Multiple sequence alignment - TraesCS3A01G462400

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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 TraesCS3A01G462400 chr3A 100.000 4450 0 0 1 4450 697562465 697558016 0.000000e+00 8218.0
1 TraesCS3A01G462400 chr3A 85.174 661 62 20 31 681 470715424 470714790 0.000000e+00 645.0
2 TraesCS3A01G462400 chr3A 93.697 238 11 4 4143 4378 714622375 714622610 1.970000e-93 353.0
3 TraesCS3A01G462400 chr3A 78.947 228 30 13 2260 2476 710614752 710614532 6.000000e-29 139.0
4 TraesCS3A01G462400 chr3A 82.955 88 9 4 3176 3261 710614446 710614363 1.720000e-09 75.0
5 TraesCS3A01G462400 chr3D 94.359 3244 119 22 946 4151 562333616 562330399 0.000000e+00 4918.0
6 TraesCS3A01G462400 chr3D 94.298 228 11 2 4138 4364 186623329 186623103 9.160000e-92 348.0
7 TraesCS3A01G462400 chr3D 83.249 197 9 9 731 926 562333774 562333601 4.610000e-35 159.0
8 TraesCS3A01G462400 chr3D 93.750 80 4 1 4362 4440 562330405 562330326 7.820000e-23 119.0
9 TraesCS3A01G462400 chr3D 86.250 80 6 4 2142 2221 513665572 513665498 1.030000e-11 82.4
10 TraesCS3A01G462400 chr3D 74.101 278 34 17 2296 2561 513665840 513665589 3.690000e-11 80.5
11 TraesCS3A01G462400 chr3B 93.767 2551 108 11 946 3461 749526006 749523472 0.000000e+00 3783.0
12 TraesCS3A01G462400 chr3B 95.513 312 13 1 3540 3851 749523474 749523164 8.600000e-137 497.0
13 TraesCS3A01G462400 chr3B 79.045 649 85 29 38 664 791408142 791408761 8.970000e-107 398.0
14 TraesCS3A01G462400 chr3B 87.050 278 15 5 3878 4150 749522857 749522596 1.210000e-75 294.0
15 TraesCS3A01G462400 chr3B 79.614 363 55 9 3033 3386 794347140 794347492 4.450000e-60 243.0
16 TraesCS3A01G462400 chr3B 79.076 368 53 10 3038 3386 794352268 794352630 9.630000e-57 231.0
17 TraesCS3A01G462400 chr3B 81.538 260 39 8 2877 3134 761601215 761601467 5.830000e-49 206.0
18 TraesCS3A01G462400 chr3B 95.238 63 3 0 4362 4424 749522601 749522539 2.830000e-17 100.0
19 TraesCS3A01G462400 chr4B 86.275 765 65 20 3 732 68655021 68655780 0.000000e+00 795.0
20 TraesCS3A01G462400 chr2B 86.733 701 67 19 3 681 664466654 664465958 0.000000e+00 756.0
21 TraesCS3A01G462400 chr1B 86.377 690 67 14 1 681 322936340 322935669 0.000000e+00 728.0
22 TraesCS3A01G462400 chr1B 86.758 657 54 14 51 679 159418202 159418853 0.000000e+00 701.0
23 TraesCS3A01G462400 chr6A 84.676 757 67 25 1 730 80798186 80797452 0.000000e+00 710.0
24 TraesCS3A01G462400 chr4A 81.722 662 88 24 38 681 45501378 45500732 5.100000e-144 521.0
25 TraesCS3A01G462400 chr6B 81.654 665 86 24 38 680 68367167 68367817 1.830000e-143 520.0
26 TraesCS3A01G462400 chr5D 80.530 755 80 32 31 735 464521936 464521199 6.600000e-143 518.0
27 TraesCS3A01G462400 chr5D 95.964 223 7 2 4143 4364 7044420 7044199 1.180000e-95 361.0
28 TraesCS3A01G462400 chr5D 95.928 221 6 3 4146 4364 164651517 164651736 5.470000e-94 355.0
29 TraesCS3A01G462400 chr7B 81.045 670 78 31 39 681 700432230 700432877 5.170000e-134 488.0
30 TraesCS3A01G462400 chr5A 95.495 222 8 2 4146 4366 680118221 680118001 1.970000e-93 353.0
31 TraesCS3A01G462400 chr5A 94.690 226 10 2 4143 4367 59028272 59028048 2.550000e-92 350.0
32 TraesCS3A01G462400 chr5B 94.348 230 10 3 4146 4374 280157113 280156886 2.550000e-92 350.0
33 TraesCS3A01G462400 chr5B 91.837 245 15 5 4132 4374 280157366 280157125 1.980000e-88 337.0
34 TraesCS3A01G462400 chr1D 94.298 228 11 2 4138 4364 335407137 335406911 9.160000e-92 348.0
35 TraesCS3A01G462400 chr7A 76.410 390 71 15 297 681 53920926 53920553 1.630000e-44 191.0
36 TraesCS3A01G462400 chr1A 83.146 89 6 6 1011 1090 95617261 95617349 6.170000e-09 73.1
37 TraesCS3A01G462400 chr7D 100.000 28 0 0 1063 1090 539123743 539123716 8.000000e-03 52.8


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 TraesCS3A01G462400 chr3A 697558016 697562465 4449 True 8218.0 8218 100.000000 1 4450 1 chr3A.!!$R2 4449
1 TraesCS3A01G462400 chr3A 470714790 470715424 634 True 645.0 645 85.174000 31 681 1 chr3A.!!$R1 650
2 TraesCS3A01G462400 chr3D 562330326 562333774 3448 True 1732.0 4918 90.452667 731 4440 3 chr3D.!!$R3 3709
3 TraesCS3A01G462400 chr3B 749522539 749526006 3467 True 1168.5 3783 92.892000 946 4424 4 chr3B.!!$R1 3478
4 TraesCS3A01G462400 chr3B 791408142 791408761 619 False 398.0 398 79.045000 38 664 1 chr3B.!!$F2 626
5 TraesCS3A01G462400 chr4B 68655021 68655780 759 False 795.0 795 86.275000 3 732 1 chr4B.!!$F1 729
6 TraesCS3A01G462400 chr2B 664465958 664466654 696 True 756.0 756 86.733000 3 681 1 chr2B.!!$R1 678
7 TraesCS3A01G462400 chr1B 322935669 322936340 671 True 728.0 728 86.377000 1 681 1 chr1B.!!$R1 680
8 TraesCS3A01G462400 chr1B 159418202 159418853 651 False 701.0 701 86.758000 51 679 1 chr1B.!!$F1 628
9 TraesCS3A01G462400 chr6A 80797452 80798186 734 True 710.0 710 84.676000 1 730 1 chr6A.!!$R1 729
10 TraesCS3A01G462400 chr4A 45500732 45501378 646 True 521.0 521 81.722000 38 681 1 chr4A.!!$R1 643
11 TraesCS3A01G462400 chr6B 68367167 68367817 650 False 520.0 520 81.654000 38 680 1 chr6B.!!$F1 642
12 TraesCS3A01G462400 chr5D 464521199 464521936 737 True 518.0 518 80.530000 31 735 1 chr5D.!!$R2 704
13 TraesCS3A01G462400 chr7B 700432230 700432877 647 False 488.0 488 81.045000 39 681 1 chr7B.!!$F1 642

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
929 990 0.485099 AGTCCAGTCCAGTCCAGTCT 59.515 55.0 0.00 0.0 0.00 3.24 F
1327 1388 0.036875 ACTGGCTTGCCTGTTCCTAC 59.963 55.0 16.65 0.0 0.00 3.18 F
2490 2584 0.396417 CTGGGACGTCATCTCCTCCT 60.396 60.0 18.91 0.0 0.00 3.69 F
3297 3393 0.179073 ATAGGTAACAGGCAGCAGCG 60.179 55.0 0.00 0.0 40.35 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1880 1.266786 CGTCGCGTGAACGTTCTCTT 61.267 55.0 27.32 0.00 42.22 2.85 R
3297 3393 0.394080 ATCTGCAGCTGCTCTTTCCC 60.394 55.0 36.61 8.49 42.66 3.97 R
3386 3482 0.110956 CAAATGCATCGATCTCCGCG 60.111 55.0 0.00 0.00 38.37 6.46 R
4156 4538 0.320421 GCACGCCCTGTAAACTGAGA 60.320 55.0 0.00 0.00 0.00 3.27 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
36 37 4.742438 TTAGCAGAAACATTCCGAACAC 57.258 40.909 0.00 0.00 0.00 3.32
218 223 8.696410 ACACGAACAATTTTTAAAAGTGTGAT 57.304 26.923 21.30 9.17 38.63 3.06
250 256 9.861138 TTTGCATTTATGAACGAAATTTGAAAG 57.139 25.926 0.00 0.00 0.00 2.62
255 261 8.586570 TTTATGAACGAAATTTGAAAGCACAT 57.413 26.923 0.00 0.00 0.00 3.21
333 343 7.204737 AGAACATTTTTGAAAGAAACGAACG 57.795 32.000 0.00 0.00 0.00 3.95
338 348 9.291664 ACATTTTTGAAAGAAACGAACGAAATA 57.708 25.926 0.14 0.00 0.00 1.40
587 631 7.604164 TCTGAATCTTCTAGATGGTTCACAAAC 59.396 37.037 23.55 5.00 34.65 2.93
622 666 1.960689 CTGGAAACCCGTGGAACATTT 59.039 47.619 0.00 0.00 44.52 2.32
739 800 4.270008 CAAATAGGAAATTCCGTCCCACT 58.730 43.478 6.35 0.00 42.75 4.00
779 840 3.803082 CGGCAACCGCATGACCTG 61.803 66.667 0.00 0.00 41.17 4.00
780 841 3.443045 GGCAACCGCATGACCTGG 61.443 66.667 0.00 0.00 41.24 4.45
781 842 2.359850 GCAACCGCATGACCTGGA 60.360 61.111 0.00 0.00 38.36 3.86
782 843 1.750399 GCAACCGCATGACCTGGAT 60.750 57.895 0.00 0.00 38.36 3.41
783 844 1.718757 GCAACCGCATGACCTGGATC 61.719 60.000 0.00 0.00 38.36 3.36
784 845 1.097547 CAACCGCATGACCTGGATCC 61.098 60.000 4.20 4.20 0.00 3.36
825 886 4.459089 GCTCGCACCTCCACCTCC 62.459 72.222 0.00 0.00 0.00 4.30
826 887 2.681778 CTCGCACCTCCACCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
827 888 2.203788 TCGCACCTCCACCTCCTT 60.204 61.111 0.00 0.00 0.00 3.36
828 889 2.046892 CGCACCTCCACCTCCTTG 60.047 66.667 0.00 0.00 0.00 3.61
829 890 2.360475 GCACCTCCACCTCCTTGC 60.360 66.667 0.00 0.00 0.00 4.01
830 891 2.046892 CACCTCCACCTCCTTGCG 60.047 66.667 0.00 0.00 0.00 4.85
831 892 2.203788 ACCTCCACCTCCTTGCGA 60.204 61.111 0.00 0.00 0.00 5.10
832 893 2.286523 ACCTCCACCTCCTTGCGAG 61.287 63.158 0.00 0.00 38.46 5.03
833 894 2.125350 CTCCACCTCCTTGCGAGC 60.125 66.667 0.00 0.00 37.27 5.03
834 895 3.672295 CTCCACCTCCTTGCGAGCC 62.672 68.421 0.00 0.00 37.27 4.70
835 896 4.020617 CCACCTCCTTGCGAGCCA 62.021 66.667 0.00 0.00 37.27 4.75
836 897 2.435586 CACCTCCTTGCGAGCCAG 60.436 66.667 0.00 0.00 37.27 4.85
837 898 2.604686 ACCTCCTTGCGAGCCAGA 60.605 61.111 0.00 0.00 37.27 3.86
838 899 2.186384 CCTCCTTGCGAGCCAGAG 59.814 66.667 0.00 0.00 37.27 3.35
839 900 2.654079 CCTCCTTGCGAGCCAGAGT 61.654 63.158 0.00 0.00 37.27 3.24
840 901 1.153667 CTCCTTGCGAGCCAGAGTC 60.154 63.158 0.00 0.00 0.00 3.36
841 902 1.603236 CTCCTTGCGAGCCAGAGTCT 61.603 60.000 0.00 0.00 0.00 3.24
842 903 1.447489 CCTTGCGAGCCAGAGTCTG 60.447 63.158 13.56 13.56 0.00 3.51
860 921 3.509575 GTCTGTGATTTGTGGGCCATTTA 59.490 43.478 10.70 0.00 0.00 1.40
863 924 3.130164 TGTGATTTGTGGGCCATTTATCG 59.870 43.478 10.70 0.00 0.00 2.92
923 984 0.605589 CAGTCCAGTCCAGTCCAGTC 59.394 60.000 0.00 0.00 0.00 3.51
924 985 0.543174 AGTCCAGTCCAGTCCAGTCC 60.543 60.000 0.00 0.00 0.00 3.85
925 986 0.832135 GTCCAGTCCAGTCCAGTCCA 60.832 60.000 0.00 0.00 0.00 4.02
926 987 0.542938 TCCAGTCCAGTCCAGTCCAG 60.543 60.000 0.00 0.00 0.00 3.86
927 988 0.833834 CCAGTCCAGTCCAGTCCAGT 60.834 60.000 0.00 0.00 0.00 4.00
928 989 0.605589 CAGTCCAGTCCAGTCCAGTC 59.394 60.000 0.00 0.00 0.00 3.51
929 990 0.485099 AGTCCAGTCCAGTCCAGTCT 59.515 55.000 0.00 0.00 0.00 3.24
930 991 1.133009 AGTCCAGTCCAGTCCAGTCTT 60.133 52.381 0.00 0.00 0.00 3.01
931 992 1.001406 GTCCAGTCCAGTCCAGTCTTG 59.999 57.143 0.00 0.00 0.00 3.02
932 993 1.051812 CCAGTCCAGTCCAGTCTTGT 58.948 55.000 0.00 0.00 0.00 3.16
933 994 1.001406 CCAGTCCAGTCCAGTCTTGTC 59.999 57.143 0.00 0.00 0.00 3.18
934 995 1.967066 CAGTCCAGTCCAGTCTTGTCT 59.033 52.381 0.00 0.00 0.00 3.41
935 996 2.029470 CAGTCCAGTCCAGTCTTGTCTC 60.029 54.545 0.00 0.00 0.00 3.36
936 997 1.964223 GTCCAGTCCAGTCTTGTCTCA 59.036 52.381 0.00 0.00 0.00 3.27
937 998 2.365617 GTCCAGTCCAGTCTTGTCTCAA 59.634 50.000 0.00 0.00 0.00 3.02
938 999 3.038280 TCCAGTCCAGTCTTGTCTCAAA 58.962 45.455 0.00 0.00 0.00 2.69
939 1000 3.454447 TCCAGTCCAGTCTTGTCTCAAAA 59.546 43.478 0.00 0.00 0.00 2.44
940 1001 4.080582 TCCAGTCCAGTCTTGTCTCAAAAA 60.081 41.667 0.00 0.00 0.00 1.94
1327 1388 0.036875 ACTGGCTTGCCTGTTCCTAC 59.963 55.000 16.65 0.00 0.00 3.18
1331 1392 0.909623 GCTTGCCTGTTCCTACCCTA 59.090 55.000 0.00 0.00 0.00 3.53
1332 1393 1.280998 GCTTGCCTGTTCCTACCCTAA 59.719 52.381 0.00 0.00 0.00 2.69
1339 1400 2.699321 CTGTTCCTACCCTAACCTAGCC 59.301 54.545 0.00 0.00 0.00 3.93
1340 1401 2.316982 TGTTCCTACCCTAACCTAGCCT 59.683 50.000 0.00 0.00 0.00 4.58
1341 1402 3.533068 TGTTCCTACCCTAACCTAGCCTA 59.467 47.826 0.00 0.00 0.00 3.93
1342 1403 4.151121 GTTCCTACCCTAACCTAGCCTAG 58.849 52.174 0.00 0.00 0.00 3.02
1350 1411 2.287251 CCTAGCCTAGGGGGTGCT 59.713 66.667 11.72 3.11 43.91 4.40
1352 1413 1.075226 CTAGCCTAGGGGGTGCTGA 60.075 63.158 11.72 0.00 43.91 4.26
1359 1423 0.913934 TAGGGGGTGCTGATGCTGAA 60.914 55.000 0.00 0.00 40.48 3.02
1380 1444 1.493446 TGCTGAATGCTGATGGATCCT 59.507 47.619 14.23 0.00 43.37 3.24
1396 1460 3.958860 CTCCATCCCATCCCCGCC 61.959 72.222 0.00 0.00 0.00 6.13
1397 1461 4.833495 TCCATCCCATCCCCGCCA 62.833 66.667 0.00 0.00 0.00 5.69
1433 1497 5.191722 TGCTCCTTAATTTCATCCTACCAGT 59.808 40.000 0.00 0.00 0.00 4.00
1443 1507 6.508030 TTCATCCTACCAGTAATATTGGCA 57.492 37.500 1.40 0.00 39.39 4.92
1489 1553 5.888161 CCCATTCAGGCTACTCTAATTTGTT 59.112 40.000 0.00 0.00 35.39 2.83
1528 1592 6.779860 TGATAATCCCAGCCCTAGTTTAATC 58.220 40.000 0.00 0.00 0.00 1.75
1566 1630 0.530650 CTAGGCATGCTGTACGTGGG 60.531 60.000 18.92 0.00 35.67 4.61
1597 1661 3.435186 GCTCCGCTCCAAGGCAAC 61.435 66.667 0.00 0.00 0.00 4.17
1645 1709 5.243283 GGAATGCTCTGCAGAAAATGGATAT 59.757 40.000 18.85 4.16 43.65 1.63
1647 1711 5.045012 TGCTCTGCAGAAAATGGATATCT 57.955 39.130 18.85 0.00 33.32 1.98
1649 1713 4.820716 GCTCTGCAGAAAATGGATATCTGT 59.179 41.667 18.85 0.00 42.00 3.41
1701 1765 8.221944 TGTGAAAACTATTCCTCCCTTTCTTAA 58.778 33.333 0.00 0.00 0.00 1.85
1840 1907 1.083015 GTTCACGCGACGCAATTGT 60.083 52.632 21.35 6.45 0.00 2.71
1842 1909 2.436997 TTCACGCGACGCAATTGTGG 62.437 55.000 22.27 10.12 0.00 4.17
1846 1913 0.454285 CGCGACGCAATTGTGGAAAT 60.454 50.000 22.27 1.66 0.00 2.17
1888 1955 2.342179 GAGAACTCCACACTTGCTAGC 58.658 52.381 8.10 8.10 0.00 3.42
1943 2010 7.893658 TCCTAGTAACGAGAGAACTTTGATTT 58.106 34.615 0.00 0.00 33.98 2.17
2017 2102 9.912634 TGTGAGTTCCTTTATTTGATTTGATTC 57.087 29.630 0.00 0.00 0.00 2.52
2289 2375 5.705441 TGCTCCACCTCATGTTTACTAAAAG 59.295 40.000 0.00 0.00 0.00 2.27
2334 2420 4.463879 CCTGCTGCTCCTCCGTGG 62.464 72.222 0.00 0.00 37.10 4.94
2335 2421 4.463879 CTGCTGCTCCTCCGTGGG 62.464 72.222 0.00 0.00 36.20 4.61
2490 2584 0.396417 CTGGGACGTCATCTCCTCCT 60.396 60.000 18.91 0.00 0.00 3.69
2548 2642 2.095364 GGTTTCTGCTCAGCAATCAGTG 60.095 50.000 0.00 0.00 38.41 3.66
2850 2946 7.519649 GCTTTCTGCTCAAGTATTATCATGTCC 60.520 40.741 0.00 0.00 38.95 4.02
2852 2948 6.888105 TCTGCTCAAGTATTATCATGTCCAA 58.112 36.000 0.00 0.00 0.00 3.53
2884 2980 1.053264 ATCTAGCAGCCCTCCCTGTG 61.053 60.000 0.00 0.00 35.28 3.66
3079 3175 1.251527 GGGCTGAAGACTGGAGACGA 61.252 60.000 0.00 0.00 0.00 4.20
3173 3269 1.439543 ATTATGAGGTCCCTCCCTGC 58.560 55.000 10.77 0.00 42.09 4.85
3251 3347 8.035394 TGAAGTCTCTTATCTTATTTTGTCGCT 58.965 33.333 0.00 0.00 0.00 4.93
3297 3393 0.179073 ATAGGTAACAGGCAGCAGCG 60.179 55.000 0.00 0.00 40.35 5.18
3386 3482 2.798364 GGAGCGGAGGGCCTACTTC 61.798 68.421 15.31 11.24 45.17 3.01
3431 3527 5.799213 CTGGTAGAGGAGTTTGTTTCATCT 58.201 41.667 0.00 0.00 38.95 2.90
3547 3643 5.295787 GGAAAAGATATATGTGTTGCACGGA 59.704 40.000 0.02 0.00 37.14 4.69
3590 3686 9.860650 AGATTAGCTGAGTCTTAATTCTAGAGA 57.139 33.333 0.00 0.00 0.00 3.10
3592 3688 9.640952 ATTAGCTGAGTCTTAATTCTAGAGAGT 57.359 33.333 0.00 0.00 0.00 3.24
3626 3722 5.373981 AGTAGTAAAGTGTTGAGTCCTCG 57.626 43.478 0.00 0.00 0.00 4.63
3653 3749 0.895100 TTGCTGCCTCGCAATTCCTT 60.895 50.000 0.00 0.00 44.30 3.36
3682 3778 4.159693 ACATGATGGTAGTCGTTAAGCTGA 59.840 41.667 0.00 0.00 0.00 4.26
3819 3916 3.937706 CCATACAGAACCTGCAGAAGAAG 59.062 47.826 17.39 4.55 34.37 2.85
3842 3939 3.620488 TGGTGGAAAGAGTATGATTGCC 58.380 45.455 0.00 0.00 0.00 4.52
3871 4071 4.407296 AGCTGTTGGTTGGTTTGGAAATAA 59.593 37.500 0.00 0.00 0.00 1.40
3872 4072 5.104735 AGCTGTTGGTTGGTTTGGAAATAAA 60.105 36.000 0.00 0.00 0.00 1.40
3874 4074 6.301169 TGTTGGTTGGTTTGGAAATAAACT 57.699 33.333 0.00 0.00 39.78 2.66
3875 4075 7.419711 TGTTGGTTGGTTTGGAAATAAACTA 57.580 32.000 0.00 0.00 39.78 2.24
3876 4076 7.266400 TGTTGGTTGGTTTGGAAATAAACTAC 58.734 34.615 0.00 0.00 39.78 2.73
3956 4332 4.276926 AGGTCACTCACATTCTTCTTTTGC 59.723 41.667 0.00 0.00 0.00 3.68
3961 4337 2.297033 TCACATTCTTCTTTTGCTGGGC 59.703 45.455 0.00 0.00 0.00 5.36
4022 4399 7.441836 TGGCATATACTAGATGTGTAAACTGG 58.558 38.462 0.00 0.00 0.00 4.00
4056 4433 5.940470 AGGAGAAAATGATTGGTGTGACTAC 59.060 40.000 0.00 0.00 0.00 2.73
4065 4442 7.376435 TGATTGGTGTGACTACATATGTTTG 57.624 36.000 14.77 10.04 39.39 2.93
4097 4479 8.309163 TGTTTGGTTGAAGATGCATTAATTTC 57.691 30.769 0.00 4.12 0.00 2.17
4100 4482 8.761575 TTGGTTGAAGATGCATTAATTTCTTC 57.238 30.769 15.46 15.46 42.74 2.87
4102 4484 8.587608 TGGTTGAAGATGCATTAATTTCTTCTT 58.412 29.630 20.46 17.07 42.82 2.52
4160 4542 8.840200 ATTAATTTGGTACTACCTCTCTCTCA 57.160 34.615 6.79 0.00 39.58 3.27
4161 4543 6.783708 AATTTGGTACTACCTCTCTCTCAG 57.216 41.667 6.79 0.00 39.58 3.35
4162 4544 4.931027 TTGGTACTACCTCTCTCTCAGT 57.069 45.455 6.79 0.00 39.58 3.41
4163 4545 4.931027 TGGTACTACCTCTCTCTCAGTT 57.069 45.455 6.79 0.00 39.58 3.16
4164 4546 5.258216 TGGTACTACCTCTCTCTCAGTTT 57.742 43.478 6.79 0.00 39.58 2.66
4165 4547 6.384342 TGGTACTACCTCTCTCTCAGTTTA 57.616 41.667 6.79 0.00 39.58 2.01
4166 4548 6.179040 TGGTACTACCTCTCTCTCAGTTTAC 58.821 44.000 6.79 0.00 39.58 2.01
4167 4549 6.179040 GGTACTACCTCTCTCTCAGTTTACA 58.821 44.000 0.00 0.00 34.73 2.41
4168 4550 6.316890 GGTACTACCTCTCTCTCAGTTTACAG 59.683 46.154 0.00 0.00 34.73 2.74
4169 4551 5.258051 ACTACCTCTCTCTCAGTTTACAGG 58.742 45.833 0.00 0.00 0.00 4.00
4170 4552 3.436243 ACCTCTCTCTCAGTTTACAGGG 58.564 50.000 0.00 0.00 0.00 4.45
4171 4553 2.167487 CCTCTCTCTCAGTTTACAGGGC 59.833 54.545 0.00 0.00 0.00 5.19
4172 4554 1.819288 TCTCTCTCAGTTTACAGGGCG 59.181 52.381 0.00 0.00 0.00 6.13
4173 4555 1.546476 CTCTCTCAGTTTACAGGGCGT 59.454 52.381 0.00 0.00 0.00 5.68
4174 4556 1.272490 TCTCTCAGTTTACAGGGCGTG 59.728 52.381 5.50 5.50 0.00 5.34
4175 4557 0.320421 TCTCAGTTTACAGGGCGTGC 60.320 55.000 7.17 0.00 0.00 5.34
4176 4558 1.626654 CTCAGTTTACAGGGCGTGCG 61.627 60.000 7.17 0.00 0.00 5.34
4177 4559 3.047877 AGTTTACAGGGCGTGCGC 61.048 61.111 7.17 8.17 41.06 6.09
4178 4560 4.439472 GTTTACAGGGCGTGCGCG 62.439 66.667 16.86 16.86 43.06 6.86
4179 4561 4.973055 TTTACAGGGCGTGCGCGT 62.973 61.111 22.18 2.94 43.06 6.01
4180 4562 3.570621 TTTACAGGGCGTGCGCGTA 62.571 57.895 22.18 0.00 43.06 4.42
4181 4563 4.781959 TACAGGGCGTGCGCGTAC 62.782 66.667 22.18 17.94 43.06 3.67
4188 4570 4.564116 CGTGCGCGTACCCCTAGG 62.564 72.222 21.71 0.06 40.04 3.02
4190 4572 3.142838 TGCGCGTACCCCTAGGTC 61.143 66.667 8.43 0.00 46.45 3.85
4191 4573 4.261781 GCGCGTACCCCTAGGTCG 62.262 72.222 8.43 8.12 46.45 4.79
4192 4574 2.825836 CGCGTACCCCTAGGTCGT 60.826 66.667 8.29 6.00 46.45 4.34
4193 4575 2.828128 CGCGTACCCCTAGGTCGTC 61.828 68.421 8.29 3.46 46.45 4.20
4194 4576 1.750399 GCGTACCCCTAGGTCGTCA 60.750 63.158 8.29 0.00 46.45 4.35
4195 4577 1.315257 GCGTACCCCTAGGTCGTCAA 61.315 60.000 8.29 0.00 46.45 3.18
4196 4578 1.396653 CGTACCCCTAGGTCGTCAAT 58.603 55.000 8.29 0.00 46.45 2.57
4197 4579 1.753073 CGTACCCCTAGGTCGTCAATT 59.247 52.381 8.29 0.00 46.45 2.32
4198 4580 2.167075 CGTACCCCTAGGTCGTCAATTT 59.833 50.000 8.29 0.00 46.45 1.82
4199 4581 3.381272 CGTACCCCTAGGTCGTCAATTTA 59.619 47.826 8.29 0.00 46.45 1.40
4200 4582 4.142182 CGTACCCCTAGGTCGTCAATTTAA 60.142 45.833 8.29 0.00 46.45 1.52
4201 4583 4.212143 ACCCCTAGGTCGTCAATTTAAC 57.788 45.455 8.29 0.00 46.45 2.01
4202 4584 3.054875 ACCCCTAGGTCGTCAATTTAACC 60.055 47.826 8.29 0.00 46.45 2.85
4203 4585 3.054948 CCCCTAGGTCGTCAATTTAACCA 60.055 47.826 8.29 0.00 34.09 3.67
4204 4586 4.566070 CCCCTAGGTCGTCAATTTAACCAA 60.566 45.833 8.29 0.00 34.09 3.67
4205 4587 4.393990 CCCTAGGTCGTCAATTTAACCAAC 59.606 45.833 8.29 0.00 34.09 3.77
4206 4588 4.393990 CCTAGGTCGTCAATTTAACCAACC 59.606 45.833 0.00 0.00 34.09 3.77
4207 4589 4.094830 AGGTCGTCAATTTAACCAACCT 57.905 40.909 0.00 0.00 34.09 3.50
4208 4590 5.231702 AGGTCGTCAATTTAACCAACCTA 57.768 39.130 7.30 0.00 34.22 3.08
4209 4591 5.623169 AGGTCGTCAATTTAACCAACCTAA 58.377 37.500 7.30 0.00 34.22 2.69
4210 4592 6.243148 AGGTCGTCAATTTAACCAACCTAAT 58.757 36.000 7.30 0.00 34.22 1.73
4211 4593 7.396418 AGGTCGTCAATTTAACCAACCTAATA 58.604 34.615 7.30 0.00 34.22 0.98
4212 4594 7.335171 AGGTCGTCAATTTAACCAACCTAATAC 59.665 37.037 7.30 0.00 34.22 1.89
4213 4595 7.119553 GGTCGTCAATTTAACCAACCTAATACA 59.880 37.037 0.00 0.00 0.00 2.29
4214 4596 8.505625 GTCGTCAATTTAACCAACCTAATACAA 58.494 33.333 0.00 0.00 0.00 2.41
4215 4597 8.723311 TCGTCAATTTAACCAACCTAATACAAG 58.277 33.333 0.00 0.00 0.00 3.16
4216 4598 8.508875 CGTCAATTTAACCAACCTAATACAAGT 58.491 33.333 0.00 0.00 0.00 3.16
4217 4599 9.836076 GTCAATTTAACCAACCTAATACAAGTC 57.164 33.333 0.00 0.00 0.00 3.01
4218 4600 9.575868 TCAATTTAACCAACCTAATACAAGTCA 57.424 29.630 0.00 0.00 0.00 3.41
4252 4634 9.716507 CAAGAAATATACCAACATAAACTTCGG 57.283 33.333 0.00 0.00 0.00 4.30
4253 4635 9.675464 AAGAAATATACCAACATAAACTTCGGA 57.325 29.630 0.00 0.00 0.00 4.55
4254 4636 9.326413 AGAAATATACCAACATAAACTTCGGAG 57.674 33.333 0.00 0.00 0.00 4.63
4255 4637 9.106070 GAAATATACCAACATAAACTTCGGAGT 57.894 33.333 0.00 0.00 37.87 3.85
4269 4651 7.619964 AACTTCGGAGTTTCTACTTTCAAAA 57.380 32.000 2.29 0.00 43.48 2.44
4270 4652 7.247929 ACTTCGGAGTTTCTACTTTCAAAAG 57.752 36.000 0.00 0.97 35.92 2.27
4271 4653 6.260271 ACTTCGGAGTTTCTACTTTCAAAAGG 59.740 38.462 7.37 0.00 34.81 3.11
4272 4654 5.677567 TCGGAGTTTCTACTTTCAAAAGGT 58.322 37.500 7.37 0.00 40.31 3.50
4273 4655 6.819284 TCGGAGTTTCTACTTTCAAAAGGTA 58.181 36.000 7.37 0.00 40.31 3.08
4274 4656 7.447594 TCGGAGTTTCTACTTTCAAAAGGTAT 58.552 34.615 7.37 0.00 40.31 2.73
4275 4657 8.587608 TCGGAGTTTCTACTTTCAAAAGGTATA 58.412 33.333 7.37 0.00 40.31 1.47
4276 4658 9.211485 CGGAGTTTCTACTTTCAAAAGGTATAA 57.789 33.333 7.37 0.00 40.31 0.98
4334 4716 7.478520 AAATTGACAACCTAGATATACGTGC 57.521 36.000 0.00 0.00 0.00 5.34
4335 4717 5.585820 TTGACAACCTAGATATACGTGCA 57.414 39.130 0.00 0.00 0.00 4.57
4336 4718 5.183014 TGACAACCTAGATATACGTGCAG 57.817 43.478 0.00 0.00 0.00 4.41
4337 4719 4.037565 TGACAACCTAGATATACGTGCAGG 59.962 45.833 4.53 4.53 0.00 4.85
4338 4720 4.212716 ACAACCTAGATATACGTGCAGGA 58.787 43.478 14.38 0.00 0.00 3.86
4339 4721 4.037684 ACAACCTAGATATACGTGCAGGAC 59.962 45.833 14.38 0.00 0.00 3.85
4340 4722 4.101645 ACCTAGATATACGTGCAGGACT 57.898 45.455 14.38 2.13 0.00 3.85
4341 4723 4.471548 ACCTAGATATACGTGCAGGACTT 58.528 43.478 14.38 0.00 0.00 3.01
4342 4724 4.278669 ACCTAGATATACGTGCAGGACTTG 59.721 45.833 14.38 5.42 0.00 3.16
4343 4725 4.278669 CCTAGATATACGTGCAGGACTTGT 59.721 45.833 14.38 0.00 0.00 3.16
4344 4726 5.472478 CCTAGATATACGTGCAGGACTTGTA 59.528 44.000 14.38 0.00 0.00 2.41
4345 4727 5.847111 AGATATACGTGCAGGACTTGTAA 57.153 39.130 14.38 0.00 0.00 2.41
4346 4728 6.216801 AGATATACGTGCAGGACTTGTAAA 57.783 37.500 14.38 0.00 0.00 2.01
4347 4729 6.040878 AGATATACGTGCAGGACTTGTAAAC 58.959 40.000 14.38 0.00 0.00 2.01
4348 4730 2.614829 ACGTGCAGGACTTGTAAACT 57.385 45.000 14.38 0.00 0.00 2.66
4349 4731 2.210116 ACGTGCAGGACTTGTAAACTG 58.790 47.619 14.38 0.00 0.00 3.16
4350 4732 2.159014 ACGTGCAGGACTTGTAAACTGA 60.159 45.455 14.38 0.00 32.86 3.41
4351 4733 2.869801 CGTGCAGGACTTGTAAACTGAA 59.130 45.455 0.00 0.00 32.86 3.02
4352 4734 3.311322 CGTGCAGGACTTGTAAACTGAAA 59.689 43.478 0.00 0.00 32.86 2.69
4353 4735 4.598062 GTGCAGGACTTGTAAACTGAAAC 58.402 43.478 0.00 0.00 32.86 2.78
4354 4736 4.095782 GTGCAGGACTTGTAAACTGAAACA 59.904 41.667 0.00 0.00 32.86 2.83
4355 4737 4.335315 TGCAGGACTTGTAAACTGAAACAG 59.665 41.667 0.00 0.00 37.52 3.16
4356 4738 4.574828 GCAGGACTTGTAAACTGAAACAGA 59.425 41.667 5.76 0.00 35.18 3.41
4357 4739 5.277538 GCAGGACTTGTAAACTGAAACAGAG 60.278 44.000 5.76 0.00 35.18 3.35
4358 4740 5.237344 CAGGACTTGTAAACTGAAACAGAGG 59.763 44.000 5.76 0.00 35.18 3.69
4359 4741 5.104485 AGGACTTGTAAACTGAAACAGAGGT 60.104 40.000 5.76 0.00 35.18 3.85
4360 4742 6.099269 AGGACTTGTAAACTGAAACAGAGGTA 59.901 38.462 5.76 0.00 35.18 3.08
4361 4743 6.424207 GGACTTGTAAACTGAAACAGAGGTAG 59.576 42.308 5.76 0.00 35.18 3.18
4362 4744 6.885922 ACTTGTAAACTGAAACAGAGGTAGT 58.114 36.000 5.76 0.00 35.18 2.73
4363 4745 8.015185 ACTTGTAAACTGAAACAGAGGTAGTA 57.985 34.615 5.76 0.00 35.18 1.82
4424 4807 2.203112 GCGATCAGCCAGCCATGA 60.203 61.111 0.00 0.00 40.81 3.07
4440 4823 7.012704 GCCAGCCATGAACGATCAATATATATT 59.987 37.037 0.00 1.91 39.49 1.28
4441 4824 9.546428 CCAGCCATGAACGATCAATATATATTA 57.454 33.333 7.65 0.00 39.49 0.98
4449 4832 9.968870 GAACGATCAATATATATTACTCCCTCC 57.031 37.037 7.65 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.398416 GTGTTCGGAATGTTTCTGCTAAAAC 59.602 40.000 0.00 7.35 39.16 2.43
228 234 8.486383 TGTGCTTTCAAATTTCGTTCATAAATG 58.514 29.630 0.00 0.00 0.00 2.32
410 420 6.207417 TCAAAACATGTTTGCCTTTTCCAAAA 59.793 30.769 23.93 0.00 34.33 2.44
528 565 8.474006 TTTCTTTCTTTTCCTTTTCCTTTTCG 57.526 30.769 0.00 0.00 0.00 3.46
535 572 8.492673 ACCATGTTTTCTTTCTTTTCCTTTTC 57.507 30.769 0.00 0.00 0.00 2.29
587 631 0.393267 TCCAGCCGGTTTATTTCGGG 60.393 55.000 1.90 0.00 45.75 5.14
622 666 2.691011 CCTTTCTGTTTCCGGTTTTGGA 59.309 45.455 0.00 0.00 35.83 3.53
697 758 1.300542 CGCACGTTGGGGCAAATTT 60.301 52.632 0.00 0.00 0.00 1.82
706 767 1.136565 CCTATTTGCCGCACGTTGG 59.863 57.895 0.00 0.00 0.00 3.77
770 831 2.592861 GCCGGATCCAGGTCATGC 60.593 66.667 13.41 0.00 0.00 4.06
772 833 2.911143 GTGCCGGATCCAGGTCAT 59.089 61.111 13.41 0.00 0.00 3.06
811 872 2.046892 CAAGGAGGTGGAGGTGCG 60.047 66.667 0.00 0.00 0.00 5.34
825 886 1.013005 CACAGACTCTGGCTCGCAAG 61.013 60.000 10.86 0.00 35.51 4.01
826 887 1.005748 CACAGACTCTGGCTCGCAA 60.006 57.895 10.86 0.00 35.51 4.85
827 888 1.253593 ATCACAGACTCTGGCTCGCA 61.254 55.000 10.86 0.00 35.51 5.10
828 889 0.108424 AATCACAGACTCTGGCTCGC 60.108 55.000 10.86 0.00 35.51 5.03
829 890 1.998315 CAAATCACAGACTCTGGCTCG 59.002 52.381 10.86 0.00 35.51 5.03
830 891 2.740981 CACAAATCACAGACTCTGGCTC 59.259 50.000 10.86 0.00 35.51 4.70
831 892 2.551721 CCACAAATCACAGACTCTGGCT 60.552 50.000 10.86 0.00 35.51 4.75
832 893 1.808945 CCACAAATCACAGACTCTGGC 59.191 52.381 10.86 0.00 35.51 4.85
833 894 2.430465 CCCACAAATCACAGACTCTGG 58.570 52.381 10.86 0.24 35.51 3.86
834 895 1.808945 GCCCACAAATCACAGACTCTG 59.191 52.381 4.36 4.36 37.52 3.35
835 896 1.271597 GGCCCACAAATCACAGACTCT 60.272 52.381 0.00 0.00 0.00 3.24
836 897 1.168714 GGCCCACAAATCACAGACTC 58.831 55.000 0.00 0.00 0.00 3.36
837 898 0.478072 TGGCCCACAAATCACAGACT 59.522 50.000 0.00 0.00 0.00 3.24
838 899 1.549203 ATGGCCCACAAATCACAGAC 58.451 50.000 0.00 0.00 0.00 3.51
839 900 2.307496 AATGGCCCACAAATCACAGA 57.693 45.000 0.00 0.00 0.00 3.41
840 901 4.685924 GATAAATGGCCCACAAATCACAG 58.314 43.478 0.00 0.00 0.00 3.66
841 902 3.130164 CGATAAATGGCCCACAAATCACA 59.870 43.478 0.00 0.00 0.00 3.58
842 903 3.490761 CCGATAAATGGCCCACAAATCAC 60.491 47.826 0.00 0.00 0.00 3.06
865 926 0.186873 ATATGGGCTTGGGCTTCAGG 59.813 55.000 0.00 0.00 38.73 3.86
941 1002 2.422945 GGTGGACTGGACTGGACTTTTT 60.423 50.000 0.00 0.00 0.00 1.94
942 1003 1.143073 GGTGGACTGGACTGGACTTTT 59.857 52.381 0.00 0.00 0.00 2.27
943 1004 0.765510 GGTGGACTGGACTGGACTTT 59.234 55.000 0.00 0.00 0.00 2.66
944 1005 1.128188 GGGTGGACTGGACTGGACTT 61.128 60.000 0.00 0.00 0.00 3.01
1331 1392 1.693103 GCACCCCCTAGGCTAGGTT 60.693 63.158 32.99 17.81 44.73 3.50
1332 1393 2.040779 GCACCCCCTAGGCTAGGT 60.041 66.667 32.99 17.43 44.73 3.08
1339 1400 1.147824 CAGCATCAGCACCCCCTAG 59.852 63.158 0.00 0.00 45.49 3.02
1340 1401 0.913934 TTCAGCATCAGCACCCCCTA 60.914 55.000 0.00 0.00 45.49 3.53
1341 1402 1.578215 ATTCAGCATCAGCACCCCCT 61.578 55.000 0.00 0.00 45.49 4.79
1342 1403 1.076485 ATTCAGCATCAGCACCCCC 60.076 57.895 0.00 0.00 45.49 5.40
1343 1404 2.012902 GCATTCAGCATCAGCACCCC 62.013 60.000 0.00 0.00 45.49 4.95
1344 1405 1.436336 GCATTCAGCATCAGCACCC 59.564 57.895 0.00 0.00 45.49 4.61
1380 1444 4.833495 TGGCGGGGATGGGATGGA 62.833 66.667 0.00 0.00 0.00 3.41
1416 1480 9.515226 GCCAATATTACTGGTAGGATGAAATTA 57.485 33.333 0.00 0.00 36.24 1.40
1443 1507 5.244626 GGGCAGTGAATGGATAATTAAGCAT 59.755 40.000 0.00 0.00 0.00 3.79
1489 1553 9.094578 CTGGGATTATCAAATTAGTAGAGGAGA 57.905 37.037 0.00 0.00 0.00 3.71
1566 1630 2.433318 GAGCACGGGTGAGAGCAC 60.433 66.667 2.38 0.00 44.39 4.40
1597 1661 1.213537 CATTGGGCAACAGAAGCGG 59.786 57.895 0.00 0.00 39.74 5.52
1645 1709 6.065374 ACAGAGAAGAAAGACTAGTGACAGA 58.935 40.000 0.00 0.00 0.00 3.41
1647 1711 6.096987 ACAACAGAGAAGAAAGACTAGTGACA 59.903 38.462 0.00 0.00 0.00 3.58
1649 1713 6.321435 TGACAACAGAGAAGAAAGACTAGTGA 59.679 38.462 0.00 0.00 0.00 3.41
1701 1765 7.275779 CGCAATATTACTTACTGTCAGTGAAGT 59.724 37.037 16.03 19.43 36.21 3.01
1760 1824 4.647853 TCGTGGAAACTAGTACATATGCCT 59.352 41.667 1.58 1.58 0.00 4.75
1812 1878 1.381429 GTCGCGTGAACGTTCTCTTAC 59.619 52.381 27.32 16.50 42.22 2.34
1814 1880 1.266786 CGTCGCGTGAACGTTCTCTT 61.267 55.000 27.32 0.00 42.22 2.85
1826 1892 1.777030 TTTCCACAATTGCGTCGCGT 61.777 50.000 13.38 0.71 0.00 6.01
1840 1907 3.805066 TTGACCAGATGACCATTTCCA 57.195 42.857 0.00 0.00 0.00 3.53
1842 1909 5.964958 TTCTTTGACCAGATGACCATTTC 57.035 39.130 0.00 0.00 0.00 2.17
1846 1913 4.782691 TCCTATTCTTTGACCAGATGACCA 59.217 41.667 0.00 0.00 0.00 4.02
1888 1955 4.003648 GGGAACAGACATAGTGAACTTGG 58.996 47.826 0.00 0.00 0.00 3.61
2017 2102 5.346281 CGTAGAAACTAGTGCCAGAAAAGAG 59.654 44.000 0.00 0.00 0.00 2.85
2257 2342 3.521126 ACATGAGGTGGAGCAGACTAAAT 59.479 43.478 0.00 0.00 0.00 1.40
2289 2375 7.967890 AAAAAGTGGAACAAATGAATGGATC 57.032 32.000 0.00 0.00 44.16 3.36
2334 2420 4.091509 CAGCGTTACACATACAGAGTTTCC 59.908 45.833 0.00 0.00 0.00 3.13
2335 2421 4.921515 TCAGCGTTACACATACAGAGTTTC 59.078 41.667 0.00 0.00 0.00 2.78
2490 2584 7.362574 GCATATACCTTCCTTGTGTTTTTGCTA 60.363 37.037 0.00 0.00 0.00 3.49
2548 2642 8.532977 AATTTCCATATGCAAACAGTTAACAC 57.467 30.769 8.61 0.00 0.00 3.32
2561 2655 6.545298 GGAGGGATCTCATAATTTCCATATGC 59.455 42.308 0.00 0.00 41.69 3.14
2612 2706 4.142026 TGTTACCAGACTATCACGAATGGG 60.142 45.833 0.00 0.00 31.95 4.00
2850 2946 6.940714 GCTGCTAGATGCCAAATAAAAATTG 58.059 36.000 0.00 0.00 42.00 2.32
3119 3215 6.951971 AGGCCTGCTAGATATATTTACCTTG 58.048 40.000 3.11 0.00 0.00 3.61
3134 3230 0.476338 TTCCACAACAAGGCCTGCTA 59.524 50.000 5.69 0.00 0.00 3.49
3288 3384 3.130160 CTCTTTCCCGCTGCTGCC 61.130 66.667 10.24 0.00 35.36 4.85
3297 3393 0.394080 ATCTGCAGCTGCTCTTTCCC 60.394 55.000 36.61 8.49 42.66 3.97
3386 3482 0.110956 CAAATGCATCGATCTCCGCG 60.111 55.000 0.00 0.00 38.37 6.46
3431 3527 0.958876 TCTACTCTGCGTCGCTTCCA 60.959 55.000 19.50 0.00 0.00 3.53
3523 3619 5.295787 TCCGTGCAACACATATATCTTTTCC 59.704 40.000 0.00 0.00 35.74 3.13
3547 3643 1.003646 TCTCTCTCTACCCAGGCTGT 58.996 55.000 14.43 0.00 0.00 4.40
3590 3686 5.780793 ACTTTACTACTTCATGGACTCCACT 59.219 40.000 0.00 0.00 35.80 4.00
3592 3688 5.542635 ACACTTTACTACTTCATGGACTCCA 59.457 40.000 0.00 0.00 38.19 3.86
3626 3722 1.986575 GCGAGGCAGCAACCAATCTC 61.987 60.000 0.00 0.00 37.05 2.75
3653 3749 2.233676 ACGACTACCATCATGTCAGCAA 59.766 45.455 0.00 0.00 0.00 3.91
3682 3778 7.898014 TCTACTGTACTTACCATCATGTCAT 57.102 36.000 0.00 0.00 0.00 3.06
3819 3916 4.276926 GGCAATCATACTCTTTCCACCATC 59.723 45.833 0.00 0.00 0.00 3.51
3842 3939 0.534203 ACCAACCAACAGCTACCACG 60.534 55.000 0.00 0.00 0.00 4.94
3961 4337 1.679944 CCTGTCTACCAATGCCAGTGG 60.680 57.143 10.11 10.11 42.28 4.00
4022 4399 7.337942 ACCAATCATTTTCTCCTCTTGTACATC 59.662 37.037 0.00 0.00 0.00 3.06
4056 4433 3.995705 CCAAACAACAGCCCAAACATATG 59.004 43.478 0.00 0.00 0.00 1.78
4065 4442 1.754226 TCTTCAACCAAACAACAGCCC 59.246 47.619 0.00 0.00 0.00 5.19
4097 4479 7.884816 ATGCATCTTTGATTCACAAAAGAAG 57.115 32.000 0.00 1.79 45.97 2.85
4147 4529 4.642885 CCCTGTAAACTGAGAGAGAGGTAG 59.357 50.000 0.00 0.00 0.00 3.18
4148 4530 4.601084 CCCTGTAAACTGAGAGAGAGGTA 58.399 47.826 0.00 0.00 0.00 3.08
4149 4531 3.436243 CCCTGTAAACTGAGAGAGAGGT 58.564 50.000 0.00 0.00 0.00 3.85
4150 4532 2.167487 GCCCTGTAAACTGAGAGAGAGG 59.833 54.545 0.00 0.00 0.00 3.69
4151 4533 2.159310 CGCCCTGTAAACTGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
4152 4534 1.819288 CGCCCTGTAAACTGAGAGAGA 59.181 52.381 0.00 0.00 0.00 3.10
4153 4535 1.546476 ACGCCCTGTAAACTGAGAGAG 59.454 52.381 0.00 0.00 0.00 3.20
4154 4536 1.272490 CACGCCCTGTAAACTGAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
4155 4537 1.714794 CACGCCCTGTAAACTGAGAG 58.285 55.000 0.00 0.00 0.00 3.20
4156 4538 0.320421 GCACGCCCTGTAAACTGAGA 60.320 55.000 0.00 0.00 0.00 3.27
4157 4539 1.626654 CGCACGCCCTGTAAACTGAG 61.627 60.000 0.00 0.00 0.00 3.35
4158 4540 1.666553 CGCACGCCCTGTAAACTGA 60.667 57.895 0.00 0.00 0.00 3.41
4159 4541 2.860293 CGCACGCCCTGTAAACTG 59.140 61.111 0.00 0.00 0.00 3.16
4160 4542 3.047877 GCGCACGCCCTGTAAACT 61.048 61.111 0.30 0.00 34.56 2.66
4161 4543 4.439472 CGCGCACGCCCTGTAAAC 62.439 66.667 8.75 0.00 37.98 2.01
4162 4544 3.570621 TACGCGCACGCCCTGTAAA 62.571 57.895 5.73 0.00 45.53 2.01
4163 4545 4.053526 TACGCGCACGCCCTGTAA 62.054 61.111 5.73 0.00 45.53 2.41
4164 4546 4.781959 GTACGCGCACGCCCTGTA 62.782 66.667 5.73 3.39 45.53 2.74
4181 4563 3.054948 TGGTTAAATTGACGACCTAGGGG 60.055 47.826 14.81 7.16 38.88 4.79
4182 4564 4.210724 TGGTTAAATTGACGACCTAGGG 57.789 45.455 14.81 0.00 33.33 3.53
4183 4565 4.393990 GGTTGGTTAAATTGACGACCTAGG 59.606 45.833 7.41 7.41 33.33 3.02
4184 4566 5.243207 AGGTTGGTTAAATTGACGACCTAG 58.757 41.667 11.08 0.00 34.50 3.02
4185 4567 5.231702 AGGTTGGTTAAATTGACGACCTA 57.768 39.130 11.08 0.91 34.50 3.08
4186 4568 4.094830 AGGTTGGTTAAATTGACGACCT 57.905 40.909 8.18 8.18 32.66 3.85
4187 4569 5.945466 TTAGGTTGGTTAAATTGACGACC 57.055 39.130 0.00 4.64 0.00 4.79
4188 4570 8.031848 TGTATTAGGTTGGTTAAATTGACGAC 57.968 34.615 0.00 0.00 0.00 4.34
4189 4571 8.618702 TTGTATTAGGTTGGTTAAATTGACGA 57.381 30.769 0.00 0.00 0.00 4.20
4190 4572 8.508875 ACTTGTATTAGGTTGGTTAAATTGACG 58.491 33.333 0.00 0.00 0.00 4.35
4191 4573 9.836076 GACTTGTATTAGGTTGGTTAAATTGAC 57.164 33.333 0.00 0.00 0.00 3.18
4192 4574 9.575868 TGACTTGTATTAGGTTGGTTAAATTGA 57.424 29.630 0.00 0.00 0.00 2.57
4226 4608 9.716507 CCGAAGTTTATGTTGGTATATTTCTTG 57.283 33.333 0.00 0.00 0.00 3.02
4227 4609 9.675464 TCCGAAGTTTATGTTGGTATATTTCTT 57.325 29.630 0.00 0.00 0.00 2.52
4228 4610 9.326413 CTCCGAAGTTTATGTTGGTATATTTCT 57.674 33.333 0.00 0.00 0.00 2.52
4229 4611 9.106070 ACTCCGAAGTTTATGTTGGTATATTTC 57.894 33.333 0.00 0.00 28.74 2.17
4230 4612 9.457436 AACTCCGAAGTTTATGTTGGTATATTT 57.543 29.630 0.00 0.00 43.28 1.40
4245 4627 7.201705 CCTTTTGAAAGTAGAAACTCCGAAGTT 60.202 37.037 3.09 0.00 39.62 2.66
4246 4628 6.260271 CCTTTTGAAAGTAGAAACTCCGAAGT 59.740 38.462 3.09 0.00 33.75 3.01
4247 4629 6.260271 ACCTTTTGAAAGTAGAAACTCCGAAG 59.740 38.462 3.09 0.00 33.75 3.79
4248 4630 6.117488 ACCTTTTGAAAGTAGAAACTCCGAA 58.883 36.000 3.09 0.00 33.75 4.30
4249 4631 5.677567 ACCTTTTGAAAGTAGAAACTCCGA 58.322 37.500 3.09 0.00 33.75 4.55
4250 4632 7.668525 ATACCTTTTGAAAGTAGAAACTCCG 57.331 36.000 3.09 0.00 33.75 4.63
4308 4690 9.037737 GCACGTATATCTAGGTTGTCAATTTTA 57.962 33.333 0.00 0.00 0.00 1.52
4309 4691 7.551262 TGCACGTATATCTAGGTTGTCAATTTT 59.449 33.333 0.00 0.00 0.00 1.82
4310 4692 7.045416 TGCACGTATATCTAGGTTGTCAATTT 58.955 34.615 0.00 0.00 0.00 1.82
4311 4693 6.578944 TGCACGTATATCTAGGTTGTCAATT 58.421 36.000 0.00 0.00 0.00 2.32
4312 4694 6.156748 TGCACGTATATCTAGGTTGTCAAT 57.843 37.500 0.00 0.00 0.00 2.57
4313 4695 5.451381 CCTGCACGTATATCTAGGTTGTCAA 60.451 44.000 0.00 0.00 0.00 3.18
4314 4696 4.037565 CCTGCACGTATATCTAGGTTGTCA 59.962 45.833 0.00 0.00 0.00 3.58
4315 4697 4.277672 TCCTGCACGTATATCTAGGTTGTC 59.722 45.833 0.00 0.00 0.00 3.18
4316 4698 4.037684 GTCCTGCACGTATATCTAGGTTGT 59.962 45.833 0.00 0.00 0.00 3.32
4317 4699 4.278669 AGTCCTGCACGTATATCTAGGTTG 59.721 45.833 0.00 0.00 0.00 3.77
4318 4700 4.471548 AGTCCTGCACGTATATCTAGGTT 58.528 43.478 0.00 0.00 0.00 3.50
4319 4701 4.101645 AGTCCTGCACGTATATCTAGGT 57.898 45.455 0.00 0.00 0.00 3.08
4320 4702 4.278669 ACAAGTCCTGCACGTATATCTAGG 59.721 45.833 0.00 0.00 0.00 3.02
4321 4703 5.440234 ACAAGTCCTGCACGTATATCTAG 57.560 43.478 0.00 0.00 0.00 2.43
4322 4704 6.947644 TTACAAGTCCTGCACGTATATCTA 57.052 37.500 0.00 0.00 0.00 1.98
4323 4705 5.847111 TTACAAGTCCTGCACGTATATCT 57.153 39.130 0.00 0.00 0.00 1.98
4324 4706 6.019801 CAGTTTACAAGTCCTGCACGTATATC 60.020 42.308 0.00 0.00 0.00 1.63
4325 4707 5.810587 CAGTTTACAAGTCCTGCACGTATAT 59.189 40.000 0.00 0.00 0.00 0.86
4326 4708 5.047872 TCAGTTTACAAGTCCTGCACGTATA 60.048 40.000 0.00 0.00 0.00 1.47
4327 4709 3.994392 CAGTTTACAAGTCCTGCACGTAT 59.006 43.478 0.00 0.00 0.00 3.06
4328 4710 3.068448 TCAGTTTACAAGTCCTGCACGTA 59.932 43.478 0.00 0.00 0.00 3.57
4329 4711 2.159014 TCAGTTTACAAGTCCTGCACGT 60.159 45.455 0.00 0.00 0.00 4.49
4330 4712 2.479837 TCAGTTTACAAGTCCTGCACG 58.520 47.619 0.00 0.00 0.00 5.34
4331 4713 4.095782 TGTTTCAGTTTACAAGTCCTGCAC 59.904 41.667 0.00 0.00 0.00 4.57
4332 4714 4.265893 TGTTTCAGTTTACAAGTCCTGCA 58.734 39.130 0.00 0.00 0.00 4.41
4333 4715 4.574828 TCTGTTTCAGTTTACAAGTCCTGC 59.425 41.667 0.00 0.00 32.61 4.85
4334 4716 5.237344 CCTCTGTTTCAGTTTACAAGTCCTG 59.763 44.000 0.00 0.00 32.61 3.86
4335 4717 5.104485 ACCTCTGTTTCAGTTTACAAGTCCT 60.104 40.000 0.00 0.00 32.61 3.85
4336 4718 5.123936 ACCTCTGTTTCAGTTTACAAGTCC 58.876 41.667 0.00 0.00 32.61 3.85
4337 4719 6.985059 ACTACCTCTGTTTCAGTTTACAAGTC 59.015 38.462 0.00 0.00 32.61 3.01
4338 4720 6.885922 ACTACCTCTGTTTCAGTTTACAAGT 58.114 36.000 0.00 0.00 32.61 3.16
4339 4721 8.142551 AGTACTACCTCTGTTTCAGTTTACAAG 58.857 37.037 0.00 0.00 32.61 3.16
4340 4722 8.015185 AGTACTACCTCTGTTTCAGTTTACAA 57.985 34.615 0.00 0.00 32.61 2.41
4341 4723 7.592885 AGTACTACCTCTGTTTCAGTTTACA 57.407 36.000 0.00 0.00 32.61 2.41
4342 4724 9.570488 CATAGTACTACCTCTGTTTCAGTTTAC 57.430 37.037 4.31 0.00 32.61 2.01
4343 4725 9.305555 ACATAGTACTACCTCTGTTTCAGTTTA 57.694 33.333 4.31 0.00 32.61 2.01
4344 4726 8.191534 ACATAGTACTACCTCTGTTTCAGTTT 57.808 34.615 4.31 0.00 32.61 2.66
4345 4727 7.778185 ACATAGTACTACCTCTGTTTCAGTT 57.222 36.000 4.31 0.00 32.61 3.16
4346 4728 9.476928 AATACATAGTACTACCTCTGTTTCAGT 57.523 33.333 4.31 0.00 32.61 3.41
4347 4729 9.737427 CAATACATAGTACTACCTCTGTTTCAG 57.263 37.037 4.31 0.00 0.00 3.02
4348 4730 8.195436 GCAATACATAGTACTACCTCTGTTTCA 58.805 37.037 4.31 0.00 0.00 2.69
4349 4731 8.414778 AGCAATACATAGTACTACCTCTGTTTC 58.585 37.037 4.31 0.00 0.00 2.78
4350 4732 8.307582 AGCAATACATAGTACTACCTCTGTTT 57.692 34.615 4.31 0.00 0.00 2.83
4351 4733 7.899648 AGCAATACATAGTACTACCTCTGTT 57.100 36.000 4.31 0.00 0.00 3.16
4352 4734 7.447853 GGTAGCAATACATAGTACTACCTCTGT 59.552 40.741 4.31 8.32 44.03 3.41
4353 4735 7.818642 GGTAGCAATACATAGTACTACCTCTG 58.181 42.308 4.31 2.13 44.03 3.35
4354 4736 7.999450 GGTAGCAATACATAGTACTACCTCT 57.001 40.000 4.31 0.00 44.03 3.69
4357 4739 7.625185 GCGTAGGTAGCAATACATAGTACTACC 60.625 44.444 4.31 8.61 46.50 3.18
4358 4740 7.118971 AGCGTAGGTAGCAATACATAGTACTAC 59.881 40.741 4.31 0.00 35.08 2.73
4359 4741 7.164122 AGCGTAGGTAGCAATACATAGTACTA 58.836 38.462 4.77 4.77 35.08 1.82
4360 4742 6.002704 AGCGTAGGTAGCAATACATAGTACT 58.997 40.000 0.00 0.00 35.08 2.73
4361 4743 6.251655 AGCGTAGGTAGCAATACATAGTAC 57.748 41.667 0.00 0.00 35.08 2.73
4362 4744 6.091305 CGTAGCGTAGGTAGCAATACATAGTA 59.909 42.308 0.00 0.00 42.96 1.82
4363 4745 5.106791 CGTAGCGTAGGTAGCAATACATAGT 60.107 44.000 0.00 0.00 42.96 2.12


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

AutoCloner maintained by Alex Coulton.