Multiple sequence alignment - TraesCS5D01G337300

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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 TraesCS5D01G337300 chr5D 100.000 2633 0 0 1 2633 426167691 426165059 0.000000e+00 4863
1 TraesCS5D01G337300 chr5B 92.955 1093 46 14 633 1722 516039456 516038392 0.000000e+00 1563
2 TraesCS5D01G337300 chr5B 85.738 610 36 19 24 608 516040678 516040095 4.850000e-167 597
3 TraesCS5D01G337300 chr5B 91.837 392 19 9 1887 2266 516033968 516033578 3.860000e-148 534
4 TraesCS5D01G337300 chr5B 93.269 208 5 1 2435 2633 516033579 516033372 5.510000e-77 298
5 TraesCS5D01G337300 chr5B 96.689 151 0 1 2267 2417 73352015 73351870 2.020000e-61 246
6 TraesCS5D01G337300 chr5B 87.778 90 6 3 1752 1841 516038399 516038315 1.670000e-17 100
7 TraesCS5D01G337300 chr5A 90.207 1205 53 28 674 1867 540368511 540367361 0.000000e+00 1511
8 TraesCS5D01G337300 chr5A 87.849 502 28 12 111 603 540369103 540368626 2.290000e-155 558
9 TraesCS5D01G337300 chr5A 91.776 304 17 5 1971 2267 540367300 540366998 1.460000e-112 416
10 TraesCS5D01G337300 chr5A 94.811 212 4 5 2427 2633 540366992 540366783 9.090000e-85 324
11 TraesCS5D01G337300 chr5A 100.000 153 0 0 2267 2419 667108028 667108180 1.540000e-72 283
12 TraesCS5D01G337300 chr5A 98.639 147 2 0 2271 2417 423043947 423044093 7.230000e-66 261
13 TraesCS5D01G337300 chr7B 100.000 151 0 0 2267 2417 565060315 565060165 2.000000e-71 279
14 TraesCS5D01G337300 chr7B 99.338 151 1 0 2267 2417 99594318 99594168 9.280000e-70 274
15 TraesCS5D01G337300 chr2B 99.351 154 1 0 2267 2420 69416114 69415961 2.000000e-71 279
16 TraesCS5D01G337300 chr3A 99.338 151 1 0 2267 2417 570664270 570664120 9.280000e-70 274
17 TraesCS5D01G337300 chr3A 89.610 154 16 0 2267 2420 658314904 658314751 2.070000e-46 196
18 TraesCS5D01G337300 chr6B 89.103 156 16 1 2267 2421 192942048 192941893 2.670000e-45 193


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 TraesCS5D01G337300 chr5D 426165059 426167691 2632 True 4863.000000 4863 100.000000 1 2633 1 chr5D.!!$R1 2632
1 TraesCS5D01G337300 chr5B 516038315 516040678 2363 True 753.333333 1563 88.823667 24 1841 3 chr5B.!!$R3 1817
2 TraesCS5D01G337300 chr5B 516033372 516033968 596 True 416.000000 534 92.553000 1887 2633 2 chr5B.!!$R2 746
3 TraesCS5D01G337300 chr5A 540366783 540369103 2320 True 702.250000 1511 91.160750 111 2633 4 chr5A.!!$R1 2522

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
625 715 0.518636 TGACAGAGAATTTGCTGCGC 59.481 50.0 0.0 0.0 35.57 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 3066 0.0982 CACATCAAGCCGCTCATGTG 59.902 55.0 22.07 22.07 40.03 3.21 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
20 21 3.629142 CCACTTACTTTGGGACCTAGG 57.371 52.381 7.41 7.41 0.00 3.02
21 22 2.238898 CCACTTACTTTGGGACCTAGGG 59.761 54.545 14.81 0.00 0.00 3.53
22 23 3.178865 CACTTACTTTGGGACCTAGGGA 58.821 50.000 14.81 0.00 0.00 4.20
34 35 4.325109 GGGACCTAGGGAGTATTTGCTTTT 60.325 45.833 14.81 0.00 0.00 2.27
35 36 5.104235 GGGACCTAGGGAGTATTTGCTTTTA 60.104 44.000 14.81 0.00 0.00 1.52
41 42 7.283354 CCTAGGGAGTATTTGCTTTTAGAAAGG 59.717 40.741 0.00 0.00 0.00 3.11
44 45 7.509318 AGGGAGTATTTGCTTTTAGAAAGGTTT 59.491 33.333 2.95 0.00 0.00 3.27
47 48 9.744468 GAGTATTTGCTTTTAGAAAGGTTTTCA 57.256 29.630 4.56 0.00 0.00 2.69
61 62 2.546789 GGTTTTCACCTCGGTTACACTG 59.453 50.000 0.00 0.00 40.44 3.66
68 69 1.071071 CCTCGGTTACACTGGAACCAA 59.929 52.381 21.18 3.81 45.70 3.67
84 85 5.838521 TGGAACCAAGAGGCTAAGAAATTTT 59.161 36.000 0.00 0.00 39.06 1.82
85 86 6.326323 TGGAACCAAGAGGCTAAGAAATTTTT 59.674 34.615 0.00 0.00 39.06 1.94
88 89 9.929180 GAACCAAGAGGCTAAGAAATTTTTATT 57.071 29.630 0.00 0.00 39.06 1.40
152 154 2.890474 GGTGGACGCGCATTCGAT 60.890 61.111 5.73 0.00 38.10 3.59
153 155 2.461110 GGTGGACGCGCATTCGATT 61.461 57.895 5.73 0.00 38.10 3.34
184 186 6.097356 TCGTGGTTAAACTAGCAATGACTAG 58.903 40.000 9.18 9.18 44.38 2.57
274 276 2.699954 CAGCCTGGTTAGTGGTTACAG 58.300 52.381 0.00 0.00 0.00 2.74
285 287 3.097614 AGTGGTTACAGCCTAGTGGTAG 58.902 50.000 0.00 0.00 35.27 3.18
286 288 1.829222 TGGTTACAGCCTAGTGGTAGC 59.171 52.381 0.00 0.00 35.27 3.58
314 322 9.601217 GTACAATCATCTGAGTGGTAGTTTTAT 57.399 33.333 11.78 0.00 43.65 1.40
323 335 8.946085 TCTGAGTGGTAGTTTTATATTTTGCTG 58.054 33.333 0.00 0.00 0.00 4.41
336 348 4.992740 TGCTGGTTTGGGCGGCAT 62.993 61.111 12.47 0.00 0.00 4.40
337 349 4.133796 GCTGGTTTGGGCGGCATC 62.134 66.667 12.47 0.00 0.00 3.91
338 350 3.814268 CTGGTTTGGGCGGCATCG 61.814 66.667 12.47 0.00 39.81 3.84
339 351 4.652131 TGGTTTGGGCGGCATCGT 62.652 61.111 12.47 0.00 38.89 3.73
356 368 4.512657 CATCGTTCGTTCTAGGTAGTACG 58.487 47.826 9.23 9.23 44.83 3.67
358 370 4.740268 TCGTTCGTTCTAGGTAGTACGTA 58.260 43.478 13.66 2.90 44.16 3.57
360 372 6.500910 TCGTTCGTTCTAGGTAGTACGTATA 58.499 40.000 13.66 0.00 44.16 1.47
361 373 7.145985 TCGTTCGTTCTAGGTAGTACGTATAT 58.854 38.462 13.66 0.00 44.16 0.86
362 374 7.114953 TCGTTCGTTCTAGGTAGTACGTATATG 59.885 40.741 13.66 8.03 44.16 1.78
363 375 6.712241 TCGTTCTAGGTAGTACGTATATGC 57.288 41.667 13.66 0.00 44.16 3.14
364 376 6.459066 TCGTTCTAGGTAGTACGTATATGCT 58.541 40.000 13.66 0.00 44.16 3.79
365 377 6.587990 TCGTTCTAGGTAGTACGTATATGCTC 59.412 42.308 13.66 0.00 44.16 4.26
366 378 6.183360 CGTTCTAGGTAGTACGTATATGCTCC 60.183 46.154 0.00 0.00 40.63 4.70
367 379 6.617782 TCTAGGTAGTACGTATATGCTCCT 57.382 41.667 0.00 4.52 0.00 3.69
368 380 6.638610 TCTAGGTAGTACGTATATGCTCCTC 58.361 44.000 0.00 0.00 0.00 3.71
369 381 5.502089 AGGTAGTACGTATATGCTCCTCT 57.498 43.478 0.00 0.00 0.00 3.69
370 382 5.878627 AGGTAGTACGTATATGCTCCTCTT 58.121 41.667 0.00 0.00 0.00 2.85
371 383 6.305411 AGGTAGTACGTATATGCTCCTCTTT 58.695 40.000 0.00 0.00 0.00 2.52
372 384 6.430616 AGGTAGTACGTATATGCTCCTCTTTC 59.569 42.308 0.00 0.00 0.00 2.62
373 385 6.430616 GGTAGTACGTATATGCTCCTCTTTCT 59.569 42.308 0.00 0.00 0.00 2.52
374 386 6.320494 AGTACGTATATGCTCCTCTTTCTG 57.680 41.667 0.00 0.00 0.00 3.02
500 523 4.202010 CCCTCGATGACACAAAACAAAACT 60.202 41.667 0.00 0.00 0.00 2.66
514 537 2.029380 ACAAAACTAAAAGATGCCGCCC 60.029 45.455 0.00 0.00 0.00 6.13
555 578 6.971184 CACGAGTGGTACTATTATTTCGTCTT 59.029 38.462 0.00 0.00 37.88 3.01
624 714 2.477357 CCATGACAGAGAATTTGCTGCG 60.477 50.000 0.00 0.00 35.57 5.18
625 715 0.518636 TGACAGAGAATTTGCTGCGC 59.481 50.000 0.00 0.00 35.57 6.09
626 716 0.801251 GACAGAGAATTTGCTGCGCT 59.199 50.000 9.73 0.00 35.57 5.92
627 717 0.520404 ACAGAGAATTTGCTGCGCTG 59.480 50.000 9.73 10.04 35.57 5.18
628 718 0.797249 CAGAGAATTTGCTGCGCTGC 60.797 55.000 29.76 29.76 0.00 5.25
712 1372 3.790437 CTGCCATGGTCGGAGCCT 61.790 66.667 14.67 0.00 0.00 4.58
713 1373 3.746949 CTGCCATGGTCGGAGCCTC 62.747 68.421 14.67 0.00 0.00 4.70
871 1538 4.127907 TCGGCTCTATACATATAGCTCCG 58.872 47.826 20.66 20.66 43.69 4.63
921 1588 2.279385 CGAGCAGAGGCAGCTAGC 60.279 66.667 6.62 6.62 43.58 3.42
979 1646 2.043450 ACCGGGGAGCAGAGAGAG 60.043 66.667 6.32 0.00 0.00 3.20
980 1647 2.277072 CCGGGGAGCAGAGAGAGA 59.723 66.667 0.00 0.00 0.00 3.10
981 1648 1.827789 CCGGGGAGCAGAGAGAGAG 60.828 68.421 0.00 0.00 0.00 3.20
982 1649 1.225983 CGGGGAGCAGAGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
1470 2137 0.246635 CGGGCGGAGAAGAAGAAGAA 59.753 55.000 0.00 0.00 0.00 2.52
1471 2138 1.737363 CGGGCGGAGAAGAAGAAGAAG 60.737 57.143 0.00 0.00 0.00 2.85
1472 2139 1.550976 GGGCGGAGAAGAAGAAGAAGA 59.449 52.381 0.00 0.00 0.00 2.87
1473 2140 2.028020 GGGCGGAGAAGAAGAAGAAGAA 60.028 50.000 0.00 0.00 0.00 2.52
1527 2194 2.509336 CGCGCGGAGGAGTTCATT 60.509 61.111 24.84 0.00 0.00 2.57
1684 2351 2.966309 CTCGCGGACCCTGTTTTGC 61.966 63.158 6.13 0.00 0.00 3.68
1697 2364 3.374745 CTGTTTTGCTCAAATCGCAGTT 58.625 40.909 0.00 0.00 38.80 3.16
1719 2425 7.857885 CAGTTAGTTTCTTTCGCTTTCTTGATT 59.142 33.333 0.00 0.00 0.00 2.57
1720 2426 7.857885 AGTTAGTTTCTTTCGCTTTCTTGATTG 59.142 33.333 0.00 0.00 0.00 2.67
1721 2427 6.136541 AGTTTCTTTCGCTTTCTTGATTGT 57.863 33.333 0.00 0.00 0.00 2.71
1722 2428 6.564328 AGTTTCTTTCGCTTTCTTGATTGTT 58.436 32.000 0.00 0.00 0.00 2.83
1723 2429 6.693113 AGTTTCTTTCGCTTTCTTGATTGTTC 59.307 34.615 0.00 0.00 0.00 3.18
1724 2430 6.377327 TTCTTTCGCTTTCTTGATTGTTCT 57.623 33.333 0.00 0.00 0.00 3.01
1725 2431 6.377327 TCTTTCGCTTTCTTGATTGTTCTT 57.623 33.333 0.00 0.00 0.00 2.52
1726 2432 6.430451 TCTTTCGCTTTCTTGATTGTTCTTC 58.570 36.000 0.00 0.00 0.00 2.87
1727 2433 6.260936 TCTTTCGCTTTCTTGATTGTTCTTCT 59.739 34.615 0.00 0.00 0.00 2.85
1728 2434 6.377327 TTCGCTTTCTTGATTGTTCTTCTT 57.623 33.333 0.00 0.00 0.00 2.52
1729 2435 5.990408 TCGCTTTCTTGATTGTTCTTCTTC 58.010 37.500 0.00 0.00 0.00 2.87
1730 2436 5.760253 TCGCTTTCTTGATTGTTCTTCTTCT 59.240 36.000 0.00 0.00 0.00 2.85
1731 2437 6.260936 TCGCTTTCTTGATTGTTCTTCTTCTT 59.739 34.615 0.00 0.00 0.00 2.52
1732 2438 6.359087 CGCTTTCTTGATTGTTCTTCTTCTTG 59.641 38.462 0.00 0.00 0.00 3.02
1733 2439 6.143598 GCTTTCTTGATTGTTCTTCTTCTTGC 59.856 38.462 0.00 0.00 0.00 4.01
1734 2440 6.949352 TTCTTGATTGTTCTTCTTCTTGCT 57.051 33.333 0.00 0.00 0.00 3.91
1735 2441 6.551385 TCTTGATTGTTCTTCTTCTTGCTC 57.449 37.500 0.00 0.00 0.00 4.26
1736 2442 6.294473 TCTTGATTGTTCTTCTTCTTGCTCT 58.706 36.000 0.00 0.00 0.00 4.09
1737 2443 5.936686 TGATTGTTCTTCTTCTTGCTCTG 57.063 39.130 0.00 0.00 0.00 3.35
1738 2444 5.371526 TGATTGTTCTTCTTCTTGCTCTGT 58.628 37.500 0.00 0.00 0.00 3.41
1739 2445 5.237996 TGATTGTTCTTCTTCTTGCTCTGTG 59.762 40.000 0.00 0.00 0.00 3.66
1740 2446 4.406648 TGTTCTTCTTCTTGCTCTGTGA 57.593 40.909 0.00 0.00 0.00 3.58
1741 2447 4.965814 TGTTCTTCTTCTTGCTCTGTGAT 58.034 39.130 0.00 0.00 0.00 3.06
1742 2448 4.993584 TGTTCTTCTTCTTGCTCTGTGATC 59.006 41.667 0.00 0.00 0.00 2.92
1743 2449 4.199432 TCTTCTTCTTGCTCTGTGATCC 57.801 45.455 0.00 0.00 0.00 3.36
1744 2450 2.662006 TCTTCTTGCTCTGTGATCCG 57.338 50.000 0.00 0.00 0.00 4.18
1745 2451 2.171003 TCTTCTTGCTCTGTGATCCGA 58.829 47.619 0.00 0.00 0.00 4.55
1746 2452 2.165234 TCTTCTTGCTCTGTGATCCGAG 59.835 50.000 0.00 0.00 0.00 4.63
1752 2458 1.638133 CTCTGTGATCCGAGCAAGTG 58.362 55.000 0.00 0.00 0.00 3.16
1753 2459 1.203287 CTCTGTGATCCGAGCAAGTGA 59.797 52.381 0.00 0.00 0.00 3.41
1754 2460 1.203287 TCTGTGATCCGAGCAAGTGAG 59.797 52.381 0.00 0.00 0.00 3.51
1781 2487 1.873591 CTACCACTGGCACTTTGACAC 59.126 52.381 0.00 0.00 28.59 3.67
1812 2518 4.784177 TGGATGAATCTTCAAGCATGCTA 58.216 39.130 23.00 4.84 41.13 3.49
1813 2519 5.382616 TGGATGAATCTTCAAGCATGCTAT 58.617 37.500 23.00 7.44 41.13 2.97
1814 2520 5.240844 TGGATGAATCTTCAAGCATGCTATG 59.759 40.000 23.00 20.01 41.13 2.23
1815 2521 4.563337 TGAATCTTCAAGCATGCTATGC 57.437 40.909 23.00 9.62 43.64 3.14
1826 2532 1.475280 CATGCTATGCTTGCTTGGTGT 59.525 47.619 0.00 0.00 33.66 4.16
1845 2551 4.391830 GGTGTTCTGAAGAAATACGCATGA 59.608 41.667 0.00 0.00 35.58 3.07
1853 2559 6.108687 TGAAGAAATACGCATGAGAATCTGT 58.891 36.000 2.50 0.00 34.92 3.41
1867 2573 8.819015 CATGAGAATCTGTAGACATTTCTTCTG 58.181 37.037 8.55 6.64 32.11 3.02
1869 2575 6.112058 AGAATCTGTAGACATTTCTTCTGGC 58.888 40.000 0.00 0.00 32.75 4.85
1870 2576 4.207891 TCTGTAGACATTTCTTCTGGCC 57.792 45.455 0.00 0.00 32.75 5.36
1871 2577 2.932614 CTGTAGACATTTCTTCTGGCCG 59.067 50.000 0.00 0.00 32.75 6.13
1872 2578 2.280628 GTAGACATTTCTTCTGGCCGG 58.719 52.381 4.71 4.71 32.75 6.13
1874 2580 1.065854 AGACATTTCTTCTGGCCGGAG 60.066 52.381 15.42 9.41 0.00 4.63
1875 2581 0.693049 ACATTTCTTCTGGCCGGAGT 59.307 50.000 15.42 5.14 0.00 3.85
1876 2582 1.906574 ACATTTCTTCTGGCCGGAGTA 59.093 47.619 15.42 3.94 0.00 2.59
1877 2583 2.093447 ACATTTCTTCTGGCCGGAGTAG 60.093 50.000 15.42 10.76 0.00 2.57
1879 2585 2.519771 TTCTTCTGGCCGGAGTAGTA 57.480 50.000 15.42 1.13 0.00 1.82
1880 2586 2.519771 TCTTCTGGCCGGAGTAGTAA 57.480 50.000 15.42 0.00 0.00 2.24
1882 2588 3.371965 TCTTCTGGCCGGAGTAGTAAAT 58.628 45.455 15.42 0.00 0.00 1.40
1885 2591 5.601313 TCTTCTGGCCGGAGTAGTAAATTAT 59.399 40.000 15.42 0.00 0.00 1.28
1889 2595 6.099269 TCTGGCCGGAGTAGTAAATTATTCTT 59.901 38.462 11.27 0.00 0.00 2.52
1969 2677 6.257423 TGCAATAAAATACTTCTCATGTGCG 58.743 36.000 0.00 0.00 0.00 5.34
1998 2708 5.240891 ACATATTCTTGGAGGCATCGTATG 58.759 41.667 0.00 0.00 0.00 2.39
2185 2904 2.825836 CCCGCCACATCTCCAAGC 60.826 66.667 0.00 0.00 0.00 4.01
2267 2986 1.063488 CGGAAATAAAAGGCGCCCG 59.937 57.895 26.15 12.59 0.00 6.13
2268 2987 1.370587 CGGAAATAAAAGGCGCCCGA 61.371 55.000 26.15 6.17 37.87 5.14
2269 2988 0.812549 GGAAATAAAAGGCGCCCGAA 59.187 50.000 26.15 6.86 0.00 4.30
2270 2989 1.202817 GGAAATAAAAGGCGCCCGAAA 59.797 47.619 26.15 7.30 0.00 3.46
2271 2990 2.256174 GAAATAAAAGGCGCCCGAAAC 58.744 47.619 26.15 3.64 0.00 2.78
2272 2991 1.541379 AATAAAAGGCGCCCGAAACT 58.459 45.000 26.15 0.00 0.00 2.66
2273 2992 2.406596 ATAAAAGGCGCCCGAAACTA 57.593 45.000 26.15 6.78 0.00 2.24
2274 2993 1.441738 TAAAAGGCGCCCGAAACTAC 58.558 50.000 26.15 0.00 0.00 2.73
2275 2994 0.250597 AAAAGGCGCCCGAAACTACT 60.251 50.000 26.15 0.00 0.00 2.57
2276 2995 0.609662 AAAGGCGCCCGAAACTACTA 59.390 50.000 26.15 0.00 0.00 1.82
2277 2996 0.828677 AAGGCGCCCGAAACTACTAT 59.171 50.000 26.15 0.00 0.00 2.12
2278 2997 1.696063 AGGCGCCCGAAACTACTATA 58.304 50.000 26.15 0.00 0.00 1.31
2279 2998 1.339291 AGGCGCCCGAAACTACTATAC 59.661 52.381 26.15 0.00 0.00 1.47
2280 2999 1.067516 GGCGCCCGAAACTACTATACA 59.932 52.381 18.11 0.00 0.00 2.29
2281 3000 2.391879 GCGCCCGAAACTACTATACAG 58.608 52.381 0.00 0.00 0.00 2.74
2282 3001 2.033801 GCGCCCGAAACTACTATACAGA 59.966 50.000 0.00 0.00 0.00 3.41
2283 3002 3.625938 CGCCCGAAACTACTATACAGAC 58.374 50.000 0.00 0.00 0.00 3.51
2284 3003 3.625938 GCCCGAAACTACTATACAGACG 58.374 50.000 0.00 0.00 0.00 4.18
2285 3004 3.313526 GCCCGAAACTACTATACAGACGA 59.686 47.826 0.00 0.00 0.00 4.20
2286 3005 4.787882 GCCCGAAACTACTATACAGACGAC 60.788 50.000 0.00 0.00 0.00 4.34
2287 3006 4.333649 CCCGAAACTACTATACAGACGACA 59.666 45.833 0.00 0.00 0.00 4.35
2288 3007 5.499935 CCGAAACTACTATACAGACGACAG 58.500 45.833 0.00 0.00 0.00 3.51
2289 3008 5.064452 CCGAAACTACTATACAGACGACAGT 59.936 44.000 0.00 0.00 0.00 3.55
2290 3009 6.256539 CCGAAACTACTATACAGACGACAGTA 59.743 42.308 0.00 0.00 0.00 2.74
2291 3010 7.116186 CGAAACTACTATACAGACGACAGTAC 58.884 42.308 0.00 0.00 0.00 2.73
2292 3011 7.009999 CGAAACTACTATACAGACGACAGTACT 59.990 40.741 0.00 0.00 0.00 2.73
2293 3012 7.769272 AACTACTATACAGACGACAGTACTC 57.231 40.000 0.00 0.00 0.00 2.59
2294 3013 6.279882 ACTACTATACAGACGACAGTACTCC 58.720 44.000 0.00 0.00 0.00 3.85
2295 3014 4.118410 ACTATACAGACGACAGTACTCCG 58.882 47.826 11.40 11.40 0.00 4.63
2296 3015 1.730501 TACAGACGACAGTACTCCGG 58.269 55.000 15.86 0.00 0.00 5.14
2297 3016 1.136984 CAGACGACAGTACTCCGGC 59.863 63.158 15.86 13.64 0.00 6.13
2298 3017 2.045131 AGACGACAGTACTCCGGCC 61.045 63.158 14.46 0.00 30.32 6.13
2299 3018 3.392595 GACGACAGTACTCCGGCCG 62.393 68.421 21.04 21.04 0.00 6.13
2300 3019 3.129502 CGACAGTACTCCGGCCGA 61.130 66.667 30.73 12.25 0.00 5.54
2301 3020 2.693762 CGACAGTACTCCGGCCGAA 61.694 63.158 30.73 4.60 0.00 4.30
2302 3021 1.153881 GACAGTACTCCGGCCGAAC 60.154 63.158 30.73 18.55 0.00 3.95
2303 3022 1.870055 GACAGTACTCCGGCCGAACA 61.870 60.000 30.73 9.20 0.00 3.18
2304 3023 1.445582 CAGTACTCCGGCCGAACAC 60.446 63.158 30.73 18.21 0.00 3.32
2305 3024 1.605738 AGTACTCCGGCCGAACACT 60.606 57.895 30.73 20.22 0.00 3.55
2306 3025 1.445582 GTACTCCGGCCGAACACTG 60.446 63.158 30.73 8.93 0.00 3.66
2307 3026 2.642254 TACTCCGGCCGAACACTGG 61.642 63.158 30.73 8.04 34.63 4.00
2308 3027 3.691342 CTCCGGCCGAACACTGGA 61.691 66.667 30.73 12.64 40.36 3.86
2309 3028 3.934391 CTCCGGCCGAACACTGGAC 62.934 68.421 30.73 0.00 37.67 4.02
2312 3031 2.264794 GGCCGAACACTGGACGAT 59.735 61.111 0.00 0.00 0.00 3.73
2313 3032 2.100631 GGCCGAACACTGGACGATG 61.101 63.158 0.00 0.00 0.00 3.84
2314 3033 1.374252 GCCGAACACTGGACGATGT 60.374 57.895 0.00 0.00 0.00 3.06
2315 3034 0.949105 GCCGAACACTGGACGATGTT 60.949 55.000 0.00 0.00 41.70 2.71
2316 3035 0.790207 CCGAACACTGGACGATGTTG 59.210 55.000 0.00 0.00 39.13 3.33
2317 3036 0.790207 CGAACACTGGACGATGTTGG 59.210 55.000 0.00 0.00 39.13 3.77
2318 3037 1.604438 CGAACACTGGACGATGTTGGA 60.604 52.381 0.00 0.00 39.13 3.53
2319 3038 2.699954 GAACACTGGACGATGTTGGAT 58.300 47.619 0.00 0.00 39.13 3.41
2320 3039 2.386661 ACACTGGACGATGTTGGATC 57.613 50.000 0.00 0.00 0.00 3.36
2321 3040 1.280982 CACTGGACGATGTTGGATCG 58.719 55.000 0.00 0.00 46.02 3.69
2322 3041 1.135112 CACTGGACGATGTTGGATCGA 60.135 52.381 10.83 0.00 43.59 3.59
2323 3042 1.548719 ACTGGACGATGTTGGATCGAA 59.451 47.619 10.83 0.00 43.59 3.71
2324 3043 1.927174 CTGGACGATGTTGGATCGAAC 59.073 52.381 13.18 13.18 43.59 3.95
2325 3044 0.921347 GGACGATGTTGGATCGAACG 59.079 55.000 14.81 6.74 43.59 3.95
2326 3045 0.921347 GACGATGTTGGATCGAACGG 59.079 55.000 14.81 9.55 43.59 4.44
2327 3046 0.245539 ACGATGTTGGATCGAACGGT 59.754 50.000 14.81 10.10 43.59 4.83
2328 3047 0.645355 CGATGTTGGATCGAACGGTG 59.355 55.000 14.81 4.22 43.59 4.94
2329 3048 1.722011 GATGTTGGATCGAACGGTGT 58.278 50.000 14.81 2.47 0.00 4.16
2330 3049 2.073816 GATGTTGGATCGAACGGTGTT 58.926 47.619 14.81 0.00 0.00 3.32
2331 3050 1.222300 TGTTGGATCGAACGGTGTTG 58.778 50.000 14.81 0.00 0.00 3.33
2332 3051 1.223187 GTTGGATCGAACGGTGTTGT 58.777 50.000 4.76 0.00 0.00 3.32
2333 3052 1.600485 GTTGGATCGAACGGTGTTGTT 59.400 47.619 4.76 0.00 34.02 2.83
2334 3053 1.956297 TGGATCGAACGGTGTTGTTT 58.044 45.000 0.00 0.00 30.75 2.83
2335 3054 3.109044 TGGATCGAACGGTGTTGTTTA 57.891 42.857 0.00 0.00 30.75 2.01
2336 3055 3.061322 TGGATCGAACGGTGTTGTTTAG 58.939 45.455 0.00 0.00 30.75 1.85
2337 3056 3.062042 GGATCGAACGGTGTTGTTTAGT 58.938 45.455 0.00 0.00 30.75 2.24
2338 3057 3.495753 GGATCGAACGGTGTTGTTTAGTT 59.504 43.478 0.00 0.00 30.75 2.24
2339 3058 4.024641 GGATCGAACGGTGTTGTTTAGTTT 60.025 41.667 0.00 0.00 30.75 2.66
2340 3059 4.943142 TCGAACGGTGTTGTTTAGTTTT 57.057 36.364 0.00 0.00 30.75 2.43
2341 3060 4.649977 TCGAACGGTGTTGTTTAGTTTTG 58.350 39.130 0.00 0.00 30.75 2.44
2342 3061 3.238798 CGAACGGTGTTGTTTAGTTTTGC 59.761 43.478 0.00 0.00 30.75 3.68
2343 3062 4.417506 GAACGGTGTTGTTTAGTTTTGCT 58.582 39.130 0.00 0.00 30.75 3.91
2344 3063 4.443913 ACGGTGTTGTTTAGTTTTGCTT 57.556 36.364 0.00 0.00 0.00 3.91
2345 3064 4.811908 ACGGTGTTGTTTAGTTTTGCTTT 58.188 34.783 0.00 0.00 0.00 3.51
2346 3065 5.952033 ACGGTGTTGTTTAGTTTTGCTTTA 58.048 33.333 0.00 0.00 0.00 1.85
2347 3066 5.801444 ACGGTGTTGTTTAGTTTTGCTTTAC 59.199 36.000 0.00 0.00 0.00 2.01
2348 3067 5.800941 CGGTGTTGTTTAGTTTTGCTTTACA 59.199 36.000 0.00 0.00 0.00 2.41
2349 3068 6.237358 CGGTGTTGTTTAGTTTTGCTTTACAC 60.237 38.462 0.00 0.00 33.35 2.90
2350 3069 6.586844 GGTGTTGTTTAGTTTTGCTTTACACA 59.413 34.615 0.00 0.00 35.20 3.72
2351 3070 7.276878 GGTGTTGTTTAGTTTTGCTTTACACAT 59.723 33.333 0.00 0.00 35.20 3.21
2352 3071 8.107564 GTGTTGTTTAGTTTTGCTTTACACATG 58.892 33.333 0.00 0.00 34.06 3.21
2353 3072 8.029522 TGTTGTTTAGTTTTGCTTTACACATGA 58.970 29.630 0.00 0.00 0.00 3.07
2354 3073 8.531530 GTTGTTTAGTTTTGCTTTACACATGAG 58.468 33.333 0.00 0.00 0.00 2.90
2355 3074 6.695278 TGTTTAGTTTTGCTTTACACATGAGC 59.305 34.615 0.00 0.00 36.95 4.26
2356 3075 3.888934 AGTTTTGCTTTACACATGAGCG 58.111 40.909 0.00 0.00 39.23 5.03
2357 3076 2.979813 GTTTTGCTTTACACATGAGCGG 59.020 45.455 0.00 0.00 39.23 5.52
2358 3077 0.521291 TTGCTTTACACATGAGCGGC 59.479 50.000 0.00 0.00 39.23 6.53
2359 3078 0.321564 TGCTTTACACATGAGCGGCT 60.322 50.000 0.00 0.00 39.23 5.52
2360 3079 0.804989 GCTTTACACATGAGCGGCTT 59.195 50.000 2.97 0.00 0.00 4.35
2361 3080 1.466360 GCTTTACACATGAGCGGCTTG 60.466 52.381 2.97 1.38 0.00 4.01
2362 3081 2.076100 CTTTACACATGAGCGGCTTGA 58.924 47.619 2.97 0.00 0.00 3.02
2363 3082 2.401583 TTACACATGAGCGGCTTGAT 57.598 45.000 2.97 0.00 0.00 2.57
2364 3083 1.655484 TACACATGAGCGGCTTGATG 58.345 50.000 16.92 16.92 0.00 3.07
2365 3084 0.321919 ACACATGAGCGGCTTGATGT 60.322 50.000 17.94 17.94 0.00 3.06
2366 3085 0.098200 CACATGAGCGGCTTGATGTG 59.902 55.000 27.45 27.45 39.68 3.21
2367 3086 1.063649 CATGAGCGGCTTGATGTGC 59.936 57.895 2.97 0.00 0.00 4.57
2368 3087 1.077930 ATGAGCGGCTTGATGTGCT 60.078 52.632 2.97 0.00 41.11 4.40
2369 3088 0.178767 ATGAGCGGCTTGATGTGCTA 59.821 50.000 2.97 0.00 37.91 3.49
2370 3089 0.740868 TGAGCGGCTTGATGTGCTAC 60.741 55.000 2.97 0.00 37.91 3.58
2371 3090 0.740868 GAGCGGCTTGATGTGCTACA 60.741 55.000 2.97 0.00 37.91 2.74
2372 3091 0.107508 AGCGGCTTGATGTGCTACAT 60.108 50.000 0.00 2.02 42.43 2.29
2380 3099 1.926561 GATGTGCTACATCGTCTGCA 58.073 50.000 11.70 0.00 44.55 4.41
2381 3100 2.270923 GATGTGCTACATCGTCTGCAA 58.729 47.619 11.70 0.00 44.55 4.08
2382 3101 2.162319 TGTGCTACATCGTCTGCAAA 57.838 45.000 0.00 0.00 37.17 3.68
2383 3102 2.698803 TGTGCTACATCGTCTGCAAAT 58.301 42.857 0.00 0.00 37.17 2.32
2384 3103 2.672874 TGTGCTACATCGTCTGCAAATC 59.327 45.455 0.00 0.00 37.17 2.17
2385 3104 1.926510 TGCTACATCGTCTGCAAATCG 59.073 47.619 0.00 0.00 32.12 3.34
2386 3105 1.927174 GCTACATCGTCTGCAAATCGT 59.073 47.619 0.00 0.00 0.00 3.73
2387 3106 2.034507 GCTACATCGTCTGCAAATCGTC 60.035 50.000 0.00 0.00 0.00 4.20
2388 3107 1.359848 ACATCGTCTGCAAATCGTCC 58.640 50.000 0.00 0.00 0.00 4.79
2389 3108 0.298707 CATCGTCTGCAAATCGTCCG 59.701 55.000 0.00 0.00 0.00 4.79
2390 3109 1.421410 ATCGTCTGCAAATCGTCCGC 61.421 55.000 0.00 0.00 0.00 5.54
2391 3110 2.785258 GTCTGCAAATCGTCCGCC 59.215 61.111 0.00 0.00 0.00 6.13
2392 3111 2.813474 TCTGCAAATCGTCCGCCG 60.813 61.111 0.00 0.00 38.13 6.46
2393 3112 3.118454 CTGCAAATCGTCCGCCGT 61.118 61.111 0.00 0.00 37.94 5.68
2394 3113 2.666862 TGCAAATCGTCCGCCGTT 60.667 55.556 0.00 0.00 37.94 4.44
2395 3114 2.182614 CTGCAAATCGTCCGCCGTTT 62.183 55.000 0.00 0.00 37.94 3.60
2396 3115 1.795962 GCAAATCGTCCGCCGTTTG 60.796 57.895 12.06 12.06 38.95 2.93
2397 3116 1.572447 CAAATCGTCCGCCGTTTGT 59.428 52.632 9.96 0.00 35.13 2.83
2398 3117 0.452122 CAAATCGTCCGCCGTTTGTC 60.452 55.000 9.96 0.00 35.13 3.18
2399 3118 1.893168 AAATCGTCCGCCGTTTGTCG 61.893 55.000 0.00 0.00 37.94 4.35
2400 3119 3.562779 ATCGTCCGCCGTTTGTCGT 62.563 57.895 0.00 0.00 37.94 4.34
2401 3120 3.759828 CGTCCGCCGTTTGTCGTC 61.760 66.667 0.00 0.00 37.94 4.20
2402 3121 2.355481 GTCCGCCGTTTGTCGTCT 60.355 61.111 0.00 0.00 37.94 4.18
2403 3122 2.355363 TCCGCCGTTTGTCGTCTG 60.355 61.111 0.00 0.00 37.94 3.51
2404 3123 2.660552 CCGCCGTTTGTCGTCTGT 60.661 61.111 0.00 0.00 37.94 3.41
2405 3124 2.544359 CGCCGTTTGTCGTCTGTG 59.456 61.111 0.00 0.00 37.94 3.66
2406 3125 2.235016 CGCCGTTTGTCGTCTGTGT 61.235 57.895 0.00 0.00 37.94 3.72
2407 3126 0.935831 CGCCGTTTGTCGTCTGTGTA 60.936 55.000 0.00 0.00 37.94 2.90
2408 3127 0.782384 GCCGTTTGTCGTCTGTGTAG 59.218 55.000 0.00 0.00 37.94 2.74
2409 3128 0.782384 CCGTTTGTCGTCTGTGTAGC 59.218 55.000 0.00 0.00 37.94 3.58
2410 3129 1.483316 CGTTTGTCGTCTGTGTAGCA 58.517 50.000 0.00 0.00 34.52 3.49
2411 3130 1.452025 CGTTTGTCGTCTGTGTAGCAG 59.548 52.381 0.00 0.00 46.34 4.24
2412 3131 1.192534 GTTTGTCGTCTGTGTAGCAGC 59.807 52.381 0.00 0.00 44.66 5.25
2413 3132 0.663269 TTGTCGTCTGTGTAGCAGCG 60.663 55.000 0.00 0.00 44.66 5.18
2414 3133 1.081376 GTCGTCTGTGTAGCAGCGT 60.081 57.895 0.00 0.00 44.66 5.07
2415 3134 0.663568 GTCGTCTGTGTAGCAGCGTT 60.664 55.000 0.00 0.00 44.66 4.84
2416 3135 0.386858 TCGTCTGTGTAGCAGCGTTC 60.387 55.000 0.00 0.00 44.66 3.95
2417 3136 0.663269 CGTCTGTGTAGCAGCGTTCA 60.663 55.000 0.00 0.00 44.66 3.18
2418 3137 1.497991 GTCTGTGTAGCAGCGTTCAA 58.502 50.000 0.00 0.00 44.66 2.69
2419 3138 1.864711 GTCTGTGTAGCAGCGTTCAAA 59.135 47.619 0.00 0.00 44.66 2.69
2420 3139 2.096713 GTCTGTGTAGCAGCGTTCAAAG 60.097 50.000 0.00 0.00 44.66 2.77
2421 3140 1.195448 CTGTGTAGCAGCGTTCAAAGG 59.805 52.381 0.00 0.00 38.52 3.11
2422 3141 0.110192 GTGTAGCAGCGTTCAAAGGC 60.110 55.000 0.00 0.00 39.92 4.35
2423 3142 1.132640 GTAGCAGCGTTCAAAGGCG 59.867 57.895 2.15 0.00 43.99 5.52
2445 3164 2.003548 CCCTTCCCCTCCCTTCCAG 61.004 68.421 0.00 0.00 0.00 3.86
2459 3183 3.174987 CCAGTCCACCCCACCACA 61.175 66.667 0.00 0.00 0.00 4.17
2518 3242 2.989253 CACCCCCAAAACCCTCGC 60.989 66.667 0.00 0.00 0.00 5.03
2519 3243 3.182996 ACCCCCAAAACCCTCGCT 61.183 61.111 0.00 0.00 0.00 4.93
2524 3248 2.434331 CAAAACCCTCGCTCCCCA 59.566 61.111 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.238898 CCCTAGGTCCCAAAGTAAGTGG 59.761 54.545 8.29 0.00 35.77 4.00
1 2 3.178865 TCCCTAGGTCCCAAAGTAAGTG 58.821 50.000 8.29 0.00 0.00 3.16
2 3 3.181398 ACTCCCTAGGTCCCAAAGTAAGT 60.181 47.826 8.29 0.00 0.00 2.24
3 4 3.451890 ACTCCCTAGGTCCCAAAGTAAG 58.548 50.000 8.29 0.00 0.00 2.34
4 5 3.572661 ACTCCCTAGGTCCCAAAGTAA 57.427 47.619 8.29 0.00 0.00 2.24
5 6 4.913154 ATACTCCCTAGGTCCCAAAGTA 57.087 45.455 8.29 6.03 0.00 2.24
6 7 3.797671 ATACTCCCTAGGTCCCAAAGT 57.202 47.619 8.29 4.05 0.00 2.66
7 8 4.781934 CAAATACTCCCTAGGTCCCAAAG 58.218 47.826 8.29 0.00 0.00 2.77
8 9 3.053917 GCAAATACTCCCTAGGTCCCAAA 60.054 47.826 8.29 0.00 0.00 3.28
9 10 2.508300 GCAAATACTCCCTAGGTCCCAA 59.492 50.000 8.29 0.00 0.00 4.12
10 11 2.124411 GCAAATACTCCCTAGGTCCCA 58.876 52.381 8.29 0.00 0.00 4.37
11 12 2.409570 AGCAAATACTCCCTAGGTCCC 58.590 52.381 8.29 0.00 0.00 4.46
12 13 4.505324 AAAGCAAATACTCCCTAGGTCC 57.495 45.455 8.29 0.00 0.00 4.46
13 14 6.885922 TCTAAAAGCAAATACTCCCTAGGTC 58.114 40.000 8.29 0.00 0.00 3.85
14 15 6.886178 TCTAAAAGCAAATACTCCCTAGGT 57.114 37.500 8.29 0.00 0.00 3.08
15 16 7.283354 CCTTTCTAAAAGCAAATACTCCCTAGG 59.717 40.741 0.06 0.06 0.00 3.02
16 17 7.829706 ACCTTTCTAAAAGCAAATACTCCCTAG 59.170 37.037 0.00 0.00 0.00 3.02
17 18 7.696017 ACCTTTCTAAAAGCAAATACTCCCTA 58.304 34.615 0.00 0.00 0.00 3.53
18 19 6.552932 ACCTTTCTAAAAGCAAATACTCCCT 58.447 36.000 0.00 0.00 0.00 4.20
19 20 6.835819 ACCTTTCTAAAAGCAAATACTCCC 57.164 37.500 0.00 0.00 0.00 4.30
20 21 9.193133 GAAAACCTTTCTAAAAGCAAATACTCC 57.807 33.333 0.00 0.00 0.00 3.85
21 22 9.744468 TGAAAACCTTTCTAAAAGCAAATACTC 57.256 29.630 1.22 0.00 0.00 2.59
22 23 9.529325 GTGAAAACCTTTCTAAAAGCAAATACT 57.471 29.630 1.22 0.00 0.00 2.12
34 35 4.426736 AACCGAGGTGAAAACCTTTCTA 57.573 40.909 0.00 0.00 40.86 2.10
35 36 3.292492 AACCGAGGTGAAAACCTTTCT 57.708 42.857 0.00 0.00 40.86 2.52
41 42 2.546789 CCAGTGTAACCGAGGTGAAAAC 59.453 50.000 0.00 0.00 37.80 2.43
44 45 1.707106 TCCAGTGTAACCGAGGTGAA 58.293 50.000 0.00 0.00 37.80 3.18
47 48 0.683412 GGTTCCAGTGTAACCGAGGT 59.317 55.000 1.38 0.00 37.26 3.85
52 53 2.779506 CCTCTTGGTTCCAGTGTAACC 58.220 52.381 10.57 10.57 45.53 2.85
56 57 1.729586 TAGCCTCTTGGTTCCAGTGT 58.270 50.000 0.00 0.00 35.27 3.55
61 62 5.984695 AAATTTCTTAGCCTCTTGGTTCC 57.015 39.130 0.00 0.00 35.27 3.62
85 86 8.236586 GCACTGAACATCATAACACAGAAAATA 58.763 33.333 0.00 0.00 0.00 1.40
88 89 5.530543 TGCACTGAACATCATAACACAGAAA 59.469 36.000 0.00 0.00 0.00 2.52
136 138 1.012234 GAATCGAATGCGCGTCCAC 60.012 57.895 8.43 0.00 37.46 4.02
152 154 6.927416 TGCTAGTTTAACCACGAGATTAGAA 58.073 36.000 0.00 0.00 0.00 2.10
153 155 6.519679 TGCTAGTTTAACCACGAGATTAGA 57.480 37.500 0.00 0.00 0.00 2.10
274 276 3.132289 TGATTGTACTGCTACCACTAGGC 59.868 47.826 0.00 0.00 39.06 3.93
285 287 3.866651 ACCACTCAGATGATTGTACTGC 58.133 45.455 0.00 0.00 0.00 4.40
286 288 6.214191 ACTACCACTCAGATGATTGTACTG 57.786 41.667 0.00 0.00 0.00 2.74
314 322 0.605589 CCGCCCAAACCAGCAAAATA 59.394 50.000 0.00 0.00 0.00 1.40
323 335 3.336715 GAACGATGCCGCCCAAACC 62.337 63.158 0.00 0.00 39.95 3.27
336 348 3.585862 ACGTACTACCTAGAACGAACGA 58.414 45.455 11.92 0.00 38.64 3.85
337 349 3.999229 ACGTACTACCTAGAACGAACG 57.001 47.619 0.23 0.00 38.64 3.95
338 350 7.012358 GCATATACGTACTACCTAGAACGAAC 58.988 42.308 0.00 0.00 38.64 3.95
339 351 6.931281 AGCATATACGTACTACCTAGAACGAA 59.069 38.462 0.00 0.00 38.64 3.85
356 368 4.562552 GGAGCCAGAAAGAGGAGCATATAC 60.563 50.000 0.00 0.00 0.00 1.47
358 370 2.371510 GGAGCCAGAAAGAGGAGCATAT 59.628 50.000 0.00 0.00 0.00 1.78
360 372 0.545646 GGAGCCAGAAAGAGGAGCAT 59.454 55.000 0.00 0.00 0.00 3.79
361 373 1.557269 GGGAGCCAGAAAGAGGAGCA 61.557 60.000 0.00 0.00 0.00 4.26
362 374 1.223211 GGGAGCCAGAAAGAGGAGC 59.777 63.158 0.00 0.00 0.00 4.70
363 375 1.911471 GGGGAGCCAGAAAGAGGAG 59.089 63.158 0.00 0.00 0.00 3.69
364 376 1.990060 CGGGGAGCCAGAAAGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
365 377 1.990060 TCGGGGAGCCAGAAAGAGG 60.990 63.158 0.00 0.00 0.00 3.69
366 378 1.219393 GTCGGGGAGCCAGAAAGAG 59.781 63.158 0.00 0.00 28.12 2.85
367 379 2.291043 GGTCGGGGAGCCAGAAAGA 61.291 63.158 0.00 0.00 28.12 2.52
368 380 2.269241 GGTCGGGGAGCCAGAAAG 59.731 66.667 0.00 0.00 28.12 2.62
500 523 0.817634 CATCCGGGCGGCATCTTTTA 60.818 55.000 12.47 0.00 34.68 1.52
531 554 6.690194 AGACGAAATAATAGTACCACTCGT 57.310 37.500 0.00 0.00 40.66 4.18
541 564 7.909267 TCACATCTGCAAAGACGAAATAATAG 58.091 34.615 0.00 0.00 0.00 1.73
555 578 1.935873 GCTCGCTAATCACATCTGCAA 59.064 47.619 0.00 0.00 0.00 4.08
584 610 1.473434 GGCTAGCAGGCGTGTTTATCT 60.473 52.381 18.24 0.00 0.00 1.98
624 714 1.369689 CAACTCAACGCAGTGCAGC 60.370 57.895 16.83 0.00 45.00 5.25
625 715 0.234106 CTCAACTCAACGCAGTGCAG 59.766 55.000 16.83 10.53 45.00 4.41
626 716 0.461870 ACTCAACTCAACGCAGTGCA 60.462 50.000 16.83 0.00 45.00 4.57
627 717 0.041839 CACTCAACTCAACGCAGTGC 60.042 55.000 4.58 4.58 45.00 4.40
628 718 0.583438 CCACTCAACTCAACGCAGTG 59.417 55.000 0.00 0.00 45.00 3.66
636 1290 2.401699 CTGCAGGGCCACTCAACTCA 62.402 60.000 6.18 0.00 0.00 3.41
670 1324 3.887716 GCAGAGCATTACATTTCTCCCAT 59.112 43.478 0.00 0.00 0.00 4.00
845 1512 3.304123 GCTATATGTATAGAGCCGAGCGG 60.304 52.174 4.20 4.20 40.67 5.52
979 1646 3.535962 CCCTGCCGCCTCTCTCTC 61.536 72.222 0.00 0.00 0.00 3.20
980 1647 3.914551 AACCCTGCCGCCTCTCTCT 62.915 63.158 0.00 0.00 0.00 3.10
981 1648 3.394836 AACCCTGCCGCCTCTCTC 61.395 66.667 0.00 0.00 0.00 3.20
982 1649 3.710722 CAACCCTGCCGCCTCTCT 61.711 66.667 0.00 0.00 0.00 3.10
1434 2101 3.630148 GTCGGCGCCATCACGATG 61.630 66.667 28.98 7.38 38.99 3.84
1470 2137 3.775654 CCGGCGGCTCCTTCTTCT 61.776 66.667 15.42 0.00 0.00 2.85
1684 2351 5.785599 CGAAAGAAACTAACTGCGATTTGAG 59.214 40.000 0.00 0.00 0.00 3.02
1697 2364 7.259290 ACAATCAAGAAAGCGAAAGAAACTA 57.741 32.000 0.00 0.00 0.00 2.24
1719 2425 4.406648 TCACAGAGCAAGAAGAAGAACA 57.593 40.909 0.00 0.00 0.00 3.18
1720 2426 4.391523 GGATCACAGAGCAAGAAGAAGAAC 59.608 45.833 0.00 0.00 0.00 3.01
1721 2427 4.573900 GGATCACAGAGCAAGAAGAAGAA 58.426 43.478 0.00 0.00 0.00 2.52
1722 2428 3.367806 CGGATCACAGAGCAAGAAGAAGA 60.368 47.826 0.00 0.00 0.00 2.87
1723 2429 2.928757 CGGATCACAGAGCAAGAAGAAG 59.071 50.000 0.00 0.00 0.00 2.85
1724 2430 2.562738 TCGGATCACAGAGCAAGAAGAA 59.437 45.455 0.00 0.00 0.00 2.52
1725 2431 2.165234 CTCGGATCACAGAGCAAGAAGA 59.835 50.000 0.00 0.00 32.42 2.87
1726 2432 2.538437 CTCGGATCACAGAGCAAGAAG 58.462 52.381 0.00 0.00 32.42 2.85
1727 2433 2.662006 CTCGGATCACAGAGCAAGAA 57.338 50.000 0.00 0.00 32.42 2.52
1733 2439 1.203287 TCACTTGCTCGGATCACAGAG 59.797 52.381 0.00 1.34 40.36 3.35
1734 2440 1.203287 CTCACTTGCTCGGATCACAGA 59.797 52.381 0.00 0.00 0.00 3.41
1735 2441 1.638133 CTCACTTGCTCGGATCACAG 58.362 55.000 0.00 0.00 0.00 3.66
1736 2442 0.390340 GCTCACTTGCTCGGATCACA 60.390 55.000 0.00 0.00 0.00 3.58
1737 2443 0.108424 AGCTCACTTGCTCGGATCAC 60.108 55.000 0.00 0.00 39.34 3.06
1738 2444 0.108472 CAGCTCACTTGCTCGGATCA 60.108 55.000 0.00 0.00 41.98 2.92
1739 2445 0.108424 ACAGCTCACTTGCTCGGATC 60.108 55.000 0.00 0.00 41.98 3.36
1740 2446 1.135915 CTACAGCTCACTTGCTCGGAT 59.864 52.381 0.00 0.00 41.98 4.18
1741 2447 0.528017 CTACAGCTCACTTGCTCGGA 59.472 55.000 0.00 0.00 41.98 4.55
1742 2448 1.080995 GCTACAGCTCACTTGCTCGG 61.081 60.000 0.00 0.00 41.98 4.63
1743 2449 2.367844 GCTACAGCTCACTTGCTCG 58.632 57.895 0.00 0.00 41.98 5.03
1754 2460 0.741221 GTGCCAGTGGTAGCTACAGC 60.741 60.000 24.75 17.64 42.49 4.40
1781 2487 4.081406 TGAAGATTCATCCAACCAGTTGG 58.919 43.478 21.26 21.26 45.43 3.77
1812 2518 1.985473 TCAGAACACCAAGCAAGCAT 58.015 45.000 0.00 0.00 0.00 3.79
1813 2519 1.677576 CTTCAGAACACCAAGCAAGCA 59.322 47.619 0.00 0.00 0.00 3.91
1814 2520 1.949525 TCTTCAGAACACCAAGCAAGC 59.050 47.619 0.00 0.00 0.00 4.01
1815 2521 4.637483 TTTCTTCAGAACACCAAGCAAG 57.363 40.909 0.00 0.00 33.13 4.01
1816 2522 5.277779 CGTATTTCTTCAGAACACCAAGCAA 60.278 40.000 0.00 0.00 33.13 3.91
1826 2532 7.010830 CAGATTCTCATGCGTATTTCTTCAGAA 59.989 37.037 0.00 0.00 0.00 3.02
1845 2551 6.112058 GCCAGAAGAAATGTCTACAGATTCT 58.888 40.000 7.68 7.68 37.48 2.40
1853 2559 2.168521 CTCCGGCCAGAAGAAATGTCTA 59.831 50.000 2.24 0.00 32.16 2.59
1867 2573 5.469084 CCAAGAATAATTTACTACTCCGGCC 59.531 44.000 0.00 0.00 0.00 6.13
1869 2575 9.991906 TTATCCAAGAATAATTTACTACTCCGG 57.008 33.333 0.00 0.00 0.00 5.14
1889 2595 9.416284 TCATGACTTGTACAGTACTATTATCCA 57.584 33.333 12.07 2.22 35.01 3.41
1896 2602 6.627287 GCCATGTCATGACTTGTACAGTACTA 60.627 42.308 29.52 8.21 35.01 1.82
1902 2608 3.073678 GTGCCATGTCATGACTTGTACA 58.926 45.455 29.52 25.13 35.46 2.90
1903 2609 2.094258 CGTGCCATGTCATGACTTGTAC 59.906 50.000 29.52 25.81 35.46 2.90
1904 2610 2.028567 TCGTGCCATGTCATGACTTGTA 60.029 45.455 29.52 19.89 35.46 2.41
1905 2611 1.159285 CGTGCCATGTCATGACTTGT 58.841 50.000 29.52 14.53 35.46 3.16
1946 2654 5.172053 GCGCACATGAGAAGTATTTTATTGC 59.828 40.000 0.30 0.00 0.00 3.56
1956 2664 1.532868 GTTTCAGCGCACATGAGAAGT 59.467 47.619 11.47 0.00 0.00 3.01
1959 2667 1.812235 ATGTTTCAGCGCACATGAGA 58.188 45.000 11.47 0.00 32.19 3.27
1969 2677 3.696051 TGCCTCCAAGAATATGTTTCAGC 59.304 43.478 0.00 0.00 0.00 4.26
2128 2847 5.389516 CCCGTTTGATGTCTCTTTTCGTTAG 60.390 44.000 0.00 0.00 0.00 2.34
2185 2904 2.442087 GGGCCCGAAAATCTGGGG 60.442 66.667 5.69 0.00 46.12 4.96
2267 2986 8.195617 AGTACTGTCGTCTGTATAGTAGTTTC 57.804 38.462 0.00 0.00 32.34 2.78
2268 2987 7.279758 GGAGTACTGTCGTCTGTATAGTAGTTT 59.720 40.741 0.00 0.00 32.34 2.66
2269 2988 6.760770 GGAGTACTGTCGTCTGTATAGTAGTT 59.239 42.308 0.00 0.00 32.34 2.24
2270 2989 6.279882 GGAGTACTGTCGTCTGTATAGTAGT 58.720 44.000 0.00 0.00 32.34 2.73
2271 2990 5.401972 CGGAGTACTGTCGTCTGTATAGTAG 59.598 48.000 0.00 0.00 32.34 2.57
2272 2991 5.284864 CGGAGTACTGTCGTCTGTATAGTA 58.715 45.833 0.00 0.00 32.34 1.82
2273 2992 4.118410 CGGAGTACTGTCGTCTGTATAGT 58.882 47.826 0.00 0.00 32.34 2.12
2274 2993 3.493877 CCGGAGTACTGTCGTCTGTATAG 59.506 52.174 0.00 0.00 32.34 1.31
2275 2994 3.461061 CCGGAGTACTGTCGTCTGTATA 58.539 50.000 0.00 0.00 32.34 1.47
2276 2995 2.286872 CCGGAGTACTGTCGTCTGTAT 58.713 52.381 0.00 0.00 32.34 2.29
2277 2996 1.730501 CCGGAGTACTGTCGTCTGTA 58.269 55.000 0.00 0.00 0.00 2.74
2278 2997 1.584380 GCCGGAGTACTGTCGTCTGT 61.584 60.000 5.05 0.00 0.00 3.41
2279 2998 1.136984 GCCGGAGTACTGTCGTCTG 59.863 63.158 5.05 0.00 0.00 3.51
2280 2999 2.045131 GGCCGGAGTACTGTCGTCT 61.045 63.158 5.05 0.00 0.00 4.18
2281 3000 2.488820 GGCCGGAGTACTGTCGTC 59.511 66.667 5.05 0.00 0.00 4.20
2282 3001 3.437795 CGGCCGGAGTACTGTCGT 61.438 66.667 20.10 0.00 0.00 4.34
2283 3002 2.693762 TTCGGCCGGAGTACTGTCG 61.694 63.158 27.83 4.03 0.00 4.35
2284 3003 1.153881 GTTCGGCCGGAGTACTGTC 60.154 63.158 27.83 0.00 0.00 3.51
2285 3004 1.904865 TGTTCGGCCGGAGTACTGT 60.905 57.895 27.83 0.00 0.00 3.55
2286 3005 1.445582 GTGTTCGGCCGGAGTACTG 60.446 63.158 27.83 0.00 0.00 2.74
2287 3006 1.605738 AGTGTTCGGCCGGAGTACT 60.606 57.895 27.83 20.91 0.00 2.73
2288 3007 1.445582 CAGTGTTCGGCCGGAGTAC 60.446 63.158 27.83 18.82 0.00 2.73
2289 3008 2.642254 CCAGTGTTCGGCCGGAGTA 61.642 63.158 27.83 5.61 0.00 2.59
2290 3009 4.003788 CCAGTGTTCGGCCGGAGT 62.004 66.667 27.83 9.84 0.00 3.85
2291 3010 3.691342 TCCAGTGTTCGGCCGGAG 61.691 66.667 27.83 3.83 0.00 4.63
2292 3011 3.998672 GTCCAGTGTTCGGCCGGA 61.999 66.667 27.83 16.16 0.00 5.14
2294 3013 3.642778 ATCGTCCAGTGTTCGGCCG 62.643 63.158 22.12 22.12 0.00 6.13
2295 3014 2.100631 CATCGTCCAGTGTTCGGCC 61.101 63.158 0.00 0.00 0.00 6.13
2296 3015 0.949105 AACATCGTCCAGTGTTCGGC 60.949 55.000 4.78 0.00 33.53 5.54
2297 3016 0.790207 CAACATCGTCCAGTGTTCGG 59.210 55.000 4.78 0.00 36.48 4.30
2298 3017 0.790207 CCAACATCGTCCAGTGTTCG 59.210 55.000 0.00 0.00 36.48 3.95
2299 3018 2.163818 TCCAACATCGTCCAGTGTTC 57.836 50.000 0.00 0.00 36.48 3.18
2300 3019 2.699954 GATCCAACATCGTCCAGTGTT 58.300 47.619 0.00 0.00 39.00 3.32
2301 3020 1.404181 CGATCCAACATCGTCCAGTGT 60.404 52.381 0.00 0.00 36.84 3.55
2302 3021 1.135112 TCGATCCAACATCGTCCAGTG 60.135 52.381 4.06 0.00 41.77 3.66
2303 3022 1.182667 TCGATCCAACATCGTCCAGT 58.817 50.000 4.06 0.00 41.77 4.00
2304 3023 1.927174 GTTCGATCCAACATCGTCCAG 59.073 52.381 0.00 0.00 41.77 3.86
2305 3024 1.734377 CGTTCGATCCAACATCGTCCA 60.734 52.381 4.06 0.00 41.77 4.02
2306 3025 0.921347 CGTTCGATCCAACATCGTCC 59.079 55.000 4.06 0.00 41.77 4.79
2307 3026 0.921347 CCGTTCGATCCAACATCGTC 59.079 55.000 4.06 0.00 41.77 4.20
2308 3027 0.245539 ACCGTTCGATCCAACATCGT 59.754 50.000 4.06 0.00 41.77 3.73
2309 3028 0.645355 CACCGTTCGATCCAACATCG 59.355 55.000 4.06 0.00 42.38 3.84
2310 3029 1.722011 ACACCGTTCGATCCAACATC 58.278 50.000 4.06 0.00 0.00 3.06
2311 3030 1.804151 CAACACCGTTCGATCCAACAT 59.196 47.619 4.06 0.00 0.00 2.71
2312 3031 1.222300 CAACACCGTTCGATCCAACA 58.778 50.000 4.06 0.00 0.00 3.33
2313 3032 1.223187 ACAACACCGTTCGATCCAAC 58.777 50.000 0.00 0.00 0.00 3.77
2314 3033 1.956297 AACAACACCGTTCGATCCAA 58.044 45.000 0.00 0.00 0.00 3.53
2315 3034 1.956297 AAACAACACCGTTCGATCCA 58.044 45.000 0.00 0.00 0.00 3.41
2316 3035 3.062042 ACTAAACAACACCGTTCGATCC 58.938 45.455 0.00 0.00 0.00 3.36
2317 3036 4.720530 AACTAAACAACACCGTTCGATC 57.279 40.909 0.00 0.00 0.00 3.69
2318 3037 5.267776 CAAAACTAAACAACACCGTTCGAT 58.732 37.500 0.00 0.00 0.00 3.59
2319 3038 4.649977 CAAAACTAAACAACACCGTTCGA 58.350 39.130 0.00 0.00 0.00 3.71
2320 3039 3.238798 GCAAAACTAAACAACACCGTTCG 59.761 43.478 0.00 0.00 0.00 3.95
2321 3040 4.417506 AGCAAAACTAAACAACACCGTTC 58.582 39.130 0.00 0.00 0.00 3.95
2322 3041 4.443913 AGCAAAACTAAACAACACCGTT 57.556 36.364 0.00 0.00 0.00 4.44
2323 3042 4.443913 AAGCAAAACTAAACAACACCGT 57.556 36.364 0.00 0.00 0.00 4.83
2324 3043 5.800941 TGTAAAGCAAAACTAAACAACACCG 59.199 36.000 0.00 0.00 0.00 4.94
2325 3044 6.586844 TGTGTAAAGCAAAACTAAACAACACC 59.413 34.615 0.00 0.00 34.16 4.16
2326 3045 7.569677 TGTGTAAAGCAAAACTAAACAACAC 57.430 32.000 0.00 0.00 35.31 3.32
2327 3046 8.029522 TCATGTGTAAAGCAAAACTAAACAACA 58.970 29.630 0.00 0.00 0.00 3.33
2328 3047 8.401046 TCATGTGTAAAGCAAAACTAAACAAC 57.599 30.769 0.00 0.00 0.00 3.32
2329 3048 7.221838 GCTCATGTGTAAAGCAAAACTAAACAA 59.778 33.333 0.00 0.00 36.06 2.83
2330 3049 6.695278 GCTCATGTGTAAAGCAAAACTAAACA 59.305 34.615 0.00 0.00 36.06 2.83
2331 3050 6.129457 CGCTCATGTGTAAAGCAAAACTAAAC 60.129 38.462 4.45 0.00 35.76 2.01
2332 3051 5.912396 CGCTCATGTGTAAAGCAAAACTAAA 59.088 36.000 4.45 0.00 35.76 1.85
2333 3052 5.448438 CGCTCATGTGTAAAGCAAAACTAA 58.552 37.500 4.45 0.00 35.76 2.24
2334 3053 4.083537 CCGCTCATGTGTAAAGCAAAACTA 60.084 41.667 4.45 0.00 35.76 2.24
2335 3054 3.304659 CCGCTCATGTGTAAAGCAAAACT 60.305 43.478 4.45 0.00 35.76 2.66
2336 3055 2.979813 CCGCTCATGTGTAAAGCAAAAC 59.020 45.455 4.45 0.00 35.76 2.43
2337 3056 2.606795 GCCGCTCATGTGTAAAGCAAAA 60.607 45.455 4.45 0.00 35.76 2.44
2338 3057 1.068610 GCCGCTCATGTGTAAAGCAAA 60.069 47.619 4.45 0.00 35.76 3.68
2339 3058 0.521291 GCCGCTCATGTGTAAAGCAA 59.479 50.000 4.45 0.00 35.76 3.91
2340 3059 0.321564 AGCCGCTCATGTGTAAAGCA 60.322 50.000 4.45 0.00 35.76 3.91
2341 3060 0.804989 AAGCCGCTCATGTGTAAAGC 59.195 50.000 0.00 0.00 0.00 3.51
2342 3061 2.076100 TCAAGCCGCTCATGTGTAAAG 58.924 47.619 0.00 0.00 0.00 1.85
2343 3062 2.177394 TCAAGCCGCTCATGTGTAAA 57.823 45.000 0.00 0.00 0.00 2.01
2344 3063 2.009051 CATCAAGCCGCTCATGTGTAA 58.991 47.619 0.00 0.00 0.00 2.41
2345 3064 1.066215 ACATCAAGCCGCTCATGTGTA 60.066 47.619 14.38 0.00 0.00 2.90
2346 3065 0.321919 ACATCAAGCCGCTCATGTGT 60.322 50.000 14.38 6.12 0.00 3.72
2347 3066 0.098200 CACATCAAGCCGCTCATGTG 59.902 55.000 22.07 22.07 40.03 3.21
2348 3067 1.651240 GCACATCAAGCCGCTCATGT 61.651 55.000 10.76 10.76 0.00 3.21
2349 3068 1.063649 GCACATCAAGCCGCTCATG 59.936 57.895 9.71 9.71 0.00 3.07
2350 3069 0.178767 TAGCACATCAAGCCGCTCAT 59.821 50.000 0.00 0.00 35.93 2.90
2351 3070 0.740868 GTAGCACATCAAGCCGCTCA 60.741 55.000 0.00 0.00 35.93 4.26
2352 3071 0.740868 TGTAGCACATCAAGCCGCTC 60.741 55.000 0.00 0.00 35.93 5.03
2353 3072 0.107508 ATGTAGCACATCAAGCCGCT 60.108 50.000 0.00 0.00 32.38 5.52
2354 3073 2.397751 ATGTAGCACATCAAGCCGC 58.602 52.632 0.00 0.00 32.38 6.53
2362 3081 2.385013 TTGCAGACGATGTAGCACAT 57.615 45.000 0.00 2.02 42.43 3.21
2363 3082 2.162319 TTTGCAGACGATGTAGCACA 57.838 45.000 0.00 0.00 36.62 4.57
2364 3083 2.285256 CGATTTGCAGACGATGTAGCAC 60.285 50.000 0.00 0.00 36.62 4.40
2365 3084 1.926510 CGATTTGCAGACGATGTAGCA 59.073 47.619 0.00 0.00 34.79 3.49
2366 3085 1.927174 ACGATTTGCAGACGATGTAGC 59.073 47.619 14.13 0.00 0.00 3.58
2367 3086 2.535984 GGACGATTTGCAGACGATGTAG 59.464 50.000 14.13 0.00 0.00 2.74
2368 3087 2.536365 GGACGATTTGCAGACGATGTA 58.464 47.619 14.13 0.00 0.00 2.29
2369 3088 1.359848 GGACGATTTGCAGACGATGT 58.640 50.000 14.13 0.00 0.00 3.06
2370 3089 0.298707 CGGACGATTTGCAGACGATG 59.701 55.000 14.13 0.00 0.00 3.84
2371 3090 1.421410 GCGGACGATTTGCAGACGAT 61.421 55.000 14.13 0.00 0.00 3.73
2372 3091 2.092291 GCGGACGATTTGCAGACGA 61.092 57.895 14.13 0.00 0.00 4.20
2373 3092 2.395690 GCGGACGATTTGCAGACG 59.604 61.111 0.00 7.49 0.00 4.18
2374 3093 2.785258 GGCGGACGATTTGCAGAC 59.215 61.111 0.00 0.00 0.00 3.51
2402 3121 1.225855 CCTTTGAACGCTGCTACACA 58.774 50.000 0.00 0.00 0.00 3.72
2403 3122 0.110192 GCCTTTGAACGCTGCTACAC 60.110 55.000 0.00 0.00 0.00 2.90
2404 3123 1.565156 CGCCTTTGAACGCTGCTACA 61.565 55.000 0.00 0.00 0.00 2.74
2405 3124 1.132640 CGCCTTTGAACGCTGCTAC 59.867 57.895 0.00 0.00 0.00 3.58
2406 3125 3.561429 CGCCTTTGAACGCTGCTA 58.439 55.556 0.00 0.00 0.00 3.49
2425 3144 2.696504 GAAGGGAGGGGAAGGGGG 60.697 72.222 0.00 0.00 0.00 5.40
2439 3158 2.153401 TGGTGGGGTGGACTGGAAG 61.153 63.158 0.00 0.00 42.29 3.46
2445 3164 2.203437 GGTTGTGGTGGGGTGGAC 60.203 66.667 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.