Multiple sequence alignment - TraesCS3B01G379500

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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 TraesCS3B01G379500 chr3B 100.000 6099 0 0 1 6099 597449444 597455542 0.000000e+00 11263.0
1 TraesCS3B01G379500 chr3B 99.303 574 3 1 5526 6099 215588231 215587659 0.000000e+00 1037.0
2 TraesCS3B01G379500 chr3B 98.087 575 10 1 5522 6096 96845728 96846301 0.000000e+00 1000.0
3 TraesCS3B01G379500 chr3D 94.061 3755 161 24 1801 5525 454671579 454675301 0.000000e+00 5642.0
4 TraesCS3B01G379500 chr3D 88.935 723 34 16 804 1489 454670215 454670928 0.000000e+00 850.0
5 TraesCS3B01G379500 chr3D 86.047 688 75 13 1 673 454665056 454665737 0.000000e+00 719.0
6 TraesCS3B01G379500 chr3D 95.349 43 2 0 1483 1525 454671333 454671375 1.100000e-07 69.4
7 TraesCS3B01G379500 chr3A 92.650 3755 194 40 1801 5521 596741360 596745066 0.000000e+00 5330.0
8 TraesCS3B01G379500 chr3A 87.029 1087 53 36 749 1758 596740297 596741372 0.000000e+00 1146.0
9 TraesCS3B01G379500 chr3A 86.767 597 62 8 27 614 596739577 596740165 0.000000e+00 649.0
10 TraesCS3B01G379500 chr7B 99.129 574 4 1 5526 6098 443744511 443745084 0.000000e+00 1031.0
11 TraesCS3B01G379500 chr7B 99.127 573 4 1 5525 6097 361161471 361160900 0.000000e+00 1029.0
12 TraesCS3B01G379500 chr7B 99.612 516 2 0 5525 6040 361159649 361160164 0.000000e+00 942.0
13 TraesCS3B01G379500 chr4A 98.780 574 6 1 5526 6098 547192580 547193153 0.000000e+00 1020.0
14 TraesCS3B01G379500 chr4A 95.000 40 2 0 413 452 705740600 705740561 5.100000e-06 63.9
15 TraesCS3B01G379500 chr2A 98.427 572 8 1 5526 6097 182316514 182315944 0.000000e+00 1005.0
16 TraesCS3B01G379500 chr6B 98.258 574 9 1 5526 6098 203972828 203972255 0.000000e+00 1003.0
17 TraesCS3B01G379500 chr7A 97.178 567 13 2 5526 6092 688201214 688200651 0.000000e+00 955.0
18 TraesCS3B01G379500 chr7A 100.000 36 0 0 413 448 711121077 711121042 3.950000e-07 67.6
19 TraesCS3B01G379500 chr7A 100.000 28 0 0 1042 1069 118104641 118104668 1.100000e-02 52.8
20 TraesCS3B01G379500 chr2D 84.694 98 15 0 517 614 202642797 202642700 1.400000e-16 99.0
21 TraesCS3B01G379500 chr6A 95.000 40 2 0 413 452 472707998 472707959 5.100000e-06 63.9
22 TraesCS3B01G379500 chr5B 95.000 40 2 0 413 452 408357332 408357293 5.100000e-06 63.9
23 TraesCS3B01G379500 chr1A 95.000 40 2 0 413 452 291531601 291531562 5.100000e-06 63.9
24 TraesCS3B01G379500 chr1A 95.000 40 2 0 413 452 374188782 374188821 5.100000e-06 63.9
25 TraesCS3B01G379500 chr1A 95.000 40 2 0 413 452 385369735 385369774 5.100000e-06 63.9
26 TraesCS3B01G379500 chr7D 96.875 32 1 0 5095 5126 31969638 31969669 3.000000e-03 54.7


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 TraesCS3B01G379500 chr3B 597449444 597455542 6098 False 11263.000000 11263 100.000000 1 6099 1 chr3B.!!$F2 6098
1 TraesCS3B01G379500 chr3B 215587659 215588231 572 True 1037.000000 1037 99.303000 5526 6099 1 chr3B.!!$R1 573
2 TraesCS3B01G379500 chr3B 96845728 96846301 573 False 1000.000000 1000 98.087000 5522 6096 1 chr3B.!!$F1 574
3 TraesCS3B01G379500 chr3D 454670215 454675301 5086 False 2187.133333 5642 92.781667 804 5525 3 chr3D.!!$F2 4721
4 TraesCS3B01G379500 chr3D 454665056 454665737 681 False 719.000000 719 86.047000 1 673 1 chr3D.!!$F1 672
5 TraesCS3B01G379500 chr3A 596739577 596745066 5489 False 2375.000000 5330 88.815333 27 5521 3 chr3A.!!$F1 5494
6 TraesCS3B01G379500 chr7B 443744511 443745084 573 False 1031.000000 1031 99.129000 5526 6098 1 chr7B.!!$F2 572
7 TraesCS3B01G379500 chr7B 361160900 361161471 571 True 1029.000000 1029 99.127000 5525 6097 1 chr7B.!!$R1 572
8 TraesCS3B01G379500 chr7B 361159649 361160164 515 False 942.000000 942 99.612000 5525 6040 1 chr7B.!!$F1 515
9 TraesCS3B01G379500 chr4A 547192580 547193153 573 False 1020.000000 1020 98.780000 5526 6098 1 chr4A.!!$F1 572
10 TraesCS3B01G379500 chr2A 182315944 182316514 570 True 1005.000000 1005 98.427000 5526 6097 1 chr2A.!!$R1 571
11 TraesCS3B01G379500 chr6B 203972255 203972828 573 True 1003.000000 1003 98.258000 5526 6098 1 chr6B.!!$R1 572
12 TraesCS3B01G379500 chr7A 688200651 688201214 563 True 955.000000 955 97.178000 5526 6092 1 chr7A.!!$R1 566

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
404 415 0.033781 CACCACCGGTCGGACTTAAA 59.966 55.0 24.32 0.0 38.96 1.52 F
616 627 0.400213 ACAAGGATGCCGTTCTTCCA 59.600 50.0 8.76 0.0 40.48 3.53 F
834 872 0.460284 AATCATCACTGGCGGACGAC 60.460 55.0 0.00 0.0 0.00 4.34 F
1888 2442 0.315568 GTTGCTCTCACGGAGTCACT 59.684 55.0 0.00 0.0 41.61 3.41 F
3278 3852 1.818959 TTGCAAGCAAGGCCATCCAC 61.819 55.0 5.01 0.0 33.74 4.02 F
4147 4727 0.462581 TGCAATCCGTGGCTCAGATC 60.463 55.0 0.00 0.0 0.00 2.75 F
4830 5421 0.616111 ACCCACCAAAAGGCAACACA 60.616 50.0 0.00 0.0 41.41 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 2108 0.445436 CGGAGTCAGCTGTGAAATGC 59.555 55.000 14.67 0.0 33.27 3.56 R
1597 2123 1.120530 ATACAGTGGTAAGGCCGGAG 58.879 55.000 5.05 0.0 41.21 4.63 R
2247 2804 2.112815 GGCAATCACACCGCCTACC 61.113 63.158 0.00 0.0 42.78 3.18 R
3583 4163 0.877071 CACATGGCACTCAGAACACC 59.123 55.000 0.00 0.0 0.00 4.16 R
4542 5122 0.108186 CTGCTGGGACTAATCGTGCA 60.108 55.000 0.00 0.0 35.37 4.57 R
4971 5562 0.179100 AGCATCATCACCGTTCCTCG 60.179 55.000 0.00 0.0 39.52 4.63 R
5928 6527 4.610605 TGGAAACCAGACGAATCACTTA 57.389 40.909 0.00 0.0 0.00 2.24 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
59 61 3.640407 GGGAGCTGGCCACACTCA 61.640 66.667 25.31 0.00 31.88 3.41
60 62 2.431683 GGAGCTGGCCACACTCAA 59.568 61.111 25.31 0.00 31.88 3.02
68 70 1.553690 GGCCACACTCAAGGGCTAGA 61.554 60.000 0.00 0.00 46.87 2.43
86 88 4.626529 GCTAGACCACTAAAAGGGCTCAAT 60.627 45.833 0.00 0.00 42.12 2.57
89 91 3.690460 ACCACTAAAAGGGCTCAATCTG 58.310 45.455 0.00 0.00 0.00 2.90
111 113 4.019321 TGGCCAGCAGTCTAATTTAGAACT 60.019 41.667 0.00 5.47 36.40 3.01
121 123 8.532819 CAGTCTAATTTAGAACTAAGTCCACCT 58.467 37.037 7.70 0.00 36.40 4.00
153 155 0.612174 CCTTGGAGAGTGTCCCTCGA 60.612 60.000 3.43 0.00 46.31 4.04
155 157 0.898789 TTGGAGAGTGTCCCTCGACC 60.899 60.000 3.43 0.00 46.31 4.79
156 158 1.000646 GGAGAGTGTCCCTCGACCT 60.001 63.158 0.00 0.00 45.44 3.85
157 159 1.316706 GGAGAGTGTCCCTCGACCTG 61.317 65.000 0.00 0.00 45.44 4.00
186 196 8.738645 TCCTTTCTATCTTAGCAAAGAAATCC 57.261 34.615 0.00 0.00 44.75 3.01
191 201 5.588958 ATCTTAGCAAAGAAATCCAAGGC 57.411 39.130 0.00 0.00 44.75 4.35
235 246 1.374947 GTCACCAGCTAGCCCACAA 59.625 57.895 12.13 0.00 0.00 3.33
237 248 0.698238 TCACCAGCTAGCCCACAATT 59.302 50.000 12.13 0.00 0.00 2.32
239 250 0.392998 ACCAGCTAGCCCACAATTCG 60.393 55.000 12.13 0.00 0.00 3.34
280 291 2.943036 AAGCCAAGGAAAACCGAGTA 57.057 45.000 0.00 0.00 0.00 2.59
282 293 3.434940 AGCCAAGGAAAACCGAGTAAT 57.565 42.857 0.00 0.00 0.00 1.89
306 317 6.824305 AGGACGATCAATTGTGAAAGATTT 57.176 33.333 5.13 0.00 37.30 2.17
310 321 9.405587 GGACGATCAATTGTGAAAGATTTAAAA 57.594 29.630 5.13 0.00 37.30 1.52
357 368 8.628882 ATTTCAAGTGCAACAAAAGTAGTTAC 57.371 30.769 0.00 0.00 41.43 2.50
398 409 4.918278 TCACCACCACCGGTCGGA 62.918 66.667 24.32 6.24 37.07 4.55
403 414 1.667151 CACCACCGGTCGGACTTAA 59.333 57.895 24.32 0.00 38.96 1.85
404 415 0.033781 CACCACCGGTCGGACTTAAA 59.966 55.000 24.32 0.00 38.96 1.52
409 420 4.002316 CCACCGGTCGGACTTAAATTAAA 58.998 43.478 16.90 0.00 38.96 1.52
450 461 5.066764 GGCATACCGAGGCAAATTTAAACTA 59.933 40.000 0.00 0.00 32.69 2.24
484 495 3.055530 CACTGCTCAGACTTAGGGTCAAT 60.056 47.826 3.60 0.00 46.72 2.57
505 516 0.832135 TCAGTCGGCTCCAGGAAGTT 60.832 55.000 0.00 0.00 0.00 2.66
509 520 0.744874 TCGGCTCCAGGAAGTTATCG 59.255 55.000 0.00 0.00 0.00 2.92
515 526 3.119101 GCTCCAGGAAGTTATCGAAGTCA 60.119 47.826 0.00 0.00 0.00 3.41
524 535 5.326200 AGTTATCGAAGTCAACGAAGGAT 57.674 39.130 0.00 0.00 42.80 3.24
526 537 1.710013 TCGAAGTCAACGAAGGATGC 58.290 50.000 0.00 0.00 36.84 3.91
527 538 0.721718 CGAAGTCAACGAAGGATGCC 59.278 55.000 0.00 0.00 0.00 4.40
532 543 1.303236 CAACGAAGGATGCCACCCA 60.303 57.895 0.00 0.00 0.00 4.51
534 545 1.779061 AACGAAGGATGCCACCCAGT 61.779 55.000 0.00 0.00 0.00 4.00
600 611 2.034179 TCTTCTTCTTGCTCGTCGACAA 59.966 45.455 17.16 0.00 0.00 3.18
615 626 1.087501 GACAAGGATGCCGTTCTTCC 58.912 55.000 0.36 0.36 38.84 3.46
616 627 0.400213 ACAAGGATGCCGTTCTTCCA 59.600 50.000 8.76 0.00 40.48 3.53
620 633 1.065854 AGGATGCCGTTCTTCCAAGAG 60.066 52.381 8.76 0.00 40.48 2.85
623 636 2.631160 TGCCGTTCTTCCAAGAGAAA 57.369 45.000 0.00 0.00 37.40 2.52
695 710 9.878599 CGTGCTAATGTATATAAAAGAAAAGGG 57.121 33.333 0.00 0.00 0.00 3.95
697 712 8.856103 TGCTAATGTATATAAAAGAAAAGGGGC 58.144 33.333 0.00 0.00 0.00 5.80
698 713 8.856103 GCTAATGTATATAAAAGAAAAGGGGCA 58.144 33.333 0.00 0.00 0.00 5.36
700 715 7.839680 ATGTATATAAAAGAAAAGGGGCAGG 57.160 36.000 0.00 0.00 0.00 4.85
701 716 6.975949 TGTATATAAAAGAAAAGGGGCAGGA 58.024 36.000 0.00 0.00 0.00 3.86
702 717 7.415086 TGTATATAAAAGAAAAGGGGCAGGAA 58.585 34.615 0.00 0.00 0.00 3.36
732 747 2.116827 TGTGTGAACGGTTTCTTGGT 57.883 45.000 0.00 0.00 32.36 3.67
733 748 2.438411 TGTGTGAACGGTTTCTTGGTT 58.562 42.857 0.00 0.00 32.36 3.67
734 749 2.162608 TGTGTGAACGGTTTCTTGGTTG 59.837 45.455 0.00 0.00 32.36 3.77
735 750 2.162809 GTGTGAACGGTTTCTTGGTTGT 59.837 45.455 0.00 0.00 32.36 3.32
736 751 3.374678 GTGTGAACGGTTTCTTGGTTGTA 59.625 43.478 0.00 0.00 32.36 2.41
737 752 3.623960 TGTGAACGGTTTCTTGGTTGTAG 59.376 43.478 0.00 0.00 32.36 2.74
738 753 3.872771 GTGAACGGTTTCTTGGTTGTAGA 59.127 43.478 0.00 0.00 32.36 2.59
739 754 3.872771 TGAACGGTTTCTTGGTTGTAGAC 59.127 43.478 0.00 0.00 32.36 2.59
740 755 3.832615 ACGGTTTCTTGGTTGTAGACT 57.167 42.857 0.00 0.00 0.00 3.24
741 756 4.146745 ACGGTTTCTTGGTTGTAGACTT 57.853 40.909 0.00 0.00 0.00 3.01
742 757 3.875134 ACGGTTTCTTGGTTGTAGACTTG 59.125 43.478 0.00 0.00 0.00 3.16
745 760 5.176958 CGGTTTCTTGGTTGTAGACTTGTAG 59.823 44.000 0.00 0.00 0.00 2.74
746 761 5.469084 GGTTTCTTGGTTGTAGACTTGTAGG 59.531 44.000 0.00 0.00 0.00 3.18
747 762 4.884668 TCTTGGTTGTAGACTTGTAGGG 57.115 45.455 0.00 0.00 0.00 3.53
754 790 2.024273 TGTAGACTTGTAGGGGGAGGAG 60.024 54.545 0.00 0.00 0.00 3.69
778 814 1.296432 CGAAGCGCAGAAGCAATCG 60.296 57.895 11.47 2.37 42.27 3.34
802 840 4.932799 GCAGTTGGTGGTTTGTTAAAGTTT 59.067 37.500 0.00 0.00 0.00 2.66
809 847 5.105269 GGTGGTTTGTTAAAGTTTCCCTTCA 60.105 40.000 0.00 0.00 31.27 3.02
810 848 6.407639 GGTGGTTTGTTAAAGTTTCCCTTCAT 60.408 38.462 0.00 0.00 31.27 2.57
833 871 1.107945 TAATCATCACTGGCGGACGA 58.892 50.000 0.00 0.00 0.00 4.20
834 872 0.460284 AATCATCACTGGCGGACGAC 60.460 55.000 0.00 0.00 0.00 4.34
870 914 0.745845 CCCACTGATTTCAGCGGAGG 60.746 60.000 14.73 8.51 46.38 4.30
957 1014 1.150536 CCCCTCCCTCTCTCTCTCG 59.849 68.421 0.00 0.00 0.00 4.04
959 1016 1.528309 CCTCCCTCTCTCTCTCGCC 60.528 68.421 0.00 0.00 0.00 5.54
1019 1078 2.047655 GCGGATTCCACGTGGACA 60.048 61.111 36.40 25.74 45.39 4.02
1064 1123 1.931705 ACCTCCTCCTCCTCCTCGT 60.932 63.158 0.00 0.00 0.00 4.18
1186 1248 3.598019 TGGTACGCCGATTTCTTTAGT 57.402 42.857 0.00 0.00 37.67 2.24
1265 1342 1.909376 AATGGTCTCGTCGTCGATTG 58.091 50.000 5.00 0.00 45.21 2.67
1481 1588 1.067142 CCTACTGCAGTTAAGCCGTCA 60.067 52.381 27.06 1.85 33.86 4.35
1529 2055 3.309506 TGGGGGTGCCAAATTGCG 61.310 61.111 0.00 0.00 0.00 4.85
1536 2062 1.134729 GGTGCCAAATTGCGGATGAAT 60.135 47.619 0.00 0.00 0.00 2.57
1552 2078 1.594397 TGAATGATGAGATTGCGCGAC 59.406 47.619 12.10 0.88 0.00 5.19
1554 2080 1.215244 ATGATGAGATTGCGCGACAG 58.785 50.000 12.10 0.00 0.00 3.51
1559 2085 1.005037 AGATTGCGCGACAGGAACA 60.005 52.632 12.10 0.00 0.00 3.18
1582 2108 4.564769 ACGCATTTGTTGTAGTGTTTTTGG 59.435 37.500 0.00 0.00 0.00 3.28
1597 2123 2.798976 TTTGGCATTTCACAGCTGAC 57.201 45.000 23.35 0.00 0.00 3.51
1601 2127 0.445436 GCATTTCACAGCTGACTCCG 59.555 55.000 23.35 5.09 0.00 4.63
1608 2134 1.153549 CAGCTGACTCCGGCCTTAC 60.154 63.158 8.42 0.00 45.76 2.34
1614 2140 1.535687 ACTCCGGCCTTACCACTGT 60.536 57.895 0.00 0.00 39.03 3.55
1661 2207 6.716934 TTTTTAGTTTGGACTGTGGCAATA 57.283 33.333 0.00 0.00 36.60 1.90
1689 2235 5.355350 GCAATAAATATAGCTGGGCCTACTG 59.645 44.000 4.53 0.00 0.00 2.74
1707 2253 6.823689 GCCTACTGTTGGATTTCTTCATTAGA 59.176 38.462 12.54 0.00 0.00 2.10
1744 2290 5.182001 GGTGTGCTCAAATTTCTGACTACAT 59.818 40.000 0.00 0.00 0.00 2.29
1753 2299 8.902806 TCAAATTTCTGACTACATGTGTTCTTT 58.097 29.630 9.11 0.00 0.00 2.52
1754 2300 9.520204 CAAATTTCTGACTACATGTGTTCTTTT 57.480 29.630 9.11 0.00 0.00 2.27
1755 2301 9.520204 AAATTTCTGACTACATGTGTTCTTTTG 57.480 29.630 9.11 0.00 0.00 2.44
1756 2302 7.857734 TTTCTGACTACATGTGTTCTTTTGA 57.142 32.000 9.11 0.58 0.00 2.69
1757 2303 7.482654 TTCTGACTACATGTGTTCTTTTGAG 57.517 36.000 9.11 0.00 0.00 3.02
1758 2304 6.582636 TCTGACTACATGTGTTCTTTTGAGT 58.417 36.000 9.11 0.00 0.00 3.41
1759 2305 7.047891 TCTGACTACATGTGTTCTTTTGAGTT 58.952 34.615 9.11 0.00 0.00 3.01
1760 2306 7.552687 TCTGACTACATGTGTTCTTTTGAGTTT 59.447 33.333 9.11 0.00 0.00 2.66
1761 2307 7.471721 TGACTACATGTGTTCTTTTGAGTTTG 58.528 34.615 9.11 0.00 0.00 2.93
1762 2308 6.265577 ACTACATGTGTTCTTTTGAGTTTGC 58.734 36.000 9.11 0.00 0.00 3.68
1763 2309 5.329035 ACATGTGTTCTTTTGAGTTTGCT 57.671 34.783 0.00 0.00 0.00 3.91
1764 2310 6.449635 ACATGTGTTCTTTTGAGTTTGCTA 57.550 33.333 0.00 0.00 0.00 3.49
1765 2311 6.862209 ACATGTGTTCTTTTGAGTTTGCTAA 58.138 32.000 0.00 0.00 0.00 3.09
1766 2312 7.319646 ACATGTGTTCTTTTGAGTTTGCTAAA 58.680 30.769 0.00 0.00 0.00 1.85
1767 2313 7.816995 ACATGTGTTCTTTTGAGTTTGCTAAAA 59.183 29.630 0.00 0.00 0.00 1.52
1768 2314 8.655092 CATGTGTTCTTTTGAGTTTGCTAAAAA 58.345 29.630 0.00 0.00 34.69 1.94
1791 2337 7.671495 AAAAATGTGTTCTTTTGAGTTTGCT 57.329 28.000 0.00 0.00 0.00 3.91
1792 2338 8.770438 AAAAATGTGTTCTTTTGAGTTTGCTA 57.230 26.923 0.00 0.00 0.00 3.49
1793 2339 8.770438 AAAATGTGTTCTTTTGAGTTTGCTAA 57.230 26.923 0.00 0.00 0.00 3.09
1794 2340 8.770438 AAATGTGTTCTTTTGAGTTTGCTAAA 57.230 26.923 0.00 0.00 0.00 1.85
1795 2341 8.770438 AATGTGTTCTTTTGAGTTTGCTAAAA 57.230 26.923 0.00 0.00 0.00 1.52
1796 2342 8.770438 ATGTGTTCTTTTGAGTTTGCTAAAAA 57.230 26.923 0.00 0.00 34.69 1.94
1847 2401 4.013728 TCAGGTTTAATGGTGTACATGCC 58.986 43.478 0.00 0.00 40.44 4.40
1876 2430 3.128938 CACTACTAACTAGGCGTTGCTCT 59.871 47.826 0.00 0.00 37.05 4.09
1880 2434 0.388649 AACTAGGCGTTGCTCTCACG 60.389 55.000 0.00 0.00 33.72 4.35
1881 2435 1.517257 CTAGGCGTTGCTCTCACGG 60.517 63.158 0.00 0.00 0.00 4.94
1888 2442 0.315568 GTTGCTCTCACGGAGTCACT 59.684 55.000 0.00 0.00 41.61 3.41
1893 2447 2.476997 GCTCTCACGGAGTCACTTTTTC 59.523 50.000 0.00 0.00 41.61 2.29
1896 2450 3.637229 TCTCACGGAGTCACTTTTTCTCT 59.363 43.478 0.00 0.00 41.61 3.10
1897 2451 4.099573 TCTCACGGAGTCACTTTTTCTCTT 59.900 41.667 0.00 0.00 41.61 2.85
1898 2452 4.369182 TCACGGAGTCACTTTTTCTCTTC 58.631 43.478 0.00 0.00 41.61 2.87
1899 2453 3.495001 CACGGAGTCACTTTTTCTCTTCC 59.505 47.826 0.00 0.00 41.61 3.46
1900 2454 3.134081 ACGGAGTCACTTTTTCTCTTCCA 59.866 43.478 0.00 0.00 29.74 3.53
1901 2455 3.743396 CGGAGTCACTTTTTCTCTTCCAG 59.257 47.826 0.00 0.00 0.00 3.86
1902 2456 4.501571 CGGAGTCACTTTTTCTCTTCCAGA 60.502 45.833 0.00 0.00 0.00 3.86
1903 2457 5.555966 GGAGTCACTTTTTCTCTTCCAGAT 58.444 41.667 0.00 0.00 0.00 2.90
1905 2459 6.488344 GGAGTCACTTTTTCTCTTCCAGATTT 59.512 38.462 0.00 0.00 0.00 2.17
1906 2460 7.661847 GGAGTCACTTTTTCTCTTCCAGATTTA 59.338 37.037 0.00 0.00 0.00 1.40
1908 2464 9.007901 AGTCACTTTTTCTCTTCCAGATTTATG 57.992 33.333 0.00 0.00 0.00 1.90
1933 2489 2.913777 TCCGTGATTGTCTAGTGTCG 57.086 50.000 0.00 0.00 0.00 4.35
1976 2532 8.201554 TGATTCATGTACAATTCACTCTTAGC 57.798 34.615 0.00 0.00 0.00 3.09
2129 2686 1.988107 TGGAAGGCATGGACTTCTCTT 59.012 47.619 11.32 0.00 46.12 2.85
2139 2696 6.823689 GGCATGGACTTCTCTTCTGTTAAATA 59.176 38.462 0.00 0.00 0.00 1.40
2247 2804 7.007456 GCAAAAGATATTTCGAGAAAAGAACCG 59.993 37.037 2.17 0.00 33.56 4.44
2600 3163 3.919216 AGGAGAGTGAAATGTTCGACTG 58.081 45.455 0.00 0.00 0.00 3.51
2709 3272 7.161773 ACATTGGTTATGGACTTCAAATGAG 57.838 36.000 0.00 0.00 38.64 2.90
2751 3314 5.851720 TCTCCATGTCAGATAATTGAGCTC 58.148 41.667 6.82 6.82 0.00 4.09
2833 3396 7.849322 AGGAGATTAAAAAGGTTTGGCTTTA 57.151 32.000 0.00 0.00 0.00 1.85
3130 3704 5.196341 TCGGTATACATAGCTTCCTGTTG 57.804 43.478 5.01 0.00 0.00 3.33
3226 3800 8.586744 ACCTTTTACAAGTGTTTTAAAACTCCA 58.413 29.630 26.76 8.79 39.59 3.86
3278 3852 1.818959 TTGCAAGCAAGGCCATCCAC 61.819 55.000 5.01 0.00 33.74 4.02
3336 3910 4.949121 ACAACTTCTCATACTAGGTCCCT 58.051 43.478 0.00 0.00 0.00 4.20
3377 3951 5.300034 TGGCCTGAAAGATATAATTGCAGTG 59.700 40.000 3.32 0.00 32.21 3.66
3583 4163 2.869801 TGGTCACTTCTGTGTTTAAGCG 59.130 45.455 0.00 0.00 44.14 4.68
3595 4175 2.869801 TGTTTAAGCGGTGTTCTGAGTG 59.130 45.455 0.00 0.00 0.00 3.51
3613 4193 4.202441 GAGTGCCATGTGTATCATCCTTT 58.798 43.478 0.00 0.00 34.09 3.11
3614 4194 4.202441 AGTGCCATGTGTATCATCCTTTC 58.798 43.478 0.00 0.00 34.09 2.62
3757 4337 0.610232 GTTCATCAGCAGGGCCAACT 60.610 55.000 6.18 0.00 0.00 3.16
3820 4400 6.984474 CACCTGTAACCAGACGAATAATATGT 59.016 38.462 0.00 0.00 41.50 2.29
3885 4465 3.452474 CTTTGCAATTGGTTCGGAAACA 58.548 40.909 3.93 3.93 37.10 2.83
3945 4525 0.526954 CTGCTTTGCGCCCATCATTC 60.527 55.000 4.18 0.00 38.05 2.67
3966 4546 3.394635 AACAGTTGCACGGACCGGT 62.395 57.895 20.00 6.92 0.00 5.28
4020 4600 8.728833 TGTTCATGCAAATTATTCATTTTTCCC 58.271 29.630 0.00 0.00 32.24 3.97
4022 4602 9.517868 TTCATGCAAATTATTCATTTTTCCCTT 57.482 25.926 0.00 0.00 32.24 3.95
4023 4603 9.165035 TCATGCAAATTATTCATTTTTCCCTTC 57.835 29.630 0.00 0.00 32.24 3.46
4143 4723 4.223800 GATGCAATCCGTGGCTCA 57.776 55.556 0.00 0.00 37.38 4.26
4147 4727 0.462581 TGCAATCCGTGGCTCAGATC 60.463 55.000 0.00 0.00 0.00 2.75
4274 4854 3.013921 GGATCCTAAATGTGTTCGGCAA 58.986 45.455 3.84 0.00 0.00 4.52
4286 4866 0.810648 TTCGGCAATCTGGTTCATGC 59.189 50.000 0.00 0.00 38.06 4.06
4317 4897 2.545532 GCTCGTTCCTGATCTGATCCTG 60.546 54.545 14.71 7.78 0.00 3.86
4327 4907 5.072872 CCTGATCTGATCCTGGGATAAACTT 59.927 44.000 14.71 0.00 34.60 2.66
4377 4957 3.062466 GTCCTTTCCGCCAAGGGC 61.062 66.667 10.17 5.53 43.40 5.19
4410 4990 4.335594 GTGCCTTTCAAGTTGAACTACACT 59.664 41.667 23.77 0.00 35.89 3.55
4425 5005 5.196341 ACTACACTGTCGAATCAGTTCAA 57.804 39.130 5.98 0.00 44.92 2.69
4518 5098 5.527951 GACGATGACTATGAAGCTCAAGAT 58.472 41.667 0.00 0.00 0.00 2.40
4521 5101 5.981915 CGATGACTATGAAGCTCAAGATCAA 59.018 40.000 0.00 0.00 0.00 2.57
4542 5122 4.052229 CCGGTGGAGCTTCGTCGT 62.052 66.667 0.00 0.00 0.00 4.34
4624 5204 8.604035 CACAATGACAATACCTATTCACTGTAC 58.396 37.037 0.00 0.00 0.00 2.90
4636 5227 4.517952 TTCACTGTACCCGAACGATTAA 57.482 40.909 0.00 0.00 0.00 1.40
4644 5235 2.301009 ACCCGAACGATTAAGGAGTTGT 59.699 45.455 0.00 0.00 0.00 3.32
4648 5239 3.985279 CGAACGATTAAGGAGTTGTGACA 59.015 43.478 0.00 0.00 0.00 3.58
4691 5282 2.801631 GGCTGATCAGGGAGGTCCG 61.802 68.421 23.89 0.00 41.52 4.79
4722 5313 2.025418 GGTTGACGCGTTCATCGGT 61.025 57.895 15.53 0.00 40.26 4.69
4830 5421 0.616111 ACCCACCAAAAGGCAACACA 60.616 50.000 0.00 0.00 41.41 3.72
4857 5448 2.359570 GAACCACAGTGACGACGGGT 62.360 60.000 0.62 0.00 0.00 5.28
4949 5540 1.993370 GCAACGGCACTACTAGAGTTG 59.007 52.381 0.00 2.21 41.07 3.16
4971 5562 4.096732 ACAGCAAGAAACTTGTTGACAC 57.903 40.909 25.97 6.07 33.69 3.67
4992 5583 0.107508 AGGAACGGTGATGATGCTGG 60.108 55.000 0.00 0.00 0.00 4.85
5145 5741 7.470900 GGCTGATGAAAGTATTGAGAAGAAAG 58.529 38.462 0.00 0.00 0.00 2.62
5220 5816 4.757149 GGGCCATAGATTGTGAGTTACATC 59.243 45.833 4.39 0.00 39.48 3.06
5221 5817 4.449068 GGCCATAGATTGTGAGTTACATCG 59.551 45.833 0.00 0.00 39.48 3.84
5270 5866 0.899720 CAGGCCACAAATTCTGCCAT 59.100 50.000 5.01 0.00 46.45 4.40
5336 5932 6.013725 TGGAGTGATGGTACTTCTTGTGTAAT 60.014 38.462 0.00 0.00 0.00 1.89
5366 5962 9.481340 AGATCTGAAAACTTTAAGCATTTTTCC 57.519 29.630 13.17 2.99 37.21 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.005791 GCCACTAAGTTCATTGCAACCTT 59.994 43.478 0.00 4.56 0.00 3.50
9 10 2.558359 AGCCACTAAGTTCATTGCAACC 59.442 45.455 0.00 0.00 0.00 3.77
10 11 3.923017 AGCCACTAAGTTCATTGCAAC 57.077 42.857 0.00 0.00 0.00 4.17
11 12 3.888323 TGAAGCCACTAAGTTCATTGCAA 59.112 39.130 0.00 0.00 0.00 4.08
13 14 4.156556 TGATGAAGCCACTAAGTTCATTGC 59.843 41.667 0.00 0.00 40.27 3.56
14 15 5.181811 TGTGATGAAGCCACTAAGTTCATTG 59.818 40.000 0.00 0.00 40.27 2.82
15 16 5.182001 GTGTGATGAAGCCACTAAGTTCATT 59.818 40.000 0.00 0.00 40.27 2.57
55 57 2.921834 TAGTGGTCTAGCCCTTGAGT 57.078 50.000 0.00 0.00 36.04 3.41
59 61 2.576648 CCCTTTTAGTGGTCTAGCCCTT 59.423 50.000 0.00 0.00 36.04 3.95
60 62 2.197465 CCCTTTTAGTGGTCTAGCCCT 58.803 52.381 0.00 0.00 36.04 5.19
68 70 3.562176 CCAGATTGAGCCCTTTTAGTGGT 60.562 47.826 0.00 0.00 0.00 4.16
86 88 3.774766 TCTAAATTAGACTGCTGGCCAGA 59.225 43.478 37.21 19.62 44.64 3.86
89 91 4.518249 AGTTCTAAATTAGACTGCTGGCC 58.482 43.478 1.61 0.00 33.84 5.36
94 96 7.278203 GGTGGACTTAGTTCTAAATTAGACTGC 59.722 40.741 1.61 0.00 33.84 4.40
121 123 2.708861 TCTCCAAGGAGTGCAACCTAAA 59.291 45.455 15.36 3.11 42.49 1.85
153 155 5.721960 TGCTAAGATAGAAAGGAGAACAGGT 59.278 40.000 0.00 0.00 0.00 4.00
155 157 8.037758 TCTTTGCTAAGATAGAAAGGAGAACAG 58.962 37.037 6.50 0.00 35.49 3.16
156 158 7.907389 TCTTTGCTAAGATAGAAAGGAGAACA 58.093 34.615 6.50 0.00 35.49 3.18
157 159 8.779354 TTCTTTGCTAAGATAGAAAGGAGAAC 57.221 34.615 11.41 0.00 40.01 3.01
186 196 1.151668 CAGTCTTCCGAGTTGCCTTG 58.848 55.000 0.00 0.00 0.00 3.61
191 201 2.609737 GGTACCACAGTCTTCCGAGTTG 60.610 54.545 7.15 0.00 0.00 3.16
257 268 3.123050 CTCGGTTTTCCTTGGCTTTTTG 58.877 45.455 0.00 0.00 37.95 2.44
265 276 4.565564 CGTCCTATTACTCGGTTTTCCTTG 59.434 45.833 0.00 0.00 37.95 3.61
280 291 8.511604 AATCTTTCACAATTGATCGTCCTATT 57.488 30.769 13.59 0.00 0.00 1.73
282 293 7.921786 AAATCTTTCACAATTGATCGTCCTA 57.078 32.000 13.59 0.00 0.00 2.94
306 317 8.062065 TGCTTTTTCTGACTCTTTTCCTTTTA 57.938 30.769 0.00 0.00 0.00 1.52
310 321 6.721704 ATTGCTTTTTCTGACTCTTTTCCT 57.278 33.333 0.00 0.00 0.00 3.36
403 414 7.088272 GCCGAGTGGAAGTGTAAAATTTAATT 58.912 34.615 0.00 0.00 37.49 1.40
404 415 6.207810 TGCCGAGTGGAAGTGTAAAATTTAAT 59.792 34.615 0.00 0.00 37.49 1.40
409 420 3.134574 TGCCGAGTGGAAGTGTAAAAT 57.865 42.857 0.00 0.00 37.49 1.82
456 467 4.220821 CCCTAAGTCTGAGCAGTGAGTTTA 59.779 45.833 0.00 0.00 0.00 2.01
466 477 5.069781 ACTGATATTGACCCTAAGTCTGAGC 59.930 44.000 0.00 0.00 46.46 4.26
475 486 2.891580 GAGCCGACTGATATTGACCCTA 59.108 50.000 0.00 0.00 0.00 3.53
484 495 1.342076 ACTTCCTGGAGCCGACTGATA 60.342 52.381 0.00 0.00 0.00 2.15
505 516 3.444916 GCATCCTTCGTTGACTTCGATA 58.555 45.455 0.00 0.00 37.18 2.92
509 520 1.464997 GTGGCATCCTTCGTTGACTTC 59.535 52.381 0.00 0.00 0.00 3.01
515 526 1.002134 CTGGGTGGCATCCTTCGTT 60.002 57.895 19.39 0.00 0.00 3.85
532 543 1.165270 GTTTCACTATGCCGCCAACT 58.835 50.000 0.00 0.00 0.00 3.16
534 545 0.037590 AGGTTTCACTATGCCGCCAA 59.962 50.000 0.00 0.00 0.00 4.52
585 596 0.888619 ATCCTTGTCGACGAGCAAGA 59.111 50.000 27.13 17.61 43.29 3.02
600 611 0.984230 TCTTGGAAGAACGGCATCCT 59.016 50.000 3.97 0.00 35.40 3.24
676 691 7.591821 TCCTGCCCCTTTTCTTTTATATACAT 58.408 34.615 0.00 0.00 0.00 2.29
677 692 6.975949 TCCTGCCCCTTTTCTTTTATATACA 58.024 36.000 0.00 0.00 0.00 2.29
678 693 7.778382 TCTTCCTGCCCCTTTTCTTTTATATAC 59.222 37.037 0.00 0.00 0.00 1.47
679 694 7.878495 TCTTCCTGCCCCTTTTCTTTTATATA 58.122 34.615 0.00 0.00 0.00 0.86
681 696 6.147437 TCTTCCTGCCCCTTTTCTTTTATA 57.853 37.500 0.00 0.00 0.00 0.98
682 697 5.010708 TCTTCCTGCCCCTTTTCTTTTAT 57.989 39.130 0.00 0.00 0.00 1.40
683 698 4.463050 TCTTCCTGCCCCTTTTCTTTTA 57.537 40.909 0.00 0.00 0.00 1.52
686 701 2.447047 TCTTCTTCCTGCCCCTTTTCTT 59.553 45.455 0.00 0.00 0.00 2.52
688 703 2.586648 TCTTCTTCCTGCCCCTTTTC 57.413 50.000 0.00 0.00 0.00 2.29
691 706 3.328535 TTTTTCTTCTTCCTGCCCCTT 57.671 42.857 0.00 0.00 0.00 3.95
723 738 5.469084 CCCTACAAGTCTACAACCAAGAAAC 59.531 44.000 0.00 0.00 0.00 2.78
725 740 4.041198 CCCCTACAAGTCTACAACCAAGAA 59.959 45.833 0.00 0.00 0.00 2.52
732 747 2.384375 TCCTCCCCCTACAAGTCTACAA 59.616 50.000 0.00 0.00 0.00 2.41
733 748 2.005350 TCCTCCCCCTACAAGTCTACA 58.995 52.381 0.00 0.00 0.00 2.74
734 749 2.668625 CTCCTCCCCCTACAAGTCTAC 58.331 57.143 0.00 0.00 0.00 2.59
735 750 1.574339 CCTCCTCCCCCTACAAGTCTA 59.426 57.143 0.00 0.00 0.00 2.59
736 751 0.340208 CCTCCTCCCCCTACAAGTCT 59.660 60.000 0.00 0.00 0.00 3.24
737 752 1.338890 GCCTCCTCCCCCTACAAGTC 61.339 65.000 0.00 0.00 0.00 3.01
738 753 1.307084 GCCTCCTCCCCCTACAAGT 60.307 63.158 0.00 0.00 0.00 3.16
739 754 2.435693 CGCCTCCTCCCCCTACAAG 61.436 68.421 0.00 0.00 0.00 3.16
740 755 2.365105 CGCCTCCTCCCCCTACAA 60.365 66.667 0.00 0.00 0.00 2.41
741 756 4.475444 CCGCCTCCTCCCCCTACA 62.475 72.222 0.00 0.00 0.00 2.74
770 806 1.526575 CCACCAACTGCCGATTGCTT 61.527 55.000 0.00 0.00 42.00 3.91
778 814 3.118920 ACTTTAACAAACCACCAACTGCC 60.119 43.478 0.00 0.00 0.00 4.85
802 840 6.716628 GCCAGTGATGATTAAATATGAAGGGA 59.283 38.462 0.00 0.00 0.00 4.20
809 847 4.690748 CGTCCGCCAGTGATGATTAAATAT 59.309 41.667 0.00 0.00 0.00 1.28
810 848 4.055360 CGTCCGCCAGTGATGATTAAATA 58.945 43.478 0.00 0.00 0.00 1.40
833 871 1.080434 GTCTCCTTCTCGCGCTTGT 60.080 57.895 5.56 0.00 0.00 3.16
834 872 1.807573 GGTCTCCTTCTCGCGCTTG 60.808 63.158 5.56 0.00 0.00 4.01
870 914 7.988028 AGATCCTGTGTTAGATTTAAGTAAGGC 59.012 37.037 0.00 0.00 0.00 4.35
1036 1095 1.229209 GGAGGAGGTGGTGGAGACA 60.229 63.158 0.00 0.00 38.70 3.41
1064 1123 2.048222 CAGCGAAACAGAGGGCGA 60.048 61.111 0.00 0.00 0.00 5.54
1110 1169 0.970937 CTTCTCCGGTGCCTCCTGTA 60.971 60.000 0.00 0.00 0.00 2.74
1186 1248 3.198068 GCTGCTGAATCGAATGGAAGTA 58.802 45.455 0.00 0.00 0.00 2.24
1265 1342 3.689346 GCTCGCCATCTGATTCTTTTTC 58.311 45.455 0.00 0.00 0.00 2.29
1339 1423 0.868602 TACGCAGTTCGCTAATCGCC 60.869 55.000 0.00 0.00 37.78 5.54
1366 1451 3.491104 GCATAGTACGAAGCCAAGCTAGT 60.491 47.826 0.00 0.00 38.25 2.57
1481 1588 2.976099 AAAAATAGCAGCCGGCCTT 58.024 47.368 26.15 11.84 46.50 4.35
1529 2055 2.412455 CGCGCAATCTCATCATTCATCC 60.412 50.000 8.75 0.00 0.00 3.51
1536 2062 0.807275 CCTGTCGCGCAATCTCATCA 60.807 55.000 8.75 0.00 0.00 3.07
1552 2078 2.490328 ACAACAAATGCGTGTTCCTG 57.510 45.000 0.00 0.00 39.73 3.86
1554 2080 3.242936 ACACTACAACAAATGCGTGTTCC 60.243 43.478 0.00 0.00 41.46 3.62
1559 2085 4.564769 CCAAAAACACTACAACAAATGCGT 59.435 37.500 0.00 0.00 0.00 5.24
1563 2089 7.335422 TGAAATGCCAAAAACACTACAACAAAT 59.665 29.630 0.00 0.00 0.00 2.32
1582 2108 0.445436 CGGAGTCAGCTGTGAAATGC 59.555 55.000 14.67 0.00 33.27 3.56
1597 2123 1.120530 ATACAGTGGTAAGGCCGGAG 58.879 55.000 5.05 0.00 41.21 4.63
1601 2127 3.815401 CTGCATAATACAGTGGTAAGGCC 59.185 47.826 0.00 0.00 32.19 5.19
1608 2134 2.923121 AGTGCCTGCATAATACAGTGG 58.077 47.619 0.00 0.00 33.09 4.00
1614 2140 6.588719 AAAAACTGAAGTGCCTGCATAATA 57.411 33.333 0.00 0.00 0.00 0.98
1643 2169 3.091545 CCATATTGCCACAGTCCAAACT 58.908 45.455 0.00 0.00 35.60 2.66
1644 2170 2.166254 CCCATATTGCCACAGTCCAAAC 59.834 50.000 0.00 0.00 0.00 2.93
1651 2197 4.669206 TTTATTGCCCATATTGCCACAG 57.331 40.909 0.00 0.00 0.00 3.66
1656 2202 7.205297 CCAGCTATATTTATTGCCCATATTGC 58.795 38.462 0.00 0.00 35.50 3.56
1661 2207 4.026052 GCCCAGCTATATTTATTGCCCAT 58.974 43.478 0.00 0.00 35.50 4.00
1707 2253 2.812011 GAGCACACCGTTTCCAACTAAT 59.188 45.455 0.00 0.00 0.00 1.73
1718 2264 2.290641 GTCAGAAATTTGAGCACACCGT 59.709 45.455 0.00 0.00 0.00 4.83
1719 2265 2.549754 AGTCAGAAATTTGAGCACACCG 59.450 45.455 0.00 0.00 0.00 4.94
1727 2273 8.450578 AAGAACACATGTAGTCAGAAATTTGA 57.549 30.769 0.00 0.00 0.00 2.69
1767 2313 7.671495 AGCAAACTCAAAAGAACACATTTTT 57.329 28.000 0.00 0.00 0.00 1.94
1768 2314 8.770438 TTAGCAAACTCAAAAGAACACATTTT 57.230 26.923 0.00 0.00 0.00 1.82
1769 2315 8.770438 TTTAGCAAACTCAAAAGAACACATTT 57.230 26.923 0.00 0.00 0.00 2.32
1770 2316 8.770438 TTTTAGCAAACTCAAAAGAACACATT 57.230 26.923 0.00 0.00 0.00 2.71
1771 2317 8.770438 TTTTTAGCAAACTCAAAAGAACACAT 57.230 26.923 0.00 0.00 28.32 3.21
1795 2341 9.971922 CTTCTTATCCTCAAAAGAACACATTTT 57.028 29.630 0.00 0.00 36.93 1.82
1796 2342 9.136323 ACTTCTTATCCTCAAAAGAACACATTT 57.864 29.630 0.00 0.00 36.93 2.32
1797 2343 8.571336 CACTTCTTATCCTCAAAAGAACACATT 58.429 33.333 0.00 0.00 36.93 2.71
1798 2344 7.939039 TCACTTCTTATCCTCAAAAGAACACAT 59.061 33.333 0.00 0.00 36.93 3.21
1799 2345 7.279615 TCACTTCTTATCCTCAAAAGAACACA 58.720 34.615 0.00 0.00 36.93 3.72
1800 2346 7.730364 TCACTTCTTATCCTCAAAAGAACAC 57.270 36.000 0.00 0.00 36.93 3.32
1801 2347 8.156820 TGATCACTTCTTATCCTCAAAAGAACA 58.843 33.333 0.00 0.00 36.93 3.18
1802 2348 8.553459 TGATCACTTCTTATCCTCAAAAGAAC 57.447 34.615 0.00 0.00 36.93 3.01
1803 2349 7.826252 CCTGATCACTTCTTATCCTCAAAAGAA 59.174 37.037 0.00 0.00 38.93 2.52
1804 2350 7.038017 ACCTGATCACTTCTTATCCTCAAAAGA 60.038 37.037 0.00 0.00 0.00 2.52
1805 2351 7.108847 ACCTGATCACTTCTTATCCTCAAAAG 58.891 38.462 0.00 0.00 0.00 2.27
1806 2352 7.020827 ACCTGATCACTTCTTATCCTCAAAA 57.979 36.000 0.00 0.00 0.00 2.44
1807 2353 6.627087 ACCTGATCACTTCTTATCCTCAAA 57.373 37.500 0.00 0.00 0.00 2.69
1847 2401 3.458189 GCCTAGTTAGTAGTGGCATGTG 58.542 50.000 0.00 0.00 42.79 3.21
1876 2430 4.369182 GAAGAGAAAAAGTGACTCCGTGA 58.631 43.478 0.00 0.00 0.00 4.35
1880 2434 4.962155 TCTGGAAGAGAAAAAGTGACTCC 58.038 43.478 0.00 0.00 38.67 3.85
1914 2470 2.429478 TCGACACTAGACAATCACGGA 58.571 47.619 0.00 0.00 0.00 4.69
1915 2471 2.913777 TCGACACTAGACAATCACGG 57.086 50.000 0.00 0.00 0.00 4.94
1916 2472 2.915463 GGTTCGACACTAGACAATCACG 59.085 50.000 0.00 0.00 0.00 4.35
1917 2473 3.909430 TGGTTCGACACTAGACAATCAC 58.091 45.455 0.00 0.00 0.00 3.06
1919 2475 5.749109 CCTTATGGTTCGACACTAGACAATC 59.251 44.000 0.00 0.00 0.00 2.67
1933 2489 7.630242 TGAATCAATTCTGACCTTATGGTTC 57.370 36.000 1.18 0.00 41.03 3.62
1950 2506 8.668353 GCTAAGAGTGAATTGTACATGAATCAA 58.332 33.333 0.00 2.07 0.00 2.57
1968 2524 6.241645 ACCATAAGAAAGCTTTGCTAAGAGT 58.758 36.000 18.30 3.04 38.25 3.24
2163 2720 5.046520 AGGTAAATCGATAGGCCCAGTAATC 60.047 44.000 0.00 0.00 0.00 1.75
2199 2756 4.183865 CAGAAATAGCATCCTTCGTGTCA 58.816 43.478 0.00 0.00 0.00 3.58
2247 2804 2.112815 GGCAATCACACCGCCTACC 61.113 63.158 0.00 0.00 42.78 3.18
2508 3065 2.360165 GTCATGCAATCCACCATCCTTC 59.640 50.000 0.00 0.00 0.00 3.46
2600 3163 4.499183 CTGTGTCATAGAGGTTTGAGGAC 58.501 47.826 0.00 0.00 0.00 3.85
2709 3272 6.668323 TGGAGATTGTCGAATCAAAAGAAAC 58.332 36.000 0.21 0.00 40.59 2.78
2751 3314 2.194201 TTGTCCTAAAAAGCTCCCCG 57.806 50.000 0.00 0.00 0.00 5.73
2786 3349 9.715121 TCCTTAAAAATACGTCAGTAAGTTCAT 57.285 29.630 0.00 0.00 36.29 2.57
2833 3396 7.658575 CCATGTGAAAAATGTGAGGAAGAAAAT 59.341 33.333 0.00 0.00 25.83 1.82
2910 3476 9.965824 CACCATACCTAATGAAAATATCAAACC 57.034 33.333 0.00 0.00 42.54 3.27
2971 3537 6.271488 TCTTTTGCTTGCTTGTATGCTAAT 57.729 33.333 0.00 0.00 0.00 1.73
3092 3666 8.078959 TGTATACCGAAAAATGTTATCGATGG 57.921 34.615 8.54 0.00 38.82 3.51
3143 3717 3.350219 TCCACACCTCCTCAATAAAGC 57.650 47.619 0.00 0.00 0.00 3.51
3175 3749 5.124936 TGAACTAGCGCAAGATACTACTGAA 59.875 40.000 11.47 0.00 43.02 3.02
3226 3800 2.255770 ATCGAGAGACTTCCCCCTTT 57.744 50.000 0.00 0.00 46.97 3.11
3377 3951 4.381505 CCCCAAGTTGTATTGTATTGTGGC 60.382 45.833 1.45 0.00 0.00 5.01
3583 4163 0.877071 CACATGGCACTCAGAACACC 59.123 55.000 0.00 0.00 0.00 4.16
3595 4175 3.947196 TGTGAAAGGATGATACACATGGC 59.053 43.478 0.00 0.00 39.56 4.40
3613 4193 1.338105 CCAGCGGACTTCAATCTGTGA 60.338 52.381 0.00 0.00 0.00 3.58
3614 4194 1.081892 CCAGCGGACTTCAATCTGTG 58.918 55.000 0.00 0.00 0.00 3.66
3697 4277 2.178912 TCCATGGGTTTCGTGTTCTC 57.821 50.000 13.02 0.00 0.00 2.87
3844 4424 2.920724 GGAACCATTCCTAGGAGAGC 57.079 55.000 12.26 0.00 46.57 4.09
3945 4525 2.604174 GGTCCGTGCAACTGTTCCG 61.604 63.158 0.00 0.00 31.75 4.30
3966 4546 2.902486 ACTCTCAGAAAGGCTCATGACA 59.098 45.455 0.00 0.00 0.00 3.58
4023 4603 7.337689 TCATTTACAAGACTGAATCCAATCTGG 59.662 37.037 0.00 0.00 39.43 3.86
4147 4727 1.729470 CGAGACGAGGGATCACCAGG 61.729 65.000 0.00 0.00 43.89 4.45
4274 4854 5.515797 CAATCTCATTGCATGAACCAGAT 57.484 39.130 0.00 0.00 39.11 2.90
4286 4866 3.264947 TCAGGAACGAGCAATCTCATTG 58.735 45.455 0.00 0.00 43.06 2.82
4292 4872 3.170791 TCAGATCAGGAACGAGCAATC 57.829 47.619 0.00 0.00 0.00 2.67
4327 4907 8.877864 ACCTGGTATTATGAAATCAAGAACAA 57.122 30.769 0.00 0.00 0.00 2.83
4377 4957 3.243068 ACTTGAAAGGCACAAACTTAGCG 60.243 43.478 0.00 0.00 0.00 4.26
4384 4964 4.799564 AGTTCAACTTGAAAGGCACAAA 57.200 36.364 5.76 0.00 38.22 2.83
4410 4990 5.491070 AGAATGGATTGAACTGATTCGACA 58.509 37.500 0.00 0.00 37.69 4.35
4425 5005 5.760253 GTCCATCGTGATGTTTAGAATGGAT 59.240 40.000 8.89 0.00 37.89 3.41
4518 5098 2.819984 GAAGCTCCACCGGCCATTGA 62.820 60.000 0.00 0.00 0.00 2.57
4521 5101 4.473520 CGAAGCTCCACCGGCCAT 62.474 66.667 0.00 0.00 0.00 4.40
4542 5122 0.108186 CTGCTGGGACTAATCGTGCA 60.108 55.000 0.00 0.00 35.37 4.57
4551 5131 1.107114 CATAGTCGACTGCTGGGACT 58.893 55.000 28.12 18.59 43.10 3.85
4589 5169 6.512297 AGGTATTGTCATTGTGTTTGGTTTC 58.488 36.000 0.00 0.00 0.00 2.78
4624 5204 2.671396 CACAACTCCTTAATCGTTCGGG 59.329 50.000 0.00 0.00 0.00 5.14
4636 5227 1.064758 TGCCTGTTTGTCACAACTCCT 60.065 47.619 0.00 0.00 33.87 3.69
4644 5235 1.811558 GCTCTCTGTGCCTGTTTGTCA 60.812 52.381 0.00 0.00 0.00 3.58
4648 5239 1.963338 GCGCTCTCTGTGCCTGTTT 60.963 57.895 0.00 0.00 45.73 2.83
4668 5259 1.124477 CCTCCCTGATCAGCCTACCC 61.124 65.000 17.76 0.00 0.00 3.69
4691 5282 0.670854 GTCAACCGTGAAGCTCTCCC 60.671 60.000 0.00 0.00 34.87 4.30
4722 5313 0.535335 GCTCCCAGTCGGTCACATTA 59.465 55.000 0.00 0.00 0.00 1.90
4830 5421 1.068741 GTCACTGTGGTTCGTCTCCTT 59.931 52.381 8.11 0.00 0.00 3.36
4949 5540 4.098416 GTGTCAACAAGTTTCTTGCTGTC 58.902 43.478 9.06 6.37 0.00 3.51
4971 5562 0.179100 AGCATCATCACCGTTCCTCG 60.179 55.000 0.00 0.00 39.52 4.63
4992 5583 5.482686 AATTCAAAACACACAAACATGGC 57.517 34.783 0.00 0.00 0.00 4.40
5053 5644 1.134371 TGTTTGTGGTGATCGGTGACA 60.134 47.619 0.00 0.00 0.00 3.58
5145 5741 2.617274 GGGAAACAGCACACGGAGC 61.617 63.158 0.00 0.00 0.00 4.70
5253 5849 1.275856 TCAATGGCAGAATTTGTGGCC 59.724 47.619 16.02 0.00 46.58 5.36
5270 5866 4.276678 CAGTTTGCACTTCTCTCCAATCAA 59.723 41.667 0.00 0.00 0.00 2.57
5365 5961 4.812626 AGAGTTTGCTTGCATTTTTCAAGG 59.187 37.500 0.00 0.00 40.79 3.61
5366 5962 5.332055 CGAGAGTTTGCTTGCATTTTTCAAG 60.332 40.000 0.00 0.00 42.72 3.02
5505 6102 7.619965 TCACTCTGTTGTATATGAATTGTGGA 58.380 34.615 0.00 0.00 0.00 4.02
5928 6527 4.610605 TGGAAACCAGACGAATCACTTA 57.389 40.909 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.