Multiple sequence alignment - TraesCS7D01G314900

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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 TraesCS7D01G314900 chr7D 100.000 5648 0 0 1 5648 400870291 400875938 0.000000e+00 10430.0
1 TraesCS7D01G314900 chr7D 89.011 91 8 2 250 339 466897322 466897233 1.660000e-20 111.0
2 TraesCS7D01G314900 chr7D 87.912 91 9 2 250 339 140920272 140920183 7.740000e-19 106.0
3 TraesCS7D01G314900 chr7A 90.664 3963 240 56 268 4192 458759597 458763467 0.000000e+00 5149.0
4 TraesCS7D01G314900 chr7A 95.533 403 16 2 4247 4648 458763495 458763896 1.330000e-180 643.0
5 TraesCS7D01G314900 chr7A 82.816 483 30 16 4660 5091 458764200 458764680 3.190000e-102 383.0
6 TraesCS7D01G314900 chr7A 81.793 368 34 16 5312 5648 458764787 458765152 1.550000e-70 278.0
7 TraesCS7D01G314900 chr7A 86.458 96 11 2 249 343 201987001 201987095 2.780000e-18 104.0
8 TraesCS7D01G314900 chr7B 91.165 3271 161 48 1 3203 409871449 409874659 0.000000e+00 4322.0
9 TraesCS7D01G314900 chr7B 91.491 2327 118 38 3360 5618 409881235 409883549 0.000000e+00 3127.0
10 TraesCS7D01G314900 chr7B 91.586 2282 114 37 3360 5575 409874668 409876937 0.000000e+00 3079.0
11 TraesCS7D01G314900 chr7B 93.595 2092 79 25 1136 3203 409879166 409881226 0.000000e+00 3070.0
12 TraesCS7D01G314900 chr7B 86.458 96 11 2 249 343 155471166 155471260 2.780000e-18 104.0
13 TraesCS7D01G314900 chrUn 92.977 1666 62 25 1562 3203 362837593 362835959 0.000000e+00 2377.0
14 TraesCS7D01G314900 chrUn 94.272 1449 54 15 3363 4785 343320408 343318963 0.000000e+00 2189.0
15 TraesCS7D01G314900 chrUn 94.272 1449 54 15 3363 4785 343342521 343341076 0.000000e+00 2189.0
16 TraesCS7D01G314900 chrUn 97.000 900 26 1 2305 3203 343321319 343320420 0.000000e+00 1511.0
17 TraesCS7D01G314900 chrUn 97.000 900 26 1 2305 3203 343343432 343342533 0.000000e+00 1511.0
18 TraesCS7D01G314900 chrUn 85.133 713 56 23 4947 5618 351743088 351742385 0.000000e+00 684.0
19 TraesCS7D01G314900 chrUn 85.133 713 56 25 4947 5618 397949947 397950650 0.000000e+00 684.0
20 TraesCS7D01G314900 chrUn 98.246 285 5 0 3363 3647 362835947 362835663 3.040000e-137 499.0
21 TraesCS7D01G314900 chr5D 83.217 143 19 4 250 388 265961978 265961837 5.940000e-25 126.0
22 TraesCS7D01G314900 chr5B 87.368 95 10 2 250 343 98663178 98663271 2.150000e-19 108.0
23 TraesCS7D01G314900 chr5A 84.906 106 13 2 239 343 86662009 86662112 2.780000e-18 104.0
24 TraesCS7D01G314900 chr4A 78.947 133 24 3 267 395 601195492 601195360 2.800000e-13 87.9
25 TraesCS7D01G314900 chr2B 95.000 40 2 0 886 925 781214031 781213992 4.720000e-06 63.9


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 TraesCS7D01G314900 chr7D 400870291 400875938 5647 False 10430.00 10430 100.00000 1 5648 1 chr7D.!!$F1 5647
1 TraesCS7D01G314900 chr7A 458759597 458765152 5555 False 1613.25 5149 87.70150 268 5648 4 chr7A.!!$F2 5380
2 TraesCS7D01G314900 chr7B 409871449 409883549 12100 False 3399.50 4322 91.95925 1 5618 4 chr7B.!!$F2 5617
3 TraesCS7D01G314900 chrUn 343318963 343321319 2356 True 1850.00 2189 95.63600 2305 4785 2 chrUn.!!$R2 2480
4 TraesCS7D01G314900 chrUn 343341076 343343432 2356 True 1850.00 2189 95.63600 2305 4785 2 chrUn.!!$R3 2480
5 TraesCS7D01G314900 chrUn 362835663 362837593 1930 True 1438.00 2377 95.61150 1562 3647 2 chrUn.!!$R4 2085
6 TraesCS7D01G314900 chrUn 351742385 351743088 703 True 684.00 684 85.13300 4947 5618 1 chrUn.!!$R1 671
7 TraesCS7D01G314900 chrUn 397949947 397950650 703 False 684.00 684 85.13300 4947 5618 1 chrUn.!!$F1 671

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
580 604 0.038890 TTGGATCCCATTTGCACGGA 59.961 50.000 9.90 0.00 31.53 4.69 F
581 605 0.258484 TGGATCCCATTTGCACGGAT 59.742 50.000 9.90 3.98 39.14 4.18 F
938 995 0.321653 AAAGATCCGCGTCCAAAGCT 60.322 50.000 4.92 0.00 0.00 3.74 F
1928 8567 2.662866 TCTATCGATCAAGGGTCCGTT 58.337 47.619 0.00 0.00 0.00 4.44 F
2714 9374 2.888834 TTTTTCAGCAAGGCCAGAAC 57.111 45.000 5.01 0.00 0.00 3.01 F
4466 11141 0.035739 TACCGGCTTGGAAGGTGTTC 59.964 55.000 0.00 0.00 42.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1621 1.014564 CACCGCCGAGAAAGAGAACC 61.015 60.000 0.0 0.0 0.00 3.62 R
1559 1623 1.374252 GCACCGCCGAGAAAGAGAA 60.374 57.895 0.0 0.0 0.00 2.87 R
2690 9350 0.108662 GGCCTTGCTGAAAAATCGGG 60.109 55.000 0.0 0.0 0.00 5.14 R
3111 9771 0.318107 CCTCAAACGCAAAGCCACAG 60.318 55.000 0.0 0.0 0.00 3.66 R
4621 11297 0.172803 GTCTACAGGATGCGGTCGTT 59.827 55.000 0.0 0.0 42.53 3.85 R
5454 12505 0.104120 CGAAGTCACTCACACCCACA 59.896 55.000 0.0 0.0 0.00 4.17 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
45 46 6.990798 TGCATTTCACAAGGAATCATTAACA 58.009 32.000 0.00 0.00 34.91 2.41
47 48 6.532657 GCATTTCACAAGGAATCATTAACAGG 59.467 38.462 0.00 0.00 34.91 4.00
48 49 5.643379 TTCACAAGGAATCATTAACAGGC 57.357 39.130 0.00 0.00 0.00 4.85
49 50 4.922206 TCACAAGGAATCATTAACAGGCT 58.078 39.130 0.00 0.00 0.00 4.58
51 52 4.096984 CACAAGGAATCATTAACAGGCTCC 59.903 45.833 0.00 0.00 0.00 4.70
55 56 3.633986 GGAATCATTAACAGGCTCCTTGG 59.366 47.826 0.00 0.00 0.00 3.61
57 58 4.591321 ATCATTAACAGGCTCCTTGGAA 57.409 40.909 0.00 0.00 0.00 3.53
58 59 3.686016 TCATTAACAGGCTCCTTGGAAC 58.314 45.455 0.00 0.00 0.00 3.62
59 60 3.330701 TCATTAACAGGCTCCTTGGAACT 59.669 43.478 0.00 0.00 0.00 3.01
60 61 3.418684 TTAACAGGCTCCTTGGAACTC 57.581 47.619 0.00 0.00 0.00 3.01
70 71 4.518970 GCTCCTTGGAACTCAAATACACAA 59.481 41.667 0.00 0.00 34.56 3.33
83 84 5.183713 TCAAATACACAAATCAAGGAGGCTG 59.816 40.000 0.00 0.00 0.00 4.85
90 91 6.041979 ACACAAATCAAGGAGGCTGTAATTTT 59.958 34.615 0.00 0.00 0.00 1.82
122 124 8.423349 ACAATGTTCTGAATTCCAAATTTGAGA 58.577 29.630 19.86 11.82 0.00 3.27
129 131 9.519191 TCTGAATTCCAAATTTGAGATGTCTTA 57.481 29.630 19.86 0.32 0.00 2.10
148 150 6.069905 TGTCTTAGCCATTGGTACCTTATCAA 60.070 38.462 14.36 0.00 32.57 2.57
150 152 7.502561 GTCTTAGCCATTGGTACCTTATCAAAT 59.497 37.037 14.36 0.00 31.65 2.32
152 154 4.821805 AGCCATTGGTACCTTATCAAATCG 59.178 41.667 14.36 0.00 31.65 3.34
162 164 6.064846 ACCTTATCAAATCGCATTGATCAC 57.935 37.500 15.77 0.00 44.64 3.06
164 166 5.008911 CCTTATCAAATCGCATTGATCACCA 59.991 40.000 15.77 0.68 44.64 4.17
168 170 6.448207 TCAAATCGCATTGATCACCATTTA 57.552 33.333 0.00 0.00 35.84 1.40
169 171 6.861144 TCAAATCGCATTGATCACCATTTAA 58.139 32.000 0.00 0.00 35.84 1.52
213 220 2.290641 CTCGTCCACCCAAACTCAAAAG 59.709 50.000 0.00 0.00 0.00 2.27
220 227 5.534654 TCCACCCAAACTCAAAAGATAACAG 59.465 40.000 0.00 0.00 0.00 3.16
236 244 8.627208 AAGATAACAGATGCCCATTATACTTG 57.373 34.615 0.00 0.00 0.00 3.16
237 245 7.977818 AGATAACAGATGCCCATTATACTTGA 58.022 34.615 0.00 0.00 0.00 3.02
238 246 8.439971 AGATAACAGATGCCCATTATACTTGAA 58.560 33.333 0.00 0.00 0.00 2.69
239 247 6.949352 AACAGATGCCCATTATACTTGAAG 57.051 37.500 0.00 0.00 0.00 3.02
240 248 5.380043 ACAGATGCCCATTATACTTGAAGG 58.620 41.667 0.00 0.00 0.00 3.46
241 249 5.132648 ACAGATGCCCATTATACTTGAAGGA 59.867 40.000 0.00 0.00 0.00 3.36
242 250 6.064060 CAGATGCCCATTATACTTGAAGGAA 58.936 40.000 0.00 0.00 0.00 3.36
247 255 6.495181 TGCCCATTATACTTGAAGGAAAACAA 59.505 34.615 0.00 0.00 0.00 2.83
258 266 4.338118 TGAAGGAAAACAAGTACTGCCTTG 59.662 41.667 0.00 6.22 45.83 3.61
264 272 3.508845 ACAAGTACTGCCTTGGTTCAT 57.491 42.857 0.00 0.00 44.89 2.57
298 306 4.874966 TGTTCTAACTTTTTCCGAAACCGA 59.125 37.500 0.00 0.00 0.00 4.69
334 342 6.533367 ACGCATTTTAGTGTGTTTGTTCATTT 59.467 30.769 0.00 0.00 39.65 2.32
396 419 3.504375 ACGGAGGGAGTACAAGTTAAGT 58.496 45.455 0.00 0.00 0.00 2.24
403 426 8.727910 GGAGGGAGTACAAGTTAAGTTAAATTG 58.272 37.037 26.15 26.15 45.95 2.32
549 573 3.614616 AGAAGCGTCTAGAAGCGAAAATG 59.385 43.478 22.34 0.00 40.72 2.32
554 578 2.352960 GTCTAGAAGCGAAAATGCCCAG 59.647 50.000 0.00 0.00 34.65 4.45
565 589 0.911769 AATGCCCAGTCGATCTTGGA 59.088 50.000 13.30 0.00 31.33 3.53
578 602 1.462616 TCTTGGATCCCATTTGCACG 58.537 50.000 9.90 0.00 31.53 5.34
579 603 0.457035 CTTGGATCCCATTTGCACGG 59.543 55.000 9.90 0.00 31.53 4.94
580 604 0.038890 TTGGATCCCATTTGCACGGA 59.961 50.000 9.90 0.00 31.53 4.69
581 605 0.258484 TGGATCCCATTTGCACGGAT 59.742 50.000 9.90 3.98 39.14 4.18
582 606 1.341877 TGGATCCCATTTGCACGGATT 60.342 47.619 9.90 0.00 36.51 3.01
583 607 1.067516 GGATCCCATTTGCACGGATTG 59.932 52.381 0.00 0.00 36.51 2.67
596 620 0.664761 CGGATTGCGCCTGATTTGAT 59.335 50.000 4.18 0.00 0.00 2.57
606 630 8.969121 TTGCGCCTGATTTGATAATAATAATG 57.031 30.769 4.18 0.00 0.00 1.90
687 722 5.681543 CGTGTAAAAAGTTTCTTGAAGGAGC 59.318 40.000 0.00 0.00 0.00 4.70
707 742 1.000607 CGACTTTCGTGGACTCTTGGA 60.001 52.381 0.00 0.00 34.72 3.53
821 858 6.917217 TTCATTCCTTCGCAAAAACATTTT 57.083 29.167 0.00 0.00 0.00 1.82
904 941 2.095466 TGTTTTTCGATTCGGGTGCATC 60.095 45.455 6.18 0.00 0.00 3.91
905 942 0.724549 TTTTCGATTCGGGTGCATCG 59.275 50.000 6.18 6.14 41.68 3.84
906 943 1.087202 TTTCGATTCGGGTGCATCGG 61.087 55.000 6.18 5.41 40.87 4.18
907 944 3.640000 CGATTCGGGTGCATCGGC 61.640 66.667 11.50 0.00 37.55 5.54
938 995 0.321653 AAAGATCCGCGTCCAAAGCT 60.322 50.000 4.92 0.00 0.00 3.74
1644 1709 7.534085 TCATTAGTTTACATCGAATGGTGAC 57.466 36.000 0.00 0.00 31.95 3.67
1690 1755 3.049708 TCATAGCCTGCATATGTGAGC 57.950 47.619 4.29 4.85 33.29 4.26
1799 1871 6.323225 GGTAGGTGCCTGTTTATAGAACTCTA 59.677 42.308 0.12 0.00 0.00 2.43
1806 1878 8.421784 TGCCTGTTTATAGAACTCTATTTCGAT 58.578 33.333 4.61 0.00 39.66 3.59
1847 1919 8.030106 GCTGTTTTGTTCAGTAGAGTAGAGTAT 58.970 37.037 0.00 0.00 35.60 2.12
1848 1920 9.915629 CTGTTTTGTTCAGTAGAGTAGAGTATT 57.084 33.333 0.00 0.00 0.00 1.89
1926 8565 3.181479 TGTTTCTATCGATCAAGGGTCCG 60.181 47.826 0.00 0.00 0.00 4.79
1928 8567 2.662866 TCTATCGATCAAGGGTCCGTT 58.337 47.619 0.00 0.00 0.00 4.44
2057 8698 7.284716 GCCCCTTTAGCACTATATTTGTTACTT 59.715 37.037 0.00 0.00 0.00 2.24
2226 8875 7.758495 AGTGTTTCTTTAAGCCGGTATAATTG 58.242 34.615 1.90 0.23 0.00 2.32
2240 8889 8.780249 GCCGGTATAATTGATTGTTTGTATAGT 58.220 33.333 1.90 0.00 0.00 2.12
2249 8898 9.959721 ATTGATTGTTTGTATAGTGTACCTCTT 57.040 29.630 0.00 0.00 0.00 2.85
2250 8899 9.787435 TTGATTGTTTGTATAGTGTACCTCTTT 57.213 29.630 0.00 0.00 0.00 2.52
2358 9017 6.266131 TCAGGCCCATTAGATAACTTGATT 57.734 37.500 0.00 0.00 0.00 2.57
2364 9023 7.503902 GGCCCATTAGATAACTTGATTCTTCTT 59.496 37.037 0.00 0.00 0.00 2.52
2385 9044 9.401058 CTTCTTTCTCCCTATTGATATTGTGTT 57.599 33.333 0.00 0.00 0.00 3.32
2575 9234 3.065095 GCTCTTGCATCCTCAATGTTCTC 59.935 47.826 0.00 0.00 37.71 2.87
2631 9290 5.906113 TGAGAAGGTTTGTGTTTGCTTAA 57.094 34.783 0.00 0.00 0.00 1.85
2661 9320 5.012239 TCTGTTGCTATTTCTGCCTTCATT 58.988 37.500 0.00 0.00 0.00 2.57
2672 9332 3.010027 TCTGCCTTCATTAATGGTGTCCA 59.990 43.478 15.36 6.19 38.19 4.02
2681 9341 9.927668 CTTCATTAATGGTGTCCAAGTTTTAAT 57.072 29.630 15.36 0.00 36.95 1.40
2690 9350 9.921637 TGGTGTCCAAGTTTTAATCATTTTATC 57.078 29.630 0.00 0.00 0.00 1.75
2695 9355 9.196139 TCCAAGTTTTAATCATTTTATCCCGAT 57.804 29.630 0.00 0.00 0.00 4.18
2714 9374 2.888834 TTTTTCAGCAAGGCCAGAAC 57.111 45.000 5.01 0.00 0.00 3.01
2756 9416 3.626670 CCTTCTGGCTGATGACATTCTTC 59.373 47.826 8.55 0.00 0.00 2.87
3018 9678 8.746922 TTTTGTCATGCTTTCTGTATCATTTC 57.253 30.769 0.00 0.00 0.00 2.17
3027 9687 9.230122 TGCTTTCTGTATCATTTCTGTTAATGA 57.770 29.630 0.00 0.00 45.64 2.57
3111 9771 5.066505 GGTATGAAATGTCCTGTCATTGTCC 59.933 44.000 0.00 0.00 37.96 4.02
3112 9772 4.371624 TGAAATGTCCTGTCATTGTCCT 57.628 40.909 0.00 0.00 37.96 3.85
3145 9805 5.503194 GCGTTTGAGGCTATTGAGATTTCTC 60.503 44.000 0.46 0.46 43.15 2.87
3150 9810 8.899427 TTGAGGCTATTGAGATTTCTCTATTG 57.101 34.615 9.28 8.75 43.25 1.90
3251 9911 6.849502 AGCAGTTGTGAATTTATGATGTGAG 58.150 36.000 0.00 0.00 0.00 3.51
3271 9931 5.005682 GTGAGCAATGGAACTTTTGTTGTTC 59.994 40.000 0.00 0.00 43.66 3.18
3278 9938 4.207955 GGAACTTTTGTTGTTCTCCTCCT 58.792 43.478 0.00 0.00 43.66 3.69
3283 9943 3.753294 TTGTTGTTCTCCTCCTGAGTC 57.247 47.619 0.00 0.00 42.12 3.36
3285 9945 2.630098 TGTTGTTCTCCTCCTGAGTCTG 59.370 50.000 0.00 0.00 42.12 3.51
3290 9950 1.958902 CTCCTCCTGAGTCTGCAGCC 61.959 65.000 9.47 0.00 36.27 4.85
3309 9969 5.517770 GCAGCCAATTGTGAACTAATGAATC 59.482 40.000 4.43 0.00 0.00 2.52
3310 9970 6.623486 CAGCCAATTGTGAACTAATGAATCA 58.377 36.000 4.43 0.00 0.00 2.57
3318 9978 9.696917 ATTGTGAACTAATGAATCAAAAACTCC 57.303 29.630 0.00 0.00 0.00 3.85
3319 9979 8.463930 TGTGAACTAATGAATCAAAAACTCCT 57.536 30.769 0.00 0.00 0.00 3.69
3320 9980 8.912988 TGTGAACTAATGAATCAAAAACTCCTT 58.087 29.630 0.00 0.00 0.00 3.36
3321 9981 9.399403 GTGAACTAATGAATCAAAAACTCCTTC 57.601 33.333 0.00 0.00 0.00 3.46
3322 9982 9.354673 TGAACTAATGAATCAAAAACTCCTTCT 57.645 29.630 0.00 0.00 0.00 2.85
3323 9983 9.617975 GAACTAATGAATCAAAAACTCCTTCTG 57.382 33.333 0.00 0.00 0.00 3.02
3324 9984 8.697507 ACTAATGAATCAAAAACTCCTTCTGT 57.302 30.769 0.00 0.00 0.00 3.41
3325 9985 9.136323 ACTAATGAATCAAAAACTCCTTCTGTT 57.864 29.630 0.00 0.00 0.00 3.16
3343 10003 8.696374 CCTTCTGTTAACACCTCTTATCATCTA 58.304 37.037 3.59 0.00 0.00 1.98
3356 10016 8.203485 CCTCTTATCATCTAGTCAAGCTTCTTT 58.797 37.037 0.00 0.00 0.00 2.52
3574 10234 5.246981 TGATCAGGGTTTGATTGAAGACT 57.753 39.130 0.00 0.00 46.51 3.24
3862 10522 6.695278 GCATAAACAGTTTAAAGCTTGTGTCA 59.305 34.615 19.24 0.00 31.55 3.58
3958 10618 4.011698 TCCGTGGGCTTTATTTTACCTTC 58.988 43.478 0.00 0.00 0.00 3.46
3997 10657 4.536765 ACAATGTAAGGGGAATGATGTCC 58.463 43.478 0.00 0.00 36.90 4.02
4050 10721 5.551760 AGTTCAAGTTGAAGTCACTTGTG 57.448 39.130 18.56 0.00 35.22 3.33
4104 10775 2.795329 AGGTACCTGCCAAATGAACTG 58.205 47.619 15.42 0.00 0.00 3.16
4197 10870 9.498176 GTAACTCTCTTGGTGGTAAATCTTTTA 57.502 33.333 0.00 0.00 0.00 1.52
4238 10913 4.939439 GGAACTCTTGGCGGTAAAATCTTA 59.061 41.667 0.00 0.00 0.00 2.10
4252 10927 6.473455 GGTAAAATCTTAATGTGCAGCATGTC 59.527 38.462 0.00 0.00 39.31 3.06
4362 11037 0.825010 CCTGTGGCCTTTTGTCTGCT 60.825 55.000 3.32 0.00 0.00 4.24
4466 11141 0.035739 TACCGGCTTGGAAGGTGTTC 59.964 55.000 0.00 0.00 42.00 3.18
4485 11160 4.520111 TGTTCTGTTTGTAGCATGCTCATT 59.480 37.500 26.57 2.21 0.00 2.57
4506 11181 1.314730 TTTCCTCGGCTTTTGACCAC 58.685 50.000 0.00 0.00 0.00 4.16
4514 11189 1.177401 GCTTTTGACCACTGGATCCC 58.823 55.000 9.90 0.00 0.00 3.85
4515 11190 1.272147 GCTTTTGACCACTGGATCCCT 60.272 52.381 9.90 0.00 0.00 4.20
4596 11272 8.730680 GGTGTATGATATGTTTTCTCTGTGTTT 58.269 33.333 0.00 0.00 0.00 2.83
4621 11297 5.749596 AAGACACATTGTTCAAATCGACA 57.250 34.783 0.00 0.00 0.00 4.35
4622 11298 5.749596 AGACACATTGTTCAAATCGACAA 57.250 34.783 0.00 0.00 39.78 3.18
4688 11656 9.146984 CGTTTTTGTACTAGAACATATCCTTGA 57.853 33.333 10.42 0.00 0.00 3.02
4724 11692 5.002516 CCACTGCAAATCTTTCTTCTCTCT 58.997 41.667 0.00 0.00 0.00 3.10
4737 11717 9.495572 TCTTTCTTCTCTCTTAATCTTTTCACC 57.504 33.333 0.00 0.00 0.00 4.02
4838 11819 8.347771 AGAACCTTTAACCTTTGTTTATCGTTC 58.652 33.333 0.00 0.00 35.87 3.95
4840 11821 6.482973 ACCTTTAACCTTTGTTTATCGTTCGA 59.517 34.615 0.00 0.00 35.87 3.71
4844 11825 6.404712 AACCTTTGTTTATCGTTCGAGATC 57.595 37.500 0.80 0.00 32.39 2.75
4846 11827 4.561606 CCTTTGTTTATCGTTCGAGATCGT 59.438 41.667 1.70 0.00 40.80 3.73
4968 11970 2.715749 TCACCCGTATCTTCTCCGTA 57.284 50.000 0.00 0.00 0.00 4.02
5010 12018 4.619227 CGTGTGTTCCCAGCCGGT 62.619 66.667 1.90 0.00 0.00 5.28
5023 12031 1.884926 GCCGGTAGCTGCAGTCATC 60.885 63.158 16.64 2.61 38.99 2.92
5043 12061 8.515414 AGTCATCTTAACCTTTGCAAATAAGTC 58.485 33.333 21.72 14.36 0.00 3.01
5091 12117 2.030562 CGTGCCAGACGGAACCTT 59.969 61.111 0.00 0.00 44.85 3.50
5093 12119 1.012486 CGTGCCAGACGGAACCTTAC 61.012 60.000 0.00 0.00 44.85 2.34
5094 12120 0.320697 GTGCCAGACGGAACCTTACT 59.679 55.000 0.00 0.00 34.16 2.24
5129 12159 6.350103 TCATATATACAAGCGGGAACAAACA 58.650 36.000 0.00 0.00 0.00 2.83
5130 12160 6.824196 TCATATATACAAGCGGGAACAAACAA 59.176 34.615 0.00 0.00 0.00 2.83
5131 12161 5.968528 ATATACAAGCGGGAACAAACAAA 57.031 34.783 0.00 0.00 0.00 2.83
5147 12177 4.365899 AACAAACTTTTCGGAGAACACC 57.634 40.909 0.00 0.00 45.90 4.16
5159 12189 2.925170 AACACCCGCTGGAGCTCT 60.925 61.111 14.64 0.00 39.32 4.09
5177 12207 1.840630 CTGCGTCGTGCCATCAACAA 61.841 55.000 0.00 0.00 45.60 2.83
5225 12255 0.112412 GGAAGCCAAGGAACAGGGAA 59.888 55.000 0.00 0.00 0.00 3.97
5270 12300 1.953559 ACTGTGCAGTGACGAACAAT 58.046 45.000 3.80 0.00 40.75 2.71
5279 12309 1.195900 GTGACGAACAATTAAGCGCCA 59.804 47.619 2.29 0.00 0.00 5.69
5280 12310 2.080693 TGACGAACAATTAAGCGCCAT 58.919 42.857 2.29 0.00 0.00 4.40
5281 12311 2.159585 TGACGAACAATTAAGCGCCATG 60.160 45.455 2.29 0.00 0.00 3.66
5282 12312 1.191096 CGAACAATTAAGCGCCATGC 58.809 50.000 2.29 0.00 46.98 4.06
5294 12342 1.507630 GCCATGCATTCTGTTCGCA 59.492 52.632 0.00 0.00 40.50 5.10
5306 12354 0.938008 TGTTCGCACACGCAATTACA 59.062 45.000 0.00 0.00 39.84 2.41
5332 12380 2.070654 CTTTTCCGGTTGTGCGGCTT 62.071 55.000 0.00 0.00 0.00 4.35
5377 12425 2.032634 GTGCACTCGATCGGCCAAA 61.033 57.895 16.41 0.00 0.00 3.28
5380 12428 2.813908 ACTCGATCGGCCAAACGC 60.814 61.111 16.41 0.00 0.00 4.84
5388 12436 2.413765 GGCCAAACGCGTTTTCCA 59.586 55.556 33.05 0.00 38.94 3.53
5390 12438 0.241481 GGCCAAACGCGTTTTCCATA 59.759 50.000 33.05 0.00 38.94 2.74
5402 12450 2.752903 GTTTTCCATACGGCACAGGATT 59.247 45.455 0.00 0.00 0.00 3.01
5433 12484 2.654404 GCGTACGGATCGAGGTGC 60.654 66.667 18.39 0.00 0.00 5.01
5454 12505 1.214367 GACGGTCAATGTCAACGTGT 58.786 50.000 2.62 0.00 37.96 4.49
5455 12506 0.934496 ACGGTCAATGTCAACGTGTG 59.066 50.000 0.00 0.00 36.32 3.82
5456 12507 0.934496 CGGTCAATGTCAACGTGTGT 59.066 50.000 0.00 0.00 0.00 3.72
5457 12508 1.332816 CGGTCAATGTCAACGTGTGTG 60.333 52.381 0.00 0.00 0.00 3.82
5458 12509 1.002900 GGTCAATGTCAACGTGTGTGG 60.003 52.381 0.00 0.00 0.00 4.17
5459 12510 1.002900 GTCAATGTCAACGTGTGTGGG 60.003 52.381 0.00 0.00 0.00 4.61
5460 12511 1.021202 CAATGTCAACGTGTGTGGGT 58.979 50.000 0.00 0.00 0.00 4.51
5461 12512 1.021202 AATGTCAACGTGTGTGGGTG 58.979 50.000 0.00 0.00 0.00 4.61
5462 12513 0.107410 ATGTCAACGTGTGTGGGTGT 60.107 50.000 0.00 0.00 0.00 4.16
5488 12539 3.259876 TGACTTCGGGCTTAAGCTTTCTA 59.740 43.478 25.88 8.23 41.70 2.10
5490 12541 2.981859 TCGGGCTTAAGCTTTCTAGG 57.018 50.000 25.88 8.55 41.70 3.02
5491 12542 1.485066 TCGGGCTTAAGCTTTCTAGGG 59.515 52.381 25.88 7.61 41.70 3.53
5495 12562 2.881513 GGCTTAAGCTTTCTAGGGCATC 59.118 50.000 25.88 1.75 41.70 3.91
5499 12566 1.781786 AGCTTTCTAGGGCATCGAGA 58.218 50.000 0.00 0.00 0.00 4.04
5523 12592 1.071987 TGAGCTGAACCTGCTGTGG 59.928 57.895 0.00 0.00 38.70 4.17
5530 12599 2.965716 GAACCTGCTGTGGTGCCACT 62.966 60.000 20.46 0.19 46.30 4.00
5533 12602 4.624364 TGCTGTGGTGCCACTCCG 62.624 66.667 20.46 10.95 46.30 4.63
5576 12645 2.341101 GCGGAGTGAAGAGGACGGA 61.341 63.158 0.00 0.00 0.00 4.69
5610 12698 0.762418 TTGTCGCTTCTTCCCTTCCA 59.238 50.000 0.00 0.00 0.00 3.53
5628 12716 1.466167 CCAAAGTCGATCTGTTGCAGG 59.534 52.381 0.00 0.00 31.51 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.330701 TGTATTTGAGTTCCAAGGAGCCT 59.669 43.478 0.00 0.00 35.94 4.58
47 48 4.072131 TGTGTATTTGAGTTCCAAGGAGC 58.928 43.478 0.00 0.00 35.94 4.70
48 49 6.633500 TTTGTGTATTTGAGTTCCAAGGAG 57.367 37.500 0.00 0.00 35.94 3.69
49 50 6.775142 TGATTTGTGTATTTGAGTTCCAAGGA 59.225 34.615 0.00 0.00 35.94 3.36
51 52 7.596248 CCTTGATTTGTGTATTTGAGTTCCAAG 59.404 37.037 0.00 0.00 35.94 3.61
55 56 7.308435 CCTCCTTGATTTGTGTATTTGAGTTC 58.692 38.462 0.00 0.00 0.00 3.01
57 58 5.183904 GCCTCCTTGATTTGTGTATTTGAGT 59.816 40.000 0.00 0.00 0.00 3.41
58 59 5.416952 AGCCTCCTTGATTTGTGTATTTGAG 59.583 40.000 0.00 0.00 0.00 3.02
59 60 5.183713 CAGCCTCCTTGATTTGTGTATTTGA 59.816 40.000 0.00 0.00 0.00 2.69
60 61 5.047802 ACAGCCTCCTTGATTTGTGTATTTG 60.048 40.000 0.00 0.00 0.00 2.32
96 97 8.423349 TCTCAAATTTGGAATTCAGAACATTGT 58.577 29.630 17.90 0.00 0.00 2.71
103 104 8.413309 AAGACATCTCAAATTTGGAATTCAGA 57.587 30.769 17.90 12.04 0.00 3.27
104 105 9.784680 CTAAGACATCTCAAATTTGGAATTCAG 57.215 33.333 17.90 7.11 0.00 3.02
106 107 7.704047 GGCTAAGACATCTCAAATTTGGAATTC 59.296 37.037 17.90 12.93 0.00 2.17
107 108 7.178983 TGGCTAAGACATCTCAAATTTGGAATT 59.821 33.333 17.90 10.07 0.00 2.17
122 124 4.862641 AAGGTACCAATGGCTAAGACAT 57.137 40.909 15.94 0.00 29.26 3.06
129 131 4.821805 CGATTTGATAAGGTACCAATGGCT 59.178 41.667 15.94 0.00 0.00 4.75
169 171 6.400568 AGGTTGATGATCAATGCGAATTTTT 58.599 32.000 11.46 0.00 38.79 1.94
174 176 2.609002 CGAGGTTGATGATCAATGCGAA 59.391 45.455 11.46 0.00 38.79 4.70
175 177 2.204237 CGAGGTTGATGATCAATGCGA 58.796 47.619 11.46 0.00 38.79 5.10
213 220 8.621532 TTCAAGTATAATGGGCATCTGTTATC 57.378 34.615 0.00 0.00 0.00 1.75
220 227 6.959639 TTTCCTTCAAGTATAATGGGCATC 57.040 37.500 0.00 0.00 0.00 3.91
236 244 4.261614 CCAAGGCAGTACTTGTTTTCCTTC 60.262 45.833 0.00 0.00 44.89 3.46
237 245 3.636764 CCAAGGCAGTACTTGTTTTCCTT 59.363 43.478 0.00 0.00 44.89 3.36
238 246 3.222603 CCAAGGCAGTACTTGTTTTCCT 58.777 45.455 0.00 0.00 44.89 3.36
239 247 2.956333 ACCAAGGCAGTACTTGTTTTCC 59.044 45.455 0.00 0.00 44.89 3.13
240 248 4.097286 TGAACCAAGGCAGTACTTGTTTTC 59.903 41.667 0.00 7.54 44.89 2.29
241 249 4.020543 TGAACCAAGGCAGTACTTGTTTT 58.979 39.130 0.00 0.00 44.89 2.43
242 250 3.626930 TGAACCAAGGCAGTACTTGTTT 58.373 40.909 0.00 0.00 44.89 2.83
247 255 9.561069 CTTATAATAATGAACCAAGGCAGTACT 57.439 33.333 0.00 0.00 0.00 2.73
290 298 4.913345 TGCGTCTATATACATTCGGTTTCG 59.087 41.667 0.00 0.00 37.82 3.46
298 306 9.542462 ACACACTAAAATGCGTCTATATACATT 57.458 29.630 0.00 0.00 34.30 2.71
357 379 6.017934 CCCTCCGTTCATTGTTATAAGATGTG 60.018 42.308 8.04 0.82 0.00 3.21
371 393 2.537143 ACTTGTACTCCCTCCGTTCAT 58.463 47.619 0.00 0.00 0.00 2.57
432 456 5.664294 ACTAATTCATGCCAAATTGCTGA 57.336 34.783 2.04 0.00 0.00 4.26
481 505 9.421399 CTTTTCTGGGTCCCTAATTTGTAATAT 57.579 33.333 10.00 0.00 0.00 1.28
526 550 3.299340 TTTCGCTTCTAGACGCTTCTT 57.701 42.857 18.01 0.00 32.75 2.52
533 557 2.352960 CTGGGCATTTTCGCTTCTAGAC 59.647 50.000 0.00 0.00 0.00 2.59
536 560 2.356135 GACTGGGCATTTTCGCTTCTA 58.644 47.619 0.00 0.00 0.00 2.10
549 573 0.250081 GGATCCAAGATCGACTGGGC 60.250 60.000 6.95 3.74 39.51 5.36
554 578 2.291741 GCAAATGGGATCCAAGATCGAC 59.708 50.000 15.23 0.00 36.95 4.20
578 602 3.988379 TTATCAAATCAGGCGCAATCC 57.012 42.857 10.83 0.00 0.00 3.01
579 603 9.793252 ATTATTATTATCAAATCAGGCGCAATC 57.207 29.630 10.83 0.00 0.00 2.67
580 604 9.577110 CATTATTATTATCAAATCAGGCGCAAT 57.423 29.630 10.83 0.00 0.00 3.56
581 605 8.575589 ACATTATTATTATCAAATCAGGCGCAA 58.424 29.630 10.83 0.00 0.00 4.85
582 606 8.109705 ACATTATTATTATCAAATCAGGCGCA 57.890 30.769 10.83 0.00 0.00 6.09
583 607 9.708222 CTACATTATTATTATCAAATCAGGCGC 57.292 33.333 0.00 0.00 0.00 6.53
775 812 7.884877 TGAATTCCATGGTATTCTAGGCAATAG 59.115 37.037 31.99 0.00 34.44 1.73
777 814 6.613699 TGAATTCCATGGTATTCTAGGCAAT 58.386 36.000 31.99 12.32 34.44 3.56
884 921 2.515912 GATGCACCCGAATCGAAAAAC 58.484 47.619 3.36 0.00 0.00 2.43
905 942 2.198304 ATCTTTGGGTCTCGGGTGCC 62.198 60.000 0.00 0.00 0.00 5.01
906 943 0.744771 GATCTTTGGGTCTCGGGTGC 60.745 60.000 0.00 0.00 0.00 5.01
907 944 0.107654 GGATCTTTGGGTCTCGGGTG 60.108 60.000 0.00 0.00 0.00 4.61
908 945 1.614241 CGGATCTTTGGGTCTCGGGT 61.614 60.000 0.00 0.00 0.00 5.28
909 946 1.144057 CGGATCTTTGGGTCTCGGG 59.856 63.158 0.00 0.00 0.00 5.14
938 995 6.303839 GCTCTTTGGGGTAATGGTAATATGA 58.696 40.000 0.00 0.00 0.00 2.15
1056 1114 2.594592 GGCACGCTGGTTTCTGGT 60.595 61.111 0.00 0.00 0.00 4.00
1145 1207 1.951130 CATCAGCGGGATCGTTCGG 60.951 63.158 4.41 0.00 38.89 4.30
1473 1537 2.058595 ATCCTCCCCGAACACCGAG 61.059 63.158 0.00 0.00 41.76 4.63
1557 1621 1.014564 CACCGCCGAGAAAGAGAACC 61.015 60.000 0.00 0.00 0.00 3.62
1559 1623 1.374252 GCACCGCCGAGAAAGAGAA 60.374 57.895 0.00 0.00 0.00 2.87
1560 1624 1.888436 ATGCACCGCCGAGAAAGAGA 61.888 55.000 0.00 0.00 0.00 3.10
1690 1755 3.544684 TCTGGGTTGCAATGCTATACAG 58.455 45.455 6.82 11.30 0.00 2.74
1707 1772 2.620251 TGTGGTTGAGACTGTTCTGG 57.380 50.000 0.00 0.00 29.47 3.86
1799 1871 9.553064 ACAGCATAGAATTTCTAGAATCGAAAT 57.447 29.630 5.89 0.00 41.46 2.17
1866 1938 9.647918 TGGAATCAGTCAGTCTAATACTCTAAT 57.352 33.333 0.00 0.00 35.76 1.73
1867 1939 9.647918 ATGGAATCAGTCAGTCTAATACTCTAA 57.352 33.333 0.00 0.00 35.76 2.10
1869 1941 9.821240 ATATGGAATCAGTCAGTCTAATACTCT 57.179 33.333 0.00 0.00 35.76 3.24
2022 8661 1.444917 GCTAAAGGGGCGTGCATACC 61.445 60.000 0.00 0.00 0.00 2.73
2057 8698 7.937700 AGAACATCTTAAGGGAGAATGGATA 57.062 36.000 1.85 0.00 0.00 2.59
2133 8782 9.521503 CTCTCTGTATTATCAAAATTCTCACGA 57.478 33.333 0.00 0.00 0.00 4.35
2214 8863 8.780249 ACTATACAAACAATCAATTATACCGGC 58.220 33.333 0.00 0.00 0.00 6.13
2226 8875 9.216117 ACAAAGAGGTACACTATACAAACAATC 57.784 33.333 0.00 0.00 0.00 2.67
2240 8889 8.598916 TGGAACAGAAATATACAAAGAGGTACA 58.401 33.333 0.00 0.00 0.00 2.90
2358 9017 8.772250 ACACAATATCAATAGGGAGAAAGAAGA 58.228 33.333 0.00 0.00 0.00 2.87
2364 9023 9.104965 CGTTTAACACAATATCAATAGGGAGAA 57.895 33.333 0.00 0.00 0.00 2.87
2575 9234 5.242393 ACAATCCATGTCTCAAAACAGAAGG 59.758 40.000 0.00 0.00 37.96 3.46
2681 9341 6.522625 TGCTGAAAAATCGGGATAAAATGA 57.477 33.333 0.00 0.00 0.00 2.57
2690 9350 0.108662 GGCCTTGCTGAAAAATCGGG 60.109 55.000 0.00 0.00 0.00 5.14
2695 9355 1.412343 GGTTCTGGCCTTGCTGAAAAA 59.588 47.619 3.32 0.00 0.00 1.94
2714 9374 3.941483 AGGTATCAAACAGCGAATCTTGG 59.059 43.478 0.00 0.00 0.00 3.61
2756 9416 5.590259 ACTTCCAACAAGGGATATTGATTCG 59.410 40.000 0.00 0.00 36.67 3.34
3111 9771 0.318107 CCTCAAACGCAAAGCCACAG 60.318 55.000 0.00 0.00 0.00 3.66
3112 9772 1.732917 CCTCAAACGCAAAGCCACA 59.267 52.632 0.00 0.00 0.00 4.17
3251 9911 4.507756 GGAGAACAACAAAAGTTCCATTGC 59.492 41.667 0.00 0.00 44.91 3.56
3278 9938 1.202794 TCACAATTGGCTGCAGACTCA 60.203 47.619 22.80 7.93 0.00 3.41
3283 9943 3.921119 TTAGTTCACAATTGGCTGCAG 57.079 42.857 10.11 10.11 0.00 4.41
3285 9945 4.439305 TCATTAGTTCACAATTGGCTGC 57.561 40.909 10.83 0.00 0.00 5.25
3309 9969 6.318900 AGAGGTGTTAACAGAAGGAGTTTTTG 59.681 38.462 8.98 0.00 0.00 2.44
3310 9970 6.424032 AGAGGTGTTAACAGAAGGAGTTTTT 58.576 36.000 8.98 0.00 0.00 1.94
3317 9977 7.560368 AGATGATAAGAGGTGTTAACAGAAGG 58.440 38.462 8.98 0.00 0.00 3.46
3318 9978 9.743057 CTAGATGATAAGAGGTGTTAACAGAAG 57.257 37.037 8.98 0.00 0.00 2.85
3319 9979 9.256228 ACTAGATGATAAGAGGTGTTAACAGAA 57.744 33.333 8.98 0.00 0.00 3.02
3320 9980 8.824756 ACTAGATGATAAGAGGTGTTAACAGA 57.175 34.615 8.98 0.00 0.00 3.41
3321 9981 8.687242 TGACTAGATGATAAGAGGTGTTAACAG 58.313 37.037 8.98 0.00 0.00 3.16
3322 9982 8.589701 TGACTAGATGATAAGAGGTGTTAACA 57.410 34.615 3.59 3.59 0.00 2.41
3323 9983 9.522804 CTTGACTAGATGATAAGAGGTGTTAAC 57.477 37.037 0.00 0.00 0.00 2.01
3324 9984 8.198109 GCTTGACTAGATGATAAGAGGTGTTAA 58.802 37.037 0.00 0.00 0.00 2.01
3325 9985 7.561722 AGCTTGACTAGATGATAAGAGGTGTTA 59.438 37.037 0.00 0.00 0.00 2.41
3326 9986 6.382570 AGCTTGACTAGATGATAAGAGGTGTT 59.617 38.462 0.00 0.00 0.00 3.32
3327 9987 5.896678 AGCTTGACTAGATGATAAGAGGTGT 59.103 40.000 0.00 0.00 0.00 4.16
3343 10003 1.133668 AGGCACCAAAGAAGCTTGACT 60.134 47.619 2.10 0.00 0.00 3.41
3574 10234 6.264518 TCTGTGAGTGTATAAGTGTGACTTCA 59.735 38.462 0.00 0.00 39.51 3.02
3806 10466 5.183713 GCTTGCAGATATACATGGGCATTAA 59.816 40.000 0.00 0.00 0.00 1.40
3842 10502 6.095440 ACTCATGACACAAGCTTTAAACTGTT 59.905 34.615 0.00 0.00 0.00 3.16
3862 10522 9.213799 GAAAGAAACAAGACTCATTAGACTCAT 57.786 33.333 0.00 0.00 0.00 2.90
3958 10618 1.640428 TGTCCTAAATCTTGCGAGCG 58.360 50.000 0.00 0.00 0.00 5.03
4035 10706 3.462021 AGCTCTCACAAGTGACTTCAAC 58.538 45.455 0.00 0.00 35.46 3.18
4050 10721 7.334421 TGTCAACCATGTAAATAGAAAGCTCTC 59.666 37.037 0.00 0.00 32.70 3.20
4104 10775 2.541120 GCTCATCATGCCTCCACGC 61.541 63.158 0.00 0.00 0.00 5.34
4211 10886 1.601419 TACCGCCAAGAGTTCCCTCG 61.601 60.000 0.00 0.00 42.86 4.63
4252 10927 2.036475 AGTGCTCTCAACCACTGTGTAG 59.964 50.000 7.08 0.00 40.55 2.74
4362 11037 3.443044 CATATGAATGCAGCCCCCA 57.557 52.632 0.00 0.00 0.00 4.96
4444 11119 1.339727 ACACCTTCCAAGCCGGTATTC 60.340 52.381 1.90 0.00 35.57 1.75
4485 11160 2.100087 GTGGTCAAAAGCCGAGGAAAAA 59.900 45.455 0.00 0.00 0.00 1.94
4506 11181 3.071023 TGCTAATTAACCGAGGGATCCAG 59.929 47.826 15.23 4.03 0.00 3.86
4596 11272 7.698628 TGTCGATTTGAACAATGTGTCTTTTA 58.301 30.769 0.00 0.00 0.00 1.52
4621 11297 0.172803 GTCTACAGGATGCGGTCGTT 59.827 55.000 0.00 0.00 42.53 3.85
4622 11298 0.963856 TGTCTACAGGATGCGGTCGT 60.964 55.000 0.00 0.00 42.53 4.34
4674 11391 4.851639 ACAAGGCTCAAGGATATGTTCT 57.148 40.909 0.00 0.00 0.00 3.01
4688 11656 1.142870 TGCAGTGGTCTTTACAAGGCT 59.857 47.619 0.00 0.00 32.49 4.58
4724 11692 7.769044 GTCAGGCATACTAGGTGAAAAGATTAA 59.231 37.037 0.00 0.00 0.00 1.40
4732 11700 1.136305 GCGTCAGGCATACTAGGTGAA 59.864 52.381 0.00 0.00 42.87 3.18
4838 11819 2.158959 GCCGACCAACACGATCTCG 61.159 63.158 0.00 0.00 46.33 4.04
4840 11821 1.079819 CAGCCGACCAACACGATCT 60.080 57.895 0.00 0.00 0.00 2.75
4844 11825 3.605749 ATCCCAGCCGACCAACACG 62.606 63.158 0.00 0.00 0.00 4.49
4846 11827 1.303236 CAATCCCAGCCGACCAACA 60.303 57.895 0.00 0.00 0.00 3.33
4968 11970 2.758979 ACGGAGATATCTTTGGTCGTGT 59.241 45.455 6.70 0.00 0.00 4.49
5010 12018 4.826274 AAGGTTAAGATGACTGCAGCTA 57.174 40.909 15.27 2.79 40.47 3.32
5021 12029 7.775053 TGGACTTATTTGCAAAGGTTAAGAT 57.225 32.000 26.45 16.04 0.00 2.40
5023 12031 8.831715 AAATGGACTTATTTGCAAAGGTTAAG 57.168 30.769 21.36 21.36 0.00 1.85
5043 12061 1.486310 TCCTGGTCTCGATGGAAATGG 59.514 52.381 0.00 0.00 0.00 3.16
5094 12120 9.546428 CCGCTTGTATATATGATGATGGAATAA 57.454 33.333 0.00 0.00 0.00 1.40
5159 12189 1.840630 CTTGTTGATGGCACGACGCA 61.841 55.000 0.00 0.00 45.17 5.24
5177 12207 0.678395 CACCTGTCTGCTGTCACTCT 59.322 55.000 0.00 0.00 0.00 3.24
5198 12228 1.056660 TCCTTGGCTTCCTTTCGTCT 58.943 50.000 0.00 0.00 0.00 4.18
5200 12230 1.133915 TGTTCCTTGGCTTCCTTTCGT 60.134 47.619 0.00 0.00 0.00 3.85
5201 12231 1.537202 CTGTTCCTTGGCTTCCTTTCG 59.463 52.381 0.00 0.00 0.00 3.46
5225 12255 1.003851 CGGTTAATGCGTCATCCGTT 58.996 50.000 8.98 0.00 39.32 4.44
5270 12300 1.462616 ACAGAATGCATGGCGCTTAA 58.537 45.000 7.64 0.00 42.53 1.85
5279 12309 0.166597 CGTGTGCGAACAGAATGCAT 59.833 50.000 0.00 0.00 41.23 3.96
5280 12310 1.569003 CGTGTGCGAACAGAATGCA 59.431 52.632 0.00 0.00 39.56 3.96
5281 12311 1.793613 GCGTGTGCGAACAGAATGC 60.794 57.895 0.00 0.00 39.56 3.56
5282 12312 4.422506 GCGTGTGCGAACAGAATG 57.577 55.556 0.00 0.00 41.30 2.67
5294 12342 0.240945 GGCAGCTTGTAATTGCGTGT 59.759 50.000 0.00 0.00 38.69 4.49
5306 12354 0.755327 ACAACCGGAAAAGGCAGCTT 60.755 50.000 9.46 0.00 33.69 3.74
5332 12380 4.409218 GCACGTAGACCGCCGTCA 62.409 66.667 7.93 0.00 41.87 4.35
5377 12425 1.668472 TGCCGTATGGAAAACGCGT 60.668 52.632 5.58 5.58 39.00 6.01
5380 12428 0.446222 CCTGTGCCGTATGGAAAACG 59.554 55.000 4.73 0.00 40.01 3.60
5388 12436 2.288030 GCGTACTAATCCTGTGCCGTAT 60.288 50.000 0.00 0.00 0.00 3.06
5390 12438 0.179119 GCGTACTAATCCTGTGCCGT 60.179 55.000 0.00 0.00 0.00 5.68
5433 12484 1.192312 CACGTTGACATTGACCGTCAG 59.808 52.381 0.64 0.00 43.85 3.51
5454 12505 0.104120 CGAAGTCACTCACACCCACA 59.896 55.000 0.00 0.00 0.00 4.17
5455 12506 0.600255 CCGAAGTCACTCACACCCAC 60.600 60.000 0.00 0.00 0.00 4.61
5456 12507 1.745890 CCGAAGTCACTCACACCCA 59.254 57.895 0.00 0.00 0.00 4.51
5457 12508 1.004918 CCCGAAGTCACTCACACCC 60.005 63.158 0.00 0.00 0.00 4.61
5458 12509 1.668151 GCCCGAAGTCACTCACACC 60.668 63.158 0.00 0.00 0.00 4.16
5459 12510 0.249911 AAGCCCGAAGTCACTCACAC 60.250 55.000 0.00 0.00 0.00 3.82
5460 12511 1.334160 TAAGCCCGAAGTCACTCACA 58.666 50.000 0.00 0.00 0.00 3.58
5461 12512 2.338500 CTTAAGCCCGAAGTCACTCAC 58.662 52.381 0.00 0.00 0.00 3.51
5462 12513 1.337823 GCTTAAGCCCGAAGTCACTCA 60.338 52.381 17.00 0.00 34.31 3.41
5488 12539 0.904865 TCACTTGGTCTCGATGCCCT 60.905 55.000 3.38 0.00 0.00 5.19
5490 12541 1.086634 GCTCACTTGGTCTCGATGCC 61.087 60.000 0.00 0.00 0.00 4.40
5491 12542 0.108424 AGCTCACTTGGTCTCGATGC 60.108 55.000 0.00 0.00 0.00 3.91
5495 12562 1.423395 GTTCAGCTCACTTGGTCTCG 58.577 55.000 0.00 0.00 0.00 4.04
5499 12566 0.536006 GCAGGTTCAGCTCACTTGGT 60.536 55.000 6.77 0.00 0.00 3.67
5576 12645 1.453155 GACAAATCTGGACACCGCAT 58.547 50.000 0.00 0.00 0.00 4.73
5610 12698 2.417719 GTCCTGCAACAGATCGACTTT 58.582 47.619 0.00 0.00 32.44 2.66
5628 12716 2.270202 CACGATCGATGCATTTCGTC 57.730 50.000 24.34 13.10 42.42 4.20


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

AutoCloner maintained by Alex Coulton.