Multiple sequence alignment - TraesCS7D01G266400

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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 TraesCS7D01G266400 chr7D 100.000 3553 0 0 1 3553 249373618 249377170 0.000000e+00 6562.0
1 TraesCS7D01G266400 chr7D 89.308 159 13 4 707 863 140786367 140786211 2.800000e-46 196.0
2 TraesCS7D01G266400 chr7D 89.172 157 11 3 708 860 135151732 135151886 1.300000e-44 191.0
3 TraesCS7D01G266400 chr7D 89.041 73 6 2 2321 2393 514765063 514764993 4.890000e-14 89.8
4 TraesCS7D01G266400 chr7D 97.297 37 1 0 2023 2059 609900849 609900885 2.960000e-06 63.9
5 TraesCS7D01G266400 chr7D 97.297 37 1 0 2023 2059 609905754 609905790 2.960000e-06 63.9
6 TraesCS7D01G266400 chr7D 97.297 37 1 0 2023 2059 609946427 609946391 2.960000e-06 63.9
7 TraesCS7D01G266400 chr7B 93.861 2427 94 26 867 3275 226332721 226335110 0.000000e+00 3605.0
8 TraesCS7D01G266400 chr7B 90.269 483 27 7 1 470 226331870 226332345 6.520000e-172 614.0
9 TraesCS7D01G266400 chr7B 89.209 278 22 4 3277 3553 226335145 226335415 1.220000e-89 340.0
10 TraesCS7D01G266400 chr7B 89.677 155 11 3 708 858 463039140 463038987 3.620000e-45 193.0
11 TraesCS7D01G266400 chr7B 74.239 427 101 4 1219 1642 697422843 697423263 1.700000e-38 171.0
12 TraesCS7D01G266400 chr7B 74.232 423 98 6 1233 1651 697120246 697119831 2.190000e-37 167.0
13 TraesCS7D01G266400 chr7B 90.278 72 5 2 2321 2392 685247560 685247491 3.780000e-15 93.5
14 TraesCS7D01G266400 chr7B 86.364 66 7 2 2325 2390 694254653 694254716 1.770000e-08 71.3
15 TraesCS7D01G266400 chr7A 94.327 2221 68 18 1088 3273 271793884 271791687 0.000000e+00 3350.0
16 TraesCS7D01G266400 chr7A 90.062 483 25 7 1 467 271794908 271794433 3.920000e-169 604.0
17 TraesCS7D01G266400 chr7A 85.561 187 19 5 867 1053 271794061 271793883 4.680000e-44 189.0
18 TraesCS7D01G266400 chr7A 75.120 418 95 5 1237 1651 700160723 700160312 1.680000e-43 187.0
19 TraesCS7D01G266400 chr7A 97.297 37 1 0 2023 2059 699925558 699925594 2.960000e-06 63.9
20 TraesCS7D01G266400 chr7A 97.297 37 1 0 2023 2059 700940860 700940824 2.960000e-06 63.9
21 TraesCS7D01G266400 chr6B 91.667 156 10 3 708 860 41607152 41606997 2.780000e-51 213.0
22 TraesCS7D01G266400 chr6B 97.297 37 1 0 2023 2059 34058217 34058181 2.960000e-06 63.9
23 TraesCS7D01G266400 chr1B 90.850 153 12 2 709 860 31175537 31175688 1.670000e-48 204.0
24 TraesCS7D01G266400 chr1B 88.961 154 16 1 708 860 12095807 12095960 4.680000e-44 189.0
25 TraesCS7D01G266400 chrUn 88.961 154 16 1 708 860 391378856 391379009 4.680000e-44 189.0
26 TraesCS7D01G266400 chrUn 88.961 154 16 1 708 860 391465443 391465596 4.680000e-44 189.0
27 TraesCS7D01G266400 chr2A 88.235 153 17 1 708 859 722814484 722814332 7.840000e-42 182.0
28 TraesCS7D01G266400 chr1A 74.772 329 73 8 1225 1545 557138710 557139036 4.780000e-29 139.0
29 TraesCS7D01G266400 chr6A 97.297 37 1 0 2023 2059 20125465 20125429 2.960000e-06 63.9


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 TraesCS7D01G266400 chr7D 249373618 249377170 3552 False 6562.000000 6562 100.000000 1 3553 1 chr7D.!!$F2 3552
1 TraesCS7D01G266400 chr7B 226331870 226335415 3545 False 1519.666667 3605 91.113000 1 3553 3 chr7B.!!$F3 3552
2 TraesCS7D01G266400 chr7A 271791687 271794908 3221 True 1381.000000 3350 89.983333 1 3273 3 chr7A.!!$R3 3272

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
722 907 0.032416 GTCTGTAGCTAGGGGGTGGA 60.032 60.0 0.0 0.0 0.00 4.02 F
841 1026 0.112218 TCATTGTTGGACCACCCTGG 59.888 55.0 0.0 0.0 45.02 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 2106 0.902531 TTTCCCAGTAGAAGAGGCCG 59.097 55.0 0.00 0.0 0.0 6.13 R
2776 3001 1.008361 CCAAACTGGCGCATTTTCCG 61.008 55.0 10.83 0.0 0.0 4.30 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
176 177 1.269206 ACTCATTGCCGCAGTTGTTTG 60.269 47.619 0.00 0.00 0.00 2.93
197 198 1.686587 TCTCAAGTCGTGCTTTCCTGA 59.313 47.619 0.00 0.00 34.69 3.86
227 234 0.318360 GGTTTTGCTACCGGTTGTGC 60.318 55.000 15.04 16.09 0.00 4.57
281 288 0.836400 ATCACCGGACACAGGAGGTT 60.836 55.000 9.46 0.00 34.25 3.50
299 316 0.461870 TTGATCGGGACTTGATGGCG 60.462 55.000 0.00 0.00 0.00 5.69
316 333 3.244582 TGGCGACTAATATGGGGTACAT 58.755 45.455 0.00 0.00 43.68 2.29
333 350 5.279809 GGGTACATGACTCCTCAAACTGTAA 60.280 44.000 0.00 0.00 0.00 2.41
336 353 6.808008 ACATGACTCCTCAAACTGTAATTG 57.192 37.500 0.00 0.00 0.00 2.32
382 399 8.884124 TGATTGGATGAACTCTCCTTAAAAAT 57.116 30.769 0.00 0.00 33.69 1.82
383 400 8.742777 TGATTGGATGAACTCTCCTTAAAAATG 58.257 33.333 0.00 0.00 33.69 2.32
384 401 6.515272 TGGATGAACTCTCCTTAAAAATGC 57.485 37.500 0.00 0.00 33.69 3.56
385 402 5.418840 TGGATGAACTCTCCTTAAAAATGCC 59.581 40.000 0.00 0.00 33.69 4.40
386 403 5.163509 GGATGAACTCTCCTTAAAAATGCCC 60.164 44.000 0.00 0.00 0.00 5.36
387 404 4.086457 TGAACTCTCCTTAAAAATGCCCC 58.914 43.478 0.00 0.00 0.00 5.80
388 405 3.825908 ACTCTCCTTAAAAATGCCCCA 57.174 42.857 0.00 0.00 0.00 4.96
389 406 4.337264 ACTCTCCTTAAAAATGCCCCAT 57.663 40.909 0.00 0.00 0.00 4.00
392 409 4.204012 TCTCCTTAAAAATGCCCCATACG 58.796 43.478 0.00 0.00 0.00 3.06
398 415 2.603075 AAATGCCCCATACGCCATAT 57.397 45.000 0.00 0.00 0.00 1.78
414 431 3.071602 GCCATATCCCCGCATATAGATGT 59.928 47.826 0.00 0.00 35.30 3.06
427 444 2.904697 TAGATGTGGAGATGCAGCTG 57.095 50.000 10.40 10.11 33.18 4.24
447 467 4.286032 GCTGTACCTATAATCCCATCACCA 59.714 45.833 0.00 0.00 0.00 4.17
471 491 4.115199 GAGCCAACCGCCTGGGAT 62.115 66.667 0.00 0.00 40.75 3.85
472 492 3.645268 GAGCCAACCGCCTGGGATT 62.645 63.158 0.00 0.00 40.75 3.01
473 493 2.679996 GCCAACCGCCTGGGATTT 60.680 61.111 0.00 0.00 40.75 2.17
474 494 2.710902 GCCAACCGCCTGGGATTTC 61.711 63.158 0.00 0.00 40.75 2.17
475 495 1.304052 CCAACCGCCTGGGATTTCA 60.304 57.895 0.00 0.00 40.75 2.69
477 497 1.674322 AACCGCCTGGGATTTCACG 60.674 57.895 0.00 0.00 40.75 4.35
478 498 2.824041 CCGCCTGGGATTTCACGG 60.824 66.667 0.00 0.00 38.47 4.94
479 499 2.046314 CGCCTGGGATTTCACGGT 60.046 61.111 0.00 0.00 0.00 4.83
480 500 2.106683 CGCCTGGGATTTCACGGTC 61.107 63.158 0.00 0.00 0.00 4.79
481 501 1.299976 GCCTGGGATTTCACGGTCT 59.700 57.895 0.00 0.00 0.00 3.85
482 502 0.539986 GCCTGGGATTTCACGGTCTA 59.460 55.000 0.00 0.00 0.00 2.59
483 503 1.473434 GCCTGGGATTTCACGGTCTAG 60.473 57.143 0.00 0.00 0.00 2.43
484 504 1.473434 CCTGGGATTTCACGGTCTAGC 60.473 57.143 0.00 0.00 0.00 3.42
485 505 0.174845 TGGGATTTCACGGTCTAGCG 59.825 55.000 0.00 0.00 0.00 4.26
486 506 1.152383 GGGATTTCACGGTCTAGCGC 61.152 60.000 0.00 0.00 0.00 5.92
487 507 1.480219 GGATTTCACGGTCTAGCGCG 61.480 60.000 0.00 0.00 0.00 6.86
488 508 2.078958 GATTTCACGGTCTAGCGCGC 62.079 60.000 26.66 26.66 0.00 6.86
489 509 4.789075 TTCACGGTCTAGCGCGCC 62.789 66.667 30.33 12.61 0.00 6.53
511 531 4.473520 CCATGACGGGCCGAAGCT 62.474 66.667 35.78 10.44 39.73 3.74
512 532 2.892425 CATGACGGGCCGAAGCTC 60.892 66.667 35.78 20.32 39.73 4.09
541 561 3.095911 CGATCACGCTGCTGCATT 58.904 55.556 16.29 0.00 39.64 3.56
544 564 0.169672 GATCACGCTGCTGCATTGTT 59.830 50.000 16.29 6.89 39.64 2.83
547 567 2.195567 ACGCTGCTGCATTGTTGGT 61.196 52.632 16.29 0.37 39.64 3.67
553 573 1.005867 CTGCATTGTTGGTGGCCAC 60.006 57.895 28.57 28.57 30.78 5.01
555 575 2.855514 GCATTGTTGGTGGCCACGT 61.856 57.895 29.08 8.13 30.78 4.49
556 576 1.007502 CATTGTTGGTGGCCACGTG 60.008 57.895 29.08 15.80 30.78 4.49
574 594 4.475135 GCCTGCCCTTCCCGAGTC 62.475 72.222 0.00 0.00 0.00 3.36
615 637 1.064758 TCCATTGATACCACACTGCCC 60.065 52.381 0.00 0.00 0.00 5.36
636 658 2.284190 GCCTTCTAGAGCAACACATCC 58.716 52.381 0.00 0.00 0.00 3.51
637 659 2.093235 GCCTTCTAGAGCAACACATCCT 60.093 50.000 0.00 0.00 0.00 3.24
677 699 5.615925 ATTAAGAGAGACCCTAAACGCAT 57.384 39.130 0.00 0.00 0.00 4.73
709 894 3.685435 GGGAACCGGTCGTCTGTA 58.315 61.111 8.04 0.00 40.86 2.74
710 895 1.509923 GGGAACCGGTCGTCTGTAG 59.490 63.158 8.04 0.00 40.86 2.74
712 897 1.593296 GGAACCGGTCGTCTGTAGCT 61.593 60.000 8.04 0.00 0.00 3.32
714 899 1.063764 GAACCGGTCGTCTGTAGCTAG 59.936 57.143 8.04 0.00 0.00 3.42
716 901 1.445716 CCGGTCGTCTGTAGCTAGGG 61.446 65.000 0.00 0.00 0.00 3.53
717 902 1.445716 CGGTCGTCTGTAGCTAGGGG 61.446 65.000 0.00 0.00 0.00 4.79
719 904 0.395448 GTCGTCTGTAGCTAGGGGGT 60.395 60.000 0.00 0.00 0.00 4.95
720 905 0.395311 TCGTCTGTAGCTAGGGGGTG 60.395 60.000 0.00 0.00 0.00 4.61
722 907 0.032416 GTCTGTAGCTAGGGGGTGGA 60.032 60.000 0.00 0.00 0.00 4.02
724 909 0.325296 CTGTAGCTAGGGGGTGGACA 60.325 60.000 0.00 0.00 0.00 4.02
725 910 0.325296 TGTAGCTAGGGGGTGGACAG 60.325 60.000 0.00 0.00 0.00 3.51
727 912 2.252012 TAGCTAGGGGGTGGACAGGG 62.252 65.000 0.00 0.00 0.00 4.45
728 913 2.454941 CTAGGGGGTGGACAGGGT 59.545 66.667 0.00 0.00 0.00 4.34
729 914 1.995626 CTAGGGGGTGGACAGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
730 915 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
732 917 3.647771 GGGGTGGACAGGGTGGTC 61.648 72.222 0.00 0.00 37.06 4.02
749 934 2.806945 GTCCATGGACCATCCTGAAA 57.193 50.000 31.37 0.00 39.08 2.69
750 935 3.085952 GTCCATGGACCATCCTGAAAA 57.914 47.619 31.37 0.00 39.08 2.29
751 936 3.635591 GTCCATGGACCATCCTGAAAAT 58.364 45.455 31.37 0.00 39.08 1.82
752 937 4.026052 GTCCATGGACCATCCTGAAAATT 58.974 43.478 31.37 0.00 39.08 1.82
753 938 4.098501 GTCCATGGACCATCCTGAAAATTC 59.901 45.833 31.37 2.86 39.08 2.17
754 939 3.385755 CCATGGACCATCCTGAAAATTCC 59.614 47.826 5.56 0.00 37.46 3.01
755 940 3.100207 TGGACCATCCTGAAAATTCCC 57.900 47.619 0.00 0.00 37.46 3.97
756 941 2.292192 TGGACCATCCTGAAAATTCCCC 60.292 50.000 0.00 0.00 37.46 4.81
757 942 2.388735 GACCATCCTGAAAATTCCCCC 58.611 52.381 0.00 0.00 0.00 5.40
758 943 1.721691 ACCATCCTGAAAATTCCCCCA 59.278 47.619 0.00 0.00 0.00 4.96
759 944 2.318822 ACCATCCTGAAAATTCCCCCAT 59.681 45.455 0.00 0.00 0.00 4.00
760 945 3.535590 ACCATCCTGAAAATTCCCCCATA 59.464 43.478 0.00 0.00 0.00 2.74
761 946 4.154942 CCATCCTGAAAATTCCCCCATAG 58.845 47.826 0.00 0.00 0.00 2.23
762 947 3.312736 TCCTGAAAATTCCCCCATAGC 57.687 47.619 0.00 0.00 0.00 2.97
763 948 2.091333 TCCTGAAAATTCCCCCATAGCC 60.091 50.000 0.00 0.00 0.00 3.93
764 949 2.359143 CCTGAAAATTCCCCCATAGCCA 60.359 50.000 0.00 0.00 0.00 4.75
765 950 3.373830 CTGAAAATTCCCCCATAGCCAA 58.626 45.455 0.00 0.00 0.00 4.52
766 951 3.969312 CTGAAAATTCCCCCATAGCCAAT 59.031 43.478 0.00 0.00 0.00 3.16
767 952 5.147032 CTGAAAATTCCCCCATAGCCAATA 58.853 41.667 0.00 0.00 0.00 1.90
768 953 5.725490 TGAAAATTCCCCCATAGCCAATAT 58.275 37.500 0.00 0.00 0.00 1.28
769 954 6.868826 TGAAAATTCCCCCATAGCCAATATA 58.131 36.000 0.00 0.00 0.00 0.86
770 955 7.486473 TGAAAATTCCCCCATAGCCAATATAT 58.514 34.615 0.00 0.00 0.00 0.86
771 956 8.628281 TGAAAATTCCCCCATAGCCAATATATA 58.372 33.333 0.00 0.00 0.00 0.86
772 957 9.136323 GAAAATTCCCCCATAGCCAATATATAG 57.864 37.037 0.00 0.00 0.00 1.31
773 958 6.786843 ATTCCCCCATAGCCAATATATAGG 57.213 41.667 0.00 0.00 0.00 2.57
774 959 5.249301 TCCCCCATAGCCAATATATAGGT 57.751 43.478 0.00 0.00 0.00 3.08
775 960 5.619926 TCCCCCATAGCCAATATATAGGTT 58.380 41.667 0.00 0.00 0.00 3.50
776 961 6.768914 TCCCCCATAGCCAATATATAGGTTA 58.231 40.000 0.00 0.00 0.00 2.85
777 962 6.849697 TCCCCCATAGCCAATATATAGGTTAG 59.150 42.308 0.00 0.00 0.00 2.34
778 963 6.849697 CCCCCATAGCCAATATATAGGTTAGA 59.150 42.308 0.00 0.00 0.00 2.10
779 964 7.349859 CCCCCATAGCCAATATATAGGTTAGAA 59.650 40.741 0.00 0.00 0.00 2.10
780 965 8.778059 CCCCATAGCCAATATATAGGTTAGAAA 58.222 37.037 0.00 0.00 0.00 2.52
831 1016 9.332301 GAATTACATGCAAATTTTCATTGTTGG 57.668 29.630 0.17 0.00 0.00 3.77
832 1017 8.618702 ATTACATGCAAATTTTCATTGTTGGA 57.381 26.923 0.17 0.00 0.00 3.53
833 1018 6.303021 ACATGCAAATTTTCATTGTTGGAC 57.697 33.333 0.17 0.00 0.00 4.02
834 1019 5.239087 ACATGCAAATTTTCATTGTTGGACC 59.761 36.000 0.17 0.00 0.00 4.46
835 1020 4.774124 TGCAAATTTTCATTGTTGGACCA 58.226 34.783 0.00 0.00 0.00 4.02
836 1021 4.574013 TGCAAATTTTCATTGTTGGACCAC 59.426 37.500 0.00 0.00 0.00 4.16
837 1022 4.024133 GCAAATTTTCATTGTTGGACCACC 60.024 41.667 0.00 0.00 0.00 4.61
838 1023 4.350368 AATTTTCATTGTTGGACCACCC 57.650 40.909 0.00 0.00 34.81 4.61
839 1024 2.765689 TTTCATTGTTGGACCACCCT 57.234 45.000 0.00 0.00 35.38 4.34
840 1025 1.993956 TTCATTGTTGGACCACCCTG 58.006 50.000 0.00 0.00 35.38 4.45
841 1026 0.112218 TCATTGTTGGACCACCCTGG 59.888 55.000 0.00 0.00 45.02 4.45
842 1027 1.228862 ATTGTTGGACCACCCTGGC 60.229 57.895 0.00 0.00 42.67 4.85
843 1028 1.729267 ATTGTTGGACCACCCTGGCT 61.729 55.000 0.00 0.00 42.67 4.75
844 1029 2.034221 GTTGGACCACCCTGGCTC 59.966 66.667 0.00 0.00 42.67 4.70
845 1030 2.449518 TTGGACCACCCTGGCTCA 60.450 61.111 0.00 0.00 42.67 4.26
846 1031 2.829384 TTGGACCACCCTGGCTCAC 61.829 63.158 0.00 0.00 42.67 3.51
847 1032 4.035102 GGACCACCCTGGCTCACC 62.035 72.222 0.00 0.00 42.67 4.02
848 1033 4.394712 GACCACCCTGGCTCACCG 62.395 72.222 0.00 0.00 42.67 4.94
849 1034 4.954118 ACCACCCTGGCTCACCGA 62.954 66.667 0.00 0.00 42.67 4.69
850 1035 4.087892 CCACCCTGGCTCACCGAG 62.088 72.222 0.00 0.00 39.70 4.63
859 1044 2.103143 CTCACCGAGCTGGCTACG 59.897 66.667 0.00 1.74 43.94 3.51
860 1045 2.675423 TCACCGAGCTGGCTACGT 60.675 61.111 0.00 0.00 43.94 3.57
861 1046 2.202623 CACCGAGCTGGCTACGTC 60.203 66.667 0.00 0.00 43.94 4.34
862 1047 2.675423 ACCGAGCTGGCTACGTCA 60.675 61.111 0.00 0.00 43.94 4.35
863 1048 2.052690 ACCGAGCTGGCTACGTCAT 61.053 57.895 0.00 0.00 43.94 3.06
864 1049 1.141881 CCGAGCTGGCTACGTCATT 59.858 57.895 0.00 0.00 0.00 2.57
865 1050 0.460284 CCGAGCTGGCTACGTCATTT 60.460 55.000 0.00 0.00 0.00 2.32
872 1057 4.700213 AGCTGGCTACGTCATTTACATTTT 59.300 37.500 0.00 0.00 0.00 1.82
876 1061 6.607689 TGGCTACGTCATTTACATTTTCAAG 58.392 36.000 0.00 0.00 0.00 3.02
1045 1231 3.620488 TGCTTTCTCAGTGTGAACCTTT 58.380 40.909 7.12 0.00 0.00 3.11
1049 1235 5.731686 GCTTTCTCAGTGTGAACCTTTCTTG 60.732 44.000 7.12 0.00 0.00 3.02
1051 1237 2.945008 CTCAGTGTGAACCTTTCTTGCA 59.055 45.455 0.00 0.00 0.00 4.08
1052 1238 3.351740 TCAGTGTGAACCTTTCTTGCAA 58.648 40.909 0.00 0.00 0.00 4.08
1053 1239 3.128589 TCAGTGTGAACCTTTCTTGCAAC 59.871 43.478 0.00 0.00 0.00 4.17
1056 1242 0.383949 TGAACCTTTCTTGCAACGCC 59.616 50.000 0.00 0.00 0.00 5.68
1057 1243 0.660300 GAACCTTTCTTGCAACGCCG 60.660 55.000 0.00 0.00 0.00 6.46
1058 1244 2.070654 AACCTTTCTTGCAACGCCGG 62.071 55.000 0.00 0.00 0.00 6.13
1059 1245 2.429069 CTTTCTTGCAACGCCGGC 60.429 61.111 19.07 19.07 0.00 6.13
1060 1246 3.896863 CTTTCTTGCAACGCCGGCC 62.897 63.158 23.46 7.25 0.00 6.13
1071 1257 4.434354 GCCGGCCCACCAATGGTA 62.434 66.667 18.11 0.00 45.66 3.25
1072 1258 2.600731 CCGGCCCACCAATGGTAT 59.399 61.111 3.85 0.00 45.66 2.73
1073 1259 1.528309 CCGGCCCACCAATGGTATC 60.528 63.158 3.85 0.00 45.66 2.24
1086 1272 1.078988 GGTATCCGCGTGAAACCCA 60.079 57.895 4.92 0.00 0.00 4.51
1169 1368 2.856988 TCAACTCCCCACCCCACC 60.857 66.667 0.00 0.00 0.00 4.61
1652 1855 2.119611 TCCCTCAAGACCTGGCGA 59.880 61.111 0.00 0.00 0.00 5.54
2021 2224 1.127567 AGGTGCTGGGCTAGACACAA 61.128 55.000 20.41 0.00 36.08 3.33
2213 2416 2.716217 ACCTGCTCCTGTTAAAGCATC 58.284 47.619 0.21 0.00 46.69 3.91
2359 2562 1.441738 CACCATCGTTGCTGTCATCA 58.558 50.000 0.00 0.00 0.00 3.07
2776 3001 3.243704 TGCTGGAATACAAAACTGCAACC 60.244 43.478 0.00 0.00 35.37 3.77
2900 3127 7.063544 GGTTATCATCGTATTGAGTATTGGCTC 59.936 40.741 0.00 0.00 36.12 4.70
2901 3128 5.791336 TCATCGTATTGAGTATTGGCTCT 57.209 39.130 0.00 0.00 36.51 4.09
2909 3136 8.297426 CGTATTGAGTATTGGCTCTACTTATCA 58.703 37.037 1.96 0.00 36.51 2.15
2920 3147 7.265673 TGGCTCTACTTATCATGTTAGTTGTC 58.734 38.462 0.00 0.00 0.00 3.18
3004 3231 5.384336 TGAACAGAAATTCCCATGTGAAGA 58.616 37.500 0.00 0.00 0.00 2.87
3016 3243 3.213506 CATGTGAAGAACAAGGACACCA 58.786 45.455 0.00 0.00 43.61 4.17
3200 3432 0.458669 GCCATCTGCCCTGTTTGATG 59.541 55.000 0.00 0.00 36.87 3.07
3208 3440 1.070601 GCCCTGTTTGATGTTTGCCTT 59.929 47.619 0.00 0.00 0.00 4.35
3221 3453 3.129638 TGTTTGCCTTCTTGTTGTGGTAC 59.870 43.478 0.00 0.00 0.00 3.34
3257 3489 4.634004 TCTTGTTCGTTGCGGATTGATTAT 59.366 37.500 0.00 0.00 0.00 1.28
3275 3507 5.356751 TGATTATGTTTTGGTTAGCAGCGAT 59.643 36.000 0.00 0.00 0.00 4.58
3276 3508 6.540551 TGATTATGTTTTGGTTAGCAGCGATA 59.459 34.615 0.00 0.00 0.00 2.92
3277 3509 4.616181 ATGTTTTGGTTAGCAGCGATAC 57.384 40.909 0.00 0.00 0.00 2.24
3278 3510 2.413796 TGTTTTGGTTAGCAGCGATACG 59.586 45.455 0.00 0.00 0.00 3.06
3279 3511 2.373540 TTTGGTTAGCAGCGATACGT 57.626 45.000 0.00 0.00 0.00 3.57
3281 3513 2.373540 TGGTTAGCAGCGATACGTTT 57.626 45.000 0.00 0.00 0.00 3.60
3282 3514 3.507103 TGGTTAGCAGCGATACGTTTA 57.493 42.857 0.00 0.00 0.00 2.01
3283 3515 4.049546 TGGTTAGCAGCGATACGTTTAT 57.950 40.909 0.00 0.00 0.00 1.40
3284 3516 4.435425 TGGTTAGCAGCGATACGTTTATT 58.565 39.130 0.00 0.00 0.00 1.40
3285 3517 4.871557 TGGTTAGCAGCGATACGTTTATTT 59.128 37.500 0.00 0.00 0.00 1.40
3286 3518 5.352016 TGGTTAGCAGCGATACGTTTATTTT 59.648 36.000 0.00 0.00 0.00 1.82
3287 3519 5.675444 GGTTAGCAGCGATACGTTTATTTTG 59.325 40.000 0.00 0.00 0.00 2.44
3288 3520 4.939509 AGCAGCGATACGTTTATTTTGT 57.060 36.364 0.00 0.00 0.00 2.83
3289 3521 4.647964 AGCAGCGATACGTTTATTTTGTG 58.352 39.130 0.00 0.00 0.00 3.33
3304 3569 1.909700 TTGTGATGAAAGTGGAGGGC 58.090 50.000 0.00 0.00 0.00 5.19
3310 3575 1.604604 TGAAAGTGGAGGGCGAAAAG 58.395 50.000 0.00 0.00 0.00 2.27
3319 3584 3.945285 TGGAGGGCGAAAAGATTGTTATC 59.055 43.478 0.00 0.00 0.00 1.75
3336 3601 1.047596 ATCTCTGCCTGCATCTCGGT 61.048 55.000 0.00 0.00 0.00 4.69
3349 3614 5.122519 TGCATCTCGGTGCTAATAAAATGA 58.877 37.500 3.60 0.00 45.27 2.57
3409 3675 7.362662 CGTGGAGATGGTAATAAAATGATTGG 58.637 38.462 0.00 0.00 0.00 3.16
3442 3708 1.845809 ACACTTGCGTGCTTGCTAGC 61.846 55.000 13.56 13.56 45.10 3.42
3463 3729 0.179006 CTGCTCCCTAGAAATGGCCC 60.179 60.000 0.00 0.00 0.00 5.80
3464 3730 0.918799 TGCTCCCTAGAAATGGCCCA 60.919 55.000 0.00 0.00 0.00 5.36
3465 3731 0.179006 GCTCCCTAGAAATGGCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
3466 3732 0.475906 CTCCCTAGAAATGGCCCAGG 59.524 60.000 0.00 0.00 0.00 4.45
3467 3733 0.045623 TCCCTAGAAATGGCCCAGGA 59.954 55.000 0.00 0.00 0.00 3.86
3468 3734 0.183731 CCCTAGAAATGGCCCAGGAC 59.816 60.000 0.00 0.00 0.00 3.85
3477 3743 2.365635 GCCCAGGACCAGGAGCTA 60.366 66.667 4.06 0.00 0.00 3.32
3479 3745 2.066999 CCCAGGACCAGGAGCTACC 61.067 68.421 4.06 0.00 39.35 3.18
3497 3763 1.642762 ACCAGGCTTCTCCATTGGAAT 59.357 47.619 6.88 0.00 34.61 3.01
3498 3764 2.029623 CCAGGCTTCTCCATTGGAATG 58.970 52.381 6.88 1.28 33.17 2.67
3531 3797 3.892104 TAGGAACGAGCCCGGTGGT 62.892 63.158 0.00 0.00 40.78 4.16
3547 3813 0.184933 TGGTTTGCTGTAGCCAAGGT 59.815 50.000 0.80 0.00 41.18 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 177 1.795286 CAGGAAAGCACGACTTGAGAC 59.205 52.381 0.00 0.00 39.09 3.36
197 198 3.055891 GGTAGCAAAACCCATGCAAGATT 60.056 43.478 0.00 0.00 46.22 2.40
227 234 3.035942 CCACGCAAGAAAAGAAGAAACG 58.964 45.455 0.00 0.00 43.62 3.60
281 288 1.143838 CGCCATCAAGTCCCGATCA 59.856 57.895 0.00 0.00 0.00 2.92
299 316 5.780793 AGGAGTCATGTACCCCATATTAGTC 59.219 44.000 0.00 0.00 30.71 2.59
316 333 9.739276 ATATTTCAATTACAGTTTGAGGAGTCA 57.261 29.630 0.00 0.00 34.76 3.41
333 350 8.240682 TCAAACGTTCGATGGAAATATTTCAAT 58.759 29.630 25.55 21.30 38.92 2.57
336 353 8.523464 CAATCAAACGTTCGATGGAAATATTTC 58.477 33.333 18.22 18.22 33.05 2.17
353 370 4.256920 AGGAGAGTTCATCCAATCAAACG 58.743 43.478 0.00 0.00 39.47 3.60
383 400 1.077716 GGGATATGGCGTATGGGGC 60.078 63.158 3.45 0.00 0.00 5.80
384 401 1.607612 GGGGATATGGCGTATGGGG 59.392 63.158 3.45 0.00 0.00 4.96
385 402 1.220749 CGGGGATATGGCGTATGGG 59.779 63.158 3.45 0.00 0.00 4.00
386 403 1.449601 GCGGGGATATGGCGTATGG 60.450 63.158 3.45 0.00 0.00 2.74
387 404 0.107703 ATGCGGGGATATGGCGTATG 60.108 55.000 3.45 0.00 0.00 2.39
388 405 1.491668 TATGCGGGGATATGGCGTAT 58.508 50.000 0.00 0.00 0.00 3.06
389 406 1.491668 ATATGCGGGGATATGGCGTA 58.508 50.000 0.00 0.00 33.18 4.42
392 409 3.071602 ACATCTATATGCGGGGATATGGC 59.928 47.826 3.29 0.00 36.50 4.40
398 415 2.179427 CTCCACATCTATATGCGGGGA 58.821 52.381 0.00 0.00 37.93 4.81
414 431 2.159179 TAGGTACAGCTGCATCTCCA 57.841 50.000 15.27 0.00 0.00 3.86
427 444 5.745227 CCATGGTGATGGGATTATAGGTAC 58.255 45.833 2.57 0.00 45.11 3.34
464 484 1.473434 GCTAGACCGTGAAATCCCAGG 60.473 57.143 0.00 0.00 0.00 4.45
470 490 2.165301 GCGCGCTAGACCGTGAAAT 61.165 57.895 26.67 0.00 40.91 2.17
471 491 2.807895 GCGCGCTAGACCGTGAAA 60.808 61.111 26.67 0.00 40.91 2.69
472 492 4.789075 GGCGCGCTAGACCGTGAA 62.789 66.667 32.29 0.00 40.91 3.18
494 514 4.473520 AGCTTCGGCCCGTCATGG 62.474 66.667 1.63 0.00 43.01 3.66
495 515 2.892425 GAGCTTCGGCCCGTCATG 60.892 66.667 1.63 0.00 43.01 3.07
496 516 4.514577 CGAGCTTCGGCCCGTCAT 62.515 66.667 1.63 0.00 43.01 3.06
527 547 1.283487 CAACAATGCAGCAGCGTGA 59.717 52.632 10.89 0.00 46.23 4.35
533 553 2.735883 GCCACCAACAATGCAGCA 59.264 55.556 0.00 0.00 0.00 4.41
585 605 3.244422 TGGTATCAATGGAGGCGGTAATC 60.244 47.826 0.00 0.00 0.00 1.75
589 609 0.180406 GTGGTATCAATGGAGGCGGT 59.820 55.000 0.00 0.00 0.00 5.68
591 611 1.134401 AGTGTGGTATCAATGGAGGCG 60.134 52.381 0.00 0.00 0.00 5.52
599 621 1.376683 GCGGGCAGTGTGGTATCAA 60.377 57.895 0.00 0.00 0.00 2.57
600 622 2.267642 GCGGGCAGTGTGGTATCA 59.732 61.111 0.00 0.00 0.00 2.15
615 637 1.929836 GATGTGTTGCTCTAGAAGGCG 59.070 52.381 0.00 0.00 0.00 5.52
658 680 3.676324 CGAATGCGTTTAGGGTCTCTCTT 60.676 47.826 0.00 0.00 0.00 2.85
659 681 2.159226 CGAATGCGTTTAGGGTCTCTCT 60.159 50.000 0.00 0.00 0.00 3.10
665 687 0.107848 CCTCCGAATGCGTTTAGGGT 60.108 55.000 12.38 0.00 35.23 4.34
674 696 1.202348 CCCTCAAAAACCTCCGAATGC 59.798 52.381 0.00 0.00 0.00 3.56
677 699 2.578786 GTTCCCTCAAAAACCTCCGAA 58.421 47.619 0.00 0.00 0.00 4.30
702 887 1.392710 CCACCCCCTAGCTACAGACG 61.393 65.000 0.00 0.00 0.00 4.18
704 889 0.032416 GTCCACCCCCTAGCTACAGA 60.032 60.000 0.00 0.00 0.00 3.41
705 890 0.325296 TGTCCACCCCCTAGCTACAG 60.325 60.000 0.00 0.00 0.00 2.74
706 891 0.325296 CTGTCCACCCCCTAGCTACA 60.325 60.000 0.00 0.00 0.00 2.74
707 892 1.049289 CCTGTCCACCCCCTAGCTAC 61.049 65.000 0.00 0.00 0.00 3.58
708 893 1.313475 CCTGTCCACCCCCTAGCTA 59.687 63.158 0.00 0.00 0.00 3.32
709 894 2.041265 CCTGTCCACCCCCTAGCT 59.959 66.667 0.00 0.00 0.00 3.32
710 895 3.090532 CCCTGTCCACCCCCTAGC 61.091 72.222 0.00 0.00 0.00 3.42
712 897 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
722 907 3.495729 GTCCATGGACCACCCTGT 58.504 61.111 31.37 0.00 39.08 4.00
730 915 2.806945 TTTCAGGATGGTCCATGGAC 57.193 50.000 33.14 33.14 39.61 4.02
731 916 4.280819 GAATTTTCAGGATGGTCCATGGA 58.719 43.478 11.44 11.44 39.61 3.41
732 917 3.385755 GGAATTTTCAGGATGGTCCATGG 59.614 47.826 9.76 4.97 39.61 3.66
733 918 3.385755 GGGAATTTTCAGGATGGTCCATG 59.614 47.826 9.76 0.00 39.61 3.66
734 919 3.630828 GGGGAATTTTCAGGATGGTCCAT 60.631 47.826 3.26 3.26 39.61 3.41
735 920 2.292192 GGGGAATTTTCAGGATGGTCCA 60.292 50.000 0.00 0.00 39.61 4.02
736 921 2.388735 GGGGAATTTTCAGGATGGTCC 58.611 52.381 0.00 0.00 36.16 4.46
737 922 2.292192 TGGGGGAATTTTCAGGATGGTC 60.292 50.000 0.00 0.00 36.16 4.02
738 923 1.721691 TGGGGGAATTTTCAGGATGGT 59.278 47.619 0.00 0.00 36.16 3.55
739 924 2.548464 TGGGGGAATTTTCAGGATGG 57.452 50.000 0.00 0.00 36.16 3.51
740 925 3.575687 GCTATGGGGGAATTTTCAGGATG 59.424 47.826 0.00 0.00 37.54 3.51
741 926 3.438520 GGCTATGGGGGAATTTTCAGGAT 60.439 47.826 0.00 0.00 0.00 3.24
742 927 2.091333 GGCTATGGGGGAATTTTCAGGA 60.091 50.000 0.00 0.00 0.00 3.86
743 928 2.319844 GGCTATGGGGGAATTTTCAGG 58.680 52.381 0.00 0.00 0.00 3.86
744 929 3.030873 TGGCTATGGGGGAATTTTCAG 57.969 47.619 0.00 0.00 0.00 3.02
745 930 3.481559 TTGGCTATGGGGGAATTTTCA 57.518 42.857 0.00 0.00 0.00 2.69
746 931 7.978099 ATATATTGGCTATGGGGGAATTTTC 57.022 36.000 0.00 0.00 0.00 2.29
747 932 8.067488 CCTATATATTGGCTATGGGGGAATTTT 58.933 37.037 0.00 0.00 0.00 1.82
748 933 7.188267 ACCTATATATTGGCTATGGGGGAATTT 59.812 37.037 12.51 0.00 32.93 1.82
749 934 6.687415 ACCTATATATTGGCTATGGGGGAATT 59.313 38.462 12.51 0.00 32.93 2.17
750 935 6.227966 ACCTATATATTGGCTATGGGGGAAT 58.772 40.000 12.51 0.00 32.93 3.01
751 936 5.619926 ACCTATATATTGGCTATGGGGGAA 58.380 41.667 12.51 0.00 32.93 3.97
752 937 5.249301 ACCTATATATTGGCTATGGGGGA 57.751 43.478 12.51 0.00 32.93 4.81
753 938 5.994416 AACCTATATATTGGCTATGGGGG 57.006 43.478 12.51 0.00 32.93 5.40
754 939 7.931015 TCTAACCTATATATTGGCTATGGGG 57.069 40.000 12.51 0.00 32.93 4.96
805 990 9.332301 CCAACAATGAAAATTTGCATGTAATTC 57.668 29.630 12.58 0.00 0.00 2.17
806 991 9.064706 TCCAACAATGAAAATTTGCATGTAATT 57.935 25.926 12.58 2.64 0.00 1.40
807 992 8.505625 GTCCAACAATGAAAATTTGCATGTAAT 58.494 29.630 12.58 0.00 0.00 1.89
808 993 7.041508 GGTCCAACAATGAAAATTTGCATGTAA 60.042 33.333 12.58 0.00 0.00 2.41
809 994 6.426328 GGTCCAACAATGAAAATTTGCATGTA 59.574 34.615 12.58 0.00 0.00 2.29
810 995 5.239087 GGTCCAACAATGAAAATTTGCATGT 59.761 36.000 12.58 9.78 0.00 3.21
811 996 5.238868 TGGTCCAACAATGAAAATTTGCATG 59.761 36.000 12.58 9.20 0.00 4.06
812 997 5.239087 GTGGTCCAACAATGAAAATTTGCAT 59.761 36.000 5.77 5.77 0.00 3.96
813 998 4.574013 GTGGTCCAACAATGAAAATTTGCA 59.426 37.500 0.07 0.07 0.00 4.08
814 999 4.024133 GGTGGTCCAACAATGAAAATTTGC 60.024 41.667 0.61 0.00 0.00 3.68
815 1000 4.514816 GGGTGGTCCAACAATGAAAATTTG 59.485 41.667 9.70 0.00 35.00 2.32
816 1001 4.411869 AGGGTGGTCCAACAATGAAAATTT 59.588 37.500 9.70 0.00 38.24 1.82
817 1002 3.973305 AGGGTGGTCCAACAATGAAAATT 59.027 39.130 9.70 0.00 38.24 1.82
818 1003 3.324556 CAGGGTGGTCCAACAATGAAAAT 59.675 43.478 9.70 0.00 38.24 1.82
819 1004 2.697751 CAGGGTGGTCCAACAATGAAAA 59.302 45.455 9.70 0.00 38.24 2.29
820 1005 2.315176 CAGGGTGGTCCAACAATGAAA 58.685 47.619 9.70 0.00 38.24 2.69
821 1006 1.480312 CCAGGGTGGTCCAACAATGAA 60.480 52.381 9.70 0.00 38.24 2.57
822 1007 0.112218 CCAGGGTGGTCCAACAATGA 59.888 55.000 9.70 0.00 38.24 2.57
823 1008 1.535204 GCCAGGGTGGTCCAACAATG 61.535 60.000 9.70 6.81 40.46 2.82
824 1009 1.228862 GCCAGGGTGGTCCAACAAT 60.229 57.895 9.70 0.00 40.46 2.71
825 1010 2.197324 GCCAGGGTGGTCCAACAA 59.803 61.111 9.70 0.00 40.46 2.83
826 1011 2.776526 AGCCAGGGTGGTCCAACA 60.777 61.111 9.70 0.00 40.46 3.33
827 1012 2.034221 GAGCCAGGGTGGTCCAAC 59.966 66.667 0.00 0.00 40.46 3.77
828 1013 2.449518 TGAGCCAGGGTGGTCCAA 60.450 61.111 0.00 0.00 40.46 3.53
829 1014 3.249189 GTGAGCCAGGGTGGTCCA 61.249 66.667 0.00 0.00 40.46 4.02
830 1015 4.035102 GGTGAGCCAGGGTGGTCC 62.035 72.222 0.00 0.00 40.46 4.46
831 1016 4.394712 CGGTGAGCCAGGGTGGTC 62.395 72.222 0.00 0.00 40.46 4.02
832 1017 4.954118 TCGGTGAGCCAGGGTGGT 62.954 66.667 0.00 0.00 40.46 4.16
833 1018 4.087892 CTCGGTGAGCCAGGGTGG 62.088 72.222 0.00 0.00 41.55 4.61
842 1027 2.103143 CGTAGCCAGCTCGGTGAG 59.897 66.667 0.00 0.00 36.97 3.51
843 1028 2.675423 ACGTAGCCAGCTCGGTGA 60.675 61.111 13.37 0.00 36.97 4.02
844 1029 2.202623 GACGTAGCCAGCTCGGTG 60.203 66.667 13.37 0.00 36.97 4.94
845 1030 1.605058 AATGACGTAGCCAGCTCGGT 61.605 55.000 13.37 5.99 36.97 4.69
846 1031 0.460284 AAATGACGTAGCCAGCTCGG 60.460 55.000 13.37 0.00 38.11 4.63
847 1032 1.852895 GTAAATGACGTAGCCAGCTCG 59.147 52.381 0.00 2.73 0.00 5.03
848 1033 2.888594 TGTAAATGACGTAGCCAGCTC 58.111 47.619 0.00 0.00 0.00 4.09
849 1034 3.543680 ATGTAAATGACGTAGCCAGCT 57.456 42.857 0.00 0.00 0.00 4.24
850 1035 4.616181 AAATGTAAATGACGTAGCCAGC 57.384 40.909 0.00 0.00 0.00 4.85
851 1036 6.176975 TGAAAATGTAAATGACGTAGCCAG 57.823 37.500 0.00 0.00 0.00 4.85
852 1037 6.348950 CCTTGAAAATGTAAATGACGTAGCCA 60.349 38.462 0.00 0.00 0.00 4.75
853 1038 6.027749 CCTTGAAAATGTAAATGACGTAGCC 58.972 40.000 0.00 0.00 0.00 3.93
854 1039 6.608610 ACCTTGAAAATGTAAATGACGTAGC 58.391 36.000 0.00 0.00 0.00 3.58
855 1040 8.932791 AGTACCTTGAAAATGTAAATGACGTAG 58.067 33.333 0.00 0.00 28.79 3.51
856 1041 8.836268 AGTACCTTGAAAATGTAAATGACGTA 57.164 30.769 0.00 0.00 28.79 3.57
857 1042 7.442969 TGAGTACCTTGAAAATGTAAATGACGT 59.557 33.333 0.00 0.00 28.79 4.34
858 1043 7.802738 TGAGTACCTTGAAAATGTAAATGACG 58.197 34.615 0.00 0.00 28.79 4.35
969 1154 8.783093 CGATTCCATGTTAATATTAGGCAAGAA 58.217 33.333 13.69 13.69 0.00 2.52
1009 1194 2.777832 AAGCAGCTACCCTTCTTCTG 57.222 50.000 0.00 0.00 0.00 3.02
1015 1201 1.981495 ACTGAGAAAGCAGCTACCCTT 59.019 47.619 0.00 0.00 39.51 3.95
1018 1204 2.072298 CACACTGAGAAAGCAGCTACC 58.928 52.381 0.00 0.00 39.51 3.18
1061 1247 0.461163 TCACGCGGATACCATTGGTG 60.461 55.000 18.83 2.51 36.19 4.17
1062 1248 0.250793 TTCACGCGGATACCATTGGT 59.749 50.000 13.94 13.94 40.16 3.67
1063 1249 1.063469 GTTTCACGCGGATACCATTGG 59.937 52.381 12.47 0.00 0.00 3.16
1064 1250 1.063469 GGTTTCACGCGGATACCATTG 59.937 52.381 22.53 7.36 44.40 2.82
1065 1251 1.375551 GGTTTCACGCGGATACCATT 58.624 50.000 22.53 0.00 44.40 3.16
1066 1252 0.463116 GGGTTTCACGCGGATACCAT 60.463 55.000 25.89 0.00 46.15 3.55
1067 1253 1.078988 GGGTTTCACGCGGATACCA 60.079 57.895 25.89 1.35 46.15 3.25
1068 1254 0.674269 TTGGGTTTCACGCGGATACC 60.674 55.000 20.67 20.67 44.30 2.73
1069 1255 1.158434 TTTGGGTTTCACGCGGATAC 58.842 50.000 12.47 10.08 33.25 2.24
1070 1256 1.893544 TTTTGGGTTTCACGCGGATA 58.106 45.000 12.47 0.00 33.25 2.59
1071 1257 1.033574 TTTTTGGGTTTCACGCGGAT 58.966 45.000 12.47 0.00 33.25 4.18
1072 1258 0.100861 GTTTTTGGGTTTCACGCGGA 59.899 50.000 12.47 1.33 33.25 5.54
1073 1259 0.101579 AGTTTTTGGGTTTCACGCGG 59.898 50.000 12.47 0.00 33.25 6.46
1086 1272 6.293900 CCTGTTTGGTTTGCTTTTGAGTTTTT 60.294 34.615 0.00 0.00 0.00 1.94
1169 1368 3.072476 CTGGTGGAGTGGAGTGGG 58.928 66.667 0.00 0.00 0.00 4.61
1611 1814 2.737830 GGAGCAGGAGGTATCGCC 59.262 66.667 0.00 0.00 37.58 5.54
1652 1855 4.699522 GCAGACCGGGTTCGCCTT 62.700 66.667 6.32 0.00 37.45 4.35
1903 2106 0.902531 TTTCCCAGTAGAAGAGGCCG 59.097 55.000 0.00 0.00 0.00 6.13
1907 2110 4.238514 CAACTCGTTTCCCAGTAGAAGAG 58.761 47.826 0.00 0.00 0.00 2.85
1908 2111 3.554337 GCAACTCGTTTCCCAGTAGAAGA 60.554 47.826 0.00 0.00 0.00 2.87
2021 2224 3.402681 CCCTGCCTCCACGATGGT 61.403 66.667 0.00 0.00 39.03 3.55
2320 2523 5.830991 TGGTGGGAAGTTGGTATATATTTGC 59.169 40.000 0.00 0.00 0.00 3.68
2359 2562 6.433093 AGCTTTACCTATTTCAAATTGTCGGT 59.567 34.615 0.00 0.00 0.00 4.69
2401 2604 4.800993 GTGATAACCATCAAGACGAGACAG 59.199 45.833 0.00 0.00 42.79 3.51
2517 2735 1.268899 GCAAGCTTCAACATGCAGAGT 59.731 47.619 0.00 0.00 38.63 3.24
2518 2736 1.268625 TGCAAGCTTCAACATGCAGAG 59.731 47.619 4.41 0.00 43.32 3.35
2556 2774 9.412460 TGGTGAGAAATATAAGATCAGCAATTT 57.588 29.630 3.17 0.00 43.20 1.82
2738 2963 3.125316 CCAGCAAATCAAACAACTGGTG 58.875 45.455 0.00 0.00 39.85 4.17
2776 3001 1.008361 CCAAACTGGCGCATTTTCCG 61.008 55.000 10.83 0.00 0.00 4.30
2837 3064 7.449704 ACAATCTTATTTTGCAGAGGAGAAGTT 59.550 33.333 0.00 0.00 0.00 2.66
2900 3127 9.737427 AATCGAGACAACTAACATGATAAGTAG 57.263 33.333 0.00 0.00 0.00 2.57
2901 3128 9.516314 CAATCGAGACAACTAACATGATAAGTA 57.484 33.333 0.00 0.00 0.00 2.24
2909 3136 6.455647 TCAGAACAATCGAGACAACTAACAT 58.544 36.000 0.00 0.00 0.00 2.71
2920 3147 2.998670 ACTGTGCATCAGAACAATCGAG 59.001 45.455 19.01 0.00 46.27 4.04
3004 3231 2.413310 ACGACTTTGGTGTCCTTGTT 57.587 45.000 0.00 0.00 33.70 2.83
3016 3243 2.496899 AGATGCCATCCAACGACTTT 57.503 45.000 0.00 0.00 0.00 2.66
3163 3395 0.737019 GCCCAAACATGCATCCAACG 60.737 55.000 0.00 0.00 0.00 4.10
3200 3432 2.959507 ACCACAACAAGAAGGCAAAC 57.040 45.000 0.00 0.00 0.00 2.93
3228 3460 1.798223 CCGCAACGAACAAGAGATTCA 59.202 47.619 0.00 0.00 0.00 2.57
3257 3489 2.413796 CGTATCGCTGCTAACCAAAACA 59.586 45.455 0.00 0.00 0.00 2.83
3275 3507 8.155821 TCCACTTTCATCACAAAATAAACGTA 57.844 30.769 0.00 0.00 0.00 3.57
3276 3508 7.033530 TCCACTTTCATCACAAAATAAACGT 57.966 32.000 0.00 0.00 0.00 3.99
3277 3509 6.582295 CCTCCACTTTCATCACAAAATAAACG 59.418 38.462 0.00 0.00 0.00 3.60
3278 3510 6.868339 CCCTCCACTTTCATCACAAAATAAAC 59.132 38.462 0.00 0.00 0.00 2.01
3279 3511 6.518200 GCCCTCCACTTTCATCACAAAATAAA 60.518 38.462 0.00 0.00 0.00 1.40
3281 3513 4.462483 GCCCTCCACTTTCATCACAAAATA 59.538 41.667 0.00 0.00 0.00 1.40
3282 3514 3.259123 GCCCTCCACTTTCATCACAAAAT 59.741 43.478 0.00 0.00 0.00 1.82
3283 3515 2.627699 GCCCTCCACTTTCATCACAAAA 59.372 45.455 0.00 0.00 0.00 2.44
3284 3516 2.238521 GCCCTCCACTTTCATCACAAA 58.761 47.619 0.00 0.00 0.00 2.83
3285 3517 1.881925 CGCCCTCCACTTTCATCACAA 60.882 52.381 0.00 0.00 0.00 3.33
3286 3518 0.321564 CGCCCTCCACTTTCATCACA 60.322 55.000 0.00 0.00 0.00 3.58
3287 3519 0.036388 TCGCCCTCCACTTTCATCAC 60.036 55.000 0.00 0.00 0.00 3.06
3288 3520 0.690192 TTCGCCCTCCACTTTCATCA 59.310 50.000 0.00 0.00 0.00 3.07
3289 3521 1.821216 TTTCGCCCTCCACTTTCATC 58.179 50.000 0.00 0.00 0.00 2.92
3304 3569 5.728898 GCAGGCAGAGATAACAATCTTTTCG 60.729 44.000 0.00 0.00 0.00 3.46
3310 3575 4.387598 AGATGCAGGCAGAGATAACAATC 58.612 43.478 0.00 0.00 0.00 2.67
3319 3584 1.521010 CACCGAGATGCAGGCAGAG 60.521 63.158 0.00 0.00 0.00 3.35
3365 3630 9.349713 TCTCCACGCCAAAAAGAATATATTATT 57.650 29.630 0.00 0.00 0.00 1.40
3373 3638 2.493278 CCATCTCCACGCCAAAAAGAAT 59.507 45.455 0.00 0.00 0.00 2.40
3374 3639 1.885887 CCATCTCCACGCCAAAAAGAA 59.114 47.619 0.00 0.00 0.00 2.52
3376 3641 1.247567 ACCATCTCCACGCCAAAAAG 58.752 50.000 0.00 0.00 0.00 2.27
3378 3643 2.570415 TTACCATCTCCACGCCAAAA 57.430 45.000 0.00 0.00 0.00 2.44
3382 3647 4.819630 TCATTTTATTACCATCTCCACGCC 59.180 41.667 0.00 0.00 0.00 5.68
3386 3652 9.486123 TTTCCAATCATTTTATTACCATCTCCA 57.514 29.630 0.00 0.00 0.00 3.86
3409 3675 5.149054 CGCAAGTGTGATTCTATCCTTTC 57.851 43.478 0.00 0.00 0.00 2.62
3442 3708 1.202746 GGCCATTTCTAGGGAGCAGAG 60.203 57.143 0.00 0.00 0.00 3.35
3463 3729 1.333636 CCTGGTAGCTCCTGGTCCTG 61.334 65.000 15.49 0.00 46.28 3.86
3464 3730 1.002274 CCTGGTAGCTCCTGGTCCT 59.998 63.158 15.49 0.00 46.28 3.85
3465 3731 3.635510 CCTGGTAGCTCCTGGTCC 58.364 66.667 15.49 0.00 46.28 4.46
3477 3743 1.075601 TTCCAATGGAGAAGCCTGGT 58.924 50.000 0.86 0.00 34.40 4.00
3497 3763 3.263369 TCCTACCCAGTACAACTTCCA 57.737 47.619 0.00 0.00 0.00 3.53
3498 3764 3.615834 CGTTCCTACCCAGTACAACTTCC 60.616 52.174 0.00 0.00 0.00 3.46
3499 3765 3.256631 TCGTTCCTACCCAGTACAACTTC 59.743 47.826 0.00 0.00 0.00 3.01
3531 3797 1.953686 GTTGACCTTGGCTACAGCAAA 59.046 47.619 3.24 0.00 44.36 3.68


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

AutoCloner maintained by Alex Coulton.