Multiple sequence alignment - TraesCS5D01G364800

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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 TraesCS5D01G364800 chr5D 100.000 9201 0 0 1 9201 442103458 442094258 0.000000e+00 16992.0
1 TraesCS5D01G364800 chr5D 80.108 739 89 35 1 720 170318571 170317872 1.780000e-136 497.0
2 TraesCS5D01G364800 chr5D 81.837 490 49 19 253 718 531503180 531502707 8.720000e-100 375.0
3 TraesCS5D01G364800 chr5D 90.952 210 15 4 6 215 52253465 52253670 7.040000e-71 279.0
4 TraesCS5D01G364800 chr5D 85.985 264 26 10 6 263 450616350 450616092 1.180000e-68 272.0
5 TraesCS5D01G364800 chr5D 83.835 266 36 6 1 264 529052206 529052466 7.140000e-61 246.0
6 TraesCS5D01G364800 chr5B 95.342 6526 192 45 1276 7746 538300615 538294147 0.000000e+00 10264.0
7 TraesCS5D01G364800 chr5B 91.568 925 46 14 7740 8659 538294118 538293221 0.000000e+00 1247.0
8 TraesCS5D01G364800 chr5B 88.361 653 65 7 6058 6700 73988581 73987930 0.000000e+00 774.0
9 TraesCS5D01G364800 chr5B 87.846 650 74 4 6056 6700 618207330 618206681 0.000000e+00 758.0
10 TraesCS5D01G364800 chr5B 81.916 741 82 31 1 720 705004900 705004191 6.190000e-161 579.0
11 TraesCS5D01G364800 chr5B 93.162 351 19 4 8856 9201 538293022 538292672 2.290000e-140 510.0
12 TraesCS5D01G364800 chr5B 94.718 284 6 3 953 1234 538300894 538300618 5.100000e-117 433.0
13 TraesCS5D01G364800 chr5B 91.558 154 9 2 727 879 538301389 538301239 9.360000e-50 209.0
14 TraesCS5D01G364800 chr5A 91.768 2466 119 25 2605 5040 558329204 558326793 0.000000e+00 3352.0
15 TraesCS5D01G364800 chr5A 87.909 1191 97 31 7740 8886 558322248 558321061 0.000000e+00 1358.0
16 TraesCS5D01G364800 chr5A 95.455 660 26 3 6697 7353 558324656 558323998 0.000000e+00 1050.0
17 TraesCS5D01G364800 chr5A 93.421 608 36 4 2015 2620 558329825 558329220 0.000000e+00 898.0
18 TraesCS5D01G364800 chr5A 92.616 474 20 6 5593 6053 558325109 558324638 0.000000e+00 667.0
19 TraesCS5D01G364800 chr5A 89.817 383 31 5 7366 7746 558322653 558322277 1.390000e-132 484.0
20 TraesCS5D01G364800 chr5A 91.168 351 28 2 5188 5535 558325455 558325105 3.010000e-129 473.0
21 TraesCS5D01G364800 chr5A 79.659 703 79 43 51 720 78903489 78904160 1.820000e-121 448.0
22 TraesCS5D01G364800 chr5A 86.364 352 24 15 910 1238 558331275 558330925 6.790000e-96 363.0
23 TraesCS5D01G364800 chr5A 86.486 296 29 6 1579 1863 558330820 558330525 1.930000e-81 315.0
24 TraesCS5D01G364800 chr5A 88.511 235 14 8 8968 9201 558321030 558320808 1.180000e-68 272.0
25 TraesCS5D01G364800 chr6D 84.375 2624 302 67 1753 4305 123774595 123777181 0.000000e+00 2475.0
26 TraesCS5D01G364800 chr6D 84.402 936 118 18 4642 5556 123777911 123778839 0.000000e+00 894.0
27 TraesCS5D01G364800 chr6D 82.603 707 75 30 1 689 329073743 329074419 1.720000e-161 580.0
28 TraesCS5D01G364800 chr6D 81.880 734 79 38 12 720 77859988 77859284 3.730000e-158 569.0
29 TraesCS5D01G364800 chr6D 82.488 611 60 27 6697 7287 123779312 123779895 8.300000e-135 492.0
30 TraesCS5D01G364800 chr6D 87.097 403 42 7 5642 6037 123778908 123779307 1.820000e-121 448.0
31 TraesCS5D01G364800 chr6D 85.663 279 15 11 939 1206 123773507 123773771 4.230000e-68 270.0
32 TraesCS5D01G364800 chr6D 82.993 294 23 16 7995 8270 123780816 123781100 3.320000e-59 241.0
33 TraesCS5D01G364800 chr6A 84.090 2621 302 68 1753 4305 157639992 157637419 0.000000e+00 2423.0
34 TraesCS5D01G364800 chr6A 83.565 937 118 20 4648 5556 157636411 157635483 0.000000e+00 845.0
35 TraesCS5D01G364800 chr6A 83.497 612 55 28 6697 7287 157635010 157634424 6.330000e-146 529.0
36 TraesCS5D01G364800 chr6A 86.352 403 45 7 5642 6037 157635414 157635015 1.840000e-116 431.0
37 TraesCS5D01G364800 chr6A 84.229 279 18 15 939 1206 157640914 157640651 1.980000e-61 248.0
38 TraesCS5D01G364800 chr6A 82.770 296 20 18 7995 8270 157633512 157633228 1.540000e-57 235.0
39 TraesCS5D01G364800 chr6A 78.517 391 57 14 253 624 445583720 445583338 2.000000e-56 231.0
40 TraesCS5D01G364800 chr6B 83.950 2623 295 69 1752 4305 218666707 218669272 0.000000e+00 2396.0
41 TraesCS5D01G364800 chr6B 82.296 932 114 38 4642 5556 218669975 218670872 0.000000e+00 760.0
42 TraesCS5D01G364800 chr6B 84.288 611 49 25 6697 7286 218671531 218672115 3.750000e-153 553.0
43 TraesCS5D01G364800 chr6B 83.099 426 51 17 272 683 688887850 688888268 1.460000e-97 368.0
44 TraesCS5D01G364800 chr6B 87.755 294 30 4 5747 6037 218671236 218671526 1.140000e-88 339.0
45 TraesCS5D01G364800 chr6B 84.588 279 17 12 939 1206 218665759 218666022 4.260000e-63 254.0
46 TraesCS5D01G364800 chr6B 82.313 294 25 16 7995 8270 218674239 218674523 7.190000e-56 230.0
47 TraesCS5D01G364800 chr1D 89.144 654 67 3 6051 6700 114006326 114005673 0.000000e+00 811.0
48 TraesCS5D01G364800 chr1D 88.685 654 70 3 6051 6700 114009693 114010346 0.000000e+00 795.0
49 TraesCS5D01G364800 chr1D 81.224 490 62 21 253 720 46391384 46391865 1.460000e-97 368.0
50 TraesCS5D01G364800 chr1D 86.957 276 28 8 1 276 360436997 360437264 4.170000e-78 303.0
51 TraesCS5D01G364800 chr7B 89.968 618 55 4 6056 6671 522151475 522150863 0.000000e+00 791.0
52 TraesCS5D01G364800 chr2D 88.550 655 68 6 6051 6700 536160339 536159687 0.000000e+00 787.0
53 TraesCS5D01G364800 chr2D 87.706 667 64 6 6051 6700 341699333 341699998 0.000000e+00 761.0
54 TraesCS5D01G364800 chr2D 80.952 735 85 36 4 720 246623980 246623283 1.760000e-146 531.0
55 TraesCS5D01G364800 chr2D 83.582 469 48 21 274 720 390728081 390728542 6.650000e-111 412.0
56 TraesCS5D01G364800 chr7D 87.963 648 68 7 6056 6700 319906577 319907217 0.000000e+00 756.0
57 TraesCS5D01G364800 chr4D 81.283 748 92 31 1 727 101675520 101676240 6.240000e-156 562.0
58 TraesCS5D01G364800 chr3D 80.811 740 85 33 1 719 111978761 111978058 2.280000e-145 527.0
59 TraesCS5D01G364800 chr3D 84.848 264 29 8 6 264 105464924 105465181 1.190000e-63 255.0
60 TraesCS5D01G364800 chr1A 77.720 772 81 49 1 727 391243469 391242744 1.120000e-103 388.0
61 TraesCS5D01G364800 chr7A 79.175 485 55 20 273 720 12906368 12905893 2.510000e-75 294.0
62 TraesCS5D01G364800 chr7A 77.143 455 65 27 294 724 80728204 80727765 2.580000e-55 228.0
63 TraesCS5D01G364800 chr7A 76.535 456 67 27 294 724 80702404 80701964 7.240000e-51 213.0
64 TraesCS5D01G364800 chr7A 76.535 456 67 27 294 724 80805335 80804895 7.240000e-51 213.0
65 TraesCS5D01G364800 chr2B 86.567 268 28 7 6 271 50710777 50710516 1.170000e-73 289.0
66 TraesCS5D01G364800 chr2B 83.667 300 33 10 5 301 470070059 470069773 1.520000e-67 268.0
67 TraesCS5D01G364800 chr3A 84.191 272 33 7 4 271 569411904 569411639 1.190000e-63 255.0
68 TraesCS5D01G364800 chr2A 84.249 273 31 10 4 271 398502327 398502592 1.190000e-63 255.0
69 TraesCS5D01G364800 chr2A 91.358 81 4 2 192 271 228395911 228395989 3.510000e-19 108.0
70 TraesCS5D01G364800 chr1B 77.097 310 45 14 450 736 395979515 395979821 1.240000e-33 156.0
71 TraesCS5D01G364800 chr4A 90.566 53 1 3 677 726 131996022 131995971 5.960000e-07 67.6


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 TraesCS5D01G364800 chr5D 442094258 442103458 9200 True 16992.000000 16992 100.000000 1 9201 1 chr5D.!!$R2 9200
1 TraesCS5D01G364800 chr5D 170317872 170318571 699 True 497.000000 497 80.108000 1 720 1 chr5D.!!$R1 719
2 TraesCS5D01G364800 chr5B 538292672 538301389 8717 True 2532.600000 10264 93.269600 727 9201 5 chr5B.!!$R4 8474
3 TraesCS5D01G364800 chr5B 73987930 73988581 651 True 774.000000 774 88.361000 6058 6700 1 chr5B.!!$R1 642
4 TraesCS5D01G364800 chr5B 618206681 618207330 649 True 758.000000 758 87.846000 6056 6700 1 chr5B.!!$R2 644
5 TraesCS5D01G364800 chr5B 705004191 705004900 709 True 579.000000 579 81.916000 1 720 1 chr5B.!!$R3 719
6 TraesCS5D01G364800 chr5A 558320808 558331275 10467 True 923.200000 3352 90.351500 910 9201 10 chr5A.!!$R1 8291
7 TraesCS5D01G364800 chr5A 78903489 78904160 671 False 448.000000 448 79.659000 51 720 1 chr5A.!!$F1 669
8 TraesCS5D01G364800 chr6D 123773507 123781100 7593 False 803.333333 2475 84.503000 939 8270 6 chr6D.!!$F2 7331
9 TraesCS5D01G364800 chr6D 329073743 329074419 676 False 580.000000 580 82.603000 1 689 1 chr6D.!!$F1 688
10 TraesCS5D01G364800 chr6D 77859284 77859988 704 True 569.000000 569 81.880000 12 720 1 chr6D.!!$R1 708
11 TraesCS5D01G364800 chr6A 157633228 157640914 7686 True 785.166667 2423 84.083833 939 8270 6 chr6A.!!$R2 7331
12 TraesCS5D01G364800 chr6B 218665759 218674523 8764 False 755.333333 2396 84.198333 939 8270 6 chr6B.!!$F2 7331
13 TraesCS5D01G364800 chr1D 114005673 114006326 653 True 811.000000 811 89.144000 6051 6700 1 chr1D.!!$R1 649
14 TraesCS5D01G364800 chr1D 114009693 114010346 653 False 795.000000 795 88.685000 6051 6700 1 chr1D.!!$F2 649
15 TraesCS5D01G364800 chr7B 522150863 522151475 612 True 791.000000 791 89.968000 6056 6671 1 chr7B.!!$R1 615
16 TraesCS5D01G364800 chr2D 536159687 536160339 652 True 787.000000 787 88.550000 6051 6700 1 chr2D.!!$R2 649
17 TraesCS5D01G364800 chr2D 341699333 341699998 665 False 761.000000 761 87.706000 6051 6700 1 chr2D.!!$F1 649
18 TraesCS5D01G364800 chr2D 246623283 246623980 697 True 531.000000 531 80.952000 4 720 1 chr2D.!!$R1 716
19 TraesCS5D01G364800 chr7D 319906577 319907217 640 False 756.000000 756 87.963000 6056 6700 1 chr7D.!!$F1 644
20 TraesCS5D01G364800 chr4D 101675520 101676240 720 False 562.000000 562 81.283000 1 727 1 chr4D.!!$F1 726
21 TraesCS5D01G364800 chr3D 111978058 111978761 703 True 527.000000 527 80.811000 1 719 1 chr3D.!!$R1 718
22 TraesCS5D01G364800 chr1A 391242744 391243469 725 True 388.000000 388 77.720000 1 727 1 chr1A.!!$R1 726

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
269 392 0.031585 CGACCGTGACTCTCACCAAA 59.968 55.000 0.00 0.00 44.20 3.28 F
1032 1511 0.032815 GTAAGATCTCTCGCCCCTGC 59.967 60.000 0.00 0.00 0.00 4.85 F
1278 1791 0.035056 ACCAGGTTGCTGTCATAGGC 60.035 55.000 0.00 0.00 0.00 3.93 F
1279 1792 0.254178 CCAGGTTGCTGTCATAGGCT 59.746 55.000 0.00 0.00 0.00 4.58 F
1446 1973 0.386476 ACATGGTGTGCTTGCTGTTG 59.614 50.000 0.00 0.00 0.00 3.33 F
1955 2831 0.667993 TTTTCTGCTTGCCCTGAACG 59.332 50.000 0.00 0.00 0.00 3.95 F
2247 3682 3.654806 CAGGAGGGATCATATGGAGGTTT 59.345 47.826 2.13 0.00 0.00 3.27 F
3849 5398 1.252175 TTATCGCTTTTGCCTTGCCA 58.748 45.000 0.00 0.00 43.93 4.92 F
5116 8595 1.066215 TCGTCTGTCAATCACCATGGG 60.066 52.381 18.09 5.22 0.00 4.00 F
6298 10035 1.068083 CGTCCGCTATGCACTGGAT 59.932 57.895 0.00 0.00 32.18 3.41 F
7733 14261 0.107508 ATGCTCAGTGGATCCCGTTG 60.108 55.000 9.90 5.10 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 1772 0.035056 GCCTATGACAGCAACCTGGT 60.035 55.000 0.00 0.00 43.53 4.00 R
2310 3746 1.908299 CCTGTTTTGTGGAGGGGGC 60.908 63.158 0.00 0.00 0.00 5.80 R
2416 3872 1.932511 GCTCAGAGCTGCATCAAGTAC 59.067 52.381 15.78 0.00 38.45 2.73 R
3235 4732 2.664402 AAGAACCAAGCAGACACCAT 57.336 45.000 0.00 0.00 0.00 3.55 R
3282 4779 5.156355 GTGCAACATATTGGTGAAGAACAG 58.844 41.667 0.00 0.00 37.20 3.16 R
3708 5218 2.026822 CAGGCAAATCACTACACCTCCT 60.027 50.000 0.00 0.00 0.00 3.69 R
4196 5751 0.958822 AACAAAGGGGCACATCGAAC 59.041 50.000 0.00 0.00 0.00 3.95 R
5434 8925 2.040947 TGTCATGACTATTTGGTGGCCA 59.959 45.455 25.55 0.00 0.00 5.36 R
6364 10101 1.668151 GAGTTGGAGTGGCACCGAC 60.668 63.158 15.27 10.22 40.90 4.79 R
7991 14570 0.244721 TCCAGACACTGCACTCATCG 59.755 55.000 0.00 0.00 0.00 3.84 R
8570 15164 0.657840 GCTGCGTACCTAAATGGCTG 59.342 55.000 0.00 0.00 40.22 4.85 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
21 22 1.404035 GTGGAAGCAAAACCGTGACTT 59.596 47.619 0.00 0.00 0.00 3.01
31 32 4.238385 CGTGACTTTCGCGGAAGA 57.762 55.556 33.16 9.49 45.61 2.87
202 321 3.381983 ATGGCCGTGACTCTCGCA 61.382 61.111 0.00 0.00 0.00 5.10
207 329 1.901650 GCCGTGACTCTCGCAAAAGG 61.902 60.000 0.00 0.00 0.00 3.11
251 374 4.488126 TTTTTCATTTCTGAGAGGCACG 57.512 40.909 0.00 0.00 31.68 5.34
252 375 3.401033 TTTCATTTCTGAGAGGCACGA 57.599 42.857 0.00 0.00 31.68 4.35
253 376 2.370281 TCATTTCTGAGAGGCACGAC 57.630 50.000 0.00 0.00 0.00 4.34
254 377 1.066858 TCATTTCTGAGAGGCACGACC 60.067 52.381 0.00 0.00 39.61 4.79
255 378 0.108615 ATTTCTGAGAGGCACGACCG 60.109 55.000 0.00 0.00 46.52 4.79
256 379 1.461091 TTTCTGAGAGGCACGACCGT 61.461 55.000 0.00 0.00 46.52 4.83
257 380 2.126307 CTGAGAGGCACGACCGTG 60.126 66.667 17.19 17.19 46.52 4.94
266 389 3.352524 ACGACCGTGACTCTCACC 58.647 61.111 0.00 0.00 44.20 4.02
267 390 1.527611 ACGACCGTGACTCTCACCA 60.528 57.895 0.00 0.00 44.20 4.17
268 391 1.105167 ACGACCGTGACTCTCACCAA 61.105 55.000 0.00 0.00 44.20 3.67
269 392 0.031585 CGACCGTGACTCTCACCAAA 59.968 55.000 0.00 0.00 44.20 3.28
270 393 1.784525 GACCGTGACTCTCACCAAAG 58.215 55.000 0.00 0.00 44.20 2.77
271 394 0.393077 ACCGTGACTCTCACCAAAGG 59.607 55.000 0.00 0.00 44.20 3.11
272 395 0.679505 CCGTGACTCTCACCAAAGGA 59.320 55.000 0.00 0.00 44.20 3.36
273 396 1.070134 CCGTGACTCTCACCAAAGGAA 59.930 52.381 0.00 0.00 44.20 3.36
274 397 2.484770 CCGTGACTCTCACCAAAGGAAA 60.485 50.000 0.00 0.00 44.20 3.13
275 398 3.202906 CGTGACTCTCACCAAAGGAAAA 58.797 45.455 0.00 0.00 44.20 2.29
276 399 3.625764 CGTGACTCTCACCAAAGGAAAAA 59.374 43.478 0.00 0.00 44.20 1.94
423 566 4.664150 TTTTTCCGTTTTCAAGAGGCAT 57.336 36.364 0.00 0.00 0.00 4.40
484 627 1.947456 GGAAGCAAAACCGTGACTCTT 59.053 47.619 0.00 0.00 0.00 2.85
522 683 4.720530 AGAAAAACTCGTATTTTCGCGT 57.279 36.364 5.77 0.00 46.41 6.01
720 916 2.719426 AGCGCTCGTTAACTAGTTGT 57.281 45.000 18.56 0.00 0.00 3.32
722 918 3.387397 AGCGCTCGTTAACTAGTTGTTT 58.613 40.909 18.56 0.00 39.89 2.83
759 955 2.074547 CGACTACGCCAGGAAGAAAA 57.925 50.000 0.00 0.00 0.00 2.29
785 981 4.409342 CGAGAGGCAATCAGACGG 57.591 61.111 0.00 0.00 0.00 4.79
830 1026 4.451150 GACCGACGCCCAGCATCA 62.451 66.667 0.00 0.00 0.00 3.07
834 1030 2.747460 GACGCCCAGCATCAGCAA 60.747 61.111 0.00 0.00 45.49 3.91
881 1077 3.464628 GAGCCAAACTCGCTCGTC 58.535 61.111 0.00 0.00 43.04 4.20
882 1078 2.430921 AGCCAAACTCGCTCGTCG 60.431 61.111 0.00 0.00 40.15 5.12
883 1079 2.733593 GCCAAACTCGCTCGTCGT 60.734 61.111 0.00 0.00 39.67 4.34
884 1080 1.443194 GCCAAACTCGCTCGTCGTA 60.443 57.895 0.00 0.00 39.67 3.43
885 1081 1.671880 GCCAAACTCGCTCGTCGTAC 61.672 60.000 0.00 0.00 39.67 3.67
886 1082 1.069378 CCAAACTCGCTCGTCGTACC 61.069 60.000 0.00 0.00 39.67 3.34
887 1083 0.109873 CAAACTCGCTCGTCGTACCT 60.110 55.000 0.00 0.00 39.67 3.08
888 1084 1.129251 CAAACTCGCTCGTCGTACCTA 59.871 52.381 0.00 0.00 39.67 3.08
889 1085 1.442769 AACTCGCTCGTCGTACCTAA 58.557 50.000 0.00 0.00 39.67 2.69
890 1086 1.005340 ACTCGCTCGTCGTACCTAAG 58.995 55.000 0.00 0.00 39.67 2.18
891 1087 0.316032 CTCGCTCGTCGTACCTAAGC 60.316 60.000 0.00 0.00 39.67 3.09
892 1088 4.281946 GCTCGTCGTACCTAAGCG 57.718 61.111 0.00 0.00 0.00 4.68
893 1089 1.427020 GCTCGTCGTACCTAAGCGT 59.573 57.895 0.00 0.00 0.00 5.07
894 1090 0.588482 GCTCGTCGTACCTAAGCGTC 60.588 60.000 0.00 0.00 0.00 5.19
895 1091 0.314898 CTCGTCGTACCTAAGCGTCG 60.315 60.000 0.00 0.00 39.93 5.12
896 1092 1.931612 CGTCGTACCTAAGCGTCGC 60.932 63.158 9.80 9.80 33.85 5.19
897 1093 1.584742 GTCGTACCTAAGCGTCGCC 60.585 63.158 14.86 0.00 0.00 5.54
898 1094 2.649975 CGTACCTAAGCGTCGCCG 60.650 66.667 14.86 4.38 37.07 6.46
1031 1510 0.676736 GGTAAGATCTCTCGCCCCTG 59.323 60.000 0.00 0.00 0.00 4.45
1032 1511 0.032815 GTAAGATCTCTCGCCCCTGC 59.967 60.000 0.00 0.00 0.00 4.85
1033 1512 1.115930 TAAGATCTCTCGCCCCTGCC 61.116 60.000 0.00 0.00 0.00 4.85
1034 1513 3.934962 GATCTCTCGCCCCTGCCC 61.935 72.222 0.00 0.00 0.00 5.36
1238 1751 3.790058 TCAAAACTGTTCGAATTACGCG 58.210 40.909 3.53 3.53 42.26 6.01
1240 1753 1.073177 AACTGTTCGAATTACGCGGG 58.927 50.000 12.47 0.00 42.26 6.13
1241 1754 1.347221 CTGTTCGAATTACGCGGGC 59.653 57.895 12.47 0.00 42.26 6.13
1242 1755 2.032185 CTGTTCGAATTACGCGGGCC 62.032 60.000 12.47 0.00 42.26 5.80
1243 1756 2.886604 TTCGAATTACGCGGGCCG 60.887 61.111 24.35 24.35 42.26 6.13
1244 1757 4.876828 TCGAATTACGCGGGCCGG 62.877 66.667 29.48 19.86 42.52 6.13
1245 1758 4.876828 CGAATTACGCGGGCCGGA 62.877 66.667 29.48 3.13 42.52 5.14
1246 1759 2.965462 GAATTACGCGGGCCGGAG 60.965 66.667 29.48 13.98 42.52 4.63
1247 1760 3.435030 GAATTACGCGGGCCGGAGA 62.435 63.158 29.48 11.67 42.52 3.71
1248 1761 3.441011 AATTACGCGGGCCGGAGAG 62.441 63.158 29.48 9.80 42.52 3.20
1254 1767 4.468689 CGGGCCGGAGAGTTTCCC 62.469 72.222 20.56 2.60 43.63 3.97
1255 1768 3.009714 GGGCCGGAGAGTTTCCCT 61.010 66.667 5.05 0.00 43.63 4.20
1256 1769 2.269241 GGCCGGAGAGTTTCCCTG 59.731 66.667 5.05 0.00 43.63 4.45
1257 1770 2.593956 GGCCGGAGAGTTTCCCTGT 61.594 63.158 5.05 0.00 43.63 4.00
1258 1771 1.079057 GCCGGAGAGTTTCCCTGTC 60.079 63.158 5.05 0.00 43.63 3.51
1259 1772 1.827399 GCCGGAGAGTTTCCCTGTCA 61.827 60.000 5.05 0.00 43.63 3.58
1260 1773 0.037232 CCGGAGAGTTTCCCTGTCAC 60.037 60.000 0.00 0.00 43.63 3.67
1261 1774 0.037232 CGGAGAGTTTCCCTGTCACC 60.037 60.000 0.00 0.00 43.63 4.02
1262 1775 1.056660 GGAGAGTTTCCCTGTCACCA 58.943 55.000 0.00 0.00 40.37 4.17
1263 1776 1.002544 GGAGAGTTTCCCTGTCACCAG 59.997 57.143 0.00 0.00 40.37 4.00
1271 1784 4.885426 CTGTCACCAGGTTGCTGT 57.115 55.556 0.00 0.00 34.90 4.40
1272 1785 2.621763 CTGTCACCAGGTTGCTGTC 58.378 57.895 0.00 0.00 34.90 3.51
1273 1786 0.179048 CTGTCACCAGGTTGCTGTCA 60.179 55.000 0.00 0.00 34.90 3.58
1274 1787 0.473755 TGTCACCAGGTTGCTGTCAT 59.526 50.000 0.00 0.00 0.00 3.06
1275 1788 1.696884 TGTCACCAGGTTGCTGTCATA 59.303 47.619 0.00 0.00 0.00 2.15
1276 1789 2.289631 TGTCACCAGGTTGCTGTCATAG 60.290 50.000 0.00 0.00 0.00 2.23
1277 1790 1.278985 TCACCAGGTTGCTGTCATAGG 59.721 52.381 0.00 0.00 0.00 2.57
1278 1791 0.035056 ACCAGGTTGCTGTCATAGGC 60.035 55.000 0.00 0.00 0.00 3.93
1279 1792 0.254178 CCAGGTTGCTGTCATAGGCT 59.746 55.000 0.00 0.00 0.00 4.58
1280 1793 1.376543 CAGGTTGCTGTCATAGGCTG 58.623 55.000 0.00 0.00 0.00 4.85
1281 1794 0.987294 AGGTTGCTGTCATAGGCTGT 59.013 50.000 0.00 0.00 0.00 4.40
1282 1795 1.352352 AGGTTGCTGTCATAGGCTGTT 59.648 47.619 0.00 0.00 0.00 3.16
1283 1796 2.162681 GGTTGCTGTCATAGGCTGTTT 58.837 47.619 0.00 0.00 0.00 2.83
1284 1797 2.558359 GGTTGCTGTCATAGGCTGTTTT 59.442 45.455 0.00 0.00 0.00 2.43
1285 1798 3.756434 GGTTGCTGTCATAGGCTGTTTTA 59.244 43.478 0.00 0.00 0.00 1.52
1290 1803 5.296780 TGCTGTCATAGGCTGTTTTATTAGC 59.703 40.000 0.00 0.00 39.17 3.09
1306 1822 1.629043 TAGCTCGTTGAACTGGGAGT 58.371 50.000 0.00 0.00 0.00 3.85
1346 1862 4.984161 GCTGAATTTGTGTGCATTACAACT 59.016 37.500 16.17 10.26 41.89 3.16
1349 1865 3.790152 TTTGTGTGCATTACAACTGCA 57.210 38.095 16.17 0.00 46.82 4.41
1445 1972 0.670162 GACATGGTGTGCTTGCTGTT 59.330 50.000 0.00 0.00 0.00 3.16
1446 1973 0.386476 ACATGGTGTGCTTGCTGTTG 59.614 50.000 0.00 0.00 0.00 3.33
1455 1982 1.401552 TGCTTGCTGTTGTGTCAGTTC 59.598 47.619 0.00 0.00 37.70 3.01
1548 2200 5.825593 TCAATCCTAAGTTGACTTCAGGT 57.174 39.130 0.00 0.00 37.40 4.00
1549 2201 5.551233 TCAATCCTAAGTTGACTTCAGGTG 58.449 41.667 0.00 2.98 37.40 4.00
1685 2347 4.659111 TGCCGCTAGCTATTAGTGTTAA 57.341 40.909 13.93 0.00 44.23 2.01
1955 2831 0.667993 TTTTCTGCTTGCCCTGAACG 59.332 50.000 0.00 0.00 0.00 3.95
2055 3490 6.591834 ACAACTTATCACACTCAGTATCTTGC 59.408 38.462 0.00 0.00 0.00 4.01
2247 3682 3.654806 CAGGAGGGATCATATGGAGGTTT 59.345 47.826 2.13 0.00 0.00 3.27
2554 4014 6.627243 TGTGTACATTTCGCTGAGTATACTT 58.373 36.000 6.88 0.00 32.15 2.24
2611 4076 4.627284 TGATTCGTTGTTTTCCCTCCTA 57.373 40.909 0.00 0.00 0.00 2.94
2649 4145 3.994392 TCGGATGCTTTGTCTTCTGTAAC 59.006 43.478 0.00 0.00 0.00 2.50
2650 4146 3.745975 CGGATGCTTTGTCTTCTGTAACA 59.254 43.478 0.00 0.00 0.00 2.41
2651 4147 4.143030 CGGATGCTTTGTCTTCTGTAACAG 60.143 45.833 0.00 0.00 0.00 3.16
2652 4148 4.378874 GGATGCTTTGTCTTCTGTAACAGC 60.379 45.833 0.00 0.00 0.00 4.40
2752 4248 8.511321 GGATCTACTATATTCTCACACTGACTG 58.489 40.741 0.00 0.00 0.00 3.51
2771 4267 5.655090 TGACTGGTTCTATATTTCAGACGGA 59.345 40.000 0.00 0.00 0.00 4.69
3175 4671 5.712152 ACCTGCTGTTTTCCTTAGAAATG 57.288 39.130 0.00 0.00 41.55 2.32
3235 4732 7.051623 AGTTTATGAACAAGTCCACTGTGTTA 58.948 34.615 7.08 0.00 38.26 2.41
3282 4779 8.758633 TTTGCTACTCTATGTCTGAAGTAAAC 57.241 34.615 0.00 0.00 0.00 2.01
3515 5023 6.715280 TCATATGAAGACTTGGAAGAAGCTT 58.285 36.000 1.98 0.00 0.00 3.74
3790 5329 5.472148 TCCAAGCTGCTTTAACATTTGATG 58.528 37.500 13.10 0.00 0.00 3.07
3849 5398 1.252175 TTATCGCTTTTGCCTTGCCA 58.748 45.000 0.00 0.00 43.93 4.92
3850 5399 1.473258 TATCGCTTTTGCCTTGCCAT 58.527 45.000 0.00 0.00 43.93 4.40
3879 5428 7.209475 TGAAGCCTTTTCTTCTACCATTTTTG 58.791 34.615 5.30 0.00 42.15 2.44
4305 5865 6.543735 AGAGGAGGGGCAAAATATACAATAC 58.456 40.000 0.00 0.00 0.00 1.89
4469 6352 8.481492 TGGCATTTCCAATATCATGAAGTAAT 57.519 30.769 0.00 0.00 43.21 1.89
4702 6956 6.983890 GTGTTTATTCTGTGAACCCATGTTTT 59.016 34.615 0.00 0.00 33.97 2.43
4788 7043 5.104374 GGTATGTTCATTGGCAAATCTGTG 58.896 41.667 3.01 0.00 0.00 3.66
5115 8471 2.385013 TCGTCTGTCAATCACCATGG 57.615 50.000 11.19 11.19 0.00 3.66
5116 8595 1.066215 TCGTCTGTCAATCACCATGGG 60.066 52.381 18.09 5.22 0.00 4.00
5434 8925 1.561076 TGTGCATGCCCTCTTCAGTAT 59.439 47.619 16.68 0.00 0.00 2.12
5460 8951 5.619981 GCCACCAAATAGTCATGACAAACTC 60.620 44.000 27.02 0.00 0.00 3.01
5662 9174 2.970987 TGCAGCCTGGTAGACCATATA 58.029 47.619 0.89 0.00 46.46 0.86
6166 9883 2.873649 GCACATGGATAGCTAGCTTCCC 60.874 54.545 28.30 25.22 0.00 3.97
6247 9984 4.335416 CCATGTCAAGTTTGGTCTACCAT 58.665 43.478 1.96 0.00 46.97 3.55
6298 10035 1.068083 CGTCCGCTATGCACTGGAT 59.932 57.895 0.00 0.00 32.18 3.41
6307 10044 4.555262 GCTATGCACTGGATCTTCTAGAC 58.445 47.826 0.00 0.00 0.00 2.59
6364 10101 5.616424 CGATTTTGGACAAGCTTCTCTTCAG 60.616 44.000 0.00 0.00 31.27 3.02
6375 10112 0.827925 TCTCTTCAGTCGGTGCCACT 60.828 55.000 0.00 0.00 0.00 4.00
6498 10242 1.079405 TCGCCTTTTAGTCGGCCAG 60.079 57.895 2.24 0.00 43.38 4.85
6516 10260 2.099592 CCAGCATTCAACGCCATACAAT 59.900 45.455 0.00 0.00 0.00 2.71
6607 10351 1.949257 CCAGAAGTTTGACGCCACC 59.051 57.895 0.00 0.00 0.00 4.61
6712 10456 4.343526 AGGTGTCCTTCAGTAGATGCTATG 59.656 45.833 0.00 0.00 0.00 2.23
7046 10794 6.715347 TGCATTGCTACTTCTCTCTACATA 57.285 37.500 10.49 0.00 0.00 2.29
7055 10803 3.993658 TCTCTCTACATACCCCCATGT 57.006 47.619 0.00 0.00 41.88 3.21
7257 11021 6.194796 TGAACAAGCTAGGATAAATGTTGC 57.805 37.500 1.08 0.00 31.68 4.17
7258 11022 5.945784 TGAACAAGCTAGGATAAATGTTGCT 59.054 36.000 1.08 0.00 31.68 3.91
7294 11060 0.950836 TCACCGTTTCCAAGCATGTG 59.049 50.000 0.00 0.00 0.00 3.21
7500 13965 6.908825 TGGTTGTTCATAAAAAGGAGAATCG 58.091 36.000 0.00 0.00 34.37 3.34
7523 14006 5.106555 CGATTGTTAAGGCTGTTGAGAATGT 60.107 40.000 0.00 0.00 0.00 2.71
7573 14098 5.474876 AGTTGATGGTGTTTTCTGAATCTCC 59.525 40.000 0.00 0.00 0.00 3.71
7616 14144 1.700042 AATGATCGCAGGAGTCCCCC 61.700 60.000 5.25 0.00 34.66 5.40
7697 14225 6.929606 GGTAAGATCCAGTATATTTGCTCGTT 59.070 38.462 0.00 0.00 0.00 3.85
7733 14261 0.107508 ATGCTCAGTGGATCCCGTTG 60.108 55.000 9.90 5.10 0.00 4.10
7753 14324 5.344884 GTTGGCAGCAAAGTAAAACTGTTA 58.655 37.500 0.00 0.00 32.65 2.41
8084 14670 6.428159 TCTCCAAAGCAGAGTAAGTTTGATTC 59.572 38.462 0.00 0.00 32.65 2.52
8134 14720 7.516943 GCTCTTTTGTATCATACGCCTAAGAAC 60.517 40.741 0.00 0.00 0.00 3.01
8138 14724 5.458015 TGTATCATACGCCTAAGAACATCG 58.542 41.667 0.00 0.00 0.00 3.84
8144 14730 3.448686 ACGCCTAAGAACATCGATCTTG 58.551 45.455 9.51 0.00 37.67 3.02
8158 14744 2.930040 CGATCTTGTCGCAAACAGGTAT 59.070 45.455 0.00 0.00 44.33 2.73
8276 14867 0.898320 ACAGTTAGATGCAGGCGACT 59.102 50.000 0.00 0.00 46.44 4.18
8301 14892 0.242825 TCTTTAGGTCCGTGAGTGCG 59.757 55.000 0.00 0.00 0.00 5.34
8403 14995 9.498176 GGGGATATTTATATTGTTGTCGTTACT 57.502 33.333 0.00 0.00 0.00 2.24
8436 15028 1.338200 GCTCCACGAGTCCAACTTGAT 60.338 52.381 1.37 0.00 33.76 2.57
8487 15079 6.551227 TGATGGTAGATACTAGCAGTTCATGT 59.449 38.462 14.26 0.00 29.74 3.21
8489 15081 5.069119 TGGTAGATACTAGCAGTTCATGTGG 59.931 44.000 6.58 0.00 0.00 4.17
8511 15103 4.398247 GTGATTTTTCTCGTCTGTGATGC 58.602 43.478 0.00 0.00 0.00 3.91
8570 15164 4.402056 TGTATCCGGGAATCAAGTCTTC 57.598 45.455 0.00 0.00 0.00 2.87
8610 15209 4.040461 AGCTGGTTCTTGAAGCTGTAACTA 59.960 41.667 16.52 0.00 45.36 2.24
8615 15214 5.123979 GGTTCTTGAAGCTGTAACTAATGGG 59.876 44.000 5.43 0.00 0.00 4.00
8629 15228 6.576778 AACTAATGGGCTACATCTTAGGTT 57.423 37.500 0.00 0.00 39.40 3.50
8632 15231 4.625607 ATGGGCTACATCTTAGGTTAGC 57.374 45.455 0.00 0.00 33.53 3.09
8643 15242 5.499004 TCTTAGGTTAGCCATGTCAAACT 57.501 39.130 0.00 0.00 37.19 2.66
8659 15258 5.163530 TGTCAAACTGTCATTGAACTTGCAT 60.164 36.000 0.00 0.00 38.44 3.96
8669 15289 6.034577 GTCATTGAACTTGCATCATTCACATG 59.965 38.462 7.17 12.10 32.21 3.21
8670 15290 4.443913 TGAACTTGCATCATTCACATGG 57.556 40.909 0.00 0.00 0.00 3.66
8676 15296 2.212652 GCATCATTCACATGGACGCTA 58.787 47.619 0.00 0.00 0.00 4.26
8683 15303 2.031870 TCACATGGACGCTATAGCTGT 58.968 47.619 21.98 19.77 39.32 4.40
8691 15311 1.215655 CGCTATAGCTGTCCGTTGCC 61.216 60.000 21.98 0.00 39.32 4.52
8717 15337 6.478344 GGTTTGCTCATGTTTGTTGTTAATGA 59.522 34.615 0.00 0.00 0.00 2.57
8732 15352 4.201980 TGTTAATGACGCTACGAGCATACT 60.202 41.667 7.47 0.00 42.58 2.12
8756 15376 2.044650 AGTGGCTGCGGCATGAAT 60.045 55.556 21.31 0.00 40.92 2.57
8757 15377 1.679977 AGTGGCTGCGGCATGAATT 60.680 52.632 21.31 0.00 40.92 2.17
8764 15384 1.135527 CTGCGGCATGAATTGGACAAT 59.864 47.619 1.75 0.00 0.00 2.71
8768 15388 4.216042 TGCGGCATGAATTGGACAATATAG 59.784 41.667 0.00 0.00 0.00 1.31
8770 15390 5.278463 GCGGCATGAATTGGACAATATAGTT 60.278 40.000 0.00 0.00 0.00 2.24
8782 15402 9.444600 TTGGACAATATAGTTTTAGTTGAGGAC 57.555 33.333 0.00 0.00 0.00 3.85
8784 15404 9.614792 GGACAATATAGTTTTAGTTGAGGACAT 57.385 33.333 0.00 0.00 0.00 3.06
8794 15416 4.422073 AGTTGAGGACATTGTTGAGTCA 57.578 40.909 0.00 0.00 36.50 3.41
8799 15421 3.733337 AGGACATTGTTGAGTCACTGAC 58.267 45.455 0.38 0.38 36.50 3.51
8835 15484 1.946768 TGCGAGCAGTTTATTATGCCC 59.053 47.619 0.00 0.00 43.60 5.36
8844 15493 5.163561 GCAGTTTATTATGCCCAGCTGTTTA 60.164 40.000 13.81 0.00 36.41 2.01
8846 15495 6.974622 CAGTTTATTATGCCCAGCTGTTTAAG 59.025 38.462 13.81 0.00 0.00 1.85
8847 15496 6.889722 AGTTTATTATGCCCAGCTGTTTAAGA 59.110 34.615 13.81 0.00 0.00 2.10
8932 15584 2.083774 GATGCAACATGGGAGAAACGA 58.916 47.619 0.00 0.00 0.00 3.85
8939 15591 5.527951 CAACATGGGAGAAACGAAAATTGA 58.472 37.500 0.00 0.00 0.00 2.57
8941 15593 5.954335 ACATGGGAGAAACGAAAATTGATC 58.046 37.500 0.00 0.00 0.00 2.92
8942 15594 5.476599 ACATGGGAGAAACGAAAATTGATCA 59.523 36.000 0.00 0.00 0.00 2.92
8943 15595 5.371115 TGGGAGAAACGAAAATTGATCAC 57.629 39.130 0.00 0.00 0.00 3.06
8944 15596 5.070001 TGGGAGAAACGAAAATTGATCACT 58.930 37.500 0.00 0.00 0.00 3.41
8945 15597 5.048782 TGGGAGAAACGAAAATTGATCACTG 60.049 40.000 0.00 0.00 0.00 3.66
8946 15598 5.048713 GGGAGAAACGAAAATTGATCACTGT 60.049 40.000 0.00 0.00 0.00 3.55
8948 15603 7.237173 GGAGAAACGAAAATTGATCACTGTAG 58.763 38.462 0.00 0.00 0.00 2.74
8962 15617 7.497595 TGATCACTGTAGGGTTTACATACATC 58.502 38.462 0.00 0.00 0.00 3.06
8965 15620 6.049149 CACTGTAGGGTTTACATACATCCAG 58.951 44.000 0.00 0.00 0.00 3.86
9060 15717 0.249489 ACGCACCACAGAACAGAGAC 60.249 55.000 0.00 0.00 0.00 3.36
9068 15725 1.143305 CAGAACAGAGACCACAAGCG 58.857 55.000 0.00 0.00 0.00 4.68
9158 15815 0.532573 TGGAGTCGATGAAGTCCTGC 59.467 55.000 0.00 0.00 39.20 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 153 2.712539 CACGGTTGTGCTTTCGCA 59.287 55.556 0.00 0.00 45.60 5.10
186 259 2.652382 TTTTGCGAGAGTCACGGCCA 62.652 55.000 11.95 0.00 0.00 5.36
231 354 3.498397 GTCGTGCCTCTCAGAAATGAAAA 59.502 43.478 0.00 0.00 0.00 2.29
232 355 3.067106 GTCGTGCCTCTCAGAAATGAAA 58.933 45.455 0.00 0.00 0.00 2.69
233 356 2.612972 GGTCGTGCCTCTCAGAAATGAA 60.613 50.000 0.00 0.00 0.00 2.57
234 357 1.066858 GGTCGTGCCTCTCAGAAATGA 60.067 52.381 0.00 0.00 0.00 2.57
235 358 1.363744 GGTCGTGCCTCTCAGAAATG 58.636 55.000 0.00 0.00 0.00 2.32
236 359 0.108615 CGGTCGTGCCTCTCAGAAAT 60.109 55.000 0.00 0.00 34.25 2.17
237 360 1.289066 CGGTCGTGCCTCTCAGAAA 59.711 57.895 0.00 0.00 34.25 2.52
238 361 1.901948 ACGGTCGTGCCTCTCAGAA 60.902 57.895 0.00 0.00 34.25 3.02
239 362 2.282251 ACGGTCGTGCCTCTCAGA 60.282 61.111 0.00 0.00 34.25 3.27
240 363 2.126307 CACGGTCGTGCCTCTCAG 60.126 66.667 10.59 0.00 39.39 3.35
241 364 2.596338 TCACGGTCGTGCCTCTCA 60.596 61.111 17.46 0.00 45.04 3.27
242 365 2.126424 GTCACGGTCGTGCCTCTC 60.126 66.667 17.46 3.53 45.04 3.20
243 366 2.597805 AGTCACGGTCGTGCCTCT 60.598 61.111 17.46 12.39 45.04 3.69
244 367 2.126424 GAGTCACGGTCGTGCCTC 60.126 66.667 16.63 16.63 42.51 4.70
245 368 2.597805 AGAGTCACGGTCGTGCCT 60.598 61.111 17.46 12.44 45.04 4.75
246 369 2.126424 GAGAGTCACGGTCGTGCC 60.126 66.667 17.46 7.52 45.04 5.01
247 370 1.729838 GTGAGAGTCACGGTCGTGC 60.730 63.158 17.46 12.68 45.04 5.34
248 371 4.535425 GTGAGAGTCACGGTCGTG 57.465 61.111 16.33 16.33 46.64 4.35
306 429 2.645567 CACAGCCGTGACTCTCGT 59.354 61.111 0.00 0.00 46.80 4.18
320 443 1.339929 TGTGCTTTAGCGAGAGTCACA 59.660 47.619 9.26 9.26 45.83 3.58
446 589 2.604174 CGCGAGAGGCACGGTTTTT 61.604 57.895 0.00 0.00 43.84 1.94
499 643 5.135330 ACGCGAAAATACGAGTTTTTCTTC 58.865 37.500 15.93 9.09 42.75 2.87
627 791 0.321671 CTCTGGGCGTTCTCTTTGGA 59.678 55.000 0.00 0.00 0.00 3.53
685 872 1.234615 CGCTTTTTCGGGAGCCTCAA 61.235 55.000 0.00 0.00 35.49 3.02
720 916 1.545428 GCACACCTCACATCAGGGAAA 60.545 52.381 0.00 0.00 37.96 3.13
722 918 1.679311 GCACACCTCACATCAGGGA 59.321 57.895 0.00 0.00 37.96 4.20
759 955 2.304761 TGATTGCCTCTCGGGTAGTTTT 59.695 45.455 0.00 0.00 37.43 2.43
761 957 1.482593 CTGATTGCCTCTCGGGTAGTT 59.517 52.381 0.00 0.00 37.43 2.24
763 959 1.067821 GTCTGATTGCCTCTCGGGTAG 59.932 57.143 0.00 0.00 37.43 3.18
819 1015 1.289694 TTTTTGCTGATGCTGGGCG 59.710 52.632 0.00 0.00 40.48 6.13
879 1075 1.584742 GGCGACGCTTAGGTACGAC 60.585 63.158 20.77 0.00 0.00 4.34
880 1076 2.793946 GGCGACGCTTAGGTACGA 59.206 61.111 20.77 0.00 0.00 3.43
979 1446 1.532794 CTGGAGATCCGGAGAGGGG 60.533 68.421 11.34 0.00 45.36 4.79
1031 1510 4.060667 TTTAGCAGGGGCAGGGGC 62.061 66.667 0.00 0.00 44.61 5.80
1032 1511 2.043953 GTTTAGCAGGGGCAGGGG 60.044 66.667 0.00 0.00 44.61 4.79
1033 1512 2.043953 GGTTTAGCAGGGGCAGGG 60.044 66.667 0.00 0.00 44.61 4.45
1034 1513 1.279025 TAGGGTTTAGCAGGGGCAGG 61.279 60.000 0.00 0.00 44.61 4.85
1035 1514 0.623723 TTAGGGTTTAGCAGGGGCAG 59.376 55.000 0.00 0.00 44.61 4.85
1036 1515 0.330267 GTTAGGGTTTAGCAGGGGCA 59.670 55.000 0.00 0.00 44.61 5.36
1238 1751 3.009714 AGGGAAACTCTCCGGCCC 61.010 66.667 0.00 0.00 46.51 5.80
1240 1753 1.079057 GACAGGGAAACTCTCCGGC 60.079 63.158 0.00 0.00 46.51 6.13
1241 1754 0.037232 GTGACAGGGAAACTCTCCGG 60.037 60.000 0.00 0.00 46.51 5.14
1242 1755 0.037232 GGTGACAGGGAAACTCTCCG 60.037 60.000 0.00 0.00 46.51 4.63
1243 1756 1.056660 TGGTGACAGGGAAACTCTCC 58.943 55.000 0.00 0.00 38.55 3.71
1259 1772 0.035056 GCCTATGACAGCAACCTGGT 60.035 55.000 0.00 0.00 43.53 4.00
1260 1773 0.254178 AGCCTATGACAGCAACCTGG 59.746 55.000 0.00 0.00 43.53 4.45
1261 1774 1.339438 ACAGCCTATGACAGCAACCTG 60.339 52.381 0.00 0.00 44.80 4.00
1262 1775 0.987294 ACAGCCTATGACAGCAACCT 59.013 50.000 0.00 0.00 0.00 3.50
1263 1776 1.826385 AACAGCCTATGACAGCAACC 58.174 50.000 0.00 0.00 0.00 3.77
1264 1777 3.923017 AAAACAGCCTATGACAGCAAC 57.077 42.857 0.00 0.00 0.00 4.17
1265 1778 6.183360 GCTAATAAAACAGCCTATGACAGCAA 60.183 38.462 0.00 0.00 0.00 3.91
1266 1779 5.296780 GCTAATAAAACAGCCTATGACAGCA 59.703 40.000 0.00 0.00 0.00 4.41
1267 1780 5.529060 AGCTAATAAAACAGCCTATGACAGC 59.471 40.000 0.00 0.00 38.61 4.40
1268 1781 6.074088 CGAGCTAATAAAACAGCCTATGACAG 60.074 42.308 0.00 0.00 38.61 3.51
1269 1782 5.753438 CGAGCTAATAAAACAGCCTATGACA 59.247 40.000 0.00 0.00 38.61 3.58
1270 1783 5.753921 ACGAGCTAATAAAACAGCCTATGAC 59.246 40.000 0.00 0.00 38.61 3.06
1271 1784 5.914033 ACGAGCTAATAAAACAGCCTATGA 58.086 37.500 0.00 0.00 38.61 2.15
1272 1785 6.257849 TCAACGAGCTAATAAAACAGCCTATG 59.742 38.462 0.00 0.00 38.61 2.23
1273 1786 6.346096 TCAACGAGCTAATAAAACAGCCTAT 58.654 36.000 0.00 0.00 38.61 2.57
1274 1787 5.726397 TCAACGAGCTAATAAAACAGCCTA 58.274 37.500 0.00 0.00 38.61 3.93
1275 1788 4.575885 TCAACGAGCTAATAAAACAGCCT 58.424 39.130 0.00 0.00 38.61 4.58
1276 1789 4.939509 TCAACGAGCTAATAAAACAGCC 57.060 40.909 0.00 0.00 38.61 4.85
1277 1790 5.790495 CAGTTCAACGAGCTAATAAAACAGC 59.210 40.000 0.00 0.00 38.09 4.40
1278 1791 6.307155 CCAGTTCAACGAGCTAATAAAACAG 58.693 40.000 0.00 0.00 0.00 3.16
1279 1792 5.180492 CCCAGTTCAACGAGCTAATAAAACA 59.820 40.000 0.00 0.00 0.00 2.83
1280 1793 5.410439 TCCCAGTTCAACGAGCTAATAAAAC 59.590 40.000 0.00 0.00 0.00 2.43
1281 1794 5.553123 TCCCAGTTCAACGAGCTAATAAAA 58.447 37.500 0.00 0.00 0.00 1.52
1282 1795 5.155278 TCCCAGTTCAACGAGCTAATAAA 57.845 39.130 0.00 0.00 0.00 1.40
1283 1796 4.222145 ACTCCCAGTTCAACGAGCTAATAA 59.778 41.667 0.00 0.00 0.00 1.40
1284 1797 3.767673 ACTCCCAGTTCAACGAGCTAATA 59.232 43.478 0.00 0.00 0.00 0.98
1285 1798 2.567615 ACTCCCAGTTCAACGAGCTAAT 59.432 45.455 0.00 0.00 0.00 1.73
1290 1803 0.679505 TCCACTCCCAGTTCAACGAG 59.320 55.000 0.00 0.00 0.00 4.18
1306 1822 2.565391 TCAGCACTAAGAATCGGTTCCA 59.435 45.455 4.40 0.00 34.81 3.53
1349 1865 1.682854 CCATCACCAGCACAAACTTGT 59.317 47.619 0.00 0.00 43.36 3.16
1445 1972 3.752747 CACTATGGCAATGAACTGACACA 59.247 43.478 0.00 0.00 37.09 3.72
1446 1973 3.127548 CCACTATGGCAATGAACTGACAC 59.872 47.826 0.00 0.00 37.09 3.67
1476 2003 1.720852 GTGCCTGCTACAAAATTTGCG 59.279 47.619 5.52 0.00 0.00 4.85
1548 2200 5.392919 CCCATCGCAGTTTATTGATTCAACA 60.393 40.000 0.15 0.00 0.00 3.33
1549 2201 5.036737 CCCATCGCAGTTTATTGATTCAAC 58.963 41.667 0.15 0.00 0.00 3.18
1685 2347 5.482908 CATGTAAGAAAGGCTCACAGTAGT 58.517 41.667 0.00 0.00 0.00 2.73
1734 2402 6.721208 TCCCATAAGACTTGAAATTCAGCTTT 59.279 34.615 11.15 2.75 0.00 3.51
1955 2831 5.783111 AGAACAACATAATTTCCAAGCACC 58.217 37.500 0.00 0.00 0.00 5.01
2055 3490 8.356657 TGAACCAACAACCTTAACATATCAAAG 58.643 33.333 0.00 0.00 0.00 2.77
2247 3682 2.303600 ACCCTTAGAATGTGCGGTTACA 59.696 45.455 0.00 0.00 34.63 2.41
2310 3746 1.908299 CCTGTTTTGTGGAGGGGGC 60.908 63.158 0.00 0.00 0.00 5.80
2339 3794 8.472413 CAATCCATAACTGTTCCATCTTTCATT 58.528 33.333 0.00 0.00 0.00 2.57
2416 3872 1.932511 GCTCAGAGCTGCATCAAGTAC 59.067 52.381 15.78 0.00 38.45 2.73
2569 4034 5.961272 TCATTTCTCGCATACTCACAACTA 58.039 37.500 0.00 0.00 0.00 2.24
2570 4035 4.820897 TCATTTCTCGCATACTCACAACT 58.179 39.130 0.00 0.00 0.00 3.16
2571 4036 5.725110 ATCATTTCTCGCATACTCACAAC 57.275 39.130 0.00 0.00 0.00 3.32
2628 4124 3.745975 TGTTACAGAAGACAAAGCATCCG 59.254 43.478 0.00 0.00 0.00 4.18
2649 4145 7.265673 TGTACTTAATCAACCTTAGCTAGCTG 58.734 38.462 27.68 13.19 0.00 4.24
2650 4146 7.419711 TGTACTTAATCAACCTTAGCTAGCT 57.580 36.000 23.12 23.12 0.00 3.32
2651 4147 7.224949 CCTTGTACTTAATCAACCTTAGCTAGC 59.775 40.741 6.62 6.62 0.00 3.42
2652 4148 8.475639 TCCTTGTACTTAATCAACCTTAGCTAG 58.524 37.037 0.00 0.00 0.00 3.42
2722 4218 8.633561 CAGTGTGAGAATATAGTAGATCCACAA 58.366 37.037 0.00 0.00 34.41 3.33
2740 4236 7.323420 TGAAATATAGAACCAGTCAGTGTGAG 58.677 38.462 0.00 0.00 0.00 3.51
2752 4248 4.039366 AGCCTCCGTCTGAAATATAGAACC 59.961 45.833 0.00 0.00 0.00 3.62
2771 4267 5.745476 GCTCTTCAGGATTGATCAATAGCCT 60.745 44.000 20.75 19.52 32.27 4.58
3057 4553 3.981071 TGTGAGAACCTGATAACCCAG 57.019 47.619 0.00 0.00 0.00 4.45
3235 4732 2.664402 AAGAACCAAGCAGACACCAT 57.336 45.000 0.00 0.00 0.00 3.55
3282 4779 5.156355 GTGCAACATATTGGTGAAGAACAG 58.844 41.667 0.00 0.00 37.20 3.16
3552 5062 6.115446 TCATGATAAAGACCCAAAGCAGTAG 58.885 40.000 0.00 0.00 0.00 2.57
3706 5216 3.844211 AGGCAAATCACTACACCTCCTAA 59.156 43.478 0.00 0.00 0.00 2.69
3707 5217 3.197766 CAGGCAAATCACTACACCTCCTA 59.802 47.826 0.00 0.00 0.00 2.94
3708 5218 2.026822 CAGGCAAATCACTACACCTCCT 60.027 50.000 0.00 0.00 0.00 3.69
3803 5342 5.221521 TGCCAGAGTCCATATGATACAACTC 60.222 44.000 3.65 8.72 34.69 3.01
3849 5398 6.306987 TGGTAGAAGAAAAGGCTTCAGAAAT 58.693 36.000 0.00 0.00 45.21 2.17
3850 5399 5.690865 TGGTAGAAGAAAAGGCTTCAGAAA 58.309 37.500 0.00 0.00 45.21 2.52
3879 5428 4.932146 ACTGCCACATGAAAACAAGTTAC 58.068 39.130 0.00 0.00 0.00 2.50
3972 5525 3.838244 AGAGAGGTGCTTACAACAACA 57.162 42.857 0.00 0.00 35.21 3.33
4196 5751 0.958822 AACAAAGGGGCACATCGAAC 59.041 50.000 0.00 0.00 0.00 3.95
4305 5865 7.735917 TGGTTATAAGACAAGGATGATAGGTG 58.264 38.462 0.00 0.00 0.00 4.00
4469 6352 2.375014 TCGATATGTACAGGGAGGCA 57.625 50.000 0.33 0.00 0.00 4.75
4577 6461 6.016777 CAGCAAGTTCAGAACCTTAGAAACAT 60.017 38.462 9.85 0.00 0.00 2.71
4580 6464 5.296780 CACAGCAAGTTCAGAACCTTAGAAA 59.703 40.000 9.85 0.00 0.00 2.52
4657 6887 5.937111 ACACCGCATAGTTTCCCTTATATT 58.063 37.500 0.00 0.00 0.00 1.28
5076 8432 6.425114 AGACGATATGCATAAAAAGTAGCCAG 59.575 38.462 11.13 0.00 0.00 4.85
5115 8471 7.646130 TGTCAAATCAGTCAAACGAATAAAACC 59.354 33.333 0.00 0.00 0.00 3.27
5116 8595 8.555166 TGTCAAATCAGTCAAACGAATAAAAC 57.445 30.769 0.00 0.00 0.00 2.43
5361 8847 9.465985 GATACACTCCAGAAAAGTAGCTATTAC 57.534 37.037 0.00 0.00 0.00 1.89
5364 8850 7.561722 TCAGATACACTCCAGAAAAGTAGCTAT 59.438 37.037 0.00 0.00 31.08 2.97
5434 8925 2.040947 TGTCATGACTATTTGGTGGCCA 59.959 45.455 25.55 0.00 0.00 5.36
5460 8951 7.149096 GGTTTTATGTCGATTTGTAAACAACGG 60.149 37.037 12.11 0.00 35.28 4.44
5662 9174 4.590850 TCGTCATAGTAGCTGCATCATT 57.409 40.909 4.12 0.00 0.00 2.57
5855 9562 6.183360 CCAACTTCAATAGTTCTGCTCAGATG 60.183 42.308 0.00 0.00 45.29 2.90
6166 9883 2.252260 CAAGAACAAGCCGTGCGG 59.748 61.111 6.22 6.22 38.57 5.69
6247 9984 5.705441 GTGTTGATAATGTGAGGAAAGGTCA 59.295 40.000 0.00 0.00 0.00 4.02
6253 9990 3.937814 AGCGTGTTGATAATGTGAGGAA 58.062 40.909 0.00 0.00 0.00 3.36
6298 10035 2.046864 AGCGCAGGCGTCTAGAAGA 61.047 57.895 11.47 0.00 46.35 2.87
6307 10044 2.250485 GCATATTCAGCGCAGGCG 59.750 61.111 11.47 9.68 46.35 5.52
6364 10101 1.668151 GAGTTGGAGTGGCACCGAC 60.668 63.158 15.27 10.22 40.90 4.79
6375 10112 6.062095 TGATGATATACGAGACAGAGTTGGA 58.938 40.000 0.00 0.00 0.00 3.53
6498 10242 4.148696 GCAATATTGTATGGCGTTGAATGC 59.851 41.667 16.61 0.00 0.00 3.56
6534 10278 6.672657 AGCTAAAAGGAAGGTTCTATAGGACA 59.327 38.462 13.33 0.00 0.00 4.02
6607 10351 2.267174 ATCAAAGCCGGATGGATGAG 57.733 50.000 5.05 0.00 37.49 2.90
6741 10487 5.598830 AGTAGAGAGGTTGAAGACAAGTCAA 59.401 40.000 2.72 0.00 36.64 3.18
6914 10662 3.198635 TGATGAAAAACAAGGGTGGCAAA 59.801 39.130 0.00 0.00 0.00 3.68
7055 10803 3.366679 CGAGTTCTTTCACTAAGCCCGTA 60.367 47.826 0.00 0.00 33.66 4.02
7119 10883 4.705023 ACAAGTTTGCAGGTGTTAGAGTTT 59.295 37.500 0.00 0.00 0.00 2.66
7130 10894 5.220931 GCTATCCAGAATACAAGTTTGCAGG 60.221 44.000 0.00 0.00 0.00 4.85
7256 11020 8.905103 ACGGTGAAAACATATAAAAATACAGC 57.095 30.769 0.00 0.00 0.00 4.40
7294 11060 9.530129 CTTCGAAGAAAACATACATAAACTGAC 57.470 33.333 20.74 0.00 45.90 3.51
7500 13965 6.259550 ACATTCTCAACAGCCTTAACAATC 57.740 37.500 0.00 0.00 0.00 2.67
7523 14006 4.934602 CCAGCAAAACCAAGACAAAAGAAA 59.065 37.500 0.00 0.00 0.00 2.52
7616 14144 0.534873 CCTTTACCCGGGCATTTTGG 59.465 55.000 24.08 12.02 0.00 3.28
7625 14153 1.000394 CTTGCCAAAACCTTTACCCGG 60.000 52.381 0.00 0.00 0.00 5.73
7697 14225 7.601073 CTGAGCATAGTCAGTTCATACAAAA 57.399 36.000 0.00 0.00 39.39 2.44
7733 14261 7.477144 AAAATAACAGTTTTACTTTGCTGCC 57.523 32.000 0.00 0.00 32.65 4.85
7753 14324 8.891671 ACTCATGTGATTAAAACAGCAAAAAT 57.108 26.923 0.94 0.00 0.00 1.82
7770 14341 6.380995 TGTTTTGCATTAAGCTACTCATGTG 58.619 36.000 0.00 0.00 45.94 3.21
7991 14570 0.244721 TCCAGACACTGCACTCATCG 59.755 55.000 0.00 0.00 0.00 3.84
8084 14670 2.427506 GCAACCAAACAGACCCTAGAG 58.572 52.381 0.00 0.00 0.00 2.43
8138 14724 3.932710 TCATACCTGTTTGCGACAAGATC 59.067 43.478 0.00 0.00 37.93 2.75
8144 14730 2.094417 GCTCTTCATACCTGTTTGCGAC 59.906 50.000 0.00 0.00 0.00 5.19
8158 14744 1.959226 GGAAACGCCGTGCTCTTCA 60.959 57.895 0.00 0.00 0.00 3.02
8276 14867 4.398358 CACTCACGGACCTAAAGATAGTCA 59.602 45.833 0.00 0.00 0.00 3.41
8301 14892 2.999355 CAGCTGAGTTTGTTCTAGAGCC 59.001 50.000 8.42 0.00 0.00 4.70
8403 14995 6.222038 ACTCGTGGAGCTAAAGATAATTCA 57.778 37.500 0.00 0.00 32.04 2.57
8436 15028 9.725019 AATGACAAGTATCAGATGAGTTTGTTA 57.275 29.630 9.37 7.07 30.97 2.41
8487 15079 4.066646 TCACAGACGAGAAAAATCACCA 57.933 40.909 0.00 0.00 0.00 4.17
8489 15081 4.083855 TGCATCACAGACGAGAAAAATCAC 60.084 41.667 0.00 0.00 0.00 3.06
8511 15103 5.334414 GGAGAGTAAACTGTTGCACATTCTG 60.334 44.000 0.00 0.00 0.00 3.02
8520 15114 4.039245 TGGAGTCTGGAGAGTAAACTGTTG 59.961 45.833 0.00 0.00 0.00 3.33
8570 15164 0.657840 GCTGCGTACCTAAATGGCTG 59.342 55.000 0.00 0.00 40.22 4.85
8610 15209 4.202472 GGCTAACCTAAGATGTAGCCCATT 60.202 45.833 9.02 0.00 42.99 3.16
8615 15214 4.962155 ACATGGCTAACCTAAGATGTAGC 58.038 43.478 0.00 0.00 36.63 3.58
8629 15228 4.650734 TCAATGACAGTTTGACATGGCTA 58.349 39.130 0.00 0.00 33.39 3.93
8632 15231 5.443185 AGTTCAATGACAGTTTGACATGG 57.557 39.130 0.00 0.00 33.39 3.66
8643 15242 5.009811 TGTGAATGATGCAAGTTCAATGACA 59.990 36.000 11.74 3.37 34.04 3.58
8659 15258 3.653344 GCTATAGCGTCCATGTGAATGA 58.347 45.455 9.40 0.00 0.00 2.57
8691 15311 2.808244 ACAACAAACATGAGCAAACCG 58.192 42.857 0.00 0.00 0.00 4.44
8697 15317 4.088496 GCGTCATTAACAACAAACATGAGC 59.912 41.667 0.00 0.00 0.00 4.26
8700 15320 5.280446 CGTAGCGTCATTAACAACAAACATG 59.720 40.000 0.00 0.00 0.00 3.21
8701 15321 5.177881 TCGTAGCGTCATTAACAACAAACAT 59.822 36.000 0.00 0.00 0.00 2.71
8717 15337 1.671979 TACCAGTATGCTCGTAGCGT 58.328 50.000 6.77 6.77 46.26 5.07
8732 15352 2.031919 CCGCAGCCACTGTTACCA 59.968 61.111 0.00 0.00 33.43 3.25
8746 15366 3.648339 ATATTGTCCAATTCATGCCGC 57.352 42.857 0.00 0.00 32.50 6.53
8747 15367 5.947228 ACTATATTGTCCAATTCATGCCG 57.053 39.130 0.00 0.00 32.50 5.69
8756 15376 9.444600 GTCCTCAACTAAAACTATATTGTCCAA 57.555 33.333 0.00 0.00 0.00 3.53
8757 15377 8.598916 TGTCCTCAACTAAAACTATATTGTCCA 58.401 33.333 0.00 0.00 0.00 4.02
8768 15388 7.027778 ACTCAACAATGTCCTCAACTAAAAC 57.972 36.000 0.00 0.00 0.00 2.43
8770 15390 6.260050 GTGACTCAACAATGTCCTCAACTAAA 59.740 38.462 0.00 0.00 32.67 1.85
8779 15399 2.476619 CGTCAGTGACTCAACAATGTCC 59.523 50.000 20.64 0.00 37.20 4.02
8782 15402 1.866601 TGCGTCAGTGACTCAACAATG 59.133 47.619 20.64 4.13 37.23 2.82
8784 15404 2.238942 ATGCGTCAGTGACTCAACAA 57.761 45.000 19.13 0.00 31.04 2.83
8786 15406 2.543848 TGAAATGCGTCAGTGACTCAAC 59.456 45.455 19.13 13.59 31.04 3.18
8787 15407 2.543848 GTGAAATGCGTCAGTGACTCAA 59.456 45.455 19.13 6.01 31.04 3.02
8794 15416 1.873591 GTTCCTGTGAAATGCGTCAGT 59.126 47.619 0.00 0.00 30.79 3.41
8832 15481 2.744741 GACTCTTCTTAAACAGCTGGGC 59.255 50.000 19.93 0.00 0.00 5.36
8833 15482 2.996621 CGACTCTTCTTAAACAGCTGGG 59.003 50.000 19.93 2.76 0.00 4.45
8835 15484 4.799678 TCTCGACTCTTCTTAAACAGCTG 58.200 43.478 13.48 13.48 0.00 4.24
8844 15493 5.184864 AGTTGTGATCATCTCGACTCTTCTT 59.815 40.000 0.00 0.00 31.03 2.52
8846 15495 4.992688 AGTTGTGATCATCTCGACTCTTC 58.007 43.478 0.00 0.00 31.03 2.87
8847 15496 4.142271 GGAGTTGTGATCATCTCGACTCTT 60.142 45.833 26.05 2.99 44.65 2.85
8911 15563 1.811965 CGTTTCTCCCATGTTGCATCA 59.188 47.619 0.00 0.00 0.00 3.07
8932 15584 8.650143 ATGTAAACCCTACAGTGATCAATTTT 57.350 30.769 0.00 0.00 0.00 1.82
8939 15591 6.385759 TGGATGTATGTAAACCCTACAGTGAT 59.614 38.462 0.00 0.00 0.00 3.06
8941 15593 5.984725 TGGATGTATGTAAACCCTACAGTG 58.015 41.667 0.00 0.00 0.00 3.66
8942 15594 5.962031 TCTGGATGTATGTAAACCCTACAGT 59.038 40.000 0.00 0.00 0.00 3.55
8943 15595 6.127168 TGTCTGGATGTATGTAAACCCTACAG 60.127 42.308 0.00 0.00 0.00 2.74
8944 15596 5.722441 TGTCTGGATGTATGTAAACCCTACA 59.278 40.000 0.00 0.00 0.00 2.74
8945 15597 6.047231 GTGTCTGGATGTATGTAAACCCTAC 58.953 44.000 0.00 0.00 0.00 3.18
8946 15598 5.129815 GGTGTCTGGATGTATGTAAACCCTA 59.870 44.000 0.00 0.00 0.00 3.53
8948 15603 4.196971 GGTGTCTGGATGTATGTAAACCC 58.803 47.826 0.00 0.00 0.00 4.11
8962 15617 1.302832 GGAACTGGCTGGTGTCTGG 60.303 63.158 0.00 0.00 0.00 3.86
8965 15620 1.003233 GGAGGAACTGGCTGGTGTC 60.003 63.158 0.00 0.00 41.55 3.67
9084 15741 1.005630 CGATCGATTCCCCTGAGCC 60.006 63.158 10.26 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.