Multiple sequence alignment - TraesCS3A01G078600

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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 TraesCS3A01G078600 chr3A 100.000 4382 0 0 1 4382 50818180 50822561 0.000000e+00 8093.0
1 TraesCS3A01G078600 chr3A 78.886 341 38 18 1130 1467 708353791 708353482 2.670000e-47 200.0
2 TraesCS3A01G078600 chr3D 88.605 2817 176 74 974 3714 39363307 39366054 0.000000e+00 3290.0
3 TraesCS3A01G078600 chr3D 81.712 946 62 38 1 909 39362441 39363312 0.000000e+00 686.0
4 TraesCS3A01G078600 chr3D 84.390 205 22 9 107 304 39361866 39362067 4.470000e-45 193.0
5 TraesCS3A01G078600 chr3D 87.931 116 11 3 1 116 39361731 39361843 2.750000e-27 134.0
6 TraesCS3A01G078600 chr3D 87.059 85 11 0 1130 1214 573704912 573704828 3.610000e-16 97.1
7 TraesCS3A01G078600 chr3B 89.628 2526 173 45 1816 4286 62417022 62419513 0.000000e+00 3131.0
8 TraesCS3A01G078600 chr3B 86.522 920 71 30 1 910 62414719 62415595 0.000000e+00 963.0
9 TraesCS3A01G078600 chr3B 92.661 327 18 2 898 1218 62416070 62416396 2.390000e-127 466.0
10 TraesCS3A01G078600 chr3B 85.079 315 25 14 1291 1584 62416428 62416741 7.120000e-78 302.0
11 TraesCS3A01G078600 chr3B 93.878 196 12 0 1583 1778 62416819 62417014 3.310000e-76 296.0
12 TraesCS3A01G078600 chr3B 77.157 197 43 2 3961 4156 647457882 647458077 3.580000e-21 113.0
13 TraesCS3A01G078600 chr6A 97.980 99 2 0 4284 4382 290343928 290343830 5.830000e-39 172.0
14 TraesCS3A01G078600 chr6A 91.525 118 7 3 4267 4382 546896928 546896812 4.540000e-35 159.0
15 TraesCS3A01G078600 chr5A 97.059 102 3 0 4281 4382 196092701 196092600 5.830000e-39 172.0
16 TraesCS3A01G078600 chr7D 96.190 105 3 1 4277 4381 415606214 415606317 2.100000e-38 171.0
17 TraesCS3A01G078600 chr7A 97.059 102 2 1 4282 4382 652656774 652656673 2.100000e-38 171.0
18 TraesCS3A01G078600 chr7B 97.000 100 3 0 4283 4382 598167010 598166911 7.540000e-38 169.0
19 TraesCS3A01G078600 chrUn 93.694 111 5 2 4273 4382 299812756 299812865 9.750000e-37 165.0
20 TraesCS3A01G078600 chrUn 93.694 111 5 2 4273 4382 299826983 299827092 9.750000e-37 165.0
21 TraesCS3A01G078600 chrUn 93.694 111 5 2 4273 4382 463865503 463865394 9.750000e-37 165.0
22 TraesCS3A01G078600 chr5B 92.405 79 6 0 1488 1566 293950282 293950204 3.580000e-21 113.0


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 TraesCS3A01G078600 chr3A 50818180 50822561 4381 False 8093.00 8093 100.0000 1 4382 1 chr3A.!!$F1 4381
1 TraesCS3A01G078600 chr3D 39361731 39366054 4323 False 1075.75 3290 85.6595 1 3714 4 chr3D.!!$F1 3713
2 TraesCS3A01G078600 chr3B 62414719 62419513 4794 False 1031.60 3131 89.5536 1 4286 5 chr3B.!!$F2 4285

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
542 1280 0.030638 CCGCATTAATTCCCGCTTGG 59.969 55.0 0.0 0.0 0.0 3.61 F
855 1616 0.524862 CATCCTTTGCTGCTGTGTCC 59.475 55.0 0.0 0.0 0.0 4.02 F
1616 2972 0.469070 CAAGAGCTGATGAGAGGGGG 59.531 60.0 0.0 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 2958 0.620556 TGAAACCCCCTCTCATCAGC 59.379 55.000 0.00 0.0 0.00 4.26 R
2470 3910 1.826024 CCTGTGGAATCGGGGAGAG 59.174 63.158 0.00 0.0 0.00 3.20 R
3591 5058 0.177836 TGGTCATGACATGCTACCGG 59.822 55.000 26.47 0.0 31.63 5.28 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 3.785505 GCACTTGCGGAATCGATGTTAAG 60.786 47.826 0.00 2.90 39.00 1.85
24 25 3.370978 CACTTGCGGAATCGATGTTAAGT 59.629 43.478 0.00 3.53 39.00 2.24
25 26 4.565166 CACTTGCGGAATCGATGTTAAGTA 59.435 41.667 0.00 0.00 39.00 2.24
26 27 4.804139 ACTTGCGGAATCGATGTTAAGTAG 59.196 41.667 0.00 0.00 39.00 2.57
32 33 6.137415 CGGAATCGATGTTAAGTAGAGACTC 58.863 44.000 0.00 0.00 39.00 3.36
48 50 0.905357 ACTCGGGTAGATGCAAAGCT 59.095 50.000 0.00 0.00 0.00 3.74
64 66 4.190772 CAAAGCTCAGGAGGAAGAATCTC 58.809 47.826 0.00 0.00 0.00 2.75
76 78 5.198965 AGGAAGAATCTCCAAACCATCATG 58.801 41.667 0.00 0.00 38.02 3.07
119 155 3.665323 CGAGCACTCAACTTACACATTGC 60.665 47.826 0.00 0.00 0.00 3.56
126 162 5.536161 ACTCAACTTACACATTGCTGGATTT 59.464 36.000 0.00 0.00 0.00 2.17
127 163 5.771469 TCAACTTACACATTGCTGGATTTG 58.229 37.500 0.00 0.00 0.00 2.32
132 168 7.047271 ACTTACACATTGCTGGATTTGTTTTT 58.953 30.769 0.00 0.00 0.00 1.94
178 215 2.359230 GCGCTCCTGCTCAAAGGT 60.359 61.111 0.00 0.00 38.58 3.50
189 235 2.809601 CAAAGGTCGGTCGCGGAG 60.810 66.667 6.13 0.00 0.00 4.63
276 322 0.462759 CTTCTCTCCCCCATTGACGC 60.463 60.000 0.00 0.00 0.00 5.19
290 336 0.319555 TGACGCCTCCGAGAGTTTTG 60.320 55.000 0.00 0.00 38.29 2.44
542 1280 0.030638 CCGCATTAATTCCCGCTTGG 59.969 55.000 0.00 0.00 0.00 3.61
543 1281 0.738389 CGCATTAATTCCCGCTTGGT 59.262 50.000 0.00 0.00 34.77 3.67
548 1286 4.142249 GCATTAATTCCCGCTTGGTTAACT 60.142 41.667 5.42 0.00 34.77 2.24
550 1288 6.404954 GCATTAATTCCCGCTTGGTTAACTTA 60.405 38.462 5.42 0.00 34.77 2.24
572 1310 1.301479 GACTATAAAGCCGGGCCCG 60.301 63.158 37.99 37.99 39.44 6.13
645 1383 1.662629 CTCGCTGTTCGCAAATCTGAT 59.337 47.619 0.00 0.00 39.08 2.90
646 1384 1.660607 TCGCTGTTCGCAAATCTGATC 59.339 47.619 0.00 0.00 39.08 2.92
647 1385 1.590679 CGCTGTTCGCAAATCTGATCG 60.591 52.381 0.00 0.00 39.08 3.69
648 1386 1.660607 GCTGTTCGCAAATCTGATCGA 59.339 47.619 0.00 0.00 38.92 3.59
649 1387 2.535732 GCTGTTCGCAAATCTGATCGAC 60.536 50.000 0.00 0.00 38.92 4.20
653 1391 1.273887 GCAAATCTGATCGACGCCG 59.726 57.895 0.00 0.00 37.07 6.46
680 1418 3.498397 CGACCTTGCTGACATTGTAAGTT 59.502 43.478 3.08 0.00 0.00 2.66
683 1421 6.293190 CGACCTTGCTGACATTGTAAGTTTTA 60.293 38.462 3.08 0.00 0.00 1.52
711 1449 0.880718 GGGGATCGTCGATTTGCTCC 60.881 60.000 9.52 6.23 0.00 4.70
720 1458 2.270923 TCGATTTGCTCCATCGACTTG 58.729 47.619 10.24 0.00 45.87 3.16
747 1494 0.540133 TTGCCCATCTTGCTCTGCAA 60.540 50.000 4.87 4.87 46.80 4.08
758 1505 3.354089 TGCTCTGCAACTGCTTTTAAC 57.646 42.857 2.95 0.00 42.66 2.01
759 1506 2.034558 TGCTCTGCAACTGCTTTTAACC 59.965 45.455 2.95 0.00 42.66 2.85
764 1517 5.108517 TCTGCAACTGCTTTTAACCTTTTG 58.891 37.500 2.95 0.00 42.66 2.44
765 1518 4.826556 TGCAACTGCTTTTAACCTTTTGT 58.173 34.783 2.95 0.00 42.66 2.83
766 1519 5.241662 TGCAACTGCTTTTAACCTTTTGTT 58.758 33.333 2.95 0.00 42.66 2.83
767 1520 5.703130 TGCAACTGCTTTTAACCTTTTGTTT 59.297 32.000 2.95 0.00 42.66 2.83
768 1521 6.205658 TGCAACTGCTTTTAACCTTTTGTTTT 59.794 30.769 2.95 0.00 42.66 2.43
769 1522 6.740905 GCAACTGCTTTTAACCTTTTGTTTTC 59.259 34.615 0.00 0.00 36.90 2.29
770 1523 7.360861 GCAACTGCTTTTAACCTTTTGTTTTCT 60.361 33.333 0.00 0.00 36.90 2.52
771 1524 9.145865 CAACTGCTTTTAACCTTTTGTTTTCTA 57.854 29.630 0.00 0.00 38.42 2.10
772 1525 8.926715 ACTGCTTTTAACCTTTTGTTTTCTAG 57.073 30.769 0.00 0.00 38.42 2.43
773 1526 8.528643 ACTGCTTTTAACCTTTTGTTTTCTAGT 58.471 29.630 0.00 0.00 38.42 2.57
788 1541 7.313646 TGTTTTCTAGTAGTTTCAGAGATCCG 58.686 38.462 0.00 0.00 0.00 4.18
812 1569 1.541310 TTGGCCACCTACCTCTGTCG 61.541 60.000 3.88 0.00 0.00 4.35
813 1574 2.184579 GCCACCTACCTCTGTCGC 59.815 66.667 0.00 0.00 0.00 5.19
855 1616 0.524862 CATCCTTTGCTGCTGTGTCC 59.475 55.000 0.00 0.00 0.00 4.02
933 2182 2.344872 TGCTCACGCTGTGCATCT 59.655 55.556 9.57 0.00 41.27 2.90
939 2193 1.822371 TCACGCTGTGCATCTAGGTTA 59.178 47.619 0.00 0.00 32.98 2.85
940 2194 2.430694 TCACGCTGTGCATCTAGGTTAT 59.569 45.455 0.00 0.00 32.98 1.89
951 2205 4.508124 GCATCTAGGTTATTGTTCTGACGG 59.492 45.833 0.00 0.00 0.00 4.79
1074 2328 1.870055 TACAGGAGGTCGCCGTGTTC 61.870 60.000 0.00 0.00 0.00 3.18
1214 2468 7.823310 GGCTGAAGATATCTGTATGTTGATCAT 59.177 37.037 5.86 0.00 40.25 2.45
1218 2472 9.149225 GAAGATATCTGTATGTTGATCATCACC 57.851 37.037 5.86 3.93 37.91 4.02
1219 2473 8.433249 AGATATCTGTATGTTGATCATCACCT 57.567 34.615 3.89 0.00 37.91 4.00
1277 2531 7.307989 CCGGCCATTTAGATTACTTGACTAATG 60.308 40.741 2.24 0.00 0.00 1.90
1279 2533 8.560374 GGCCATTTAGATTACTTGACTAATGAC 58.440 37.037 0.00 0.00 0.00 3.06
1289 2543 5.940595 ACTTGACTAATGACGAGTGAGTAC 58.059 41.667 0.00 0.00 32.78 2.73
1300 2554 5.868258 TGACGAGTGAGTACTGAGTAGTAAG 59.132 44.000 0.00 0.00 40.89 2.34
1302 2556 6.462500 ACGAGTGAGTACTGAGTAGTAAGAA 58.538 40.000 0.00 0.00 40.89 2.52
1303 2557 7.104939 ACGAGTGAGTACTGAGTAGTAAGAAT 58.895 38.462 0.00 0.00 40.89 2.40
1305 2559 9.096160 CGAGTGAGTACTGAGTAGTAAGAATTA 57.904 37.037 0.00 0.00 40.89 1.40
1313 2567 8.534954 ACTGAGTAGTAAGAATTATGTGCCTA 57.465 34.615 0.00 0.00 34.74 3.93
1334 2588 8.855110 TGCCTATTATTTTTCTGAACTGTTGAA 58.145 29.630 0.00 0.00 0.00 2.69
1375 2630 2.941453 TATGTCGGCTGTCTCTGAAC 57.059 50.000 0.00 0.00 0.00 3.18
1389 2644 3.660111 GAACTGCAACGCGCCCTT 61.660 61.111 5.73 0.00 41.33 3.95
1425 2680 4.321230 CCTGTTGTTCTTGGATTAACAGCC 60.321 45.833 0.00 0.00 44.08 4.85
1439 2694 2.736670 ACAGCCAAAGGTCTGAACTT 57.263 45.000 1.18 1.18 33.40 2.66
1450 2705 2.769095 GGTCTGAACTTCAGCCTATCCT 59.231 50.000 13.24 0.00 43.95 3.24
1491 2768 5.776173 AGTAGTACTCAATCGCTATTGCT 57.224 39.130 0.00 0.95 41.96 3.91
1601 2957 6.422333 TGCCATACTTATTGGTTGATCAAGA 58.578 36.000 8.80 0.00 36.57 3.02
1602 2958 6.543465 TGCCATACTTATTGGTTGATCAAGAG 59.457 38.462 8.80 3.30 36.57 2.85
1615 2971 1.493861 TCAAGAGCTGATGAGAGGGG 58.506 55.000 0.00 0.00 0.00 4.79
1616 2972 0.469070 CAAGAGCTGATGAGAGGGGG 59.531 60.000 0.00 0.00 0.00 5.40
1638 2994 1.189752 TCATCCAGGAGTGCTGTCTC 58.810 55.000 11.04 0.00 0.00 3.36
1702 3058 0.518636 GATGCTTGCGCTGTTTGAGA 59.481 50.000 9.73 0.00 36.97 3.27
1741 3097 1.373570 GAGAGACGGCCAAAATGGAG 58.626 55.000 2.24 0.00 40.96 3.86
1778 3134 5.344743 TCTGAAGGTCAGTTCCATGTATC 57.655 43.478 5.23 0.00 44.58 2.24
1785 3141 5.187186 AGGTCAGTTCCATGTATCTACGTTT 59.813 40.000 0.00 0.00 0.00 3.60
1803 3159 5.569413 ACGTTTGATTCAAAGAGACAACAC 58.431 37.500 12.02 0.00 33.82 3.32
1808 3164 5.192927 TGATTCAAAGAGACAACACCACTT 58.807 37.500 0.00 0.00 0.00 3.16
1888 3252 6.211184 TCACAGTGAAATTAATGAAATGGCCT 59.789 34.615 3.32 0.00 0.00 5.19
1889 3253 6.532657 CACAGTGAAATTAATGAAATGGCCTC 59.467 38.462 3.32 0.00 0.00 4.70
1927 3300 7.678947 ACTAGATTCAAAGAAGGATGTTGTG 57.321 36.000 0.00 0.00 0.00 3.33
1985 3358 3.000041 TCCGTGCATCACATACTTGTTC 59.000 45.455 0.00 0.00 32.34 3.18
1987 3360 3.188254 CCGTGCATCACATACTTGTTCAA 59.812 43.478 0.00 0.00 32.34 2.69
2034 3424 5.197451 ACAAAACCTGTGACCAGTTATCAA 58.803 37.500 0.00 0.00 36.69 2.57
2036 3426 4.706842 AACCTGTGACCAGTTATCAACT 57.293 40.909 0.00 0.00 44.06 3.16
2037 3427 4.706842 ACCTGTGACCAGTTATCAACTT 57.293 40.909 0.00 0.00 40.46 2.66
2038 3428 5.048846 ACCTGTGACCAGTTATCAACTTT 57.951 39.130 0.00 0.00 40.46 2.66
2040 3430 6.597562 ACCTGTGACCAGTTATCAACTTTTA 58.402 36.000 0.00 0.00 40.46 1.52
2041 3431 6.485648 ACCTGTGACCAGTTATCAACTTTTAC 59.514 38.462 0.00 0.00 40.46 2.01
2042 3432 6.710744 CCTGTGACCAGTTATCAACTTTTACT 59.289 38.462 0.00 0.00 40.46 2.24
2043 3433 7.876068 CCTGTGACCAGTTATCAACTTTTACTA 59.124 37.037 0.00 0.00 40.46 1.82
2044 3434 8.597662 TGTGACCAGTTATCAACTTTTACTAC 57.402 34.615 0.00 0.00 40.46 2.73
2045 3435 8.426489 TGTGACCAGTTATCAACTTTTACTACT 58.574 33.333 0.00 0.00 40.46 2.57
2046 3436 9.918630 GTGACCAGTTATCAACTTTTACTACTA 57.081 33.333 0.00 0.00 40.46 1.82
2047 3437 9.918630 TGACCAGTTATCAACTTTTACTACTAC 57.081 33.333 0.00 0.00 40.46 2.73
2048 3438 9.363763 GACCAGTTATCAACTTTTACTACTACC 57.636 37.037 0.00 0.00 40.46 3.18
2049 3439 8.873144 ACCAGTTATCAACTTTTACTACTACCA 58.127 33.333 0.00 0.00 40.46 3.25
2050 3440 9.148104 CCAGTTATCAACTTTTACTACTACCAC 57.852 37.037 0.00 0.00 40.46 4.16
2051 3441 9.924650 CAGTTATCAACTTTTACTACTACCACT 57.075 33.333 0.00 0.00 40.46 4.00
2055 3445 7.838079 TCAACTTTTACTACTACCACTACCA 57.162 36.000 0.00 0.00 0.00 3.25
2056 3446 8.426569 TCAACTTTTACTACTACCACTACCAT 57.573 34.615 0.00 0.00 0.00 3.55
2057 3447 8.873144 TCAACTTTTACTACTACCACTACCATT 58.127 33.333 0.00 0.00 0.00 3.16
2058 3448 8.932791 CAACTTTTACTACTACCACTACCATTG 58.067 37.037 0.00 0.00 0.00 2.82
2059 3449 8.426569 ACTTTTACTACTACCACTACCATTGA 57.573 34.615 0.00 0.00 0.00 2.57
2098 3488 5.006386 AGCTCACCTTTGAATTACAGGAAG 58.994 41.667 4.42 3.29 0.00 3.46
2099 3489 5.003804 GCTCACCTTTGAATTACAGGAAGA 58.996 41.667 4.42 2.17 0.00 2.87
2101 3491 6.187727 TCACCTTTGAATTACAGGAAGAGT 57.812 37.500 4.42 0.00 0.00 3.24
2165 3555 3.402628 TTCAGTCTTTGGCTCAGGTAC 57.597 47.619 0.00 0.00 0.00 3.34
2269 3704 7.707035 GCGATCCTTATACTTTACCTATGATGG 59.293 40.741 0.00 0.00 0.00 3.51
2285 3720 6.536582 CCTATGATGGAAAACAGTGTGTAGAG 59.463 42.308 0.00 0.00 0.00 2.43
2294 3729 6.835819 AAACAGTGTGTAGAGATACAGCTA 57.164 37.500 0.00 0.00 0.00 3.32
2380 3815 7.428826 CAAGTCAGCTATTTTTCAAAGGTCTT 58.571 34.615 0.00 0.00 0.00 3.01
2429 3868 5.056894 AGCAAGTTTCATCAGCATCTTTC 57.943 39.130 0.00 0.00 0.00 2.62
2470 3910 3.347216 TCTTTTCATACTGGCTTCCTGC 58.653 45.455 0.00 0.00 41.94 4.85
2478 3918 4.168291 GGCTTCCTGCTCTCCCCG 62.168 72.222 0.00 0.00 42.39 5.73
2505 3945 1.889170 CAGGCTCACTACTGTCTGTCA 59.111 52.381 0.00 0.00 0.00 3.58
2565 4005 2.751806 GCTCTTCCTCAAGTGGAAATGG 59.248 50.000 5.27 0.98 44.49 3.16
2581 4021 0.680921 ATGGATGGACGCCAAGGTTG 60.681 55.000 2.68 0.00 39.21 3.77
2833 4273 1.615883 GGTCTGACTGAGAGTTCTGCA 59.384 52.381 7.85 0.00 0.00 4.41
2982 4439 5.408909 TGTCGCGTACAAGAAATTCCAAATA 59.591 36.000 5.77 0.00 34.29 1.40
2985 4442 8.280497 GTCGCGTACAAGAAATTCCAAATATAT 58.720 33.333 5.77 0.00 0.00 0.86
3020 4477 4.511826 CGAGCAAGACAAGAAAAGGTAAGT 59.488 41.667 0.00 0.00 0.00 2.24
3042 4499 3.383698 AAGTCCTCCGGTATCAAGAGA 57.616 47.619 0.00 0.00 0.00 3.10
3091 4548 8.695456 AGATTCCAAAGTTAAAAGCTTCTTCAA 58.305 29.630 0.00 0.00 0.00 2.69
3151 4608 1.296392 CCCAAGGACACGCATGAGA 59.704 57.895 2.50 0.00 0.00 3.27
3152 4609 0.321564 CCCAAGGACACGCATGAGAA 60.322 55.000 2.50 0.00 0.00 2.87
3358 4818 1.439644 GAGCATCTGGAGGACGACC 59.560 63.158 0.00 0.00 0.00 4.79
3503 4965 8.490355 GGCAGAACAAAATTGAAAACAGAATAG 58.510 33.333 0.00 0.00 0.00 1.73
3512 4974 5.862924 TGAAAACAGAATAGTAGCTGTGC 57.137 39.130 0.00 4.13 44.06 4.57
3522 4984 6.656693 AGAATAGTAGCTGTGCAAGTGAAAAT 59.343 34.615 0.00 0.00 0.00 1.82
3615 5082 0.393944 AGCATGTCATGACCAGGCAG 60.394 55.000 25.54 12.18 0.00 4.85
3667 5134 5.804692 TCAAAAGAAGTGTAAAGCGTCAA 57.195 34.783 0.00 0.00 0.00 3.18
3720 5194 6.235231 TCCATTGTTCCTGATCCTAAGTAC 57.765 41.667 0.00 0.00 0.00 2.73
3739 5213 1.537814 CCACTAGGTACCACCGCACA 61.538 60.000 15.94 0.00 44.90 4.57
3742 5216 0.810031 CTAGGTACCACCGCACATGC 60.810 60.000 15.94 0.00 44.90 4.06
3788 5262 7.820386 TCAGTAACCGTAGCTTGAAATCATAAA 59.180 33.333 0.00 0.00 0.00 1.40
3789 5263 8.116753 CAGTAACCGTAGCTTGAAATCATAAAG 58.883 37.037 0.00 0.00 0.00 1.85
3797 5272 7.709149 AGCTTGAAATCATAAAGTTTAGGCT 57.291 32.000 2.38 0.00 0.00 4.58
3804 5279 7.730364 AATCATAAAGTTTAGGCTACCATCG 57.270 36.000 2.38 0.00 0.00 3.84
3827 5302 6.304445 TCGCAATGAACGAATAACAATTGAAC 59.696 34.615 13.59 0.00 36.44 3.18
3865 5340 6.827586 TTATGATAAGGTTGGAAAAAGCGT 57.172 33.333 0.00 0.00 0.00 5.07
3866 5341 7.925043 TTATGATAAGGTTGGAAAAAGCGTA 57.075 32.000 0.00 0.00 0.00 4.42
3867 5342 5.873179 TGATAAGGTTGGAAAAAGCGTAG 57.127 39.130 0.00 0.00 0.00 3.51
3875 5351 3.460103 TGGAAAAAGCGTAGTCGAAAGT 58.540 40.909 0.00 0.00 39.71 2.66
3904 5380 1.290639 GCCTTAGCCTAGCGCCTAG 59.709 63.158 2.29 5.30 38.78 3.02
3918 5394 1.679311 CCTAGGTGGCACTTCAGCA 59.321 57.895 18.45 0.00 37.59 4.41
3919 5395 0.674895 CCTAGGTGGCACTTCAGCAC 60.675 60.000 18.45 0.00 37.59 4.40
3934 5426 1.041447 AGCACCCTAGGCGAACGTAT 61.041 55.000 2.05 0.00 36.08 3.06
3938 5430 1.952296 ACCCTAGGCGAACGTATAGTG 59.048 52.381 2.05 0.00 0.00 2.74
4041 5533 4.889409 CCATTGTATTATGGCTCAGTTGGT 59.111 41.667 0.00 0.00 38.75 3.67
4044 5536 7.094634 CCATTGTATTATGGCTCAGTTGGTATC 60.095 40.741 0.00 0.00 38.75 2.24
4081 5573 6.374333 TGGTCTAATTTATTGCTTGAGTGGAC 59.626 38.462 0.00 0.00 0.00 4.02
4096 5588 3.989817 GAGTGGACAATTTCATGTTTGCC 59.010 43.478 0.00 3.28 32.57 4.52
4099 5591 3.006752 TGGACAATTTCATGTTTGCCCTC 59.993 43.478 10.54 2.00 32.57 4.30
4101 5593 3.242011 ACAATTTCATGTTTGCCCTCCT 58.758 40.909 0.00 0.00 0.00 3.69
4136 5628 1.648467 GCTCTAGGCAAGGCGTTTGG 61.648 60.000 0.00 0.00 41.35 3.28
4144 5636 3.175976 AAGGCGTTTGGTCGTTGCG 62.176 57.895 0.00 0.00 0.00 4.85
4167 5659 1.348594 GCCTAAGCGTGCTTAAGCG 59.651 57.895 21.97 10.25 45.83 4.68
4168 5660 1.359459 GCCTAAGCGTGCTTAAGCGT 61.359 55.000 21.97 7.65 45.83 5.07
4169 5661 0.645868 CCTAAGCGTGCTTAAGCGTC 59.354 55.000 21.97 15.90 45.83 5.19
4170 5662 1.630148 CTAAGCGTGCTTAAGCGTCT 58.370 50.000 21.97 15.01 45.83 4.18
4171 5663 1.584308 CTAAGCGTGCTTAAGCGTCTC 59.416 52.381 21.97 12.53 45.83 3.36
4172 5664 1.014564 AAGCGTGCTTAAGCGTCTCC 61.015 55.000 21.97 8.78 45.83 3.71
4173 5665 1.446272 GCGTGCTTAAGCGTCTCCT 60.446 57.895 21.97 0.00 45.83 3.69
4174 5666 0.179145 GCGTGCTTAAGCGTCTCCTA 60.179 55.000 21.97 0.00 45.83 2.94
4175 5667 1.828832 CGTGCTTAAGCGTCTCCTAG 58.171 55.000 21.97 3.88 45.83 3.02
4176 5668 1.534175 CGTGCTTAAGCGTCTCCTAGG 60.534 57.143 21.97 0.82 45.83 3.02
4177 5669 0.460311 TGCTTAAGCGTCTCCTAGGC 59.540 55.000 21.97 0.00 45.83 3.93
4182 5674 2.837371 AAGCGTCTCCTAGGCGTTGC 62.837 60.000 2.96 6.88 46.51 4.17
4192 5684 4.336581 GGCGTTGCCTTTTCCAAC 57.663 55.556 0.00 0.00 46.69 3.77
4200 5692 5.469479 CGTTGCCTTTTCCAACAGATTTAT 58.531 37.500 5.30 0.00 41.94 1.40
4217 5709 5.876460 AGATTTATGATGGCTTTTGTTTGGC 59.124 36.000 0.00 0.00 0.00 4.52
4220 5712 1.344114 TGATGGCTTTTGTTTGGCCTC 59.656 47.619 3.32 0.00 45.45 4.70
4224 5716 0.319813 GCTTTTGTTTGGCCTCGCAT 60.320 50.000 3.32 0.00 0.00 4.73
4236 5728 2.609244 GGCCTCGCATCTACTGATTCTC 60.609 54.545 0.00 0.00 0.00 2.87
4238 5730 3.491619 GCCTCGCATCTACTGATTCTCAA 60.492 47.826 0.00 0.00 0.00 3.02
4246 5738 7.864882 CGCATCTACTGATTCTCAAATTCTAGA 59.135 37.037 0.00 0.00 0.00 2.43
4253 5745 8.991275 ACTGATTCTCAAATTCTAGATCTTCCT 58.009 33.333 0.00 0.00 0.00 3.36
4286 5778 5.063204 TCTCAAACAAACACATCGGATTCT 58.937 37.500 0.00 0.00 0.00 2.40
4287 5779 5.049474 TCTCAAACAAACACATCGGATTCTG 60.049 40.000 0.00 0.00 0.00 3.02
4288 5780 4.578516 TCAAACAAACACATCGGATTCTGT 59.421 37.500 0.00 0.00 0.00 3.41
4289 5781 5.067153 TCAAACAAACACATCGGATTCTGTT 59.933 36.000 5.38 5.38 0.00 3.16
4290 5782 4.488126 ACAAACACATCGGATTCTGTTG 57.512 40.909 10.21 2.61 0.00 3.33
4291 5783 4.133820 ACAAACACATCGGATTCTGTTGA 58.866 39.130 9.95 0.00 0.00 3.18
4292 5784 4.024048 ACAAACACATCGGATTCTGTTGAC 60.024 41.667 9.95 0.00 0.00 3.18
4293 5785 3.401033 ACACATCGGATTCTGTTGACA 57.599 42.857 9.95 0.00 0.00 3.58
4294 5786 3.067106 ACACATCGGATTCTGTTGACAC 58.933 45.455 9.95 0.00 0.00 3.67
4295 5787 3.066380 CACATCGGATTCTGTTGACACA 58.934 45.455 9.95 0.00 0.00 3.72
4296 5788 3.067106 ACATCGGATTCTGTTGACACAC 58.933 45.455 9.95 0.00 0.00 3.82
4297 5789 1.778334 TCGGATTCTGTTGACACACG 58.222 50.000 0.00 0.00 0.00 4.49
4298 5790 1.338655 TCGGATTCTGTTGACACACGA 59.661 47.619 0.00 0.00 0.00 4.35
4299 5791 2.131972 CGGATTCTGTTGACACACGAA 58.868 47.619 0.00 0.00 0.00 3.85
4300 5792 2.096909 CGGATTCTGTTGACACACGAAC 60.097 50.000 0.00 0.00 0.00 3.95
4301 5793 2.869801 GGATTCTGTTGACACACGAACA 59.130 45.455 0.00 0.00 0.00 3.18
4302 5794 3.303132 GGATTCTGTTGACACACGAACAC 60.303 47.826 0.00 0.00 0.00 3.32
4303 5795 1.273688 TCTGTTGACACACGAACACG 58.726 50.000 0.00 0.00 0.00 4.49
4304 5796 0.996462 CTGTTGACACACGAACACGT 59.004 50.000 0.00 0.00 41.02 4.49
4305 5797 0.993532 TGTTGACACACGAACACGTC 59.006 50.000 0.00 0.00 38.21 4.34
4306 5798 0.993532 GTTGACACACGAACACGTCA 59.006 50.000 0.00 0.00 38.21 4.35
4307 5799 0.993532 TTGACACACGAACACGTCAC 59.006 50.000 0.00 0.00 38.07 3.67
4308 5800 1.135114 TGACACACGAACACGTCACG 61.135 55.000 0.00 0.00 38.21 4.35
4309 5801 1.135699 GACACACGAACACGTCACGT 61.136 55.000 0.00 0.00 42.36 4.49
4318 5810 2.949106 ACGTCACGTGTACCCTCG 59.051 61.111 16.51 13.30 39.18 4.63
4319 5811 1.597854 ACGTCACGTGTACCCTCGA 60.598 57.895 16.51 0.00 39.18 4.04
4320 5812 1.154338 CGTCACGTGTACCCTCGAC 60.154 63.158 16.51 2.42 0.00 4.20
4321 5813 1.844771 CGTCACGTGTACCCTCGACA 61.845 60.000 16.51 0.00 0.00 4.35
4322 5814 0.386478 GTCACGTGTACCCTCGACAC 60.386 60.000 16.51 0.00 43.10 3.67
4323 5815 1.080974 CACGTGTACCCTCGACACC 60.081 63.158 7.58 0.00 43.53 4.16
4324 5816 2.177531 CGTGTACCCTCGACACCG 59.822 66.667 0.61 0.00 43.53 4.94
4325 5817 2.570181 GTGTACCCTCGACACCGG 59.430 66.667 0.00 0.00 41.13 5.28
4326 5818 2.677524 TGTACCCTCGACACCGGG 60.678 66.667 6.32 5.93 46.26 5.73
4338 5830 4.033776 ACCGGGGGTGATGCACAG 62.034 66.667 6.32 0.00 35.86 3.66
4343 5835 2.360852 GGGTGATGCACAGCAGCT 60.361 61.111 16.48 0.00 45.80 4.24
4344 5836 2.404995 GGGTGATGCACAGCAGCTC 61.405 63.158 16.48 4.87 45.80 4.09
4345 5837 1.673337 GGTGATGCACAGCAGCTCA 60.673 57.895 10.57 0.19 45.80 4.26
4346 5838 1.500844 GTGATGCACAGCAGCTCAC 59.499 57.895 8.76 9.01 45.80 3.51
4347 5839 2.030958 TGATGCACAGCAGCTCACG 61.031 57.895 8.76 0.00 45.80 4.35
4348 5840 2.031516 GATGCACAGCAGCTCACGT 61.032 57.895 0.00 0.00 43.65 4.49
4349 5841 1.964290 GATGCACAGCAGCTCACGTC 61.964 60.000 0.00 0.00 43.65 4.34
4350 5842 3.771491 GCACAGCAGCTCACGTCG 61.771 66.667 0.00 0.00 0.00 5.12
4351 5843 2.050077 CACAGCAGCTCACGTCGA 60.050 61.111 0.00 0.00 0.00 4.20
4352 5844 1.661509 CACAGCAGCTCACGTCGAA 60.662 57.895 0.00 0.00 0.00 3.71
4353 5845 1.372251 ACAGCAGCTCACGTCGAAG 60.372 57.895 0.00 0.00 0.00 3.79
4354 5846 2.091112 CAGCAGCTCACGTCGAAGG 61.091 63.158 0.00 0.00 0.00 3.46
4355 5847 2.258591 GCAGCTCACGTCGAAGGA 59.741 61.111 0.00 0.00 0.00 3.36
4356 5848 1.803519 GCAGCTCACGTCGAAGGAG 60.804 63.158 0.00 7.74 0.00 3.69
4357 5849 1.876664 CAGCTCACGTCGAAGGAGA 59.123 57.895 16.63 7.92 0.00 3.71
4358 5850 0.179176 CAGCTCACGTCGAAGGAGAG 60.179 60.000 16.63 15.92 0.00 3.20
4359 5851 1.515304 GCTCACGTCGAAGGAGAGC 60.515 63.158 23.69 23.69 43.95 4.09
4360 5852 1.137825 CTCACGTCGAAGGAGAGCC 59.862 63.158 0.00 0.00 0.00 4.70
4361 5853 2.202492 CACGTCGAAGGAGAGCCG 60.202 66.667 0.00 0.00 39.96 5.52
4362 5854 2.359602 ACGTCGAAGGAGAGCCGA 60.360 61.111 0.00 0.00 39.96 5.54
4363 5855 2.100603 CGTCGAAGGAGAGCCGAC 59.899 66.667 0.00 0.00 46.27 4.79
4364 5856 2.490685 GTCGAAGGAGAGCCGACC 59.509 66.667 0.00 0.00 44.67 4.79
4365 5857 3.132139 TCGAAGGAGAGCCGACCG 61.132 66.667 0.00 0.00 39.96 4.79
4366 5858 3.132139 CGAAGGAGAGCCGACCGA 61.132 66.667 0.00 0.00 39.96 4.69
4367 5859 2.490685 GAAGGAGAGCCGACCGAC 59.509 66.667 0.00 0.00 39.96 4.79
4368 5860 2.282958 AAGGAGAGCCGACCGACA 60.283 61.111 0.00 0.00 39.96 4.35
4369 5861 2.272918 GAAGGAGAGCCGACCGACAG 62.273 65.000 0.00 0.00 39.96 3.51
4370 5862 4.500116 GGAGAGCCGACCGACAGC 62.500 72.222 0.00 0.00 0.00 4.40
4371 5863 4.838486 GAGAGCCGACCGACAGCG 62.838 72.222 0.00 0.00 37.24 5.18
4376 5868 4.246206 CCGACCGACAGCGCGATA 62.246 66.667 12.10 0.00 35.83 2.92
4377 5869 3.017314 CGACCGACAGCGCGATAC 61.017 66.667 12.10 0.00 35.83 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.062434 AGTCTCTACTTAACATCGATTCCG 57.938 41.667 0.00 0.00 29.00 4.30
23 24 2.573369 TGCATCTACCCGAGTCTCTAC 58.427 52.381 0.00 0.00 0.00 2.59
24 25 3.292492 TTGCATCTACCCGAGTCTCTA 57.708 47.619 0.00 0.00 0.00 2.43
25 26 2.145397 TTGCATCTACCCGAGTCTCT 57.855 50.000 0.00 0.00 0.00 3.10
26 27 2.815478 CTTTGCATCTACCCGAGTCTC 58.185 52.381 0.00 0.00 0.00 3.36
32 33 1.293924 CTGAGCTTTGCATCTACCCG 58.706 55.000 0.00 0.00 0.00 5.28
64 66 3.634504 TGGGATCTTCATGATGGTTTGG 58.365 45.455 8.60 0.00 35.14 3.28
76 78 1.521681 CGTCGGGCTTGGGATCTTC 60.522 63.158 0.00 0.00 0.00 2.87
132 168 1.200252 CACGCTCGAGGAAGAAGAGAA 59.800 52.381 15.58 0.00 34.13 2.87
133 169 0.805614 CACGCTCGAGGAAGAAGAGA 59.194 55.000 15.58 0.00 34.13 3.10
134 170 0.805614 TCACGCTCGAGGAAGAAGAG 59.194 55.000 15.58 0.00 35.28 2.85
136 172 1.833860 GATCACGCTCGAGGAAGAAG 58.166 55.000 15.58 0.00 0.00 2.85
142 178 2.024871 GGACGATCACGCTCGAGG 59.975 66.667 15.58 6.97 43.96 4.63
206 252 1.517913 GCGGAGTAGTACAACGGGC 60.518 63.158 15.41 7.30 0.00 6.13
208 254 0.522076 GTCGCGGAGTAGTACAACGG 60.522 60.000 6.13 8.85 0.00 4.44
366 1085 1.304713 TGTACTGTCCCGGGGAGAC 60.305 63.158 23.50 12.81 29.39 3.36
374 1093 3.310652 GGGAGGCTGTACTGTCCC 58.689 66.667 11.25 11.25 42.07 4.46
375 1094 2.368011 GGGGGAGGCTGTACTGTCC 61.368 68.421 0.00 1.16 0.00 4.02
376 1095 0.910088 AAGGGGGAGGCTGTACTGTC 60.910 60.000 0.00 0.00 0.00 3.51
377 1096 0.910088 GAAGGGGGAGGCTGTACTGT 60.910 60.000 0.00 0.00 0.00 3.55
542 1280 5.174579 CGGCTTTATAGTCGGCTAAGTTAAC 59.825 44.000 0.00 0.00 45.50 2.01
543 1281 5.284079 CGGCTTTATAGTCGGCTAAGTTAA 58.716 41.667 0.00 0.00 45.50 2.01
578 1316 2.187163 GTACAAGGAGGCTCGCCC 59.813 66.667 8.69 0.00 36.58 6.13
653 1391 3.426568 GTCAGCAAGGTCGCAGGC 61.427 66.667 0.00 0.00 0.00 4.85
689 1427 1.436983 GCAAATCGACGATCCCCACC 61.437 60.000 11.42 0.00 0.00 4.61
691 1429 0.179084 GAGCAAATCGACGATCCCCA 60.179 55.000 11.42 0.00 0.00 4.96
711 1449 2.414559 GGCAACCATCAACAAGTCGATG 60.415 50.000 0.00 0.00 39.00 3.84
747 1494 8.528643 ACTAGAAAACAAAAGGTTAAAAGCAGT 58.471 29.630 0.00 0.00 39.29 4.40
758 1505 9.326413 TCTCTGAAACTACTAGAAAACAAAAGG 57.674 33.333 0.00 0.00 0.00 3.11
764 1517 6.752815 CCGGATCTCTGAAACTACTAGAAAAC 59.247 42.308 0.00 0.00 0.00 2.43
765 1518 6.662234 TCCGGATCTCTGAAACTACTAGAAAA 59.338 38.462 0.00 0.00 0.00 2.29
766 1519 6.185511 TCCGGATCTCTGAAACTACTAGAAA 58.814 40.000 0.00 0.00 0.00 2.52
767 1520 5.752650 TCCGGATCTCTGAAACTACTAGAA 58.247 41.667 0.00 0.00 0.00 2.10
768 1521 5.369409 TCCGGATCTCTGAAACTACTAGA 57.631 43.478 0.00 0.00 0.00 2.43
769 1522 4.023536 GCTCCGGATCTCTGAAACTACTAG 60.024 50.000 3.57 0.00 0.00 2.57
770 1523 3.884091 GCTCCGGATCTCTGAAACTACTA 59.116 47.826 3.57 0.00 0.00 1.82
771 1524 2.691011 GCTCCGGATCTCTGAAACTACT 59.309 50.000 3.57 0.00 0.00 2.57
772 1525 2.691011 AGCTCCGGATCTCTGAAACTAC 59.309 50.000 3.57 0.00 0.00 2.73
773 1526 3.019799 AGCTCCGGATCTCTGAAACTA 57.980 47.619 3.57 0.00 0.00 2.24
788 1541 2.258748 GAGGTAGGTGGCCAAGCTCC 62.259 65.000 19.99 12.26 37.85 4.70
812 1569 7.871853 TGAACAGAAGTTAGTAAAGAAATGGC 58.128 34.615 0.00 0.00 38.30 4.40
930 2179 5.934402 ACCGTCAGAACAATAACCTAGAT 57.066 39.130 0.00 0.00 0.00 1.98
931 2180 5.711506 TGTACCGTCAGAACAATAACCTAGA 59.288 40.000 0.00 0.00 0.00 2.43
932 2181 5.957798 TGTACCGTCAGAACAATAACCTAG 58.042 41.667 0.00 0.00 0.00 3.02
933 2182 5.981088 TGTACCGTCAGAACAATAACCTA 57.019 39.130 0.00 0.00 0.00 3.08
939 2193 3.007506 TGGACATGTACCGTCAGAACAAT 59.992 43.478 5.38 0.00 34.97 2.71
940 2194 2.365941 TGGACATGTACCGTCAGAACAA 59.634 45.455 5.38 0.00 34.97 2.83
964 2218 0.543277 GCAGGGGATCATGTCACTGA 59.457 55.000 15.90 0.00 36.19 3.41
1074 2328 1.227263 GACACGGATGGTCGGGATG 60.227 63.158 0.00 0.00 36.96 3.51
1214 2468 2.169769 AGACAAAGAACGGTGAAGGTGA 59.830 45.455 0.00 0.00 0.00 4.02
1218 2472 3.877508 AGGAAAGACAAAGAACGGTGAAG 59.122 43.478 0.00 0.00 0.00 3.02
1219 2473 3.625764 CAGGAAAGACAAAGAACGGTGAA 59.374 43.478 0.00 0.00 0.00 3.18
1277 2531 6.098679 TCTTACTACTCAGTACTCACTCGTC 58.901 44.000 0.00 0.00 36.98 4.20
1279 2533 6.964741 TTCTTACTACTCAGTACTCACTCG 57.035 41.667 0.00 0.00 36.98 4.18
1289 2543 9.988815 AATAGGCACATAATTCTTACTACTCAG 57.011 33.333 0.00 0.00 0.00 3.35
1305 2559 8.353423 ACAGTTCAGAAAAATAATAGGCACAT 57.647 30.769 0.00 0.00 0.00 3.21
1307 2561 8.296713 TCAACAGTTCAGAAAAATAATAGGCAC 58.703 33.333 0.00 0.00 0.00 5.01
1308 2562 8.402798 TCAACAGTTCAGAAAAATAATAGGCA 57.597 30.769 0.00 0.00 0.00 4.75
1309 2563 9.860898 ATTCAACAGTTCAGAAAAATAATAGGC 57.139 29.630 0.00 0.00 0.00 3.93
1334 2588 8.396388 ACATATCCCCATGATCTTCATACAAAT 58.604 33.333 0.00 0.00 34.28 2.32
1338 2592 6.045318 CGACATATCCCCATGATCTTCATAC 58.955 44.000 0.00 0.00 34.28 2.39
1339 2593 5.129320 CCGACATATCCCCATGATCTTCATA 59.871 44.000 0.00 0.00 34.28 2.15
1340 2594 4.080695 CCGACATATCCCCATGATCTTCAT 60.081 45.833 0.00 0.00 37.65 2.57
1389 2644 0.976641 CAACAGGCAGGTACTCCTCA 59.023 55.000 0.00 0.00 43.07 3.86
1404 2659 4.211125 TGGCTGTTAATCCAAGAACAACA 58.789 39.130 0.00 0.00 35.24 3.33
1439 2694 9.693739 TTAAAATTCACATAAAGGATAGGCTGA 57.306 29.630 0.00 0.00 0.00 4.26
1601 2957 0.915364 GAAACCCCCTCTCATCAGCT 59.085 55.000 0.00 0.00 0.00 4.24
1602 2958 0.620556 TGAAACCCCCTCTCATCAGC 59.379 55.000 0.00 0.00 0.00 4.26
1615 2971 1.271597 ACAGCACTCCTGGATGAAACC 60.272 52.381 0.00 0.00 46.14 3.27
1616 2972 2.079925 GACAGCACTCCTGGATGAAAC 58.920 52.381 0.00 0.00 46.14 2.78
1647 3003 5.850614 ACAACAGAAAGTACTTCGTACCAT 58.149 37.500 8.95 0.00 39.58 3.55
1702 3058 2.105821 TCGGGATGAGTTTGAGGTTTGT 59.894 45.455 0.00 0.00 0.00 2.83
1731 3087 4.039609 ACCTTCTTTTCAGCTCCATTTTGG 59.960 41.667 0.00 0.00 39.43 3.28
1741 3097 5.249420 ACCTTCAGATACCTTCTTTTCAGC 58.751 41.667 0.00 0.00 29.93 4.26
1778 3134 6.846283 GTGTTGTCTCTTTGAATCAAACGTAG 59.154 38.462 4.03 3.43 0.00 3.51
1785 3141 4.780815 AGTGGTGTTGTCTCTTTGAATCA 58.219 39.130 0.00 0.00 0.00 2.57
1803 3159 6.043411 GCAAAGAGTACTACTCCATAAGTGG 58.957 44.000 11.94 0.00 46.18 4.00
1808 3164 5.715279 ACTGTGCAAAGAGTACTACTCCATA 59.285 40.000 11.93 2.20 46.18 2.74
1812 3168 5.122512 TCACTGTGCAAAGAGTACTACTC 57.877 43.478 11.93 8.02 45.38 2.59
1813 3169 5.730296 ATCACTGTGCAAAGAGTACTACT 57.270 39.130 11.93 0.00 33.54 2.57
1814 3170 6.787085 AAATCACTGTGCAAAGAGTACTAC 57.213 37.500 11.93 0.00 33.54 2.73
1899 3272 7.741554 ACATCCTTCTTTGAATCTAGTAGGT 57.258 36.000 0.00 0.00 32.53 3.08
1901 3274 8.877779 CACAACATCCTTCTTTGAATCTAGTAG 58.122 37.037 0.00 0.00 0.00 2.57
1927 3300 4.232310 GCCCTGAGCAATGAGTCC 57.768 61.111 0.00 0.00 42.97 3.85
1985 3358 7.758980 TGCATACTTAATTTGTGCAGGTATTTG 59.241 33.333 4.99 0.00 40.51 2.32
1987 3360 7.093988 TGTGCATACTTAATTTGTGCAGGTATT 60.094 33.333 8.37 0.00 45.32 1.89
2034 3424 8.426569 TCAATGGTAGTGGTAGTAGTAAAAGT 57.573 34.615 0.00 0.00 0.00 2.66
2036 3426 9.038072 TGATCAATGGTAGTGGTAGTAGTAAAA 57.962 33.333 0.00 0.00 0.00 1.52
2037 3427 8.598202 TGATCAATGGTAGTGGTAGTAGTAAA 57.402 34.615 0.00 0.00 0.00 2.01
2038 3428 8.598202 TTGATCAATGGTAGTGGTAGTAGTAA 57.402 34.615 3.38 0.00 0.00 2.24
2040 3430 6.668283 ACTTGATCAATGGTAGTGGTAGTAGT 59.332 38.462 8.96 0.00 0.00 2.73
2041 3431 7.113658 ACTTGATCAATGGTAGTGGTAGTAG 57.886 40.000 8.96 0.00 0.00 2.57
2042 3432 7.837689 AGTACTTGATCAATGGTAGTGGTAGTA 59.162 37.037 8.96 0.07 0.00 1.82
2043 3433 6.668283 AGTACTTGATCAATGGTAGTGGTAGT 59.332 38.462 8.96 5.33 0.00 2.73
2044 3434 7.113658 AGTACTTGATCAATGGTAGTGGTAG 57.886 40.000 8.96 0.00 0.00 3.18
2045 3435 6.666113 TGAGTACTTGATCAATGGTAGTGGTA 59.334 38.462 16.04 7.57 0.00 3.25
2046 3436 5.483937 TGAGTACTTGATCAATGGTAGTGGT 59.516 40.000 16.04 8.38 0.00 4.16
2047 3437 5.812642 GTGAGTACTTGATCAATGGTAGTGG 59.187 44.000 16.04 3.45 0.00 4.00
2048 3438 6.634805 AGTGAGTACTTGATCAATGGTAGTG 58.365 40.000 16.04 4.07 31.66 2.74
2049 3439 6.859112 AGTGAGTACTTGATCAATGGTAGT 57.141 37.500 8.96 11.22 31.66 2.73
2050 3440 7.323420 TGAAGTGAGTACTTGATCAATGGTAG 58.677 38.462 8.96 0.00 46.79 3.18
2051 3441 7.239763 TGAAGTGAGTACTTGATCAATGGTA 57.760 36.000 8.96 6.04 46.79 3.25
2052 3442 6.114187 TGAAGTGAGTACTTGATCAATGGT 57.886 37.500 8.96 7.08 46.79 3.55
2053 3443 5.064452 GCTGAAGTGAGTACTTGATCAATGG 59.936 44.000 8.96 0.48 46.79 3.16
2054 3444 5.873712 AGCTGAAGTGAGTACTTGATCAATG 59.126 40.000 8.96 6.02 46.79 2.82
2055 3445 6.047511 AGCTGAAGTGAGTACTTGATCAAT 57.952 37.500 8.96 2.32 46.79 2.57
2056 3446 5.011023 TGAGCTGAAGTGAGTACTTGATCAA 59.989 40.000 8.12 8.12 46.79 2.57
2057 3447 4.524328 TGAGCTGAAGTGAGTACTTGATCA 59.476 41.667 0.00 0.00 46.79 2.92
2058 3448 4.862018 GTGAGCTGAAGTGAGTACTTGATC 59.138 45.833 0.00 0.00 46.79 2.92
2059 3449 4.322349 GGTGAGCTGAAGTGAGTACTTGAT 60.322 45.833 0.00 0.00 46.79 2.57
2232 3667 9.832445 AAAGTATAAGGATCGCTTTTAGAATCA 57.168 29.630 2.37 0.00 0.00 2.57
2235 3670 9.538508 GGTAAAGTATAAGGATCGCTTTTAGAA 57.461 33.333 2.37 0.00 32.52 2.10
2236 3671 8.921205 AGGTAAAGTATAAGGATCGCTTTTAGA 58.079 33.333 2.37 0.00 32.52 2.10
2239 3674 9.490379 CATAGGTAAAGTATAAGGATCGCTTTT 57.510 33.333 2.37 0.00 32.52 2.27
2240 3675 8.867097 TCATAGGTAAAGTATAAGGATCGCTTT 58.133 33.333 2.37 0.00 34.35 3.51
2241 3676 8.418597 TCATAGGTAAAGTATAAGGATCGCTT 57.581 34.615 2.61 2.61 0.00 4.68
2242 3677 8.470805 CATCATAGGTAAAGTATAAGGATCGCT 58.529 37.037 0.00 0.00 0.00 4.93
2243 3678 7.707035 CCATCATAGGTAAAGTATAAGGATCGC 59.293 40.741 0.00 0.00 0.00 4.58
2244 3679 8.967918 TCCATCATAGGTAAAGTATAAGGATCG 58.032 37.037 0.00 0.00 0.00 3.69
2257 3692 6.539173 ACACACTGTTTTCCATCATAGGTAA 58.461 36.000 0.00 0.00 0.00 2.85
2269 3704 6.159988 AGCTGTATCTCTACACACTGTTTTC 58.840 40.000 0.00 0.00 34.20 2.29
2285 3720 4.039730 TCAGAAGCCAATCCTAGCTGTATC 59.960 45.833 0.00 0.00 39.87 2.24
2294 3729 1.980765 TCACACTCAGAAGCCAATCCT 59.019 47.619 0.00 0.00 0.00 3.24
2391 3829 6.949352 AACTTGCTATGGTTATGAGATTGG 57.051 37.500 0.00 0.00 0.00 3.16
2402 3840 3.689347 TGCTGATGAAACTTGCTATGGT 58.311 40.909 0.00 0.00 0.00 3.55
2429 3868 9.670719 GAAAAGAAGTTCAGTAGGAAAAAGATG 57.329 33.333 5.50 0.00 37.23 2.90
2470 3910 1.826024 CCTGTGGAATCGGGGAGAG 59.174 63.158 0.00 0.00 0.00 3.20
2478 3918 2.234908 ACAGTAGTGAGCCTGTGGAATC 59.765 50.000 4.09 0.00 40.30 2.52
2505 3945 3.440415 TCGCTCGTGTCGCATCCT 61.440 61.111 0.00 0.00 0.00 3.24
2565 4005 2.700773 GGCAACCTTGGCGTCCATC 61.701 63.158 0.00 0.00 43.97 3.51
2581 4021 2.094906 GGGTTTGAGTTGTTATTCGGGC 60.095 50.000 0.00 0.00 0.00 6.13
2640 4080 3.284617 TGCCTGAAATGTGATGAGATGG 58.715 45.455 0.00 0.00 0.00 3.51
2982 4439 3.213206 TGCTCGAAAAGATGCCCATAT 57.787 42.857 0.00 0.00 0.00 1.78
2985 4442 1.167851 CTTGCTCGAAAAGATGCCCA 58.832 50.000 2.06 0.00 0.00 5.36
3134 4591 1.081892 CTTCTCATGCGTGTCCTTGG 58.918 55.000 5.68 0.00 0.00 3.61
3185 4642 1.703513 AGGAAAGGGGAGGTGTAACAC 59.296 52.381 0.00 0.00 39.98 3.32
3197 4657 2.270986 GCACTGCACCAGGAAAGGG 61.271 63.158 0.00 0.00 35.51 3.95
3358 4818 7.693969 ACTATTTTGAATCCTCTGTTTCTGG 57.306 36.000 0.00 0.00 0.00 3.86
3503 4965 6.002062 AGTAATTTTCACTTGCACAGCTAC 57.998 37.500 0.00 0.00 0.00 3.58
3512 4974 8.517878 ACAATCAGATGGAGTAATTTTCACTTG 58.482 33.333 0.00 0.00 0.00 3.16
3591 5058 0.177836 TGGTCATGACATGCTACCGG 59.822 55.000 26.47 0.00 31.63 5.28
3615 5082 4.201881 ACACTCCAGTTAGCGAAACAAAAC 60.202 41.667 7.58 0.00 40.83 2.43
3667 5134 3.222603 ACGGGATTTTGTGCTCTTCTTT 58.777 40.909 0.00 0.00 0.00 2.52
3720 5194 1.217244 GTGCGGTGGTACCTAGTGG 59.783 63.158 14.36 0.00 35.66 4.00
3757 5231 6.870971 TTCAAGCTACGGTTACTGAATTTT 57.129 33.333 0.00 0.00 0.00 1.82
3759 5233 6.653320 TGATTTCAAGCTACGGTTACTGAATT 59.347 34.615 0.00 0.00 0.00 2.17
3771 5245 8.678199 AGCCTAAACTTTATGATTTCAAGCTAC 58.322 33.333 0.00 0.00 0.00 3.58
3775 5249 8.956426 TGGTAGCCTAAACTTTATGATTTCAAG 58.044 33.333 0.00 0.00 0.00 3.02
3788 5262 3.118408 TCATTGCGATGGTAGCCTAAACT 60.118 43.478 14.12 0.00 33.93 2.66
3789 5263 3.202906 TCATTGCGATGGTAGCCTAAAC 58.797 45.455 14.12 0.00 33.93 2.01
3797 5272 4.870991 TGTTATTCGTTCATTGCGATGGTA 59.129 37.500 14.12 0.03 38.21 3.25
3804 5279 7.566858 AGTTCAATTGTTATTCGTTCATTGC 57.433 32.000 5.13 0.00 0.00 3.56
3846 5321 5.445540 CGACTACGCTTTTTCCAACCTTATC 60.446 44.000 0.00 0.00 0.00 1.75
3853 5328 3.872771 ACTTTCGACTACGCTTTTTCCAA 59.127 39.130 0.00 0.00 39.58 3.53
3856 5331 4.376109 CCTCACTTTCGACTACGCTTTTTC 60.376 45.833 0.00 0.00 39.58 2.29
3861 5336 0.109226 GCCTCACTTTCGACTACGCT 60.109 55.000 0.00 0.00 39.58 5.07
3865 5340 2.288825 CCAACTGCCTCACTTTCGACTA 60.289 50.000 0.00 0.00 0.00 2.59
3866 5341 1.541233 CCAACTGCCTCACTTTCGACT 60.541 52.381 0.00 0.00 0.00 4.18
3867 5342 0.868406 CCAACTGCCTCACTTTCGAC 59.132 55.000 0.00 0.00 0.00 4.20
3904 5380 2.124507 TAGGGTGCTGAAGTGCCACC 62.125 60.000 0.00 0.54 35.17 4.61
3913 5389 2.978824 GTTCGCCTAGGGTGCTGA 59.021 61.111 11.72 0.00 32.51 4.26
3918 5394 1.952296 CACTATACGTTCGCCTAGGGT 59.048 52.381 11.72 1.56 0.00 4.34
3919 5395 1.952296 ACACTATACGTTCGCCTAGGG 59.048 52.381 11.72 0.44 0.00 3.53
3934 5426 7.635648 ACCCAAATACTTATAGCCAAACACTA 58.364 34.615 0.00 0.00 0.00 2.74
4011 5503 9.200817 ACTGAGCCATAATACAATGGTAAAAAT 57.799 29.630 4.89 0.00 46.93 1.82
4014 5506 7.068103 CCAACTGAGCCATAATACAATGGTAAA 59.932 37.037 4.89 0.00 46.93 2.01
4026 5518 5.647658 CACAAAGATACCAACTGAGCCATAA 59.352 40.000 0.00 0.00 0.00 1.90
4034 5526 6.127647 ACCATATTGCACAAAGATACCAACTG 60.128 38.462 0.00 0.00 0.00 3.16
4036 5528 6.095440 AGACCATATTGCACAAAGATACCAAC 59.905 38.462 0.00 0.00 0.00 3.77
4081 5573 3.967332 AGGAGGGCAAACATGAAATTG 57.033 42.857 0.00 2.99 0.00 2.32
4096 5588 5.189180 AGCATAAGCAAAACTCTAAGGAGG 58.811 41.667 0.00 0.00 45.49 4.30
4099 5591 6.481644 CCTAGAGCATAAGCAAAACTCTAAGG 59.518 42.308 0.00 0.00 45.49 2.69
4101 5593 5.817816 GCCTAGAGCATAAGCAAAACTCTAA 59.182 40.000 0.00 0.00 45.49 2.10
4130 5622 1.154727 GCTACGCAACGACCAAACG 60.155 57.895 0.00 0.00 39.31 3.60
4158 5650 0.460311 GCCTAGGAGACGCTTAAGCA 59.540 55.000 26.29 4.80 42.21 3.91
4159 5651 0.595310 CGCCTAGGAGACGCTTAAGC 60.595 60.000 17.83 17.83 37.78 3.09
4160 5652 0.739561 ACGCCTAGGAGACGCTTAAG 59.260 55.000 20.46 0.00 0.00 1.85
4161 5653 1.135199 CAACGCCTAGGAGACGCTTAA 60.135 52.381 20.46 0.00 0.00 1.85
4162 5654 0.454600 CAACGCCTAGGAGACGCTTA 59.545 55.000 20.46 0.00 0.00 3.09
4163 5655 1.215647 CAACGCCTAGGAGACGCTT 59.784 57.895 20.46 0.00 0.00 4.68
4166 5658 2.202756 GGCAACGCCTAGGAGACG 60.203 66.667 20.46 12.53 46.69 4.18
4176 5668 0.383949 TCTGTTGGAAAAGGCAACGC 59.616 50.000 0.00 0.00 46.39 4.84
4177 5669 3.369546 AATCTGTTGGAAAAGGCAACG 57.630 42.857 0.00 0.00 46.39 4.10
4182 5674 6.044682 GCCATCATAAATCTGTTGGAAAAGG 58.955 40.000 5.56 0.00 37.95 3.11
4192 5684 6.183360 GCCAAACAAAAGCCATCATAAATCTG 60.183 38.462 0.00 0.00 0.00 2.90
4217 5709 3.998099 TGAGAATCAGTAGATGCGAGG 57.002 47.619 0.00 0.00 42.56 4.63
4258 5750 6.227522 TCCGATGTGTTTGTTTGAGATTCTA 58.772 36.000 0.00 0.00 0.00 2.10
4301 5793 1.597854 TCGAGGGTACACGTGACGT 60.598 57.895 25.01 4.10 42.36 4.34
4302 5794 1.154338 GTCGAGGGTACACGTGACG 60.154 63.158 25.01 16.05 0.00 4.35
4303 5795 0.386478 GTGTCGAGGGTACACGTGAC 60.386 60.000 25.01 15.43 38.03 3.67
4304 5796 1.518056 GGTGTCGAGGGTACACGTGA 61.518 60.000 25.01 2.68 46.57 4.35
4305 5797 1.080974 GGTGTCGAGGGTACACGTG 60.081 63.158 15.48 15.48 46.57 4.49
4306 5798 2.620112 CGGTGTCGAGGGTACACGT 61.620 63.158 0.00 0.00 46.57 4.49
4307 5799 2.177531 CGGTGTCGAGGGTACACG 59.822 66.667 0.00 0.00 46.57 4.49
4308 5800 2.570181 CCGGTGTCGAGGGTACAC 59.430 66.667 0.00 0.00 45.21 2.90
4309 5801 2.677524 CCCGGTGTCGAGGGTACA 60.678 66.667 0.00 0.00 42.67 2.90
4310 5802 3.455469 CCCCGGTGTCGAGGGTAC 61.455 72.222 0.00 0.00 46.17 3.34
4321 5813 4.033776 CTGTGCATCACCCCCGGT 62.034 66.667 0.00 0.00 35.62 5.28
4323 5815 4.720902 TGCTGTGCATCACCCCCG 62.721 66.667 0.00 0.00 31.71 5.73
4324 5816 2.753043 CTGCTGTGCATCACCCCC 60.753 66.667 0.00 0.00 38.13 5.40
4325 5817 3.446570 GCTGCTGTGCATCACCCC 61.447 66.667 0.00 0.00 38.13 4.95
4326 5818 2.360852 AGCTGCTGTGCATCACCC 60.361 61.111 0.00 0.00 38.13 4.61
4327 5819 1.673337 TGAGCTGCTGTGCATCACC 60.673 57.895 7.01 0.00 38.13 4.02
4328 5820 1.500844 GTGAGCTGCTGTGCATCAC 59.499 57.895 7.01 4.11 38.13 3.06
4329 5821 2.030958 CGTGAGCTGCTGTGCATCA 61.031 57.895 7.01 0.00 38.13 3.07
4330 5822 1.964290 GACGTGAGCTGCTGTGCATC 61.964 60.000 7.01 0.00 38.13 3.91
4331 5823 2.031516 GACGTGAGCTGCTGTGCAT 61.032 57.895 7.01 0.00 38.13 3.96
4332 5824 2.662857 GACGTGAGCTGCTGTGCA 60.663 61.111 7.01 0.00 36.92 4.57
4333 5825 3.771491 CGACGTGAGCTGCTGTGC 61.771 66.667 7.01 0.00 0.00 4.57
4334 5826 1.612469 CTTCGACGTGAGCTGCTGTG 61.612 60.000 7.01 0.00 0.00 3.66
4335 5827 1.372251 CTTCGACGTGAGCTGCTGT 60.372 57.895 7.01 0.00 0.00 4.40
4336 5828 2.091112 CCTTCGACGTGAGCTGCTG 61.091 63.158 7.01 0.00 0.00 4.41
4337 5829 2.206515 CTCCTTCGACGTGAGCTGCT 62.207 60.000 0.00 0.00 0.00 4.24
4338 5830 1.803519 CTCCTTCGACGTGAGCTGC 60.804 63.158 0.00 0.00 0.00 5.25
4339 5831 0.179176 CTCTCCTTCGACGTGAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
4340 5832 1.928706 GCTCTCCTTCGACGTGAGCT 61.929 60.000 20.50 0.00 44.52 4.09
4341 5833 1.515304 GCTCTCCTTCGACGTGAGC 60.515 63.158 15.85 15.85 42.31 4.26
4342 5834 1.137825 GGCTCTCCTTCGACGTGAG 59.862 63.158 0.00 0.00 0.00 3.51
4343 5835 2.687805 CGGCTCTCCTTCGACGTGA 61.688 63.158 0.00 0.00 0.00 4.35
4344 5836 2.202492 CGGCTCTCCTTCGACGTG 60.202 66.667 0.00 0.00 0.00 4.49
4345 5837 2.359602 TCGGCTCTCCTTCGACGT 60.360 61.111 0.00 0.00 0.00 4.34
4346 5838 2.100603 GTCGGCTCTCCTTCGACG 59.899 66.667 0.00 0.00 42.60 5.12
4348 5840 3.132139 CGGTCGGCTCTCCTTCGA 61.132 66.667 0.00 0.00 0.00 3.71
4349 5841 3.132139 TCGGTCGGCTCTCCTTCG 61.132 66.667 0.00 0.00 0.00 3.79
4350 5842 2.272918 CTGTCGGTCGGCTCTCCTTC 62.273 65.000 0.00 0.00 0.00 3.46
4351 5843 2.282958 TGTCGGTCGGCTCTCCTT 60.283 61.111 0.00 0.00 0.00 3.36
4352 5844 2.752238 CTGTCGGTCGGCTCTCCT 60.752 66.667 0.00 0.00 0.00 3.69
4353 5845 4.500116 GCTGTCGGTCGGCTCTCC 62.500 72.222 0.00 0.00 44.39 3.71
4354 5846 4.838486 CGCTGTCGGTCGGCTCTC 62.838 72.222 4.63 0.00 45.50 3.20
4359 5851 4.246206 TATCGCGCTGTCGGTCGG 62.246 66.667 5.56 0.00 35.95 4.79
4360 5852 3.017314 GTATCGCGCTGTCGGTCG 61.017 66.667 5.56 0.00 35.95 4.79
4361 5853 3.017314 CGTATCGCGCTGTCGGTC 61.017 66.667 5.56 0.00 35.95 4.79


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

AutoCloner maintained by Alex Coulton.