Multiple sequence alignment - TraesCS4A01G389500

Loading Multiple Alignment...

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 TraesCS4A01G389500 chr4A 100.000 5534 0 0 1 5534 666953836 666948303 0.000000e+00 10220
1 TraesCS4A01G389500 chr4A 82.830 1258 183 23 935 2179 17898559 17897322 0.000000e+00 1096
2 TraesCS4A01G389500 chr4A 81.225 1241 192 27 932 2161 731006985 731005775 0.000000e+00 963
3 TraesCS4A01G389500 chr4A 81.728 706 106 16 4794 5496 17893064 17892379 8.050000e-158 568
4 TraesCS4A01G389500 chr4A 76.722 1031 209 25 3390 4406 18273966 18274979 3.770000e-151 545
5 TraesCS4A01G389500 chr4A 80.343 641 91 13 4475 5113 18275618 18276225 2.350000e-123 453
6 TraesCS4A01G389500 chr4A 82.796 186 22 7 415 597 17899578 17899400 2.060000e-34 158
7 TraesCS4A01G389500 chr7D 95.753 1931 71 9 2500 4421 52354062 52352134 0.000000e+00 3101
8 TraesCS4A01G389500 chr7D 93.096 1767 109 6 2670 4427 52470630 52468868 0.000000e+00 2575
9 TraesCS4A01G389500 chr7D 89.680 1124 83 19 4414 5534 52457554 52456461 0.000000e+00 1402
10 TraesCS4A01G389500 chr7D 95.011 882 40 2 1565 2446 52354928 52354051 0.000000e+00 1382
11 TraesCS4A01G389500 chr7D 87.530 1243 93 34 372 1572 52356325 52355103 0.000000e+00 1380
12 TraesCS4A01G389500 chr7D 93.490 722 37 5 1672 2391 52474416 52473703 0.000000e+00 1064
13 TraesCS4A01G389500 chr7D 86.246 967 83 23 328 1266 52483593 52482649 0.000000e+00 1003
14 TraesCS4A01G389500 chr7D 90.789 684 36 4 4410 5092 52350746 52350089 0.000000e+00 889
15 TraesCS4A01G389500 chr7D 95.759 448 18 1 5087 5534 52340663 52340217 0.000000e+00 721
16 TraesCS4A01G389500 chr7D 93.602 422 26 1 1266 1687 52475419 52474999 3.640000e-176 628
17 TraesCS4A01G389500 chr7D 92.357 157 8 2 2522 2675 52473668 52473513 2.600000e-53 220
18 TraesCS4A01G389500 chr5D 83.975 1429 196 22 3002 4405 4052711 4051291 0.000000e+00 1339
19 TraesCS4A01G389500 chr5D 83.917 1343 181 24 948 2278 4054915 4053596 0.000000e+00 1251
20 TraesCS4A01G389500 chr5D 82.546 974 165 4 3252 4221 27351158 27350186 0.000000e+00 852
21 TraesCS4A01G389500 chr5D 81.936 1002 168 9 3418 4409 4253154 4252156 0.000000e+00 835
22 TraesCS4A01G389500 chr5D 84.008 519 61 15 2494 3002 4053412 4052906 3.880000e-131 479
23 TraesCS4A01G389500 chr5D 78.358 670 103 18 4435 5100 4267501 4266870 4.020000e-106 396
24 TraesCS4A01G389500 chr5D 77.740 292 54 5 4418 4706 4049825 4049542 9.530000e-38 169
25 TraesCS4A01G389500 chr5D 80.233 172 23 7 457 619 4055989 4055820 9.740000e-23 119
26 TraesCS4A01G389500 chr7A 93.666 821 49 2 1024 1841 54853468 54852648 0.000000e+00 1225
27 TraesCS4A01G389500 chr7A 93.929 560 24 4 1837 2396 54852000 54851451 0.000000e+00 837
28 TraesCS4A01G389500 chr7A 84.158 606 50 23 454 1032 54854129 54853543 3.770000e-151 545
29 TraesCS4A01G389500 chr7A 87.692 130 9 2 328 450 54854365 54854236 1.610000e-30 145
30 TraesCS4A01G389500 chr7A 88.785 107 10 1 147 253 54854966 54854862 4.500000e-26 130
31 TraesCS4A01G389500 chr5B 83.452 1263 175 20 916 2167 19745121 19743882 0.000000e+00 1144
32 TraesCS4A01G389500 chr5B 81.702 1175 190 17 936 2105 6927803 6926649 0.000000e+00 955
33 TraesCS4A01G389500 chr5B 81.948 1119 187 8 3287 4393 7022459 7021344 0.000000e+00 933
34 TraesCS4A01G389500 chr5B 84.197 772 103 3 3639 4409 19737217 19736464 0.000000e+00 732
35 TraesCS4A01G389500 chr5B 78.224 1070 190 26 4425 5491 64734681 64733652 0.000000e+00 645
36 TraesCS4A01G389500 chr5B 77.629 1046 187 18 4453 5492 7018449 7017445 4.770000e-165 592
37 TraesCS4A01G389500 chr5B 76.916 1070 180 44 4443 5493 6880462 6879441 3.770000e-151 545
38 TraesCS4A01G389500 chr5B 80.601 732 113 15 4440 5169 19730823 19730119 6.310000e-149 538
39 TraesCS4A01G389500 chr5B 75.755 1027 211 18 3393 4409 64736877 64735879 3.000000e-132 483
40 TraesCS4A01G389500 chr5B 76.626 984 162 38 4437 5406 64721157 64722086 1.080000e-131 481
41 TraesCS4A01G389500 chr5B 78.535 396 76 8 3252 3641 19742513 19742121 9.200000e-63 252
42 TraesCS4A01G389500 chr5A 83.171 1028 164 7 3385 4409 4289127 4290148 0.000000e+00 931
43 TraesCS4A01G389500 chr5A 76.584 1089 197 34 4415 5488 4292653 4293698 3.770000e-151 545
44 TraesCS4A01G389500 chr3D 84.641 599 85 7 962 1557 418560560 418561154 1.720000e-164 590
45 TraesCS4A01G389500 chr3D 83.189 577 81 7 982 1557 418443164 418443725 1.060000e-141 514
46 TraesCS4A01G389500 chr3D 82.682 537 77 13 1596 2128 418704339 418704863 3.910000e-126 462
47 TraesCS4A01G389500 chr3B 85.304 313 45 1 982 1294 544927701 544928012 6.920000e-84 322
48 TraesCS4A01G389500 chr3B 88.298 94 10 1 982 1075 544835333 544835425 1.630000e-20 111
49 TraesCS4A01G389500 chr6B 80.889 225 35 8 2747 2970 169231715 169231498 2.650000e-38 171
50 TraesCS4A01G389500 chr6D 77.372 274 47 14 2732 2998 88885608 88885343 1.240000e-31 148
51 TraesCS4A01G389500 chrUn 88.298 94 10 1 982 1075 438150910 438151002 1.630000e-20 111


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 TraesCS4A01G389500 chr4A 666948303 666953836 5533 True 10220.00 10220 100.00000 1 5534 1 chr4A.!!$R2 5533
1 TraesCS4A01G389500 chr4A 731005775 731006985 1210 True 963.00 963 81.22500 932 2161 1 chr4A.!!$R3 1229
2 TraesCS4A01G389500 chr4A 17897322 17899578 2256 True 627.00 1096 82.81300 415 2179 2 chr4A.!!$R4 1764
3 TraesCS4A01G389500 chr4A 17892379 17893064 685 True 568.00 568 81.72800 4794 5496 1 chr4A.!!$R1 702
4 TraesCS4A01G389500 chr4A 18273966 18276225 2259 False 499.00 545 78.53250 3390 5113 2 chr4A.!!$F1 1723
5 TraesCS4A01G389500 chr7D 52350089 52356325 6236 True 1688.00 3101 92.27075 372 5092 4 chr7D.!!$R4 4720
6 TraesCS4A01G389500 chr7D 52456461 52457554 1093 True 1402.00 1402 89.68000 4414 5534 1 chr7D.!!$R2 1120
7 TraesCS4A01G389500 chr7D 52468868 52475419 6551 True 1121.75 2575 93.13625 1266 4427 4 chr7D.!!$R5 3161
8 TraesCS4A01G389500 chr7D 52482649 52483593 944 True 1003.00 1003 86.24600 328 1266 1 chr7D.!!$R3 938
9 TraesCS4A01G389500 chr5D 27350186 27351158 972 True 852.00 852 82.54600 3252 4221 1 chr5D.!!$R3 969
10 TraesCS4A01G389500 chr5D 4252156 4253154 998 True 835.00 835 81.93600 3418 4409 1 chr5D.!!$R1 991
11 TraesCS4A01G389500 chr5D 4049542 4055989 6447 True 671.40 1339 81.97460 457 4706 5 chr5D.!!$R4 4249
12 TraesCS4A01G389500 chr5D 4266870 4267501 631 True 396.00 396 78.35800 4435 5100 1 chr5D.!!$R2 665
13 TraesCS4A01G389500 chr7A 54851451 54854966 3515 True 576.40 1225 89.64600 147 2396 5 chr7A.!!$R1 2249
14 TraesCS4A01G389500 chr5B 6926649 6927803 1154 True 955.00 955 81.70200 936 2105 1 chr5B.!!$R2 1169
15 TraesCS4A01G389500 chr5B 7017445 7022459 5014 True 762.50 933 79.78850 3287 5492 2 chr5B.!!$R5 2205
16 TraesCS4A01G389500 chr5B 19736464 19737217 753 True 732.00 732 84.19700 3639 4409 1 chr5B.!!$R4 770
17 TraesCS4A01G389500 chr5B 19742121 19745121 3000 True 698.00 1144 80.99350 916 3641 2 chr5B.!!$R6 2725
18 TraesCS4A01G389500 chr5B 64733652 64736877 3225 True 564.00 645 76.98950 3393 5491 2 chr5B.!!$R7 2098
19 TraesCS4A01G389500 chr5B 6879441 6880462 1021 True 545.00 545 76.91600 4443 5493 1 chr5B.!!$R1 1050
20 TraesCS4A01G389500 chr5B 19730119 19730823 704 True 538.00 538 80.60100 4440 5169 1 chr5B.!!$R3 729
21 TraesCS4A01G389500 chr5B 64721157 64722086 929 False 481.00 481 76.62600 4437 5406 1 chr5B.!!$F1 969
22 TraesCS4A01G389500 chr5A 4289127 4293698 4571 False 738.00 931 79.87750 3385 5488 2 chr5A.!!$F1 2103
23 TraesCS4A01G389500 chr3D 418560560 418561154 594 False 590.00 590 84.64100 962 1557 1 chr3D.!!$F2 595
24 TraesCS4A01G389500 chr3D 418443164 418443725 561 False 514.00 514 83.18900 982 1557 1 chr3D.!!$F1 575
25 TraesCS4A01G389500 chr3D 418704339 418704863 524 False 462.00 462 82.68200 1596 2128 1 chr3D.!!$F3 532

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
79 80 0.106769 AGGCAATCACACACCACACA 60.107 50.0 0.00 0.00 0.00 3.72 F
244 245 0.107654 GTGTCATCCAGCTGGTACCC 60.108 60.0 31.58 18.25 36.34 3.69 F
388 818 0.453793 CGATCGCTTCAGAGGACTGT 59.546 55.0 0.26 0.00 43.81 3.55 F
2239 5016 0.665369 GCTGCGCAAGAAACAAGCAT 60.665 50.0 13.05 0.00 43.02 3.79 F
2240 5017 1.774639 CTGCGCAAGAAACAAGCATT 58.225 45.0 13.05 0.00 43.02 3.56 F
2702 8559 2.847327 AGATATGCGGAAGATGGGTG 57.153 50.0 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 3894 0.390492 AGCCTGGCTTTGCTTTTCAC 59.610 50.000 17.22 0.0 33.89 3.18 R
2153 4903 5.972935 TGCTACGTCTAAATGGAAGAATGA 58.027 37.500 0.00 0.0 0.00 2.57 R
2377 5165 6.134535 AGGATGTAAGGACAATTTACCACA 57.865 37.500 0.00 0.0 39.59 4.17 R
3604 9860 4.913784 GGACACATAGACCCAAACCTTAA 58.086 43.478 0.00 0.0 0.00 1.85 R
3803 10066 4.943705 ACACCAACTCTTAACATAGCCATG 59.056 41.667 0.00 0.0 38.21 3.66 R
4627 15787 3.816842 GCATAGAGGCATCCATTTCCCAT 60.817 47.826 0.00 0.0 0.00 4.00 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
28 29 8.737168 TTCATTTTCATCGAGGAAGAATATGT 57.263 30.769 12.75 0.00 33.71 2.29
29 30 8.737168 TCATTTTCATCGAGGAAGAATATGTT 57.263 30.769 12.75 0.00 33.71 2.71
30 31 8.615211 TCATTTTCATCGAGGAAGAATATGTTG 58.385 33.333 12.75 3.19 33.71 3.33
31 32 7.921786 TTTTCATCGAGGAAGAATATGTTGT 57.078 32.000 12.75 0.00 0.00 3.32
32 33 6.908870 TTCATCGAGGAAGAATATGTTGTG 57.091 37.500 8.70 0.00 0.00 3.33
33 34 5.359756 TCATCGAGGAAGAATATGTTGTGG 58.640 41.667 0.00 0.00 0.00 4.17
34 35 4.819105 TCGAGGAAGAATATGTTGTGGT 57.181 40.909 0.00 0.00 0.00 4.16
35 36 5.925506 TCGAGGAAGAATATGTTGTGGTA 57.074 39.130 0.00 0.00 0.00 3.25
36 37 5.657474 TCGAGGAAGAATATGTTGTGGTAC 58.343 41.667 0.00 0.00 0.00 3.34
37 38 5.186215 TCGAGGAAGAATATGTTGTGGTACA 59.814 40.000 0.00 0.00 0.00 2.90
38 39 5.520288 CGAGGAAGAATATGTTGTGGTACAG 59.480 44.000 0.00 0.00 41.80 2.74
39 40 6.620877 AGGAAGAATATGTTGTGGTACAGA 57.379 37.500 0.00 0.00 41.80 3.41
40 41 7.016153 AGGAAGAATATGTTGTGGTACAGAA 57.984 36.000 0.00 0.00 41.80 3.02
41 42 7.458397 AGGAAGAATATGTTGTGGTACAGAAA 58.542 34.615 0.00 0.00 45.15 2.52
42 43 7.607991 AGGAAGAATATGTTGTGGTACAGAAAG 59.392 37.037 0.00 0.00 45.15 2.62
43 44 7.606456 GGAAGAATATGTTGTGGTACAGAAAGA 59.394 37.037 0.00 0.00 45.15 2.52
44 45 9.167311 GAAGAATATGTTGTGGTACAGAAAGAT 57.833 33.333 0.00 0.00 45.15 2.40
45 46 9.520515 AAGAATATGTTGTGGTACAGAAAGATT 57.479 29.630 0.00 0.00 45.15 2.40
46 47 8.950210 AGAATATGTTGTGGTACAGAAAGATTG 58.050 33.333 0.00 0.00 45.15 2.67
47 48 8.862325 AATATGTTGTGGTACAGAAAGATTGA 57.138 30.769 0.00 0.00 45.15 2.57
48 49 8.862325 ATATGTTGTGGTACAGAAAGATTGAA 57.138 30.769 0.00 0.00 45.15 2.69
49 50 6.371809 TGTTGTGGTACAGAAAGATTGAAC 57.628 37.500 0.00 0.00 45.15 3.18
50 51 5.298276 TGTTGTGGTACAGAAAGATTGAACC 59.702 40.000 0.00 0.00 45.15 3.62
51 52 5.042463 TGTGGTACAGAAAGATTGAACCA 57.958 39.130 0.00 0.00 41.80 3.67
52 53 5.063204 TGTGGTACAGAAAGATTGAACCAG 58.937 41.667 0.00 0.00 41.80 4.00
53 54 4.072131 TGGTACAGAAAGATTGAACCAGC 58.928 43.478 0.00 0.00 32.07 4.85
54 55 3.440522 GGTACAGAAAGATTGAACCAGCC 59.559 47.826 0.00 0.00 0.00 4.85
55 56 3.228188 ACAGAAAGATTGAACCAGCCA 57.772 42.857 0.00 0.00 0.00 4.75
56 57 3.771216 ACAGAAAGATTGAACCAGCCAT 58.229 40.909 0.00 0.00 0.00 4.40
57 58 4.154942 ACAGAAAGATTGAACCAGCCATT 58.845 39.130 0.00 0.00 0.00 3.16
58 59 4.590222 ACAGAAAGATTGAACCAGCCATTT 59.410 37.500 0.00 0.00 0.00 2.32
59 60 4.927425 CAGAAAGATTGAACCAGCCATTTG 59.073 41.667 0.00 0.00 0.00 2.32
60 61 4.834496 AGAAAGATTGAACCAGCCATTTGA 59.166 37.500 0.00 0.00 0.00 2.69
61 62 4.796038 AAGATTGAACCAGCCATTTGAG 57.204 40.909 0.00 0.00 0.00 3.02
62 63 3.094572 AGATTGAACCAGCCATTTGAGG 58.905 45.455 0.00 0.00 0.00 3.86
73 74 2.950433 CCATTTGAGGCAATCACACAC 58.050 47.619 0.00 0.00 37.77 3.82
74 75 2.353011 CCATTTGAGGCAATCACACACC 60.353 50.000 0.00 0.00 37.77 4.16
75 76 2.064434 TTTGAGGCAATCACACACCA 57.936 45.000 0.00 0.00 37.77 4.17
76 77 1.317613 TTGAGGCAATCACACACCAC 58.682 50.000 0.00 0.00 37.77 4.16
77 78 0.182299 TGAGGCAATCACACACCACA 59.818 50.000 0.00 0.00 31.12 4.17
78 79 0.593128 GAGGCAATCACACACCACAC 59.407 55.000 0.00 0.00 0.00 3.82
79 80 0.106769 AGGCAATCACACACCACACA 60.107 50.000 0.00 0.00 0.00 3.72
80 81 0.743688 GGCAATCACACACCACACAA 59.256 50.000 0.00 0.00 0.00 3.33
81 82 1.340889 GGCAATCACACACCACACAAT 59.659 47.619 0.00 0.00 0.00 2.71
82 83 2.224018 GGCAATCACACACCACACAATT 60.224 45.455 0.00 0.00 0.00 2.32
83 84 3.456280 GCAATCACACACCACACAATTT 58.544 40.909 0.00 0.00 0.00 1.82
84 85 3.870419 GCAATCACACACCACACAATTTT 59.130 39.130 0.00 0.00 0.00 1.82
85 86 4.332268 GCAATCACACACCACACAATTTTT 59.668 37.500 0.00 0.00 0.00 1.94
104 105 5.934935 TTTTTCCACGGACTTATCACTTC 57.065 39.130 0.00 0.00 0.00 3.01
105 106 3.604875 TTCCACGGACTTATCACTTCC 57.395 47.619 0.00 0.00 0.00 3.46
106 107 1.829222 TCCACGGACTTATCACTTCCC 59.171 52.381 0.00 0.00 0.00 3.97
107 108 1.831736 CCACGGACTTATCACTTCCCT 59.168 52.381 0.00 0.00 0.00 4.20
108 109 2.159085 CCACGGACTTATCACTTCCCTC 60.159 54.545 0.00 0.00 0.00 4.30
109 110 2.761208 CACGGACTTATCACTTCCCTCT 59.239 50.000 0.00 0.00 0.00 3.69
110 111 3.025262 ACGGACTTATCACTTCCCTCTC 58.975 50.000 0.00 0.00 0.00 3.20
111 112 3.024547 CGGACTTATCACTTCCCTCTCA 58.975 50.000 0.00 0.00 0.00 3.27
112 113 3.181485 CGGACTTATCACTTCCCTCTCAC 60.181 52.174 0.00 0.00 0.00 3.51
113 114 3.769844 GGACTTATCACTTCCCTCTCACA 59.230 47.826 0.00 0.00 0.00 3.58
114 115 4.142049 GGACTTATCACTTCCCTCTCACAG 60.142 50.000 0.00 0.00 0.00 3.66
115 116 3.772025 ACTTATCACTTCCCTCTCACAGG 59.228 47.826 0.00 0.00 43.01 4.00
124 125 2.363018 TCTCACAGGAGAGCCGGG 60.363 66.667 2.18 0.00 45.12 5.73
125 126 4.154347 CTCACAGGAGAGCCGGGC 62.154 72.222 12.11 12.11 44.26 6.13
126 127 4.704103 TCACAGGAGAGCCGGGCT 62.704 66.667 24.13 24.13 43.88 5.19
127 128 4.463879 CACAGGAGAGCCGGGCTG 62.464 72.222 29.31 15.21 39.88 4.85
129 130 2.759973 CAGGAGAGCCGGGCTGTA 60.760 66.667 29.31 0.00 39.88 2.74
130 131 2.760385 AGGAGAGCCGGGCTGTAC 60.760 66.667 29.31 24.54 39.88 2.90
131 132 3.075005 GGAGAGCCGGGCTGTACA 61.075 66.667 29.31 0.00 39.88 2.90
132 133 2.656069 GGAGAGCCGGGCTGTACAA 61.656 63.158 29.31 0.00 39.88 2.41
133 134 1.522569 GAGAGCCGGGCTGTACAAT 59.477 57.895 29.31 0.00 39.88 2.71
134 135 0.530870 GAGAGCCGGGCTGTACAATC 60.531 60.000 29.31 10.38 39.88 2.67
135 136 1.523938 GAGCCGGGCTGTACAATCC 60.524 63.158 29.31 5.15 39.88 3.01
136 137 2.516225 GCCGGGCTGTACAATCCC 60.516 66.667 12.87 18.48 36.68 3.85
137 138 2.192175 CCGGGCTGTACAATCCCC 59.808 66.667 21.11 17.35 36.69 4.81
138 139 2.675242 CCGGGCTGTACAATCCCCA 61.675 63.158 21.11 0.00 37.36 4.96
139 140 1.451387 CGGGCTGTACAATCCCCAC 60.451 63.158 21.11 3.85 37.36 4.61
140 141 1.076995 GGGCTGTACAATCCCCACC 60.077 63.158 17.92 2.95 37.46 4.61
141 142 1.571773 GGGCTGTACAATCCCCACCT 61.572 60.000 17.92 0.00 37.46 4.00
142 143 1.209621 GGCTGTACAATCCCCACCTA 58.790 55.000 0.00 0.00 0.00 3.08
143 144 1.141053 GGCTGTACAATCCCCACCTAG 59.859 57.143 0.00 0.00 0.00 3.02
144 145 1.838077 GCTGTACAATCCCCACCTAGT 59.162 52.381 0.00 0.00 0.00 2.57
145 146 2.238898 GCTGTACAATCCCCACCTAGTT 59.761 50.000 0.00 0.00 0.00 2.24
155 156 2.291282 CCCCACCTAGTTGGCAATGTTA 60.291 50.000 1.92 0.00 40.22 2.41
171 172 5.051508 GCAATGTTAACAAGCAACTCTGTTG 60.052 40.000 23.58 15.47 33.15 3.33
172 173 6.264832 CAATGTTAACAAGCAACTCTGTTGA 58.735 36.000 13.23 0.00 0.00 3.18
221 222 7.024768 GCAAGTAAACTTTCAACCGCATATTA 58.975 34.615 0.00 0.00 33.11 0.98
226 227 4.261801 ACTTTCAACCGCATATTAGCAGT 58.738 39.130 0.00 0.00 0.00 4.40
233 234 2.738846 CCGCATATTAGCAGTGTCATCC 59.261 50.000 0.00 0.00 0.00 3.51
238 239 2.391616 TTAGCAGTGTCATCCAGCTG 57.608 50.000 6.78 6.78 36.80 4.24
241 242 0.250234 GCAGTGTCATCCAGCTGGTA 59.750 55.000 31.58 18.83 36.34 3.25
244 245 0.107654 GTGTCATCCAGCTGGTACCC 60.108 60.000 31.58 18.25 36.34 3.69
246 247 2.203070 CATCCAGCTGGTACCCGC 60.203 66.667 31.58 19.77 36.34 6.13
250 251 2.742372 CAGCTGGTACCCGCACAC 60.742 66.667 27.48 1.06 0.00 3.82
268 373 4.150098 GCACACGGAGTAATCGGATATTTC 59.850 45.833 4.65 0.00 41.61 2.17
279 384 6.551385 AATCGGATATTTCTGATGCAGTTC 57.449 37.500 8.09 0.00 45.41 3.01
308 416 6.127054 TGTCCTATTTGTGTTCAGGATCTAGG 60.127 42.308 0.00 0.00 39.33 3.02
311 419 6.098982 CCTATTTGTGTTCAGGATCTAGGTCT 59.901 42.308 2.34 0.00 0.00 3.85
312 420 5.407407 TTTGTGTTCAGGATCTAGGTCTC 57.593 43.478 2.34 0.00 0.00 3.36
334 757 4.522789 TCACCTCTTTGCTGTAAAAATCCC 59.477 41.667 0.00 0.00 0.00 3.85
369 792 3.256631 ACTGGGCAACATCTGAAATTCAC 59.743 43.478 0.00 0.00 39.74 3.18
377 800 3.935203 ACATCTGAAATTCACGATCGCTT 59.065 39.130 16.60 0.80 0.00 4.68
388 818 0.453793 CGATCGCTTCAGAGGACTGT 59.546 55.000 0.26 0.00 43.81 3.55
402 832 2.495669 AGGACTGTAGCTGAGCTTCTTC 59.504 50.000 14.14 8.39 40.44 2.87
531 1064 5.434408 AGATGACATGCTGCTTCTTTATCA 58.566 37.500 0.00 0.00 0.00 2.15
611 1153 4.289410 TCCCATTGGAATTCTGAGAAGTGA 59.711 41.667 0.00 0.00 37.86 3.41
700 1242 6.554605 TGAGGATTCTGTTCTTTGGGATTTTT 59.445 34.615 0.00 0.00 0.00 1.94
776 1343 6.072112 ACTATTTCACACGCAGTTCAAAAT 57.928 33.333 0.00 0.00 41.61 1.82
782 1349 6.125327 TCACACGCAGTTCAAAATAAGAAA 57.875 33.333 0.00 0.00 41.61 2.52
783 1350 5.968848 TCACACGCAGTTCAAAATAAGAAAC 59.031 36.000 0.00 0.00 41.61 2.78
789 1356 9.394477 ACGCAGTTCAAAATAAGAAACTTTATC 57.606 29.630 0.00 0.00 37.78 1.75
828 1957 7.355332 GGATTTGTTCCATTCAAAATGTGAG 57.645 36.000 0.00 0.00 44.74 3.51
829 1958 7.153985 GGATTTGTTCCATTCAAAATGTGAGA 58.846 34.615 0.00 0.00 44.74 3.27
830 1959 7.820872 GGATTTGTTCCATTCAAAATGTGAGAT 59.179 33.333 0.00 0.00 44.74 2.75
831 1960 7.949903 TTTGTTCCATTCAAAATGTGAGATG 57.050 32.000 0.00 0.00 37.61 2.90
872 2009 6.042638 ACATGTCTCATGCTAAAGTGTAGT 57.957 37.500 9.27 0.00 0.00 2.73
1009 2213 1.396648 TGTAACTGCAAATGGATCGCG 59.603 47.619 0.00 0.00 0.00 5.87
1094 2381 2.483188 CCCTACCGTTATCACTTCTGGC 60.483 54.545 0.00 0.00 0.00 4.85
1095 2382 2.167693 CCTACCGTTATCACTTCTGGCA 59.832 50.000 0.00 0.00 0.00 4.92
1113 2400 2.548493 GGCACACATCACCAGCAATTTT 60.548 45.455 0.00 0.00 0.00 1.82
1160 2447 1.686052 TGGCTTTGCAAGGGTTTACAG 59.314 47.619 10.89 0.00 0.00 2.74
1276 2567 3.809832 CGGTTATAGGGAATGCTTGACAG 59.190 47.826 0.00 0.00 0.00 3.51
1302 2593 1.069636 CGGTTGCTGTGAAGAAGCTTC 60.070 52.381 19.11 19.11 41.42 3.86
1303 2594 1.949525 GGTTGCTGTGAAGAAGCTTCA 59.050 47.619 27.57 5.80 41.42 3.02
1400 2691 9.765295 AATATAGTACGGTTCCTAGGATATTGT 57.235 33.333 13.57 11.47 0.00 2.71
1426 2717 2.445525 ACACACAAGGGGAAATGGTAGT 59.554 45.455 0.00 0.00 0.00 2.73
1584 3062 8.779354 ATTTAGTGTTTAGTGATTGAGGACTC 57.221 34.615 0.00 0.00 0.00 3.36
1764 3850 7.010552 CCGGCAAATATACTGCTAGATGATAAC 59.989 40.741 9.02 0.00 39.82 1.89
1797 3883 7.312154 CGAAAATTGGTGATTTTGGTCTATCA 58.688 34.615 1.82 0.00 45.54 2.15
1808 3894 3.071874 TGGTCTATCAAGGTGCTTTGG 57.928 47.619 0.00 0.00 0.00 3.28
2179 4956 7.652105 TCATTCTTCCATTTAGACGTAGCATAC 59.348 37.037 0.00 0.00 38.50 2.39
2184 4961 5.538813 TCCATTTAGACGTAGCATACCATCT 59.461 40.000 0.00 0.00 38.71 2.90
2211 4988 8.840833 TTTTGTATCACATAGTACTGCAAAGA 57.159 30.769 5.39 0.00 0.00 2.52
2225 5002 3.307674 TGCAAAGAACAAATTAGCTGCG 58.692 40.909 0.00 0.00 0.00 5.18
2232 5009 3.641437 ACAAATTAGCTGCGCAAGAAA 57.359 38.095 13.05 5.95 43.02 2.52
2236 5013 2.686558 TTAGCTGCGCAAGAAACAAG 57.313 45.000 13.05 0.00 43.02 3.16
2239 5016 0.665369 GCTGCGCAAGAAACAAGCAT 60.665 50.000 13.05 0.00 43.02 3.79
2240 5017 1.774639 CTGCGCAAGAAACAAGCATT 58.225 45.000 13.05 0.00 43.02 3.56
2381 5169 8.175069 GTGTAACATGTTTATAGTGATGTGTGG 58.825 37.037 17.78 0.00 36.32 4.17
2468 5424 7.624360 TTGGTTGCTATAATACAGTTTCCTG 57.376 36.000 0.00 0.00 44.68 3.86
2489 5446 7.060421 TCCTGTCTAAAATGTTTCTCCTTTGT 58.940 34.615 0.00 0.00 0.00 2.83
2492 5449 8.287439 TGTCTAAAATGTTTCTCCTTTGTCAA 57.713 30.769 0.00 0.00 0.00 3.18
2536 5493 8.301252 TCTAGGCTCATTATGTTAGTGTGTTA 57.699 34.615 0.00 0.00 0.00 2.41
2702 8559 2.847327 AGATATGCGGAAGATGGGTG 57.153 50.000 0.00 0.00 0.00 4.61
2758 8619 3.213506 CCCATGATGGCAATTTCGTAGA 58.786 45.455 5.79 0.00 35.79 2.59
3015 9237 7.759489 TGCCTTATGAAACTTCTTATGTGTT 57.241 32.000 0.00 0.00 0.00 3.32
3189 9418 9.128404 ACAGATATGTACAATTTTGCATCTCAT 57.872 29.630 0.00 0.00 0.00 2.90
3228 9458 9.996554 ACGAAATTATGACCATGATATCTGTTA 57.003 29.630 3.98 0.00 0.00 2.41
3238 9468 9.941325 GACCATGATATCTGTTATGATCTTTCT 57.059 33.333 3.98 0.00 0.00 2.52
3300 9542 3.019564 CCCACAATTGGTCCAGAGAATC 58.980 50.000 10.83 0.00 42.10 2.52
3454 9704 6.220726 TGTGGAAGAATCACTAATCATCGA 57.779 37.500 0.00 0.00 36.21 3.59
3479 9729 7.555087 AGAGGACTGAAGAAAGAGATAACATG 58.445 38.462 0.00 0.00 0.00 3.21
3482 9732 7.400339 AGGACTGAAGAAAGAGATAACATGGTA 59.600 37.037 0.00 0.00 0.00 3.25
3604 9860 2.930950 TGCTCAGTTTGCAGGTTACTT 58.069 42.857 0.00 0.00 35.31 2.24
3870 10133 4.318332 TGTAACCACAAGAGATGAAGCAG 58.682 43.478 0.00 0.00 0.00 4.24
4531 15691 2.113807 TGCTGCAGAGTGATAGATGGT 58.886 47.619 20.43 0.00 0.00 3.55
4613 15773 3.334691 TCTTGGCCGATCAAGTAAACAG 58.665 45.455 14.30 0.00 43.25 3.16
4627 15787 6.993308 TCAAGTAAACAGTAATGGCAGTGTTA 59.007 34.615 0.00 0.00 40.39 2.41
4779 15940 4.035675 GCATTTTCACTAGGTACATGCCTC 59.964 45.833 0.00 0.00 39.94 4.70
4780 15941 3.906720 TTTCACTAGGTACATGCCTCC 57.093 47.619 0.00 0.00 39.94 4.30
4781 15942 1.789523 TCACTAGGTACATGCCTCCC 58.210 55.000 0.00 0.00 39.94 4.30
4782 15943 1.291033 TCACTAGGTACATGCCTCCCT 59.709 52.381 0.00 0.00 39.94 4.20
4783 15944 1.414181 CACTAGGTACATGCCTCCCTG 59.586 57.143 0.00 0.00 39.94 4.45
4784 15945 1.008449 ACTAGGTACATGCCTCCCTGT 59.992 52.381 0.00 0.00 39.94 4.00
4785 15946 1.689273 CTAGGTACATGCCTCCCTGTC 59.311 57.143 0.00 0.00 39.94 3.51
4786 15947 0.043334 AGGTACATGCCTCCCTGTCT 59.957 55.000 0.00 0.00 32.39 3.41
4787 15948 0.912486 GGTACATGCCTCCCTGTCTT 59.088 55.000 0.00 0.00 0.00 3.01
4788 15949 1.407437 GGTACATGCCTCCCTGTCTTG 60.407 57.143 0.00 0.00 0.00 3.02
4789 15950 0.911769 TACATGCCTCCCTGTCTTGG 59.088 55.000 0.00 0.00 0.00 3.61
4790 15951 0.842030 ACATGCCTCCCTGTCTTGGA 60.842 55.000 0.00 0.00 0.00 3.53
4791 15952 0.549950 CATGCCTCCCTGTCTTGGAT 59.450 55.000 0.00 0.00 0.00 3.41
4792 15953 1.064166 CATGCCTCCCTGTCTTGGATT 60.064 52.381 0.00 0.00 0.00 3.01
4793 15954 1.075601 TGCCTCCCTGTCTTGGATTT 58.924 50.000 0.00 0.00 0.00 2.17
4794 15955 2.274542 TGCCTCCCTGTCTTGGATTTA 58.725 47.619 0.00 0.00 0.00 1.40
4795 15956 2.647299 TGCCTCCCTGTCTTGGATTTAA 59.353 45.455 0.00 0.00 0.00 1.52
4796 15957 3.282885 GCCTCCCTGTCTTGGATTTAAG 58.717 50.000 0.00 0.00 0.00 1.85
4797 15958 3.308473 GCCTCCCTGTCTTGGATTTAAGT 60.308 47.826 0.00 0.00 0.00 2.24
4798 15959 4.265073 CCTCCCTGTCTTGGATTTAAGTG 58.735 47.826 0.00 0.00 0.00 3.16
4799 15960 4.019321 CCTCCCTGTCTTGGATTTAAGTGA 60.019 45.833 0.00 0.00 0.00 3.41
4800 15961 5.514834 CCTCCCTGTCTTGGATTTAAGTGAA 60.515 44.000 0.00 0.00 0.00 3.18
4801 15962 6.139679 TCCCTGTCTTGGATTTAAGTGAAT 57.860 37.500 0.00 0.00 0.00 2.57
4802 15963 5.945784 TCCCTGTCTTGGATTTAAGTGAATG 59.054 40.000 0.00 0.00 0.00 2.67
4905 16066 1.270041 GCTCCAAGGATCCGAGATCAC 60.270 57.143 16.75 0.00 0.00 3.06
5007 16174 5.563475 GCCGGATTCAATTGGTGATATGAAG 60.563 44.000 5.05 0.00 35.70 3.02
5148 16318 1.792367 GCTTTTGGCGGCTTTACAAAG 59.208 47.619 11.43 11.27 35.74 2.77
5311 16484 2.105006 TGACATCTTGCTTGGCTCTC 57.895 50.000 0.00 0.00 0.00 3.20
5367 16546 2.183679 ACTGAGAATCGAGGGCTTTCT 58.816 47.619 0.00 0.00 38.61 2.52
5400 16579 2.745968 AGTTTTGGCAACCTCAGGAAA 58.254 42.857 0.00 0.00 0.00 3.13
5508 16687 9.191995 CTAAATGTGGACAACTTTGTTAAATCC 57.808 33.333 0.00 0.00 42.43 3.01
5517 16696 2.413310 TTGTTAAATCCGGGCTCTCC 57.587 50.000 0.00 0.00 0.00 3.71
5527 16706 1.954927 CGGGCTCTCCTGGTTAAATC 58.045 55.000 0.00 0.00 35.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.615211 CAACATATTCTTCCTCGATGAAAATGA 58.385 33.333 15.23 4.98 31.36 2.57
6 7 8.400947 CACAACATATTCTTCCTCGATGAAAAT 58.599 33.333 4.66 9.28 31.36 1.82
7 8 7.148255 CCACAACATATTCTTCCTCGATGAAAA 60.148 37.037 4.66 3.38 31.36 2.29
8 9 6.316140 CCACAACATATTCTTCCTCGATGAAA 59.684 38.462 4.66 0.00 31.36 2.69
9 10 5.817296 CCACAACATATTCTTCCTCGATGAA 59.183 40.000 3.05 3.05 31.95 2.57
10 11 5.104941 ACCACAACATATTCTTCCTCGATGA 60.105 40.000 0.00 0.00 0.00 2.92
11 12 5.118990 ACCACAACATATTCTTCCTCGATG 58.881 41.667 0.00 0.00 0.00 3.84
12 13 5.359194 ACCACAACATATTCTTCCTCGAT 57.641 39.130 0.00 0.00 0.00 3.59
13 14 4.819105 ACCACAACATATTCTTCCTCGA 57.181 40.909 0.00 0.00 0.00 4.04
14 15 5.416083 TGTACCACAACATATTCTTCCTCG 58.584 41.667 0.00 0.00 0.00 4.63
15 16 6.640518 TCTGTACCACAACATATTCTTCCTC 58.359 40.000 0.00 0.00 0.00 3.71
16 17 6.620877 TCTGTACCACAACATATTCTTCCT 57.379 37.500 0.00 0.00 0.00 3.36
17 18 7.606456 TCTTTCTGTACCACAACATATTCTTCC 59.394 37.037 0.00 0.00 0.00 3.46
18 19 8.547967 TCTTTCTGTACCACAACATATTCTTC 57.452 34.615 0.00 0.00 0.00 2.87
19 20 9.520515 AATCTTTCTGTACCACAACATATTCTT 57.479 29.630 0.00 0.00 0.00 2.52
20 21 8.950210 CAATCTTTCTGTACCACAACATATTCT 58.050 33.333 0.00 0.00 0.00 2.40
21 22 8.946085 TCAATCTTTCTGTACCACAACATATTC 58.054 33.333 0.00 0.00 0.00 1.75
22 23 8.862325 TCAATCTTTCTGTACCACAACATATT 57.138 30.769 0.00 0.00 0.00 1.28
23 24 8.730680 GTTCAATCTTTCTGTACCACAACATAT 58.269 33.333 0.00 0.00 0.00 1.78
24 25 7.174253 GGTTCAATCTTTCTGTACCACAACATA 59.826 37.037 0.00 0.00 35.09 2.29
25 26 6.016276 GGTTCAATCTTTCTGTACCACAACAT 60.016 38.462 0.00 0.00 35.09 2.71
26 27 5.298276 GGTTCAATCTTTCTGTACCACAACA 59.702 40.000 0.00 0.00 35.09 3.33
27 28 5.298276 TGGTTCAATCTTTCTGTACCACAAC 59.702 40.000 0.00 0.00 38.77 3.32
28 29 5.441500 TGGTTCAATCTTTCTGTACCACAA 58.558 37.500 0.00 0.00 38.77 3.33
29 30 5.042463 TGGTTCAATCTTTCTGTACCACA 57.958 39.130 0.00 0.00 38.77 4.17
30 31 4.083271 GCTGGTTCAATCTTTCTGTACCAC 60.083 45.833 0.00 0.00 38.77 4.16
31 32 4.072131 GCTGGTTCAATCTTTCTGTACCA 58.928 43.478 0.00 0.00 40.64 3.25
32 33 3.440522 GGCTGGTTCAATCTTTCTGTACC 59.559 47.826 0.00 0.00 35.43 3.34
33 34 4.072131 TGGCTGGTTCAATCTTTCTGTAC 58.928 43.478 0.00 0.00 0.00 2.90
34 35 4.365514 TGGCTGGTTCAATCTTTCTGTA 57.634 40.909 0.00 0.00 0.00 2.74
35 36 3.228188 TGGCTGGTTCAATCTTTCTGT 57.772 42.857 0.00 0.00 0.00 3.41
36 37 4.796038 AATGGCTGGTTCAATCTTTCTG 57.204 40.909 0.00 0.00 0.00 3.02
37 38 4.834496 TCAAATGGCTGGTTCAATCTTTCT 59.166 37.500 0.00 0.00 0.00 2.52
38 39 5.138125 TCAAATGGCTGGTTCAATCTTTC 57.862 39.130 0.00 0.00 0.00 2.62
39 40 4.020839 CCTCAAATGGCTGGTTCAATCTTT 60.021 41.667 0.00 0.00 0.00 2.52
40 41 3.512724 CCTCAAATGGCTGGTTCAATCTT 59.487 43.478 0.00 0.00 0.00 2.40
41 42 3.094572 CCTCAAATGGCTGGTTCAATCT 58.905 45.455 0.00 0.00 0.00 2.40
42 43 3.515330 CCTCAAATGGCTGGTTCAATC 57.485 47.619 0.00 0.00 0.00 2.67
53 54 2.353011 GGTGTGTGATTGCCTCAAATGG 60.353 50.000 0.00 0.00 35.07 3.16
54 55 2.296752 TGGTGTGTGATTGCCTCAAATG 59.703 45.455 0.00 0.00 35.07 2.32
55 56 2.297033 GTGGTGTGTGATTGCCTCAAAT 59.703 45.455 0.00 0.00 35.07 2.32
56 57 1.680735 GTGGTGTGTGATTGCCTCAAA 59.319 47.619 0.00 0.00 35.07 2.69
57 58 1.317613 GTGGTGTGTGATTGCCTCAA 58.682 50.000 0.00 0.00 35.07 3.02
58 59 0.182299 TGTGGTGTGTGATTGCCTCA 59.818 50.000 0.00 0.00 0.00 3.86
59 60 0.593128 GTGTGGTGTGTGATTGCCTC 59.407 55.000 0.00 0.00 0.00 4.70
60 61 0.106769 TGTGTGGTGTGTGATTGCCT 60.107 50.000 0.00 0.00 0.00 4.75
61 62 0.743688 TTGTGTGGTGTGTGATTGCC 59.256 50.000 0.00 0.00 0.00 4.52
62 63 2.798976 ATTGTGTGGTGTGTGATTGC 57.201 45.000 0.00 0.00 0.00 3.56
82 83 4.758165 GGAAGTGATAAGTCCGTGGAAAAA 59.242 41.667 0.00 0.00 0.00 1.94
83 84 4.320870 GGAAGTGATAAGTCCGTGGAAAA 58.679 43.478 0.00 0.00 0.00 2.29
84 85 3.307199 GGGAAGTGATAAGTCCGTGGAAA 60.307 47.826 0.00 0.00 31.73 3.13
85 86 2.235402 GGGAAGTGATAAGTCCGTGGAA 59.765 50.000 0.00 0.00 31.73 3.53
86 87 1.829222 GGGAAGTGATAAGTCCGTGGA 59.171 52.381 0.00 0.00 31.73 4.02
87 88 1.831736 AGGGAAGTGATAAGTCCGTGG 59.168 52.381 0.00 0.00 31.73 4.94
88 89 2.761208 AGAGGGAAGTGATAAGTCCGTG 59.239 50.000 0.00 0.00 31.73 4.94
89 90 3.025262 GAGAGGGAAGTGATAAGTCCGT 58.975 50.000 0.00 0.00 31.73 4.69
90 91 3.024547 TGAGAGGGAAGTGATAAGTCCG 58.975 50.000 0.00 0.00 31.73 4.79
91 92 3.769844 TGTGAGAGGGAAGTGATAAGTCC 59.230 47.826 0.00 0.00 0.00 3.85
92 93 4.142049 CCTGTGAGAGGGAAGTGATAAGTC 60.142 50.000 0.00 0.00 38.36 3.01
93 94 3.772025 CCTGTGAGAGGGAAGTGATAAGT 59.228 47.826 0.00 0.00 38.36 2.24
94 95 4.026744 TCCTGTGAGAGGGAAGTGATAAG 58.973 47.826 0.00 0.00 43.06 1.73
95 96 4.026744 CTCCTGTGAGAGGGAAGTGATAA 58.973 47.826 0.00 0.00 43.06 1.75
96 97 3.269643 TCTCCTGTGAGAGGGAAGTGATA 59.730 47.826 0.00 0.00 42.73 2.15
97 98 2.043664 TCTCCTGTGAGAGGGAAGTGAT 59.956 50.000 0.00 0.00 42.73 3.06
98 99 1.429299 TCTCCTGTGAGAGGGAAGTGA 59.571 52.381 0.00 0.00 42.73 3.41
99 100 1.930251 TCTCCTGTGAGAGGGAAGTG 58.070 55.000 0.00 0.00 42.73 3.16
107 108 2.363018 CCCGGCTCTCCTGTGAGA 60.363 66.667 0.00 0.00 45.39 3.27
108 109 4.154347 GCCCGGCTCTCCTGTGAG 62.154 72.222 0.71 0.00 40.17 3.51
109 110 4.704103 AGCCCGGCTCTCCTGTGA 62.704 66.667 5.94 0.00 30.62 3.58
110 111 4.463879 CAGCCCGGCTCTCCTGTG 62.464 72.222 9.68 0.00 36.40 3.66
111 112 3.602075 TACAGCCCGGCTCTCCTGT 62.602 63.158 9.68 7.75 36.40 4.00
112 113 2.759973 TACAGCCCGGCTCTCCTG 60.760 66.667 9.68 0.85 36.40 3.86
113 114 2.760385 GTACAGCCCGGCTCTCCT 60.760 66.667 9.68 0.00 36.40 3.69
114 115 1.972660 ATTGTACAGCCCGGCTCTCC 61.973 60.000 9.68 0.02 36.40 3.71
115 116 0.530870 GATTGTACAGCCCGGCTCTC 60.531 60.000 9.68 3.52 36.40 3.20
116 117 1.522569 GATTGTACAGCCCGGCTCT 59.477 57.895 9.68 0.00 36.40 4.09
117 118 1.523938 GGATTGTACAGCCCGGCTC 60.524 63.158 9.68 0.00 36.40 4.70
118 119 2.590092 GGATTGTACAGCCCGGCT 59.410 61.111 5.94 5.94 40.77 5.52
119 120 2.516225 GGGATTGTACAGCCCGGC 60.516 66.667 17.16 0.00 31.06 6.13
120 121 2.192175 GGGGATTGTACAGCCCGG 59.808 66.667 22.47 0.00 42.99 5.73
121 122 1.451387 GTGGGGATTGTACAGCCCG 60.451 63.158 22.47 0.00 42.99 6.13
122 123 1.076995 GGTGGGGATTGTACAGCCC 60.077 63.158 21.69 21.69 41.28 5.19
123 124 1.141053 CTAGGTGGGGATTGTACAGCC 59.859 57.143 8.02 8.02 33.38 4.85
124 125 1.838077 ACTAGGTGGGGATTGTACAGC 59.162 52.381 0.00 0.00 0.00 4.40
125 126 3.370527 CCAACTAGGTGGGGATTGTACAG 60.371 52.174 20.00 0.00 34.77 2.74
126 127 2.574369 CCAACTAGGTGGGGATTGTACA 59.426 50.000 20.00 0.00 34.77 2.90
127 128 2.682858 GCCAACTAGGTGGGGATTGTAC 60.683 54.545 28.13 4.98 39.26 2.90
128 129 1.562475 GCCAACTAGGTGGGGATTGTA 59.438 52.381 28.13 0.00 39.26 2.41
129 130 0.331616 GCCAACTAGGTGGGGATTGT 59.668 55.000 28.13 0.00 39.26 2.71
130 131 0.331278 TGCCAACTAGGTGGGGATTG 59.669 55.000 28.13 4.52 39.26 2.67
131 132 1.080638 TTGCCAACTAGGTGGGGATT 58.919 50.000 28.13 0.00 39.26 3.01
132 133 1.063717 CATTGCCAACTAGGTGGGGAT 60.064 52.381 28.13 0.00 39.26 3.85
133 134 0.331278 CATTGCCAACTAGGTGGGGA 59.669 55.000 28.13 7.64 39.26 4.81
134 135 0.039618 ACATTGCCAACTAGGTGGGG 59.960 55.000 28.13 4.13 39.26 4.96
135 136 1.923356 AACATTGCCAACTAGGTGGG 58.077 50.000 28.13 13.74 39.26 4.61
136 137 3.823873 TGTTAACATTGCCAACTAGGTGG 59.176 43.478 23.41 23.41 42.05 4.61
137 138 5.446143 TTGTTAACATTGCCAACTAGGTG 57.554 39.130 9.56 0.00 40.61 4.00
138 139 4.022329 GCTTGTTAACATTGCCAACTAGGT 60.022 41.667 9.56 0.00 40.61 3.08
139 140 4.022416 TGCTTGTTAACATTGCCAACTAGG 60.022 41.667 22.77 0.00 41.84 3.02
140 141 5.119931 TGCTTGTTAACATTGCCAACTAG 57.880 39.130 22.77 11.12 0.00 2.57
141 142 5.068460 AGTTGCTTGTTAACATTGCCAACTA 59.932 36.000 25.55 11.49 32.73 2.24
142 143 4.119136 GTTGCTTGTTAACATTGCCAACT 58.881 39.130 22.77 0.00 0.00 3.16
143 144 4.119136 AGTTGCTTGTTAACATTGCCAAC 58.881 39.130 22.77 21.91 0.00 3.77
144 145 4.099266 AGAGTTGCTTGTTAACATTGCCAA 59.901 37.500 22.77 14.89 0.00 4.52
145 146 3.636300 AGAGTTGCTTGTTAACATTGCCA 59.364 39.130 22.77 14.27 0.00 4.92
155 156 4.999950 CCTATCTCAACAGAGTTGCTTGTT 59.000 41.667 5.06 0.00 29.82 2.83
171 172 0.375106 GCAAACGCAGTGCCTATCTC 59.625 55.000 10.11 0.00 45.00 2.75
172 173 0.321564 TGCAAACGCAGTGCCTATCT 60.322 50.000 10.11 0.00 45.00 1.98
221 222 1.298993 CCAGCTGGATGACACTGCT 59.701 57.895 29.88 0.00 42.74 4.24
244 245 0.248907 ATCCGATTACTCCGTGTGCG 60.249 55.000 0.00 0.00 37.95 5.34
246 247 5.402568 CAGAAATATCCGATTACTCCGTGTG 59.597 44.000 0.00 0.00 0.00 3.82
250 251 5.289675 GCATCAGAAATATCCGATTACTCCG 59.710 44.000 0.00 0.00 0.00 4.63
268 373 6.506500 AATAGGACAAAAGAACTGCATCAG 57.493 37.500 0.00 0.00 37.52 2.90
279 384 6.633500 TCCTGAACACAAATAGGACAAAAG 57.367 37.500 0.00 0.00 34.54 2.27
334 757 1.668101 GCCCAGTCCTGTCTAGACGG 61.668 65.000 22.75 22.75 39.31 4.79
369 792 0.453793 ACAGTCCTCTGAAGCGATCG 59.546 55.000 11.69 11.69 43.76 3.69
377 800 1.005332 AGCTCAGCTACAGTCCTCTGA 59.995 52.381 0.00 0.00 43.94 3.27
388 818 4.202060 CGATTACCTGAAGAAGCTCAGCTA 60.202 45.833 0.00 0.00 41.36 3.32
402 832 2.093973 AGTCCTGTGAAGCGATTACCTG 60.094 50.000 0.00 0.00 0.00 4.00
509 1042 5.746307 TGATAAAGAAGCAGCATGTCATC 57.254 39.130 0.00 0.00 39.31 2.92
511 1044 4.945543 ACATGATAAAGAAGCAGCATGTCA 59.054 37.500 0.00 0.00 41.55 3.58
531 1064 1.812571 GGTCCAAAGCGTCATGAACAT 59.187 47.619 0.00 0.00 0.00 2.71
637 1179 7.848223 ATTCCTTTGAAACAAGAAAAGGTTG 57.152 32.000 11.94 0.00 46.63 3.77
675 1217 4.934797 ATCCCAAAGAACAGAATCCTCA 57.065 40.909 0.00 0.00 0.00 3.86
741 1292 7.119116 TGCGTGTGAAATAGTTCATAGTCAAAT 59.881 33.333 9.08 0.00 45.38 2.32
742 1293 6.425417 TGCGTGTGAAATAGTTCATAGTCAAA 59.575 34.615 9.08 0.00 45.38 2.69
743 1294 5.929415 TGCGTGTGAAATAGTTCATAGTCAA 59.071 36.000 9.08 0.00 45.38 3.18
744 1295 5.474825 TGCGTGTGAAATAGTTCATAGTCA 58.525 37.500 9.08 4.58 45.38 3.41
745 1296 5.577164 ACTGCGTGTGAAATAGTTCATAGTC 59.423 40.000 9.08 2.11 45.38 2.59
746 1297 5.479306 ACTGCGTGTGAAATAGTTCATAGT 58.521 37.500 9.08 6.44 45.38 2.12
747 1298 6.408858 AACTGCGTGTGAAATAGTTCATAG 57.591 37.500 9.08 5.09 45.38 2.23
748 1299 6.403333 GAACTGCGTGTGAAATAGTTCATA 57.597 37.500 9.08 3.33 45.38 2.15
749 1300 5.283060 GAACTGCGTGTGAAATAGTTCAT 57.717 39.130 9.08 0.00 45.38 2.57
750 1301 4.725556 GAACTGCGTGTGAAATAGTTCA 57.274 40.909 0.56 0.56 43.98 3.18
751 1302 4.725556 TGAACTGCGTGTGAAATAGTTC 57.274 40.909 0.00 0.00 44.50 3.01
752 1303 5.493133 TTTGAACTGCGTGTGAAATAGTT 57.507 34.783 0.00 0.00 34.56 2.24
753 1304 5.493133 TTTTGAACTGCGTGTGAAATAGT 57.507 34.783 0.00 0.00 0.00 2.12
754 1305 8.015087 TCTTATTTTGAACTGCGTGTGAAATAG 58.985 33.333 0.00 0.00 0.00 1.73
755 1306 7.866729 TCTTATTTTGAACTGCGTGTGAAATA 58.133 30.769 0.00 0.00 0.00 1.40
763 1314 9.394477 GATAAAGTTTCTTATTTTGAACTGCGT 57.606 29.630 0.00 0.00 0.00 5.24
823 1952 6.038161 CACAAAACCACTCTTAACATCTCACA 59.962 38.462 0.00 0.00 0.00 3.58
824 1953 6.260050 TCACAAAACCACTCTTAACATCTCAC 59.740 38.462 0.00 0.00 0.00 3.51
825 1954 6.260050 GTCACAAAACCACTCTTAACATCTCA 59.740 38.462 0.00 0.00 0.00 3.27
826 1955 6.260050 TGTCACAAAACCACTCTTAACATCTC 59.740 38.462 0.00 0.00 0.00 2.75
827 1956 6.119536 TGTCACAAAACCACTCTTAACATCT 58.880 36.000 0.00 0.00 0.00 2.90
828 1957 6.371809 TGTCACAAAACCACTCTTAACATC 57.628 37.500 0.00 0.00 0.00 3.06
829 1958 6.321181 ACATGTCACAAAACCACTCTTAACAT 59.679 34.615 0.00 0.00 0.00 2.71
830 1959 5.650266 ACATGTCACAAAACCACTCTTAACA 59.350 36.000 0.00 0.00 0.00 2.41
831 1960 6.038271 AGACATGTCACAAAACCACTCTTAAC 59.962 38.462 27.02 0.00 0.00 2.01
872 2009 8.458573 TTCTTTTAGGAAAACATTAGACAGCA 57.541 30.769 0.00 0.00 0.00 4.41
973 2176 7.589395 TGCAGTTACAAACACAATACTATTGG 58.411 34.615 12.48 5.17 0.00 3.16
977 2180 8.079203 CCATTTGCAGTTACAAACACAATACTA 58.921 33.333 0.00 0.00 42.01 1.82
1094 2381 4.446385 CAGAAAAATTGCTGGTGATGTGTG 59.554 41.667 0.00 0.00 0.00 3.82
1095 2382 4.341806 TCAGAAAAATTGCTGGTGATGTGT 59.658 37.500 1.35 0.00 33.05 3.72
1113 2400 5.302568 ACAGCCAATTTCTTTGTCATCAGAA 59.697 36.000 0.00 0.00 33.15 3.02
1160 2447 7.014422 ACTGAGAGTTACTGTATAAGCATACCC 59.986 40.741 0.00 0.00 36.90 3.69
1302 2593 5.759763 TCTCATCCATATCAACCAAATCGTG 59.240 40.000 0.00 0.00 0.00 4.35
1303 2594 5.928976 TCTCATCCATATCAACCAAATCGT 58.071 37.500 0.00 0.00 0.00 3.73
1308 2599 8.827832 AATTTCTTCTCATCCATATCAACCAA 57.172 30.769 0.00 0.00 0.00 3.67
1400 2691 3.221771 CATTTCCCCTTGTGTGTCAGAA 58.778 45.455 0.00 0.00 0.00 3.02
1426 2717 4.503714 AAGACAAGTTTTCCCTCACAGA 57.496 40.909 0.00 0.00 0.00 3.41
1577 3051 6.231211 TGTATTTGAGAAACTTGGAGTCCTC 58.769 40.000 11.33 0.00 0.00 3.71
1584 3062 7.763985 AGTTGGTTTTGTATTTGAGAAACTTGG 59.236 33.333 0.00 0.00 33.65 3.61
1764 3850 3.023946 TCACCAATTTTCGGCAACATG 57.976 42.857 0.00 0.00 0.00 3.21
1808 3894 0.390492 AGCCTGGCTTTGCTTTTCAC 59.610 50.000 17.22 0.00 33.89 3.18
2152 4902 6.582636 TGCTACGTCTAAATGGAAGAATGAT 58.417 36.000 0.00 0.00 0.00 2.45
2153 4903 5.972935 TGCTACGTCTAAATGGAAGAATGA 58.027 37.500 0.00 0.00 0.00 2.57
2377 5165 6.134535 AGGATGTAAGGACAATTTACCACA 57.865 37.500 0.00 0.00 39.59 4.17
2381 5169 6.766467 CCCAGTAGGATGTAAGGACAATTTAC 59.234 42.308 0.00 0.00 39.59 2.01
2462 5418 8.413229 CAAAGGAGAAACATTTTAGACAGGAAA 58.587 33.333 0.00 0.00 29.81 3.13
2463 5419 7.559897 ACAAAGGAGAAACATTTTAGACAGGAA 59.440 33.333 0.00 0.00 29.81 3.36
2465 5421 7.013274 TGACAAAGGAGAAACATTTTAGACAGG 59.987 37.037 0.00 0.00 29.81 4.00
2466 5422 7.930217 TGACAAAGGAGAAACATTTTAGACAG 58.070 34.615 0.00 0.00 29.81 3.51
2467 5423 7.873719 TGACAAAGGAGAAACATTTTAGACA 57.126 32.000 0.00 0.00 29.81 3.41
2468 5424 9.750125 ATTTGACAAAGGAGAAACATTTTAGAC 57.250 29.630 6.77 0.00 29.81 2.59
2473 5429 8.260114 ACTCAATTTGACAAAGGAGAAACATTT 58.740 29.630 26.64 9.77 32.90 2.32
2474 5430 7.785033 ACTCAATTTGACAAAGGAGAAACATT 58.215 30.769 26.64 10.27 32.90 2.71
2476 5432 6.773976 ACTCAATTTGACAAAGGAGAAACA 57.226 33.333 26.64 0.00 32.90 2.83
2477 5433 7.931275 ACTACTCAATTTGACAAAGGAGAAAC 58.069 34.615 26.64 0.00 32.90 2.78
2478 5434 8.519799 AACTACTCAATTTGACAAAGGAGAAA 57.480 30.769 26.64 17.55 32.90 2.52
2479 5435 8.519799 AAACTACTCAATTTGACAAAGGAGAA 57.480 30.769 26.64 5.77 32.90 2.87
2511 5468 6.791867 ACACACTAACATAATGAGCCTAGA 57.208 37.500 0.00 0.00 0.00 2.43
2536 5493 9.447596 ACAAAGACTTGTAATTGCACAGCAAGT 62.448 37.037 18.78 18.78 46.66 3.16
2555 5512 1.745653 GCCTCCAGCCATTACAAAGAC 59.254 52.381 0.00 0.00 34.35 3.01
2577 5534 1.630369 TCATGCCACCTAGAAGCAACT 59.370 47.619 5.57 0.00 40.46 3.16
2738 8599 5.702670 AGTATCTACGAAATTGCCATCATGG 59.297 40.000 0.00 0.00 41.55 3.66
2758 8619 5.205056 CCTACTTCTCCACCTCTCAAGTAT 58.795 45.833 0.00 0.00 30.96 2.12
2844 8705 0.438830 GGTTAAAGTCAGCGCACTCG 59.561 55.000 11.47 0.00 39.07 4.18
3015 9237 0.250684 TGGAGAAAATGCAGCACCGA 60.251 50.000 0.00 0.00 0.00 4.69
3300 9542 7.396540 ACTTCTTTAACTCATTAGCCATTGG 57.603 36.000 0.00 0.00 0.00 3.16
3454 9704 7.364585 CCATGTTATCTCTTTCTTCAGTCCTCT 60.365 40.741 0.00 0.00 0.00 3.69
3479 9729 6.949463 AGATACTCCCAGATAAAGTAGCTACC 59.051 42.308 20.31 4.64 39.67 3.18
3482 9732 6.492087 GTGAGATACTCCCAGATAAAGTAGCT 59.508 42.308 0.00 0.00 42.99 3.32
3604 9860 4.913784 GGACACATAGACCCAAACCTTAA 58.086 43.478 0.00 0.00 0.00 1.85
3803 10066 4.943705 ACACCAACTCTTAACATAGCCATG 59.056 41.667 0.00 0.00 38.21 3.66
3870 10133 5.537188 TGTATGACAAATTTCCCTTGCAAC 58.463 37.500 0.00 0.00 0.00 4.17
3988 10271 6.365970 TCTCCCTTCCTATATGCTTCAATC 57.634 41.667 0.00 0.00 0.00 2.67
4488 15633 7.389053 AGCAAAGAAGACCTAATTGTGTTAGAG 59.611 37.037 0.00 0.00 0.00 2.43
4531 15691 6.257849 GTGAACAGTGTAACATCTTTGTCTCA 59.742 38.462 0.00 0.00 41.43 3.27
4613 15773 5.451798 CCATTTCCCATAACACTGCCATTAC 60.452 44.000 0.00 0.00 0.00 1.89
4627 15787 3.816842 GCATAGAGGCATCCATTTCCCAT 60.817 47.826 0.00 0.00 0.00 4.00
4779 15940 5.393461 GCATTCACTTAAATCCAAGACAGGG 60.393 44.000 0.00 0.00 0.00 4.45
4780 15941 5.393461 GGCATTCACTTAAATCCAAGACAGG 60.393 44.000 0.00 0.00 0.00 4.00
4781 15942 5.644644 GGCATTCACTTAAATCCAAGACAG 58.355 41.667 0.00 0.00 0.00 3.51
4782 15943 4.155826 CGGCATTCACTTAAATCCAAGACA 59.844 41.667 0.00 0.00 0.00 3.41
4783 15944 4.156008 ACGGCATTCACTTAAATCCAAGAC 59.844 41.667 0.00 0.00 0.00 3.01
4784 15945 4.155826 CACGGCATTCACTTAAATCCAAGA 59.844 41.667 0.00 0.00 0.00 3.02
4785 15946 4.082787 ACACGGCATTCACTTAAATCCAAG 60.083 41.667 0.00 0.00 0.00 3.61
4786 15947 3.823873 ACACGGCATTCACTTAAATCCAA 59.176 39.130 0.00 0.00 0.00 3.53
4787 15948 3.417101 ACACGGCATTCACTTAAATCCA 58.583 40.909 0.00 0.00 0.00 3.41
4788 15949 3.689649 AGACACGGCATTCACTTAAATCC 59.310 43.478 0.00 0.00 0.00 3.01
4789 15950 4.946784 AGACACGGCATTCACTTAAATC 57.053 40.909 0.00 0.00 0.00 2.17
4790 15951 4.082787 CCAAGACACGGCATTCACTTAAAT 60.083 41.667 0.00 0.00 0.00 1.40
4791 15952 3.252215 CCAAGACACGGCATTCACTTAAA 59.748 43.478 0.00 0.00 0.00 1.52
4792 15953 2.811431 CCAAGACACGGCATTCACTTAA 59.189 45.455 0.00 0.00 0.00 1.85
4793 15954 2.037902 TCCAAGACACGGCATTCACTTA 59.962 45.455 0.00 0.00 0.00 2.24
4794 15955 1.202758 TCCAAGACACGGCATTCACTT 60.203 47.619 0.00 0.00 0.00 3.16
4795 15956 0.396435 TCCAAGACACGGCATTCACT 59.604 50.000 0.00 0.00 0.00 3.41
4796 15957 1.453155 ATCCAAGACACGGCATTCAC 58.547 50.000 0.00 0.00 0.00 3.18
4797 15958 2.198827 AATCCAAGACACGGCATTCA 57.801 45.000 0.00 0.00 0.00 2.57
4798 15959 4.156008 ACTTAAATCCAAGACACGGCATTC 59.844 41.667 0.00 0.00 0.00 2.67
4799 15960 4.079253 ACTTAAATCCAAGACACGGCATT 58.921 39.130 0.00 0.00 0.00 3.56
4800 15961 3.440173 CACTTAAATCCAAGACACGGCAT 59.560 43.478 0.00 0.00 0.00 4.40
4801 15962 2.811431 CACTTAAATCCAAGACACGGCA 59.189 45.455 0.00 0.00 0.00 5.69
4802 15963 3.071479 TCACTTAAATCCAAGACACGGC 58.929 45.455 0.00 0.00 0.00 5.68
4905 16066 4.821260 TCGGTGATACAATTGGGAATCATG 59.179 41.667 17.83 14.63 31.49 3.07
5007 16174 3.488778 AGATCAAGATGCATCAGACCC 57.511 47.619 27.81 18.10 0.00 4.46
5121 16291 1.134551 AAGCCGCCAAAAGCTTTTGAA 60.135 42.857 40.43 0.00 46.99 2.69
5184 16354 4.402793 GTCAGACCTCTCCTATTTGCTACA 59.597 45.833 0.00 0.00 0.00 2.74
5297 16470 0.036577 GCTGAGAGAGCCAAGCAAGA 60.037 55.000 0.00 0.00 42.54 3.02
5311 16484 5.336150 TCTAGATTGGAAAGAGTGCTGAG 57.664 43.478 0.00 0.00 0.00 3.35
5319 16492 4.964897 TCCAGATGCTCTAGATTGGAAAGA 59.035 41.667 0.00 0.00 32.15 2.52
5347 16520 2.183679 AGAAAGCCCTCGATTCTCAGT 58.816 47.619 0.00 0.00 0.00 3.41
5367 16546 6.431852 GGTTGCCAAAACTTTCTGGTATACTA 59.568 38.462 2.25 0.00 34.97 1.82
5400 16579 5.455326 GCCTATGAGGTCCAATGTATGAAGT 60.455 44.000 0.00 0.00 37.80 3.01
5508 16687 1.486726 AGATTTAACCAGGAGAGCCCG 59.513 52.381 0.00 0.00 40.87 6.13


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

AutoCloner maintained by Alex Coulton.