Multiple sequence alignment - TraesCS7A01G404100

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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 TraesCS7A01G404100 chr7A 100.000 4393 0 0 824 5216 585055082 585059474 0.000000e+00 8113.0
1 TraesCS7A01G404100 chr7A 100.000 568 0 0 1 568 585054259 585054826 0.000000e+00 1050.0
2 TraesCS7A01G404100 chr7A 100.000 192 0 0 5598 5789 585059856 585060047 7.130000e-94 355.0
3 TraesCS7A01G404100 chr7A 78.832 137 29 0 4626 4762 585064741 585064877 6.180000e-15 93.5
4 TraesCS7A01G404100 chr7D 91.159 4468 219 82 861 5213 512269559 512273965 0.000000e+00 5901.0
5 TraesCS7A01G404100 chr7D 88.679 318 27 6 40 357 512268999 512269307 4.230000e-101 379.0
6 TraesCS7A01G404100 chr7D 93.122 189 4 2 375 563 512269290 512269469 9.560000e-68 268.0
7 TraesCS7A01G404100 chr7D 91.146 192 10 2 5598 5789 512274104 512274288 2.680000e-63 254.0
8 TraesCS7A01G404100 chr7B 89.912 2726 174 56 1406 4074 544123077 544125758 0.000000e+00 3417.0
9 TraesCS7A01G404100 chr7B 91.455 1182 63 26 4055 5213 544131711 544132877 0.000000e+00 1589.0
10 TraesCS7A01G404100 chr7B 96.737 429 5 4 991 1410 544117373 544117801 0.000000e+00 706.0
11 TraesCS7A01G404100 chr7B 93.714 175 6 2 5598 5772 544133007 544133176 2.070000e-64 257.0
12 TraesCS7A01G404100 chr7B 98.473 131 2 0 861 991 544117207 544117337 1.250000e-56 231.0
13 TraesCS7A01G404100 chr7B 73.711 388 66 28 4381 4762 544137586 544137943 1.020000e-22 119.0
14 TraesCS7A01G404100 chr4B 88.550 262 19 9 3612 3872 355228073 355228324 2.030000e-79 307.0
15 TraesCS7A01G404100 chr4B 88.550 262 18 10 3612 3872 355245994 355246244 2.030000e-79 307.0
16 TraesCS7A01G404100 chr4B 88.168 262 19 10 3612 3872 355237026 355237276 9.430000e-78 302.0
17 TraesCS7A01G404100 chr3A 89.105 257 15 10 3618 3872 84678992 84679237 2.030000e-79 307.0
18 TraesCS7A01G404100 chr1B 88.550 262 18 7 3612 3872 546252497 546252747 2.030000e-79 307.0
19 TraesCS7A01G404100 chr1A 100.000 37 0 0 2482 2518 6301345 6301381 1.040000e-07 69.4


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 TraesCS7A01G404100 chr7A 585054259 585060047 5788 False 3172.666667 8113 100.0000 1 5789 3 chr7A.!!$F2 5788
1 TraesCS7A01G404100 chr7D 512268999 512274288 5289 False 1700.500000 5901 91.0265 40 5789 4 chr7D.!!$F1 5749
2 TraesCS7A01G404100 chr7B 544123077 544125758 2681 False 3417.000000 3417 89.9120 1406 4074 1 chr7B.!!$F1 2668
3 TraesCS7A01G404100 chr7B 544131711 544133176 1465 False 923.000000 1589 92.5845 4055 5772 2 chr7B.!!$F4 1717
4 TraesCS7A01G404100 chr7B 544117207 544117801 594 False 468.500000 706 97.6050 861 1410 2 chr7B.!!$F3 549

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
165 166 0.593128 ACGCAGGTTGCAGATTGTTC 59.407 50.0 1.69 0.00 45.36 3.18 F
1903 2021 0.627451 TCATGCAAGGCCTTCTGGAT 59.373 50.0 17.29 10.68 34.57 3.41 F
3386 3549 0.319555 CGAGCACCTTCGACTGGAAA 60.320 55.0 10.28 0.00 43.03 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2056 0.321564 CGTCATCCACACCACCATGT 60.322 55.0 0.0 0.0 0.00 3.21 R
3645 3808 0.167470 CAGAGTTGCCATTGCGTCAG 59.833 55.0 0.0 0.0 41.78 3.51 R
4815 5003 0.034616 AAGCTCTGGTCTGTCTGCAC 59.965 55.0 0.0 0.0 0.00 4.57 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
22 23 4.718961 ACATCTTTCAGTGGTTGCTAAGT 58.281 39.130 0.00 0.00 0.00 2.24
23 24 5.865085 ACATCTTTCAGTGGTTGCTAAGTA 58.135 37.500 0.00 0.00 0.00 2.24
24 25 5.701290 ACATCTTTCAGTGGTTGCTAAGTAC 59.299 40.000 0.00 0.00 0.00 2.73
25 26 5.546621 TCTTTCAGTGGTTGCTAAGTACT 57.453 39.130 0.00 0.00 0.00 2.73
26 27 6.659745 TCTTTCAGTGGTTGCTAAGTACTA 57.340 37.500 0.00 0.00 0.00 1.82
27 28 6.453092 TCTTTCAGTGGTTGCTAAGTACTAC 58.547 40.000 0.00 0.00 0.00 2.73
28 29 5.794726 TTCAGTGGTTGCTAAGTACTACA 57.205 39.130 0.00 0.00 0.00 2.74
29 30 5.130292 TCAGTGGTTGCTAAGTACTACAC 57.870 43.478 0.00 0.00 0.00 2.90
30 31 4.021719 TCAGTGGTTGCTAAGTACTACACC 60.022 45.833 0.00 0.00 0.00 4.16
31 32 3.260128 AGTGGTTGCTAAGTACTACACCC 59.740 47.826 0.00 0.00 0.00 4.61
32 33 3.260128 GTGGTTGCTAAGTACTACACCCT 59.740 47.826 0.00 0.00 0.00 4.34
33 34 3.512724 TGGTTGCTAAGTACTACACCCTC 59.487 47.826 0.00 0.00 0.00 4.30
34 35 3.118847 GGTTGCTAAGTACTACACCCTCC 60.119 52.174 0.00 0.00 0.00 4.30
35 36 3.461378 TGCTAAGTACTACACCCTCCA 57.539 47.619 0.00 0.00 0.00 3.86
36 37 3.990369 TGCTAAGTACTACACCCTCCAT 58.010 45.455 0.00 0.00 0.00 3.41
37 38 4.359105 TGCTAAGTACTACACCCTCCATT 58.641 43.478 0.00 0.00 0.00 3.16
38 39 4.404715 TGCTAAGTACTACACCCTCCATTC 59.595 45.833 0.00 0.00 0.00 2.67
48 49 5.408079 ACACCCTCCATTCCATGATTATT 57.592 39.130 0.00 0.00 0.00 1.40
57 58 9.123902 CTCCATTCCATGATTATTGTTGAACTA 57.876 33.333 0.00 0.00 0.00 2.24
69 70 5.828299 TTGTTGAACTAAAACCAGGACAG 57.172 39.130 0.00 0.00 0.00 3.51
70 71 4.850680 TGTTGAACTAAAACCAGGACAGT 58.149 39.130 0.00 0.00 0.00 3.55
79 80 7.116736 ACTAAAACCAGGACAGTAATTATGGG 58.883 38.462 0.00 0.00 31.95 4.00
87 88 3.381335 ACAGTAATTATGGGACGGAGGT 58.619 45.455 0.00 0.00 0.00 3.85
152 153 1.655484 TGTGCATCATAGAACGCAGG 58.345 50.000 0.00 0.00 34.49 4.85
162 163 0.877071 AGAACGCAGGTTGCAGATTG 59.123 50.000 1.69 0.00 45.36 2.67
165 166 0.593128 ACGCAGGTTGCAGATTGTTC 59.407 50.000 1.69 0.00 45.36 3.18
179 180 4.689812 CAGATTGTTCTCTTCCACTGTCTG 59.310 45.833 0.00 0.00 0.00 3.51
184 185 4.893524 TGTTCTCTTCCACTGTCTGAAGTA 59.106 41.667 13.36 4.47 39.19 2.24
185 186 5.221263 TGTTCTCTTCCACTGTCTGAAGTAC 60.221 44.000 13.36 11.18 39.19 2.73
186 187 4.470602 TCTCTTCCACTGTCTGAAGTACA 58.529 43.478 13.36 0.00 39.19 2.90
187 188 5.080337 TCTCTTCCACTGTCTGAAGTACAT 58.920 41.667 13.36 0.00 39.19 2.29
189 190 6.719829 TCTCTTCCACTGTCTGAAGTACATTA 59.280 38.462 13.36 0.00 39.19 1.90
190 191 6.688578 TCTTCCACTGTCTGAAGTACATTAC 58.311 40.000 13.36 0.00 39.19 1.89
191 192 6.266786 TCTTCCACTGTCTGAAGTACATTACA 59.733 38.462 13.36 0.00 39.19 2.41
192 193 6.605471 TCCACTGTCTGAAGTACATTACAT 57.395 37.500 0.00 0.00 0.00 2.29
193 194 7.712204 TCCACTGTCTGAAGTACATTACATA 57.288 36.000 0.00 0.00 0.00 2.29
194 195 7.544622 TCCACTGTCTGAAGTACATTACATAC 58.455 38.462 0.00 0.00 0.00 2.39
195 196 7.177744 TCCACTGTCTGAAGTACATTACATACA 59.822 37.037 0.00 0.00 0.00 2.29
196 197 7.489435 CCACTGTCTGAAGTACATTACATACAG 59.511 40.741 16.81 16.81 40.60 2.74
197 198 7.009631 CACTGTCTGAAGTACATTACATACAGC 59.990 40.741 17.58 0.00 39.40 4.40
204 205 9.008965 TGAAGTACATTACATACAGCACAAAAT 57.991 29.630 0.00 0.00 0.00 1.82
246 247 4.023963 GGTTGTACTTCTCTTCAACAAGGC 60.024 45.833 8.68 0.00 40.96 4.35
252 253 3.373565 CTTCAACAAGGCCGGCCC 61.374 66.667 41.72 23.87 36.58 5.80
288 289 2.205074 CCCGTTCCTCATTCATTCTCG 58.795 52.381 0.00 0.00 0.00 4.04
291 292 2.565841 GTTCCTCATTCATTCTCGGGG 58.434 52.381 0.00 0.00 0.00 5.73
307 308 1.744456 CGGGGCGCTAAAGGTAATTCA 60.744 52.381 7.64 0.00 0.00 2.57
323 324 6.205853 AGGTAATTCATTCACACACGCTAAAA 59.794 34.615 0.00 0.00 0.00 1.52
324 325 6.523201 GGTAATTCATTCACACACGCTAAAAG 59.477 38.462 0.00 0.00 0.00 2.27
330 331 6.425417 TCATTCACACACGCTAAAAGAATGTA 59.575 34.615 0.00 0.00 40.79 2.29
339 340 8.440833 ACACGCTAAAAGAATGTACTGTAATTC 58.559 33.333 11.47 11.47 33.77 2.17
340 341 7.903431 CACGCTAAAAGAATGTACTGTAATTCC 59.097 37.037 13.91 0.00 34.02 3.01
341 342 7.822822 ACGCTAAAAGAATGTACTGTAATTCCT 59.177 33.333 13.91 4.70 34.02 3.36
342 343 9.309516 CGCTAAAAGAATGTACTGTAATTCCTA 57.690 33.333 13.91 7.28 34.02 2.94
349 350 9.435570 AGAATGTACTGTAATTCCTATACACCT 57.564 33.333 13.91 0.00 34.02 4.00
350 351 9.694137 GAATGTACTGTAATTCCTATACACCTC 57.306 37.037 0.00 0.00 0.00 3.85
351 352 8.777578 ATGTACTGTAATTCCTATACACCTCA 57.222 34.615 0.00 0.00 0.00 3.86
352 353 8.004087 TGTACTGTAATTCCTATACACCTCAC 57.996 38.462 0.00 0.00 0.00 3.51
353 354 6.481434 ACTGTAATTCCTATACACCTCACC 57.519 41.667 0.00 0.00 0.00 4.02
354 355 6.203072 ACTGTAATTCCTATACACCTCACCT 58.797 40.000 0.00 0.00 0.00 4.00
355 356 6.672657 ACTGTAATTCCTATACACCTCACCTT 59.327 38.462 0.00 0.00 0.00 3.50
356 357 7.182206 ACTGTAATTCCTATACACCTCACCTTT 59.818 37.037 0.00 0.00 0.00 3.11
357 358 7.924541 TGTAATTCCTATACACCTCACCTTTT 58.075 34.615 0.00 0.00 0.00 2.27
358 359 8.387813 TGTAATTCCTATACACCTCACCTTTTT 58.612 33.333 0.00 0.00 0.00 1.94
410 411 6.817140 CACCTTTGGTAGTGTTTAGAGATACC 59.183 42.308 0.00 0.00 37.09 2.73
414 415 4.885907 TGGTAGTGTTTAGAGATACCGGAG 59.114 45.833 9.46 0.00 39.00 4.63
450 451 4.143543 TGGAAGCTTTCATGTGACATGAA 58.856 39.130 30.87 30.87 36.37 2.57
451 452 4.768448 TGGAAGCTTTCATGTGACATGAAT 59.232 37.500 33.63 22.53 37.79 2.57
452 453 5.945191 TGGAAGCTTTCATGTGACATGAATA 59.055 36.000 33.63 24.02 37.79 1.75
453 454 6.127925 TGGAAGCTTTCATGTGACATGAATAC 60.128 38.462 33.63 27.74 37.79 1.89
454 455 6.127925 GGAAGCTTTCATGTGACATGAATACA 60.128 38.462 33.63 21.64 37.79 2.29
455 456 7.400599 AAGCTTTCATGTGACATGAATACAT 57.599 32.000 33.63 21.48 37.79 2.29
484 485 2.959707 ACCGTGTTTTCCTTAATGCCAA 59.040 40.909 0.00 0.00 0.00 4.52
563 589 4.642429 TCTTCCTTAGTTTTCTCACCTGC 58.358 43.478 0.00 0.00 0.00 4.85
890 934 0.802607 GTGATCTCAACCGACCGCTC 60.803 60.000 0.00 0.00 0.00 5.03
1541 1635 5.104374 CGGCTACATTTCTTGCATTTCATT 58.896 37.500 0.00 0.00 0.00 2.57
1548 1642 8.786826 ACATTTCTTGCATTTCATTTGATCAT 57.213 26.923 0.00 0.00 0.00 2.45
1550 1644 8.878769 CATTTCTTGCATTTCATTTGATCATGA 58.121 29.630 0.00 0.00 0.00 3.07
1559 1653 4.078537 TCATTTGATCATGAAACCGGTGT 58.921 39.130 8.52 0.00 29.81 4.16
1560 1654 5.249420 TCATTTGATCATGAAACCGGTGTA 58.751 37.500 8.52 0.00 29.81 2.90
1561 1655 5.123186 TCATTTGATCATGAAACCGGTGTAC 59.877 40.000 8.52 3.07 29.81 2.90
1563 1657 2.028839 TGATCATGAAACCGGTGTACGT 60.029 45.455 8.52 0.76 42.24 3.57
1698 1798 3.406595 GAGGAAGATGGGCACGGGG 62.407 68.421 0.00 0.00 0.00 5.73
1724 1824 3.073101 GGCTTACCCCGACGAGGT 61.073 66.667 6.23 6.23 41.64 3.85
1845 1945 8.472007 TTTTAGTGTGATTTGGTTCCAGTTAT 57.528 30.769 0.00 0.00 0.00 1.89
1849 1949 6.016276 AGTGTGATTTGGTTCCAGTTATTGAC 60.016 38.462 0.00 0.00 0.00 3.18
1851 1951 6.493115 TGTGATTTGGTTCCAGTTATTGACAT 59.507 34.615 0.00 0.00 0.00 3.06
1903 2021 0.627451 TCATGCAAGGCCTTCTGGAT 59.373 50.000 17.29 10.68 34.57 3.41
1918 2036 0.973632 TGGATCAGTACACGTTGGCT 59.026 50.000 0.00 0.00 0.00 4.75
1919 2037 1.346395 TGGATCAGTACACGTTGGCTT 59.654 47.619 0.00 0.00 0.00 4.35
1920 2038 2.000447 GGATCAGTACACGTTGGCTTC 59.000 52.381 0.00 0.00 0.00 3.86
1924 2042 2.066262 CAGTACACGTTGGCTTCGAAT 58.934 47.619 0.00 0.00 0.00 3.34
1938 2056 0.611200 TCGAATCGAAAGGGCCTTGA 59.389 50.000 21.72 14.36 31.06 3.02
2045 2163 4.816984 ACGAGGAGACCGGCGGAT 62.817 66.667 35.78 21.08 32.36 4.18
2065 2183 5.234116 CGGATTGAACGATGTCATGTATCAA 59.766 40.000 11.39 0.00 0.00 2.57
2071 2189 7.264947 TGAACGATGTCATGTATCAACTGTAT 58.735 34.615 11.39 0.00 0.00 2.29
2074 2192 7.145985 ACGATGTCATGTATCAACTGTATACC 58.854 38.462 0.00 0.00 0.00 2.73
2132 2250 6.046593 AGTAGTGTTTTGTGATCTTCGTTCA 58.953 36.000 0.00 0.00 0.00 3.18
2141 2259 3.807622 GTGATCTTCGTTCAGGTTGTGAA 59.192 43.478 0.00 0.00 43.26 3.18
2151 2269 0.393808 AGGTTGTGAACTTGCGGTGT 60.394 50.000 0.00 0.00 0.00 4.16
2152 2270 1.134340 AGGTTGTGAACTTGCGGTGTA 60.134 47.619 0.00 0.00 0.00 2.90
2153 2271 1.003223 GGTTGTGAACTTGCGGTGTAC 60.003 52.381 0.00 0.00 0.00 2.90
2154 2272 1.666700 GTTGTGAACTTGCGGTGTACA 59.333 47.619 0.00 0.00 0.00 2.90
2170 2288 6.128553 GCGGTGTACATATGTATCAAATCCTG 60.129 42.308 18.27 11.39 32.54 3.86
2172 2290 7.116376 CGGTGTACATATGTATCAAATCCTGAC 59.884 40.741 18.27 4.65 36.69 3.51
2173 2291 7.931407 GGTGTACATATGTATCAAATCCTGACA 59.069 37.037 18.27 7.15 36.69 3.58
2178 2296 7.443575 ACATATGTATCAAATCCTGACAAGAGC 59.556 37.037 6.56 0.00 36.69 4.09
2202 2320 6.183360 GCTGTTTTCTATCTCTGCAGAAAGAG 60.183 42.308 18.85 11.96 44.34 2.85
2214 2332 2.613977 GCAGAAAGAGCAGAAGCACCTA 60.614 50.000 0.00 0.00 45.49 3.08
2294 2412 5.301805 TCAGGAGAACTTTGGGTTTCATTTC 59.698 40.000 0.00 0.00 38.41 2.17
2305 2423 5.312895 TGGGTTTCATTTCGATTTCTGAGA 58.687 37.500 0.00 0.00 0.00 3.27
2330 2448 4.915704 TCAGAAGTTTTAAGCAACGGTTG 58.084 39.130 16.35 16.35 0.00 3.77
2375 2493 2.768527 CAGGATGATGATATAGCGGGGT 59.231 50.000 0.00 0.00 39.69 4.95
2416 2534 2.260434 GTCCTAGTCGGTGCGCAA 59.740 61.111 14.00 0.00 0.00 4.85
2457 2575 4.390909 CGGTGACCATCTTTACAAGGTAAC 59.609 45.833 1.11 0.00 35.18 2.50
2490 2626 5.515797 TCTTAGAATCGTCGATGGACAAT 57.484 39.130 8.83 0.00 43.61 2.71
2497 2633 4.379339 TCGTCGATGGACAATGTCATAA 57.621 40.909 15.86 0.40 43.61 1.90
2498 2634 4.359706 TCGTCGATGGACAATGTCATAAG 58.640 43.478 15.86 4.00 43.61 1.73
2534 2670 6.172630 TGTAACTGTGCAACTATCATGTCAT 58.827 36.000 0.00 0.00 38.04 3.06
2535 2671 5.556355 AACTGTGCAACTATCATGTCATG 57.444 39.130 6.47 6.47 38.04 3.07
2536 2672 4.582869 ACTGTGCAACTATCATGTCATGT 58.417 39.130 12.54 3.37 38.04 3.21
2537 2673 5.005740 ACTGTGCAACTATCATGTCATGTT 58.994 37.500 12.54 7.13 38.04 2.71
2538 2674 6.172630 ACTGTGCAACTATCATGTCATGTTA 58.827 36.000 12.54 7.90 38.04 2.41
2539 2675 6.092670 ACTGTGCAACTATCATGTCATGTTAC 59.907 38.462 12.54 0.04 38.04 2.50
2540 2676 6.172630 TGTGCAACTATCATGTCATGTTACT 58.827 36.000 12.54 0.06 38.04 2.24
2541 2677 6.313658 TGTGCAACTATCATGTCATGTTACTC 59.686 38.462 12.54 0.00 38.04 2.59
2542 2678 6.313658 GTGCAACTATCATGTCATGTTACTCA 59.686 38.462 12.54 1.86 0.00 3.41
2543 2679 7.011763 GTGCAACTATCATGTCATGTTACTCAT 59.988 37.037 12.54 0.74 37.22 2.90
2544 2680 8.203485 TGCAACTATCATGTCATGTTACTCATA 58.797 33.333 12.54 1.84 34.67 2.15
2545 2681 9.045223 GCAACTATCATGTCATGTTACTCATAA 57.955 33.333 12.54 0.00 34.67 1.90
2551 2687 7.751732 TCATGTCATGTTACTCATAAAACAGC 58.248 34.615 12.54 0.00 38.87 4.40
2552 2688 7.390162 TCATGTCATGTTACTCATAAAACAGCA 59.610 33.333 12.54 0.00 38.87 4.41
2553 2689 7.503521 TGTCATGTTACTCATAAAACAGCAA 57.496 32.000 0.00 0.00 38.87 3.91
2554 2690 7.935520 TGTCATGTTACTCATAAAACAGCAAA 58.064 30.769 0.00 0.00 38.87 3.68
2555 2691 8.075574 TGTCATGTTACTCATAAAACAGCAAAG 58.924 33.333 0.00 0.00 38.87 2.77
2556 2692 8.289618 GTCATGTTACTCATAAAACAGCAAAGA 58.710 33.333 0.00 0.00 38.87 2.52
2557 2693 8.506437 TCATGTTACTCATAAAACAGCAAAGAG 58.494 33.333 0.00 0.00 38.87 2.85
2558 2694 8.506437 CATGTTACTCATAAAACAGCAAAGAGA 58.494 33.333 0.00 0.00 38.87 3.10
2559 2695 8.445275 TGTTACTCATAAAACAGCAAAGAGAA 57.555 30.769 0.00 0.00 32.11 2.87
2560 2696 8.898761 TGTTACTCATAAAACAGCAAAGAGAAA 58.101 29.630 0.00 0.00 32.11 2.52
2561 2697 9.899226 GTTACTCATAAAACAGCAAAGAGAAAT 57.101 29.630 0.00 0.00 0.00 2.17
2562 2698 9.897744 TTACTCATAAAACAGCAAAGAGAAATG 57.102 29.630 0.00 0.00 0.00 2.32
2563 2699 8.169977 ACTCATAAAACAGCAAAGAGAAATGA 57.830 30.769 0.00 0.00 0.00 2.57
2564 2700 8.078596 ACTCATAAAACAGCAAAGAGAAATGAC 58.921 33.333 0.00 0.00 0.00 3.06
2565 2701 7.939782 TCATAAAACAGCAAAGAGAAATGACA 58.060 30.769 0.00 0.00 0.00 3.58
2588 2724 7.734942 ACACAGTACCATCCATTTTTCAAAAT 58.265 30.769 0.00 0.00 39.07 1.82
2608 2744 7.925483 TCAAAATTTTGGTGAACTGAATACTGG 59.075 33.333 26.45 0.00 38.66 4.00
2621 2757 3.118038 TGAATACTGGACTAACCCATGGC 60.118 47.826 6.09 0.00 38.00 4.40
2669 2805 2.370849 ACGTTGTAAACTCCTCCCACAT 59.629 45.455 0.00 0.00 46.99 3.21
2676 2812 3.737559 AACTCCTCCCACATATTTGCA 57.262 42.857 0.00 0.00 0.00 4.08
2695 2831 1.556911 CAACAGGAGGCACATCTACCT 59.443 52.381 0.00 0.00 39.65 3.08
2743 2881 1.949525 CCTCACCATATTTCCGCCTTG 59.050 52.381 0.00 0.00 0.00 3.61
2744 2882 1.334869 CTCACCATATTTCCGCCTTGC 59.665 52.381 0.00 0.00 0.00 4.01
2771 2912 1.207593 CCCGCTCAAGTTCTTTGCG 59.792 57.895 16.71 16.71 45.22 4.85
2772 2913 1.441016 CCGCTCAAGTTCTTTGCGC 60.441 57.895 17.61 0.00 44.44 6.09
2776 2917 1.334054 CTCAAGTTCTTTGCGCATGC 58.666 50.000 12.75 7.91 43.20 4.06
2783 2924 4.360964 TTTGCGCATGCCAGGCAC 62.361 61.111 19.10 4.22 43.04 5.01
2847 2988 0.389948 GGAGACTTGCACCACCTACG 60.390 60.000 0.00 0.00 0.00 3.51
2892 3033 4.141937 GCACTCAATCTACCATCACAGGTA 60.142 45.833 0.00 0.00 43.08 3.08
2897 3038 8.938883 ACTCAATCTACCATCACAGGTATTAAT 58.061 33.333 0.00 0.00 42.92 1.40
2940 3082 0.536260 AACTTGCCTTTTGCTGTGCA 59.464 45.000 0.00 0.00 42.00 4.57
2995 3137 3.056035 GGTGGACGAAGGAAGTCAAGTAT 60.056 47.826 0.00 0.00 40.20 2.12
3025 3167 0.829333 ACGAGAGGCTGCTCATCAAT 59.171 50.000 0.00 0.00 34.56 2.57
3203 3345 1.338389 GCTGCTACGGGACAGGTAAAA 60.338 52.381 0.00 0.00 34.38 1.52
3205 3347 3.606687 CTGCTACGGGACAGGTAAAATT 58.393 45.455 0.00 0.00 0.00 1.82
3236 3399 1.740380 GCGGAAGTGATCTTGCTGCTA 60.740 52.381 0.00 0.00 39.36 3.49
3356 3519 4.647615 CCGGGGCTCTACATCGCG 62.648 72.222 0.00 0.00 36.76 5.87
3386 3549 0.319555 CGAGCACCTTCGACTGGAAA 60.320 55.000 10.28 0.00 43.03 3.13
3389 3552 0.884704 GCACCTTCGACTGGAAAGCA 60.885 55.000 10.28 0.00 33.34 3.91
3438 3601 1.517257 CCACTGCTGTCGACGGATC 60.517 63.158 28.38 11.64 0.00 3.36
3452 3615 3.858238 CGACGGATCCTTACTTTGAAGTC 59.142 47.826 10.75 4.71 40.37 3.01
3493 3656 5.337571 CCAAGGTAGCTTCTGAATGACACTA 60.338 44.000 3.68 0.00 0.00 2.74
3514 3677 2.104267 CAGCCATGGTGCTTAGCTG 58.896 57.895 14.67 8.51 44.31 4.24
3523 3686 2.123982 GCTTAGCTGGGCCTGCAT 60.124 61.111 32.94 21.18 0.00 3.96
3525 3688 1.530771 CTTAGCTGGGCCTGCATCT 59.469 57.895 32.94 17.76 0.00 2.90
3550 3713 5.241506 TCTTTGACCCAAGCAAGAATTAGTG 59.758 40.000 0.00 0.00 0.00 2.74
3552 3715 5.235850 TGACCCAAGCAAGAATTAGTGTA 57.764 39.130 0.00 0.00 0.00 2.90
3553 3716 5.626142 TGACCCAAGCAAGAATTAGTGTAA 58.374 37.500 0.00 0.00 0.00 2.41
3554 3717 5.472137 TGACCCAAGCAAGAATTAGTGTAAC 59.528 40.000 0.00 0.00 0.00 2.50
3654 3817 0.321919 ACATCCACAGCTGACGCAAT 60.322 50.000 23.35 3.42 39.10 3.56
3724 3887 5.836821 TCACTGATGGACTGTACTGATAC 57.163 43.478 6.77 0.00 0.00 2.24
3738 3905 7.011576 ACTGTACTGATACTTCATACGAGACTG 59.988 40.741 6.77 0.00 32.00 3.51
3877 4044 5.163519 CCGAGGCAATCAAAGGTATGAAATT 60.164 40.000 0.00 0.00 32.06 1.82
3883 4050 7.490402 GGCAATCAAAGGTATGAAATTTCAGAG 59.510 37.037 24.17 9.36 41.08 3.35
3884 4051 8.031277 GCAATCAAAGGTATGAAATTTCAGAGT 58.969 33.333 24.17 11.76 41.08 3.24
3887 4054 9.739276 ATCAAAGGTATGAAATTTCAGAGTACA 57.261 29.630 24.17 8.02 41.08 2.90
3888 4055 9.567776 TCAAAGGTATGAAATTTCAGAGTACAA 57.432 29.630 24.17 5.85 41.08 2.41
3907 4079 3.760684 ACAATGTCTGAATCTTTCTGGGC 59.239 43.478 0.00 0.00 0.00 5.36
3912 4084 3.688673 GTCTGAATCTTTCTGGGCAGAAG 59.311 47.826 0.00 0.00 46.80 2.85
3919 4091 1.742308 TTCTGGGCAGAAGGTTAGGT 58.258 50.000 0.00 0.00 42.06 3.08
3924 4096 1.339151 GGGCAGAAGGTTAGGTGTCTG 60.339 57.143 0.00 0.00 40.40 3.51
3925 4097 1.623811 GGCAGAAGGTTAGGTGTCTGA 59.376 52.381 3.78 0.00 39.94 3.27
3926 4098 2.038557 GGCAGAAGGTTAGGTGTCTGAA 59.961 50.000 3.78 0.00 39.94 3.02
3927 4099 3.067833 GCAGAAGGTTAGGTGTCTGAAC 58.932 50.000 3.78 0.00 39.94 3.18
3928 4100 3.244249 GCAGAAGGTTAGGTGTCTGAACT 60.244 47.826 3.78 0.00 39.94 3.01
3929 4101 4.743955 GCAGAAGGTTAGGTGTCTGAACTT 60.744 45.833 3.78 0.00 38.95 2.66
3930 4102 5.510861 GCAGAAGGTTAGGTGTCTGAACTTA 60.511 44.000 3.78 0.00 36.77 2.24
3931 4103 6.522054 CAGAAGGTTAGGTGTCTGAACTTAA 58.478 40.000 0.00 0.00 36.77 1.85
3932 4104 6.647067 CAGAAGGTTAGGTGTCTGAACTTAAG 59.353 42.308 0.00 0.00 36.77 1.85
3933 4105 6.553852 AGAAGGTTAGGTGTCTGAACTTAAGA 59.446 38.462 10.09 0.00 36.77 2.10
3939 4111 8.890718 GTTAGGTGTCTGAACTTAAGAAAAAGT 58.109 33.333 10.09 0.00 41.46 2.66
3950 4122 9.634300 GAACTTAAGAAAAAGTAGTCTGAAACG 57.366 33.333 10.09 0.00 38.76 3.60
4048 4220 1.648720 CTGACACACGGCAACAAGG 59.351 57.895 0.00 0.00 0.00 3.61
4254 4426 3.181367 GGCACGCTGACAATGGAG 58.819 61.111 0.00 0.00 0.00 3.86
4255 4427 2.482374 GCACGCTGACAATGGAGC 59.518 61.111 0.00 0.00 0.00 4.70
4538 4710 2.743928 GCCAGGGTGCTTCGTGAG 60.744 66.667 0.00 0.00 0.00 3.51
4793 4981 3.036084 CGCCGACAGCTGAAACGT 61.036 61.111 23.35 0.00 40.39 3.99
4806 4994 0.937304 GAAACGTGCTGCTGAACTGA 59.063 50.000 0.00 0.00 0.00 3.41
4813 5001 1.367471 CTGCTGAACTGACGACCCA 59.633 57.895 0.00 0.00 0.00 4.51
4814 5002 0.036952 CTGCTGAACTGACGACCCAT 60.037 55.000 0.00 0.00 0.00 4.00
4815 5003 0.320683 TGCTGAACTGACGACCCATG 60.321 55.000 0.00 0.00 0.00 3.66
4816 5004 0.320771 GCTGAACTGACGACCCATGT 60.321 55.000 0.00 0.00 0.00 3.21
4819 5022 0.602638 GAACTGACGACCCATGTGCA 60.603 55.000 0.00 0.00 0.00 4.57
4842 5050 2.170166 CAGACCAGAGCTTCAGAGAGT 58.830 52.381 0.00 0.00 0.00 3.24
4864 5072 2.125188 GCAGTCTGGCTCTGGCTC 60.125 66.667 1.14 0.00 38.73 4.70
4959 5167 5.069516 GCATCTCCCATCACCAAAACAATAT 59.930 40.000 0.00 0.00 0.00 1.28
4963 5171 8.062065 TCTCCCATCACCAAAACAATATTAAC 57.938 34.615 0.00 0.00 0.00 2.01
4995 5203 1.865865 TCCTCGAGTGAAAACAGTGC 58.134 50.000 12.31 0.00 0.00 4.40
5017 5229 1.300266 TGTGCATGCATCTCGGTGTG 61.300 55.000 25.64 0.00 0.00 3.82
5029 5241 3.771160 GGTGTGAGATCGGCCCGT 61.771 66.667 1.63 0.00 0.00 5.28
5030 5242 2.509336 GTGTGAGATCGGCCCGTG 60.509 66.667 1.63 0.00 0.00 4.94
5031 5243 2.994995 TGTGAGATCGGCCCGTGT 60.995 61.111 1.63 0.00 0.00 4.49
5032 5244 2.202756 GTGAGATCGGCCCGTGTC 60.203 66.667 1.63 2.87 0.00 3.67
5068 5280 1.065854 AGATTTCTCGAGGTTGGCCAG 60.066 52.381 13.56 0.00 37.19 4.85
5089 5301 3.053095 AGGATCTTGATCCATGCACCTTT 60.053 43.478 25.91 4.83 43.14 3.11
5101 5313 0.803380 GCACCTTTCATTCATGCCGC 60.803 55.000 0.00 0.00 0.00 6.53
5103 5315 0.960364 ACCTTTCATTCATGCCGCGT 60.960 50.000 4.92 0.00 0.00 6.01
5105 5317 0.587242 CTTTCATTCATGCCGCGTCG 60.587 55.000 4.92 0.00 0.00 5.12
5176 5388 1.689813 TGTGGACGTGTGGTACAATCT 59.310 47.619 0.00 0.00 42.45 2.40
5183 5395 5.258456 ACGTGTGGTACAATCTTCGATAT 57.742 39.130 0.00 0.00 44.16 1.63
5202 5414 4.978099 ATATGTAGGCATATGGCATAGCC 58.022 43.478 28.82 26.88 44.22 3.93
5213 5425 0.679505 GGCATAGCCTACCGTGATGA 59.320 55.000 0.00 0.00 46.69 2.92
5634 5846 2.185867 CACCGCGGGCTAAGCTAA 59.814 61.111 31.76 0.00 0.00 3.09
5635 5847 1.883084 CACCGCGGGCTAAGCTAAG 60.883 63.158 31.76 0.00 0.00 2.18
5636 5848 2.967615 CCGCGGGCTAAGCTAAGC 60.968 66.667 20.10 0.00 41.99 3.09
5637 5849 2.107141 CGCGGGCTAAGCTAAGCT 59.893 61.111 0.00 0.00 42.37 3.74
5638 5850 1.362717 CGCGGGCTAAGCTAAGCTA 59.637 57.895 0.00 0.00 42.37 3.32
5695 5907 1.606668 GGGAATGCAACGTGACAAAGA 59.393 47.619 0.00 0.00 0.00 2.52
5713 5925 0.166814 GAGGACGCAATGTGACAAGC 59.833 55.000 0.00 3.65 0.00 4.01
5778 5990 1.286553 AGCCAGCAGTAGAGTAGAGGT 59.713 52.381 0.00 0.00 0.00 3.85
5781 5993 3.626930 CCAGCAGTAGAGTAGAGGTCTT 58.373 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.718961 ACTTAGCAACCACTGAAAGATGT 58.281 39.130 0.00 0.00 37.43 3.06
1 2 5.934625 AGTACTTAGCAACCACTGAAAGATG 59.065 40.000 0.00 0.00 37.43 2.90
2 3 6.115448 AGTACTTAGCAACCACTGAAAGAT 57.885 37.500 0.00 0.00 37.43 2.40
3 4 5.546621 AGTACTTAGCAACCACTGAAAGA 57.453 39.130 0.00 0.00 37.43 2.52
4 5 6.145696 GTGTAGTACTTAGCAACCACTGAAAG 59.854 42.308 0.00 0.00 42.29 2.62
5 6 5.987347 GTGTAGTACTTAGCAACCACTGAAA 59.013 40.000 0.00 0.00 0.00 2.69
6 7 5.510179 GGTGTAGTACTTAGCAACCACTGAA 60.510 44.000 0.00 0.00 0.00 3.02
7 8 4.021719 GGTGTAGTACTTAGCAACCACTGA 60.022 45.833 0.00 0.00 0.00 3.41
8 9 4.243270 GGTGTAGTACTTAGCAACCACTG 58.757 47.826 0.00 0.00 0.00 3.66
9 10 3.260128 GGGTGTAGTACTTAGCAACCACT 59.740 47.826 18.26 0.00 38.50 4.00
10 11 3.260128 AGGGTGTAGTACTTAGCAACCAC 59.740 47.826 22.48 6.46 40.94 4.16
11 12 3.512724 GAGGGTGTAGTACTTAGCAACCA 59.487 47.826 22.48 0.00 40.94 3.67
12 13 3.118847 GGAGGGTGTAGTACTTAGCAACC 60.119 52.174 16.45 16.45 38.90 3.77
13 14 3.512724 TGGAGGGTGTAGTACTTAGCAAC 59.487 47.826 0.00 0.82 0.00 4.17
14 15 3.781808 TGGAGGGTGTAGTACTTAGCAA 58.218 45.455 0.00 0.00 0.00 3.91
15 16 3.461378 TGGAGGGTGTAGTACTTAGCA 57.539 47.619 0.00 0.00 0.00 3.49
16 17 4.202233 GGAATGGAGGGTGTAGTACTTAGC 60.202 50.000 0.00 0.27 0.00 3.09
17 18 4.960469 TGGAATGGAGGGTGTAGTACTTAG 59.040 45.833 0.00 0.00 0.00 2.18
18 19 4.950361 TGGAATGGAGGGTGTAGTACTTA 58.050 43.478 0.00 0.00 0.00 2.24
19 20 3.798515 TGGAATGGAGGGTGTAGTACTT 58.201 45.455 0.00 0.00 0.00 2.24
20 21 3.484953 TGGAATGGAGGGTGTAGTACT 57.515 47.619 0.00 0.00 0.00 2.73
21 22 3.709653 TCATGGAATGGAGGGTGTAGTAC 59.290 47.826 0.00 0.00 46.73 2.73
22 23 4.002256 TCATGGAATGGAGGGTGTAGTA 57.998 45.455 0.00 0.00 46.73 1.82
23 24 2.845659 TCATGGAATGGAGGGTGTAGT 58.154 47.619 0.00 0.00 46.73 2.73
24 25 4.443978 AATCATGGAATGGAGGGTGTAG 57.556 45.455 0.00 0.00 46.73 2.74
25 26 6.126215 ACAATAATCATGGAATGGAGGGTGTA 60.126 38.462 0.00 0.00 46.73 2.90
26 27 5.142639 CAATAATCATGGAATGGAGGGTGT 58.857 41.667 0.00 0.00 46.73 4.16
27 28 5.142639 ACAATAATCATGGAATGGAGGGTG 58.857 41.667 0.00 0.00 46.73 4.61
28 29 5.408079 ACAATAATCATGGAATGGAGGGT 57.592 39.130 0.00 0.00 46.73 4.34
29 30 5.834742 TCAACAATAATCATGGAATGGAGGG 59.165 40.000 0.00 0.00 46.73 4.30
30 31 6.964807 TCAACAATAATCATGGAATGGAGG 57.035 37.500 0.00 0.00 46.73 4.30
31 32 8.004087 AGTTCAACAATAATCATGGAATGGAG 57.996 34.615 0.00 0.00 46.73 3.86
32 33 7.959658 AGTTCAACAATAATCATGGAATGGA 57.040 32.000 0.00 0.00 46.73 3.41
36 37 9.921637 GGTTTTAGTTCAACAATAATCATGGAA 57.078 29.630 0.00 0.00 0.00 3.53
37 38 9.083422 TGGTTTTAGTTCAACAATAATCATGGA 57.917 29.630 0.00 0.00 0.00 3.41
38 39 9.357652 CTGGTTTTAGTTCAACAATAATCATGG 57.642 33.333 0.00 0.00 0.00 3.66
48 49 4.850680 ACTGTCCTGGTTTTAGTTCAACA 58.149 39.130 0.00 0.00 0.00 3.33
57 58 5.949952 GTCCCATAATTACTGTCCTGGTTTT 59.050 40.000 0.00 0.00 0.00 2.43
69 70 5.772169 ACTACTACCTCCGTCCCATAATTAC 59.228 44.000 0.00 0.00 0.00 1.89
70 71 5.957132 ACTACTACCTCCGTCCCATAATTA 58.043 41.667 0.00 0.00 0.00 1.40
79 80 7.599998 TCAAAACAAAATACTACTACCTCCGTC 59.400 37.037 0.00 0.00 0.00 4.79
112 113 7.116819 GCACAAAGCAACAAGTTTATTACAAC 58.883 34.615 0.00 0.00 44.79 3.32
152 153 3.817647 AGTGGAAGAGAACAATCTGCAAC 59.182 43.478 0.00 0.00 35.54 4.17
162 163 4.329462 ACTTCAGACAGTGGAAGAGAAC 57.671 45.455 15.37 0.00 42.39 3.01
165 166 4.855715 TGTACTTCAGACAGTGGAAGAG 57.144 45.455 15.37 0.00 42.39 2.85
217 218 6.550108 TGTTGAAGAGAAGTACAACCTCTAGT 59.450 38.462 10.69 0.00 40.91 2.57
271 272 2.565841 CCCCGAGAATGAATGAGGAAC 58.434 52.381 0.00 0.00 0.00 3.62
288 289 2.047002 TGAATTACCTTTAGCGCCCC 57.953 50.000 2.29 0.00 0.00 5.80
291 292 5.028375 GTGTGAATGAATTACCTTTAGCGC 58.972 41.667 0.00 0.00 0.00 5.92
307 308 5.689383 ACATTCTTTTAGCGTGTGTGAAT 57.311 34.783 0.00 0.00 0.00 2.57
323 324 9.435570 AGGTGTATAGGAATTACAGTACATTCT 57.564 33.333 8.01 6.84 31.16 2.40
324 325 9.694137 GAGGTGTATAGGAATTACAGTACATTC 57.306 37.037 8.01 0.00 0.00 2.67
330 331 6.203072 AGGTGAGGTGTATAGGAATTACAGT 58.797 40.000 0.00 0.00 0.00 3.55
368 369 3.644335 AGGTGAGGTGTATAGGTTCCTC 58.356 50.000 0.00 0.00 44.54 3.71
369 370 3.778622 AGGTGAGGTGTATAGGTTCCT 57.221 47.619 0.00 0.00 0.00 3.36
370 371 4.514401 CAAAGGTGAGGTGTATAGGTTCC 58.486 47.826 0.00 0.00 0.00 3.62
371 372 4.019591 ACCAAAGGTGAGGTGTATAGGTTC 60.020 45.833 0.00 0.00 36.60 3.62
372 373 3.914435 ACCAAAGGTGAGGTGTATAGGTT 59.086 43.478 0.00 0.00 36.60 3.50
373 374 3.527937 ACCAAAGGTGAGGTGTATAGGT 58.472 45.455 0.00 0.00 36.60 3.08
410 411 0.249784 CATGGCAGATGTCTCCTCCG 60.250 60.000 0.00 0.00 0.00 4.63
414 415 1.964552 CTTCCATGGCAGATGTCTCC 58.035 55.000 5.31 0.00 0.00 3.71
461 462 3.502979 TGGCATTAAGGAAAACACGGTAC 59.497 43.478 0.00 0.00 0.00 3.34
484 485 3.797865 GCGTAGGTGTAGCATTTCCGTAT 60.798 47.826 0.00 0.00 0.00 3.06
827 853 3.338275 TAGGCGCCATTCCACACCC 62.338 63.158 31.54 0.00 0.00 4.61
828 854 1.819632 CTAGGCGCCATTCCACACC 60.820 63.158 31.54 0.00 0.00 4.16
829 855 2.472909 GCTAGGCGCCATTCCACAC 61.473 63.158 31.54 4.76 0.00 3.82
830 856 2.124736 GCTAGGCGCCATTCCACA 60.125 61.111 31.54 2.99 0.00 4.17
908 952 1.086634 AGATGGCGCGAAAGAAGCTC 61.087 55.000 12.10 0.00 36.69 4.09
1301 1390 2.768344 AGTACATGGAGCCGGGGG 60.768 66.667 2.18 0.00 0.00 5.40
1452 1541 3.726595 TACGAAATGGCCGCGGAGG 62.727 63.158 33.48 11.04 44.97 4.30
1503 1592 1.727062 AGCCGGAATGGAGAGATGAT 58.273 50.000 5.05 0.00 42.00 2.45
1541 1635 2.997303 CGTACACCGGTTTCATGATCAA 59.003 45.455 2.97 0.00 0.00 2.57
1548 1642 0.665835 ACGTACGTACACCGGTTTCA 59.334 50.000 21.41 0.00 42.24 2.69
1550 1644 0.383949 ACACGTACGTACACCGGTTT 59.616 50.000 22.34 0.00 42.24 3.27
1553 1647 1.059657 CGAACACGTACGTACACCGG 61.060 60.000 22.34 10.15 42.24 5.28
1555 1649 1.318251 GACGAACACGTACGTACACC 58.682 55.000 22.34 9.60 42.74 4.16
1563 1657 2.256158 CCTGCGGACGAACACGTA 59.744 61.111 0.00 0.00 40.41 3.57
1635 1735 1.704007 CCCTGGCCATCTTCTCCCTC 61.704 65.000 5.51 0.00 0.00 4.30
1704 1804 2.676121 TCGTCGGGGTAAGCCGAA 60.676 61.111 0.00 0.00 40.15 4.30
1724 1824 1.135489 GCTCCTCGTACATGTCGAACA 60.135 52.381 17.09 8.81 36.89 3.18
1812 1912 7.360113 ACCAAATCACACTAAAAGTTGGATT 57.640 32.000 7.70 0.46 37.93 3.01
1849 1949 9.950680 AAAACAGTAAGTAAAGTGACATGAATG 57.049 29.630 0.00 0.00 0.00 2.67
1851 1951 9.391006 AGAAAACAGTAAGTAAAGTGACATGAA 57.609 29.630 0.00 0.00 0.00 2.57
1903 2021 0.669619 TCGAAGCCAACGTGTACTGA 59.330 50.000 0.00 0.00 0.00 3.41
1918 2036 1.002659 TCAAGGCCCTTTCGATTCGAA 59.997 47.619 17.08 17.08 44.28 3.71
1919 2037 0.611200 TCAAGGCCCTTTCGATTCGA 59.389 50.000 4.29 4.29 0.00 3.71
1920 2038 0.727398 GTCAAGGCCCTTTCGATTCG 59.273 55.000 0.00 0.00 0.00 3.34
1924 2042 0.322456 CCATGTCAAGGCCCTTTCGA 60.322 55.000 0.00 0.00 0.00 3.71
1938 2056 0.321564 CGTCATCCACACCACCATGT 60.322 55.000 0.00 0.00 0.00 3.21
2045 2163 5.931724 ACAGTTGATACATGACATCGTTCAA 59.068 36.000 0.00 0.00 0.00 2.69
2074 2192 4.514441 AGATAGTACGATGTTACCGTCAGG 59.486 45.833 0.00 0.00 40.95 3.86
2085 2203 7.142021 ACTAGTTGCAATGAGATAGTACGATG 58.858 38.462 15.30 0.00 0.00 3.84
2132 2250 0.393808 ACACCGCAAGTTCACAACCT 60.394 50.000 0.00 0.00 0.00 3.50
2141 2259 5.270893 TGATACATATGTACACCGCAAGT 57.729 39.130 17.69 0.00 32.72 3.16
2146 2264 7.116376 GTCAGGATTTGATACATATGTACACCG 59.884 40.741 17.69 10.89 38.29 4.94
2151 2269 9.987272 CTCTTGTCAGGATTTGATACATATGTA 57.013 33.333 17.65 17.65 38.29 2.29
2152 2270 7.443575 GCTCTTGTCAGGATTTGATACATATGT 59.556 37.037 13.93 13.93 38.29 2.29
2153 2271 7.660617 AGCTCTTGTCAGGATTTGATACATATG 59.339 37.037 0.00 0.00 38.29 1.78
2154 2272 7.660617 CAGCTCTTGTCAGGATTTGATACATAT 59.339 37.037 0.00 0.00 38.29 1.78
2170 2288 5.063312 GCAGAGATAGAAAACAGCTCTTGTC 59.937 44.000 0.00 0.00 39.73 3.18
2172 2290 4.934001 TGCAGAGATAGAAAACAGCTCTTG 59.066 41.667 0.00 0.00 33.94 3.02
2173 2291 5.046735 TCTGCAGAGATAGAAAACAGCTCTT 60.047 40.000 13.74 0.00 33.94 2.85
2178 2296 6.183360 GCTCTTTCTGCAGAGATAGAAAACAG 60.183 42.308 19.97 8.02 42.81 3.16
2202 2320 1.009829 CCATCGTTAGGTGCTTCTGC 58.990 55.000 0.00 0.00 40.20 4.26
2214 2332 1.094785 CGAAAAGATGGGCCATCGTT 58.905 50.000 33.11 33.11 44.67 3.85
2305 2423 6.144078 ACCGTTGCTTAAAACTTCTGAAAT 57.856 33.333 0.00 0.00 0.00 2.17
2330 2448 0.526211 GAAAAAGGCCGACATCACCC 59.474 55.000 0.00 0.00 0.00 4.61
2375 2493 4.826733 AGGAATGTGAGTGTTAACATGCAA 59.173 37.500 12.26 5.16 37.11 4.08
2416 2534 4.398358 TCACCGACGACTTCATATCTCTTT 59.602 41.667 0.00 0.00 0.00 2.52
2457 2575 9.760660 ATCGACGATTCTAAGAAAAATTTCAAG 57.239 29.630 4.05 5.56 39.61 3.02
2467 2585 4.976224 TGTCCATCGACGATTCTAAGAA 57.024 40.909 7.83 0.00 42.37 2.52
2480 2598 4.571984 TGAAGCTTATGACATTGTCCATCG 59.428 41.667 14.05 2.29 0.00 3.84
2490 2626 7.661437 AGTTACAAGTTGATGAAGCTTATGACA 59.339 33.333 10.54 0.00 0.00 3.58
2497 2633 4.023707 GCACAGTTACAAGTTGATGAAGCT 60.024 41.667 10.54 0.00 0.00 3.74
2498 2634 4.222114 GCACAGTTACAAGTTGATGAAGC 58.778 43.478 10.54 8.58 0.00 3.86
2534 2670 8.445275 TTCTCTTTGCTGTTTTATGAGTAACA 57.555 30.769 0.00 0.00 33.54 2.41
2535 2671 9.899226 ATTTCTCTTTGCTGTTTTATGAGTAAC 57.101 29.630 0.00 0.00 0.00 2.50
2536 2672 9.897744 CATTTCTCTTTGCTGTTTTATGAGTAA 57.102 29.630 0.00 0.00 0.00 2.24
2537 2673 9.283768 TCATTTCTCTTTGCTGTTTTATGAGTA 57.716 29.630 0.00 0.00 0.00 2.59
2538 2674 8.078596 GTCATTTCTCTTTGCTGTTTTATGAGT 58.921 33.333 0.00 0.00 0.00 3.41
2539 2675 8.077991 TGTCATTTCTCTTTGCTGTTTTATGAG 58.922 33.333 0.00 0.00 0.00 2.90
2540 2676 7.862372 GTGTCATTTCTCTTTGCTGTTTTATGA 59.138 33.333 0.00 0.00 0.00 2.15
2541 2677 7.648908 TGTGTCATTTCTCTTTGCTGTTTTATG 59.351 33.333 0.00 0.00 0.00 1.90
2542 2678 7.715657 TGTGTCATTTCTCTTTGCTGTTTTAT 58.284 30.769 0.00 0.00 0.00 1.40
2543 2679 7.094508 TGTGTCATTTCTCTTTGCTGTTTTA 57.905 32.000 0.00 0.00 0.00 1.52
2544 2680 5.964758 TGTGTCATTTCTCTTTGCTGTTTT 58.035 33.333 0.00 0.00 0.00 2.43
2545 2681 5.126061 ACTGTGTCATTTCTCTTTGCTGTTT 59.874 36.000 0.00 0.00 0.00 2.83
2546 2682 4.641989 ACTGTGTCATTTCTCTTTGCTGTT 59.358 37.500 0.00 0.00 0.00 3.16
2547 2683 4.202441 ACTGTGTCATTTCTCTTTGCTGT 58.798 39.130 0.00 0.00 0.00 4.40
2548 2684 4.825546 ACTGTGTCATTTCTCTTTGCTG 57.174 40.909 0.00 0.00 0.00 4.41
2549 2685 4.757149 GGTACTGTGTCATTTCTCTTTGCT 59.243 41.667 0.00 0.00 0.00 3.91
2550 2686 4.515191 TGGTACTGTGTCATTTCTCTTTGC 59.485 41.667 0.00 0.00 0.00 3.68
2551 2687 6.128172 GGATGGTACTGTGTCATTTCTCTTTG 60.128 42.308 0.00 0.00 0.00 2.77
2552 2688 5.940470 GGATGGTACTGTGTCATTTCTCTTT 59.060 40.000 0.00 0.00 0.00 2.52
2553 2689 5.013079 TGGATGGTACTGTGTCATTTCTCTT 59.987 40.000 0.00 0.00 0.00 2.85
2554 2690 4.532126 TGGATGGTACTGTGTCATTTCTCT 59.468 41.667 0.00 0.00 0.00 3.10
2555 2691 4.832248 TGGATGGTACTGTGTCATTTCTC 58.168 43.478 0.00 0.00 0.00 2.87
2556 2692 4.908601 TGGATGGTACTGTGTCATTTCT 57.091 40.909 0.00 0.00 0.00 2.52
2557 2693 6.515272 AAATGGATGGTACTGTGTCATTTC 57.485 37.500 0.00 0.00 30.53 2.17
2558 2694 6.916360 AAAATGGATGGTACTGTGTCATTT 57.084 33.333 0.00 0.00 35.64 2.32
2559 2695 6.493115 TGAAAAATGGATGGTACTGTGTCATT 59.507 34.615 0.00 0.00 0.00 2.57
2560 2696 6.009589 TGAAAAATGGATGGTACTGTGTCAT 58.990 36.000 0.00 0.00 0.00 3.06
2561 2697 5.380900 TGAAAAATGGATGGTACTGTGTCA 58.619 37.500 0.00 0.00 0.00 3.58
2562 2698 5.957842 TGAAAAATGGATGGTACTGTGTC 57.042 39.130 0.00 0.00 0.00 3.67
2563 2699 6.723298 TTTGAAAAATGGATGGTACTGTGT 57.277 33.333 0.00 0.00 0.00 3.72
2564 2700 8.606040 AATTTTGAAAAATGGATGGTACTGTG 57.394 30.769 1.91 0.00 38.53 3.66
2565 2701 9.625747 AAAATTTTGAAAAATGGATGGTACTGT 57.374 25.926 1.75 0.00 38.53 3.55
2588 2724 5.690865 AGTCCAGTATTCAGTTCACCAAAA 58.309 37.500 0.00 0.00 0.00 2.44
2608 2744 0.618458 TCCTGTGCCATGGGTTAGTC 59.382 55.000 15.13 0.00 0.00 2.59
2621 2757 3.928727 AGAATGTTGCAATGTCCTGTG 57.071 42.857 0.59 0.00 0.00 3.66
2669 2805 2.284754 TGTGCCTCCTGTTGCAAATA 57.715 45.000 0.00 0.00 39.57 1.40
2676 2812 1.958288 AGGTAGATGTGCCTCCTGTT 58.042 50.000 0.00 0.00 32.15 3.16
2695 2831 1.532604 ATCGCTCACCAGTGTTCCGA 61.533 55.000 10.63 10.63 33.27 4.55
2696 2832 0.172578 TATCGCTCACCAGTGTTCCG 59.827 55.000 0.00 0.28 0.00 4.30
2744 2882 0.673644 ACTTGAGCGGGGAAATGTCG 60.674 55.000 0.00 0.00 0.00 4.35
2747 2885 1.826385 AGAACTTGAGCGGGGAAATG 58.174 50.000 0.00 0.00 0.00 2.32
2748 2886 2.558359 CAAAGAACTTGAGCGGGGAAAT 59.442 45.455 0.00 0.00 37.17 2.17
2752 2893 1.581447 GCAAAGAACTTGAGCGGGG 59.419 57.895 0.00 0.00 37.17 5.73
2783 2924 0.304098 CTACTAGTCGCTTCGGGTCG 59.696 60.000 0.00 0.00 0.00 4.79
2940 3082 4.787551 TCGGGACACCTGCAATTTATATT 58.212 39.130 0.00 0.00 33.28 1.28
2945 3087 1.339929 GTTTCGGGACACCTGCAATTT 59.660 47.619 0.00 0.00 33.28 1.82
2946 3088 0.958822 GTTTCGGGACACCTGCAATT 59.041 50.000 0.00 0.00 33.28 2.32
2995 3137 1.725557 GCCTCTCGTAGTGATCGGCA 61.726 60.000 0.00 0.00 40.00 5.69
3025 3167 1.213619 TCTGGTTGCCCATGATCCCA 61.214 55.000 0.00 0.00 40.90 4.37
3203 3345 1.002773 ACTTCCGCGGGTACTGAAAAT 59.997 47.619 27.83 0.00 36.31 1.82
3205 3347 0.320073 CACTTCCGCGGGTACTGAAA 60.320 55.000 27.83 9.34 36.31 2.69
3236 3399 5.532406 TCTTTGATTTAGAAACAGCAGCAGT 59.468 36.000 0.00 0.00 0.00 4.40
3356 3519 2.464459 GGTGCTCGGTATGTGCTGC 61.464 63.158 0.00 0.00 37.94 5.25
3426 3589 3.119602 TCAAAGTAAGGATCCGTCGACAG 60.120 47.826 17.16 3.99 0.00 3.51
3431 3594 4.626172 GTGACTTCAAAGTAAGGATCCGTC 59.374 45.833 2.45 2.84 39.88 4.79
3438 3601 5.997746 TGGAGATTGTGACTTCAAAGTAAGG 59.002 40.000 0.00 0.00 39.88 2.69
3452 3615 3.119245 CCTTGGCAGAAATGGAGATTGTG 60.119 47.826 0.00 0.00 0.00 3.33
3514 3677 0.813821 GTCAAAGAAGATGCAGGCCC 59.186 55.000 0.00 0.00 0.00 5.80
3523 3686 3.576078 TCTTGCTTGGGTCAAAGAAGA 57.424 42.857 0.00 0.00 0.00 2.87
3525 3688 5.833131 ACTAATTCTTGCTTGGGTCAAAGAA 59.167 36.000 0.00 0.00 0.00 2.52
3565 3728 5.414360 TGTGTGCATTAGAAAGCAAAACAA 58.586 33.333 0.00 0.00 43.20 2.83
3645 3808 0.167470 CAGAGTTGCCATTGCGTCAG 59.833 55.000 0.00 0.00 41.78 3.51
3654 3817 1.702182 TTTGCCATTCAGAGTTGCCA 58.298 45.000 0.00 0.00 0.00 4.92
3711 3874 7.225145 AGTCTCGTATGAAGTATCAGTACAGTC 59.775 40.741 0.00 0.00 39.39 3.51
3724 3887 5.277779 GGATCTCTCACAGTCTCGTATGAAG 60.278 48.000 0.00 0.00 0.00 3.02
3738 3905 1.487976 TGAAGCATGGGGATCTCTCAC 59.512 52.381 0.00 0.00 0.00 3.51
3883 4050 5.163713 GCCCAGAAAGATTCAGACATTGTAC 60.164 44.000 0.00 0.00 0.00 2.90
3884 4051 4.943705 GCCCAGAAAGATTCAGACATTGTA 59.056 41.667 0.00 0.00 0.00 2.41
3885 4052 3.760684 GCCCAGAAAGATTCAGACATTGT 59.239 43.478 0.00 0.00 0.00 2.71
3886 4053 3.760151 TGCCCAGAAAGATTCAGACATTG 59.240 43.478 0.00 0.00 0.00 2.82
3887 4054 4.015084 CTGCCCAGAAAGATTCAGACATT 58.985 43.478 0.00 0.00 0.00 2.71
3888 4055 3.265221 TCTGCCCAGAAAGATTCAGACAT 59.735 43.478 0.00 0.00 33.91 3.06
3889 4056 2.639347 TCTGCCCAGAAAGATTCAGACA 59.361 45.455 0.00 0.00 33.91 3.41
3890 4057 3.340814 TCTGCCCAGAAAGATTCAGAC 57.659 47.619 0.00 0.00 33.91 3.51
3907 4079 4.608948 AGTTCAGACACCTAACCTTCTG 57.391 45.455 0.00 0.00 37.43 3.02
3912 4084 7.797038 TTTTCTTAAGTTCAGACACCTAACC 57.203 36.000 1.63 0.00 0.00 2.85
3919 4091 9.314321 CAGACTACTTTTTCTTAAGTTCAGACA 57.686 33.333 1.63 0.00 39.08 3.41
3924 4096 9.634300 CGTTTCAGACTACTTTTTCTTAAGTTC 57.366 33.333 1.63 0.00 39.08 3.01
3925 4097 8.610035 CCGTTTCAGACTACTTTTTCTTAAGTT 58.390 33.333 1.63 0.00 39.08 2.66
3926 4098 7.767659 ACCGTTTCAGACTACTTTTTCTTAAGT 59.232 33.333 1.63 0.00 41.13 2.24
3927 4099 8.139521 ACCGTTTCAGACTACTTTTTCTTAAG 57.860 34.615 0.00 0.00 0.00 1.85
3928 4100 9.252962 CTACCGTTTCAGACTACTTTTTCTTAA 57.747 33.333 0.00 0.00 0.00 1.85
3929 4101 8.416329 ACTACCGTTTCAGACTACTTTTTCTTA 58.584 33.333 0.00 0.00 0.00 2.10
3930 4102 7.270779 ACTACCGTTTCAGACTACTTTTTCTT 58.729 34.615 0.00 0.00 0.00 2.52
3931 4103 6.814043 ACTACCGTTTCAGACTACTTTTTCT 58.186 36.000 0.00 0.00 0.00 2.52
3932 4104 7.474398 AACTACCGTTTCAGACTACTTTTTC 57.526 36.000 0.00 0.00 0.00 2.29
3933 4105 7.854557 AAACTACCGTTTCAGACTACTTTTT 57.145 32.000 0.00 0.00 39.00 1.94
3939 4111 6.921857 CAGAAGAAAACTACCGTTTCAGACTA 59.078 38.462 0.00 0.00 42.28 2.59
3950 4122 4.393371 GGTCATCTGCAGAAGAAAACTACC 59.607 45.833 22.30 14.88 38.79 3.18
3964 4136 4.899239 CTCCGGCCGGTCATCTGC 62.899 72.222 41.57 0.00 36.47 4.26
4048 4220 3.003478 CTCGGTCGCGTTAATGGC 58.997 61.111 5.77 0.00 0.00 4.40
4793 4981 1.300931 GGTCGTCAGTTCAGCAGCA 60.301 57.895 0.00 0.00 0.00 4.41
4806 4994 1.004560 CTGTCTGCACATGGGTCGT 60.005 57.895 0.00 0.00 0.00 4.34
4813 5001 0.036577 GCTCTGGTCTGTCTGCACAT 60.037 55.000 0.00 0.00 0.00 3.21
4814 5002 1.117749 AGCTCTGGTCTGTCTGCACA 61.118 55.000 0.00 0.00 0.00 4.57
4815 5003 0.034616 AAGCTCTGGTCTGTCTGCAC 59.965 55.000 0.00 0.00 0.00 4.57
4816 5004 0.319728 GAAGCTCTGGTCTGTCTGCA 59.680 55.000 0.00 0.00 0.00 4.41
4819 5022 2.170166 CTCTGAAGCTCTGGTCTGTCT 58.830 52.381 0.00 0.00 0.00 3.41
4863 5071 4.025858 GCCACTGCCAGAGCCAGA 62.026 66.667 0.00 0.00 38.69 3.86
4864 5072 4.340246 TGCCACTGCCAGAGCCAG 62.340 66.667 0.00 0.00 38.69 4.85
4959 5167 2.225491 GAGGAACATGCAACAGCGTTAA 59.775 45.455 0.00 0.00 0.00 2.01
4963 5171 1.133253 CGAGGAACATGCAACAGCG 59.867 57.895 0.00 0.00 0.00 5.18
4995 5203 1.022982 ACCGAGATGCATGCACACAG 61.023 55.000 25.37 14.77 0.00 3.66
5017 5229 2.105128 CAGACACGGGCCGATCTC 59.895 66.667 35.78 21.84 0.00 2.75
5021 5233 4.293648 CACACAGACACGGGCCGA 62.294 66.667 35.78 0.00 0.00 5.54
5029 5241 2.433970 TCTCAACCACATCACACAGACA 59.566 45.455 0.00 0.00 0.00 3.41
5030 5242 3.111853 TCTCAACCACATCACACAGAC 57.888 47.619 0.00 0.00 0.00 3.51
5031 5243 4.356405 AATCTCAACCACATCACACAGA 57.644 40.909 0.00 0.00 0.00 3.41
5032 5244 4.758674 AGAAATCTCAACCACATCACACAG 59.241 41.667 0.00 0.00 0.00 3.66
5089 5301 3.563088 GCGACGCGGCATGAATGA 61.563 61.111 14.85 0.00 0.00 2.57
5105 5317 2.094762 AACAGGACGACACTTATGGC 57.905 50.000 0.00 0.00 0.00 4.40
5176 5388 4.817318 TGCCATATGCCTACATATCGAA 57.183 40.909 0.00 0.00 44.55 3.71
5617 5829 1.883084 CTTAGCTTAGCCCGCGGTG 60.883 63.158 26.12 16.79 0.00 4.94
5634 5846 1.065854 CCAGTACAAGGCAAGCTAGCT 60.066 52.381 12.68 12.68 34.17 3.32
5635 5847 1.373570 CCAGTACAAGGCAAGCTAGC 58.626 55.000 6.62 6.62 0.00 3.42
5695 5907 1.237285 GGCTTGTCACATTGCGTCCT 61.237 55.000 0.00 0.00 0.00 3.85
5731 5943 2.509052 TTTACTCGGCGATCCATCAG 57.491 50.000 11.27 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.