Multiple sequence alignment - TraesCS1D01G172700

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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 TraesCS1D01G172700 chr1D 100.000 2522 0 0 1 2522 246680959 246678438 0.000000e+00 4658
1 TraesCS1D01G172700 chr1D 90.018 561 48 5 986 1539 246970669 246970110 0.000000e+00 719
2 TraesCS1D01G172700 chr1D 87.838 518 48 3 1017 1528 247123316 247122808 6.010000e-166 593
3 TraesCS1D01G172700 chr1D 95.671 231 9 1 2292 2522 493967841 493968070 1.100000e-98 370
4 TraesCS1D01G172700 chr1D 85.053 281 36 5 612 891 247123859 247123584 5.310000e-72 281
5 TraesCS1D01G172700 chr1B 95.130 1499 57 10 298 1783 331362790 331364285 0.000000e+00 2350
6 TraesCS1D01G172700 chr1B 89.382 518 43 5 1017 1522 331084060 331084577 2.120000e-180 641
7 TraesCS1D01G172700 chr1B 88.760 516 46 6 1025 1528 330991499 330992014 2.760000e-174 621
8 TraesCS1D01G172700 chr1B 85.053 281 34 6 612 891 330990967 330991240 1.910000e-71 279
9 TraesCS1D01G172700 chr1A 94.610 1410 59 8 565 1962 300943650 300945054 0.000000e+00 2167
10 TraesCS1D01G172700 chr1A 90.737 529 42 4 1017 1539 300672657 300673184 0.000000e+00 699
11 TraesCS1D01G172700 chr1A 89.453 512 48 3 1017 1528 300577030 300577535 2.120000e-180 641
12 TraesCS1D01G172700 chr1A 89.671 426 34 7 1 419 300939138 300939560 3.690000e-148 534
13 TraesCS1D01G172700 chr1A 91.020 245 11 5 2055 2290 300945058 300945300 1.130000e-83 320
14 TraesCS1D01G172700 chr1A 84.859 284 32 10 612 891 300576484 300576760 2.470000e-70 276
15 TraesCS1D01G172700 chr1A 88.750 160 17 1 409 567 300941912 300942071 7.120000e-46 195
16 TraesCS1D01G172700 chr5A 81.607 560 82 12 993 1537 491301900 491302453 6.400000e-121 444
17 TraesCS1D01G172700 chr5A 95.279 233 9 1 2292 2522 23928301 23928533 3.960000e-98 368
18 TraesCS1D01G172700 chr4B 94.805 231 10 2 2292 2522 553513620 553513392 2.390000e-95 359
19 TraesCS1D01G172700 chr6B 80.831 433 49 14 636 1050 116106804 116107220 2.440000e-80 309
20 TraesCS1D01G172700 chr6D 81.714 350 41 10 637 968 46860941 46861285 1.150000e-68 270
21 TraesCS1D01G172700 chr7A 84.342 281 37 5 246 522 544890877 544891154 4.140000e-68 268
22 TraesCS1D01G172700 chr5D 85.047 107 7 5 1774 1871 565748856 565748962 1.600000e-17 100


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 TraesCS1D01G172700 chr1D 246678438 246680959 2521 True 4658.0 4658 100.00000 1 2522 1 chr1D.!!$R1 2521
1 TraesCS1D01G172700 chr1D 246970110 246970669 559 True 719.0 719 90.01800 986 1539 1 chr1D.!!$R2 553
2 TraesCS1D01G172700 chr1D 247122808 247123859 1051 True 437.0 593 86.44550 612 1528 2 chr1D.!!$R3 916
3 TraesCS1D01G172700 chr1B 331362790 331364285 1495 False 2350.0 2350 95.13000 298 1783 1 chr1B.!!$F2 1485
4 TraesCS1D01G172700 chr1B 331084060 331084577 517 False 641.0 641 89.38200 1017 1522 1 chr1B.!!$F1 505
5 TraesCS1D01G172700 chr1B 330990967 330992014 1047 False 450.0 621 86.90650 612 1528 2 chr1B.!!$F3 916
6 TraesCS1D01G172700 chr1A 300939138 300945300 6162 False 804.0 2167 91.01275 1 2290 4 chr1A.!!$F3 2289
7 TraesCS1D01G172700 chr1A 300672657 300673184 527 False 699.0 699 90.73700 1017 1539 1 chr1A.!!$F1 522
8 TraesCS1D01G172700 chr1A 300576484 300577535 1051 False 458.5 641 87.15600 612 1528 2 chr1A.!!$F2 916
9 TraesCS1D01G172700 chr5A 491301900 491302453 553 False 444.0 444 81.60700 993 1537 1 chr5A.!!$F2 544

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
465 2840 0.24912 ACCAATGTCGCGAATCTCCA 59.751 50.0 12.06 4.17 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2395 6559 0.038166 TTGGGCTGATTGACTGACCC 59.962 55.0 0.0 0.0 43.82 4.46 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
63 64 4.723248 CGTTCTTATGTTTGAAGCCCTTC 58.277 43.478 1.12 1.12 39.91 3.46
69 70 2.159382 TGTTTGAAGCCCTTCGAATCC 58.841 47.619 12.48 3.73 42.84 3.01
93 94 6.019156 CCGTAAAGAAAGAAGATGATCTCTGC 60.019 42.308 0.00 0.00 33.29 4.26
138 139 4.887655 TCTCCAAGAAACTTGTCCCTTTTC 59.112 41.667 9.99 0.00 0.00 2.29
146 147 7.395617 AGAAACTTGTCCCTTTTCCTATCTAC 58.604 38.462 0.00 0.00 30.82 2.59
157 158 6.015688 CCTTTTCCTATCTACATACTGCCGTA 60.016 42.308 0.00 0.00 0.00 4.02
216 217 2.739913 CGATTCAAAGTCGGCTTAACCA 59.260 45.455 0.94 0.00 39.03 3.67
217 218 3.374058 CGATTCAAAGTCGGCTTAACCAT 59.626 43.478 0.94 0.00 39.03 3.55
218 219 4.662145 GATTCAAAGTCGGCTTAACCATG 58.338 43.478 0.94 0.00 39.03 3.66
219 220 2.432444 TCAAAGTCGGCTTAACCATGG 58.568 47.619 11.19 11.19 39.03 3.66
222 223 4.080807 TCAAAGTCGGCTTAACCATGGATA 60.081 41.667 21.47 8.52 39.03 2.59
223 224 4.706842 AAGTCGGCTTAACCATGGATAT 57.293 40.909 21.47 6.72 39.03 1.63
224 225 4.706842 AGTCGGCTTAACCATGGATATT 57.293 40.909 21.47 4.85 39.03 1.28
226 227 5.063880 AGTCGGCTTAACCATGGATATTTC 58.936 41.667 21.47 3.12 39.03 2.17
251 255 7.371126 GTGGAACAGGAAGATAAGAAGAAAG 57.629 40.000 0.00 0.00 41.80 2.62
272 276 8.884726 AGAAAGAAGAACTAAGAAGAACAACAC 58.115 33.333 0.00 0.00 0.00 3.32
287 291 5.984926 AGAACAACACAACAATGGCTTAATG 59.015 36.000 0.00 0.00 0.00 1.90
291 295 4.545610 ACACAACAATGGCTTAATGAACG 58.454 39.130 0.00 0.00 0.00 3.95
332 336 9.804758 CCTATATTAGTTCATATCTTCCCGTTC 57.195 37.037 0.00 0.00 0.00 3.95
342 346 7.367285 TCATATCTTCCCGTTCTTTGTTTTTG 58.633 34.615 0.00 0.00 0.00 2.44
362 367 2.708861 TGAGACCCACACCAAACAGTAT 59.291 45.455 0.00 0.00 0.00 2.12
372 377 4.248859 CACCAAACAGTATCAGACCAGAG 58.751 47.826 0.00 0.00 0.00 3.35
465 2840 0.249120 ACCAATGTCGCGAATCTCCA 59.751 50.000 12.06 4.17 0.00 3.86
477 2852 3.421231 GCGAATCTCCACGTAGATTAACG 59.579 47.826 12.45 13.13 44.38 3.18
510 2885 1.075836 TGCCCCCTTATTTGCGTGT 59.924 52.632 0.00 0.00 0.00 4.49
522 2900 0.319555 TTGCGTGTCCTTCCTCTTCG 60.320 55.000 0.00 0.00 0.00 3.79
567 2948 1.137825 GAACTCTCCAGACGGCTCG 59.862 63.158 0.00 0.00 0.00 5.03
708 4671 9.049523 AGAAAGCTTTGATTTTGGAATTTTCTC 57.950 29.630 18.30 0.00 26.96 2.87
722 4685 5.123027 GGAATTTTCTCTGCTTGGAGTAGTG 59.877 44.000 0.00 0.00 35.11 2.74
743 4706 5.533903 AGTGAAAACTGGTACGTTCTCTCTA 59.466 40.000 0.00 0.00 0.00 2.43
773 4736 1.071987 CTGCTGTGTTCTGCCCTCA 59.928 57.895 0.00 0.00 37.65 3.86
945 5036 1.537202 GAACCAGCCACAACTCATCAC 59.463 52.381 0.00 0.00 0.00 3.06
965 5056 0.947244 CACCCACAGCAAGTCAAGTC 59.053 55.000 0.00 0.00 0.00 3.01
1447 5591 0.250124 GACCAACATCGTGGACACCA 60.250 55.000 0.00 0.00 41.65 4.17
1554 5701 2.505777 CGTGAGCAGTCTCGGCAG 60.506 66.667 0.00 0.00 42.26 4.85
1555 5702 2.813042 GTGAGCAGTCTCGGCAGC 60.813 66.667 0.00 0.00 42.26 5.25
1811 5964 6.292381 CGTATTACACAAGAAATGCTAGCTCC 60.292 42.308 17.23 2.33 0.00 4.70
1838 5991 8.229811 CGATTCTTCACTGTATCTCTATCTGAG 58.770 40.741 0.00 0.00 43.96 3.35
1871 6024 5.396484 TGTGCTTGTGTACGTTATCTAGAC 58.604 41.667 0.00 0.00 0.00 2.59
1872 6025 5.182570 TGTGCTTGTGTACGTTATCTAGACT 59.817 40.000 0.00 0.00 0.00 3.24
1876 6029 4.267536 TGTGTACGTTATCTAGACTGGCT 58.732 43.478 0.00 0.00 0.00 4.75
1950 6106 8.870075 AGGGAGTTTTATTCCATCAATATAGC 57.130 34.615 0.00 0.00 36.40 2.97
1954 6110 8.396272 AGTTTTATTCCATCAATATAGCGCTT 57.604 30.769 18.68 6.25 0.00 4.68
1963 6119 9.582431 TCCATCAATATAGCGCTTAAAGTATAC 57.418 33.333 18.68 0.00 0.00 1.47
1964 6120 9.366216 CCATCAATATAGCGCTTAAAGTATACA 57.634 33.333 18.68 0.00 0.00 2.29
1967 6123 9.419297 TCAATATAGCGCTTAAAGTATACAAGG 57.581 33.333 18.68 0.00 0.00 3.61
1968 6124 8.656849 CAATATAGCGCTTAAAGTATACAAGGG 58.343 37.037 18.68 9.44 35.85 3.95
1969 6125 4.748277 AGCGCTTAAAGTATACAAGGGA 57.252 40.909 2.64 0.00 35.01 4.20
1970 6126 4.439968 AGCGCTTAAAGTATACAAGGGAC 58.560 43.478 2.64 11.06 35.01 4.46
1971 6127 3.244579 GCGCTTAAAGTATACAAGGGACG 59.755 47.826 17.48 10.36 35.01 4.79
1972 6128 3.244579 CGCTTAAAGTATACAAGGGACGC 59.755 47.826 5.50 0.00 35.01 5.19
1973 6129 3.244579 GCTTAAAGTATACAAGGGACGCG 59.755 47.826 3.53 3.53 0.00 6.01
1974 6130 2.304751 AAAGTATACAAGGGACGCGG 57.695 50.000 12.47 0.00 0.00 6.46
1975 6131 0.462789 AAGTATACAAGGGACGCGGG 59.537 55.000 12.47 0.00 0.00 6.13
1976 6132 1.068585 GTATACAAGGGACGCGGGG 59.931 63.158 12.47 0.00 0.00 5.73
1977 6133 2.135581 TATACAAGGGACGCGGGGG 61.136 63.158 12.47 0.00 0.00 5.40
1993 6149 1.755384 GGGGGTGCTCTATGTAGCC 59.245 63.158 0.00 0.00 46.13 3.93
1995 6151 3.997672 GGGTGCTCTATGTAGCCAG 57.002 57.895 0.00 0.00 46.13 4.85
1996 6152 0.250081 GGGTGCTCTATGTAGCCAGC 60.250 60.000 0.00 0.00 46.13 4.85
1997 6153 0.465705 GGTGCTCTATGTAGCCAGCA 59.534 55.000 0.00 0.74 42.05 4.41
1998 6154 1.134401 GGTGCTCTATGTAGCCAGCAA 60.134 52.381 5.35 0.00 43.35 3.91
1999 6155 2.208431 GTGCTCTATGTAGCCAGCAAG 58.792 52.381 5.35 0.00 43.35 4.01
2000 6156 1.224965 GCTCTATGTAGCCAGCAAGC 58.775 55.000 0.00 0.00 36.45 4.01
2001 6157 1.876322 CTCTATGTAGCCAGCAAGCC 58.124 55.000 0.00 0.00 0.00 4.35
2002 6158 1.139654 CTCTATGTAGCCAGCAAGCCA 59.860 52.381 0.00 0.00 0.00 4.75
2003 6159 1.770658 TCTATGTAGCCAGCAAGCCAT 59.229 47.619 0.00 0.00 0.00 4.40
2004 6160 1.878088 CTATGTAGCCAGCAAGCCATG 59.122 52.381 0.00 0.00 0.00 3.66
2017 6173 4.025015 CAAGCCATGCTACATTCAGTTC 57.975 45.455 0.00 0.00 38.25 3.01
2018 6174 3.354948 AGCCATGCTACATTCAGTTCA 57.645 42.857 0.00 0.00 36.99 3.18
2019 6175 3.689347 AGCCATGCTACATTCAGTTCAA 58.311 40.909 0.00 0.00 36.99 2.69
2020 6176 3.441572 AGCCATGCTACATTCAGTTCAAC 59.558 43.478 0.00 0.00 36.99 3.18
2021 6177 3.428045 GCCATGCTACATTCAGTTCAACC 60.428 47.826 0.00 0.00 0.00 3.77
2022 6178 3.758023 CCATGCTACATTCAGTTCAACCA 59.242 43.478 0.00 0.00 0.00 3.67
2023 6179 4.400251 CCATGCTACATTCAGTTCAACCAT 59.600 41.667 0.00 0.00 0.00 3.55
2024 6180 5.337554 CATGCTACATTCAGTTCAACCATG 58.662 41.667 0.00 0.00 0.00 3.66
2025 6181 4.650734 TGCTACATTCAGTTCAACCATGA 58.349 39.130 0.00 0.00 0.00 3.07
2026 6182 5.255687 TGCTACATTCAGTTCAACCATGAT 58.744 37.500 0.00 0.00 34.96 2.45
2027 6183 5.711506 TGCTACATTCAGTTCAACCATGATT 59.288 36.000 0.00 0.00 34.96 2.57
2028 6184 6.209192 TGCTACATTCAGTTCAACCATGATTT 59.791 34.615 0.00 0.00 34.96 2.17
2029 6185 7.092716 GCTACATTCAGTTCAACCATGATTTT 58.907 34.615 0.00 0.00 34.96 1.82
2030 6186 7.599998 GCTACATTCAGTTCAACCATGATTTTT 59.400 33.333 0.00 0.00 34.96 1.94
2094 6250 4.814224 ATGCCCATATTTTAGGACAGGT 57.186 40.909 0.00 0.00 0.00 4.00
2106 6262 5.762179 TTAGGACAGGTGAGTCATTTGAT 57.238 39.130 12.23 3.06 40.29 2.57
2138 6294 2.362077 ACATTGTCCCACAAGCTTGAAC 59.638 45.455 32.50 21.75 41.94 3.18
2140 6296 2.363306 TGTCCCACAAGCTTGAACAT 57.637 45.000 32.50 7.52 0.00 2.71
2184 6340 8.476142 ACAAAATCAAATTTGAACGTGTATTCG 58.524 29.630 23.91 9.64 41.73 3.34
2189 6353 4.852609 ATTTGAACGTGTATTCGGCTAC 57.147 40.909 0.00 0.00 34.94 3.58
2193 6357 3.861113 TGAACGTGTATTCGGCTACATTC 59.139 43.478 0.00 4.05 34.33 2.67
2219 6383 9.698309 CATATATAGTTTCAAGTACCCAGTCAG 57.302 37.037 0.00 0.00 0.00 3.51
2292 6456 9.739276 TCTTATGATATAGGGTAATTTGCAAGG 57.261 33.333 0.00 0.00 0.00 3.61
2293 6457 9.739276 CTTATGATATAGGGTAATTTGCAAGGA 57.261 33.333 0.00 0.00 0.00 3.36
2294 6458 9.739276 TTATGATATAGGGTAATTTGCAAGGAG 57.261 33.333 0.00 0.00 0.00 3.69
2295 6459 6.003950 TGATATAGGGTAATTTGCAAGGAGC 58.996 40.000 0.00 0.00 45.96 4.70
2304 6468 2.512515 GCAAGGAGCGGCTACAGG 60.513 66.667 15.89 6.88 0.00 4.00
2305 6469 2.982130 CAAGGAGCGGCTACAGGT 59.018 61.111 15.89 0.00 0.00 4.00
2306 6470 1.153549 CAAGGAGCGGCTACAGGTC 60.154 63.158 15.89 0.00 35.57 3.85
2307 6471 1.609501 AAGGAGCGGCTACAGGTCA 60.610 57.895 15.89 0.00 37.81 4.02
2308 6472 1.192146 AAGGAGCGGCTACAGGTCAA 61.192 55.000 15.89 0.00 37.81 3.18
2309 6473 0.978146 AGGAGCGGCTACAGGTCAAT 60.978 55.000 15.89 0.00 37.81 2.57
2310 6474 0.530870 GGAGCGGCTACAGGTCAATC 60.531 60.000 7.50 0.00 37.81 2.67
2311 6475 0.872021 GAGCGGCTACAGGTCAATCG 60.872 60.000 0.60 0.00 36.27 3.34
2312 6476 1.141019 GCGGCTACAGGTCAATCGA 59.859 57.895 0.00 0.00 0.00 3.59
2313 6477 1.146358 GCGGCTACAGGTCAATCGAC 61.146 60.000 0.00 0.00 41.80 4.20
2314 6478 0.456221 CGGCTACAGGTCAATCGACT 59.544 55.000 0.00 0.00 42.21 4.18
2315 6479 1.799181 CGGCTACAGGTCAATCGACTG 60.799 57.143 0.00 0.00 42.21 3.51
2316 6480 1.476891 GGCTACAGGTCAATCGACTGA 59.523 52.381 6.95 0.00 42.21 3.41
2317 6481 2.101582 GGCTACAGGTCAATCGACTGAT 59.898 50.000 0.00 0.00 42.21 2.90
2318 6482 3.430929 GGCTACAGGTCAATCGACTGATT 60.431 47.826 0.00 0.00 45.70 2.57
2330 6494 4.801330 TCGACTGATTGTAGAATGTGGT 57.199 40.909 0.00 0.00 0.00 4.16
2331 6495 4.744570 TCGACTGATTGTAGAATGTGGTC 58.255 43.478 0.00 0.00 0.00 4.02
2332 6496 4.219725 TCGACTGATTGTAGAATGTGGTCA 59.780 41.667 0.00 0.00 0.00 4.02
2333 6497 4.564372 CGACTGATTGTAGAATGTGGTCAG 59.436 45.833 0.00 0.00 38.01 3.51
2334 6498 5.482908 GACTGATTGTAGAATGTGGTCAGT 58.517 41.667 5.72 5.72 45.16 3.41
2335 6499 5.869579 ACTGATTGTAGAATGTGGTCAGTT 58.130 37.500 1.14 0.00 41.22 3.16
2336 6500 5.702670 ACTGATTGTAGAATGTGGTCAGTTG 59.297 40.000 1.14 0.00 41.22 3.16
2337 6501 5.863965 TGATTGTAGAATGTGGTCAGTTGA 58.136 37.500 0.00 0.00 0.00 3.18
2338 6502 6.475504 TGATTGTAGAATGTGGTCAGTTGAT 58.524 36.000 0.00 0.00 0.00 2.57
2339 6503 6.942005 TGATTGTAGAATGTGGTCAGTTGATT 59.058 34.615 0.00 0.00 0.00 2.57
2340 6504 8.100164 TGATTGTAGAATGTGGTCAGTTGATTA 58.900 33.333 0.00 0.00 0.00 1.75
2341 6505 7.667043 TTGTAGAATGTGGTCAGTTGATTAC 57.333 36.000 0.00 0.00 0.00 1.89
2342 6506 7.004555 TGTAGAATGTGGTCAGTTGATTACT 57.995 36.000 0.00 0.00 37.68 2.24
2343 6507 8.129496 TGTAGAATGTGGTCAGTTGATTACTA 57.871 34.615 0.00 0.00 34.56 1.82
2344 6508 8.033038 TGTAGAATGTGGTCAGTTGATTACTAC 58.967 37.037 0.00 0.00 34.56 2.73
2345 6509 7.004555 AGAATGTGGTCAGTTGATTACTACA 57.995 36.000 0.00 0.00 38.68 2.74
2346 6510 7.450074 AGAATGTGGTCAGTTGATTACTACAA 58.550 34.615 0.00 0.00 37.99 2.41
2347 6511 7.387948 AGAATGTGGTCAGTTGATTACTACAAC 59.612 37.037 0.00 0.00 45.15 3.32
2348 6512 5.919755 TGTGGTCAGTTGATTACTACAACA 58.080 37.500 12.15 0.00 46.58 3.33
2349 6513 6.350103 TGTGGTCAGTTGATTACTACAACAA 58.650 36.000 12.15 0.00 46.58 2.83
2350 6514 6.824196 TGTGGTCAGTTGATTACTACAACAAA 59.176 34.615 12.15 0.00 46.58 2.83
2351 6515 7.011950 TGTGGTCAGTTGATTACTACAACAAAG 59.988 37.037 12.15 3.60 46.58 2.77
2352 6516 6.485313 TGGTCAGTTGATTACTACAACAAAGG 59.515 38.462 12.15 1.33 46.58 3.11
2353 6517 6.708949 GGTCAGTTGATTACTACAACAAAGGA 59.291 38.462 12.15 3.22 46.58 3.36
2354 6518 7.227910 GGTCAGTTGATTACTACAACAAAGGAA 59.772 37.037 12.15 0.00 46.58 3.36
2355 6519 8.617809 GTCAGTTGATTACTACAACAAAGGAAA 58.382 33.333 12.15 0.00 46.58 3.13
2356 6520 9.179909 TCAGTTGATTACTACAACAAAGGAAAA 57.820 29.630 12.15 0.00 46.58 2.29
2357 6521 9.450807 CAGTTGATTACTACAACAAAGGAAAAG 57.549 33.333 12.15 0.00 46.58 2.27
2358 6522 9.403583 AGTTGATTACTACAACAAAGGAAAAGA 57.596 29.630 12.15 0.00 46.58 2.52
2365 6529 7.772166 ACTACAACAAAGGAAAAGAAAAGAGG 58.228 34.615 0.00 0.00 0.00 3.69
2366 6530 6.850752 ACAACAAAGGAAAAGAAAAGAGGA 57.149 33.333 0.00 0.00 0.00 3.71
2367 6531 6.631016 ACAACAAAGGAAAAGAAAAGAGGAC 58.369 36.000 0.00 0.00 0.00 3.85
2368 6532 6.210584 ACAACAAAGGAAAAGAAAAGAGGACA 59.789 34.615 0.00 0.00 0.00 4.02
2369 6533 6.456795 ACAAAGGAAAAGAAAAGAGGACAG 57.543 37.500 0.00 0.00 0.00 3.51
2370 6534 6.187682 ACAAAGGAAAAGAAAAGAGGACAGA 58.812 36.000 0.00 0.00 0.00 3.41
2371 6535 6.663523 ACAAAGGAAAAGAAAAGAGGACAGAA 59.336 34.615 0.00 0.00 0.00 3.02
2372 6536 6.951062 AAGGAAAAGAAAAGAGGACAGAAG 57.049 37.500 0.00 0.00 0.00 2.85
2373 6537 6.253946 AGGAAAAGAAAAGAGGACAGAAGA 57.746 37.500 0.00 0.00 0.00 2.87
2374 6538 6.663734 AGGAAAAGAAAAGAGGACAGAAGAA 58.336 36.000 0.00 0.00 0.00 2.52
2375 6539 7.119387 AGGAAAAGAAAAGAGGACAGAAGAAA 58.881 34.615 0.00 0.00 0.00 2.52
2376 6540 7.615757 AGGAAAAGAAAAGAGGACAGAAGAAAA 59.384 33.333 0.00 0.00 0.00 2.29
2377 6541 7.702772 GGAAAAGAAAAGAGGACAGAAGAAAAC 59.297 37.037 0.00 0.00 0.00 2.43
2378 6542 7.946381 AAAGAAAAGAGGACAGAAGAAAACT 57.054 32.000 0.00 0.00 0.00 2.66
2379 6543 6.934048 AGAAAAGAGGACAGAAGAAAACTG 57.066 37.500 0.00 0.00 40.68 3.16
2380 6544 6.653989 AGAAAAGAGGACAGAAGAAAACTGA 58.346 36.000 0.00 0.00 38.55 3.41
2381 6545 6.540551 AGAAAAGAGGACAGAAGAAAACTGAC 59.459 38.462 0.00 0.00 38.55 3.51
2382 6546 5.622346 AAGAGGACAGAAGAAAACTGACT 57.378 39.130 0.00 0.00 38.55 3.41
2383 6547 4.954875 AGAGGACAGAAGAAAACTGACTG 58.045 43.478 0.00 0.00 38.55 3.51
2384 6548 4.651503 AGAGGACAGAAGAAAACTGACTGA 59.348 41.667 0.00 0.00 38.55 3.41
2385 6549 4.698575 AGGACAGAAGAAAACTGACTGAC 58.301 43.478 0.00 0.00 38.55 3.51
2386 6550 3.810386 GGACAGAAGAAAACTGACTGACC 59.190 47.826 0.00 0.00 38.55 4.02
2387 6551 3.809905 ACAGAAGAAAACTGACTGACCC 58.190 45.455 0.00 0.00 38.55 4.46
2388 6552 3.199946 ACAGAAGAAAACTGACTGACCCA 59.800 43.478 0.00 0.00 38.55 4.51
2389 6553 4.199310 CAGAAGAAAACTGACTGACCCAA 58.801 43.478 0.00 0.00 37.54 4.12
2390 6554 4.640201 CAGAAGAAAACTGACTGACCCAAA 59.360 41.667 0.00 0.00 37.54 3.28
2391 6555 4.884164 AGAAGAAAACTGACTGACCCAAAG 59.116 41.667 0.00 0.00 0.00 2.77
2392 6556 4.236527 AGAAAACTGACTGACCCAAAGT 57.763 40.909 0.00 0.00 0.00 2.66
2393 6557 4.600062 AGAAAACTGACTGACCCAAAGTT 58.400 39.130 0.00 0.00 32.60 2.66
2394 6558 5.751586 AGAAAACTGACTGACCCAAAGTTA 58.248 37.500 0.00 0.00 31.09 2.24
2395 6559 5.823045 AGAAAACTGACTGACCCAAAGTTAG 59.177 40.000 0.00 0.00 37.31 2.34
2396 6560 3.771577 ACTGACTGACCCAAAGTTAGG 57.228 47.619 0.00 0.00 36.41 2.69
2405 6569 3.502123 CCCAAAGTTAGGGTCAGTCAA 57.498 47.619 0.00 0.00 41.61 3.18
2406 6570 4.034285 CCCAAAGTTAGGGTCAGTCAAT 57.966 45.455 0.00 0.00 41.61 2.57
2407 6571 4.010349 CCCAAAGTTAGGGTCAGTCAATC 58.990 47.826 0.00 0.00 41.61 2.67
2408 6572 4.506625 CCCAAAGTTAGGGTCAGTCAATCA 60.507 45.833 0.00 0.00 41.61 2.57
2409 6573 4.697352 CCAAAGTTAGGGTCAGTCAATCAG 59.303 45.833 0.00 0.00 0.00 2.90
2410 6574 3.618690 AGTTAGGGTCAGTCAATCAGC 57.381 47.619 0.00 0.00 0.00 4.26
2411 6575 2.237392 AGTTAGGGTCAGTCAATCAGCC 59.763 50.000 0.00 0.00 0.00 4.85
2412 6576 1.204146 TAGGGTCAGTCAATCAGCCC 58.796 55.000 0.00 0.00 36.46 5.19
2413 6577 0.842030 AGGGTCAGTCAATCAGCCCA 60.842 55.000 0.00 0.00 38.56 5.36
2414 6578 0.038166 GGGTCAGTCAATCAGCCCAA 59.962 55.000 0.00 0.00 36.25 4.12
2415 6579 1.168714 GGTCAGTCAATCAGCCCAAC 58.831 55.000 0.00 0.00 0.00 3.77
2416 6580 1.545428 GGTCAGTCAATCAGCCCAACA 60.545 52.381 0.00 0.00 0.00 3.33
2417 6581 2.229792 GTCAGTCAATCAGCCCAACAA 58.770 47.619 0.00 0.00 0.00 2.83
2418 6582 2.030805 GTCAGTCAATCAGCCCAACAAC 60.031 50.000 0.00 0.00 0.00 3.32
2419 6583 1.270550 CAGTCAATCAGCCCAACAACC 59.729 52.381 0.00 0.00 0.00 3.77
2420 6584 1.133513 AGTCAATCAGCCCAACAACCA 60.134 47.619 0.00 0.00 0.00 3.67
2421 6585 1.686052 GTCAATCAGCCCAACAACCAA 59.314 47.619 0.00 0.00 0.00 3.67
2422 6586 2.102252 GTCAATCAGCCCAACAACCAAA 59.898 45.455 0.00 0.00 0.00 3.28
2423 6587 2.102252 TCAATCAGCCCAACAACCAAAC 59.898 45.455 0.00 0.00 0.00 2.93
2424 6588 2.086610 ATCAGCCCAACAACCAAACT 57.913 45.000 0.00 0.00 0.00 2.66
2425 6589 1.110442 TCAGCCCAACAACCAAACTG 58.890 50.000 0.00 0.00 0.00 3.16
2426 6590 0.104671 CAGCCCAACAACCAAACTGG 59.895 55.000 0.00 0.00 45.02 4.00
2427 6591 1.227527 GCCCAACAACCAAACTGGC 60.228 57.895 0.00 0.00 42.67 4.85
2428 6592 1.685355 GCCCAACAACCAAACTGGCT 61.685 55.000 0.00 0.00 42.67 4.75
2429 6593 0.104671 CCCAACAACCAAACTGGCTG 59.895 55.000 0.00 0.00 42.67 4.85
2430 6594 1.110442 CCAACAACCAAACTGGCTGA 58.890 50.000 3.16 0.00 42.67 4.26
2431 6595 1.480137 CCAACAACCAAACTGGCTGAA 59.520 47.619 3.16 0.00 42.67 3.02
2432 6596 2.093764 CCAACAACCAAACTGGCTGAAA 60.094 45.455 3.16 0.00 42.67 2.69
2433 6597 3.594134 CAACAACCAAACTGGCTGAAAA 58.406 40.909 3.16 0.00 42.67 2.29
2434 6598 3.971245 ACAACCAAACTGGCTGAAAAA 57.029 38.095 3.16 0.00 42.67 1.94
2454 6618 3.949842 AATTCTCTTGCCCTCTTTTGC 57.050 42.857 0.00 0.00 0.00 3.68
2455 6619 1.620822 TTCTCTTGCCCTCTTTTGCC 58.379 50.000 0.00 0.00 0.00 4.52
2456 6620 0.773644 TCTCTTGCCCTCTTTTGCCT 59.226 50.000 0.00 0.00 0.00 4.75
2457 6621 1.145738 TCTCTTGCCCTCTTTTGCCTT 59.854 47.619 0.00 0.00 0.00 4.35
2458 6622 1.543358 CTCTTGCCCTCTTTTGCCTTC 59.457 52.381 0.00 0.00 0.00 3.46
2459 6623 1.145738 TCTTGCCCTCTTTTGCCTTCT 59.854 47.619 0.00 0.00 0.00 2.85
2460 6624 1.271656 CTTGCCCTCTTTTGCCTTCTG 59.728 52.381 0.00 0.00 0.00 3.02
2461 6625 0.185901 TGCCCTCTTTTGCCTTCTGT 59.814 50.000 0.00 0.00 0.00 3.41
2462 6626 0.884514 GCCCTCTTTTGCCTTCTGTC 59.115 55.000 0.00 0.00 0.00 3.51
2463 6627 1.539157 CCCTCTTTTGCCTTCTGTCC 58.461 55.000 0.00 0.00 0.00 4.02
2464 6628 1.202927 CCCTCTTTTGCCTTCTGTCCA 60.203 52.381 0.00 0.00 0.00 4.02
2465 6629 2.157738 CCTCTTTTGCCTTCTGTCCAG 58.842 52.381 0.00 0.00 0.00 3.86
2466 6630 2.224621 CCTCTTTTGCCTTCTGTCCAGA 60.225 50.000 0.00 0.00 35.27 3.86
2467 6631 2.810852 CTCTTTTGCCTTCTGTCCAGAC 59.189 50.000 0.00 0.00 37.14 3.51
2468 6632 1.882623 CTTTTGCCTTCTGTCCAGACC 59.117 52.381 0.00 0.00 37.14 3.85
2469 6633 0.843309 TTTGCCTTCTGTCCAGACCA 59.157 50.000 0.00 0.00 37.14 4.02
2470 6634 0.843309 TTGCCTTCTGTCCAGACCAA 59.157 50.000 0.00 0.00 37.14 3.67
2471 6635 0.843309 TGCCTTCTGTCCAGACCAAA 59.157 50.000 0.00 0.00 37.14 3.28
2472 6636 1.214175 TGCCTTCTGTCCAGACCAAAA 59.786 47.619 0.00 0.00 37.14 2.44
2473 6637 2.306847 GCCTTCTGTCCAGACCAAAAA 58.693 47.619 0.00 0.00 37.14 1.94
2493 6657 4.806640 AAAAAGGGCCTGACAATATGTG 57.193 40.909 6.92 0.00 0.00 3.21
2494 6658 3.737559 AAAGGGCCTGACAATATGTGA 57.262 42.857 6.92 0.00 0.00 3.58
2495 6659 2.717639 AGGGCCTGACAATATGTGAC 57.282 50.000 4.50 0.00 0.00 3.67
2496 6660 1.915489 AGGGCCTGACAATATGTGACA 59.085 47.619 4.50 0.00 0.00 3.58
2497 6661 2.308570 AGGGCCTGACAATATGTGACAA 59.691 45.455 4.50 0.00 31.39 3.18
2498 6662 2.423538 GGGCCTGACAATATGTGACAAC 59.576 50.000 0.84 0.00 31.39 3.32
2499 6663 2.423538 GGCCTGACAATATGTGACAACC 59.576 50.000 0.00 0.00 31.39 3.77
2500 6664 3.347216 GCCTGACAATATGTGACAACCT 58.653 45.455 0.00 0.00 31.39 3.50
2501 6665 3.127548 GCCTGACAATATGTGACAACCTG 59.872 47.826 0.00 0.00 31.39 4.00
2502 6666 4.578871 CCTGACAATATGTGACAACCTGA 58.421 43.478 0.00 0.00 31.39 3.86
2503 6667 4.393062 CCTGACAATATGTGACAACCTGAC 59.607 45.833 0.00 0.00 31.39 3.51
2504 6668 4.967036 TGACAATATGTGACAACCTGACA 58.033 39.130 0.00 0.00 0.00 3.58
2505 6669 5.372373 TGACAATATGTGACAACCTGACAA 58.628 37.500 0.00 0.00 0.00 3.18
2506 6670 6.003326 TGACAATATGTGACAACCTGACAAT 58.997 36.000 0.00 0.00 0.00 2.71
2507 6671 6.489700 TGACAATATGTGACAACCTGACAATT 59.510 34.615 0.00 0.00 0.00 2.32
2508 6672 7.014134 TGACAATATGTGACAACCTGACAATTT 59.986 33.333 0.00 0.00 0.00 1.82
2509 6673 7.147312 ACAATATGTGACAACCTGACAATTTG 58.853 34.615 0.00 0.00 0.00 2.32
2510 6674 4.589216 ATGTGACAACCTGACAATTTGG 57.411 40.909 0.78 0.00 0.00 3.28
2511 6675 3.360867 TGTGACAACCTGACAATTTGGT 58.639 40.909 0.78 0.00 35.29 3.67
2512 6676 3.130164 TGTGACAACCTGACAATTTGGTG 59.870 43.478 0.78 0.00 33.89 4.17
2513 6677 3.130340 GTGACAACCTGACAATTTGGTGT 59.870 43.478 0.78 0.00 33.89 4.16
2514 6678 3.766591 TGACAACCTGACAATTTGGTGTT 59.233 39.130 0.78 0.00 33.89 3.32
2515 6679 4.221703 TGACAACCTGACAATTTGGTGTTT 59.778 37.500 0.78 0.00 33.89 2.83
2516 6680 5.159273 ACAACCTGACAATTTGGTGTTTT 57.841 34.783 0.78 0.00 33.89 2.43
2517 6681 4.934602 ACAACCTGACAATTTGGTGTTTTG 59.065 37.500 0.78 1.89 33.89 2.44
2518 6682 5.174395 CAACCTGACAATTTGGTGTTTTGA 58.826 37.500 0.78 0.00 33.89 2.69
2519 6683 5.612725 ACCTGACAATTTGGTGTTTTGAT 57.387 34.783 0.78 0.00 32.16 2.57
2520 6684 5.988287 ACCTGACAATTTGGTGTTTTGATT 58.012 33.333 0.78 0.00 32.16 2.57
2521 6685 6.413892 ACCTGACAATTTGGTGTTTTGATTT 58.586 32.000 0.78 0.00 32.16 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.454504 TCGAAGGGCTTCAAACATAAGAAC 59.545 41.667 0.00 0.00 39.46 3.01
63 64 6.887376 TCATCTTCTTTCTTTACGGATTCG 57.113 37.500 0.00 0.00 43.02 3.34
69 70 6.291532 CGCAGAGATCATCTTCTTTCTTTACG 60.292 42.308 0.00 0.00 35.47 3.18
110 111 4.645136 GGGACAAGTTTCTTGGAGAAGTTT 59.355 41.667 12.95 0.00 35.37 2.66
119 120 6.717084 AGATAGGAAAAGGGACAAGTTTCTTG 59.283 38.462 7.78 7.78 32.89 3.02
157 158 5.923733 AGGTCTCGAAGATAAGAACACAT 57.076 39.130 0.00 0.00 33.89 3.21
161 162 8.973378 CATATTGAAGGTCTCGAAGATAAGAAC 58.027 37.037 0.00 0.00 33.89 3.01
216 217 4.771114 TCCTGTTCCACGAAATATCCAT 57.229 40.909 0.00 0.00 0.00 3.41
217 218 4.224147 TCTTCCTGTTCCACGAAATATCCA 59.776 41.667 0.00 0.00 0.00 3.41
218 219 4.766375 TCTTCCTGTTCCACGAAATATCC 58.234 43.478 0.00 0.00 0.00 2.59
219 220 7.926555 TCTTATCTTCCTGTTCCACGAAATATC 59.073 37.037 0.00 0.00 0.00 1.63
222 223 6.049955 TCTTATCTTCCTGTTCCACGAAAT 57.950 37.500 0.00 0.00 0.00 2.17
223 224 5.477607 TCTTATCTTCCTGTTCCACGAAA 57.522 39.130 0.00 0.00 0.00 3.46
224 225 5.245301 TCTTCTTATCTTCCTGTTCCACGAA 59.755 40.000 0.00 0.00 0.00 3.85
226 227 5.073311 TCTTCTTATCTTCCTGTTCCACG 57.927 43.478 0.00 0.00 0.00 4.94
244 248 9.923786 GTTGTTCTTCTTAGTTCTTCTTTCTTC 57.076 33.333 0.00 0.00 0.00 2.87
251 255 7.748847 TGTTGTGTTGTTCTTCTTAGTTCTTC 58.251 34.615 0.00 0.00 0.00 2.87
272 276 5.227805 CGATTCGTTCATTAAGCCATTGTTG 59.772 40.000 0.00 0.00 0.00 3.33
303 307 8.967918 CGGGAAGATATGAACTAATATAGGACA 58.032 37.037 0.00 0.00 0.00 4.02
304 308 8.968969 ACGGGAAGATATGAACTAATATAGGAC 58.031 37.037 0.00 0.00 0.00 3.85
306 310 9.804758 GAACGGGAAGATATGAACTAATATAGG 57.195 37.037 0.00 0.00 0.00 2.57
319 323 7.447238 TCTCAAAAACAAAGAACGGGAAGATAT 59.553 33.333 0.00 0.00 0.00 1.63
332 336 3.194542 TGGTGTGGGTCTCAAAAACAAAG 59.805 43.478 0.00 0.00 0.00 2.77
342 346 2.922740 TACTGTTTGGTGTGGGTCTC 57.077 50.000 0.00 0.00 0.00 3.36
362 367 1.177401 CATGTCGGTCTCTGGTCTGA 58.823 55.000 0.00 0.00 0.00 3.27
465 2840 0.179129 CGTGGGCCGTTAATCTACGT 60.179 55.000 0.00 0.00 39.81 3.57
484 2859 0.679960 AATAAGGGGGCACGCACTTC 60.680 55.000 5.55 0.00 45.96 3.01
529 2907 9.862149 AGAGTTCTTTTTAGTAAAATGGAGGAA 57.138 29.630 16.85 10.49 33.05 3.36
534 2912 9.284968 TCTGGAGAGTTCTTTTTAGTAAAATGG 57.715 33.333 16.85 10.33 33.05 3.16
549 2929 1.137825 CGAGCCGTCTGGAGAGTTC 59.862 63.158 0.00 0.00 37.49 3.01
567 2948 4.345271 AATGTTGTTTAATCCCGTACGC 57.655 40.909 10.49 0.00 0.00 4.42
683 4645 9.049523 AGAGAAAATTCCAAAATCAAAGCTTTC 57.950 29.630 9.23 0.00 0.00 2.62
708 4671 3.499918 CCAGTTTTCACTACTCCAAGCAG 59.500 47.826 0.00 0.00 0.00 4.24
722 4685 5.159925 GGTAGAGAGAACGTACCAGTTTTC 58.840 45.833 0.00 0.00 36.89 2.29
945 5036 0.466189 ACTTGACTTGCTGTGGGTGG 60.466 55.000 0.00 0.00 0.00 4.61
965 5056 0.610232 AGCTTACCTGCTGCCCTTTG 60.610 55.000 0.00 0.00 42.33 2.77
1122 5245 1.604593 GTGCTTGTGGACCATGCCT 60.605 57.895 0.00 0.00 42.11 4.75
1449 5593 3.056328 GCCTTCCACACGGCTTCC 61.056 66.667 0.00 0.00 42.98 3.46
1786 5936 6.292381 GGAGCTAGCATTTCTTGTGTAATACG 60.292 42.308 18.83 0.00 0.00 3.06
1811 5964 7.174080 TCAGATAGAGATACAGTGAAGAATCGG 59.826 40.741 0.00 0.00 0.00 4.18
1838 5991 4.670621 CGTACACAAGCACAAAAGATGAAC 59.329 41.667 0.00 0.00 0.00 3.18
1950 6106 3.244579 GCGTCCCTTGTATACTTTAAGCG 59.755 47.826 4.17 4.14 0.00 4.68
1954 6110 2.101249 CCCGCGTCCCTTGTATACTTTA 59.899 50.000 4.92 0.00 0.00 1.85
1975 6131 1.054406 TGGCTACATAGAGCACCCCC 61.054 60.000 0.00 0.00 44.76 5.40
1976 6132 0.394565 CTGGCTACATAGAGCACCCC 59.605 60.000 0.00 0.00 44.76 4.95
1977 6133 0.250081 GCTGGCTACATAGAGCACCC 60.250 60.000 0.00 0.00 44.76 4.61
1978 6134 0.465705 TGCTGGCTACATAGAGCACC 59.534 55.000 0.00 0.00 44.76 5.01
1979 6135 2.208431 CTTGCTGGCTACATAGAGCAC 58.792 52.381 0.00 0.00 44.76 4.40
1980 6136 1.473965 GCTTGCTGGCTACATAGAGCA 60.474 52.381 0.00 0.00 44.76 4.26
1981 6137 1.224965 GCTTGCTGGCTACATAGAGC 58.775 55.000 0.00 0.00 42.05 4.09
1982 6138 1.139654 TGGCTTGCTGGCTACATAGAG 59.860 52.381 5.59 0.00 42.34 2.43
1983 6139 1.203237 TGGCTTGCTGGCTACATAGA 58.797 50.000 5.59 0.00 42.34 1.98
1984 6140 1.878088 CATGGCTTGCTGGCTACATAG 59.122 52.381 5.59 0.00 42.34 2.23
1985 6141 1.971481 CATGGCTTGCTGGCTACATA 58.029 50.000 5.59 0.00 42.34 2.29
1986 6142 2.803203 CATGGCTTGCTGGCTACAT 58.197 52.632 5.59 0.00 42.34 2.29
1987 6143 4.324471 CATGGCTTGCTGGCTACA 57.676 55.556 5.59 0.00 42.34 2.74
1996 6152 3.441222 TGAACTGAATGTAGCATGGCTTG 59.559 43.478 0.00 0.00 40.44 4.01
1997 6153 3.689347 TGAACTGAATGTAGCATGGCTT 58.311 40.909 0.00 0.00 40.44 4.35
1998 6154 3.354948 TGAACTGAATGTAGCATGGCT 57.645 42.857 0.00 0.00 43.41 4.75
1999 6155 3.428045 GGTTGAACTGAATGTAGCATGGC 60.428 47.826 0.00 0.00 0.00 4.40
2000 6156 3.758023 TGGTTGAACTGAATGTAGCATGG 59.242 43.478 0.00 0.00 0.00 3.66
2001 6157 5.124297 TCATGGTTGAACTGAATGTAGCATG 59.876 40.000 0.00 0.00 39.81 4.06
2002 6158 5.255687 TCATGGTTGAACTGAATGTAGCAT 58.744 37.500 0.00 0.00 0.00 3.79
2003 6159 4.650734 TCATGGTTGAACTGAATGTAGCA 58.349 39.130 0.00 0.00 0.00 3.49
2004 6160 5.824904 ATCATGGTTGAACTGAATGTAGC 57.175 39.130 0.00 0.00 34.96 3.58
2035 6191 8.783833 TCATGGTTGAACTGAATTTTCAAAAA 57.216 26.923 5.56 0.00 42.98 1.94
2036 6192 8.961294 ATCATGGTTGAACTGAATTTTCAAAA 57.039 26.923 5.56 0.00 42.98 2.44
2037 6193 8.961294 AATCATGGTTGAACTGAATTTTCAAA 57.039 26.923 5.56 0.00 42.98 2.69
2038 6194 8.828644 CAAATCATGGTTGAACTGAATTTTCAA 58.171 29.630 0.00 0.62 39.99 2.69
2039 6195 7.041916 GCAAATCATGGTTGAACTGAATTTTCA 60.042 33.333 12.56 0.00 34.96 2.69
2040 6196 7.172019 AGCAAATCATGGTTGAACTGAATTTTC 59.828 33.333 12.56 0.00 35.94 2.29
2041 6197 6.993902 AGCAAATCATGGTTGAACTGAATTTT 59.006 30.769 12.56 0.00 35.94 1.82
2042 6198 6.527423 AGCAAATCATGGTTGAACTGAATTT 58.473 32.000 12.56 0.00 35.94 1.82
2043 6199 6.105397 AGCAAATCATGGTTGAACTGAATT 57.895 33.333 12.56 0.00 35.94 2.17
2044 6200 5.733620 AGCAAATCATGGTTGAACTGAAT 57.266 34.783 12.56 0.00 35.94 2.57
2045 6201 6.433716 TGATAGCAAATCATGGTTGAACTGAA 59.566 34.615 12.56 0.00 40.93 3.02
2046 6202 5.945191 TGATAGCAAATCATGGTTGAACTGA 59.055 36.000 12.56 0.00 40.93 3.41
2047 6203 6.032094 GTGATAGCAAATCATGGTTGAACTG 58.968 40.000 12.56 0.00 40.93 3.16
2048 6204 5.948162 AGTGATAGCAAATCATGGTTGAACT 59.052 36.000 12.56 4.42 40.93 3.01
2049 6205 6.199937 AGTGATAGCAAATCATGGTTGAAC 57.800 37.500 12.56 0.00 40.93 3.18
2050 6206 7.469043 GCATAGTGATAGCAAATCATGGTTGAA 60.469 37.037 12.56 2.48 40.93 2.69
2051 6207 6.016860 GCATAGTGATAGCAAATCATGGTTGA 60.017 38.462 12.56 0.00 40.93 3.18
2052 6208 6.147581 GCATAGTGATAGCAAATCATGGTTG 58.852 40.000 5.21 0.00 40.93 3.77
2053 6209 5.242393 GGCATAGTGATAGCAAATCATGGTT 59.758 40.000 5.21 0.00 40.93 3.67
2094 6250 4.286808 TCCTGGTCTCAATCAAATGACTCA 59.713 41.667 0.00 0.00 0.00 3.41
2193 6357 9.698309 CTGACTGGGTACTTGAAACTATATATG 57.302 37.037 0.00 0.00 0.00 1.78
2204 6368 2.256306 TCATGCTGACTGGGTACTTGA 58.744 47.619 0.00 0.00 0.00 3.02
2215 6379 8.806177 TGATTTGCATTATAAATCATGCTGAC 57.194 30.769 6.65 1.78 44.90 3.51
2266 6430 9.739276 CCTTGCAAATTACCCTATATCATAAGA 57.261 33.333 0.00 0.00 0.00 2.10
2287 6451 2.512515 CCTGTAGCCGCTCCTTGC 60.513 66.667 0.00 0.00 38.57 4.01
2288 6452 1.153549 GACCTGTAGCCGCTCCTTG 60.154 63.158 0.00 0.00 0.00 3.61
2289 6453 1.192146 TTGACCTGTAGCCGCTCCTT 61.192 55.000 0.00 0.00 0.00 3.36
2291 6455 0.530870 GATTGACCTGTAGCCGCTCC 60.531 60.000 0.00 0.00 0.00 4.70
2292 6456 0.872021 CGATTGACCTGTAGCCGCTC 60.872 60.000 0.00 0.00 0.00 5.03
2293 6457 1.141881 CGATTGACCTGTAGCCGCT 59.858 57.895 0.00 0.00 0.00 5.52
2294 6458 1.141019 TCGATTGACCTGTAGCCGC 59.859 57.895 0.00 0.00 0.00 6.53
2295 6459 0.456221 AGTCGATTGACCTGTAGCCG 59.544 55.000 9.62 0.00 46.74 5.52
2296 6460 1.476891 TCAGTCGATTGACCTGTAGCC 59.523 52.381 6.51 0.00 46.74 3.93
2297 6461 2.941453 TCAGTCGATTGACCTGTAGC 57.059 50.000 6.51 0.00 46.74 3.58
2307 6471 5.734720 ACCACATTCTACAATCAGTCGATT 58.265 37.500 0.00 0.00 42.81 3.34
2308 6472 5.105351 TGACCACATTCTACAATCAGTCGAT 60.105 40.000 0.00 0.00 0.00 3.59
2309 6473 4.219725 TGACCACATTCTACAATCAGTCGA 59.780 41.667 0.00 0.00 0.00 4.20
2310 6474 4.494484 TGACCACATTCTACAATCAGTCG 58.506 43.478 0.00 0.00 0.00 4.18
2311 6475 5.482908 ACTGACCACATTCTACAATCAGTC 58.517 41.667 0.00 0.00 40.95 3.51
2312 6476 5.489792 ACTGACCACATTCTACAATCAGT 57.510 39.130 0.00 0.00 40.26 3.41
2313 6477 5.934043 TCAACTGACCACATTCTACAATCAG 59.066 40.000 0.00 0.00 38.42 2.90
2314 6478 5.863965 TCAACTGACCACATTCTACAATCA 58.136 37.500 0.00 0.00 0.00 2.57
2315 6479 6.992063 ATCAACTGACCACATTCTACAATC 57.008 37.500 0.00 0.00 0.00 2.67
2316 6480 8.103305 AGTAATCAACTGACCACATTCTACAAT 58.897 33.333 0.00 0.00 36.93 2.71
2317 6481 7.450074 AGTAATCAACTGACCACATTCTACAA 58.550 34.615 0.00 0.00 36.93 2.41
2318 6482 7.004555 AGTAATCAACTGACCACATTCTACA 57.995 36.000 0.00 0.00 36.93 2.74
2319 6483 8.033038 TGTAGTAATCAACTGACCACATTCTAC 58.967 37.037 0.00 0.00 39.39 2.59
2320 6484 8.129496 TGTAGTAATCAACTGACCACATTCTA 57.871 34.615 0.00 0.00 39.39 2.10
2321 6485 7.004555 TGTAGTAATCAACTGACCACATTCT 57.995 36.000 0.00 0.00 39.39 2.40
2322 6486 7.172532 TGTTGTAGTAATCAACTGACCACATTC 59.827 37.037 9.57 0.00 43.54 2.67
2323 6487 6.995686 TGTTGTAGTAATCAACTGACCACATT 59.004 34.615 9.57 0.00 43.54 2.71
2324 6488 6.530120 TGTTGTAGTAATCAACTGACCACAT 58.470 36.000 9.57 0.00 43.54 3.21
2325 6489 5.919755 TGTTGTAGTAATCAACTGACCACA 58.080 37.500 9.57 0.00 43.54 4.17
2326 6490 6.854496 TTGTTGTAGTAATCAACTGACCAC 57.146 37.500 9.57 0.00 43.54 4.16
2327 6491 6.485313 CCTTTGTTGTAGTAATCAACTGACCA 59.515 38.462 9.57 0.00 43.54 4.02
2328 6492 6.708949 TCCTTTGTTGTAGTAATCAACTGACC 59.291 38.462 9.57 0.00 43.54 4.02
2329 6493 7.724305 TCCTTTGTTGTAGTAATCAACTGAC 57.276 36.000 9.57 0.00 43.54 3.51
2330 6494 8.740123 TTTCCTTTGTTGTAGTAATCAACTGA 57.260 30.769 9.57 0.00 43.54 3.41
2331 6495 9.450807 CTTTTCCTTTGTTGTAGTAATCAACTG 57.549 33.333 9.57 2.03 43.54 3.16
2332 6496 9.403583 TCTTTTCCTTTGTTGTAGTAATCAACT 57.596 29.630 9.57 0.00 43.54 3.16
2339 6503 8.899771 CCTCTTTTCTTTTCCTTTGTTGTAGTA 58.100 33.333 0.00 0.00 0.00 1.82
2340 6504 7.614192 TCCTCTTTTCTTTTCCTTTGTTGTAGT 59.386 33.333 0.00 0.00 0.00 2.73
2341 6505 7.915923 GTCCTCTTTTCTTTTCCTTTGTTGTAG 59.084 37.037 0.00 0.00 0.00 2.74
2342 6506 7.394923 TGTCCTCTTTTCTTTTCCTTTGTTGTA 59.605 33.333 0.00 0.00 0.00 2.41
2343 6507 6.210584 TGTCCTCTTTTCTTTTCCTTTGTTGT 59.789 34.615 0.00 0.00 0.00 3.32
2344 6508 6.630071 TGTCCTCTTTTCTTTTCCTTTGTTG 58.370 36.000 0.00 0.00 0.00 3.33
2345 6509 6.663523 TCTGTCCTCTTTTCTTTTCCTTTGTT 59.336 34.615 0.00 0.00 0.00 2.83
2346 6510 6.187682 TCTGTCCTCTTTTCTTTTCCTTTGT 58.812 36.000 0.00 0.00 0.00 2.83
2347 6511 6.699575 TCTGTCCTCTTTTCTTTTCCTTTG 57.300 37.500 0.00 0.00 0.00 2.77
2348 6512 7.119387 TCTTCTGTCCTCTTTTCTTTTCCTTT 58.881 34.615 0.00 0.00 0.00 3.11
2349 6513 6.663734 TCTTCTGTCCTCTTTTCTTTTCCTT 58.336 36.000 0.00 0.00 0.00 3.36
2350 6514 6.253946 TCTTCTGTCCTCTTTTCTTTTCCT 57.746 37.500 0.00 0.00 0.00 3.36
2351 6515 6.944234 TTCTTCTGTCCTCTTTTCTTTTCC 57.056 37.500 0.00 0.00 0.00 3.13
2352 6516 8.462811 AGTTTTCTTCTGTCCTCTTTTCTTTTC 58.537 33.333 0.00 0.00 0.00 2.29
2353 6517 8.246871 CAGTTTTCTTCTGTCCTCTTTTCTTTT 58.753 33.333 0.00 0.00 0.00 2.27
2354 6518 7.611855 TCAGTTTTCTTCTGTCCTCTTTTCTTT 59.388 33.333 0.00 0.00 34.86 2.52
2355 6519 7.066404 GTCAGTTTTCTTCTGTCCTCTTTTCTT 59.934 37.037 0.00 0.00 34.86 2.52
2356 6520 6.540551 GTCAGTTTTCTTCTGTCCTCTTTTCT 59.459 38.462 0.00 0.00 34.86 2.52
2357 6521 6.540551 AGTCAGTTTTCTTCTGTCCTCTTTTC 59.459 38.462 0.00 0.00 34.86 2.29
2358 6522 6.317391 CAGTCAGTTTTCTTCTGTCCTCTTTT 59.683 38.462 0.00 0.00 34.86 2.27
2359 6523 5.819901 CAGTCAGTTTTCTTCTGTCCTCTTT 59.180 40.000 0.00 0.00 34.86 2.52
2360 6524 5.129485 TCAGTCAGTTTTCTTCTGTCCTCTT 59.871 40.000 0.00 0.00 33.86 2.85
2361 6525 4.651503 TCAGTCAGTTTTCTTCTGTCCTCT 59.348 41.667 0.00 0.00 33.86 3.69
2362 6526 4.747605 GTCAGTCAGTTTTCTTCTGTCCTC 59.252 45.833 0.00 0.00 33.86 3.71
2363 6527 4.443598 GGTCAGTCAGTTTTCTTCTGTCCT 60.444 45.833 0.00 0.00 36.15 3.85
2364 6528 3.810386 GGTCAGTCAGTTTTCTTCTGTCC 59.190 47.826 0.00 0.00 34.07 4.02
2365 6529 3.810386 GGGTCAGTCAGTTTTCTTCTGTC 59.190 47.826 0.00 0.00 33.86 3.51
2366 6530 3.199946 TGGGTCAGTCAGTTTTCTTCTGT 59.800 43.478 0.00 0.00 33.86 3.41
2367 6531 3.808728 TGGGTCAGTCAGTTTTCTTCTG 58.191 45.455 0.00 0.00 33.62 3.02
2368 6532 4.503714 TTGGGTCAGTCAGTTTTCTTCT 57.496 40.909 0.00 0.00 0.00 2.85
2369 6533 4.640647 ACTTTGGGTCAGTCAGTTTTCTTC 59.359 41.667 0.00 0.00 0.00 2.87
2370 6534 4.600062 ACTTTGGGTCAGTCAGTTTTCTT 58.400 39.130 0.00 0.00 0.00 2.52
2371 6535 4.236527 ACTTTGGGTCAGTCAGTTTTCT 57.763 40.909 0.00 0.00 0.00 2.52
2372 6536 4.983671 AACTTTGGGTCAGTCAGTTTTC 57.016 40.909 0.00 0.00 0.00 2.29
2373 6537 4.887655 CCTAACTTTGGGTCAGTCAGTTTT 59.112 41.667 0.00 0.00 0.00 2.43
2374 6538 4.461198 CCTAACTTTGGGTCAGTCAGTTT 58.539 43.478 0.00 0.00 0.00 2.66
2375 6539 3.181443 CCCTAACTTTGGGTCAGTCAGTT 60.181 47.826 0.28 0.00 39.82 3.16
2376 6540 2.372172 CCCTAACTTTGGGTCAGTCAGT 59.628 50.000 0.28 0.00 39.82 3.41
2377 6541 3.059352 CCCTAACTTTGGGTCAGTCAG 57.941 52.381 0.28 0.00 39.82 3.51
2386 6550 4.651778 TGATTGACTGACCCTAACTTTGG 58.348 43.478 0.00 0.00 0.00 3.28
2387 6551 4.154918 GCTGATTGACTGACCCTAACTTTG 59.845 45.833 0.00 0.00 0.00 2.77
2388 6552 4.327680 GCTGATTGACTGACCCTAACTTT 58.672 43.478 0.00 0.00 0.00 2.66
2389 6553 3.307762 GGCTGATTGACTGACCCTAACTT 60.308 47.826 0.00 0.00 0.00 2.66
2390 6554 2.237392 GGCTGATTGACTGACCCTAACT 59.763 50.000 0.00 0.00 0.00 2.24
2391 6555 2.633488 GGCTGATTGACTGACCCTAAC 58.367 52.381 0.00 0.00 0.00 2.34
2392 6556 1.559682 GGGCTGATTGACTGACCCTAA 59.440 52.381 0.00 0.00 39.36 2.69
2393 6557 1.204146 GGGCTGATTGACTGACCCTA 58.796 55.000 0.00 0.00 39.36 3.53
2394 6558 0.842030 TGGGCTGATTGACTGACCCT 60.842 55.000 0.00 0.00 43.82 4.34
2395 6559 0.038166 TTGGGCTGATTGACTGACCC 59.962 55.000 0.00 0.00 43.82 4.46
2396 6560 1.168714 GTTGGGCTGATTGACTGACC 58.831 55.000 0.00 0.00 44.57 4.02
2397 6561 1.896220 TGTTGGGCTGATTGACTGAC 58.104 50.000 0.00 0.00 0.00 3.51
2398 6562 2.229792 GTTGTTGGGCTGATTGACTGA 58.770 47.619 0.00 0.00 0.00 3.41
2399 6563 1.270550 GGTTGTTGGGCTGATTGACTG 59.729 52.381 0.00 0.00 0.00 3.51
2400 6564 1.133513 TGGTTGTTGGGCTGATTGACT 60.134 47.619 0.00 0.00 0.00 3.41
2401 6565 1.327303 TGGTTGTTGGGCTGATTGAC 58.673 50.000 0.00 0.00 0.00 3.18
2402 6566 2.079170 TTGGTTGTTGGGCTGATTGA 57.921 45.000 0.00 0.00 0.00 2.57
2403 6567 2.102925 AGTTTGGTTGTTGGGCTGATTG 59.897 45.455 0.00 0.00 0.00 2.67
2404 6568 2.102925 CAGTTTGGTTGTTGGGCTGATT 59.897 45.455 0.00 0.00 0.00 2.57
2405 6569 1.688197 CAGTTTGGTTGTTGGGCTGAT 59.312 47.619 0.00 0.00 0.00 2.90
2406 6570 1.110442 CAGTTTGGTTGTTGGGCTGA 58.890 50.000 0.00 0.00 0.00 4.26
2407 6571 0.104671 CCAGTTTGGTTGTTGGGCTG 59.895 55.000 0.00 0.00 31.35 4.85
2408 6572 1.685355 GCCAGTTTGGTTGTTGGGCT 61.685 55.000 0.00 0.00 40.46 5.19
2409 6573 1.227527 GCCAGTTTGGTTGTTGGGC 60.228 57.895 0.00 0.00 40.46 5.36
2410 6574 0.104671 CAGCCAGTTTGGTTGTTGGG 59.895 55.000 4.03 0.00 42.83 4.12
2411 6575 3.665544 CAGCCAGTTTGGTTGTTGG 57.334 52.632 4.03 0.00 42.83 3.77
2431 6595 5.059161 GCAAAAGAGGGCAAGAGAATTTTT 58.941 37.500 0.00 0.00 0.00 1.94
2432 6596 4.503817 GGCAAAAGAGGGCAAGAGAATTTT 60.504 41.667 0.00 0.00 0.00 1.82
2433 6597 3.007290 GGCAAAAGAGGGCAAGAGAATTT 59.993 43.478 0.00 0.00 0.00 1.82
2434 6598 2.564504 GGCAAAAGAGGGCAAGAGAATT 59.435 45.455 0.00 0.00 0.00 2.17
2435 6599 2.174360 GGCAAAAGAGGGCAAGAGAAT 58.826 47.619 0.00 0.00 0.00 2.40
2436 6600 1.145738 AGGCAAAAGAGGGCAAGAGAA 59.854 47.619 0.00 0.00 0.00 2.87
2437 6601 0.773644 AGGCAAAAGAGGGCAAGAGA 59.226 50.000 0.00 0.00 0.00 3.10
2438 6602 1.543358 GAAGGCAAAAGAGGGCAAGAG 59.457 52.381 0.00 0.00 0.00 2.85
2439 6603 1.145738 AGAAGGCAAAAGAGGGCAAGA 59.854 47.619 0.00 0.00 0.00 3.02
2440 6604 1.271656 CAGAAGGCAAAAGAGGGCAAG 59.728 52.381 0.00 0.00 0.00 4.01
2441 6605 1.331214 CAGAAGGCAAAAGAGGGCAA 58.669 50.000 0.00 0.00 0.00 4.52
2442 6606 0.185901 ACAGAAGGCAAAAGAGGGCA 59.814 50.000 0.00 0.00 0.00 5.36
2443 6607 0.884514 GACAGAAGGCAAAAGAGGGC 59.115 55.000 0.00 0.00 0.00 5.19
2444 6608 1.202927 TGGACAGAAGGCAAAAGAGGG 60.203 52.381 0.00 0.00 0.00 4.30
2445 6609 2.157738 CTGGACAGAAGGCAAAAGAGG 58.842 52.381 0.00 0.00 0.00 3.69
2446 6610 2.810852 GTCTGGACAGAAGGCAAAAGAG 59.189 50.000 3.18 0.00 39.48 2.85
2447 6611 2.487265 GGTCTGGACAGAAGGCAAAAGA 60.487 50.000 3.18 0.00 39.48 2.52
2448 6612 1.882623 GGTCTGGACAGAAGGCAAAAG 59.117 52.381 3.18 0.00 39.48 2.27
2449 6613 1.214175 TGGTCTGGACAGAAGGCAAAA 59.786 47.619 3.18 0.00 39.48 2.44
2450 6614 0.843309 TGGTCTGGACAGAAGGCAAA 59.157 50.000 3.18 0.00 39.48 3.68
2451 6615 0.843309 TTGGTCTGGACAGAAGGCAA 59.157 50.000 3.18 0.00 39.48 4.52
2452 6616 0.843309 TTTGGTCTGGACAGAAGGCA 59.157 50.000 3.18 0.00 39.48 4.75
2453 6617 1.981256 TTTTGGTCTGGACAGAAGGC 58.019 50.000 3.18 0.00 39.48 4.35
2472 6636 4.220602 GTCACATATTGTCAGGCCCTTTTT 59.779 41.667 0.00 0.00 0.00 1.94
2473 6637 3.763897 GTCACATATTGTCAGGCCCTTTT 59.236 43.478 0.00 0.00 0.00 2.27
2474 6638 3.245229 TGTCACATATTGTCAGGCCCTTT 60.245 43.478 0.00 0.00 0.00 3.11
2475 6639 2.308570 TGTCACATATTGTCAGGCCCTT 59.691 45.455 0.00 0.00 0.00 3.95
2476 6640 1.915489 TGTCACATATTGTCAGGCCCT 59.085 47.619 0.00 0.00 0.00 5.19
2477 6641 2.418368 TGTCACATATTGTCAGGCCC 57.582 50.000 0.00 0.00 0.00 5.80
2478 6642 2.423538 GGTTGTCACATATTGTCAGGCC 59.576 50.000 0.00 0.00 0.00 5.19
2479 6643 3.127548 CAGGTTGTCACATATTGTCAGGC 59.872 47.826 0.00 0.00 0.00 4.85
2480 6644 4.393062 GTCAGGTTGTCACATATTGTCAGG 59.607 45.833 0.00 0.00 0.00 3.86
2481 6645 4.996758 TGTCAGGTTGTCACATATTGTCAG 59.003 41.667 0.00 0.00 0.00 3.51
2482 6646 4.967036 TGTCAGGTTGTCACATATTGTCA 58.033 39.130 0.00 0.00 0.00 3.58
2483 6647 5.940192 TTGTCAGGTTGTCACATATTGTC 57.060 39.130 0.00 0.00 0.00 3.18
2484 6648 6.899393 AATTGTCAGGTTGTCACATATTGT 57.101 33.333 0.00 0.00 0.00 2.71
2485 6649 6.587226 CCAAATTGTCAGGTTGTCACATATTG 59.413 38.462 0.00 0.00 0.00 1.90
2486 6650 6.267471 ACCAAATTGTCAGGTTGTCACATATT 59.733 34.615 0.00 0.00 29.58 1.28
2487 6651 5.774690 ACCAAATTGTCAGGTTGTCACATAT 59.225 36.000 0.00 0.00 29.58 1.78
2488 6652 5.009510 CACCAAATTGTCAGGTTGTCACATA 59.990 40.000 0.00 0.00 32.15 2.29
2489 6653 3.960102 ACCAAATTGTCAGGTTGTCACAT 59.040 39.130 0.00 0.00 29.58 3.21
2490 6654 3.130164 CACCAAATTGTCAGGTTGTCACA 59.870 43.478 0.00 0.00 32.15 3.58
2491 6655 3.130340 ACACCAAATTGTCAGGTTGTCAC 59.870 43.478 0.00 0.00 32.15 3.67
2492 6656 3.360867 ACACCAAATTGTCAGGTTGTCA 58.639 40.909 0.00 0.00 32.15 3.58
2493 6657 4.385358 AACACCAAATTGTCAGGTTGTC 57.615 40.909 0.00 0.00 32.15 3.18
2494 6658 4.817318 AAACACCAAATTGTCAGGTTGT 57.183 36.364 0.00 0.00 32.15 3.32
2495 6659 5.174395 TCAAAACACCAAATTGTCAGGTTG 58.826 37.500 0.00 0.00 32.15 3.77
2496 6660 5.413309 TCAAAACACCAAATTGTCAGGTT 57.587 34.783 0.00 0.00 32.15 3.50
2497 6661 5.612725 ATCAAAACACCAAATTGTCAGGT 57.387 34.783 0.00 0.00 35.65 4.00
2498 6662 6.923928 AAATCAAAACACCAAATTGTCAGG 57.076 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.