Multiple sequence alignment - TraesCS3A01G027700

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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 TraesCS3A01G027700 chr3A 100.000 5194 0 0 682 5875 14848453 14853646 0.000000e+00 9592.0
1 TraesCS3A01G027700 chr3A 86.645 629 69 7 3857 4484 14860314 14860928 0.000000e+00 682.0
2 TraesCS3A01G027700 chr3A 100.000 365 0 0 1 365 14847772 14848136 0.000000e+00 675.0
3 TraesCS3A01G027700 chr3A 93.676 253 15 1 4487 4739 14861015 14861266 1.550000e-100 377.0
4 TraesCS3A01G027700 chr3A 92.893 197 14 0 5028 5224 14883554 14883750 2.680000e-73 287.0
5 TraesCS3A01G027700 chr3A 93.960 149 8 1 4732 4879 14883245 14883393 2.130000e-54 224.0
6 TraesCS3A01G027700 chr3A 92.188 128 9 1 5309 5436 14895384 14895510 4.680000e-41 180.0
7 TraesCS3A01G027700 chr3A 87.850 107 4 6 4870 4976 14883444 14883541 3.720000e-22 117.0
8 TraesCS3A01G027700 chr3D 93.191 3334 147 23 842 4134 6149962 6146668 0.000000e+00 4826.0
9 TraesCS3A01G027700 chr3D 92.160 574 18 3 4487 5034 6146282 6145710 0.000000e+00 785.0
10 TraesCS3A01G027700 chr3D 96.277 376 14 0 5423 5798 6145491 6145116 8.360000e-173 617.0
11 TraesCS3A01G027700 chr3D 84.466 309 30 8 4181 4484 6146666 6146371 7.450000e-74 289.0
12 TraesCS3A01G027700 chr3D 100.000 40 0 0 5397 5436 6145559 6145520 2.270000e-09 75.0
13 TraesCS3A01G027700 chr3B 92.771 3168 158 30 880 4014 7371165 7374294 0.000000e+00 4516.0
14 TraesCS3A01G027700 chr3B 90.435 460 31 9 5423 5874 7375487 7375941 1.410000e-165 593.0
15 TraesCS3A01G027700 chr3B 92.055 365 23 2 1 365 7370635 7370993 5.250000e-140 508.0
16 TraesCS3A01G027700 chr3B 92.369 249 18 1 115 363 7367920 7368167 2.600000e-93 353.0
17 TraesCS3A01G027700 chr3B 87.156 109 10 1 5005 5109 7374950 7375058 2.880000e-23 121.0
18 TraesCS3A01G027700 chr3B 84.783 92 6 2 4872 4963 7374686 7374769 1.050000e-12 86.1
19 TraesCS3A01G027700 chr3B 91.837 49 4 0 5395 5443 7375417 7375465 1.060000e-07 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G027700 chr3A 14847772 14853646 5874 False 5133.500000 9592 100.000000 1 5875 2 chr3A.!!$F2 5874
1 TraesCS3A01G027700 chr3A 14860314 14861266 952 False 529.500000 682 90.160500 3857 4739 2 chr3A.!!$F3 882
2 TraesCS3A01G027700 chr3A 14883245 14883750 505 False 209.333333 287 91.567667 4732 5224 3 chr3A.!!$F4 492
3 TraesCS3A01G027700 chr3D 6145116 6149962 4846 True 1318.400000 4826 93.218800 842 5798 5 chr3D.!!$R1 4956
4 TraesCS3A01G027700 chr3B 7367920 7375941 8021 False 892.357143 4516 90.200857 1 5874 7 chr3B.!!$F1 5873

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
816 3532 0.168128 GGGATGTTTTGGAGTTCGCG 59.832 55.0 0.00 0.0 0.00 5.87 F
818 3534 0.168128 GATGTTTTGGAGTTCGCGGG 59.832 55.0 6.13 0.0 0.00 6.13 F
2585 5336 0.179084 CAACACGGACACCTGTCACT 60.179 55.0 7.71 0.0 46.47 3.41 F
2939 5690 0.108138 GGAGTCACGGGAACATGGAG 60.108 60.0 0.00 0.0 0.00 3.86 F
4124 6903 0.108963 TCCGGCGGGAAAGAAGAAAA 59.891 50.0 27.98 0.0 40.15 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 4652 0.120377 TCCCCTTAAAGGCCCTCAGA 59.880 55.0 0.00 0.00 32.73 3.27 R
2622 5373 0.467474 TGTATCGCATCTCGGGACCT 60.467 55.0 0.00 0.00 39.76 3.85 R
3656 6415 0.099436 GCAAACGGACATCTCATGGC 59.901 55.0 0.00 0.00 37.65 4.40 R
4574 7443 0.380733 GGGCTAATGTTTACGCCTGC 59.619 55.0 0.00 0.00 42.13 4.85 R
5379 8864 0.033796 AGCAATGCTACATGGGCAGT 60.034 50.0 5.69 13.86 43.15 4.40 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
20 2736 0.877071 GGTCTCGTTACGGTCTCACA 59.123 55.000 4.53 0.00 0.00 3.58
21 2737 1.471684 GGTCTCGTTACGGTCTCACAT 59.528 52.381 4.53 0.00 0.00 3.21
22 2738 2.477525 GGTCTCGTTACGGTCTCACATC 60.478 54.545 4.53 0.00 0.00 3.06
23 2739 2.161012 GTCTCGTTACGGTCTCACATCA 59.839 50.000 4.53 0.00 0.00 3.07
24 2740 2.161012 TCTCGTTACGGTCTCACATCAC 59.839 50.000 4.53 0.00 0.00 3.06
63 2779 5.239525 GCACAATGTTATATCCTCCTCCAAC 59.760 44.000 0.00 0.00 0.00 3.77
67 2783 7.092444 ACAATGTTATATCCTCCTCCAACTTGA 60.092 37.037 0.00 0.00 0.00 3.02
90 2806 4.715527 ATTGCTCAATCTTCCAAGCTTC 57.284 40.909 0.00 0.00 35.76 3.86
97 2813 4.692625 TCAATCTTCCAAGCTTCTTCTTCG 59.307 41.667 0.00 0.00 0.00 3.79
111 2827 1.428448 TCTTCGTGTTGCAATCTCGG 58.572 50.000 0.59 0.00 0.00 4.63
121 2837 0.749454 GCAATCTCGGCCTCAACCAT 60.749 55.000 0.00 0.00 0.00 3.55
256 2972 2.480224 AATCATGTTGCGCACTATGC 57.520 45.000 21.98 7.84 40.69 3.14
304 3020 5.973565 AGAAGAAGAAAACAAGTTGCATTCG 59.026 36.000 1.81 0.00 0.00 3.34
313 3029 3.573967 ACAAGTTGCATTCGAGGGATTTT 59.426 39.130 1.81 0.00 0.00 1.82
337 3053 1.758592 GGTACTTGGTGTGCCCTCA 59.241 57.895 0.00 0.00 44.32 3.86
340 3056 0.322456 TACTTGGTGTGCCCTCATGC 60.322 55.000 0.00 0.00 0.00 4.06
341 3057 2.283101 TTGGTGTGCCCTCATGCC 60.283 61.111 0.00 0.00 0.00 4.40
350 3066 2.659063 CCCTCATGCCGGTGTCAGA 61.659 63.158 1.90 0.00 0.00 3.27
353 3069 0.738762 CTCATGCCGGTGTCAGAGTG 60.739 60.000 1.90 0.00 0.00 3.51
361 3077 1.276421 CGGTGTCAGAGTGAAGGGATT 59.724 52.381 0.00 0.00 0.00 3.01
715 3431 2.665603 GCTCTGCCGGTTTCCTCT 59.334 61.111 1.90 0.00 0.00 3.69
717 3433 0.606673 GCTCTGCCGGTTTCCTCTTT 60.607 55.000 1.90 0.00 0.00 2.52
726 3442 3.244249 CCGGTTTCCTCTTTCTCTTCAGT 60.244 47.826 0.00 0.00 0.00 3.41
732 3448 2.064762 CTCTTTCTCTTCAGTGGTGCG 58.935 52.381 0.00 0.00 0.00 5.34
736 3452 1.112916 TCTCTTCAGTGGTGCGGTGA 61.113 55.000 0.00 0.00 0.00 4.02
740 3456 1.811645 TTCAGTGGTGCGGTGATCGA 61.812 55.000 0.00 0.00 42.43 3.59
745 3461 2.167861 GGTGCGGTGATCGAAGCTC 61.168 63.158 0.00 4.29 41.45 4.09
756 3472 2.169789 CGAAGCTCGATGCCAGGTG 61.170 63.158 0.00 0.00 43.74 4.00
783 3499 4.660938 GTGGCCGGCCCTCTTGTT 62.661 66.667 41.75 0.00 34.56 2.83
784 3500 3.897122 TGGCCGGCCCTCTTGTTT 61.897 61.111 41.75 0.00 34.56 2.83
785 3501 2.353573 GGCCGGCCCTCTTGTTTA 59.646 61.111 36.64 0.00 0.00 2.01
786 3502 2.044555 GGCCGGCCCTCTTGTTTAC 61.045 63.158 36.64 4.38 0.00 2.01
787 3503 2.396157 GCCGGCCCTCTTGTTTACG 61.396 63.158 18.11 0.00 0.00 3.18
788 3504 2.396157 CCGGCCCTCTTGTTTACGC 61.396 63.158 0.00 0.00 0.00 4.42
789 3505 1.669760 CGGCCCTCTTGTTTACGCA 60.670 57.895 0.00 0.00 0.00 5.24
790 3506 1.635663 CGGCCCTCTTGTTTACGCAG 61.636 60.000 0.00 0.00 0.00 5.18
791 3507 0.321298 GGCCCTCTTGTTTACGCAGA 60.321 55.000 0.00 0.00 0.00 4.26
792 3508 1.519408 GCCCTCTTGTTTACGCAGAA 58.481 50.000 0.00 0.00 0.00 3.02
793 3509 1.197036 GCCCTCTTGTTTACGCAGAAC 59.803 52.381 0.00 0.00 0.00 3.01
794 3510 1.804748 CCCTCTTGTTTACGCAGAACC 59.195 52.381 0.00 0.00 0.00 3.62
795 3511 1.459592 CCTCTTGTTTACGCAGAACCG 59.540 52.381 0.00 0.00 0.00 4.44
796 3512 1.459592 CTCTTGTTTACGCAGAACCGG 59.540 52.381 0.00 0.00 0.00 5.28
797 3513 0.515564 CTTGTTTACGCAGAACCGGG 59.484 55.000 6.32 0.00 0.00 5.73
798 3514 0.885596 TTGTTTACGCAGAACCGGGG 60.886 55.000 6.32 0.00 0.00 5.73
799 3515 2.036571 GTTTACGCAGAACCGGGGG 61.037 63.158 6.32 0.00 0.00 5.40
800 3516 2.215625 TTTACGCAGAACCGGGGGA 61.216 57.895 6.32 0.00 0.00 4.81
801 3517 1.555477 TTTACGCAGAACCGGGGGAT 61.555 55.000 6.32 0.00 0.00 3.85
802 3518 2.246761 TTACGCAGAACCGGGGGATG 62.247 60.000 6.32 0.00 0.00 3.51
803 3519 4.096003 CGCAGAACCGGGGGATGT 62.096 66.667 6.32 0.00 0.00 3.06
804 3520 2.355115 GCAGAACCGGGGGATGTT 59.645 61.111 6.32 0.00 0.00 2.71
805 3521 1.304134 GCAGAACCGGGGGATGTTT 60.304 57.895 6.32 0.00 0.00 2.83
806 3522 0.898326 GCAGAACCGGGGGATGTTTT 60.898 55.000 6.32 0.00 0.00 2.43
807 3523 0.887933 CAGAACCGGGGGATGTTTTG 59.112 55.000 6.32 0.00 0.00 2.44
808 3524 0.251608 AGAACCGGGGGATGTTTTGG 60.252 55.000 6.32 0.00 0.00 3.28
809 3525 0.251430 GAACCGGGGGATGTTTTGGA 60.251 55.000 6.32 0.00 0.00 3.53
810 3526 0.251608 AACCGGGGGATGTTTTGGAG 60.252 55.000 6.32 0.00 0.00 3.86
811 3527 1.382629 CCGGGGGATGTTTTGGAGT 59.617 57.895 0.00 0.00 0.00 3.85
812 3528 0.251608 CCGGGGGATGTTTTGGAGTT 60.252 55.000 0.00 0.00 0.00 3.01
813 3529 1.173913 CGGGGGATGTTTTGGAGTTC 58.826 55.000 0.00 0.00 0.00 3.01
814 3530 1.173913 GGGGGATGTTTTGGAGTTCG 58.826 55.000 0.00 0.00 0.00 3.95
815 3531 0.526211 GGGGATGTTTTGGAGTTCGC 59.474 55.000 0.00 0.00 0.00 4.70
816 3532 0.168128 GGGATGTTTTGGAGTTCGCG 59.832 55.000 0.00 0.00 0.00 5.87
817 3533 0.168128 GGATGTTTTGGAGTTCGCGG 59.832 55.000 6.13 0.00 0.00 6.46
818 3534 0.168128 GATGTTTTGGAGTTCGCGGG 59.832 55.000 6.13 0.00 0.00 6.13
819 3535 0.536460 ATGTTTTGGAGTTCGCGGGT 60.536 50.000 6.13 0.00 0.00 5.28
820 3536 0.748729 TGTTTTGGAGTTCGCGGGTT 60.749 50.000 6.13 0.00 0.00 4.11
821 3537 0.382873 GTTTTGGAGTTCGCGGGTTT 59.617 50.000 6.13 0.00 0.00 3.27
822 3538 1.104630 TTTTGGAGTTCGCGGGTTTT 58.895 45.000 6.13 0.00 0.00 2.43
823 3539 0.664224 TTTGGAGTTCGCGGGTTTTC 59.336 50.000 6.13 0.00 0.00 2.29
824 3540 1.167781 TTGGAGTTCGCGGGTTTTCC 61.168 55.000 6.13 7.65 39.75 3.13
840 3556 6.791867 GGTTTTCCCTAATATTTGAGGCTT 57.208 37.500 0.00 0.00 0.00 4.35
841 3557 6.573434 GGTTTTCCCTAATATTTGAGGCTTG 58.427 40.000 0.00 0.00 0.00 4.01
842 3558 6.379988 GGTTTTCCCTAATATTTGAGGCTTGA 59.620 38.462 0.00 0.00 0.00 3.02
843 3559 7.069950 GGTTTTCCCTAATATTTGAGGCTTGAT 59.930 37.037 0.00 0.00 0.00 2.57
844 3560 7.587037 TTTCCCTAATATTTGAGGCTTGATG 57.413 36.000 0.00 0.00 0.00 3.07
875 3591 3.535280 TGGTTGGCCAGAAAAGAAAAC 57.465 42.857 5.11 0.00 40.46 2.43
878 3594 3.194861 GTTGGCCAGAAAAGAAAACACC 58.805 45.455 5.11 0.00 0.00 4.16
903 3629 1.398692 GGATGGGCCTTTAAATCGCA 58.601 50.000 4.53 8.96 0.00 5.10
909 3636 2.033424 GGGCCTTTAAATCGCATGTCTC 59.967 50.000 0.84 0.00 0.00 3.36
923 3650 1.185618 TGTCTCTTGGGCGCTACAGT 61.186 55.000 7.64 0.00 0.00 3.55
951 3678 5.964958 TTGGATGCCAGAAAGAAAACTAG 57.035 39.130 0.00 0.00 33.81 2.57
982 3712 7.893124 TTTGGGATAGATTAGAGTACGAGTT 57.107 36.000 0.00 0.00 0.00 3.01
1095 3825 2.262774 CTGGCCATCTCCCCTGTCAC 62.263 65.000 5.51 0.00 0.00 3.67
1099 3829 1.604378 CATCTCCCCTGTCACACCC 59.396 63.158 0.00 0.00 0.00 4.61
1210 3946 1.009389 CGGCTTCGACAAGGTGACTC 61.009 60.000 0.00 0.00 36.06 3.36
1225 3961 4.898861 AGGTGACTCTCTCTTCTCTGTTTT 59.101 41.667 0.00 0.00 32.90 2.43
1228 3964 6.462347 GGTGACTCTCTCTTCTCTGTTTTCTT 60.462 42.308 0.00 0.00 0.00 2.52
1239 3975 4.075682 CTCTGTTTTCTTCCCCTTCTTCC 58.924 47.826 0.00 0.00 0.00 3.46
1364 4106 3.359950 GGAAAATGGCAGATTGGAGAGT 58.640 45.455 0.00 0.00 0.00 3.24
1427 4169 3.382832 CTGAAGGACGGCCGGACT 61.383 66.667 31.76 23.64 39.96 3.85
1457 4199 1.815421 GATGTACGTGCCCCTGCTG 60.815 63.158 0.00 0.00 38.71 4.41
1478 4220 3.733960 CGGTGCGTCGAGACCAGA 61.734 66.667 12.74 0.00 31.97 3.86
1562 4313 3.376078 GTGGCGACGTCCCTGGTA 61.376 66.667 19.61 1.88 0.00 3.25
1655 4406 3.706373 ACCTGGACGGCGCTGATT 61.706 61.111 25.98 0.00 35.61 2.57
1661 4412 1.141019 GACGGCGCTGATTACAGGA 59.859 57.895 25.98 0.00 43.62 3.86
1662 4413 0.249489 GACGGCGCTGATTACAGGAT 60.249 55.000 25.98 0.00 43.62 3.24
1818 4569 1.676678 GCAGGTCCATGGCTACTCGA 61.677 60.000 6.96 0.00 0.00 4.04
1820 4571 1.000283 CAGGTCCATGGCTACTCGATC 60.000 57.143 6.96 0.00 0.00 3.69
1832 4583 1.794714 ACTCGATCAAGTATGGGGCT 58.205 50.000 0.00 0.00 0.00 5.19
1851 4602 2.546584 GCTGATACCATCACGAGCATGA 60.547 50.000 0.00 0.00 35.06 3.07
1901 4652 4.810191 GTCTGGAGACTTACAATCTGGT 57.190 45.455 0.00 0.00 41.65 4.00
1976 4727 2.332362 TATCGTCCTGCGCCGAAGAC 62.332 60.000 4.18 5.51 41.07 3.01
2060 4811 2.910688 ATGAGTTCACGTTGACCAGT 57.089 45.000 0.00 0.00 0.00 4.00
2096 4847 0.671781 GCGCGAGGCTGGATATGAAT 60.672 55.000 12.10 0.00 39.11 2.57
2207 4958 4.736896 GGCGAAACGGACGAGGCT 62.737 66.667 0.00 0.00 0.00 4.58
2378 5129 3.265221 TGAGGTCTGAATTGAAGCCTGAT 59.735 43.478 0.00 0.00 0.00 2.90
2450 5201 0.610232 AGCAGGGTGAGCAAATCCAC 60.610 55.000 0.00 0.00 0.00 4.02
2455 5206 0.387239 GGTGAGCAAATCCACGCAAC 60.387 55.000 0.00 0.00 34.30 4.17
2459 5210 1.372872 GCAAATCCACGCAACCACC 60.373 57.895 0.00 0.00 0.00 4.61
2501 5252 0.737804 ATGTTGTTGTGAACAGCGCA 59.262 45.000 11.47 0.00 44.41 6.09
2516 5267 2.677836 CAGCGCACTGGTAAACATGTAT 59.322 45.455 11.47 0.00 40.48 2.29
2542 5293 2.528743 GCGGATGCATCGAGTGTGG 61.529 63.158 20.15 4.79 42.15 4.17
2585 5336 0.179084 CAACACGGACACCTGTCACT 60.179 55.000 7.71 0.00 46.47 3.41
2622 5373 2.125147 GGTACTCGCAGCATGGCA 60.125 61.111 0.00 0.00 35.86 4.92
2684 5435 2.343163 CTGGCGCCAAACCAAACGAA 62.343 55.000 32.09 1.95 36.56 3.85
2918 5669 3.197983 GGTCTAGTTTGGTAGCTGGATGT 59.802 47.826 0.00 0.00 0.00 3.06
2927 5678 1.103803 TAGCTGGATGTCGGAGTCAC 58.896 55.000 0.00 0.00 0.00 3.67
2939 5690 0.108138 GGAGTCACGGGAACATGGAG 60.108 60.000 0.00 0.00 0.00 3.86
2954 5705 0.321671 TGGAGCTTGCTTTCTACGCT 59.678 50.000 0.00 0.00 0.00 5.07
3087 5838 2.436417 CCAAACATGAAGATGTCGGGT 58.564 47.619 0.00 0.00 42.30 5.28
3137 5888 7.308830 GCAATCAGAGACAAGGTGTATTTCTTT 60.309 37.037 0.00 0.00 0.00 2.52
3170 5921 1.267121 TGACTCACCCTCAAGCTACC 58.733 55.000 0.00 0.00 0.00 3.18
3215 5966 0.405585 TGCTGGAAAAGGCTAAGGCT 59.594 50.000 0.00 0.00 41.24 4.58
3265 6016 3.681897 CCTGAGTTGTTATCTGACAGCAC 59.318 47.826 0.00 0.00 33.75 4.40
3509 6260 1.450312 CAAGGATGGTCGGTGCTCC 60.450 63.158 0.00 0.00 0.00 4.70
3562 6320 1.131126 CCGAAAAATCTCATGCGCACT 59.869 47.619 14.90 0.00 0.00 4.40
3647 6406 6.037830 TGAAGAACTTGTTTACTGCAAGGTAC 59.962 38.462 9.42 0.00 43.15 3.34
3648 6407 4.510340 AGAACTTGTTTACTGCAAGGTACG 59.490 41.667 9.42 0.00 43.15 3.67
3649 6408 3.800531 ACTTGTTTACTGCAAGGTACGT 58.199 40.909 9.42 0.00 45.38 3.57
3650 6409 4.947645 ACTTGTTTACTGCAAGGTACGTA 58.052 39.130 9.42 0.00 45.38 3.57
3651 6410 4.746611 ACTTGTTTACTGCAAGGTACGTAC 59.253 41.667 17.56 17.56 45.38 3.67
3652 6411 3.652274 TGTTTACTGCAAGGTACGTACC 58.348 45.455 33.16 33.16 46.82 3.34
3713 6472 5.771153 TGAAAGCATGATTTGTTCAGTCA 57.229 34.783 14.71 0.43 37.89 3.41
3756 6519 8.390143 AGTATATATGACCATGCATAAACCCAA 58.610 33.333 0.00 0.00 34.67 4.12
3832 6601 3.254657 TGTAACTGTTGTAAATGCTGGCC 59.745 43.478 2.69 0.00 0.00 5.36
3833 6602 1.993956 ACTGTTGTAAATGCTGGCCA 58.006 45.000 4.71 4.71 0.00 5.36
3844 6613 0.407528 TGCTGGCCAATTAGGGTCAA 59.592 50.000 7.01 0.00 43.10 3.18
3845 6614 0.817654 GCTGGCCAATTAGGGTCAAC 59.182 55.000 7.01 0.00 43.10 3.18
3863 6636 7.651704 AGGGTCAACTTTCATTGTTTTAATTCG 59.348 33.333 0.00 0.00 0.00 3.34
3883 6656 5.369685 TCGCAATGCTGACTCAAATTTTA 57.630 34.783 2.94 0.00 0.00 1.52
3937 6710 8.965819 AGCATTGTGTACCATATGAAACAAATA 58.034 29.630 3.65 0.00 31.90 1.40
4036 6809 5.129815 ACAAGATTTTATCCTGCTACCGGTA 59.870 40.000 14.95 14.95 0.00 4.02
4124 6903 0.108963 TCCGGCGGGAAAGAAGAAAA 59.891 50.000 27.98 0.00 40.15 2.29
4127 6906 2.750712 CCGGCGGGAAAGAAGAAAAATA 59.249 45.455 20.56 0.00 34.06 1.40
4134 6913 5.016831 GGGAAAGAAGAAAAATAGGGCTCA 58.983 41.667 0.00 0.00 0.00 4.26
4143 6922 3.382083 AAATAGGGCTCAATTCCGGTT 57.618 42.857 0.00 0.00 0.00 4.44
4147 6926 1.304134 GGCTCAATTCCGGTTGGGT 60.304 57.895 0.00 0.00 37.00 4.51
4150 6929 1.471287 GCTCAATTCCGGTTGGGTAAC 59.529 52.381 0.00 0.00 37.00 2.50
4151 6930 1.735571 CTCAATTCCGGTTGGGTAACG 59.264 52.381 0.00 0.00 37.69 3.18
4167 6946 3.306434 GGTAACGAAAAGGCTCTTCGATC 59.694 47.826 27.95 16.24 46.73 3.69
4168 6947 3.320673 AACGAAAAGGCTCTTCGATCT 57.679 42.857 27.95 10.05 46.73 2.75
4270 7049 3.128188 CAGCAGCAGCAGCAGGAG 61.128 66.667 12.92 0.00 45.49 3.69
4277 7056 1.376942 CAGCAGCAGGAGGAGTTGG 60.377 63.158 0.00 0.00 0.00 3.77
4278 7057 2.749441 GCAGCAGGAGGAGTTGGC 60.749 66.667 0.00 0.00 0.00 4.52
4302 7081 4.493747 CGGCGTCGGGAAGAGGAC 62.494 72.222 0.00 0.00 39.31 3.85
4314 7093 3.119096 GAGGACGAAGGTTGCGGC 61.119 66.667 0.00 0.00 35.64 6.53
4331 7110 4.778143 CGGCGTTGGGAAGGGAGG 62.778 72.222 0.00 0.00 0.00 4.30
4332 7111 3.327404 GGCGTTGGGAAGGGAGGA 61.327 66.667 0.00 0.00 0.00 3.71
4333 7112 2.754375 GCGTTGGGAAGGGAGGAA 59.246 61.111 0.00 0.00 0.00 3.36
4334 7113 1.377333 GCGTTGGGAAGGGAGGAAG 60.377 63.158 0.00 0.00 0.00 3.46
4335 7114 1.299976 CGTTGGGAAGGGAGGAAGG 59.700 63.158 0.00 0.00 0.00 3.46
4336 7115 1.489560 CGTTGGGAAGGGAGGAAGGT 61.490 60.000 0.00 0.00 0.00 3.50
4360 7139 1.895131 GTCACCATGAACCTTGGCATT 59.105 47.619 0.00 0.00 37.81 3.56
4363 7142 2.564062 CACCATGAACCTTGGCATTCTT 59.436 45.455 0.00 0.00 37.81 2.52
4373 7152 3.190878 GCATTCTTGACTGCCCCG 58.809 61.111 2.12 0.00 32.15 5.73
4393 7172 1.751927 CTGCTTCCATCCCCTGCAC 60.752 63.158 0.00 0.00 0.00 4.57
4431 7214 1.302511 CCCTGTCCCTGTTGGTTCG 60.303 63.158 0.00 0.00 34.77 3.95
4469 7252 1.286553 ACTGAAACCCCACAAACTCCA 59.713 47.619 0.00 0.00 0.00 3.86
4471 7254 3.139397 ACTGAAACCCCACAAACTCCATA 59.861 43.478 0.00 0.00 0.00 2.74
4484 7267 2.547990 ACTCCATAAGGAAGGACGGTT 58.452 47.619 0.00 0.00 45.19 4.44
4485 7268 2.910977 ACTCCATAAGGAAGGACGGTTT 59.089 45.455 0.00 0.00 45.19 3.27
4492 7361 1.493446 AGGAAGGACGGTTTTGGAACT 59.507 47.619 0.00 0.00 36.03 3.01
4529 7398 2.422377 GGACCTGTGGTTTTGTAGTGGT 60.422 50.000 0.00 0.00 35.25 4.16
4569 7438 7.389053 AGGTTGACATCTCTGAACAATTAGAAC 59.611 37.037 0.00 0.00 0.00 3.01
4574 7443 9.604626 GACATCTCTGAACAATTAGAACAAAAG 57.395 33.333 0.00 0.00 0.00 2.27
4654 7523 6.000246 TGTTGCCTTCAGTCCATATATGAA 58.000 37.500 14.54 0.04 0.00 2.57
4790 7660 3.952931 AGCTCATCATTGCTCAGAAACT 58.047 40.909 0.00 0.00 33.90 2.66
4804 7677 7.175104 TGCTCAGAAACTATAAACAAGGGAAT 58.825 34.615 0.00 0.00 0.00 3.01
5063 8357 3.071023 ACAGTTTCATCTCCGTTCCTCAA 59.929 43.478 0.00 0.00 0.00 3.02
5081 8375 2.203523 TGCACTGTTGGGCATGCT 60.204 55.556 18.92 0.00 38.90 3.79
5110 8404 1.743252 CTTGCCACGAGAAGCTCCC 60.743 63.158 0.00 0.00 0.00 4.30
5123 8417 1.968540 GCTCCCTGACAAGTGCCAC 60.969 63.158 0.00 0.00 0.00 5.01
5125 8419 0.604780 CTCCCTGACAAGTGCCACTG 60.605 60.000 0.00 0.00 0.00 3.66
5210 8695 0.179134 GATCGAGGTCCACAACTCCG 60.179 60.000 0.00 0.00 0.00 4.63
5215 8700 1.194781 AGGTCCACAACTCCGCATCT 61.195 55.000 0.00 0.00 0.00 2.90
5307 8792 2.037136 GCAGTGTCAGCCTCGCATT 61.037 57.895 0.00 0.00 0.00 3.56
5308 8793 1.792301 CAGTGTCAGCCTCGCATTG 59.208 57.895 0.00 0.00 0.00 2.82
5313 8798 0.462581 GTCAGCCTCGCATTGATGGA 60.463 55.000 0.00 0.00 0.00 3.41
5314 8799 0.471191 TCAGCCTCGCATTGATGGAT 59.529 50.000 0.00 0.00 0.00 3.41
5318 8803 1.520494 CCTCGCATTGATGGATCCAG 58.480 55.000 21.33 7.10 0.00 3.86
5320 8805 0.839277 TCGCATTGATGGATCCAGGT 59.161 50.000 21.33 3.64 0.00 4.00
5321 8806 1.212688 TCGCATTGATGGATCCAGGTT 59.787 47.619 21.33 2.76 0.00 3.50
5322 8807 1.605710 CGCATTGATGGATCCAGGTTC 59.394 52.381 21.33 13.51 0.00 3.62
5323 8808 2.658285 GCATTGATGGATCCAGGTTCA 58.342 47.619 21.33 16.09 0.00 3.18
5324 8809 2.621998 GCATTGATGGATCCAGGTTCAG 59.378 50.000 21.33 9.26 0.00 3.02
5325 8810 3.686405 GCATTGATGGATCCAGGTTCAGA 60.686 47.826 21.33 10.09 0.00 3.27
5326 8811 4.726583 CATTGATGGATCCAGGTTCAGAT 58.273 43.478 21.33 11.69 0.00 2.90
5327 8812 3.851458 TGATGGATCCAGGTTCAGATG 57.149 47.619 21.33 0.00 0.00 2.90
5328 8813 2.158711 TGATGGATCCAGGTTCAGATGC 60.159 50.000 21.33 0.14 0.00 3.91
5329 8814 1.288188 TGGATCCAGGTTCAGATGCA 58.712 50.000 11.44 0.00 38.35 3.96
5330 8815 1.211212 TGGATCCAGGTTCAGATGCAG 59.789 52.381 11.44 0.00 36.12 4.41
5331 8816 1.476471 GGATCCAGGTTCAGATGCAGG 60.476 57.143 6.95 0.00 31.71 4.85
5332 8817 0.106819 ATCCAGGTTCAGATGCAGGC 60.107 55.000 0.00 0.00 0.00 4.85
5333 8818 1.203441 TCCAGGTTCAGATGCAGGCT 61.203 55.000 0.00 0.00 0.00 4.58
5334 8819 1.030488 CCAGGTTCAGATGCAGGCTG 61.030 60.000 10.94 10.94 34.71 4.85
5335 8820 1.030488 CAGGTTCAGATGCAGGCTGG 61.030 60.000 17.64 0.00 34.20 4.85
5336 8821 2.413142 GGTTCAGATGCAGGCTGGC 61.413 63.158 17.64 9.25 34.20 4.85
5343 8828 2.115695 TGCAGGCTGGCATTGTCA 59.884 55.556 17.64 0.15 39.25 3.58
5344 8829 1.304630 TGCAGGCTGGCATTGTCAT 60.305 52.632 17.64 0.00 39.25 3.06
5345 8830 1.141019 GCAGGCTGGCATTGTCATG 59.859 57.895 17.64 0.00 0.00 3.07
5354 8839 3.583054 CATTGTCATGCCCTGGAGT 57.417 52.632 0.00 0.00 0.00 3.85
5355 8840 1.100510 CATTGTCATGCCCTGGAGTG 58.899 55.000 0.00 0.00 0.00 3.51
5356 8841 0.700564 ATTGTCATGCCCTGGAGTGT 59.299 50.000 0.00 0.00 0.00 3.55
5357 8842 0.478072 TTGTCATGCCCTGGAGTGTT 59.522 50.000 0.00 0.00 0.00 3.32
5358 8843 1.357137 TGTCATGCCCTGGAGTGTTA 58.643 50.000 0.00 0.00 0.00 2.41
5359 8844 1.915489 TGTCATGCCCTGGAGTGTTAT 59.085 47.619 0.00 0.00 0.00 1.89
5360 8845 3.111484 TGTCATGCCCTGGAGTGTTATA 58.889 45.455 0.00 0.00 0.00 0.98
5361 8846 3.716353 TGTCATGCCCTGGAGTGTTATAT 59.284 43.478 0.00 0.00 0.00 0.86
5362 8847 4.202357 TGTCATGCCCTGGAGTGTTATATC 60.202 45.833 0.00 0.00 0.00 1.63
5363 8848 3.973305 TCATGCCCTGGAGTGTTATATCA 59.027 43.478 0.00 0.00 0.00 2.15
5364 8849 4.040829 TCATGCCCTGGAGTGTTATATCAG 59.959 45.833 0.00 0.00 0.00 2.90
5365 8850 2.705658 TGCCCTGGAGTGTTATATCAGG 59.294 50.000 0.00 0.00 43.26 3.86
5366 8851 2.972713 GCCCTGGAGTGTTATATCAGGA 59.027 50.000 9.02 0.00 45.66 3.86
5367 8852 3.584848 GCCCTGGAGTGTTATATCAGGAT 59.415 47.826 9.02 0.00 45.66 3.24
5368 8853 4.777896 GCCCTGGAGTGTTATATCAGGATA 59.222 45.833 9.02 0.00 45.66 2.59
5369 8854 5.337652 GCCCTGGAGTGTTATATCAGGATAC 60.338 48.000 9.02 0.00 45.66 2.24
5370 8855 5.780282 CCCTGGAGTGTTATATCAGGATACA 59.220 44.000 9.02 0.00 45.66 2.29
5371 8856 6.071108 CCCTGGAGTGTTATATCAGGATACAG 60.071 46.154 9.02 0.00 45.66 2.74
5372 8857 6.495181 CCTGGAGTGTTATATCAGGATACAGT 59.505 42.308 0.00 0.00 45.66 3.55
5373 8858 7.670140 CCTGGAGTGTTATATCAGGATACAGTA 59.330 40.741 0.00 0.00 45.66 2.74
5374 8859 9.249053 CTGGAGTGTTATATCAGGATACAGTAT 57.751 37.037 0.00 0.00 41.41 2.12
5375 8860 9.601810 TGGAGTGTTATATCAGGATACAGTATT 57.398 33.333 0.00 0.00 41.41 1.89
5389 8874 3.281727 CAGTATTACCACTGCCCATGT 57.718 47.619 0.00 0.00 39.54 3.21
5390 8875 4.415881 CAGTATTACCACTGCCCATGTA 57.584 45.455 0.00 0.00 39.54 2.29
5391 8876 4.380531 CAGTATTACCACTGCCCATGTAG 58.619 47.826 0.00 0.00 39.54 2.74
5392 8877 2.348411 ATTACCACTGCCCATGTAGC 57.652 50.000 0.00 0.00 0.00 3.58
5393 8878 0.988063 TTACCACTGCCCATGTAGCA 59.012 50.000 7.38 7.38 38.82 3.49
5546 9074 4.302559 ACATTACCCCTCAGAAGAAACC 57.697 45.455 0.00 0.00 0.00 3.27
5559 9087 4.455877 CAGAAGAAACCACACAGGGTATTC 59.544 45.833 0.00 0.00 41.32 1.75
5638 9166 1.538047 TCAGGCTTTTCACATCCTGC 58.462 50.000 2.44 0.00 44.27 4.85
5745 9273 4.219288 AGCCAATCTTGACCATTGAAACTC 59.781 41.667 0.00 0.00 33.69 3.01
5815 9346 5.848406 AGTTCTACACTAGATATTGCCTGC 58.152 41.667 0.00 0.00 34.22 4.85
5817 9348 4.483950 TCTACACTAGATATTGCCTGCCT 58.516 43.478 0.00 0.00 0.00 4.75
5818 9349 3.482156 ACACTAGATATTGCCTGCCTG 57.518 47.619 0.00 0.00 0.00 4.85
5819 9350 2.105477 ACACTAGATATTGCCTGCCTGG 59.895 50.000 0.00 0.00 39.35 4.45
5874 9407 7.264373 TCAGTTGAAATCTTTTGAGTCCTTC 57.736 36.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.163554 GTGAGACCGTAACGAGACCT 58.836 55.000 0.00 0.00 0.00 3.85
1 2 0.877071 TGTGAGACCGTAACGAGACC 59.123 55.000 0.00 0.00 0.00 3.85
2 3 2.161012 TGATGTGAGACCGTAACGAGAC 59.839 50.000 0.00 0.00 0.00 3.36
3 4 2.161012 GTGATGTGAGACCGTAACGAGA 59.839 50.000 0.00 0.00 0.00 4.04
4 5 2.095415 TGTGATGTGAGACCGTAACGAG 60.095 50.000 0.00 0.00 0.00 4.18
20 2736 2.439135 TGCTATGCATGGGTACTGTGAT 59.561 45.455 10.16 0.00 31.71 3.06
21 2737 1.836802 TGCTATGCATGGGTACTGTGA 59.163 47.619 10.16 0.00 31.71 3.58
22 2738 1.942657 GTGCTATGCATGGGTACTGTG 59.057 52.381 10.16 0.00 41.91 3.66
23 2739 1.559219 TGTGCTATGCATGGGTACTGT 59.441 47.619 10.16 0.00 41.91 3.55
24 2740 2.330440 TGTGCTATGCATGGGTACTG 57.670 50.000 10.16 0.00 41.91 2.74
63 2779 5.347907 GCTTGGAAGATTGAGCAATTTCAAG 59.652 40.000 10.92 10.92 40.16 3.02
67 2783 5.245526 AGAAGCTTGGAAGATTGAGCAATTT 59.754 36.000 2.10 0.00 34.31 1.82
90 2806 2.159787 CCGAGATTGCAACACGAAGAAG 60.160 50.000 18.57 3.21 0.00 2.85
97 2813 0.955428 TGAGGCCGAGATTGCAACAC 60.955 55.000 0.00 0.00 0.00 3.32
111 2827 2.238395 AGAGGAGAAAGATGGTTGAGGC 59.762 50.000 0.00 0.00 0.00 4.70
121 2837 1.978580 GGTGGACCAAGAGGAGAAAGA 59.021 52.381 0.00 0.00 38.69 2.52
155 2871 0.966920 GGACCTCAACTTCTCGGTGA 59.033 55.000 0.00 0.00 0.00 4.02
198 2914 5.488645 TTAAAAGTTTCACTGGTTCGACC 57.511 39.130 0.00 0.00 39.22 4.79
201 2917 7.248437 AGAGTTTTAAAAGTTTCACTGGTTCG 58.752 34.615 9.60 0.00 0.00 3.95
256 2972 2.743928 GAGGTCAGCGCACTTGGG 60.744 66.667 11.47 0.00 0.00 4.12
304 3020 4.017126 CAAGTACCCAAGGAAAATCCCTC 58.983 47.826 0.00 0.00 37.19 4.30
313 3029 0.109723 GCACACCAAGTACCCAAGGA 59.890 55.000 0.00 0.00 0.00 3.36
333 3049 1.153489 CTCTGACACCGGCATGAGG 60.153 63.158 0.00 0.69 0.00 3.86
337 3053 0.036952 CTTCACTCTGACACCGGCAT 60.037 55.000 0.00 0.00 0.00 4.40
340 3056 1.185618 TCCCTTCACTCTGACACCGG 61.186 60.000 0.00 0.00 0.00 5.28
341 3057 0.898320 ATCCCTTCACTCTGACACCG 59.102 55.000 0.00 0.00 0.00 4.94
684 3400 4.208686 GAGCCGCCGACCACTAGG 62.209 72.222 0.00 0.00 42.21 3.02
685 3401 3.141488 AGAGCCGCCGACCACTAG 61.141 66.667 0.00 0.00 0.00 2.57
715 3431 0.468226 ACCGCACCACTGAAGAGAAA 59.532 50.000 0.00 0.00 0.00 2.52
717 3433 1.112916 TCACCGCACCACTGAAGAGA 61.113 55.000 0.00 0.00 0.00 3.10
726 3442 2.434185 GCTTCGATCACCGCACCA 60.434 61.111 0.00 0.00 38.37 4.17
740 3456 2.270205 CCACCTGGCATCGAGCTT 59.730 61.111 0.00 0.00 44.79 3.74
766 3482 2.757980 TAAACAAGAGGGCCGGCCAC 62.758 60.000 44.46 35.07 37.98 5.01
767 3483 2.530672 TAAACAAGAGGGCCGGCCA 61.531 57.895 44.46 20.41 37.98 5.36
769 3485 2.396157 CGTAAACAAGAGGGCCGGC 61.396 63.158 21.18 21.18 0.00 6.13
771 3487 1.635663 CTGCGTAAACAAGAGGGCCG 61.636 60.000 0.00 0.00 0.00 6.13
773 3489 1.197036 GTTCTGCGTAAACAAGAGGGC 59.803 52.381 0.00 0.00 0.00 5.19
775 3491 1.459592 CGGTTCTGCGTAAACAAGAGG 59.540 52.381 0.00 0.00 0.00 3.69
776 3492 1.459592 CCGGTTCTGCGTAAACAAGAG 59.540 52.381 0.00 0.00 0.00 2.85
777 3493 1.504359 CCGGTTCTGCGTAAACAAGA 58.496 50.000 0.00 0.00 0.00 3.02
778 3494 0.515564 CCCGGTTCTGCGTAAACAAG 59.484 55.000 0.00 0.00 0.00 3.16
779 3495 0.885596 CCCCGGTTCTGCGTAAACAA 60.886 55.000 0.00 0.00 0.00 2.83
780 3496 1.301874 CCCCGGTTCTGCGTAAACA 60.302 57.895 0.00 0.00 0.00 2.83
781 3497 2.036571 CCCCCGGTTCTGCGTAAAC 61.037 63.158 0.00 0.00 0.00 2.01
782 3498 1.555477 ATCCCCCGGTTCTGCGTAAA 61.555 55.000 0.00 0.00 0.00 2.01
783 3499 1.991167 ATCCCCCGGTTCTGCGTAA 60.991 57.895 0.00 0.00 0.00 3.18
784 3500 2.364579 ATCCCCCGGTTCTGCGTA 60.365 61.111 0.00 0.00 0.00 4.42
785 3501 4.096003 CATCCCCCGGTTCTGCGT 62.096 66.667 0.00 0.00 0.00 5.24
786 3502 3.622060 AACATCCCCCGGTTCTGCG 62.622 63.158 0.00 0.00 0.00 5.18
787 3503 0.898326 AAAACATCCCCCGGTTCTGC 60.898 55.000 0.00 0.00 0.00 4.26
788 3504 0.887933 CAAAACATCCCCCGGTTCTG 59.112 55.000 0.00 0.00 0.00 3.02
789 3505 0.251608 CCAAAACATCCCCCGGTTCT 60.252 55.000 0.00 0.00 0.00 3.01
790 3506 0.251430 TCCAAAACATCCCCCGGTTC 60.251 55.000 0.00 0.00 0.00 3.62
791 3507 0.251608 CTCCAAAACATCCCCCGGTT 60.252 55.000 0.00 0.00 0.00 4.44
792 3508 1.382629 CTCCAAAACATCCCCCGGT 59.617 57.895 0.00 0.00 0.00 5.28
793 3509 0.251608 AACTCCAAAACATCCCCCGG 60.252 55.000 0.00 0.00 0.00 5.73
794 3510 1.173913 GAACTCCAAAACATCCCCCG 58.826 55.000 0.00 0.00 0.00 5.73
795 3511 1.173913 CGAACTCCAAAACATCCCCC 58.826 55.000 0.00 0.00 0.00 5.40
796 3512 0.526211 GCGAACTCCAAAACATCCCC 59.474 55.000 0.00 0.00 0.00 4.81
797 3513 0.168128 CGCGAACTCCAAAACATCCC 59.832 55.000 0.00 0.00 0.00 3.85
798 3514 0.168128 CCGCGAACTCCAAAACATCC 59.832 55.000 8.23 0.00 0.00 3.51
799 3515 0.168128 CCCGCGAACTCCAAAACATC 59.832 55.000 8.23 0.00 0.00 3.06
800 3516 0.536460 ACCCGCGAACTCCAAAACAT 60.536 50.000 8.23 0.00 0.00 2.71
801 3517 0.748729 AACCCGCGAACTCCAAAACA 60.749 50.000 8.23 0.00 0.00 2.83
802 3518 0.382873 AAACCCGCGAACTCCAAAAC 59.617 50.000 8.23 0.00 0.00 2.43
803 3519 1.065851 GAAAACCCGCGAACTCCAAAA 59.934 47.619 8.23 0.00 0.00 2.44
804 3520 0.664224 GAAAACCCGCGAACTCCAAA 59.336 50.000 8.23 0.00 0.00 3.28
805 3521 1.167781 GGAAAACCCGCGAACTCCAA 61.168 55.000 8.23 0.00 0.00 3.53
806 3522 1.598685 GGAAAACCCGCGAACTCCA 60.599 57.895 8.23 0.00 0.00 3.86
807 3523 2.330372 GGGAAAACCCGCGAACTCC 61.330 63.158 8.23 5.89 35.07 3.85
808 3524 0.037046 TAGGGAAAACCCGCGAACTC 60.037 55.000 8.23 0.00 41.63 3.01
809 3525 0.397564 TTAGGGAAAACCCGCGAACT 59.602 50.000 8.23 0.00 41.63 3.01
810 3526 1.456296 ATTAGGGAAAACCCGCGAAC 58.544 50.000 8.23 0.00 41.63 3.95
811 3527 3.564053 ATATTAGGGAAAACCCGCGAA 57.436 42.857 8.23 0.00 41.63 4.70
812 3528 3.564053 AATATTAGGGAAAACCCGCGA 57.436 42.857 8.23 0.00 41.63 5.87
813 3529 3.628487 TCAAATATTAGGGAAAACCCGCG 59.372 43.478 0.00 0.00 41.63 6.46
814 3530 4.037565 CCTCAAATATTAGGGAAAACCCGC 59.962 45.833 0.00 0.00 41.63 6.13
815 3531 4.037565 GCCTCAAATATTAGGGAAAACCCG 59.962 45.833 6.44 0.00 41.63 5.28
816 3532 5.208890 AGCCTCAAATATTAGGGAAAACCC 58.791 41.667 6.44 0.00 41.63 4.11
817 3533 6.379988 TCAAGCCTCAAATATTAGGGAAAACC 59.620 38.462 6.44 0.00 40.67 3.27
818 3534 7.404671 TCAAGCCTCAAATATTAGGGAAAAC 57.595 36.000 6.44 0.00 33.17 2.43
819 3535 7.069826 CCATCAAGCCTCAAATATTAGGGAAAA 59.930 37.037 6.44 0.00 33.17 2.29
820 3536 6.550854 CCATCAAGCCTCAAATATTAGGGAAA 59.449 38.462 6.44 0.00 33.17 3.13
821 3537 6.070656 CCATCAAGCCTCAAATATTAGGGAA 58.929 40.000 6.44 0.00 33.17 3.97
822 3538 5.372363 TCCATCAAGCCTCAAATATTAGGGA 59.628 40.000 6.44 0.00 33.17 4.20
823 3539 5.634118 TCCATCAAGCCTCAAATATTAGGG 58.366 41.667 6.44 2.57 33.17 3.53
824 3540 7.771927 AATCCATCAAGCCTCAAATATTAGG 57.228 36.000 0.44 0.44 35.86 2.69
860 3576 3.653344 GATGGTGTTTTCTTTTCTGGCC 58.347 45.455 0.00 0.00 0.00 5.36
866 3582 2.952116 TCCCCGATGGTGTTTTCTTTT 58.048 42.857 0.00 0.00 34.77 2.27
867 3583 2.668144 TCCCCGATGGTGTTTTCTTT 57.332 45.000 0.00 0.00 34.77 2.52
878 3594 0.184933 TTAAAGGCCCATCCCCGATG 59.815 55.000 0.00 0.00 39.52 3.84
903 3629 0.176680 CTGTAGCGCCCAAGAGACAT 59.823 55.000 2.29 0.00 0.00 3.06
978 3708 3.075148 GGACCAGGTTTAAGAGCAACTC 58.925 50.000 0.00 0.00 0.00 3.01
980 3710 2.858745 TGGACCAGGTTTAAGAGCAAC 58.141 47.619 0.00 0.00 0.00 4.17
982 3712 2.879756 GCATGGACCAGGTTTAAGAGCA 60.880 50.000 8.14 0.00 0.00 4.26
1088 3818 3.567579 ATTGGCGGGGTGTGACAGG 62.568 63.158 0.00 0.00 0.00 4.00
1210 3946 4.285775 AGGGGAAGAAAACAGAGAAGAGAG 59.714 45.833 0.00 0.00 0.00 3.20
1225 3961 0.496382 TCCAGGGAAGAAGGGGAAGA 59.504 55.000 0.00 0.00 0.00 2.87
1228 3964 1.229853 GGTCCAGGGAAGAAGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
1239 3975 1.821136 GGCAATCTTTCTTGGTCCAGG 59.179 52.381 0.00 0.00 0.00 4.45
1275 4016 6.146673 GCAATGGTGAAAGAAAAAGAATGAGG 59.853 38.462 0.00 0.00 0.00 3.86
1427 4169 1.445410 GTACATCGCCGACTGCACA 60.445 57.895 0.00 0.00 41.33 4.57
1436 4178 4.157120 AGGGGCACGTACATCGCC 62.157 66.667 5.31 5.31 45.47 5.54
1562 4313 1.144969 CGCACCTCATGTACACGTTT 58.855 50.000 0.00 0.00 0.00 3.60
1655 4406 7.229707 GCTTCAGAGTTCAGAGTATATCCTGTA 59.770 40.741 0.00 0.00 0.00 2.74
1661 4412 4.890581 ACCGCTTCAGAGTTCAGAGTATAT 59.109 41.667 0.00 0.00 0.00 0.86
1662 4413 4.096532 CACCGCTTCAGAGTTCAGAGTATA 59.903 45.833 0.00 0.00 0.00 1.47
1818 4569 3.326521 TGGTATCAGCCCCATACTTGAT 58.673 45.455 0.00 0.00 34.81 2.57
1820 4571 3.072915 TGATGGTATCAGCCCCATACTTG 59.927 47.826 0.00 0.00 41.51 3.16
1832 4583 2.546584 GCTCATGCTCGTGATGGTATCA 60.547 50.000 0.00 0.00 34.85 2.15
1851 4602 6.372659 CAGTACATCCTACAAAGTGAATTGCT 59.627 38.462 0.00 0.00 33.52 3.91
1892 4643 0.548682 AGGCCCTCAGACCAGATTGT 60.549 55.000 0.00 0.00 0.00 2.71
1893 4644 0.622665 AAGGCCCTCAGACCAGATTG 59.377 55.000 0.00 0.00 0.00 2.67
1895 4646 2.270434 TAAAGGCCCTCAGACCAGAT 57.730 50.000 0.00 0.00 0.00 2.90
1901 4652 0.120377 TCCCCTTAAAGGCCCTCAGA 59.880 55.000 0.00 0.00 32.73 3.27
1976 4727 1.134965 CCAAGCTCCAGGTAGTTCTCG 60.135 57.143 0.00 0.00 0.00 4.04
2060 4811 1.229975 CGCCACACAAGCTCATGACA 61.230 55.000 4.26 0.00 0.00 3.58
2096 4847 2.922503 TGGACCTGCTTGCCGAGA 60.923 61.111 0.00 0.00 0.00 4.04
2153 4904 4.348168 AGGTACATTGTGGAGTTCTTCACT 59.652 41.667 11.80 0.00 39.07 3.41
2207 4958 3.689161 CCATCTCTTCAAACAACCGCATA 59.311 43.478 0.00 0.00 0.00 3.14
2378 5129 3.557898 GGATGCTTGAGAAGGTGAACAGA 60.558 47.826 0.00 0.00 0.00 3.41
2450 5201 1.468520 CCAGTCTTTATGGTGGTTGCG 59.531 52.381 0.00 0.00 32.85 4.85
2501 5252 6.128391 CGCACTTGTTATACATGTTTACCAGT 60.128 38.462 2.30 4.78 34.74 4.00
2542 5293 1.005394 TCGACGAAGGCTTTGGTCC 60.005 57.895 18.48 6.58 38.40 4.46
2585 5336 4.111577 ACCCTGAAATCATAGAGGTCCAA 58.888 43.478 0.00 0.00 0.00 3.53
2622 5373 0.467474 TGTATCGCATCTCGGGACCT 60.467 55.000 0.00 0.00 39.76 3.85
2684 5435 5.238432 TGACAGCAAACTTACGAATGTGATT 59.762 36.000 0.00 0.00 0.00 2.57
2885 5636 2.237143 CAAACTAGACCAGATGGCCTCA 59.763 50.000 3.32 0.00 39.32 3.86
2900 5651 2.167693 CCGACATCCAGCTACCAAACTA 59.832 50.000 0.00 0.00 0.00 2.24
2918 5669 1.589630 CATGTTCCCGTGACTCCGA 59.410 57.895 0.00 0.00 0.00 4.55
2927 5678 0.962356 AAGCAAGCTCCATGTTCCCG 60.962 55.000 0.00 0.00 0.00 5.14
2939 5690 0.179205 CAGCAGCGTAGAAAGCAAGC 60.179 55.000 0.00 0.00 37.89 4.01
3087 5838 1.819288 CCAGCTACGGTCTCTGAGAAA 59.181 52.381 9.31 0.00 0.00 2.52
3137 5888 3.382865 GGTGAGTCATGTCATCAGCTCTA 59.617 47.826 14.90 0.00 38.20 2.43
3170 5921 6.480524 TTCTCCAACAATTGATACAACTCG 57.519 37.500 13.59 0.00 0.00 4.18
3239 5990 3.182967 GTCAGATAACAACTCAGGAGCG 58.817 50.000 0.00 0.00 0.00 5.03
3265 6016 3.758088 CTGTCGTCATCGCCCTCCG 62.758 68.421 0.00 0.00 36.96 4.63
3443 6194 3.565482 GGACAACAATCTCTCTGTTTGCA 59.435 43.478 0.00 0.00 34.80 4.08
3509 6260 1.586028 CGCACCAAAATCCCCACAG 59.414 57.895 0.00 0.00 0.00 3.66
3562 6320 5.262588 TGTTCTCAGAATAGAATAGCGCA 57.737 39.130 11.47 0.00 37.78 6.09
3647 6406 2.545526 GACATCTCATGGCATTGGTACG 59.454 50.000 0.00 0.00 38.49 3.67
3648 6407 2.880890 GGACATCTCATGGCATTGGTAC 59.119 50.000 0.00 0.00 41.20 3.34
3649 6408 2.485302 CGGACATCTCATGGCATTGGTA 60.485 50.000 0.00 0.00 41.20 3.25
3650 6409 1.748244 CGGACATCTCATGGCATTGGT 60.748 52.381 0.00 0.00 41.20 3.67
3651 6410 0.949397 CGGACATCTCATGGCATTGG 59.051 55.000 0.00 0.00 41.20 3.16
3652 6411 1.671979 ACGGACATCTCATGGCATTG 58.328 50.000 0.00 0.00 41.20 2.82
3653 6412 2.424601 CAAACGGACATCTCATGGCATT 59.575 45.455 0.00 0.00 41.20 3.56
3654 6413 2.019249 CAAACGGACATCTCATGGCAT 58.981 47.619 0.00 0.00 41.20 4.40
3655 6414 1.452110 CAAACGGACATCTCATGGCA 58.548 50.000 0.00 0.00 41.20 4.92
3656 6415 0.099436 GCAAACGGACATCTCATGGC 59.901 55.000 0.00 0.00 37.65 4.40
3713 6472 9.828039 CATATATACTCATATGTCACCAATGCT 57.172 33.333 1.90 0.00 35.18 3.79
3832 6601 8.661352 AAAACAATGAAAGTTGACCCTAATTG 57.339 30.769 0.00 0.00 33.37 2.32
3863 6636 8.715088 AGAATTTAAAATTTGAGTCAGCATTGC 58.285 29.630 0.00 0.00 0.00 3.56
3883 6656 7.202029 CCACTCAAATTATGGGCCATAGAATTT 60.202 37.037 24.58 24.58 30.00 1.82
3890 6663 3.686227 TCCACTCAAATTATGGGCCAT 57.314 42.857 24.69 24.69 34.03 4.40
3963 6736 8.709386 AGACATGCTACAAATACTCTTTACAG 57.291 34.615 0.00 0.00 0.00 2.74
4036 6809 3.439857 AACACACATGGGAGCAACTAT 57.560 42.857 0.00 0.00 0.00 2.12
4124 6903 2.654863 CAACCGGAATTGAGCCCTATT 58.345 47.619 9.46 0.00 0.00 1.73
4127 6906 1.000896 CCAACCGGAATTGAGCCCT 60.001 57.895 9.46 0.00 0.00 5.19
4134 6913 2.565046 TTCGTTACCCAACCGGAATT 57.435 45.000 9.46 0.00 34.64 2.17
4143 6922 2.774687 GAAGAGCCTTTTCGTTACCCA 58.225 47.619 0.00 0.00 0.00 4.51
4180 6959 4.309950 GACAGGGAACGGCGGTGT 62.310 66.667 13.24 6.33 0.00 4.16
4183 6962 2.175035 TTAAGGACAGGGAACGGCGG 62.175 60.000 13.24 0.00 0.00 6.13
4187 6966 2.038033 TGGAACTTAAGGACAGGGAACG 59.962 50.000 7.53 0.00 0.00 3.95
4198 6977 4.022849 CAGGGAAAAGCACTGGAACTTAAG 60.023 45.833 0.00 0.00 44.59 1.85
4199 6978 3.888930 CAGGGAAAAGCACTGGAACTTAA 59.111 43.478 0.00 0.00 44.59 1.85
4231 7010 2.369668 TTCCCATACCTTTCCTCCCA 57.630 50.000 0.00 0.00 0.00 4.37
4238 7017 2.381911 CTGCTGCATTCCCATACCTTT 58.618 47.619 1.31 0.00 0.00 3.11
4260 7039 3.076092 CCAACTCCTCCTGCTGCT 58.924 61.111 0.00 0.00 0.00 4.24
4265 7044 2.581354 CTCCGCCAACTCCTCCTG 59.419 66.667 0.00 0.00 0.00 3.86
4268 7047 4.475135 GCCCTCCGCCAACTCCTC 62.475 72.222 0.00 0.00 0.00 3.71
4295 7074 1.004918 CCGCAACCTTCGTCCTCTT 60.005 57.895 0.00 0.00 0.00 2.85
4314 7093 4.778143 CCTCCCTTCCCAACGCCG 62.778 72.222 0.00 0.00 0.00 6.46
4318 7097 1.665137 TACCTTCCTCCCTTCCCAAC 58.335 55.000 0.00 0.00 0.00 3.77
4319 7098 2.580783 CAATACCTTCCTCCCTTCCCAA 59.419 50.000 0.00 0.00 0.00 4.12
4320 7099 2.205342 CAATACCTTCCTCCCTTCCCA 58.795 52.381 0.00 0.00 0.00 4.37
4321 7100 2.172930 GACAATACCTTCCTCCCTTCCC 59.827 54.545 0.00 0.00 0.00 3.97
4323 7102 3.370633 GGTGACAATACCTTCCTCCCTTC 60.371 52.174 0.00 0.00 37.74 3.46
4324 7103 2.576648 GGTGACAATACCTTCCTCCCTT 59.423 50.000 0.00 0.00 37.74 3.95
4325 7104 2.197465 GGTGACAATACCTTCCTCCCT 58.803 52.381 0.00 0.00 37.74 4.20
4326 7105 1.913419 TGGTGACAATACCTTCCTCCC 59.087 52.381 0.00 0.00 41.43 4.30
4360 7139 3.059982 CAGACGGGGCAGTCAAGA 58.940 61.111 13.46 0.00 43.24 3.02
4363 7142 3.240134 GAAGCAGACGGGGCAGTCA 62.240 63.158 13.46 0.00 43.24 3.41
4373 7152 1.452833 GCAGGGGATGGAAGCAGAC 60.453 63.158 0.00 0.00 0.00 3.51
4448 7231 1.681264 GGAGTTTGTGGGGTTTCAGTG 59.319 52.381 0.00 0.00 0.00 3.66
4469 7252 4.077108 GTTCCAAAACCGTCCTTCCTTAT 58.923 43.478 0.00 0.00 0.00 1.73
4471 7254 2.092049 AGTTCCAAAACCGTCCTTCCTT 60.092 45.455 0.00 0.00 35.92 3.36
4484 7267 1.497286 ACCTGGCACCTAAGTTCCAAA 59.503 47.619 0.00 0.00 38.93 3.28
4485 7268 1.145571 ACCTGGCACCTAAGTTCCAA 58.854 50.000 0.00 0.00 38.93 3.53
4492 7361 1.479757 GGTCCAAAACCTGGCACCTAA 60.480 52.381 0.00 0.00 45.98 2.69
4569 7438 3.608073 GCTAATGTTTACGCCTGCTTTTG 59.392 43.478 0.00 0.00 0.00 2.44
4574 7443 0.380733 GGGCTAATGTTTACGCCTGC 59.619 55.000 0.00 0.00 42.13 4.85
4654 7523 9.582431 CAATGATGAGCAGAAAGATTTTACAAT 57.418 29.630 0.00 0.00 0.00 2.71
4708 7578 4.318332 CAACCAGTGATTGCTAGAGAACA 58.682 43.478 0.00 0.00 0.00 3.18
4804 7677 8.988060 TCAATACTTCCAGGAATACAGTATTCA 58.012 33.333 27.41 10.31 44.92 2.57
5081 8375 5.529581 TCTCGTGGCAAGATGAACATATA 57.470 39.130 3.00 0.00 0.00 0.86
5110 8404 1.947013 CAGCAGTGGCACTTGTCAG 59.053 57.895 19.43 7.53 44.61 3.51
5210 8695 1.751437 GGTTGGTCCCAGTTAGATGC 58.249 55.000 0.00 0.00 0.00 3.91
5246 8731 6.613755 GTTAACAAGTAACAAGCTCCTCAA 57.386 37.500 0.00 0.00 41.62 3.02
5291 8776 0.251354 ATCAATGCGAGGCTGACACT 59.749 50.000 0.00 0.00 0.00 3.55
5298 8783 0.535780 TGGATCCATCAATGCGAGGC 60.536 55.000 11.44 0.00 0.00 4.70
5301 8786 0.839277 ACCTGGATCCATCAATGCGA 59.161 50.000 16.63 0.00 0.00 5.10
5304 8789 4.160642 TCTGAACCTGGATCCATCAATG 57.839 45.455 16.63 5.87 0.00 2.82
5305 8790 4.726583 CATCTGAACCTGGATCCATCAAT 58.273 43.478 16.63 9.62 0.00 2.57
5307 8792 2.158711 GCATCTGAACCTGGATCCATCA 60.159 50.000 16.63 15.29 0.00 3.07
5308 8793 2.158711 TGCATCTGAACCTGGATCCATC 60.159 50.000 16.63 11.02 0.00 3.51
5313 8798 0.106819 GCCTGCATCTGAACCTGGAT 60.107 55.000 0.00 0.00 0.00 3.41
5314 8799 1.203441 AGCCTGCATCTGAACCTGGA 61.203 55.000 0.00 0.00 0.00 3.86
5318 8803 2.413142 GCCAGCCTGCATCTGAACC 61.413 63.158 15.32 2.98 33.54 3.62
5320 8805 2.758434 TGCCAGCCTGCATCTGAA 59.242 55.556 15.32 3.48 36.04 3.02
5326 8811 1.304630 ATGACAATGCCAGCCTGCA 60.305 52.632 0.00 0.00 46.94 4.41
5327 8812 1.141019 CATGACAATGCCAGCCTGC 59.859 57.895 0.00 0.00 0.00 4.85
5336 8821 1.100510 CACTCCAGGGCATGACAATG 58.899 55.000 0.00 0.00 36.82 2.82
5337 8822 0.700564 ACACTCCAGGGCATGACAAT 59.299 50.000 0.00 0.00 0.00 2.71
5338 8823 0.478072 AACACTCCAGGGCATGACAA 59.522 50.000 0.00 0.00 0.00 3.18
5339 8824 1.357137 TAACACTCCAGGGCATGACA 58.643 50.000 0.00 0.00 0.00 3.58
5340 8825 2.717639 ATAACACTCCAGGGCATGAC 57.282 50.000 0.00 0.00 0.00 3.06
5341 8826 3.973305 TGATATAACACTCCAGGGCATGA 59.027 43.478 0.00 0.00 0.00 3.07
5342 8827 4.321718 CTGATATAACACTCCAGGGCATG 58.678 47.826 0.00 0.00 0.00 4.06
5343 8828 3.328931 CCTGATATAACACTCCAGGGCAT 59.671 47.826 0.00 0.00 40.39 4.40
5344 8829 2.705658 CCTGATATAACACTCCAGGGCA 59.294 50.000 0.00 0.00 40.39 5.36
5345 8830 2.972713 TCCTGATATAACACTCCAGGGC 59.027 50.000 0.00 0.00 43.34 5.19
5346 8831 5.780282 TGTATCCTGATATAACACTCCAGGG 59.220 44.000 0.00 0.00 43.34 4.45
5347 8832 6.495181 ACTGTATCCTGATATAACACTCCAGG 59.505 42.308 0.00 0.00 44.23 4.45
5348 8833 7.531857 ACTGTATCCTGATATAACACTCCAG 57.468 40.000 0.00 0.00 0.00 3.86
5349 8834 9.601810 AATACTGTATCCTGATATAACACTCCA 57.398 33.333 0.00 0.00 0.00 3.86
5370 8855 3.181454 GCTACATGGGCAGTGGTAATACT 60.181 47.826 0.00 0.00 0.00 2.12
5371 8856 3.139077 GCTACATGGGCAGTGGTAATAC 58.861 50.000 0.00 0.00 0.00 1.89
5372 8857 2.774809 TGCTACATGGGCAGTGGTAATA 59.225 45.455 10.80 0.00 34.56 0.98
5373 8858 1.563879 TGCTACATGGGCAGTGGTAAT 59.436 47.619 10.80 0.00 34.56 1.89
5374 8859 0.988063 TGCTACATGGGCAGTGGTAA 59.012 50.000 10.80 0.00 34.56 2.85
5375 8860 1.212375 ATGCTACATGGGCAGTGGTA 58.788 50.000 17.85 0.00 43.15 3.25
5376 8861 0.332632 AATGCTACATGGGCAGTGGT 59.667 50.000 17.85 2.40 43.15 4.16
5377 8862 3.196040 AATGCTACATGGGCAGTGG 57.804 52.632 17.85 0.00 43.15 4.00
5379 8864 0.033796 AGCAATGCTACATGGGCAGT 60.034 50.000 5.69 13.86 43.15 4.40
5380 8865 1.108776 AAGCAATGCTACATGGGCAG 58.891 50.000 8.68 8.94 43.15 4.85
5381 8866 1.559368 AAAGCAATGCTACATGGGCA 58.441 45.000 8.68 15.88 38.25 5.36
5382 8867 2.094078 TCAAAAGCAATGCTACATGGGC 60.094 45.455 8.68 1.45 38.25 5.36
5383 8868 3.056678 TGTCAAAAGCAATGCTACATGGG 60.057 43.478 8.68 0.00 38.25 4.00
5384 8869 4.171005 CTGTCAAAAGCAATGCTACATGG 58.829 43.478 8.68 0.00 38.25 3.66
5385 8870 4.171005 CCTGTCAAAAGCAATGCTACATG 58.829 43.478 8.68 8.29 38.25 3.21
5386 8871 3.828451 ACCTGTCAAAAGCAATGCTACAT 59.172 39.130 8.68 0.00 38.25 2.29
5387 8872 3.004629 CACCTGTCAAAAGCAATGCTACA 59.995 43.478 8.68 8.34 38.25 2.74
5388 8873 3.253188 TCACCTGTCAAAAGCAATGCTAC 59.747 43.478 8.68 3.21 38.25 3.58
5389 8874 3.485394 TCACCTGTCAAAAGCAATGCTA 58.515 40.909 8.68 0.00 38.25 3.49
5390 8875 2.295349 CTCACCTGTCAAAAGCAATGCT 59.705 45.455 0.00 0.00 42.56 3.79
5391 8876 2.035066 ACTCACCTGTCAAAAGCAATGC 59.965 45.455 0.00 0.00 0.00 3.56
5392 8877 3.996150 ACTCACCTGTCAAAAGCAATG 57.004 42.857 0.00 0.00 0.00 2.82
5393 8878 4.718961 AGTACTCACCTGTCAAAAGCAAT 58.281 39.130 0.00 0.00 0.00 3.56
5466 8994 0.034337 TGCCCCGAGTACAAACAGTC 59.966 55.000 0.00 0.00 0.00 3.51
5500 9028 5.427036 TGTGTAATTCCTTTCAACGGTTC 57.573 39.130 0.00 0.00 0.00 3.62
5546 9074 3.259374 AGTGACAGAGAATACCCTGTGTG 59.741 47.826 0.00 0.00 43.02 3.82
5638 9166 5.689514 TGAAAATTTGAACAGCCAACATACG 59.310 36.000 0.00 0.00 0.00 3.06
5745 9273 9.053840 TGGAGTTACTATCTAAGACTACAATCG 57.946 37.037 0.00 0.00 28.68 3.34
5818 9349 2.324541 ACTGATAGAGATGGACCTGCC 58.675 52.381 0.00 0.00 37.10 4.85
5819 9350 4.342378 TGTAACTGATAGAGATGGACCTGC 59.658 45.833 0.00 0.00 0.00 4.85
5820 9351 6.493115 AGATGTAACTGATAGAGATGGACCTG 59.507 42.308 0.00 0.00 0.00 4.00
5821 9352 6.619464 AGATGTAACTGATAGAGATGGACCT 58.381 40.000 0.00 0.00 0.00 3.85
5822 9353 6.909550 AGATGTAACTGATAGAGATGGACC 57.090 41.667 0.00 0.00 0.00 4.46
5823 9354 8.177119 AGAAGATGTAACTGATAGAGATGGAC 57.823 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.