Multiple sequence alignment - TraesCS2D01G500700

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 TraesCS2D01G500700 chr2D 100.000 1935 0 0 798 2732 595168117 595166183 0.000000e+00 3574.0
1 TraesCS2D01G500700 chr2D 100.000 593 0 0 1 593 595168914 595168322 0.000000e+00 1096.0
2 TraesCS2D01G500700 chr2D 100.000 29 0 0 1 29 146303421 146303393 1.000000e-03 54.7
3 TraesCS2D01G500700 chr2A 88.553 1057 78 19 908 1944 729299543 729298510 0.000000e+00 1242.0
4 TraesCS2D01G500700 chr2A 87.040 571 65 6 24 593 729301027 729300465 1.070000e-178 636.0
5 TraesCS2D01G500700 chr2A 83.404 235 21 7 2512 2730 729298061 729297829 4.610000e-48 202.0
6 TraesCS2D01G500700 chr2A 93.814 97 5 1 1962 2057 729298401 729298305 7.880000e-31 145.0
7 TraesCS2D01G500700 chr2A 100.000 29 0 0 1 29 31878383 31878411 1.000000e-03 54.7
8 TraesCS2D01G500700 chr2B 84.015 1051 90 33 908 1931 722638519 722637520 0.000000e+00 939.0
9 TraesCS2D01G500700 chr2B 85.306 245 22 10 2099 2339 722635014 722634780 9.780000e-60 241.0
10 TraesCS2D01G500700 chr2B 81.633 245 13 13 2516 2732 722634701 722634461 1.010000e-39 174.0
11 TraesCS2D01G500700 chr2B 80.420 143 11 7 1928 2057 722637415 722637277 2.900000e-15 93.5
12 TraesCS2D01G500700 chr3D 96.512 86 3 0 2425 2510 372318643 372318728 2.840000e-30 143.0
13 TraesCS2D01G500700 chr3D 100.000 29 0 0 1 29 551347552 551347524 1.000000e-03 54.7
14 TraesCS2D01G500700 chr3B 94.253 87 5 0 2424 2510 486382224 486382310 1.710000e-27 134.0
15 TraesCS2D01G500700 chr3B 94.286 35 2 0 845 879 133828220 133828186 1.000000e-03 54.7
16 TraesCS2D01G500700 chr4A 91.765 85 7 0 2426 2510 187263801 187263717 4.780000e-23 119.0
17 TraesCS2D01G500700 chr7D 89.655 87 9 0 2425 2511 602187767 602187853 8.000000e-21 111.0
18 TraesCS2D01G500700 chr5D 88.043 92 11 0 2426 2517 354501968 354502059 2.880000e-20 110.0
19 TraesCS2D01G500700 chr5D 100.000 30 0 0 844 873 46306466 46306437 3.800000e-04 56.5
20 TraesCS2D01G500700 chr4B 90.411 73 4 2 2442 2514 370424107 370424038 2.900000e-15 93.5
21 TraesCS2D01G500700 chr1D 83.516 91 14 1 2425 2514 494146256 494146346 1.740000e-12 84.2
22 TraesCS2D01G500700 chr1B 88.571 70 7 1 2425 2493 687410542 687410611 1.740000e-12 84.2
23 TraesCS2D01G500700 chr1B 100.000 29 0 0 1 29 541385224 541385252 1.000000e-03 54.7
24 TraesCS2D01G500700 chr7A 85.897 78 10 1 2443 2520 651088032 651087956 6.270000e-12 82.4
25 TraesCS2D01G500700 chr7A 100.000 29 0 0 1 29 504735073 504735101 1.000000e-03 54.7
26 TraesCS2D01G500700 chr6B 100.000 29 0 0 1 29 332417171 332417199 1.000000e-03 54.7
27 TraesCS2D01G500700 chr6B 100.000 29 0 0 1 29 423195909 423195881 1.000000e-03 54.7
28 TraesCS2D01G500700 chr5B 100.000 29 0 0 1 29 448283739 448283767 1.000000e-03 54.7
29 TraesCS2D01G500700 chr4D 100.000 29 0 0 1 29 473811873 473811901 1.000000e-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 TraesCS2D01G500700 chr2D 595166183 595168914 2731 True 2335.000 3574 100.00000 1 2732 2 chr2D.!!$R2 2731
1 TraesCS2D01G500700 chr2A 729297829 729301027 3198 True 556.250 1242 88.20275 24 2730 4 chr2A.!!$R1 2706
2 TraesCS2D01G500700 chr2B 722634461 722638519 4058 True 361.875 939 82.84350 908 2732 4 chr2B.!!$R1 1824

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
215 216 0.673333 TGCAACTCCACCGCACTATG 60.673 55.0 0.0 0.0 0.0 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2780 0.17668 ACTCCTACCATGCAGCGAAG 59.823 55.0 0.0 0.0 0.0 3.79 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
34 35 1.123928 GGGAGTAGATGTCACCCCTG 58.876 60.000 0.00 0.00 35.00 4.45
40 41 4.104086 AGTAGATGTCACCCCTGATCAAA 58.896 43.478 0.00 0.00 0.00 2.69
69 70 7.280876 TGTTTGAAAACATAGCTAGCCTATCTG 59.719 37.037 12.13 4.66 43.45 2.90
76 77 1.275856 AGCTAGCCTATCTGCATCAGC 59.724 52.381 12.13 0.00 42.57 4.26
90 91 1.284657 ATCAGCGTTTGATGCTCGAG 58.715 50.000 8.45 8.45 44.84 4.04
111 112 8.149973 TCGAGCTTCAAAAGTAAACTTACAAT 57.850 30.769 2.63 0.00 36.12 2.71
154 155 8.802267 CATTTTTCTAAGTTATTCTTCCCACCA 58.198 33.333 0.00 0.00 37.56 4.17
166 167 7.797121 ATTCTTCCCACCAATTTTCTTGTAT 57.203 32.000 0.00 0.00 0.00 2.29
212 213 2.116983 ATCTGCAACTCCACCGCACT 62.117 55.000 0.00 0.00 0.00 4.40
215 216 0.673333 TGCAACTCCACCGCACTATG 60.673 55.000 0.00 0.00 0.00 2.23
226 227 1.933181 CCGCACTATGTACCACATGTG 59.067 52.381 19.31 19.31 39.53 3.21
244 245 6.635641 CACATGTGACTTCTCAATGTTGAAAG 59.364 38.462 21.64 12.14 36.64 2.62
285 286 7.013559 CCAGAGGTGATCATACAATATTTTGCA 59.986 37.037 0.00 0.00 36.22 4.08
293 294 7.894753 TCATACAATATTTTGCATTCCCTCA 57.105 32.000 0.00 0.00 36.22 3.86
295 296 5.343307 ACAATATTTTGCATTCCCTCACC 57.657 39.130 0.00 0.00 36.22 4.02
314 315 1.602237 CGTAGGTGGTCAGGGCAAT 59.398 57.895 0.00 0.00 0.00 3.56
315 316 0.744414 CGTAGGTGGTCAGGGCAATG 60.744 60.000 0.00 0.00 0.00 2.82
338 339 2.674220 CCTCCCCTCCAAGCTCCAC 61.674 68.421 0.00 0.00 0.00 4.02
339 340 2.610859 TCCCCTCCAAGCTCCACC 60.611 66.667 0.00 0.00 0.00 4.61
360 361 3.512680 CGATTAGACCATAGATTCGCCC 58.487 50.000 0.00 0.00 0.00 6.13
361 362 3.676324 CGATTAGACCATAGATTCGCCCC 60.676 52.174 0.00 0.00 0.00 5.80
362 363 1.640917 TAGACCATAGATTCGCCCCC 58.359 55.000 0.00 0.00 0.00 5.40
384 385 3.854669 CCCTACCCTGCCGCTCTG 61.855 72.222 0.00 0.00 0.00 3.35
385 386 3.854669 CCTACCCTGCCGCTCTGG 61.855 72.222 0.00 0.00 42.50 3.86
410 411 3.158648 TGGCGGGTAGGGGAATCG 61.159 66.667 0.00 0.00 0.00 3.34
411 412 3.159347 GGCGGGTAGGGGAATCGT 61.159 66.667 0.00 0.00 0.00 3.73
421 422 2.511600 GGAATCGTGGTGCCTCGG 60.512 66.667 11.92 0.00 34.27 4.63
439 440 5.241285 GCCTCGGTTCTAGCTAGTAGTTTAT 59.759 44.000 20.10 0.00 0.00 1.40
447 448 8.358895 GTTCTAGCTAGTAGTTTATGTTAGGGG 58.641 40.741 20.10 0.00 0.00 4.79
448 449 7.589993 TCTAGCTAGTAGTTTATGTTAGGGGT 58.410 38.462 20.10 0.00 0.00 4.95
453 454 9.671279 GCTAGTAGTTTATGTTAGGGGTTTTTA 57.329 33.333 0.00 0.00 0.00 1.52
461 462 3.005554 GTTAGGGGTTTTTAGTCCTCGC 58.994 50.000 0.00 0.00 0.00 5.03
484 485 0.734889 AGCGGTGCTCAAACATATGC 59.265 50.000 1.58 0.00 30.62 3.14
488 489 2.094675 GGTGCTCAAACATATGCTGGT 58.905 47.619 1.58 0.00 0.00 4.00
503 504 2.234661 TGCTGGTGATTCATCTTCGAGT 59.765 45.455 0.00 0.00 0.00 4.18
507 508 3.007940 TGGTGATTCATCTTCGAGTTGGT 59.992 43.478 0.00 0.00 0.00 3.67
511 512 6.984474 GGTGATTCATCTTCGAGTTGGTATTA 59.016 38.462 0.00 0.00 0.00 0.98
512 513 7.042658 GGTGATTCATCTTCGAGTTGGTATTAC 60.043 40.741 0.00 0.00 0.00 1.89
513 514 7.491372 GTGATTCATCTTCGAGTTGGTATTACA 59.509 37.037 0.00 0.00 0.00 2.41
517 518 5.401531 TCTTCGAGTTGGTATTACAAGCT 57.598 39.130 0.00 0.00 0.00 3.74
521 522 3.306166 CGAGTTGGTATTACAAGCTTCGG 59.694 47.826 0.00 0.00 31.70 4.30
535 536 2.010497 GCTTCGGTCCTCCTCAAATTC 58.990 52.381 0.00 0.00 0.00 2.17
554 555 0.716108 CGTGCATCGAGACAAAGTCC 59.284 55.000 0.00 0.00 42.86 3.85
560 561 3.854666 CATCGAGACAAAGTCCACAGAT 58.145 45.455 0.00 0.00 32.18 2.90
568 569 6.806017 AGACAAAGTCCACAGATATCTGGCA 61.806 44.000 31.19 15.10 39.67 4.92
578 579 6.296317 CCACAGATATCTGGCATAGATTCCTT 60.296 42.308 31.19 7.60 43.68 3.36
579 580 7.166851 CACAGATATCTGGCATAGATTCCTTT 58.833 38.462 31.19 7.19 43.68 3.11
822 824 1.333435 GGGTTTCTTGTTGTACGTGCG 60.333 52.381 0.00 0.00 0.00 5.34
829 831 1.007580 TGTTGTACGTGCGCAAAAGA 58.992 45.000 14.00 0.00 0.00 2.52
830 832 1.267632 TGTTGTACGTGCGCAAAAGAC 60.268 47.619 14.00 8.95 0.00 3.01
832 834 0.870735 TGTACGTGCGCAAAAGACGA 60.871 50.000 21.94 5.15 36.90 4.20
835 837 1.128611 CGTGCGCAAAAGACGAGAG 59.871 57.895 14.00 0.00 35.05 3.20
842 844 3.473367 CGCAAAAGACGAGAGATGTTTG 58.527 45.455 0.00 0.00 0.00 2.93
868 870 6.944862 AGGCACTTTAGATCAATTCAAGAGTT 59.055 34.615 0.00 0.00 27.25 3.01
873 875 9.342308 ACTTTAGATCAATTCAAGAGTTCAACA 57.658 29.630 0.00 0.00 0.00 3.33
883 885 8.958119 ATTCAAGAGTTCAACAACTACAACTA 57.042 30.769 0.00 0.00 43.37 2.24
884 886 8.958119 TTCAAGAGTTCAACAACTACAACTAT 57.042 30.769 0.00 0.00 43.37 2.12
895 897 3.951663 ACTACAACTATGGTTCCAAGGC 58.048 45.455 0.00 0.00 32.73 4.35
896 898 2.969821 ACAACTATGGTTCCAAGGCA 57.030 45.000 0.00 0.00 32.73 4.75
897 899 3.237268 ACAACTATGGTTCCAAGGCAA 57.763 42.857 0.00 0.00 32.73 4.52
911 1705 0.839946 AGGCAAGGCGTTGATCCTAT 59.160 50.000 22.64 0.00 35.46 2.57
940 1734 2.035961 GGGCAAGGAAGACTTTTTGACC 59.964 50.000 17.57 17.57 41.17 4.02
947 1741 3.188667 GGAAGACTTTTTGACCGTCATCC 59.811 47.826 1.09 0.00 38.06 3.51
961 1755 2.093890 GTCATCCACAATGTCATGCCA 58.906 47.619 0.00 0.00 36.68 4.92
962 1756 2.098607 GTCATCCACAATGTCATGCCAG 59.901 50.000 0.00 0.00 36.68 4.85
992 1787 4.399978 CCGATTACGTGGTGACATTTTTC 58.600 43.478 0.00 0.00 46.14 2.29
993 1788 4.399978 CGATTACGTGGTGACATTTTTCC 58.600 43.478 0.00 0.00 46.14 3.13
1011 1806 1.719378 TCCCTTCAAATGGGGCCTAAA 59.281 47.619 0.84 0.00 44.67 1.85
1014 1809 3.523157 CCCTTCAAATGGGGCCTAAATTT 59.477 43.478 0.84 5.05 40.97 1.82
1015 1810 4.516323 CCTTCAAATGGGGCCTAAATTTG 58.484 43.478 22.71 22.71 40.86 2.32
1077 1873 0.671796 CATCGCCCGATGTGTACCTA 59.328 55.000 19.46 0.00 44.93 3.08
1093 1890 4.400251 TGTACCTAGTAAAGACACGGATGG 59.600 45.833 0.00 0.00 0.00 3.51
1119 1916 2.352814 GCGTTCTACAAGAGCTTCCTCA 60.353 50.000 0.00 0.00 40.68 3.86
1142 1950 5.314718 TCTCCATTATTGTCATCTGCCAT 57.685 39.130 0.00 0.00 0.00 4.40
1145 1953 5.005740 TCCATTATTGTCATCTGCCATAGC 58.994 41.667 0.00 0.00 40.48 2.97
1152 1960 0.107066 CATCTGCCATAGCCACCACA 60.107 55.000 0.00 0.00 38.69 4.17
1354 2168 0.826715 GGAGCAGCATGAGGTCAGTA 59.173 55.000 16.29 0.00 39.69 2.74
1358 2172 2.158986 AGCAGCATGAGGTCAGTACATC 60.159 50.000 0.00 0.00 39.69 3.06
1376 2191 0.039618 TCTGCCCCCACCAAGAAATC 59.960 55.000 0.00 0.00 0.00 2.17
1389 2204 4.344968 ACCAAGAAATCCAGAAACCCAAAG 59.655 41.667 0.00 0.00 0.00 2.77
1398 2213 3.565902 CCAGAAACCCAAAGACAGAGTTC 59.434 47.826 0.00 0.00 0.00 3.01
1478 2294 2.033299 CGAAGCACACACCATTTTCTGT 59.967 45.455 0.00 0.00 0.00 3.41
1480 2296 3.441496 AGCACACACCATTTTCTGTTG 57.559 42.857 0.00 0.00 0.00 3.33
1515 2331 9.921637 TTTGTTTTGTTCAGAAGAAAATGTACT 57.078 25.926 18.40 0.00 36.27 2.73
1516 2332 9.921637 TTGTTTTGTTCAGAAGAAAATGTACTT 57.078 25.926 18.40 0.00 36.27 2.24
1533 2349 5.479306 TGTACTTAGCACCATCAGAGTTTC 58.521 41.667 0.00 0.00 0.00 2.78
1534 2350 4.899352 ACTTAGCACCATCAGAGTTTCT 57.101 40.909 0.00 0.00 0.00 2.52
1535 2351 4.826556 ACTTAGCACCATCAGAGTTTCTC 58.173 43.478 0.00 0.00 0.00 2.87
1542 2358 3.257393 CCATCAGAGTTTCTCTTGACGG 58.743 50.000 0.00 0.00 38.99 4.79
1577 2393 2.193248 GGTGGTGCCTATGGGAGC 59.807 66.667 0.00 0.00 41.84 4.70
1586 2402 1.467678 CCTATGGGAGCGGAGAGTGG 61.468 65.000 0.00 0.00 33.58 4.00
1587 2403 2.093537 CTATGGGAGCGGAGAGTGGC 62.094 65.000 0.00 0.00 0.00 5.01
1604 2420 0.176910 GGCGAAGAGAGGAAGAAGGG 59.823 60.000 0.00 0.00 0.00 3.95
1606 2422 1.550976 GCGAAGAGAGGAAGAAGGGAA 59.449 52.381 0.00 0.00 0.00 3.97
1608 2424 2.829120 CGAAGAGAGGAAGAAGGGAAGT 59.171 50.000 0.00 0.00 0.00 3.01
1719 2535 2.049248 CCGGCGCACAAAAAGCAT 60.049 55.556 10.83 0.00 0.00 3.79
1760 2576 3.679980 CGCCTCCGGATATTATTCAGTTG 59.320 47.826 3.57 0.00 0.00 3.16
1790 2606 4.073293 TCTTGTCCAGTTCAGTTTCCTC 57.927 45.455 0.00 0.00 0.00 3.71
1797 2613 5.590663 GTCCAGTTCAGTTTCCTCTTCTTTT 59.409 40.000 0.00 0.00 0.00 2.27
1798 2614 6.095580 GTCCAGTTCAGTTTCCTCTTCTTTTT 59.904 38.462 0.00 0.00 0.00 1.94
1799 2615 6.318900 TCCAGTTCAGTTTCCTCTTCTTTTTC 59.681 38.462 0.00 0.00 0.00 2.29
1800 2616 6.195165 CAGTTCAGTTTCCTCTTCTTTTTCG 58.805 40.000 0.00 0.00 0.00 3.46
1830 2646 4.587976 AGCAAGTACTCCTAGTAGTCCA 57.412 45.455 0.00 0.00 33.44 4.02
1834 2650 5.163632 GCAAGTACTCCTAGTAGTCCAGTTC 60.164 48.000 0.00 0.00 33.44 3.01
1852 2668 6.867662 CAGTTCTATGGAATTGGTGTATCC 57.132 41.667 6.44 0.00 36.12 2.59
1856 2672 7.072961 AGTTCTATGGAATTGGTGTATCCTGAT 59.927 37.037 0.00 0.00 33.90 2.90
1903 2729 7.170828 TCCACGATTTTATATGGATCTTCGTTG 59.829 37.037 0.00 0.00 36.30 4.10
1932 2768 9.436957 AAGAAAAATCGAGATACATAGTTGTGT 57.563 29.630 0.00 0.00 36.53 3.72
1944 2780 9.760660 GATACATAGTTGTGTCTTTGTTGATTC 57.239 33.333 0.00 0.00 39.95 2.52
1952 2892 3.229552 GTCTTTGTTGATTCTTCGCTGC 58.770 45.455 0.00 0.00 0.00 5.25
1959 2899 2.554142 TGATTCTTCGCTGCATGGTAG 58.446 47.619 0.00 0.00 0.00 3.18
1960 2900 1.869767 GATTCTTCGCTGCATGGTAGG 59.130 52.381 0.00 0.00 0.00 3.18
1976 2916 3.389983 TGGTAGGAGTAGCTGTTTGTTGT 59.610 43.478 0.00 0.00 0.00 3.32
2041 2993 1.392589 CACCCAGCAGTTTCAACACT 58.607 50.000 0.00 0.00 0.00 3.55
2043 2995 2.549754 CACCCAGCAGTTTCAACACTAG 59.450 50.000 0.00 0.00 0.00 2.57
2065 3018 1.446792 CGCAGAACGCTCTCCACAT 60.447 57.895 0.00 0.00 39.08 3.21
2066 3019 1.416813 CGCAGAACGCTCTCCACATC 61.417 60.000 0.00 0.00 39.08 3.06
2067 3020 1.416813 GCAGAACGCTCTCCACATCG 61.417 60.000 0.00 0.00 37.77 3.84
2068 3021 0.803768 CAGAACGCTCTCCACATCGG 60.804 60.000 0.00 0.00 0.00 4.18
2070 3023 3.665675 AACGCTCTCCACATCGGCC 62.666 63.158 0.00 0.00 33.14 6.13
2072 3025 4.148825 GCTCTCCACATCGGCCGT 62.149 66.667 27.15 10.00 33.14 5.68
2073 3026 2.579201 CTCTCCACATCGGCCGTT 59.421 61.111 27.15 15.26 33.14 4.44
2074 3027 1.813859 CTCTCCACATCGGCCGTTA 59.186 57.895 27.15 7.11 33.14 3.18
2075 3028 0.249073 CTCTCCACATCGGCCGTTAG 60.249 60.000 27.15 18.12 33.14 2.34
2076 3029 1.883084 CTCCACATCGGCCGTTAGC 60.883 63.158 27.15 0.00 42.60 3.09
2092 3045 4.521062 GCCTCCAGCGCGATGAGT 62.521 66.667 28.29 0.00 0.00 3.41
2093 3046 2.584418 CCTCCAGCGCGATGAGTG 60.584 66.667 28.29 15.81 0.00 3.51
2102 3055 4.457496 CGATGAGTGCGCACCCCT 62.457 66.667 35.51 18.90 0.00 4.79
2103 3056 2.821366 GATGAGTGCGCACCCCTG 60.821 66.667 35.51 0.00 0.00 4.45
2104 3057 4.415150 ATGAGTGCGCACCCCTGG 62.415 66.667 35.51 0.00 0.00 4.45
2106 3059 4.329545 GAGTGCGCACCCCTGGAA 62.330 66.667 35.51 0.00 0.00 3.53
2107 3060 3.628646 GAGTGCGCACCCCTGGAAT 62.629 63.158 35.51 15.83 0.00 3.01
2108 3061 3.134127 GTGCGCACCCCTGGAATC 61.134 66.667 30.12 0.00 0.00 2.52
2110 3063 4.424711 GCGCACCCCTGGAATCCA 62.425 66.667 0.30 0.48 0.00 3.41
2120 3073 1.685224 TGGAATCCAGGACAGTGGC 59.315 57.895 0.00 0.00 37.53 5.01
2121 3074 1.133181 TGGAATCCAGGACAGTGGCA 61.133 55.000 0.00 0.00 37.53 4.92
2122 3075 0.678048 GGAATCCAGGACAGTGGCAC 60.678 60.000 10.29 10.29 37.53 5.01
2173 5355 3.513225 GCCATTGCGCAGTGGTAT 58.487 55.556 40.90 18.66 40.01 2.73
2174 5356 1.356624 GCCATTGCGCAGTGGTATC 59.643 57.895 40.90 26.84 40.01 2.24
2175 5357 1.643292 CCATTGCGCAGTGGTATCG 59.357 57.895 36.17 16.18 33.95 2.92
2179 5361 2.105128 GCGCAGTGGTATCGCTCT 59.895 61.111 0.30 0.00 44.79 4.09
2180 5362 1.946650 GCGCAGTGGTATCGCTCTC 60.947 63.158 0.30 0.00 44.79 3.20
2181 5363 1.730487 CGCAGTGGTATCGCTCTCT 59.270 57.895 0.00 0.00 0.00 3.10
2182 5364 0.945099 CGCAGTGGTATCGCTCTCTA 59.055 55.000 0.00 0.00 0.00 2.43
2183 5365 1.537638 CGCAGTGGTATCGCTCTCTAT 59.462 52.381 0.00 0.00 0.00 1.98
2184 5366 2.413502 CGCAGTGGTATCGCTCTCTATC 60.414 54.545 0.00 0.00 0.00 2.08
2195 5377 1.107114 CTCTCTATCGCACAGGGTGT 58.893 55.000 0.00 0.00 35.75 4.16
2196 5378 2.298610 CTCTCTATCGCACAGGGTGTA 58.701 52.381 0.00 0.00 35.75 2.90
2198 5380 2.623416 TCTCTATCGCACAGGGTGTATG 59.377 50.000 0.00 0.00 35.75 2.39
2219 5401 0.098552 CGGCATAATTCAGTTGCGCA 59.901 50.000 5.66 5.66 37.25 6.09
2263 5446 3.564511 CAAAATCGACAGGCGTTTTCAT 58.435 40.909 5.17 0.00 40.05 2.57
2265 5448 3.471495 AATCGACAGGCGTTTTCATTC 57.529 42.857 0.00 0.00 41.80 2.67
2269 5452 0.238289 ACAGGCGTTTTCATTCAGCG 59.762 50.000 0.00 0.00 0.00 5.18
2293 5476 7.564988 CGGTTTCTTCACTACTTTTCTGTTAG 58.435 38.462 0.00 0.00 0.00 2.34
2298 5481 8.019656 TCTTCACTACTTTTCTGTTAGGTTCT 57.980 34.615 0.00 0.00 0.00 3.01
2343 5526 4.077188 GTGCTCCGTGCGTTCAGC 62.077 66.667 0.00 0.00 46.63 4.26
2353 5536 3.470567 CGTTCAGCCGTGTCGCTC 61.471 66.667 0.00 0.00 36.82 5.03
2354 5537 3.112709 GTTCAGCCGTGTCGCTCC 61.113 66.667 0.00 0.00 36.82 4.70
2355 5538 4.373116 TTCAGCCGTGTCGCTCCC 62.373 66.667 0.00 0.00 36.82 4.30
2361 5544 4.436998 CGTGTCGCTCCCCTGGAC 62.437 72.222 0.00 0.00 0.00 4.02
2362 5545 2.997897 GTGTCGCTCCCCTGGACT 60.998 66.667 0.00 0.00 0.00 3.85
2363 5546 2.997315 TGTCGCTCCCCTGGACTG 60.997 66.667 0.00 0.00 0.00 3.51
2364 5547 3.775654 GTCGCTCCCCTGGACTGG 61.776 72.222 0.00 0.00 0.00 4.00
2365 5548 3.992641 TCGCTCCCCTGGACTGGA 61.993 66.667 0.00 0.00 0.00 3.86
2366 5549 3.775654 CGCTCCCCTGGACTGGAC 61.776 72.222 0.00 0.00 0.00 4.02
2367 5550 2.284995 GCTCCCCTGGACTGGACT 60.285 66.667 0.00 0.00 0.00 3.85
2423 5606 3.256631 GGAATTGTGGAGTCAGTTGCAAT 59.743 43.478 0.59 0.00 0.00 3.56
2425 5608 2.936919 TGTGGAGTCAGTTGCAATCT 57.063 45.000 0.59 0.00 0.00 2.40
2426 5609 4.350368 TTGTGGAGTCAGTTGCAATCTA 57.650 40.909 0.59 0.00 0.00 1.98
2427 5610 3.664107 TGTGGAGTCAGTTGCAATCTAC 58.336 45.455 0.59 4.42 0.00 2.59
2428 5611 3.324846 TGTGGAGTCAGTTGCAATCTACT 59.675 43.478 0.59 6.32 0.00 2.57
2429 5612 3.929610 GTGGAGTCAGTTGCAATCTACTC 59.070 47.826 20.91 20.91 34.08 2.59
2430 5613 3.526534 GGAGTCAGTTGCAATCTACTCC 58.473 50.000 27.25 27.25 44.36 3.85
2431 5614 3.526534 GAGTCAGTTGCAATCTACTCCC 58.473 50.000 19.45 0.25 0.00 4.30
2432 5615 3.177228 AGTCAGTTGCAATCTACTCCCT 58.823 45.455 0.59 0.00 0.00 4.20
2433 5616 3.196685 AGTCAGTTGCAATCTACTCCCTC 59.803 47.826 0.59 0.00 0.00 4.30
2434 5617 2.166459 TCAGTTGCAATCTACTCCCTCG 59.834 50.000 0.59 0.00 0.00 4.63
2435 5618 1.482593 AGTTGCAATCTACTCCCTCGG 59.517 52.381 0.59 0.00 0.00 4.63
2436 5619 1.207329 GTTGCAATCTACTCCCTCGGT 59.793 52.381 0.59 0.00 0.00 4.69
2437 5620 2.429610 GTTGCAATCTACTCCCTCGGTA 59.570 50.000 0.59 0.00 0.00 4.02
2438 5621 2.029623 TGCAATCTACTCCCTCGGTAC 58.970 52.381 0.00 0.00 0.00 3.34
2439 5622 1.340568 GCAATCTACTCCCTCGGTACC 59.659 57.143 0.16 0.16 0.00 3.34
2440 5623 2.662866 CAATCTACTCCCTCGGTACCA 58.337 52.381 13.54 0.00 0.00 3.25
2441 5624 3.231818 CAATCTACTCCCTCGGTACCAT 58.768 50.000 13.54 0.00 0.00 3.55
2442 5625 4.404640 CAATCTACTCCCTCGGTACCATA 58.595 47.826 13.54 0.00 0.00 2.74
2443 5626 4.736611 ATCTACTCCCTCGGTACCATAA 57.263 45.455 13.54 0.00 0.00 1.90
2444 5627 4.736611 TCTACTCCCTCGGTACCATAAT 57.263 45.455 13.54 0.00 0.00 1.28
2445 5628 5.848286 TCTACTCCCTCGGTACCATAATA 57.152 43.478 13.54 0.00 0.00 0.98
2446 5629 6.398655 TCTACTCCCTCGGTACCATAATAT 57.601 41.667 13.54 0.00 0.00 1.28
2447 5630 7.515004 TCTACTCCCTCGGTACCATAATATA 57.485 40.000 13.54 0.00 0.00 0.86
2448 5631 7.932134 TCTACTCCCTCGGTACCATAATATAA 58.068 38.462 13.54 0.00 0.00 0.98
2449 5632 8.393259 TCTACTCCCTCGGTACCATAATATAAA 58.607 37.037 13.54 0.00 0.00 1.40
2450 5633 7.860649 ACTCCCTCGGTACCATAATATAAAA 57.139 36.000 13.54 0.00 0.00 1.52
2451 5634 7.674120 ACTCCCTCGGTACCATAATATAAAAC 58.326 38.462 13.54 0.00 0.00 2.43
2452 5635 6.690530 TCCCTCGGTACCATAATATAAAACG 58.309 40.000 13.54 0.00 0.00 3.60
2453 5636 6.267471 TCCCTCGGTACCATAATATAAAACGT 59.733 38.462 13.54 0.00 0.00 3.99
2454 5637 6.930722 CCCTCGGTACCATAATATAAAACGTT 59.069 38.462 13.54 0.00 0.00 3.99
2455 5638 7.442062 CCCTCGGTACCATAATATAAAACGTTT 59.558 37.037 13.54 7.96 0.00 3.60
2456 5639 8.829612 CCTCGGTACCATAATATAAAACGTTTT 58.170 33.333 27.65 27.65 0.00 2.43
2458 5641 9.985318 TCGGTACCATAATATAAAACGTTTTTG 57.015 29.630 29.42 19.75 0.00 2.44
2459 5642 8.735837 CGGTACCATAATATAAAACGTTTTTGC 58.264 33.333 29.42 12.57 0.00 3.68
2460 5643 9.570488 GGTACCATAATATAAAACGTTTTTGCA 57.430 29.630 29.42 13.85 0.00 4.08
2463 5646 9.699703 ACCATAATATAAAACGTTTTTGCAGTT 57.300 25.926 29.42 18.54 0.00 3.16
2473 5656 8.648422 AAACGTTTTTGCAGTTCAAATTTAAC 57.352 26.923 7.96 0.00 43.53 2.01
2474 5657 7.589574 ACGTTTTTGCAGTTCAAATTTAACT 57.410 28.000 0.00 0.00 43.53 2.24
2483 5666 7.859891 CAGTTCAAATTTAACTGCAAAAACG 57.140 32.000 18.80 0.00 45.15 3.60
2484 5667 7.452231 CAGTTCAAATTTAACTGCAAAAACGT 58.548 30.769 18.80 0.00 45.15 3.99
2485 5668 7.630606 CAGTTCAAATTTAACTGCAAAAACGTC 59.369 33.333 18.80 0.00 45.15 4.34
2486 5669 7.544217 AGTTCAAATTTAACTGCAAAAACGTCT 59.456 29.630 10.38 0.00 35.87 4.18
2487 5670 7.820044 TCAAATTTAACTGCAAAAACGTCTT 57.180 28.000 0.00 0.00 0.00 3.01
2488 5671 8.912787 TCAAATTTAACTGCAAAAACGTCTTA 57.087 26.923 0.00 0.00 0.00 2.10
2489 5672 9.522804 TCAAATTTAACTGCAAAAACGTCTTAT 57.477 25.926 0.00 0.00 0.00 1.73
2497 5680 8.276252 ACTGCAAAAACGTCTTATATTATGGT 57.724 30.769 0.00 0.00 0.00 3.55
2498 5681 9.386010 ACTGCAAAAACGTCTTATATTATGGTA 57.614 29.630 0.00 0.00 0.00 3.25
2499 5682 9.646336 CTGCAAAAACGTCTTATATTATGGTAC 57.354 33.333 0.00 0.00 0.00 3.34
2500 5683 8.614346 TGCAAAAACGTCTTATATTATGGTACC 58.386 33.333 4.43 4.43 0.00 3.34
2501 5684 7.795272 GCAAAAACGTCTTATATTATGGTACCG 59.205 37.037 7.57 0.00 0.00 4.02
2502 5685 9.033481 CAAAAACGTCTTATATTATGGTACCGA 57.967 33.333 7.57 0.00 0.00 4.69
2503 5686 8.807667 AAAACGTCTTATATTATGGTACCGAG 57.192 34.615 7.57 0.00 0.00 4.63
2504 5687 6.506500 ACGTCTTATATTATGGTACCGAGG 57.493 41.667 7.57 3.36 0.00 4.63
2505 5688 5.416952 ACGTCTTATATTATGGTACCGAGGG 59.583 44.000 7.57 0.00 0.00 4.30
2506 5689 5.649395 CGTCTTATATTATGGTACCGAGGGA 59.351 44.000 7.57 0.00 0.00 4.20
2507 5690 6.183360 CGTCTTATATTATGGTACCGAGGGAG 60.183 46.154 7.57 0.00 0.00 4.30
2508 5691 6.662663 GTCTTATATTATGGTACCGAGGGAGT 59.337 42.308 7.57 0.00 0.00 3.85
2509 5692 7.831193 GTCTTATATTATGGTACCGAGGGAGTA 59.169 40.741 7.57 0.00 0.00 2.59
2510 5693 8.051535 TCTTATATTATGGTACCGAGGGAGTAG 58.948 40.741 7.57 0.00 0.00 2.57
2521 5709 0.755686 AGGGAGTAGTATGCAGCAGC 59.244 55.000 0.00 0.00 42.57 5.25
2593 5783 2.798262 GCAGAACTTTGCGCTGCG 60.798 61.111 19.17 19.17 44.52 5.18
2620 5810 3.637229 TCCTTGTCTCGTTTCTTCAGAGT 59.363 43.478 0.00 0.00 33.96 3.24
2626 5816 2.201732 TCGTTTCTTCAGAGTGTGTGC 58.798 47.619 0.00 0.00 0.00 4.57
2627 5817 2.159099 TCGTTTCTTCAGAGTGTGTGCT 60.159 45.455 0.00 0.00 0.00 4.40
2629 5819 2.140065 TTCTTCAGAGTGTGTGCTCG 57.860 50.000 0.00 0.00 40.26 5.03
2631 5821 1.287730 CTTCAGAGTGTGTGCTCGCC 61.288 60.000 0.00 0.00 40.26 5.54
2632 5822 3.108289 CAGAGTGTGTGCTCGCCG 61.108 66.667 0.00 0.00 40.26 6.46
2634 5824 2.807045 GAGTGTGTGCTCGCCGAG 60.807 66.667 10.36 10.36 0.00 4.63
2647 5844 2.441901 CCGAGCAGAGAGAGGGCT 60.442 66.667 0.00 0.00 41.35 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
1 2 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2 3 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3 4 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4 5 3.053095 ACATCTACTCCCTCCGTTCCTAA 60.053 47.826 0.00 0.00 0.00 2.69
5 6 2.512896 ACATCTACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
6 7 1.288335 ACATCTACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
7 8 1.682323 GACATCTACTCCCTCCGTTCC 59.318 57.143 0.00 0.00 0.00 3.62
8 9 2.099427 GTGACATCTACTCCCTCCGTTC 59.901 54.545 0.00 0.00 0.00 3.95
9 10 2.100989 GTGACATCTACTCCCTCCGTT 58.899 52.381 0.00 0.00 0.00 4.44
10 11 1.685491 GGTGACATCTACTCCCTCCGT 60.685 57.143 0.00 0.00 0.00 4.69
11 12 1.033574 GGTGACATCTACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
12 13 1.415200 GGGTGACATCTACTCCCTCC 58.585 60.000 0.00 0.00 37.86 4.30
13 14 1.062810 AGGGGTGACATCTACTCCCTC 60.063 57.143 0.00 0.00 40.48 4.30
14 15 1.019650 AGGGGTGACATCTACTCCCT 58.980 55.000 0.00 0.00 39.62 4.20
15 16 1.123928 CAGGGGTGACATCTACTCCC 58.876 60.000 0.00 0.00 39.62 4.30
16 17 2.160721 TCAGGGGTGACATCTACTCC 57.839 55.000 0.00 0.00 39.05 3.85
17 18 3.300388 TGATCAGGGGTGACATCTACTC 58.700 50.000 0.00 0.00 0.00 2.59
18 19 3.404869 TGATCAGGGGTGACATCTACT 57.595 47.619 0.00 0.00 0.00 2.57
19 20 4.487714 TTTGATCAGGGGTGACATCTAC 57.512 45.455 0.00 0.00 0.00 2.59
20 21 4.536090 ACTTTTGATCAGGGGTGACATCTA 59.464 41.667 0.00 0.00 0.00 1.98
21 22 3.331889 ACTTTTGATCAGGGGTGACATCT 59.668 43.478 0.00 0.00 0.00 2.90
22 23 3.441572 CACTTTTGATCAGGGGTGACATC 59.558 47.826 14.62 0.00 0.00 3.06
54 55 3.132646 GCTGATGCAGATAGGCTAGCTAT 59.867 47.826 12.63 10.24 39.41 2.97
57 58 1.724429 GCTGATGCAGATAGGCTAGC 58.276 55.000 6.04 6.04 39.41 3.42
61 62 1.003116 CAAACGCTGATGCAGATAGGC 60.003 52.381 0.00 0.00 39.64 3.93
62 63 2.554142 TCAAACGCTGATGCAGATAGG 58.446 47.619 0.00 0.00 39.64 2.57
76 77 1.070821 TGAAGCTCGAGCATCAAACG 58.929 50.000 35.51 0.26 44.42 3.60
86 87 7.542534 TTGTAAGTTTACTTTTGAAGCTCGA 57.457 32.000 0.00 0.00 37.40 4.04
142 143 7.797121 ATACAAGAAAATTGGTGGGAAGAAT 57.203 32.000 0.00 0.00 0.00 2.40
144 145 8.713708 TTTATACAAGAAAATTGGTGGGAAGA 57.286 30.769 0.00 0.00 0.00 2.87
166 167 9.944376 GGAGCAGTAGTTATCCATGAATATTTA 57.056 33.333 0.00 0.00 0.00 1.40
181 182 2.304180 AGTTGCAGATGGAGCAGTAGTT 59.696 45.455 0.00 0.00 43.75 2.24
187 188 0.321919 GTGGAGTTGCAGATGGAGCA 60.322 55.000 0.00 0.00 40.85 4.26
212 213 5.993748 TGAGAAGTCACATGTGGTACATA 57.006 39.130 25.16 2.02 44.52 2.29
215 216 4.997395 ACATTGAGAAGTCACATGTGGTAC 59.003 41.667 25.16 16.72 35.19 3.34
226 227 6.963796 ACACATCTTTCAACATTGAGAAGTC 58.036 36.000 12.29 0.00 38.61 3.01
244 245 3.452627 ACCTCTGGGTGAGAATACACATC 59.547 47.826 0.00 0.00 45.43 3.06
295 296 1.910580 ATTGCCCTGACCACCTACGG 61.911 60.000 0.00 0.00 0.00 4.02
304 305 1.546029 GGAGGAAAACATTGCCCTGAC 59.454 52.381 0.00 0.00 0.00 3.51
306 307 0.897621 GGGAGGAAAACATTGCCCTG 59.102 55.000 0.00 0.00 32.78 4.45
310 311 1.186200 GGAGGGGAGGAAAACATTGC 58.814 55.000 0.00 0.00 0.00 3.56
314 315 0.112412 GCTTGGAGGGGAGGAAAACA 59.888 55.000 0.00 0.00 0.00 2.83
315 316 0.405973 AGCTTGGAGGGGAGGAAAAC 59.594 55.000 0.00 0.00 0.00 2.43
338 339 3.512680 GGCGAATCTATGGTCTAATCGG 58.487 50.000 0.00 0.00 0.00 4.18
339 340 3.512680 GGGCGAATCTATGGTCTAATCG 58.487 50.000 0.00 0.00 0.00 3.34
404 405 2.511600 CCGAGGCACCACGATTCC 60.512 66.667 8.14 0.00 0.00 3.01
410 411 1.448013 GCTAGAACCGAGGCACCAC 60.448 63.158 0.00 0.00 0.00 4.16
411 412 0.323999 TAGCTAGAACCGAGGCACCA 60.324 55.000 0.00 0.00 0.00 4.17
421 422 8.358895 CCCCTAACATAAACTACTAGCTAGAAC 58.641 40.741 27.45 0.00 0.00 3.01
439 440 3.557686 GCGAGGACTAAAAACCCCTAACA 60.558 47.826 0.00 0.00 0.00 2.41
470 471 3.070476 TCACCAGCATATGTTTGAGCA 57.930 42.857 4.29 0.00 0.00 4.26
475 476 6.238566 CGAAGATGAATCACCAGCATATGTTT 60.239 38.462 4.29 0.00 0.00 2.83
476 477 5.237996 CGAAGATGAATCACCAGCATATGTT 59.762 40.000 4.29 0.00 0.00 2.71
480 481 4.100035 ACTCGAAGATGAATCACCAGCATA 59.900 41.667 0.00 0.00 33.89 3.14
484 485 3.620374 CCAACTCGAAGATGAATCACCAG 59.380 47.826 0.00 0.00 33.89 4.00
488 489 7.552459 TGTAATACCAACTCGAAGATGAATCA 58.448 34.615 0.00 0.00 33.89 2.57
503 504 3.262405 AGGACCGAAGCTTGTAATACCAA 59.738 43.478 2.10 0.00 0.00 3.67
507 508 3.371965 AGGAGGACCGAAGCTTGTAATA 58.628 45.455 2.10 0.00 41.83 0.98
511 512 0.832135 TGAGGAGGACCGAAGCTTGT 60.832 55.000 2.10 0.00 41.83 3.16
512 513 0.321671 TTGAGGAGGACCGAAGCTTG 59.678 55.000 2.10 0.00 41.83 4.01
513 514 1.056660 TTTGAGGAGGACCGAAGCTT 58.943 50.000 0.00 0.00 41.83 3.74
517 518 1.621814 ACGAATTTGAGGAGGACCGAA 59.378 47.619 0.00 0.00 41.83 4.30
521 522 1.808411 TGCACGAATTTGAGGAGGAC 58.192 50.000 0.00 0.00 0.00 3.85
535 536 0.716108 GGACTTTGTCTCGATGCACG 59.284 55.000 0.00 0.00 44.09 5.34
544 545 4.383552 GCCAGATATCTGTGGACTTTGTCT 60.384 45.833 27.03 0.00 42.27 3.41
549 550 5.150715 TCTATGCCAGATATCTGTGGACTT 58.849 41.667 27.03 15.20 42.27 3.01
554 555 6.297080 AGGAATCTATGCCAGATATCTGTG 57.703 41.667 27.03 19.95 43.56 3.66
560 561 7.577303 AGACAAAAAGGAATCTATGCCAGATA 58.423 34.615 0.00 0.00 43.56 1.98
568 569 7.709149 CCAAAGGAGACAAAAAGGAATCTAT 57.291 36.000 0.00 0.00 0.00 1.98
799 800 3.560896 GCACGTACAACAAGAAACCCTAA 59.439 43.478 0.00 0.00 0.00 2.69
822 824 4.377841 CCTCAAACATCTCTCGTCTTTTGC 60.378 45.833 0.00 0.00 0.00 3.68
829 831 1.620819 AGTGCCTCAAACATCTCTCGT 59.379 47.619 0.00 0.00 0.00 4.18
830 832 2.376808 AGTGCCTCAAACATCTCTCG 57.623 50.000 0.00 0.00 0.00 4.04
832 834 5.489792 TCTAAAGTGCCTCAAACATCTCT 57.510 39.130 0.00 0.00 0.00 3.10
835 837 6.500684 TTGATCTAAAGTGCCTCAAACATC 57.499 37.500 0.00 0.00 0.00 3.06
842 844 6.597280 ACTCTTGAATTGATCTAAAGTGCCTC 59.403 38.462 0.00 0.00 0.00 4.70
868 870 5.931294 TGGAACCATAGTTGTAGTTGTTGA 58.069 37.500 0.00 0.00 35.94 3.18
873 875 4.202524 TGCCTTGGAACCATAGTTGTAGTT 60.203 41.667 0.00 0.00 35.94 2.24
883 885 1.978617 CGCCTTGCCTTGGAACCAT 60.979 57.895 0.00 0.00 0.00 3.55
884 886 2.597217 CGCCTTGCCTTGGAACCA 60.597 61.111 0.00 0.00 0.00 3.67
895 897 3.199880 AGGAATAGGATCAACGCCTTG 57.800 47.619 0.00 0.00 36.96 3.61
896 898 3.933861 AAGGAATAGGATCAACGCCTT 57.066 42.857 0.00 0.00 36.96 4.35
897 899 4.608948 CTAAGGAATAGGATCAACGCCT 57.391 45.455 0.00 0.00 39.56 5.52
940 1734 1.064505 GGCATGACATTGTGGATGACG 59.935 52.381 0.00 0.00 39.15 4.35
947 1741 0.454600 GGAGCTGGCATGACATTGTG 59.545 55.000 0.00 0.00 0.00 3.33
961 1755 0.460284 CACGTAATCGGCTTGGAGCT 60.460 55.000 0.00 0.00 41.99 4.09
962 1756 1.429148 CCACGTAATCGGCTTGGAGC 61.429 60.000 0.00 0.00 41.46 4.70
993 1788 4.516323 CAAATTTAGGCCCCATTTGAAGG 58.484 43.478 20.11 1.15 39.34 3.46
1015 1810 0.593128 CCTGGGCTACGCATATTTGC 59.407 55.000 0.00 0.00 45.78 3.68
1025 1820 3.482232 ATGATGGCGCCTGGGCTAC 62.482 63.158 29.70 11.02 42.84 3.58
1031 1827 0.179094 AAAATGCATGATGGCGCCTG 60.179 50.000 29.70 18.76 36.28 4.85
1041 1837 1.061421 GATGGTTGCGCAAAATGCATG 59.939 47.619 26.87 0.00 45.36 4.06
1059 1855 0.959553 CTAGGTACACATCGGGCGAT 59.040 55.000 0.00 0.00 34.81 4.58
1065 1861 5.026462 CGTGTCTTTACTAGGTACACATCG 58.974 45.833 0.00 4.94 40.29 3.84
1066 1862 5.124457 TCCGTGTCTTTACTAGGTACACATC 59.876 44.000 0.00 0.00 40.29 3.06
1077 1873 2.761208 CTCTCCCATCCGTGTCTTTACT 59.239 50.000 0.00 0.00 0.00 2.24
1093 1890 1.474879 AGCTCTTGTAGAACGCTCTCC 59.525 52.381 0.00 0.00 32.70 3.71
1119 1916 5.314718 TGGCAGATGACAATAATGGAGAT 57.685 39.130 0.00 0.00 0.00 2.75
1142 1950 1.892474 GCTTTTCCATTGTGGTGGCTA 59.108 47.619 0.00 0.00 39.03 3.93
1145 1953 1.606224 GCAGCTTTTCCATTGTGGTGG 60.606 52.381 0.00 0.00 39.03 4.61
1152 1960 0.883833 CGGTGAGCAGCTTTTCCATT 59.116 50.000 0.00 0.00 0.00 3.16
1255 2066 3.119566 CCTAGAACACGACCTTGTAGACC 60.120 52.174 0.00 0.00 0.00 3.85
1354 2168 1.434513 TTCTTGGTGGGGGCAGATGT 61.435 55.000 0.00 0.00 0.00 3.06
1358 2172 0.972471 GGATTTCTTGGTGGGGGCAG 60.972 60.000 0.00 0.00 0.00 4.85
1376 2191 3.214696 ACTCTGTCTTTGGGTTTCTGG 57.785 47.619 0.00 0.00 0.00 3.86
1478 2294 9.703892 TTCTGAACAAAACAAATTTCTTCTCAA 57.296 25.926 0.00 0.00 0.00 3.02
1480 2296 9.573133 TCTTCTGAACAAAACAAATTTCTTCTC 57.427 29.630 0.00 0.00 0.00 2.87
1514 2330 5.083533 AGAGAAACTCTGATGGTGCTAAG 57.916 43.478 0.25 0.00 39.62 2.18
1515 2331 5.012046 TCAAGAGAAACTCTGATGGTGCTAA 59.988 40.000 1.97 0.00 40.28 3.09
1516 2332 4.528206 TCAAGAGAAACTCTGATGGTGCTA 59.472 41.667 1.97 0.00 40.28 3.49
1517 2333 3.326006 TCAAGAGAAACTCTGATGGTGCT 59.674 43.478 1.97 0.00 40.28 4.40
1533 2349 1.664649 TGCACTTCGCCGTCAAGAG 60.665 57.895 0.00 0.00 41.33 2.85
1534 2350 1.954146 GTGCACTTCGCCGTCAAGA 60.954 57.895 10.32 0.00 41.33 3.02
1535 2351 1.568612 ATGTGCACTTCGCCGTCAAG 61.569 55.000 19.41 0.00 41.33 3.02
1563 2379 3.161450 TCCGCTCCCATAGGCACC 61.161 66.667 0.00 0.00 0.00 5.01
1577 2393 1.431440 CTCTCTTCGCCACTCTCCG 59.569 63.158 0.00 0.00 0.00 4.63
1586 2402 1.187087 TCCCTTCTTCCTCTCTTCGC 58.813 55.000 0.00 0.00 0.00 4.70
1587 2403 2.829120 ACTTCCCTTCTTCCTCTCTTCG 59.171 50.000 0.00 0.00 0.00 3.79
1604 2420 1.669211 CGTCCTCGTTCCTCCAACTTC 60.669 57.143 0.00 0.00 32.09 3.01
1606 2422 0.538977 TCGTCCTCGTTCCTCCAACT 60.539 55.000 0.00 0.00 38.33 3.16
1608 2424 1.248785 CCTCGTCCTCGTTCCTCCAA 61.249 60.000 0.00 0.00 38.33 3.53
1639 2455 2.110006 GGAGATCAGCCCTTCCGC 59.890 66.667 0.00 0.00 0.00 5.54
1760 2576 4.385825 TGAACTGGACAAGATTACACACC 58.614 43.478 0.00 0.00 0.00 4.16
1790 2606 3.565516 GCTAAAGGCACCGAAAAAGAAG 58.434 45.455 0.00 0.00 41.35 2.85
1814 2630 6.711645 CCATAGAACTGGACTACTAGGAGTAC 59.288 46.154 10.83 10.83 38.69 2.73
1815 2631 6.618610 TCCATAGAACTGGACTACTAGGAGTA 59.381 42.308 7.87 0.00 40.43 2.59
1816 2632 5.432390 TCCATAGAACTGGACTACTAGGAGT 59.568 44.000 7.55 7.55 40.43 3.85
1817 2633 5.942961 TCCATAGAACTGGACTACTAGGAG 58.057 45.833 0.00 0.00 40.43 3.69
1818 2634 5.988865 TCCATAGAACTGGACTACTAGGA 57.011 43.478 0.00 0.00 40.43 2.94
1819 2635 7.437748 CAATTCCATAGAACTGGACTACTAGG 58.562 42.308 0.00 0.00 44.97 3.02
1830 2646 6.386927 TCAGGATACACCAATTCCATAGAACT 59.613 38.462 0.00 0.00 42.04 3.01
1834 2650 7.456725 AGAATCAGGATACACCAATTCCATAG 58.543 38.462 0.00 0.00 40.66 2.23
1852 2668 9.092876 GACTTGGTATCTTTTACAGAGAATCAG 57.907 37.037 0.00 0.00 37.82 2.90
1856 2672 7.159372 GTGGACTTGGTATCTTTTACAGAGAA 58.841 38.462 0.00 0.00 33.87 2.87
1871 2697 5.996644 TCCATATAAAATCGTGGACTTGGT 58.003 37.500 0.00 0.00 35.91 3.67
1932 2768 2.877786 TGCAGCGAAGAATCAACAAAGA 59.122 40.909 0.00 0.00 0.00 2.52
1941 2777 1.486310 TCCTACCATGCAGCGAAGAAT 59.514 47.619 0.00 0.00 0.00 2.40
1944 2780 0.176680 ACTCCTACCATGCAGCGAAG 59.823 55.000 0.00 0.00 0.00 3.79
1952 2892 4.207891 ACAAACAGCTACTCCTACCATG 57.792 45.455 0.00 0.00 0.00 3.66
1959 2899 1.880027 CCCACAACAAACAGCTACTCC 59.120 52.381 0.00 0.00 0.00 3.85
1960 2900 2.572290 ACCCACAACAAACAGCTACTC 58.428 47.619 0.00 0.00 0.00 2.59
2032 2984 2.556257 TCTGCGTTGCTAGTGTTGAAA 58.444 42.857 0.00 0.00 0.00 2.69
2057 3010 1.813859 CTAACGGCCGATGTGGAGA 59.186 57.895 35.90 1.87 42.00 3.71
2059 3012 2.185867 GCTAACGGCCGATGTGGA 59.814 61.111 35.90 3.23 42.00 4.02
2070 3023 3.774959 ATCGCGCTGGAGGCTAACG 62.775 63.158 5.56 0.00 39.13 3.18
2071 3024 2.107141 ATCGCGCTGGAGGCTAAC 59.893 61.111 5.56 0.00 39.13 2.34
2072 3025 2.106938 CATCGCGCTGGAGGCTAA 59.893 61.111 5.56 0.00 39.13 3.09
2073 3026 2.833121 TCATCGCGCTGGAGGCTA 60.833 61.111 10.42 0.00 39.13 3.93
2074 3027 4.218578 CTCATCGCGCTGGAGGCT 62.219 66.667 10.42 0.00 39.13 4.58
2075 3028 4.521062 ACTCATCGCGCTGGAGGC 62.521 66.667 20.24 0.00 32.98 4.70
2076 3029 2.584418 CACTCATCGCGCTGGAGG 60.584 66.667 20.24 7.54 32.98 4.30
2077 3030 3.260483 GCACTCATCGCGCTGGAG 61.260 66.667 10.42 14.00 34.85 3.86
2085 3038 4.457496 AGGGGTGCGCACTCATCG 62.457 66.667 38.91 0.00 32.11 3.84
2086 3039 2.821366 CAGGGGTGCGCACTCATC 60.821 66.667 38.91 24.12 32.11 2.92
2087 3040 4.415150 CCAGGGGTGCGCACTCAT 62.415 66.667 38.91 32.36 32.11 2.90
2089 3042 3.628646 ATTCCAGGGGTGCGCACTC 62.629 63.158 36.84 34.78 0.00 3.51
2090 3043 3.628646 GATTCCAGGGGTGCGCACT 62.629 63.158 36.84 17.75 0.00 4.40
2092 3045 4.424711 GGATTCCAGGGGTGCGCA 62.425 66.667 5.66 5.66 0.00 6.09
2093 3046 4.424711 TGGATTCCAGGGGTGCGC 62.425 66.667 0.00 0.00 0.00 6.09
2102 3055 1.133181 TGCCACTGTCCTGGATTCCA 61.133 55.000 5.05 5.05 32.30 3.53
2103 3056 0.678048 GTGCCACTGTCCTGGATTCC 60.678 60.000 0.00 0.00 32.30 3.01
2104 3057 0.678048 GGTGCCACTGTCCTGGATTC 60.678 60.000 0.00 0.00 32.30 2.52
2106 3059 2.959484 CGGTGCCACTGTCCTGGAT 61.959 63.158 0.00 0.00 32.30 3.41
2107 3060 3.625897 CGGTGCCACTGTCCTGGA 61.626 66.667 0.00 0.00 32.30 3.86
2108 3061 4.704833 CCGGTGCCACTGTCCTGG 62.705 72.222 2.45 0.00 0.00 4.45
2131 5305 2.094659 CGACATGTCCACACGGCTC 61.095 63.158 20.03 0.00 0.00 4.70
2171 5353 1.807142 CCTGTGCGATAGAGAGCGATA 59.193 52.381 0.00 0.00 36.26 2.92
2172 5354 0.595588 CCTGTGCGATAGAGAGCGAT 59.404 55.000 0.00 0.00 36.26 4.58
2173 5355 1.448119 CCCTGTGCGATAGAGAGCGA 61.448 60.000 0.00 0.00 36.26 4.93
2174 5356 1.007964 CCCTGTGCGATAGAGAGCG 60.008 63.158 0.00 0.00 37.58 5.03
2175 5357 0.249238 CACCCTGTGCGATAGAGAGC 60.249 60.000 0.00 0.00 39.76 4.09
2176 5358 1.107114 ACACCCTGTGCGATAGAGAG 58.893 55.000 0.00 0.00 36.98 3.20
2177 5359 2.430248 TACACCCTGTGCGATAGAGA 57.570 50.000 0.00 0.00 36.98 3.10
2178 5360 2.362397 ACATACACCCTGTGCGATAGAG 59.638 50.000 0.00 0.00 36.98 2.43
2179 5361 2.361119 GACATACACCCTGTGCGATAGA 59.639 50.000 0.00 0.00 36.98 1.98
2180 5362 2.743938 GACATACACCCTGTGCGATAG 58.256 52.381 0.00 0.00 36.98 2.08
2181 5363 1.066454 CGACATACACCCTGTGCGATA 59.934 52.381 0.00 0.00 36.98 2.92
2182 5364 0.179111 CGACATACACCCTGTGCGAT 60.179 55.000 0.00 0.00 36.98 4.58
2183 5365 1.214325 CGACATACACCCTGTGCGA 59.786 57.895 0.00 0.00 36.98 5.10
2184 5366 1.809619 CCGACATACACCCTGTGCG 60.810 63.158 0.00 0.00 36.98 5.34
2195 5377 3.247411 CGCAACTGAATTATGCCGACATA 59.753 43.478 0.00 0.00 37.74 2.29
2196 5378 2.032054 CGCAACTGAATTATGCCGACAT 59.968 45.455 0.00 0.00 40.49 3.06
2198 5380 1.856014 GCGCAACTGAATTATGCCGAC 60.856 52.381 0.30 0.00 36.75 4.79
2219 5401 2.008752 GCCATGGCAGCGTTTATTTT 57.991 45.000 32.08 0.00 41.49 1.82
2263 5446 3.746045 AGTAGTGAAGAAACCGCTGAA 57.254 42.857 0.00 0.00 0.00 3.02
2265 5448 4.511826 AGAAAAGTAGTGAAGAAACCGCTG 59.488 41.667 0.00 0.00 0.00 5.18
2269 5452 7.498239 ACCTAACAGAAAAGTAGTGAAGAAACC 59.502 37.037 0.00 0.00 0.00 3.27
2293 5476 2.359900 CCCTTGTGCAGATACAGAACC 58.640 52.381 0.00 0.00 0.00 3.62
2298 5481 0.673333 CGTGCCCTTGTGCAGATACA 60.673 55.000 0.00 0.00 43.02 2.29
2344 5527 4.436998 GTCCAGGGGAGCGACACG 62.437 72.222 0.00 0.00 29.39 4.49
2345 5528 2.997897 AGTCCAGGGGAGCGACAC 60.998 66.667 0.00 0.00 29.39 3.67
2346 5529 2.997315 CAGTCCAGGGGAGCGACA 60.997 66.667 0.00 0.00 29.39 4.35
2347 5530 3.775654 CCAGTCCAGGGGAGCGAC 61.776 72.222 0.00 0.00 29.39 5.19
2348 5531 3.992641 TCCAGTCCAGGGGAGCGA 61.993 66.667 0.00 0.00 29.39 4.93
2349 5532 3.775654 GTCCAGTCCAGGGGAGCG 61.776 72.222 0.00 0.00 32.85 5.03
2351 5534 1.687493 GGAGTCCAGTCCAGGGGAG 60.687 68.421 3.60 0.00 36.51 4.30
2352 5535 2.450243 GGAGTCCAGTCCAGGGGA 59.550 66.667 3.60 0.00 36.51 4.81
2353 5536 2.122729 TGGAGTCCAGTCCAGGGG 59.877 66.667 8.12 0.00 41.99 4.79
2366 5549 4.803426 GAGGTCGTGCCGCTGGAG 62.803 72.222 0.00 0.00 43.70 3.86
2381 5564 3.770040 TGCCATCCCACGGACGAG 61.770 66.667 0.00 0.00 32.98 4.18
2403 5586 4.147321 AGATTGCAACTGACTCCACAATT 58.853 39.130 0.00 0.00 0.00 2.32
2414 5597 2.544685 CGAGGGAGTAGATTGCAACTG 58.455 52.381 0.00 0.00 0.00 3.16
2423 5606 4.736611 ATTATGGTACCGAGGGAGTAGA 57.263 45.455 7.57 0.00 0.00 2.59
2425 5608 8.806146 GTTTTATATTATGGTACCGAGGGAGTA 58.194 37.037 7.57 0.00 0.00 2.59
2426 5609 7.524367 CGTTTTATATTATGGTACCGAGGGAGT 60.524 40.741 7.57 0.00 0.00 3.85
2427 5610 6.810182 CGTTTTATATTATGGTACCGAGGGAG 59.190 42.308 7.57 0.00 0.00 4.30
2428 5611 6.267471 ACGTTTTATATTATGGTACCGAGGGA 59.733 38.462 7.57 0.00 0.00 4.20
2429 5612 6.458210 ACGTTTTATATTATGGTACCGAGGG 58.542 40.000 7.57 0.00 0.00 4.30
2430 5613 7.951530 AACGTTTTATATTATGGTACCGAGG 57.048 36.000 7.57 0.00 0.00 4.63
2432 5615 9.985318 CAAAAACGTTTTATATTATGGTACCGA 57.015 29.630 25.44 0.00 0.00 4.69
2433 5616 8.735837 GCAAAAACGTTTTATATTATGGTACCG 58.264 33.333 25.44 0.00 0.00 4.02
2434 5617 9.570488 TGCAAAAACGTTTTATATTATGGTACC 57.430 29.630 25.44 4.43 0.00 3.34
2437 5620 9.699703 AACTGCAAAAACGTTTTATATTATGGT 57.300 25.926 25.44 13.28 0.00 3.55
2460 5643 7.544217 AGACGTTTTTGCAGTTAAATTTGAACT 59.456 29.630 0.00 4.37 37.64 3.01
2461 5644 7.671827 AGACGTTTTTGCAGTTAAATTTGAAC 58.328 30.769 0.00 2.17 0.00 3.18
2462 5645 7.820044 AGACGTTTTTGCAGTTAAATTTGAA 57.180 28.000 0.00 0.00 0.00 2.69
2463 5646 7.820044 AAGACGTTTTTGCAGTTAAATTTGA 57.180 28.000 0.00 0.00 0.00 2.69
2471 5654 8.736244 ACCATAATATAAGACGTTTTTGCAGTT 58.264 29.630 0.00 0.00 0.00 3.16
2472 5655 8.276252 ACCATAATATAAGACGTTTTTGCAGT 57.724 30.769 0.00 0.00 0.00 4.40
2473 5656 9.646336 GTACCATAATATAAGACGTTTTTGCAG 57.354 33.333 0.00 0.00 0.00 4.41
2474 5657 8.614346 GGTACCATAATATAAGACGTTTTTGCA 58.386 33.333 7.15 0.00 0.00 4.08
2475 5658 7.795272 CGGTACCATAATATAAGACGTTTTTGC 59.205 37.037 13.54 0.00 0.00 3.68
2476 5659 9.033481 TCGGTACCATAATATAAGACGTTTTTG 57.967 33.333 13.54 0.00 0.00 2.44
2477 5660 9.252962 CTCGGTACCATAATATAAGACGTTTTT 57.747 33.333 13.54 0.00 0.00 1.94
2478 5661 7.869429 CCTCGGTACCATAATATAAGACGTTTT 59.131 37.037 13.54 0.00 0.00 2.43
2479 5662 7.373493 CCTCGGTACCATAATATAAGACGTTT 58.627 38.462 13.54 0.00 0.00 3.60
2480 5663 6.071728 CCCTCGGTACCATAATATAAGACGTT 60.072 42.308 13.54 0.00 0.00 3.99
2481 5664 5.416952 CCCTCGGTACCATAATATAAGACGT 59.583 44.000 13.54 0.00 0.00 4.34
2482 5665 5.649395 TCCCTCGGTACCATAATATAAGACG 59.351 44.000 13.54 0.00 0.00 4.18
2483 5666 6.662663 ACTCCCTCGGTACCATAATATAAGAC 59.337 42.308 13.54 0.00 0.00 3.01
2484 5667 6.797707 ACTCCCTCGGTACCATAATATAAGA 58.202 40.000 13.54 0.00 0.00 2.10
2485 5668 7.833183 ACTACTCCCTCGGTACCATAATATAAG 59.167 40.741 13.54 3.37 0.00 1.73
2486 5669 7.702785 ACTACTCCCTCGGTACCATAATATAA 58.297 38.462 13.54 0.00 0.00 0.98
2487 5670 7.276088 ACTACTCCCTCGGTACCATAATATA 57.724 40.000 13.54 0.00 0.00 0.86
2488 5671 6.150034 ACTACTCCCTCGGTACCATAATAT 57.850 41.667 13.54 0.00 0.00 1.28
2489 5672 5.589367 ACTACTCCCTCGGTACCATAATA 57.411 43.478 13.54 0.00 0.00 0.98
2490 5673 4.466255 ACTACTCCCTCGGTACCATAAT 57.534 45.455 13.54 0.00 0.00 1.28
2491 5674 3.959495 ACTACTCCCTCGGTACCATAA 57.041 47.619 13.54 0.00 0.00 1.90
2492 5675 4.808665 GCATACTACTCCCTCGGTACCATA 60.809 50.000 13.54 0.00 0.00 2.74
2493 5676 3.764218 CATACTACTCCCTCGGTACCAT 58.236 50.000 13.54 0.00 0.00 3.55
2494 5677 2.750807 GCATACTACTCCCTCGGTACCA 60.751 54.545 13.54 0.00 0.00 3.25
2495 5678 1.885233 GCATACTACTCCCTCGGTACC 59.115 57.143 0.16 0.16 0.00 3.34
2496 5679 2.553172 CTGCATACTACTCCCTCGGTAC 59.447 54.545 0.00 0.00 0.00 3.34
2497 5680 2.860009 CTGCATACTACTCCCTCGGTA 58.140 52.381 0.00 0.00 0.00 4.02
2498 5681 1.693627 CTGCATACTACTCCCTCGGT 58.306 55.000 0.00 0.00 0.00 4.69
2499 5682 0.315568 GCTGCATACTACTCCCTCGG 59.684 60.000 0.00 0.00 0.00 4.63
2500 5683 1.000827 CTGCTGCATACTACTCCCTCG 60.001 57.143 1.31 0.00 0.00 4.63
2501 5684 1.270041 GCTGCTGCATACTACTCCCTC 60.270 57.143 11.11 0.00 39.41 4.30
2502 5685 0.755686 GCTGCTGCATACTACTCCCT 59.244 55.000 11.11 0.00 39.41 4.20
2503 5686 0.465705 TGCTGCTGCATACTACTCCC 59.534 55.000 14.93 0.00 45.31 4.30
2521 5709 2.066262 AGTAAAACAGATCGTGCCGTG 58.934 47.619 0.00 0.00 0.00 4.94
2593 5783 4.024048 TGAAGAAACGAGACAAGGAATTGC 60.024 41.667 0.00 0.00 0.00 3.56
2594 5784 5.466728 TCTGAAGAAACGAGACAAGGAATTG 59.533 40.000 0.00 0.00 0.00 2.32
2626 5816 2.715005 CTCTCTCTGCTCGGCGAG 59.285 66.667 31.40 31.40 33.22 5.03
2627 5817 2.826287 CCTCTCTCTGCTCGGCGA 60.826 66.667 10.14 10.14 0.00 5.54
2629 5819 4.219999 GCCCTCTCTCTGCTCGGC 62.220 72.222 0.00 0.00 0.00 5.54
2631 5821 2.003658 GACAGCCCTCTCTCTGCTCG 62.004 65.000 0.00 0.00 33.80 5.03
2632 5822 1.675720 GGACAGCCCTCTCTCTGCTC 61.676 65.000 0.00 0.00 33.80 4.26
2634 5824 2.899505 GGACAGCCCTCTCTCTGC 59.100 66.667 0.00 0.00 33.80 4.26
2635 5825 2.422231 CCGGACAGCCCTCTCTCTG 61.422 68.421 0.00 0.00 36.45 3.35
2636 5826 2.043450 CCGGACAGCCCTCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
2637 5827 3.844090 GCCGGACAGCCCTCTCTC 61.844 72.222 5.05 0.00 0.00 3.20
2647 5844 4.451150 GATGGTCGCTGCCGGACA 62.451 66.667 5.05 1.09 34.56 4.02
2680 5893 0.179000 CTATGACCACTGTGGAGGGC 59.821 60.000 32.30 17.66 40.96 5.19
2681 5894 0.179000 GCTATGACCACTGTGGAGGG 59.821 60.000 32.30 16.87 40.96 4.30


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

AutoCloner maintained by Alex Coulton.