Multiple sequence alignment - TraesCS5B01G180200

Loading Multiple Alignment...

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 TraesCS5B01G180200 chr5B 100.000 6138 0 0 1 6138 328103325 328109462 0.000000e+00 11335.0
1 TraesCS5B01G180200 chr5B 91.549 71 6 0 1 71 511297866 511297936 1.410000e-16 99.0
2 TraesCS5B01G180200 chr5A 90.793 4540 263 66 68 4499 382067578 382072070 0.000000e+00 5925.0
3 TraesCS5B01G180200 chr5A 89.559 1427 104 17 4736 6138 382072199 382073604 0.000000e+00 1768.0
4 TraesCS5B01G180200 chr5A 91.429 70 5 1 1 70 17237758 17237690 1.820000e-15 95.3
5 TraesCS5B01G180200 chr5D 91.393 2463 109 46 68 2469 288544921 288547341 0.000000e+00 3278.0
6 TraesCS5B01G180200 chr5D 93.772 1991 63 21 2518 4499 288547337 288549275 0.000000e+00 2933.0
7 TraesCS5B01G180200 chr5D 88.172 1395 105 21 4736 6083 288549423 288550804 0.000000e+00 1607.0
8 TraesCS5B01G180200 chr5D 87.121 132 11 4 4518 4648 288549260 288549386 1.780000e-30 145.0
9 TraesCS5B01G180200 chr5D 92.105 76 5 1 1 76 23382137 23382063 8.410000e-19 106.0
10 TraesCS5B01G180200 chr3A 88.398 905 70 15 1294 2178 512327921 512328810 0.000000e+00 1057.0
11 TraesCS5B01G180200 chr3A 86.842 76 7 3 1 74 623352745 623352671 1.420000e-11 82.4
12 TraesCS5B01G180200 chr3D 87.934 547 49 10 1635 2179 392350332 392350863 4.040000e-176 628.0
13 TraesCS5B01G180200 chr3D 90.000 70 6 1 1 70 554997740 554997672 8.470000e-14 89.8
14 TraesCS5B01G180200 chr3D 97.436 39 1 0 4647 4685 373324973 373325011 3.970000e-07 67.6
15 TraesCS5B01G180200 chr1A 94.231 156 8 1 2411 2565 395177601 395177446 2.860000e-58 237.0
16 TraesCS5B01G180200 chr1A 95.349 43 0 2 4639 4680 505514572 505514531 3.970000e-07 67.6
17 TraesCS5B01G180200 chr4A 92.025 163 10 3 2402 2562 690411280 690411441 6.190000e-55 226.0
18 TraesCS5B01G180200 chr4D 92.857 154 9 2 2411 2562 74079351 74079504 8.010000e-54 222.0
19 TraesCS5B01G180200 chr2D 92.357 157 11 1 2411 2566 79056167 79056323 8.010000e-54 222.0
20 TraesCS5B01G180200 chr2D 91.429 70 5 1 1 70 195723745 195723813 1.820000e-15 95.3
21 TraesCS5B01G180200 chr2D 88.571 70 4 3 1 70 2754177 2754112 1.420000e-11 82.4
22 TraesCS5B01G180200 chr1B 91.925 161 9 4 2411 2570 632021077 632020920 8.010000e-54 222.0
23 TraesCS5B01G180200 chr4B 91.824 159 11 2 2411 2568 146469216 146469373 2.880000e-53 220.0
24 TraesCS5B01G180200 chr6D 91.304 161 12 2 2411 2570 256728450 256728609 1.040000e-52 219.0
25 TraesCS5B01G180200 chr6D 91.304 161 12 2 2411 2570 256729247 256729406 1.040000e-52 219.0
26 TraesCS5B01G180200 chr6D 97.500 40 1 0 4647 4686 175718975 175719014 1.100000e-07 69.4
27 TraesCS5B01G180200 chr7D 91.429 70 5 1 1 70 398063387 398063455 1.820000e-15 95.3
28 TraesCS5B01G180200 chr2B 91.429 70 5 1 1 70 734042518 734042586 1.820000e-15 95.3
29 TraesCS5B01G180200 chr2B 100.000 38 0 0 1531 1568 753640355 753640392 3.070000e-08 71.3
30 TraesCS5B01G180200 chr2A 78.014 141 24 6 5944 6080 628789845 628789708 1.420000e-11 82.4
31 TraesCS5B01G180200 chr6A 97.500 40 1 0 4647 4686 237755308 237755269 1.100000e-07 69.4
32 TraesCS5B01G180200 chr6A 97.500 40 1 0 4647 4686 237756337 237756298 1.100000e-07 69.4
33 TraesCS5B01G180200 chr6A 97.500 40 1 0 4647 4686 237757363 237757324 1.100000e-07 69.4
34 TraesCS5B01G180200 chr3B 97.500 40 1 0 4647 4686 487045481 487045520 1.100000e-07 69.4
35 TraesCS5B01G180200 chr1D 97.500 40 1 0 4647 4686 201495069 201495030 1.100000e-07 69.4
36 TraesCS5B01G180200 chr7A 91.667 48 3 1 4640 4686 209620804 209620757 1.430000e-06 65.8


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 TraesCS5B01G180200 chr5B 328103325 328109462 6137 False 11335.00 11335 100.0000 1 6138 1 chr5B.!!$F1 6137
1 TraesCS5B01G180200 chr5A 382067578 382073604 6026 False 3846.50 5925 90.1760 68 6138 2 chr5A.!!$F1 6070
2 TraesCS5B01G180200 chr5D 288544921 288550804 5883 False 1990.75 3278 90.1145 68 6083 4 chr5D.!!$F1 6015
3 TraesCS5B01G180200 chr3A 512327921 512328810 889 False 1057.00 1057 88.3980 1294 2178 1 chr3A.!!$F1 884
4 TraesCS5B01G180200 chr3D 392350332 392350863 531 False 628.00 628 87.9340 1635 2179 1 chr3D.!!$F2 544
5 TraesCS5B01G180200 chr6D 256728450 256729406 956 False 219.00 219 91.3040 2411 2570 2 chr6D.!!$F2 159

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
42 43 0.108472 TCGTTCAGATGCAGAGGCTG 60.108 55.0 0.00 0.0 41.91 4.85 F
957 1030 0.179189 CCTTTCATTCAACCGAGCGC 60.179 55.0 0.00 0.0 0.00 5.92 F
969 1042 0.798776 CCGAGCGCAAAGATTGTTCT 59.201 50.0 11.47 0.0 0.00 3.01 F
1112 1185 0.980231 GGTCTGTGCCATCTCCTCCT 60.980 60.0 0.00 0.0 0.00 3.69 F
2035 2156 0.481567 TACTATCCTGGTCCCTCCGG 59.518 60.0 0.00 0.0 42.06 5.14 F
3803 3960 0.324552 ATGGGCTATTTGGCACTGCA 60.325 50.0 2.82 0.0 43.83 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1806 0.718343 GTGTCGCTCTCATTGTCTGC 59.282 55.000 0.0 0.0 0.00 4.26 R
1765 1879 1.942657 CCTCGAACATATTGCCCACAG 59.057 52.381 0.0 0.0 0.00 3.66 R
2015 2136 2.376695 CGGAGGGACCAGGATAGTAA 57.623 55.000 0.0 0.0 38.90 2.24 R
2469 2591 4.029750 GTGAACAAACACAGTAAAACGTGC 59.970 41.667 0.0 0.0 40.11 5.34 R
3913 4070 2.036733 TGTAGACCCAAGAAGACCAACG 59.963 50.000 0.0 0.0 0.00 4.10 R
5587 6021 0.169009 ACCGCTCGTAAACCGACTAC 59.831 55.000 0.0 0.0 41.60 2.73 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
29 30 6.691754 AATATTGGTTGTATGCATCGTTCA 57.308 33.333 0.19 0.00 0.00 3.18
30 31 4.621068 ATTGGTTGTATGCATCGTTCAG 57.379 40.909 0.19 0.00 0.00 3.02
31 32 3.326836 TGGTTGTATGCATCGTTCAGA 57.673 42.857 0.19 0.00 0.00 3.27
32 33 3.872696 TGGTTGTATGCATCGTTCAGAT 58.127 40.909 0.19 0.00 41.01 2.90
40 41 3.376218 ATCGTTCAGATGCAGAGGC 57.624 52.632 0.00 0.00 38.36 4.70
41 42 0.829333 ATCGTTCAGATGCAGAGGCT 59.171 50.000 0.00 0.00 41.91 4.58
42 43 0.108472 TCGTTCAGATGCAGAGGCTG 60.108 55.000 0.00 0.00 41.91 4.85
43 44 1.088340 CGTTCAGATGCAGAGGCTGG 61.088 60.000 0.00 0.00 41.91 4.85
44 45 0.747283 GTTCAGATGCAGAGGCTGGG 60.747 60.000 0.00 0.00 41.91 4.45
45 46 1.918467 TTCAGATGCAGAGGCTGGGG 61.918 60.000 0.00 0.00 41.91 4.96
46 47 2.285969 AGATGCAGAGGCTGGGGT 60.286 61.111 0.00 0.00 41.91 4.95
47 48 2.124403 GATGCAGAGGCTGGGGTG 60.124 66.667 0.00 0.00 41.91 4.61
48 49 2.611800 ATGCAGAGGCTGGGGTGA 60.612 61.111 0.00 0.00 41.91 4.02
49 50 2.202236 GATGCAGAGGCTGGGGTGAA 62.202 60.000 0.00 0.00 41.91 3.18
50 51 2.360475 GCAGAGGCTGGGGTGAAC 60.360 66.667 0.00 0.00 36.96 3.18
51 52 2.352805 CAGAGGCTGGGGTGAACC 59.647 66.667 0.00 0.00 39.11 3.62
150 152 6.016443 CCTCTAGCAAAAATGGGAATCAGATC 60.016 42.308 0.00 0.00 0.00 2.75
218 222 2.396157 GGGGCGACAAATCCGACAC 61.396 63.158 0.00 0.00 36.63 3.67
306 317 1.133976 CCTCTGATCCGAGGCCATTTT 60.134 52.381 18.92 0.00 43.69 1.82
382 398 3.374058 CGAAAGAAACCGATGCTTGGTAT 59.626 43.478 0.00 0.00 39.29 2.73
401 419 2.701780 CGTAGCGAGGGAGTGCAGT 61.702 63.158 0.00 0.00 0.00 4.40
465 490 2.958355 CTGCCTCTTTTGACCTTTTCCA 59.042 45.455 0.00 0.00 0.00 3.53
608 652 2.499289 GACCTCTCTTCTCTTGCATCCA 59.501 50.000 0.00 0.00 0.00 3.41
609 653 3.113824 ACCTCTCTTCTCTTGCATCCAT 58.886 45.455 0.00 0.00 0.00 3.41
610 654 3.134442 ACCTCTCTTCTCTTGCATCCATC 59.866 47.826 0.00 0.00 0.00 3.51
611 655 3.494749 CCTCTCTTCTCTTGCATCCATCC 60.495 52.174 0.00 0.00 0.00 3.51
746 806 6.471146 AGCATCTTGAGTGACAGACTATTTT 58.529 36.000 0.00 0.00 33.83 1.82
778 841 4.890158 TTCTTGTGGAACTGATCTAGCA 57.110 40.909 0.00 0.00 38.04 3.49
780 843 5.426689 TCTTGTGGAACTGATCTAGCAAT 57.573 39.130 0.00 0.00 38.04 3.56
787 850 7.828717 TGTGGAACTGATCTAGCAATTTGATAA 59.171 33.333 0.00 0.00 38.04 1.75
825 888 3.791973 TCGTTTTGCAGATTGGTTTGT 57.208 38.095 0.00 0.00 0.00 2.83
834 897 3.854784 GCAGATTGGTTTGTGAGCTTGAC 60.855 47.826 0.00 0.00 0.00 3.18
848 911 4.263639 TGAGCTTGACAGGATTCCTTGATT 60.264 41.667 1.28 0.00 0.00 2.57
851 914 4.142293 GCTTGACAGGATTCCTTGATTTCC 60.142 45.833 1.28 0.00 0.00 3.13
852 915 4.934797 TGACAGGATTCCTTGATTTCCT 57.065 40.909 1.28 0.00 39.18 3.36
855 918 5.222109 TGACAGGATTCCTTGATTTCCTTGA 60.222 40.000 1.28 0.00 36.45 3.02
895 958 6.533730 TCTTGCTCTTGATTTCCAGTTTAGA 58.466 36.000 0.00 0.00 0.00 2.10
897 960 7.502226 TCTTGCTCTTGATTTCCAGTTTAGAAA 59.498 33.333 0.00 0.00 37.61 2.52
957 1030 0.179189 CCTTTCATTCAACCGAGCGC 60.179 55.000 0.00 0.00 0.00 5.92
969 1042 0.798776 CCGAGCGCAAAGATTGTTCT 59.201 50.000 11.47 0.00 0.00 3.01
972 1045 2.158449 CGAGCGCAAAGATTGTTCTTCT 59.842 45.455 11.47 0.00 41.42 2.85
1108 1181 2.262774 CTGGGGTCTGTGCCATCTCC 62.263 65.000 0.00 0.00 0.00 3.71
1111 1184 1.524482 GGTCTGTGCCATCTCCTCC 59.476 63.158 0.00 0.00 0.00 4.30
1112 1185 0.980231 GGTCTGTGCCATCTCCTCCT 60.980 60.000 0.00 0.00 0.00 3.69
1117 1190 1.280133 TGTGCCATCTCCTCCTTCAAG 59.720 52.381 0.00 0.00 0.00 3.02
1140 1213 2.416680 TGGCATGTTGGATCAATCGA 57.583 45.000 0.00 0.00 0.00 3.59
1198 1271 1.632589 GAGAGGCAATTGGTTTGGGT 58.367 50.000 7.72 0.00 35.75 4.51
1503 1587 2.028420 TGGCGGCTCATATGCATATC 57.972 50.000 16.46 5.84 34.04 1.63
1692 1806 3.196469 TGTTCTATCTGCAGAGGTTCCTG 59.804 47.826 22.96 6.76 37.23 3.86
1798 1912 4.931661 TGTTCGAGGTACAAGAAACTCT 57.068 40.909 0.00 0.00 0.00 3.24
1816 1935 6.732896 AACTCTCACTTCTCCTTTAACTGA 57.267 37.500 0.00 0.00 0.00 3.41
1817 1936 6.091718 ACTCTCACTTCTCCTTTAACTGAC 57.908 41.667 0.00 0.00 0.00 3.51
1818 1937 5.122512 TCTCACTTCTCCTTTAACTGACG 57.877 43.478 0.00 0.00 0.00 4.35
1819 1938 4.825634 TCTCACTTCTCCTTTAACTGACGA 59.174 41.667 0.00 0.00 0.00 4.20
1820 1939 5.477291 TCTCACTTCTCCTTTAACTGACGAT 59.523 40.000 0.00 0.00 0.00 3.73
1821 1940 5.470368 TCACTTCTCCTTTAACTGACGATG 58.530 41.667 0.00 0.00 0.00 3.84
1822 1941 5.243060 TCACTTCTCCTTTAACTGACGATGA 59.757 40.000 0.00 0.00 0.00 2.92
1853 1972 7.826260 TTTCAGTCCAAAAGTTCAAACATTC 57.174 32.000 0.00 0.00 0.00 2.67
1863 1982 8.667463 CAAAAGTTCAAACATTCATTTCTTGGT 58.333 29.630 0.00 0.00 0.00 3.67
1866 1985 8.791327 AGTTCAAACATTCATTTCTTGGTTTT 57.209 26.923 0.00 0.00 0.00 2.43
1880 1999 9.750125 ATTTCTTGGTTTTTGTCAGAATCTTAC 57.250 29.630 0.00 0.00 0.00 2.34
1882 2001 9.621629 TTCTTGGTTTTTGTCAGAATCTTACTA 57.378 29.630 0.00 0.00 0.00 1.82
1987 2107 4.127566 ACTGGACCAAATATGCAATTGC 57.872 40.909 23.69 23.69 42.50 3.56
1993 2113 4.870363 ACCAAATATGCAATTGCGGATAC 58.130 39.130 24.58 0.00 45.83 2.24
2033 2154 8.445361 TTTATTATTACTATCCTGGTCCCTCC 57.555 38.462 0.00 0.00 0.00 4.30
2034 2155 2.376695 TTACTATCCTGGTCCCTCCG 57.623 55.000 0.00 0.00 39.52 4.63
2035 2156 0.481567 TACTATCCTGGTCCCTCCGG 59.518 60.000 0.00 0.00 42.06 5.14
2321 2442 2.259012 TCCCGGTGGTAAAAGCTCTAA 58.741 47.619 0.00 0.00 0.00 2.10
2438 2559 5.470098 CCCTCCGTTCACAAATATAAGATGG 59.530 44.000 0.00 0.00 0.00 3.51
2479 2601 6.897259 TCAGATGTTATAGGCACGTTTTAC 57.103 37.500 0.00 0.00 0.00 2.01
2677 2799 6.196918 AGCATGGATCTCTTATTGATTGGA 57.803 37.500 0.00 0.00 0.00 3.53
2691 2813 4.846779 TGATTGGAACTTTAGCAACACC 57.153 40.909 0.00 0.00 0.00 4.16
2693 2815 4.832266 TGATTGGAACTTTAGCAACACCAT 59.168 37.500 0.00 0.00 0.00 3.55
2753 2875 6.711277 TGCACTTAGTACCAGATCATTTCTT 58.289 36.000 0.00 0.00 29.93 2.52
3270 3394 5.579047 TCCACACCACTTATTCATTTCCAT 58.421 37.500 0.00 0.00 0.00 3.41
3273 3398 7.285172 TCCACACCACTTATTCATTTCCATATG 59.715 37.037 0.00 0.00 0.00 1.78
3387 3517 2.203195 GGCATGATGGCCGCAGTA 60.203 61.111 7.90 0.00 45.40 2.74
3413 3543 4.763793 GGTGTCGCTAATAGAGGTACCATA 59.236 45.833 15.94 7.01 0.00 2.74
3665 3795 7.668052 AGTCTAGTAGTTCTCATGAAGTTGAGT 59.332 37.037 0.00 0.00 43.02 3.41
3729 3869 2.949451 ACTCCGTAATCACTGCTGAG 57.051 50.000 0.00 0.00 0.00 3.35
3731 3871 1.135915 CTCCGTAATCACTGCTGAGCT 59.864 52.381 5.83 0.00 0.00 4.09
3803 3960 0.324552 ATGGGCTATTTGGCACTGCA 60.325 50.000 2.82 0.00 43.83 4.41
3841 3998 1.895131 TGTGTGAGTGCATCTGAGCTA 59.105 47.619 0.00 0.00 34.99 3.32
3848 4005 3.298619 AGTGCATCTGAGCTATCACTCT 58.701 45.455 0.00 0.00 37.58 3.24
3913 4070 1.814394 TGGATGCAATGCAGTGAGAAC 59.186 47.619 20.00 5.39 40.85 3.01
4120 4277 7.185318 TGCTTCCATTCCATTCACAATATTT 57.815 32.000 0.00 0.00 0.00 1.40
4132 4289 8.255206 CCATTCACAATATTTGCTGCCATATAT 58.745 33.333 0.00 0.00 30.12 0.86
4171 4328 7.386851 GCATTATTGGTAAGTATCCTAGCAGA 58.613 38.462 0.00 0.00 0.00 4.26
4187 4345 6.428159 TCCTAGCAGAAAAAGTGAAGATGTTC 59.572 38.462 0.00 0.00 0.00 3.18
4206 4365 3.314541 TCTCCTTTGTAGTTTCCGAGC 57.685 47.619 0.00 0.00 0.00 5.03
4213 4372 4.698583 TTGTAGTTTCCGAGCTCTCTAC 57.301 45.455 12.85 14.84 0.00 2.59
4215 4374 2.217510 AGTTTCCGAGCTCTCTACCA 57.782 50.000 12.85 0.00 0.00 3.25
4217 4376 3.100671 AGTTTCCGAGCTCTCTACCAAT 58.899 45.455 12.85 0.00 0.00 3.16
4220 4379 5.010213 AGTTTCCGAGCTCTCTACCAATATC 59.990 44.000 12.85 0.00 0.00 1.63
4227 4386 6.806249 CGAGCTCTCTACCAATATCTGAATTC 59.194 42.308 12.85 0.00 0.00 2.17
4228 4387 6.686630 AGCTCTCTACCAATATCTGAATTCG 58.313 40.000 0.04 0.00 0.00 3.34
4229 4388 5.347364 GCTCTCTACCAATATCTGAATTCGC 59.653 44.000 0.04 0.00 0.00 4.70
4230 4389 6.405278 TCTCTACCAATATCTGAATTCGCA 57.595 37.500 0.04 0.00 0.00 5.10
4231 4390 6.216569 TCTCTACCAATATCTGAATTCGCAC 58.783 40.000 0.04 0.00 0.00 5.34
4234 4393 5.895636 ACCAATATCTGAATTCGCACAAA 57.104 34.783 0.04 0.00 0.00 2.83
4235 4394 6.455360 ACCAATATCTGAATTCGCACAAAT 57.545 33.333 0.04 0.00 0.00 2.32
4237 4396 7.995289 ACCAATATCTGAATTCGCACAAATAA 58.005 30.769 0.04 0.00 0.00 1.40
4238 4397 8.632679 ACCAATATCTGAATTCGCACAAATAAT 58.367 29.630 0.04 0.00 0.00 1.28
4283 4442 2.595655 GCGGTGGGGCTATCCTTT 59.404 61.111 0.00 0.00 35.33 3.11
4459 4618 3.862309 ACTATCCCCCACACCCTTAATTT 59.138 43.478 0.00 0.00 0.00 1.82
4460 4619 2.614134 TCCCCCACACCCTTAATTTG 57.386 50.000 0.00 0.00 0.00 2.32
4461 4620 1.790157 TCCCCCACACCCTTAATTTGT 59.210 47.619 0.00 0.00 0.00 2.83
4462 4621 2.994581 TCCCCCACACCCTTAATTTGTA 59.005 45.455 0.00 0.00 0.00 2.41
4463 4622 3.093814 CCCCCACACCCTTAATTTGTAC 58.906 50.000 0.00 0.00 0.00 2.90
4472 4631 7.064253 CACACCCTTAATTTGTACTGTACTAGC 59.936 40.741 17.98 0.00 0.00 3.42
4499 4658 0.035458 CCCACAAGTCCACTGTCTCC 59.965 60.000 0.00 0.00 0.00 3.71
4500 4659 1.051812 CCACAAGTCCACTGTCTCCT 58.948 55.000 0.00 0.00 0.00 3.69
4501 4660 1.417890 CCACAAGTCCACTGTCTCCTT 59.582 52.381 0.00 0.00 0.00 3.36
4502 4661 2.158755 CCACAAGTCCACTGTCTCCTTT 60.159 50.000 0.00 0.00 0.00 3.11
4503 4662 3.545703 CACAAGTCCACTGTCTCCTTTT 58.454 45.455 0.00 0.00 0.00 2.27
4510 4669 5.358160 AGTCCACTGTCTCCTTTTCAAAAAG 59.642 40.000 8.02 8.02 43.82 2.27
4590 4844 5.294552 GTCCATCTAGTATCTGGCACAAAAC 59.705 44.000 0.00 0.00 38.70 2.43
4610 4886 9.145865 ACAAAACAATAACACAAACTTAACTGG 57.854 29.630 0.00 0.00 0.00 4.00
4623 4899 7.762159 ACAAACTTAACTGGTGGTAAAATGTTG 59.238 33.333 0.00 0.00 0.00 3.33
4624 4900 7.412853 AACTTAACTGGTGGTAAAATGTTGT 57.587 32.000 0.00 0.00 0.00 3.32
4625 4901 6.801575 ACTTAACTGGTGGTAAAATGTTGTG 58.198 36.000 0.00 0.00 0.00 3.33
4626 4902 4.664150 AACTGGTGGTAAAATGTTGTGG 57.336 40.909 0.00 0.00 0.00 4.17
4628 4904 2.363680 CTGGTGGTAAAATGTTGTGGCA 59.636 45.455 0.00 0.00 0.00 4.92
4629 4905 2.968574 TGGTGGTAAAATGTTGTGGCAT 59.031 40.909 0.00 0.00 0.00 4.40
4632 4908 5.247110 TGGTGGTAAAATGTTGTGGCATATT 59.753 36.000 0.00 0.00 0.00 1.28
4633 4909 5.580297 GGTGGTAAAATGTTGTGGCATATTG 59.420 40.000 0.00 0.00 0.00 1.90
4635 4911 5.046735 TGGTAAAATGTTGTGGCATATTGCT 60.047 36.000 0.00 0.00 44.28 3.91
4636 4912 5.291614 GGTAAAATGTTGTGGCATATTGCTG 59.708 40.000 0.00 0.00 44.28 4.41
4641 5030 3.829026 TGTTGTGGCATATTGCTGGTAAA 59.171 39.130 0.00 0.00 44.28 2.01
4643 5032 5.046735 TGTTGTGGCATATTGCTGGTAAAAT 60.047 36.000 0.00 0.00 44.28 1.82
4644 5033 5.008619 TGTGGCATATTGCTGGTAAAATG 57.991 39.130 0.00 0.00 44.28 2.32
4645 5034 4.465660 TGTGGCATATTGCTGGTAAAATGT 59.534 37.500 0.00 0.00 44.28 2.71
4650 5039 7.093552 TGGCATATTGCTGGTAAAATGTTACTT 60.094 33.333 5.76 0.00 44.28 2.24
4656 5045 4.094442 GCTGGTAAAATGTTACTTCCTCCG 59.906 45.833 5.76 0.00 39.73 4.63
4658 5047 5.240121 TGGTAAAATGTTACTTCCTCCGTC 58.760 41.667 5.76 0.00 39.73 4.79
4660 5049 3.345508 AAATGTTACTTCCTCCGTCCC 57.654 47.619 0.00 0.00 0.00 4.46
4661 5050 1.946984 ATGTTACTTCCTCCGTCCCA 58.053 50.000 0.00 0.00 0.00 4.37
4672 5061 5.286267 TCCTCCGTCCCAAAATATAAGAC 57.714 43.478 0.00 0.00 0.00 3.01
4676 5065 5.490159 TCCGTCCCAAAATATAAGACGTTT 58.510 37.500 9.63 0.00 46.62 3.60
4677 5066 5.939296 TCCGTCCCAAAATATAAGACGTTTT 59.061 36.000 9.63 0.00 46.62 2.43
4678 5067 6.430616 TCCGTCCCAAAATATAAGACGTTTTT 59.569 34.615 9.63 0.00 46.62 1.94
4679 5068 6.525280 CCGTCCCAAAATATAAGACGTTTTTG 59.475 38.462 11.96 11.96 46.62 2.44
4681 5070 6.864165 GTCCCAAAATATAAGACGTTTTTGCA 59.136 34.615 13.03 0.00 37.60 4.08
4682 5071 7.061789 GTCCCAAAATATAAGACGTTTTTGCAG 59.938 37.037 13.03 8.28 37.60 4.41
4685 5074 8.424731 CCAAAATATAAGACGTTTTTGCAGTTC 58.575 33.333 13.03 0.00 37.60 3.01
4687 5076 8.728088 AAATATAAGACGTTTTTGCAGTTCTG 57.272 30.769 0.00 0.00 0.00 3.02
4688 5077 2.475200 AGACGTTTTTGCAGTTCTGC 57.525 45.000 16.65 16.65 0.00 4.26
4698 5087 2.836262 TGCAGTTCTGCAAAAATTGGG 58.164 42.857 22.60 0.00 42.40 4.12
4699 5088 2.433604 TGCAGTTCTGCAAAAATTGGGA 59.566 40.909 22.60 0.00 42.40 4.37
4700 5089 2.802247 GCAGTTCTGCAAAAATTGGGAC 59.198 45.455 18.26 0.00 34.41 4.46
4701 5090 3.052036 CAGTTCTGCAAAAATTGGGACG 58.948 45.455 0.00 0.00 0.00 4.79
4702 5091 2.035832 AGTTCTGCAAAAATTGGGACGG 59.964 45.455 0.00 0.00 0.00 4.79
4703 5092 1.988293 TCTGCAAAAATTGGGACGGA 58.012 45.000 0.00 0.00 0.00 4.69
4704 5093 1.885887 TCTGCAAAAATTGGGACGGAG 59.114 47.619 0.00 0.00 0.00 4.63
4705 5094 0.965439 TGCAAAAATTGGGACGGAGG 59.035 50.000 0.00 0.00 0.00 4.30
4706 5095 0.966179 GCAAAAATTGGGACGGAGGT 59.034 50.000 0.00 0.00 0.00 3.85
4707 5096 2.164338 GCAAAAATTGGGACGGAGGTA 58.836 47.619 0.00 0.00 0.00 3.08
4708 5097 2.163613 GCAAAAATTGGGACGGAGGTAG 59.836 50.000 0.00 0.00 0.00 3.18
4715 5104 1.358787 TGGGACGGAGGTAGTAGGAAA 59.641 52.381 0.00 0.00 0.00 3.13
4823 5225 8.798859 AATCTACTCATACATCAATAATGGCC 57.201 34.615 0.00 0.00 39.90 5.36
4834 5236 6.606796 ACATCAATAATGGCCTGTCAATGTTA 59.393 34.615 3.32 0.00 39.90 2.41
4918 5321 2.153034 TGTATCATCCCTGACCGTCA 57.847 50.000 0.29 0.29 33.22 4.35
4954 5357 2.183478 ACATCAACACCATCTTCGCA 57.817 45.000 0.00 0.00 0.00 5.10
4960 5363 1.224315 CACCATCTTCGCATCCCCA 59.776 57.895 0.00 0.00 0.00 4.96
5005 5408 1.792949 GTAGTCCTTGACAACACGCTG 59.207 52.381 0.00 0.00 34.60 5.18
5083 5486 2.370445 CCGAGGGGACAGCAGGAAT 61.370 63.158 0.00 0.00 34.06 3.01
5092 5495 3.006247 GGACAGCAGGAATGAAGAGTTC 58.994 50.000 0.00 0.00 0.00 3.01
5170 5573 1.481056 AAGTCCGGGTACTGCAAGCT 61.481 55.000 0.00 0.00 37.60 3.74
5199 5602 5.163322 ACCAAATGAAGAAACCTTTGCATCA 60.163 36.000 0.00 0.00 0.00 3.07
5205 5608 7.230849 TGAAGAAACCTTTGCATCACAATAT 57.769 32.000 0.00 0.00 38.31 1.28
5286 5689 0.725117 GCATGCCGTTTTACTAGCGT 59.275 50.000 6.36 0.00 0.00 5.07
5299 5702 2.588620 ACTAGCGTAGGATGGAGGAAG 58.411 52.381 0.00 0.00 0.00 3.46
5309 5712 0.912486 ATGGAGGAAGTTCCCTTCGG 59.088 55.000 18.65 0.00 46.72 4.30
5362 5769 8.725405 TTCCGTAGACAATGAATTAATGCTAA 57.275 30.769 0.00 0.00 0.00 3.09
5403 5817 6.545508 TGTAAGATCTCATGAAACATTTGCG 58.454 36.000 0.00 0.00 0.00 4.85
5404 5818 4.627611 AGATCTCATGAAACATTTGCGG 57.372 40.909 0.00 0.00 0.00 5.69
5405 5819 3.379372 AGATCTCATGAAACATTTGCGGG 59.621 43.478 0.00 0.00 0.00 6.13
5406 5820 1.202114 TCTCATGAAACATTTGCGGGC 59.798 47.619 0.00 0.00 0.00 6.13
5407 5821 0.964700 TCATGAAACATTTGCGGGCA 59.035 45.000 0.00 0.00 0.00 5.36
5408 5822 1.067706 TCATGAAACATTTGCGGGCAG 60.068 47.619 0.00 0.00 0.00 4.85
5434 5849 3.367703 GCAAATGAGGCACATTGTTAGCT 60.368 43.478 10.93 0.00 46.90 3.32
5445 5860 5.277779 GCACATTGTTAGCTGTAGTTGAACA 60.278 40.000 0.00 0.00 0.00 3.18
5461 5876 1.534163 GAACACACCGTAGAAAAGGGC 59.466 52.381 0.00 0.00 36.53 5.19
5497 5912 5.623169 CAAAAATTATAGCATGGCCCCAAT 58.377 37.500 0.00 0.00 0.00 3.16
5507 5922 1.727062 TGGCCCCAATTGAAATGTGT 58.273 45.000 7.12 0.00 0.00 3.72
5534 5949 1.667830 CTTGTCGGCACACATCCGT 60.668 57.895 0.00 0.00 46.49 4.69
5587 6021 4.843728 TGCAATAAGACCCTTGTAAGAGG 58.156 43.478 0.00 0.00 36.52 3.69
5629 6063 0.328258 GGTAGGTTGATGTGGCACCT 59.672 55.000 16.26 4.83 34.79 4.00
5631 6065 2.172717 GGTAGGTTGATGTGGCACCTAT 59.827 50.000 16.26 2.12 35.76 2.57
5676 6110 7.174253 GTGAATCGGTTATGGCCTTATTTGATA 59.826 37.037 3.32 0.00 0.00 2.15
5679 6113 8.650143 ATCGGTTATGGCCTTATTTGATAAAT 57.350 30.769 3.32 0.00 34.90 1.40
5681 6115 8.919145 TCGGTTATGGCCTTATTTGATAAATTT 58.081 29.630 3.32 0.00 32.38 1.82
5682 6116 8.977505 CGGTTATGGCCTTATTTGATAAATTTG 58.022 33.333 3.32 0.00 32.38 2.32
5705 6162 4.526970 ACCATTACTGAGTTATTGGCCTG 58.473 43.478 3.32 0.00 0.00 4.85
5710 6167 6.614694 TTACTGAGTTATTGGCCTGAAGTA 57.385 37.500 3.32 0.00 0.00 2.24
5727 6184 6.988580 CCTGAAGTATGCAATCAGATTGAGTA 59.011 38.462 24.92 13.73 42.48 2.59
5810 6272 2.261671 GAGACCGCCACACATCGT 59.738 61.111 0.00 0.00 0.00 3.73
5817 6285 2.272678 CCGCCACACATCGTTTGTATA 58.727 47.619 0.00 0.00 36.57 1.47
5818 6286 2.029970 CCGCCACACATCGTTTGTATAC 59.970 50.000 0.00 0.00 36.57 1.47
5819 6287 2.668945 CGCCACACATCGTTTGTATACA 59.331 45.455 0.08 0.08 36.57 2.29
5826 6294 5.584251 ACACATCGTTTGTATACATCATGCA 59.416 36.000 6.36 0.00 36.57 3.96
5833 6301 6.465781 CGTTTGTATACATCATGCACACTTTC 59.534 38.462 6.36 0.00 30.33 2.62
5843 6311 3.878086 TGCACACTTTCGATGAAGAAC 57.122 42.857 3.89 0.00 0.00 3.01
5861 6329 7.434492 TGAAGAACCAACAACACAAGTAAAAA 58.566 30.769 0.00 0.00 0.00 1.94
5862 6330 7.596995 TGAAGAACCAACAACACAAGTAAAAAG 59.403 33.333 0.00 0.00 0.00 2.27
5863 6331 6.988522 AGAACCAACAACACAAGTAAAAAGT 58.011 32.000 0.00 0.00 0.00 2.66
5864 6332 8.113173 AGAACCAACAACACAAGTAAAAAGTA 57.887 30.769 0.00 0.00 0.00 2.24
5866 6334 9.194271 GAACCAACAACACAAGTAAAAAGTAAA 57.806 29.630 0.00 0.00 0.00 2.01
5868 6336 9.198837 ACCAACAACACAAGTAAAAAGTAAAAG 57.801 29.630 0.00 0.00 0.00 2.27
5869 6337 9.198837 CCAACAACACAAGTAAAAAGTAAAAGT 57.801 29.630 0.00 0.00 0.00 2.66
5884 6352 0.527565 AAAGTATACACCCGTCGCGT 59.472 50.000 5.77 0.00 0.00 6.01
5905 6373 2.505407 TGATCCAACCACCATAGGTCAG 59.495 50.000 0.00 0.00 42.25 3.51
5907 6375 0.255890 CCAACCACCATAGGTCAGGG 59.744 60.000 0.00 0.00 42.25 4.45
5908 6376 1.285280 CAACCACCATAGGTCAGGGA 58.715 55.000 0.00 0.00 42.25 4.20
5933 6401 3.751698 GGGTTTTCATCCGGATAGTATGC 59.248 47.826 18.63 6.11 0.00 3.14
5935 6403 3.695830 TTTCATCCGGATAGTATGCCC 57.304 47.619 18.63 0.00 0.00 5.36
5966 6434 5.936956 ACTTCAAAACAATGCCTTCAACAAA 59.063 32.000 0.00 0.00 0.00 2.83
5974 6442 4.942761 ATGCCTTCAACAAAGACACAAT 57.057 36.364 0.00 0.00 37.12 2.71
5975 6443 4.305989 TGCCTTCAACAAAGACACAATC 57.694 40.909 0.00 0.00 37.12 2.67
5985 6453 6.385649 ACAAAGACACAATCGGTAAAACAT 57.614 33.333 0.00 0.00 0.00 2.71
5986 6454 6.801575 ACAAAGACACAATCGGTAAAACATT 58.198 32.000 0.00 0.00 0.00 2.71
6050 6518 2.438392 TCACCCTAGAGCTCGATACTCA 59.562 50.000 8.37 3.96 36.58 3.41
6103 6571 3.157949 TGTGTCGCTGTCACCCCA 61.158 61.111 0.00 0.00 35.25 4.96
6107 6575 1.668151 GTCGCTGTCACCCCACTTC 60.668 63.158 0.00 0.00 0.00 3.01
6108 6576 2.137528 TCGCTGTCACCCCACTTCA 61.138 57.895 0.00 0.00 0.00 3.02
6130 6598 0.038526 GAAGAAGGCGTCACGGAAGA 60.039 55.000 0.00 0.00 0.00 2.87
6132 6600 2.048127 AAGGCGTCACGGAAGAGC 60.048 61.111 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.845227 TGAACGATGCATACAACCAATATTATT 58.155 29.630 0.00 0.00 0.00 1.40
4 5 8.389779 TGAACGATGCATACAACCAATATTAT 57.610 30.769 0.00 0.00 0.00 1.28
5 6 7.713073 TCTGAACGATGCATACAACCAATATTA 59.287 33.333 0.00 0.00 0.00 0.98
6 7 6.542005 TCTGAACGATGCATACAACCAATATT 59.458 34.615 0.00 0.00 0.00 1.28
7 8 6.054941 TCTGAACGATGCATACAACCAATAT 58.945 36.000 0.00 0.00 0.00 1.28
8 9 5.423886 TCTGAACGATGCATACAACCAATA 58.576 37.500 0.00 0.00 0.00 1.90
9 10 4.260985 TCTGAACGATGCATACAACCAAT 58.739 39.130 0.00 0.00 0.00 3.16
10 11 3.669536 TCTGAACGATGCATACAACCAA 58.330 40.909 0.00 0.00 0.00 3.67
11 12 3.326836 TCTGAACGATGCATACAACCA 57.673 42.857 0.00 0.00 0.00 3.67
12 13 4.201208 CATCTGAACGATGCATACAACC 57.799 45.455 0.00 0.00 42.75 3.77
22 23 0.829333 AGCCTCTGCATCTGAACGAT 59.171 50.000 0.00 0.00 41.13 3.73
23 24 0.108472 CAGCCTCTGCATCTGAACGA 60.108 55.000 0.00 0.00 41.13 3.85
24 25 1.088340 CCAGCCTCTGCATCTGAACG 61.088 60.000 6.89 0.00 41.13 3.95
25 26 0.747283 CCCAGCCTCTGCATCTGAAC 60.747 60.000 6.89 0.00 41.13 3.18
26 27 1.605992 CCCAGCCTCTGCATCTGAA 59.394 57.895 6.89 0.00 41.13 3.02
27 28 2.372890 CCCCAGCCTCTGCATCTGA 61.373 63.158 6.89 0.00 41.13 3.27
28 29 2.192443 CCCCAGCCTCTGCATCTG 59.808 66.667 0.00 0.00 41.13 2.90
29 30 2.285969 ACCCCAGCCTCTGCATCT 60.286 61.111 0.00 0.00 41.13 2.90
30 31 2.124403 CACCCCAGCCTCTGCATC 60.124 66.667 0.00 0.00 41.13 3.91
31 32 2.233566 TTCACCCCAGCCTCTGCAT 61.234 57.895 0.00 0.00 41.13 3.96
32 33 2.853542 TTCACCCCAGCCTCTGCA 60.854 61.111 0.00 0.00 41.13 4.41
33 34 2.360475 GTTCACCCCAGCCTCTGC 60.360 66.667 0.00 0.00 37.95 4.26
34 35 2.352805 GGTTCACCCCAGCCTCTG 59.647 66.667 0.00 0.00 0.00 3.35
117 118 5.241064 CCCATTTTTGCTAGAGGATGATCTG 59.759 44.000 0.00 0.00 0.00 2.90
121 122 4.860802 TCCCATTTTTGCTAGAGGATGA 57.139 40.909 0.00 0.00 0.00 2.92
150 152 1.702886 ATCTTCAGAGAACACGTGCG 58.297 50.000 17.22 0.00 35.07 5.34
218 222 2.747855 GTGAAAGGCTGGCCGGAG 60.748 66.667 18.31 0.00 41.95 4.63
228 232 5.296748 CAGTAAATTTTGGTGGGTGAAAGG 58.703 41.667 0.00 0.00 0.00 3.11
274 285 4.775780 TCGGATCAGAGGTTTTAAGGAGAA 59.224 41.667 0.00 0.00 0.00 2.87
306 317 1.606994 CCGTTGTGATTTCTGGGACGA 60.607 52.381 0.00 0.00 0.00 4.20
382 398 2.360726 TGCACTCCCTCGCTACGA 60.361 61.111 0.00 0.00 0.00 3.43
401 419 1.299648 CGAGGGATGAGTGGGCAAA 59.700 57.895 0.00 0.00 0.00 3.68
465 490 6.434340 GCGGGATATATCAAAGGGAAAAAGAT 59.566 38.462 14.60 0.00 0.00 2.40
608 652 2.560080 GAGAGGGATGGATGGATGGAT 58.440 52.381 0.00 0.00 0.00 3.41
609 653 1.828857 CGAGAGGGATGGATGGATGGA 60.829 57.143 0.00 0.00 0.00 3.41
610 654 0.612229 CGAGAGGGATGGATGGATGG 59.388 60.000 0.00 0.00 0.00 3.51
675 735 1.205417 GCAAGCAATTGCATACCAGGT 59.795 47.619 30.89 5.95 46.60 4.00
759 819 6.149973 TCAAATTGCTAGATCAGTTCCACAAG 59.850 38.462 0.00 0.00 0.00 3.16
787 850 8.487176 GCAAAACGAACATCAATAATTTTGAGT 58.513 29.630 9.95 5.26 37.62 3.41
807 870 3.245990 GCTCACAAACCAATCTGCAAAAC 59.754 43.478 0.00 0.00 0.00 2.43
825 888 2.639347 TCAAGGAATCCTGTCAAGCTCA 59.361 45.455 0.90 0.00 32.13 4.26
834 897 6.127793 AGATCAAGGAAATCAAGGAATCCTG 58.872 40.000 0.90 0.00 41.39 3.86
848 911 8.372877 AGATGAAAAGTAGAGAGATCAAGGAA 57.627 34.615 0.00 0.00 0.00 3.36
851 914 7.765360 AGCAAGATGAAAAGTAGAGAGATCAAG 59.235 37.037 0.00 0.00 0.00 3.02
852 915 7.619050 AGCAAGATGAAAAGTAGAGAGATCAA 58.381 34.615 0.00 0.00 0.00 2.57
855 918 7.422465 AGAGCAAGATGAAAAGTAGAGAGAT 57.578 36.000 0.00 0.00 0.00 2.75
895 958 4.210331 CCAAGATTTCCTCGGGATGATTT 58.790 43.478 0.00 0.00 0.00 2.17
897 960 2.107204 CCCAAGATTTCCTCGGGATGAT 59.893 50.000 0.00 0.00 39.44 2.45
899 962 1.972872 CCCAAGATTTCCTCGGGATG 58.027 55.000 0.00 0.00 39.44 3.51
900 963 0.183731 GCCCAAGATTTCCTCGGGAT 59.816 55.000 0.00 0.00 39.44 3.85
903 966 1.133976 AGATGCCCAAGATTTCCTCGG 60.134 52.381 0.00 0.00 0.00 4.63
904 967 2.338577 AGATGCCCAAGATTTCCTCG 57.661 50.000 0.00 0.00 0.00 4.63
939 1004 0.516877 TGCGCTCGGTTGAATGAAAG 59.483 50.000 9.73 0.00 0.00 2.62
945 1017 1.069296 CAATCTTTGCGCTCGGTTGAA 60.069 47.619 9.73 0.00 0.00 2.69
952 1024 3.820777 AGAAGAACAATCTTTGCGCTC 57.179 42.857 9.73 0.00 45.91 5.03
957 1030 6.309712 TCTGCTCAAGAAGAACAATCTTTG 57.690 37.500 0.00 0.00 45.91 2.77
969 1042 3.733337 GAACTGTTCCTCTGCTCAAGAA 58.267 45.455 9.38 0.00 33.37 2.52
972 1045 1.686587 TCGAACTGTTCCTCTGCTCAA 59.313 47.619 14.48 0.00 0.00 3.02
1108 1181 2.233271 ACATGCCAACACTTGAAGGAG 58.767 47.619 0.00 0.00 0.00 3.69
1111 1184 2.361757 TCCAACATGCCAACACTTGAAG 59.638 45.455 0.00 0.00 0.00 3.02
1112 1185 2.382882 TCCAACATGCCAACACTTGAA 58.617 42.857 0.00 0.00 0.00 2.69
1117 1190 3.514645 GATTGATCCAACATGCCAACAC 58.485 45.455 0.00 0.00 0.00 3.32
1140 1213 8.960591 CAAATATTCAGGGTAAGAAACACAGAT 58.039 33.333 0.00 0.00 31.97 2.90
1298 1371 6.016276 ACCAAGGAGTGTAGCAAACATAAAAG 60.016 38.462 0.00 0.00 41.10 2.27
1503 1587 4.826274 TTATGGAGAGGACTGGAACAAG 57.174 45.455 0.00 0.00 38.70 3.16
1692 1806 0.718343 GTGTCGCTCTCATTGTCTGC 59.282 55.000 0.00 0.00 0.00 4.26
1765 1879 1.942657 CCTCGAACATATTGCCCACAG 59.057 52.381 0.00 0.00 0.00 3.66
1798 1912 5.243060 TCATCGTCAGTTAAAGGAGAAGTGA 59.757 40.000 0.00 0.00 34.58 3.41
1816 1935 5.160607 TGGACTGAAAAACCTATCATCGT 57.839 39.130 0.00 0.00 0.00 3.73
1817 1936 6.494893 TTTGGACTGAAAAACCTATCATCG 57.505 37.500 0.00 0.00 0.00 3.84
1818 1937 7.886338 ACTTTTGGACTGAAAAACCTATCATC 58.114 34.615 0.00 0.00 0.00 2.92
1819 1938 7.839680 ACTTTTGGACTGAAAAACCTATCAT 57.160 32.000 0.00 0.00 0.00 2.45
1820 1939 7.340743 TGAACTTTTGGACTGAAAAACCTATCA 59.659 33.333 0.00 0.00 0.00 2.15
1821 1940 7.712797 TGAACTTTTGGACTGAAAAACCTATC 58.287 34.615 0.00 0.00 0.00 2.08
1822 1941 7.654022 TGAACTTTTGGACTGAAAAACCTAT 57.346 32.000 0.00 0.00 0.00 2.57
1853 1972 8.652810 AAGATTCTGACAAAAACCAAGAAATG 57.347 30.769 0.00 0.00 0.00 2.32
2010 2131 6.192773 CGGAGGGACCAGGATAGTAATAATA 58.807 44.000 0.00 0.00 38.90 0.98
2011 2132 5.024118 CGGAGGGACCAGGATAGTAATAAT 58.976 45.833 0.00 0.00 38.90 1.28
2013 2134 4.043608 CGGAGGGACCAGGATAGTAATA 57.956 50.000 0.00 0.00 38.90 0.98
2014 2135 2.890814 CGGAGGGACCAGGATAGTAAT 58.109 52.381 0.00 0.00 38.90 1.89
2015 2136 2.376695 CGGAGGGACCAGGATAGTAA 57.623 55.000 0.00 0.00 38.90 2.24
2321 2442 5.869649 AAACAGAACAAAAGTAAGGCCAT 57.130 34.783 5.01 0.00 0.00 4.40
2453 2574 9.037737 GTAAAACGTGCCTATAACATCTGATTA 57.962 33.333 0.00 0.00 0.00 1.75
2469 2591 4.029750 GTGAACAAACACAGTAAAACGTGC 59.970 41.667 0.00 0.00 40.11 5.34
2479 2601 5.883661 ACTGAAATGAGTGAACAAACACAG 58.116 37.500 0.00 0.00 42.45 3.66
2640 2762 7.067981 AGAGATCCATGCTCCAAATAAACTTTC 59.932 37.037 0.00 0.00 32.82 2.62
2677 2799 6.245408 TCTATTGGATGGTGTTGCTAAAGTT 58.755 36.000 0.00 0.00 0.00 2.66
2850 2973 7.962995 TGCCTGGGTAAATATGAACAATTAA 57.037 32.000 0.00 0.00 0.00 1.40
2912 3036 6.899393 TCTCATGGTGCTAAATGTTTTTCT 57.101 33.333 0.00 0.00 0.00 2.52
3387 3517 4.038883 GGTACCTCTATTAGCGACACCATT 59.961 45.833 4.06 0.00 0.00 3.16
3413 3543 9.857656 AGGAATCATGTATTTGACAAGTATGAT 57.142 29.630 4.08 4.08 42.78 2.45
3477 3607 6.152661 ACTGAAGAACTCAAATGGTTTCAACA 59.847 34.615 0.00 0.00 32.17 3.33
3729 3869 7.538303 TGTTTCATTTCCTTTCAGAAAAAGC 57.462 32.000 0.00 0.00 39.11 3.51
3731 3871 8.881743 CACATGTTTCATTTCCTTTCAGAAAAA 58.118 29.630 0.00 0.00 39.11 1.94
3803 3960 3.134804 ACACAGAAACAGTAGAGCCAGTT 59.865 43.478 0.00 0.00 0.00 3.16
3841 3998 7.173907 CCACAACAGAACAATCTTAAGAGTGAT 59.826 37.037 33.01 24.34 42.16 3.06
3848 4005 5.771469 CATGCCACAACAGAACAATCTTAA 58.229 37.500 0.00 0.00 32.03 1.85
3913 4070 2.036733 TGTAGACCCAAGAAGACCAACG 59.963 50.000 0.00 0.00 0.00 4.10
3943 4100 4.935352 AATCTGTATCACTCTCCTGCTC 57.065 45.455 0.00 0.00 0.00 4.26
4030 4187 5.221884 ACCCTGAAAAATCCAATGCAAATGA 60.222 36.000 4.54 0.00 0.00 2.57
4120 4277 6.957920 AACATAACACAATATATGGCAGCA 57.042 33.333 0.00 0.00 34.52 4.41
4132 4289 6.763355 ACCAATAATGCCAAACATAACACAA 58.237 32.000 0.00 0.00 38.34 3.33
4171 4328 7.410120 ACAAAGGAGAACATCTTCACTTTTT 57.590 32.000 2.28 0.00 35.42 1.94
4187 4345 3.056465 AGAGCTCGGAAACTACAAAGGAG 60.056 47.826 8.37 0.00 0.00 3.69
4206 4365 6.364706 GTGCGAATTCAGATATTGGTAGAGAG 59.635 42.308 6.22 0.00 0.00 3.20
4213 4372 9.467258 AATTATTTGTGCGAATTCAGATATTGG 57.533 29.630 6.22 0.00 0.00 3.16
4220 4379 7.512297 AGCAAAAATTATTTGTGCGAATTCAG 58.488 30.769 22.39 0.00 37.49 3.02
4227 4386 4.884257 ACGAGCAAAAATTATTTGTGCG 57.116 36.364 22.39 14.17 37.49 5.34
4228 4387 6.418141 ACAAACGAGCAAAAATTATTTGTGC 58.582 32.000 21.50 21.50 37.40 4.57
4229 4388 7.902403 ACAACAAACGAGCAAAAATTATTTGTG 59.098 29.630 3.60 3.60 38.44 3.33
4230 4389 7.902403 CACAACAAACGAGCAAAAATTATTTGT 59.098 29.630 11.90 0.00 39.72 2.83
4231 4390 7.902403 ACACAACAAACGAGCAAAAATTATTTG 59.098 29.630 0.00 8.06 0.00 2.32
4234 4393 6.978080 AGACACAACAAACGAGCAAAAATTAT 59.022 30.769 0.00 0.00 0.00 1.28
4235 4394 6.326375 AGACACAACAAACGAGCAAAAATTA 58.674 32.000 0.00 0.00 0.00 1.40
4237 4396 4.743493 AGACACAACAAACGAGCAAAAAT 58.257 34.783 0.00 0.00 0.00 1.82
4238 4397 4.162812 GAGACACAACAAACGAGCAAAAA 58.837 39.130 0.00 0.00 0.00 1.94
4283 4442 2.636647 TCATGTTGGTGAACTGCAGA 57.363 45.000 23.35 0.00 32.79 4.26
4434 4593 0.326618 AGGGTGTGGGGGATAGTGAG 60.327 60.000 0.00 0.00 0.00 3.51
4459 4618 3.952323 GGAGTCCATGCTAGTACAGTACA 59.048 47.826 13.37 0.00 0.00 2.90
4460 4619 3.318557 GGGAGTCCATGCTAGTACAGTAC 59.681 52.174 12.30 2.05 0.00 2.73
4461 4620 3.053170 TGGGAGTCCATGCTAGTACAGTA 60.053 47.826 12.30 0.00 38.32 2.74
4462 4621 2.292257 TGGGAGTCCATGCTAGTACAGT 60.292 50.000 12.30 0.00 38.32 3.55
4463 4622 2.101582 GTGGGAGTCCATGCTAGTACAG 59.898 54.545 12.30 0.00 46.09 2.74
4516 4675 2.307768 TCTCGAGACAGTGGACTTGTT 58.692 47.619 12.08 0.00 0.00 2.83
4520 4679 3.157881 TCAAATCTCGAGACAGTGGACT 58.842 45.455 19.30 0.00 0.00 3.85
4521 4680 3.577649 TCAAATCTCGAGACAGTGGAC 57.422 47.619 19.30 0.00 0.00 4.02
4522 4681 4.808414 ATTCAAATCTCGAGACAGTGGA 57.192 40.909 19.30 11.13 0.00 4.02
4523 4682 4.032217 CGAATTCAAATCTCGAGACAGTGG 59.968 45.833 19.30 3.89 34.52 4.00
4524 4683 4.859245 TCGAATTCAAATCTCGAGACAGTG 59.141 41.667 19.30 15.54 36.72 3.66
4525 4684 5.060662 TCGAATTCAAATCTCGAGACAGT 57.939 39.130 19.30 2.99 36.72 3.55
4527 4686 6.589907 TCATTTCGAATTCAAATCTCGAGACA 59.410 34.615 19.30 0.00 42.09 3.41
4528 4687 6.897138 GTCATTTCGAATTCAAATCTCGAGAC 59.103 38.462 19.30 0.91 42.09 3.36
4529 4688 6.589907 TGTCATTTCGAATTCAAATCTCGAGA 59.410 34.615 19.19 19.19 42.09 4.04
4530 4689 6.765089 TGTCATTTCGAATTCAAATCTCGAG 58.235 36.000 5.93 5.93 42.09 4.04
4531 4690 6.720012 TGTCATTTCGAATTCAAATCTCGA 57.280 33.333 6.22 0.00 39.68 4.04
4532 4691 7.372657 CAGATGTCATTTCGAATTCAAATCTCG 59.627 37.037 6.22 0.00 0.00 4.04
4590 4844 6.801575 ACCACCAGTTAAGTTTGTGTTATTG 58.198 36.000 8.27 0.00 0.00 1.90
4610 4886 5.063312 GCAATATGCCACAACATTTTACCAC 59.937 40.000 0.00 0.00 37.42 4.16
4623 4899 5.009854 ACATTTTACCAGCAATATGCCAC 57.990 39.130 0.00 0.00 46.52 5.01
4624 4900 5.674052 AACATTTTACCAGCAATATGCCA 57.326 34.783 0.00 0.00 46.52 4.92
4625 4901 6.805713 AGTAACATTTTACCAGCAATATGCC 58.194 36.000 0.00 0.00 40.47 4.40
4626 4902 7.435192 GGAAGTAACATTTTACCAGCAATATGC 59.565 37.037 0.00 0.00 40.17 3.14
4628 4904 8.823220 AGGAAGTAACATTTTACCAGCAATAT 57.177 30.769 0.00 0.00 38.79 1.28
4629 4905 7.338449 GGAGGAAGTAACATTTTACCAGCAATA 59.662 37.037 0.00 0.00 38.79 1.90
4632 4908 5.007682 GGAGGAAGTAACATTTTACCAGCA 58.992 41.667 0.00 0.00 38.79 4.41
4633 4909 4.094442 CGGAGGAAGTAACATTTTACCAGC 59.906 45.833 0.00 0.00 38.79 4.85
4635 4911 5.231702 ACGGAGGAAGTAACATTTTACCA 57.768 39.130 0.00 0.00 38.79 3.25
4636 4912 4.633126 GGACGGAGGAAGTAACATTTTACC 59.367 45.833 0.00 0.00 38.79 2.85
4641 5030 2.262637 TGGGACGGAGGAAGTAACATT 58.737 47.619 0.00 0.00 0.00 2.71
4643 5032 1.719529 TTGGGACGGAGGAAGTAACA 58.280 50.000 0.00 0.00 0.00 2.41
4644 5033 2.845363 TTTGGGACGGAGGAAGTAAC 57.155 50.000 0.00 0.00 0.00 2.50
4645 5034 5.703730 ATATTTTGGGACGGAGGAAGTAA 57.296 39.130 0.00 0.00 0.00 2.24
4650 5039 4.202182 CGTCTTATATTTTGGGACGGAGGA 60.202 45.833 0.00 0.00 43.69 3.71
4656 5045 6.864165 TGCAAAAACGTCTTATATTTTGGGAC 59.136 34.615 17.78 6.55 41.02 4.46
4658 5047 6.866248 ACTGCAAAAACGTCTTATATTTTGGG 59.134 34.615 17.78 0.48 41.02 4.12
4660 5049 9.180678 AGAACTGCAAAAACGTCTTATATTTTG 57.819 29.630 13.82 13.82 42.66 2.44
4661 5050 9.180678 CAGAACTGCAAAAACGTCTTATATTTT 57.819 29.630 0.00 0.00 0.00 1.82
4681 5070 2.035832 CCGTCCCAATTTTTGCAGAACT 59.964 45.455 0.00 0.00 0.00 3.01
4682 5071 2.035321 TCCGTCCCAATTTTTGCAGAAC 59.965 45.455 0.00 0.00 0.00 3.01
4685 5074 1.067635 CCTCCGTCCCAATTTTTGCAG 60.068 52.381 0.00 0.00 0.00 4.41
4687 5076 0.966179 ACCTCCGTCCCAATTTTTGC 59.034 50.000 0.00 0.00 0.00 3.68
4688 5077 3.418047 ACTACCTCCGTCCCAATTTTTG 58.582 45.455 0.00 0.00 0.00 2.44
4692 5081 2.023695 TCCTACTACCTCCGTCCCAATT 60.024 50.000 0.00 0.00 0.00 2.32
4693 5082 1.572415 TCCTACTACCTCCGTCCCAAT 59.428 52.381 0.00 0.00 0.00 3.16
4694 5083 1.002069 TCCTACTACCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
4695 5084 1.002069 TTCCTACTACCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
4696 5085 2.149973 TTTCCTACTACCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
4697 5086 5.859205 TTAATTTCCTACTACCTCCGTCC 57.141 43.478 0.00 0.00 0.00 4.79
4698 5087 8.583296 ACATATTAATTTCCTACTACCTCCGTC 58.417 37.037 0.00 0.00 0.00 4.79
4699 5088 8.488308 ACATATTAATTTCCTACTACCTCCGT 57.512 34.615 0.00 0.00 0.00 4.69
4818 5220 5.999205 TTTTGATAACATTGACAGGCCAT 57.001 34.783 5.01 0.00 0.00 4.40
4823 5225 8.291740 TGACAGACATTTTGATAACATTGACAG 58.708 33.333 0.00 0.00 0.00 3.51
4834 5236 5.067413 GCATGGAGATGACAGACATTTTGAT 59.933 40.000 0.00 0.00 39.56 2.57
4954 5357 3.771160 GCGACAGTCGGTGGGGAT 61.771 66.667 24.13 0.00 40.84 3.85
5005 5408 2.583593 GCCGCGTCTCTGACATCC 60.584 66.667 4.92 0.00 32.09 3.51
5062 5465 2.266055 CTGCTGTCCCCTCGGAAC 59.734 66.667 0.00 0.00 40.92 3.62
5083 5486 1.623811 GGCAGGGTGTAGAACTCTTCA 59.376 52.381 0.00 0.00 37.59 3.02
5092 5495 0.322546 GGTTGAAGGGCAGGGTGTAG 60.323 60.000 0.00 0.00 0.00 2.74
5170 5573 6.460953 GCAAAGGTTTCTTCATTTGGTACTCA 60.461 38.462 6.09 0.00 38.81 3.41
5199 5602 5.597182 AGAATTCAGAAGCATGCCATATTGT 59.403 36.000 15.66 0.00 0.00 2.71
5205 5608 3.076079 TCAGAATTCAGAAGCATGCCA 57.924 42.857 15.66 0.00 0.00 4.92
5309 5712 3.728076 TCTATGTACAATCGGACAGCC 57.272 47.619 0.00 0.00 0.00 4.85
5339 5742 9.950680 AAATTAGCATTAATTCATTGTCTACGG 57.049 29.630 0.00 0.00 38.27 4.02
5403 5817 3.830192 CTCATTTGCCCGCTGCCC 61.830 66.667 0.00 0.00 40.16 5.36
5404 5818 3.830192 CCTCATTTGCCCGCTGCC 61.830 66.667 0.00 0.00 40.16 4.85
5405 5819 4.503314 GCCTCATTTGCCCGCTGC 62.503 66.667 0.00 0.00 41.77 5.25
5406 5820 3.063704 TGCCTCATTTGCCCGCTG 61.064 61.111 0.00 0.00 0.00 5.18
5407 5821 3.064324 GTGCCTCATTTGCCCGCT 61.064 61.111 0.00 0.00 0.00 5.52
5408 5822 2.229690 AATGTGCCTCATTTGCCCGC 62.230 55.000 0.00 0.00 43.33 6.13
5409 5823 0.458889 CAATGTGCCTCATTTGCCCG 60.459 55.000 2.17 0.00 43.33 6.13
5412 5827 2.925563 GCTAACAATGTGCCTCATTTGC 59.074 45.455 0.00 2.51 43.33 3.68
5434 5849 4.652421 TTCTACGGTGTGTTCAACTACA 57.348 40.909 0.00 0.00 0.00 2.74
5445 5860 2.433436 GAATGCCCTTTTCTACGGTGT 58.567 47.619 0.00 0.00 0.00 4.16
5461 5876 8.719648 TGCTATAATTTTTGCTTGTTTGGAATG 58.280 29.630 4.30 0.00 0.00 2.67
5497 5912 7.304735 CGACAAGGATTAATGACACATTTCAA 58.695 34.615 0.00 0.00 0.00 2.69
5507 5922 3.006940 GTGTGCCGACAAGGATTAATGA 58.993 45.455 0.00 0.00 45.00 2.57
5534 5949 4.566987 GACATGATCTGAGCAGCATATCA 58.433 43.478 0.00 9.12 42.19 2.15
5587 6021 0.169009 ACCGCTCGTAAACCGACTAC 59.831 55.000 0.00 0.00 41.60 2.73
5629 6063 1.279846 GAGGGAAAACCGGACCACATA 59.720 52.381 9.46 0.00 46.96 2.29
5631 6065 1.452801 GAGGGAAAACCGGACCACA 59.547 57.895 9.46 0.00 46.96 4.17
5638 6072 0.719465 CGATTCACGAGGGAAAACCG 59.281 55.000 0.00 0.00 46.96 4.44
5676 6110 8.034804 GCCAATAACTCAGTAATGGTCAAATTT 58.965 33.333 5.58 0.00 0.00 1.82
5679 6113 5.417580 GGCCAATAACTCAGTAATGGTCAAA 59.582 40.000 0.00 0.00 32.89 2.69
5681 6115 4.227300 AGGCCAATAACTCAGTAATGGTCA 59.773 41.667 5.01 0.00 35.05 4.02
5682 6116 4.576463 CAGGCCAATAACTCAGTAATGGTC 59.424 45.833 5.01 0.76 32.80 4.02
5685 6119 5.882557 ACTTCAGGCCAATAACTCAGTAATG 59.117 40.000 5.01 0.00 0.00 1.90
5692 6149 4.199310 TGCATACTTCAGGCCAATAACTC 58.801 43.478 5.01 0.00 31.20 3.01
5734 6191 8.725405 TTTACTCAATCCGATTGCATAGTTTA 57.275 30.769 15.21 4.73 40.05 2.01
5740 6202 5.009010 GTCCATTTACTCAATCCGATTGCAT 59.991 40.000 15.21 8.70 40.05 3.96
5810 6272 6.370166 TCGAAAGTGTGCATGATGTATACAAA 59.630 34.615 10.14 1.70 0.00 2.83
5817 6285 3.337358 TCATCGAAAGTGTGCATGATGT 58.663 40.909 0.00 0.00 35.78 3.06
5818 6286 4.093850 TCTTCATCGAAAGTGTGCATGATG 59.906 41.667 0.00 0.00 35.66 3.07
5819 6287 4.256110 TCTTCATCGAAAGTGTGCATGAT 58.744 39.130 0.00 0.00 0.00 2.45
5826 6294 4.196193 TGTTGGTTCTTCATCGAAAGTGT 58.804 39.130 0.00 0.00 0.00 3.55
5833 6301 3.961477 TGTGTTGTTGGTTCTTCATCG 57.039 42.857 0.00 0.00 0.00 3.84
5843 6311 9.198837 ACTTTTACTTTTTACTTGTGTTGTTGG 57.801 29.630 0.00 0.00 0.00 3.77
5861 6329 3.731867 CGCGACGGGTGTATACTTTTACT 60.732 47.826 0.00 0.00 0.00 2.24
5862 6330 2.531508 CGCGACGGGTGTATACTTTTAC 59.468 50.000 0.00 0.00 0.00 2.01
5863 6331 2.163412 ACGCGACGGGTGTATACTTTTA 59.837 45.455 15.93 0.00 37.67 1.52
5864 6332 1.067635 ACGCGACGGGTGTATACTTTT 60.068 47.619 15.93 0.00 37.67 2.27
5866 6334 0.179156 CACGCGACGGGTGTATACTT 60.179 55.000 30.39 0.00 40.76 2.24
5868 6336 0.029834 ATCACGCGACGGGTGTATAC 59.970 55.000 34.68 0.00 44.89 1.47
5869 6337 0.308684 GATCACGCGACGGGTGTATA 59.691 55.000 34.68 21.85 44.89 1.47
5870 6338 1.065273 GATCACGCGACGGGTGTAT 59.935 57.895 34.68 27.33 44.89 2.29
5871 6339 2.486504 GATCACGCGACGGGTGTA 59.513 61.111 34.68 24.72 44.89 2.90
5872 6340 4.430765 GGATCACGCGACGGGTGT 62.431 66.667 34.68 25.11 44.89 4.16
5873 6341 3.925362 TTGGATCACGCGACGGGTG 62.925 63.158 32.20 32.20 45.77 4.61
5874 6342 3.687102 TTGGATCACGCGACGGGT 61.687 61.111 15.93 12.27 0.00 5.28
5884 6352 2.505407 CTGACCTATGGTGGTTGGATCA 59.495 50.000 0.00 0.00 41.00 2.92
5905 6373 1.111277 CCGGATGAAAACCCAATCCC 58.889 55.000 0.00 0.00 0.00 3.85
5907 6375 4.461198 ACTATCCGGATGAAAACCCAATC 58.539 43.478 27.55 0.00 0.00 2.67
5908 6376 4.519906 ACTATCCGGATGAAAACCCAAT 57.480 40.909 27.55 0.00 0.00 3.16
5933 6401 1.593196 TGTTTTGAAGTCTGCTCGGG 58.407 50.000 0.00 0.00 0.00 5.14
5935 6403 2.975851 GCATTGTTTTGAAGTCTGCTCG 59.024 45.455 0.00 0.00 0.00 5.03
5966 6434 5.529430 TGACAATGTTTTACCGATTGTGTCT 59.471 36.000 0.00 0.00 39.77 3.41
5974 6442 3.570125 TGGCAATGACAATGTTTTACCGA 59.430 39.130 0.00 0.00 0.00 4.69
5975 6443 3.906998 TGGCAATGACAATGTTTTACCG 58.093 40.909 0.00 0.00 0.00 4.02
6025 6493 4.896482 AGTATCGAGCTCTAGGGTGAAAAT 59.104 41.667 12.85 0.00 0.00 1.82
6085 6553 2.665185 GGGGTGACAGCGACACAC 60.665 66.667 11.55 8.46 40.46 3.82
6103 6571 1.412710 TGACGCCTTCTTCTGTGAAGT 59.587 47.619 7.13 0.00 41.17 3.01
6107 6575 1.284982 CCGTGACGCCTTCTTCTGTG 61.285 60.000 0.00 0.00 0.00 3.66
6108 6576 1.006102 CCGTGACGCCTTCTTCTGT 60.006 57.895 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.