Multiple sequence alignment - TraesCS4D01G057700

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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 TraesCS4D01G057700 chr4D 100.000 2901 0 0 1 2901 32503942 32501042 0.000000e+00 5358.0
1 TraesCS4D01G057700 chr4A 88.226 1257 57 34 829 2039 569877308 569878519 0.000000e+00 1417.0
2 TraesCS4D01G057700 chr4A 90.888 428 19 9 2046 2454 569878490 569878916 9.080000e-155 556.0
3 TraesCS4D01G057700 chr4A 85.919 419 29 16 97 487 569876879 569877295 1.240000e-113 420.0
4 TraesCS4D01G057700 chr4A 81.974 466 29 27 2470 2901 569878975 569879419 7.700000e-91 344.0
5 TraesCS4D01G057700 chr4A 91.133 203 18 0 619 821 153353093 153352891 2.850000e-70 276.0
6 TraesCS4D01G057700 chr4A 93.600 125 6 1 489 611 153353275 153353151 4.940000e-43 185.0
7 TraesCS4D01G057700 chr4B 85.009 1154 59 40 817 1923 47504137 47503051 0.000000e+00 1068.0
8 TraesCS4D01G057700 chr4B 91.791 402 13 9 97 492 47504520 47504133 2.540000e-150 542.0
9 TraesCS4D01G057700 chr4B 90.076 393 15 10 2494 2871 47502489 47502106 3.360000e-134 488.0
10 TraesCS4D01G057700 chr4B 85.096 416 22 16 2067 2455 47502985 47502583 3.510000e-104 388.0
11 TraesCS4D01G057700 chr4B 89.785 186 19 0 634 819 67486326 67486511 3.740000e-59 239.0
12 TraesCS4D01G057700 chr5D 97.305 334 9 0 488 821 374383996 374383663 4.200000e-158 568.0
13 TraesCS4D01G057700 chr5D 92.195 205 16 0 619 823 488934785 488934581 1.020000e-74 291.0
14 TraesCS4D01G057700 chr5D 95.455 88 4 0 489 576 488937499 488937412 1.080000e-29 141.0
15 TraesCS4D01G057700 chr1D 96.997 333 10 0 489 821 221873409 221873077 7.020000e-156 560.0
16 TraesCS4D01G057700 chr2D 95.266 338 12 1 486 819 629214345 629214682 1.530000e-147 532.0
17 TraesCS4D01G057700 chr1A 91.089 202 18 0 619 820 113475421 113475622 1.020000e-69 274.0
18 TraesCS4D01G057700 chr1A 89.381 113 6 1 489 601 113475244 113475350 1.400000e-28 137.0
19 TraesCS4D01G057700 chr6B 92.800 125 8 1 488 611 642911902 642911778 2.300000e-41 180.0
20 TraesCS4D01G057700 chr6B 91.304 115 9 1 705 819 642909892 642909779 3.870000e-34 156.0
21 TraesCS4D01G057700 chrUn 82.178 101 10 8 489 585 87126127 87126031 2.400000e-11 80.5
22 TraesCS4D01G057700 chrUn 81.176 85 9 6 743 824 314868016 314868096 8.680000e-06 62.1


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 TraesCS4D01G057700 chr4D 32501042 32503942 2900 True 5358.00 5358 100.00000 1 2901 1 chr4D.!!$R1 2900
1 TraesCS4D01G057700 chr4A 569876879 569879419 2540 False 684.25 1417 86.75175 97 2901 4 chr4A.!!$F1 2804
2 TraesCS4D01G057700 chr4B 47502106 47504520 2414 True 621.50 1068 87.99300 97 2871 4 chr4B.!!$R1 2774
3 TraesCS4D01G057700 chr5D 488934581 488937499 2918 True 216.00 291 93.82500 489 823 2 chr5D.!!$R2 334

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
576 612 0.793104 GGCGCGTTGACATTTACTGC 60.793 55.0 8.43 0.0 0.0 4.4 F
1575 4252 0.177604 CGAGGCCTGCTCAAGAAGAT 59.822 55.0 12.00 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 4528 0.036022 GGGAACTCAGAAGCAGCTGT 59.964 55.0 16.64 0.0 37.2 4.40 R
2390 5128 0.774908 TGGGGAAAAACGACCTCCAT 59.225 50.0 0.00 0.0 0.0 3.41 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
21 22 3.773418 TCCACCGAACATTAGTTTCCA 57.227 42.857 0.00 0.00 38.30 3.53
22 23 4.295141 TCCACCGAACATTAGTTTCCAT 57.705 40.909 0.00 0.00 38.30 3.41
23 24 5.423704 TCCACCGAACATTAGTTTCCATA 57.576 39.130 0.00 0.00 38.30 2.74
24 25 5.996644 TCCACCGAACATTAGTTTCCATAT 58.003 37.500 0.00 0.00 38.30 1.78
25 26 5.820423 TCCACCGAACATTAGTTTCCATATG 59.180 40.000 0.00 0.00 38.30 1.78
26 27 5.820423 CCACCGAACATTAGTTTCCATATGA 59.180 40.000 3.65 0.00 38.30 2.15
27 28 6.486657 CCACCGAACATTAGTTTCCATATGAT 59.513 38.462 3.65 0.00 38.30 2.45
28 29 7.659799 CCACCGAACATTAGTTTCCATATGATA 59.340 37.037 3.65 0.00 38.30 2.15
29 30 9.051679 CACCGAACATTAGTTTCCATATGATAA 57.948 33.333 3.65 0.00 38.30 1.75
30 31 9.273016 ACCGAACATTAGTTTCCATATGATAAG 57.727 33.333 3.65 0.00 38.30 1.73
31 32 9.489084 CCGAACATTAGTTTCCATATGATAAGA 57.511 33.333 3.65 0.00 38.30 2.10
44 45 9.850198 TCCATATGATAAGAATCACAAACATCA 57.150 29.630 3.65 0.00 44.79 3.07
51 52 9.565213 GATAAGAATCACAAACATCAAAGAAGG 57.435 33.333 0.00 0.00 31.93 3.46
52 53 7.587037 AAGAATCACAAACATCAAAGAAGGA 57.413 32.000 0.00 0.00 0.00 3.36
53 54 7.211966 AGAATCACAAACATCAAAGAAGGAG 57.788 36.000 0.00 0.00 0.00 3.69
54 55 7.000472 AGAATCACAAACATCAAAGAAGGAGA 59.000 34.615 0.00 0.00 0.00 3.71
55 56 7.668886 AGAATCACAAACATCAAAGAAGGAGAT 59.331 33.333 0.00 0.00 0.00 2.75
56 57 6.564709 TCACAAACATCAAAGAAGGAGATG 57.435 37.500 0.00 0.00 43.56 2.90
57 58 5.048504 TCACAAACATCAAAGAAGGAGATGC 60.049 40.000 0.00 0.00 42.12 3.91
58 59 4.828939 ACAAACATCAAAGAAGGAGATGCA 59.171 37.500 0.00 0.00 42.12 3.96
59 60 5.302568 ACAAACATCAAAGAAGGAGATGCAA 59.697 36.000 0.00 0.00 42.12 4.08
60 61 6.183360 ACAAACATCAAAGAAGGAGATGCAAA 60.183 34.615 0.00 0.00 42.12 3.68
61 62 6.600882 AACATCAAAGAAGGAGATGCAAAT 57.399 33.333 0.00 0.00 42.12 2.32
62 63 7.707624 AACATCAAAGAAGGAGATGCAAATA 57.292 32.000 0.00 0.00 42.12 1.40
63 64 7.093322 ACATCAAAGAAGGAGATGCAAATAC 57.907 36.000 0.00 0.00 42.12 1.89
64 65 6.660521 ACATCAAAGAAGGAGATGCAAATACA 59.339 34.615 0.00 0.00 42.12 2.29
65 66 7.177216 ACATCAAAGAAGGAGATGCAAATACAA 59.823 33.333 0.00 0.00 42.12 2.41
66 67 7.149569 TCAAAGAAGGAGATGCAAATACAAG 57.850 36.000 0.00 0.00 0.00 3.16
67 68 6.942005 TCAAAGAAGGAGATGCAAATACAAGA 59.058 34.615 0.00 0.00 0.00 3.02
68 69 7.448161 TCAAAGAAGGAGATGCAAATACAAGAA 59.552 33.333 0.00 0.00 0.00 2.52
69 70 7.951347 AAGAAGGAGATGCAAATACAAGAAT 57.049 32.000 0.00 0.00 0.00 2.40
70 71 7.565323 AGAAGGAGATGCAAATACAAGAATC 57.435 36.000 0.00 0.00 0.00 2.52
71 72 7.344913 AGAAGGAGATGCAAATACAAGAATCT 58.655 34.615 0.00 0.00 32.75 2.40
72 73 7.833183 AGAAGGAGATGCAAATACAAGAATCTT 59.167 33.333 0.00 0.00 30.18 2.40
73 74 7.565323 AGGAGATGCAAATACAAGAATCTTC 57.435 36.000 0.00 0.00 30.18 2.87
74 75 6.545298 AGGAGATGCAAATACAAGAATCTTCC 59.455 38.462 0.00 0.00 30.18 3.46
75 76 6.238869 GGAGATGCAAATACAAGAATCTTCCC 60.239 42.308 0.00 0.00 30.18 3.97
76 77 5.595952 AGATGCAAATACAAGAATCTTCCCC 59.404 40.000 0.00 0.00 24.81 4.81
77 78 4.023291 TGCAAATACAAGAATCTTCCCCC 58.977 43.478 0.00 0.00 0.00 5.40
78 79 4.264352 TGCAAATACAAGAATCTTCCCCCT 60.264 41.667 0.00 0.00 0.00 4.79
79 80 5.044476 TGCAAATACAAGAATCTTCCCCCTA 60.044 40.000 0.00 0.00 0.00 3.53
80 81 5.891551 GCAAATACAAGAATCTTCCCCCTAA 59.108 40.000 0.00 0.00 0.00 2.69
81 82 6.039829 GCAAATACAAGAATCTTCCCCCTAAG 59.960 42.308 0.00 0.00 0.00 2.18
82 83 7.346471 CAAATACAAGAATCTTCCCCCTAAGA 58.654 38.462 0.00 0.00 39.71 2.10
83 84 6.755542 ATACAAGAATCTTCCCCCTAAGAG 57.244 41.667 0.00 0.00 38.81 2.85
84 85 4.439860 ACAAGAATCTTCCCCCTAAGAGT 58.560 43.478 0.00 0.00 38.81 3.24
85 86 4.852697 ACAAGAATCTTCCCCCTAAGAGTT 59.147 41.667 0.00 0.00 38.81 3.01
86 87 6.030082 ACAAGAATCTTCCCCCTAAGAGTTA 58.970 40.000 0.00 0.00 38.81 2.24
87 88 6.504279 ACAAGAATCTTCCCCCTAAGAGTTAA 59.496 38.462 0.00 0.00 38.81 2.01
88 89 7.184753 ACAAGAATCTTCCCCCTAAGAGTTAAT 59.815 37.037 0.00 0.00 38.81 1.40
89 90 7.142995 AGAATCTTCCCCCTAAGAGTTAATG 57.857 40.000 0.00 0.00 38.81 1.90
90 91 5.913946 ATCTTCCCCCTAAGAGTTAATGG 57.086 43.478 0.00 0.00 38.81 3.16
91 92 4.706616 TCTTCCCCCTAAGAGTTAATGGT 58.293 43.478 0.00 0.00 31.85 3.55
92 93 5.105853 TCTTCCCCCTAAGAGTTAATGGTT 58.894 41.667 0.00 0.00 31.85 3.67
93 94 4.855298 TCCCCCTAAGAGTTAATGGTTG 57.145 45.455 0.00 0.00 0.00 3.77
94 95 3.053917 TCCCCCTAAGAGTTAATGGTTGC 60.054 47.826 0.00 0.00 0.00 4.17
95 96 3.288092 CCCCTAAGAGTTAATGGTTGCC 58.712 50.000 0.00 0.00 0.00 4.52
201 203 4.161102 TGCATCTCATCTCATCTCATCCT 58.839 43.478 0.00 0.00 0.00 3.24
202 204 4.021016 TGCATCTCATCTCATCTCATCCTG 60.021 45.833 0.00 0.00 0.00 3.86
204 206 3.847081 TCTCATCTCATCTCATCCTGCT 58.153 45.455 0.00 0.00 0.00 4.24
206 208 4.281435 TCTCATCTCATCTCATCCTGCTTC 59.719 45.833 0.00 0.00 0.00 3.86
207 209 3.005578 TCATCTCATCTCATCCTGCTTCG 59.994 47.826 0.00 0.00 0.00 3.79
223 243 2.667137 CTTCGTTTCTCTCGAGCTGTT 58.333 47.619 7.81 0.00 38.52 3.16
236 256 4.950050 TCGAGCTGTTCTCTTCTTTTCTT 58.050 39.130 0.00 0.00 39.70 2.52
244 264 3.759581 TCTCTTCTTTTCTTGCATGGCT 58.240 40.909 0.00 0.00 0.00 4.75
245 265 3.504906 TCTCTTCTTTTCTTGCATGGCTG 59.495 43.478 0.00 0.00 0.00 4.85
320 340 2.912956 AGTGCAATGTAAAGGAGGGAGA 59.087 45.455 0.00 0.00 0.00 3.71
322 342 2.293170 GCAATGTAAAGGAGGGAGAGC 58.707 52.381 0.00 0.00 0.00 4.09
478 514 2.578128 GCCGCATTCAATGGCCAA 59.422 55.556 10.96 0.00 43.06 4.52
498 534 1.304713 GTCCGTGGTACTCCCTCCA 60.305 63.158 0.00 0.00 0.00 3.86
521 557 6.071952 CCATCACAGTTTATAAGGCACACTTT 60.072 38.462 0.00 0.00 40.64 2.66
552 588 6.379133 ACATGCATTTTCAGAATATGTGAGGT 59.621 34.615 13.31 7.12 0.00 3.85
554 590 7.230849 TGCATTTTCAGAATATGTGAGGTTT 57.769 32.000 13.31 0.00 0.00 3.27
576 612 0.793104 GGCGCGTTGACATTTACTGC 60.793 55.000 8.43 0.00 0.00 4.40
609 3176 8.694581 AGTTAATTAGACTAGTACTAGGCAGG 57.305 38.462 32.55 10.99 43.65 4.85
610 3177 7.231115 AGTTAATTAGACTAGTACTAGGCAGGC 59.769 40.741 32.55 12.97 43.65 4.85
611 3178 4.792513 TTAGACTAGTACTAGGCAGGCT 57.207 45.455 32.55 19.23 43.65 4.58
612 3179 3.673543 AGACTAGTACTAGGCAGGCTT 57.326 47.619 32.55 12.90 43.65 4.35
613 3180 3.983821 AGACTAGTACTAGGCAGGCTTT 58.016 45.455 32.55 12.20 43.65 3.51
614 3181 5.126699 AGACTAGTACTAGGCAGGCTTTA 57.873 43.478 32.55 0.00 43.65 1.85
615 3182 4.888823 AGACTAGTACTAGGCAGGCTTTAC 59.111 45.833 32.55 4.60 43.65 2.01
616 3183 4.869451 ACTAGTACTAGGCAGGCTTTACT 58.131 43.478 29.05 17.38 37.49 2.24
617 3184 6.011122 ACTAGTACTAGGCAGGCTTTACTA 57.989 41.667 29.05 17.65 37.49 1.82
624 3244 1.278127 GGCAGGCTTTACTACTCCACA 59.722 52.381 0.00 0.00 0.00 4.17
652 3272 1.079681 ATGCGGACGGCTCGTTTAA 60.080 52.632 6.55 0.00 41.37 1.52
658 3278 1.712018 GACGGCTCGTTTAATGGCCC 61.712 60.000 0.00 0.00 41.37 5.80
662 3282 1.310216 GCTCGTTTAATGGCCCGGTT 61.310 55.000 0.00 0.00 0.00 4.44
670 3290 1.253100 AATGGCCCGGTTGTTTACTG 58.747 50.000 0.00 0.00 0.00 2.74
674 3294 1.170290 GCCCGGTTGTTTACTGTGCT 61.170 55.000 0.00 0.00 34.13 4.40
707 3327 4.393680 CAGCTAATTAGGCGTTGTGGTTTA 59.606 41.667 14.28 0.00 34.52 2.01
709 3329 5.090757 GCTAATTAGGCGTTGTGGTTTAAC 58.909 41.667 14.28 0.00 0.00 2.01
756 3376 5.242615 AGAGGAAAGAAAACTGAAGCCAATC 59.757 40.000 0.00 0.00 0.00 2.67
814 3434 3.793559 CCTTATAAACTGTGACGGAGGG 58.206 50.000 0.00 0.00 0.00 4.30
823 3443 1.340405 TGTGACGGAGGGAGTAGTACC 60.340 57.143 0.00 0.00 0.00 3.34
827 3447 2.192187 GGAGGGAGTAGTACCGGCG 61.192 68.421 0.00 0.00 0.00 6.46
874 3506 1.040339 CAACCCCTCTCCCTCTCTCG 61.040 65.000 0.00 0.00 0.00 4.04
878 3510 1.531748 CCTCTCCCTCTCTCGCTCT 59.468 63.158 0.00 0.00 0.00 4.09
879 3511 0.819259 CCTCTCCCTCTCTCGCTCTG 60.819 65.000 0.00 0.00 0.00 3.35
1052 3687 2.354539 GAGCCGATCGAGCTGAGC 60.355 66.667 28.07 17.31 41.75 4.26
1053 3688 2.832661 AGCCGATCGAGCTGAGCT 60.833 61.111 24.18 6.69 43.88 4.09
1099 3741 2.300437 ACTTTACTCCTCGCTTCTGCTT 59.700 45.455 0.00 0.00 36.97 3.91
1180 3830 6.437477 TGCCAAGATCTTCTTACTGTCTCTAA 59.563 38.462 4.57 0.00 33.78 2.10
1195 3845 2.032620 CTCTAATACTCCACACCGCCT 58.967 52.381 0.00 0.00 0.00 5.52
1218 3868 2.329267 TCTTCCTCACTTTCTCTGCCA 58.671 47.619 0.00 0.00 0.00 4.92
1304 3964 1.303643 GAGCTCCAAAGGTGGTGGG 60.304 63.158 0.87 0.00 46.11 4.61
1305 3965 2.283173 GCTCCAAAGGTGGTGGGG 60.283 66.667 0.00 0.00 46.11 4.96
1306 3966 2.440599 CTCCAAAGGTGGTGGGGG 59.559 66.667 0.00 0.00 46.11 5.40
1307 3967 2.370403 TCCAAAGGTGGTGGGGGT 60.370 61.111 0.00 0.00 46.11 4.95
1308 3968 2.203625 CCAAAGGTGGTGGGGGTG 60.204 66.667 0.00 0.00 40.42 4.61
1309 3969 2.917227 CAAAGGTGGTGGGGGTGC 60.917 66.667 0.00 0.00 0.00 5.01
1559 4225 1.605058 ATCCTCAACCCGTGACCGAG 61.605 60.000 0.00 0.00 35.63 4.63
1575 4252 0.177604 CGAGGCCTGCTCAAGAAGAT 59.822 55.000 12.00 0.00 0.00 2.40
1608 4285 1.590932 CCTCCAGCATCTTTGATCCG 58.409 55.000 0.00 0.00 0.00 4.18
1708 4390 1.823250 GCAAGGAGTGGTTGTTGGGAT 60.823 52.381 0.00 0.00 0.00 3.85
1799 4493 0.250553 TAGTTTGGAGCCGGTGTTGG 60.251 55.000 1.90 0.00 0.00 3.77
1816 4510 1.016627 TGGCGCTGCACTAATTGATC 58.983 50.000 7.64 0.00 0.00 2.92
1817 4511 1.016627 GGCGCTGCACTAATTGATCA 58.983 50.000 7.64 0.00 0.00 2.92
1818 4512 1.401552 GGCGCTGCACTAATTGATCAA 59.598 47.619 11.26 11.26 0.00 2.57
1819 4513 2.540361 GGCGCTGCACTAATTGATCAAG 60.540 50.000 14.54 2.68 0.00 3.02
1820 4514 2.540361 GCGCTGCACTAATTGATCAAGG 60.540 50.000 14.54 8.95 0.00 3.61
1821 4515 2.938451 CGCTGCACTAATTGATCAAGGA 59.062 45.455 14.54 3.21 0.00 3.36
1822 4516 3.002042 CGCTGCACTAATTGATCAAGGAG 59.998 47.826 14.54 14.68 0.00 3.69
1823 4517 3.243002 GCTGCACTAATTGATCAAGGAGC 60.243 47.826 17.92 17.92 0.00 4.70
1824 4518 4.197750 CTGCACTAATTGATCAAGGAGCT 58.802 43.478 14.54 0.00 0.00 4.09
1825 4519 3.943381 TGCACTAATTGATCAAGGAGCTG 59.057 43.478 14.54 13.23 0.00 4.24
1826 4520 3.243002 GCACTAATTGATCAAGGAGCTGC 60.243 47.826 14.54 17.68 0.00 5.25
1827 4521 4.197750 CACTAATTGATCAAGGAGCTGCT 58.802 43.478 14.54 0.00 0.00 4.24
1828 4522 5.363101 CACTAATTGATCAAGGAGCTGCTA 58.637 41.667 8.68 0.00 0.00 3.49
1829 4523 5.996513 CACTAATTGATCAAGGAGCTGCTAT 59.003 40.000 8.68 0.00 0.00 2.97
1830 4524 5.996513 ACTAATTGATCAAGGAGCTGCTATG 59.003 40.000 8.68 9.47 0.00 2.23
1831 4525 3.920231 TTGATCAAGGAGCTGCTATGT 57.080 42.857 8.68 0.00 0.00 2.29
1832 4526 3.920231 TGATCAAGGAGCTGCTATGTT 57.080 42.857 8.68 4.57 0.00 2.71
1833 4527 5.357742 TTGATCAAGGAGCTGCTATGTTA 57.642 39.130 8.68 0.00 0.00 2.41
1834 4528 5.357742 TGATCAAGGAGCTGCTATGTTAA 57.642 39.130 8.68 0.00 0.00 2.01
1916 4641 2.273370 TCACTTCGTATTGTCGCTCC 57.727 50.000 0.00 0.00 0.00 4.70
1934 4659 2.496070 CTCCGATGGACTAACAAGGTCA 59.504 50.000 0.00 0.00 35.61 4.02
1941 4666 5.241403 TGGACTAACAAGGTCATGTCAAT 57.759 39.130 0.00 0.00 35.61 2.57
1947 4672 8.635765 ACTAACAAGGTCATGTCAATACATTT 57.364 30.769 0.00 0.00 44.07 2.32
1956 4681 8.604035 GGTCATGTCAATACATTTGTACTACTG 58.396 37.037 0.00 0.00 44.07 2.74
1957 4682 8.604035 GTCATGTCAATACATTTGTACTACTGG 58.396 37.037 0.00 0.00 44.07 4.00
1958 4683 6.978343 TGTCAATACATTTGTACTACTGGC 57.022 37.500 0.00 0.00 32.72 4.85
1959 4684 6.707290 TGTCAATACATTTGTACTACTGGCT 58.293 36.000 0.00 0.00 32.72 4.75
1960 4685 7.165485 TGTCAATACATTTGTACTACTGGCTT 58.835 34.615 0.00 0.00 32.72 4.35
1980 4705 4.570772 GCTTACATATGCGACCTTTTCTGA 59.429 41.667 1.58 0.00 0.00 3.27
2022 4747 9.912634 AAAATGAATGTTGAATGTAAATCGAGT 57.087 25.926 0.00 0.00 0.00 4.18
2023 4748 9.912634 AAATGAATGTTGAATGTAAATCGAGTT 57.087 25.926 2.72 2.72 0.00 3.01
2024 4749 9.559958 AATGAATGTTGAATGTAAATCGAGTTC 57.440 29.630 0.00 0.00 0.00 3.01
2025 4750 8.093659 TGAATGTTGAATGTAAATCGAGTTCA 57.906 30.769 0.00 0.63 0.00 3.18
2026 4751 8.729756 TGAATGTTGAATGTAAATCGAGTTCAT 58.270 29.630 0.00 3.16 0.00 2.57
2027 4752 9.559958 GAATGTTGAATGTAAATCGAGTTCATT 57.440 29.630 17.13 17.13 0.00 2.57
2028 4753 9.912634 AATGTTGAATGTAAATCGAGTTCATTT 57.087 25.926 17.76 5.72 0.00 2.32
2029 4754 9.912634 ATGTTGAATGTAAATCGAGTTCATTTT 57.087 25.926 17.76 5.14 0.00 1.82
2030 4755 9.179552 TGTTGAATGTAAATCGAGTTCATTTTG 57.820 29.630 17.76 0.00 0.00 2.44
2031 4756 9.393249 GTTGAATGTAAATCGAGTTCATTTTGA 57.607 29.630 17.76 9.24 0.00 2.69
2032 4757 9.958234 TTGAATGTAAATCGAGTTCATTTTGAA 57.042 25.926 17.76 11.69 33.32 2.69
2033 4758 9.611284 TGAATGTAAATCGAGTTCATTTTGAAG 57.389 29.630 17.76 0.00 37.00 3.02
2034 4759 9.825972 GAATGTAAATCGAGTTCATTTTGAAGA 57.174 29.630 17.76 0.00 37.00 2.87
2087 4822 4.457466 ACAAGAAAAATGGTACGTGTCCT 58.543 39.130 0.00 0.00 0.00 3.85
2199 4935 3.753272 TCATTGCTGTAGCCTTGTCTTTC 59.247 43.478 0.80 0.00 41.18 2.62
2255 4993 1.412710 GATTCGCTCCCAGGACATGTA 59.587 52.381 0.00 0.00 0.00 2.29
2276 5014 3.801997 CAGGCCCAGGGATTCGCT 61.802 66.667 10.89 0.00 0.00 4.93
2354 5092 2.052237 CGCGTCAGCCAACAACAC 60.052 61.111 0.00 0.00 41.18 3.32
2360 5098 0.391793 TCAGCCAACAACACACGTGA 60.392 50.000 25.01 0.00 0.00 4.35
2373 5111 2.508944 CACGTGATTTGATCGTGTGG 57.491 50.000 10.90 0.00 46.11 4.17
2377 5115 3.314080 ACGTGATTTGATCGTGTGGTTTT 59.686 39.130 0.00 0.00 36.46 2.43
2390 5128 4.570772 CGTGTGGTTTTTCTCTTCTTCTCA 59.429 41.667 0.00 0.00 0.00 3.27
2405 5160 4.315803 TCTTCTCATGGAGGTCGTTTTTC 58.684 43.478 0.00 0.00 0.00 2.29
2410 5165 0.179012 TGGAGGTCGTTTTTCCCCAC 60.179 55.000 0.00 0.00 0.00 4.61
2421 5176 5.104527 TCGTTTTTCCCCACTGATGATCTAT 60.105 40.000 0.00 0.00 0.00 1.98
2422 5177 5.237344 CGTTTTTCCCCACTGATGATCTATC 59.763 44.000 0.00 0.00 36.29 2.08
2456 5214 8.016229 CAGAATTTCAAGTTCAGTGAGAGAATG 58.984 37.037 0.00 0.00 0.00 2.67
2457 5215 6.814506 ATTTCAAGTTCAGTGAGAGAATGG 57.185 37.500 0.00 0.00 0.00 3.16
2459 5217 3.326006 TCAAGTTCAGTGAGAGAATGGCT 59.674 43.478 0.00 0.00 0.00 4.75
2460 5218 4.528206 TCAAGTTCAGTGAGAGAATGGCTA 59.472 41.667 0.00 0.00 0.00 3.93
2461 5219 5.012046 TCAAGTTCAGTGAGAGAATGGCTAA 59.988 40.000 0.00 0.00 0.00 3.09
2463 5221 4.530161 AGTTCAGTGAGAGAATGGCTAACT 59.470 41.667 0.00 0.00 0.00 2.24
2465 5223 4.089361 TCAGTGAGAGAATGGCTAACTCA 58.911 43.478 9.47 0.00 35.65 3.41
2466 5224 4.528206 TCAGTGAGAGAATGGCTAACTCAA 59.472 41.667 0.00 0.00 38.90 3.02
2467 5225 4.629200 CAGTGAGAGAATGGCTAACTCAAC 59.371 45.833 0.00 7.48 38.90 3.18
2504 5330 6.376581 TGAGCAAAGGTTACTAGAGTAGTACC 59.623 42.308 0.00 3.30 40.74 3.34
2507 5333 5.443230 AAGGTTACTAGAGTAGTACCGGT 57.557 43.478 13.98 13.98 40.74 5.28
2636 5465 1.271001 TGCTCCAGTGAGTGAATGTGG 60.271 52.381 0.00 0.00 40.95 4.17
2647 5476 2.203337 AATGTGGGTGCGCAGTGT 60.203 55.556 12.22 0.00 0.00 3.55
2726 5565 0.241213 TTCAAGCGTCTGTCTCCTCG 59.759 55.000 0.00 0.00 0.00 4.63
2731 5570 2.344203 CGTCTGTCTCCTCGGCCTT 61.344 63.158 0.00 0.00 0.00 4.35
2732 5571 1.878656 CGTCTGTCTCCTCGGCCTTT 61.879 60.000 0.00 0.00 0.00 3.11
2733 5572 0.321996 GTCTGTCTCCTCGGCCTTTT 59.678 55.000 0.00 0.00 0.00 2.27
2734 5573 0.608640 TCTGTCTCCTCGGCCTTTTC 59.391 55.000 0.00 0.00 0.00 2.29
2735 5574 0.391793 CTGTCTCCTCGGCCTTTTCC 60.392 60.000 0.00 0.00 0.00 3.13
2740 5599 0.613777 TCCTCGGCCTTTTCCTCTTC 59.386 55.000 0.00 0.00 0.00 2.87
2741 5600 0.324943 CCTCGGCCTTTTCCTCTTCA 59.675 55.000 0.00 0.00 0.00 3.02
2743 5602 2.284190 CTCGGCCTTTTCCTCTTCATC 58.716 52.381 0.00 0.00 0.00 2.92
2802 5661 2.699954 ACTCATGACAAAGCGTAAGGG 58.300 47.619 0.00 0.00 38.28 3.95
2828 5697 4.448537 GCTTAACAGCAAGAGAGAGAGA 57.551 45.455 0.00 0.00 46.49 3.10
2829 5698 4.423732 GCTTAACAGCAAGAGAGAGAGAG 58.576 47.826 0.00 0.00 46.49 3.20
2830 5699 4.157656 GCTTAACAGCAAGAGAGAGAGAGA 59.842 45.833 0.00 0.00 46.49 3.10
2831 5700 5.677091 GCTTAACAGCAAGAGAGAGAGAGAG 60.677 48.000 0.00 0.00 46.49 3.20
2832 5701 3.719268 ACAGCAAGAGAGAGAGAGAGA 57.281 47.619 0.00 0.00 0.00 3.10
2833 5702 3.347216 ACAGCAAGAGAGAGAGAGAGAC 58.653 50.000 0.00 0.00 0.00 3.36
2834 5703 3.009473 ACAGCAAGAGAGAGAGAGAGACT 59.991 47.826 0.00 0.00 0.00 3.24
2835 5704 4.225042 ACAGCAAGAGAGAGAGAGAGACTA 59.775 45.833 0.00 0.00 0.00 2.59
2836 5705 4.813161 CAGCAAGAGAGAGAGAGAGACTAG 59.187 50.000 0.00 0.00 0.00 2.57
2876 5745 0.882042 ACAGCAGCAGTCAAACCTCG 60.882 55.000 0.00 0.00 0.00 4.63
2877 5746 1.963338 AGCAGCAGTCAAACCTCGC 60.963 57.895 0.00 0.00 0.00 5.03
2878 5747 2.970974 GCAGCAGTCAAACCTCGCC 61.971 63.158 0.00 0.00 0.00 5.54
2879 5748 1.302033 CAGCAGTCAAACCTCGCCT 60.302 57.895 0.00 0.00 0.00 5.52
2880 5749 1.004440 AGCAGTCAAACCTCGCCTC 60.004 57.895 0.00 0.00 0.00 4.70
2881 5750 2.383527 GCAGTCAAACCTCGCCTCG 61.384 63.158 0.00 0.00 0.00 4.63
2891 5760 0.038159 CCTCGCCTCGAAACAAGTCT 60.038 55.000 0.00 0.00 34.74 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.088056 TGGAAACTAATGTTCGGTGGAA 57.912 40.909 0.00 0.00 34.96 3.53
1 2 3.773418 TGGAAACTAATGTTCGGTGGA 57.227 42.857 0.00 0.00 34.96 4.02
2 3 5.820423 TCATATGGAAACTAATGTTCGGTGG 59.180 40.000 2.13 0.00 34.96 4.61
3 4 6.918892 TCATATGGAAACTAATGTTCGGTG 57.081 37.500 2.13 0.00 34.96 4.94
4 5 9.273016 CTTATCATATGGAAACTAATGTTCGGT 57.727 33.333 2.13 0.00 34.96 4.69
5 6 9.489084 TCTTATCATATGGAAACTAATGTTCGG 57.511 33.333 2.13 0.00 34.96 4.30
18 19 9.850198 TGATGTTTGTGATTCTTATCATATGGA 57.150 29.630 2.13 0.00 42.49 3.41
25 26 9.565213 CCTTCTTTGATGTTTGTGATTCTTATC 57.435 33.333 0.00 0.00 0.00 1.75
26 27 9.300681 TCCTTCTTTGATGTTTGTGATTCTTAT 57.699 29.630 0.00 0.00 0.00 1.73
27 28 8.690203 TCCTTCTTTGATGTTTGTGATTCTTA 57.310 30.769 0.00 0.00 0.00 2.10
28 29 7.503566 TCTCCTTCTTTGATGTTTGTGATTCTT 59.496 33.333 0.00 0.00 0.00 2.52
29 30 7.000472 TCTCCTTCTTTGATGTTTGTGATTCT 59.000 34.615 0.00 0.00 0.00 2.40
30 31 7.206981 TCTCCTTCTTTGATGTTTGTGATTC 57.793 36.000 0.00 0.00 0.00 2.52
31 32 7.600065 CATCTCCTTCTTTGATGTTTGTGATT 58.400 34.615 0.00 0.00 34.55 2.57
32 33 6.349944 GCATCTCCTTCTTTGATGTTTGTGAT 60.350 38.462 0.00 0.00 39.58 3.06
33 34 5.048504 GCATCTCCTTCTTTGATGTTTGTGA 60.049 40.000 0.00 0.00 39.58 3.58
34 35 5.159209 GCATCTCCTTCTTTGATGTTTGTG 58.841 41.667 0.00 0.00 39.58 3.33
35 36 4.828939 TGCATCTCCTTCTTTGATGTTTGT 59.171 37.500 0.00 0.00 39.58 2.83
36 37 5.381174 TGCATCTCCTTCTTTGATGTTTG 57.619 39.130 0.00 0.00 39.58 2.93
37 38 6.409524 TTTGCATCTCCTTCTTTGATGTTT 57.590 33.333 0.00 0.00 39.58 2.83
38 39 6.600882 ATTTGCATCTCCTTCTTTGATGTT 57.399 33.333 0.00 0.00 39.58 2.71
39 40 6.660521 TGTATTTGCATCTCCTTCTTTGATGT 59.339 34.615 0.00 0.00 39.58 3.06
40 41 7.092137 TGTATTTGCATCTCCTTCTTTGATG 57.908 36.000 0.00 0.00 40.16 3.07
41 42 7.613022 TCTTGTATTTGCATCTCCTTCTTTGAT 59.387 33.333 0.00 0.00 0.00 2.57
42 43 6.942005 TCTTGTATTTGCATCTCCTTCTTTGA 59.058 34.615 0.00 0.00 0.00 2.69
43 44 7.149569 TCTTGTATTTGCATCTCCTTCTTTG 57.850 36.000 0.00 0.00 0.00 2.77
44 45 7.765695 TTCTTGTATTTGCATCTCCTTCTTT 57.234 32.000 0.00 0.00 0.00 2.52
45 46 7.833183 AGATTCTTGTATTTGCATCTCCTTCTT 59.167 33.333 0.00 0.00 0.00 2.52
46 47 7.344913 AGATTCTTGTATTTGCATCTCCTTCT 58.655 34.615 0.00 0.00 0.00 2.85
47 48 7.565323 AGATTCTTGTATTTGCATCTCCTTC 57.435 36.000 0.00 0.00 0.00 3.46
48 49 7.067981 GGAAGATTCTTGTATTTGCATCTCCTT 59.932 37.037 3.03 0.00 0.00 3.36
49 50 6.545298 GGAAGATTCTTGTATTTGCATCTCCT 59.455 38.462 3.03 0.00 0.00 3.69
50 51 6.238869 GGGAAGATTCTTGTATTTGCATCTCC 60.239 42.308 3.03 0.00 0.00 3.71
51 52 6.238869 GGGGAAGATTCTTGTATTTGCATCTC 60.239 42.308 3.03 0.00 0.00 2.75
52 53 5.595952 GGGGAAGATTCTTGTATTTGCATCT 59.404 40.000 3.03 0.00 0.00 2.90
53 54 5.221322 GGGGGAAGATTCTTGTATTTGCATC 60.221 44.000 3.03 0.00 0.00 3.91
54 55 4.651045 GGGGGAAGATTCTTGTATTTGCAT 59.349 41.667 3.03 0.00 0.00 3.96
55 56 4.023291 GGGGGAAGATTCTTGTATTTGCA 58.977 43.478 3.03 0.00 0.00 4.08
56 57 4.281657 AGGGGGAAGATTCTTGTATTTGC 58.718 43.478 3.03 0.00 0.00 3.68
57 58 7.346471 TCTTAGGGGGAAGATTCTTGTATTTG 58.654 38.462 3.03 0.00 30.36 2.32
58 59 7.184753 ACTCTTAGGGGGAAGATTCTTGTATTT 59.815 37.037 3.03 0.00 34.95 1.40
59 60 6.678857 ACTCTTAGGGGGAAGATTCTTGTATT 59.321 38.462 3.03 0.00 34.95 1.89
60 61 6.213525 ACTCTTAGGGGGAAGATTCTTGTAT 58.786 40.000 3.03 0.00 34.95 2.29
61 62 5.600749 ACTCTTAGGGGGAAGATTCTTGTA 58.399 41.667 3.03 0.00 34.95 2.41
62 63 4.439860 ACTCTTAGGGGGAAGATTCTTGT 58.560 43.478 3.03 0.00 34.95 3.16
63 64 5.443230 AACTCTTAGGGGGAAGATTCTTG 57.557 43.478 3.03 0.00 34.95 3.02
64 65 7.366913 CCATTAACTCTTAGGGGGAAGATTCTT 60.367 40.741 0.00 0.00 34.95 2.52
65 66 6.101881 CCATTAACTCTTAGGGGGAAGATTCT 59.898 42.308 0.00 0.00 34.95 2.40
66 67 6.126449 ACCATTAACTCTTAGGGGGAAGATTC 60.126 42.308 0.00 0.00 34.95 2.52
67 68 5.736616 ACCATTAACTCTTAGGGGGAAGATT 59.263 40.000 0.00 0.00 34.95 2.40
68 69 5.297799 ACCATTAACTCTTAGGGGGAAGAT 58.702 41.667 0.00 0.00 34.95 2.40
69 70 4.706616 ACCATTAACTCTTAGGGGGAAGA 58.293 43.478 0.00 0.00 34.30 2.87
70 71 5.193679 CAACCATTAACTCTTAGGGGGAAG 58.806 45.833 0.00 0.00 0.00 3.46
71 72 4.569015 GCAACCATTAACTCTTAGGGGGAA 60.569 45.833 0.00 0.00 0.00 3.97
72 73 3.053917 GCAACCATTAACTCTTAGGGGGA 60.054 47.826 0.00 0.00 0.00 4.81
73 74 3.288092 GCAACCATTAACTCTTAGGGGG 58.712 50.000 0.00 0.00 0.00 5.40
74 75 3.288092 GGCAACCATTAACTCTTAGGGG 58.712 50.000 0.00 0.00 0.00 4.79
75 76 2.943033 CGGCAACCATTAACTCTTAGGG 59.057 50.000 0.00 0.00 0.00 3.53
76 77 3.869065 TCGGCAACCATTAACTCTTAGG 58.131 45.455 0.00 0.00 0.00 2.69
77 78 5.175859 TCTTCGGCAACCATTAACTCTTAG 58.824 41.667 0.00 0.00 0.00 2.18
78 79 5.155278 TCTTCGGCAACCATTAACTCTTA 57.845 39.130 0.00 0.00 0.00 2.10
79 80 4.015872 TCTTCGGCAACCATTAACTCTT 57.984 40.909 0.00 0.00 0.00 2.85
80 81 3.695830 TCTTCGGCAACCATTAACTCT 57.304 42.857 0.00 0.00 0.00 3.24
81 82 3.127030 CCTTCTTCGGCAACCATTAACTC 59.873 47.826 0.00 0.00 0.00 3.01
82 83 3.081804 CCTTCTTCGGCAACCATTAACT 58.918 45.455 0.00 0.00 0.00 2.24
83 84 2.163613 CCCTTCTTCGGCAACCATTAAC 59.836 50.000 0.00 0.00 0.00 2.01
84 85 2.224917 ACCCTTCTTCGGCAACCATTAA 60.225 45.455 0.00 0.00 0.00 1.40
85 86 1.353022 ACCCTTCTTCGGCAACCATTA 59.647 47.619 0.00 0.00 0.00 1.90
86 87 0.112412 ACCCTTCTTCGGCAACCATT 59.888 50.000 0.00 0.00 0.00 3.16
87 88 0.322546 GACCCTTCTTCGGCAACCAT 60.323 55.000 0.00 0.00 0.00 3.55
88 89 1.072505 GACCCTTCTTCGGCAACCA 59.927 57.895 0.00 0.00 0.00 3.67
89 90 0.955919 CAGACCCTTCTTCGGCAACC 60.956 60.000 0.00 0.00 0.00 3.77
90 91 1.578206 GCAGACCCTTCTTCGGCAAC 61.578 60.000 0.00 0.00 34.66 4.17
91 92 1.302511 GCAGACCCTTCTTCGGCAA 60.303 57.895 0.00 0.00 34.66 4.52
92 93 2.347490 GCAGACCCTTCTTCGGCA 59.653 61.111 0.00 0.00 34.66 5.69
93 94 2.815647 CGCAGACCCTTCTTCGGC 60.816 66.667 0.00 0.00 35.16 5.54
94 95 2.815647 GCGCAGACCCTTCTTCGG 60.816 66.667 0.30 0.00 38.74 4.30
95 96 2.048222 TGCGCAGACCCTTCTTCG 60.048 61.111 5.66 0.00 40.97 3.79
185 187 3.005578 CGAAGCAGGATGAGATGAGATGA 59.994 47.826 0.00 0.00 39.69 2.92
201 203 0.598562 AGCTCGAGAGAAACGAAGCA 59.401 50.000 18.75 0.00 41.32 3.91
202 204 0.988439 CAGCTCGAGAGAAACGAAGC 59.012 55.000 18.75 0.00 41.32 3.86
204 206 2.293677 AGAACAGCTCGAGAGAAACGAA 59.706 45.455 18.75 0.00 41.32 3.85
206 208 2.246789 GAGAACAGCTCGAGAGAAACG 58.753 52.381 18.75 0.00 41.32 3.60
223 243 3.504906 CAGCCATGCAAGAAAAGAAGAGA 59.495 43.478 0.00 0.00 0.00 3.10
251 271 1.743252 CGAGGTCCTTTGCTCCAGC 60.743 63.158 0.00 0.00 42.50 4.85
252 272 1.743252 GCGAGGTCCTTTGCTCCAG 60.743 63.158 9.25 0.00 0.00 3.86
253 273 0.902984 TAGCGAGGTCCTTTGCTCCA 60.903 55.000 19.59 4.57 38.82 3.86
309 329 0.043334 TGCCTAGCTCTCCCTCCTTT 59.957 55.000 0.00 0.00 0.00 3.11
320 340 3.746949 GACGCATGCCTGCCTAGCT 62.747 63.158 13.15 0.00 46.07 3.32
322 342 2.963854 CGACGCATGCCTGCCTAG 60.964 66.667 13.15 0.00 46.07 3.02
410 441 4.154347 GCGTCAGAGCCAGAGGGG 62.154 72.222 0.00 0.00 40.85 4.79
478 514 1.676967 GAGGGAGTACCACGGACGT 60.677 63.158 0.00 0.00 43.89 4.34
498 534 6.128282 CGAAAGTGTGCCTTATAAACTGTGAT 60.128 38.462 0.00 0.00 31.48 3.06
521 557 8.458052 ACATATTCTGAAAATGCATGTAAACGA 58.542 29.630 0.00 0.00 0.00 3.85
552 588 3.499157 AGTAAATGTCAACGCGCCTTAAA 59.501 39.130 5.73 0.00 0.00 1.52
554 590 2.413796 CAGTAAATGTCAACGCGCCTTA 59.586 45.455 5.73 0.00 0.00 2.69
593 3160 4.888823 AGTAAAGCCTGCCTAGTACTAGTC 59.111 45.833 24.84 15.60 0.00 2.59
604 3171 1.278127 TGTGGAGTAGTAAAGCCTGCC 59.722 52.381 0.00 0.00 0.00 4.85
605 3172 2.742589 GTTGTGGAGTAGTAAAGCCTGC 59.257 50.000 0.00 0.00 0.00 4.85
606 3173 3.997021 CAGTTGTGGAGTAGTAAAGCCTG 59.003 47.826 0.00 0.00 0.00 4.85
607 3174 3.557264 GCAGTTGTGGAGTAGTAAAGCCT 60.557 47.826 0.00 0.00 0.00 4.58
609 3176 3.399330 TGCAGTTGTGGAGTAGTAAAGC 58.601 45.455 0.00 0.00 0.00 3.51
610 3177 4.142816 GCATGCAGTTGTGGAGTAGTAAAG 60.143 45.833 14.21 0.00 0.00 1.85
611 3178 3.751175 GCATGCAGTTGTGGAGTAGTAAA 59.249 43.478 14.21 0.00 0.00 2.01
612 3179 3.244387 TGCATGCAGTTGTGGAGTAGTAA 60.244 43.478 18.46 0.00 0.00 2.24
613 3180 2.301583 TGCATGCAGTTGTGGAGTAGTA 59.698 45.455 18.46 0.00 0.00 1.82
614 3181 1.072173 TGCATGCAGTTGTGGAGTAGT 59.928 47.619 18.46 0.00 0.00 2.73
615 3182 1.812235 TGCATGCAGTTGTGGAGTAG 58.188 50.000 18.46 0.00 0.00 2.57
616 3183 2.086094 CATGCATGCAGTTGTGGAGTA 58.914 47.619 26.69 0.00 0.00 2.59
617 3184 0.885879 CATGCATGCAGTTGTGGAGT 59.114 50.000 26.69 2.26 0.00 3.85
652 3272 0.111639 ACAGTAAACAACCGGGCCAT 59.888 50.000 6.32 0.00 0.00 4.40
658 3278 3.684103 TCAAAGCACAGTAAACAACCG 57.316 42.857 0.00 0.00 0.00 4.44
662 3282 6.691754 TGAGAAATCAAAGCACAGTAAACA 57.308 33.333 0.00 0.00 0.00 2.83
670 3290 7.192232 CCTAATTAGCTGAGAAATCAAAGCAC 58.808 38.462 6.99 0.00 38.14 4.40
674 3294 5.880332 ACGCCTAATTAGCTGAGAAATCAAA 59.120 36.000 6.99 0.00 0.00 2.69
726 3346 7.444487 GGCTTCAGTTTTCTTTCCTCTAAACTA 59.556 37.037 0.00 0.00 38.41 2.24
730 3350 5.690865 TGGCTTCAGTTTTCTTTCCTCTAA 58.309 37.500 0.00 0.00 0.00 2.10
731 3351 5.304686 TGGCTTCAGTTTTCTTTCCTCTA 57.695 39.130 0.00 0.00 0.00 2.43
741 3361 2.582052 TCCACGATTGGCTTCAGTTTT 58.418 42.857 0.00 0.00 43.56 2.43
748 3368 0.620556 AGGTGATCCACGATTGGCTT 59.379 50.000 0.00 0.00 43.56 4.35
756 3376 1.078426 GGGACCAAGGTGATCCACG 60.078 63.158 0.00 0.00 34.83 4.94
793 3413 3.449737 TCCCTCCGTCACAGTTTATAAGG 59.550 47.826 0.00 0.00 0.00 2.69
814 3434 2.103736 GGTGCGCCGGTACTACTC 59.896 66.667 4.18 0.00 0.00 2.59
827 3447 0.533491 TATCTACGGTGGTGTGGTGC 59.467 55.000 0.00 0.00 0.00 5.01
839 3459 1.068741 GGTTGGCCCTGTCTATCTACG 59.931 57.143 0.00 0.00 0.00 3.51
874 3506 3.378427 GGAATAAATGGTCCACACAGAGC 59.622 47.826 0.00 0.00 33.79 4.09
878 3510 3.696045 CTGGGAATAAATGGTCCACACA 58.304 45.455 0.00 0.00 35.44 3.72
879 3511 2.427095 GCTGGGAATAAATGGTCCACAC 59.573 50.000 0.00 0.00 35.44 3.82
1075 3717 3.735514 GCAGAAGCGAGGAGTAAAGTAGG 60.736 52.174 0.00 0.00 0.00 3.18
1099 3741 3.521126 AGGATAGCAAAAGGAGAAGCAGA 59.479 43.478 0.00 0.00 0.00 4.26
1180 3830 0.753262 GATGAGGCGGTGTGGAGTAT 59.247 55.000 0.00 0.00 0.00 2.12
1195 3845 3.055530 GGCAGAGAAAGTGAGGAAGATGA 60.056 47.826 0.00 0.00 0.00 2.92
1218 3868 4.384056 GGCAACATGATACATCAGCTAGT 58.616 43.478 0.00 0.00 40.64 2.57
1559 4225 1.948145 CATCATCTTCTTGAGCAGGCC 59.052 52.381 0.00 0.00 0.00 5.19
1575 4252 2.942752 GCTGGAGGCTCATCAAACATCA 60.943 50.000 17.69 0.43 38.06 3.07
1608 4285 2.569059 CCATGTGATCTGTGATGGGAC 58.431 52.381 0.00 0.00 33.06 4.46
1708 4390 7.706100 ACCTAAACAAACTGACCAAAACTTA 57.294 32.000 0.00 0.00 0.00 2.24
1799 4493 2.540361 CCTTGATCAATTAGTGCAGCGC 60.540 50.000 8.96 0.00 0.00 5.92
1800 4494 2.938451 TCCTTGATCAATTAGTGCAGCG 59.062 45.455 8.96 0.00 0.00 5.18
1801 4495 3.243002 GCTCCTTGATCAATTAGTGCAGC 60.243 47.826 8.96 0.00 0.00 5.25
1802 4496 4.035324 CAGCTCCTTGATCAATTAGTGCAG 59.965 45.833 20.23 13.33 0.00 4.41
1803 4497 3.943381 CAGCTCCTTGATCAATTAGTGCA 59.057 43.478 20.23 0.00 0.00 4.57
1804 4498 3.243002 GCAGCTCCTTGATCAATTAGTGC 60.243 47.826 8.96 15.29 0.00 4.40
1816 4510 4.871993 CTGTTAACATAGCAGCTCCTTG 57.128 45.455 9.13 0.00 30.37 3.61
1823 4517 3.937706 AGAAGCAGCTGTTAACATAGCAG 59.062 43.478 16.64 13.21 42.29 4.24
1824 4518 3.686241 CAGAAGCAGCTGTTAACATAGCA 59.314 43.478 16.64 0.00 42.29 3.49
1825 4519 3.935203 TCAGAAGCAGCTGTTAACATAGC 59.065 43.478 16.64 10.18 40.18 2.97
1826 4520 5.174395 ACTCAGAAGCAGCTGTTAACATAG 58.826 41.667 16.64 10.52 37.20 2.23
1827 4521 5.152623 ACTCAGAAGCAGCTGTTAACATA 57.847 39.130 16.64 0.00 37.20 2.29
1828 4522 4.013267 ACTCAGAAGCAGCTGTTAACAT 57.987 40.909 16.64 0.00 37.20 2.71
1829 4523 3.475566 ACTCAGAAGCAGCTGTTAACA 57.524 42.857 16.64 8.28 37.20 2.41
1830 4524 3.187432 GGAACTCAGAAGCAGCTGTTAAC 59.813 47.826 16.64 7.53 37.20 2.01
1831 4525 3.403038 GGAACTCAGAAGCAGCTGTTAA 58.597 45.455 16.64 0.00 37.20 2.01
1832 4526 2.289694 GGGAACTCAGAAGCAGCTGTTA 60.290 50.000 16.64 0.00 37.20 2.41
1833 4527 1.544314 GGGAACTCAGAAGCAGCTGTT 60.544 52.381 16.64 6.37 37.20 3.16
1834 4528 0.036022 GGGAACTCAGAAGCAGCTGT 59.964 55.000 16.64 0.00 37.20 4.40
1916 4641 3.861840 ACATGACCTTGTTAGTCCATCG 58.138 45.455 0.00 0.00 33.09 3.84
1941 4666 9.758651 CATATGTAAGCCAGTAGTACAAATGTA 57.241 33.333 2.52 0.00 31.85 2.29
1947 4672 4.581409 TCGCATATGTAAGCCAGTAGTACA 59.419 41.667 4.29 0.00 32.58 2.90
1956 4681 3.877508 AGAAAAGGTCGCATATGTAAGCC 59.122 43.478 4.29 2.51 0.00 4.35
1957 4682 4.570772 TCAGAAAAGGTCGCATATGTAAGC 59.429 41.667 4.29 2.81 0.00 3.09
1958 4683 6.662414 TTCAGAAAAGGTCGCATATGTAAG 57.338 37.500 4.29 0.00 0.00 2.34
1959 4684 6.019075 CGATTCAGAAAAGGTCGCATATGTAA 60.019 38.462 4.29 0.00 0.00 2.41
1960 4685 5.462068 CGATTCAGAAAAGGTCGCATATGTA 59.538 40.000 4.29 0.00 0.00 2.29
1966 4691 2.066262 GACGATTCAGAAAAGGTCGCA 58.934 47.619 4.17 0.00 35.86 5.10
2000 4725 8.093659 TGAACTCGATTTACATTCAACATTCA 57.906 30.769 0.00 0.00 0.00 2.57
2001 4726 9.559958 AATGAACTCGATTTACATTCAACATTC 57.440 29.630 0.00 0.00 33.29 2.67
2002 4727 9.912634 AAATGAACTCGATTTACATTCAACATT 57.087 25.926 10.97 0.00 33.29 2.71
2006 4731 9.958234 TTCAAAATGAACTCGATTTACATTCAA 57.042 25.926 10.97 5.48 33.29 2.69
2007 4732 9.611284 CTTCAAAATGAACTCGATTTACATTCA 57.389 29.630 10.97 0.00 32.21 2.57
2008 4733 9.825972 TCTTCAAAATGAACTCGATTTACATTC 57.174 29.630 10.97 0.00 32.21 2.67
2199 4935 1.528129 GGCACAAGTTCTTCAGAGGG 58.472 55.000 0.00 0.00 0.00 4.30
2255 4993 2.003548 GAATCCCTGGGCCTGGAGT 61.004 63.158 29.31 21.38 33.27 3.85
2276 5014 2.028112 GTCTGTGTGCAAGGAGATGGTA 60.028 50.000 0.00 0.00 0.00 3.25
2360 5098 6.263168 AGAAGAGAAAAACCACACGATCAAAT 59.737 34.615 0.00 0.00 0.00 2.32
2373 5111 6.000840 ACCTCCATGAGAAGAAGAGAAAAAC 58.999 40.000 0.00 0.00 0.00 2.43
2377 5115 3.445450 CGACCTCCATGAGAAGAAGAGAA 59.555 47.826 0.00 0.00 0.00 2.87
2390 5128 0.774908 TGGGGAAAAACGACCTCCAT 59.225 50.000 0.00 0.00 0.00 3.41
2421 5176 8.956426 ACTGAACTTGAAATTCTGTAAAACTGA 58.044 29.630 0.00 0.00 36.73 3.41
2422 5177 9.013490 CACTGAACTTGAAATTCTGTAAAACTG 57.987 33.333 0.00 0.00 36.45 3.16
2456 5214 3.055747 AGGCTTGAGTAGTTGAGTTAGCC 60.056 47.826 0.00 0.00 45.57 3.93
2457 5215 4.195225 AGGCTTGAGTAGTTGAGTTAGC 57.805 45.455 0.00 0.00 0.00 3.09
2459 5217 5.801531 TCAAGGCTTGAGTAGTTGAGTTA 57.198 39.130 25.38 0.00 34.08 2.24
2460 5218 4.689612 TCAAGGCTTGAGTAGTTGAGTT 57.310 40.909 25.38 0.00 34.08 3.01
2504 5330 2.811431 TCTTGGTTGAATGCAGTTACCG 59.189 45.455 12.71 2.76 0.00 4.02
2507 5333 2.819608 GGCTCTTGGTTGAATGCAGTTA 59.180 45.455 0.00 0.00 0.00 2.24
2658 5488 1.813786 ACTCAGTACAGCCGAGAGAAC 59.186 52.381 0.00 0.00 0.00 3.01
2659 5489 1.813178 CACTCAGTACAGCCGAGAGAA 59.187 52.381 0.00 0.00 0.00 2.87
2660 5490 1.003233 TCACTCAGTACAGCCGAGAGA 59.997 52.381 0.00 0.00 0.00 3.10
2726 5565 5.474578 AAAAAGATGAAGAGGAAAAGGCC 57.525 39.130 0.00 0.00 0.00 5.19
2731 5570 6.490040 CCCTGTGTAAAAAGATGAAGAGGAAA 59.510 38.462 0.00 0.00 0.00 3.13
2732 5571 6.003950 CCCTGTGTAAAAAGATGAAGAGGAA 58.996 40.000 0.00 0.00 0.00 3.36
2733 5572 5.309543 TCCCTGTGTAAAAAGATGAAGAGGA 59.690 40.000 0.00 0.00 0.00 3.71
2734 5573 5.560724 TCCCTGTGTAAAAAGATGAAGAGG 58.439 41.667 0.00 0.00 0.00 3.69
2735 5574 6.467677 TCTCCCTGTGTAAAAAGATGAAGAG 58.532 40.000 0.00 0.00 0.00 2.85
2740 5599 3.372206 CGCTCTCCCTGTGTAAAAAGATG 59.628 47.826 0.00 0.00 0.00 2.90
2741 5600 3.600388 CGCTCTCCCTGTGTAAAAAGAT 58.400 45.455 0.00 0.00 0.00 2.40
2743 5602 2.076863 CCGCTCTCCCTGTGTAAAAAG 58.923 52.381 0.00 0.00 0.00 2.27
2826 5695 1.075600 GGCCTGGCCTAGTCTCTCT 60.076 63.158 30.42 0.00 46.69 3.10
2827 5696 3.544772 GGCCTGGCCTAGTCTCTC 58.455 66.667 30.42 0.00 46.69 3.20
2848 5717 3.837570 CTGCTGCTGTGGCTGTGGA 62.838 63.158 0.00 0.00 39.19 4.02
2876 5745 0.884704 TGGCAGACTTGTTTCGAGGC 60.885 55.000 0.00 0.00 0.00 4.70
2877 5746 0.868406 GTGGCAGACTTGTTTCGAGG 59.132 55.000 0.00 0.00 0.00 4.63
2878 5747 1.261619 GTGTGGCAGACTTGTTTCGAG 59.738 52.381 7.64 0.00 0.00 4.04
2879 5748 1.295792 GTGTGGCAGACTTGTTTCGA 58.704 50.000 7.64 0.00 0.00 3.71
2880 5749 1.013596 TGTGTGGCAGACTTGTTTCG 58.986 50.000 16.26 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.