Multiple sequence alignment - TraesCS1B01G273500

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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 TraesCS1B01G273500 chr1B 100.000 4842 0 0 462 5303 480652949 480657790 0.000000e+00 8942.0
1 TraesCS1B01G273500 chr1B 100.000 58 0 0 1 58 480652488 480652545 2.020000e-19 108.0
2 TraesCS1B01G273500 chr1B 80.435 138 25 2 4092 4228 582544985 582545121 2.610000e-18 104.0
3 TraesCS1B01G273500 chr1A 91.163 2184 80 43 2406 4555 458395173 458397277 0.000000e+00 2859.0
4 TraesCS1B01G273500 chr1A 91.555 1338 56 21 597 1896 458393806 458395124 0.000000e+00 1792.0
5 TraesCS1B01G273500 chr1A 87.616 323 23 10 4647 4960 458397337 458397651 5.050000e-95 359.0
6 TraesCS1B01G273500 chr1A 89.256 121 13 0 2265 2385 592836089 592836209 9.200000e-33 152.0
7 TraesCS1B01G273500 chr1A 94.382 89 5 0 5073 5161 458397720 458397808 2.580000e-28 137.0
8 TraesCS1B01G273500 chr1A 80.435 138 25 2 4092 4228 529665401 529665537 2.610000e-18 104.0
9 TraesCS1B01G273500 chr1A 85.333 75 8 2 3597 3668 529664993 529665067 2.050000e-09 75.0
10 TraesCS1B01G273500 chr1D 96.361 1374 29 6 651 2007 357211674 357213043 0.000000e+00 2241.0
11 TraesCS1B01G273500 chr1D 93.608 1361 42 14 3348 4690 357214192 357215525 0.000000e+00 1989.0
12 TraesCS1B01G273500 chr1D 94.209 708 28 8 2236 2936 357213042 357213743 0.000000e+00 1068.0
13 TraesCS1B01G273500 chr1D 85.150 633 42 26 4680 5303 357215774 357216363 7.600000e-168 601.0
14 TraesCS1B01G273500 chr1D 85.154 357 32 10 2895 3233 357213738 357214091 3.930000e-91 346.0
15 TraesCS1B01G273500 chr1D 90.099 202 11 4 5102 5303 357219699 357219891 2.450000e-63 254.0
16 TraesCS1B01G273500 chr1D 89.604 202 11 4 5102 5303 357217935 357218126 1.140000e-61 248.0
17 TraesCS1B01G273500 chr1D 89.604 202 12 4 5102 5303 357221463 357221655 1.140000e-61 248.0
18 TraesCS1B01G273500 chr1D 81.159 138 24 2 4092 4228 431427074 431427210 5.610000e-20 110.0
19 TraesCS1B01G273500 chr1D 96.552 58 1 1 1 58 357210932 357210988 1.570000e-15 95.3
20 TraesCS1B01G273500 chr7D 86.611 239 28 3 2003 2237 176959069 176959307 1.460000e-65 261.0
21 TraesCS1B01G273500 chr7D 84.436 257 35 4 1987 2238 484967478 484967222 1.140000e-61 248.0
22 TraesCS1B01G273500 chr7D 84.314 255 36 3 1987 2237 214019183 214019437 4.100000e-61 246.0
23 TraesCS1B01G273500 chr2D 86.066 244 28 5 2000 2238 525078063 525077821 1.890000e-64 257.0
24 TraesCS1B01G273500 chr2D 84.436 257 32 5 1987 2238 444860802 444861055 4.100000e-61 246.0
25 TraesCS1B01G273500 chr2D 87.302 126 13 2 2262 2385 563960656 563960780 1.990000e-29 141.0
26 TraesCS1B01G273500 chr2D 96.429 84 2 1 5088 5170 97216090 97216007 2.580000e-28 137.0
27 TraesCS1B01G273500 chr3D 84.496 258 33 6 1987 2238 85475923 85476179 1.140000e-61 248.0
28 TraesCS1B01G273500 chr3D 84.496 258 33 7 1987 2238 591845295 591845039 1.140000e-61 248.0
29 TraesCS1B01G273500 chr3D 85.185 243 32 3 2000 2238 354440443 354440201 4.100000e-61 246.0
30 TraesCS1B01G273500 chr3D 97.561 82 0 1 5088 5167 147815690 147815609 7.160000e-29 139.0
31 TraesCS1B01G273500 chr3D 88.506 87 6 3 3586 3668 44823302 44823388 9.400000e-18 102.0
32 TraesCS1B01G273500 chr3D 78.832 137 22 5 3597 3728 378035004 378034870 9.460000e-13 86.1
33 TraesCS1B01G273500 chr3D 77.778 135 30 0 4073 4207 44823834 44823968 3.400000e-12 84.2
34 TraesCS1B01G273500 chr2B 84.436 257 32 5 1987 2238 69734075 69734328 4.100000e-61 246.0
35 TraesCS1B01G273500 chr2B 84.436 257 32 5 1987 2238 69753327 69753580 4.100000e-61 246.0
36 TraesCS1B01G273500 chr2B 97.561 82 1 1 5088 5168 148205393 148205312 7.160000e-29 139.0
37 TraesCS1B01G273500 chr2B 100.000 32 0 0 15 46 571731045 571731014 5.740000e-05 60.2
38 TraesCS1B01G273500 chr2B 100.000 32 0 0 15 46 571741631 571741600 5.740000e-05 60.2
39 TraesCS1B01G273500 chrUn 87.421 159 11 4 5145 5303 479438655 479438506 1.960000e-39 174.0
40 TraesCS1B01G273500 chr4D 90.756 119 11 0 2267 2385 16356825 16356943 5.500000e-35 159.0
41 TraesCS1B01G273500 chr5B 88.618 123 14 0 2263 2385 294566366 294566488 3.310000e-32 150.0
42 TraesCS1B01G273500 chr6D 89.076 119 13 0 2267 2385 456668613 456668495 1.190000e-31 148.0
43 TraesCS1B01G273500 chr4B 89.076 119 13 0 2267 2385 68958138 68958020 1.190000e-31 148.0
44 TraesCS1B01G273500 chr4B 91.304 46 4 0 13 58 68732677 68732632 4.430000e-06 63.9
45 TraesCS1B01G273500 chr2A 89.076 119 13 0 2267 2385 176566638 176566520 1.190000e-31 148.0
46 TraesCS1B01G273500 chr6A 88.333 120 14 0 2266 2385 387992008 387992127 1.540000e-30 145.0
47 TraesCS1B01G273500 chr3B 92.308 104 5 2 5088 5188 214568914 214569017 1.540000e-30 145.0
48 TraesCS1B01G273500 chr3B 90.123 81 5 2 3587 3664 69644339 69644419 9.400000e-18 102.0
49 TraesCS1B01G273500 chr3B 78.519 135 29 0 4073 4207 69644867 69645001 7.310000e-14 89.8
50 TraesCS1B01G273500 chr3B 92.982 57 2 2 3597 3652 492611967 492611912 1.220000e-11 82.4
51 TraesCS1B01G273500 chr3A 100.000 74 0 0 5088 5161 165422451 165422524 2.580000e-28 137.0
52 TraesCS1B01G273500 chr3A 90.244 82 5 2 3586 3664 56591323 56591404 2.610000e-18 104.0
53 TraesCS1B01G273500 chr3A 80.000 135 27 0 4073 4207 56591858 56591992 3.380000e-17 100.0
54 TraesCS1B01G273500 chr3A 92.982 57 2 2 3597 3652 502166634 502166579 1.220000e-11 82.4
55 TraesCS1B01G273500 chr5D 92.857 56 3 1 4 58 340539685 340539630 4.400000e-11 80.5
56 TraesCS1B01G273500 chr5D 93.750 48 2 1 4 50 548944770 548944817 2.650000e-08 71.3
57 TraesCS1B01G273500 chr7A 78.333 120 18 6 3354 3472 459517552 459517440 2.650000e-08 71.3
58 TraesCS1B01G273500 chr4A 93.750 48 2 1 4 50 40453130 40453083 2.650000e-08 71.3
59 TraesCS1B01G273500 chr6B 94.595 37 2 0 4180 4216 455415808 455415844 2.060000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G273500 chr1B 480652488 480657790 5302 False 4525.000000 8942 100.000 1 5303 2 chr1B.!!$F2 5302
1 TraesCS1B01G273500 chr1A 458393806 458397808 4002 False 1286.750000 2859 91.179 597 5161 4 chr1A.!!$F2 4564
2 TraesCS1B01G273500 chr1D 357210932 357221655 10723 False 787.811111 2241 91.149 1 5303 9 chr1D.!!$F2 5302

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
543 549 0.253044 CCCATTTCGCTCCTCCTTCA 59.747 55.0 0.00 0.0 0.00 3.02 F
582 588 0.909610 TTGAGGGGTGAAGGCGAGAT 60.910 55.0 0.00 0.0 0.00 2.75 F
1580 1787 0.319405 AAATCAGCTGGCAAAGTGGC 59.681 50.0 15.13 0.0 44.03 5.01 F
2976 3240 0.242825 GTGTAGCACAGCGGTACTCA 59.757 55.0 0.00 0.0 46.66 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 1599 0.904649 GGAAAGGAAAATGGCCAGGG 59.095 55.0 13.05 0.0 0.00 4.45 R
1708 1919 1.745232 TGACAGAAAAACAGCCGTGT 58.255 45.0 0.00 0.0 39.19 4.49 R
3180 3455 0.317160 GCCCCTGGTTAGTTTTGTGC 59.683 55.0 0.00 0.0 0.00 4.57 R
4973 5579 0.235665 GATGCCGGTACATGCGATTG 59.764 55.0 1.90 0.0 0.00 2.67 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
507 513 2.477845 AAAAATGAGGCCATGGTTGC 57.522 45.000 14.67 3.23 32.36 4.17
535 541 3.436728 GGCCATCCCATTTCGCTC 58.563 61.111 0.00 0.00 0.00 5.03
536 542 2.196245 GGCCATCCCATTTCGCTCC 61.196 63.158 0.00 0.00 0.00 4.70
537 543 1.152881 GCCATCCCATTTCGCTCCT 60.153 57.895 0.00 0.00 0.00 3.69
538 544 1.169034 GCCATCCCATTTCGCTCCTC 61.169 60.000 0.00 0.00 0.00 3.71
539 545 0.536006 CCATCCCATTTCGCTCCTCC 60.536 60.000 0.00 0.00 0.00 4.30
540 546 0.471617 CATCCCATTTCGCTCCTCCT 59.528 55.000 0.00 0.00 0.00 3.69
541 547 1.133976 CATCCCATTTCGCTCCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
542 548 0.541863 TCCCATTTCGCTCCTCCTTC 59.458 55.000 0.00 0.00 0.00 3.46
543 549 0.253044 CCCATTTCGCTCCTCCTTCA 59.747 55.000 0.00 0.00 0.00 3.02
544 550 1.661341 CCATTTCGCTCCTCCTTCAG 58.339 55.000 0.00 0.00 0.00 3.02
545 551 1.012841 CATTTCGCTCCTCCTTCAGC 58.987 55.000 0.00 0.00 0.00 4.26
549 555 3.293702 GCTCCTCCTTCAGCGAGT 58.706 61.111 0.00 0.00 0.00 4.18
550 556 1.140804 GCTCCTCCTTCAGCGAGTC 59.859 63.158 0.00 0.00 0.00 3.36
551 557 1.431440 CTCCTCCTTCAGCGAGTCG 59.569 63.158 8.54 8.54 0.00 4.18
582 588 0.909610 TTGAGGGGTGAAGGCGAGAT 60.910 55.000 0.00 0.00 0.00 2.75
614 623 4.562963 GCCCTTTTACTACTGTACTGTGCT 60.563 45.833 15.01 3.08 0.00 4.40
666 835 3.900888 CCGTAGGCCCATACCCAT 58.099 61.111 0.00 0.00 46.14 4.00
687 856 3.418684 AGAACCGCAAAACCATACTCT 57.581 42.857 0.00 0.00 0.00 3.24
688 857 3.335579 AGAACCGCAAAACCATACTCTC 58.664 45.455 0.00 0.00 0.00 3.20
1043 1228 4.459089 GACGGTGCTCCTCCTGGC 62.459 72.222 2.85 0.00 0.00 4.85
1382 1579 2.747460 TGCTCCACGCATGCTTCC 60.747 61.111 17.13 0.00 45.47 3.46
1426 1623 3.430453 TGGCCATTTTCCTTTCCTACTG 58.570 45.455 0.00 0.00 0.00 2.74
1518 1725 5.742453 CGCCGGTAGTATATGATGTGTTATC 59.258 44.000 1.90 0.00 0.00 1.75
1580 1787 0.319405 AAATCAGCTGGCAAAGTGGC 59.681 50.000 15.13 0.00 44.03 5.01
1639 1846 4.599047 ACATCCTAGAATGAGCTAGTGC 57.401 45.455 0.00 0.00 36.88 4.40
2014 2226 8.879342 TCTATGTAAGTACTACTAACTCCGTC 57.121 38.462 0.00 0.00 0.00 4.79
2015 2227 6.934048 ATGTAAGTACTACTAACTCCGTCC 57.066 41.667 0.00 0.00 0.00 4.79
2016 2228 6.054860 TGTAAGTACTACTAACTCCGTCCT 57.945 41.667 0.00 0.00 0.00 3.85
2017 2229 5.877012 TGTAAGTACTACTAACTCCGTCCTG 59.123 44.000 0.00 0.00 0.00 3.86
2018 2230 3.883669 AGTACTACTAACTCCGTCCTGG 58.116 50.000 0.00 0.00 40.09 4.45
2019 2231 2.895242 ACTACTAACTCCGTCCTGGT 57.105 50.000 0.00 0.00 39.52 4.00
2020 2232 3.166560 ACTACTAACTCCGTCCTGGTT 57.833 47.619 0.00 0.00 39.52 3.67
2021 2233 3.504375 ACTACTAACTCCGTCCTGGTTT 58.496 45.455 0.00 0.00 39.52 3.27
2022 2234 4.666512 ACTACTAACTCCGTCCTGGTTTA 58.333 43.478 0.00 0.00 39.52 2.01
2023 2235 5.267587 ACTACTAACTCCGTCCTGGTTTAT 58.732 41.667 0.00 0.00 39.52 1.40
2024 2236 5.718607 ACTACTAACTCCGTCCTGGTTTATT 59.281 40.000 0.00 0.00 39.52 1.40
2025 2237 4.828829 ACTAACTCCGTCCTGGTTTATTG 58.171 43.478 0.00 0.00 39.52 1.90
2026 2238 2.781681 ACTCCGTCCTGGTTTATTGG 57.218 50.000 0.00 0.00 39.52 3.16
2027 2239 1.982958 ACTCCGTCCTGGTTTATTGGT 59.017 47.619 0.00 0.00 39.52 3.67
2028 2240 2.374170 ACTCCGTCCTGGTTTATTGGTT 59.626 45.455 0.00 0.00 39.52 3.67
2029 2241 3.007635 CTCCGTCCTGGTTTATTGGTTC 58.992 50.000 0.00 0.00 39.52 3.62
2030 2242 2.089201 CCGTCCTGGTTTATTGGTTCC 58.911 52.381 0.00 0.00 0.00 3.62
2031 2243 2.089201 CGTCCTGGTTTATTGGTTCCC 58.911 52.381 0.00 0.00 0.00 3.97
2032 2244 2.290705 CGTCCTGGTTTATTGGTTCCCT 60.291 50.000 0.00 0.00 0.00 4.20
2033 2245 3.774734 GTCCTGGTTTATTGGTTCCCTT 58.225 45.455 0.00 0.00 0.00 3.95
2034 2246 3.762288 GTCCTGGTTTATTGGTTCCCTTC 59.238 47.826 0.00 0.00 0.00 3.46
2035 2247 3.399644 TCCTGGTTTATTGGTTCCCTTCA 59.600 43.478 0.00 0.00 0.00 3.02
2036 2248 4.140900 TCCTGGTTTATTGGTTCCCTTCAA 60.141 41.667 0.00 0.00 0.00 2.69
2037 2249 4.591072 CCTGGTTTATTGGTTCCCTTCAAA 59.409 41.667 0.00 0.00 0.00 2.69
2038 2250 5.071115 CCTGGTTTATTGGTTCCCTTCAAAA 59.929 40.000 0.00 0.00 0.00 2.44
2039 2251 6.239858 CCTGGTTTATTGGTTCCCTTCAAAAT 60.240 38.462 0.00 0.00 0.00 1.82
2040 2252 6.529220 TGGTTTATTGGTTCCCTTCAAAATG 58.471 36.000 0.00 0.00 0.00 2.32
2041 2253 6.100424 TGGTTTATTGGTTCCCTTCAAAATGT 59.900 34.615 0.00 0.00 0.00 2.71
2042 2254 6.426633 GGTTTATTGGTTCCCTTCAAAATGTG 59.573 38.462 0.00 0.00 0.00 3.21
2043 2255 6.739331 TTATTGGTTCCCTTCAAAATGTGT 57.261 33.333 0.00 0.00 0.00 3.72
2044 2256 4.399004 TTGGTTCCCTTCAAAATGTGTG 57.601 40.909 0.00 0.00 0.00 3.82
2045 2257 2.697751 TGGTTCCCTTCAAAATGTGTGG 59.302 45.455 0.00 0.00 0.00 4.17
2046 2258 2.547855 GGTTCCCTTCAAAATGTGTGGC 60.548 50.000 0.00 0.00 0.00 5.01
2047 2259 2.079170 TCCCTTCAAAATGTGTGGCA 57.921 45.000 0.00 0.00 0.00 4.92
2048 2260 2.392662 TCCCTTCAAAATGTGTGGCAA 58.607 42.857 0.00 0.00 0.00 4.52
2049 2261 2.768527 TCCCTTCAAAATGTGTGGCAAA 59.231 40.909 0.00 0.00 0.00 3.68
2050 2262 3.390639 TCCCTTCAAAATGTGTGGCAAAT 59.609 39.130 0.00 0.00 0.00 2.32
2051 2263 4.136051 CCCTTCAAAATGTGTGGCAAATT 58.864 39.130 0.00 0.00 0.00 1.82
2052 2264 4.579753 CCCTTCAAAATGTGTGGCAAATTT 59.420 37.500 0.00 0.00 33.24 1.82
2053 2265 5.067544 CCCTTCAAAATGTGTGGCAAATTTT 59.932 36.000 9.68 9.68 40.59 1.82
2057 2269 5.497635 AAAATGTGTGGCAAATTTTGACC 57.502 34.783 12.38 12.60 39.10 4.02
2058 2270 3.834489 ATGTGTGGCAAATTTTGACCA 57.166 38.095 12.38 14.75 38.13 4.02
2059 2271 3.616956 TGTGTGGCAAATTTTGACCAA 57.383 38.095 19.85 11.73 38.13 3.67
2060 2272 3.942829 TGTGTGGCAAATTTTGACCAAA 58.057 36.364 19.85 14.99 38.13 3.28
2061 2273 4.521146 TGTGTGGCAAATTTTGACCAAAT 58.479 34.783 19.85 0.00 38.13 2.32
2062 2274 5.674525 TGTGTGGCAAATTTTGACCAAATA 58.325 33.333 19.85 13.68 38.13 1.40
2063 2275 6.115446 TGTGTGGCAAATTTTGACCAAATAA 58.885 32.000 19.85 9.93 38.13 1.40
2064 2276 6.769822 TGTGTGGCAAATTTTGACCAAATAAT 59.230 30.769 19.85 0.00 38.13 1.28
2065 2277 7.284034 TGTGTGGCAAATTTTGACCAAATAATT 59.716 29.630 19.85 0.00 38.13 1.40
2066 2278 8.778358 GTGTGGCAAATTTTGACCAAATAATTA 58.222 29.630 19.85 0.00 38.13 1.40
2067 2279 9.342308 TGTGGCAAATTTTGACCAAATAATTAA 57.658 25.926 19.85 0.00 38.13 1.40
2068 2280 9.605955 GTGGCAAATTTTGACCAAATAATTAAC 57.394 29.630 19.85 3.82 38.13 2.01
2069 2281 9.566432 TGGCAAATTTTGACCAAATAATTAACT 57.434 25.926 12.38 0.00 38.13 2.24
2089 2301 9.685828 ATTAACTAACAAAATGTTAACGCATGT 57.314 25.926 0.26 1.10 41.70 3.21
2090 2302 7.995463 AACTAACAAAATGTTAACGCATGTT 57.005 28.000 17.28 17.28 41.70 2.71
2092 2304 9.517609 AACTAACAAAATGTTAACGCATGTTAA 57.482 25.926 18.40 0.00 45.76 2.01
2167 2379 6.615264 TTTTTGTAACATGCATGCACATTT 57.385 29.167 25.37 17.89 0.00 2.32
2168 2380 6.615264 TTTTGTAACATGCATGCACATTTT 57.385 29.167 25.37 15.38 0.00 1.82
2169 2381 5.593183 TTGTAACATGCATGCACATTTTG 57.407 34.783 25.37 19.32 0.00 2.44
2170 2382 4.629092 TGTAACATGCATGCACATTTTGT 58.371 34.783 25.37 20.04 0.00 2.83
2171 2383 5.055144 TGTAACATGCATGCACATTTTGTT 58.945 33.333 29.31 29.31 0.00 2.83
2172 2384 6.218746 TGTAACATGCATGCACATTTTGTTA 58.781 32.000 27.72 27.72 0.00 2.41
2173 2385 5.849357 AACATGCATGCACATTTTGTTAG 57.151 34.783 26.92 10.09 0.00 2.34
2174 2386 4.885413 ACATGCATGCACATTTTGTTAGT 58.115 34.783 25.37 0.00 0.00 2.24
2175 2387 5.299148 ACATGCATGCACATTTTGTTAGTT 58.701 33.333 25.37 0.00 0.00 2.24
2176 2388 6.453943 ACATGCATGCACATTTTGTTAGTTA 58.546 32.000 25.37 0.00 0.00 2.24
2177 2389 6.927936 ACATGCATGCACATTTTGTTAGTTAA 59.072 30.769 25.37 0.00 0.00 2.01
2178 2390 7.603404 ACATGCATGCACATTTTGTTAGTTAAT 59.397 29.630 25.37 0.00 0.00 1.40
2179 2391 7.959689 TGCATGCACATTTTGTTAGTTAATT 57.040 28.000 18.46 0.00 0.00 1.40
2180 2392 8.375608 TGCATGCACATTTTGTTAGTTAATTT 57.624 26.923 18.46 0.00 0.00 1.82
2181 2393 9.481340 TGCATGCACATTTTGTTAGTTAATTTA 57.519 25.926 18.46 0.00 0.00 1.40
2185 2397 9.988815 TGCACATTTTGTTAGTTAATTTATGGT 57.011 25.926 0.00 0.00 0.00 3.55
2221 2433 8.876181 ACAAAATATAATGGGGGCTAATAAACC 58.124 33.333 0.00 0.00 0.00 3.27
2222 2434 8.875168 CAAAATATAATGGGGGCTAATAAACCA 58.125 33.333 0.00 0.00 35.39 3.67
2223 2435 9.628244 AAAATATAATGGGGGCTAATAAACCAT 57.372 29.630 0.00 0.00 43.39 3.55
2226 2438 9.709387 ATATAATGGGGGCTAATAAACCATAAC 57.291 33.333 0.00 0.00 40.84 1.89
2227 2439 4.883021 TGGGGGCTAATAAACCATAACA 57.117 40.909 0.00 0.00 0.00 2.41
2228 2440 4.798882 TGGGGGCTAATAAACCATAACAG 58.201 43.478 0.00 0.00 0.00 3.16
2229 2441 4.479056 TGGGGGCTAATAAACCATAACAGA 59.521 41.667 0.00 0.00 0.00 3.41
2230 2442 5.070685 GGGGGCTAATAAACCATAACAGAG 58.929 45.833 0.00 0.00 0.00 3.35
2231 2443 5.070685 GGGGCTAATAAACCATAACAGAGG 58.929 45.833 0.00 0.00 0.00 3.69
2232 2444 5.070685 GGGCTAATAAACCATAACAGAGGG 58.929 45.833 0.00 0.00 34.11 4.30
2233 2445 5.163131 GGGCTAATAAACCATAACAGAGGGA 60.163 44.000 0.00 0.00 31.54 4.20
2234 2446 5.998363 GGCTAATAAACCATAACAGAGGGAG 59.002 44.000 0.00 0.00 31.54 4.30
2235 2447 6.409349 GGCTAATAAACCATAACAGAGGGAGT 60.409 42.308 0.00 0.00 31.54 3.85
2236 2448 7.202066 GGCTAATAAACCATAACAGAGGGAGTA 60.202 40.741 0.00 0.00 31.54 2.59
2239 2451 8.849543 AATAAACCATAACAGAGGGAGTACTA 57.150 34.615 0.00 0.00 31.54 1.82
2247 2459 9.624373 CATAACAGAGGGAGTACTAGTTAACTA 57.376 37.037 14.52 14.52 0.00 2.24
2253 2465 9.372189 AGAGGGAGTACTAGTTAACTACAAAAA 57.628 33.333 11.38 0.00 0.00 1.94
2307 2519 1.108776 AAGTCTTGCGCGTATCCCTA 58.891 50.000 8.43 0.00 0.00 3.53
2345 2557 7.710907 TGACCAACATAAGATGAGTTGTATAGC 59.289 37.037 0.00 0.00 40.64 2.97
2461 2673 5.572252 TGGAATTGGATATGCTCATATGCA 58.428 37.500 16.64 16.64 45.97 3.96
2462 2674 7.344612 AATGGAATTGGATATGCTCATATGCAT 59.655 33.333 19.79 3.79 46.55 3.96
2672 2891 4.941263 TGCATGTACTACTCCAATGGAAAC 59.059 41.667 2.61 0.00 0.00 2.78
2689 2908 4.409574 TGGAAACCCACACTTGAGTACTAA 59.590 41.667 0.00 0.00 0.00 2.24
2696 2915 7.686434 ACCCACACTTGAGTACTAATGTTTAT 58.314 34.615 0.00 0.00 0.00 1.40
2843 3065 3.430513 GCTTGAAGCCTAGTACCAGTACC 60.431 52.174 5.74 0.00 34.29 3.34
2891 3113 3.079578 CTCCATGTGCTCATTCAAGTGT 58.920 45.455 0.00 0.00 31.15 3.55
2903 3125 6.462552 TCATTCAAGTGTATGAGAGAGAGG 57.537 41.667 0.00 0.00 30.15 3.69
2907 3129 4.017958 TCAAGTGTATGAGAGAGAGGGAGT 60.018 45.833 0.00 0.00 0.00 3.85
2911 3133 3.525609 TGTATGAGAGAGAGGGAGTGAGT 59.474 47.826 0.00 0.00 0.00 3.41
2976 3240 0.242825 GTGTAGCACAGCGGTACTCA 59.757 55.000 0.00 0.00 46.66 3.41
3157 3427 7.926555 TGTATAGTACTCTACTACGGTGGTAAC 59.073 40.741 16.68 1.62 43.46 2.50
3180 3455 7.730364 ACTAAATACTCCGCCAATAATTCAG 57.270 36.000 0.00 0.00 0.00 3.02
3210 3485 1.377725 CCAGGGGCTGCAACTGTAG 60.378 63.158 17.59 4.20 0.00 2.74
3235 3510 8.582437 AGCAAATCTTAGTTACTGTACAGTACA 58.418 33.333 30.76 20.09 43.02 2.90
3241 3516 9.687210 TCTTAGTTACTGTACAGTACAAACATG 57.313 33.333 30.76 20.67 43.02 3.21
3242 3517 9.687210 CTTAGTTACTGTACAGTACAAACATGA 57.313 33.333 30.76 14.14 43.02 3.07
3245 3520 9.555727 AGTTACTGTACAGTACAAACATGATTT 57.444 29.630 30.76 11.86 43.02 2.17
3298 3573 7.745015 TGATTAGTTACCGCAAACAATTACTC 58.255 34.615 1.65 0.00 0.00 2.59
3299 3574 4.657075 AGTTACCGCAAACAATTACTCG 57.343 40.909 1.65 0.00 0.00 4.18
3321 3609 3.206150 ACGTACCGTGGATTATACGAGT 58.794 45.455 12.10 0.00 43.82 4.18
3372 3666 3.790437 GCTGAGCTGCTGGGGCTA 61.790 66.667 7.01 0.00 40.40 3.93
3387 3681 3.077556 CTACCCCTGCTGCCGTCT 61.078 66.667 0.00 0.00 0.00 4.18
3743 4037 0.940126 CTCACCGTAAGCCATGCATC 59.060 55.000 0.00 0.00 0.00 3.91
3744 4038 0.251634 TCACCGTAAGCCATGCATCA 59.748 50.000 0.00 0.00 0.00 3.07
3745 4039 1.134128 TCACCGTAAGCCATGCATCAT 60.134 47.619 0.00 0.00 0.00 2.45
3746 4040 1.677576 CACCGTAAGCCATGCATCATT 59.322 47.619 0.00 0.00 0.00 2.57
3747 4041 2.877786 CACCGTAAGCCATGCATCATTA 59.122 45.455 0.00 0.00 0.00 1.90
3748 4042 2.878406 ACCGTAAGCCATGCATCATTAC 59.122 45.455 0.00 5.74 0.00 1.89
3749 4043 3.141398 CCGTAAGCCATGCATCATTACT 58.859 45.455 16.95 2.12 0.00 2.24
3750 4044 4.202315 ACCGTAAGCCATGCATCATTACTA 60.202 41.667 16.95 0.00 0.00 1.82
3751 4045 4.152402 CCGTAAGCCATGCATCATTACTAC 59.848 45.833 16.95 6.79 0.00 2.73
3752 4046 4.749598 CGTAAGCCATGCATCATTACTACA 59.250 41.667 16.95 0.00 0.00 2.74
3753 4047 5.409520 CGTAAGCCATGCATCATTACTACAT 59.590 40.000 16.95 0.00 0.00 2.29
3754 4048 5.954296 AAGCCATGCATCATTACTACATC 57.046 39.130 0.00 0.00 0.00 3.06
3755 4049 5.238624 AGCCATGCATCATTACTACATCT 57.761 39.130 0.00 0.00 0.00 2.90
3756 4050 5.243981 AGCCATGCATCATTACTACATCTC 58.756 41.667 0.00 0.00 0.00 2.75
3757 4051 4.999311 GCCATGCATCATTACTACATCTCA 59.001 41.667 0.00 0.00 0.00 3.27
3758 4052 5.646793 GCCATGCATCATTACTACATCTCAT 59.353 40.000 0.00 0.00 0.00 2.90
3794 4091 7.544622 AGTAATTGTAAGTTGCATCGTCTCTA 58.455 34.615 0.00 0.00 0.00 2.43
3803 4109 3.937814 TGCATCGTCTCTAAAACCATGT 58.062 40.909 0.00 0.00 0.00 3.21
3807 4113 5.220416 GCATCGTCTCTAAAACCATGTACAC 60.220 44.000 0.00 0.00 0.00 2.90
3816 4122 2.323968 ACCATGTACACGCATGCATA 57.676 45.000 19.57 3.75 43.46 3.14
3817 4123 2.849942 ACCATGTACACGCATGCATAT 58.150 42.857 19.57 4.04 43.46 1.78
3818 4124 2.549329 ACCATGTACACGCATGCATATG 59.451 45.455 19.57 14.71 43.46 1.78
3819 4125 2.549329 CCATGTACACGCATGCATATGT 59.451 45.455 19.57 19.54 43.46 2.29
3843 4151 1.377333 GAGCCTGTACAACCTGGGC 60.377 63.158 13.74 13.74 42.74 5.36
4374 4690 8.958119 ACAGTGTTTCTTCTGTGAGTTAATTA 57.042 30.769 0.00 0.00 42.30 1.40
4379 4695 7.444183 TGTTTCTTCTGTGAGTTAATTACCAGG 59.556 37.037 0.00 0.00 0.00 4.45
4384 4700 7.786046 TCTGTGAGTTAATTACCAGGTTAGA 57.214 36.000 0.00 0.00 0.00 2.10
4476 4798 1.031235 CAATGGTGTTGTGGCTGTCA 58.969 50.000 0.00 0.00 0.00 3.58
4568 4902 4.082625 TGAGATCTTTGCGACCGTACTTAA 60.083 41.667 0.00 0.00 0.00 1.85
4569 4903 5.007385 AGATCTTTGCGACCGTACTTAAT 57.993 39.130 0.00 0.00 0.00 1.40
4570 4904 5.041940 AGATCTTTGCGACCGTACTTAATC 58.958 41.667 0.00 0.00 0.00 1.75
4571 4905 4.177165 TCTTTGCGACCGTACTTAATCA 57.823 40.909 0.00 0.00 0.00 2.57
4619 4953 5.008118 GCCACTGAACTAAGATTTAGATGGC 59.992 44.000 3.04 0.00 36.37 4.40
4641 4975 2.480759 GGCAATCTAGTTACGCCGAGAA 60.481 50.000 0.00 0.00 32.14 2.87
4644 4978 1.456296 TCTAGTTACGCCGAGAAGCA 58.544 50.000 0.00 0.00 0.00 3.91
4649 4983 0.179181 TTACGCCGAGAAGCACGTAG 60.179 55.000 0.00 0.00 41.46 3.51
4663 5001 1.134075 CGTAGCGCGTACAGACTGT 59.866 57.895 13.68 13.68 35.54 3.55
4669 5007 1.521411 CGCGTACAGACTGTAAGACG 58.479 55.000 26.48 23.24 34.90 4.18
4673 5011 3.607775 GCGTACAGACTGTAAGACGAACA 60.608 47.826 25.91 0.00 34.90 3.18
4685 5023 4.410492 AAGACGAACACAATGCTGAATC 57.590 40.909 0.00 0.00 0.00 2.52
4752 5349 1.183549 ACAGAATTACGGAGCCGACT 58.816 50.000 16.83 0.00 42.83 4.18
4823 5420 1.973137 TTTTAATCGCTGCCGCCGTC 61.973 55.000 0.00 0.00 0.00 4.79
4837 5438 0.305313 GCCGTCTCTACAGTAGCTCG 59.695 60.000 2.26 7.19 0.00 5.03
4889 5495 3.886505 ACGGTGGTTTTTCTATTTGCTCA 59.113 39.130 0.00 0.00 0.00 4.26
4950 5556 3.319198 GGTGGAACGGGAGCCTGA 61.319 66.667 1.59 0.00 38.12 3.86
4960 5566 2.373707 GGAGCCTGACCAGCTGGAT 61.374 63.158 39.19 22.71 41.75 3.41
4961 5567 1.153208 GAGCCTGACCAGCTGGATG 60.153 63.158 39.19 24.77 41.75 3.51
4962 5568 1.614525 AGCCTGACCAGCTGGATGA 60.615 57.895 39.19 19.74 39.69 2.92
4963 5569 1.153208 GCCTGACCAGCTGGATGAG 60.153 63.158 39.19 26.74 37.79 2.90
4964 5570 1.908340 GCCTGACCAGCTGGATGAGT 61.908 60.000 39.19 16.91 37.79 3.41
4965 5571 0.107800 CCTGACCAGCTGGATGAGTG 60.108 60.000 39.19 19.81 37.79 3.51
4966 5572 0.612229 CTGACCAGCTGGATGAGTGT 59.388 55.000 39.19 15.22 38.94 3.55
4967 5573 0.322648 TGACCAGCTGGATGAGTGTG 59.677 55.000 39.19 9.60 38.94 3.82
4968 5574 0.392193 GACCAGCTGGATGAGTGTGG 60.392 60.000 39.19 9.95 38.94 4.17
4969 5575 1.748122 CCAGCTGGATGAGTGTGGC 60.748 63.158 29.88 0.00 37.39 5.01
4970 5576 1.298993 CAGCTGGATGAGTGTGGCT 59.701 57.895 5.57 0.00 0.00 4.75
4971 5577 0.743701 CAGCTGGATGAGTGTGGCTC 60.744 60.000 5.57 0.00 44.36 4.70
4986 5592 1.276844 GCTCGCAATCGCATGTACC 59.723 57.895 0.00 0.00 38.40 3.34
4987 5593 1.559814 CTCGCAATCGCATGTACCG 59.440 57.895 0.00 0.00 38.40 4.02
4997 5603 1.215655 GCATGTACCGGCATCTCGAC 61.216 60.000 0.00 0.00 0.00 4.20
4999 5605 0.385751 ATGTACCGGCATCTCGACAG 59.614 55.000 0.00 0.00 0.00 3.51
5009 5615 2.528125 CATCTCGACAGCTCTTCACTG 58.472 52.381 0.00 0.00 41.08 3.66
5019 5625 2.365617 AGCTCTTCACTGACGAGGAAAA 59.634 45.455 13.03 0.00 30.15 2.29
5033 5641 7.083858 TGACGAGGAAAAGCTAAATTCATTTG 58.916 34.615 8.53 3.99 0.00 2.32
5035 5643 7.308435 ACGAGGAAAAGCTAAATTCATTTGAG 58.692 34.615 8.53 0.40 0.00 3.02
5216 11109 4.836125 TTCCTGCACTTTTCATCACTTC 57.164 40.909 0.00 0.00 0.00 3.01
5225 11118 6.420903 GCACTTTTCATCACTTCCTTAAAACC 59.579 38.462 0.00 0.00 0.00 3.27
5230 11123 5.560724 TCATCACTTCCTTAAAACCTCCAG 58.439 41.667 0.00 0.00 0.00 3.86
5232 11125 4.969484 TCACTTCCTTAAAACCTCCAGAC 58.031 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
518 524 2.196245 GGAGCGAAATGGGATGGCC 61.196 63.158 0.00 0.00 0.00 5.36
519 525 1.152881 AGGAGCGAAATGGGATGGC 60.153 57.895 0.00 0.00 0.00 4.40
520 526 0.536006 GGAGGAGCGAAATGGGATGG 60.536 60.000 0.00 0.00 0.00 3.51
521 527 0.471617 AGGAGGAGCGAAATGGGATG 59.528 55.000 0.00 0.00 0.00 3.51
522 528 1.141858 GAAGGAGGAGCGAAATGGGAT 59.858 52.381 0.00 0.00 0.00 3.85
523 529 0.541863 GAAGGAGGAGCGAAATGGGA 59.458 55.000 0.00 0.00 0.00 4.37
524 530 0.253044 TGAAGGAGGAGCGAAATGGG 59.747 55.000 0.00 0.00 0.00 4.00
525 531 1.661341 CTGAAGGAGGAGCGAAATGG 58.339 55.000 0.00 0.00 0.00 3.16
526 532 1.012841 GCTGAAGGAGGAGCGAAATG 58.987 55.000 0.00 0.00 0.00 2.32
527 533 3.467776 GCTGAAGGAGGAGCGAAAT 57.532 52.632 0.00 0.00 0.00 2.17
532 538 1.140804 GACTCGCTGAAGGAGGAGC 59.859 63.158 0.00 0.00 35.82 4.70
533 539 1.431440 CGACTCGCTGAAGGAGGAG 59.569 63.158 0.00 0.00 35.82 3.69
534 540 3.592070 CGACTCGCTGAAGGAGGA 58.408 61.111 0.00 0.00 35.82 3.71
560 566 0.183971 TCGCCTTCACCCCTCAAAAA 59.816 50.000 0.00 0.00 0.00 1.94
561 567 0.250727 CTCGCCTTCACCCCTCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
562 568 1.125093 TCTCGCCTTCACCCCTCAAA 61.125 55.000 0.00 0.00 0.00 2.69
563 569 0.909610 ATCTCGCCTTCACCCCTCAA 60.910 55.000 0.00 0.00 0.00 3.02
564 570 0.909610 AATCTCGCCTTCACCCCTCA 60.910 55.000 0.00 0.00 0.00 3.86
565 571 0.253327 AAATCTCGCCTTCACCCCTC 59.747 55.000 0.00 0.00 0.00 4.30
566 572 1.486726 CTAAATCTCGCCTTCACCCCT 59.513 52.381 0.00 0.00 0.00 4.79
567 573 1.475213 CCTAAATCTCGCCTTCACCCC 60.475 57.143 0.00 0.00 0.00 4.95
570 576 1.954927 CCCCTAAATCTCGCCTTCAC 58.045 55.000 0.00 0.00 0.00 3.18
614 623 2.014128 GGCTAATAAACGGCTTGCTGA 58.986 47.619 8.57 0.00 0.00 4.26
666 835 4.501071 GAGAGTATGGTTTTGCGGTTCTA 58.499 43.478 0.00 0.00 0.00 2.10
687 856 2.622942 GTGCCTGTGATTTGTCAAAGGA 59.377 45.455 16.89 1.87 45.82 3.36
688 857 2.605338 CGTGCCTGTGATTTGTCAAAGG 60.605 50.000 9.78 9.78 45.73 3.11
779 948 3.321950 AGATGGAGAGAGTAAATGGGGG 58.678 50.000 0.00 0.00 0.00 5.40
1101 1286 2.665185 GTGAAGTTCCACGGCGCT 60.665 61.111 6.90 0.00 0.00 5.92
1137 1322 4.767255 CTGGTCCCTGCTGCGTCC 62.767 72.222 0.00 0.00 0.00 4.79
1375 1572 2.050350 ATGCAGCGCAAGGAAGCAT 61.050 52.632 11.47 12.06 43.62 3.79
1402 1599 0.904649 GGAAAGGAAAATGGCCAGGG 59.095 55.000 13.05 0.00 0.00 4.45
1426 1623 3.650139 TGAAGAACTCAAGAAGTACGCC 58.350 45.455 0.00 0.00 37.17 5.68
1518 1725 8.131100 ACAAAATGGCTCGATTTATATGTGAAG 58.869 33.333 0.00 0.00 0.00 3.02
1580 1787 3.995199 TCTACTCAAAAGAGGCACTGTG 58.005 45.455 2.76 2.76 41.55 3.66
1708 1919 1.745232 TGACAGAAAAACAGCCGTGT 58.255 45.000 0.00 0.00 39.19 4.49
1909 2121 7.665559 ACACATACCAATCTAAGCTTCTTTTCA 59.334 33.333 0.00 0.00 0.00 2.69
1916 2128 5.109903 GTCGACACATACCAATCTAAGCTT 58.890 41.667 11.55 3.48 0.00 3.74
2008 2220 2.781681 ACCAATAAACCAGGACGGAG 57.218 50.000 0.00 0.00 38.63 4.63
2010 2222 2.089201 GGAACCAATAAACCAGGACGG 58.911 52.381 0.00 0.00 42.50 4.79
2026 2238 2.102252 TGCCACACATTTTGAAGGGAAC 59.898 45.455 0.00 0.00 0.00 3.62
2027 2239 2.392662 TGCCACACATTTTGAAGGGAA 58.607 42.857 0.00 0.00 0.00 3.97
2028 2240 2.079170 TGCCACACATTTTGAAGGGA 57.921 45.000 0.00 0.00 0.00 4.20
2029 2241 2.906691 TTGCCACACATTTTGAAGGG 57.093 45.000 0.00 0.00 0.00 3.95
2030 2242 5.754543 AAATTTGCCACACATTTTGAAGG 57.245 34.783 0.00 0.00 0.00 3.46
2034 2246 5.163683 TGGTCAAAATTTGCCACACATTTTG 60.164 36.000 18.88 18.88 45.23 2.44
2035 2247 4.946157 TGGTCAAAATTTGCCACACATTTT 59.054 33.333 14.66 0.00 35.13 1.82
2036 2248 4.521146 TGGTCAAAATTTGCCACACATTT 58.479 34.783 14.66 0.00 33.81 2.32
2037 2249 4.148128 TGGTCAAAATTTGCCACACATT 57.852 36.364 14.66 0.00 33.81 2.71
2038 2250 3.834489 TGGTCAAAATTTGCCACACAT 57.166 38.095 14.66 0.00 33.81 3.21
2039 2251 3.616956 TTGGTCAAAATTTGCCACACA 57.383 38.095 17.15 5.20 36.85 3.72
2040 2252 6.610741 TTATTTGGTCAAAATTTGCCACAC 57.389 33.333 17.15 4.54 39.29 3.82
2041 2253 7.814264 AATTATTTGGTCAAAATTTGCCACA 57.186 28.000 17.15 13.15 39.29 4.17
2042 2254 9.605955 GTTAATTATTTGGTCAAAATTTGCCAC 57.394 29.630 17.15 5.46 39.29 5.01
2043 2255 9.566432 AGTTAATTATTTGGTCAAAATTTGCCA 57.434 25.926 14.66 14.66 39.29 4.92
2063 2275 9.685828 ACATGCGTTAACATTTTGTTAGTTAAT 57.314 25.926 6.39 0.00 42.93 1.40
2064 2276 9.517609 AACATGCGTTAACATTTTGTTAGTTAA 57.482 25.926 6.39 0.00 42.93 2.01
2066 2278 7.995463 AACATGCGTTAACATTTTGTTAGTT 57.005 28.000 6.39 0.00 42.93 2.24
2144 2356 6.615264 AAATGTGCATGCATGTTACAAAAA 57.385 29.167 29.45 15.31 33.29 1.94
2145 2357 6.037940 ACAAAATGTGCATGCATGTTACAAAA 59.962 30.769 29.45 15.57 33.29 2.44
2146 2358 5.526479 ACAAAATGTGCATGCATGTTACAAA 59.474 32.000 29.45 16.92 33.29 2.83
2147 2359 5.055144 ACAAAATGTGCATGCATGTTACAA 58.945 33.333 29.45 18.97 33.29 2.41
2148 2360 4.629092 ACAAAATGTGCATGCATGTTACA 58.371 34.783 28.56 28.56 33.78 2.41
2149 2361 5.594724 AACAAAATGTGCATGCATGTTAC 57.405 34.783 26.92 23.87 0.00 2.50
2150 2362 6.453943 ACTAACAAAATGTGCATGCATGTTA 58.546 32.000 28.67 28.67 0.00 2.41
2151 2363 5.299148 ACTAACAAAATGTGCATGCATGTT 58.701 33.333 29.31 29.31 0.00 2.71
2152 2364 4.885413 ACTAACAAAATGTGCATGCATGT 58.115 34.783 25.64 20.28 0.00 3.21
2153 2365 5.849357 AACTAACAAAATGTGCATGCATG 57.151 34.783 25.64 22.70 0.00 4.06
2154 2366 8.550710 AATTAACTAACAAAATGTGCATGCAT 57.449 26.923 25.64 5.67 0.00 3.96
2155 2367 7.959689 AATTAACTAACAAAATGTGCATGCA 57.040 28.000 18.46 18.46 0.00 3.96
2159 2371 9.988815 ACCATAAATTAACTAACAAAATGTGCA 57.011 25.926 0.00 0.00 0.00 4.57
2195 2407 8.876181 GGTTTATTAGCCCCCATTATATTTTGT 58.124 33.333 0.00 0.00 0.00 2.83
2196 2408 8.875168 TGGTTTATTAGCCCCCATTATATTTTG 58.125 33.333 0.00 0.00 0.00 2.44
2197 2409 9.628244 ATGGTTTATTAGCCCCCATTATATTTT 57.372 29.630 0.00 0.00 31.99 1.82
2200 2412 9.709387 GTTATGGTTTATTAGCCCCCATTATAT 57.291 33.333 0.00 0.00 37.17 0.86
2201 2413 8.679725 TGTTATGGTTTATTAGCCCCCATTATA 58.320 33.333 0.00 0.00 37.17 0.98
2202 2414 7.540183 TGTTATGGTTTATTAGCCCCCATTAT 58.460 34.615 0.00 0.00 37.17 1.28
2203 2415 6.923670 TGTTATGGTTTATTAGCCCCCATTA 58.076 36.000 0.00 0.00 37.17 1.90
2204 2416 5.782925 TGTTATGGTTTATTAGCCCCCATT 58.217 37.500 0.00 0.00 37.17 3.16
2205 2417 5.135362 TCTGTTATGGTTTATTAGCCCCCAT 59.865 40.000 0.00 0.00 39.22 4.00
2206 2418 4.479056 TCTGTTATGGTTTATTAGCCCCCA 59.521 41.667 0.00 0.00 0.00 4.96
2207 2419 5.056553 TCTGTTATGGTTTATTAGCCCCC 57.943 43.478 0.00 0.00 0.00 5.40
2208 2420 5.070685 CCTCTGTTATGGTTTATTAGCCCC 58.929 45.833 0.00 0.00 0.00 5.80
2209 2421 5.070685 CCCTCTGTTATGGTTTATTAGCCC 58.929 45.833 0.00 0.00 0.00 5.19
2210 2422 5.937111 TCCCTCTGTTATGGTTTATTAGCC 58.063 41.667 0.00 0.00 0.00 3.93
2211 2423 6.592870 ACTCCCTCTGTTATGGTTTATTAGC 58.407 40.000 0.00 0.00 0.00 3.09
2212 2424 8.925338 AGTACTCCCTCTGTTATGGTTTATTAG 58.075 37.037 0.00 0.00 0.00 1.73
2213 2425 8.849543 AGTACTCCCTCTGTTATGGTTTATTA 57.150 34.615 0.00 0.00 0.00 0.98
2214 2426 7.750947 AGTACTCCCTCTGTTATGGTTTATT 57.249 36.000 0.00 0.00 0.00 1.40
2215 2427 8.066247 ACTAGTACTCCCTCTGTTATGGTTTAT 58.934 37.037 0.00 0.00 0.00 1.40
2216 2428 7.416731 ACTAGTACTCCCTCTGTTATGGTTTA 58.583 38.462 0.00 0.00 0.00 2.01
2217 2429 6.262207 ACTAGTACTCCCTCTGTTATGGTTT 58.738 40.000 0.00 0.00 0.00 3.27
2218 2430 5.840081 ACTAGTACTCCCTCTGTTATGGTT 58.160 41.667 0.00 0.00 0.00 3.67
2219 2431 5.469210 ACTAGTACTCCCTCTGTTATGGT 57.531 43.478 0.00 0.00 0.00 3.55
2220 2432 7.560626 AGTTAACTAGTACTCCCTCTGTTATGG 59.439 40.741 6.26 0.00 0.00 2.74
2221 2433 8.522542 AGTTAACTAGTACTCCCTCTGTTATG 57.477 38.462 6.26 0.00 0.00 1.90
2222 2434 9.625747 GTAGTTAACTAGTACTCCCTCTGTTAT 57.374 37.037 15.68 0.00 31.17 1.89
2223 2435 8.605947 TGTAGTTAACTAGTACTCCCTCTGTTA 58.394 37.037 15.68 0.00 34.35 2.41
2224 2436 7.465116 TGTAGTTAACTAGTACTCCCTCTGTT 58.535 38.462 15.68 0.00 34.35 3.16
2225 2437 7.025520 TGTAGTTAACTAGTACTCCCTCTGT 57.974 40.000 15.68 0.00 34.35 3.41
2226 2438 7.934855 TTGTAGTTAACTAGTACTCCCTCTG 57.065 40.000 15.68 0.00 34.35 3.35
2227 2439 8.946797 TTTTGTAGTTAACTAGTACTCCCTCT 57.053 34.615 15.68 0.00 34.35 3.69
2256 2468 9.720769 CCAGAAATGAGGTAGTAGTTCTTTTTA 57.279 33.333 0.00 0.00 29.77 1.52
2275 2487 5.447279 CGCGCAAGACTTATAAACCAGAAAT 60.447 40.000 8.75 0.00 43.02 2.17
2281 2493 4.084693 GGATACGCGCAAGACTTATAAACC 60.085 45.833 5.73 0.00 43.02 3.27
2461 2673 5.190528 CCCTGAGGAATGTACCTGCATATAT 59.809 44.000 0.00 0.00 40.73 0.86
2462 2674 4.532126 CCCTGAGGAATGTACCTGCATATA 59.468 45.833 0.00 0.00 40.73 0.86
2523 2735 8.121305 ACATTACACAATGAAATTCTAGCCAA 57.879 30.769 4.46 0.00 43.67 4.52
2672 2891 7.065803 CCATAAACATTAGTACTCAAGTGTGGG 59.934 40.741 0.00 0.00 0.00 4.61
2689 2908 6.156602 TGATTTGCTTGGATTCCCATAAACAT 59.843 34.615 0.00 0.00 43.12 2.71
2818 3040 3.447944 ACTGGTACTAGGCTTCAAGCTAC 59.552 47.826 9.83 3.65 41.99 3.58
2843 3065 4.595116 CCGGTCAGTAGTTATTACAGTCG 58.405 47.826 0.00 0.00 34.56 4.18
2891 3113 3.783082 TCACTCACTCCCTCTCTCTCATA 59.217 47.826 0.00 0.00 0.00 2.15
2903 3125 4.592485 TTTCACTCTTCTCACTCACTCC 57.408 45.455 0.00 0.00 0.00 3.85
2907 3129 5.596361 ACTCTCTTTTCACTCTTCTCACTCA 59.404 40.000 0.00 0.00 0.00 3.41
2911 3133 5.830457 TCTCACTCTCTTTTCACTCTTCTCA 59.170 40.000 0.00 0.00 0.00 3.27
3142 3412 7.519008 CGGAGTATTTAGTTACCACCGTAGTAG 60.519 44.444 0.00 0.00 37.56 2.57
3157 3427 6.204688 TGCTGAATTATTGGCGGAGTATTTAG 59.795 38.462 0.00 0.00 0.00 1.85
3180 3455 0.317160 GCCCCTGGTTAGTTTTGTGC 59.683 55.000 0.00 0.00 0.00 4.57
3210 3485 8.752766 TGTACTGTACAGTAACTAAGATTTGC 57.247 34.615 32.02 17.67 44.62 3.68
3249 3524 2.634815 TGTACTACCACGGGCAAAAA 57.365 45.000 0.00 0.00 0.00 1.94
3250 3525 2.617774 GTTTGTACTACCACGGGCAAAA 59.382 45.455 0.00 0.00 0.00 2.44
3251 3526 2.220313 GTTTGTACTACCACGGGCAAA 58.780 47.619 0.00 0.00 0.00 3.68
3252 3527 1.140452 TGTTTGTACTACCACGGGCAA 59.860 47.619 0.00 0.00 0.00 4.52
3253 3528 0.757512 TGTTTGTACTACCACGGGCA 59.242 50.000 0.00 0.00 0.00 5.36
3254 3529 1.735571 CATGTTTGTACTACCACGGGC 59.264 52.381 0.00 0.00 0.00 6.13
3255 3530 3.322211 TCATGTTTGTACTACCACGGG 57.678 47.619 0.00 0.00 0.00 5.28
3256 3531 6.103997 ACTAATCATGTTTGTACTACCACGG 58.896 40.000 0.00 0.00 0.00 4.94
3257 3532 7.591006 AACTAATCATGTTTGTACTACCACG 57.409 36.000 0.00 0.00 0.00 4.94
3258 3533 8.876790 GGTAACTAATCATGTTTGTACTACCAC 58.123 37.037 0.00 0.00 0.00 4.16
3259 3534 7.760794 CGGTAACTAATCATGTTTGTACTACCA 59.239 37.037 15.14 0.00 0.00 3.25
3260 3535 7.254218 GCGGTAACTAATCATGTTTGTACTACC 60.254 40.741 0.00 6.43 0.00 3.18
3261 3536 7.276218 TGCGGTAACTAATCATGTTTGTACTAC 59.724 37.037 0.00 0.00 0.00 2.73
3262 3537 7.321908 TGCGGTAACTAATCATGTTTGTACTA 58.678 34.615 0.00 0.00 0.00 1.82
3321 3609 7.862372 ACAAACACGTCGAGAGTTAATTAACTA 59.138 33.333 26.80 11.78 45.84 2.24
3336 3624 0.993251 CTGCATGCACAAACACGTCG 60.993 55.000 18.46 0.00 0.00 5.12
3372 3666 2.606519 TTAGACGGCAGCAGGGGT 60.607 61.111 0.00 0.00 0.00 4.95
3387 3681 0.320073 CGTTGGAGGCCTCGTTGTTA 60.320 55.000 26.36 5.58 0.00 2.41
3794 4091 1.611006 TGCATGCGTGTACATGGTTTT 59.389 42.857 16.68 0.00 46.14 2.43
3803 4109 1.790043 GCGTACATATGCATGCGTGTA 59.210 47.619 22.77 21.10 38.10 2.90
3807 4113 1.125566 CTCTGCGTACATATGCATGCG 59.874 52.381 14.09 7.40 46.08 4.73
3816 4122 1.182667 TGTACAGGCTCTGCGTACAT 58.817 50.000 10.49 0.00 40.29 2.29
3817 4123 0.963225 TTGTACAGGCTCTGCGTACA 59.037 50.000 10.49 10.49 42.70 2.90
3818 4124 1.347320 GTTGTACAGGCTCTGCGTAC 58.653 55.000 6.04 6.04 34.37 3.67
3819 4125 0.245539 GGTTGTACAGGCTCTGCGTA 59.754 55.000 0.00 0.00 34.37 4.42
3843 4151 4.143333 ATCACGAACCTCCGGGCG 62.143 66.667 0.00 0.50 35.63 6.13
4379 4695 3.734293 GCACACGGTACTCCAGATCTAAC 60.734 52.174 0.00 0.00 0.00 2.34
4384 4700 0.818296 GAGCACACGGTACTCCAGAT 59.182 55.000 0.00 0.00 0.00 2.90
4649 4983 1.257539 GTCTTACAGTCTGTACGCGC 58.742 55.000 12.37 0.00 31.69 6.86
4663 5001 4.091365 CGATTCAGCATTGTGTTCGTCTTA 59.909 41.667 0.00 0.00 0.00 2.10
4669 5007 2.160219 TCAGCGATTCAGCATTGTGTTC 59.840 45.455 0.00 0.00 40.15 3.18
4673 5011 1.065102 GCATCAGCGATTCAGCATTGT 59.935 47.619 0.00 0.00 40.15 2.71
4735 5332 0.381089 CGAGTCGGCTCCGTAATTCT 59.619 55.000 12.25 1.30 38.49 2.40
4757 5354 0.397187 AAAACCAAGCCATGCATGCA 59.603 45.000 25.04 25.04 0.00 3.96
4758 5355 2.383368 TAAAACCAAGCCATGCATGC 57.617 45.000 21.69 11.82 0.00 4.06
4759 5356 4.919168 CGATATAAAACCAAGCCATGCATG 59.081 41.667 20.19 20.19 0.00 4.06
4760 5357 4.559300 GCGATATAAAACCAAGCCATGCAT 60.559 41.667 0.00 0.00 0.00 3.96
4823 5420 1.649815 CCGCCGAGCTACTGTAGAG 59.350 63.158 18.64 8.39 0.00 2.43
4950 5556 1.681666 CCACACTCATCCAGCTGGT 59.318 57.895 31.58 16.68 36.34 4.00
4960 5566 1.737735 CGATTGCGAGCCACACTCA 60.738 57.895 0.00 0.00 46.63 3.41
4961 5567 3.084579 CGATTGCGAGCCACACTC 58.915 61.111 0.00 0.00 42.47 3.51
4962 5568 3.121030 GCGATTGCGAGCCACACT 61.121 61.111 0.00 0.00 40.82 3.55
4972 5578 1.785041 ATGCCGGTACATGCGATTGC 61.785 55.000 1.90 0.00 43.20 3.56
4973 5579 0.235665 GATGCCGGTACATGCGATTG 59.764 55.000 1.90 0.00 0.00 2.67
4986 5592 0.869454 GAAGAGCTGTCGAGATGCCG 60.869 60.000 0.00 0.00 0.00 5.69
4987 5593 0.174389 TGAAGAGCTGTCGAGATGCC 59.826 55.000 0.00 0.00 0.00 4.40
4997 5603 0.884514 TCCTCGTCAGTGAAGAGCTG 59.115 55.000 25.40 15.52 36.97 4.24
4999 5605 2.440539 TTTCCTCGTCAGTGAAGAGC 57.559 50.000 25.40 0.00 36.97 4.09
5009 5615 7.305474 TCAAATGAATTTAGCTTTTCCTCGTC 58.695 34.615 0.00 0.00 0.00 4.20
5063 5671 8.776470 GGCGCCTTTTGTTATATACACTTTATA 58.224 33.333 22.15 0.00 36.21 0.98
5068 5676 3.881089 GGGCGCCTTTTGTTATATACACT 59.119 43.478 28.56 0.00 36.21 3.55
5069 5677 3.004002 GGGGCGCCTTTTGTTATATACAC 59.996 47.826 28.56 2.65 36.21 2.90
5071 5679 2.555325 GGGGGCGCCTTTTGTTATATAC 59.445 50.000 28.56 3.90 0.00 1.47
5074 5682 0.748729 CGGGGGCGCCTTTTGTTATA 60.749 55.000 28.56 0.00 0.00 0.98
5086 5695 3.771160 AACTGAGCTACGGGGGCG 61.771 66.667 0.00 0.00 34.52 6.13
5190 9327 4.507756 GTGATGAAAAGTGCAGGAAAAACC 59.492 41.667 0.00 0.00 39.35 3.27
5191 9328 5.351458 AGTGATGAAAAGTGCAGGAAAAAC 58.649 37.500 0.00 0.00 0.00 2.43
5197 11090 3.152341 AGGAAGTGATGAAAAGTGCAGG 58.848 45.455 0.00 0.00 0.00 4.85
5200 11093 6.420903 GGTTTTAAGGAAGTGATGAAAAGTGC 59.579 38.462 0.00 0.00 0.00 4.40
5210 11103 4.410883 TGTCTGGAGGTTTTAAGGAAGTGA 59.589 41.667 0.00 0.00 0.00 3.41
5216 11109 3.790089 AGGTGTCTGGAGGTTTTAAGG 57.210 47.619 0.00 0.00 0.00 2.69
5225 11118 6.531948 CGTATAAGAAAAGAAGGTGTCTGGAG 59.468 42.308 0.00 0.00 36.40 3.86
5230 11123 8.530269 TTTCTCGTATAAGAAAAGAAGGTGTC 57.470 34.615 0.00 0.00 41.17 3.67
5232 11125 8.535690 ACTTTCTCGTATAAGAAAAGAAGGTG 57.464 34.615 19.54 5.25 42.93 4.00


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

AutoCloner maintained by Alex Coulton.