Multiple sequence alignment - TraesCS5B01G144100

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 TraesCS5B01G144100 chr5B 100.000 4885 0 0 1 4885 271299574 271304458 0.000000e+00 9022.0
1 TraesCS5B01G144100 chr5A 88.567 2624 149 42 1 2552 321721944 321719400 0.000000e+00 3044.0
2 TraesCS5B01G144100 chr5A 90.139 1440 76 35 2853 4265 321719076 321717676 0.000000e+00 1812.0
3 TraesCS5B01G144100 chr5A 88.542 288 23 6 2570 2850 321719415 321719131 1.680000e-89 340.0
4 TraesCS5B01G144100 chr5A 78.292 281 32 11 4286 4546 321717598 321717327 2.350000e-33 154.0
5 TraesCS5B01G144100 chr5A 79.845 129 12 3 4749 4869 321717126 321717004 1.130000e-11 82.4
6 TraesCS5B01G144100 chr5D 94.376 1209 45 12 3064 4265 233506427 233505235 0.000000e+00 1834.0
7 TraesCS5B01G144100 chr5D 90.153 1046 51 16 975 1979 233508479 233507445 0.000000e+00 1314.0
8 TraesCS5B01G144100 chr5D 92.382 827 36 15 2044 2850 233507410 233506591 0.000000e+00 1153.0
9 TraesCS5B01G144100 chr5D 88.421 950 71 14 1 934 233509765 233508839 0.000000e+00 1109.0
10 TraesCS5B01G144100 chr5D 84.906 371 34 13 999 1348 320921212 320920843 6.010000e-94 355.0
11 TraesCS5B01G144100 chr5D 83.558 371 39 12 999 1348 531913357 531913726 1.310000e-85 327.0
12 TraesCS5B01G144100 chr5D 80.906 309 28 14 4320 4626 233505083 233504804 1.060000e-51 215.0
13 TraesCS5B01G144100 chr5D 98.165 109 1 1 2853 2960 233506536 233506428 6.450000e-44 189.0
14 TraesCS5B01G144100 chr5D 96.104 77 3 0 4747 4823 233493115 233493039 5.130000e-25 126.0
15 TraesCS5B01G144100 chr5D 96.970 33 0 1 528 559 482858003 482858035 2.000000e-03 54.7
16 TraesCS5B01G144100 chr4A 86.849 365 33 7 999 1348 472918001 472918365 1.270000e-105 394.0
17 TraesCS5B01G144100 chr4A 100.000 31 0 0 534 564 552889917 552889947 1.900000e-04 58.4
18 TraesCS5B01G144100 chr4A 100.000 28 0 0 534 561 646585302 646585329 9.000000e-03 52.8
19 TraesCS5B01G144100 chr4B 86.301 365 35 7 999 1348 146498330 146497966 2.760000e-102 383.0
20 TraesCS5B01G144100 chr4B 95.238 42 2 0 4661 4702 423356735 423356776 3.160000e-07 67.6
21 TraesCS5B01G144100 chr4D 86.104 367 32 10 999 1348 102168629 102168265 1.280000e-100 377.0
22 TraesCS5B01G144100 chr3A 82.480 371 43 13 999 1348 645742378 645742009 6.140000e-79 305.0
23 TraesCS5B01G144100 chr3A 80.811 370 49 11 1000 1348 260681283 260680915 2.240000e-68 270.0
24 TraesCS5B01G144100 chr3D 81.579 228 25 7 1137 1348 418847006 418847232 6.500000e-39 172.0
25 TraesCS5B01G144100 chr3D 93.750 48 3 0 4658 4705 5400429 5400382 6.780000e-09 73.1
26 TraesCS5B01G144100 chr3D 100.000 31 0 0 534 564 47799616 47799586 1.900000e-04 58.4
27 TraesCS5B01G144100 chr7D 95.556 45 2 0 4661 4705 571261994 571261950 6.780000e-09 73.1
28 TraesCS5B01G144100 chr2B 93.333 45 3 0 4661 4705 3463080 3463036 3.160000e-07 67.6
29 TraesCS5B01G144100 chr2D 92.857 42 3 0 4661 4702 115586270 115586311 1.470000e-05 62.1
30 TraesCS5B01G144100 chr1B 90.909 44 3 1 4656 4699 633196527 633196569 1.900000e-04 58.4
31 TraesCS5B01G144100 chr7B 96.875 32 1 0 534 565 595349585 595349616 2.000000e-03 54.7


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 TraesCS5B01G144100 chr5B 271299574 271304458 4884 False 9022.00 9022 100.000000 1 4885 1 chr5B.!!$F1 4884
1 TraesCS5B01G144100 chr5A 321717004 321721944 4940 True 1086.48 3044 85.077000 1 4869 5 chr5A.!!$R1 4868
2 TraesCS5B01G144100 chr5D 233504804 233509765 4961 True 969.00 1834 90.733833 1 4626 6 chr5D.!!$R3 4625

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
491 516 0.108615 CTCGTCATCTTTGTCCGGCT 60.109 55.000 0.0 0.0 0.00 5.52 F
1377 1729 0.246635 ATCTCCGTCCCAACAACGAG 59.753 55.000 0.0 0.0 42.62 4.18 F
2197 2593 0.526739 GTTCCGTGGTGTTTGTTGCC 60.527 55.000 0.0 0.0 0.00 4.52 F
2202 2598 1.399215 CGTGGTGTTTGTTGCCGATAC 60.399 52.381 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1937 0.320683 TGTCCTCCACAGCAACATCG 60.321 55.000 0.00 0.0 0.00 3.84 R
2999 3501 1.063616 CCTTGACAAGATGCATGCGAG 59.936 52.381 16.99 3.2 0.00 5.03 R
3583 4119 0.745845 GCACATACTCCAGGCCACTG 60.746 60.000 5.01 0.0 44.51 3.66 R
4051 4587 1.210967 ACAGTTTCCGACCACCAGAAA 59.789 47.619 0.00 0.0 0.00 2.52 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
35 36 3.738282 CGAAATCACACTAGCTCATAGCC 59.262 47.826 0.00 0.00 43.77 3.93
109 110 3.194542 ACTGTCTCATAGCTGGAGTGTTC 59.805 47.826 14.58 7.08 34.04 3.18
155 156 0.472471 TTCCGTCCACTGGAAGCTTT 59.528 50.000 0.00 0.00 40.51 3.51
170 171 1.841663 GCTTTCGTGCTTTGAGCGGA 61.842 55.000 0.00 0.00 46.26 5.54
273 285 2.884012 ACATCAATGGAGACGCAAAACA 59.116 40.909 0.00 0.00 0.00 2.83
290 312 4.486125 AAACAACACCATCTTTTTGCCT 57.514 36.364 0.00 0.00 0.00 4.75
317 339 9.950680 GTTGTATTTGGTAATCGATCATGAATT 57.049 29.630 0.00 0.00 0.00 2.17
337 359 3.399105 TTGTGTGCCAGCCGTCACT 62.399 57.895 9.72 0.00 34.49 3.41
354 376 0.916086 ACTGTCAAGTGGGTGGTTCA 59.084 50.000 0.00 0.00 34.48 3.18
363 385 0.393673 TGGGTGGTTCATATGTGGCG 60.394 55.000 1.90 0.00 0.00 5.69
379 401 1.209261 TGGCGGATAACTGAAGATGCA 59.791 47.619 0.00 0.00 0.00 3.96
380 402 1.599542 GGCGGATAACTGAAGATGCAC 59.400 52.381 0.00 0.00 0.00 4.57
381 403 2.555199 GCGGATAACTGAAGATGCACT 58.445 47.619 0.00 0.00 0.00 4.40
382 404 2.286294 GCGGATAACTGAAGATGCACTG 59.714 50.000 0.00 0.00 0.00 3.66
395 420 3.386078 AGATGCACTGTACCATCTCGAAT 59.614 43.478 14.01 0.00 43.37 3.34
464 489 5.300539 TGAGCAAGTTGTAATTGTTTGCCTA 59.699 36.000 4.48 0.00 43.77 3.93
491 516 0.108615 CTCGTCATCTTTGTCCGGCT 60.109 55.000 0.00 0.00 0.00 5.52
496 521 2.093658 GTCATCTTTGTCCGGCTAAGGA 60.094 50.000 15.64 10.91 38.11 3.36
518 543 9.614792 AAGGAATAGTCGCTGAACTAAAATATT 57.385 29.630 0.00 0.00 35.47 1.28
543 568 7.356089 TCGCTCCTAATTATTACTTCCTTCA 57.644 36.000 0.00 0.00 0.00 3.02
591 616 1.416030 ACCAAACAAAGCAATGGGACC 59.584 47.619 0.00 0.00 37.26 4.46
596 621 0.388907 CAAAGCAATGGGACCAAGCG 60.389 55.000 11.75 0.00 36.56 4.68
607 632 1.594862 GGACCAAGCGAAAGATGATCG 59.405 52.381 0.00 0.00 42.99 3.69
653 680 2.534042 TCTTGAGAATCGGACCTCCT 57.466 50.000 6.74 0.00 38.61 3.69
654 681 2.379972 TCTTGAGAATCGGACCTCCTC 58.620 52.381 6.74 0.00 38.61 3.71
655 682 1.410882 CTTGAGAATCGGACCTCCTCC 59.589 57.143 6.74 0.00 38.61 4.30
713 740 2.102946 GCATAGCCGTTGCCAAGC 59.897 61.111 0.00 0.00 38.69 4.01
714 741 2.800736 CATAGCCGTTGCCAAGCC 59.199 61.111 0.00 0.00 38.69 4.35
715 742 2.045708 CATAGCCGTTGCCAAGCCA 61.046 57.895 0.00 0.00 38.69 4.75
725 752 3.371063 CCAAGCCAGCCAGCACAG 61.371 66.667 0.00 0.00 34.23 3.66
731 758 4.007644 CAGCCAGCACAGACGGGA 62.008 66.667 0.00 0.00 0.00 5.14
850 880 0.535328 TCAATTCGACCGTTGCCCAA 60.535 50.000 0.00 0.00 0.00 4.12
852 882 1.520600 AATTCGACCGTTGCCCAACC 61.521 55.000 5.64 0.00 38.03 3.77
1029 1379 0.892063 ACGAGAAGCTGGAGAAGGTC 59.108 55.000 0.00 0.00 34.84 3.85
1364 1716 6.094325 GTCAAGGTATCTATCTACCATCTCCG 59.906 46.154 3.32 0.00 43.12 4.63
1367 1719 4.883006 GGTATCTATCTACCATCTCCGTCC 59.117 50.000 0.00 0.00 40.81 4.79
1372 1724 1.191535 CTACCATCTCCGTCCCAACA 58.808 55.000 0.00 0.00 0.00 3.33
1377 1729 0.246635 ATCTCCGTCCCAACAACGAG 59.753 55.000 0.00 0.00 42.62 4.18
1401 1753 9.425577 GAGCTTTTTCTTCAGTATACTGTACTT 57.574 33.333 27.83 7.96 44.12 2.24
1412 1764 8.900781 TCAGTATACTGTACTTACCATCTTGTC 58.099 37.037 27.83 0.00 44.12 3.18
1418 1770 3.795623 ACTTACCATCTTGTCGCGTAT 57.204 42.857 5.77 0.00 0.00 3.06
1539 1914 3.698040 ACGGTATGAATCGTAAGTGGACT 59.302 43.478 0.00 0.00 37.88 3.85
1541 1916 5.357878 ACGGTATGAATCGTAAGTGGACTAA 59.642 40.000 0.00 0.00 37.88 2.24
1542 1917 5.913514 CGGTATGAATCGTAAGTGGACTAAG 59.086 44.000 0.00 0.00 39.48 2.18
1543 1918 6.459298 CGGTATGAATCGTAAGTGGACTAAGT 60.459 42.308 0.00 0.00 39.48 2.24
1544 1919 7.254898 CGGTATGAATCGTAAGTGGACTAAGTA 60.255 40.741 0.00 0.00 39.48 2.24
1545 1920 8.408601 GGTATGAATCGTAAGTGGACTAAGTAA 58.591 37.037 0.00 0.00 39.48 2.24
1546 1921 9.962783 GTATGAATCGTAAGTGGACTAAGTAAT 57.037 33.333 0.00 0.00 39.48 1.89
1549 1925 9.146984 TGAATCGTAAGTGGACTAAGTAATTTG 57.853 33.333 0.00 0.00 39.48 2.32
1561 1937 7.201652 GGACTAAGTAATTTGGAAGCACTGATC 60.202 40.741 0.00 0.00 0.00 2.92
1661 2041 8.443898 AAAGGTCTAATTTTTCGTAAATTCGC 57.556 30.769 12.10 6.41 32.64 4.70
1680 2060 2.472235 CGCGCATATATAGTTGCAACGG 60.472 50.000 23.21 9.47 38.80 4.44
1700 2080 5.177326 ACGGCAAATTAGGAATGTAACGTA 58.823 37.500 0.00 0.00 0.00 3.57
1715 2095 7.843490 ATGTAACGTATCAGCATTTACAGTT 57.157 32.000 0.00 0.00 36.40 3.16
1733 2113 1.667724 GTTCCTTGCTGGTGATGATCG 59.332 52.381 0.00 0.00 37.07 3.69
1801 2182 2.833794 AGTGAAAGAACGCTGTGCTTA 58.166 42.857 2.90 0.00 28.68 3.09
1811 2192 2.290641 ACGCTGTGCTTACTTTGGAAAG 59.709 45.455 0.00 0.00 41.73 2.62
1839 2220 3.745975 ACATATAACGCACCATCAATCCG 59.254 43.478 0.00 0.00 0.00 4.18
1847 2228 0.532862 ACCATCAATCCGCCATCGTC 60.533 55.000 0.00 0.00 0.00 4.20
1887 2272 4.040584 AGAAACCTTCTACTTGTCTCCACC 59.959 45.833 0.00 0.00 38.49 4.61
1896 2281 6.527423 TCTACTTGTCTCCACCGTAAAATTT 58.473 36.000 0.00 0.00 0.00 1.82
1943 2329 1.139734 CAGTCGTCACAGGATCGGG 59.860 63.158 0.00 0.00 0.00 5.14
1957 2346 2.264794 CGGGAGCCGTTAACTGCT 59.735 61.111 22.54 22.54 42.73 4.24
1960 2349 0.605589 GGGAGCCGTTAACTGCTTGT 60.606 55.000 23.08 4.13 36.55 3.16
1972 2361 8.665685 CCGTTAACTGCTTGTAATTCTATCTTT 58.334 33.333 3.71 0.00 0.00 2.52
1979 2368 8.677148 TGCTTGTAATTCTATCTTTATCCACC 57.323 34.615 0.00 0.00 0.00 4.61
1981 2370 7.095187 GCTTGTAATTCTATCTTTATCCACCGG 60.095 40.741 0.00 0.00 0.00 5.28
1991 2380 2.287457 TATCCACCGGCTCCGTTTCG 62.287 60.000 0.00 0.00 37.81 3.46
1999 2388 1.461897 CGGCTCCGTTTCGTATTTTGT 59.538 47.619 0.00 0.00 34.35 2.83
2033 2422 1.209019 CTTCTACCATGCACCTGAGCT 59.791 52.381 0.00 0.00 34.99 4.09
2039 2428 2.031616 TGCACCTGAGCTGCACTC 59.968 61.111 1.02 8.75 46.45 3.51
2040 2429 2.745492 GCACCTGAGCTGCACTCC 60.745 66.667 1.02 0.00 45.61 3.85
2041 2430 2.433838 CACCTGAGCTGCACTCCG 60.434 66.667 1.02 7.11 45.61 4.63
2078 2474 8.525316 TGATTACTTCTGCATGAAAATGACAAT 58.475 29.630 0.00 0.00 33.79 2.71
2079 2475 8.922058 ATTACTTCTGCATGAAAATGACAATC 57.078 30.769 0.00 0.00 33.79 2.67
2080 2476 6.335471 ACTTCTGCATGAAAATGACAATCA 57.665 33.333 0.00 0.00 33.79 2.57
2081 2477 6.751157 ACTTCTGCATGAAAATGACAATCAA 58.249 32.000 0.00 0.00 33.79 2.57
2175 2571 1.000506 TGTGCTTCACCGGTTAGACTC 59.999 52.381 2.97 4.08 32.73 3.36
2197 2593 0.526739 GTTCCGTGGTGTTTGTTGCC 60.527 55.000 0.00 0.00 0.00 4.52
2199 2595 2.473760 CCGTGGTGTTTGTTGCCGA 61.474 57.895 0.00 0.00 0.00 5.54
2200 2596 1.652012 CGTGGTGTTTGTTGCCGAT 59.348 52.632 0.00 0.00 0.00 4.18
2202 2598 1.399215 CGTGGTGTTTGTTGCCGATAC 60.399 52.381 0.00 0.00 0.00 2.24
2203 2599 1.604755 GTGGTGTTTGTTGCCGATACA 59.395 47.619 0.00 0.00 0.00 2.29
2246 2657 4.854173 TGGTTAATGCTATCCTGCTTGAA 58.146 39.130 0.00 0.00 0.00 2.69
2247 2658 5.260424 TGGTTAATGCTATCCTGCTTGAAA 58.740 37.500 0.00 0.00 0.00 2.69
2248 2659 5.714333 TGGTTAATGCTATCCTGCTTGAAAA 59.286 36.000 0.00 0.00 0.00 2.29
2249 2660 6.036470 GGTTAATGCTATCCTGCTTGAAAAC 58.964 40.000 0.00 0.00 0.00 2.43
2383 2794 3.133362 CCCATGAGGTACCGCTTAGTAAA 59.867 47.826 17.09 0.00 0.00 2.01
2558 3001 3.004024 GCATCTTTGGTATGCCGATTG 57.996 47.619 0.00 0.00 43.17 2.67
2559 3002 2.859806 GCATCTTTGGTATGCCGATTGC 60.860 50.000 0.00 0.28 43.17 3.56
2570 3013 2.584492 GCCGATTGCAATTAGGCTTT 57.416 45.000 33.95 8.35 44.06 3.51
2571 3014 2.195922 GCCGATTGCAATTAGGCTTTG 58.804 47.619 33.95 11.84 44.06 2.77
2572 3015 2.159254 GCCGATTGCAATTAGGCTTTGA 60.159 45.455 33.95 1.18 44.06 2.69
2573 3016 3.491447 GCCGATTGCAATTAGGCTTTGAT 60.491 43.478 33.95 6.56 44.06 2.57
2574 3017 4.293415 CCGATTGCAATTAGGCTTTGATC 58.707 43.478 14.33 0.00 34.04 2.92
2575 3018 4.037208 CCGATTGCAATTAGGCTTTGATCT 59.963 41.667 14.33 0.00 34.04 2.75
2576 3019 5.450965 CCGATTGCAATTAGGCTTTGATCTT 60.451 40.000 14.33 0.00 34.04 2.40
2577 3020 6.038356 CGATTGCAATTAGGCTTTGATCTTT 58.962 36.000 14.33 0.00 34.04 2.52
2578 3021 6.020121 CGATTGCAATTAGGCTTTGATCTTTG 60.020 38.462 14.33 0.00 34.04 2.77
2579 3022 5.726980 TGCAATTAGGCTTTGATCTTTGT 57.273 34.783 3.14 0.00 34.04 2.83
2580 3023 6.100404 TGCAATTAGGCTTTGATCTTTGTT 57.900 33.333 3.14 0.00 34.04 2.83
2581 3024 7.225784 TGCAATTAGGCTTTGATCTTTGTTA 57.774 32.000 3.14 0.00 34.04 2.41
2582 3025 7.839907 TGCAATTAGGCTTTGATCTTTGTTAT 58.160 30.769 3.14 0.00 34.04 1.89
2583 3026 7.760794 TGCAATTAGGCTTTGATCTTTGTTATG 59.239 33.333 3.14 0.00 34.04 1.90
2819 3267 8.129161 TGTTTTACATTGCATCAAGACAAAAG 57.871 30.769 0.00 0.00 0.00 2.27
2827 3276 8.857216 CATTGCATCAAGACAAAAGATCTTAAC 58.143 33.333 8.75 1.09 34.59 2.01
2938 3440 6.080648 ACAATAGCATATGAATTGCCACAG 57.919 37.500 21.83 6.72 41.06 3.66
2999 3501 9.736023 AGTTTATCTCACATCAAACAAAAGAAC 57.264 29.630 0.00 0.00 34.15 3.01
3001 3503 9.950680 TTTATCTCACATCAAACAAAAGAACTC 57.049 29.630 0.00 0.00 0.00 3.01
3006 3508 4.977963 ACATCAAACAAAAGAACTCGCATG 59.022 37.500 0.00 0.00 0.00 4.06
3022 3551 2.286831 CGCATGCATCTTGTCAAGGATC 60.287 50.000 19.57 2.95 0.00 3.36
3023 3552 2.286831 GCATGCATCTTGTCAAGGATCG 60.287 50.000 14.21 0.75 0.00 3.69
3029 3558 4.035558 GCATCTTGTCAAGGATCGCATTTA 59.964 41.667 12.66 0.00 0.00 1.40
3036 3565 6.976088 TGTCAAGGATCGCATTTAAAAGAAA 58.024 32.000 0.00 0.00 0.00 2.52
3123 3652 7.657761 CAGTCCTTGTGTTATCTGAACTAAACT 59.342 37.037 0.00 0.00 0.00 2.66
3127 3656 7.657761 CCTTGTGTTATCTGAACTAAACTCACT 59.342 37.037 0.00 0.00 0.00 3.41
3393 3925 6.373005 TGATGGGATGGTGTATTAGTATGG 57.627 41.667 0.00 0.00 0.00 2.74
3394 3926 5.849475 TGATGGGATGGTGTATTAGTATGGT 59.151 40.000 0.00 0.00 0.00 3.55
3468 4004 8.167392 TGGATAAATAACTTCTGACTTGGGAAA 58.833 33.333 0.00 0.00 0.00 3.13
3482 4018 4.630069 ACTTGGGAAATCGATTGAAGTACG 59.370 41.667 12.25 1.11 0.00 3.67
3485 4021 5.104374 TGGGAAATCGATTGAAGTACGTAC 58.896 41.667 18.10 18.10 0.00 3.67
3583 4119 2.119495 TGGGGACTCCTAATGAAGAGC 58.881 52.381 0.00 0.00 36.20 4.09
3667 4203 0.730265 GTCACGTGCAGTTCCAACAA 59.270 50.000 11.67 0.00 0.00 2.83
3684 4220 1.707427 ACAATGGAGCCTGAAGGACTT 59.293 47.619 0.00 0.00 37.39 3.01
3694 4230 3.307762 GCCTGAAGGACTTGACCTGTTAT 60.308 47.826 0.00 0.00 40.49 1.89
3708 4244 9.158233 CTTGACCTGTTATCGGTAAATTAAGAA 57.842 33.333 0.00 0.00 34.19 2.52
3724 4260 7.406799 AATTAAGAAAAACATGAAACGCCAG 57.593 32.000 0.00 0.00 0.00 4.85
3781 4317 2.224314 AGCTAACAGTTTCTTGCTTCGC 59.776 45.455 0.00 0.00 0.00 4.70
4071 4607 0.834612 TTCTGGTGGTCGGAAACTGT 59.165 50.000 0.00 0.00 37.78 3.55
4078 4614 0.320697 GGTCGGAAACTGTACTGCCT 59.679 55.000 0.00 0.00 0.00 4.75
4093 4629 1.895798 CTGCCTCTCAGTAACTGGTCA 59.104 52.381 0.00 0.00 38.02 4.02
4095 4631 1.896465 GCCTCTCAGTAACTGGTCAGT 59.104 52.381 0.00 0.00 44.94 3.41
4106 4642 3.492102 ACTGGTCAGTTGCACTGTAAT 57.508 42.857 13.59 0.00 46.03 1.89
4107 4643 3.141398 ACTGGTCAGTTGCACTGTAATG 58.859 45.455 13.59 0.00 46.03 1.90
4108 4644 3.141398 CTGGTCAGTTGCACTGTAATGT 58.859 45.455 13.59 0.00 46.03 2.71
4109 4645 3.550820 TGGTCAGTTGCACTGTAATGTT 58.449 40.909 13.59 0.00 46.03 2.71
4110 4646 4.709250 TGGTCAGTTGCACTGTAATGTTA 58.291 39.130 13.59 0.00 46.03 2.41
4111 4647 5.312895 TGGTCAGTTGCACTGTAATGTTAT 58.687 37.500 13.59 0.00 46.03 1.89
4112 4648 5.181056 TGGTCAGTTGCACTGTAATGTTATG 59.819 40.000 13.59 0.00 46.03 1.90
4113 4649 5.181245 GGTCAGTTGCACTGTAATGTTATGT 59.819 40.000 13.59 0.00 46.03 2.29
4114 4650 6.293955 GGTCAGTTGCACTGTAATGTTATGTT 60.294 38.462 13.59 0.00 46.03 2.71
4115 4651 7.138736 GTCAGTTGCACTGTAATGTTATGTTT 58.861 34.615 13.59 0.00 46.03 2.83
4116 4652 7.323656 GTCAGTTGCACTGTAATGTTATGTTTC 59.676 37.037 13.59 0.00 46.03 2.78
4117 4653 6.582295 CAGTTGCACTGTAATGTTATGTTTCC 59.418 38.462 7.80 0.00 41.19 3.13
4240 4776 6.522165 GCGGGAAAAGAAAAGTAATTACTTCG 59.478 38.462 26.87 22.05 45.17 3.79
4301 4907 3.339141 GGAAGAAGAAGCGACATCCTTT 58.661 45.455 0.00 0.00 0.00 3.11
4314 4920 3.690460 ACATCCTTTGTCCCTTGTGATC 58.310 45.455 0.00 0.00 30.89 2.92
4386 5024 5.277683 GCACAATCACTAGGCATGATGTAAG 60.278 44.000 0.00 0.00 36.89 2.34
4407 5046 2.282180 GCCCGAGCCAACCTTGAA 60.282 61.111 0.00 0.00 0.00 2.69
4456 5095 1.334869 CATTGGTAAAGGAGATGCGCC 59.665 52.381 4.18 0.00 0.00 6.53
4460 5099 3.750373 TAAAGGAGATGCGCCGCCC 62.750 63.158 6.63 0.00 0.00 6.13
4477 5131 2.556287 CGCCGGTTCTGCAAAGAC 59.444 61.111 1.90 0.00 0.00 3.01
4485 5139 2.545742 GGTTCTGCAAAGACGGCAAAAT 60.546 45.455 0.00 0.00 41.39 1.82
4486 5140 3.305064 GGTTCTGCAAAGACGGCAAAATA 60.305 43.478 0.00 0.00 41.39 1.40
4520 5174 1.038280 CCCCTACGCCGAAGTCTATT 58.962 55.000 0.00 0.00 0.00 1.73
4522 5176 1.407979 CCCTACGCCGAAGTCTATTGT 59.592 52.381 0.00 0.00 0.00 2.71
4526 5180 0.870307 CGCCGAAGTCTATTGTCCGG 60.870 60.000 0.00 0.00 39.88 5.14
4536 5190 3.322828 GTCTATTGTCCGGCCATAACCTA 59.677 47.826 2.24 0.00 0.00 3.08
4537 5191 2.632987 ATTGTCCGGCCATAACCTAC 57.367 50.000 2.24 0.00 0.00 3.18
4538 5192 1.575419 TTGTCCGGCCATAACCTACT 58.425 50.000 2.24 0.00 0.00 2.57
4539 5193 0.828022 TGTCCGGCCATAACCTACTG 59.172 55.000 2.24 0.00 0.00 2.74
4540 5194 0.828677 GTCCGGCCATAACCTACTGT 59.171 55.000 2.24 0.00 0.00 3.55
4541 5195 0.828022 TCCGGCCATAACCTACTGTG 59.172 55.000 2.24 0.00 0.00 3.66
4542 5196 0.179056 CCGGCCATAACCTACTGTGG 60.179 60.000 2.24 0.00 34.84 4.17
4543 5197 0.828022 CGGCCATAACCTACTGTGGA 59.172 55.000 2.24 0.00 33.53 4.02
4544 5198 1.416401 CGGCCATAACCTACTGTGGAT 59.584 52.381 2.24 0.00 33.53 3.41
4545 5199 2.631062 CGGCCATAACCTACTGTGGATA 59.369 50.000 2.24 0.00 33.53 2.59
4546 5200 3.070446 CGGCCATAACCTACTGTGGATAA 59.930 47.826 2.24 0.00 33.53 1.75
4547 5201 4.386711 GGCCATAACCTACTGTGGATAAC 58.613 47.826 0.00 0.00 33.53 1.89
4548 5202 4.386711 GCCATAACCTACTGTGGATAACC 58.613 47.826 0.00 0.00 33.53 2.85
4549 5203 4.141574 GCCATAACCTACTGTGGATAACCA 60.142 45.833 0.00 0.00 44.76 3.67
4592 5246 3.521560 TCATTAACACATGTCTCTCCGC 58.478 45.455 0.00 0.00 0.00 5.54
4642 5296 7.250569 AGTTAAATTCATTTACATGTCCAGCG 58.749 34.615 0.00 0.00 32.42 5.18
4643 5297 4.637483 AATTCATTTACATGTCCAGCGG 57.363 40.909 0.00 0.00 0.00 5.52
4644 5298 3.342377 TTCATTTACATGTCCAGCGGA 57.658 42.857 0.00 0.00 0.00 5.54
4645 5299 3.558931 TCATTTACATGTCCAGCGGAT 57.441 42.857 0.00 0.00 32.73 4.18
4646 5300 3.466836 TCATTTACATGTCCAGCGGATC 58.533 45.455 0.00 0.00 32.73 3.36
4647 5301 2.325583 TTTACATGTCCAGCGGATCC 57.674 50.000 0.00 0.00 32.73 3.36
4648 5302 1.199615 TTACATGTCCAGCGGATCCA 58.800 50.000 13.41 0.00 32.73 3.41
4649 5303 1.423584 TACATGTCCAGCGGATCCAT 58.576 50.000 13.41 0.00 32.73 3.41
4650 5304 0.179037 ACATGTCCAGCGGATCCATG 60.179 55.000 13.41 18.10 40.10 3.66
4651 5305 0.179037 CATGTCCAGCGGATCCATGT 60.179 55.000 13.41 0.00 33.93 3.21
4652 5306 0.179037 ATGTCCAGCGGATCCATGTG 60.179 55.000 13.41 5.29 32.73 3.21
4654 5308 0.107456 GTCCAGCGGATCCATGTGAT 59.893 55.000 13.41 0.00 32.73 3.06
4656 5310 0.949397 CCAGCGGATCCATGTGATTG 59.051 55.000 13.41 0.00 32.41 2.67
4657 5311 1.475571 CCAGCGGATCCATGTGATTGA 60.476 52.381 13.41 0.00 32.41 2.57
4658 5312 2.501261 CAGCGGATCCATGTGATTGAT 58.499 47.619 13.41 0.00 32.41 2.57
4659 5313 3.557686 CCAGCGGATCCATGTGATTGATA 60.558 47.826 13.41 0.00 32.41 2.15
4660 5314 4.259356 CAGCGGATCCATGTGATTGATAT 58.741 43.478 13.41 0.00 32.41 1.63
4661 5315 5.422145 CAGCGGATCCATGTGATTGATATA 58.578 41.667 13.41 0.00 32.41 0.86
4662 5316 5.292834 CAGCGGATCCATGTGATTGATATAC 59.707 44.000 13.41 0.00 32.41 1.47
4663 5317 5.188555 AGCGGATCCATGTGATTGATATACT 59.811 40.000 13.41 0.00 32.41 2.12
4664 5318 5.521735 GCGGATCCATGTGATTGATATACTC 59.478 44.000 13.41 0.00 32.41 2.59
4665 5319 6.045318 CGGATCCATGTGATTGATATACTCC 58.955 44.000 13.41 0.00 32.41 3.85
4670 5324 6.212187 TCCATGTGATTGATATACTCCCTCTG 59.788 42.308 0.00 0.00 0.00 3.35
4671 5325 6.013898 CCATGTGATTGATATACTCCCTCTGT 60.014 42.308 0.00 0.00 0.00 3.41
4674 5328 5.698545 GTGATTGATATACTCCCTCTGTTGC 59.301 44.000 0.00 0.00 0.00 4.17
4675 5329 5.604231 TGATTGATATACTCCCTCTGTTGCT 59.396 40.000 0.00 0.00 0.00 3.91
4676 5330 6.782494 TGATTGATATACTCCCTCTGTTGCTA 59.218 38.462 0.00 0.00 0.00 3.49
4677 5331 7.290014 TGATTGATATACTCCCTCTGTTGCTAA 59.710 37.037 0.00 0.00 0.00 3.09
4685 5339 7.618019 ACTCCCTCTGTTGCTAAATATATGA 57.382 36.000 0.00 0.00 0.00 2.15
4686 5340 7.445945 ACTCCCTCTGTTGCTAAATATATGAC 58.554 38.462 0.00 0.00 0.00 3.06
4687 5341 7.071196 ACTCCCTCTGTTGCTAAATATATGACA 59.929 37.037 0.00 0.00 0.00 3.58
4688 5342 7.977818 TCCCTCTGTTGCTAAATATATGACAT 58.022 34.615 0.00 0.00 0.00 3.06
4689 5343 8.439971 TCCCTCTGTTGCTAAATATATGACATT 58.560 33.333 0.00 0.00 0.00 2.71
4690 5344 9.071276 CCCTCTGTTGCTAAATATATGACATTT 57.929 33.333 0.00 0.00 0.00 2.32
4747 5437 8.474006 TTTGAGATTCAAAATGCATCTTCATG 57.526 30.769 0.00 0.00 42.72 3.07
4797 5511 0.941542 CCAAAAGACGCGACAAAGGA 59.058 50.000 15.93 0.00 0.00 3.36
4799 5513 2.223386 CCAAAAGACGCGACAAAGGAAA 60.223 45.455 15.93 0.00 0.00 3.13
4801 5515 3.537793 AAAGACGCGACAAAGGAAATC 57.462 42.857 15.93 0.00 0.00 2.17
4806 5520 1.193650 CGCGACAAAGGAAATCGTTGA 59.806 47.619 0.00 0.00 38.06 3.18
4814 5528 7.910162 CGACAAAGGAAATCGTTGATGAAATAT 59.090 33.333 0.00 0.00 38.06 1.28
4842 5556 1.078848 ATGCAAGAGTCGTCCCAGC 60.079 57.895 0.00 0.00 0.00 4.85
4846 5560 2.948720 AAGAGTCGTCCCAGCCTGC 61.949 63.158 0.00 0.00 0.00 4.85
4860 5574 3.130633 CAGCCTGCGCAATAGTACATAA 58.869 45.455 13.05 0.00 37.52 1.90
4864 5578 4.272504 GCCTGCGCAATAGTACATAAAAGA 59.727 41.667 13.05 0.00 34.03 2.52
4869 5583 8.880878 TGCGCAATAGTACATAAAAGATAGAA 57.119 30.769 8.16 0.00 0.00 2.10
4870 5584 8.761497 TGCGCAATAGTACATAAAAGATAGAAC 58.239 33.333 8.16 0.00 0.00 3.01
4871 5585 8.761497 GCGCAATAGTACATAAAAGATAGAACA 58.239 33.333 0.30 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.738282 GGCTATGAGCTAGTGTGATTTCG 59.262 47.826 0.00 0.00 41.99 3.46
155 156 2.357034 GGTCCGCTCAAAGCACGA 60.357 61.111 0.00 0.00 42.58 4.35
167 168 1.006832 CACGCTTCAATTAGGGTCCG 58.993 55.000 0.00 0.00 39.04 4.79
170 171 2.017049 GATGCACGCTTCAATTAGGGT 58.983 47.619 0.00 0.00 41.42 4.34
273 285 3.197549 ACAACAGGCAAAAAGATGGTGTT 59.802 39.130 0.00 0.00 40.58 3.32
290 312 8.499403 TTCATGATCGATTACCAAATACAACA 57.501 30.769 0.00 0.00 0.00 3.33
317 339 2.280797 GACGGCTGGCACACAAGA 60.281 61.111 0.00 0.00 0.00 3.02
320 342 3.860605 AGTGACGGCTGGCACACA 61.861 61.111 32.70 4.52 37.48 3.72
337 359 3.073798 ACATATGAACCACCCACTTGACA 59.926 43.478 10.38 0.00 0.00 3.58
346 368 0.107410 TCCGCCACATATGAACCACC 60.107 55.000 10.38 0.00 0.00 4.61
352 374 4.343814 TCTTCAGTTATCCGCCACATATGA 59.656 41.667 10.38 0.00 0.00 2.15
354 376 4.955811 TCTTCAGTTATCCGCCACATAT 57.044 40.909 0.00 0.00 0.00 1.78
363 385 4.811557 GGTACAGTGCATCTTCAGTTATCC 59.188 45.833 0.00 0.00 0.00 2.59
382 404 3.357166 AAGAGCGATTCGAGATGGTAC 57.643 47.619 10.88 0.00 0.00 3.34
395 420 0.944311 GACAACTGGCGAAAGAGCGA 60.944 55.000 0.00 0.00 38.18 4.93
435 460 7.909641 GCAAACAATTACAACTTGCTCAAAAAT 59.090 29.630 0.00 0.00 39.39 1.82
470 495 1.939838 GCCGGACAAAGATGACGAGTT 60.940 52.381 5.05 0.00 34.21 3.01
477 502 2.691409 TCCTTAGCCGGACAAAGATG 57.309 50.000 5.05 0.00 0.00 2.90
496 521 8.062448 GCGAAATATTTTAGTTCAGCGACTATT 58.938 33.333 1.43 0.00 32.71 1.73
518 543 7.788026 TGAAGGAAGTAATAATTAGGAGCGAA 58.212 34.615 0.00 0.00 0.00 4.70
537 562 9.832445 AACGCTCTTATATTTCTTTATGAAGGA 57.168 29.630 0.00 0.00 35.89 3.36
565 590 3.377798 CCATTGCTTTGTTTGGTGCTTTT 59.622 39.130 0.00 0.00 0.00 2.27
567 592 2.563702 CCATTGCTTTGTTTGGTGCTT 58.436 42.857 0.00 0.00 0.00 3.91
570 595 2.482864 GTCCCATTGCTTTGTTTGGTG 58.517 47.619 0.00 0.00 0.00 4.17
630 657 4.123506 GGAGGTCCGATTCTCAAGATTTC 58.876 47.826 0.00 0.00 0.00 2.17
674 701 0.733150 CCGATCGTCACTCACTGCTA 59.267 55.000 15.09 0.00 0.00 3.49
675 702 1.244697 ACCGATCGTCACTCACTGCT 61.245 55.000 15.09 0.00 0.00 4.24
676 703 0.798771 GACCGATCGTCACTCACTGC 60.799 60.000 15.09 0.00 41.54 4.40
698 725 1.750399 CTGGCTTGGCAACGGCTAT 60.750 57.895 18.61 0.00 40.87 2.97
714 741 4.007644 TCCCGTCTGTGCTGGCTG 62.008 66.667 0.00 0.00 0.00 4.85
715 742 4.008933 GTCCCGTCTGTGCTGGCT 62.009 66.667 0.00 0.00 0.00 4.75
740 767 3.350612 TGTAAAGTGCGGTGCGGC 61.351 61.111 0.00 0.00 0.00 6.53
1364 1716 2.357952 AGAAAAAGCTCGTTGTTGGGAC 59.642 45.455 0.00 0.00 0.00 4.46
1367 1719 4.027572 TGAAGAAAAAGCTCGTTGTTGG 57.972 40.909 0.00 0.00 0.00 3.77
1372 1724 6.929606 ACAGTATACTGAAGAAAAAGCTCGTT 59.070 34.615 34.16 7.64 46.59 3.85
1401 1753 1.941975 TCGATACGCGACAAGATGGTA 59.058 47.619 15.93 0.00 45.59 3.25
1412 1764 8.432302 AAAGTAACTATAAGAATCGATACGCG 57.568 34.615 3.53 3.53 42.69 6.01
1418 1770 7.198390 CGTGGGAAAGTAACTATAAGAATCGA 58.802 38.462 0.00 0.00 0.00 3.59
1452 1804 3.115892 CGCCGCGCTTCAAGGTAA 61.116 61.111 5.56 0.00 0.00 2.85
1522 1897 9.886132 AAATTACTTAGTCCACTTACGATTCAT 57.114 29.630 0.00 0.00 0.00 2.57
1539 1914 6.403049 TCGATCAGTGCTTCCAAATTACTTA 58.597 36.000 0.00 0.00 0.00 2.24
1541 1916 4.832248 TCGATCAGTGCTTCCAAATTACT 58.168 39.130 0.00 0.00 0.00 2.24
1542 1917 5.065218 ACATCGATCAGTGCTTCCAAATTAC 59.935 40.000 0.00 0.00 0.00 1.89
1543 1918 5.185454 ACATCGATCAGTGCTTCCAAATTA 58.815 37.500 0.00 0.00 0.00 1.40
1544 1919 4.012374 ACATCGATCAGTGCTTCCAAATT 58.988 39.130 0.00 0.00 0.00 1.82
1545 1920 3.614092 ACATCGATCAGTGCTTCCAAAT 58.386 40.909 0.00 0.00 0.00 2.32
1546 1921 3.057969 ACATCGATCAGTGCTTCCAAA 57.942 42.857 0.00 0.00 0.00 3.28
1549 1925 1.063174 GCAACATCGATCAGTGCTTCC 59.937 52.381 14.32 0.00 0.00 3.46
1561 1937 0.320683 TGTCCTCCACAGCAACATCG 60.321 55.000 0.00 0.00 0.00 3.84
1661 2041 2.478514 TGCCGTTGCAACTATATATGCG 59.521 45.455 26.09 10.34 46.66 4.73
1680 2060 6.851330 GCTGATACGTTACATTCCTAATTTGC 59.149 38.462 0.00 0.00 0.00 3.68
1700 2080 4.338879 AGCAAGGAACTGTAAATGCTGAT 58.661 39.130 8.77 0.00 44.59 2.90
1715 2095 0.462581 GCGATCATCACCAGCAAGGA 60.463 55.000 1.83 0.00 41.22 3.36
1811 2192 4.334203 TGATGGTGCGTTATATGTTTCCAC 59.666 41.667 0.00 0.00 0.00 4.02
1812 2193 4.518249 TGATGGTGCGTTATATGTTTCCA 58.482 39.130 0.00 0.00 0.00 3.53
1813 2194 5.493133 TTGATGGTGCGTTATATGTTTCC 57.507 39.130 0.00 0.00 0.00 3.13
1814 2195 6.142817 GGATTGATGGTGCGTTATATGTTTC 58.857 40.000 0.00 0.00 0.00 2.78
1815 2196 5.277779 CGGATTGATGGTGCGTTATATGTTT 60.278 40.000 0.00 0.00 0.00 2.83
1816 2197 4.213270 CGGATTGATGGTGCGTTATATGTT 59.787 41.667 0.00 0.00 0.00 2.71
1817 2198 3.745975 CGGATTGATGGTGCGTTATATGT 59.254 43.478 0.00 0.00 0.00 2.29
1839 2220 1.852067 AACCAAGCAACGACGATGGC 61.852 55.000 0.00 1.62 34.45 4.40
1847 2228 4.497473 TTTCTATGGAAACCAAGCAACG 57.503 40.909 0.00 0.00 36.95 4.10
1887 2272 3.223157 AGCGCGTGAAGAAAATTTTACG 58.777 40.909 16.06 16.06 41.32 3.18
1896 2281 2.363788 ACTGAATAGCGCGTGAAGAA 57.636 45.000 8.43 0.00 0.00 2.52
1943 2329 4.392138 AGAATTACAAGCAGTTAACGGCTC 59.608 41.667 29.32 17.00 46.30 4.70
1957 2346 6.708949 GCCGGTGGATAAAGATAGAATTACAA 59.291 38.462 1.90 0.00 0.00 2.41
1960 2349 6.295688 GGAGCCGGTGGATAAAGATAGAATTA 60.296 42.308 1.90 0.00 0.00 1.40
1972 2361 1.518774 GAAACGGAGCCGGTGGATA 59.481 57.895 14.07 0.00 40.27 2.59
1979 2368 1.461897 ACAAAATACGAAACGGAGCCG 59.538 47.619 7.48 7.48 46.03 5.52
1981 2370 4.779987 AGAAACAAAATACGAAACGGAGC 58.220 39.130 0.00 0.00 0.00 4.70
1991 2380 8.951243 AGAAGCTAATGGAGAGAAACAAAATAC 58.049 33.333 0.00 0.00 0.00 1.89
1999 2388 6.586344 CATGGTAGAAGCTAATGGAGAGAAA 58.414 40.000 0.00 0.00 0.00 2.52
2039 2428 7.064134 TGCAGAAGTAATCAAGTTATAACACGG 59.936 37.037 17.65 6.61 0.00 4.94
2040 2429 7.959733 TGCAGAAGTAATCAAGTTATAACACG 58.040 34.615 17.65 8.00 0.00 4.49
2041 2430 9.708222 CATGCAGAAGTAATCAAGTTATAACAC 57.292 33.333 17.65 5.96 0.00 3.32
2078 2474 5.182001 GCAAGAGGAGCAAGAAAGTTATTGA 59.818 40.000 2.68 0.00 31.34 2.57
2079 2475 5.048504 TGCAAGAGGAGCAAGAAAGTTATTG 60.049 40.000 0.00 0.00 39.39 1.90
2080 2476 5.072741 TGCAAGAGGAGCAAGAAAGTTATT 58.927 37.500 0.00 0.00 39.39 1.40
2081 2477 4.655963 TGCAAGAGGAGCAAGAAAGTTAT 58.344 39.130 0.00 0.00 39.39 1.89
2155 2551 1.000506 GAGTCTAACCGGTGAAGCACA 59.999 52.381 8.52 0.00 35.86 4.57
2158 2554 2.288886 ACAAGAGTCTAACCGGTGAAGC 60.289 50.000 8.52 5.75 0.00 3.86
2175 2571 2.525055 CAACAAACACCACGGAACAAG 58.475 47.619 0.00 0.00 0.00 3.16
2223 2634 5.052693 TCAAGCAGGATAGCATTAACCAT 57.947 39.130 0.00 0.00 36.85 3.55
2246 2657 6.723977 TGTGGCTTTAAATCCCTATGAAGTTT 59.276 34.615 5.65 0.00 0.00 2.66
2247 2658 6.252995 TGTGGCTTTAAATCCCTATGAAGTT 58.747 36.000 5.65 0.00 0.00 2.66
2248 2659 5.826643 TGTGGCTTTAAATCCCTATGAAGT 58.173 37.500 5.65 0.00 0.00 3.01
2249 2660 6.773976 TTGTGGCTTTAAATCCCTATGAAG 57.226 37.500 5.65 0.00 0.00 3.02
2383 2794 8.691661 TGCTCAGTAAAATCTTAGGAACTTTT 57.308 30.769 0.00 0.00 41.75 2.27
2552 2995 3.781079 TCAAAGCCTAATTGCAATCGG 57.219 42.857 13.38 16.62 0.00 4.18
2553 2996 5.179045 AGATCAAAGCCTAATTGCAATCG 57.821 39.130 13.38 7.04 0.00 3.34
2554 2997 6.815142 ACAAAGATCAAAGCCTAATTGCAATC 59.185 34.615 13.38 0.00 0.00 2.67
2555 2998 6.704310 ACAAAGATCAAAGCCTAATTGCAAT 58.296 32.000 5.99 5.99 0.00 3.56
2556 2999 6.100404 ACAAAGATCAAAGCCTAATTGCAA 57.900 33.333 0.00 0.00 0.00 4.08
2557 3000 5.726980 ACAAAGATCAAAGCCTAATTGCA 57.273 34.783 0.00 0.00 0.00 4.08
2558 3001 7.975616 TCATAACAAAGATCAAAGCCTAATTGC 59.024 33.333 0.00 0.00 0.00 3.56
2559 3002 9.859427 TTCATAACAAAGATCAAAGCCTAATTG 57.141 29.630 0.00 0.00 0.00 2.32
2562 3005 9.859427 CATTTCATAACAAAGATCAAAGCCTAA 57.141 29.630 0.00 0.00 0.00 2.69
2563 3006 7.975616 GCATTTCATAACAAAGATCAAAGCCTA 59.024 33.333 0.00 0.00 0.00 3.93
2564 3007 6.815142 GCATTTCATAACAAAGATCAAAGCCT 59.185 34.615 0.00 0.00 0.00 4.58
2565 3008 6.036408 GGCATTTCATAACAAAGATCAAAGCC 59.964 38.462 0.00 0.00 0.00 4.35
2566 3009 6.815142 AGGCATTTCATAACAAAGATCAAAGC 59.185 34.615 0.00 0.00 0.00 3.51
2567 3010 8.767478 AAGGCATTTCATAACAAAGATCAAAG 57.233 30.769 0.00 0.00 0.00 2.77
2573 3016 9.859427 CAAGAATAAGGCATTTCATAACAAAGA 57.141 29.630 0.00 0.00 0.00 2.52
2574 3017 9.643693 ACAAGAATAAGGCATTTCATAACAAAG 57.356 29.630 0.00 0.00 0.00 2.77
2581 3024 9.412460 TCTGAATACAAGAATAAGGCATTTCAT 57.588 29.630 0.00 0.00 0.00 2.57
2582 3025 8.806429 TCTGAATACAAGAATAAGGCATTTCA 57.194 30.769 0.00 0.00 0.00 2.69
2583 3026 9.508567 GTTCTGAATACAAGAATAAGGCATTTC 57.491 33.333 0.00 0.00 0.00 2.17
2632 3075 5.243507 TGCTAATGCATTTTTGTTCTGGAGA 59.756 36.000 18.75 0.00 45.31 3.71
2719 3165 9.643693 AAGATGCATGAAAATATCGAACTTTTT 57.356 25.926 2.46 6.45 0.00 1.94
2724 3170 9.882996 TTCATAAGATGCATGAAAATATCGAAC 57.117 29.630 2.46 0.00 38.98 3.95
2727 3175 8.019094 TGCTTCATAAGATGCATGAAAATATCG 58.981 33.333 2.46 0.00 46.27 2.92
2802 3250 8.800332 AGTTAAGATCTTTTGTCTTGATGCAAT 58.200 29.630 14.36 0.00 36.63 3.56
2834 3283 7.122650 AGACATACAATTTCATAAGGTGGTTGG 59.877 37.037 0.00 0.00 0.00 3.77
2837 3286 9.920946 ATAAGACATACAATTTCATAAGGTGGT 57.079 29.630 0.00 0.00 0.00 4.16
2938 3440 6.486253 TCTGCTTAACTGATTGTGATCAAC 57.514 37.500 0.00 0.00 41.55 3.18
2982 3484 4.350346 TGCGAGTTCTTTTGTTTGATGTG 58.650 39.130 0.00 0.00 0.00 3.21
2998 3500 1.736126 CTTGACAAGATGCATGCGAGT 59.264 47.619 14.09 6.60 0.00 4.18
2999 3501 1.063616 CCTTGACAAGATGCATGCGAG 59.936 52.381 16.99 3.20 0.00 5.03
3001 3503 1.089112 TCCTTGACAAGATGCATGCG 58.911 50.000 16.99 0.00 0.00 4.73
3006 3508 1.372582 TGCGATCCTTGACAAGATGC 58.627 50.000 16.99 13.67 0.00 3.91
3022 3551 9.464248 GCTTATCAAATGTTTCTTTTAAATGCG 57.536 29.630 0.00 0.00 0.00 4.73
3052 3581 9.950680 TTCTTCTCAAACAAAAGCATTTAGTAG 57.049 29.630 0.00 0.00 37.28 2.57
3058 3587 7.436376 GCTTACTTCTTCTCAAACAAAAGCATT 59.564 33.333 0.00 0.00 36.50 3.56
3073 3602 5.049336 GTGGAAAACTGGAGCTTACTTCTTC 60.049 44.000 0.00 0.00 0.00 2.87
3123 3652 7.334421 GGAAGAACTTGAAGCACAATATAGTGA 59.666 37.037 7.27 0.00 42.05 3.41
3127 3656 6.721318 AGGGAAGAACTTGAAGCACAATATA 58.279 36.000 0.00 0.00 37.88 0.86
3353 3885 1.859302 TCAACCAACCAGGCAAAGTT 58.141 45.000 0.00 0.00 43.14 2.66
3360 3892 1.477553 CATCCCATCAACCAACCAGG 58.522 55.000 0.00 0.00 45.67 4.45
3393 3925 7.440523 ACAAGAACAATTCACTAGGATCAAC 57.559 36.000 0.00 0.00 0.00 3.18
3394 3926 7.939039 AGAACAAGAACAATTCACTAGGATCAA 59.061 33.333 0.00 0.00 0.00 2.57
3408 3940 7.004086 AGGAATAATGGACAGAACAAGAACAA 58.996 34.615 0.00 0.00 0.00 2.83
3468 4004 7.776933 TGTAGTAGTACGTACTTCAATCGAT 57.223 36.000 31.58 12.96 39.06 3.59
3583 4119 0.745845 GCACATACTCCAGGCCACTG 60.746 60.000 5.01 0.00 44.51 3.66
3667 4203 1.280421 GTCAAGTCCTTCAGGCTCCAT 59.720 52.381 0.00 0.00 34.44 3.41
3684 4220 9.504708 TTTTCTTAATTTACCGATAACAGGTCA 57.495 29.630 0.00 0.00 42.81 4.02
3694 4230 9.171701 CGTTTCATGTTTTTCTTAATTTACCGA 57.828 29.630 0.00 0.00 0.00 4.69
3724 4260 3.927142 CCTCAAGGACAGACATACGAAAC 59.073 47.826 0.00 0.00 37.39 2.78
4000 4536 5.835257 CAAATCGATTGCCCACTCAATAAT 58.165 37.500 12.25 0.00 36.85 1.28
4051 4587 1.210967 ACAGTTTCCGACCACCAGAAA 59.789 47.619 0.00 0.00 0.00 2.52
4093 4629 6.264292 TGGAAACATAACATTACAGTGCAACT 59.736 34.615 0.00 0.00 43.29 3.16
4095 4631 6.641169 TGGAAACATAACATTACAGTGCAA 57.359 33.333 0.00 0.00 33.40 4.08
4107 4643 7.308229 GAGCATCATACCAGATGGAAACATAAC 60.308 40.741 5.72 0.00 44.11 1.89
4108 4644 6.712095 GAGCATCATACCAGATGGAAACATAA 59.288 38.462 5.72 0.00 44.11 1.90
4109 4645 6.043590 AGAGCATCATACCAGATGGAAACATA 59.956 38.462 5.72 0.00 46.50 2.29
4110 4646 5.068636 GAGCATCATACCAGATGGAAACAT 58.931 41.667 5.72 0.00 46.11 2.71
4111 4647 4.164796 AGAGCATCATACCAGATGGAAACA 59.835 41.667 5.72 0.00 44.33 2.83
4112 4648 4.514441 CAGAGCATCATACCAGATGGAAAC 59.486 45.833 5.72 0.00 44.33 2.78
4113 4649 4.164796 ACAGAGCATCATACCAGATGGAAA 59.835 41.667 5.72 0.00 44.33 3.13
4114 4650 3.713248 ACAGAGCATCATACCAGATGGAA 59.287 43.478 5.72 0.00 44.33 3.53
4115 4651 3.311990 ACAGAGCATCATACCAGATGGA 58.688 45.455 5.72 0.00 44.33 3.41
4116 4652 3.766068 ACAGAGCATCATACCAGATGG 57.234 47.619 6.13 0.00 44.33 3.51
4117 4653 7.660617 AGATAAAACAGAGCATCATACCAGATG 59.339 37.037 0.00 0.00 46.36 2.90
4158 4694 7.175641 TGGAAATCTTTTTGCCTTGTTTCAAAA 59.824 29.630 0.00 0.00 39.53 2.44
4208 4744 2.880963 TTTCTTTTCCCGCTTTGTGG 57.119 45.000 0.00 0.00 0.00 4.17
4213 4749 7.520451 AGTAATTACTTTTCTTTTCCCGCTT 57.480 32.000 12.50 0.00 31.13 4.68
4240 4776 1.032014 TCAAAGAGTGCCAAGCAACC 58.968 50.000 0.00 0.00 41.47 3.77
4301 4907 3.907474 TCCTTACAAGATCACAAGGGACA 59.093 43.478 12.14 0.00 38.47 4.02
4304 4910 4.202441 CCATCCTTACAAGATCACAAGGG 58.798 47.826 12.14 1.21 38.47 3.95
4314 4920 3.081804 GGACCAACACCATCCTTACAAG 58.918 50.000 0.00 0.00 0.00 3.16
4386 5024 3.553095 AAGGTTGGCTCGGGCTCAC 62.553 63.158 7.48 3.69 38.73 3.51
4407 5046 4.748892 CACGACTAGAGTGTGGAATGATT 58.251 43.478 12.65 0.00 35.08 2.57
4460 5099 2.556287 GTCTTTGCAGAACCGGCG 59.444 61.111 0.00 0.00 0.00 6.46
4462 5101 2.966309 GCCGTCTTTGCAGAACCGG 61.966 63.158 0.00 0.00 40.24 5.28
4463 5102 1.781025 TTGCCGTCTTTGCAGAACCG 61.781 55.000 0.00 0.00 40.35 4.44
4464 5103 0.383949 TTTGCCGTCTTTGCAGAACC 59.616 50.000 0.00 0.00 40.35 3.62
4465 5104 2.202295 TTTTGCCGTCTTTGCAGAAC 57.798 45.000 0.00 0.00 40.35 3.01
4467 5106 2.881513 TGTATTTTGCCGTCTTTGCAGA 59.118 40.909 0.00 0.00 40.35 4.26
4477 5131 4.355437 TCGCCAAATTATGTATTTTGCCG 58.645 39.130 5.11 5.11 40.16 5.69
4485 5139 3.655615 AGGGGTTCGCCAAATTATGTA 57.344 42.857 8.53 0.00 39.65 2.29
4486 5140 2.525105 AGGGGTTCGCCAAATTATGT 57.475 45.000 8.53 0.00 39.65 2.29
4510 5164 0.174845 TGGCCGGACAATAGACTTCG 59.825 55.000 8.12 0.00 0.00 3.79
4520 5174 0.828022 CAGTAGGTTATGGCCGGACA 59.172 55.000 15.46 15.46 0.00 4.02
4522 5176 0.828022 CACAGTAGGTTATGGCCGGA 59.172 55.000 5.05 0.00 0.00 5.14
4526 5180 4.141574 TGGTTATCCACAGTAGGTTATGGC 60.142 45.833 0.00 0.00 39.03 4.40
4536 5190 2.108250 AGCTTGGTTGGTTATCCACAGT 59.892 45.455 0.00 0.00 44.22 3.55
4537 5191 2.795329 AGCTTGGTTGGTTATCCACAG 58.205 47.619 0.00 0.00 44.22 3.66
4538 5192 2.969821 AGCTTGGTTGGTTATCCACA 57.030 45.000 0.00 0.00 44.22 4.17
4539 5193 3.153919 TGAAGCTTGGTTGGTTATCCAC 58.846 45.455 2.10 0.00 44.22 4.02
4540 5194 3.517296 TGAAGCTTGGTTGGTTATCCA 57.483 42.857 2.10 0.00 42.66 3.41
4541 5195 4.273318 AGATGAAGCTTGGTTGGTTATCC 58.727 43.478 2.10 0.00 0.00 2.59
4542 5196 5.904362 AAGATGAAGCTTGGTTGGTTATC 57.096 39.130 2.10 0.00 0.00 1.75
4543 5197 6.267471 TCAAAAGATGAAGCTTGGTTGGTTAT 59.733 34.615 2.10 0.00 34.30 1.89
4544 5198 5.596361 TCAAAAGATGAAGCTTGGTTGGTTA 59.404 36.000 2.10 0.00 34.30 2.85
4545 5199 4.405358 TCAAAAGATGAAGCTTGGTTGGTT 59.595 37.500 2.10 0.00 34.30 3.67
4546 5200 3.960102 TCAAAAGATGAAGCTTGGTTGGT 59.040 39.130 2.10 0.00 34.30 3.67
4547 5201 4.279169 TCTCAAAAGATGAAGCTTGGTTGG 59.721 41.667 2.10 0.00 37.67 3.77
4548 5202 5.443185 TCTCAAAAGATGAAGCTTGGTTG 57.557 39.130 2.10 0.00 37.67 3.77
4549 5203 5.771666 TGATCTCAAAAGATGAAGCTTGGTT 59.228 36.000 2.10 0.00 42.46 3.67
4550 5204 5.319453 TGATCTCAAAAGATGAAGCTTGGT 58.681 37.500 2.10 0.00 42.46 3.67
4551 5205 5.892160 TGATCTCAAAAGATGAAGCTTGG 57.108 39.130 2.10 0.00 42.46 3.61
4552 5206 9.286946 GTTAATGATCTCAAAAGATGAAGCTTG 57.713 33.333 2.10 0.00 42.46 4.01
4553 5207 9.017509 TGTTAATGATCTCAAAAGATGAAGCTT 57.982 29.630 0.00 0.00 42.46 3.74
4554 5208 8.457261 GTGTTAATGATCTCAAAAGATGAAGCT 58.543 33.333 0.00 0.00 42.46 3.74
4555 5209 8.239314 TGTGTTAATGATCTCAAAAGATGAAGC 58.761 33.333 0.00 0.00 42.46 3.86
4558 5212 9.234827 ACATGTGTTAATGATCTCAAAAGATGA 57.765 29.630 0.00 0.00 42.46 2.92
4559 5213 9.499585 GACATGTGTTAATGATCTCAAAAGATG 57.500 33.333 1.15 0.00 42.46 2.90
4592 5246 9.838975 CTATGCTCTCTACTAATGTACAATCAG 57.161 37.037 0.00 0.00 0.00 2.90
4626 5280 2.549754 GGATCCGCTGGACATGTAAATG 59.450 50.000 0.00 0.00 32.98 2.32
4627 5281 2.172505 TGGATCCGCTGGACATGTAAAT 59.827 45.455 7.39 0.00 32.98 1.40
4628 5282 1.557371 TGGATCCGCTGGACATGTAAA 59.443 47.619 7.39 0.00 32.98 2.01
4629 5283 1.199615 TGGATCCGCTGGACATGTAA 58.800 50.000 7.39 0.00 32.98 2.41
4630 5284 1.070601 CATGGATCCGCTGGACATGTA 59.929 52.381 7.39 0.00 33.93 2.29
4632 5286 0.179037 ACATGGATCCGCTGGACATG 60.179 55.000 16.18 18.10 40.10 3.21
4633 5287 0.179037 CACATGGATCCGCTGGACAT 60.179 55.000 16.18 0.00 32.98 3.06
4634 5288 1.221566 CACATGGATCCGCTGGACA 59.778 57.895 16.18 0.00 32.98 4.02
4635 5289 0.107456 ATCACATGGATCCGCTGGAC 59.893 55.000 16.18 0.00 32.98 4.02
4636 5290 0.839277 AATCACATGGATCCGCTGGA 59.161 50.000 16.18 11.39 34.28 3.86
4637 5291 0.949397 CAATCACATGGATCCGCTGG 59.051 55.000 16.18 4.96 34.28 4.85
4638 5292 1.957668 TCAATCACATGGATCCGCTG 58.042 50.000 7.39 9.85 34.28 5.18
4639 5293 2.945080 ATCAATCACATGGATCCGCT 57.055 45.000 7.39 0.00 34.28 5.52
4640 5294 5.423015 AGTATATCAATCACATGGATCCGC 58.577 41.667 7.39 0.00 34.28 5.54
4641 5295 6.045318 GGAGTATATCAATCACATGGATCCG 58.955 44.000 7.39 0.00 34.28 4.18
4642 5296 6.157645 AGGGAGTATATCAATCACATGGATCC 59.842 42.308 4.20 4.20 34.28 3.36
4643 5297 7.125507 AGAGGGAGTATATCAATCACATGGATC 59.874 40.741 0.00 0.00 34.28 3.36
4644 5298 6.964679 AGAGGGAGTATATCAATCACATGGAT 59.035 38.462 0.00 0.00 38.05 3.41
4645 5299 6.212187 CAGAGGGAGTATATCAATCACATGGA 59.788 42.308 0.00 0.00 0.00 3.41
4646 5300 6.013898 ACAGAGGGAGTATATCAATCACATGG 60.014 42.308 0.00 0.00 0.00 3.66
4647 5301 7.002250 ACAGAGGGAGTATATCAATCACATG 57.998 40.000 0.00 0.00 0.00 3.21
4648 5302 7.448420 CAACAGAGGGAGTATATCAATCACAT 58.552 38.462 0.00 0.00 0.00 3.21
4649 5303 6.686378 GCAACAGAGGGAGTATATCAATCACA 60.686 42.308 0.00 0.00 0.00 3.58
4650 5304 5.698545 GCAACAGAGGGAGTATATCAATCAC 59.301 44.000 0.00 0.00 0.00 3.06
4651 5305 5.604231 AGCAACAGAGGGAGTATATCAATCA 59.396 40.000 0.00 0.00 0.00 2.57
4652 5306 6.107901 AGCAACAGAGGGAGTATATCAATC 57.892 41.667 0.00 0.00 0.00 2.67
4654 5308 7.432148 TTTAGCAACAGAGGGAGTATATCAA 57.568 36.000 0.00 0.00 0.00 2.57
4659 5313 9.326489 TCATATATTTAGCAACAGAGGGAGTAT 57.674 33.333 0.00 0.00 0.00 2.12
4660 5314 8.585881 GTCATATATTTAGCAACAGAGGGAGTA 58.414 37.037 0.00 0.00 0.00 2.59
4661 5315 7.071196 TGTCATATATTTAGCAACAGAGGGAGT 59.929 37.037 0.00 0.00 0.00 3.85
4662 5316 7.445121 TGTCATATATTTAGCAACAGAGGGAG 58.555 38.462 0.00 0.00 0.00 4.30
4663 5317 7.373617 TGTCATATATTTAGCAACAGAGGGA 57.626 36.000 0.00 0.00 0.00 4.20
4664 5318 8.627208 AATGTCATATATTTAGCAACAGAGGG 57.373 34.615 0.00 0.00 0.00 4.30
4689 5343 9.689976 CATGTGATGTAAAATTGAACTACCAAA 57.310 29.630 0.00 0.00 0.00 3.28
4690 5344 7.812191 GCATGTGATGTAAAATTGAACTACCAA 59.188 33.333 0.00 0.00 0.00 3.67
4691 5345 7.040132 TGCATGTGATGTAAAATTGAACTACCA 60.040 33.333 0.00 0.00 0.00 3.25
4693 5347 8.741101 TTGCATGTGATGTAAAATTGAACTAC 57.259 30.769 0.00 0.00 31.88 2.73
4694 5348 9.409312 CTTTGCATGTGATGTAAAATTGAACTA 57.591 29.630 0.00 0.00 42.73 2.24
4695 5349 7.095523 GCTTTGCATGTGATGTAAAATTGAACT 60.096 33.333 0.00 0.00 42.73 3.01
4696 5350 7.011189 GCTTTGCATGTGATGTAAAATTGAAC 58.989 34.615 0.00 0.00 42.73 3.18
4697 5351 6.930164 AGCTTTGCATGTGATGTAAAATTGAA 59.070 30.769 0.00 0.00 42.73 2.69
4699 5353 6.715344 AGCTTTGCATGTGATGTAAAATTG 57.285 33.333 0.00 0.00 42.73 2.32
4700 5354 7.441760 TCAAAGCTTTGCATGTGATGTAAAATT 59.558 29.630 30.35 0.00 42.73 1.82
4707 5365 4.168922 TCTCAAAGCTTTGCATGTGATG 57.831 40.909 30.35 8.38 38.05 3.07
4801 5515 9.964253 GCATGAGAGTAATATATTTCATCAACG 57.036 33.333 2.68 5.07 0.00 4.10
4830 5544 4.803426 CGCAGGCTGGGACGACTC 62.803 72.222 25.76 0.00 31.21 3.36
4836 5550 1.334384 TACTATTGCGCAGGCTGGGA 61.334 55.000 32.71 15.10 40.82 4.37
4842 5556 5.984233 TCTTTTATGTACTATTGCGCAGG 57.016 39.130 11.31 7.90 0.00 4.85


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

AutoCloner maintained by Alex Coulton.