Multiple sequence alignment - TraesCS6B01G174700

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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 TraesCS6B01G174700 chr6B 100.000 4616 0 0 1 4616 189221948 189217333 0.000000e+00 8525.0
1 TraesCS6B01G174700 chr6B 90.000 60 4 2 4550 4608 611931272 611931330 4.950000e-10 76.8
2 TraesCS6B01G174700 chr6D 92.039 3291 167 53 642 3884 104141607 104138364 0.000000e+00 4538.0
3 TraesCS6B01G174700 chr6D 88.123 261 22 8 3904 4161 35001839 35002093 7.510000e-78 302.0
4 TraesCS6B01G174700 chr6D 91.935 62 4 1 4556 4616 224427038 224426977 8.230000e-13 86.1
5 TraesCS6B01G174700 chr6A 91.297 1896 116 31 562 2432 125499246 125497375 0.000000e+00 2542.0
6 TraesCS6B01G174700 chr6A 93.417 1352 58 15 2450 3795 125497310 125495984 0.000000e+00 1975.0
7 TraesCS6B01G174700 chr6A 82.037 540 67 16 25 558 79406068 79405553 2.550000e-117 433.0
8 TraesCS6B01G174700 chr3D 94.152 513 26 4 46 558 298577284 298577792 0.000000e+00 778.0
9 TraesCS6B01G174700 chr1B 86.240 516 51 14 3 515 486351185 486350687 4.060000e-150 542.0
10 TraesCS6B01G174700 chr1B 89.091 55 4 2 4563 4616 265018356 265018303 2.980000e-07 67.6
11 TraesCS6B01G174700 chr5A 85.545 505 64 9 24 525 113585964 113585466 1.900000e-143 520.0
12 TraesCS6B01G174700 chr5A 82.630 403 64 3 4163 4563 619442373 619441975 7.350000e-93 351.0
13 TraesCS6B01G174700 chr5A 86.154 260 29 7 3904 4161 647398548 647398294 1.640000e-69 274.0
14 TraesCS6B01G174700 chr2D 81.042 691 94 19 3899 4568 410413335 410414009 2.460000e-142 516.0
15 TraesCS6B01G174700 chr2D 85.502 269 29 8 3903 4168 505775616 505775355 5.880000e-69 272.0
16 TraesCS6B01G174700 chr2A 84.162 543 69 13 25 558 738801887 738802421 1.150000e-140 510.0
17 TraesCS6B01G174700 chr2A 85.789 190 21 5 25 213 142330600 142330784 3.640000e-46 196.0
18 TraesCS6B01G174700 chr5B 86.266 466 57 7 11 473 679047400 679046939 2.480000e-137 499.0
19 TraesCS6B01G174700 chr5B 86.364 264 29 4 3899 4161 47594085 47594342 9.780000e-72 281.0
20 TraesCS6B01G174700 chr5B 89.091 55 4 2 4563 4616 576878411 576878358 2.980000e-07 67.6
21 TraesCS6B01G174700 chr3B 84.038 520 56 17 3 515 384329676 384330175 4.180000e-130 475.0
22 TraesCS6B01G174700 chr3B 90.602 266 16 8 3899 4161 766625797 766626056 1.230000e-90 344.0
23 TraesCS6B01G174700 chr3B 91.667 60 3 2 4550 4608 534832529 534832587 1.060000e-11 82.4
24 TraesCS6B01G174700 chr5D 84.653 404 52 6 4160 4561 24920983 24920588 1.200000e-105 394.0
25 TraesCS6B01G174700 chr5D 82.921 404 58 7 4165 4566 507868471 507868865 2.040000e-93 353.0
26 TraesCS6B01G174700 chr5D 82.843 408 52 8 4163 4566 28039465 28039072 2.640000e-92 350.0
27 TraesCS6B01G174700 chr5D 84.091 88 11 3 606 691 483987795 483987881 1.060000e-11 82.4
28 TraesCS6B01G174700 chr5D 80.952 84 13 3 610 691 483827354 483827436 3.860000e-06 63.9
29 TraesCS6B01G174700 chr3A 82.439 410 64 7 4156 4563 711215339 711215742 7.350000e-93 351.0
30 TraesCS6B01G174700 chr3A 82.266 406 64 7 4160 4563 711214175 711214574 1.230000e-90 344.0
31 TraesCS6B01G174700 chr3A 87.121 264 27 5 3899 4161 711211979 711212236 4.520000e-75 292.0
32 TraesCS6B01G174700 chr4B 82.382 403 56 11 4166 4563 67116508 67116900 2.060000e-88 337.0
33 TraesCS6B01G174700 chr4B 85.824 261 28 8 3903 4161 650774913 650774660 7.610000e-68 268.0
34 TraesCS6B01G174700 chr4B 81.739 115 16 4 606 718 387439478 387439589 1.770000e-14 91.6
35 TraesCS6B01G174700 chr4D 82.353 408 48 15 4163 4565 324470684 324470296 2.660000e-87 333.0
36 TraesCS6B01G174700 chr7D 91.266 229 18 2 3934 4161 205495415 205495188 1.250000e-80 311.0
37 TraesCS6B01G174700 chr7D 85.390 308 32 10 258 555 508334479 508334175 1.610000e-79 307.0
38 TraesCS6B01G174700 chr1A 83.509 285 37 8 3880 4161 351472287 351472010 1.650000e-64 257.0
39 TraesCS6B01G174700 chr7A 87.500 88 9 2 25 112 725683550 725683465 2.940000e-17 100.0
40 TraesCS6B01G174700 chr7B 96.000 50 2 0 4565 4614 395605399 395605350 1.060000e-11 82.4
41 TraesCS6B01G174700 chr1D 92.727 55 4 0 4562 4616 434362661 434362607 3.830000e-11 80.5
42 TraesCS6B01G174700 chr2B 91.379 58 2 3 4557 4613 769883417 769883472 4.950000e-10 76.8
43 TraesCS6B01G174700 chr2B 90.385 52 3 2 4563 4613 98616530 98616480 2.980000e-07 67.6


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 TraesCS6B01G174700 chr6B 189217333 189221948 4615 True 8525.0 8525 100.000 1 4616 1 chr6B.!!$R1 4615
1 TraesCS6B01G174700 chr6D 104138364 104141607 3243 True 4538.0 4538 92.039 642 3884 1 chr6D.!!$R1 3242
2 TraesCS6B01G174700 chr6A 125495984 125499246 3262 True 2258.5 2542 92.357 562 3795 2 chr6A.!!$R2 3233
3 TraesCS6B01G174700 chr6A 79405553 79406068 515 True 433.0 433 82.037 25 558 1 chr6A.!!$R1 533
4 TraesCS6B01G174700 chr3D 298577284 298577792 508 False 778.0 778 94.152 46 558 1 chr3D.!!$F1 512
5 TraesCS6B01G174700 chr2D 410413335 410414009 674 False 516.0 516 81.042 3899 4568 1 chr2D.!!$F1 669
6 TraesCS6B01G174700 chr2A 738801887 738802421 534 False 510.0 510 84.162 25 558 1 chr2A.!!$F2 533
7 TraesCS6B01G174700 chr3A 711211979 711215742 3763 False 329.0 351 83.942 3899 4563 3 chr3A.!!$F1 664

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
52 53 0.107361 CCAGCAGCCATGAGATGTGA 60.107 55.0 0.00 0.00 0.00 3.58 F
1236 1248 0.033366 TGAACTCGCTGCAGCTTGTA 59.967 50.0 34.22 16.82 39.32 2.41 F
1758 1780 0.028770 CAACGAAATGTGCACCGTGT 59.971 50.0 17.53 5.70 35.28 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1654 0.038526 AACACGGACGGCTTAGTGAG 60.039 55.000 16.47 0.00 37.95 3.51 R
2755 2857 0.107703 TTCTGCATGATGTCCCGGAC 60.108 55.000 10.96 10.96 0.00 4.79 R
3624 3732 1.749033 GGCGCCTTAGCAGATAGGT 59.251 57.895 22.15 0.00 39.83 3.08 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
17 18 3.382832 CTCCCCTCTGCGGTCGTT 61.383 66.667 0.00 0.00 0.00 3.85
18 19 3.649277 CTCCCCTCTGCGGTCGTTG 62.649 68.421 0.00 0.00 0.00 4.10
19 20 3.691342 CCCCTCTGCGGTCGTTGA 61.691 66.667 0.00 0.00 0.00 3.18
20 21 2.579201 CCCTCTGCGGTCGTTGAT 59.421 61.111 0.00 0.00 0.00 2.57
21 22 1.811266 CCCTCTGCGGTCGTTGATG 60.811 63.158 0.00 0.00 0.00 3.07
22 23 1.215382 CCTCTGCGGTCGTTGATGA 59.785 57.895 0.00 0.00 0.00 2.92
23 24 0.179100 CCTCTGCGGTCGTTGATGAT 60.179 55.000 0.00 0.00 0.00 2.45
52 53 0.107361 CCAGCAGCCATGAGATGTGA 60.107 55.000 0.00 0.00 0.00 3.58
69 71 2.762459 AGCGCGAGGGGGATAACA 60.762 61.111 12.10 0.00 0.00 2.41
85 87 2.514458 AACATGGGATGAACTCACCC 57.486 50.000 0.00 0.00 43.51 4.61
90 92 0.698818 GGGATGAACTCACCCAGGTT 59.301 55.000 10.67 0.00 42.81 3.50
99 101 2.030562 ACCCAGGTTGTCGAAGCG 59.969 61.111 0.00 0.00 34.60 4.68
169 171 4.741239 GCTCCACCCTCTCCCCCA 62.741 72.222 0.00 0.00 0.00 4.96
347 352 2.464459 GCGTGATTTGGCTCCTCGG 61.464 63.158 0.00 0.00 0.00 4.63
368 373 0.896019 CGGAGAGAGTGTGAGGTGGT 60.896 60.000 0.00 0.00 0.00 4.16
372 377 2.365617 GAGAGAGTGTGAGGTGGTGAAA 59.634 50.000 0.00 0.00 0.00 2.69
393 398 1.975680 GGGGAAACGGCAGGATAGATA 59.024 52.381 0.00 0.00 0.00 1.98
398 404 1.617322 ACGGCAGGATAGATAAGCGA 58.383 50.000 0.00 0.00 0.00 4.93
402 408 1.068194 GCAGGATAGATAAGCGACGCT 60.068 52.381 18.46 18.46 42.56 5.07
418 424 1.539827 ACGCTTCTCCCAAAATTTCGG 59.460 47.619 0.00 0.00 0.00 4.30
422 428 3.005367 GCTTCTCCCAAAATTTCGGAACA 59.995 43.478 0.00 0.00 0.00 3.18
505 513 1.371337 CGAGATGGACGGTCGTGGTA 61.371 60.000 0.00 0.00 0.00 3.25
508 516 1.926511 GATGGACGGTCGTGGTACGT 61.927 60.000 0.00 0.00 43.14 3.57
558 566 0.462375 CACCGGACATCGATTGGGTA 59.538 55.000 9.46 0.00 42.43 3.69
559 567 1.134640 CACCGGACATCGATTGGGTAA 60.135 52.381 9.46 0.00 42.43 2.85
560 568 1.134610 ACCGGACATCGATTGGGTAAC 60.135 52.381 9.46 0.00 42.43 2.50
572 580 7.136289 TCGATTGGGTAACTTTTATGTTGTC 57.864 36.000 0.00 0.00 0.00 3.18
613 621 5.620206 TCAGAGTGTTAACAATGGATGTGT 58.380 37.500 14.13 0.00 42.99 3.72
614 622 5.469760 TCAGAGTGTTAACAATGGATGTGTG 59.530 40.000 14.13 0.77 42.99 3.82
663 671 7.504238 GGTGTTACCCATCATAATTTGTATCCA 59.496 37.037 0.00 0.00 30.04 3.41
886 897 6.319658 TCAGGAAGCAATTATCAAGAACATCC 59.680 38.462 0.00 0.00 0.00 3.51
896 907 1.273327 CAAGAACATCCAAGCCCCAAC 59.727 52.381 0.00 0.00 0.00 3.77
897 908 0.251787 AGAACATCCAAGCCCCAACC 60.252 55.000 0.00 0.00 0.00 3.77
898 909 1.229177 AACATCCAAGCCCCAACCC 60.229 57.895 0.00 0.00 0.00 4.11
899 910 2.364186 CATCCAAGCCCCAACCCC 60.364 66.667 0.00 0.00 0.00 4.95
900 911 3.683518 ATCCAAGCCCCAACCCCC 61.684 66.667 0.00 0.00 0.00 5.40
902 913 4.010018 CCAAGCCCCAACCCCCAT 62.010 66.667 0.00 0.00 0.00 4.00
963 974 9.286170 CATCAGATTCAGATGGATTGATAGTTT 57.714 33.333 10.37 0.00 39.30 2.66
966 977 9.286170 CAGATTCAGATGGATTGATAGTTTGAT 57.714 33.333 0.00 0.00 0.00 2.57
1008 1020 4.431131 CCTGACCCAATGGCCGCT 62.431 66.667 0.00 0.00 33.59 5.52
1035 1047 2.088104 TACGCTTCCATCTCCATCCT 57.912 50.000 0.00 0.00 0.00 3.24
1056 1068 1.333636 CCGCCTTCTCCTCTGTCCAT 61.334 60.000 0.00 0.00 0.00 3.41
1072 1084 1.004161 TCCATCCGTCCAATTCAAGCA 59.996 47.619 0.00 0.00 0.00 3.91
1131 1143 0.251077 CTGCAGGAAGAAGGTGCCTT 60.251 55.000 5.57 2.68 39.23 4.35
1204 1216 2.633509 GGTACTCGGACGTGCACCT 61.634 63.158 12.15 0.00 0.00 4.00
1236 1248 0.033366 TGAACTCGCTGCAGCTTGTA 59.967 50.000 34.22 16.82 39.32 2.41
1373 1385 2.892425 GCCTCCGGTGATCTTGCG 60.892 66.667 4.76 0.00 0.00 4.85
1441 1453 1.002773 GCTCCCCGAGGTTTCAGTTAA 59.997 52.381 0.00 0.00 0.00 2.01
1446 1458 3.887110 CCCCGAGGTTTCAGTTAACTTTT 59.113 43.478 5.07 0.00 0.00 2.27
1447 1459 4.023450 CCCCGAGGTTTCAGTTAACTTTTC 60.023 45.833 5.07 0.00 0.00 2.29
1458 1470 5.875910 TCAGTTAACTTTTCGTGGTTCTTCA 59.124 36.000 5.07 0.00 0.00 3.02
1461 1473 6.373495 AGTTAACTTTTCGTGGTTCTTCAGTT 59.627 34.615 1.12 0.00 0.00 3.16
1593 1607 3.780294 TGATTAGCATGACCCTAACCTGT 59.220 43.478 0.00 0.00 0.00 4.00
1621 1638 8.207545 GGATTGATCAGAGGTACTTACAAATCT 58.792 37.037 0.00 0.00 41.55 2.40
1637 1654 2.725221 ATCTTCATGCTTGGTCCCTC 57.275 50.000 0.00 0.00 0.00 4.30
1639 1656 1.556911 TCTTCATGCTTGGTCCCTCTC 59.443 52.381 0.00 0.00 0.00 3.20
1640 1657 1.280133 CTTCATGCTTGGTCCCTCTCA 59.720 52.381 0.00 0.00 0.00 3.27
1643 1664 1.833630 CATGCTTGGTCCCTCTCACTA 59.166 52.381 0.00 0.00 0.00 2.74
1646 1667 1.406205 GCTTGGTCCCTCTCACTAAGC 60.406 57.143 5.34 5.34 46.81 3.09
1651 1672 0.683504 TCCCTCTCACTAAGCCGTCC 60.684 60.000 0.00 0.00 0.00 4.79
1665 1686 0.587768 CCGTCCGTGTTGGTTTTACC 59.412 55.000 0.00 0.00 39.52 2.85
1674 1695 6.204495 TCCGTGTTGGTTTTACCTGTAATTAC 59.796 38.462 8.75 8.75 39.58 1.89
1680 1701 7.319052 TGGTTTTACCTGTAATTACCTGAGA 57.681 36.000 13.01 0.00 39.58 3.27
1681 1702 7.391620 TGGTTTTACCTGTAATTACCTGAGAG 58.608 38.462 13.01 3.35 39.58 3.20
1751 1773 3.543670 CAAATTTGGCAACGAAATGTGC 58.456 40.909 10.49 0.00 45.05 4.57
1753 1775 1.565305 TTTGGCAACGAAATGTGCAC 58.435 45.000 10.75 10.75 36.89 4.57
1754 1776 0.249238 TTGGCAACGAAATGTGCACC 60.249 50.000 15.69 0.00 42.51 5.01
1755 1777 1.729131 GGCAACGAAATGTGCACCG 60.729 57.895 15.69 13.01 0.00 4.94
1757 1779 1.268113 GCAACGAAATGTGCACCGTG 61.268 55.000 17.53 12.94 35.28 4.94
1758 1780 0.028770 CAACGAAATGTGCACCGTGT 59.971 50.000 17.53 5.70 35.28 4.49
1759 1781 1.261885 CAACGAAATGTGCACCGTGTA 59.738 47.619 17.53 0.00 35.28 2.90
1809 1831 8.772705 TCCTGAAATATTTGTTTGATTTTGCAC 58.227 29.630 5.17 0.00 0.00 4.57
1829 1879 5.123820 TGCACTAGGTCAACTCAATTTATGC 59.876 40.000 0.00 0.00 0.00 3.14
1839 1889 6.433716 TCAACTCAATTTATGCTGTCCATTGA 59.566 34.615 0.00 0.00 35.34 2.57
1840 1890 7.123098 TCAACTCAATTTATGCTGTCCATTGAT 59.877 33.333 0.00 0.00 34.24 2.57
1847 1897 6.484364 TTATGCTGTCCATTGATGTAGAGA 57.516 37.500 0.00 0.00 35.34 3.10
1849 1899 4.953667 TGCTGTCCATTGATGTAGAGATC 58.046 43.478 0.00 0.00 0.00 2.75
1857 1907 8.753133 GTCCATTGATGTAGAGATCCATATGTA 58.247 37.037 1.24 0.00 0.00 2.29
1874 1924 6.491062 CCATATGTATTTTGAATCTCTGGGCA 59.509 38.462 1.24 0.00 0.00 5.36
1885 1935 5.104402 TGAATCTCTGGGCACATATTCAGAA 60.104 40.000 14.26 0.00 36.06 3.02
1896 1946 6.914215 GGCACATATTCAGAATGTAACACATG 59.086 38.462 5.85 2.53 37.97 3.21
1899 1949 9.659830 CACATATTCAGAATGTAACACATGATG 57.340 33.333 5.85 0.00 37.97 3.07
1950 2000 7.281774 TGCAGTGAGAAGATGGATAAATTTCTC 59.718 37.037 0.00 5.77 42.42 2.87
2047 2097 3.345508 AAGAGGTAACCCCGAATTCAC 57.654 47.619 6.22 0.00 38.74 3.18
2067 2117 5.865085 TCACAGTACATGTTTTTCTAGCCT 58.135 37.500 2.30 0.00 41.41 4.58
2072 2122 8.784043 ACAGTACATGTTTTTCTAGCCTTTTAG 58.216 33.333 2.30 0.00 39.96 1.85
2085 2135 8.410673 TCTAGCCTTTTAGTATGAGATACCAG 57.589 38.462 0.00 0.00 36.40 4.00
2089 2139 7.735321 AGCCTTTTAGTATGAGATACCAGGTAT 59.265 37.037 12.36 12.36 36.40 2.73
2106 2157 8.499288 ACCAGGTATTTATTCCCAAAGAAAAA 57.501 30.769 0.00 0.00 38.21 1.94
2107 2158 8.593679 ACCAGGTATTTATTCCCAAAGAAAAAG 58.406 33.333 0.00 0.00 38.21 2.27
2108 2159 8.811994 CCAGGTATTTATTCCCAAAGAAAAAGA 58.188 33.333 0.00 0.00 38.21 2.52
2109 2160 9.860898 CAGGTATTTATTCCCAAAGAAAAAGAG 57.139 33.333 0.00 0.00 38.21 2.85
2110 2161 9.822727 AGGTATTTATTCCCAAAGAAAAAGAGA 57.177 29.630 0.00 0.00 38.21 3.10
2115 2166 6.759497 ATTCCCAAAGAAAAAGAGATACCG 57.241 37.500 0.00 0.00 38.21 4.02
2116 2167 5.492855 TCCCAAAGAAAAAGAGATACCGA 57.507 39.130 0.00 0.00 0.00 4.69
2117 2168 5.488341 TCCCAAAGAAAAAGAGATACCGAG 58.512 41.667 0.00 0.00 0.00 4.63
2118 2169 4.095036 CCCAAAGAAAAAGAGATACCGAGC 59.905 45.833 0.00 0.00 0.00 5.03
2146 2197 3.616821 CACTGCAGAATTCATGGCAAATG 59.383 43.478 23.35 14.25 35.59 2.32
2230 2283 5.746990 ACAGGCTGTTCTACTTGTCTATT 57.253 39.130 15.88 0.00 0.00 1.73
2257 2310 4.025229 CCAAATATATTCGTGGACGTGGTG 60.025 45.833 9.72 0.00 40.80 4.17
2362 2415 1.381463 GTCCTCGGGGGAGCTTACT 60.381 63.158 0.00 0.00 46.10 2.24
2428 2519 9.243105 AGGTAACATATAAATGCAGAGTGTTTT 57.757 29.630 0.00 0.00 36.50 2.43
2438 2529 3.132824 TGCAGAGTGTTTTCAGAGACTCA 59.867 43.478 5.02 0.00 0.00 3.41
2538 2639 0.974383 TCCTCCGTTTCTCCAACCTC 59.026 55.000 0.00 0.00 30.65 3.85
2595 2696 4.387598 GGAATGTGCAGCTCATATTCTCT 58.612 43.478 22.33 0.00 46.34 3.10
2685 2787 2.236644 TGTTCATTCATTGGCCAATGGG 59.763 45.455 43.41 34.24 46.08 4.00
2686 2788 2.236893 GTTCATTCATTGGCCAATGGGT 59.763 45.455 43.41 32.86 46.08 4.51
2687 2789 3.395054 TCATTCATTGGCCAATGGGTA 57.605 42.857 43.41 32.39 46.08 3.69
2688 2790 3.298619 TCATTCATTGGCCAATGGGTAG 58.701 45.455 43.41 32.50 46.08 3.18
2689 2791 2.157640 TTCATTGGCCAATGGGTAGG 57.842 50.000 43.41 26.13 46.08 3.18
2755 2857 1.131883 ACTTCGACAACTACGGGATCG 59.868 52.381 0.00 0.00 43.02 3.69
2817 2919 1.153349 GTTCGCCATGGAGACTCCC 60.153 63.158 18.72 2.95 35.03 4.30
2823 2925 0.972983 CCATGGAGACTCCCGTCAGT 60.973 60.000 19.11 0.00 42.73 3.41
2863 2965 2.159627 CGCAACGAGAAGGTAGCAAAAT 59.840 45.455 0.00 0.00 0.00 1.82
2866 2968 5.447279 CGCAACGAGAAGGTAGCAAAATAAT 60.447 40.000 0.00 0.00 0.00 1.28
2900 3002 4.391155 ACCAATTAAACGTACAGCCTGAA 58.609 39.130 0.00 0.00 0.00 3.02
3153 3257 4.043200 GGCAAGGCGCTTCACACC 62.043 66.667 7.64 0.00 41.91 4.16
3216 3320 2.421399 CCTCTACCGGGGGAACGTC 61.421 68.421 6.32 0.00 0.00 4.34
3354 3458 3.617775 GCAACCTCAACCTCTTCTACTCC 60.618 52.174 0.00 0.00 0.00 3.85
3606 3710 3.558411 GACATCAGCAGCGACGGC 61.558 66.667 0.00 0.00 40.37 5.68
3624 3732 2.035632 GGCTCCTTCTAGCAAGCTCTA 58.964 52.381 0.00 0.00 44.64 2.43
3690 3798 1.133790 GCCATCAAGTGACAGCCAATC 59.866 52.381 0.00 0.00 0.00 2.67
3709 3826 6.541641 GCCAATCTTACTCAGACTCAATCAAT 59.458 38.462 0.00 0.00 32.83 2.57
3716 3833 5.477510 ACTCAGACTCAATCAATCTGTGAC 58.522 41.667 8.95 0.00 39.72 3.67
3795 3912 4.511082 TGCATTTTCCTTACTTTTGCAAGC 59.489 37.500 0.00 0.00 35.85 4.01
3797 3914 5.333568 GCATTTTCCTTACTTTTGCAAGCTG 60.334 40.000 0.00 0.00 32.57 4.24
3814 3932 1.610522 GCTGAAAATCTGCCACACACT 59.389 47.619 0.00 0.00 35.62 3.55
3815 3933 2.813754 GCTGAAAATCTGCCACACACTA 59.186 45.455 0.00 0.00 35.62 2.74
3816 3934 3.365364 GCTGAAAATCTGCCACACACTAC 60.365 47.826 0.00 0.00 35.62 2.73
3817 3935 3.814625 TGAAAATCTGCCACACACTACA 58.185 40.909 0.00 0.00 0.00 2.74
3832 3950 7.651304 CCACACACTACAGCAAAATCAAATAAA 59.349 33.333 0.00 0.00 0.00 1.40
3836 3954 6.867816 CACTACAGCAAAATCAAATAAAGCCA 59.132 34.615 0.00 0.00 0.00 4.75
3876 3994 5.763876 AGGTCAGTTTAACCTCAGCTTAT 57.236 39.130 0.00 0.00 43.85 1.73
3877 3995 6.869206 AGGTCAGTTTAACCTCAGCTTATA 57.131 37.500 0.00 0.00 43.85 0.98
3878 3996 6.641474 AGGTCAGTTTAACCTCAGCTTATAC 58.359 40.000 0.00 0.00 43.85 1.47
3881 3999 8.422566 GGTCAGTTTAACCTCAGCTTATACTAT 58.577 37.037 0.00 0.00 33.78 2.12
3887 4005 9.760077 TTTAACCTCAGCTTATACTATAACAGC 57.240 33.333 0.00 0.00 0.00 4.40
3888 4006 6.978674 ACCTCAGCTTATACTATAACAGCA 57.021 37.500 0.00 0.00 32.58 4.41
3889 4007 7.546250 ACCTCAGCTTATACTATAACAGCAT 57.454 36.000 0.00 0.00 32.58 3.79
3890 4008 7.607250 ACCTCAGCTTATACTATAACAGCATC 58.393 38.462 0.00 0.00 32.58 3.91
3891 4009 7.453126 ACCTCAGCTTATACTATAACAGCATCT 59.547 37.037 0.00 0.00 32.58 2.90
3892 4010 7.973388 CCTCAGCTTATACTATAACAGCATCTC 59.027 40.741 0.00 0.00 32.58 2.75
3893 4011 7.831753 TCAGCTTATACTATAACAGCATCTCC 58.168 38.462 0.00 0.00 32.58 3.71
3894 4012 7.451566 TCAGCTTATACTATAACAGCATCTCCA 59.548 37.037 0.00 0.00 32.58 3.86
3895 4013 8.090831 CAGCTTATACTATAACAGCATCTCCAA 58.909 37.037 0.00 0.00 32.58 3.53
3896 4014 8.091449 AGCTTATACTATAACAGCATCTCCAAC 58.909 37.037 3.60 0.00 32.58 3.77
3897 4015 7.872993 GCTTATACTATAACAGCATCTCCAACA 59.127 37.037 0.00 0.00 0.00 3.33
3900 4018 4.471386 ACTATAACAGCATCTCCAACAGGT 59.529 41.667 0.00 0.00 0.00 4.00
3941 4059 2.592861 CTGCCCGGAATAGCCAGC 60.593 66.667 0.73 0.00 36.39 4.85
4025 4145 1.065358 GCAGACGCGCTAAACTACAA 58.935 50.000 5.73 0.00 0.00 2.41
4058 4179 1.133025 GCTGACGCTTGCCATATGTTT 59.867 47.619 1.24 0.00 0.00 2.83
4161 7389 7.487484 TGACATAAAAGTTCAAAATCACTGCA 58.513 30.769 0.00 0.00 0.00 4.41
4165 7393 6.892310 AAAAGTTCAAAATCACTGCAAGAC 57.108 33.333 0.00 0.00 37.43 3.01
4174 7402 0.602638 CACTGCAAGACCGGTGCTTA 60.603 55.000 14.63 0.50 42.69 3.09
4190 7418 1.001764 TTAGAGGAGCACCGACGGA 60.002 57.895 23.38 0.00 41.83 4.69
4191 7419 1.030488 TTAGAGGAGCACCGACGGAG 61.030 60.000 23.38 14.88 41.83 4.63
4287 7515 2.687566 GGTGAGGGGGATGTCGGT 60.688 66.667 0.00 0.00 0.00 4.69
4319 7547 4.313675 GATGAATTCGCCGGCGGC 62.314 66.667 44.95 39.60 46.75 6.53
4363 7591 4.101448 GCGGAGAGGGTGTGGCAT 62.101 66.667 0.00 0.00 0.00 4.40
4385 7613 3.474034 GCTCGAGTGTGCAGCGTC 61.474 66.667 15.13 0.00 34.77 5.19
4410 7638 1.928706 GCGGGCGGACAAAATAAGCA 61.929 55.000 0.00 0.00 0.00 3.91
4428 7656 4.535094 GCGCGCGATGCCATTTCA 62.535 61.111 37.18 0.00 42.08 2.69
4532 7762 1.539388 CTGTATTTTTCCAGTGCGGCA 59.461 47.619 0.00 0.00 33.14 5.69
4533 7763 2.164219 CTGTATTTTTCCAGTGCGGCAT 59.836 45.455 5.72 0.00 33.14 4.40
4539 7769 4.364415 TTTTCCAGTGCGGCATTTATAC 57.636 40.909 5.72 0.00 33.14 1.47
4541 7771 1.210722 TCCAGTGCGGCATTTATACCA 59.789 47.619 5.72 0.00 33.14 3.25
4548 7778 1.281656 GCATTTATACCACGCGGCC 59.718 57.895 12.47 0.00 34.57 6.13
4568 7798 1.137872 CGTTGGAGATGCTCTAAGGCT 59.862 52.381 0.00 0.00 31.92 4.58
4569 7799 2.559440 GTTGGAGATGCTCTAAGGCTG 58.441 52.381 0.00 0.00 31.92 4.85
4570 7800 1.126488 TGGAGATGCTCTAAGGCTGG 58.874 55.000 0.00 0.00 0.00 4.85
4571 7801 0.250252 GGAGATGCTCTAAGGCTGGC 60.250 60.000 0.00 0.00 0.00 4.85
4572 7802 0.250252 GAGATGCTCTAAGGCTGGCC 60.250 60.000 3.00 3.00 0.00 5.36
4573 7803 0.984961 AGATGCTCTAAGGCTGGCCA 60.985 55.000 14.39 4.71 38.92 5.36
4574 7804 0.110104 GATGCTCTAAGGCTGGCCAT 59.890 55.000 5.51 4.39 38.92 4.40
4575 7805 1.349026 GATGCTCTAAGGCTGGCCATA 59.651 52.381 5.51 5.41 38.92 2.74
4576 7806 0.761187 TGCTCTAAGGCTGGCCATAG 59.239 55.000 5.51 15.26 38.38 2.23
4577 7807 0.761802 GCTCTAAGGCTGGCCATAGT 59.238 55.000 19.10 0.00 38.24 2.12
4578 7808 1.542108 GCTCTAAGGCTGGCCATAGTG 60.542 57.143 19.10 17.79 38.24 2.74
4579 7809 2.042464 CTCTAAGGCTGGCCATAGTGA 58.958 52.381 19.10 0.00 38.24 3.41
4580 7810 2.036992 CTCTAAGGCTGGCCATAGTGAG 59.963 54.545 19.10 6.07 38.24 3.51
4581 7811 1.071385 CTAAGGCTGGCCATAGTGAGG 59.929 57.143 5.51 0.00 38.92 3.86
4582 7812 1.639635 AAGGCTGGCCATAGTGAGGG 61.640 60.000 5.51 0.00 38.92 4.30
4583 7813 2.378634 GGCTGGCCATAGTGAGGGT 61.379 63.158 5.51 0.00 35.81 4.34
4584 7814 1.054406 GGCTGGCCATAGTGAGGGTA 61.054 60.000 5.51 0.00 35.81 3.69
4585 7815 0.837272 GCTGGCCATAGTGAGGGTAA 59.163 55.000 5.51 0.00 0.00 2.85
4586 7816 1.475213 GCTGGCCATAGTGAGGGTAAC 60.475 57.143 5.51 0.00 0.00 2.50
4587 7817 1.837439 CTGGCCATAGTGAGGGTAACA 59.163 52.381 5.51 0.00 39.74 2.41
4588 7818 2.439507 CTGGCCATAGTGAGGGTAACAT 59.560 50.000 5.51 0.00 39.74 2.71
4589 7819 3.646162 CTGGCCATAGTGAGGGTAACATA 59.354 47.826 5.51 0.00 39.74 2.29
4590 7820 4.041464 TGGCCATAGTGAGGGTAACATAA 58.959 43.478 0.00 0.00 39.74 1.90
4591 7821 4.141574 TGGCCATAGTGAGGGTAACATAAC 60.142 45.833 0.00 0.00 39.74 1.89
4592 7822 4.386711 GCCATAGTGAGGGTAACATAACC 58.613 47.826 0.00 0.00 38.94 2.85
4603 7833 7.144234 AGGGTAACATAACCTATAACATGCA 57.856 36.000 0.00 0.00 46.26 3.96
4604 7834 6.996282 AGGGTAACATAACCTATAACATGCAC 59.004 38.462 0.00 0.00 46.26 4.57
4605 7835 6.996282 GGGTAACATAACCTATAACATGCACT 59.004 38.462 0.00 0.00 39.65 4.40
4606 7836 7.501225 GGGTAACATAACCTATAACATGCACTT 59.499 37.037 0.00 0.00 39.65 3.16
4607 7837 8.342634 GGTAACATAACCTATAACATGCACTTG 58.657 37.037 0.00 0.00 36.53 3.16
4608 7838 9.104965 GTAACATAACCTATAACATGCACTTGA 57.895 33.333 0.00 0.00 0.00 3.02
4609 7839 7.792374 ACATAACCTATAACATGCACTTGAG 57.208 36.000 0.00 0.00 0.00 3.02
4610 7840 7.564793 ACATAACCTATAACATGCACTTGAGA 58.435 34.615 0.00 0.00 0.00 3.27
4611 7841 7.495934 ACATAACCTATAACATGCACTTGAGAC 59.504 37.037 0.00 0.00 0.00 3.36
4612 7842 5.683876 ACCTATAACATGCACTTGAGACT 57.316 39.130 0.00 0.00 0.00 3.24
4613 7843 6.791867 ACCTATAACATGCACTTGAGACTA 57.208 37.500 0.00 0.00 0.00 2.59
4614 7844 6.810911 ACCTATAACATGCACTTGAGACTAG 58.189 40.000 0.00 0.00 0.00 2.57
4615 7845 5.694006 CCTATAACATGCACTTGAGACTAGC 59.306 44.000 0.00 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.382832 AACGACCGCAGAGGGGAG 61.383 66.667 7.14 3.42 46.96 4.30
1 2 3.691342 CAACGACCGCAGAGGGGA 61.691 66.667 7.14 0.00 46.96 4.81
2 3 3.019003 ATCAACGACCGCAGAGGGG 62.019 63.158 0.00 0.00 46.96 4.79
3 4 1.811266 CATCAACGACCGCAGAGGG 60.811 63.158 0.00 0.00 46.96 4.30
5 6 0.926155 CATCATCAACGACCGCAGAG 59.074 55.000 0.00 0.00 0.00 3.35
6 7 0.530288 TCATCATCAACGACCGCAGA 59.470 50.000 0.00 0.00 0.00 4.26
7 8 0.647410 GTCATCATCAACGACCGCAG 59.353 55.000 0.00 0.00 0.00 5.18
8 9 1.075979 CGTCATCATCAACGACCGCA 61.076 55.000 0.00 0.00 41.29 5.69
9 10 0.800683 TCGTCATCATCAACGACCGC 60.801 55.000 0.00 0.00 42.49 5.68
10 11 1.320555 GTTCGTCATCATCAACGACCG 59.679 52.381 0.00 0.00 46.56 4.79
11 12 1.659098 GGTTCGTCATCATCAACGACC 59.341 52.381 0.00 0.00 46.56 4.79
12 13 1.659098 GGGTTCGTCATCATCAACGAC 59.341 52.381 0.00 0.00 46.56 4.34
13 14 1.404986 GGGGTTCGTCATCATCAACGA 60.405 52.381 0.00 0.00 45.37 3.85
14 15 1.006832 GGGGTTCGTCATCATCAACG 58.993 55.000 0.00 0.00 40.17 4.10
15 16 1.339631 TGGGGGTTCGTCATCATCAAC 60.340 52.381 0.00 0.00 0.00 3.18
16 17 0.988063 TGGGGGTTCGTCATCATCAA 59.012 50.000 0.00 0.00 0.00 2.57
17 18 0.541392 CTGGGGGTTCGTCATCATCA 59.459 55.000 0.00 0.00 0.00 3.07
18 19 0.815615 GCTGGGGGTTCGTCATCATC 60.816 60.000 0.00 0.00 0.00 2.92
19 20 1.224592 GCTGGGGGTTCGTCATCAT 59.775 57.895 0.00 0.00 0.00 2.45
20 21 2.184020 CTGCTGGGGGTTCGTCATCA 62.184 60.000 0.00 0.00 0.00 3.07
21 22 1.450312 CTGCTGGGGGTTCGTCATC 60.450 63.158 0.00 0.00 0.00 2.92
22 23 2.671070 CTGCTGGGGGTTCGTCAT 59.329 61.111 0.00 0.00 0.00 3.06
23 24 4.329545 GCTGCTGGGGGTTCGTCA 62.330 66.667 0.00 0.00 0.00 4.35
52 53 2.140792 ATGTTATCCCCCTCGCGCT 61.141 57.895 5.56 0.00 0.00 5.92
64 65 3.527253 TGGGTGAGTTCATCCCATGTTAT 59.473 43.478 8.88 0.00 46.59 1.89
65 66 2.916269 TGGGTGAGTTCATCCCATGTTA 59.084 45.455 8.88 0.00 46.59 2.41
69 71 0.921896 CCTGGGTGAGTTCATCCCAT 59.078 55.000 17.20 0.00 46.59 4.00
85 87 1.221466 TGCTTCGCTTCGACAACCTG 61.221 55.000 0.00 0.00 34.89 4.00
90 92 0.458543 GATCCTGCTTCGCTTCGACA 60.459 55.000 0.00 0.00 34.89 4.35
99 101 0.317770 CGAGAGCGAGATCCTGCTTC 60.318 60.000 10.33 8.91 42.60 3.86
169 171 1.043673 AGGAGAAGGTAGCGGCGAAT 61.044 55.000 12.98 0.00 0.00 3.34
261 266 1.798813 GGCGAGTTCAATTCAACGAGT 59.201 47.619 0.00 0.00 0.00 4.18
347 352 1.979693 ACCTCACACTCTCTCCGGC 60.980 63.158 0.00 0.00 0.00 6.13
349 354 0.896019 ACCACCTCACACTCTCTCCG 60.896 60.000 0.00 0.00 0.00 4.63
368 373 1.228429 CCTGCCGTTTCCCCTTTCA 60.228 57.895 0.00 0.00 0.00 2.69
372 377 0.326238 TCTATCCTGCCGTTTCCCCT 60.326 55.000 0.00 0.00 0.00 4.79
398 404 1.539827 CCGAAATTTTGGGAGAAGCGT 59.460 47.619 15.89 0.00 0.00 5.07
402 408 5.538433 AGATTGTTCCGAAATTTTGGGAGAA 59.462 36.000 22.07 18.97 38.83 2.87
418 424 4.368315 GGTGGGTTTTGTTGAGATTGTTC 58.632 43.478 0.00 0.00 0.00 3.18
422 428 1.339929 GCGGTGGGTTTTGTTGAGATT 59.660 47.619 0.00 0.00 0.00 2.40
548 556 6.128499 CGACAACATAAAAGTTACCCAATCGA 60.128 38.462 0.00 0.00 0.00 3.59
593 601 4.023279 TGCACACATCCATTGTTAACACTC 60.023 41.667 8.07 0.00 36.00 3.51
600 608 5.477984 AGTTAGAATGCACACATCCATTGTT 59.522 36.000 0.00 0.00 36.00 2.83
601 609 5.012239 AGTTAGAATGCACACATCCATTGT 58.988 37.500 0.00 0.00 39.91 2.71
602 610 5.571784 AGTTAGAATGCACACATCCATTG 57.428 39.130 0.00 0.00 34.62 2.82
604 612 6.872628 CATAGTTAGAATGCACACATCCAT 57.127 37.500 0.00 0.00 34.62 3.41
707 716 7.541783 CCCATTGGTATGCGAACATATTTATTG 59.458 37.037 1.20 0.00 40.79 1.90
720 729 3.243501 CCTTTTCATCCCATTGGTATGCG 60.244 47.826 3.45 0.00 0.00 4.73
724 733 9.944079 TTTATTATCCTTTTCATCCCATTGGTA 57.056 29.630 1.20 0.00 0.00 3.25
886 897 1.989508 GAATGGGGGTTGGGGCTTG 60.990 63.158 0.00 0.00 0.00 4.01
896 907 2.190578 GGCTCTGACGAATGGGGG 59.809 66.667 0.00 0.00 0.00 5.40
897 908 0.745845 CTTGGCTCTGACGAATGGGG 60.746 60.000 0.00 0.00 0.00 4.96
898 909 1.372087 GCTTGGCTCTGACGAATGGG 61.372 60.000 0.00 0.00 0.00 4.00
899 910 0.674581 TGCTTGGCTCTGACGAATGG 60.675 55.000 0.00 0.00 0.00 3.16
900 911 1.329906 GATGCTTGGCTCTGACGAATG 59.670 52.381 0.00 0.00 0.00 2.67
901 912 1.661341 GATGCTTGGCTCTGACGAAT 58.339 50.000 0.00 0.00 0.00 3.34
902 913 0.391661 GGATGCTTGGCTCTGACGAA 60.392 55.000 0.00 0.00 0.00 3.85
963 974 7.037586 AGGAAACAAGAATAGTTGGGAGTATCA 60.038 37.037 0.00 0.00 36.25 2.15
966 977 6.697641 AGGAAACAAGAATAGTTGGGAGTA 57.302 37.500 0.00 0.00 0.00 2.59
1008 1020 3.252701 GGAGATGGAAGCGTAAGTCGATA 59.747 47.826 0.00 0.00 42.86 2.92
1035 1047 2.604686 ACAGAGGAGAAGGCGGCA 60.605 61.111 13.08 0.00 0.00 5.69
1056 1068 0.109532 TGGTGCTTGAATTGGACGGA 59.890 50.000 0.00 0.00 0.00 4.69
1072 1084 4.966787 ATGGCGGTGCGGTTTGGT 62.967 61.111 0.00 0.00 0.00 3.67
1131 1143 3.214328 GTTTGAAGACTTTGCCCTGAGA 58.786 45.455 0.00 0.00 0.00 3.27
1140 1152 1.029681 GGTGCCCGTTTGAAGACTTT 58.970 50.000 0.00 0.00 0.00 2.66
1204 1216 0.243907 GAGTTCAGACAGCCGTGCTA 59.756 55.000 0.00 0.00 36.40 3.49
1236 1248 6.106673 CCACTTCTCGGTACAATATTCTTGT 58.893 40.000 0.00 0.00 36.49 3.16
1326 1338 0.175073 GTGATACTGACGGTGTCCCC 59.825 60.000 8.53 0.00 35.57 4.81
1327 1339 0.892755 TGTGATACTGACGGTGTCCC 59.107 55.000 8.53 0.00 35.57 4.46
1328 1340 1.544691 ACTGTGATACTGACGGTGTCC 59.455 52.381 8.53 1.71 35.57 4.02
1329 1341 2.728225 CGACTGTGATACTGACGGTGTC 60.728 54.545 4.29 4.29 32.91 3.67
1340 1352 0.393944 AGGCTCCGACGACTGTGATA 60.394 55.000 0.00 0.00 0.00 2.15
1441 1453 4.142469 CCAAACTGAAGAACCACGAAAAGT 60.142 41.667 0.00 0.00 0.00 2.66
1446 1458 1.961793 CCCAAACTGAAGAACCACGA 58.038 50.000 0.00 0.00 0.00 4.35
1447 1459 0.310854 GCCCAAACTGAAGAACCACG 59.689 55.000 0.00 0.00 0.00 4.94
1458 1470 1.203100 AGCATCTCCAAAGCCCAAACT 60.203 47.619 0.00 0.00 0.00 2.66
1461 1473 1.635487 ACTAGCATCTCCAAAGCCCAA 59.365 47.619 0.00 0.00 0.00 4.12
1593 1607 5.198207 TGTAAGTACCTCTGATCAATCCGA 58.802 41.667 0.00 0.00 0.00 4.55
1621 1638 1.003580 GTGAGAGGGACCAAGCATGAA 59.996 52.381 0.00 0.00 0.00 2.57
1637 1654 0.038526 AACACGGACGGCTTAGTGAG 60.039 55.000 16.47 0.00 37.95 3.51
1639 1656 1.289109 CCAACACGGACGGCTTAGTG 61.289 60.000 9.79 9.79 40.17 2.74
1640 1657 1.005394 CCAACACGGACGGCTTAGT 60.005 57.895 0.00 0.00 36.56 2.24
1643 1664 1.033202 AAAACCAACACGGACGGCTT 61.033 50.000 0.00 0.00 38.63 4.35
1646 1667 0.587768 GGTAAAACCAACACGGACGG 59.412 55.000 0.00 0.00 38.42 4.79
1651 1672 6.205270 AGGTAATTACAGGTAAAACCAACACG 59.795 38.462 17.16 0.00 41.95 4.49
1665 1686 3.452627 AGGGCACTCTCAGGTAATTACAG 59.547 47.826 17.16 9.10 0.00 2.74
1747 1769 2.409012 CATTGTACTACACGGTGCACA 58.591 47.619 20.43 4.83 32.04 4.57
1748 1770 1.730064 CCATTGTACTACACGGTGCAC 59.270 52.381 8.80 8.80 32.04 4.57
1751 1773 2.087501 TGCCATTGTACTACACGGTG 57.912 50.000 6.58 6.58 0.00 4.94
1753 1775 1.939934 CCATGCCATTGTACTACACGG 59.060 52.381 0.00 0.00 0.00 4.94
1754 1776 1.330521 GCCATGCCATTGTACTACACG 59.669 52.381 0.00 0.00 0.00 4.49
1755 1777 2.097466 GTGCCATGCCATTGTACTACAC 59.903 50.000 0.00 0.00 0.00 2.90
1757 1779 2.364632 TGTGCCATGCCATTGTACTAC 58.635 47.619 0.00 0.00 0.00 2.73
1758 1780 2.797177 TGTGCCATGCCATTGTACTA 57.203 45.000 0.00 0.00 0.00 1.82
1759 1781 1.921982 TTGTGCCATGCCATTGTACT 58.078 45.000 0.00 0.00 0.00 2.73
1809 1831 6.037610 GGACAGCATAAATTGAGTTGACCTAG 59.962 42.308 0.00 0.00 0.00 3.02
1829 1879 5.541953 TGGATCTCTACATCAATGGACAG 57.458 43.478 0.00 0.00 0.00 3.51
1847 1897 7.395489 GCCCAGAGATTCAAAATACATATGGAT 59.605 37.037 7.80 0.00 0.00 3.41
1849 1899 6.491062 TGCCCAGAGATTCAAAATACATATGG 59.509 38.462 7.80 0.00 0.00 2.74
1857 1907 6.608405 TGAATATGTGCCCAGAGATTCAAAAT 59.392 34.615 11.50 0.00 30.92 1.82
1860 1910 5.104402 TCTGAATATGTGCCCAGAGATTCAA 60.104 40.000 13.89 5.70 32.33 2.69
1874 1924 9.399797 ACATCATGTGTTACATTCTGAATATGT 57.600 29.630 1.98 2.32 36.53 2.29
1914 1964 0.898326 TCTCACTGCAGTTCGCCCTA 60.898 55.000 18.94 0.00 41.33 3.53
1950 2000 4.297510 CGGACTGATAGAAGCATCTCTTG 58.702 47.826 0.00 0.00 37.10 3.02
2047 2097 8.784043 ACTAAAAGGCTAGAAAAACATGTACTG 58.216 33.333 0.00 0.00 0.00 2.74
2072 2122 8.822805 TGGGAATAAATACCTGGTATCTCATAC 58.177 37.037 19.19 7.82 35.00 2.39
2089 2139 8.736244 CGGTATCTCTTTTTCTTTGGGAATAAA 58.264 33.333 0.00 0.00 33.53 1.40
2106 2157 2.169352 AGTGCAATTGCTCGGTATCTCT 59.831 45.455 29.37 6.41 42.66 3.10
2107 2158 2.286294 CAGTGCAATTGCTCGGTATCTC 59.714 50.000 29.37 9.61 42.66 2.75
2108 2159 2.283298 CAGTGCAATTGCTCGGTATCT 58.717 47.619 29.37 13.46 42.66 1.98
2109 2160 2.744787 CAGTGCAATTGCTCGGTATC 57.255 50.000 29.37 11.71 42.66 2.24
2118 2169 3.616821 CCATGAATTCTGCAGTGCAATTG 59.383 43.478 20.22 7.94 38.41 2.32
2146 2197 4.319549 CCTCAACTCCTTTTTCTACGCAAC 60.320 45.833 0.00 0.00 0.00 4.17
2230 2283 4.141892 ACGTCCACGAATATATTTGGTGGA 60.142 41.667 29.83 29.83 44.30 4.02
2362 2415 6.209589 CCTCTAAATACATCTTCAGGGATCGA 59.790 42.308 0.00 0.00 0.00 3.59
2428 2519 5.894393 CCTAAGAAATAGGGTGAGTCTCTGA 59.106 44.000 0.65 0.00 46.55 3.27
2538 2639 2.253758 CCACAGTGGCTGGAACACG 61.254 63.158 6.67 0.00 43.41 4.49
2595 2696 3.450507 TCGGTGCCGAAGTCTTCA 58.549 55.556 11.22 0.00 46.01 3.02
2643 2744 1.342074 TCTTATCAGATCCGGCTGGG 58.658 55.000 12.87 0.00 36.55 4.45
2648 2749 6.707608 TGAATGAACATTCTTATCAGATCCGG 59.292 38.462 22.35 0.00 45.55 5.14
2704 2806 2.804647 CAACCCAACAAAGAAACCGTC 58.195 47.619 0.00 0.00 0.00 4.79
2706 2808 1.134965 TGCAACCCAACAAAGAAACCG 60.135 47.619 0.00 0.00 0.00 4.44
2709 2811 2.941720 GCAATGCAACCCAACAAAGAAA 59.058 40.909 0.00 0.00 0.00 2.52
2713 2815 1.950828 CTGCAATGCAACCCAACAAA 58.049 45.000 9.92 0.00 38.41 2.83
2755 2857 0.107703 TTCTGCATGATGTCCCGGAC 60.108 55.000 10.96 10.96 0.00 4.79
2863 2965 7.306953 GTTTAATTGGTCAACCGTGCTTATTA 58.693 34.615 0.00 0.00 39.43 0.98
2866 2968 4.319622 CGTTTAATTGGTCAACCGTGCTTA 60.320 41.667 0.00 0.00 39.43 3.09
3024 3128 2.482374 GTCGGGTCGTCCACGTAG 59.518 66.667 0.04 0.00 40.80 3.51
3216 3320 4.082523 ATGTCCAGGTCCGTGCCG 62.083 66.667 0.00 0.00 0.00 5.69
3459 3563 2.124151 GGCGTGAAGATGGCCCAT 60.124 61.111 0.00 0.00 41.01 4.00
3606 3710 3.295973 AGGTAGAGCTTGCTAGAAGGAG 58.704 50.000 0.00 0.00 0.00 3.69
3624 3732 1.749033 GGCGCCTTAGCAGATAGGT 59.251 57.895 22.15 0.00 39.83 3.08
3690 3798 7.275341 GTCACAGATTGATTGAGTCTGAGTAAG 59.725 40.741 8.44 0.00 41.38 2.34
3709 3826 2.297315 AGCTTCTCATGTTCGTCACAGA 59.703 45.455 0.00 0.00 39.40 3.41
3736 3853 6.369615 GGCAGAAGACAAAACAATTGCAATAT 59.630 34.615 13.39 0.84 32.24 1.28
3737 3854 5.695816 GGCAGAAGACAAAACAATTGCAATA 59.304 36.000 13.39 0.00 32.24 1.90
3738 3855 4.512571 GGCAGAAGACAAAACAATTGCAAT 59.487 37.500 5.99 5.99 32.24 3.56
3739 3856 3.870419 GGCAGAAGACAAAACAATTGCAA 59.130 39.130 5.05 0.00 32.24 4.08
3746 3863 4.385825 ACGATTAGGCAGAAGACAAAACA 58.614 39.130 0.00 0.00 0.00 2.83
3795 3912 3.814842 TGTAGTGTGTGGCAGATTTTCAG 59.185 43.478 0.00 0.00 0.00 3.02
3797 3914 3.365364 GCTGTAGTGTGTGGCAGATTTTC 60.365 47.826 0.00 0.00 0.00 2.29
3814 3932 7.225784 TCTGGCTTTATTTGATTTTGCTGTA 57.774 32.000 0.00 0.00 0.00 2.74
3815 3933 6.100404 TCTGGCTTTATTTGATTTTGCTGT 57.900 33.333 0.00 0.00 0.00 4.40
3816 3934 8.761497 CATATCTGGCTTTATTTGATTTTGCTG 58.239 33.333 0.00 0.00 0.00 4.41
3817 3935 7.929785 CCATATCTGGCTTTATTTGATTTTGCT 59.070 33.333 0.00 0.00 35.23 3.91
3832 3950 5.279708 CCTCGAGTATTTTCCATATCTGGCT 60.280 44.000 12.31 0.00 42.80 4.75
3836 3954 6.551601 ACTGACCTCGAGTATTTTCCATATCT 59.448 38.462 12.31 0.00 0.00 1.98
3876 3994 5.661312 ACCTGTTGGAGATGCTGTTATAGTA 59.339 40.000 0.00 0.00 37.04 1.82
3877 3995 4.471386 ACCTGTTGGAGATGCTGTTATAGT 59.529 41.667 0.00 0.00 37.04 2.12
3878 3996 4.813161 CACCTGTTGGAGATGCTGTTATAG 59.187 45.833 0.00 0.00 37.04 1.31
3881 3999 2.875672 GCACCTGTTGGAGATGCTGTTA 60.876 50.000 0.00 0.00 37.04 2.41
3882 4000 1.901591 CACCTGTTGGAGATGCTGTT 58.098 50.000 0.00 0.00 37.04 3.16
3883 4001 0.607489 GCACCTGTTGGAGATGCTGT 60.607 55.000 0.00 0.00 37.04 4.40
3884 4002 1.642037 CGCACCTGTTGGAGATGCTG 61.642 60.000 0.00 0.00 32.59 4.41
3885 4003 1.376424 CGCACCTGTTGGAGATGCT 60.376 57.895 0.00 0.00 32.59 3.79
3886 4004 3.044059 GCGCACCTGTTGGAGATGC 62.044 63.158 0.30 0.00 37.04 3.91
3887 4005 0.108186 TAGCGCACCTGTTGGAGATG 60.108 55.000 11.47 0.00 37.04 2.90
3888 4006 0.613260 TTAGCGCACCTGTTGGAGAT 59.387 50.000 11.47 0.00 37.04 2.75
3889 4007 0.394938 TTTAGCGCACCTGTTGGAGA 59.605 50.000 11.47 0.00 37.04 3.71
3890 4008 1.234821 TTTTAGCGCACCTGTTGGAG 58.765 50.000 11.47 0.00 37.04 3.86
3891 4009 1.681538 TTTTTAGCGCACCTGTTGGA 58.318 45.000 11.47 0.00 37.04 3.53
3922 4040 3.089874 TGGCTATTCCGGGCAGCT 61.090 61.111 18.24 0.00 37.80 4.24
3925 4043 2.210144 AAAGCTGGCTATTCCGGGCA 62.210 55.000 0.00 0.00 41.76 5.36
3926 4044 1.037579 AAAAGCTGGCTATTCCGGGC 61.038 55.000 0.00 0.00 41.76 6.13
3927 4045 0.740737 CAAAAGCTGGCTATTCCGGG 59.259 55.000 0.00 0.00 41.76 5.73
3941 4059 2.202222 CTTCTCGGCGCGCAAAAG 60.202 61.111 34.42 24.71 0.00 2.27
4040 4160 5.574891 AAATAAACATATGGCAAGCGTCA 57.425 34.783 7.80 0.00 0.00 4.35
4042 4162 5.105554 TCCAAAATAAACATATGGCAAGCGT 60.106 36.000 7.80 0.00 0.00 5.07
4126 4248 9.515020 TTTGAACTTTTATGTCATGAACTTGTC 57.485 29.630 0.00 0.00 0.00 3.18
4157 4279 0.037326 TCTAAGCACCGGTCTTGCAG 60.037 55.000 22.04 15.24 42.83 4.41
4158 4280 0.037326 CTCTAAGCACCGGTCTTGCA 60.037 55.000 22.04 11.68 42.83 4.08
4161 7389 1.187087 CTCCTCTAAGCACCGGTCTT 58.813 55.000 18.91 18.91 0.00 3.01
4165 7393 3.298958 TGCTCCTCTAAGCACCGG 58.701 61.111 0.00 0.00 47.00 5.28
4174 7402 2.752238 CTCCGTCGGTGCTCCTCT 60.752 66.667 11.88 0.00 0.00 3.69
4186 7414 1.248785 TTAGCTTCGCCTGACTCCGT 61.249 55.000 0.00 0.00 0.00 4.69
4190 7418 3.145228 GCTTTAGCTTCGCCTGACT 57.855 52.632 0.00 0.00 38.21 3.41
4203 7431 1.141019 CCTAGCGCGTGGAGCTTTA 59.859 57.895 15.09 0.00 43.24 1.85
4398 7626 1.455908 CGCGCGCTGCTTATTTTGTC 61.456 55.000 30.48 0.00 43.27 3.18
4410 7638 4.241999 GAAATGGCATCGCGCGCT 62.242 61.111 30.48 14.34 43.84 5.92
4423 7651 2.255172 TTCAACGCGCGGGTGAAAT 61.255 52.632 34.40 11.28 0.00 2.17
4428 7656 2.704342 AAGTAGTTCAACGCGCGGGT 62.704 55.000 35.22 24.30 0.00 5.28
4437 7666 1.003851 GCGCGGCATAAGTAGTTCAA 58.996 50.000 8.83 0.00 0.00 2.69
4526 7756 1.767127 CGCGTGGTATAAATGCCGCA 61.767 55.000 10.61 0.00 42.26 5.69
4532 7762 0.462403 AACGGCCGCGTGGTATAAAT 60.462 50.000 28.58 0.00 37.67 1.40
4533 7763 1.079266 AACGGCCGCGTGGTATAAA 60.079 52.632 28.58 0.00 37.67 1.40
4568 7798 1.959710 TGTTACCCTCACTATGGCCA 58.040 50.000 8.56 8.56 0.00 5.36
4569 7799 4.386711 GTTATGTTACCCTCACTATGGCC 58.613 47.826 0.00 0.00 0.00 5.36
4570 7800 4.102681 AGGTTATGTTACCCTCACTATGGC 59.897 45.833 0.00 0.00 39.08 4.40
4571 7801 5.888982 AGGTTATGTTACCCTCACTATGG 57.111 43.478 0.00 0.00 39.08 2.74
4572 7802 9.924650 GTTATAGGTTATGTTACCCTCACTATG 57.075 37.037 0.00 0.00 39.08 2.23
4573 7803 9.664777 TGTTATAGGTTATGTTACCCTCACTAT 57.335 33.333 0.00 0.00 39.08 2.12
4574 7804 9.664777 ATGTTATAGGTTATGTTACCCTCACTA 57.335 33.333 0.00 0.00 39.08 2.74
4575 7805 7.983166 TGTTATAGGTTATGTTACCCTCACT 57.017 36.000 0.00 0.00 39.08 3.41
4576 7806 7.172703 GCATGTTATAGGTTATGTTACCCTCAC 59.827 40.741 0.00 0.00 39.08 3.51
4577 7807 7.147461 TGCATGTTATAGGTTATGTTACCCTCA 60.147 37.037 0.00 0.00 39.08 3.86
4578 7808 7.172703 GTGCATGTTATAGGTTATGTTACCCTC 59.827 40.741 0.00 0.00 39.08 4.30
4579 7809 6.996282 GTGCATGTTATAGGTTATGTTACCCT 59.004 38.462 0.00 0.00 39.08 4.34
4580 7810 6.996282 AGTGCATGTTATAGGTTATGTTACCC 59.004 38.462 0.00 0.00 39.08 3.69
4581 7811 8.342634 CAAGTGCATGTTATAGGTTATGTTACC 58.657 37.037 0.00 0.00 38.53 2.85
4582 7812 9.104965 TCAAGTGCATGTTATAGGTTATGTTAC 57.895 33.333 0.00 0.00 0.00 2.50
4583 7813 9.325198 CTCAAGTGCATGTTATAGGTTATGTTA 57.675 33.333 0.00 0.00 0.00 2.41
4584 7814 8.046708 TCTCAAGTGCATGTTATAGGTTATGTT 58.953 33.333 0.00 0.00 0.00 2.71
4585 7815 7.495934 GTCTCAAGTGCATGTTATAGGTTATGT 59.504 37.037 0.00 0.00 0.00 2.29
4586 7816 7.712639 AGTCTCAAGTGCATGTTATAGGTTATG 59.287 37.037 0.00 0.00 0.00 1.90
4587 7817 7.796054 AGTCTCAAGTGCATGTTATAGGTTAT 58.204 34.615 0.00 0.00 0.00 1.89
4588 7818 7.182817 AGTCTCAAGTGCATGTTATAGGTTA 57.817 36.000 0.00 0.00 0.00 2.85
4589 7819 6.054860 AGTCTCAAGTGCATGTTATAGGTT 57.945 37.500 0.00 0.00 0.00 3.50
4590 7820 5.683876 AGTCTCAAGTGCATGTTATAGGT 57.316 39.130 0.00 0.00 0.00 3.08
4591 7821 5.694006 GCTAGTCTCAAGTGCATGTTATAGG 59.306 44.000 0.00 0.00 0.00 2.57
4592 7822 6.761731 GCTAGTCTCAAGTGCATGTTATAG 57.238 41.667 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.