Multiple sequence alignment - TraesCS3B01G427500

Loading Multiple Alignment...

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 TraesCS3B01G427500 chr3B 100.000 7436 0 0 1 7436 666454053 666461488 0.000000e+00 13732.0
1 TraesCS3B01G427500 chr3A 95.041 4719 176 26 1750 6436 642931364 642936056 0.000000e+00 7365.0
2 TraesCS3B01G427500 chr3A 84.037 1303 92 42 74 1316 642929586 642930832 0.000000e+00 1147.0
3 TraesCS3B01G427500 chr3A 86.106 511 48 15 1320 1811 642930864 642931370 5.110000e-146 529.0
4 TraesCS3B01G427500 chr3A 90.541 296 16 6 6457 6747 642936163 642936451 1.510000e-101 381.0
5 TraesCS3B01G427500 chr3A 82.671 277 36 10 3817 4092 144472909 144473174 1.250000e-57 235.0
6 TraesCS3B01G427500 chr3A 97.561 41 1 0 15 55 642929555 642929595 3.720000e-08 71.3
7 TraesCS3B01G427500 chr3D 94.010 2688 120 15 3773 6434 504749903 504752575 0.000000e+00 4034.0
8 TraesCS3B01G427500 chr3D 94.765 2044 79 14 1750 3777 504745156 504747187 0.000000e+00 3157.0
9 TraesCS3B01G427500 chr3D 86.750 1366 93 32 1 1322 504743324 504744645 0.000000e+00 1439.0
10 TraesCS3B01G427500 chr3D 90.323 496 41 6 1320 1811 504744670 504745162 1.750000e-180 643.0
11 TraesCS3B01G427500 chr3D 89.615 260 17 5 6497 6751 504752810 504753064 9.310000e-84 322.0
12 TraesCS3B01G427500 chr6B 87.043 656 59 17 6805 7436 34919057 34918404 0.000000e+00 717.0
13 TraesCS3B01G427500 chr2D 87.809 607 60 11 6843 7436 19607389 19606784 0.000000e+00 699.0
14 TraesCS3B01G427500 chr2D 81.250 192 27 6 4407 4596 606502888 606503072 6.010000e-31 147.0
15 TraesCS3B01G427500 chr1A 87.438 605 61 11 6843 7435 548799770 548800371 0.000000e+00 682.0
16 TraesCS3B01G427500 chr6D 87.331 592 63 9 6843 7424 455913858 455914447 0.000000e+00 667.0
17 TraesCS3B01G427500 chr7D 86.842 608 64 8 6843 7436 69077538 69078143 0.000000e+00 665.0
18 TraesCS3B01G427500 chr7D 86.184 608 67 9 6843 7436 554278499 554277895 6.290000e-180 641.0
19 TraesCS3B01G427500 chr7B 87.022 601 64 7 6848 7436 556454210 556454808 0.000000e+00 665.0
20 TraesCS3B01G427500 chr4B 85.870 644 69 14 6808 7435 537827084 537826447 0.000000e+00 665.0
21 TraesCS3B01G427500 chr5B 87.065 603 55 14 6846 7431 440565510 440566106 0.000000e+00 660.0


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 TraesCS3B01G427500 chr3B 666454053 666461488 7435 False 13732.00 13732 100.0000 1 7436 1 chr3B.!!$F1 7435
1 TraesCS3B01G427500 chr3A 642929555 642936451 6896 False 1898.66 7365 90.6572 15 6747 5 chr3A.!!$F2 6732
2 TraesCS3B01G427500 chr3D 504743324 504753064 9740 False 1919.00 4034 91.0926 1 6751 5 chr3D.!!$F1 6750
3 TraesCS3B01G427500 chr6B 34918404 34919057 653 True 717.00 717 87.0430 6805 7436 1 chr6B.!!$R1 631
4 TraesCS3B01G427500 chr2D 19606784 19607389 605 True 699.00 699 87.8090 6843 7436 1 chr2D.!!$R1 593
5 TraesCS3B01G427500 chr1A 548799770 548800371 601 False 682.00 682 87.4380 6843 7435 1 chr1A.!!$F1 592
6 TraesCS3B01G427500 chr6D 455913858 455914447 589 False 667.00 667 87.3310 6843 7424 1 chr6D.!!$F1 581
7 TraesCS3B01G427500 chr7D 69077538 69078143 605 False 665.00 665 86.8420 6843 7436 1 chr7D.!!$F1 593
8 TraesCS3B01G427500 chr7D 554277895 554278499 604 True 641.00 641 86.1840 6843 7436 1 chr7D.!!$R1 593
9 TraesCS3B01G427500 chr7B 556454210 556454808 598 False 665.00 665 87.0220 6848 7436 1 chr7B.!!$F1 588
10 TraesCS3B01G427500 chr4B 537826447 537827084 637 True 665.00 665 85.8700 6808 7435 1 chr4B.!!$R1 627
11 TraesCS3B01G427500 chr5B 440565510 440566106 596 False 660.00 660 87.0650 6846 7431 1 chr5B.!!$F1 585

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
988 1079 0.036858 AGGAAAACAGAGGAGCGAGC 60.037 55.000 0.00 0.00 0.00 5.03 F
1467 1610 0.035439 GGCTGGAGGATTTGGTCGAA 60.035 55.000 0.00 0.00 0.00 3.71 F
1718 1866 0.252881 TGGGAGGAGGAATGCTGACT 60.253 55.000 0.00 0.00 0.00 3.41 F
3187 3400 0.888736 CCATGTGGTGCCTCGTCAAA 60.889 55.000 0.00 0.00 0.00 2.69 F
4003 6943 0.380733 GGTGTATAAAAGCTGCGCCC 59.619 55.000 4.18 0.00 0.00 6.13 F
5775 8739 1.320555 CAGGCGTTATCTGAACGTTCG 59.679 52.381 22.48 16.77 44.69 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2701 2913 1.700955 TAGTACAGCGGGAGGGATTC 58.299 55.000 0.00 0.00 0.00 2.52 R
3339 3552 1.331399 TGGCACCATCCGTTCCGATA 61.331 55.000 0.00 0.00 28.74 2.92 R
3599 3812 1.996898 TGTATTGAACGCATCGTCACC 59.003 47.619 0.00 0.00 39.99 4.02 R
4421 7362 2.082231 AGCAACTATGAGCAAGCTGTG 58.918 47.619 0.00 0.00 0.00 3.66 R
5808 8772 0.241749 TCACGGTCTTGCGATAACGT 59.758 50.000 0.00 0.00 41.98 3.99 R
7060 10273 0.103026 TGAAGATGGGTCAGCGATCG 59.897 55.000 11.69 11.69 0.00 3.69 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
20 21 0.108329 ATCGTCATCGTGGGTGGAAC 60.108 55.000 0.00 0.00 38.33 3.62
63 64 3.918220 CAGCCGATCGTGCGCTTC 61.918 66.667 15.09 0.35 0.00 3.86
117 121 1.298859 GCGTTGCAGATTCCTTCCGT 61.299 55.000 0.00 0.00 0.00 4.69
143 147 1.003464 GGCCCAAACTTTGATGCCAAT 59.997 47.619 21.18 0.00 43.49 3.16
149 153 5.338219 CCCAAACTTTGATGCCAATGGAATA 60.338 40.000 2.05 0.00 32.91 1.75
156 160 7.342799 ACTTTGATGCCAATGGAATAGTACAAT 59.657 33.333 2.05 0.00 33.28 2.71
175 179 4.962362 ACAATTTGGAAGACATATTCCCCC 59.038 41.667 2.91 0.00 46.98 5.40
369 393 2.343387 GCCCAACACCAACATGGC 59.657 61.111 0.00 0.00 42.67 4.40
399 423 0.690192 TGAGACCCTGCCGATTTTCA 59.310 50.000 0.00 0.00 0.00 2.69
431 455 5.900865 AAAAAGAAAACTACACCGTTCCA 57.099 34.783 0.00 0.00 0.00 3.53
433 457 5.432885 AAAGAAAACTACACCGTTCCATG 57.567 39.130 0.00 0.00 0.00 3.66
434 458 4.345859 AGAAAACTACACCGTTCCATGA 57.654 40.909 0.00 0.00 0.00 3.07
435 459 4.062991 AGAAAACTACACCGTTCCATGAC 58.937 43.478 0.00 0.00 0.00 3.06
436 460 2.467566 AACTACACCGTTCCATGACC 57.532 50.000 0.00 0.00 0.00 4.02
437 461 0.245539 ACTACACCGTTCCATGACCG 59.754 55.000 0.00 0.00 0.00 4.79
438 462 0.528924 CTACACCGTTCCATGACCGA 59.471 55.000 0.00 0.00 0.00 4.69
469 528 6.940298 ACAAGAAAATCGAAGGAAATGGAGTA 59.060 34.615 0.00 0.00 0.00 2.59
470 529 7.611855 ACAAGAAAATCGAAGGAAATGGAGTAT 59.388 33.333 0.00 0.00 0.00 2.12
564 623 0.250684 ACCGCCAACACATGTGATCA 60.251 50.000 31.94 0.00 0.00 2.92
609 676 0.700564 AGTGTCCCTGCCAACATCAT 59.299 50.000 0.00 0.00 0.00 2.45
637 704 2.364722 TTTAGCAGCAGTGGGGCCAA 62.365 55.000 4.39 0.00 0.00 4.52
658 725 3.391965 ACACGGTACACTTTAAATGCGA 58.608 40.909 0.00 0.00 0.00 5.10
677 744 3.050619 CGAAAATTACCCTCGAGATCCG 58.949 50.000 15.71 0.40 40.25 4.18
714 781 4.290155 CAACCGAACCAAAAACATCTCAG 58.710 43.478 0.00 0.00 0.00 3.35
739 811 1.959747 CTGTGCGTTGCATTCAGAAG 58.040 50.000 4.00 0.00 41.91 2.85
750 829 6.492007 TTGCATTCAGAAGCAAAAACAAAA 57.508 29.167 14.15 0.00 46.65 2.44
751 830 6.492007 TGCATTCAGAAGCAAAAACAAAAA 57.508 29.167 5.19 0.00 37.90 1.94
775 854 8.479313 AAAACATTCAGAAAACAAGAGAAACC 57.521 30.769 0.00 0.00 0.00 3.27
776 855 5.821204 ACATTCAGAAAACAAGAGAAACCG 58.179 37.500 0.00 0.00 0.00 4.44
778 857 5.734855 TTCAGAAAACAAGAGAAACCGAG 57.265 39.130 0.00 0.00 0.00 4.63
779 858 4.127171 TCAGAAAACAAGAGAAACCGAGG 58.873 43.478 0.00 0.00 0.00 4.63
803 882 5.458891 CAAGAATCTGCAGTTTCAAAGAGG 58.541 41.667 29.91 14.18 0.00 3.69
814 893 5.767168 CAGTTTCAAAGAGGGAAGAATCTGT 59.233 40.000 0.00 0.00 35.04 3.41
815 894 6.000840 AGTTTCAAAGAGGGAAGAATCTGTC 58.999 40.000 0.00 0.00 0.00 3.51
816 895 4.559862 TCAAAGAGGGAAGAATCTGTCC 57.440 45.455 3.80 3.80 0.00 4.02
828 907 2.610438 ATCTGTCCCCAACTGCAAAT 57.390 45.000 0.00 0.00 0.00 2.32
836 915 7.180051 TCTGTCCCCAACTGCAAATATAAAAAT 59.820 33.333 0.00 0.00 0.00 1.82
975 1066 1.482365 GGGAAAAGGGGCAGAGGAAAA 60.482 52.381 0.00 0.00 0.00 2.29
976 1067 1.618837 GGAAAAGGGGCAGAGGAAAAC 59.381 52.381 0.00 0.00 0.00 2.43
977 1068 2.316108 GAAAAGGGGCAGAGGAAAACA 58.684 47.619 0.00 0.00 0.00 2.83
978 1069 2.001076 AAAGGGGCAGAGGAAAACAG 57.999 50.000 0.00 0.00 0.00 3.16
979 1070 1.149101 AAGGGGCAGAGGAAAACAGA 58.851 50.000 0.00 0.00 0.00 3.41
980 1071 0.695347 AGGGGCAGAGGAAAACAGAG 59.305 55.000 0.00 0.00 0.00 3.35
981 1072 0.322906 GGGGCAGAGGAAAACAGAGG 60.323 60.000 0.00 0.00 0.00 3.69
982 1073 0.693049 GGGCAGAGGAAAACAGAGGA 59.307 55.000 0.00 0.00 0.00 3.71
983 1074 1.339535 GGGCAGAGGAAAACAGAGGAG 60.340 57.143 0.00 0.00 0.00 3.69
984 1075 1.447945 GCAGAGGAAAACAGAGGAGC 58.552 55.000 0.00 0.00 0.00 4.70
985 1076 1.719600 CAGAGGAAAACAGAGGAGCG 58.280 55.000 0.00 0.00 0.00 5.03
986 1077 1.273606 CAGAGGAAAACAGAGGAGCGA 59.726 52.381 0.00 0.00 0.00 4.93
987 1078 1.548269 AGAGGAAAACAGAGGAGCGAG 59.452 52.381 0.00 0.00 0.00 5.03
988 1079 0.036858 AGGAAAACAGAGGAGCGAGC 60.037 55.000 0.00 0.00 0.00 5.03
989 1080 1.355066 GGAAAACAGAGGAGCGAGCG 61.355 60.000 0.00 0.00 0.00 5.03
990 1081 0.388649 GAAAACAGAGGAGCGAGCGA 60.389 55.000 0.00 0.00 0.00 4.93
991 1082 0.389166 AAAACAGAGGAGCGAGCGAG 60.389 55.000 0.00 0.00 0.00 5.03
992 1083 2.219325 AAACAGAGGAGCGAGCGAGG 62.219 60.000 0.00 0.00 0.00 4.63
993 1084 4.567385 CAGAGGAGCGAGCGAGGC 62.567 72.222 0.00 0.00 0.00 4.70
1065 1156 4.767255 CCAGCCACCGCCACTCTC 62.767 72.222 0.00 0.00 34.57 3.20
1124 1215 2.515057 TCGAGAGAGCGAGGGAGC 60.515 66.667 0.00 0.00 35.01 4.70
1168 1259 5.178797 CGGCCGATATCATATTTTCCTCTT 58.821 41.667 24.07 0.00 0.00 2.85
1180 1271 1.807814 TTCCTCTTATCCTGCCCTCC 58.192 55.000 0.00 0.00 0.00 4.30
1242 1339 2.659016 CTGGCGAGCTGAAGGTGA 59.341 61.111 0.00 0.00 0.00 4.02
1316 1417 0.676782 TCTGTCTGCGTGATCTCGGA 60.677 55.000 17.94 14.51 0.00 4.55
1317 1418 0.524392 CTGTCTGCGTGATCTCGGAC 60.524 60.000 17.94 16.43 0.00 4.79
1318 1419 1.241315 TGTCTGCGTGATCTCGGACA 61.241 55.000 18.82 18.82 32.75 4.02
1467 1610 0.035439 GGCTGGAGGATTTGGTCGAA 60.035 55.000 0.00 0.00 0.00 3.71
1470 1613 2.205074 CTGGAGGATTTGGTCGAATCG 58.795 52.381 0.00 0.00 36.99 3.34
1478 1621 3.306917 TTTGGTCGAATCGCTTCTGTA 57.693 42.857 0.00 0.00 0.00 2.74
1479 1622 2.273370 TGGTCGAATCGCTTCTGTAC 57.727 50.000 0.00 0.00 0.00 2.90
1481 1624 3.011818 TGGTCGAATCGCTTCTGTACTA 58.988 45.455 0.00 0.00 0.00 1.82
1502 1645 2.082366 GCGTGCGATTTTGTGCTGG 61.082 57.895 0.00 0.00 0.00 4.85
1566 1709 2.750350 CCCACCAGAAAGCGAGGT 59.250 61.111 0.00 0.00 35.65 3.85
1568 1711 3.257933 CACCAGAAAGCGAGGTGC 58.742 61.111 0.00 0.00 45.39 5.01
1597 1740 2.755952 AGGGTTATGGATTGAAGGGC 57.244 50.000 0.00 0.00 0.00 5.19
1599 1742 1.217942 GGGTTATGGATTGAAGGGCCT 59.782 52.381 0.00 0.00 0.00 5.19
1600 1743 2.310538 GGTTATGGATTGAAGGGCCTG 58.689 52.381 6.92 0.00 0.00 4.85
1604 1751 2.220653 TGGATTGAAGGGCCTGAAAG 57.779 50.000 6.92 0.00 0.00 2.62
1610 1757 3.652057 TGAAGGGCCTGAAAGAATAGG 57.348 47.619 6.92 0.00 34.07 2.57
1621 1768 7.215998 CCTGAAAGAATAGGATTTGCGGAGC 62.216 48.000 0.00 0.00 45.99 4.70
1635 1782 0.801067 CGGAGCGTGCTAGTGGTTAC 60.801 60.000 0.00 0.00 0.00 2.50
1680 1828 1.971357 AGAGTGGCTCTTTTCTTCGGA 59.029 47.619 0.00 0.00 37.60 4.55
1718 1866 0.252881 TGGGAGGAGGAATGCTGACT 60.253 55.000 0.00 0.00 0.00 3.41
1719 1867 0.915364 GGGAGGAGGAATGCTGACTT 59.085 55.000 0.00 0.00 0.00 3.01
1720 1868 1.407989 GGGAGGAGGAATGCTGACTTG 60.408 57.143 0.00 0.00 0.00 3.16
1723 1871 3.055094 GGAGGAGGAATGCTGACTTGTTA 60.055 47.826 0.00 0.00 0.00 2.41
1724 1872 4.187694 GAGGAGGAATGCTGACTTGTTAG 58.812 47.826 0.00 0.00 0.00 2.34
1725 1873 3.840666 AGGAGGAATGCTGACTTGTTAGA 59.159 43.478 0.00 0.00 0.00 2.10
1726 1874 4.472833 AGGAGGAATGCTGACTTGTTAGAT 59.527 41.667 0.00 0.00 0.00 1.98
1729 1877 6.823689 GGAGGAATGCTGACTTGTTAGATTTA 59.176 38.462 0.00 0.00 0.00 1.40
1730 1878 7.201652 GGAGGAATGCTGACTTGTTAGATTTAC 60.202 40.741 0.00 0.00 0.00 2.01
1777 1980 8.363390 GTTCTTTTCAAAATCATCTTTCTCCCT 58.637 33.333 0.00 0.00 0.00 4.20
1791 1994 7.125792 TCTTTCTCCCTATTTGTATCCAGTC 57.874 40.000 0.00 0.00 0.00 3.51
1826 2031 3.777106 AGTCTGCTGTGATTTGAGGAA 57.223 42.857 0.00 0.00 0.00 3.36
1854 2059 6.313519 AGAATCTAGATGGTTGGCTTGTTA 57.686 37.500 5.86 0.00 0.00 2.41
1976 2181 7.444299 AGTGCCATTGATTAATTGTTTCAGTT 58.556 30.769 0.00 0.00 0.00 3.16
1977 2182 7.933033 AGTGCCATTGATTAATTGTTTCAGTTT 59.067 29.630 0.00 0.00 0.00 2.66
2003 2208 8.634444 TCTGCTTTAGCCATTTTTACTTGTAAA 58.366 29.630 0.00 2.22 41.18 2.01
2013 2218 8.167985 CCATTTTTACTTGTAAATTGGCGATTG 58.832 33.333 16.00 0.00 32.50 2.67
2017 2222 5.895636 ACTTGTAAATTGGCGATTGATGA 57.104 34.783 0.00 0.00 0.00 2.92
2074 2286 9.937577 GTTTGTCGTAAAAGAAAAATCATATGC 57.062 29.630 0.00 0.00 30.89 3.14
2140 2352 6.199393 CACAGTGCTTTTCTTAGTTACCAAC 58.801 40.000 0.00 0.00 0.00 3.77
2235 2447 2.378208 TGGATCAGAACCCCATTTCACA 59.622 45.455 0.00 0.00 0.00 3.58
2269 2481 8.519799 TTTCATGACTTCTCAAGTTTAAGGTT 57.480 30.769 0.00 0.00 43.03 3.50
2283 2495 5.012871 AGTTTAAGGTTACTCCCTCCTTCAC 59.987 44.000 0.00 0.00 41.17 3.18
2531 2743 4.429108 TCAAAGAACGCCCAAAGAAAAAG 58.571 39.130 0.00 0.00 0.00 2.27
2662 2874 3.555966 AGCAATGACTATAAAGTGCCCC 58.444 45.455 0.00 0.00 35.56 5.80
2754 2966 4.320861 CGTTTGCTGGACAATGTTTCCATA 60.321 41.667 0.00 0.00 42.43 2.74
2988 3200 7.875971 ACATTTTCTTTCAAGTACCTGATGAC 58.124 34.615 0.00 0.00 0.00 3.06
3053 3265 4.734266 AGATGGCTTCTGTTTCCTTTTCT 58.266 39.130 1.57 0.00 31.79 2.52
3071 3283 2.239400 TCTGTCGGTGTGTCTCTTGAT 58.761 47.619 0.00 0.00 0.00 2.57
3117 3329 3.457560 AGTGGTCTACTGACAGGCA 57.542 52.632 7.51 0.00 44.61 4.75
3118 3330 1.717032 AGTGGTCTACTGACAGGCAA 58.283 50.000 7.51 0.00 44.61 4.52
3170 3383 7.363705 CCATTTTGAGTTGCATTATAAGGACCA 60.364 37.037 0.32 0.00 0.00 4.02
3187 3400 0.888736 CCATGTGGTGCCTCGTCAAA 60.889 55.000 0.00 0.00 0.00 2.69
3276 3489 4.541973 TCTCAAGTGTAGTGTGCATCAT 57.458 40.909 0.00 0.00 0.00 2.45
3339 3552 6.541641 TGGCATTTTTATTGCAGACAGTTTTT 59.458 30.769 0.00 0.00 41.95 1.94
3599 3812 2.632996 TCTTATAGAGTGGGGAATGCCG 59.367 50.000 0.00 0.00 33.83 5.69
3784 6723 5.370880 ACCCAGAACAATCTTAGCCTATCAT 59.629 40.000 0.00 0.00 32.03 2.45
3910 6849 5.804944 AGATATGCACTCAGCTAGTCAAT 57.195 39.130 0.00 0.00 45.94 2.57
3920 6859 7.678218 GCACTCAGCTAGTCAATGGAAAATAAG 60.678 40.741 0.00 0.00 41.15 1.73
4003 6943 0.380733 GGTGTATAAAAGCTGCGCCC 59.619 55.000 4.18 0.00 0.00 6.13
4151 7092 5.456173 TGCATTCCGTTTCGAAAAAGTAAAC 59.544 36.000 13.10 0.00 0.00 2.01
4339 7280 5.071115 AGGATACCTGAGACCTGCTTTTATC 59.929 44.000 0.00 0.00 29.57 1.75
4380 7321 6.480763 TGAGGAGTTTATTTGGTGCTGAATA 58.519 36.000 0.00 0.00 0.00 1.75
4421 7362 4.744795 TCTAATTGGAGAGGTGCTTCTC 57.255 45.455 3.11 3.11 42.31 2.87
4422 7363 4.096681 TCTAATTGGAGAGGTGCTTCTCA 58.903 43.478 12.32 0.00 44.34 3.27
4605 7546 7.716998 AGTTACTTGCCTTGAACATCCATATAG 59.283 37.037 0.00 0.00 0.00 1.31
4606 7547 5.380043 ACTTGCCTTGAACATCCATATAGG 58.620 41.667 0.00 0.00 39.47 2.57
4608 7549 6.101150 ACTTGCCTTGAACATCCATATAGGTA 59.899 38.462 0.00 0.00 39.02 3.08
4757 7698 3.944015 CAGGTAAAGCATCCCTCTTCAAG 59.056 47.826 0.00 0.00 0.00 3.02
4780 7721 4.046462 CCAATGCTTTCAGTTGACAAGTG 58.954 43.478 15.66 15.66 0.00 3.16
4793 7734 6.146837 CAGTTGACAAGTGAAGGATAGTTCAG 59.853 42.308 16.64 0.00 37.12 3.02
4868 7809 4.032960 TGGCTTGGTAGTCATCATGTTT 57.967 40.909 0.00 0.00 29.10 2.83
5221 8162 5.361857 AGCCTGAAATTTAATCCTGGTGATG 59.638 40.000 0.00 0.00 32.68 3.07
5249 8207 7.854422 GTGTGAACTTGCATATGAACTATCATG 59.146 37.037 6.97 0.00 45.82 3.07
5698 8662 6.292923 GTGGGTTATTGGGCTTAAACTTTTT 58.707 36.000 0.00 0.00 0.00 1.94
5775 8739 1.320555 CAGGCGTTATCTGAACGTTCG 59.679 52.381 22.48 16.77 44.69 3.95
5893 8857 2.344741 GCTTCGAACGCCTAACAGTAAG 59.655 50.000 0.00 0.00 0.00 2.34
5907 8871 2.037772 ACAGTAAGCTGGTGAGGACAAG 59.962 50.000 0.00 0.00 46.62 3.16
6031 8995 0.457853 TCGATCGAGGTTTCGGCTTG 60.458 55.000 15.15 0.00 46.67 4.01
6038 9002 2.668550 GTTTCGGCTTGGTCGGCT 60.669 61.111 0.00 0.00 0.00 5.52
6039 9003 1.375013 GTTTCGGCTTGGTCGGCTA 60.375 57.895 0.00 0.00 0.00 3.93
6082 9046 5.055265 TGGTTTCTGACAAATAAGGTGGA 57.945 39.130 0.00 0.00 0.00 4.02
6083 9047 5.640147 TGGTTTCTGACAAATAAGGTGGAT 58.360 37.500 0.00 0.00 0.00 3.41
6117 9081 1.815421 GCATCCTTGGATGCGACGT 60.815 57.895 30.88 0.00 46.69 4.34
6157 9121 1.956043 GCAATCTGCAACCGACCAA 59.044 52.632 0.00 0.00 44.26 3.67
6166 9130 1.399727 GCAACCGACCAAGTTTCATCG 60.400 52.381 0.00 0.00 0.00 3.84
6276 9249 7.536622 CGACGTCTTCTTACATGTAACTAACTT 59.463 37.037 14.35 4.70 0.00 2.66
6306 9279 3.500680 TCCGTTTCCTTTACATGCTGAAC 59.499 43.478 0.00 0.00 0.00 3.18
6338 9324 2.965572 ATATTTTGCGCCAACATGCT 57.034 40.000 4.18 0.00 0.00 3.79
6361 9347 2.065512 TGTCGAAACATCGATGGTGTG 58.934 47.619 28.09 17.95 44.29 3.82
6364 9350 1.453155 GAAACATCGATGGTGTGGCT 58.547 50.000 28.09 7.36 0.00 4.75
6373 9359 2.094803 CGATGGTGTGGCTGCAATAAAA 60.095 45.455 0.50 0.00 0.00 1.52
6374 9360 3.613671 CGATGGTGTGGCTGCAATAAAAA 60.614 43.478 0.50 0.00 0.00 1.94
6397 9383 8.696410 AAATATTACTTTGCCGTTATGTTTGG 57.304 30.769 0.00 0.00 0.00 3.28
6402 9388 2.107950 TGCCGTTATGTTTGGAGAGG 57.892 50.000 0.00 0.00 0.00 3.69
6436 9422 2.698803 ACATGCTTATCGTGCAGAACA 58.301 42.857 0.00 0.00 44.04 3.18
6437 9423 3.073678 ACATGCTTATCGTGCAGAACAA 58.926 40.909 0.00 0.00 44.04 2.83
6438 9424 3.501828 ACATGCTTATCGTGCAGAACAAA 59.498 39.130 0.00 0.00 44.04 2.83
6439 9425 4.156556 ACATGCTTATCGTGCAGAACAAAT 59.843 37.500 0.00 0.00 44.04 2.32
6440 9426 4.082274 TGCTTATCGTGCAGAACAAATG 57.918 40.909 0.00 0.00 35.31 2.32
6441 9427 3.501828 TGCTTATCGTGCAGAACAAATGT 59.498 39.130 0.00 0.00 35.31 2.71
6443 9429 4.917415 GCTTATCGTGCAGAACAAATGTTT 59.083 37.500 0.00 0.00 38.56 2.83
6444 9430 5.164158 GCTTATCGTGCAGAACAAATGTTTG 60.164 40.000 0.00 4.04 43.62 2.93
6445 9431 3.077229 TCGTGCAGAACAAATGTTTGG 57.923 42.857 9.98 0.00 42.34 3.28
6446 9432 1.522258 CGTGCAGAACAAATGTTTGGC 59.478 47.619 9.98 13.07 42.34 4.52
6447 9433 2.799207 CGTGCAGAACAAATGTTTGGCT 60.799 45.455 17.85 4.37 42.34 4.75
6450 9436 2.823984 CAGAACAAATGTTTGGCTGCA 58.176 42.857 9.98 0.00 42.34 4.41
6453 9439 4.989797 CAGAACAAATGTTTGGCTGCAATA 59.010 37.500 9.98 0.00 42.34 1.90
6454 9440 5.466058 CAGAACAAATGTTTGGCTGCAATAA 59.534 36.000 9.98 0.00 42.34 1.40
6455 9441 6.018098 CAGAACAAATGTTTGGCTGCAATAAA 60.018 34.615 9.98 0.00 42.34 1.40
6472 9544 5.106317 GCAATAAAAAGATTGTGACCGGAGA 60.106 40.000 9.46 0.00 38.77 3.71
6657 9841 4.541779 GAGCGTAGATCGACTGAATGAAT 58.458 43.478 4.39 0.00 42.86 2.57
6660 9844 4.740205 GCGTAGATCGACTGAATGAATGAA 59.260 41.667 4.39 0.00 42.86 2.57
6661 9845 5.232202 GCGTAGATCGACTGAATGAATGAAA 59.768 40.000 4.39 0.00 42.86 2.69
6662 9846 6.237835 GCGTAGATCGACTGAATGAATGAAAA 60.238 38.462 4.39 0.00 42.86 2.29
6663 9847 7.333269 CGTAGATCGACTGAATGAATGAAAAG 58.667 38.462 4.39 0.00 42.86 2.27
6665 9849 6.176183 AGATCGACTGAATGAATGAAAAGGT 58.824 36.000 0.00 0.00 0.00 3.50
6666 9850 5.862924 TCGACTGAATGAATGAAAAGGTC 57.137 39.130 0.00 0.00 0.00 3.85
6667 9851 4.388773 TCGACTGAATGAATGAAAAGGTCG 59.611 41.667 0.00 0.00 43.16 4.79
6668 9852 4.406943 GACTGAATGAATGAAAAGGTCGC 58.593 43.478 0.00 0.00 0.00 5.19
6669 9853 4.074970 ACTGAATGAATGAAAAGGTCGCT 58.925 39.130 0.00 0.00 0.00 4.93
6670 9854 4.083110 ACTGAATGAATGAAAAGGTCGCTG 60.083 41.667 0.00 0.00 0.00 5.18
6671 9855 3.191162 TGAATGAATGAAAAGGTCGCTGG 59.809 43.478 0.00 0.00 0.00 4.85
6672 9856 2.559698 TGAATGAAAAGGTCGCTGGA 57.440 45.000 0.00 0.00 0.00 3.86
6686 9870 3.618780 CTGGACTGGACTGGCCTGC 62.619 68.421 9.95 2.57 39.08 4.85
6709 9893 3.463704 TGGGAGAGCCTCTATCAGTCTAA 59.536 47.826 0.00 0.00 0.00 2.10
6751 9935 5.010282 AGGAAACGCAGGATTTAGATGTTT 58.990 37.500 0.00 0.00 0.00 2.83
6752 9936 5.476945 AGGAAACGCAGGATTTAGATGTTTT 59.523 36.000 0.00 0.00 0.00 2.43
6753 9937 6.015434 AGGAAACGCAGGATTTAGATGTTTTT 60.015 34.615 0.00 0.00 0.00 1.94
6776 9960 9.717942 TTTTTCTTTTCTTTTGGAATGACAGAA 57.282 25.926 0.00 0.00 33.53 3.02
6777 9961 9.889128 TTTTCTTTTCTTTTGGAATGACAGAAT 57.111 25.926 0.00 0.00 33.53 2.40
6778 9962 9.889128 TTTCTTTTCTTTTGGAATGACAGAATT 57.111 25.926 0.00 0.00 33.53 2.17
6779 9963 9.533253 TTCTTTTCTTTTGGAATGACAGAATTC 57.467 29.630 0.00 0.00 36.08 2.17
6790 9974 6.540438 AATGACAGAATTCCTGCATTCATT 57.460 33.333 0.65 8.48 46.81 2.57
6791 9975 5.319140 TGACAGAATTCCTGCATTCATTG 57.681 39.130 0.65 0.00 46.81 2.82
6792 9976 5.011586 TGACAGAATTCCTGCATTCATTGA 58.988 37.500 0.65 0.00 46.81 2.57
6793 9977 5.124936 TGACAGAATTCCTGCATTCATTGAG 59.875 40.000 0.65 0.00 46.81 3.02
6794 9978 5.258841 ACAGAATTCCTGCATTCATTGAGA 58.741 37.500 0.65 0.00 46.81 3.27
6795 9979 5.713389 ACAGAATTCCTGCATTCATTGAGAA 59.287 36.000 0.65 0.00 46.81 2.87
6796 9980 6.034591 CAGAATTCCTGCATTCATTGAGAAC 58.965 40.000 0.65 0.00 36.07 3.01
6797 9981 5.713389 AGAATTCCTGCATTCATTGAGAACA 59.287 36.000 0.65 0.00 39.49 3.18
6798 9982 5.988310 ATTCCTGCATTCATTGAGAACAA 57.012 34.783 0.00 0.00 39.49 2.83
6799 9983 5.787953 TTCCTGCATTCATTGAGAACAAA 57.212 34.783 0.00 0.00 39.49 2.83
6800 9984 5.988310 TCCTGCATTCATTGAGAACAAAT 57.012 34.783 0.00 0.00 39.49 2.32
6801 9985 5.716094 TCCTGCATTCATTGAGAACAAATG 58.284 37.500 0.00 0.00 39.49 2.32
6802 9986 5.477637 TCCTGCATTCATTGAGAACAAATGA 59.522 36.000 0.00 0.00 39.49 2.57
6803 9987 5.805486 CCTGCATTCATTGAGAACAAATGAG 59.195 40.000 0.00 0.00 39.49 2.90
6804 9988 6.335471 TGCATTCATTGAGAACAAATGAGT 57.665 33.333 0.00 0.00 39.49 3.41
6805 9989 6.751157 TGCATTCATTGAGAACAAATGAGTT 58.249 32.000 0.00 0.00 39.49 3.01
6806 9990 7.211573 TGCATTCATTGAGAACAAATGAGTTT 58.788 30.769 0.00 0.00 39.49 2.66
6841 10025 2.271173 GTTAAGACCCCCGGCCTG 59.729 66.667 0.00 0.00 0.00 4.85
6935 10134 6.367695 CACACACCTACAAAACTCGATAATGA 59.632 38.462 0.00 0.00 0.00 2.57
6993 10201 6.791299 GTCGATCCATCTATATAACGTATCGC 59.209 42.308 4.53 0.00 35.06 4.58
7041 10249 3.328382 AACGTACACCACATGCATACT 57.672 42.857 0.00 0.00 0.00 2.12
7042 10250 4.459390 AACGTACACCACATGCATACTA 57.541 40.909 0.00 0.00 0.00 1.82
7053 10266 0.462937 TGCATACTAACGCCGCCATT 60.463 50.000 0.00 0.00 0.00 3.16
7060 10273 0.736053 TAACGCCGCCATTTTCATCC 59.264 50.000 0.00 0.00 0.00 3.51
7087 10300 3.307506 CTGACCCATCTTCAGGAGAGAT 58.692 50.000 0.00 0.00 37.93 2.75
7301 10516 1.633852 GCAAGACGAAGCTGCTCCAG 61.634 60.000 1.00 0.00 34.12 3.86
7325 10540 1.446966 GCCTCTGTCTTCCAGCGTC 60.447 63.158 0.00 0.00 41.25 5.19
7326 10541 1.967535 CCTCTGTCTTCCAGCGTCA 59.032 57.895 0.00 0.00 41.25 4.35
7330 10545 0.600557 CTGTCTTCCAGCGTCACTCT 59.399 55.000 0.00 0.00 33.59 3.24
7362 10577 3.866449 GCTCCCAAGAGAGAAAACGACAT 60.866 47.826 0.00 0.00 43.39 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.081892 CAGGCGAGGAACAAGACATG 58.918 55.000 0.00 0.00 0.00 3.21
117 121 1.228429 CAAAGTTTGGGCCTCCGGA 60.228 57.895 2.93 2.93 35.24 5.14
149 153 6.833933 GGGGAATATGTCTTCCAAATTGTACT 59.166 38.462 5.31 0.00 45.51 2.73
156 160 2.685522 GCGGGGGAATATGTCTTCCAAA 60.686 50.000 5.31 0.00 45.51 3.28
231 235 2.272146 CAGTTGGGATGGGACGGG 59.728 66.667 0.00 0.00 0.00 5.28
234 238 1.755179 CATGTCAGTTGGGATGGGAC 58.245 55.000 0.00 0.00 0.00 4.46
369 393 1.871676 CAGGGTCTCATTCATCATGCG 59.128 52.381 0.00 0.00 32.13 4.73
414 438 3.187842 GGTCATGGAACGGTGTAGTTTTC 59.812 47.826 0.00 0.00 34.00 2.29
418 442 0.245539 CGGTCATGGAACGGTGTAGT 59.754 55.000 0.00 0.00 39.28 2.73
419 443 0.528924 TCGGTCATGGAACGGTGTAG 59.471 55.000 3.65 0.00 43.55 2.74
420 444 0.528924 CTCGGTCATGGAACGGTGTA 59.471 55.000 3.65 0.00 43.55 2.90
421 445 1.292223 CTCGGTCATGGAACGGTGT 59.708 57.895 3.65 0.00 43.55 4.16
422 446 0.320421 AACTCGGTCATGGAACGGTG 60.320 55.000 3.65 0.58 43.55 4.94
425 449 1.459592 GTCAAACTCGGTCATGGAACG 59.540 52.381 0.00 0.00 44.86 3.95
426 450 2.489971 TGTCAAACTCGGTCATGGAAC 58.510 47.619 0.00 0.00 0.00 3.62
427 451 2.920724 TGTCAAACTCGGTCATGGAA 57.079 45.000 0.00 0.00 0.00 3.53
428 452 2.367241 TCTTGTCAAACTCGGTCATGGA 59.633 45.455 0.00 0.00 0.00 3.41
429 453 2.766313 TCTTGTCAAACTCGGTCATGG 58.234 47.619 0.00 0.00 0.00 3.66
430 454 4.811555 TTTCTTGTCAAACTCGGTCATG 57.188 40.909 0.00 0.00 0.00 3.07
431 455 5.334105 CGATTTTCTTGTCAAACTCGGTCAT 60.334 40.000 0.00 0.00 35.76 3.06
433 457 4.210537 TCGATTTTCTTGTCAAACTCGGTC 59.789 41.667 6.03 0.00 38.37 4.79
434 458 4.124238 TCGATTTTCTTGTCAAACTCGGT 58.876 39.130 6.03 0.00 38.37 4.69
435 459 4.725556 TCGATTTTCTTGTCAAACTCGG 57.274 40.909 6.03 0.00 38.37 4.63
436 460 5.050363 TCCTTCGATTTTCTTGTCAAACTCG 60.050 40.000 0.00 0.00 38.88 4.18
437 461 6.300354 TCCTTCGATTTTCTTGTCAAACTC 57.700 37.500 0.00 0.00 0.00 3.01
438 462 6.693315 TTCCTTCGATTTTCTTGTCAAACT 57.307 33.333 0.00 0.00 0.00 2.66
501 560 1.550976 ACTCCCCGCAAAACAAAACAA 59.449 42.857 0.00 0.00 0.00 2.83
564 623 7.801716 TGGCTCACGCTTTAATTATTCTAAT 57.198 32.000 0.00 0.00 36.09 1.73
609 676 3.503363 CCACTGCTGCTAAAATGAGTGAA 59.497 43.478 13.57 0.00 34.06 3.18
637 704 3.391965 TCGCATTTAAAGTGTACCGTGT 58.608 40.909 0.00 0.00 0.00 4.49
658 725 2.434702 AGCGGATCTCGAGGGTAATTTT 59.565 45.455 13.56 0.00 42.43 1.82
677 744 1.603739 GTTGGGGTTGGTGAGGAGC 60.604 63.158 0.00 0.00 0.00 4.70
749 828 8.935844 GGTTTCTCTTGTTTTCTGAATGTTTTT 58.064 29.630 0.00 0.00 0.00 1.94
750 829 7.275560 CGGTTTCTCTTGTTTTCTGAATGTTTT 59.724 33.333 0.00 0.00 0.00 2.43
751 830 6.751888 CGGTTTCTCTTGTTTTCTGAATGTTT 59.248 34.615 0.00 0.00 0.00 2.83
752 831 6.094881 TCGGTTTCTCTTGTTTTCTGAATGTT 59.905 34.615 0.00 0.00 0.00 2.71
753 832 5.588648 TCGGTTTCTCTTGTTTTCTGAATGT 59.411 36.000 0.00 0.00 0.00 2.71
754 833 6.060028 TCGGTTTCTCTTGTTTTCTGAATG 57.940 37.500 0.00 0.00 0.00 2.67
755 834 5.239525 CCTCGGTTTCTCTTGTTTTCTGAAT 59.760 40.000 0.00 0.00 0.00 2.57
775 854 1.446907 AACTGCAGATTCTTGCCTCG 58.553 50.000 23.35 0.00 43.43 4.63
776 855 2.816087 TGAAACTGCAGATTCTTGCCTC 59.184 45.455 29.71 9.80 43.43 4.70
778 857 3.648339 TTGAAACTGCAGATTCTTGCC 57.352 42.857 29.71 10.87 43.43 4.52
779 858 4.863491 TCTTTGAAACTGCAGATTCTTGC 58.137 39.130 29.71 11.27 44.33 4.01
803 882 2.716217 CAGTTGGGGACAGATTCTTCC 58.284 52.381 6.42 6.42 44.54 3.46
814 893 7.609532 CCAAATTTTTATATTTGCAGTTGGGGA 59.390 33.333 0.00 0.00 41.82 4.81
815 894 7.392953 ACCAAATTTTTATATTTGCAGTTGGGG 59.607 33.333 0.00 0.00 41.82 4.96
816 895 8.334263 ACCAAATTTTTATATTTGCAGTTGGG 57.666 30.769 0.00 0.00 41.82 4.12
820 899 9.566432 TCCAAACCAAATTTTTATATTTGCAGT 57.434 25.926 0.00 0.00 41.82 4.40
828 907 8.495260 ACCCAAGTTCCAAACCAAATTTTTATA 58.505 29.630 0.00 0.00 0.00 0.98
836 915 2.763448 CTGACCCAAGTTCCAAACCAAA 59.237 45.455 0.00 0.00 0.00 3.28
900 990 0.744771 CACTAGGGAGGGCGCTTTTC 60.745 60.000 7.64 2.31 38.40 2.29
958 1049 2.091333 TCTGTTTTCCTCTGCCCCTTTT 60.091 45.455 0.00 0.00 0.00 2.27
975 1066 3.137459 CCTCGCTCGCTCCTCTGT 61.137 66.667 0.00 0.00 0.00 3.41
976 1067 4.567385 GCCTCGCTCGCTCCTCTG 62.567 72.222 0.00 0.00 0.00 3.35
989 1080 4.168291 CTCTCCTTGGCCCGCCTC 62.168 72.222 7.35 0.00 36.94 4.70
990 1081 4.722535 TCTCTCCTTGGCCCGCCT 62.723 66.667 7.35 0.00 36.94 5.52
991 1082 2.764637 TTTTCTCTCCTTGGCCCGCC 62.765 60.000 0.00 0.00 0.00 6.13
992 1083 0.681243 ATTTTCTCTCCTTGGCCCGC 60.681 55.000 0.00 0.00 0.00 6.13
993 1084 2.565841 CTATTTTCTCTCCTTGGCCCG 58.434 52.381 0.00 0.00 0.00 6.13
994 1085 2.937519 CCTATTTTCTCTCCTTGGCCC 58.062 52.381 0.00 0.00 0.00 5.80
995 1086 2.092158 AGCCTATTTTCTCTCCTTGGCC 60.092 50.000 0.00 0.00 39.90 5.36
996 1087 3.210227 GAGCCTATTTTCTCTCCTTGGC 58.790 50.000 0.00 0.00 39.40 4.52
997 1088 3.814625 GGAGCCTATTTTCTCTCCTTGG 58.185 50.000 0.00 0.00 41.35 3.61
1039 1130 2.362120 GGTGGCTGGCTGCAGAAT 60.362 61.111 20.43 0.00 45.15 2.40
1147 1238 8.207545 AGGATAAGAGGAAAATATGATATCGGC 58.792 37.037 0.00 0.00 0.00 5.54
1151 1242 8.277918 GGGCAGGATAAGAGGAAAATATGATAT 58.722 37.037 0.00 0.00 0.00 1.63
1152 1243 7.462328 AGGGCAGGATAAGAGGAAAATATGATA 59.538 37.037 0.00 0.00 0.00 2.15
1154 1245 5.612688 AGGGCAGGATAAGAGGAAAATATGA 59.387 40.000 0.00 0.00 0.00 2.15
1155 1246 5.885465 AGGGCAGGATAAGAGGAAAATATG 58.115 41.667 0.00 0.00 0.00 1.78
1168 1259 2.445845 CACGGGGAGGGCAGGATA 60.446 66.667 0.00 0.00 0.00 2.59
1266 1367 4.635765 CGCAGTCAATCTTAATTGGAGGAA 59.364 41.667 0.00 0.00 42.19 3.36
1267 1368 4.081142 TCGCAGTCAATCTTAATTGGAGGA 60.081 41.667 0.00 0.00 42.19 3.71
1316 1417 2.704190 TCTGTTCTCCTCCTCCTTGT 57.296 50.000 0.00 0.00 0.00 3.16
1317 1418 2.903135 ACTTCTGTTCTCCTCCTCCTTG 59.097 50.000 0.00 0.00 0.00 3.61
1318 1419 3.268034 ACTTCTGTTCTCCTCCTCCTT 57.732 47.619 0.00 0.00 0.00 3.36
1384 1513 3.023949 GCACCGATGGAGAGGCAGT 62.024 63.158 0.00 0.00 0.00 4.40
1388 1531 0.742281 CAGTTGCACCGATGGAGAGG 60.742 60.000 0.00 0.00 0.00 3.69
1393 1536 0.240945 GGAAACAGTTGCACCGATGG 59.759 55.000 0.00 0.00 0.00 3.51
1467 1610 2.032302 CACGCTCTAGTACAGAAGCGAT 59.968 50.000 29.93 17.53 45.63 4.58
1470 1613 1.551145 GCACGCTCTAGTACAGAAGC 58.449 55.000 0.00 0.00 31.12 3.86
1478 1621 1.726791 CACAAAATCGCACGCTCTAGT 59.273 47.619 0.00 0.00 0.00 2.57
1479 1622 1.527793 GCACAAAATCGCACGCTCTAG 60.528 52.381 0.00 0.00 0.00 2.43
1481 1624 1.207593 GCACAAAATCGCACGCTCT 59.792 52.632 0.00 0.00 0.00 4.09
1518 1661 2.096248 TCAAGAACACCGGCAAAACTT 58.904 42.857 0.00 0.00 0.00 2.66
1528 1671 1.941325 CCTAGCGGATCAAGAACACC 58.059 55.000 0.00 0.00 0.00 4.16
1566 1709 2.771943 CCATAACCCTAGTTCCTGAGCA 59.228 50.000 0.00 0.00 37.42 4.26
1568 1711 5.366768 TCAATCCATAACCCTAGTTCCTGAG 59.633 44.000 0.00 0.00 37.42 3.35
1597 1740 4.199310 TCCGCAAATCCTATTCTTTCAGG 58.801 43.478 0.00 0.00 0.00 3.86
1599 1742 3.627577 GCTCCGCAAATCCTATTCTTTCA 59.372 43.478 0.00 0.00 0.00 2.69
1600 1743 3.303395 CGCTCCGCAAATCCTATTCTTTC 60.303 47.826 0.00 0.00 0.00 2.62
1604 1751 1.261619 CACGCTCCGCAAATCCTATTC 59.738 52.381 0.00 0.00 0.00 1.75
1610 1757 1.084370 ACTAGCACGCTCCGCAAATC 61.084 55.000 0.00 0.00 0.00 2.17
1621 1768 2.030185 ACTCACAGTAACCACTAGCACG 60.030 50.000 0.00 0.00 32.21 5.34
1627 1774 1.128200 TGCCACTCACAGTAACCACT 58.872 50.000 0.00 0.00 34.42 4.00
1628 1775 1.961793 TTGCCACTCACAGTAACCAC 58.038 50.000 0.00 0.00 0.00 4.16
1635 1782 0.110056 GTGCGAATTGCCACTCACAG 60.110 55.000 0.00 0.00 45.60 3.66
1680 1828 4.012374 CCCAACTGCAATTCTACATGTCT 58.988 43.478 0.00 0.00 0.00 3.41
1726 1874 9.593134 ACAAACAACAGCTCATTTAAATGTAAA 57.407 25.926 23.95 7.78 37.65 2.01
1729 1877 7.981225 AGAACAAACAACAGCTCATTTAAATGT 59.019 29.630 23.95 6.80 37.65 2.71
1730 1878 8.356533 AGAACAAACAACAGCTCATTTAAATG 57.643 30.769 20.13 20.13 37.75 2.32
1736 1884 6.397272 TGAAAAGAACAAACAACAGCTCATT 58.603 32.000 0.00 0.00 0.00 2.57
1742 1890 9.693157 GATGATTTTGAAAAGAACAAACAACAG 57.307 29.630 0.00 0.00 37.05 3.16
1751 1899 8.363390 AGGGAGAAAGATGATTTTGAAAAGAAC 58.637 33.333 0.00 0.00 0.00 3.01
1791 1994 2.992543 GCAGACTAACAGAGCACAGAAG 59.007 50.000 0.00 0.00 0.00 2.85
1826 2031 5.463154 AGCCAACCATCTAGATTCTAGAGT 58.537 41.667 23.87 16.26 0.00 3.24
1832 2037 6.514048 GCATAACAAGCCAACCATCTAGATTC 60.514 42.308 1.33 0.00 0.00 2.52
1833 2038 5.300286 GCATAACAAGCCAACCATCTAGATT 59.700 40.000 1.33 0.00 0.00 2.40
1834 2039 4.823989 GCATAACAAGCCAACCATCTAGAT 59.176 41.667 0.00 0.00 0.00 1.98
1835 2040 4.080356 AGCATAACAAGCCAACCATCTAGA 60.080 41.667 0.00 0.00 0.00 2.43
1836 2041 4.202441 AGCATAACAAGCCAACCATCTAG 58.798 43.478 0.00 0.00 0.00 2.43
1837 2042 4.235079 AGCATAACAAGCCAACCATCTA 57.765 40.909 0.00 0.00 0.00 1.98
1838 2043 3.091633 AGCATAACAAGCCAACCATCT 57.908 42.857 0.00 0.00 0.00 2.90
1854 2059 4.411540 AGTGATCCCAATTCAGAGTAGCAT 59.588 41.667 0.00 0.00 0.00 3.79
1951 2156 6.996509 ACTGAAACAATTAATCAATGGCACT 58.003 32.000 0.00 0.00 0.00 4.40
1952 2157 7.656707 AACTGAAACAATTAATCAATGGCAC 57.343 32.000 0.00 0.00 0.00 5.01
1976 2181 7.049799 ACAAGTAAAAATGGCTAAAGCAGAA 57.950 32.000 4.07 0.00 44.36 3.02
1977 2182 6.648879 ACAAGTAAAAATGGCTAAAGCAGA 57.351 33.333 4.07 0.00 44.36 4.26
2003 2208 4.022068 ACAAAAGTGTCATCAATCGCCAAT 60.022 37.500 0.00 0.00 29.49 3.16
2140 2352 5.794687 TTATGTCTGCGAAAATACACCAG 57.205 39.130 0.00 0.00 0.00 4.00
2208 2420 3.713826 TGGGGTTCTGATCCAGTTTAC 57.286 47.619 7.06 0.00 32.61 2.01
2235 2447 4.533707 TGAGAAGTCATGAAATCTCTGGGT 59.466 41.667 26.81 4.14 39.21 4.51
2269 2481 2.180276 GAAGCAGTGAAGGAGGGAGTA 58.820 52.381 0.00 0.00 0.00 2.59
2283 2495 6.655003 TCATTTAAGGGAGTAAGTTGAAGCAG 59.345 38.462 0.00 0.00 0.00 4.24
2531 2743 5.724328 TCTACATCTGTCAGTGAAATGTCC 58.276 41.667 16.23 0.00 33.01 4.02
2626 2838 7.042797 AGTCATTGCTATGCCGAATTAAAAT 57.957 32.000 3.00 0.00 0.00 1.82
2662 2874 3.165058 TGTATGCTCAGACTTAAGCCG 57.835 47.619 1.29 0.00 37.73 5.52
2701 2913 1.700955 TAGTACAGCGGGAGGGATTC 58.299 55.000 0.00 0.00 0.00 2.52
2754 2966 3.701040 CCCTTGCTATTTGCCTACACAAT 59.299 43.478 0.00 0.00 42.00 2.71
2879 3091 7.144722 TCTTCTGTAAAATATGTGCTTGTGG 57.855 36.000 0.00 0.00 0.00 4.17
2881 3093 9.236006 AGATTCTTCTGTAAAATATGTGCTTGT 57.764 29.630 0.00 0.00 0.00 3.16
2917 3129 3.084039 AGTGTTAGATGCACAACATGGG 58.916 45.455 12.05 0.00 39.84 4.00
3036 3248 3.304057 CCGACAGAAAAGGAAACAGAAGC 60.304 47.826 0.00 0.00 0.00 3.86
3053 3265 3.614150 GCTTATCAAGAGACACACCGACA 60.614 47.826 0.00 0.00 0.00 4.35
3100 3312 2.543777 TTTGCCTGTCAGTAGACCAC 57.456 50.000 0.00 0.00 44.33 4.16
3118 3330 5.930837 TTGGAAGACAGTGAACCATTTTT 57.069 34.783 0.00 0.00 0.00 1.94
3123 3335 3.888930 GGAATTTGGAAGACAGTGAACCA 59.111 43.478 0.00 0.00 0.00 3.67
3170 3383 1.909700 AATTTGACGAGGCACCACAT 58.090 45.000 0.00 0.00 0.00 3.21
3179 3392 5.509972 CAGACTCGAGAACTAATTTGACGAG 59.490 44.000 21.68 0.00 46.80 4.18
3187 3400 8.304596 TCACAAAATACAGACTCGAGAACTAAT 58.695 33.333 21.68 11.31 0.00 1.73
3276 3489 4.782019 AATATTCTTGCAGCCAAAACGA 57.218 36.364 0.00 0.00 0.00 3.85
3301 3514 8.920665 CAATAAAAATGCCATTTCAGTCGTAAA 58.079 29.630 2.61 0.00 0.00 2.01
3339 3552 1.331399 TGGCACCATCCGTTCCGATA 61.331 55.000 0.00 0.00 28.74 2.92
3511 3724 7.229306 GGAGAGCATCAATAATGACATGGTTTA 59.771 37.037 0.00 0.00 38.69 2.01
3599 3812 1.996898 TGTATTGAACGCATCGTCACC 59.003 47.619 0.00 0.00 39.99 4.02
3808 6747 7.264373 AGCAAATCTTGAATTCTTATACCCG 57.736 36.000 7.05 0.00 0.00 5.28
4003 6943 2.886523 TCAGCAATCCACTCCAGTTTTG 59.113 45.455 0.00 0.00 0.00 2.44
4151 7092 2.842457 TGCTAGCCAATGCATCTACTG 58.158 47.619 13.29 0.00 41.13 2.74
4339 7280 6.626302 ACTCCTCAAATAAGACTCTTCTTCG 58.374 40.000 0.00 0.00 41.48 3.79
4380 7321 2.779755 TGAATAACCATCGGCACTGT 57.220 45.000 0.00 0.00 0.00 3.55
4421 7362 2.082231 AGCAACTATGAGCAAGCTGTG 58.918 47.619 0.00 0.00 0.00 3.66
4422 7363 2.486472 AGCAACTATGAGCAAGCTGT 57.514 45.000 0.00 0.00 0.00 4.40
4757 7698 2.798976 TGTCAACTGAAAGCATTGGC 57.201 45.000 0.00 0.00 37.60 4.52
4780 7721 8.569641 AGTAATACATCGACTGAACTATCCTTC 58.430 37.037 0.00 0.00 0.00 3.46
4868 7809 8.190122 GTGGATCAATCATAAACTGCAACAATA 58.810 33.333 0.00 0.00 0.00 1.90
5197 8138 4.934356 TCACCAGGATTAAATTTCAGGCT 58.066 39.130 0.00 0.00 0.00 4.58
5221 8162 5.362556 AGTTCATATGCAAGTTCACACAC 57.637 39.130 0.00 0.00 0.00 3.82
5249 8207 5.185828 ACCAGGATTAAATTTCAGGTGAAGC 59.814 40.000 0.00 0.00 35.21 3.86
5698 8662 4.919774 TGGAAATGCCAGAGGTACTTTA 57.080 40.909 0.00 0.00 43.33 1.85
5713 8677 5.901276 AGGTTATTCTGGATTGCATGGAAAT 59.099 36.000 2.94 0.00 0.00 2.17
5746 8710 3.751175 TCAGATAACGCCTGAAACCAAAG 59.249 43.478 0.00 0.00 37.68 2.77
5775 8739 1.202076 CGCTTGATCTTCTTTTCGGCC 60.202 52.381 0.00 0.00 0.00 6.13
5808 8772 0.241749 TCACGGTCTTGCGATAACGT 59.758 50.000 0.00 0.00 41.98 3.99
5831 8795 4.094887 GCTAACATTCATCTTCAGCGGAAA 59.905 41.667 0.00 0.00 31.35 3.13
5866 8830 3.808726 TGTTAGGCGTTCGAAGCTAAAAA 59.191 39.130 15.80 6.47 34.52 1.94
5893 8857 2.352805 CCCCTTGTCCTCACCAGC 59.647 66.667 0.00 0.00 0.00 4.85
5907 8871 2.034221 GAGTTCCCTGCACACCCC 59.966 66.667 0.00 0.00 0.00 4.95
6031 8995 2.963548 GGCCTTCTATATAGCCGACC 57.036 55.000 4.75 1.07 35.30 4.79
6038 9002 2.158279 TGGGTGGTCGGCCTTCTATATA 60.158 50.000 7.97 0.00 35.27 0.86
6039 9003 1.349067 GGGTGGTCGGCCTTCTATAT 58.651 55.000 7.97 0.00 35.27 0.86
6082 9046 3.199508 GGATGCTCCTCTATACATGGCAT 59.800 47.826 0.00 0.00 40.83 4.40
6083 9047 2.568956 GGATGCTCCTCTATACATGGCA 59.431 50.000 0.00 0.00 32.53 4.92
6117 9081 3.822192 CGACACCGGATCGCCTCA 61.822 66.667 9.46 0.00 31.96 3.86
6157 9121 4.941873 GGGAAACTTATGACCGATGAAACT 59.058 41.667 0.00 0.00 0.00 2.66
6166 9130 5.805728 TCTTTCAGAGGGAAACTTATGACC 58.194 41.667 0.00 0.00 40.51 4.02
6196 9160 3.719268 TGTATCCTGTGTTTCCTGCAT 57.281 42.857 0.00 0.00 0.00 3.96
6276 9249 2.859165 AAAGGAAACGGATGAGAGCA 57.141 45.000 0.00 0.00 0.00 4.26
6325 9298 4.045771 CAGCAGCATGTTGGCGCA 62.046 61.111 10.83 0.00 44.15 6.09
6361 9347 7.516627 CGGCAAAGTAATATTTTTATTGCAGCC 60.517 37.037 20.05 11.59 42.45 4.85
6364 9350 8.764524 AACGGCAAAGTAATATTTTTATTGCA 57.235 26.923 20.05 0.00 42.45 4.08
6373 9359 8.057536 TCCAAACATAACGGCAAAGTAATATT 57.942 30.769 0.00 0.00 0.00 1.28
6374 9360 7.554835 TCTCCAAACATAACGGCAAAGTAATAT 59.445 33.333 0.00 0.00 0.00 1.28
6391 9377 1.699083 TGTCTGATGCCTCTCCAAACA 59.301 47.619 0.00 0.00 0.00 2.83
6397 9383 3.603532 TGTTTCATGTCTGATGCCTCTC 58.396 45.455 0.00 0.00 0.00 3.20
6402 9388 3.777465 AGCATGTTTCATGTCTGATGC 57.223 42.857 10.68 11.89 35.05 3.91
6436 9422 7.748691 ATCTTTTTATTGCAGCCAAACATTT 57.251 28.000 0.00 0.00 34.05 2.32
6437 9423 7.229106 ACAATCTTTTTATTGCAGCCAAACATT 59.771 29.630 0.00 0.00 39.93 2.71
6438 9424 6.711645 ACAATCTTTTTATTGCAGCCAAACAT 59.288 30.769 0.00 0.00 39.93 2.71
6439 9425 6.018098 CACAATCTTTTTATTGCAGCCAAACA 60.018 34.615 0.00 0.00 39.93 2.83
6440 9426 6.202570 TCACAATCTTTTTATTGCAGCCAAAC 59.797 34.615 0.00 0.00 39.93 2.93
6441 9427 6.202570 GTCACAATCTTTTTATTGCAGCCAAA 59.797 34.615 0.00 0.00 39.93 3.28
6443 9429 5.229423 GTCACAATCTTTTTATTGCAGCCA 58.771 37.500 0.00 0.00 39.93 4.75
6444 9430 4.627035 GGTCACAATCTTTTTATTGCAGCC 59.373 41.667 0.00 0.00 39.93 4.85
6445 9431 4.324402 CGGTCACAATCTTTTTATTGCAGC 59.676 41.667 0.00 0.00 39.93 5.25
6446 9432 4.858692 CCGGTCACAATCTTTTTATTGCAG 59.141 41.667 0.00 0.00 39.93 4.41
6447 9433 4.520874 TCCGGTCACAATCTTTTTATTGCA 59.479 37.500 0.00 0.00 39.93 4.08
6449 9435 6.371548 TCTCTCCGGTCACAATCTTTTTATTG 59.628 38.462 0.00 0.00 41.65 1.90
6450 9436 6.472887 TCTCTCCGGTCACAATCTTTTTATT 58.527 36.000 0.00 0.00 0.00 1.40
6453 9439 4.351874 TCTCTCCGGTCACAATCTTTTT 57.648 40.909 0.00 0.00 0.00 1.94
6454 9440 4.559862 ATCTCTCCGGTCACAATCTTTT 57.440 40.909 0.00 0.00 0.00 2.27
6455 9441 4.559862 AATCTCTCCGGTCACAATCTTT 57.440 40.909 0.00 0.00 0.00 2.52
6472 9544 9.757227 GTATGAGCAAACACTATCTTCTAATCT 57.243 33.333 0.00 0.00 0.00 2.40
6645 9829 4.641954 CGACCTTTTCATTCATTCAGTCG 58.358 43.478 0.00 0.00 38.63 4.18
6649 9833 3.191162 CCAGCGACCTTTTCATTCATTCA 59.809 43.478 0.00 0.00 0.00 2.57
6657 9841 0.250295 CCAGTCCAGCGACCTTTTCA 60.250 55.000 0.00 0.00 40.12 2.69
6660 9844 1.122019 AGTCCAGTCCAGCGACCTTT 61.122 55.000 0.00 0.00 40.12 3.11
6661 9845 1.534235 AGTCCAGTCCAGCGACCTT 60.534 57.895 0.00 0.00 40.12 3.50
6662 9846 2.118513 AGTCCAGTCCAGCGACCT 59.881 61.111 0.00 0.00 40.12 3.85
6663 9847 2.262915 CAGTCCAGTCCAGCGACC 59.737 66.667 0.00 0.00 40.12 4.79
6665 9849 3.695606 GCCAGTCCAGTCCAGCGA 61.696 66.667 0.00 0.00 0.00 4.93
6666 9850 4.767255 GGCCAGTCCAGTCCAGCG 62.767 72.222 0.00 0.00 34.01 5.18
6667 9851 3.325753 AGGCCAGTCCAGTCCAGC 61.326 66.667 5.01 0.00 37.29 4.85
6668 9852 2.667418 CAGGCCAGTCCAGTCCAG 59.333 66.667 5.01 0.00 37.29 3.86
6669 9853 3.640407 GCAGGCCAGTCCAGTCCA 61.640 66.667 5.01 0.00 37.29 4.02
6670 9854 3.325753 AGCAGGCCAGTCCAGTCC 61.326 66.667 5.01 0.00 37.29 3.85
6671 9855 2.046507 CAGCAGGCCAGTCCAGTC 60.047 66.667 5.01 0.00 37.29 3.51
6672 9856 3.644606 CCAGCAGGCCAGTCCAGT 61.645 66.667 5.01 0.00 37.29 4.00
6686 9870 2.158475 AGACTGATAGAGGCTCTCCCAG 60.158 54.545 29.24 29.24 32.82 4.45
6751 9935 9.889128 ATTCTGTCATTCCAAAAGAAAAGAAAA 57.111 25.926 0.00 0.00 38.21 2.29
6752 9936 9.889128 AATTCTGTCATTCCAAAAGAAAAGAAA 57.111 25.926 0.00 0.00 38.21 2.52
6753 9937 9.533253 GAATTCTGTCATTCCAAAAGAAAAGAA 57.467 29.630 0.00 0.00 38.21 2.52
6767 9951 6.153851 TCAATGAATGCAGGAATTCTGTCATT 59.846 34.615 5.23 11.30 44.66 2.57
6768 9952 5.655090 TCAATGAATGCAGGAATTCTGTCAT 59.345 36.000 5.23 3.59 45.08 3.06
6769 9953 5.011586 TCAATGAATGCAGGAATTCTGTCA 58.988 37.500 5.23 1.31 45.08 3.58
6770 9954 5.356190 TCTCAATGAATGCAGGAATTCTGTC 59.644 40.000 5.23 0.00 45.08 3.51
6771 9955 5.258841 TCTCAATGAATGCAGGAATTCTGT 58.741 37.500 5.23 0.00 45.08 3.41
6772 9956 5.830000 TCTCAATGAATGCAGGAATTCTG 57.170 39.130 5.23 3.21 46.03 3.02
6773 9957 5.713389 TGTTCTCAATGAATGCAGGAATTCT 59.287 36.000 5.23 0.00 37.44 2.40
6774 9958 5.957798 TGTTCTCAATGAATGCAGGAATTC 58.042 37.500 0.00 0.00 36.99 2.17
6775 9959 5.988310 TGTTCTCAATGAATGCAGGAATT 57.012 34.783 0.00 0.00 36.99 2.17
6776 9960 5.988310 TTGTTCTCAATGAATGCAGGAAT 57.012 34.783 0.00 0.00 36.99 3.01
6777 9961 5.787953 TTTGTTCTCAATGAATGCAGGAA 57.212 34.783 0.00 0.00 36.99 3.36
6778 9962 5.477637 TCATTTGTTCTCAATGAATGCAGGA 59.522 36.000 0.00 0.00 36.99 3.86
6779 9963 5.716094 TCATTTGTTCTCAATGAATGCAGG 58.284 37.500 0.00 0.00 36.99 4.85
6780 9964 6.387465 ACTCATTTGTTCTCAATGAATGCAG 58.613 36.000 0.00 0.00 36.99 4.41
6781 9965 6.335471 ACTCATTTGTTCTCAATGAATGCA 57.665 33.333 0.00 0.00 36.99 3.96
6782 9966 7.647907 AAACTCATTTGTTCTCAATGAATGC 57.352 32.000 0.00 0.00 36.99 3.56
6841 10025 7.865385 TGTTGAATAATAAATAAAGATGGCCGC 59.135 33.333 0.00 0.00 0.00 6.53
6911 10110 6.460781 TCATTATCGAGTTTTGTAGGTGTGT 58.539 36.000 0.00 0.00 0.00 3.72
6993 10201 3.198236 CTGCACCGGCTGTTGGTTG 62.198 63.158 0.00 0.00 37.72 3.77
7041 10249 0.736053 GGATGAAAATGGCGGCGTTA 59.264 50.000 17.60 1.73 0.00 3.18
7042 10250 1.510844 GGATGAAAATGGCGGCGTT 59.489 52.632 11.16 11.16 0.00 4.84
7053 10266 0.179084 GGGTCAGCGATCGGATGAAA 60.179 55.000 18.30 0.00 43.79 2.69
7060 10273 0.103026 TGAAGATGGGTCAGCGATCG 59.897 55.000 11.69 11.69 0.00 3.69
7087 10300 2.158769 ACTGGCAAGGATGATGCGAATA 60.159 45.455 0.00 0.00 44.75 1.75
7301 10516 1.220477 GGAAGACAGAGGCAGGAGC 59.780 63.158 0.00 0.00 41.10 4.70
7325 10540 2.271800 GGGAGCATCGTTTGTAGAGTG 58.728 52.381 0.00 0.00 34.37 3.51
7326 10541 1.899814 TGGGAGCATCGTTTGTAGAGT 59.100 47.619 0.00 0.00 34.37 3.24
7330 10545 2.565391 TCTCTTGGGAGCATCGTTTGTA 59.435 45.455 0.00 0.00 39.31 2.41
7362 10577 3.405592 GACGATGGCGGTACTGCGA 62.406 63.158 20.17 17.26 43.17 5.10
7414 10629 2.919856 ACCCACTCGTGCTGCTCT 60.920 61.111 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.