Multiple sequence alignment - TraesCS4A01G138200

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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 TraesCS4A01G138200 chr4A 100.000 2718 0 0 1 2718 202726996 202724279 0.000000e+00 5020.0
1 TraesCS4A01G138200 chr4A 90.319 909 81 7 1 905 202620688 202619783 0.000000e+00 1184.0
2 TraesCS4A01G138200 chr4A 91.598 726 53 5 1995 2718 202607182 202606463 0.000000e+00 996.0
3 TraesCS4A01G138200 chr4A 89.849 729 67 6 1996 2718 212779574 212780301 0.000000e+00 929.0
4 TraesCS4A01G138200 chr4A 89.821 727 66 7 1995 2717 230848360 230847638 0.000000e+00 926.0
5 TraesCS4A01G138200 chr4A 89.835 728 65 8 1995 2718 230885386 230884664 0.000000e+00 926.0
6 TraesCS4A01G138200 chr4A 88.163 566 62 4 1023 1585 202608608 202608045 0.000000e+00 669.0
7 TraesCS4A01G138200 chr4A 86.804 485 54 6 791 1268 247376950 247377431 1.430000e-147 532.0
8 TraesCS4A01G138200 chr4A 85.170 499 66 5 768 1259 296146619 296147116 3.120000e-139 505.0
9 TraesCS4A01G138200 chr4A 83.800 500 70 7 768 1259 296167237 296167733 5.300000e-127 464.0
10 TraesCS4A01G138200 chr4A 85.273 421 52 6 791 1202 247384142 247384561 2.500000e-115 425.0
11 TraesCS4A01G138200 chr4A 91.503 153 12 1 1434 1585 450384779 450384931 2.740000e-50 209.0
12 TraesCS4A01G138200 chr4A 90.580 138 13 0 1240 1377 541699428 541699565 1.660000e-42 183.0
13 TraesCS4A01G138200 chr4A 75.964 441 44 30 1579 1992 362171833 362172238 1.290000e-38 171.0
14 TraesCS4A01G138200 chr4A 87.786 131 16 0 1579 1709 324266427 324266297 1.300000e-33 154.0
15 TraesCS4A01G138200 chr4A 87.786 131 16 0 1579 1709 362163590 362163720 1.300000e-33 154.0
16 TraesCS4A01G138200 chr4A 75.166 302 44 19 1734 2012 209426272 209425979 2.210000e-21 113.0
17 TraesCS4A01G138200 chr4A 89.706 68 7 0 1579 1646 184762778 184762845 1.340000e-13 87.9
18 TraesCS4A01G138200 chr3A 90.496 726 66 3 1995 2718 371309906 371309182 0.000000e+00 955.0
19 TraesCS4A01G138200 chr3A 90.083 726 69 3 1995 2718 371302117 371301393 0.000000e+00 939.0
20 TraesCS4A01G138200 chr3A 91.874 443 27 8 1 436 352851129 352851569 6.430000e-171 610.0
21 TraesCS4A01G138200 chr3A 90.672 461 33 7 1 457 596121886 596122340 2.990000e-169 604.0
22 TraesCS4A01G138200 chr3A 90.065 463 33 11 1 454 352842925 352843383 3.010000e-164 588.0
23 TraesCS4A01G138200 chr3A 89.849 463 38 7 1 457 172657006 172656547 1.080000e-163 586.0
24 TraesCS4A01G138200 chr3A 89.610 462 39 8 1 457 441685507 441685050 1.810000e-161 579.0
25 TraesCS4A01G138200 chr3A 89.177 462 41 8 1 457 441706027 441705570 3.930000e-158 568.0
26 TraesCS4A01G138200 chr3A 85.287 401 44 13 862 1259 502392289 502392677 1.520000e-107 399.0
27 TraesCS4A01G138200 chr3A 82.317 328 38 11 1688 1996 304940416 304940090 1.600000e-67 267.0
28 TraesCS4A01G138200 chr3A 91.503 153 12 1 1434 1585 723914275 723914427 2.740000e-50 209.0
29 TraesCS4A01G138200 chr3A 91.045 134 12 0 1244 1377 444946480 444946347 5.980000e-42 182.0
30 TraesCS4A01G138200 chr3A 90.299 134 13 0 1244 1377 444966006 444965873 2.780000e-40 176.0
31 TraesCS4A01G138200 chr3A 81.111 180 18 10 1483 1646 220774019 220773840 2.200000e-26 130.0
32 TraesCS4A01G138200 chr3A 88.542 96 7 3 667 760 564976568 564976475 2.210000e-21 113.0
33 TraesCS4A01G138200 chr6D 90.220 726 62 9 1997 2718 58765144 58764424 0.000000e+00 939.0
34 TraesCS4A01G138200 chr1A 90.223 716 66 3 1999 2710 189138059 189138774 0.000000e+00 931.0
35 TraesCS4A01G138200 chr1A 89.655 725 69 5 1995 2713 224360924 224360200 0.000000e+00 918.0
36 TraesCS4A01G138200 chr1A 91.503 153 12 1 1434 1585 236550745 236550593 2.740000e-50 209.0
37 TraesCS4A01G138200 chr1A 91.071 112 10 0 1885 1996 204302797 204302686 4.690000e-33 152.0
38 TraesCS4A01G138200 chr1A 90.000 60 6 0 1387 1446 345653490 345653549 8.070000e-11 78.7
39 TraesCS4A01G138200 chr1A 90.000 60 6 0 1387 1446 345659363 345659422 8.070000e-11 78.7
40 TraesCS4A01G138200 chr1A 94.872 39 0 2 1674 1712 395592760 395592724 2.920000e-05 60.2
41 TraesCS4A01G138200 chr6A 91.304 437 31 6 1 434 244166302 244166734 8.380000e-165 590.0
42 TraesCS4A01G138200 chr6A 83.721 129 12 6 763 883 346130569 346130696 2.210000e-21 113.0
43 TraesCS4A01G138200 chr6A 83.721 129 12 7 763 883 346159612 346159739 2.210000e-21 113.0
44 TraesCS4A01G138200 chr6A 85.057 87 9 3 1627 1711 119576358 119576274 4.820000e-13 86.1
45 TraesCS4A01G138200 chr6A 91.667 60 5 0 1387 1446 398096165 398096224 1.730000e-12 84.2
46 TraesCS4A01G138200 chr6A 91.071 56 5 0 1391 1446 398039788 398039843 2.900000e-10 76.8
47 TraesCS4A01G138200 chr6A 88.889 54 6 0 1393 1446 188126309 188126256 1.750000e-07 67.6
48 TraesCS4A01G138200 chr6A 89.796 49 2 2 581 628 333662030 333661984 2.920000e-05 60.2
49 TraesCS4A01G138200 chr2A 89.474 437 36 8 2 433 299248116 299247685 6.620000e-151 544.0
50 TraesCS4A01G138200 chr2A 87.821 312 31 3 791 1095 159902112 159901801 2.570000e-95 359.0
51 TraesCS4A01G138200 chr2A 92.810 153 10 1 1434 1585 90469798 90469950 1.270000e-53 220.0
52 TraesCS4A01G138200 chr2A 91.503 153 12 1 1434 1585 90477694 90477846 2.740000e-50 209.0
53 TraesCS4A01G138200 chr2A 91.241 137 12 0 1240 1376 288354107 288354243 1.280000e-43 187.0
54 TraesCS4A01G138200 chr2A 90.299 134 13 0 1244 1377 567795814 567795681 2.780000e-40 176.0
55 TraesCS4A01G138200 chr2A 89.130 138 15 0 1240 1377 288366936 288367073 3.600000e-39 172.0
56 TraesCS4A01G138200 chr2A 74.177 395 69 26 1610 1992 12483132 12483505 1.700000e-27 134.0
57 TraesCS4A01G138200 chr2A 91.176 68 6 0 1579 1646 119991518 119991451 2.880000e-15 93.5
58 TraesCS4A01G138200 chr2A 90.000 60 6 0 1387 1446 165123350 165123291 8.070000e-11 78.7
59 TraesCS4A01G138200 chr7A 87.640 267 15 4 497 761 340138464 340138714 7.360000e-76 294.0
60 TraesCS4A01G138200 chr7A 92.810 153 10 1 1434 1585 378926742 378926894 1.270000e-53 220.0
61 TraesCS4A01G138200 chr7A 91.045 134 12 0 1244 1377 354075015 354075148 5.980000e-42 182.0
62 TraesCS4A01G138200 chr7A 90.000 60 6 0 1600 1659 404445094 404445153 8.070000e-11 78.7
63 TraesCS4A01G138200 chr2B 86.087 230 24 3 1022 1251 268892922 268893143 9.720000e-60 241.0
64 TraesCS4A01G138200 chr2B 93.458 107 7 0 1890 1996 273591620 273591514 2.800000e-35 159.0
65 TraesCS4A01G138200 chr2B 77.741 301 34 20 1722 2000 100685811 100685522 1.300000e-33 154.0
66 TraesCS4A01G138200 chr5A 92.157 153 11 1 1434 1585 32623383 32623535 5.890000e-52 215.0
67 TraesCS4A01G138200 chr5A 91.503 153 12 1 1434 1585 621684346 621684498 2.740000e-50 209.0
68 TraesCS4A01G138200 chr5A 90.132 152 10 5 1245 1394 191314271 191314419 2.760000e-45 193.0
69 TraesCS4A01G138200 chr5A 88.235 51 5 1 579 628 371560632 371560582 2.920000e-05 60.2
70 TraesCS4A01G138200 chr1B 87.429 175 14 3 1082 1256 671021538 671021704 7.680000e-46 195.0
71 TraesCS4A01G138200 chr1B 76.531 294 38 17 1722 1993 593823019 593823303 6.110000e-27 132.0
72 TraesCS4A01G138200 chr1B 76.689 296 32 21 1723 1993 274822520 274822237 2.200000e-26 130.0
73 TraesCS4A01G138200 chr1B 76.582 158 25 10 1690 1842 193234460 193234310 2.900000e-10 76.8
74 TraesCS4A01G138200 chr1B 87.719 57 5 1 572 628 209771203 209771257 6.280000e-07 65.8
75 TraesCS4A01G138200 chrUn 85.475 179 17 4 1079 1256 401105451 401105281 7.730000e-41 178.0
76 TraesCS4A01G138200 chrUn 91.667 120 10 0 1137 1256 399500270 399500389 1.670000e-37 167.0
77 TraesCS4A01G138200 chrUn 81.618 136 15 7 1722 1853 158543631 158543760 1.330000e-18 104.0
78 TraesCS4A01G138200 chr4D 80.233 258 27 8 1755 1993 128789172 128789424 3.600000e-39 172.0
79 TraesCS4A01G138200 chr4D 79.845 258 28 8 1755 1993 128797293 128797545 1.670000e-37 167.0
80 TraesCS4A01G138200 chr4D 92.523 107 8 0 1890 1996 162752104 162751998 1.300000e-33 154.0
81 TraesCS4A01G138200 chr1D 80.233 258 27 8 1755 1993 139489625 139489877 3.600000e-39 172.0
82 TraesCS4A01G138200 chr1D 79.845 258 28 9 1755 1993 379164471 379164723 1.670000e-37 167.0
83 TraesCS4A01G138200 chr5B 92.241 116 9 0 1885 2000 267083090 267082975 6.020000e-37 165.0
84 TraesCS4A01G138200 chr3D 83.974 156 21 2 1736 1888 287274468 287274314 2.180000e-31 147.0
85 TraesCS4A01G138200 chr3D 86.131 137 11 5 768 897 503502142 503502007 1.010000e-29 141.0
86 TraesCS4A01G138200 chr3D 91.071 56 4 1 1391 1446 240173621 240173675 1.040000e-09 75.0
87 TraesCS4A01G138200 chr5D 87.200 125 9 5 777 894 242559470 242559346 4.720000e-28 135.0
88 TraesCS4A01G138200 chr2D 85.401 137 12 4 768 897 350146509 350146644 4.720000e-28 135.0
89 TraesCS4A01G138200 chr7D 79.695 197 28 7 1694 1885 507488557 507488746 6.110000e-27 132.0
90 TraesCS4A01G138200 chr7D 85.938 128 10 7 774 894 175970393 175970267 2.200000e-26 130.0
91 TraesCS4A01G138200 chr3B 76.370 292 38 18 1722 1991 714799436 714799718 7.900000e-26 128.0
92 TraesCS4A01G138200 chr3B 76.027 292 39 17 1722 1991 714791797 714792079 3.680000e-24 122.0
93 TraesCS4A01G138200 chr3B 76.211 227 25 21 1678 1885 568517882 568518098 2.880000e-15 93.5
94 TraesCS4A01G138200 chr4B 92.857 56 4 0 1391 1446 297575774 297575719 6.240000e-12 82.4


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 TraesCS4A01G138200 chr4A 202724279 202726996 2717 True 5020.0 5020 100.0000 1 2718 1 chr4A.!!$R2 2717
1 TraesCS4A01G138200 chr4A 202619783 202620688 905 True 1184.0 1184 90.3190 1 905 1 chr4A.!!$R1 904
2 TraesCS4A01G138200 chr4A 212779574 212780301 727 False 929.0 929 89.8490 1996 2718 1 chr4A.!!$F2 722
3 TraesCS4A01G138200 chr4A 230847638 230848360 722 True 926.0 926 89.8210 1995 2717 1 chr4A.!!$R4 722
4 TraesCS4A01G138200 chr4A 230884664 230885386 722 True 926.0 926 89.8350 1995 2718 1 chr4A.!!$R5 723
5 TraesCS4A01G138200 chr4A 202606463 202608608 2145 True 832.5 996 89.8805 1023 2718 2 chr4A.!!$R7 1695
6 TraesCS4A01G138200 chr3A 371309182 371309906 724 True 955.0 955 90.4960 1995 2718 1 chr3A.!!$R5 723
7 TraesCS4A01G138200 chr3A 371301393 371302117 724 True 939.0 939 90.0830 1995 2718 1 chr3A.!!$R4 723
8 TraesCS4A01G138200 chr6D 58764424 58765144 720 True 939.0 939 90.2200 1997 2718 1 chr6D.!!$R1 721
9 TraesCS4A01G138200 chr1A 189138059 189138774 715 False 931.0 931 90.2230 1999 2710 1 chr1A.!!$F1 711
10 TraesCS4A01G138200 chr1A 224360200 224360924 724 True 918.0 918 89.6550 1995 2713 1 chr1A.!!$R2 718

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
521 524 0.106469 CTCTCGATCCCACTCCCTCA 60.106 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1884 0.037326 AATGAGGAACGAGCAAGCGA 60.037 50.0 0.0 0.0 34.83 4.93 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 21 3.169355 GGGAATGCACATGGTGATTTC 57.831 47.619 0.00 2.51 35.23 2.17
75 76 8.322906 TGGAGCTACAATAAATATTCCATTCG 57.677 34.615 0.00 0.00 0.00 3.34
97 98 6.210078 TCGTATGAAATCAACCCAAACAAAC 58.790 36.000 0.00 0.00 0.00 2.93
111 112 6.183360 ACCCAAACAAACTTGCATTTCAAATC 60.183 34.615 0.00 0.00 33.65 2.17
117 118 7.495055 ACAAACTTGCATTTCAAATCTCTTCT 58.505 30.769 0.00 0.00 33.65 2.85
137 138 7.607250 TCTTCTGTTTCCAGATTCTAGAGTTC 58.393 38.462 0.00 0.00 46.80 3.01
163 164 5.768980 TCTCATCTCTTTTGGTCTCCATT 57.231 39.130 0.00 0.00 31.53 3.16
170 171 9.362539 CATCTCTTTTGGTCTCCATTTAAATTG 57.637 33.333 0.00 0.00 31.53 2.32
291 293 3.869065 TGTCTCCGGGAAAATATGTCAC 58.131 45.455 0.00 0.00 0.00 3.67
381 383 5.542848 AAGGAAAGAATTTGGAGGGAGAT 57.457 39.130 0.00 0.00 39.27 2.75
384 386 5.973124 AGGAAAGAATTTGGAGGGAGATAGA 59.027 40.000 0.00 0.00 39.27 1.98
387 389 3.323403 AGAATTTGGAGGGAGATAGAGCG 59.677 47.826 0.00 0.00 0.00 5.03
408 410 3.655211 CAGCCAGTCCCCCTGCTT 61.655 66.667 0.00 0.00 40.06 3.91
422 424 4.120755 GCTTCCCTCAGCCCCCAG 62.121 72.222 0.00 0.00 33.21 4.45
423 425 3.415087 CTTCCCTCAGCCCCCAGG 61.415 72.222 0.00 0.00 0.00 4.45
436 438 4.528039 CCAGGCCGGCCCATTCAT 62.528 66.667 41.72 20.42 36.58 2.57
464 467 1.929494 TCCTATGGCCCAAATCCAACT 59.071 47.619 0.00 0.00 37.13 3.16
475 478 1.562672 AATCCAACTAGCCGGTGCCT 61.563 55.000 1.90 0.00 38.69 4.75
493 496 1.688627 CCTCGTCTAAACCCTAGGCCT 60.689 57.143 11.78 11.78 0.00 5.19
520 523 0.825840 CCTCTCGATCCCACTCCCTC 60.826 65.000 0.00 0.00 0.00 4.30
521 524 0.106469 CTCTCGATCCCACTCCCTCA 60.106 60.000 0.00 0.00 0.00 3.86
531 534 0.179936 CACTCCCTCATTCCCTCTGC 59.820 60.000 0.00 0.00 0.00 4.26
533 536 1.694169 TCCCTCATTCCCTCTGCCC 60.694 63.158 0.00 0.00 0.00 5.36
556 559 4.161295 CGCTTGCCCGATCCCTCA 62.161 66.667 0.00 0.00 0.00 3.86
566 569 1.527844 GATCCCTCACATGCAGCCC 60.528 63.158 0.00 0.00 0.00 5.19
569 572 4.100084 CCTCACATGCAGCCCCGA 62.100 66.667 0.00 0.00 0.00 5.14
577 580 2.592861 GCAGCCCCGATCCACATC 60.593 66.667 0.00 0.00 0.00 3.06
585 588 1.885887 CCCGATCCACATCTCTCTCTC 59.114 57.143 0.00 0.00 0.00 3.20
609 612 2.196229 CCTCGTCCTCCTCCCGAT 59.804 66.667 0.00 0.00 0.00 4.18
611 614 0.606944 CCTCGTCCTCCTCCCGATAG 60.607 65.000 0.00 0.00 0.00 2.08
612 615 0.108963 CTCGTCCTCCTCCCGATAGT 59.891 60.000 0.00 0.00 0.00 2.12
615 618 1.152525 TCCTCCTCCCGATAGTGCC 60.153 63.158 0.00 0.00 0.00 5.01
616 619 1.152440 CCTCCTCCCGATAGTGCCT 60.152 63.158 0.00 0.00 0.00 4.75
620 623 1.467678 CCTCCCGATAGTGCCTCCAG 61.468 65.000 0.00 0.00 0.00 3.86
664 667 2.161855 CTCATCCCTCTCCTCGATCTG 58.838 57.143 0.00 0.00 0.00 2.90
675 678 2.107141 CGATCTGCCTCGAACCCC 59.893 66.667 0.00 0.00 41.12 4.95
677 680 1.443828 GATCTGCCTCGAACCCCTC 59.556 63.158 0.00 0.00 0.00 4.30
685 688 2.088674 CTCGAACCCCTCCTATGGCG 62.089 65.000 0.00 0.00 0.00 5.69
686 689 2.111251 GAACCCCTCCTATGGCGC 59.889 66.667 0.00 0.00 0.00 6.53
723 726 2.445845 CGCCACCATCCCCCTCTA 60.446 66.667 0.00 0.00 0.00 2.43
725 728 1.384643 GCCACCATCCCCCTCTACT 60.385 63.158 0.00 0.00 0.00 2.57
737 740 1.429825 CTCTACTGACCACCTCGCG 59.570 63.158 0.00 0.00 0.00 5.87
761 764 4.521062 CCCTGCCTCGAGCTTCGG 62.521 72.222 6.99 4.17 44.23 4.30
783 786 1.677217 CGCTAGCCTTCCTTTCTGCTT 60.677 52.381 9.66 0.00 35.34 3.91
789 792 1.321474 CTTCCTTTCTGCTTGCACCA 58.679 50.000 0.00 0.00 0.00 4.17
794 797 1.891150 CTTTCTGCTTGCACCATCCTT 59.109 47.619 0.00 0.00 0.00 3.36
822 825 2.599597 CCCCTCCATGGCCTTCTG 59.400 66.667 6.96 0.00 0.00 3.02
841 844 4.636435 CCGAGCCACCAACCCGTT 62.636 66.667 0.00 0.00 0.00 4.44
851 855 2.106683 CAACCCGTTCGCCTCCATC 61.107 63.158 0.00 0.00 0.00 3.51
855 859 4.514577 CGTTCGCCTCCATCCGCT 62.515 66.667 0.00 0.00 0.00 5.52
905 909 4.441695 CAAGCCGCTCGAGCCTCA 62.442 66.667 30.66 0.00 37.91 3.86
906 910 4.443266 AAGCCGCTCGAGCCTCAC 62.443 66.667 30.66 17.27 37.91 3.51
919 923 2.978010 CTCACCGCCGTTGCCTTT 60.978 61.111 0.00 0.00 0.00 3.11
920 924 3.254014 CTCACCGCCGTTGCCTTTG 62.254 63.158 0.00 0.00 0.00 2.77
921 925 4.999939 CACCGCCGTTGCCTTTGC 63.000 66.667 0.00 0.00 38.26 3.68
923 927 3.977244 CCGCCGTTGCCTTTGCTT 61.977 61.111 0.00 0.00 38.71 3.91
924 928 2.429069 CGCCGTTGCCTTTGCTTC 60.429 61.111 0.00 0.00 38.71 3.86
925 929 2.727544 GCCGTTGCCTTTGCTTCA 59.272 55.556 0.00 0.00 38.71 3.02
926 930 1.661509 GCCGTTGCCTTTGCTTCAC 60.662 57.895 0.00 0.00 38.71 3.18
927 931 1.007387 CCGTTGCCTTTGCTTCACC 60.007 57.895 0.00 0.00 38.71 4.02
928 932 1.455383 CCGTTGCCTTTGCTTCACCT 61.455 55.000 0.00 0.00 38.71 4.00
929 933 0.318107 CGTTGCCTTTGCTTCACCTG 60.318 55.000 0.00 0.00 38.71 4.00
930 934 1.032014 GTTGCCTTTGCTTCACCTGA 58.968 50.000 0.00 0.00 38.71 3.86
931 935 1.000938 GTTGCCTTTGCTTCACCTGAG 60.001 52.381 0.00 0.00 38.71 3.35
932 936 1.174712 TGCCTTTGCTTCACCTGAGC 61.175 55.000 0.00 0.00 38.71 4.26
933 937 1.871126 GCCTTTGCTTCACCTGAGCC 61.871 60.000 0.00 0.00 33.53 4.70
934 938 1.580845 CCTTTGCTTCACCTGAGCCG 61.581 60.000 0.00 0.00 0.00 5.52
935 939 2.192608 CTTTGCTTCACCTGAGCCGC 62.193 60.000 0.00 0.00 0.00 6.53
960 964 2.435059 GCCCTCTGCTTCGTGGAC 60.435 66.667 0.00 0.00 36.87 4.02
961 965 2.125912 CCCTCTGCTTCGTGGACG 60.126 66.667 0.00 0.00 41.45 4.79
962 966 2.651361 CCTCTGCTTCGTGGACGT 59.349 61.111 0.00 0.00 40.80 4.34
963 967 1.734477 CCTCTGCTTCGTGGACGTG 60.734 63.158 0.00 0.00 40.80 4.49
964 968 2.355837 TCTGCTTCGTGGACGTGC 60.356 61.111 0.00 0.00 40.80 5.34
965 969 2.356313 CTGCTTCGTGGACGTGCT 60.356 61.111 8.99 0.00 40.80 4.40
966 970 2.355837 TGCTTCGTGGACGTGCTC 60.356 61.111 8.99 3.45 40.80 4.26
967 971 3.470567 GCTTCGTGGACGTGCTCG 61.471 66.667 22.92 22.92 40.80 5.03
977 981 3.250323 CGTGCTCGTCCTGCATCG 61.250 66.667 0.00 0.00 42.69 3.84
978 982 3.558411 GTGCTCGTCCTGCATCGC 61.558 66.667 0.00 0.00 42.69 4.58
979 983 4.819761 TGCTCGTCCTGCATCGCC 62.820 66.667 0.00 0.00 35.31 5.54
980 984 4.521062 GCTCGTCCTGCATCGCCT 62.521 66.667 0.00 0.00 0.00 5.52
981 985 2.584418 CTCGTCCTGCATCGCCTG 60.584 66.667 0.00 0.00 0.00 4.85
982 986 3.068064 TCGTCCTGCATCGCCTGA 61.068 61.111 0.00 0.00 0.00 3.86
983 987 2.887568 CGTCCTGCATCGCCTGAC 60.888 66.667 0.00 0.00 0.00 3.51
984 988 2.512515 GTCCTGCATCGCCTGACC 60.513 66.667 0.00 0.00 0.00 4.02
985 989 3.002583 TCCTGCATCGCCTGACCA 61.003 61.111 0.00 0.00 0.00 4.02
986 990 2.821366 CCTGCATCGCCTGACCAC 60.821 66.667 0.00 0.00 0.00 4.16
987 991 2.267006 CTGCATCGCCTGACCACT 59.733 61.111 0.00 0.00 0.00 4.00
988 992 1.812922 CTGCATCGCCTGACCACTC 60.813 63.158 0.00 0.00 0.00 3.51
989 993 2.236223 CTGCATCGCCTGACCACTCT 62.236 60.000 0.00 0.00 0.00 3.24
990 994 1.078848 GCATCGCCTGACCACTCTT 60.079 57.895 0.00 0.00 0.00 2.85
991 995 1.086634 GCATCGCCTGACCACTCTTC 61.087 60.000 0.00 0.00 0.00 2.87
992 996 0.803768 CATCGCCTGACCACTCTTCG 60.804 60.000 0.00 0.00 0.00 3.79
993 997 0.965866 ATCGCCTGACCACTCTTCGA 60.966 55.000 0.00 0.00 0.00 3.71
994 998 1.444553 CGCCTGACCACTCTTCGAC 60.445 63.158 0.00 0.00 0.00 4.20
995 999 1.079750 GCCTGACCACTCTTCGACC 60.080 63.158 0.00 0.00 0.00 4.79
996 1000 1.536943 GCCTGACCACTCTTCGACCT 61.537 60.000 0.00 0.00 0.00 3.85
997 1001 0.244994 CCTGACCACTCTTCGACCTG 59.755 60.000 0.00 0.00 0.00 4.00
998 1002 0.389166 CTGACCACTCTTCGACCTGC 60.389 60.000 0.00 0.00 0.00 4.85
999 1003 1.079750 GACCACTCTTCGACCTGCC 60.080 63.158 0.00 0.00 0.00 4.85
1000 1004 1.816863 GACCACTCTTCGACCTGCCA 61.817 60.000 0.00 0.00 0.00 4.92
1001 1005 1.194781 ACCACTCTTCGACCTGCCAT 61.195 55.000 0.00 0.00 0.00 4.40
1002 1006 0.742281 CCACTCTTCGACCTGCCATG 60.742 60.000 0.00 0.00 0.00 3.66
1003 1007 0.742281 CACTCTTCGACCTGCCATGG 60.742 60.000 7.63 7.63 0.00 3.66
1004 1008 1.153289 CTCTTCGACCTGCCATGGG 60.153 63.158 15.13 0.00 0.00 4.00
1005 1009 2.124570 CTTCGACCTGCCATGGGG 60.125 66.667 15.13 9.85 37.18 4.96
1006 1010 3.704231 CTTCGACCTGCCATGGGGG 62.704 68.421 15.13 0.00 40.85 5.40
1016 1020 4.447342 CATGGGGGCCGCCTTCTT 62.447 66.667 36.11 17.58 0.00 2.52
1017 1021 2.694616 ATGGGGGCCGCCTTCTTA 60.695 61.111 36.11 18.79 0.00 2.10
1018 1022 2.313427 ATGGGGGCCGCCTTCTTAA 61.313 57.895 36.11 18.03 0.00 1.85
1019 1023 2.439701 GGGGGCCGCCTTCTTAAC 60.440 66.667 30.90 1.81 0.00 2.01
1020 1024 2.353573 GGGGCCGCCTTCTTAACA 59.646 61.111 9.05 0.00 0.00 2.41
1021 1025 1.749258 GGGGCCGCCTTCTTAACAG 60.749 63.158 9.05 0.00 0.00 3.16
1037 1041 2.925170 AGACGCCTCAAGCCACCT 60.925 61.111 0.00 0.00 38.78 4.00
1096 1100 2.993853 CCCAACTCTGGCCTCTCC 59.006 66.667 3.32 0.00 41.99 3.71
1097 1101 1.614824 CCCAACTCTGGCCTCTCCT 60.615 63.158 3.32 0.00 41.99 3.69
1105 1109 4.025858 GGCCTCTCCTGCAGCACA 62.026 66.667 8.66 0.00 0.00 4.57
1109 1113 1.670015 CTCTCCTGCAGCACACTCA 59.330 57.895 8.66 0.00 0.00 3.41
1112 1116 1.226686 CTCCTGCAGCACACTCACAC 61.227 60.000 8.66 0.00 0.00 3.82
1113 1117 1.524393 CCTGCAGCACACTCACACA 60.524 57.895 8.66 0.00 0.00 3.72
1114 1118 0.887836 CCTGCAGCACACTCACACAT 60.888 55.000 8.66 0.00 0.00 3.21
1116 1120 1.730612 CTGCAGCACACTCACACATAG 59.269 52.381 0.00 0.00 0.00 2.23
1120 1124 0.036010 GCACACTCACACATAGCCCT 60.036 55.000 0.00 0.00 0.00 5.19
1148 1152 2.224719 CCTATGAGGCTTTGATCCCCTG 60.225 54.545 0.00 0.00 0.00 4.45
1154 1158 1.452108 CTTTGATCCCCTGCCCGAC 60.452 63.158 0.00 0.00 0.00 4.79
1204 1208 2.231721 GACACTAAGCTCTCTTTCGGGT 59.768 50.000 0.00 0.00 33.85 5.28
1207 1211 3.444388 CACTAAGCTCTCTTTCGGGTACT 59.556 47.826 0.00 0.00 33.85 2.73
1224 1228 3.306849 GGTACTTCCTCAAGACCAGGAAC 60.307 52.174 0.00 0.00 43.84 3.62
1226 1230 0.034896 TTCCTCAAGACCAGGAACGC 59.965 55.000 0.00 0.00 43.84 4.84
1233 1237 3.222354 GACCAGGAACGCCGTGACT 62.222 63.158 0.00 0.00 39.96 3.41
1245 1249 0.387367 CCGTGACTGAGACCGACAAG 60.387 60.000 0.00 0.00 0.00 3.16
1267 1271 4.722700 ACCACGACCTGCATGCCC 62.723 66.667 16.68 0.70 0.00 5.36
1274 1278 2.439701 CCTGCATGCCCTGTCCAG 60.440 66.667 16.68 3.39 0.00 3.86
1315 1319 0.250424 CCCGCTATCATCATGCACCA 60.250 55.000 0.00 0.00 0.00 4.17
1316 1320 1.596603 CCGCTATCATCATGCACCAA 58.403 50.000 0.00 0.00 0.00 3.67
1323 1327 1.270274 TCATCATGCACCAACACTTGC 59.730 47.619 0.00 0.00 39.33 4.01
1336 1340 2.026641 ACACTTGCTGTTGCTGTTGAT 58.973 42.857 0.00 0.00 40.48 2.57
1337 1341 2.223641 ACACTTGCTGTTGCTGTTGATG 60.224 45.455 0.00 0.00 40.48 3.07
1349 1353 1.197721 CTGTTGATGCCAAGTTCGACC 59.802 52.381 0.00 0.00 32.06 4.79
1373 1377 0.328258 AACAGGGAATAGCGCCAAGT 59.672 50.000 2.29 0.00 0.00 3.16
1379 1383 1.690352 GGAATAGCGCCAAGTACCCTA 59.310 52.381 2.29 0.00 0.00 3.53
1381 1385 3.326747 GAATAGCGCCAAGTACCCTATG 58.673 50.000 2.29 0.00 0.00 2.23
1388 1392 1.336887 CCAAGTACCCTATGCGGATCG 60.337 57.143 0.00 0.00 33.16 3.69
1403 1407 1.189403 GATCGCCAAGTTCGACTACG 58.811 55.000 0.00 0.00 38.88 3.51
1405 1409 2.774951 CGCCAAGTTCGACTACGCG 61.775 63.158 3.53 3.53 38.74 6.01
1416 1420 0.040246 GACTACGCGGCTATGACCTC 60.040 60.000 12.47 0.00 0.00 3.85
1434 1438 1.466167 CTCAGATTTGGACCACAAGCG 59.534 52.381 0.00 0.00 40.82 4.68
1476 1480 0.178929 AAGTCCCTCGAAGGTCCACT 60.179 55.000 0.00 0.00 31.93 4.00
1481 1485 0.460987 CCTCGAAGGTCCACTGATGC 60.461 60.000 0.00 0.00 0.00 3.91
1493 1497 2.033550 CCACTGATGCCTAGTACGACTC 59.966 54.545 0.00 0.00 0.00 3.36
1494 1498 2.946329 CACTGATGCCTAGTACGACTCT 59.054 50.000 0.00 0.00 0.00 3.24
1506 1510 0.037303 ACGACTCTAGGACCGGAACA 59.963 55.000 9.46 0.00 0.00 3.18
1513 1517 3.762823 CTCTAGGACCGGAACAAAGTACT 59.237 47.826 9.46 0.00 0.00 2.73
1537 1541 4.556233 CGATGACCGTTGATATGTACCAT 58.444 43.478 0.00 0.00 0.00 3.55
1543 1547 5.362263 ACCGTTGATATGTACCATTACACC 58.638 41.667 0.00 0.00 41.12 4.16
1548 1552 2.032680 ATGTACCATTACACCGCACC 57.967 50.000 0.00 0.00 41.12 5.01
1554 1558 0.179235 CATTACACCGCACCGAAACG 60.179 55.000 0.00 0.00 0.00 3.60
1567 1571 2.663852 AAACGCCAAGACCGTCCG 60.664 61.111 0.00 0.00 38.06 4.79
1617 1650 4.748102 TGTTCCATCAAGTTCGACTACAAC 59.252 41.667 0.00 0.00 0.00 3.32
1627 1660 4.035558 AGTTCGACTACAACGACTACAACA 59.964 41.667 0.00 0.00 39.46 3.33
1642 1675 3.756933 ACAACATGTACCACTACCGTT 57.243 42.857 0.00 0.00 0.00 4.44
1648 1681 0.733909 GTACCACTACCGTTGCCGAC 60.734 60.000 0.00 0.00 35.63 4.79
1662 1695 1.294138 CCGACAACCCGTGTACCAT 59.706 57.895 0.00 0.00 41.96 3.55
1666 1699 2.094597 CGACAACCCGTGTACCATAAGA 60.095 50.000 0.00 0.00 41.96 2.10
1681 1714 5.169295 ACCATAAGAAGCAAGTTCGACTAC 58.831 41.667 0.00 0.00 40.49 2.73
1682 1715 4.567159 CCATAAGAAGCAAGTTCGACTACC 59.433 45.833 0.00 0.00 40.49 3.18
1708 1741 3.933332 GCATGAACCACTACTTCCACTAC 59.067 47.826 0.00 0.00 0.00 2.73
1719 1752 2.635915 ACTTCCACTACGACCCATGAAA 59.364 45.455 0.00 0.00 0.00 2.69
1720 1753 3.071892 ACTTCCACTACGACCCATGAAAA 59.928 43.478 0.00 0.00 0.00 2.29
1734 1767 3.303329 CCATGAAAATCTACACCGCATCG 60.303 47.826 0.00 0.00 0.00 3.84
1744 1777 2.189257 CCGCATCGAACCCATCCA 59.811 61.111 0.00 0.00 0.00 3.41
1747 1780 1.823899 GCATCGAACCCATCCACCC 60.824 63.158 0.00 0.00 0.00 4.61
1749 1782 1.618143 ATCGAACCCATCCACCCCA 60.618 57.895 0.00 0.00 0.00 4.96
1750 1783 1.211567 ATCGAACCCATCCACCCCAA 61.212 55.000 0.00 0.00 0.00 4.12
1751 1784 1.075836 CGAACCCATCCACCCCAAA 59.924 57.895 0.00 0.00 0.00 3.28
1757 1790 1.288752 CATCCACCCCAAAACGCAC 59.711 57.895 0.00 0.00 0.00 5.34
1773 1806 2.124903 CGCACGCTTCGAAGGTATAAT 58.875 47.619 25.77 0.00 0.00 1.28
1776 1809 2.153247 CACGCTTCGAAGGTATAATCGC 59.847 50.000 25.77 8.60 38.87 4.58
1796 1829 2.214920 GGAACGACACCCCTGGACT 61.215 63.158 0.00 0.00 0.00 3.85
1797 1830 0.901580 GGAACGACACCCCTGGACTA 60.902 60.000 0.00 0.00 0.00 2.59
1824 1857 5.648960 TGCATGTGATGTGTTGTATGAGATT 59.351 36.000 0.00 0.00 0.00 2.40
1844 1877 2.045524 TCCCATGTTTGCACCATGTTT 58.954 42.857 19.10 0.00 38.39 2.83
1847 1880 3.464907 CCATGTTTGCACCATGTTTGAA 58.535 40.909 19.10 0.00 38.39 2.69
1849 1882 4.515944 CCATGTTTGCACCATGTTTGAATT 59.484 37.500 19.10 0.00 38.39 2.17
1851 1884 4.511527 TGTTTGCACCATGTTTGAATTGT 58.488 34.783 0.00 0.00 0.00 2.71
1860 1893 2.998772 TGTTTGAATTGTCGCTTGCTC 58.001 42.857 0.00 0.00 0.00 4.26
1872 1905 1.464687 CGCTTGCTCGTTCCTCATTTG 60.465 52.381 0.00 0.00 0.00 2.32
1880 1913 0.179129 GTTCCTCATTTGCCATGCCG 60.179 55.000 0.00 0.00 0.00 5.69
1886 1919 0.101040 CATTTGCCATGCCGTCGATT 59.899 50.000 0.00 0.00 0.00 3.34
1888 1921 0.957888 TTTGCCATGCCGTCGATTCA 60.958 50.000 0.00 0.00 0.00 2.57
1912 1962 0.258484 CACCCCACCATCCTTGCATA 59.742 55.000 0.00 0.00 0.00 3.14
1916 1966 1.750778 CCCACCATCCTTGCATAACAC 59.249 52.381 0.00 0.00 0.00 3.32
1923 1973 1.705337 CCTTGCATAACACGCTCCCG 61.705 60.000 0.00 0.00 41.14 5.14
1943 1993 0.030638 CCACACTTCCTTTTGCACCG 59.969 55.000 0.00 0.00 0.00 4.94
1960 2010 2.828520 CACCGGTATCTCCATGAGCTAT 59.171 50.000 6.87 0.00 35.57 2.97
1962 2012 2.098280 CCGGTATCTCCATGAGCTATCG 59.902 54.545 0.00 1.71 35.50 2.92
1963 2013 3.010420 CGGTATCTCCATGAGCTATCGA 58.990 50.000 0.00 0.00 37.14 3.59
1976 2026 7.359849 CCATGAGCTATCGAAACTGATATGTTG 60.360 40.741 0.00 0.00 30.79 3.33
1978 2028 5.605534 AGCTATCGAAACTGATATGTTGCT 58.394 37.500 0.00 0.00 30.79 3.91
1979 2029 5.464722 AGCTATCGAAACTGATATGTTGCTG 59.535 40.000 0.00 0.00 31.37 4.41
2067 2530 9.646427 TTGTTTACTATGTTGTTTGCTTCTTTT 57.354 25.926 0.00 0.00 0.00 2.27
2078 2541 1.333619 TGCTTCTTTTCGGTTGTGCTC 59.666 47.619 0.00 0.00 0.00 4.26
2092 2555 4.246458 GTTGTGCTCCTTCTCGATAGTTT 58.754 43.478 0.00 0.00 37.40 2.66
2170 2637 1.473278 CTCGTTCTTCTTCCTAGCGGT 59.527 52.381 0.00 0.00 0.00 5.68
2182 2649 1.940613 CCTAGCGGTATTTCAGGCAAC 59.059 52.381 0.00 0.00 0.00 4.17
2296 2765 2.699846 GCCTCCCAAATTGCCATGATAA 59.300 45.455 0.00 0.00 0.00 1.75
2335 2805 6.786122 ACCCTTCCTAGCAAACTATTGTTTA 58.214 36.000 4.94 0.00 43.75 2.01
2358 2828 2.472695 ATGTTACCGCTTTGCTCAGA 57.527 45.000 0.00 0.00 0.00 3.27
2366 2836 1.447945 GCTTTGCTCAGACCCTCTTC 58.552 55.000 0.00 0.00 0.00 2.87
2415 2885 1.499007 AGGTTGTTCCATGTTGGGACT 59.501 47.619 6.53 0.00 46.50 3.85
2452 2922 9.771534 GGGATATCACAATATCTCCTATTTAGC 57.228 37.037 4.83 0.00 42.32 3.09
2490 2960 0.992695 GGTAAAGGGTGGAAGGCTCT 59.007 55.000 0.00 0.00 0.00 4.09
2503 2973 3.957288 GGCTCTACCTTTTGCCTGA 57.043 52.632 0.00 0.00 41.92 3.86
2514 2984 4.162131 ACCTTTTGCCTGATGTTTTGTTCT 59.838 37.500 0.00 0.00 0.00 3.01
2516 2986 5.922544 CCTTTTGCCTGATGTTTTGTTCTAG 59.077 40.000 0.00 0.00 0.00 2.43
2530 3000 1.413077 GTTCTAGTCTTGCCGCCCTAT 59.587 52.381 0.00 0.00 0.00 2.57
2568 3039 5.388371 GGTGTTATGTTTCTTGATTTTGCGC 60.388 40.000 0.00 0.00 0.00 6.09
2594 3066 1.211949 ACACGATGAGGGTTTATGGGG 59.788 52.381 0.00 0.00 26.81 4.96
2604 3076 1.006639 GGTTTATGGGGCCCTCTTGAA 59.993 52.381 25.93 10.15 0.00 2.69
2638 3111 5.070313 TGAATAAAACTTTTCCAGCAAGGCT 59.930 36.000 0.00 0.00 40.77 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 6.542821 TGTAGCTCCATAAAATATTGGGAGG 58.457 40.000 19.27 8.55 39.75 4.30
50 51 7.936847 ACGAATGGAATATTTATTGTAGCTCCA 59.063 33.333 0.00 0.00 0.00 3.86
70 71 6.385843 TGTTTGGGTTGATTTCATACGAATG 58.614 36.000 0.00 0.00 0.00 2.67
75 76 7.518211 GCAAGTTTGTTTGGGTTGATTTCATAC 60.518 37.037 0.00 0.00 0.00 2.39
80 81 4.583871 TGCAAGTTTGTTTGGGTTGATTT 58.416 34.783 0.00 0.00 0.00 2.17
97 98 7.115947 GGAAACAGAAGAGATTTGAAATGCAAG 59.884 37.037 0.00 0.00 37.87 4.01
117 118 9.261035 AGATAAGAACTCTAGAATCTGGAAACA 57.739 33.333 8.15 0.00 39.59 2.83
137 138 6.882656 TGGAGACCAAAAGAGATGAGATAAG 58.117 40.000 0.00 0.00 0.00 1.73
170 171 9.045223 AAACTCAAACTATTTGAATTTGGAAGC 57.955 29.630 9.26 0.00 44.44 3.86
269 271 3.871594 GTGACATATTTTCCCGGAGACAG 59.128 47.826 0.73 0.00 0.00 3.51
291 293 2.185004 AGGAGTGGAATTCCAACACG 57.815 50.000 28.64 0.00 46.78 4.49
398 400 2.285668 CTGAGGGAAGCAGGGGGA 60.286 66.667 0.00 0.00 0.00 4.81
421 423 0.909133 AAAAATGAATGGGCCGGCCT 60.909 50.000 42.70 26.22 36.10 5.19
422 424 1.601703 AAAAATGAATGGGCCGGCC 59.398 52.632 38.57 38.57 0.00 6.13
447 449 2.424234 GGCTAGTTGGATTTGGGCCATA 60.424 50.000 7.26 1.88 38.16 2.74
449 451 0.324275 GGCTAGTTGGATTTGGGCCA 60.324 55.000 0.00 0.00 38.16 5.36
457 459 1.972660 GAGGCACCGGCTAGTTGGAT 61.973 60.000 0.00 0.00 38.98 3.41
458 460 2.606519 AGGCACCGGCTAGTTGGA 60.607 61.111 0.00 0.00 40.87 3.53
475 478 1.006281 TCAGGCCTAGGGTTTAGACGA 59.994 52.381 3.98 0.00 0.00 4.20
493 496 1.230497 GGATCGAGAGGAGGGGTCA 59.770 63.158 0.00 0.00 0.00 4.02
538 541 3.849951 GAGGGATCGGGCAAGCGA 61.850 66.667 0.00 0.00 0.00 4.93
540 543 2.514824 GTGAGGGATCGGGCAAGC 60.515 66.667 0.00 0.00 0.00 4.01
556 559 3.410628 TGGATCGGGGCTGCATGT 61.411 61.111 0.50 0.00 0.00 3.21
566 569 1.535028 CGAGAGAGAGATGTGGATCGG 59.465 57.143 0.00 0.00 33.34 4.18
569 572 2.582052 GGTCGAGAGAGAGATGTGGAT 58.418 52.381 0.00 0.00 43.49 3.41
634 637 3.934962 GGGATGAGGGGCTCGAGC 61.935 72.222 29.38 29.38 41.14 5.03
664 667 1.749033 CATAGGAGGGGTTCGAGGC 59.251 63.158 0.00 0.00 0.00 4.70
706 709 2.445845 TAGAGGGGGATGGTGGCG 60.446 66.667 0.00 0.00 0.00 5.69
721 724 1.154016 CACGCGAGGTGGTCAGTAG 60.154 63.158 15.93 0.00 43.16 2.57
761 764 1.092345 CAGAAAGGAAGGCTAGCGGC 61.092 60.000 9.00 0.00 40.90 6.53
766 769 1.073763 TGCAAGCAGAAAGGAAGGCTA 59.926 47.619 0.00 0.00 35.11 3.93
771 774 3.511362 TGGTGCAAGCAGAAAGGAA 57.489 47.368 0.00 0.00 40.88 3.36
783 786 2.677524 GCTGGCAAGGATGGTGCA 60.678 61.111 0.00 0.00 44.07 4.57
906 910 3.896863 GAAGCAAAGGCAACGGCGG 62.897 63.158 13.24 0.00 44.61 6.13
907 911 2.429069 GAAGCAAAGGCAACGGCG 60.429 61.111 4.80 4.80 44.61 6.46
908 912 1.661509 GTGAAGCAAAGGCAACGGC 60.662 57.895 0.00 0.00 44.61 5.68
909 913 1.007387 GGTGAAGCAAAGGCAACGG 60.007 57.895 0.00 0.00 44.61 4.44
910 914 0.318107 CAGGTGAAGCAAAGGCAACG 60.318 55.000 0.00 0.00 44.61 4.10
911 915 1.000938 CTCAGGTGAAGCAAAGGCAAC 60.001 52.381 0.00 0.00 44.61 4.17
912 916 1.321474 CTCAGGTGAAGCAAAGGCAA 58.679 50.000 0.00 0.00 44.61 4.52
913 917 1.174712 GCTCAGGTGAAGCAAAGGCA 61.175 55.000 0.00 0.00 44.61 4.75
914 918 1.583477 GCTCAGGTGAAGCAAAGGC 59.417 57.895 0.00 0.00 41.61 4.35
915 919 1.580845 CGGCTCAGGTGAAGCAAAGG 61.581 60.000 0.00 0.00 0.00 3.11
916 920 1.871772 CGGCTCAGGTGAAGCAAAG 59.128 57.895 0.00 0.00 0.00 2.77
917 921 2.260869 GCGGCTCAGGTGAAGCAAA 61.261 57.895 0.00 0.00 0.00 3.68
918 922 2.669569 GCGGCTCAGGTGAAGCAA 60.670 61.111 0.00 0.00 0.00 3.91
943 947 2.435059 GTCCACGAAGCAGAGGGC 60.435 66.667 0.00 0.00 45.30 5.19
944 948 2.125912 CGTCCACGAAGCAGAGGG 60.126 66.667 0.00 0.00 43.02 4.30
945 949 1.734477 CACGTCCACGAAGCAGAGG 60.734 63.158 6.03 0.00 43.02 3.69
946 950 2.375766 GCACGTCCACGAAGCAGAG 61.376 63.158 6.03 0.00 43.02 3.35
947 951 2.355837 GCACGTCCACGAAGCAGA 60.356 61.111 6.03 0.00 43.02 4.26
948 952 2.356313 AGCACGTCCACGAAGCAG 60.356 61.111 18.32 1.74 42.67 4.24
949 953 2.355837 GAGCACGTCCACGAAGCA 60.356 61.111 18.32 0.00 42.67 3.91
950 954 3.470567 CGAGCACGTCCACGAAGC 61.471 66.667 6.03 9.38 43.02 3.86
960 964 3.250323 CGATGCAGGACGAGCACG 61.250 66.667 0.76 0.76 45.95 5.34
961 965 3.558411 GCGATGCAGGACGAGCAC 61.558 66.667 13.36 0.00 45.95 4.40
963 967 4.521062 AGGCGATGCAGGACGAGC 62.521 66.667 13.36 2.80 0.00 5.03
964 968 2.584418 CAGGCGATGCAGGACGAG 60.584 66.667 13.36 0.00 0.00 4.18
965 969 3.068064 TCAGGCGATGCAGGACGA 61.068 61.111 13.36 0.61 0.00 4.20
966 970 2.887568 GTCAGGCGATGCAGGACG 60.888 66.667 0.00 0.00 0.00 4.79
967 971 2.512515 GGTCAGGCGATGCAGGAC 60.513 66.667 0.00 4.19 34.17 3.85
968 972 3.002583 TGGTCAGGCGATGCAGGA 61.003 61.111 0.00 0.00 0.00 3.86
969 973 2.821366 GTGGTCAGGCGATGCAGG 60.821 66.667 0.00 0.00 0.00 4.85
970 974 1.812922 GAGTGGTCAGGCGATGCAG 60.813 63.158 0.00 0.00 0.00 4.41
971 975 1.830587 AAGAGTGGTCAGGCGATGCA 61.831 55.000 0.00 0.00 0.00 3.96
972 976 1.078848 AAGAGTGGTCAGGCGATGC 60.079 57.895 0.00 0.00 0.00 3.91
973 977 0.803768 CGAAGAGTGGTCAGGCGATG 60.804 60.000 0.00 0.00 0.00 3.84
974 978 0.965866 TCGAAGAGTGGTCAGGCGAT 60.966 55.000 0.00 0.00 0.00 4.58
975 979 1.602605 TCGAAGAGTGGTCAGGCGA 60.603 57.895 0.00 0.00 0.00 5.54
976 980 1.444553 GTCGAAGAGTGGTCAGGCG 60.445 63.158 0.00 0.00 36.95 5.52
977 981 1.079750 GGTCGAAGAGTGGTCAGGC 60.080 63.158 0.00 0.00 36.95 4.85
978 982 0.244994 CAGGTCGAAGAGTGGTCAGG 59.755 60.000 0.00 0.00 36.95 3.86
979 983 0.389166 GCAGGTCGAAGAGTGGTCAG 60.389 60.000 0.00 0.00 36.95 3.51
980 984 1.666011 GCAGGTCGAAGAGTGGTCA 59.334 57.895 0.00 0.00 36.95 4.02
981 985 1.079750 GGCAGGTCGAAGAGTGGTC 60.080 63.158 0.00 0.00 36.95 4.02
982 986 1.194781 ATGGCAGGTCGAAGAGTGGT 61.195 55.000 0.00 0.00 36.95 4.16
983 987 0.742281 CATGGCAGGTCGAAGAGTGG 60.742 60.000 0.00 0.00 36.95 4.00
984 988 0.742281 CCATGGCAGGTCGAAGAGTG 60.742 60.000 0.00 0.00 36.95 3.51
985 989 1.599047 CCATGGCAGGTCGAAGAGT 59.401 57.895 0.00 0.00 36.95 3.24
986 990 1.153289 CCCATGGCAGGTCGAAGAG 60.153 63.158 6.09 0.00 36.95 2.85
987 991 2.669133 CCCCATGGCAGGTCGAAGA 61.669 63.158 6.09 0.00 0.00 2.87
988 992 2.124570 CCCCATGGCAGGTCGAAG 60.125 66.667 6.09 0.00 0.00 3.79
989 993 3.727258 CCCCCATGGCAGGTCGAA 61.727 66.667 6.09 0.00 0.00 3.71
999 1003 2.566111 TTAAGAAGGCGGCCCCCATG 62.566 60.000 17.02 0.00 0.00 3.66
1000 1004 2.313427 TTAAGAAGGCGGCCCCCAT 61.313 57.895 17.02 0.00 0.00 4.00
1001 1005 2.936584 TTAAGAAGGCGGCCCCCA 60.937 61.111 17.02 0.00 0.00 4.96
1002 1006 2.439701 GTTAAGAAGGCGGCCCCC 60.440 66.667 17.02 7.83 0.00 5.40
1003 1007 1.749258 CTGTTAAGAAGGCGGCCCC 60.749 63.158 17.02 8.24 0.00 5.80
1004 1008 1.025113 GTCTGTTAAGAAGGCGGCCC 61.025 60.000 17.02 0.38 33.05 5.80
1005 1009 1.359459 CGTCTGTTAAGAAGGCGGCC 61.359 60.000 12.11 12.11 39.06 6.13
1006 1010 1.967597 GCGTCTGTTAAGAAGGCGGC 61.968 60.000 12.53 0.00 42.87 6.53
1007 1011 1.359459 GGCGTCTGTTAAGAAGGCGG 61.359 60.000 12.53 0.00 44.91 6.13
1008 1012 2.079049 GGCGTCTGTTAAGAAGGCG 58.921 57.895 7.55 7.55 44.91 5.52
1010 1014 2.743636 TGAGGCGTCTGTTAAGAAGG 57.256 50.000 8.06 0.00 33.05 3.46
1011 1015 2.413453 GCTTGAGGCGTCTGTTAAGAAG 59.587 50.000 8.06 2.37 33.05 2.85
1012 1016 2.413837 GCTTGAGGCGTCTGTTAAGAA 58.586 47.619 8.06 0.00 33.05 2.52
1013 1017 1.337823 GGCTTGAGGCGTCTGTTAAGA 60.338 52.381 8.06 0.00 42.94 2.10
1014 1018 1.079503 GGCTTGAGGCGTCTGTTAAG 58.920 55.000 8.06 0.00 42.94 1.85
1015 1019 0.394938 TGGCTTGAGGCGTCTGTTAA 59.605 50.000 8.06 0.00 44.42 2.01
1016 1020 0.320421 GTGGCTTGAGGCGTCTGTTA 60.320 55.000 8.06 0.00 44.42 2.41
1017 1021 1.598130 GTGGCTTGAGGCGTCTGTT 60.598 57.895 8.06 0.00 44.42 3.16
1018 1022 2.031163 GTGGCTTGAGGCGTCTGT 59.969 61.111 8.06 0.00 44.42 3.41
1019 1023 2.743928 GGTGGCTTGAGGCGTCTG 60.744 66.667 8.06 2.10 44.42 3.51
1020 1024 2.925170 AGGTGGCTTGAGGCGTCT 60.925 61.111 8.06 0.00 44.42 4.18
1021 1025 2.435059 GAGGTGGCTTGAGGCGTC 60.435 66.667 0.00 0.00 44.42 5.19
1096 1100 1.730612 CTATGTGTGAGTGTGCTGCAG 59.269 52.381 10.11 10.11 0.00 4.41
1097 1101 1.799544 CTATGTGTGAGTGTGCTGCA 58.200 50.000 0.00 0.00 0.00 4.41
1105 1109 1.066858 CAACGAGGGCTATGTGTGAGT 60.067 52.381 0.00 0.00 0.00 3.41
1127 1131 2.061061 AGGGGATCAAAGCCTCATAGG 58.939 52.381 0.00 0.00 38.80 2.57
1130 1134 0.106318 GCAGGGGATCAAAGCCTCAT 60.106 55.000 0.00 0.00 0.00 2.90
1131 1135 1.304282 GCAGGGGATCAAAGCCTCA 59.696 57.895 0.00 0.00 0.00 3.86
1156 1160 2.110967 CATGGAGCTGCGGTCTTGG 61.111 63.158 0.00 0.00 0.00 3.61
1181 1185 2.520979 CGAAAGAGAGCTTAGTGTCCG 58.479 52.381 0.00 0.00 32.98 4.79
1185 1189 3.444388 AGTACCCGAAAGAGAGCTTAGTG 59.556 47.826 0.00 0.00 32.98 2.74
1186 1190 3.699413 AGTACCCGAAAGAGAGCTTAGT 58.301 45.455 0.00 0.00 32.98 2.24
1188 1192 3.446516 GGAAGTACCCGAAAGAGAGCTTA 59.553 47.826 0.00 0.00 32.98 3.09
1207 1211 0.034896 GCGTTCCTGGTCTTGAGGAA 59.965 55.000 0.00 0.00 45.57 3.36
1224 1228 3.733960 TCGGTCTCAGTCACGGCG 61.734 66.667 4.80 4.80 0.00 6.46
1226 1230 0.387367 CTTGTCGGTCTCAGTCACGG 60.387 60.000 0.00 0.00 0.00 4.94
1233 1237 0.963962 GGTGGTACTTGTCGGTCTCA 59.036 55.000 0.00 0.00 0.00 3.27
1245 1249 1.019278 CATGCAGGTCGTGGTGGTAC 61.019 60.000 0.00 0.00 0.00 3.34
1293 1297 2.393768 GCATGATGATAGCGGGGCG 61.394 63.158 0.00 0.00 0.00 6.13
1299 1303 2.947652 AGTGTTGGTGCATGATGATAGC 59.052 45.455 0.00 0.00 0.00 2.97
1300 1304 4.732647 GCAAGTGTTGGTGCATGATGATAG 60.733 45.833 0.00 0.00 40.58 2.08
1302 1306 2.094390 GCAAGTGTTGGTGCATGATGAT 60.094 45.455 0.00 0.00 40.58 2.45
1316 1320 1.462616 TCAACAGCAACAGCAAGTGT 58.537 45.000 0.00 0.00 43.24 3.55
1323 1327 1.338973 ACTTGGCATCAACAGCAACAG 59.661 47.619 0.00 0.00 0.00 3.16
1331 1335 1.069227 GTGGTCGAACTTGGCATCAAC 60.069 52.381 0.33 0.00 0.00 3.18
1336 1340 2.280524 CGGTGGTCGAACTTGGCA 60.281 61.111 0.33 0.00 42.43 4.92
1337 1341 2.029964 TCGGTGGTCGAACTTGGC 59.970 61.111 0.33 0.00 45.86 4.52
1349 1353 1.429148 GCGCTATTCCCTGTTCGGTG 61.429 60.000 0.00 0.00 0.00 4.94
1388 1392 2.442188 CCGCGTAGTCGAACTTGGC 61.442 63.158 4.92 0.00 39.71 4.52
1403 1407 1.869767 CAAATCTGAGGTCATAGCCGC 59.130 52.381 0.00 0.00 0.00 6.53
1405 1409 3.471680 GTCCAAATCTGAGGTCATAGCC 58.528 50.000 0.00 0.00 0.00 3.93
1416 1420 0.109597 GCGCTTGTGGTCCAAATCTG 60.110 55.000 0.00 0.00 31.20 2.90
1476 1480 3.741249 CCTAGAGTCGTACTAGGCATCA 58.259 50.000 15.04 0.00 46.52 3.07
1493 1497 4.437930 CGTAGTACTTTGTTCCGGTCCTAG 60.438 50.000 0.00 0.00 0.00 3.02
1494 1498 3.440173 CGTAGTACTTTGTTCCGGTCCTA 59.560 47.826 0.00 0.00 0.00 2.94
1500 1504 3.855950 GGTCATCGTAGTACTTTGTTCCG 59.144 47.826 0.00 0.00 0.00 4.30
1537 1541 2.596795 GCGTTTCGGTGCGGTGTAA 61.597 57.895 0.00 0.00 0.00 2.41
1543 1547 3.342627 TCTTGGCGTTTCGGTGCG 61.343 61.111 0.00 0.00 0.00 5.34
1548 1552 2.664436 GGACGGTCTTGGCGTTTCG 61.664 63.158 8.23 0.00 0.00 3.46
1554 1558 0.106149 AATATCCGGACGGTCTTGGC 59.894 55.000 6.12 0.00 36.47 4.52
1567 1571 4.275936 GTGTCATGGTACTTGGCAATATCC 59.724 45.833 0.00 4.15 29.08 2.59
1597 1630 3.253921 TCGTTGTAGTCGAACTTGATGGA 59.746 43.478 0.00 0.00 34.36 3.41
1600 1633 4.500603 AGTCGTTGTAGTCGAACTTGAT 57.499 40.909 0.00 0.00 39.01 2.57
1617 1650 4.418392 GGTAGTGGTACATGTTGTAGTCG 58.582 47.826 2.30 0.00 44.52 4.18
1627 1660 3.846955 GGCAACGGTAGTGGTACAT 57.153 52.632 0.00 0.00 44.52 2.29
1642 1675 2.029369 GTACACGGGTTGTCGGCA 59.971 61.111 0.00 0.00 39.91 5.69
1662 1695 3.254166 ACGGTAGTCGAACTTGCTTCTTA 59.746 43.478 0.00 0.00 42.43 2.10
1666 1699 2.061740 GACGGTAGTCGAACTTGCTT 57.938 50.000 0.00 0.00 42.43 3.91
1681 1714 0.108804 AGTAGTGGTTCATGCGACGG 60.109 55.000 0.00 0.00 0.00 4.79
1682 1715 1.654105 GAAGTAGTGGTTCATGCGACG 59.346 52.381 0.00 0.00 0.00 5.12
1708 1741 2.607635 CGGTGTAGATTTTCATGGGTCG 59.392 50.000 0.00 0.00 0.00 4.79
1719 1752 1.472728 GGGTTCGATGCGGTGTAGATT 60.473 52.381 0.00 0.00 0.00 2.40
1720 1753 0.104304 GGGTTCGATGCGGTGTAGAT 59.896 55.000 0.00 0.00 0.00 1.98
1734 1767 0.973632 GTTTTGGGGTGGATGGGTTC 59.026 55.000 0.00 0.00 0.00 3.62
1744 1777 2.831284 AAGCGTGCGTTTTGGGGT 60.831 55.556 0.00 0.00 0.00 4.95
1747 1780 0.991770 CTTCGAAGCGTGCGTTTTGG 60.992 55.000 13.09 0.00 0.00 3.28
1749 1782 1.278637 CCTTCGAAGCGTGCGTTTT 59.721 52.632 19.99 0.00 0.00 2.43
1750 1783 0.598158 TACCTTCGAAGCGTGCGTTT 60.598 50.000 19.99 0.00 0.00 3.60
1751 1784 0.389426 ATACCTTCGAAGCGTGCGTT 60.389 50.000 19.99 4.24 0.00 4.84
1757 1790 1.719780 GGCGATTATACCTTCGAAGCG 59.280 52.381 19.99 15.80 37.55 4.68
1776 1809 4.388499 CCAGGGGTGTCGTTCCGG 62.388 72.222 0.00 0.00 0.00 5.14
1785 1818 2.373169 ACATGCATATAGTCCAGGGGTG 59.627 50.000 0.00 0.00 0.00 4.61
1786 1819 2.373169 CACATGCATATAGTCCAGGGGT 59.627 50.000 0.00 0.00 0.00 4.95
1790 1823 5.303165 ACACATCACATGCATATAGTCCAG 58.697 41.667 0.00 0.00 0.00 3.86
1796 1829 8.149647 TCTCATACAACACATCACATGCATATA 58.850 33.333 0.00 0.00 0.00 0.86
1797 1830 6.993902 TCTCATACAACACATCACATGCATAT 59.006 34.615 0.00 0.00 0.00 1.78
1844 1877 1.194547 GAACGAGCAAGCGACAATTCA 59.805 47.619 0.00 0.00 34.83 2.57
1847 1880 0.320771 AGGAACGAGCAAGCGACAAT 60.321 50.000 0.00 0.00 34.83 2.71
1849 1882 1.372997 GAGGAACGAGCAAGCGACA 60.373 57.895 0.00 0.00 34.83 4.35
1851 1884 0.037326 AATGAGGAACGAGCAAGCGA 60.037 50.000 0.00 0.00 34.83 4.93
1860 1893 0.179129 GGCATGGCAAATGAGGAACG 60.179 55.000 15.47 0.00 0.00 3.95
1872 1905 2.537560 CCTGAATCGACGGCATGGC 61.538 63.158 9.69 9.69 0.00 4.40
1880 1913 0.830648 TGGGGTGATCCTGAATCGAC 59.169 55.000 0.00 0.00 37.17 4.20
1886 1919 0.988145 GGATGGTGGGGTGATCCTGA 60.988 60.000 0.00 0.00 34.00 3.86
1888 1921 0.253820 AAGGATGGTGGGGTGATCCT 60.254 55.000 0.00 0.00 46.65 3.24
1923 1973 0.249447 GGTGCAAAAGGAAGTGTGGC 60.249 55.000 0.00 0.00 0.00 5.01
1943 1993 5.047660 AGTTTCGATAGCTCATGGAGATACC 60.048 44.000 0.00 0.00 33.30 2.73
1960 2010 3.684305 CCACAGCAACATATCAGTTTCGA 59.316 43.478 0.00 0.00 0.00 3.71
1962 2012 3.762779 GCCACAGCAACATATCAGTTTC 58.237 45.455 0.00 0.00 39.53 2.78
1963 2013 3.855689 GCCACAGCAACATATCAGTTT 57.144 42.857 0.00 0.00 39.53 2.66
1976 2026 2.229543 TGTCTGAAAATGATGCCACAGC 59.770 45.455 0.00 0.00 40.48 4.40
1978 2028 3.367600 GCATGTCTGAAAATGATGCCACA 60.368 43.478 5.93 0.00 34.58 4.17
1979 2029 3.184541 GCATGTCTGAAAATGATGCCAC 58.815 45.455 5.93 0.00 34.58 5.01
1993 2043 4.397103 CACAACCAAGTATGATGCATGTCT 59.603 41.667 2.46 0.00 0.00 3.41
2067 2530 1.176619 TCGAGAAGGAGCACAACCGA 61.177 55.000 0.00 0.00 0.00 4.69
2092 2555 3.054166 CTCACAATCACAACGTAACCGA 58.946 45.455 0.00 0.00 37.88 4.69
2170 2637 3.006940 GACGGTCATGTTGCCTGAAATA 58.993 45.455 2.62 0.00 0.00 1.40
2182 2649 1.208052 AGATCCAAGGTGACGGTCATG 59.792 52.381 14.78 8.58 0.00 3.07
2296 2765 4.918273 AGGAAGGGTAAAAAGGTTAGAGGT 59.082 41.667 0.00 0.00 0.00 3.85
2335 2805 2.280628 GAGCAAAGCGGTAACATAGCT 58.719 47.619 0.00 0.00 43.90 3.32
2490 2960 5.362430 AGAACAAAACATCAGGCAAAAGGTA 59.638 36.000 0.00 0.00 0.00 3.08
2503 2973 3.058224 GCGGCAAGACTAGAACAAAACAT 60.058 43.478 0.00 0.00 0.00 2.71
2514 2984 2.420967 GGAAAATAGGGCGGCAAGACTA 60.421 50.000 12.47 2.93 0.00 2.59
2516 2986 0.738975 GGAAAATAGGGCGGCAAGAC 59.261 55.000 12.47 0.00 0.00 3.01
2594 3066 3.632145 TCAAAGTGAACTTTCAAGAGGGC 59.368 43.478 5.46 0.00 43.72 5.19
2604 3076 9.936759 TGGAAAAGTTTTATTCAAAGTGAACTT 57.063 25.926 0.00 0.00 39.45 2.66
2625 3098 1.999648 ATGTTGAGCCTTGCTGGAAA 58.000 45.000 0.00 0.00 39.88 3.13


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

AutoCloner maintained by Alex Coulton.