Multiple sequence alignment - TraesCS2D01G476200

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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 TraesCS2D01G476200 chr2D 100.000 5345 0 0 1 5345 578698311 578703655 0.000000e+00 9871
1 TraesCS2D01G476200 chr2B 92.698 2876 144 31 2490 5345 695591710 695594539 0.000000e+00 4087
2 TraesCS2D01G476200 chr2B 93.680 1788 93 11 1 1773 695589207 695590989 0.000000e+00 2658
3 TraesCS2D01G476200 chr2B 88.922 334 27 6 2122 2446 695591372 695591704 2.320000e-108 403
4 TraesCS2D01G476200 chr2B 90.435 230 17 3 1813 2037 695591141 695591370 1.130000e-76 298
5 TraesCS2D01G476200 chr2B 92.157 102 6 2 2026 2125 756555468 756555367 5.580000e-30 143
6 TraesCS2D01G476200 chr2B 91.262 103 8 1 2024 2126 731610533 731610634 7.220000e-29 139
7 TraesCS2D01G476200 chr2A 92.684 2064 125 12 2483 4539 716231760 716233804 0.000000e+00 2952
8 TraesCS2D01G476200 chr2A 93.768 1781 92 11 1 1768 716229271 716231045 0.000000e+00 2656
9 TraesCS2D01G476200 chr2A 90.332 331 29 2 2120 2447 716231432 716231762 1.060000e-116 431
10 TraesCS2D01G476200 chr2A 81.873 502 28 24 4873 5345 716234035 716234502 1.090000e-96 364
11 TraesCS2D01G476200 chr2A 93.304 224 10 4 4632 4855 716233828 716234046 5.160000e-85 326
12 TraesCS2D01G476200 chr2A 91.775 231 15 2 1813 2039 716231204 716231434 8.640000e-83 318
13 TraesCS2D01G476200 chr4A 97.753 89 2 0 2037 2125 614251515 614251427 2.580000e-33 154
14 TraesCS2D01G476200 chr7B 95.745 94 3 1 2034 2126 460585042 460584949 3.330000e-32 150
15 TraesCS2D01G476200 chr7B 95.604 91 4 0 2035 2125 654925856 654925766 4.310000e-31 147
16 TraesCS2D01G476200 chr3B 95.745 94 2 1 2038 2131 187335764 187335673 3.330000e-32 150
17 TraesCS2D01G476200 chrUn 97.674 86 2 0 2037 2122 119047542 119047627 1.200000e-31 148
18 TraesCS2D01G476200 chr6B 94.681 94 5 0 2030 2123 218219332 218219425 4.310000e-31 147
19 TraesCS2D01G476200 chr6A 94.624 93 5 0 2037 2129 101438363 101438271 1.550000e-30 145


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 TraesCS2D01G476200 chr2D 578698311 578703655 5344 False 9871.0 9871 100.000000 1 5345 1 chr2D.!!$F1 5344
1 TraesCS2D01G476200 chr2B 695589207 695594539 5332 False 1861.5 4087 91.433750 1 5345 4 chr2B.!!$F2 5344
2 TraesCS2D01G476200 chr2A 716229271 716234502 5231 False 1174.5 2952 90.622667 1 5345 6 chr2A.!!$F1 5344

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
182 183 0.256752 TGGGAGATGTGGCATTGGAG 59.743 55.0 0.0 0.0 0.0 3.86 F
2050 2200 0.042881 AACTGGTACTCCCTCCCTCC 59.957 60.0 0.0 0.0 0.0 4.30 F
2227 2377 0.036388 ACATCCACGCTAACCACAGG 60.036 55.0 0.0 0.0 0.0 4.00 F
3255 3415 0.100861 GAGACGGGTTGAGATCGGTC 59.899 60.0 0.0 0.0 34.7 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2256 0.635009 AATCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37 R
3282 3442 0.251742 TGGCATCAGAAAAGGGTGGG 60.252 55.000 0.00 0.00 0.00 4.61 R
3536 3696 1.000385 GCTTAGGTGTGCATGCAAACA 60.000 47.619 35.64 22.66 35.94 2.83 R
4392 4556 0.038166 ACAATACCCACAGGCCACAG 59.962 55.000 5.01 0.00 36.11 3.66 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
170 171 2.235402 CAAAAAGCAGCCAATGGGAGAT 59.765 45.455 0.00 0.00 35.59 2.75
182 183 0.256752 TGGGAGATGTGGCATTGGAG 59.743 55.000 0.00 0.00 0.00 3.86
209 210 6.761242 ACGCTCTAGTTGATATGTATGCAAAA 59.239 34.615 0.00 0.00 0.00 2.44
215 216 5.887598 AGTTGATATGTATGCAAAAGCAGGA 59.112 36.000 0.00 0.00 0.00 3.86
345 346 3.181440 TGTGAGCCTTTTTGAGAGGATGT 60.181 43.478 0.00 0.00 36.33 3.06
371 372 0.951558 ATGGTGTGAAGCCAAACGAC 59.048 50.000 0.00 0.00 39.72 4.34
418 419 2.839486 TGTGGTCATTCTGGTCTGAC 57.161 50.000 0.00 0.00 40.82 3.51
419 420 2.046292 TGTGGTCATTCTGGTCTGACA 58.954 47.619 10.38 0.00 42.83 3.58
487 488 4.492494 TTGATCCAAGAGCTGAGCATTA 57.508 40.909 7.39 0.00 0.00 1.90
518 519 2.747686 GACCTTCTTGGCCGTGGA 59.252 61.111 0.00 0.00 40.22 4.02
549 550 1.432270 GGATGCGTGGAAGCTAGTGC 61.432 60.000 0.00 0.00 38.13 4.40
654 655 3.893813 AGAAACTGCAGCCAAGAATCTTT 59.106 39.130 15.27 3.03 0.00 2.52
764 765 6.670695 ACAAGGAAATTAATGGCTGAAACT 57.329 33.333 0.00 0.00 0.00 2.66
794 795 0.536006 AGGAAGCTGGTTGCAGTGTC 60.536 55.000 13.45 0.00 45.94 3.67
805 806 2.999355 GTTGCAGTGTCCTCTGAAGATC 59.001 50.000 0.78 0.00 37.61 2.75
807 808 2.634453 TGCAGTGTCCTCTGAAGATCAA 59.366 45.455 0.00 0.00 37.61 2.57
869 870 3.548745 TTGTCCTGATAGATGCACCAG 57.451 47.619 0.00 0.00 0.00 4.00
938 940 1.555075 TCCAACATGTAGAGCCTCCAC 59.445 52.381 0.00 0.00 0.00 4.02
949 951 3.944087 AGAGCCTCCACATCTTTGTAAC 58.056 45.455 0.00 0.00 33.76 2.50
965 967 5.733620 TTGTAACCTCTAACCGACTTCAT 57.266 39.130 0.00 0.00 0.00 2.57
972 974 6.807789 ACCTCTAACCGACTTCATAATCTTC 58.192 40.000 0.00 0.00 0.00 2.87
976 978 3.112263 ACCGACTTCATAATCTTCCCCA 58.888 45.455 0.00 0.00 0.00 4.96
995 997 4.337555 CCCCATTTGATTAAGCAGTGAGAG 59.662 45.833 9.05 0.39 0.00 3.20
1025 1027 3.630769 ACTTATCAGCAGCCATCATGTTG 59.369 43.478 0.00 0.00 0.00 3.33
1086 1096 9.744468 AACTTTTGTATAGTTGTTCATTTGGAC 57.256 29.630 0.00 0.00 34.68 4.02
1088 1098 9.180678 CTTTTGTATAGTTGTTCATTTGGACAC 57.819 33.333 0.00 0.00 0.00 3.67
1099 1109 1.327303 TTTGGACACATCTGTTGGGC 58.673 50.000 0.00 0.00 28.72 5.36
1104 1114 2.076863 GACACATCTGTTGGGCTACAC 58.923 52.381 0.00 0.00 28.72 2.90
1174 1184 3.251729 GCGGATGCATGTTTGACTCATAT 59.748 43.478 2.46 0.00 42.15 1.78
1203 1213 6.358974 TGTCAGTATTCTCAATTCTGTCCA 57.641 37.500 3.64 0.86 37.50 4.02
1204 1214 6.768483 TGTCAGTATTCTCAATTCTGTCCAA 58.232 36.000 3.64 0.00 37.50 3.53
1206 1216 7.884877 TGTCAGTATTCTCAATTCTGTCCAATT 59.115 33.333 3.64 0.00 37.50 2.32
1240 1250 6.592994 GGACAGTTACAGGTTTATGGTCTTAC 59.407 42.308 0.00 0.00 0.00 2.34
1270 1283 2.936919 ACTCCAACTTGTCTGCATCA 57.063 45.000 0.00 0.00 0.00 3.07
1271 1284 3.213206 ACTCCAACTTGTCTGCATCAA 57.787 42.857 0.00 0.00 0.00 2.57
1272 1285 3.759581 ACTCCAACTTGTCTGCATCAAT 58.240 40.909 5.21 0.00 0.00 2.57
1348 1362 7.914427 TTCCCTTCTGTACATGACTATATGT 57.086 36.000 0.00 0.00 43.34 2.29
1368 1382 3.181453 TGTCGATACCCTGTTTTTCCACA 60.181 43.478 0.00 0.00 0.00 4.17
1377 1391 3.432252 CCTGTTTTTCCACACTACGCTAG 59.568 47.826 0.00 0.00 0.00 3.42
1401 1415 5.127682 GCCATTTCTCTTTTGATGTGGGTAT 59.872 40.000 0.00 0.00 0.00 2.73
1492 1507 4.455533 TGTTGAATCTGACAGTGCCAATAC 59.544 41.667 1.59 0.00 0.00 1.89
1523 1538 5.372343 TGATCTATTGCATACCCTGTGTT 57.628 39.130 0.00 0.00 0.00 3.32
1586 1601 0.249280 CCAAAAGCCACCACGTTTCC 60.249 55.000 0.00 0.00 0.00 3.13
1658 1674 7.596995 TGACTTAAGTTTTGTTTGTTGAGTTGG 59.403 33.333 10.02 0.00 0.00 3.77
1672 1688 8.441312 TTGTTGAGTTGGTTTACCTAGTAAAG 57.559 34.615 0.30 0.00 38.44 1.85
1792 1937 8.400184 TCAGTACTGTAGCATAATACGGTTAT 57.600 34.615 21.99 0.00 41.46 1.89
1797 1942 8.813643 ACTGTAGCATAATACGGTTATTCTTC 57.186 34.615 0.00 0.00 41.46 2.87
1798 1943 8.639761 ACTGTAGCATAATACGGTTATTCTTCT 58.360 33.333 0.00 0.00 41.46 2.85
1799 1944 9.477484 CTGTAGCATAATACGGTTATTCTTCTT 57.523 33.333 0.00 0.00 0.00 2.52
1800 1945 9.826574 TGTAGCATAATACGGTTATTCTTCTTT 57.173 29.630 0.00 0.00 0.00 2.52
1802 1947 8.958119 AGCATAATACGGTTATTCTTCTTTCA 57.042 30.769 0.00 0.00 0.00 2.69
1803 1948 8.827677 AGCATAATACGGTTATTCTTCTTTCAC 58.172 33.333 0.00 0.00 0.00 3.18
1804 1949 8.609176 GCATAATACGGTTATTCTTCTTTCACA 58.391 33.333 0.00 0.00 0.00 3.58
1811 1956 9.840427 ACGGTTATTCTTCTTTCACATTATTTG 57.160 29.630 0.00 0.00 0.00 2.32
1909 2058 4.991687 AGCTAGCAACTTACAGTTCAAGTC 59.008 41.667 18.83 0.00 36.03 3.01
1932 2082 6.642540 GTCTTTGATTTGGCACTTTTAGGAAG 59.357 38.462 0.00 0.00 0.00 3.46
1937 2087 3.439857 TGGCACTTTTAGGAAGATGCT 57.560 42.857 0.00 0.00 33.57 3.79
1954 2104 5.911752 AGATGCTGTAGTCACATCTTAAGG 58.088 41.667 1.85 0.00 46.38 2.69
1959 2109 5.147330 TGTAGTCACATCTTAAGGGTGTG 57.853 43.478 24.20 24.20 43.41 3.82
1993 2143 2.203209 GGGCCACGATGGATGGTC 60.203 66.667 4.39 0.00 40.96 4.02
2020 2170 6.938596 TCATTCATCCAATATCTGTTGGCTAG 59.061 38.462 1.13 0.00 46.58 3.42
2040 2190 6.864360 CTAGAATAGCTCGTAACTGGTACT 57.136 41.667 0.85 0.00 0.00 2.73
2041 2191 5.754543 AGAATAGCTCGTAACTGGTACTC 57.245 43.478 0.85 0.00 0.00 2.59
2042 2192 4.579753 AGAATAGCTCGTAACTGGTACTCC 59.420 45.833 0.85 0.00 0.00 3.85
2043 2193 1.472188 AGCTCGTAACTGGTACTCCC 58.528 55.000 0.85 0.00 0.00 4.30
2044 2194 1.005687 AGCTCGTAACTGGTACTCCCT 59.994 52.381 0.85 0.00 0.00 4.20
2045 2195 1.404748 GCTCGTAACTGGTACTCCCTC 59.595 57.143 0.85 0.00 0.00 4.30
2046 2196 2.022934 CTCGTAACTGGTACTCCCTCC 58.977 57.143 0.85 0.00 0.00 4.30
2047 2197 1.109609 CGTAACTGGTACTCCCTCCC 58.890 60.000 0.85 0.00 0.00 4.30
2048 2198 1.341778 CGTAACTGGTACTCCCTCCCT 60.342 57.143 0.85 0.00 0.00 4.20
2049 2199 2.386779 GTAACTGGTACTCCCTCCCTC 58.613 57.143 0.00 0.00 0.00 4.30
2050 2200 0.042881 AACTGGTACTCCCTCCCTCC 59.957 60.000 0.00 0.00 0.00 4.30
2051 2201 1.075151 CTGGTACTCCCTCCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
2052 2202 1.865045 TGGTACTCCCTCCCTCCCA 60.865 63.158 0.00 0.00 0.00 4.37
2053 2203 1.236026 TGGTACTCCCTCCCTCCCAT 61.236 60.000 0.00 0.00 0.00 4.00
2054 2204 0.865362 GGTACTCCCTCCCTCCCATA 59.135 60.000 0.00 0.00 0.00 2.74
2055 2205 1.222298 GGTACTCCCTCCCTCCCATAA 59.778 57.143 0.00 0.00 0.00 1.90
2056 2206 2.157989 GGTACTCCCTCCCTCCCATAAT 60.158 54.545 0.00 0.00 0.00 1.28
2057 2207 2.124560 ACTCCCTCCCTCCCATAATG 57.875 55.000 0.00 0.00 0.00 1.90
2058 2208 1.298382 ACTCCCTCCCTCCCATAATGT 59.702 52.381 0.00 0.00 0.00 2.71
2059 2209 2.527057 ACTCCCTCCCTCCCATAATGTA 59.473 50.000 0.00 0.00 0.00 2.29
2060 2210 3.050564 ACTCCCTCCCTCCCATAATGTAA 60.051 47.826 0.00 0.00 0.00 2.41
2061 2211 3.584848 CTCCCTCCCTCCCATAATGTAAG 59.415 52.174 0.00 0.00 0.00 2.34
2062 2212 3.211232 TCCCTCCCTCCCATAATGTAAGA 59.789 47.826 0.00 0.00 0.00 2.10
2063 2213 3.328050 CCCTCCCTCCCATAATGTAAGAC 59.672 52.174 0.00 0.00 0.00 3.01
2064 2214 3.006967 CCTCCCTCCCATAATGTAAGACG 59.993 52.174 0.00 0.00 0.00 4.18
2065 2215 3.641906 CTCCCTCCCATAATGTAAGACGT 59.358 47.826 0.00 0.00 0.00 4.34
2066 2216 4.035112 TCCCTCCCATAATGTAAGACGTT 58.965 43.478 0.00 0.00 0.00 3.99
2067 2217 4.472108 TCCCTCCCATAATGTAAGACGTTT 59.528 41.667 0.00 0.00 0.00 3.60
2068 2218 5.045432 TCCCTCCCATAATGTAAGACGTTTT 60.045 40.000 0.00 0.00 0.00 2.43
2069 2219 5.650703 CCCTCCCATAATGTAAGACGTTTTT 59.349 40.000 0.00 0.00 0.00 1.94
2114 2264 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2115 2265 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2116 2266 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2117 2267 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2118 2268 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2119 2269 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2120 2270 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2130 2280 2.885894 GACGGAGGGAGTAGATTACAGG 59.114 54.545 0.00 0.00 0.00 4.00
2131 2281 1.614413 CGGAGGGAGTAGATTACAGGC 59.386 57.143 0.00 0.00 0.00 4.85
2145 2295 0.698818 ACAGGCCCTTAACTTCTGGG 59.301 55.000 0.00 0.00 43.62 4.45
2154 2304 2.561478 TAACTTCTGGGACACTTGCC 57.439 50.000 0.00 0.00 0.00 4.52
2164 2314 1.616725 GGACACTTGCCATCCCATCAA 60.617 52.381 0.00 0.00 0.00 2.57
2197 2347 3.300388 TGCCTCATCCGAGACTATTCTT 58.700 45.455 0.00 0.00 42.34 2.52
2207 2357 6.936279 TCCGAGACTATTCTTCAATTCTTGT 58.064 36.000 0.00 0.00 29.47 3.16
2227 2377 0.036388 ACATCCACGCTAACCACAGG 60.036 55.000 0.00 0.00 0.00 4.00
2293 2443 2.800881 TCTACTGGCTGCGTGATATG 57.199 50.000 0.00 0.00 0.00 1.78
2299 2449 2.543012 CTGGCTGCGTGATATGAGAAAG 59.457 50.000 0.00 0.00 0.00 2.62
2312 2462 7.976734 GTGATATGAGAAAGTAGTACAGCTGTT 59.023 37.037 27.06 10.85 0.00 3.16
2314 2464 9.672086 GATATGAGAAAGTAGTACAGCTGTTAG 57.328 37.037 27.06 0.00 0.00 2.34
2318 2468 1.749634 AGTAGTACAGCTGTTAGGGCG 59.250 52.381 27.06 0.00 34.52 6.13
2325 2475 0.903454 AGCTGTTAGGGCGTGTAGGT 60.903 55.000 0.00 0.00 34.52 3.08
2333 2483 2.532843 AGGGCGTGTAGGTTTCTAGAA 58.467 47.619 0.00 0.00 0.00 2.10
2358 2508 9.601217 AACCACTATACTAATACTGAGCAAAAG 57.399 33.333 0.00 0.00 0.00 2.27
2360 2510 7.171678 CCACTATACTAATACTGAGCAAAAGGC 59.828 40.741 0.00 0.00 45.30 4.35
2385 2536 5.584649 TGGCTTACTATCACTTATGTGCAAC 59.415 40.000 3.90 0.00 43.49 4.17
2418 2576 4.020218 TGAACTATAAAGCAGGCTGTGAGT 60.020 41.667 17.16 7.67 0.00 3.41
2431 2589 3.580731 GCTGTGAGTTCTAGTTCACCTC 58.419 50.000 16.47 8.66 42.30 3.85
2440 2598 7.939039 TGAGTTCTAGTTCACCTCAAAAATCAT 59.061 33.333 0.00 0.00 0.00 2.45
2447 2605 6.550854 AGTTCACCTCAAAAATCATCAAGGAA 59.449 34.615 0.00 0.00 0.00 3.36
2448 2606 6.579666 TCACCTCAAAAATCATCAAGGAAG 57.420 37.500 0.00 0.00 0.00 3.46
2449 2607 5.047802 TCACCTCAAAAATCATCAAGGAAGC 60.048 40.000 0.00 0.00 0.00 3.86
2450 2608 4.834496 ACCTCAAAAATCATCAAGGAAGCA 59.166 37.500 0.00 0.00 0.00 3.91
2451 2609 5.305128 ACCTCAAAAATCATCAAGGAAGCAA 59.695 36.000 0.00 0.00 0.00 3.91
2452 2610 5.636543 CCTCAAAAATCATCAAGGAAGCAAC 59.363 40.000 0.00 0.00 0.00 4.17
2453 2611 6.409524 TCAAAAATCATCAAGGAAGCAACT 57.590 33.333 0.00 0.00 0.00 3.16
2454 2612 6.449698 TCAAAAATCATCAAGGAAGCAACTC 58.550 36.000 0.00 0.00 0.00 3.01
2455 2613 5.397142 AAAATCATCAAGGAAGCAACTCC 57.603 39.130 0.00 0.00 35.51 3.85
2456 2614 3.726557 ATCATCAAGGAAGCAACTCCA 57.273 42.857 2.75 0.00 38.02 3.86
2457 2615 2.783135 TCATCAAGGAAGCAACTCCAC 58.217 47.619 2.75 0.00 38.02 4.02
2458 2616 1.815003 CATCAAGGAAGCAACTCCACC 59.185 52.381 2.75 0.00 38.02 4.61
2459 2617 0.250295 TCAAGGAAGCAACTCCACCG 60.250 55.000 2.75 0.00 38.02 4.94
2460 2618 1.600916 AAGGAAGCAACTCCACCGC 60.601 57.895 2.75 0.00 38.02 5.68
2461 2619 2.032681 GGAAGCAACTCCACCGCT 59.967 61.111 0.00 0.00 37.68 5.52
2462 2620 2.328099 GGAAGCAACTCCACCGCTG 61.328 63.158 0.00 0.00 35.79 5.18
2463 2621 1.598130 GAAGCAACTCCACCGCTGT 60.598 57.895 0.00 0.00 35.79 4.40
2464 2622 0.320421 GAAGCAACTCCACCGCTGTA 60.320 55.000 0.00 0.00 35.79 2.74
2465 2623 0.320771 AAGCAACTCCACCGCTGTAG 60.321 55.000 0.00 0.00 35.79 2.74
2466 2624 2.391389 GCAACTCCACCGCTGTAGC 61.391 63.158 0.00 0.00 37.78 3.58
2467 2625 1.293498 CAACTCCACCGCTGTAGCT 59.707 57.895 2.04 0.00 39.32 3.32
2468 2626 0.530744 CAACTCCACCGCTGTAGCTA 59.469 55.000 2.04 0.00 39.32 3.32
2469 2627 0.818296 AACTCCACCGCTGTAGCTAG 59.182 55.000 0.00 0.00 39.32 3.42
2470 2628 1.038130 ACTCCACCGCTGTAGCTAGG 61.038 60.000 0.00 0.00 39.32 3.02
2471 2629 1.739338 CTCCACCGCTGTAGCTAGGG 61.739 65.000 0.00 0.00 39.32 3.53
2474 2632 3.630289 CCGCTGTAGCTAGGGGTT 58.370 61.111 10.72 0.00 43.63 4.11
2475 2633 1.144057 CCGCTGTAGCTAGGGGTTG 59.856 63.158 10.72 0.00 43.63 3.77
2476 2634 1.614241 CCGCTGTAGCTAGGGGTTGT 61.614 60.000 10.72 0.00 43.63 3.32
2477 2635 1.108776 CGCTGTAGCTAGGGGTTGTA 58.891 55.000 0.00 0.00 39.32 2.41
2478 2636 1.202382 CGCTGTAGCTAGGGGTTGTAC 60.202 57.143 0.00 0.00 39.32 2.90
2479 2637 1.829222 GCTGTAGCTAGGGGTTGTACA 59.171 52.381 0.00 0.00 38.21 2.90
2480 2638 2.434702 GCTGTAGCTAGGGGTTGTACAT 59.565 50.000 0.00 0.00 38.21 2.29
2481 2639 3.118371 GCTGTAGCTAGGGGTTGTACATT 60.118 47.826 0.00 0.00 38.21 2.71
2482 2640 4.442706 CTGTAGCTAGGGGTTGTACATTG 58.557 47.826 0.00 0.00 0.00 2.82
2483 2641 3.199071 TGTAGCTAGGGGTTGTACATTGG 59.801 47.826 0.00 0.00 0.00 3.16
2484 2642 2.557869 AGCTAGGGGTTGTACATTGGA 58.442 47.619 0.00 0.00 0.00 3.53
2485 2643 2.238898 AGCTAGGGGTTGTACATTGGAC 59.761 50.000 0.00 0.00 0.00 4.02
2486 2644 2.026636 GCTAGGGGTTGTACATTGGACA 60.027 50.000 0.00 0.00 0.00 4.02
2487 2645 2.579410 AGGGGTTGTACATTGGACAC 57.421 50.000 0.00 0.00 0.00 3.67
2488 2646 1.161843 GGGGTTGTACATTGGACACG 58.838 55.000 0.00 0.00 0.00 4.49
2493 2651 1.507562 TGTACATTGGACACGCACAG 58.492 50.000 0.00 0.00 0.00 3.66
2527 2685 4.469586 AGACTCCTCTTTGGATTTCTCCTC 59.530 45.833 0.00 0.00 45.16 3.71
2534 2692 4.226168 TCTTTGGATTTCTCCTCCCTCTTC 59.774 45.833 0.00 0.00 42.59 2.87
2537 2695 2.703536 GGATTTCTCCTCCCTCTTCTCC 59.296 54.545 0.00 0.00 38.65 3.71
2541 2699 1.491332 TCTCCTCCCTCTTCTCCTACG 59.509 57.143 0.00 0.00 0.00 3.51
2558 2716 3.631227 CCTACGACCCTCCTTAGTGTTAG 59.369 52.174 0.00 0.00 0.00 2.34
2561 2719 1.136500 GACCCTCCTTAGTGTTAGGCG 59.864 57.143 0.00 0.00 32.59 5.52
2573 2731 0.824759 GTTAGGCGATCCACCAGAGT 59.175 55.000 2.46 0.00 33.74 3.24
2605 2763 3.194542 GCTTTTACCAATACACATGCCCA 59.805 43.478 0.00 0.00 0.00 5.36
2610 2768 4.183223 ACCAATACACATGCCCATATGT 57.817 40.909 1.24 0.00 41.77 2.29
2635 2793 4.186926 AGGTCATTGTTCGTGATGAGATG 58.813 43.478 0.00 0.00 33.27 2.90
2665 2823 2.852075 TCCCACGTCCCAAGCCTT 60.852 61.111 0.00 0.00 0.00 4.35
2670 2828 3.741476 CGTCCCAAGCCTTGCTGC 61.741 66.667 0.00 0.00 39.62 5.25
2710 2868 3.945285 ACTTCCACGACTGTTTTGTGAAT 59.055 39.130 9.43 0.00 41.77 2.57
2733 2891 1.599542 GTGCACACACCTTTGTCTCTC 59.400 52.381 13.17 0.00 41.21 3.20
2736 2894 2.760374 CACACACCTTTGTCTCTCCTC 58.240 52.381 0.00 0.00 31.66 3.71
2807 2965 3.709653 AGGGTTGCGATGGTTCTATTCTA 59.290 43.478 0.00 0.00 0.00 2.10
2858 3016 3.790089 AAGGAATCAGAACCGAACCTT 57.210 42.857 0.00 0.00 33.72 3.50
2951 3109 3.577848 CCTGTGCTGATATCCTAGCTCTT 59.422 47.826 14.24 0.00 40.52 2.85
3008 3166 8.299570 ACTAGCAGTTCTGTTCATTAATTTTGG 58.700 33.333 1.78 0.00 0.00 3.28
3054 3213 8.862325 AGTTGACATAGTTCATAAAATGGTGA 57.138 30.769 0.00 0.00 0.00 4.02
3056 3215 8.730680 GTTGACATAGTTCATAAAATGGTGAGT 58.269 33.333 0.00 0.00 0.00 3.41
3071 3231 7.862274 AATGGTGAGTATAGGATGATTCAGA 57.138 36.000 0.00 0.00 0.00 3.27
3078 3238 7.060383 AGTATAGGATGATTCAGACCAACAG 57.940 40.000 12.90 0.00 0.00 3.16
3106 3266 3.938334 GCAAAACCCACACATTTTTGACT 59.062 39.130 9.60 0.00 40.96 3.41
3108 3268 2.888834 ACCCACACATTTTTGACTGC 57.111 45.000 0.00 0.00 0.00 4.40
3113 3273 3.181477 CCACACATTTTTGACTGCCTTCA 60.181 43.478 0.00 0.00 0.00 3.02
3116 3276 4.887071 ACACATTTTTGACTGCCTTCACTA 59.113 37.500 0.00 0.00 0.00 2.74
3171 3331 4.464069 AAGTACCTGCTCTCTTGCTAAG 57.536 45.455 0.00 0.00 0.00 2.18
3178 3338 1.736681 GCTCTCTTGCTAAGCCAACTG 59.263 52.381 0.00 0.00 0.00 3.16
3181 3341 1.728971 CTCTTGCTAAGCCAACTGTCG 59.271 52.381 0.00 0.00 0.00 4.35
3222 3382 2.301346 CATGGGCCTTACTGGAATGTC 58.699 52.381 4.53 0.00 38.35 3.06
3255 3415 0.100861 GAGACGGGTTGAGATCGGTC 59.899 60.000 0.00 0.00 34.70 4.79
3261 3421 1.405661 GGGTTGAGATCGGTCAAGGAC 60.406 57.143 0.00 0.00 37.12 3.85
3264 3424 0.809385 TGAGATCGGTCAAGGACGAC 59.191 55.000 0.00 0.00 42.39 4.34
3282 3442 1.534163 GACGCTTTGAACAACCTACCC 59.466 52.381 0.00 0.00 0.00 3.69
3288 3448 1.381463 GAACAACCTACCCCCACCC 59.619 63.158 0.00 0.00 0.00 4.61
3293 3453 0.781920 AACCTACCCCCACCCTTTTC 59.218 55.000 0.00 0.00 0.00 2.29
3318 3478 2.000447 GCCACTCGTAATCTGAACCAC 59.000 52.381 0.00 0.00 0.00 4.16
3325 3485 5.010719 ACTCGTAATCTGAACCACTTCTTCA 59.989 40.000 0.00 0.00 0.00 3.02
3449 3609 4.220821 TCTCTCCTAGTTTTGTGTAGCCTG 59.779 45.833 0.00 0.00 0.00 4.85
3536 3696 2.501316 GCATTCCCCAATAAAGGTGCTT 59.499 45.455 0.00 0.00 0.00 3.91
3550 3710 2.974845 TGCTTGTTTGCATGCACAC 58.025 47.368 26.37 26.37 46.40 3.82
3625 3785 3.679824 ACAGAGACGGGGAAAACTAAG 57.320 47.619 0.00 0.00 0.00 2.18
3642 3802 3.560068 ACTAAGCTTTGTCGGTTCTTGTG 59.440 43.478 3.20 0.00 0.00 3.33
3758 3922 0.934436 GCTGTTCATTTTGCACGCGT 60.934 50.000 5.58 5.58 0.00 6.01
3872 4036 0.403271 AGCTCTGCAGGAAACCATGT 59.597 50.000 15.13 0.00 0.00 3.21
3897 4061 6.619801 AACTGACACATTCTAACTTGTTCC 57.380 37.500 0.00 0.00 0.00 3.62
4148 4312 2.182030 GCTCTTCACCTCGGACGG 59.818 66.667 0.00 0.00 0.00 4.79
4237 4401 1.601419 CTACCCCGCGGAGTTCTTCA 61.601 60.000 30.73 2.07 0.00 3.02
4309 4473 2.997315 CGCAGGGTGAGGTGAGGA 60.997 66.667 0.00 0.00 0.00 3.71
4387 4551 1.730064 CATCGGCCCGTAAATTATCGG 59.270 52.381 1.63 12.42 45.42 4.18
4397 4561 5.637104 CGTAAATTATCGGAAGTCTGTGG 57.363 43.478 0.00 0.00 0.00 4.17
4398 4562 4.025979 CGTAAATTATCGGAAGTCTGTGGC 60.026 45.833 0.00 0.00 0.00 5.01
4471 4636 7.464178 GCATCATTGTCTTTCTTCATTTGCATC 60.464 37.037 0.00 0.00 0.00 3.91
4541 4707 7.490079 TGCTTGATTGATTCAGTGAAATAATGC 59.510 33.333 10.14 12.44 35.27 3.56
4553 4719 1.392589 AATAATGCCCTCTGCCAACG 58.607 50.000 0.00 0.00 40.16 4.10
4626 4792 1.804326 GGCTGCGTACACGGTACAG 60.804 63.158 12.62 4.00 40.23 2.74
4627 4793 2.442188 GCTGCGTACACGGTACAGC 61.442 63.158 14.13 14.13 42.37 4.40
4628 4794 2.126773 TGCGTACACGGTACAGCG 60.127 61.111 12.62 0.00 40.23 5.18
4629 4795 2.877582 GCGTACACGGTACAGCGG 60.878 66.667 5.75 0.00 40.23 5.52
4654 4820 1.713078 AGGAAACTTGAGGCTGGGATT 59.287 47.619 0.00 0.00 37.44 3.01
4698 4864 5.283457 ACTTGGTGCTCTGGATATTCTAC 57.717 43.478 0.00 0.00 0.00 2.59
4699 4865 4.716784 ACTTGGTGCTCTGGATATTCTACA 59.283 41.667 0.00 0.00 0.00 2.74
4700 4866 4.944619 TGGTGCTCTGGATATTCTACAG 57.055 45.455 0.00 0.00 0.00 2.74
4701 4867 4.290093 TGGTGCTCTGGATATTCTACAGT 58.710 43.478 0.00 0.00 34.02 3.55
4702 4868 5.454966 TGGTGCTCTGGATATTCTACAGTA 58.545 41.667 0.00 0.00 34.02 2.74
4703 4869 6.077993 TGGTGCTCTGGATATTCTACAGTAT 58.922 40.000 0.00 0.00 34.02 2.12
4704 4870 6.209589 TGGTGCTCTGGATATTCTACAGTATC 59.790 42.308 0.00 0.00 34.02 2.24
4835 5001 4.466827 TGTCTCACACTCCTTGTACACTA 58.533 43.478 0.00 0.00 35.67 2.74
4836 5002 4.891168 TGTCTCACACTCCTTGTACACTAA 59.109 41.667 0.00 0.00 35.67 2.24
4856 5022 3.032265 ACTTTCCAGCCTTTTGGTCTT 57.968 42.857 0.00 0.00 42.99 3.01
4857 5023 3.374764 ACTTTCCAGCCTTTTGGTCTTT 58.625 40.909 0.00 0.00 42.99 2.52
4930 5100 4.072839 AGGCCAGTTGAGTAGTAAAAAGC 58.927 43.478 5.01 0.00 0.00 3.51
4936 5106 6.073548 CCAGTTGAGTAGTAAAAAGCAGACAG 60.074 42.308 0.00 0.00 0.00 3.51
4940 5110 7.941795 TGAGTAGTAAAAAGCAGACAGTTAC 57.058 36.000 0.00 0.00 0.00 2.50
4943 5113 9.688592 GAGTAGTAAAAAGCAGACAGTTACTTA 57.311 33.333 0.00 0.00 36.61 2.24
4990 5160 6.980978 ACCAGATGTACGATAATTTCAGACAG 59.019 38.462 0.00 0.00 0.00 3.51
5001 5171 8.276325 CGATAATTTCAGACAGCTAATAACCAC 58.724 37.037 0.00 0.00 0.00 4.16
5005 5175 5.435686 TCAGACAGCTAATAACCACCAAT 57.564 39.130 0.00 0.00 0.00 3.16
5036 5224 6.954616 TTTTGCTCGAAATCGTCTTGTATA 57.045 33.333 2.41 0.00 40.80 1.47
5037 5225 5.944049 TTGCTCGAAATCGTCTTGTATAC 57.056 39.130 2.41 0.00 40.80 1.47
5038 5226 4.989044 TGCTCGAAATCGTCTTGTATACA 58.011 39.130 0.08 0.08 40.80 2.29
5039 5227 5.034797 TGCTCGAAATCGTCTTGTATACAG 58.965 41.667 5.56 1.19 40.80 2.74
5040 5228 5.035443 GCTCGAAATCGTCTTGTATACAGT 58.965 41.667 5.56 0.00 40.80 3.55
5041 5229 5.515626 GCTCGAAATCGTCTTGTATACAGTT 59.484 40.000 5.56 0.00 40.80 3.16
5042 5230 6.690098 GCTCGAAATCGTCTTGTATACAGTTA 59.310 38.462 5.56 0.00 40.80 2.24
5043 5231 7.305304 GCTCGAAATCGTCTTGTATACAGTTAC 60.305 40.741 5.56 5.17 40.80 2.50
5092 5310 1.429463 CCAACCGAAAGACGAGGAAG 58.571 55.000 0.00 0.00 45.77 3.46
5095 5313 1.211969 CCGAAAGACGAGGAAGCGA 59.788 57.895 0.00 0.00 45.77 4.93
5096 5314 0.179134 CCGAAAGACGAGGAAGCGAT 60.179 55.000 0.00 0.00 45.77 4.58
5104 5322 1.001597 ACGAGGAAGCGATCGGAATAC 60.002 52.381 18.30 0.00 43.12 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.532417 AGCTCCATCGCATCTTCAGC 60.532 55.000 0.00 0.00 0.00 4.26
20 21 2.687700 TCTTGCAGAAGAGCTCCATC 57.312 50.000 10.93 9.61 32.98 3.51
170 171 0.955428 GAGCGTTCTCCAATGCCACA 60.955 55.000 0.00 0.00 44.59 4.17
182 183 5.920840 TGCATACATATCAACTAGAGCGTTC 59.079 40.000 0.00 0.00 0.00 3.95
209 210 3.022406 GGCATCTGAAAATTCTCCTGCT 58.978 45.455 11.35 0.00 0.00 4.24
215 216 1.747355 CGCCTGGCATCTGAAAATTCT 59.253 47.619 20.29 0.00 0.00 2.40
345 346 0.038166 GGCTTCACACCATCCTCCAA 59.962 55.000 0.00 0.00 0.00 3.53
371 372 4.310769 ACAGAAGAGAAAGGAATGTCACG 58.689 43.478 0.00 0.00 0.00 4.35
418 419 4.706476 TGAAATACTCCATCCCTTTGCTTG 59.294 41.667 0.00 0.00 0.00 4.01
419 420 4.706962 GTGAAATACTCCATCCCTTTGCTT 59.293 41.667 0.00 0.00 0.00 3.91
487 488 3.093057 AGAAGGTCGATAGCAGAACTGT 58.907 45.455 3.77 0.00 35.56 3.55
518 519 1.478510 CACGCATCCTCTAACTGACCT 59.521 52.381 0.00 0.00 0.00 3.85
549 550 4.220693 TGGGTTCAGTATCCACATTCTG 57.779 45.455 0.00 0.00 0.00 3.02
626 627 0.183492 TGGCTGCAGTTTCTCCAAGT 59.817 50.000 16.64 0.00 0.00 3.16
654 655 4.345257 AGAACTCTCAGCACCTTTACTGAA 59.655 41.667 0.00 0.00 42.12 3.02
764 765 0.538057 CAGCTTCCTTGCCACCAGAA 60.538 55.000 0.00 0.00 0.00 3.02
869 870 5.163612 GGTCTGAGGGTAATTCAAAAGCATC 60.164 44.000 0.00 0.00 0.00 3.91
874 875 6.133356 ACAAAGGTCTGAGGGTAATTCAAAA 58.867 36.000 0.00 0.00 0.00 2.44
876 877 5.313712 GACAAAGGTCTGAGGGTAATTCAA 58.686 41.667 0.00 0.00 40.99 2.69
879 880 3.655777 TGGACAAAGGTCTGAGGGTAATT 59.344 43.478 0.00 0.00 43.77 1.40
938 940 5.721232 AGTCGGTTAGAGGTTACAAAGATG 58.279 41.667 0.00 0.00 0.00 2.90
949 951 6.217294 GGAAGATTATGAAGTCGGTTAGAGG 58.783 44.000 0.00 0.00 0.00 3.69
965 967 7.068593 CACTGCTTAATCAAATGGGGAAGATTA 59.931 37.037 0.00 0.00 33.22 1.75
972 974 4.272489 TCTCACTGCTTAATCAAATGGGG 58.728 43.478 0.00 0.00 0.00 4.96
976 978 9.107177 CATTAGACTCTCACTGCTTAATCAAAT 57.893 33.333 0.00 0.00 0.00 2.32
995 997 4.697514 TGGCTGCTGATAAGTCATTAGAC 58.302 43.478 0.00 0.00 45.31 2.59
1025 1027 2.200373 ATGTGCACTTACCCTGAACC 57.800 50.000 19.41 0.00 0.00 3.62
1086 1096 2.350522 GAGTGTAGCCCAACAGATGTG 58.649 52.381 0.00 0.00 0.00 3.21
1088 1098 1.407437 GGGAGTGTAGCCCAACAGATG 60.407 57.143 0.00 0.00 45.31 2.90
1136 1146 4.085107 GCATCCGCAAAACTTTTACAGTTG 60.085 41.667 0.00 0.00 40.78 3.16
1174 1184 8.807118 ACAGAATTGAGAATACTGACAAGACTA 58.193 33.333 0.00 0.00 33.53 2.59
1203 1213 8.650143 ACCTGTAACTGTCCAATCAATAAATT 57.350 30.769 0.00 0.00 0.00 1.82
1204 1214 8.650143 AACCTGTAACTGTCCAATCAATAAAT 57.350 30.769 0.00 0.00 0.00 1.40
1206 1216 9.747898 ATAAACCTGTAACTGTCCAATCAATAA 57.252 29.630 0.00 0.00 0.00 1.40
1222 1232 7.563724 AAAGGAGTAAGACCATAAACCTGTA 57.436 36.000 0.00 0.00 0.00 2.74
1251 1261 2.936919 TGATGCAGACAAGTTGGAGT 57.063 45.000 7.96 0.00 0.00 3.85
1252 1262 4.216902 TCAATTGATGCAGACAAGTTGGAG 59.783 41.667 3.38 0.00 0.00 3.86
1258 1271 7.741027 ATAGGTATCAATTGATGCAGACAAG 57.259 36.000 29.86 3.37 38.64 3.16
1296 1309 6.323739 ACAAACTGGTTTATCCACTGATGTTT 59.676 34.615 0.00 0.00 41.93 2.83
1348 1362 3.071892 AGTGTGGAAAAACAGGGTATCGA 59.928 43.478 0.00 0.00 0.00 3.59
1368 1382 4.473477 AAAGAGAAATGGCTAGCGTAGT 57.527 40.909 9.00 0.00 0.00 2.73
1377 1391 3.259123 ACCCACATCAAAAGAGAAATGGC 59.741 43.478 0.00 0.00 0.00 4.40
1492 1507 2.589720 TGCAATAGATCAAGGCCATGG 58.410 47.619 7.63 7.63 0.00 3.66
1523 1538 0.969149 ATCTGCTTCACTCGACACCA 59.031 50.000 0.00 0.00 0.00 4.17
1586 1601 8.982685 ACATATTCAATTATTCACTGAGTAGCG 58.017 33.333 0.00 0.00 0.00 4.26
1615 1631 0.888736 TCAACAGCACATGGGTTCGG 60.889 55.000 0.00 0.00 0.00 4.30
1773 1791 9.477484 AAGAAGAATAACCGTATTATGCTACAG 57.523 33.333 0.00 0.00 27.16 2.74
1774 1792 9.826574 AAAGAAGAATAACCGTATTATGCTACA 57.173 29.630 0.00 0.00 27.16 2.74
1792 1937 9.814899 TTGAAAGCAAATAATGTGAAAGAAGAA 57.185 25.926 0.00 0.00 0.00 2.52
1808 1953 8.719924 TATCCTCAGATGCCATTTGAAAGCAAA 61.720 37.037 0.00 0.00 40.46 3.68
1809 1954 3.056393 CCTCAGATGCCATTTGAAAGCAA 60.056 43.478 0.00 0.00 40.46 3.91
1810 1955 2.494471 CCTCAGATGCCATTTGAAAGCA 59.506 45.455 0.00 0.00 41.50 3.91
1811 1956 2.756760 TCCTCAGATGCCATTTGAAAGC 59.243 45.455 0.00 0.00 0.00 3.51
1874 2023 3.713764 AGTTGCTAGCTGTTATCATCCCT 59.286 43.478 17.23 0.00 0.00 4.20
1909 2058 6.748132 TCTTCCTAAAAGTGCCAAATCAAAG 58.252 36.000 0.00 0.00 0.00 2.77
1932 2082 5.053145 CCCTTAAGATGTGACTACAGCATC 58.947 45.833 3.36 0.00 45.39 3.91
1937 2087 4.020573 CCACACCCTTAAGATGTGACTACA 60.021 45.833 27.97 0.00 45.34 2.74
1959 2109 0.738389 CCCATGCGATTGTGTAACCC 59.262 55.000 0.00 0.00 34.36 4.11
1970 2120 4.854924 CCATCGTGGCCCATGCGA 62.855 66.667 0.00 5.72 38.85 5.10
1971 2121 4.854924 TCCATCGTGGCCCATGCG 62.855 66.667 0.00 0.00 37.47 4.73
2020 2170 4.261530 GGGAGTACCAGTTACGAGCTATTC 60.262 50.000 0.00 0.00 39.85 1.75
2038 2188 1.298382 ACATTATGGGAGGGAGGGAGT 59.702 52.381 0.00 0.00 0.00 3.85
2039 2189 2.124560 ACATTATGGGAGGGAGGGAG 57.875 55.000 0.00 0.00 0.00 4.30
2040 2190 3.211232 TCTTACATTATGGGAGGGAGGGA 59.789 47.826 0.00 0.00 0.00 4.20
2041 2191 3.328050 GTCTTACATTATGGGAGGGAGGG 59.672 52.174 0.00 0.00 0.00 4.30
2042 2192 3.006967 CGTCTTACATTATGGGAGGGAGG 59.993 52.174 0.00 0.00 0.00 4.30
2043 2193 3.641906 ACGTCTTACATTATGGGAGGGAG 59.358 47.826 0.00 0.00 0.00 4.30
2044 2194 3.649843 ACGTCTTACATTATGGGAGGGA 58.350 45.455 0.00 0.00 0.00 4.20
2045 2195 4.417426 AACGTCTTACATTATGGGAGGG 57.583 45.455 0.00 0.00 0.00 4.30
2046 2196 6.753107 AAAAACGTCTTACATTATGGGAGG 57.247 37.500 0.00 1.06 0.00 4.30
2089 2239 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2090 2240 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2091 2241 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2092 2242 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2093 2243 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2095 2245 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2096 2246 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2097 2247 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2098 2248 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2099 2249 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2100 2250 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2101 2251 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2102 2252 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2103 2253 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2104 2254 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2105 2255 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
2106 2256 0.635009 AATCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2107 2257 2.237643 GTAATCTACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
2108 2258 2.885894 CTGTAATCTACTCCCTCCGTCC 59.114 54.545 0.00 0.00 0.00 4.79
2109 2259 2.885894 CCTGTAATCTACTCCCTCCGTC 59.114 54.545 0.00 0.00 0.00 4.79
2110 2260 2.946785 CCTGTAATCTACTCCCTCCGT 58.053 52.381 0.00 0.00 0.00 4.69
2111 2261 1.614413 GCCTGTAATCTACTCCCTCCG 59.386 57.143 0.00 0.00 0.00 4.63
2112 2262 1.972075 GGCCTGTAATCTACTCCCTCC 59.028 57.143 0.00 0.00 0.00 4.30
2113 2263 1.972075 GGGCCTGTAATCTACTCCCTC 59.028 57.143 0.84 0.00 33.64 4.30
2114 2264 1.581149 AGGGCCTGTAATCTACTCCCT 59.419 52.381 4.50 0.00 38.21 4.20
2115 2265 2.104669 AGGGCCTGTAATCTACTCCC 57.895 55.000 4.50 0.00 35.30 4.30
2116 2266 4.654724 AGTTAAGGGCCTGTAATCTACTCC 59.345 45.833 6.92 0.00 0.00 3.85
2117 2267 5.873146 AGTTAAGGGCCTGTAATCTACTC 57.127 43.478 6.92 0.00 0.00 2.59
2118 2268 5.965091 AGAAGTTAAGGGCCTGTAATCTACT 59.035 40.000 6.92 0.07 0.00 2.57
2119 2269 6.049790 CAGAAGTTAAGGGCCTGTAATCTAC 58.950 44.000 6.92 0.00 0.00 2.59
2120 2270 5.130477 CCAGAAGTTAAGGGCCTGTAATCTA 59.870 44.000 6.92 0.00 0.00 1.98
2130 2280 1.351350 AGTGTCCCAGAAGTTAAGGGC 59.649 52.381 7.15 4.17 42.52 5.19
2131 2281 3.412386 CAAGTGTCCCAGAAGTTAAGGG 58.588 50.000 5.86 5.86 44.22 3.95
2145 2295 1.838112 TTGATGGGATGGCAAGTGTC 58.162 50.000 0.00 0.00 0.00 3.67
2154 2304 5.628666 GCATCTAGGGAGTATTGATGGGATG 60.629 48.000 0.00 0.00 36.14 3.51
2164 2314 3.718723 GGATGAGGCATCTAGGGAGTAT 58.281 50.000 0.00 0.00 40.39 2.12
2207 2357 1.206132 CCTGTGGTTAGCGTGGATGTA 59.794 52.381 0.00 0.00 0.00 2.29
2272 2422 2.800881 TATCACGCAGCCAGTAGATG 57.199 50.000 0.00 0.00 0.00 2.90
2285 2435 6.634837 CAGCTGTACTACTTTCTCATATCACG 59.365 42.308 5.25 0.00 0.00 4.35
2293 2443 5.652518 CCCTAACAGCTGTACTACTTTCTC 58.347 45.833 22.01 0.00 0.00 2.87
2299 2449 1.475682 ACGCCCTAACAGCTGTACTAC 59.524 52.381 22.01 8.20 0.00 2.73
2312 2462 3.370840 TCTAGAAACCTACACGCCCTA 57.629 47.619 0.00 0.00 0.00 3.53
2314 2464 2.614779 GTTCTAGAAACCTACACGCCC 58.385 52.381 6.78 0.00 0.00 6.13
2318 2468 8.291191 AGTATAGTGGTTCTAGAAACCTACAC 57.709 38.462 17.85 15.89 40.88 2.90
2333 2483 8.204836 CCTTTTGCTCAGTATTAGTATAGTGGT 58.795 37.037 0.00 0.00 37.96 4.16
2358 2508 4.962155 ACATAAGTGATAGTAAGCCAGCC 58.038 43.478 0.00 0.00 0.00 4.85
2385 2536 6.037610 CCTGCTTTATAGTTCAGTTGCTTAGG 59.962 42.308 0.00 0.00 0.00 2.69
2418 2576 8.690203 TTGATGATTTTTGAGGTGAACTAGAA 57.310 30.769 0.00 0.00 0.00 2.10
2431 2589 5.636543 GGAGTTGCTTCCTTGATGATTTTTG 59.363 40.000 0.00 0.00 34.27 2.44
2440 2598 0.250295 CGGTGGAGTTGCTTCCTTGA 60.250 55.000 4.52 0.00 38.12 3.02
2447 2605 1.293498 CTACAGCGGTGGAGTTGCT 59.707 57.895 18.92 0.00 40.16 3.91
2448 2606 2.391389 GCTACAGCGGTGGAGTTGC 61.391 63.158 26.71 11.18 36.91 4.17
2449 2607 3.876300 GCTACAGCGGTGGAGTTG 58.124 61.111 26.71 4.38 36.91 3.16
2459 2617 1.829222 TGTACAACCCCTAGCTACAGC 59.171 52.381 0.00 0.00 42.49 4.40
2460 2618 4.442706 CAATGTACAACCCCTAGCTACAG 58.557 47.826 0.00 0.00 0.00 2.74
2461 2619 3.199071 CCAATGTACAACCCCTAGCTACA 59.801 47.826 0.00 0.00 0.00 2.74
2462 2620 3.453353 TCCAATGTACAACCCCTAGCTAC 59.547 47.826 0.00 0.00 0.00 3.58
2463 2621 3.453353 GTCCAATGTACAACCCCTAGCTA 59.547 47.826 0.00 0.00 0.00 3.32
2464 2622 2.238898 GTCCAATGTACAACCCCTAGCT 59.761 50.000 0.00 0.00 0.00 3.32
2465 2623 2.026636 TGTCCAATGTACAACCCCTAGC 60.027 50.000 0.00 0.00 0.00 3.42
2466 2624 3.606687 GTGTCCAATGTACAACCCCTAG 58.393 50.000 0.00 0.00 0.00 3.02
2467 2625 2.027929 CGTGTCCAATGTACAACCCCTA 60.028 50.000 0.00 0.00 0.00 3.53
2468 2626 1.271163 CGTGTCCAATGTACAACCCCT 60.271 52.381 0.00 0.00 0.00 4.79
2469 2627 1.161843 CGTGTCCAATGTACAACCCC 58.838 55.000 0.00 0.00 0.00 4.95
2470 2628 0.519961 GCGTGTCCAATGTACAACCC 59.480 55.000 0.00 0.00 0.00 4.11
2471 2629 1.069500 GTGCGTGTCCAATGTACAACC 60.069 52.381 0.00 0.00 31.22 3.77
2472 2630 1.600013 TGTGCGTGTCCAATGTACAAC 59.400 47.619 0.00 0.00 37.45 3.32
2473 2631 1.870402 CTGTGCGTGTCCAATGTACAA 59.130 47.619 0.00 0.00 39.54 2.41
2474 2632 1.507562 CTGTGCGTGTCCAATGTACA 58.492 50.000 0.00 0.00 37.98 2.90
2475 2633 0.165944 GCTGTGCGTGTCCAATGTAC 59.834 55.000 0.00 0.00 0.00 2.90
2476 2634 0.250081 TGCTGTGCGTGTCCAATGTA 60.250 50.000 0.00 0.00 0.00 2.29
2477 2635 0.890542 ATGCTGTGCGTGTCCAATGT 60.891 50.000 0.00 0.00 0.00 2.71
2478 2636 0.455464 CATGCTGTGCGTGTCCAATG 60.455 55.000 3.82 0.00 40.30 2.82
2479 2637 1.588824 CCATGCTGTGCGTGTCCAAT 61.589 55.000 10.32 0.00 43.26 3.16
2480 2638 2.260154 CCATGCTGTGCGTGTCCAA 61.260 57.895 10.32 0.00 43.26 3.53
2481 2639 2.669229 CCATGCTGTGCGTGTCCA 60.669 61.111 10.32 0.00 43.26 4.02
2482 2640 1.795170 AAACCATGCTGTGCGTGTCC 61.795 55.000 10.32 0.00 43.26 4.02
2483 2641 0.871722 TAAACCATGCTGTGCGTGTC 59.128 50.000 10.32 0.00 43.26 3.67
2484 2642 0.591170 GTAAACCATGCTGTGCGTGT 59.409 50.000 10.32 0.00 43.26 4.49
2485 2643 0.590682 TGTAAACCATGCTGTGCGTG 59.409 50.000 4.91 4.91 44.25 5.34
2486 2644 0.874390 CTGTAAACCATGCTGTGCGT 59.126 50.000 0.00 0.00 0.00 5.24
2487 2645 1.135972 GTCTGTAAACCATGCTGTGCG 60.136 52.381 0.00 0.00 0.00 5.34
2488 2646 2.154462 AGTCTGTAAACCATGCTGTGC 58.846 47.619 0.00 0.00 0.00 4.57
2493 2651 3.618690 AGAGGAGTCTGTAAACCATGC 57.381 47.619 0.00 0.00 0.00 4.06
2527 2685 0.259356 AGGGTCGTAGGAGAAGAGGG 59.741 60.000 0.00 0.00 0.00 4.30
2534 2692 2.299521 CACTAAGGAGGGTCGTAGGAG 58.700 57.143 0.00 0.00 0.00 3.69
2537 2695 3.631227 CCTAACACTAAGGAGGGTCGTAG 59.369 52.174 0.00 0.00 38.88 3.51
2541 2699 1.136500 CGCCTAACACTAAGGAGGGTC 59.864 57.143 0.00 0.00 38.88 4.46
2558 2716 0.036388 TTCAACTCTGGTGGATCGCC 60.036 55.000 0.00 0.00 34.12 5.54
2561 2719 3.077359 CAACCTTCAACTCTGGTGGATC 58.923 50.000 0.00 0.00 33.89 3.36
2605 2763 6.465439 TCACGAACAATGACCTCTACATAT 57.535 37.500 0.00 0.00 0.00 1.78
2610 2768 4.705023 TCTCATCACGAACAATGACCTCTA 59.295 41.667 0.00 0.00 0.00 2.43
2665 2823 2.263852 CGAAGCAGAGGAGCAGCA 59.736 61.111 0.00 0.00 36.85 4.41
2726 2884 2.298446 CTGAAGCAGTTGAGGAGAGACA 59.702 50.000 0.00 0.00 0.00 3.41
2807 2965 5.606749 TGGTAATCCTGGTATGCTATCAAGT 59.393 40.000 0.00 0.00 34.23 3.16
2846 3004 0.036294 GCAGGCTAAGGTTCGGTTCT 60.036 55.000 0.00 0.00 0.00 3.01
2873 3031 2.064434 TGACAAGGTCAATTGTGCCA 57.936 45.000 18.80 2.50 43.32 4.92
2930 3088 4.039004 ACAAGAGCTAGGATATCAGCACAG 59.961 45.833 15.30 9.36 40.36 3.66
2933 3091 3.323115 CCACAAGAGCTAGGATATCAGCA 59.677 47.826 15.30 0.00 40.36 4.41
2951 3109 1.423541 AGTACAACATCCCTTGCCACA 59.576 47.619 0.00 0.00 0.00 4.17
3049 3208 5.540337 GGTCTGAATCATCCTATACTCACCA 59.460 44.000 0.00 0.00 0.00 4.17
3050 3209 5.540337 TGGTCTGAATCATCCTATACTCACC 59.460 44.000 6.27 0.00 0.00 4.02
3052 3211 6.611236 TGTTGGTCTGAATCATCCTATACTCA 59.389 38.462 6.27 0.00 0.00 3.41
3053 3212 7.055667 TGTTGGTCTGAATCATCCTATACTC 57.944 40.000 6.27 0.00 0.00 2.59
3054 3213 6.613271 ACTGTTGGTCTGAATCATCCTATACT 59.387 38.462 6.27 0.00 0.00 2.12
3056 3215 6.183361 CCACTGTTGGTCTGAATCATCCTATA 60.183 42.308 6.27 0.00 38.23 1.31
3098 3258 6.151985 TCAAACTTAGTGAAGGCAGTCAAAAA 59.848 34.615 0.00 0.00 36.95 1.94
3106 3266 5.809001 AGATGATCAAACTTAGTGAAGGCA 58.191 37.500 0.00 0.00 36.95 4.75
3142 3302 6.173339 CAAGAGAGCAGGTACTTTCCATAAA 58.827 40.000 0.00 0.00 34.60 1.40
3143 3303 5.734720 CAAGAGAGCAGGTACTTTCCATAA 58.265 41.667 0.00 0.00 34.60 1.90
3144 3304 4.383118 GCAAGAGAGCAGGTACTTTCCATA 60.383 45.833 0.00 0.00 34.60 2.74
3145 3305 3.620966 GCAAGAGAGCAGGTACTTTCCAT 60.621 47.826 0.00 0.00 34.60 3.41
3150 3310 3.368948 GCTTAGCAAGAGAGCAGGTACTT 60.369 47.826 0.00 0.00 34.60 2.24
3171 3331 3.810373 CATAGTGAAAACGACAGTTGGC 58.190 45.455 0.00 0.00 41.05 4.52
3178 3338 4.455124 GTCTGTTGCATAGTGAAAACGAC 58.545 43.478 0.00 0.00 0.00 4.34
3181 3341 3.568007 TGGGTCTGTTGCATAGTGAAAAC 59.432 43.478 0.00 0.00 0.00 2.43
3240 3400 0.460284 CCTTGACCGATCTCAACCCG 60.460 60.000 0.00 0.00 0.00 5.28
3255 3415 0.934496 TGTTCAAAGCGTCGTCCTTG 59.066 50.000 0.00 0.00 0.00 3.61
3261 3421 1.193874 GGTAGGTTGTTCAAAGCGTCG 59.806 52.381 0.00 0.00 0.00 5.12
3264 3424 0.879090 GGGGTAGGTTGTTCAAAGCG 59.121 55.000 0.00 0.00 0.00 4.68
3282 3442 0.251742 TGGCATCAGAAAAGGGTGGG 60.252 55.000 0.00 0.00 0.00 4.61
3288 3448 4.872691 AGATTACGAGTGGCATCAGAAAAG 59.127 41.667 0.00 0.00 0.00 2.27
3293 3453 3.443099 TCAGATTACGAGTGGCATCAG 57.557 47.619 0.00 0.00 0.00 2.90
3449 3609 3.195396 ACAGAGAGGAATCAGAAGAGCAC 59.805 47.826 0.00 0.00 0.00 4.40
3536 3696 1.000385 GCTTAGGTGTGCATGCAAACA 60.000 47.619 35.64 22.66 35.94 2.83
3550 3710 4.402155 TGCTTGATTAACCCATTGCTTAGG 59.598 41.667 0.00 0.00 0.00 2.69
3625 3785 1.021968 ACCACAAGAACCGACAAAGC 58.978 50.000 0.00 0.00 0.00 3.51
3758 3922 5.952347 GGTTTTCTACCCCATCTCTTCTA 57.048 43.478 0.00 0.00 41.43 2.10
3872 4036 7.990886 AGGAACAAGTTAGAATGTGTCAGTTTA 59.009 33.333 0.00 0.00 0.00 2.01
3924 4088 4.767255 GAGCAGTGGGAGGTGCCG 62.767 72.222 0.00 0.00 40.81 5.69
3927 4091 2.262915 GACGAGCAGTGGGAGGTG 59.737 66.667 0.00 0.00 0.00 4.00
4016 4180 2.740055 ACTTGCTCTTCAGCCGCG 60.740 61.111 0.00 0.00 46.26 6.46
4049 4213 2.355986 ATCTCCACCAGCGCCGTAA 61.356 57.895 2.29 0.00 0.00 3.18
4299 4463 3.385384 CAGCGCCTCCTCACCTCA 61.385 66.667 2.29 0.00 0.00 3.86
4387 4551 1.302832 CCCACAGGCCACAGACTTC 60.303 63.158 5.01 0.00 0.00 3.01
4392 4556 0.038166 ACAATACCCACAGGCCACAG 59.962 55.000 5.01 0.00 36.11 3.66
4393 4557 1.363246 TACAATACCCACAGGCCACA 58.637 50.000 5.01 0.00 36.11 4.17
4394 4558 2.729028 ATACAATACCCACAGGCCAC 57.271 50.000 5.01 0.00 36.11 5.01
4395 4559 5.103898 TCAATTATACAATACCCACAGGCCA 60.104 40.000 5.01 0.00 36.11 5.36
4396 4560 5.381757 TCAATTATACAATACCCACAGGCC 58.618 41.667 0.00 0.00 36.11 5.19
4397 4561 6.490040 ACATCAATTATACAATACCCACAGGC 59.510 38.462 0.00 0.00 36.11 4.85
4398 4562 7.502226 ACACATCAATTATACAATACCCACAGG 59.498 37.037 0.00 0.00 40.04 4.00
4541 4707 1.811266 CATCGACGTTGGCAGAGGG 60.811 63.158 2.20 0.00 0.00 4.30
4553 4719 2.909244 CTGTCGTAGTGTGTTCATCGAC 59.091 50.000 8.26 8.26 40.85 4.20
4605 4771 2.624868 TACCGTGTACGCAGCCGAA 61.625 57.895 7.29 0.00 38.18 4.30
4612 4778 2.877582 CCGCTGTACCGTGTACGC 60.878 66.667 0.00 14.52 38.18 4.42
4626 4792 1.439679 CTCAAGTTTCCTGTACCCGC 58.560 55.000 0.00 0.00 0.00 6.13
4627 4793 1.944430 GCCTCAAGTTTCCTGTACCCG 60.944 57.143 0.00 0.00 0.00 5.28
4628 4794 1.351350 AGCCTCAAGTTTCCTGTACCC 59.649 52.381 0.00 0.00 0.00 3.69
4629 4795 2.427506 CAGCCTCAAGTTTCCTGTACC 58.572 52.381 0.00 0.00 0.00 3.34
4667 4833 4.137543 CCAGAGCACCAAGTAAACTCTTT 58.862 43.478 0.00 0.00 35.57 2.52
4835 5001 3.032265 AGACCAAAAGGCTGGAAAGTT 57.968 42.857 0.00 0.00 38.96 2.66
4836 5002 2.755952 AGACCAAAAGGCTGGAAAGT 57.244 45.000 0.00 0.00 38.96 2.66
4903 5069 5.811796 TTACTACTCAACTGGCCTTAACA 57.188 39.130 3.32 0.00 0.00 2.41
4943 5113 8.314143 TGGTTCTCGTCTCGTAAAATTATTTT 57.686 30.769 8.07 8.07 36.67 1.82
4944 5114 7.816031 TCTGGTTCTCGTCTCGTAAAATTATTT 59.184 33.333 0.00 0.00 0.00 1.40
4961 5131 7.921214 TCTGAAATTATCGTACATCTGGTTCTC 59.079 37.037 0.00 0.00 0.00 2.87
4962 5132 7.707035 GTCTGAAATTATCGTACATCTGGTTCT 59.293 37.037 0.00 0.00 0.00 3.01
4963 5133 7.491372 TGTCTGAAATTATCGTACATCTGGTTC 59.509 37.037 0.00 0.00 0.00 3.62
4965 5135 6.873997 TGTCTGAAATTATCGTACATCTGGT 58.126 36.000 0.00 0.00 0.00 4.00
4966 5136 6.074088 GCTGTCTGAAATTATCGTACATCTGG 60.074 42.308 0.00 0.00 0.00 3.86
5027 5199 5.636543 GGTGGTGTGTAACTGTATACAAGAC 59.363 44.000 7.06 5.87 37.52 3.01
5029 5217 5.790593 AGGTGGTGTGTAACTGTATACAAG 58.209 41.667 7.06 4.14 37.52 3.16
5036 5224 3.926058 AGAAAGGTGGTGTGTAACTGT 57.074 42.857 0.00 0.00 38.04 3.55
5037 5225 4.733523 GCAAAGAAAGGTGGTGTGTAACTG 60.734 45.833 0.00 0.00 38.04 3.16
5038 5226 3.380320 GCAAAGAAAGGTGGTGTGTAACT 59.620 43.478 0.00 0.00 38.04 2.24
5039 5227 3.380320 AGCAAAGAAAGGTGGTGTGTAAC 59.620 43.478 0.00 0.00 37.35 2.50
5040 5228 3.626930 AGCAAAGAAAGGTGGTGTGTAA 58.373 40.909 0.00 0.00 0.00 2.41
5041 5229 3.211045 GAGCAAAGAAAGGTGGTGTGTA 58.789 45.455 0.00 0.00 0.00 2.90
5042 5230 2.024414 GAGCAAAGAAAGGTGGTGTGT 58.976 47.619 0.00 0.00 0.00 3.72
5043 5231 1.002468 CGAGCAAAGAAAGGTGGTGTG 60.002 52.381 0.00 0.00 0.00 3.82
5104 5322 0.319211 TCGAGCTTTGGTGTACGGTG 60.319 55.000 0.00 0.00 0.00 4.94
5276 5494 4.367023 TGGTCGCCCTACGTGTGC 62.367 66.667 0.00 0.00 44.19 4.57


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

AutoCloner maintained by Alex Coulton.