Multiple sequence alignment - TraesCS6D01G199900

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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 TraesCS6D01G199900 chr6D 100.000 7700 0 0 1 7700 277679483 277671784 0.000000e+00 14220.0
1 TraesCS6D01G199900 chr6B 97.185 4156 82 13 3563 7700 439405825 439401687 0.000000e+00 6994.0
2 TraesCS6D01G199900 chr6B 95.777 734 28 2 2796 3526 439406545 439405812 0.000000e+00 1181.0
3 TraesCS6D01G199900 chr6B 82.200 691 71 24 84 741 439463920 439463249 1.460000e-151 547.0
4 TraesCS6D01G199900 chr6B 86.937 444 32 13 1708 2140 696411244 696411672 6.990000e-130 475.0
5 TraesCS6D01G199900 chr6B 93.836 146 7 1 2190 2335 696411676 696411819 1.300000e-52 219.0
6 TraesCS6D01G199900 chr6B 94.286 35 2 0 428 462 54863909 54863943 4.000000e-03 54.7
7 TraesCS6D01G199900 chr6A 97.106 4146 92 5 3563 7700 400126934 400122809 0.000000e+00 6966.0
8 TraesCS6D01G199900 chr6A 89.981 2066 111 40 781 2801 400129605 400127591 0.000000e+00 2580.0
9 TraesCS6D01G199900 chr6A 92.754 690 32 6 2839 3526 400127594 400126921 0.000000e+00 981.0
10 TraesCS6D01G199900 chr6A 85.372 417 30 19 1 388 400131209 400130795 3.350000e-108 403.0
11 TraesCS6D01G199900 chr6A 86.364 66 9 0 699 764 400130231 400130166 1.070000e-08 73.1
12 TraesCS6D01G199900 chr6A 95.238 42 2 0 627 668 400130329 400130288 4.990000e-07 67.6
13 TraesCS6D01G199900 chr6A 94.286 35 2 0 428 462 28672928 28672962 4.000000e-03 54.7
14 TraesCS6D01G199900 chr6A 100.000 28 0 0 1684 1711 214804828 214804855 1.400000e-02 52.8
15 TraesCS6D01G199900 chr7A 87.879 66 8 0 422 487 169649352 169649287 2.300000e-10 78.7
16 TraesCS6D01G199900 chr7A 97.436 39 0 1 3524 3561 641455484 641455522 1.790000e-06 65.8
17 TraesCS6D01G199900 chr1A 95.349 43 2 0 3524 3566 571219695 571219737 1.390000e-07 69.4
18 TraesCS6D01G199900 chr1A 95.349 43 2 0 3524 3566 571259876 571259918 1.390000e-07 69.4
19 TraesCS6D01G199900 chr5D 97.500 40 0 1 3523 3561 284106078 284106039 4.990000e-07 67.6
20 TraesCS6D01G199900 chr4B 97.368 38 1 0 3524 3561 592546552 592546515 1.790000e-06 65.8
21 TraesCS6D01G199900 chr4B 94.737 38 0 2 1684 1720 389466800 389466764 3.000000e-04 58.4
22 TraesCS6D01G199900 chr2B 97.436 39 0 1 3524 3561 66491846 66491808 1.790000e-06 65.8
23 TraesCS6D01G199900 chr2D 95.122 41 0 2 3524 3562 37959912 37959872 6.450000e-06 63.9
24 TraesCS6D01G199900 chr2D 95.122 41 0 2 3524 3562 37986563 37986523 6.450000e-06 63.9
25 TraesCS6D01G199900 chr2A 95.122 41 0 2 3524 3562 42790591 42790551 6.450000e-06 63.9
26 TraesCS6D01G199900 chr2A 94.595 37 1 1 1683 1718 516743594 516743630 1.000000e-03 56.5
27 TraesCS6D01G199900 chr5A 100.000 30 0 0 1681 1710 553098660 553098689 1.000000e-03 56.5
28 TraesCS6D01G199900 chr1B 100.000 29 0 0 1683 1711 604574434 604574462 4.000000e-03 54.7
29 TraesCS6D01G199900 chr4D 100.000 28 0 0 1683 1710 319254381 319254354 1.400000e-02 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 TraesCS6D01G199900 chr6D 277671784 277679483 7699 True 14220.000000 14220 100.000000 1 7700 1 chr6D.!!$R1 7699
1 TraesCS6D01G199900 chr6B 439401687 439406545 4858 True 4087.500000 6994 96.481000 2796 7700 2 chr6B.!!$R2 4904
2 TraesCS6D01G199900 chr6B 439463249 439463920 671 True 547.000000 547 82.200000 84 741 1 chr6B.!!$R1 657
3 TraesCS6D01G199900 chr6B 696411244 696411819 575 False 347.000000 475 90.386500 1708 2335 2 chr6B.!!$F2 627
4 TraesCS6D01G199900 chr6A 400122809 400131209 8400 True 1845.116667 6966 91.135833 1 7700 6 chr6A.!!$R1 7699

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
417 447 0.249699 TGCTCGGTGATGTTGTCGTT 60.250 50.000 0.00 0.00 0.00 3.85 F
1377 2320 0.034476 TCTTGTGGCTGACAGCTCTG 59.966 55.000 25.92 15.23 41.99 3.35 F
1577 2520 0.107831 CCAACTTGAACGGGACCTCA 59.892 55.000 0.00 0.00 0.00 3.86 F
2335 3293 0.112218 AAGCACAGGGTGTATGCCAA 59.888 50.000 0.00 0.00 40.33 4.52 F
3549 4532 0.392998 GCAGCAAGCCTGGTAAGCTA 60.393 55.000 8.22 0.00 40.49 3.32 F
4531 5521 1.269726 CGAAGGCACCAACAGCAAAAT 60.270 47.619 0.00 0.00 0.00 1.82 F
5076 6076 2.642171 TCCCTGGTACACCTGAGAAT 57.358 50.000 6.84 0.00 37.15 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 2506 0.395312 GGTTCTGAGGTCCCGTTCAA 59.605 55.000 0.00 0.00 0.00 2.69 R
2949 3928 0.029300 TCACACTTTTGAGCAAGCGC 59.971 50.000 0.00 0.00 38.99 5.92 R
3530 4513 0.392998 TAGCTTACCAGGCTTGCTGC 60.393 55.000 10.05 0.00 40.74 5.25 R
4111 5095 1.202627 GCTGGCTCCTCCTTATCTGTG 60.203 57.143 0.00 0.00 35.26 3.66 R
4696 5689 3.188786 CGGTAACTCTGCAGCGCC 61.189 66.667 9.47 5.39 0.00 6.53 R
5656 6659 1.348064 TGAATCGTGTCCAGAAGGGT 58.652 50.000 0.00 0.00 38.11 4.34 R
6763 7785 0.457337 CGCAAGCAGCCTCCAAATTC 60.457 55.000 0.00 0.00 41.38 2.17 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
121 122 3.827008 TGCTTCTCTTCCGCATCTATT 57.173 42.857 0.00 0.00 0.00 1.73
123 124 3.118629 TGCTTCTCTTCCGCATCTATTGT 60.119 43.478 0.00 0.00 0.00 2.71
126 127 4.471904 TCTCTTCCGCATCTATTGTTGT 57.528 40.909 0.00 0.00 0.00 3.32
156 157 1.671850 CGCGTATGTTGGTGTTCCTCT 60.672 52.381 0.00 0.00 34.23 3.69
214 224 2.472029 TCCTCTTCTCTCCCACAATCC 58.528 52.381 0.00 0.00 0.00 3.01
217 227 3.201708 CCTCTTCTCTCCCACAATCCATT 59.798 47.826 0.00 0.00 0.00 3.16
218 228 4.450053 CTCTTCTCTCCCACAATCCATTC 58.550 47.826 0.00 0.00 0.00 2.67
219 229 2.988010 TCTCTCCCACAATCCATTCG 57.012 50.000 0.00 0.00 0.00 3.34
221 231 0.617935 TCTCCCACAATCCATTCGCA 59.382 50.000 0.00 0.00 0.00 5.10
222 232 0.734889 CTCCCACAATCCATTCGCAC 59.265 55.000 0.00 0.00 0.00 5.34
223 233 0.327924 TCCCACAATCCATTCGCACT 59.672 50.000 0.00 0.00 0.00 4.40
225 235 0.452987 CCACAATCCATTCGCACTGG 59.547 55.000 0.00 0.00 34.93 4.00
226 236 1.167851 CACAATCCATTCGCACTGGT 58.832 50.000 0.00 0.00 35.19 4.00
228 238 1.271325 ACAATCCATTCGCACTGGTCA 60.271 47.619 0.00 0.00 35.19 4.02
230 240 1.959042 ATCCATTCGCACTGGTCATC 58.041 50.000 0.00 0.00 35.19 2.92
231 241 0.612744 TCCATTCGCACTGGTCATCA 59.387 50.000 0.00 0.00 35.19 3.07
298 328 1.225168 ACCCATCTCCTCATCCTCCAT 59.775 52.381 0.00 0.00 0.00 3.41
334 364 4.008933 GGTGCAGAGGAGCGTGGT 62.009 66.667 0.00 0.00 37.31 4.16
337 367 3.695606 GCAGAGGAGCGTGGTGGA 61.696 66.667 0.00 0.00 0.00 4.02
340 370 1.305297 AGAGGAGCGTGGTGGATCA 60.305 57.895 0.00 0.00 0.00 2.92
363 393 0.455464 CCGATGCTGCAACATGTGTG 60.455 55.000 7.46 1.20 0.00 3.82
385 415 3.006537 GTGTGTTGTAAGAGGTGGAGCTA 59.993 47.826 0.00 0.00 0.00 3.32
388 418 4.081642 GTGTTGTAAGAGGTGGAGCTATGA 60.082 45.833 0.00 0.00 0.00 2.15
390 420 2.688446 TGTAAGAGGTGGAGCTATGACG 59.312 50.000 0.00 0.00 0.00 4.35
413 443 1.672356 GGCTGCTCGGTGATGTTGT 60.672 57.895 0.00 0.00 0.00 3.32
417 447 0.249699 TGCTCGGTGATGTTGTCGTT 60.250 50.000 0.00 0.00 0.00 3.85
422 452 2.413796 TCGGTGATGTTGTCGTTATTGC 59.586 45.455 0.00 0.00 0.00 3.56
428 458 2.422597 TGTTGTCGTTATTGCTGGAGG 58.577 47.619 0.00 0.00 0.00 4.30
432 462 2.000447 GTCGTTATTGCTGGAGGTGAC 59.000 52.381 0.00 0.00 0.00 3.67
451 481 3.938334 TGACGACAACATGGTCCATATTG 59.062 43.478 19.37 19.37 34.81 1.90
454 484 3.128415 CGACAACATGGTCCATATTGCAA 59.872 43.478 20.63 0.00 32.22 4.08
455 485 4.202040 CGACAACATGGTCCATATTGCAAT 60.202 41.667 20.63 17.56 32.22 3.56
456 486 5.013568 ACAACATGGTCCATATTGCAATG 57.986 39.130 20.63 7.66 32.22 2.82
457 487 4.141892 ACAACATGGTCCATATTGCAATGG 60.142 41.667 20.63 16.94 46.69 3.16
458 488 2.967201 ACATGGTCCATATTGCAATGGG 59.033 45.455 22.27 21.10 45.57 4.00
459 489 2.844654 TGGTCCATATTGCAATGGGT 57.155 45.000 22.27 5.15 45.57 4.51
460 490 2.386779 TGGTCCATATTGCAATGGGTG 58.613 47.619 22.27 16.14 45.57 4.61
461 491 2.024560 TGGTCCATATTGCAATGGGTGA 60.025 45.455 22.27 9.96 45.57 4.02
462 492 2.362077 GGTCCATATTGCAATGGGTGAC 59.638 50.000 22.27 19.42 45.57 3.67
518 548 1.308069 CCCCACGTCATTCAAGCTGG 61.308 60.000 0.00 0.00 0.00 4.85
521 551 1.511850 CACGTCATTCAAGCTGGTGA 58.488 50.000 0.00 0.00 0.00 4.02
526 556 2.421424 GTCATTCAAGCTGGTGATGACC 59.579 50.000 20.47 0.00 43.48 4.02
537 570 2.479566 GTGATGACCACACCATGTCT 57.520 50.000 0.00 0.00 45.03 3.41
580 613 3.732212 AGCACATGTCATGTATACGCAT 58.268 40.909 18.00 5.44 42.70 4.73
583 616 5.934043 AGCACATGTCATGTATACGCATAAT 59.066 36.000 18.00 0.00 42.70 1.28
623 656 2.693069 CAAACCAACCAAGCACAACAA 58.307 42.857 0.00 0.00 0.00 2.83
656 998 1.303806 TGACGTGGTGGGAGATCGA 60.304 57.895 0.00 0.00 0.00 3.59
669 1011 1.331138 GAGATCGAACGGATGTCTCGT 59.669 52.381 0.00 0.00 41.13 4.18
671 1013 0.525668 ATCGAACGGATGTCTCGTGC 60.526 55.000 0.00 0.00 40.96 5.34
673 1015 2.789203 GAACGGATGTCTCGTGCGC 61.789 63.158 0.00 0.00 40.96 6.09
674 1016 4.796231 ACGGATGTCTCGTGCGCC 62.796 66.667 4.18 0.00 37.72 6.53
675 1017 4.794439 CGGATGTCTCGTGCGCCA 62.794 66.667 4.18 0.00 0.00 5.69
676 1018 2.202932 GGATGTCTCGTGCGCCAT 60.203 61.111 4.18 0.00 0.00 4.40
708 1050 1.784525 GAGGCGGTCGATCTAATTGG 58.215 55.000 0.00 0.00 0.00 3.16
711 1053 1.597663 GGCGGTCGATCTAATTGGTTG 59.402 52.381 0.00 0.00 0.00 3.77
712 1054 1.597663 GCGGTCGATCTAATTGGTTGG 59.402 52.381 0.00 0.00 0.00 3.77
755 1140 2.169330 AGGTAAACGTCCTCAGTCTCC 58.831 52.381 0.00 0.00 0.00 3.71
778 1285 4.381612 CGAGAGAAGTACTTTGCACCCATA 60.382 45.833 10.02 0.00 0.00 2.74
860 1789 1.006832 CGGTGAGGCATCCGTAAAAG 58.993 55.000 0.00 0.00 41.58 2.27
1156 2097 2.117423 CCACCTCCCCGCCTTTTT 59.883 61.111 0.00 0.00 0.00 1.94
1173 2114 4.626172 CCTTTTTCCACGACTAAGAGCTAC 59.374 45.833 0.00 0.00 0.00 3.58
1185 2126 3.452024 GAGCTACGACCGAGACCGC 62.452 68.421 0.00 0.00 0.00 5.68
1186 2127 4.549516 GCTACGACCGAGACCGCC 62.550 72.222 0.00 0.00 0.00 6.13
1225 2166 2.282462 CAAAGGGAAGCAGGGCGT 60.282 61.111 0.00 0.00 0.00 5.68
1226 2167 1.903404 CAAAGGGAAGCAGGGCGTT 60.903 57.895 0.00 0.00 0.00 4.84
1263 2204 2.024871 GGCGACGAGGTGAGATCG 59.975 66.667 0.00 0.00 45.54 3.69
1269 2210 1.193650 GACGAGGTGAGATCGATCGAG 59.806 57.143 23.84 8.71 42.76 4.04
1274 2215 1.059173 GTGAGATCGATCGAGCATGC 58.941 55.000 32.33 21.39 32.23 4.06
1292 2235 1.802314 CGTACACGGCGTGCATACA 60.802 57.895 37.21 16.19 36.98 2.29
1293 2236 1.143373 CGTACACGGCGTGCATACAT 61.143 55.000 37.21 20.57 36.98 2.29
1294 2237 1.003851 GTACACGGCGTGCATACATT 58.996 50.000 37.21 19.85 36.98 2.71
1297 2240 0.247655 CACGGCGTGCATACATTGAC 60.248 55.000 28.30 0.00 0.00 3.18
1342 2285 4.786425 AGGACAGCTTATTTTCCCTGATC 58.214 43.478 0.00 0.00 0.00 2.92
1377 2320 0.034476 TCTTGTGGCTGACAGCTCTG 59.966 55.000 25.92 15.23 41.99 3.35
1414 2357 1.553308 GCGTACGTGATCAAGGTACC 58.447 55.000 22.76 2.73 43.96 3.34
1434 2377 4.810345 ACCCTTTTATCCAAGTTCCAACA 58.190 39.130 0.00 0.00 0.00 3.33
1439 2382 7.832187 CCCTTTTATCCAAGTTCCAACATACTA 59.168 37.037 0.00 0.00 0.00 1.82
1441 2384 9.449719 CTTTTATCCAAGTTCCAACATACTACT 57.550 33.333 0.00 0.00 0.00 2.57
1502 2445 1.215647 CGGCGCCTGTTCTTACTCT 59.784 57.895 26.68 0.00 0.00 3.24
1563 2506 2.355986 TACCTGATCGGCGCCAACT 61.356 57.895 28.98 10.04 35.61 3.16
1575 2518 1.228154 GCCAACTTGAACGGGACCT 60.228 57.895 0.00 0.00 0.00 3.85
1577 2520 0.107831 CCAACTTGAACGGGACCTCA 59.892 55.000 0.00 0.00 0.00 3.86
1605 2548 3.147595 CCGTCATCTCCCTCGGCA 61.148 66.667 0.00 0.00 36.68 5.69
1625 2568 1.963338 GCAGAAGCGCTTCAGGTGT 60.963 57.895 42.14 24.71 41.84 4.16
1627 2570 1.963338 AGAAGCGCTTCAGGTGTGC 60.963 57.895 42.14 20.71 41.84 4.57
1651 2594 6.576442 GCAATAACACTCCCTCCTCTTCTTAA 60.576 42.308 0.00 0.00 0.00 1.85
1657 2600 7.985589 ACACTCCCTCCTCTTCTTAAATTTTA 58.014 34.615 0.00 0.00 0.00 1.52
1658 2601 8.615705 ACACTCCCTCCTCTTCTTAAATTTTAT 58.384 33.333 0.00 0.00 0.00 1.40
1660 2603 9.688091 ACTCCCTCCTCTTCTTAAATTTTATTC 57.312 33.333 0.00 0.00 0.00 1.75
1662 2605 8.846804 TCCCTCCTCTTCTTAAATTTTATTCCT 58.153 33.333 0.00 0.00 0.00 3.36
1682 2625 7.628769 TTCCTTTTTACTACCAAAACTTCGT 57.371 32.000 0.00 0.00 0.00 3.85
1683 2626 8.729805 TTCCTTTTTACTACCAAAACTTCGTA 57.270 30.769 0.00 0.00 0.00 3.43
1684 2627 8.907222 TCCTTTTTACTACCAAAACTTCGTAT 57.093 30.769 0.00 0.00 0.00 3.06
1696 2639 8.899771 ACCAAAACTTCGTATATTTAGGAATGG 58.100 33.333 11.33 11.33 36.08 3.16
1697 2640 9.116067 CCAAAACTTCGTATATTTAGGAATGGA 57.884 33.333 8.89 0.00 34.00 3.41
1699 2642 8.904099 AAACTTCGTATATTTAGGAATGGAGG 57.096 34.615 0.00 0.00 33.17 4.30
1705 2648 8.120538 TCGTATATTTAGGAATGGAGGGAGTAT 58.879 37.037 0.00 0.00 0.00 2.12
1710 2653 4.917906 AGGAATGGAGGGAGTATAATGC 57.082 45.455 0.00 0.00 0.00 3.56
1715 2658 2.634940 TGGAGGGAGTATAATGCTGCTC 59.365 50.000 0.00 0.00 0.00 4.26
1754 2697 6.986817 AGGTGTTCATATAGTTCATACTGTGC 59.013 38.462 0.00 0.00 35.78 4.57
1880 2827 5.389935 CGAACAGCTTCCTACACATTCTTTC 60.390 44.000 0.00 0.00 0.00 2.62
1943 2894 9.658799 TTTCTTCTCCTAGAACATAGAAATGTG 57.341 33.333 0.00 0.00 45.79 3.21
2142 3098 9.959721 AACAAAAATGTCTCAGTATATACCACT 57.040 29.630 9.32 0.00 0.00 4.00
2150 3106 5.545335 TCTCAGTATATACCACTACCTCCGA 59.455 44.000 9.32 0.00 0.00 4.55
2151 3107 6.215023 TCTCAGTATATACCACTACCTCCGAT 59.785 42.308 9.32 0.00 0.00 4.18
2155 3111 3.544698 ATACCACTACCTCCGATCCAT 57.455 47.619 0.00 0.00 0.00 3.41
2157 3113 3.544698 ACCACTACCTCCGATCCATAT 57.455 47.619 0.00 0.00 0.00 1.78
2160 3116 5.399991 ACCACTACCTCCGATCCATATTAA 58.600 41.667 0.00 0.00 0.00 1.40
2162 3118 6.500751 ACCACTACCTCCGATCCATATTAAAT 59.499 38.462 0.00 0.00 0.00 1.40
2164 3120 7.386851 CACTACCTCCGATCCATATTAAATGT 58.613 38.462 0.00 0.00 0.00 2.71
2165 3121 7.878127 CACTACCTCCGATCCATATTAAATGTT 59.122 37.037 0.00 0.00 0.00 2.71
2167 3123 6.837312 ACCTCCGATCCATATTAAATGTTGA 58.163 36.000 0.00 0.00 0.00 3.18
2168 3124 6.936900 ACCTCCGATCCATATTAAATGTTGAG 59.063 38.462 0.00 0.00 0.00 3.02
2169 3125 6.372659 CCTCCGATCCATATTAAATGTTGAGG 59.627 42.308 0.00 0.00 0.00 3.86
2171 3127 7.969004 TCCGATCCATATTAAATGTTGAGGTA 58.031 34.615 0.00 0.00 0.00 3.08
2172 3128 7.876068 TCCGATCCATATTAAATGTTGAGGTAC 59.124 37.037 0.00 0.00 0.00 3.34
2174 3130 9.923143 CGATCCATATTAAATGTTGAGGTACTA 57.077 33.333 0.00 0.00 41.55 1.82
2182 3138 8.749026 TTAAATGTTGAGGTACTAAAACCACA 57.251 30.769 0.00 0.00 41.55 4.17
2183 3139 7.648039 AAATGTTGAGGTACTAAAACCACAA 57.352 32.000 2.36 2.36 44.54 3.33
2187 3143 3.810941 TGAGGTACTAAAACCACAAAGCG 59.189 43.478 0.00 0.00 41.55 4.68
2189 3145 3.562557 AGGTACTAAAACCACAAAGCGTG 59.437 43.478 0.00 0.00 42.40 5.34
2191 3147 6.480689 AGGTACTAAAACCACAAAGCGTGAG 61.481 44.000 0.00 0.00 43.65 3.51
2218 3174 4.585879 TGAGTTAAATTAGCCGGCTCTTT 58.414 39.130 36.73 31.86 0.00 2.52
2222 3178 5.652452 AGTTAAATTAGCCGGCTCTTTGATT 59.348 36.000 36.73 22.28 0.00 2.57
2250 3206 3.440173 AGCGTGGTTCCAGTTTGAATATG 59.560 43.478 0.00 0.00 0.00 1.78
2291 3249 4.240888 CAATACGGCATGATGGAGTAGAG 58.759 47.826 0.00 0.00 0.00 2.43
2292 3250 2.073252 ACGGCATGATGGAGTAGAGA 57.927 50.000 0.00 0.00 0.00 3.10
2335 3293 0.112218 AAGCACAGGGTGTATGCCAA 59.888 50.000 0.00 0.00 40.33 4.52
2343 3301 2.781681 GGTGTATGCCAACCTACAGT 57.218 50.000 0.00 0.00 0.00 3.55
2344 3302 2.356135 GGTGTATGCCAACCTACAGTG 58.644 52.381 0.00 0.00 0.00 3.66
2345 3303 2.290071 GGTGTATGCCAACCTACAGTGT 60.290 50.000 0.00 0.00 0.00 3.55
2346 3304 3.408634 GTGTATGCCAACCTACAGTGTT 58.591 45.455 0.00 0.00 0.00 3.32
2347 3305 4.563993 GGTGTATGCCAACCTACAGTGTTA 60.564 45.833 0.00 0.00 0.00 2.41
2348 3306 4.630069 GTGTATGCCAACCTACAGTGTTAG 59.370 45.833 0.00 0.00 0.00 2.34
2401 3367 6.437928 CAGTGCTGCTGTTAGTTTTATTTCA 58.562 36.000 0.00 0.00 40.27 2.69
2446 3412 5.060662 AGCACGGCATACATATAGTAGTG 57.939 43.478 0.00 0.00 35.85 2.74
2448 3414 4.174009 CACGGCATACATATAGTAGTGCC 58.826 47.826 17.07 17.07 44.75 5.01
2450 3416 4.713824 GGCATACATATAGTAGTGCCGA 57.286 45.455 14.77 0.00 42.22 5.54
2451 3417 4.673441 GGCATACATATAGTAGTGCCGAG 58.327 47.826 14.77 0.00 42.22 4.63
2453 3419 4.673441 CATACATATAGTAGTGCCGAGCC 58.327 47.826 0.00 0.00 35.85 4.70
2455 3421 5.697483 ATACATATAGTAGTGCCGAGCCGG 61.697 50.000 9.03 9.03 42.49 6.13
2485 3456 0.673644 ATCTTTCGGAACCGTGGCAG 60.674 55.000 12.93 5.53 40.74 4.85
2493 3464 1.270678 GGAACCGTGGCAGAAAGTAGT 60.271 52.381 0.00 0.00 0.00 2.73
2504 3475 6.708054 GTGGCAGAAAGTAGTAGCATCATAAT 59.292 38.462 0.00 0.00 0.00 1.28
2505 3476 7.227512 GTGGCAGAAAGTAGTAGCATCATAATT 59.772 37.037 0.00 0.00 0.00 1.40
2506 3477 7.775093 TGGCAGAAAGTAGTAGCATCATAATTT 59.225 33.333 0.00 0.00 0.00 1.82
2532 3503 3.625745 AGGCACTTACTTTCCCACG 57.374 52.632 0.00 0.00 27.25 4.94
2547 3518 3.678921 CACGAAGACAGTGGTCCAA 57.321 52.632 0.00 0.00 45.48 3.53
2585 3556 3.490759 GTGCACCTGACGCCATCG 61.491 66.667 5.22 0.00 42.43 3.84
2589 3560 1.592669 CACCTGACGCCATCGATCC 60.593 63.158 0.00 0.00 39.41 3.36
2618 3589 5.620206 TCAGGCTTTGAATAGTGAACTGAA 58.380 37.500 0.00 0.00 31.34 3.02
2625 3596 6.573664 TTGAATAGTGAACTGAACAATGGG 57.426 37.500 0.00 0.00 0.00 4.00
2633 3604 0.896940 CTGAACAATGGGCTGCAGGT 60.897 55.000 17.12 0.00 0.00 4.00
2646 3617 2.618709 GCTGCAGGTTGTCAAAAGTAGT 59.381 45.455 17.12 0.00 0.00 2.73
2710 3686 2.144730 GCATCATAGCCAGCTTCTCTG 58.855 52.381 0.00 0.00 42.49 3.35
2718 3694 1.888215 CCAGCTTCTCTGAAGCAACA 58.112 50.000 27.06 0.00 45.72 3.33
2723 3699 2.483876 CTTCTCTGAAGCAACAACCGA 58.516 47.619 0.00 0.00 0.00 4.69
2793 3769 4.440525 GGAACCTGGCACAAACATCATATG 60.441 45.833 0.00 0.00 38.70 1.78
2839 3815 5.379706 AATGAAACCTGGCTAGCTAGATT 57.620 39.130 28.01 21.01 0.00 2.40
2859 3835 4.604843 TTTATCTGCTCAGCATGTTTCG 57.395 40.909 0.00 0.00 38.13 3.46
2949 3928 2.819422 CATTTGATGCCAGAGACACG 57.181 50.000 0.00 0.00 0.00 4.49
2950 3929 1.089920 ATTTGATGCCAGAGACACGC 58.910 50.000 0.00 0.00 0.00 5.34
3219 4202 1.390123 CCGCTCACAACACAAGTATCG 59.610 52.381 0.00 0.00 0.00 2.92
3280 4263 2.582687 GTCGACTTCTGACAGGTAACG 58.417 52.381 8.70 4.89 46.39 3.18
3398 4381 2.646798 AGCCAAGTCCCAGAGAAAGATT 59.353 45.455 0.00 0.00 0.00 2.40
3405 4388 6.642707 AGTCCCAGAGAAAGATTATACTCG 57.357 41.667 0.00 0.00 34.98 4.18
3464 4447 2.603110 TCTGCACGCTACAATCGAATTC 59.397 45.455 0.00 0.00 0.00 2.17
3525 4508 8.962884 ATTGCACATACAGTATTTCATACTCA 57.037 30.769 0.00 0.00 43.93 3.41
3526 4509 7.770801 TGCACATACAGTATTTCATACTCAC 57.229 36.000 0.00 0.00 43.93 3.51
3527 4510 6.761242 TGCACATACAGTATTTCATACTCACC 59.239 38.462 0.00 0.00 43.93 4.02
3528 4511 6.761242 GCACATACAGTATTTCATACTCACCA 59.239 38.462 0.00 0.00 43.93 4.17
3529 4512 7.042456 GCACATACAGTATTTCATACTCACCAG 60.042 40.741 0.00 0.00 43.93 4.00
3530 4513 7.439356 CACATACAGTATTTCATACTCACCAGG 59.561 40.741 0.00 0.00 43.93 4.45
3531 4514 4.770795 ACAGTATTTCATACTCACCAGGC 58.229 43.478 0.00 0.00 43.93 4.85
3532 4515 4.225042 ACAGTATTTCATACTCACCAGGCA 59.775 41.667 0.00 0.00 43.93 4.75
3533 4516 4.813161 CAGTATTTCATACTCACCAGGCAG 59.187 45.833 0.00 0.00 43.93 4.85
3534 4517 2.113860 TTTCATACTCACCAGGCAGC 57.886 50.000 0.00 0.00 0.00 5.25
3535 4518 0.983467 TTCATACTCACCAGGCAGCA 59.017 50.000 0.00 0.00 0.00 4.41
3536 4519 0.983467 TCATACTCACCAGGCAGCAA 59.017 50.000 0.00 0.00 0.00 3.91
3537 4520 1.065926 TCATACTCACCAGGCAGCAAG 60.066 52.381 0.00 0.00 0.00 4.01
3538 4521 0.393537 ATACTCACCAGGCAGCAAGC 60.394 55.000 0.00 0.00 44.65 4.01
3547 4530 2.880648 GCAGCAAGCCTGGTAAGC 59.119 61.111 0.00 0.00 42.03 3.09
3548 4531 1.676967 GCAGCAAGCCTGGTAAGCT 60.677 57.895 0.00 0.00 44.19 3.74
3549 4532 0.392998 GCAGCAAGCCTGGTAAGCTA 60.393 55.000 8.22 0.00 40.49 3.32
3550 4533 1.748591 GCAGCAAGCCTGGTAAGCTAT 60.749 52.381 8.22 0.00 40.49 2.97
3551 4534 2.216898 CAGCAAGCCTGGTAAGCTATC 58.783 52.381 8.22 0.00 40.49 2.08
3552 4535 2.122768 AGCAAGCCTGGTAAGCTATCT 58.877 47.619 7.04 0.00 40.49 1.98
3553 4536 3.070159 CAGCAAGCCTGGTAAGCTATCTA 59.930 47.826 8.22 0.00 40.49 1.98
3554 4537 3.711704 AGCAAGCCTGGTAAGCTATCTAA 59.288 43.478 7.04 0.00 40.49 2.10
3555 4538 4.164221 AGCAAGCCTGGTAAGCTATCTAAA 59.836 41.667 7.04 0.00 40.49 1.85
3556 4539 4.881850 GCAAGCCTGGTAAGCTATCTAAAA 59.118 41.667 0.00 0.00 40.49 1.52
3557 4540 5.357032 GCAAGCCTGGTAAGCTATCTAAAAA 59.643 40.000 0.00 0.00 40.49 1.94
3597 4580 3.157087 ACTGAACCGAATGATTGCCTTT 58.843 40.909 0.00 0.00 0.00 3.11
3598 4581 3.573967 ACTGAACCGAATGATTGCCTTTT 59.426 39.130 0.00 0.00 0.00 2.27
3910 4893 3.062234 GCTGCAGAAAATCGGTACAGTAC 59.938 47.826 20.43 1.59 0.00 2.73
4111 5095 1.826720 ACACATGCATGATTTCACCCC 59.173 47.619 32.75 0.00 0.00 4.95
4531 5521 1.269726 CGAAGGCACCAACAGCAAAAT 60.270 47.619 0.00 0.00 0.00 1.82
4696 5689 3.684103 ACATTTCGAGCTCTAGAGACG 57.316 47.619 24.24 24.07 0.00 4.18
4821 5814 3.244078 CCTGTACTTGTACAAGCAGGTGA 60.244 47.826 33.10 16.53 40.63 4.02
5076 6076 2.642171 TCCCTGGTACACCTGAGAAT 57.358 50.000 6.84 0.00 37.15 2.40
5131 6131 5.064558 TGTTTTTCCAGCAGTACCGAAATA 58.935 37.500 0.00 0.00 0.00 1.40
5260 6260 5.522456 ACGACGTAACAGTCAAATGTTCTA 58.478 37.500 0.00 0.00 42.33 2.10
5262 6262 6.476380 ACGACGTAACAGTCAAATGTTCTAAA 59.524 34.615 0.00 0.00 42.33 1.85
5611 6611 6.053650 ACATCCATGATTCTGACATGTAGTG 58.946 40.000 0.00 0.00 42.16 2.74
5674 6677 2.232941 TGTACCCTTCTGGACACGATTC 59.767 50.000 0.00 0.00 38.00 2.52
5682 6685 4.443913 TCTGGACACGATTCAATAACGA 57.556 40.909 0.00 0.00 0.00 3.85
5814 6836 8.026026 GTGAACAACAAACAAAATTCCCATTTT 58.974 29.630 0.00 0.00 42.37 1.82
5888 6910 9.774413 AGTAGATACGTAAATATTTTTCCCTGG 57.226 33.333 5.91 0.00 0.00 4.45
5982 7004 5.934043 TCTAGTTCAACATGTCAAGTGGATG 59.066 40.000 0.00 0.00 0.00 3.51
6269 7291 7.224297 TGGCATAGTTTAGGATTCTAACCATC 58.776 38.462 0.00 0.00 35.40 3.51
6386 7408 3.556999 TGAAAGAACAAAATGTCCGGGA 58.443 40.909 0.00 0.00 0.00 5.14
6637 7659 2.407562 TGGAGGCTGCCAGTGATTATA 58.592 47.619 22.65 0.00 33.10 0.98
6709 7731 2.736721 TCTTCAGCATAACGAACTGCAC 59.263 45.455 9.70 0.00 40.88 4.57
6763 7785 6.605849 GCATACATACAGGACATATTTGCAG 58.394 40.000 0.00 0.00 0.00 4.41
6908 7930 1.268999 GCACACAAAATGCTTCCGACA 60.269 47.619 0.00 0.00 40.08 4.35
7282 8305 7.119709 TCATTATTTCCGTGACCTAAGATCA 57.880 36.000 0.00 0.00 0.00 2.92
7574 8597 6.549364 AGGATTCAACAATTACAACTTGGTGA 59.451 34.615 0.00 0.00 45.89 4.02
7577 8600 6.142818 TCAACAATTACAACTTGGTGAAGG 57.857 37.500 1.51 0.00 44.91 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.808958 CGATAAGCGGTGCGTTGGG 61.809 63.158 0.00 0.00 36.03 4.12
140 141 2.028476 CGACCAGAGGAACACCAACATA 60.028 50.000 0.00 0.00 0.00 2.29
214 224 0.376152 GCTGATGACCAGTGCGAATG 59.624 55.000 0.00 0.00 44.71 2.67
217 227 1.216444 GAGCTGATGACCAGTGCGA 59.784 57.895 0.00 0.00 44.71 5.10
218 228 0.461516 ATGAGCTGATGACCAGTGCG 60.462 55.000 0.00 0.00 44.71 5.34
219 229 1.297664 GATGAGCTGATGACCAGTGC 58.702 55.000 0.00 0.00 44.71 4.40
221 231 2.186243 AGTGATGAGCTGATGACCAGT 58.814 47.619 0.00 0.00 44.71 4.00
222 232 2.937149 CAAGTGATGAGCTGATGACCAG 59.063 50.000 0.00 0.00 45.67 4.00
223 233 2.568509 TCAAGTGATGAGCTGATGACCA 59.431 45.455 0.00 0.00 33.04 4.02
363 393 2.143925 GCTCCACCTCTTACAACACAC 58.856 52.381 0.00 0.00 0.00 3.82
396 426 1.790387 GACAACATCACCGAGCAGC 59.210 57.895 0.00 0.00 0.00 5.25
404 434 3.435327 TCCAGCAATAACGACAACATCAC 59.565 43.478 0.00 0.00 0.00 3.06
413 443 1.403647 CGTCACCTCCAGCAATAACGA 60.404 52.381 0.00 0.00 0.00 3.85
417 447 1.262417 TGTCGTCACCTCCAGCAATA 58.738 50.000 0.00 0.00 0.00 1.90
422 452 1.432514 CATGTTGTCGTCACCTCCAG 58.567 55.000 0.00 0.00 0.00 3.86
428 458 1.808411 ATGGACCATGTTGTCGTCAC 58.192 50.000 6.06 0.00 36.07 3.67
432 462 2.682352 TGCAATATGGACCATGTTGTCG 59.318 45.455 32.31 16.70 42.29 4.35
451 481 1.876497 ATGTTGCGGTCACCCATTGC 61.876 55.000 0.00 0.00 0.00 3.56
454 484 1.678635 CCATGTTGCGGTCACCCAT 60.679 57.895 0.00 0.00 0.00 4.00
455 485 2.282110 CCATGTTGCGGTCACCCA 60.282 61.111 0.00 0.00 0.00 4.51
456 486 1.460273 AAACCATGTTGCGGTCACCC 61.460 55.000 0.00 0.00 34.99 4.61
457 487 1.240256 TAAACCATGTTGCGGTCACC 58.760 50.000 0.00 0.00 34.99 4.02
458 488 2.227865 ACATAAACCATGTTGCGGTCAC 59.772 45.455 0.00 0.00 46.01 3.67
459 489 2.509569 ACATAAACCATGTTGCGGTCA 58.490 42.857 0.00 0.00 46.01 4.02
502 532 1.511850 TCACCAGCTTGAATGACGTG 58.488 50.000 0.00 0.00 0.00 4.49
518 548 2.289631 TGAGACATGGTGTGGTCATCAC 60.290 50.000 0.00 0.00 46.23 3.06
521 551 2.306805 ACATGAGACATGGTGTGGTCAT 59.693 45.455 14.70 0.00 36.56 3.06
526 556 1.881324 TGCAACATGAGACATGGTGTG 59.119 47.619 24.10 15.38 38.87 3.82
527 557 2.275134 TGCAACATGAGACATGGTGT 57.725 45.000 24.10 5.64 38.87 4.16
537 570 2.805194 TGGTCATCCATTGCAACATGA 58.195 42.857 0.00 7.37 39.03 3.07
565 598 7.140048 TGTTACGATTATGCGTATACATGACA 58.860 34.615 0.00 0.00 45.03 3.58
580 613 3.940209 ACACGGACCTTGTTACGATTA 57.060 42.857 0.00 0.00 0.00 1.75
583 616 1.855513 CAACACGGACCTTGTTACGA 58.144 50.000 15.41 0.00 35.38 3.43
607 640 0.175302 TGCTTGTTGTGCTTGGTTGG 59.825 50.000 0.00 0.00 0.00 3.77
613 646 2.620242 CAACCTTTGCTTGTTGTGCTT 58.380 42.857 0.00 0.00 37.62 3.91
656 998 2.809601 GCGCACGAGACATCCGTT 60.810 61.111 0.30 0.00 38.29 4.44
669 1011 1.809619 GCAGACGTTAGATGGCGCA 60.810 57.895 10.83 0.00 0.00 6.09
671 1013 3.706140 GGCAGACGTTAGATGGCG 58.294 61.111 0.00 0.00 0.00 5.69
673 1015 0.249073 CCTCGGCAGACGTTAGATGG 60.249 60.000 0.00 0.00 44.69 3.51
674 1016 0.872021 GCCTCGGCAGACGTTAGATG 60.872 60.000 2.41 0.00 44.69 2.90
675 1017 1.437986 GCCTCGGCAGACGTTAGAT 59.562 57.895 2.41 0.00 44.69 1.98
676 1018 2.882876 GCCTCGGCAGACGTTAGA 59.117 61.111 2.41 0.00 44.69 2.10
712 1054 2.801483 TTTACTGCCGGCCGGGTTAC 62.801 60.000 43.31 27.76 38.44 2.50
723 1065 4.083643 GGACGTTTACCTTTCTTTACTGCC 60.084 45.833 0.00 0.00 0.00 4.85
724 1066 4.753610 AGGACGTTTACCTTTCTTTACTGC 59.246 41.667 0.00 0.00 33.55 4.40
755 1140 2.288825 TGGGTGCAAAGTACTTCTCTCG 60.289 50.000 8.95 0.00 0.00 4.04
778 1285 1.956477 GTAATTGGCTCCCGCAATCAT 59.044 47.619 0.00 0.00 38.10 2.45
794 1723 9.558396 AATTGGTTGTTTGAAACATCATGTAAT 57.442 25.926 11.97 7.62 41.79 1.89
844 1773 3.168773 GGCTTTTACGGATGCCTCA 57.831 52.632 0.00 0.00 41.92 3.86
849 1778 1.006832 CACGGAGGCTTTTACGGATG 58.993 55.000 0.00 0.00 0.00 3.51
860 1789 3.371063 TCACGGTCTCACGGAGGC 61.371 66.667 1.76 0.00 38.39 4.70
924 1858 3.708734 CAACCAACCGTCGCCGTC 61.709 66.667 0.00 0.00 0.00 4.79
1149 2090 2.159824 GCTCTTAGTCGTGGAAAAAGGC 59.840 50.000 0.00 0.00 0.00 4.35
1150 2091 3.665190 AGCTCTTAGTCGTGGAAAAAGG 58.335 45.455 0.00 0.00 0.00 3.11
1152 2093 4.022935 TCGTAGCTCTTAGTCGTGGAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
1154 2095 3.076621 TCGTAGCTCTTAGTCGTGGAAA 58.923 45.455 0.00 0.00 0.00 3.13
1156 2097 2.005451 GTCGTAGCTCTTAGTCGTGGA 58.995 52.381 0.00 0.00 0.00 4.02
1225 2166 4.301505 GCATCCTGGTTCAGCGAA 57.698 55.556 0.00 0.00 0.00 4.70
1263 2204 1.540607 CCGTGTACGCATGCTCGATC 61.541 60.000 17.13 2.73 38.18 3.69
1269 2210 4.499023 CACGCCGTGTACGCATGC 62.499 66.667 9.53 7.91 38.18 4.06
1274 2215 1.143373 ATGTATGCACGCCGTGTACG 61.143 55.000 19.57 0.00 35.75 3.67
1321 2264 4.526970 TGATCAGGGAAAATAAGCTGTCC 58.473 43.478 0.00 0.00 0.00 4.02
1322 2265 5.163612 GGTTGATCAGGGAAAATAAGCTGTC 60.164 44.000 0.00 0.00 0.00 3.51
1342 2285 2.082231 CAAGAGTGATCTGCAGGGTTG 58.918 52.381 15.13 3.86 0.00 3.77
1389 2332 1.864725 TTGATCACGTACGCGGTGGA 61.865 55.000 16.72 5.92 43.45 4.02
1414 2357 7.703058 AGTATGTTGGAACTTGGATAAAAGG 57.297 36.000 0.00 0.00 0.00 3.11
1434 2377 9.001542 GTGCTAGCTGTGTAGTATTAGTAGTAT 57.998 37.037 17.23 0.00 0.00 2.12
1439 2382 5.067936 CAGGTGCTAGCTGTGTAGTATTAGT 59.932 44.000 17.23 0.00 38.80 2.24
1441 2384 4.341235 CCAGGTGCTAGCTGTGTAGTATTA 59.659 45.833 17.23 0.00 41.84 0.98
1442 2385 3.133003 CCAGGTGCTAGCTGTGTAGTATT 59.867 47.826 17.23 0.00 41.84 1.89
1443 2386 2.695666 CCAGGTGCTAGCTGTGTAGTAT 59.304 50.000 17.23 0.00 41.84 2.12
1502 2445 0.516877 GACGCAGCAACACATAAGCA 59.483 50.000 0.00 0.00 0.00 3.91
1563 2506 0.395312 GGTTCTGAGGTCCCGTTCAA 59.605 55.000 0.00 0.00 0.00 2.69
1575 2518 0.968901 ATGACGGCGTAGGGTTCTGA 60.969 55.000 14.74 0.00 0.00 3.27
1577 2520 0.683504 AGATGACGGCGTAGGGTTCT 60.684 55.000 14.74 8.16 0.00 3.01
1605 2548 2.046507 CCTGAAGCGCTTCTGCCT 60.047 61.111 40.70 14.40 40.14 4.75
1625 2568 2.551270 AGAGGAGGGAGTGTTATTGCA 58.449 47.619 0.00 0.00 0.00 4.08
1627 2570 5.428184 AAGAAGAGGAGGGAGTGTTATTG 57.572 43.478 0.00 0.00 0.00 1.90
1635 2578 9.126151 GGAATAAAATTTAAGAAGAGGAGGGAG 57.874 37.037 0.00 0.00 0.00 4.30
1657 2600 8.229253 ACGAAGTTTTGGTAGTAAAAAGGAAT 57.771 30.769 0.00 0.00 37.78 3.01
1658 2601 7.628769 ACGAAGTTTTGGTAGTAAAAAGGAA 57.371 32.000 0.00 0.00 37.78 3.36
1670 2613 8.899771 CCATTCCTAAATATACGAAGTTTTGGT 58.100 33.333 0.00 0.00 37.78 3.67
1671 2614 9.116067 TCCATTCCTAAATATACGAAGTTTTGG 57.884 33.333 0.00 0.00 37.78 3.28
1674 2617 7.937394 CCCTCCATTCCTAAATATACGAAGTTT 59.063 37.037 0.00 0.00 37.78 2.66
1675 2618 7.291651 TCCCTCCATTCCTAAATATACGAAGTT 59.708 37.037 0.00 0.00 37.78 2.66
1677 2620 7.038941 ACTCCCTCCATTCCTAAATATACGAAG 60.039 40.741 0.00 0.00 0.00 3.79
1680 2623 6.607004 ACTCCCTCCATTCCTAAATATACG 57.393 41.667 0.00 0.00 0.00 3.06
1684 2627 8.548877 GCATTATACTCCCTCCATTCCTAAATA 58.451 37.037 0.00 0.00 0.00 1.40
1686 2629 6.562608 AGCATTATACTCCCTCCATTCCTAAA 59.437 38.462 0.00 0.00 0.00 1.85
1687 2630 6.013379 CAGCATTATACTCCCTCCATTCCTAA 60.013 42.308 0.00 0.00 0.00 2.69
1688 2631 5.485353 CAGCATTATACTCCCTCCATTCCTA 59.515 44.000 0.00 0.00 0.00 2.94
1691 2634 4.006319 GCAGCATTATACTCCCTCCATTC 58.994 47.826 0.00 0.00 0.00 2.67
1692 2635 3.654806 AGCAGCATTATACTCCCTCCATT 59.345 43.478 0.00 0.00 0.00 3.16
1693 2636 3.254960 AGCAGCATTATACTCCCTCCAT 58.745 45.455 0.00 0.00 0.00 3.41
1694 2637 2.634940 GAGCAGCATTATACTCCCTCCA 59.365 50.000 0.00 0.00 0.00 3.86
1695 2638 2.903135 AGAGCAGCATTATACTCCCTCC 59.097 50.000 0.00 0.00 0.00 4.30
1696 2639 3.864160 GCAGAGCAGCATTATACTCCCTC 60.864 52.174 0.00 0.00 0.00 4.30
1697 2640 2.038295 GCAGAGCAGCATTATACTCCCT 59.962 50.000 0.00 0.00 0.00 4.20
1698 2641 2.224378 TGCAGAGCAGCATTATACTCCC 60.224 50.000 0.00 0.00 40.11 4.30
1699 2642 3.117491 TGCAGAGCAGCATTATACTCC 57.883 47.619 0.00 0.00 40.11 3.85
1705 2648 3.760151 ACTTGAATTGCAGAGCAGCATTA 59.240 39.130 0.00 0.00 45.19 1.90
1710 2653 2.161808 CCTCACTTGAATTGCAGAGCAG 59.838 50.000 0.00 0.00 40.61 4.24
1715 2658 3.316029 TGAACACCTCACTTGAATTGCAG 59.684 43.478 0.00 0.00 0.00 4.41
1754 2697 1.968017 ATGGGACTGCACGCACAAG 60.968 57.895 0.00 0.00 35.70 3.16
1880 2827 5.007430 GTGTTTGCTGTGGATAGAGATGATG 59.993 44.000 0.00 0.00 0.00 3.07
2142 3098 7.969004 TCAACATTTAATATGGATCGGAGGTA 58.031 34.615 0.00 0.00 0.00 3.08
2157 3113 8.749026 TGTGGTTTTAGTACCTCAACATTTAA 57.251 30.769 0.00 0.00 38.39 1.52
2160 3116 7.648039 TTTGTGGTTTTAGTACCTCAACATT 57.352 32.000 9.14 0.00 45.92 2.71
2162 3118 5.066764 GCTTTGTGGTTTTAGTACCTCAACA 59.933 40.000 9.14 0.00 45.92 3.33
2164 3120 4.273969 CGCTTTGTGGTTTTAGTACCTCAA 59.726 41.667 6.27 6.27 45.11 3.02
2165 3121 3.810941 CGCTTTGTGGTTTTAGTACCTCA 59.189 43.478 0.00 0.00 39.27 3.86
2167 3123 3.562557 CACGCTTTGTGGTTTTAGTACCT 59.437 43.478 0.00 0.00 45.21 3.08
2168 3124 3.880610 CACGCTTTGTGGTTTTAGTACC 58.119 45.455 0.00 0.00 45.21 3.34
2183 3139 8.979574 GCTAATTTAACTCATATACTCACGCTT 58.020 33.333 0.00 0.00 0.00 4.68
2187 3143 7.148623 GCCGGCTAATTTAACTCATATACTCAC 60.149 40.741 22.15 0.00 0.00 3.51
2189 3145 7.097834 AGCCGGCTAATTTAACTCATATACTC 58.902 38.462 31.86 0.00 0.00 2.59
2191 3147 7.097834 AGAGCCGGCTAATTTAACTCATATAC 58.902 38.462 32.97 10.57 0.00 1.47
2250 3206 4.468095 TTGCTCTTCTTTCACGCTTAAC 57.532 40.909 0.00 0.00 0.00 2.01
2335 3293 6.266103 TGCTTTGTACTACTAACACTGTAGGT 59.734 38.462 0.00 0.00 41.03 3.08
2338 3296 7.117236 GCATTGCTTTGTACTACTAACACTGTA 59.883 37.037 0.16 0.00 0.00 2.74
2339 3297 6.073222 GCATTGCTTTGTACTACTAACACTGT 60.073 38.462 0.16 0.00 0.00 3.55
2340 3298 6.147821 AGCATTGCTTTGTACTACTAACACTG 59.852 38.462 5.03 0.00 33.89 3.66
2341 3299 6.231211 AGCATTGCTTTGTACTACTAACACT 58.769 36.000 5.03 0.00 33.89 3.55
2342 3300 6.481954 AGCATTGCTTTGTACTACTAACAC 57.518 37.500 5.03 0.00 33.89 3.32
2455 3421 1.345176 CGAAAGATCGTCGGCAAGC 59.655 57.895 12.46 0.00 44.06 4.01
2506 3477 5.187967 TGGGAAAGTAAGTGCCTTTCAAAAA 59.812 36.000 13.15 0.00 46.15 1.94
2522 3493 1.202651 CCACTGTCTTCGTGGGAAAGT 60.203 52.381 1.34 0.00 46.38 2.66
2523 3494 1.512926 CCACTGTCTTCGTGGGAAAG 58.487 55.000 1.34 0.00 46.38 2.62
2524 3495 3.698250 CCACTGTCTTCGTGGGAAA 57.302 52.632 1.34 0.00 46.38 3.13
2531 3502 7.385205 CCTATATTATTTGGACCACTGTCTTCG 59.615 40.741 0.00 0.00 41.47 3.79
2532 3503 7.661847 CCCTATATTATTTGGACCACTGTCTTC 59.338 40.741 0.00 0.00 41.47 2.87
2585 3556 3.185246 TCAAAGCCTGAATCGAGGATC 57.815 47.619 0.00 0.00 34.69 3.36
2618 3589 1.152483 ACAACCTGCAGCCCATTGT 60.152 52.632 8.66 12.46 0.00 2.71
2625 3596 2.618709 ACTACTTTTGACAACCTGCAGC 59.381 45.455 8.66 0.00 0.00 5.25
2633 3604 6.934645 CACTCTCCCATAACTACTTTTGACAA 59.065 38.462 0.00 0.00 0.00 3.18
2646 3617 0.108186 CGCACTGCACTCTCCCATAA 60.108 55.000 1.11 0.00 0.00 1.90
2710 3686 1.368850 GTGCGTCGGTTGTTGCTTC 60.369 57.895 0.00 0.00 0.00 3.86
2718 3694 3.616721 AGGAGCAGTGCGTCGGTT 61.617 61.111 10.00 0.00 0.00 4.44
2723 3699 0.952497 CATTGACAGGAGCAGTGCGT 60.952 55.000 10.00 0.54 0.00 5.24
2766 3742 0.755327 GTTTGTGCCAGGTTCCAGGT 60.755 55.000 2.41 0.00 0.00 4.00
2767 3743 0.754957 TGTTTGTGCCAGGTTCCAGG 60.755 55.000 0.00 0.00 0.00 4.45
2768 3744 1.270550 GATGTTTGTGCCAGGTTCCAG 59.729 52.381 0.00 0.00 0.00 3.86
2769 3745 1.327303 GATGTTTGTGCCAGGTTCCA 58.673 50.000 0.00 0.00 0.00 3.53
2770 3746 1.327303 TGATGTTTGTGCCAGGTTCC 58.673 50.000 0.00 0.00 0.00 3.62
2771 3747 4.398988 TCATATGATGTTTGTGCCAGGTTC 59.601 41.667 0.00 0.00 0.00 3.62
2772 3748 4.343231 TCATATGATGTTTGTGCCAGGTT 58.657 39.130 0.00 0.00 0.00 3.50
2793 3769 5.784578 ACAACTTGGTTCCCATAAAGTTC 57.215 39.130 0.00 0.00 31.97 3.01
2839 3815 3.599343 ACGAAACATGCTGAGCAGATAA 58.401 40.909 14.36 0.00 43.65 1.75
2859 3835 4.449405 GTCTCAGTTCCAGCTTCTGTTTAC 59.551 45.833 0.00 0.00 0.00 2.01
2947 3926 1.009675 CACTTTTGAGCAAGCGCGT 60.010 52.632 8.43 0.00 45.49 6.01
2948 3927 1.009675 ACACTTTTGAGCAAGCGCG 60.010 52.632 0.00 0.00 45.49 6.86
2949 3928 0.029300 TCACACTTTTGAGCAAGCGC 59.971 50.000 0.00 0.00 38.99 5.92
2950 3929 2.287188 ACATCACACTTTTGAGCAAGCG 60.287 45.455 0.00 0.00 0.00 4.68
3280 4263 8.922058 ATGCTGTTCATATTTCTCAAATCAAC 57.078 30.769 0.00 0.00 32.59 3.18
3398 4381 1.683943 ACCGTTGCCTAGCGAGTATA 58.316 50.000 0.00 0.00 31.68 1.47
3405 4388 1.595093 ATTGCCAACCGTTGCCTAGC 61.595 55.000 5.68 4.69 0.00 3.42
3438 4421 0.898320 ATTGTAGCGTGCAGAGGACT 59.102 50.000 0.00 0.00 0.00 3.85
3464 4447 6.865726 CGAGAATTAGTACTTCATCATGAGGG 59.134 42.308 7.64 0.00 0.00 4.30
3514 4497 2.025981 TGCTGCCTGGTGAGTATGAAAT 60.026 45.455 0.00 0.00 0.00 2.17
3515 4498 1.350684 TGCTGCCTGGTGAGTATGAAA 59.649 47.619 0.00 0.00 0.00 2.69
3516 4499 0.983467 TGCTGCCTGGTGAGTATGAA 59.017 50.000 0.00 0.00 0.00 2.57
3517 4500 0.983467 TTGCTGCCTGGTGAGTATGA 59.017 50.000 0.00 0.00 0.00 2.15
3518 4501 1.376543 CTTGCTGCCTGGTGAGTATG 58.623 55.000 0.00 0.00 0.00 2.39
3519 4502 0.393537 GCTTGCTGCCTGGTGAGTAT 60.394 55.000 0.00 0.00 35.15 2.12
3520 4503 1.003355 GCTTGCTGCCTGGTGAGTA 60.003 57.895 0.00 0.00 35.15 2.59
3521 4504 2.282040 GCTTGCTGCCTGGTGAGT 60.282 61.111 0.00 0.00 35.15 3.41
3530 4513 0.392998 TAGCTTACCAGGCTTGCTGC 60.393 55.000 10.05 0.00 40.74 5.25
3531 4514 2.158842 AGATAGCTTACCAGGCTTGCTG 60.159 50.000 10.05 0.00 40.74 4.41
3532 4515 2.122768 AGATAGCTTACCAGGCTTGCT 58.877 47.619 0.00 6.04 40.74 3.91
3533 4516 2.629336 AGATAGCTTACCAGGCTTGC 57.371 50.000 0.00 0.00 40.74 4.01
3563 4546 5.079689 TCGGTTCAGTTGAGTATGCAATA 57.920 39.130 0.00 0.00 0.00 1.90
3597 4580 6.353323 TGTGGTGAACAATCTGAAAGTAGAA 58.647 36.000 0.00 0.00 35.24 2.10
3598 4581 5.924356 TGTGGTGAACAATCTGAAAGTAGA 58.076 37.500 0.00 0.00 35.24 2.59
3910 4893 6.479990 TCTGAACTTGCTTGTCAATATATCCG 59.520 38.462 0.00 0.00 33.57 4.18
4090 5073 2.234414 GGGGTGAAATCATGCATGTGTT 59.766 45.455 25.43 19.45 0.00 3.32
4111 5095 1.202627 GCTGGCTCCTCCTTATCTGTG 60.203 57.143 0.00 0.00 35.26 3.66
4172 5156 4.720902 CCATGACCACCTGCGCCA 62.721 66.667 4.18 0.00 0.00 5.69
4190 5174 1.312815 GGCAGCACAATGGAGATACC 58.687 55.000 0.00 0.00 39.54 2.73
4306 5290 8.799367 GTTTTACAACTAGGGGTGTGATTTATT 58.201 33.333 6.31 0.00 0.00 1.40
4338 5322 5.699839 CGTACACATCGAATCCATGATAGA 58.300 41.667 0.00 0.00 0.00 1.98
4531 5521 7.947332 ACAGCAGATCTATATTTCTAGGACTCA 59.053 37.037 0.00 0.00 0.00 3.41
4696 5689 3.188786 CGGTAACTCTGCAGCGCC 61.189 66.667 9.47 5.39 0.00 6.53
4821 5814 6.772716 TCTCCTTTAAGAAGCAAATGTGAACT 59.227 34.615 0.00 0.00 0.00 3.01
5131 6131 8.504005 CACCTTTAAATCTGTATCTTTTCGTGT 58.496 33.333 0.00 0.00 0.00 4.49
5459 6459 8.139989 AGATGCTTGCATTAAAGGATGAAATAC 58.860 33.333 9.59 0.00 38.22 1.89
5656 6659 1.348064 TGAATCGTGTCCAGAAGGGT 58.652 50.000 0.00 0.00 38.11 4.34
5674 6677 3.815401 CTGAAAGGGGGCTATCGTTATTG 59.185 47.826 0.00 0.00 0.00 1.90
5682 6685 4.956075 CACAATTAACTGAAAGGGGGCTAT 59.044 41.667 0.00 0.00 39.30 2.97
5765 6787 9.824216 TCACTAGCATTTATATCTTAGTAGGGT 57.176 33.333 0.00 0.00 0.00 4.34
5888 6910 1.661341 CATCAGCTACAGTTGGCCTC 58.339 55.000 3.32 0.00 0.00 4.70
6269 7291 4.398044 ACAGTTATTATTCAAAGTGGGCGG 59.602 41.667 0.00 0.00 31.60 6.13
6299 7321 8.442632 TGAAATAACTTCTGAATGCTGGATAG 57.557 34.615 0.00 0.00 34.86 2.08
6637 7659 2.325583 TTTGACTCAGCTTTGACGGT 57.674 45.000 0.00 0.00 0.00 4.83
6709 7731 5.865552 CAGAAATATGCAGGTGGTTTTCTTG 59.134 40.000 0.00 0.00 32.65 3.02
6763 7785 0.457337 CGCAAGCAGCCTCCAAATTC 60.457 55.000 0.00 0.00 41.38 2.17
6887 7909 1.028130 TCGGAAGCATTTTGTGTGCA 58.972 45.000 0.69 0.00 44.87 4.57
6908 7930 4.843728 TCCTTCTCAACAGTCAACACTTT 58.156 39.130 0.00 0.00 0.00 2.66
7081 8104 9.577110 TTTTCAGATCAGTTGATAATTTGATGC 57.423 29.630 0.00 0.00 34.37 3.91
7108 8131 9.740710 AATATAGGTTGTAGAAAAGTCAGCTTT 57.259 29.630 0.00 0.00 46.01 3.51
7282 8305 7.830099 AACAAGGATGAAGAAACTTGAGAAT 57.170 32.000 9.90 0.00 42.07 2.40
7574 8597 9.990868 ACATTACAAAGAGGGTAATATTTCCTT 57.009 29.630 10.57 3.35 38.91 3.36


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

AutoCloner maintained by Alex Coulton.