Multiple sequence alignment - TraesCS2B01G545800

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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 TraesCS2B01G545800 chr2B 100.000 3158 0 0 1 3158 742549138 742545981 0.000000e+00 5832.0
1 TraesCS2B01G545800 chr2B 98.404 564 9 0 1 564 416824814 416824251 0.000000e+00 992.0
2 TraesCS2B01G545800 chr2B 98.404 564 9 0 1 564 640106794 640106231 0.000000e+00 992.0
3 TraesCS2B01G545800 chr2B 98.050 564 11 0 1 564 683670853 683670290 0.000000e+00 981.0
4 TraesCS2B01G545800 chr2B 99.652 287 1 0 564 850 640105917 640105631 2.790000e-145 525.0
5 TraesCS2B01G545800 chr2B 97.917 288 6 0 564 851 683669976 683669689 1.690000e-137 499.0
6 TraesCS2B01G545800 chr3D 95.941 2316 73 10 851 3158 77344559 77346861 0.000000e+00 3736.0
7 TraesCS2B01G545800 chr3D 97.378 1144 29 1 851 1993 604383153 604382010 0.000000e+00 1945.0
8 TraesCS2B01G545800 chr3D 96.251 987 19 3 2173 3158 604381671 604380702 0.000000e+00 1602.0
9 TraesCS2B01G545800 chr3D 87.719 57 3 2 2116 2168 196388142 196388198 2.630000e-06 63.9
10 TraesCS2B01G545800 chr3A 95.408 2330 80 8 851 3158 24108845 24106521 0.000000e+00 3685.0
11 TraesCS2B01G545800 chr3A 93.863 1222 55 4 851 2053 37970915 37972135 0.000000e+00 1823.0
12 TraesCS2B01G545800 chr3A 95.361 776 29 4 2100 2873 37972397 37973167 0.000000e+00 1227.0
13 TraesCS2B01G545800 chr3A 95.533 291 12 1 2869 3158 37981710 37982000 6.170000e-127 464.0
14 TraesCS2B01G545800 chr7B 94.721 2330 94 10 851 3158 252387995 252385673 0.000000e+00 3594.0
15 TraesCS2B01G545800 chr7B 96.233 292 11 0 561 852 15037225 15037516 2.200000e-131 479.0
16 TraesCS2B01G545800 chr6D 94.193 1481 58 16 1694 3158 458414976 458413508 0.000000e+00 2233.0
17 TraesCS2B01G545800 chr6D 95.275 783 28 2 851 1624 458415758 458414976 0.000000e+00 1232.0
18 TraesCS2B01G545800 chr6D 94.891 783 31 2 851 1624 458425499 458424717 0.000000e+00 1216.0
19 TraesCS2B01G545800 chr6D 97.118 694 18 2 2467 3158 458423586 458422893 0.000000e+00 1170.0
20 TraesCS2B01G545800 chr6D 93.924 395 13 2 1694 2078 458424717 458424324 1.260000e-163 586.0
21 TraesCS2B01G545800 chr7D 90.770 1246 71 21 851 2065 540633397 540634629 0.000000e+00 1624.0
22 TraesCS2B01G545800 chr4B 91.154 927 67 5 2235 3158 133361787 133362701 0.000000e+00 1243.0
23 TraesCS2B01G545800 chr4B 82.070 976 102 33 1176 2115 133360442 133361380 0.000000e+00 765.0
24 TraesCS2B01G545800 chr4B 98.276 290 5 0 564 853 66093080 66092791 2.810000e-140 508.0
25 TraesCS2B01G545800 chr4B 93.548 62 4 0 2115 2176 133361414 133361475 3.350000e-15 93.5
26 TraesCS2B01G545800 chr2D 90.183 927 59 9 2235 3158 615215477 615216374 0.000000e+00 1179.0
27 TraesCS2B01G545800 chr2D 97.872 564 12 0 1 564 178273752 178274315 0.000000e+00 976.0
28 TraesCS2B01G545800 chr2D 85.163 984 80 19 1176 2115 615213990 615214951 0.000000e+00 948.0
29 TraesCS2B01G545800 chr6A 88.216 925 85 15 2235 3151 113308774 113309682 0.000000e+00 1083.0
30 TraesCS2B01G545800 chr6A 87.581 926 91 14 2235 3151 113085659 113086569 0.000000e+00 1051.0
31 TraesCS2B01G545800 chr6A 82.816 902 87 31 1225 2084 113307547 113308422 0.000000e+00 745.0
32 TraesCS2B01G545800 chr6A 82.652 807 85 19 1225 2001 113071035 113071816 0.000000e+00 664.0
33 TraesCS2B01G545800 chr3B 98.404 564 9 0 1 564 752282641 752283204 0.000000e+00 992.0
34 TraesCS2B01G545800 chr3B 98.621 290 4 0 561 850 752283515 752283804 6.040000e-142 514.0
35 TraesCS2B01G545800 chr3B 97.938 291 6 0 561 851 312175152 312175442 3.640000e-139 505.0
36 TraesCS2B01G545800 chr6B 98.227 564 10 0 1 564 440784159 440784722 0.000000e+00 987.0
37 TraesCS2B01G545800 chr6B 98.227 564 10 0 1 564 646623960 646623397 0.000000e+00 987.0
38 TraesCS2B01G545800 chr6B 98.258 287 5 0 564 850 646623083 646622797 1.310000e-138 503.0
39 TraesCS2B01G545800 chr6B 97.251 291 7 1 561 851 440785033 440785322 2.830000e-135 492.0
40 TraesCS2B01G545800 chr1B 98.227 564 10 0 1 564 277435094 277434531 0.000000e+00 987.0
41 TraesCS2B01G545800 chr1B 97.586 290 4 1 564 853 277434217 277433931 7.870000e-136 494.0
42 TraesCS2B01G545800 chr4A 98.050 564 11 0 1 564 647217954 647218517 0.000000e+00 981.0
43 TraesCS2B01G545800 chr4A 86.885 61 4 2 2112 2168 571128024 571128084 7.310000e-07 65.8
44 TraesCS2B01G545800 chr7A 85.714 217 25 3 851 1067 109848358 109848148 1.140000e-54 224.0
45 TraesCS2B01G545800 chr7A 84.112 214 25 5 853 1064 732710041 732710247 6.910000e-47 198.0
46 TraesCS2B01G545800 chr1D 86.885 61 4 2 2112 2168 125788204 125788264 7.310000e-07 65.8


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 TraesCS2B01G545800 chr2B 742545981 742549138 3157 True 5832.000000 5832 100.0000 1 3158 1 chr2B.!!$R2 3157
1 TraesCS2B01G545800 chr2B 416824251 416824814 563 True 992.000000 992 98.4040 1 564 1 chr2B.!!$R1 563
2 TraesCS2B01G545800 chr2B 640105631 640106794 1163 True 758.500000 992 99.0280 1 850 2 chr2B.!!$R3 849
3 TraesCS2B01G545800 chr2B 683669689 683670853 1164 True 740.000000 981 97.9835 1 851 2 chr2B.!!$R4 850
4 TraesCS2B01G545800 chr3D 77344559 77346861 2302 False 3736.000000 3736 95.9410 851 3158 1 chr3D.!!$F1 2307
5 TraesCS2B01G545800 chr3D 604380702 604383153 2451 True 1773.500000 1945 96.8145 851 3158 2 chr3D.!!$R1 2307
6 TraesCS2B01G545800 chr3A 24106521 24108845 2324 True 3685.000000 3685 95.4080 851 3158 1 chr3A.!!$R1 2307
7 TraesCS2B01G545800 chr3A 37970915 37973167 2252 False 1525.000000 1823 94.6120 851 2873 2 chr3A.!!$F2 2022
8 TraesCS2B01G545800 chr7B 252385673 252387995 2322 True 3594.000000 3594 94.7210 851 3158 1 chr7B.!!$R1 2307
9 TraesCS2B01G545800 chr6D 458413508 458415758 2250 True 1732.500000 2233 94.7340 851 3158 2 chr6D.!!$R1 2307
10 TraesCS2B01G545800 chr6D 458422893 458425499 2606 True 990.666667 1216 95.3110 851 3158 3 chr6D.!!$R2 2307
11 TraesCS2B01G545800 chr7D 540633397 540634629 1232 False 1624.000000 1624 90.7700 851 2065 1 chr7D.!!$F1 1214
12 TraesCS2B01G545800 chr4B 133360442 133362701 2259 False 700.500000 1243 88.9240 1176 3158 3 chr4B.!!$F1 1982
13 TraesCS2B01G545800 chr2D 615213990 615216374 2384 False 1063.500000 1179 87.6730 1176 3158 2 chr2D.!!$F2 1982
14 TraesCS2B01G545800 chr2D 178273752 178274315 563 False 976.000000 976 97.8720 1 564 1 chr2D.!!$F1 563
15 TraesCS2B01G545800 chr6A 113085659 113086569 910 False 1051.000000 1051 87.5810 2235 3151 1 chr6A.!!$F2 916
16 TraesCS2B01G545800 chr6A 113307547 113309682 2135 False 914.000000 1083 85.5160 1225 3151 2 chr6A.!!$F3 1926
17 TraesCS2B01G545800 chr6A 113071035 113071816 781 False 664.000000 664 82.6520 1225 2001 1 chr6A.!!$F1 776
18 TraesCS2B01G545800 chr3B 752282641 752283804 1163 False 753.000000 992 98.5125 1 850 2 chr3B.!!$F2 849
19 TraesCS2B01G545800 chr6B 646622797 646623960 1163 True 745.000000 987 98.2425 1 850 2 chr6B.!!$R1 849
20 TraesCS2B01G545800 chr6B 440784159 440785322 1163 False 739.500000 987 97.7390 1 851 2 chr6B.!!$F1 850
21 TraesCS2B01G545800 chr1B 277433931 277435094 1163 True 740.500000 987 97.9065 1 853 2 chr1B.!!$R1 852
22 TraesCS2B01G545800 chr4A 647217954 647218517 563 False 981.000000 981 98.0500 1 564 1 chr4A.!!$F2 563

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
754 755 0.032615 CCTGGGCCTCACTCTAGACT 60.033 60.0 4.53 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 3140 6.292865 GCTAGTGTGATAAATGCTCGCAAATA 60.293 38.462 0.0 0.0 35.11 1.4 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
122 123 1.222661 CTAGCTGCCCAGTGATGCA 59.777 57.895 0.00 7.04 35.86 3.96
213 214 4.973168 ACAAGGAGAAATGAAGTGCACTA 58.027 39.130 22.01 5.63 0.00 2.74
219 220 3.327757 AGAAATGAAGTGCACTACTGGGA 59.672 43.478 22.01 0.72 40.26 4.37
270 271 7.907389 TCCATATCTCTTTAGTTGAAGTGTGT 58.093 34.615 0.00 0.00 0.00 3.72
280 281 4.202441 AGTTGAAGTGTGTTGCTCAAGAT 58.798 39.130 0.00 0.00 0.00 2.40
282 283 5.126061 AGTTGAAGTGTGTTGCTCAAGATTT 59.874 36.000 0.00 0.00 0.00 2.17
564 565 2.806434 ACACCCAATTTGATAGCAGCA 58.194 42.857 0.00 0.00 0.00 4.41
566 567 3.018856 CACCCAATTTGATAGCAGCAGA 58.981 45.455 0.00 0.00 0.00 4.26
567 568 3.019564 ACCCAATTTGATAGCAGCAGAC 58.980 45.455 0.00 0.00 0.00 3.51
568 569 3.018856 CCCAATTTGATAGCAGCAGACA 58.981 45.455 0.00 0.00 0.00 3.41
570 571 3.943381 CCAATTTGATAGCAGCAGACAGA 59.057 43.478 0.00 0.00 0.00 3.41
571 572 4.579340 CCAATTTGATAGCAGCAGACAGAT 59.421 41.667 0.00 0.00 0.00 2.90
572 573 5.277876 CCAATTTGATAGCAGCAGACAGATC 60.278 44.000 0.00 0.00 0.00 2.75
575 576 0.033228 ATAGCAGCAGACAGATCCGC 59.967 55.000 0.00 0.00 0.00 5.54
577 578 2.898738 CAGCAGACAGATCCGCCT 59.101 61.111 0.00 0.00 0.00 5.52
578 579 1.521010 CAGCAGACAGATCCGCCTG 60.521 63.158 0.00 0.00 39.93 4.85
579 580 1.683707 AGCAGACAGATCCGCCTGA 60.684 57.895 0.00 0.00 37.59 3.86
581 582 0.179062 GCAGACAGATCCGCCTGAAT 60.179 55.000 0.00 0.00 37.59 2.57
582 583 1.863267 CAGACAGATCCGCCTGAATC 58.137 55.000 0.00 0.00 37.59 2.52
583 584 1.137675 CAGACAGATCCGCCTGAATCA 59.862 52.381 0.00 0.00 37.59 2.57
584 585 1.137872 AGACAGATCCGCCTGAATCAC 59.862 52.381 0.00 0.00 37.59 3.06
585 586 0.179000 ACAGATCCGCCTGAATCACC 59.821 55.000 0.00 0.00 37.59 4.02
586 587 0.467384 CAGATCCGCCTGAATCACCT 59.533 55.000 0.00 0.00 36.29 4.00
589 590 0.179000 ATCCGCCTGAATCACCTCAC 59.821 55.000 0.00 0.00 0.00 3.51
591 592 1.811266 CGCCTGAATCACCTCACCG 60.811 63.158 0.00 0.00 0.00 4.94
593 594 1.450312 CCTGAATCACCTCACCGGC 60.450 63.158 0.00 0.00 35.61 6.13
594 595 1.296392 CTGAATCACCTCACCGGCA 59.704 57.895 0.00 0.00 35.61 5.69
595 596 0.742281 CTGAATCACCTCACCGGCAG 60.742 60.000 0.00 0.00 35.61 4.85
596 597 2.045926 AATCACCTCACCGGCAGC 60.046 61.111 0.00 0.00 35.61 5.25
597 598 3.958147 AATCACCTCACCGGCAGCG 62.958 63.158 0.00 0.00 35.61 5.18
599 600 4.457496 CACCTCACCGGCAGCGAT 62.457 66.667 0.00 0.00 35.61 4.58
600 601 3.706373 ACCTCACCGGCAGCGATT 61.706 61.111 0.00 0.00 35.61 3.34
601 602 2.436646 CCTCACCGGCAGCGATTT 60.437 61.111 0.00 0.00 0.00 2.17
602 603 2.464459 CCTCACCGGCAGCGATTTC 61.464 63.158 0.00 0.00 0.00 2.17
603 604 1.741401 CTCACCGGCAGCGATTTCA 60.741 57.895 0.00 0.00 0.00 2.69
604 605 1.078497 TCACCGGCAGCGATTTCAT 60.078 52.632 0.00 0.00 0.00 2.57
605 606 1.063006 CACCGGCAGCGATTTCATG 59.937 57.895 0.00 0.00 0.00 3.07
606 607 2.114670 ACCGGCAGCGATTTCATGG 61.115 57.895 0.00 0.00 0.00 3.66
607 608 2.717485 CGGCAGCGATTTCATGGG 59.283 61.111 0.00 0.00 0.00 4.00
608 609 2.114670 CGGCAGCGATTTCATGGGT 61.115 57.895 0.00 0.00 0.00 4.51
609 610 1.434696 GGCAGCGATTTCATGGGTG 59.565 57.895 0.00 0.00 39.13 4.61
610 611 1.434696 GCAGCGATTTCATGGGTGG 59.565 57.895 0.00 0.00 37.05 4.61
611 612 1.434696 CAGCGATTTCATGGGTGGC 59.565 57.895 0.00 0.00 33.63 5.01
612 613 2.114670 AGCGATTTCATGGGTGGCG 61.115 57.895 0.00 0.00 0.00 5.69
613 614 3.110139 CGATTTCATGGGTGGCGG 58.890 61.111 0.00 0.00 0.00 6.13
614 615 2.807622 GATTTCATGGGTGGCGGC 59.192 61.111 0.00 0.00 0.00 6.53
615 616 1.754234 GATTTCATGGGTGGCGGCT 60.754 57.895 11.43 0.00 0.00 5.52
616 617 2.008268 GATTTCATGGGTGGCGGCTG 62.008 60.000 11.43 0.00 0.00 4.85
617 618 4.738998 TTCATGGGTGGCGGCTGG 62.739 66.667 11.43 0.00 0.00 4.85
619 620 4.738998 CATGGGTGGCGGCTGGAA 62.739 66.667 11.43 0.00 0.00 3.53
620 621 4.431131 ATGGGTGGCGGCTGGAAG 62.431 66.667 11.43 0.00 0.00 3.46
622 623 4.785453 GGGTGGCGGCTGGAAGAG 62.785 72.222 11.43 0.00 34.07 2.85
623 624 4.785453 GGTGGCGGCTGGAAGAGG 62.785 72.222 11.43 0.00 34.07 3.69
624 625 4.785453 GTGGCGGCTGGAAGAGGG 62.785 72.222 11.43 0.00 34.07 4.30
626 627 4.475135 GGCGGCTGGAAGAGGGAC 62.475 72.222 0.00 0.00 34.07 4.46
628 629 2.058595 GCGGCTGGAAGAGGGACTA 61.059 63.158 0.00 0.00 41.55 2.59
629 630 2.022240 GCGGCTGGAAGAGGGACTAG 62.022 65.000 0.00 0.00 41.55 2.57
630 631 1.395826 CGGCTGGAAGAGGGACTAGG 61.396 65.000 0.00 0.00 41.55 3.02
631 632 1.051556 GGCTGGAAGAGGGACTAGGG 61.052 65.000 0.00 0.00 41.55 3.53
632 633 0.325765 GCTGGAAGAGGGACTAGGGT 60.326 60.000 0.00 0.00 41.55 4.34
633 634 1.902141 GCTGGAAGAGGGACTAGGGTT 60.902 57.143 0.00 0.00 41.55 4.11
634 635 2.552367 CTGGAAGAGGGACTAGGGTTT 58.448 52.381 0.00 0.00 41.55 3.27
635 636 2.237392 CTGGAAGAGGGACTAGGGTTTG 59.763 54.545 0.00 0.00 41.55 2.93
636 637 1.560146 GGAAGAGGGACTAGGGTTTGG 59.440 57.143 0.00 0.00 41.55 3.28
637 638 2.267192 GAAGAGGGACTAGGGTTTGGT 58.733 52.381 0.00 0.00 41.55 3.67
638 639 1.954035 AGAGGGACTAGGGTTTGGTC 58.046 55.000 0.00 0.00 41.55 4.02
639 640 0.910338 GAGGGACTAGGGTTTGGTCC 59.090 60.000 0.00 0.00 46.14 4.46
640 641 0.496841 AGGGACTAGGGTTTGGTCCT 59.503 55.000 9.17 0.00 46.11 3.85
641 642 0.618981 GGGACTAGGGTTTGGTCCTG 59.381 60.000 9.17 0.00 46.11 3.86
642 643 0.618981 GGACTAGGGTTTGGTCCTGG 59.381 60.000 0.00 0.00 44.21 4.45
643 644 1.359168 GACTAGGGTTTGGTCCTGGT 58.641 55.000 0.00 0.00 46.61 4.00
644 645 1.359168 ACTAGGGTTTGGTCCTGGTC 58.641 55.000 0.00 0.00 41.37 4.02
645 646 1.132495 ACTAGGGTTTGGTCCTGGTCT 60.132 52.381 0.00 0.00 41.37 3.85
646 647 1.279271 CTAGGGTTTGGTCCTGGTCTG 59.721 57.143 0.00 0.00 35.92 3.51
647 648 0.401395 AGGGTTTGGTCCTGGTCTGA 60.401 55.000 0.00 0.00 32.53 3.27
648 649 0.698818 GGGTTTGGTCCTGGTCTGAT 59.301 55.000 0.00 0.00 0.00 2.90
649 650 1.913419 GGGTTTGGTCCTGGTCTGATA 59.087 52.381 0.00 0.00 0.00 2.15
650 651 2.355818 GGGTTTGGTCCTGGTCTGATAC 60.356 54.545 0.00 0.00 0.00 2.24
665 666 6.963049 GTCTGATACCATGTTAGAAAACGT 57.037 37.500 0.00 0.00 38.53 3.99
675 676 5.524971 TGTTAGAAAACGTGAGGAAGAGA 57.475 39.130 0.00 0.00 38.53 3.10
676 677 5.529791 TGTTAGAAAACGTGAGGAAGAGAG 58.470 41.667 0.00 0.00 38.53 3.20
677 678 5.301045 TGTTAGAAAACGTGAGGAAGAGAGA 59.699 40.000 0.00 0.00 38.53 3.10
678 679 4.939052 AGAAAACGTGAGGAAGAGAGAA 57.061 40.909 0.00 0.00 0.00 2.87
679 680 5.476091 AGAAAACGTGAGGAAGAGAGAAT 57.524 39.130 0.00 0.00 0.00 2.40
680 681 5.233988 AGAAAACGTGAGGAAGAGAGAATG 58.766 41.667 0.00 0.00 0.00 2.67
681 682 4.873746 AAACGTGAGGAAGAGAGAATGA 57.126 40.909 0.00 0.00 0.00 2.57
682 683 3.859411 ACGTGAGGAAGAGAGAATGAC 57.141 47.619 0.00 0.00 0.00 3.06
683 684 2.494073 ACGTGAGGAAGAGAGAATGACC 59.506 50.000 0.00 0.00 0.00 4.02
684 685 2.478709 CGTGAGGAAGAGAGAATGACCG 60.479 54.545 0.00 0.00 0.00 4.79
685 686 2.755655 GTGAGGAAGAGAGAATGACCGA 59.244 50.000 0.00 0.00 0.00 4.69
686 687 3.193691 GTGAGGAAGAGAGAATGACCGAA 59.806 47.826 0.00 0.00 0.00 4.30
687 688 3.193691 TGAGGAAGAGAGAATGACCGAAC 59.806 47.826 0.00 0.00 0.00 3.95
688 689 3.165875 AGGAAGAGAGAATGACCGAACA 58.834 45.455 0.00 0.00 0.00 3.18
689 690 3.194542 AGGAAGAGAGAATGACCGAACAG 59.805 47.826 0.00 0.00 0.00 3.16
690 691 3.056465 GGAAGAGAGAATGACCGAACAGT 60.056 47.826 0.00 0.00 0.00 3.55
691 692 4.561105 GAAGAGAGAATGACCGAACAGTT 58.439 43.478 0.00 0.00 0.00 3.16
692 693 4.608948 AGAGAGAATGACCGAACAGTTT 57.391 40.909 0.00 0.00 0.00 2.66
693 694 4.962155 AGAGAGAATGACCGAACAGTTTT 58.038 39.130 0.00 0.00 0.00 2.43
694 695 4.991687 AGAGAGAATGACCGAACAGTTTTC 59.008 41.667 0.00 0.00 0.00 2.29
695 696 4.962155 AGAGAATGACCGAACAGTTTTCT 58.038 39.130 0.00 0.00 0.00 2.52
710 711 6.042638 CAGTTTTCTGTATTGAGGAGGAGA 57.957 41.667 0.00 0.00 42.48 3.71
711 712 6.105333 CAGTTTTCTGTATTGAGGAGGAGAG 58.895 44.000 0.00 0.00 42.48 3.20
712 713 6.019748 AGTTTTCTGTATTGAGGAGGAGAGA 58.980 40.000 0.00 0.00 0.00 3.10
713 714 6.154363 AGTTTTCTGTATTGAGGAGGAGAGAG 59.846 42.308 0.00 0.00 0.00 3.20
714 715 5.458451 TTCTGTATTGAGGAGGAGAGAGA 57.542 43.478 0.00 0.00 0.00 3.10
715 716 5.047566 TCTGTATTGAGGAGGAGAGAGAG 57.952 47.826 0.00 0.00 0.00 3.20
716 717 4.724293 TCTGTATTGAGGAGGAGAGAGAGA 59.276 45.833 0.00 0.00 0.00 3.10
717 718 5.372363 TCTGTATTGAGGAGGAGAGAGAGAT 59.628 44.000 0.00 0.00 0.00 2.75
718 719 6.560687 TCTGTATTGAGGAGGAGAGAGAGATA 59.439 42.308 0.00 0.00 0.00 1.98
719 720 7.239563 TCTGTATTGAGGAGGAGAGAGAGATAT 59.760 40.741 0.00 0.00 0.00 1.63
720 721 8.456221 TGTATTGAGGAGGAGAGAGAGATATA 57.544 38.462 0.00 0.00 0.00 0.86
721 722 8.325787 TGTATTGAGGAGGAGAGAGAGATATAC 58.674 40.741 0.00 0.00 0.00 1.47
722 723 6.771934 TTGAGGAGGAGAGAGAGATATACA 57.228 41.667 0.00 0.00 0.00 2.29
723 724 6.771934 TGAGGAGGAGAGAGAGATATACAA 57.228 41.667 0.00 0.00 0.00 2.41
724 725 6.778821 TGAGGAGGAGAGAGAGATATACAAG 58.221 44.000 0.00 0.00 0.00 3.16
725 726 6.139679 AGGAGGAGAGAGAGATATACAAGG 57.860 45.833 0.00 0.00 0.00 3.61
726 727 5.615261 AGGAGGAGAGAGAGATATACAAGGT 59.385 44.000 0.00 0.00 0.00 3.50
727 728 6.104094 AGGAGGAGAGAGAGATATACAAGGTT 59.896 42.308 0.00 0.00 0.00 3.50
728 729 7.296150 AGGAGGAGAGAGAGATATACAAGGTTA 59.704 40.741 0.00 0.00 0.00 2.85
729 730 7.392393 GGAGGAGAGAGAGATATACAAGGTTAC 59.608 44.444 0.00 0.00 0.00 2.50
730 731 7.817440 AGGAGAGAGAGATATACAAGGTTACA 58.183 38.462 0.00 0.00 0.00 2.41
731 732 8.452868 AGGAGAGAGAGATATACAAGGTTACAT 58.547 37.037 0.00 0.00 0.00 2.29
732 733 8.519526 GGAGAGAGAGATATACAAGGTTACATG 58.480 40.741 0.00 0.00 0.00 3.21
733 734 8.415950 AGAGAGAGATATACAAGGTTACATGG 57.584 38.462 0.00 0.00 0.00 3.66
734 735 7.453126 AGAGAGAGATATACAAGGTTACATGGG 59.547 40.741 0.00 0.00 0.00 4.00
735 736 6.014156 AGAGAGATATACAAGGTTACATGGGC 60.014 42.308 0.00 0.00 0.00 5.36
736 737 5.013183 AGAGATATACAAGGTTACATGGGCC 59.987 44.000 0.00 0.00 0.00 5.80
737 738 4.913968 AGATATACAAGGTTACATGGGCCT 59.086 41.667 4.53 0.00 0.00 5.19
738 739 2.799126 TACAAGGTTACATGGGCCTG 57.201 50.000 4.53 3.00 32.16 4.85
739 740 0.039618 ACAAGGTTACATGGGCCTGG 59.960 55.000 4.53 1.46 32.16 4.45
740 741 0.684153 CAAGGTTACATGGGCCTGGG 60.684 60.000 4.53 0.00 32.16 4.45
741 742 2.442087 GGTTACATGGGCCTGGGC 60.442 66.667 12.58 12.58 41.06 5.36
751 752 3.225235 GCCTGGGCCTCACTCTAG 58.775 66.667 4.53 0.00 34.56 2.43
752 753 1.381872 GCCTGGGCCTCACTCTAGA 60.382 63.158 4.53 0.00 34.56 2.43
753 754 1.681486 GCCTGGGCCTCACTCTAGAC 61.681 65.000 4.53 0.00 34.56 2.59
754 755 0.032615 CCTGGGCCTCACTCTAGACT 60.033 60.000 4.53 0.00 0.00 3.24
755 756 1.215673 CCTGGGCCTCACTCTAGACTA 59.784 57.143 4.53 0.00 0.00 2.59
756 757 2.158385 CCTGGGCCTCACTCTAGACTAT 60.158 54.545 4.53 0.00 0.00 2.12
757 758 2.890311 CTGGGCCTCACTCTAGACTATG 59.110 54.545 4.53 0.00 0.00 2.23
758 759 2.243810 GGGCCTCACTCTAGACTATGG 58.756 57.143 0.84 0.00 0.00 2.74
759 760 2.243810 GGCCTCACTCTAGACTATGGG 58.756 57.143 0.00 0.00 0.00 4.00
760 761 1.616374 GCCTCACTCTAGACTATGGGC 59.384 57.143 0.00 0.32 0.00 5.36
761 762 2.243810 CCTCACTCTAGACTATGGGCC 58.756 57.143 0.00 0.00 0.00 5.80
762 763 2.158385 CCTCACTCTAGACTATGGGCCT 60.158 54.545 4.53 0.00 0.00 5.19
763 764 2.890311 CTCACTCTAGACTATGGGCCTG 59.110 54.545 4.53 0.00 0.00 4.85
764 765 1.967066 CACTCTAGACTATGGGCCTGG 59.033 57.143 4.53 0.00 0.00 4.45
765 766 1.133009 ACTCTAGACTATGGGCCTGGG 60.133 57.143 4.53 0.00 0.00 4.45
766 767 0.471971 TCTAGACTATGGGCCTGGGC 60.472 60.000 12.58 12.58 41.06 5.36
776 777 3.077907 GCCTGGGCCTGTACAAGA 58.922 61.111 4.53 0.00 34.56 3.02
777 778 1.377333 GCCTGGGCCTGTACAAGAC 60.377 63.158 4.53 0.00 34.56 3.01
778 779 2.066340 CCTGGGCCTGTACAAGACA 58.934 57.895 4.53 0.00 36.35 3.41
779 780 0.400213 CCTGGGCCTGTACAAGACAA 59.600 55.000 4.53 0.00 37.70 3.18
780 781 1.202879 CCTGGGCCTGTACAAGACAAA 60.203 52.381 4.53 0.00 37.70 2.83
781 782 1.880027 CTGGGCCTGTACAAGACAAAC 59.120 52.381 4.53 0.00 37.70 2.93
782 783 1.213182 TGGGCCTGTACAAGACAAACA 59.787 47.619 4.53 0.00 37.70 2.83
783 784 1.607148 GGGCCTGTACAAGACAAACAC 59.393 52.381 0.84 0.00 37.70 3.32
784 785 2.294074 GGCCTGTACAAGACAAACACA 58.706 47.619 0.00 0.00 37.70 3.72
785 786 2.685897 GGCCTGTACAAGACAAACACAA 59.314 45.455 0.00 0.00 37.70 3.33
786 787 3.488553 GGCCTGTACAAGACAAACACAAC 60.489 47.826 0.00 0.00 37.70 3.32
787 788 3.127895 GCCTGTACAAGACAAACACAACA 59.872 43.478 0.00 0.00 37.70 3.33
788 789 4.202010 GCCTGTACAAGACAAACACAACAT 60.202 41.667 0.00 0.00 37.70 2.71
789 790 5.008217 GCCTGTACAAGACAAACACAACATA 59.992 40.000 0.00 0.00 37.70 2.29
790 791 6.427150 CCTGTACAAGACAAACACAACATAC 58.573 40.000 0.00 0.00 37.70 2.39
791 792 6.260050 CCTGTACAAGACAAACACAACATACT 59.740 38.462 0.00 0.00 37.70 2.12
792 793 7.201696 CCTGTACAAGACAAACACAACATACTT 60.202 37.037 0.00 0.00 37.70 2.24
793 794 7.690228 TGTACAAGACAAACACAACATACTTC 58.310 34.615 0.00 0.00 34.15 3.01
794 795 6.751514 ACAAGACAAACACAACATACTTCA 57.248 33.333 0.00 0.00 0.00 3.02
795 796 6.551736 ACAAGACAAACACAACATACTTCAC 58.448 36.000 0.00 0.00 0.00 3.18
796 797 6.374333 ACAAGACAAACACAACATACTTCACT 59.626 34.615 0.00 0.00 0.00 3.41
797 798 6.604735 AGACAAACACAACATACTTCACTC 57.395 37.500 0.00 0.00 0.00 3.51
798 799 6.349300 AGACAAACACAACATACTTCACTCT 58.651 36.000 0.00 0.00 0.00 3.24
799 800 7.497595 AGACAAACACAACATACTTCACTCTA 58.502 34.615 0.00 0.00 0.00 2.43
800 801 7.653713 AGACAAACACAACATACTTCACTCTAG 59.346 37.037 0.00 0.00 0.00 2.43
801 802 7.497595 ACAAACACAACATACTTCACTCTAGA 58.502 34.615 0.00 0.00 0.00 2.43
802 803 7.438459 ACAAACACAACATACTTCACTCTAGAC 59.562 37.037 0.00 0.00 0.00 2.59
803 804 6.902771 ACACAACATACTTCACTCTAGACT 57.097 37.500 0.00 0.00 0.00 3.24
804 805 7.997773 ACACAACATACTTCACTCTAGACTA 57.002 36.000 0.00 0.00 0.00 2.59
805 806 8.582657 ACACAACATACTTCACTCTAGACTAT 57.417 34.615 0.00 0.00 0.00 2.12
806 807 8.462811 ACACAACATACTTCACTCTAGACTATG 58.537 37.037 0.00 0.00 0.00 2.23
807 808 7.918033 CACAACATACTTCACTCTAGACTATGG 59.082 40.741 0.00 0.00 0.00 2.74
808 809 7.068839 ACAACATACTTCACTCTAGACTATGGG 59.931 40.741 0.00 0.00 0.00 4.00
809 810 5.536916 ACATACTTCACTCTAGACTATGGGC 59.463 44.000 0.00 0.00 0.00 5.36
810 811 3.301274 ACTTCACTCTAGACTATGGGCC 58.699 50.000 0.00 0.00 0.00 5.80
811 812 3.052490 ACTTCACTCTAGACTATGGGCCT 60.052 47.826 4.53 0.00 0.00 5.19
812 813 2.950781 TCACTCTAGACTATGGGCCTG 58.049 52.381 4.53 0.00 0.00 4.85
813 814 1.967066 CACTCTAGACTATGGGCCTGG 59.033 57.143 4.53 0.00 0.00 4.45
814 815 1.133009 ACTCTAGACTATGGGCCTGGG 60.133 57.143 4.53 0.00 0.00 4.45
815 816 0.471971 TCTAGACTATGGGCCTGGGC 60.472 60.000 12.58 12.58 41.06 5.36
825 826 3.077907 GCCTGGGCCTGTACAAGA 58.922 61.111 4.53 0.00 34.56 3.02
826 827 1.377333 GCCTGGGCCTGTACAAGAC 60.377 63.158 4.53 0.00 34.56 3.01
827 828 2.066340 CCTGGGCCTGTACAAGACA 58.934 57.895 4.53 0.00 36.35 3.41
828 829 0.400213 CCTGGGCCTGTACAAGACAA 59.600 55.000 4.53 0.00 37.70 3.18
829 830 1.611673 CCTGGGCCTGTACAAGACAAG 60.612 57.143 4.53 0.00 37.70 3.16
830 831 0.250727 TGGGCCTGTACAAGACAAGC 60.251 55.000 4.53 0.00 43.69 4.01
831 832 0.250727 GGGCCTGTACAAGACAAGCA 60.251 55.000 0.84 0.00 45.85 3.91
832 833 0.875059 GGCCTGTACAAGACAAGCAC 59.125 55.000 0.00 0.00 45.85 4.40
833 834 1.593196 GCCTGTACAAGACAAGCACA 58.407 50.000 0.00 0.00 43.84 4.57
834 835 1.946768 GCCTGTACAAGACAAGCACAA 59.053 47.619 0.00 0.00 43.84 3.33
835 836 2.287009 GCCTGTACAAGACAAGCACAAC 60.287 50.000 0.00 0.00 43.84 3.32
836 837 2.942376 CCTGTACAAGACAAGCACAACA 59.058 45.455 0.00 0.00 37.70 3.33
837 838 3.565482 CCTGTACAAGACAAGCACAACAT 59.435 43.478 0.00 0.00 37.70 2.71
838 839 4.754618 CCTGTACAAGACAAGCACAACATA 59.245 41.667 0.00 0.00 37.70 2.29
839 840 5.412594 CCTGTACAAGACAAGCACAACATAT 59.587 40.000 0.00 0.00 37.70 1.78
840 841 6.593770 CCTGTACAAGACAAGCACAACATATA 59.406 38.462 0.00 0.00 37.70 0.86
841 842 7.280876 CCTGTACAAGACAAGCACAACATATAT 59.719 37.037 0.00 0.00 37.70 0.86
842 843 9.313118 CTGTACAAGACAAGCACAACATATATA 57.687 33.333 0.00 0.00 37.70 0.86
843 844 9.093970 TGTACAAGACAAGCACAACATATATAC 57.906 33.333 0.00 0.00 34.15 1.47
844 845 9.314321 GTACAAGACAAGCACAACATATATACT 57.686 33.333 0.00 0.00 0.00 2.12
845 846 8.792830 ACAAGACAAGCACAACATATATACTT 57.207 30.769 0.00 0.00 0.00 2.24
846 847 9.884636 ACAAGACAAGCACAACATATATACTTA 57.115 29.630 0.00 0.00 0.00 2.24
849 850 9.884636 AGACAAGCACAACATATATACTTAACA 57.115 29.630 0.00 0.00 0.00 2.41
941 942 1.098712 GCGCCGGGGATGATGTTTTA 61.099 55.000 24.68 0.00 0.00 1.52
958 959 5.314529 TGTTTTATATCCCGTTGACACCAA 58.685 37.500 0.00 0.00 0.00 3.67
1045 1046 1.063027 CATCGAAGATGCATGCGTTGT 59.937 47.619 14.88 4.84 45.12 3.32
1345 1379 3.464828 TCCCTAATCTCAGCTTCCCTTT 58.535 45.455 0.00 0.00 0.00 3.11
1461 1495 3.788333 ATTTCATTTGGCTCCATCGTG 57.212 42.857 0.00 0.00 0.00 4.35
1529 1590 9.976511 CTTGCATTATCCAAGATAAATCATTGT 57.023 29.630 1.43 0.00 41.64 2.71
2078 2178 4.478317 TGGATTGGATAGTTGTCCTTCCAT 59.522 41.667 12.64 0.00 41.83 3.41
2291 3023 8.994429 TGCCAAATTTATTTAGTACATGGTTG 57.006 30.769 0.00 0.00 0.00 3.77
2332 3067 9.190858 TGCAATGTTGTTTAATAAACTCATGTC 57.809 29.630 15.80 13.78 41.90 3.06
2429 3164 5.469373 TTTGCGAGCATTTATCACACTAG 57.531 39.130 0.00 0.00 0.00 2.57
2430 3165 2.866156 TGCGAGCATTTATCACACTAGC 59.134 45.455 0.00 0.00 0.00 3.42
2431 3166 3.126831 GCGAGCATTTATCACACTAGCT 58.873 45.455 0.00 0.00 0.00 3.32
2432 3167 4.202111 TGCGAGCATTTATCACACTAGCTA 60.202 41.667 0.00 0.00 31.33 3.32
2772 3513 3.427161 GGCATTCAACTTCTGTATGGC 57.573 47.619 2.95 2.95 46.27 4.40
2782 3523 0.178932 TCTGTATGGCGCCCCTCTAT 60.179 55.000 26.77 13.13 0.00 1.98
2839 3581 8.918202 ACCTAAGTTACTCATGTCATTTTTCA 57.082 30.769 0.00 0.00 0.00 2.69
2983 3726 4.437239 AGTAGATTGCAAGGTCGAGAATG 58.563 43.478 4.94 0.00 0.00 2.67
3051 3794 3.855858 TCTATGCAACGCTACACAATCA 58.144 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 6.439058 AGAAGAGTACTATGGAGCTTTCACTT 59.561 38.462 0.00 0.00 0.00 3.16
213 214 0.978146 AGCGCTACCTTCATCCCAGT 60.978 55.000 8.99 0.00 0.00 4.00
219 220 0.250234 TTGAGCAGCGCTACCTTCAT 59.750 50.000 10.99 0.00 39.88 2.57
260 261 5.581126 AAATCTTGAGCAACACACTTCAA 57.419 34.783 0.00 0.00 0.00 2.69
270 271 5.487433 TCACTCCGAATAAATCTTGAGCAA 58.513 37.500 0.00 0.00 31.35 3.91
280 281 4.202377 TGTTGAACCCTCACTCCGAATAAA 60.202 41.667 0.00 0.00 0.00 1.40
282 283 2.901192 TGTTGAACCCTCACTCCGAATA 59.099 45.455 0.00 0.00 0.00 1.75
564 565 1.137872 GTGATTCAGGCGGATCTGTCT 59.862 52.381 1.77 1.77 36.25 3.41
566 567 0.179000 GGTGATTCAGGCGGATCTGT 59.821 55.000 2.89 0.00 36.25 3.41
567 568 0.467384 AGGTGATTCAGGCGGATCTG 59.533 55.000 0.00 0.00 36.17 2.90
568 569 0.755686 GAGGTGATTCAGGCGGATCT 59.244 55.000 0.00 0.00 0.00 2.75
570 571 0.179000 GTGAGGTGATTCAGGCGGAT 59.821 55.000 0.00 0.00 0.00 4.18
571 572 1.596934 GTGAGGTGATTCAGGCGGA 59.403 57.895 0.00 0.00 0.00 5.54
572 573 1.450312 GGTGAGGTGATTCAGGCGG 60.450 63.158 0.00 0.00 0.00 6.13
575 576 1.450312 GCCGGTGAGGTGATTCAGG 60.450 63.158 1.90 0.00 43.70 3.86
577 578 1.296392 CTGCCGGTGAGGTGATTCA 59.704 57.895 1.90 0.00 43.70 2.57
578 579 2.109126 GCTGCCGGTGAGGTGATTC 61.109 63.158 1.90 0.00 43.70 2.52
579 580 2.045926 GCTGCCGGTGAGGTGATT 60.046 61.111 1.90 0.00 43.70 2.57
582 583 3.958147 AATCGCTGCCGGTGAGGTG 62.958 63.158 1.90 0.00 43.70 4.00
583 584 3.254024 AAATCGCTGCCGGTGAGGT 62.254 57.895 1.90 0.00 43.70 3.85
584 585 2.436646 AAATCGCTGCCGGTGAGG 60.437 61.111 1.90 0.00 44.97 3.86
585 586 1.091771 ATGAAATCGCTGCCGGTGAG 61.092 55.000 1.90 0.00 37.90 3.51
586 587 1.078497 ATGAAATCGCTGCCGGTGA 60.078 52.632 1.90 0.00 38.92 4.02
589 590 2.717485 CCATGAAATCGCTGCCGG 59.283 61.111 0.00 0.00 34.56 6.13
591 592 1.434696 CACCCATGAAATCGCTGCC 59.565 57.895 0.00 0.00 0.00 4.85
593 594 1.434696 GCCACCCATGAAATCGCTG 59.565 57.895 0.00 0.00 0.00 5.18
594 595 2.114670 CGCCACCCATGAAATCGCT 61.115 57.895 0.00 0.00 0.00 4.93
595 596 2.408835 CGCCACCCATGAAATCGC 59.591 61.111 0.00 0.00 0.00 4.58
596 597 3.110139 CCGCCACCCATGAAATCG 58.890 61.111 0.00 0.00 0.00 3.34
597 598 1.754234 AGCCGCCACCCATGAAATC 60.754 57.895 0.00 0.00 0.00 2.17
598 599 2.053865 CAGCCGCCACCCATGAAAT 61.054 57.895 0.00 0.00 0.00 2.17
599 600 2.676121 CAGCCGCCACCCATGAAA 60.676 61.111 0.00 0.00 0.00 2.69
600 601 4.738998 CCAGCCGCCACCCATGAA 62.739 66.667 0.00 0.00 0.00 2.57
602 603 4.738998 TTCCAGCCGCCACCCATG 62.739 66.667 0.00 0.00 0.00 3.66
603 604 4.431131 CTTCCAGCCGCCACCCAT 62.431 66.667 0.00 0.00 0.00 4.00
605 606 4.785453 CTCTTCCAGCCGCCACCC 62.785 72.222 0.00 0.00 0.00 4.61
606 607 4.785453 CCTCTTCCAGCCGCCACC 62.785 72.222 0.00 0.00 0.00 4.61
607 608 4.785453 CCCTCTTCCAGCCGCCAC 62.785 72.222 0.00 0.00 0.00 5.01
609 610 4.475135 GTCCCTCTTCCAGCCGCC 62.475 72.222 0.00 0.00 0.00 6.13
610 611 2.022240 CTAGTCCCTCTTCCAGCCGC 62.022 65.000 0.00 0.00 0.00 6.53
611 612 1.395826 CCTAGTCCCTCTTCCAGCCG 61.396 65.000 0.00 0.00 0.00 5.52
612 613 1.051556 CCCTAGTCCCTCTTCCAGCC 61.052 65.000 0.00 0.00 0.00 4.85
613 614 0.325765 ACCCTAGTCCCTCTTCCAGC 60.326 60.000 0.00 0.00 0.00 4.85
614 615 2.237392 CAAACCCTAGTCCCTCTTCCAG 59.763 54.545 0.00 0.00 0.00 3.86
615 616 2.266279 CAAACCCTAGTCCCTCTTCCA 58.734 52.381 0.00 0.00 0.00 3.53
616 617 1.560146 CCAAACCCTAGTCCCTCTTCC 59.440 57.143 0.00 0.00 0.00 3.46
617 618 2.236644 GACCAAACCCTAGTCCCTCTTC 59.763 54.545 0.00 0.00 0.00 2.87
618 619 2.267192 GACCAAACCCTAGTCCCTCTT 58.733 52.381 0.00 0.00 0.00 2.85
619 620 1.555058 GGACCAAACCCTAGTCCCTCT 60.555 57.143 0.00 0.00 43.60 3.69
620 621 0.910338 GGACCAAACCCTAGTCCCTC 59.090 60.000 0.00 0.00 43.60 4.30
621 622 3.100039 GGACCAAACCCTAGTCCCT 57.900 57.895 0.00 0.00 43.60 4.20
624 625 1.278413 GACCAGGACCAAACCCTAGTC 59.722 57.143 0.00 0.00 35.82 2.59
625 626 1.132495 AGACCAGGACCAAACCCTAGT 60.132 52.381 0.00 0.00 31.64 2.57
626 627 1.279271 CAGACCAGGACCAAACCCTAG 59.721 57.143 0.00 0.00 31.64 3.02
627 628 1.132657 TCAGACCAGGACCAAACCCTA 60.133 52.381 0.00 0.00 31.64 3.53
628 629 0.401395 TCAGACCAGGACCAAACCCT 60.401 55.000 0.00 0.00 0.00 4.34
629 630 0.698818 ATCAGACCAGGACCAAACCC 59.301 55.000 0.00 0.00 0.00 4.11
630 631 2.987232 GTATCAGACCAGGACCAAACC 58.013 52.381 0.00 0.00 0.00 3.27
641 642 5.873164 ACGTTTTCTAACATGGTATCAGACC 59.127 40.000 0.00 0.00 40.42 3.85
642 643 6.588756 TCACGTTTTCTAACATGGTATCAGAC 59.411 38.462 0.00 0.00 33.75 3.51
643 644 6.693466 TCACGTTTTCTAACATGGTATCAGA 58.307 36.000 0.00 0.00 33.75 3.27
644 645 6.036083 CCTCACGTTTTCTAACATGGTATCAG 59.964 42.308 0.00 0.00 33.75 2.90
645 646 5.872617 CCTCACGTTTTCTAACATGGTATCA 59.127 40.000 0.00 0.00 33.75 2.15
646 647 6.103997 TCCTCACGTTTTCTAACATGGTATC 58.896 40.000 0.00 0.00 33.75 2.24
647 648 6.045072 TCCTCACGTTTTCTAACATGGTAT 57.955 37.500 0.00 0.00 33.75 2.73
648 649 5.471556 TCCTCACGTTTTCTAACATGGTA 57.528 39.130 0.00 0.00 33.75 3.25
649 650 4.345859 TCCTCACGTTTTCTAACATGGT 57.654 40.909 0.00 0.00 33.75 3.55
650 651 4.994852 TCTTCCTCACGTTTTCTAACATGG 59.005 41.667 0.00 0.00 33.75 3.66
651 652 5.926542 TCTCTTCCTCACGTTTTCTAACATG 59.073 40.000 0.00 0.00 33.75 3.21
652 653 6.015350 TCTCTCTTCCTCACGTTTTCTAACAT 60.015 38.462 0.00 0.00 33.75 2.71
653 654 5.301045 TCTCTCTTCCTCACGTTTTCTAACA 59.699 40.000 0.00 0.00 33.75 2.41
654 655 5.770417 TCTCTCTTCCTCACGTTTTCTAAC 58.230 41.667 0.00 0.00 0.00 2.34
655 656 6.401047 TTCTCTCTTCCTCACGTTTTCTAA 57.599 37.500 0.00 0.00 0.00 2.10
656 657 6.208797 TCATTCTCTCTTCCTCACGTTTTCTA 59.791 38.462 0.00 0.00 0.00 2.10
657 658 4.939052 TTCTCTCTTCCTCACGTTTTCT 57.061 40.909 0.00 0.00 0.00 2.52
658 659 5.119434 GTCATTCTCTCTTCCTCACGTTTTC 59.881 44.000 0.00 0.00 0.00 2.29
659 660 4.991687 GTCATTCTCTCTTCCTCACGTTTT 59.008 41.667 0.00 0.00 0.00 2.43
660 661 4.561105 GTCATTCTCTCTTCCTCACGTTT 58.439 43.478 0.00 0.00 0.00 3.60
661 662 3.056465 GGTCATTCTCTCTTCCTCACGTT 60.056 47.826 0.00 0.00 0.00 3.99
662 663 2.494073 GGTCATTCTCTCTTCCTCACGT 59.506 50.000 0.00 0.00 0.00 4.49
663 664 2.478709 CGGTCATTCTCTCTTCCTCACG 60.479 54.545 0.00 0.00 0.00 4.35
664 665 2.755655 TCGGTCATTCTCTCTTCCTCAC 59.244 50.000 0.00 0.00 0.00 3.51
665 666 3.087370 TCGGTCATTCTCTCTTCCTCA 57.913 47.619 0.00 0.00 0.00 3.86
666 667 3.193691 TGTTCGGTCATTCTCTCTTCCTC 59.806 47.826 0.00 0.00 0.00 3.71
667 668 3.165875 TGTTCGGTCATTCTCTCTTCCT 58.834 45.455 0.00 0.00 0.00 3.36
668 669 3.056465 ACTGTTCGGTCATTCTCTCTTCC 60.056 47.826 0.00 0.00 0.00 3.46
669 670 4.181309 ACTGTTCGGTCATTCTCTCTTC 57.819 45.455 0.00 0.00 0.00 2.87
670 671 4.608948 AACTGTTCGGTCATTCTCTCTT 57.391 40.909 0.00 0.00 0.00 2.85
671 672 4.608948 AAACTGTTCGGTCATTCTCTCT 57.391 40.909 0.00 0.00 0.00 3.10
672 673 4.991687 AGAAAACTGTTCGGTCATTCTCTC 59.008 41.667 0.00 0.00 0.00 3.20
673 674 4.752101 CAGAAAACTGTTCGGTCATTCTCT 59.248 41.667 0.00 0.00 0.00 3.10
674 675 4.511826 ACAGAAAACTGTTCGGTCATTCTC 59.488 41.667 0.00 0.00 33.11 2.87
675 676 4.451900 ACAGAAAACTGTTCGGTCATTCT 58.548 39.130 0.00 0.00 33.11 2.40
676 677 4.813296 ACAGAAAACTGTTCGGTCATTC 57.187 40.909 0.00 0.00 33.11 2.67
677 678 6.485313 TCAATACAGAAAACTGTTCGGTCATT 59.515 34.615 8.14 0.00 38.64 2.57
678 679 5.995282 TCAATACAGAAAACTGTTCGGTCAT 59.005 36.000 8.14 0.00 38.64 3.06
679 680 5.361427 TCAATACAGAAAACTGTTCGGTCA 58.639 37.500 8.14 0.00 38.64 4.02
680 681 5.107065 CCTCAATACAGAAAACTGTTCGGTC 60.107 44.000 8.14 0.00 38.64 4.79
681 682 4.755123 CCTCAATACAGAAAACTGTTCGGT 59.245 41.667 8.14 0.00 38.64 4.69
682 683 4.994852 TCCTCAATACAGAAAACTGTTCGG 59.005 41.667 8.14 3.47 38.64 4.30
683 684 5.120830 CCTCCTCAATACAGAAAACTGTTCG 59.879 44.000 8.14 0.00 38.64 3.95
684 685 6.231211 TCCTCCTCAATACAGAAAACTGTTC 58.769 40.000 8.14 0.00 38.64 3.18
685 686 6.043243 TCTCCTCCTCAATACAGAAAACTGTT 59.957 38.462 8.14 0.00 38.64 3.16
686 687 5.544176 TCTCCTCCTCAATACAGAAAACTGT 59.456 40.000 7.94 7.94 41.00 3.55
687 688 6.042638 TCTCCTCCTCAATACAGAAAACTG 57.957 41.667 0.00 0.00 0.00 3.16
688 689 6.019748 TCTCTCCTCCTCAATACAGAAAACT 58.980 40.000 0.00 0.00 0.00 2.66
689 690 6.153680 TCTCTCTCCTCCTCAATACAGAAAAC 59.846 42.308 0.00 0.00 0.00 2.43
690 691 6.256819 TCTCTCTCCTCCTCAATACAGAAAA 58.743 40.000 0.00 0.00 0.00 2.29
691 692 5.832221 TCTCTCTCCTCCTCAATACAGAAA 58.168 41.667 0.00 0.00 0.00 2.52
692 693 5.192722 TCTCTCTCTCCTCCTCAATACAGAA 59.807 44.000 0.00 0.00 0.00 3.02
693 694 4.724293 TCTCTCTCTCCTCCTCAATACAGA 59.276 45.833 0.00 0.00 0.00 3.41
694 695 5.047566 TCTCTCTCTCCTCCTCAATACAG 57.952 47.826 0.00 0.00 0.00 2.74
695 696 5.661503 ATCTCTCTCTCCTCCTCAATACA 57.338 43.478 0.00 0.00 0.00 2.29
696 697 8.325787 TGTATATCTCTCTCTCCTCCTCAATAC 58.674 40.741 0.00 0.00 0.00 1.89
697 698 8.456221 TGTATATCTCTCTCTCCTCCTCAATA 57.544 38.462 0.00 0.00 0.00 1.90
698 699 7.341885 TGTATATCTCTCTCTCCTCCTCAAT 57.658 40.000 0.00 0.00 0.00 2.57
699 700 6.771934 TGTATATCTCTCTCTCCTCCTCAA 57.228 41.667 0.00 0.00 0.00 3.02
700 701 6.240147 CCTTGTATATCTCTCTCTCCTCCTCA 60.240 46.154 0.00 0.00 0.00 3.86
701 702 6.180472 CCTTGTATATCTCTCTCTCCTCCTC 58.820 48.000 0.00 0.00 0.00 3.71
702 703 5.615261 ACCTTGTATATCTCTCTCTCCTCCT 59.385 44.000 0.00 0.00 0.00 3.69
703 704 5.887754 ACCTTGTATATCTCTCTCTCCTCC 58.112 45.833 0.00 0.00 0.00 4.30
704 705 7.940137 TGTAACCTTGTATATCTCTCTCTCCTC 59.060 40.741 0.00 0.00 0.00 3.71
705 706 7.817440 TGTAACCTTGTATATCTCTCTCTCCT 58.183 38.462 0.00 0.00 0.00 3.69
706 707 8.519526 CATGTAACCTTGTATATCTCTCTCTCC 58.480 40.741 0.00 0.00 0.00 3.71
707 708 8.519526 CCATGTAACCTTGTATATCTCTCTCTC 58.480 40.741 0.00 0.00 0.00 3.20
708 709 7.453126 CCCATGTAACCTTGTATATCTCTCTCT 59.547 40.741 0.00 0.00 0.00 3.10
709 710 7.607250 CCCATGTAACCTTGTATATCTCTCTC 58.393 42.308 0.00 0.00 0.00 3.20
710 711 6.014156 GCCCATGTAACCTTGTATATCTCTCT 60.014 42.308 0.00 0.00 0.00 3.10
711 712 6.166982 GCCCATGTAACCTTGTATATCTCTC 58.833 44.000 0.00 0.00 0.00 3.20
712 713 5.013183 GGCCCATGTAACCTTGTATATCTCT 59.987 44.000 0.00 0.00 0.00 3.10
713 714 5.013183 AGGCCCATGTAACCTTGTATATCTC 59.987 44.000 0.00 0.00 0.00 2.75
714 715 4.913968 AGGCCCATGTAACCTTGTATATCT 59.086 41.667 0.00 0.00 0.00 1.98
715 716 5.003804 CAGGCCCATGTAACCTTGTATATC 58.996 45.833 0.00 0.00 0.00 1.63
716 717 4.202567 CCAGGCCCATGTAACCTTGTATAT 60.203 45.833 0.00 0.00 0.00 0.86
717 718 3.137544 CCAGGCCCATGTAACCTTGTATA 59.862 47.826 0.00 0.00 0.00 1.47
718 719 2.091885 CCAGGCCCATGTAACCTTGTAT 60.092 50.000 0.00 0.00 0.00 2.29
719 720 1.283613 CCAGGCCCATGTAACCTTGTA 59.716 52.381 0.00 0.00 0.00 2.41
720 721 0.039618 CCAGGCCCATGTAACCTTGT 59.960 55.000 0.00 0.00 0.00 3.16
721 722 0.684153 CCCAGGCCCATGTAACCTTG 60.684 60.000 0.00 0.00 0.00 3.61
722 723 1.697297 CCCAGGCCCATGTAACCTT 59.303 57.895 0.00 0.00 0.00 3.50
723 724 2.996330 GCCCAGGCCCATGTAACCT 61.996 63.158 0.00 0.00 34.56 3.50
724 725 2.442087 GCCCAGGCCCATGTAACC 60.442 66.667 0.00 0.00 34.56 2.85
734 735 1.381872 TCTAGAGTGAGGCCCAGGC 60.382 63.158 0.00 0.00 41.06 4.85
735 736 0.032615 AGTCTAGAGTGAGGCCCAGG 60.033 60.000 0.00 0.00 0.00 4.45
736 737 2.738587 TAGTCTAGAGTGAGGCCCAG 57.261 55.000 10.51 0.00 0.00 4.45
737 738 2.424957 CCATAGTCTAGAGTGAGGCCCA 60.425 54.545 10.51 0.00 0.00 5.36
738 739 2.243810 CCATAGTCTAGAGTGAGGCCC 58.756 57.143 10.51 0.00 0.00 5.80
739 740 2.243810 CCCATAGTCTAGAGTGAGGCC 58.756 57.143 10.51 0.00 0.00 5.19
740 741 1.616374 GCCCATAGTCTAGAGTGAGGC 59.384 57.143 16.84 16.84 0.00 4.70
741 742 2.158385 AGGCCCATAGTCTAGAGTGAGG 60.158 54.545 10.51 11.01 0.00 3.86
742 743 2.890311 CAGGCCCATAGTCTAGAGTGAG 59.110 54.545 10.51 2.55 0.00 3.51
743 744 2.424957 CCAGGCCCATAGTCTAGAGTGA 60.425 54.545 10.51 0.00 0.00 3.41
744 745 1.967066 CCAGGCCCATAGTCTAGAGTG 59.033 57.143 10.51 1.84 0.00 3.51
745 746 1.133009 CCCAGGCCCATAGTCTAGAGT 60.133 57.143 0.00 5.21 0.00 3.24
746 747 1.638529 CCCAGGCCCATAGTCTAGAG 58.361 60.000 0.00 0.00 0.00 2.43
747 748 0.471971 GCCCAGGCCCATAGTCTAGA 60.472 60.000 0.00 0.00 34.56 2.43
748 749 2.062070 GCCCAGGCCCATAGTCTAG 58.938 63.158 0.00 0.00 34.56 2.43
749 750 4.313523 GCCCAGGCCCATAGTCTA 57.686 61.111 0.00 0.00 34.56 2.59
759 760 1.377333 GTCTTGTACAGGCCCAGGC 60.377 63.158 0.00 0.00 41.06 4.85
760 761 0.400213 TTGTCTTGTACAGGCCCAGG 59.600 55.000 0.00 0.00 39.87 4.45
761 762 1.880027 GTTTGTCTTGTACAGGCCCAG 59.120 52.381 0.00 0.00 39.87 4.45
762 763 1.213182 TGTTTGTCTTGTACAGGCCCA 59.787 47.619 0.00 0.00 39.87 5.36
763 764 1.607148 GTGTTTGTCTTGTACAGGCCC 59.393 52.381 0.00 0.00 39.87 5.80
764 765 2.294074 TGTGTTTGTCTTGTACAGGCC 58.706 47.619 0.00 0.00 39.87 5.19
765 766 3.127895 TGTTGTGTTTGTCTTGTACAGGC 59.872 43.478 0.00 0.00 39.87 4.85
766 767 4.955925 TGTTGTGTTTGTCTTGTACAGG 57.044 40.909 0.00 0.00 39.87 4.00
767 768 7.246674 AGTATGTTGTGTTTGTCTTGTACAG 57.753 36.000 0.00 0.00 39.87 2.74
768 769 7.334671 TGAAGTATGTTGTGTTTGTCTTGTACA 59.665 33.333 0.00 0.00 35.88 2.90
769 770 7.638683 GTGAAGTATGTTGTGTTTGTCTTGTAC 59.361 37.037 0.00 0.00 0.00 2.90
770 771 7.551262 AGTGAAGTATGTTGTGTTTGTCTTGTA 59.449 33.333 0.00 0.00 0.00 2.41
771 772 6.374333 AGTGAAGTATGTTGTGTTTGTCTTGT 59.626 34.615 0.00 0.00 0.00 3.16
772 773 6.785191 AGTGAAGTATGTTGTGTTTGTCTTG 58.215 36.000 0.00 0.00 0.00 3.02
773 774 6.823689 AGAGTGAAGTATGTTGTGTTTGTCTT 59.176 34.615 0.00 0.00 0.00 3.01
774 775 6.349300 AGAGTGAAGTATGTTGTGTTTGTCT 58.651 36.000 0.00 0.00 0.00 3.41
775 776 6.604735 AGAGTGAAGTATGTTGTGTTTGTC 57.395 37.500 0.00 0.00 0.00 3.18
776 777 7.438459 GTCTAGAGTGAAGTATGTTGTGTTTGT 59.562 37.037 0.00 0.00 0.00 2.83
777 778 7.653713 AGTCTAGAGTGAAGTATGTTGTGTTTG 59.346 37.037 0.00 0.00 0.00 2.93
778 779 7.727181 AGTCTAGAGTGAAGTATGTTGTGTTT 58.273 34.615 0.00 0.00 0.00 2.83
779 780 7.291411 AGTCTAGAGTGAAGTATGTTGTGTT 57.709 36.000 0.00 0.00 0.00 3.32
780 781 6.902771 AGTCTAGAGTGAAGTATGTTGTGT 57.097 37.500 0.00 0.00 0.00 3.72
781 782 7.918033 CCATAGTCTAGAGTGAAGTATGTTGTG 59.082 40.741 10.51 0.00 0.00 3.33
782 783 7.068839 CCCATAGTCTAGAGTGAAGTATGTTGT 59.931 40.741 10.51 0.00 0.00 3.32
783 784 7.429633 CCCATAGTCTAGAGTGAAGTATGTTG 58.570 42.308 10.51 0.00 0.00 3.33
784 785 6.041069 GCCCATAGTCTAGAGTGAAGTATGTT 59.959 42.308 10.51 0.00 0.00 2.71
785 786 5.536916 GCCCATAGTCTAGAGTGAAGTATGT 59.463 44.000 10.51 0.00 0.00 2.29
786 787 5.047660 GGCCCATAGTCTAGAGTGAAGTATG 60.048 48.000 10.51 5.45 0.00 2.39
787 788 5.081032 GGCCCATAGTCTAGAGTGAAGTAT 58.919 45.833 10.51 0.00 0.00 2.12
788 789 4.168283 AGGCCCATAGTCTAGAGTGAAGTA 59.832 45.833 10.51 0.00 0.00 2.24
789 790 3.052490 AGGCCCATAGTCTAGAGTGAAGT 60.052 47.826 10.51 0.00 0.00 3.01
790 791 3.320541 CAGGCCCATAGTCTAGAGTGAAG 59.679 52.174 10.51 0.13 0.00 3.02
791 792 3.300388 CAGGCCCATAGTCTAGAGTGAA 58.700 50.000 10.51 0.00 0.00 3.18
792 793 2.424957 CCAGGCCCATAGTCTAGAGTGA 60.425 54.545 10.51 0.00 0.00 3.41
793 794 1.967066 CCAGGCCCATAGTCTAGAGTG 59.033 57.143 10.51 1.84 0.00 3.51
794 795 1.133009 CCCAGGCCCATAGTCTAGAGT 60.133 57.143 0.00 5.21 0.00 3.24
795 796 1.638529 CCCAGGCCCATAGTCTAGAG 58.361 60.000 0.00 0.00 0.00 2.43
796 797 0.471971 GCCCAGGCCCATAGTCTAGA 60.472 60.000 0.00 0.00 34.56 2.43
797 798 2.062070 GCCCAGGCCCATAGTCTAG 58.938 63.158 0.00 0.00 34.56 2.43
798 799 4.313523 GCCCAGGCCCATAGTCTA 57.686 61.111 0.00 0.00 34.56 2.59
808 809 1.377333 GTCTTGTACAGGCCCAGGC 60.377 63.158 0.00 0.00 41.06 4.85
809 810 0.400213 TTGTCTTGTACAGGCCCAGG 59.600 55.000 0.00 0.00 39.87 4.45
810 811 1.813513 CTTGTCTTGTACAGGCCCAG 58.186 55.000 0.00 0.00 39.87 4.45
815 816 2.942376 TGTTGTGCTTGTCTTGTACAGG 59.058 45.455 0.00 0.00 39.87 4.00
816 817 4.818534 ATGTTGTGCTTGTCTTGTACAG 57.181 40.909 0.00 0.00 39.87 2.74
817 818 9.093970 GTATATATGTTGTGCTTGTCTTGTACA 57.906 33.333 0.00 0.00 35.88 2.90
818 819 9.314321 AGTATATATGTTGTGCTTGTCTTGTAC 57.686 33.333 0.00 0.00 0.00 2.90
819 820 9.884636 AAGTATATATGTTGTGCTTGTCTTGTA 57.115 29.630 0.00 0.00 0.00 2.41
820 821 8.792830 AAGTATATATGTTGTGCTTGTCTTGT 57.207 30.769 0.00 0.00 0.00 3.16
823 824 9.884636 TGTTAAGTATATATGTTGTGCTTGTCT 57.115 29.630 0.00 0.00 0.00 3.41
825 826 9.667107 ACTGTTAAGTATATATGTTGTGCTTGT 57.333 29.630 0.00 0.00 33.79 3.16
839 840 8.184192 GCTCCTACGTTTGTACTGTTAAGTATA 58.816 37.037 0.00 0.00 40.95 1.47
840 841 7.031975 GCTCCTACGTTTGTACTGTTAAGTAT 58.968 38.462 0.00 0.00 40.95 2.12
841 842 6.016360 TGCTCCTACGTTTGTACTGTTAAGTA 60.016 38.462 0.00 0.00 37.88 2.24
842 843 5.221303 TGCTCCTACGTTTGTACTGTTAAGT 60.221 40.000 0.00 0.00 40.67 2.24
843 844 5.224888 TGCTCCTACGTTTGTACTGTTAAG 58.775 41.667 0.00 0.00 0.00 1.85
844 845 5.009911 TCTGCTCCTACGTTTGTACTGTTAA 59.990 40.000 0.00 0.00 0.00 2.01
845 846 4.520111 TCTGCTCCTACGTTTGTACTGTTA 59.480 41.667 0.00 0.00 0.00 2.41
846 847 3.319972 TCTGCTCCTACGTTTGTACTGTT 59.680 43.478 0.00 0.00 0.00 3.16
847 848 2.889045 TCTGCTCCTACGTTTGTACTGT 59.111 45.455 0.00 0.00 0.00 3.55
848 849 3.057456 AGTCTGCTCCTACGTTTGTACTG 60.057 47.826 0.00 0.00 0.00 2.74
849 850 3.155501 AGTCTGCTCCTACGTTTGTACT 58.844 45.455 0.00 0.00 0.00 2.73
1156 1189 0.465705 GGCATGAGATCCTCGGTTGA 59.534 55.000 0.00 0.00 32.35 3.18
1345 1379 3.569701 GCAAGGTCAATTTCAGAACCTGA 59.430 43.478 0.00 0.00 38.87 3.86
2405 3140 6.292865 GCTAGTGTGATAAATGCTCGCAAATA 60.293 38.462 0.00 0.00 35.11 1.40
2517 3252 6.753744 GCAGCTTTCCAGAAAATACAAATAGG 59.246 38.462 0.00 0.00 0.00 2.57
2772 3513 3.214328 AGCAACAAAATATAGAGGGGCG 58.786 45.455 0.00 0.00 0.00 6.13
2839 3581 8.636213 CCATTTATCTTGGCAATCTACAGAAAT 58.364 33.333 0.00 0.00 0.00 2.17
3080 3823 5.791336 TCAATACTGTATAGGAGCCACAG 57.209 43.478 0.00 4.47 44.20 3.66


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

AutoCloner maintained by Alex Coulton.