Multiple sequence alignment - TraesCS2B01G438600

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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 TraesCS2B01G438600 chr2B 100.000 4830 0 0 1 4830 631105568 631100739 0.000000e+00 8920.0
1 TraesCS2B01G438600 chr2B 89.320 1030 101 7 2697 3720 630136898 630135872 0.000000e+00 1284.0
2 TraesCS2B01G438600 chr2B 86.879 282 16 9 4115 4394 631175694 631175432 3.660000e-76 296.0
3 TraesCS2B01G438600 chr2B 83.884 242 26 8 3939 4173 630135722 630135487 8.140000e-53 219.0
4 TraesCS2B01G438600 chr2B 90.588 85 6 1 3931 4013 631101597 631101513 1.420000e-20 111.0
5 TraesCS2B01G438600 chr2B 90.588 85 6 1 3972 4056 631101638 631101556 1.420000e-20 111.0
6 TraesCS2B01G438600 chr2D 92.315 3318 177 30 760 4056 531265969 531262709 0.000000e+00 4643.0
7 TraesCS2B01G438600 chr2D 89.591 1028 99 8 2697 3720 530260023 530259000 0.000000e+00 1299.0
8 TraesCS2B01G438600 chr2D 94.957 694 28 5 1 693 531266659 531265972 0.000000e+00 1081.0
9 TraesCS2B01G438600 chr2D 89.730 370 31 5 3931 4297 531262793 531262428 2.630000e-127 466.0
10 TraesCS2B01G438600 chr2D 91.617 334 22 1 4503 4830 531259985 531259652 1.580000e-124 457.0
11 TraesCS2B01G438600 chr2D 87.189 281 17 8 4115 4394 531335069 531334807 7.860000e-78 302.0
12 TraesCS2B01G438600 chr2D 95.489 133 5 1 4374 4506 531260150 531260019 1.360000e-50 211.0
13 TraesCS2B01G438600 chr2D 89.412 85 5 3 3938 4019 530258750 530258667 2.380000e-18 104.0
14 TraesCS2B01G438600 chr2D 90.667 75 7 0 4522 4596 615384506 615384580 3.080000e-17 100.0
15 TraesCS2B01G438600 chr2D 92.857 56 1 1 4439 4494 615384379 615384431 1.440000e-10 78.7
16 TraesCS2B01G438600 chr2A 91.249 3371 199 42 760 4063 675749859 675746518 0.000000e+00 4503.0
17 TraesCS2B01G438600 chr2A 89.192 1027 105 6 2697 3720 675081125 675080102 0.000000e+00 1277.0
18 TraesCS2B01G438600 chr2A 94.813 694 29 5 1 693 675750549 675749862 0.000000e+00 1075.0
19 TraesCS2B01G438600 chr2A 90.659 364 25 7 3939 4297 675746602 675746243 4.370000e-130 475.0
20 TraesCS2B01G438600 chr2A 92.216 334 20 2 4503 4830 675745927 675745594 7.320000e-128 468.0
21 TraesCS2B01G438600 chr2A 94.811 212 9 2 4295 4506 675746170 675745961 3.600000e-86 329.0
22 TraesCS2B01G438600 chr2A 76.680 253 32 16 3792 4019 675080057 675079807 1.100000e-21 115.0
23 TraesCS2B01G438600 chr2A 89.333 75 8 0 4522 4596 745393194 745393268 1.430000e-15 95.3
24 TraesCS2B01G438600 chr2A 92.982 57 1 1 4438 4494 745393067 745393120 4.010000e-11 80.5
25 TraesCS2B01G438600 chr2A 97.297 37 1 0 4458 4494 745395694 745395730 4.040000e-06 63.9
26 TraesCS2B01G438600 chr4D 85.000 160 20 2 4527 4682 47288659 47288818 5.000000e-35 159.0


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 TraesCS2B01G438600 chr2B 631100739 631105568 4829 True 8920.0 8920 100.0000 1 4830 1 chr2B.!!$R1 4829
1 TraesCS2B01G438600 chr2B 630135487 630136898 1411 True 751.5 1284 86.6020 2697 4173 2 chr2B.!!$R3 1476
2 TraesCS2B01G438600 chr2D 531259652 531266659 7007 True 1371.6 4643 92.8216 1 4830 5 chr2D.!!$R3 4829
3 TraesCS2B01G438600 chr2D 530258667 530260023 1356 True 701.5 1299 89.5015 2697 4019 2 chr2D.!!$R2 1322
4 TraesCS2B01G438600 chr2A 675745594 675750549 4955 True 1370.0 4503 92.7496 1 4830 5 chr2A.!!$R2 4829
5 TraesCS2B01G438600 chr2A 675079807 675081125 1318 True 696.0 1277 82.9360 2697 4019 2 chr2A.!!$R1 1322

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
716 718 0.250124 TTGGGTAACTGCAGTGTCCG 60.250 55.0 22.49 0.0 0.00 4.79 F
973 977 0.455005 GGCTTCAGGAAGATTGCAGC 59.545 55.0 13.01 0.0 40.79 5.25 F
996 1000 0.461961 CCCTGTCAGATCGGAGGTTC 59.538 60.0 0.00 0.0 0.00 3.62 F
2788 2810 0.318441 AGCACACGCAGAAGAAGCTA 59.682 50.0 0.00 0.0 42.27 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1640 0.097674 GTGATAAGTTGCGCAGGCTG 59.902 55.0 11.31 10.94 40.82 4.85 R
2710 2732 0.321653 GTTTGCCCGGATCAGACAGT 60.322 55.0 0.73 0.00 0.00 3.55 R
2911 2936 0.766674 ACAAGTACTGGTCCTGGCCA 60.767 55.0 4.71 4.71 36.97 5.36 R
4613 6984 0.181114 GCCTATCCCAGTGACATGCA 59.819 55.0 0.00 0.00 0.00 3.96 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 60 2.939103 CCCTTAGCTGCATTGTCTGTAC 59.061 50.000 1.02 0.00 0.00 2.90
67 68 1.129998 GCATTGTCTGTACTGCAGCTG 59.870 52.381 15.27 10.11 44.66 4.24
103 104 7.930325 CAGCTATTGATCCATCTTGTTCTCTTA 59.070 37.037 0.00 0.00 0.00 2.10
199 200 3.767131 TGGAAGATACGGTGATGAACTCA 59.233 43.478 0.00 0.00 0.00 3.41
217 218 5.483685 ACTCACCTACATGCTAACTGAAA 57.516 39.130 0.00 0.00 0.00 2.69
218 219 5.865085 ACTCACCTACATGCTAACTGAAAA 58.135 37.500 0.00 0.00 0.00 2.29
219 220 6.296026 ACTCACCTACATGCTAACTGAAAAA 58.704 36.000 0.00 0.00 0.00 1.94
220 221 6.428159 ACTCACCTACATGCTAACTGAAAAAG 59.572 38.462 0.00 0.00 0.00 2.27
222 223 6.204688 TCACCTACATGCTAACTGAAAAAGTG 59.795 38.462 0.00 0.00 39.81 3.16
223 224 5.473504 ACCTACATGCTAACTGAAAAAGTGG 59.526 40.000 0.00 0.00 39.81 4.00
225 226 6.206634 CCTACATGCTAACTGAAAAAGTGGAA 59.793 38.462 0.00 0.00 39.81 3.53
226 227 6.076981 ACATGCTAACTGAAAAAGTGGAAG 57.923 37.500 0.00 0.00 39.81 3.46
227 228 5.827797 ACATGCTAACTGAAAAAGTGGAAGA 59.172 36.000 0.00 0.00 39.81 2.87
229 230 7.665559 ACATGCTAACTGAAAAAGTGGAAGATA 59.334 33.333 0.00 0.00 39.81 1.98
230 231 7.435068 TGCTAACTGAAAAAGTGGAAGATAC 57.565 36.000 0.00 0.00 39.81 2.24
231 232 6.147164 TGCTAACTGAAAAAGTGGAAGATACG 59.853 38.462 0.00 0.00 39.81 3.06
232 233 5.941948 AACTGAAAAAGTGGAAGATACGG 57.058 39.130 0.00 0.00 39.81 4.02
233 234 5.223449 ACTGAAAAAGTGGAAGATACGGA 57.777 39.130 0.00 0.00 37.88 4.69
234 235 5.238583 ACTGAAAAAGTGGAAGATACGGAG 58.761 41.667 0.00 0.00 37.88 4.63
254 255 5.505324 CGGAGTATTAGTAACCTCTGTTCCG 60.505 48.000 10.25 0.00 35.87 4.30
263 264 2.582052 ACCTCTGTTCCGCAATTTTGA 58.418 42.857 0.00 0.00 0.00 2.69
274 275 7.094162 TGTTCCGCAATTTTGAGATGGTAATAA 60.094 33.333 0.00 0.00 0.00 1.40
398 399 4.403432 ACCGTATCCTTTATCCGAAGACAA 59.597 41.667 0.00 0.00 0.00 3.18
453 454 6.660949 CCTGTATCTGATTCTTTTTGGGACTT 59.339 38.462 0.00 0.00 0.00 3.01
462 463 9.367160 TGATTCTTTTTGGGACTTTTCTCTTAT 57.633 29.630 0.00 0.00 0.00 1.73
656 658 3.738982 TGAAGTTCAAAAGGATGAGCGA 58.261 40.909 2.20 0.00 35.89 4.93
673 675 2.229302 AGCGATTTCCTCTCCGTATAGC 59.771 50.000 0.00 0.00 0.00 2.97
697 699 9.933723 AGCTACATTTTCTTCTGCATTTTAATT 57.066 25.926 0.00 0.00 0.00 1.40
701 703 8.785946 ACATTTTCTTCTGCATTTTAATTTGGG 58.214 29.630 0.00 0.00 0.00 4.12
702 704 8.785946 CATTTTCTTCTGCATTTTAATTTGGGT 58.214 29.630 0.00 0.00 0.00 4.51
704 706 9.838339 TTTTCTTCTGCATTTTAATTTGGGTAA 57.162 25.926 0.00 0.00 0.00 2.85
705 707 8.825667 TTCTTCTGCATTTTAATTTGGGTAAC 57.174 30.769 0.00 0.00 0.00 2.50
706 708 8.189119 TCTTCTGCATTTTAATTTGGGTAACT 57.811 30.769 0.00 0.00 0.00 2.24
707 709 8.087750 TCTTCTGCATTTTAATTTGGGTAACTG 58.912 33.333 0.00 0.00 0.00 3.16
708 710 6.162777 TCTGCATTTTAATTTGGGTAACTGC 58.837 36.000 0.00 0.00 0.00 4.40
709 711 5.858381 TGCATTTTAATTTGGGTAACTGCA 58.142 33.333 0.00 0.00 31.72 4.41
710 712 5.931146 TGCATTTTAATTTGGGTAACTGCAG 59.069 36.000 13.48 13.48 31.12 4.41
711 713 5.931724 GCATTTTAATTTGGGTAACTGCAGT 59.068 36.000 15.25 15.25 0.00 4.40
712 714 6.128580 GCATTTTAATTTGGGTAACTGCAGTG 60.129 38.462 22.49 2.20 0.00 3.66
713 715 6.472686 TTTTAATTTGGGTAACTGCAGTGT 57.527 33.333 22.49 13.05 0.00 3.55
714 716 5.699097 TTAATTTGGGTAACTGCAGTGTC 57.301 39.130 22.49 15.92 0.00 3.67
715 717 1.975660 TTTGGGTAACTGCAGTGTCC 58.024 50.000 22.49 23.46 0.00 4.02
716 718 0.250124 TTGGGTAACTGCAGTGTCCG 60.250 55.000 22.49 0.00 0.00 4.79
717 719 1.375523 GGGTAACTGCAGTGTCCGG 60.376 63.158 22.49 0.00 0.00 5.14
718 720 2.033194 GGTAACTGCAGTGTCCGGC 61.033 63.158 22.49 7.04 0.00 6.13
719 721 2.033194 GTAACTGCAGTGTCCGGCC 61.033 63.158 22.49 0.00 0.00 6.13
720 722 3.583276 TAACTGCAGTGTCCGGCCG 62.583 63.158 22.49 21.04 0.00 6.13
722 724 4.680237 CTGCAGTGTCCGGCCGAA 62.680 66.667 30.73 1.10 0.00 4.30
723 725 4.243008 TGCAGTGTCCGGCCGAAA 62.243 61.111 30.73 12.10 0.00 3.46
724 726 3.723348 GCAGTGTCCGGCCGAAAC 61.723 66.667 30.73 24.17 0.00 2.78
725 727 2.030562 CAGTGTCCGGCCGAAACT 59.969 61.111 30.73 22.99 39.92 2.66
726 728 1.597027 CAGTGTCCGGCCGAAACTT 60.597 57.895 30.73 13.64 36.88 2.66
727 729 1.147600 AGTGTCCGGCCGAAACTTT 59.852 52.632 30.73 13.30 35.28 2.66
728 730 1.164041 AGTGTCCGGCCGAAACTTTG 61.164 55.000 30.73 8.04 35.28 2.77
729 731 1.146485 TGTCCGGCCGAAACTTTGA 59.854 52.632 30.73 10.80 0.00 2.69
730 732 0.882927 TGTCCGGCCGAAACTTTGAG 60.883 55.000 30.73 6.27 0.00 3.02
731 733 1.302192 TCCGGCCGAAACTTTGAGG 60.302 57.895 30.73 5.39 0.00 3.86
732 734 2.332654 CCGGCCGAAACTTTGAGGG 61.333 63.158 30.73 0.00 0.00 4.30
733 735 1.302192 CGGCCGAAACTTTGAGGGA 60.302 57.895 24.07 0.00 0.00 4.20
734 736 0.887387 CGGCCGAAACTTTGAGGGAA 60.887 55.000 24.07 0.00 0.00 3.97
735 737 1.324383 GGCCGAAACTTTGAGGGAAA 58.676 50.000 0.00 0.00 0.00 3.13
736 738 1.000607 GGCCGAAACTTTGAGGGAAAC 60.001 52.381 0.00 0.00 0.00 2.78
737 739 1.954382 GCCGAAACTTTGAGGGAAACT 59.046 47.619 0.00 0.00 0.00 2.66
738 740 2.287608 GCCGAAACTTTGAGGGAAACTG 60.288 50.000 0.00 0.00 0.00 3.16
739 741 2.287608 CCGAAACTTTGAGGGAAACTGC 60.288 50.000 0.00 0.00 0.00 4.40
740 742 2.357637 CGAAACTTTGAGGGAAACTGCA 59.642 45.455 0.00 0.00 0.00 4.41
741 743 3.548818 CGAAACTTTGAGGGAAACTGCAG 60.549 47.826 13.48 13.48 0.00 4.41
742 744 1.322442 ACTTTGAGGGAAACTGCAGC 58.678 50.000 15.27 0.00 0.00 5.25
743 745 1.133668 ACTTTGAGGGAAACTGCAGCT 60.134 47.619 15.27 0.00 0.00 4.24
744 746 1.959282 CTTTGAGGGAAACTGCAGCTT 59.041 47.619 15.27 8.13 0.00 3.74
745 747 2.071778 TTGAGGGAAACTGCAGCTTT 57.928 45.000 15.27 13.39 0.00 3.51
746 748 2.071778 TGAGGGAAACTGCAGCTTTT 57.928 45.000 15.27 7.92 0.00 2.27
747 749 1.956477 TGAGGGAAACTGCAGCTTTTC 59.044 47.619 15.27 16.57 0.00 2.29
748 750 0.954452 AGGGAAACTGCAGCTTTTCG 59.046 50.000 15.27 0.00 33.29 3.46
749 751 0.668535 GGGAAACTGCAGCTTTTCGT 59.331 50.000 15.27 0.00 33.29 3.85
750 752 1.600413 GGGAAACTGCAGCTTTTCGTG 60.600 52.381 15.27 0.00 33.29 4.35
751 753 1.333619 GGAAACTGCAGCTTTTCGTGA 59.666 47.619 15.27 0.00 33.29 4.35
752 754 2.030805 GGAAACTGCAGCTTTTCGTGAT 60.031 45.455 15.27 0.00 33.29 3.06
753 755 2.977405 AACTGCAGCTTTTCGTGATC 57.023 45.000 15.27 0.00 0.00 2.92
754 756 1.160137 ACTGCAGCTTTTCGTGATCC 58.840 50.000 15.27 0.00 0.00 3.36
755 757 1.271054 ACTGCAGCTTTTCGTGATCCT 60.271 47.619 15.27 0.00 0.00 3.24
756 758 1.808945 CTGCAGCTTTTCGTGATCCTT 59.191 47.619 0.00 0.00 0.00 3.36
757 759 1.806542 TGCAGCTTTTCGTGATCCTTC 59.193 47.619 0.00 0.00 0.00 3.46
758 760 1.806542 GCAGCTTTTCGTGATCCTTCA 59.193 47.619 0.00 0.00 0.00 3.02
795 798 3.254166 CAGCAGCCACATTACTGTTTTCT 59.746 43.478 0.00 0.00 36.26 2.52
927 931 6.904626 AGGATCAACTATCTTTTGCTATGGT 58.095 36.000 0.00 0.00 34.75 3.55
936 940 4.621991 TCTTTTGCTATGGTATCGAGCTC 58.378 43.478 2.73 2.73 37.12 4.09
955 959 1.208052 TCGGCCAAGATTCTTCTGAGG 59.792 52.381 2.24 0.00 33.30 3.86
970 974 2.015587 CTGAGGCTTCAGGAAGATTGC 58.984 52.381 17.73 0.00 45.79 3.56
971 975 1.352017 TGAGGCTTCAGGAAGATTGCA 59.648 47.619 13.01 2.50 40.79 4.08
972 976 2.015587 GAGGCTTCAGGAAGATTGCAG 58.984 52.381 13.01 0.00 40.79 4.41
973 977 0.455005 GGCTTCAGGAAGATTGCAGC 59.545 55.000 13.01 0.00 40.79 5.25
974 978 1.461559 GCTTCAGGAAGATTGCAGCT 58.538 50.000 13.01 0.00 40.79 4.24
975 979 1.817447 GCTTCAGGAAGATTGCAGCTT 59.183 47.619 13.01 3.84 40.79 3.74
976 980 2.230750 GCTTCAGGAAGATTGCAGCTTT 59.769 45.455 13.01 0.00 40.79 3.51
977 981 3.672781 GCTTCAGGAAGATTGCAGCTTTC 60.673 47.826 13.01 3.91 40.79 2.62
978 982 2.440409 TCAGGAAGATTGCAGCTTTCC 58.560 47.619 14.08 14.08 0.00 3.13
979 983 1.475682 CAGGAAGATTGCAGCTTTCCC 59.524 52.381 16.83 9.87 0.00 3.97
980 984 1.357079 AGGAAGATTGCAGCTTTCCCT 59.643 47.619 16.83 11.47 0.00 4.20
981 985 1.475682 GGAAGATTGCAGCTTTCCCTG 59.524 52.381 11.91 0.00 35.93 4.45
982 986 2.165998 GAAGATTGCAGCTTTCCCTGT 58.834 47.619 5.52 0.00 35.28 4.00
983 987 1.831580 AGATTGCAGCTTTCCCTGTC 58.168 50.000 0.00 0.00 35.28 3.51
984 988 1.074405 AGATTGCAGCTTTCCCTGTCA 59.926 47.619 0.00 0.00 35.28 3.58
985 989 1.471684 GATTGCAGCTTTCCCTGTCAG 59.528 52.381 0.00 0.00 35.28 3.51
989 993 1.649664 CAGCTTTCCCTGTCAGATCG 58.350 55.000 0.00 0.00 0.00 3.69
996 1000 0.461961 CCCTGTCAGATCGGAGGTTC 59.538 60.000 0.00 0.00 0.00 3.62
1001 1005 0.824109 TCAGATCGGAGGTTCGCAAT 59.176 50.000 0.00 0.00 0.00 3.56
1165 1169 4.704833 TGCTCAAGCCGGACCTGC 62.705 66.667 5.05 0.00 41.18 4.85
1386 1390 1.379044 GCAAGGGCTGGTGCTATGT 60.379 57.895 1.25 0.00 37.78 2.29
1427 1431 1.269448 GTTTTGCCGAGATGGAAGCAA 59.731 47.619 0.00 0.00 43.09 3.91
1428 1432 3.337834 TTGCCGAGATGGAAGCAAA 57.662 47.368 0.00 0.00 41.93 3.68
1432 1436 1.131315 GCCGAGATGGAAGCAAAGTTC 59.869 52.381 0.00 0.00 42.00 3.01
1514 1518 1.203523 AGCTCTAGACCAGAAGCAACG 59.796 52.381 2.67 0.00 32.80 4.10
1530 1534 3.378427 AGCAACGGAAATATTTGGAGAGC 59.622 43.478 5.17 4.62 0.00 4.09
1531 1535 3.128589 GCAACGGAAATATTTGGAGAGCA 59.871 43.478 5.17 0.00 0.00 4.26
1636 1640 2.576615 AGGTTCAAGGTTTGACAGCTC 58.423 47.619 0.00 0.00 39.87 4.09
1660 1664 2.223340 CCTGCGCAACTTATCACATTCC 60.223 50.000 13.05 0.00 0.00 3.01
1678 1682 1.635487 TCCAGGACTTTGATTCAGGGG 59.365 52.381 0.00 0.00 0.00 4.79
1683 1687 1.283321 GACTTTGATTCAGGGGAGCCT 59.717 52.381 0.00 0.00 0.00 4.58
1685 1689 1.563410 CTTTGATTCAGGGGAGCCTCT 59.437 52.381 0.00 0.00 0.00 3.69
1714 1721 3.248602 CGTTGAGCATTATGGTAAGGAGC 59.751 47.826 0.00 0.00 0.00 4.70
1718 1725 3.755378 GAGCATTATGGTAAGGAGCATGG 59.245 47.826 0.00 0.00 43.60 3.66
1722 1729 5.513094 GCATTATGGTAAGGAGCATGGAGTA 60.513 44.000 0.00 0.00 43.60 2.59
1724 1731 1.762957 TGGTAAGGAGCATGGAGTAGC 59.237 52.381 0.00 0.00 0.00 3.58
1725 1732 1.070914 GGTAAGGAGCATGGAGTAGCC 59.929 57.143 0.00 0.00 37.10 3.93
1766 1773 1.603456 TGCTTGGATTTGAGCACGAA 58.397 45.000 0.00 0.00 43.46 3.85
1768 1775 2.287547 TGCTTGGATTTGAGCACGAAAC 60.288 45.455 0.00 0.00 43.46 2.78
1805 1812 6.516739 TTATATCCCGATTGAGCTCTGTAG 57.483 41.667 16.19 3.82 0.00 2.74
1814 1821 5.449725 CGATTGAGCTCTGTAGTCTTCATCA 60.450 44.000 16.19 0.00 0.00 3.07
1857 1864 2.109425 ATACGCTCAAGGGTTCCAAC 57.891 50.000 4.97 0.00 41.61 3.77
1880 1887 2.991540 GCCAAGGGACAAGCCACC 60.992 66.667 0.00 0.00 38.95 4.61
1904 1911 4.216257 CGAATCAAATGCCCGGAAAGATAT 59.784 41.667 0.73 0.00 0.00 1.63
2017 2024 7.499895 ACCATGCATTCTTTCTTTTTGTCAAAT 59.500 29.630 0.00 0.00 0.00 2.32
2021 2028 7.225145 TGCATTCTTTCTTTTTGTCAAATCTGG 59.775 33.333 0.00 0.00 0.00 3.86
2022 2029 7.307573 GCATTCTTTCTTTTTGTCAAATCTGGG 60.308 37.037 0.00 0.00 0.00 4.45
2023 2030 7.416964 TTCTTTCTTTTTGTCAAATCTGGGA 57.583 32.000 0.00 0.00 0.00 4.37
2064 2071 7.148672 TGCTGTTTATTTGTTAAATCCAATGCG 60.149 33.333 0.00 0.00 32.56 4.73
2079 2086 3.489568 CCAATGCGATGCAATTTGCTAGA 60.490 43.478 21.19 2.71 45.31 2.43
2084 2091 6.075762 TGCGATGCAATTTGCTAGATATTT 57.924 33.333 21.19 0.00 45.31 1.40
2160 2169 9.613428 AGTTGTGCTAACATTAGATGCTAATTA 57.387 29.630 2.75 0.00 35.83 1.40
2196 2205 6.151144 AGTTTAACCATGCTTGGATTCAGTAC 59.849 38.462 24.48 11.96 46.92 2.73
2199 2208 4.603131 ACCATGCTTGGATTCAGTACAAT 58.397 39.130 24.48 0.00 46.92 2.71
2226 2235 8.647143 ATGAAGTTTAACCATGTTTGTTCAAG 57.353 30.769 0.00 0.00 0.00 3.02
2227 2236 7.607250 TGAAGTTTAACCATGTTTGTTCAAGT 58.393 30.769 0.00 0.00 0.00 3.16
2228 2237 8.091449 TGAAGTTTAACCATGTTTGTTCAAGTT 58.909 29.630 0.00 0.00 29.62 2.66
2229 2238 9.575783 GAAGTTTAACCATGTTTGTTCAAGTTA 57.424 29.630 0.00 0.00 28.03 2.24
2231 2240 9.744468 AGTTTAACCATGTTTGTTCAAGTTATC 57.256 29.630 0.00 0.00 0.00 1.75
2274 2286 4.104383 TGGAACTGATCTTTGCCTTTCT 57.896 40.909 0.00 0.00 0.00 2.52
2295 2307 8.930846 TTTCTTTCAAGAAAGGATCTGATCTT 57.069 30.769 19.27 7.04 46.80 2.40
2463 2476 0.895530 CTTACACTCGGCTCCTCCAA 59.104 55.000 0.00 0.00 34.01 3.53
2471 2484 4.496336 GCTCCTCCAATGGCCGCT 62.496 66.667 0.00 0.00 0.00 5.52
2476 2489 3.060020 CTCCAATGGCCGCTGCAAG 62.060 63.158 1.55 0.00 40.13 4.01
2480 2493 2.398554 AATGGCCGCTGCAAGTACG 61.399 57.895 1.55 0.00 40.13 3.67
2488 2501 2.054363 CGCTGCAAGTACGATATCAGG 58.946 52.381 3.12 0.00 35.30 3.86
2603 2622 1.280133 CATCTCACTCTGGCCAGGAAA 59.720 52.381 32.23 12.84 0.00 3.13
2675 2697 4.946157 ACCTTGGTATTCAGATGCAAAGAG 59.054 41.667 0.00 0.00 32.38 2.85
2710 2732 1.795872 CGTTGTTCAGCAATGTCGGTA 59.204 47.619 0.00 0.00 39.55 4.02
2713 2735 2.412870 TGTTCAGCAATGTCGGTACTG 58.587 47.619 0.00 0.00 0.00 2.74
2735 2757 0.390603 TGATCCGGGCAAACTACGTG 60.391 55.000 0.00 0.00 0.00 4.49
2764 2786 0.620556 TCCAGGTGAAGAAGGATGCC 59.379 55.000 0.00 0.00 0.00 4.40
2788 2810 0.318441 AGCACACGCAGAAGAAGCTA 59.682 50.000 0.00 0.00 42.27 3.32
2940 2965 2.508300 ACCAGTACTTGTCCAACCTTGT 59.492 45.455 0.00 0.00 0.00 3.16
3031 3056 2.736721 CTCACGTTTCATGTTCATCGGT 59.263 45.455 0.00 0.00 0.00 4.69
3066 3091 2.680352 GCCTCCAGGAGACACGGA 60.680 66.667 19.21 0.00 37.39 4.69
3168 3193 3.082579 GCGGCAAGGAGGAGATCGT 62.083 63.158 0.00 0.00 0.00 3.73
3222 3247 3.436577 AGTCTACAAGGAGAGGAACGA 57.563 47.619 0.00 0.00 0.00 3.85
3256 3281 5.419542 CCAGACAAGATCATTTACTTCCGA 58.580 41.667 0.00 0.00 0.00 4.55
3259 3284 6.254589 CAGACAAGATCATTTACTTCCGAGAC 59.745 42.308 0.00 0.00 0.00 3.36
3285 3310 4.053067 CGACGAGCAGTTCCGTAC 57.947 61.111 0.00 0.00 39.30 3.67
3317 3342 2.028130 AGGAGCTAGTGTCGATGAAGG 58.972 52.381 0.00 0.00 0.00 3.46
3322 3347 1.067821 CTAGTGTCGATGAAGGAGGGC 59.932 57.143 0.00 0.00 0.00 5.19
3336 3361 4.899239 GGGCATCTGCGAGGACGG 62.899 72.222 0.00 0.00 43.26 4.79
3359 3384 2.178273 CGCCGACGATCACAGTGA 59.822 61.111 5.50 5.50 43.93 3.41
3409 3434 1.961793 TGTTCCCCAACGACAGAAAG 58.038 50.000 0.00 0.00 34.95 2.62
3417 3442 0.946221 AACGACAGAAAGGAGCTGCG 60.946 55.000 0.00 0.00 36.86 5.18
3421 3446 2.097038 CAGAAAGGAGCTGCGGACG 61.097 63.158 0.00 0.00 0.00 4.79
3422 3447 2.815647 GAAAGGAGCTGCGGACGG 60.816 66.667 0.00 0.00 0.00 4.79
3423 3448 3.296709 GAAAGGAGCTGCGGACGGA 62.297 63.158 0.00 0.00 0.00 4.69
3424 3449 2.579684 GAAAGGAGCTGCGGACGGAT 62.580 60.000 0.00 0.00 0.00 4.18
3427 3452 1.591863 GGAGCTGCGGACGGATAAC 60.592 63.158 0.00 0.00 0.00 1.89
3461 3486 4.634133 GCACGGTCGTCGACACCA 62.634 66.667 25.64 6.41 42.43 4.17
3462 3487 2.728383 CACGGTCGTCGACACCAC 60.728 66.667 25.64 15.86 42.43 4.16
3672 3700 1.870055 ATCAAGTACGCCGACACCGT 61.870 55.000 0.00 0.00 42.26 4.83
3702 3730 1.180029 GGCAGGGACTACTACGACAA 58.820 55.000 0.00 0.00 36.02 3.18
3839 3906 0.179065 CTTCATCTGATGCCGCCTGA 60.179 55.000 12.78 0.00 0.00 3.86
4107 4240 9.431887 TCTGTTACTGATTACTGTAAATCAACC 57.568 33.333 4.11 0.00 43.42 3.77
4170 4303 5.695851 ATTTCATATTCCGGCAGATGTTC 57.304 39.130 8.56 0.00 0.00 3.18
4179 4312 1.469767 CGGCAGATGTTCGATGTGAGA 60.470 52.381 0.00 0.00 0.00 3.27
4189 4322 5.003160 TGTTCGATGTGAGATTTCCAACAT 58.997 37.500 0.00 0.00 0.00 2.71
4208 4341 2.533266 TGTTGAGAACTGCAGTCCTC 57.467 50.000 24.89 24.89 0.00 3.71
4209 4342 1.269778 TGTTGAGAACTGCAGTCCTCG 60.270 52.381 25.62 0.00 0.00 4.63
4277 4410 5.359576 GGGATCAGCCAAATGTTGTATGTAA 59.640 40.000 0.00 0.00 38.95 2.41
4284 4417 5.348451 GCCAAATGTTGTATGTAAAAGGCAG 59.652 40.000 0.00 0.00 37.23 4.85
4301 4509 6.560253 AAGGCAGACAGTTACATACAAAAG 57.440 37.500 0.00 0.00 0.00 2.27
4308 4516 7.278868 CAGACAGTTACATACAAAAGATCCCTC 59.721 40.741 0.00 0.00 0.00 4.30
4344 4552 2.002586 CATAAGAACACTCAGGGCACG 58.997 52.381 0.00 0.00 0.00 5.34
4372 4580 6.646240 ACAATGAATTTGACAATGGCAGTTAC 59.354 34.615 0.00 0.00 38.76 2.50
4399 6733 3.944015 GCCAAACAAGCTCATATCACTCT 59.056 43.478 0.00 0.00 0.00 3.24
4425 6759 6.324601 AGATTGGAGGAAAGACTCATCATT 57.675 37.500 0.00 0.00 36.54 2.57
4434 6768 7.865820 AGGAAAGACTCATCATTTAGATTGGA 58.134 34.615 0.00 0.00 33.72 3.53
4462 6796 4.037222 TCTGCCTCTTATTACATGTGGGA 58.963 43.478 9.11 0.00 0.00 4.37
4496 6830 4.820173 GGGTAGCATTATAACTGAACCACC 59.180 45.833 9.75 0.00 0.00 4.61
4541 6912 1.358152 TCGGAGAAAATCCCACACCT 58.642 50.000 0.00 0.00 46.50 4.00
4613 6984 1.354337 CTACATGAACTGCAGCGCGT 61.354 55.000 15.27 4.29 0.00 6.01
4614 6985 1.625759 TACATGAACTGCAGCGCGTG 61.626 55.000 15.27 18.81 0.00 5.34
4624 6995 3.417224 AGCGCGTGCATGTCACTG 61.417 61.111 24.79 10.95 46.23 3.66
4637 7008 2.109799 CACTGGGATAGGCCTGCG 59.890 66.667 17.99 0.00 36.66 5.18
4655 7026 1.019278 CGGCAGTGTACCATCGCTTT 61.019 55.000 0.00 0.00 0.00 3.51
4667 7038 4.207165 ACCATCGCTTTAACTATGGCATT 58.793 39.130 4.78 0.00 42.21 3.56
4682 7053 8.627208 ACTATGGCATTAAGAATGGTATGAAG 57.373 34.615 4.78 0.00 39.31 3.02
4700 7071 4.847198 TGAAGCACACCTCACAATATGAT 58.153 39.130 0.00 0.00 36.48 2.45
4703 7074 4.847198 AGCACACCTCACAATATGATTGA 58.153 39.130 6.21 0.00 36.48 2.57
4722 7093 6.487668 TGATTGAATATACCATGCAGTCAAGG 59.512 38.462 0.00 0.00 37.12 3.61
4736 7107 5.157067 GCAGTCAAGGCTTCAGAATTAAAC 58.843 41.667 0.00 0.00 0.00 2.01
4748 7119 9.899226 GCTTCAGAATTAAACAACTACTTCATT 57.101 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.462174 CTTGTCATACAGAGAGATAATCTTCAC 57.538 37.037 0.00 0.00 38.84 3.18
15 16 7.566879 AGGGAACTTGTCATACAGAGAGATAAT 59.433 37.037 0.00 0.00 37.44 1.28
67 68 8.474025 AGATGGATCAATAGCTGCTATAAGTAC 58.526 37.037 21.56 11.72 0.00 2.73
103 104 8.464404 CAAACACTTCATATGGATTCAAGACAT 58.536 33.333 2.13 0.00 0.00 3.06
199 200 5.473504 CCACTTTTTCAGTTAGCATGTAGGT 59.526 40.000 0.00 0.00 30.92 3.08
200 201 5.705441 TCCACTTTTTCAGTTAGCATGTAGG 59.295 40.000 0.00 0.00 30.92 3.18
217 218 7.657023 ACTAATACTCCGTATCTTCCACTTT 57.343 36.000 0.00 0.00 0.00 2.66
218 219 8.628280 GTTACTAATACTCCGTATCTTCCACTT 58.372 37.037 0.00 0.00 0.00 3.16
219 220 7.230309 GGTTACTAATACTCCGTATCTTCCACT 59.770 40.741 0.00 0.00 0.00 4.00
220 221 7.230309 AGGTTACTAATACTCCGTATCTTCCAC 59.770 40.741 0.00 0.00 0.00 4.02
222 223 7.665145 AGAGGTTACTAATACTCCGTATCTTCC 59.335 40.741 0.00 0.00 0.00 3.46
223 224 8.505625 CAGAGGTTACTAATACTCCGTATCTTC 58.494 40.741 0.00 0.00 0.00 2.87
225 226 7.516452 ACAGAGGTTACTAATACTCCGTATCT 58.484 38.462 0.00 0.00 0.00 1.98
226 227 7.742556 ACAGAGGTTACTAATACTCCGTATC 57.257 40.000 0.00 0.00 0.00 2.24
227 228 7.230309 GGAACAGAGGTTACTAATACTCCGTAT 59.770 40.741 0.00 0.00 37.36 3.06
229 230 5.359292 GGAACAGAGGTTACTAATACTCCGT 59.641 44.000 0.00 0.00 37.36 4.69
230 231 5.505324 CGGAACAGAGGTTACTAATACTCCG 60.505 48.000 0.00 0.00 37.36 4.63
231 232 5.735638 GCGGAACAGAGGTTACTAATACTCC 60.736 48.000 0.00 0.00 37.36 3.85
232 233 5.163581 TGCGGAACAGAGGTTACTAATACTC 60.164 44.000 0.00 0.00 37.36 2.59
233 234 4.708421 TGCGGAACAGAGGTTACTAATACT 59.292 41.667 0.00 0.00 37.36 2.12
234 235 5.002464 TGCGGAACAGAGGTTACTAATAC 57.998 43.478 0.00 0.00 37.36 1.89
377 378 5.828747 TCTTGTCTTCGGATAAAGGATACG 58.171 41.667 0.00 0.00 43.95 3.06
398 399 3.953612 TGGTGAAAACTGTGATGCTTTCT 59.046 39.130 4.21 0.00 0.00 2.52
453 454 9.554395 TGTGAAATAACACACTCATAAGAGAAA 57.446 29.630 1.17 0.00 43.33 2.52
656 658 6.919775 AATGTAGCTATACGGAGAGGAAAT 57.080 37.500 0.00 0.00 34.39 2.17
693 695 4.076394 GGACACTGCAGTTACCCAAATTA 58.924 43.478 18.94 0.00 0.00 1.40
694 696 2.890945 GGACACTGCAGTTACCCAAATT 59.109 45.455 18.94 0.00 0.00 1.82
695 697 2.514803 GGACACTGCAGTTACCCAAAT 58.485 47.619 18.94 0.00 0.00 2.32
696 698 1.812324 CGGACACTGCAGTTACCCAAA 60.812 52.381 18.94 0.00 0.00 3.28
697 699 0.250124 CGGACACTGCAGTTACCCAA 60.250 55.000 18.94 0.00 0.00 4.12
698 700 1.369692 CGGACACTGCAGTTACCCA 59.630 57.895 18.94 0.00 0.00 4.51
699 701 1.375523 CCGGACACTGCAGTTACCC 60.376 63.158 18.94 16.74 0.00 3.69
700 702 2.033194 GCCGGACACTGCAGTTACC 61.033 63.158 18.94 21.00 0.00 2.85
701 703 2.033194 GGCCGGACACTGCAGTTAC 61.033 63.158 18.94 13.81 0.00 2.50
702 704 2.345991 GGCCGGACACTGCAGTTA 59.654 61.111 18.94 0.00 0.00 2.24
703 705 4.988598 CGGCCGGACACTGCAGTT 62.989 66.667 18.94 9.02 0.00 3.16
705 707 4.680237 TTCGGCCGGACACTGCAG 62.680 66.667 27.83 13.48 0.00 4.41
706 708 4.243008 TTTCGGCCGGACACTGCA 62.243 61.111 27.83 0.00 0.00 4.41
707 709 3.723348 GTTTCGGCCGGACACTGC 61.723 66.667 27.83 5.17 0.00 4.40
708 710 1.164041 AAAGTTTCGGCCGGACACTG 61.164 55.000 27.83 0.00 35.87 3.66
709 711 1.147600 AAAGTTTCGGCCGGACACT 59.852 52.632 27.83 20.96 37.27 3.55
710 712 1.161563 TCAAAGTTTCGGCCGGACAC 61.162 55.000 27.83 18.97 0.00 3.67
711 713 0.882927 CTCAAAGTTTCGGCCGGACA 60.883 55.000 27.83 6.94 0.00 4.02
712 714 1.574702 CCTCAAAGTTTCGGCCGGAC 61.575 60.000 27.83 23.42 0.00 4.79
713 715 1.302192 CCTCAAAGTTTCGGCCGGA 60.302 57.895 27.83 16.16 0.00 5.14
714 716 2.332654 CCCTCAAAGTTTCGGCCGG 61.333 63.158 27.83 7.21 0.00 6.13
715 717 0.887387 TTCCCTCAAAGTTTCGGCCG 60.887 55.000 22.12 22.12 0.00 6.13
716 718 1.000607 GTTTCCCTCAAAGTTTCGGCC 60.001 52.381 0.00 0.00 0.00 6.13
717 719 1.954382 AGTTTCCCTCAAAGTTTCGGC 59.046 47.619 0.00 0.00 0.00 5.54
718 720 2.287608 GCAGTTTCCCTCAAAGTTTCGG 60.288 50.000 0.00 0.00 0.00 4.30
719 721 2.357637 TGCAGTTTCCCTCAAAGTTTCG 59.642 45.455 0.00 0.00 0.00 3.46
720 722 3.796844 GCTGCAGTTTCCCTCAAAGTTTC 60.797 47.826 16.64 0.00 0.00 2.78
721 723 2.101415 GCTGCAGTTTCCCTCAAAGTTT 59.899 45.455 16.64 0.00 0.00 2.66
722 724 1.683385 GCTGCAGTTTCCCTCAAAGTT 59.317 47.619 16.64 0.00 0.00 2.66
723 725 1.133668 AGCTGCAGTTTCCCTCAAAGT 60.134 47.619 16.64 0.00 0.00 2.66
724 726 1.613836 AGCTGCAGTTTCCCTCAAAG 58.386 50.000 16.64 0.00 0.00 2.77
725 727 2.071778 AAGCTGCAGTTTCCCTCAAA 57.928 45.000 16.64 0.00 0.00 2.69
726 728 2.071778 AAAGCTGCAGTTTCCCTCAA 57.928 45.000 16.65 0.00 0.00 3.02
727 729 1.956477 GAAAAGCTGCAGTTTCCCTCA 59.044 47.619 16.65 0.00 0.00 3.86
728 730 1.068954 CGAAAAGCTGCAGTTTCCCTC 60.069 52.381 16.65 11.95 31.34 4.30
729 731 0.954452 CGAAAAGCTGCAGTTTCCCT 59.046 50.000 16.65 4.34 31.34 4.20
730 732 0.668535 ACGAAAAGCTGCAGTTTCCC 59.331 50.000 16.65 10.02 31.34 3.97
731 733 1.333619 TCACGAAAAGCTGCAGTTTCC 59.666 47.619 16.65 10.36 31.34 3.13
732 734 2.755836 TCACGAAAAGCTGCAGTTTC 57.244 45.000 16.65 16.36 0.00 2.78
733 735 2.030805 GGATCACGAAAAGCTGCAGTTT 60.031 45.455 16.64 13.48 0.00 2.66
734 736 1.537202 GGATCACGAAAAGCTGCAGTT 59.463 47.619 16.64 6.37 0.00 3.16
735 737 1.160137 GGATCACGAAAAGCTGCAGT 58.840 50.000 16.64 0.00 0.00 4.40
736 738 1.446907 AGGATCACGAAAAGCTGCAG 58.553 50.000 10.11 10.11 0.00 4.41
737 739 1.806542 GAAGGATCACGAAAAGCTGCA 59.193 47.619 1.02 0.00 0.00 4.41
738 740 1.806542 TGAAGGATCACGAAAAGCTGC 59.193 47.619 0.00 0.00 0.00 5.25
739 741 4.394300 AGAATGAAGGATCACGAAAAGCTG 59.606 41.667 0.00 0.00 38.69 4.24
740 742 4.583871 AGAATGAAGGATCACGAAAAGCT 58.416 39.130 0.00 0.00 38.69 3.74
741 743 4.201861 GGAGAATGAAGGATCACGAAAAGC 60.202 45.833 0.00 0.00 38.69 3.51
742 744 4.333926 GGGAGAATGAAGGATCACGAAAAG 59.666 45.833 0.00 0.00 38.69 2.27
743 745 4.019321 AGGGAGAATGAAGGATCACGAAAA 60.019 41.667 0.00 0.00 38.69 2.29
744 746 3.519510 AGGGAGAATGAAGGATCACGAAA 59.480 43.478 0.00 0.00 38.69 3.46
745 747 3.107601 AGGGAGAATGAAGGATCACGAA 58.892 45.455 0.00 0.00 38.69 3.85
746 748 2.695666 GAGGGAGAATGAAGGATCACGA 59.304 50.000 0.00 0.00 38.69 4.35
747 749 2.697751 AGAGGGAGAATGAAGGATCACG 59.302 50.000 0.00 0.00 38.69 4.35
748 750 3.966665 AGAGAGGGAGAATGAAGGATCAC 59.033 47.826 0.00 0.00 38.69 3.06
749 751 3.966006 CAGAGAGGGAGAATGAAGGATCA 59.034 47.826 0.00 0.00 40.57 2.92
750 752 4.039124 GTCAGAGAGGGAGAATGAAGGATC 59.961 50.000 0.00 0.00 0.00 3.36
751 753 3.966665 GTCAGAGAGGGAGAATGAAGGAT 59.033 47.826 0.00 0.00 0.00 3.24
752 754 3.245766 TGTCAGAGAGGGAGAATGAAGGA 60.246 47.826 0.00 0.00 0.00 3.36
753 755 3.102972 TGTCAGAGAGGGAGAATGAAGG 58.897 50.000 0.00 0.00 0.00 3.46
754 756 3.430651 GCTGTCAGAGAGGGAGAATGAAG 60.431 52.174 3.32 0.00 0.00 3.02
755 757 2.499289 GCTGTCAGAGAGGGAGAATGAA 59.501 50.000 3.32 0.00 0.00 2.57
756 758 2.106566 GCTGTCAGAGAGGGAGAATGA 58.893 52.381 3.32 0.00 0.00 2.57
757 759 1.829849 TGCTGTCAGAGAGGGAGAATG 59.170 52.381 3.32 0.00 0.00 2.67
758 760 2.109774 CTGCTGTCAGAGAGGGAGAAT 58.890 52.381 3.32 0.00 42.95 2.40
927 931 1.000163 GAATCTTGGCCGAGCTCGATA 60.000 52.381 36.59 19.00 43.02 2.92
936 940 1.661341 CCTCAGAAGAATCTTGGCCG 58.339 55.000 0.00 0.00 32.03 6.13
955 959 1.461559 AGCTGCAATCTTCCTGAAGC 58.538 50.000 1.02 0.00 44.70 3.86
962 966 2.163211 GACAGGGAAAGCTGCAATCTTC 59.837 50.000 1.02 0.00 0.00 2.87
963 967 2.165998 GACAGGGAAAGCTGCAATCTT 58.834 47.619 1.02 0.00 0.00 2.40
964 968 1.074405 TGACAGGGAAAGCTGCAATCT 59.926 47.619 1.02 0.00 0.00 2.40
965 969 1.471684 CTGACAGGGAAAGCTGCAATC 59.528 52.381 1.02 0.00 0.00 2.67
966 970 1.074405 TCTGACAGGGAAAGCTGCAAT 59.926 47.619 1.02 0.00 0.00 3.56
967 971 0.473755 TCTGACAGGGAAAGCTGCAA 59.526 50.000 1.02 0.00 0.00 4.08
968 972 0.694771 ATCTGACAGGGAAAGCTGCA 59.305 50.000 1.02 0.00 0.00 4.41
969 973 1.377536 GATCTGACAGGGAAAGCTGC 58.622 55.000 1.81 0.00 0.00 5.25
970 974 1.649664 CGATCTGACAGGGAAAGCTG 58.350 55.000 1.81 0.00 0.00 4.24
971 975 0.539051 CCGATCTGACAGGGAAAGCT 59.461 55.000 1.81 0.00 0.00 3.74
972 976 0.537188 TCCGATCTGACAGGGAAAGC 59.463 55.000 1.81 0.00 0.00 3.51
973 977 1.137872 CCTCCGATCTGACAGGGAAAG 59.862 57.143 1.81 0.00 0.00 2.62
974 978 1.195115 CCTCCGATCTGACAGGGAAA 58.805 55.000 1.81 0.00 0.00 3.13
975 979 0.041238 ACCTCCGATCTGACAGGGAA 59.959 55.000 1.81 0.00 0.00 3.97
976 980 0.041238 AACCTCCGATCTGACAGGGA 59.959 55.000 1.81 0.65 0.00 4.20
977 981 0.461961 GAACCTCCGATCTGACAGGG 59.538 60.000 1.81 0.00 0.00 4.45
978 982 0.101399 CGAACCTCCGATCTGACAGG 59.899 60.000 1.81 0.00 0.00 4.00
979 983 0.526524 GCGAACCTCCGATCTGACAG 60.527 60.000 0.00 0.00 0.00 3.51
980 984 1.248101 TGCGAACCTCCGATCTGACA 61.248 55.000 0.00 0.00 0.00 3.58
981 985 0.108804 TTGCGAACCTCCGATCTGAC 60.109 55.000 0.00 0.00 0.00 3.51
982 986 0.824109 ATTGCGAACCTCCGATCTGA 59.176 50.000 0.00 0.00 0.00 3.27
983 987 0.933097 CATTGCGAACCTCCGATCTG 59.067 55.000 0.00 0.00 0.00 2.90
984 988 0.179073 CCATTGCGAACCTCCGATCT 60.179 55.000 0.00 0.00 0.00 2.75
985 989 1.776034 GCCATTGCGAACCTCCGATC 61.776 60.000 0.00 0.00 0.00 3.69
989 993 1.132453 GTTTAGCCATTGCGAACCTCC 59.868 52.381 0.00 0.00 44.33 4.30
996 1000 2.083774 TCCAAGAGTTTAGCCATTGCG 58.916 47.619 0.00 0.00 44.33 4.85
1001 1005 5.734720 CAAGTATCTCCAAGAGTTTAGCCA 58.265 41.667 0.00 0.00 0.00 4.75
1139 1143 1.801332 GGCTTGAGCACTGCTGATG 59.199 57.895 8.69 3.49 39.88 3.07
1381 1385 7.726216 TCCATAACTGAATAGTCCACACATAG 58.274 38.462 0.00 0.00 35.69 2.23
1383 1387 6.156949 ACTCCATAACTGAATAGTCCACACAT 59.843 38.462 0.00 0.00 35.69 3.21
1386 1390 6.620877 AACTCCATAACTGAATAGTCCACA 57.379 37.500 0.00 0.00 35.69 4.17
1427 1431 5.625150 AGTGCTTAACAAGATCCAGAACTT 58.375 37.500 0.00 0.00 0.00 2.66
1428 1432 5.234466 AGTGCTTAACAAGATCCAGAACT 57.766 39.130 0.00 0.00 0.00 3.01
1432 1436 4.074970 ACCAAGTGCTTAACAAGATCCAG 58.925 43.478 0.00 0.00 0.00 3.86
1504 1508 5.123820 TCTCCAAATATTTCCGTTGCTTCTG 59.876 40.000 0.00 0.00 0.00 3.02
1514 1518 4.641989 TCAGCTTGCTCTCCAAATATTTCC 59.358 41.667 0.00 0.00 31.94 3.13
1530 1534 2.479566 TACAGAGGCCTTTCAGCTTG 57.520 50.000 6.77 0.00 0.00 4.01
1531 1535 2.573462 TGATACAGAGGCCTTTCAGCTT 59.427 45.455 6.77 0.00 0.00 3.74
1636 1640 0.097674 GTGATAAGTTGCGCAGGCTG 59.902 55.000 11.31 10.94 40.82 4.85
1660 1664 2.943199 GCTCCCCTGAATCAAAGTCCTG 60.943 54.545 0.00 0.00 0.00 3.86
1692 1699 3.248602 GCTCCTTACCATAATGCTCAACG 59.751 47.826 0.00 0.00 0.00 4.10
1699 1706 4.978099 ACTCCATGCTCCTTACCATAATG 58.022 43.478 0.00 0.00 0.00 1.90
1705 1712 1.070914 GGCTACTCCATGCTCCTTACC 59.929 57.143 0.00 0.00 34.01 2.85
1708 1715 3.012153 TGGCTACTCCATGCTCCTT 57.988 52.632 0.00 0.00 40.72 3.36
1718 1725 4.865365 GCATCTTATACCGAATGGCTACTC 59.135 45.833 0.00 0.00 39.70 2.59
1722 1729 4.319177 GAAGCATCTTATACCGAATGGCT 58.681 43.478 0.00 0.00 39.70 4.75
1724 1731 4.641396 TGGAAGCATCTTATACCGAATGG 58.359 43.478 0.00 0.00 42.84 3.16
1725 1732 5.391310 GCATGGAAGCATCTTATACCGAATG 60.391 44.000 0.00 0.00 0.00 2.67
1730 1737 5.368256 CAAGCATGGAAGCATCTTATACC 57.632 43.478 0.00 0.00 36.85 2.73
1755 1762 1.001487 CTGCCATGTTTCGTGCTCAAA 60.001 47.619 0.00 0.00 0.00 2.69
1766 1773 5.539955 GGGATATAATTTGGTCTGCCATGTT 59.460 40.000 0.00 0.00 45.56 2.71
1768 1775 4.156556 CGGGATATAATTTGGTCTGCCATG 59.843 45.833 0.00 0.00 45.56 3.66
1786 1793 2.625790 GACTACAGAGCTCAATCGGGAT 59.374 50.000 17.77 0.00 0.00 3.85
1805 1812 2.417719 ACTTCTGCCGTTGATGAAGAC 58.582 47.619 8.32 0.00 39.17 3.01
1814 1821 1.065418 CCTTGGGATACTTCTGCCGTT 60.065 52.381 0.00 0.00 0.00 4.44
1857 1864 1.246737 GCTTGTCCCTTGGCTTCAGG 61.247 60.000 0.00 0.00 0.00 3.86
1859 1866 1.228552 GGCTTGTCCCTTGGCTTCA 60.229 57.895 0.00 0.00 0.00 3.02
1880 1887 0.814457 TTTCCGGGCATTTGATTCGG 59.186 50.000 0.00 0.00 41.80 4.30
1904 1911 6.159575 TGGAGGTTTTACCATATCCAGAATCA 59.840 38.462 2.21 0.00 41.95 2.57
2017 2024 8.052748 ACAGCACATATAAATTAAGTTCCCAGA 58.947 33.333 0.00 0.00 0.00 3.86
2040 2047 8.459521 TCGCATTGGATTTAACAAATAAACAG 57.540 30.769 0.00 0.00 36.35 3.16
2120 2129 9.081997 TGTTAGCACAACTTTCAAGTTTTATTG 57.918 29.630 2.01 0.00 46.52 1.90
2160 2169 8.829612 CAAGCATGGTTAAACTTCATTCTTTTT 58.170 29.630 10.31 0.00 0.00 1.94
2229 2238 9.413734 CCATCCAAAGAAAGGAAATACTTAGAT 57.586 33.333 0.00 0.00 38.93 1.98
2230 2239 8.611257 TCCATCCAAAGAAAGGAAATACTTAGA 58.389 33.333 0.00 0.00 38.93 2.10
2231 2240 8.807948 TCCATCCAAAGAAAGGAAATACTTAG 57.192 34.615 0.00 0.00 38.93 2.18
2233 2242 7.730332 AGTTCCATCCAAAGAAAGGAAATACTT 59.270 33.333 0.00 0.00 40.13 2.24
2234 2243 7.177392 CAGTTCCATCCAAAGAAAGGAAATACT 59.823 37.037 0.00 0.00 40.13 2.12
2235 2244 7.176690 TCAGTTCCATCCAAAGAAAGGAAATAC 59.823 37.037 0.00 0.00 40.13 1.89
2241 2253 5.259632 AGATCAGTTCCATCCAAAGAAAGG 58.740 41.667 0.00 0.00 0.00 3.11
2253 2265 4.104383 AGAAAGGCAAAGATCAGTTCCA 57.896 40.909 0.00 0.00 0.00 3.53
2254 2266 5.010012 TGAAAGAAAGGCAAAGATCAGTTCC 59.990 40.000 0.00 0.00 0.00 3.62
2274 2286 9.745018 ACAATAAGATCAGATCCTTTCTTGAAA 57.255 29.630 6.80 0.00 29.93 2.69
2362 2375 1.617018 ATTGCTCGCCTCTGCTACCA 61.617 55.000 0.00 0.00 34.43 3.25
2363 2376 0.462759 AATTGCTCGCCTCTGCTACC 60.463 55.000 0.00 0.00 34.43 3.18
2375 2388 9.624697 TCTGTTCAATGTAATGTTAAATTGCTC 57.375 29.630 9.74 6.79 37.96 4.26
2446 2459 0.824109 CATTGGAGGAGCCGAGTGTA 59.176 55.000 0.00 0.00 40.66 2.90
2450 2463 2.203126 GCCATTGGAGGAGCCGAG 60.203 66.667 6.95 0.00 40.66 4.63
2463 2476 2.593468 ATCGTACTTGCAGCGGCCAT 62.593 55.000 6.32 0.00 40.13 4.40
2471 2484 5.592104 TTCTTCCTGATATCGTACTTGCA 57.408 39.130 0.00 0.00 0.00 4.08
2474 2487 7.064728 GCAGTTTTTCTTCCTGATATCGTACTT 59.935 37.037 0.00 0.00 0.00 2.24
2476 2489 6.238130 GGCAGTTTTTCTTCCTGATATCGTAC 60.238 42.308 0.00 0.00 0.00 3.67
2480 2493 5.649831 ACTGGCAGTTTTTCTTCCTGATATC 59.350 40.000 15.88 0.00 33.97 1.63
2488 2501 3.490933 GGTTCCACTGGCAGTTTTTCTTC 60.491 47.826 19.43 5.03 0.00 2.87
2603 2622 3.565307 TGAACTTGTTTCCATGAAGCCT 58.435 40.909 0.00 0.00 32.58 4.58
2615 2637 7.905604 TGACGATATTCTCAATGAACTTGTT 57.094 32.000 0.00 0.00 37.52 2.83
2629 2651 6.071463 GTGAACACACTTGTTGACGATATTC 58.929 40.000 0.00 0.00 46.43 1.75
2675 2697 1.199624 CAACGCACAAAACAGCCTTC 58.800 50.000 0.00 0.00 0.00 3.46
2710 2732 0.321653 GTTTGCCCGGATCAGACAGT 60.322 55.000 0.73 0.00 0.00 3.55
2713 2735 1.653151 GTAGTTTGCCCGGATCAGAC 58.347 55.000 0.73 6.11 0.00 3.51
2735 2757 3.034635 TCTTCACCTGGATAAGCTCCTC 58.965 50.000 0.00 0.00 45.21 3.71
2764 2786 2.049156 TTCTGCGTGTGCTCCTCG 60.049 61.111 0.00 0.00 43.34 4.63
2788 2810 0.832135 TCGGGCAGAAGAGGAGTTGT 60.832 55.000 0.00 0.00 0.00 3.32
2834 2856 4.201960 TGTCTCGCAGATCATCTTCAGTAC 60.202 45.833 0.00 0.00 33.89 2.73
2909 2934 0.912486 AAGTACTGGTCCTGGCCATC 59.088 55.000 5.51 0.00 37.96 3.51
2911 2936 0.766674 ACAAGTACTGGTCCTGGCCA 60.767 55.000 4.71 4.71 36.97 5.36
2940 2965 4.511527 GAGCTTGATGTTGATCTTGAGGA 58.488 43.478 0.00 0.00 0.00 3.71
3031 3056 4.612412 GGGTGGTTCACGTCCGCA 62.612 66.667 7.53 0.00 37.22 5.69
3066 3091 1.675483 CAGCTGCTATCGACAGACTCT 59.325 52.381 0.00 0.00 37.32 3.24
3168 3193 4.081531 CCTTACACATGGTACCGAGGTTAA 60.082 45.833 7.57 1.54 0.00 2.01
3281 3306 4.759564 CTTGTCGAGGACCGTACG 57.240 61.111 8.69 8.69 39.75 3.67
3310 3335 0.883814 CGCAGATGCCCTCCTTCATC 60.884 60.000 0.00 0.00 39.38 2.92
3317 3342 2.107953 GTCCTCGCAGATGCCCTC 59.892 66.667 0.00 0.00 37.91 4.30
3322 3347 1.299468 GTAGCCGTCCTCGCAGATG 60.299 63.158 0.00 0.00 33.89 2.90
3359 3384 2.436646 CCGCTTCTTGGCCACGAT 60.437 61.111 13.43 0.00 0.00 3.73
3389 3414 2.294074 CTTTCTGTCGTTGGGGAACAA 58.706 47.619 0.00 0.00 36.54 2.83
3400 3425 2.097038 CCGCAGCTCCTTTCTGTCG 61.097 63.158 0.00 0.00 34.21 4.35
3404 3429 2.262915 CGTCCGCAGCTCCTTTCT 59.737 61.111 0.00 0.00 0.00 2.52
3405 3430 2.579684 ATCCGTCCGCAGCTCCTTTC 62.580 60.000 0.00 0.00 0.00 2.62
3409 3434 1.591863 GTTATCCGTCCGCAGCTCC 60.592 63.158 0.00 0.00 0.00 4.70
3417 3442 0.655733 CACATTGCCGTTATCCGTCC 59.344 55.000 0.00 0.00 33.66 4.79
3421 3446 0.663153 GGAGCACATTGCCGTTATCC 59.337 55.000 0.00 0.00 46.52 2.59
3422 3447 0.663153 GGGAGCACATTGCCGTTATC 59.337 55.000 0.00 0.00 46.52 1.75
3423 3448 0.255890 AGGGAGCACATTGCCGTTAT 59.744 50.000 0.00 0.00 46.52 1.89
3424 3449 0.676466 CAGGGAGCACATTGCCGTTA 60.676 55.000 0.00 0.00 46.52 3.18
3427 3452 3.136123 CCAGGGAGCACATTGCCG 61.136 66.667 0.00 0.00 46.52 5.69
3776 3813 1.148273 GCACCTCGGGCATATCCAA 59.852 57.895 0.00 0.00 36.21 3.53
3777 3814 2.069430 TGCACCTCGGGCATATCCA 61.069 57.895 0.00 0.00 36.11 3.41
3796 3833 1.219124 GCTGTCCTTGAGATCCGCA 59.781 57.895 0.00 0.00 0.00 5.69
3839 3906 2.097825 GGAGCTCACCATGCTGAAAAT 58.902 47.619 17.19 0.00 41.30 1.82
4022 4152 2.414481 GAGCATGTACAGAACACAGCAG 59.586 50.000 0.33 0.00 42.09 4.24
4060 4191 4.398988 AGAATGTGTGCAGAACAAGTTTGA 59.601 37.500 6.27 0.00 41.57 2.69
4107 4240 8.655651 AGAAGAAAGACTGAAACTAGTTCTTG 57.344 34.615 8.95 4.53 37.13 3.02
4160 4293 2.299993 TCTCACATCGAACATCTGCC 57.700 50.000 0.00 0.00 0.00 4.85
4170 4303 4.952262 ACATGTTGGAAATCTCACATCG 57.048 40.909 0.00 0.00 0.00 3.84
4179 4312 4.341806 TGCAGTTCTCAACATGTTGGAAAT 59.658 37.500 32.54 27.79 40.78 2.17
4245 4378 2.190578 GGCTGATCCCAGGAACGG 59.809 66.667 0.00 0.00 40.72 4.44
4247 4380 1.753073 CATTTGGCTGATCCCAGGAAC 59.247 52.381 0.00 0.00 40.72 3.62
4251 4384 2.173519 ACAACATTTGGCTGATCCCAG 58.826 47.619 0.00 0.00 43.22 4.45
4277 4410 6.770785 TCTTTTGTATGTAACTGTCTGCCTTT 59.229 34.615 0.00 0.00 0.00 3.11
4284 4417 7.278868 CAGAGGGATCTTTTGTATGTAACTGTC 59.721 40.741 0.00 0.00 0.00 3.51
4328 4536 1.367840 GACGTGCCCTGAGTGTTCT 59.632 57.895 0.00 0.00 0.00 3.01
4344 4552 4.989797 TGCCATTGTCAAATTCATTGTGAC 59.010 37.500 1.06 1.06 41.66 3.67
4372 4580 4.883585 TGATATGAGCTTGTTTGGCTTAGG 59.116 41.667 0.00 0.00 40.40 2.69
4399 6733 5.721480 TGATGAGTCTTTCCTCCAATCTACA 59.279 40.000 0.00 0.00 0.00 2.74
4425 6759 4.225942 AGAGGCAGATGTTGTCCAATCTAA 59.774 41.667 0.00 0.00 29.16 2.10
4434 6768 6.317140 CACATGTAATAAGAGGCAGATGTTGT 59.683 38.462 0.00 0.00 0.00 3.32
4462 6796 3.086600 GCTACCCTGCCAGCCTCT 61.087 66.667 0.00 0.00 0.00 3.69
4496 6830 2.290883 GGTTATTACCGGTGCGTCG 58.709 57.895 19.93 0.00 34.01 5.12
4517 6888 2.289565 GTGGGATTTTCTCCGATCACC 58.710 52.381 0.00 0.00 46.01 4.02
4541 6912 4.212214 CGATCAGAGTCAGTCATCGATACA 59.788 45.833 0.00 0.00 38.92 2.29
4577 6948 0.256752 TAGACGAATCCCCAGACCGA 59.743 55.000 0.00 0.00 0.00 4.69
4613 6984 0.181114 GCCTATCCCAGTGACATGCA 59.819 55.000 0.00 0.00 0.00 3.96
4614 6985 0.536006 GGCCTATCCCAGTGACATGC 60.536 60.000 0.00 0.00 0.00 4.06
4667 7038 5.045942 TGAGGTGTGCTTCATACCATTCTTA 60.046 40.000 13.80 0.00 45.99 2.10
4682 7053 5.565592 TTCAATCATATTGTGAGGTGTGC 57.434 39.130 0.00 0.00 40.92 4.57
4700 7071 4.580167 GCCTTGACTGCATGGTATATTCAA 59.420 41.667 0.00 0.00 40.50 2.69
4703 7074 4.443978 AGCCTTGACTGCATGGTATATT 57.556 40.909 0.00 0.00 40.50 1.28
4722 7093 9.899226 AATGAAGTAGTTGTTTAATTCTGAAGC 57.101 29.630 0.00 0.00 31.02 3.86
4736 7107 7.962964 TCTTGTCCACTTAATGAAGTAGTTG 57.037 36.000 0.00 0.00 44.39 3.16
4796 7173 6.094742 TGAGTTGTTTCAAATCACTGCTTGTA 59.905 34.615 8.22 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.