Multiple sequence alignment - TraesCS6B01G114300

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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 TraesCS6B01G114300 chr6B 100.000 6136 0 0 1 6136 96643716 96637581 0.000000e+00 11332.0
1 TraesCS6B01G114300 chr6B 99.043 2613 11 2 2292 4890 522329929 522327317 0.000000e+00 4674.0
2 TraesCS6B01G114300 chr6B 95.254 885 38 2 2577 3460 422974859 422975740 0.000000e+00 1399.0
3 TraesCS6B01G114300 chr6B 84.446 1318 179 16 677 1981 13440997 13439693 0.000000e+00 1275.0
4 TraesCS6B01G114300 chr6B 92.517 147 10 1 5990 6136 523343636 523343781 6.230000e-50 209.0
5 TraesCS6B01G114300 chr6B 79.767 257 32 8 5152 5389 13652007 13651752 1.060000e-37 169.0
6 TraesCS6B01G114300 chr6B 88.043 92 5 6 5900 5990 127746630 127746544 3.030000e-18 104.0
7 TraesCS6B01G114300 chr6A 99.082 2613 10 2 2292 4890 234188651 234186039 0.000000e+00 4680.0
8 TraesCS6B01G114300 chr6A 99.043 2613 11 2 2292 4890 222651086 222648474 0.000000e+00 4674.0
9 TraesCS6B01G114300 chr6A 98.967 2613 13 2 2292 4890 409143023 409140411 0.000000e+00 4663.0
10 TraesCS6B01G114300 chr6A 95.072 1461 49 4 677 2126 51879828 51881276 0.000000e+00 2278.0
11 TraesCS6B01G114300 chr6A 97.643 1103 23 1 4890 5992 51881260 51882359 0.000000e+00 1890.0
12 TraesCS6B01G114300 chr6A 85.018 1355 186 7 677 2019 7186414 7185065 0.000000e+00 1362.0
13 TraesCS6B01G114300 chr6A 90.351 570 37 3 26 594 51851532 51852084 0.000000e+00 732.0
14 TraesCS6B01G114300 chr6A 100.000 174 0 0 2122 2295 515931848 515931675 7.670000e-84 322.0
15 TraesCS6B01G114300 chr6A 86.957 92 6 6 5900 5990 71700182 71700096 1.410000e-16 99.0
16 TraesCS6B01G114300 chr6A 97.674 43 0 1 594 635 51852111 51852153 8.530000e-09 73.1
17 TraesCS6B01G114300 chr6A 100.000 30 0 0 1 30 51848061 51848090 8.590000e-04 56.5
18 TraesCS6B01G114300 chr1B 99.043 2613 10 3 2292 4890 151845558 151842947 0.000000e+00 4673.0
19 TraesCS6B01G114300 chr1B 93.197 147 9 1 5990 6136 520524973 520524828 1.340000e-51 215.0
20 TraesCS6B01G114300 chr2B 99.005 2613 12 6 2292 4890 683125733 683123121 0.000000e+00 4669.0
21 TraesCS6B01G114300 chr2B 98.890 2613 15 6 2292 4890 674787416 674790028 0.000000e+00 4652.0
22 TraesCS6B01G114300 chr2B 98.925 2605 14 6 2292 4882 504688488 504691092 0.000000e+00 4643.0
23 TraesCS6B01G114300 chr2B 92.517 147 9 1 5990 6136 399350442 399350586 6.230000e-50 209.0
24 TraesCS6B01G114300 chr7B 98.967 2613 13 2 2292 4890 700427366 700429978 0.000000e+00 4663.0
25 TraesCS6B01G114300 chr7B 98.928 2613 14 6 2292 4890 433476015 433473403 0.000000e+00 4658.0
26 TraesCS6B01G114300 chr7B 87.939 2562 229 26 2298 4845 490604717 490602222 0.000000e+00 2946.0
27 TraesCS6B01G114300 chr7B 99.425 174 1 0 2122 2295 443304072 443304245 3.570000e-82 316.0
28 TraesCS6B01G114300 chr7B 77.703 296 50 12 297 577 638559995 638559701 3.800000e-37 167.0
29 TraesCS6B01G114300 chr5B 98.928 2613 14 2 2292 4890 292189191 292191803 0.000000e+00 4658.0
30 TraesCS6B01G114300 chr5B 84.711 1367 190 11 666 2019 432983061 432984421 0.000000e+00 1349.0
31 TraesCS6B01G114300 chr5B 85.463 454 62 2 2981 3430 248397722 248397269 2.590000e-128 470.0
32 TraesCS6B01G114300 chr5B 100.000 171 0 0 2125 2295 554032966 554033136 3.570000e-82 316.0
33 TraesCS6B01G114300 chr5B 96.237 186 5 2 2110 2295 666212167 666212350 2.780000e-78 303.0
34 TraesCS6B01G114300 chr5B 80.156 257 31 8 5152 5389 432984597 432984852 2.270000e-39 174.0
35 TraesCS6B01G114300 chr5B 85.000 140 21 0 442 581 432982708 432982847 6.410000e-30 143.0
36 TraesCS6B01G114300 chr4A 98.852 2613 14 4 2292 4890 578159034 578156424 0.000000e+00 4645.0
37 TraesCS6B01G114300 chr4A 98.324 179 2 1 2118 2295 537197838 537197660 4.620000e-81 313.0
38 TraesCS6B01G114300 chr3B 98.887 2605 12 3 2300 4890 53353973 53351372 0.000000e+00 4634.0
39 TraesCS6B01G114300 chr3B 96.562 2414 75 6 2478 4890 306263026 306265432 0.000000e+00 3991.0
40 TraesCS6B01G114300 chr6D 96.646 1461 30 3 677 2126 41234396 41235848 0.000000e+00 2409.0
41 TraesCS6B01G114300 chr6D 98.277 1103 18 1 4890 5992 41235832 41236933 0.000000e+00 1930.0
42 TraesCS6B01G114300 chr6D 84.723 1355 190 11 677 2019 7345579 7344230 0.000000e+00 1339.0
43 TraesCS6B01G114300 chr6D 84.377 1357 191 13 677 2019 7359118 7357769 0.000000e+00 1312.0
44 TraesCS6B01G114300 chr6D 83.049 1463 230 7 677 2126 22183019 22184476 0.000000e+00 1312.0
45 TraesCS6B01G114300 chr6D 84.713 1256 156 16 677 1912 7696986 7698225 0.000000e+00 1223.0
46 TraesCS6B01G114300 chr6D 96.471 595 18 1 1 592 41233589 41234183 0.000000e+00 979.0
47 TraesCS6B01G114300 chr6D 91.096 146 11 2 5233 5376 22184867 22185012 4.850000e-46 196.0
48 TraesCS6B01G114300 chr6D 91.509 106 7 2 575 679 41234194 41234298 1.780000e-30 145.0
49 TraesCS6B01G114300 chr6D 88.043 92 5 6 5900 5990 57109780 57109694 3.030000e-18 104.0
50 TraesCS6B01G114300 chr7D 85.103 1356 184 10 677 2019 597676747 597675397 0.000000e+00 1369.0
51 TraesCS6B01G114300 chr7D 91.772 158 9 3 5979 6136 31062091 31061938 3.720000e-52 217.0
52 TraesCS6B01G114300 chr7D 91.447 152 11 2 5986 6136 170559352 170559502 2.240000e-49 207.0
53 TraesCS6B01G114300 chrUn 84.915 1359 182 14 677 2019 80036754 80035403 0.000000e+00 1352.0
54 TraesCS6B01G114300 chrUn 84.718 1348 190 9 679 2015 79937494 79938836 0.000000e+00 1334.0
55 TraesCS6B01G114300 chrUn 84.365 1260 179 11 677 1923 79930963 79932217 0.000000e+00 1219.0
56 TraesCS6B01G114300 chrUn 84.193 1183 169 10 679 1848 79855038 79856215 0.000000e+00 1133.0
57 TraesCS6B01G114300 chrUn 99.425 174 1 0 2122 2295 1039317 1039144 3.570000e-82 316.0
58 TraesCS6B01G114300 chrUn 99.425 174 1 0 2122 2295 388234301 388234128 3.570000e-82 316.0
59 TraesCS6B01G114300 chrUn 100.000 170 0 0 2126 2295 87050786 87050617 1.280000e-81 315.0
60 TraesCS6B01G114300 chrUn 100.000 170 0 0 2126 2295 419797222 419797053 1.280000e-81 315.0
61 TraesCS6B01G114300 chrUn 100.000 170 0 0 2126 2295 435604261 435604092 1.280000e-81 315.0
62 TraesCS6B01G114300 chrUn 99.422 173 1 0 2123 2295 442546695 442546867 1.280000e-81 315.0
63 TraesCS6B01G114300 chrUn 99.405 168 1 0 2128 2295 468628733 468628566 7.730000e-79 305.0
64 TraesCS6B01G114300 chrUn 98.824 170 2 0 2126 2295 17585401 17585232 2.780000e-78 303.0
65 TraesCS6B01G114300 chrUn 98.830 171 1 1 2126 2295 27369918 27369748 2.780000e-78 303.0
66 TraesCS6B01G114300 chr4D 100.000 173 0 0 2123 2295 323566426 323566254 2.760000e-83 320.0
67 TraesCS6B01G114300 chr4D 100.000 170 0 0 2126 2295 83143560 83143729 1.280000e-81 315.0
68 TraesCS6B01G114300 chr4D 98.857 175 1 1 2121 2295 93830042 93830215 1.660000e-80 311.0
69 TraesCS6B01G114300 chr4D 93.056 144 9 1 5993 6136 26896015 26895873 6.230000e-50 209.0
70 TraesCS6B01G114300 chr2A 100.000 173 0 0 2123 2295 67523370 67523542 2.760000e-83 320.0
71 TraesCS6B01G114300 chr2A 98.333 180 2 1 2117 2295 488710997 488710818 1.280000e-81 315.0
72 TraesCS6B01G114300 chr2A 93.970 199 8 4 2099 2295 535256654 535256850 1.290000e-76 298.0
73 TraesCS6B01G114300 chr2A 93.836 146 9 0 5991 6136 362446136 362445991 2.880000e-53 220.0
74 TraesCS6B01G114300 chr4B 100.000 172 0 0 2124 2295 172477749 172477578 9.930000e-83 318.0
75 TraesCS6B01G114300 chr4B 98.864 176 2 0 2120 2295 639254009 639254184 1.280000e-81 315.0
76 TraesCS6B01G114300 chr1A 99.425 174 1 0 2122 2295 136929358 136929531 3.570000e-82 316.0
77 TraesCS6B01G114300 chr1A 100.000 171 0 0 2125 2295 491264687 491264857 3.570000e-82 316.0
78 TraesCS6B01G114300 chr1A 99.425 174 1 0 2122 2295 538329921 538330094 3.570000e-82 316.0
79 TraesCS6B01G114300 chr7A 93.836 146 8 1 5991 6136 631367419 631367563 1.040000e-52 219.0
80 TraesCS6B01G114300 chr5A 93.151 146 9 1 5991 6136 568401611 568401467 4.820000e-51 213.0


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 TraesCS6B01G114300 chr6B 96637581 96643716 6135 True 11332.000000 11332 100.000000 1 6136 1 chr6B.!!$R3 6135
1 TraesCS6B01G114300 chr6B 522327317 522329929 2612 True 4674.000000 4674 99.043000 2292 4890 1 chr6B.!!$R5 2598
2 TraesCS6B01G114300 chr6B 422974859 422975740 881 False 1399.000000 1399 95.254000 2577 3460 1 chr6B.!!$F1 883
3 TraesCS6B01G114300 chr6B 13439693 13440997 1304 True 1275.000000 1275 84.446000 677 1981 1 chr6B.!!$R1 1304
4 TraesCS6B01G114300 chr6A 234186039 234188651 2612 True 4680.000000 4680 99.082000 2292 4890 1 chr6A.!!$R4 2598
5 TraesCS6B01G114300 chr6A 222648474 222651086 2612 True 4674.000000 4674 99.043000 2292 4890 1 chr6A.!!$R3 2598
6 TraesCS6B01G114300 chr6A 409140411 409143023 2612 True 4663.000000 4663 98.967000 2292 4890 1 chr6A.!!$R5 2598
7 TraesCS6B01G114300 chr6A 51879828 51882359 2531 False 2084.000000 2278 96.357500 677 5992 2 chr6A.!!$F2 5315
8 TraesCS6B01G114300 chr6A 7185065 7186414 1349 True 1362.000000 1362 85.018000 677 2019 1 chr6A.!!$R1 1342
9 TraesCS6B01G114300 chr6A 51848061 51852153 4092 False 287.200000 732 96.008333 1 635 3 chr6A.!!$F1 634
10 TraesCS6B01G114300 chr1B 151842947 151845558 2611 True 4673.000000 4673 99.043000 2292 4890 1 chr1B.!!$R1 2598
11 TraesCS6B01G114300 chr2B 683123121 683125733 2612 True 4669.000000 4669 99.005000 2292 4890 1 chr2B.!!$R1 2598
12 TraesCS6B01G114300 chr2B 674787416 674790028 2612 False 4652.000000 4652 98.890000 2292 4890 1 chr2B.!!$F3 2598
13 TraesCS6B01G114300 chr2B 504688488 504691092 2604 False 4643.000000 4643 98.925000 2292 4882 1 chr2B.!!$F2 2590
14 TraesCS6B01G114300 chr7B 700427366 700429978 2612 False 4663.000000 4663 98.967000 2292 4890 1 chr7B.!!$F2 2598
15 TraesCS6B01G114300 chr7B 433473403 433476015 2612 True 4658.000000 4658 98.928000 2292 4890 1 chr7B.!!$R1 2598
16 TraesCS6B01G114300 chr7B 490602222 490604717 2495 True 2946.000000 2946 87.939000 2298 4845 1 chr7B.!!$R2 2547
17 TraesCS6B01G114300 chr5B 292189191 292191803 2612 False 4658.000000 4658 98.928000 2292 4890 1 chr5B.!!$F1 2598
18 TraesCS6B01G114300 chr5B 432982708 432984852 2144 False 555.333333 1349 83.289000 442 5389 3 chr5B.!!$F4 4947
19 TraesCS6B01G114300 chr4A 578156424 578159034 2610 True 4645.000000 4645 98.852000 2292 4890 1 chr4A.!!$R2 2598
20 TraesCS6B01G114300 chr3B 53351372 53353973 2601 True 4634.000000 4634 98.887000 2300 4890 1 chr3B.!!$R1 2590
21 TraesCS6B01G114300 chr3B 306263026 306265432 2406 False 3991.000000 3991 96.562000 2478 4890 1 chr3B.!!$F1 2412
22 TraesCS6B01G114300 chr6D 41233589 41236933 3344 False 1365.750000 2409 95.725750 1 5992 4 chr6D.!!$F3 5991
23 TraesCS6B01G114300 chr6D 7344230 7345579 1349 True 1339.000000 1339 84.723000 677 2019 1 chr6D.!!$R1 1342
24 TraesCS6B01G114300 chr6D 7357769 7359118 1349 True 1312.000000 1312 84.377000 677 2019 1 chr6D.!!$R2 1342
25 TraesCS6B01G114300 chr6D 7696986 7698225 1239 False 1223.000000 1223 84.713000 677 1912 1 chr6D.!!$F1 1235
26 TraesCS6B01G114300 chr6D 22183019 22185012 1993 False 754.000000 1312 87.072500 677 5376 2 chr6D.!!$F2 4699
27 TraesCS6B01G114300 chr7D 597675397 597676747 1350 True 1369.000000 1369 85.103000 677 2019 1 chr7D.!!$R2 1342
28 TraesCS6B01G114300 chrUn 80035403 80036754 1351 True 1352.000000 1352 84.915000 677 2019 1 chrUn.!!$R4 1342
29 TraesCS6B01G114300 chrUn 79937494 79938836 1342 False 1334.000000 1334 84.718000 679 2015 1 chrUn.!!$F3 1336
30 TraesCS6B01G114300 chrUn 79930963 79932217 1254 False 1219.000000 1219 84.365000 677 1923 1 chrUn.!!$F2 1246
31 TraesCS6B01G114300 chrUn 79855038 79856215 1177 False 1133.000000 1133 84.193000 679 1848 1 chrUn.!!$F1 1169

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
865 998 0.480690 TGCCAACCTAATGTGGTGGT 59.519 50.000 0.00 0.00 40.73 4.16 F
2133 2287 0.034337 TGACCTACAACAACTCCGCC 59.966 55.000 0.00 0.00 0.00 6.13 F
2197 2351 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.000 0.00 0.00 0.00 4.52 F
2213 2367 0.308376 TGGCGAGCCAACGTAAAAAC 59.692 50.000 15.24 0.00 44.12 2.43 F
2214 2368 0.589708 GGCGAGCCAACGTAAAAACT 59.410 50.000 9.58 0.00 35.81 2.66 F
2265 2419 0.883153 ATTTTCGTTGGGGCGTAACC 59.117 50.000 0.00 0.00 37.93 2.85 F
2277 2431 1.226323 CGTAACCCTCTCAGCGACG 60.226 63.158 0.00 0.00 0.00 5.12 F
2278 2432 1.516603 GTAACCCTCTCAGCGACGC 60.517 63.158 13.03 13.03 0.00 5.19 F
2279 2433 3.047718 TAACCCTCTCAGCGACGCG 62.048 63.158 15.18 3.53 0.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2332 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34 R
3741 6080 4.702131 ACACCATATGCAAGTCCTTCTTTC 59.298 41.667 0.00 0.00 33.63 2.62 R
4894 7786 6.013725 ACCACTGAGAATTATGTTGTAGGTCA 60.014 38.462 0.00 0.00 0.00 4.02 R
4896 7788 6.213600 AGACCACTGAGAATTATGTTGTAGGT 59.786 38.462 0.00 0.00 0.00 3.08 R
4897 7789 6.536582 CAGACCACTGAGAATTATGTTGTAGG 59.463 42.308 0.00 0.00 46.03 3.18 R
4938 7830 6.660521 TGAAACATTCTTAGTGCTTCATCCAT 59.339 34.615 0.00 0.00 29.52 3.41 R
4978 7870 8.729805 AGTCCTGATCTCAAGTTGATAATTTC 57.270 34.615 5.91 0.65 0.00 2.17 R
5024 7916 3.259123 CCTTCCTGCCAACTTTAAGCAAT 59.741 43.478 0.00 0.00 35.79 3.56 R
5551 8510 6.653020 AGTCAGCCATATAGATGAAACACAA 58.347 36.000 0.00 0.00 34.73 3.33 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
236 237 2.880879 CTCGCCATGTCGGTGTCG 60.881 66.667 0.00 0.00 46.24 4.35
321 322 1.760029 GCTAGCCTCCTAACTCTGCTT 59.240 52.381 2.29 0.00 33.63 3.91
408 412 1.216710 GTCCTCTCCTGTTGCGAGG 59.783 63.158 0.00 0.00 44.48 4.63
412 416 0.605589 CTCTCCTGTTGCGAGGTTCT 59.394 55.000 0.00 0.00 34.36 3.01
508 512 0.804989 GAAACATTGGCACCGAGGAG 59.195 55.000 0.00 0.00 0.00 3.69
538 542 2.002586 CTGTTCGACGAATTGCTCCAT 58.997 47.619 14.27 0.00 0.00 3.41
586 590 1.174783 TCAACTGCCTCCTCTACGTC 58.825 55.000 0.00 0.00 0.00 4.34
592 596 1.449246 CCTCCTCTACGTCGTCGGT 60.449 63.158 0.00 0.00 41.85 4.69
648 680 3.370421 CCCACAATGTCACCTACAGCATA 60.370 47.826 0.00 0.00 42.70 3.14
717 849 1.899437 AATGGACATCGCACTCCGGT 61.899 55.000 0.00 0.00 37.59 5.28
724 856 2.244117 ATCGCACTCCGGTGAATGCT 62.244 55.000 11.17 0.00 45.61 3.79
864 997 1.176527 CTGCCAACCTAATGTGGTGG 58.823 55.000 0.00 0.00 40.73 4.61
865 998 0.480690 TGCCAACCTAATGTGGTGGT 59.519 50.000 0.00 0.00 40.73 4.16
866 999 0.887933 GCCAACCTAATGTGGTGGTG 59.112 55.000 0.00 0.00 40.73 4.17
1183 1329 7.503566 AGCCAGATATTGCAACTTACAACATAT 59.496 33.333 0.00 0.00 0.00 1.78
1251 1397 3.563808 CGATTTTTGATTCTATGGCCGGA 59.436 43.478 5.05 0.00 0.00 5.14
1269 1415 2.542205 CGGAAAGGACCAAAAACCGAAC 60.542 50.000 0.00 0.00 41.09 3.95
1363 1509 8.252417 TCATTGAATTGATGGTAGAAAATGGTG 58.748 33.333 0.00 0.00 0.00 4.17
1400 1546 8.966868 TCATTCTGTGTACAACATACTGATAGA 58.033 33.333 0.00 0.00 38.39 1.98
1401 1547 9.025020 CATTCTGTGTACAACATACTGATAGAC 57.975 37.037 0.00 0.00 38.39 2.59
1431 1579 4.651045 GCTAAGGGGAAAATGGTTGATGAT 59.349 41.667 0.00 0.00 0.00 2.45
1440 1588 6.256321 GGAAAATGGTTGATGATGTAATGCAC 59.744 38.462 0.00 0.00 0.00 4.57
1675 1828 4.539870 ACTTGCTGAAATGTTGAATCGTG 58.460 39.130 0.00 0.00 0.00 4.35
2109 2263 1.933853 GACAGCGGAATATGTGTGGAC 59.066 52.381 0.00 0.00 0.00 4.02
2131 2285 2.519377 TGTGACCTACAACAACTCCG 57.481 50.000 0.00 0.00 36.06 4.63
2132 2286 1.145803 GTGACCTACAACAACTCCGC 58.854 55.000 0.00 0.00 0.00 5.54
2133 2287 0.034337 TGACCTACAACAACTCCGCC 59.966 55.000 0.00 0.00 0.00 6.13
2134 2288 0.320697 GACCTACAACAACTCCGCCT 59.679 55.000 0.00 0.00 0.00 5.52
2135 2289 1.547372 GACCTACAACAACTCCGCCTA 59.453 52.381 0.00 0.00 0.00 3.93
2136 2290 2.167900 GACCTACAACAACTCCGCCTAT 59.832 50.000 0.00 0.00 0.00 2.57
2137 2291 2.093658 ACCTACAACAACTCCGCCTATG 60.094 50.000 0.00 0.00 0.00 2.23
2138 2292 2.093658 CCTACAACAACTCCGCCTATGT 60.094 50.000 0.00 0.00 0.00 2.29
2139 2293 2.561478 ACAACAACTCCGCCTATGTT 57.439 45.000 0.00 0.00 36.49 2.71
2140 2294 2.900122 CAACAACTCCGCCTATGTTG 57.100 50.000 3.45 3.45 44.40 3.33
2143 2297 2.386661 CAACTCCGCCTATGTTGTCT 57.613 50.000 0.00 0.00 37.05 3.41
2144 2298 2.271800 CAACTCCGCCTATGTTGTCTC 58.728 52.381 0.00 0.00 37.05 3.36
2145 2299 1.557099 ACTCCGCCTATGTTGTCTCA 58.443 50.000 0.00 0.00 0.00 3.27
2146 2300 1.899814 ACTCCGCCTATGTTGTCTCAA 59.100 47.619 0.00 0.00 0.00 3.02
2147 2301 2.271800 CTCCGCCTATGTTGTCTCAAC 58.728 52.381 5.78 5.78 0.00 3.18
2148 2302 1.621317 TCCGCCTATGTTGTCTCAACA 59.379 47.619 15.83 15.83 34.31 3.33
2149 2303 2.236146 TCCGCCTATGTTGTCTCAACAT 59.764 45.455 24.50 24.50 42.82 2.71
2150 2304 3.449377 TCCGCCTATGTTGTCTCAACATA 59.551 43.478 24.21 24.21 40.87 2.29
2155 2309 2.093306 TGTTGTCTCAACATAGCCGG 57.907 50.000 10.63 0.00 34.73 6.13
2156 2310 1.346395 TGTTGTCTCAACATAGCCGGT 59.654 47.619 1.90 0.00 34.73 5.28
2157 2311 2.000447 GTTGTCTCAACATAGCCGGTC 59.000 52.381 1.90 0.00 34.73 4.79
2158 2312 0.535335 TGTCTCAACATAGCCGGTCC 59.465 55.000 1.90 0.00 0.00 4.46
2159 2313 0.179081 GTCTCAACATAGCCGGTCCC 60.179 60.000 1.90 0.00 0.00 4.46
2160 2314 0.616395 TCTCAACATAGCCGGTCCCA 60.616 55.000 1.90 0.00 0.00 4.37
2161 2315 0.251916 CTCAACATAGCCGGTCCCAA 59.748 55.000 1.90 0.00 0.00 4.12
2162 2316 0.251916 TCAACATAGCCGGTCCCAAG 59.748 55.000 1.90 0.00 0.00 3.61
2163 2317 1.077716 AACATAGCCGGTCCCAAGC 60.078 57.895 1.90 0.00 0.00 4.01
2164 2318 2.203209 CATAGCCGGTCCCAAGCC 60.203 66.667 1.90 0.00 0.00 4.35
2165 2319 3.489513 ATAGCCGGTCCCAAGCCC 61.490 66.667 1.90 0.00 0.00 5.19
2174 2328 2.044352 CCCAAGCCCGGGTAAAGG 60.044 66.667 24.63 18.41 41.83 3.11
2175 2329 2.608550 CCCAAGCCCGGGTAAAGGA 61.609 63.158 24.63 0.00 41.83 3.36
2176 2330 1.077716 CCAAGCCCGGGTAAAGGAG 60.078 63.158 24.63 5.31 0.00 3.69
2177 2331 1.077716 CAAGCCCGGGTAAAGGAGG 60.078 63.158 24.63 0.00 0.00 4.30
2178 2332 1.229723 AAGCCCGGGTAAAGGAGGA 60.230 57.895 24.63 0.00 0.00 3.71
2179 2333 1.272554 AAGCCCGGGTAAAGGAGGAG 61.273 60.000 24.63 0.00 0.00 3.69
2180 2334 2.743179 GCCCGGGTAAAGGAGGAGG 61.743 68.421 24.63 0.00 0.00 4.30
2181 2335 2.070650 CCCGGGTAAAGGAGGAGGG 61.071 68.421 14.18 0.00 0.00 4.30
2182 2336 1.306739 CCGGGTAAAGGAGGAGGGT 60.307 63.158 0.00 0.00 0.00 4.34
2183 2337 0.912968 CCGGGTAAAGGAGGAGGGTT 60.913 60.000 0.00 0.00 0.00 4.11
2184 2338 0.252197 CGGGTAAAGGAGGAGGGTTG 59.748 60.000 0.00 0.00 0.00 3.77
2185 2339 1.369403 GGGTAAAGGAGGAGGGTTGT 58.631 55.000 0.00 0.00 0.00 3.32
2186 2340 1.004394 GGGTAAAGGAGGAGGGTTGTG 59.996 57.143 0.00 0.00 0.00 3.33
2187 2341 1.982958 GGTAAAGGAGGAGGGTTGTGA 59.017 52.381 0.00 0.00 0.00 3.58
2188 2342 2.576648 GGTAAAGGAGGAGGGTTGTGAT 59.423 50.000 0.00 0.00 0.00 3.06
2189 2343 3.778629 GGTAAAGGAGGAGGGTTGTGATA 59.221 47.826 0.00 0.00 0.00 2.15
2190 2344 4.141688 GGTAAAGGAGGAGGGTTGTGATAG 60.142 50.000 0.00 0.00 0.00 2.08
2191 2345 2.182516 AGGAGGAGGGTTGTGATAGG 57.817 55.000 0.00 0.00 0.00 2.57
2192 2346 0.470341 GGAGGAGGGTTGTGATAGGC 59.530 60.000 0.00 0.00 0.00 3.93
2193 2347 1.501582 GAGGAGGGTTGTGATAGGCT 58.498 55.000 0.00 0.00 0.00 4.58
2194 2348 1.840635 GAGGAGGGTTGTGATAGGCTT 59.159 52.381 0.00 0.00 0.00 4.35
2195 2349 1.561542 AGGAGGGTTGTGATAGGCTTG 59.438 52.381 0.00 0.00 0.00 4.01
2196 2350 1.408822 GGAGGGTTGTGATAGGCTTGG 60.409 57.143 0.00 0.00 0.00 3.61
2197 2351 0.034089 AGGGTTGTGATAGGCTTGGC 60.034 55.000 0.00 0.00 0.00 4.52
2198 2352 1.376609 GGGTTGTGATAGGCTTGGCG 61.377 60.000 0.00 0.00 0.00 5.69
2199 2353 0.392461 GGTTGTGATAGGCTTGGCGA 60.392 55.000 0.00 0.00 0.00 5.54
2200 2354 1.009829 GTTGTGATAGGCTTGGCGAG 58.990 55.000 0.00 0.00 0.00 5.03
2211 2365 4.458666 TGGCGAGCCAACGTAAAA 57.541 50.000 15.24 0.00 44.12 1.52
2212 2366 2.704108 TGGCGAGCCAACGTAAAAA 58.296 47.368 15.24 0.00 44.12 1.94
2213 2367 0.308376 TGGCGAGCCAACGTAAAAAC 59.692 50.000 15.24 0.00 44.12 2.43
2214 2368 0.589708 GGCGAGCCAACGTAAAAACT 59.410 50.000 9.58 0.00 35.81 2.66
2215 2369 1.399343 GGCGAGCCAACGTAAAAACTC 60.399 52.381 9.58 0.00 35.81 3.01
2216 2370 1.262151 GCGAGCCAACGTAAAAACTCA 59.738 47.619 0.00 0.00 35.59 3.41
2217 2371 2.661979 GCGAGCCAACGTAAAAACTCAG 60.662 50.000 0.00 0.00 35.59 3.35
2218 2372 2.661979 CGAGCCAACGTAAAAACTCAGC 60.662 50.000 0.00 0.00 0.00 4.26
2219 2373 1.607148 AGCCAACGTAAAAACTCAGCC 59.393 47.619 0.00 0.00 0.00 4.85
2220 2374 1.335496 GCCAACGTAAAAACTCAGCCA 59.665 47.619 0.00 0.00 0.00 4.75
2221 2375 2.857104 GCCAACGTAAAAACTCAGCCAC 60.857 50.000 0.00 0.00 0.00 5.01
2222 2376 2.616842 CCAACGTAAAAACTCAGCCACT 59.383 45.455 0.00 0.00 0.00 4.00
2223 2377 3.303791 CCAACGTAAAAACTCAGCCACTC 60.304 47.826 0.00 0.00 0.00 3.51
2224 2378 3.470645 ACGTAAAAACTCAGCCACTCT 57.529 42.857 0.00 0.00 0.00 3.24
2225 2379 3.805207 ACGTAAAAACTCAGCCACTCTT 58.195 40.909 0.00 0.00 0.00 2.85
2226 2380 4.952460 ACGTAAAAACTCAGCCACTCTTA 58.048 39.130 0.00 0.00 0.00 2.10
2227 2381 5.548406 ACGTAAAAACTCAGCCACTCTTAT 58.452 37.500 0.00 0.00 0.00 1.73
2228 2382 5.408604 ACGTAAAAACTCAGCCACTCTTATG 59.591 40.000 0.00 0.00 0.00 1.90
2229 2383 5.163854 CGTAAAAACTCAGCCACTCTTATGG 60.164 44.000 0.00 0.00 43.26 2.74
2230 2384 4.640771 AAAACTCAGCCACTCTTATGGA 57.359 40.909 0.00 0.00 43.02 3.41
2231 2385 3.902881 AACTCAGCCACTCTTATGGAG 57.097 47.619 0.00 0.00 43.02 3.86
2232 2386 3.107402 ACTCAGCCACTCTTATGGAGA 57.893 47.619 0.00 0.00 44.45 3.71
2233 2387 3.652055 ACTCAGCCACTCTTATGGAGAT 58.348 45.455 0.00 0.00 44.45 2.75
2234 2388 3.387374 ACTCAGCCACTCTTATGGAGATG 59.613 47.826 0.00 0.00 44.45 2.90
2235 2389 3.640498 CTCAGCCACTCTTATGGAGATGA 59.360 47.826 0.00 0.00 44.45 2.92
2236 2390 4.033009 TCAGCCACTCTTATGGAGATGAA 58.967 43.478 0.00 0.00 44.45 2.57
2237 2391 4.471025 TCAGCCACTCTTATGGAGATGAAA 59.529 41.667 0.00 0.00 44.45 2.69
2238 2392 4.574013 CAGCCACTCTTATGGAGATGAAAC 59.426 45.833 0.00 0.00 44.45 2.78
2239 2393 3.879892 GCCACTCTTATGGAGATGAAACC 59.120 47.826 0.00 0.00 44.45 3.27
2240 2394 4.455606 CCACTCTTATGGAGATGAAACCC 58.544 47.826 4.83 0.00 44.45 4.11
2241 2395 4.080356 CCACTCTTATGGAGATGAAACCCA 60.080 45.833 4.83 0.00 44.45 4.51
2242 2396 5.500234 CACTCTTATGGAGATGAAACCCAA 58.500 41.667 4.83 0.00 44.45 4.12
2243 2397 5.945784 CACTCTTATGGAGATGAAACCCAAA 59.054 40.000 4.83 0.00 44.45 3.28
2244 2398 6.434028 CACTCTTATGGAGATGAAACCCAAAA 59.566 38.462 4.83 0.00 44.45 2.44
2245 2399 6.660949 ACTCTTATGGAGATGAAACCCAAAAG 59.339 38.462 4.83 0.00 44.45 2.27
2246 2400 6.789268 TCTTATGGAGATGAAACCCAAAAGA 58.211 36.000 0.00 0.00 33.15 2.52
2247 2401 7.413446 TCTTATGGAGATGAAACCCAAAAGAT 58.587 34.615 0.00 0.00 33.15 2.40
2248 2402 7.895429 TCTTATGGAGATGAAACCCAAAAGATT 59.105 33.333 0.00 0.00 33.15 2.40
2249 2403 6.940430 ATGGAGATGAAACCCAAAAGATTT 57.060 33.333 0.00 0.00 33.15 2.17
2250 2404 6.745794 TGGAGATGAAACCCAAAAGATTTT 57.254 33.333 0.00 0.00 0.00 1.82
2251 2405 6.758254 TGGAGATGAAACCCAAAAGATTTTC 58.242 36.000 0.00 0.00 0.00 2.29
2252 2406 5.863935 GGAGATGAAACCCAAAAGATTTTCG 59.136 40.000 0.00 0.00 31.76 3.46
2253 2407 6.405278 AGATGAAACCCAAAAGATTTTCGT 57.595 33.333 0.00 0.00 31.76 3.85
2254 2408 6.816136 AGATGAAACCCAAAAGATTTTCGTT 58.184 32.000 0.00 0.00 31.76 3.85
2255 2409 6.701400 AGATGAAACCCAAAAGATTTTCGTTG 59.299 34.615 0.00 0.00 31.76 4.10
2256 2410 5.112686 TGAAACCCAAAAGATTTTCGTTGG 58.887 37.500 0.00 0.00 36.67 3.77
2258 2412 3.038788 CCCAAAAGATTTTCGTTGGGG 57.961 47.619 17.61 11.08 45.27 4.96
2259 2413 2.412870 CCAAAAGATTTTCGTTGGGGC 58.587 47.619 0.00 0.00 34.69 5.80
2260 2414 2.058057 CAAAAGATTTTCGTTGGGGCG 58.942 47.619 0.00 0.00 0.00 6.13
2261 2415 1.324383 AAAGATTTTCGTTGGGGCGT 58.676 45.000 0.00 0.00 0.00 5.68
2262 2416 2.188062 AAGATTTTCGTTGGGGCGTA 57.812 45.000 0.00 0.00 0.00 4.42
2263 2417 2.188062 AGATTTTCGTTGGGGCGTAA 57.812 45.000 0.00 0.00 0.00 3.18
2264 2418 1.808343 AGATTTTCGTTGGGGCGTAAC 59.192 47.619 0.00 0.00 0.00 2.50
2265 2419 0.883153 ATTTTCGTTGGGGCGTAACC 59.117 50.000 0.00 0.00 37.93 2.85
2274 2428 2.202756 GGCGTAACCCTCTCAGCG 60.203 66.667 0.00 0.00 0.00 5.18
2275 2429 2.707849 GGCGTAACCCTCTCAGCGA 61.708 63.158 0.00 0.00 0.00 4.93
2276 2430 1.516603 GCGTAACCCTCTCAGCGAC 60.517 63.158 0.00 0.00 0.00 5.19
2277 2431 1.226323 CGTAACCCTCTCAGCGACG 60.226 63.158 0.00 0.00 0.00 5.12
2278 2432 1.516603 GTAACCCTCTCAGCGACGC 60.517 63.158 13.03 13.03 0.00 5.19
2279 2433 3.047718 TAACCCTCTCAGCGACGCG 62.048 63.158 15.18 3.53 0.00 6.01
3741 6080 4.037446 GCTTATGGAGAGATATAGGGAGCG 59.963 50.000 0.00 0.00 0.00 5.03
4890 7782 6.292381 GCTTTGTTGTTGTTGTTGTTGTTGTA 60.292 34.615 0.00 0.00 0.00 2.41
4891 7783 7.570324 GCTTTGTTGTTGTTGTTGTTGTTGTAT 60.570 33.333 0.00 0.00 0.00 2.29
4892 7784 7.715265 TTGTTGTTGTTGTTGTTGTTGTATT 57.285 28.000 0.00 0.00 0.00 1.89
4893 7785 7.110179 TGTTGTTGTTGTTGTTGTTGTATTG 57.890 32.000 0.00 0.00 0.00 1.90
4894 7786 6.701841 TGTTGTTGTTGTTGTTGTTGTATTGT 59.298 30.769 0.00 0.00 0.00 2.71
4895 7787 6.696825 TGTTGTTGTTGTTGTTGTATTGTG 57.303 33.333 0.00 0.00 0.00 3.33
4896 7788 6.447162 TGTTGTTGTTGTTGTTGTATTGTGA 58.553 32.000 0.00 0.00 0.00 3.58
4897 7789 6.363626 TGTTGTTGTTGTTGTTGTATTGTGAC 59.636 34.615 0.00 0.00 0.00 3.67
4938 7830 7.231925 TCAGTGGTCTGTGTAGAAATAACTGTA 59.768 37.037 0.00 0.00 41.91 2.74
4978 7870 6.813152 AGAATGTTTCAAAACCTGTGTTCAAG 59.187 34.615 3.33 0.00 38.11 3.02
5551 8510 7.279615 TGGTACCATTTTGATGATCGACTATT 58.720 34.615 11.60 0.00 0.00 1.73
5604 8563 1.927487 TCCATGGAGCTGCACATTTT 58.073 45.000 11.23 0.00 0.00 1.82
5683 8642 0.815213 TGTGCCTGTTCACTCACTGC 60.815 55.000 0.00 0.00 37.81 4.40
5688 8647 2.292267 CCTGTTCACTCACTGCAGTTT 58.708 47.619 18.94 0.91 0.00 2.66
5710 8669 5.924475 TTTAGCAGTAAGTTGACTTCTGC 57.076 39.130 24.61 24.61 45.93 4.26
5998 8957 9.847224 TTATTCAAAATACCTCAATACTCCCTC 57.153 33.333 0.00 0.00 0.00 4.30
5999 8958 6.248569 TCAAAATACCTCAATACTCCCTCC 57.751 41.667 0.00 0.00 0.00 4.30
6000 8959 5.729229 TCAAAATACCTCAATACTCCCTCCA 59.271 40.000 0.00 0.00 0.00 3.86
6001 8960 6.389869 TCAAAATACCTCAATACTCCCTCCAT 59.610 38.462 0.00 0.00 0.00 3.41
6002 8961 6.848562 AAATACCTCAATACTCCCTCCATT 57.151 37.500 0.00 0.00 0.00 3.16
6003 8962 6.441088 AATACCTCAATACTCCCTCCATTC 57.559 41.667 0.00 0.00 0.00 2.67
6004 8963 3.049344 ACCTCAATACTCCCTCCATTCC 58.951 50.000 0.00 0.00 0.00 3.01
6005 8964 3.048600 CCTCAATACTCCCTCCATTCCA 58.951 50.000 0.00 0.00 0.00 3.53
6006 8965 3.459598 CCTCAATACTCCCTCCATTCCAA 59.540 47.826 0.00 0.00 0.00 3.53
6007 8966 4.079787 CCTCAATACTCCCTCCATTCCAAA 60.080 45.833 0.00 0.00 0.00 3.28
6008 8967 5.399497 CCTCAATACTCCCTCCATTCCAAAT 60.399 44.000 0.00 0.00 0.00 2.32
6009 8968 6.091076 TCAATACTCCCTCCATTCCAAATT 57.909 37.500 0.00 0.00 0.00 1.82
6010 8969 7.219601 TCAATACTCCCTCCATTCCAAATTA 57.780 36.000 0.00 0.00 0.00 1.40
6011 8970 7.825709 TCAATACTCCCTCCATTCCAAATTAT 58.174 34.615 0.00 0.00 0.00 1.28
6012 8971 8.954729 TCAATACTCCCTCCATTCCAAATTATA 58.045 33.333 0.00 0.00 0.00 0.98
6013 8972 9.236006 CAATACTCCCTCCATTCCAAATTATAG 57.764 37.037 0.00 0.00 0.00 1.31
6014 8973 8.757307 ATACTCCCTCCATTCCAAATTATAGA 57.243 34.615 0.00 0.00 0.00 1.98
6015 8974 7.084268 ACTCCCTCCATTCCAAATTATAGAG 57.916 40.000 0.00 0.00 0.00 2.43
6016 8975 5.880901 TCCCTCCATTCCAAATTATAGAGC 58.119 41.667 0.00 0.00 0.00 4.09
6017 8976 4.697352 CCCTCCATTCCAAATTATAGAGCG 59.303 45.833 0.00 0.00 0.00 5.03
6018 8977 4.154918 CCTCCATTCCAAATTATAGAGCGC 59.845 45.833 0.00 0.00 0.00 5.92
6019 8978 4.072131 TCCATTCCAAATTATAGAGCGCC 58.928 43.478 2.29 0.00 0.00 6.53
6020 8979 3.191371 CCATTCCAAATTATAGAGCGCCC 59.809 47.826 2.29 0.00 0.00 6.13
6021 8980 2.163818 TCCAAATTATAGAGCGCCCG 57.836 50.000 2.29 0.00 0.00 6.13
6022 8981 0.517316 CCAAATTATAGAGCGCCCGC 59.483 55.000 2.29 4.20 42.33 6.13
6037 8996 4.735132 CGCGCTTCCCGAGGTCAA 62.735 66.667 5.56 0.00 40.02 3.18
6038 8997 2.358247 GCGCTTCCCGAGGTCAAA 60.358 61.111 0.00 0.00 40.02 2.69
6039 8998 2.677979 GCGCTTCCCGAGGTCAAAC 61.678 63.158 0.00 0.00 40.02 2.93
6040 8999 1.004918 CGCTTCCCGAGGTCAAACT 60.005 57.895 0.00 0.00 40.02 2.66
6041 9000 0.602905 CGCTTCCCGAGGTCAAACTT 60.603 55.000 0.00 0.00 40.02 2.66
6042 9001 1.605753 GCTTCCCGAGGTCAAACTTT 58.394 50.000 0.00 0.00 0.00 2.66
6043 9002 1.266989 GCTTCCCGAGGTCAAACTTTG 59.733 52.381 0.00 0.00 0.00 2.77
6044 9003 2.846193 CTTCCCGAGGTCAAACTTTGA 58.154 47.619 0.00 0.00 37.33 2.69
6062 9021 8.582433 AACTTTGACCATAAATTTAACCAACG 57.418 30.769 1.21 5.06 0.00 4.10
6063 9022 7.942990 ACTTTGACCATAAATTTAACCAACGA 58.057 30.769 1.21 0.00 0.00 3.85
6064 9023 8.079809 ACTTTGACCATAAATTTAACCAACGAG 58.920 33.333 1.21 3.35 0.00 4.18
6065 9024 7.747155 TTGACCATAAATTTAACCAACGAGA 57.253 32.000 1.21 0.00 0.00 4.04
6066 9025 7.136289 TGACCATAAATTTAACCAACGAGAC 57.864 36.000 1.21 0.00 0.00 3.36
6067 9026 6.149807 TGACCATAAATTTAACCAACGAGACC 59.850 38.462 1.21 0.00 0.00 3.85
6068 9027 5.122711 ACCATAAATTTAACCAACGAGACCG 59.877 40.000 1.21 0.00 42.50 4.79
6069 9028 5.352016 CCATAAATTTAACCAACGAGACCGA 59.648 40.000 1.21 0.00 39.50 4.69
6070 9029 6.037830 CCATAAATTTAACCAACGAGACCGAT 59.962 38.462 1.21 0.00 39.50 4.18
6071 9030 5.952526 AAATTTAACCAACGAGACCGATT 57.047 34.783 0.00 0.00 39.50 3.34
6072 9031 4.939509 ATTTAACCAACGAGACCGATTG 57.060 40.909 0.00 0.00 39.50 2.67
6073 9032 1.717194 TAACCAACGAGACCGATTGC 58.283 50.000 0.00 0.00 39.50 3.56
6074 9033 1.289109 AACCAACGAGACCGATTGCG 61.289 55.000 0.00 0.00 39.50 4.85
6084 9043 4.294523 CGATTGCGGTGGGAGAAA 57.705 55.556 0.00 0.00 0.00 2.52
6085 9044 2.550487 CGATTGCGGTGGGAGAAAA 58.450 52.632 0.00 0.00 0.00 2.29
6086 9045 0.878416 CGATTGCGGTGGGAGAAAAA 59.122 50.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 4.357947 GGTGTCTGCTGTCCGCGA 62.358 66.667 8.23 0.00 43.27 5.87
91 92 2.606519 TTCCACACCCTCCCTCGG 60.607 66.667 0.00 0.00 0.00 4.63
92 93 1.913762 AGTTCCACACCCTCCCTCG 60.914 63.158 0.00 0.00 0.00 4.63
321 322 4.360951 ACCTGGGATTAGAAACAACGAA 57.639 40.909 0.00 0.00 0.00 3.85
408 412 4.366684 CCCCCACCTGGCCAGAAC 62.367 72.222 34.91 0.00 0.00 3.01
451 455 0.389817 CGATGTTCCGCTCCAAGACA 60.390 55.000 0.00 0.00 0.00 3.41
491 495 1.002134 CCTCCTCGGTGCCAATGTT 60.002 57.895 0.00 0.00 0.00 2.71
508 512 1.668151 GTCGAACAGGTGGAGTGCC 60.668 63.158 0.00 0.00 0.00 5.01
553 557 3.053291 TTGATGGCGCGGGTCAAC 61.053 61.111 11.93 9.44 0.00 3.18
555 559 4.015406 AGTTGATGGCGCGGGTCA 62.015 61.111 9.93 9.93 0.00 4.02
592 596 1.750341 TTGCGACCCGGTTGAAGAGA 61.750 55.000 9.22 0.00 0.00 3.10
648 680 4.731612 CAGCAGCAGCCGACGAGT 62.732 66.667 0.00 0.00 43.56 4.18
717 849 3.186409 GTGCAGTTAAACTCGAGCATTCA 59.814 43.478 13.61 0.00 34.24 2.57
724 856 1.067364 TCGGTGTGCAGTTAAACTCGA 59.933 47.619 0.00 0.00 0.00 4.04
864 997 5.578005 TCAACTACAGTGCTATAGGACAC 57.422 43.478 24.25 13.52 38.96 3.67
865 998 5.069119 CCATCAACTACAGTGCTATAGGACA 59.931 44.000 24.25 5.09 38.96 4.02
866 999 5.533482 CCATCAACTACAGTGCTATAGGAC 58.467 45.833 16.04 16.04 36.57 3.85
1087 1232 6.015095 TCGCACTGTCCTGATGAATAATATCT 60.015 38.462 0.00 0.00 0.00 1.98
1251 1397 2.093890 ACGTTCGGTTTTTGGTCCTTT 58.906 42.857 0.00 0.00 0.00 3.11
1269 1415 6.062434 AGCAGAATACTGTAGCTAGTAACG 57.938 41.667 0.00 0.00 45.04 3.18
1363 1509 3.981211 ACACAGAATGATTTGGTGCAAC 58.019 40.909 0.00 0.00 39.69 4.17
1431 1579 8.590470 CGCATTTTTGTAAATATGTGCATTACA 58.410 29.630 5.87 5.87 36.40 2.41
1440 1588 4.565962 TGCTGCCGCATTTTTGTAAATATG 59.434 37.500 0.00 4.17 42.25 1.78
1512 1660 0.664761 CCATTCGGCCAATACTGCAG 59.335 55.000 13.48 13.48 0.00 4.41
1619 1772 4.588528 CCTTCTCCCATTTTCCACAAGAAA 59.411 41.667 0.00 0.00 42.82 2.52
1675 1828 0.104304 ACGTTGTCGGGATAGATGCC 59.896 55.000 0.00 0.00 41.85 4.40
2126 2280 1.557099 TGAGACAACATAGGCGGAGT 58.443 50.000 0.00 0.00 0.00 3.85
2127 2281 2.271800 GTTGAGACAACATAGGCGGAG 58.728 52.381 9.32 0.00 0.00 4.63
2128 2282 1.621317 TGTTGAGACAACATAGGCGGA 59.379 47.619 12.32 0.00 31.49 5.54
2129 2283 2.093306 TGTTGAGACAACATAGGCGG 57.907 50.000 12.32 0.00 31.49 6.13
2134 2288 3.196901 ACCGGCTATGTTGAGACAACATA 59.803 43.478 25.32 25.32 40.87 2.29
2135 2289 2.027192 ACCGGCTATGTTGAGACAACAT 60.027 45.455 25.70 25.70 42.82 2.71
2136 2290 1.346395 ACCGGCTATGTTGAGACAACA 59.654 47.619 17.39 17.39 39.66 3.33
2137 2291 2.000447 GACCGGCTATGTTGAGACAAC 59.000 52.381 0.00 7.55 39.66 3.32
2138 2292 1.066430 GGACCGGCTATGTTGAGACAA 60.066 52.381 0.00 0.00 39.66 3.18
2139 2293 0.535335 GGACCGGCTATGTTGAGACA 59.465 55.000 0.00 0.00 40.71 3.41
2140 2294 0.179081 GGGACCGGCTATGTTGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
2141 2295 0.616395 TGGGACCGGCTATGTTGAGA 60.616 55.000 0.00 0.00 0.00 3.27
2142 2296 0.251916 TTGGGACCGGCTATGTTGAG 59.748 55.000 0.00 0.00 0.00 3.02
2143 2297 0.251916 CTTGGGACCGGCTATGTTGA 59.748 55.000 0.00 0.00 0.00 3.18
2144 2298 1.376609 GCTTGGGACCGGCTATGTTG 61.377 60.000 0.00 0.00 0.00 3.33
2145 2299 1.077716 GCTTGGGACCGGCTATGTT 60.078 57.895 0.00 0.00 0.00 2.71
2146 2300 2.590092 GCTTGGGACCGGCTATGT 59.410 61.111 0.00 0.00 0.00 2.29
2147 2301 2.203209 GGCTTGGGACCGGCTATG 60.203 66.667 0.00 0.00 0.00 2.23
2148 2302 3.489513 GGGCTTGGGACCGGCTAT 61.490 66.667 0.00 0.00 0.00 2.97
2158 2312 1.077716 CTCCTTTACCCGGGCTTGG 60.078 63.158 24.08 17.99 0.00 3.61
2159 2313 1.077716 CCTCCTTTACCCGGGCTTG 60.078 63.158 24.08 8.51 0.00 4.01
2160 2314 1.229723 TCCTCCTTTACCCGGGCTT 60.230 57.895 24.08 4.08 0.00 4.35
2161 2315 1.689582 CTCCTCCTTTACCCGGGCT 60.690 63.158 24.08 10.93 0.00 5.19
2162 2316 2.743179 CCTCCTCCTTTACCCGGGC 61.743 68.421 24.08 0.00 0.00 6.13
2163 2317 2.070650 CCCTCCTCCTTTACCCGGG 61.071 68.421 22.25 22.25 0.00 5.73
2164 2318 0.912968 AACCCTCCTCCTTTACCCGG 60.913 60.000 0.00 0.00 0.00 5.73
2165 2319 0.252197 CAACCCTCCTCCTTTACCCG 59.748 60.000 0.00 0.00 0.00 5.28
2166 2320 1.004394 CACAACCCTCCTCCTTTACCC 59.996 57.143 0.00 0.00 0.00 3.69
2167 2321 1.982958 TCACAACCCTCCTCCTTTACC 59.017 52.381 0.00 0.00 0.00 2.85
2168 2322 4.141688 CCTATCACAACCCTCCTCCTTTAC 60.142 50.000 0.00 0.00 0.00 2.01
2169 2323 4.037927 CCTATCACAACCCTCCTCCTTTA 58.962 47.826 0.00 0.00 0.00 1.85
2170 2324 2.846827 CCTATCACAACCCTCCTCCTTT 59.153 50.000 0.00 0.00 0.00 3.11
2171 2325 2.482494 CCTATCACAACCCTCCTCCTT 58.518 52.381 0.00 0.00 0.00 3.36
2172 2326 1.972207 GCCTATCACAACCCTCCTCCT 60.972 57.143 0.00 0.00 0.00 3.69
2173 2327 0.470341 GCCTATCACAACCCTCCTCC 59.530 60.000 0.00 0.00 0.00 4.30
2174 2328 1.501582 AGCCTATCACAACCCTCCTC 58.498 55.000 0.00 0.00 0.00 3.71
2175 2329 1.561542 CAAGCCTATCACAACCCTCCT 59.438 52.381 0.00 0.00 0.00 3.69
2176 2330 1.408822 CCAAGCCTATCACAACCCTCC 60.409 57.143 0.00 0.00 0.00 4.30
2177 2331 2.019156 GCCAAGCCTATCACAACCCTC 61.019 57.143 0.00 0.00 0.00 4.30
2178 2332 0.034089 GCCAAGCCTATCACAACCCT 60.034 55.000 0.00 0.00 0.00 4.34
2179 2333 1.376609 CGCCAAGCCTATCACAACCC 61.377 60.000 0.00 0.00 0.00 4.11
2180 2334 0.392461 TCGCCAAGCCTATCACAACC 60.392 55.000 0.00 0.00 0.00 3.77
2181 2335 1.009829 CTCGCCAAGCCTATCACAAC 58.990 55.000 0.00 0.00 0.00 3.32
2182 2336 0.744414 GCTCGCCAAGCCTATCACAA 60.744 55.000 0.00 0.00 45.92 3.33
2183 2337 1.153369 GCTCGCCAAGCCTATCACA 60.153 57.895 0.00 0.00 45.92 3.58
2184 2338 3.724494 GCTCGCCAAGCCTATCAC 58.276 61.111 0.00 0.00 45.92 3.06
2194 2348 0.308376 GTTTTTACGTTGGCTCGCCA 59.692 50.000 6.52 6.52 45.63 5.69
2195 2349 0.589708 AGTTTTTACGTTGGCTCGCC 59.410 50.000 0.00 0.00 0.00 5.54
2196 2350 1.262151 TGAGTTTTTACGTTGGCTCGC 59.738 47.619 0.00 0.00 0.00 5.03
2197 2351 2.661979 GCTGAGTTTTTACGTTGGCTCG 60.662 50.000 0.00 1.70 0.00 5.03
2198 2352 2.350484 GGCTGAGTTTTTACGTTGGCTC 60.350 50.000 0.00 0.00 0.00 4.70
2199 2353 1.607148 GGCTGAGTTTTTACGTTGGCT 59.393 47.619 0.00 0.00 0.00 4.75
2200 2354 1.335496 TGGCTGAGTTTTTACGTTGGC 59.665 47.619 0.00 0.00 0.00 4.52
2201 2355 2.616842 AGTGGCTGAGTTTTTACGTTGG 59.383 45.455 0.00 0.00 0.00 3.77
2202 2356 3.560068 AGAGTGGCTGAGTTTTTACGTTG 59.440 43.478 0.00 0.00 0.00 4.10
2203 2357 3.805207 AGAGTGGCTGAGTTTTTACGTT 58.195 40.909 0.00 0.00 0.00 3.99
2204 2358 3.470645 AGAGTGGCTGAGTTTTTACGT 57.529 42.857 0.00 0.00 0.00 3.57
2205 2359 5.163854 CCATAAGAGTGGCTGAGTTTTTACG 60.164 44.000 0.00 0.00 31.43 3.18
2206 2360 5.938125 TCCATAAGAGTGGCTGAGTTTTTAC 59.062 40.000 0.00 0.00 39.19 2.01
2207 2361 6.013725 TCTCCATAAGAGTGGCTGAGTTTTTA 60.014 38.462 0.00 0.00 43.71 1.52
2208 2362 4.985538 TCCATAAGAGTGGCTGAGTTTTT 58.014 39.130 0.00 0.00 39.19 1.94
2209 2363 4.287067 TCTCCATAAGAGTGGCTGAGTTTT 59.713 41.667 0.00 0.00 43.71 2.43
2210 2364 3.840666 TCTCCATAAGAGTGGCTGAGTTT 59.159 43.478 0.00 0.00 43.71 2.66
2211 2365 3.445008 TCTCCATAAGAGTGGCTGAGTT 58.555 45.455 0.00 0.00 43.71 3.01
2212 2366 3.107402 TCTCCATAAGAGTGGCTGAGT 57.893 47.619 0.00 0.00 43.71 3.41
2213 2367 3.640498 TCATCTCCATAAGAGTGGCTGAG 59.360 47.826 0.00 0.00 43.71 3.35
2214 2368 3.646534 TCATCTCCATAAGAGTGGCTGA 58.353 45.455 0.00 0.00 43.71 4.26
2215 2369 4.412796 TTCATCTCCATAAGAGTGGCTG 57.587 45.455 0.00 0.00 43.71 4.85
2216 2370 4.384647 GGTTTCATCTCCATAAGAGTGGCT 60.385 45.833 0.00 0.00 43.71 4.75
2217 2371 3.879892 GGTTTCATCTCCATAAGAGTGGC 59.120 47.826 0.00 0.00 43.71 5.01
2218 2372 4.080356 TGGGTTTCATCTCCATAAGAGTGG 60.080 45.833 0.00 0.00 43.71 4.00
2219 2373 5.102953 TGGGTTTCATCTCCATAAGAGTG 57.897 43.478 0.00 0.00 43.71 3.51
2220 2374 5.779241 TTGGGTTTCATCTCCATAAGAGT 57.221 39.130 0.00 0.00 43.71 3.24
2221 2375 6.886459 TCTTTTGGGTTTCATCTCCATAAGAG 59.114 38.462 9.33 0.00 40.80 2.85
2222 2376 6.789268 TCTTTTGGGTTTCATCTCCATAAGA 58.211 36.000 9.33 9.33 42.22 2.10
2223 2377 7.651027 ATCTTTTGGGTTTCATCTCCATAAG 57.349 36.000 0.00 0.00 39.39 1.73
2224 2378 8.434589 AAATCTTTTGGGTTTCATCTCCATAA 57.565 30.769 0.00 0.00 0.00 1.90
2225 2379 8.434589 AAAATCTTTTGGGTTTCATCTCCATA 57.565 30.769 0.00 0.00 0.00 2.74
2226 2380 6.940430 AAATCTTTTGGGTTTCATCTCCAT 57.060 33.333 0.00 0.00 0.00 3.41
2227 2381 6.516527 CGAAAATCTTTTGGGTTTCATCTCCA 60.517 38.462 0.00 0.00 31.66 3.86
2228 2382 5.863935 CGAAAATCTTTTGGGTTTCATCTCC 59.136 40.000 0.00 0.00 31.66 3.71
2229 2383 6.447162 ACGAAAATCTTTTGGGTTTCATCTC 58.553 36.000 0.00 0.00 31.27 2.75
2230 2384 6.405278 ACGAAAATCTTTTGGGTTTCATCT 57.595 33.333 0.00 0.00 31.27 2.90
2231 2385 6.073819 CCAACGAAAATCTTTTGGGTTTCATC 60.074 38.462 0.00 0.00 35.76 2.92
2232 2386 5.757808 CCAACGAAAATCTTTTGGGTTTCAT 59.242 36.000 0.00 0.00 35.76 2.57
2233 2387 5.112686 CCAACGAAAATCTTTTGGGTTTCA 58.887 37.500 0.00 0.00 35.76 2.69
2234 2388 5.651172 CCAACGAAAATCTTTTGGGTTTC 57.349 39.130 0.00 0.00 35.76 2.78
2239 2393 2.412870 GCCCCAACGAAAATCTTTTGG 58.587 47.619 0.00 0.00 38.62 3.28
2240 2394 2.058057 CGCCCCAACGAAAATCTTTTG 58.942 47.619 0.00 0.00 34.06 2.44
2241 2395 1.684450 ACGCCCCAACGAAAATCTTTT 59.316 42.857 0.00 0.00 36.70 2.27
2242 2396 1.324383 ACGCCCCAACGAAAATCTTT 58.676 45.000 0.00 0.00 36.70 2.52
2243 2397 2.188062 TACGCCCCAACGAAAATCTT 57.812 45.000 0.00 0.00 36.70 2.40
2244 2398 1.808343 GTTACGCCCCAACGAAAATCT 59.192 47.619 0.00 0.00 36.70 2.40
2245 2399 1.135603 GGTTACGCCCCAACGAAAATC 60.136 52.381 0.00 0.00 36.70 2.17
2246 2400 0.883153 GGTTACGCCCCAACGAAAAT 59.117 50.000 0.00 0.00 36.70 1.82
2247 2401 2.329244 GGTTACGCCCCAACGAAAA 58.671 52.632 0.00 0.00 36.70 2.29
2248 2402 4.061949 GGTTACGCCCCAACGAAA 57.938 55.556 0.00 0.00 36.70 3.46
2257 2411 2.202756 CGCTGAGAGGGTTACGCC 60.203 66.667 0.00 0.00 0.00 5.68
2258 2412 1.516603 GTCGCTGAGAGGGTTACGC 60.517 63.158 0.00 0.00 0.00 4.42
2259 2413 1.226323 CGTCGCTGAGAGGGTTACG 60.226 63.158 0.00 0.00 0.00 3.18
2260 2414 1.516603 GCGTCGCTGAGAGGGTTAC 60.517 63.158 10.68 0.00 35.42 2.50
2261 2415 2.882876 GCGTCGCTGAGAGGGTTA 59.117 61.111 10.68 0.00 35.42 2.85
2262 2416 4.421479 CGCGTCGCTGAGAGGGTT 62.421 66.667 16.36 0.00 35.42 4.11
2274 2428 3.849953 GTTCCGATGTGGCGCGTC 61.850 66.667 2.29 2.29 37.80 5.19
2287 2441 2.437895 GGCCTACTTGCGGGTTCC 60.438 66.667 0.00 0.00 0.00 3.62
2288 2442 2.038837 GTGGCCTACTTGCGGGTTC 61.039 63.158 3.32 0.00 0.00 3.62
2289 2443 2.033602 GTGGCCTACTTGCGGGTT 59.966 61.111 3.32 0.00 0.00 4.11
2290 2444 2.137177 ATTGTGGCCTACTTGCGGGT 62.137 55.000 3.32 0.00 0.00 5.28
3601 5940 4.718774 TCAATGACTCTCTCCCATAGCTTT 59.281 41.667 0.00 0.00 0.00 3.51
3741 6080 4.702131 ACACCATATGCAAGTCCTTCTTTC 59.298 41.667 0.00 0.00 33.63 2.62
4891 7783 7.387673 CACTGAGAATTATGTTGTAGGTCACAA 59.612 37.037 0.00 0.00 44.97 3.33
4892 7784 6.873605 CACTGAGAATTATGTTGTAGGTCACA 59.126 38.462 0.00 0.00 34.51 3.58
4893 7785 6.313905 CCACTGAGAATTATGTTGTAGGTCAC 59.686 42.308 0.00 0.00 0.00 3.67
4894 7786 6.013725 ACCACTGAGAATTATGTTGTAGGTCA 60.014 38.462 0.00 0.00 0.00 4.02
4895 7787 6.407202 ACCACTGAGAATTATGTTGTAGGTC 58.593 40.000 0.00 0.00 0.00 3.85
4896 7788 6.213600 AGACCACTGAGAATTATGTTGTAGGT 59.786 38.462 0.00 0.00 0.00 3.08
4897 7789 6.536582 CAGACCACTGAGAATTATGTTGTAGG 59.463 42.308 0.00 0.00 46.03 3.18
4938 7830 6.660521 TGAAACATTCTTAGTGCTTCATCCAT 59.339 34.615 0.00 0.00 29.52 3.41
4978 7870 8.729805 AGTCCTGATCTCAAGTTGATAATTTC 57.270 34.615 5.91 0.65 0.00 2.17
5024 7916 3.259123 CCTTCCTGCCAACTTTAAGCAAT 59.741 43.478 0.00 0.00 35.79 3.56
5551 8510 6.653020 AGTCAGCCATATAGATGAAACACAA 58.347 36.000 0.00 0.00 34.73 3.33
5683 8642 7.852945 CAGAAGTCAACTTACTGCTAAAAACTG 59.147 37.037 0.00 0.00 32.65 3.16
5688 8647 5.364778 TGCAGAAGTCAACTTACTGCTAAA 58.635 37.500 27.72 16.63 45.86 1.85
5992 8951 5.942826 GCTCTATAATTTGGAATGGAGGGAG 59.057 44.000 2.61 0.00 32.87 4.30
5993 8952 5.513094 CGCTCTATAATTTGGAATGGAGGGA 60.513 44.000 9.44 0.00 42.51 4.20
5994 8953 4.697352 CGCTCTATAATTTGGAATGGAGGG 59.303 45.833 3.17 3.17 37.33 4.30
5995 8954 4.154918 GCGCTCTATAATTTGGAATGGAGG 59.845 45.833 0.00 0.00 32.87 4.30
5996 8955 4.154918 GGCGCTCTATAATTTGGAATGGAG 59.845 45.833 7.64 0.00 34.73 3.86
5997 8956 4.072131 GGCGCTCTATAATTTGGAATGGA 58.928 43.478 7.64 0.00 0.00 3.41
5998 8957 3.191371 GGGCGCTCTATAATTTGGAATGG 59.809 47.826 7.64 0.00 0.00 3.16
5999 8958 3.120199 CGGGCGCTCTATAATTTGGAATG 60.120 47.826 5.36 0.00 0.00 2.67
6000 8959 3.074412 CGGGCGCTCTATAATTTGGAAT 58.926 45.455 5.36 0.00 0.00 3.01
6001 8960 2.489971 CGGGCGCTCTATAATTTGGAA 58.510 47.619 5.36 0.00 0.00 3.53
6002 8961 1.876416 GCGGGCGCTCTATAATTTGGA 60.876 52.381 5.36 0.00 38.26 3.53
6003 8962 0.517316 GCGGGCGCTCTATAATTTGG 59.483 55.000 5.36 0.00 38.26 3.28
6004 8963 0.163788 CGCGGGCGCTCTATAATTTG 59.836 55.000 5.36 0.00 39.32 2.32
6005 8964 2.528797 CGCGGGCGCTCTATAATTT 58.471 52.632 5.36 0.00 39.32 1.82
6006 8965 4.261888 CGCGGGCGCTCTATAATT 57.738 55.556 5.36 0.00 39.32 1.40
6020 8979 4.735132 TTGACCTCGGGAAGCGCG 62.735 66.667 0.00 0.00 41.10 6.86
6021 8980 2.358247 TTTGACCTCGGGAAGCGC 60.358 61.111 0.00 0.00 0.00 5.92
6022 8981 0.602905 AAGTTTGACCTCGGGAAGCG 60.603 55.000 0.00 0.00 0.00 4.68
6023 8982 1.266989 CAAAGTTTGACCTCGGGAAGC 59.733 52.381 10.19 0.00 0.00 3.86
6024 8983 2.846193 TCAAAGTTTGACCTCGGGAAG 58.154 47.619 14.35 0.00 34.08 3.46
6036 8995 9.036671 CGTTGGTTAAATTTATGGTCAAAGTTT 57.963 29.630 0.00 0.00 29.44 2.66
6037 8996 8.414778 TCGTTGGTTAAATTTATGGTCAAAGTT 58.585 29.630 0.00 0.00 31.36 2.66
6038 8997 7.942990 TCGTTGGTTAAATTTATGGTCAAAGT 58.057 30.769 0.00 0.00 0.00 2.66
6039 8998 8.293867 TCTCGTTGGTTAAATTTATGGTCAAAG 58.706 33.333 0.00 4.88 0.00 2.77
6040 8999 8.077386 GTCTCGTTGGTTAAATTTATGGTCAAA 58.923 33.333 0.00 0.00 0.00 2.69
6041 9000 7.308710 GGTCTCGTTGGTTAAATTTATGGTCAA 60.309 37.037 0.00 0.00 0.00 3.18
6042 9001 6.149807 GGTCTCGTTGGTTAAATTTATGGTCA 59.850 38.462 0.00 0.00 0.00 4.02
6043 9002 6.549061 GGTCTCGTTGGTTAAATTTATGGTC 58.451 40.000 0.00 0.00 0.00 4.02
6044 9003 5.122711 CGGTCTCGTTGGTTAAATTTATGGT 59.877 40.000 0.00 0.00 0.00 3.55
6045 9004 5.352016 TCGGTCTCGTTGGTTAAATTTATGG 59.648 40.000 0.00 0.00 37.69 2.74
6046 9005 6.411630 TCGGTCTCGTTGGTTAAATTTATG 57.588 37.500 0.00 0.00 37.69 1.90
6047 9006 7.469260 CAATCGGTCTCGTTGGTTAAATTTAT 58.531 34.615 0.00 0.00 37.69 1.40
6048 9007 6.621164 GCAATCGGTCTCGTTGGTTAAATTTA 60.621 38.462 0.00 0.00 37.69 1.40
6049 9008 5.695818 CAATCGGTCTCGTTGGTTAAATTT 58.304 37.500 0.00 0.00 37.69 1.82
6050 9009 4.379082 GCAATCGGTCTCGTTGGTTAAATT 60.379 41.667 0.00 0.00 37.69 1.82
6051 9010 3.126343 GCAATCGGTCTCGTTGGTTAAAT 59.874 43.478 0.00 0.00 37.69 1.40
6052 9011 2.481185 GCAATCGGTCTCGTTGGTTAAA 59.519 45.455 0.00 0.00 37.69 1.52
6053 9012 2.070783 GCAATCGGTCTCGTTGGTTAA 58.929 47.619 0.00 0.00 37.69 2.01
6054 9013 1.717194 GCAATCGGTCTCGTTGGTTA 58.283 50.000 0.00 0.00 37.69 2.85
6055 9014 1.289109 CGCAATCGGTCTCGTTGGTT 61.289 55.000 0.00 0.00 37.69 3.67
6056 9015 1.736645 CGCAATCGGTCTCGTTGGT 60.737 57.895 0.00 0.00 37.69 3.67
6057 9016 3.081133 CGCAATCGGTCTCGTTGG 58.919 61.111 0.00 0.00 37.69 3.77
6067 9026 0.878416 TTTTTCTCCCACCGCAATCG 59.122 50.000 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.