Multiple sequence alignment - TraesCS1A01G040400

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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 TraesCS1A01G040400 chr1A 100.000 5827 0 0 1 5827 22292553 22286727 0.000000e+00 10761.0
1 TraesCS1A01G040400 chr1A 87.075 441 53 4 4063 4501 22288362 22287924 4.060000e-136 496.0
2 TraesCS1A01G040400 chr1A 87.075 441 53 4 4192 4630 22288491 22288053 4.060000e-136 496.0
3 TraesCS1A01G040400 chr1D 94.093 2404 111 10 2639 5018 20055039 20057435 0.000000e+00 3624.0
4 TraesCS1A01G040400 chr1D 86.270 1646 129 54 211 1790 20052542 20054156 0.000000e+00 1698.0
5 TraesCS1A01G040400 chr1D 94.538 476 22 3 1785 2258 20054267 20054740 0.000000e+00 732.0
6 TraesCS1A01G040400 chr1D 89.116 588 40 11 5236 5813 20057531 20058104 0.000000e+00 710.0
7 TraesCS1A01G040400 chr1D 85.204 588 64 8 5236 5813 20178916 20179490 3.030000e-162 582.0
8 TraesCS1A01G040400 chr1D 87.025 447 54 4 4186 4630 20056475 20056919 8.720000e-138 501.0
9 TraesCS1A01G040400 chr1D 85.906 447 59 4 4057 4501 20056604 20057048 1.900000e-129 473.0
10 TraesCS1A01G040400 chr1D 82.759 319 49 6 4315 4630 20056475 20056790 4.450000e-71 279.0
11 TraesCS1A01G040400 chr1B 93.434 2315 103 23 3000 5292 33978722 33976435 0.000000e+00 3387.0
12 TraesCS1A01G040400 chr1B 89.697 1223 86 17 1785 2996 33980022 33978829 0.000000e+00 1524.0
13 TraesCS1A01G040400 chr1B 84.385 1601 126 61 282 1790 33981701 33980133 0.000000e+00 1458.0
14 TraesCS1A01G040400 chr1B 88.439 519 30 12 5236 5727 33926126 33925611 3.000000e-167 599.0
15 TraesCS1A01G040400 chr1B 93.931 379 19 4 5236 5614 33950829 33950455 2.360000e-158 569.0
16 TraesCS1A01G040400 chr1B 87.075 441 53 4 4063 4501 33977530 33977092 4.060000e-136 496.0
17 TraesCS1A01G040400 chr1B 87.075 441 53 4 4192 4630 33977659 33977221 4.060000e-136 496.0
18 TraesCS1A01G040400 chr1B 83.228 316 47 6 4060 4372 33977404 33977092 9.560000e-73 285.0
19 TraesCS1A01G040400 chr1B 77.612 134 22 6 5595 5727 33971040 33970914 2.250000e-09 75.0
20 TraesCS1A01G040400 chr5D 89.695 689 58 9 14 694 189930599 189929916 0.000000e+00 867.0
21 TraesCS1A01G040400 chr5D 91.000 100 8 1 2501 2600 367591429 367591331 3.660000e-27 134.0
22 TraesCS1A01G040400 chr2D 88.393 112 12 1 2489 2600 538391411 538391521 3.660000e-27 134.0
23 TraesCS1A01G040400 chr5B 90.000 100 9 1 2501 2600 434923520 434923422 1.700000e-25 128.0
24 TraesCS1A01G040400 chr3D 92.222 90 6 1 2511 2600 464060792 464060704 6.130000e-25 126.0
25 TraesCS1A01G040400 chr3D 93.151 73 5 0 2528 2600 32175354 32175282 2.220000e-19 108.0
26 TraesCS1A01G040400 chr7D 91.781 73 6 0 2528 2600 580058325 580058253 1.030000e-17 102.0
27 TraesCS1A01G040400 chr7B 93.443 61 3 1 2575 2635 209401774 209401833 8.040000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G040400 chr1A 22286727 22292553 5826 True 10761.000000 10761 100.000000 1 5827 1 chr1A.!!$R1 5826
1 TraesCS1A01G040400 chr1A 22287924 22288491 567 True 496.000000 496 87.075000 4063 4630 2 chr1A.!!$R2 567
2 TraesCS1A01G040400 chr1D 20052542 20058104 5562 False 1145.285714 3624 88.529571 211 5813 7 chr1D.!!$F2 5602
3 TraesCS1A01G040400 chr1D 20178916 20179490 574 False 582.000000 582 85.204000 5236 5813 1 chr1D.!!$F1 577
4 TraesCS1A01G040400 chr1B 33976435 33981701 5266 True 1274.333333 3387 87.482333 282 5292 6 chr1B.!!$R4 5010
5 TraesCS1A01G040400 chr1B 33925611 33926126 515 True 599.000000 599 88.439000 5236 5727 1 chr1B.!!$R1 491
6 TraesCS1A01G040400 chr5D 189929916 189930599 683 True 867.000000 867 89.695000 14 694 1 chr5D.!!$R1 680

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
931 989 0.108019 CCCGGCCCACTATAAACCTC 59.892 60.000 0.00 0.00 0.00 3.85 F
1702 1830 0.040514 CGCTTCGACAAATTGGTGCA 60.041 50.000 0.00 0.00 0.00 4.57 F
1714 1842 0.592637 TTGGTGCATTTGTGCTCGAG 59.407 50.000 8.45 8.45 35.49 4.04 F
2459 2715 1.133407 GCTCGGACTTGGACTGTCTAG 59.867 57.143 7.85 8.12 35.04 2.43 F
3324 3861 2.074547 TTGTCGTCGTTTGGAGGATC 57.925 50.000 0.00 0.00 41.23 3.36 F
3896 4439 2.699846 AGGTGAATTCAAAGGCTTTGCA 59.300 40.909 30.40 22.97 40.43 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2380 0.325671 TCCTTCGCCTCTCCTTCCAT 60.326 55.000 0.00 0.00 0.00 3.41 R
3312 3849 0.036010 ACAGGCAGATCCTCCAAACG 60.036 55.000 3.96 0.00 45.52 3.60 R
3403 3940 0.389948 GGTGGTACAAGCTGACTCCG 60.390 60.000 0.00 0.00 44.16 4.63 R
3934 4477 1.795286 CGTTCTGGTCAAGCTTCAGAC 59.205 52.381 14.15 11.21 37.28 3.51 R
4736 5282 0.958822 TCTTTTTCTTTGGAGGCGCC 59.041 50.000 21.89 21.89 37.10 6.53 R
5789 6372 1.097547 CGAGGCGCCAAAATCCTCAT 61.098 55.000 31.54 2.38 45.04 2.90 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
23 24 2.280628 CGAACAGGGCCTTAATGTCTC 58.719 52.381 1.32 0.00 0.00 3.36
28 29 1.095807 GGGCCTTAATGTCTCGTGGC 61.096 60.000 0.84 0.00 39.61 5.01
30 31 1.679032 GGCCTTAATGTCTCGTGGCTT 60.679 52.381 0.00 0.00 40.15 4.35
31 32 2.419574 GGCCTTAATGTCTCGTGGCTTA 60.420 50.000 0.00 0.00 40.15 3.09
153 154 5.066375 TCGAGCAAATAAACCCTGATGATTG 59.934 40.000 0.00 0.00 0.00 2.67
165 166 3.504906 CCTGATGATTGAAACAGCACACT 59.495 43.478 0.00 0.00 30.61 3.55
179 180 3.862267 CAGCACACTCAAGCTACTGATAC 59.138 47.826 0.00 0.00 39.50 2.24
186 187 2.432146 TCAAGCTACTGATACCAGCCAG 59.568 50.000 0.00 0.00 44.16 4.85
206 207 5.007034 CCAGGAAACACATGGTTACATACA 58.993 41.667 0.00 0.00 44.34 2.29
246 247 2.543848 AGCACGGCATTGATTATACACG 59.456 45.455 0.00 0.00 0.00 4.49
247 248 2.349438 GCACGGCATTGATTATACACGG 60.349 50.000 0.00 0.00 0.00 4.94
299 305 0.606401 ACACCGGATGGCAAACTGAG 60.606 55.000 9.46 0.00 39.70 3.35
315 321 3.136763 ACTGAGACAACATGAAGCACAG 58.863 45.455 0.00 4.54 0.00 3.66
320 326 2.227388 GACAACATGAAGCACAGAAGGG 59.773 50.000 0.00 0.00 0.00 3.95
321 327 1.068055 CAACATGAAGCACAGAAGGGC 60.068 52.381 0.00 0.00 0.00 5.19
425 437 5.440234 AAACAAACCAAACCAAACCAAAC 57.560 34.783 0.00 0.00 0.00 2.93
428 440 3.790089 AACCAAACCAAACCAAACCAA 57.210 38.095 0.00 0.00 0.00 3.67
429 441 3.342377 ACCAAACCAAACCAAACCAAG 57.658 42.857 0.00 0.00 0.00 3.61
430 442 2.640332 ACCAAACCAAACCAAACCAAGT 59.360 40.909 0.00 0.00 0.00 3.16
431 443 3.073209 ACCAAACCAAACCAAACCAAGTT 59.927 39.130 0.00 0.00 0.00 2.66
432 444 4.286291 ACCAAACCAAACCAAACCAAGTTA 59.714 37.500 0.00 0.00 0.00 2.24
433 445 5.221864 ACCAAACCAAACCAAACCAAGTTAA 60.222 36.000 0.00 0.00 0.00 2.01
454 466 2.503356 ACCAGGCATCGAGAAGAGAAAT 59.497 45.455 0.00 0.00 0.00 2.17
459 471 1.260033 CATCGAGAAGAGAAATGGCGC 59.740 52.381 0.00 0.00 0.00 6.53
460 472 0.246360 TCGAGAAGAGAAATGGCGCA 59.754 50.000 10.83 0.00 0.00 6.09
462 474 1.737029 CGAGAAGAGAAATGGCGCAGA 60.737 52.381 10.83 0.00 0.00 4.26
463 475 2.559440 GAGAAGAGAAATGGCGCAGAT 58.441 47.619 10.83 0.00 0.00 2.90
464 476 2.941720 GAGAAGAGAAATGGCGCAGATT 59.058 45.455 10.83 3.54 0.00 2.40
465 477 2.681848 AGAAGAGAAATGGCGCAGATTG 59.318 45.455 10.83 0.00 0.00 2.67
490 517 1.615262 GTGGAGGGAAATGGGGGAG 59.385 63.158 0.00 0.00 0.00 4.30
797 830 4.936248 CGCTCTCTCGCTCGCTCG 62.936 72.222 0.00 0.00 0.00 5.03
799 832 3.572539 CTCTCTCGCTCGCTCGCT 61.573 66.667 0.00 0.00 0.00 4.93
800 833 3.506312 CTCTCTCGCTCGCTCGCTC 62.506 68.421 0.00 0.00 0.00 5.03
807 840 4.320928 CTCGCTCGCTCGCTAGGG 62.321 72.222 0.00 0.00 37.02 3.53
809 842 4.194720 CGCTCGCTCGCTAGGGTT 62.195 66.667 6.70 0.00 37.01 4.11
838 890 1.689813 GGCCTAGGGTAAGAGAAGAGC 59.310 57.143 11.72 0.00 0.00 4.09
847 899 3.004315 GGTAAGAGAAGAGCAGAGATCGG 59.996 52.174 0.00 0.00 0.00 4.18
848 900 1.691196 AGAGAAGAGCAGAGATCGGG 58.309 55.000 0.00 0.00 0.00 5.14
893 951 3.850923 GAACCGCACGTTCGATCA 58.149 55.556 9.73 0.00 41.51 2.92
895 953 0.719465 GAACCGCACGTTCGATCAAT 59.281 50.000 9.73 0.00 41.51 2.57
896 954 0.442310 AACCGCACGTTCGATCAATG 59.558 50.000 9.73 0.00 0.00 2.82
897 955 0.669318 ACCGCACGTTCGATCAATGT 60.669 50.000 9.73 0.00 34.22 2.71
898 956 1.273688 CCGCACGTTCGATCAATGTA 58.726 50.000 9.73 0.00 31.94 2.29
899 957 1.656594 CCGCACGTTCGATCAATGTAA 59.343 47.619 9.73 0.00 31.94 2.41
906 964 2.325583 TCGATCAATGTAAGGCCCAC 57.674 50.000 0.00 0.00 0.00 4.61
931 989 0.108019 CCCGGCCCACTATAAACCTC 59.892 60.000 0.00 0.00 0.00 3.85
943 1006 1.236616 TAAACCTCGCCGTCTCGTCA 61.237 55.000 0.00 0.00 0.00 4.35
944 1007 2.079020 AAACCTCGCCGTCTCGTCAA 62.079 55.000 0.00 0.00 0.00 3.18
961 1027 1.719378 TCAAGTCTCTTCCTCTCCCCT 59.281 52.381 0.00 0.00 0.00 4.79
966 1032 1.850345 TCTCTTCCTCTCCCCTCTCTC 59.150 57.143 0.00 0.00 0.00 3.20
968 1034 1.568597 TCTTCCTCTCCCCTCTCTCTG 59.431 57.143 0.00 0.00 0.00 3.35
970 1036 0.923358 TCCTCTCCCCTCTCTCTGTC 59.077 60.000 0.00 0.00 0.00 3.51
972 1038 1.287739 CCTCTCCCCTCTCTCTGTCTT 59.712 57.143 0.00 0.00 0.00 3.01
975 1041 2.652348 TCTCCCCTCTCTCTGTCTTTCT 59.348 50.000 0.00 0.00 0.00 2.52
976 1042 3.023832 CTCCCCTCTCTCTGTCTTTCTC 58.976 54.545 0.00 0.00 0.00 2.87
977 1043 2.652348 TCCCCTCTCTCTGTCTTTCTCT 59.348 50.000 0.00 0.00 0.00 3.10
979 1045 3.023832 CCCTCTCTCTGTCTTTCTCTCC 58.976 54.545 0.00 0.00 0.00 3.71
981 1047 3.443681 CCTCTCTCTGTCTTTCTCTCCAC 59.556 52.174 0.00 0.00 0.00 4.02
982 1048 4.335416 CTCTCTCTGTCTTTCTCTCCACT 58.665 47.826 0.00 0.00 0.00 4.00
1167 1242 3.787001 CCTCCCCGGACCAAGAGC 61.787 72.222 0.73 0.00 33.16 4.09
1371 1491 1.524849 GAAGGAGAAGATGCGGGCC 60.525 63.158 0.00 0.00 0.00 5.80
1445 1565 4.035102 GAAGCAGGGCCCGGAAGT 62.035 66.667 27.79 9.26 0.00 3.01
1449 1569 3.411517 CAGGGCCCGGAAGTGGAT 61.412 66.667 18.42 0.00 0.00 3.41
1454 1574 2.272146 CCCGGAAGTGGATGGTGG 59.728 66.667 0.73 0.00 0.00 4.61
1464 1584 1.125093 TGGATGGTGGTGACGACCTT 61.125 55.000 17.63 11.43 43.58 3.50
1472 1592 1.079750 GTGACGACCTTGAGGAGCC 60.080 63.158 3.59 0.00 38.94 4.70
1475 1595 4.821589 CGACCTTGAGGAGCCGGC 62.822 72.222 21.89 21.89 38.94 6.13
1638 1758 1.216710 GGAGAAGCAGGACGTGGAG 59.783 63.158 0.00 0.00 0.00 3.86
1668 1788 2.025589 CTGATGCAGCTGTGTCAGAT 57.974 50.000 30.48 10.87 40.30 2.90
1681 1801 5.077134 TGTGTCAGATGATAGGTGAGTTG 57.923 43.478 0.00 0.00 0.00 3.16
1682 1802 4.081476 TGTGTCAGATGATAGGTGAGTTGG 60.081 45.833 0.00 0.00 0.00 3.77
1687 1807 0.613260 TGATAGGTGAGTTGGCGCTT 59.387 50.000 7.64 0.00 0.00 4.68
1691 1811 2.668280 GGTGAGTTGGCGCTTCGAC 61.668 63.158 7.64 0.93 34.27 4.20
1702 1830 0.040514 CGCTTCGACAAATTGGTGCA 60.041 50.000 0.00 0.00 0.00 4.57
1709 1837 2.096811 CGACAAATTGGTGCATTTGTGC 60.097 45.455 18.26 10.33 47.00 4.57
1711 1839 3.132925 ACAAATTGGTGCATTTGTGCTC 58.867 40.909 13.83 0.00 45.79 4.26
1714 1842 0.592637 TTGGTGCATTTGTGCTCGAG 59.407 50.000 8.45 8.45 35.49 4.04
1721 1849 2.675317 GCATTTGTGCTCGAGTACCTCT 60.675 50.000 27.59 11.33 0.00 3.69
1726 1854 1.727335 GTGCTCGAGTACCTCTTTTGC 59.273 52.381 21.57 0.00 0.00 3.68
1755 1883 4.757149 GGTTCATGCCATGTAGATAGGAAC 59.243 45.833 4.31 0.00 33.30 3.62
1769 1897 6.426646 AGATAGGAACTGTGTTGAACTCTT 57.573 37.500 0.00 0.00 41.52 2.85
1770 1898 6.226787 AGATAGGAACTGTGTTGAACTCTTG 58.773 40.000 0.00 0.00 41.52 3.02
1788 2034 5.163581 ACTCTTGATGTTAAGATGCCATTGC 60.164 40.000 0.00 0.00 36.21 3.56
1808 2054 9.859427 CCATTGCTTAGTTTTATCATTCAGAAA 57.141 29.630 0.00 0.00 0.00 2.52
1857 2103 7.281100 CCTTCATCCATCTAGTTTGGTAACTTC 59.719 40.741 12.29 0.00 41.85 3.01
1868 2114 6.068010 AGTTTGGTAACTTCATCATGTTGGA 58.932 36.000 3.98 0.00 41.85 3.53
1911 2157 6.483640 GCAACTATCTGGTTATCTAGTTTGGG 59.516 42.308 0.00 0.00 33.34 4.12
1918 2164 7.110155 TCTGGTTATCTAGTTTGGGTTTGATC 58.890 38.462 0.00 0.00 0.00 2.92
2076 2324 4.832266 TGTCTGGTCCTTGCATTAACATTT 59.168 37.500 0.00 0.00 0.00 2.32
2077 2325 5.163513 GTCTGGTCCTTGCATTAACATTTG 58.836 41.667 0.00 0.00 0.00 2.32
2132 2380 3.244078 ACACAATCTAGACGCCACAAAGA 60.244 43.478 0.00 0.00 0.00 2.52
2259 2507 8.101419 AGATAGGTGAGTTAAAACTGTAAAGGG 58.899 37.037 0.00 0.00 39.88 3.95
2260 2508 4.825634 AGGTGAGTTAAAACTGTAAAGGGC 59.174 41.667 0.00 0.00 39.88 5.19
2262 2510 5.278315 GGTGAGTTAAAACTGTAAAGGGCAG 60.278 44.000 0.00 0.00 39.88 4.85
2277 2532 1.903183 GGGCAGAGTTCTTGAGTACCT 59.097 52.381 0.00 0.00 0.00 3.08
2286 2541 6.551601 AGAGTTCTTGAGTACCTTCTTTCTCA 59.448 38.462 0.00 0.00 35.54 3.27
2290 2545 9.145865 GTTCTTGAGTACCTTCTTTCTCATTAG 57.854 37.037 0.00 0.00 36.91 1.73
2305 2560 9.083422 CTTTCTCATTAGATAGGTATGAGGACA 57.917 37.037 10.43 0.00 43.39 4.02
2308 2563 7.885922 TCTCATTAGATAGGTATGAGGACAGAC 59.114 40.741 10.43 0.00 43.39 3.51
2314 2569 7.051623 AGATAGGTATGAGGACAGACGATATC 58.948 42.308 0.00 0.00 38.88 1.63
2318 2573 5.184096 GGTATGAGGACAGACGATATCACAT 59.816 44.000 3.12 0.00 38.88 3.21
2321 2576 6.073327 TGAGGACAGACGATATCACATAAC 57.927 41.667 3.12 0.00 0.00 1.89
2330 2585 5.233225 ACGATATCACATAACAGAGGCATG 58.767 41.667 3.12 0.00 0.00 4.06
2346 2601 3.071602 AGGCATGTAAGACAAGACACTGT 59.928 43.478 0.00 0.00 24.59 3.55
2403 2658 7.486551 CACAGTGAGTTAGTGACTAAGAATAGC 59.513 40.741 5.10 0.00 39.19 2.97
2412 2667 5.835819 AGTGACTAAGAATAGCATAGCAGGA 59.164 40.000 0.00 0.00 31.96 3.86
2417 2672 3.524826 AGAATAGCATAGCAGGATGGGA 58.475 45.455 0.00 0.00 35.86 4.37
2418 2673 3.262915 AGAATAGCATAGCAGGATGGGAC 59.737 47.826 0.00 0.00 35.86 4.46
2421 2676 2.694397 AGCATAGCAGGATGGGACTTA 58.306 47.619 0.00 0.00 35.86 2.24
2424 2679 3.755378 GCATAGCAGGATGGGACTTATTG 59.245 47.826 0.00 0.00 35.86 1.90
2425 2680 2.355010 AGCAGGATGGGACTTATTGC 57.645 50.000 0.00 0.00 35.86 3.56
2426 2681 1.565759 AGCAGGATGGGACTTATTGCA 59.434 47.619 0.00 0.00 35.86 4.08
2427 2682 2.176364 AGCAGGATGGGACTTATTGCAT 59.824 45.455 0.00 0.00 35.86 3.96
2429 2684 3.755378 GCAGGATGGGACTTATTGCATAG 59.245 47.826 0.00 0.00 35.86 2.23
2430 2685 4.747931 GCAGGATGGGACTTATTGCATAGT 60.748 45.833 0.00 0.00 35.86 2.12
2432 2687 6.533730 CAGGATGGGACTTATTGCATAGTTA 58.466 40.000 0.00 0.00 0.00 2.24
2433 2688 6.652481 CAGGATGGGACTTATTGCATAGTTAG 59.348 42.308 0.00 0.00 0.00 2.34
2434 2689 6.558775 AGGATGGGACTTATTGCATAGTTAGA 59.441 38.462 0.00 0.00 0.00 2.10
2442 2698 8.202745 ACTTATTGCATAGTTAGAAGTTGCTC 57.797 34.615 0.00 0.00 34.47 4.26
2452 2708 1.149148 GAAGTTGCTCGGACTTGGAC 58.851 55.000 0.00 0.00 37.46 4.02
2459 2715 1.133407 GCTCGGACTTGGACTGTCTAG 59.867 57.143 7.85 8.12 35.04 2.43
2464 2720 3.330267 GGACTTGGACTGTCTAGCTTTG 58.670 50.000 7.85 0.00 35.04 2.77
2479 2735 6.147821 GTCTAGCTTTGCTGTTGACTCAAATA 59.852 38.462 0.00 0.00 40.10 1.40
2483 2739 5.277974 GCTTTGCTGTTGACTCAAATAGTGA 60.278 40.000 0.00 0.00 39.07 3.41
2484 2740 6.569226 GCTTTGCTGTTGACTCAAATAGTGAT 60.569 38.462 0.00 0.00 39.07 3.06
2485 2741 5.868043 TGCTGTTGACTCAAATAGTGATG 57.132 39.130 0.00 0.00 39.07 3.07
2488 2744 7.105588 TGCTGTTGACTCAAATAGTGATGTAT 58.894 34.615 0.00 0.00 39.07 2.29
2489 2745 7.064966 TGCTGTTGACTCAAATAGTGATGTATG 59.935 37.037 0.00 0.00 39.07 2.39
2491 2747 8.846943 TGTTGACTCAAATAGTGATGTATGTT 57.153 30.769 0.00 0.00 39.07 2.71
2492 2748 8.720562 TGTTGACTCAAATAGTGATGTATGTTG 58.279 33.333 0.00 0.00 39.07 3.33
2493 2749 8.935844 GTTGACTCAAATAGTGATGTATGTTGA 58.064 33.333 0.00 0.00 39.07 3.18
2494 2750 8.479313 TGACTCAAATAGTGATGTATGTTGAC 57.521 34.615 0.00 0.00 39.07 3.18
2495 2751 8.314021 TGACTCAAATAGTGATGTATGTTGACT 58.686 33.333 0.00 0.00 39.07 3.41
2496 2752 8.709386 ACTCAAATAGTGATGTATGTTGACTC 57.291 34.615 0.00 0.00 36.93 3.36
2497 2753 8.314021 ACTCAAATAGTGATGTATGTTGACTCA 58.686 33.333 0.00 0.00 36.93 3.41
2498 2754 9.154847 CTCAAATAGTGATGTATGTTGACTCAA 57.845 33.333 0.00 0.00 35.07 3.02
2499 2755 9.500785 TCAAATAGTGATGTATGTTGACTCAAA 57.499 29.630 0.00 0.00 0.00 2.69
2504 2760 8.484641 AGTGATGTATGTTGACTCAAATAGTG 57.515 34.615 0.00 0.00 39.07 2.74
2505 2761 7.065085 AGTGATGTATGTTGACTCAAATAGTGC 59.935 37.037 0.00 0.00 39.07 4.40
2506 2762 7.065085 GTGATGTATGTTGACTCAAATAGTGCT 59.935 37.037 0.00 0.00 39.07 4.40
2507 2763 6.726258 TGTATGTTGACTCAAATAGTGCTG 57.274 37.500 0.00 0.00 39.07 4.41
2508 2764 6.230472 TGTATGTTGACTCAAATAGTGCTGT 58.770 36.000 0.00 0.00 39.07 4.40
2509 2765 7.382898 TGTATGTTGACTCAAATAGTGCTGTA 58.617 34.615 0.00 0.00 39.07 2.74
2510 2766 7.875554 TGTATGTTGACTCAAATAGTGCTGTAA 59.124 33.333 0.00 0.00 39.07 2.41
2511 2767 6.539649 TGTTGACTCAAATAGTGCTGTAAC 57.460 37.500 0.00 0.00 39.07 2.50
2512 2768 6.288294 TGTTGACTCAAATAGTGCTGTAACT 58.712 36.000 0.00 0.00 39.07 2.24
2513 2769 6.202762 TGTTGACTCAAATAGTGCTGTAACTG 59.797 38.462 0.00 0.00 39.07 3.16
2562 2818 4.621068 TCAGACTTTGTTGTGAGCTTTG 57.379 40.909 0.00 0.00 0.00 2.77
2597 2853 5.738619 AAAACTGTTTGGTCTGGAAGTTT 57.261 34.783 6.53 0.00 38.99 2.66
2636 2892 5.237048 TGGCAATTTTATTGCTTTCTGGTC 58.763 37.500 20.07 5.55 44.36 4.02
2650 3069 6.597672 TGCTTTCTGGTCGTATGTTTATTGAT 59.402 34.615 0.00 0.00 0.00 2.57
2654 3073 7.915293 TCTGGTCGTATGTTTATTGATTTGT 57.085 32.000 0.00 0.00 0.00 2.83
2669 3088 6.554334 TTGATTTGTTAAGGAGTGCAGTAC 57.446 37.500 0.00 0.00 0.00 2.73
2683 3102 2.108168 GCAGTACACAGGGTGGAGATA 58.892 52.381 0.00 0.00 37.94 1.98
2823 3242 5.449553 AGAAGTTTCTTTGAAGGATGTGGT 58.550 37.500 0.00 0.00 32.55 4.16
2907 3326 3.668447 TCTCACATTCAAGGTCAGCTTC 58.332 45.455 0.00 0.00 0.00 3.86
2919 3338 2.913590 GGTCAGCTTCGAAACGTAGTAC 59.086 50.000 0.00 0.00 45.00 2.73
2933 3352 5.382618 ACGTAGTACCCTTTGTTCTAGTG 57.617 43.478 0.00 0.00 41.94 2.74
2937 3356 5.625568 AGTACCCTTTGTTCTAGTGTTGT 57.374 39.130 0.00 0.00 0.00 3.32
2942 3361 4.638421 CCCTTTGTTCTAGTGTTGTGTTCA 59.362 41.667 0.00 0.00 0.00 3.18
3030 3552 8.181904 ACTGAATGTTTAAGGTTTGATGACAT 57.818 30.769 0.00 0.00 0.00 3.06
3047 3569 4.880759 TGACATTGGCGTTTTGATTCAAT 58.119 34.783 0.00 0.00 0.00 2.57
3178 3715 5.815740 CCCTTGCGTCTTATGTTACTACAAT 59.184 40.000 0.00 0.00 37.91 2.71
3272 3809 5.365025 AGATGCTCTTAATCTGCTTGGTAGA 59.635 40.000 0.00 0.00 33.08 2.59
3283 3820 2.704572 GCTTGGTAGAGCACATGACTT 58.295 47.619 0.00 0.00 42.25 3.01
3292 3829 3.197333 AGAGCACATGACTTATCAGCAGT 59.803 43.478 0.00 0.00 38.57 4.40
3310 3847 3.846023 GCAGTGTGTTTCAGTCATTGTCG 60.846 47.826 0.00 0.00 0.00 4.35
3312 3849 3.555956 AGTGTGTTTCAGTCATTGTCGTC 59.444 43.478 0.00 0.00 0.00 4.20
3324 3861 2.074547 TTGTCGTCGTTTGGAGGATC 57.925 50.000 0.00 0.00 41.23 3.36
3359 3896 7.397892 TTGAATCTTGTGGTACAACTTTTGA 57.602 32.000 1.23 0.00 44.16 2.69
3360 3897 7.397892 TGAATCTTGTGGTACAACTTTTGAA 57.602 32.000 1.23 0.00 44.16 2.69
3364 3901 5.708230 TCTTGTGGTACAACTTTTGAACAGT 59.292 36.000 1.23 0.00 44.16 3.55
3378 3915 7.880195 ACTTTTGAACAGTGCTCTTATCTACAT 59.120 33.333 0.00 0.00 0.00 2.29
3379 3916 8.621532 TTTTGAACAGTGCTCTTATCTACATT 57.378 30.769 0.00 0.00 0.00 2.71
3380 3917 8.621532 TTTGAACAGTGCTCTTATCTACATTT 57.378 30.769 0.00 0.00 0.00 2.32
3381 3918 8.621532 TTGAACAGTGCTCTTATCTACATTTT 57.378 30.769 0.00 0.00 0.00 1.82
3453 3994 7.329588 TGCTCTTAATCTGTTATCACGAGTA 57.670 36.000 0.00 0.00 0.00 2.59
3454 3995 7.418408 TGCTCTTAATCTGTTATCACGAGTAG 58.582 38.462 0.00 0.00 0.00 2.57
3455 3996 7.282450 TGCTCTTAATCTGTTATCACGAGTAGA 59.718 37.037 0.00 0.00 0.00 2.59
3456 3997 8.293867 GCTCTTAATCTGTTATCACGAGTAGAT 58.706 37.037 0.00 0.00 0.00 1.98
3638 4181 6.466308 TTCAGTTGTGATTCATAAGTGACG 57.534 37.500 24.78 6.76 41.89 4.35
3639 4182 5.538118 TCAGTTGTGATTCATAAGTGACGT 58.462 37.500 22.48 0.00 39.02 4.34
3743 4286 3.766051 ACCATGAGAAGGAAGATTTTGCC 59.234 43.478 0.00 0.00 0.00 4.52
3893 4436 4.218312 AGACAGGTGAATTCAAAGGCTTT 58.782 39.130 10.35 6.68 0.00 3.51
3896 4439 2.699846 AGGTGAATTCAAAGGCTTTGCA 59.300 40.909 30.40 22.97 40.43 4.08
4004 4547 4.518211 AGATGTGCTGTTCCAAAGAAAGAG 59.482 41.667 0.00 0.00 32.58 2.85
4017 4560 5.221126 CCAAAGAAAGAGAACCAGAAACCAG 60.221 44.000 0.00 0.00 0.00 4.00
4037 4583 4.320057 CCAGATGACAAAGCAACTTCAGAC 60.320 45.833 0.00 0.00 0.00 3.51
4649 5195 3.584733 AAGGCCACTGAGATTAATCCC 57.415 47.619 11.92 0.39 0.00 3.85
4660 5206 3.041946 AGATTAATCCCGAGGAAGCAGT 58.958 45.455 11.92 0.00 34.34 4.40
4761 5307 4.319839 CGCCTCCAAAGAAAAAGAAGAGAC 60.320 45.833 0.00 0.00 0.00 3.36
4853 5399 4.277423 CGGTGGACCAGTTACTTTTTGATT 59.723 41.667 0.00 0.00 35.14 2.57
4962 5508 8.340618 ACATTTTACAGAGCAATCTTGTATGT 57.659 30.769 0.00 0.00 0.00 2.29
5001 5547 9.574516 GTTGTATCTTCCATTTACCCTTATCAT 57.425 33.333 0.00 0.00 0.00 2.45
5056 5602 1.538047 AGTTTGGCTGCGTGATGAAT 58.462 45.000 0.00 0.00 0.00 2.57
5061 5607 0.308993 GGCTGCGTGATGAATTAGGC 59.691 55.000 0.00 0.00 0.00 3.93
5068 5617 2.868583 CGTGATGAATTAGGCAGTCCAG 59.131 50.000 0.00 0.00 33.74 3.86
5101 5650 8.365399 TCTATGTGCACTGTATTTGCTATTAC 57.635 34.615 19.41 0.00 40.86 1.89
5126 5675 9.255029 ACAGCTTATTAATACCAGGAACAAATT 57.745 29.630 0.00 0.00 0.00 1.82
5128 5677 8.197439 AGCTTATTAATACCAGGAACAAATTGC 58.803 33.333 0.00 0.00 0.00 3.56
5141 5690 6.601613 AGGAACAAATTGCAGTATCCGAAATA 59.398 34.615 0.00 0.00 0.00 1.40
5143 5692 7.379529 GGAACAAATTGCAGTATCCGAAATATG 59.620 37.037 0.00 0.00 0.00 1.78
5149 5698 6.358118 TGCAGTATCCGAAATATGTTGTTC 57.642 37.500 0.00 0.00 0.00 3.18
5163 5712 8.925161 AATATGTTGTTCCAACCATTATTTCG 57.075 30.769 4.78 0.00 0.00 3.46
5164 5713 5.776173 TGTTGTTCCAACCATTATTTCGT 57.224 34.783 4.78 0.00 0.00 3.85
5165 5714 6.150396 TGTTGTTCCAACCATTATTTCGTT 57.850 33.333 4.78 0.00 0.00 3.85
5179 5728 7.254455 CCATTATTTCGTTCCTGTGCTAACTAG 60.254 40.741 0.00 0.00 0.00 2.57
5234 5783 9.988815 AATTACTAGAGATAGTATTGGCTTGTG 57.011 33.333 0.00 0.00 33.10 3.33
5387 5959 5.816777 TGTATGTGTGTGATGACATGTATGG 59.183 40.000 0.00 0.00 34.60 2.74
5549 6129 0.984230 CAGGCAGGGAGGTTCTAACA 59.016 55.000 0.00 0.00 0.00 2.41
5603 6183 3.136763 CTGCTGCTCTTTTCTCTGACAA 58.863 45.455 0.00 0.00 0.00 3.18
5634 6214 9.705290 TTAACTCTTTCTCAAAAAGCAAGTTTT 57.295 25.926 8.82 0.00 40.26 2.43
5637 6217 8.090831 ACTCTTTCTCAAAAAGCAAGTTTTTCT 58.909 29.630 0.00 0.00 44.93 2.52
5667 6247 2.070262 TGTCACTCATGAGAGCAACG 57.930 50.000 29.27 9.65 46.09 4.10
5681 6261 0.385473 GCAACGGGTTGTTCATGACG 60.385 55.000 12.65 0.00 42.31 4.35
5692 6275 4.082274 TGTTCATGACGATGATTTGTGC 57.918 40.909 0.00 0.00 38.43 4.57
5700 6283 3.888934 ACGATGATTTGTGCTTGTCAAC 58.111 40.909 0.00 0.00 0.00 3.18
5728 6311 3.098774 TGCCTTCTTTATCCATTGGCA 57.901 42.857 0.00 0.00 45.31 4.92
5730 6313 3.290710 GCCTTCTTTATCCATTGGCAGA 58.709 45.455 0.00 0.00 38.79 4.26
5731 6314 3.701040 GCCTTCTTTATCCATTGGCAGAA 59.299 43.478 0.00 2.63 38.79 3.02
5736 6319 6.271488 TCTTTATCCATTGGCAGAACAAAG 57.729 37.500 0.00 1.93 33.48 2.77
5772 6355 8.348285 TCACTTTCCATTATTTCTTTGGTAGG 57.652 34.615 0.00 0.00 0.00 3.18
5788 6371 2.038952 GGTAGGTGGTTTCGGTTAACCT 59.961 50.000 22.12 2.63 46.28 3.50
5789 6372 3.260632 GGTAGGTGGTTTCGGTTAACCTA 59.739 47.826 22.12 9.06 46.28 3.08
5792 6375 3.583966 AGGTGGTTTCGGTTAACCTATGA 59.416 43.478 22.12 9.66 46.28 2.15
5795 6378 3.839490 TGGTTTCGGTTAACCTATGAGGA 59.161 43.478 22.12 8.21 46.28 3.71
5797 6380 5.045432 TGGTTTCGGTTAACCTATGAGGATT 60.045 40.000 22.12 0.00 46.28 3.01
5799 6382 6.376299 GGTTTCGGTTAACCTATGAGGATTTT 59.624 38.462 22.12 0.00 43.44 1.82
5801 6384 5.433526 TCGGTTAACCTATGAGGATTTTGG 58.566 41.667 22.12 1.85 37.67 3.28
5826 6409 2.664567 GCAAATGGCGCACATAACC 58.335 52.632 10.83 0.00 39.40 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.065418 AGACATTAAGGCCCTGTTCGG 60.065 52.381 0.00 0.00 0.00 4.30
3 4 2.280628 GAGACATTAAGGCCCTGTTCG 58.719 52.381 0.00 0.00 0.00 3.95
4 5 2.280628 CGAGACATTAAGGCCCTGTTC 58.719 52.381 0.00 0.00 0.00 3.18
5 6 1.628846 ACGAGACATTAAGGCCCTGTT 59.371 47.619 0.00 0.00 0.00 3.16
6 7 1.066143 CACGAGACATTAAGGCCCTGT 60.066 52.381 0.00 0.00 0.00 4.00
7 8 1.656652 CACGAGACATTAAGGCCCTG 58.343 55.000 0.00 0.00 0.00 4.45
8 9 0.541863 CCACGAGACATTAAGGCCCT 59.458 55.000 0.00 0.00 0.00 5.19
9 10 1.095807 GCCACGAGACATTAAGGCCC 61.096 60.000 0.00 0.00 36.17 5.80
10 11 0.107654 AGCCACGAGACATTAAGGCC 60.108 55.000 0.00 0.00 42.97 5.19
11 12 1.739067 AAGCCACGAGACATTAAGGC 58.261 50.000 0.00 0.00 42.31 4.35
12 13 6.692486 AGATATAAGCCACGAGACATTAAGG 58.308 40.000 0.00 0.00 0.00 2.69
54 55 0.940126 GCCATAACTGGAGTCATGCG 59.060 55.000 0.00 0.00 46.37 4.73
63 64 4.881273 TGTTGTAAGCATAGCCATAACTGG 59.119 41.667 0.00 0.00 46.17 4.00
126 127 1.084289 AGGGTTTATTTGCTCGACGC 58.916 50.000 0.00 0.58 39.77 5.19
136 137 6.211184 TGCTGTTTCAATCATCAGGGTTTATT 59.789 34.615 0.00 0.00 0.00 1.40
142 143 2.821378 TGTGCTGTTTCAATCATCAGGG 59.179 45.455 0.00 0.00 0.00 4.45
143 144 3.504906 AGTGTGCTGTTTCAATCATCAGG 59.495 43.478 0.00 0.00 0.00 3.86
153 154 3.059325 CAGTAGCTTGAGTGTGCTGTTTC 60.059 47.826 0.00 0.00 40.08 2.78
165 166 2.432146 CTGGCTGGTATCAGTAGCTTGA 59.568 50.000 4.60 0.00 42.78 3.02
179 180 0.540365 ACCATGTGTTTCCTGGCTGG 60.540 55.000 3.65 3.65 35.65 4.85
186 187 6.569179 AGTTGTATGTAACCATGTGTTTCC 57.431 37.500 5.12 0.00 38.42 3.13
206 207 4.878397 GTGCTGAGCAATCCTTGTATAGTT 59.122 41.667 9.51 0.00 41.47 2.24
225 226 2.543848 CGTGTATAATCAATGCCGTGCT 59.456 45.455 0.00 0.00 0.00 4.40
284 290 1.197721 GTTGTCTCAGTTTGCCATCCG 59.802 52.381 0.00 0.00 0.00 4.18
299 305 2.227388 CCCTTCTGTGCTTCATGTTGTC 59.773 50.000 0.00 0.00 0.00 3.18
425 437 2.009774 CTCGATGCCTGGTTAACTTGG 58.990 52.381 5.42 9.02 0.00 3.61
428 440 2.832129 TCTTCTCGATGCCTGGTTAACT 59.168 45.455 5.42 0.00 0.00 2.24
429 441 3.119101 TCTCTTCTCGATGCCTGGTTAAC 60.119 47.826 0.00 0.00 0.00 2.01
430 442 3.096852 TCTCTTCTCGATGCCTGGTTAA 58.903 45.455 0.00 0.00 0.00 2.01
431 443 2.735151 TCTCTTCTCGATGCCTGGTTA 58.265 47.619 0.00 0.00 0.00 2.85
432 444 1.561643 TCTCTTCTCGATGCCTGGTT 58.438 50.000 0.00 0.00 0.00 3.67
433 445 1.561643 TTCTCTTCTCGATGCCTGGT 58.438 50.000 0.00 0.00 0.00 4.00
454 466 4.113815 CCCTCCCAATCTGCGCCA 62.114 66.667 4.18 0.00 0.00 5.69
459 471 1.639635 CCTCCACCCCTCCCAATCTG 61.640 65.000 0.00 0.00 0.00 2.90
460 472 1.308216 CCTCCACCCCTCCCAATCT 60.308 63.158 0.00 0.00 0.00 2.40
462 474 2.287194 CCCTCCACCCCTCCCAAT 60.287 66.667 0.00 0.00 0.00 3.16
463 475 2.662971 TTTCCCTCCACCCCTCCCAA 62.663 60.000 0.00 0.00 0.00 4.12
464 476 2.446337 ATTTCCCTCCACCCCTCCCA 62.446 60.000 0.00 0.00 0.00 4.37
465 477 1.622752 ATTTCCCTCCACCCCTCCC 60.623 63.158 0.00 0.00 0.00 4.30
490 517 0.876342 CCGCCGAGAAGTAATGAGCC 60.876 60.000 0.00 0.00 0.00 4.70
780 813 4.936248 CGAGCGAGCGAGAGAGCG 62.936 72.222 0.00 0.00 43.00 5.03
789 822 4.973360 CCTAGCGAGCGAGCGAGC 62.973 72.222 10.12 9.12 43.00 5.03
790 823 4.320928 CCCTAGCGAGCGAGCGAG 62.321 72.222 8.97 8.97 43.00 5.03
792 825 4.194720 AACCCTAGCGAGCGAGCG 62.195 66.667 0.00 0.00 43.00 5.03
892 950 1.406539 GCTGATGTGGGCCTTACATTG 59.593 52.381 21.59 18.28 38.78 2.82
893 951 1.686115 GGCTGATGTGGGCCTTACATT 60.686 52.381 21.59 10.03 44.48 2.71
895 953 1.302949 GGCTGATGTGGGCCTTACA 59.697 57.895 14.26 14.26 44.48 2.41
896 954 1.453928 GGGCTGATGTGGGCCTTAC 60.454 63.158 4.53 2.84 46.80 2.34
897 955 3.006677 GGGCTGATGTGGGCCTTA 58.993 61.111 4.53 0.00 46.80 2.69
898 956 4.431131 CGGGCTGATGTGGGCCTT 62.431 66.667 4.53 0.00 46.80 4.35
906 964 1.480212 TATAGTGGGCCGGGCTGATG 61.480 60.000 28.80 0.00 0.00 3.07
921 979 1.332997 ACGAGACGGCGAGGTTTATAG 59.667 52.381 16.62 0.00 34.83 1.31
931 989 1.512310 GAGACTTGACGAGACGGCG 60.512 63.158 4.80 4.80 37.93 6.46
943 1006 2.007636 AGAGGGGAGAGGAAGAGACTT 58.992 52.381 0.00 0.00 0.00 3.01
944 1007 1.569072 GAGAGGGGAGAGGAAGAGACT 59.431 57.143 0.00 0.00 0.00 3.24
961 1027 4.331968 GAGTGGAGAGAAAGACAGAGAGA 58.668 47.826 0.00 0.00 0.00 3.10
966 1032 1.403514 GCGGAGTGGAGAGAAAGACAG 60.404 57.143 0.00 0.00 0.00 3.51
968 1034 0.108567 GGCGGAGTGGAGAGAAAGAC 60.109 60.000 0.00 0.00 0.00 3.01
970 1036 1.153745 CGGCGGAGTGGAGAGAAAG 60.154 63.158 0.00 0.00 0.00 2.62
972 1038 3.760035 GCGGCGGAGTGGAGAGAA 61.760 66.667 9.78 0.00 0.00 2.87
1085 1160 2.237392 AGCCGCACCTTTATCTTCTTCT 59.763 45.455 0.00 0.00 0.00 2.85
1088 1163 1.407437 CCAGCCGCACCTTTATCTTCT 60.407 52.381 0.00 0.00 0.00 2.85
1305 1425 2.131067 CCTCCTCTCCTTCCTCCGC 61.131 68.421 0.00 0.00 0.00 5.54
1371 1491 2.747855 GCCTCCGCCAACTTCCTG 60.748 66.667 0.00 0.00 0.00 3.86
1398 1518 1.347817 CGTCAGACTTCTTGCTCGCC 61.348 60.000 0.00 0.00 0.00 5.54
1403 1523 1.989430 CTCTCCGTCAGACTTCTTGC 58.011 55.000 0.00 0.00 0.00 4.01
1445 1565 1.125093 AAGGTCGTCACCACCATCCA 61.125 55.000 0.00 0.00 46.68 3.41
1449 1569 1.745890 CTCAAGGTCGTCACCACCA 59.254 57.895 0.00 0.00 46.68 4.17
1454 1574 1.079750 GGCTCCTCAAGGTCGTCAC 60.080 63.158 0.00 0.00 36.34 3.67
1590 1710 0.716108 CAGACTTCTTGTTAGCCGCG 59.284 55.000 0.00 0.00 0.00 6.46
1596 1716 5.423015 GCCTCATCATCAGACTTCTTGTTA 58.577 41.667 0.00 0.00 0.00 2.41
1654 1774 2.158986 ACCTATCATCTGACACAGCTGC 60.159 50.000 15.27 0.00 29.04 5.25
1656 1776 3.369175 TCACCTATCATCTGACACAGCT 58.631 45.455 0.00 0.00 0.00 4.24
1659 1779 4.081476 CCAACTCACCTATCATCTGACACA 60.081 45.833 0.00 0.00 0.00 3.72
1663 1783 2.101415 CGCCAACTCACCTATCATCTGA 59.899 50.000 0.00 0.00 0.00 3.27
1668 1788 0.613260 AAGCGCCAACTCACCTATCA 59.387 50.000 2.29 0.00 0.00 2.15
1681 1801 0.729140 CACCAATTTGTCGAAGCGCC 60.729 55.000 2.29 0.00 0.00 6.53
1682 1802 1.337110 GCACCAATTTGTCGAAGCGC 61.337 55.000 0.00 0.00 0.00 5.92
1714 1842 5.061179 TGAACCTAACAGCAAAAGAGGTAC 58.939 41.667 0.00 0.00 39.65 3.34
1721 1849 2.961741 TGGCATGAACCTAACAGCAAAA 59.038 40.909 0.00 0.00 0.00 2.44
1726 1854 4.769688 TCTACATGGCATGAACCTAACAG 58.230 43.478 32.74 14.87 0.00 3.16
1755 1883 7.482654 TCTTAACATCAAGAGTTCAACACAG 57.517 36.000 0.00 0.00 31.01 3.66
1769 1897 5.887598 ACTAAGCAATGGCATCTTAACATCA 59.112 36.000 0.00 0.00 44.61 3.07
1770 1898 6.382869 ACTAAGCAATGGCATCTTAACATC 57.617 37.500 0.00 0.00 44.61 3.06
1808 2054 8.807948 AGGCATTTACAATGTTATGACTACTT 57.192 30.769 12.84 0.00 34.66 2.24
1809 2055 8.807948 AAGGCATTTACAATGTTATGACTACT 57.192 30.769 14.26 1.33 35.35 2.57
1810 2056 8.673711 TGAAGGCATTTACAATGTTATGACTAC 58.326 33.333 14.26 4.23 35.35 2.73
1811 2057 8.800370 TGAAGGCATTTACAATGTTATGACTA 57.200 30.769 14.26 1.33 35.35 2.59
1857 2103 4.511527 ACTACAGCTCTTCCAACATGATG 58.488 43.478 0.00 0.00 0.00 3.07
1868 2114 4.217983 AGTTGCTTACGTACTACAGCTCTT 59.782 41.667 15.84 1.73 33.15 2.85
1911 2157 7.464577 GCAAAAGGTGTTTTTCTCAGATCAAAC 60.465 37.037 0.00 3.83 36.87 2.93
1918 2164 4.033243 GCAAGCAAAAGGTGTTTTTCTCAG 59.967 41.667 0.00 0.00 36.87 3.35
2132 2380 0.325671 TCCTTCGCCTCTCCTTCCAT 60.326 55.000 0.00 0.00 0.00 3.41
2249 2497 3.391296 TCAAGAACTCTGCCCTTTACAGT 59.609 43.478 0.00 0.00 36.50 3.55
2259 2507 4.529109 AGAAGGTACTCAAGAACTCTGC 57.471 45.455 0.00 0.00 38.49 4.26
2260 2508 6.754193 AGAAAGAAGGTACTCAAGAACTCTG 58.246 40.000 0.00 0.00 38.49 3.35
2262 2510 6.750148 TGAGAAAGAAGGTACTCAAGAACTC 58.250 40.000 0.00 0.00 38.49 3.01
2277 2532 9.883293 TCCTCATACCTATCTAATGAGAAAGAA 57.117 33.333 12.01 0.00 46.22 2.52
2286 2541 6.780901 TCGTCTGTCCTCATACCTATCTAAT 58.219 40.000 0.00 0.00 0.00 1.73
2290 2545 6.824196 TGATATCGTCTGTCCTCATACCTATC 59.176 42.308 0.00 0.00 0.00 2.08
2298 2553 5.592688 TGTTATGTGATATCGTCTGTCCTCA 59.407 40.000 0.00 0.00 0.00 3.86
2305 2560 4.584743 TGCCTCTGTTATGTGATATCGTCT 59.415 41.667 0.00 0.00 0.00 4.18
2308 2563 5.233225 ACATGCCTCTGTTATGTGATATCG 58.767 41.667 0.00 0.00 34.04 2.92
2314 2569 5.178061 TGTCTTACATGCCTCTGTTATGTG 58.822 41.667 0.00 0.00 36.52 3.21
2318 2573 5.011635 TGTCTTGTCTTACATGCCTCTGTTA 59.988 40.000 0.00 0.00 0.00 2.41
2321 2576 3.681897 GTGTCTTGTCTTACATGCCTCTG 59.318 47.826 0.00 0.00 0.00 3.35
2330 2585 4.570772 TGCAGAAACAGTGTCTTGTCTTAC 59.429 41.667 0.00 0.00 0.00 2.34
2371 2626 9.477484 CTTAGTCACTAACTCACTGTGTTATTT 57.523 33.333 7.79 0.26 39.55 1.40
2379 2634 7.539436 TGCTATTCTTAGTCACTAACTCACTG 58.461 38.462 0.00 0.00 39.55 3.66
2391 2646 6.105333 CCATCCTGCTATGCTATTCTTAGTC 58.895 44.000 0.00 0.00 0.00 2.59
2395 2650 3.912528 TCCCATCCTGCTATGCTATTCTT 59.087 43.478 0.00 0.00 0.00 2.52
2403 2658 3.755378 GCAATAAGTCCCATCCTGCTATG 59.245 47.826 0.00 0.00 0.00 2.23
2412 2667 7.806180 ACTTCTAACTATGCAATAAGTCCCAT 58.194 34.615 0.00 0.00 0.00 4.00
2417 2672 7.010552 CGAGCAACTTCTAACTATGCAATAAGT 59.989 37.037 0.00 0.00 39.42 2.24
2418 2673 7.340699 CGAGCAACTTCTAACTATGCAATAAG 58.659 38.462 0.00 0.00 39.42 1.73
2421 2676 4.572389 CCGAGCAACTTCTAACTATGCAAT 59.428 41.667 0.00 0.00 39.42 3.56
2424 2679 3.552294 GTCCGAGCAACTTCTAACTATGC 59.448 47.826 0.00 0.00 37.28 3.14
2425 2680 5.000012 AGTCCGAGCAACTTCTAACTATG 58.000 43.478 0.00 0.00 0.00 2.23
2426 2681 5.411781 CAAGTCCGAGCAACTTCTAACTAT 58.588 41.667 0.00 0.00 34.79 2.12
2427 2682 4.321750 CCAAGTCCGAGCAACTTCTAACTA 60.322 45.833 0.00 0.00 34.79 2.24
2429 2684 2.737252 CCAAGTCCGAGCAACTTCTAAC 59.263 50.000 0.00 0.00 34.79 2.34
2430 2685 2.631062 TCCAAGTCCGAGCAACTTCTAA 59.369 45.455 0.00 0.00 34.79 2.10
2432 2687 1.048601 TCCAAGTCCGAGCAACTTCT 58.951 50.000 0.00 0.00 34.79 2.85
2433 2688 1.149148 GTCCAAGTCCGAGCAACTTC 58.851 55.000 0.00 0.00 34.79 3.01
2434 2689 0.759346 AGTCCAAGTCCGAGCAACTT 59.241 50.000 0.00 0.00 37.44 2.66
2442 2698 1.178276 AGCTAGACAGTCCAAGTCCG 58.822 55.000 0.00 0.00 36.68 4.79
2452 2708 3.397482 AGTCAACAGCAAAGCTAGACAG 58.603 45.455 15.71 0.00 36.40 3.51
2459 2715 4.913924 CACTATTTGAGTCAACAGCAAAGC 59.086 41.667 4.68 0.00 35.64 3.51
2464 2720 5.869753 ACATCACTATTTGAGTCAACAGC 57.130 39.130 4.68 0.00 37.77 4.40
2479 2735 7.065085 GCACTATTTGAGTCAACATACATCACT 59.935 37.037 4.68 0.00 35.64 3.41
2483 2739 6.881065 ACAGCACTATTTGAGTCAACATACAT 59.119 34.615 4.68 0.00 35.64 2.29
2484 2740 6.230472 ACAGCACTATTTGAGTCAACATACA 58.770 36.000 4.68 0.00 35.64 2.29
2485 2741 6.727824 ACAGCACTATTTGAGTCAACATAC 57.272 37.500 4.68 0.00 35.64 2.39
2488 2744 6.202762 CAGTTACAGCACTATTTGAGTCAACA 59.797 38.462 4.68 0.00 35.64 3.33
2489 2745 6.202954 ACAGTTACAGCACTATTTGAGTCAAC 59.797 38.462 4.68 0.00 35.64 3.18
2491 2747 5.853936 ACAGTTACAGCACTATTTGAGTCA 58.146 37.500 0.00 0.00 35.64 3.41
2492 2748 6.866770 TGTACAGTTACAGCACTATTTGAGTC 59.133 38.462 0.00 0.00 32.42 3.36
2493 2749 6.755206 TGTACAGTTACAGCACTATTTGAGT 58.245 36.000 0.00 0.00 34.05 3.41
2494 2750 7.283254 CTGTACAGTTACAGCACTATTTGAG 57.717 40.000 15.06 0.00 46.80 3.02
2506 2762 9.203421 CAATTTCTGATGTACTGTACAGTTACA 57.797 33.333 32.15 28.51 42.77 2.41
2507 2763 9.204570 ACAATTTCTGATGTACTGTACAGTTAC 57.795 33.333 32.15 24.75 42.77 2.50
2508 2764 9.772973 AACAATTTCTGATGTACTGTACAGTTA 57.227 29.630 32.15 21.62 42.77 2.24
2509 2765 8.677148 AACAATTTCTGATGTACTGTACAGTT 57.323 30.769 32.15 15.94 42.77 3.16
2510 2766 8.559536 CAAACAATTTCTGATGTACTGTACAGT 58.440 33.333 30.13 30.13 42.77 3.55
2511 2767 7.535258 GCAAACAATTTCTGATGTACTGTACAG 59.465 37.037 23.35 21.44 42.77 2.74
2512 2768 7.228507 AGCAAACAATTTCTGATGTACTGTACA 59.771 33.333 21.68 21.68 43.80 2.90
2513 2769 7.584987 AGCAAACAATTTCTGATGTACTGTAC 58.415 34.615 10.98 10.98 0.00 2.90
2669 3088 2.840651 AGAACCTTATCTCCACCCTGTG 59.159 50.000 0.00 0.00 0.00 3.66
2683 3102 5.440610 CTGCCAACATCCTATAAGAACCTT 58.559 41.667 0.00 0.00 0.00 3.50
2823 3242 1.405463 CAGTCCAGCGCAGTGATACTA 59.595 52.381 11.47 0.00 0.00 1.82
2907 3326 4.301628 AGAACAAAGGGTACTACGTTTCG 58.698 43.478 0.00 0.00 0.00 3.46
2919 3338 4.638421 TGAACACAACACTAGAACAAAGGG 59.362 41.667 0.00 0.00 0.00 3.95
2933 3352 3.311106 CCTGCATGAACATGAACACAAC 58.689 45.455 17.40 0.32 41.20 3.32
2937 3356 1.618487 TGCCTGCATGAACATGAACA 58.382 45.000 17.40 6.89 41.20 3.18
3030 3552 6.199908 CACAGTTAATTGAATCAAAACGCCAA 59.800 34.615 4.81 0.00 0.00 4.52
3047 3569 6.071051 TCAGACTGCCATACATACACAGTTAA 60.071 38.462 0.00 0.00 41.45 2.01
3112 3649 6.267471 ACCAAAAGACCTTAAAGATGAATGCA 59.733 34.615 0.00 0.00 0.00 3.96
3178 3715 3.005791 TCGATGAGAGTTCTGCTCAAACA 59.994 43.478 0.00 0.00 46.47 2.83
3221 3758 2.238646 TGGTATCGAGCCAACTCCAATT 59.761 45.455 8.81 0.00 40.03 2.32
3272 3809 3.268330 CACTGCTGATAAGTCATGTGCT 58.732 45.455 0.00 0.00 32.98 4.40
3283 3820 4.335400 TGACTGAAACACACTGCTGATA 57.665 40.909 0.00 0.00 0.00 2.15
3292 3829 2.538037 CGACGACAATGACTGAAACACA 59.462 45.455 0.00 0.00 0.00 3.72
3310 3847 0.250513 AGGCAGATCCTCCAAACGAC 59.749 55.000 0.00 0.00 43.20 4.34
3312 3849 0.036010 ACAGGCAGATCCTCCAAACG 60.036 55.000 3.96 0.00 45.52 3.60
3324 3861 3.126514 CACAAGATTCAAGCTACAGGCAG 59.873 47.826 0.00 0.00 44.79 4.85
3380 3917 9.069082 TCCGATGGACTAAAATGAAACTAAAAA 57.931 29.630 0.00 0.00 0.00 1.94
3381 3918 8.624367 TCCGATGGACTAAAATGAAACTAAAA 57.376 30.769 0.00 0.00 0.00 1.52
3403 3940 0.389948 GGTGGTACAAGCTGACTCCG 60.390 60.000 0.00 0.00 44.16 4.63
3453 3994 7.052248 TGCTGATGAGTCATGTGAATTAATCT 58.948 34.615 11.20 0.00 32.98 2.40
3454 3995 7.255491 TGCTGATGAGTCATGTGAATTAATC 57.745 36.000 11.20 0.00 32.98 1.75
3455 3996 6.238676 GCTGCTGATGAGTCATGTGAATTAAT 60.239 38.462 11.20 0.00 32.98 1.40
3456 3997 5.065602 GCTGCTGATGAGTCATGTGAATTAA 59.934 40.000 11.20 0.00 32.98 1.40
3562 4105 4.214971 GCTTACATATCTGCACCATCAAGG 59.785 45.833 0.00 0.00 45.67 3.61
3638 4181 7.042119 CCCCTGTGATTGTTTAACAAAAATGAC 60.042 37.037 14.70 3.86 41.96 3.06
3639 4182 6.989169 CCCCTGTGATTGTTTAACAAAAATGA 59.011 34.615 14.70 0.00 41.96 2.57
3743 4286 6.439636 TTGTATCCCTCTATCATCTTTGGG 57.560 41.667 0.00 0.00 36.14 4.12
3893 4436 6.094719 GCTATCAGAAAAATCAACATGTGCA 58.905 36.000 0.00 0.00 0.00 4.57
3896 4439 7.218228 TGTGCTATCAGAAAAATCAACATGT 57.782 32.000 0.00 0.00 0.00 3.21
3934 4477 1.795286 CGTTCTGGTCAAGCTTCAGAC 59.205 52.381 14.15 11.21 37.28 3.51
4004 4547 4.557496 GCTTTGTCATCTGGTTTCTGGTTC 60.557 45.833 0.00 0.00 0.00 3.62
4017 4560 4.512944 TGAGTCTGAAGTTGCTTTGTCATC 59.487 41.667 0.00 0.00 0.00 2.92
4037 4583 5.408299 TGTACGGATGTTGTTCTTTGATGAG 59.592 40.000 0.00 0.00 0.00 2.90
4649 5195 2.767505 ACAGGTTTAACTGCTTCCTCG 58.232 47.619 0.00 0.00 42.21 4.63
4660 5206 2.738587 TGAGCCACCAACAGGTTTAA 57.261 45.000 0.00 0.00 31.84 1.52
4736 5282 0.958822 TCTTTTTCTTTGGAGGCGCC 59.041 50.000 21.89 21.89 37.10 6.53
4761 5307 1.559814 CGCATTCATAGCACGTCCG 59.440 57.895 0.00 0.00 0.00 4.79
4853 5399 1.675219 GAACGAAGGGGCACTACCA 59.325 57.895 0.00 0.00 42.05 3.25
4962 5508 6.210584 TGGAAGATACAACATGTGTCTACTGA 59.789 38.462 9.69 0.00 46.04 3.41
5056 5602 4.353777 AGATTGAGTACTGGACTGCCTAA 58.646 43.478 0.00 0.00 39.06 2.69
5061 5607 5.046529 GCACATAGATTGAGTACTGGACTG 58.953 45.833 0.00 0.00 39.06 3.51
5063 5609 4.806247 GTGCACATAGATTGAGTACTGGAC 59.194 45.833 13.17 0.00 30.83 4.02
5068 5617 8.331022 CAAATACAGTGCACATAGATTGAGTAC 58.669 37.037 21.04 0.00 33.00 2.73
5101 5650 9.520204 CAATTTGTTCCTGGTATTAATAAGCTG 57.480 33.333 0.00 0.00 0.00 4.24
5110 5659 6.096846 GGATACTGCAATTTGTTCCTGGTATT 59.903 38.462 0.00 0.00 0.00 1.89
5126 5675 5.295787 GGAACAACATATTTCGGATACTGCA 59.704 40.000 0.00 0.00 0.00 4.41
5128 5677 6.918892 TGGAACAACATATTTCGGATACTG 57.081 37.500 0.00 0.00 31.92 2.74
5149 5698 4.732784 CACAGGAACGAAATAATGGTTGG 58.267 43.478 0.00 0.00 29.21 3.77
5179 5728 5.967674 CAGATGTATCTTCAAAACCGAATGC 59.032 40.000 0.00 0.00 34.22 3.56
5213 5762 7.721402 AGTTCACAAGCCAATACTATCTCTAG 58.279 38.462 0.00 0.00 0.00 2.43
5223 5772 5.076182 TCCATTTGAGTTCACAAGCCAATA 58.924 37.500 0.00 0.00 0.00 1.90
5234 5783 5.901552 TGTTTGGTTTCTCCATTTGAGTTC 58.098 37.500 0.00 0.00 46.60 3.01
5270 5819 5.235186 CCTAATGCTTTGTAAGATCTCACGG 59.765 44.000 0.00 0.00 0.00 4.94
5549 6129 2.883828 CGGGGCTGGAACTCACACT 61.884 63.158 0.00 0.00 0.00 3.55
5603 6183 8.225603 TGCTTTTTGAGAAAGAGTTAAGTCAT 57.774 30.769 12.77 0.00 0.00 3.06
5634 6214 3.054728 TGAGTGACAAACTGGGTGAAGAA 60.055 43.478 0.00 0.00 40.07 2.52
5635 6215 2.503765 TGAGTGACAAACTGGGTGAAGA 59.496 45.455 0.00 0.00 40.07 2.87
5637 6217 3.118075 TCATGAGTGACAAACTGGGTGAA 60.118 43.478 0.00 0.00 40.07 3.18
5667 6247 4.082787 ACAAATCATCGTCATGAACAACCC 60.083 41.667 0.00 0.00 42.53 4.11
5681 6261 5.978919 TGAAAGTTGACAAGCACAAATCATC 59.021 36.000 0.00 0.00 0.00 2.92
5692 6275 5.594926 AGAAGGCAATTGAAAGTTGACAAG 58.405 37.500 10.34 0.00 37.05 3.16
5700 6283 7.279313 CCAATGGATAAAGAAGGCAATTGAAAG 59.721 37.037 10.34 0.00 0.00 2.62
5746 6329 8.971073 CCTACCAAAGAAATAATGGAAAGTGAT 58.029 33.333 0.00 0.00 37.66 3.06
5748 6331 8.028938 CACCTACCAAAGAAATAATGGAAAGTG 58.971 37.037 0.00 0.00 37.66 3.16
5749 6332 7.178451 CCACCTACCAAAGAAATAATGGAAAGT 59.822 37.037 0.00 0.00 37.66 2.66
5751 6334 7.013834 ACCACCTACCAAAGAAATAATGGAAA 58.986 34.615 0.00 0.00 37.66 3.13
5752 6335 6.557568 ACCACCTACCAAAGAAATAATGGAA 58.442 36.000 0.00 0.00 37.66 3.53
5754 6337 6.850752 AACCACCTACCAAAGAAATAATGG 57.149 37.500 0.00 0.00 40.16 3.16
5755 6338 7.027161 CGAAACCACCTACCAAAGAAATAATG 58.973 38.462 0.00 0.00 0.00 1.90
5762 6345 1.770061 ACCGAAACCACCTACCAAAGA 59.230 47.619 0.00 0.00 0.00 2.52
5766 6349 2.224499 GGTTAACCGAAACCACCTACCA 60.224 50.000 9.34 0.00 46.85 3.25
5788 6371 1.810031 CGAGGCGCCAAAATCCTCATA 60.810 52.381 31.54 0.00 45.04 2.15
5789 6372 1.097547 CGAGGCGCCAAAATCCTCAT 61.098 55.000 31.54 2.38 45.04 2.90


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

AutoCloner maintained by Alex Coulton.