Multiple sequence alignment - TraesCS4A01G082600

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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 TraesCS4A01G082600 chr4A 100.000 5716 0 0 1737 7452 85907738 85902023 0.000000e+00 10556.0
1 TraesCS4A01G082600 chr4A 100.000 1445 0 0 1 1445 85909474 85908030 0.000000e+00 2669.0
2 TraesCS4A01G082600 chr4A 91.045 67 4 2 4910 4975 507583438 507583503 1.030000e-13 89.8
3 TraesCS4A01G082600 chr4A 92.982 57 1 3 4919 4975 552263187 552263240 6.200000e-11 80.5
4 TraesCS4A01G082600 chr4D 93.970 2156 82 21 4973 7102 379149209 379151342 0.000000e+00 3217.0
5 TraesCS4A01G082600 chr4D 93.035 1967 74 24 2980 4916 379147276 379149209 0.000000e+00 2815.0
6 TraesCS4A01G082600 chr4D 96.494 1255 33 4 1737 2982 379145943 379147195 0.000000e+00 2063.0
7 TraesCS4A01G082600 chr4D 83.855 799 84 24 2 783 379143616 379144386 0.000000e+00 719.0
8 TraesCS4A01G082600 chr4D 90.775 542 23 7 779 1320 379145210 379145724 0.000000e+00 699.0
9 TraesCS4A01G082600 chr4D 87.571 354 25 6 7103 7452 379151440 379151778 7.010000e-105 392.0
10 TraesCS4A01G082600 chr4D 89.231 65 4 2 4911 4974 3694961 3694899 2.230000e-10 78.7
11 TraesCS4A01G082600 chr4D 90.909 44 2 2 463 505 67238414 67238372 2.900000e-04 58.4
12 TraesCS4A01G082600 chr4B 95.422 1813 69 10 1737 3541 465730429 465732235 0.000000e+00 2876.0
13 TraesCS4A01G082600 chr4B 93.378 1933 72 23 5197 7087 465736474 465738392 0.000000e+00 2809.0
14 TraesCS4A01G082600 chr4B 95.174 1409 44 9 3539 4933 465732315 465733713 0.000000e+00 2204.0
15 TraesCS4A01G082600 chr4B 92.496 613 32 8 709 1320 465729611 465730210 0.000000e+00 865.0
16 TraesCS4A01G082600 chr4B 86.534 453 42 4 253 705 465728973 465729406 1.450000e-131 481.0
17 TraesCS4A01G082600 chr4B 87.679 349 22 13 7111 7452 465738459 465738793 3.260000e-103 387.0
18 TraesCS4A01G082600 chr4B 82.143 448 50 16 2 435 465728525 465728956 2.560000e-94 357.0
19 TraesCS4A01G082600 chr4B 85.560 277 15 7 4934 5206 465733741 465733996 4.430000e-67 267.0
20 TraesCS4A01G082600 chr4B 96.639 119 4 0 1325 1443 465730275 465730393 1.640000e-46 198.0
21 TraesCS4A01G082600 chr4B 87.379 103 13 0 404 506 34717231 34717129 1.310000e-22 119.0
22 TraesCS4A01G082600 chr4B 88.889 90 9 1 4458 4547 604049701 604049613 7.910000e-20 110.0
23 TraesCS4A01G082600 chr4B 97.059 34 0 1 719 751 510349144 510349177 1.000000e-03 56.5
24 TraesCS4A01G082600 chr2A 83.791 364 45 7 5531 5893 203005107 203004757 4.310000e-87 333.0
25 TraesCS4A01G082600 chr2A 87.209 86 11 0 4461 4546 569278807 569278892 1.710000e-16 99.0
26 TraesCS4A01G082600 chr2B 86.513 304 32 8 5592 5893 245009322 245009026 7.210000e-85 326.0
27 TraesCS4A01G082600 chr2D 76.578 602 101 22 5527 6104 188884859 188884274 2.030000e-75 294.0
28 TraesCS4A01G082600 chr2D 95.556 45 2 0 4462 4506 13914897 13914941 1.040000e-08 73.1
29 TraesCS4A01G082600 chr7D 89.011 91 7 3 4462 4551 410057986 410057898 7.910000e-20 110.0
30 TraesCS4A01G082600 chr7D 97.143 35 0 1 713 746 34029367 34029333 2.900000e-04 58.4
31 TraesCS4A01G082600 chr7B 87.500 80 10 0 4462 4541 385504433 385504354 7.960000e-15 93.5
32 TraesCS4A01G082600 chr7B 92.982 57 2 1 4918 4974 743311757 743311811 1.720000e-11 82.4
33 TraesCS4A01G082600 chr7B 88.710 62 4 1 4934 4995 654925813 654925871 1.040000e-08 73.1
34 TraesCS4A01G082600 chr6D 90.625 64 5 1 4918 4981 114870622 114870560 4.790000e-12 84.2
35 TraesCS4A01G082600 chr6D 96.970 33 0 1 719 750 245567891 245567923 4.000000e-03 54.7
36 TraesCS4A01G082600 chr5B 89.394 66 6 1 4455 4519 47729065 47729000 1.720000e-11 82.4
37 TraesCS4A01G082600 chr3B 91.803 61 2 2 4918 4977 351292252 351292310 1.720000e-11 82.4
38 TraesCS4A01G082600 chr3B 82.105 95 16 1 397 491 669630721 669630814 6.200000e-11 80.5
39 TraesCS4A01G082600 chr7A 91.525 59 3 2 4918 4975 26167207 26167150 6.200000e-11 80.5
40 TraesCS4A01G082600 chr5D 82.927 82 14 0 4466 4547 419388726 419388645 2.880000e-09 75.0
41 TraesCS4A01G082600 chr5D 96.970 33 0 1 719 750 375070171 375070203 4.000000e-03 54.7
42 TraesCS4A01G082600 chr6A 97.143 35 1 0 712 746 158049131 158049165 8.070000e-05 60.2
43 TraesCS4A01G082600 chrUn 96.970 33 0 1 719 750 104889276 104889244 4.000000e-03 54.7
44 TraesCS4A01G082600 chr6B 100.000 29 0 0 718 746 217157826 217157798 4.000000e-03 54.7
45 TraesCS4A01G082600 chr3D 96.875 32 1 0 715 746 507041040 507041071 4.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G082600 chr4A 85902023 85909474 7451 True 6612.500000 10556 100.000000 1 7452 2 chr4A.!!$R1 7451
1 TraesCS4A01G082600 chr4D 379143616 379151778 8162 False 1650.833333 3217 90.950000 2 7452 6 chr4D.!!$F1 7450
2 TraesCS4A01G082600 chr4B 465728525 465738793 10268 False 1160.444444 2876 90.558333 2 7452 9 chr4B.!!$F2 7450
3 TraesCS4A01G082600 chr2D 188884274 188884859 585 True 294.000000 294 76.578000 5527 6104 1 chr2D.!!$R1 577

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
113 114 0.968901 CAATGGCAGCAGGGACACAT 60.969 55.000 0.00 0.00 0.00 3.21 F
662 875 1.130777 TGAATGGGCGGATCATCTGA 58.869 50.000 0.00 0.00 0.00 3.27 F
1321 2580 0.460311 AAGTAGCAATCGGTCCTCGG 59.540 55.000 0.00 0.00 39.77 4.63 F
1989 3310 1.053424 TGGTCTTCTGGCTACCGTTT 58.947 50.000 0.00 0.00 35.98 3.60 F
2533 3861 1.452108 GTGCACCTGGATGCCCTAC 60.452 63.158 5.22 6.62 45.50 3.18 F
4200 5728 1.472662 ATCCCTTCGATGCCCCTACG 61.473 60.000 0.00 0.00 0.00 3.51 F
4928 6459 0.035439 TCAAAATGCTCCCTCCGTCC 60.035 55.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 2414 0.865111 CATTGCGTCGAACACCTTGA 59.135 50.000 0.0 0.0 0.00 3.02 R
2003 3324 1.336755 CCGACCACCAGGAACAAAAAG 59.663 52.381 0.0 0.0 38.69 2.27 R
2578 3906 1.550524 TGAGTACCACTGGCTGATGAC 59.449 52.381 0.0 0.0 0.00 3.06 R
3658 5161 1.349259 CGTGATTGTCCCGTTCCGAC 61.349 60.000 0.0 0.0 0.00 4.79 R
4221 5749 0.111253 CCCCCTCAGCAAAAGTCACT 59.889 55.000 0.0 0.0 0.00 3.41 R
5249 9354 1.000060 GAAATGCAGGCACAAAGCTGA 60.000 47.619 0.0 0.0 44.79 4.26 R
6685 10814 0.176449 CGTCCAGTGATCAGGCATCA 59.824 55.000 0.0 0.0 39.39 3.07 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
47 48 6.391649 TGGGGGTTTGATGGTAAGTATCTTAT 59.608 38.462 0.00 0.00 0.00 1.73
113 114 0.968901 CAATGGCAGCAGGGACACAT 60.969 55.000 0.00 0.00 0.00 3.21
145 146 1.831736 GAGCTTCTGGTACCTTGGCTA 59.168 52.381 14.36 0.00 0.00 3.93
146 147 2.436173 GAGCTTCTGGTACCTTGGCTAT 59.564 50.000 14.36 0.00 0.00 2.97
149 150 3.641906 GCTTCTGGTACCTTGGCTATAGA 59.358 47.826 14.36 1.58 0.00 1.98
151 152 3.573695 TCTGGTACCTTGGCTATAGACC 58.426 50.000 14.36 4.75 0.00 3.85
154 155 4.105577 TGGTACCTTGGCTATAGACCAAA 58.894 43.478 21.43 10.44 46.24 3.28
159 160 4.016444 CCTTGGCTATAGACCAAAAAGCA 58.984 43.478 21.43 6.51 46.24 3.91
173 174 4.382685 CCAAAAAGCAATGGATCATGCTCT 60.383 41.667 17.00 4.31 39.12 4.09
177 178 6.726490 AAAGCAATGGATCATGCTCTTTAT 57.274 33.333 17.00 2.65 36.51 1.40
179 180 4.022242 AGCAATGGATCATGCTCTTTATGC 60.022 41.667 12.51 3.45 31.18 3.14
185 196 3.770263 TCATGCTCTTTATGCTTGTGC 57.230 42.857 0.00 0.00 37.05 4.57
186 197 2.096335 TCATGCTCTTTATGCTTGTGCG 59.904 45.455 0.00 0.00 43.34 5.34
189 200 2.006888 GCTCTTTATGCTTGTGCGGTA 58.993 47.619 0.00 0.00 43.34 4.02
190 201 2.614057 GCTCTTTATGCTTGTGCGGTAT 59.386 45.455 0.00 0.00 43.34 2.73
191 202 3.065371 GCTCTTTATGCTTGTGCGGTATT 59.935 43.478 0.00 0.00 43.34 1.89
192 203 4.272504 GCTCTTTATGCTTGTGCGGTATTA 59.727 41.667 0.00 0.00 43.34 0.98
193 204 5.049405 GCTCTTTATGCTTGTGCGGTATTAT 60.049 40.000 0.00 0.00 43.34 1.28
194 205 6.299023 TCTTTATGCTTGTGCGGTATTATG 57.701 37.500 0.00 0.00 43.34 1.90
195 206 5.238432 TCTTTATGCTTGTGCGGTATTATGG 59.762 40.000 0.00 0.00 43.34 2.74
196 207 2.411628 TGCTTGTGCGGTATTATGGT 57.588 45.000 0.00 0.00 43.34 3.55
223 234 2.963782 AGAGTCCGAGTGGTAGTTTTGT 59.036 45.455 0.00 0.00 36.30 2.83
278 303 4.782019 ACATAACAAAATGCGGTGACAT 57.218 36.364 0.00 0.00 0.00 3.06
284 309 4.072131 ACAAAATGCGGTGACATAGAAGT 58.928 39.130 0.00 0.00 0.00 3.01
361 573 9.658799 TTCAAAATAACTGAATCTCTAGGACTG 57.341 33.333 0.00 0.00 0.00 3.51
370 582 8.598041 ACTGAATCTCTAGGACTGTTTTATGTT 58.402 33.333 0.00 0.00 0.00 2.71
448 660 6.914215 TGAATCTATCGAAGCAAATTTGATGC 59.086 34.615 22.31 13.56 41.37 3.91
520 732 6.481313 AGTTTGACTTAAAACGGACTAGAACC 59.519 38.462 0.00 0.00 43.39 3.62
566 778 7.148689 GGGAGTACACTATTAAACGTGTTTCAG 60.149 40.741 15.48 1.49 41.24 3.02
594 806 5.163322 TGGATCATTTCACCTTGCAAAAAGT 60.163 36.000 0.00 0.00 0.00 2.66
619 831 9.264719 GTATGATGACATGATAAACACATGAGA 57.735 33.333 13.54 1.79 45.22 3.27
639 852 5.356751 TGAGATAAGCAACACACACAAAACT 59.643 36.000 0.00 0.00 0.00 2.66
643 856 4.981806 AGCAACACACACAAAACTATGT 57.018 36.364 0.00 0.00 0.00 2.29
662 875 1.130777 TGAATGGGCGGATCATCTGA 58.869 50.000 0.00 0.00 0.00 3.27
677 890 7.278875 GGATCATCTGAACCTAGAGTCAAATT 58.721 38.462 0.00 0.00 34.54 1.82
687 900 5.251700 ACCTAGAGTCAAATTCAGAACCCAT 59.748 40.000 0.00 0.00 0.00 4.00
688 901 5.587844 CCTAGAGTCAAATTCAGAACCCATG 59.412 44.000 0.00 0.00 0.00 3.66
706 919 1.656587 TGGGTCCAAGCATGTACTCT 58.343 50.000 0.00 0.00 0.00 3.24
707 1121 1.555075 TGGGTCCAAGCATGTACTCTC 59.445 52.381 0.00 0.00 0.00 3.20
711 1125 4.081087 GGGTCCAAGCATGTACTCTCTTTA 60.081 45.833 0.00 0.00 0.00 1.85
941 2185 2.365617 CAACCGCAGTCCATACTCCTAT 59.634 50.000 0.00 0.00 31.97 2.57
988 2232 2.037847 CCCCTCCCCCAAGCAAAG 59.962 66.667 0.00 0.00 0.00 2.77
1016 2260 1.598962 CAATGGCCGCTCGGATCAT 60.599 57.895 13.11 11.39 37.50 2.45
1155 2414 3.930592 AGTAGATAGCCCTATACCCCACT 59.069 47.826 0.00 0.00 0.00 4.00
1206 2465 2.175811 GACGCCATTGTCGTTGCC 59.824 61.111 0.00 0.00 40.59 4.52
1223 2482 1.351017 TGCCTCCTGATTTCTTCGGTT 59.649 47.619 0.00 0.00 0.00 4.44
1224 2483 2.010497 GCCTCCTGATTTCTTCGGTTC 58.990 52.381 0.00 0.00 0.00 3.62
1227 2486 3.686726 CCTCCTGATTTCTTCGGTTCAAG 59.313 47.826 0.00 0.00 0.00 3.02
1247 2506 2.167900 AGTGGGACTTGTTCTATACCGC 59.832 50.000 0.00 0.00 0.00 5.68
1248 2507 2.093869 GTGGGACTTGTTCTATACCGCA 60.094 50.000 0.00 0.00 0.00 5.69
1249 2508 2.568062 TGGGACTTGTTCTATACCGCAA 59.432 45.455 0.00 0.00 0.00 4.85
1251 2510 4.406326 TGGGACTTGTTCTATACCGCAATA 59.594 41.667 0.00 0.00 0.00 1.90
1266 2525 4.191544 CCGCAATATCTTCTTTGGTCTCA 58.808 43.478 0.00 0.00 0.00 3.27
1273 2532 4.908601 TCTTCTTTGGTCTCATAAGGCA 57.091 40.909 0.00 0.00 0.00 4.75
1275 2534 5.003804 TCTTCTTTGGTCTCATAAGGCAAC 58.996 41.667 0.00 0.00 0.00 4.17
1276 2535 3.686016 TCTTTGGTCTCATAAGGCAACC 58.314 45.455 0.00 0.00 37.17 3.77
1277 2536 2.507407 TTGGTCTCATAAGGCAACCC 57.493 50.000 0.00 0.00 37.17 4.11
1278 2537 1.367346 TGGTCTCATAAGGCAACCCA 58.633 50.000 0.00 0.00 37.17 4.51
1279 2538 1.707989 TGGTCTCATAAGGCAACCCAA 59.292 47.619 0.00 0.00 37.17 4.12
1280 2539 2.311542 TGGTCTCATAAGGCAACCCAAT 59.688 45.455 0.00 0.00 37.17 3.16
1281 2540 2.689983 GGTCTCATAAGGCAACCCAATG 59.310 50.000 0.00 0.00 37.17 2.82
1282 2541 2.099756 GTCTCATAAGGCAACCCAATGC 59.900 50.000 0.00 0.00 45.67 3.56
1288 2547 4.917474 GCAACCCAATGCATGACC 57.083 55.556 0.00 0.00 45.70 4.02
1320 2579 1.134367 TGAAGTAGCAATCGGTCCTCG 59.866 52.381 0.00 0.00 40.90 4.63
1321 2580 0.460311 AAGTAGCAATCGGTCCTCGG 59.540 55.000 0.00 0.00 39.77 4.63
1416 2736 9.044150 TGAATGATTCCTGTGAAATTTTGTTTC 57.956 29.630 2.26 0.00 33.32 2.78
1443 2763 1.810532 CAGCACTCCTCTCGTACCC 59.189 63.158 0.00 0.00 0.00 3.69
1444 2764 1.749638 AGCACTCCTCTCGTACCCG 60.750 63.158 0.00 0.00 0.00 5.28
1920 3241 4.582869 TCTTGAAGCTTGCTGTATGATGT 58.417 39.130 2.10 0.00 0.00 3.06
1989 3310 1.053424 TGGTCTTCTGGCTACCGTTT 58.947 50.000 0.00 0.00 35.98 3.60
2003 3324 5.177696 GGCTACCGTTTCATCTGTGATATTC 59.822 44.000 0.00 0.00 33.56 1.75
2126 3447 8.131455 ACAATGCAGTTATAATAGAGTGTTCG 57.869 34.615 0.00 0.00 0.00 3.95
2213 3537 5.440685 CATGAACTAACTTTGTCCAACGAC 58.559 41.667 0.00 0.00 39.66 4.34
2372 3696 7.871463 GCTGTTACCGAAATATACCAGATTAGT 59.129 37.037 0.00 0.00 0.00 2.24
2529 3857 3.434319 CACGTGCACCTGGATGCC 61.434 66.667 12.15 8.38 45.50 4.40
2533 3861 1.452108 GTGCACCTGGATGCCCTAC 60.452 63.158 5.22 6.62 45.50 3.18
2550 3878 4.442893 GCCCTACATGCACTACTTACATGA 60.443 45.833 0.00 0.00 43.04 3.07
2565 3893 7.124573 ACTTACATGATGGCTGATGTAGTAA 57.875 36.000 0.00 0.00 36.62 2.24
2578 3906 5.496556 TGATGTAGTAACCACCCAGAAATG 58.503 41.667 0.00 0.00 0.00 2.32
2592 3920 2.422479 CAGAAATGTCATCAGCCAGTGG 59.578 50.000 4.20 4.20 0.00 4.00
2608 3936 4.003648 CCAGTGGTACTCAGGATTTTGTC 58.996 47.826 0.00 0.00 29.68 3.18
3019 4437 3.120792 CTCTTCCGTTCTTTGTTGTCGA 58.879 45.455 0.00 0.00 0.00 4.20
3020 4438 3.523547 TCTTCCGTTCTTTGTTGTCGAA 58.476 40.909 0.00 0.00 0.00 3.71
3448 4868 9.562408 TGAAATTATTAGTTGTGTCACCTTGTA 57.438 29.630 0.00 0.00 0.00 2.41
3747 5250 3.823304 AGGTGCTTCTTTGGTCTTGAATC 59.177 43.478 0.00 0.00 0.00 2.52
3839 5342 3.889538 GGCAAGGTAGGAATTAATGGTCC 59.110 47.826 0.00 0.00 0.00 4.46
3840 5343 3.564225 GCAAGGTAGGAATTAATGGTCCG 59.436 47.826 1.33 0.00 39.06 4.79
4114 5642 6.154445 GCCGATGCTGAATCATATTTCATTT 58.846 36.000 0.00 0.00 35.20 2.32
4200 5728 1.472662 ATCCCTTCGATGCCCCTACG 61.473 60.000 0.00 0.00 0.00 3.51
4221 5749 5.012239 ACGTATAATATACCCGAGAAGCCA 58.988 41.667 4.96 0.00 0.00 4.75
4337 5865 8.487970 GCTTATTTTTGAACCAAAAGAGTAAGC 58.512 33.333 23.39 23.39 42.91 3.09
4488 6016 6.681729 ACCTCTGTTCCTAAATGTAAGACA 57.318 37.500 0.00 0.00 0.00 3.41
4490 6018 7.106239 ACCTCTGTTCCTAAATGTAAGACATG 58.894 38.462 0.00 0.00 37.97 3.21
4558 6086 0.958876 GGGTGTACTTTCCAAGGGCG 60.959 60.000 0.00 0.00 0.00 6.13
4594 6122 3.596214 ACTGCCACTAAGAAATACCACG 58.404 45.455 0.00 0.00 0.00 4.94
4739 6267 1.181786 GGGCCCATGATTTTTCGTGA 58.818 50.000 19.95 0.00 0.00 4.35
4790 6321 2.496899 TTTTGGCTTGGCTCTCCTAG 57.503 50.000 0.00 0.00 38.11 3.02
4922 6453 9.652114 AATATTTCTTATCTCAAAATGCTCCCT 57.348 29.630 0.00 0.00 0.00 4.20
4923 6454 7.579761 ATTTCTTATCTCAAAATGCTCCCTC 57.420 36.000 0.00 0.00 0.00 4.30
4924 6455 5.041191 TCTTATCTCAAAATGCTCCCTCC 57.959 43.478 0.00 0.00 0.00 4.30
4925 6456 2.338577 ATCTCAAAATGCTCCCTCCG 57.661 50.000 0.00 0.00 0.00 4.63
4926 6457 0.984230 TCTCAAAATGCTCCCTCCGT 59.016 50.000 0.00 0.00 0.00 4.69
4927 6458 1.066143 TCTCAAAATGCTCCCTCCGTC 60.066 52.381 0.00 0.00 0.00 4.79
4928 6459 0.035439 TCAAAATGCTCCCTCCGTCC 60.035 55.000 0.00 0.00 0.00 4.79
4929 6460 1.032114 CAAAATGCTCCCTCCGTCCC 61.032 60.000 0.00 0.00 0.00 4.46
4930 6461 1.497309 AAAATGCTCCCTCCGTCCCA 61.497 55.000 0.00 0.00 0.00 4.37
4931 6462 1.281925 AAATGCTCCCTCCGTCCCAT 61.282 55.000 0.00 0.00 0.00 4.00
4932 6463 0.399949 AATGCTCCCTCCGTCCCATA 60.400 55.000 0.00 0.00 0.00 2.74
4933 6464 0.178891 ATGCTCCCTCCGTCCCATAT 60.179 55.000 0.00 0.00 0.00 1.78
4934 6465 0.485543 TGCTCCCTCCGTCCCATATA 59.514 55.000 0.00 0.00 0.00 0.86
4935 6466 1.132977 TGCTCCCTCCGTCCCATATAA 60.133 52.381 0.00 0.00 0.00 0.98
4936 6467 2.188817 GCTCCCTCCGTCCCATATAAT 58.811 52.381 0.00 0.00 0.00 1.28
4937 6468 2.093447 GCTCCCTCCGTCCCATATAATG 60.093 54.545 0.00 0.00 0.00 1.90
4938 6469 3.173965 CTCCCTCCGTCCCATATAATGT 58.826 50.000 0.00 0.00 0.00 2.71
4939 6470 3.170717 TCCCTCCGTCCCATATAATGTC 58.829 50.000 0.00 0.00 0.00 3.06
4940 6471 2.903784 CCCTCCGTCCCATATAATGTCA 59.096 50.000 0.00 0.00 0.00 3.58
4941 6472 3.326588 CCCTCCGTCCCATATAATGTCAA 59.673 47.826 0.00 0.00 0.00 3.18
4942 6473 4.202419 CCCTCCGTCCCATATAATGTCAAA 60.202 45.833 0.00 0.00 0.00 2.69
4943 6474 5.373222 CCTCCGTCCCATATAATGTCAAAA 58.627 41.667 0.00 0.00 0.00 2.44
4944 6475 5.825679 CCTCCGTCCCATATAATGTCAAAAA 59.174 40.000 0.00 0.00 0.00 1.94
4965 6496 6.693315 AAAACGTCTTACATTATGGGATGG 57.307 37.500 0.00 0.00 0.00 3.51
4966 6497 5.623956 AACGTCTTACATTATGGGATGGA 57.376 39.130 0.00 0.00 0.00 3.41
4967 6498 5.215252 ACGTCTTACATTATGGGATGGAG 57.785 43.478 0.00 0.00 0.00 3.86
4968 6499 4.040461 ACGTCTTACATTATGGGATGGAGG 59.960 45.833 0.00 0.00 0.00 4.30
4969 6500 4.563580 CGTCTTACATTATGGGATGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
4970 6501 4.597507 GTCTTACATTATGGGATGGAGGGA 59.402 45.833 0.00 0.00 0.00 4.20
4971 6502 4.846367 TCTTACATTATGGGATGGAGGGAG 59.154 45.833 0.00 0.00 0.00 4.30
5010 6625 3.141398 TGAACTGCAGGAATTCACTGTC 58.859 45.455 19.93 13.87 38.22 3.51
5021 6636 7.414098 GCAGGAATTCACTGTCGTTAATATTGT 60.414 37.037 19.00 0.00 38.22 2.71
5169 6787 2.639839 ACCTGGTTGATGTTCTAGCTGT 59.360 45.455 0.00 0.00 0.00 4.40
5219 9324 9.136952 GTCGTTCATTAGTAATCTACACACTTT 57.863 33.333 0.00 0.00 0.00 2.66
5295 9400 9.383519 CTTGGCATCTTTTACTCTTACTAATGA 57.616 33.333 0.00 0.00 0.00 2.57
5382 9487 7.897575 TTTTGTTTAGCATGTTGTCAGTTTT 57.102 28.000 0.00 0.00 0.00 2.43
5405 9510 8.651589 TTTCGTATATGGATTGATACTCTCCT 57.348 34.615 0.00 0.00 0.00 3.69
5455 9560 6.532302 TGCATCAAATGATATGTTTTGTCAGC 59.468 34.615 0.00 8.91 35.01 4.26
5718 9824 9.256228 TGACATAGTATTGTAGTTTTCCTCTCT 57.744 33.333 0.00 0.00 0.00 3.10
6184 10310 5.884232 AGAATTCAGATGATGCTTTGCTACA 59.116 36.000 8.44 0.00 0.00 2.74
6206 10332 3.010420 GTGGAAAGGAACACTAGGATGC 58.990 50.000 0.00 0.00 34.84 3.91
6253 10379 3.719924 CATTGCAAGCCTTCAAACTTGA 58.280 40.909 4.94 0.00 44.89 3.02
6465 10591 1.482182 AGCGTAAGGATGCATGAGACA 59.518 47.619 2.46 0.00 40.34 3.41
6510 10637 0.613853 TGGGTCGAGGAACTGGGTAG 60.614 60.000 0.00 0.00 41.55 3.18
6699 10853 4.232188 AGAACAATGATGCCTGATCACT 57.768 40.909 0.00 0.00 44.12 3.41
6703 10857 2.617308 CAATGATGCCTGATCACTGGAC 59.383 50.000 5.19 0.00 44.12 4.02
6787 10941 4.935205 TGCATGTGCTACCTACTGTAAAAG 59.065 41.667 6.55 0.00 42.66 2.27
6788 10942 4.332819 GCATGTGCTACCTACTGTAAAAGG 59.667 45.833 0.00 0.00 37.19 3.11
6789 10943 4.546829 TGTGCTACCTACTGTAAAAGGG 57.453 45.455 0.54 0.00 37.18 3.95
6790 10944 3.905591 TGTGCTACCTACTGTAAAAGGGT 59.094 43.478 0.54 1.61 37.18 4.34
6838 10992 8.198109 GCTCTTTCTATGATTGGAGTAGTTGTA 58.802 37.037 0.00 0.00 0.00 2.41
6875 11029 5.241506 TCTGGAAAGAAATGTTTCGAAGCAT 59.758 36.000 20.26 20.26 41.92 3.79
6903 11057 9.398921 ACCCTAATTGTATGGATAGATTCTTCT 57.601 33.333 0.00 0.00 35.90 2.85
6930 11084 8.334263 TGACTAATTTAGAACATGTCATTGCA 57.666 30.769 10.39 0.00 0.00 4.08
6938 11092 8.746922 TTAGAACATGTCATTGCATTTTCTTC 57.253 30.769 18.65 0.00 40.76 2.87
6975 11134 7.600065 TGGTACTTGCAACTACTTCTAGTTAG 58.400 38.462 13.68 0.00 40.64 2.34
6976 11135 7.232127 TGGTACTTGCAACTACTTCTAGTTAGT 59.768 37.037 13.68 5.76 40.64 2.24
6977 11136 8.087136 GGTACTTGCAACTACTTCTAGTTAGTT 58.913 37.037 13.68 6.88 40.64 2.24
7006 11165 7.642071 ACATGATTTCCTTTGTGAATTTTCG 57.358 32.000 0.00 0.00 0.00 3.46
7069 11228 6.542821 TCAATTAGGTGAGGTGATTGTTCTT 58.457 36.000 0.00 0.00 0.00 2.52
7102 11261 8.717717 TGGTTCCTGATAGATAATCTTGTTCAT 58.282 33.333 0.00 0.00 35.45 2.57
7103 11262 9.213799 GGTTCCTGATAGATAATCTTGTTCATC 57.786 37.037 0.00 0.00 35.45 2.92
7104 11263 9.770097 GTTCCTGATAGATAATCTTGTTCATCA 57.230 33.333 0.00 0.00 35.45 3.07
7124 11380 9.794685 TTCATCAGATATTCTATAGTTCGATGC 57.205 33.333 0.00 0.00 0.00 3.91
7189 11445 3.787001 CCCCTCCCACGCCTTCTC 61.787 72.222 0.00 0.00 0.00 2.87
7234 11490 1.005156 GCCGATGAGGAGGATGAGC 60.005 63.158 0.00 0.00 45.00 4.26
7239 11495 2.045524 GATGAGGAGGATGAGCTTGGA 58.954 52.381 0.00 0.00 0.00 3.53
7244 11500 1.773653 GGAGGATGAGCTTGGAAGGAT 59.226 52.381 0.00 0.00 0.00 3.24
7256 11512 3.468326 GAAGGATGCGAGGGGAGCC 62.468 68.421 0.00 0.00 40.87 4.70
7344 11601 4.636249 CATTATCCTAGAGCACCTCCAAC 58.364 47.826 0.00 0.00 0.00 3.77
7373 11630 5.611374 ACATATAATCAGTCCCCGAAAGTG 58.389 41.667 0.00 0.00 0.00 3.16
7392 11649 3.004734 AGTGGCATGCTACACTTTGTTTC 59.995 43.478 32.23 4.99 45.03 2.78
7405 11666 9.389570 CTACACTTTGTTTCCCTTAAAATAACG 57.610 33.333 0.00 0.00 0.00 3.18
7447 11708 2.678336 CCTTTCCTGCGAGTATCAAACC 59.322 50.000 0.00 0.00 33.17 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.215399 CACCACATCCGACACAGTTTTAAT 59.785 41.667 0.00 0.00 0.00 1.40
7 8 1.375908 CCCACCACATCCGACACAG 60.376 63.158 0.00 0.00 0.00 3.66
17 18 1.154921 CCATCAAACCCCCACCACA 59.845 57.895 0.00 0.00 0.00 4.17
47 48 7.506114 ACTTTACAAGTGTTGACTCCTTCATA 58.494 34.615 0.00 0.00 41.01 2.15
108 109 0.617413 CTCTTCCCCTCAGCATGTGT 59.383 55.000 0.00 0.00 37.40 3.72
113 114 0.546267 AGAAGCTCTTCCCCTCAGCA 60.546 55.000 6.04 0.00 40.33 4.41
145 146 6.684613 GCATGATCCATTGCTTTTTGGTCTAT 60.685 38.462 0.00 0.00 34.48 1.98
146 147 5.394443 GCATGATCCATTGCTTTTTGGTCTA 60.394 40.000 0.00 0.00 34.48 2.59
149 150 3.262405 AGCATGATCCATTGCTTTTTGGT 59.738 39.130 8.60 0.00 33.34 3.67
151 152 4.755411 AGAGCATGATCCATTGCTTTTTG 58.245 39.130 7.49 0.00 37.79 2.44
154 155 6.513180 CATAAAGAGCATGATCCATTGCTTT 58.487 36.000 7.49 3.22 37.79 3.51
159 160 5.597182 ACAAGCATAAAGAGCATGATCCATT 59.403 36.000 7.49 6.11 34.97 3.16
173 174 4.884744 ACCATAATACCGCACAAGCATAAA 59.115 37.500 0.00 0.00 42.27 1.40
177 178 2.013400 CACCATAATACCGCACAAGCA 58.987 47.619 0.00 0.00 42.27 3.91
179 180 1.946768 CCCACCATAATACCGCACAAG 59.053 52.381 0.00 0.00 0.00 3.16
185 196 4.377897 GACTCTTTCCCACCATAATACCG 58.622 47.826 0.00 0.00 0.00 4.02
186 197 4.715713 GGACTCTTTCCCACCATAATACC 58.284 47.826 0.00 0.00 38.70 2.73
189 200 3.112263 TCGGACTCTTTCCCACCATAAT 58.888 45.455 0.00 0.00 42.27 1.28
190 201 2.500098 CTCGGACTCTTTCCCACCATAA 59.500 50.000 0.00 0.00 42.27 1.90
191 202 2.108168 CTCGGACTCTTTCCCACCATA 58.892 52.381 0.00 0.00 42.27 2.74
192 203 0.905357 CTCGGACTCTTTCCCACCAT 59.095 55.000 0.00 0.00 42.27 3.55
193 204 0.471211 ACTCGGACTCTTTCCCACCA 60.471 55.000 0.00 0.00 42.27 4.17
194 205 0.037232 CACTCGGACTCTTTCCCACC 60.037 60.000 0.00 0.00 42.27 4.61
195 206 0.037232 CCACTCGGACTCTTTCCCAC 60.037 60.000 0.00 0.00 42.27 4.61
196 207 0.471211 ACCACTCGGACTCTTTCCCA 60.471 55.000 0.00 0.00 42.27 4.37
241 252 8.812147 TTTGTTATGTACCATCGCTTCTATAG 57.188 34.615 0.00 0.00 0.00 1.31
244 255 7.466725 GCATTTTGTTATGTACCATCGCTTCTA 60.467 37.037 0.00 0.00 0.00 2.10
246 257 5.455525 GCATTTTGTTATGTACCATCGCTTC 59.544 40.000 0.00 0.00 0.00 3.86
248 259 4.495679 CGCATTTTGTTATGTACCATCGCT 60.496 41.667 0.00 0.00 0.00 4.93
278 303 2.715749 TACGTCGGGGATCACTTCTA 57.284 50.000 0.00 0.00 0.00 2.10
284 309 5.477637 TCAAATGTATATACGTCGGGGATCA 59.522 40.000 8.05 0.00 0.00 2.92
370 582 9.388506 ACATTTGAAATGGTTGATGTTTGTTTA 57.611 25.926 20.69 0.00 0.00 2.01
493 705 8.393366 GTTCTAGTCCGTTTTAAGTCAAACTTT 58.607 33.333 0.00 0.00 39.51 2.66
520 732 4.761739 TCCCTTTGTTGCAGACTAATTGAG 59.238 41.667 0.00 0.00 0.00 3.02
566 778 3.507233 TGCAAGGTGAAATGATCCACTTC 59.493 43.478 0.00 0.00 33.99 3.01
614 826 6.039717 AGTTTTGTGTGTGTTGCTTATCTCAT 59.960 34.615 0.00 0.00 0.00 2.90
615 827 5.356751 AGTTTTGTGTGTGTTGCTTATCTCA 59.643 36.000 0.00 0.00 0.00 3.27
619 831 6.917477 CACATAGTTTTGTGTGTGTTGCTTAT 59.083 34.615 0.00 0.00 41.65 1.73
639 852 2.639347 AGATGATCCGCCCATTCACATA 59.361 45.455 0.00 0.00 0.00 2.29
643 856 1.130777 TCAGATGATCCGCCCATTCA 58.869 50.000 0.00 0.00 0.00 2.57
647 860 0.982852 AGGTTCAGATGATCCGCCCA 60.983 55.000 4.65 0.00 38.59 5.36
662 875 5.073144 TGGGTTCTGAATTTGACTCTAGGTT 59.927 40.000 0.00 0.00 0.00 3.50
687 900 1.555075 GAGAGTACATGCTTGGACCCA 59.445 52.381 11.21 0.00 37.40 4.51
688 901 1.834263 AGAGAGTACATGCTTGGACCC 59.166 52.381 11.21 0.00 37.40 4.46
693 906 9.173939 CTTGTTTTTAAAGAGAGTACATGCTTG 57.826 33.333 0.00 0.00 0.00 4.01
807 2051 1.315690 GGGATAGACGTCATCCGACA 58.684 55.000 26.58 5.28 42.57 4.35
941 2185 1.302949 CAGGCGAGATGGGGGAAAA 59.697 57.895 0.00 0.00 0.00 2.29
988 2232 1.169034 GCGGCCATTGATCCTTCTCC 61.169 60.000 2.24 0.00 0.00 3.71
1016 2260 3.640407 GGTGGTGGAGCAGCCTCA 61.640 66.667 0.00 0.00 39.96 3.86
1155 2414 0.865111 CATTGCGTCGAACACCTTGA 59.135 50.000 0.00 0.00 0.00 3.02
1206 2465 4.153117 CACTTGAACCGAAGAAATCAGGAG 59.847 45.833 0.00 0.00 0.00 3.69
1227 2486 2.093869 TGCGGTATAGAACAAGTCCCAC 60.094 50.000 0.00 0.00 0.00 4.61
1236 2495 7.441458 ACCAAAGAAGATATTGCGGTATAGAAC 59.559 37.037 0.00 0.00 0.00 3.01
1247 2506 7.500227 TGCCTTATGAGACCAAAGAAGATATTG 59.500 37.037 0.00 0.00 0.00 1.90
1248 2507 7.577303 TGCCTTATGAGACCAAAGAAGATATT 58.423 34.615 0.00 0.00 0.00 1.28
1249 2508 7.141758 TGCCTTATGAGACCAAAGAAGATAT 57.858 36.000 0.00 0.00 0.00 1.63
1251 2510 5.441718 TGCCTTATGAGACCAAAGAAGAT 57.558 39.130 0.00 0.00 0.00 2.40
1266 2525 2.431782 GTCATGCATTGGGTTGCCTTAT 59.568 45.455 0.00 0.00 42.06 1.73
1273 2532 1.076549 ACGGGTCATGCATTGGGTT 59.923 52.632 0.00 0.00 0.00 4.11
1275 2534 1.656818 GACACGGGTCATGCATTGGG 61.657 60.000 14.30 0.00 43.73 4.12
1276 2535 1.802636 GACACGGGTCATGCATTGG 59.197 57.895 14.30 0.00 43.73 3.16
1285 2544 2.767505 ACTTCAAATCTGACACGGGTC 58.232 47.619 11.93 11.93 44.57 4.46
1288 2547 3.325870 TGCTACTTCAAATCTGACACGG 58.674 45.455 0.00 0.00 0.00 4.94
1301 2560 1.536284 CCGAGGACCGATTGCTACTTC 60.536 57.143 0.00 0.00 41.76 3.01
1320 2579 3.826221 TGTGAGCAGCAACACACC 58.174 55.556 17.57 0.00 41.19 4.16
1416 2736 3.488384 CGAGAGGAGTGCTGCTAGTTTAG 60.488 52.174 0.00 0.00 0.00 1.85
1424 2744 1.139947 GGTACGAGAGGAGTGCTGC 59.860 63.158 0.00 0.00 0.00 5.25
1989 3310 8.733458 CAGGAACAAAAAGAATATCACAGATGA 58.267 33.333 0.00 0.00 39.83 2.92
2003 3324 1.336755 CCGACCACCAGGAACAAAAAG 59.663 52.381 0.00 0.00 38.69 2.27
2118 3439 9.422196 GTTTAAGCATCAAATATACGAACACTC 57.578 33.333 0.00 0.00 0.00 3.51
2126 3447 7.441458 AGGACTCCGTTTAAGCATCAAATATAC 59.559 37.037 0.00 0.00 0.00 1.47
2213 3537 8.029642 ACTATCCAATCTCAGTTTACAAAACG 57.970 34.615 0.00 0.00 0.00 3.60
2529 3857 5.698089 CCATCATGTAAGTAGTGCATGTAGG 59.302 44.000 12.37 11.54 46.98 3.18
2550 3878 2.172717 GGGTGGTTACTACATCAGCCAT 59.827 50.000 0.61 0.00 44.45 4.40
2565 3893 2.881403 GCTGATGACATTTCTGGGTGGT 60.881 50.000 0.00 0.00 0.00 4.16
2578 3906 1.550524 TGAGTACCACTGGCTGATGAC 59.449 52.381 0.00 0.00 0.00 3.06
2592 3920 9.220767 ACAGAAAATAGACAAAATCCTGAGTAC 57.779 33.333 0.00 0.00 0.00 2.73
3003 4421 4.670621 CAGATTTTCGACAACAAAGAACGG 59.329 41.667 0.00 0.00 0.00 4.44
3019 4437 6.777580 AGTAAATGACTGTTGGTCCAGATTTT 59.222 34.615 0.00 0.00 43.89 1.82
3020 4438 6.306987 AGTAAATGACTGTTGGTCCAGATTT 58.693 36.000 0.00 0.00 43.89 2.17
3049 4467 3.204505 CACAGCAAAAGTGGGCATG 57.795 52.632 0.00 0.00 33.43 4.06
3658 5161 1.349259 CGTGATTGTCCCGTTCCGAC 61.349 60.000 0.00 0.00 0.00 4.79
3747 5250 3.998099 TCTCATGCGAGAACATCTAGG 57.002 47.619 0.00 0.00 45.47 3.02
3871 5387 5.250200 AGAGAACAGACATACTCGACTCTT 58.750 41.667 0.00 0.00 34.98 2.85
3872 5388 4.839121 AGAGAACAGACATACTCGACTCT 58.161 43.478 0.00 0.00 34.98 3.24
3877 5393 5.570973 CACAAGAAGAGAACAGACATACTCG 59.429 44.000 0.00 0.00 34.98 4.18
4114 5642 8.605947 AGGGCAGTGATCTATAAGCAATATAAA 58.394 33.333 0.00 0.00 0.00 1.40
4161 5689 4.503991 GGATCTCCAACAGTTGACAAGTCT 60.504 45.833 15.36 2.43 35.64 3.24
4200 5728 6.152323 TCACTGGCTTCTCGGGTATATTATAC 59.848 42.308 5.42 5.42 0.00 1.47
4221 5749 0.111253 CCCCCTCAGCAAAAGTCACT 59.889 55.000 0.00 0.00 0.00 3.41
4337 5865 6.453092 AGTTCAATCAGAAGAATGCAAAAGG 58.547 36.000 0.00 0.00 36.78 3.11
4558 6086 5.078256 AGTGGCAGTACATACTCCCTATAC 58.922 45.833 0.78 0.00 35.13 1.47
4594 6122 0.593128 AAACTTCGCACATGCCTGAC 59.407 50.000 0.00 0.00 37.91 3.51
4677 6205 3.966665 AGGGAGAGAACAGAATGAGATCC 59.033 47.826 0.00 0.00 39.69 3.36
4739 6267 4.322499 CCATAACTTACTCCGTCACCAACT 60.322 45.833 0.00 0.00 0.00 3.16
4790 6321 1.678101 GGCTTGGTGATACATGAAGGC 59.322 52.381 0.00 0.00 32.84 4.35
4908 6439 1.373570 GACGGAGGGAGCATTTTGAG 58.626 55.000 0.00 0.00 0.00 3.02
4915 6446 0.485543 TATATGGGACGGAGGGAGCA 59.514 55.000 0.00 0.00 0.00 4.26
4916 6447 1.640917 TTATATGGGACGGAGGGAGC 58.359 55.000 0.00 0.00 0.00 4.70
4917 6448 3.173965 ACATTATATGGGACGGAGGGAG 58.826 50.000 0.00 0.00 33.60 4.30
4918 6449 3.170717 GACATTATATGGGACGGAGGGA 58.829 50.000 0.00 0.00 33.60 4.20
4919 6450 2.903784 TGACATTATATGGGACGGAGGG 59.096 50.000 0.00 0.00 33.60 4.30
4920 6451 4.617253 TTGACATTATATGGGACGGAGG 57.383 45.455 0.00 0.00 33.60 4.30
4921 6452 6.935741 TTTTTGACATTATATGGGACGGAG 57.064 37.500 0.00 0.00 33.60 4.63
4941 6472 6.887545 TCCATCCCATAATGTAAGACGTTTTT 59.112 34.615 0.00 0.00 0.00 1.94
4942 6473 6.419791 TCCATCCCATAATGTAAGACGTTTT 58.580 36.000 0.00 0.00 0.00 2.43
4943 6474 5.996644 TCCATCCCATAATGTAAGACGTTT 58.003 37.500 0.00 0.00 0.00 3.60
4944 6475 5.454755 CCTCCATCCCATAATGTAAGACGTT 60.455 44.000 0.00 0.00 0.00 3.99
4945 6476 4.040461 CCTCCATCCCATAATGTAAGACGT 59.960 45.833 0.00 0.00 0.00 4.34
4946 6477 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
4947 6478 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
4948 6479 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
4949 6480 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
4950 6481 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
4951 6482 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
4952 6483 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
4953 6484 4.171234 AGTACTCCCTCCATCCCATAATG 58.829 47.826 0.00 0.00 0.00 1.90
4954 6485 4.510303 AGTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
4955 6486 3.973973 CAAGTACTCCCTCCATCCCATAA 59.026 47.826 0.00 0.00 0.00 1.90
4956 6487 3.587498 CAAGTACTCCCTCCATCCCATA 58.413 50.000 0.00 0.00 0.00 2.74
4957 6488 2.412591 CAAGTACTCCCTCCATCCCAT 58.587 52.381 0.00 0.00 0.00 4.00
4958 6489 1.879575 CAAGTACTCCCTCCATCCCA 58.120 55.000 0.00 0.00 0.00 4.37
4959 6490 0.470341 GCAAGTACTCCCTCCATCCC 59.530 60.000 0.00 0.00 0.00 3.85
4960 6491 1.204146 TGCAAGTACTCCCTCCATCC 58.796 55.000 0.00 0.00 0.00 3.51
4961 6492 3.209410 CATTGCAAGTACTCCCTCCATC 58.791 50.000 4.94 0.00 0.00 3.51
4962 6493 2.578021 ACATTGCAAGTACTCCCTCCAT 59.422 45.455 4.94 0.00 0.00 3.41
4963 6494 1.985159 ACATTGCAAGTACTCCCTCCA 59.015 47.619 4.94 0.00 0.00 3.86
4964 6495 2.237392 AGACATTGCAAGTACTCCCTCC 59.763 50.000 4.94 0.00 0.00 4.30
4965 6496 3.618690 AGACATTGCAAGTACTCCCTC 57.381 47.619 4.94 0.00 0.00 4.30
4966 6497 4.965532 AGATAGACATTGCAAGTACTCCCT 59.034 41.667 4.94 2.41 0.00 4.20
4967 6498 5.053145 CAGATAGACATTGCAAGTACTCCC 58.947 45.833 4.94 0.00 0.00 4.30
4968 6499 5.907207 TCAGATAGACATTGCAAGTACTCC 58.093 41.667 4.94 0.00 0.00 3.85
4969 6500 7.009999 CAGTTCAGATAGACATTGCAAGTACTC 59.990 40.741 4.94 0.00 0.00 2.59
4970 6501 6.815641 CAGTTCAGATAGACATTGCAAGTACT 59.184 38.462 4.94 6.31 0.00 2.73
4971 6502 6.456181 GCAGTTCAGATAGACATTGCAAGTAC 60.456 42.308 4.94 0.00 0.00 2.73
5021 6636 7.386848 AGCAGACTTTTTCGCTAACAAAGTATA 59.613 33.333 9.55 0.00 40.15 1.47
5066 6681 5.716703 CCACAAGGTCCTCCAGATTTTAAAT 59.283 40.000 0.00 0.00 35.89 1.40
5102 6717 9.315363 TGAAAAGGGGAAATAGCATACTTTTAA 57.685 29.630 0.00 0.00 36.96 1.52
5103 6718 8.887264 TGAAAAGGGGAAATAGCATACTTTTA 57.113 30.769 0.00 0.00 36.96 1.52
5104 6719 7.790782 TGAAAAGGGGAAATAGCATACTTTT 57.209 32.000 0.00 0.00 38.80 2.27
5105 6720 7.978099 ATGAAAAGGGGAAATAGCATACTTT 57.022 32.000 0.00 0.00 0.00 2.66
5106 6721 7.400052 ACAATGAAAAGGGGAAATAGCATACTT 59.600 33.333 0.00 0.00 0.00 2.24
5107 6722 6.897413 ACAATGAAAAGGGGAAATAGCATACT 59.103 34.615 0.00 0.00 0.00 2.12
5108 6723 6.980397 CACAATGAAAAGGGGAAATAGCATAC 59.020 38.462 0.00 0.00 0.00 2.39
5169 6787 4.039488 AGCATGATTTTCTGCAAGTTGGAA 59.961 37.500 4.75 0.00 40.88 3.53
5249 9354 1.000060 GAAATGCAGGCACAAAGCTGA 60.000 47.619 0.00 0.00 44.79 4.26
5261 9366 5.717119 AGTAAAAGATGCCAAGAAATGCAG 58.283 37.500 0.00 0.00 41.46 4.41
5382 9487 6.095580 GCAGGAGAGTATCAATCCATATACGA 59.904 42.308 0.00 0.00 37.82 3.43
5405 9510 7.652909 CACAAAAGAAATTCAGTAAATCTGGCA 59.347 33.333 0.00 0.00 43.76 4.92
5488 9593 4.880886 GCCAAAAGCAATGTGAAAAACT 57.119 36.364 0.00 0.00 42.97 2.66
6116 10242 3.120321 AGAAGCCATTACACGACAACA 57.880 42.857 0.00 0.00 0.00 3.33
6117 10243 3.810373 CAAGAAGCCATTACACGACAAC 58.190 45.455 0.00 0.00 0.00 3.32
6184 10310 3.307762 GCATCCTAGTGTTCCTTTCCACT 60.308 47.826 0.00 0.00 43.90 4.00
6206 10332 9.736023 GCAACTATGGAAACTCTTATAAAATGG 57.264 33.333 0.00 0.00 0.00 3.16
6253 10379 7.768582 TGTATGTCGATTCAAGTGACCAATAAT 59.231 33.333 0.00 0.00 0.00 1.28
6465 10591 4.929146 ACCAAGGTTCCTAGCAACTATT 57.071 40.909 0.00 0.00 0.00 1.73
6685 10814 0.176449 CGTCCAGTGATCAGGCATCA 59.824 55.000 0.00 0.00 39.39 3.07
6686 10815 0.176680 ACGTCCAGTGATCAGGCATC 59.823 55.000 0.00 0.00 0.00 3.91
6699 10853 2.631160 AACATCCACAAGAACGTCCA 57.369 45.000 0.00 0.00 0.00 4.02
6787 10941 4.460263 TGGACATCATGTGCTATAAACCC 58.540 43.478 10.99 0.00 39.59 4.11
6788 10942 6.441274 CATTGGACATCATGTGCTATAAACC 58.559 40.000 10.99 0.00 39.59 3.27
6789 10943 5.916883 GCATTGGACATCATGTGCTATAAAC 59.083 40.000 10.99 0.00 39.59 2.01
6790 10944 5.829391 AGCATTGGACATCATGTGCTATAAA 59.171 36.000 10.99 0.00 42.20 1.40
6855 11009 5.343325 GGTCATGCTTCGAAACATTTCTTTC 59.657 40.000 11.26 0.23 35.07 2.62
6869 11023 5.376625 TCCATACAATTAGGGTCATGCTTC 58.623 41.667 0.00 0.00 30.59 3.86
6875 11029 8.742125 AGAATCTATCCATACAATTAGGGTCA 57.258 34.615 0.00 0.00 30.59 4.02
6903 11057 9.624697 GCAATGACATGTTCTAAATTAGTCAAA 57.375 29.630 0.00 0.00 37.95 2.69
6930 11084 0.254747 TCGCCATCCCCGAAGAAAAT 59.745 50.000 0.00 0.00 0.00 1.82
6938 11092 2.030562 GTACCATCGCCATCCCCG 59.969 66.667 0.00 0.00 0.00 5.73
7029 11188 6.542370 ACCTAATTGATCCCAACGTTTGATAG 59.458 38.462 0.00 0.00 34.72 2.08
7069 11228 8.328758 AGATTATCTATCAGGAACCACAAACAA 58.671 33.333 0.00 0.00 35.59 2.83
7102 11261 7.946381 AGGCATCGAACTATAGAATATCTGA 57.054 36.000 6.78 2.79 0.00 3.27
7103 11262 8.994429 AAAGGCATCGAACTATAGAATATCTG 57.006 34.615 6.78 0.00 0.00 2.90
7109 11365 7.332557 TGGTAAAAAGGCATCGAACTATAGAA 58.667 34.615 6.78 0.00 0.00 2.10
7119 11375 6.361899 CAAACATTTTGGTAAAAAGGCATCG 58.638 36.000 0.00 0.00 39.98 3.84
7145 11401 3.896888 AGTGATGAATTCAAACCCAGCAA 59.103 39.130 13.09 0.00 35.70 3.91
7220 11476 2.187239 TCCAAGCTCATCCTCCTCAT 57.813 50.000 0.00 0.00 0.00 2.90
7234 11490 1.153086 CCCCTCGCATCCTTCCAAG 60.153 63.158 0.00 0.00 0.00 3.61
7239 11495 3.483869 GGCTCCCCTCGCATCCTT 61.484 66.667 0.00 0.00 0.00 3.36
7296 11553 2.061790 GCTCCCCTGATCCATCACCC 62.062 65.000 0.00 0.00 32.50 4.61
7344 11601 3.307480 GGGGACTGATTATATGTTCCCCG 60.307 52.174 7.76 0.00 45.20 5.73
7373 11630 2.352715 GGGAAACAAAGTGTAGCATGCC 60.353 50.000 15.66 0.00 0.00 4.40
7392 11649 1.469308 TGCACGCCGTTATTTTAAGGG 59.531 47.619 0.00 2.41 0.00 3.95
7426 11687 2.678336 GGTTTGATACTCGCAGGAAAGG 59.322 50.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.