Multiple sequence alignment - TraesCS5D01G540200

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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 TraesCS5D01G540200 chr5D 100.000 3510 0 0 1 3510 551470838 551467329 0.000000e+00 6482.0
1 TraesCS5D01G540200 chr5D 80.942 1338 217 25 944 2258 551545969 551544647 0.000000e+00 1024.0
2 TraesCS5D01G540200 chr5D 79.797 1282 229 24 995 2258 552407684 552408953 0.000000e+00 905.0
3 TraesCS5D01G540200 chr5D 80.016 1236 206 27 976 2192 542411225 542410012 0.000000e+00 876.0
4 TraesCS5D01G540200 chr5D 100.000 412 0 0 3738 4149 551467101 551466690 0.000000e+00 761.0
5 TraesCS5D01G540200 chr5D 83.197 613 91 7 1606 2216 552068206 552068808 6.060000e-153 551.0
6 TraesCS5D01G540200 chr5D 84.766 512 66 7 2477 2986 552409069 552409570 1.720000e-138 503.0
7 TraesCS5D01G540200 chr5D 78.550 676 116 21 2478 3140 551544519 551543860 6.420000e-113 418.0
8 TraesCS5D01G540200 chr5D 80.261 537 85 16 2650 3175 557952009 557951483 6.510000e-103 385.0
9 TraesCS5D01G540200 chr5D 81.624 468 65 13 2833 3279 552739986 552739519 6.550000e-98 368.0
10 TraesCS5D01G540200 chr5D 86.822 258 29 3 999 1255 551409722 551409469 2.440000e-72 283.0
11 TraesCS5D01G540200 chr4A 95.380 3333 108 13 149 3468 616661245 616664544 0.000000e+00 5260.0
12 TraesCS5D01G540200 chr4A 80.049 1233 205 27 998 2216 616120852 616119647 0.000000e+00 876.0
13 TraesCS5D01G540200 chr4A 80.202 495 88 9 1422 1912 626748513 626749001 3.050000e-96 363.0
14 TraesCS5D01G540200 chr4A 99.459 185 0 1 3966 4149 616665015 616665199 6.650000e-88 335.0
15 TraesCS5D01G540200 chr4A 98.315 178 3 0 3738 3915 616664836 616665013 3.110000e-81 313.0
16 TraesCS5D01G540200 chr4A 75.000 732 148 20 1438 2163 615375621 615374919 5.210000e-79 305.0
17 TraesCS5D01G540200 chr4A 92.063 189 13 1 2294 2480 506704232 506704044 8.840000e-67 265.0
18 TraesCS5D01G540200 chr5B 89.441 1610 113 26 574 2174 699731610 699730049 0.000000e+00 1978.0
19 TraesCS5D01G540200 chr5B 78.698 1643 250 60 643 2258 699282875 699281306 0.000000e+00 1003.0
20 TraesCS5D01G540200 chr5B 76.667 1560 257 53 643 2157 697869456 697867959 0.000000e+00 765.0
21 TraesCS5D01G540200 chr5B 86.623 613 75 3 1650 2258 703894156 703893547 0.000000e+00 671.0
22 TraesCS5D01G540200 chr5B 76.122 1248 250 40 995 2218 703859469 703858246 9.860000e-171 610.0
23 TraesCS5D01G540200 chr5B 78.676 891 160 16 1302 2185 699645474 699644607 2.160000e-157 566.0
24 TraesCS5D01G540200 chr5B 91.166 283 23 2 149 429 445179331 445179613 2.340000e-102 383.0
25 TraesCS5D01G540200 chr5B 93.506 231 13 1 470 700 699774017 699773789 3.970000e-90 342.0
26 TraesCS5D01G540200 chr5B 81.772 395 63 6 2811 3196 697809425 697809819 5.170000e-84 322.0
27 TraesCS5D01G540200 chr5B 82.720 353 52 3 1302 1654 699615365 699615022 5.210000e-79 305.0
28 TraesCS5D01G540200 chr5B 83.537 328 28 9 867 1188 699616416 699616109 2.440000e-72 283.0
29 TraesCS5D01G540200 chr5B 80.702 399 35 13 844 1233 699615731 699615366 5.290000e-69 272.0
30 TraesCS5D01G540200 chr5B 80.702 399 35 13 844 1233 699645840 699645475 5.290000e-69 272.0
31 TraesCS5D01G540200 chr5B 80.159 252 26 17 2477 2720 703893420 703893185 2.570000e-37 167.0
32 TraesCS5D01G540200 chr1A 77.058 1312 234 48 995 2258 33229343 33228051 0.000000e+00 693.0
33 TraesCS5D01G540200 chr1A 77.072 929 179 26 1286 2194 33236677 33235763 4.790000e-139 505.0
34 TraesCS5D01G540200 chr1A 84.527 433 60 4 2696 3124 33227533 33227104 4.960000e-114 422.0
35 TraesCS5D01G540200 chr1A 84.491 432 60 4 2696 3123 33302842 33302414 1.780000e-113 420.0
36 TraesCS5D01G540200 chr1A 93.122 189 11 1 2294 2480 92956463 92956651 4.090000e-70 276.0
37 TraesCS5D01G540200 chr1A 93.122 189 11 1 2294 2480 169082830 169083018 4.090000e-70 276.0
38 TraesCS5D01G540200 chr1A 76.131 398 80 10 1535 1922 33344821 33344429 1.180000e-45 195.0
39 TraesCS5D01G540200 chr1A 89.552 67 7 0 3213 3279 33226983 33226917 7.390000e-13 86.1
40 TraesCS5D01G540200 chr1A 97.222 36 1 0 2261 2296 33227853 33227818 1.250000e-05 62.1
41 TraesCS5D01G540200 chr7A 75.561 1248 246 42 995 2220 618171090 618172300 1.010000e-155 560.0
42 TraesCS5D01G540200 chr7A 91.197 284 23 2 149 430 10222389 10222106 6.510000e-103 385.0
43 TraesCS5D01G540200 chr7A 93.158 190 11 1 2294 2481 641845563 641845752 1.140000e-70 278.0
44 TraesCS5D01G540200 chr7B 74.822 1267 257 38 975 2220 577284109 577282884 2.210000e-142 516.0
45 TraesCS5D01G540200 chr7B 78.076 634 103 26 2662 3269 151064410 151065033 6.550000e-98 368.0
46 TraesCS5D01G540200 chr1D 84.516 465 65 4 2684 3144 34654683 34654222 1.760000e-123 453.0
47 TraesCS5D01G540200 chr1D 88.525 61 7 0 3219 3279 34654115 34654055 1.600000e-09 75.0
48 TraesCS5D01G540200 chr1B 83.480 454 66 6 2696 3144 53075861 53075412 8.300000e-112 414.0
49 TraesCS5D01G540200 chr1B 83.627 397 30 15 1884 2258 53082364 53081981 1.430000e-89 340.0
50 TraesCS5D01G540200 chr1B 91.045 67 6 0 3213 3279 53075311 53075245 1.590000e-14 91.6
51 TraesCS5D01G540200 chr7D 91.228 285 21 2 151 434 11043716 11043435 6.510000e-103 385.0
52 TraesCS5D01G540200 chr7D 89.796 294 27 3 149 441 406805768 406806059 1.410000e-99 374.0
53 TraesCS5D01G540200 chr7D 98.387 124 2 0 1 124 476623865 476623742 6.980000e-53 219.0
54 TraesCS5D01G540200 chr7D 98.387 124 2 0 1 124 570917071 570916948 6.980000e-53 219.0
55 TraesCS5D01G540200 chr4B 90.559 286 25 2 149 433 546575877 546575593 1.090000e-100 377.0
56 TraesCS5D01G540200 chr4B 90.559 286 25 2 149 433 546598244 546597960 1.090000e-100 377.0
57 TraesCS5D01G540200 chr4B 91.866 209 12 4 2277 2480 130063324 130063532 1.890000e-73 287.0
58 TraesCS5D01G540200 chr6B 89.691 291 29 1 149 438 502012413 502012123 1.820000e-98 370.0
59 TraesCS5D01G540200 chr3B 89.527 296 25 6 149 441 758628576 758628868 1.820000e-98 370.0
60 TraesCS5D01G540200 chr6A 90.952 210 17 1 2294 2501 425147627 425147418 8.780000e-72 281.0
61 TraesCS5D01G540200 chr6A 92.000 200 14 1 2283 2480 489613556 489613357 3.160000e-71 279.0
62 TraesCS5D01G540200 chr6A 91.176 136 10 2 3924 4059 290256976 290256843 2.550000e-42 183.0
63 TraesCS5D01G540200 chr6A 79.570 186 30 8 1882 2063 23595855 23595674 4.350000e-25 126.0
64 TraesCS5D01G540200 chr5A 92.347 196 12 2 2288 2480 166733909 166733714 4.090000e-70 276.0
65 TraesCS5D01G540200 chr3D 98.387 124 2 0 1 124 70255649 70255526 6.980000e-53 219.0
66 TraesCS5D01G540200 chr3D 100.000 33 0 0 471 503 610002862 610002894 1.250000e-05 62.1
67 TraesCS5D01G540200 chrUn 97.581 124 3 0 1 124 20426232 20426109 3.250000e-51 213.0
68 TraesCS5D01G540200 chrUn 97.500 40 0 1 464 503 108274323 108274285 2.680000e-07 67.6
69 TraesCS5D01G540200 chr6D 97.581 124 3 0 1 124 91556122 91556245 3.250000e-51 213.0
70 TraesCS5D01G540200 chr6D 97.581 124 3 0 1 124 186518296 186518419 3.250000e-51 213.0
71 TraesCS5D01G540200 chr6D 97.581 124 3 0 1 124 355019977 355020100 3.250000e-51 213.0
72 TraesCS5D01G540200 chr6D 97.581 124 3 0 1 124 362828001 362828124 3.250000e-51 213.0
73 TraesCS5D01G540200 chr6D 88.889 99 10 1 3961 4059 202976771 202976868 2.030000e-23 121.0
74 TraesCS5D01G540200 chr4D 97.581 124 3 0 1 124 45518462 45518585 3.250000e-51 213.0
75 TraesCS5D01G540200 chr2B 87.805 82 3 6 3978 4059 87413464 87413538 5.710000e-14 89.8
76 TraesCS5D01G540200 chr2A 86.905 84 5 4 3978 4059 55969927 55970006 5.710000e-14 89.8
77 TraesCS5D01G540200 chr2D 86.585 82 4 6 3978 4059 55260699 55260773 2.660000e-12 84.2
78 TraesCS5D01G540200 chr2D 84.706 85 9 3 3977 4059 55245751 55245833 9.560000e-12 82.4
79 TraesCS5D01G540200 chr2D 86.250 80 4 6 3978 4057 55239484 55239556 3.440000e-11 80.5


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 TraesCS5D01G540200 chr5D 551466690 551470838 4148 True 3621.500000 6482 100.000000 1 4149 2 chr5D.!!$R5 4148
1 TraesCS5D01G540200 chr5D 542410012 542411225 1213 True 876.000000 876 80.016000 976 2192 1 chr5D.!!$R1 1216
2 TraesCS5D01G540200 chr5D 551543860 551545969 2109 True 721.000000 1024 79.746000 944 3140 2 chr5D.!!$R6 2196
3 TraesCS5D01G540200 chr5D 552407684 552409570 1886 False 704.000000 905 82.281500 995 2986 2 chr5D.!!$F2 1991
4 TraesCS5D01G540200 chr5D 552068206 552068808 602 False 551.000000 551 83.197000 1606 2216 1 chr5D.!!$F1 610
5 TraesCS5D01G540200 chr5D 557951483 557952009 526 True 385.000000 385 80.261000 2650 3175 1 chr5D.!!$R4 525
6 TraesCS5D01G540200 chr4A 616661245 616665199 3954 False 1969.333333 5260 97.718000 149 4149 3 chr4A.!!$F2 4000
7 TraesCS5D01G540200 chr4A 616119647 616120852 1205 True 876.000000 876 80.049000 998 2216 1 chr4A.!!$R3 1218
8 TraesCS5D01G540200 chr4A 615374919 615375621 702 True 305.000000 305 75.000000 1438 2163 1 chr4A.!!$R2 725
9 TraesCS5D01G540200 chr5B 699730049 699731610 1561 True 1978.000000 1978 89.441000 574 2174 1 chr5B.!!$R3 1600
10 TraesCS5D01G540200 chr5B 699281306 699282875 1569 True 1003.000000 1003 78.698000 643 2258 1 chr5B.!!$R2 1615
11 TraesCS5D01G540200 chr5B 697867959 697869456 1497 True 765.000000 765 76.667000 643 2157 1 chr5B.!!$R1 1514
12 TraesCS5D01G540200 chr5B 703858246 703859469 1223 True 610.000000 610 76.122000 995 2218 1 chr5B.!!$R5 1223
13 TraesCS5D01G540200 chr5B 699644607 699645840 1233 True 419.000000 566 79.689000 844 2185 2 chr5B.!!$R7 1341
14 TraesCS5D01G540200 chr5B 703893185 703894156 971 True 419.000000 671 83.391000 1650 2720 2 chr5B.!!$R8 1070
15 TraesCS5D01G540200 chr5B 699615022 699616416 1394 True 286.666667 305 82.319667 844 1654 3 chr5B.!!$R6 810
16 TraesCS5D01G540200 chr1A 33235763 33236677 914 True 505.000000 505 77.072000 1286 2194 1 chr1A.!!$R1 908
17 TraesCS5D01G540200 chr1A 33226917 33229343 2426 True 315.800000 693 87.089750 995 3279 4 chr1A.!!$R4 2284
18 TraesCS5D01G540200 chr7A 618171090 618172300 1210 False 560.000000 560 75.561000 995 2220 1 chr7A.!!$F1 1225
19 TraesCS5D01G540200 chr7B 577282884 577284109 1225 True 516.000000 516 74.822000 975 2220 1 chr7B.!!$R1 1245
20 TraesCS5D01G540200 chr7B 151064410 151065033 623 False 368.000000 368 78.076000 2662 3269 1 chr7B.!!$F1 607
21 TraesCS5D01G540200 chr1D 34654055 34654683 628 True 264.000000 453 86.520500 2684 3279 2 chr1D.!!$R1 595
22 TraesCS5D01G540200 chr1B 53075245 53075861 616 True 252.800000 414 87.262500 2696 3279 2 chr1B.!!$R2 583

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
211 212 0.179015 TTTTGGTGCGCTGGTCCTAA 60.179 50.000 9.73 6.62 0.00 2.69 F
268 269 0.818040 AACAAGTTGTGCCCGACTCC 60.818 55.000 9.79 0.00 34.00 3.85 F
319 320 0.819259 TTTGGCTCGCTTCAGTGCTT 60.819 50.000 0.00 0.00 0.00 3.91 F
334 335 1.129998 GTGCTTGTAGTCGTCGCTAGA 59.870 52.381 0.00 0.00 0.00 2.43 F
2145 2992 1.602888 CTTGAAGCTGCACCTGCCT 60.603 57.895 0.00 0.00 41.18 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 2454 2.961741 TCGAGATCCTTGATCCCAGAAG 59.038 50.000 0.59 0.0 39.66 2.85 R
2145 2992 4.714632 AGGCTTACTGTAAACTTCTGCAA 58.285 39.130 1.46 0.0 0.00 4.08 R
2315 3369 3.604875 TTGGTCGACTGATAAGTTCCC 57.395 47.619 16.46 0.0 0.00 3.97 R
2363 3417 2.451132 GTGATATCGACCGATATGCCG 58.549 52.381 24.27 0.0 44.91 5.69 R
3487 4678 1.077787 CACACACACACACAGGGGT 60.078 57.895 0.00 0.0 0.00 4.95 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
25 26 2.385013 TGATCATTGCCCGGATATCG 57.615 50.000 0.73 0.00 38.88 2.92
26 27 1.623311 TGATCATTGCCCGGATATCGT 59.377 47.619 0.73 0.00 37.11 3.73
27 28 2.271800 GATCATTGCCCGGATATCGTC 58.728 52.381 0.73 0.00 37.11 4.20
28 29 1.044611 TCATTGCCCGGATATCGTCA 58.955 50.000 0.73 0.00 37.11 4.35
29 30 1.623311 TCATTGCCCGGATATCGTCAT 59.377 47.619 0.73 0.00 37.11 3.06
30 31 1.733912 CATTGCCCGGATATCGTCATG 59.266 52.381 0.73 0.00 37.11 3.07
31 32 1.044611 TTGCCCGGATATCGTCATGA 58.955 50.000 0.73 0.00 37.11 3.07
32 33 1.266178 TGCCCGGATATCGTCATGAT 58.734 50.000 0.73 0.00 41.30 2.45
33 34 1.623311 TGCCCGGATATCGTCATGATT 59.377 47.619 0.73 0.00 38.57 2.57
34 35 2.829120 TGCCCGGATATCGTCATGATTA 59.171 45.455 0.73 0.00 38.57 1.75
35 36 3.450817 TGCCCGGATATCGTCATGATTAT 59.549 43.478 0.73 0.00 38.57 1.28
36 37 4.081142 TGCCCGGATATCGTCATGATTATT 60.081 41.667 0.73 0.00 38.57 1.40
37 38 4.876107 GCCCGGATATCGTCATGATTATTT 59.124 41.667 0.73 0.00 38.57 1.40
38 39 5.220662 GCCCGGATATCGTCATGATTATTTG 60.221 44.000 0.73 0.00 38.57 2.32
39 40 6.106003 CCCGGATATCGTCATGATTATTTGA 58.894 40.000 0.73 0.00 38.57 2.69
40 41 6.593770 CCCGGATATCGTCATGATTATTTGAA 59.406 38.462 0.73 0.00 38.57 2.69
41 42 7.119116 CCCGGATATCGTCATGATTATTTGAAA 59.881 37.037 0.73 0.00 38.57 2.69
42 43 8.668353 CCGGATATCGTCATGATTATTTGAAAT 58.332 33.333 0.00 0.00 38.57 2.17
59 60 7.903995 TTTGAAATTCTATCAATTGCCCAAC 57.096 32.000 0.00 0.00 36.72 3.77
60 61 6.602410 TGAAATTCTATCAATTGCCCAACA 57.398 33.333 0.00 0.00 0.00 3.33
61 62 6.632909 TGAAATTCTATCAATTGCCCAACAG 58.367 36.000 0.00 0.00 0.00 3.16
62 63 6.211184 TGAAATTCTATCAATTGCCCAACAGT 59.789 34.615 0.00 0.00 0.00 3.55
63 64 7.395772 TGAAATTCTATCAATTGCCCAACAGTA 59.604 33.333 0.00 0.00 0.00 2.74
64 65 7.716799 AATTCTATCAATTGCCCAACAGTAA 57.283 32.000 0.00 0.00 0.00 2.24
65 66 7.902920 ATTCTATCAATTGCCCAACAGTAAT 57.097 32.000 0.00 0.00 0.00 1.89
66 67 7.716799 TTCTATCAATTGCCCAACAGTAATT 57.283 32.000 0.00 0.00 33.04 1.40
67 68 7.716799 TCTATCAATTGCCCAACAGTAATTT 57.283 32.000 0.00 0.00 30.78 1.82
68 69 7.546358 TCTATCAATTGCCCAACAGTAATTTG 58.454 34.615 0.00 0.00 30.78 2.32
69 70 5.543507 TCAATTGCCCAACAGTAATTTGT 57.456 34.783 0.00 0.00 30.78 2.83
70 71 5.923204 TCAATTGCCCAACAGTAATTTGTT 58.077 33.333 0.00 0.00 41.77 2.83
71 72 6.352516 TCAATTGCCCAACAGTAATTTGTTT 58.647 32.000 0.00 0.00 39.17 2.83
72 73 7.500992 TCAATTGCCCAACAGTAATTTGTTTA 58.499 30.769 0.00 0.00 39.17 2.01
73 74 7.439655 TCAATTGCCCAACAGTAATTTGTTTAC 59.560 33.333 0.00 0.00 39.17 2.01
74 75 5.203060 TGCCCAACAGTAATTTGTTTACC 57.797 39.130 0.00 0.00 41.01 2.85
75 76 4.039366 TGCCCAACAGTAATTTGTTTACCC 59.961 41.667 0.00 0.00 41.01 3.69
76 77 4.039366 GCCCAACAGTAATTTGTTTACCCA 59.961 41.667 0.00 0.00 41.01 4.51
77 78 5.534407 CCCAACAGTAATTTGTTTACCCAC 58.466 41.667 0.00 0.00 41.01 4.61
78 79 5.510009 CCCAACAGTAATTTGTTTACCCACC 60.510 44.000 0.00 0.00 41.01 4.61
79 80 5.216648 CAACAGTAATTTGTTTACCCACCG 58.783 41.667 0.00 0.00 41.01 4.94
80 81 4.463070 ACAGTAATTTGTTTACCCACCGT 58.537 39.130 0.00 0.00 41.01 4.83
81 82 4.888823 ACAGTAATTTGTTTACCCACCGTT 59.111 37.500 0.00 0.00 41.01 4.44
82 83 5.360429 ACAGTAATTTGTTTACCCACCGTTT 59.640 36.000 0.00 0.00 41.01 3.60
83 84 5.688176 CAGTAATTTGTTTACCCACCGTTTG 59.312 40.000 0.00 0.00 41.01 2.93
84 85 2.580966 TTTGTTTACCCACCGTTTGC 57.419 45.000 0.00 0.00 0.00 3.68
85 86 1.765230 TTGTTTACCCACCGTTTGCT 58.235 45.000 0.00 0.00 0.00 3.91
86 87 2.634815 TGTTTACCCACCGTTTGCTA 57.365 45.000 0.00 0.00 0.00 3.49
87 88 3.143211 TGTTTACCCACCGTTTGCTAT 57.857 42.857 0.00 0.00 0.00 2.97
88 89 3.488363 TGTTTACCCACCGTTTGCTATT 58.512 40.909 0.00 0.00 0.00 1.73
89 90 3.890147 TGTTTACCCACCGTTTGCTATTT 59.110 39.130 0.00 0.00 0.00 1.40
90 91 4.341520 TGTTTACCCACCGTTTGCTATTTT 59.658 37.500 0.00 0.00 0.00 1.82
91 92 5.163437 TGTTTACCCACCGTTTGCTATTTTT 60.163 36.000 0.00 0.00 0.00 1.94
92 93 3.653539 ACCCACCGTTTGCTATTTTTC 57.346 42.857 0.00 0.00 0.00 2.29
93 94 3.227614 ACCCACCGTTTGCTATTTTTCT 58.772 40.909 0.00 0.00 0.00 2.52
94 95 3.254903 ACCCACCGTTTGCTATTTTTCTC 59.745 43.478 0.00 0.00 0.00 2.87
95 96 3.488489 CCACCGTTTGCTATTTTTCTCG 58.512 45.455 0.00 0.00 0.00 4.04
96 97 3.187637 CCACCGTTTGCTATTTTTCTCGA 59.812 43.478 0.00 0.00 0.00 4.04
97 98 4.394795 CACCGTTTGCTATTTTTCTCGAG 58.605 43.478 5.93 5.93 0.00 4.04
98 99 4.151689 CACCGTTTGCTATTTTTCTCGAGA 59.848 41.667 12.08 12.08 0.00 4.04
99 100 4.389077 ACCGTTTGCTATTTTTCTCGAGAG 59.611 41.667 15.94 3.92 0.00 3.20
100 101 4.625742 CCGTTTGCTATTTTTCTCGAGAGA 59.374 41.667 15.94 8.62 39.12 3.10
101 102 5.120208 CCGTTTGCTATTTTTCTCGAGAGAA 59.880 40.000 15.94 14.90 44.94 2.87
102 103 6.237073 CGTTTGCTATTTTTCTCGAGAGAAG 58.763 40.000 15.94 6.98 46.80 2.85
103 104 5.786401 TTGCTATTTTTCTCGAGAGAAGC 57.214 39.130 15.94 16.61 46.80 3.86
104 105 4.184629 TGCTATTTTTCTCGAGAGAAGCC 58.815 43.478 19.68 10.79 46.80 4.35
105 106 4.184629 GCTATTTTTCTCGAGAGAAGCCA 58.815 43.478 15.94 3.14 46.80 4.75
106 107 4.033472 GCTATTTTTCTCGAGAGAAGCCAC 59.967 45.833 15.94 5.36 46.80 5.01
107 108 3.753294 TTTTTCTCGAGAGAAGCCACT 57.247 42.857 15.94 0.00 46.80 4.00
108 109 4.866508 TTTTTCTCGAGAGAAGCCACTA 57.133 40.909 15.94 0.00 46.80 2.74
109 110 4.442375 TTTTCTCGAGAGAAGCCACTAG 57.558 45.455 15.94 0.00 46.80 2.57
110 111 2.791347 TCTCGAGAGAAGCCACTAGT 57.209 50.000 12.08 0.00 41.32 2.57
111 112 2.360844 TCTCGAGAGAAGCCACTAGTG 58.639 52.381 16.34 16.34 41.32 2.74
112 113 2.027100 TCTCGAGAGAAGCCACTAGTGA 60.027 50.000 24.68 0.00 41.32 3.41
113 114 2.750166 CTCGAGAGAAGCCACTAGTGAA 59.250 50.000 24.68 0.00 41.32 3.18
114 115 3.154710 TCGAGAGAAGCCACTAGTGAAA 58.845 45.455 24.68 0.00 37.03 2.69
115 116 3.057456 TCGAGAGAAGCCACTAGTGAAAC 60.057 47.826 24.68 12.76 37.03 2.78
116 117 3.591023 GAGAGAAGCCACTAGTGAAACC 58.409 50.000 24.68 10.28 37.80 3.27
117 118 3.243724 AGAGAAGCCACTAGTGAAACCT 58.756 45.455 24.68 14.61 37.80 3.50
118 119 4.417437 AGAGAAGCCACTAGTGAAACCTA 58.583 43.478 24.68 0.00 37.80 3.08
119 120 5.026790 AGAGAAGCCACTAGTGAAACCTAT 58.973 41.667 24.68 9.95 37.80 2.57
120 121 5.091261 AGAAGCCACTAGTGAAACCTATG 57.909 43.478 24.68 5.82 37.80 2.23
121 122 3.914426 AGCCACTAGTGAAACCTATGG 57.086 47.619 24.68 5.15 37.80 2.74
122 123 2.289565 GCCACTAGTGAAACCTATGGC 58.710 52.381 24.68 11.74 43.89 4.40
123 124 2.919228 CCACTAGTGAAACCTATGGCC 58.081 52.381 24.68 0.00 37.80 5.36
124 125 2.550978 CACTAGTGAAACCTATGGCCG 58.449 52.381 18.45 0.00 37.80 6.13
125 126 1.485066 ACTAGTGAAACCTATGGCCGG 59.515 52.381 0.00 0.00 37.80 6.13
126 127 1.760613 CTAGTGAAACCTATGGCCGGA 59.239 52.381 5.05 0.00 37.80 5.14
127 128 0.988832 AGTGAAACCTATGGCCGGAA 59.011 50.000 5.05 0.00 37.80 4.30
128 129 1.353022 AGTGAAACCTATGGCCGGAAA 59.647 47.619 5.05 0.00 37.80 3.13
129 130 2.164338 GTGAAACCTATGGCCGGAAAA 58.836 47.619 5.05 0.00 0.00 2.29
130 131 2.559231 GTGAAACCTATGGCCGGAAAAA 59.441 45.455 5.05 0.00 0.00 1.94
131 132 3.194755 GTGAAACCTATGGCCGGAAAAAT 59.805 43.478 5.05 0.00 0.00 1.82
132 133 4.399934 GTGAAACCTATGGCCGGAAAAATA 59.600 41.667 5.05 0.00 0.00 1.40
133 134 4.642885 TGAAACCTATGGCCGGAAAAATAG 59.357 41.667 5.05 5.91 0.00 1.73
134 135 4.513406 AACCTATGGCCGGAAAAATAGA 57.487 40.909 5.05 0.00 0.00 1.98
135 136 3.816994 ACCTATGGCCGGAAAAATAGAC 58.183 45.455 5.05 0.00 0.00 2.59
136 137 3.146847 CCTATGGCCGGAAAAATAGACC 58.853 50.000 5.05 0.00 0.00 3.85
137 138 2.818751 ATGGCCGGAAAAATAGACCA 57.181 45.000 5.05 0.00 0.00 4.02
138 139 1.828979 TGGCCGGAAAAATAGACCAC 58.171 50.000 5.05 0.00 0.00 4.16
139 140 1.100510 GGCCGGAAAAATAGACCACC 58.899 55.000 5.05 0.00 0.00 4.61
140 141 1.614850 GGCCGGAAAAATAGACCACCA 60.615 52.381 5.05 0.00 0.00 4.17
141 142 2.375146 GCCGGAAAAATAGACCACCAT 58.625 47.619 5.05 0.00 0.00 3.55
142 143 2.758423 GCCGGAAAAATAGACCACCATT 59.242 45.455 5.05 0.00 0.00 3.16
143 144 3.194755 GCCGGAAAAATAGACCACCATTT 59.805 43.478 5.05 0.00 0.00 2.32
144 145 4.743493 CCGGAAAAATAGACCACCATTTG 58.257 43.478 0.00 0.00 0.00 2.32
145 146 4.173256 CGGAAAAATAGACCACCATTTGC 58.827 43.478 0.00 0.00 0.00 3.68
146 147 4.082245 CGGAAAAATAGACCACCATTTGCT 60.082 41.667 0.00 0.00 0.00 3.91
147 148 5.410924 GGAAAAATAGACCACCATTTGCTC 58.589 41.667 0.00 0.00 0.00 4.26
156 157 1.672881 CACCATTTGCTCGGATCCTTC 59.327 52.381 10.75 0.00 0.00 3.46
160 161 2.386661 TTTGCTCGGATCCTTCTGAC 57.613 50.000 10.75 0.00 33.60 3.51
173 174 5.831702 TCCTTCTGACCTACGTTATTCTC 57.168 43.478 0.00 0.00 0.00 2.87
178 179 4.275196 TCTGACCTACGTTATTCTCCATCG 59.725 45.833 0.00 0.00 0.00 3.84
179 180 3.317149 TGACCTACGTTATTCTCCATCGG 59.683 47.826 0.00 0.00 0.00 4.18
200 201 0.869880 GACGGTTGCTGTTTTGGTGC 60.870 55.000 0.00 0.00 0.00 5.01
211 212 0.179015 TTTTGGTGCGCTGGTCCTAA 60.179 50.000 9.73 6.62 0.00 2.69
213 214 1.476845 TTGGTGCGCTGGTCCTAAGA 61.477 55.000 9.73 0.00 0.00 2.10
234 235 1.145803 GCCTTAGCACGACGACTTTT 58.854 50.000 0.00 0.00 39.53 2.27
260 261 6.033619 CGACTGTCTACTATAACAAGTTGTGC 59.966 42.308 9.79 0.00 0.00 4.57
268 269 0.818040 AACAAGTTGTGCCCGACTCC 60.818 55.000 9.79 0.00 34.00 3.85
292 293 3.399181 GGAGGGGTGATGACGGCA 61.399 66.667 0.00 0.00 0.00 5.69
319 320 0.819259 TTTGGCTCGCTTCAGTGCTT 60.819 50.000 0.00 0.00 0.00 3.91
334 335 1.129998 GTGCTTGTAGTCGTCGCTAGA 59.870 52.381 0.00 0.00 0.00 2.43
351 352 2.002505 AGATGGTCTACGGATCTGGG 57.997 55.000 6.47 0.00 0.00 4.45
360 361 4.100498 GTCTACGGATCTGGGTGGAATTTA 59.900 45.833 6.47 0.00 0.00 1.40
362 363 3.820557 ACGGATCTGGGTGGAATTTATG 58.179 45.455 6.47 0.00 0.00 1.90
387 388 8.600625 TGTTATTTCTGATATTCGTTGTACTGC 58.399 33.333 0.00 0.00 0.00 4.40
410 412 6.433093 TGCCATGATTGAAGATGATAGATTGG 59.567 38.462 0.00 0.00 0.00 3.16
572 574 4.648651 ACACAAAGTCCGGCTAGTTTAAT 58.351 39.130 0.00 0.00 0.00 1.40
588 590 5.423886 AGTTTAATCCTTCTCTAGCACAGC 58.576 41.667 0.00 0.00 0.00 4.40
589 591 5.046304 AGTTTAATCCTTCTCTAGCACAGCA 60.046 40.000 0.00 0.00 0.00 4.41
711 713 2.158769 TCCAATCGAATCCACCATCCAG 60.159 50.000 0.00 0.00 0.00 3.86
713 715 2.615447 CAATCGAATCCACCATCCAGTG 59.385 50.000 0.00 0.00 37.51 3.66
716 718 1.748244 CGAATCCACCATCCAGTGCAT 60.748 52.381 0.00 0.00 36.38 3.96
748 750 2.634815 AGCTAACCATGCATCTCAGG 57.365 50.000 0.00 0.00 0.00 3.86
960 1004 3.429135 GGTCAGTTCTAGCTAGGGTTTCG 60.429 52.174 20.58 5.37 0.00 3.46
1646 2454 1.618861 CTCAAGATCGACACACCGTC 58.381 55.000 0.00 0.00 41.62 4.79
1744 2552 4.084265 TGCAGTGCACATCTTGGG 57.916 55.556 21.04 0.22 31.71 4.12
2145 2992 1.602888 CTTGAAGCTGCACCTGCCT 60.603 57.895 0.00 0.00 41.18 4.75
2315 3369 5.964958 AATGTTGGGGATATTGCTTATCG 57.035 39.130 0.00 0.00 38.08 2.92
2363 3417 2.882761 GGGGTAAATCGGCCAGTTTATC 59.117 50.000 2.24 7.54 0.00 1.75
2419 3475 9.087424 TGATTTATCAGCCGATTTATCTTATCG 57.913 33.333 0.00 0.00 37.47 2.92
2444 3500 1.529865 GGCACCGGTAAGCGATAAATC 59.470 52.381 6.87 0.00 0.00 2.17
2553 3609 8.573885 CAGAGAAATAATGTCCATGCAATATGT 58.426 33.333 0.00 0.00 0.00 2.29
2562 3624 7.984002 TGTCCATGCAATATGTAAAAATTCG 57.016 32.000 0.00 0.00 0.00 3.34
2962 4099 0.900647 AGGAGGAGGACAAGGTGACG 60.901 60.000 0.00 0.00 0.00 4.35
3331 4522 0.951040 GCCCGAGAAGTGTGTCAAGG 60.951 60.000 0.00 0.00 0.00 3.61
3364 4555 6.183360 GCTTAGTTCTGGAGCTCAATTACAAG 60.183 42.308 17.19 10.70 33.72 3.16
3481 4672 4.645809 GGTGATCCCTGCTTGACC 57.354 61.111 0.00 0.00 0.00 4.02
3482 4673 1.685224 GGTGATCCCTGCTTGACCA 59.315 57.895 0.00 0.00 0.00 4.02
3483 4674 0.678048 GGTGATCCCTGCTTGACCAC 60.678 60.000 0.00 0.00 0.00 4.16
3484 4675 0.678048 GTGATCCCTGCTTGACCACC 60.678 60.000 0.00 0.00 0.00 4.61
3485 4676 1.077429 GATCCCTGCTTGACCACCC 60.077 63.158 0.00 0.00 0.00 4.61
3486 4677 2.876368 GATCCCTGCTTGACCACCCG 62.876 65.000 0.00 0.00 0.00 5.28
3487 4678 3.636231 CCCTGCTTGACCACCCGA 61.636 66.667 0.00 0.00 0.00 5.14
3488 4679 2.358737 CCTGCTTGACCACCCGAC 60.359 66.667 0.00 0.00 0.00 4.79
3489 4680 2.358737 CTGCTTGACCACCCGACC 60.359 66.667 0.00 0.00 0.00 4.79
3490 4681 3.901797 CTGCTTGACCACCCGACCC 62.902 68.421 0.00 0.00 0.00 4.46
3491 4682 4.717313 GCTTGACCACCCGACCCC 62.717 72.222 0.00 0.00 0.00 4.95
3492 4683 2.928396 CTTGACCACCCGACCCCT 60.928 66.667 0.00 0.00 0.00 4.79
3493 4684 3.246112 TTGACCACCCGACCCCTG 61.246 66.667 0.00 0.00 0.00 4.45
3494 4685 4.567597 TGACCACCCGACCCCTGT 62.568 66.667 0.00 0.00 0.00 4.00
3495 4686 4.016706 GACCACCCGACCCCTGTG 62.017 72.222 0.00 0.00 0.00 3.66
3496 4687 4.892291 ACCACCCGACCCCTGTGT 62.892 66.667 0.00 0.00 0.00 3.72
3497 4688 4.329545 CCACCCGACCCCTGTGTG 62.330 72.222 0.00 0.00 0.00 3.82
3498 4689 3.556306 CACCCGACCCCTGTGTGT 61.556 66.667 0.00 0.00 0.00 3.72
3499 4690 3.556306 ACCCGACCCCTGTGTGTG 61.556 66.667 0.00 0.00 0.00 3.82
3500 4691 3.556306 CCCGACCCCTGTGTGTGT 61.556 66.667 0.00 0.00 0.00 3.72
3501 4692 2.280797 CCGACCCCTGTGTGTGTG 60.281 66.667 0.00 0.00 0.00 3.82
3502 4693 2.504032 CGACCCCTGTGTGTGTGT 59.496 61.111 0.00 0.00 0.00 3.72
3503 4694 1.887242 CGACCCCTGTGTGTGTGTG 60.887 63.158 0.00 0.00 0.00 3.82
3504 4695 1.223487 GACCCCTGTGTGTGTGTGT 59.777 57.895 0.00 0.00 0.00 3.72
3505 4696 1.077787 ACCCCTGTGTGTGTGTGTG 60.078 57.895 0.00 0.00 0.00 3.82
3506 4697 1.823470 CCCCTGTGTGTGTGTGTGG 60.823 63.158 0.00 0.00 0.00 4.17
3507 4698 1.823470 CCCTGTGTGTGTGTGTGGG 60.823 63.158 0.00 0.00 0.00 4.61
3508 4699 1.823470 CCTGTGTGTGTGTGTGGGG 60.823 63.158 0.00 0.00 0.00 4.96
3509 4700 1.823470 CTGTGTGTGTGTGTGGGGG 60.823 63.158 0.00 0.00 0.00 5.40
3797 5010 4.646572 TGTGTGTACCATCTGTATTTGCA 58.353 39.130 0.00 0.00 0.00 4.08
3814 5027 5.913137 TTTGCATTGGTAAACCCTATCAG 57.087 39.130 0.00 0.00 34.29 2.90
3920 5133 4.427394 GCACAGGGCAGATACGAG 57.573 61.111 0.00 0.00 43.97 4.18
3921 5134 1.816537 GCACAGGGCAGATACGAGA 59.183 57.895 0.00 0.00 43.97 4.04
3922 5135 0.175760 GCACAGGGCAGATACGAGAA 59.824 55.000 0.00 0.00 43.97 2.87
3923 5136 1.927895 CACAGGGCAGATACGAGAAC 58.072 55.000 0.00 0.00 0.00 3.01
3924 5137 1.204704 CACAGGGCAGATACGAGAACA 59.795 52.381 0.00 0.00 0.00 3.18
3925 5138 1.899814 ACAGGGCAGATACGAGAACAA 59.100 47.619 0.00 0.00 0.00 2.83
3926 5139 2.501723 ACAGGGCAGATACGAGAACAAT 59.498 45.455 0.00 0.00 0.00 2.71
3927 5140 3.704566 ACAGGGCAGATACGAGAACAATA 59.295 43.478 0.00 0.00 0.00 1.90
3928 5141 4.161565 ACAGGGCAGATACGAGAACAATAA 59.838 41.667 0.00 0.00 0.00 1.40
3929 5142 5.163301 ACAGGGCAGATACGAGAACAATAAT 60.163 40.000 0.00 0.00 0.00 1.28
3930 5143 5.178252 CAGGGCAGATACGAGAACAATAATG 59.822 44.000 0.00 0.00 0.00 1.90
3931 5144 4.083802 GGGCAGATACGAGAACAATAATGC 60.084 45.833 0.00 0.00 0.00 3.56
3932 5145 4.511454 GGCAGATACGAGAACAATAATGCA 59.489 41.667 0.00 0.00 0.00 3.96
3933 5146 5.007626 GGCAGATACGAGAACAATAATGCAA 59.992 40.000 0.00 0.00 0.00 4.08
3934 5147 6.458206 GGCAGATACGAGAACAATAATGCAAA 60.458 38.462 0.00 0.00 0.00 3.68
3935 5148 6.630443 GCAGATACGAGAACAATAATGCAAAG 59.370 38.462 0.00 0.00 0.00 2.77
3936 5149 7.677276 GCAGATACGAGAACAATAATGCAAAGT 60.677 37.037 0.00 0.00 0.00 2.66
3937 5150 8.177663 CAGATACGAGAACAATAATGCAAAGTT 58.822 33.333 0.00 0.00 0.00 2.66
3938 5151 9.378551 AGATACGAGAACAATAATGCAAAGTTA 57.621 29.630 0.00 0.00 0.00 2.24
3942 5155 9.341899 ACGAGAACAATAATGCAAAGTTATTTC 57.658 29.630 0.00 0.00 31.28 2.17
3943 5156 9.340695 CGAGAACAATAATGCAAAGTTATTTCA 57.659 29.630 0.00 0.00 31.28 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.875726 CGATATCCGGGCAATGATCATTATAT 59.124 38.462 20.32 16.96 33.91 0.86
1 2 6.183360 ACGATATCCGGGCAATGATCATTATA 60.183 38.462 20.32 13.34 43.93 0.98
2 3 5.059161 CGATATCCGGGCAATGATCATTAT 58.941 41.667 20.32 11.66 33.91 1.28
3 4 4.081142 ACGATATCCGGGCAATGATCATTA 60.081 41.667 20.32 4.74 43.93 1.90
5 6 2.237143 ACGATATCCGGGCAATGATCAT 59.763 45.455 1.18 1.18 43.93 2.45
6 7 1.623311 ACGATATCCGGGCAATGATCA 59.377 47.619 0.00 0.00 43.93 2.92
7 8 2.271800 GACGATATCCGGGCAATGATC 58.728 52.381 0.00 0.00 43.93 2.92
8 9 1.623311 TGACGATATCCGGGCAATGAT 59.377 47.619 0.00 0.00 43.93 2.45
9 10 1.044611 TGACGATATCCGGGCAATGA 58.955 50.000 0.00 0.00 43.93 2.57
10 11 1.733912 CATGACGATATCCGGGCAATG 59.266 52.381 0.00 0.00 43.93 2.82
11 12 1.623311 TCATGACGATATCCGGGCAAT 59.377 47.619 0.00 0.00 43.93 3.56
12 13 1.044611 TCATGACGATATCCGGGCAA 58.955 50.000 0.00 0.00 43.93 4.52
13 14 1.266178 ATCATGACGATATCCGGGCA 58.734 50.000 0.00 0.00 43.93 5.36
14 15 2.386661 AATCATGACGATATCCGGGC 57.613 50.000 0.00 0.00 43.93 6.13
15 16 6.106003 TCAAATAATCATGACGATATCCGGG 58.894 40.000 0.00 0.00 43.93 5.73
16 17 7.595311 TTCAAATAATCATGACGATATCCGG 57.405 36.000 0.00 0.00 43.93 5.14
33 34 9.598517 GTTGGGCAATTGATAGAATTTCAAATA 57.401 29.630 10.34 0.00 36.72 1.40
34 35 8.102047 TGTTGGGCAATTGATAGAATTTCAAAT 58.898 29.630 10.34 0.00 36.72 2.32
35 36 7.448420 TGTTGGGCAATTGATAGAATTTCAAA 58.552 30.769 10.34 0.00 36.72 2.69
36 37 7.002250 TGTTGGGCAATTGATAGAATTTCAA 57.998 32.000 10.34 0.00 37.49 2.69
37 38 6.211184 ACTGTTGGGCAATTGATAGAATTTCA 59.789 34.615 10.34 0.00 0.00 2.69
38 39 6.633856 ACTGTTGGGCAATTGATAGAATTTC 58.366 36.000 10.34 0.00 0.00 2.17
39 40 6.610075 ACTGTTGGGCAATTGATAGAATTT 57.390 33.333 10.34 0.00 0.00 1.82
40 41 7.716799 TTACTGTTGGGCAATTGATAGAATT 57.283 32.000 10.34 0.00 0.00 2.17
41 42 7.902920 ATTACTGTTGGGCAATTGATAGAAT 57.097 32.000 10.34 0.00 0.00 2.40
42 43 7.716799 AATTACTGTTGGGCAATTGATAGAA 57.283 32.000 10.34 0.00 0.00 2.10
43 44 7.178274 ACAAATTACTGTTGGGCAATTGATAGA 59.822 33.333 10.34 0.00 0.00 1.98
44 45 7.322664 ACAAATTACTGTTGGGCAATTGATAG 58.677 34.615 10.34 0.00 0.00 2.08
45 46 7.238486 ACAAATTACTGTTGGGCAATTGATA 57.762 32.000 10.34 0.00 0.00 2.15
46 47 6.112927 ACAAATTACTGTTGGGCAATTGAT 57.887 33.333 10.34 0.00 0.00 2.57
47 48 5.543507 ACAAATTACTGTTGGGCAATTGA 57.456 34.783 10.34 0.00 0.00 2.57
48 49 6.616774 AAACAAATTACTGTTGGGCAATTG 57.383 33.333 0.00 0.00 39.47 2.32
49 50 6.708502 GGTAAACAAATTACTGTTGGGCAATT 59.291 34.615 0.00 0.00 42.93 2.32
50 51 6.227522 GGTAAACAAATTACTGTTGGGCAAT 58.772 36.000 0.00 0.00 42.93 3.56
51 52 5.453480 GGGTAAACAAATTACTGTTGGGCAA 60.453 40.000 0.00 0.00 42.93 4.52
52 53 4.039366 GGGTAAACAAATTACTGTTGGGCA 59.961 41.667 0.00 0.00 42.93 5.36
53 54 4.039366 TGGGTAAACAAATTACTGTTGGGC 59.961 41.667 0.00 0.00 42.93 5.36
54 55 5.510009 GGTGGGTAAACAAATTACTGTTGGG 60.510 44.000 0.00 0.00 42.93 4.12
55 56 5.534407 GGTGGGTAAACAAATTACTGTTGG 58.466 41.667 0.00 0.00 42.93 3.77
56 57 5.216648 CGGTGGGTAAACAAATTACTGTTG 58.783 41.667 0.00 0.00 42.93 3.33
57 58 4.888823 ACGGTGGGTAAACAAATTACTGTT 59.111 37.500 0.00 0.00 42.93 3.16
58 59 4.463070 ACGGTGGGTAAACAAATTACTGT 58.537 39.130 0.00 0.00 42.93 3.55
59 60 5.441709 AACGGTGGGTAAACAAATTACTG 57.558 39.130 0.00 0.00 42.93 2.74
60 61 5.736777 GCAAACGGTGGGTAAACAAATTACT 60.737 40.000 0.00 0.00 42.93 2.24
61 62 4.445052 GCAAACGGTGGGTAAACAAATTAC 59.555 41.667 0.00 0.00 42.68 1.89
62 63 4.341520 AGCAAACGGTGGGTAAACAAATTA 59.658 37.500 0.00 0.00 0.00 1.40
63 64 3.133183 AGCAAACGGTGGGTAAACAAATT 59.867 39.130 0.00 0.00 0.00 1.82
64 65 2.696187 AGCAAACGGTGGGTAAACAAAT 59.304 40.909 0.00 0.00 0.00 2.32
65 66 2.100989 AGCAAACGGTGGGTAAACAAA 58.899 42.857 0.00 0.00 0.00 2.83
66 67 1.765230 AGCAAACGGTGGGTAAACAA 58.235 45.000 0.00 0.00 0.00 2.83
67 68 2.634815 TAGCAAACGGTGGGTAAACA 57.365 45.000 0.00 0.00 0.00 2.83
68 69 4.508461 AAATAGCAAACGGTGGGTAAAC 57.492 40.909 0.00 0.00 0.00 2.01
69 70 5.302313 AGAAAAATAGCAAACGGTGGGTAAA 59.698 36.000 0.00 0.00 0.00 2.01
70 71 4.828387 AGAAAAATAGCAAACGGTGGGTAA 59.172 37.500 0.00 0.00 0.00 2.85
71 72 4.400120 AGAAAAATAGCAAACGGTGGGTA 58.600 39.130 0.00 0.00 0.00 3.69
72 73 3.227614 AGAAAAATAGCAAACGGTGGGT 58.772 40.909 0.00 0.00 0.00 4.51
73 74 3.669557 CGAGAAAAATAGCAAACGGTGGG 60.670 47.826 0.00 0.00 0.00 4.61
74 75 3.187637 TCGAGAAAAATAGCAAACGGTGG 59.812 43.478 0.00 0.00 0.00 4.61
75 76 4.151689 TCTCGAGAAAAATAGCAAACGGTG 59.848 41.667 14.01 0.00 0.00 4.94
76 77 4.312443 TCTCGAGAAAAATAGCAAACGGT 58.688 39.130 14.01 0.00 0.00 4.83
77 78 4.625742 TCTCTCGAGAAAAATAGCAAACGG 59.374 41.667 17.36 0.00 33.91 4.44
78 79 5.763444 TCTCTCGAGAAAAATAGCAAACG 57.237 39.130 17.36 0.00 33.91 3.60
79 80 6.018542 GCTTCTCTCGAGAAAAATAGCAAAC 58.981 40.000 17.36 0.00 45.75 2.93
80 81 5.122396 GGCTTCTCTCGAGAAAAATAGCAAA 59.878 40.000 17.36 0.00 45.75 3.68
81 82 4.631813 GGCTTCTCTCGAGAAAAATAGCAA 59.368 41.667 17.36 0.40 45.75 3.91
82 83 4.184629 GGCTTCTCTCGAGAAAAATAGCA 58.815 43.478 17.36 0.00 45.75 3.49
83 84 4.033472 GTGGCTTCTCTCGAGAAAAATAGC 59.967 45.833 17.36 17.89 45.75 2.97
84 85 5.415221 AGTGGCTTCTCTCGAGAAAAATAG 58.585 41.667 17.36 9.97 45.75 1.73
85 86 5.407407 AGTGGCTTCTCTCGAGAAAAATA 57.593 39.130 17.36 0.00 45.75 1.40
86 87 4.278975 AGTGGCTTCTCTCGAGAAAAAT 57.721 40.909 17.36 0.00 45.75 1.82
87 88 3.753294 AGTGGCTTCTCTCGAGAAAAA 57.247 42.857 17.36 12.48 45.75 1.94
88 89 3.827302 ACTAGTGGCTTCTCTCGAGAAAA 59.173 43.478 17.36 9.00 45.75 2.29
89 90 3.191581 CACTAGTGGCTTCTCTCGAGAAA 59.808 47.826 17.36 12.26 45.75 2.52
90 91 2.750166 CACTAGTGGCTTCTCTCGAGAA 59.250 50.000 17.36 8.88 44.47 2.87
91 92 2.027100 TCACTAGTGGCTTCTCTCGAGA 60.027 50.000 22.48 15.70 35.27 4.04
92 93 2.360844 TCACTAGTGGCTTCTCTCGAG 58.639 52.381 22.48 5.93 0.00 4.04
93 94 2.491675 TCACTAGTGGCTTCTCTCGA 57.508 50.000 22.48 0.00 0.00 4.04
94 95 3.246619 GTTTCACTAGTGGCTTCTCTCG 58.753 50.000 22.48 0.00 0.00 4.04
95 96 3.259625 AGGTTTCACTAGTGGCTTCTCTC 59.740 47.826 22.48 5.24 0.00 3.20
96 97 3.243724 AGGTTTCACTAGTGGCTTCTCT 58.756 45.455 22.48 10.05 0.00 3.10
97 98 3.686916 AGGTTTCACTAGTGGCTTCTC 57.313 47.619 22.48 8.10 0.00 2.87
98 99 4.080863 CCATAGGTTTCACTAGTGGCTTCT 60.081 45.833 22.48 16.20 0.00 2.85
99 100 4.192317 CCATAGGTTTCACTAGTGGCTTC 58.808 47.826 22.48 10.36 0.00 3.86
100 101 3.622455 GCCATAGGTTTCACTAGTGGCTT 60.622 47.826 22.48 11.79 40.50 4.35
101 102 2.092914 GCCATAGGTTTCACTAGTGGCT 60.093 50.000 22.48 6.62 40.50 4.75
102 103 2.289565 GCCATAGGTTTCACTAGTGGC 58.710 52.381 22.48 10.96 38.82 5.01
103 104 2.741878 CGGCCATAGGTTTCACTAGTGG 60.742 54.545 22.48 4.49 0.00 4.00
104 105 2.550978 CGGCCATAGGTTTCACTAGTG 58.449 52.381 17.17 17.17 0.00 2.74
105 106 1.485066 CCGGCCATAGGTTTCACTAGT 59.515 52.381 2.24 0.00 0.00 2.57
106 107 1.760613 TCCGGCCATAGGTTTCACTAG 59.239 52.381 2.24 0.00 0.00 2.57
107 108 1.868713 TCCGGCCATAGGTTTCACTA 58.131 50.000 2.24 0.00 0.00 2.74
108 109 0.988832 TTCCGGCCATAGGTTTCACT 59.011 50.000 2.24 0.00 0.00 3.41
109 110 1.828979 TTTCCGGCCATAGGTTTCAC 58.171 50.000 2.24 0.00 0.00 3.18
110 111 2.588464 TTTTCCGGCCATAGGTTTCA 57.412 45.000 2.24 0.00 0.00 2.69
111 112 4.885325 TCTATTTTTCCGGCCATAGGTTTC 59.115 41.667 2.24 0.00 0.00 2.78
112 113 4.643334 GTCTATTTTTCCGGCCATAGGTTT 59.357 41.667 2.24 0.00 0.00 3.27
113 114 4.204799 GTCTATTTTTCCGGCCATAGGTT 58.795 43.478 2.24 0.00 0.00 3.50
114 115 3.434596 GGTCTATTTTTCCGGCCATAGGT 60.435 47.826 2.24 0.00 0.00 3.08
115 116 3.146847 GGTCTATTTTTCCGGCCATAGG 58.853 50.000 2.24 0.00 0.00 2.57
116 117 3.564225 GTGGTCTATTTTTCCGGCCATAG 59.436 47.826 2.24 0.92 0.00 2.23
117 118 3.547746 GTGGTCTATTTTTCCGGCCATA 58.452 45.455 2.24 0.00 0.00 2.74
118 119 2.375146 GTGGTCTATTTTTCCGGCCAT 58.625 47.619 2.24 0.00 0.00 4.40
119 120 1.614850 GGTGGTCTATTTTTCCGGCCA 60.615 52.381 2.24 0.00 0.00 5.36
120 121 1.100510 GGTGGTCTATTTTTCCGGCC 58.899 55.000 0.00 0.00 0.00 6.13
121 122 1.828979 TGGTGGTCTATTTTTCCGGC 58.171 50.000 0.00 0.00 0.00 6.13
122 123 4.743493 CAAATGGTGGTCTATTTTTCCGG 58.257 43.478 0.00 0.00 33.56 5.14
123 124 4.082245 AGCAAATGGTGGTCTATTTTTCCG 60.082 41.667 0.00 0.00 33.56 4.30
124 125 5.405935 AGCAAATGGTGGTCTATTTTTCC 57.594 39.130 0.00 0.00 33.56 3.13
134 135 0.394352 GGATCCGAGCAAATGGTGGT 60.394 55.000 0.00 0.00 41.89 4.16
135 136 0.107017 AGGATCCGAGCAAATGGTGG 60.107 55.000 5.98 0.00 0.00 4.61
136 137 1.672881 GAAGGATCCGAGCAAATGGTG 59.327 52.381 5.98 0.00 0.00 4.17
137 138 1.561542 AGAAGGATCCGAGCAAATGGT 59.438 47.619 5.98 0.00 0.00 3.55
138 139 1.945394 CAGAAGGATCCGAGCAAATGG 59.055 52.381 5.98 0.00 0.00 3.16
139 140 2.611292 GTCAGAAGGATCCGAGCAAATG 59.389 50.000 5.98 0.23 0.00 2.32
140 141 2.420687 GGTCAGAAGGATCCGAGCAAAT 60.421 50.000 5.98 0.00 0.00 2.32
141 142 1.066143 GGTCAGAAGGATCCGAGCAAA 60.066 52.381 5.98 0.00 0.00 3.68
142 143 0.537188 GGTCAGAAGGATCCGAGCAA 59.463 55.000 5.98 0.00 0.00 3.91
143 144 0.324738 AGGTCAGAAGGATCCGAGCA 60.325 55.000 15.93 0.00 0.00 4.26
144 145 1.338655 GTAGGTCAGAAGGATCCGAGC 59.661 57.143 5.98 7.27 0.00 5.03
145 146 1.604755 CGTAGGTCAGAAGGATCCGAG 59.395 57.143 5.98 0.00 0.00 4.63
146 147 1.064906 ACGTAGGTCAGAAGGATCCGA 60.065 52.381 5.98 0.00 0.00 4.55
147 148 1.390565 ACGTAGGTCAGAAGGATCCG 58.609 55.000 5.98 0.00 0.00 4.18
156 157 4.537965 CGATGGAGAATAACGTAGGTCAG 58.462 47.826 0.00 0.00 0.00 3.51
160 161 2.673833 GCCGATGGAGAATAACGTAGG 58.326 52.381 0.00 0.00 0.00 3.18
178 179 1.657181 CAAAACAGCAACCGTCGCC 60.657 57.895 0.00 0.00 0.00 5.54
179 180 1.657181 CCAAAACAGCAACCGTCGC 60.657 57.895 0.00 0.00 0.00 5.19
185 186 1.226945 AGCGCACCAAAACAGCAAC 60.227 52.632 11.47 0.00 0.00 4.17
189 190 1.008538 GACCAGCGCACCAAAACAG 60.009 57.895 11.47 0.00 0.00 3.16
194 195 1.003839 CTTAGGACCAGCGCACCAA 60.004 57.895 11.47 4.35 0.00 3.67
200 201 2.501610 GGCCTCTTAGGACCAGCG 59.498 66.667 0.00 0.00 37.46 5.18
211 212 1.677966 TCGTCGTGCTAAGGCCTCT 60.678 57.895 5.23 0.00 37.74 3.69
213 214 1.533469 AAGTCGTCGTGCTAAGGCCT 61.533 55.000 0.00 0.00 37.74 5.19
234 235 7.303261 CACAACTTGTTATAGTAGACAGTCGA 58.697 38.462 0.00 0.00 0.00 4.20
238 239 5.581085 GGGCACAACTTGTTATAGTAGACAG 59.419 44.000 0.00 0.00 0.00 3.51
242 243 4.565564 GTCGGGCACAACTTGTTATAGTAG 59.434 45.833 0.00 0.00 0.00 2.57
248 249 1.541670 GGAGTCGGGCACAACTTGTTA 60.542 52.381 0.00 0.00 0.00 2.41
268 269 3.550431 ATCACCCCTCCATCGCCG 61.550 66.667 0.00 0.00 0.00 6.46
299 300 1.208614 GCACTGAAGCGAGCCAAAG 59.791 57.895 0.00 0.00 0.00 2.77
302 303 1.962822 CAAGCACTGAAGCGAGCCA 60.963 57.895 0.00 0.00 40.15 4.75
308 309 1.721926 GACGACTACAAGCACTGAAGC 59.278 52.381 0.00 0.00 0.00 3.86
309 310 1.979469 CGACGACTACAAGCACTGAAG 59.021 52.381 0.00 0.00 0.00 3.02
319 320 1.938577 GACCATCTAGCGACGACTACA 59.061 52.381 0.00 0.00 0.00 2.74
334 335 1.414158 CACCCAGATCCGTAGACCAT 58.586 55.000 0.00 0.00 0.00 3.55
362 363 8.062448 GGCAGTACAACGAATATCAGAAATAAC 58.938 37.037 0.00 0.00 0.00 1.89
387 388 8.631480 TTCCAATCTATCATCTTCAATCATGG 57.369 34.615 0.00 0.00 0.00 3.66
505 507 0.182537 AGTGTGCCAGTGTTGCCTAA 59.817 50.000 0.00 0.00 0.00 2.69
513 515 0.523072 GTAATGCCAGTGTGCCAGTG 59.477 55.000 3.72 3.72 34.85 3.66
514 516 0.955428 CGTAATGCCAGTGTGCCAGT 60.955 55.000 1.78 0.00 0.00 4.00
532 534 5.570262 TGTGTAAATTTCACTTCGAGTCG 57.430 39.130 6.09 6.09 36.83 4.18
572 574 1.273606 GTGTGCTGTGCTAGAGAAGGA 59.726 52.381 0.00 0.00 0.00 3.36
588 590 2.633657 GCGGTGCTGTCTTGTGTG 59.366 61.111 0.00 0.00 0.00 3.82
589 591 2.591715 GGCGGTGCTGTCTTGTGT 60.592 61.111 0.00 0.00 0.00 3.72
711 713 1.468054 GCTTCGATTTGGTGGATGCAC 60.468 52.381 9.16 9.16 36.27 4.57
713 715 1.098050 AGCTTCGATTTGGTGGATGC 58.902 50.000 0.00 0.00 36.42 3.91
716 718 2.039216 TGGTTAGCTTCGATTTGGTGGA 59.961 45.455 0.00 0.00 0.00 4.02
748 750 2.844839 ATCCCCTCCGGCTAGTGC 60.845 66.667 0.00 0.00 38.76 4.40
766 784 3.213402 GGCTCCTCCTCGTCCTCG 61.213 72.222 0.00 0.00 38.55 4.63
767 785 1.671901 CTTGGCTCCTCCTCGTCCTC 61.672 65.000 0.00 0.00 35.26 3.71
768 786 1.684049 CTTGGCTCCTCCTCGTCCT 60.684 63.158 0.00 0.00 35.26 3.85
769 787 1.671901 CTCTTGGCTCCTCCTCGTCC 61.672 65.000 0.00 0.00 35.26 4.79
770 788 1.813192 CTCTTGGCTCCTCCTCGTC 59.187 63.158 0.00 0.00 35.26 4.20
771 789 2.355193 GCTCTTGGCTCCTCCTCGT 61.355 63.158 0.00 0.00 38.06 4.18
960 1004 1.469767 GCCGATTTGGATTTGCTGGTC 60.470 52.381 0.00 0.00 42.00 4.02
1646 2454 2.961741 TCGAGATCCTTGATCCCAGAAG 59.038 50.000 0.59 0.00 39.66 2.85
2145 2992 4.714632 AGGCTTACTGTAAACTTCTGCAA 58.285 39.130 1.46 0.00 0.00 4.08
2307 3361 4.499188 CGACTGATAAGTTCCCGATAAGCA 60.499 45.833 0.00 0.00 0.00 3.91
2315 3369 3.604875 TTGGTCGACTGATAAGTTCCC 57.395 47.619 16.46 0.00 0.00 3.97
2363 3417 2.451132 GTGATATCGACCGATATGCCG 58.549 52.381 24.27 0.00 44.91 5.69
2419 3475 2.436115 GCTTACCGGTGCCTGACC 60.436 66.667 19.93 0.00 42.07 4.02
2425 3481 1.191647 CGATTTATCGCTTACCGGTGC 59.808 52.381 19.93 12.67 43.84 5.01
2444 3500 3.551890 CCGATATTCCGATAAATCAGCCG 59.448 47.826 0.00 0.00 0.00 5.52
2448 3504 9.967346 GATATCTTCCGATATTCCGATAAATCA 57.033 33.333 0.00 0.00 41.70 2.57
2553 3609 5.933463 AGGTACGATCCAACACGAATTTTTA 59.067 36.000 0.00 0.00 0.00 1.52
2562 3624 1.068055 ACACGAGGTACGATCCAACAC 60.068 52.381 0.00 0.00 45.77 3.32
2962 4099 6.406692 TCCATGACTAGCCTTATGTAGTTC 57.593 41.667 0.00 0.00 29.34 3.01
3157 4329 6.183810 TGATGAGACATAGCATTCCTTGAT 57.816 37.500 0.00 0.00 0.00 2.57
3331 4522 5.483811 AGCTCCAGAACTAAGCTTTCTTAC 58.516 41.667 3.20 0.00 43.67 2.34
3364 4555 7.916128 CAGAACATACTGTAGTACTATGCAC 57.084 40.000 5.75 0.00 32.72 4.57
3468 4659 2.971598 CGGGTGGTCAAGCAGGGAT 61.972 63.158 0.00 0.00 0.00 3.85
3469 4660 3.636231 CGGGTGGTCAAGCAGGGA 61.636 66.667 0.00 0.00 0.00 4.20
3470 4661 3.636231 TCGGGTGGTCAAGCAGGG 61.636 66.667 0.00 0.00 0.00 4.45
3471 4662 2.358737 GTCGGGTGGTCAAGCAGG 60.359 66.667 0.00 0.00 0.00 4.85
3472 4663 2.358737 GGTCGGGTGGTCAAGCAG 60.359 66.667 0.00 0.00 0.00 4.24
3473 4664 3.948719 GGGTCGGGTGGTCAAGCA 61.949 66.667 0.00 0.00 0.00 3.91
3474 4665 4.717313 GGGGTCGGGTGGTCAAGC 62.717 72.222 0.00 0.00 0.00 4.01
3475 4666 2.928396 AGGGGTCGGGTGGTCAAG 60.928 66.667 0.00 0.00 0.00 3.02
3476 4667 3.246112 CAGGGGTCGGGTGGTCAA 61.246 66.667 0.00 0.00 0.00 3.18
3477 4668 4.567597 ACAGGGGTCGGGTGGTCA 62.568 66.667 0.00 0.00 0.00 4.02
3478 4669 4.016706 CACAGGGGTCGGGTGGTC 62.017 72.222 0.00 0.00 0.00 4.02
3479 4670 4.892291 ACACAGGGGTCGGGTGGT 62.892 66.667 0.00 0.00 36.87 4.16
3480 4671 4.329545 CACACAGGGGTCGGGTGG 62.330 72.222 0.00 0.00 36.87 4.61
3481 4672 3.556306 ACACACAGGGGTCGGGTG 61.556 66.667 0.00 0.00 38.47 4.61
3482 4673 3.556306 CACACACAGGGGTCGGGT 61.556 66.667 0.00 0.00 0.00 5.28
3483 4674 3.556306 ACACACACAGGGGTCGGG 61.556 66.667 0.00 0.00 0.00 5.14
3484 4675 2.280797 CACACACACAGGGGTCGG 60.281 66.667 0.00 0.00 0.00 4.79
3485 4676 1.887242 CACACACACACAGGGGTCG 60.887 63.158 0.00 0.00 0.00 4.79
3486 4677 1.095228 CACACACACACACAGGGGTC 61.095 60.000 0.00 0.00 0.00 4.46
3487 4678 1.077787 CACACACACACACAGGGGT 60.078 57.895 0.00 0.00 0.00 4.95
3488 4679 1.823470 CCACACACACACACAGGGG 60.823 63.158 0.00 0.00 0.00 4.79
3489 4680 1.823470 CCCACACACACACACAGGG 60.823 63.158 0.00 0.00 0.00 4.45
3490 4681 1.823470 CCCCACACACACACACAGG 60.823 63.158 0.00 0.00 0.00 4.00
3491 4682 1.823470 CCCCCACACACACACACAG 60.823 63.158 0.00 0.00 0.00 3.66
3492 4683 2.273776 CCCCCACACACACACACA 59.726 61.111 0.00 0.00 0.00 3.72
3743 4956 6.042093 CCAAATAGGAGATGTTAGCAGGAGTA 59.958 42.308 0.00 0.00 41.22 2.59
3797 5010 8.282256 AGCTAAAATCTGATAGGGTTTACCAAT 58.718 33.333 0.69 0.00 43.89 3.16
3814 5027 3.561310 TCGTGATCCATGCAGCTAAAATC 59.439 43.478 0.00 0.00 0.00 2.17
3916 5129 9.341899 GAAATAACTTTGCATTATTGTTCTCGT 57.658 29.630 4.89 0.00 33.51 4.18
3917 5130 9.340695 TGAAATAACTTTGCATTATTGTTCTCG 57.659 29.630 4.89 0.00 33.51 4.04
3945 5158 9.528018 GTTGTTTTCATGGAATTCAAGTTAGAA 57.472 29.630 7.93 0.02 0.00 2.10
3946 5159 8.690884 TGTTGTTTTCATGGAATTCAAGTTAGA 58.309 29.630 7.93 0.00 0.00 2.10
3947 5160 8.870160 TGTTGTTTTCATGGAATTCAAGTTAG 57.130 30.769 7.93 0.00 0.00 2.34
3948 5161 9.829507 ATTGTTGTTTTCATGGAATTCAAGTTA 57.170 25.926 7.93 0.00 0.00 2.24
3949 5162 8.735692 ATTGTTGTTTTCATGGAATTCAAGTT 57.264 26.923 7.93 0.00 0.00 2.66
3950 5163 8.735692 AATTGTTGTTTTCATGGAATTCAAGT 57.264 26.923 7.93 0.00 0.00 3.16
3951 5164 8.828644 TGAATTGTTGTTTTCATGGAATTCAAG 58.171 29.630 7.93 0.00 36.81 3.02
3952 5165 8.728337 TGAATTGTTGTTTTCATGGAATTCAA 57.272 26.923 7.93 0.00 36.81 2.69
3953 5166 8.202811 TCTGAATTGTTGTTTTCATGGAATTCA 58.797 29.630 7.93 0.00 37.07 2.57
3954 5167 8.592105 TCTGAATTGTTGTTTTCATGGAATTC 57.408 30.769 0.00 0.00 33.93 2.17
3955 5168 8.423349 TCTCTGAATTGTTGTTTTCATGGAATT 58.577 29.630 0.00 0.00 31.83 2.17
3956 5169 7.954835 TCTCTGAATTGTTGTTTTCATGGAAT 58.045 30.769 0.00 0.00 31.83 3.01
3957 5170 7.345422 TCTCTGAATTGTTGTTTTCATGGAA 57.655 32.000 0.00 0.00 31.83 3.53
3958 5171 6.515531 GCTCTCTGAATTGTTGTTTTCATGGA 60.516 38.462 0.00 0.00 31.83 3.41
3959 5172 5.632347 GCTCTCTGAATTGTTGTTTTCATGG 59.368 40.000 0.00 0.00 31.83 3.66
3960 5173 6.210796 TGCTCTCTGAATTGTTGTTTTCATG 58.789 36.000 0.00 0.00 31.83 3.07
3961 5174 6.395426 TGCTCTCTGAATTGTTGTTTTCAT 57.605 33.333 0.00 0.00 31.83 2.57
3962 5175 5.833406 TGCTCTCTGAATTGTTGTTTTCA 57.167 34.783 0.00 0.00 0.00 2.69
3963 5176 6.035843 TGTTGCTCTCTGAATTGTTGTTTTC 58.964 36.000 0.00 0.00 0.00 2.29
3964 5177 5.964758 TGTTGCTCTCTGAATTGTTGTTTT 58.035 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.