Multiple sequence alignment - TraesCS2D01G376100

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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 TraesCS2D01G376100 chr2D 100.000 3891 0 0 1 3891 480326533 480322643 0.000000e+00 7186.0
1 TraesCS2D01G376100 chr2D 84.628 1802 139 81 666 2357 480182021 480180248 0.000000e+00 1666.0
2 TraesCS2D01G376100 chr2D 87.130 575 74 0 1046 1620 159573859 159574433 0.000000e+00 652.0
3 TraesCS2D01G376100 chr2D 81.925 426 58 12 2537 2943 480179916 480179491 3.720000e-90 342.0
4 TraesCS2D01G376100 chr2D 80.617 227 31 9 172 395 480182509 480182293 3.110000e-36 163.0
5 TraesCS2D01G376100 chr2D 88.372 129 12 2 41 168 14895231 14895105 6.730000e-33 152.0
6 TraesCS2D01G376100 chr2D 82.353 136 23 1 2401 2536 480180082 480179948 2.460000e-22 117.0
7 TraesCS2D01G376100 chr2D 98.148 54 1 0 1 54 480327814 480327867 1.150000e-15 95.3
8 TraesCS2D01G376100 chr2A 89.173 2928 181 55 666 3542 622854084 622851242 0.000000e+00 3526.0
9 TraesCS2D01G376100 chr2A 84.769 1405 132 43 667 2030 622748405 622747042 0.000000e+00 1334.0
10 TraesCS2D01G376100 chr2A 87.304 575 73 0 1046 1620 170602964 170603538 0.000000e+00 658.0
11 TraesCS2D01G376100 chr2A 89.521 334 22 8 237 566 622855153 622854829 1.010000e-110 411.0
12 TraesCS2D01G376100 chr2A 78.723 611 73 29 2377 2943 622746500 622745903 4.780000e-94 355.0
13 TraesCS2D01G376100 chr2A 85.312 320 24 15 2059 2358 622746954 622746638 3.780000e-80 309.0
14 TraesCS2D01G376100 chr2A 90.991 111 9 1 63 172 762743643 762743753 8.710000e-32 148.0
15 TraesCS2D01G376100 chr2A 96.226 53 2 0 1 53 374719622 374719674 1.930000e-13 87.9
16 TraesCS2D01G376100 chr2B 90.308 1816 100 32 1772 3542 563183890 563182106 0.000000e+00 2309.0
17 TraesCS2D01G376100 chr2B 91.437 1635 78 23 167 1777 563185785 563184189 0.000000e+00 2187.0
18 TraesCS2D01G376100 chr2B 85.644 1421 120 47 666 2030 563046795 563045403 0.000000e+00 1417.0
19 TraesCS2D01G376100 chr2B 87.478 575 72 0 1046 1620 216708506 216709080 0.000000e+00 664.0
20 TraesCS2D01G376100 chr2B 89.356 357 27 5 3544 3891 563182073 563181719 4.620000e-119 438.0
21 TraesCS2D01G376100 chr2B 78.374 615 70 32 2377 2943 563044397 563043798 1.340000e-89 340.0
22 TraesCS2D01G376100 chr2B 96.988 166 5 0 2066 2231 563045293 563045128 2.960000e-71 279.0
23 TraesCS2D01G376100 chr2B 80.263 228 25 8 170 395 563047168 563046959 1.870000e-33 154.0
24 TraesCS2D01G376100 chr2B 88.983 118 12 1 57 173 376116745 376116862 1.130000e-30 145.0
25 TraesCS2D01G376100 chr2B 86.047 86 5 2 2279 2358 563044614 563044530 6.930000e-13 86.1
26 TraesCS2D01G376100 chr5D 86.292 569 73 4 1051 1618 128565428 128564864 7.150000e-172 614.0
27 TraesCS2D01G376100 chr5D 86.429 140 19 0 2079 2218 562029601 562029740 1.870000e-33 154.0
28 TraesCS2D01G376100 chr5D 85.075 134 20 0 2077 2210 128564783 128564650 1.890000e-28 137.0
29 TraesCS2D01G376100 chr5A 90.517 116 8 3 58 172 246293577 246293690 2.420000e-32 150.0
30 TraesCS2D01G376100 chr5A 85.821 134 19 0 2077 2210 143552250 143552117 4.050000e-30 143.0
31 TraesCS2D01G376100 chr5A 98.113 53 1 0 1 53 568581462 568581514 4.140000e-15 93.5
32 TraesCS2D01G376100 chr5B 91.667 108 8 1 63 169 42689696 42689589 8.710000e-32 148.0
33 TraesCS2D01G376100 chr4B 91.667 108 8 1 62 168 41036708 41036601 8.710000e-32 148.0
34 TraesCS2D01G376100 chr3B 90.991 111 9 1 63 172 590268422 590268312 8.710000e-32 148.0
35 TraesCS2D01G376100 chr3B 90.991 111 9 1 63 172 590273034 590272924 8.710000e-32 148.0
36 TraesCS2D01G376100 chr6D 93.878 98 5 1 2766 2863 302040144 302040240 3.130000e-31 147.0
37 TraesCS2D01G376100 chr6D 95.000 60 2 1 1 60 278370451 278370393 4.140000e-15 93.5
38 TraesCS2D01G376100 chr6D 98.113 53 1 0 1 53 278371746 278371798 4.140000e-15 93.5
39 TraesCS2D01G376100 chr6D 94.737 57 3 0 1 57 470688304 470688248 5.350000e-14 89.8
40 TraesCS2D01G376100 chr6D 96.296 54 2 0 1 54 470689784 470689837 5.350000e-14 89.8
41 TraesCS2D01G376100 chr7B 90.179 112 10 1 59 169 555654396 555654507 1.130000e-30 145.0
42 TraesCS2D01G376100 chr7B 82.500 120 21 0 2076 2195 111269804 111269923 5.320000e-19 106.0
43 TraesCS2D01G376100 chr6B 93.684 95 5 1 2766 2860 467450590 467450683 1.460000e-29 141.0
44 TraesCS2D01G376100 chr6A 92.079 101 7 1 2766 2866 414875611 414875512 1.460000e-29 141.0
45 TraesCS2D01G376100 chr3A 94.737 57 2 1 1 56 705278271 705278327 1.930000e-13 87.9
46 TraesCS2D01G376100 chr3D 94.340 53 3 0 1 53 382119652 382119704 8.960000e-12 82.4


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 TraesCS2D01G376100 chr2D 480322643 480326533 3890 True 7186.000000 7186 100.000000 1 3891 1 chr2D.!!$R2 3890
1 TraesCS2D01G376100 chr2D 159573859 159574433 574 False 652.000000 652 87.130000 1046 1620 1 chr2D.!!$F1 574
2 TraesCS2D01G376100 chr2D 480179491 480182509 3018 True 572.000000 1666 82.380750 172 2943 4 chr2D.!!$R3 2771
3 TraesCS2D01G376100 chr2A 622851242 622855153 3911 True 1968.500000 3526 89.347000 237 3542 2 chr2A.!!$R2 3305
4 TraesCS2D01G376100 chr2A 622745903 622748405 2502 True 666.000000 1334 82.934667 667 2943 3 chr2A.!!$R1 2276
5 TraesCS2D01G376100 chr2A 170602964 170603538 574 False 658.000000 658 87.304000 1046 1620 1 chr2A.!!$F1 574
6 TraesCS2D01G376100 chr2B 563181719 563185785 4066 True 1644.666667 2309 90.367000 167 3891 3 chr2B.!!$R2 3724
7 TraesCS2D01G376100 chr2B 216708506 216709080 574 False 664.000000 664 87.478000 1046 1620 1 chr2B.!!$F1 574
8 TraesCS2D01G376100 chr2B 563043798 563047168 3370 True 455.220000 1417 85.463200 170 2943 5 chr2B.!!$R1 2773
9 TraesCS2D01G376100 chr5D 128564650 128565428 778 True 375.500000 614 85.683500 1051 2210 2 chr5D.!!$R1 1159

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
929 1799 0.532862 GTCACCTCACACCACCACAG 60.533 60.0 0.0 0.0 0.0 3.66 F
1059 1939 0.039911 ACGGAGCCAAGGACTACTCT 59.960 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 4515 0.741221 GTGGGGAGTGACATCGCTTC 60.741 60.0 0.00 0.0 36.74 3.86 R
2958 5048 0.442310 ACGCGTGCACAATACATCAC 59.558 50.0 12.93 0.0 0.00 3.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.502093 TAGCCGCATGTTACCCCG 59.498 61.111 0.00 0.00 0.00 5.73
18 19 2.360767 TAGCCGCATGTTACCCCGT 61.361 57.895 0.00 0.00 0.00 5.28
19 20 2.581208 TAGCCGCATGTTACCCCGTG 62.581 60.000 0.00 0.00 0.00 4.94
20 21 2.266372 CCGCATGTTACCCCGTGA 59.734 61.111 0.00 0.00 0.00 4.35
21 22 2.104253 CCGCATGTTACCCCGTGAC 61.104 63.158 0.00 0.00 0.00 3.67
22 23 1.079405 CGCATGTTACCCCGTGACT 60.079 57.895 0.00 0.00 0.00 3.41
23 24 1.358725 CGCATGTTACCCCGTGACTG 61.359 60.000 0.00 0.00 0.00 3.51
24 25 1.644786 GCATGTTACCCCGTGACTGC 61.645 60.000 0.00 0.00 0.00 4.40
25 26 1.024579 CATGTTACCCCGTGACTGCC 61.025 60.000 0.00 0.00 0.00 4.85
26 27 1.485294 ATGTTACCCCGTGACTGCCA 61.485 55.000 0.00 0.00 0.00 4.92
27 28 1.071814 GTTACCCCGTGACTGCCAA 59.928 57.895 0.00 0.00 0.00 4.52
28 29 0.953960 GTTACCCCGTGACTGCCAAG 60.954 60.000 0.00 0.00 0.00 3.61
29 30 1.122632 TTACCCCGTGACTGCCAAGA 61.123 55.000 0.00 0.00 0.00 3.02
30 31 1.541310 TACCCCGTGACTGCCAAGAG 61.541 60.000 0.00 0.00 0.00 2.85
31 32 2.046892 CCCGTGACTGCCAAGAGG 60.047 66.667 0.00 0.00 38.23 3.69
43 44 2.189594 CCAAGAGGCATGTCACTTGA 57.810 50.000 31.09 0.00 41.16 3.02
44 45 2.719739 CCAAGAGGCATGTCACTTGAT 58.280 47.619 31.09 0.44 41.16 2.57
45 46 2.681848 CCAAGAGGCATGTCACTTGATC 59.318 50.000 31.09 6.48 41.16 2.92
46 47 2.681848 CAAGAGGCATGTCACTTGATCC 59.318 50.000 27.15 2.01 41.16 3.36
47 48 1.211457 AGAGGCATGTCACTTGATCCC 59.789 52.381 0.00 0.00 0.00 3.85
48 49 0.994247 AGGCATGTCACTTGATCCCA 59.006 50.000 0.00 0.00 0.00 4.37
49 50 1.064906 AGGCATGTCACTTGATCCCAG 60.065 52.381 0.00 0.00 0.00 4.45
50 51 1.340405 GGCATGTCACTTGATCCCAGT 60.340 52.381 0.00 0.00 0.00 4.00
51 52 2.012673 GCATGTCACTTGATCCCAGTC 58.987 52.381 0.00 0.00 0.00 3.51
52 53 2.636830 CATGTCACTTGATCCCAGTCC 58.363 52.381 0.00 0.00 0.00 3.85
53 54 0.984230 TGTCACTTGATCCCAGTCCC 59.016 55.000 0.00 0.00 0.00 4.46
54 55 1.280457 GTCACTTGATCCCAGTCCCT 58.720 55.000 0.00 0.00 0.00 4.20
55 56 1.630878 GTCACTTGATCCCAGTCCCTT 59.369 52.381 0.00 0.00 0.00 3.95
56 57 1.630369 TCACTTGATCCCAGTCCCTTG 59.370 52.381 0.00 0.00 0.00 3.61
57 58 1.352352 CACTTGATCCCAGTCCCTTGT 59.648 52.381 0.00 0.00 0.00 3.16
58 59 2.065799 ACTTGATCCCAGTCCCTTGTT 58.934 47.619 0.00 0.00 0.00 2.83
59 60 3.009033 CACTTGATCCCAGTCCCTTGTTA 59.991 47.826 0.00 0.00 0.00 2.41
60 61 3.009143 ACTTGATCCCAGTCCCTTGTTAC 59.991 47.826 0.00 0.00 0.00 2.50
61 62 1.553248 TGATCCCAGTCCCTTGTTACG 59.447 52.381 0.00 0.00 0.00 3.18
62 63 1.553704 GATCCCAGTCCCTTGTTACGT 59.446 52.381 0.00 0.00 0.00 3.57
63 64 2.307496 TCCCAGTCCCTTGTTACGTA 57.693 50.000 0.00 0.00 0.00 3.57
64 65 1.895131 TCCCAGTCCCTTGTTACGTAC 59.105 52.381 0.00 0.00 0.00 3.67
65 66 1.897802 CCCAGTCCCTTGTTACGTACT 59.102 52.381 0.00 0.00 0.00 2.73
66 67 2.094338 CCCAGTCCCTTGTTACGTACTC 60.094 54.545 0.00 0.00 0.00 2.59
67 68 2.094338 CCAGTCCCTTGTTACGTACTCC 60.094 54.545 0.00 0.00 0.00 3.85
68 69 2.094338 CAGTCCCTTGTTACGTACTCCC 60.094 54.545 0.00 0.00 0.00 4.30
69 70 2.174360 GTCCCTTGTTACGTACTCCCT 58.826 52.381 0.00 0.00 0.00 4.20
70 71 2.165234 GTCCCTTGTTACGTACTCCCTC 59.835 54.545 0.00 0.00 0.00 4.30
71 72 1.479730 CCCTTGTTACGTACTCCCTCC 59.520 57.143 0.00 0.00 0.00 4.30
72 73 1.133790 CCTTGTTACGTACTCCCTCCG 59.866 57.143 0.00 0.00 0.00 4.63
73 74 1.815003 CTTGTTACGTACTCCCTCCGT 59.185 52.381 0.00 0.00 38.53 4.69
74 75 1.909700 TGTTACGTACTCCCTCCGTT 58.090 50.000 0.00 0.00 36.12 4.44
75 76 1.812571 TGTTACGTACTCCCTCCGTTC 59.187 52.381 0.00 0.00 36.12 3.95
76 77 1.086696 TTACGTACTCCCTCCGTTCG 58.913 55.000 0.00 0.00 36.12 3.95
77 78 0.744414 TACGTACTCCCTCCGTTCGG 60.744 60.000 4.74 4.74 36.12 4.30
78 79 1.746615 CGTACTCCCTCCGTTCGGA 60.747 63.158 13.34 13.34 0.00 4.55
79 80 1.308069 CGTACTCCCTCCGTTCGGAA 61.308 60.000 14.79 0.04 33.41 4.30
80 81 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
81 82 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
82 83 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
83 84 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
84 85 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
85 86 1.479323 TCCCTCCGTTCGGAATTACTG 59.521 52.381 14.79 2.64 33.41 2.74
86 87 1.472728 CCCTCCGTTCGGAATTACTGG 60.473 57.143 14.79 10.82 33.41 4.00
87 88 1.206371 CCTCCGTTCGGAATTACTGGT 59.794 52.381 14.79 0.00 33.41 4.00
88 89 2.537401 CTCCGTTCGGAATTACTGGTC 58.463 52.381 14.79 0.00 33.41 4.02
89 90 2.165845 CTCCGTTCGGAATTACTGGTCT 59.834 50.000 14.79 0.00 33.41 3.85
90 91 2.165030 TCCGTTCGGAATTACTGGTCTC 59.835 50.000 11.66 0.00 0.00 3.36
91 92 2.182825 CGTTCGGAATTACTGGTCTCG 58.817 52.381 0.00 0.00 0.00 4.04
92 93 2.159476 CGTTCGGAATTACTGGTCTCGA 60.159 50.000 0.00 0.00 0.00 4.04
93 94 3.671433 CGTTCGGAATTACTGGTCTCGAA 60.671 47.826 0.00 0.00 33.66 3.71
94 95 4.240096 GTTCGGAATTACTGGTCTCGAAA 58.760 43.478 0.00 0.00 37.00 3.46
95 96 4.524316 TCGGAATTACTGGTCTCGAAAA 57.476 40.909 0.00 0.00 0.00 2.29
96 97 5.080969 TCGGAATTACTGGTCTCGAAAAT 57.919 39.130 0.00 0.00 0.00 1.82
97 98 4.868171 TCGGAATTACTGGTCTCGAAAATG 59.132 41.667 0.00 0.00 0.00 2.32
98 99 4.034048 CGGAATTACTGGTCTCGAAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
99 100 5.183228 GGAATTACTGGTCTCGAAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
100 101 5.823045 GGAATTACTGGTCTCGAAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
101 102 6.238484 GGAATTACTGGTCTCGAAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
102 103 3.703001 ACTGGTCTCGAAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
103 104 4.819105 ACTGGTCTCGAAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
104 105 5.359194 ACTGGTCTCGAAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
105 106 5.745227 ACTGGTCTCGAAAATGGATGTATT 58.255 37.500 0.00 0.00 0.00 1.89
106 107 6.180472 ACTGGTCTCGAAAATGGATGTATTT 58.820 36.000 0.00 0.00 31.87 1.40
107 108 7.335627 ACTGGTCTCGAAAATGGATGTATTTA 58.664 34.615 0.00 0.00 30.47 1.40
108 109 7.495934 ACTGGTCTCGAAAATGGATGTATTTAG 59.504 37.037 0.00 0.00 30.47 1.85
109 110 7.561251 TGGTCTCGAAAATGGATGTATTTAGA 58.439 34.615 0.00 0.00 30.47 2.10
110 111 8.044309 TGGTCTCGAAAATGGATGTATTTAGAA 58.956 33.333 0.00 0.00 30.47 2.10
111 112 9.057089 GGTCTCGAAAATGGATGTATTTAGAAT 57.943 33.333 0.00 0.00 30.47 2.40
159 160 5.954434 TTTCGATAAGTAATTCCGAACGG 57.046 39.130 6.94 6.94 38.69 4.44
160 161 4.898829 TCGATAAGTAATTCCGAACGGA 57.101 40.909 12.04 12.04 43.52 4.69
161 162 4.852138 TCGATAAGTAATTCCGAACGGAG 58.148 43.478 15.34 1.44 46.06 4.63
162 163 3.979495 CGATAAGTAATTCCGAACGGAGG 59.021 47.826 15.34 0.00 46.06 4.30
163 164 2.685850 AAGTAATTCCGAACGGAGGG 57.314 50.000 15.34 0.00 46.06 4.30
164 165 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
165 166 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
166 167 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
167 168 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
168 169 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
226 250 5.956563 TCGGATAGAAACTTTTAGAGACCCT 59.043 40.000 0.00 0.00 0.00 4.34
227 251 6.043411 CGGATAGAAACTTTTAGAGACCCTG 58.957 44.000 0.00 0.00 0.00 4.45
359 388 2.920490 CAACAATACAAAATTCCCGCCG 59.080 45.455 0.00 0.00 0.00 6.46
434 463 4.383861 TCCACTCCAGCTGCTGCG 62.384 66.667 23.86 17.91 45.42 5.18
438 471 2.202851 CTCCAGCTGCTGCGGTAG 60.203 66.667 23.86 13.33 45.42 3.18
462 495 4.628074 AGTAAAACAGCTTCTTCGTAGCA 58.372 39.130 0.00 0.00 41.11 3.49
464 497 3.879932 AAACAGCTTCTTCGTAGCAAC 57.120 42.857 0.00 0.00 41.11 4.17
500 537 2.467826 GCTCCGGAGTGCAATCTGC 61.468 63.158 31.43 12.03 45.29 4.26
516 553 5.563475 GCAATCTGCAGTTCAGTAATTGTGT 60.563 40.000 14.67 0.00 44.26 3.72
550 587 6.601613 TGCCTACATTTTGATTACTTACCAGG 59.398 38.462 0.00 0.00 0.00 4.45
571 1247 2.489329 GGCATAACAGCACACTCAACAT 59.511 45.455 0.00 0.00 35.83 2.71
572 1248 3.495193 GCATAACAGCACACTCAACATG 58.505 45.455 0.00 0.00 0.00 3.21
573 1249 3.495193 CATAACAGCACACTCAACATGC 58.505 45.455 0.00 0.00 39.74 4.06
574 1250 1.391577 AACAGCACACTCAACATGCA 58.608 45.000 0.00 0.00 41.97 3.96
575 1251 1.391577 ACAGCACACTCAACATGCAA 58.608 45.000 0.00 0.00 41.97 4.08
576 1252 1.958579 ACAGCACACTCAACATGCAAT 59.041 42.857 0.00 0.00 41.97 3.56
577 1253 2.363038 ACAGCACACTCAACATGCAATT 59.637 40.909 0.00 0.00 41.97 2.32
578 1254 3.569277 ACAGCACACTCAACATGCAATTA 59.431 39.130 0.00 0.00 41.97 1.40
579 1255 4.037803 ACAGCACACTCAACATGCAATTAA 59.962 37.500 0.00 0.00 41.97 1.40
580 1256 4.619760 CAGCACACTCAACATGCAATTAAG 59.380 41.667 0.00 0.00 41.97 1.85
581 1257 3.365820 GCACACTCAACATGCAATTAAGC 59.634 43.478 0.00 0.00 39.23 3.09
582 1258 4.801891 CACACTCAACATGCAATTAAGCT 58.198 39.130 0.00 0.00 34.99 3.74
583 1259 4.619760 CACACTCAACATGCAATTAAGCTG 59.380 41.667 0.00 0.00 34.99 4.24
584 1260 4.520111 ACACTCAACATGCAATTAAGCTGA 59.480 37.500 0.00 0.00 34.99 4.26
585 1261 4.855388 CACTCAACATGCAATTAAGCTGAC 59.145 41.667 0.00 0.00 34.99 3.51
586 1262 4.763793 ACTCAACATGCAATTAAGCTGACT 59.236 37.500 0.00 0.00 34.99 3.41
604 1280 3.943381 TGACTGCCAATTAAGCTGATGAG 59.057 43.478 11.83 0.00 33.78 2.90
631 1486 1.743995 CCGGAAGTAAACTGGGCCG 60.744 63.158 0.00 10.59 36.43 6.13
641 1496 2.109425 AACTGGGCCGCTAACTAAAG 57.891 50.000 0.00 0.00 0.00 1.85
650 1505 5.295152 GGCCGCTAACTAAAGCTAAGAATA 58.705 41.667 3.13 0.00 40.49 1.75
655 1510 7.329717 CCGCTAACTAAAGCTAAGAATATCCAG 59.670 40.741 3.13 0.00 40.49 3.86
656 1511 7.868415 CGCTAACTAAAGCTAAGAATATCCAGT 59.132 37.037 3.13 0.00 40.49 4.00
685 1540 2.620115 CGTAAGCTCCACCGTATTAGGA 59.380 50.000 0.00 0.00 34.73 2.94
709 1564 1.294459 CACCAGTGAGCTAGCTGCA 59.706 57.895 24.99 16.72 45.94 4.41
785 1649 1.069935 GGGAGACGCCTTATCTGCC 59.930 63.158 0.00 0.00 45.96 4.85
929 1799 0.532862 GTCACCTCACACCACCACAG 60.533 60.000 0.00 0.00 0.00 3.66
936 1806 0.969149 CACACCACCACAGAGAGCTA 59.031 55.000 0.00 0.00 0.00 3.32
1059 1939 0.039911 ACGGAGCCAAGGACTACTCT 59.960 55.000 0.00 0.00 0.00 3.24
1176 2056 0.902984 TCTACATCACCGTGGCCACT 60.903 55.000 32.28 13.41 0.00 4.00
1626 2506 2.101917 CCACGTCCCGGTAAGTTATCAT 59.898 50.000 0.00 0.00 0.00 2.45
1687 2587 7.944729 ACTAGTGAAGTTTGCATGGAAATAT 57.055 32.000 15.83 7.70 33.35 1.28
1720 2628 5.184864 CAGCTGGTCTCCGAATATTCTCTAT 59.815 44.000 13.45 0.00 0.00 1.98
1755 2676 4.639334 AGTTCGTCACTACTCAGTACTCA 58.361 43.478 0.00 0.00 31.97 3.41
1756 2677 4.451774 AGTTCGTCACTACTCAGTACTCAC 59.548 45.833 0.00 0.00 31.97 3.51
1757 2678 4.268797 TCGTCACTACTCAGTACTCACT 57.731 45.455 0.00 0.00 32.21 3.41
1758 2679 5.397142 TCGTCACTACTCAGTACTCACTA 57.603 43.478 0.00 0.00 32.21 2.74
1759 2680 5.409211 TCGTCACTACTCAGTACTCACTAG 58.591 45.833 0.00 0.00 32.21 2.57
1760 2681 5.184671 TCGTCACTACTCAGTACTCACTAGA 59.815 44.000 0.00 0.00 32.21 2.43
1761 2682 6.044046 CGTCACTACTCAGTACTCACTAGAT 58.956 44.000 0.00 0.00 32.21 1.98
1845 3072 4.435425 ACCGCTTGTGATTAACGCTATAA 58.565 39.130 0.00 0.00 0.00 0.98
2017 3274 4.082787 GCCAGCTCTACTTTTTGTTGCATA 60.083 41.667 0.00 0.00 0.00 3.14
2018 3275 5.393461 GCCAGCTCTACTTTTTGTTGCATAT 60.393 40.000 0.00 0.00 0.00 1.78
2019 3276 6.183360 GCCAGCTCTACTTTTTGTTGCATATA 60.183 38.462 0.00 0.00 0.00 0.86
2020 3277 7.469181 GCCAGCTCTACTTTTTGTTGCATATAT 60.469 37.037 0.00 0.00 0.00 0.86
2021 3278 7.859377 CCAGCTCTACTTTTTGTTGCATATATG 59.141 37.037 8.45 8.45 0.00 1.78
2022 3279 7.859377 CAGCTCTACTTTTTGTTGCATATATGG 59.141 37.037 14.51 0.00 0.00 2.74
2023 3280 7.557719 AGCTCTACTTTTTGTTGCATATATGGT 59.442 33.333 14.51 3.27 0.00 3.55
2024 3281 8.190784 GCTCTACTTTTTGTTGCATATATGGTT 58.809 33.333 14.51 0.00 0.00 3.67
2025 3282 9.722056 CTCTACTTTTTGTTGCATATATGGTTC 57.278 33.333 14.51 0.00 0.00 3.62
2026 3283 9.461312 TCTACTTTTTGTTGCATATATGGTTCT 57.539 29.630 14.51 0.00 0.00 3.01
2027 3284 9.507280 CTACTTTTTGTTGCATATATGGTTCTG 57.493 33.333 14.51 0.00 0.00 3.02
2028 3285 8.121305 ACTTTTTGTTGCATATATGGTTCTGA 57.879 30.769 14.51 0.00 0.00 3.27
2029 3286 8.584157 ACTTTTTGTTGCATATATGGTTCTGAA 58.416 29.630 14.51 0.00 0.00 3.02
2030 3287 9.590451 CTTTTTGTTGCATATATGGTTCTGAAT 57.410 29.630 14.51 0.00 0.00 2.57
2031 3288 9.941325 TTTTTGTTGCATATATGGTTCTGAATT 57.059 25.926 14.51 0.00 0.00 2.17
2032 3289 9.941325 TTTTGTTGCATATATGGTTCTGAATTT 57.059 25.926 14.51 0.00 0.00 1.82
2033 3290 8.929827 TTGTTGCATATATGGTTCTGAATTTG 57.070 30.769 14.51 0.00 0.00 2.32
2034 3291 8.065473 TGTTGCATATATGGTTCTGAATTTGT 57.935 30.769 14.51 0.00 0.00 2.83
2035 3292 8.530311 TGTTGCATATATGGTTCTGAATTTGTT 58.470 29.630 14.51 0.00 0.00 2.83
2036 3293 8.810427 GTTGCATATATGGTTCTGAATTTGTTG 58.190 33.333 14.51 0.00 0.00 3.33
2037 3294 6.979817 TGCATATATGGTTCTGAATTTGTTGC 59.020 34.615 14.51 0.00 0.00 4.17
2038 3295 6.979817 GCATATATGGTTCTGAATTTGTTGCA 59.020 34.615 14.51 0.00 0.00 4.08
2039 3296 7.654520 GCATATATGGTTCTGAATTTGTTGCAT 59.345 33.333 14.51 0.00 0.00 3.96
2042 3299 6.594788 ATGGTTCTGAATTTGTTGCATACT 57.405 33.333 0.00 0.00 0.00 2.12
2228 3597 0.107897 GGATGACCACGTATGTGCCA 60.108 55.000 9.72 9.74 45.04 4.92
2318 4167 8.936864 CAATCACCTCGAAGACTATAAAACTTT 58.063 33.333 0.00 0.00 0.00 2.66
2320 4169 9.804758 ATCACCTCGAAGACTATAAAACTTTAG 57.195 33.333 0.00 0.00 0.00 1.85
2492 4515 7.420800 CAGGATAAGGCTTAATTAACAAGCTG 58.579 38.462 11.59 7.55 46.15 4.24
2522 4551 1.134280 CACTCCCCACTGATTAGCCTG 60.134 57.143 0.00 0.00 0.00 4.85
2525 4554 1.143813 CCCCACTGATTAGCCTGGAT 58.856 55.000 0.00 0.00 0.00 3.41
2526 4555 1.496429 CCCCACTGATTAGCCTGGATT 59.504 52.381 0.00 0.00 0.00 3.01
2611 4673 2.986728 ACTCCCACTTCCAACTACCATT 59.013 45.455 0.00 0.00 0.00 3.16
2669 4742 6.040616 TGCCTAACTAGTTAGTGCTATCTTCC 59.959 42.308 32.76 17.11 40.59 3.46
2671 4744 7.201929 GCCTAACTAGTTAGTGCTATCTTCCTT 60.202 40.741 31.28 0.14 40.59 3.36
2708 4782 4.320494 CCATGGTTTTGTAGAGAGTGCAAC 60.320 45.833 2.57 0.00 29.32 4.17
2899 4982 1.735376 GCAGGAACTAGATCGGCCGA 61.735 60.000 33.12 33.12 36.02 5.54
2901 4984 0.106619 AGGAACTAGATCGGCCGACT 60.107 55.000 33.75 28.86 36.02 4.18
2904 4987 1.320344 AACTAGATCGGCCGACTGCA 61.320 55.000 33.75 15.10 43.89 4.41
2960 5050 2.743636 AGTGTGATACTGTTCGGGTG 57.256 50.000 0.00 0.00 38.49 4.61
3018 5108 5.348164 CGTTTGGGTGTCTTCAAAATTTCT 58.652 37.500 0.00 0.00 35.08 2.52
3128 5219 6.380079 AACTAGGAAGAAGTGGATCACATT 57.620 37.500 0.00 0.00 36.74 2.71
3144 5235 6.238897 GGATCACATTGTTTTACAACAGGACA 60.239 38.462 0.00 0.00 43.92 4.02
3147 5238 6.824196 TCACATTGTTTTACAACAGGACACTA 59.176 34.615 0.00 0.00 43.92 2.74
3162 5253 8.926715 ACAGGACACTAAAAGAAAAATGAAAC 57.073 30.769 0.00 0.00 0.00 2.78
3197 5288 5.104652 TGCCTAGTTATTACAAAGAGGACCC 60.105 44.000 0.00 0.00 0.00 4.46
3207 5298 0.328258 AAGAGGACCCCCAAATGTCG 59.672 55.000 0.00 0.00 33.88 4.35
3263 5354 2.427453 TCACAAGCCCGAATCTAGTCTC 59.573 50.000 0.00 0.00 0.00 3.36
3310 5401 3.147595 CGACGAGCCCTCCATGGA 61.148 66.667 15.27 15.27 38.35 3.41
3349 5440 1.751924 AGACGAAGATGTAGTGCCTCC 59.248 52.381 0.00 0.00 0.00 4.30
3363 5454 1.919600 GCCTCCATCTGGCTCTTGGT 61.920 60.000 0.00 0.00 46.38 3.67
3406 5497 5.180492 TCACCATTCGTCCAACAGATTTAAC 59.820 40.000 0.00 0.00 0.00 2.01
3431 5522 0.324614 TGATTGGCATCGACCACAGT 59.675 50.000 0.00 0.00 40.19 3.55
3449 5540 2.521451 TAGTGGGCGCCAAAGTCCA 61.521 57.895 30.85 13.29 44.73 4.02
3454 5545 1.754234 GGCGCCAAAGTCCATCCAT 60.754 57.895 24.80 0.00 0.00 3.41
3516 5607 1.283321 ACCTTTCCCATGCTTCTCCTC 59.717 52.381 0.00 0.00 0.00 3.71
3542 5633 1.143183 ACGGTAACCATGCTAGGCG 59.857 57.895 0.00 0.00 0.00 5.52
3558 5680 1.438814 GCGGCCATGCAAGCTTATT 59.561 52.632 2.24 0.00 32.70 1.40
3559 5681 0.595825 GCGGCCATGCAAGCTTATTC 60.596 55.000 2.24 0.00 32.70 1.75
3560 5682 0.317269 CGGCCATGCAAGCTTATTCG 60.317 55.000 2.24 3.29 0.00 3.34
3561 5683 0.740737 GGCCATGCAAGCTTATTCGT 59.259 50.000 11.41 0.00 0.00 3.85
3562 5684 1.268743 GGCCATGCAAGCTTATTCGTC 60.269 52.381 11.41 0.00 0.00 4.20
3568 5690 3.000041 TGCAAGCTTATTCGTCAATCGT 59.000 40.909 0.00 0.00 40.80 3.73
3571 5693 3.416119 AGCTTATTCGTCAATCGTCGA 57.584 42.857 0.00 0.00 40.80 4.20
3572 5694 3.966154 AGCTTATTCGTCAATCGTCGAT 58.034 40.909 0.75 0.75 40.80 3.59
3584 5706 0.817654 TCGTCGATGATGCACTCCTT 59.182 50.000 2.39 0.00 0.00 3.36
3585 5707 0.926155 CGTCGATGATGCACTCCTTG 59.074 55.000 0.00 0.00 0.00 3.61
3628 5750 0.549950 ATAGCCAGGATTGCAGCTGT 59.450 50.000 16.64 0.00 36.79 4.40
3647 5769 2.125512 GCTAGCCACCGACCACTG 60.126 66.667 2.29 0.00 0.00 3.66
3658 5780 0.388520 CGACCACTGCTCAATCACGA 60.389 55.000 0.00 0.00 0.00 4.35
3662 5784 1.633561 CACTGCTCAATCACGACGAT 58.366 50.000 0.00 0.00 35.12 3.73
3685 5807 2.277591 TGCTCCACCATGGCAAAGC 61.278 57.895 20.41 20.41 37.47 3.51
3687 5809 3.346631 CTCCACCATGGCAAAGCGC 62.347 63.158 13.04 0.00 37.47 5.92
3703 5825 4.043200 GCCAAACGCCACAGGAGC 62.043 66.667 0.00 0.00 0.00 4.70
3715 5837 3.003763 AGGAGCAGGACGGAACCC 61.004 66.667 0.00 0.00 0.00 4.11
3721 5843 1.913762 CAGGACGGAACCCAGACCT 60.914 63.158 0.00 0.00 0.00 3.85
3751 5873 1.277580 AAGGGTCCTCCATGCTCCTG 61.278 60.000 0.00 0.00 38.24 3.86
3780 5902 1.705337 CGGGCATGAAACACCGCTAG 61.705 60.000 0.00 0.00 39.85 3.42
3801 5923 1.272769 GGAAGATTAGGGATCGGGTCG 59.727 57.143 0.00 0.00 39.85 4.79
3806 5928 2.376695 TTAGGGATCGGGTCGAGAAT 57.623 50.000 0.00 0.00 39.91 2.40
3808 5930 0.753262 AGGGATCGGGTCGAGAATTG 59.247 55.000 0.00 0.00 39.91 2.32
3809 5931 0.249911 GGGATCGGGTCGAGAATTGG 60.250 60.000 0.00 0.00 39.91 3.16
3843 5971 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
3844 5972 3.885901 CTCTCTCTCTCTCTCTCTCTCGA 59.114 52.174 0.00 0.00 0.00 4.04
3854 5984 2.027653 TCTCTCTCTCGACTCTCAGCAA 60.028 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.505184 CACGGGGTAACATGCGGC 61.505 66.667 0.00 0.00 39.74 6.53
3 4 2.104253 GTCACGGGGTAACATGCGG 61.104 63.158 0.00 0.00 39.74 5.69
4 5 1.079405 AGTCACGGGGTAACATGCG 60.079 57.895 0.00 0.00 39.74 4.73
5 6 1.644786 GCAGTCACGGGGTAACATGC 61.645 60.000 0.00 0.00 39.74 4.06
6 7 1.024579 GGCAGTCACGGGGTAACATG 61.025 60.000 0.00 0.00 39.74 3.21
7 8 1.298667 GGCAGTCACGGGGTAACAT 59.701 57.895 0.00 0.00 39.74 2.71
8 9 1.697082 TTGGCAGTCACGGGGTAACA 61.697 55.000 0.00 0.00 39.74 2.41
9 10 0.953960 CTTGGCAGTCACGGGGTAAC 60.954 60.000 0.00 0.00 0.00 2.50
10 11 1.122632 TCTTGGCAGTCACGGGGTAA 61.123 55.000 0.00 0.00 0.00 2.85
11 12 1.534476 TCTTGGCAGTCACGGGGTA 60.534 57.895 0.00 0.00 0.00 3.69
12 13 2.847234 TCTTGGCAGTCACGGGGT 60.847 61.111 0.00 0.00 0.00 4.95
13 14 2.046892 CTCTTGGCAGTCACGGGG 60.047 66.667 0.00 0.00 0.00 5.73
14 15 2.046892 CCTCTTGGCAGTCACGGG 60.047 66.667 0.00 0.00 0.00 5.28
24 25 2.189594 TCAAGTGACATGCCTCTTGG 57.810 50.000 19.43 5.76 37.89 3.61
25 26 2.681848 GGATCAAGTGACATGCCTCTTG 59.318 50.000 15.24 15.24 38.37 3.02
26 27 2.356535 GGGATCAAGTGACATGCCTCTT 60.357 50.000 0.00 0.00 0.00 2.85
27 28 1.211457 GGGATCAAGTGACATGCCTCT 59.789 52.381 0.00 0.00 0.00 3.69
28 29 1.065199 TGGGATCAAGTGACATGCCTC 60.065 52.381 0.00 0.00 31.85 4.70
29 30 0.994247 TGGGATCAAGTGACATGCCT 59.006 50.000 0.00 0.00 31.85 4.75
30 31 1.340405 ACTGGGATCAAGTGACATGCC 60.340 52.381 0.00 0.00 0.00 4.40
31 32 2.012673 GACTGGGATCAAGTGACATGC 58.987 52.381 5.11 0.00 0.00 4.06
32 33 2.636830 GGACTGGGATCAAGTGACATG 58.363 52.381 5.11 0.00 0.00 3.21
33 34 1.561542 GGGACTGGGATCAAGTGACAT 59.438 52.381 5.11 0.00 0.00 3.06
34 35 0.984230 GGGACTGGGATCAAGTGACA 59.016 55.000 5.11 0.00 0.00 3.58
35 36 1.280457 AGGGACTGGGATCAAGTGAC 58.720 55.000 5.11 0.00 37.18 3.67
36 37 1.630369 CAAGGGACTGGGATCAAGTGA 59.370 52.381 5.11 0.00 40.86 3.41
37 38 1.352352 ACAAGGGACTGGGATCAAGTG 59.648 52.381 5.11 0.00 40.86 3.16
38 39 1.747444 ACAAGGGACTGGGATCAAGT 58.253 50.000 0.17 0.17 40.86 3.16
39 40 2.887151 AACAAGGGACTGGGATCAAG 57.113 50.000 0.00 0.00 40.86 3.02
40 41 2.027561 CGTAACAAGGGACTGGGATCAA 60.028 50.000 0.00 0.00 40.86 2.57
41 42 1.553248 CGTAACAAGGGACTGGGATCA 59.447 52.381 0.00 0.00 40.86 2.92
42 43 1.553704 ACGTAACAAGGGACTGGGATC 59.446 52.381 0.00 0.00 40.86 3.36
43 44 1.652947 ACGTAACAAGGGACTGGGAT 58.347 50.000 0.00 0.00 40.86 3.85
44 45 1.895131 GTACGTAACAAGGGACTGGGA 59.105 52.381 0.00 0.00 40.86 4.37
45 46 1.897802 AGTACGTAACAAGGGACTGGG 59.102 52.381 0.00 0.00 40.86 4.45
46 47 2.094338 GGAGTACGTAACAAGGGACTGG 60.094 54.545 0.00 0.00 40.86 4.00
47 48 2.094338 GGGAGTACGTAACAAGGGACTG 60.094 54.545 0.00 0.00 40.86 3.51
49 50 2.165234 GAGGGAGTACGTAACAAGGGAC 59.835 54.545 0.00 0.00 0.00 4.46
50 51 2.450476 GAGGGAGTACGTAACAAGGGA 58.550 52.381 0.00 0.00 0.00 4.20
51 52 1.479730 GGAGGGAGTACGTAACAAGGG 59.520 57.143 0.00 0.00 0.00 3.95
52 53 1.133790 CGGAGGGAGTACGTAACAAGG 59.866 57.143 0.00 0.00 0.00 3.61
53 54 1.815003 ACGGAGGGAGTACGTAACAAG 59.185 52.381 0.00 0.00 39.30 3.16
54 55 1.909700 ACGGAGGGAGTACGTAACAA 58.090 50.000 0.00 0.00 39.30 2.83
55 56 1.812571 GAACGGAGGGAGTACGTAACA 59.187 52.381 0.00 0.00 40.31 2.41
56 57 1.202076 CGAACGGAGGGAGTACGTAAC 60.202 57.143 0.00 0.00 40.31 2.50
57 58 1.086696 CGAACGGAGGGAGTACGTAA 58.913 55.000 0.00 0.00 40.31 3.18
58 59 0.744414 CCGAACGGAGGGAGTACGTA 60.744 60.000 7.53 0.00 40.31 3.57
59 60 2.042831 CCGAACGGAGGGAGTACGT 61.043 63.158 7.53 0.00 43.43 3.57
60 61 1.308069 TTCCGAACGGAGGGAGTACG 61.308 60.000 15.34 0.00 46.06 3.67
61 62 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
62 63 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
63 64 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
64 65 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
65 66 1.479323 CAGTAATTCCGAACGGAGGGA 59.521 52.381 15.34 2.49 46.06 4.20
66 67 1.472728 CCAGTAATTCCGAACGGAGGG 60.473 57.143 15.34 8.37 46.06 4.30
67 68 1.206371 ACCAGTAATTCCGAACGGAGG 59.794 52.381 15.34 14.00 46.06 4.30
68 69 2.165845 AGACCAGTAATTCCGAACGGAG 59.834 50.000 15.34 5.60 46.06 4.63
69 70 2.165030 GAGACCAGTAATTCCGAACGGA 59.835 50.000 12.04 12.04 43.52 4.69
70 71 2.537401 GAGACCAGTAATTCCGAACGG 58.463 52.381 6.94 6.94 0.00 4.44
71 72 2.159476 TCGAGACCAGTAATTCCGAACG 60.159 50.000 0.00 0.00 0.00 3.95
72 73 3.498927 TCGAGACCAGTAATTCCGAAC 57.501 47.619 0.00 0.00 0.00 3.95
73 74 4.524316 TTTCGAGACCAGTAATTCCGAA 57.476 40.909 0.00 0.00 33.57 4.30
74 75 4.524316 TTTTCGAGACCAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
75 76 4.034048 CCATTTTCGAGACCAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
76 77 5.183228 TCCATTTTCGAGACCAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
77 78 6.316390 ACATCCATTTTCGAGACCAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
78 79 6.180472 ACATCCATTTTCGAGACCAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
79 80 5.745227 ACATCCATTTTCGAGACCAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
80 81 5.160607 ACATCCATTTTCGAGACCAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
81 82 4.819105 ACATCCATTTTCGAGACCAGTA 57.181 40.909 0.00 0.00 0.00 2.74
82 83 3.703001 ACATCCATTTTCGAGACCAGT 57.297 42.857 0.00 0.00 0.00 4.00
83 84 6.683974 AAATACATCCATTTTCGAGACCAG 57.316 37.500 0.00 0.00 0.00 4.00
84 85 7.561251 TCTAAATACATCCATTTTCGAGACCA 58.439 34.615 0.00 0.00 30.84 4.02
85 86 8.433421 TTCTAAATACATCCATTTTCGAGACC 57.567 34.615 0.00 0.00 30.84 3.85
135 136 6.589523 TCCGTTCGGAATTACTTATCGAAAAA 59.410 34.615 11.66 0.00 40.67 1.94
136 137 6.098679 TCCGTTCGGAATTACTTATCGAAAA 58.901 36.000 11.66 0.00 40.67 2.29
137 138 5.649557 TCCGTTCGGAATTACTTATCGAAA 58.350 37.500 11.66 0.00 40.67 3.46
138 139 5.247507 TCCGTTCGGAATTACTTATCGAA 57.752 39.130 11.66 0.00 37.48 3.71
139 140 4.261322 CCTCCGTTCGGAATTACTTATCGA 60.261 45.833 14.79 0.00 33.41 3.59
140 141 3.979495 CCTCCGTTCGGAATTACTTATCG 59.021 47.826 14.79 0.00 33.41 2.92
141 142 4.038402 TCCCTCCGTTCGGAATTACTTATC 59.962 45.833 14.79 0.00 33.41 1.75
142 143 3.962718 TCCCTCCGTTCGGAATTACTTAT 59.037 43.478 14.79 0.00 33.41 1.73
143 144 3.364549 TCCCTCCGTTCGGAATTACTTA 58.635 45.455 14.79 0.00 33.41 2.24
144 145 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
145 146 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
146 147 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
147 148 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
148 149 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
149 150 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
150 151 1.308069 CGTACTCCCTCCGTTCGGAA 61.308 60.000 14.79 0.04 33.41 4.30
151 152 1.746615 CGTACTCCCTCCGTTCGGA 60.747 63.158 13.34 13.34 0.00 4.55
152 153 0.744414 TACGTACTCCCTCCGTTCGG 60.744 60.000 4.74 4.74 36.12 4.30
153 154 0.375106 GTACGTACTCCCTCCGTTCG 59.625 60.000 18.47 0.00 36.12 3.95
154 155 1.399791 CTGTACGTACTCCCTCCGTTC 59.600 57.143 25.12 0.00 36.12 3.95
155 156 1.457346 CTGTACGTACTCCCTCCGTT 58.543 55.000 25.12 0.00 36.12 4.44
156 157 1.028868 GCTGTACGTACTCCCTCCGT 61.029 60.000 25.12 0.00 38.53 4.69
157 158 1.722636 GGCTGTACGTACTCCCTCCG 61.723 65.000 25.12 7.24 0.00 4.63
158 159 1.722636 CGGCTGTACGTACTCCCTCC 61.723 65.000 25.12 16.42 0.00 4.30
159 160 0.745845 TCGGCTGTACGTACTCCCTC 60.746 60.000 25.12 10.12 34.94 4.30
160 161 0.106819 ATCGGCTGTACGTACTCCCT 60.107 55.000 25.12 12.45 34.94 4.20
161 162 0.030369 CATCGGCTGTACGTACTCCC 59.970 60.000 25.12 21.68 34.94 4.30
162 163 0.594284 GCATCGGCTGTACGTACTCC 60.594 60.000 25.12 22.46 36.96 3.85
163 164 2.869354 GCATCGGCTGTACGTACTC 58.131 57.895 25.12 16.47 36.96 2.59
250 276 1.931551 CACGTCACAAGAACCACCG 59.068 57.895 0.00 0.00 0.00 4.94
438 471 5.176958 TGCTACGAAGAAGCTGTTTTACTTC 59.823 40.000 0.00 0.00 42.13 3.01
462 495 3.119495 AGCTCTGCAAACAAAAGAACGTT 60.119 39.130 0.00 0.00 0.00 3.99
464 497 3.038710 GAGCTCTGCAAACAAAAGAACG 58.961 45.455 6.43 0.00 0.00 3.95
476 513 4.074526 GCACTCCGGAGCTCTGCA 62.075 66.667 30.44 0.31 30.93 4.41
500 537 6.129393 CGAGAAACACACAATTACTGAACTG 58.871 40.000 0.00 0.00 0.00 3.16
516 553 4.130857 TCAAAATGTAGGCACGAGAAACA 58.869 39.130 0.00 0.00 0.00 2.83
550 587 1.879380 TGTTGAGTGTGCTGTTATGCC 59.121 47.619 0.00 0.00 0.00 4.40
571 1247 1.908344 TGGCAGTCAGCTTAATTGCA 58.092 45.000 13.34 0.00 44.79 4.08
572 1248 3.515330 ATTGGCAGTCAGCTTAATTGC 57.485 42.857 5.12 5.12 44.79 3.56
573 1249 5.517770 GCTTAATTGGCAGTCAGCTTAATTG 59.482 40.000 6.83 0.00 44.79 2.32
574 1250 5.420104 AGCTTAATTGGCAGTCAGCTTAATT 59.580 36.000 9.93 0.00 44.79 1.40
575 1251 4.952335 AGCTTAATTGGCAGTCAGCTTAAT 59.048 37.500 9.93 0.00 44.79 1.40
576 1252 4.156556 CAGCTTAATTGGCAGTCAGCTTAA 59.843 41.667 12.31 0.00 44.79 1.85
577 1253 3.691118 CAGCTTAATTGGCAGTCAGCTTA 59.309 43.478 12.31 0.00 44.79 3.09
578 1254 2.490903 CAGCTTAATTGGCAGTCAGCTT 59.509 45.455 12.31 0.00 44.79 3.74
579 1255 2.089980 CAGCTTAATTGGCAGTCAGCT 58.910 47.619 9.93 9.93 44.79 4.24
580 1256 2.086869 TCAGCTTAATTGGCAGTCAGC 58.913 47.619 6.14 6.14 44.65 4.26
581 1257 3.943381 TCATCAGCTTAATTGGCAGTCAG 59.057 43.478 7.73 0.00 0.00 3.51
582 1258 3.943381 CTCATCAGCTTAATTGGCAGTCA 59.057 43.478 7.73 0.00 0.00 3.41
583 1259 3.314635 CCTCATCAGCTTAATTGGCAGTC 59.685 47.826 7.73 0.00 0.00 3.51
584 1260 3.054139 TCCTCATCAGCTTAATTGGCAGT 60.054 43.478 7.73 0.00 0.00 4.40
585 1261 3.314635 GTCCTCATCAGCTTAATTGGCAG 59.685 47.826 7.73 0.90 0.00 4.85
586 1262 3.282021 GTCCTCATCAGCTTAATTGGCA 58.718 45.455 7.73 0.00 0.00 4.92
641 1496 8.321650 ACGTACTAGTACTGGATATTCTTAGC 57.678 38.462 26.36 0.00 34.04 3.09
650 1505 5.062528 GGAGCTTACGTACTAGTACTGGAT 58.937 45.833 26.36 14.15 34.04 3.41
655 1510 3.001736 CGGTGGAGCTTACGTACTAGTAC 59.998 52.174 21.06 21.06 0.00 2.73
656 1511 3.198068 CGGTGGAGCTTACGTACTAGTA 58.802 50.000 0.00 0.00 0.00 1.82
657 1512 2.012673 CGGTGGAGCTTACGTACTAGT 58.987 52.381 0.00 0.00 0.00 2.57
658 1513 2.012673 ACGGTGGAGCTTACGTACTAG 58.987 52.381 0.00 0.00 37.85 2.57
659 1514 2.113860 ACGGTGGAGCTTACGTACTA 57.886 50.000 0.00 0.00 37.85 1.82
660 1515 2.113860 TACGGTGGAGCTTACGTACT 57.886 50.000 0.00 0.00 40.38 2.73
661 1516 3.427161 AATACGGTGGAGCTTACGTAC 57.573 47.619 12.90 0.00 43.43 3.67
662 1517 3.565482 CCTAATACGGTGGAGCTTACGTA 59.435 47.826 12.98 12.98 44.51 3.57
663 1518 2.360165 CCTAATACGGTGGAGCTTACGT 59.640 50.000 10.04 10.04 42.71 3.57
664 1519 2.620115 TCCTAATACGGTGGAGCTTACG 59.380 50.000 0.00 0.00 0.00 3.18
685 1540 1.536418 TAGCTCACTGGTGGCTGGT 60.536 57.895 19.32 10.78 37.56 4.00
709 1564 3.542648 CTCATCATTGCATCACTCCAGT 58.457 45.455 0.00 0.00 0.00 4.00
777 1640 5.430417 TGGGTTTATTAGTGGAGGCAGATAA 59.570 40.000 0.00 0.00 0.00 1.75
785 1649 3.054361 AGTGGCTGGGTTTATTAGTGGAG 60.054 47.826 0.00 0.00 0.00 3.86
1032 1912 1.686110 CTTGGCTCCGTACTCCCCT 60.686 63.158 0.00 0.00 0.00 4.79
1044 1924 1.562783 GGTCAGAGTAGTCCTTGGCT 58.437 55.000 0.00 0.00 0.00 4.75
1176 2056 0.036765 GGTGCTTGTACCCGATGACA 60.037 55.000 0.00 0.00 34.56 3.58
1626 2506 0.326595 TGAAATCGGTAGGCAGGCAA 59.673 50.000 0.00 0.00 0.00 4.52
1700 2608 7.782897 ATCAATAGAGAATATTCGGAGACCA 57.217 36.000 9.78 0.00 34.32 4.02
1701 2609 8.962679 AGTATCAATAGAGAATATTCGGAGACC 58.037 37.037 9.78 0.00 34.32 3.85
1702 2610 9.781834 CAGTATCAATAGAGAATATTCGGAGAC 57.218 37.037 9.78 9.01 34.32 3.36
1720 2628 6.570672 AGTGACGAACTACTTCAGTATCAA 57.429 37.500 0.00 0.00 37.36 2.57
1749 2670 3.702045 AGCAAGGGACATCTAGTGAGTAC 59.298 47.826 0.00 0.00 0.00 2.73
1752 2673 3.957497 ACTAGCAAGGGACATCTAGTGAG 59.043 47.826 0.00 0.00 39.92 3.51
1755 2676 5.520751 ACTAACTAGCAAGGGACATCTAGT 58.479 41.667 0.00 0.00 42.31 2.57
1756 2677 6.472686 AACTAACTAGCAAGGGACATCTAG 57.527 41.667 0.00 0.00 35.77 2.43
1757 2678 7.966339 TTAACTAACTAGCAAGGGACATCTA 57.034 36.000 0.00 0.00 0.00 1.98
1758 2679 6.869206 TTAACTAACTAGCAAGGGACATCT 57.131 37.500 0.00 0.00 0.00 2.90
1759 2680 8.398665 CAAATTAACTAACTAGCAAGGGACATC 58.601 37.037 0.00 0.00 0.00 3.06
1760 2681 7.339466 CCAAATTAACTAACTAGCAAGGGACAT 59.661 37.037 0.00 0.00 0.00 3.06
1761 2682 6.657541 CCAAATTAACTAACTAGCAAGGGACA 59.342 38.462 0.00 0.00 0.00 4.02
2017 3274 8.297470 AGTATGCAACAAATTCAGAACCATAT 57.703 30.769 0.00 0.00 0.00 1.78
2018 3275 7.701539 AGTATGCAACAAATTCAGAACCATA 57.298 32.000 0.00 0.00 0.00 2.74
2019 3276 6.594788 AGTATGCAACAAATTCAGAACCAT 57.405 33.333 0.00 0.00 0.00 3.55
2020 3277 7.701539 ATAGTATGCAACAAATTCAGAACCA 57.298 32.000 0.00 0.00 0.00 3.67
2021 3278 9.669353 CATATAGTATGCAACAAATTCAGAACC 57.331 33.333 0.00 0.00 0.00 3.62
2022 3279 9.669353 CCATATAGTATGCAACAAATTCAGAAC 57.331 33.333 0.00 0.00 0.00 3.01
2023 3280 9.407380 ACCATATAGTATGCAACAAATTCAGAA 57.593 29.630 0.00 0.00 0.00 3.02
2024 3281 8.978874 ACCATATAGTATGCAACAAATTCAGA 57.021 30.769 0.00 0.00 0.00 3.27
2040 3297 9.723601 ATTGCAACAAATTCAAAACCATATAGT 57.276 25.926 0.00 0.00 0.00 2.12
2041 3298 9.976255 CATTGCAACAAATTCAAAACCATATAG 57.024 29.630 0.00 0.00 0.00 1.31
2042 3299 9.716531 TCATTGCAACAAATTCAAAACCATATA 57.283 25.926 0.00 0.00 0.00 0.86
2228 3597 3.369471 GCAGACATGGTATAGTGTGTGGT 60.369 47.826 0.00 0.00 39.29 4.16
2240 3609 5.518865 ACCCATTAAATTAGCAGACATGGT 58.481 37.500 0.00 0.00 40.99 3.55
2318 4167 6.349777 CCACACAAGTTCTGTTTGGTTTTCTA 60.350 38.462 2.54 0.00 46.70 2.10
2320 4169 4.625311 CCACACAAGTTCTGTTTGGTTTTC 59.375 41.667 2.54 0.00 46.70 2.29
2439 4458 7.646922 GCCATTCTTCAAAATAATCTAGCTGTG 59.353 37.037 0.00 0.00 0.00 3.66
2492 4515 0.741221 GTGGGGAGTGACATCGCTTC 60.741 60.000 0.00 0.00 36.74 3.86
2611 4673 4.323417 AGTAGATTTTGTGGCGTGATTGA 58.677 39.130 0.00 0.00 0.00 2.57
2669 4742 6.899393 AACCATGGGCATATGTATGTAAAG 57.101 37.500 18.09 0.00 36.11 1.85
2671 4744 6.609212 ACAAAACCATGGGCATATGTATGTAA 59.391 34.615 18.09 0.00 36.11 2.41
2886 4969 1.729470 CTGCAGTCGGCCGATCTAGT 61.729 60.000 33.58 8.89 43.89 2.57
2899 4982 2.319844 TCCGATCATCCATACTGCAGT 58.680 47.619 25.12 25.12 0.00 4.40
2901 4984 2.548707 GCTTCCGATCATCCATACTGCA 60.549 50.000 0.00 0.00 0.00 4.41
2904 4987 2.288457 CGTGCTTCCGATCATCCATACT 60.288 50.000 0.00 0.00 0.00 2.12
2958 5048 0.442310 ACGCGTGCACAATACATCAC 59.558 50.000 12.93 0.00 0.00 3.06
2960 5050 0.999406 AGACGCGTGCACAATACATC 59.001 50.000 20.70 5.12 0.00 3.06
2996 5086 6.573434 AGAGAAATTTTGAAGACACCCAAAC 58.427 36.000 0.00 0.00 32.67 2.93
3018 5108 6.876789 TCCTTCGAATTTAGTGCAATTGTAGA 59.123 34.615 7.40 0.00 0.00 2.59
3083 5174 3.636153 ATGCAACTTCTAGGTCCTTCC 57.364 47.619 0.00 0.00 0.00 3.46
3092 5183 8.594550 ACTTCTTCCTAGTTAATGCAACTTCTA 58.405 33.333 0.00 0.00 45.54 2.10
3111 5202 7.648142 TGTAAAACAATGTGATCCACTTCTTC 58.352 34.615 0.00 0.00 35.11 2.87
3114 5205 7.199766 TGTTGTAAAACAATGTGATCCACTTC 58.800 34.615 0.00 0.00 40.59 3.01
3128 5219 7.925043 TCTTTTAGTGTCCTGTTGTAAAACA 57.075 32.000 0.00 0.00 0.00 2.83
3174 5265 5.366460 GGGTCCTCTTTGTAATAACTAGGC 58.634 45.833 0.00 0.00 0.00 3.93
3197 5288 2.916111 CGAGTTTCAACGACATTTGGG 58.084 47.619 0.00 0.00 0.00 4.12
3207 5298 2.607038 GGACCCAATTGCGAGTTTCAAC 60.607 50.000 0.00 0.00 0.00 3.18
3244 5335 1.405821 CGAGACTAGATTCGGGCTTGT 59.594 52.381 0.00 0.00 33.39 3.16
3263 5354 0.320683 TGTCATGCCTGGTGAAGACG 60.321 55.000 0.00 0.00 0.00 4.18
3295 5386 1.488705 TTGTTCCATGGAGGGCTCGT 61.489 55.000 15.53 0.00 38.24 4.18
3310 5401 1.608590 CTTGGAGTTCATGGCGTTGTT 59.391 47.619 0.00 0.00 0.00 2.83
3313 5404 1.523758 GTCTTGGAGTTCATGGCGTT 58.476 50.000 0.00 0.00 0.00 4.84
3349 5440 0.329261 TCCCAACCAAGAGCCAGATG 59.671 55.000 0.00 0.00 0.00 2.90
3363 5454 1.073923 GACCTTGCTTCTTCCTCCCAA 59.926 52.381 0.00 0.00 0.00 4.12
3427 5518 1.302511 CTTTGGCGCCCACTACTGT 60.303 57.895 26.77 0.00 30.78 3.55
3431 5522 1.847798 ATGGACTTTGGCGCCCACTA 61.848 55.000 26.77 0.59 30.78 2.74
3449 5540 0.752743 CACCGATGGCAACCATGGAT 60.753 55.000 21.47 2.68 45.26 3.41
3454 5545 0.392863 CTCATCACCGATGGCAACCA 60.393 55.000 4.24 0.00 40.15 3.67
3458 5549 1.450134 GTGCTCATCACCGATGGCA 60.450 57.895 12.91 12.91 40.78 4.92
3516 5607 1.017177 CATGGTTACCGTGGTCGTGG 61.017 60.000 15.44 0.00 36.92 4.94
3542 5633 0.740737 ACGAATAAGCTTGCATGGCC 59.259 50.000 9.86 0.00 0.00 5.36
3558 5680 1.202245 TGCATCATCGACGATTGACGA 60.202 47.619 7.83 9.90 45.54 4.20
3560 5682 2.196749 AGTGCATCATCGACGATTGAC 58.803 47.619 7.83 5.95 0.00 3.18
3561 5683 2.463876 GAGTGCATCATCGACGATTGA 58.536 47.619 7.83 9.71 0.00 2.57
3562 5684 1.524355 GGAGTGCATCATCGACGATTG 59.476 52.381 7.83 6.38 0.00 2.67
3584 5706 2.124024 GGGAGCCAGATGCATGCA 60.124 61.111 25.04 25.04 44.83 3.96
3585 5707 1.755395 TTGGGAGCCAGATGCATGC 60.755 57.895 11.82 11.82 44.83 4.06
3595 5717 0.250510 GGCTATGCTAGTTGGGAGCC 60.251 60.000 7.29 7.29 42.45 4.70
3647 5769 0.567968 CGTCATCGTCGTGATTGAGC 59.432 55.000 0.00 0.00 34.13 4.26
3662 5784 2.347114 CCATGGTGGAGCACGTCA 59.653 61.111 2.57 0.00 40.96 4.35
3685 5807 3.726517 CTCCTGTGGCGTTTGGCG 61.727 66.667 0.00 0.00 44.92 5.69
3687 5809 2.594303 TGCTCCTGTGGCGTTTGG 60.594 61.111 0.00 0.00 0.00 3.28
3701 5823 2.203788 TCTGGGTTCCGTCCTGCT 60.204 61.111 0.00 0.00 0.00 4.24
3703 5825 0.613853 TAGGTCTGGGTTCCGTCCTG 60.614 60.000 0.00 0.00 0.00 3.86
3715 5837 8.493787 AGGACCCTTATAAAATACTAGGTCTG 57.506 38.462 0.00 0.00 41.80 3.51
3721 5843 7.516209 AGCATGGAGGACCCTTATAAAATACTA 59.484 37.037 0.00 0.00 35.38 1.82
3763 5885 1.376609 CCCTAGCGGTGTTTCATGCC 61.377 60.000 0.00 0.00 0.00 4.40
3766 5888 1.906574 TCTTCCCTAGCGGTGTTTCAT 59.093 47.619 0.00 0.00 0.00 2.57
3769 5891 3.118371 CCTAATCTTCCCTAGCGGTGTTT 60.118 47.826 0.00 0.00 0.00 2.83
3780 5902 1.624312 GACCCGATCCCTAATCTTCCC 59.376 57.143 0.00 0.00 31.68 3.97
3801 5923 4.210331 AGAGAGAGAGAGAGCCAATTCTC 58.790 47.826 0.00 0.00 43.16 2.87
3806 5928 2.846206 AGAGAGAGAGAGAGAGAGCCAA 59.154 50.000 0.00 0.00 0.00 4.52
3808 5930 2.703007 AGAGAGAGAGAGAGAGAGAGCC 59.297 54.545 0.00 0.00 0.00 4.70
3809 5931 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
3843 5971 0.948141 AAGCGCACTTGCTGAGAGTC 60.948 55.000 11.47 0.00 46.60 3.36
3844 5972 1.070445 AAGCGCACTTGCTGAGAGT 59.930 52.632 11.47 0.00 46.60 3.24
3854 5984 1.896220 TTGATCCTTTCAAGCGCACT 58.104 45.000 11.47 0.00 39.44 4.40


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

AutoCloner maintained by Alex Coulton.