Multiple sequence alignment - TraesCS6D01G255000

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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 TraesCS6D01G255000 chr6D 100.000 4088 0 0 1 4088 360338523 360342610 0.000000e+00 7550.0
1 TraesCS6D01G255000 chr6B 94.406 2592 107 19 1523 4086 542009624 542012205 0.000000e+00 3949.0
2 TraesCS6D01G255000 chr6B 86.158 1481 129 49 3 1441 542008160 542009606 0.000000e+00 1530.0
3 TraesCS6D01G255000 chr6A 94.967 2305 88 18 1804 4086 501498314 501500612 0.000000e+00 3589.0
4 TraesCS6D01G255000 chr6A 93.878 441 16 4 1 430 501496188 501496628 0.000000e+00 654.0
5 TraesCS6D01G255000 chr6A 93.510 416 15 5 448 852 501496613 501497027 3.490000e-170 608.0
6 TraesCS6D01G255000 chr6A 98.333 240 4 0 889 1128 501497464 501497703 4.890000e-114 422.0
7 TraesCS6D01G255000 chr6A 93.676 253 10 3 1184 1435 501497805 501498052 1.390000e-99 374.0
8 TraesCS6D01G255000 chr6A 90.517 232 22 0 1523 1754 501498080 501498311 1.430000e-79 307.0
9 TraesCS6D01G255000 chr3B 75.255 392 70 14 3711 4080 181295752 181296138 1.180000e-35 161.0
10 TraesCS6D01G255000 chr3B 73.196 388 73 19 3710 4079 778675219 778675593 1.200000e-20 111.0
11 TraesCS6D01G255000 chr4A 78.298 235 42 6 3808 4034 540477847 540478080 4.260000e-30 143.0
12 TraesCS6D01G255000 chr7A 76.779 267 44 14 3824 4080 734469908 734469650 2.560000e-27 134.0
13 TraesCS6D01G255000 chr7A 82.353 153 22 3 3712 3859 64845162 64845314 1.190000e-25 128.0
14 TraesCS6D01G255000 chr7A 79.085 153 26 4 3847 3994 707622201 707622352 2.600000e-17 100.0
15 TraesCS6D01G255000 chr7A 76.355 203 36 8 3779 3975 55436739 55436543 9.350000e-17 99.0
16 TraesCS6D01G255000 chr5B 73.902 387 74 20 3712 4080 10097089 10096712 3.320000e-26 130.0
17 TraesCS6D01G255000 chr4D 75.694 288 52 10 3808 4082 509802057 509802339 1.190000e-25 128.0
18 TraesCS6D01G255000 chr3D 76.891 238 41 8 3766 3994 385432442 385432674 5.550000e-24 122.0
19 TraesCS6D01G255000 chr2B 76.812 207 40 8 3808 4008 373090710 373090914 4.320000e-20 110.0
20 TraesCS6D01G255000 chr2B 75.980 204 40 8 3808 4004 373064276 373064477 3.360000e-16 97.1
21 TraesCS6D01G255000 chr7D 83.168 101 13 3 3882 3978 53561349 53561449 5.630000e-14 89.8


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 TraesCS6D01G255000 chr6D 360338523 360342610 4087 False 7550.000000 7550 100.000000 1 4088 1 chr6D.!!$F1 4087
1 TraesCS6D01G255000 chr6B 542008160 542012205 4045 False 2739.500000 3949 90.282000 3 4086 2 chr6B.!!$F1 4083
2 TraesCS6D01G255000 chr6A 501496188 501500612 4424 False 992.333333 3589 94.146833 1 4086 6 chr6A.!!$F1 4085

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
418 438 0.026674 CACGCGTGATGGTGCTATTG 59.973 55.0 34.93 1.01 0.0 1.90 F
1379 1917 0.034337 TACCAGCAAACTCCACGACC 59.966 55.0 0.00 0.00 0.0 4.79 F
1645 2191 0.597637 CCGCCAGATATCACCGTCAC 60.598 60.0 5.32 0.00 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 2269 0.250252 GGGAGCTCTAGCATCCAAGC 60.250 60.000 14.64 1.25 45.16 4.01 R
2407 2974 1.973281 CTTTGCGGTGTCCCTGCAT 60.973 57.895 0.00 0.00 39.08 3.96 R
3140 3716 3.868661 GCGGTATGATGTATGTTGACACA 59.131 43.478 0.00 0.00 37.31 3.72 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
260 269 5.692204 GCAATATAGACATCACGTTGTAGCT 59.308 40.000 0.00 0.00 0.00 3.32
372 382 8.836413 ACAAATAATTCCTTACATCCACATACG 58.164 33.333 0.00 0.00 0.00 3.06
373 383 7.979444 AATAATTCCTTACATCCACATACGG 57.021 36.000 0.00 0.00 0.00 4.02
374 384 2.902705 TCCTTACATCCACATACGGC 57.097 50.000 0.00 0.00 0.00 5.68
375 385 2.394632 TCCTTACATCCACATACGGCT 58.605 47.619 0.00 0.00 0.00 5.52
377 387 3.131396 CCTTACATCCACATACGGCTTC 58.869 50.000 0.00 0.00 0.00 3.86
378 388 2.502213 TACATCCACATACGGCTTCG 57.498 50.000 0.00 0.00 40.22 3.79
395 415 4.154918 GGCTTCGAGAAAACATGTCTTGAT 59.845 41.667 0.00 0.00 35.81 2.57
403 423 0.523072 ACATGTCTTGATTGGCACGC 59.477 50.000 0.00 0.00 0.00 5.34
418 438 0.026674 CACGCGTGATGGTGCTATTG 59.973 55.000 34.93 1.01 0.00 1.90
422 442 1.795162 GCGTGATGGTGCTATTGTTGC 60.795 52.381 0.00 0.00 0.00 4.17
426 446 3.441572 GTGATGGTGCTATTGTTGCTCTT 59.558 43.478 0.00 0.00 0.00 2.85
427 447 4.081406 TGATGGTGCTATTGTTGCTCTTT 58.919 39.130 0.00 0.00 0.00 2.52
428 448 4.523943 TGATGGTGCTATTGTTGCTCTTTT 59.476 37.500 0.00 0.00 0.00 2.27
429 449 4.935352 TGGTGCTATTGTTGCTCTTTTT 57.065 36.364 0.00 0.00 0.00 1.94
430 450 6.208402 TGATGGTGCTATTGTTGCTCTTTTTA 59.792 34.615 0.00 0.00 0.00 1.52
431 451 5.768317 TGGTGCTATTGTTGCTCTTTTTAC 58.232 37.500 0.00 0.00 0.00 2.01
432 452 5.534654 TGGTGCTATTGTTGCTCTTTTTACT 59.465 36.000 0.00 0.00 0.00 2.24
433 453 6.040391 TGGTGCTATTGTTGCTCTTTTTACTT 59.960 34.615 0.00 0.00 0.00 2.24
434 454 6.923508 GGTGCTATTGTTGCTCTTTTTACTTT 59.076 34.615 0.00 0.00 0.00 2.66
435 455 7.438160 GGTGCTATTGTTGCTCTTTTTACTTTT 59.562 33.333 0.00 0.00 0.00 2.27
436 456 8.817100 GTGCTATTGTTGCTCTTTTTACTTTTT 58.183 29.630 0.00 0.00 0.00 1.94
456 476 3.444703 TTTTGCGGTTGTATTGTTGCT 57.555 38.095 0.00 0.00 0.00 3.91
457 477 2.697431 TTGCGGTTGTATTGTTGCTC 57.303 45.000 0.00 0.00 0.00 4.26
531 580 1.135139 ACATCGATGACGTGGAAGAGG 59.865 52.381 31.33 0.47 40.69 3.69
540 595 3.830178 TGACGTGGAAGAGGATAGACAAA 59.170 43.478 0.00 0.00 0.00 2.83
542 597 5.221561 TGACGTGGAAGAGGATAGACAAAAA 60.222 40.000 0.00 0.00 0.00 1.94
636 693 5.986135 ACGAGATGCTATCTTTCCATTACAC 59.014 40.000 0.00 0.00 40.38 2.90
842 907 3.444034 TCACGTAGGGATTTGAGTCTCTG 59.556 47.826 0.65 0.00 29.97 3.35
850 915 7.630005 AGGGATTTGAGTCTCTGATATCATT 57.370 36.000 5.72 0.00 0.00 2.57
851 916 8.733092 AGGGATTTGAGTCTCTGATATCATTA 57.267 34.615 5.72 0.00 0.00 1.90
852 917 8.592809 AGGGATTTGAGTCTCTGATATCATTAC 58.407 37.037 5.72 5.13 0.00 1.89
853 918 7.543868 GGGATTTGAGTCTCTGATATCATTACG 59.456 40.741 5.72 0.00 0.00 3.18
854 919 8.300286 GGATTTGAGTCTCTGATATCATTACGA 58.700 37.037 5.72 0.00 0.00 3.43
855 920 9.340695 GATTTGAGTCTCTGATATCATTACGAG 57.659 37.037 5.72 9.37 0.00 4.18
859 936 8.368668 TGAGTCTCTGATATCATTACGAGTAGA 58.631 37.037 15.53 3.42 0.00 2.59
928 1419 3.636153 ATGACAGTCTAAGGGGCTTTC 57.364 47.619 1.31 0.00 0.00 2.62
991 1482 2.012937 TAAATAGGCGTTCCCACACG 57.987 50.000 0.00 0.00 43.36 4.49
1131 1638 6.565234 TGAGAAACGCCATTTTTCTTAACAA 58.435 32.000 0.20 0.00 42.21 2.83
1143 1650 8.981647 CATTTTTCTTAACAAACTGCAATAGCT 58.018 29.630 0.00 0.00 42.74 3.32
1146 1653 5.234752 TCTTAACAAACTGCAATAGCTCGA 58.765 37.500 0.00 0.00 42.74 4.04
1149 1656 2.744202 ACAAACTGCAATAGCTCGAAGG 59.256 45.455 0.00 0.00 42.74 3.46
1150 1657 3.002791 CAAACTGCAATAGCTCGAAGGA 58.997 45.455 0.00 0.00 42.74 3.36
1151 1658 3.334583 AACTGCAATAGCTCGAAGGAA 57.665 42.857 0.00 0.00 42.74 3.36
1152 1659 2.898705 ACTGCAATAGCTCGAAGGAAG 58.101 47.619 0.00 0.00 42.74 3.46
1155 1662 1.134371 GCAATAGCTCGAAGGAAGGGT 60.134 52.381 0.00 0.00 37.91 4.34
1156 1663 2.555199 CAATAGCTCGAAGGAAGGGTG 58.445 52.381 0.00 0.00 0.00 4.61
1159 1666 0.251832 AGCTCGAAGGAAGGGTGAGA 60.252 55.000 0.00 0.00 0.00 3.27
1161 1668 2.032620 GCTCGAAGGAAGGGTGAGATA 58.967 52.381 0.00 0.00 0.00 1.98
1164 1671 3.288964 TCGAAGGAAGGGTGAGATAGAC 58.711 50.000 0.00 0.00 0.00 2.59
1166 1673 1.404843 AGGAAGGGTGAGATAGACGC 58.595 55.000 0.00 0.00 0.00 5.19
1168 1675 1.757699 GGAAGGGTGAGATAGACGCTT 59.242 52.381 0.00 0.00 46.09 4.68
1376 1914 0.320771 AGCTACCAGCAAACTCCACG 60.321 55.000 0.38 0.00 45.56 4.94
1379 1917 0.034337 TACCAGCAAACTCCACGACC 59.966 55.000 0.00 0.00 0.00 4.79
1380 1918 1.227823 CCAGCAAACTCCACGACCA 60.228 57.895 0.00 0.00 0.00 4.02
1384 1922 1.098712 GCAAACTCCACGACCACCAA 61.099 55.000 0.00 0.00 0.00 3.67
1398 1940 2.240667 ACCACCAAATCTCTAGCTGCAT 59.759 45.455 1.02 0.00 0.00 3.96
1399 1941 2.617308 CCACCAAATCTCTAGCTGCATG 59.383 50.000 1.02 0.00 0.00 4.06
1402 1944 2.686405 CCAAATCTCTAGCTGCATGCAA 59.314 45.455 22.88 6.07 45.94 4.08
1403 1945 3.129813 CCAAATCTCTAGCTGCATGCAAA 59.870 43.478 22.88 9.26 45.94 3.68
1404 1946 4.103357 CAAATCTCTAGCTGCATGCAAAC 58.897 43.478 22.88 16.60 45.94 2.93
1405 1947 2.477845 TCTCTAGCTGCATGCAAACA 57.522 45.000 22.88 8.16 45.94 2.83
1406 1948 2.995283 TCTCTAGCTGCATGCAAACAT 58.005 42.857 22.88 10.08 45.94 2.71
1407 1949 2.941064 TCTCTAGCTGCATGCAAACATC 59.059 45.455 22.88 8.46 45.94 3.06
1447 1993 2.250485 CAGCTGAACTGTGCACGC 59.750 61.111 8.42 8.23 41.86 5.34
1448 1994 2.109799 AGCTGAACTGTGCACGCT 59.890 55.556 13.13 10.60 0.00 5.07
1449 1995 2.249535 AGCTGAACTGTGCACGCTG 61.250 57.895 13.13 7.54 0.00 5.18
1450 1996 2.941333 CTGAACTGTGCACGCTGG 59.059 61.111 13.13 4.94 0.00 4.85
1451 1997 2.591429 TGAACTGTGCACGCTGGG 60.591 61.111 13.13 2.40 0.00 4.45
1452 1998 4.030452 GAACTGTGCACGCTGGGC 62.030 66.667 13.13 0.00 0.00 5.36
1454 2000 4.996434 ACTGTGCACGCTGGGCTC 62.996 66.667 13.13 1.73 0.00 4.70
1455 2001 4.994471 CTGTGCACGCTGGGCTCA 62.994 66.667 13.13 5.98 34.10 4.26
1456 2002 4.334118 TGTGCACGCTGGGCTCAT 62.334 61.111 13.13 0.00 30.64 2.90
1457 2003 3.807538 GTGCACGCTGGGCTCATG 61.808 66.667 0.00 0.00 0.00 3.07
1460 2006 2.827190 CACGCTGGGCTCATGCAT 60.827 61.111 8.44 0.00 41.91 3.96
1461 2007 2.515523 ACGCTGGGCTCATGCATC 60.516 61.111 0.00 0.00 41.91 3.91
1462 2008 2.203167 CGCTGGGCTCATGCATCT 60.203 61.111 0.00 0.00 41.91 2.90
1463 2009 1.822613 CGCTGGGCTCATGCATCTT 60.823 57.895 0.00 0.00 41.91 2.40
1464 2010 1.381928 CGCTGGGCTCATGCATCTTT 61.382 55.000 0.00 0.00 41.91 2.52
1465 2011 0.822164 GCTGGGCTCATGCATCTTTT 59.178 50.000 0.00 0.00 41.91 2.27
1466 2012 2.026641 GCTGGGCTCATGCATCTTTTA 58.973 47.619 0.00 0.00 41.91 1.52
1467 2013 2.626743 GCTGGGCTCATGCATCTTTTAT 59.373 45.455 0.00 0.00 41.91 1.40
1468 2014 3.822735 GCTGGGCTCATGCATCTTTTATA 59.177 43.478 0.00 0.00 41.91 0.98
1469 2015 4.461781 GCTGGGCTCATGCATCTTTTATAT 59.538 41.667 0.00 0.00 41.91 0.86
1470 2016 5.047519 GCTGGGCTCATGCATCTTTTATATT 60.048 40.000 0.00 0.00 41.91 1.28
1471 2017 6.579666 TGGGCTCATGCATCTTTTATATTC 57.420 37.500 0.00 0.00 41.91 1.75
1472 2018 6.309357 TGGGCTCATGCATCTTTTATATTCT 58.691 36.000 0.00 0.00 41.91 2.40
1473 2019 6.432162 TGGGCTCATGCATCTTTTATATTCTC 59.568 38.462 0.00 0.00 41.91 2.87
1474 2020 6.127786 GGGCTCATGCATCTTTTATATTCTCC 60.128 42.308 0.00 0.00 41.91 3.71
1475 2021 6.127786 GGCTCATGCATCTTTTATATTCTCCC 60.128 42.308 0.00 0.00 41.91 4.30
1476 2022 6.402983 GCTCATGCATCTTTTATATTCTCCCG 60.403 42.308 0.00 0.00 39.41 5.14
1477 2023 6.533730 TCATGCATCTTTTATATTCTCCCGT 58.466 36.000 0.00 0.00 0.00 5.28
1478 2024 6.650807 TCATGCATCTTTTATATTCTCCCGTC 59.349 38.462 0.00 0.00 0.00 4.79
1479 2025 5.305585 TGCATCTTTTATATTCTCCCGTCC 58.694 41.667 0.00 0.00 0.00 4.79
1480 2026 4.389077 GCATCTTTTATATTCTCCCGTCCG 59.611 45.833 0.00 0.00 0.00 4.79
1481 2027 5.779922 CATCTTTTATATTCTCCCGTCCGA 58.220 41.667 0.00 0.00 0.00 4.55
1482 2028 6.398918 CATCTTTTATATTCTCCCGTCCGAT 58.601 40.000 0.00 0.00 0.00 4.18
1483 2029 6.022163 TCTTTTATATTCTCCCGTCCGATC 57.978 41.667 0.00 0.00 0.00 3.69
1484 2030 5.773680 TCTTTTATATTCTCCCGTCCGATCT 59.226 40.000 0.00 0.00 0.00 2.75
1485 2031 6.267014 TCTTTTATATTCTCCCGTCCGATCTT 59.733 38.462 0.00 0.00 0.00 2.40
1486 2032 6.415206 TTTATATTCTCCCGTCCGATCTTT 57.585 37.500 0.00 0.00 0.00 2.52
1487 2033 2.604046 ATTCTCCCGTCCGATCTTTG 57.396 50.000 0.00 0.00 0.00 2.77
1488 2034 1.552578 TTCTCCCGTCCGATCTTTGA 58.447 50.000 0.00 0.00 0.00 2.69
1489 2035 1.552578 TCTCCCGTCCGATCTTTGAA 58.447 50.000 0.00 0.00 0.00 2.69
1490 2036 1.476891 TCTCCCGTCCGATCTTTGAAG 59.523 52.381 0.00 0.00 0.00 3.02
1491 2037 1.204941 CTCCCGTCCGATCTTTGAAGT 59.795 52.381 0.00 0.00 0.00 3.01
1492 2038 2.426024 CTCCCGTCCGATCTTTGAAGTA 59.574 50.000 0.00 0.00 0.00 2.24
1493 2039 3.028850 TCCCGTCCGATCTTTGAAGTAT 58.971 45.455 0.00 0.00 0.00 2.12
1494 2040 3.123804 CCCGTCCGATCTTTGAAGTATG 58.876 50.000 0.00 0.00 0.00 2.39
1495 2041 3.430374 CCCGTCCGATCTTTGAAGTATGT 60.430 47.826 0.00 0.00 0.00 2.29
1496 2042 3.797256 CCGTCCGATCTTTGAAGTATGTC 59.203 47.826 0.00 0.00 0.00 3.06
1497 2043 3.797256 CGTCCGATCTTTGAAGTATGTCC 59.203 47.826 0.00 0.00 0.00 4.02
1498 2044 4.440250 CGTCCGATCTTTGAAGTATGTCCT 60.440 45.833 0.00 0.00 0.00 3.85
1499 2045 4.806247 GTCCGATCTTTGAAGTATGTCCTG 59.194 45.833 0.00 0.00 0.00 3.86
1500 2046 4.709886 TCCGATCTTTGAAGTATGTCCTGA 59.290 41.667 0.00 0.00 0.00 3.86
1501 2047 4.806247 CCGATCTTTGAAGTATGTCCTGAC 59.194 45.833 0.00 0.00 0.00 3.51
1502 2048 5.410924 CGATCTTTGAAGTATGTCCTGACA 58.589 41.667 1.93 1.93 46.44 3.58
1503 2049 5.518128 CGATCTTTGAAGTATGTCCTGACAG 59.482 44.000 6.13 0.00 45.48 3.51
1504 2050 5.808366 TCTTTGAAGTATGTCCTGACAGT 57.192 39.130 6.13 0.00 45.48 3.55
1505 2051 6.911250 TCTTTGAAGTATGTCCTGACAGTA 57.089 37.500 6.13 0.00 45.48 2.74
1506 2052 7.482169 TCTTTGAAGTATGTCCTGACAGTAT 57.518 36.000 6.13 0.00 45.48 2.12
1507 2053 8.589701 TCTTTGAAGTATGTCCTGACAGTATA 57.410 34.615 6.13 0.00 45.48 1.47
1508 2054 9.201989 TCTTTGAAGTATGTCCTGACAGTATAT 57.798 33.333 6.13 0.00 45.48 0.86
1512 2058 9.588096 TGAAGTATGTCCTGACAGTATATATGT 57.412 33.333 6.13 0.00 45.48 2.29
1514 2060 9.815306 AAGTATGTCCTGACAGTATATATGTCT 57.185 33.333 17.17 0.00 45.87 3.41
1515 2061 9.815306 AGTATGTCCTGACAGTATATATGTCTT 57.185 33.333 17.17 4.10 45.87 3.01
1516 2062 9.847706 GTATGTCCTGACAGTATATATGTCTTG 57.152 37.037 17.17 11.80 45.87 3.02
1517 2063 7.898014 TGTCCTGACAGTATATATGTCTTGT 57.102 36.000 17.17 6.66 45.87 3.16
1518 2064 8.306313 TGTCCTGACAGTATATATGTCTTGTT 57.694 34.615 17.17 0.00 45.87 2.83
1519 2065 8.197439 TGTCCTGACAGTATATATGTCTTGTTG 58.803 37.037 17.17 6.27 45.87 3.33
1520 2066 7.169982 GTCCTGACAGTATATATGTCTTGTTGC 59.830 40.741 17.17 0.00 45.87 4.17
1521 2067 6.425114 CCTGACAGTATATATGTCTTGTTGCC 59.575 42.308 17.17 0.00 45.87 4.52
1526 2072 7.928706 ACAGTATATATGTCTTGTTGCCTCTTC 59.071 37.037 0.00 0.00 0.00 2.87
1546 2092 2.041485 TCATCTTGGCAATGAAGGTCCA 59.959 45.455 0.00 0.00 30.37 4.02
1547 2093 2.905415 TCTTGGCAATGAAGGTCCAT 57.095 45.000 0.00 0.00 0.00 3.41
1645 2191 0.597637 CCGCCAGATATCACCGTCAC 60.598 60.000 5.32 0.00 0.00 3.67
1679 2225 1.590525 CGCGCTGCTCCGGTAATTA 60.591 57.895 5.56 0.00 0.00 1.40
1680 2226 1.548973 CGCGCTGCTCCGGTAATTAG 61.549 60.000 5.56 0.00 0.00 1.73
1699 2245 1.784525 GTGTTCTCCACTCCGTTCAG 58.215 55.000 0.00 0.00 41.11 3.02
1702 2248 1.614413 GTTCTCCACTCCGTTCAGTCT 59.386 52.381 0.00 0.00 0.00 3.24
1705 2251 1.213013 CCACTCCGTTCAGTCTCCG 59.787 63.158 0.00 0.00 0.00 4.63
1710 2256 1.811266 CCGTTCAGTCTCCGCCATG 60.811 63.158 0.00 0.00 0.00 3.66
1720 2266 1.989508 TCCGCCATGGAGCTCTTCA 60.990 57.895 18.40 4.20 43.74 3.02
1723 2269 1.607509 CCGCCATGGAGCTCTTCATAG 60.608 57.143 18.40 3.94 42.00 2.23
1754 2304 1.152546 AGCTCCCGGCCAACTTTTT 60.153 52.632 2.24 0.00 43.05 1.94
1758 2308 1.957877 CTCCCGGCCAACTTTTTACAA 59.042 47.619 2.24 0.00 0.00 2.41
1767 2317 5.741510 GGCCAACTTTTTACAAAAATGTTGC 59.258 36.000 24.24 20.66 40.57 4.17
1768 2318 6.404184 GGCCAACTTTTTACAAAAATGTTGCT 60.404 34.615 24.24 4.34 40.57 3.91
1770 2320 6.966066 CCAACTTTTTACAAAAATGTTGCTGG 59.034 34.615 24.24 15.63 40.57 4.85
1788 2338 3.269178 CTGGGAGAGCAGAAATCAGAAC 58.731 50.000 0.00 0.00 0.00 3.01
1810 2360 3.774216 CCTGATGTTTCTCTTCTCCCTCT 59.226 47.826 0.00 0.00 0.00 3.69
1814 2364 5.545723 TGATGTTTCTCTTCTCCCTCTCTTT 59.454 40.000 0.00 0.00 0.00 2.52
1816 2366 5.615289 TGTTTCTCTTCTCCCTCTCTTTTG 58.385 41.667 0.00 0.00 0.00 2.44
1817 2367 3.971245 TCTCTTCTCCCTCTCTTTTGC 57.029 47.619 0.00 0.00 0.00 3.68
1818 2368 2.232452 TCTCTTCTCCCTCTCTTTTGCG 59.768 50.000 0.00 0.00 0.00 4.85
1819 2369 1.971357 TCTTCTCCCTCTCTTTTGCGT 59.029 47.619 0.00 0.00 0.00 5.24
1820 2370 2.368875 TCTTCTCCCTCTCTTTTGCGTT 59.631 45.455 0.00 0.00 0.00 4.84
1821 2371 2.457366 TCTCCCTCTCTTTTGCGTTC 57.543 50.000 0.00 0.00 0.00 3.95
1984 2534 5.116882 CAGACCTATGTAAAACCTACAGCC 58.883 45.833 0.00 0.00 0.00 4.85
1987 2537 3.458487 CCTATGTAAAACCTACAGCCCCT 59.542 47.826 0.00 0.00 0.00 4.79
2007 2557 3.326747 CTGTCACAAACTACAGGTAGCC 58.673 50.000 6.38 0.00 39.55 3.93
2008 2558 2.969950 TGTCACAAACTACAGGTAGCCT 59.030 45.455 6.38 0.00 36.66 4.58
2026 2576 5.700402 AGCCTACCATGAAACTCATTACT 57.300 39.130 0.00 0.00 34.28 2.24
2027 2577 5.431765 AGCCTACCATGAAACTCATTACTG 58.568 41.667 0.00 0.00 34.28 2.74
2031 2581 5.505181 ACCATGAAACTCATTACTGGTCT 57.495 39.130 0.00 0.00 34.28 3.85
2034 2584 5.707298 CCATGAAACTCATTACTGGTCTTGT 59.293 40.000 0.00 0.00 34.28 3.16
2036 2586 6.861065 TGAAACTCATTACTGGTCTTGTTC 57.139 37.500 0.00 0.00 0.00 3.18
2038 2588 6.826231 TGAAACTCATTACTGGTCTTGTTCAA 59.174 34.615 0.00 0.00 0.00 2.69
2039 2589 6.867662 AACTCATTACTGGTCTTGTTCAAG 57.132 37.500 6.24 6.24 0.00 3.02
2041 2591 5.992217 ACTCATTACTGGTCTTGTTCAAGAC 59.008 40.000 27.44 27.44 46.36 3.01
2051 2610 6.952935 GTCTTGTTCAAGACGATCAACTAT 57.047 37.500 23.59 0.00 39.66 2.12
2347 2912 4.688021 CTCAGTGAGCTATTGTTCCTACC 58.312 47.826 7.33 0.00 0.00 3.18
2350 2915 5.897250 TCAGTGAGCTATTGTTCCTACCATA 59.103 40.000 0.00 0.00 0.00 2.74
2407 2974 9.967451 TTTCTTAACACTATTTATCCATGGACA 57.033 29.630 18.99 0.87 0.00 4.02
2514 3082 6.560003 TGGGTATGTCACTTGATAACTGAT 57.440 37.500 0.00 0.00 0.00 2.90
2584 3153 1.975680 GATTGCCCCTCTATCCCGTTA 59.024 52.381 0.00 0.00 0.00 3.18
2765 3334 1.688197 GAGAGGATGAGCCCAGAAGAG 59.312 57.143 0.00 0.00 37.37 2.85
2952 3528 9.520515 GTGGGATTGAGTATAATATTGGTGATT 57.479 33.333 0.00 0.00 0.00 2.57
3089 3665 6.940298 GGCAGATAAACAGGCCTATAACAATA 59.060 38.462 3.98 0.00 43.09 1.90
3140 3716 4.767409 TGTACAGCTTGTCAGACTATGTCT 59.233 41.667 1.31 0.00 44.44 3.41
3196 3772 3.066342 CCTGTGCAAATCAGTGATGATCC 59.934 47.826 6.34 0.00 0.00 3.36
3292 3868 2.045536 CTGCCTGCTTGGGGTCTC 60.046 66.667 0.00 0.00 36.00 3.36
3595 4171 3.786635 ACAATTAGACTAAGCCTCGCTG 58.213 45.455 0.73 0.00 39.62 5.18
3603 4179 2.036475 ACTAAGCCTCGCTGACATATGG 59.964 50.000 7.80 0.00 39.62 2.74
3682 4258 5.055265 TCATCACCCTTAACTCCAAACAA 57.945 39.130 0.00 0.00 0.00 2.83
3702 4278 9.798994 CAAACAAATCTAACTAGGACGTATACT 57.201 33.333 0.56 0.00 0.00 2.12
3728 4304 2.613223 GGATACTAGAAGGATTGGGCGC 60.613 54.545 0.00 0.00 0.00 6.53
3854 4431 3.153919 GGCTTTCTTGGTGGTGTGATTA 58.846 45.455 0.00 0.00 0.00 1.75
4028 4606 6.289834 TGTTACCGATTACTTTGAGAAACCA 58.710 36.000 0.00 0.00 0.00 3.67
4086 4664 2.558359 TCAACTGAATGAGAGCTCGTCA 59.442 45.455 8.37 12.64 0.00 4.35
4087 4665 3.005791 TCAACTGAATGAGAGCTCGTCAA 59.994 43.478 16.42 2.31 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
360 370 0.821517 TCGAAGCCGTATGTGGATGT 59.178 50.000 0.00 0.00 37.05 3.06
372 382 3.498397 TCAAGACATGTTTTCTCGAAGCC 59.502 43.478 0.00 0.00 0.00 4.35
373 383 4.732285 TCAAGACATGTTTTCTCGAAGC 57.268 40.909 0.00 0.00 0.00 3.86
374 384 6.082338 CCAATCAAGACATGTTTTCTCGAAG 58.918 40.000 0.00 0.00 0.00 3.79
375 385 5.562696 GCCAATCAAGACATGTTTTCTCGAA 60.563 40.000 0.00 0.00 0.00 3.71
377 387 4.161333 GCCAATCAAGACATGTTTTCTCG 58.839 43.478 0.00 0.00 0.00 4.04
378 388 4.919754 GTGCCAATCAAGACATGTTTTCTC 59.080 41.667 0.00 0.00 0.00 2.87
395 415 3.353029 CACCATCACGCGTGCCAA 61.353 61.111 33.63 18.10 0.00 4.52
403 423 1.739466 AGCAACAATAGCACCATCACG 59.261 47.619 0.00 0.00 0.00 4.35
435 455 3.786635 AGCAACAATACAACCGCAAAAA 58.213 36.364 0.00 0.00 0.00 1.94
436 456 3.067461 AGAGCAACAATACAACCGCAAAA 59.933 39.130 0.00 0.00 0.00 2.44
437 457 2.621055 AGAGCAACAATACAACCGCAAA 59.379 40.909 0.00 0.00 0.00 3.68
438 458 2.226330 AGAGCAACAATACAACCGCAA 58.774 42.857 0.00 0.00 0.00 4.85
439 459 1.890876 AGAGCAACAATACAACCGCA 58.109 45.000 0.00 0.00 0.00 5.69
440 460 2.989422 AAGAGCAACAATACAACCGC 57.011 45.000 0.00 0.00 0.00 5.68
441 461 5.338559 CGTAAAAAGAGCAACAATACAACCG 59.661 40.000 0.00 0.00 0.00 4.44
442 462 5.627780 CCGTAAAAAGAGCAACAATACAACC 59.372 40.000 0.00 0.00 0.00 3.77
443 463 6.203647 ACCGTAAAAAGAGCAACAATACAAC 58.796 36.000 0.00 0.00 0.00 3.32
444 464 6.380095 ACCGTAAAAAGAGCAACAATACAA 57.620 33.333 0.00 0.00 0.00 2.41
445 465 6.482641 TGTACCGTAAAAAGAGCAACAATACA 59.517 34.615 0.00 0.00 0.00 2.29
446 466 6.890558 TGTACCGTAAAAAGAGCAACAATAC 58.109 36.000 0.00 0.00 0.00 1.89
447 467 7.493743 TTGTACCGTAAAAAGAGCAACAATA 57.506 32.000 0.00 0.00 0.00 1.90
448 468 6.380095 TTGTACCGTAAAAAGAGCAACAAT 57.620 33.333 0.00 0.00 0.00 2.71
449 469 5.814764 TTGTACCGTAAAAAGAGCAACAA 57.185 34.783 0.00 0.00 0.00 2.83
450 470 5.278071 CCATTGTACCGTAAAAAGAGCAACA 60.278 40.000 0.00 0.00 0.00 3.33
451 471 5.151389 CCATTGTACCGTAAAAAGAGCAAC 58.849 41.667 0.00 0.00 0.00 4.17
452 472 4.822896 ACCATTGTACCGTAAAAAGAGCAA 59.177 37.500 0.00 0.00 0.00 3.91
453 473 4.214545 CACCATTGTACCGTAAAAAGAGCA 59.785 41.667 0.00 0.00 0.00 4.26
454 474 4.719040 CACCATTGTACCGTAAAAAGAGC 58.281 43.478 0.00 0.00 0.00 4.09
455 475 4.454504 AGCACCATTGTACCGTAAAAAGAG 59.545 41.667 0.00 0.00 0.00 2.85
456 476 4.391155 AGCACCATTGTACCGTAAAAAGA 58.609 39.130 0.00 0.00 0.00 2.52
457 477 4.759516 AGCACCATTGTACCGTAAAAAG 57.240 40.909 0.00 0.00 0.00 2.27
500 547 6.688813 CCACGTCATCGATGTCATATATACAG 59.311 42.308 24.09 11.09 40.62 2.74
581 636 6.795399 ACGTGAATTGTCTTGTCTTTCATTT 58.205 32.000 0.00 0.00 0.00 2.32
850 915 6.432936 CAGGCGTTGTTAATATCTACTCGTA 58.567 40.000 0.00 0.00 0.00 3.43
851 916 5.279384 CAGGCGTTGTTAATATCTACTCGT 58.721 41.667 0.00 0.00 0.00 4.18
852 917 4.148348 GCAGGCGTTGTTAATATCTACTCG 59.852 45.833 0.00 0.00 0.00 4.18
853 918 5.047847 TGCAGGCGTTGTTAATATCTACTC 58.952 41.667 0.00 0.00 0.00 2.59
854 919 5.018539 TGCAGGCGTTGTTAATATCTACT 57.981 39.130 0.00 0.00 0.00 2.57
855 920 5.679906 CATGCAGGCGTTGTTAATATCTAC 58.320 41.667 0.00 0.00 0.00 2.59
859 936 2.687425 TGCATGCAGGCGTTGTTAATAT 59.313 40.909 18.46 0.00 36.28 1.28
862 939 0.240678 CTGCATGCAGGCGTTGTTAA 59.759 50.000 35.39 2.69 40.17 2.01
991 1482 0.744771 GAGGTTGGCGAGGATGAACC 60.745 60.000 0.00 0.00 38.54 3.62
1124 1615 5.530519 TCGAGCTATTGCAGTTTGTTAAG 57.469 39.130 1.12 0.00 42.74 1.85
1131 1638 3.265791 CTTCCTTCGAGCTATTGCAGTT 58.734 45.455 1.12 0.00 42.74 3.16
1143 1650 3.288964 GTCTATCTCACCCTTCCTTCGA 58.711 50.000 0.00 0.00 0.00 3.71
1146 1653 1.757699 GCGTCTATCTCACCCTTCCTT 59.242 52.381 0.00 0.00 0.00 3.36
1149 1656 2.482142 CCAAGCGTCTATCTCACCCTTC 60.482 54.545 0.00 0.00 0.00 3.46
1150 1657 1.482593 CCAAGCGTCTATCTCACCCTT 59.517 52.381 0.00 0.00 0.00 3.95
1151 1658 1.115467 CCAAGCGTCTATCTCACCCT 58.885 55.000 0.00 0.00 0.00 4.34
1152 1659 0.530870 GCCAAGCGTCTATCTCACCC 60.531 60.000 0.00 0.00 0.00 4.61
1155 1662 2.067365 TAGGCCAAGCGTCTATCTCA 57.933 50.000 5.01 0.00 0.00 3.27
1156 1663 2.362717 AGTTAGGCCAAGCGTCTATCTC 59.637 50.000 5.01 0.00 0.00 2.75
1159 1666 2.108168 TCAGTTAGGCCAAGCGTCTAT 58.892 47.619 5.01 0.00 0.00 1.98
1161 1668 0.685097 TTCAGTTAGGCCAAGCGTCT 59.315 50.000 5.01 0.00 0.00 4.18
1164 1671 0.955428 TGCTTCAGTTAGGCCAAGCG 60.955 55.000 15.98 0.00 43.55 4.68
1166 1673 2.421424 GACATGCTTCAGTTAGGCCAAG 59.579 50.000 5.01 0.00 0.00 3.61
1168 1675 1.630369 AGACATGCTTCAGTTAGGCCA 59.370 47.619 5.01 0.00 0.00 5.36
1365 1903 1.098712 TTGGTGGTCGTGGAGTTTGC 61.099 55.000 0.00 0.00 0.00 3.68
1366 1904 1.384525 TTTGGTGGTCGTGGAGTTTG 58.615 50.000 0.00 0.00 0.00 2.93
1367 1905 2.158667 AGATTTGGTGGTCGTGGAGTTT 60.159 45.455 0.00 0.00 0.00 2.66
1371 1909 1.348064 AGAGATTTGGTGGTCGTGGA 58.652 50.000 0.00 0.00 0.00 4.02
1373 1911 2.093973 AGCTAGAGATTTGGTGGTCGTG 60.094 50.000 0.00 0.00 0.00 4.35
1376 1914 2.284190 GCAGCTAGAGATTTGGTGGTC 58.716 52.381 0.00 0.00 31.91 4.02
1379 1917 2.033049 GCATGCAGCTAGAGATTTGGTG 59.967 50.000 14.21 0.00 41.15 4.17
1380 1918 2.295885 GCATGCAGCTAGAGATTTGGT 58.704 47.619 14.21 0.00 41.15 3.67
1384 1922 3.349927 TGTTTGCATGCAGCTAGAGATT 58.650 40.909 21.50 0.00 45.94 2.40
1398 1940 5.221702 TGCCATAGCTATAGAGATGTTTGCA 60.222 40.000 5.77 7.95 40.80 4.08
1399 1941 5.240891 TGCCATAGCTATAGAGATGTTTGC 58.759 41.667 5.77 5.71 40.80 3.68
1402 1944 6.864151 TGATGCCATAGCTATAGAGATGTT 57.136 37.500 5.77 0.00 40.80 2.71
1403 1945 6.212187 TGTTGATGCCATAGCTATAGAGATGT 59.788 38.462 5.77 0.00 40.80 3.06
1404 1946 6.637657 TGTTGATGCCATAGCTATAGAGATG 58.362 40.000 5.77 5.69 40.80 2.90
1405 1947 6.629963 GCTGTTGATGCCATAGCTATAGAGAT 60.630 42.308 5.77 0.00 40.80 2.75
1406 1948 5.337089 GCTGTTGATGCCATAGCTATAGAGA 60.337 44.000 5.77 0.00 40.80 3.10
1407 1949 4.869297 GCTGTTGATGCCATAGCTATAGAG 59.131 45.833 5.77 0.00 40.80 2.43
1444 1990 2.515523 GATGCATGAGCCCAGCGT 60.516 61.111 2.46 0.00 41.13 5.07
1446 1992 0.822164 AAAAGATGCATGAGCCCAGC 59.178 50.000 2.46 0.00 41.13 4.85
1447 1993 6.433404 AGAATATAAAAGATGCATGAGCCCAG 59.567 38.462 2.46 0.00 41.13 4.45
1448 1994 6.309357 AGAATATAAAAGATGCATGAGCCCA 58.691 36.000 2.46 0.00 41.13 5.36
1449 1995 6.127786 GGAGAATATAAAAGATGCATGAGCCC 60.128 42.308 2.46 0.00 41.13 5.19
1450 1996 6.127786 GGGAGAATATAAAAGATGCATGAGCC 60.128 42.308 2.46 0.00 41.13 4.70
1451 1997 6.402983 CGGGAGAATATAAAAGATGCATGAGC 60.403 42.308 2.46 0.00 42.57 4.26
1452 1998 6.652481 ACGGGAGAATATAAAAGATGCATGAG 59.348 38.462 2.46 0.00 0.00 2.90
1454 2000 6.128172 GGACGGGAGAATATAAAAGATGCATG 60.128 42.308 2.46 0.00 0.00 4.06
1455 2001 5.940470 GGACGGGAGAATATAAAAGATGCAT 59.060 40.000 0.00 0.00 0.00 3.96
1456 2002 5.305585 GGACGGGAGAATATAAAAGATGCA 58.694 41.667 0.00 0.00 0.00 3.96
1457 2003 4.389077 CGGACGGGAGAATATAAAAGATGC 59.611 45.833 0.00 0.00 0.00 3.91
1458 2004 5.779922 TCGGACGGGAGAATATAAAAGATG 58.220 41.667 0.00 0.00 0.00 2.90
1459 2005 6.437793 AGATCGGACGGGAGAATATAAAAGAT 59.562 38.462 0.00 0.00 0.00 2.40
1460 2006 5.773680 AGATCGGACGGGAGAATATAAAAGA 59.226 40.000 0.00 0.00 0.00 2.52
1461 2007 6.026947 AGATCGGACGGGAGAATATAAAAG 57.973 41.667 0.00 0.00 0.00 2.27
1462 2008 6.415206 AAGATCGGACGGGAGAATATAAAA 57.585 37.500 0.00 0.00 0.00 1.52
1463 2009 6.041182 TCAAAGATCGGACGGGAGAATATAAA 59.959 38.462 0.00 0.00 0.00 1.40
1464 2010 5.537295 TCAAAGATCGGACGGGAGAATATAA 59.463 40.000 0.00 0.00 0.00 0.98
1465 2011 5.074804 TCAAAGATCGGACGGGAGAATATA 58.925 41.667 0.00 0.00 0.00 0.86
1466 2012 3.895656 TCAAAGATCGGACGGGAGAATAT 59.104 43.478 0.00 0.00 0.00 1.28
1467 2013 3.293337 TCAAAGATCGGACGGGAGAATA 58.707 45.455 0.00 0.00 0.00 1.75
1468 2014 2.108168 TCAAAGATCGGACGGGAGAAT 58.892 47.619 0.00 0.00 0.00 2.40
1469 2015 1.552578 TCAAAGATCGGACGGGAGAA 58.447 50.000 0.00 0.00 0.00 2.87
1470 2016 1.476891 CTTCAAAGATCGGACGGGAGA 59.523 52.381 0.00 0.00 0.00 3.71
1471 2017 1.204941 ACTTCAAAGATCGGACGGGAG 59.795 52.381 0.00 0.00 0.00 4.30
1472 2018 1.263356 ACTTCAAAGATCGGACGGGA 58.737 50.000 0.00 0.00 0.00 5.14
1473 2019 2.953466 TACTTCAAAGATCGGACGGG 57.047 50.000 0.00 0.00 0.00 5.28
1474 2020 3.782046 ACATACTTCAAAGATCGGACGG 58.218 45.455 0.00 0.00 0.00 4.79
1475 2021 3.797256 GGACATACTTCAAAGATCGGACG 59.203 47.826 0.00 0.00 0.00 4.79
1476 2022 4.806247 CAGGACATACTTCAAAGATCGGAC 59.194 45.833 0.00 0.00 0.00 4.79
1477 2023 4.709886 TCAGGACATACTTCAAAGATCGGA 59.290 41.667 0.00 0.00 0.00 4.55
1478 2024 4.806247 GTCAGGACATACTTCAAAGATCGG 59.194 45.833 0.00 0.00 0.00 4.18
1479 2025 5.410924 TGTCAGGACATACTTCAAAGATCG 58.589 41.667 0.00 0.00 36.21 3.69
1480 2026 6.402222 ACTGTCAGGACATACTTCAAAGATC 58.598 40.000 4.53 0.00 41.01 2.75
1481 2027 6.365970 ACTGTCAGGACATACTTCAAAGAT 57.634 37.500 4.53 0.00 41.01 2.40
1482 2028 5.808366 ACTGTCAGGACATACTTCAAAGA 57.192 39.130 4.53 0.00 41.01 2.52
1486 2032 9.588096 ACATATATACTGTCAGGACATACTTCA 57.412 33.333 4.53 0.00 41.01 3.02
1488 2034 9.815306 AGACATATATACTGTCAGGACATACTT 57.185 33.333 18.99 0.00 44.37 2.24
1489 2035 9.815306 AAGACATATATACTGTCAGGACATACT 57.185 33.333 18.99 0.00 44.37 2.12
1490 2036 9.847706 CAAGACATATATACTGTCAGGACATAC 57.152 37.037 18.99 0.00 44.37 2.39
1491 2037 9.588096 ACAAGACATATATACTGTCAGGACATA 57.412 33.333 18.99 0.00 44.37 2.29
1492 2038 8.484214 ACAAGACATATATACTGTCAGGACAT 57.516 34.615 18.99 0.00 44.37 3.06
1493 2039 7.898014 ACAAGACATATATACTGTCAGGACA 57.102 36.000 18.99 1.70 44.37 4.02
1494 2040 7.169982 GCAACAAGACATATATACTGTCAGGAC 59.830 40.741 18.99 0.00 44.37 3.85
1495 2041 7.210174 GCAACAAGACATATATACTGTCAGGA 58.790 38.462 18.99 0.00 44.37 3.86
1496 2042 6.425114 GGCAACAAGACATATATACTGTCAGG 59.575 42.308 18.99 14.67 44.37 3.86
1497 2043 7.212976 AGGCAACAAGACATATATACTGTCAG 58.787 38.462 18.99 0.00 42.05 3.51
1498 2044 7.069950 AGAGGCAACAAGACATATATACTGTCA 59.930 37.037 18.99 0.00 42.05 3.58
1499 2045 7.437748 AGAGGCAACAAGACATATATACTGTC 58.562 38.462 13.25 13.25 40.77 3.51
1500 2046 7.366847 AGAGGCAACAAGACATATATACTGT 57.633 36.000 0.00 0.00 41.41 3.55
1501 2047 7.928167 TGAAGAGGCAACAAGACATATATACTG 59.072 37.037 0.00 0.00 41.41 2.74
1502 2048 8.023021 TGAAGAGGCAACAAGACATATATACT 57.977 34.615 0.00 0.00 41.41 2.12
1503 2049 8.839310 ATGAAGAGGCAACAAGACATATATAC 57.161 34.615 0.00 0.00 41.41 1.47
1504 2050 8.874156 AGATGAAGAGGCAACAAGACATATATA 58.126 33.333 0.00 0.00 41.41 0.86
1505 2051 7.743749 AGATGAAGAGGCAACAAGACATATAT 58.256 34.615 0.00 0.00 41.41 0.86
1506 2052 7.129457 AGATGAAGAGGCAACAAGACATATA 57.871 36.000 0.00 0.00 41.41 0.86
1507 2053 5.999044 AGATGAAGAGGCAACAAGACATAT 58.001 37.500 0.00 0.00 41.41 1.78
1508 2054 5.426689 AGATGAAGAGGCAACAAGACATA 57.573 39.130 0.00 0.00 41.41 2.29
1509 2055 4.298103 AGATGAAGAGGCAACAAGACAT 57.702 40.909 0.00 0.00 41.41 3.06
1510 2056 3.777106 AGATGAAGAGGCAACAAGACA 57.223 42.857 0.00 0.00 41.41 3.41
1511 2057 3.190118 CCAAGATGAAGAGGCAACAAGAC 59.810 47.826 0.00 0.00 41.41 3.01
1512 2058 3.415212 CCAAGATGAAGAGGCAACAAGA 58.585 45.455 0.00 0.00 41.41 3.02
1513 2059 2.094854 GCCAAGATGAAGAGGCAACAAG 60.095 50.000 0.00 0.00 46.26 3.16
1514 2060 1.888512 GCCAAGATGAAGAGGCAACAA 59.111 47.619 0.00 0.00 46.26 2.83
1515 2061 1.538047 GCCAAGATGAAGAGGCAACA 58.462 50.000 0.00 0.00 46.26 3.33
1526 2072 2.449464 TGGACCTTCATTGCCAAGATG 58.551 47.619 0.00 0.00 0.00 2.90
1645 2191 2.588877 CGGGAGTATTGGCAGGCG 60.589 66.667 0.00 0.00 0.00 5.52
1654 2200 3.917760 GGAGCAGCGCGGGAGTAT 61.918 66.667 8.83 0.00 0.00 2.12
1680 2226 1.068741 ACTGAACGGAGTGGAGAACAC 59.931 52.381 0.00 0.00 45.00 3.32
1702 2248 1.340399 ATGAAGAGCTCCATGGCGGA 61.340 55.000 10.93 0.00 43.61 5.54
1705 2251 1.521580 GCTATGAAGAGCTCCATGGC 58.478 55.000 19.93 19.93 39.42 4.40
1713 2259 2.848691 AGCATCCAAGCTATGAAGAGC 58.151 47.619 0.00 0.00 44.50 4.09
1720 2266 2.566724 GGAGCTCTAGCATCCAAGCTAT 59.433 50.000 14.64 0.00 44.77 2.97
1723 2269 0.250252 GGGAGCTCTAGCATCCAAGC 60.250 60.000 14.64 1.25 45.16 4.01
1725 2275 1.402896 CCGGGAGCTCTAGCATCCAA 61.403 60.000 14.64 0.00 45.16 3.53
1767 2317 3.269178 GTTCTGATTTCTGCTCTCCCAG 58.731 50.000 0.00 0.00 0.00 4.45
1768 2318 2.026822 GGTTCTGATTTCTGCTCTCCCA 60.027 50.000 0.00 0.00 0.00 4.37
1770 2320 3.055530 TCAGGTTCTGATTTCTGCTCTCC 60.056 47.826 0.00 0.00 35.39 3.71
1788 2338 3.774216 AGAGGGAGAAGAGAAACATCAGG 59.226 47.826 0.00 0.00 0.00 3.86
1796 2346 3.306364 CGCAAAAGAGAGGGAGAAGAGAA 60.306 47.826 0.00 0.00 0.00 2.87
1810 2360 5.811399 TCTGAGAAAAAGAACGCAAAAGA 57.189 34.783 0.00 0.00 0.00 2.52
1814 2364 3.304659 GGCATCTGAGAAAAAGAACGCAA 60.305 43.478 0.00 0.00 31.25 4.85
1816 2366 2.226437 TGGCATCTGAGAAAAAGAACGC 59.774 45.455 0.00 0.00 0.00 4.84
1817 2367 4.488126 TTGGCATCTGAGAAAAAGAACG 57.512 40.909 0.00 0.00 0.00 3.95
1818 2368 5.225642 CCTTTGGCATCTGAGAAAAAGAAC 58.774 41.667 10.13 0.00 0.00 3.01
1819 2369 4.281688 CCCTTTGGCATCTGAGAAAAAGAA 59.718 41.667 10.13 0.00 0.00 2.52
1820 2370 3.828451 CCCTTTGGCATCTGAGAAAAAGA 59.172 43.478 10.13 0.00 0.00 2.52
1821 2371 3.575687 ACCCTTTGGCATCTGAGAAAAAG 59.424 43.478 0.00 0.00 33.59 2.27
1876 2426 0.931468 TCCCTCCTCCGACCATCTTA 59.069 55.000 0.00 0.00 0.00 2.10
1906 2456 3.114616 CTTGCGCAGAGGTCCACG 61.115 66.667 11.31 0.00 0.00 4.94
1987 2537 2.969950 AGGCTACCTGTAGTTTGTGACA 59.030 45.455 6.22 0.00 35.65 3.58
2007 2557 6.644347 AGACCAGTAATGAGTTTCATGGTAG 58.356 40.000 0.00 0.00 37.15 3.18
2008 2558 6.620877 AGACCAGTAATGAGTTTCATGGTA 57.379 37.500 0.00 0.00 37.15 3.25
2012 2562 6.998074 TGAACAAGACCAGTAATGAGTTTCAT 59.002 34.615 0.00 0.00 39.09 2.57
2015 2565 7.054124 TCTTGAACAAGACCAGTAATGAGTTT 58.946 34.615 12.40 0.00 42.06 2.66
2031 2581 7.552459 TCCATATAGTTGATCGTCTTGAACAA 58.448 34.615 0.00 0.00 37.07 2.83
2034 2584 8.204160 ACAATCCATATAGTTGATCGTCTTGAA 58.796 33.333 0.00 0.00 0.00 2.69
2036 2586 7.953158 ACAATCCATATAGTTGATCGTCTTG 57.047 36.000 0.00 0.00 0.00 3.02
2038 2588 8.964476 AAAACAATCCATATAGTTGATCGTCT 57.036 30.769 0.00 0.00 0.00 4.18
2039 2589 9.046296 AGAAAACAATCCATATAGTTGATCGTC 57.954 33.333 0.00 0.00 0.00 4.20
2041 2591 9.045223 TCAGAAAACAATCCATATAGTTGATCG 57.955 33.333 0.00 0.00 0.00 3.69
2051 2610 7.950512 TCTTTTGCTTCAGAAAACAATCCATA 58.049 30.769 0.29 0.00 0.00 2.74
2338 2899 7.719633 GCAATTAAGGAAGATATGGTAGGAACA 59.280 37.037 0.00 0.00 0.00 3.18
2347 2912 7.496529 TTTCGAGGCAATTAAGGAAGATATG 57.503 36.000 0.00 0.00 0.00 1.78
2350 2915 7.410120 AAATTTCGAGGCAATTAAGGAAGAT 57.590 32.000 0.00 0.00 0.00 2.40
2391 2957 4.703575 CCCTGCATGTCCATGGATAAATAG 59.296 45.833 19.62 13.75 38.47 1.73
2392 2958 4.353489 TCCCTGCATGTCCATGGATAAATA 59.647 41.667 19.62 4.84 38.47 1.40
2407 2974 1.973281 CTTTGCGGTGTCCCTGCAT 60.973 57.895 0.00 0.00 39.08 3.96
2514 3082 7.974504 AGGGTTCAGAGAGTTTGTTTTATAGA 58.025 34.615 0.00 0.00 0.00 1.98
2572 3141 7.013464 GGACATCATACCTATAACGGGATAGAG 59.987 44.444 7.27 1.85 32.00 2.43
2645 3214 8.694540 GCTTGTGATCTCATCCTGATATATAGT 58.305 37.037 0.00 0.00 0.00 2.12
3140 3716 3.868661 GCGGTATGATGTATGTTGACACA 59.131 43.478 0.00 0.00 37.31 3.72
3196 3772 7.128331 GCATTTCTATAGTTGTGCACATACAG 58.872 38.462 22.39 9.91 33.09 2.74
3292 3868 9.267084 GCTAAATAGGAGTCAAAAGGATAAGAG 57.733 37.037 0.00 0.00 0.00 2.85
3702 4278 6.380274 CGCCCAATCCTTCTAGTATCCTATAA 59.620 42.308 0.00 0.00 0.00 0.98
3820 4397 3.306472 AGAAAGCCCACTAAAACACCA 57.694 42.857 0.00 0.00 0.00 4.17
3854 4431 5.372343 TGGTGGATTAGCAGATAACACAT 57.628 39.130 0.00 0.00 32.05 3.21
3994 4572 0.035439 ATCGGTAACAACCAGCCTGG 60.035 55.000 9.83 9.83 45.02 4.45
4016 4594 8.289618 TCACTATTTTTCGATGGTTTCTCAAAG 58.710 33.333 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.