Multiple sequence alignment - TraesCS6B01G260500

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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 TraesCS6B01G260500 chr6B 100.000 7427 0 0 1 7427 470832479 470825053 0.000000e+00 13716.0
1 TraesCS6B01G260500 chr6B 100.000 29 0 0 6062 6090 25016544 25016516 4.000000e-03 54.7
2 TraesCS6B01G260500 chr6A 94.479 3876 144 27 867 4706 440233421 440237262 0.000000e+00 5908.0
3 TraesCS6B01G260500 chr6A 96.186 944 29 4 4702 5643 440242921 440243859 0.000000e+00 1537.0
4 TraesCS6B01G260500 chr6A 93.445 778 37 5 5814 6589 440255462 440256227 0.000000e+00 1142.0
5 TraesCS6B01G260500 chr6A 88.907 613 28 19 6585 7192 440257302 440257879 0.000000e+00 719.0
6 TraesCS6B01G260500 chr6A 94.167 240 14 0 7188 7427 440258184 440258423 4.230000e-97 366.0
7 TraesCS6B01G260500 chr6A 92.529 174 9 2 5644 5816 440243912 440244082 5.760000e-61 246.0
8 TraesCS6B01G260500 chr6D 93.910 3120 138 29 2468 5568 305732178 305735264 0.000000e+00 4662.0
9 TraesCS6B01G260500 chr6D 92.078 1641 87 14 867 2483 305730513 305732134 0.000000e+00 2270.0
10 TraesCS6B01G260500 chr6D 93.455 1146 49 15 5645 6782 305735457 305736584 0.000000e+00 1677.0
11 TraesCS6B01G260500 chr6D 91.646 395 25 6 6800 7192 305736664 305737052 2.360000e-149 540.0
12 TraesCS6B01G260500 chr6D 95.000 240 12 0 7188 7427 305737362 305737601 1.960000e-100 377.0
13 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23418337 23418374 3.720000e-08 71.3
14 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23420568 23420605 3.720000e-08 71.3
15 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23620258 23620295 3.720000e-08 71.3
16 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23623473 23623510 3.720000e-08 71.3
17 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23628333 23628370 3.720000e-08 71.3
18 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23639670 23639707 3.720000e-08 71.3
19 TraesCS6B01G260500 chr6D 100.000 38 0 0 829 866 23783083 23783120 3.720000e-08 71.3
20 TraesCS6B01G260500 chr6D 100.000 33 0 0 5611 5643 305735365 305735397 2.240000e-05 62.1
21 TraesCS6B01G260500 chr3B 92.552 725 47 6 10 730 754774990 754774269 0.000000e+00 1033.0
22 TraesCS6B01G260500 chr2D 83.197 488 68 12 250 728 36773190 36773672 1.140000e-117 435.0
23 TraesCS6B01G260500 chr3D 85.194 412 58 3 7 418 8907944 8907536 3.200000e-113 420.0
24 TraesCS6B01G260500 chr3D 86.709 316 34 5 418 730 8907197 8906887 1.980000e-90 344.0
25 TraesCS6B01G260500 chrUn 100.000 38 0 0 829 866 87037913 87037876 3.720000e-08 71.3
26 TraesCS6B01G260500 chr7B 90.909 55 2 3 829 880 417897332 417897386 3.720000e-08 71.3
27 TraesCS6B01G260500 chr5B 100.000 29 0 0 6062 6090 344265171 344265143 4.000000e-03 54.7
28 TraesCS6B01G260500 chr4B 100.000 29 0 0 6062 6090 333049744 333049772 4.000000e-03 54.7
29 TraesCS6B01G260500 chr4B 100.000 29 0 0 6062 6090 469615962 469615934 4.000000e-03 54.7
30 TraesCS6B01G260500 chr4B 100.000 29 0 0 6062 6090 476897917 476897945 4.000000e-03 54.7
31 TraesCS6B01G260500 chr1B 100.000 29 0 0 6062 6090 115654262 115654234 4.000000e-03 54.7
32 TraesCS6B01G260500 chr1B 100.000 29 0 0 6062 6090 419243375 419243347 4.000000e-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 TraesCS6B01G260500 chr6B 470825053 470832479 7426 True 13716.000000 13716 100.000000 1 7427 1 chr6B.!!$R2 7426
1 TraesCS6B01G260500 chr6A 440233421 440237262 3841 False 5908.000000 5908 94.479000 867 4706 1 chr6A.!!$F1 3839
2 TraesCS6B01G260500 chr6A 440242921 440244082 1161 False 891.500000 1537 94.357500 4702 5816 2 chr6A.!!$F2 1114
3 TraesCS6B01G260500 chr6A 440255462 440258423 2961 False 742.333333 1142 92.173000 5814 7427 3 chr6A.!!$F3 1613
4 TraesCS6B01G260500 chr6D 305730513 305737601 7088 False 1598.016667 4662 94.348167 867 7427 6 chr6D.!!$F6 6560
5 TraesCS6B01G260500 chr3B 754774269 754774990 721 True 1033.000000 1033 92.552000 10 730 1 chr3B.!!$R1 720
6 TraesCS6B01G260500 chr3D 8906887 8907944 1057 True 382.000000 420 85.951500 7 730 2 chr3D.!!$R1 723

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
911 1257 0.818445 CCCATCTGGCTAGCAGCAAG 60.818 60.0 18.24 8.25 43.74 4.01 F
1370 1732 0.108186 CAGCTCATGGTAAGTGGCGA 60.108 55.0 0.00 0.00 0.00 5.54 F
1533 1895 0.753867 TTGCGGAGGTACAAGACACA 59.246 50.0 0.00 0.00 0.00 3.72 F
2355 2741 1.511850 TGTGTTGTTCTGATCTGCGG 58.488 50.0 0.00 0.00 0.00 5.69 F
3319 3777 0.111446 TTGTTCCGCCTCCCATTTCA 59.889 50.0 0.00 0.00 0.00 2.69 F
3996 4455 0.321996 TACCAACCGCATGTGCTACA 59.678 50.0 0.00 0.00 39.32 2.74 F
5506 5977 0.109319 GCAACACTGCCATAAACCCG 60.109 55.0 0.00 0.00 43.26 5.28 F
6169 6785 0.541863 ACAGCGAGAAATAGGTGGGG 59.458 55.0 0.00 0.00 39.87 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2453 3.084786 GCCAGAATACAGAGGTTTTGCT 58.915 45.455 0.00 0.00 0.00 3.91 R
2483 2872 3.799281 ACAGGGACAACAACAACATTG 57.201 42.857 0.00 0.00 0.00 2.82 R
2970 3428 4.726317 TGGATAAGATCATCAAAGGGTGGA 59.274 41.667 0.00 0.00 0.00 4.02 R
4310 4771 2.783135 ACTCCAGATGCATCAACGTTT 58.217 42.857 27.81 3.64 0.00 3.60 R
5172 5635 1.675552 GGGGCACACGCTTGTATTAT 58.324 50.000 0.00 0.00 38.60 1.28 R
5724 6333 2.082140 ACCGACATACTGGCTATGGA 57.918 50.000 0.00 0.00 37.18 3.41 R
6381 6997 0.040958 CCGCTGCATTAAATCGGCTC 60.041 55.000 0.00 0.00 33.36 4.70 R
7360 9441 0.331616 AGGAGGGGTACATTGTTGCC 59.668 55.000 0.00 0.00 0.00 4.52 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
125 126 4.036734 ACATTCACAAACCTACAACAGCAG 59.963 41.667 0.00 0.00 0.00 4.24
146 147 4.153117 CAGCAGCGAGTTCTAAGTTCAAAT 59.847 41.667 0.00 0.00 0.00 2.32
148 149 6.036517 CAGCAGCGAGTTCTAAGTTCAAATAT 59.963 38.462 0.00 0.00 0.00 1.28
151 152 7.222999 GCAGCGAGTTCTAAGTTCAAATATACT 59.777 37.037 0.00 0.00 0.00 2.12
164 165 9.084164 AGTTCAAATATACTGACGTCATTACAC 57.916 33.333 20.40 8.89 0.00 2.90
180 181 2.254152 ACACTCATCCAGGCTAAGGA 57.746 50.000 0.00 0.00 39.97 3.36
181 182 2.769209 ACACTCATCCAGGCTAAGGAT 58.231 47.619 0.62 0.62 46.61 3.24
223 224 3.963129 ACCAAGACAACAAAAGGACAGA 58.037 40.909 0.00 0.00 0.00 3.41
322 323 4.935808 GGCCGCATATACTTTACTTGCTAT 59.064 41.667 0.00 0.00 0.00 2.97
390 392 6.455360 TTGCTCCTTTATCTGCAAAATAGG 57.545 37.500 0.00 0.00 41.58 2.57
484 826 1.315257 CCCATTCCTGGCTTTCCACG 61.315 60.000 0.00 0.00 41.64 4.94
514 857 0.893727 CACTTGGCAACCCCTACCAC 60.894 60.000 0.00 0.00 31.83 4.16
520 863 2.083715 CAACCCCTACCACCACCAT 58.916 57.895 0.00 0.00 0.00 3.55
591 934 5.818336 TCTTGAACTGACGATGGTGTTTTTA 59.182 36.000 0.00 0.00 0.00 1.52
644 987 2.114488 TTAAGGAGGCGGCCGAACAA 62.114 55.000 33.48 9.00 0.00 2.83
650 993 0.965363 AGGCGGCCGAACAATCAAAT 60.965 50.000 33.48 0.00 0.00 2.32
652 995 1.268539 GGCGGCCGAACAATCAAATAG 60.269 52.381 33.48 0.00 0.00 1.73
657 1000 4.025979 CGGCCGAACAATCAAATAGTAGAC 60.026 45.833 24.07 0.00 0.00 2.59
673 1016 9.823647 AAATAGTAGACGATCAACTGATTCATT 57.176 29.630 0.00 0.00 34.37 2.57
676 1019 8.190888 AGTAGACGATCAACTGATTCATTTTC 57.809 34.615 0.00 0.00 34.37 2.29
677 1020 8.037758 AGTAGACGATCAACTGATTCATTTTCT 58.962 33.333 0.00 0.00 34.37 2.52
689 1033 7.230108 ACTGATTCATTTTCTCACAGAACACAT 59.770 33.333 0.00 0.00 33.26 3.21
691 1035 8.724229 TGATTCATTTTCTCACAGAACACATAG 58.276 33.333 0.00 0.00 33.26 2.23
703 1049 4.156739 CAGAACACATAGCTTTTCCCCTTC 59.843 45.833 0.00 0.00 0.00 3.46
730 1076 7.256655 CCATCCCCTTTTTAATAATGAATCCCC 60.257 40.741 0.00 0.00 0.00 4.81
731 1077 6.757317 TCCCCTTTTTAATAATGAATCCCCA 58.243 36.000 0.00 0.00 0.00 4.96
732 1078 7.377513 TCCCCTTTTTAATAATGAATCCCCAT 58.622 34.615 0.00 0.00 0.00 4.00
733 1079 7.512402 TCCCCTTTTTAATAATGAATCCCCATC 59.488 37.037 0.00 0.00 0.00 3.51
734 1080 7.292120 CCCCTTTTTAATAATGAATCCCCATCA 59.708 37.037 0.00 0.00 0.00 3.07
735 1081 8.713036 CCCTTTTTAATAATGAATCCCCATCAA 58.287 33.333 0.00 0.00 0.00 2.57
748 1094 9.258629 TGAATCCCCATCAAATATAATGAATCC 57.741 33.333 0.00 0.00 0.00 3.01
749 1095 8.613922 AATCCCCATCAAATATAATGAATCCC 57.386 34.615 0.00 0.00 0.00 3.85
750 1096 6.186957 TCCCCATCAAATATAATGAATCCCG 58.813 40.000 0.00 0.00 0.00 5.14
751 1097 5.951747 CCCCATCAAATATAATGAATCCCGT 59.048 40.000 0.00 0.00 0.00 5.28
752 1098 6.437162 CCCCATCAAATATAATGAATCCCGTT 59.563 38.462 0.00 0.00 0.00 4.44
753 1099 7.039082 CCCCATCAAATATAATGAATCCCGTTT 60.039 37.037 0.00 0.00 0.00 3.60
754 1100 9.019656 CCCATCAAATATAATGAATCCCGTTTA 57.980 33.333 0.00 0.00 0.00 2.01
756 1102 9.559958 CATCAAATATAATGAATCCCGTTTAGC 57.440 33.333 0.00 0.00 0.00 3.09
757 1103 8.684386 TCAAATATAATGAATCCCGTTTAGCA 57.316 30.769 0.00 0.00 0.00 3.49
758 1104 9.295825 TCAAATATAATGAATCCCGTTTAGCAT 57.704 29.630 0.00 0.00 0.00 3.79
759 1105 9.912634 CAAATATAATGAATCCCGTTTAGCATT 57.087 29.630 0.00 0.00 0.00 3.56
768 1114 9.959749 TGAATCCCGTTTAGCATTTTTATTATC 57.040 29.630 0.00 0.00 0.00 1.75
769 1115 9.406828 GAATCCCGTTTAGCATTTTTATTATCC 57.593 33.333 0.00 0.00 0.00 2.59
770 1116 6.961576 TCCCGTTTAGCATTTTTATTATCCG 58.038 36.000 0.00 0.00 0.00 4.18
771 1117 6.766944 TCCCGTTTAGCATTTTTATTATCCGA 59.233 34.615 0.00 0.00 0.00 4.55
772 1118 7.282675 TCCCGTTTAGCATTTTTATTATCCGAA 59.717 33.333 0.00 0.00 0.00 4.30
773 1119 7.916450 CCCGTTTAGCATTTTTATTATCCGAAA 59.084 33.333 0.00 0.00 0.00 3.46
774 1120 9.291664 CCGTTTAGCATTTTTATTATCCGAAAA 57.708 29.630 0.00 0.00 0.00 2.29
788 1134 5.734855 ATCCGAAAATTATGGTTCAGACG 57.265 39.130 0.00 0.00 0.00 4.18
789 1135 4.823157 TCCGAAAATTATGGTTCAGACGA 58.177 39.130 0.00 0.00 0.00 4.20
790 1136 5.239351 TCCGAAAATTATGGTTCAGACGAA 58.761 37.500 0.00 0.00 0.00 3.85
791 1137 5.701750 TCCGAAAATTATGGTTCAGACGAAA 59.298 36.000 0.00 0.00 31.43 3.46
792 1138 6.373216 TCCGAAAATTATGGTTCAGACGAAAT 59.627 34.615 0.00 0.00 31.43 2.17
793 1139 7.549842 TCCGAAAATTATGGTTCAGACGAAATA 59.450 33.333 0.00 0.00 31.43 1.40
794 1140 8.178964 CCGAAAATTATGGTTCAGACGAAATAA 58.821 33.333 0.00 0.00 31.43 1.40
795 1141 9.549509 CGAAAATTATGGTTCAGACGAAATAAA 57.450 29.630 0.00 0.00 31.43 1.40
803 1149 8.964420 TGGTTCAGACGAAATAAATGAATTTC 57.036 30.769 0.00 3.87 40.79 2.17
804 1150 8.792633 TGGTTCAGACGAAATAAATGAATTTCT 58.207 29.630 9.93 0.80 41.62 2.52
819 1165 9.862585 AAATGAATTTCTAAACATTTTTCGTGC 57.137 25.926 0.00 0.00 39.03 5.34
820 1166 7.993821 TGAATTTCTAAACATTTTTCGTGCA 57.006 28.000 0.00 0.00 0.00 4.57
821 1167 8.586570 TGAATTTCTAAACATTTTTCGTGCAT 57.413 26.923 0.00 0.00 0.00 3.96
822 1168 8.698854 TGAATTTCTAAACATTTTTCGTGCATC 58.301 29.630 0.00 0.00 0.00 3.91
823 1169 8.586570 AATTTCTAAACATTTTTCGTGCATCA 57.413 26.923 0.00 0.00 0.00 3.07
824 1170 7.993821 TTTCTAAACATTTTTCGTGCATCAA 57.006 28.000 0.00 0.00 0.00 2.57
825 1171 8.586570 TTTCTAAACATTTTTCGTGCATCAAT 57.413 26.923 0.00 0.00 0.00 2.57
826 1172 8.586570 TTCTAAACATTTTTCGTGCATCAATT 57.413 26.923 0.00 0.00 0.00 2.32
827 1173 8.586570 TCTAAACATTTTTCGTGCATCAATTT 57.413 26.923 0.00 0.00 0.00 1.82
828 1174 9.684448 TCTAAACATTTTTCGTGCATCAATTTA 57.316 25.926 0.00 0.00 0.00 1.40
829 1175 9.941991 CTAAACATTTTTCGTGCATCAATTTAG 57.058 29.630 0.00 0.00 0.00 1.85
830 1176 6.393720 ACATTTTTCGTGCATCAATTTAGC 57.606 33.333 0.00 0.00 0.00 3.09
831 1177 5.060816 ACATTTTTCGTGCATCAATTTAGCG 59.939 36.000 0.00 0.00 0.00 4.26
832 1178 2.823196 TTCGTGCATCAATTTAGCGG 57.177 45.000 0.00 0.00 0.00 5.52
833 1179 1.732941 TCGTGCATCAATTTAGCGGT 58.267 45.000 0.00 0.00 0.00 5.68
834 1180 2.894902 TCGTGCATCAATTTAGCGGTA 58.105 42.857 0.00 0.00 0.00 4.02
835 1181 2.605818 TCGTGCATCAATTTAGCGGTAC 59.394 45.455 0.00 0.00 0.00 3.34
853 1199 5.299582 GGTACGAGCCTATAGAACAGATC 57.700 47.826 0.00 0.00 0.00 2.75
854 1200 4.156373 GGTACGAGCCTATAGAACAGATCC 59.844 50.000 0.00 0.00 0.00 3.36
855 1201 4.107127 ACGAGCCTATAGAACAGATCCT 57.893 45.455 0.00 0.00 0.00 3.24
856 1202 3.823873 ACGAGCCTATAGAACAGATCCTG 59.176 47.826 0.00 0.00 37.52 3.86
896 1242 1.377202 GACACGCCACATCACCCAT 60.377 57.895 0.00 0.00 0.00 4.00
909 1255 1.997311 ACCCATCTGGCTAGCAGCA 60.997 57.895 18.24 5.21 44.75 4.41
911 1257 0.818445 CCCATCTGGCTAGCAGCAAG 60.818 60.000 18.24 8.25 43.74 4.01
929 1278 2.747460 CCACCCCGTGCATGACAG 60.747 66.667 7.72 0.00 31.34 3.51
944 1293 2.670934 CAGACACACCAGCCAGCC 60.671 66.667 0.00 0.00 0.00 4.85
1077 1430 3.198853 GTGTTATGCCCTTCTTCCTCTCT 59.801 47.826 0.00 0.00 0.00 3.10
1157 1519 3.798511 CTTCCGCCTCCCTTCCCC 61.799 72.222 0.00 0.00 0.00 4.81
1329 1691 2.202987 GACGAGCAGCTCATGGGG 60.203 66.667 22.49 7.90 0.00 4.96
1370 1732 0.108186 CAGCTCATGGTAAGTGGCGA 60.108 55.000 0.00 0.00 0.00 5.54
1377 1739 0.834687 TGGTAAGTGGCGAGGAACCT 60.835 55.000 0.00 0.00 0.00 3.50
1403 1765 1.372087 CCCGCTCTCATTTCACCTGC 61.372 60.000 0.00 0.00 0.00 4.85
1411 1773 4.713553 TCTCATTTCACCTGCTGTTGTTA 58.286 39.130 0.00 0.00 0.00 2.41
1414 1776 1.225855 TTCACCTGCTGTTGTTAGCG 58.774 50.000 0.00 0.00 46.61 4.26
1451 1813 2.267324 GCCCTCTGGTGCTGACTC 59.733 66.667 0.00 0.00 0.00 3.36
1468 1830 3.588842 TGACTCCTTGATTTGATCTGGGT 59.411 43.478 0.00 0.00 0.00 4.51
1509 1871 2.806237 GGGCTAAGCGTCGCTACT 59.194 61.111 22.04 8.57 38.25 2.57
1515 1877 2.203972 TAAGCGTCGCTACTGCCGTT 62.204 55.000 22.04 4.45 38.25 4.44
1533 1895 0.753867 TTGCGGAGGTACAAGACACA 59.246 50.000 0.00 0.00 0.00 3.72
1625 1991 4.883083 CAGTTAGCTGGTTAGTTGTCTGA 58.117 43.478 0.00 0.00 39.01 3.27
1626 1992 4.926238 CAGTTAGCTGGTTAGTTGTCTGAG 59.074 45.833 0.00 0.00 39.01 3.35
1627 1993 4.589374 AGTTAGCTGGTTAGTTGTCTGAGT 59.411 41.667 0.00 0.00 0.00 3.41
1628 1994 5.773680 AGTTAGCTGGTTAGTTGTCTGAGTA 59.226 40.000 0.00 0.00 0.00 2.59
1629 1995 6.267014 AGTTAGCTGGTTAGTTGTCTGAGTAA 59.733 38.462 0.00 0.00 0.00 2.24
1735 2113 6.884280 AAGGACCACTACAAAGAAAATGAG 57.116 37.500 0.00 0.00 0.00 2.90
1830 2208 9.339850 TGATCAGACATAGAAGGTAGTACTAAC 57.660 37.037 10.12 10.12 0.00 2.34
1961 2339 7.012044 ACACAGGTTTATAAGTTGAGTGAACAC 59.988 37.037 11.54 0.00 36.98 3.32
2075 2453 6.973474 CCTTTGTTTGTTATCCAAAACGTACA 59.027 34.615 0.00 0.00 44.36 2.90
2145 2523 4.473444 ACTCCATGATTTTCTTGGTGTGT 58.527 39.130 13.23 7.50 42.77 3.72
2263 2641 4.503991 CCTCAGGATTTATCAGGGCAGTAC 60.504 50.000 0.00 0.00 0.00 2.73
2355 2741 1.511850 TGTGTTGTTCTGATCTGCGG 58.488 50.000 0.00 0.00 0.00 5.69
2447 2836 9.181061 CCATGTGAATATTCTATGCCATATGAA 57.819 33.333 16.24 0.00 0.00 2.57
2760 3213 6.351966 GGAATATAGGTATACAGAAGGGTGCC 60.352 46.154 5.01 0.00 0.00 5.01
2970 3428 3.650023 TGTTCAGGAACACCCCGT 58.350 55.556 10.63 0.00 45.42 5.28
3054 3512 1.880027 AGACCGCCAATTGTTTCTGTC 59.120 47.619 4.43 5.58 0.00 3.51
3319 3777 0.111446 TTGTTCCGCCTCCCATTTCA 59.889 50.000 0.00 0.00 0.00 2.69
3703 4162 9.341899 CTTGCAAAACTGGTTACTAATAATGAC 57.658 33.333 0.00 0.00 0.00 3.06
3848 4307 6.843752 TCCAGTGAACCTCCTTACAATTTTA 58.156 36.000 0.00 0.00 0.00 1.52
3906 4365 3.481112 AATTACGGTAGCCAAAAAGCG 57.519 42.857 0.00 0.00 42.03 4.68
3990 4449 2.230266 GGTGATTTTACCAACCGCATGT 59.770 45.455 0.00 0.00 40.54 3.21
3996 4455 0.321996 TACCAACCGCATGTGCTACA 59.678 50.000 0.00 0.00 39.32 2.74
3997 4456 0.955428 ACCAACCGCATGTGCTACAG 60.955 55.000 0.00 0.00 39.32 2.74
3998 4457 1.647545 CCAACCGCATGTGCTACAGG 61.648 60.000 0.00 0.00 39.32 4.00
4067 4526 4.082949 GCAACACAATGGTAGTCCTTTACC 60.083 45.833 0.00 0.00 42.83 2.85
4132 4591 5.128205 TCACATCTTTCAGCATAATCTGGG 58.872 41.667 0.00 0.00 34.91 4.45
4139 4598 2.754552 TCAGCATAATCTGGGTTTGCAC 59.245 45.455 0.00 0.00 35.79 4.57
4173 4632 7.049799 AGCTGATCTGTTAAGTAATCCTCTC 57.950 40.000 1.27 0.00 0.00 3.20
4276 4737 5.954150 ACTAGGCCTCATTTCATGTTTCATT 59.046 36.000 9.68 0.00 0.00 2.57
4310 4771 9.038072 TGGTACCAGTTATAAGTGAGAACAATA 57.962 33.333 19.87 4.89 31.28 1.90
4328 4789 4.699735 ACAATAAACGTTGATGCATCTGGA 59.300 37.500 26.32 10.59 33.37 3.86
4340 4801 5.985530 TGATGCATCTGGAGTATTCGTTTAG 59.014 40.000 26.32 0.00 0.00 1.85
4362 4823 3.619038 GCAAGGAGTAAGGAATGAACTCG 59.381 47.826 0.00 0.00 40.44 4.18
4413 4874 5.806654 ACATAGTTTTCAAACCAGGCAAT 57.193 34.783 0.00 0.00 39.71 3.56
4427 4888 6.469782 ACCAGGCAATAGATTTACCAAATG 57.530 37.500 0.00 0.00 0.00 2.32
4517 4978 4.082190 GGGTCTTCAAGGCAAATAAAGGAC 60.082 45.833 0.00 0.00 0.00 3.85
4564 5025 6.016693 TCAGTTTGGTGTTGGTACATTACATG 60.017 38.462 0.00 0.00 39.30 3.21
4594 5055 7.497925 TGTTTTTAAAACCAAATACCATGCC 57.502 32.000 16.62 0.00 0.00 4.40
4595 5056 7.054124 TGTTTTTAAAACCAAATACCATGCCA 58.946 30.769 16.62 0.00 0.00 4.92
4651 5114 5.293079 GTCAGGTGCTCAGTTCATTCTTATC 59.707 44.000 0.00 0.00 0.00 1.75
4671 5134 2.103432 TCTTTAACGCTCCAGTGGAACA 59.897 45.455 14.17 0.00 41.43 3.18
4739 5202 0.807496 GTTGGCTGATGCTGACCTTC 59.193 55.000 0.00 0.00 39.59 3.46
5085 5548 7.110155 TCCTTGGGTGTTTTAAAGATAGCTAG 58.890 38.462 0.00 0.00 0.00 3.42
5103 5566 3.140332 GCTAGGGGATTGGGGAGTAAAAT 59.860 47.826 0.00 0.00 0.00 1.82
5369 5835 4.724074 TTTGTCATCCATGCCATTTCTC 57.276 40.909 0.00 0.00 0.00 2.87
5454 5921 2.933906 CCACGTTAATGGTAACTGCGAT 59.066 45.455 0.00 0.00 37.97 4.58
5506 5977 0.109319 GCAACACTGCCATAAACCCG 60.109 55.000 0.00 0.00 43.26 5.28
5547 6018 7.659390 TGTCAAAGTGCTAAAATTTATTTGGGG 59.341 33.333 8.69 0.00 0.00 4.96
5716 6325 1.044611 GGGAGATGGAGAGTACAGCC 58.955 60.000 0.00 0.00 0.00 4.85
5824 6437 7.361713 GCCTATTAACTGCAGTTATTGTGTCAA 60.362 37.037 33.72 21.31 39.89 3.18
5865 6478 6.934645 TGTAACAATCTTTAGTTAGCTGCTGT 59.065 34.615 13.43 0.00 31.45 4.40
6100 6714 7.389803 TCATTTGAATATCCGTGAACATGTT 57.610 32.000 11.78 11.78 0.00 2.71
6103 6717 9.009327 CATTTGAATATCCGTGAACATGTTAAC 57.991 33.333 15.25 15.25 0.00 2.01
6160 6776 4.174009 GCTACAGTATTCACAGCGAGAAA 58.826 43.478 0.00 0.00 0.00 2.52
6169 6785 0.541863 ACAGCGAGAAATAGGTGGGG 59.458 55.000 0.00 0.00 39.87 4.96
6212 6828 3.264450 AGGTTGTCCCCTTGATCAGTAAG 59.736 47.826 0.00 0.00 0.00 2.34
6276 6892 3.595758 GGCACCTGCGCACACTTT 61.596 61.111 5.66 0.00 43.26 2.66
6277 6893 2.412937 GCACCTGCGCACACTTTT 59.587 55.556 5.66 0.00 0.00 2.27
6320 6936 4.565564 GCAATTTCTTGATTGGAGATGTGC 59.434 41.667 0.00 0.00 37.47 4.57
6335 6951 5.237344 GGAGATGTGCGCTAGATGTATTTTT 59.763 40.000 9.73 0.00 0.00 1.94
6381 6997 2.362397 AGCAGGATACGTGAGGTGTATG 59.638 50.000 0.00 0.00 46.39 2.39
6399 7015 0.657312 TGAGCCGATTTAATGCAGCG 59.343 50.000 0.00 0.00 0.00 5.18
6446 7062 5.009911 TGTGAAGATTGCTGTTATGTTGCTT 59.990 36.000 0.00 0.00 0.00 3.91
6476 7092 2.107141 GCTGGCGCTACTCCGAAT 59.893 61.111 7.64 0.00 0.00 3.34
6482 7098 0.645868 GCGCTACTCCGAATTCACAC 59.354 55.000 0.00 0.00 0.00 3.82
6493 7109 2.478335 AATTCACACGGGCCATCGGT 62.478 55.000 4.39 0.00 0.00 4.69
6543 7160 0.543410 TTCCAGCCTGTAACCGAGGA 60.543 55.000 0.00 0.00 31.48 3.71
6544 7161 1.218316 CCAGCCTGTAACCGAGGAC 59.782 63.158 0.00 0.00 31.48 3.85
6545 7162 1.258445 CCAGCCTGTAACCGAGGACT 61.258 60.000 0.00 0.00 31.48 3.85
6557 7174 2.163509 CCGAGGACTCTCTCTTCACAA 58.836 52.381 0.00 0.00 37.86 3.33
6637 8333 2.297701 TGGTGAAAGTCTGAACTTGCC 58.702 47.619 0.00 0.00 45.07 4.52
6791 8490 8.574251 ACTTGTATTGGTACATAGATTGCAAA 57.426 30.769 1.71 0.00 40.35 3.68
6792 8491 9.019656 ACTTGTATTGGTACATAGATTGCAAAA 57.980 29.630 1.71 0.00 40.35 2.44
6808 8507 9.349713 AGATTGCAAAATTATCTTATTACGGGA 57.650 29.630 1.71 0.00 0.00 5.14
6818 8579 0.569204 TATTACGGGATGGAGGGGGT 59.431 55.000 0.00 0.00 0.00 4.95
6819 8580 1.060163 ATTACGGGATGGAGGGGGTG 61.060 60.000 0.00 0.00 0.00 4.61
6829 8590 2.543635 TGGAGGGGGTGTTAGTTAGAC 58.456 52.381 0.00 0.00 0.00 2.59
6867 8628 3.243704 GCATTGGGCACAAAACAGAGTAA 60.244 43.478 4.97 0.00 43.97 2.24
6916 8677 2.739913 CCATGCTTGTTGCTTTGATTGG 59.260 45.455 0.00 0.00 43.37 3.16
6923 8684 5.007921 GCTTGTTGCTTTGATTGGTTTTGAT 59.992 36.000 0.00 0.00 38.95 2.57
6924 8685 6.458615 GCTTGTTGCTTTGATTGGTTTTGATT 60.459 34.615 0.00 0.00 38.95 2.57
6925 8686 6.360844 TGTTGCTTTGATTGGTTTTGATTG 57.639 33.333 0.00 0.00 0.00 2.67
6926 8687 6.111382 TGTTGCTTTGATTGGTTTTGATTGA 58.889 32.000 0.00 0.00 0.00 2.57
7007 8768 9.512588 CCCTTGATAGCTCATGAGTTAATTAAT 57.487 33.333 21.25 7.35 0.00 1.40
7091 8853 5.243060 TGAAGATCTTGTGTCTACCGAGAAA 59.757 40.000 14.00 0.00 31.96 2.52
7094 8856 3.585862 TCTTGTGTCTACCGAGAAATGC 58.414 45.455 0.00 0.00 31.96 3.56
7120 8882 9.099454 CTTGTACCTACAGTTTCTATGGATTTC 57.901 37.037 0.00 0.00 37.52 2.17
7173 8936 2.287393 TGCGTCATAGCAACGTACAT 57.713 45.000 0.00 0.00 45.06 2.29
7297 9378 6.931838 ACTAGTTAGTTAGTTGCAGCACATA 58.068 36.000 2.55 0.00 31.13 2.29
7360 9441 6.016777 GCATATTCCTTGGTTCTTGATAGTGG 60.017 42.308 0.00 0.00 0.00 4.00
7391 9472 2.354328 ACCCCTCCTTACAACCATCAA 58.646 47.619 0.00 0.00 0.00 2.57
7413 9494 8.868522 TCAATGTGAATCCTCTTATCTGTTTT 57.131 30.769 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.557205 GTCCTTGTAGTTCTGAACGATGT 58.443 43.478 14.35 0.42 36.23 3.06
1 2 3.927142 GGTCCTTGTAGTTCTGAACGATG 59.073 47.826 14.35 5.77 36.23 3.84
2 3 3.576982 TGGTCCTTGTAGTTCTGAACGAT 59.423 43.478 14.35 1.48 36.23 3.73
3 4 2.960384 TGGTCCTTGTAGTTCTGAACGA 59.040 45.455 14.35 7.07 36.23 3.85
4 5 3.318017 CTGGTCCTTGTAGTTCTGAACG 58.682 50.000 14.35 0.65 36.23 3.95
5 6 3.067833 GCTGGTCCTTGTAGTTCTGAAC 58.932 50.000 12.54 12.54 0.00 3.18
96 97 6.151985 TGTTGTAGGTTTGTGAATGTTGTCTT 59.848 34.615 0.00 0.00 0.00 3.01
125 126 4.670227 ATTTGAACTTAGAACTCGCTGC 57.330 40.909 0.00 0.00 0.00 5.25
146 147 6.544564 TGGATGAGTGTAATGACGTCAGTATA 59.455 38.462 26.34 21.59 0.00 1.47
148 149 4.703093 TGGATGAGTGTAATGACGTCAGTA 59.297 41.667 24.41 22.58 0.00 2.74
151 152 3.119137 CCTGGATGAGTGTAATGACGTCA 60.119 47.826 22.48 22.48 0.00 4.35
164 165 7.201992 GGATATAAGATCCTTAGCCTGGATGAG 60.202 44.444 0.00 0.00 43.68 2.90
180 181 7.872138 TGGTTCTGTCTTTTGGGATATAAGAT 58.128 34.615 0.00 0.00 31.25 2.40
181 182 7.265599 TGGTTCTGTCTTTTGGGATATAAGA 57.734 36.000 0.00 0.00 0.00 2.10
223 224 2.555547 GCGGCTGGCTCACTTGTTT 61.556 57.895 0.00 0.00 39.11 2.83
252 253 2.288666 GCGGCTGGAATCATAAACTCA 58.711 47.619 0.00 0.00 0.00 3.41
313 314 6.590068 AGACTACTAGAACGGATAGCAAGTA 58.410 40.000 0.00 0.00 0.00 2.24
322 323 2.097825 GGGCAAGACTACTAGAACGGA 58.902 52.381 0.00 0.00 0.00 4.69
450 791 3.554129 GGAATGGGGTCGTTTTTGAAAGG 60.554 47.826 0.00 0.00 0.00 3.11
484 826 3.977244 CCAAGTGTGTTGGGCGCC 61.977 66.667 21.18 21.18 35.96 6.53
547 890 6.782988 TCAAGATTGTTTTGGGGTATGGTTAA 59.217 34.615 0.00 0.00 0.00 2.01
644 987 9.469807 GAATCAGTTGATCGTCTACTATTTGAT 57.530 33.333 0.00 0.00 30.99 2.57
650 993 9.302345 GAAAATGAATCAGTTGATCGTCTACTA 57.698 33.333 0.00 0.00 30.99 1.82
652 995 8.190888 AGAAAATGAATCAGTTGATCGTCTAC 57.809 34.615 0.00 0.00 32.75 2.59
657 1000 6.834876 TGTGAGAAAATGAATCAGTTGATCG 58.165 36.000 0.00 0.00 32.75 3.69
673 1016 6.017109 GGAAAAGCTATGTGTTCTGTGAGAAA 60.017 38.462 0.00 0.00 35.75 2.52
676 1019 4.154918 GGGAAAAGCTATGTGTTCTGTGAG 59.845 45.833 0.00 0.00 0.00 3.51
677 1020 4.072131 GGGAAAAGCTATGTGTTCTGTGA 58.928 43.478 0.00 0.00 0.00 3.58
689 1033 1.569072 GGATGGGAAGGGGAAAAGCTA 59.431 52.381 0.00 0.00 0.00 3.32
691 1035 0.687757 GGGATGGGAAGGGGAAAAGC 60.688 60.000 0.00 0.00 0.00 3.51
703 1049 7.256655 GGGATTCATTATTAAAAAGGGGATGGG 60.257 40.741 0.00 0.00 0.00 4.00
730 1076 9.559958 GCTAAACGGGATTCATTATATTTGATG 57.440 33.333 0.00 0.00 0.00 3.07
731 1077 9.295825 TGCTAAACGGGATTCATTATATTTGAT 57.704 29.630 0.00 0.00 0.00 2.57
732 1078 8.684386 TGCTAAACGGGATTCATTATATTTGA 57.316 30.769 0.00 0.00 0.00 2.69
733 1079 9.912634 AATGCTAAACGGGATTCATTATATTTG 57.087 29.630 0.00 0.00 0.00 2.32
742 1088 9.959749 GATAATAAAAATGCTAAACGGGATTCA 57.040 29.630 0.00 0.00 0.00 2.57
743 1089 9.406828 GGATAATAAAAATGCTAAACGGGATTC 57.593 33.333 0.00 0.00 0.00 2.52
744 1090 8.079809 CGGATAATAAAAATGCTAAACGGGATT 58.920 33.333 0.00 0.00 0.00 3.01
745 1091 7.446013 TCGGATAATAAAAATGCTAAACGGGAT 59.554 33.333 0.00 0.00 0.00 3.85
746 1092 6.766944 TCGGATAATAAAAATGCTAAACGGGA 59.233 34.615 0.00 0.00 0.00 5.14
747 1093 6.961576 TCGGATAATAAAAATGCTAAACGGG 58.038 36.000 0.00 0.00 0.00 5.28
748 1094 8.844441 TTTCGGATAATAAAAATGCTAAACGG 57.156 30.769 0.00 0.00 0.00 4.44
762 1108 8.984764 CGTCTGAACCATAATTTTCGGATAATA 58.015 33.333 3.14 0.00 38.93 0.98
763 1109 7.713507 TCGTCTGAACCATAATTTTCGGATAAT 59.286 33.333 3.14 0.00 38.93 1.28
764 1110 7.042950 TCGTCTGAACCATAATTTTCGGATAA 58.957 34.615 3.14 0.00 38.93 1.75
765 1111 6.575267 TCGTCTGAACCATAATTTTCGGATA 58.425 36.000 3.14 0.00 38.93 2.59
766 1112 5.424757 TCGTCTGAACCATAATTTTCGGAT 58.575 37.500 3.14 0.00 38.93 4.18
767 1113 4.823157 TCGTCTGAACCATAATTTTCGGA 58.177 39.130 0.00 0.00 35.23 4.55
768 1114 5.539582 TTCGTCTGAACCATAATTTTCGG 57.460 39.130 0.00 0.00 0.00 4.30
769 1115 9.549509 TTTATTTCGTCTGAACCATAATTTTCG 57.450 29.630 0.00 0.00 32.71 3.46
777 1123 9.573133 GAAATTCATTTATTTCGTCTGAACCAT 57.427 29.630 0.00 0.00 35.50 3.55
778 1124 8.792633 AGAAATTCATTTATTTCGTCTGAACCA 58.207 29.630 0.00 0.00 45.08 3.67
793 1139 9.862585 GCACGAAAAATGTTTAGAAATTCATTT 57.137 25.926 0.00 0.00 40.62 2.32
794 1140 9.039870 TGCACGAAAAATGTTTAGAAATTCATT 57.960 25.926 0.00 0.00 32.86 2.57
795 1141 8.586570 TGCACGAAAAATGTTTAGAAATTCAT 57.413 26.923 0.00 0.00 0.00 2.57
796 1142 7.993821 TGCACGAAAAATGTTTAGAAATTCA 57.006 28.000 0.00 0.00 0.00 2.57
797 1143 8.698854 TGATGCACGAAAAATGTTTAGAAATTC 58.301 29.630 0.00 0.00 0.00 2.17
798 1144 8.586570 TGATGCACGAAAAATGTTTAGAAATT 57.413 26.923 0.00 0.00 0.00 1.82
799 1145 8.586570 TTGATGCACGAAAAATGTTTAGAAAT 57.413 26.923 0.00 0.00 0.00 2.17
800 1146 7.993821 TTGATGCACGAAAAATGTTTAGAAA 57.006 28.000 0.00 0.00 0.00 2.52
801 1147 8.586570 AATTGATGCACGAAAAATGTTTAGAA 57.413 26.923 0.00 0.00 0.00 2.10
802 1148 8.586570 AAATTGATGCACGAAAAATGTTTAGA 57.413 26.923 0.00 0.00 0.00 2.10
803 1149 9.941991 CTAAATTGATGCACGAAAAATGTTTAG 57.058 29.630 0.00 0.00 0.00 1.85
804 1150 8.431593 GCTAAATTGATGCACGAAAAATGTTTA 58.568 29.630 0.00 0.00 0.00 2.01
805 1151 7.290118 GCTAAATTGATGCACGAAAAATGTTT 58.710 30.769 0.00 0.00 0.00 2.83
806 1152 6.399880 CGCTAAATTGATGCACGAAAAATGTT 60.400 34.615 0.00 0.00 0.00 2.71
807 1153 5.060816 CGCTAAATTGATGCACGAAAAATGT 59.939 36.000 0.00 0.00 0.00 2.71
808 1154 5.474545 CGCTAAATTGATGCACGAAAAATG 58.525 37.500 0.00 0.00 0.00 2.32
809 1155 4.562394 CCGCTAAATTGATGCACGAAAAAT 59.438 37.500 0.00 0.00 0.00 1.82
810 1156 3.917380 CCGCTAAATTGATGCACGAAAAA 59.083 39.130 0.00 0.00 0.00 1.94
811 1157 3.057876 ACCGCTAAATTGATGCACGAAAA 60.058 39.130 0.00 0.00 0.00 2.29
812 1158 2.486203 ACCGCTAAATTGATGCACGAAA 59.514 40.909 0.00 0.00 0.00 3.46
813 1159 2.080693 ACCGCTAAATTGATGCACGAA 58.919 42.857 0.00 0.00 0.00 3.85
814 1160 1.732941 ACCGCTAAATTGATGCACGA 58.267 45.000 0.00 0.00 0.00 4.35
815 1161 2.596575 CGTACCGCTAAATTGATGCACG 60.597 50.000 0.00 0.00 0.00 5.34
816 1162 2.605818 TCGTACCGCTAAATTGATGCAC 59.394 45.455 0.00 0.00 0.00 4.57
817 1163 2.863740 CTCGTACCGCTAAATTGATGCA 59.136 45.455 0.00 0.00 0.00 3.96
818 1164 2.348591 GCTCGTACCGCTAAATTGATGC 60.349 50.000 0.00 0.00 0.00 3.91
819 1165 2.221055 GGCTCGTACCGCTAAATTGATG 59.779 50.000 2.32 0.00 0.00 3.07
820 1166 2.102588 AGGCTCGTACCGCTAAATTGAT 59.897 45.455 2.32 0.00 33.69 2.57
821 1167 1.479323 AGGCTCGTACCGCTAAATTGA 59.521 47.619 2.32 0.00 33.69 2.57
822 1168 1.935933 AGGCTCGTACCGCTAAATTG 58.064 50.000 2.32 0.00 33.69 2.32
823 1169 4.763793 TCTATAGGCTCGTACCGCTAAATT 59.236 41.667 0.00 0.00 33.69 1.82
824 1170 4.330250 TCTATAGGCTCGTACCGCTAAAT 58.670 43.478 0.00 0.00 33.69 1.40
825 1171 3.743521 TCTATAGGCTCGTACCGCTAAA 58.256 45.455 0.00 0.00 33.69 1.85
826 1172 3.407424 TCTATAGGCTCGTACCGCTAA 57.593 47.619 0.00 0.00 33.69 3.09
827 1173 3.070018 GTTCTATAGGCTCGTACCGCTA 58.930 50.000 0.00 0.00 33.69 4.26
828 1174 1.878734 GTTCTATAGGCTCGTACCGCT 59.121 52.381 0.00 0.00 33.69 5.52
829 1175 1.605710 TGTTCTATAGGCTCGTACCGC 59.394 52.381 0.00 0.00 33.69 5.68
830 1176 3.136763 TCTGTTCTATAGGCTCGTACCG 58.863 50.000 0.00 0.00 33.69 4.02
831 1177 4.156373 GGATCTGTTCTATAGGCTCGTACC 59.844 50.000 0.00 0.00 0.00 3.34
832 1178 5.005094 AGGATCTGTTCTATAGGCTCGTAC 58.995 45.833 0.00 0.00 0.00 3.67
833 1179 5.004448 CAGGATCTGTTCTATAGGCTCGTA 58.996 45.833 0.00 0.00 0.00 3.43
834 1180 3.823873 CAGGATCTGTTCTATAGGCTCGT 59.176 47.826 0.00 0.00 0.00 4.18
835 1181 3.823873 ACAGGATCTGTTCTATAGGCTCG 59.176 47.826 0.00 0.00 42.59 5.03
848 1194 9.046296 GGTTACATATTACTTGAACAGGATCTG 57.954 37.037 0.00 0.00 37.52 2.90
849 1195 8.211629 GGGTTACATATTACTTGAACAGGATCT 58.788 37.037 0.00 0.00 0.00 2.75
850 1196 8.211629 AGGGTTACATATTACTTGAACAGGATC 58.788 37.037 0.00 0.00 0.00 3.36
851 1197 8.102484 AGGGTTACATATTACTTGAACAGGAT 57.898 34.615 0.00 0.00 0.00 3.24
852 1198 7.504926 AGGGTTACATATTACTTGAACAGGA 57.495 36.000 0.00 0.00 0.00 3.86
853 1199 7.827236 TCAAGGGTTACATATTACTTGAACAGG 59.173 37.037 0.00 0.00 40.68 4.00
854 1200 8.665685 GTCAAGGGTTACATATTACTTGAACAG 58.334 37.037 6.50 0.00 43.82 3.16
855 1201 8.158132 TGTCAAGGGTTACATATTACTTGAACA 58.842 33.333 6.50 5.37 43.82 3.18
856 1202 8.448615 GTGTCAAGGGTTACATATTACTTGAAC 58.551 37.037 6.50 4.80 43.82 3.18
857 1203 7.332430 CGTGTCAAGGGTTACATATTACTTGAA 59.668 37.037 6.50 0.00 43.82 2.69
858 1204 6.814644 CGTGTCAAGGGTTACATATTACTTGA 59.185 38.462 0.00 0.00 41.16 3.02
859 1205 6.456449 GCGTGTCAAGGGTTACATATTACTTG 60.456 42.308 0.00 0.00 37.31 3.16
860 1206 5.583457 GCGTGTCAAGGGTTACATATTACTT 59.417 40.000 0.00 0.00 0.00 2.24
861 1207 5.114081 GCGTGTCAAGGGTTACATATTACT 58.886 41.667 0.00 0.00 0.00 2.24
862 1208 4.271776 GGCGTGTCAAGGGTTACATATTAC 59.728 45.833 0.00 0.00 0.00 1.89
863 1209 4.081031 TGGCGTGTCAAGGGTTACATATTA 60.081 41.667 0.00 0.00 0.00 0.98
864 1210 3.275999 GGCGTGTCAAGGGTTACATATT 58.724 45.455 0.00 0.00 0.00 1.28
865 1211 2.237643 TGGCGTGTCAAGGGTTACATAT 59.762 45.455 0.00 0.00 0.00 1.78
909 1255 3.965258 TCATGCACGGGGTGGCTT 61.965 61.111 0.00 0.00 33.64 4.35
914 1260 2.347490 GTCTGTCATGCACGGGGT 59.653 61.111 0.00 0.00 31.32 4.95
915 1261 2.034879 GTGTCTGTCATGCACGGGG 61.035 63.158 0.00 0.00 31.32 5.73
916 1262 1.301637 TGTGTCTGTCATGCACGGG 60.302 57.895 0.00 0.00 36.04 5.28
917 1263 1.568612 GGTGTGTCTGTCATGCACGG 61.569 60.000 0.00 0.00 36.04 4.94
919 1265 0.870393 CTGGTGTGTCTGTCATGCAC 59.130 55.000 0.00 0.00 0.00 4.57
922 1268 0.250424 TGGCTGGTGTGTCTGTCATG 60.250 55.000 0.00 0.00 0.00 3.07
923 1269 0.035881 CTGGCTGGTGTGTCTGTCAT 59.964 55.000 0.00 0.00 0.00 3.06
1097 1459 4.154347 GAGGGCAGAGCGGAGTGG 62.154 72.222 0.00 0.00 0.00 4.00
1329 1691 4.699522 ACGCTGAAACCGAGGGGC 62.700 66.667 0.00 0.00 36.48 5.80
1403 1765 4.147322 CCGCGGCGCTAACAACAG 62.147 66.667 30.54 11.30 0.00 3.16
1432 1794 3.325753 GTCAGCACCAGAGGGCCT 61.326 66.667 5.25 5.25 37.90 5.19
1443 1805 4.259356 CAGATCAAATCAAGGAGTCAGCA 58.741 43.478 0.00 0.00 0.00 4.41
1451 1813 3.512724 AGCAAACCCAGATCAAATCAAGG 59.487 43.478 0.00 0.00 0.00 3.61
1468 1830 2.260869 GCTCCTGCACGGAAGCAAA 61.261 57.895 15.09 0.00 45.13 3.68
1515 1877 0.973632 ATGTGTCTTGTACCTCCGCA 59.026 50.000 0.00 0.00 0.00 5.69
1525 1887 3.562973 AGCACAGAAAGTCATGTGTCTTG 59.437 43.478 7.12 0.00 46.75 3.02
1533 1895 2.812591 CAAGAGCAGCACAGAAAGTCAT 59.187 45.455 0.00 0.00 0.00 3.06
1577 1939 1.008538 GCACGGCAACCAGAACAAG 60.009 57.895 0.00 0.00 0.00 3.16
1617 1983 6.647067 AGTGCTAGACAATTTACTCAGACAAC 59.353 38.462 0.00 0.00 0.00 3.32
1618 1984 6.759272 AGTGCTAGACAATTTACTCAGACAA 58.241 36.000 0.00 0.00 0.00 3.18
1619 1985 6.346477 AGTGCTAGACAATTTACTCAGACA 57.654 37.500 0.00 0.00 0.00 3.41
1620 1986 7.763356 TCTAGTGCTAGACAATTTACTCAGAC 58.237 38.462 4.93 0.00 37.28 3.51
1621 1987 7.939784 TCTAGTGCTAGACAATTTACTCAGA 57.060 36.000 4.93 0.00 37.28 3.27
1672 2038 2.458951 TCATTTCGCAACAACAGCAAC 58.541 42.857 0.00 0.00 0.00 4.17
1735 2113 4.101119 AGACCATAGTACTGTATTGCCCAC 59.899 45.833 5.39 0.00 0.00 4.61
1961 2339 4.637534 CCACAGATGATAAGAACCCTTGTG 59.362 45.833 0.00 0.00 33.94 3.33
2075 2453 3.084786 GCCAGAATACAGAGGTTTTGCT 58.915 45.455 0.00 0.00 0.00 3.91
2263 2641 4.836455 ACATCGCATCAATAACAATGTCG 58.164 39.130 0.00 0.00 0.00 4.35
2355 2741 6.194796 TGAGCTTTACATAAAATCAGTGGC 57.805 37.500 0.00 0.00 0.00 5.01
2483 2872 3.799281 ACAGGGACAACAACAACATTG 57.201 42.857 0.00 0.00 0.00 2.82
2693 3146 5.014202 GGAACAGTAACCCCATGTGTTTAT 58.986 41.667 3.52 0.00 31.57 1.40
2970 3428 4.726317 TGGATAAGATCATCAAAGGGTGGA 59.274 41.667 0.00 0.00 0.00 4.02
3361 3819 6.514870 GCACTTTTCCAATTCTCACACACATA 60.515 38.462 0.00 0.00 0.00 2.29
3848 4307 4.079558 AGACCCAATGAAGGCATGAGTAAT 60.080 41.667 0.00 0.00 34.26 1.89
3906 4365 7.795272 GCATTTGAATTTTCCGATAAATCATGC 59.205 33.333 0.00 0.00 0.00 4.06
4067 4526 4.692625 AGACAGCAAGCACAGTATAGTTTG 59.307 41.667 0.00 0.00 0.00 2.93
4113 4572 5.163478 GCAAACCCAGATTATGCTGAAAGAT 60.163 40.000 0.00 0.00 38.14 2.40
4132 4591 7.272084 CAGATCAGCTTACAAATAAGTGCAAAC 59.728 37.037 0.00 0.00 40.13 2.93
4178 4637 8.688747 AAAGATCAGAAAAGAAGAACACAGAT 57.311 30.769 0.00 0.00 0.00 2.90
4180 4639 8.619546 AGAAAAGATCAGAAAAGAAGAACACAG 58.380 33.333 0.00 0.00 0.00 3.66
4276 4737 9.575868 TCACTTATAACTGGTACCAAAAATCAA 57.424 29.630 17.11 5.33 0.00 2.57
4310 4771 2.783135 ACTCCAGATGCATCAACGTTT 58.217 42.857 27.81 3.64 0.00 3.60
4328 4789 6.154021 TCCTTACTCCTTGCTAAACGAATACT 59.846 38.462 0.00 0.00 0.00 2.12
4340 4801 3.619038 CGAGTTCATTCCTTACTCCTTGC 59.381 47.826 0.00 0.00 35.91 4.01
4362 4823 9.248291 CATAAAAATATACCAAACATGCCTCAC 57.752 33.333 0.00 0.00 0.00 3.51
4517 4978 5.757320 TGAAATTACCAAGCAAACCAACATG 59.243 36.000 0.00 0.00 0.00 3.21
4651 5114 2.489971 TGTTCCACTGGAGCGTTAAAG 58.510 47.619 7.37 0.00 35.65 1.85
4671 5134 7.630242 TTTCTCAGTCAGTTTGAAACAGATT 57.370 32.000 11.02 1.67 0.00 2.40
4739 5202 7.863375 CCTTCTACTCTAACCTATGAAACGATG 59.137 40.741 0.00 0.00 0.00 3.84
5085 5548 6.713731 TCTATATTTTACTCCCCAATCCCC 57.286 41.667 0.00 0.00 0.00 4.81
5103 5566 8.866093 TCCCTTGTTCGTCATCAATAATCTATA 58.134 33.333 0.00 0.00 0.00 1.31
5172 5635 1.675552 GGGGCACACGCTTGTATTAT 58.324 50.000 0.00 0.00 38.60 1.28
5369 5835 9.072294 GGGTGAATTATTCGTGTCAATAAAAAG 57.928 33.333 0.23 0.00 33.05 2.27
5454 5921 9.144298 CTTGGATCTAGGAGTATTAAACTGGTA 57.856 37.037 0.00 0.00 39.07 3.25
5506 5977 3.750639 TTGACAACTGTTCACGAAACC 57.249 42.857 0.00 0.00 37.03 3.27
5547 6018 7.916914 ACATATTAAGGTTGTTGAGTACACC 57.083 36.000 0.00 0.00 36.21 4.16
5724 6333 2.082140 ACCGACATACTGGCTATGGA 57.918 50.000 0.00 0.00 37.18 3.41
5725 6334 4.537135 AATACCGACATACTGGCTATGG 57.463 45.455 0.00 0.00 37.18 2.74
5726 6335 6.093404 CACTAATACCGACATACTGGCTATG 58.907 44.000 0.00 0.00 38.65 2.23
5727 6336 5.185249 CCACTAATACCGACATACTGGCTAT 59.815 44.000 0.00 0.00 0.00 2.97
5816 6429 5.997746 ACTTTAGCAGCTTAGATTGACACAA 59.002 36.000 0.00 0.00 0.00 3.33
5824 6437 8.043710 AGATTGTTACACTTTAGCAGCTTAGAT 58.956 33.333 0.00 0.00 0.00 1.98
5865 6478 7.577303 AGAAGCCAGAATTCAGGATTAACATA 58.423 34.615 18.96 0.00 31.14 2.29
6160 6776 2.418669 CCATTCTGTACCCCCACCTAT 58.581 52.381 0.00 0.00 0.00 2.57
6169 6785 2.418368 TGGATGTGCCATTCTGTACC 57.582 50.000 0.00 0.00 43.33 3.34
6276 6892 3.054655 GCAGTCCATTAGGTACCAGGAAA 60.055 47.826 15.94 3.05 35.89 3.13
6277 6893 2.504175 GCAGTCCATTAGGTACCAGGAA 59.496 50.000 15.94 5.50 35.89 3.36
6335 6951 9.649167 CTTCTCTGCATTCACATATATATCACA 57.351 33.333 0.00 0.00 0.00 3.58
6358 6974 1.204941 ACACCTCACGTATCCTGCTTC 59.795 52.381 0.00 0.00 0.00 3.86
6370 6986 2.604046 AATCGGCTCATACACCTCAC 57.396 50.000 0.00 0.00 0.00 3.51
6381 6997 0.040958 CCGCTGCATTAAATCGGCTC 60.041 55.000 0.00 0.00 33.36 4.70
6446 7062 1.435515 GCCAGCCGTCAAACAAACA 59.564 52.632 0.00 0.00 0.00 2.83
6476 7092 3.599285 GACCGATGGCCCGTGTGAA 62.599 63.158 0.00 0.00 0.00 3.18
6493 7109 1.367346 TAAGGGTTGCACATCCTGGA 58.633 50.000 0.00 0.00 0.00 3.86
6543 7160 6.667414 AGAAGTATCCATTGTGAAGAGAGAGT 59.333 38.462 0.00 0.00 0.00 3.24
6544 7161 7.111247 AGAAGTATCCATTGTGAAGAGAGAG 57.889 40.000 0.00 0.00 0.00 3.20
6545 7162 6.665248 TGAGAAGTATCCATTGTGAAGAGAGA 59.335 38.462 0.00 0.00 0.00 3.10
6557 7174 7.789202 ATAGTAGCACATGAGAAGTATCCAT 57.211 36.000 0.00 0.00 0.00 3.41
6637 8333 7.495934 AGGAAAATGGACTCTACATATTTGTCG 59.504 37.037 0.00 0.00 37.28 4.35
6746 8445 6.978080 ACAAGTTTTAAACCATGTGCAGTTAG 59.022 34.615 13.57 0.00 32.67 2.34
6753 8452 9.187455 GTACCAATACAAGTTTTAAACCATGTG 57.813 33.333 20.03 10.36 34.82 3.21
6782 8481 9.349713 TCCCGTAATAAGATAATTTTGCAATCT 57.650 29.630 0.00 0.00 0.00 2.40
6784 8483 9.912634 CATCCCGTAATAAGATAATTTTGCAAT 57.087 29.630 0.00 0.00 0.00 3.56
6787 8486 8.106247 TCCATCCCGTAATAAGATAATTTTGC 57.894 34.615 0.00 0.00 0.00 3.68
6788 8487 8.730680 CCTCCATCCCGTAATAAGATAATTTTG 58.269 37.037 0.00 0.00 0.00 2.44
6791 8490 6.069615 CCCCTCCATCCCGTAATAAGATAATT 60.070 42.308 0.00 0.00 0.00 1.40
6792 8491 5.428783 CCCCTCCATCCCGTAATAAGATAAT 59.571 44.000 0.00 0.00 0.00 1.28
6794 8493 4.359105 CCCCTCCATCCCGTAATAAGATA 58.641 47.826 0.00 0.00 0.00 1.98
6795 8494 3.182152 CCCCTCCATCCCGTAATAAGAT 58.818 50.000 0.00 0.00 0.00 2.40
6797 8496 1.628846 CCCCCTCCATCCCGTAATAAG 59.371 57.143 0.00 0.00 0.00 1.73
6801 8500 1.691337 CACCCCCTCCATCCCGTAA 60.691 63.158 0.00 0.00 0.00 3.18
6803 8502 2.480255 TAACACCCCCTCCATCCCGT 62.480 60.000 0.00 0.00 0.00 5.28
6805 8504 0.623617 ACTAACACCCCCTCCATCCC 60.624 60.000 0.00 0.00 0.00 3.85
6806 8505 1.296002 AACTAACACCCCCTCCATCC 58.704 55.000 0.00 0.00 0.00 3.51
6807 8506 3.134262 GTCTAACTAACACCCCCTCCATC 59.866 52.174 0.00 0.00 0.00 3.51
6808 8507 3.113043 GTCTAACTAACACCCCCTCCAT 58.887 50.000 0.00 0.00 0.00 3.41
6809 8508 2.113052 AGTCTAACTAACACCCCCTCCA 59.887 50.000 0.00 0.00 0.00 3.86
6818 8579 5.473846 CAGAGGTGTCTCAGTCTAACTAACA 59.526 44.000 0.00 0.00 42.34 2.41
6819 8580 5.706369 TCAGAGGTGTCTCAGTCTAACTAAC 59.294 44.000 0.00 0.00 42.34 2.34
6829 8590 2.937149 CAATGCATCAGAGGTGTCTCAG 59.063 50.000 0.00 0.00 42.34 3.35
6867 8628 4.690748 CACAGTTCACATTGTAACTCGGAT 59.309 41.667 8.01 0.00 33.72 4.18
6925 8686 8.414778 ACATTACCACTGACTAGCTAATTAGTC 58.585 37.037 13.91 7.32 46.27 2.59
6926 8687 8.307582 ACATTACCACTGACTAGCTAATTAGT 57.692 34.615 13.91 0.00 36.61 2.24
7007 8768 8.753133 ACTATATGTCTGTTCACATCAGAAAGA 58.247 33.333 0.00 0.00 42.42 2.52
7091 8853 6.156256 TCCATAGAAACTGTAGGTACAAGCAT 59.844 38.462 0.00 0.00 35.50 3.79
7094 8856 9.099454 GAAATCCATAGAAACTGTAGGTACAAG 57.901 37.037 0.00 0.00 35.50 3.16
7120 8882 2.615447 CCAGTCCCAATTCATGATCACG 59.385 50.000 0.00 0.00 0.00 4.35
7173 8936 0.673333 CCAACAGCTGCATCCGTACA 60.673 55.000 15.27 0.00 0.00 2.90
7263 9344 8.381387 GCAACTAACTAACTAGTAATGCAGAAC 58.619 37.037 0.00 0.00 34.99 3.01
7297 9378 4.042187 ACACTCCTAAGGACAAATCAAGCT 59.958 41.667 0.00 0.00 0.00 3.74
7360 9441 0.331616 AGGAGGGGTACATTGTTGCC 59.668 55.000 0.00 0.00 0.00 4.52
7391 9472 9.911788 ATACAAAACAGATAAGAGGATTCACAT 57.088 29.630 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.