Multiple sequence alignment - TraesCS7A01G313900

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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 TraesCS7A01G313900 chr7A 100.000 5436 0 0 1 5436 447754866 447749431 0.000000e+00 10039
1 TraesCS7A01G313900 chr7D 95.859 3912 140 10 936 4834 394117755 394113853 0.000000e+00 6307
2 TraesCS7A01G313900 chr7D 90.106 940 61 13 1 919 394118667 394117739 0.000000e+00 1192
3 TraesCS7A01G313900 chr7D 91.387 476 37 4 4829 5302 394113799 394113326 0.000000e+00 649
4 TraesCS7A01G313900 chr7D 92.409 303 19 4 4842 5142 137612594 137612894 3.890000e-116 429
5 TraesCS7A01G313900 chr7D 94.048 84 5 0 5353 5436 394113312 394113229 1.590000e-25 128
6 TraesCS7A01G313900 chr7B 94.971 3858 137 17 936 4791 393870193 393866391 0.000000e+00 5997
7 TraesCS7A01G313900 chr7B 89.396 943 64 12 1 919 393871107 393870177 0.000000e+00 1155
8 TraesCS7A01G313900 chrUn 92.739 303 18 4 4842 5142 91678789 91679089 8.360000e-118 435
9 TraesCS7A01G313900 chr3D 92.409 303 20 3 4842 5142 144329941 144330242 3.890000e-116 429
10 TraesCS7A01G313900 chr3D 91.803 305 22 3 4840 5142 206620485 206620788 6.510000e-114 422
11 TraesCS7A01G313900 chr4A 91.803 305 22 3 4840 5142 557403966 557403663 6.510000e-114 422
12 TraesCS7A01G313900 chr6D 91.776 304 22 3 4840 5142 193622877 193623178 2.340000e-113 420
13 TraesCS7A01G313900 chr5D 91.475 305 22 4 4840 5142 376126777 376127079 3.030000e-112 416
14 TraesCS7A01G313900 chr2A 91.503 306 20 6 4840 5142 185990100 185990402 3.030000e-112 416


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 TraesCS7A01G313900 chr7A 447749431 447754866 5435 True 10039 10039 100.0000 1 5436 1 chr7A.!!$R1 5435
1 TraesCS7A01G313900 chr7D 394113229 394118667 5438 True 2069 6307 92.8500 1 5436 4 chr7D.!!$R1 5435
2 TraesCS7A01G313900 chr7B 393866391 393871107 4716 True 3576 5997 92.1835 1 4791 2 chr7B.!!$R1 4790

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
951 986 0.319405 AAAGGCCTGCATTTGCTGTC 59.681 50.0 5.69 0.00 42.66 3.51 F
1119 1154 0.317160 CGTCTGCAGTCCTACAACCA 59.683 55.0 14.67 0.00 0.00 3.67 F
1121 1156 0.321671 TCTGCAGTCCTACAACCAGC 59.678 55.0 14.67 0.00 0.00 4.85 F
1332 1374 0.322456 AGGCAAGCAATTACGGCAGA 60.322 50.0 0.00 0.00 0.00 4.26 F
1602 1644 0.323957 AGAAGTACCGGCCAAAGTCC 59.676 55.0 0.00 0.00 0.00 3.85 F
3548 3594 0.031994 AAATGTTCGCACCTGCCAAC 59.968 50.0 1.24 1.24 41.48 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2773 2816 0.664761 GCAGCTGAGAAGTTGCACAA 59.335 50.000 20.43 0.00 43.87 3.33 R
3294 3337 4.276678 TGACAACTTTCCATCTTTCTGCAG 59.723 41.667 7.63 7.63 0.00 4.41 R
3352 3395 7.431084 CGCAACAAAGTAAAAGTTCTAACACAT 59.569 33.333 0.00 0.00 0.00 3.21 R
3376 3419 3.825308 TGACAAATGAATCTTGCTTCGC 58.175 40.909 0.00 0.00 0.00 4.70 R
3695 3743 1.355563 CTCAGCGAGCATGCAATGG 59.644 57.895 21.98 6.70 46.86 3.16 R
5310 5421 0.033504 TGAAGGTGACTCTGTTCCGC 59.966 55.000 0.00 0.00 42.68 5.54 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
67 79 2.237143 TGACATCCTCTCGCCAAAAGAT 59.763 45.455 0.00 0.00 0.00 2.40
215 228 2.582498 CCATCCGTCGACTTCGGC 60.582 66.667 14.70 0.00 46.49 5.54
273 287 4.722700 TTCTTGCTCCTGCGGCCC 62.723 66.667 0.00 0.00 43.34 5.80
404 424 2.101233 GCCGCTTTTCGTCTCCTCC 61.101 63.158 0.00 0.00 36.19 4.30
462 482 1.136500 CAGGGACGTAGGGTAAGCTTC 59.864 57.143 0.00 0.00 0.00 3.86
499 519 2.417719 CCACCTTTCCTCTTCTGTTCG 58.582 52.381 0.00 0.00 0.00 3.95
504 524 2.440539 TTCCTCTTCTGTTCGTGCTC 57.559 50.000 0.00 0.00 0.00 4.26
509 529 0.784778 CTTCTGTTCGTGCTCGGTTC 59.215 55.000 8.49 0.40 37.69 3.62
536 556 1.518792 TTGTTCGGTTCGCGTGTCA 60.519 52.632 5.77 0.00 0.00 3.58
544 564 1.007336 GTTCGCGTGTCACCGAGATT 61.007 55.000 5.77 0.00 36.56 2.40
557 577 4.098654 TCACCGAGATTCTCTGATTCTTCC 59.901 45.833 11.53 0.00 0.00 3.46
568 588 8.986929 TTCTCTGATTCTTCCTTTTCTTTTCT 57.013 30.769 0.00 0.00 0.00 2.52
571 591 9.460906 CTCTGATTCTTCCTTTTCTTTTCTTTG 57.539 33.333 0.00 0.00 0.00 2.77
572 592 7.922811 TCTGATTCTTCCTTTTCTTTTCTTTGC 59.077 33.333 0.00 0.00 0.00 3.68
573 593 6.986231 TGATTCTTCCTTTTCTTTTCTTTGCC 59.014 34.615 0.00 0.00 0.00 4.52
574 594 6.544928 TTCTTCCTTTTCTTTTCTTTGCCT 57.455 33.333 0.00 0.00 0.00 4.75
575 595 6.544928 TCTTCCTTTTCTTTTCTTTGCCTT 57.455 33.333 0.00 0.00 0.00 4.35
576 596 6.573434 TCTTCCTTTTCTTTTCTTTGCCTTC 58.427 36.000 0.00 0.00 0.00 3.46
617 637 3.682292 GAATTGCGCCCCCGTCTCT 62.682 63.158 4.18 0.00 36.67 3.10
664 686 4.889995 CAGGTTTTTCTTCCAAGAACCTCT 59.110 41.667 7.85 0.17 44.18 3.69
706 728 8.581253 TTTCTTTCCTCTTGTTTTCTCTTCTT 57.419 30.769 0.00 0.00 0.00 2.52
733 755 4.037690 GCATTCTGCATTCACGATTTACC 58.962 43.478 0.00 0.00 44.26 2.85
734 756 4.438608 GCATTCTGCATTCACGATTTACCA 60.439 41.667 0.00 0.00 44.26 3.25
792 827 3.529634 TGATTTGCTCAAAACCGTACG 57.470 42.857 8.69 8.69 33.56 3.67
799 834 1.129811 CTCAAAACCGTACGCCCAATC 59.870 52.381 10.49 0.00 0.00 2.67
829 864 5.653769 CCTTTTCTGCTCCCAAGATTGATTA 59.346 40.000 0.00 0.00 0.00 1.75
830 865 6.405176 CCTTTTCTGCTCCCAAGATTGATTAC 60.405 42.308 0.00 0.00 0.00 1.89
836 871 2.238646 TCCCAAGATTGATTACCTGCGT 59.761 45.455 0.00 0.00 0.00 5.24
885 920 1.626825 CGGGAGGGAGTTTGTTTCCTA 59.373 52.381 0.00 0.00 35.01 2.94
919 954 1.276989 CATGGCCTGCATTTCCTGTTT 59.723 47.619 3.32 0.00 0.00 2.83
920 955 2.300956 TGGCCTGCATTTCCTGTTTA 57.699 45.000 3.32 0.00 0.00 2.01
921 956 2.818921 TGGCCTGCATTTCCTGTTTAT 58.181 42.857 3.32 0.00 0.00 1.40
922 957 3.172339 TGGCCTGCATTTCCTGTTTATT 58.828 40.909 3.32 0.00 0.00 1.40
923 958 3.582208 TGGCCTGCATTTCCTGTTTATTT 59.418 39.130 3.32 0.00 0.00 1.40
924 959 4.774726 TGGCCTGCATTTCCTGTTTATTTA 59.225 37.500 3.32 0.00 0.00 1.40
925 960 5.424895 TGGCCTGCATTTCCTGTTTATTTAT 59.575 36.000 3.32 0.00 0.00 1.40
926 961 6.070309 TGGCCTGCATTTCCTGTTTATTTATT 60.070 34.615 3.32 0.00 0.00 1.40
927 962 6.823182 GGCCTGCATTTCCTGTTTATTTATTT 59.177 34.615 0.00 0.00 0.00 1.40
928 963 7.984617 GGCCTGCATTTCCTGTTTATTTATTTA 59.015 33.333 0.00 0.00 0.00 1.40
929 964 9.034544 GCCTGCATTTCCTGTTTATTTATTTAG 57.965 33.333 0.00 0.00 0.00 1.85
941 976 9.430623 TGTTTATTTATTTAGAAAAAGGCCTGC 57.569 29.630 5.69 0.00 0.00 4.85
942 977 9.430623 GTTTATTTATTTAGAAAAAGGCCTGCA 57.569 29.630 5.69 0.00 0.00 4.41
946 981 7.903995 TTATTTAGAAAAAGGCCTGCATTTG 57.096 32.000 5.69 0.00 30.04 2.32
947 982 2.174363 AGAAAAAGGCCTGCATTTGC 57.826 45.000 5.69 1.27 42.50 3.68
948 983 1.695788 AGAAAAAGGCCTGCATTTGCT 59.304 42.857 5.69 4.20 42.66 3.91
949 984 1.802365 GAAAAAGGCCTGCATTTGCTG 59.198 47.619 5.69 3.30 42.66 4.41
950 985 0.760572 AAAAGGCCTGCATTTGCTGT 59.239 45.000 5.69 0.00 42.66 4.40
951 986 0.319405 AAAGGCCTGCATTTGCTGTC 59.681 50.000 5.69 0.00 42.66 3.51
990 1025 8.496534 AAATAGATGGAAATTTTAGATGGGGG 57.503 34.615 0.00 0.00 0.00 5.40
1009 1044 3.703052 GGGGATCTGCTTCATGTTTCAAT 59.297 43.478 0.00 0.00 0.00 2.57
1010 1045 4.161001 GGGGATCTGCTTCATGTTTCAATT 59.839 41.667 0.00 0.00 0.00 2.32
1049 1084 2.412325 GCAATGCATGTGCTTTTCTTGC 60.412 45.455 19.93 11.22 42.66 4.01
1062 1097 4.391523 GCTTTTCTTGCCACAAGTCAAAAA 59.608 37.500 7.18 6.32 0.00 1.94
1064 1099 6.403527 GCTTTTCTTGCCACAAGTCAAAAATT 60.404 34.615 7.18 0.00 0.00 1.82
1065 1100 6.419980 TTTCTTGCCACAAGTCAAAAATTG 57.580 33.333 7.18 0.00 0.00 2.32
1067 1102 5.486526 TCTTGCCACAAGTCAAAAATTGTT 58.513 33.333 7.18 0.00 37.54 2.83
1069 1104 4.187694 TGCCACAAGTCAAAAATTGTTCC 58.812 39.130 0.00 0.00 37.54 3.62
1070 1105 4.081198 TGCCACAAGTCAAAAATTGTTCCT 60.081 37.500 0.00 0.00 37.54 3.36
1071 1106 4.270808 GCCACAAGTCAAAAATTGTTCCTG 59.729 41.667 0.00 0.00 37.54 3.86
1111 1146 1.078848 ATTCAGCCGTCTGCAGTCC 60.079 57.895 14.67 4.83 44.83 3.85
1114 1149 1.153745 CAGCCGTCTGCAGTCCTAC 60.154 63.158 14.67 3.17 44.83 3.18
1115 1150 1.606601 AGCCGTCTGCAGTCCTACA 60.607 57.895 14.67 0.00 44.83 2.74
1117 1152 1.014564 GCCGTCTGCAGTCCTACAAC 61.015 60.000 14.67 1.17 40.77 3.32
1119 1154 0.317160 CGTCTGCAGTCCTACAACCA 59.683 55.000 14.67 0.00 0.00 3.67
1120 1155 1.670087 CGTCTGCAGTCCTACAACCAG 60.670 57.143 14.67 0.00 0.00 4.00
1121 1156 0.321671 TCTGCAGTCCTACAACCAGC 59.678 55.000 14.67 0.00 0.00 4.85
1123 1158 1.127567 TGCAGTCCTACAACCAGCCT 61.128 55.000 0.00 0.00 0.00 4.58
1125 1160 0.687354 CAGTCCTACAACCAGCCTGT 59.313 55.000 0.00 0.00 0.00 4.00
1142 1184 1.815003 CTGTGGAGTTGATTGGAAGCC 59.185 52.381 0.00 0.00 0.00 4.35
1165 1207 1.978454 CAAGATGATTGAGGGGAGGC 58.022 55.000 0.00 0.00 0.00 4.70
1332 1374 0.322456 AGGCAAGCAATTACGGCAGA 60.322 50.000 0.00 0.00 0.00 4.26
1482 1524 3.079478 TGCTGCTCTGCGATCCCT 61.079 61.111 0.00 0.00 35.36 4.20
1602 1644 0.323957 AGAAGTACCGGCCAAAGTCC 59.676 55.000 0.00 0.00 0.00 3.85
1624 1666 2.241479 CTCTGAGCTGGCTGGACAGG 62.241 65.000 5.55 0.00 38.90 4.00
1653 1695 2.294233 TGCACAGTCTCTTTCAAATGCC 59.706 45.455 0.00 0.00 0.00 4.40
1701 1743 0.765903 ATCTCCTCCATGGTCCGCAT 60.766 55.000 12.58 0.00 37.07 4.73
1914 1956 3.470709 CTGTGAAGTTCCTGCTTCTTCA 58.529 45.455 0.00 0.00 43.74 3.02
2037 2079 7.572523 ATTTGTCATGATAACATCCGACATT 57.427 32.000 4.14 0.00 38.38 2.71
2118 2160 1.960040 ATGCAGAGATTGTCCGCCGA 61.960 55.000 0.00 0.00 0.00 5.54
2265 2307 5.166398 GGAAAAAGGATCAGCAAATCAGTG 58.834 41.667 0.00 0.00 0.00 3.66
2299 2341 8.035984 ACCTAGTAAGTTGATTTACTCAAGCTC 58.964 37.037 2.68 0.00 44.44 4.09
2622 2665 1.067071 GTACGTCCACTTCCCTTCCTG 60.067 57.143 0.00 0.00 0.00 3.86
2688 2731 4.739716 ACACAAATCTGCGATTTTGTTGAC 59.260 37.500 11.96 0.00 41.90 3.18
2716 2759 3.827008 AGCACTATCCCTATGTGTGTG 57.173 47.619 0.00 0.00 34.52 3.82
2731 2774 6.968131 ATGTGTGTGTATAAGCTTACAGTG 57.032 37.500 8.70 0.00 32.92 3.66
2732 2775 5.849510 TGTGTGTGTATAAGCTTACAGTGT 58.150 37.500 8.70 0.00 32.92 3.55
2733 2776 6.983984 TGTGTGTGTATAAGCTTACAGTGTA 58.016 36.000 8.70 0.00 32.92 2.90
3294 3337 7.518052 GCACATCTAAGTCACTTCATAATCTGC 60.518 40.741 0.00 0.00 0.00 4.26
3351 3394 7.066525 ACACAACCCAAGGTAATTGATATAACG 59.933 37.037 0.00 0.00 41.83 3.18
3352 3395 7.281324 CACAACCCAAGGTAATTGATATAACGA 59.719 37.037 0.00 0.00 41.83 3.85
3376 3419 8.943925 CGATGTGTTAGAACTTTTACTTTGTTG 58.056 33.333 0.00 0.00 0.00 3.33
3474 3520 4.660303 TCCACCATACATCTTTATCCAGCT 59.340 41.667 0.00 0.00 0.00 4.24
3548 3594 0.031994 AAATGTTCGCACCTGCCAAC 59.968 50.000 1.24 1.24 41.48 3.77
3562 3608 5.863397 CACCTGCCAACATAAGTTATTGTTG 59.137 40.000 20.13 20.13 40.68 3.33
3619 3665 3.984018 TCTTTTAACGCGTGCACTATC 57.016 42.857 14.98 2.93 0.00 2.08
3725 3773 1.396301 CTCGCTGAGGATGTTTCAAGC 59.604 52.381 0.00 0.00 0.00 4.01
3766 3814 3.443045 CGGATTGCAGGTGTGGCC 61.443 66.667 0.00 0.00 37.58 5.36
3912 3960 4.600547 TCCAATCTCCATCAGCAATAGGAT 59.399 41.667 0.00 0.00 0.00 3.24
3916 3964 6.692849 ATCTCCATCAGCAATAGGATTGTA 57.307 37.500 1.47 0.00 0.00 2.41
3960 4008 2.295885 GGTCATGCAATCCAGAGAAGG 58.704 52.381 0.00 0.00 0.00 3.46
3983 4031 1.078918 CAGGCGCAGAATCCAGTCA 60.079 57.895 10.83 0.00 0.00 3.41
4144 4192 3.034635 GAGGATCCTGAGCTACCAGAAA 58.965 50.000 22.02 0.00 36.29 2.52
4212 4260 4.393155 TGGAGAGCGCACGCCAAT 62.393 61.111 26.24 0.00 43.17 3.16
4318 4366 3.716006 CCGCACGACAAGCACAGG 61.716 66.667 0.00 0.00 0.00 4.00
4372 4420 0.449388 GTTTCTGCAAGATCAGGCCG 59.551 55.000 0.00 0.00 46.36 6.13
4386 4434 2.357034 GCCGGACTGCAGAACGAA 60.357 61.111 27.39 0.00 0.00 3.85
4408 4456 0.598562 CTGACGCTGTGTACAGGTCT 59.401 55.000 22.39 1.67 43.94 3.85
4437 4485 0.462047 GAGGTGTTCCATGGGTAGCG 60.462 60.000 13.02 0.00 35.89 4.26
4460 4508 5.005779 CGAGCATGTTGTAGCTTAAGTTAGG 59.994 44.000 4.02 0.00 42.04 2.69
4461 4509 6.049955 AGCATGTTGTAGCTTAAGTTAGGA 57.950 37.500 4.02 0.00 38.01 2.94
4674 4722 5.817296 GGTAGCGCAATGATATAATCCATCA 59.183 40.000 11.47 0.00 36.86 3.07
4682 4730 9.403110 GCAATGATATAATCCATCAGAAAACAC 57.597 33.333 0.00 0.00 35.93 3.32
4698 4746 0.458260 ACACCCTTTTGTTGCGTTCC 59.542 50.000 0.00 0.00 0.00 3.62
4708 4756 2.555123 TTGCGTTCCTGAGCAATCC 58.445 52.632 0.00 0.00 46.83 3.01
4782 4830 9.113838 GAGATTGCTGTAGAGAATTAAAATGGA 57.886 33.333 0.00 0.00 0.00 3.41
4783 4831 9.638176 AGATTGCTGTAGAGAATTAAAATGGAT 57.362 29.630 0.00 0.00 0.00 3.41
4848 4957 0.254462 CTCCTCCTTTTCAGGGCCTC 59.746 60.000 0.95 0.00 41.25 4.70
4861 4970 1.379642 GGGCCTCTTTGATTCGCAGG 61.380 60.000 0.84 0.00 0.00 4.85
4873 4982 4.225984 TGATTCGCAGGATTTTGAAAACG 58.774 39.130 0.00 0.00 0.00 3.60
4874 4983 2.044888 TCGCAGGATTTTGAAAACGC 57.955 45.000 0.00 0.00 0.00 4.84
4877 4986 2.604373 CGCAGGATTTTGAAAACGCAGA 60.604 45.455 0.00 0.00 0.00 4.26
4878 4987 3.578688 GCAGGATTTTGAAAACGCAGAT 58.421 40.909 0.00 0.00 0.00 2.90
4883 4992 7.134815 CAGGATTTTGAAAACGCAGATATAGG 58.865 38.462 0.00 0.00 0.00 2.57
4899 5008 9.606631 GCAGATATAGGAAAAGTATAGGATTGG 57.393 37.037 0.00 0.00 0.00 3.16
4913 5022 1.616725 GGATTGGAGTGTCATGCCCAA 60.617 52.381 0.00 0.00 42.16 4.12
4922 5031 2.821969 GTGTCATGCCCAACTTGAATCT 59.178 45.455 0.00 0.00 34.50 2.40
4955 5064 3.853307 GCAAGGAGTGTTTGATTTCACGG 60.853 47.826 0.00 0.00 39.25 4.94
4962 5071 4.401202 AGTGTTTGATTTCACGGGAAAAGT 59.599 37.500 18.20 0.49 45.52 2.66
4966 5076 5.699097 TTGATTTCACGGGAAAAGTAAGG 57.301 39.130 18.20 0.00 45.52 2.69
4976 5086 7.284944 TCACGGGAAAAGTAAGGAATTGTAAAA 59.715 33.333 0.00 0.00 0.00 1.52
5080 5190 6.816640 TCCTATGAATCAAAGGACAAACGTAG 59.183 38.462 0.00 0.00 34.46 3.51
5085 5195 6.319152 TGAATCAAAGGACAAACGTAGGAAAA 59.681 34.615 0.00 0.00 0.00 2.29
5090 5200 7.703197 TCAAAGGACAAACGTAGGAAAATTTTC 59.297 33.333 20.51 20.51 36.46 2.29
5174 5285 2.422803 CCTTTTCAATGGGGCTATCCGA 60.423 50.000 0.00 0.00 36.01 4.55
5190 5301 0.734253 CCGACGCCAGAGAAAGTCAG 60.734 60.000 0.00 0.00 33.56 3.51
5238 5349 0.463204 AGCACGGAGATCCATGTCAG 59.537 55.000 0.00 0.00 30.68 3.51
5245 5356 2.042464 GAGATCCATGTCAGGCTACCA 58.958 52.381 0.00 0.00 0.00 3.25
5266 5377 1.936547 GAGATGGCGTCACCTTCAATC 59.063 52.381 9.78 0.00 43.58 2.67
5268 5379 2.766263 AGATGGCGTCACCTTCAATCTA 59.234 45.455 9.78 0.00 43.58 1.98
5269 5380 3.197766 AGATGGCGTCACCTTCAATCTAA 59.802 43.478 9.78 0.00 43.58 2.10
5302 5413 2.251642 GCGGAACAGAGGCACGTTT 61.252 57.895 0.00 0.00 0.00 3.60
5303 5414 1.782028 GCGGAACAGAGGCACGTTTT 61.782 55.000 0.00 0.00 0.00 2.43
5304 5415 0.234884 CGGAACAGAGGCACGTTTTC 59.765 55.000 0.00 0.00 0.00 2.29
5305 5416 1.594331 GGAACAGAGGCACGTTTTCT 58.406 50.000 0.00 0.00 0.00 2.52
5306 5417 1.264288 GGAACAGAGGCACGTTTTCTG 59.736 52.381 15.47 15.47 43.04 3.02
5307 5418 2.210116 GAACAGAGGCACGTTTTCTGA 58.790 47.619 21.16 0.00 40.54 3.27
5308 5419 2.550830 ACAGAGGCACGTTTTCTGAT 57.449 45.000 21.16 8.12 40.54 2.90
5309 5420 2.146342 ACAGAGGCACGTTTTCTGATG 58.854 47.619 21.16 8.09 40.54 3.07
5310 5421 1.466167 CAGAGGCACGTTTTCTGATGG 59.534 52.381 12.94 0.00 40.54 3.51
5312 5423 1.154225 GGCACGTTTTCTGATGGCG 60.154 57.895 0.00 0.00 0.00 5.69
5313 5424 1.154225 GCACGTTTTCTGATGGCGG 60.154 57.895 0.00 0.00 0.00 6.13
5314 5425 1.573829 GCACGTTTTCTGATGGCGGA 61.574 55.000 0.00 0.00 0.00 5.54
5315 5426 0.871722 CACGTTTTCTGATGGCGGAA 59.128 50.000 0.00 0.00 37.62 4.30
5316 5427 0.872388 ACGTTTTCTGATGGCGGAAC 59.128 50.000 0.00 0.00 39.06 3.62
5317 5428 0.871722 CGTTTTCTGATGGCGGAACA 59.128 50.000 0.00 0.00 39.06 3.18
5318 5429 1.135972 CGTTTTCTGATGGCGGAACAG 60.136 52.381 0.00 0.00 39.06 3.16
5319 5430 2.151202 GTTTTCTGATGGCGGAACAGA 58.849 47.619 0.00 0.00 39.06 3.41
5320 5431 2.099141 TTTCTGATGGCGGAACAGAG 57.901 50.000 0.00 0.00 40.82 3.35
5321 5432 0.976641 TTCTGATGGCGGAACAGAGT 59.023 50.000 0.00 0.00 40.82 3.24
5322 5433 0.532573 TCTGATGGCGGAACAGAGTC 59.467 55.000 0.00 0.00 36.04 3.36
5323 5434 0.247460 CTGATGGCGGAACAGAGTCA 59.753 55.000 0.00 0.00 34.07 3.41
5324 5435 0.037326 TGATGGCGGAACAGAGTCAC 60.037 55.000 0.00 0.00 0.00 3.67
5325 5436 0.741221 GATGGCGGAACAGAGTCACC 60.741 60.000 0.00 0.00 0.00 4.02
5326 5437 1.194781 ATGGCGGAACAGAGTCACCT 61.195 55.000 0.00 0.00 0.00 4.00
5327 5438 1.371558 GGCGGAACAGAGTCACCTT 59.628 57.895 0.00 0.00 0.00 3.50
5328 5439 0.670854 GGCGGAACAGAGTCACCTTC 60.671 60.000 0.00 0.00 0.00 3.46
5329 5440 0.033504 GCGGAACAGAGTCACCTTCA 59.966 55.000 0.00 0.00 0.00 3.02
5330 5441 1.540363 GCGGAACAGAGTCACCTTCAA 60.540 52.381 0.00 0.00 0.00 2.69
5331 5442 2.872038 GCGGAACAGAGTCACCTTCAAT 60.872 50.000 0.00 0.00 0.00 2.57
5332 5443 2.996621 CGGAACAGAGTCACCTTCAATC 59.003 50.000 0.00 0.00 0.00 2.67
5333 5444 3.306364 CGGAACAGAGTCACCTTCAATCT 60.306 47.826 0.00 0.00 0.00 2.40
5334 5445 4.082190 CGGAACAGAGTCACCTTCAATCTA 60.082 45.833 0.00 0.00 0.00 1.98
5335 5446 5.172205 GGAACAGAGTCACCTTCAATCTAC 58.828 45.833 0.00 0.00 0.00 2.59
5336 5447 4.810191 ACAGAGTCACCTTCAATCTACC 57.190 45.455 0.00 0.00 0.00 3.18
5337 5448 4.160329 ACAGAGTCACCTTCAATCTACCA 58.840 43.478 0.00 0.00 0.00 3.25
5338 5449 4.221703 ACAGAGTCACCTTCAATCTACCAG 59.778 45.833 0.00 0.00 0.00 4.00
5339 5450 4.464244 CAGAGTCACCTTCAATCTACCAGA 59.536 45.833 0.00 0.00 0.00 3.86
5340 5451 4.709397 AGAGTCACCTTCAATCTACCAGAG 59.291 45.833 0.00 0.00 0.00 3.35
5341 5452 4.678256 AGTCACCTTCAATCTACCAGAGA 58.322 43.478 0.00 0.00 39.01 3.10
5342 5453 4.464597 AGTCACCTTCAATCTACCAGAGAC 59.535 45.833 0.00 0.00 36.87 3.36
5343 5454 3.444034 TCACCTTCAATCTACCAGAGACG 59.556 47.826 0.00 0.00 36.87 4.18
5344 5455 2.761208 ACCTTCAATCTACCAGAGACGG 59.239 50.000 0.00 0.00 36.87 4.79
5345 5456 2.482142 CCTTCAATCTACCAGAGACGGC 60.482 54.545 0.00 0.00 36.87 5.68
5346 5457 2.145397 TCAATCTACCAGAGACGGCT 57.855 50.000 0.00 0.00 36.87 5.52
5347 5458 2.025155 TCAATCTACCAGAGACGGCTC 58.975 52.381 11.39 11.39 41.62 4.70
5348 5459 1.751351 CAATCTACCAGAGACGGCTCA 59.249 52.381 22.94 0.00 43.81 4.26
5349 5460 1.394618 ATCTACCAGAGACGGCTCAC 58.605 55.000 22.94 0.00 43.81 3.51
5350 5461 0.680280 TCTACCAGAGACGGCTCACC 60.680 60.000 22.94 0.00 43.81 4.02
5351 5462 0.681564 CTACCAGAGACGGCTCACCT 60.682 60.000 22.94 3.77 43.81 4.00
5361 5472 3.515901 AGACGGCTCACCTAGAAAATTCT 59.484 43.478 0.77 0.77 41.24 2.40
5387 5498 5.248640 GTCCTCATCACCTCATCAAAGAAA 58.751 41.667 0.00 0.00 0.00 2.52
5419 5530 4.023291 GGAGGGAGCAATCCACAATAAAA 58.977 43.478 0.00 0.00 35.54 1.52
5421 5532 5.129320 GGAGGGAGCAATCCACAATAAAAAT 59.871 40.000 0.00 0.00 35.54 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 95 2.427453 ACAGCCGTAGATACCTGTGAAG 59.573 50.000 0.00 0.00 37.18 3.02
147 159 1.415200 GTAGAGGAAATCGGAGGCCT 58.585 55.000 3.86 3.86 0.00 5.19
306 320 4.980903 GCCGCCGCCGCATTAATG 62.981 66.667 11.27 11.27 34.03 1.90
331 345 3.284197 CGCTCCCGGTATTTACCAG 57.716 57.895 0.00 0.00 46.80 4.00
390 410 1.466024 CGACGAGGAGGAGACGAAAAG 60.466 57.143 0.00 0.00 0.00 2.27
396 416 1.694955 GACGACGACGAGGAGGAGAC 61.695 65.000 15.32 0.00 42.66 3.36
509 529 1.235724 GAACCGAACAACCAGAAGGG 58.764 55.000 0.00 0.00 44.81 3.95
544 564 8.986929 AAGAAAAGAAAAGGAAGAATCAGAGA 57.013 30.769 0.00 0.00 0.00 3.10
557 577 6.478016 CCTCAAGAAGGCAAAGAAAAGAAAAG 59.522 38.462 0.00 0.00 38.67 2.27
608 628 3.542648 GGGATTAAAAAGAGAGACGGGG 58.457 50.000 0.00 0.00 0.00 5.73
633 655 1.463553 AAGAAAAACCTGGCAGCGGG 61.464 55.000 9.56 0.00 0.00 6.13
634 656 0.039165 GAAGAAAAACCTGGCAGCGG 60.039 55.000 9.56 0.00 0.00 5.52
635 657 0.039165 GGAAGAAAAACCTGGCAGCG 60.039 55.000 9.56 5.16 0.00 5.18
686 708 7.389053 GCATCTAAGAAGAGAAAACAAGAGGAA 59.611 37.037 0.00 0.00 34.49 3.36
723 745 6.024049 GCAAAGAAGAAGATGGTAAATCGTG 58.976 40.000 0.00 0.00 0.00 4.35
731 753 3.409026 AGTCGCAAAGAAGAAGATGGT 57.591 42.857 0.00 0.00 0.00 3.55
732 754 4.756084 AAAGTCGCAAAGAAGAAGATGG 57.244 40.909 0.00 0.00 0.00 3.51
792 827 3.567585 GCAGAAAAGGATAGAGATTGGGC 59.432 47.826 0.00 0.00 0.00 5.36
799 834 4.163078 TCTTGGGAGCAGAAAAGGATAGAG 59.837 45.833 0.00 0.00 0.00 2.43
830 865 4.331717 CCTAAACAGTATTTACCACGCAGG 59.668 45.833 0.00 0.00 45.67 4.85
836 871 7.280652 GCGATTTACCCTAAACAGTATTTACCA 59.719 37.037 0.00 0.00 0.00 3.25
844 879 3.007635 GCTGCGATTTACCCTAAACAGT 58.992 45.455 0.00 0.00 0.00 3.55
901 936 2.300956 TAAACAGGAAATGCAGGCCA 57.699 45.000 5.01 0.00 0.00 5.36
920 955 8.949177 CAAATGCAGGCCTTTTTCTAAATAAAT 58.051 29.630 0.00 0.00 0.00 1.40
921 956 7.094848 GCAAATGCAGGCCTTTTTCTAAATAAA 60.095 33.333 0.00 0.00 41.59 1.40
922 957 6.371271 GCAAATGCAGGCCTTTTTCTAAATAA 59.629 34.615 0.00 0.00 41.59 1.40
923 958 5.874261 GCAAATGCAGGCCTTTTTCTAAATA 59.126 36.000 0.00 0.00 41.59 1.40
924 959 4.696877 GCAAATGCAGGCCTTTTTCTAAAT 59.303 37.500 0.00 0.00 41.59 1.40
925 960 4.064388 GCAAATGCAGGCCTTTTTCTAAA 58.936 39.130 0.00 0.00 41.59 1.85
926 961 3.324556 AGCAAATGCAGGCCTTTTTCTAA 59.675 39.130 0.00 0.00 45.16 2.10
927 962 2.899256 AGCAAATGCAGGCCTTTTTCTA 59.101 40.909 0.00 0.00 45.16 2.10
928 963 1.695788 AGCAAATGCAGGCCTTTTTCT 59.304 42.857 0.00 0.00 45.16 2.52
929 964 1.802365 CAGCAAATGCAGGCCTTTTTC 59.198 47.619 0.00 0.00 45.16 2.29
930 965 1.141455 ACAGCAAATGCAGGCCTTTTT 59.859 42.857 0.00 0.08 45.16 1.94
931 966 0.760572 ACAGCAAATGCAGGCCTTTT 59.239 45.000 0.00 0.00 45.16 2.27
932 967 0.319405 GACAGCAAATGCAGGCCTTT 59.681 50.000 0.00 0.00 45.16 3.11
933 968 0.828762 TGACAGCAAATGCAGGCCTT 60.829 50.000 0.00 0.00 45.16 4.35
934 969 1.228644 TGACAGCAAATGCAGGCCT 60.229 52.632 0.00 0.00 45.16 5.19
935 970 1.080298 GTGACAGCAAATGCAGGCC 60.080 57.895 8.28 0.00 45.16 5.19
936 971 1.080298 GGTGACAGCAAATGCAGGC 60.080 57.895 8.28 2.01 45.16 4.85
937 972 0.675083 TTGGTGACAGCAAATGCAGG 59.325 50.000 17.35 1.98 44.54 4.85
938 973 1.338973 ACTTGGTGACAGCAAATGCAG 59.661 47.619 19.77 10.94 44.54 4.41
939 974 1.401761 ACTTGGTGACAGCAAATGCA 58.598 45.000 19.77 0.00 44.54 3.96
940 975 3.441572 AGATACTTGGTGACAGCAAATGC 59.558 43.478 19.77 8.15 44.54 3.56
941 976 6.741992 TTAGATACTTGGTGACAGCAAATG 57.258 37.500 19.77 12.24 44.54 2.32
942 977 7.759489 TTTTAGATACTTGGTGACAGCAAAT 57.241 32.000 19.77 13.50 44.54 2.32
943 978 7.575414 TTTTTAGATACTTGGTGACAGCAAA 57.425 32.000 19.77 7.77 44.54 3.68
944 979 7.759489 ATTTTTAGATACTTGGTGACAGCAA 57.241 32.000 18.43 18.43 44.54 3.91
945 980 8.318412 TCTATTTTTAGATACTTGGTGACAGCA 58.682 33.333 2.50 2.50 44.54 4.41
946 981 8.718102 TCTATTTTTAGATACTTGGTGACAGC 57.282 34.615 0.00 0.00 44.54 4.40
948 983 9.613428 CCATCTATTTTTAGATACTTGGTGACA 57.387 33.333 0.00 0.00 35.21 3.58
949 984 9.832445 TCCATCTATTTTTAGATACTTGGTGAC 57.168 33.333 0.00 0.00 35.21 3.67
1014 1049 2.550180 TGCATTGCACGCTAGTAACAAA 59.450 40.909 7.38 0.00 31.71 2.83
1015 1050 2.147150 TGCATTGCACGCTAGTAACAA 58.853 42.857 7.38 0.00 31.71 2.83
1049 1084 5.659463 TCAGGAACAATTTTTGACTTGTGG 58.341 37.500 0.00 0.00 35.82 4.17
1065 1100 1.282930 GCGGACGAGTGTTCAGGAAC 61.283 60.000 5.23 5.23 41.50 3.62
1067 1102 1.532604 ATGCGGACGAGTGTTCAGGA 61.533 55.000 0.00 0.00 0.00 3.86
1069 1104 0.439985 CAATGCGGACGAGTGTTCAG 59.560 55.000 0.00 0.00 0.00 3.02
1070 1105 1.565156 GCAATGCGGACGAGTGTTCA 61.565 55.000 0.00 0.00 0.00 3.18
1071 1106 1.132640 GCAATGCGGACGAGTGTTC 59.867 57.895 0.00 0.00 0.00 3.18
1111 1146 0.687354 ACTCCACAGGCTGGTTGTAG 59.313 55.000 20.34 7.76 41.52 2.74
1114 1149 0.179020 TCAACTCCACAGGCTGGTTG 60.179 55.000 20.34 20.86 41.52 3.77
1115 1150 0.773644 ATCAACTCCACAGGCTGGTT 59.226 50.000 20.34 10.15 41.52 3.67
1117 1152 1.171308 CAATCAACTCCACAGGCTGG 58.829 55.000 20.34 7.72 42.29 4.85
1119 1154 1.067295 TCCAATCAACTCCACAGGCT 58.933 50.000 0.00 0.00 0.00 4.58
1120 1155 1.815003 CTTCCAATCAACTCCACAGGC 59.185 52.381 0.00 0.00 0.00 4.85
1121 1156 1.815003 GCTTCCAATCAACTCCACAGG 59.185 52.381 0.00 0.00 0.00 4.00
1123 1158 1.425066 AGGCTTCCAATCAACTCCACA 59.575 47.619 0.00 0.00 0.00 4.17
1125 1160 2.517959 CAAGGCTTCCAATCAACTCCA 58.482 47.619 0.00 0.00 0.00 3.86
1142 1184 2.950309 CTCCCCTCAATCATCTTGCAAG 59.050 50.000 20.81 20.81 0.00 4.01
1165 1207 1.156736 GGGATATCAACCGAATGCCG 58.843 55.000 4.83 0.00 38.18 5.69
1188 1230 4.200283 GCGACCAGAGCCCTCGAG 62.200 72.222 5.13 5.13 34.09 4.04
1206 1248 2.034432 CAGAGATCTGGACCTCATGACG 59.966 54.545 0.00 0.00 40.20 4.35
1482 1524 2.725312 GGCAGCTCTCGACATCCCA 61.725 63.158 0.00 0.00 0.00 4.37
1569 1611 2.470983 ACTTCTGGAGCAAGCTTCTC 57.529 50.000 14.11 14.11 0.00 2.87
1602 1644 0.108233 GTCCAGCCAGCTCAGAGAAG 60.108 60.000 0.00 0.00 0.00 2.85
1701 1743 1.314534 CGGATGTCTTGCCAATGCCA 61.315 55.000 0.00 0.00 36.33 4.92
1776 1818 2.809861 ATTCCTCGCAGTGCCCACAG 62.810 60.000 10.11 0.26 0.00 3.66
1900 1942 3.206150 TGAAGTGTGAAGAAGCAGGAAC 58.794 45.455 0.00 0.00 0.00 3.62
1914 1956 8.812972 TCATCTACAATAAGTACCTTGAAGTGT 58.187 33.333 7.26 0.00 0.00 3.55
2037 2079 4.250464 CGGAGTTGCTTGGTAGTTTATCA 58.750 43.478 0.00 0.00 0.00 2.15
2145 2187 1.726853 CTTCGGCTTCGAACTCCATT 58.273 50.000 11.09 0.00 46.42 3.16
2265 2307 9.230932 GTAAATCAACTTACTAGGTCGTATGTC 57.769 37.037 0.00 0.00 30.33 3.06
2622 2665 4.749976 TCACACAACTTTAAAGTTTGCCC 58.250 39.130 27.12 0.00 46.52 5.36
2642 2685 2.294512 CCGCTATGTCTCATGTAGCTCA 59.705 50.000 9.74 0.00 38.87 4.26
2688 2731 7.489435 CACACATAGGGATAGTGCTATAAATCG 59.511 40.741 0.00 0.00 36.76 3.34
2716 2759 8.627403 TCCATGTACTACACTGTAAGCTTATAC 58.373 37.037 9.88 6.11 37.60 1.47
2771 2814 2.288030 GCAGCTGAGAAGTTGCACAAAT 60.288 45.455 20.43 0.00 43.87 2.32
2773 2816 0.664761 GCAGCTGAGAAGTTGCACAA 59.335 50.000 20.43 0.00 43.87 3.33
3294 3337 4.276678 TGACAACTTTCCATCTTTCTGCAG 59.723 41.667 7.63 7.63 0.00 4.41
3351 3394 8.743099 GCAACAAAGTAAAAGTTCTAACACATC 58.257 33.333 0.00 0.00 0.00 3.06
3352 3395 7.431084 CGCAACAAAGTAAAAGTTCTAACACAT 59.569 33.333 0.00 0.00 0.00 3.21
3376 3419 3.825308 TGACAAATGAATCTTGCTTCGC 58.175 40.909 0.00 0.00 0.00 4.70
3548 3594 8.347771 CCATCTGATGGTCAACAATAACTTATG 58.652 37.037 25.34 0.00 45.54 1.90
3639 3685 2.751259 CTCACACTGTGCCAATTGCTAT 59.249 45.455 7.90 0.00 42.00 2.97
3695 3743 1.355563 CTCAGCGAGCATGCAATGG 59.644 57.895 21.98 6.70 46.86 3.16
3706 3754 1.442769 GCTTGAAACATCCTCAGCGA 58.557 50.000 0.00 0.00 0.00 4.93
3766 3814 4.211164 TGACAGAATTGTAACTCAGCAACG 59.789 41.667 0.00 0.00 37.76 4.10
3916 3964 2.749621 GCTGACCAACGAATTCTTGGAT 59.250 45.455 28.53 18.71 40.76 3.41
3930 3978 2.066700 TTGCATGACCAGGCTGACCA 62.067 55.000 17.94 13.41 39.14 4.02
3960 4008 0.955428 TGGATTCTGCGCCTGTTGAC 60.955 55.000 4.18 0.00 0.00 3.18
3983 4031 2.426023 GGTTCTGCAGTCCGTGGT 59.574 61.111 14.67 0.00 0.00 4.16
4037 4085 0.631753 TTGGGTTGTTGTCCTGGGAA 59.368 50.000 0.00 0.00 0.00 3.97
4090 4138 1.592400 CGCATCGCTATCTGCACCA 60.592 57.895 0.00 0.00 43.06 4.17
4144 4192 4.564782 TGCTTCAGGAATGACAGAGATT 57.435 40.909 0.00 0.00 0.00 2.40
4212 4260 0.748450 ACCTTTGACTTCGTCGACCA 59.252 50.000 10.58 0.00 34.95 4.02
4372 4420 0.514691 CAGCTTTCGTTCTGCAGTCC 59.485 55.000 14.67 4.44 0.00 3.85
4437 4485 6.106673 TCCTAACTTAAGCTACAACATGCTC 58.893 40.000 1.29 0.00 38.75 4.26
4460 4508 2.370281 TTCAACGGTGCTCATCTCTC 57.630 50.000 0.00 0.00 0.00 3.20
4461 4509 2.224281 TGTTTCAACGGTGCTCATCTCT 60.224 45.455 0.00 0.00 0.00 3.10
4537 4585 6.981559 AGACTCGCCTAAATTGATCTAACTTC 59.018 38.462 0.00 0.00 0.00 3.01
4674 4722 2.232696 ACGCAACAAAAGGGTGTTTTCT 59.767 40.909 0.00 0.00 39.73 2.52
4682 4730 1.001378 CTCAGGAACGCAACAAAAGGG 60.001 52.381 0.00 0.00 0.00 3.95
4698 4746 6.521151 ACAAAGAATAAAGGGATTGCTCAG 57.479 37.500 0.00 0.00 0.00 3.35
4782 4830 3.306088 CGGTCTCGCCAACATCCTATAAT 60.306 47.826 0.00 0.00 36.97 1.28
4783 4831 2.035449 CGGTCTCGCCAACATCCTATAA 59.965 50.000 0.00 0.00 36.97 0.98
4848 4957 6.584056 GTTTTCAAAATCCTGCGAATCAAAG 58.416 36.000 0.00 0.00 0.00 2.77
4861 4970 9.567848 TTTTCCTATATCTGCGTTTTCAAAATC 57.432 29.630 0.00 0.00 0.00 2.17
4873 4982 9.606631 CCAATCCTATACTTTTCCTATATCTGC 57.393 37.037 0.00 0.00 0.00 4.26
4878 4987 9.670442 ACACTCCAATCCTATACTTTTCCTATA 57.330 33.333 0.00 0.00 0.00 1.31
4883 4992 7.254932 GCATGACACTCCAATCCTATACTTTTC 60.255 40.741 0.00 0.00 0.00 2.29
4899 5008 1.896220 TCAAGTTGGGCATGACACTC 58.104 50.000 0.00 0.00 0.00 3.51
4903 5012 5.841957 ATAAGATTCAAGTTGGGCATGAC 57.158 39.130 2.34 0.00 0.00 3.06
4913 5022 8.938883 TCCTTGCTAATCCTATAAGATTCAAGT 58.061 33.333 16.64 0.00 36.88 3.16
4922 5031 7.857456 TCAAACACTCCTTGCTAATCCTATAA 58.143 34.615 0.00 0.00 0.00 0.98
4978 5088 8.552296 AGGAAATCTAACATCCACTCTAACATT 58.448 33.333 0.00 0.00 35.62 2.71
4980 5090 7.496346 AGGAAATCTAACATCCACTCTAACA 57.504 36.000 0.00 0.00 35.62 2.41
5057 5167 6.816640 TCCTACGTTTGTCCTTTGATTCATAG 59.183 38.462 0.00 0.00 0.00 2.23
5174 5285 1.373497 CGCTGACTTTCTCTGGCGT 60.373 57.895 0.00 0.00 37.19 5.68
5180 5291 0.246635 TGGTAGGCGCTGACTTTCTC 59.753 55.000 7.64 0.00 0.00 2.87
5190 5301 1.227674 CCCTTGAGATGGTAGGCGC 60.228 63.158 0.00 0.00 0.00 6.53
5222 5333 0.689080 AGCCTGACATGGATCTCCGT 60.689 55.000 0.00 0.00 39.43 4.69
5238 5349 1.068250 GACGCCATCTCTGGTAGCC 59.932 63.158 0.00 0.00 45.10 3.93
5245 5356 0.976641 TTGAAGGTGACGCCATCTCT 59.023 50.000 11.31 0.00 40.61 3.10
5266 5377 5.828299 TCCGCCATTTTTATTCACCTTAG 57.172 39.130 0.00 0.00 0.00 2.18
5268 5379 4.282195 TGTTCCGCCATTTTTATTCACCTT 59.718 37.500 0.00 0.00 0.00 3.50
5269 5380 3.829601 TGTTCCGCCATTTTTATTCACCT 59.170 39.130 0.00 0.00 0.00 4.00
5302 5413 0.976641 ACTCTGTTCCGCCATCAGAA 59.023 50.000 0.00 0.00 37.68 3.02
5303 5414 0.532573 GACTCTGTTCCGCCATCAGA 59.467 55.000 0.00 0.00 36.85 3.27
5304 5415 0.247460 TGACTCTGTTCCGCCATCAG 59.753 55.000 0.00 0.00 0.00 2.90
5305 5416 0.037326 GTGACTCTGTTCCGCCATCA 60.037 55.000 0.00 0.00 0.00 3.07
5306 5417 0.741221 GGTGACTCTGTTCCGCCATC 60.741 60.000 0.00 0.00 0.00 3.51
5307 5418 1.194781 AGGTGACTCTGTTCCGCCAT 61.195 55.000 0.00 0.00 32.90 4.40
5308 5419 1.407656 AAGGTGACTCTGTTCCGCCA 61.408 55.000 0.00 0.00 42.68 5.69
5309 5420 0.670854 GAAGGTGACTCTGTTCCGCC 60.671 60.000 0.00 0.00 42.68 6.13
5310 5421 0.033504 TGAAGGTGACTCTGTTCCGC 59.966 55.000 0.00 0.00 42.68 5.54
5312 5423 4.278975 AGATTGAAGGTGACTCTGTTCC 57.721 45.455 0.00 0.00 42.68 3.62
5313 5424 5.172205 GGTAGATTGAAGGTGACTCTGTTC 58.828 45.833 0.00 0.00 42.68 3.18
5314 5425 4.593206 TGGTAGATTGAAGGTGACTCTGTT 59.407 41.667 0.00 0.00 42.68 3.16
5315 5426 4.160329 TGGTAGATTGAAGGTGACTCTGT 58.840 43.478 0.00 0.00 42.68 3.41
5316 5427 4.464244 TCTGGTAGATTGAAGGTGACTCTG 59.536 45.833 0.00 0.00 42.68 3.35
5317 5428 4.678256 TCTGGTAGATTGAAGGTGACTCT 58.322 43.478 0.00 0.00 42.68 3.24
5318 5429 4.707448 TCTCTGGTAGATTGAAGGTGACTC 59.293 45.833 0.00 0.00 42.68 3.36
5319 5430 4.464597 GTCTCTGGTAGATTGAAGGTGACT 59.535 45.833 0.00 0.00 38.60 3.41
5320 5431 4.675671 CGTCTCTGGTAGATTGAAGGTGAC 60.676 50.000 0.00 0.00 36.36 3.67
5321 5432 3.444034 CGTCTCTGGTAGATTGAAGGTGA 59.556 47.826 0.00 0.00 36.36 4.02
5322 5433 3.429547 CCGTCTCTGGTAGATTGAAGGTG 60.430 52.174 0.00 0.00 36.36 4.00
5323 5434 2.761208 CCGTCTCTGGTAGATTGAAGGT 59.239 50.000 0.00 0.00 36.36 3.50
5324 5435 2.482142 GCCGTCTCTGGTAGATTGAAGG 60.482 54.545 0.00 0.00 36.36 3.46
5325 5436 2.428890 AGCCGTCTCTGGTAGATTGAAG 59.571 50.000 0.00 0.00 36.36 3.02
5326 5437 2.427453 GAGCCGTCTCTGGTAGATTGAA 59.573 50.000 0.00 0.00 36.36 2.69
5327 5438 2.025155 GAGCCGTCTCTGGTAGATTGA 58.975 52.381 0.00 0.00 36.36 2.57
5328 5439 1.751351 TGAGCCGTCTCTGGTAGATTG 59.249 52.381 0.00 0.00 40.03 2.67
5329 5440 1.751924 GTGAGCCGTCTCTGGTAGATT 59.248 52.381 0.00 0.00 40.03 2.40
5330 5441 1.394618 GTGAGCCGTCTCTGGTAGAT 58.605 55.000 0.00 0.00 40.03 1.98
5331 5442 0.680280 GGTGAGCCGTCTCTGGTAGA 60.680 60.000 0.00 0.00 40.03 2.59
5332 5443 0.681564 AGGTGAGCCGTCTCTGGTAG 60.682 60.000 0.00 0.00 40.03 3.18
5333 5444 0.622136 TAGGTGAGCCGTCTCTGGTA 59.378 55.000 0.00 0.00 40.03 3.25
5334 5445 0.681564 CTAGGTGAGCCGTCTCTGGT 60.682 60.000 0.00 0.00 40.03 4.00
5335 5446 0.394488 TCTAGGTGAGCCGTCTCTGG 60.394 60.000 0.00 0.00 40.03 3.86
5336 5447 1.464734 TTCTAGGTGAGCCGTCTCTG 58.535 55.000 0.00 0.00 40.03 3.35
5337 5448 2.217510 TTTCTAGGTGAGCCGTCTCT 57.782 50.000 0.00 0.00 40.03 3.10
5338 5449 3.528597 ATTTTCTAGGTGAGCCGTCTC 57.471 47.619 0.00 0.00 40.50 3.36
5339 5450 3.515901 AGAATTTTCTAGGTGAGCCGTCT 59.484 43.478 0.00 0.00 40.50 4.18
5340 5451 3.619038 CAGAATTTTCTAGGTGAGCCGTC 59.381 47.826 0.00 0.00 36.05 4.79
5341 5452 3.600388 CAGAATTTTCTAGGTGAGCCGT 58.400 45.455 0.00 0.00 36.05 5.68
5342 5453 2.939103 CCAGAATTTTCTAGGTGAGCCG 59.061 50.000 0.00 0.00 36.05 5.52
5343 5454 3.282885 CCCAGAATTTTCTAGGTGAGCC 58.717 50.000 0.00 0.00 35.34 4.70
5344 5455 3.942115 GACCCAGAATTTTCTAGGTGAGC 59.058 47.826 14.02 0.00 46.94 4.26
5345 5456 4.226168 AGGACCCAGAATTTTCTAGGTGAG 59.774 45.833 14.02 0.71 46.94 3.51
5346 5457 4.175962 AGGACCCAGAATTTTCTAGGTGA 58.824 43.478 14.02 0.00 46.94 4.02
5347 5458 4.019321 TGAGGACCCAGAATTTTCTAGGTG 60.019 45.833 14.02 5.81 46.94 4.00
5349 5460 4.844349 TGAGGACCCAGAATTTTCTAGG 57.156 45.455 3.59 3.59 41.18 3.02
5350 5461 5.819901 GTGATGAGGACCCAGAATTTTCTAG 59.180 44.000 0.00 0.00 35.34 2.43
5351 5462 5.339200 GGTGATGAGGACCCAGAATTTTCTA 60.339 44.000 0.00 0.00 35.34 2.10
5361 5472 1.273781 TGATGAGGTGATGAGGACCCA 60.274 52.381 0.00 0.00 33.51 4.51
5368 5479 4.012374 GGCTTTCTTTGATGAGGTGATGA 58.988 43.478 0.00 0.00 0.00 2.92
5387 5498 2.363172 GCTCCCTCCTTTCTCGGCT 61.363 63.158 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.