Multiple sequence alignment - TraesCS5B01G082600

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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 TraesCS5B01G082600 chr5B 100.000 7765 0 0 1 7765 103470488 103462724 0.000000e+00 14340.0
1 TraesCS5B01G082600 chr5B 98.053 3235 45 6 2751 5976 105698908 105695683 0.000000e+00 5609.0
2 TraesCS5B01G082600 chr5B 93.095 2433 86 23 354 2749 105701364 105698977 0.000000e+00 3487.0
3 TraesCS5B01G082600 chr5B 93.088 680 19 9 6531 7192 105689118 105688449 0.000000e+00 970.0
4 TraesCS5B01G082600 chr5B 93.952 463 19 3 7191 7648 105688191 105687733 0.000000e+00 691.0
5 TraesCS5B01G082600 chr5B 98.000 350 5 1 1 348 105702065 105701716 2.400000e-169 606.0
6 TraesCS5B01G082600 chr5B 97.863 234 5 0 5972 6205 105693798 105693565 9.380000e-109 405.0
7 TraesCS5B01G082600 chr5B 95.522 201 9 0 6335 6535 105693567 105693367 9.720000e-84 322.0
8 TraesCS5B01G082600 chr5B 92.188 64 5 0 7519 7582 430166122 430166185 2.980000e-14 91.6
9 TraesCS5B01G082600 chr5B 92.188 64 5 0 7519 7582 430264171 430264234 2.980000e-14 91.6
10 TraesCS5B01G082600 chr5D 88.921 2085 129 54 1 2004 97274746 97272683 0.000000e+00 2477.0
11 TraesCS5B01G082600 chr5D 91.868 1611 102 14 2751 4355 97266104 97264517 0.000000e+00 2222.0
12 TraesCS5B01G082600 chr5D 90.538 1300 94 16 4340 5628 97264497 97263216 0.000000e+00 1692.0
13 TraesCS5B01G082600 chr5D 92.296 649 40 6 6341 6986 97262751 97262110 0.000000e+00 913.0
14 TraesCS5B01G082600 chr5D 92.883 548 24 5 7200 7739 97261994 97261454 0.000000e+00 782.0
15 TraesCS5B01G082600 chr5D 94.092 457 19 6 2126 2580 97271984 97271534 0.000000e+00 688.0
16 TraesCS5B01G082600 chr5D 88.199 483 31 7 5724 6205 97263207 97262750 3.170000e-153 553.0
17 TraesCS5B01G082600 chr5D 89.213 445 23 7 6760 7188 97074130 97073695 4.120000e-147 532.0
18 TraesCS5B01G082600 chr5D 92.444 225 11 2 6552 6775 97187568 97187349 4.520000e-82 316.0
19 TraesCS5B01G082600 chr5D 91.477 176 13 1 2574 2749 97266347 97266174 2.800000e-59 241.0
20 TraesCS5B01G082600 chr5D 91.071 168 14 1 7008 7174 204324442 204324609 7.840000e-55 226.0
21 TraesCS5B01G082600 chr5D 86.765 204 12 2 5792 5995 97187750 97187562 6.100000e-51 213.0
22 TraesCS5B01G082600 chr5D 93.878 98 5 1 5625 5721 87186600 87186503 6.280000e-31 147.0
23 TraesCS5B01G082600 chr5D 88.983 118 9 4 5623 5738 216627857 216627742 8.120000e-30 143.0
24 TraesCS5B01G082600 chr5D 89.908 109 9 2 5854 5962 97073685 97073579 1.050000e-28 139.0
25 TraesCS5B01G082600 chr5D 85.926 135 14 4 2751 2884 291507904 291508034 1.050000e-28 139.0
26 TraesCS5B01G082600 chr5D 87.500 96 6 2 2030 2125 97272179 97272090 1.070000e-18 106.0
27 TraesCS5B01G082600 chr3A 83.638 2732 302 77 2901 5587 110315430 110318061 0.000000e+00 2435.0
28 TraesCS5B01G082600 chr3A 86.864 944 110 11 875 1811 110310004 110310940 0.000000e+00 1044.0
29 TraesCS5B01G082600 chr3A 86.283 452 51 8 5715 6162 110318094 110318538 1.520000e-131 481.0
30 TraesCS5B01G082600 chr3A 82.042 568 67 22 2098 2641 110314869 110315425 1.190000e-122 451.0
31 TraesCS5B01G082600 chr3A 84.935 385 53 4 6531 6914 110319152 110319532 1.220000e-102 385.0
32 TraesCS5B01G082600 chr3A 92.593 162 12 0 7012 7173 600921016 600920855 4.680000e-57 233.0
33 TraesCS5B01G082600 chr3D 83.552 2742 301 77 2884 5572 114322332 114324976 0.000000e+00 2427.0
34 TraesCS5B01G082600 chr3D 86.850 943 113 9 875 1811 114318714 114319651 0.000000e+00 1044.0
35 TraesCS5B01G082600 chr3D 83.533 583 75 12 6336 6916 114325542 114326105 6.900000e-145 525.0
36 TraesCS5B01G082600 chr3D 86.406 434 48 8 5722 6151 114325071 114325497 1.530000e-126 464.0
37 TraesCS5B01G082600 chr3D 82.074 569 72 15 2098 2641 114321781 114322344 7.100000e-125 459.0
38 TraesCS5B01G082600 chr3D 92.381 105 4 4 5617 5720 526509288 526509389 6.280000e-31 147.0
39 TraesCS5B01G082600 chr5A 90.985 1431 108 12 2771 4192 92438556 92437138 0.000000e+00 1908.0
40 TraesCS5B01G082600 chr5A 92.037 1281 92 8 537 1809 92442193 92440915 0.000000e+00 1792.0
41 TraesCS5B01G082600 chr5A 91.331 1292 91 10 4340 5628 92431337 92430064 0.000000e+00 1746.0
42 TraesCS5B01G082600 chr5A 90.741 648 46 7 6341 6986 92429599 92428964 0.000000e+00 852.0
43 TraesCS5B01G082600 chr5A 92.746 579 18 7 7200 7765 92428849 92428282 0.000000e+00 815.0
44 TraesCS5B01G082600 chr5A 87.405 659 65 16 2101 2749 92439260 92438610 0.000000e+00 741.0
45 TraesCS5B01G082600 chr5A 88.091 529 25 15 1 509 92442780 92442270 1.870000e-165 593.0
46 TraesCS5B01G082600 chr5A 89.027 483 27 7 5724 6205 92430055 92429598 6.760000e-160 575.0
47 TraesCS5B01G082600 chr5A 90.047 211 15 2 1826 2035 92440865 92440660 1.280000e-67 268.0
48 TraesCS5B01G082600 chr5A 94.156 154 6 2 6194 6345 48729086 48728934 1.690000e-56 231.0
49 TraesCS5B01G082600 chr5A 88.304 171 18 2 5792 5962 92223050 92222882 3.670000e-48 204.0
50 TraesCS5B01G082600 chr3B 82.942 1489 155 53 2901 4358 166516880 166515460 0.000000e+00 1251.0
51 TraesCS5B01G082600 chr3B 85.926 945 115 12 875 1814 166520554 166519623 0.000000e+00 992.0
52 TraesCS5B01G082600 chr3B 85.873 899 100 15 4593 5479 166515419 166514536 0.000000e+00 931.0
53 TraesCS5B01G082600 chr3B 82.872 578 76 16 6343 6916 166514015 166513457 1.500000e-136 497.0
54 TraesCS5B01G082600 chr3B 85.872 453 52 9 5715 6162 166514504 166514059 9.120000e-129 472.0
55 TraesCS5B01G082600 chr3B 81.836 523 66 22 2141 2641 166517400 166516885 5.610000e-111 412.0
56 TraesCS5B01G082600 chr3B 92.188 64 5 0 7519 7582 202592084 202592021 2.980000e-14 91.6
57 TraesCS5B01G082600 chr2D 92.593 162 12 0 7012 7173 134301649 134301488 4.680000e-57 233.0
58 TraesCS5B01G082600 chr2D 91.975 162 13 0 7012 7173 560153887 560154048 2.180000e-55 228.0
59 TraesCS5B01G082600 chr2D 96.667 90 2 1 5628 5716 203023987 203023898 1.750000e-31 148.0
60 TraesCS5B01G082600 chr2D 93.878 98 4 2 5626 5722 164992770 164992674 6.280000e-31 147.0
61 TraesCS5B01G082600 chr2D 83.516 91 14 1 2794 2884 498530905 498530816 4.990000e-12 84.2
62 TraesCS5B01G082600 chr1B 91.765 170 11 3 7012 7180 314565539 314565706 4.680000e-57 233.0
63 TraesCS5B01G082600 chr1B 82.946 129 20 2 2753 2880 249519847 249519974 1.770000e-21 115.0
64 TraesCS5B01G082600 chr1A 91.667 168 14 0 7012 7179 59114658 59114491 4.680000e-57 233.0
65 TraesCS5B01G082600 chr1A 96.296 135 5 0 6203 6337 539280687 539280553 1.010000e-53 222.0
66 TraesCS5B01G082600 chr1A 82.883 111 17 2 2777 2886 227259067 227258958 1.780000e-16 99.0
67 TraesCS5B01G082600 chr4A 95.833 144 4 2 6205 6346 644456550 644456407 1.690000e-56 231.0
68 TraesCS5B01G082600 chr6B 97.059 136 4 0 6202 6337 135790408 135790543 6.060000e-56 230.0
69 TraesCS5B01G082600 chr6B 97.710 131 3 0 6205 6335 341984739 341984869 7.840000e-55 226.0
70 TraesCS5B01G082600 chr6B 97.015 134 3 1 6205 6337 508476816 508476949 2.820000e-54 224.0
71 TraesCS5B01G082600 chr6B 95.000 100 3 2 5621 5719 8403543 8403641 1.040000e-33 156.0
72 TraesCS5B01G082600 chr2A 96.350 137 5 0 6203 6339 444641509 444641373 7.840000e-55 226.0
73 TraesCS5B01G082600 chr2A 96.324 136 5 0 6200 6335 715929166 715929031 2.820000e-54 224.0
74 TraesCS5B01G082600 chr2A 96.296 135 5 0 6203 6337 718966124 718966258 1.010000e-53 222.0
75 TraesCS5B01G082600 chr2A 83.721 129 17 2 2760 2884 500525744 500525872 1.370000e-22 119.0
76 TraesCS5B01G082600 chr2A 87.755 98 12 0 2787 2884 500525318 500525415 1.770000e-21 115.0
77 TraesCS5B01G082600 chr6A 91.411 163 14 0 7011 7173 91902405 91902567 2.820000e-54 224.0
78 TraesCS5B01G082600 chr7D 96.774 93 2 1 5625 5716 519264543 519264635 3.750000e-33 154.0
79 TraesCS5B01G082600 chr1D 90.826 109 5 5 5611 5715 355171678 355171571 2.920000e-29 141.0
80 TraesCS5B01G082600 chrUn 92.188 64 5 0 7519 7582 342508728 342508665 2.980000e-14 91.6
81 TraesCS5B01G082600 chrUn 92.188 64 5 0 7519 7582 382684882 382684945 2.980000e-14 91.6
82 TraesCS5B01G082600 chrUn 92.188 64 5 0 7519 7582 399641449 399641512 2.980000e-14 91.6
83 TraesCS5B01G082600 chr7A 87.097 62 6 2 2776 2836 724037881 724037821 1.400000e-07 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G082600 chr5B 103462724 103470488 7764 True 14340.000000 14340 100.000000 1 7765 1 chr5B.!!$R1 7764
1 TraesCS5B01G082600 chr5B 105693367 105702065 8698 True 2085.800000 5609 96.506600 1 6535 5 chr5B.!!$R3 6534
2 TraesCS5B01G082600 chr5B 105687733 105689118 1385 True 830.500000 970 93.520000 6531 7648 2 chr5B.!!$R2 1117
3 TraesCS5B01G082600 chr5D 97271534 97274746 3212 True 1090.333333 2477 90.171000 1 2580 3 chr5D.!!$R6 2579
4 TraesCS5B01G082600 chr5D 97261454 97266347 4893 True 1067.166667 2222 91.210167 2574 7739 6 chr5D.!!$R5 5165
5 TraesCS5B01G082600 chr5D 97073579 97074130 551 True 335.500000 532 89.560500 5854 7188 2 chr5D.!!$R3 1334
6 TraesCS5B01G082600 chr3A 110310004 110319532 9528 False 959.200000 2435 84.752400 875 6914 5 chr3A.!!$F1 6039
7 TraesCS5B01G082600 chr3D 114318714 114326105 7391 False 983.800000 2427 84.483000 875 6916 5 chr3D.!!$F2 6041
8 TraesCS5B01G082600 chr5A 92437138 92442780 5642 True 1060.400000 1908 89.713000 1 4192 5 chr5A.!!$R4 4191
9 TraesCS5B01G082600 chr5A 92428282 92431337 3055 True 997.000000 1746 90.961250 4340 7765 4 chr5A.!!$R3 3425
10 TraesCS5B01G082600 chr3B 166513457 166520554 7097 True 759.166667 1251 84.220167 875 6916 6 chr3B.!!$R2 6041

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
492 869 0.339162 TGGACGGTTAGGGATGGGTA 59.661 55.000 0.00 0.0 0.00 3.69 F
1098 1532 0.758734 CCTTCCGCTATCACCATCCA 59.241 55.000 0.00 0.0 0.00 3.41 F
2749 8277 2.491086 GGCCTACTCCTATGAGCACCTA 60.491 54.545 0.00 0.0 42.74 3.08 F
3134 8742 2.035066 AGCATGCCTTGTTGTGAACTTC 59.965 45.455 15.66 0.0 0.00 3.01 F
3882 9518 4.363991 AAGATGGCTGGGTCTTGATATC 57.636 45.455 0.00 0.0 33.64 1.63 F
5386 11106 2.047830 CCTCCCCCAAGTCTATGTACC 58.952 57.143 0.00 0.0 0.00 3.34 F
6246 13909 0.179134 CTCTGTTAACTCCGCTCCCG 60.179 60.000 7.22 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 2001 1.069935 GGCCATCTTAGGAGCGACC 59.930 63.158 0.0 0.00 39.35 4.79 R
2852 8449 0.034089 ATGGCTAGGTTCCTTGTGGC 60.034 55.000 0.0 1.91 0.00 5.01 R
3882 9518 2.033602 GGACCACCACCTTTCCGG 59.966 66.667 0.0 0.00 39.35 5.14 R
4229 9891 2.156117 CAGCATGACAAATGGCAAAACG 59.844 45.455 0.0 0.00 39.69 3.60 R
5755 11524 5.999600 TCCAAGCAATCATGACACCTATATG 59.000 40.000 0.0 0.00 0.00 1.78 R
6275 13938 0.109132 GTTGGATTTTGGCAGCTCCG 60.109 55.000 0.0 0.00 37.80 4.63 R
7421 15825 2.755103 CAAGGTTTGGGTGCCTTCTATC 59.245 50.000 0.0 0.00 42.68 2.08 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
374 743 7.367285 CCCTCTGTAATCTTTTCTCTATCTCG 58.633 42.308 0.00 0.00 0.00 4.04
375 744 6.861055 CCTCTGTAATCTTTTCTCTATCTCGC 59.139 42.308 0.00 0.00 0.00 5.03
377 746 8.678593 TCTGTAATCTTTTCTCTATCTCGCTA 57.321 34.615 0.00 0.00 0.00 4.26
378 747 9.121658 TCTGTAATCTTTTCTCTATCTCGCTAA 57.878 33.333 0.00 0.00 0.00 3.09
379 748 9.737427 CTGTAATCTTTTCTCTATCTCGCTAAA 57.263 33.333 0.00 0.00 0.00 1.85
438 811 4.436998 GCGTCGAGGTGGGAGGTG 62.437 72.222 7.01 0.00 0.00 4.00
439 812 2.675423 CGTCGAGGTGGGAGGTGA 60.675 66.667 0.00 0.00 0.00 4.02
440 813 2.701780 CGTCGAGGTGGGAGGTGAG 61.702 68.421 0.00 0.00 0.00 3.51
441 814 2.680352 TCGAGGTGGGAGGTGAGC 60.680 66.667 0.00 0.00 0.00 4.26
481 858 2.100879 GAGTGAGGCAGTGGACGGTT 62.101 60.000 0.00 0.00 0.00 4.44
492 869 0.339162 TGGACGGTTAGGGATGGGTA 59.661 55.000 0.00 0.00 0.00 3.69
532 943 2.691252 GAGGGTTGGGTCCGGGAT 60.691 66.667 0.00 0.00 0.00 3.85
600 1025 1.774894 TTATGCTATGGCCGGGGGTC 61.775 60.000 2.18 0.00 37.74 4.46
611 1036 2.519302 GGGGGTCGCCATTGGATG 60.519 66.667 6.95 0.00 0.00 3.51
667 1097 3.361786 GGCTCTCCTCTGTACTTCTCTT 58.638 50.000 0.00 0.00 0.00 2.85
668 1098 3.767131 GGCTCTCCTCTGTACTTCTCTTT 59.233 47.826 0.00 0.00 0.00 2.52
672 1102 2.231478 TCCTCTGTACTTCTCTTTGCCG 59.769 50.000 0.00 0.00 0.00 5.69
987 1421 3.948719 GGGTCACCTGCCGGAACA 61.949 66.667 5.05 0.00 0.00 3.18
1035 1469 2.189521 CCGACCTTATTGCCGCCT 59.810 61.111 0.00 0.00 0.00 5.52
1044 1478 1.917782 TATTGCCGCCTGTTTCACGC 61.918 55.000 0.00 0.00 0.00 5.34
1072 1506 0.983378 CTTCCTCCTCCGAACCCCAT 60.983 60.000 0.00 0.00 0.00 4.00
1075 1509 1.522569 CTCCTCCGAACCCCATCAC 59.477 63.158 0.00 0.00 0.00 3.06
1098 1532 0.758734 CCTTCCGCTATCACCATCCA 59.241 55.000 0.00 0.00 0.00 3.41
1152 1586 2.626950 CCCATCAACCTCTCCTACTCCA 60.627 54.545 0.00 0.00 0.00 3.86
1558 2001 3.005540 GCTTGTGAAATGGGGCGGG 62.006 63.158 0.00 0.00 0.00 6.13
1708 2155 3.930336 TGTTCAGAAAGCACTCGATGAT 58.070 40.909 0.00 0.00 0.00 2.45
1911 2392 3.867857 TGTAAGCTTGCACATCGGATAA 58.132 40.909 13.67 0.00 0.00 1.75
2219 7726 4.282496 AGTAGACCACTGTATCTTCTGGG 58.718 47.826 0.00 0.00 35.62 4.45
2541 8063 6.434340 ACATCACACCGAATCAGCTATATAGA 59.566 38.462 14.16 0.00 0.00 1.98
2749 8277 2.491086 GGCCTACTCCTATGAGCACCTA 60.491 54.545 0.00 0.00 42.74 3.08
2812 8409 3.563512 AGGAAACTGCGACCACCT 58.436 55.556 0.00 0.00 41.13 4.00
2896 8493 3.935203 GAGCTATGCTTACAAACTGCTCA 59.065 43.478 0.00 0.00 43.33 4.26
2987 8585 3.988379 AGCTGCGAAAACTGAAAATCA 57.012 38.095 0.00 0.00 0.00 2.57
3134 8742 2.035066 AGCATGCCTTGTTGTGAACTTC 59.965 45.455 15.66 0.00 0.00 3.01
3204 8812 5.680594 TTCATATTTGCAATGAAGGCCTT 57.319 34.783 20.65 20.65 38.19 4.35
3595 9227 7.410120 AATTGAGGTTTCCATCCACTATTTC 57.590 36.000 0.00 0.00 0.00 2.17
3600 9232 7.508977 TGAGGTTTCCATCCACTATTTCTTTTT 59.491 33.333 0.00 0.00 0.00 1.94
3882 9518 4.363991 AAGATGGCTGGGTCTTGATATC 57.636 45.455 0.00 0.00 33.64 1.63
3997 9648 7.027161 CCACAGTAATTATGTTTACTTGCCAC 58.973 38.462 0.00 0.00 39.75 5.01
4229 9891 4.160736 GGTGTCTTCAATACAACCTTGC 57.839 45.455 0.00 0.00 0.00 4.01
4467 10165 6.808212 CCTAATCTCAAACACGCAAAATTCAT 59.192 34.615 0.00 0.00 0.00 2.57
5386 11106 2.047830 CCTCCCCCAAGTCTATGTACC 58.952 57.143 0.00 0.00 0.00 3.34
5756 11525 8.236585 ACATATGCTATGTTCCTTTATTTGCA 57.763 30.769 1.58 0.00 0.00 4.08
5958 11727 5.722021 AAATAAGTGCCCAAAGTAACTGG 57.278 39.130 0.00 0.00 0.00 4.00
5986 13644 4.778213 TGCACTATAGGAAGCTCCATTT 57.222 40.909 4.43 0.00 39.61 2.32
6205 13868 8.327941 TCATCATCAAAGGTTGAAGAGTTAAG 57.672 34.615 2.82 0.00 43.95 1.85
6206 13869 7.391554 TCATCATCAAAGGTTGAAGAGTTAAGG 59.608 37.037 2.82 0.00 43.95 2.69
6207 13870 5.473504 TCATCAAAGGTTGAAGAGTTAAGGC 59.526 40.000 0.00 0.00 43.95 4.35
6208 13871 5.048846 TCAAAGGTTGAAGAGTTAAGGCT 57.951 39.130 0.00 0.00 36.59 4.58
6209 13872 4.821805 TCAAAGGTTGAAGAGTTAAGGCTG 59.178 41.667 0.00 0.00 36.59 4.85
6210 13873 4.439253 AAGGTTGAAGAGTTAAGGCTGT 57.561 40.909 0.00 0.00 0.00 4.40
6211 13874 3.744660 AGGTTGAAGAGTTAAGGCTGTG 58.255 45.455 0.00 0.00 0.00 3.66
6212 13875 3.136626 AGGTTGAAGAGTTAAGGCTGTGT 59.863 43.478 0.00 0.00 0.00 3.72
6213 13876 3.883489 GGTTGAAGAGTTAAGGCTGTGTT 59.117 43.478 0.00 0.00 0.00 3.32
6214 13877 4.023963 GGTTGAAGAGTTAAGGCTGTGTTC 60.024 45.833 0.00 0.00 0.00 3.18
6215 13878 3.390135 TGAAGAGTTAAGGCTGTGTTCG 58.610 45.455 0.00 0.00 0.00 3.95
6216 13879 2.457366 AGAGTTAAGGCTGTGTTCGG 57.543 50.000 0.00 0.00 0.00 4.30
6217 13880 1.692519 AGAGTTAAGGCTGTGTTCGGT 59.307 47.619 0.00 0.00 0.00 4.69
6218 13881 2.104281 AGAGTTAAGGCTGTGTTCGGTT 59.896 45.455 0.00 0.00 0.00 4.44
6219 13882 2.876550 GAGTTAAGGCTGTGTTCGGTTT 59.123 45.455 0.00 0.00 0.00 3.27
6220 13883 2.876550 AGTTAAGGCTGTGTTCGGTTTC 59.123 45.455 0.00 0.00 0.00 2.78
6221 13884 2.876550 GTTAAGGCTGTGTTCGGTTTCT 59.123 45.455 0.00 0.00 0.00 2.52
6222 13885 1.594331 AAGGCTGTGTTCGGTTTCTC 58.406 50.000 0.00 0.00 0.00 2.87
6223 13886 0.759346 AGGCTGTGTTCGGTTTCTCT 59.241 50.000 0.00 0.00 0.00 3.10
6224 13887 1.149148 GGCTGTGTTCGGTTTCTCTC 58.851 55.000 0.00 0.00 0.00 3.20
6225 13888 1.270358 GGCTGTGTTCGGTTTCTCTCT 60.270 52.381 0.00 0.00 0.00 3.10
6226 13889 1.795286 GCTGTGTTCGGTTTCTCTCTG 59.205 52.381 0.00 0.00 0.00 3.35
6227 13890 1.795286 CTGTGTTCGGTTTCTCTCTGC 59.205 52.381 0.00 0.00 0.00 4.26
6228 13891 1.412710 TGTGTTCGGTTTCTCTCTGCT 59.587 47.619 0.00 0.00 0.00 4.24
6229 13892 2.062519 GTGTTCGGTTTCTCTCTGCTC 58.937 52.381 0.00 0.00 0.00 4.26
6230 13893 1.964223 TGTTCGGTTTCTCTCTGCTCT 59.036 47.619 0.00 0.00 0.00 4.09
6231 13894 2.288457 TGTTCGGTTTCTCTCTGCTCTG 60.288 50.000 0.00 0.00 0.00 3.35
6232 13895 1.621992 TCGGTTTCTCTCTGCTCTGT 58.378 50.000 0.00 0.00 0.00 3.41
6233 13896 1.964223 TCGGTTTCTCTCTGCTCTGTT 59.036 47.619 0.00 0.00 0.00 3.16
6234 13897 3.154710 TCGGTTTCTCTCTGCTCTGTTA 58.845 45.455 0.00 0.00 0.00 2.41
6235 13898 3.572682 TCGGTTTCTCTCTGCTCTGTTAA 59.427 43.478 0.00 0.00 0.00 2.01
6236 13899 3.675698 CGGTTTCTCTCTGCTCTGTTAAC 59.324 47.826 0.00 0.00 0.00 2.01
6237 13900 4.559704 CGGTTTCTCTCTGCTCTGTTAACT 60.560 45.833 7.22 0.00 0.00 2.24
6238 13901 4.926832 GGTTTCTCTCTGCTCTGTTAACTC 59.073 45.833 7.22 0.00 0.00 3.01
6239 13902 4.792521 TTCTCTCTGCTCTGTTAACTCC 57.207 45.455 7.22 0.00 0.00 3.85
6240 13903 2.750166 TCTCTCTGCTCTGTTAACTCCG 59.250 50.000 7.22 0.00 0.00 4.63
6241 13904 1.202582 TCTCTGCTCTGTTAACTCCGC 59.797 52.381 7.22 6.86 0.00 5.54
6242 13905 1.203523 CTCTGCTCTGTTAACTCCGCT 59.796 52.381 7.22 0.00 0.00 5.52
6243 13906 1.202582 TCTGCTCTGTTAACTCCGCTC 59.797 52.381 7.22 0.00 0.00 5.03
6244 13907 0.246635 TGCTCTGTTAACTCCGCTCC 59.753 55.000 7.22 0.00 0.00 4.70
6245 13908 0.460459 GCTCTGTTAACTCCGCTCCC 60.460 60.000 7.22 0.00 0.00 4.30
6246 13909 0.179134 CTCTGTTAACTCCGCTCCCG 60.179 60.000 7.22 0.00 0.00 5.14
6262 13925 2.584608 CGGAGCGGACCATCCTTT 59.415 61.111 10.30 0.00 33.30 3.11
6263 13926 1.820581 CGGAGCGGACCATCCTTTA 59.179 57.895 10.30 0.00 33.30 1.85
6264 13927 0.249489 CGGAGCGGACCATCCTTTAG 60.249 60.000 10.30 0.00 33.30 1.85
6265 13928 0.533085 GGAGCGGACCATCCTTTAGC 60.533 60.000 5.62 0.00 33.30 3.09
6266 13929 0.466124 GAGCGGACCATCCTTTAGCT 59.534 55.000 0.00 0.00 33.22 3.32
6267 13930 0.912486 AGCGGACCATCCTTTAGCTT 59.088 50.000 0.00 0.00 33.30 3.74
6268 13931 2.102588 GAGCGGACCATCCTTTAGCTTA 59.897 50.000 0.00 0.00 31.19 3.09
6269 13932 2.504175 AGCGGACCATCCTTTAGCTTAA 59.496 45.455 0.00 0.00 33.30 1.85
6270 13933 3.136626 AGCGGACCATCCTTTAGCTTAAT 59.863 43.478 0.00 0.00 33.30 1.40
6271 13934 3.883489 GCGGACCATCCTTTAGCTTAATT 59.117 43.478 0.00 0.00 33.30 1.40
6272 13935 5.061179 GCGGACCATCCTTTAGCTTAATTA 58.939 41.667 0.00 0.00 33.30 1.40
6273 13936 5.179555 GCGGACCATCCTTTAGCTTAATTAG 59.820 44.000 0.00 0.00 33.30 1.73
6274 13937 5.701290 CGGACCATCCTTTAGCTTAATTAGG 59.299 44.000 0.00 0.00 33.30 2.69
6275 13938 5.473846 GGACCATCCTTTAGCTTAATTAGGC 59.526 44.000 11.42 11.42 32.53 3.93
6276 13939 5.063880 ACCATCCTTTAGCTTAATTAGGCG 58.936 41.667 13.28 0.18 33.04 5.52
6277 13940 4.455877 CCATCCTTTAGCTTAATTAGGCGG 59.544 45.833 13.28 8.96 33.04 6.13
6278 13941 5.305585 CATCCTTTAGCTTAATTAGGCGGA 58.694 41.667 13.28 13.48 33.04 5.54
6279 13942 4.957296 TCCTTTAGCTTAATTAGGCGGAG 58.043 43.478 13.28 11.75 33.04 4.63
6292 13955 4.001248 CGGAGCTGCCAAAATCCA 57.999 55.556 0.00 0.00 35.94 3.41
6293 13956 2.266070 CGGAGCTGCCAAAATCCAA 58.734 52.632 0.00 0.00 35.94 3.53
6294 13957 0.109132 CGGAGCTGCCAAAATCCAAC 60.109 55.000 0.00 0.00 35.94 3.77
6295 13958 1.260544 GGAGCTGCCAAAATCCAACT 58.739 50.000 0.00 0.00 36.34 3.16
6296 13959 1.203287 GGAGCTGCCAAAATCCAACTC 59.797 52.381 0.00 0.00 36.34 3.01
6297 13960 1.203287 GAGCTGCCAAAATCCAACTCC 59.797 52.381 0.00 0.00 0.00 3.85
6298 13961 0.247460 GCTGCCAAAATCCAACTCCC 59.753 55.000 0.00 0.00 0.00 4.30
6299 13962 0.897621 CTGCCAAAATCCAACTCCCC 59.102 55.000 0.00 0.00 0.00 4.81
6300 13963 0.189574 TGCCAAAATCCAACTCCCCA 59.810 50.000 0.00 0.00 0.00 4.96
6301 13964 1.347062 GCCAAAATCCAACTCCCCAA 58.653 50.000 0.00 0.00 0.00 4.12
6302 13965 1.001974 GCCAAAATCCAACTCCCCAAC 59.998 52.381 0.00 0.00 0.00 3.77
6303 13966 2.608623 CCAAAATCCAACTCCCCAACT 58.391 47.619 0.00 0.00 0.00 3.16
6304 13967 2.562738 CCAAAATCCAACTCCCCAACTC 59.437 50.000 0.00 0.00 0.00 3.01
6305 13968 2.562738 CAAAATCCAACTCCCCAACTCC 59.437 50.000 0.00 0.00 0.00 3.85
6306 13969 1.455822 AATCCAACTCCCCAACTCCA 58.544 50.000 0.00 0.00 0.00 3.86
6307 13970 0.698818 ATCCAACTCCCCAACTCCAC 59.301 55.000 0.00 0.00 0.00 4.02
6308 13971 0.696143 TCCAACTCCCCAACTCCACA 60.696 55.000 0.00 0.00 0.00 4.17
6309 13972 0.250901 CCAACTCCCCAACTCCACAG 60.251 60.000 0.00 0.00 0.00 3.66
6310 13973 0.764890 CAACTCCCCAACTCCACAGA 59.235 55.000 0.00 0.00 0.00 3.41
6311 13974 1.059913 AACTCCCCAACTCCACAGAG 58.940 55.000 0.00 0.00 46.36 3.35
6312 13975 1.298014 CTCCCCAACTCCACAGAGC 59.702 63.158 0.00 0.00 44.65 4.09
6313 13976 2.046892 CCCCAACTCCACAGAGCG 60.047 66.667 0.00 0.00 44.65 5.03
6314 13977 2.046892 CCCAACTCCACAGAGCGG 60.047 66.667 0.00 0.00 44.65 5.52
6315 13978 2.046892 CCAACTCCACAGAGCGGG 60.047 66.667 0.00 0.00 44.65 6.13
6316 13979 2.046892 CAACTCCACAGAGCGGGG 60.047 66.667 0.00 0.00 44.65 5.73
6317 13980 2.203788 AACTCCACAGAGCGGGGA 60.204 61.111 0.00 0.00 44.65 4.81
6318 13981 1.841556 AACTCCACAGAGCGGGGAA 60.842 57.895 0.00 0.00 44.65 3.97
6319 13982 1.831652 AACTCCACAGAGCGGGGAAG 61.832 60.000 0.00 0.00 44.65 3.46
6320 13983 2.203788 TCCACAGAGCGGGGAAGT 60.204 61.111 0.00 0.00 0.00 3.01
6321 13984 1.831652 CTCCACAGAGCGGGGAAGTT 61.832 60.000 0.00 0.00 32.13 2.66
6322 13985 1.376037 CCACAGAGCGGGGAAGTTC 60.376 63.158 0.00 0.00 0.00 3.01
6323 13986 1.376037 CACAGAGCGGGGAAGTTCC 60.376 63.158 13.99 13.99 35.23 3.62
6330 13993 4.716003 GGGGAAGTTCCGAACAGG 57.284 61.111 15.80 0.00 37.43 4.00
6331 13994 1.002502 GGGGAAGTTCCGAACAGGG 60.003 63.158 15.80 0.00 41.52 4.45
6332 13995 1.674651 GGGAAGTTCCGAACAGGGC 60.675 63.158 15.80 0.00 41.52 5.19
6333 13996 1.674651 GGAAGTTCCGAACAGGGCC 60.675 63.158 13.69 0.00 41.52 5.80
6334 13997 1.375326 GAAGTTCCGAACAGGGCCT 59.625 57.895 13.69 0.00 41.52 5.19
6397 14064 3.814842 TGAATAGTGTTGACAACCAGCTG 59.185 43.478 15.59 6.78 0.00 4.24
6425 14092 4.792528 AAACACACAATTGAATTTGGCG 57.207 36.364 13.59 0.00 0.00 5.69
6452 14119 5.295431 TGTTGAAGCTCGGTCATTTAATG 57.705 39.130 0.00 0.00 0.00 1.90
6529 14596 2.821378 TGAATCAGGCCATTGTCTTGTG 59.179 45.455 5.01 0.00 0.00 3.33
6539 14606 4.635765 GCCATTGTCTTGTGCTGATAAGTA 59.364 41.667 0.00 0.00 0.00 2.24
6604 14672 1.608590 TGTTCTGGCTGTTTTGCTAGC 59.391 47.619 8.10 8.10 40.64 3.42
6917 14987 4.814147 TGACTAGCAGTTCATCTGTTCAG 58.186 43.478 0.00 0.00 45.23 3.02
6918 14988 4.281941 TGACTAGCAGTTCATCTGTTCAGT 59.718 41.667 0.00 0.00 45.23 3.41
6919 14989 5.220710 ACTAGCAGTTCATCTGTTCAGTT 57.779 39.130 0.00 0.00 45.23 3.16
6920 14990 5.233988 ACTAGCAGTTCATCTGTTCAGTTC 58.766 41.667 0.00 0.00 45.23 3.01
6921 14991 4.077300 AGCAGTTCATCTGTTCAGTTCA 57.923 40.909 0.00 0.00 45.23 3.18
6922 14992 3.812053 AGCAGTTCATCTGTTCAGTTCAC 59.188 43.478 0.00 0.00 45.23 3.18
6939 15009 7.276658 TCAGTTCACATAGAAGTTGTTTACCA 58.723 34.615 0.00 0.00 37.81 3.25
6982 15052 5.597806 AGCATCCATGTTAAATGATTGCAG 58.402 37.500 10.54 0.00 32.75 4.41
6986 15056 6.587206 TCCATGTTAAATGATTGCAGTCAA 57.413 33.333 16.42 0.00 36.51 3.18
6988 15058 7.036829 TCCATGTTAAATGATTGCAGTCAATG 58.963 34.615 16.42 12.99 42.60 2.82
6989 15059 6.256975 CCATGTTAAATGATTGCAGTCAATGG 59.743 38.462 16.42 17.59 42.60 3.16
6990 15060 5.722263 TGTTAAATGATTGCAGTCAATGGG 58.278 37.500 16.42 0.00 42.60 4.00
7024 15111 6.842676 AGGATACCAATTACTCCTTCCATTC 58.157 40.000 0.00 0.00 34.42 2.67
7026 15113 4.251103 ACCAATTACTCCTTCCATTCCC 57.749 45.455 0.00 0.00 0.00 3.97
7371 15771 9.754382 ATATTCTGGATCAAAATACAATTGCAC 57.246 29.630 5.05 0.00 0.00 4.57
7376 15776 6.038356 GGATCAAAATACAATTGCACCTCAG 58.962 40.000 5.05 0.00 0.00 3.35
7403 15807 5.106197 GGAACTGCATATCAACATGTCACAA 60.106 40.000 0.00 0.00 0.00 3.33
7404 15808 5.556355 ACTGCATATCAACATGTCACAAG 57.444 39.130 0.00 0.00 0.00 3.16
7405 15809 4.397103 ACTGCATATCAACATGTCACAAGG 59.603 41.667 0.00 0.00 0.00 3.61
7406 15810 4.587891 TGCATATCAACATGTCACAAGGA 58.412 39.130 0.00 0.00 0.00 3.36
7416 15820 3.924114 TGTCACAAGGAAGAAGAACCA 57.076 42.857 0.00 0.00 0.00 3.67
7421 15825 5.872070 GTCACAAGGAAGAAGAACCATCTAG 59.128 44.000 0.00 0.00 33.77 2.43
7431 15835 6.139671 AGAAGAACCATCTAGATAGAAGGCA 58.860 40.000 4.54 0.00 43.18 4.75
7707 16116 4.454728 TGAGTCACATCGTTCATGATGA 57.545 40.909 14.70 0.00 46.98 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
430 803 2.284625 ACCATCGCTCACCTCCCA 60.285 61.111 0.00 0.00 0.00 4.37
431 804 2.187946 CACCATCGCTCACCTCCC 59.812 66.667 0.00 0.00 0.00 4.30
432 805 2.187946 CCACCATCGCTCACCTCC 59.812 66.667 0.00 0.00 0.00 4.30
433 806 1.448540 CACCACCATCGCTCACCTC 60.449 63.158 0.00 0.00 0.00 3.85
434 807 2.665000 CACCACCATCGCTCACCT 59.335 61.111 0.00 0.00 0.00 4.00
435 808 2.436646 CCACCACCATCGCTCACC 60.437 66.667 0.00 0.00 0.00 4.02
436 809 2.436646 CCCACCACCATCGCTCAC 60.437 66.667 0.00 0.00 0.00 3.51
437 810 4.408821 GCCCACCACCATCGCTCA 62.409 66.667 0.00 0.00 0.00 4.26
469 842 0.462047 CATCCCTAACCGTCCACTGC 60.462 60.000 0.00 0.00 0.00 4.40
481 858 1.046472 CCGCACACTACCCATCCCTA 61.046 60.000 0.00 0.00 0.00 3.53
511 922 3.246112 CGGACCCAACCCTCACCA 61.246 66.667 0.00 0.00 0.00 4.17
532 943 2.268920 GGTCTGCCTCATTCGCCA 59.731 61.111 0.00 0.00 0.00 5.69
572 997 1.901591 CCATAGCATAAGCCACCTGG 58.098 55.000 0.00 0.00 43.56 4.45
611 1036 5.048013 CCCAGTGTCTAAAACTGAAATTCCC 60.048 44.000 5.17 0.00 46.55 3.97
798 1230 1.072266 ATGGGGTTCCTGTGTGCTTA 58.928 50.000 0.00 0.00 0.00 3.09
987 1421 2.973082 GCCATTTTTCCAGGCGCT 59.027 55.556 7.64 0.00 38.86 5.92
1072 1506 1.066430 GTGATAGCGGAAGGGTTGTGA 60.066 52.381 0.00 0.00 0.00 3.58
1075 1509 0.251916 TGGTGATAGCGGAAGGGTTG 59.748 55.000 0.00 0.00 0.00 3.77
1098 1532 1.003233 GAGGAGGCTGCGGAAAAGT 60.003 57.895 0.00 0.00 0.00 2.66
1164 1598 0.690744 TAGCTGCAGAGGCCATGGTA 60.691 55.000 20.43 0.00 40.13 3.25
1558 2001 1.069935 GGCCATCTTAGGAGCGACC 59.930 63.158 0.00 0.00 39.35 4.79
1708 2155 3.473923 TCACTCTCTGACACATTTGCA 57.526 42.857 0.00 0.00 0.00 4.08
1911 2392 9.574516 CCATACCTAAAGCCTAACTGATAAAAT 57.425 33.333 0.00 0.00 0.00 1.82
2341 7851 5.621422 CAATTTGACAGGTCATTACACTCG 58.379 41.667 2.52 0.00 39.64 4.18
2541 8063 5.106442 GTGTCCTCGAACCAAAAACAAATT 58.894 37.500 0.00 0.00 0.00 1.82
2749 8277 0.178068 ATTCGTTCAGCGGTATGGCT 59.822 50.000 0.00 0.00 46.13 4.75
2852 8449 0.034089 ATGGCTAGGTTCCTTGTGGC 60.034 55.000 0.00 1.91 0.00 5.01
2896 8493 6.100714 AGGGGAAAACATAATGTAGGACGTAT 59.899 38.462 0.00 0.00 0.00 3.06
3882 9518 2.033602 GGACCACCACCTTTCCGG 59.966 66.667 0.00 0.00 39.35 5.14
4004 9655 9.243637 GCAAGTAACATGTCAAATTGAACTAAA 57.756 29.630 19.54 0.00 0.00 1.85
4229 9891 2.156117 CAGCATGACAAATGGCAAAACG 59.844 45.455 0.00 0.00 39.69 3.60
5386 11106 6.611381 AATGACAAACTCATTACCATTGTCG 58.389 36.000 11.06 0.00 46.17 4.35
5755 11524 5.999600 TCCAAGCAATCATGACACCTATATG 59.000 40.000 0.00 0.00 0.00 1.78
5756 11525 6.000219 GTCCAAGCAATCATGACACCTATAT 59.000 40.000 0.00 0.00 0.00 0.86
5958 11727 6.542370 TGGAGCTTCCTATAGTGCAATTTAAC 59.458 38.462 0.00 0.00 37.46 2.01
6205 13868 1.149148 GAGAGAAACCGAACACAGCC 58.851 55.000 0.00 0.00 0.00 4.85
6206 13869 1.795286 CAGAGAGAAACCGAACACAGC 59.205 52.381 0.00 0.00 0.00 4.40
6207 13870 1.795286 GCAGAGAGAAACCGAACACAG 59.205 52.381 0.00 0.00 0.00 3.66
6208 13871 1.412710 AGCAGAGAGAAACCGAACACA 59.587 47.619 0.00 0.00 0.00 3.72
6209 13872 2.062519 GAGCAGAGAGAAACCGAACAC 58.937 52.381 0.00 0.00 0.00 3.32
6210 13873 1.964223 AGAGCAGAGAGAAACCGAACA 59.036 47.619 0.00 0.00 0.00 3.18
6211 13874 2.288518 ACAGAGCAGAGAGAAACCGAAC 60.289 50.000 0.00 0.00 0.00 3.95
6212 13875 1.964223 ACAGAGCAGAGAGAAACCGAA 59.036 47.619 0.00 0.00 0.00 4.30
6213 13876 1.621992 ACAGAGCAGAGAGAAACCGA 58.378 50.000 0.00 0.00 0.00 4.69
6214 13877 2.447244 AACAGAGCAGAGAGAAACCG 57.553 50.000 0.00 0.00 0.00 4.44
6215 13878 4.888917 AGTTAACAGAGCAGAGAGAAACC 58.111 43.478 8.61 0.00 0.00 3.27
6216 13879 4.926832 GGAGTTAACAGAGCAGAGAGAAAC 59.073 45.833 8.61 0.00 0.00 2.78
6217 13880 4.321304 CGGAGTTAACAGAGCAGAGAGAAA 60.321 45.833 8.61 0.00 0.00 2.52
6218 13881 3.191581 CGGAGTTAACAGAGCAGAGAGAA 59.808 47.826 8.61 0.00 0.00 2.87
6219 13882 2.750166 CGGAGTTAACAGAGCAGAGAGA 59.250 50.000 8.61 0.00 0.00 3.10
6220 13883 2.733858 GCGGAGTTAACAGAGCAGAGAG 60.734 54.545 8.61 0.00 0.00 3.20
6221 13884 1.202582 GCGGAGTTAACAGAGCAGAGA 59.797 52.381 8.61 0.00 0.00 3.10
6222 13885 1.203523 AGCGGAGTTAACAGAGCAGAG 59.796 52.381 17.25 0.00 0.00 3.35
6223 13886 1.202582 GAGCGGAGTTAACAGAGCAGA 59.797 52.381 17.25 0.00 0.00 4.26
6224 13887 1.634702 GAGCGGAGTTAACAGAGCAG 58.365 55.000 17.25 3.75 0.00 4.24
6225 13888 0.246635 GGAGCGGAGTTAACAGAGCA 59.753 55.000 17.25 0.00 0.00 4.26
6226 13889 0.460459 GGGAGCGGAGTTAACAGAGC 60.460 60.000 8.61 9.47 0.00 4.09
6227 13890 0.179134 CGGGAGCGGAGTTAACAGAG 60.179 60.000 8.61 0.00 0.00 3.35
6228 13891 1.601419 CCGGGAGCGGAGTTAACAGA 61.601 60.000 8.61 0.00 0.00 3.41
6229 13892 1.153628 CCGGGAGCGGAGTTAACAG 60.154 63.158 8.61 0.00 0.00 3.16
6230 13893 1.607178 TCCGGGAGCGGAGTTAACA 60.607 57.895 8.61 0.00 33.62 2.41
6231 13894 3.291611 TCCGGGAGCGGAGTTAAC 58.708 61.111 0.00 0.00 33.62 2.01
6245 13908 0.249489 CTAAAGGATGGTCCGCTCCG 60.249 60.000 4.97 0.00 42.75 4.63
6246 13909 0.533085 GCTAAAGGATGGTCCGCTCC 60.533 60.000 2.63 2.63 42.75 4.70
6247 13910 0.466124 AGCTAAAGGATGGTCCGCTC 59.534 55.000 0.00 0.00 42.75 5.03
6248 13911 0.912486 AAGCTAAAGGATGGTCCGCT 59.088 50.000 0.00 0.00 42.75 5.52
6249 13912 2.614829 TAAGCTAAAGGATGGTCCGC 57.385 50.000 0.00 0.00 42.75 5.54
6250 13913 5.701290 CCTAATTAAGCTAAAGGATGGTCCG 59.299 44.000 0.00 0.00 42.75 4.79
6251 13914 5.473846 GCCTAATTAAGCTAAAGGATGGTCC 59.526 44.000 0.00 0.00 36.58 4.46
6252 13915 5.179555 CGCCTAATTAAGCTAAAGGATGGTC 59.820 44.000 4.61 0.00 0.00 4.02
6253 13916 5.063880 CGCCTAATTAAGCTAAAGGATGGT 58.936 41.667 4.61 0.00 0.00 3.55
6254 13917 4.455877 CCGCCTAATTAAGCTAAAGGATGG 59.544 45.833 4.61 0.00 0.00 3.51
6255 13918 5.305585 TCCGCCTAATTAAGCTAAAGGATG 58.694 41.667 4.61 0.00 0.00 3.51
6256 13919 5.552178 CTCCGCCTAATTAAGCTAAAGGAT 58.448 41.667 4.61 0.00 0.00 3.24
6257 13920 4.742743 GCTCCGCCTAATTAAGCTAAAGGA 60.743 45.833 4.61 3.08 0.00 3.36
6258 13921 3.498777 GCTCCGCCTAATTAAGCTAAAGG 59.501 47.826 4.61 0.00 0.00 3.11
6259 13922 4.212214 CAGCTCCGCCTAATTAAGCTAAAG 59.788 45.833 8.02 2.73 41.19 1.85
6260 13923 4.127171 CAGCTCCGCCTAATTAAGCTAAA 58.873 43.478 8.02 0.00 41.19 1.85
6261 13924 3.728845 CAGCTCCGCCTAATTAAGCTAA 58.271 45.455 8.02 0.00 41.19 3.09
6262 13925 2.548067 GCAGCTCCGCCTAATTAAGCTA 60.548 50.000 8.02 0.00 41.19 3.32
6263 13926 1.811941 GCAGCTCCGCCTAATTAAGCT 60.812 52.381 4.61 3.92 43.81 3.74
6264 13927 0.588737 GCAGCTCCGCCTAATTAAGC 59.411 55.000 0.00 0.00 0.00 3.09
6274 13937 1.876497 TTGGATTTTGGCAGCTCCGC 61.876 55.000 0.00 0.00 37.80 5.54
6275 13938 0.109132 GTTGGATTTTGGCAGCTCCG 60.109 55.000 0.00 0.00 37.80 4.63
6276 13939 1.203287 GAGTTGGATTTTGGCAGCTCC 59.797 52.381 0.00 5.41 0.00 4.70
6277 13940 1.203287 GGAGTTGGATTTTGGCAGCTC 59.797 52.381 0.00 0.00 0.00 4.09
6278 13941 1.260544 GGAGTTGGATTTTGGCAGCT 58.739 50.000 0.00 0.00 0.00 4.24
6279 13942 0.247460 GGGAGTTGGATTTTGGCAGC 59.753 55.000 0.00 0.00 0.00 5.25
6280 13943 0.897621 GGGGAGTTGGATTTTGGCAG 59.102 55.000 0.00 0.00 0.00 4.85
6281 13944 0.189574 TGGGGAGTTGGATTTTGGCA 59.810 50.000 0.00 0.00 0.00 4.92
6282 13945 1.001974 GTTGGGGAGTTGGATTTTGGC 59.998 52.381 0.00 0.00 0.00 4.52
6283 13946 2.562738 GAGTTGGGGAGTTGGATTTTGG 59.437 50.000 0.00 0.00 0.00 3.28
6284 13947 2.562738 GGAGTTGGGGAGTTGGATTTTG 59.437 50.000 0.00 0.00 0.00 2.44
6285 13948 2.178984 TGGAGTTGGGGAGTTGGATTTT 59.821 45.455 0.00 0.00 0.00 1.82
6286 13949 1.786441 TGGAGTTGGGGAGTTGGATTT 59.214 47.619 0.00 0.00 0.00 2.17
6287 13950 1.075536 GTGGAGTTGGGGAGTTGGATT 59.924 52.381 0.00 0.00 0.00 3.01
6288 13951 0.698818 GTGGAGTTGGGGAGTTGGAT 59.301 55.000 0.00 0.00 0.00 3.41
6289 13952 0.696143 TGTGGAGTTGGGGAGTTGGA 60.696 55.000 0.00 0.00 0.00 3.53
6290 13953 0.250901 CTGTGGAGTTGGGGAGTTGG 60.251 60.000 0.00 0.00 0.00 3.77
6291 13954 0.764890 TCTGTGGAGTTGGGGAGTTG 59.235 55.000 0.00 0.00 0.00 3.16
6292 13955 1.059913 CTCTGTGGAGTTGGGGAGTT 58.940 55.000 0.00 0.00 35.03 3.01
6293 13956 1.484444 GCTCTGTGGAGTTGGGGAGT 61.484 60.000 0.00 0.00 41.38 3.85
6294 13957 1.298014 GCTCTGTGGAGTTGGGGAG 59.702 63.158 0.00 0.00 41.38 4.30
6295 13958 2.583441 CGCTCTGTGGAGTTGGGGA 61.583 63.158 0.00 0.00 41.38 4.81
6296 13959 2.046892 CGCTCTGTGGAGTTGGGG 60.047 66.667 0.00 0.00 41.38 4.96
6297 13960 2.046892 CCGCTCTGTGGAGTTGGG 60.047 66.667 0.00 0.00 41.38 4.12
6298 13961 2.046892 CCCGCTCTGTGGAGTTGG 60.047 66.667 0.00 0.00 41.38 3.77
6299 13962 2.046892 CCCCGCTCTGTGGAGTTG 60.047 66.667 0.00 0.00 41.38 3.16
6300 13963 1.831652 CTTCCCCGCTCTGTGGAGTT 61.832 60.000 0.00 0.00 41.38 3.01
6301 13964 2.203788 TTCCCCGCTCTGTGGAGT 60.204 61.111 0.00 0.00 41.38 3.85
6302 13965 1.831652 AACTTCCCCGCTCTGTGGAG 61.832 60.000 0.00 0.00 42.18 3.86
6303 13966 1.827399 GAACTTCCCCGCTCTGTGGA 61.827 60.000 0.00 0.00 34.74 4.02
6304 13967 1.376037 GAACTTCCCCGCTCTGTGG 60.376 63.158 0.00 0.00 0.00 4.17
6305 13968 1.376037 GGAACTTCCCCGCTCTGTG 60.376 63.158 0.00 0.00 0.00 3.66
6306 13969 2.943978 CGGAACTTCCCCGCTCTGT 61.944 63.158 1.97 0.00 40.54 3.41
6307 13970 2.125512 CGGAACTTCCCCGCTCTG 60.126 66.667 1.97 0.00 40.54 3.35
6308 13971 1.911766 TTCGGAACTTCCCCGCTCT 60.912 57.895 1.97 0.00 46.10 4.09
6309 13972 1.740664 GTTCGGAACTTCCCCGCTC 60.741 63.158 13.49 0.00 46.10 5.03
6310 13973 2.346365 GTTCGGAACTTCCCCGCT 59.654 61.111 13.49 0.00 46.10 5.52
6311 13974 2.031465 TGTTCGGAACTTCCCCGC 59.969 61.111 20.53 0.00 46.10 6.13
6313 13976 1.002502 CCCTGTTCGGAACTTCCCC 60.003 63.158 20.53 0.00 31.13 4.81
6314 13977 1.674651 GCCCTGTTCGGAACTTCCC 60.675 63.158 20.53 4.79 31.13 3.97
6315 13978 1.674651 GGCCCTGTTCGGAACTTCC 60.675 63.158 20.53 12.27 33.16 3.46
6316 13979 0.611714 TAGGCCCTGTTCGGAACTTC 59.388 55.000 20.53 7.76 33.16 3.01
6317 13980 1.061546 TTAGGCCCTGTTCGGAACTT 58.938 50.000 20.53 3.85 33.16 2.66
6318 13981 1.061546 TTTAGGCCCTGTTCGGAACT 58.938 50.000 20.53 3.18 33.16 3.01
6319 13982 2.124277 ATTTAGGCCCTGTTCGGAAC 57.876 50.000 13.86 13.86 33.16 3.62
6320 13983 4.304048 TTTATTTAGGCCCTGTTCGGAA 57.696 40.909 0.00 0.00 33.16 4.30
6321 13984 4.304048 TTTTATTTAGGCCCTGTTCGGA 57.696 40.909 0.00 0.00 33.16 4.55
6322 13985 6.264518 ACATATTTTATTTAGGCCCTGTTCGG 59.735 38.462 0.00 0.00 0.00 4.30
6323 13986 7.012894 TGACATATTTTATTTAGGCCCTGTTCG 59.987 37.037 0.00 0.00 0.00 3.95
6324 13987 8.232913 TGACATATTTTATTTAGGCCCTGTTC 57.767 34.615 0.00 0.00 0.00 3.18
6325 13988 8.602472 TTGACATATTTTATTTAGGCCCTGTT 57.398 30.769 0.00 0.00 0.00 3.16
6326 13989 8.602472 TTTGACATATTTTATTTAGGCCCTGT 57.398 30.769 0.00 0.00 0.00 4.00
6397 14064 9.701355 CCAAATTCAATTGTGTGTTTTTCTAAC 57.299 29.630 5.13 0.00 0.00 2.34
6425 14092 2.143122 TGACCGAGCTTCAACAATCAC 58.857 47.619 0.00 0.00 0.00 3.06
6452 14119 0.674534 CGGGTGCTCATAGTCCCTAC 59.325 60.000 0.00 0.00 37.92 3.18
6529 14596 9.757227 AATACTCAGTGAAAGATACTTATCAGC 57.243 33.333 0.00 0.00 35.17 4.26
6604 14672 6.171921 AGACAAAAACTGATCAGAGAGGATG 58.828 40.000 29.27 19.20 0.00 3.51
6910 14980 6.851222 ACAACTTCTATGTGAACTGAACAG 57.149 37.500 0.00 0.00 0.00 3.16
6917 14987 6.360329 CGTGGTAAACAACTTCTATGTGAAC 58.640 40.000 0.00 0.00 0.00 3.18
6918 14988 5.049954 GCGTGGTAAACAACTTCTATGTGAA 60.050 40.000 0.00 0.00 0.00 3.18
6919 14989 4.449743 GCGTGGTAAACAACTTCTATGTGA 59.550 41.667 0.00 0.00 0.00 3.58
6920 14990 4.378046 GGCGTGGTAAACAACTTCTATGTG 60.378 45.833 0.00 0.00 0.00 3.21
6921 14991 3.749609 GGCGTGGTAAACAACTTCTATGT 59.250 43.478 0.00 0.00 0.00 2.29
6922 14992 3.749088 TGGCGTGGTAAACAACTTCTATG 59.251 43.478 0.00 0.00 0.00 2.23
6939 15009 3.470709 CTCAAATATCAGGTCATGGCGT 58.529 45.455 0.00 0.00 0.00 5.68
6982 15052 8.380099 TGGTATCCTATAAATACACCCATTGAC 58.620 37.037 7.07 0.00 32.35 3.18
7060 15147 5.670485 TCACTCATTTTGCTCCGTATGTAT 58.330 37.500 0.00 0.00 0.00 2.29
7330 15730 4.400251 CCAGAATATCAACACTGCAACCAT 59.600 41.667 0.00 0.00 0.00 3.55
7371 15771 4.412796 TGATATGCAGTTCCTTCTGAGG 57.587 45.455 0.00 0.00 45.02 3.86
7376 15776 5.355071 TGACATGTTGATATGCAGTTCCTTC 59.645 40.000 0.00 0.00 0.00 3.46
7403 15807 7.508977 CCTTCTATCTAGATGGTTCTTCTTCCT 59.491 40.741 15.79 0.00 40.73 3.36
7404 15808 7.666623 CCTTCTATCTAGATGGTTCTTCTTCC 58.333 42.308 15.79 0.00 40.73 3.46
7405 15809 7.151976 GCCTTCTATCTAGATGGTTCTTCTTC 58.848 42.308 15.79 0.00 44.90 2.87
7406 15810 6.613271 TGCCTTCTATCTAGATGGTTCTTCTT 59.387 38.462 15.79 0.00 44.90 2.52
7416 15820 4.103311 GGTTTGGGTGCCTTCTATCTAGAT 59.897 45.833 10.73 10.73 31.40 1.98
7421 15825 2.755103 CAAGGTTTGGGTGCCTTCTATC 59.245 50.000 0.00 0.00 42.68 2.08
7585 15993 3.988976 TTAGAGCCTGAGCACTTTCAT 57.011 42.857 0.00 0.00 40.65 2.57
7586 15994 3.769739 TTTAGAGCCTGAGCACTTTCA 57.230 42.857 0.00 0.00 40.65 2.69
7707 16116 5.438761 ACGCTGAAGAAAAATAGCACTTT 57.561 34.783 0.00 0.00 35.98 2.66
7742 16151 3.435671 CCACAGGACTTTCAAATACGTCC 59.564 47.826 0.00 0.00 44.84 4.79
7743 16152 4.663636 CCACAGGACTTTCAAATACGTC 57.336 45.455 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.