Multiple sequence alignment - TraesCS2A01G145400

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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 TraesCS2A01G145400 chr2A 100.000 3491 0 0 1 3491 90510895 90507405 0.000000e+00 6447.0
1 TraesCS2A01G145400 chr2A 83.654 728 73 27 2797 3491 100137246 100137960 0.000000e+00 643.0
2 TraesCS2A01G145400 chr2A 77.273 880 155 23 1352 2192 90428874 90428001 3.150000e-130 475.0
3 TraesCS2A01G145400 chr2A 79.602 201 28 12 680 874 566852087 566852280 7.860000e-27 132.0
4 TraesCS2A01G145400 chr2A 100.000 28 0 0 2603 2630 90508171 90508144 6.000000e-03 52.8
5 TraesCS2A01G145400 chr2A 100.000 28 0 0 2725 2752 90508293 90508266 6.000000e-03 52.8
6 TraesCS2A01G145400 chr2D 93.187 1688 54 14 1121 2765 89216218 89214549 0.000000e+00 2423.0
7 TraesCS2A01G145400 chr2D 93.238 976 30 7 1121 2071 104876374 104877338 0.000000e+00 1404.0
8 TraesCS2A01G145400 chr2D 95.750 400 7 5 2797 3192 89213946 89213553 1.370000e-178 636.0
9 TraesCS2A01G145400 chr2D 95.718 397 7 5 2797 3189 104887405 104887795 6.360000e-177 630.0
10 TraesCS2A01G145400 chr2D 94.203 414 15 3 2068 2475 104885966 104886376 1.060000e-174 623.0
11 TraesCS2A01G145400 chr2D 94.717 265 6 3 3228 3491 104887795 104888052 4.200000e-109 405.0
12 TraesCS2A01G145400 chr2D 90.260 308 12 8 2460 2753 104886429 104886732 1.520000e-103 387.0
13 TraesCS2A01G145400 chr2D 92.803 264 7 3 3228 3491 89213556 89213305 4.260000e-99 372.0
14 TraesCS2A01G145400 chr2D 89.855 276 21 3 3219 3491 100320914 100321185 7.170000e-92 348.0
15 TraesCS2A01G145400 chr2D 81.818 341 29 14 2797 3107 100320418 100320755 4.470000e-64 255.0
16 TraesCS2A01G145400 chr2D 94.578 166 6 2 2604 2769 104886644 104886806 1.610000e-63 254.0
17 TraesCS2A01G145400 chr2D 94.505 91 5 0 2662 2752 89214711 89214621 1.310000e-29 141.0
18 TraesCS2A01G145400 chr2D 94.444 90 3 1 2603 2692 89214648 89214561 1.690000e-28 137.0
19 TraesCS2A01G145400 chr2D 95.238 84 4 0 1043 1126 104876212 104876295 2.190000e-27 134.0
20 TraesCS2A01G145400 chr2D 95.122 82 4 0 1045 1126 89216378 89216297 2.830000e-26 130.0
21 TraesCS2A01G145400 chr2D 92.222 90 5 1 2603 2692 104886704 104886791 3.660000e-25 126.0
22 TraesCS2A01G145400 chr2D 82.653 98 8 4 154 250 113921393 113921482 1.040000e-10 78.7
23 TraesCS2A01G145400 chr2D 100.000 30 0 0 12 41 89216406 89216377 4.870000e-04 56.5
24 TraesCS2A01G145400 chr2B 93.949 1570 58 11 1207 2753 143483818 143485373 0.000000e+00 2338.0
25 TraesCS2A01G145400 chr2B 97.623 589 8 2 2903 3491 143486406 143486988 0.000000e+00 1005.0
26 TraesCS2A01G145400 chr2B 83.586 725 62 27 2797 3491 152181267 152181964 8.230000e-176 627.0
27 TraesCS2A01G145400 chr2B 75.144 1388 196 96 1207 2504 143282120 143280792 6.680000e-142 514.0
28 TraesCS2A01G145400 chr2B 86.636 434 23 8 41 448 430235645 430236069 6.870000e-122 448.0
29 TraesCS2A01G145400 chr2B 85.279 394 44 8 3105 3491 152179426 152179812 9.080000e-106 394.0
30 TraesCS2A01G145400 chr2B 91.979 187 11 1 492 674 430236065 430236251 3.460000e-65 259.0
31 TraesCS2A01G145400 chr2B 92.308 169 10 2 2603 2769 143485282 143485449 1.620000e-58 237.0
32 TraesCS2A01G145400 chr2B 80.938 341 27 21 2797 3107 152179033 152179365 5.830000e-58 235.0
33 TraesCS2A01G145400 chr2B 95.604 91 4 0 2662 2752 143485219 143485309 2.810000e-31 147.0
34 TraesCS2A01G145400 chr2B 98.387 62 1 0 972 1033 430236386 430236447 3.680000e-20 110.0
35 TraesCS2A01G145400 chr2B 98.214 56 1 0 1043 1098 143483724 143483779 7.970000e-17 99.0
36 TraesCS2A01G145400 chr2B 100.000 30 0 0 2723 2752 143485219 143485248 4.870000e-04 56.5
37 TraesCS2A01G145400 chr6A 96.648 179 6 0 685 863 531395988 531396166 7.330000e-77 298.0
38 TraesCS2A01G145400 chr6A 90.338 207 16 3 658 860 589716897 589717103 5.740000e-68 268.0
39 TraesCS2A01G145400 chr5A 94.764 191 7 3 666 856 361454810 361454623 9.480000e-76 294.0
40 TraesCS2A01G145400 chr3B 96.571 175 4 2 682 856 45447698 45447526 4.410000e-74 289.0
41 TraesCS2A01G145400 chr3B 96.000 175 6 1 682 856 651427719 651427892 2.050000e-72 283.0
42 TraesCS2A01G145400 chr3B 88.421 190 16 5 691 875 604490679 604490491 1.260000e-54 224.0
43 TraesCS2A01G145400 chr3B 87.435 191 18 5 690 875 680074643 680074832 7.590000e-52 215.0
44 TraesCS2A01G145400 chr4A 95.028 181 8 1 685 865 677942341 677942162 2.050000e-72 283.0
45 TraesCS2A01G145400 chr3A 95.028 181 8 1 682 861 80489270 80489090 2.050000e-72 283.0
46 TraesCS2A01G145400 chr3A 83.246 191 21 10 685 872 375818400 375818218 7.750000e-37 165.0
47 TraesCS2A01G145400 chr7B 93.651 189 10 2 665 851 739630086 739630274 7.380000e-72 281.0
48 TraesCS2A01G145400 chr7B 79.537 259 42 10 1766 2020 424537129 424537380 1.290000e-39 174.0
49 TraesCS2A01G145400 chr7A 76.678 596 86 37 1927 2504 570183066 570182506 7.380000e-72 281.0
50 TraesCS2A01G145400 chr5B 93.617 188 10 2 668 853 396856572 396856759 2.650000e-71 279.0


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 TraesCS2A01G145400 chr2A 90507405 90510895 3490 True 2184.200000 6447 100.000000 1 3491 3 chr2A.!!$R2 3490
1 TraesCS2A01G145400 chr2A 100137246 100137960 714 False 643.000000 643 83.654000 2797 3491 1 chr2A.!!$F1 694
2 TraesCS2A01G145400 chr2A 90428001 90428874 873 True 475.000000 475 77.273000 1352 2192 1 chr2A.!!$R1 840
3 TraesCS2A01G145400 chr2D 104876212 104877338 1126 False 769.000000 1404 94.238000 1043 2071 2 chr2D.!!$F3 1028
4 TraesCS2A01G145400 chr2D 89213305 89216406 3101 True 556.500000 2423 95.115857 12 3491 7 chr2D.!!$R1 3479
5 TraesCS2A01G145400 chr2D 104885966 104888052 2086 False 404.166667 630 93.616333 2068 3491 6 chr2D.!!$F4 1423
6 TraesCS2A01G145400 chr2D 100320418 100321185 767 False 301.500000 348 85.836500 2797 3491 2 chr2D.!!$F2 694
7 TraesCS2A01G145400 chr2B 143483724 143486988 3264 False 647.083333 2338 96.283000 1043 3491 6 chr2B.!!$F1 2448
8 TraesCS2A01G145400 chr2B 143280792 143282120 1328 True 514.000000 514 75.144000 1207 2504 1 chr2B.!!$R1 1297
9 TraesCS2A01G145400 chr2B 152179033 152181964 2931 False 418.666667 627 83.267667 2797 3491 3 chr2B.!!$F2 694
10 TraesCS2A01G145400 chr2B 430235645 430236447 802 False 272.333333 448 92.334000 41 1033 3 chr2B.!!$F3 992
11 TraesCS2A01G145400 chr7A 570182506 570183066 560 True 281.000000 281 76.678000 1927 2504 1 chr7A.!!$R1 577

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
476 503 0.106521 GCCAGAGATGCTCCTCCTTC 59.893 60.0 2.94 0.00 33.76 3.46 F
937 968 0.251077 CAGCTTGAAAGTCCAGGGCT 60.251 55.0 0.00 0.00 0.00 5.19 F
2119 2372 0.320421 TCTGTTAAGTGAGCGCCCAC 60.320 55.0 14.98 14.98 37.32 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2502 0.026027 ACGATAGAAGCGACGACGAC 59.974 55.00 12.29 2.46 40.29 4.34 R
2250 2503 0.299895 GACGATAGAAGCGACGACGA 59.700 55.00 12.29 0.00 40.29 4.20 R
3163 4584 4.886579 ACGTACTTCCCATCGTTACTTTT 58.113 39.13 0.00 0.00 32.62 2.27 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
30 31 9.975218 ATTATAATTATAAGCCAACGATCCCTT 57.025 29.630 19.81 0.00 32.24 3.95
31 32 7.923414 ATAATTATAAGCCAACGATCCCTTC 57.077 36.000 0.00 0.00 0.00 3.46
41 42 1.571919 CGATCCCTTCGCTACTTTGG 58.428 55.000 0.00 0.00 41.69 3.28
42 43 1.136305 CGATCCCTTCGCTACTTTGGA 59.864 52.381 0.00 0.00 41.69 3.53
43 44 2.552031 GATCCCTTCGCTACTTTGGAC 58.448 52.381 0.00 0.00 0.00 4.02
44 45 0.245539 TCCCTTCGCTACTTTGGACG 59.754 55.000 0.00 0.00 0.00 4.79
45 46 0.739813 CCCTTCGCTACTTTGGACGG 60.740 60.000 0.00 0.00 0.00 4.79
67 68 1.987855 CGGTAGCCCTCCAACTCCA 60.988 63.158 0.00 0.00 0.00 3.86
71 72 1.416772 GTAGCCCTCCAACTCCATACC 59.583 57.143 0.00 0.00 0.00 2.73
123 124 2.701951 ACGGTCTAACTCCTGGTTTTGA 59.298 45.455 0.00 0.00 39.17 2.69
128 129 5.826208 GGTCTAACTCCTGGTTTTGAAGAAA 59.174 40.000 0.00 0.00 39.17 2.52
131 132 7.282450 GTCTAACTCCTGGTTTTGAAGAAAAGA 59.718 37.037 0.00 0.00 39.17 2.52
132 133 6.850752 AACTCCTGGTTTTGAAGAAAAGAA 57.149 33.333 0.00 0.00 33.90 2.52
133 134 6.456795 ACTCCTGGTTTTGAAGAAAAGAAG 57.543 37.500 0.00 0.00 31.57 2.85
134 135 5.163509 ACTCCTGGTTTTGAAGAAAAGAAGC 60.164 40.000 0.00 0.00 31.57 3.86
135 136 4.956075 TCCTGGTTTTGAAGAAAAGAAGCT 59.044 37.500 0.00 0.00 31.57 3.74
136 137 6.126409 TCCTGGTTTTGAAGAAAAGAAGCTA 58.874 36.000 0.00 0.00 31.57 3.32
137 138 6.263168 TCCTGGTTTTGAAGAAAAGAAGCTAG 59.737 38.462 0.00 0.00 31.57 3.42
138 139 5.831997 TGGTTTTGAAGAAAAGAAGCTAGC 58.168 37.500 6.62 6.62 31.57 3.42
139 140 5.594317 TGGTTTTGAAGAAAAGAAGCTAGCT 59.406 36.000 12.68 12.68 31.57 3.32
167 168 6.651225 GCTTGTAGTGTAAAATCTGAGGAGTT 59.349 38.462 0.00 0.00 0.00 3.01
216 217 2.943036 AACTTGGAAGCGGGAGTTAA 57.057 45.000 0.00 0.00 31.05 2.01
226 227 6.661805 TGGAAGCGGGAGTTAAGAAAAATTAT 59.338 34.615 0.00 0.00 0.00 1.28
259 260 1.293179 GCCAAGTAACCCGTACCGT 59.707 57.895 0.00 0.00 32.58 4.83
271 298 0.590732 CGTACCGTTTCGATCCCTCG 60.591 60.000 0.00 0.00 46.41 4.63
304 331 3.991051 ACTGGTGCACCTCGTCCG 61.991 66.667 34.75 18.04 36.82 4.79
365 392 1.225855 GTGATTGAACTGGCACGTGA 58.774 50.000 22.23 0.00 0.00 4.35
443 470 1.522569 CCCATCGTTCACCTCCTCC 59.477 63.158 0.00 0.00 0.00 4.30
444 471 1.264749 CCCATCGTTCACCTCCTCCA 61.265 60.000 0.00 0.00 0.00 3.86
445 472 0.108138 CCATCGTTCACCTCCTCCAC 60.108 60.000 0.00 0.00 0.00 4.02
446 473 0.108138 CATCGTTCACCTCCTCCACC 60.108 60.000 0.00 0.00 0.00 4.61
447 474 0.252284 ATCGTTCACCTCCTCCACCT 60.252 55.000 0.00 0.00 0.00 4.00
448 475 0.898789 TCGTTCACCTCCTCCACCTC 60.899 60.000 0.00 0.00 0.00 3.85
449 476 1.592223 GTTCACCTCCTCCACCTCG 59.408 63.158 0.00 0.00 0.00 4.63
450 477 0.898789 GTTCACCTCCTCCACCTCGA 60.899 60.000 0.00 0.00 0.00 4.04
451 478 0.612174 TTCACCTCCTCCACCTCGAG 60.612 60.000 5.13 5.13 0.00 4.04
452 479 2.363147 ACCTCCTCCACCTCGAGC 60.363 66.667 6.99 0.00 0.00 5.03
453 480 2.043450 CCTCCTCCACCTCGAGCT 60.043 66.667 6.99 0.00 0.00 4.09
454 481 2.124693 CCTCCTCCACCTCGAGCTC 61.125 68.421 6.99 2.73 0.00 4.09
455 482 2.438614 TCCTCCACCTCGAGCTCG 60.439 66.667 30.03 30.03 41.45 5.03
464 491 2.269241 TCGAGCTCGAGCCAGAGA 59.731 61.111 33.84 22.68 44.22 3.10
465 492 1.153066 TCGAGCTCGAGCCAGAGAT 60.153 57.895 33.84 14.37 44.22 2.75
466 493 1.008652 CGAGCTCGAGCCAGAGATG 60.009 63.158 32.94 11.68 43.38 2.90
467 494 1.300080 GAGCTCGAGCCAGAGATGC 60.300 63.158 32.94 6.59 43.38 3.91
468 495 1.737355 GAGCTCGAGCCAGAGATGCT 61.737 60.000 32.94 11.94 43.38 3.79
473 500 3.968773 AGCCAGAGATGCTCCTCC 58.031 61.111 2.94 0.00 32.41 4.30
474 501 1.314170 AGCCAGAGATGCTCCTCCT 59.686 57.895 2.94 0.00 32.41 3.69
475 502 0.326427 AGCCAGAGATGCTCCTCCTT 60.326 55.000 2.94 0.00 32.41 3.36
476 503 0.106521 GCCAGAGATGCTCCTCCTTC 59.893 60.000 2.94 0.00 33.76 3.46
477 504 0.758123 CCAGAGATGCTCCTCCTTCC 59.242 60.000 2.94 0.00 33.76 3.46
478 505 0.758123 CAGAGATGCTCCTCCTTCCC 59.242 60.000 2.94 0.00 33.76 3.97
479 506 0.641601 AGAGATGCTCCTCCTTCCCT 59.358 55.000 2.94 0.00 33.76 4.20
480 507 1.047801 GAGATGCTCCTCCTTCCCTC 58.952 60.000 0.00 0.00 0.00 4.30
481 508 0.758685 AGATGCTCCTCCTTCCCTCG 60.759 60.000 0.00 0.00 0.00 4.63
482 509 1.753368 GATGCTCCTCCTTCCCTCGG 61.753 65.000 0.00 0.00 0.00 4.63
483 510 3.855853 GCTCCTCCTTCCCTCGGC 61.856 72.222 0.00 0.00 0.00 5.54
484 511 2.042435 CTCCTCCTTCCCTCGGCT 60.042 66.667 0.00 0.00 0.00 5.52
485 512 1.687493 CTCCTCCTTCCCTCGGCTT 60.687 63.158 0.00 0.00 0.00 4.35
486 513 1.965754 CTCCTCCTTCCCTCGGCTTG 61.966 65.000 0.00 0.00 0.00 4.01
487 514 2.294078 CCTCCTTCCCTCGGCTTGT 61.294 63.158 0.00 0.00 0.00 3.16
488 515 1.219393 CTCCTTCCCTCGGCTTGTC 59.781 63.158 0.00 0.00 0.00 3.18
489 516 2.125512 CCTTCCCTCGGCTTGTCG 60.126 66.667 0.00 0.00 0.00 4.35
490 517 2.646175 CCTTCCCTCGGCTTGTCGA 61.646 63.158 0.00 0.00 37.60 4.20
524 551 0.534203 GCCTCCTCGGTGAAACAACA 60.534 55.000 0.00 0.00 39.98 3.33
529 556 1.069022 CCTCGGTGAAACAACATGCTG 60.069 52.381 0.00 0.00 39.98 4.41
593 620 1.078848 GCCGCACTGACCATCTCTT 60.079 57.895 0.00 0.00 0.00 2.85
597 624 1.738365 CGCACTGACCATCTCTTCTGG 60.738 57.143 0.00 0.00 39.80 3.86
599 626 0.908198 ACTGACCATCTCTTCTGGGC 59.092 55.000 0.00 0.00 42.62 5.36
619 650 3.394719 GCGAGGAGGGAATTGTAATCTC 58.605 50.000 0.00 0.00 0.00 2.75
623 654 6.058183 CGAGGAGGGAATTGTAATCTCATTT 58.942 40.000 0.00 0.00 0.00 2.32
636 667 9.618890 TTGTAATCTCATTTTGATTCCTAGAGG 57.381 33.333 0.00 0.00 35.90 3.69
697 728 7.662604 TTTTTGAGTAATACTTCCTCCGTTC 57.337 36.000 0.00 0.00 0.00 3.95
698 729 4.996788 TGAGTAATACTTCCTCCGTTCC 57.003 45.455 0.00 0.00 0.00 3.62
699 730 4.607239 TGAGTAATACTTCCTCCGTTCCT 58.393 43.478 0.00 0.00 0.00 3.36
700 731 5.759059 TGAGTAATACTTCCTCCGTTCCTA 58.241 41.667 0.00 0.00 0.00 2.94
701 732 6.189859 TGAGTAATACTTCCTCCGTTCCTAA 58.810 40.000 0.00 0.00 0.00 2.69
702 733 6.664816 TGAGTAATACTTCCTCCGTTCCTAAA 59.335 38.462 0.00 0.00 0.00 1.85
703 734 7.343833 TGAGTAATACTTCCTCCGTTCCTAAAT 59.656 37.037 0.00 0.00 0.00 1.40
704 735 8.773033 AGTAATACTTCCTCCGTTCCTAAATA 57.227 34.615 0.00 0.00 0.00 1.40
705 736 8.637099 AGTAATACTTCCTCCGTTCCTAAATAC 58.363 37.037 0.00 0.00 0.00 1.89
706 737 7.672122 AATACTTCCTCCGTTCCTAAATACT 57.328 36.000 0.00 0.00 0.00 2.12
707 738 7.672122 ATACTTCCTCCGTTCCTAAATACTT 57.328 36.000 0.00 0.00 0.00 2.24
708 739 5.731591 ACTTCCTCCGTTCCTAAATACTTG 58.268 41.667 0.00 0.00 0.00 3.16
709 740 5.247792 ACTTCCTCCGTTCCTAAATACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
710 741 5.334724 TCCTCCGTTCCTAAATACTTGTC 57.665 43.478 0.00 0.00 0.00 3.18
711 742 5.021458 TCCTCCGTTCCTAAATACTTGTCT 58.979 41.667 0.00 0.00 0.00 3.41
712 743 5.482878 TCCTCCGTTCCTAAATACTTGTCTT 59.517 40.000 0.00 0.00 0.00 3.01
713 744 6.013984 TCCTCCGTTCCTAAATACTTGTCTTT 60.014 38.462 0.00 0.00 0.00 2.52
714 745 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
715 746 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
716 747 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
717 748 8.587608 TCCGTTCCTAAATACTTGTCTTTCTAA 58.412 33.333 0.00 0.00 0.00 2.10
718 749 8.870879 CCGTTCCTAAATACTTGTCTTTCTAAG 58.129 37.037 0.00 0.00 0.00 2.18
719 750 8.381387 CGTTCCTAAATACTTGTCTTTCTAAGC 58.619 37.037 0.00 0.00 0.00 3.09
720 751 9.216117 GTTCCTAAATACTTGTCTTTCTAAGCA 57.784 33.333 0.00 0.00 0.00 3.91
721 752 9.959721 TTCCTAAATACTTGTCTTTCTAAGCAT 57.040 29.630 0.00 0.00 0.00 3.79
722 753 9.959721 TCCTAAATACTTGTCTTTCTAAGCATT 57.040 29.630 0.00 0.00 0.00 3.56
727 758 9.899226 AATACTTGTCTTTCTAAGCATTTCAAC 57.101 29.630 0.00 0.00 0.00 3.18
728 759 7.333528 ACTTGTCTTTCTAAGCATTTCAACA 57.666 32.000 0.00 0.00 0.00 3.33
729 760 7.771183 ACTTGTCTTTCTAAGCATTTCAACAA 58.229 30.769 0.00 0.00 0.00 2.83
730 761 7.917505 ACTTGTCTTTCTAAGCATTTCAACAAG 59.082 33.333 0.00 0.00 43.26 3.16
731 762 7.333528 TGTCTTTCTAAGCATTTCAACAAGT 57.666 32.000 0.00 0.00 0.00 3.16
732 763 7.195646 TGTCTTTCTAAGCATTTCAACAAGTG 58.804 34.615 0.00 0.00 0.00 3.16
733 764 7.066887 TGTCTTTCTAAGCATTTCAACAAGTGA 59.933 33.333 0.00 0.00 0.00 3.41
734 765 7.377131 GTCTTTCTAAGCATTTCAACAAGTGAC 59.623 37.037 0.00 0.00 35.39 3.67
735 766 6.942532 TTCTAAGCATTTCAACAAGTGACT 57.057 33.333 0.00 0.00 35.39 3.41
736 767 8.445275 TTTCTAAGCATTTCAACAAGTGACTA 57.555 30.769 0.00 0.00 35.39 2.59
737 768 7.421530 TCTAAGCATTTCAACAAGTGACTAC 57.578 36.000 0.00 0.00 35.39 2.73
738 769 6.989759 TCTAAGCATTTCAACAAGTGACTACA 59.010 34.615 0.00 0.00 35.39 2.74
739 770 6.639632 AAGCATTTCAACAAGTGACTACAT 57.360 33.333 0.00 0.00 35.39 2.29
740 771 7.744087 AAGCATTTCAACAAGTGACTACATA 57.256 32.000 0.00 0.00 35.39 2.29
741 772 7.133891 AGCATTTCAACAAGTGACTACATAC 57.866 36.000 0.00 0.00 35.39 2.39
742 773 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
743 774 6.128661 GCATTTCAACAAGTGACTACATACGA 60.129 38.462 0.00 0.00 35.39 3.43
744 775 7.570507 GCATTTCAACAAGTGACTACATACGAA 60.571 37.037 0.00 0.00 35.39 3.85
745 776 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
746 777 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
747 778 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
748 779 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
749 780 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
750 781 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
751 782 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
752 783 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
753 784 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
754 785 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
755 786 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
756 787 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
757 788 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
758 789 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
759 790 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
760 791 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
761 792 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
762 793 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
763 794 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
764 795 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
765 796 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
810 841 9.647797 ACATTCGTATGTAGTAGTCATTTGAAA 57.352 29.630 5.81 0.00 43.12 2.69
813 844 9.647797 TTCGTATGTAGTAGTCATTTGAAATGT 57.352 29.630 16.62 2.38 0.00 2.71
814 845 9.297586 TCGTATGTAGTAGTCATTTGAAATGTC 57.702 33.333 16.62 11.74 0.00 3.06
815 846 9.302345 CGTATGTAGTAGTCATTTGAAATGTCT 57.698 33.333 18.62 18.62 0.00 3.41
839 870 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
840 871 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
841 872 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
842 873 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
843 874 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
844 875 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
845 876 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
846 877 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
847 878 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
848 879 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
849 880 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
850 881 3.463048 TTAGGAACGGAGGGAGTAGTT 57.537 47.619 0.00 0.00 0.00 2.24
851 882 4.591321 TTAGGAACGGAGGGAGTAGTTA 57.409 45.455 0.00 0.00 0.00 2.24
852 883 3.684408 AGGAACGGAGGGAGTAGTTAT 57.316 47.619 0.00 0.00 0.00 1.89
853 884 3.991683 AGGAACGGAGGGAGTAGTTATT 58.008 45.455 0.00 0.00 0.00 1.40
854 885 4.359996 AGGAACGGAGGGAGTAGTTATTT 58.640 43.478 0.00 0.00 0.00 1.40
855 886 5.522641 AGGAACGGAGGGAGTAGTTATTTA 58.477 41.667 0.00 0.00 0.00 1.40
856 887 6.141790 AGGAACGGAGGGAGTAGTTATTTAT 58.858 40.000 0.00 0.00 0.00 1.40
857 888 6.614496 AGGAACGGAGGGAGTAGTTATTTATT 59.386 38.462 0.00 0.00 0.00 1.40
858 889 7.126879 AGGAACGGAGGGAGTAGTTATTTATTT 59.873 37.037 0.00 0.00 0.00 1.40
859 890 7.772292 GGAACGGAGGGAGTAGTTATTTATTTT 59.228 37.037 0.00 0.00 0.00 1.82
860 891 8.728337 AACGGAGGGAGTAGTTATTTATTTTC 57.272 34.615 0.00 0.00 0.00 2.29
861 892 8.087303 ACGGAGGGAGTAGTTATTTATTTTCT 57.913 34.615 0.00 0.00 0.00 2.52
862 893 9.205513 ACGGAGGGAGTAGTTATTTATTTTCTA 57.794 33.333 0.00 0.00 0.00 2.10
935 966 1.349026 TCTCAGCTTGAAAGTCCAGGG 59.651 52.381 0.00 0.00 0.00 4.45
937 968 0.251077 CAGCTTGAAAGTCCAGGGCT 60.251 55.000 0.00 0.00 0.00 5.19
939 970 1.280421 AGCTTGAAAGTCCAGGGCTAG 59.720 52.381 0.00 0.00 0.00 3.42
999 1059 2.014857 CGAACGTATCCTGACTCCAGA 58.985 52.381 0.00 0.00 43.02 3.86
1033 1093 2.151502 TCTAGGCTGAGGAGTTGAGG 57.848 55.000 0.00 0.00 0.00 3.86
1034 1094 1.641192 TCTAGGCTGAGGAGTTGAGGA 59.359 52.381 0.00 0.00 0.00 3.71
1035 1095 2.246067 TCTAGGCTGAGGAGTTGAGGAT 59.754 50.000 0.00 0.00 0.00 3.24
1036 1096 1.963985 AGGCTGAGGAGTTGAGGATT 58.036 50.000 0.00 0.00 0.00 3.01
1037 1097 2.273619 AGGCTGAGGAGTTGAGGATTT 58.726 47.619 0.00 0.00 0.00 2.17
1038 1098 2.646798 AGGCTGAGGAGTTGAGGATTTT 59.353 45.455 0.00 0.00 0.00 1.82
1039 1099 3.846588 AGGCTGAGGAGTTGAGGATTTTA 59.153 43.478 0.00 0.00 0.00 1.52
1040 1100 4.080638 AGGCTGAGGAGTTGAGGATTTTAG 60.081 45.833 0.00 0.00 0.00 1.85
1041 1101 4.195416 GCTGAGGAGTTGAGGATTTTAGG 58.805 47.826 0.00 0.00 0.00 2.69
1100 1160 3.256631 GTCTCCCAACACAATCAATTGCT 59.743 43.478 0.00 0.00 41.38 3.91
1101 1161 4.458989 GTCTCCCAACACAATCAATTGCTA 59.541 41.667 0.00 0.00 41.38 3.49
1255 1424 3.677121 CGCCGAATCTAAGGAATCAGATG 59.323 47.826 0.00 0.00 31.87 2.90
1264 1433 7.493743 TCTAAGGAATCAGATGTACGAGTAC 57.506 40.000 6.46 6.46 36.63 2.73
1265 1434 4.815040 AGGAATCAGATGTACGAGTACG 57.185 45.455 8.62 0.00 45.75 3.67
1266 1435 4.449131 AGGAATCAGATGTACGAGTACGA 58.551 43.478 8.62 1.07 42.66 3.43
1267 1436 4.512198 AGGAATCAGATGTACGAGTACGAG 59.488 45.833 8.62 0.00 42.66 4.18
1268 1437 4.272991 GGAATCAGATGTACGAGTACGAGT 59.727 45.833 8.62 2.13 42.66 4.18
1269 1438 5.464722 GGAATCAGATGTACGAGTACGAGTA 59.535 44.000 8.62 0.36 42.66 2.59
1270 1439 6.018425 GGAATCAGATGTACGAGTACGAGTAA 60.018 42.308 8.62 0.00 42.66 2.24
1271 1440 7.307870 GGAATCAGATGTACGAGTACGAGTAAT 60.308 40.741 8.62 0.00 42.66 1.89
1272 1441 8.599055 AATCAGATGTACGAGTACGAGTAATA 57.401 34.615 8.62 0.28 42.66 0.98
1273 1442 8.599055 ATCAGATGTACGAGTACGAGTAATAA 57.401 34.615 8.62 0.00 42.66 1.40
1274 1443 8.599055 TCAGATGTACGAGTACGAGTAATAAT 57.401 34.615 8.62 1.66 42.66 1.28
1275 1444 8.706936 TCAGATGTACGAGTACGAGTAATAATC 58.293 37.037 8.62 8.59 42.66 1.75
1276 1445 7.956403 CAGATGTACGAGTACGAGTAATAATCC 59.044 40.741 8.62 0.00 42.66 3.01
1277 1446 7.658982 AGATGTACGAGTACGAGTAATAATCCA 59.341 37.037 8.62 0.51 42.66 3.41
1278 1447 7.182361 TGTACGAGTACGAGTAATAATCCAG 57.818 40.000 8.62 0.00 42.66 3.86
1279 1448 5.686159 ACGAGTACGAGTAATAATCCAGG 57.314 43.478 0.00 0.00 42.66 4.45
1280 1449 5.371526 ACGAGTACGAGTAATAATCCAGGA 58.628 41.667 0.00 0.00 42.66 3.86
1423 1616 2.852449 TCCGCATGGTAAACTTGTTGA 58.148 42.857 0.00 0.00 36.30 3.18
1604 1830 3.033764 GTTGGACGTTCGCTCGCA 61.034 61.111 0.00 0.00 0.00 5.10
1659 1885 5.378985 TCCTATTCCTCCCATCTACTACCTT 59.621 44.000 0.00 0.00 0.00 3.50
1836 2086 3.181467 CCTCCTACTCTTTGCATCCTGAG 60.181 52.174 0.00 0.00 0.00 3.35
1900 2150 1.544759 CCACCTACACCTTTGACACCC 60.545 57.143 0.00 0.00 0.00 4.61
2032 2282 0.607620 TGGCCAAATTTACAGCTGCC 59.392 50.000 15.27 6.28 37.90 4.85
2119 2372 0.320421 TCTGTTAAGTGAGCGCCCAC 60.320 55.000 14.98 14.98 37.32 4.61
2237 2490 2.227968 GACGACGTTGCTCATGGTGC 62.228 60.000 0.13 0.00 0.00 5.01
2364 2620 1.523758 AAGTGCCTAAAGAAGCCACG 58.476 50.000 0.00 0.00 0.00 4.94
2518 2866 2.805671 TGTGCACGTCTGATTTGGTAAG 59.194 45.455 13.13 0.00 0.00 2.34
2529 2877 7.562135 GTCTGATTTGGTAAGTGTATTCCCTA 58.438 38.462 0.00 0.00 0.00 3.53
2571 2933 8.824159 ATAAGATTATGAAATGACACCTCTCG 57.176 34.615 0.00 0.00 0.00 4.04
2585 2950 3.741344 CACCTCTCGTTTTCCTGTAAGTG 59.259 47.826 0.00 0.00 0.00 3.16
2643 3008 1.204704 CGTCATTCAGCCTGTCACCTA 59.795 52.381 0.00 0.00 0.00 3.08
2691 3056 6.197364 TCTGTTTTTGTTGTACCGTCATTT 57.803 33.333 0.00 0.00 0.00 2.32
2693 3058 7.932335 TCTGTTTTTGTTGTACCGTCATTTAT 58.068 30.769 0.00 0.00 0.00 1.40
2769 3198 8.353684 ACCGTCATTTTACTATCTGATCTAGTG 58.646 37.037 0.00 0.00 31.96 2.74
2770 3199 7.810282 CCGTCATTTTACTATCTGATCTAGTGG 59.190 40.741 0.00 0.00 31.96 4.00
2771 3200 8.353684 CGTCATTTTACTATCTGATCTAGTGGT 58.646 37.037 0.00 0.00 31.96 4.16
2772 3201 9.469807 GTCATTTTACTATCTGATCTAGTGGTG 57.530 37.037 0.00 0.00 31.96 4.17
2774 3203 6.978674 TTTACTATCTGATCTAGTGGTGGG 57.021 41.667 0.00 0.00 31.96 4.61
2775 3204 4.816048 ACTATCTGATCTAGTGGTGGGA 57.184 45.455 0.00 0.00 0.00 4.37
2776 3205 4.735369 ACTATCTGATCTAGTGGTGGGAG 58.265 47.826 0.00 0.00 0.00 4.30
2777 3206 3.981516 ATCTGATCTAGTGGTGGGAGA 57.018 47.619 0.00 0.00 0.00 3.71
2785 3524 7.872138 TGATCTAGTGGTGGGAGATTATTTTT 58.128 34.615 0.00 0.00 30.01 1.94
2824 3849 2.551504 GGTGGGAGATGTTTACCGTTGT 60.552 50.000 0.00 0.00 0.00 3.32
3111 4532 2.797156 GGCGTCATACAAGATACAGCTG 59.203 50.000 13.48 13.48 0.00 4.24
3162 4583 4.730613 GCAACGTTTCTTGCTTTGAGAAGA 60.731 41.667 0.00 0.00 42.84 2.87
3163 4584 5.331902 CAACGTTTCTTGCTTTGAGAAGAA 58.668 37.500 0.00 0.00 36.60 2.52
3284 4748 1.212935 CTCCCACCGATTCCTGGAAAT 59.787 52.381 14.03 2.17 0.00 2.17
3285 4749 2.438021 CTCCCACCGATTCCTGGAAATA 59.562 50.000 14.03 0.00 0.00 1.40
3286 4750 2.438021 TCCCACCGATTCCTGGAAATAG 59.562 50.000 14.03 7.26 0.00 1.73
3287 4751 2.438021 CCCACCGATTCCTGGAAATAGA 59.562 50.000 14.03 0.00 0.00 1.98
3288 4752 3.073062 CCCACCGATTCCTGGAAATAGAT 59.927 47.826 14.03 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.975218 AAGGGATCGTTGGCTTATAATTATAAT 57.025 29.630 16.41 1.75 0.00 1.28
6 7 7.762615 CGAAGGGATCGTTGGCTTATAATTATA 59.237 37.037 0.81 0.81 46.52 0.98
7 8 6.594159 CGAAGGGATCGTTGGCTTATAATTAT 59.406 38.462 2.97 2.97 46.52 1.28
8 9 5.929992 CGAAGGGATCGTTGGCTTATAATTA 59.070 40.000 0.00 0.00 46.52 1.40
9 10 4.755123 CGAAGGGATCGTTGGCTTATAATT 59.245 41.667 0.00 0.00 46.52 1.40
10 11 4.315803 CGAAGGGATCGTTGGCTTATAAT 58.684 43.478 0.00 0.00 46.52 1.28
23 24 2.552031 GTCCAAAGTAGCGAAGGGATC 58.448 52.381 0.00 0.00 0.00 3.36
24 25 1.134788 CGTCCAAAGTAGCGAAGGGAT 60.135 52.381 0.00 0.00 0.00 3.85
25 26 0.245539 CGTCCAAAGTAGCGAAGGGA 59.754 55.000 0.00 0.00 0.00 4.20
26 27 0.739813 CCGTCCAAAGTAGCGAAGGG 60.740 60.000 0.00 0.00 0.00 3.95
27 28 0.739813 CCCGTCCAAAGTAGCGAAGG 60.740 60.000 0.00 0.00 0.00 3.46
28 29 0.037605 ACCCGTCCAAAGTAGCGAAG 60.038 55.000 0.00 0.00 0.00 3.79
29 30 0.393820 AACCCGTCCAAAGTAGCGAA 59.606 50.000 0.00 0.00 0.00 4.70
30 31 0.037975 GAACCCGTCCAAAGTAGCGA 60.038 55.000 0.00 0.00 0.00 4.93
31 32 1.349259 CGAACCCGTCCAAAGTAGCG 61.349 60.000 0.00 0.00 0.00 4.26
32 33 1.017701 CCGAACCCGTCCAAAGTAGC 61.018 60.000 0.00 0.00 0.00 3.58
33 34 0.319405 ACCGAACCCGTCCAAAGTAG 59.681 55.000 0.00 0.00 0.00 2.57
34 35 1.545582 CTACCGAACCCGTCCAAAGTA 59.454 52.381 0.00 0.00 0.00 2.24
35 36 0.319405 CTACCGAACCCGTCCAAAGT 59.681 55.000 0.00 0.00 0.00 2.66
36 37 1.017701 GCTACCGAACCCGTCCAAAG 61.018 60.000 0.00 0.00 0.00 2.77
37 38 1.004679 GCTACCGAACCCGTCCAAA 60.005 57.895 0.00 0.00 0.00 3.28
38 39 2.658422 GCTACCGAACCCGTCCAA 59.342 61.111 0.00 0.00 0.00 3.53
39 40 3.384532 GGCTACCGAACCCGTCCA 61.385 66.667 0.00 0.00 0.00 4.02
40 41 4.152964 GGGCTACCGAACCCGTCC 62.153 72.222 0.00 0.00 36.07 4.79
45 46 1.078637 GTTGGAGGGCTACCGAACC 60.079 63.158 0.00 0.00 43.47 3.62
86 87 4.329545 GTTCGGGGCAGCTCCACA 62.330 66.667 13.26 0.00 38.54 4.17
134 135 8.812329 CAGATTTTACACTACAAGCTTAGCTAG 58.188 37.037 7.32 3.83 38.25 3.42
135 136 8.528643 TCAGATTTTACACTACAAGCTTAGCTA 58.471 33.333 7.32 0.00 38.25 3.32
136 137 7.386851 TCAGATTTTACACTACAAGCTTAGCT 58.613 34.615 0.00 0.00 42.56 3.32
137 138 7.201565 CCTCAGATTTTACACTACAAGCTTAGC 60.202 40.741 0.00 0.00 0.00 3.09
138 139 8.035394 TCCTCAGATTTTACACTACAAGCTTAG 58.965 37.037 0.00 0.00 0.00 2.18
139 140 7.903145 TCCTCAGATTTTACACTACAAGCTTA 58.097 34.615 0.00 0.00 0.00 3.09
147 148 6.269077 TCCACAACTCCTCAGATTTTACACTA 59.731 38.462 0.00 0.00 0.00 2.74
167 168 1.149627 CGGGTTTCCCAACTCCACA 59.850 57.895 5.64 0.00 45.83 4.17
193 194 1.133915 ACTCCCGCTTCCAAGTTTTCA 60.134 47.619 0.00 0.00 0.00 2.69
259 260 1.776662 ATGGAGACGAGGGATCGAAA 58.223 50.000 4.44 0.00 36.85 3.46
271 298 0.543749 CAGTGGAGGGGAATGGAGAC 59.456 60.000 0.00 0.00 0.00 3.36
335 362 2.813226 TTCAATCACGGCGGGGGAAG 62.813 60.000 10.28 0.00 0.00 3.46
340 367 2.398554 CCAGTTCAATCACGGCGGG 61.399 63.158 13.24 7.61 0.00 6.13
349 376 0.396435 TCCTCACGTGCCAGTTCAAT 59.604 50.000 11.67 0.00 0.00 2.57
362 389 0.457851 ACTGCGCTCTGTATCCTCAC 59.542 55.000 9.73 0.00 0.00 3.51
365 392 1.407258 GAAGACTGCGCTCTGTATCCT 59.593 52.381 9.73 0.00 0.00 3.24
397 424 1.805869 CTCTTGCTCAAGGTGGAGTG 58.194 55.000 9.48 0.00 38.88 3.51
428 455 0.252284 AGGTGGAGGAGGTGAACGAT 60.252 55.000 0.00 0.00 0.00 3.73
429 456 0.898789 GAGGTGGAGGAGGTGAACGA 60.899 60.000 0.00 0.00 0.00 3.85
448 475 1.008652 CATCTCTGGCTCGAGCTCG 60.009 63.158 34.46 30.03 41.70 5.03
449 476 1.300080 GCATCTCTGGCTCGAGCTC 60.300 63.158 34.46 24.64 41.70 4.09
450 477 1.757731 AGCATCTCTGGCTCGAGCT 60.758 57.895 34.46 13.16 36.81 4.09
451 478 2.813901 AGCATCTCTGGCTCGAGC 59.186 61.111 29.38 29.38 36.81 5.03
456 483 0.326427 AAGGAGGAGCATCTCTGGCT 60.326 55.000 6.34 0.00 46.07 4.75
457 484 0.106521 GAAGGAGGAGCATCTCTGGC 59.893 60.000 6.34 0.00 34.39 4.85
458 485 0.758123 GGAAGGAGGAGCATCTCTGG 59.242 60.000 6.34 0.00 34.39 3.86
459 486 0.758123 GGGAAGGAGGAGCATCTCTG 59.242 60.000 6.34 0.00 34.39 3.35
460 487 0.641601 AGGGAAGGAGGAGCATCTCT 59.358 55.000 6.34 0.00 34.39 3.10
461 488 1.047801 GAGGGAAGGAGGAGCATCTC 58.952 60.000 0.00 0.00 33.73 2.75
462 489 0.758685 CGAGGGAAGGAGGAGCATCT 60.759 60.000 0.00 0.00 33.73 2.90
463 490 1.745264 CGAGGGAAGGAGGAGCATC 59.255 63.158 0.00 0.00 0.00 3.91
464 491 1.764054 CCGAGGGAAGGAGGAGCAT 60.764 63.158 0.00 0.00 0.00 3.79
465 492 2.364317 CCGAGGGAAGGAGGAGCA 60.364 66.667 0.00 0.00 0.00 4.26
466 493 3.855853 GCCGAGGGAAGGAGGAGC 61.856 72.222 0.00 0.00 0.00 4.70
467 494 1.687493 AAGCCGAGGGAAGGAGGAG 60.687 63.158 0.00 0.00 0.00 3.69
468 495 1.990060 CAAGCCGAGGGAAGGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
469 496 2.245438 GACAAGCCGAGGGAAGGAGG 62.245 65.000 0.00 0.00 0.00 4.30
470 497 1.219393 GACAAGCCGAGGGAAGGAG 59.781 63.158 0.00 0.00 0.00 3.69
471 498 2.646175 CGACAAGCCGAGGGAAGGA 61.646 63.158 0.00 0.00 0.00 3.36
472 499 2.125512 CGACAAGCCGAGGGAAGG 60.126 66.667 0.00 0.00 0.00 3.46
473 500 1.446272 GTCGACAAGCCGAGGGAAG 60.446 63.158 11.55 0.00 39.43 3.46
474 501 2.654877 GTCGACAAGCCGAGGGAA 59.345 61.111 11.55 0.00 39.43 3.97
475 502 3.744719 CGTCGACAAGCCGAGGGA 61.745 66.667 17.16 0.00 39.77 4.20
482 509 1.805945 CTGGTAGGCGTCGACAAGC 60.806 63.158 17.16 11.63 0.00 4.01
483 510 0.038526 AACTGGTAGGCGTCGACAAG 60.039 55.000 17.16 2.80 0.00 3.16
484 511 0.319211 CAACTGGTAGGCGTCGACAA 60.319 55.000 17.16 0.00 0.00 3.18
485 512 1.287815 CAACTGGTAGGCGTCGACA 59.712 57.895 17.16 0.00 0.00 4.35
486 513 1.007336 CACAACTGGTAGGCGTCGAC 61.007 60.000 5.18 5.18 0.00 4.20
487 514 1.287815 CACAACTGGTAGGCGTCGA 59.712 57.895 0.00 0.00 0.00 4.20
488 515 2.380410 GCACAACTGGTAGGCGTCG 61.380 63.158 0.00 0.00 0.00 5.12
489 516 2.033194 GGCACAACTGGTAGGCGTC 61.033 63.158 0.00 0.00 0.00 5.19
490 517 2.032071 GGCACAACTGGTAGGCGT 59.968 61.111 0.00 0.00 0.00 5.68
593 620 1.306997 AATTCCCTCCTCGCCCAGA 60.307 57.895 0.00 0.00 0.00 3.86
597 624 2.104963 AGATTACAATTCCCTCCTCGCC 59.895 50.000 0.00 0.00 0.00 5.54
599 626 4.672587 TGAGATTACAATTCCCTCCTCG 57.327 45.455 0.00 0.00 0.00 4.63
619 650 6.096001 CAGAAACCCCTCTAGGAATCAAAATG 59.904 42.308 0.00 0.00 38.24 2.32
623 654 4.435137 TCAGAAACCCCTCTAGGAATCAA 58.565 43.478 0.00 0.00 38.24 2.57
634 665 4.292306 ACCAGAACATTATCAGAAACCCCT 59.708 41.667 0.00 0.00 0.00 4.79
636 667 7.881775 ATAACCAGAACATTATCAGAAACCC 57.118 36.000 0.00 0.00 0.00 4.11
679 710 7.672122 ATTTAGGAACGGAGGAAGTATTACT 57.328 36.000 0.00 0.00 46.66 2.24
680 711 8.637099 AGTATTTAGGAACGGAGGAAGTATTAC 58.363 37.037 0.00 0.00 0.00 1.89
681 712 8.773033 AGTATTTAGGAACGGAGGAAGTATTA 57.227 34.615 0.00 0.00 0.00 0.98
682 713 7.672122 AGTATTTAGGAACGGAGGAAGTATT 57.328 36.000 0.00 0.00 0.00 1.89
683 714 7.125356 ACAAGTATTTAGGAACGGAGGAAGTAT 59.875 37.037 0.00 0.00 0.00 2.12
684 715 6.438425 ACAAGTATTTAGGAACGGAGGAAGTA 59.562 38.462 0.00 0.00 0.00 2.24
685 716 5.247792 ACAAGTATTTAGGAACGGAGGAAGT 59.752 40.000 0.00 0.00 0.00 3.01
686 717 5.731591 ACAAGTATTTAGGAACGGAGGAAG 58.268 41.667 0.00 0.00 0.00 3.46
687 718 5.482878 AGACAAGTATTTAGGAACGGAGGAA 59.517 40.000 0.00 0.00 0.00 3.36
688 719 5.021458 AGACAAGTATTTAGGAACGGAGGA 58.979 41.667 0.00 0.00 0.00 3.71
689 720 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
690 721 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
691 722 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
692 723 8.767478 TTAGAAAGACAAGTATTTAGGAACGG 57.233 34.615 0.00 0.00 0.00 4.44
693 724 8.381387 GCTTAGAAAGACAAGTATTTAGGAACG 58.619 37.037 0.00 0.00 0.00 3.95
694 725 9.216117 TGCTTAGAAAGACAAGTATTTAGGAAC 57.784 33.333 0.00 0.00 0.00 3.62
695 726 9.959721 ATGCTTAGAAAGACAAGTATTTAGGAA 57.040 29.630 0.00 0.00 0.00 3.36
696 727 9.959721 AATGCTTAGAAAGACAAGTATTTAGGA 57.040 29.630 0.00 0.00 34.65 2.94
701 732 9.899226 GTTGAAATGCTTAGAAAGACAAGTATT 57.101 29.630 0.00 0.00 38.29 1.89
702 733 9.066892 TGTTGAAATGCTTAGAAAGACAAGTAT 57.933 29.630 0.00 0.00 0.00 2.12
703 734 8.445275 TGTTGAAATGCTTAGAAAGACAAGTA 57.555 30.769 0.00 0.00 0.00 2.24
704 735 7.333528 TGTTGAAATGCTTAGAAAGACAAGT 57.666 32.000 0.00 0.00 0.00 3.16
705 736 7.917505 ACTTGTTGAAATGCTTAGAAAGACAAG 59.082 33.333 0.00 0.00 43.36 3.16
706 737 7.701924 CACTTGTTGAAATGCTTAGAAAGACAA 59.298 33.333 0.00 0.00 0.00 3.18
707 738 7.066887 TCACTTGTTGAAATGCTTAGAAAGACA 59.933 33.333 0.00 0.00 0.00 3.41
708 739 7.377131 GTCACTTGTTGAAATGCTTAGAAAGAC 59.623 37.037 0.00 0.00 35.39 3.01
709 740 7.283127 AGTCACTTGTTGAAATGCTTAGAAAGA 59.717 33.333 0.00 0.00 35.39 2.52
710 741 7.420800 AGTCACTTGTTGAAATGCTTAGAAAG 58.579 34.615 0.00 0.00 35.39 2.62
711 742 7.333528 AGTCACTTGTTGAAATGCTTAGAAA 57.666 32.000 0.00 0.00 35.39 2.52
712 743 6.942532 AGTCACTTGTTGAAATGCTTAGAA 57.057 33.333 0.00 0.00 35.39 2.10
713 744 6.989759 TGTAGTCACTTGTTGAAATGCTTAGA 59.010 34.615 0.00 0.00 35.39 2.10
714 745 7.189693 TGTAGTCACTTGTTGAAATGCTTAG 57.810 36.000 0.00 0.00 35.39 2.18
715 746 7.744087 ATGTAGTCACTTGTTGAAATGCTTA 57.256 32.000 0.00 0.00 35.39 3.09
716 747 6.639632 ATGTAGTCACTTGTTGAAATGCTT 57.360 33.333 0.00 0.00 35.39 3.91
717 748 6.128553 CGTATGTAGTCACTTGTTGAAATGCT 60.129 38.462 0.00 0.00 35.39 3.79
718 749 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
719 750 7.346208 TCGTATGTAGTCACTTGTTGAAATG 57.654 36.000 0.00 0.00 35.39 2.32
720 751 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
721 752 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
722 753 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
723 754 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
724 755 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
725 756 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
726 757 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
727 758 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
728 759 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
729 760 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
730 761 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
731 762 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
732 763 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
733 764 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
734 765 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
735 766 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
736 767 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
737 768 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
738 769 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
739 770 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
740 771 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
741 772 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
742 773 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
787 818 9.647797 ACATTTCAAATGACTACTACATACGAA 57.352 29.630 17.30 0.00 0.00 3.85
788 819 9.297586 GACATTTCAAATGACTACTACATACGA 57.702 33.333 17.30 0.00 0.00 3.43
789 820 9.302345 AGACATTTCAAATGACTACTACATACG 57.698 33.333 17.30 0.00 0.00 3.06
813 844 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
814 845 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
815 846 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
816 847 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
817 848 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
818 849 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
819 850 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
820 851 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
821 852 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
822 853 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
823 854 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
824 855 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
825 856 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
826 857 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
827 858 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
828 859 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
829 860 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
830 861 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
831 862 4.803329 ATAACTACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
832 863 3.684408 ATAACTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
833 864 4.750021 AAATAACTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
834 865 8.728337 AAAATAAATAACTACTCCCTCCGTTC 57.272 34.615 0.00 0.00 0.00 3.95
835 866 8.546322 AGAAAATAAATAACTACTCCCTCCGTT 58.454 33.333 0.00 0.00 0.00 4.44
836 867 8.087303 AGAAAATAAATAACTACTCCCTCCGT 57.913 34.615 0.00 0.00 0.00 4.69
865 896 5.116882 GGATGAGTTGGTATTGTCTGTACC 58.883 45.833 0.00 0.00 41.59 3.34
866 897 5.116882 GGGATGAGTTGGTATTGTCTGTAC 58.883 45.833 0.00 0.00 0.00 2.90
867 898 4.142026 CGGGATGAGTTGGTATTGTCTGTA 60.142 45.833 0.00 0.00 0.00 2.74
901 932 2.232298 CTGAGAACGGAGGCCTGGAC 62.232 65.000 12.00 0.00 0.00 4.02
912 943 2.478134 CTGGACTTTCAAGCTGAGAACG 59.522 50.000 1.62 3.31 0.00 3.95
937 968 1.681793 GGCTAGAATGTGGCTCGACTA 59.318 52.381 0.00 0.00 0.00 2.59
939 970 0.461961 AGGCTAGAATGTGGCTCGAC 59.538 55.000 0.00 0.00 33.73 4.20
967 998 3.317430 GGATACGTTCGGGAGTACATTCT 59.683 47.826 0.00 0.00 0.00 2.40
969 1000 3.067742 CAGGATACGTTCGGGAGTACATT 59.932 47.826 0.00 0.00 46.39 2.71
999 1059 7.281100 CCTCAGCCTAGATTCTCGTTTAAAATT 59.719 37.037 0.00 0.00 0.00 1.82
1033 1093 3.679083 CGGTGGGAGACAGACCTAAAATC 60.679 52.174 0.00 0.00 33.31 2.17
1034 1094 2.236395 CGGTGGGAGACAGACCTAAAAT 59.764 50.000 0.00 0.00 33.31 1.82
1035 1095 1.621814 CGGTGGGAGACAGACCTAAAA 59.378 52.381 0.00 0.00 33.31 1.52
1036 1096 1.263356 CGGTGGGAGACAGACCTAAA 58.737 55.000 0.00 0.00 33.31 1.85
1037 1097 1.255667 GCGGTGGGAGACAGACCTAA 61.256 60.000 0.00 0.00 33.31 2.69
1038 1098 1.681327 GCGGTGGGAGACAGACCTA 60.681 63.158 0.00 0.00 33.31 3.08
1039 1099 2.997897 GCGGTGGGAGACAGACCT 60.998 66.667 0.00 0.00 33.31 3.85
1040 1100 4.083862 GGCGGTGGGAGACAGACC 62.084 72.222 0.00 0.00 0.00 3.85
1041 1101 4.436998 CGGCGGTGGGAGACAGAC 62.437 72.222 0.00 0.00 0.00 3.51
1100 1160 0.106335 TCACCAACGGAGCGGTTTTA 59.894 50.000 0.00 0.00 34.08 1.52
1101 1161 1.153127 TCACCAACGGAGCGGTTTT 60.153 52.632 0.00 0.00 34.08 2.43
1255 1424 6.425114 TCCTGGATTATTACTCGTACTCGTAC 59.575 42.308 0.00 0.00 38.33 3.67
1332 1501 0.387622 CACGCTTTGGCATCCTTGTG 60.388 55.000 0.00 0.00 38.60 3.33
1491 1708 1.534595 GTGAAGTACGACACGAGAGGT 59.465 52.381 9.03 0.00 0.00 3.85
1604 1830 2.594592 GGGCAAAGGTGACGCACT 60.595 61.111 9.31 0.00 31.03 4.40
1659 1885 0.892755 ATAACTCGTTGCCGACAGGA 59.107 50.000 0.00 0.00 41.02 3.86
1836 2086 0.974383 TGAAGAGGAAGGTCCGTTCC 59.026 55.000 10.10 10.10 45.76 3.62
1872 2122 3.391382 GTGTAGGTGGCCTCGGCT 61.391 66.667 3.32 0.00 41.60 5.52
1873 2123 4.468689 GGTGTAGGTGGCCTCGGC 62.469 72.222 3.32 0.00 41.06 5.54
1900 2150 3.815401 AGGAGTTTCCATGAACGTTTCTG 59.185 43.478 0.46 3.05 39.61 3.02
1955 2205 2.359975 GGCCCGGGTCAAAGTGAG 60.360 66.667 23.50 0.00 0.00 3.51
2032 2282 2.941064 CAGTGTCATAGATGGGCACTTG 59.059 50.000 13.92 8.90 40.00 3.16
2119 2372 2.109609 GCACCAACATGCATATCACG 57.890 50.000 0.00 0.00 45.39 4.35
2237 2490 4.849329 GACGACCGGGTAGCTGCG 62.849 72.222 6.32 5.45 0.00 5.18
2249 2502 0.026027 ACGATAGAAGCGACGACGAC 59.974 55.000 12.29 2.46 40.29 4.34
2250 2503 0.299895 GACGATAGAAGCGACGACGA 59.700 55.000 12.29 0.00 40.29 4.20
2251 2504 0.301088 AGACGATAGAAGCGACGACG 59.699 55.000 2.12 2.12 40.64 5.12
2364 2620 2.010497 GGATCTTGAAGGAACGGCTTC 58.990 52.381 0.00 0.00 0.00 3.86
2410 2671 4.758674 AGGAAGTGACTCATGACACAATTG 59.241 41.667 16.30 3.24 40.37 2.32
2566 2928 2.737252 GCCACTTACAGGAAAACGAGAG 59.263 50.000 0.00 0.00 0.00 3.20
2568 2930 2.767505 AGCCACTTACAGGAAAACGAG 58.232 47.619 0.00 0.00 0.00 4.18
2569 2931 2.922740 AGCCACTTACAGGAAAACGA 57.077 45.000 0.00 0.00 0.00 3.85
2570 2932 2.875933 TGAAGCCACTTACAGGAAAACG 59.124 45.455 0.00 0.00 0.00 3.60
2571 2933 3.883489 ACTGAAGCCACTTACAGGAAAAC 59.117 43.478 0.00 0.00 35.08 2.43
2585 2950 1.921243 AAACGTTTGCAACTGAAGCC 58.079 45.000 13.81 0.00 0.00 4.35
2601 2966 5.289917 ACGGTGCAACAAAAACAGATTAAAC 59.710 36.000 0.98 0.00 39.98 2.01
2681 3046 4.028131 AGGTGACAGGATAAATGACGGTA 58.972 43.478 0.00 0.00 0.00 4.02
2691 3056 1.622449 CCAGGGTCAGGTGACAGGATA 60.622 57.143 12.09 0.00 46.47 2.59
2693 3058 1.536418 CCAGGGTCAGGTGACAGGA 60.536 63.158 12.09 0.00 46.47 3.86
2734 3163 5.000012 AGTAAAATGACGGTGCAACAAAA 58.000 34.783 0.98 0.00 39.98 2.44
2735 3164 4.640789 AGTAAAATGACGGTGCAACAAA 57.359 36.364 0.98 0.00 39.98 2.83
2795 3534 2.795231 ACATCTCCCACCACAGAATG 57.205 50.000 0.00 0.00 46.00 2.67
3111 4532 9.774742 GTTTGATCATATTACTTGTTTCTGGAC 57.225 33.333 0.00 0.00 0.00 4.02
3162 4583 5.299949 ACGTACTTCCCATCGTTACTTTTT 58.700 37.500 0.00 0.00 32.62 1.94
3163 4584 4.886579 ACGTACTTCCCATCGTTACTTTT 58.113 39.130 0.00 0.00 32.62 2.27


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

AutoCloner maintained by Alex Coulton.