Multiple sequence alignment - TraesCS5D01G562000

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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 TraesCS5D01G562000 chr5D 100.000 3352 0 0 1 3352 562065211 562061860 0.000000e+00 6191.0
1 TraesCS5D01G562000 chr5D 87.678 211 20 5 324 530 422461469 422461677 1.200000e-59 241.0
2 TraesCS5D01G562000 chr5D 82.784 273 25 5 265 535 202399597 202399345 1.210000e-54 224.0
3 TraesCS5D01G562000 chr7B 86.403 2221 143 73 542 2708 640727 642842 0.000000e+00 2281.0
4 TraesCS5D01G562000 chr7B 87.650 583 46 15 2771 3346 642944 643507 0.000000e+00 654.0
5 TraesCS5D01G562000 chr7B 88.785 107 3 4 162 259 640605 640711 4.540000e-24 122.0
6 TraesCS5D01G562000 chr5B 88.242 1854 106 56 906 2708 712438085 712436293 0.000000e+00 2113.0
7 TraesCS5D01G562000 chr5B 87.067 433 31 10 2716 3139 712435962 712435546 1.820000e-127 466.0
8 TraesCS5D01G562000 chr5B 79.576 377 18 27 547 891 712438500 712438151 7.280000e-52 215.0
9 TraesCS5D01G562000 chr5B 79.710 276 34 5 263 536 544533178 544533433 2.660000e-41 180.0
10 TraesCS5D01G562000 chr5B 85.185 162 15 3 2 158 712438848 712438691 1.250000e-34 158.0
11 TraesCS5D01G562000 chr5B 92.391 92 7 0 3261 3352 712435545 712435454 7.550000e-27 132.0
12 TraesCS5D01G562000 chr5B 94.030 67 4 0 196 262 712438570 712438504 5.920000e-18 102.0
13 TraesCS5D01G562000 chr5B 97.436 39 1 0 2303 2341 708961333 708961295 2.160000e-07 67.6
14 TraesCS5D01G562000 chr5B 96.875 32 1 0 162 193 712438625 712438594 2.000000e-03 54.7
15 TraesCS5D01G562000 chr4B 89.806 206 19 2 331 534 15428164 15428369 2.560000e-66 263.0
16 TraesCS5D01G562000 chr4B 92.500 40 3 0 2301 2340 543399191 543399152 1.300000e-04 58.4
17 TraesCS5D01G562000 chr7A 88.350 206 22 2 332 535 679064149 679063944 2.580000e-61 246.0
18 TraesCS5D01G562000 chr7A 88.038 209 22 3 332 537 566530079 566529871 9.290000e-61 244.0
19 TraesCS5D01G562000 chr2A 88.725 204 20 3 332 533 746759332 746759130 2.580000e-61 246.0
20 TraesCS5D01G562000 chr2A 81.124 249 26 8 260 507 457220874 457221102 2.660000e-41 180.0
21 TraesCS5D01G562000 chr2A 79.562 274 34 13 263 534 156681899 156682152 3.440000e-40 176.0
22 TraesCS5D01G562000 chr6B 87.923 207 23 2 330 534 214870551 214870345 3.340000e-60 243.0
23 TraesCS5D01G562000 chr6B 86.636 217 23 5 331 544 536831229 536831442 5.590000e-58 235.0
24 TraesCS5D01G562000 chr6B 80.669 269 30 4 267 533 78027703 78027455 4.410000e-44 189.0
25 TraesCS5D01G562000 chr6B 80.370 270 29 6 267 533 78058904 78058656 2.050000e-42 183.0
26 TraesCS5D01G562000 chr4A 86.977 215 26 2 324 536 207362740 207362954 1.200000e-59 241.0
27 TraesCS5D01G562000 chr4A 97.436 39 1 0 2303 2341 606346172 606346134 2.160000e-07 67.6
28 TraesCS5D01G562000 chr4A 97.143 35 1 0 2306 2340 28600744 28600710 3.610000e-05 60.2
29 TraesCS5D01G562000 chr3A 87.264 212 23 4 327 536 246937287 246937078 4.320000e-59 239.0
30 TraesCS5D01G562000 chr2D 86.977 215 25 3 322 533 455942439 455942225 4.320000e-59 239.0
31 TraesCS5D01G562000 chr1A 80.137 292 33 8 257 546 446090732 446090464 9.490000e-46 195.0
32 TraesCS5D01G562000 chr1A 97.368 38 1 0 2303 2340 237746066 237746103 7.760000e-07 65.8
33 TraesCS5D01G562000 chr3B 94.444 72 4 0 263 334 770248285 770248214 9.830000e-21 111.0
34 TraesCS5D01G562000 chr2B 97.561 41 1 0 2649 2689 693095026 693094986 1.670000e-08 71.3
35 TraesCS5D01G562000 chr1D 97.368 38 1 0 2303 2340 191861268 191861305 7.760000e-07 65.8
36 TraesCS5D01G562000 chr1B 97.368 38 1 0 2303 2340 265648385 265648422 7.760000e-07 65.8
37 TraesCS5D01G562000 chr4D 97.143 35 1 0 2306 2340 439291816 439291782 3.610000e-05 60.2


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 TraesCS5D01G562000 chr5D 562061860 562065211 3351 True 6191.000000 6191 100.000000 1 3352 1 chr5D.!!$R2 3351
1 TraesCS5D01G562000 chr7B 640605 643507 2902 False 1019.000000 2281 87.612667 162 3346 3 chr7B.!!$F1 3184
2 TraesCS5D01G562000 chr5B 712435454 712438848 3394 True 462.957143 2113 89.052286 2 3352 7 chr5B.!!$R2 3350

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
813 946 0.178953 ACACCCAAAGCCTTGCTCAT 60.179 50.0 0.0 0.0 38.25 2.90 F
1239 1454 0.174617 GGAGAAGAAGGACGAGGCAG 59.825 60.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 2070 0.112995 TGCTTCATCCTTTGGTGGCT 59.887 50.0 0.0 0.0 0.0 4.75 R
2372 2623 0.552363 CCCATGTGGTGATCCATCCA 59.448 55.0 0.0 0.0 46.2 3.41 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
55 56 2.300850 TATAGGTCGCCCGCACAACC 62.301 60.000 0.00 0.00 35.12 3.77
88 94 1.927895 GCAGCTGCTACGAATACACT 58.072 50.000 31.33 0.00 38.21 3.55
94 100 5.520288 CAGCTGCTACGAATACACTAAACAT 59.480 40.000 0.00 0.00 0.00 2.71
96 102 7.382488 CAGCTGCTACGAATACACTAAACATAT 59.618 37.037 0.00 0.00 0.00 1.78
97 103 7.926555 AGCTGCTACGAATACACTAAACATATT 59.073 33.333 0.00 0.00 0.00 1.28
130 136 4.216366 TCGATGATGCTAGAAAGACGAG 57.784 45.455 0.00 0.00 0.00 4.18
133 139 4.907010 CGATGATGCTAGAAAGACGAGTAC 59.093 45.833 0.00 0.00 0.00 2.73
160 228 4.430765 GCATGTGGGTGCTGCTGC 62.431 66.667 8.89 8.89 41.82 5.25
194 262 5.074584 GGAATCCTCCCTCACGTAATATC 57.925 47.826 0.00 0.00 35.42 1.63
236 325 2.159393 GGTACATGCATGCACATTCGTT 60.159 45.455 27.14 1.29 0.00 3.85
295 384 8.451908 AATTTACTCTGCATATTAGGGTTGAC 57.548 34.615 0.00 0.00 30.08 3.18
296 385 6.808321 TTACTCTGCATATTAGGGTTGACT 57.192 37.500 0.00 0.00 30.08 3.41
297 386 5.028549 ACTCTGCATATTAGGGTTGACTG 57.971 43.478 0.00 0.00 0.00 3.51
298 387 4.716784 ACTCTGCATATTAGGGTTGACTGA 59.283 41.667 0.00 0.00 0.00 3.41
299 388 5.189736 ACTCTGCATATTAGGGTTGACTGAA 59.810 40.000 0.00 0.00 0.00 3.02
300 389 5.674525 TCTGCATATTAGGGTTGACTGAAG 58.325 41.667 0.00 0.00 0.00 3.02
301 390 5.189736 TCTGCATATTAGGGTTGACTGAAGT 59.810 40.000 0.00 0.00 0.00 3.01
302 391 5.428253 TGCATATTAGGGTTGACTGAAGTC 58.572 41.667 3.41 3.41 44.97 3.01
489 578 9.516314 ACTTTGTCAAAATTTACTAAGCTTGAC 57.484 29.630 9.86 5.05 38.27 3.18
490 579 9.736023 CTTTGTCAAAATTTACTAAGCTTGACT 57.264 29.630 9.86 0.00 38.43 3.41
501 590 6.073327 ACTAAGCTTGACTTTAACCAAAGC 57.927 37.500 9.86 0.00 44.27 3.51
502 591 5.828328 ACTAAGCTTGACTTTAACCAAAGCT 59.172 36.000 9.86 2.50 44.27 3.74
503 592 6.996282 ACTAAGCTTGACTTTAACCAAAGCTA 59.004 34.615 9.86 0.00 44.27 3.32
504 593 6.709018 AAGCTTGACTTTAACCAAAGCTAA 57.291 33.333 8.49 0.00 44.27 3.09
505 594 6.901081 AGCTTGACTTTAACCAAAGCTAAT 57.099 33.333 6.43 0.00 44.27 1.73
506 595 7.996098 AGCTTGACTTTAACCAAAGCTAATA 57.004 32.000 6.43 0.00 44.27 0.98
507 596 8.045176 AGCTTGACTTTAACCAAAGCTAATAG 57.955 34.615 6.43 0.00 44.27 1.73
508 597 7.121315 AGCTTGACTTTAACCAAAGCTAATAGG 59.879 37.037 6.43 0.00 44.27 2.57
509 598 6.753107 TGACTTTAACCAAAGCTAATAGGC 57.247 37.500 0.00 0.00 44.27 3.93
510 599 6.242396 TGACTTTAACCAAAGCTAATAGGCA 58.758 36.000 0.00 0.00 44.27 4.75
511 600 6.374333 TGACTTTAACCAAAGCTAATAGGCAG 59.626 38.462 0.00 0.00 44.27 4.85
512 601 6.481643 ACTTTAACCAAAGCTAATAGGCAGA 58.518 36.000 0.00 0.00 44.27 4.26
513 602 6.374613 ACTTTAACCAAAGCTAATAGGCAGAC 59.625 38.462 0.00 0.00 44.27 3.51
514 603 4.301072 AACCAAAGCTAATAGGCAGACA 57.699 40.909 0.00 0.00 34.17 3.41
515 604 4.301072 ACCAAAGCTAATAGGCAGACAA 57.699 40.909 0.00 0.00 34.17 3.18
516 605 4.662278 ACCAAAGCTAATAGGCAGACAAA 58.338 39.130 0.00 0.00 34.17 2.83
517 606 5.076873 ACCAAAGCTAATAGGCAGACAAAA 58.923 37.500 0.00 0.00 34.17 2.44
518 607 5.538433 ACCAAAGCTAATAGGCAGACAAAAA 59.462 36.000 0.00 0.00 34.17 1.94
546 635 5.469421 CGAATGGAGTACTACCTACCTACAG 59.531 48.000 1.66 0.00 0.00 2.74
549 638 7.645132 ATGGAGTACTACCTACCTACAGTAT 57.355 40.000 1.66 0.00 0.00 2.12
593 682 2.968574 GCTACTCCATCTCCATCTCCAA 59.031 50.000 0.00 0.00 0.00 3.53
637 741 5.476254 GGCCGGAATAGTAGTAAGTACATCT 59.524 44.000 5.05 0.00 33.55 2.90
695 816 1.209504 GAATGTAGCTGGCCACCTACA 59.790 52.381 33.01 33.01 45.47 2.74
709 830 5.394115 GGCCACCTACATACCTTTGAATTTG 60.394 44.000 0.00 0.00 0.00 2.32
712 833 7.666623 CCACCTACATACCTTTGAATTTGTTT 58.333 34.615 0.00 0.00 0.00 2.83
713 834 7.598493 CCACCTACATACCTTTGAATTTGTTTG 59.402 37.037 0.00 0.00 0.00 2.93
722 843 3.558608 TGAATTTGTTTGGGGGATCCT 57.441 42.857 12.58 0.00 36.20 3.24
737 858 3.475575 GGATCCTTTCCAGATGCTTCTC 58.524 50.000 3.84 0.00 44.74 2.87
738 859 3.118112 GGATCCTTTCCAGATGCTTCTCA 60.118 47.826 3.84 0.00 44.74 3.27
757 886 2.778270 TCACTGAGGTAGCTAGCTAGGA 59.222 50.000 24.78 16.01 33.58 2.94
758 887 3.146066 CACTGAGGTAGCTAGCTAGGAG 58.854 54.545 24.78 20.72 33.58 3.69
762 891 2.640826 GAGGTAGCTAGCTAGGAGAGGA 59.359 54.545 24.78 0.00 33.58 3.71
763 892 2.642807 AGGTAGCTAGCTAGGAGAGGAG 59.357 54.545 24.78 0.00 31.28 3.69
764 893 2.433436 GTAGCTAGCTAGGAGAGGAGC 58.567 57.143 24.78 7.82 39.08 4.70
765 894 0.850100 AGCTAGCTAGGAGAGGAGCA 59.150 55.000 17.69 0.00 41.36 4.26
766 895 0.958822 GCTAGCTAGGAGAGGAGCAC 59.041 60.000 22.10 0.00 41.36 4.40
767 896 1.478654 GCTAGCTAGGAGAGGAGCACT 60.479 57.143 22.10 0.00 41.36 4.40
768 897 2.224670 GCTAGCTAGGAGAGGAGCACTA 60.225 54.545 22.10 0.00 41.36 2.74
769 898 3.561313 GCTAGCTAGGAGAGGAGCACTAT 60.561 52.174 22.10 0.00 41.36 2.12
800 933 2.930019 CTCCTGCCTCCACACCCA 60.930 66.667 0.00 0.00 0.00 4.51
812 945 1.108727 CACACCCAAAGCCTTGCTCA 61.109 55.000 0.00 0.00 38.25 4.26
813 946 0.178953 ACACCCAAAGCCTTGCTCAT 60.179 50.000 0.00 0.00 38.25 2.90
843 977 1.077212 CCCTCCCTTGTGCCATCTG 60.077 63.158 0.00 0.00 0.00 2.90
851 985 0.675837 TTGTGCCATCTGCTCTGCTC 60.676 55.000 0.00 0.00 42.00 4.26
855 989 0.249573 GCCATCTGCTCTGCTCTCTC 60.250 60.000 0.00 0.00 36.87 3.20
857 991 1.405872 CATCTGCTCTGCTCTCTCCT 58.594 55.000 0.00 0.00 0.00 3.69
858 992 2.585330 CATCTGCTCTGCTCTCTCCTA 58.415 52.381 0.00 0.00 0.00 2.94
859 993 3.159472 CATCTGCTCTGCTCTCTCCTAT 58.841 50.000 0.00 0.00 0.00 2.57
860 994 2.862541 TCTGCTCTGCTCTCTCCTATC 58.137 52.381 0.00 0.00 0.00 2.08
861 995 2.174424 TCTGCTCTGCTCTCTCCTATCA 59.826 50.000 0.00 0.00 0.00 2.15
862 996 3.159472 CTGCTCTGCTCTCTCCTATCAT 58.841 50.000 0.00 0.00 0.00 2.45
863 997 3.156293 TGCTCTGCTCTCTCCTATCATC 58.844 50.000 0.00 0.00 0.00 2.92
887 1021 8.442632 TCTATCTAGCAACTCAATTCCATTTG 57.557 34.615 0.00 0.00 0.00 2.32
891 1025 4.250464 AGCAACTCAATTCCATTTGCATG 58.750 39.130 7.31 0.00 44.06 4.06
892 1026 3.181514 GCAACTCAATTCCATTTGCATGC 60.182 43.478 11.82 11.82 41.77 4.06
893 1027 3.255969 ACTCAATTCCATTTGCATGCC 57.744 42.857 16.68 0.00 0.00 4.40
894 1028 2.835764 ACTCAATTCCATTTGCATGCCT 59.164 40.909 16.68 0.00 0.00 4.75
896 1030 4.142093 ACTCAATTCCATTTGCATGCCTAC 60.142 41.667 16.68 0.00 0.00 3.18
897 1031 3.768215 TCAATTCCATTTGCATGCCTACA 59.232 39.130 16.68 0.00 0.00 2.74
898 1032 3.806625 ATTCCATTTGCATGCCTACAC 57.193 42.857 16.68 0.00 0.00 2.90
899 1033 2.212812 TCCATTTGCATGCCTACACA 57.787 45.000 16.68 0.00 0.00 3.72
906 1046 3.625649 TGCATGCCTACACACATCTTA 57.374 42.857 16.68 0.00 0.00 2.10
950 1145 3.235200 CACTCCACCCTAGCTAAGCTAT 58.765 50.000 0.00 0.00 40.54 2.97
962 1157 4.230455 AGCTAAGCTATCTTCACCTCCAT 58.770 43.478 0.00 0.00 36.99 3.41
979 1175 5.047847 CCTCCATCACAAATCATCAATTGC 58.952 41.667 0.00 0.00 0.00 3.56
980 1176 5.163447 CCTCCATCACAAATCATCAATTGCT 60.163 40.000 0.00 0.00 0.00 3.91
981 1177 6.288941 TCCATCACAAATCATCAATTGCTT 57.711 33.333 0.00 0.00 0.00 3.91
982 1178 6.334989 TCCATCACAAATCATCAATTGCTTC 58.665 36.000 0.00 0.00 0.00 3.86
983 1179 6.071278 TCCATCACAAATCATCAATTGCTTCA 60.071 34.615 0.00 0.00 0.00 3.02
984 1180 6.255670 CCATCACAAATCATCAATTGCTTCAG 59.744 38.462 0.00 0.00 0.00 3.02
985 1181 6.335471 TCACAAATCATCAATTGCTTCAGT 57.665 33.333 0.00 0.00 0.00 3.41
986 1182 6.751157 TCACAAATCATCAATTGCTTCAGTT 58.249 32.000 0.00 0.00 0.00 3.16
987 1183 7.211573 TCACAAATCATCAATTGCTTCAGTTT 58.788 30.769 0.00 0.00 0.00 2.66
988 1184 7.170151 TCACAAATCATCAATTGCTTCAGTTTG 59.830 33.333 0.00 9.26 0.00 2.93
989 1185 7.170151 CACAAATCATCAATTGCTTCAGTTTGA 59.830 33.333 18.60 0.00 33.06 2.69
990 1186 7.876068 ACAAATCATCAATTGCTTCAGTTTGAT 59.124 29.630 18.60 0.00 38.89 2.57
991 1187 8.380644 CAAATCATCAATTGCTTCAGTTTGATC 58.619 33.333 0.00 0.00 36.84 2.92
1028 1224 2.723273 GCAAGTAGCCACCAAGGTAAT 58.277 47.619 0.00 0.00 40.61 1.89
1040 1236 7.039993 AGCCACCAAGGTAATTAACTAAACAAG 60.040 37.037 2.78 0.00 40.61 3.16
1059 1255 8.674263 AAACAAGCCATTAATCTCTCATCTAG 57.326 34.615 0.00 0.00 0.00 2.43
1060 1256 7.372260 ACAAGCCATTAATCTCTCATCTAGT 57.628 36.000 0.00 0.00 0.00 2.57
1061 1257 7.215789 ACAAGCCATTAATCTCTCATCTAGTG 58.784 38.462 0.00 0.00 0.00 2.74
1065 1261 6.368516 GCCATTAATCTCTCATCTAGTGCTTC 59.631 42.308 0.00 0.00 0.00 3.86
1066 1262 7.440198 CCATTAATCTCTCATCTAGTGCTTCA 58.560 38.462 0.00 0.00 0.00 3.02
1067 1263 8.095792 CCATTAATCTCTCATCTAGTGCTTCAT 58.904 37.037 0.00 0.00 0.00 2.57
1112 1309 4.555906 CGGCCGGTGATCCATTTAATTAAC 60.556 45.833 20.10 0.00 0.00 2.01
1113 1310 4.261867 GGCCGGTGATCCATTTAATTAACC 60.262 45.833 1.90 0.00 0.00 2.85
1202 1408 3.730761 GCACCTGAAGCTGCACCG 61.731 66.667 1.02 0.00 33.31 4.94
1235 1441 1.134175 GCAGAGGAGAAGAAGGACGAG 59.866 57.143 0.00 0.00 0.00 4.18
1239 1454 0.174617 GGAGAAGAAGGACGAGGCAG 59.825 60.000 0.00 0.00 0.00 4.85
1259 1474 1.073199 AGCCGACCAAGACCCAAAG 59.927 57.895 0.00 0.00 0.00 2.77
1277 1492 0.768221 AGAAGGAGGAACCACCAGCA 60.768 55.000 9.72 0.00 42.04 4.41
1279 1494 2.360475 GGAGGAACCACCAGCAGC 60.360 66.667 2.57 0.00 42.04 5.25
1280 1495 2.360475 GAGGAACCACCAGCAGCC 60.360 66.667 0.00 0.00 42.04 4.85
1410 1634 2.257371 CCGTCCACGTCGACATGT 59.743 61.111 17.16 0.00 37.74 3.21
1505 1729 2.501610 GACGCCACCCTCATCTCC 59.498 66.667 0.00 0.00 0.00 3.71
1509 1733 2.447714 GCCACCCTCATCTCCCCTC 61.448 68.421 0.00 0.00 0.00 4.30
1511 1735 1.053264 CCACCCTCATCTCCCCTCTG 61.053 65.000 0.00 0.00 0.00 3.35
1514 1738 1.383664 CCTCATCTCCCCTCTGCCA 60.384 63.158 0.00 0.00 0.00 4.92
1517 1741 1.692042 CATCTCCCCTCTGCCACCT 60.692 63.158 0.00 0.00 0.00 4.00
1730 1954 3.626924 AGTGCCACCGTGGAGGAC 61.627 66.667 22.37 13.27 45.00 3.85
1830 2054 1.599576 GAGGAGGAACCACCAGCTC 59.400 63.158 9.72 0.00 42.04 4.09
1844 2068 2.124653 GCTCCTGCTGCTGATGCT 60.125 61.111 8.20 0.00 40.48 3.79
1845 2069 2.473760 GCTCCTGCTGCTGATGCTG 61.474 63.158 8.20 0.00 40.48 4.41
1846 2070 1.221021 CTCCTGCTGCTGATGCTGA 59.779 57.895 8.20 0.00 40.01 4.26
1847 2071 0.812014 CTCCTGCTGCTGATGCTGAG 60.812 60.000 8.20 2.19 40.01 3.35
1848 2072 2.473760 CCTGCTGCTGATGCTGAGC 61.474 63.158 8.20 0.00 40.01 4.26
1849 2073 2.437895 TGCTGCTGATGCTGAGCC 60.438 61.111 0.23 0.00 37.40 4.70
1850 2074 2.437895 GCTGCTGATGCTGAGCCA 60.438 61.111 0.23 0.00 40.01 4.75
1851 2075 2.762234 GCTGCTGATGCTGAGCCAC 61.762 63.158 0.23 0.00 40.01 5.01
1852 2076 2.045634 TGCTGATGCTGAGCCACC 60.046 61.111 0.23 0.00 40.48 4.61
1853 2077 2.045634 GCTGATGCTGAGCCACCA 60.046 61.111 0.23 0.00 36.03 4.17
1859 2083 0.333993 ATGCTGAGCCACCAAAGGAT 59.666 50.000 0.23 0.00 0.00 3.24
1898 2128 2.047179 AAAGAAGAGGCCGGCGAC 60.047 61.111 22.54 16.84 0.00 5.19
1925 2155 4.379174 GCTGAAGACGGCAAAGGA 57.621 55.556 0.00 0.00 46.56 3.36
2045 2284 2.411904 GAGATGATGAAGCGGATGGTC 58.588 52.381 0.00 0.00 0.00 4.02
2370 2621 2.980568 AGTCCTAGCTATCTCGGATCG 58.019 52.381 3.01 0.00 36.68 3.69
2371 2622 2.568062 AGTCCTAGCTATCTCGGATCGA 59.432 50.000 3.01 0.00 36.68 3.59
2372 2623 3.199071 AGTCCTAGCTATCTCGGATCGAT 59.801 47.826 0.00 0.00 36.68 3.59
2373 2624 3.311322 GTCCTAGCTATCTCGGATCGATG 59.689 52.174 0.54 0.00 36.68 3.84
2374 2625 2.616376 CCTAGCTATCTCGGATCGATGG 59.384 54.545 0.54 0.00 34.61 3.51
2375 2626 2.498644 AGCTATCTCGGATCGATGGA 57.501 50.000 0.54 0.00 34.61 3.41
2376 2627 3.011566 AGCTATCTCGGATCGATGGAT 57.988 47.619 0.54 3.99 34.61 3.41
2377 2628 2.687425 AGCTATCTCGGATCGATGGATG 59.313 50.000 0.54 0.00 34.61 3.51
2378 2629 2.223688 GCTATCTCGGATCGATGGATGG 60.224 54.545 0.54 4.66 34.61 3.51
2379 2630 2.222227 ATCTCGGATCGATGGATGGA 57.778 50.000 0.54 0.00 34.61 3.41
2380 2631 2.222227 TCTCGGATCGATGGATGGAT 57.778 50.000 0.54 0.00 34.61 3.41
2381 2632 2.095461 TCTCGGATCGATGGATGGATC 58.905 52.381 0.54 3.66 40.12 3.36
2518 2770 8.798748 AAGCAGTAGTTATTGTACTATTAGCG 57.201 34.615 0.00 0.00 33.49 4.26
2613 2870 2.543653 CGAAAAATCAATGGATCGCCCC 60.544 50.000 0.00 0.00 31.88 5.80
2678 2935 6.931790 ATGTCTCAGTCCATGCTATATTCT 57.068 37.500 0.00 0.00 0.00 2.40
2743 3330 0.894835 TCACTGAGACATAGCCGCAA 59.105 50.000 0.00 0.00 0.00 4.85
2784 3373 1.887854 CACCAGTTGCAACATGATCCA 59.112 47.619 30.11 0.00 0.00 3.41
2786 3375 2.559668 ACCAGTTGCAACATGATCCAAG 59.440 45.455 30.11 13.38 0.00 3.61
2810 3399 4.222810 GGTGGAAAGTTGGCAAATCCTTAT 59.777 41.667 21.47 6.53 35.26 1.73
2818 3407 5.951747 AGTTGGCAAATCCTTATGCTTCTAA 59.048 36.000 0.00 0.00 42.20 2.10
2820 3409 5.509498 TGGCAAATCCTTATGCTTCTAACT 58.491 37.500 0.00 0.00 42.20 2.24
2821 3410 5.357878 TGGCAAATCCTTATGCTTCTAACTG 59.642 40.000 0.00 0.00 42.20 3.16
2855 3451 2.453601 CCTATAAGTCCTACCCCCTCCA 59.546 54.545 0.00 0.00 0.00 3.86
2909 3507 1.021202 CTGTAGCTCGGACCTCTCAG 58.979 60.000 0.00 0.00 0.00 3.35
2939 3538 6.818644 TGACAACTATCTAGAAGATGCCAAAC 59.181 38.462 0.00 0.00 35.37 2.93
2948 3547 2.787473 AGATGCCAAACGGAAGATGA 57.213 45.000 0.00 0.00 0.00 2.92
2973 3572 3.064207 GTGTGAGAATAACGACAAGCCA 58.936 45.455 0.00 0.00 0.00 4.75
2987 3586 2.692557 ACAAGCCAAGTGTTGCAATACA 59.307 40.909 25.58 8.14 0.00 2.29
2988 3587 3.321682 ACAAGCCAAGTGTTGCAATACAT 59.678 39.130 25.58 13.29 0.00 2.29
2992 3591 3.119029 GCCAAGTGTTGCAATACATGGAT 60.119 43.478 38.47 15.08 40.07 3.41
3015 3614 4.830046 TGATACCCTGATTCTACTCTGAGC 59.170 45.833 4.19 0.00 0.00 4.26
3044 3643 3.386078 TGCTCATGTGGCCAAACTAAAAA 59.614 39.130 7.24 0.00 0.00 1.94
3045 3644 4.040217 TGCTCATGTGGCCAAACTAAAAAT 59.960 37.500 7.24 0.00 0.00 1.82
3052 3651 3.898123 TGGCCAAACTAAAAATGGTGCTA 59.102 39.130 0.61 0.00 36.57 3.49
3092 3691 0.555769 TGGCCTCACCCTCAACTTTT 59.444 50.000 3.32 0.00 37.83 2.27
3174 3773 4.108673 GGGTGTCCGGTGACTAGT 57.891 61.111 0.00 0.00 42.28 2.57
3176 3775 0.245813 GGGTGTCCGGTGACTAGTTC 59.754 60.000 0.00 0.00 42.28 3.01
3185 3784 2.186076 GGTGACTAGTTCTTCGCATCG 58.814 52.381 0.00 0.00 0.00 3.84
3241 3841 0.613260 ATCGCTGACCTTAGCACCAA 59.387 50.000 0.00 0.00 43.87 3.67
3266 3866 2.030457 GGTAGCGTTGACAAATGGATCG 59.970 50.000 0.00 0.00 0.00 3.69
3269 3869 1.663643 GCGTTGACAAATGGATCGCTA 59.336 47.619 10.34 0.00 39.26 4.26
3308 3908 2.046023 CATCGGCTGGCAAGTGGA 60.046 61.111 1.08 0.00 0.00 4.02
3347 3947 0.179056 CATTGCCCTACCCACCTACG 60.179 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.605275 CTATATCTCAATCTCTCTCTCACCTAG 57.395 40.741 0.00 0.00 0.00 3.02
4 5 8.846943 TGTCTATATCTCAATCTCTCTCTCAC 57.153 38.462 0.00 0.00 0.00 3.51
103 109 6.318628 GTCTTTCTAGCATCATCGATCGTAT 58.681 40.000 15.94 4.64 0.00 3.06
105 111 4.541779 GTCTTTCTAGCATCATCGATCGT 58.458 43.478 15.94 0.00 0.00 3.73
106 112 3.601636 CGTCTTTCTAGCATCATCGATCG 59.398 47.826 9.36 9.36 0.00 3.69
110 116 3.958704 ACTCGTCTTTCTAGCATCATCG 58.041 45.455 0.00 0.00 0.00 3.84
130 136 1.393539 CCACATGCACGCAACTAGTAC 59.606 52.381 0.00 0.00 0.00 2.73
133 139 0.955428 ACCCACATGCACGCAACTAG 60.955 55.000 0.00 0.00 0.00 2.57
271 360 7.716998 CAGTCAACCCTAATATGCAGAGTAAAT 59.283 37.037 0.00 0.00 0.00 1.40
273 362 6.382859 TCAGTCAACCCTAATATGCAGAGTAA 59.617 38.462 0.00 0.00 0.00 2.24
274 363 5.897250 TCAGTCAACCCTAATATGCAGAGTA 59.103 40.000 0.00 0.00 0.00 2.59
275 364 4.716784 TCAGTCAACCCTAATATGCAGAGT 59.283 41.667 0.00 0.00 0.00 3.24
276 365 5.282055 TCAGTCAACCCTAATATGCAGAG 57.718 43.478 0.00 0.00 0.00 3.35
277 366 5.189736 ACTTCAGTCAACCCTAATATGCAGA 59.810 40.000 0.00 0.00 0.00 4.26
278 367 5.431765 ACTTCAGTCAACCCTAATATGCAG 58.568 41.667 0.00 0.00 0.00 4.41
279 368 5.428253 GACTTCAGTCAACCCTAATATGCA 58.572 41.667 1.86 0.00 44.18 3.96
280 369 5.993106 GACTTCAGTCAACCCTAATATGC 57.007 43.478 1.86 0.00 44.18 3.14
463 552 9.516314 GTCAAGCTTAGTAAATTTTGACAAAGT 57.484 29.630 19.08 0.00 42.25 2.66
464 553 9.736023 AGTCAAGCTTAGTAAATTTTGACAAAG 57.264 29.630 22.59 6.27 44.04 2.77
475 564 8.132995 GCTTTGGTTAAAGTCAAGCTTAGTAAA 58.867 33.333 0.00 0.00 44.11 2.01
476 565 7.501225 AGCTTTGGTTAAAGTCAAGCTTAGTAA 59.499 33.333 0.00 0.00 44.11 2.24
477 566 6.996282 AGCTTTGGTTAAAGTCAAGCTTAGTA 59.004 34.615 0.00 0.00 44.11 1.82
478 567 5.828328 AGCTTTGGTTAAAGTCAAGCTTAGT 59.172 36.000 0.00 0.00 44.11 2.24
479 568 6.319141 AGCTTTGGTTAAAGTCAAGCTTAG 57.681 37.500 0.00 0.00 44.11 2.18
480 569 7.811117 TTAGCTTTGGTTAAAGTCAAGCTTA 57.189 32.000 9.81 0.00 44.11 3.09
481 570 6.709018 TTAGCTTTGGTTAAAGTCAAGCTT 57.291 33.333 9.81 0.00 44.11 3.74
482 571 6.901081 ATTAGCTTTGGTTAAAGTCAAGCT 57.099 33.333 9.50 9.50 44.11 3.74
483 572 7.251281 CCTATTAGCTTTGGTTAAAGTCAAGC 58.749 38.462 0.00 0.00 44.11 4.01
484 573 7.094377 TGCCTATTAGCTTTGGTTAAAGTCAAG 60.094 37.037 0.00 0.00 44.11 3.02
485 574 6.717540 TGCCTATTAGCTTTGGTTAAAGTCAA 59.282 34.615 0.00 0.00 44.11 3.18
486 575 6.242396 TGCCTATTAGCTTTGGTTAAAGTCA 58.758 36.000 0.00 0.00 44.11 3.41
487 576 6.598064 TCTGCCTATTAGCTTTGGTTAAAGTC 59.402 38.462 0.00 0.00 44.11 3.01
488 577 6.374613 GTCTGCCTATTAGCTTTGGTTAAAGT 59.625 38.462 0.00 0.00 44.11 2.66
489 578 6.374333 TGTCTGCCTATTAGCTTTGGTTAAAG 59.626 38.462 0.00 0.00 44.86 1.85
490 579 6.242396 TGTCTGCCTATTAGCTTTGGTTAAA 58.758 36.000 0.00 0.00 0.00 1.52
491 580 5.811190 TGTCTGCCTATTAGCTTTGGTTAA 58.189 37.500 0.00 0.00 0.00 2.01
492 581 5.429681 TGTCTGCCTATTAGCTTTGGTTA 57.570 39.130 0.00 0.00 0.00 2.85
493 582 4.301072 TGTCTGCCTATTAGCTTTGGTT 57.699 40.909 0.00 0.00 0.00 3.67
494 583 4.301072 TTGTCTGCCTATTAGCTTTGGT 57.699 40.909 0.00 0.00 0.00 3.67
495 584 5.643379 TTTTGTCTGCCTATTAGCTTTGG 57.357 39.130 0.00 0.00 0.00 3.28
517 606 6.212187 AGGTAGGTAGTACTCCATTCGTTTTT 59.788 38.462 0.00 0.00 0.00 1.94
518 607 5.718607 AGGTAGGTAGTACTCCATTCGTTTT 59.281 40.000 0.00 0.00 0.00 2.43
519 608 5.267587 AGGTAGGTAGTACTCCATTCGTTT 58.732 41.667 0.00 0.00 0.00 3.60
520 609 4.864726 AGGTAGGTAGTACTCCATTCGTT 58.135 43.478 0.00 0.00 0.00 3.85
521 610 4.516652 AGGTAGGTAGTACTCCATTCGT 57.483 45.455 0.00 0.00 0.00 3.85
522 611 5.371526 TGTAGGTAGGTAGTACTCCATTCG 58.628 45.833 0.00 0.00 0.00 3.34
523 612 6.363882 ACTGTAGGTAGGTAGTACTCCATTC 58.636 44.000 0.00 0.00 0.00 2.67
524 613 6.338591 ACTGTAGGTAGGTAGTACTCCATT 57.661 41.667 0.00 0.00 0.00 3.16
525 614 5.990713 ACTGTAGGTAGGTAGTACTCCAT 57.009 43.478 0.00 0.00 0.00 3.41
526 615 7.420680 GGAATACTGTAGGTAGGTAGTACTCCA 60.421 44.444 0.00 0.00 40.14 3.86
527 616 6.939730 GGAATACTGTAGGTAGGTAGTACTCC 59.060 46.154 0.00 0.48 35.65 3.85
528 617 7.512992 TGGAATACTGTAGGTAGGTAGTACTC 58.487 42.308 0.00 0.00 33.51 2.59
529 618 7.128573 ACTGGAATACTGTAGGTAGGTAGTACT 59.871 40.741 0.00 0.00 33.51 2.73
530 619 7.286313 ACTGGAATACTGTAGGTAGGTAGTAC 58.714 42.308 0.00 0.00 33.51 2.73
531 620 7.420680 GGACTGGAATACTGTAGGTAGGTAGTA 60.421 44.444 0.00 0.00 33.51 1.82
532 621 6.338591 ACTGGAATACTGTAGGTAGGTAGT 57.661 41.667 0.00 0.00 33.51 2.73
533 622 5.769162 GGACTGGAATACTGTAGGTAGGTAG 59.231 48.000 0.00 0.00 33.51 3.18
534 623 5.434376 AGGACTGGAATACTGTAGGTAGGTA 59.566 44.000 0.00 0.00 33.51 3.08
535 624 4.232354 AGGACTGGAATACTGTAGGTAGGT 59.768 45.833 0.00 0.00 33.51 3.08
536 625 4.805744 AGGACTGGAATACTGTAGGTAGG 58.194 47.826 0.00 0.00 33.51 3.18
537 626 5.657302 ACAAGGACTGGAATACTGTAGGTAG 59.343 44.000 0.00 0.00 33.51 3.18
538 627 5.586877 ACAAGGACTGGAATACTGTAGGTA 58.413 41.667 0.00 0.00 34.62 3.08
539 628 4.426704 ACAAGGACTGGAATACTGTAGGT 58.573 43.478 0.00 0.00 0.00 3.08
540 629 5.422214 AACAAGGACTGGAATACTGTAGG 57.578 43.478 0.00 0.00 0.00 3.18
546 635 4.982295 GCAAACAAACAAGGACTGGAATAC 59.018 41.667 0.00 0.00 0.00 1.89
549 638 3.096092 AGCAAACAAACAAGGACTGGAA 58.904 40.909 0.00 0.00 0.00 3.53
593 682 1.672356 GCGTGCATGGAGTTGGAGT 60.672 57.895 8.27 0.00 0.00 3.85
695 816 5.158889 TCCCCCAAACAAATTCAAAGGTAT 58.841 37.500 0.00 0.00 0.00 2.73
722 843 3.307269 CCTCAGTGAGAAGCATCTGGAAA 60.307 47.826 22.09 0.00 35.54 3.13
728 849 2.430332 AGCTACCTCAGTGAGAAGCATC 59.570 50.000 31.85 15.21 39.34 3.91
737 858 3.146066 CTCCTAGCTAGCTACCTCAGTG 58.854 54.545 20.67 8.95 0.00 3.66
738 859 3.050089 TCTCCTAGCTAGCTACCTCAGT 58.950 50.000 20.67 0.00 0.00 3.41
757 886 6.492087 GTCCAACTTATAGATAGTGCTCCTCT 59.508 42.308 0.00 0.00 0.00 3.69
758 887 6.294843 GGTCCAACTTATAGATAGTGCTCCTC 60.295 46.154 0.00 0.00 0.00 3.71
762 891 5.540719 GGAGGTCCAACTTATAGATAGTGCT 59.459 44.000 0.00 0.00 35.64 4.40
763 892 5.540719 AGGAGGTCCAACTTATAGATAGTGC 59.459 44.000 0.00 0.00 38.89 4.40
764 893 6.517529 GCAGGAGGTCCAACTTATAGATAGTG 60.518 46.154 0.00 0.00 38.89 2.74
765 894 5.540719 GCAGGAGGTCCAACTTATAGATAGT 59.459 44.000 0.00 0.00 38.89 2.12
766 895 5.046950 GGCAGGAGGTCCAACTTATAGATAG 60.047 48.000 0.00 0.00 38.89 2.08
767 896 4.838986 GGCAGGAGGTCCAACTTATAGATA 59.161 45.833 0.00 0.00 38.89 1.98
768 897 3.648545 GGCAGGAGGTCCAACTTATAGAT 59.351 47.826 0.00 0.00 38.89 1.98
769 898 3.039011 GGCAGGAGGTCCAACTTATAGA 58.961 50.000 0.00 0.00 38.89 1.98
800 933 3.054582 TGAGATGAGATGAGCAAGGCTTT 60.055 43.478 0.00 0.00 39.88 3.51
812 945 3.651904 CAAGGGAGGGAATGAGATGAGAT 59.348 47.826 0.00 0.00 0.00 2.75
813 946 3.044156 CAAGGGAGGGAATGAGATGAGA 58.956 50.000 0.00 0.00 0.00 3.27
843 977 3.424703 AGATGATAGGAGAGAGCAGAGC 58.575 50.000 0.00 0.00 0.00 4.09
851 985 7.828717 TGAGTTGCTAGATAGATGATAGGAGAG 59.171 40.741 0.00 0.00 0.00 3.20
855 989 9.585099 GAATTGAGTTGCTAGATAGATGATAGG 57.415 37.037 0.00 0.00 0.00 2.57
857 991 9.093458 TGGAATTGAGTTGCTAGATAGATGATA 57.907 33.333 0.00 0.00 0.00 2.15
858 992 7.971201 TGGAATTGAGTTGCTAGATAGATGAT 58.029 34.615 0.00 0.00 0.00 2.45
859 993 7.365497 TGGAATTGAGTTGCTAGATAGATGA 57.635 36.000 0.00 0.00 0.00 2.92
860 994 8.618702 AATGGAATTGAGTTGCTAGATAGATG 57.381 34.615 0.00 0.00 33.44 2.90
861 995 9.064706 CAAATGGAATTGAGTTGCTAGATAGAT 57.935 33.333 0.00 0.00 36.10 1.98
862 996 7.012704 GCAAATGGAATTGAGTTGCTAGATAGA 59.987 37.037 10.49 0.00 40.39 1.98
863 997 7.137426 GCAAATGGAATTGAGTTGCTAGATAG 58.863 38.462 10.49 0.00 40.39 2.08
887 1021 3.270027 TGTAAGATGTGTGTAGGCATGC 58.730 45.455 9.90 9.90 0.00 4.06
891 1025 5.178797 AGTGAATGTAAGATGTGTGTAGGC 58.821 41.667 0.00 0.00 0.00 3.93
892 1026 6.757010 GGTAGTGAATGTAAGATGTGTGTAGG 59.243 42.308 0.00 0.00 0.00 3.18
893 1027 7.548097 AGGTAGTGAATGTAAGATGTGTGTAG 58.452 38.462 0.00 0.00 0.00 2.74
894 1028 7.177744 TGAGGTAGTGAATGTAAGATGTGTGTA 59.822 37.037 0.00 0.00 0.00 2.90
896 1030 6.398095 TGAGGTAGTGAATGTAAGATGTGTG 58.602 40.000 0.00 0.00 0.00 3.82
897 1031 6.605471 TGAGGTAGTGAATGTAAGATGTGT 57.395 37.500 0.00 0.00 0.00 3.72
898 1032 6.873605 TGTTGAGGTAGTGAATGTAAGATGTG 59.126 38.462 0.00 0.00 0.00 3.21
899 1033 6.874134 GTGTTGAGGTAGTGAATGTAAGATGT 59.126 38.462 0.00 0.00 0.00 3.06
906 1046 5.071250 TGGTAAGTGTTGAGGTAGTGAATGT 59.929 40.000 0.00 0.00 0.00 2.71
950 1145 4.639078 TGATTTGTGATGGAGGTGAAGA 57.361 40.909 0.00 0.00 0.00 2.87
962 1157 6.335471 ACTGAAGCAATTGATGATTTGTGA 57.665 33.333 10.34 0.00 37.88 3.58
979 1175 3.689347 TGGTGATGGGATCAAACTGAAG 58.311 45.455 0.00 0.00 41.69 3.02
980 1176 3.805066 TGGTGATGGGATCAAACTGAA 57.195 42.857 0.00 0.00 41.69 3.02
981 1177 3.623703 CATGGTGATGGGATCAAACTGA 58.376 45.455 0.00 0.00 41.69 3.41
982 1178 2.691526 CCATGGTGATGGGATCAAACTG 59.308 50.000 2.57 0.00 45.11 3.16
983 1179 3.022557 CCATGGTGATGGGATCAAACT 57.977 47.619 2.57 0.00 45.11 2.66
1028 1224 9.733556 TGAGAGATTAATGGCTTGTTTAGTTAA 57.266 29.630 0.00 0.00 0.00 2.01
1040 1236 5.792741 AGCACTAGATGAGAGATTAATGGC 58.207 41.667 0.00 0.00 0.00 4.40
1065 1261 7.974501 CCGGGAGCAAGTAATACTAGTTATATG 59.025 40.741 0.00 0.00 0.00 1.78
1066 1262 7.363617 GCCGGGAGCAAGTAATACTAGTTATAT 60.364 40.741 2.18 0.00 42.97 0.86
1067 1263 6.071728 GCCGGGAGCAAGTAATACTAGTTATA 60.072 42.308 2.18 0.00 42.97 0.98
1068 1264 5.279356 GCCGGGAGCAAGTAATACTAGTTAT 60.279 44.000 2.18 0.00 42.97 1.89
1069 1265 4.038402 GCCGGGAGCAAGTAATACTAGTTA 59.962 45.833 2.18 0.00 42.97 2.24
1070 1266 3.181468 GCCGGGAGCAAGTAATACTAGTT 60.181 47.826 2.18 0.00 42.97 2.24
1071 1267 2.364647 GCCGGGAGCAAGTAATACTAGT 59.635 50.000 2.18 0.00 42.97 2.57
1072 1268 2.288886 GGCCGGGAGCAAGTAATACTAG 60.289 54.545 2.18 0.00 46.50 2.57
1075 1271 0.878961 CGGCCGGGAGCAAGTAATAC 60.879 60.000 20.10 0.00 46.50 1.89
1112 1309 4.889995 GGGTTAATTTGGAGAAGATGGAGG 59.110 45.833 0.00 0.00 0.00 4.30
1113 1310 5.760131 AGGGTTAATTTGGAGAAGATGGAG 58.240 41.667 0.00 0.00 0.00 3.86
1239 1454 3.842925 TTGGGTCTTGGTCGGCTGC 62.843 63.158 0.00 0.00 0.00 5.25
1259 1474 0.322008 CTGCTGGTGGTTCCTCCTTC 60.322 60.000 10.65 4.11 37.07 3.46
1410 1634 3.948719 GGTGACCTGGTTGGCGGA 61.949 66.667 0.00 0.00 40.22 5.54
1505 1729 3.086600 GGAGGAGGTGGCAGAGGG 61.087 72.222 0.00 0.00 0.00 4.30
1592 1816 1.005630 GTTGACGAGCAGCTCCACT 60.006 57.895 17.16 0.00 0.00 4.00
1730 1954 4.363999 GGATGTACTCCACAATCTTCTCG 58.636 47.826 6.51 0.00 44.26 4.04
1830 2054 2.473760 GCTCAGCATCAGCAGCAGG 61.474 63.158 0.00 0.00 45.49 4.85
1838 2062 0.609957 CCTTTGGTGGCTCAGCATCA 60.610 55.000 0.00 0.00 41.53 3.07
1841 2065 0.609957 CATCCTTTGGTGGCTCAGCA 60.610 55.000 0.00 3.38 40.20 4.41
1842 2066 0.322816 TCATCCTTTGGTGGCTCAGC 60.323 55.000 0.00 0.00 0.00 4.26
1844 2068 1.887956 GCTTCATCCTTTGGTGGCTCA 60.888 52.381 0.00 0.00 0.00 4.26
1845 2069 0.813821 GCTTCATCCTTTGGTGGCTC 59.186 55.000 0.00 0.00 0.00 4.70
1846 2070 0.112995 TGCTTCATCCTTTGGTGGCT 59.887 50.000 0.00 0.00 0.00 4.75
1847 2071 0.244721 GTGCTTCATCCTTTGGTGGC 59.755 55.000 0.00 0.00 0.00 5.01
1848 2072 0.890683 GGTGCTTCATCCTTTGGTGG 59.109 55.000 0.00 0.00 0.00 4.61
1849 2073 1.542915 CTGGTGCTTCATCCTTTGGTG 59.457 52.381 0.00 0.00 0.00 4.17
1850 2074 1.915141 CTGGTGCTTCATCCTTTGGT 58.085 50.000 0.00 0.00 0.00 3.67
1851 2075 0.529378 GCTGGTGCTTCATCCTTTGG 59.471 55.000 0.00 0.00 36.03 3.28
1852 2076 0.529378 GGCTGGTGCTTCATCCTTTG 59.471 55.000 0.00 0.00 39.59 2.77
1853 2077 0.962356 CGGCTGGTGCTTCATCCTTT 60.962 55.000 0.00 0.00 39.59 3.11
1859 2083 4.680237 CCGTCGGCTGGTGCTTCA 62.680 66.667 0.00 0.00 39.59 3.02
1898 2128 1.576421 GTCTTCAGCCGCCTTGTTG 59.424 57.895 0.00 0.00 0.00 3.33
1905 2135 3.314388 CTTTGCCGTCTTCAGCCGC 62.314 63.158 0.00 0.00 0.00 6.53
2370 2621 2.511659 CCATGTGGTGATCCATCCATC 58.488 52.381 5.01 1.60 46.20 3.51
2371 2622 1.146359 CCCATGTGGTGATCCATCCAT 59.854 52.381 5.01 0.00 46.20 3.41
2372 2623 0.552363 CCCATGTGGTGATCCATCCA 59.448 55.000 0.00 0.00 46.20 3.41
2373 2624 0.825010 GCCCATGTGGTGATCCATCC 60.825 60.000 0.00 0.00 46.20 3.51
2374 2625 0.825010 GGCCCATGTGGTGATCCATC 60.825 60.000 0.00 0.00 46.20 3.51
2375 2626 1.231068 GGCCCATGTGGTGATCCAT 59.769 57.895 0.00 0.00 46.20 3.41
2376 2627 1.582853 ATGGCCCATGTGGTGATCCA 61.583 55.000 0.00 0.95 42.05 3.41
2377 2628 1.111116 CATGGCCCATGTGGTGATCC 61.111 60.000 15.89 0.00 37.12 3.36
2378 2629 1.111116 CCATGGCCCATGTGGTGATC 61.111 60.000 21.88 0.00 39.94 2.92
2379 2630 1.075822 CCATGGCCCATGTGGTGAT 60.076 57.895 21.88 0.00 39.94 3.06
2380 2631 2.359797 CCATGGCCCATGTGGTGA 59.640 61.111 21.88 0.00 39.94 4.02
2381 2632 3.463585 GCCATGGCCCATGTGGTG 61.464 66.667 27.24 8.06 39.94 4.17
2475 2727 5.900339 TGCTTATAATTACGCAGCAGTAC 57.100 39.130 9.84 0.00 35.56 2.73
2513 2765 6.402766 CCAATGTCCTTTAATTTCGTCGCTAA 60.403 38.462 0.00 0.00 0.00 3.09
2516 2768 4.095610 CCAATGTCCTTTAATTTCGTCGC 58.904 43.478 0.00 0.00 0.00 5.19
2517 2769 5.106869 TGACCAATGTCCTTTAATTTCGTCG 60.107 40.000 0.00 0.00 41.01 5.12
2518 2770 6.084277 GTGACCAATGTCCTTTAATTTCGTC 58.916 40.000 0.00 0.00 41.01 4.20
2584 2841 2.736192 CCATTGATTTTTCGGTTGGTGC 59.264 45.455 0.00 0.00 0.00 5.01
2591 2848 2.543653 GGGCGATCCATTGATTTTTCGG 60.544 50.000 0.00 0.00 35.00 4.30
2613 2870 4.378616 CGAATTGTTCGCCAACTAAAAGTG 59.621 41.667 0.00 0.00 46.97 3.16
2678 2935 9.187996 TGCATAAATCTCCATACAAGATCAAAA 57.812 29.630 0.00 0.00 32.29 2.44
2713 2970 6.091441 GCTATGTCTCAGTGACTTAACCAAAG 59.909 42.308 4.31 0.00 45.54 2.77
2740 3320 5.200454 CACGTGCATATACTCTTTCATTGC 58.800 41.667 0.82 0.00 0.00 3.56
2768 3355 2.173519 CCCTTGGATCATGTTGCAACT 58.826 47.619 28.61 9.99 0.00 3.16
2784 3373 1.872773 TTTGCCAACTTTCCACCCTT 58.127 45.000 0.00 0.00 0.00 3.95
2786 3375 1.001974 GGATTTGCCAACTTTCCACCC 59.998 52.381 0.00 0.00 36.34 4.61
2810 3399 3.055094 GGAATGAGGTCCAGTTAGAAGCA 60.055 47.826 0.00 0.00 37.65 3.91
2818 3407 3.715648 ATAGGAGGAATGAGGTCCAGT 57.284 47.619 0.00 0.00 40.48 4.00
2820 3409 5.148502 GACTTATAGGAGGAATGAGGTCCA 58.851 45.833 0.00 0.00 40.48 4.02
2821 3410 4.528987 GGACTTATAGGAGGAATGAGGTCC 59.471 50.000 0.00 0.00 38.03 4.46
2909 3507 7.223777 GGCATCTTCTAGATAGTTGTCAACTTC 59.776 40.741 22.81 17.98 42.81 3.01
2939 3538 3.857549 TCTCACACTTCTCATCTTCCG 57.142 47.619 0.00 0.00 0.00 4.30
2948 3547 4.686554 GCTTGTCGTTATTCTCACACTTCT 59.313 41.667 0.00 0.00 0.00 2.85
2973 3572 6.039717 GGTATCATCCATGTATTGCAACACTT 59.960 38.462 9.63 0.00 30.75 3.16
2987 3586 6.440010 CAGAGTAGAATCAGGGTATCATCCAT 59.560 42.308 0.00 0.00 0.00 3.41
2988 3587 5.777223 CAGAGTAGAATCAGGGTATCATCCA 59.223 44.000 0.00 0.00 0.00 3.41
2992 3591 4.830046 GCTCAGAGTAGAATCAGGGTATCA 59.170 45.833 0.00 0.00 0.00 2.15
3015 3614 2.831366 GCCACATGAGCAGCATCCG 61.831 63.158 0.00 0.00 34.15 4.18
3044 3643 2.437281 CCATGAAGGAGTCTAGCACCAT 59.563 50.000 0.00 0.00 41.22 3.55
3045 3644 1.833630 CCATGAAGGAGTCTAGCACCA 59.166 52.381 0.00 0.00 41.22 4.17
3052 3651 0.976641 TGTTCGCCATGAAGGAGTCT 59.023 50.000 0.00 0.00 41.22 3.24
3141 3740 1.133025 CACCCGAAGATTGATGCCAAC 59.867 52.381 0.00 0.00 34.72 3.77
3174 3773 2.483013 CCCAAGGTATCGATGCGAAGAA 60.483 50.000 8.54 0.00 39.99 2.52
3176 3775 1.502231 CCCAAGGTATCGATGCGAAG 58.498 55.000 8.54 0.00 39.99 3.79
3241 3841 4.839121 TCCATTTGTCAACGCTACCTATT 58.161 39.130 0.00 0.00 0.00 1.73
3250 3850 2.285220 CCTAGCGATCCATTTGTCAACG 59.715 50.000 0.00 0.00 0.00 4.10
3266 3866 1.821332 GCATGCCTCACCACCTAGC 60.821 63.158 6.36 0.00 0.00 3.42
3269 3869 0.911525 AGTAGCATGCCTCACCACCT 60.912 55.000 15.66 0.00 0.00 4.00
3308 3908 2.098607 TGAGAACAACGTCGACAAGAGT 59.901 45.455 17.16 5.26 0.00 3.24


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

AutoCloner maintained by Alex Coulton.