Multiple sequence alignment - TraesCS4B01G214600

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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 TraesCS4B01G214600 chr4B 100.000 4925 0 0 1 4925 454042636 454037712 0.000000e+00 9095
1 TraesCS4B01G214600 chr4B 88.525 122 8 6 2189 2307 454040324 454040442 5.140000e-30 143
2 TraesCS4B01G214600 chr4B 79.535 215 20 6 2129 2342 517959145 517958954 1.110000e-26 132
3 TraesCS4B01G214600 chr4B 86.325 117 13 3 2192 2306 14343815 14343930 1.860000e-24 124
4 TraesCS4B01G214600 chr4B 94.805 77 4 0 2269 2345 634413189 634413113 2.410000e-23 121
5 TraesCS4B01G214600 chr4A 95.800 2405 69 18 2341 4720 96016483 96018880 0.000000e+00 3853
6 TraesCS4B01G214600 chr4A 91.689 2202 81 48 1 2138 96014321 96016484 0.000000e+00 2959
7 TraesCS4B01G214600 chr4A 86.538 260 19 5 4676 4925 96018881 96019134 6.280000e-69 272
8 TraesCS4B01G214600 chr4D 92.849 2615 116 35 2341 4897 368872369 368869768 0.000000e+00 3727
9 TraesCS4B01G214600 chr4D 87.165 1231 82 27 354 1519 368874070 368872851 0.000000e+00 1328
10 TraesCS4B01G214600 chr4D 92.638 489 26 5 1654 2138 368872850 368872368 0.000000e+00 695
11 TraesCS4B01G214600 chr4D 89.944 358 13 8 1 358 368875554 368875220 1.630000e-119 440
12 TraesCS4B01G214600 chr6B 87.923 207 5 7 2136 2342 503548066 503547880 4.960000e-55 226
13 TraesCS4B01G214600 chr3D 80.444 225 24 16 2136 2342 382748071 382747849 2.370000e-33 154
14 TraesCS4B01G214600 chr3D 84.459 148 17 5 4522 4663 441388671 441388818 1.850000e-29 141
15 TraesCS4B01G214600 chr3D 82.432 148 19 6 4522 4663 375193763 375193909 6.690000e-24 122
16 TraesCS4B01G214600 chr3D 81.457 151 18 8 4522 4664 170537803 170537951 1.120000e-21 115
17 TraesCS4B01G214600 chr3A 85.135 148 16 5 4522 4663 582283219 582283366 3.970000e-31 147
18 TraesCS4B01G214600 chr3A 83.673 147 19 3 4522 4663 498229939 498230085 3.090000e-27 134
19 TraesCS4B01G214600 chr5B 80.357 224 15 15 2137 2343 368502998 368502787 5.140000e-30 143
20 TraesCS4B01G214600 chr5B 85.124 121 14 4 2193 2310 356309482 356309363 2.410000e-23 121
21 TraesCS4B01G214600 chr2B 81.720 186 16 13 2177 2345 211528010 211527826 6.650000e-29 139
22 TraesCS4B01G214600 chr2B 87.288 118 7 6 2196 2307 757137578 757137463 1.440000e-25 128
23 TraesCS4B01G214600 chr2B 95.775 71 3 0 2128 2198 694052141 694052211 1.120000e-21 115
24 TraesCS4B01G214600 chr7B 88.136 118 6 7 2196 2307 513127946 513127831 3.090000e-27 134
25 TraesCS4B01G214600 chr1D 87.500 120 7 7 2196 2309 118811994 118811877 1.110000e-26 132
26 TraesCS4B01G214600 chr1D 84.906 106 9 3 2136 2235 470083732 470083628 3.140000e-17 100
27 TraesCS4B01G214600 chr5A 83.108 148 19 2 4522 4663 329991804 329991951 4.000000e-26 130
28 TraesCS4B01G214600 chr3B 87.719 114 8 5 2194 2306 700323751 700323643 1.440000e-25 128
29 TraesCS4B01G214600 chr3B 82.313 147 21 3 4522 4663 489352729 489352875 6.690000e-24 122
30 TraesCS4B01G214600 chr3B 85.124 121 14 4 2193 2310 797794374 797794255 2.410000e-23 121
31 TraesCS4B01G214600 chr3B 84.298 121 11 8 2193 2310 485594717 485594602 1.450000e-20 111
32 TraesCS4B01G214600 chr1B 87.069 116 9 5 2194 2306 282236451 282236339 5.180000e-25 126
33 TraesCS4B01G214600 chr1B 78.125 224 25 17 2135 2338 623732171 623731952 2.410000e-23 121
34 TraesCS4B01G214600 chr1B 84.298 121 15 4 2193 2310 320564968 320564849 1.120000e-21 115
35 TraesCS4B01G214600 chrUn 94.521 73 2 2 2126 2197 305213121 305213192 1.450000e-20 111
36 TraesCS4B01G214600 chr2D 92.405 79 2 3 2122 2198 562902809 562902733 5.210000e-20 110
37 TraesCS4B01G214600 chr2A 88.506 87 8 2 2112 2197 603084763 603084678 2.420000e-18 104


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 TraesCS4B01G214600 chr4B 454037712 454042636 4924 True 9095.000000 9095 100.000000 1 4925 1 chr4B.!!$R1 4924
1 TraesCS4B01G214600 chr4A 96014321 96019134 4813 False 2361.333333 3853 91.342333 1 4925 3 chr4A.!!$F1 4924
2 TraesCS4B01G214600 chr4D 368869768 368875554 5786 True 1547.500000 3727 90.649000 1 4897 4 chr4D.!!$R1 4896

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
402 1569 0.107703 CTCTCATGCAGCCGGGTTTA 60.108 55.0 1.64 0.0 0.0 2.01 F
1248 2478 0.036732 TGTCCTGCTTAGCCAACCAG 59.963 55.0 0.29 0.0 0.0 4.00 F
2212 3464 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.0 0.0 3.28 F
2307 3559 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.0 0.00 0.0 0.0 2.90 F
2310 3562 0.535797 GGGACGGAGGGAGTACAAAG 59.464 60.0 0.00 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 3445 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73 R
2535 3787 0.111639 TTACAAGGTTGGGGTGCCTC 59.888 55.000 0.00 0.00 33.24 4.70 R
3295 4552 0.538057 CTTCAAGAAGCAGCACCCCA 60.538 55.000 0.00 0.00 0.00 4.96 R
3658 4934 1.815196 CTGTTGCTTGGGTGCACAA 59.185 52.632 20.43 4.21 43.20 3.33 R
4229 5505 2.048222 TTCAGCCTGTTCCTCGCG 60.048 61.111 0.00 0.00 0.00 5.87 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
70 71 8.916628 AGAAAAAGAAAAGTCAATCTAGAGCT 57.083 30.769 0.00 0.00 0.00 4.09
161 162 0.533491 CGTTTCTACACGGGATCCCA 59.467 55.000 30.42 10.08 36.47 4.37
162 163 1.138266 CGTTTCTACACGGGATCCCAT 59.862 52.381 30.42 13.83 36.47 4.00
163 164 2.802057 CGTTTCTACACGGGATCCCATC 60.802 54.545 30.42 7.25 36.47 3.51
271 276 1.011968 TCCATGAACGAACGAAGCCG 61.012 55.000 0.00 0.00 42.50 5.52
272 277 1.225745 CATGAACGAACGAAGCCGC 60.226 57.895 0.14 0.00 39.95 6.53
273 278 2.726691 ATGAACGAACGAAGCCGCG 61.727 57.895 0.00 0.00 39.95 6.46
385 1552 3.237522 CGACGGACGGAATTCTCTC 57.762 57.895 5.23 0.15 38.46 3.20
386 1553 0.733729 CGACGGACGGAATTCTCTCT 59.266 55.000 5.23 0.00 38.46 3.10
387 1554 1.268133 CGACGGACGGAATTCTCTCTC 60.268 57.143 5.23 0.00 38.46 3.20
392 1559 2.159043 GGACGGAATTCTCTCTCATGCA 60.159 50.000 5.23 0.00 0.00 3.96
401 1568 1.377725 CTCTCATGCAGCCGGGTTT 60.378 57.895 1.64 0.00 0.00 3.27
402 1569 0.107703 CTCTCATGCAGCCGGGTTTA 60.108 55.000 1.64 0.00 0.00 2.01
404 1571 1.718757 CTCATGCAGCCGGGTTTAGC 61.719 60.000 1.64 5.25 0.00 3.09
483 1656 2.660552 CCGGTCAGTGCGTTCGTT 60.661 61.111 0.00 0.00 0.00 3.85
484 1657 2.654912 CCGGTCAGTGCGTTCGTTC 61.655 63.158 0.00 0.00 0.00 3.95
486 1659 1.947642 GGTCAGTGCGTTCGTTCGT 60.948 57.895 4.37 0.00 0.00 3.85
489 1662 1.660575 CAGTGCGTTCGTTCGTCCT 60.661 57.895 4.37 0.00 0.00 3.85
491 1664 0.529119 AGTGCGTTCGTTCGTCCTTT 60.529 50.000 4.37 0.00 0.00 3.11
492 1665 0.382636 GTGCGTTCGTTCGTCCTTTG 60.383 55.000 4.37 0.00 0.00 2.77
497 1684 3.053896 CGTTCGTCCTTTGCCCCC 61.054 66.667 0.00 0.00 0.00 5.40
559 1746 1.244816 GGTAAAACTTCCGCCTGCTT 58.755 50.000 0.00 0.00 0.00 3.91
570 1773 1.299321 GCCTGCTTTGCTCTCCTCT 59.701 57.895 0.00 0.00 0.00 3.69
599 1807 2.997315 CTCCTCGGCCTGTCCACA 60.997 66.667 0.00 0.00 34.01 4.17
614 1822 1.891919 CACAACACCACCACGAGGG 60.892 63.158 3.29 0.00 44.81 4.30
654 1862 1.001815 CAAAACATTCGGTTGGCTCGT 60.002 47.619 0.00 0.00 40.35 4.18
811 2021 3.120477 TCGCCGTACAAATTTACAAGCTG 60.120 43.478 0.00 0.00 0.00 4.24
812 2022 3.498082 GCCGTACAAATTTACAAGCTGG 58.502 45.455 0.00 0.00 0.00 4.85
813 2023 3.189702 GCCGTACAAATTTACAAGCTGGA 59.810 43.478 0.00 0.00 0.00 3.86
814 2024 4.671766 GCCGTACAAATTTACAAGCTGGAG 60.672 45.833 0.00 0.00 0.00 3.86
815 2025 4.454504 CCGTACAAATTTACAAGCTGGAGT 59.545 41.667 0.00 0.00 0.00 3.85
822 2032 6.575162 AATTTACAAGCTGGAGTAGGTTTG 57.425 37.500 0.00 0.00 44.32 2.93
886 2103 1.374252 GAGTAGGCCCGTGTGTGTG 60.374 63.158 0.00 0.00 0.00 3.82
887 2104 2.095978 GAGTAGGCCCGTGTGTGTGT 62.096 60.000 0.00 0.00 0.00 3.72
888 2105 1.959226 GTAGGCCCGTGTGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
889 2106 3.818121 TAGGCCCGTGTGTGTGTGC 62.818 63.158 0.00 0.00 0.00 4.57
909 2126 1.408422 GTTGTTTGCTCAATCGTGCC 58.592 50.000 0.00 0.00 0.00 5.01
981 2198 1.068741 CTTCGGATAAAGGTCTCGGGG 59.931 57.143 0.00 0.00 0.00 5.73
996 2214 3.467226 GGGAGGCCACGGATTCGA 61.467 66.667 5.01 0.00 40.11 3.71
1043 2261 3.760035 GAGCGGCTCCAAGTCGGA 61.760 66.667 19.20 0.00 44.68 4.55
1061 2279 0.329596 GAGCCAGGTCCAAATGGTCT 59.670 55.000 0.00 0.00 38.91 3.85
1161 2380 4.925646 CCTGCTTAAAGCTTTCCAACATTC 59.074 41.667 16.57 0.00 42.97 2.67
1164 2383 6.677913 TGCTTAAAGCTTTCCAACATTCTAC 58.322 36.000 16.57 0.00 42.97 2.59
1193 2412 7.021196 TCGAATTTTAAGAACATACTTGCTGC 58.979 34.615 0.00 0.00 0.00 5.25
1202 2421 2.751259 ACATACTTGCTGCTTGACATGG 59.249 45.455 0.00 0.00 0.00 3.66
1227 2446 0.614812 GTGGGGGATTTGCTGCAAAT 59.385 50.000 33.67 33.67 45.25 2.32
1248 2478 0.036732 TGTCCTGCTTAGCCAACCAG 59.963 55.000 0.29 0.00 0.00 4.00
1285 2515 9.892130 CTCCTTACTAGTTGTTCCAATTATTCT 57.108 33.333 0.00 0.00 0.00 2.40
1302 2532 2.654749 TCTAGTGTTGCAGATGGACG 57.345 50.000 0.00 0.00 0.00 4.79
1303 2533 2.167662 TCTAGTGTTGCAGATGGACGA 58.832 47.619 0.00 0.00 0.00 4.20
1304 2534 2.164422 TCTAGTGTTGCAGATGGACGAG 59.836 50.000 0.00 0.00 0.00 4.18
1368 2614 9.717942 TTGATAAAAGTCAATTTAACAATGGGG 57.282 29.630 0.00 0.00 34.58 4.96
1429 2675 9.066892 AGAACACTATGAATTCTAACAGCAAAA 57.933 29.630 7.05 0.00 30.88 2.44
1520 2767 7.161404 TGATAGTGCTATTGGTATGATGTTCC 58.839 38.462 0.00 0.00 0.00 3.62
1649 2897 5.065090 GCCTTTTGTGTTCTGCATTTCTTTT 59.935 36.000 0.00 0.00 0.00 2.27
1701 2949 6.811665 GGCTTAAATGAAACATTTCCTACACC 59.188 38.462 12.02 5.06 36.36 4.16
1719 2967 1.988107 ACCAGAGGTTGTGTGATCCAT 59.012 47.619 0.00 0.00 27.29 3.41
1720 2968 2.026822 ACCAGAGGTTGTGTGATCCATC 60.027 50.000 0.00 0.00 27.29 3.51
1721 2969 2.026915 CCAGAGGTTGTGTGATCCATCA 60.027 50.000 0.00 0.00 0.00 3.07
1818 3069 4.039488 TGAACTAGTAAGCCGAGGTTTTGA 59.961 41.667 0.00 0.00 0.00 2.69
2058 3310 3.367292 GCCACACGGAATTTTCACATGAT 60.367 43.478 0.00 0.00 0.00 2.45
2138 3390 7.437267 TCGTATTGCTGCCTTCTTACTTTATAC 59.563 37.037 0.00 0.00 0.00 1.47
2139 3391 7.438459 CGTATTGCTGCCTTCTTACTTTATACT 59.562 37.037 0.00 0.00 0.00 2.12
2140 3392 7.793927 ATTGCTGCCTTCTTACTTTATACTC 57.206 36.000 0.00 0.00 0.00 2.59
2141 3393 5.671493 TGCTGCCTTCTTACTTTATACTCC 58.329 41.667 0.00 0.00 0.00 3.85
2142 3394 5.057819 GCTGCCTTCTTACTTTATACTCCC 58.942 45.833 0.00 0.00 0.00 4.30
2143 3395 5.163290 GCTGCCTTCTTACTTTATACTCCCT 60.163 44.000 0.00 0.00 0.00 4.20
2144 3396 6.481434 TGCCTTCTTACTTTATACTCCCTC 57.519 41.667 0.00 0.00 0.00 4.30
2145 3397 5.365895 TGCCTTCTTACTTTATACTCCCTCC 59.634 44.000 0.00 0.00 0.00 4.30
2146 3398 5.509332 GCCTTCTTACTTTATACTCCCTCCG 60.509 48.000 0.00 0.00 0.00 4.63
2147 3399 5.597594 CCTTCTTACTTTATACTCCCTCCGT 59.402 44.000 0.00 0.00 0.00 4.69
2148 3400 6.097981 CCTTCTTACTTTATACTCCCTCCGTT 59.902 42.308 0.00 0.00 0.00 4.44
2149 3401 6.705863 TCTTACTTTATACTCCCTCCGTTC 57.294 41.667 0.00 0.00 0.00 3.95
2150 3402 5.595952 TCTTACTTTATACTCCCTCCGTTCC 59.404 44.000 0.00 0.00 0.00 3.62
2151 3403 3.716431 ACTTTATACTCCCTCCGTTCCA 58.284 45.455 0.00 0.00 0.00 3.53
2152 3404 4.098894 ACTTTATACTCCCTCCGTTCCAA 58.901 43.478 0.00 0.00 0.00 3.53
2153 3405 4.533311 ACTTTATACTCCCTCCGTTCCAAA 59.467 41.667 0.00 0.00 0.00 3.28
2154 3406 5.013391 ACTTTATACTCCCTCCGTTCCAAAA 59.987 40.000 0.00 0.00 0.00 2.44
2155 3407 5.703730 TTATACTCCCTCCGTTCCAAAAT 57.296 39.130 0.00 0.00 0.00 1.82
2156 3408 6.811634 TTATACTCCCTCCGTTCCAAAATA 57.188 37.500 0.00 0.00 0.00 1.40
2157 3409 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2158 3410 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2159 3411 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2160 3412 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2161 3413 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2162 3414 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2163 3415 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2164 3416 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2165 3417 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2166 3418 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2167 3419 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2168 3420 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2169 3421 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2170 3422 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2171 3423 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2172 3424 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2173 3425 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2174 3426 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2175 3427 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2176 3428 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2177 3429 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2178 3430 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
2179 3431 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
2180 3432 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
2181 3433 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
2182 3434 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
2183 3435 5.591067 TGACCCAACTTTGTACTAACTTTGG 59.409 40.000 14.15 14.15 33.25 3.28
2184 3436 5.512298 ACCCAACTTTGTACTAACTTTGGT 58.488 37.500 17.29 10.13 31.82 3.67
2185 3437 6.661777 ACCCAACTTTGTACTAACTTTGGTA 58.338 36.000 17.29 0.00 31.82 3.25
2186 3438 6.543465 ACCCAACTTTGTACTAACTTTGGTAC 59.457 38.462 17.29 8.31 43.06 3.34
2203 3455 5.990120 TGGTACAAAGTTAGTACTCCCTC 57.010 43.478 0.00 0.00 41.16 4.30
2204 3456 4.774200 TGGTACAAAGTTAGTACTCCCTCC 59.226 45.833 0.00 0.00 41.16 4.30
2205 3457 4.142293 GGTACAAAGTTAGTACTCCCTCCG 60.142 50.000 0.00 0.00 41.16 4.63
2206 3458 3.504375 ACAAAGTTAGTACTCCCTCCGT 58.496 45.455 0.00 0.00 31.99 4.69
2207 3459 3.509184 ACAAAGTTAGTACTCCCTCCGTC 59.491 47.826 0.00 0.00 31.99 4.79
2208 3460 2.433662 AGTTAGTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
2209 3461 1.064091 AGTTAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
2210 3462 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2211 3463 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2212 3464 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2213 3465 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2214 3466 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2215 3467 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2216 3468 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2217 3469 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2218 3470 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2219 3471 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2220 3472 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2221 3473 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2222 3474 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2223 3475 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2224 3476 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2225 3477 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2226 3478 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2227 3479 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2228 3480 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2229 3481 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2230 3482 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2231 3483 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2232 3484 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2233 3485 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2241 3493 9.961264 TCTTGTCTTAGATTTGTCTAGTCTAGA 57.039 33.333 5.41 5.41 0.00 2.43
2293 3545 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2294 3546 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2295 3547 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2296 3548 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2297 3549 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2298 3550 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2299 3551 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2300 3552 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2301 3553 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2302 3554 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2303 3555 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2304 3556 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2305 3557 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2306 3558 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2307 3559 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
2308 3560 0.178926 TTGGGACGGAGGGAGTACAA 60.179 55.000 0.00 0.00 0.00 2.41
2309 3561 0.178926 TGGGACGGAGGGAGTACAAA 60.179 55.000 0.00 0.00 0.00 2.83
2310 3562 0.535797 GGGACGGAGGGAGTACAAAG 59.464 60.000 0.00 0.00 0.00 2.77
2311 3563 1.264295 GGACGGAGGGAGTACAAAGT 58.736 55.000 0.00 0.00 0.00 2.66
2312 3564 1.622312 GGACGGAGGGAGTACAAAGTT 59.378 52.381 0.00 0.00 0.00 2.66
2313 3565 2.612221 GGACGGAGGGAGTACAAAGTTG 60.612 54.545 0.00 0.00 0.00 3.16
2314 3566 2.298163 GACGGAGGGAGTACAAAGTTGA 59.702 50.000 0.00 0.00 0.00 3.18
2315 3567 2.299297 ACGGAGGGAGTACAAAGTTGAG 59.701 50.000 0.00 0.00 0.00 3.02
2316 3568 2.299297 CGGAGGGAGTACAAAGTTGAGT 59.701 50.000 0.00 0.00 0.00 3.41
2317 3569 3.614390 CGGAGGGAGTACAAAGTTGAGTC 60.614 52.174 0.00 0.00 0.00 3.36
2318 3570 3.323979 GGAGGGAGTACAAAGTTGAGTCA 59.676 47.826 0.00 0.00 0.00 3.41
2319 3571 4.020128 GGAGGGAGTACAAAGTTGAGTCAT 60.020 45.833 0.00 0.00 0.00 3.06
2320 3572 5.153950 AGGGAGTACAAAGTTGAGTCATC 57.846 43.478 0.00 0.00 0.00 2.92
2321 3573 4.841246 AGGGAGTACAAAGTTGAGTCATCT 59.159 41.667 0.00 0.00 0.00 2.90
2322 3574 6.017192 AGGGAGTACAAAGTTGAGTCATCTA 58.983 40.000 4.14 0.00 0.00 1.98
2323 3575 6.670027 AGGGAGTACAAAGTTGAGTCATCTAT 59.330 38.462 4.14 0.00 0.00 1.98
2324 3576 7.181125 AGGGAGTACAAAGTTGAGTCATCTATT 59.819 37.037 4.14 0.00 0.00 1.73
2325 3577 7.824779 GGGAGTACAAAGTTGAGTCATCTATTT 59.175 37.037 4.14 0.00 0.00 1.40
2326 3578 9.220767 GGAGTACAAAGTTGAGTCATCTATTTT 57.779 33.333 4.14 0.00 0.00 1.82
2328 3580 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2329 3581 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2330 3582 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2331 3583 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2332 3584 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2333 3585 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2334 3586 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2335 3587 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2336 3588 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2337 3589 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2338 3590 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2339 3591 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2340 3592 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2341 3593 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2425 3677 4.566004 TGAATAACAGTGGTTCTCCTTCG 58.434 43.478 0.00 0.00 38.45 3.79
2535 3787 7.384387 ACAGAGATCGATGTCATATCAAATGTG 59.616 37.037 23.01 11.34 0.00 3.21
2745 3997 7.345653 TGATCAGGACCAAAGAGTAGATGTATT 59.654 37.037 0.00 0.00 0.00 1.89
2955 4207 1.511887 CATTAGCACGCGTGTTGCC 60.512 57.895 36.80 22.00 42.08 4.52
3019 4271 7.568199 ACTTGCTTTTACAGTGTGAGTTATT 57.432 32.000 5.88 0.00 0.00 1.40
3067 4319 6.534079 GGAACAAATATCGTGCAGTACTTACT 59.466 38.462 0.00 0.00 36.90 2.24
3295 4552 9.686683 ACCAAGAAAGCAGACATATATAGTTTT 57.313 29.630 0.00 0.00 0.00 2.43
3399 4656 3.244770 TGGGTAATTCACTTTCGCCTCTT 60.245 43.478 0.00 0.00 0.00 2.85
3462 4738 3.858812 GCATCATAAATCTGCGCACAAAA 59.141 39.130 5.66 0.00 0.00 2.44
3606 4882 6.097412 GGCTTTTGGAAATTGTAGATCCAGAT 59.903 38.462 0.00 0.00 43.69 2.90
3658 4934 2.034558 CGTTTCATCAAGGTGGCACTTT 59.965 45.455 18.45 13.99 0.00 2.66
4012 5288 3.128349 GAGTGCTGACGAGGTTTTTGTA 58.872 45.455 0.00 0.00 0.00 2.41
4229 5505 5.341872 AGGCAGCATATGAGATAGATGTC 57.658 43.478 6.97 0.00 30.65 3.06
4254 5530 0.868406 GAACAGGCTGAACAGTTCCG 59.132 55.000 23.66 5.59 35.52 4.30
4257 5533 0.951040 CAGGCTGAACAGTTCCGTCC 60.951 60.000 9.42 9.74 0.00 4.79
4339 5619 8.268850 AGTGAACATGTGTAGAAATTATGGTC 57.731 34.615 0.00 0.00 36.32 4.02
4379 5659 8.678510 CGTTGATACATTGTACTTTTTGTTCAC 58.321 33.333 0.00 0.00 0.00 3.18
4383 5663 5.956642 ACATTGTACTTTTTGTTCACGGTT 58.043 33.333 0.00 0.00 0.00 4.44
4425 5705 0.899720 TTTACTGGACCGCACCTAGG 59.100 55.000 7.41 7.41 0.00 3.02
4427 5707 2.159101 TACTGGACCGCACCTAGGGT 62.159 60.000 14.81 0.07 39.83 4.34
4456 5736 5.750352 ATTGGAGCCAAATGTTTTCTCAT 57.250 34.783 5.98 0.00 39.55 2.90
4474 5754 5.188434 TCTCATGGGATCTTTGAATGACAC 58.812 41.667 0.00 0.00 0.00 3.67
4477 5757 6.720309 TCATGGGATCTTTGAATGACACTTA 58.280 36.000 0.00 0.00 0.00 2.24
4498 5778 7.432252 CACTTACACATGTCAGGAAAGAAAAAC 59.568 37.037 0.00 0.00 0.00 2.43
4547 5830 7.067008 CCCTCCGTTCACAAATATAAGATGTTT 59.933 37.037 0.00 0.00 0.00 2.83
4597 5885 6.004408 ACGTTTTAGTGTGTTTGTTCACTT 57.996 33.333 3.25 0.00 43.39 3.16
4626 5914 9.976511 TTCTATCCGTTTGTAGTCCATATTAAG 57.023 33.333 0.00 0.00 0.00 1.85
4663 5952 6.338146 TCTTATATTTGTGACGAAGGGAGTG 58.662 40.000 0.00 0.00 0.00 3.51
4671 5960 1.205893 GACGAAGGGAGTGCTGAGAAT 59.794 52.381 0.00 0.00 0.00 2.40
4746 6075 6.293735 CCAAATGATTTTGACATTGCAAGCTT 60.294 34.615 4.94 0.00 44.11 3.74
4799 6141 8.856247 CAAATGTCAATATATGAATCCAATGCG 58.144 33.333 0.00 0.00 40.50 4.73
4809 6165 0.592637 ATCCAATGCGTGTGTGTGTG 59.407 50.000 0.00 0.00 0.00 3.82
4859 6215 5.860941 TTTGAATTGGGTGCAAGTAAAGA 57.139 34.783 0.00 0.00 0.00 2.52
4862 6218 7.531857 TTGAATTGGGTGCAAGTAAAGATAA 57.468 32.000 0.00 0.00 0.00 1.75
4903 6261 4.260948 GCAAGTAGAATGAATGTGCTAGGC 60.261 45.833 0.00 0.00 0.00 3.93
4906 6264 2.928334 AGAATGAATGTGCTAGGCTGG 58.072 47.619 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.604174 GCCCGTCGTCAAAGGTGTG 61.604 63.158 0.00 0.00 0.00 3.82
18 19 2.348411 AATTAATAGCTGCTGCCCGT 57.652 45.000 13.43 0.00 40.80 5.28
70 71 3.678056 ACGTGTCAGGAAGCAATTCTA 57.322 42.857 0.00 0.00 0.00 2.10
108 109 2.483877 TGTTATCAGCCGTTTTGCAGAG 59.516 45.455 0.00 0.00 29.89 3.35
230 231 1.331161 CGAAAGATCCGCGTTTCATCG 60.331 52.381 16.87 15.56 33.07 3.84
384 1551 0.107703 CTAAACCCGGCTGCATGAGA 60.108 55.000 0.50 0.00 0.00 3.27
385 1552 1.718757 GCTAAACCCGGCTGCATGAG 61.719 60.000 0.50 0.00 0.00 2.90
386 1553 1.748879 GCTAAACCCGGCTGCATGA 60.749 57.895 0.50 0.00 0.00 3.07
387 1554 1.750399 AGCTAAACCCGGCTGCATG 60.750 57.895 0.50 0.00 37.41 4.06
392 1559 2.535331 AACCCAGCTAAACCCGGCT 61.535 57.895 0.00 0.00 39.60 5.52
401 1568 3.399181 CTCGGCCCAACCCAGCTA 61.399 66.667 0.00 0.00 33.26 3.32
419 1591 2.604174 CCACGTTTCTGGGTCACGC 61.604 63.158 0.00 0.00 37.44 5.34
457 1630 1.298859 GCACTGACCGGTTGACCATC 61.299 60.000 9.42 0.00 35.14 3.51
483 1656 1.110518 GTTTTGGGGGCAAAGGACGA 61.111 55.000 0.00 0.00 0.00 4.20
484 1657 1.365999 GTTTTGGGGGCAAAGGACG 59.634 57.895 0.00 0.00 0.00 4.79
486 1659 0.397254 TTCGTTTTGGGGGCAAAGGA 60.397 50.000 0.00 0.00 0.00 3.36
489 1662 0.902531 TTGTTCGTTTTGGGGGCAAA 59.097 45.000 0.00 0.00 0.00 3.68
491 1664 0.902531 TTTTGTTCGTTTTGGGGGCA 59.097 45.000 0.00 0.00 0.00 5.36
492 1665 1.577468 CTTTTGTTCGTTTTGGGGGC 58.423 50.000 0.00 0.00 0.00 5.80
497 1684 1.073054 GCGTCGCTTTTGTTCGTTTTG 60.073 47.619 10.68 0.00 0.00 2.44
559 1746 2.364317 CGGGGGAGAGGAGAGCAA 60.364 66.667 0.00 0.00 0.00 3.91
570 1773 4.153330 GAGGAGGTAGGCGGGGGA 62.153 72.222 0.00 0.00 0.00 4.81
591 1794 1.436195 CGTGGTGGTGTTGTGGACAG 61.436 60.000 0.00 0.00 39.39 3.51
599 1807 2.770904 ACCCCTCGTGGTGGTGTT 60.771 61.111 13.71 0.00 37.20 3.32
671 1879 2.513204 CAGATGGGTGGAGCTGCG 60.513 66.667 0.00 0.00 0.00 5.18
811 2021 2.838813 AGGGAAGCTACAAACCTACTCC 59.161 50.000 0.00 0.00 0.00 3.85
812 2022 3.863041 CAGGGAAGCTACAAACCTACTC 58.137 50.000 0.00 0.00 0.00 2.59
813 2023 2.027100 GCAGGGAAGCTACAAACCTACT 60.027 50.000 0.00 0.00 0.00 2.57
814 2024 2.027100 AGCAGGGAAGCTACAAACCTAC 60.027 50.000 0.00 0.00 44.50 3.18
815 2025 2.266279 AGCAGGGAAGCTACAAACCTA 58.734 47.619 0.00 0.00 44.50 3.08
822 2032 1.454201 GGAACAAGCAGGGAAGCTAC 58.546 55.000 0.00 0.00 45.89 3.58
886 2103 1.044725 CGATTGAGCAAACAACGCAC 58.955 50.000 0.00 0.00 32.50 5.34
887 2104 0.660488 ACGATTGAGCAAACAACGCA 59.340 45.000 0.00 0.00 32.50 5.24
888 2105 1.044725 CACGATTGAGCAAACAACGC 58.955 50.000 0.00 0.00 32.50 4.84
889 2106 1.044725 GCACGATTGAGCAAACAACG 58.955 50.000 0.00 0.00 32.50 4.10
890 2107 1.408422 GGCACGATTGAGCAAACAAC 58.592 50.000 4.67 0.00 32.83 3.32
909 2126 2.870411 GGGGACGAAATTAACCATCTCG 59.130 50.000 0.00 0.00 35.68 4.04
981 2198 2.582498 CGTCGAATCCGTGGCCTC 60.582 66.667 3.32 0.00 37.05 4.70
1043 2261 1.561542 CTAGACCATTTGGACCTGGCT 59.438 52.381 3.01 0.63 38.94 4.75
1074 2292 1.310933 TACCAGAACGAGGAGACGCC 61.311 60.000 0.00 0.00 36.70 5.68
1164 2383 9.267096 GCAAGTATGTTCTTAAAATTCGAAGAG 57.733 33.333 3.35 0.00 38.43 2.85
1193 2412 2.440409 CCCCACTCTTTCCATGTCAAG 58.560 52.381 0.00 0.00 0.00 3.02
1202 2421 1.821136 CAGCAAATCCCCCACTCTTTC 59.179 52.381 0.00 0.00 0.00 2.62
1227 2446 0.324943 GGTTGGCTAAGCAGGACAGA 59.675 55.000 7.17 0.00 34.50 3.41
1285 2515 1.893137 ACTCGTCCATCTGCAACACTA 59.107 47.619 0.00 0.00 0.00 2.74
1302 2532 4.336713 GGCACCCTAAATTTCTCATCACTC 59.663 45.833 0.00 0.00 0.00 3.51
1303 2533 4.018050 AGGCACCCTAAATTTCTCATCACT 60.018 41.667 0.00 0.00 28.47 3.41
1304 2534 4.273318 AGGCACCCTAAATTTCTCATCAC 58.727 43.478 0.00 0.00 28.47 3.06
1368 2614 1.270518 TGGAAGTCTCTGTGCTTCAGC 60.271 52.381 6.62 0.00 43.32 4.26
1465 2711 6.325919 TGAAAAAGCCGACAAACATCTAAT 57.674 33.333 0.00 0.00 0.00 1.73
1466 2712 5.759506 TGAAAAAGCCGACAAACATCTAA 57.240 34.783 0.00 0.00 0.00 2.10
1536 2783 4.143543 CAATGTTTTGGAATTTTGGGCCT 58.856 39.130 4.53 0.00 0.00 5.19
1547 2794 2.975732 TGTTGCTGCAATGTTTTGGA 57.024 40.000 19.11 0.00 33.22 3.53
1582 2830 8.814733 TTATTTTGCGTGAACTTACGATTATG 57.185 30.769 2.14 0.00 46.46 1.90
1649 2897 4.817318 TGCAGATGACACAGGTAACATA 57.183 40.909 0.00 0.00 41.41 2.29
1701 2949 3.339253 TGATGGATCACACAACCTCTG 57.661 47.619 0.00 0.00 0.00 3.35
1719 2967 7.882791 AGATGTGTGTCATGGTATAGTTTTTGA 59.117 33.333 0.00 0.00 36.83 2.69
1720 2968 7.964559 CAGATGTGTGTCATGGTATAGTTTTTG 59.035 37.037 0.00 0.00 36.83 2.44
1721 2969 7.121168 CCAGATGTGTGTCATGGTATAGTTTTT 59.879 37.037 0.00 0.00 36.83 1.94
2058 3310 2.267351 CCACGGCCAATGCAGTTCA 61.267 57.895 2.24 0.00 43.70 3.18
2138 3390 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2139 3391 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2140 3392 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2141 3393 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2142 3394 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2143 3395 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2144 3396 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2145 3397 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2146 3398 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2147 3399 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2148 3400 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2149 3401 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2150 3402 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2151 3403 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2152 3404 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
2153 3405 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
2154 3406 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
2155 3407 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
2156 3408 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
2157 3409 7.360361 CAAAGTTAGTACAAAGTTGGGTCATC 58.640 38.462 0.00 0.00 0.00 2.92
2158 3410 6.264518 CCAAAGTTAGTACAAAGTTGGGTCAT 59.735 38.462 0.00 0.00 30.84 3.06
2159 3411 5.591067 CCAAAGTTAGTACAAAGTTGGGTCA 59.409 40.000 0.00 0.00 30.84 4.02
2160 3412 5.591472 ACCAAAGTTAGTACAAAGTTGGGTC 59.409 40.000 15.46 0.00 40.62 4.46
2161 3413 5.512298 ACCAAAGTTAGTACAAAGTTGGGT 58.488 37.500 15.46 6.01 40.05 4.51
2162 3414 6.543100 TGTACCAAAGTTAGTACAAAGTTGGG 59.457 38.462 13.64 5.51 44.32 4.12
2163 3415 7.556733 TGTACCAAAGTTAGTACAAAGTTGG 57.443 36.000 13.64 11.57 44.32 3.77
2175 3427 8.150296 GGGAGTACTAACTTTGTACCAAAGTTA 58.850 37.037 27.48 27.48 45.51 2.24
2177 3429 6.328410 AGGGAGTACTAACTTTGTACCAAAGT 59.672 38.462 14.80 14.80 41.82 2.66
2178 3430 6.766429 AGGGAGTACTAACTTTGTACCAAAG 58.234 40.000 13.62 13.62 40.61 2.77
2179 3431 6.239686 GGAGGGAGTACTAACTTTGTACCAAA 60.240 42.308 0.00 0.00 40.61 3.28
2180 3432 5.246883 GGAGGGAGTACTAACTTTGTACCAA 59.753 44.000 0.00 0.00 40.61 3.67
2181 3433 4.774200 GGAGGGAGTACTAACTTTGTACCA 59.226 45.833 0.00 0.00 40.61 3.25
2182 3434 4.142293 CGGAGGGAGTACTAACTTTGTACC 60.142 50.000 0.00 0.00 40.61 3.34
2183 3435 4.460731 ACGGAGGGAGTACTAACTTTGTAC 59.539 45.833 0.00 5.63 40.19 2.90
2184 3436 4.666512 ACGGAGGGAGTACTAACTTTGTA 58.333 43.478 0.00 0.00 35.56 2.41
2185 3437 3.504375 ACGGAGGGAGTACTAACTTTGT 58.496 45.455 0.00 0.00 35.56 2.83
2186 3438 3.119209 GGACGGAGGGAGTACTAACTTTG 60.119 52.174 0.00 0.00 35.56 2.77
2187 3439 3.095332 GGACGGAGGGAGTACTAACTTT 58.905 50.000 0.00 0.00 35.56 2.66
2188 3440 2.622714 GGGACGGAGGGAGTACTAACTT 60.623 54.545 0.00 0.00 35.56 2.66
2189 3441 1.064091 GGGACGGAGGGAGTACTAACT 60.064 57.143 0.00 0.00 39.21 2.24
2190 3442 1.341383 TGGGACGGAGGGAGTACTAAC 60.341 57.143 0.00 0.00 0.00 2.34
2191 3443 1.002069 TGGGACGGAGGGAGTACTAA 58.998 55.000 0.00 0.00 0.00 2.24
2192 3444 1.002069 TTGGGACGGAGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
2193 3445 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
2194 3446 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2195 3447 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2196 3448 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2197 3449 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2198 3450 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2199 3451 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2200 3452 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2201 3453 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2202 3454 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2203 3455 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2204 3456 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2205 3457 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2206 3458 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2207 3459 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2215 3467 9.961264 TCTAGACTAGACAAATCTAAGACAAGA 57.039 33.333 8.17 0.00 36.98 3.02
2267 3519 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2268 3520 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2269 3521 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2270 3522 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2271 3523 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2272 3524 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2273 3525 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2274 3526 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2275 3527 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2276 3528 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2277 3529 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2278 3530 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2279 3531 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2280 3532 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2281 3533 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2282 3534 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2283 3535 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2284 3536 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2285 3537 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2286 3538 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2287 3539 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2288 3540 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2289 3541 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
2290 3542 0.178926 TTTGTACTCCCTCCGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
2291 3543 0.535797 CTTTGTACTCCCTCCGTCCC 59.464 60.000 0.00 0.00 0.00 4.46
2292 3544 1.264295 ACTTTGTACTCCCTCCGTCC 58.736 55.000 0.00 0.00 0.00 4.79
2293 3545 2.298163 TCAACTTTGTACTCCCTCCGTC 59.702 50.000 0.00 0.00 0.00 4.79
2294 3546 2.299297 CTCAACTTTGTACTCCCTCCGT 59.701 50.000 0.00 0.00 0.00 4.69
2295 3547 2.299297 ACTCAACTTTGTACTCCCTCCG 59.701 50.000 0.00 0.00 0.00 4.63
2296 3548 3.323979 TGACTCAACTTTGTACTCCCTCC 59.676 47.826 0.00 0.00 0.00 4.30
2297 3549 4.602340 TGACTCAACTTTGTACTCCCTC 57.398 45.455 0.00 0.00 0.00 4.30
2298 3550 4.841246 AGATGACTCAACTTTGTACTCCCT 59.159 41.667 0.00 0.00 0.00 4.20
2299 3551 5.153950 AGATGACTCAACTTTGTACTCCC 57.846 43.478 0.00 0.00 0.00 4.30
2300 3552 8.779354 AAATAGATGACTCAACTTTGTACTCC 57.221 34.615 0.00 0.00 0.00 3.85
2302 3554 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2303 3555 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2304 3556 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2305 3557 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2306 3558 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2307 3559 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2308 3560 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2309 3561 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2310 3562 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2311 3563 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2312 3564 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2313 3565 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2314 3566 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2315 3567 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2316 3568 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2317 3569 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2318 3570 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2319 3571 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2320 3572 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2321 3573 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
2322 3574 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
2323 3575 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
2324 3576 2.235402 GACATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
2325 3577 1.829222 GACATACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
2326 3578 1.481871 GACATACTCCCTCCGTTCCA 58.518 55.000 0.00 0.00 0.00 3.53
2327 3579 0.384669 CGACATACTCCCTCCGTTCC 59.615 60.000 0.00 0.00 0.00 3.62
2328 3580 1.101331 ACGACATACTCCCTCCGTTC 58.899 55.000 0.00 0.00 0.00 3.95
2329 3581 2.425143 TACGACATACTCCCTCCGTT 57.575 50.000 0.00 0.00 0.00 4.44
2330 3582 2.228059 CATACGACATACTCCCTCCGT 58.772 52.381 0.00 0.00 0.00 4.69
2331 3583 2.228059 ACATACGACATACTCCCTCCG 58.772 52.381 0.00 0.00 0.00 4.63
2332 3584 5.475909 TGATAACATACGACATACTCCCTCC 59.524 44.000 0.00 0.00 0.00 4.30
2333 3585 6.207025 AGTGATAACATACGACATACTCCCTC 59.793 42.308 0.00 0.00 0.00 4.30
2334 3586 6.016192 CAGTGATAACATACGACATACTCCCT 60.016 42.308 0.00 0.00 0.00 4.20
2335 3587 6.150318 CAGTGATAACATACGACATACTCCC 58.850 44.000 0.00 0.00 0.00 4.30
2336 3588 5.629849 GCAGTGATAACATACGACATACTCC 59.370 44.000 0.00 0.00 0.00 3.85
2337 3589 6.439599 AGCAGTGATAACATACGACATACTC 58.560 40.000 0.00 0.00 0.00 2.59
2338 3590 6.039382 TGAGCAGTGATAACATACGACATACT 59.961 38.462 0.00 0.00 0.00 2.12
2339 3591 6.206498 TGAGCAGTGATAACATACGACATAC 58.794 40.000 0.00 0.00 0.00 2.39
2340 3592 6.385649 TGAGCAGTGATAACATACGACATA 57.614 37.500 0.00 0.00 0.00 2.29
2341 3593 5.262588 TGAGCAGTGATAACATACGACAT 57.737 39.130 0.00 0.00 0.00 3.06
2425 3677 2.445682 TCTCTCAGGTCTCCCTAAGC 57.554 55.000 0.00 0.00 39.89 3.09
2535 3787 0.111639 TTACAAGGTTGGGGTGCCTC 59.888 55.000 0.00 0.00 33.24 4.70
2745 3997 3.360867 TCTTGTTTGCCAGTTCAAAGGA 58.639 40.909 0.00 0.00 36.71 3.36
2955 4207 2.232452 AGAGAGGACTGACATTGTTCCG 59.768 50.000 0.00 0.00 0.00 4.30
3019 4271 9.893634 TTCCGGAGAAAATCTACATAAATACAA 57.106 29.630 3.34 0.00 0.00 2.41
3295 4552 0.538057 CTTCAAGAAGCAGCACCCCA 60.538 55.000 0.00 0.00 0.00 4.96
3399 4656 5.369404 TGGTATTGCATCCTATGGAGAAAGA 59.631 40.000 0.00 0.00 34.05 2.52
3462 4738 3.474920 ACCATGGGGAAATCTAGGACTT 58.525 45.455 18.09 0.00 38.05 3.01
3606 4882 3.107601 CTCCTCTGGGTATTCTTCCACA 58.892 50.000 0.00 0.00 0.00 4.17
3658 4934 1.815196 CTGTTGCTTGGGTGCACAA 59.185 52.632 20.43 4.21 43.20 3.33
4012 5288 9.369904 GTACATTATGTGCAATTTTCCATTTCT 57.630 29.630 8.26 0.00 33.03 2.52
4229 5505 2.048222 TTCAGCCTGTTCCTCGCG 60.048 61.111 0.00 0.00 0.00 5.87
4254 5530 3.319972 TGACTAGGGTTATATGCACGGAC 59.680 47.826 0.00 0.00 0.00 4.79
4257 5533 4.316205 TGTGACTAGGGTTATATGCACG 57.684 45.455 0.00 0.00 0.00 5.34
4339 5619 1.581934 TCAACGGTCTGCAGAAACTG 58.418 50.000 20.19 15.23 34.12 3.16
4379 5659 3.848272 ATAAACTGCAACATCCAACCG 57.152 42.857 0.00 0.00 0.00 4.44
4425 5705 0.324275 TTGGCTCCAATTGGGCTACC 60.324 55.000 26.82 21.14 36.21 3.18
4427 5707 2.109774 CATTTGGCTCCAATTGGGCTA 58.890 47.619 26.82 21.95 35.13 3.93
4456 5736 5.705441 GTGTAAGTGTCATTCAAAGATCCCA 59.295 40.000 0.00 0.00 0.00 4.37
4474 5754 7.707104 AGTTTTTCTTTCCTGACATGTGTAAG 58.293 34.615 1.15 0.00 0.00 2.34
4477 5757 5.888161 AGAGTTTTTCTTTCCTGACATGTGT 59.112 36.000 1.15 0.00 29.61 3.72
4498 5778 3.113260 ACTCCGTTTGGAACAGAAGAG 57.887 47.619 0.00 0.00 45.87 2.85
4564 5847 9.577003 CAAACACACTAAAACGTCTCTTTATAC 57.423 33.333 0.00 0.00 0.00 1.47
4565 5848 9.316730 ACAAACACACTAAAACGTCTCTTTATA 57.683 29.630 0.00 0.00 0.00 0.98
4566 5849 8.205131 ACAAACACACTAAAACGTCTCTTTAT 57.795 30.769 0.00 0.00 0.00 1.40
4567 5850 7.599630 ACAAACACACTAAAACGTCTCTTTA 57.400 32.000 0.00 0.00 0.00 1.85
4568 5851 6.490566 ACAAACACACTAAAACGTCTCTTT 57.509 33.333 0.00 0.00 0.00 2.52
4569 5852 6.148150 TGAACAAACACACTAAAACGTCTCTT 59.852 34.615 0.00 0.00 0.00 2.85
4597 5885 5.471556 TGGACTACAAACGGATAGAAACA 57.528 39.130 0.00 0.00 0.00 2.83
4845 6201 5.067805 CCCTTCATTATCTTTACTTGCACCC 59.932 44.000 0.00 0.00 0.00 4.61
4856 6212 5.590259 CACCGAATTCACCCTTCATTATCTT 59.410 40.000 6.22 0.00 0.00 2.40
4857 6213 5.126067 CACCGAATTCACCCTTCATTATCT 58.874 41.667 6.22 0.00 0.00 1.98
4858 6214 4.261197 GCACCGAATTCACCCTTCATTATC 60.261 45.833 6.22 0.00 0.00 1.75
4859 6215 3.632145 GCACCGAATTCACCCTTCATTAT 59.368 43.478 6.22 0.00 0.00 1.28
4862 6218 1.271871 TGCACCGAATTCACCCTTCAT 60.272 47.619 6.22 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.