Multiple sequence alignment - TraesCS2A01G500700

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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 TraesCS2A01G500700 chr2A 100.000 3692 0 0 1 3692 729502714 729499023 0.000000e+00 6818.0
1 TraesCS2A01G500700 chr2A 80.909 110 19 2 2077 2185 196504816 196504924 6.570000e-13 86.1
2 TraesCS2A01G500700 chr2A 94.737 38 2 0 1840 1877 758551736 758551773 3.980000e-05 60.2
3 TraesCS2A01G500700 chr2D 89.785 3495 177 88 7 3421 595292268 595288874 0.000000e+00 4311.0
4 TraesCS2A01G500700 chr2D 95.238 126 5 1 3559 3684 595288433 595288309 8.090000e-47 198.0
5 TraesCS2A01G500700 chr2B 93.125 1629 62 21 1462 3069 723043942 723042343 0.000000e+00 2342.0
6 TraesCS2A01G500700 chr2B 91.266 1374 79 20 80 1436 723045287 723043938 0.000000e+00 1834.0
7 TraesCS2A01G500700 chr2B 94.737 38 2 0 1840 1877 771194956 771194919 3.980000e-05 60.2
8 TraesCS2A01G500700 chr2B 94.737 38 2 0 1840 1877 771216931 771216968 3.980000e-05 60.2
9 TraesCS2A01G500700 chr5D 81.560 141 23 3 1794 1932 322005200 322005339 3.010000e-21 113.0
10 TraesCS2A01G500700 chr5A 81.560 141 23 3 1794 1932 417255808 417255947 3.010000e-21 113.0
11 TraesCS2A01G500700 chr5B 80.851 141 24 3 1794 1932 373217039 373216900 1.400000e-19 108.0
12 TraesCS2A01G500700 chr3A 81.319 91 13 3 2091 2179 651588269 651588181 1.840000e-08 71.3
13 TraesCS2A01G500700 chr3D 80.220 91 14 3 2091 2179 516385312 516385224 8.560000e-07 65.8
14 TraesCS2A01G500700 chr3D 97.297 37 1 0 1842 1878 28210075 28210039 3.080000e-06 63.9
15 TraesCS2A01G500700 chr3B 80.220 91 14 3 2091 2179 679646178 679646090 8.560000e-07 65.8


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 TraesCS2A01G500700 chr2A 729499023 729502714 3691 True 6818.0 6818 100.0000 1 3692 1 chr2A.!!$R1 3691
1 TraesCS2A01G500700 chr2D 595288309 595292268 3959 True 2254.5 4311 92.5115 7 3684 2 chr2D.!!$R1 3677
2 TraesCS2A01G500700 chr2B 723042343 723045287 2944 True 2088.0 2342 92.1955 80 3069 2 chr2B.!!$R2 2989

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
665 691 0.101399 TTCGCGAAGGATCTGAGCTC 59.899 55.0 19.38 6.82 0.00 4.09 F
2071 2160 0.032952 TGCTCCTACGGTGTTGTCAC 59.967 55.0 0.00 0.00 43.19 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2347 0.108615 AGTGCGATTCTTCAGTCCGG 60.109 55.0 0.00 0.0 0.0 5.14 R
3425 3548 0.039165 CCGCAGCTGGAACCTTTTTC 60.039 55.0 17.12 0.0 0.0 2.29 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
42 43 6.261826 CCATAGCTGATTGGGAAAGAAGTAAG 59.738 42.308 0.00 0.00 0.00 2.34
46 47 5.703876 CTGATTGGGAAAGAAGTAAGCAAC 58.296 41.667 0.00 0.00 0.00 4.17
48 49 3.586470 TGGGAAAGAAGTAAGCAACCA 57.414 42.857 0.00 0.00 0.00 3.67
58 60 2.162338 TAAGCAACCACGACGGGGAG 62.162 60.000 26.07 15.96 40.22 4.30
76 78 2.175715 GGAGTTGGGGATATTTCAGCCT 59.824 50.000 0.00 0.00 31.34 4.58
78 80 2.091665 AGTTGGGGATATTTCAGCCTGG 60.092 50.000 0.00 0.00 31.34 4.45
157 171 2.649975 CGCCACGGTCGTATCGTC 60.650 66.667 0.00 0.00 38.94 4.20
158 172 2.649975 GCCACGGTCGTATCGTCG 60.650 66.667 0.00 0.00 38.94 5.12
159 173 2.787249 CCACGGTCGTATCGTCGT 59.213 61.111 0.00 7.21 38.94 4.34
267 282 2.159057 TCCTCGGGCGATTAACTTAACC 60.159 50.000 0.00 0.00 0.00 2.85
297 312 4.032987 CCGGACGCCAAAAACCCG 62.033 66.667 0.00 0.00 39.85 5.28
298 313 4.032987 CGGACGCCAAAAACCCGG 62.033 66.667 0.00 0.00 36.81 5.73
299 314 4.351938 GGACGCCAAAAACCCGGC 62.352 66.667 0.00 0.00 45.28 6.13
320 335 0.952010 ATTAACAACGCCGGTCGCTT 60.952 50.000 16.48 8.60 43.23 4.68
323 338 4.424430 CAACGCCGGTCGCTTTCG 62.424 66.667 16.48 6.05 43.23 3.46
394 409 1.424493 CCTGATCGCTTTCGTCAGCC 61.424 60.000 3.48 0.00 39.84 4.85
397 412 3.296709 ATCGCTTTCGTCAGCCCGT 62.297 57.895 3.48 0.00 36.31 5.28
567 590 2.356313 CGAGCGCTCACTGGTTGT 60.356 61.111 34.69 0.00 0.00 3.32
569 592 2.959357 GAGCGCTCACTGGTTGTGC 61.959 63.158 31.91 0.00 45.81 4.57
573 596 1.891919 GCTCACTGGTTGTGCGGAA 60.892 57.895 0.00 0.00 45.81 4.30
575 598 0.813610 CTCACTGGTTGTGCGGAACA 60.814 55.000 0.00 0.00 45.81 3.18
636 659 4.643387 ACCGGCAAGGGTGACTGC 62.643 66.667 0.00 0.00 46.96 4.40
637 660 4.335647 CCGGCAAGGGTGACTGCT 62.336 66.667 0.00 0.00 35.97 4.24
665 691 0.101399 TTCGCGAAGGATCTGAGCTC 59.899 55.000 19.38 6.82 0.00 4.09
673 699 0.955905 GGATCTGAGCTCCGAGGTAC 59.044 60.000 12.15 0.00 0.00 3.34
697 723 1.070443 CGACGTATTCTCTCCTCGCTC 60.070 57.143 0.00 0.00 0.00 5.03
708 734 0.685785 TCCTCGCTCCTCTGCAAGAT 60.686 55.000 0.00 0.00 45.62 2.40
720 746 4.442612 CCTCTGCAAGATCTAGCTTTGCTA 60.443 45.833 18.21 8.06 45.62 3.49
733 759 4.636249 AGCTTTGCTAGGATATACTGTGC 58.364 43.478 0.00 2.79 36.99 4.57
735 761 4.450419 GCTTTGCTAGGATATACTGTGCAG 59.550 45.833 14.40 7.98 34.53 4.41
793 822 5.005779 CCAAACTCGTATGATACAAGTCAGC 59.994 44.000 0.00 0.00 0.00 4.26
810 845 3.441572 GTCAGCTTGTGATTTGCCTGTAT 59.558 43.478 0.00 0.00 37.56 2.29
831 866 4.320608 TTTGTTCATCCTTTGCAACTCC 57.679 40.909 0.00 0.00 0.00 3.85
844 879 1.612199 GCAACTCCGAATTACACCCCA 60.612 52.381 0.00 0.00 0.00 4.96
860 921 1.603802 CCCCAGCATTATGTTAGCGTG 59.396 52.381 0.00 0.00 0.00 5.34
1045 1106 5.845065 TCAATCTTCCTCATCCTGATCATCT 59.155 40.000 0.00 0.00 0.00 2.90
1128 1189 2.686835 AGGAGACTGCTCAGGCCC 60.687 66.667 0.00 0.95 43.14 5.80
1161 1222 0.667993 CAGGTGAACGTGTTGCCATT 59.332 50.000 0.00 0.00 0.00 3.16
1165 1226 2.604614 GGTGAACGTGTTGCCATTTCTC 60.605 50.000 0.00 0.00 0.00 2.87
1178 1241 4.160626 TGCCATTTCTCAATTGATCATGCA 59.839 37.500 8.96 10.39 0.00 3.96
1179 1242 4.745125 GCCATTTCTCAATTGATCATGCAG 59.255 41.667 8.96 0.00 0.00 4.41
1190 1253 8.294577 TCAATTGATCATGCAGCAGATTAATAC 58.705 33.333 17.44 5.22 31.66 1.89
1198 1261 4.332543 TGCAGCAGATTAATACGAAACCAG 59.667 41.667 0.00 0.00 0.00 4.00
1227 1290 4.640201 TCATAAGAAATGGTGTGCTAAGCC 59.360 41.667 0.00 0.00 0.00 4.35
1230 1293 2.756760 AGAAATGGTGTGCTAAGCCATG 59.243 45.455 0.00 0.00 41.68 3.66
1248 1311 2.360553 TGCAATTATGTTTGTGCCCG 57.639 45.000 0.00 0.00 36.12 6.13
1266 1329 0.999406 CGTAATCAACAGAGGTGCCG 59.001 55.000 0.00 0.00 0.00 5.69
1302 1365 4.704833 ATGAGCGGCAACCTGCGT 62.705 61.111 1.45 0.00 46.21 5.24
1377 1440 0.113190 AGAAAAACCAGCTGGGGAGG 59.887 55.000 35.42 11.85 42.91 4.30
1416 1479 8.190784 CCTGTTTATCTGGTACAATTCCATTTC 58.809 37.037 0.00 0.00 38.70 2.17
1431 1494 4.355549 TCCATTTCAATCCCAGCAATCTT 58.644 39.130 0.00 0.00 0.00 2.40
1432 1495 5.517924 TCCATTTCAATCCCAGCAATCTTA 58.482 37.500 0.00 0.00 0.00 2.10
1433 1496 5.595542 TCCATTTCAATCCCAGCAATCTTAG 59.404 40.000 0.00 0.00 0.00 2.18
1434 1497 4.989279 TTTCAATCCCAGCAATCTTAGC 57.011 40.909 0.00 0.00 0.00 3.09
1435 1498 3.650281 TCAATCCCAGCAATCTTAGCA 57.350 42.857 0.00 0.00 0.00 3.49
1436 1499 3.966979 TCAATCCCAGCAATCTTAGCAA 58.033 40.909 0.00 0.00 0.00 3.91
1437 1500 3.949754 TCAATCCCAGCAATCTTAGCAAG 59.050 43.478 0.00 0.00 0.00 4.01
1438 1501 3.939740 ATCCCAGCAATCTTAGCAAGA 57.060 42.857 1.85 1.85 42.69 3.02
1452 1515 6.993079 TCTTAGCAAGATAGTGTTCAGTTCA 58.007 36.000 0.00 0.00 31.20 3.18
1453 1516 7.441836 TCTTAGCAAGATAGTGTTCAGTTCAA 58.558 34.615 0.00 0.00 31.20 2.69
1454 1517 8.097038 TCTTAGCAAGATAGTGTTCAGTTCAAT 58.903 33.333 0.00 0.00 31.20 2.57
1455 1518 8.621532 TTAGCAAGATAGTGTTCAGTTCAATT 57.378 30.769 0.00 0.00 0.00 2.32
1456 1519 7.516198 AGCAAGATAGTGTTCAGTTCAATTT 57.484 32.000 0.00 0.00 0.00 1.82
1457 1520 7.365741 AGCAAGATAGTGTTCAGTTCAATTTG 58.634 34.615 0.00 0.00 0.00 2.32
1458 1521 7.013655 AGCAAGATAGTGTTCAGTTCAATTTGT 59.986 33.333 0.00 0.00 0.00 2.83
1459 1522 8.289618 GCAAGATAGTGTTCAGTTCAATTTGTA 58.710 33.333 0.00 0.00 0.00 2.41
1460 1523 9.817365 CAAGATAGTGTTCAGTTCAATTTGTAG 57.183 33.333 0.00 0.00 0.00 2.74
2008 2097 2.186076 GATCAACATCACCGTCGAGTC 58.814 52.381 0.00 0.00 0.00 3.36
2048 2137 0.158096 CGACGAAACGGTTCTTGACG 59.842 55.000 12.14 5.16 0.00 4.35
2056 2145 2.472049 GTTCTTGACGCGCTGCTC 59.528 61.111 5.73 0.00 0.00 4.26
2065 2154 4.436998 GCGCTGCTCCTACGGTGT 62.437 66.667 0.00 0.00 0.00 4.16
2066 2155 2.261671 CGCTGCTCCTACGGTGTT 59.738 61.111 0.00 0.00 0.00 3.32
2067 2156 2.094659 CGCTGCTCCTACGGTGTTG 61.095 63.158 0.00 0.00 0.00 3.33
2068 2157 1.004918 GCTGCTCCTACGGTGTTGT 60.005 57.895 0.00 0.00 0.00 3.32
2069 2158 1.014564 GCTGCTCCTACGGTGTTGTC 61.015 60.000 0.00 0.00 0.00 3.18
2070 2159 0.317160 CTGCTCCTACGGTGTTGTCA 59.683 55.000 0.00 0.00 0.00 3.58
2071 2160 0.032952 TGCTCCTACGGTGTTGTCAC 59.967 55.000 0.00 0.00 43.19 3.67
2247 2336 0.750850 ACGTACACTGAACTGCCACT 59.249 50.000 0.00 0.00 0.00 4.00
2252 2341 1.069823 ACACTGAACTGCCACTCTCTG 59.930 52.381 0.00 0.00 0.00 3.35
2253 2342 1.342496 CACTGAACTGCCACTCTCTGA 59.658 52.381 0.00 0.00 0.00 3.27
2254 2343 2.042464 ACTGAACTGCCACTCTCTGAA 58.958 47.619 0.00 0.00 0.00 3.02
2255 2344 2.036992 ACTGAACTGCCACTCTCTGAAG 59.963 50.000 0.00 0.00 0.00 3.02
2256 2345 2.298446 CTGAACTGCCACTCTCTGAAGA 59.702 50.000 0.00 0.00 0.00 2.87
2257 2346 2.700371 TGAACTGCCACTCTCTGAAGAA 59.300 45.455 0.00 0.00 0.00 2.52
2258 2347 2.829741 ACTGCCACTCTCTGAAGAAC 57.170 50.000 0.00 0.00 0.00 3.01
2259 2348 1.346068 ACTGCCACTCTCTGAAGAACC 59.654 52.381 0.00 0.00 0.00 3.62
2260 2349 0.318441 TGCCACTCTCTGAAGAACCG 59.682 55.000 0.00 0.00 0.00 4.44
2261 2350 0.390472 GCCACTCTCTGAAGAACCGG 60.390 60.000 0.00 0.00 0.00 5.28
2262 2351 1.257743 CCACTCTCTGAAGAACCGGA 58.742 55.000 9.46 0.00 0.00 5.14
2271 2360 3.578716 TCTGAAGAACCGGACTGAAGAAT 59.421 43.478 9.46 0.00 0.00 2.40
2272 2361 3.926616 TGAAGAACCGGACTGAAGAATC 58.073 45.455 9.46 1.23 0.00 2.52
2273 2362 2.656560 AGAACCGGACTGAAGAATCG 57.343 50.000 9.46 0.00 0.00 3.34
2274 2363 1.000145 GAACCGGACTGAAGAATCGC 59.000 55.000 9.46 0.00 0.00 4.58
2275 2364 0.320374 AACCGGACTGAAGAATCGCA 59.680 50.000 9.46 0.00 0.00 5.10
2276 2365 0.389948 ACCGGACTGAAGAATCGCAC 60.390 55.000 9.46 0.00 0.00 5.34
2278 2367 1.272781 CGGACTGAAGAATCGCACTC 58.727 55.000 0.00 0.00 0.00 3.51
2284 2373 2.690497 CTGAAGAATCGCACTCCTCCTA 59.310 50.000 0.00 0.00 0.00 2.94
2298 2387 2.310349 TCCTCCTACTCTGCTCTGAACT 59.690 50.000 0.00 0.00 0.00 3.01
2366 2455 4.087892 CCTGGAGCTGGTGGACGG 62.088 72.222 0.00 0.00 0.00 4.79
2562 2651 1.375523 CCGGAAGAACCTCAACGGG 60.376 63.158 0.00 0.00 37.80 5.28
2704 2801 2.848858 AAATGATCCATGGCGCGGC 61.849 57.895 27.61 27.61 0.00 6.53
2731 2828 3.253955 ACGCAGCACCGTGAAATC 58.746 55.556 1.65 0.00 40.40 2.17
2935 3036 9.098355 CGATTCAGAGAACAATAAAGATGGTAA 57.902 33.333 0.00 0.00 0.00 2.85
2983 3091 9.462606 TGACTTGATCTAACTATGTCAGTTCTA 57.537 33.333 0.00 0.00 44.48 2.10
3016 3124 6.625532 AAACTCCCCCGTAAGATAAAGTTA 57.374 37.500 0.00 0.00 43.02 2.24
3082 3203 5.127845 TCCTAACAGAGCTCAAATACTCCTG 59.872 44.000 17.77 4.32 33.18 3.86
3092 3213 9.113838 GAGCTCAAATACTCCTGATATGAAAAA 57.886 33.333 9.40 0.00 0.00 1.94
3130 3251 8.329203 TGTAGCAAAACATTGAAAACCTTTTT 57.671 26.923 0.00 0.00 0.00 1.94
3165 3287 9.039870 CAACAAACATTGCTTAATTTTCTACCA 57.960 29.630 0.00 0.00 0.00 3.25
3168 3290 5.640732 ACATTGCTTAATTTTCTACCAGCG 58.359 37.500 0.00 0.00 0.00 5.18
3183 3305 6.811954 TCTACCAGCGTGTATATTTTCATGA 58.188 36.000 0.00 0.00 0.00 3.07
3200 3322 9.726232 ATTTTCATGATGAAATGACATTCGTAG 57.274 29.630 20.04 0.00 44.75 3.51
3202 3324 7.468922 TCATGATGAAATGACATTCGTAGAC 57.531 36.000 0.05 0.00 30.44 2.59
3205 3327 7.468922 TGATGAAATGACATTCGTAGACATC 57.531 36.000 0.05 9.99 34.32 3.06
3207 3329 6.892310 TGAAATGACATTCGTAGACATCTG 57.108 37.500 0.05 0.00 34.32 2.90
3208 3330 5.812127 TGAAATGACATTCGTAGACATCTGG 59.188 40.000 0.05 0.00 34.32 3.86
3246 3369 7.933577 TCAAGCTTCAAAGAATAGTCTTCTTGA 59.066 33.333 20.87 20.87 43.59 3.02
3301 3424 3.454042 TTCTTCACGAAACATCGCATG 57.546 42.857 0.00 0.00 36.44 4.06
3304 3427 0.443478 TCACGAAACATCGCATGCAG 59.557 50.000 19.57 10.78 36.44 4.41
3319 3442 3.307782 GCATGCAGGTGAAACATTATTGC 59.692 43.478 14.21 0.00 39.98 3.56
3327 3450 4.996758 GGTGAAACATTATTGCAAAAGGCT 59.003 37.500 1.71 0.00 41.11 4.58
3384 3507 2.027003 ACAAAGACAACCGAAACCGA 57.973 45.000 0.00 0.00 0.00 4.69
3404 3527 2.276732 AGGTCCACACACCAGAATTG 57.723 50.000 0.00 0.00 39.16 2.32
3405 3528 1.494721 AGGTCCACACACCAGAATTGT 59.505 47.619 0.00 0.00 39.16 2.71
3421 3544 7.839705 ACCAGAATTGTAGAGGTACATAAGAGA 59.160 37.037 0.00 0.00 38.98 3.10
3422 3545 8.356657 CCAGAATTGTAGAGGTACATAAGAGAG 58.643 40.741 0.00 0.00 38.98 3.20
3423 3546 8.356657 CAGAATTGTAGAGGTACATAAGAGAGG 58.643 40.741 0.00 0.00 38.98 3.69
3424 3547 8.282982 AGAATTGTAGAGGTACATAAGAGAGGA 58.717 37.037 0.00 0.00 38.98 3.71
3425 3548 8.472007 AATTGTAGAGGTACATAAGAGAGGAG 57.528 38.462 0.00 0.00 38.98 3.69
3427 3550 7.209340 TGTAGAGGTACATAAGAGAGGAGAA 57.791 40.000 0.00 0.00 34.02 2.87
3430 3553 8.968969 GTAGAGGTACATAAGAGAGGAGAAAAA 58.031 37.037 0.00 0.00 0.00 1.94
3431 3554 8.073467 AGAGGTACATAAGAGAGGAGAAAAAG 57.927 38.462 0.00 0.00 0.00 2.27
3433 3556 6.731448 AGGTACATAAGAGAGGAGAAAAAGGT 59.269 38.462 0.00 0.00 0.00 3.50
3434 3557 7.237887 AGGTACATAAGAGAGGAGAAAAAGGTT 59.762 37.037 0.00 0.00 0.00 3.50
3437 3560 6.044404 ACATAAGAGAGGAGAAAAAGGTTCCA 59.956 38.462 0.00 0.00 33.32 3.53
3438 3561 4.632327 AGAGAGGAGAAAAAGGTTCCAG 57.368 45.455 0.00 0.00 33.32 3.86
3439 3562 3.078097 GAGAGGAGAAAAAGGTTCCAGC 58.922 50.000 0.00 0.00 33.32 4.85
3440 3563 2.713708 AGAGGAGAAAAAGGTTCCAGCT 59.286 45.455 0.00 0.00 33.32 4.24
3441 3564 2.816672 GAGGAGAAAAAGGTTCCAGCTG 59.183 50.000 6.78 6.78 33.32 4.24
3442 3565 1.270826 GGAGAAAAAGGTTCCAGCTGC 59.729 52.381 8.66 0.00 0.00 5.25
3443 3566 0.954452 AGAAAAAGGTTCCAGCTGCG 59.046 50.000 8.66 1.56 0.00 5.18
3444 3567 0.039165 GAAAAAGGTTCCAGCTGCGG 60.039 55.000 8.66 0.00 0.00 5.69
3445 3568 1.463553 AAAAAGGTTCCAGCTGCGGG 61.464 55.000 12.93 12.93 0.00 6.13
3460 3738 2.026014 GGGCAACAGCACAACACG 59.974 61.111 0.00 0.00 39.74 4.49
3461 3739 2.655044 GGCAACAGCACAACACGC 60.655 61.111 0.00 0.00 0.00 5.34
3464 3742 3.582120 AACAGCACAACACGCCCG 61.582 61.111 0.00 0.00 0.00 6.13
3465 3743 4.539083 ACAGCACAACACGCCCGA 62.539 61.111 0.00 0.00 0.00 5.14
3471 3749 1.335142 GCACAACACGCCCGAAAATTA 60.335 47.619 0.00 0.00 0.00 1.40
3472 3750 2.859032 GCACAACACGCCCGAAAATTAA 60.859 45.455 0.00 0.00 0.00 1.40
3474 3752 3.797256 CACAACACGCCCGAAAATTAAAA 59.203 39.130 0.00 0.00 0.00 1.52
3475 3753 4.045783 ACAACACGCCCGAAAATTAAAAG 58.954 39.130 0.00 0.00 0.00 2.27
3477 3755 4.776795 ACACGCCCGAAAATTAAAAGAT 57.223 36.364 0.00 0.00 0.00 2.40
3479 3757 5.633927 ACACGCCCGAAAATTAAAAGATAC 58.366 37.500 0.00 0.00 0.00 2.24
3480 3758 5.181622 ACACGCCCGAAAATTAAAAGATACA 59.818 36.000 0.00 0.00 0.00 2.29
3482 3760 5.413523 ACGCCCGAAAATTAAAAGATACACT 59.586 36.000 0.00 0.00 0.00 3.55
3483 3761 5.963586 CGCCCGAAAATTAAAAGATACACTC 59.036 40.000 0.00 0.00 0.00 3.51
3484 3762 6.402766 CGCCCGAAAATTAAAAGATACACTCA 60.403 38.462 0.00 0.00 0.00 3.41
3486 3764 7.484959 GCCCGAAAATTAAAAGATACACTCAAG 59.515 37.037 0.00 0.00 0.00 3.02
3487 3765 7.968405 CCCGAAAATTAAAAGATACACTCAAGG 59.032 37.037 0.00 0.00 0.00 3.61
3488 3766 8.726988 CCGAAAATTAAAAGATACACTCAAGGA 58.273 33.333 0.00 0.00 0.00 3.36
3489 3767 9.760660 CGAAAATTAAAAGATACACTCAAGGAG 57.239 33.333 0.00 0.00 35.52 3.69
3491 3769 9.807921 AAAATTAAAAGATACACTCAAGGAGGA 57.192 29.630 0.00 0.00 33.35 3.71
3496 3774 7.741554 AAAGATACACTCAAGGAGGATAAGT 57.258 36.000 0.00 0.00 33.35 2.24
3497 3775 6.723298 AGATACACTCAAGGAGGATAAGTG 57.277 41.667 0.00 0.00 42.33 3.16
3498 3776 6.436027 AGATACACTCAAGGAGGATAAGTGA 58.564 40.000 7.73 0.00 39.72 3.41
3501 3779 3.515502 CACTCAAGGAGGATAAGTGACCA 59.484 47.826 0.00 0.00 39.72 4.02
3502 3780 4.163078 CACTCAAGGAGGATAAGTGACCAT 59.837 45.833 0.00 0.00 39.72 3.55
3503 3781 4.163078 ACTCAAGGAGGATAAGTGACCATG 59.837 45.833 0.00 0.00 33.35 3.66
3504 3782 4.361783 TCAAGGAGGATAAGTGACCATGA 58.638 43.478 0.00 0.00 0.00 3.07
3506 3784 4.271807 AGGAGGATAAGTGACCATGAGA 57.728 45.455 0.00 0.00 0.00 3.27
3507 3785 4.624913 AGGAGGATAAGTGACCATGAGAA 58.375 43.478 0.00 0.00 0.00 2.87
3508 3786 5.032846 AGGAGGATAAGTGACCATGAGAAA 58.967 41.667 0.00 0.00 0.00 2.52
3509 3787 5.130145 AGGAGGATAAGTGACCATGAGAAAG 59.870 44.000 0.00 0.00 0.00 2.62
3510 3788 5.104735 GGAGGATAAGTGACCATGAGAAAGT 60.105 44.000 0.00 0.00 0.00 2.66
3511 3789 5.738909 AGGATAAGTGACCATGAGAAAGTG 58.261 41.667 0.00 0.00 0.00 3.16
3512 3790 4.333926 GGATAAGTGACCATGAGAAAGTGC 59.666 45.833 0.00 0.00 0.00 4.40
3513 3791 3.498774 AAGTGACCATGAGAAAGTGCT 57.501 42.857 0.00 0.00 0.00 4.40
3514 3792 4.623932 AAGTGACCATGAGAAAGTGCTA 57.376 40.909 0.00 0.00 0.00 3.49
3515 3793 3.931578 AGTGACCATGAGAAAGTGCTAC 58.068 45.455 0.00 0.00 0.00 3.58
3516 3794 2.668457 GTGACCATGAGAAAGTGCTACG 59.332 50.000 0.00 0.00 0.00 3.51
3519 3802 1.675714 CCATGAGAAAGTGCTACGCCA 60.676 52.381 0.00 0.00 0.00 5.69
3531 3814 1.888436 CTACGCCAGCTCCTTGACCA 61.888 60.000 0.00 0.00 0.00 4.02
3537 3820 0.463295 CAGCTCCTTGACCATCGCAT 60.463 55.000 0.00 0.00 0.00 4.73
3541 3824 2.711311 CTTGACCATCGCATGCCG 59.289 61.111 13.15 7.68 38.61 5.69
3542 3825 2.823593 TTGACCATCGCATGCCGG 60.824 61.111 13.15 12.85 37.59 6.13
3543 3826 3.620419 TTGACCATCGCATGCCGGT 62.620 57.895 18.29 18.29 37.59 5.28
3548 3831 3.187058 ATCGCATGCCGGTGAAAC 58.813 55.556 13.15 0.00 37.59 2.78
3549 3832 1.673993 ATCGCATGCCGGTGAAACA 60.674 52.632 13.15 0.00 39.98 2.83
3550 3833 1.031571 ATCGCATGCCGGTGAAACAT 61.032 50.000 13.15 0.00 39.98 2.71
3551 3834 1.212490 CGCATGCCGGTGAAACATT 59.788 52.632 13.15 0.00 39.98 2.71
3552 3835 0.798009 CGCATGCCGGTGAAACATTC 60.798 55.000 13.15 0.00 39.98 2.67
3553 3836 0.243365 GCATGCCGGTGAAACATTCA 59.757 50.000 6.36 0.00 39.98 2.57
3554 3837 1.135024 GCATGCCGGTGAAACATTCAT 60.135 47.619 6.36 0.00 42.47 2.57
3556 3839 2.198827 TGCCGGTGAAACATTCATCT 57.801 45.000 1.90 0.00 42.47 2.90
3576 4002 6.599244 TCATCTATGTTTGTCAGAAACATCCC 59.401 38.462 15.80 0.00 44.83 3.85
3590 4016 8.869109 TCAGAAACATCCCATTCTTTTGTATTT 58.131 29.630 0.00 0.00 33.73 1.40
3653 4079 1.004394 ACCGGGGATCCAAAACTCTTC 59.996 52.381 15.23 0.00 0.00 2.87
3684 4110 7.454260 ACCTTATTTAGCAAAGTTTCTCCTG 57.546 36.000 0.00 0.00 0.00 3.86
3685 4111 6.071896 ACCTTATTTAGCAAAGTTTCTCCTGC 60.072 38.462 0.00 0.00 34.96 4.85
3686 4112 6.151817 CCTTATTTAGCAAAGTTTCTCCTGCT 59.848 38.462 4.52 4.52 46.50 4.24
3687 4113 5.635417 ATTTAGCAAAGTTTCTCCTGCTC 57.365 39.130 2.32 0.00 43.85 4.26
3688 4114 2.947127 AGCAAAGTTTCTCCTGCTCT 57.053 45.000 0.00 0.00 41.18 4.09
3689 4115 3.220674 AGCAAAGTTTCTCCTGCTCTT 57.779 42.857 0.00 0.00 41.18 2.85
3690 4116 3.560105 AGCAAAGTTTCTCCTGCTCTTT 58.440 40.909 0.00 0.00 41.18 2.52
3691 4117 3.317430 AGCAAAGTTTCTCCTGCTCTTTG 59.683 43.478 10.35 10.35 41.18 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.451894 GCTCCATTGGCCCGTTGG 61.452 66.667 0.00 4.64 0.00 3.77
1 2 3.451894 GGCTCCATTGGCCCGTTG 61.452 66.667 0.00 0.00 43.49 4.10
21 22 4.013050 GCTTACTTCTTTCCCAATCAGCT 58.987 43.478 0.00 0.00 0.00 4.24
23 24 5.335976 GGTTGCTTACTTCTTTCCCAATCAG 60.336 44.000 0.00 0.00 0.00 2.90
42 43 3.819877 AACTCCCCGTCGTGGTTGC 62.820 63.158 0.00 0.00 35.15 4.17
46 47 4.388499 CCCAACTCCCCGTCGTGG 62.388 72.222 0.00 0.00 37.55 4.94
48 49 2.519119 TATCCCCAACTCCCCGTCGT 62.519 60.000 0.00 0.00 0.00 4.34
58 60 2.091885 TCCAGGCTGAAATATCCCCAAC 60.092 50.000 17.94 0.00 0.00 3.77
76 78 0.669318 CGCCAGTTAGCTTCGTTCCA 60.669 55.000 0.00 0.00 0.00 3.53
78 80 0.389426 TCCGCCAGTTAGCTTCGTTC 60.389 55.000 0.00 0.00 0.00 3.95
157 171 5.549454 CCGGAGAGGTTTCGTACAGTACG 62.549 56.522 24.60 24.60 43.62 3.67
158 172 2.159462 CCGGAGAGGTTTCGTACAGTAC 60.159 54.545 0.00 0.00 34.51 2.73
159 173 2.086869 CCGGAGAGGTTTCGTACAGTA 58.913 52.381 0.00 0.00 34.51 2.74
267 282 3.781307 TCCGGCCGGGATTGACTG 61.781 66.667 42.36 15.31 40.94 3.51
288 303 3.060205 CGTTGTTAATTGCCGGGTTTTTG 60.060 43.478 2.18 0.00 0.00 2.44
289 304 3.124560 CGTTGTTAATTGCCGGGTTTTT 58.875 40.909 2.18 0.00 0.00 1.94
290 305 2.745102 CGTTGTTAATTGCCGGGTTTT 58.255 42.857 2.18 0.00 0.00 2.43
291 306 1.603425 GCGTTGTTAATTGCCGGGTTT 60.603 47.619 2.18 0.00 0.00 3.27
292 307 0.038983 GCGTTGTTAATTGCCGGGTT 60.039 50.000 2.18 0.00 0.00 4.11
293 308 1.582461 GCGTTGTTAATTGCCGGGT 59.418 52.632 2.18 0.00 0.00 5.28
295 310 4.469052 GGCGTTGTTAATTGCCGG 57.531 55.556 0.00 0.00 37.81 6.13
297 312 0.455464 GACCGGCGTTGTTAATTGCC 60.455 55.000 6.01 0.00 44.09 4.52
298 313 0.791610 CGACCGGCGTTGTTAATTGC 60.792 55.000 6.01 0.00 34.64 3.56
299 314 0.791610 GCGACCGGCGTTGTTAATTG 60.792 55.000 17.38 0.00 43.41 2.32
300 315 1.498611 GCGACCGGCGTTGTTAATT 59.501 52.632 17.38 0.00 43.41 1.40
301 316 3.171056 GCGACCGGCGTTGTTAAT 58.829 55.556 17.38 0.00 43.41 1.40
567 590 4.742201 GCGCCTCTCTGTTCCGCA 62.742 66.667 0.00 0.00 43.67 5.69
590 613 1.524002 GGAGCACTAGCAGCATGGA 59.476 57.895 10.05 0.00 45.49 3.41
684 710 1.034838 GCAGAGGAGCGAGGAGAGAA 61.035 60.000 0.00 0.00 0.00 2.87
685 711 1.453015 GCAGAGGAGCGAGGAGAGA 60.453 63.158 0.00 0.00 0.00 3.10
690 716 0.249405 GATCTTGCAGAGGAGCGAGG 60.249 60.000 3.57 0.00 44.50 4.63
697 723 2.613133 GCAAAGCTAGATCTTGCAGAGG 59.387 50.000 27.14 15.77 33.84 3.69
720 746 6.843752 ACTACTACTCTGCACAGTATATCCT 58.156 40.000 2.05 0.00 0.00 3.24
721 747 8.505625 GTTACTACTACTCTGCACAGTATATCC 58.494 40.741 2.05 0.00 0.00 2.59
722 748 9.053840 TGTTACTACTACTCTGCACAGTATATC 57.946 37.037 2.05 0.00 0.00 1.63
723 749 8.975663 TGTTACTACTACTCTGCACAGTATAT 57.024 34.615 2.05 0.00 0.00 0.86
724 750 8.975663 ATGTTACTACTACTCTGCACAGTATA 57.024 34.615 2.05 0.00 0.00 1.47
725 751 7.883391 ATGTTACTACTACTCTGCACAGTAT 57.117 36.000 2.05 0.00 0.00 2.12
726 752 7.698506 AATGTTACTACTACTCTGCACAGTA 57.301 36.000 1.68 1.68 0.00 2.74
727 753 6.591750 AATGTTACTACTACTCTGCACAGT 57.408 37.500 0.00 0.00 0.00 3.55
763 789 4.873827 TGTATCATACGAGTTTGGGCTTTC 59.126 41.667 0.00 0.00 0.00 2.62
793 822 6.215121 TGAACAAATACAGGCAAATCACAAG 58.785 36.000 0.00 0.00 0.00 3.16
810 845 3.243367 CGGAGTTGCAAAGGATGAACAAA 60.243 43.478 0.00 0.00 0.00 2.83
831 866 3.882888 ACATAATGCTGGGGTGTAATTCG 59.117 43.478 0.00 0.00 0.00 3.34
844 879 1.942657 CAGCCACGCTAACATAATGCT 59.057 47.619 0.00 0.00 36.40 3.79
860 921 1.678970 AAATCAACTCGGCCCAGCC 60.679 57.895 0.00 0.00 46.75 4.85
1045 1106 2.219458 GACGATGACTATGACGAGGGA 58.781 52.381 0.00 0.00 0.00 4.20
1161 1222 4.266714 TCTGCTGCATGATCAATTGAGAA 58.733 39.130 14.54 4.83 0.00 2.87
1165 1226 7.270579 CGTATTAATCTGCTGCATGATCAATTG 59.729 37.037 1.31 0.00 0.00 2.32
1178 1241 6.407202 ACTTCTGGTTTCGTATTAATCTGCT 58.593 36.000 0.00 0.00 0.00 4.24
1179 1242 6.535508 AGACTTCTGGTTTCGTATTAATCTGC 59.464 38.462 0.00 0.00 0.00 4.26
1190 1253 7.413438 CCATTTCTTATGAGACTTCTGGTTTCG 60.413 40.741 0.00 0.00 32.43 3.46
1198 1261 5.645497 AGCACACCATTTCTTATGAGACTTC 59.355 40.000 0.00 0.00 0.00 3.01
1227 1290 2.604011 CGGGCACAAACATAATTGCATG 59.396 45.455 0.00 0.00 36.66 4.06
1230 1293 2.362169 ACGGGCACAAACATAATTGC 57.638 45.000 0.00 0.00 33.52 3.56
1248 1311 1.066430 TCCGGCACCTCTGTTGATTAC 60.066 52.381 0.00 0.00 0.00 1.89
1266 1329 0.320421 TGTTGCCGCTGAAGTACTCC 60.320 55.000 0.00 0.00 0.00 3.85
1302 1365 3.873361 CGTAGTCGAAGTAGGTGATGGTA 59.127 47.826 0.00 0.00 39.71 3.25
1377 1440 2.211468 AAACAGGGCCGAATCCTCCC 62.211 60.000 0.00 0.00 40.36 4.30
1416 1479 3.949754 TCTTGCTAAGATTGCTGGGATTG 59.050 43.478 0.00 0.00 31.20 2.67
1431 1494 8.506437 CAAATTGAACTGAACACTATCTTGCTA 58.494 33.333 0.00 0.00 0.00 3.49
1432 1495 7.013655 ACAAATTGAACTGAACACTATCTTGCT 59.986 33.333 0.00 0.00 0.00 3.91
1433 1496 7.141363 ACAAATTGAACTGAACACTATCTTGC 58.859 34.615 0.00 0.00 0.00 4.01
1434 1497 9.817365 CTACAAATTGAACTGAACACTATCTTG 57.183 33.333 0.00 0.00 0.00 3.02
1435 1498 9.561069 ACTACAAATTGAACTGAACACTATCTT 57.439 29.630 0.00 0.00 0.00 2.40
1438 1501 8.936864 GCTACTACAAATTGAACTGAACACTAT 58.063 33.333 0.00 0.00 0.00 2.12
1439 1502 7.929245 TGCTACTACAAATTGAACTGAACACTA 59.071 33.333 0.00 0.00 0.00 2.74
1440 1503 6.765989 TGCTACTACAAATTGAACTGAACACT 59.234 34.615 0.00 0.00 0.00 3.55
1441 1504 6.851330 GTGCTACTACAAATTGAACTGAACAC 59.149 38.462 0.00 0.00 0.00 3.32
1442 1505 6.540551 TGTGCTACTACAAATTGAACTGAACA 59.459 34.615 0.00 0.00 0.00 3.18
1443 1506 6.954944 TGTGCTACTACAAATTGAACTGAAC 58.045 36.000 0.00 0.00 0.00 3.18
1444 1507 7.282224 AGTTGTGCTACTACAAATTGAACTGAA 59.718 33.333 0.00 0.00 41.75 3.02
1445 1508 6.765989 AGTTGTGCTACTACAAATTGAACTGA 59.234 34.615 0.00 0.00 41.75 3.41
1446 1509 6.852853 CAGTTGTGCTACTACAAATTGAACTG 59.147 38.462 0.00 2.27 41.75 3.16
1447 1510 6.765989 TCAGTTGTGCTACTACAAATTGAACT 59.234 34.615 0.00 0.00 41.75 3.01
1448 1511 6.954944 TCAGTTGTGCTACTACAAATTGAAC 58.045 36.000 0.00 0.00 41.75 3.18
1449 1512 7.066404 TGTTCAGTTGTGCTACTACAAATTGAA 59.934 33.333 0.00 12.08 41.75 2.69
1450 1513 6.540551 TGTTCAGTTGTGCTACTACAAATTGA 59.459 34.615 0.00 0.00 41.75 2.57
1451 1514 6.724263 TGTTCAGTTGTGCTACTACAAATTG 58.276 36.000 0.00 0.00 41.75 2.32
1452 1515 6.765989 TCTGTTCAGTTGTGCTACTACAAATT 59.234 34.615 0.00 0.00 41.75 1.82
1453 1516 6.288294 TCTGTTCAGTTGTGCTACTACAAAT 58.712 36.000 0.00 0.00 41.75 2.32
1454 1517 5.666462 TCTGTTCAGTTGTGCTACTACAAA 58.334 37.500 0.00 0.00 41.75 2.83
1455 1518 5.270893 TCTGTTCAGTTGTGCTACTACAA 57.729 39.130 0.00 0.00 38.17 2.41
1456 1519 4.262036 CCTCTGTTCAGTTGTGCTACTACA 60.262 45.833 0.00 0.00 0.00 2.74
1457 1520 4.238514 CCTCTGTTCAGTTGTGCTACTAC 58.761 47.826 0.00 0.00 0.00 2.73
1458 1521 3.895656 ACCTCTGTTCAGTTGTGCTACTA 59.104 43.478 0.00 0.00 0.00 1.82
1459 1522 2.700897 ACCTCTGTTCAGTTGTGCTACT 59.299 45.455 0.00 0.00 0.00 2.57
1460 1523 2.802816 CACCTCTGTTCAGTTGTGCTAC 59.197 50.000 9.82 0.00 0.00 3.58
2008 2097 0.387202 CAGGCGATCAGAGGTAGGTG 59.613 60.000 0.00 0.00 0.00 4.00
2065 2154 1.418637 GTACCCCCTGACAAGTGACAA 59.581 52.381 0.00 0.00 0.00 3.18
2066 2155 1.053424 GTACCCCCTGACAAGTGACA 58.947 55.000 0.00 0.00 0.00 3.58
2067 2156 1.053424 TGTACCCCCTGACAAGTGAC 58.947 55.000 0.00 0.00 0.00 3.67
2068 2157 1.053424 GTGTACCCCCTGACAAGTGA 58.947 55.000 0.00 0.00 0.00 3.41
2069 2158 0.320421 CGTGTACCCCCTGACAAGTG 60.320 60.000 0.00 0.00 0.00 3.16
2070 2159 1.477685 CCGTGTACCCCCTGACAAGT 61.478 60.000 0.00 0.00 0.00 3.16
2071 2160 1.295423 CCGTGTACCCCCTGACAAG 59.705 63.158 0.00 0.00 0.00 3.16
2247 2336 2.287977 TCAGTCCGGTTCTTCAGAGA 57.712 50.000 0.00 0.00 0.00 3.10
2252 2341 2.924290 CGATTCTTCAGTCCGGTTCTTC 59.076 50.000 0.00 0.00 0.00 2.87
2253 2342 2.931320 GCGATTCTTCAGTCCGGTTCTT 60.931 50.000 0.00 0.00 0.00 2.52
2254 2343 1.404315 GCGATTCTTCAGTCCGGTTCT 60.404 52.381 0.00 0.00 0.00 3.01
2255 2344 1.000145 GCGATTCTTCAGTCCGGTTC 59.000 55.000 0.00 0.00 0.00 3.62
2256 2345 0.320374 TGCGATTCTTCAGTCCGGTT 59.680 50.000 0.00 0.00 0.00 4.44
2257 2346 0.389948 GTGCGATTCTTCAGTCCGGT 60.390 55.000 0.00 0.00 0.00 5.28
2258 2347 0.108615 AGTGCGATTCTTCAGTCCGG 60.109 55.000 0.00 0.00 0.00 5.14
2259 2348 1.272781 GAGTGCGATTCTTCAGTCCG 58.727 55.000 0.00 0.00 0.00 4.79
2260 2349 1.646189 GGAGTGCGATTCTTCAGTCC 58.354 55.000 11.46 11.46 43.22 3.85
2261 2350 2.535331 GAGGAGTGCGATTCTTCAGTC 58.465 52.381 0.00 0.00 33.16 3.51
2262 2351 1.205893 GGAGGAGTGCGATTCTTCAGT 59.794 52.381 0.00 0.00 0.00 3.41
2271 2360 1.032657 GCAGAGTAGGAGGAGTGCGA 61.033 60.000 0.00 0.00 0.00 5.10
2272 2361 1.034838 AGCAGAGTAGGAGGAGTGCG 61.035 60.000 0.00 0.00 36.04 5.34
2273 2362 0.744281 GAGCAGAGTAGGAGGAGTGC 59.256 60.000 0.00 0.00 0.00 4.40
2274 2363 2.023673 CAGAGCAGAGTAGGAGGAGTG 58.976 57.143 0.00 0.00 0.00 3.51
2275 2364 1.919654 TCAGAGCAGAGTAGGAGGAGT 59.080 52.381 0.00 0.00 0.00 3.85
2276 2365 2.687935 GTTCAGAGCAGAGTAGGAGGAG 59.312 54.545 0.00 0.00 0.00 3.69
2278 2367 2.733956 AGTTCAGAGCAGAGTAGGAGG 58.266 52.381 0.00 0.00 0.00 4.30
2284 2373 7.573968 AAACATAAAAAGTTCAGAGCAGAGT 57.426 32.000 0.00 0.00 0.00 3.24
2394 2483 0.179936 CCTGCATCACCTCCTTCTCC 59.820 60.000 0.00 0.00 0.00 3.71
2545 2634 1.375523 CCCCGTTGAGGTTCTTCCG 60.376 63.158 0.00 0.00 41.99 4.30
2731 2828 1.600957 GCATGGAATCATCGGTCACAG 59.399 52.381 0.00 0.00 0.00 3.66
2822 2920 6.624423 GGTATACCGTATACATACTGTTGGG 58.376 44.000 23.87 0.00 42.16 4.12
2935 3036 6.422400 GTCACGTTTGAGAGAAGAGAAAATCT 59.578 38.462 0.00 0.00 33.58 2.40
2936 3037 6.422400 AGTCACGTTTGAGAGAAGAGAAAATC 59.578 38.462 0.00 0.00 30.10 2.17
2983 3091 6.842807 TCTTACGGGGGAGTTTATTCTAGAAT 59.157 38.462 21.28 21.28 34.93 2.40
3092 3213 7.856145 TGTTTTGCTACATTTTTGGATTTGT 57.144 28.000 0.00 0.00 0.00 2.83
3138 3259 9.040939 GGTAGAAAATTAAGCAATGTTTGTTGT 57.959 29.630 0.00 0.00 0.00 3.32
3139 3260 9.039870 TGGTAGAAAATTAAGCAATGTTTGTTG 57.960 29.630 0.00 0.00 0.00 3.33
3140 3261 9.260002 CTGGTAGAAAATTAAGCAATGTTTGTT 57.740 29.630 0.00 0.00 0.00 2.83
3183 3305 6.481313 CCAGATGTCTACGAATGTCATTTCAT 59.519 38.462 0.00 0.00 0.00 2.57
3219 3341 8.562892 CAAGAAGACTATTCTTTGAAGCTTGAA 58.437 33.333 2.10 0.00 42.53 2.69
3222 3344 8.682936 TTCAAGAAGACTATTCTTTGAAGCTT 57.317 30.769 0.00 0.00 42.53 3.74
3260 3383 9.604626 GAAGAAAAACATCTGTAATGTTCTGAG 57.395 33.333 4.05 0.00 40.94 3.35
3301 3424 5.106987 CCTTTTGCAATAATGTTTCACCTGC 60.107 40.000 0.00 0.00 0.00 4.85
3304 3427 4.996758 AGCCTTTTGCAATAATGTTTCACC 59.003 37.500 0.00 0.00 44.83 4.02
3327 3450 3.838244 ATCTATAAAGCAGGGCGTGAA 57.162 42.857 12.03 0.00 0.00 3.18
3363 3486 2.865551 TCGGTTTCGGTTGTCTTTGTAC 59.134 45.455 0.00 0.00 36.95 2.90
3366 3489 2.286772 CCTTCGGTTTCGGTTGTCTTTG 60.287 50.000 0.00 0.00 36.95 2.77
3384 3507 2.091885 ACAATTCTGGTGTGTGGACCTT 60.092 45.455 0.00 0.00 36.88 3.50
3396 3519 8.239038 TCTCTTATGTACCTCTACAATTCTGG 57.761 38.462 0.00 0.00 36.43 3.86
3397 3520 8.356657 CCTCTCTTATGTACCTCTACAATTCTG 58.643 40.741 0.00 0.00 36.43 3.02
3404 3527 8.522542 TTTTCTCCTCTCTTATGTACCTCTAC 57.477 38.462 0.00 0.00 0.00 2.59
3405 3528 9.191479 CTTTTTCTCCTCTCTTATGTACCTCTA 57.809 37.037 0.00 0.00 0.00 2.43
3421 3544 2.868899 CAGCTGGAACCTTTTTCTCCT 58.131 47.619 5.57 0.00 0.00 3.69
3422 3545 1.270826 GCAGCTGGAACCTTTTTCTCC 59.729 52.381 17.12 0.00 0.00 3.71
3423 3546 1.068954 CGCAGCTGGAACCTTTTTCTC 60.069 52.381 17.12 0.00 0.00 2.87
3424 3547 0.954452 CGCAGCTGGAACCTTTTTCT 59.046 50.000 17.12 0.00 0.00 2.52
3425 3548 0.039165 CCGCAGCTGGAACCTTTTTC 60.039 55.000 17.12 0.00 0.00 2.29
3427 3550 1.903404 CCCGCAGCTGGAACCTTTT 60.903 57.895 17.12 0.00 0.00 2.27
3433 3556 4.577677 TGTTGCCCGCAGCTGGAA 62.578 61.111 17.12 0.00 44.23 3.53
3439 3562 3.594775 TTGTGCTGTTGCCCGCAG 61.595 61.111 0.00 0.00 36.73 5.18
3440 3563 3.898509 GTTGTGCTGTTGCCCGCA 61.899 61.111 0.00 0.00 38.71 5.69
3441 3564 3.898509 TGTTGTGCTGTTGCCCGC 61.899 61.111 0.00 0.00 38.71 6.13
3442 3565 2.026014 GTGTTGTGCTGTTGCCCG 59.974 61.111 0.00 0.00 38.71 6.13
3443 3566 2.026014 CGTGTTGTGCTGTTGCCC 59.974 61.111 0.00 0.00 38.71 5.36
3444 3567 2.655044 GCGTGTTGTGCTGTTGCC 60.655 61.111 0.00 0.00 38.71 4.52
3445 3568 2.655044 GGCGTGTTGTGCTGTTGC 60.655 61.111 0.00 0.00 40.20 4.17
3447 3725 3.582120 CGGGCGTGTTGTGCTGTT 61.582 61.111 0.00 0.00 0.00 3.16
3453 3731 3.712091 TTTAATTTTCGGGCGTGTTGT 57.288 38.095 0.00 0.00 0.00 3.32
3455 3733 4.571372 TCTTTTAATTTTCGGGCGTGTT 57.429 36.364 0.00 0.00 0.00 3.32
3458 3736 5.413523 AGTGTATCTTTTAATTTTCGGGCGT 59.586 36.000 0.00 0.00 0.00 5.68
3460 3738 6.848451 TGAGTGTATCTTTTAATTTTCGGGC 58.152 36.000 0.00 0.00 0.00 6.13
3461 3739 7.968405 CCTTGAGTGTATCTTTTAATTTTCGGG 59.032 37.037 0.00 0.00 0.00 5.14
3465 3743 9.807921 TCCTCCTTGAGTGTATCTTTTAATTTT 57.192 29.630 0.00 0.00 0.00 1.82
3471 3749 8.043710 CACTTATCCTCCTTGAGTGTATCTTTT 58.956 37.037 0.00 0.00 34.51 2.27
3472 3750 7.400339 TCACTTATCCTCCTTGAGTGTATCTTT 59.600 37.037 0.00 0.00 38.95 2.52
3474 3752 6.322712 GTCACTTATCCTCCTTGAGTGTATCT 59.677 42.308 0.00 0.00 38.95 1.98
3475 3753 6.461788 GGTCACTTATCCTCCTTGAGTGTATC 60.462 46.154 0.00 0.00 38.95 2.24
3477 3755 4.710375 GGTCACTTATCCTCCTTGAGTGTA 59.290 45.833 0.00 0.00 38.95 2.90
3479 3757 3.515502 TGGTCACTTATCCTCCTTGAGTG 59.484 47.826 0.00 0.00 39.16 3.51
3480 3758 3.791320 TGGTCACTTATCCTCCTTGAGT 58.209 45.455 0.00 0.00 0.00 3.41
3482 3760 4.361783 TCATGGTCACTTATCCTCCTTGA 58.638 43.478 0.00 0.00 32.57 3.02
3483 3761 4.406972 TCTCATGGTCACTTATCCTCCTTG 59.593 45.833 0.00 0.00 0.00 3.61
3484 3762 4.624913 TCTCATGGTCACTTATCCTCCTT 58.375 43.478 0.00 0.00 0.00 3.36
3486 3764 5.104735 ACTTTCTCATGGTCACTTATCCTCC 60.105 44.000 0.00 0.00 0.00 4.30
3487 3765 5.814705 CACTTTCTCATGGTCACTTATCCTC 59.185 44.000 0.00 0.00 0.00 3.71
3488 3766 5.738909 CACTTTCTCATGGTCACTTATCCT 58.261 41.667 0.00 0.00 0.00 3.24
3489 3767 4.333926 GCACTTTCTCATGGTCACTTATCC 59.666 45.833 0.00 0.00 0.00 2.59
3490 3768 5.181748 AGCACTTTCTCATGGTCACTTATC 58.818 41.667 0.00 0.00 0.00 1.75
3491 3769 5.171339 AGCACTTTCTCATGGTCACTTAT 57.829 39.130 0.00 0.00 0.00 1.73
3493 3771 3.498774 AGCACTTTCTCATGGTCACTT 57.501 42.857 0.00 0.00 0.00 3.16
3494 3772 3.615110 CGTAGCACTTTCTCATGGTCACT 60.615 47.826 0.00 0.00 0.00 3.41
3495 3773 2.668457 CGTAGCACTTTCTCATGGTCAC 59.332 50.000 0.00 0.00 0.00 3.67
3496 3774 2.959516 CGTAGCACTTTCTCATGGTCA 58.040 47.619 0.00 0.00 0.00 4.02
3512 3790 1.153549 GGTCAAGGAGCTGGCGTAG 60.154 63.158 0.00 0.00 0.00 3.51
3513 3791 1.264749 ATGGTCAAGGAGCTGGCGTA 61.265 55.000 0.00 0.00 0.00 4.42
3514 3792 2.527951 GATGGTCAAGGAGCTGGCGT 62.528 60.000 0.00 0.00 0.00 5.68
3515 3793 1.817099 GATGGTCAAGGAGCTGGCG 60.817 63.158 0.00 0.00 0.00 5.69
3516 3794 1.817099 CGATGGTCAAGGAGCTGGC 60.817 63.158 0.00 0.00 0.00 4.85
3519 3802 0.463295 CATGCGATGGTCAAGGAGCT 60.463 55.000 0.00 0.00 0.00 4.09
3522 3805 1.451927 GGCATGCGATGGTCAAGGA 60.452 57.895 12.44 0.00 0.00 3.36
3525 3808 2.823593 CCGGCATGCGATGGTCAA 60.824 61.111 12.44 0.00 0.00 3.18
3526 3809 4.094646 ACCGGCATGCGATGGTCA 62.095 61.111 18.83 0.00 0.00 4.02
3531 3814 1.031571 ATGTTTCACCGGCATGCGAT 61.032 50.000 12.44 0.00 0.00 4.58
3537 3820 2.198827 AGATGAATGTTTCACCGGCA 57.801 45.000 0.00 0.00 43.48 5.69
3547 3830 8.394971 TGTTTCTGACAAACATAGATGAATGT 57.605 30.769 0.00 1.08 36.03 2.71
3636 4062 3.721087 TCTGAAGAGTTTTGGATCCCC 57.279 47.619 9.90 0.00 0.00 4.81
3638 4064 5.644206 GGTAGTTCTGAAGAGTTTTGGATCC 59.356 44.000 4.20 4.20 0.00 3.36
3653 4079 9.827411 GAAACTTTGCTAAATAAGGTAGTTCTG 57.173 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.