Multiple sequence alignment - TraesCS3B01G125500

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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 TraesCS3B01G125500 chr3B 100.000 3681 0 0 1 3681 101310393 101314073 0.000000e+00 6798
1 TraesCS3B01G125500 chr3D 89.093 2118 113 45 1 2045 62327799 62329871 0.000000e+00 2523
2 TraesCS3B01G125500 chr3D 91.816 1283 64 13 2288 3556 62329900 62331155 0.000000e+00 1749
3 TraesCS3B01G125500 chr3A 88.144 1670 95 44 433 2050 71223325 71224943 0.000000e+00 1892
4 TraesCS3B01G125500 chr3A 89.764 762 29 18 2288 3004 71224961 71225718 0.000000e+00 929
5 TraesCS3B01G125500 chr3A 82.148 661 70 18 3030 3681 71225716 71226337 1.170000e-144 523
6 TraesCS3B01G125500 chr3A 89.573 422 19 9 1 411 71222787 71223194 2.540000e-141 512
7 TraesCS3B01G125500 chr3A 93.916 263 13 3 2031 2290 41099305 41099567 9.580000e-106 394
8 TraesCS3B01G125500 chr2A 97.531 243 6 0 2048 2290 206048656 206048898 2.040000e-112 416
9 TraesCS3B01G125500 chr2A 96.429 252 8 1 2040 2290 487349692 487349943 7.350000e-112 414
10 TraesCS3B01G125500 chr4A 97.521 242 6 0 2049 2290 642034746 642034987 7.350000e-112 414
11 TraesCS3B01G125500 chr7B 97.107 242 7 0 2049 2290 119705888 119706129 3.420000e-110 409
12 TraesCS3B01G125500 chr7B 96.721 244 8 0 2047 2290 11963765 11963522 1.230000e-109 407
13 TraesCS3B01G125500 chr6B 96.735 245 8 0 2046 2290 140675178 140674934 3.420000e-110 409
14 TraesCS3B01G125500 chr1B 96.708 243 8 0 2048 2290 265967331 265967089 4.430000e-109 405
15 TraesCS3B01G125500 chr4B 95.984 249 9 1 2042 2290 373764695 373764942 1.590000e-108 403


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 TraesCS3B01G125500 chr3B 101310393 101314073 3680 False 6798 6798 100.00000 1 3681 1 chr3B.!!$F1 3680
1 TraesCS3B01G125500 chr3D 62327799 62331155 3356 False 2136 2523 90.45450 1 3556 2 chr3D.!!$F1 3555
2 TraesCS3B01G125500 chr3A 71222787 71226337 3550 False 964 1892 87.40725 1 3681 4 chr3A.!!$F2 3680

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
729 873 0.107214 GCAGATTCCACCGGATTCCA 60.107 55.0 9.46 0.0 33.91 3.53 F
1434 1615 0.796312 CACGCTTCATTAACCGTGCT 59.204 50.0 0.00 0.0 43.40 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2228 0.103208 AACGAGGATGACGATGAGGC 59.897 55.0 0.00 0.0 34.70 4.70 R
3059 3358 0.038618 TCGTTGTCAGTGATCCACGG 60.039 55.0 16.89 0.0 39.64 4.94 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
150 158 2.980568 TGGCACCTAACCTTGATAACG 58.019 47.619 0.00 0.00 0.00 3.18
182 195 1.134401 TGCATAGAAAGGCCTCTTCCG 60.134 52.381 5.23 5.53 31.82 4.30
183 196 1.587547 CATAGAAAGGCCTCTTCCGC 58.412 55.000 5.23 0.00 31.82 5.54
184 197 1.139853 CATAGAAAGGCCTCTTCCGCT 59.860 52.381 5.23 0.00 31.82 5.52
185 198 0.824759 TAGAAAGGCCTCTTCCGCTC 59.175 55.000 5.23 0.00 31.82 5.03
186 199 1.450491 GAAAGGCCTCTTCCGCTCC 60.450 63.158 5.23 0.00 31.82 4.70
187 200 1.904990 GAAAGGCCTCTTCCGCTCCT 61.905 60.000 5.23 0.00 31.82 3.69
188 201 1.904990 AAAGGCCTCTTCCGCTCCTC 61.905 60.000 5.23 0.00 31.82 3.71
189 202 3.855853 GGCCTCTTCCGCTCCTCC 61.856 72.222 0.00 0.00 0.00 4.30
190 203 2.762043 GCCTCTTCCGCTCCTCCT 60.762 66.667 0.00 0.00 0.00 3.69
191 204 2.791868 GCCTCTTCCGCTCCTCCTC 61.792 68.421 0.00 0.00 0.00 3.71
192 205 2.131067 CCTCTTCCGCTCCTCCTCC 61.131 68.421 0.00 0.00 0.00 4.30
247 260 2.755103 CCTTGAAACAATGGAGGCCTAC 59.245 50.000 8.55 8.55 0.00 3.18
291 306 4.468510 TGTTAATCACAACCCTATCTCCGT 59.531 41.667 0.00 0.00 29.87 4.69
357 372 6.226787 AGAATATAAGATTCCAAGCCACTCG 58.773 40.000 0.00 0.00 0.00 4.18
387 406 5.652994 AGCGAAACAGTATCTTTCTCTCT 57.347 39.130 0.00 0.00 0.00 3.10
435 563 2.586838 TGGATCTGGGGGTGAATGAAAT 59.413 45.455 0.00 0.00 0.00 2.17
446 574 4.463891 GGGTGAATGAAATGTCTTCCATGT 59.536 41.667 0.00 0.00 32.82 3.21
521 656 5.348997 GTGACTTTCAGTGGTCATTAGTAGC 59.651 44.000 4.34 0.00 43.07 3.58
522 657 5.011635 TGACTTTCAGTGGTCATTAGTAGCA 59.988 40.000 0.00 0.00 37.52 3.49
525 660 4.188247 TCAGTGGTCATTAGTAGCACAC 57.812 45.455 7.99 0.00 45.49 3.82
526 661 3.576550 TCAGTGGTCATTAGTAGCACACA 59.423 43.478 7.99 0.00 45.49 3.72
535 670 7.387948 GGTCATTAGTAGCACACAATTATAGGG 59.612 40.741 0.00 0.00 0.00 3.53
536 671 7.931948 GTCATTAGTAGCACACAATTATAGGGT 59.068 37.037 0.00 0.00 0.00 4.34
538 673 9.772973 CATTAGTAGCACACAATTATAGGGTTA 57.227 33.333 0.00 0.00 0.00 2.85
577 714 4.216257 GCTAGCACAAGACTTTTCCAATCA 59.784 41.667 10.63 0.00 0.00 2.57
592 729 2.097466 CCAATCAGTTAACCATGTCGGC 59.903 50.000 0.88 0.00 39.03 5.54
653 796 4.492646 TCCTGATATGAGCCATACAGGAA 58.507 43.478 24.15 16.38 43.21 3.36
661 804 5.372343 TGAGCCATACAGGAACAACATAT 57.628 39.130 0.00 0.00 41.22 1.78
691 835 2.901840 CGACGGGGGATGGCATTG 60.902 66.667 0.00 0.00 0.00 2.82
719 863 0.907486 CAGAGACTGGGCAGATTCCA 59.093 55.000 0.00 0.00 0.00 3.53
729 873 0.107214 GCAGATTCCACCGGATTCCA 60.107 55.000 9.46 0.00 33.91 3.53
744 888 4.821805 CGGATTCCAGGTGCAGTTAAATAT 59.178 41.667 3.09 0.00 0.00 1.28
751 895 2.426738 GGTGCAGTTAAATATGCCAGCA 59.573 45.455 0.00 0.00 41.85 4.41
757 901 3.053693 AGTTAAATATGCCAGCACTCCCA 60.054 43.478 0.00 0.00 0.00 4.37
811 955 3.204827 GATGCCAATGCGTCGCCT 61.205 61.111 15.88 0.88 43.20 5.52
814 958 3.430862 GCCAATGCGTCGCCTTCA 61.431 61.111 15.88 0.00 0.00 3.02
884 1028 2.598288 TTCTCCCCTATTAAGCCCCA 57.402 50.000 0.00 0.00 0.00 4.96
948 1104 1.755783 CCAGGGCCAGAGGAATTGC 60.756 63.158 6.18 0.00 0.00 3.56
974 1130 2.821437 TCTTCTCCATCCTTCCTTCGT 58.179 47.619 0.00 0.00 0.00 3.85
996 1159 1.291877 GAGCTTGTGTGCCGTCGATT 61.292 55.000 0.00 0.00 0.00 3.34
1254 1420 4.419957 TCGTCGTCGTCGTCGCTG 62.420 66.667 15.28 2.44 44.86 5.18
1290 1456 2.507944 CCGGAGAAGATGGGCCAG 59.492 66.667 13.78 0.00 0.00 4.85
1317 1483 1.753078 CTCCGACGGACTCATGGGA 60.753 63.158 13.88 0.00 0.00 4.37
1361 1527 4.219944 AGGTGAGTTCGTGTGTGTATGTAT 59.780 41.667 0.00 0.00 0.00 2.29
1369 1539 5.750650 TCGTGTGTGTATGTATGTATACCG 58.249 41.667 0.00 0.00 33.56 4.02
1376 1546 6.015772 TGTGTATGTATGTATACCGTGCTGAT 60.016 38.462 0.00 0.00 33.56 2.90
1387 1557 3.214328 ACCGTGCTGATTTTCTTGAACT 58.786 40.909 0.00 0.00 0.00 3.01
1404 1574 1.856802 ACTGTTCGTTGGTTCGGTAC 58.143 50.000 0.00 0.00 0.00 3.34
1428 1609 3.363970 CCACTGTGACACGCTTCATTAAC 60.364 47.826 9.86 0.00 0.00 2.01
1429 1610 2.806244 ACTGTGACACGCTTCATTAACC 59.194 45.455 0.22 0.00 0.00 2.85
1430 1611 1.795872 TGTGACACGCTTCATTAACCG 59.204 47.619 0.22 0.00 0.00 4.44
1431 1612 1.796459 GTGACACGCTTCATTAACCGT 59.204 47.619 0.00 0.00 0.00 4.83
1433 1614 3.290098 CACGCTTCATTAACCGTGC 57.710 52.632 0.00 0.00 43.40 5.34
1434 1615 0.796312 CACGCTTCATTAACCGTGCT 59.204 50.000 0.00 0.00 43.40 4.40
1435 1616 1.196808 CACGCTTCATTAACCGTGCTT 59.803 47.619 0.00 0.00 43.40 3.91
1436 1617 1.877443 ACGCTTCATTAACCGTGCTTT 59.123 42.857 0.00 0.00 32.07 3.51
1584 1792 2.303022 TCCTCTTAGTTGCTGTCCCAAG 59.697 50.000 0.00 0.00 0.00 3.61
1664 1872 1.689959 GCAACTTGCAACTTCCATCG 58.310 50.000 8.97 0.00 44.26 3.84
1792 2018 3.213206 ACTGAACTTGCAAGTGGATCA 57.787 42.857 31.73 27.25 39.66 2.92
1796 2022 3.503363 TGAACTTGCAAGTGGATCATGAC 59.497 43.478 31.73 14.39 39.66 3.06
1996 2222 1.444553 GTCCAGCCTCTTCGACGTG 60.445 63.158 0.00 0.00 0.00 4.49
2050 2289 3.607209 GCACTTGCACGTAGTAGAAGTAC 59.393 47.826 0.00 0.00 41.61 2.73
2051 2290 4.615452 GCACTTGCACGTAGTAGAAGTACT 60.615 45.833 0.00 0.00 41.61 2.73
2052 2291 5.087397 CACTTGCACGTAGTAGAAGTACTC 58.913 45.833 0.00 0.00 41.61 2.59
2053 2292 4.155644 ACTTGCACGTAGTAGAAGTACTCC 59.844 45.833 0.00 0.00 41.61 3.85
2055 2294 3.277715 GCACGTAGTAGAAGTACTCCCT 58.722 50.000 0.00 0.00 41.61 4.20
2057 2296 3.876320 CACGTAGTAGAAGTACTCCCTCC 59.124 52.174 0.00 0.00 41.61 4.30
2059 2298 3.181471 CGTAGTAGAAGTACTCCCTCCGA 60.181 52.174 0.00 0.00 40.23 4.55
2061 2300 4.089408 AGTAGAAGTACTCCCTCCGATC 57.911 50.000 0.00 0.00 34.00 3.69
2062 2301 2.368311 AGAAGTACTCCCTCCGATCC 57.632 55.000 0.00 0.00 0.00 3.36
2063 2302 1.854280 AGAAGTACTCCCTCCGATCCT 59.146 52.381 0.00 0.00 0.00 3.24
2064 2303 2.245287 AGAAGTACTCCCTCCGATCCTT 59.755 50.000 0.00 0.00 0.00 3.36
2066 2305 3.117552 AGTACTCCCTCCGATCCTTTT 57.882 47.619 0.00 0.00 0.00 2.27
2067 2306 3.451890 AGTACTCCCTCCGATCCTTTTT 58.548 45.455 0.00 0.00 0.00 1.94
2068 2307 4.617593 AGTACTCCCTCCGATCCTTTTTA 58.382 43.478 0.00 0.00 0.00 1.52
2069 2308 3.908643 ACTCCCTCCGATCCTTTTTAC 57.091 47.619 0.00 0.00 0.00 2.01
2070 2309 3.451890 ACTCCCTCCGATCCTTTTTACT 58.548 45.455 0.00 0.00 0.00 2.24
2071 2310 3.451540 ACTCCCTCCGATCCTTTTTACTC 59.548 47.826 0.00 0.00 0.00 2.59
2072 2311 3.707102 CTCCCTCCGATCCTTTTTACTCT 59.293 47.826 0.00 0.00 0.00 3.24
2073 2312 3.451178 TCCCTCCGATCCTTTTTACTCTG 59.549 47.826 0.00 0.00 0.00 3.35
2074 2313 3.198872 CCTCCGATCCTTTTTACTCTGC 58.801 50.000 0.00 0.00 0.00 4.26
2075 2314 3.369471 CCTCCGATCCTTTTTACTCTGCA 60.369 47.826 0.00 0.00 0.00 4.41
2076 2315 3.596214 TCCGATCCTTTTTACTCTGCAC 58.404 45.455 0.00 0.00 0.00 4.57
2077 2316 3.007506 TCCGATCCTTTTTACTCTGCACA 59.992 43.478 0.00 0.00 0.00 4.57
2078 2317 3.941483 CCGATCCTTTTTACTCTGCACAT 59.059 43.478 0.00 0.00 0.00 3.21
2079 2318 4.396166 CCGATCCTTTTTACTCTGCACATT 59.604 41.667 0.00 0.00 0.00 2.71
2080 2319 5.327091 CGATCCTTTTTACTCTGCACATTG 58.673 41.667 0.00 0.00 0.00 2.82
2081 2320 5.644644 GATCCTTTTTACTCTGCACATTGG 58.355 41.667 0.00 0.00 0.00 3.16
2082 2321 4.724399 TCCTTTTTACTCTGCACATTGGA 58.276 39.130 0.00 0.00 0.00 3.53
2083 2322 5.324409 TCCTTTTTACTCTGCACATTGGAT 58.676 37.500 0.00 0.00 0.00 3.41
2084 2323 5.774690 TCCTTTTTACTCTGCACATTGGATT 59.225 36.000 0.00 0.00 0.00 3.01
2085 2324 6.267471 TCCTTTTTACTCTGCACATTGGATTT 59.733 34.615 0.00 0.00 0.00 2.17
2086 2325 6.366877 CCTTTTTACTCTGCACATTGGATTTG 59.633 38.462 0.00 0.00 0.00 2.32
2087 2326 4.439305 TTACTCTGCACATTGGATTTGC 57.561 40.909 0.00 0.00 36.76 3.68
2088 2327 1.547372 ACTCTGCACATTGGATTTGCC 59.453 47.619 0.00 0.00 35.26 4.52
2089 2328 0.527113 TCTGCACATTGGATTTGCCG 59.473 50.000 0.00 0.00 40.66 5.69
2090 2329 0.527113 CTGCACATTGGATTTGCCGA 59.473 50.000 0.00 0.00 40.66 5.54
2091 2330 0.964700 TGCACATTGGATTTGCCGAA 59.035 45.000 0.00 0.00 40.66 4.30
2092 2331 1.342496 TGCACATTGGATTTGCCGAAA 59.658 42.857 0.00 0.00 40.66 3.46
2093 2332 2.224137 TGCACATTGGATTTGCCGAAAA 60.224 40.909 0.00 0.00 40.66 2.29
2094 2333 3.002102 GCACATTGGATTTGCCGAAAAT 58.998 40.909 0.00 0.00 41.33 1.82
2105 2344 4.846779 TTGCCGAAAATCAAACTTAGCT 57.153 36.364 0.00 0.00 0.00 3.32
2106 2345 5.950758 TTGCCGAAAATCAAACTTAGCTA 57.049 34.783 0.00 0.00 0.00 3.32
2107 2346 5.950758 TGCCGAAAATCAAACTTAGCTAA 57.049 34.783 5.94 5.94 0.00 3.09
2108 2347 5.938322 TGCCGAAAATCAAACTTAGCTAAG 58.062 37.500 28.16 28.16 39.18 2.18
2201 2440 7.263100 TCCGAAATGAATCTAATGATGTTGG 57.737 36.000 0.00 0.00 32.44 3.77
2202 2441 6.828273 TCCGAAATGAATCTAATGATGTTGGT 59.172 34.615 0.00 0.00 32.44 3.67
2203 2442 6.914215 CCGAAATGAATCTAATGATGTTGGTG 59.086 38.462 0.00 0.00 32.44 4.17
2204 2443 7.415541 CCGAAATGAATCTAATGATGTTGGTGT 60.416 37.037 0.00 0.00 32.44 4.16
2205 2444 7.970061 CGAAATGAATCTAATGATGTTGGTGTT 59.030 33.333 0.00 0.00 32.44 3.32
2206 2445 8.991243 AAATGAATCTAATGATGTTGGTGTTG 57.009 30.769 0.00 0.00 32.44 3.33
2207 2446 7.707624 ATGAATCTAATGATGTTGGTGTTGT 57.292 32.000 0.00 0.00 32.44 3.32
2208 2447 7.523293 TGAATCTAATGATGTTGGTGTTGTT 57.477 32.000 0.00 0.00 32.44 2.83
2209 2448 8.628630 TGAATCTAATGATGTTGGTGTTGTTA 57.371 30.769 0.00 0.00 32.44 2.41
2210 2449 9.241919 TGAATCTAATGATGTTGGTGTTGTTAT 57.758 29.630 0.00 0.00 32.44 1.89
2211 2450 9.507280 GAATCTAATGATGTTGGTGTTGTTATG 57.493 33.333 0.00 0.00 32.44 1.90
2212 2451 7.994425 TCTAATGATGTTGGTGTTGTTATGT 57.006 32.000 0.00 0.00 0.00 2.29
2213 2452 9.679661 ATCTAATGATGTTGGTGTTGTTATGTA 57.320 29.630 0.00 0.00 0.00 2.29
2214 2453 9.508642 TCTAATGATGTTGGTGTTGTTATGTAA 57.491 29.630 0.00 0.00 0.00 2.41
2217 2456 8.984891 ATGATGTTGGTGTTGTTATGTAAATG 57.015 30.769 0.00 0.00 0.00 2.32
2218 2457 7.946207 TGATGTTGGTGTTGTTATGTAAATGT 58.054 30.769 0.00 0.00 0.00 2.71
2219 2458 8.079203 TGATGTTGGTGTTGTTATGTAAATGTC 58.921 33.333 0.00 0.00 0.00 3.06
2220 2459 7.334844 TGTTGGTGTTGTTATGTAAATGTCA 57.665 32.000 0.00 0.00 0.00 3.58
2221 2460 7.772166 TGTTGGTGTTGTTATGTAAATGTCAA 58.228 30.769 0.00 0.00 0.00 3.18
2222 2461 8.417106 TGTTGGTGTTGTTATGTAAATGTCAAT 58.583 29.630 0.00 0.00 0.00 2.57
2223 2462 9.900710 GTTGGTGTTGTTATGTAAATGTCAATA 57.099 29.630 0.00 0.00 0.00 1.90
2257 2496 3.045601 ACTTGGTCAAAGTCGGATGAG 57.954 47.619 0.00 0.00 46.60 2.90
2258 2497 2.368875 ACTTGGTCAAAGTCGGATGAGT 59.631 45.455 0.00 0.00 46.60 3.41
2259 2498 3.181454 ACTTGGTCAAAGTCGGATGAGTT 60.181 43.478 0.00 0.00 46.60 3.01
2260 2499 3.485463 TGGTCAAAGTCGGATGAGTTT 57.515 42.857 0.00 0.00 46.27 2.66
2267 2506 4.336889 AAGTCGGATGAGTTTGACTTCA 57.663 40.909 0.90 0.00 45.79 3.02
2268 2507 3.919216 AGTCGGATGAGTTTGACTTCAG 58.081 45.455 0.00 0.00 38.48 3.02
2269 2508 3.574396 AGTCGGATGAGTTTGACTTCAGA 59.426 43.478 0.00 0.00 38.48 3.27
2270 2509 3.675698 GTCGGATGAGTTTGACTTCAGAC 59.324 47.826 0.00 0.00 33.08 3.51
2271 2510 3.320826 TCGGATGAGTTTGACTTCAGACA 59.679 43.478 3.03 0.00 33.85 3.41
2272 2511 4.058124 CGGATGAGTTTGACTTCAGACAA 58.942 43.478 3.03 0.00 33.85 3.18
2273 2512 4.511454 CGGATGAGTTTGACTTCAGACAAA 59.489 41.667 3.03 1.04 37.36 2.83
2283 2522 6.985188 TGACTTCAGACAAACCTAATATGC 57.015 37.500 0.00 0.00 0.00 3.14
2284 2523 6.472016 TGACTTCAGACAAACCTAATATGCA 58.528 36.000 0.00 0.00 0.00 3.96
2285 2524 6.595326 TGACTTCAGACAAACCTAATATGCAG 59.405 38.462 0.00 0.00 0.00 4.41
2286 2525 6.711277 ACTTCAGACAAACCTAATATGCAGA 58.289 36.000 0.00 0.00 0.00 4.26
2292 2531 6.096423 AGACAAACCTAATATGCAGAGTACGA 59.904 38.462 0.00 0.00 0.00 3.43
2374 2613 1.377725 CAGGCTGAAACCCGATGCT 60.378 57.895 9.42 0.00 0.00 3.79
2470 2709 4.063967 CTACCGCCGTGCCTGACA 62.064 66.667 0.00 0.00 0.00 3.58
2563 2817 1.037030 TGGCAAATGCGAATCCTCCC 61.037 55.000 0.00 0.00 43.26 4.30
2602 2856 1.398739 GAGCTCAAGATCTCGTCGACA 59.601 52.381 17.16 1.87 0.00 4.35
2699 2968 1.901650 GAGCGAGCAAAAGACCACCG 61.902 60.000 0.00 0.00 0.00 4.94
2700 2969 2.251642 GCGAGCAAAAGACCACCGT 61.252 57.895 0.00 0.00 0.00 4.83
2724 2993 3.804193 GCGGCGGCTGAAAAGAGG 61.804 66.667 14.15 0.00 35.83 3.69
2753 3022 2.480224 AGACGACGACGAAGAACAAA 57.520 45.000 15.32 0.00 42.66 2.83
2812 3091 9.938670 CTACATTAACAGTAGTATGTCAGTCTC 57.061 37.037 8.18 0.00 35.39 3.36
2816 3095 9.682465 ATTAACAGTAGTATGTCAGTCTCAGTA 57.318 33.333 0.00 0.00 31.50 2.74
2888 3172 4.931601 CCATCCTGTATTATCACCATCACG 59.068 45.833 0.00 0.00 0.00 4.35
2891 3175 5.137551 TCCTGTATTATCACCATCACGAGA 58.862 41.667 0.00 0.00 0.00 4.04
3006 3293 0.460459 GGGTCTTTGTCTCTAGCGCC 60.460 60.000 2.29 0.00 0.00 6.53
3051 3350 5.769662 TGAGCTCACAAAATATTCACCTGTT 59.230 36.000 13.74 0.00 0.00 3.16
3052 3351 6.017400 AGCTCACAAAATATTCACCTGTTG 57.983 37.500 0.00 0.00 0.00 3.33
3053 3352 5.536161 AGCTCACAAAATATTCACCTGTTGT 59.464 36.000 0.00 0.00 0.00 3.32
3054 3353 5.630680 GCTCACAAAATATTCACCTGTTGTG 59.369 40.000 16.90 16.90 46.88 3.33
3055 3354 5.527951 TCACAAAATATTCACCTGTTGTGC 58.472 37.500 17.71 0.00 45.03 4.57
3056 3355 4.685628 CACAAAATATTCACCTGTTGTGCC 59.314 41.667 12.90 0.00 45.03 5.01
3057 3356 4.244862 CAAAATATTCACCTGTTGTGCCC 58.755 43.478 0.00 0.00 45.03 5.36
3058 3357 1.750193 ATATTCACCTGTTGTGCCCG 58.250 50.000 0.00 0.00 45.03 6.13
3059 3358 0.958382 TATTCACCTGTTGTGCCCGC 60.958 55.000 0.00 0.00 45.03 6.13
3060 3359 4.947147 TCACCTGTTGTGCCCGCC 62.947 66.667 0.00 0.00 45.03 6.13
3076 3375 1.626654 CGCCGTGGATCACTGACAAC 61.627 60.000 0.00 0.00 31.34 3.32
3079 3378 1.404181 CCGTGGATCACTGACAACGAT 60.404 52.381 10.18 0.00 31.34 3.73
3114 3413 3.194116 ACCGGCTACGTTCAAGATTTCTA 59.806 43.478 0.00 0.00 38.78 2.10
3205 3504 1.746861 CGGAGCTGCATAATTCACCCA 60.747 52.381 5.91 0.00 0.00 4.51
3333 3632 3.334272 GCTCGTTGCTTGTTAACTTGT 57.666 42.857 7.22 0.00 38.95 3.16
3340 3639 3.263261 TGCTTGTTAACTTGTCACGACA 58.737 40.909 7.22 0.00 39.98 4.35
3407 3706 3.053291 GGATGTTCCGGCGTTGCA 61.053 61.111 6.01 1.15 0.00 4.08
3411 3710 3.578272 GTTCCGGCGTTGCACACA 61.578 61.111 6.01 0.00 0.00 3.72
3412 3711 2.593148 TTCCGGCGTTGCACACAT 60.593 55.556 6.01 0.00 0.00 3.21
3413 3712 2.612567 TTCCGGCGTTGCACACATC 61.613 57.895 6.01 0.00 0.00 3.06
3425 3724 5.459762 CGTTGCACACATCAGAATTTCTTTT 59.540 36.000 0.00 0.00 0.00 2.27
3480 3784 3.681835 GCCGTCTCGTCAGGTGGT 61.682 66.667 0.00 0.00 0.00 4.16
3483 3787 1.239296 CCGTCTCGTCAGGTGGTACA 61.239 60.000 0.00 0.00 0.00 2.90
3556 3860 0.250467 ATCGCGCCATTAGCAAGGAT 60.250 50.000 0.00 0.00 44.04 3.24
3557 3861 1.159713 TCGCGCCATTAGCAAGGATG 61.160 55.000 0.00 0.00 44.04 3.51
3558 3862 1.656441 GCGCCATTAGCAAGGATGG 59.344 57.895 0.00 0.00 44.52 3.51
3559 3863 1.799258 GCGCCATTAGCAAGGATGGG 61.799 60.000 0.00 0.00 42.46 4.00
3560 3864 1.174712 CGCCATTAGCAAGGATGGGG 61.175 60.000 5.25 5.25 45.83 4.96
3561 3865 0.185901 GCCATTAGCAAGGATGGGGA 59.814 55.000 4.70 0.00 42.46 4.81
3562 3866 1.203100 GCCATTAGCAAGGATGGGGAT 60.203 52.381 4.70 0.00 42.46 3.85
3563 3867 2.041620 GCCATTAGCAAGGATGGGGATA 59.958 50.000 4.70 0.00 42.46 2.59
3566 3879 5.336102 CCATTAGCAAGGATGGGGATAATT 58.664 41.667 0.00 0.00 39.30 1.40
3577 3890 3.301274 TGGGGATAATTAAAAAGGCGGG 58.699 45.455 0.00 0.00 0.00 6.13
3578 3891 3.302161 GGGGATAATTAAAAAGGCGGGT 58.698 45.455 0.00 0.00 0.00 5.28
3580 3893 3.069016 GGGATAATTAAAAAGGCGGGTGG 59.931 47.826 0.00 0.00 0.00 4.61
3582 3895 1.271856 AATTAAAAAGGCGGGTGGGG 58.728 50.000 0.00 0.00 0.00 4.96
3583 3896 0.410270 ATTAAAAAGGCGGGTGGGGA 59.590 50.000 0.00 0.00 0.00 4.81
3584 3897 0.410270 TTAAAAAGGCGGGTGGGGAT 59.590 50.000 0.00 0.00 0.00 3.85
3585 3898 0.410270 TAAAAAGGCGGGTGGGGATT 59.590 50.000 0.00 0.00 0.00 3.01
3586 3899 0.410270 AAAAAGGCGGGTGGGGATTA 59.590 50.000 0.00 0.00 0.00 1.75
3587 3900 0.033503 AAAAGGCGGGTGGGGATTAG 60.034 55.000 0.00 0.00 0.00 1.73
3588 3901 0.917333 AAAGGCGGGTGGGGATTAGA 60.917 55.000 0.00 0.00 0.00 2.10
3589 3902 0.697854 AAGGCGGGTGGGGATTAGAT 60.698 55.000 0.00 0.00 0.00 1.98
3590 3903 0.697854 AGGCGGGTGGGGATTAGATT 60.698 55.000 0.00 0.00 0.00 2.40
3591 3904 1.061546 GGCGGGTGGGGATTAGATTA 58.938 55.000 0.00 0.00 0.00 1.75
3592 3905 1.003233 GGCGGGTGGGGATTAGATTAG 59.997 57.143 0.00 0.00 0.00 1.73
3593 3906 1.697982 GCGGGTGGGGATTAGATTAGT 59.302 52.381 0.00 0.00 0.00 2.24
3594 3907 2.550208 GCGGGTGGGGATTAGATTAGTG 60.550 54.545 0.00 0.00 0.00 2.74
3595 3908 2.038557 CGGGTGGGGATTAGATTAGTGG 59.961 54.545 0.00 0.00 0.00 4.00
3596 3909 3.323775 GGGTGGGGATTAGATTAGTGGA 58.676 50.000 0.00 0.00 0.00 4.02
3599 3912 4.597507 GGTGGGGATTAGATTAGTGGATGA 59.402 45.833 0.00 0.00 0.00 2.92
3607 3920 8.097662 GGATTAGATTAGTGGATGAGTAAAGGG 58.902 40.741 0.00 0.00 0.00 3.95
3608 3921 8.798975 ATTAGATTAGTGGATGAGTAAAGGGA 57.201 34.615 0.00 0.00 0.00 4.20
3615 3928 4.884164 GTGGATGAGTAAAGGGAAAGGATG 59.116 45.833 0.00 0.00 0.00 3.51
3616 3929 4.788075 TGGATGAGTAAAGGGAAAGGATGA 59.212 41.667 0.00 0.00 0.00 2.92
3627 3940 1.639635 AAAGGATGAGATGCGCCCCT 61.640 55.000 4.18 0.49 0.00 4.79
3642 3955 0.549950 CCCCTCTGCACATGAAGGAT 59.450 55.000 0.00 0.00 0.00 3.24
3644 3957 2.173356 CCCCTCTGCACATGAAGGATTA 59.827 50.000 0.00 0.00 0.00 1.75
3655 3968 9.183368 TGCACATGAAGGATTATTGTTATGTTA 57.817 29.630 0.00 0.00 0.00 2.41
3671 3984 2.485903 TGTTAGTTGACGTGCGGAAAT 58.514 42.857 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 52 9.857957 GTATTATCTACCTTCCACAGCTATTAC 57.142 37.037 0.00 0.00 0.00 1.89
49 57 6.209788 GCTAGTATTATCTACCTTCCACAGCT 59.790 42.308 0.00 0.00 0.00 4.24
182 195 1.305718 ACTGACAGGGAGGAGGAGC 60.306 63.158 7.51 0.00 0.00 4.70
183 196 0.686112 GGACTGACAGGGAGGAGGAG 60.686 65.000 7.51 0.00 0.00 3.69
184 197 1.149782 AGGACTGACAGGGAGGAGGA 61.150 60.000 7.51 0.00 0.00 3.71
185 198 0.975040 CAGGACTGACAGGGAGGAGG 60.975 65.000 7.51 0.00 0.00 4.30
186 199 0.252012 ACAGGACTGACAGGGAGGAG 60.252 60.000 7.51 0.00 0.00 3.69
187 200 0.191064 AACAGGACTGACAGGGAGGA 59.809 55.000 7.51 0.00 0.00 3.71
188 201 1.938585 TAACAGGACTGACAGGGAGG 58.061 55.000 7.51 0.00 0.00 4.30
189 202 4.442192 GCTAATAACAGGACTGACAGGGAG 60.442 50.000 7.51 0.00 0.00 4.30
190 203 3.451178 GCTAATAACAGGACTGACAGGGA 59.549 47.826 7.51 0.00 0.00 4.20
191 204 3.432326 GGCTAATAACAGGACTGACAGGG 60.432 52.174 7.51 0.00 0.00 4.45
192 205 3.197766 TGGCTAATAACAGGACTGACAGG 59.802 47.826 7.51 0.00 0.00 4.00
247 260 6.391227 ACAAAACTCAGAATACAAGGTTGG 57.609 37.500 0.00 0.00 0.00 3.77
279 294 2.966516 GGAGATTCAACGGAGATAGGGT 59.033 50.000 0.00 0.00 0.00 4.34
320 335 5.902681 TCTTATATTCTAGTGCACGCAACT 58.097 37.500 12.01 0.23 0.00 3.16
321 336 6.771188 ATCTTATATTCTAGTGCACGCAAC 57.229 37.500 12.01 0.00 0.00 4.17
322 337 6.423905 GGAATCTTATATTCTAGTGCACGCAA 59.576 38.462 12.01 5.91 0.00 4.85
357 372 0.527565 TACTGTTTCGCTACGTCCCC 59.472 55.000 0.00 0.00 0.00 4.81
387 406 2.294074 AGTTGCGGCAGTAAACAAGAA 58.706 42.857 1.67 0.00 0.00 2.52
435 563 2.103094 GGATGGATCGACATGGAAGACA 59.897 50.000 0.00 0.00 0.00 3.41
446 574 5.079643 TCTACAGATCAATGGATGGATCGA 58.920 41.667 0.00 0.00 43.61 3.59
521 656 8.257306 AGGCAAAAATAACCCTATAATTGTGTG 58.743 33.333 0.00 0.00 0.00 3.82
522 657 8.374184 AGGCAAAAATAACCCTATAATTGTGT 57.626 30.769 0.00 0.00 0.00 3.72
577 714 1.613255 CCAAGGCCGACATGGTTAACT 60.613 52.381 5.42 0.00 41.21 2.24
607 744 1.924731 TATACCCTCGCCTCTCCATG 58.075 55.000 0.00 0.00 0.00 3.66
609 746 1.497716 TCTTATACCCTCGCCTCTCCA 59.502 52.381 0.00 0.00 0.00 3.86
610 747 2.289592 TCTTATACCCTCGCCTCTCC 57.710 55.000 0.00 0.00 0.00 3.71
612 749 3.166679 GGAATCTTATACCCTCGCCTCT 58.833 50.000 0.00 0.00 0.00 3.69
653 796 2.872245 GCCGTCATGCTGTATATGTTGT 59.128 45.455 0.00 0.00 0.00 3.32
661 804 2.202557 CGTCGCCGTCATGCTGTA 60.203 61.111 0.00 0.00 0.00 2.74
719 863 1.779061 AACTGCACCTGGAATCCGGT 61.779 55.000 7.43 8.56 32.45 5.28
729 873 2.689983 GCTGGCATATTTAACTGCACCT 59.310 45.455 0.00 0.00 40.18 4.00
751 895 0.976641 TTCAATCAGACGCTGGGAGT 59.023 50.000 0.00 0.00 31.51 3.85
811 955 4.377370 CACACCTGTGCCGATGAA 57.623 55.556 0.00 0.00 39.39 2.57
884 1028 2.491022 GCGGGGAGACGTAGCATCT 61.491 63.158 0.00 0.00 35.98 2.90
948 1104 3.779738 AGGAAGGATGGAGAAGAAGGAAG 59.220 47.826 0.00 0.00 0.00 3.46
974 1130 1.954146 GACGGCACACAAGCTCGAA 60.954 57.895 0.00 0.00 34.07 3.71
996 1159 2.417257 GCATTTCCTCGCCATGCCA 61.417 57.895 0.00 0.00 37.88 4.92
1086 1252 3.058160 CCAAACAGCCTCAGCCCG 61.058 66.667 0.00 0.00 41.25 6.13
1254 1420 2.419739 GCTCTCCTCCACCGAGACC 61.420 68.421 0.00 0.00 38.52 3.85
1290 1456 2.832201 CCGTCGGAGAGGTACCCC 60.832 72.222 8.74 1.41 41.34 4.95
1308 1474 0.622665 CTTGAGCCCTTCCCATGAGT 59.377 55.000 0.00 0.00 0.00 3.41
1317 1483 2.334006 TCTTCCTCTCTTGAGCCCTT 57.666 50.000 0.00 0.00 38.93 3.95
1361 1527 5.483811 TCAAGAAAATCAGCACGGTATACA 58.516 37.500 5.01 0.00 0.00 2.29
1369 1539 4.672413 CGAACAGTTCAAGAAAATCAGCAC 59.328 41.667 13.82 0.00 0.00 4.40
1376 1546 5.379732 AACCAACGAACAGTTCAAGAAAA 57.620 34.783 13.82 0.00 42.02 2.29
1387 1557 1.214373 GCGTACCGAACCAACGAACA 61.214 55.000 0.00 0.00 38.89 3.18
1404 1574 2.943345 GAAGCGTGTCACAGTGGCG 61.943 63.158 0.00 4.86 0.00 5.69
1428 1609 0.745845 CTCCCAGATCCAAAGCACGG 60.746 60.000 0.00 0.00 0.00 4.94
1429 1610 0.250234 TCTCCCAGATCCAAAGCACG 59.750 55.000 0.00 0.00 0.00 5.34
1430 1611 2.725221 ATCTCCCAGATCCAAAGCAC 57.275 50.000 0.00 0.00 25.75 4.40
1431 1612 6.514012 TTATAATCTCCCAGATCCAAAGCA 57.486 37.500 0.00 0.00 32.89 3.91
1432 1613 7.336427 CAGATTATAATCTCCCAGATCCAAAGC 59.664 40.741 22.54 0.00 43.65 3.51
1433 1614 8.381636 ACAGATTATAATCTCCCAGATCCAAAG 58.618 37.037 22.54 10.82 43.65 2.77
1434 1615 8.159447 CACAGATTATAATCTCCCAGATCCAAA 58.841 37.037 22.54 0.00 43.65 3.28
1435 1616 7.513781 TCACAGATTATAATCTCCCAGATCCAA 59.486 37.037 22.54 0.71 43.65 3.53
1436 1617 7.018769 TCACAGATTATAATCTCCCAGATCCA 58.981 38.462 22.54 0.48 43.65 3.41
1544 1730 3.018856 GGATCCAAACACTCATGCATCA 58.981 45.455 6.95 0.00 0.00 3.07
1584 1792 2.157738 GCCATGCTATCCCTCATCAAC 58.842 52.381 0.00 0.00 0.00 3.18
1664 1872 3.565905 AAATGACAAAGTAGCTGCAGC 57.434 42.857 31.53 31.53 42.49 5.25
1753 1979 6.882610 TCAGTACCGTACCGTTATATGAAT 57.117 37.500 5.02 0.00 0.00 2.57
1761 1987 2.863704 GCAAGTTCAGTACCGTACCGTT 60.864 50.000 5.02 0.00 0.00 4.44
1762 1988 1.336240 GCAAGTTCAGTACCGTACCGT 60.336 52.381 5.02 0.00 0.00 4.83
1764 1990 2.443887 TGCAAGTTCAGTACCGTACC 57.556 50.000 5.02 0.00 0.00 3.34
1765 1991 3.183775 CACTTGCAAGTTCAGTACCGTAC 59.816 47.826 29.23 0.00 37.08 3.67
1766 1992 3.386486 CACTTGCAAGTTCAGTACCGTA 58.614 45.455 29.23 0.00 37.08 4.02
1769 1995 2.846193 TCCACTTGCAAGTTCAGTACC 58.154 47.619 29.23 0.00 37.08 3.34
1782 2008 1.409241 CCCCTGGTCATGATCCACTTG 60.409 57.143 2.86 0.25 0.00 3.16
1792 2018 0.552367 TCCATGGAACCCCTGGTCAT 60.552 55.000 13.46 0.00 33.12 3.06
1796 2022 2.683475 GGTCCATGGAACCCCTGG 59.317 66.667 19.95 1.45 34.22 4.45
1996 2222 0.318784 GATGACGATGAGGCCGTACC 60.319 60.000 0.00 0.00 40.67 3.34
2002 2228 0.103208 AACGAGGATGACGATGAGGC 59.897 55.000 0.00 0.00 34.70 4.70
2050 2289 3.707102 AGAGTAAAAAGGATCGGAGGGAG 59.293 47.826 0.00 0.00 0.00 4.30
2051 2290 3.451178 CAGAGTAAAAAGGATCGGAGGGA 59.549 47.826 0.00 0.00 0.00 4.20
2052 2291 3.798202 CAGAGTAAAAAGGATCGGAGGG 58.202 50.000 0.00 0.00 0.00 4.30
2053 2292 3.198872 GCAGAGTAAAAAGGATCGGAGG 58.801 50.000 0.00 0.00 0.00 4.30
2055 2294 3.007506 TGTGCAGAGTAAAAAGGATCGGA 59.992 43.478 0.00 0.00 0.00 4.55
2057 2296 5.327091 CAATGTGCAGAGTAAAAAGGATCG 58.673 41.667 0.00 0.00 0.00 3.69
2059 2298 5.324409 TCCAATGTGCAGAGTAAAAAGGAT 58.676 37.500 0.00 0.00 0.00 3.24
2061 2300 5.649782 ATCCAATGTGCAGAGTAAAAAGG 57.350 39.130 0.00 0.00 0.00 3.11
2062 2301 6.128742 GCAAATCCAATGTGCAGAGTAAAAAG 60.129 38.462 0.00 0.00 38.19 2.27
2063 2302 5.695816 GCAAATCCAATGTGCAGAGTAAAAA 59.304 36.000 0.00 0.00 38.19 1.94
2064 2303 5.229423 GCAAATCCAATGTGCAGAGTAAAA 58.771 37.500 0.00 0.00 38.19 1.52
2066 2305 3.193267 GGCAAATCCAATGTGCAGAGTAA 59.807 43.478 4.59 0.00 40.12 2.24
2067 2306 2.754552 GGCAAATCCAATGTGCAGAGTA 59.245 45.455 4.59 0.00 40.12 2.59
2068 2307 1.547372 GGCAAATCCAATGTGCAGAGT 59.453 47.619 4.59 0.00 40.12 3.24
2069 2308 1.468565 CGGCAAATCCAATGTGCAGAG 60.469 52.381 4.59 0.00 40.12 3.35
2070 2309 0.527113 CGGCAAATCCAATGTGCAGA 59.473 50.000 4.59 0.00 40.12 4.26
2071 2310 0.527113 TCGGCAAATCCAATGTGCAG 59.473 50.000 4.59 0.65 40.12 4.41
2072 2311 0.964700 TTCGGCAAATCCAATGTGCA 59.035 45.000 4.59 0.00 40.12 4.57
2073 2312 2.077413 TTTCGGCAAATCCAATGTGC 57.923 45.000 0.00 0.00 37.55 4.57
2074 2313 4.845621 GATTTTCGGCAAATCCAATGTG 57.154 40.909 2.22 0.00 43.65 3.21
2082 2321 5.783111 AGCTAAGTTTGATTTTCGGCAAAT 58.217 33.333 0.00 0.00 37.84 2.32
2083 2322 5.195001 AGCTAAGTTTGATTTTCGGCAAA 57.805 34.783 0.00 0.00 0.00 3.68
2084 2323 4.846779 AGCTAAGTTTGATTTTCGGCAA 57.153 36.364 0.00 0.00 0.00 4.52
2085 2324 5.472137 ACTTAGCTAAGTTTGATTTTCGGCA 59.528 36.000 29.48 0.00 43.57 5.69
2086 2325 5.939457 ACTTAGCTAAGTTTGATTTTCGGC 58.061 37.500 29.48 0.00 43.57 5.54
2175 2414 8.355169 CCAACATCATTAGATTCATTTCGGAAT 58.645 33.333 0.00 0.00 40.10 3.01
2176 2415 7.339212 ACCAACATCATTAGATTCATTTCGGAA 59.661 33.333 0.00 0.00 30.20 4.30
2177 2416 6.828273 ACCAACATCATTAGATTCATTTCGGA 59.172 34.615 0.00 0.00 30.20 4.55
2178 2417 6.914215 CACCAACATCATTAGATTCATTTCGG 59.086 38.462 0.00 0.00 30.20 4.30
2179 2418 7.475015 ACACCAACATCATTAGATTCATTTCG 58.525 34.615 0.00 0.00 30.20 3.46
2180 2419 9.079833 CAACACCAACATCATTAGATTCATTTC 57.920 33.333 0.00 0.00 30.20 2.17
2181 2420 8.587608 ACAACACCAACATCATTAGATTCATTT 58.412 29.630 0.00 0.00 30.20 2.32
2182 2421 8.125978 ACAACACCAACATCATTAGATTCATT 57.874 30.769 0.00 0.00 30.20 2.57
2183 2422 7.707624 ACAACACCAACATCATTAGATTCAT 57.292 32.000 0.00 0.00 30.20 2.57
2184 2423 7.523293 AACAACACCAACATCATTAGATTCA 57.477 32.000 0.00 0.00 30.20 2.57
2185 2424 9.507280 CATAACAACACCAACATCATTAGATTC 57.493 33.333 0.00 0.00 30.20 2.52
2186 2425 9.023962 ACATAACAACACCAACATCATTAGATT 57.976 29.630 0.00 0.00 30.20 2.40
2187 2426 8.579850 ACATAACAACACCAACATCATTAGAT 57.420 30.769 0.00 0.00 33.87 1.98
2188 2427 7.994425 ACATAACAACACCAACATCATTAGA 57.006 32.000 0.00 0.00 0.00 2.10
2191 2430 9.421806 CATTTACATAACAACACCAACATCATT 57.578 29.630 0.00 0.00 0.00 2.57
2192 2431 8.584157 ACATTTACATAACAACACCAACATCAT 58.416 29.630 0.00 0.00 0.00 2.45
2193 2432 7.946207 ACATTTACATAACAACACCAACATCA 58.054 30.769 0.00 0.00 0.00 3.07
2194 2433 8.079203 TGACATTTACATAACAACACCAACATC 58.921 33.333 0.00 0.00 0.00 3.06
2195 2434 7.946207 TGACATTTACATAACAACACCAACAT 58.054 30.769 0.00 0.00 0.00 2.71
2196 2435 7.334844 TGACATTTACATAACAACACCAACA 57.665 32.000 0.00 0.00 0.00 3.33
2197 2436 8.810652 ATTGACATTTACATAACAACACCAAC 57.189 30.769 0.00 0.00 0.00 3.77
2227 2466 9.504708 TCCGACTTTGACCAAGTTTATATAAAA 57.495 29.630 9.48 0.00 46.53 1.52
2228 2467 9.675464 ATCCGACTTTGACCAAGTTTATATAAA 57.325 29.630 3.71 3.71 46.53 1.40
2229 2468 9.104965 CATCCGACTTTGACCAAGTTTATATAA 57.895 33.333 0.00 0.00 46.53 0.98
2230 2469 8.479689 TCATCCGACTTTGACCAAGTTTATATA 58.520 33.333 0.00 0.00 46.53 0.86
2231 2470 7.335627 TCATCCGACTTTGACCAAGTTTATAT 58.664 34.615 0.00 0.00 46.53 0.86
2232 2471 6.703319 TCATCCGACTTTGACCAAGTTTATA 58.297 36.000 0.00 0.00 46.53 0.98
2233 2472 5.556915 TCATCCGACTTTGACCAAGTTTAT 58.443 37.500 0.00 0.00 46.53 1.40
2234 2473 4.963373 TCATCCGACTTTGACCAAGTTTA 58.037 39.130 0.00 0.00 46.53 2.01
2235 2474 3.815401 CTCATCCGACTTTGACCAAGTTT 59.185 43.478 0.00 0.00 46.53 2.66
2236 2475 3.181454 ACTCATCCGACTTTGACCAAGTT 60.181 43.478 0.00 0.00 46.53 2.66
2238 2477 3.045601 ACTCATCCGACTTTGACCAAG 57.954 47.619 0.00 0.00 38.64 3.61
2239 2478 3.485463 AACTCATCCGACTTTGACCAA 57.515 42.857 0.00 0.00 0.00 3.67
2240 2479 3.138304 CAAACTCATCCGACTTTGACCA 58.862 45.455 0.00 0.00 30.67 4.02
2241 2480 3.186613 GTCAAACTCATCCGACTTTGACC 59.813 47.826 9.86 0.00 42.77 4.02
2242 2481 4.058817 AGTCAAACTCATCCGACTTTGAC 58.941 43.478 12.19 12.19 45.59 3.18
2243 2482 4.336889 AGTCAAACTCATCCGACTTTGA 57.663 40.909 0.00 0.00 35.18 2.69
2244 2483 4.511454 TGAAGTCAAACTCATCCGACTTTG 59.489 41.667 5.23 0.00 46.04 2.77
2245 2484 4.703897 TGAAGTCAAACTCATCCGACTTT 58.296 39.130 5.23 0.00 46.04 2.66
2247 2486 3.574396 TCTGAAGTCAAACTCATCCGACT 59.426 43.478 0.00 0.00 40.38 4.18
2248 2487 3.675698 GTCTGAAGTCAAACTCATCCGAC 59.324 47.826 0.00 0.00 0.00 4.79
2249 2488 3.320826 TGTCTGAAGTCAAACTCATCCGA 59.679 43.478 0.00 0.00 0.00 4.55
2250 2489 3.653344 TGTCTGAAGTCAAACTCATCCG 58.347 45.455 0.00 0.00 0.00 4.18
2251 2490 5.278022 GGTTTGTCTGAAGTCAAACTCATCC 60.278 44.000 23.08 10.18 46.04 3.51
2252 2491 5.529060 AGGTTTGTCTGAAGTCAAACTCATC 59.471 40.000 23.08 12.57 46.04 2.92
2253 2492 5.440610 AGGTTTGTCTGAAGTCAAACTCAT 58.559 37.500 23.08 12.77 46.04 2.90
2254 2493 4.843728 AGGTTTGTCTGAAGTCAAACTCA 58.156 39.130 23.08 0.00 46.04 3.41
2255 2494 6.920569 TTAGGTTTGTCTGAAGTCAAACTC 57.079 37.500 23.08 16.54 46.04 3.01
2256 2495 9.003658 CATATTAGGTTTGTCTGAAGTCAAACT 57.996 33.333 23.08 15.50 46.04 2.66
2257 2496 7.750903 GCATATTAGGTTTGTCTGAAGTCAAAC 59.249 37.037 18.75 18.75 46.05 2.93
2258 2497 7.446931 TGCATATTAGGTTTGTCTGAAGTCAAA 59.553 33.333 0.00 0.00 32.37 2.69
2259 2498 6.939730 TGCATATTAGGTTTGTCTGAAGTCAA 59.060 34.615 0.00 0.00 0.00 3.18
2260 2499 6.472016 TGCATATTAGGTTTGTCTGAAGTCA 58.528 36.000 0.00 0.00 0.00 3.41
2261 2500 6.818644 TCTGCATATTAGGTTTGTCTGAAGTC 59.181 38.462 0.00 0.00 0.00 3.01
2262 2501 6.711277 TCTGCATATTAGGTTTGTCTGAAGT 58.289 36.000 0.00 0.00 0.00 3.01
2263 2502 6.820656 ACTCTGCATATTAGGTTTGTCTGAAG 59.179 38.462 0.00 0.00 0.00 3.02
2264 2503 6.711277 ACTCTGCATATTAGGTTTGTCTGAA 58.289 36.000 0.00 0.00 0.00 3.02
2265 2504 6.299805 ACTCTGCATATTAGGTTTGTCTGA 57.700 37.500 0.00 0.00 0.00 3.27
2266 2505 6.199154 CGTACTCTGCATATTAGGTTTGTCTG 59.801 42.308 0.00 0.00 0.00 3.51
2267 2506 6.096423 TCGTACTCTGCATATTAGGTTTGTCT 59.904 38.462 0.00 0.00 0.00 3.41
2268 2507 6.198591 GTCGTACTCTGCATATTAGGTTTGTC 59.801 42.308 0.00 0.00 0.00 3.18
2269 2508 6.040878 GTCGTACTCTGCATATTAGGTTTGT 58.959 40.000 0.00 0.00 0.00 2.83
2270 2509 5.462398 GGTCGTACTCTGCATATTAGGTTTG 59.538 44.000 0.00 0.00 0.00 2.93
2271 2510 5.363005 AGGTCGTACTCTGCATATTAGGTTT 59.637 40.000 0.00 0.00 0.00 3.27
2272 2511 4.894114 AGGTCGTACTCTGCATATTAGGTT 59.106 41.667 0.00 0.00 0.00 3.50
2273 2512 4.471548 AGGTCGTACTCTGCATATTAGGT 58.528 43.478 0.00 0.00 0.00 3.08
2274 2513 4.762765 AGAGGTCGTACTCTGCATATTAGG 59.237 45.833 10.11 0.00 45.70 2.69
2275 2514 5.950758 AGAGGTCGTACTCTGCATATTAG 57.049 43.478 10.11 0.00 45.70 1.73
2276 2515 5.241064 GGAAGAGGTCGTACTCTGCATATTA 59.759 44.000 15.65 0.00 46.70 0.98
2277 2516 4.038162 GGAAGAGGTCGTACTCTGCATATT 59.962 45.833 15.65 0.71 46.70 1.28
2278 2517 3.570550 GGAAGAGGTCGTACTCTGCATAT 59.429 47.826 15.65 1.28 46.70 1.78
2279 2518 2.950309 GGAAGAGGTCGTACTCTGCATA 59.050 50.000 15.65 0.00 46.70 3.14
2280 2519 1.751924 GGAAGAGGTCGTACTCTGCAT 59.248 52.381 15.65 1.86 46.70 3.96
2281 2520 1.174783 GGAAGAGGTCGTACTCTGCA 58.825 55.000 15.65 0.00 46.70 4.41
2282 2521 1.465794 AGGAAGAGGTCGTACTCTGC 58.534 55.000 11.33 9.70 46.70 4.26
2283 2522 4.200874 ACATAGGAAGAGGTCGTACTCTG 58.799 47.826 11.33 3.39 46.70 3.35
2285 2524 5.341617 CAAACATAGGAAGAGGTCGTACTC 58.658 45.833 0.00 1.69 37.77 2.59
2286 2525 4.381718 GCAAACATAGGAAGAGGTCGTACT 60.382 45.833 0.00 0.00 29.63 2.73
2292 2531 4.566488 CCTGAAGCAAACATAGGAAGAGGT 60.566 45.833 0.00 0.00 0.00 3.85
2339 2578 4.338539 GTGACGACGCTCGGTGGT 62.339 66.667 11.13 0.00 45.59 4.16
2374 2613 3.755628 GCGTCCACGGAGCTGGTA 61.756 66.667 0.00 0.00 40.23 3.25
2470 2709 2.186384 GAGCAGCTCGGCATCAGT 59.814 61.111 6.67 0.00 35.83 3.41
2710 2979 1.197949 GAAAGACCTCTTTTCAGCCGC 59.802 52.381 1.85 0.00 45.37 6.53
2746 3015 7.637631 AGCTCTTTCTTCTTCTTTTTGTTCT 57.362 32.000 0.00 0.00 0.00 3.01
2749 3018 7.063898 GCAAAAGCTCTTTCTTCTTCTTTTTGT 59.936 33.333 0.00 0.00 33.19 2.83
2750 3019 7.277319 AGCAAAAGCTCTTTCTTCTTCTTTTTG 59.723 33.333 0.00 0.00 33.19 2.44
2753 3022 6.462552 AGCAAAAGCTCTTTCTTCTTCTTT 57.537 33.333 0.00 0.00 31.45 2.52
2812 3091 0.166597 CCAGCAACACACGCATACTG 59.833 55.000 0.00 0.00 0.00 2.74
2816 3095 1.808531 AATGCCAGCAACACACGCAT 61.809 50.000 0.00 0.00 41.77 4.73
2888 3172 1.351350 AGGCCAGTAAAGTTGGGTCTC 59.649 52.381 5.01 0.00 36.19 3.36
2891 3175 4.397919 AATTAGGCCAGTAAAGTTGGGT 57.602 40.909 5.01 0.00 36.19 4.51
2979 3263 1.623811 GAGACAAAGACCCACTGGCTA 59.376 52.381 0.00 0.00 33.59 3.93
3006 3293 4.148825 CTCACCTTCTCCCGCGGG 62.149 72.222 39.13 39.13 0.00 6.13
3010 3297 1.153289 CATGCCTCACCTTCTCCCG 60.153 63.158 0.00 0.00 0.00 5.14
3055 3354 3.770040 TCAGTGATCCACGGCGGG 61.770 66.667 13.24 7.16 39.64 6.13
3056 3355 2.509336 GTCAGTGATCCACGGCGG 60.509 66.667 13.24 0.00 39.64 6.13
3057 3356 1.374125 TTGTCAGTGATCCACGGCG 60.374 57.895 4.80 4.80 39.64 6.46
3058 3357 1.626654 CGTTGTCAGTGATCCACGGC 61.627 60.000 11.78 0.00 39.64 5.68
3059 3358 0.038618 TCGTTGTCAGTGATCCACGG 60.039 55.000 16.89 0.00 39.64 4.94
3060 3359 1.655597 CATCGTTGTCAGTGATCCACG 59.344 52.381 12.91 12.91 39.64 4.94
3061 3360 1.394917 GCATCGTTGTCAGTGATCCAC 59.605 52.381 0.00 0.00 34.10 4.02
3062 3361 1.725641 GCATCGTTGTCAGTGATCCA 58.274 50.000 0.00 0.00 0.00 3.41
3076 3375 2.404789 GTGATTGGCCACGCATCG 59.595 61.111 3.88 0.00 0.00 3.84
3098 3397 9.531942 TTTACTGTTGTAGAAATCTTGAACGTA 57.468 29.630 0.00 0.00 0.00 3.57
3131 3430 7.539712 TCATCATCATCATCATCGATTCATG 57.460 36.000 0.00 1.14 0.00 3.07
3139 3438 7.041984 CCGAACCATATCATCATCATCATCATC 60.042 40.741 0.00 0.00 0.00 2.92
3140 3439 6.766467 CCGAACCATATCATCATCATCATCAT 59.234 38.462 0.00 0.00 0.00 2.45
3141 3440 6.110707 CCGAACCATATCATCATCATCATCA 58.889 40.000 0.00 0.00 0.00 3.07
3142 3441 6.111382 ACCGAACCATATCATCATCATCATC 58.889 40.000 0.00 0.00 0.00 2.92
3143 3442 6.058553 ACCGAACCATATCATCATCATCAT 57.941 37.500 0.00 0.00 0.00 2.45
3333 3632 1.005512 CCACCGTGGATTGTCGTGA 60.006 57.895 12.68 0.00 40.96 4.35
3340 3639 2.671619 CGCCAACCACCGTGGATT 60.672 61.111 24.80 11.49 40.96 3.01
3484 3788 4.142687 CCAAAGCAACGAATTACCACTAGG 60.143 45.833 0.00 0.00 42.21 3.02
3556 3860 3.301274 CCCGCCTTTTTAATTATCCCCA 58.699 45.455 0.00 0.00 0.00 4.96
3557 3861 3.069016 CACCCGCCTTTTTAATTATCCCC 59.931 47.826 0.00 0.00 0.00 4.81
3558 3862 3.069016 CCACCCGCCTTTTTAATTATCCC 59.931 47.826 0.00 0.00 0.00 3.85
3559 3863 3.069016 CCCACCCGCCTTTTTAATTATCC 59.931 47.826 0.00 0.00 0.00 2.59
3560 3864 3.069016 CCCCACCCGCCTTTTTAATTATC 59.931 47.826 0.00 0.00 0.00 1.75
3561 3865 3.035363 CCCCACCCGCCTTTTTAATTAT 58.965 45.455 0.00 0.00 0.00 1.28
3562 3866 2.042706 TCCCCACCCGCCTTTTTAATTA 59.957 45.455 0.00 0.00 0.00 1.40
3563 3867 1.203199 TCCCCACCCGCCTTTTTAATT 60.203 47.619 0.00 0.00 0.00 1.40
3566 3879 0.410270 AATCCCCACCCGCCTTTTTA 59.590 50.000 0.00 0.00 0.00 1.52
3577 3890 5.308237 ACTCATCCACTAATCTAATCCCCAC 59.692 44.000 0.00 0.00 0.00 4.61
3578 3891 5.476983 ACTCATCCACTAATCTAATCCCCA 58.523 41.667 0.00 0.00 0.00 4.96
3580 3893 8.097662 CCTTTACTCATCCACTAATCTAATCCC 58.902 40.741 0.00 0.00 0.00 3.85
3582 3895 8.871125 TCCCTTTACTCATCCACTAATCTAATC 58.129 37.037 0.00 0.00 0.00 1.75
3583 3896 8.798975 TCCCTTTACTCATCCACTAATCTAAT 57.201 34.615 0.00 0.00 0.00 1.73
3584 3897 8.618240 TTCCCTTTACTCATCCACTAATCTAA 57.382 34.615 0.00 0.00 0.00 2.10
3585 3898 8.618240 TTTCCCTTTACTCATCCACTAATCTA 57.382 34.615 0.00 0.00 0.00 1.98
3586 3899 7.366011 CCTTTCCCTTTACTCATCCACTAATCT 60.366 40.741 0.00 0.00 0.00 2.40
3587 3900 6.768381 CCTTTCCCTTTACTCATCCACTAATC 59.232 42.308 0.00 0.00 0.00 1.75
3588 3901 6.447084 TCCTTTCCCTTTACTCATCCACTAAT 59.553 38.462 0.00 0.00 0.00 1.73
3589 3902 5.788533 TCCTTTCCCTTTACTCATCCACTAA 59.211 40.000 0.00 0.00 0.00 2.24
3590 3903 5.347124 TCCTTTCCCTTTACTCATCCACTA 58.653 41.667 0.00 0.00 0.00 2.74
3591 3904 4.175962 TCCTTTCCCTTTACTCATCCACT 58.824 43.478 0.00 0.00 0.00 4.00
3592 3905 4.569719 TCCTTTCCCTTTACTCATCCAC 57.430 45.455 0.00 0.00 0.00 4.02
3593 3906 4.788075 TCATCCTTTCCCTTTACTCATCCA 59.212 41.667 0.00 0.00 0.00 3.41
3594 3907 5.131142 TCTCATCCTTTCCCTTTACTCATCC 59.869 44.000 0.00 0.00 0.00 3.51
3595 3908 6.240549 TCTCATCCTTTCCCTTTACTCATC 57.759 41.667 0.00 0.00 0.00 2.92
3596 3909 6.599445 CATCTCATCCTTTCCCTTTACTCAT 58.401 40.000 0.00 0.00 0.00 2.90
3599 3912 4.684485 CGCATCTCATCCTTTCCCTTTACT 60.684 45.833 0.00 0.00 0.00 2.24
3607 3920 1.169034 GGGGCGCATCTCATCCTTTC 61.169 60.000 10.83 0.00 0.00 2.62
3608 3921 1.152881 GGGGCGCATCTCATCCTTT 60.153 57.895 10.83 0.00 0.00 3.11
3615 3928 4.166888 TGCAGAGGGGCGCATCTC 62.167 66.667 15.63 15.30 36.28 2.75
3616 3929 4.479993 GTGCAGAGGGGCGCATCT 62.480 66.667 12.63 12.63 43.57 2.90
3627 3940 7.557358 ACATAACAATAATCCTTCATGTGCAGA 59.443 33.333 0.00 0.00 0.00 4.26
3642 3955 6.401260 CCGCACGTCAACTAACATAACAATAA 60.401 38.462 0.00 0.00 0.00 1.40
3644 3957 4.142988 CCGCACGTCAACTAACATAACAAT 60.143 41.667 0.00 0.00 0.00 2.71
3655 3968 0.534203 ACCATTTCCGCACGTCAACT 60.534 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.