACCAACTTT 59.586 36.000 0.00 0.00 0.00 2.66
8181 10098 2.808244 ACACATGCGAACCAACTTTTG 58.192 42.857 0.00 0.00 0.00 2.44
8182 10099 2.165437 ACACATGCGAACCAACTTTTGT 59.835 40.909 0.00 0.00 0.00 2.83
8185 10102 3.616379 ACATGCGAACCAACTTTTGTTTG 59.384 39.130 0.00 0.00 41.35 2.93
8197 10114 7.147567 ACCAACTTTTGTTTGGATGGTTAGAAT 60.148 33.333 8.10 0.00 41.35 2.40
8198 10115 8.364142 CCAACTTTTGTTTGGATGGTTAGAATA 58.636 33.333 0.00 0.00 41.35 1.75
8199 10116 9.927668 CAACTTTTGTTTGGATGGTTAGAATAT 57.072 29.630 0.00 0.00 41.35 1.28
8201 10118 9.533831 ACTTTTGTTTGGATGGTTAGAATATCT 57.466 29.630 0.00 0.00 0.00 1.98
8204 10121 9.527157 TTTGTTTGGATGGTTAGAATATCTTCA 57.473 29.630 0.00 0.00 33.56 3.02
8205 10122 8.737168 TGTTTGGATGGTTAGAATATCTTCAG 57.263 34.615 0.00 0.00 33.56 3.02
8206 10123 8.328758 TGTTTGGATGGTTAGAATATCTTCAGT 58.671 33.333 0.00 0.00 33.56 3.41
8207 10124 9.832445 GTTTGGATGGTTAGAATATCTTCAGTA 57.168 33.333 0.00 0.00 33.56 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.821033 ACTGCCTACTTTTCATGGTGTTC 59.179 43.478 0.00 0.00 0.00 3.18
50 51 7.371159 GGAACTTTTATGCCATATTTAGCCTC 58.629 38.462 0.00 0.00 0.00 4.70
61 62 0.251386 TGCGGGGAACTTTTATGCCA 60.251 50.000 0.00 0.00 0.00 4.92
84 85 3.640967 TGACCTGCACTTTTATGCCTTTT 59.359 39.130 0.00 0.00 45.50 2.27
85 86 3.230134 TGACCTGCACTTTTATGCCTTT 58.770 40.909 0.00 0.00 45.50 3.11
86 87 2.875296 TGACCTGCACTTTTATGCCTT 58.125 42.857 0.00 0.00 45.50 4.35
87 88 2.584835 TGACCTGCACTTTTATGCCT 57.415 45.000 0.00 0.00 45.50 4.75
88 89 2.558359 ACTTGACCTGCACTTTTATGCC 59.442 45.455 0.00 0.00 45.50 4.40
89 90 3.568538 CACTTGACCTGCACTTTTATGC 58.431 45.455 0.00 0.00 46.32 3.14
90 91 3.004629 TGCACTTGACCTGCACTTTTATG 59.995 43.478 0.00 0.00 39.76 1.90
91 92 3.221771 TGCACTTGACCTGCACTTTTAT 58.778 40.909 0.00 0.00 39.76 1.40
92 93 2.649190 TGCACTTGACCTGCACTTTTA 58.351 42.857 0.00 0.00 39.76 1.52
104 105 2.622470 TGCTAACATGCTTTGCACTTGA 59.378 40.909 11.00 0.00 43.04 3.02
134 135 1.384525 AACTTTGTGTTGCGCCACTA 58.615 45.000 13.27 5.06 37.52 2.74
207 210 4.301072 TTTGACCAATGGAAGTAGGAGG 57.699 45.455 6.16 0.00 0.00 4.30
210 213 5.982890 ACAATTTGACCAATGGAAGTAGG 57.017 39.130 6.16 0.00 0.00 3.18
278 298 2.160721 ATGACCACGACCAGAGGTAT 57.839 50.000 0.00 0.00 44.02 2.73
280 300 1.183549 GTATGACCACGACCAGAGGT 58.816 55.000 0.00 0.00 46.71 3.85
286 306 0.037697 TGTGCAGTATGACCACGACC 60.038 55.000 0.00 0.00 39.69 4.79
287 307 1.068474 GTGTGCAGTATGACCACGAC 58.932 55.000 0.00 0.00 39.69 4.34
289 309 1.725641 ATGTGTGCAGTATGACCACG 58.274 50.000 0.00 0.00 39.69 4.94
290 310 2.162208 CCAATGTGTGCAGTATGACCAC 59.838 50.000 0.00 0.00 39.69 4.16
292 312 1.133025 GCCAATGTGTGCAGTATGACC 59.867 52.381 0.00 0.00 39.69 4.02
296 340 1.656818 GCCGCCAATGTGTGCAGTAT 61.657 55.000 0.00 0.00 0.00 2.12
307 351 1.047801 AAACAAAAGGAGCCGCCAAT 58.952 45.000 0.00 0.00 40.02 3.16
324 368 4.761975 ACTCGGTTCCTAATTGCGATAAA 58.238 39.130 0.00 0.00 0.00 1.40
491 538 1.291906 GTCCAAATTGCCGGTTGGG 59.708 57.895 18.62 6.09 43.82 4.12
496 543 1.291906 GTTGGGTCCAAATTGCCGG 59.708 57.895 3.74 0.00 37.70 6.13
553 604 1.826720 GACGGGTTGGGAGTGTGTATA 59.173 52.381 0.00 0.00 0.00 1.47
554 605 0.611714 GACGGGTTGGGAGTGTGTAT 59.388 55.000 0.00 0.00 0.00 2.29
555 606 1.808531 CGACGGGTTGGGAGTGTGTA 61.809 60.000 0.00 0.00 0.00 2.90
558 609 1.911766 ATCGACGGGTTGGGAGTGT 60.912 57.895 0.00 0.00 0.00 3.55
561 612 2.511600 GCATCGACGGGTTGGGAG 60.512 66.667 0.00 0.00 0.00 4.30
614 666 0.036577 CTGATGGGATCGGATGGAGC 60.037 60.000 0.00 0.00 37.90 4.70
660 1026 1.886542 GACCCGCTCTGGTTTTCAATT 59.113 47.619 0.00 0.00 39.24 2.32
661 1027 1.202879 TGACCCGCTCTGGTTTTCAAT 60.203 47.619 0.00 0.00 39.24 2.57
662 1028 0.181587 TGACCCGCTCTGGTTTTCAA 59.818 50.000 0.00 0.00 39.24 2.69
663 1029 0.534203 GTGACCCGCTCTGGTTTTCA 60.534 55.000 0.00 0.00 39.24 2.69
664 1030 1.566018 CGTGACCCGCTCTGGTTTTC 61.566 60.000 0.00 0.00 39.24 2.29
665 1031 1.597027 CGTGACCCGCTCTGGTTTT 60.597 57.895 0.00 0.00 39.24 2.43
666 1032 2.030562 CGTGACCCGCTCTGGTTT 59.969 61.111 0.00 0.00 39.24 3.27
667 1033 4.003788 CCGTGACCCGCTCTGGTT 62.004 66.667 0.00 0.00 39.24 3.67
886 1265 2.283894 GCAAAAGGTGGGGAGGGG 60.284 66.667 0.00 0.00 0.00 4.79
968 1371 0.168128 GAAATGGAAACCTCGGCGTG 59.832 55.000 6.85 3.87 0.00 5.34
969 1372 1.296056 CGAAATGGAAACCTCGGCGT 61.296 55.000 6.85 0.00 0.00 5.68
970 1373 1.423845 CGAAATGGAAACCTCGGCG 59.576 57.895 0.00 0.00 0.00 6.46
971 1374 1.136774 GCGAAATGGAAACCTCGGC 59.863 57.895 0.00 0.00 0.00 5.54
972 1375 0.727398 GAGCGAAATGGAAACCTCGG 59.273 55.000 0.00 0.00 0.00 4.63
973 1376 0.370273 CGAGCGAAATGGAAACCTCG 59.630 55.000 0.00 0.00 36.65 4.63
974 1377 0.097150 GCGAGCGAAATGGAAACCTC 59.903 55.000 0.00 0.00 0.00 3.85
975 1378 1.305930 GGCGAGCGAAATGGAAACCT 61.306 55.000 0.00 0.00 0.00 3.50
976 1379 1.136774 GGCGAGCGAAATGGAAACC 59.863 57.895 0.00 0.00 0.00 3.27
977 1380 1.226018 CGGCGAGCGAAATGGAAAC 60.226 57.895 0.00 0.00 0.00 2.78
978 1381 2.395360 CCGGCGAGCGAAATGGAAA 61.395 57.895 9.30 0.00 0.00 3.13
990 1393 1.252215 TTATATCCATCGGCCGGCGA 61.252 55.000 27.83 20.18 0.00 5.54
994 1397 0.528924 TCCGTTATATCCATCGGCCG 59.471 55.000 22.12 22.12 42.28 6.13
995 1398 1.134788 CCTCCGTTATATCCATCGGCC 60.135 57.143 0.00 0.00 42.28 6.13
1168 1595 4.888325 ATCAGGGAGGGGCCGAGG 62.888 72.222 0.00 0.00 37.63 4.63
1169 1596 3.237741 GATCAGGGAGGGGCCGAG 61.238 72.222 0.00 0.00 37.63 4.63
1173 1600 3.468326 GAAGCGATCAGGGAGGGGC 62.468 68.421 0.00 0.00 0.00 5.80
1174 1601 2.812619 GGAAGCGATCAGGGAGGGG 61.813 68.421 0.00 0.00 0.00 4.79
1175 1602 2.812619 GGGAAGCGATCAGGGAGGG 61.813 68.421 0.00 0.00 0.00 4.30
1235 1668 4.025979 CGGGTCGATTTAGACAATAGCAAC 60.026 45.833 0.00 0.00 42.62 4.17
1245 1678 5.047847 CAGATTAAAGCGGGTCGATTTAGA 58.952 41.667 9.94 4.12 45.65 2.10
1256 1689 5.371115 TCAAAGGTTTCAGATTAAAGCGG 57.629 39.130 0.00 0.00 40.80 5.52
1258 1691 7.062255 CGGAAATCAAAGGTTTCAGATTAAAGC 59.938 37.037 5.26 0.00 37.32 3.51
1312 1747 0.916358 CCCCCAGGAACCAGATGACT 60.916 60.000 0.00 0.00 33.47 3.41
1337 1774 2.835605 TCGCAACCGAACTCCATTC 58.164 52.632 0.00 0.00 41.17 2.67
1380 1821 7.650217 CAATTTGTGTAAAAATTACTACCGCG 58.350 34.615 0.00 0.00 37.59 6.46
1406 1847 2.599645 ATTAGCAGCCGAGCACCAGG 62.600 60.000 0.00 0.00 36.85 4.45
1414 1855 2.441750 AGGGGAAATTATTAGCAGCCGA 59.558 45.455 0.00 0.00 0.00 5.54
1433 1874 3.200593 GCACAGCGATGGAGCAGG 61.201 66.667 14.22 0.00 40.15 4.85
1617 2076 4.566907 GGCAGTCACCCCTTGATAGTTTTA 60.567 45.833 0.00 0.00 36.32 1.52
1702 2161 2.878406 TGACAGCTTCGAAAAAGGAAGG 59.122 45.455 0.00 0.00 40.92 3.46
1777 2236 1.817740 GCTTGTAACCCAGTCTGCCAA 60.818 52.381 0.00 0.00 0.00 4.52
1782 2241 1.073923 CCTTGGCTTGTAACCCAGTCT 59.926 52.381 0.00 0.00 31.73 3.24
2114 2576 3.658398 CCACCAGTGGCAGAATTCT 57.342 52.632 9.78 0.88 44.73 2.40
2136 2598 2.491152 CATCGTGGGCCATGTTGC 59.509 61.111 24.48 3.13 0.00 4.17
2157 2619 3.897239 TGTTATCATCCCAACACATCCC 58.103 45.455 0.00 0.00 29.93 3.85
2163 2625 5.178096 AGACATGTGTTATCATCCCAACA 57.822 39.130 1.15 0.00 32.40 3.33
2164 2626 6.823689 AGTTAGACATGTGTTATCATCCCAAC 59.176 38.462 1.15 0.00 0.00 3.77
2165 2627 6.823182 CAGTTAGACATGTGTTATCATCCCAA 59.177 38.462 1.15 0.00 0.00 4.12
2166 2628 6.156083 TCAGTTAGACATGTGTTATCATCCCA 59.844 38.462 1.15 0.00 0.00 4.37
2228 2690 2.634982 TGCTTTGATTAAGGCTTGCG 57.365 45.000 10.69 0.00 39.43 4.85
2446 2908 4.095483 CCAGTGTAATGGCTCTGAACATTC 59.905 45.833 9.63 4.80 38.24 2.67
2628 3097 9.270640 CCATTCAAGAAACAAATTACCAAATCA 57.729 29.630 0.00 0.00 0.00 2.57
2768 3245 7.944729 AATTCTAGTAACCAATGCAGTCATT 57.055 32.000 0.00 0.00 43.31 2.57
2804 3281 5.636121 CAGAACATTTGCACAGCACAAATAT 59.364 36.000 1.74 0.00 43.94 1.28
2826 3303 2.733552 CAGCGCAATAGTATACCTGCAG 59.266 50.000 11.47 6.78 33.56 4.41
2943 3420 6.019779 ACTCAGACTCATGTTAGTGAAGAC 57.980 41.667 0.00 0.00 0.00 3.01
3046 3523 9.787435 AACACACTCCAAAACAGTATATCTTAA 57.213 29.630 0.00 0.00 0.00 1.85
3104 3581 7.575155 GCCTAGGAAAGTCAAACTTGATTAACC 60.575 40.741 14.75 0.11 38.66 2.85
3217 3695 6.593770 ACAAGTTTTGTGGTTCCAAAATCTTC 59.406 34.615 2.80 0.00 43.82 2.87
3218 3696 6.472016 ACAAGTTTTGTGGTTCCAAAATCTT 58.528 32.000 2.80 6.28 43.82 2.40
3270 3748 1.068333 GCACTTGGTTCAATGCGACAT 60.068 47.619 0.00 0.00 0.00 3.06
3734 4303 6.903883 AATTACACCTAAGAAGTGCATACG 57.096 37.500 0.00 0.00 38.87 3.06
3900 4469 2.048601 TGCAACCCTTTCCATGCAC 58.951 52.632 0.00 0.00 43.32 4.57
4116 4685 4.568592 CCCAAGTAAAGGCTTTGGATCTCT 60.569 45.833 22.32 7.95 34.31 3.10
4238 4807 5.658634 AGATTTATGCAGTGAGTACCAGAGA 59.341 40.000 0.00 0.00 0.00 3.10
4354 4923 2.027100 ACCAAACCCGAATCTCTTCCTC 60.027 50.000 0.00 0.00 0.00 3.71
4366 4935 3.253677 TGTTTGCTGTAATACCAAACCCG 59.746 43.478 16.78 0.00 44.58 5.28
4436 5005 5.175126 CGTAAAGCCTGTAGGTCATAAATCG 59.825 44.000 0.00 0.00 37.57 3.34
4491 5060 9.753674 AGGATATTAAAAGAATGGACTTCACAA 57.246 29.630 0.00 0.00 36.24 3.33
4492 5061 9.753674 AAGGATATTAAAAGAATGGACTTCACA 57.246 29.630 0.00 0.00 36.24 3.58
4739 5310 3.259064 CACCAACAAGGACCTATACACG 58.741 50.000 0.00 0.00 41.22 4.49
4804 5375 2.226962 ATGGAGGCTCAACAAAGCAT 57.773 45.000 17.69 5.61 44.35 3.79
5031 5602 7.540474 TGACTTCTGTAATCTAACCTCAACT 57.460 36.000 0.00 0.00 0.00 3.16
5156 5727 7.736447 ATACAAAGAGAGAACAAGAAACTGG 57.264 36.000 0.00 0.00 0.00 4.00
5157 5728 9.261180 TGTATACAAAGAGAGAACAAGAAACTG 57.739 33.333 2.20 0.00 0.00 3.16
5202 5798 7.599998 AGCATGTTAGGCTGTAAAAGAAATTTG 59.400 33.333 0.00 0.00 40.80 2.32
5256 5852 4.996788 TTTACCTGTAGATTCCGACTCC 57.003 45.455 0.00 0.00 0.00 3.85
5333 5929 3.411446 ACGCAAATCAATTCCAGACAGA 58.589 40.909 0.00 0.00 0.00 3.41
5457 6053 4.082245 GGTGTTGAGAACATACCATTTGGG 60.082 45.833 0.96 0.00 44.35 4.12
5691 6289 8.577296 TCTCGAACTTGAAGAGAAAGAAGATTA 58.423 33.333 0.00 0.00 38.00 1.75
5759 6357 5.565439 GCAAGAGATGTTATGGCTTTGTTGT 60.565 40.000 0.00 0.00 0.00 3.32
5797 6395 5.545658 AAGCATGTAATCAACCGTACAAG 57.454 39.130 0.00 0.00 34.08 3.16
5805 6403 6.715464 AGTATACGCAAAGCATGTAATCAAC 58.285 36.000 0.00 0.00 0.00 3.18
5861 6459 2.937591 ACTGATTGAACAATTGCTGCG 58.062 42.857 5.05 0.00 0.00 5.18
5883 6481 4.826274 TGTCCTCCTCTCAGTTTATTGG 57.174 45.455 0.00 0.00 0.00 3.16
6072 6670 1.651240 CCGTGAGCATTTCAGCCTGG 61.651 60.000 0.00 0.00 36.21 4.45
6107 6705 9.621629 TTCTGAGTTCAAAATTCCAGTAAAGTA 57.378 29.630 0.00 0.00 0.00 2.24
6116 6714 9.827411 GTTATAGTGTTCTGAGTTCAAAATTCC 57.173 33.333 0.00 0.00 0.00 3.01
6119 6717 9.003658 CCTGTTATAGTGTTCTGAGTTCAAAAT 57.996 33.333 0.00 0.00 0.00 1.82
6167 6765 7.091947 GGGGACTGGGCCTTATTAAATATAGAT 60.092 40.741 4.53 0.00 0.00 1.98
6195 6793 3.423154 GAAAGGCGAGCACCACCG 61.423 66.667 0.00 0.00 0.00 4.94
6213 6811 4.082026 CCTTGGTGGCATTCTTTTAAGGAG 60.082 45.833 0.00 0.00 36.43 3.69
6215 6813 3.055891 CCCTTGGTGGCATTCTTTTAAGG 60.056 47.826 0.00 0.00 34.63 2.69
6292 6891 4.162131 TGCTACTGCATCTCCATCAGTTAA 59.838 41.667 0.00 0.00 45.31 2.01
6306 6905 4.875536 CACAATGGTAGTATTGCTACTGCA 59.124 41.667 11.07 3.32 46.99 4.41
6314 6913 7.429633 TCCAAACAAACACAATGGTAGTATTG 58.570 34.615 0.00 0.00 42.38 1.90
6323 6922 6.143758 CGGTTTCTATCCAAACAAACACAATG 59.856 38.462 0.00 0.00 37.91 2.82
6364 6963 5.706833 TCATGCATGGTTCAGCGATAATAAT 59.293 36.000 25.97 0.00 0.00 1.28
6367 6966 3.479489 TCATGCATGGTTCAGCGATAAT 58.521 40.909 25.97 0.00 0.00 1.28
6370 6969 1.753930 TTCATGCATGGTTCAGCGAT 58.246 45.000 25.97 0.00 0.00 4.58
6400 6999 6.466413 CGACTAGCTCGCATTAAGATACATAC 59.534 42.308 0.00 0.00 35.06 2.39
6464 7063 4.149511 TGTTCCACACAGTTCATCTTCA 57.850 40.909 0.00 0.00 0.00 3.02
6809 7408 3.664025 CTTGCGGAGGTGGCGATGA 62.664 63.158 0.00 0.00 0.00 2.92
6902 7501 0.942410 TTTCGCACGGAGAGGTTTCG 60.942 55.000 0.00 0.00 0.00 3.46
6990 7589 3.136123 CATGCTGCTGTTCCCGGG 61.136 66.667 16.85 16.85 0.00 5.73
6992 7591 2.046023 TCCATGCTGCTGTTCCCG 60.046 61.111 0.00 0.00 0.00 5.14
6997 7596 3.677284 CTCCGCTCCATGCTGCTGT 62.677 63.158 0.00 0.00 40.11 4.40
7026 7625 4.463879 CTCGGGGCTGGAGTGCTG 62.464 72.222 0.00 0.00 0.00 4.41
7027 7626 4.704103 TCTCGGGGCTGGAGTGCT 62.704 66.667 5.50 0.00 33.26 4.40
7052 7651 1.801913 CTTTGTCGGGCTCTCGTCG 60.802 63.158 0.00 0.00 0.00 5.12
7157 7756 1.774254 TCTTCCTTGCCCTTGTCAAGA 59.226 47.619 14.42 0.00 42.52 3.02
7293 7892 2.837591 TGCTACCCAGATTCTACAGCAA 59.162 45.455 7.72 0.00 34.82 3.91
7294 7893 2.432146 CTGCTACCCAGATTCTACAGCA 59.568 50.000 9.14 9.14 44.64 4.41
7313 7913 5.710984 AGAAACGTCAACCTCTATGTACTG 58.289 41.667 0.00 0.00 0.00 2.74
7505 8852 7.227873 TCGGAGATACTACATTTCTCTCTGAT 58.772 38.462 5.51 0.00 41.25 2.90
7520 8867 3.314307 TCCATGTTCCTCGGAGATACT 57.686 47.619 6.58 0.00 33.89 2.12
7531 9114 3.303881 GAGCCAAAAACTCCATGTTCC 57.696 47.619 0.00 0.00 38.03 3.62
7609 9192 7.998212 CGCTGATAAACACTCAAAAATGTTTTC 59.002 33.333 7.58 6.44 44.61 2.29
7613 9196 5.914635 CACGCTGATAAACACTCAAAAATGT 59.085 36.000 0.00 0.00 0.00 2.71
7639 9222 9.381033 ACTGAATGTTTTTCATCACAAAAATCA 57.619 25.926 0.00 0.00 37.52 2.57
7640 9223 9.640974 CACTGAATGTTTTTCATCACAAAAATC 57.359 29.630 0.00 0.00 37.52 2.17
7688 9271 1.251251 GCCTGGAGCACTGAATGTTT 58.749 50.000 0.00 0.00 42.97 2.83
7718 9301 7.494298 ACGCTTTTGAAACATCCTGTTATTTTT 59.506 29.630 0.00 0.00 40.14 1.94
7719 9302 6.983890 ACGCTTTTGAAACATCCTGTTATTTT 59.016 30.769 0.00 0.00 40.14 1.82
7722 9305 5.705609 ACGCTTTTGAAACATCCTGTTAT 57.294 34.783 0.00 0.00 40.14 1.89
7738 9321 3.181476 ACAAGAATGCTCCAAAACGCTTT 60.181 39.130 0.00 0.00 0.00 3.51
7741 9324 2.422276 ACAAGAATGCTCCAAAACGC 57.578 45.000 0.00 0.00 0.00 4.84
7742 9325 5.063312 ACAAAAACAAGAATGCTCCAAAACG 59.937 36.000 0.00 0.00 0.00 3.60
7743 9326 6.421377 ACAAAAACAAGAATGCTCCAAAAC 57.579 33.333 0.00 0.00 0.00 2.43
7744 9327 6.622462 GCAACAAAAACAAGAATGCTCCAAAA 60.622 34.615 0.00 0.00 0.00 2.44
7748 9331 4.122046 AGCAACAAAAACAAGAATGCTCC 58.878 39.130 0.00 0.00 38.16 4.70
7750 9333 5.068987 TCCTAGCAACAAAAACAAGAATGCT 59.931 36.000 0.00 0.00 44.17 3.79
7751 9334 5.288804 TCCTAGCAACAAAAACAAGAATGC 58.711 37.500 0.00 0.00 0.00 3.56
7752 9335 7.202526 TCTTCCTAGCAACAAAAACAAGAATG 58.797 34.615 0.00 0.00 0.00 2.67
7753 9336 7.346751 TCTTCCTAGCAACAAAAACAAGAAT 57.653 32.000 0.00 0.00 0.00 2.40
7803 9390 2.631418 AGTCTTCATACACGTGTCCG 57.369 50.000 27.16 17.41 40.83 4.79
7804 9391 4.084013 CCAAAAGTCTTCATACACGTGTCC 60.084 45.833 27.16 5.55 0.00 4.02
7805 9392 4.084013 CCCAAAAGTCTTCATACACGTGTC 60.084 45.833 27.16 8.96 0.00 3.67
7806 9393 3.813166 CCCAAAAGTCTTCATACACGTGT 59.187 43.478 26.52 26.52 0.00 4.49
7809 9396 3.364964 GCACCCAAAAGTCTTCATACACG 60.365 47.826 0.00 0.00 0.00 4.49
7810 9397 3.057526 GGCACCCAAAAGTCTTCATACAC 60.058 47.826 0.00 0.00 0.00 2.90
7811 9398 3.153919 GGCACCCAAAAGTCTTCATACA 58.846 45.455 0.00 0.00 0.00 2.29
7813 9400 2.432444 CGGCACCCAAAAGTCTTCATA 58.568 47.619 0.00 0.00 0.00 2.15
7814 9401 1.247567 CGGCACCCAAAAGTCTTCAT 58.752 50.000 0.00 0.00 0.00 2.57
7816 9403 1.956802 CCGGCACCCAAAAGTCTTC 59.043 57.895 0.00 0.00 0.00 2.87
7817 9404 2.200337 GCCGGCACCCAAAAGTCTT 61.200 57.895 24.80 0.00 0.00 3.01
7818 9405 2.597510 GCCGGCACCCAAAAGTCT 60.598 61.111 24.80 0.00 0.00 3.24
7819 9406 2.200337 AAGCCGGCACCCAAAAGTC 61.200 57.895 31.54 0.00 0.00 3.01
7820 9407 2.123468 AAGCCGGCACCCAAAAGT 60.123 55.556 31.54 0.00 0.00 2.66
7821 9408 2.026945 AACAAGCCGGCACCCAAAAG 62.027 55.000 31.54 10.84 0.00 2.27
7822 9409 2.022240 GAACAAGCCGGCACCCAAAA 62.022 55.000 31.54 0.00 0.00 2.44
7824 9411 2.058125 TAGAACAAGCCGGCACCCAA 62.058 55.000 31.54 4.33 0.00 4.12
7825 9412 2.463589 CTAGAACAAGCCGGCACCCA 62.464 60.000 31.54 5.52 0.00 4.51
7826 9413 1.745489 CTAGAACAAGCCGGCACCC 60.745 63.158 31.54 12.61 0.00 4.61
7827 9414 0.741221 CTCTAGAACAAGCCGGCACC 60.741 60.000 31.54 12.22 0.00 5.01
7831 9418 2.029838 AATGCTCTAGAACAAGCCGG 57.970 50.000 0.00 0.00 37.73 6.13
7832 9419 3.484229 CGAAAATGCTCTAGAACAAGCCG 60.484 47.826 0.00 0.00 37.73 5.52
7833 9420 3.437049 ACGAAAATGCTCTAGAACAAGCC 59.563 43.478 0.00 0.00 37.73 4.35
7834 9421 4.152402 TCACGAAAATGCTCTAGAACAAGC 59.848 41.667 0.00 0.00 39.02 4.01
7835 9422 5.845985 TCACGAAAATGCTCTAGAACAAG 57.154 39.130 0.00 0.00 0.00 3.16
7837 9424 5.297547 AGTTCACGAAAATGCTCTAGAACA 58.702 37.500 0.00 0.00 37.25 3.18
7839 9426 6.861065 AAAGTTCACGAAAATGCTCTAGAA 57.139 33.333 0.00 0.00 0.00 2.10
7843 9430 9.559958 CATTATAAAAGTTCACGAAAATGCTCT 57.440 29.630 0.00 0.00 0.00 4.09
7939 9855 2.143122 GACCAGCATGAACAACGAGAA 58.857 47.619 0.00 0.00 39.69 2.87
7942 9858 1.225855 GTGACCAGCATGAACAACGA 58.774 50.000 0.00 0.00 39.69 3.85
7962 9878 5.507974 CATCTTCGTGATGGAATGACATTG 58.492 41.667 5.14 0.00 46.55 2.82
7991 9907 6.420913 ACACTGGTCAGTTTTCTACATACT 57.579 37.500 0.20 0.00 40.20 2.12
8011 9927 5.235305 TGAACTCTTTCTTTCAGCAACAC 57.765 39.130 0.00 0.00 32.36 3.32
8052 9969 8.059461 TGAACAGTAGGAACCTGAGAATATAGA 58.941 37.037 3.36 0.00 34.04 1.98
8057 9974 5.338708 CCATGAACAGTAGGAACCTGAGAAT 60.339 44.000 3.36 0.00 34.04 2.40
8065 9982 4.878397 CAGATTCCCATGAACAGTAGGAAC 59.122 45.833 0.00 0.00 39.32 3.62
8073 9990 4.726317 TCTAATCCCAGATTCCCATGAACA 59.274 41.667 0.00 0.00 32.13 3.18
8135 10052 2.175878 TGAAAGAAGTGCTGAGGAGC 57.824 50.000 0.00 0.00 46.44 4.70
8138 10055 6.595326 TGTATATGTTGAAAGAAGTGCTGAGG 59.405 38.462 0.00 0.00 0.00 3.86
8155 10072 4.513442 AGTTGGTTCGCATGTGTATATGT 58.487 39.130 6.09 0.00 0.00 2.29
8156 10073 5.484173 AAGTTGGTTCGCATGTGTATATG 57.516 39.130 6.09 0.00 0.00 1.78
8179 10096 9.177608 CTGAAGATATTCTAACCATCCAAACAA 57.822 33.333 1.19 0.00 0.00 2.83
8181 10098 8.738645 ACTGAAGATATTCTAACCATCCAAAC 57.261 34.615 1.19 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.