Multiple sequence alignment - TraesCS1B01G238900

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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 TraesCS1B01G238900 chr1B 100.000 4743 0 0 1 4743 427207298 427212040 0.000000e+00 8759
1 TraesCS1B01G238900 chr1B 96.667 120 4 0 4497 4616 73093974 73094093 2.890000e-47 200
2 TraesCS1B01G238900 chr1B 96.667 120 4 0 4497 4616 73198849 73198968 2.890000e-47 200
3 TraesCS1B01G238900 chr1B 95.192 104 4 1 152 255 427207329 427207431 3.800000e-36 163
4 TraesCS1B01G238900 chr1B 95.192 104 4 1 32 134 427207449 427207552 3.800000e-36 163
5 TraesCS1B01G238900 chr1D 92.191 4405 202 62 152 4498 315544852 315540532 0.000000e+00 6098
6 TraesCS1B01G238900 chr1D 96.269 134 5 0 4610 4743 315540535 315540402 2.220000e-53 220
7 TraesCS1B01G238900 chr1D 95.522 134 5 1 3 135 315544972 315544839 3.720000e-51 213
8 TraesCS1B01G238900 chr1D 93.388 121 7 1 5 125 315544879 315544760 1.360000e-40 178
9 TraesCS1B01G238900 chr1A 90.122 4434 228 95 152 4498 396108875 396104565 0.000000e+00 5568
10 TraesCS1B01G238900 chr1A 97.015 134 4 0 4610 4743 396104568 396104435 4.780000e-55 226
11 TraesCS1B01G238900 chr1A 92.481 133 8 1 4 134 396108903 396108771 6.270000e-44 189
12 TraesCS1B01G238900 chr1A 97.647 85 0 2 3 86 396109180 396109097 1.380000e-30 145
13 TraesCS1B01G238900 chr6A 96.694 121 4 0 4493 4613 540792404 540792284 8.050000e-48 202
14 TraesCS1B01G238900 chr2A 96.694 121 4 0 4493 4613 758744758 758744878 8.050000e-48 202
15 TraesCS1B01G238900 chr4A 97.436 117 3 0 4497 4613 650851814 650851930 2.890000e-47 200
16 TraesCS1B01G238900 chr4A 97.436 117 3 0 4497 4613 650861978 650862094 2.890000e-47 200
17 TraesCS1B01G238900 chr2B 97.436 117 3 0 4497 4613 655786580 655786464 2.890000e-47 200
18 TraesCS1B01G238900 chr2B 92.481 133 8 2 4493 4624 569246625 569246756 6.270000e-44 189
19 TraesCS1B01G238900 chr6B 94.531 128 6 1 4494 4620 119980385 119980258 3.740000e-46 196


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 TraesCS1B01G238900 chr1B 427207298 427212040 4742 False 8759.00 8759 100.00000 1 4743 1 chr1B.!!$F3 4742
1 TraesCS1B01G238900 chr1D 315540402 315544972 4570 True 1677.25 6098 94.34250 3 4743 4 chr1D.!!$R1 4740
2 TraesCS1B01G238900 chr1A 396104435 396109180 4745 True 1532.00 5568 94.31625 3 4743 4 chr1A.!!$R1 4740

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
475 675 0.448593 GCACGCGCCCTAATTACAAA 59.551 50.0 5.73 0.00 0.0 2.83 F
1283 1508 0.725784 CCATGTTGCTGTTTCGTCGC 60.726 55.0 0.00 0.00 0.0 5.19 F
2730 3013 0.324614 TGACCTGTACATGTGGGCTG 59.675 55.0 9.11 3.04 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 1633 0.037326 AGAAATCGAGGAGCGTGCAA 60.037 50.0 0.00 0.0 41.80 4.08 R
3215 3516 0.035458 GAACCCAGGTGACAGACAGG 59.965 60.0 0.00 0.0 0.00 4.00 R
4590 4916 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
115 303 9.066892 ACCTGATATTAACGTGCAATCAATATT 57.933 29.630 0.00 0.00 0.00 1.28
125 313 8.633075 ACGTGCAATCAATATTTTTCCTAATG 57.367 30.769 0.00 0.00 0.00 1.90
126 314 8.250332 ACGTGCAATCAATATTTTTCCTAATGT 58.750 29.630 0.00 0.00 0.00 2.71
127 315 8.745837 CGTGCAATCAATATTTTTCCTAATGTC 58.254 33.333 0.00 0.00 0.00 3.06
128 316 9.585099 GTGCAATCAATATTTTTCCTAATGTCA 57.415 29.630 0.00 0.00 0.00 3.58
138 326 6.618287 TTTTCCTAATGTCAATATGCTCCG 57.382 37.500 0.00 0.00 0.00 4.63
139 327 4.955811 TCCTAATGTCAATATGCTCCGT 57.044 40.909 0.00 0.00 0.00 4.69
140 328 5.290493 TCCTAATGTCAATATGCTCCGTT 57.710 39.130 0.00 0.00 0.00 4.44
141 329 6.413783 TCCTAATGTCAATATGCTCCGTTA 57.586 37.500 0.00 0.00 0.00 3.18
142 330 6.220930 TCCTAATGTCAATATGCTCCGTTAC 58.779 40.000 0.00 0.00 0.00 2.50
143 331 5.118664 CCTAATGTCAATATGCTCCGTTACG 59.881 44.000 0.00 0.00 0.00 3.18
144 332 3.786516 TGTCAATATGCTCCGTTACGA 57.213 42.857 6.24 0.00 0.00 3.43
145 333 4.112716 TGTCAATATGCTCCGTTACGAA 57.887 40.909 6.24 0.00 0.00 3.85
146 334 4.496360 TGTCAATATGCTCCGTTACGAAA 58.504 39.130 6.24 0.00 0.00 3.46
147 335 4.930405 TGTCAATATGCTCCGTTACGAAAA 59.070 37.500 6.24 0.00 0.00 2.29
148 336 5.583061 TGTCAATATGCTCCGTTACGAAAAT 59.417 36.000 6.24 0.00 0.00 1.82
149 337 6.757478 TGTCAATATGCTCCGTTACGAAAATA 59.243 34.615 6.24 0.00 0.00 1.40
150 338 7.278203 TGTCAATATGCTCCGTTACGAAAATAA 59.722 33.333 6.24 0.00 0.00 1.40
340 532 6.127196 ACCAAGTAAGAGATCATCAGGTTCTC 60.127 42.308 0.00 0.00 40.96 2.87
440 640 5.129368 ACAATTATCCTAGGTGGCATTGT 57.871 39.130 17.99 17.99 36.61 2.71
454 654 3.192422 TGGCATTGTTAACATAGCACCAC 59.808 43.478 24.98 13.66 0.00 4.16
472 672 1.087771 ACTGCACGCGCCCTAATTAC 61.088 55.000 5.73 0.00 37.32 1.89
475 675 0.448593 GCACGCGCCCTAATTACAAA 59.551 50.000 5.73 0.00 0.00 2.83
514 714 2.711311 CCAATGATGGCACGCGAG 59.289 61.111 15.93 5.97 40.58 5.03
515 715 1.815003 CCAATGATGGCACGCGAGA 60.815 57.895 15.93 0.00 40.58 4.04
516 716 1.640069 CAATGATGGCACGCGAGAG 59.360 57.895 15.93 2.87 0.00 3.20
517 717 1.522355 AATGATGGCACGCGAGAGG 60.522 57.895 15.93 0.00 0.00 3.69
518 718 2.244117 AATGATGGCACGCGAGAGGT 62.244 55.000 15.93 0.00 0.00 3.85
519 719 2.583593 GATGGCACGCGAGAGGTC 60.584 66.667 15.93 0.60 0.00 3.85
520 720 3.356639 GATGGCACGCGAGAGGTCA 62.357 63.158 15.93 7.41 0.00 4.02
526 726 2.392181 ACGCGAGAGGTCAGACGAG 61.392 63.158 15.93 0.00 0.00 4.18
632 832 6.731292 AAACAAAGGCCATATAGGGAATTC 57.269 37.500 7.83 0.00 38.09 2.17
678 887 6.856135 AAAACTTTACCGTACAAAGAGAGG 57.144 37.500 10.27 0.00 36.65 3.69
693 902 2.499289 AGAGAGGGCATGTGTACTCAAG 59.501 50.000 1.11 0.00 32.52 3.02
776 986 2.788515 GCCTAACAGCGGCCAATTA 58.211 52.632 2.24 0.00 41.73 1.40
810 1020 6.776116 CCCATAATTGCATATGATAGGCTGAT 59.224 38.462 10.59 2.20 35.69 2.90
811 1021 7.255486 CCCATAATTGCATATGATAGGCTGATG 60.255 40.741 10.59 7.98 35.69 3.07
826 1036 1.303561 GATGGCAGCTGGTTCACCA 60.304 57.895 17.12 14.09 45.30 4.17
945 1156 4.250464 GCCTTTTGGTGCCTATTTAAACC 58.750 43.478 0.00 0.00 42.99 3.27
970 1181 2.574824 ACCCCTTACGGCTTACAAGAAT 59.425 45.455 0.00 0.00 0.00 2.40
979 1190 3.375299 CGGCTTACAAGAATGGAAAGAGG 59.625 47.826 0.00 0.00 0.00 3.69
999 1210 3.203263 AGGGAGGAAAAGAAAGGATAGCC 59.797 47.826 0.00 0.00 0.00 3.93
1066 1286 0.899019 GGACGGCCTCTCTTCTTCTT 59.101 55.000 0.00 0.00 0.00 2.52
1067 1287 1.134936 GGACGGCCTCTCTTCTTCTTC 60.135 57.143 0.00 0.00 0.00 2.87
1068 1288 0.899019 ACGGCCTCTCTTCTTCTTCC 59.101 55.000 0.00 0.00 0.00 3.46
1131 1351 1.600058 TTTGCCATGAGGAGGAGGAT 58.400 50.000 0.00 0.00 36.89 3.24
1161 1381 1.903877 CGGCAATGGAGTCTCCCTGT 61.904 60.000 16.60 0.00 35.03 4.00
1220 1440 0.766288 ATCTCTCCCTTGCCTAGCCC 60.766 60.000 0.00 0.00 0.00 5.19
1249 1469 5.183713 TCAGTTAACTGCTTGCATGCTAATT 59.816 36.000 27.49 16.50 43.46 1.40
1262 1487 2.997980 TGCTAATTTCTTGGCCGATCA 58.002 42.857 0.00 0.00 38.02 2.92
1272 1497 1.102809 TGGCCGATCATCCATGTTGC 61.103 55.000 0.00 0.00 0.00 4.17
1277 1502 2.424601 CCGATCATCCATGTTGCTGTTT 59.575 45.455 0.00 0.00 0.00 2.83
1278 1503 3.488047 CCGATCATCCATGTTGCTGTTTC 60.488 47.826 0.00 0.00 0.00 2.78
1279 1504 3.688272 GATCATCCATGTTGCTGTTTCG 58.312 45.455 0.00 0.00 0.00 3.46
1280 1505 2.503331 TCATCCATGTTGCTGTTTCGT 58.497 42.857 0.00 0.00 0.00 3.85
1282 1507 0.865111 TCCATGTTGCTGTTTCGTCG 59.135 50.000 0.00 0.00 0.00 5.12
1283 1508 0.725784 CCATGTTGCTGTTTCGTCGC 60.726 55.000 0.00 0.00 0.00 5.19
1284 1509 1.054348 CATGTTGCTGTTTCGTCGCG 61.054 55.000 0.00 0.00 0.00 5.87
1285 1510 2.764251 ATGTTGCTGTTTCGTCGCGC 62.764 55.000 0.00 0.00 0.00 6.86
1334 1560 4.063967 CAGTACGCGCACAGGGGA 62.064 66.667 12.80 0.00 37.07 4.81
1433 1659 1.066143 GCTCCTCGATTTCTTGTGGGA 60.066 52.381 0.00 0.00 0.00 4.37
1435 1661 3.003480 CTCCTCGATTTCTTGTGGGAAC 58.997 50.000 0.00 0.00 0.00 3.62
1460 1686 2.755469 CCCAGGGTCCAATTGCGG 60.755 66.667 0.00 0.00 0.00 5.69
1480 1706 2.609459 GGTCGCATCATTCATTTCGTCT 59.391 45.455 0.00 0.00 0.00 4.18
1485 1711 4.024438 GCATCATTCATTTCGTCTCGTTG 58.976 43.478 0.00 0.00 0.00 4.10
1486 1712 3.722555 TCATTCATTTCGTCTCGTTGC 57.277 42.857 0.00 0.00 0.00 4.17
1487 1713 3.325870 TCATTCATTTCGTCTCGTTGCT 58.674 40.909 0.00 0.00 0.00 3.91
1488 1714 4.490743 TCATTCATTTCGTCTCGTTGCTA 58.509 39.130 0.00 0.00 0.00 3.49
1620 1849 3.609853 TCCTAATCAAGTGTCCACATGC 58.390 45.455 0.00 0.00 30.79 4.06
1710 1939 7.697691 AGCCTTTTCGTGTAATAATCAATCAG 58.302 34.615 0.00 0.00 0.00 2.90
1828 2067 4.762289 AGTGCCTTCATCTTTAGTAGGG 57.238 45.455 0.00 0.00 0.00 3.53
1892 2136 3.445857 GAGCCGTATAAAGTGTCCTCAC 58.554 50.000 0.00 0.00 44.15 3.51
1985 2229 2.781595 GAAAGCTCCGGCCGTTGAGA 62.782 60.000 28.78 16.88 39.73 3.27
2013 2257 1.613630 CTGTCAGGTAGGCCCCACT 60.614 63.158 0.00 0.00 34.57 4.00
2019 2263 1.307084 GGTAGGCCCCACTCCTCTT 60.307 63.158 0.00 0.00 35.21 2.85
2025 2269 1.467920 GCCCCACTCCTCTTTCATTG 58.532 55.000 0.00 0.00 0.00 2.82
2089 2335 7.629866 GCATTGTCAATTCAATCTGAAGGATGA 60.630 37.037 0.00 0.00 40.05 2.92
2277 2534 3.691118 TCAGAACAGCAACTAATCATGCC 59.309 43.478 0.00 0.00 43.57 4.40
2297 2560 0.331616 AAGGCAATCAGGGTGGGTAC 59.668 55.000 0.00 0.00 0.00 3.34
2309 2572 2.686491 TGGGTACGCTAACCACCAT 58.314 52.632 11.59 0.00 41.60 3.55
2315 2578 0.907704 ACGCTAACCACCATGGAGGA 60.908 55.000 32.26 11.97 40.96 3.71
2444 2710 2.814835 CCACGGGGCAGGTATACCC 61.815 68.421 18.65 2.75 46.24 3.69
2517 2786 2.831333 AGTAAGATCCAAGCGATGCTG 58.169 47.619 0.00 0.00 39.62 4.41
2520 2789 0.532417 AGATCCAAGCGATGCTGCTC 60.532 55.000 0.00 0.00 46.60 4.26
2521 2790 0.812811 GATCCAAGCGATGCTGCTCA 60.813 55.000 0.00 0.00 46.60 4.26
2526 2809 1.296755 AAGCGATGCTGCTCACTGTG 61.297 55.000 0.17 0.17 46.60 3.66
2527 2810 2.031516 GCGATGCTGCTCACTGTGT 61.032 57.895 7.79 0.00 0.00 3.72
2528 2811 0.737367 GCGATGCTGCTCACTGTGTA 60.737 55.000 7.79 0.00 0.00 2.90
2529 2812 1.275505 CGATGCTGCTCACTGTGTAG 58.724 55.000 7.79 5.42 0.00 2.74
2530 2813 1.135286 CGATGCTGCTCACTGTGTAGA 60.135 52.381 7.79 0.00 0.00 2.59
2543 2826 7.274686 GCTCACTGTGTAGATAGAGAAAGAAAC 59.725 40.741 7.79 0.00 0.00 2.78
2709 2992 5.244755 AGAGAAAAGACAGCCAGAAGAATC 58.755 41.667 0.00 0.00 0.00 2.52
2726 3009 3.198635 AGAATCCTGACCTGTACATGTGG 59.801 47.826 9.11 3.60 0.00 4.17
2727 3010 1.275666 TCCTGACCTGTACATGTGGG 58.724 55.000 9.11 10.42 0.00 4.61
2728 3011 0.392998 CCTGACCTGTACATGTGGGC 60.393 60.000 9.11 3.78 0.00 5.36
2729 3012 0.615331 CTGACCTGTACATGTGGGCT 59.385 55.000 9.11 0.00 0.00 5.19
2730 3013 0.324614 TGACCTGTACATGTGGGCTG 59.675 55.000 9.11 3.04 0.00 4.85
2731 3014 0.324943 GACCTGTACATGTGGGCTGT 59.675 55.000 9.11 0.00 0.00 4.40
2732 3015 0.771127 ACCTGTACATGTGGGCTGTT 59.229 50.000 9.11 0.00 0.00 3.16
2763 3046 4.148825 CGTTGGCGAGAGGGAGGG 62.149 72.222 0.00 0.00 41.33 4.30
2764 3047 2.683933 GTTGGCGAGAGGGAGGGA 60.684 66.667 0.00 0.00 0.00 4.20
2765 3048 2.364317 TTGGCGAGAGGGAGGGAG 60.364 66.667 0.00 0.00 0.00 4.30
2766 3049 3.984186 TTGGCGAGAGGGAGGGAGG 62.984 68.421 0.00 0.00 0.00 4.30
2813 3097 3.593442 ACTCCAAATCTCACCAAACCA 57.407 42.857 0.00 0.00 0.00 3.67
2881 3165 1.031571 TTTGGCTCCAGCTAATGCGG 61.032 55.000 0.00 0.00 41.12 5.69
2981 3265 2.365941 TGTACCGTCCATCAACTGAACA 59.634 45.455 0.00 0.00 0.00 3.18
3107 3400 3.299977 CGATGGACGGCCCGGATA 61.300 66.667 3.83 0.00 37.93 2.59
3184 3481 1.135689 GCGCCAAACTGAACCATACTG 60.136 52.381 0.00 0.00 0.00 2.74
3215 3516 3.562779 ATGCTTTGCTGCGTGGTGC 62.563 57.895 0.00 0.00 46.70 5.01
3291 3592 1.004628 TCATACTGCTGGTGTGGCATT 59.995 47.619 0.00 0.00 39.07 3.56
3363 3667 1.754745 ACGGTGAGTGAGCCACATT 59.245 52.632 7.86 0.00 36.74 2.71
3364 3668 0.603707 ACGGTGAGTGAGCCACATTG 60.604 55.000 7.86 0.00 36.74 2.82
3365 3669 1.300971 CGGTGAGTGAGCCACATTGG 61.301 60.000 7.86 0.00 41.55 3.16
3405 3709 5.641783 TCTGAAGACAAGAGATCAGAGTG 57.358 43.478 0.00 0.00 42.36 3.51
3412 3716 4.636249 ACAAGAGATCAGAGTGACAAACC 58.364 43.478 0.00 0.00 0.00 3.27
3426 3731 3.924073 TGACAAACCGTAACAGATCGATG 59.076 43.478 0.54 0.00 0.00 3.84
3436 3741 4.844998 AACAGATCGATGAGATGACGAT 57.155 40.909 0.54 0.00 46.79 3.73
3449 3754 4.184629 AGATGACGATGAAACTAACAGCC 58.815 43.478 0.00 0.00 0.00 4.85
3450 3755 2.695359 TGACGATGAAACTAACAGCCC 58.305 47.619 0.00 0.00 0.00 5.19
3475 3780 0.370273 CGTCGCTTTGCAGATGTACC 59.630 55.000 0.00 0.00 0.00 3.34
3611 3916 5.422331 TGACTTCTTACCTGTCATTCCTAGG 59.578 44.000 0.82 0.82 36.03 3.02
3612 3917 4.162509 ACTTCTTACCTGTCATTCCTAGGC 59.837 45.833 2.96 0.00 34.93 3.93
3613 3918 3.719871 TCTTACCTGTCATTCCTAGGCA 58.280 45.455 2.96 0.00 34.93 4.75
3614 3919 3.451178 TCTTACCTGTCATTCCTAGGCAC 59.549 47.826 2.96 0.00 34.93 5.01
3622 3927 1.331756 CATTCCTAGGCACGAACATGC 59.668 52.381 2.96 0.00 45.34 4.06
3634 3939 1.195448 CGAACATGCTGTGGTTGACTC 59.805 52.381 0.00 0.00 29.61 3.36
3909 4214 4.731773 GCCTCAAATGTGAATAAAGGCTCG 60.732 45.833 5.96 0.00 37.21 5.03
3914 4219 7.693952 TCAAATGTGAATAAAGGCTCGAATAC 58.306 34.615 0.00 0.00 0.00 1.89
3960 4265 4.499037 AAGAAAAATTGTCCCTGCGTAC 57.501 40.909 0.00 0.00 0.00 3.67
3973 4278 2.333926 CTGCGTACGAATTCACTTCCA 58.666 47.619 21.65 1.92 0.00 3.53
3977 4282 2.670905 CGTACGAATTCACTTCCATGCA 59.329 45.455 10.44 0.00 0.00 3.96
4151 4476 1.283029 CTCCATTCCCTCCACACACAT 59.717 52.381 0.00 0.00 0.00 3.21
4224 4550 8.700722 CAGATATATCAGAATCTGTACAAGGC 57.299 38.462 15.08 0.00 42.67 4.35
4228 4554 2.012673 CAGAATCTGTACAAGGCTGGC 58.987 52.381 1.31 0.00 0.00 4.85
4242 4568 1.804748 GGCTGGCAGTAGTACAACAAC 59.195 52.381 17.16 0.00 0.00 3.32
4293 4619 9.419297 GTAATATGAAAAGGAAAAACAAGACCC 57.581 33.333 0.00 0.00 0.00 4.46
4298 4624 0.747852 GGAAAAACAAGACCCCGCAA 59.252 50.000 0.00 0.00 0.00 4.85
4494 4820 1.117150 GTACTCACGGGGGCTCAATA 58.883 55.000 0.00 0.00 0.00 1.90
4495 4821 1.068741 GTACTCACGGGGGCTCAATAG 59.931 57.143 0.00 0.00 0.00 1.73
4496 4822 0.617820 ACTCACGGGGGCTCAATAGT 60.618 55.000 0.00 0.00 0.00 2.12
4497 4823 1.342674 ACTCACGGGGGCTCAATAGTA 60.343 52.381 0.00 0.00 0.00 1.82
4498 4824 1.068741 CTCACGGGGGCTCAATAGTAC 59.931 57.143 0.00 0.00 0.00 2.73
4499 4825 1.120530 CACGGGGGCTCAATAGTACT 58.879 55.000 0.00 0.00 0.00 2.73
4500 4826 1.068741 CACGGGGGCTCAATAGTACTC 59.931 57.143 0.00 0.00 0.00 2.59
4501 4827 0.680061 CGGGGGCTCAATAGTACTCC 59.320 60.000 0.00 0.00 0.00 3.85
4502 4828 1.057471 GGGGGCTCAATAGTACTCCC 58.943 60.000 0.00 2.06 0.00 4.30
4503 4829 1.414685 GGGGGCTCAATAGTACTCCCT 60.415 57.143 13.29 0.00 34.28 4.20
4504 4830 1.972075 GGGGCTCAATAGTACTCCCTC 59.028 57.143 13.29 2.59 34.28 4.30
4505 4831 1.972075 GGGCTCAATAGTACTCCCTCC 59.028 57.143 0.00 0.00 0.00 4.30
4506 4832 1.614413 GGCTCAATAGTACTCCCTCCG 59.386 57.143 0.00 0.00 0.00 4.63
4507 4833 2.308690 GCTCAATAGTACTCCCTCCGT 58.691 52.381 0.00 0.00 0.00 4.69
4508 4834 2.293955 GCTCAATAGTACTCCCTCCGTC 59.706 54.545 0.00 0.00 0.00 4.79
4509 4835 2.885894 CTCAATAGTACTCCCTCCGTCC 59.114 54.545 0.00 0.00 0.00 4.79
4510 4836 1.962100 CAATAGTACTCCCTCCGTCCC 59.038 57.143 0.00 0.00 0.00 4.46
4511 4837 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
4512 4838 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
4513 4839 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
4514 4840 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
4515 4841 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
4516 4842 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
4517 4843 1.558294 ACTCCCTCCGTCCCAAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
4518 4844 1.838077 CTCCCTCCGTCCCAAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
4519 4845 2.238898 CTCCCTCCGTCCCAAAATACTT 59.761 50.000 0.00 0.00 0.00 2.24
4520 4846 2.026636 TCCCTCCGTCCCAAAATACTTG 60.027 50.000 0.00 0.00 0.00 3.16
4521 4847 2.290705 CCCTCCGTCCCAAAATACTTGT 60.291 50.000 0.00 0.00 0.00 3.16
4522 4848 3.007635 CCTCCGTCCCAAAATACTTGTC 58.992 50.000 0.00 0.00 0.00 3.18
4523 4849 2.671396 CTCCGTCCCAAAATACTTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
4524 4850 1.735571 CCGTCCCAAAATACTTGTCGG 59.264 52.381 0.00 0.00 0.00 4.79
4525 4851 2.613474 CCGTCCCAAAATACTTGTCGGA 60.613 50.000 0.00 0.00 38.03 4.55
4526 4852 2.671396 CGTCCCAAAATACTTGTCGGAG 59.329 50.000 0.00 0.00 0.00 4.63
4527 4853 3.615592 CGTCCCAAAATACTTGTCGGAGA 60.616 47.826 0.00 0.00 0.00 3.71
4528 4854 4.320870 GTCCCAAAATACTTGTCGGAGAA 58.679 43.478 0.00 0.00 39.69 2.87
4529 4855 4.758165 GTCCCAAAATACTTGTCGGAGAAA 59.242 41.667 0.00 0.00 39.69 2.52
4530 4856 5.414765 GTCCCAAAATACTTGTCGGAGAAAT 59.585 40.000 0.00 0.00 39.69 2.17
4531 4857 5.414454 TCCCAAAATACTTGTCGGAGAAATG 59.586 40.000 0.00 0.00 39.69 2.32
4532 4858 5.393027 CCCAAAATACTTGTCGGAGAAATGG 60.393 44.000 0.00 0.00 39.69 3.16
4533 4859 5.414454 CCAAAATACTTGTCGGAGAAATGGA 59.586 40.000 0.00 0.00 39.69 3.41
4534 4860 6.095440 CCAAAATACTTGTCGGAGAAATGGAT 59.905 38.462 0.00 0.00 39.69 3.41
4535 4861 7.282224 CCAAAATACTTGTCGGAGAAATGGATA 59.718 37.037 0.00 0.00 39.69 2.59
4536 4862 8.673711 CAAAATACTTGTCGGAGAAATGGATAA 58.326 33.333 0.00 0.00 39.69 1.75
4537 4863 8.801882 AAATACTTGTCGGAGAAATGGATAAA 57.198 30.769 0.00 0.00 39.69 1.40
4538 4864 8.801882 AATACTTGTCGGAGAAATGGATAAAA 57.198 30.769 0.00 0.00 39.69 1.52
4539 4865 8.801882 ATACTTGTCGGAGAAATGGATAAAAA 57.198 30.769 0.00 0.00 39.69 1.94
4540 4866 7.703058 ACTTGTCGGAGAAATGGATAAAAAT 57.297 32.000 0.00 0.00 39.69 1.82
4541 4867 8.801882 ACTTGTCGGAGAAATGGATAAAAATA 57.198 30.769 0.00 0.00 39.69 1.40
4542 4868 8.893727 ACTTGTCGGAGAAATGGATAAAAATAG 58.106 33.333 0.00 0.00 39.69 1.73
4543 4869 9.109393 CTTGTCGGAGAAATGGATAAAAATAGA 57.891 33.333 0.00 0.00 39.69 1.98
4544 4870 9.627123 TTGTCGGAGAAATGGATAAAAATAGAT 57.373 29.630 0.00 0.00 39.69 1.98
4545 4871 9.056005 TGTCGGAGAAATGGATAAAAATAGATG 57.944 33.333 0.00 0.00 39.69 2.90
4546 4872 9.057089 GTCGGAGAAATGGATAAAAATAGATGT 57.943 33.333 0.00 0.00 39.69 3.06
4583 4909 9.781425 AAGATATGTCTAGATACATCCATTCCT 57.219 33.333 4.30 0.00 40.52 3.36
4584 4910 9.781425 AGATATGTCTAGATACATCCATTCCTT 57.219 33.333 4.30 0.00 40.52 3.36
4587 4913 7.675161 TGTCTAGATACATCCATTCCTTTGA 57.325 36.000 0.00 0.00 0.00 2.69
4588 4914 7.500992 TGTCTAGATACATCCATTCCTTTGAC 58.499 38.462 0.00 0.00 0.00 3.18
4589 4915 7.125659 TGTCTAGATACATCCATTCCTTTGACA 59.874 37.037 0.00 0.00 0.00 3.58
4590 4916 7.987458 GTCTAGATACATCCATTCCTTTGACAA 59.013 37.037 0.00 0.00 0.00 3.18
4591 4917 8.206867 TCTAGATACATCCATTCCTTTGACAAG 58.793 37.037 0.00 0.00 0.00 3.16
4592 4918 6.725364 AGATACATCCATTCCTTTGACAAGT 58.275 36.000 0.00 0.00 0.00 3.16
4593 4919 7.861629 AGATACATCCATTCCTTTGACAAGTA 58.138 34.615 0.00 0.00 0.00 2.24
4594 4920 8.497745 AGATACATCCATTCCTTTGACAAGTAT 58.502 33.333 0.00 0.00 0.00 2.12
4595 4921 9.125026 GATACATCCATTCCTTTGACAAGTATT 57.875 33.333 0.00 0.00 0.00 1.89
4596 4922 7.781324 ACATCCATTCCTTTGACAAGTATTT 57.219 32.000 0.00 0.00 0.00 1.40
4597 4923 7.830739 ACATCCATTCCTTTGACAAGTATTTC 58.169 34.615 0.00 0.00 0.00 2.17
4598 4924 6.834168 TCCATTCCTTTGACAAGTATTTCC 57.166 37.500 0.00 0.00 0.00 3.13
4599 4925 5.414454 TCCATTCCTTTGACAAGTATTTCCG 59.586 40.000 0.00 0.00 0.00 4.30
4600 4926 5.393027 CCATTCCTTTGACAAGTATTTCCGG 60.393 44.000 0.00 0.00 0.00 5.14
4601 4927 4.627284 TCCTTTGACAAGTATTTCCGGA 57.373 40.909 0.00 0.00 0.00 5.14
4602 4928 4.320870 TCCTTTGACAAGTATTTCCGGAC 58.679 43.478 1.83 0.00 0.00 4.79
4603 4929 3.124636 CCTTTGACAAGTATTTCCGGACG 59.875 47.826 1.83 0.00 0.00 4.79
4604 4930 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4605 4931 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4606 4932 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4607 4933 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4608 4934 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4616 4942 2.269023 TCCGGACGGAGGGAGTATATA 58.731 52.381 9.76 0.00 39.76 0.86
4624 4950 7.059156 GGACGGAGGGAGTATATATTAGCTAA 58.941 42.308 8.99 8.99 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 303 6.119536 ACGGAGCATATTGACATTAGGAAAA 58.880 36.000 0.00 0.00 0.00 2.29
121 309 5.834169 TCGTAACGGAGCATATTGACATTA 58.166 37.500 0.00 0.00 0.00 1.90
122 310 4.689071 TCGTAACGGAGCATATTGACATT 58.311 39.130 0.00 0.00 0.00 2.71
123 311 4.316205 TCGTAACGGAGCATATTGACAT 57.684 40.909 0.00 0.00 0.00 3.06
124 312 3.786516 TCGTAACGGAGCATATTGACA 57.213 42.857 0.00 0.00 0.00 3.58
125 313 5.459110 TTTTCGTAACGGAGCATATTGAC 57.541 39.130 0.00 0.00 0.00 3.18
126 314 7.773864 TTATTTTCGTAACGGAGCATATTGA 57.226 32.000 0.00 0.00 0.00 2.57
132 320 9.478768 TGATATTATTATTTTCGTAACGGAGCA 57.521 29.630 0.00 0.00 0.00 4.26
298 490 5.589192 ACTTGGTATGACTAGTAATCGTGC 58.411 41.667 0.00 0.00 0.00 5.34
362 554 5.127356 GGGCTTGTCTTCTCTTAGCTAAGTA 59.873 44.000 28.31 17.38 34.93 2.24
454 654 1.087202 TGTAATTAGGGCGCGTGCAG 61.087 55.000 24.18 0.00 45.35 4.41
472 672 6.470235 GCTCGATTCAAACATACCATCTTTTG 59.530 38.462 0.00 0.00 0.00 2.44
475 675 4.576463 GGCTCGATTCAAACATACCATCTT 59.424 41.667 0.00 0.00 0.00 2.40
506 706 2.505118 GTCTGACCTCTCGCGTGC 60.505 66.667 5.77 0.00 0.00 5.34
512 712 4.004982 ACTCTTTACTCGTCTGACCTCTC 58.995 47.826 1.55 0.00 0.00 3.20
513 713 4.023726 ACTCTTTACTCGTCTGACCTCT 57.976 45.455 1.55 0.00 0.00 3.69
514 714 5.876612 TTACTCTTTACTCGTCTGACCTC 57.123 43.478 1.55 0.00 0.00 3.85
515 715 6.645790 TTTTACTCTTTACTCGTCTGACCT 57.354 37.500 1.55 0.00 0.00 3.85
516 716 7.062022 GTCATTTTACTCTTTACTCGTCTGACC 59.938 40.741 1.55 0.00 0.00 4.02
517 717 7.594015 TGTCATTTTACTCTTTACTCGTCTGAC 59.406 37.037 0.00 0.00 0.00 3.51
518 718 7.654568 TGTCATTTTACTCTTTACTCGTCTGA 58.345 34.615 0.00 0.00 0.00 3.27
519 719 7.869016 TGTCATTTTACTCTTTACTCGTCTG 57.131 36.000 0.00 0.00 0.00 3.51
520 720 7.384387 GGTTGTCATTTTACTCTTTACTCGTCT 59.616 37.037 0.00 0.00 0.00 4.18
526 726 9.744468 ATGTTTGGTTGTCATTTTACTCTTTAC 57.256 29.630 0.00 0.00 0.00 2.01
632 832 4.307032 TTTGGAGGATCTTTGGAAGAGG 57.693 45.455 0.00 0.00 41.61 3.69
659 859 3.259902 GCCCTCTCTTTGTACGGTAAAG 58.740 50.000 0.00 0.00 36.67 1.85
660 860 2.633967 TGCCCTCTCTTTGTACGGTAAA 59.366 45.455 0.00 0.00 0.00 2.01
661 861 2.250031 TGCCCTCTCTTTGTACGGTAA 58.750 47.619 0.00 0.00 0.00 2.85
663 863 1.066143 CATGCCCTCTCTTTGTACGGT 60.066 52.381 0.00 0.00 0.00 4.83
664 864 1.066143 ACATGCCCTCTCTTTGTACGG 60.066 52.381 0.00 0.00 0.00 4.02
666 866 3.059352 ACACATGCCCTCTCTTTGTAC 57.941 47.619 0.00 0.00 0.00 2.90
669 869 3.265791 GAGTACACATGCCCTCTCTTTG 58.734 50.000 0.00 0.00 0.00 2.77
678 887 1.337823 ACCGACTTGAGTACACATGCC 60.338 52.381 6.17 0.00 0.00 4.40
693 902 2.277084 CCAGCTACCATTTACACCGAC 58.723 52.381 0.00 0.00 0.00 4.79
826 1036 1.073199 CGGTGCCCTCTGTTCCTTT 59.927 57.895 0.00 0.00 0.00 3.11
970 1181 4.447762 CCTTTCTTTTCCTCCCTCTTTCCA 60.448 45.833 0.00 0.00 0.00 3.53
979 1190 4.236527 TGGCTATCCTTTCTTTTCCTCC 57.763 45.455 0.00 0.00 0.00 4.30
999 1210 1.750206 TCCAATTCAATGGCGGTCATG 59.250 47.619 0.00 0.00 40.46 3.07
1066 1286 1.997256 GAGGAGGCGTAGGAGGAGGA 61.997 65.000 0.00 0.00 0.00 3.71
1067 1287 1.529713 GAGGAGGCGTAGGAGGAGG 60.530 68.421 0.00 0.00 0.00 4.30
1068 1288 0.106419 AAGAGGAGGCGTAGGAGGAG 60.106 60.000 0.00 0.00 0.00 3.69
1161 1381 3.079478 AGAGAGCCGGAGCATGCA 61.079 61.111 21.98 0.00 43.56 3.96
1220 1440 2.613595 TGCAAGCAGTTAACTGACACAG 59.386 45.455 34.43 20.06 46.59 3.66
1249 1469 1.212688 ACATGGATGATCGGCCAAGAA 59.787 47.619 13.69 0.00 37.78 2.52
1262 1487 1.464608 CGACGAAACAGCAACATGGAT 59.535 47.619 0.00 0.00 0.00 3.41
1272 1497 1.586679 CGATTAAGCGCGACGAAACAG 60.587 52.381 12.10 0.00 0.00 3.16
1277 1502 2.239201 CATATCGATTAAGCGCGACGA 58.761 47.619 12.10 15.96 39.56 4.20
1278 1503 1.976728 ACATATCGATTAAGCGCGACG 59.023 47.619 12.10 5.08 39.56 5.12
1279 1504 4.370620 AAACATATCGATTAAGCGCGAC 57.629 40.909 12.10 0.04 39.56 5.19
1280 1505 4.269123 ACAAAACATATCGATTAAGCGCGA 59.731 37.500 12.10 4.30 41.14 5.87
1282 1507 5.963004 TGAACAAAACATATCGATTAAGCGC 59.037 36.000 8.54 0.00 0.00 5.92
1283 1508 7.356719 GCATGAACAAAACATATCGATTAAGCG 60.357 37.037 6.82 6.82 0.00 4.68
1284 1509 7.431960 TGCATGAACAAAACATATCGATTAAGC 59.568 33.333 1.71 0.00 0.00 3.09
1285 1510 8.839947 TGCATGAACAAAACATATCGATTAAG 57.160 30.769 1.71 0.00 0.00 1.85
1334 1560 1.601759 GCACCACCTCTGCACACAT 60.602 57.895 0.00 0.00 34.56 3.21
1407 1633 0.037326 AGAAATCGAGGAGCGTGCAA 60.037 50.000 0.00 0.00 41.80 4.08
1433 1659 1.623542 GGACCCTGGGCGATACAGTT 61.624 60.000 14.08 0.00 34.16 3.16
1435 1661 1.622607 TTGGACCCTGGGCGATACAG 61.623 60.000 14.08 0.00 35.74 2.74
1460 1686 3.600235 CGAGACGAAATGAATGATGCGAC 60.600 47.826 0.00 0.00 0.00 5.19
1486 1712 1.040646 TTCATGGACGGGCTAGCTAG 58.959 55.000 16.84 16.84 0.00 3.42
1487 1713 1.491668 TTTCATGGACGGGCTAGCTA 58.508 50.000 15.72 0.00 0.00 3.32
1488 1714 0.839946 ATTTCATGGACGGGCTAGCT 59.160 50.000 15.72 0.00 0.00 3.32
1594 1823 7.521099 GCATGTGGACACTTGATTAGGATTATG 60.521 40.741 18.85 4.87 38.35 1.90
1595 1824 6.488006 GCATGTGGACACTTGATTAGGATTAT 59.512 38.462 18.85 0.00 38.35 1.28
1596 1825 5.822519 GCATGTGGACACTTGATTAGGATTA 59.177 40.000 18.85 0.00 38.35 1.75
1597 1826 4.641989 GCATGTGGACACTTGATTAGGATT 59.358 41.667 18.85 0.00 38.35 3.01
1620 1849 2.597305 GCGTGTACAGAATCAAGTACCG 59.403 50.000 0.00 13.63 39.79 4.02
1777 2016 1.977854 TGGAGTGTGCTGTAATGGACT 59.022 47.619 0.00 0.00 0.00 3.85
1985 2229 2.501723 CCTACCTGACAGTAACCAGCAT 59.498 50.000 0.93 0.00 0.00 3.79
2013 2257 5.957771 ACTACCATAGCAATGAAAGAGGA 57.042 39.130 0.00 0.00 34.84 3.71
2019 2263 6.092944 CCGTTTTGTACTACCATAGCAATGAA 59.907 38.462 0.00 0.00 34.84 2.57
2025 2269 2.610833 GGCCGTTTTGTACTACCATAGC 59.389 50.000 0.00 0.00 0.00 2.97
2089 2335 6.139671 ACCTAGAGTGTGTATCTGATCCATT 58.860 40.000 0.00 0.00 0.00 3.16
2277 2534 0.331278 TACCCACCCTGATTGCCTTG 59.669 55.000 0.00 0.00 0.00 3.61
2297 2560 0.179073 CTCCTCCATGGTGGTTAGCG 60.179 60.000 27.90 11.83 39.03 4.26
2309 2572 1.942776 TCTCATCAGCAACTCCTCCA 58.057 50.000 0.00 0.00 0.00 3.86
2315 2578 2.738000 GCGACAGATCTCATCAGCAACT 60.738 50.000 0.00 0.00 0.00 3.16
2357 2623 2.351244 TGTCTACCTGGCTGGCTCG 61.351 63.158 10.71 0.00 40.22 5.03
2444 2710 1.469308 CCTAAGCGGCCTAGATCGTAG 59.531 57.143 7.19 0.00 0.00 3.51
2517 2786 6.443934 TCTTTCTCTATCTACACAGTGAGC 57.556 41.667 7.81 0.00 0.00 4.26
2520 2789 7.306213 TCGTTTCTTTCTCTATCTACACAGTG 58.694 38.462 0.00 0.00 0.00 3.66
2521 2790 7.450124 TCGTTTCTTTCTCTATCTACACAGT 57.550 36.000 0.00 0.00 0.00 3.55
2526 2809 6.628185 TGGGTTCGTTTCTTTCTCTATCTAC 58.372 40.000 0.00 0.00 0.00 2.59
2527 2810 6.436532 ACTGGGTTCGTTTCTTTCTCTATCTA 59.563 38.462 0.00 0.00 0.00 1.98
2528 2811 5.246429 ACTGGGTTCGTTTCTTTCTCTATCT 59.754 40.000 0.00 0.00 0.00 1.98
2529 2812 5.480205 ACTGGGTTCGTTTCTTTCTCTATC 58.520 41.667 0.00 0.00 0.00 2.08
2530 2813 5.485209 ACTGGGTTCGTTTCTTTCTCTAT 57.515 39.130 0.00 0.00 0.00 1.98
2543 2826 1.741770 GCTGGTGCTACTGGGTTCG 60.742 63.158 0.00 0.00 36.03 3.95
2653 2936 1.627864 TCAACACGGGATCACAGAGA 58.372 50.000 0.00 0.00 0.00 3.10
2709 2992 0.392998 GCCCACATGTACAGGTCAGG 60.393 60.000 10.79 15.12 0.00 3.86
2726 3009 0.877213 CAAAGCAACAGCCAACAGCC 60.877 55.000 0.00 0.00 45.47 4.85
2727 3010 1.493134 GCAAAGCAACAGCCAACAGC 61.493 55.000 0.00 0.00 44.25 4.40
2728 3011 1.210545 CGCAAAGCAACAGCCAACAG 61.211 55.000 0.00 0.00 0.00 3.16
2729 3012 1.226916 CGCAAAGCAACAGCCAACA 60.227 52.632 0.00 0.00 0.00 3.33
2730 3013 0.805711 AACGCAAAGCAACAGCCAAC 60.806 50.000 0.00 0.00 0.00 3.77
2731 3014 0.805322 CAACGCAAAGCAACAGCCAA 60.805 50.000 0.00 0.00 0.00 4.52
2732 3015 1.226916 CAACGCAAAGCAACAGCCA 60.227 52.632 0.00 0.00 0.00 4.75
2813 3097 1.117150 GGATGGGCATTGACATTGCT 58.883 50.000 18.85 2.88 40.03 3.91
2905 3189 1.098129 GGGCAAAGAGAAGATCGGGC 61.098 60.000 0.00 0.00 0.00 6.13
2907 3191 1.432270 GCGGGCAAAGAGAAGATCGG 61.432 60.000 0.00 0.00 0.00 4.18
2981 3265 1.089920 GCGTCAGTCAATCAGGCAAT 58.910 50.000 0.00 0.00 0.00 3.56
3166 3463 3.189287 CAGACAGTATGGTTCAGTTTGGC 59.811 47.826 0.00 0.00 43.62 4.52
3184 3481 2.351157 GCAAAGCATGAACCTGACAGAC 60.351 50.000 3.32 0.00 0.00 3.51
3193 3494 1.005294 CCACGCAGCAAAGCATGAAC 61.005 55.000 0.00 0.00 0.00 3.18
3215 3516 0.035458 GAACCCAGGTGACAGACAGG 59.965 60.000 0.00 0.00 0.00 4.00
3291 3592 2.047655 GGTCACCACGGCGATGAA 60.048 61.111 16.62 0.00 0.00 2.57
3329 3630 2.811317 GTGAGGAGGCTGAACGCG 60.811 66.667 3.53 3.53 40.44 6.01
3389 3693 4.688413 GGTTTGTCACTCTGATCTCTTGTC 59.312 45.833 0.00 0.00 0.00 3.18
3391 3695 3.677121 CGGTTTGTCACTCTGATCTCTTG 59.323 47.826 0.00 0.00 0.00 3.02
3398 3702 3.382227 TCTGTTACGGTTTGTCACTCTGA 59.618 43.478 0.00 0.00 0.00 3.27
3405 3709 4.171005 TCATCGATCTGTTACGGTTTGTC 58.829 43.478 0.00 0.00 0.00 3.18
3412 3716 3.903054 CGTCATCTCATCGATCTGTTACG 59.097 47.826 0.00 0.00 0.00 3.18
3426 3731 4.268884 GGCTGTTAGTTTCATCGTCATCTC 59.731 45.833 0.00 0.00 0.00 2.75
3436 3741 0.404040 CCCCTGGGCTGTTAGTTTCA 59.596 55.000 7.39 0.00 0.00 2.69
3456 3761 0.370273 GGTACATCTGCAAAGCGACG 59.630 55.000 0.00 0.00 0.00 5.12
3457 3762 1.726853 AGGTACATCTGCAAAGCGAC 58.273 50.000 0.00 0.00 0.00 5.19
3459 3764 2.350522 AGAAGGTACATCTGCAAAGCG 58.649 47.619 0.00 0.00 33.98 4.68
3462 3767 3.334691 CCGAAGAAGGTACATCTGCAAA 58.665 45.455 6.68 0.00 36.13 3.68
3595 3900 1.754803 CGTGCCTAGGAATGACAGGTA 59.245 52.381 14.75 0.00 0.00 3.08
3597 3902 0.824109 TCGTGCCTAGGAATGACAGG 59.176 55.000 14.75 6.33 0.00 4.00
3622 3927 1.869767 GAGCACTTGAGTCAACCACAG 59.130 52.381 0.08 0.00 0.00 3.66
3634 3939 5.904941 AGAGAGAAGATACATGAGCACTTG 58.095 41.667 0.00 0.00 0.00 3.16
3705 4010 4.719106 GCTGCTGCTGCTCCTGGT 62.719 66.667 22.10 0.00 40.48 4.00
3777 4082 7.360113 AGTTTACAACTGATGGAATTGGTTT 57.640 32.000 0.00 0.00 41.01 3.27
3940 4245 2.482721 CGTACGCAGGGACAATTTTTCT 59.517 45.455 0.52 0.00 0.00 2.52
3947 4252 1.001068 TGAATTCGTACGCAGGGACAA 59.999 47.619 11.24 0.00 0.00 3.18
3960 4265 6.603237 TTATAGTGCATGGAAGTGAATTCG 57.397 37.500 0.04 0.00 38.95 3.34
4014 4321 0.610785 TGCCCGGGGAAAAGTTGATC 60.611 55.000 25.28 0.18 0.00 2.92
4016 4323 1.110518 GTTGCCCGGGGAAAAGTTGA 61.111 55.000 30.81 1.63 0.00 3.18
4017 4324 1.112916 AGTTGCCCGGGGAAAAGTTG 61.113 55.000 30.81 0.00 0.00 3.16
4027 4334 0.035056 ATTTCTCTCCAGTTGCCCGG 60.035 55.000 0.00 0.00 0.00 5.73
4151 4476 4.020218 AGGATTGTCTCAACTCGGATTTCA 60.020 41.667 0.00 0.00 0.00 2.69
4224 4550 3.067106 CCAGTTGTTGTACTACTGCCAG 58.933 50.000 13.49 0.00 45.93 4.85
4228 4554 3.402628 AGGCCAGTTGTTGTACTACTG 57.597 47.619 5.01 12.42 46.52 2.74
4242 4568 4.037208 CCTACATTAATCTTGCAAGGCCAG 59.963 45.833 25.73 13.35 0.00 4.85
4280 4606 2.035321 TGATTGCGGGGTCTTGTTTTTC 59.965 45.455 0.00 0.00 0.00 2.29
4291 4617 4.718940 AAAGAAAATACTGATTGCGGGG 57.281 40.909 0.00 0.00 0.00 5.73
4293 4619 7.809806 AGAAGAAAAAGAAAATACTGATTGCGG 59.190 33.333 0.00 0.00 0.00 5.69
4330 4656 5.528600 TTAATCTTCCCAGGACCATTTGA 57.471 39.130 0.00 0.00 0.00 2.69
4369 4695 6.456718 GCAGTGATCTAGATCTTGTTTTCTGC 60.457 42.308 28.51 25.83 38.60 4.26
4494 4820 0.115745 TTTGGGACGGAGGGAGTACT 59.884 55.000 0.00 0.00 0.00 2.73
4495 4821 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
4496 4822 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4497 4823 1.558294 GTATTTTGGGACGGAGGGAGT 59.442 52.381 0.00 0.00 0.00 3.85
4498 4824 1.838077 AGTATTTTGGGACGGAGGGAG 59.162 52.381 0.00 0.00 0.00 4.30
4499 4825 1.961133 AGTATTTTGGGACGGAGGGA 58.039 50.000 0.00 0.00 0.00 4.20
4500 4826 2.290705 ACAAGTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
4501 4827 3.007635 GACAAGTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
4502 4828 2.671396 CGACAAGTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
4503 4829 2.613474 CCGACAAGTATTTTGGGACGGA 60.613 50.000 0.00 0.00 37.12 4.69
4504 4830 1.735571 CCGACAAGTATTTTGGGACGG 59.264 52.381 0.00 0.00 0.00 4.79
4505 4831 2.671396 CTCCGACAAGTATTTTGGGACG 59.329 50.000 0.00 0.00 0.00 4.79
4506 4832 3.934068 TCTCCGACAAGTATTTTGGGAC 58.066 45.455 0.00 0.00 0.00 4.46
4507 4833 4.627284 TTCTCCGACAAGTATTTTGGGA 57.373 40.909 0.00 0.00 0.00 4.37
4508 4834 5.393027 CCATTTCTCCGACAAGTATTTTGGG 60.393 44.000 0.00 0.00 0.00 4.12
4509 4835 5.414454 TCCATTTCTCCGACAAGTATTTTGG 59.586 40.000 0.00 0.00 0.00 3.28
4510 4836 6.494893 TCCATTTCTCCGACAAGTATTTTG 57.505 37.500 0.00 0.00 0.00 2.44
4511 4837 8.801882 TTATCCATTTCTCCGACAAGTATTTT 57.198 30.769 0.00 0.00 0.00 1.82
4512 4838 8.801882 TTTATCCATTTCTCCGACAAGTATTT 57.198 30.769 0.00 0.00 0.00 1.40
4513 4839 8.801882 TTTTATCCATTTCTCCGACAAGTATT 57.198 30.769 0.00 0.00 0.00 1.89
4514 4840 8.801882 TTTTTATCCATTTCTCCGACAAGTAT 57.198 30.769 0.00 0.00 0.00 2.12
4515 4841 8.801882 ATTTTTATCCATTTCTCCGACAAGTA 57.198 30.769 0.00 0.00 0.00 2.24
4516 4842 7.703058 ATTTTTATCCATTTCTCCGACAAGT 57.297 32.000 0.00 0.00 0.00 3.16
4517 4843 9.109393 TCTATTTTTATCCATTTCTCCGACAAG 57.891 33.333 0.00 0.00 0.00 3.16
4518 4844 9.627123 ATCTATTTTTATCCATTTCTCCGACAA 57.373 29.630 0.00 0.00 0.00 3.18
4519 4845 9.056005 CATCTATTTTTATCCATTTCTCCGACA 57.944 33.333 0.00 0.00 0.00 4.35
4520 4846 9.057089 ACATCTATTTTTATCCATTTCTCCGAC 57.943 33.333 0.00 0.00 0.00 4.79
4557 4883 9.781425 AGGAATGGATGTATCTAGACATATCTT 57.219 33.333 7.57 0.00 40.18 2.40
4558 4884 9.781425 AAGGAATGGATGTATCTAGACATATCT 57.219 33.333 7.57 0.00 40.18 1.98
4561 4887 9.379770 TCAAAGGAATGGATGTATCTAGACATA 57.620 33.333 0.00 0.00 40.18 2.29
4562 4888 8.153550 GTCAAAGGAATGGATGTATCTAGACAT 58.846 37.037 0.00 0.00 42.82 3.06
4563 4889 7.125659 TGTCAAAGGAATGGATGTATCTAGACA 59.874 37.037 0.00 0.00 0.00 3.41
4564 4890 7.500992 TGTCAAAGGAATGGATGTATCTAGAC 58.499 38.462 0.00 0.00 0.00 2.59
4565 4891 7.675161 TGTCAAAGGAATGGATGTATCTAGA 57.325 36.000 0.00 0.00 0.00 2.43
4566 4892 7.989741 ACTTGTCAAAGGAATGGATGTATCTAG 59.010 37.037 0.00 0.00 37.76 2.43
4567 4893 7.861629 ACTTGTCAAAGGAATGGATGTATCTA 58.138 34.615 0.00 0.00 37.76 1.98
4568 4894 6.725364 ACTTGTCAAAGGAATGGATGTATCT 58.275 36.000 0.00 0.00 37.76 1.98
4569 4895 8.682936 ATACTTGTCAAAGGAATGGATGTATC 57.317 34.615 0.00 0.00 37.76 2.24
4570 4896 9.479549 AAATACTTGTCAAAGGAATGGATGTAT 57.520 29.630 0.00 0.00 37.76 2.29
4571 4897 8.877864 AAATACTTGTCAAAGGAATGGATGTA 57.122 30.769 0.00 0.00 37.76 2.29
4572 4898 7.093771 GGAAATACTTGTCAAAGGAATGGATGT 60.094 37.037 0.00 0.00 37.76 3.06
4573 4899 7.260603 GGAAATACTTGTCAAAGGAATGGATG 58.739 38.462 0.00 0.00 37.76 3.51
4574 4900 6.095440 CGGAAATACTTGTCAAAGGAATGGAT 59.905 38.462 0.00 0.00 37.76 3.41
4575 4901 5.414454 CGGAAATACTTGTCAAAGGAATGGA 59.586 40.000 0.00 0.00 37.76 3.41
4576 4902 5.393027 CCGGAAATACTTGTCAAAGGAATGG 60.393 44.000 0.00 0.00 37.76 3.16
4577 4903 5.414454 TCCGGAAATACTTGTCAAAGGAATG 59.586 40.000 0.00 0.00 37.76 2.67
4578 4904 5.414765 GTCCGGAAATACTTGTCAAAGGAAT 59.585 40.000 5.23 0.00 37.76 3.01
4579 4905 4.758165 GTCCGGAAATACTTGTCAAAGGAA 59.242 41.667 5.23 0.00 37.76 3.36
4580 4906 4.320870 GTCCGGAAATACTTGTCAAAGGA 58.679 43.478 5.23 0.00 37.76 3.36
4581 4907 3.124636 CGTCCGGAAATACTTGTCAAAGG 59.875 47.826 5.23 0.00 37.76 3.11
4582 4908 3.124636 CCGTCCGGAAATACTTGTCAAAG 59.875 47.826 5.23 0.00 37.11 2.77
4583 4909 3.068560 CCGTCCGGAAATACTTGTCAAA 58.931 45.455 5.23 0.00 37.50 2.69
4584 4910 2.299582 TCCGTCCGGAAATACTTGTCAA 59.700 45.455 5.23 0.00 42.05 3.18
4585 4911 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4586 4912 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4587 4913 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4588 4914 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4589 4915 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4590 4916 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4591 4917 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4592 4918 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4593 4919 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4594 4920 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
4595 4921 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
4596 4922 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
4597 4923 2.795231 TATATACTCCCTCCGTCCGG 57.205 55.000 0.00 0.00 0.00 5.14
4598 4924 4.275443 GCTAATATATACTCCCTCCGTCCG 59.725 50.000 0.00 0.00 0.00 4.79
4599 4925 5.447757 AGCTAATATATACTCCCTCCGTCC 58.552 45.833 0.00 0.00 0.00 4.79
4600 4926 8.569641 CATTAGCTAATATATACTCCCTCCGTC 58.430 40.741 18.45 0.00 0.00 4.79
4601 4927 7.014422 GCATTAGCTAATATATACTCCCTCCGT 59.986 40.741 18.45 0.00 37.91 4.69
4602 4928 7.371936 GCATTAGCTAATATATACTCCCTCCG 58.628 42.308 18.45 2.91 37.91 4.63
4603 4929 7.511028 AGGCATTAGCTAATATATACTCCCTCC 59.489 40.741 18.45 5.99 41.70 4.30
4604 4930 8.485578 AGGCATTAGCTAATATATACTCCCTC 57.514 38.462 18.45 0.00 41.70 4.30
4605 4931 8.068110 TGAGGCATTAGCTAATATATACTCCCT 58.932 37.037 18.45 12.64 41.70 4.20
4606 4932 8.251383 TGAGGCATTAGCTAATATATACTCCC 57.749 38.462 18.45 8.85 41.70 4.30
4616 4942 5.163099 TGGTTGGTATGAGGCATTAGCTAAT 60.163 40.000 13.37 13.37 41.70 1.73
4624 4950 2.726821 CACTTGGTTGGTATGAGGCAT 58.273 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.