Multiple sequence alignment - TraesCS5B01G518500

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 TraesCS5B01G518500 chr5B 100.000 4025 0 0 1 4025 681619288 681615264 0.000000e+00 7433.0
1 TraesCS5B01G518500 chr5B 93.768 1412 63 11 859 2265 681344934 681343543 0.000000e+00 2097.0
2 TraesCS5B01G518500 chr5B 89.368 649 57 7 212 853 681345734 681345091 0.000000e+00 806.0
3 TraesCS5B01G518500 chr5B 88.555 533 55 4 3497 4025 114906306 114905776 3.390000e-180 641.0
4 TraesCS5B01G518500 chr5B 90.741 432 33 3 2789 3216 681343164 681342736 1.620000e-158 569.0
5 TraesCS5B01G518500 chr5B 86.174 528 52 12 3497 4016 297113304 297113818 5.880000e-153 551.0
6 TraesCS5B01G518500 chr5B 85.478 544 60 14 3497 4025 643150782 643150243 2.110000e-152 549.0
7 TraesCS5B01G518500 chr5B 93.519 216 11 2 1 215 9496542 9496329 6.490000e-83 318.0
8 TraesCS5B01G518500 chr5B 92.342 222 14 2 1 221 634337380 634337161 3.020000e-81 313.0
9 TraesCS5B01G518500 chr5B 94.565 184 8 2 3097 3279 681587634 681587452 2.370000e-72 283.0
10 TraesCS5B01G518500 chr5B 82.724 301 41 5 1062 1355 681737610 681737906 1.440000e-64 257.0
11 TraesCS5B01G518500 chr5B 86.486 222 16 10 3278 3494 681587291 681587079 8.700000e-57 231.0
12 TraesCS5B01G518500 chr4A 94.130 1465 68 12 859 2310 628848650 628850109 0.000000e+00 2213.0
13 TraesCS5B01G518500 chr4A 88.022 910 77 12 2320 3213 628850253 628851146 0.000000e+00 1048.0
14 TraesCS5B01G518500 chr4A 94.009 217 9 3 1 215 726413835 726414049 3.880000e-85 326.0
15 TraesCS5B01G518500 chr4A 93.488 215 10 3 1 213 718499533 718499321 2.330000e-82 316.0
16 TraesCS5B01G518500 chr4A 75.071 706 118 40 1411 2069 595283643 595282949 3.960000e-70 276.0
17 TraesCS5B01G518500 chr4A 95.041 121 5 1 742 862 628848458 628848577 5.310000e-44 189.0
18 TraesCS5B01G518500 chrUn 93.576 1183 64 7 928 2103 67357568 67358745 0.000000e+00 1753.0
19 TraesCS5B01G518500 chrUn 94.516 547 21 6 323 862 67356931 67357475 0.000000e+00 835.0
20 TraesCS5B01G518500 chrUn 87.838 296 25 5 2822 3109 67358742 67359034 1.790000e-88 337.0
21 TraesCS5B01G518500 chrUn 94.565 184 8 2 3097 3279 299312132 299312314 2.370000e-72 283.0
22 TraesCS5B01G518500 chrUn 82.392 301 42 5 1062 1355 67332364 67332660 6.680000e-63 252.0
23 TraesCS5B01G518500 chrUn 86.486 222 16 10 3278 3494 299312475 299312687 8.700000e-57 231.0
24 TraesCS5B01G518500 chrUn 89.286 84 9 0 217 300 67356851 67356934 5.500000e-19 106.0
25 TraesCS5B01G518500 chr5D 95.581 792 24 6 863 1654 539676124 539675344 0.000000e+00 1258.0
26 TraesCS5B01G518500 chr5D 86.474 1109 96 21 1637 2711 539675323 539674235 0.000000e+00 1168.0
27 TraesCS5B01G518500 chr5D 87.160 514 38 10 2714 3216 539674169 539673673 3.510000e-155 558.0
28 TraesCS5B01G518500 chr5D 95.139 144 7 0 680 823 539676369 539676226 1.130000e-55 228.0
29 TraesCS5B01G518500 chr5D 88.000 125 5 3 565 682 539677666 539677545 5.420000e-29 139.0
30 TraesCS5B01G518500 chr4B 88.550 524 53 4 3499 4020 520269654 520269136 2.640000e-176 628.0
31 TraesCS5B01G518500 chr4B 86.064 531 53 12 3497 4025 592201101 592200590 5.880000e-153 551.0
32 TraesCS5B01G518500 chr4B 87.088 364 39 4 3660 4020 598453187 598452829 4.840000e-109 405.0
33 TraesCS5B01G518500 chr4B 75.975 795 129 44 1313 2070 14653607 14652838 1.780000e-93 353.0
34 TraesCS5B01G518500 chr7B 87.689 528 50 9 3499 4025 55742843 55742330 5.760000e-168 601.0
35 TraesCS5B01G518500 chr7B 86.338 527 52 6 3499 4025 320260308 320259802 1.260000e-154 556.0
36 TraesCS5B01G518500 chr7B 87.444 446 41 10 3591 4025 659253184 659252743 2.160000e-137 499.0
37 TraesCS5B01G518500 chr7B 94.444 216 8 3 1 214 611626325 611626112 3.000000e-86 329.0
38 TraesCS5B01G518500 chr7B 93.488 215 10 3 2 214 733020639 733020427 2.330000e-82 316.0
39 TraesCS5B01G518500 chr7B 93.488 215 10 3 1 213 740915856 740916068 2.330000e-82 316.0
40 TraesCS5B01G518500 chr3B 85.635 543 60 12 3495 4025 349953293 349952757 4.550000e-154 555.0
41 TraesCS5B01G518500 chr3B 90.402 323 27 3 3700 4021 125634924 125635243 4.810000e-114 422.0
42 TraesCS5B01G518500 chr3B 94.444 216 8 3 3 216 758712045 758712258 3.000000e-86 329.0
43 TraesCS5B01G518500 chr1B 85.609 542 57 16 3492 4025 600665415 600665943 2.110000e-152 549.0
44 TraesCS5B01G518500 chr2B 84.404 545 67 11 3496 4025 497802957 497802416 1.660000e-143 520.0
45 TraesCS5B01G518500 chr2B 92.308 169 12 1 3497 3665 599206700 599206867 5.200000e-59 239.0
46 TraesCS5B01G518500 chr2B 94.444 36 2 0 2674 2709 6535122 6535157 5.620000e-04 56.5
47 TraesCS5B01G518500 chr6B 84.268 553 54 20 3499 4021 716308890 716309439 3.590000e-140 508.0
48 TraesCS5B01G518500 chr6B 89.820 334 31 2 3692 4025 35225975 35225645 3.720000e-115 425.0
49 TraesCS5B01G518500 chr6B 93.519 216 10 3 1 214 116423441 116423654 6.490000e-83 318.0
50 TraesCS5B01G518500 chr6B 93.413 167 10 1 3499 3665 632557069 632556904 3.110000e-61 246.0
51 TraesCS5B01G518500 chr6B 86.000 50 7 0 2422 2471 330981980 330981931 2.000000e-03 54.7
52 TraesCS5B01G518500 chr4D 74.895 713 122 35 1411 2073 8137044 8136339 5.130000e-69 272.0
53 TraesCS5B01G518500 chr4D 81.915 188 23 8 1411 1588 8011132 8011318 9.010000e-32 148.0
54 TraesCS5B01G518500 chr4D 92.553 94 7 0 1495 1588 8150922 8150829 7.020000e-28 135.0
55 TraesCS5B01G518500 chr3D 91.954 174 13 1 3492 3665 338545481 338545309 4.020000e-60 243.0


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 TraesCS5B01G518500 chr5B 681615264 681619288 4024 True 7433.000000 7433 100.000000 1 4025 1 chr5B.!!$R5 4024
1 TraesCS5B01G518500 chr5B 681342736 681345734 2998 True 1157.333333 2097 91.292333 212 3216 3 chr5B.!!$R6 3004
2 TraesCS5B01G518500 chr5B 114905776 114906306 530 True 641.000000 641 88.555000 3497 4025 1 chr5B.!!$R2 528
3 TraesCS5B01G518500 chr5B 297113304 297113818 514 False 551.000000 551 86.174000 3497 4016 1 chr5B.!!$F1 519
4 TraesCS5B01G518500 chr5B 643150243 643150782 539 True 549.000000 549 85.478000 3497 4025 1 chr5B.!!$R4 528
5 TraesCS5B01G518500 chr5B 681587079 681587634 555 True 257.000000 283 90.525500 3097 3494 2 chr5B.!!$R7 397
6 TraesCS5B01G518500 chr4A 628848458 628851146 2688 False 1150.000000 2213 92.397667 742 3213 3 chr4A.!!$F2 2471
7 TraesCS5B01G518500 chr4A 595282949 595283643 694 True 276.000000 276 75.071000 1411 2069 1 chr4A.!!$R1 658
8 TraesCS5B01G518500 chrUn 67356851 67359034 2183 False 757.750000 1753 91.304000 217 3109 4 chrUn.!!$F2 2892
9 TraesCS5B01G518500 chrUn 299312132 299312687 555 False 257.000000 283 90.525500 3097 3494 2 chrUn.!!$F3 397
10 TraesCS5B01G518500 chr5D 539673673 539677666 3993 True 670.200000 1258 90.470800 565 3216 5 chr5D.!!$R1 2651
11 TraesCS5B01G518500 chr4B 520269136 520269654 518 True 628.000000 628 88.550000 3499 4020 1 chr4B.!!$R2 521
12 TraesCS5B01G518500 chr4B 592200590 592201101 511 True 551.000000 551 86.064000 3497 4025 1 chr4B.!!$R3 528
13 TraesCS5B01G518500 chr4B 14652838 14653607 769 True 353.000000 353 75.975000 1313 2070 1 chr4B.!!$R1 757
14 TraesCS5B01G518500 chr7B 55742330 55742843 513 True 601.000000 601 87.689000 3499 4025 1 chr7B.!!$R1 526
15 TraesCS5B01G518500 chr7B 320259802 320260308 506 True 556.000000 556 86.338000 3499 4025 1 chr7B.!!$R2 526
16 TraesCS5B01G518500 chr3B 349952757 349953293 536 True 555.000000 555 85.635000 3495 4025 1 chr3B.!!$R1 530
17 TraesCS5B01G518500 chr1B 600665415 600665943 528 False 549.000000 549 85.609000 3492 4025 1 chr1B.!!$F1 533
18 TraesCS5B01G518500 chr2B 497802416 497802957 541 True 520.000000 520 84.404000 3496 4025 1 chr2B.!!$R1 529
19 TraesCS5B01G518500 chr6B 716308890 716309439 549 False 508.000000 508 84.268000 3499 4021 1 chr6B.!!$F2 522
20 TraesCS5B01G518500 chr4D 8136339 8137044 705 True 272.000000 272 74.895000 1411 2073 1 chr4D.!!$R1 662

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
39 40 0.035725 CCACCCTTTAGTCCCGGTTC 60.036 60.0 0.0 0.0 0.00 3.62 F
46 47 0.035820 TTAGTCCCGGTTCATGGCAC 60.036 55.0 0.0 0.0 0.00 5.01 F
1823 3354 0.035152 TCCAACAGCGATGATGGCTT 60.035 50.0 23.6 0.0 39.08 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 2749 1.376037 GCCGAGGTGAAGTTCCAGG 60.376 63.158 0.00 0.0 0.00 4.45 R
1874 3432 1.541015 CGATCTCCGGCAATGGAATCA 60.541 52.381 0.00 0.0 37.64 2.57 R
3772 5821 0.031585 TCTTATAACGAGCGCCGCAT 59.968 50.000 13.36 12.6 43.32 4.73 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
18 19 3.464207 CCGGTACTAAAATGGGCGT 57.536 52.632 0.00 0.00 0.00 5.68
19 20 1.292992 CCGGTACTAAAATGGGCGTC 58.707 55.000 0.00 0.00 0.00 5.19
20 21 1.292992 CGGTACTAAAATGGGCGTCC 58.707 55.000 0.00 0.00 0.00 4.79
21 22 1.671979 GGTACTAAAATGGGCGTCCC 58.328 55.000 2.12 5.67 45.71 4.46
30 31 2.271173 GGGCGTCCCACCCTTTAG 59.729 66.667 9.72 0.00 44.65 1.85
31 32 2.599757 GGGCGTCCCACCCTTTAGT 61.600 63.158 9.72 0.00 44.65 2.24
32 33 1.078637 GGCGTCCCACCCTTTAGTC 60.079 63.158 0.00 0.00 0.00 2.59
33 34 1.078637 GCGTCCCACCCTTTAGTCC 60.079 63.158 0.00 0.00 0.00 3.85
34 35 1.600638 CGTCCCACCCTTTAGTCCC 59.399 63.158 0.00 0.00 0.00 4.46
35 36 1.600638 GTCCCACCCTTTAGTCCCG 59.399 63.158 0.00 0.00 0.00 5.14
36 37 1.614226 TCCCACCCTTTAGTCCCGG 60.614 63.158 0.00 0.00 0.00 5.73
37 38 1.921857 CCCACCCTTTAGTCCCGGT 60.922 63.158 0.00 0.00 0.00 5.28
38 39 1.494716 CCCACCCTTTAGTCCCGGTT 61.495 60.000 0.00 0.00 0.00 4.44
39 40 0.035725 CCACCCTTTAGTCCCGGTTC 60.036 60.000 0.00 0.00 0.00 3.62
40 41 0.688487 CACCCTTTAGTCCCGGTTCA 59.312 55.000 0.00 0.00 0.00 3.18
41 42 1.280998 CACCCTTTAGTCCCGGTTCAT 59.719 52.381 0.00 0.00 0.00 2.57
42 43 1.280998 ACCCTTTAGTCCCGGTTCATG 59.719 52.381 0.00 0.00 0.00 3.07
43 44 1.408266 CCCTTTAGTCCCGGTTCATGG 60.408 57.143 0.00 0.00 0.00 3.66
44 45 1.379527 CTTTAGTCCCGGTTCATGGC 58.620 55.000 0.00 0.00 0.00 4.40
45 46 0.693622 TTTAGTCCCGGTTCATGGCA 59.306 50.000 0.00 0.00 0.00 4.92
46 47 0.035820 TTAGTCCCGGTTCATGGCAC 60.036 55.000 0.00 0.00 0.00 5.01
47 48 1.906105 TAGTCCCGGTTCATGGCACC 61.906 60.000 0.00 5.18 0.00 5.01
48 49 3.253061 TCCCGGTTCATGGCACCA 61.253 61.111 13.57 0.00 33.36 4.17
49 50 2.282816 CCCGGTTCATGGCACCAA 60.283 61.111 13.57 0.00 33.36 3.67
50 51 2.635443 CCCGGTTCATGGCACCAAC 61.635 63.158 13.57 0.00 33.36 3.77
51 52 2.635443 CCGGTTCATGGCACCAACC 61.635 63.158 16.24 16.24 36.91 3.77
52 53 2.961768 GGTTCATGGCACCAACCG 59.038 61.111 12.38 0.00 34.04 4.44
53 54 2.635443 GGTTCATGGCACCAACCGG 61.635 63.158 12.38 0.00 34.04 5.28
54 55 2.282816 TTCATGGCACCAACCGGG 60.283 61.111 6.32 0.00 44.81 5.73
55 56 2.835049 TTCATGGCACCAACCGGGA 61.835 57.895 6.32 0.00 41.15 5.14
56 57 3.061848 CATGGCACCAACCGGGAC 61.062 66.667 6.32 0.00 41.15 4.46
57 58 3.256960 ATGGCACCAACCGGGACT 61.257 61.111 6.32 0.00 41.15 3.85
58 59 1.921346 ATGGCACCAACCGGGACTA 60.921 57.895 6.32 0.00 41.15 2.59
59 60 1.493854 ATGGCACCAACCGGGACTAA 61.494 55.000 6.32 0.00 41.15 2.24
60 61 1.073548 GGCACCAACCGGGACTAAA 59.926 57.895 6.32 0.00 41.15 1.85
61 62 0.537828 GGCACCAACCGGGACTAAAA 60.538 55.000 6.32 0.00 41.15 1.52
62 63 0.879090 GCACCAACCGGGACTAAAAG 59.121 55.000 6.32 0.00 41.15 2.27
63 64 1.530323 CACCAACCGGGACTAAAAGG 58.470 55.000 6.32 0.00 41.15 3.11
64 65 1.142936 ACCAACCGGGACTAAAAGGT 58.857 50.000 6.32 0.00 41.15 3.50
65 66 1.072806 ACCAACCGGGACTAAAAGGTC 59.927 52.381 6.32 0.00 41.15 3.85
75 76 3.324117 GACTAAAAGGTCCAGACGAACC 58.676 50.000 0.00 0.00 35.69 3.62
76 77 2.288640 ACTAAAAGGTCCAGACGAACCG 60.289 50.000 0.00 0.00 40.63 4.44
77 78 0.250166 AAAAGGTCCAGACGAACCGG 60.250 55.000 0.00 0.00 40.63 5.28
78 79 2.108278 AAAGGTCCAGACGAACCGGG 62.108 60.000 6.32 0.00 40.63 5.73
79 80 2.993264 GGTCCAGACGAACCGGGA 60.993 66.667 6.32 0.00 0.00 5.14
80 81 2.260743 GTCCAGACGAACCGGGAC 59.739 66.667 6.32 9.54 42.60 4.46
81 82 2.203523 TCCAGACGAACCGGGACA 60.204 61.111 6.32 0.00 0.00 4.02
82 83 1.833492 TCCAGACGAACCGGGACAA 60.833 57.895 6.32 0.00 0.00 3.18
83 84 1.070105 CCAGACGAACCGGGACAAA 59.930 57.895 6.32 0.00 0.00 2.83
84 85 0.321298 CCAGACGAACCGGGACAAAT 60.321 55.000 6.32 0.00 0.00 2.32
85 86 0.796312 CAGACGAACCGGGACAAATG 59.204 55.000 6.32 0.00 0.00 2.32
86 87 0.321298 AGACGAACCGGGACAAATGG 60.321 55.000 6.32 0.00 0.00 3.16
87 88 1.918868 GACGAACCGGGACAAATGGC 61.919 60.000 6.32 0.00 0.00 4.40
88 89 2.696759 CGAACCGGGACAAATGGCC 61.697 63.158 6.32 0.00 44.61 5.36
94 95 2.961768 GGACAAATGGCCCACGTG 59.038 61.111 9.08 9.08 37.19 4.49
95 96 2.635443 GGACAAATGGCCCACGTGG 61.635 63.158 28.26 28.26 37.19 4.94
122 123 2.359975 CCCCTTGGCTCACGAACC 60.360 66.667 0.00 0.00 0.00 3.62
123 124 2.742372 CCCTTGGCTCACGAACCG 60.742 66.667 0.00 0.00 0.00 4.44
124 125 2.742372 CCTTGGCTCACGAACCGG 60.742 66.667 0.00 0.00 0.00 5.28
125 126 2.742372 CTTGGCTCACGAACCGGG 60.742 66.667 6.32 0.00 0.00 5.73
126 127 3.234630 CTTGGCTCACGAACCGGGA 62.235 63.158 6.32 0.00 36.75 5.14
127 128 3.524648 TTGGCTCACGAACCGGGAC 62.525 63.158 6.32 0.00 32.99 4.46
128 129 4.754667 GGCTCACGAACCGGGACC 62.755 72.222 6.32 0.00 32.99 4.46
129 130 3.998672 GCTCACGAACCGGGACCA 61.999 66.667 6.32 0.00 32.99 4.02
130 131 2.738480 CTCACGAACCGGGACCAA 59.262 61.111 6.32 0.00 32.99 3.67
131 132 1.295423 CTCACGAACCGGGACCAAT 59.705 57.895 6.32 0.00 32.99 3.16
132 133 1.004320 TCACGAACCGGGACCAATG 60.004 57.895 6.32 0.00 32.99 2.82
133 134 2.359478 ACGAACCGGGACCAATGC 60.359 61.111 6.32 0.00 0.00 3.56
134 135 3.131478 CGAACCGGGACCAATGCC 61.131 66.667 6.32 0.00 0.00 4.40
135 136 2.754254 GAACCGGGACCAATGCCC 60.754 66.667 6.32 0.00 42.41 5.36
136 137 4.376170 AACCGGGACCAATGCCCC 62.376 66.667 6.32 0.00 42.92 5.80
138 139 4.141876 CCGGGACCAATGCCCCAT 62.142 66.667 9.10 0.00 42.92 4.00
139 140 2.834505 CGGGACCAATGCCCCATG 60.835 66.667 9.10 0.00 42.92 3.66
140 141 2.364160 GGGACCAATGCCCCATGT 59.636 61.111 4.42 0.00 42.24 3.21
141 142 2.059786 GGGACCAATGCCCCATGTG 61.060 63.158 4.42 0.00 42.24 3.21
142 143 1.305213 GGACCAATGCCCCATGTGT 60.305 57.895 0.00 0.00 0.00 3.72
143 144 1.322538 GGACCAATGCCCCATGTGTC 61.323 60.000 0.00 0.00 0.00 3.67
144 145 1.305213 ACCAATGCCCCATGTGTCC 60.305 57.895 0.00 0.00 0.00 4.02
145 146 2.059786 CCAATGCCCCATGTGTCCC 61.060 63.158 0.00 0.00 0.00 4.46
146 147 2.044053 AATGCCCCATGTGTCCCG 60.044 61.111 0.00 0.00 0.00 5.14
147 148 3.660422 AATGCCCCATGTGTCCCGG 62.660 63.158 0.00 0.00 0.00 5.73
149 150 4.360405 GCCCCATGTGTCCCGGTT 62.360 66.667 0.00 0.00 0.00 4.44
150 151 2.045340 CCCCATGTGTCCCGGTTC 60.045 66.667 0.00 0.00 0.00 3.62
151 152 2.602676 CCCCATGTGTCCCGGTTCT 61.603 63.158 0.00 0.00 0.00 3.01
152 153 1.377202 CCCATGTGTCCCGGTTCTG 60.377 63.158 0.00 0.00 0.00 3.02
153 154 1.377202 CCATGTGTCCCGGTTCTGG 60.377 63.158 0.00 0.00 0.00 3.86
154 155 1.676968 CATGTGTCCCGGTTCTGGA 59.323 57.895 0.00 0.00 0.00 3.86
159 160 4.631493 TCCCGGTTCTGGACTGAA 57.369 55.556 0.00 0.00 36.72 3.02
160 161 2.055299 TCCCGGTTCTGGACTGAAC 58.945 57.895 12.04 12.04 43.88 3.18
164 165 4.695560 GTTCTGGACTGAACCGGG 57.304 61.111 6.32 0.00 40.10 5.73
165 166 2.055299 GTTCTGGACTGAACCGGGA 58.945 57.895 6.32 0.00 40.10 5.14
166 167 0.320508 GTTCTGGACTGAACCGGGAC 60.321 60.000 6.32 0.00 40.10 4.46
167 168 0.471211 TTCTGGACTGAACCGGGACT 60.471 55.000 6.32 0.00 36.97 3.85
168 169 0.406750 TCTGGACTGAACCGGGACTA 59.593 55.000 6.32 0.00 36.97 2.59
169 170 1.203087 TCTGGACTGAACCGGGACTAA 60.203 52.381 6.32 0.00 36.97 2.24
170 171 1.831736 CTGGACTGAACCGGGACTAAT 59.168 52.381 6.32 0.00 33.06 1.73
171 172 1.553248 TGGACTGAACCGGGACTAATG 59.447 52.381 6.32 0.00 0.00 1.90
172 173 1.134491 GGACTGAACCGGGACTAATGG 60.134 57.143 6.32 0.00 0.00 3.16
173 174 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
174 175 0.463833 CTGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
175 176 0.912487 TGAACCGGGACTAATGGGCT 60.912 55.000 6.32 0.00 0.00 5.19
176 177 1.125633 GAACCGGGACTAATGGGCTA 58.874 55.000 6.32 0.00 0.00 3.93
177 178 1.487558 GAACCGGGACTAATGGGCTAA 59.512 52.381 6.32 0.00 0.00 3.09
178 179 0.835276 ACCGGGACTAATGGGCTAAC 59.165 55.000 6.32 0.00 0.00 2.34
179 180 0.108019 CCGGGACTAATGGGCTAACC 59.892 60.000 0.00 0.00 40.81 2.85
189 190 2.820261 GGCTAACCCGGCCTAGAC 59.180 66.667 11.22 5.35 45.57 2.59
190 191 2.804912 GGCTAACCCGGCCTAGACC 61.805 68.421 11.22 8.32 45.57 3.85
191 192 2.062177 GCTAACCCGGCCTAGACCA 61.062 63.158 11.22 0.00 0.00 4.02
192 193 1.619807 GCTAACCCGGCCTAGACCAA 61.620 60.000 11.22 0.00 0.00 3.67
193 194 0.906775 CTAACCCGGCCTAGACCAAA 59.093 55.000 0.00 0.00 0.00 3.28
194 195 0.906775 TAACCCGGCCTAGACCAAAG 59.093 55.000 0.00 0.00 0.00 2.77
195 196 2.124695 CCCGGCCTAGACCAAAGC 60.125 66.667 0.00 0.00 0.00 3.51
196 197 2.124695 CCGGCCTAGACCAAAGCC 60.125 66.667 0.00 0.00 42.18 4.35
197 198 2.124695 CGGCCTAGACCAAAGCCC 60.125 66.667 0.00 0.00 42.66 5.19
198 199 2.670148 CGGCCTAGACCAAAGCCCT 61.670 63.158 0.00 0.00 42.66 5.19
199 200 1.224870 GGCCTAGACCAAAGCCCTC 59.775 63.158 0.00 0.00 39.60 4.30
200 201 1.275421 GGCCTAGACCAAAGCCCTCT 61.275 60.000 0.00 0.00 39.60 3.69
201 202 0.621082 GCCTAGACCAAAGCCCTCTT 59.379 55.000 0.00 0.00 0.00 2.85
202 203 1.004862 GCCTAGACCAAAGCCCTCTTT 59.995 52.381 0.00 0.00 42.92 2.52
203 204 2.555448 GCCTAGACCAAAGCCCTCTTTT 60.555 50.000 0.00 0.00 40.35 2.27
204 205 3.348119 CCTAGACCAAAGCCCTCTTTTC 58.652 50.000 0.00 0.00 40.35 2.29
205 206 3.009584 CCTAGACCAAAGCCCTCTTTTCT 59.990 47.826 0.00 0.00 40.35 2.52
206 207 4.225267 CCTAGACCAAAGCCCTCTTTTCTA 59.775 45.833 0.00 0.00 40.35 2.10
207 208 4.022413 AGACCAAAGCCCTCTTTTCTAC 57.978 45.455 0.00 0.00 40.35 2.59
208 209 3.653352 AGACCAAAGCCCTCTTTTCTACT 59.347 43.478 0.00 0.00 40.35 2.57
209 210 4.844655 AGACCAAAGCCCTCTTTTCTACTA 59.155 41.667 0.00 0.00 40.35 1.82
210 211 5.046231 AGACCAAAGCCCTCTTTTCTACTAG 60.046 44.000 0.00 0.00 40.35 2.57
222 223 0.541392 TCTACTAGTGTCGGGGCGTA 59.459 55.000 5.39 0.00 0.00 4.42
229 230 4.424566 GTCGGGGCGTACGCTTCA 62.425 66.667 36.24 17.32 41.60 3.02
282 283 3.752747 TGATGATGGTGGCAAATATAGCG 59.247 43.478 0.00 0.00 0.00 4.26
294 295 0.182537 ATATAGCGGGGTTGCAGCAA 59.817 50.000 2.83 2.83 37.31 3.91
304 305 1.200948 GGTTGCAGCAAGTCCTTCATC 59.799 52.381 8.49 0.00 0.00 2.92
307 308 0.723981 GCAGCAAGTCCTTCATCGTC 59.276 55.000 0.00 0.00 0.00 4.20
313 314 2.167861 GTCCTTCATCGTCGGCAGC 61.168 63.158 0.00 0.00 0.00 5.25
329 330 2.032681 GCCGGCTTGTTCCTGAGT 59.967 61.111 22.15 0.00 0.00 3.41
339 340 5.009610 GGCTTGTTCCTGAGTGTTAATTCAA 59.990 40.000 0.00 0.00 0.00 2.69
380 382 1.934463 CGCCTGCAACGATACCATC 59.066 57.895 2.74 0.00 0.00 3.51
441 443 9.665264 CTTTGTAAAGCTTGGTAGAAACTTAAG 57.335 33.333 0.00 0.00 0.00 1.85
447 449 9.569122 AAAGCTTGGTAGAAACTTAAGATTACA 57.431 29.630 10.09 0.00 32.32 2.41
558 560 1.535896 TGTTTCAGAGTCCTCGTCGAG 59.464 52.381 15.53 15.53 34.09 4.04
733 1930 8.264347 GGCCTCCAAAAATAATCAAGGATTAAA 58.736 33.333 0.00 0.00 37.92 1.52
736 1933 9.599866 CTCCAAAAATAATCAAGGATTAAACCC 57.400 33.333 0.00 0.00 37.92 4.11
850 2136 5.626142 TGCTTCTTGTTTCCCATAGTACAA 58.374 37.500 0.00 0.00 0.00 2.41
986 2397 9.159254 TGTGTGATTTATAGGTTAGATCCATCT 57.841 33.333 0.00 0.00 40.86 2.90
1182 2594 1.564818 TCCCGTCATCACTCCTAGAGT 59.435 52.381 0.00 0.00 44.44 3.24
1823 3354 0.035152 TCCAACAGCGATGATGGCTT 60.035 50.000 23.60 0.00 39.08 4.35
1862 3420 1.611851 CAGCAGGTGGAGGAGGTCT 60.612 63.158 0.00 0.00 0.00 3.85
1866 3424 1.079438 AGGTGGAGGAGGTCTGACC 59.921 63.158 19.20 19.20 38.99 4.02
1874 3432 0.608640 GGAGGTCTGACCACGACAAT 59.391 55.000 27.48 5.90 41.95 2.71
1878 3436 2.303022 AGGTCTGACCACGACAATGATT 59.697 45.455 27.48 0.27 41.95 2.57
2152 3721 4.992688 AGACGTTTTTGCAGTTCAAATCA 58.007 34.783 0.00 0.00 43.53 2.57
2166 3736 9.176181 GCAGTTCAAATCAAACTATAAAAACGA 57.824 29.630 0.00 0.00 35.25 3.85
2204 3774 4.279169 AGAGTTAGTACTTGTTGCCGTACA 59.721 41.667 0.00 0.00 38.69 2.90
2344 4070 2.915738 ACCTTACTTGAGTCGTAGCG 57.084 50.000 0.00 0.00 0.00 4.26
2364 4090 3.967470 GCGAATTGCCACAAATGTTTTTG 59.033 39.130 0.00 0.00 42.07 2.44
2371 4097 3.242252 GCCACAAATGTTTTTGGAACACG 60.242 43.478 13.37 0.00 45.34 4.49
2372 4098 3.308323 CCACAAATGTTTTTGGAACACGG 59.692 43.478 4.99 0.00 45.34 4.94
2385 4111 4.062293 TGGAACACGGTGTAATCAAAGAG 58.938 43.478 15.11 0.00 0.00 2.85
2391 4117 5.171476 CACGGTGTAATCAAAGAGACTCAT 58.829 41.667 5.02 0.00 0.00 2.90
2394 4120 6.980978 ACGGTGTAATCAAAGAGACTCATATG 59.019 38.462 5.02 0.00 0.00 1.78
2416 4142 3.000322 GCACGCACATACACTCATTCTAC 60.000 47.826 0.00 0.00 0.00 2.59
2421 4147 5.912955 CGCACATACACTCATTCTACGAATA 59.087 40.000 0.00 0.00 0.00 1.75
2456 4187 1.106351 ATGTGAGCACCAACGCCAAA 61.106 50.000 0.00 0.00 0.00 3.28
2462 4193 3.202906 GAGCACCAACGCCAAATCTATA 58.797 45.455 0.00 0.00 0.00 1.31
2474 4205 5.220854 CGCCAAATCTATAACTTGAACCCTG 60.221 44.000 0.00 0.00 0.00 4.45
2475 4206 5.450550 GCCAAATCTATAACTTGAACCCTGC 60.451 44.000 0.00 0.00 0.00 4.85
2476 4207 5.888161 CCAAATCTATAACTTGAACCCTGCT 59.112 40.000 0.00 0.00 0.00 4.24
2477 4208 6.183360 CCAAATCTATAACTTGAACCCTGCTG 60.183 42.308 0.00 0.00 0.00 4.41
2479 4210 1.839424 ATAACTTGAACCCTGCTGGC 58.161 50.000 3.63 0.00 37.83 4.85
2496 4227 1.301954 GCCGGGTTAGTTCCACCAT 59.698 57.895 2.18 0.00 35.80 3.55
2501 4232 3.431766 CCGGGTTAGTTCCACCATAAGAG 60.432 52.174 0.00 0.00 35.80 2.85
2512 4243 9.710818 AGTTCCACCATAAGAGAACTAACTATA 57.289 33.333 2.57 0.00 45.31 1.31
2525 4256 8.542497 AGAACTAACTATATGAGCTACTCTCG 57.458 38.462 0.00 0.00 44.86 4.04
2530 4261 5.622180 ACTATATGAGCTACTCTCGGTTCA 58.378 41.667 0.00 0.00 44.86 3.18
2548 4279 4.260702 GGTTCACAATTGCCACAAATGTTG 60.261 41.667 5.05 0.00 0.00 3.33
2705 4454 8.336235 ACTCCCTCCATTTCAAAATGTAAGATA 58.664 33.333 12.99 3.56 43.24 1.98
2775 4589 7.338449 ACTGGTACAAAGTTTAAGTCACACAAT 59.662 33.333 0.00 0.00 38.70 2.71
2818 4632 6.596106 TCGTCAGCCATATTAAACTTAAGCAA 59.404 34.615 1.29 0.00 0.00 3.91
2823 4637 7.915397 CAGCCATATTAAACTTAAGCAACGATT 59.085 33.333 1.29 0.00 0.00 3.34
2830 4644 5.607119 AACTTAAGCAACGATTGTCGAAT 57.393 34.783 1.29 0.00 43.74 3.34
2939 4760 1.444553 GACGAGGGCTTCACTGTCG 60.445 63.158 0.00 0.00 36.71 4.35
2950 4771 3.749064 ACTGTCGCAGCGGACGAT 61.749 61.111 16.42 1.59 42.26 3.73
2999 4820 0.583438 CCGACATCATAGCGGCAAAG 59.417 55.000 1.45 0.00 38.46 2.77
3016 4845 4.311606 GCAAAGGATAGTTCTAGCTAGGC 58.688 47.826 20.58 13.44 0.00 3.93
3093 4923 6.694411 GCTTATGTCCAATTAGCATGTTCAAG 59.306 38.462 0.00 0.00 0.00 3.02
3105 4945 3.559655 GCATGTTCAAGTAGTGTGTGTGA 59.440 43.478 0.00 0.00 0.00 3.58
3112 4952 3.032017 AGTAGTGTGTGTGAGTGCATC 57.968 47.619 0.00 0.00 0.00 3.91
3162 5002 1.737838 TCTCGGGCACATGTTCAATC 58.262 50.000 0.00 0.00 0.00 2.67
3221 5061 2.876550 CACTACAGCATCATGGTCATGG 59.123 50.000 10.61 0.00 39.24 3.66
3244 5084 0.035439 CCAAAGTGGTACATCCGGCT 60.035 55.000 0.00 0.00 44.52 5.52
3252 5092 1.472728 GGTACATCCGGCTCGTTGATT 60.473 52.381 0.00 0.00 0.00 2.57
3323 5326 7.500227 GGTAGGGTCCTATGTAACAAAATTACC 59.500 40.741 0.00 0.00 0.00 2.85
3325 5328 5.595542 GGGTCCTATGTAACAAAATTACCCC 59.404 44.000 0.00 0.00 37.45 4.95
3339 5342 2.916527 TACCCCTAAGCGCGCCTAGT 62.917 60.000 29.36 20.02 0.00 2.57
3342 5345 0.388649 CCCTAAGCGCGCCTAGTATG 60.389 60.000 29.36 17.25 0.00 2.39
3349 5352 1.803625 GCGCGCCTAGTATGTTTGGTA 60.804 52.381 23.24 0.00 0.00 3.25
3352 5355 3.558418 CGCGCCTAGTATGTTTGGTATTT 59.442 43.478 0.00 0.00 0.00 1.40
3359 5362 7.465513 GCCTAGTATGTTTGGTATTTTCTCGTG 60.466 40.741 0.00 0.00 0.00 4.35
3363 5366 6.817765 ATGTTTGGTATTTTCTCGTGTCAT 57.182 33.333 0.00 0.00 0.00 3.06
3364 5367 7.915293 ATGTTTGGTATTTTCTCGTGTCATA 57.085 32.000 0.00 0.00 0.00 2.15
3380 5383 3.315470 TGTCATACTCCATCGTGCTAGAC 59.685 47.826 0.00 0.00 0.00 2.59
3394 5399 1.332375 GCTAGACAGAGAGCGTACTGG 59.668 57.143 0.00 0.00 38.30 4.00
3399 5404 4.270834 AGACAGAGAGCGTACTGGAATAA 58.729 43.478 10.61 0.00 38.30 1.40
3432 5440 9.667107 TGAGTGAAAAGTACTGGGATATTTTAG 57.333 33.333 0.00 0.00 0.00 1.85
3433 5441 9.668497 GAGTGAAAAGTACTGGGATATTTTAGT 57.332 33.333 0.00 0.00 0.00 2.24
3519 5527 2.281208 CAACTCCAACGGGCCGAA 60.281 61.111 35.78 13.68 0.00 4.30
3810 5861 1.122019 AAGACGCTCCCTCCACACTT 61.122 55.000 0.00 0.00 0.00 3.16
3819 5876 0.320374 CCTCCACACTTAGTTCGCCA 59.680 55.000 0.00 0.00 0.00 5.69
3821 5878 1.000955 CTCCACACTTAGTTCGCCACT 59.999 52.381 0.00 0.00 39.87 4.00
3833 5891 2.505118 GCCACTCACTCGTCTCGC 60.505 66.667 0.00 0.00 0.00 5.03
3834 5892 2.179517 CCACTCACTCGTCTCGCC 59.820 66.667 0.00 0.00 0.00 5.54
3880 5938 3.037992 GCGCCAACATGTCGATGCA 62.038 57.895 9.39 0.00 32.14 3.96
3983 6041 1.604378 CCTCATCCTCGGCACCTTT 59.396 57.895 0.00 0.00 0.00 3.11
3989 6047 1.071471 CCTCGGCACCTTTGACACT 59.929 57.895 0.00 0.00 0.00 3.55
3996 6054 1.811558 GCACCTTTGACACTGCAGAGA 60.812 52.381 23.35 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.292992 GGACGCCCATTTTAGTACCG 58.707 55.000 0.00 0.00 0.00 4.02
15 16 1.078637 GGACTAAAGGGTGGGACGC 60.079 63.158 0.00 0.00 38.67 5.19
16 17 1.600638 GGGACTAAAGGGTGGGACG 59.399 63.158 0.00 0.00 0.00 4.79
17 18 1.600638 CGGGACTAAAGGGTGGGAC 59.399 63.158 0.00 0.00 0.00 4.46
18 19 1.614226 CCGGGACTAAAGGGTGGGA 60.614 63.158 0.00 0.00 0.00 4.37
19 20 1.494716 AACCGGGACTAAAGGGTGGG 61.495 60.000 6.32 0.00 31.96 4.61
20 21 0.035725 GAACCGGGACTAAAGGGTGG 60.036 60.000 6.32 0.00 31.96 4.61
21 22 0.688487 TGAACCGGGACTAAAGGGTG 59.312 55.000 6.32 0.00 31.96 4.61
22 23 1.280998 CATGAACCGGGACTAAAGGGT 59.719 52.381 6.32 0.00 0.00 4.34
23 24 1.408266 CCATGAACCGGGACTAAAGGG 60.408 57.143 6.32 0.00 0.00 3.95
24 25 2.017113 GCCATGAACCGGGACTAAAGG 61.017 57.143 6.32 0.00 0.00 3.11
25 26 1.339631 TGCCATGAACCGGGACTAAAG 60.340 52.381 6.32 0.00 0.00 1.85
26 27 0.693622 TGCCATGAACCGGGACTAAA 59.306 50.000 6.32 0.00 0.00 1.85
27 28 0.035820 GTGCCATGAACCGGGACTAA 60.036 55.000 6.32 0.00 41.35 2.24
28 29 1.600107 GTGCCATGAACCGGGACTA 59.400 57.895 6.32 0.00 41.35 2.59
29 30 2.351276 GTGCCATGAACCGGGACT 59.649 61.111 6.32 0.00 41.35 3.85
30 31 2.750237 GGTGCCATGAACCGGGAC 60.750 66.667 6.32 0.00 43.66 4.46
31 32 2.835049 TTGGTGCCATGAACCGGGA 61.835 57.895 6.32 0.00 40.86 5.14
32 33 2.282816 TTGGTGCCATGAACCGGG 60.283 61.111 6.32 0.00 40.86 5.73
33 34 2.635443 GGTTGGTGCCATGAACCGG 61.635 63.158 0.00 0.00 40.86 5.28
34 35 2.961768 GGTTGGTGCCATGAACCG 59.038 61.111 11.54 0.00 40.86 4.44
35 36 2.635443 CCGGTTGGTGCCATGAACC 61.635 63.158 9.87 9.87 38.26 3.62
36 37 2.635443 CCCGGTTGGTGCCATGAAC 61.635 63.158 0.00 0.00 0.00 3.18
37 38 2.282816 CCCGGTTGGTGCCATGAA 60.283 61.111 0.00 0.00 0.00 2.57
38 39 3.253061 TCCCGGTTGGTGCCATGA 61.253 61.111 0.00 0.00 34.77 3.07
39 40 2.191786 TAGTCCCGGTTGGTGCCATG 62.192 60.000 0.00 0.00 34.77 3.66
40 41 1.493854 TTAGTCCCGGTTGGTGCCAT 61.494 55.000 0.00 0.00 34.77 4.40
41 42 1.706995 TTTAGTCCCGGTTGGTGCCA 61.707 55.000 0.00 0.00 34.77 4.92
42 43 0.537828 TTTTAGTCCCGGTTGGTGCC 60.538 55.000 0.00 0.00 34.77 5.01
43 44 0.879090 CTTTTAGTCCCGGTTGGTGC 59.121 55.000 0.00 0.00 34.77 5.01
44 45 1.202842 ACCTTTTAGTCCCGGTTGGTG 60.203 52.381 0.00 0.00 34.77 4.17
45 46 1.072806 GACCTTTTAGTCCCGGTTGGT 59.927 52.381 0.00 0.00 34.77 3.67
46 47 1.817357 GACCTTTTAGTCCCGGTTGG 58.183 55.000 0.00 0.00 0.00 3.77
54 55 3.324117 GGTTCGTCTGGACCTTTTAGTC 58.676 50.000 0.00 0.00 35.95 2.59
55 56 2.288640 CGGTTCGTCTGGACCTTTTAGT 60.289 50.000 0.00 0.00 0.00 2.24
56 57 2.334838 CGGTTCGTCTGGACCTTTTAG 58.665 52.381 0.00 0.00 0.00 1.85
57 58 1.001181 CCGGTTCGTCTGGACCTTTTA 59.999 52.381 0.00 0.00 45.09 1.52
58 59 0.250166 CCGGTTCGTCTGGACCTTTT 60.250 55.000 0.00 0.00 45.09 2.27
59 60 1.370064 CCGGTTCGTCTGGACCTTT 59.630 57.895 0.00 0.00 45.09 3.11
60 61 2.580601 CCCGGTTCGTCTGGACCTT 61.581 63.158 0.00 0.00 45.09 3.50
61 62 2.995574 CCCGGTTCGTCTGGACCT 60.996 66.667 0.00 0.00 45.09 3.85
62 63 2.993264 TCCCGGTTCGTCTGGACC 60.993 66.667 0.00 0.00 45.09 4.46
63 64 2.091102 TTGTCCCGGTTCGTCTGGAC 62.091 60.000 0.00 0.00 45.09 4.02
64 65 1.401318 TTTGTCCCGGTTCGTCTGGA 61.401 55.000 0.00 0.00 45.09 3.86
65 66 0.321298 ATTTGTCCCGGTTCGTCTGG 60.321 55.000 0.00 2.18 42.06 3.86
66 67 0.796312 CATTTGTCCCGGTTCGTCTG 59.204 55.000 0.00 0.00 0.00 3.51
67 68 0.321298 CCATTTGTCCCGGTTCGTCT 60.321 55.000 0.00 0.00 0.00 4.18
68 69 1.918868 GCCATTTGTCCCGGTTCGTC 61.919 60.000 0.00 0.00 0.00 4.20
69 70 1.969589 GCCATTTGTCCCGGTTCGT 60.970 57.895 0.00 0.00 0.00 3.85
70 71 2.696759 GGCCATTTGTCCCGGTTCG 61.697 63.158 0.00 0.00 0.00 3.95
71 72 2.348104 GGGCCATTTGTCCCGGTTC 61.348 63.158 4.39 0.00 32.00 3.62
72 73 2.283604 GGGCCATTTGTCCCGGTT 60.284 61.111 4.39 0.00 32.00 4.44
73 74 3.585428 TGGGCCATTTGTCCCGGT 61.585 61.111 0.00 0.00 45.60 5.28
74 75 3.068064 GTGGGCCATTTGTCCCGG 61.068 66.667 10.70 0.00 45.60 5.73
75 76 3.439540 CGTGGGCCATTTGTCCCG 61.440 66.667 10.70 2.04 45.60 5.14
76 77 2.282887 ACGTGGGCCATTTGTCCC 60.283 61.111 10.70 0.00 42.93 4.46
77 78 2.635443 CCACGTGGGCCATTTGTCC 61.635 63.158 27.57 0.00 0.00 4.02
78 79 2.961768 CCACGTGGGCCATTTGTC 59.038 61.111 27.57 0.00 0.00 3.18
105 106 2.359975 GGTTCGTGAGCCAAGGGG 60.360 66.667 0.00 0.00 37.18 4.79
106 107 2.742372 CGGTTCGTGAGCCAAGGG 60.742 66.667 3.61 0.00 0.00 3.95
107 108 2.742372 CCGGTTCGTGAGCCAAGG 60.742 66.667 3.61 0.00 0.00 3.61
108 109 2.742372 CCCGGTTCGTGAGCCAAG 60.742 66.667 0.00 0.00 0.00 3.61
109 110 3.235481 TCCCGGTTCGTGAGCCAA 61.235 61.111 0.00 0.00 0.00 4.52
110 111 3.998672 GTCCCGGTTCGTGAGCCA 61.999 66.667 0.00 0.00 0.00 4.75
111 112 4.754667 GGTCCCGGTTCGTGAGCC 62.755 72.222 0.00 0.00 0.00 4.70
112 113 2.798148 ATTGGTCCCGGTTCGTGAGC 62.798 60.000 0.00 0.00 32.96 4.26
113 114 1.019278 CATTGGTCCCGGTTCGTGAG 61.019 60.000 0.00 0.00 0.00 3.51
114 115 1.004320 CATTGGTCCCGGTTCGTGA 60.004 57.895 0.00 0.00 0.00 4.35
115 116 2.686816 GCATTGGTCCCGGTTCGTG 61.687 63.158 0.00 0.00 0.00 4.35
116 117 2.359478 GCATTGGTCCCGGTTCGT 60.359 61.111 0.00 0.00 0.00 3.85
117 118 3.131478 GGCATTGGTCCCGGTTCG 61.131 66.667 0.00 0.00 0.00 3.95
118 119 2.754254 GGGCATTGGTCCCGGTTC 60.754 66.667 0.00 0.00 33.43 3.62
124 125 1.305213 ACACATGGGGCATTGGTCC 60.305 57.895 0.00 0.00 38.40 4.46
125 126 1.322538 GGACACATGGGGCATTGGTC 61.323 60.000 1.52 0.00 0.00 4.02
126 127 1.305213 GGACACATGGGGCATTGGT 60.305 57.895 1.52 0.00 0.00 3.67
127 128 2.059786 GGGACACATGGGGCATTGG 61.060 63.158 1.52 0.00 0.00 3.16
128 129 2.417257 CGGGACACATGGGGCATTG 61.417 63.158 1.52 0.00 0.00 2.82
129 130 2.044053 CGGGACACATGGGGCATT 60.044 61.111 1.52 0.00 0.00 3.56
130 131 4.127744 CCGGGACACATGGGGCAT 62.128 66.667 1.52 0.00 0.00 4.40
132 133 4.360405 AACCGGGACACATGGGGC 62.360 66.667 6.32 0.00 0.00 5.80
133 134 2.045340 GAACCGGGACACATGGGG 60.045 66.667 6.32 0.00 0.00 4.96
134 135 1.377202 CAGAACCGGGACACATGGG 60.377 63.158 6.32 0.00 0.00 4.00
135 136 1.377202 CCAGAACCGGGACACATGG 60.377 63.158 6.32 0.80 0.00 3.66
136 137 1.676968 TCCAGAACCGGGACACATG 59.323 57.895 6.32 0.00 0.00 3.21
137 138 4.225860 TCCAGAACCGGGACACAT 57.774 55.556 6.32 0.00 0.00 3.21
142 143 2.055299 GTTCAGTCCAGAACCGGGA 58.945 57.895 6.32 0.00 41.52 5.14
143 144 4.695560 GTTCAGTCCAGAACCGGG 57.304 61.111 6.32 0.00 41.52 5.73
147 148 0.320508 GTCCCGGTTCAGTCCAGAAC 60.321 60.000 0.00 0.00 45.50 3.01
148 149 0.471211 AGTCCCGGTTCAGTCCAGAA 60.471 55.000 0.00 0.00 0.00 3.02
149 150 0.406750 TAGTCCCGGTTCAGTCCAGA 59.593 55.000 0.00 0.00 0.00 3.86
150 151 1.263356 TTAGTCCCGGTTCAGTCCAG 58.737 55.000 0.00 0.00 0.00 3.86
151 152 1.553248 CATTAGTCCCGGTTCAGTCCA 59.447 52.381 0.00 0.00 0.00 4.02
152 153 1.134491 CCATTAGTCCCGGTTCAGTCC 60.134 57.143 0.00 0.00 0.00 3.85
153 154 1.134491 CCCATTAGTCCCGGTTCAGTC 60.134 57.143 0.00 0.00 0.00 3.51
154 155 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
155 156 0.463833 GCCCATTAGTCCCGGTTCAG 60.464 60.000 0.00 0.00 0.00 3.02
156 157 0.912487 AGCCCATTAGTCCCGGTTCA 60.912 55.000 0.00 0.00 0.00 3.18
157 158 1.125633 TAGCCCATTAGTCCCGGTTC 58.874 55.000 0.00 0.00 0.00 3.62
158 159 1.211212 GTTAGCCCATTAGTCCCGGTT 59.789 52.381 0.00 0.00 0.00 4.44
159 160 0.835276 GTTAGCCCATTAGTCCCGGT 59.165 55.000 0.00 0.00 0.00 5.28
160 161 0.108019 GGTTAGCCCATTAGTCCCGG 59.892 60.000 0.00 0.00 0.00 5.73
161 162 3.700198 GGTTAGCCCATTAGTCCCG 57.300 57.895 0.00 0.00 0.00 5.14
173 174 1.619807 TTGGTCTAGGCCGGGTTAGC 61.620 60.000 9.28 0.00 0.00 3.09
174 175 0.906775 TTTGGTCTAGGCCGGGTTAG 59.093 55.000 9.28 0.00 0.00 2.34
175 176 0.906775 CTTTGGTCTAGGCCGGGTTA 59.093 55.000 9.28 0.00 0.00 2.85
176 177 1.683441 CTTTGGTCTAGGCCGGGTT 59.317 57.895 9.28 0.00 0.00 4.11
177 178 2.967946 GCTTTGGTCTAGGCCGGGT 61.968 63.158 9.28 0.00 0.00 5.28
178 179 2.124695 GCTTTGGTCTAGGCCGGG 60.125 66.667 9.28 2.25 0.00 5.73
179 180 2.124695 GGCTTTGGTCTAGGCCGG 60.125 66.667 9.28 0.00 35.08 6.13
180 181 2.124695 GGGCTTTGGTCTAGGCCG 60.125 66.667 9.28 0.00 46.65 6.13
182 183 0.621082 AAGAGGGCTTTGGTCTAGGC 59.379 55.000 0.00 0.00 37.45 3.93
183 184 3.009584 AGAAAAGAGGGCTTTGGTCTAGG 59.990 47.826 0.00 0.00 43.32 3.02
184 185 4.293662 AGAAAAGAGGGCTTTGGTCTAG 57.706 45.455 0.00 0.00 43.32 2.43
185 186 4.844655 AGTAGAAAAGAGGGCTTTGGTCTA 59.155 41.667 0.00 0.00 43.32 2.59
186 187 3.653352 AGTAGAAAAGAGGGCTTTGGTCT 59.347 43.478 0.00 0.00 43.32 3.85
187 188 4.022413 AGTAGAAAAGAGGGCTTTGGTC 57.978 45.455 0.00 0.00 43.32 4.02
188 189 4.597940 ACTAGTAGAAAAGAGGGCTTTGGT 59.402 41.667 3.59 0.00 43.32 3.67
189 190 4.938226 CACTAGTAGAAAAGAGGGCTTTGG 59.062 45.833 3.59 0.00 43.32 3.28
190 191 5.552178 ACACTAGTAGAAAAGAGGGCTTTG 58.448 41.667 3.59 0.00 43.32 2.77
191 192 5.567025 CGACACTAGTAGAAAAGAGGGCTTT 60.567 44.000 3.59 0.00 45.95 3.51
192 193 4.082136 CGACACTAGTAGAAAAGAGGGCTT 60.082 45.833 3.59 0.00 35.37 4.35
193 194 3.444388 CGACACTAGTAGAAAAGAGGGCT 59.556 47.826 3.59 0.00 0.00 5.19
194 195 3.429135 CCGACACTAGTAGAAAAGAGGGC 60.429 52.174 3.59 0.00 0.00 5.19
195 196 3.130693 CCCGACACTAGTAGAAAAGAGGG 59.869 52.174 3.59 5.18 0.00 4.30
196 197 3.130693 CCCCGACACTAGTAGAAAAGAGG 59.869 52.174 3.59 0.00 0.00 3.69
197 198 3.429135 GCCCCGACACTAGTAGAAAAGAG 60.429 52.174 3.59 0.00 0.00 2.85
198 199 2.494870 GCCCCGACACTAGTAGAAAAGA 59.505 50.000 3.59 0.00 0.00 2.52
199 200 2.734492 CGCCCCGACACTAGTAGAAAAG 60.734 54.545 3.59 0.00 0.00 2.27
200 201 1.203052 CGCCCCGACACTAGTAGAAAA 59.797 52.381 3.59 0.00 0.00 2.29
201 202 0.813184 CGCCCCGACACTAGTAGAAA 59.187 55.000 3.59 0.00 0.00 2.52
202 203 0.322816 ACGCCCCGACACTAGTAGAA 60.323 55.000 3.59 0.00 0.00 2.10
203 204 0.541392 TACGCCCCGACACTAGTAGA 59.459 55.000 3.59 0.00 0.00 2.59
204 205 0.659957 GTACGCCCCGACACTAGTAG 59.340 60.000 0.00 0.00 0.00 2.57
205 206 1.089481 CGTACGCCCCGACACTAGTA 61.089 60.000 0.52 0.00 0.00 1.82
206 207 2.401766 CGTACGCCCCGACACTAGT 61.402 63.158 0.52 0.00 0.00 2.57
207 208 2.406401 CGTACGCCCCGACACTAG 59.594 66.667 0.52 0.00 0.00 2.57
208 209 3.814268 GCGTACGCCCCGACACTA 61.814 66.667 29.51 0.00 34.56 2.74
210 211 4.729856 AAGCGTACGCCCCGACAC 62.730 66.667 34.88 6.89 43.17 3.67
222 223 2.332654 GCCACCGGATTTGAAGCGT 61.333 57.895 9.46 0.00 0.00 5.07
229 230 3.732892 CGCAACGCCACCGGATTT 61.733 61.111 9.46 0.00 39.22 2.17
282 283 1.527433 GAAGGACTTGCTGCAACCCC 61.527 60.000 11.69 14.54 0.00 4.95
294 295 1.513158 CTGCCGACGATGAAGGACT 59.487 57.895 0.00 0.00 0.00 3.85
313 314 0.535102 AACACTCAGGAACAAGCCGG 60.535 55.000 0.00 0.00 0.00 6.13
316 317 5.689383 TGAATTAACACTCAGGAACAAGC 57.311 39.130 0.00 0.00 0.00 4.01
329 330 5.347342 CAGTGCCACAACTTTGAATTAACA 58.653 37.500 0.00 0.00 0.00 2.41
339 340 0.670162 GTCATGCAGTGCCACAACTT 59.330 50.000 13.72 0.00 0.00 2.66
360 361 3.925238 GGTATCGTTGCAGGCGCG 61.925 66.667 0.00 0.00 42.97 6.86
364 366 2.036958 TTGGATGGTATCGTTGCAGG 57.963 50.000 0.00 0.00 0.00 4.85
380 382 0.753111 GAGCCCTACTTGCCCATTGG 60.753 60.000 0.00 0.00 0.00 3.16
457 459 9.856162 TTAAAACTTGGTAAGAACTAAGGATGT 57.144 29.630 6.59 0.00 45.71 3.06
618 627 7.153985 TCCCATGCTTTTCAATTGACTTTTAG 58.846 34.615 7.89 2.77 0.00 1.85
733 1930 0.469705 TTGTCCTTTGCATGCAGGGT 60.470 50.000 28.72 0.00 0.00 4.34
736 1933 3.306917 TGATTTGTCCTTTGCATGCAG 57.693 42.857 21.50 10.33 0.00 4.41
850 2136 6.644347 TCTCAAGCTTTTACTTGCTAGCTAT 58.356 36.000 17.23 3.71 45.43 2.97
1169 2581 3.444388 GGTTGTCGAACTCTAGGAGTGAT 59.556 47.826 0.74 0.00 42.59 3.06
1182 2594 4.367023 CTCCGCCGGGTTGTCGAA 62.367 66.667 1.90 0.00 33.83 3.71
1337 2749 1.376037 GCCGAGGTGAAGTTCCAGG 60.376 63.158 0.00 0.00 0.00 4.45
1850 3393 1.878656 CGTGGTCAGACCTCCTCCAC 61.879 65.000 20.82 8.24 43.27 4.02
1862 3420 2.849294 TGGAATCATTGTCGTGGTCA 57.151 45.000 0.00 0.00 0.00 4.02
1874 3432 1.541015 CGATCTCCGGCAATGGAATCA 60.541 52.381 0.00 0.00 37.64 2.57
1878 3436 1.742146 CTCGATCTCCGGCAATGGA 59.258 57.895 0.00 0.00 39.14 3.41
2166 3736 8.648693 AGTACTAACTCTGTACCAAAATGAAGT 58.351 33.333 0.00 0.00 40.61 3.01
2344 4070 5.747951 TCCAAAAACATTTGTGGCAATTC 57.252 34.783 8.50 0.00 43.81 2.17
2364 4090 4.151867 GTCTCTTTGATTACACCGTGTTCC 59.848 45.833 9.98 0.44 0.00 3.62
2371 4097 6.763135 TGCATATGAGTCTCTTTGATTACACC 59.237 38.462 6.97 0.00 0.00 4.16
2372 4098 7.515841 CGTGCATATGAGTCTCTTTGATTACAC 60.516 40.741 6.97 0.00 0.00 2.90
2385 4111 3.060272 GTGTATGTGCGTGCATATGAGTC 60.060 47.826 13.47 3.60 34.35 3.36
2391 4117 2.663826 TGAGTGTATGTGCGTGCATA 57.336 45.000 0.00 0.00 0.00 3.14
2394 4120 2.002586 AGAATGAGTGTATGTGCGTGC 58.997 47.619 0.00 0.00 0.00 5.34
2421 4147 9.435688 GGTGCTCACATTTTCCTAAATTTATTT 57.564 29.630 0.00 0.00 31.63 1.40
2456 4187 4.687219 GCCAGCAGGGTTCAAGTTATAGAT 60.687 45.833 0.00 0.00 39.65 1.98
2462 4193 1.531602 GGCCAGCAGGGTTCAAGTT 60.532 57.895 0.00 0.00 39.65 2.66
2474 4205 2.437895 GGAACTAACCCGGCCAGC 60.438 66.667 2.24 0.00 0.00 4.85
2475 4206 1.376812 GTGGAACTAACCCGGCCAG 60.377 63.158 2.24 0.00 0.00 4.85
2476 4207 2.751688 GTGGAACTAACCCGGCCA 59.248 61.111 2.24 0.00 0.00 5.36
2477 4208 2.045634 GGTGGAACTAACCCGGCC 60.046 66.667 0.00 0.00 36.74 6.13
2479 4210 2.502538 TCTTATGGTGGAACTAACCCGG 59.497 50.000 0.00 0.00 36.83 5.73
2486 4217 6.936968 AGTTAGTTCTCTTATGGTGGAACT 57.063 37.500 11.10 11.10 46.43 3.01
2501 4232 7.388500 ACCGAGAGTAGCTCATATAGTTAGTTC 59.612 40.741 0.00 0.00 44.15 3.01
2512 4243 2.447443 TGTGAACCGAGAGTAGCTCAT 58.553 47.619 0.00 0.00 44.15 2.90
2525 4256 3.465871 ACATTTGTGGCAATTGTGAACC 58.534 40.909 7.40 0.00 0.00 3.62
2530 4261 5.609423 ACATACAACATTTGTGGCAATTGT 58.391 33.333 7.40 4.26 45.03 2.71
2572 4303 9.642327 TCAACATTTCCTTATGATTGTGATTTG 57.358 29.630 0.00 0.00 0.00 2.32
2669 4418 8.575649 TTGAAATGGAGGGAGTATTTTCTAAC 57.424 34.615 0.00 0.00 0.00 2.34
2775 4589 8.851145 GGCTGACGATTATTCCATATATCTAGA 58.149 37.037 0.00 0.00 0.00 2.43
2786 4600 8.324163 AGTTTAATATGGCTGACGATTATTCC 57.676 34.615 0.00 0.00 0.00 3.01
2818 4632 5.991328 ATAAGATGCAATTCGACAATCGT 57.009 34.783 0.00 0.00 41.35 3.73
2823 4637 9.929722 GTTAACAATATAAGATGCAATTCGACA 57.070 29.630 0.00 0.00 0.00 4.35
2939 4760 1.726791 CCATACAATATCGTCCGCTGC 59.273 52.381 0.00 0.00 0.00 5.25
2950 4771 4.499865 GCAGAGTCGAGCTTCCATACAATA 60.500 45.833 3.70 0.00 0.00 1.90
2999 4820 2.750712 CCTCGCCTAGCTAGAACTATCC 59.249 54.545 22.70 0.85 0.00 2.59
3016 4845 4.032900 CGTCTTCATGTTTATTGGTCCTCG 59.967 45.833 0.00 0.00 0.00 4.63
3071 4901 8.046708 ACTACTTGAACATGCTAATTGGACATA 58.953 33.333 0.00 0.00 0.00 2.29
3093 4923 1.721389 CGATGCACTCACACACACTAC 59.279 52.381 0.00 0.00 0.00 2.73
3221 5061 1.084289 GGATGTACCACTTTGGACGC 58.916 55.000 0.00 0.00 40.96 5.19
3244 5084 3.165875 AGGGACTGAGAAGAATCAACGA 58.834 45.455 0.00 0.00 37.18 3.85
3252 5092 2.398754 TTGTGGAGGGACTGAGAAGA 57.601 50.000 0.00 0.00 41.55 2.87
3323 5326 0.388649 CATACTAGGCGCGCTTAGGG 60.389 60.000 41.13 29.72 30.99 3.53
3325 5328 2.135664 AACATACTAGGCGCGCTTAG 57.864 50.000 38.68 38.68 0.00 2.18
3339 5342 7.915293 ATGACACGAGAAAATACCAAACATA 57.085 32.000 0.00 0.00 0.00 2.29
3342 5345 7.360575 AGTATGACACGAGAAAATACCAAAC 57.639 36.000 0.00 0.00 0.00 2.93
3349 5352 5.043903 CGATGGAGTATGACACGAGAAAAT 58.956 41.667 0.00 0.00 0.00 1.82
3352 5355 3.014623 ACGATGGAGTATGACACGAGAA 58.985 45.455 0.00 0.00 0.00 2.87
3359 5362 3.315470 TGTCTAGCACGATGGAGTATGAC 59.685 47.826 0.00 0.00 0.00 3.06
3363 5366 3.118371 TCTCTGTCTAGCACGATGGAGTA 60.118 47.826 0.00 0.00 0.00 2.59
3364 5367 2.020720 CTCTGTCTAGCACGATGGAGT 58.979 52.381 0.00 0.00 0.00 3.85
3399 5404 8.073467 TCCCAGTACTTTTCACTCAAATTTTT 57.927 30.769 0.00 0.00 0.00 1.94
3404 5409 8.934023 AAATATCCCAGTACTTTTCACTCAAA 57.066 30.769 0.00 0.00 0.00 2.69
3405 5410 8.934023 AAAATATCCCAGTACTTTTCACTCAA 57.066 30.769 0.00 0.00 0.00 3.02
3438 5446 8.957466 GCAGAGTAAACAAATAAGGAAGGTAAT 58.043 33.333 0.00 0.00 0.00 1.89
3454 5462 8.808092 AGGAGACCTAATATATGCAGAGTAAAC 58.192 37.037 0.00 0.00 28.47 2.01
3473 5481 5.077564 ACAAAGGTTTATTCCAAGGAGACC 58.922 41.667 5.44 5.44 0.00 3.85
3519 5527 4.922026 AAGCGCCGTCCGTTTGGT 62.922 61.111 2.29 0.00 38.97 3.67
3545 5553 1.339929 GCCGACCCAAACAGACAAAAT 59.660 47.619 0.00 0.00 0.00 1.82
3623 5631 1.305219 ACGCGGTCATGAAATGGGTG 61.305 55.000 12.47 0.00 46.73 4.61
3772 5821 0.031585 TCTTATAACGAGCGCCGCAT 59.968 50.000 13.36 12.60 43.32 4.73
3773 5822 0.179132 TTCTTATAACGAGCGCCGCA 60.179 50.000 13.36 6.86 43.32 5.69
3774 5823 0.503117 CTTCTTATAACGAGCGCCGC 59.497 55.000 16.48 0.00 43.32 6.53
3810 5861 0.520404 GACGAGTGAGTGGCGAACTA 59.480 55.000 0.00 0.00 40.07 2.24
3819 5876 3.063084 GGGGCGAGACGAGTGAGT 61.063 66.667 0.00 0.00 0.00 3.41
3868 5926 1.945387 GAGGATGTGCATCGACATGT 58.055 50.000 0.00 0.00 36.67 3.21
3880 5938 4.514577 CCGAAGCGCCGAGGATGT 62.515 66.667 2.29 0.00 0.00 3.06
3983 6041 2.135890 TGCCTTCTCTGCAGTGTCA 58.864 52.632 14.67 6.21 34.05 3.58
3989 6047 4.399395 CGGGCTGCCTTCTCTGCA 62.399 66.667 19.68 0.00 37.17 4.41


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

AutoCloner maintained by Alex Coulton.