Multiple sequence alignment - TraesCS5A01G398900

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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 TraesCS5A01G398900 chr5A 100.000 4273 0 0 1 4273 592639925 592635653 0.000000e+00 7891.0
1 TraesCS5A01G398900 chr5B 90.759 2370 123 57 894 3227 580366861 580364552 0.000000e+00 3075.0
2 TraesCS5A01G398900 chr5B 92.612 582 22 9 3291 3856 580364541 580363965 0.000000e+00 817.0
3 TraesCS5A01G398900 chr5B 88.034 351 33 3 3907 4255 580363965 580363622 1.430000e-109 407.0
4 TraesCS5A01G398900 chr5B 84.314 306 26 9 506 798 580367389 580367093 3.250000e-71 279.0
5 TraesCS5A01G398900 chr5B 97.826 46 1 0 1 46 580367868 580367823 3.540000e-11 80.5
6 TraesCS5A01G398900 chr5D 87.550 2265 122 79 53 2240 473004438 473002257 0.000000e+00 2473.0
7 TraesCS5A01G398900 chr5D 91.515 990 57 15 3291 4259 473001309 473000326 0.000000e+00 1338.0
8 TraesCS5A01G398900 chr5D 91.561 948 53 8 2289 3227 473002249 473001320 0.000000e+00 1282.0
9 TraesCS5A01G398900 chr5D 82.040 696 101 9 2369 3052 551984531 551985214 4.790000e-159 571.0
10 TraesCS5A01G398900 chrUn 83.808 667 88 7 2395 3051 376497646 376496990 2.180000e-172 616.0
11 TraesCS5A01G398900 chrUn 83.808 667 88 7 2395 3051 376510421 376509765 2.180000e-172 616.0
12 TraesCS5A01G398900 chrUn 83.808 667 88 7 2395 3051 456468594 456467938 2.180000e-172 616.0
13 TraesCS5A01G398900 chr1A 83.784 666 88 7 2396 3051 564320579 564319924 7.850000e-172 614.0
14 TraesCS5A01G398900 chr7A 82.459 667 95 10 2395 3051 367840874 367841528 8.020000e-157 564.0
15 TraesCS5A01G398900 chr4A 81.275 502 76 10 2560 3051 616429362 616428869 1.440000e-104 390.0
16 TraesCS5A01G398900 chr4A 83.140 172 25 3 1089 1258 40860255 40860424 2.060000e-33 154.0
17 TraesCS5A01G398900 chr4B 84.000 175 24 3 1089 1261 519824585 519824413 9.510000e-37 165.0
18 TraesCS5A01G398900 chr4D 82.286 175 27 3 1089 1261 423429821 423429649 9.570000e-32 148.0
19 TraesCS5A01G398900 chr2A 79.762 168 26 7 1065 1228 705068466 705068629 9.710000e-22 115.0
20 TraesCS5A01G398900 chr3D 81.022 137 20 6 2940 3075 501051428 501051297 2.100000e-18 104.0
21 TraesCS5A01G398900 chr2D 80.000 140 24 4 1091 1228 564384018 564384155 2.720000e-17 100.0
22 TraesCS5A01G398900 chr2B 77.711 166 33 4 1065 1228 675514528 675514691 9.780000e-17 99.0
23 TraesCS5A01G398900 chr3B 88.333 60 7 0 1169 1228 823029111 823029170 5.930000e-09 73.1


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 TraesCS5A01G398900 chr5A 592635653 592639925 4272 True 7891.000000 7891 100.000000 1 4273 1 chr5A.!!$R1 4272
1 TraesCS5A01G398900 chr5B 580363622 580367868 4246 True 931.700000 3075 90.709000 1 4255 5 chr5B.!!$R1 4254
2 TraesCS5A01G398900 chr5D 473000326 473004438 4112 True 1697.666667 2473 90.208667 53 4259 3 chr5D.!!$R1 4206
3 TraesCS5A01G398900 chr5D 551984531 551985214 683 False 571.000000 571 82.040000 2369 3052 1 chr5D.!!$F1 683
4 TraesCS5A01G398900 chrUn 376496990 376497646 656 True 616.000000 616 83.808000 2395 3051 1 chrUn.!!$R1 656
5 TraesCS5A01G398900 chrUn 376509765 376510421 656 True 616.000000 616 83.808000 2395 3051 1 chrUn.!!$R2 656
6 TraesCS5A01G398900 chrUn 456467938 456468594 656 True 616.000000 616 83.808000 2395 3051 1 chrUn.!!$R3 656
7 TraesCS5A01G398900 chr1A 564319924 564320579 655 True 614.000000 614 83.784000 2396 3051 1 chr1A.!!$R1 655
8 TraesCS5A01G398900 chr7A 367840874 367841528 654 False 564.000000 564 82.459000 2395 3051 1 chr7A.!!$F1 656

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
129 543 0.106918 TTGTTCCAGAAACGGCCACT 60.107 50.0 2.24 0.0 41.02 4.00 F
1003 1631 0.038166 TTGGTGGTGAAGGAGGATGC 59.962 55.0 0.00 0.0 0.00 3.91 F
1305 1933 0.252197 CCTTCCCCTTCCGTCGATTT 59.748 55.0 0.00 0.0 0.00 2.17 F
3228 3919 0.260230 CTACTCCTCCTCCAGCTCCA 59.740 60.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1905 0.626382 GAAGGGGAAGGGGAAGGAAG 59.374 60.0 0.00 0.00 0.00 3.46 R
2742 3420 0.670546 GTGGTTCAGCGCTAAGAGCA 60.671 55.0 10.99 12.14 42.58 4.26 R
3247 3938 0.108756 GGAGTCACGGTAAGCCTGAC 60.109 60.0 0.00 5.66 40.26 3.51 R
4074 4796 0.109226 GACGCACCACTAGTCACCTC 60.109 60.0 0.00 0.00 35.19 3.85 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
42 43 2.485814 CCAACTTGTGCTCTCTTTAGCC 59.514 50.000 0.00 0.00 42.05 3.93
46 47 0.532573 TGTGCTCTCTTTAGCCGAGG 59.467 55.000 0.00 0.00 42.05 4.63
47 48 0.533032 GTGCTCTCTTTAGCCGAGGT 59.467 55.000 0.00 0.00 42.05 3.85
48 49 1.749634 GTGCTCTCTTTAGCCGAGGTA 59.250 52.381 0.00 0.00 42.05 3.08
49 50 2.165845 GTGCTCTCTTTAGCCGAGGTAA 59.834 50.000 0.00 0.00 42.05 2.85
51 52 3.259876 TGCTCTCTTTAGCCGAGGTAAAA 59.740 43.478 8.79 0.00 42.05 1.52
77 490 4.228567 TGCACCTCCACGCGACAA 62.229 61.111 15.93 0.00 0.00 3.18
80 493 3.231736 ACCTCCACGCGACAAGGT 61.232 61.111 15.93 18.65 37.30 3.50
104 517 0.815734 TCCAAGTAGAGTAGCGTGCC 59.184 55.000 0.00 0.00 0.00 5.01
111 525 0.977395 AGAGTAGCGTGCCCTTTCTT 59.023 50.000 0.00 0.00 0.00 2.52
116 530 1.172812 AGCGTGCCCTTTCTTGTTCC 61.173 55.000 0.00 0.00 0.00 3.62
123 537 2.287608 GCCCTTTCTTGTTCCAGAAACG 60.288 50.000 0.00 0.00 41.02 3.60
124 538 2.293399 CCCTTTCTTGTTCCAGAAACGG 59.707 50.000 0.00 0.00 41.02 4.44
125 539 2.287608 CCTTTCTTGTTCCAGAAACGGC 60.288 50.000 0.00 0.00 41.02 5.68
126 540 1.314730 TTCTTGTTCCAGAAACGGCC 58.685 50.000 0.00 0.00 41.02 6.13
127 541 0.181587 TCTTGTTCCAGAAACGGCCA 59.818 50.000 2.24 0.00 41.02 5.36
128 542 0.310854 CTTGTTCCAGAAACGGCCAC 59.689 55.000 2.24 0.00 41.02 5.01
129 543 0.106918 TTGTTCCAGAAACGGCCACT 60.107 50.000 2.24 0.00 41.02 4.00
130 544 0.759959 TGTTCCAGAAACGGCCACTA 59.240 50.000 2.24 0.00 41.02 2.74
131 545 1.270625 TGTTCCAGAAACGGCCACTAG 60.271 52.381 2.24 0.00 41.02 2.57
229 666 5.415701 TGGTTGCTTTCCATCATCTCTTTAC 59.584 40.000 0.00 0.00 0.00 2.01
230 667 5.447818 GGTTGCTTTCCATCATCTCTTTACG 60.448 44.000 0.00 0.00 0.00 3.18
231 668 4.832248 TGCTTTCCATCATCTCTTTACGT 58.168 39.130 0.00 0.00 0.00 3.57
232 669 4.631377 TGCTTTCCATCATCTCTTTACGTG 59.369 41.667 0.00 0.00 0.00 4.49
249 686 2.582498 GCGTACGTAGGCAGCTGG 60.582 66.667 29.72 0.00 37.08 4.85
272 709 2.203126 CGCTCCCTCCTCAATGCC 60.203 66.667 0.00 0.00 0.00 4.40
291 728 3.053896 CACCGCCTCCCGTTTTCC 61.054 66.667 0.00 0.00 34.38 3.13
297 734 1.677820 CGCCTCCCGTTTTCCTGTTAT 60.678 52.381 0.00 0.00 0.00 1.89
333 773 4.154942 TCTCCCCGTATTCCTGTTATACC 58.845 47.826 0.00 0.00 0.00 2.73
334 774 2.892852 TCCCCGTATTCCTGTTATACCG 59.107 50.000 0.00 0.00 0.00 4.02
335 775 2.028748 CCCCGTATTCCTGTTATACCGG 60.029 54.545 0.00 0.00 31.03 5.28
336 776 2.629617 CCCGTATTCCTGTTATACCGGT 59.370 50.000 13.98 13.98 0.00 5.28
338 778 4.321230 CCCGTATTCCTGTTATACCGGTAC 60.321 50.000 18.55 7.89 0.00 3.34
369 809 3.533606 ACCTCGATCCAGTCATTCTTG 57.466 47.619 0.00 0.00 0.00 3.02
370 810 2.834549 ACCTCGATCCAGTCATTCTTGT 59.165 45.455 0.00 0.00 0.00 3.16
394 853 4.736896 GGTCGCCACCTCGTCACC 62.737 72.222 0.00 0.00 40.00 4.02
395 854 4.736896 GTCGCCACCTCGTCACCC 62.737 72.222 0.00 0.00 0.00 4.61
416 875 3.461982 GTCACGCTCACGCTCACG 61.462 66.667 0.00 0.00 45.53 4.35
464 925 1.973812 GGCCCACCTCTGCAAACTC 60.974 63.158 0.00 0.00 0.00 3.01
480 941 2.892640 TCGGAGAGCATCAACGGG 59.107 61.111 0.00 0.00 37.82 5.28
527 988 3.129287 CAGCAGGGATTGTTTATGACACC 59.871 47.826 0.00 0.00 38.18 4.16
544 1005 4.062991 GACACCCCGTTATAATTAGGCTG 58.937 47.826 0.00 0.00 0.00 4.85
546 1007 4.202326 ACACCCCGTTATAATTAGGCTGAG 60.202 45.833 0.00 0.00 0.00 3.35
564 1029 2.162408 TGAGATGTGATAGATAGCGGCG 59.838 50.000 0.51 0.51 0.00 6.46
578 1043 2.025727 GGCGACGACCTATCACCG 59.974 66.667 0.00 0.00 0.00 4.94
608 1073 0.227234 GTCGATTAGTGATGCACGCG 59.773 55.000 3.53 3.53 39.64 6.01
634 1100 0.944386 CACCTGTCGGAAACCAACAG 59.056 55.000 2.30 2.30 39.27 3.16
666 1132 1.977009 CACCGGGGAAAGGAAAGGC 60.977 63.158 6.32 0.00 0.00 4.35
667 1133 2.750237 CCGGGGAAAGGAAAGGCG 60.750 66.667 0.00 0.00 0.00 5.52
728 1198 0.866061 CCAATCCTACGACGCGACAG 60.866 60.000 15.93 5.82 0.00 3.51
757 1227 0.324645 TAACCACCGTAGACCCCCTC 60.325 60.000 0.00 0.00 0.00 4.30
758 1228 3.145551 CCACCGTAGACCCCCTCG 61.146 72.222 0.00 0.00 0.00 4.63
763 1233 4.791069 GTAGACCCCCTCGCCCCA 62.791 72.222 0.00 0.00 0.00 4.96
764 1234 4.791069 TAGACCCCCTCGCCCCAC 62.791 72.222 0.00 0.00 0.00 4.61
818 1295 2.212652 CCCGGCGTTATTACTTAACCC 58.787 52.381 6.01 0.00 37.49 4.11
826 1303 4.445453 GTTATTACTTAACCCACCCCTCG 58.555 47.826 0.00 0.00 35.17 4.63
830 1307 4.660611 TAACCCACCCCTCGCCCA 62.661 66.667 0.00 0.00 0.00 5.36
855 1332 3.449688 CCCCCATTCCCATTCCCA 58.550 61.111 0.00 0.00 0.00 4.37
856 1333 1.948640 CCCCCATTCCCATTCCCAT 59.051 57.895 0.00 0.00 0.00 4.00
857 1334 0.268566 CCCCCATTCCCATTCCCATT 59.731 55.000 0.00 0.00 0.00 3.16
878 1355 2.381618 TCCCATTCCACTTCCATTTCCA 59.618 45.455 0.00 0.00 0.00 3.53
879 1356 3.012730 TCCCATTCCACTTCCATTTCCAT 59.987 43.478 0.00 0.00 0.00 3.41
880 1357 3.776417 CCCATTCCACTTCCATTTCCATT 59.224 43.478 0.00 0.00 0.00 3.16
881 1358 4.225717 CCCATTCCACTTCCATTTCCATTT 59.774 41.667 0.00 0.00 0.00 2.32
882 1359 5.422145 CCATTCCACTTCCATTTCCATTTC 58.578 41.667 0.00 0.00 0.00 2.17
883 1360 4.782019 TTCCACTTCCATTTCCATTTCG 57.218 40.909 0.00 0.00 0.00 3.46
884 1361 3.761897 TCCACTTCCATTTCCATTTCGT 58.238 40.909 0.00 0.00 0.00 3.85
909 1522 3.874543 CGTCCCCATTCATTCATTCGTTA 59.125 43.478 0.00 0.00 0.00 3.18
923 1536 2.756840 TCGTTACCAGAGAGACGAGA 57.243 50.000 0.00 0.00 39.33 4.04
933 1561 1.583404 GAGAGACGAGACGACGACTAC 59.417 57.143 0.00 0.00 38.20 2.73
935 1563 1.075425 AGACGAGACGACGACTACGG 61.075 60.000 17.33 7.26 44.46 4.02
962 1590 1.045911 GGGGCAGAGTTCGGATCTCT 61.046 60.000 11.86 11.86 42.16 3.10
963 1591 1.693627 GGGCAGAGTTCGGATCTCTA 58.306 55.000 16.14 0.00 39.84 2.43
964 1592 2.243810 GGGCAGAGTTCGGATCTCTAT 58.756 52.381 16.14 0.00 39.84 1.98
965 1593 2.630580 GGGCAGAGTTCGGATCTCTATT 59.369 50.000 16.14 0.00 39.84 1.73
1003 1631 0.038166 TTGGTGGTGAAGGAGGATGC 59.962 55.000 0.00 0.00 0.00 3.91
1257 1885 2.221299 CCTCTTCCCCCACGTCCAA 61.221 63.158 0.00 0.00 0.00 3.53
1277 1905 2.350136 CGTACGTACGCTCTTCTCTC 57.650 55.000 32.36 0.00 43.14 3.20
1278 1906 1.925847 CGTACGTACGCTCTTCTCTCT 59.074 52.381 32.36 0.00 43.14 3.10
1305 1933 0.252197 CCTTCCCCTTCCGTCGATTT 59.748 55.000 0.00 0.00 0.00 2.17
1319 1947 1.621814 TCGATTTGAGTTTCTCCCGGT 59.378 47.619 0.00 0.00 0.00 5.28
1325 1953 2.326428 TGAGTTTCTCCCGGTTTCTCT 58.674 47.619 0.00 0.00 0.00 3.10
1331 1969 1.480954 TCTCCCGGTTTCTCTGTATGC 59.519 52.381 0.00 0.00 0.00 3.14
1335 1973 1.135083 CCGGTTTCTCTGTATGCTCGT 60.135 52.381 0.00 0.00 0.00 4.18
1354 1992 2.574212 CGCGCGGTGCTGATTTTC 60.574 61.111 24.84 0.00 43.27 2.29
1359 1997 1.135315 CGGTGCTGATTTTCCTGCG 59.865 57.895 0.00 0.00 34.31 5.18
1367 2005 0.517316 GATTTTCCTGCGCGTCTTGT 59.483 50.000 8.43 0.00 0.00 3.16
1368 2006 0.517316 ATTTTCCTGCGCGTCTTGTC 59.483 50.000 8.43 0.00 0.00 3.18
1369 2007 0.531974 TTTTCCTGCGCGTCTTGTCT 60.532 50.000 8.43 0.00 0.00 3.41
1370 2008 0.531974 TTTCCTGCGCGTCTTGTCTT 60.532 50.000 8.43 0.00 0.00 3.01
1371 2009 1.221466 TTCCTGCGCGTCTTGTCTTG 61.221 55.000 8.43 0.00 0.00 3.02
1756 2399 4.286813 AGGGGATAATTCAGGTGAGAGA 57.713 45.455 0.00 0.00 0.00 3.10
1773 2416 0.683973 AGACCGATGATGAGGATGCC 59.316 55.000 0.00 0.00 0.00 4.40
1775 2418 0.839277 ACCGATGATGAGGATGCCAA 59.161 50.000 0.00 0.00 0.00 4.52
1776 2419 1.422781 ACCGATGATGAGGATGCCAAT 59.577 47.619 0.00 0.00 0.00 3.16
1777 2420 2.158564 ACCGATGATGAGGATGCCAATT 60.159 45.455 0.00 0.00 0.00 2.32
1779 2422 4.074259 CCGATGATGAGGATGCCAATTTA 58.926 43.478 0.00 0.00 0.00 1.40
1783 2430 6.150641 CGATGATGAGGATGCCAATTTATCTT 59.849 38.462 0.00 0.00 0.00 2.40
1785 2432 7.750229 TGATGAGGATGCCAATTTATCTTAC 57.250 36.000 0.00 0.00 0.00 2.34
1797 2444 9.196552 GCCAATTTATCTTACTAATTTCATGCC 57.803 33.333 0.00 0.00 0.00 4.40
1802 2449 5.708736 TCTTACTAATTTCATGCCTCCCA 57.291 39.130 0.00 0.00 0.00 4.37
1803 2450 6.073447 TCTTACTAATTTCATGCCTCCCAA 57.927 37.500 0.00 0.00 0.00 4.12
1804 2451 6.672593 TCTTACTAATTTCATGCCTCCCAAT 58.327 36.000 0.00 0.00 0.00 3.16
1805 2452 6.772716 TCTTACTAATTTCATGCCTCCCAATC 59.227 38.462 0.00 0.00 0.00 2.67
1806 2453 4.870636 ACTAATTTCATGCCTCCCAATCA 58.129 39.130 0.00 0.00 0.00 2.57
1816 2463 3.975982 TGCCTCCCAATCATCAGAGATTA 59.024 43.478 0.00 0.00 36.13 1.75
1824 2471 6.060136 CCAATCATCAGAGATTAGAGGCAAA 58.940 40.000 0.00 0.00 36.13 3.68
1825 2472 6.544931 CCAATCATCAGAGATTAGAGGCAAAA 59.455 38.462 0.00 0.00 36.13 2.44
1826 2473 7.230913 CCAATCATCAGAGATTAGAGGCAAAAT 59.769 37.037 0.00 0.00 36.13 1.82
1926 2574 5.067674 GCTTGCACACTGAAATATGGGATAA 59.932 40.000 0.00 0.00 0.00 1.75
1927 2575 6.405731 GCTTGCACACTGAAATATGGGATAAA 60.406 38.462 0.00 0.00 0.00 1.40
1931 2586 6.498304 CACACTGAAATATGGGATAAACTGC 58.502 40.000 0.00 0.00 0.00 4.40
2002 2657 4.197750 GCAGAGCCATTAGATCCCATATG 58.802 47.826 0.00 0.00 0.00 1.78
2048 2709 4.149598 AGTGGGTTTCCAGGTAACAATTC 58.850 43.478 10.86 0.00 45.05 2.17
2142 2803 6.942576 GGCCATATGTCAGAAATGGTAACTAT 59.057 38.462 0.00 0.00 41.87 2.12
2196 2857 3.686726 GGAAACTTGCTGACCATACTGAG 59.313 47.826 0.00 0.00 0.00 3.35
2336 2999 0.548031 TCCAGGATTGCTGGGATCAC 59.452 55.000 22.42 0.00 42.03 3.06
2354 3017 2.307686 TCACAAAGTATCCTGGGTTCCC 59.692 50.000 0.12 0.12 0.00 3.97
2425 3096 7.202047 GGATTCCTGGGATCATAGTCCATATAC 60.202 44.444 16.75 0.00 40.17 1.47
2451 3127 8.449397 CAGTTTCTCTCTTTTGGTGATAAGATG 58.551 37.037 0.00 0.00 30.57 2.90
2468 3144 3.480470 AGATGCTCCATTTATCGTTGGG 58.520 45.455 0.00 0.00 33.62 4.12
2506 3182 7.385778 TGTTATTGTTTGGTGATTAGCCTAC 57.614 36.000 0.00 0.00 0.00 3.18
2541 3219 8.450578 TTTGTCATCACTCATCAGTTAGTTTT 57.549 30.769 0.00 0.00 0.00 2.43
2692 3370 4.466726 ACTTGAAGAAACCGGAGTATAGCT 59.533 41.667 9.46 0.00 0.00 3.32
2742 3420 3.698040 CTGTTATTGCATTGAAGAGGCCT 59.302 43.478 3.86 3.86 33.12 5.19
2905 3586 8.191446 CGGTAGGTTCTGATATATCAATACCAG 58.809 40.741 29.59 20.24 40.25 4.00
2924 3606 3.211865 CAGTTGATGATCTCATGTGGGG 58.788 50.000 0.00 0.00 36.57 4.96
2925 3607 3.117745 AGTTGATGATCTCATGTGGGGA 58.882 45.455 0.00 0.00 36.57 4.81
2932 3615 2.879103 TCTCATGTGGGGAGGTTTTC 57.121 50.000 0.00 0.00 33.18 2.29
2953 3636 3.062763 CCTCCACGTATGAATGATCTGC 58.937 50.000 0.00 0.00 0.00 4.26
2958 3641 5.301805 TCCACGTATGAATGATCTGCTAGAA 59.698 40.000 0.00 0.00 0.00 2.10
2969 3652 9.234384 GAATGATCTGCTAGAACAAATGAAATG 57.766 33.333 0.00 0.00 30.72 2.32
2983 3674 8.356533 ACAAATGAAATGACTTGTGTGAAATC 57.643 30.769 0.00 0.00 31.00 2.17
2988 3679 7.546358 TGAAATGACTTGTGTGAAATCACTTT 58.454 30.769 14.15 4.42 46.55 2.66
3227 3918 0.553819 TCTACTCCTCCTCCAGCTCC 59.446 60.000 0.00 0.00 0.00 4.70
3228 3919 0.260230 CTACTCCTCCTCCAGCTCCA 59.740 60.000 0.00 0.00 0.00 3.86
3229 3920 0.937441 TACTCCTCCTCCAGCTCCAT 59.063 55.000 0.00 0.00 0.00 3.41
3230 3921 0.398381 ACTCCTCCTCCAGCTCCATC 60.398 60.000 0.00 0.00 0.00 3.51
3231 3922 1.074926 TCCTCCTCCAGCTCCATCC 60.075 63.158 0.00 0.00 0.00 3.51
3232 3923 1.383664 CCTCCTCCAGCTCCATCCA 60.384 63.158 0.00 0.00 0.00 3.41
3233 3924 1.409251 CCTCCTCCAGCTCCATCCAG 61.409 65.000 0.00 0.00 0.00 3.86
3234 3925 0.690411 CTCCTCCAGCTCCATCCAGT 60.690 60.000 0.00 0.00 0.00 4.00
3235 3926 0.689080 TCCTCCAGCTCCATCCAGTC 60.689 60.000 0.00 0.00 0.00 3.51
3236 3927 1.440893 CTCCAGCTCCATCCAGTCG 59.559 63.158 0.00 0.00 0.00 4.18
3237 3928 2.025767 CTCCAGCTCCATCCAGTCGG 62.026 65.000 0.00 0.00 0.00 4.79
3238 3929 2.362369 CCAGCTCCATCCAGTCGGT 61.362 63.158 0.00 0.00 0.00 4.69
3239 3930 1.153489 CAGCTCCATCCAGTCGGTG 60.153 63.158 0.00 0.00 0.00 4.94
3240 3931 2.512515 GCTCCATCCAGTCGGTGC 60.513 66.667 0.00 0.00 34.92 5.01
3241 3932 2.981302 CTCCATCCAGTCGGTGCA 59.019 61.111 0.00 0.00 0.00 4.57
3242 3933 1.153489 CTCCATCCAGTCGGTGCAG 60.153 63.158 0.00 0.00 0.00 4.41
3243 3934 2.821366 CCATCCAGTCGGTGCAGC 60.821 66.667 5.64 5.64 0.00 5.25
3244 3935 2.821366 CATCCAGTCGGTGCAGCC 60.821 66.667 10.90 2.64 0.00 4.85
3245 3936 3.321648 ATCCAGTCGGTGCAGCCA 61.322 61.111 10.90 0.00 36.97 4.75
3246 3937 3.612247 ATCCAGTCGGTGCAGCCAC 62.612 63.158 10.90 8.10 41.32 5.01
3248 3939 4.969196 CAGTCGGTGCAGCCACGT 62.969 66.667 10.90 0.00 43.00 4.49
3249 3940 4.664677 AGTCGGTGCAGCCACGTC 62.665 66.667 10.90 0.00 43.00 4.34
3250 3941 4.961511 GTCGGTGCAGCCACGTCA 62.962 66.667 10.90 0.00 43.00 4.35
3260 3951 2.654877 CCACGTCAGGCTTACCGT 59.345 61.111 0.00 0.00 42.76 4.83
3282 3973 4.341520 GTGACTCCGGTTAATAGACCAGAT 59.658 45.833 0.00 0.00 39.78 2.90
3283 3974 5.533903 GTGACTCCGGTTAATAGACCAGATA 59.466 44.000 0.00 0.00 39.78 1.98
3284 3975 6.040166 GTGACTCCGGTTAATAGACCAGATAA 59.960 42.308 0.00 0.00 39.78 1.75
3285 3976 6.264744 TGACTCCGGTTAATAGACCAGATAAG 59.735 42.308 0.00 0.00 39.78 1.73
3286 3977 6.371278 ACTCCGGTTAATAGACCAGATAAGA 58.629 40.000 0.00 0.00 39.78 2.10
3287 3978 6.264970 ACTCCGGTTAATAGACCAGATAAGAC 59.735 42.308 0.00 0.00 39.78 3.01
3288 3979 5.240183 TCCGGTTAATAGACCAGATAAGACG 59.760 44.000 0.00 0.00 39.78 4.18
3289 3980 5.458891 CGGTTAATAGACCAGATAAGACGG 58.541 45.833 0.00 0.00 39.78 4.79
3290 3981 5.564259 CGGTTAATAGACCAGATAAGACGGG 60.564 48.000 0.00 0.00 39.78 5.28
3291 3982 5.537674 GGTTAATAGACCAGATAAGACGGGA 59.462 44.000 0.00 0.00 39.57 5.14
3292 3983 6.445475 GTTAATAGACCAGATAAGACGGGAC 58.555 44.000 0.00 0.00 0.00 4.46
3293 3984 2.830651 AGACCAGATAAGACGGGACT 57.169 50.000 0.00 0.00 0.00 3.85
3294 3985 2.657143 AGACCAGATAAGACGGGACTC 58.343 52.381 0.00 0.00 0.00 3.36
3295 3986 1.682323 GACCAGATAAGACGGGACTCC 59.318 57.143 0.00 0.00 0.00 3.85
3307 3998 1.397672 GGGACTCCGGTTAGTAGACC 58.602 60.000 0.00 0.05 36.31 3.85
3308 3999 1.341383 GGGACTCCGGTTAGTAGACCA 60.341 57.143 0.00 0.00 39.78 4.02
3309 4000 2.022934 GGACTCCGGTTAGTAGACCAG 58.977 57.143 0.00 0.00 39.78 4.00
3310 4001 2.356535 GGACTCCGGTTAGTAGACCAGA 60.357 54.545 0.00 0.00 39.78 3.86
3311 4002 3.553904 GACTCCGGTTAGTAGACCAGAT 58.446 50.000 0.00 0.00 39.78 2.90
3312 4003 4.445448 GGACTCCGGTTAGTAGACCAGATA 60.445 50.000 0.00 0.00 39.78 1.98
3385 4084 3.569902 TGCAGATCAGCAACGCAG 58.430 55.556 10.74 0.00 42.46 5.18
3386 4085 1.004679 TGCAGATCAGCAACGCAGA 60.005 52.632 10.74 0.00 42.46 4.26
3573 4281 2.029649 GTGAACTAGAACGGTGGCAGTA 60.030 50.000 0.00 0.00 0.00 2.74
3574 4282 2.829720 TGAACTAGAACGGTGGCAGTAT 59.170 45.455 0.00 0.00 0.00 2.12
3676 4389 5.644644 TCGGGTTATCTTTCTACTTTCGAC 58.355 41.667 0.00 0.00 0.00 4.20
3701 4414 1.057847 CGTTCTCGTGTTCGCTGAATC 59.942 52.381 0.00 0.00 34.30 2.52
3705 4418 1.006825 TCGTGTTCGCTGAATCGTGG 61.007 55.000 13.28 0.00 36.96 4.94
3711 4424 0.669318 TCGCTGAATCGTGGTTCCAC 60.669 55.000 11.53 11.53 0.00 4.02
3856 4577 3.516586 GGGGAAAAGGGGAAATTCTGAA 58.483 45.455 0.00 0.00 0.00 3.02
3875 4596 2.615489 ACTAGTGTCGTCTCGCTTTC 57.385 50.000 0.00 0.00 0.00 2.62
3954 4675 4.227300 AGTGCTTACCATGACCTAATTCCA 59.773 41.667 0.00 0.00 0.00 3.53
3979 4700 4.034048 CACCAAGTTATGAGTTATCCGTGC 59.966 45.833 0.00 0.00 0.00 5.34
4074 4796 5.390567 GCTACCAAATGTCTTTGTAACGAGG 60.391 44.000 0.00 0.00 40.15 4.63
4076 4798 4.755123 ACCAAATGTCTTTGTAACGAGGAG 59.245 41.667 0.00 0.00 40.15 3.69
4093 4815 0.109226 GAGGTGACTAGTGGTGCGTC 60.109 60.000 0.00 0.00 44.43 5.19
4097 4819 0.902984 TGACTAGTGGTGCGTCCCAT 60.903 55.000 0.00 0.00 36.74 4.00
4113 4836 1.511850 CCATGCGACAGACTTTGTGA 58.488 50.000 0.00 0.00 41.05 3.58
4157 4880 1.542375 AGCCCAGGAGGATGGTTGT 60.542 57.895 0.00 0.00 38.81 3.32
4188 4911 6.887626 ATTCGGAATCTTCTACTCCTAGTC 57.112 41.667 0.00 0.00 0.00 2.59
4232 4956 0.698818 AGGCCTCGTTTCAAGGGATT 59.301 50.000 0.00 0.00 34.26 3.01
4234 4958 1.095600 GCCTCGTTTCAAGGGATTCC 58.904 55.000 0.00 0.00 34.26 3.01
4259 4984 1.962306 GTACCTGGGCGAACGCAAA 60.962 57.895 20.16 7.14 44.11 3.68
4260 4985 1.003112 TACCTGGGCGAACGCAAAT 60.003 52.632 20.16 4.15 44.11 2.32
4261 4986 0.249676 TACCTGGGCGAACGCAAATA 59.750 50.000 20.16 3.27 44.11 1.40
4262 4987 1.303091 ACCTGGGCGAACGCAAATAC 61.303 55.000 20.16 2.97 44.11 1.89
4263 4988 1.060308 CTGGGCGAACGCAAATACG 59.940 57.895 20.16 0.00 44.11 3.06
4271 4996 3.215244 CGAACGCAAATACGCAATATCC 58.785 45.455 0.00 0.00 36.19 2.59
4272 4997 2.941891 ACGCAAATACGCAATATCCG 57.058 45.000 0.00 0.00 36.19 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.497286 TGGAGGTGCACCCTACTTTTT 59.503 47.619 32.29 11.32 45.67 1.94
51 52 0.400594 GTGGAGGTGCACCCTACTTT 59.599 55.000 32.29 13.00 45.67 2.66
62 475 2.738521 CCTTGTCGCGTGGAGGTG 60.739 66.667 5.77 0.00 0.00 4.00
99 512 0.593128 CTGGAACAAGAAAGGGCACG 59.407 55.000 0.00 0.00 38.70 5.34
104 517 2.287608 GCCGTTTCTGGAACAAGAAAGG 60.288 50.000 13.95 13.95 38.70 3.11
111 525 0.759959 TAGTGGCCGTTTCTGGAACA 59.240 50.000 0.00 0.00 38.18 3.18
116 530 2.489971 TGTTTCTAGTGGCCGTTTCTG 58.510 47.619 0.00 0.00 0.00 3.02
123 537 4.649088 ACTTTGTTTGTTTCTAGTGGCC 57.351 40.909 0.00 0.00 0.00 5.36
124 538 7.422399 TCATAACTTTGTTTGTTTCTAGTGGC 58.578 34.615 0.00 0.00 0.00 5.01
125 539 9.965824 AATCATAACTTTGTTTGTTTCTAGTGG 57.034 29.630 0.00 0.00 0.00 4.00
128 542 9.626045 GGGAATCATAACTTTGTTTGTTTCTAG 57.374 33.333 0.00 0.00 0.00 2.43
129 543 8.293867 CGGGAATCATAACTTTGTTTGTTTCTA 58.706 33.333 0.00 0.00 0.00 2.10
130 544 7.145323 CGGGAATCATAACTTTGTTTGTTTCT 58.855 34.615 0.00 0.00 0.00 2.52
131 545 6.921307 ACGGGAATCATAACTTTGTTTGTTTC 59.079 34.615 0.00 0.00 0.00 2.78
177 599 2.514505 GAAAAGAAGTGAGCGGCGGC 62.515 60.000 9.78 8.43 40.37 6.53
181 603 1.069906 CCGTTGAAAAGAAGTGAGCGG 60.070 52.381 0.00 0.00 0.00 5.52
182 604 1.864711 TCCGTTGAAAAGAAGTGAGCG 59.135 47.619 0.00 0.00 0.00 5.03
183 605 2.872858 ACTCCGTTGAAAAGAAGTGAGC 59.127 45.455 0.00 0.00 0.00 4.26
184 606 4.260784 CCAACTCCGTTGAAAAGAAGTGAG 60.261 45.833 8.21 0.00 45.28 3.51
185 607 3.625764 CCAACTCCGTTGAAAAGAAGTGA 59.374 43.478 8.21 0.00 45.28 3.41
186 608 3.377172 ACCAACTCCGTTGAAAAGAAGTG 59.623 43.478 8.21 0.00 45.28 3.16
206 643 5.447818 CGTAAAGAGATGATGGAAAGCAACC 60.448 44.000 0.00 0.00 0.00 3.77
215 652 2.540515 ACGCACGTAAAGAGATGATGG 58.459 47.619 0.00 0.00 0.00 3.51
230 667 2.158959 CAGCTGCCTACGTACGCAC 61.159 63.158 16.72 11.39 0.00 5.34
231 668 2.180769 CAGCTGCCTACGTACGCA 59.819 61.111 16.72 16.64 0.00 5.24
232 669 2.582498 CCAGCTGCCTACGTACGC 60.582 66.667 16.72 9.31 0.00 4.42
309 749 5.105432 GGTATAACAGGAATACGGGGAGATC 60.105 48.000 0.00 0.00 31.76 2.75
314 754 2.028748 CCGGTATAACAGGAATACGGGG 60.029 54.545 10.41 1.54 42.35 5.73
333 773 4.299155 TCGAGGTAGATAAGTACGTACCG 58.701 47.826 21.80 13.53 40.03 4.02
334 774 5.350091 GGATCGAGGTAGATAAGTACGTACC 59.650 48.000 21.80 6.94 36.01 3.34
335 775 5.928839 TGGATCGAGGTAGATAAGTACGTAC 59.071 44.000 18.10 18.10 0.00 3.67
336 776 6.101650 TGGATCGAGGTAGATAAGTACGTA 57.898 41.667 0.00 0.00 0.00 3.57
338 778 4.996122 ACTGGATCGAGGTAGATAAGTACG 59.004 45.833 9.72 0.00 30.46 3.67
447 906 2.328099 CGAGTTTGCAGAGGTGGGC 61.328 63.158 0.00 0.00 0.00 5.36
457 918 1.129437 GTTGATGCTCTCCGAGTTTGC 59.871 52.381 0.00 0.25 31.39 3.68
464 925 2.892425 GCCCGTTGATGCTCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
501 962 3.444742 TCATAAACAATCCCTGCTGCAAG 59.555 43.478 3.02 0.00 0.00 4.01
510 971 2.021457 CGGGGTGTCATAAACAATCCC 58.979 52.381 7.43 7.43 44.31 3.85
527 988 5.639506 CACATCTCAGCCTAATTATAACGGG 59.360 44.000 0.00 0.00 0.00 5.28
544 1005 2.420372 TCGCCGCTATCTATCACATCTC 59.580 50.000 0.00 0.00 0.00 2.75
546 1007 2.520979 GTCGCCGCTATCTATCACATC 58.479 52.381 0.00 0.00 0.00 3.06
564 1029 1.793134 ATCGGCGGTGATAGGTCGTC 61.793 60.000 7.21 0.00 32.22 4.20
578 1043 3.250280 TCACTAATCGACTGACTATCGGC 59.750 47.826 0.00 0.00 40.05 5.54
623 1088 4.216472 GTCTTCTGGAATCTGTTGGTTTCC 59.784 45.833 0.00 0.00 41.69 3.13
634 1100 1.084370 CCGGTGCGTCTTCTGGAATC 61.084 60.000 0.00 0.00 32.26 2.52
666 1132 1.608283 GGTTTGACTTGTCTCCTCCCG 60.608 57.143 2.35 0.00 0.00 5.14
667 1133 1.420138 TGGTTTGACTTGTCTCCTCCC 59.580 52.381 2.35 0.00 0.00 4.30
728 1198 3.199891 GGTGGTTATCCCGTGCGC 61.200 66.667 0.00 0.00 35.15 6.09
734 1204 0.755079 GGGTCTACGGTGGTTATCCC 59.245 60.000 0.00 0.00 0.00 3.85
763 1233 3.276846 GAAAGCGCGTGGGTGTGT 61.277 61.111 8.43 0.00 0.00 3.72
764 1234 4.025401 GGAAAGCGCGTGGGTGTG 62.025 66.667 8.43 0.00 0.00 3.82
808 1285 0.614812 GCGAGGGGTGGGTTAAGTAA 59.385 55.000 0.00 0.00 0.00 2.24
810 1287 2.599757 GGCGAGGGGTGGGTTAAGT 61.600 63.158 0.00 0.00 0.00 2.24
811 1288 2.271173 GGCGAGGGGTGGGTTAAG 59.729 66.667 0.00 0.00 0.00 1.85
812 1289 3.332385 GGGCGAGGGGTGGGTTAA 61.332 66.667 0.00 0.00 0.00 2.01
813 1290 4.660611 TGGGCGAGGGGTGGGTTA 62.661 66.667 0.00 0.00 0.00 2.85
845 1322 1.220236 GGAATGGGAATGGGAATGGGA 59.780 52.381 0.00 0.00 0.00 4.37
846 1323 1.062275 TGGAATGGGAATGGGAATGGG 60.062 52.381 0.00 0.00 0.00 4.00
847 1324 2.041701 GTGGAATGGGAATGGGAATGG 58.958 52.381 0.00 0.00 0.00 3.16
848 1325 3.036452 AGTGGAATGGGAATGGGAATG 57.964 47.619 0.00 0.00 0.00 2.67
849 1326 3.630828 GGAAGTGGAATGGGAATGGGAAT 60.631 47.826 0.00 0.00 0.00 3.01
850 1327 2.292192 GGAAGTGGAATGGGAATGGGAA 60.292 50.000 0.00 0.00 0.00 3.97
851 1328 1.287739 GGAAGTGGAATGGGAATGGGA 59.712 52.381 0.00 0.00 0.00 4.37
852 1329 1.006998 TGGAAGTGGAATGGGAATGGG 59.993 52.381 0.00 0.00 0.00 4.00
853 1330 2.530460 TGGAAGTGGAATGGGAATGG 57.470 50.000 0.00 0.00 0.00 3.16
854 1331 4.141869 GGAAATGGAAGTGGAATGGGAATG 60.142 45.833 0.00 0.00 0.00 2.67
855 1332 4.033009 GGAAATGGAAGTGGAATGGGAAT 58.967 43.478 0.00 0.00 0.00 3.01
856 1333 3.181413 TGGAAATGGAAGTGGAATGGGAA 60.181 43.478 0.00 0.00 0.00 3.97
857 1334 2.381618 TGGAAATGGAAGTGGAATGGGA 59.618 45.455 0.00 0.00 0.00 4.37
883 1360 0.254747 TGAATGAATGGGGACGGGAC 59.745 55.000 0.00 0.00 0.00 4.46
884 1361 1.221635 ATGAATGAATGGGGACGGGA 58.778 50.000 0.00 0.00 0.00 5.14
909 1522 1.015085 CGTCGTCTCGTCTCTCTGGT 61.015 60.000 0.00 0.00 0.00 4.00
923 1536 3.130160 GCTCCCCGTAGTCGTCGT 61.130 66.667 0.00 0.00 35.01 4.34
962 1590 6.821665 CCAACTAGACAAAAATCTCCGGAATA 59.178 38.462 5.23 0.00 0.00 1.75
963 1591 5.648092 CCAACTAGACAAAAATCTCCGGAAT 59.352 40.000 5.23 0.00 0.00 3.01
964 1592 5.001232 CCAACTAGACAAAAATCTCCGGAA 58.999 41.667 5.23 0.00 0.00 4.30
965 1593 4.041198 ACCAACTAGACAAAAATCTCCGGA 59.959 41.667 2.93 2.93 0.00 5.14
1003 1631 4.463879 CCTCGCCACAGCCCTCAG 62.464 72.222 0.00 0.00 34.57 3.35
1264 1892 3.018149 GGAAGGAAGAGAGAAGAGCGTA 58.982 50.000 0.00 0.00 0.00 4.42
1265 1893 1.822371 GGAAGGAAGAGAGAAGAGCGT 59.178 52.381 0.00 0.00 0.00 5.07
1267 1895 1.484653 GGGGAAGGAAGAGAGAAGAGC 59.515 57.143 0.00 0.00 0.00 4.09
1277 1905 0.626382 GAAGGGGAAGGGGAAGGAAG 59.374 60.000 0.00 0.00 0.00 3.46
1278 1906 0.849540 GGAAGGGGAAGGGGAAGGAA 60.850 60.000 0.00 0.00 0.00 3.36
1305 1933 2.037251 CAGAGAAACCGGGAGAAACTCA 59.963 50.000 6.32 0.00 31.08 3.41
1319 1947 1.629013 CGCACGAGCATACAGAGAAA 58.371 50.000 5.50 0.00 42.27 2.52
1354 1992 1.891060 GACAAGACAAGACGCGCAGG 61.891 60.000 5.73 0.00 0.00 4.85
1359 1997 1.618640 GCCGAGACAAGACAAGACGC 61.619 60.000 0.00 0.00 0.00 5.19
1367 2005 1.293498 GAAGCCTGCCGAGACAAGA 59.707 57.895 0.00 0.00 0.00 3.02
1368 2006 2.097038 CGAAGCCTGCCGAGACAAG 61.097 63.158 0.00 0.00 0.00 3.16
1369 2007 2.048222 CGAAGCCTGCCGAGACAA 60.048 61.111 0.00 0.00 0.00 3.18
1756 2399 0.839277 TTGGCATCCTCATCATCGGT 59.161 50.000 0.00 0.00 0.00 4.69
1760 2403 8.168725 AGTAAGATAAATTGGCATCCTCATCAT 58.831 33.333 0.00 0.00 0.00 2.45
1775 2418 9.301897 GGGAGGCATGAAATTAGTAAGATAAAT 57.698 33.333 0.00 0.00 0.00 1.40
1776 2419 8.278639 TGGGAGGCATGAAATTAGTAAGATAAA 58.721 33.333 0.00 0.00 0.00 1.40
1777 2420 7.811282 TGGGAGGCATGAAATTAGTAAGATAA 58.189 34.615 0.00 0.00 0.00 1.75
1779 2422 6.266131 TGGGAGGCATGAAATTAGTAAGAT 57.734 37.500 0.00 0.00 0.00 2.40
1783 2430 6.012337 TGATTGGGAGGCATGAAATTAGTA 57.988 37.500 0.00 0.00 0.00 1.82
1785 2432 5.537295 TGATGATTGGGAGGCATGAAATTAG 59.463 40.000 0.00 0.00 0.00 1.73
1797 2444 5.569227 GCCTCTAATCTCTGATGATTGGGAG 60.569 48.000 10.59 13.91 37.27 4.30
1800 2447 5.224821 TGCCTCTAATCTCTGATGATTGG 57.775 43.478 10.59 8.66 37.27 3.16
1805 2452 8.881743 GCTATATTTTGCCTCTAATCTCTGATG 58.118 37.037 0.00 0.00 0.00 3.07
1806 2453 8.824783 AGCTATATTTTGCCTCTAATCTCTGAT 58.175 33.333 0.00 0.00 0.00 2.90
1816 2463 7.739825 TCTACAATCAGCTATATTTTGCCTCT 58.260 34.615 0.00 0.00 0.00 3.69
1825 2472 9.814899 GCAGATGTTATCTACAATCAGCTATAT 57.185 33.333 0.00 0.00 40.89 0.86
1826 2473 7.970614 CGCAGATGTTATCTACAATCAGCTATA 59.029 37.037 0.00 0.00 40.89 1.31
1829 2476 4.987285 CGCAGATGTTATCTACAATCAGCT 59.013 41.667 0.00 0.00 40.89 4.24
1839 2486 2.684881 CCAAAAGCCGCAGATGTTATCT 59.315 45.455 0.00 0.00 41.15 1.98
1899 2547 4.171005 CCATATTTCAGTGTGCAAGCAAG 58.829 43.478 0.00 0.00 0.00 4.01
1931 2586 5.155643 TGAATCTGTGATGCAATTTCGTTG 58.844 37.500 0.00 0.00 40.90 4.10
2002 2657 7.119846 ACTCAAGGTCAATGACATTAGTTAAGC 59.880 37.037 13.08 0.00 34.27 3.09
2048 2709 4.944048 ACAAAAGGGGTCAATTTCTTTCG 58.056 39.130 0.00 0.00 0.00 3.46
2142 2803 9.123902 CACAGTGAATATCATCTTAAATTGGGA 57.876 33.333 0.00 0.00 0.00 4.37
2155 2816 8.006298 AGTTTCCAAAAACACAGTGAATATCA 57.994 30.769 7.81 0.00 45.94 2.15
2196 2857 7.385205 GCTTTAAAGTGGAAAGAGGAAAATTCC 59.615 37.037 16.38 3.93 42.39 3.01
2210 2871 3.799366 TCAGTGTTCGCTTTAAAGTGGA 58.201 40.909 24.64 16.35 37.15 4.02
2211 2872 4.545823 TTCAGTGTTCGCTTTAAAGTGG 57.454 40.909 24.64 13.75 37.15 4.00
2274 2937 9.840034 CCAGGAATCCAGGACTGAGGATACTAT 62.840 48.148 4.49 0.00 43.67 2.12
2281 2944 0.835941 CCAGGAATCCAGGACTGAGG 59.164 60.000 4.49 0.00 31.24 3.86
2354 3017 4.682778 TCCTGGATAGTTTATGAACCCG 57.317 45.455 0.00 0.00 36.39 5.28
2425 3096 7.969536 TCTTATCACCAAAAGAGAGAAACTG 57.030 36.000 0.00 0.00 0.00 3.16
2451 3127 2.033424 GCTTCCCAACGATAAATGGAGC 59.967 50.000 0.00 0.00 39.12 4.70
2506 3182 2.053627 GTGATGACAAAAAGGCAAGCG 58.946 47.619 0.00 0.00 39.98 4.68
2541 3219 5.016459 AGGTTCTCCTAACTCCTAAGAGGAA 59.984 44.000 0.00 0.00 42.63 3.36
2692 3370 2.025793 TCTGCCGAAATAATGGGTCCAA 60.026 45.455 0.00 0.00 0.00 3.53
2742 3420 0.670546 GTGGTTCAGCGCTAAGAGCA 60.671 55.000 10.99 12.14 42.58 4.26
2846 3527 4.038282 TCTTGAAGACAATTTGCACAGCAT 59.962 37.500 0.00 0.00 35.34 3.79
2905 3586 3.474600 CTCCCCACATGAGATCATCAAC 58.525 50.000 0.00 0.00 42.53 3.18
2911 3592 3.282885 GAAAACCTCCCCACATGAGATC 58.717 50.000 0.00 0.00 31.26 2.75
2924 3606 3.604875 TCATACGTGGAGGAAAACCTC 57.395 47.619 0.00 7.64 36.20 3.85
2925 3607 4.019681 TCATTCATACGTGGAGGAAAACCT 60.020 41.667 0.00 0.00 0.00 3.50
2932 3615 3.062763 GCAGATCATTCATACGTGGAGG 58.937 50.000 0.00 0.00 0.00 4.30
2953 3636 8.344831 TCACACAAGTCATTTCATTTGTTCTAG 58.655 33.333 0.00 0.00 31.84 2.43
2958 3641 7.980662 TGATTTCACACAAGTCATTTCATTTGT 59.019 29.630 0.00 0.00 34.31 2.83
2988 3679 1.279558 TCGGTTTGCTATACCCTGCAA 59.720 47.619 0.00 0.00 45.83 4.08
3227 3918 2.821366 GGCTGCACCGACTGGATG 60.821 66.667 0.50 0.00 39.21 3.51
3228 3919 3.321648 TGGCTGCACCGACTGGAT 61.322 61.111 0.50 0.00 43.94 3.41
3229 3920 4.314440 GTGGCTGCACCGACTGGA 62.314 66.667 0.50 0.00 43.94 3.86
3231 3922 4.969196 ACGTGGCTGCACCGACTG 62.969 66.667 15.49 0.80 43.94 3.51
3232 3923 4.664677 GACGTGGCTGCACCGACT 62.665 66.667 15.49 0.00 43.94 4.18
3233 3924 4.961511 TGACGTGGCTGCACCGAC 62.962 66.667 15.49 10.49 43.94 4.79
3234 3925 4.662961 CTGACGTGGCTGCACCGA 62.663 66.667 15.49 0.00 43.94 4.69
3243 3934 2.654877 ACGGTAAGCCTGACGTGG 59.345 61.111 0.00 0.00 38.24 4.94
3245 3936 1.177256 AGTCACGGTAAGCCTGACGT 61.177 55.000 0.00 0.00 42.45 4.34
3246 3937 0.456312 GAGTCACGGTAAGCCTGACG 60.456 60.000 7.37 0.00 42.45 4.35
3247 3938 0.108756 GGAGTCACGGTAAGCCTGAC 60.109 60.000 0.00 5.66 40.26 3.51
3248 3939 1.592400 CGGAGTCACGGTAAGCCTGA 61.592 60.000 0.00 0.00 0.00 3.86
3249 3940 1.153823 CGGAGTCACGGTAAGCCTG 60.154 63.158 0.00 0.00 0.00 4.85
3250 3941 3.285371 CGGAGTCACGGTAAGCCT 58.715 61.111 0.00 0.00 0.00 4.58
3276 3967 1.777941 GGAGTCCCGTCTTATCTGGT 58.222 55.000 0.00 0.00 0.00 4.00
3288 3979 1.341383 TGGTCTACTAACCGGAGTCCC 60.341 57.143 9.46 4.11 42.62 4.46
3289 3980 2.022934 CTGGTCTACTAACCGGAGTCC 58.977 57.143 9.46 1.92 46.94 3.85
3294 3985 4.024218 CGTCTTATCTGGTCTACTAACCGG 60.024 50.000 0.00 0.00 45.59 5.28
3295 3986 4.024218 CCGTCTTATCTGGTCTACTAACCG 60.024 50.000 0.00 0.00 42.62 4.44
3296 3987 4.277921 CCCGTCTTATCTGGTCTACTAACC 59.722 50.000 0.00 0.00 39.94 2.85
3297 3988 4.261530 GCCCGTCTTATCTGGTCTACTAAC 60.262 50.000 0.00 0.00 0.00 2.34
3298 3989 3.887716 GCCCGTCTTATCTGGTCTACTAA 59.112 47.826 0.00 0.00 0.00 2.24
3299 3990 3.117776 TGCCCGTCTTATCTGGTCTACTA 60.118 47.826 0.00 0.00 0.00 1.82
3300 3991 2.308690 GCCCGTCTTATCTGGTCTACT 58.691 52.381 0.00 0.00 0.00 2.57
3301 3992 2.029623 TGCCCGTCTTATCTGGTCTAC 58.970 52.381 0.00 0.00 0.00 2.59
3302 3993 2.307768 CTGCCCGTCTTATCTGGTCTA 58.692 52.381 0.00 0.00 0.00 2.59
3303 3994 1.115467 CTGCCCGTCTTATCTGGTCT 58.885 55.000 0.00 0.00 0.00 3.85
3304 3995 0.530870 GCTGCCCGTCTTATCTGGTC 60.531 60.000 0.00 0.00 0.00 4.02
3305 3996 1.264749 TGCTGCCCGTCTTATCTGGT 61.265 55.000 0.00 0.00 0.00 4.00
3306 3997 0.531532 CTGCTGCCCGTCTTATCTGG 60.532 60.000 0.00 0.00 0.00 3.86
3307 3998 0.461548 TCTGCTGCCCGTCTTATCTG 59.538 55.000 0.00 0.00 0.00 2.90
3308 3999 1.137872 CTTCTGCTGCCCGTCTTATCT 59.862 52.381 0.00 0.00 0.00 1.98
3309 4000 1.576356 CTTCTGCTGCCCGTCTTATC 58.424 55.000 0.00 0.00 0.00 1.75
3310 4001 0.462759 GCTTCTGCTGCCCGTCTTAT 60.463 55.000 0.00 0.00 36.03 1.73
3311 4002 1.079127 GCTTCTGCTGCCCGTCTTA 60.079 57.895 0.00 0.00 36.03 2.10
3312 4003 2.359230 GCTTCTGCTGCCCGTCTT 60.359 61.111 0.00 0.00 36.03 3.01
3599 4307 1.678970 GCTGAAATTCGGGGTGCCT 60.679 57.895 3.77 0.00 0.00 4.75
3676 4389 1.730593 GCGAACACGAGAACGATCGG 61.731 60.000 20.98 3.20 46.91 4.18
3705 4418 4.943705 TGATTCCTGATAAGCAAGTGGAAC 59.056 41.667 0.00 0.00 36.57 3.62
3711 4424 4.201990 GCCAAGTGATTCCTGATAAGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
3837 4558 6.010850 ACTAGTTCAGAATTTCCCCTTTTCC 58.989 40.000 0.00 0.00 0.00 3.13
3838 4559 6.490381 ACACTAGTTCAGAATTTCCCCTTTTC 59.510 38.462 0.00 0.00 0.00 2.29
3856 4577 2.152830 AGAAAGCGAGACGACACTAGT 58.847 47.619 0.00 0.00 0.00 2.57
3954 4675 4.081087 ACGGATAACTCATAACTTGGTGCT 60.081 41.667 0.00 0.00 0.00 4.40
3979 4700 1.066454 TGTCACGGTGTCACTAGTGTG 59.934 52.381 21.99 12.04 45.07 3.82
4074 4796 0.109226 GACGCACCACTAGTCACCTC 60.109 60.000 0.00 0.00 35.19 3.85
4076 4798 1.080025 GGACGCACCACTAGTCACC 60.080 63.158 0.00 0.00 38.79 4.02
4082 4804 2.267642 GCATGGGACGCACCACTA 59.732 61.111 0.19 0.00 44.72 2.74
4093 4815 0.518636 CACAAAGTCTGTCGCATGGG 59.481 55.000 2.76 2.76 35.47 4.00
4097 4819 0.750249 TCCTCACAAAGTCTGTCGCA 59.250 50.000 0.00 0.00 35.47 5.10
4113 4836 3.198635 ACGAATTGGACATCACTGATCCT 59.801 43.478 0.00 0.00 33.34 3.24
4124 4847 0.608035 GGGCTGGAACGAATTGGACA 60.608 55.000 0.00 0.00 0.00 4.02
4127 4850 1.315257 CCTGGGCTGGAACGAATTGG 61.315 60.000 0.00 0.00 0.00 3.16
4131 4854 2.592993 CCTCCTGGGCTGGAACGAA 61.593 63.158 0.00 0.00 35.43 3.85
4152 4875 4.941873 AGATTCCGAATTCCACTTACAACC 59.058 41.667 0.00 0.00 0.00 3.77
4157 4880 7.417570 GGAGTAGAAGATTCCGAATTCCACTTA 60.418 40.741 0.00 0.00 27.37 2.24
4247 4972 2.277057 GCGTATTTGCGTTCGCCC 60.277 61.111 14.44 0.00 42.33 6.13


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

AutoCloner maintained by Alex Coulton.