Multiple sequence alignment - TraesCS3B01G345900

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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 TraesCS3B01G345900 chr3B 100.000 3672 0 0 948 4619 555546366 555542695 0.000000e+00 6782.0
1 TraesCS3B01G345900 chr3B 100.000 398 0 0 1 398 555547313 555546916 0.000000e+00 736.0
2 TraesCS3B01G345900 chr3B 93.333 45 1 2 2693 2737 824388969 824388927 1.070000e-06 65.8
3 TraesCS3B01G345900 chr3B 92.857 42 1 1 95 136 495813310 495813349 4.990000e-05 60.2
4 TraesCS3B01G345900 chr3B 92.683 41 1 2 85 125 130118223 130118261 1.800000e-04 58.4
5 TraesCS3B01G345900 chr3B 87.755 49 4 1 3784 3832 53239791 53239837 6.460000e-04 56.5
6 TraesCS3B01G345900 chr3A 92.526 1659 75 21 1128 2765 562791574 562793204 0.000000e+00 2331.0
7 TraesCS3B01G345900 chr3A 91.946 745 36 13 3068 3789 562793671 562794414 0.000000e+00 1022.0
8 TraesCS3B01G345900 chr3A 87.324 355 28 11 4270 4619 562794996 562795338 1.560000e-104 390.0
9 TraesCS3B01G345900 chr3A 92.896 183 12 1 2764 2945 562793498 562793680 9.850000e-67 265.0
10 TraesCS3B01G345900 chr3A 84.871 271 18 11 90 355 562790701 562790953 7.670000e-63 252.0
11 TraesCS3B01G345900 chr3A 85.714 189 19 4 3975 4163 562794729 562794909 4.720000e-45 193.0
12 TraesCS3B01G345900 chr3A 84.615 91 13 1 1 90 601965309 601965399 6.370000e-14 89.8
13 TraesCS3B01G345900 chr3A 82.609 69 8 4 2674 2740 293585576 293585642 1.800000e-04 58.4
14 TraesCS3B01G345900 chr3D 92.647 1088 52 13 1693 2767 425565620 425566692 0.000000e+00 1541.0
15 TraesCS3B01G345900 chr3D 91.612 1061 54 26 2759 3800 425566986 425568030 0.000000e+00 1434.0
16 TraesCS3B01G345900 chr3D 93.577 794 36 5 948 1739 425564855 425565635 0.000000e+00 1170.0
17 TraesCS3B01G345900 chr3D 86.301 292 21 8 4329 4619 425568496 425568769 2.700000e-77 300.0
18 TraesCS3B01G345900 chr3D 94.872 39 0 2 87 125 595760593 595760557 4.990000e-05 60.2
19 TraesCS3B01G345900 chr6A 91.017 590 30 13 3225 3792 318065233 318064645 0.000000e+00 774.0
20 TraesCS3B01G345900 chr6A 95.116 389 16 3 3222 3608 77904684 77905071 1.100000e-170 610.0
21 TraesCS3B01G345900 chr6A 93.316 389 23 3 3222 3608 78045753 78046140 5.180000e-159 571.0
22 TraesCS3B01G345900 chr6A 85.567 97 10 4 9 102 4519065 4518970 1.060000e-16 99.0
23 TraesCS3B01G345900 chr1A 95.373 389 14 4 3222 3608 130933818 130934204 2.360000e-172 616.0
24 TraesCS3B01G345900 chr1A 85.938 64 6 3 2685 2747 556171686 556171625 1.070000e-06 65.8
25 TraesCS3B01G345900 chr4A 95.116 389 16 3 3225 3611 28768878 28768491 1.100000e-170 610.0
26 TraesCS3B01G345900 chr4A 93.137 102 5 2 4 103 729642201 729642100 1.040000e-31 148.0
27 TraesCS3B01G345900 chr4A 93.617 47 3 0 3800 3846 476748752 476748706 2.310000e-08 71.3
28 TraesCS3B01G345900 chr4A 100.000 28 0 0 2137 2164 467667580 467667607 8.000000e-03 52.8
29 TraesCS3B01G345900 chr2A 94.859 389 17 3 3225 3611 306092195 306091808 5.110000e-169 604.0
30 TraesCS3B01G345900 chr2A 93.878 392 18 4 3225 3611 360683850 360683460 1.850000e-163 586.0
31 TraesCS3B01G345900 chr2A 90.000 50 2 3 3783 3832 19379033 19379079 1.390000e-05 62.1
32 TraesCS3B01G345900 chr2A 97.297 37 0 1 3800 3836 337606831 337606796 1.390000e-05 62.1
33 TraesCS3B01G345900 chr4B 98.889 90 1 0 1 90 16790489 16790578 1.330000e-35 161.0
34 TraesCS3B01G345900 chr4B 80.469 128 17 8 1 120 16226270 16226143 1.770000e-14 91.6
35 TraesCS3B01G345900 chr5B 85.870 92 12 1 2 92 465008598 465008689 3.800000e-16 97.1
36 TraesCS3B01G345900 chr5B 100.000 28 0 0 2137 2164 83464083 83464110 8.000000e-03 52.8
37 TraesCS3B01G345900 chrUn 83.838 99 15 1 1 99 2929166 2929069 4.920000e-15 93.5
38 TraesCS3B01G345900 chrUn 85.246 61 6 2 2688 2746 284001354 284001413 4.990000e-05 60.2
39 TraesCS3B01G345900 chrUn 100.000 29 0 0 2138 2166 92781410 92781382 2.000000e-03 54.7
40 TraesCS3B01G345900 chr5D 84.783 92 11 2 1 91 22580187 22580276 6.370000e-14 89.8
41 TraesCS3B01G345900 chr5D 100.000 29 0 0 2136 2164 447431244 447431216 2.000000e-03 54.7
42 TraesCS3B01G345900 chr7B 82.692 104 13 5 1 102 42353206 42353306 2.290000e-13 87.9
43 TraesCS3B01G345900 chr7B 91.111 45 3 1 3792 3836 12236898 12236941 4.990000e-05 60.2
44 TraesCS3B01G345900 chr7B 94.872 39 0 2 87 125 395736130 395736094 4.990000e-05 60.2
45 TraesCS3B01G345900 chr7B 94.872 39 0 2 87 125 639228161 639228125 4.990000e-05 60.2
46 TraesCS3B01G345900 chr6D 93.333 45 1 2 2693 2737 321773521 321773563 1.070000e-06 65.8
47 TraesCS3B01G345900 chr5A 95.122 41 2 0 2138 2178 360079169 360079129 1.070000e-06 65.8
48 TraesCS3B01G345900 chr7A 93.182 44 1 2 3793 3835 635683873 635683915 3.860000e-06 63.9
49 TraesCS3B01G345900 chr7A 85.246 61 6 2 2688 2746 1755788 1755729 4.990000e-05 60.2
50 TraesCS3B01G345900 chr2D 91.489 47 1 3 3787 3832 395597215 395597171 1.390000e-05 62.1
51 TraesCS3B01G345900 chr2B 91.111 45 4 0 3788 3832 7173213 7173257 1.390000e-05 62.1
52 TraesCS3B01G345900 chr2B 90.000 50 2 3 3783 3832 746033028 746033074 1.390000e-05 62.1
53 TraesCS3B01G345900 chr2B 91.111 45 3 1 95 138 37007526 37007570 4.990000e-05 60.2
54 TraesCS3B01G345900 chr2B 84.127 63 5 4 2674 2734 209085881 209085822 6.460000e-04 56.5
55 TraesCS3B01G345900 chr7D 94.737 38 0 2 86 123 121200576 121200611 1.800000e-04 58.4
56 TraesCS3B01G345900 chr1B 100.000 31 0 0 95 125 453517050 453517020 1.800000e-04 58.4
57 TraesCS3B01G345900 chr4D 100.000 28 0 0 2137 2164 108632644 108632617 8.000000e-03 52.8


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 TraesCS3B01G345900 chr3B 555542695 555547313 4618 True 3759.000000 6782 100.000000 1 4619 2 chr3B.!!$R2 4618
1 TraesCS3B01G345900 chr3A 562790701 562795338 4637 False 742.166667 2331 89.212833 90 4619 6 chr3A.!!$F3 4529
2 TraesCS3B01G345900 chr3D 425564855 425568769 3914 False 1111.250000 1541 91.034250 948 4619 4 chr3D.!!$F1 3671
3 TraesCS3B01G345900 chr6A 318064645 318065233 588 True 774.000000 774 91.017000 3225 3792 1 chr6A.!!$R2 567

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
87 88 0.037139 ACGCACGGGCATTTGTACTA 60.037 50.0 11.77 0.0 41.24 1.82 F
394 400 0.179100 AGACAGATCATTCGCCACCG 60.179 55.0 0.00 0.0 0.00 4.94 F
2018 2562 0.250295 ATGACCACTGGACACGGTTG 60.250 55.0 0.71 0.0 32.69 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1926 0.319728 ATCGGATCCGGATTCTGCAG 59.68 55.0 32.79 7.63 40.25 4.41 R
2352 2896 0.250124 TGTAAACACCGGTCAGGCTG 60.25 55.0 2.59 8.58 46.52 4.85 R
3960 4897 0.309612 AATGTTTCGTCCCGCACAAC 59.69 50.0 0.00 0.00 0.00 3.32 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.617540 TGGCACACGAAGTATGTTTTG 57.382 42.857 0.00 0.00 41.61 2.44
48 49 2.946329 TGGCACACGAAGTATGTTTTGT 59.054 40.909 0.00 0.00 41.61 2.83
49 50 4.127907 TGGCACACGAAGTATGTTTTGTA 58.872 39.130 0.00 0.00 41.61 2.41
50 51 4.575236 TGGCACACGAAGTATGTTTTGTAA 59.425 37.500 0.00 0.00 41.61 2.41
51 52 5.239744 TGGCACACGAAGTATGTTTTGTAAT 59.760 36.000 0.00 0.00 41.61 1.89
52 53 6.146898 GGCACACGAAGTATGTTTTGTAATT 58.853 36.000 0.00 0.00 41.61 1.40
53 54 6.639279 GGCACACGAAGTATGTTTTGTAATTT 59.361 34.615 0.00 0.00 41.61 1.82
54 55 7.168469 GGCACACGAAGTATGTTTTGTAATTTT 59.832 33.333 0.00 0.00 41.61 1.82
55 56 8.536407 GCACACGAAGTATGTTTTGTAATTTTT 58.464 29.630 0.00 0.00 41.61 1.94
69 70 4.403976 TTTTTCGCCCGTTGCAAC 57.596 50.000 19.89 19.89 41.33 4.17
79 80 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
80 81 3.600694 TTGCAACGCACGGGCATT 61.601 55.556 11.77 0.00 38.71 3.56
81 82 3.144120 TTGCAACGCACGGGCATTT 62.144 52.632 11.77 0.00 38.71 2.32
82 83 3.105157 GCAACGCACGGGCATTTG 61.105 61.111 11.77 13.80 41.24 2.32
83 84 2.334653 CAACGCACGGGCATTTGT 59.665 55.556 11.77 0.00 41.24 2.83
84 85 1.576920 CAACGCACGGGCATTTGTA 59.423 52.632 11.77 0.00 41.24 2.41
85 86 0.727793 CAACGCACGGGCATTTGTAC 60.728 55.000 11.77 0.00 41.24 2.90
86 87 0.887387 AACGCACGGGCATTTGTACT 60.887 50.000 11.77 0.00 41.24 2.73
87 88 0.037139 ACGCACGGGCATTTGTACTA 60.037 50.000 11.77 0.00 41.24 1.82
88 89 0.650512 CGCACGGGCATTTGTACTAG 59.349 55.000 11.77 0.00 41.24 2.57
92 93 4.624015 GCACGGGCATTTGTACTAGTATA 58.376 43.478 3.77 0.00 40.72 1.47
126 127 8.325477 ACTCTTATATTTCTTTACAGAGGGCT 57.675 34.615 0.00 0.00 32.21 5.19
127 128 9.435570 ACTCTTATATTTCTTTACAGAGGGCTA 57.564 33.333 0.00 0.00 32.21 3.93
128 129 9.699703 CTCTTATATTTCTTTACAGAGGGCTAC 57.300 37.037 0.00 0.00 0.00 3.58
129 130 9.435570 TCTTATATTTCTTTACAGAGGGCTACT 57.564 33.333 0.00 0.00 0.00 2.57
166 169 6.943899 AATACCAGATCTAGAATCCCTTCC 57.056 41.667 0.00 0.00 31.27 3.46
206 209 6.315912 AAGGTAAACTTCGATGGTAAGCCAC 61.316 44.000 3.12 0.00 40.98 5.01
229 232 0.955919 CTCCTCCGGTGCACTTTTCC 60.956 60.000 17.98 0.00 0.00 3.13
252 255 7.291566 TCCCACAAAATAAACAACTCTCCTTA 58.708 34.615 0.00 0.00 0.00 2.69
323 326 9.113876 CAATATAAACGTCCAAGAGAAAACAAC 57.886 33.333 0.00 0.00 0.00 3.32
325 328 5.379732 AAACGTCCAAGAGAAAACAACAA 57.620 34.783 0.00 0.00 0.00 2.83
329 335 5.820947 ACGTCCAAGAGAAAACAACAATAGT 59.179 36.000 0.00 0.00 0.00 2.12
339 345 9.783256 GAGAAAACAACAATAGTAAACAACACT 57.217 29.630 0.00 0.00 0.00 3.55
350 356 5.657474 AGTAAACAACACTTCTCGACAGAA 58.343 37.500 0.00 0.00 37.11 3.02
355 361 4.508124 ACAACACTTCTCGACAGAACATTC 59.492 41.667 0.00 0.00 34.71 2.67
357 363 2.663602 CACTTCTCGACAGAACATTCGG 59.336 50.000 0.00 0.00 34.71 4.30
358 364 2.557056 ACTTCTCGACAGAACATTCGGA 59.443 45.455 0.00 0.00 34.71 4.55
359 365 2.631418 TCTCGACAGAACATTCGGAC 57.369 50.000 0.00 0.00 35.89 4.79
360 366 1.201647 TCTCGACAGAACATTCGGACC 59.798 52.381 0.00 0.00 35.89 4.46
361 367 0.245539 TCGACAGAACATTCGGACCC 59.754 55.000 0.00 0.00 35.89 4.46
362 368 0.246635 CGACAGAACATTCGGACCCT 59.753 55.000 0.00 0.00 0.00 4.34
363 369 1.736032 CGACAGAACATTCGGACCCTC 60.736 57.143 0.00 0.00 0.00 4.30
364 370 1.275291 GACAGAACATTCGGACCCTCA 59.725 52.381 0.00 0.00 0.00 3.86
365 371 1.697432 ACAGAACATTCGGACCCTCAA 59.303 47.619 0.00 0.00 0.00 3.02
366 372 2.105821 ACAGAACATTCGGACCCTCAAA 59.894 45.455 0.00 0.00 0.00 2.69
367 373 3.146066 CAGAACATTCGGACCCTCAAAA 58.854 45.455 0.00 0.00 0.00 2.44
368 374 3.568007 CAGAACATTCGGACCCTCAAAAA 59.432 43.478 0.00 0.00 0.00 1.94
392 398 4.425577 AAAAAGACAGATCATTCGCCAC 57.574 40.909 0.00 0.00 0.00 5.01
393 399 2.029838 AAGACAGATCATTCGCCACC 57.970 50.000 0.00 0.00 0.00 4.61
394 400 0.179100 AGACAGATCATTCGCCACCG 60.179 55.000 0.00 0.00 0.00 4.94
395 401 1.153369 ACAGATCATTCGCCACCGG 60.153 57.895 0.00 0.00 34.56 5.28
396 402 1.143838 CAGATCATTCGCCACCGGA 59.856 57.895 9.46 0.00 34.56 5.14
397 403 1.144057 AGATCATTCGCCACCGGAC 59.856 57.895 9.46 0.00 34.56 4.79
1341 1847 3.055080 TACGTACCGCTCCGCCTTG 62.055 63.158 0.00 0.00 0.00 3.61
1343 1849 4.078516 GTACCGCTCCGCCTTGGT 62.079 66.667 0.00 0.00 39.52 3.67
1344 1850 3.315949 TACCGCTCCGCCTTGGTT 61.316 61.111 0.00 0.00 39.52 3.67
1345 1851 2.886134 TACCGCTCCGCCTTGGTTT 61.886 57.895 0.00 0.00 39.52 3.27
1346 1852 2.400269 TACCGCTCCGCCTTGGTTTT 62.400 55.000 0.00 0.00 39.52 2.43
1396 1903 1.821966 TAGGTGAGGGGAGGCCTGAA 61.822 60.000 12.00 0.00 32.90 3.02
1419 1926 3.524095 TGATCCCCATCTCTCTCTCTC 57.476 52.381 0.00 0.00 0.00 3.20
1420 1927 3.062889 TGATCCCCATCTCTCTCTCTCT 58.937 50.000 0.00 0.00 0.00 3.10
1560 2067 4.837218 ACAAATCCATCTATCCCTCTCCT 58.163 43.478 0.00 0.00 0.00 3.69
1566 2073 6.086011 TCCATCTATCCCTCTCCTTATCTC 57.914 45.833 0.00 0.00 0.00 2.75
1577 2084 3.252701 TCTCCTTATCTCATCGTTACGCC 59.747 47.826 0.00 0.00 0.00 5.68
1580 2087 2.787601 TATCTCATCGTTACGCCCAC 57.212 50.000 0.00 0.00 0.00 4.61
1621 2128 2.846039 AGCAGTATCTGACCGTTACG 57.154 50.000 0.00 0.00 32.44 3.18
1622 2129 1.197910 GCAGTATCTGACCGTTACGC 58.802 55.000 0.00 0.00 32.44 4.42
1623 2130 1.836383 CAGTATCTGACCGTTACGCC 58.164 55.000 0.00 0.00 32.44 5.68
1625 2132 2.615447 CAGTATCTGACCGTTACGCCTA 59.385 50.000 0.00 0.00 32.44 3.93
1630 2137 1.924524 CTGACCGTTACGCCTATGTTG 59.075 52.381 0.00 0.00 0.00 3.33
1657 2164 4.507710 TCTAGCTGTTGAATGGTGTGATC 58.492 43.478 0.00 0.00 0.00 2.92
1660 2167 4.847198 AGCTGTTGAATGGTGTGATCATA 58.153 39.130 0.00 0.00 0.00 2.15
1665 2172 7.523293 TGTTGAATGGTGTGATCATAGTTTT 57.477 32.000 0.00 0.00 0.00 2.43
1700 2211 5.220548 CGTGCCATGTTTCTCTTCTATTCTG 60.221 44.000 0.00 0.00 0.00 3.02
1762 2304 6.723515 TGGTTGAATAAATCCACTTGATTCCA 59.276 34.615 0.00 0.00 42.97 3.53
1796 2340 1.860641 TAGGTTGATTCCGCCTCTGA 58.139 50.000 0.14 0.00 34.07 3.27
1814 2358 6.688922 GCCTCTGATTGGATACTTTGGTGATA 60.689 42.308 0.00 0.00 37.61 2.15
1829 2373 2.482721 GGTGATAGTGGTTGTTCGTTGG 59.517 50.000 0.00 0.00 0.00 3.77
1838 2382 4.454504 GTGGTTGTTCGTTGGTTATCATCT 59.545 41.667 0.00 0.00 0.00 2.90
1856 2400 4.097286 TCATCTGTAGTTGTGTGCGCTATA 59.903 41.667 9.73 0.00 0.00 1.31
1975 2519 8.400947 AGCAATCATGTAATTAGTGATGTGTTC 58.599 33.333 11.90 3.73 33.19 3.18
2011 2555 5.394333 GGAAACTAGTCTATGACCACTGGAC 60.394 48.000 0.71 0.00 32.18 4.02
2018 2562 0.250295 ATGACCACTGGACACGGTTG 60.250 55.000 0.71 0.00 32.69 3.77
2027 2571 3.275143 CTGGACACGGTTGGCATTATAA 58.725 45.455 0.00 0.00 28.57 0.98
2072 2616 9.581289 TCTCTAATTTGATAAAAGAAACCACCA 57.419 29.630 0.00 0.00 0.00 4.17
2116 2660 4.437772 TGTTTGCATATCATGGTGTGTG 57.562 40.909 4.51 0.00 0.00 3.82
2142 2686 8.235905 GTGTTTACGTCAGAACTCTTATACTCT 58.764 37.037 0.00 0.00 0.00 3.24
2178 2722 4.162096 ACTTGTCGCAGTCTTAGTACAG 57.838 45.455 0.00 0.00 0.00 2.74
2232 2776 6.075984 ACAAGTAATATGTATCGGAGGGAGT 58.924 40.000 0.00 0.00 0.00 3.85
2233 2777 7.236529 ACAAGTAATATGTATCGGAGGGAGTA 58.763 38.462 0.00 0.00 0.00 2.59
2234 2778 7.176340 ACAAGTAATATGTATCGGAGGGAGTAC 59.824 40.741 0.00 0.00 0.00 2.73
2235 2779 7.030234 AGTAATATGTATCGGAGGGAGTACT 57.970 40.000 0.00 0.00 0.00 2.73
2236 2780 8.155620 AGTAATATGTATCGGAGGGAGTACTA 57.844 38.462 0.00 0.00 0.00 1.82
2277 2821 4.206375 TCTCTTGTTGATGGTTTCAAGCA 58.794 39.130 0.00 0.00 44.89 3.91
2293 2837 6.872628 TTCAAGCATCTAAATGGATAGCTG 57.127 37.500 0.00 0.00 33.70 4.24
2352 2896 2.772287 AGTTCAGTTAGCTGTGCCTTC 58.228 47.619 6.47 0.00 43.05 3.46
2427 2973 9.357652 GCTTGTTTATCTTTCATTTTCTGCATA 57.642 29.630 0.00 0.00 0.00 3.14
2487 3042 5.615984 GCCAAAATGTGAAATGTTGCAGATG 60.616 40.000 0.00 0.00 0.00 2.90
2704 3260 9.699410 TTGATGAGTTATGAAGTATTCCCAAAT 57.301 29.630 0.00 0.00 46.93 2.32
2740 3297 7.521871 TCTTTACGGAGGGAGTATCTTTATC 57.478 40.000 0.00 0.00 33.73 1.75
2741 3298 7.296098 TCTTTACGGAGGGAGTATCTTTATCT 58.704 38.462 0.00 0.00 33.73 1.98
2742 3299 7.783596 TCTTTACGGAGGGAGTATCTTTATCTT 59.216 37.037 0.00 0.00 33.73 2.40
2743 3300 7.909485 TTACGGAGGGAGTATCTTTATCTTT 57.091 36.000 0.00 0.00 33.73 2.52
2744 3301 9.425248 TTTACGGAGGGAGTATCTTTATCTTTA 57.575 33.333 0.00 0.00 33.73 1.85
2745 3302 9.597681 TTACGGAGGGAGTATCTTTATCTTTAT 57.402 33.333 0.00 0.00 33.73 1.40
2746 3303 8.493787 ACGGAGGGAGTATCTTTATCTTTATT 57.506 34.615 0.00 0.00 33.73 1.40
2780 3638 2.092968 GTGTTGATCAGTAGGGCCATCA 60.093 50.000 6.18 2.31 0.00 3.07
2792 3650 3.250617 AGGGCCATCAAACCTTTCATTT 58.749 40.909 6.18 0.00 0.00 2.32
2800 3658 2.531522 AACCTTTCATTTGCAGTGGC 57.468 45.000 0.00 0.00 41.68 5.01
2818 3676 2.057137 GCCTCAGCCAACCATAATCA 57.943 50.000 0.00 0.00 0.00 2.57
2826 3684 3.119029 AGCCAACCATAATCATGTGCAAC 60.119 43.478 0.00 0.00 37.35 4.17
3148 4006 6.017852 GGTTCTCTTGGTAGTTGTTGAAGAAG 60.018 42.308 0.00 0.00 0.00 2.85
3185 4043 6.969043 TGACCTCCTTATATTGTGGATTGTT 58.031 36.000 0.00 0.00 0.00 2.83
3198 4056 7.513190 TTGTGGATTGTTTTTGTAAGAAACG 57.487 32.000 0.00 0.00 39.30 3.60
3204 4062 5.049398 TGTTTTTGTAAGAAACGTGCACT 57.951 34.783 16.19 0.00 39.30 4.40
3208 4066 3.352554 TGTAAGAAACGTGCACTCGTA 57.647 42.857 16.19 5.74 43.38 3.43
3210 4068 5.045668 TGTAAGAAACGTGCACTCGTATA 57.954 39.130 16.19 4.27 43.38 1.47
3211 4069 5.643664 TGTAAGAAACGTGCACTCGTATAT 58.356 37.500 16.19 0.00 43.38 0.86
3212 4070 5.740569 TGTAAGAAACGTGCACTCGTATATC 59.259 40.000 16.19 8.38 43.38 1.63
3238 4098 2.868044 GCTGTGATATCGGCCTACTTGG 60.868 54.545 0.00 0.00 39.35 3.61
3248 4108 1.298859 GCCTACTTGGTCGGCAAGTG 61.299 60.000 12.96 5.49 42.82 3.16
3423 4286 2.568956 TGCCTGATGAAGCTACAAGACT 59.431 45.455 0.00 0.00 0.00 3.24
3424 4287 3.008375 TGCCTGATGAAGCTACAAGACTT 59.992 43.478 0.00 0.00 0.00 3.01
3632 4507 2.814280 ACTCGTGAACCGTTGAGAAT 57.186 45.000 4.55 0.00 37.94 2.40
3656 4531 2.574006 TGCTGAGTTGCCAAGAGAAT 57.426 45.000 0.00 0.00 0.00 2.40
3692 4569 7.103641 GGTACAAATCACCATCTCTCTTTGTA 58.896 38.462 0.00 0.00 37.78 2.41
3694 4571 5.940470 ACAAATCACCATCTCTCTTTGTACC 59.060 40.000 0.00 0.00 35.66 3.34
3695 4572 4.762289 ATCACCATCTCTCTTTGTACCC 57.238 45.455 0.00 0.00 0.00 3.69
3696 4573 3.791320 TCACCATCTCTCTTTGTACCCT 58.209 45.455 0.00 0.00 0.00 4.34
3697 4574 4.168101 TCACCATCTCTCTTTGTACCCTT 58.832 43.478 0.00 0.00 0.00 3.95
3698 4575 5.338632 TCACCATCTCTCTTTGTACCCTTA 58.661 41.667 0.00 0.00 0.00 2.69
3699 4576 5.783360 TCACCATCTCTCTTTGTACCCTTAA 59.217 40.000 0.00 0.00 0.00 1.85
3700 4577 6.271391 TCACCATCTCTCTTTGTACCCTTAAA 59.729 38.462 0.00 0.00 0.00 1.52
3701 4578 6.595716 CACCATCTCTCTTTGTACCCTTAAAG 59.404 42.308 0.00 0.00 35.70 1.85
3726 4621 4.946784 AGTTGTTCGATTACATCAAGGC 57.053 40.909 0.00 0.00 0.00 4.35
3782 4677 6.670695 ACCCTATGCTTGAAAATTCAGTTT 57.329 33.333 0.00 0.00 38.61 2.66
3818 4713 8.422577 AAGCATTACTCCCTTTGTAAAGAAAT 57.577 30.769 5.95 0.00 38.28 2.17
3826 4721 9.397280 ACTCCCTTTGTAAAGAAATATAAGAGC 57.603 33.333 5.95 0.00 38.28 4.09
3827 4722 8.433421 TCCCTTTGTAAAGAAATATAAGAGCG 57.567 34.615 5.95 0.00 38.28 5.03
3828 4723 8.044908 TCCCTTTGTAAAGAAATATAAGAGCGT 58.955 33.333 5.95 0.00 38.28 5.07
3829 4724 8.674607 CCCTTTGTAAAGAAATATAAGAGCGTT 58.325 33.333 5.95 0.00 38.28 4.84
3846 4741 7.772332 AGAGCGTTTAATATAGGAGTGTTTG 57.228 36.000 0.00 0.00 0.00 2.93
3847 4742 6.761714 AGAGCGTTTAATATAGGAGTGTTTGG 59.238 38.462 0.00 0.00 0.00 3.28
3848 4743 5.820947 AGCGTTTAATATAGGAGTGTTTGGG 59.179 40.000 0.00 0.00 0.00 4.12
3849 4744 5.587443 GCGTTTAATATAGGAGTGTTTGGGT 59.413 40.000 0.00 0.00 0.00 4.51
3850 4745 6.762661 GCGTTTAATATAGGAGTGTTTGGGTA 59.237 38.462 0.00 0.00 0.00 3.69
3851 4746 7.280652 GCGTTTAATATAGGAGTGTTTGGGTAA 59.719 37.037 0.00 0.00 0.00 2.85
3852 4747 9.165035 CGTTTAATATAGGAGTGTTTGGGTAAA 57.835 33.333 0.00 0.00 0.00 2.01
3857 4752 9.990868 AATATAGGAGTGTTTGGGTAAAGAAAT 57.009 29.630 0.00 0.00 0.00 2.17
3862 4757 9.628500 AGGAGTGTTTGGGTAAAGAAATATATC 57.372 33.333 0.00 0.00 0.00 1.63
3863 4758 9.628500 GGAGTGTTTGGGTAAAGAAATATATCT 57.372 33.333 0.00 0.00 0.00 1.98
3957 4894 3.320826 GGCATACCTTCACCTTTTGTGTT 59.679 43.478 0.00 0.00 45.61 3.32
3959 4896 2.959507 ACCTTCACCTTTTGTGTTGC 57.040 45.000 0.00 0.00 45.61 4.17
3960 4897 1.134175 ACCTTCACCTTTTGTGTTGCG 59.866 47.619 0.00 0.00 45.61 4.85
3961 4898 1.134175 CCTTCACCTTTTGTGTTGCGT 59.866 47.619 0.00 0.00 45.61 5.24
3962 4899 2.416701 CCTTCACCTTTTGTGTTGCGTT 60.417 45.455 0.00 0.00 45.61 4.84
3966 4903 0.644843 CCTTTTGTGTTGCGTTGTGC 59.355 50.000 0.00 0.00 46.70 4.57
4072 5141 4.033587 CGTATGGGTTTGTTATTGTCGGAG 59.966 45.833 0.00 0.00 0.00 4.63
4079 5148 1.271379 TGTTATTGTCGGAGTGCGACT 59.729 47.619 32.54 19.13 37.29 4.18
4086 5155 0.039798 TCGGAGTGCGACTTGTACAC 60.040 55.000 1.26 0.00 35.35 2.90
4087 5156 1.334992 CGGAGTGCGACTTGTACACG 61.335 60.000 0.00 0.00 39.31 4.49
4089 5158 1.601162 GGAGTGCGACTTGTACACGAA 60.601 52.381 6.33 0.00 39.31 3.85
4090 5159 2.325761 GAGTGCGACTTGTACACGAAT 58.674 47.619 6.33 0.00 39.31 3.34
4092 5161 3.240069 AGTGCGACTTGTACACGAATAC 58.760 45.455 6.33 3.24 39.31 1.89
4104 5173 4.600012 ACACGAATACTACAAAGCATGC 57.400 40.909 10.51 10.51 0.00 4.06
4114 5183 1.226491 AAAGCATGCAATCGAGCGC 60.226 52.632 21.98 0.00 37.31 5.92
4115 5184 1.925415 AAAGCATGCAATCGAGCGCA 61.925 50.000 21.98 13.27 43.45 6.09
4116 5185 1.925415 AAGCATGCAATCGAGCGCAA 61.925 50.000 21.98 0.00 42.37 4.85
4129 5198 1.660264 GCGCAAAAGAAACGGGTGG 60.660 57.895 0.30 0.00 0.00 4.61
4130 5199 1.731093 CGCAAAAGAAACGGGTGGT 59.269 52.632 0.00 0.00 0.00 4.16
4156 5225 8.408043 TGACTGAATTGTTGGTTGAATTAGAT 57.592 30.769 0.00 0.00 0.00 1.98
4159 5228 8.960591 ACTGAATTGTTGGTTGAATTAGATAGG 58.039 33.333 0.00 0.00 0.00 2.57
4176 5275 5.289510 AGATAGGGACTTGGGTATGAACTT 58.710 41.667 0.00 0.00 41.75 2.66
4249 5348 3.964875 GCGTGGCCACAACACAGG 61.965 66.667 34.16 17.58 38.74 4.00
4254 5353 4.603535 GCCACAACACAGGCCCCT 62.604 66.667 0.00 0.00 45.18 4.79
4255 5354 3.166434 CCACAACACAGGCCCCTA 58.834 61.111 0.00 0.00 0.00 3.53
4256 5355 1.002134 CCACAACACAGGCCCCTAG 60.002 63.158 0.00 0.00 0.00 3.02
4257 5356 1.761174 CACAACACAGGCCCCTAGT 59.239 57.895 0.00 0.00 0.00 2.57
4258 5357 0.321653 CACAACACAGGCCCCTAGTC 60.322 60.000 0.00 0.00 0.00 2.59
4259 5358 1.299976 CAACACAGGCCCCTAGTCC 59.700 63.158 0.00 0.00 0.00 3.85
4260 5359 1.161113 AACACAGGCCCCTAGTCCT 59.839 57.895 0.00 0.00 0.00 3.85
4261 5360 0.475828 AACACAGGCCCCTAGTCCTT 60.476 55.000 0.00 0.00 0.00 3.36
4262 5361 1.201429 ACACAGGCCCCTAGTCCTTG 61.201 60.000 0.00 0.00 0.00 3.61
4263 5362 1.616628 ACAGGCCCCTAGTCCTTGG 60.617 63.158 0.00 0.00 0.00 3.61
4264 5363 2.042930 AGGCCCCTAGTCCTTGGG 59.957 66.667 0.00 6.82 43.89 4.12
4268 5367 3.480133 CCCTAGTCCTTGGGGCGG 61.480 72.222 5.97 0.00 41.15 6.13
4269 5368 2.687566 CCTAGTCCTTGGGGCGGT 60.688 66.667 0.00 0.00 0.00 5.68
4270 5369 2.584608 CTAGTCCTTGGGGCGGTG 59.415 66.667 0.00 0.00 0.00 4.94
4271 5370 3.682292 CTAGTCCTTGGGGCGGTGC 62.682 68.421 0.00 0.00 0.00 5.01
4352 5451 1.868251 CACGCTCGCTCCGTTCTAC 60.868 63.158 0.00 0.00 36.69 2.59
4353 5452 2.278013 CGCTCGCTCCGTTCTACC 60.278 66.667 0.00 0.00 0.00 3.18
4354 5453 2.278013 GCTCGCTCCGTTCTACCG 60.278 66.667 0.00 0.00 0.00 4.02
4355 5454 2.278013 CTCGCTCCGTTCTACCGC 60.278 66.667 0.00 0.00 0.00 5.68
4356 5455 3.047718 CTCGCTCCGTTCTACCGCA 62.048 63.158 0.00 0.00 0.00 5.69
4357 5456 2.104331 CGCTCCGTTCTACCGCAT 59.896 61.111 0.00 0.00 0.00 4.73
4358 5457 2.230940 CGCTCCGTTCTACCGCATG 61.231 63.158 0.00 0.00 0.00 4.06
4359 5458 2.526120 GCTCCGTTCTACCGCATGC 61.526 63.158 7.91 7.91 0.00 4.06
4360 5459 2.202690 TCCGTTCTACCGCATGCG 60.203 61.111 32.60 32.60 39.44 4.73
4361 5460 2.508439 CCGTTCTACCGCATGCGT 60.508 61.111 35.55 25.53 37.81 5.24
4362 5461 2.695055 CGTTCTACCGCATGCGTG 59.305 61.111 35.55 28.11 37.81 5.34
4363 5462 2.092291 CGTTCTACCGCATGCGTGT 61.092 57.895 35.55 31.51 37.81 4.49
4365 5464 1.447140 TTCTACCGCATGCGTGTCC 60.447 57.895 35.55 0.00 37.81 4.02
4366 5465 1.884075 TTCTACCGCATGCGTGTCCT 61.884 55.000 35.55 16.18 37.81 3.85
4368 5467 2.557059 CTACCGCATGCGTGTCCTCA 62.557 60.000 35.55 17.53 37.81 3.86
4369 5468 2.161078 TACCGCATGCGTGTCCTCAA 62.161 55.000 35.55 16.08 37.81 3.02
4396 5496 1.521457 GATGCGAATCACGGCCAGA 60.521 57.895 2.24 0.00 42.83 3.86
4426 5526 2.355444 TGATGCGTGAAACATATGCCAG 59.645 45.455 1.58 0.00 35.74 4.85
4460 5560 0.179163 CTGCTACTCACGATCGTGCA 60.179 55.000 37.14 29.80 45.04 4.57
4491 5591 4.873129 CCGGTGGACCATCGCTCG 62.873 72.222 22.14 4.47 36.57 5.03
4498 5598 3.825833 GACCATCGCTCGCTACGGG 62.826 68.421 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.492344 CCTTGTGCCATTTCTTATAACCAATTC 59.508 37.037 0.00 0.00 0.00 2.17
1 2 7.038373 ACCTTGTGCCATTTCTTATAACCAATT 60.038 33.333 0.00 0.00 0.00 2.32
2 3 6.440328 ACCTTGTGCCATTTCTTATAACCAAT 59.560 34.615 0.00 0.00 0.00 3.16
3 4 5.777732 ACCTTGTGCCATTTCTTATAACCAA 59.222 36.000 0.00 0.00 0.00 3.67
4 5 5.184864 CACCTTGTGCCATTTCTTATAACCA 59.815 40.000 0.00 0.00 0.00 3.67
5 6 5.394115 CCACCTTGTGCCATTTCTTATAACC 60.394 44.000 0.00 0.00 31.34 2.85
6 7 5.650543 CCACCTTGTGCCATTTCTTATAAC 58.349 41.667 0.00 0.00 31.34 1.89
7 8 4.159506 GCCACCTTGTGCCATTTCTTATAA 59.840 41.667 0.00 0.00 31.34 0.98
8 9 3.699038 GCCACCTTGTGCCATTTCTTATA 59.301 43.478 0.00 0.00 31.34 0.98
9 10 2.497273 GCCACCTTGTGCCATTTCTTAT 59.503 45.455 0.00 0.00 31.34 1.73
10 11 1.892474 GCCACCTTGTGCCATTTCTTA 59.108 47.619 0.00 0.00 31.34 2.10
11 12 0.681175 GCCACCTTGTGCCATTTCTT 59.319 50.000 0.00 0.00 31.34 2.52
12 13 0.469705 TGCCACCTTGTGCCATTTCT 60.470 50.000 0.00 0.00 31.34 2.52
13 14 0.319813 GTGCCACCTTGTGCCATTTC 60.320 55.000 0.00 0.00 31.34 2.17
14 15 1.047596 TGTGCCACCTTGTGCCATTT 61.048 50.000 0.00 0.00 31.34 2.32
15 16 1.457267 TGTGCCACCTTGTGCCATT 60.457 52.632 0.00 0.00 31.34 3.16
16 17 2.198150 TGTGCCACCTTGTGCCAT 59.802 55.556 0.00 0.00 31.34 4.40
17 18 2.832661 GTGTGCCACCTTGTGCCA 60.833 61.111 0.00 0.00 31.34 4.92
18 19 3.964875 CGTGTGCCACCTTGTGCC 61.965 66.667 0.00 0.00 31.34 5.01
19 20 2.392613 CTTCGTGTGCCACCTTGTGC 62.393 60.000 0.00 0.00 31.34 4.57
20 21 1.095228 ACTTCGTGTGCCACCTTGTG 61.095 55.000 0.00 0.00 0.00 3.33
21 22 0.466543 TACTTCGTGTGCCACCTTGT 59.533 50.000 0.00 0.51 0.00 3.16
22 23 1.464608 CATACTTCGTGTGCCACCTTG 59.535 52.381 0.00 0.00 0.00 3.61
23 24 1.071699 ACATACTTCGTGTGCCACCTT 59.928 47.619 0.00 0.00 0.00 3.50
24 25 0.685097 ACATACTTCGTGTGCCACCT 59.315 50.000 0.00 0.00 0.00 4.00
25 26 1.519408 AACATACTTCGTGTGCCACC 58.481 50.000 0.00 0.00 0.00 4.61
26 27 3.242936 ACAAAACATACTTCGTGTGCCAC 60.243 43.478 0.00 0.00 0.00 5.01
27 28 2.946329 ACAAAACATACTTCGTGTGCCA 59.054 40.909 0.00 0.00 0.00 4.92
28 29 3.619233 ACAAAACATACTTCGTGTGCC 57.381 42.857 0.00 0.00 0.00 5.01
29 30 7.617533 AAATTACAAAACATACTTCGTGTGC 57.382 32.000 0.00 0.00 0.00 4.57
62 63 3.839642 AATGCCCGTGCGTTGCAAC 62.840 57.895 19.89 19.89 44.90 4.17
63 64 3.144120 AAATGCCCGTGCGTTGCAA 62.144 52.632 0.00 0.00 45.88 4.08
64 65 3.600694 AAATGCCCGTGCGTTGCA 61.601 55.556 0.00 8.11 45.88 4.08
65 66 2.465097 TACAAATGCCCGTGCGTTGC 62.465 55.000 0.00 0.00 45.88 4.17
66 67 0.727793 GTACAAATGCCCGTGCGTTG 60.728 55.000 0.00 1.29 45.88 4.10
68 69 0.037139 TAGTACAAATGCCCGTGCGT 60.037 50.000 0.00 0.00 41.78 5.24
69 70 0.650512 CTAGTACAAATGCCCGTGCG 59.349 55.000 0.00 0.00 41.78 5.34
70 71 1.734163 ACTAGTACAAATGCCCGTGC 58.266 50.000 0.00 0.00 38.26 5.34
71 72 5.839621 AGTATACTAGTACAAATGCCCGTG 58.160 41.667 4.31 0.00 0.00 4.94
72 73 5.832060 AGAGTATACTAGTACAAATGCCCGT 59.168 40.000 5.09 0.00 0.00 5.28
73 74 6.328641 AGAGTATACTAGTACAAATGCCCG 57.671 41.667 5.09 0.00 0.00 6.13
100 101 9.435570 AGCCCTCTGTAAAGAAATATAAGAGTA 57.564 33.333 0.00 0.00 0.00 2.59
101 102 8.325477 AGCCCTCTGTAAAGAAATATAAGAGT 57.675 34.615 0.00 0.00 0.00 3.24
154 157 5.502089 TTTAAACACGGGAAGGGATTCTA 57.498 39.130 0.00 0.00 0.00 2.10
181 184 4.698780 GGCTTACCATCGAAGTTTACCTTT 59.301 41.667 0.00 0.00 31.82 3.11
182 185 4.259356 GGCTTACCATCGAAGTTTACCTT 58.741 43.478 0.00 0.00 33.61 3.50
183 186 3.262405 TGGCTTACCATCGAAGTTTACCT 59.738 43.478 0.00 0.00 42.67 3.08
184 187 3.602483 TGGCTTACCATCGAAGTTTACC 58.398 45.455 0.00 0.00 42.67 2.85
272 275 9.204337 TGGTCAAGGTATTAGTGCTAGTTATTA 57.796 33.333 0.00 0.00 0.00 0.98
273 276 8.086143 TGGTCAAGGTATTAGTGCTAGTTATT 57.914 34.615 0.00 0.00 0.00 1.40
274 277 7.670605 TGGTCAAGGTATTAGTGCTAGTTAT 57.329 36.000 0.00 0.00 0.00 1.89
286 289 7.340256 TGGACGTTTATATTGGTCAAGGTATT 58.660 34.615 0.00 0.00 0.00 1.89
287 290 6.891388 TGGACGTTTATATTGGTCAAGGTAT 58.109 36.000 0.00 0.00 0.00 2.73
323 326 7.381408 TCTGTCGAGAAGTGTTGTTTACTATTG 59.619 37.037 0.00 0.00 0.00 1.90
325 328 6.978338 TCTGTCGAGAAGTGTTGTTTACTAT 58.022 36.000 0.00 0.00 0.00 2.12
329 335 5.412640 TGTTCTGTCGAGAAGTGTTGTTTA 58.587 37.500 0.00 0.00 38.95 2.01
339 345 2.352421 GGTCCGAATGTTCTGTCGAGAA 60.352 50.000 0.00 0.00 39.64 2.87
371 377 3.191371 GGTGGCGAATGATCTGTCTTTTT 59.809 43.478 0.00 0.00 0.00 1.94
372 378 2.749621 GGTGGCGAATGATCTGTCTTTT 59.250 45.455 0.00 0.00 0.00 2.27
373 379 2.359900 GGTGGCGAATGATCTGTCTTT 58.640 47.619 0.00 0.00 0.00 2.52
374 380 1.740380 CGGTGGCGAATGATCTGTCTT 60.740 52.381 0.00 0.00 0.00 3.01
375 381 0.179100 CGGTGGCGAATGATCTGTCT 60.179 55.000 0.00 0.00 0.00 3.41
376 382 1.154205 CCGGTGGCGAATGATCTGTC 61.154 60.000 0.00 0.00 0.00 3.51
377 383 1.153369 CCGGTGGCGAATGATCTGT 60.153 57.895 0.00 0.00 0.00 3.41
378 384 1.143838 TCCGGTGGCGAATGATCTG 59.856 57.895 0.00 0.00 0.00 2.90
379 385 1.144057 GTCCGGTGGCGAATGATCT 59.856 57.895 0.00 0.00 0.00 2.75
380 386 3.719214 GTCCGGTGGCGAATGATC 58.281 61.111 0.00 0.00 0.00 2.92
1341 1847 5.122554 ACGAAAATTGAACCAAACCAAAACC 59.877 36.000 0.00 0.00 0.00 3.27
1342 1848 6.171932 ACGAAAATTGAACCAAACCAAAAC 57.828 33.333 0.00 0.00 0.00 2.43
1343 1849 5.062308 CGACGAAAATTGAACCAAACCAAAA 59.938 36.000 0.00 0.00 0.00 2.44
1344 1850 4.563184 CGACGAAAATTGAACCAAACCAAA 59.437 37.500 0.00 0.00 0.00 3.28
1345 1851 4.106197 CGACGAAAATTGAACCAAACCAA 58.894 39.130 0.00 0.00 0.00 3.67
1346 1852 3.489398 CCGACGAAAATTGAACCAAACCA 60.489 43.478 0.00 0.00 0.00 3.67
1396 1903 4.830138 AGAGAGAGAGATGGGGATCAAAT 58.170 43.478 0.00 0.00 0.00 2.32
1419 1926 0.319728 ATCGGATCCGGATTCTGCAG 59.680 55.000 32.79 7.63 40.25 4.41
1420 1927 1.546029 CTATCGGATCCGGATTCTGCA 59.454 52.381 32.79 12.37 40.25 4.41
1560 2067 2.542205 CGTGGGCGTAACGATGAGATAA 60.542 50.000 0.00 0.00 43.68 1.75
1577 2084 4.495422 ACAGCTACTAGATCAAAACGTGG 58.505 43.478 0.00 0.00 0.00 4.94
1580 2087 5.683743 GCTAGACAGCTACTAGATCAAAACG 59.316 44.000 22.93 0.00 44.93 3.60
1614 2121 0.918619 CGACAACATAGGCGTAACGG 59.081 55.000 0.00 0.00 0.00 4.44
1621 2128 3.243569 ACAGCTAGATCGACAACATAGGC 60.244 47.826 0.00 0.00 0.00 3.93
1622 2129 4.576216 ACAGCTAGATCGACAACATAGG 57.424 45.455 0.00 0.00 0.00 2.57
1623 2130 5.582550 TCAACAGCTAGATCGACAACATAG 58.417 41.667 0.00 0.00 0.00 2.23
1625 2132 4.456280 TCAACAGCTAGATCGACAACAT 57.544 40.909 0.00 0.00 0.00 2.71
1630 2137 3.553511 CACCATTCAACAGCTAGATCGAC 59.446 47.826 0.00 0.00 0.00 4.20
1657 2164 4.466828 CACGCTTCACCTCAAAAACTATG 58.533 43.478 0.00 0.00 0.00 2.23
1660 2167 1.065551 GCACGCTTCACCTCAAAAACT 59.934 47.619 0.00 0.00 0.00 2.66
1665 2172 1.073025 ATGGCACGCTTCACCTCAA 59.927 52.632 0.00 0.00 0.00 3.02
1729 2240 6.325545 AGTGGATTTATTCAACCATGATGCAT 59.674 34.615 0.00 0.00 34.96 3.96
1796 2340 6.327386 ACCACTATCACCAAAGTATCCAAT 57.673 37.500 0.00 0.00 0.00 3.16
1814 2358 3.811083 TGATAACCAACGAACAACCACT 58.189 40.909 0.00 0.00 0.00 4.00
1829 2373 4.492570 GCGCACACAACTACAGATGATAAC 60.493 45.833 0.30 0.00 0.00 1.89
1838 2382 3.861276 AGTATAGCGCACACAACTACA 57.139 42.857 11.47 0.00 0.00 2.74
1856 2400 6.010219 AGAACATGTGTGGGCTAATAAAAGT 58.990 36.000 0.00 0.00 0.00 2.66
1975 2519 4.065789 GACTAGTTTCCCACAACAGAAGG 58.934 47.826 0.00 0.00 0.00 3.46
2011 2555 3.692101 TGAACCTTATAATGCCAACCGTG 59.308 43.478 0.00 0.00 0.00 4.94
2018 2562 8.466798 ACTGTAAAACATGAACCTTATAATGCC 58.533 33.333 0.00 0.00 0.00 4.40
2072 2616 6.015688 ACAAACAATGATCTCAGACAATTGCT 60.016 34.615 5.05 0.69 0.00 3.91
2116 2660 8.235905 AGAGTATAAGAGTTCTGACGTAAACAC 58.764 37.037 9.71 4.62 0.00 3.32
2142 2686 4.321008 GCGACAAGTAATATGGATCGGAGA 60.321 45.833 0.00 0.00 45.75 3.71
2184 2728 5.700832 TCACAGTCCTAGTGCAAATTTGTAG 59.299 40.000 19.03 12.41 36.93 2.74
2233 2777 9.554053 AGAGAATGAAATGGGCTATAGTATAGT 57.446 33.333 16.76 0.00 0.00 2.12
2236 2780 8.664079 ACAAGAGAATGAAATGGGCTATAGTAT 58.336 33.333 0.84 0.00 0.00 2.12
2293 2837 9.793252 GGATGCCATATATGTGACAATTTATTC 57.207 33.333 11.73 1.54 0.00 1.75
2352 2896 0.250124 TGTAAACACCGGTCAGGCTG 60.250 55.000 2.59 8.58 46.52 4.85
2487 3042 6.385033 AGCAAATGACTTTTGACTGCTTATC 58.615 36.000 15.85 0.00 46.36 1.75
2704 3260 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
2742 3299 9.952030 TGATCAACACATACTTGGAGTTAATAA 57.048 29.630 0.00 0.00 0.00 1.40
2743 3300 9.599866 CTGATCAACACATACTTGGAGTTAATA 57.400 33.333 0.00 0.00 0.00 0.98
2744 3301 8.103305 ACTGATCAACACATACTTGGAGTTAAT 58.897 33.333 0.00 0.00 0.00 1.40
2745 3302 7.450074 ACTGATCAACACATACTTGGAGTTAA 58.550 34.615 0.00 0.00 0.00 2.01
2746 3303 7.004555 ACTGATCAACACATACTTGGAGTTA 57.995 36.000 0.00 0.00 0.00 2.24
2780 3638 2.485302 GGCCACTGCAAATGAAAGGTTT 60.485 45.455 0.00 0.00 40.13 3.27
2800 3658 3.317149 CACATGATTATGGTTGGCTGAGG 59.683 47.826 0.00 0.00 38.66 3.86
2818 3676 3.636300 TGCTTAAACCAGAAGTTGCACAT 59.364 39.130 0.00 0.00 39.19 3.21
2826 3684 5.552178 ACTAGGAAGTGCTTAAACCAGAAG 58.448 41.667 0.00 0.00 33.57 2.85
2916 3774 4.214545 CCAAAAGCTATACACAACGACCAA 59.785 41.667 0.00 0.00 0.00 3.67
2917 3775 3.749088 CCAAAAGCTATACACAACGACCA 59.251 43.478 0.00 0.00 0.00 4.02
3034 3892 8.729157 CAGAATACTGACACTACCACAGGGTG 62.729 50.000 0.00 0.00 42.62 4.61
3045 3903 7.099764 CCAATTACTGACAGAATACTGACACT 58.900 38.462 10.08 0.00 46.03 3.55
3185 4043 3.371591 ACGAGTGCACGTTTCTTACAAAA 59.628 39.130 12.01 0.00 44.14 2.44
3198 4056 3.604198 CAGCGTATGATATACGAGTGCAC 59.396 47.826 21.44 9.40 42.94 4.57
3204 4062 6.292703 CCGATATCACAGCGTATGATATACGA 60.293 42.308 21.44 4.36 45.56 3.43
3210 4068 2.417379 GGCCGATATCACAGCGTATGAT 60.417 50.000 3.12 5.82 40.02 2.45
3211 4069 1.067846 GGCCGATATCACAGCGTATGA 60.068 52.381 3.12 0.00 33.06 2.15
3212 4070 1.067565 AGGCCGATATCACAGCGTATG 60.068 52.381 3.12 0.00 33.06 2.39
3238 4098 1.086634 GGAGATCAGCACTTGCCGAC 61.087 60.000 0.00 0.00 43.38 4.79
3248 4108 3.936564 ACAAGAAGTGAAGGAGATCAGC 58.063 45.455 0.00 0.00 0.00 4.26
3270 4130 1.275856 TCCATGAACTGCAAAATGGGC 59.724 47.619 13.64 0.00 40.07 5.36
3423 4286 1.448985 GTGGGCTCGTCTATTTGCAA 58.551 50.000 0.00 0.00 0.00 4.08
3424 4287 0.739462 CGTGGGCTCGTCTATTTGCA 60.739 55.000 0.00 0.00 0.00 4.08
3617 4492 4.154195 AGCATTGTATTCTCAACGGTTCAC 59.846 41.667 0.00 0.00 0.00 3.18
3621 4496 3.935203 CTCAGCATTGTATTCTCAACGGT 59.065 43.478 0.00 0.00 0.00 4.83
3632 4507 3.076621 CTCTTGGCAACTCAGCATTGTA 58.923 45.455 0.00 0.00 35.83 2.41
3656 4531 5.419155 TGGTGATTTGTACCACACTTTTTGA 59.581 36.000 0.00 0.00 43.00 2.69
3692 4569 6.954487 ATCGAACAACTTTTCTTTAAGGGT 57.046 33.333 0.00 0.00 0.00 4.34
3694 4571 9.893305 ATGTAATCGAACAACTTTTCTTTAAGG 57.107 29.630 0.00 0.00 32.02 2.69
3759 4654 6.670695 AAACTGAATTTTCAAGCATAGGGT 57.329 33.333 0.00 0.00 36.64 4.34
3792 4687 8.927675 TTTCTTTACAAAGGGAGTAATGCTTA 57.072 30.769 2.04 0.00 36.67 3.09
3793 4688 7.833285 TTTCTTTACAAAGGGAGTAATGCTT 57.167 32.000 2.04 0.00 36.67 3.91
3794 4689 9.700831 ATATTTCTTTACAAAGGGAGTAATGCT 57.299 29.630 2.04 0.00 36.67 3.79
3801 4696 8.552034 CGCTCTTATATTTCTTTACAAAGGGAG 58.448 37.037 2.04 0.00 36.67 4.30
3802 4697 8.044908 ACGCTCTTATATTTCTTTACAAAGGGA 58.955 33.333 2.04 0.00 36.67 4.20
3803 4698 8.209917 ACGCTCTTATATTTCTTTACAAAGGG 57.790 34.615 2.04 0.00 36.67 3.95
3823 4718 6.018180 CCCAAACACTCCTATATTAAACGCTC 60.018 42.308 0.00 0.00 0.00 5.03
3825 4720 5.587443 ACCCAAACACTCCTATATTAAACGC 59.413 40.000 0.00 0.00 0.00 4.84
3826 4721 8.721019 TTACCCAAACACTCCTATATTAAACG 57.279 34.615 0.00 0.00 0.00 3.60
3837 4732 9.628500 AGATATATTTCTTTACCCAAACACTCC 57.372 33.333 0.00 0.00 0.00 3.85
3878 4773 9.686683 AAAAGGTTGCTCTCACATATAAGTATT 57.313 29.630 0.00 0.00 0.00 1.89
3879 4774 9.686683 AAAAAGGTTGCTCTCACATATAAGTAT 57.313 29.630 0.00 0.00 0.00 2.12
3880 4775 9.162764 GAAAAAGGTTGCTCTCACATATAAGTA 57.837 33.333 0.00 0.00 0.00 2.24
3881 4776 7.148407 CGAAAAAGGTTGCTCTCACATATAAGT 60.148 37.037 0.00 0.00 0.00 2.24
3882 4777 7.182761 CGAAAAAGGTTGCTCTCACATATAAG 58.817 38.462 0.00 0.00 0.00 1.73
3883 4778 6.403200 GCGAAAAAGGTTGCTCTCACATATAA 60.403 38.462 0.00 0.00 0.00 0.98
3884 4779 5.064707 GCGAAAAAGGTTGCTCTCACATATA 59.935 40.000 0.00 0.00 0.00 0.86
3885 4780 4.142600 GCGAAAAAGGTTGCTCTCACATAT 60.143 41.667 0.00 0.00 0.00 1.78
3886 4781 3.188460 GCGAAAAAGGTTGCTCTCACATA 59.812 43.478 0.00 0.00 0.00 2.29
3887 4782 2.030805 GCGAAAAAGGTTGCTCTCACAT 60.031 45.455 0.00 0.00 0.00 3.21
3888 4783 1.333619 GCGAAAAAGGTTGCTCTCACA 59.666 47.619 0.00 0.00 0.00 3.58
3957 4894 4.893601 TTCGTCCCGCACAACGCA 62.894 61.111 0.00 0.00 42.60 5.24
3959 4896 1.837538 ATGTTTCGTCCCGCACAACG 61.838 55.000 0.00 0.00 43.15 4.10
3960 4897 0.309612 AATGTTTCGTCCCGCACAAC 59.690 50.000 0.00 0.00 0.00 3.32
3961 4898 1.025812 AAATGTTTCGTCCCGCACAA 58.974 45.000 0.00 0.00 0.00 3.33
3962 4899 1.025812 AAAATGTTTCGTCCCGCACA 58.974 45.000 0.00 0.00 0.00 4.57
3966 4903 1.414378 GCCAAAAATGTTTCGTCCCG 58.586 50.000 0.00 0.00 0.00 5.14
3968 4905 2.128367 ACGCCAAAAATGTTTCGTCC 57.872 45.000 0.00 0.00 0.00 4.79
3973 4910 5.175127 ACAAGAGAAACGCCAAAAATGTTT 58.825 33.333 0.00 0.00 38.44 2.83
3985 5054 4.629065 GCTTTCGTCATACAAGAGAAACG 58.371 43.478 0.00 0.00 0.00 3.60
4015 5084 5.588240 TCCATTCGTACTAGTGCAGTATTG 58.412 41.667 11.70 0.00 41.77 1.90
4022 5091 2.544069 GGAGCTCCATTCGTACTAGTGC 60.544 54.545 28.43 2.60 35.64 4.40
4024 5093 2.308690 GGGAGCTCCATTCGTACTAGT 58.691 52.381 33.29 0.00 37.91 2.57
4025 5094 1.614413 GGGGAGCTCCATTCGTACTAG 59.386 57.143 33.29 0.00 37.91 2.57
4026 5095 1.217183 AGGGGAGCTCCATTCGTACTA 59.783 52.381 33.29 0.00 37.91 1.82
4027 5096 0.032017 AGGGGAGCTCCATTCGTACT 60.032 55.000 33.29 15.62 37.91 2.73
4028 5097 0.389757 GAGGGGAGCTCCATTCGTAC 59.610 60.000 33.29 14.34 37.91 3.67
4029 5098 0.759436 GGAGGGGAGCTCCATTCGTA 60.759 60.000 33.29 0.00 40.57 3.43
4030 5099 2.066999 GGAGGGGAGCTCCATTCGT 61.067 63.158 33.29 17.83 40.57 3.85
4031 5100 2.812619 GGGAGGGGAGCTCCATTCG 61.813 68.421 33.29 0.00 42.56 3.34
4072 5141 3.240069 AGTATTCGTGTACAAGTCGCAC 58.760 45.455 8.68 3.74 0.00 5.34
4079 5148 6.401688 GCATGCTTTGTAGTATTCGTGTACAA 60.402 38.462 11.37 0.00 35.39 2.41
4086 5155 4.900182 CGATTGCATGCTTTGTAGTATTCG 59.100 41.667 20.33 9.39 0.00 3.34
4087 5156 6.048073 TCGATTGCATGCTTTGTAGTATTC 57.952 37.500 20.33 1.10 0.00 1.75
4089 5158 4.024556 GCTCGATTGCATGCTTTGTAGTAT 60.025 41.667 20.33 0.00 0.00 2.12
4090 5159 3.309682 GCTCGATTGCATGCTTTGTAGTA 59.690 43.478 20.33 0.00 0.00 1.82
4092 5161 2.713011 GCTCGATTGCATGCTTTGTAG 58.287 47.619 20.33 11.79 0.00 2.74
4104 5173 1.638996 CGTTTCTTTTGCGCTCGATTG 59.361 47.619 9.73 0.00 0.00 2.67
4114 5183 2.425668 AGTCAACCACCCGTTTCTTTTG 59.574 45.455 0.00 0.00 29.93 2.44
4115 5184 2.425668 CAGTCAACCACCCGTTTCTTTT 59.574 45.455 0.00 0.00 29.93 2.27
4116 5185 2.021457 CAGTCAACCACCCGTTTCTTT 58.979 47.619 0.00 0.00 29.93 2.52
4129 5198 8.134895 TCTAATTCAACCAACAATTCAGTCAAC 58.865 33.333 0.00 0.00 0.00 3.18
4130 5199 8.231692 TCTAATTCAACCAACAATTCAGTCAA 57.768 30.769 0.00 0.00 0.00 3.18
4156 5225 3.521937 CCAAGTTCATACCCAAGTCCCTA 59.478 47.826 0.00 0.00 0.00 3.53
4159 5228 3.081804 CACCAAGTTCATACCCAAGTCC 58.918 50.000 0.00 0.00 0.00 3.85
4176 5275 0.599204 GAAAGGAACTCGCGTCACCA 60.599 55.000 5.77 0.00 38.49 4.17
4232 5331 3.964875 CCTGTGTTGTGGCCACGC 61.965 66.667 30.07 24.35 35.56 5.34
4233 5332 3.964875 GCCTGTGTTGTGGCCACG 61.965 66.667 30.07 15.28 43.11 4.94
4238 5337 1.002134 CTAGGGGCCTGTGTTGTGG 60.002 63.158 0.84 0.00 0.00 4.17
4239 5338 0.321653 GACTAGGGGCCTGTGTTGTG 60.322 60.000 0.84 0.00 0.00 3.33
4240 5339 1.489560 GGACTAGGGGCCTGTGTTGT 61.490 60.000 0.84 0.00 0.00 3.32
4241 5340 1.201429 AGGACTAGGGGCCTGTGTTG 61.201 60.000 0.84 0.00 32.06 3.33
4242 5341 0.475828 AAGGACTAGGGGCCTGTGTT 60.476 55.000 0.84 0.00 34.00 3.32
4243 5342 1.161113 AAGGACTAGGGGCCTGTGT 59.839 57.895 0.84 0.00 34.00 3.72
4244 5343 1.604378 CAAGGACTAGGGGCCTGTG 59.396 63.158 0.84 0.00 34.00 3.66
4245 5344 1.616628 CCAAGGACTAGGGGCCTGT 60.617 63.158 0.84 0.00 34.00 4.00
4246 5345 2.378634 CCCAAGGACTAGGGGCCTG 61.379 68.421 0.84 0.00 41.58 4.85
4247 5346 2.042930 CCCAAGGACTAGGGGCCT 59.957 66.667 0.84 0.00 41.58 5.19
4251 5350 3.480133 CCGCCCCAAGGACTAGGG 61.480 72.222 0.00 3.54 45.04 3.53
4252 5351 2.687566 ACCGCCCCAAGGACTAGG 60.688 66.667 0.00 0.00 33.47 3.02
4253 5352 2.584608 CACCGCCCCAAGGACTAG 59.415 66.667 0.00 0.00 33.47 2.57
4254 5353 3.712907 GCACCGCCCCAAGGACTA 61.713 66.667 0.00 0.00 33.47 2.59
4277 5376 4.323477 TTTCCGGTGCGTGGGGAG 62.323 66.667 0.00 0.00 0.00 4.30
4301 5400 1.936547 GTGTGGATGGAGCTTTCGATC 59.063 52.381 0.00 0.00 0.00 3.69
4352 5451 1.647545 AATTGAGGACACGCATGCGG 61.648 55.000 39.95 30.20 44.69 5.69
4353 5452 0.247814 GAATTGAGGACACGCATGCG 60.248 55.000 36.79 36.79 46.03 4.73
4354 5453 0.099436 GGAATTGAGGACACGCATGC 59.901 55.000 7.91 7.91 0.00 4.06
4355 5454 0.734889 GGGAATTGAGGACACGCATG 59.265 55.000 0.00 0.00 0.00 4.06
4356 5455 0.327924 TGGGAATTGAGGACACGCAT 59.672 50.000 0.00 0.00 0.00 4.73
4357 5456 0.327924 ATGGGAATTGAGGACACGCA 59.672 50.000 0.00 0.00 0.00 5.24
4358 5457 0.734889 CATGGGAATTGAGGACACGC 59.265 55.000 0.00 0.00 0.00 5.34
4359 5458 1.065491 TCCATGGGAATTGAGGACACG 60.065 52.381 13.02 0.00 0.00 4.49
4360 5459 2.806945 TCCATGGGAATTGAGGACAC 57.193 50.000 13.02 0.00 0.00 3.67
4361 5460 2.687614 GCATCCATGGGAATTGAGGACA 60.688 50.000 13.02 0.00 34.34 4.02
4362 5461 1.959282 GCATCCATGGGAATTGAGGAC 59.041 52.381 13.02 0.00 34.34 3.85
4363 5462 1.477377 CGCATCCATGGGAATTGAGGA 60.477 52.381 13.02 0.00 42.66 3.71
4365 5464 1.971481 TCGCATCCATGGGAATTGAG 58.029 50.000 13.02 7.06 45.15 3.02
4396 5496 2.684881 GTTTCACGCATCAATCCATCCT 59.315 45.455 0.00 0.00 0.00 3.24
4426 5526 1.733399 GCAGACCGTCGTGTTCCTC 60.733 63.158 0.00 0.00 0.00 3.71
4491 5591 4.752879 TGCGCAGAACCCCGTAGC 62.753 66.667 5.66 0.00 0.00 3.58
4527 5627 2.988684 TTGCGTTGCATGGTCCCC 60.989 61.111 0.00 0.00 38.76 4.81
4528 5628 2.568090 CTTGCGTTGCATGGTCCC 59.432 61.111 0.00 0.00 38.76 4.46
4529 5629 1.305219 TAGCTTGCGTTGCATGGTCC 61.305 55.000 11.80 0.00 41.96 4.46
4530 5630 0.097674 CTAGCTTGCGTTGCATGGTC 59.902 55.000 11.80 0.00 41.96 4.02
4531 5631 1.926511 GCTAGCTTGCGTTGCATGGT 61.927 55.000 7.70 12.81 44.29 3.55
4532 5632 1.226491 GCTAGCTTGCGTTGCATGG 60.226 57.895 7.70 0.00 38.76 3.66
4556 5658 3.747976 GTTGCGGTGGTGCCCATC 61.748 66.667 0.00 0.00 35.28 3.51
4572 5674 1.591594 CTGAATGCCGATACGCCGT 60.592 57.895 0.00 0.00 0.00 5.68
4573 5675 2.943345 GCTGAATGCCGATACGCCG 61.943 63.158 0.00 0.00 35.15 6.46
4574 5676 1.887242 TGCTGAATGCCGATACGCC 60.887 57.895 0.00 0.00 42.00 5.68
4575 5677 1.154205 AGTGCTGAATGCCGATACGC 61.154 55.000 0.00 0.00 42.00 4.42
4576 5678 0.578683 CAGTGCTGAATGCCGATACG 59.421 55.000 0.00 0.00 42.00 3.06
4577 5679 0.940126 CCAGTGCTGAATGCCGATAC 59.060 55.000 0.02 0.00 42.00 2.24
4578 5680 0.815213 GCCAGTGCTGAATGCCGATA 60.815 55.000 0.02 0.00 42.00 2.92
4579 5681 2.117156 GCCAGTGCTGAATGCCGAT 61.117 57.895 0.02 0.00 42.00 4.18
4580 5682 2.747460 GCCAGTGCTGAATGCCGA 60.747 61.111 0.02 0.00 42.00 5.54


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

AutoCloner maintained by Alex Coulton.