Multiple sequence alignment - TraesCS5B01G007900

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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 TraesCS5B01G007900 chr5B 100.000 4536 0 0 1 4536 8936800 8932265 0.000000e+00 8377
1 TraesCS5B01G007900 chr5B 97.840 972 20 1 3566 4536 452126144 452127115 0.000000e+00 1677
2 TraesCS5B01G007900 chr5B 93.527 448 29 0 1 448 8943539 8943092 0.000000e+00 667
3 TraesCS5B01G007900 chr5B 87.841 403 36 9 3094 3494 8902627 8902236 1.150000e-125 460
4 TraesCS5B01G007900 chr5B 93.227 251 14 2 2997 3247 8900277 8900030 2.580000e-97 366
5 TraesCS5B01G007900 chr5D 91.090 1863 116 25 1723 3566 8547769 8545938 0.000000e+00 2475
6 TraesCS5B01G007900 chr5D 91.751 1382 87 9 1887 3247 8497077 8495702 0.000000e+00 1895
7 TraesCS5B01G007900 chr5D 94.013 451 27 0 1 451 8593528 8593078 0.000000e+00 684
8 TraesCS5B01G007900 chr5D 94.463 307 17 0 414 720 8592890 8592584 1.480000e-129 473
9 TraesCS5B01G007900 chr5D 84.058 414 45 17 1293 1693 8548602 8548197 3.310000e-101 379
10 TraesCS5B01G007900 chr5D 87.216 352 12 16 977 1311 8548949 8548614 1.990000e-98 370
11 TraesCS5B01G007900 chr5A 91.939 1650 99 18 1724 3356 6725869 6724237 0.000000e+00 2279
12 TraesCS5B01G007900 chr5A 89.403 670 52 10 1900 2558 6675832 6675171 0.000000e+00 826
13 TraesCS5B01G007900 chr5A 92.461 451 34 0 1 451 6774011 6773561 0.000000e+00 645
14 TraesCS5B01G007900 chr5A 92.461 451 34 0 1 451 14864440 14863990 0.000000e+00 645
15 TraesCS5B01G007900 chr5A 96.286 350 13 0 2898 3247 6669791 6669442 3.940000e-160 575
16 TraesCS5B01G007900 chr5A 90.554 307 29 0 414 720 6773373 6773067 1.520000e-109 407
17 TraesCS5B01G007900 chr5A 93.015 272 19 0 414 685 14863802 14863531 9.140000e-107 398
18 TraesCS5B01G007900 chr5A 86.040 351 16 13 977 1311 6726987 6726654 3.360000e-91 346
19 TraesCS5B01G007900 chr5A 93.529 170 8 3 3378 3547 6718831 6718665 2.710000e-62 250
20 TraesCS5B01G007900 chr3B 97.942 972 19 1 3566 4536 232640521 232639550 0.000000e+00 1683
21 TraesCS5B01G007900 chr3B 79.425 452 79 6 1 448 617439075 617438634 1.590000e-79 307
22 TraesCS5B01G007900 chr7B 97.840 972 20 1 3566 4536 457405751 457406722 0.000000e+00 1677
23 TraesCS5B01G007900 chr7B 97.840 972 20 1 3566 4536 458482291 458481320 0.000000e+00 1677
24 TraesCS5B01G007900 chr7B 97.368 988 22 4 3552 4536 571400269 571399283 0.000000e+00 1677
25 TraesCS5B01G007900 chr7B 97.077 992 24 5 3547 4535 433878818 433877829 0.000000e+00 1666
26 TraesCS5B01G007900 chr4A 97.840 972 20 1 3566 4536 467531794 467532765 0.000000e+00 1677
27 TraesCS5B01G007900 chr2B 97.840 972 20 1 3566 4536 178706385 178705414 0.000000e+00 1677
28 TraesCS5B01G007900 chr1B 97.840 972 20 1 3566 4536 146735622 146736593 0.000000e+00 1677
29 TraesCS5B01G007900 chr1D 81.761 318 41 11 1927 2241 203311325 203311022 2.710000e-62 250
30 TraesCS5B01G007900 chr1A 76.892 489 71 28 1923 2403 257566241 257565787 5.860000e-59 239


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 TraesCS5B01G007900 chr5B 8932265 8936800 4535 True 8377.000000 8377 100.000000 1 4536 1 chr5B.!!$R1 4535
1 TraesCS5B01G007900 chr5B 452126144 452127115 971 False 1677.000000 1677 97.840000 3566 4536 1 chr5B.!!$F1 970
2 TraesCS5B01G007900 chr5B 8900030 8902627 2597 True 413.000000 460 90.534000 2997 3494 2 chr5B.!!$R3 497
3 TraesCS5B01G007900 chr5D 8495702 8497077 1375 True 1895.000000 1895 91.751000 1887 3247 1 chr5D.!!$R1 1360
4 TraesCS5B01G007900 chr5D 8545938 8548949 3011 True 1074.666667 2475 87.454667 977 3566 3 chr5D.!!$R2 2589
5 TraesCS5B01G007900 chr5D 8592584 8593528 944 True 578.500000 684 94.238000 1 720 2 chr5D.!!$R3 719
6 TraesCS5B01G007900 chr5A 6724237 6726987 2750 True 1312.500000 2279 88.989500 977 3356 2 chr5A.!!$R4 2379
7 TraesCS5B01G007900 chr5A 6675171 6675832 661 True 826.000000 826 89.403000 1900 2558 1 chr5A.!!$R2 658
8 TraesCS5B01G007900 chr5A 6773067 6774011 944 True 526.000000 645 91.507500 1 720 2 chr5A.!!$R5 719
9 TraesCS5B01G007900 chr5A 14863531 14864440 909 True 521.500000 645 92.738000 1 685 2 chr5A.!!$R6 684
10 TraesCS5B01G007900 chr3B 232639550 232640521 971 True 1683.000000 1683 97.942000 3566 4536 1 chr3B.!!$R1 970
11 TraesCS5B01G007900 chr7B 457405751 457406722 971 False 1677.000000 1677 97.840000 3566 4536 1 chr7B.!!$F1 970
12 TraesCS5B01G007900 chr7B 458481320 458482291 971 True 1677.000000 1677 97.840000 3566 4536 1 chr7B.!!$R2 970
13 TraesCS5B01G007900 chr7B 571399283 571400269 986 True 1677.000000 1677 97.368000 3552 4536 1 chr7B.!!$R3 984
14 TraesCS5B01G007900 chr7B 433877829 433878818 989 True 1666.000000 1666 97.077000 3547 4535 1 chr7B.!!$R1 988
15 TraesCS5B01G007900 chr4A 467531794 467532765 971 False 1677.000000 1677 97.840000 3566 4536 1 chr4A.!!$F1 970
16 TraesCS5B01G007900 chr2B 178705414 178706385 971 True 1677.000000 1677 97.840000 3566 4536 1 chr2B.!!$R1 970
17 TraesCS5B01G007900 chr1B 146735622 146736593 971 False 1677.000000 1677 97.840000 3566 4536 1 chr1B.!!$F1 970

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
826 1052 0.037232 ACTGCACTCGGTCTTAAGCC 60.037 55.0 0.00 1.75 0.00 4.35 F
827 1053 0.037326 CTGCACTCGGTCTTAAGCCA 60.037 55.0 13.93 3.64 0.00 4.75 F
1448 1747 0.175760 TGCGCAGTTCTAGGTGGATC 59.824 55.0 5.66 0.00 0.00 3.36 F
3301 4041 0.103572 GGCACCGGCTCGATTAAGTA 59.896 55.0 0.00 0.00 40.87 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 3524 0.320946 AAGCATGCCACATTTGGTGC 60.321 50.000 15.66 5.55 46.50 5.01 R
2860 3600 2.093711 GGGCTGTTTTCAACAACCTTGT 60.094 45.455 8.56 0.00 44.98 3.16 R
3368 4108 0.113580 GAAAAAGGGGCCTGGGTACA 59.886 55.000 0.84 0.00 0.00 2.90 R
4207 5824 2.136863 TCTCCTCTCCCGGATCTTAGT 58.863 52.381 0.73 0.00 31.43 2.24 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
58 59 4.148825 GTCCTGAGCGCCACCGAT 62.149 66.667 2.29 0.00 36.29 4.18
320 321 1.065491 TGAACATGGGGATGGAGAACG 60.065 52.381 0.00 0.00 0.00 3.95
427 428 1.219773 ACACTGGGATGGAGATGCAT 58.780 50.000 0.00 0.00 0.00 3.96
567 793 3.034635 TCCCATACTGAGGAGAAGAAGC 58.965 50.000 0.00 0.00 0.00 3.86
602 828 2.085320 AGTTCTGAGTACGAGTGCGAT 58.915 47.619 0.00 0.00 41.64 4.58
611 837 1.941734 CGAGTGCGATTCCGAGAGC 60.942 63.158 0.00 0.00 40.82 4.09
641 867 5.180868 TCTGAGTCTGTCCGAGTTAAACTAC 59.819 44.000 0.00 0.00 0.00 2.73
674 900 1.728425 CGTATGCATGGATGGATGTCG 59.272 52.381 10.16 5.37 39.29 4.35
723 949 8.589335 AGTTATATTATTCATCGTGCTTTCGT 57.411 30.769 0.00 0.00 0.00 3.85
724 950 8.700644 AGTTATATTATTCATCGTGCTTTCGTC 58.299 33.333 0.00 0.00 0.00 4.20
725 951 8.700644 GTTATATTATTCATCGTGCTTTCGTCT 58.299 33.333 0.00 0.00 0.00 4.18
726 952 4.840401 TTATTCATCGTGCTTTCGTCTG 57.160 40.909 0.00 0.00 0.00 3.51
727 953 2.148916 TTCATCGTGCTTTCGTCTGT 57.851 45.000 0.00 0.00 0.00 3.41
728 954 3.291809 TTCATCGTGCTTTCGTCTGTA 57.708 42.857 0.00 0.00 0.00 2.74
729 955 2.592194 TCATCGTGCTTTCGTCTGTAC 58.408 47.619 0.00 0.00 0.00 2.90
730 956 2.228103 TCATCGTGCTTTCGTCTGTACT 59.772 45.455 0.00 0.00 0.00 2.73
731 957 2.046283 TCGTGCTTTCGTCTGTACTG 57.954 50.000 0.00 0.00 0.00 2.74
732 958 1.335810 TCGTGCTTTCGTCTGTACTGT 59.664 47.619 0.00 0.00 0.00 3.55
733 959 1.452025 CGTGCTTTCGTCTGTACTGTG 59.548 52.381 0.00 0.00 0.00 3.66
734 960 2.470821 GTGCTTTCGTCTGTACTGTGT 58.529 47.619 0.00 0.00 0.00 3.72
735 961 2.864343 GTGCTTTCGTCTGTACTGTGTT 59.136 45.455 0.00 0.00 0.00 3.32
736 962 3.060473 GTGCTTTCGTCTGTACTGTGTTC 60.060 47.826 0.00 0.00 0.00 3.18
737 963 3.120792 GCTTTCGTCTGTACTGTGTTCA 58.879 45.455 0.00 0.00 0.00 3.18
738 964 3.554324 GCTTTCGTCTGTACTGTGTTCAA 59.446 43.478 0.00 0.00 0.00 2.69
739 965 4.033587 GCTTTCGTCTGTACTGTGTTCAAA 59.966 41.667 0.00 0.00 0.00 2.69
740 966 5.446741 GCTTTCGTCTGTACTGTGTTCAAAA 60.447 40.000 0.00 0.00 0.00 2.44
741 967 5.712217 TTCGTCTGTACTGTGTTCAAAAG 57.288 39.130 0.00 0.00 0.00 2.27
742 968 5.001237 TCGTCTGTACTGTGTTCAAAAGA 57.999 39.130 0.00 0.00 0.00 2.52
743 969 5.412640 TCGTCTGTACTGTGTTCAAAAGAA 58.587 37.500 0.00 0.00 0.00 2.52
744 970 5.870433 TCGTCTGTACTGTGTTCAAAAGAAA 59.130 36.000 0.00 0.00 0.00 2.52
745 971 6.369340 TCGTCTGTACTGTGTTCAAAAGAAAA 59.631 34.615 0.00 0.00 0.00 2.29
746 972 6.464834 CGTCTGTACTGTGTTCAAAAGAAAAC 59.535 38.462 0.00 0.00 0.00 2.43
747 973 7.302524 GTCTGTACTGTGTTCAAAAGAAAACA 58.697 34.615 1.70 1.70 32.03 2.83
748 974 7.968405 GTCTGTACTGTGTTCAAAAGAAAACAT 59.032 33.333 2.03 0.00 37.67 2.71
749 975 9.168451 TCTGTACTGTGTTCAAAAGAAAACATA 57.832 29.630 2.03 0.00 37.67 2.29
750 976 9.221775 CTGTACTGTGTTCAAAAGAAAACATAC 57.778 33.333 2.03 7.51 37.67 2.39
751 977 8.952278 TGTACTGTGTTCAAAAGAAAACATACT 58.048 29.630 2.03 0.00 37.67 2.12
752 978 9.783256 GTACTGTGTTCAAAAGAAAACATACTT 57.217 29.630 2.03 0.00 37.67 2.24
756 982 9.279904 TGTGTTCAAAAGAAAACATACTTTACG 57.720 29.630 0.00 0.00 37.67 3.18
757 983 9.281075 GTGTTCAAAAGAAAACATACTTTACGT 57.719 29.630 0.00 0.00 37.67 3.57
758 984 9.843334 TGTTCAAAAGAAAACATACTTTACGTT 57.157 25.926 0.00 0.00 35.66 3.99
760 986 8.844441 TCAAAAGAAAACATACTTTACGTTGG 57.156 30.769 0.00 0.00 35.66 3.77
761 987 8.675504 TCAAAAGAAAACATACTTTACGTTGGA 58.324 29.630 0.00 0.00 35.66 3.53
762 988 9.458374 CAAAAGAAAACATACTTTACGTTGGAT 57.542 29.630 0.00 0.00 35.66 3.41
796 1022 9.716507 TTTTATGTAGTACGTCGGATTTACTAC 57.283 33.333 21.10 21.10 44.44 2.73
798 1024 6.925610 TGTAGTACGTCGGATTTACTACAT 57.074 37.500 24.02 2.70 46.81 2.29
799 1025 6.718388 TGTAGTACGTCGGATTTACTACATG 58.282 40.000 24.02 0.00 46.81 3.21
800 1026 6.538381 TGTAGTACGTCGGATTTACTACATGA 59.462 38.462 24.02 11.91 46.81 3.07
801 1027 6.441093 AGTACGTCGGATTTACTACATGAA 57.559 37.500 0.00 0.00 0.00 2.57
802 1028 6.261118 AGTACGTCGGATTTACTACATGAAC 58.739 40.000 0.00 0.00 0.00 3.18
803 1029 4.100529 ACGTCGGATTTACTACATGAACG 58.899 43.478 0.00 0.00 0.00 3.95
804 1030 3.484649 CGTCGGATTTACTACATGAACGG 59.515 47.826 0.00 0.00 0.00 4.44
805 1031 4.675510 GTCGGATTTACTACATGAACGGA 58.324 43.478 0.00 0.00 0.00 4.69
806 1032 5.287226 GTCGGATTTACTACATGAACGGAT 58.713 41.667 0.00 0.00 0.00 4.18
807 1033 6.441274 GTCGGATTTACTACATGAACGGATA 58.559 40.000 0.00 0.00 0.00 2.59
808 1034 6.361748 GTCGGATTTACTACATGAACGGATAC 59.638 42.308 0.00 0.00 0.00 2.24
809 1035 6.263842 TCGGATTTACTACATGAACGGATACT 59.736 38.462 0.00 0.00 0.00 2.12
810 1036 6.362551 CGGATTTACTACATGAACGGATACTG 59.637 42.308 0.00 0.00 0.00 2.74
811 1037 6.145696 GGATTTACTACATGAACGGATACTGC 59.854 42.308 0.00 0.00 0.00 4.40
812 1038 5.585820 TTACTACATGAACGGATACTGCA 57.414 39.130 0.00 0.00 0.00 4.41
813 1039 3.782046 ACTACATGAACGGATACTGCAC 58.218 45.455 0.00 0.00 0.00 4.57
814 1040 3.447586 ACTACATGAACGGATACTGCACT 59.552 43.478 0.00 0.00 0.00 4.40
815 1041 2.893637 ACATGAACGGATACTGCACTC 58.106 47.619 0.00 0.00 0.00 3.51
816 1042 1.854743 CATGAACGGATACTGCACTCG 59.145 52.381 0.00 0.00 0.00 4.18
817 1043 0.172578 TGAACGGATACTGCACTCGG 59.827 55.000 0.00 0.00 0.00 4.63
818 1044 0.172803 GAACGGATACTGCACTCGGT 59.827 55.000 0.00 0.00 35.61 4.69
819 1045 0.172803 AACGGATACTGCACTCGGTC 59.827 55.000 0.00 0.00 33.08 4.79
820 1046 0.680280 ACGGATACTGCACTCGGTCT 60.680 55.000 0.00 0.00 33.08 3.85
821 1047 0.456221 CGGATACTGCACTCGGTCTT 59.544 55.000 0.00 0.00 33.08 3.01
822 1048 1.674441 CGGATACTGCACTCGGTCTTA 59.326 52.381 0.00 0.00 33.08 2.10
823 1049 2.098607 CGGATACTGCACTCGGTCTTAA 59.901 50.000 0.00 0.00 33.08 1.85
824 1050 3.707793 GGATACTGCACTCGGTCTTAAG 58.292 50.000 0.00 0.00 33.08 1.85
825 1051 2.649331 TACTGCACTCGGTCTTAAGC 57.351 50.000 0.00 0.00 33.08 3.09
826 1052 0.037232 ACTGCACTCGGTCTTAAGCC 60.037 55.000 0.00 1.75 0.00 4.35
827 1053 0.037326 CTGCACTCGGTCTTAAGCCA 60.037 55.000 13.93 3.64 0.00 4.75
828 1054 0.394938 TGCACTCGGTCTTAAGCCAA 59.605 50.000 13.93 0.00 0.00 4.52
829 1055 1.202710 TGCACTCGGTCTTAAGCCAAA 60.203 47.619 13.93 3.52 0.00 3.28
830 1056 1.877443 GCACTCGGTCTTAAGCCAAAA 59.123 47.619 13.93 1.63 0.00 2.44
831 1057 2.095718 GCACTCGGTCTTAAGCCAAAAG 60.096 50.000 13.93 10.49 0.00 2.27
832 1058 2.484264 CACTCGGTCTTAAGCCAAAAGG 59.516 50.000 13.93 0.00 0.00 3.11
833 1059 2.084546 CTCGGTCTTAAGCCAAAAGGG 58.915 52.381 13.93 0.00 40.85 3.95
834 1060 1.700739 TCGGTCTTAAGCCAAAAGGGA 59.299 47.619 13.93 2.41 40.01 4.20
835 1061 2.084546 CGGTCTTAAGCCAAAAGGGAG 58.915 52.381 13.93 0.00 40.01 4.30
836 1062 2.290071 CGGTCTTAAGCCAAAAGGGAGA 60.290 50.000 13.93 0.00 40.01 3.71
837 1063 3.348119 GGTCTTAAGCCAAAAGGGAGAG 58.652 50.000 10.08 0.00 40.01 3.20
838 1064 3.009143 GGTCTTAAGCCAAAAGGGAGAGA 59.991 47.826 10.08 0.00 40.01 3.10
839 1065 4.506802 GGTCTTAAGCCAAAAGGGAGAGAA 60.507 45.833 10.08 0.00 40.01 2.87
840 1066 5.070685 GTCTTAAGCCAAAAGGGAGAGAAA 58.929 41.667 0.00 0.00 40.01 2.52
841 1067 5.712446 GTCTTAAGCCAAAAGGGAGAGAAAT 59.288 40.000 0.00 0.00 40.01 2.17
842 1068 5.711976 TCTTAAGCCAAAAGGGAGAGAAATG 59.288 40.000 0.00 0.00 40.01 2.32
843 1069 3.532641 AGCCAAAAGGGAGAGAAATGT 57.467 42.857 0.00 0.00 40.01 2.71
844 1070 4.657814 AGCCAAAAGGGAGAGAAATGTA 57.342 40.909 0.00 0.00 40.01 2.29
845 1071 5.198602 AGCCAAAAGGGAGAGAAATGTAT 57.801 39.130 0.00 0.00 40.01 2.29
846 1072 5.196695 AGCCAAAAGGGAGAGAAATGTATC 58.803 41.667 0.00 0.00 40.01 2.24
847 1073 4.949856 GCCAAAAGGGAGAGAAATGTATCA 59.050 41.667 0.00 0.00 40.01 2.15
848 1074 5.418840 GCCAAAAGGGAGAGAAATGTATCAA 59.581 40.000 0.00 0.00 40.01 2.57
849 1075 6.625960 GCCAAAAGGGAGAGAAATGTATCAAC 60.626 42.308 0.00 0.00 40.01 3.18
850 1076 6.434028 CCAAAAGGGAGAGAAATGTATCAACA 59.566 38.462 0.00 0.00 40.01 3.33
851 1077 7.308435 CAAAAGGGAGAGAAATGTATCAACAC 58.692 38.462 0.00 0.00 38.78 3.32
852 1078 5.762179 AGGGAGAGAAATGTATCAACACA 57.238 39.130 0.00 0.00 38.78 3.72
853 1079 6.319048 AGGGAGAGAAATGTATCAACACAT 57.681 37.500 0.00 0.00 40.90 3.21
855 1081 6.600822 AGGGAGAGAAATGTATCAACACATTG 59.399 38.462 2.48 0.00 46.00 2.82
856 1082 6.375455 GGGAGAGAAATGTATCAACACATTGT 59.625 38.462 2.48 0.00 46.00 2.71
857 1083 7.094205 GGGAGAGAAATGTATCAACACATTGTT 60.094 37.037 2.48 0.00 46.00 2.83
858 1084 8.299570 GGAGAGAAATGTATCAACACATTGTTT 58.700 33.333 2.48 0.00 46.00 2.83
859 1085 9.683069 GAGAGAAATGTATCAACACATTGTTTT 57.317 29.630 2.48 0.00 46.00 2.43
894 1120 9.889128 TGAGATAAGAAATGTATCAACACATGA 57.111 29.630 0.00 0.00 43.67 3.07
896 1122 9.113838 AGATAAGAAATGTATCAACACATGACC 57.886 33.333 0.00 0.00 41.93 4.02
897 1123 6.515272 AAGAAATGTATCAACACATGACCC 57.485 37.500 0.00 0.00 41.93 4.46
898 1124 4.635765 AGAAATGTATCAACACATGACCCG 59.364 41.667 0.00 0.00 41.93 5.28
899 1125 2.394930 TGTATCAACACATGACCCGG 57.605 50.000 0.00 0.00 41.93 5.73
900 1126 1.626321 TGTATCAACACATGACCCGGT 59.374 47.619 0.00 0.00 41.93 5.28
901 1127 2.039216 TGTATCAACACATGACCCGGTT 59.961 45.455 0.00 0.00 41.93 4.44
902 1128 2.286365 ATCAACACATGACCCGGTTT 57.714 45.000 0.00 0.00 41.93 3.27
903 1129 2.932855 TCAACACATGACCCGGTTTA 57.067 45.000 0.00 0.00 31.50 2.01
904 1130 3.426787 TCAACACATGACCCGGTTTAT 57.573 42.857 0.00 0.00 31.50 1.40
905 1131 3.757270 TCAACACATGACCCGGTTTATT 58.243 40.909 0.00 0.00 31.50 1.40
906 1132 4.145807 TCAACACATGACCCGGTTTATTT 58.854 39.130 0.00 0.00 31.50 1.40
907 1133 4.585162 TCAACACATGACCCGGTTTATTTT 59.415 37.500 0.00 0.00 31.50 1.82
908 1134 5.069251 TCAACACATGACCCGGTTTATTTTT 59.931 36.000 0.00 0.00 31.50 1.94
940 1166 1.816074 TTTCGAGGAAAATGACCCGG 58.184 50.000 0.00 0.00 0.00 5.73
941 1167 0.688487 TTCGAGGAAAATGACCCGGT 59.312 50.000 0.00 0.00 0.00 5.28
942 1168 0.688487 TCGAGGAAAATGACCCGGTT 59.312 50.000 0.00 0.00 0.00 4.44
943 1169 1.072648 TCGAGGAAAATGACCCGGTTT 59.927 47.619 0.00 0.00 0.00 3.27
944 1170 2.302445 TCGAGGAAAATGACCCGGTTTA 59.698 45.455 0.00 0.00 0.00 2.01
945 1171 3.054948 TCGAGGAAAATGACCCGGTTTAT 60.055 43.478 0.00 0.00 0.00 1.40
946 1172 3.692593 CGAGGAAAATGACCCGGTTTATT 59.307 43.478 0.00 0.00 0.00 1.40
947 1173 4.201881 CGAGGAAAATGACCCGGTTTATTC 60.202 45.833 0.00 0.00 0.00 1.75
948 1174 3.692593 AGGAAAATGACCCGGTTTATTCG 59.307 43.478 0.00 0.00 0.00 3.34
949 1175 3.181494 GGAAAATGACCCGGTTTATTCGG 60.181 47.826 0.00 0.00 46.43 4.30
950 1176 2.793288 AATGACCCGGTTTATTCGGT 57.207 45.000 0.00 0.00 45.51 4.69
951 1177 2.793288 ATGACCCGGTTTATTCGGTT 57.207 45.000 0.00 0.00 45.51 4.44
952 1178 2.565046 TGACCCGGTTTATTCGGTTT 57.435 45.000 0.00 0.00 45.51 3.27
953 1179 3.692257 TGACCCGGTTTATTCGGTTTA 57.308 42.857 0.00 0.00 45.51 2.01
954 1180 3.598299 TGACCCGGTTTATTCGGTTTAG 58.402 45.455 0.00 0.00 45.51 1.85
955 1181 3.260380 TGACCCGGTTTATTCGGTTTAGA 59.740 43.478 0.00 0.00 45.51 2.10
956 1182 4.252878 GACCCGGTTTATTCGGTTTAGAA 58.747 43.478 0.00 0.00 45.51 2.10
957 1183 4.650734 ACCCGGTTTATTCGGTTTAGAAA 58.349 39.130 0.00 0.00 45.51 2.52
958 1184 5.069318 ACCCGGTTTATTCGGTTTAGAAAA 58.931 37.500 0.00 0.00 45.51 2.29
959 1185 5.711506 ACCCGGTTTATTCGGTTTAGAAAAT 59.288 36.000 0.00 0.00 45.51 1.82
960 1186 6.031471 CCCGGTTTATTCGGTTTAGAAAATG 58.969 40.000 0.00 0.00 45.51 2.32
961 1187 6.127952 CCCGGTTTATTCGGTTTAGAAAATGA 60.128 38.462 0.00 0.00 45.51 2.57
962 1188 6.744082 CCGGTTTATTCGGTTTAGAAAATGAC 59.256 38.462 0.00 0.00 42.33 3.06
963 1189 6.744082 CGGTTTATTCGGTTTAGAAAATGACC 59.256 38.462 0.00 0.00 33.43 4.02
964 1190 7.031372 GGTTTATTCGGTTTAGAAAATGACCC 58.969 38.462 0.00 0.00 33.43 4.46
965 1191 4.957759 ATTCGGTTTAGAAAATGACCCG 57.042 40.909 0.00 0.00 33.43 5.28
966 1192 2.702261 TCGGTTTAGAAAATGACCCGG 58.298 47.619 0.00 0.00 0.00 5.73
967 1193 2.038820 TCGGTTTAGAAAATGACCCGGT 59.961 45.455 0.00 0.00 0.00 5.28
968 1194 2.160813 CGGTTTAGAAAATGACCCGGTG 59.839 50.000 0.00 0.00 0.00 4.94
969 1195 3.151554 GGTTTAGAAAATGACCCGGTGT 58.848 45.455 0.00 0.00 0.00 4.16
970 1196 4.325972 GGTTTAGAAAATGACCCGGTGTA 58.674 43.478 0.00 0.00 0.00 2.90
971 1197 4.945543 GGTTTAGAAAATGACCCGGTGTAT 59.054 41.667 0.00 0.00 0.00 2.29
972 1198 5.065602 GGTTTAGAAAATGACCCGGTGTATC 59.934 44.000 0.00 0.00 0.00 2.24
973 1199 3.992943 AGAAAATGACCCGGTGTATCA 57.007 42.857 0.00 0.00 0.00 2.15
974 1200 4.295141 AGAAAATGACCCGGTGTATCAA 57.705 40.909 0.00 0.00 0.00 2.57
975 1201 4.007659 AGAAAATGACCCGGTGTATCAAC 58.992 43.478 0.00 0.00 0.00 3.18
997 1223 3.000773 CACTTTTGTTTTCTGTTCTGCGC 60.001 43.478 0.00 0.00 0.00 6.09
998 1224 1.821336 TTTGTTTTCTGTTCTGCGCG 58.179 45.000 0.00 0.00 0.00 6.86
999 1225 1.010580 TTGTTTTCTGTTCTGCGCGA 58.989 45.000 12.10 0.00 0.00 5.87
1000 1226 0.581529 TGTTTTCTGTTCTGCGCGAG 59.418 50.000 12.10 4.52 0.00 5.03
1057 1283 2.408241 CGACCGTCTCTCCCCTCAC 61.408 68.421 0.00 0.00 0.00 3.51
1058 1284 2.361357 ACCGTCTCTCCCCTCACG 60.361 66.667 0.00 0.00 0.00 4.35
1131 1374 4.147449 CACCGCCTCGCCATCAGA 62.147 66.667 0.00 0.00 0.00 3.27
1224 1467 3.866582 GGCGATCCCCACTCCCTG 61.867 72.222 0.00 0.00 0.00 4.45
1225 1468 4.554036 GCGATCCCCACTCCCTGC 62.554 72.222 0.00 0.00 0.00 4.85
1226 1469 3.866582 CGATCCCCACTCCCTGCC 61.867 72.222 0.00 0.00 0.00 4.85
1227 1470 3.493303 GATCCCCACTCCCTGCCC 61.493 72.222 0.00 0.00 0.00 5.36
1265 1508 3.199071 AGCCACAGGTAATAAATCGACCA 59.801 43.478 0.00 0.00 35.56 4.02
1266 1509 4.134563 GCCACAGGTAATAAATCGACCAT 58.865 43.478 0.00 0.00 35.56 3.55
1294 1537 0.385751 CTGACCGGTGTATCGCTGAT 59.614 55.000 14.63 0.00 0.00 2.90
1382 1657 1.762222 CGACCCGCGGCTAATCTTTG 61.762 60.000 22.85 4.97 36.03 2.77
1384 1659 0.743345 ACCCGCGGCTAATCTTTGAC 60.743 55.000 22.85 0.00 0.00 3.18
1388 1663 1.062587 CGCGGCTAATCTTTGACCAAG 59.937 52.381 0.00 0.00 0.00 3.61
1391 1666 2.159517 CGGCTAATCTTTGACCAAGCAC 60.160 50.000 0.00 0.00 31.70 4.40
1392 1667 2.159517 GGCTAATCTTTGACCAAGCACG 60.160 50.000 0.00 0.00 31.70 5.34
1397 1672 4.853924 ATCTTTGACCAAGCACGAAATT 57.146 36.364 0.00 0.00 31.70 1.82
1399 1674 5.004922 TCTTTGACCAAGCACGAAATTTT 57.995 34.783 0.00 0.00 31.70 1.82
1419 1718 2.725490 TGTGTTTGTTGCTGTTATGCG 58.275 42.857 0.00 0.00 35.36 4.73
1448 1747 0.175760 TGCGCAGTTCTAGGTGGATC 59.824 55.000 5.66 0.00 0.00 3.36
1481 1780 3.351740 TCAGCAACCACAGAGAAACAAA 58.648 40.909 0.00 0.00 0.00 2.83
1506 1805 5.751243 TTTTTGTCTAGTCTTCAGCAACC 57.249 39.130 0.00 0.00 0.00 3.77
1507 1806 4.415881 TTTGTCTAGTCTTCAGCAACCA 57.584 40.909 0.00 0.00 0.00 3.67
1508 1807 3.386768 TGTCTAGTCTTCAGCAACCAC 57.613 47.619 0.00 0.00 0.00 4.16
1509 1808 2.288213 TGTCTAGTCTTCAGCAACCACG 60.288 50.000 0.00 0.00 0.00 4.94
1552 1855 1.226491 GCTTGCTGTTATGCCGCAG 60.226 57.895 0.00 0.00 34.82 5.18
1578 1881 2.096713 CACCGAGAAGCGAAACTGAAAG 60.097 50.000 0.00 0.00 44.57 2.62
1601 1904 2.508867 GATTGTGCTGTTGTACGCATG 58.491 47.619 0.00 0.00 38.56 4.06
1661 1965 2.473664 CCTTCTCCGCGAAGTCGTGT 62.474 60.000 8.23 0.00 46.23 4.49
1667 1971 2.081212 CGCGAAGTCGTGTCCTGTC 61.081 63.158 0.00 0.00 44.02 3.51
1693 2007 4.137872 CCAGGCGGCATGCTTTGG 62.138 66.667 18.92 15.38 45.43 3.28
1695 2009 3.376078 AGGCGGCATGCTTTGGTG 61.376 61.111 18.92 2.16 45.43 4.17
1714 2028 1.825474 TGTTAGGCACAGCTCTCTACC 59.175 52.381 0.00 0.00 0.00 3.18
1715 2029 1.137282 GTTAGGCACAGCTCTCTACCC 59.863 57.143 0.00 0.00 0.00 3.69
1716 2030 0.631753 TAGGCACAGCTCTCTACCCT 59.368 55.000 0.00 0.00 0.00 4.34
1717 2031 0.975040 AGGCACAGCTCTCTACCCTG 60.975 60.000 0.00 0.00 0.00 4.45
1718 2032 1.261238 GGCACAGCTCTCTACCCTGT 61.261 60.000 0.00 0.00 40.22 4.00
1790 2507 2.799017 TGCTCAGTTCAGGCATCAATT 58.201 42.857 0.00 0.00 0.00 2.32
1794 2511 4.624452 GCTCAGTTCAGGCATCAATTTTTC 59.376 41.667 0.00 0.00 0.00 2.29
1795 2512 5.775686 CTCAGTTCAGGCATCAATTTTTCA 58.224 37.500 0.00 0.00 0.00 2.69
1803 2520 5.344128 CAGGCATCAATTTTTCAAGTCTTCG 59.656 40.000 0.00 0.00 0.00 3.79
1814 2531 4.563337 TCAAGTCTTCGGGTATCATACG 57.437 45.455 0.00 0.00 0.00 3.06
2029 2746 1.464734 TCGCCCTCTCTACAGTTCTG 58.535 55.000 0.00 0.00 0.00 3.02
2064 2781 8.886719 GTGAACAGATTGATTCTTGATGATGTA 58.113 33.333 0.00 0.00 29.93 2.29
2243 2960 2.994699 CCACGGCCCAAGGTATGA 59.005 61.111 0.00 0.00 0.00 2.15
2277 2994 9.540538 TGACCTTTAATTTATTTCTTGGATGGA 57.459 29.630 0.00 0.00 0.00 3.41
2310 3027 1.830477 TGCTGAGGCCTTTTGTTTTGT 59.170 42.857 6.77 0.00 37.74 2.83
2326 3043 7.840342 TTGTTTTGTTGCAAGATATGTGTTT 57.160 28.000 0.00 0.00 0.00 2.83
2400 3117 6.450545 TCAGAGCTTCCAATAGATAATGTCG 58.549 40.000 0.00 0.00 0.00 4.35
2421 3143 6.183360 TGTCGATACATACTGTGACTTGAGAG 60.183 42.308 0.00 0.00 0.00 3.20
2518 3244 8.798859 ACATAGACTAAAACTGATTTGCATCT 57.201 30.769 0.00 0.00 32.27 2.90
2535 3261 3.614092 CATCTGTGAACTGCCATAACCT 58.386 45.455 0.00 0.00 0.00 3.50
2605 3339 6.072508 TGAGATGCAATTCAGACAACCTTTAC 60.073 38.462 0.00 0.00 0.00 2.01
2643 3377 8.999220 TTTTGTCTGCAAATATTTCATATGCA 57.001 26.923 10.49 10.49 43.26 3.96
2645 3379 8.582433 TTGTCTGCAAATATTTCATATGCATG 57.418 30.769 10.16 0.00 45.03 4.06
2666 3400 6.238759 GCATGGTTAGGCTTTACTGAAATAGG 60.239 42.308 0.00 0.00 0.00 2.57
2738 3478 5.092105 CACGTTGAACACTGAAAACATGAA 58.908 37.500 0.00 0.00 0.00 2.57
2748 3488 9.912634 AACACTGAAAACATGAAACTAATATGG 57.087 29.630 0.00 0.00 0.00 2.74
2784 3524 6.570692 AGTTCTATCGGGTTATATTATGCGG 58.429 40.000 0.00 0.00 0.00 5.69
2857 3597 5.192722 TCAGAGGAGGTGAATCTCTCTTCTA 59.807 44.000 14.28 5.61 42.17 2.10
2858 3598 5.299279 CAGAGGAGGTGAATCTCTCTTCTAC 59.701 48.000 14.28 0.00 42.17 2.59
2859 3599 5.193728 AGAGGAGGTGAATCTCTCTTCTACT 59.806 44.000 13.53 0.00 42.23 2.57
2860 3600 6.388689 AGAGGAGGTGAATCTCTCTTCTACTA 59.611 42.308 13.53 0.00 42.23 1.82
2891 3631 2.297701 GAAAACAGCCCTGAACACTCA 58.702 47.619 1.69 0.00 0.00 3.41
2917 3657 3.627577 TCGCCAATGCTTATCTTCCTTTC 59.372 43.478 0.00 0.00 34.43 2.62
2934 3674 4.821805 TCCTTTCACCTGAATGTTGAGTTC 59.178 41.667 0.00 0.00 33.54 3.01
3093 3833 4.129737 CTGGGCACGACGATCGGT 62.130 66.667 20.98 5.55 45.59 4.69
3283 4023 3.198417 CCCATGAAAGAAATTGGGGAAGG 59.802 47.826 0.00 0.00 44.29 3.46
3286 4026 2.632512 TGAAAGAAATTGGGGAAGGCAC 59.367 45.455 0.00 0.00 0.00 5.01
3301 4041 0.103572 GGCACCGGCTCGATTAAGTA 59.896 55.000 0.00 0.00 40.87 2.24
3315 4055 9.831737 GCTCGATTAAGTATTTTGCATTGATAT 57.168 29.630 0.00 0.00 0.00 1.63
3359 4099 4.726825 TCCTGGGATAAAGTTAGATGCCTT 59.273 41.667 8.96 0.00 34.77 4.35
3360 4100 5.193728 TCCTGGGATAAAGTTAGATGCCTTT 59.806 40.000 8.96 0.00 34.77 3.11
3361 4101 5.532779 CCTGGGATAAAGTTAGATGCCTTTC 59.467 44.000 8.96 0.00 34.77 2.62
3362 4102 5.445964 TGGGATAAAGTTAGATGCCTTTCC 58.554 41.667 8.96 0.00 34.77 3.13
3363 4103 5.044476 TGGGATAAAGTTAGATGCCTTTCCA 60.044 40.000 8.96 0.00 34.77 3.53
3364 4104 5.532779 GGGATAAAGTTAGATGCCTTTCCAG 59.467 44.000 2.06 0.00 33.24 3.86
3365 4105 5.532779 GGATAAAGTTAGATGCCTTTCCAGG 59.467 44.000 0.00 0.00 44.28 4.45
3374 4114 3.266240 CCTTTCCAGGCTTGTACCC 57.734 57.895 0.00 0.00 31.53 3.69
3375 4115 0.404040 CCTTTCCAGGCTTGTACCCA 59.596 55.000 0.00 0.00 31.53 4.51
3376 4116 1.614317 CCTTTCCAGGCTTGTACCCAG 60.614 57.143 0.00 0.00 31.53 4.45
3377 4117 0.404040 TTTCCAGGCTTGTACCCAGG 59.596 55.000 0.00 0.00 0.00 4.45
3378 4118 2.044946 CCAGGCTTGTACCCAGGC 60.045 66.667 7.46 7.46 42.60 4.85
3389 4129 0.407918 TACCCAGGCCCCTTTTTCTG 59.592 55.000 0.00 0.00 0.00 3.02
3392 4132 1.156095 CAGGCCCCTTTTTCTGGGT 59.844 57.895 0.00 0.00 44.20 4.51
3406 4146 7.450323 CCTTTTTCTGGGTGGAGATTAAGTAAA 59.550 37.037 0.00 0.00 0.00 2.01
3408 4148 8.950007 TTTTCTGGGTGGAGATTAAGTAAATT 57.050 30.769 0.00 0.00 0.00 1.82
3424 4164 0.323725 AATTCGGTTGCATCCAGGCT 60.324 50.000 14.13 0.00 34.04 4.58
3439 4179 3.333680 TCCAGGCTTTGTATTCCTTTCCT 59.666 43.478 0.00 0.00 0.00 3.36
3448 4188 7.574030 GCTTTGTATTCCTTTCCTCTGTCTTTC 60.574 40.741 0.00 0.00 0.00 2.62
3454 4194 3.823304 CCTTTCCTCTGTCTTTCTTTGGG 59.177 47.826 0.00 0.00 0.00 4.12
3543 4283 8.803799 CGCTGGTTTAATGATTTAATTTGTACC 58.196 33.333 0.00 0.00 0.00 3.34
3641 4554 3.185797 GTGACTTTTAGTAGTGGCCAACG 59.814 47.826 7.24 0.00 0.00 4.10
3664 4577 5.307204 GCTCTAGCCAGATTGATTTCATCT 58.693 41.667 0.00 0.00 34.31 2.90
3713 4626 4.645588 GTGCCTAGACTGTAAGGTGATACT 59.354 45.833 9.65 0.00 39.30 2.12
3900 4813 2.150051 GGAAGGAGGGGATGCGGAT 61.150 63.158 0.00 0.00 0.00 4.18
4027 5373 2.028420 TGATGTCCAGAAGGCGATTG 57.972 50.000 0.00 0.00 33.74 2.67
4294 5912 1.344763 ACTCTTGGTGAAGGACGAAGG 59.655 52.381 0.00 0.00 40.03 3.46
4432 6050 1.974236 CCAAGAGTCTGAGGTGAAGGT 59.026 52.381 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.293955 GGTGCAACTTCTTCAGCTTGTTATTA 60.294 38.462 0.00 0.00 36.74 0.98
170 171 2.597340 CGCAATCTGGTCCCCCAT 59.403 61.111 0.00 0.00 40.90 4.00
189 190 0.906775 TAGTTCGGGGTTAAGCCAGG 59.093 55.000 24.42 15.49 39.65 4.45
277 278 0.179200 GTACCTGGTTTGCGCATTCG 60.179 55.000 12.75 0.00 39.07 3.34
305 306 0.326618 AGGACGTTCTCCATCCCCAT 60.327 55.000 0.00 0.00 42.46 4.00
427 428 0.104855 GCATCGCCATAGTCACCTGA 59.895 55.000 0.00 0.00 0.00 3.86
506 732 1.793134 GCCTGCTGCACCATATCTGC 61.793 60.000 0.00 0.00 40.77 4.26
567 793 5.010516 ACTCAGAACTCGATATGGATCTTGG 59.989 44.000 0.00 0.00 0.00 3.61
602 828 2.046864 CAGACCCTCGCTCTCGGAA 61.047 63.158 0.00 0.00 36.13 4.30
611 837 1.649390 CGGACAGACTCAGACCCTCG 61.649 65.000 0.00 0.00 0.00 4.63
674 900 7.930865 ACTAGATTGGCAATGAACTAAGAGATC 59.069 37.037 19.07 0.00 0.00 2.75
720 946 5.001237 TCTTTTGAACACAGTACAGACGA 57.999 39.130 0.00 0.00 0.00 4.20
721 947 5.712217 TTCTTTTGAACACAGTACAGACG 57.288 39.130 0.00 0.00 32.77 4.18
722 948 7.302524 TGTTTTCTTTTGAACACAGTACAGAC 58.697 34.615 0.00 0.00 42.20 3.51
723 949 7.441890 TGTTTTCTTTTGAACACAGTACAGA 57.558 32.000 0.00 0.00 42.20 3.41
731 957 9.281075 ACGTAAAGTATGTTTTCTTTTGAACAC 57.719 29.630 0.00 0.00 38.46 3.32
732 958 9.843334 AACGTAAAGTATGTTTTCTTTTGAACA 57.157 25.926 0.00 0.00 38.30 3.18
734 960 9.291664 CCAACGTAAAGTATGTTTTCTTTTGAA 57.708 29.630 0.00 0.00 35.79 2.69
735 961 8.675504 TCCAACGTAAAGTATGTTTTCTTTTGA 58.324 29.630 0.00 0.00 35.79 2.69
736 962 8.844441 TCCAACGTAAAGTATGTTTTCTTTTG 57.156 30.769 0.00 0.00 35.79 2.44
770 996 9.716507 GTAGTAAATCCGACGTACTACATAAAA 57.283 33.333 20.21 0.00 44.94 1.52
776 1002 6.948353 TCATGTAGTAAATCCGACGTACTAC 58.052 40.000 19.11 19.11 45.43 2.73
777 1003 7.409697 GTTCATGTAGTAAATCCGACGTACTA 58.590 38.462 0.00 0.00 30.81 1.82
778 1004 6.261118 GTTCATGTAGTAAATCCGACGTACT 58.739 40.000 0.00 0.00 32.87 2.73
779 1005 5.170270 CGTTCATGTAGTAAATCCGACGTAC 59.830 44.000 0.00 0.00 0.00 3.67
780 1006 5.265477 CGTTCATGTAGTAAATCCGACGTA 58.735 41.667 0.00 0.00 0.00 3.57
781 1007 4.100529 CGTTCATGTAGTAAATCCGACGT 58.899 43.478 0.00 0.00 0.00 4.34
782 1008 3.484649 CCGTTCATGTAGTAAATCCGACG 59.515 47.826 0.00 0.00 0.00 5.12
783 1009 4.675510 TCCGTTCATGTAGTAAATCCGAC 58.324 43.478 0.00 0.00 0.00 4.79
784 1010 4.987408 TCCGTTCATGTAGTAAATCCGA 57.013 40.909 0.00 0.00 0.00 4.55
785 1011 6.362551 CAGTATCCGTTCATGTAGTAAATCCG 59.637 42.308 0.00 0.00 0.00 4.18
786 1012 6.145696 GCAGTATCCGTTCATGTAGTAAATCC 59.854 42.308 0.00 0.00 0.00 3.01
787 1013 6.700081 TGCAGTATCCGTTCATGTAGTAAATC 59.300 38.462 0.00 0.00 0.00 2.17
788 1014 6.479001 GTGCAGTATCCGTTCATGTAGTAAAT 59.521 38.462 0.00 0.00 0.00 1.40
789 1015 5.808540 GTGCAGTATCCGTTCATGTAGTAAA 59.191 40.000 0.00 0.00 0.00 2.01
790 1016 5.126545 AGTGCAGTATCCGTTCATGTAGTAA 59.873 40.000 0.00 0.00 0.00 2.24
791 1017 4.643334 AGTGCAGTATCCGTTCATGTAGTA 59.357 41.667 0.00 0.00 0.00 1.82
792 1018 3.447586 AGTGCAGTATCCGTTCATGTAGT 59.552 43.478 0.00 0.00 0.00 2.73
793 1019 4.045104 GAGTGCAGTATCCGTTCATGTAG 58.955 47.826 0.00 0.00 0.00 2.74
794 1020 3.488553 CGAGTGCAGTATCCGTTCATGTA 60.489 47.826 0.00 0.00 0.00 2.29
795 1021 2.735444 CGAGTGCAGTATCCGTTCATGT 60.735 50.000 0.00 0.00 0.00 3.21
796 1022 1.854743 CGAGTGCAGTATCCGTTCATG 59.145 52.381 0.00 0.00 0.00 3.07
797 1023 1.202417 CCGAGTGCAGTATCCGTTCAT 60.202 52.381 0.00 0.00 0.00 2.57
798 1024 0.172578 CCGAGTGCAGTATCCGTTCA 59.827 55.000 0.00 0.00 0.00 3.18
799 1025 0.172803 ACCGAGTGCAGTATCCGTTC 59.827 55.000 0.00 0.00 0.00 3.95
800 1026 0.172803 GACCGAGTGCAGTATCCGTT 59.827 55.000 0.00 0.00 0.00 4.44
801 1027 0.680280 AGACCGAGTGCAGTATCCGT 60.680 55.000 0.00 0.00 0.00 4.69
802 1028 0.456221 AAGACCGAGTGCAGTATCCG 59.544 55.000 0.00 0.00 0.00 4.18
803 1029 3.707793 CTTAAGACCGAGTGCAGTATCC 58.292 50.000 0.00 0.00 0.00 2.59
804 1030 3.117046 GCTTAAGACCGAGTGCAGTATC 58.883 50.000 6.67 0.00 0.00 2.24
805 1031 2.159085 GGCTTAAGACCGAGTGCAGTAT 60.159 50.000 6.67 0.00 0.00 2.12
806 1032 1.203994 GGCTTAAGACCGAGTGCAGTA 59.796 52.381 6.67 0.00 0.00 2.74
807 1033 0.037232 GGCTTAAGACCGAGTGCAGT 60.037 55.000 6.67 0.00 0.00 4.40
808 1034 0.037326 TGGCTTAAGACCGAGTGCAG 60.037 55.000 5.69 0.00 0.00 4.41
809 1035 0.394938 TTGGCTTAAGACCGAGTGCA 59.605 50.000 5.69 0.00 0.00 4.57
810 1036 1.519408 TTTGGCTTAAGACCGAGTGC 58.481 50.000 5.69 0.00 0.00 4.40
811 1037 2.484264 CCTTTTGGCTTAAGACCGAGTG 59.516 50.000 5.69 3.91 0.00 3.51
812 1038 2.552373 CCCTTTTGGCTTAAGACCGAGT 60.552 50.000 5.69 0.00 38.58 4.18
813 1039 2.084546 CCCTTTTGGCTTAAGACCGAG 58.915 52.381 5.69 0.83 38.58 4.63
814 1040 1.700739 TCCCTTTTGGCTTAAGACCGA 59.299 47.619 5.69 3.89 38.58 4.69
815 1041 2.084546 CTCCCTTTTGGCTTAAGACCG 58.915 52.381 5.69 0.00 38.58 4.79
816 1042 3.009143 TCTCTCCCTTTTGGCTTAAGACC 59.991 47.826 5.69 7.40 38.58 3.85
817 1043 4.287766 TCTCTCCCTTTTGGCTTAAGAC 57.712 45.455 6.67 3.27 38.58 3.01
818 1044 4.993705 TTCTCTCCCTTTTGGCTTAAGA 57.006 40.909 6.67 0.00 38.58 2.10
819 1045 5.478332 ACATTTCTCTCCCTTTTGGCTTAAG 59.522 40.000 0.00 0.00 38.58 1.85
820 1046 5.393866 ACATTTCTCTCCCTTTTGGCTTAA 58.606 37.500 0.00 0.00 38.58 1.85
821 1047 4.998051 ACATTTCTCTCCCTTTTGGCTTA 58.002 39.130 0.00 0.00 38.58 3.09
822 1048 3.849527 ACATTTCTCTCCCTTTTGGCTT 58.150 40.909 0.00 0.00 38.58 4.35
823 1049 3.532641 ACATTTCTCTCCCTTTTGGCT 57.467 42.857 0.00 0.00 38.58 4.75
824 1050 4.949856 TGATACATTTCTCTCCCTTTTGGC 59.050 41.667 0.00 0.00 38.58 4.52
825 1051 6.434028 TGTTGATACATTTCTCTCCCTTTTGG 59.566 38.462 0.00 0.00 39.97 3.28
826 1052 7.040478 TGTGTTGATACATTTCTCTCCCTTTTG 60.040 37.037 0.00 0.00 36.50 2.44
827 1053 7.004086 TGTGTTGATACATTTCTCTCCCTTTT 58.996 34.615 0.00 0.00 36.50 2.27
828 1054 6.542821 TGTGTTGATACATTTCTCTCCCTTT 58.457 36.000 0.00 0.00 36.50 3.11
829 1055 6.126863 TGTGTTGATACATTTCTCTCCCTT 57.873 37.500 0.00 0.00 36.50 3.95
830 1056 5.762179 TGTGTTGATACATTTCTCTCCCT 57.238 39.130 0.00 0.00 36.50 4.20
831 1057 6.375455 ACAATGTGTTGATACATTTCTCTCCC 59.625 38.462 3.72 0.00 46.18 4.30
832 1058 7.383102 ACAATGTGTTGATACATTTCTCTCC 57.617 36.000 3.72 0.00 46.18 3.71
833 1059 9.683069 AAAACAATGTGTTGATACATTTCTCTC 57.317 29.630 3.72 0.00 46.18 3.20
868 1094 9.889128 TCATGTGTTGATACATTTCTTATCTCA 57.111 29.630 0.00 0.00 39.17 3.27
870 1096 9.113838 GGTCATGTGTTGATACATTTCTTATCT 57.886 33.333 0.00 0.00 39.17 1.98
871 1097 8.345565 GGGTCATGTGTTGATACATTTCTTATC 58.654 37.037 0.00 0.00 39.17 1.75
872 1098 7.012327 CGGGTCATGTGTTGATACATTTCTTAT 59.988 37.037 0.00 0.00 39.17 1.73
873 1099 6.315144 CGGGTCATGTGTTGATACATTTCTTA 59.685 38.462 0.00 0.00 39.17 2.10
874 1100 5.123820 CGGGTCATGTGTTGATACATTTCTT 59.876 40.000 0.00 0.00 39.17 2.52
875 1101 4.635765 CGGGTCATGTGTTGATACATTTCT 59.364 41.667 0.00 0.00 39.17 2.52
876 1102 4.201910 CCGGGTCATGTGTTGATACATTTC 60.202 45.833 0.00 0.00 39.17 2.17
877 1103 3.694072 CCGGGTCATGTGTTGATACATTT 59.306 43.478 0.00 0.00 39.17 2.32
878 1104 3.278574 CCGGGTCATGTGTTGATACATT 58.721 45.455 0.00 0.00 39.17 2.71
879 1105 2.238646 ACCGGGTCATGTGTTGATACAT 59.761 45.455 6.32 0.00 41.77 2.29
880 1106 1.626321 ACCGGGTCATGTGTTGATACA 59.374 47.619 6.32 0.00 36.54 2.29
881 1107 2.396590 ACCGGGTCATGTGTTGATAC 57.603 50.000 6.32 0.00 36.54 2.24
882 1108 3.426787 AAACCGGGTCATGTGTTGATA 57.573 42.857 6.32 0.00 36.54 2.15
883 1109 2.286365 AAACCGGGTCATGTGTTGAT 57.714 45.000 6.32 0.00 36.54 2.57
884 1110 2.932855 TAAACCGGGTCATGTGTTGA 57.067 45.000 6.32 0.00 0.00 3.18
885 1111 4.513198 AAATAAACCGGGTCATGTGTTG 57.487 40.909 6.32 0.00 0.00 3.33
886 1112 5.538849 AAAAATAAACCGGGTCATGTGTT 57.461 34.783 6.32 0.00 0.00 3.32
914 1140 6.864165 CGGGTCATTTTCCTCGAAAATAAAAA 59.136 34.615 11.02 0.00 46.37 1.94
915 1141 6.383415 CGGGTCATTTTCCTCGAAAATAAAA 58.617 36.000 11.02 0.00 46.37 1.52
916 1142 5.106078 CCGGGTCATTTTCCTCGAAAATAAA 60.106 40.000 11.02 2.34 46.37 1.40
917 1143 4.396790 CCGGGTCATTTTCCTCGAAAATAA 59.603 41.667 11.02 0.00 46.37 1.40
918 1144 3.942748 CCGGGTCATTTTCCTCGAAAATA 59.057 43.478 11.02 0.59 46.37 1.40
920 1146 2.156098 CCGGGTCATTTTCCTCGAAAA 58.844 47.619 0.00 2.29 44.04 2.29
921 1147 1.072648 ACCGGGTCATTTTCCTCGAAA 59.927 47.619 6.32 0.00 0.00 3.46
922 1148 0.688487 ACCGGGTCATTTTCCTCGAA 59.312 50.000 6.32 0.00 0.00 3.71
923 1149 0.688487 AACCGGGTCATTTTCCTCGA 59.312 50.000 6.32 0.00 0.00 4.04
924 1150 1.530323 AAACCGGGTCATTTTCCTCG 58.470 50.000 6.32 0.00 0.00 4.63
925 1151 4.201881 CGAATAAACCGGGTCATTTTCCTC 60.202 45.833 6.32 0.00 0.00 3.71
926 1152 3.692593 CGAATAAACCGGGTCATTTTCCT 59.307 43.478 6.32 0.00 0.00 3.36
927 1153 3.181494 CCGAATAAACCGGGTCATTTTCC 60.181 47.826 6.32 0.00 43.05 3.13
928 1154 4.023739 CCGAATAAACCGGGTCATTTTC 57.976 45.455 6.32 3.39 43.05 2.29
929 1155 3.827876 AACCGAATAAACCGGGTCATTTT 59.172 39.130 6.32 0.00 45.07 1.82
930 1156 3.423749 AACCGAATAAACCGGGTCATTT 58.576 40.909 6.32 0.00 45.07 2.32
931 1157 3.076079 AACCGAATAAACCGGGTCATT 57.924 42.857 6.32 0.00 45.07 2.57
932 1158 2.793288 AACCGAATAAACCGGGTCAT 57.207 45.000 6.32 0.00 45.07 3.06
938 1164 6.744082 GGTCATTTTCTAAACCGAATAAACCG 59.256 38.462 0.00 0.00 0.00 4.44
939 1165 7.031372 GGGTCATTTTCTAAACCGAATAAACC 58.969 38.462 0.00 0.00 32.34 3.27
940 1166 6.744082 CGGGTCATTTTCTAAACCGAATAAAC 59.256 38.462 0.00 0.00 42.19 2.01
941 1167 6.127952 CCGGGTCATTTTCTAAACCGAATAAA 60.128 38.462 0.00 0.00 42.19 1.40
942 1168 5.354792 CCGGGTCATTTTCTAAACCGAATAA 59.645 40.000 0.00 0.00 42.19 1.40
943 1169 4.877251 CCGGGTCATTTTCTAAACCGAATA 59.123 41.667 0.00 0.00 42.19 1.75
944 1170 3.692593 CCGGGTCATTTTCTAAACCGAAT 59.307 43.478 0.00 0.00 42.19 3.34
945 1171 3.075884 CCGGGTCATTTTCTAAACCGAA 58.924 45.455 0.00 0.00 42.19 4.30
946 1172 2.038820 ACCGGGTCATTTTCTAAACCGA 59.961 45.455 6.32 0.00 42.19 4.69
947 1173 2.160813 CACCGGGTCATTTTCTAAACCG 59.839 50.000 6.32 0.00 39.54 4.44
948 1174 3.151554 ACACCGGGTCATTTTCTAAACC 58.848 45.455 6.32 0.00 0.00 3.27
949 1175 5.644636 TGATACACCGGGTCATTTTCTAAAC 59.355 40.000 6.32 0.00 0.00 2.01
950 1176 5.806818 TGATACACCGGGTCATTTTCTAAA 58.193 37.500 6.32 0.00 0.00 1.85
951 1177 5.423704 TGATACACCGGGTCATTTTCTAA 57.576 39.130 6.32 0.00 0.00 2.10
952 1178 5.180271 GTTGATACACCGGGTCATTTTCTA 58.820 41.667 6.32 0.00 0.00 2.10
953 1179 3.992943 TGATACACCGGGTCATTTTCT 57.007 42.857 6.32 0.00 0.00 2.52
954 1180 3.754323 TGTTGATACACCGGGTCATTTTC 59.246 43.478 6.32 0.00 0.00 2.29
955 1181 3.757270 TGTTGATACACCGGGTCATTTT 58.243 40.909 6.32 0.00 0.00 1.82
956 1182 3.426787 TGTTGATACACCGGGTCATTT 57.573 42.857 6.32 0.00 0.00 2.32
974 1200 4.165779 CGCAGAACAGAAAACAAAAGTGT 58.834 39.130 0.00 0.00 40.75 3.55
975 1201 3.000773 GCGCAGAACAGAAAACAAAAGTG 60.001 43.478 0.30 0.00 0.00 3.16
1246 1489 5.236478 GGTGATGGTCGATTTATTACCTGTG 59.764 44.000 10.95 0.00 34.23 3.66
1265 1508 3.009115 CCGGTCAGGGGTGGTGAT 61.009 66.667 0.00 0.00 35.97 3.06
1266 1509 4.567597 ACCGGTCAGGGGTGGTGA 62.568 66.667 0.00 0.00 46.96 4.02
1382 1657 3.443976 ACACAAAATTTCGTGCTTGGTC 58.556 40.909 9.18 0.00 36.57 4.02
1384 1659 4.092675 ACAAACACAAAATTTCGTGCTTGG 59.907 37.500 22.63 11.56 41.35 3.61
1388 1663 3.778199 GCAACAAACACAAAATTTCGTGC 59.222 39.130 9.18 0.00 36.57 5.34
1391 1666 5.202046 ACAGCAACAAACACAAAATTTCG 57.798 34.783 0.00 0.00 0.00 3.46
1392 1667 7.164008 GCATAACAGCAACAAACACAAAATTTC 59.836 33.333 0.00 0.00 0.00 2.17
1397 1672 3.549471 CGCATAACAGCAACAAACACAAA 59.451 39.130 0.00 0.00 0.00 2.83
1399 1674 2.098280 ACGCATAACAGCAACAAACACA 59.902 40.909 0.00 0.00 0.00 3.72
1419 1718 3.747099 AGAACTGCGCATTCATGTAAC 57.253 42.857 24.50 12.61 0.00 2.50
1448 1747 2.288213 TGGTTGCTGAAGACTAGACGTG 60.288 50.000 0.00 0.00 0.00 4.49
1489 1788 2.329379 CGTGGTTGCTGAAGACTAGAC 58.671 52.381 0.00 0.00 0.00 2.59
1490 1789 1.272490 CCGTGGTTGCTGAAGACTAGA 59.728 52.381 0.00 0.00 0.00 2.43
1491 1790 1.000955 ACCGTGGTTGCTGAAGACTAG 59.999 52.381 0.00 0.00 0.00 2.57
1492 1791 1.045407 ACCGTGGTTGCTGAAGACTA 58.955 50.000 0.00 0.00 0.00 2.59
1493 1792 0.532862 CACCGTGGTTGCTGAAGACT 60.533 55.000 0.00 0.00 0.00 3.24
1494 1793 0.814010 ACACCGTGGTTGCTGAAGAC 60.814 55.000 3.03 0.00 0.00 3.01
1495 1794 0.813610 CACACCGTGGTTGCTGAAGA 60.814 55.000 3.03 0.00 0.00 2.87
1498 1797 1.817520 CACACACCGTGGTTGCTGA 60.818 57.895 3.03 0.00 42.34 4.26
1507 1806 1.153269 TGCATGACACACACACCGT 60.153 52.632 0.00 0.00 0.00 4.83
1508 1807 3.729804 TGCATGACACACACACCG 58.270 55.556 0.00 0.00 0.00 4.94
1552 1855 0.038526 TTTCGCTTCTCGGTGACCTC 60.039 55.000 0.00 0.00 39.05 3.85
1578 1881 0.179225 CGTACAACAGCACAATCGGC 60.179 55.000 0.00 0.00 0.00 5.54
1661 1965 3.610619 CTGGCGCCACATGACAGGA 62.611 63.158 29.03 0.00 0.00 3.86
1695 2009 1.137282 GGGTAGAGAGCTGTGCCTAAC 59.863 57.143 0.00 0.00 0.00 2.34
1765 2482 2.391616 TGCCTGAACTGAGCATAGTG 57.608 50.000 0.00 0.00 0.00 2.74
1790 2507 5.808540 CGTATGATACCCGAAGACTTGAAAA 59.191 40.000 0.00 0.00 0.00 2.29
1794 2511 3.050619 GCGTATGATACCCGAAGACTTG 58.949 50.000 0.00 0.00 0.00 3.16
1795 2512 2.287427 CGCGTATGATACCCGAAGACTT 60.287 50.000 3.72 0.00 32.05 3.01
1803 2520 2.666619 CGTAGGAACGCGTATGATACCC 60.667 54.545 14.46 5.51 43.12 3.69
1835 2552 7.968405 AGTGAAATTATTCGAAACATAAGTGGC 59.032 33.333 0.00 0.00 38.46 5.01
1838 2555 9.010029 ACCAGTGAAATTATTCGAAACATAAGT 57.990 29.630 0.00 0.00 38.46 2.24
2009 2726 1.819288 CAGAACTGTAGAGAGGGCGAA 59.181 52.381 0.00 0.00 0.00 4.70
2029 2746 4.305989 TCAATCTGTTCACAAGCCAAAC 57.694 40.909 0.00 0.00 0.00 2.93
2064 2781 4.281688 CCCCACAAATCAACAAGAACAGAT 59.718 41.667 0.00 0.00 0.00 2.90
2326 3043 8.534954 ACAGCAGGATAGACTTATTTGTACTA 57.465 34.615 0.00 0.00 0.00 1.82
2340 3057 6.257411 CAGAAACAGAACATACAGCAGGATAG 59.743 42.308 0.00 0.00 0.00 2.08
2341 3058 6.108687 CAGAAACAGAACATACAGCAGGATA 58.891 40.000 0.00 0.00 0.00 2.59
2421 3143 3.314635 GGACACTGCTGGATCAATTCATC 59.685 47.826 0.00 0.00 0.00 2.92
2518 3244 2.884012 CAACAGGTTATGGCAGTTCACA 59.116 45.455 0.00 0.00 0.00 3.58
2605 3339 4.578516 TGCAGACAAAATATAATCCCCACG 59.421 41.667 0.00 0.00 0.00 4.94
2643 3377 6.970191 ACCTATTTCAGTAAAGCCTAACCAT 58.030 36.000 0.00 0.00 0.00 3.55
2645 3379 6.315642 GTGACCTATTTCAGTAAAGCCTAACC 59.684 42.308 0.00 0.00 0.00 2.85
2666 3400 1.504359 TGGACGACCGAAAATGTGAC 58.496 50.000 0.00 0.00 39.42 3.67
2784 3524 0.320946 AAGCATGCCACATTTGGTGC 60.321 50.000 15.66 5.55 46.50 5.01
2857 3597 4.142249 GGCTGTTTTCAACAACCTTGTAGT 60.142 41.667 2.39 0.00 42.88 2.73
2858 3598 4.359706 GGCTGTTTTCAACAACCTTGTAG 58.640 43.478 2.39 0.00 42.88 2.74
2859 3599 3.131400 GGGCTGTTTTCAACAACCTTGTA 59.869 43.478 8.56 0.00 44.98 2.41
2860 3600 2.093711 GGGCTGTTTTCAACAACCTTGT 60.094 45.455 8.56 0.00 44.98 3.16
2885 3625 2.352503 GCATTGGCGAAAATGAGTGT 57.647 45.000 12.99 0.00 39.46 3.55
2917 3657 9.388506 AGAAATATAGAACTCAACATTCAGGTG 57.611 33.333 0.00 0.00 35.78 4.00
2959 3699 3.837731 TCCTGGGGAAATGATTTGGAAAC 59.162 43.478 0.00 0.00 0.00 2.78
3045 3785 3.118956 CGCTCTTTATGAACTCCTCCACT 60.119 47.826 0.00 0.00 0.00 4.00
3280 4020 0.462047 CTTAATCGAGCCGGTGCCTT 60.462 55.000 1.90 0.00 38.69 4.35
3283 4023 2.150397 ATACTTAATCGAGCCGGTGC 57.850 50.000 1.90 0.00 37.95 5.01
3286 4026 3.311322 TGCAAAATACTTAATCGAGCCGG 59.689 43.478 0.00 0.00 0.00 6.13
3316 4056 8.204160 CCCAGGAAAATGTTTCTTCTACTTTTT 58.796 33.333 0.00 0.00 36.30 1.94
3317 4057 7.563556 TCCCAGGAAAATGTTTCTTCTACTTTT 59.436 33.333 0.00 0.00 0.00 2.27
3320 4060 6.200878 TCCCAGGAAAATGTTTCTTCTACT 57.799 37.500 0.00 0.00 0.00 2.57
3335 4075 4.726825 AGGCATCTAACTTTATCCCAGGAA 59.273 41.667 0.00 0.00 0.00 3.36
3336 4076 4.307259 AGGCATCTAACTTTATCCCAGGA 58.693 43.478 0.00 0.00 0.00 3.86
3365 4105 2.441035 AAAGGGGCCTGGGTACAAGC 62.441 60.000 0.84 0.00 33.22 4.01
3367 4107 0.563672 AAAAAGGGGCCTGGGTACAA 59.436 50.000 0.84 0.00 0.00 2.41
3368 4108 0.113580 GAAAAAGGGGCCTGGGTACA 59.886 55.000 0.84 0.00 0.00 2.90
3369 4109 0.408309 AGAAAAAGGGGCCTGGGTAC 59.592 55.000 0.84 0.00 0.00 3.34
3370 4110 0.407918 CAGAAAAAGGGGCCTGGGTA 59.592 55.000 0.84 0.00 0.00 3.69
3371 4111 1.156095 CAGAAAAAGGGGCCTGGGT 59.844 57.895 0.84 0.00 0.00 4.51
3372 4112 1.610379 CCAGAAAAAGGGGCCTGGG 60.610 63.158 0.84 0.00 41.76 4.45
3373 4113 1.610379 CCCAGAAAAAGGGGCCTGG 60.610 63.158 0.84 0.24 42.90 4.45
3374 4114 4.118584 CCCAGAAAAAGGGGCCTG 57.881 61.111 0.84 0.00 42.90 4.85
3389 4129 5.434408 ACCGAATTTACTTAATCTCCACCC 58.566 41.667 0.00 0.00 0.00 4.61
3392 4132 5.941058 TGCAACCGAATTTACTTAATCTCCA 59.059 36.000 0.00 0.00 0.00 3.86
3406 4146 0.323725 AAGCCTGGATGCAACCGAAT 60.324 50.000 8.65 0.00 0.00 3.34
3408 4148 1.074775 AAAGCCTGGATGCAACCGA 59.925 52.632 8.65 0.00 0.00 4.69
3424 4164 7.518188 AGAAAGACAGAGGAAAGGAATACAAA 58.482 34.615 0.00 0.00 0.00 2.83
3439 4179 9.807921 ACTTATTTAATCCCAAAGAAAGACAGA 57.192 29.630 0.00 0.00 0.00 3.41
3448 4188 9.771534 TGGAAAACAACTTATTTAATCCCAAAG 57.228 29.630 0.00 0.00 0.00 2.77
3543 4283 5.460091 GGCAGCAGACAGTTTAAAGAAAAAG 59.540 40.000 0.00 0.00 0.00 2.27
3641 4554 5.610235 GATGAAATCAATCTGGCTAGAGC 57.390 43.478 5.82 0.00 44.70 4.09
3713 4626 1.061546 GGGTACAACACTCTCCCCAA 58.938 55.000 0.00 0.00 32.66 4.12
3900 4813 3.118445 TCGCCATCTTCATCCACACATTA 60.118 43.478 0.00 0.00 0.00 1.90
4027 5373 6.400940 CGTCTGAAGCAATCTTTCTTCTCTTC 60.401 42.308 4.42 0.00 39.41 2.87
4207 5824 2.136863 TCTCCTCTCCCGGATCTTAGT 58.863 52.381 0.73 0.00 31.43 2.24
4273 5891 2.610727 CCTTCGTCCTTCACCAAGAGTC 60.611 54.545 0.00 0.00 0.00 3.36
4294 5912 5.941788 ACTCCCACCATCTATGTTTAATCC 58.058 41.667 0.00 0.00 0.00 3.01
4432 6050 5.245977 CCTCCTTTCATCCTTTTTAAAGCCA 59.754 40.000 0.00 0.00 34.69 4.75


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

AutoCloner maintained by Alex Coulton.