Multiple sequence alignment - TraesCS6A01G186900

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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 TraesCS6A01G186900 chr6A 100.000 3334 0 0 1 3334 222683783 222680450 0.000000e+00 6157.0
1 TraesCS6A01G186900 chr6A 93.935 676 36 2 2659 3334 222136911 222136241 0.000000e+00 1016.0
2 TraesCS6A01G186900 chr6A 100.000 151 0 0 955 1105 109115269 109115419 2.530000e-71 279.0
3 TraesCS6A01G186900 chr6A 90.728 151 12 2 1823 1971 32463978 32463828 2.030000e-47 200.0
4 TraesCS6A01G186900 chr6A 75.956 183 28 13 524 705 597773449 597773282 2.760000e-11 80.5
5 TraesCS6A01G186900 chr6A 90.909 55 2 1 2578 2632 222136970 222136919 1.660000e-08 71.3
6 TraesCS6A01G186900 chr6D 95.827 1390 44 7 1956 3334 162957451 162956065 0.000000e+00 2233.0
7 TraesCS6A01G186900 chr6D 92.693 739 41 7 1105 1832 162958185 162957449 0.000000e+00 1053.0
8 TraesCS6A01G186900 chr6D 75.298 672 106 30 47 697 407824105 407824737 1.970000e-67 267.0
9 TraesCS6A01G186900 chr6D 97.931 145 2 1 812 955 162958320 162958176 1.990000e-62 250.0
10 TraesCS6A01G186900 chr6B 95.979 970 21 5 1956 2913 299601372 299602335 0.000000e+00 1559.0
11 TraesCS6A01G186900 chr6B 89.348 751 48 15 1105 1832 299600633 299601374 0.000000e+00 915.0
12 TraesCS6A01G186900 chr6B 93.772 562 31 1 2773 3334 299823993 299824550 0.000000e+00 841.0
13 TraesCS6A01G186900 chr6B 96.606 383 11 2 2952 3334 299602333 299602713 4.690000e-178 634.0
14 TraesCS6A01G186900 chr6B 82.619 443 47 14 150 586 299599286 299599704 6.800000e-97 364.0
15 TraesCS6A01G186900 chr6B 82.639 432 47 15 148 578 299599903 299600307 1.140000e-94 357.0
16 TraesCS6A01G186900 chr6B 85.174 344 29 15 625 955 299600308 299600642 1.920000e-87 333.0
17 TraesCS6A01G186900 chr6B 91.282 195 17 0 4 198 299599107 299599301 1.970000e-67 267.0
18 TraesCS6A01G186900 chr6B 89.352 216 11 6 2578 2789 299821893 299822100 9.170000e-66 261.0
19 TraesCS6A01G186900 chr6B 73.684 779 146 32 8 777 40429732 40429004 7.140000e-62 248.0
20 TraesCS6A01G186900 chr6B 75.874 572 87 27 135 697 612129865 612130394 9.240000e-61 244.0
21 TraesCS6A01G186900 chr6B 81.429 140 20 3 59 195 701611485 701611349 3.520000e-20 110.0
22 TraesCS6A01G186900 chr7A 88.462 546 49 10 2788 3332 438261031 438260499 0.000000e+00 647.0
23 TraesCS6A01G186900 chr7D 87.302 504 47 11 2788 3290 388035950 388035463 8.080000e-156 560.0
24 TraesCS6A01G186900 chr7B 84.644 547 46 14 2787 3332 383515562 383515053 8.250000e-141 510.0
25 TraesCS6A01G186900 chr7B 98.667 150 2 0 956 1105 40086138 40085989 1.970000e-67 267.0
26 TraesCS6A01G186900 chr7B 94.853 136 7 0 1823 1958 675661961 675662096 2.610000e-51 213.0
27 TraesCS6A01G186900 chr7B 94.815 135 7 0 1830 1964 506990563 506990697 9.370000e-51 211.0
28 TraesCS6A01G186900 chr7B 94.161 137 8 0 1822 1958 523328270 523328134 3.370000e-50 209.0
29 TraesCS6A01G186900 chr7B 92.754 138 10 0 1823 1960 376045976 376046113 2.030000e-47 200.0
30 TraesCS6A01G186900 chr7B 72.989 522 103 32 192 705 102261729 102261238 7.450000e-32 148.0
31 TraesCS6A01G186900 chr1D 76.018 663 102 33 57 704 357223594 357222974 1.170000e-74 291.0
32 TraesCS6A01G186900 chr1D 74.857 700 131 29 10 705 68438022 68437364 3.280000e-70 276.0
33 TraesCS6A01G186900 chr1D 73.000 300 61 13 228 514 375756838 375756546 1.650000e-13 87.9
34 TraesCS6A01G186900 chr3A 97.590 166 4 0 952 1117 429461053 429460888 5.440000e-73 285.0
35 TraesCS6A01G186900 chr3A 90.728 151 12 2 1823 1971 346245384 346245234 2.030000e-47 200.0
36 TraesCS6A01G186900 chr2B 99.351 154 1 0 953 1106 273752397 273752550 2.530000e-71 279.0
37 TraesCS6A01G186900 chr2B 98.065 155 2 1 956 1110 169501300 169501453 5.480000e-68 268.0
38 TraesCS6A01G186900 chr5B 100.000 150 0 0 956 1105 652825219 652825070 9.110000e-71 278.0
39 TraesCS6A01G186900 chr5B 98.684 152 2 0 954 1105 697513471 697513622 1.520000e-68 270.0
40 TraesCS6A01G186900 chr3B 99.346 153 1 0 953 1105 824153840 824153992 9.110000e-71 278.0
41 TraesCS6A01G186900 chr1B 97.436 156 4 0 956 1111 101247786 101247631 1.970000e-67 267.0
42 TraesCS6A01G186900 chr1B 96.875 32 1 0 629 660 1745651 1745620 2.000000e-03 54.7
43 TraesCS6A01G186900 chr5A 75.459 599 106 26 109 701 440951970 440952533 1.540000e-63 254.0
44 TraesCS6A01G186900 chr5A 91.837 49 3 1 623 670 414094105 414094153 2.150000e-07 67.6
45 TraesCS6A01G186900 chr3D 86.364 220 26 4 184 401 165593255 165593038 1.550000e-58 237.0
46 TraesCS6A01G186900 chr2A 75.309 567 91 28 140 691 717177162 717177694 3.350000e-55 226.0
47 TraesCS6A01G186900 chr2A 73.684 513 105 16 185 694 19612560 19612075 4.420000e-39 172.0
48 TraesCS6A01G186900 chr2A 78.750 160 29 5 418 574 773806067 773805910 5.880000e-18 102.0
49 TraesCS6A01G186900 chr4B 94.853 136 7 0 1823 1958 384045706 384045571 2.610000e-51 213.0
50 TraesCS6A01G186900 chr4B 91.837 147 11 1 1823 1968 170678366 170678512 1.570000e-48 204.0
51 TraesCS6A01G186900 chr5D 94.737 133 7 0 1830 1962 56233838 56233706 1.210000e-49 207.0
52 TraesCS6A01G186900 chr2D 76.882 186 37 4 417 598 315082561 315082378 2.120000e-17 100.0


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 TraesCS6A01G186900 chr6A 222680450 222683783 3333 True 6157.000000 6157 100.000000 1 3334 1 chr6A.!!$R2 3333
1 TraesCS6A01G186900 chr6A 222136241 222136970 729 True 543.650000 1016 92.422000 2578 3334 2 chr6A.!!$R4 756
2 TraesCS6A01G186900 chr6D 162956065 162958320 2255 True 1178.666667 2233 95.483667 812 3334 3 chr6D.!!$R1 2522
3 TraesCS6A01G186900 chr6D 407824105 407824737 632 False 267.000000 267 75.298000 47 697 1 chr6D.!!$F1 650
4 TraesCS6A01G186900 chr6B 299599107 299602713 3606 False 632.714286 1559 89.092429 4 3334 7 chr6B.!!$F2 3330
5 TraesCS6A01G186900 chr6B 299821893 299824550 2657 False 551.000000 841 91.562000 2578 3334 2 chr6B.!!$F3 756
6 TraesCS6A01G186900 chr6B 40429004 40429732 728 True 248.000000 248 73.684000 8 777 1 chr6B.!!$R1 769
7 TraesCS6A01G186900 chr6B 612129865 612130394 529 False 244.000000 244 75.874000 135 697 1 chr6B.!!$F1 562
8 TraesCS6A01G186900 chr7A 438260499 438261031 532 True 647.000000 647 88.462000 2788 3332 1 chr7A.!!$R1 544
9 TraesCS6A01G186900 chr7B 383515053 383515562 509 True 510.000000 510 84.644000 2787 3332 1 chr7B.!!$R3 545
10 TraesCS6A01G186900 chr1D 357222974 357223594 620 True 291.000000 291 76.018000 57 704 1 chr1D.!!$R2 647
11 TraesCS6A01G186900 chr1D 68437364 68438022 658 True 276.000000 276 74.857000 10 705 1 chr1D.!!$R1 695
12 TraesCS6A01G186900 chr5A 440951970 440952533 563 False 254.000000 254 75.459000 109 701 1 chr5A.!!$F2 592
13 TraesCS6A01G186900 chr2A 717177162 717177694 532 False 226.000000 226 75.309000 140 691 1 chr2A.!!$F1 551

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
599 1337 0.029035 CTCCATCGTTAGTCCGACGG 59.971 60.0 7.84 7.84 41.32 4.79 F
1003 1754 0.025513 GCACGACAGATGAACGATGC 59.974 55.0 0.00 0.00 0.00 3.91 F
1014 1765 0.026285 GAACGATGCGGGATCAAACG 59.974 55.0 10.19 0.00 0.00 3.60 F
1098 1849 0.033366 ACAGCATCGTGTGTGTAGCA 59.967 50.0 0.00 0.00 0.00 3.49 F
1110 1861 0.110644 GTGTAGCACTGCTCGTTTGC 60.111 55.0 6.86 0.00 40.44 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2525 0.756070 GGAGGTTAGAGCTAGCCGGT 60.756 60.0 12.13 0.0 40.77 5.28 R
1828 2614 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.0 0.00 0.0 0.00 2.90 R
1829 2615 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.0 0.00 0.0 0.00 2.73 R
2280 3078 2.887151 AGAGATCCAAAACCCTGTGG 57.113 50.0 0.00 0.0 36.13 4.17 R
2518 3316 2.941415 GCAGGCAATAACTACAGGCACT 60.941 50.0 0.00 0.0 43.88 4.40 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
44 45 2.698803 CAACCATGTCATCGACTTCCA 58.301 47.619 0.00 0.00 33.15 3.53
48 49 0.175760 ATGTCATCGACTTCCACGGG 59.824 55.000 0.00 0.00 33.15 5.28
165 203 0.264359 ACATCCTCCTCCTCCTCCTG 59.736 60.000 0.00 0.00 0.00 3.86
173 211 3.073735 CCTCCTCCTGCTGCTCGT 61.074 66.667 0.00 0.00 0.00 4.18
182 274 3.071206 GCTGCTCGTCCTCCTCCA 61.071 66.667 0.00 0.00 0.00 3.86
222 341 1.486726 GTCCTCCTTTGGATCCATCGT 59.513 52.381 17.06 0.00 38.52 3.73
293 412 4.399395 CAAGGAGCTGCAGCCGGA 62.399 66.667 34.39 0.00 43.38 5.14
446 1183 1.646912 TGTGGACGGATAGGGTTTCA 58.353 50.000 0.00 0.00 0.00 2.69
457 1194 2.258726 GGGTTTCAGTGCCGGTGAC 61.259 63.158 1.90 0.00 0.00 3.67
458 1195 1.525077 GGTTTCAGTGCCGGTGACA 60.525 57.895 1.90 0.00 0.00 3.58
581 1319 1.474498 GGAGTGTTTTCGTGTGGGACT 60.474 52.381 0.00 0.00 0.00 3.85
589 1327 1.183030 TCGTGTGGGACTCCATCGTT 61.183 55.000 0.00 0.00 46.09 3.85
599 1337 0.029035 CTCCATCGTTAGTCCGACGG 59.971 60.000 7.84 7.84 41.32 4.79
600 1338 0.392863 TCCATCGTTAGTCCGACGGA 60.393 55.000 13.88 13.88 45.86 4.69
601 1339 0.666913 CCATCGTTAGTCCGACGGAT 59.333 55.000 21.53 11.58 42.49 4.18
602 1340 1.599667 CCATCGTTAGTCCGACGGATG 60.600 57.143 21.53 12.01 42.49 3.51
604 1342 0.729116 TCGTTAGTCCGACGGATGAC 59.271 55.000 21.53 16.80 40.70 3.06
605 1343 0.248377 CGTTAGTCCGACGGATGACC 60.248 60.000 21.53 7.02 36.90 4.02
616 1354 2.420568 GGATGACCGGTCGTGCCTA 61.421 63.158 33.52 13.53 31.75 3.93
618 1356 1.379443 ATGACCGGTCGTGCCTAGA 60.379 57.895 28.38 9.08 34.25 2.43
619 1357 0.755698 ATGACCGGTCGTGCCTAGAT 60.756 55.000 28.38 11.15 34.25 1.98
620 1358 1.359475 GACCGGTCGTGCCTAGATC 59.641 63.158 20.85 0.00 34.25 2.75
621 1359 1.076923 ACCGGTCGTGCCTAGATCT 60.077 57.895 0.00 0.00 34.25 2.75
627 1366 0.188587 TCGTGCCTAGATCTCCCCAT 59.811 55.000 0.00 0.00 0.00 4.00
670 1409 0.779997 ATGAGGGGTTTTGGTCAGCT 59.220 50.000 0.00 0.00 0.00 4.24
673 1412 0.779997 AGGGGTTTTGGTCAGCTCAT 59.220 50.000 0.00 0.00 0.00 2.90
705 1444 0.034896 GGTTTGAGAAGCCCGTCTGA 59.965 55.000 0.00 0.00 0.00 3.27
706 1445 1.542547 GGTTTGAGAAGCCCGTCTGAA 60.543 52.381 0.00 0.00 0.00 3.02
742 1483 3.650950 ATTGGCCAGGCTGTCCGT 61.651 61.111 12.43 0.00 37.47 4.69
766 1507 0.178975 ACATTTGAGGCGGGTTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
767 1508 0.527565 CATTTGAGGCGGGTTTGGAG 59.472 55.000 0.00 0.00 0.00 3.86
768 1509 0.112412 ATTTGAGGCGGGTTTGGAGT 59.888 50.000 0.00 0.00 0.00 3.85
777 1518 1.675219 GGTTTGGAGTGCCCGACTA 59.325 57.895 0.00 0.00 37.93 2.59
800 1546 6.006759 ACTCTTAGTCAGAAAATTTGCTGC 57.993 37.500 19.94 14.85 32.27 5.25
801 1547 5.767168 ACTCTTAGTCAGAAAATTTGCTGCT 59.233 36.000 19.94 20.08 32.27 4.24
805 1551 7.649306 TCTTAGTCAGAAAATTTGCTGCTTTTC 59.351 33.333 19.94 14.28 40.18 2.29
962 1713 2.712077 GCGTTTGCAATCGGAACTG 58.288 52.632 26.27 8.34 42.15 3.16
963 1714 1.337110 GCGTTTGCAATCGGAACTGC 61.337 55.000 26.27 13.31 42.15 4.40
964 1715 0.238289 CGTTTGCAATCGGAACTGCT 59.762 50.000 19.72 0.00 39.38 4.24
965 1716 1.689959 GTTTGCAATCGGAACTGCTG 58.310 50.000 0.00 0.00 39.38 4.41
966 1717 0.039256 TTTGCAATCGGAACTGCTGC 60.039 50.000 0.00 0.00 39.38 5.25
967 1718 2.099062 GCAATCGGAACTGCTGCG 59.901 61.111 7.88 0.00 40.85 5.18
968 1719 2.099062 CAATCGGAACTGCTGCGC 59.901 61.111 0.00 0.00 39.03 6.09
969 1720 3.490759 AATCGGAACTGCTGCGCG 61.491 61.111 0.00 0.00 39.03 6.86
980 1731 3.767230 CTGCGCGGACGACAACAG 61.767 66.667 11.90 0.00 43.93 3.16
981 1732 4.578898 TGCGCGGACGACAACAGT 62.579 61.111 8.83 0.00 43.93 3.55
982 1733 2.429571 GCGCGGACGACAACAGTA 60.430 61.111 8.83 0.00 43.93 2.74
983 1734 1.804326 GCGCGGACGACAACAGTAT 60.804 57.895 8.83 0.00 43.93 2.12
984 1735 1.988409 CGCGGACGACAACAGTATG 59.012 57.895 0.00 0.00 43.93 2.39
985 1736 1.708027 GCGGACGACAACAGTATGC 59.292 57.895 0.00 0.00 42.53 3.14
986 1737 1.011968 GCGGACGACAACAGTATGCA 61.012 55.000 0.00 0.00 42.53 3.96
987 1738 0.713883 CGGACGACAACAGTATGCAC 59.286 55.000 0.00 0.00 42.53 4.57
988 1739 0.713883 GGACGACAACAGTATGCACG 59.286 55.000 0.00 0.00 42.53 5.34
989 1740 1.667756 GGACGACAACAGTATGCACGA 60.668 52.381 0.00 0.00 42.53 4.35
990 1741 1.385743 GACGACAACAGTATGCACGAC 59.614 52.381 0.00 0.00 42.53 4.34
991 1742 1.269361 ACGACAACAGTATGCACGACA 60.269 47.619 0.00 0.00 42.53 4.35
992 1743 1.386748 CGACAACAGTATGCACGACAG 59.613 52.381 0.00 0.00 42.53 3.51
993 1744 2.672714 GACAACAGTATGCACGACAGA 58.327 47.619 0.00 0.00 42.53 3.41
994 1745 3.254060 GACAACAGTATGCACGACAGAT 58.746 45.455 0.00 0.00 42.53 2.90
995 1746 2.995939 ACAACAGTATGCACGACAGATG 59.004 45.455 0.00 0.00 42.53 2.90
996 1747 3.253230 CAACAGTATGCACGACAGATGA 58.747 45.455 0.00 0.00 42.53 2.92
997 1748 3.592898 ACAGTATGCACGACAGATGAA 57.407 42.857 0.00 0.00 42.53 2.57
998 1749 3.254060 ACAGTATGCACGACAGATGAAC 58.746 45.455 0.00 0.00 42.53 3.18
999 1750 2.279921 CAGTATGCACGACAGATGAACG 59.720 50.000 0.00 0.00 0.00 3.95
1000 1751 2.163613 AGTATGCACGACAGATGAACGA 59.836 45.455 0.00 0.00 0.00 3.85
1001 1752 2.299993 ATGCACGACAGATGAACGAT 57.700 45.000 0.00 0.00 0.00 3.73
1002 1753 1.349234 TGCACGACAGATGAACGATG 58.651 50.000 0.00 0.00 0.00 3.84
1003 1754 0.025513 GCACGACAGATGAACGATGC 59.974 55.000 0.00 0.00 0.00 3.91
1004 1755 0.295763 CACGACAGATGAACGATGCG 59.704 55.000 0.00 0.00 0.00 4.73
1005 1756 0.802222 ACGACAGATGAACGATGCGG 60.802 55.000 0.00 0.00 0.00 5.69
1006 1757 1.482621 CGACAGATGAACGATGCGGG 61.483 60.000 0.00 0.00 0.00 6.13
1007 1758 0.179111 GACAGATGAACGATGCGGGA 60.179 55.000 0.00 0.00 0.00 5.14
1008 1759 0.465705 ACAGATGAACGATGCGGGAT 59.534 50.000 0.00 0.00 0.00 3.85
1009 1760 1.143305 CAGATGAACGATGCGGGATC 58.857 55.000 0.00 0.00 0.00 3.36
1010 1761 0.752658 AGATGAACGATGCGGGATCA 59.247 50.000 10.19 0.00 0.00 2.92
1011 1762 1.138859 AGATGAACGATGCGGGATCAA 59.861 47.619 10.19 0.00 0.00 2.57
1012 1763 1.939934 GATGAACGATGCGGGATCAAA 59.060 47.619 10.19 0.00 0.00 2.69
1013 1764 1.083489 TGAACGATGCGGGATCAAAC 58.917 50.000 10.19 0.95 0.00 2.93
1014 1765 0.026285 GAACGATGCGGGATCAAACG 59.974 55.000 10.19 0.00 0.00 3.60
1015 1766 1.366111 AACGATGCGGGATCAAACGG 61.366 55.000 10.19 0.00 0.00 4.44
1016 1767 1.813753 CGATGCGGGATCAAACGGT 60.814 57.895 10.19 0.00 0.00 4.83
1017 1768 1.762222 CGATGCGGGATCAAACGGTC 61.762 60.000 10.19 0.00 0.00 4.79
1018 1769 0.462047 GATGCGGGATCAAACGGTCT 60.462 55.000 4.47 0.00 0.00 3.85
1019 1770 0.744414 ATGCGGGATCAAACGGTCTG 60.744 55.000 0.00 0.00 0.00 3.51
1020 1771 2.750888 GCGGGATCAAACGGTCTGC 61.751 63.158 0.00 0.00 0.00 4.26
1021 1772 1.079127 CGGGATCAAACGGTCTGCT 60.079 57.895 0.00 0.00 0.00 4.24
1022 1773 1.361668 CGGGATCAAACGGTCTGCTG 61.362 60.000 0.00 0.00 0.00 4.41
1023 1774 1.026718 GGGATCAAACGGTCTGCTGG 61.027 60.000 0.00 0.00 0.00 4.85
1024 1775 0.036388 GGATCAAACGGTCTGCTGGA 60.036 55.000 0.00 0.00 0.00 3.86
1025 1776 1.079503 GATCAAACGGTCTGCTGGAC 58.920 55.000 2.54 2.54 43.79 4.02
1026 1777 0.687354 ATCAAACGGTCTGCTGGACT 59.313 50.000 9.50 0.00 43.97 3.85
1027 1778 0.033504 TCAAACGGTCTGCTGGACTC 59.966 55.000 9.50 1.51 43.97 3.36
1028 1779 0.034059 CAAACGGTCTGCTGGACTCT 59.966 55.000 9.50 0.00 43.97 3.24
1029 1780 0.034059 AAACGGTCTGCTGGACTCTG 59.966 55.000 9.50 4.32 43.97 3.35
1030 1781 2.125753 CGGTCTGCTGGACTCTGC 60.126 66.667 9.50 0.00 43.97 4.26
1031 1782 2.644212 CGGTCTGCTGGACTCTGCT 61.644 63.158 9.50 0.00 43.97 4.24
1032 1783 1.315981 CGGTCTGCTGGACTCTGCTA 61.316 60.000 9.50 0.00 43.97 3.49
1033 1784 0.174617 GGTCTGCTGGACTCTGCTAC 59.825 60.000 9.50 0.00 43.97 3.58
1034 1785 0.891373 GTCTGCTGGACTCTGCTACA 59.109 55.000 3.73 0.00 41.46 2.74
1035 1786 1.480137 GTCTGCTGGACTCTGCTACAT 59.520 52.381 3.73 0.00 41.46 2.29
1036 1787 1.479730 TCTGCTGGACTCTGCTACATG 59.520 52.381 0.00 0.00 38.45 3.21
1037 1788 0.107993 TGCTGGACTCTGCTACATGC 60.108 55.000 0.00 0.00 43.25 4.06
1046 1797 4.855105 GCTACATGCATGGACGGA 57.145 55.556 29.41 9.11 42.31 4.69
1047 1798 2.311294 GCTACATGCATGGACGGAC 58.689 57.895 29.41 9.72 42.31 4.79
1048 1799 0.461870 GCTACATGCATGGACGGACA 60.462 55.000 29.41 5.67 42.31 4.02
1049 1800 1.575244 CTACATGCATGGACGGACAG 58.425 55.000 29.41 5.40 0.00 3.51
1050 1801 0.177836 TACATGCATGGACGGACAGG 59.822 55.000 29.41 1.63 0.00 4.00
1051 1802 1.820906 CATGCATGGACGGACAGGG 60.821 63.158 19.40 0.00 0.00 4.45
1052 1803 1.995066 ATGCATGGACGGACAGGGA 60.995 57.895 0.00 0.00 0.00 4.20
1053 1804 1.348008 ATGCATGGACGGACAGGGAT 61.348 55.000 0.00 0.00 0.00 3.85
1054 1805 1.227674 GCATGGACGGACAGGGATC 60.228 63.158 0.00 0.00 0.00 3.36
1055 1806 1.690219 GCATGGACGGACAGGGATCT 61.690 60.000 0.00 0.00 0.00 2.75
1056 1807 0.105593 CATGGACGGACAGGGATCTG 59.894 60.000 0.00 0.00 46.10 2.90
1065 1816 2.460330 CAGGGATCTGTTGTCGTGC 58.540 57.895 0.00 0.00 36.30 5.34
1066 1817 0.320683 CAGGGATCTGTTGTCGTGCA 60.321 55.000 0.00 0.00 36.30 4.57
1067 1818 0.615331 AGGGATCTGTTGTCGTGCAT 59.385 50.000 0.00 0.00 0.00 3.96
1068 1819 0.729116 GGGATCTGTTGTCGTGCATG 59.271 55.000 0.00 0.00 0.00 4.06
1069 1820 1.675714 GGGATCTGTTGTCGTGCATGA 60.676 52.381 3.97 3.97 0.00 3.07
1070 1821 2.076100 GGATCTGTTGTCGTGCATGAA 58.924 47.619 10.93 0.00 0.00 2.57
1071 1822 2.679837 GGATCTGTTGTCGTGCATGAAT 59.320 45.455 10.93 0.00 0.00 2.57
1072 1823 3.242543 GGATCTGTTGTCGTGCATGAATC 60.243 47.826 10.93 8.70 0.00 2.52
1073 1824 1.726248 TCTGTTGTCGTGCATGAATCG 59.274 47.619 10.93 0.00 0.00 3.34
1074 1825 1.460743 CTGTTGTCGTGCATGAATCGT 59.539 47.619 10.93 0.00 0.00 3.73
1075 1826 1.194322 TGTTGTCGTGCATGAATCGTG 59.806 47.619 10.93 0.00 0.00 4.35
1076 1827 0.165727 TTGTCGTGCATGAATCGTGC 59.834 50.000 19.69 19.69 45.53 5.34
1081 1832 2.480102 GCATGAATCGTGCGCACA 59.520 55.556 37.03 24.97 36.64 4.57
1082 1833 1.581912 GCATGAATCGTGCGCACAG 60.582 57.895 37.03 28.44 36.64 3.66
1097 1848 0.439985 CACAGCATCGTGTGTGTAGC 59.560 55.000 0.00 0.00 42.52 3.58
1098 1849 0.033366 ACAGCATCGTGTGTGTAGCA 59.967 50.000 0.00 0.00 0.00 3.49
1106 1857 4.655527 GTGTGTAGCACTGCTCGT 57.344 55.556 6.86 0.00 44.41 4.18
1107 1858 2.900528 GTGTGTAGCACTGCTCGTT 58.099 52.632 6.86 0.00 44.41 3.85
1108 1859 1.217882 GTGTGTAGCACTGCTCGTTT 58.782 50.000 6.86 0.00 44.41 3.60
1109 1860 1.070577 GTGTGTAGCACTGCTCGTTTG 60.071 52.381 6.86 0.00 44.41 2.93
1110 1861 0.110644 GTGTAGCACTGCTCGTTTGC 60.111 55.000 6.86 0.00 40.44 3.68
1111 1862 0.531753 TGTAGCACTGCTCGTTTGCA 60.532 50.000 6.86 0.00 40.44 4.08
1112 1863 0.586319 GTAGCACTGCTCGTTTGCAA 59.414 50.000 6.86 0.00 42.83 4.08
1113 1864 1.197721 GTAGCACTGCTCGTTTGCAAT 59.802 47.619 6.86 0.00 42.83 3.56
1114 1865 0.239347 AGCACTGCTCGTTTGCAATC 59.761 50.000 0.00 0.00 42.83 2.67
1415 2166 1.400941 ACCAACCCCTACCTCTCCTA 58.599 55.000 0.00 0.00 0.00 2.94
1471 2227 4.078537 TGGGTACTTGGATGTGAATTGTG 58.921 43.478 0.00 0.00 0.00 3.33
1534 2298 0.883833 GCTTATTGGCTGTGTGCTGT 59.116 50.000 0.00 0.00 42.39 4.40
1568 2337 8.039538 TGTAGGATGTAGTACTATCGGATGTAG 58.960 40.741 5.75 0.00 0.00 2.74
1611 2380 2.051692 ACAGGGGCACTAGTAACACAA 58.948 47.619 0.00 0.00 0.00 3.33
1615 2384 4.081087 CAGGGGCACTAGTAACACAACTAT 60.081 45.833 0.00 0.00 31.70 2.12
1635 2404 2.736144 ACATTGGCACTTGCATTCTG 57.264 45.000 3.15 0.00 44.36 3.02
1700 2469 2.791383 TGTTTGGTACATGTGCTTGC 57.209 45.000 13.86 0.00 39.30 4.01
1704 2473 0.536233 TGGTACATGTGCTTGCCGTT 60.536 50.000 13.86 0.00 0.00 4.44
1756 2525 4.141135 TGGACCTCAGGGAAAATTTGTGTA 60.141 41.667 0.00 0.00 36.25 2.90
1758 2527 4.149598 ACCTCAGGGAAAATTTGTGTACC 58.850 43.478 0.00 0.00 36.25 3.34
1765 2534 3.427098 GGAAAATTTGTGTACCGGCTAGC 60.427 47.826 6.04 6.04 0.00 3.42
1773 2542 1.064166 TGTACCGGCTAGCTCTAACCT 60.064 52.381 15.72 0.00 0.00 3.50
1775 2544 0.756070 ACCGGCTAGCTCTAACCTCC 60.756 60.000 15.72 0.00 0.00 4.30
1792 2578 4.745649 ACCTCCGATTCTCTCTTTTTACG 58.254 43.478 0.00 0.00 0.00 3.18
1828 2614 2.396590 ATTTGCGAGTGGGTTATCGT 57.603 45.000 0.00 0.00 40.97 3.73
1829 2615 1.434555 TTTGCGAGTGGGTTATCGTG 58.565 50.000 0.00 0.00 40.97 4.35
1830 2616 0.319083 TTGCGAGTGGGTTATCGTGT 59.681 50.000 0.00 0.00 40.97 4.49
1831 2617 1.175654 TGCGAGTGGGTTATCGTGTA 58.824 50.000 0.00 0.00 40.97 2.90
1832 2618 1.135315 TGCGAGTGGGTTATCGTGTAC 60.135 52.381 0.00 0.00 40.97 2.90
1833 2619 1.133790 GCGAGTGGGTTATCGTGTACT 59.866 52.381 0.00 0.00 40.97 2.73
1834 2620 2.793933 GCGAGTGGGTTATCGTGTACTC 60.794 54.545 0.00 0.00 40.97 2.59
1835 2621 2.223433 CGAGTGGGTTATCGTGTACTCC 60.223 54.545 0.00 0.00 34.30 3.85
1836 2622 2.100418 GAGTGGGTTATCGTGTACTCCC 59.900 54.545 0.00 0.00 35.85 4.30
1837 2623 2.105766 GTGGGTTATCGTGTACTCCCT 58.894 52.381 0.00 0.00 36.23 4.20
1838 2624 2.100418 GTGGGTTATCGTGTACTCCCTC 59.900 54.545 0.00 0.00 36.23 4.30
1839 2625 1.685517 GGGTTATCGTGTACTCCCTCC 59.314 57.143 0.00 0.00 32.89 4.30
1840 2626 1.336125 GGTTATCGTGTACTCCCTCCG 59.664 57.143 0.00 0.00 0.00 4.63
1841 2627 2.019984 GTTATCGTGTACTCCCTCCGT 58.980 52.381 0.00 0.00 0.00 4.69
1842 2628 2.424956 GTTATCGTGTACTCCCTCCGTT 59.575 50.000 0.00 0.00 0.00 4.44
1843 2629 1.101331 ATCGTGTACTCCCTCCGTTC 58.899 55.000 0.00 0.00 0.00 3.95
1844 2630 0.962356 TCGTGTACTCCCTCCGTTCC 60.962 60.000 0.00 0.00 0.00 3.62
1845 2631 1.246056 CGTGTACTCCCTCCGTTCCA 61.246 60.000 0.00 0.00 0.00 3.53
1846 2632 0.971386 GTGTACTCCCTCCGTTCCAA 59.029 55.000 0.00 0.00 0.00 3.53
1847 2633 1.345415 GTGTACTCCCTCCGTTCCAAA 59.655 52.381 0.00 0.00 0.00 3.28
1848 2634 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
1849 2635 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
1850 2636 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
1851 2637 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
1852 2638 2.910977 ACTCCCTCCGTTCCAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
1853 2639 3.329814 ACTCCCTCCGTTCCAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
1854 2640 3.681593 TCCCTCCGTTCCAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
1855 2641 3.328343 TCCCTCCGTTCCAAAATACTTGA 59.672 43.478 0.00 0.00 0.00 3.02
1856 2642 3.439129 CCCTCCGTTCCAAAATACTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
1857 2643 4.324267 CCTCCGTTCCAAAATACTTGACT 58.676 43.478 0.00 0.00 0.00 3.41
1858 2644 4.760204 CCTCCGTTCCAAAATACTTGACTT 59.240 41.667 0.00 0.00 0.00 3.01
1859 2645 5.106673 CCTCCGTTCCAAAATACTTGACTTC 60.107 44.000 0.00 0.00 0.00 3.01
1860 2646 4.758165 TCCGTTCCAAAATACTTGACTTCC 59.242 41.667 0.00 0.00 0.00 3.46
1861 2647 4.517453 CCGTTCCAAAATACTTGACTTCCA 59.483 41.667 0.00 0.00 0.00 3.53
1862 2648 5.183140 CCGTTCCAAAATACTTGACTTCCAT 59.817 40.000 0.00 0.00 0.00 3.41
1863 2649 6.294508 CCGTTCCAAAATACTTGACTTCCATT 60.295 38.462 0.00 0.00 0.00 3.16
1864 2650 7.145323 CGTTCCAAAATACTTGACTTCCATTT 58.855 34.615 0.00 0.00 0.00 2.32
1865 2651 7.114811 CGTTCCAAAATACTTGACTTCCATTTG 59.885 37.037 0.00 0.00 0.00 2.32
1866 2652 7.595819 TCCAAAATACTTGACTTCCATTTGT 57.404 32.000 0.00 0.00 0.00 2.83
1867 2653 7.657336 TCCAAAATACTTGACTTCCATTTGTC 58.343 34.615 0.00 0.00 0.00 3.18
1868 2654 6.868339 CCAAAATACTTGACTTCCATTTGTCC 59.132 38.462 0.00 0.00 32.67 4.02
1869 2655 7.432869 CAAAATACTTGACTTCCATTTGTCCA 58.567 34.615 0.00 0.00 32.67 4.02
1870 2656 7.595819 AAATACTTGACTTCCATTTGTCCAA 57.404 32.000 0.00 0.00 32.67 3.53
1871 2657 7.595819 AATACTTGACTTCCATTTGTCCAAA 57.404 32.000 0.00 0.00 32.67 3.28
1872 2658 5.930837 ACTTGACTTCCATTTGTCCAAAA 57.069 34.783 0.00 0.00 33.56 2.44
1873 2659 6.293004 ACTTGACTTCCATTTGTCCAAAAA 57.707 33.333 0.00 0.00 33.56 1.94
1874 2660 6.888105 ACTTGACTTCCATTTGTCCAAAAAT 58.112 32.000 0.00 0.00 33.56 1.82
1875 2661 6.762661 ACTTGACTTCCATTTGTCCAAAAATG 59.237 34.615 0.00 3.25 43.94 2.32
1944 2730 8.224389 TGATAAATGGAAGACATGTATTGTGG 57.776 34.615 11.08 0.00 39.57 4.17
1945 2731 8.052141 TGATAAATGGAAGACATGTATTGTGGA 58.948 33.333 11.08 0.00 39.57 4.02
1946 2732 8.821686 ATAAATGGAAGACATGTATTGTGGAA 57.178 30.769 11.08 0.00 36.76 3.53
1947 2733 6.515272 AATGGAAGACATGTATTGTGGAAC 57.485 37.500 11.08 0.00 40.44 3.62
1948 2734 5.241403 TGGAAGACATGTATTGTGGAACT 57.759 39.130 11.08 0.00 39.18 3.01
1949 2735 5.003160 TGGAAGACATGTATTGTGGAACTG 58.997 41.667 11.08 0.00 39.18 3.16
1950 2736 5.221823 TGGAAGACATGTATTGTGGAACTGA 60.222 40.000 11.08 0.00 39.18 3.41
1951 2737 5.352569 GGAAGACATGTATTGTGGAACTGAG 59.647 44.000 11.08 0.00 39.18 3.35
1952 2738 4.836825 AGACATGTATTGTGGAACTGAGG 58.163 43.478 0.00 0.00 39.18 3.86
1953 2739 3.941483 GACATGTATTGTGGAACTGAGGG 59.059 47.826 0.00 0.00 39.18 4.30
1954 2740 3.587061 ACATGTATTGTGGAACTGAGGGA 59.413 43.478 0.00 0.00 37.11 4.20
2021 2807 7.642194 TCGTTCTTTGTTCATGTTGAATTACAC 59.358 33.333 0.00 0.00 38.79 2.90
2126 2924 0.323302 TGCCAGTTATGAAGCGACCA 59.677 50.000 0.00 0.00 0.00 4.02
2565 3364 8.682016 CAAACTGAAGCAAGTTAACTTTTATCG 58.318 33.333 18.25 8.06 39.48 2.92
2566 3365 7.492352 ACTGAAGCAAGTTAACTTTTATCGT 57.508 32.000 18.25 13.70 33.11 3.73
2712 3517 4.406456 TGACCTGCATTATTTGTTCTGGT 58.594 39.130 0.00 0.00 0.00 4.00
2882 5596 4.563337 TGACATAATACCGGAGAACTCG 57.437 45.455 9.46 0.00 0.00 4.18
2884 5598 4.641541 TGACATAATACCGGAGAACTCGAA 59.358 41.667 9.46 0.00 0.00 3.71
2935 5649 4.217118 ACAATTCAACAGAATGGAGCTGTC 59.783 41.667 0.00 0.00 45.27 3.51
3038 5752 2.282251 AGGAGGTCAGCGACGTCA 60.282 61.111 22.95 0.00 45.59 4.35
3122 5836 0.792640 CACGAGCAACGAAGCTGATT 59.207 50.000 10.83 0.00 46.75 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.428890 CGTATATGGATGAGGAGGAGGC 59.571 54.545 0.00 0.00 0.00 4.70
44 45 3.003763 GGAGGCAGAGAACCCCGT 61.004 66.667 0.00 0.00 0.00 5.28
165 203 3.071206 TGGAGGAGGACGAGCAGC 61.071 66.667 0.00 0.00 0.00 5.25
173 211 1.547755 AGGAGGAGGTGGAGGAGGA 60.548 63.158 0.00 0.00 0.00 3.71
182 274 1.156322 TTGGAGGAGGAGGAGGAGGT 61.156 60.000 0.00 0.00 0.00 3.85
222 341 2.363795 CAGGGCTACCTCCGGACA 60.364 66.667 0.00 0.00 46.95 4.02
293 412 3.567397 ACCCATATCTAACGTCAGAGCT 58.433 45.455 0.00 0.00 0.00 4.09
408 531 2.585523 ATTTCCTCCTCCCCTCCCCC 62.586 65.000 0.00 0.00 0.00 5.40
409 532 1.006227 ATTTCCTCCTCCCCTCCCC 59.994 63.158 0.00 0.00 0.00 4.81
410 533 0.624795 ACATTTCCTCCTCCCCTCCC 60.625 60.000 0.00 0.00 0.00 4.30
411 534 0.548510 CACATTTCCTCCTCCCCTCC 59.451 60.000 0.00 0.00 0.00 4.30
412 535 0.548510 CCACATTTCCTCCTCCCCTC 59.451 60.000 0.00 0.00 0.00 4.30
413 536 0.121197 TCCACATTTCCTCCTCCCCT 59.879 55.000 0.00 0.00 0.00 4.79
414 537 0.256177 GTCCACATTTCCTCCTCCCC 59.744 60.000 0.00 0.00 0.00 4.81
415 538 0.107654 CGTCCACATTTCCTCCTCCC 60.108 60.000 0.00 0.00 0.00 4.30
416 539 0.107654 CCGTCCACATTTCCTCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
417 540 0.902531 TCCGTCCACATTTCCTCCTC 59.097 55.000 0.00 0.00 0.00 3.71
481 1219 0.465705 TCTAGCAGGCCACATAGTGC 59.534 55.000 5.01 4.58 36.10 4.40
511 1249 1.143183 GTCGGACATATGGCACCGT 59.857 57.895 25.51 0.00 44.72 4.83
521 1259 2.113433 CGTCTCCTCCGTCGGACAT 61.113 63.158 10.71 0.00 0.00 3.06
599 1337 1.065928 CTAGGCACGACCGGTCATC 59.934 63.158 32.80 20.02 46.52 2.92
600 1338 0.755698 ATCTAGGCACGACCGGTCAT 60.756 55.000 32.80 17.77 46.52 3.06
601 1339 1.379443 ATCTAGGCACGACCGGTCA 60.379 57.895 32.80 12.38 46.52 4.02
602 1340 1.102222 AGATCTAGGCACGACCGGTC 61.102 60.000 25.28 25.28 46.52 4.79
604 1342 1.655329 GAGATCTAGGCACGACCGG 59.345 63.158 0.00 0.00 46.52 5.28
605 1343 1.655329 GGAGATCTAGGCACGACCG 59.345 63.158 0.00 0.00 46.52 4.79
606 1344 1.465200 GGGGAGATCTAGGCACGACC 61.465 65.000 0.00 0.00 39.61 4.79
609 1347 1.924731 TATGGGGAGATCTAGGCACG 58.075 55.000 0.00 0.00 0.00 5.34
610 1348 2.428890 CGATATGGGGAGATCTAGGCAC 59.571 54.545 0.00 0.00 0.00 5.01
612 1350 1.410882 GCGATATGGGGAGATCTAGGC 59.589 57.143 0.00 0.00 0.00 3.93
613 1351 2.035632 GGCGATATGGGGAGATCTAGG 58.964 57.143 0.00 0.00 0.00 3.02
614 1352 2.955660 GAGGCGATATGGGGAGATCTAG 59.044 54.545 0.00 0.00 0.00 2.43
616 1354 1.077828 TGAGGCGATATGGGGAGATCT 59.922 52.381 0.00 0.00 0.00 2.75
618 1356 2.260639 ATGAGGCGATATGGGGAGAT 57.739 50.000 0.00 0.00 0.00 2.75
619 1357 2.919772 TATGAGGCGATATGGGGAGA 57.080 50.000 0.00 0.00 0.00 3.71
620 1358 4.080919 TCAAATATGAGGCGATATGGGGAG 60.081 45.833 0.00 0.00 0.00 4.30
621 1359 3.843619 TCAAATATGAGGCGATATGGGGA 59.156 43.478 0.00 0.00 0.00 4.81
670 1409 0.400213 AACCGGCCTCAAACTCATGA 59.600 50.000 0.00 0.00 0.00 3.07
673 1412 0.181587 TCAAACCGGCCTCAAACTCA 59.818 50.000 0.00 0.00 0.00 3.41
742 1483 2.267642 CCGCCTCAAATGTCCCGA 59.732 61.111 0.00 0.00 0.00 5.14
744 1485 0.898326 AAACCCGCCTCAAATGTCCC 60.898 55.000 0.00 0.00 0.00 4.46
747 1488 0.178975 TCCAAACCCGCCTCAAATGT 60.179 50.000 0.00 0.00 0.00 2.71
766 1507 2.367486 GACTAAGAGTAGTCGGGCACT 58.633 52.381 0.00 0.00 45.16 4.40
767 1508 2.847959 GACTAAGAGTAGTCGGGCAC 57.152 55.000 0.00 0.00 45.16 5.01
774 1515 7.095017 GCAGCAAATTTTCTGACTAAGAGTAGT 60.095 37.037 20.11 0.00 43.56 2.73
777 1518 5.767168 AGCAGCAAATTTTCTGACTAAGAGT 59.233 36.000 20.11 0.00 35.91 3.24
800 1546 7.373493 ACATTTATGAGCACCTTTCAGAAAAG 58.627 34.615 0.00 0.00 38.69 2.27
801 1547 7.288810 ACATTTATGAGCACCTTTCAGAAAA 57.711 32.000 0.00 0.00 38.69 2.29
805 1551 7.383102 ACTTACATTTATGAGCACCTTTCAG 57.617 36.000 0.00 0.00 0.00 3.02
807 1553 8.947115 AGTAACTTACATTTATGAGCACCTTTC 58.053 33.333 1.79 0.00 0.00 2.62
963 1714 3.767230 CTGTTGTCGTCCGCGCAG 61.767 66.667 8.75 0.00 38.14 5.18
964 1715 2.480853 ATACTGTTGTCGTCCGCGCA 62.481 55.000 8.75 0.00 38.14 6.09
965 1716 1.804326 ATACTGTTGTCGTCCGCGC 60.804 57.895 0.00 0.00 38.14 6.86
966 1717 1.988409 CATACTGTTGTCGTCCGCG 59.012 57.895 0.00 0.00 39.92 6.46
967 1718 1.011968 TGCATACTGTTGTCGTCCGC 61.012 55.000 0.00 0.00 0.00 5.54
968 1719 0.713883 GTGCATACTGTTGTCGTCCG 59.286 55.000 0.00 0.00 0.00 4.79
969 1720 0.713883 CGTGCATACTGTTGTCGTCC 59.286 55.000 0.00 0.00 0.00 4.79
970 1721 1.385743 GTCGTGCATACTGTTGTCGTC 59.614 52.381 0.00 0.00 0.00 4.20
971 1722 1.269361 TGTCGTGCATACTGTTGTCGT 60.269 47.619 0.00 0.00 0.00 4.34
972 1723 1.386748 CTGTCGTGCATACTGTTGTCG 59.613 52.381 0.00 0.00 0.00 4.35
973 1724 2.672714 TCTGTCGTGCATACTGTTGTC 58.327 47.619 0.00 0.00 0.00 3.18
974 1725 2.812358 TCTGTCGTGCATACTGTTGT 57.188 45.000 0.00 0.00 0.00 3.32
975 1726 3.253230 TCATCTGTCGTGCATACTGTTG 58.747 45.455 0.00 2.06 0.00 3.33
976 1727 3.592898 TCATCTGTCGTGCATACTGTT 57.407 42.857 0.00 0.00 0.00 3.16
977 1728 3.254060 GTTCATCTGTCGTGCATACTGT 58.746 45.455 0.00 0.00 0.00 3.55
978 1729 2.279921 CGTTCATCTGTCGTGCATACTG 59.720 50.000 0.00 0.00 0.00 2.74
979 1730 2.163613 TCGTTCATCTGTCGTGCATACT 59.836 45.455 0.00 0.00 0.00 2.12
980 1731 2.526077 TCGTTCATCTGTCGTGCATAC 58.474 47.619 0.00 0.00 0.00 2.39
981 1732 2.931512 TCGTTCATCTGTCGTGCATA 57.068 45.000 0.00 0.00 0.00 3.14
982 1733 1.929169 CATCGTTCATCTGTCGTGCAT 59.071 47.619 0.00 0.00 0.00 3.96
983 1734 1.349234 CATCGTTCATCTGTCGTGCA 58.651 50.000 0.00 0.00 0.00 4.57
984 1735 0.025513 GCATCGTTCATCTGTCGTGC 59.974 55.000 0.00 0.00 0.00 5.34
985 1736 0.295763 CGCATCGTTCATCTGTCGTG 59.704 55.000 0.00 0.00 0.00 4.35
986 1737 0.802222 CCGCATCGTTCATCTGTCGT 60.802 55.000 0.00 0.00 0.00 4.34
987 1738 1.482621 CCCGCATCGTTCATCTGTCG 61.483 60.000 0.00 0.00 0.00 4.35
988 1739 0.179111 TCCCGCATCGTTCATCTGTC 60.179 55.000 0.00 0.00 0.00 3.51
989 1740 0.465705 ATCCCGCATCGTTCATCTGT 59.534 50.000 0.00 0.00 0.00 3.41
990 1741 1.143305 GATCCCGCATCGTTCATCTG 58.857 55.000 0.00 0.00 0.00 2.90
991 1742 0.752658 TGATCCCGCATCGTTCATCT 59.247 50.000 0.00 0.00 33.61 2.90
992 1743 1.581934 TTGATCCCGCATCGTTCATC 58.418 50.000 0.00 0.00 33.61 2.92
993 1744 1.670811 GTTTGATCCCGCATCGTTCAT 59.329 47.619 0.00 0.00 33.61 2.57
994 1745 1.083489 GTTTGATCCCGCATCGTTCA 58.917 50.000 0.00 0.00 33.61 3.18
995 1746 0.026285 CGTTTGATCCCGCATCGTTC 59.974 55.000 0.00 0.00 33.61 3.95
996 1747 1.366111 CCGTTTGATCCCGCATCGTT 61.366 55.000 0.00 0.00 33.61 3.85
997 1748 1.813753 CCGTTTGATCCCGCATCGT 60.814 57.895 0.00 0.00 33.61 3.73
998 1749 1.762222 GACCGTTTGATCCCGCATCG 61.762 60.000 0.00 0.00 33.61 3.84
999 1750 0.462047 AGACCGTTTGATCCCGCATC 60.462 55.000 0.00 0.00 0.00 3.91
1000 1751 0.744414 CAGACCGTTTGATCCCGCAT 60.744 55.000 0.00 0.00 0.00 4.73
1001 1752 1.375396 CAGACCGTTTGATCCCGCA 60.375 57.895 0.00 0.00 0.00 5.69
1002 1753 2.750888 GCAGACCGTTTGATCCCGC 61.751 63.158 0.00 0.00 0.00 6.13
1003 1754 1.079127 AGCAGACCGTTTGATCCCG 60.079 57.895 0.00 0.00 0.00 5.14
1004 1755 1.026718 CCAGCAGACCGTTTGATCCC 61.027 60.000 0.00 0.00 0.00 3.85
1005 1756 0.036388 TCCAGCAGACCGTTTGATCC 60.036 55.000 0.00 0.00 0.00 3.36
1006 1757 1.079503 GTCCAGCAGACCGTTTGATC 58.920 55.000 0.00 0.00 39.84 2.92
1007 1758 3.233355 GTCCAGCAGACCGTTTGAT 57.767 52.632 0.00 0.00 39.84 2.57
1008 1759 4.771127 GTCCAGCAGACCGTTTGA 57.229 55.556 0.00 0.00 39.84 2.69
1015 1766 0.891373 TGTAGCAGAGTCCAGCAGAC 59.109 55.000 7.79 0.00 46.71 3.51
1016 1767 1.479730 CATGTAGCAGAGTCCAGCAGA 59.520 52.381 7.79 0.00 0.00 4.26
1017 1768 1.937278 CATGTAGCAGAGTCCAGCAG 58.063 55.000 7.79 0.00 0.00 4.24
1018 1769 0.107993 GCATGTAGCAGAGTCCAGCA 60.108 55.000 7.79 0.00 44.79 4.41
1019 1770 2.687842 GCATGTAGCAGAGTCCAGC 58.312 57.895 0.00 0.00 44.79 4.85
1029 1780 0.461870 TGTCCGTCCATGCATGTAGC 60.462 55.000 24.58 12.98 45.96 3.58
1030 1781 1.575244 CTGTCCGTCCATGCATGTAG 58.425 55.000 24.58 14.67 0.00 2.74
1031 1782 0.177836 CCTGTCCGTCCATGCATGTA 59.822 55.000 24.58 6.94 0.00 2.29
1032 1783 1.078214 CCTGTCCGTCCATGCATGT 60.078 57.895 24.58 0.00 0.00 3.21
1033 1784 1.820906 CCCTGTCCGTCCATGCATG 60.821 63.158 20.19 20.19 0.00 4.06
1034 1785 1.348008 ATCCCTGTCCGTCCATGCAT 61.348 55.000 0.00 0.00 0.00 3.96
1035 1786 1.971505 GATCCCTGTCCGTCCATGCA 61.972 60.000 0.00 0.00 0.00 3.96
1036 1787 1.227674 GATCCCTGTCCGTCCATGC 60.228 63.158 0.00 0.00 0.00 4.06
1037 1788 0.105593 CAGATCCCTGTCCGTCCATG 59.894 60.000 0.00 0.00 35.70 3.66
1038 1789 2.521103 CAGATCCCTGTCCGTCCAT 58.479 57.895 0.00 0.00 35.70 3.41
1039 1790 4.034246 CAGATCCCTGTCCGTCCA 57.966 61.111 0.00 0.00 35.70 4.02
1047 1798 0.320683 TGCACGACAACAGATCCCTG 60.321 55.000 0.00 0.00 45.76 4.45
1048 1799 0.615331 ATGCACGACAACAGATCCCT 59.385 50.000 0.00 0.00 0.00 4.20
1049 1800 0.729116 CATGCACGACAACAGATCCC 59.271 55.000 0.00 0.00 0.00 3.85
1050 1801 1.725641 TCATGCACGACAACAGATCC 58.274 50.000 0.00 0.00 0.00 3.36
1051 1802 3.542875 CGATTCATGCACGACAACAGATC 60.543 47.826 0.00 0.00 0.00 2.75
1052 1803 2.349580 CGATTCATGCACGACAACAGAT 59.650 45.455 0.00 0.00 0.00 2.90
1053 1804 1.726248 CGATTCATGCACGACAACAGA 59.274 47.619 0.00 0.00 0.00 3.41
1054 1805 1.460743 ACGATTCATGCACGACAACAG 59.539 47.619 11.51 0.00 0.00 3.16
1055 1806 1.194322 CACGATTCATGCACGACAACA 59.806 47.619 11.51 0.00 0.00 3.33
1056 1807 1.869503 CACGATTCATGCACGACAAC 58.130 50.000 11.51 0.00 0.00 3.32
1057 1808 0.165727 GCACGATTCATGCACGACAA 59.834 50.000 0.00 0.00 42.88 3.18
1058 1809 1.787215 GCACGATTCATGCACGACA 59.213 52.632 0.00 0.00 42.88 4.35
1059 1810 1.296145 CGCACGATTCATGCACGAC 60.296 57.895 5.49 4.37 43.57 4.34
1060 1811 3.080274 CGCACGATTCATGCACGA 58.920 55.556 5.49 0.00 43.57 4.35
1061 1812 2.645628 GCGCACGATTCATGCACG 60.646 61.111 0.30 0.00 43.57 5.34
1062 1813 2.480102 TGCGCACGATTCATGCAC 59.520 55.556 5.66 0.00 43.57 4.57
1063 1814 2.243160 CTGTGCGCACGATTCATGCA 62.243 55.000 33.22 13.31 43.57 3.96
1064 1815 1.581912 CTGTGCGCACGATTCATGC 60.582 57.895 33.22 8.99 39.81 4.06
1065 1816 1.581912 GCTGTGCGCACGATTCATG 60.582 57.895 33.22 17.72 38.92 3.07
1066 1817 2.034317 TGCTGTGCGCACGATTCAT 61.034 52.632 33.22 0.00 45.47 2.57
1067 1818 2.664518 TGCTGTGCGCACGATTCA 60.665 55.556 33.22 23.77 45.47 2.57
1075 1826 3.716006 ACACACGATGCTGTGCGC 61.716 61.111 0.00 0.00 44.73 6.09
1076 1827 1.281566 TACACACACGATGCTGTGCG 61.282 55.000 3.88 0.00 44.73 5.34
1077 1828 0.439985 CTACACACACGATGCTGTGC 59.560 55.000 3.88 0.00 44.73 4.57
1078 1829 0.439985 GCTACACACACGATGCTGTG 59.560 55.000 2.49 2.49 46.06 3.66
1079 1830 0.033366 TGCTACACACACGATGCTGT 59.967 50.000 0.00 0.00 0.00 4.40
1080 1831 2.826277 TGCTACACACACGATGCTG 58.174 52.632 0.00 0.00 0.00 4.41
1090 1841 1.217001 CAAACGAGCAGTGCTACACA 58.783 50.000 19.77 0.00 39.88 3.72
1091 1842 0.110644 GCAAACGAGCAGTGCTACAC 60.111 55.000 19.77 4.76 39.88 2.90
1092 1843 0.531753 TGCAAACGAGCAGTGCTACA 60.532 50.000 19.77 6.96 39.88 2.74
1093 1844 0.586319 TTGCAAACGAGCAGTGCTAC 59.414 50.000 19.77 10.86 46.54 3.58
1094 1845 1.464608 GATTGCAAACGAGCAGTGCTA 59.535 47.619 19.77 0.00 46.54 3.49
1095 1846 0.239347 GATTGCAAACGAGCAGTGCT 59.761 50.000 19.86 19.86 46.54 4.40
1096 1847 1.061799 CGATTGCAAACGAGCAGTGC 61.062 55.000 22.96 7.13 46.54 4.40
1097 1848 1.061799 GCGATTGCAAACGAGCAGTG 61.062 55.000 30.07 2.45 46.54 3.66
1098 1849 1.207593 GCGATTGCAAACGAGCAGT 59.792 52.632 30.07 0.00 46.54 4.40
1099 1850 4.047030 GCGATTGCAAACGAGCAG 57.953 55.556 30.07 3.87 46.54 4.24
1110 1861 4.101790 GTGGCCGGTGTGCGATTG 62.102 66.667 1.90 0.00 0.00 2.67
1111 1862 4.329545 AGTGGCCGGTGTGCGATT 62.330 61.111 1.90 0.00 0.00 3.34
1112 1863 4.760047 GAGTGGCCGGTGTGCGAT 62.760 66.667 1.90 0.00 0.00 4.58
1130 1881 2.633481 GTCCTCAGGTCAGGTACACTTT 59.367 50.000 0.00 0.00 34.76 2.66
1415 2166 1.051556 GGAGCGGAGGGGAGAAGAAT 61.052 60.000 0.00 0.00 0.00 2.40
1471 2227 3.612247 ATCGCCACTGGGTCACTGC 62.612 63.158 0.00 0.00 36.17 4.40
1534 2298 9.736414 GATAGTACTACATCCTACAGGTTATCA 57.264 37.037 4.31 0.00 36.34 2.15
1568 2337 8.470040 TGTAATATGTTCGTGTTTTCTACTCC 57.530 34.615 0.00 0.00 0.00 3.85
1611 2380 5.066893 CAGAATGCAAGTGCCAATGTATAGT 59.933 40.000 0.00 0.00 41.18 2.12
1615 2384 3.156293 ACAGAATGCAAGTGCCAATGTA 58.844 40.909 0.00 0.00 42.53 2.29
1700 2469 1.009900 CTAGTAGGCGCGAGAACGG 60.010 63.158 12.10 0.00 40.15 4.44
1704 2473 1.525535 GTCCCTAGTAGGCGCGAGA 60.526 63.158 12.10 0.00 32.73 4.04
1756 2525 0.756070 GGAGGTTAGAGCTAGCCGGT 60.756 60.000 12.13 0.00 40.77 5.28
1758 2527 0.818445 TCGGAGGTTAGAGCTAGCCG 60.818 60.000 12.13 4.42 40.77 5.52
1765 2534 5.845391 AAAGAGAGAATCGGAGGTTAGAG 57.155 43.478 0.00 0.00 42.67 2.43
1773 2542 4.673580 CGTCCGTAAAAAGAGAGAATCGGA 60.674 45.833 0.00 0.00 42.67 4.55
1775 2544 4.164294 ACGTCCGTAAAAAGAGAGAATCG 58.836 43.478 0.00 0.00 42.67 3.34
1792 2578 3.485743 GCAAATTGAGTTGTGAAACGTCC 59.514 43.478 0.00 0.00 42.39 4.79
1828 2614 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
1829 2615 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1830 2616 4.098894 AGTATTTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1831 2617 2.910977 AGTATTTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1832 2618 3.629142 AGTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1833 2619 3.328343 TCAAGTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
1834 2620 3.439129 GTCAAGTATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
1835 2621 4.324267 AGTCAAGTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
1836 2622 5.106673 GGAAGTCAAGTATTTTGGAACGGAG 60.107 44.000 0.00 0.00 0.00 4.63
1837 2623 4.758165 GGAAGTCAAGTATTTTGGAACGGA 59.242 41.667 0.00 0.00 0.00 4.69
1838 2624 4.517453 TGGAAGTCAAGTATTTTGGAACGG 59.483 41.667 0.00 0.00 0.00 4.44
1839 2625 5.682943 TGGAAGTCAAGTATTTTGGAACG 57.317 39.130 0.00 0.00 0.00 3.95
1840 2626 7.926018 ACAAATGGAAGTCAAGTATTTTGGAAC 59.074 33.333 0.00 0.00 29.41 3.62
1841 2627 8.017418 ACAAATGGAAGTCAAGTATTTTGGAA 57.983 30.769 0.00 0.00 29.41 3.53
1842 2628 7.255801 GGACAAATGGAAGTCAAGTATTTTGGA 60.256 37.037 0.00 0.00 36.50 3.53
1843 2629 6.868339 GGACAAATGGAAGTCAAGTATTTTGG 59.132 38.462 0.00 0.00 36.50 3.28
1844 2630 7.432869 TGGACAAATGGAAGTCAAGTATTTTG 58.567 34.615 0.00 0.00 36.50 2.44
1845 2631 7.595819 TGGACAAATGGAAGTCAAGTATTTT 57.404 32.000 0.00 0.00 36.50 1.82
1846 2632 7.595819 TTGGACAAATGGAAGTCAAGTATTT 57.404 32.000 0.00 0.00 36.50 1.40
1847 2633 7.595819 TTTGGACAAATGGAAGTCAAGTATT 57.404 32.000 0.00 0.00 36.50 1.89
1848 2634 7.595819 TTTTGGACAAATGGAAGTCAAGTAT 57.404 32.000 0.00 0.00 36.50 2.12
1849 2635 7.411486 TTTTTGGACAAATGGAAGTCAAGTA 57.589 32.000 0.00 0.00 36.50 2.24
1850 2636 5.930837 TTTTGGACAAATGGAAGTCAAGT 57.069 34.783 0.00 0.00 36.50 3.16
1851 2637 7.181143 CATTTTTGGACAAATGGAAGTCAAG 57.819 36.000 0.00 0.00 39.53 3.02
1918 2704 8.685427 CCACAATACATGTCTTCCATTTATCAA 58.315 33.333 0.00 0.00 41.46 2.57
1919 2705 8.052141 TCCACAATACATGTCTTCCATTTATCA 58.948 33.333 0.00 0.00 41.46 2.15
1920 2706 8.450578 TCCACAATACATGTCTTCCATTTATC 57.549 34.615 0.00 0.00 41.46 1.75
1921 2707 8.686334 GTTCCACAATACATGTCTTCCATTTAT 58.314 33.333 0.00 0.00 41.46 1.40
1922 2708 7.888021 AGTTCCACAATACATGTCTTCCATTTA 59.112 33.333 0.00 0.00 41.46 1.40
1923 2709 6.721208 AGTTCCACAATACATGTCTTCCATTT 59.279 34.615 0.00 0.00 41.46 2.32
1924 2710 6.151648 CAGTTCCACAATACATGTCTTCCATT 59.848 38.462 0.00 0.00 41.46 3.16
1925 2711 5.649395 CAGTTCCACAATACATGTCTTCCAT 59.351 40.000 0.00 0.00 41.46 3.41
1926 2712 5.003160 CAGTTCCACAATACATGTCTTCCA 58.997 41.667 0.00 0.00 41.46 3.53
1927 2713 5.245531 TCAGTTCCACAATACATGTCTTCC 58.754 41.667 0.00 0.00 41.46 3.46
1928 2714 5.352569 CCTCAGTTCCACAATACATGTCTTC 59.647 44.000 0.00 0.00 41.46 2.87
1929 2715 5.248640 CCTCAGTTCCACAATACATGTCTT 58.751 41.667 0.00 0.00 41.46 3.01
1930 2716 4.323792 CCCTCAGTTCCACAATACATGTCT 60.324 45.833 0.00 0.00 41.46 3.41
1931 2717 3.941483 CCCTCAGTTCCACAATACATGTC 59.059 47.826 0.00 0.00 41.46 3.06
1932 2718 3.587061 TCCCTCAGTTCCACAATACATGT 59.413 43.478 2.69 2.69 45.34 3.21
1933 2719 4.194640 CTCCCTCAGTTCCACAATACATG 58.805 47.826 0.00 0.00 0.00 3.21
1934 2720 3.846588 ACTCCCTCAGTTCCACAATACAT 59.153 43.478 0.00 0.00 26.56 2.29
1935 2721 3.248024 ACTCCCTCAGTTCCACAATACA 58.752 45.455 0.00 0.00 26.56 2.29
1936 2722 3.983044 ACTCCCTCAGTTCCACAATAC 57.017 47.619 0.00 0.00 26.56 1.89
1937 2723 6.844388 ACATATACTCCCTCAGTTCCACAATA 59.156 38.462 0.00 0.00 36.43 1.90
1938 2724 5.667626 ACATATACTCCCTCAGTTCCACAAT 59.332 40.000 0.00 0.00 36.43 2.71
1939 2725 5.030147 ACATATACTCCCTCAGTTCCACAA 58.970 41.667 0.00 0.00 36.43 3.33
1940 2726 4.620723 ACATATACTCCCTCAGTTCCACA 58.379 43.478 0.00 0.00 36.43 4.17
1941 2727 5.615925 AACATATACTCCCTCAGTTCCAC 57.384 43.478 0.00 0.00 36.43 4.02
1942 2728 5.629133 GCAAACATATACTCCCTCAGTTCCA 60.629 44.000 0.00 0.00 36.43 3.53
1943 2729 4.816925 GCAAACATATACTCCCTCAGTTCC 59.183 45.833 0.00 0.00 36.43 3.62
1944 2730 5.428253 TGCAAACATATACTCCCTCAGTTC 58.572 41.667 0.00 0.00 36.43 3.01
1945 2731 5.045578 ACTGCAAACATATACTCCCTCAGTT 60.046 40.000 0.00 0.00 36.43 3.16
1946 2732 4.471386 ACTGCAAACATATACTCCCTCAGT 59.529 41.667 0.00 0.00 39.41 3.41
1947 2733 5.028549 ACTGCAAACATATACTCCCTCAG 57.971 43.478 0.00 0.00 0.00 3.35
1948 2734 5.428253 GAACTGCAAACATATACTCCCTCA 58.572 41.667 0.00 0.00 0.00 3.86
1949 2735 4.816925 GGAACTGCAAACATATACTCCCTC 59.183 45.833 0.00 0.00 0.00 4.30
1950 2736 4.475016 AGGAACTGCAAACATATACTCCCT 59.525 41.667 0.00 0.00 37.18 4.20
1951 2737 4.781934 AGGAACTGCAAACATATACTCCC 58.218 43.478 0.00 0.00 37.18 4.30
1952 2738 5.066505 CCAAGGAACTGCAAACATATACTCC 59.933 44.000 0.00 0.00 40.86 3.85
1953 2739 5.648092 ACCAAGGAACTGCAAACATATACTC 59.352 40.000 0.00 0.00 40.86 2.59
1954 2740 5.570320 ACCAAGGAACTGCAAACATATACT 58.430 37.500 0.00 0.00 40.86 2.12
2126 2924 3.439513 TTCGGCTGCGCGTGGATAT 62.440 57.895 8.43 0.00 0.00 1.63
2280 3078 2.887151 AGAGATCCAAAACCCTGTGG 57.113 50.000 0.00 0.00 36.13 4.17
2518 3316 2.941415 GCAGGCAATAACTACAGGCACT 60.941 50.000 0.00 0.00 43.88 4.40
2565 3364 7.584987 TCTGGTGTTAGTACTAGTACGAAAAC 58.415 38.462 28.07 28.07 40.80 2.43
2566 3365 7.744087 TCTGGTGTTAGTACTAGTACGAAAA 57.256 36.000 24.52 18.98 40.80 2.29
2576 3375 7.099764 CACTGAATGAATCTGGTGTTAGTACT 58.900 38.462 0.00 0.00 32.15 2.73
2712 3517 6.016610 GCACACAGGTTACAGAATCCTTTAAA 60.017 38.462 0.00 0.00 0.00 1.52
2882 5596 4.976116 CGTCTTGTGGGATTGAAACTTTTC 59.024 41.667 0.00 0.00 37.69 2.29
2884 5598 4.204012 TCGTCTTGTGGGATTGAAACTTT 58.796 39.130 0.00 0.00 0.00 2.66
2969 5683 6.268617 TGCACAGATGGCTATCTAGACTATTT 59.731 38.462 12.76 0.00 41.71 1.40
2971 5685 5.184864 GTGCACAGATGGCTATCTAGACTAT 59.815 44.000 12.76 0.00 41.71 2.12
2972 5686 4.520874 GTGCACAGATGGCTATCTAGACTA 59.479 45.833 12.76 0.00 41.71 2.59
3122 5836 2.184020 CTGGAGGGATTGGTGTCGCA 62.184 60.000 0.00 0.00 33.85 5.10


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

AutoCloner maintained by Alex Coulton.