Multiple sequence alignment - TraesCS7D01G024300

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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 TraesCS7D01G024300 chr7D 100.000 3821 0 0 1 3821 11431353 11427533 0.000000e+00 7057.0
1 TraesCS7D01G024300 chr7A 91.697 2168 150 16 545 2705 10907631 10905487 0.000000e+00 2979.0
2 TraesCS7D01G024300 chr7A 94.086 186 10 1 6 190 10908347 10908162 8.080000e-72 281.0
3 TraesCS7D01G024300 chr7A 76.757 370 39 30 3471 3821 10904826 10904485 3.050000e-36 163.0
4 TraesCS7D01G024300 chr7A 100.000 32 0 0 3082 3113 10905149 10905118 4.120000e-05 60.2
5 TraesCS7D01G024300 chr4A 92.933 1415 95 3 1295 2705 726442782 726444195 0.000000e+00 2054.0
6 TraesCS7D01G024300 chr4A 89.765 596 51 7 684 1276 726441841 726442429 0.000000e+00 754.0
7 TraesCS7D01G024300 chr4A 94.426 305 10 3 1 305 726440759 726441056 2.690000e-126 462.0
8 TraesCS7D01G024300 chr4A 78.979 333 36 23 3447 3772 726444847 726445152 3.010000e-46 196.0
9 TraesCS7D01G024300 chr4A 83.333 78 3 1 3046 3113 726444499 726444576 3.190000e-06 63.9
10 TraesCS7D01G024300 chr5A 89.203 954 84 5 2082 3030 292253977 292254916 0.000000e+00 1173.0
11 TraesCS7D01G024300 chr5A 88.924 957 87 6 2082 3033 472472882 472471940 0.000000e+00 1162.0
12 TraesCS7D01G024300 chrUn 97.015 67 2 0 485 551 87037930 87037864 3.120000e-21 113.0
13 TraesCS7D01G024300 chrUn 100.000 61 0 0 485 545 339968876 339968936 3.120000e-21 113.0
14 TraesCS7D01G024300 chr7B 97.015 67 2 0 485 551 660639700 660639634 3.120000e-21 113.0
15 TraesCS7D01G024300 chr6D 100.000 61 0 0 485 545 23418320 23418380 3.120000e-21 113.0
16 TraesCS7D01G024300 chr6D 100.000 61 0 0 485 545 23420551 23420611 3.120000e-21 113.0
17 TraesCS7D01G024300 chr6D 100.000 61 0 0 485 545 23620241 23620301 3.120000e-21 113.0
18 TraesCS7D01G024300 chr6D 100.000 61 0 0 485 545 23623456 23623516 3.120000e-21 113.0
19 TraesCS7D01G024300 chr6D 100.000 61 0 0 485 545 23783066 23783126 3.120000e-21 113.0
20 TraesCS7D01G024300 chr6B 98.438 64 1 0 485 548 46671417 46671354 3.120000e-21 113.0
21 TraesCS7D01G024300 chr1D 92.500 40 3 0 1708 1747 440046155 440046116 1.480000e-04 58.4


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 TraesCS7D01G024300 chr7D 11427533 11431353 3820 True 7057.00 7057 100.0000 1 3821 1 chr7D.!!$R1 3820
1 TraesCS7D01G024300 chr7A 10904485 10908347 3862 True 870.80 2979 90.6350 6 3821 4 chr7A.!!$R1 3815
2 TraesCS7D01G024300 chr4A 726440759 726445152 4393 False 705.98 2054 87.8872 1 3772 5 chr4A.!!$F1 3771
3 TraesCS7D01G024300 chr5A 292253977 292254916 939 False 1173.00 1173 89.2030 2082 3030 1 chr5A.!!$F1 948
4 TraesCS7D01G024300 chr5A 472471940 472472882 942 True 1162.00 1162 88.9240 2082 3033 1 chr5A.!!$R1 951

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
506 943 0.037590 TTGGTAAAGGATGCAGCGGT 59.962 50.0 0.0 0.0 0.0 5.68 F
1659 2542 0.036388 GGAACTCGATGCTTGGTGGA 60.036 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 3187 0.252421 AGAGCCTGACCATCCTGTCA 60.252 55.0 0.0 0.0 42.75 3.58 R
2954 3901 0.036294 GCTACCCCTCGTCTTGCTTT 60.036 55.0 0.0 0.0 0.00 3.51 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
222 224 1.544246 GGTTTTTACCAGGAATGCGCT 59.456 47.619 9.73 0.00 0.00 5.92
251 253 8.525316 TCCATCATGCATATTTGTTATGAATCC 58.475 33.333 0.00 0.00 40.22 3.01
317 746 2.305635 GGTTTCAAGGAATGGGGCAAAT 59.694 45.455 0.00 0.00 0.00 2.32
374 804 8.684386 TTTTAAAGGAAAAATGTGGGAATTCC 57.316 30.769 16.74 16.74 39.85 3.01
426 863 4.944962 TTTCTATGCACGATGAACAAGG 57.055 40.909 0.00 0.00 0.00 3.61
439 876 7.604164 CACGATGAACAAGGCTAATATCCTTAT 59.396 37.037 0.00 0.00 41.73 1.73
442 879 9.507329 GATGAACAAGGCTAATATCCTTATCAA 57.493 33.333 11.83 1.55 41.73 2.57
504 941 4.601019 CTTTATTGGTAAAGGATGCAGCG 58.399 43.478 0.00 0.00 41.92 5.18
505 942 1.392589 ATTGGTAAAGGATGCAGCGG 58.607 50.000 0.00 0.00 0.00 5.52
506 943 0.037590 TTGGTAAAGGATGCAGCGGT 59.962 50.000 0.00 0.00 0.00 5.68
507 944 0.906066 TGGTAAAGGATGCAGCGGTA 59.094 50.000 0.00 0.00 0.00 4.02
508 945 1.296727 GGTAAAGGATGCAGCGGTAC 58.703 55.000 0.00 0.00 0.00 3.34
526 963 5.299582 GGTACGAGCCTATAGAACAGATC 57.700 47.826 0.00 0.00 0.00 2.75
527 964 4.156373 GGTACGAGCCTATAGAACAGATCC 59.844 50.000 0.00 0.00 0.00 3.36
528 965 4.107127 ACGAGCCTATAGAACAGATCCT 57.893 45.455 0.00 0.00 0.00 3.24
529 966 3.823873 ACGAGCCTATAGAACAGATCCTG 59.176 47.826 0.00 0.00 37.52 3.86
542 979 5.153950 ACAGATCCTGTTCAAGTAAGGTC 57.846 43.478 0.00 0.00 42.59 3.85
543 980 4.177026 CAGATCCTGTTCAAGTAAGGTCG 58.823 47.826 0.00 0.00 32.59 4.79
544 981 3.833070 AGATCCTGTTCAAGTAAGGTCGT 59.167 43.478 0.00 0.00 32.59 4.34
555 993 6.950545 TCAAGTAAGGTCGTTATGTGTTTTG 58.049 36.000 0.00 0.00 0.00 2.44
602 1040 9.626045 ATTAGAATTCACGTTCTTTTCCAATTC 57.374 29.630 8.44 0.00 39.15 2.17
608 1046 2.351350 CGTTCTTTTCCAATTCCCGTGG 60.351 50.000 0.00 0.00 37.51 4.94
623 1061 0.958091 CGTGGACCAAAGCATCCAAA 59.042 50.000 0.00 0.00 46.53 3.28
640 1086 9.412460 AGCATCCAAATTGACAGAATTTCTATA 57.588 29.630 0.00 0.00 0.00 1.31
682 1221 7.438459 ACATACGTTCCTCTATTATTTCTGCAC 59.562 37.037 0.00 0.00 0.00 4.57
697 1236 3.002791 TCTGCACTTTTAGAATCCTGCG 58.997 45.455 0.00 0.00 0.00 5.18
702 1241 3.751175 CACTTTTAGAATCCTGCGAACCA 59.249 43.478 0.00 0.00 0.00 3.67
705 1244 5.048713 ACTTTTAGAATCCTGCGAACCAAAG 60.049 40.000 0.00 0.00 0.00 2.77
720 1259 3.441101 ACCAAAGGAGCCCTAAAATTCC 58.559 45.455 0.00 0.00 31.13 3.01
721 1260 3.181412 ACCAAAGGAGCCCTAAAATTCCA 60.181 43.478 0.00 0.00 31.13 3.53
726 1265 4.281657 AGGAGCCCTAAAATTCCAACATC 58.718 43.478 0.00 0.00 32.02 3.06
732 1271 6.880529 AGCCCTAAAATTCCAACATCAATTTG 59.119 34.615 0.00 0.00 33.44 2.32
766 1311 2.844946 TGCTTGAATTCAACGTGAGGA 58.155 42.857 16.91 5.52 0.00 3.71
805 1350 4.897224 TGAATTCGATGAAAATCTCGCAC 58.103 39.130 0.04 0.00 34.94 5.34
809 1354 1.267732 CGATGAAAATCTCGCACTGCC 60.268 52.381 0.00 0.00 0.00 4.85
901 1448 0.956902 TAAAAACCCGCCTTCGCCTC 60.957 55.000 0.00 0.00 0.00 4.70
908 1455 4.388499 GCCTTCGCCTCCCGTTCA 62.388 66.667 0.00 0.00 38.35 3.18
914 1461 2.203972 TCGCCTCCCGTTCACGTAAG 62.204 60.000 0.00 0.00 40.37 2.34
915 1462 1.588082 GCCTCCCGTTCACGTAAGA 59.412 57.895 0.00 0.00 43.62 2.10
916 1463 0.458025 GCCTCCCGTTCACGTAAGAG 60.458 60.000 0.00 2.09 43.62 2.85
921 1468 2.486982 TCCCGTTCACGTAAGAGAGAAG 59.513 50.000 0.00 0.00 38.45 2.85
922 1469 2.486982 CCCGTTCACGTAAGAGAGAAGA 59.513 50.000 0.00 0.00 38.45 2.87
923 1470 3.057736 CCCGTTCACGTAAGAGAGAAGAA 60.058 47.826 0.00 0.00 38.45 2.52
935 1482 2.952978 GAGAGAAGAATACGCCTCCTCA 59.047 50.000 0.00 0.00 0.00 3.86
937 1484 1.410882 AGAAGAATACGCCTCCTCAGC 59.589 52.381 0.00 0.00 0.00 4.26
1200 1749 1.684049 CCTCAACTCGCTCCTCCCT 60.684 63.158 0.00 0.00 0.00 4.20
1239 1788 3.465403 CACCTCCTCCGCCTCCTG 61.465 72.222 0.00 0.00 0.00 3.86
1374 2257 2.507992 CTCGCCAACTCGCTCCTG 60.508 66.667 0.00 0.00 0.00 3.86
1527 2410 1.154225 GCTGTTCGACCAAATGCCG 60.154 57.895 0.00 0.00 0.00 5.69
1611 2494 2.863153 GCGCAACAGCTGTTCGAT 59.137 55.556 34.69 16.66 35.83 3.59
1612 2495 1.225854 GCGCAACAGCTGTTCGATC 60.226 57.895 34.69 22.88 35.83 3.69
1613 2496 1.900585 GCGCAACAGCTGTTCGATCA 61.901 55.000 34.69 0.00 35.83 2.92
1637 2520 2.878429 CGAGAGGGACGTGGTCAG 59.122 66.667 0.00 0.00 33.68 3.51
1653 2536 0.610174 TCAGCTGGAACTCGATGCTT 59.390 50.000 15.13 0.00 0.00 3.91
1655 2538 0.392193 AGCTGGAACTCGATGCTTGG 60.392 55.000 0.00 0.00 0.00 3.61
1656 2539 0.674895 GCTGGAACTCGATGCTTGGT 60.675 55.000 0.00 0.00 0.00 3.67
1659 2542 0.036388 GGAACTCGATGCTTGGTGGA 60.036 55.000 0.00 0.00 0.00 4.02
1662 2545 3.495100 GGAACTCGATGCTTGGTGGATAT 60.495 47.826 0.00 0.00 0.00 1.63
1944 2827 0.241481 AGAAGACCTTCGTGAGCGTC 59.759 55.000 4.32 0.00 43.97 5.19
2023 2906 1.000771 CGACAGAGGTGGGAGAGGA 60.001 63.158 0.00 0.00 0.00 3.71
2136 3019 2.506438 GAAAGGAGCGTCCCGTCG 60.506 66.667 1.06 0.00 37.19 5.12
2196 3079 3.111939 GAGAAGGCGCTCGAGCTA 58.888 61.111 32.88 0.00 39.32 3.32
2304 3187 2.116125 GAGGGCTGGTGGTGCTTT 59.884 61.111 0.00 0.00 0.00 3.51
2331 3214 1.227380 GGTCAGGCTCTACGGCATG 60.227 63.158 0.00 0.00 44.06 4.06
2352 3235 4.507969 CCCAAGGCAGAGCACTTT 57.492 55.556 0.00 0.00 0.00 2.66
2626 3515 0.034616 GAGGGAGATGATGAAGCGGG 59.965 60.000 0.00 0.00 0.00 6.13
2678 3570 3.834799 GGGATCGAGCGAACCGGT 61.835 66.667 0.00 0.00 41.33 5.28
2760 3703 2.815647 CTGAAGAAGCCGGCGACC 60.816 66.667 23.20 14.25 0.00 4.79
2796 3739 2.003548 GTGCAGGGAGGGAAGGGAT 61.004 63.158 0.00 0.00 0.00 3.85
2799 3742 2.368878 AGGGAGGGAAGGGATGCC 60.369 66.667 0.00 0.00 40.55 4.40
2823 3766 1.498865 GGACCTGTTGTGCGTGACAG 61.499 60.000 6.27 6.27 42.21 3.51
2844 3789 4.141883 CAACGCAGAGCATGTTGC 57.858 55.556 8.37 8.37 45.46 4.17
2868 3813 1.585267 TTACTACGCCTCGCCGTTGA 61.585 55.000 10.18 0.00 42.20 3.18
2870 3815 1.944676 CTACGCCTCGCCGTTGATC 60.945 63.158 1.31 0.00 42.20 2.92
2886 3831 2.034124 TGATCATCACGGAGCATCAGA 58.966 47.619 0.00 0.00 36.25 3.27
2887 3832 2.631545 TGATCATCACGGAGCATCAGAT 59.368 45.455 0.00 0.00 36.25 2.90
2900 3845 1.404391 CATCAGATTTCCTGCTGGTGC 59.596 52.381 9.73 0.00 42.62 5.01
2922 3867 0.737715 GTGGTCCTCTGTCGTCATGC 60.738 60.000 0.00 0.00 0.00 4.06
2962 3909 1.658114 CAGCAGCAGCAAAGCAAGA 59.342 52.632 3.17 0.00 45.49 3.02
2978 3925 0.630134 AAGACGAGGGGTAGCCTACT 59.370 55.000 11.48 0.00 0.00 2.57
2979 3926 0.106619 AGACGAGGGGTAGCCTACTG 60.107 60.000 11.48 1.38 0.00 2.74
2980 3927 1.736365 GACGAGGGGTAGCCTACTGC 61.736 65.000 11.48 0.00 41.71 4.40
3015 3962 2.564771 TGAGCAAGCGATGGAATAAGG 58.435 47.619 0.00 0.00 0.00 2.69
3033 3980 1.404035 AGGCAGAAAACACGTTTGGAC 59.596 47.619 0.00 0.00 32.36 4.02
3034 3981 1.404035 GGCAGAAAACACGTTTGGACT 59.596 47.619 0.00 0.00 32.36 3.85
3036 3983 3.507786 GCAGAAAACACGTTTGGACTTT 58.492 40.909 0.00 0.00 32.36 2.66
3039 3986 3.759618 AGAAAACACGTTTGGACTTTGGA 59.240 39.130 0.00 0.00 32.36 3.53
3040 3987 3.775661 AAACACGTTTGGACTTTGGAG 57.224 42.857 0.00 0.00 0.00 3.86
3042 3989 1.064979 ACACGTTTGGACTTTGGAGGT 60.065 47.619 0.00 0.00 0.00 3.85
3043 3990 1.333619 CACGTTTGGACTTTGGAGGTG 59.666 52.381 0.00 0.00 0.00 4.00
3052 4035 0.251742 CTTTGGAGGTGGGCCAATGA 60.252 55.000 8.40 0.00 44.30 2.57
3090 4074 4.711949 CCGGCTGGCTGCTCAACT 62.712 66.667 16.14 0.00 42.39 3.16
3091 4075 3.429141 CGGCTGGCTGCTCAACTG 61.429 66.667 16.14 0.00 42.39 3.16
3092 4076 2.033141 GGCTGGCTGCTCAACTGA 59.967 61.111 16.14 0.00 42.39 3.41
3093 4077 1.378250 GGCTGGCTGCTCAACTGAT 60.378 57.895 16.14 0.00 42.39 2.90
3094 4078 1.375098 GGCTGGCTGCTCAACTGATC 61.375 60.000 16.14 0.00 42.39 2.92
3095 4079 0.392729 GCTGGCTGCTCAACTGATCT 60.393 55.000 9.31 0.00 38.95 2.75
3096 4080 1.370609 CTGGCTGCTCAACTGATCTG 58.629 55.000 0.00 0.00 0.00 2.90
3097 4081 0.035725 TGGCTGCTCAACTGATCTGG 60.036 55.000 0.00 0.00 0.00 3.86
3098 4082 1.375098 GGCTGCTCAACTGATCTGGC 61.375 60.000 0.00 0.00 0.00 4.85
3099 4083 1.375098 GCTGCTCAACTGATCTGGCC 61.375 60.000 0.00 0.00 0.00 5.36
3100 4084 1.078918 TGCTCAACTGATCTGGCCG 60.079 57.895 0.00 0.00 0.00 6.13
3101 4085 1.817099 GCTCAACTGATCTGGCCGG 60.817 63.158 4.71 4.71 0.00 6.13
3102 4086 1.817099 CTCAACTGATCTGGCCGGC 60.817 63.158 21.18 21.18 0.00 6.13
3103 4087 3.197790 CAACTGATCTGGCCGGCG 61.198 66.667 22.54 7.85 0.00 6.46
3104 4088 3.390521 AACTGATCTGGCCGGCGA 61.391 61.111 22.54 17.25 0.00 5.54
3105 4089 2.735772 AACTGATCTGGCCGGCGAT 61.736 57.895 22.54 18.70 0.00 4.58
3106 4090 2.664185 CTGATCTGGCCGGCGATG 60.664 66.667 22.54 13.04 0.00 3.84
3107 4091 3.451556 CTGATCTGGCCGGCGATGT 62.452 63.158 22.54 8.00 0.00 3.06
3108 4092 2.969238 GATCTGGCCGGCGATGTG 60.969 66.667 22.54 4.90 0.00 3.21
3109 4093 3.445518 GATCTGGCCGGCGATGTGA 62.446 63.158 22.54 11.11 0.00 3.58
3110 4094 2.721971 GATCTGGCCGGCGATGTGAT 62.722 60.000 22.54 15.83 0.00 3.06
3111 4095 3.274586 CTGGCCGGCGATGTGATG 61.275 66.667 22.54 0.00 0.00 3.07
3112 4096 4.094646 TGGCCGGCGATGTGATGT 62.095 61.111 22.54 0.00 0.00 3.06
3113 4097 2.824041 GGCCGGCGATGTGATGTT 60.824 61.111 22.54 0.00 0.00 2.71
3114 4098 2.404789 GCCGGCGATGTGATGTTG 59.595 61.111 12.58 0.00 0.00 3.33
3115 4099 2.404789 CCGGCGATGTGATGTTGC 59.595 61.111 9.30 0.00 0.00 4.17
3134 4118 1.712401 CTCTGCTCTGCTCAACTGAC 58.288 55.000 0.00 0.00 0.00 3.51
3156 4140 2.528743 GCCGGCGATGTGATGTGAG 61.529 63.158 12.58 0.00 0.00 3.51
3157 4141 1.153568 CCGGCGATGTGATGTGAGT 60.154 57.895 9.30 0.00 0.00 3.41
3158 4142 1.148157 CCGGCGATGTGATGTGAGTC 61.148 60.000 9.30 0.00 0.00 3.36
3159 4143 0.179127 CGGCGATGTGATGTGAGTCT 60.179 55.000 0.00 0.00 0.00 3.24
3160 4144 1.284657 GGCGATGTGATGTGAGTCTG 58.715 55.000 0.00 0.00 0.00 3.51
3161 4145 1.404717 GGCGATGTGATGTGAGTCTGT 60.405 52.381 0.00 0.00 0.00 3.41
3162 4146 1.657594 GCGATGTGATGTGAGTCTGTG 59.342 52.381 0.00 0.00 0.00 3.66
3163 4147 2.672195 GCGATGTGATGTGAGTCTGTGA 60.672 50.000 0.00 0.00 0.00 3.58
3174 4158 4.100035 TGTGAGTCTGTGACAAGTGAAGAT 59.900 41.667 0.46 0.00 34.60 2.40
3183 4167 3.006859 TGACAAGTGAAGATGGTGACGAT 59.993 43.478 0.00 0.00 0.00 3.73
3184 4168 3.329386 ACAAGTGAAGATGGTGACGATG 58.671 45.455 0.00 0.00 0.00 3.84
3185 4169 3.006859 ACAAGTGAAGATGGTGACGATGA 59.993 43.478 0.00 0.00 0.00 2.92
3186 4170 4.186926 CAAGTGAAGATGGTGACGATGAT 58.813 43.478 0.00 0.00 0.00 2.45
3187 4171 4.478206 AGTGAAGATGGTGACGATGATT 57.522 40.909 0.00 0.00 0.00 2.57
3188 4172 4.186926 AGTGAAGATGGTGACGATGATTG 58.813 43.478 0.00 0.00 0.00 2.67
3189 4173 2.938451 TGAAGATGGTGACGATGATTGC 59.062 45.455 0.00 0.00 0.00 3.56
3190 4174 1.575244 AGATGGTGACGATGATTGCG 58.425 50.000 0.00 0.00 0.00 4.85
3191 4175 1.134699 AGATGGTGACGATGATTGCGT 60.135 47.619 0.00 0.00 45.79 5.24
3197 4181 3.812577 ACGATGATTGCGTCAGTCA 57.187 47.368 7.31 7.31 40.92 3.41
3198 4182 1.633561 ACGATGATTGCGTCAGTCAG 58.366 50.000 9.90 2.39 40.92 3.51
3199 4183 0.299895 CGATGATTGCGTCAGTCAGC 59.700 55.000 9.39 9.39 40.92 4.26
3230 4214 4.811364 GGCAAGGCAGGGAGAGGC 62.811 72.222 0.00 0.00 0.00 4.70
3285 4306 1.681780 GGGCATTCGGATCTGTGGAAA 60.682 52.381 0.42 0.00 0.00 3.13
3288 4309 3.009723 GCATTCGGATCTGTGGAAAGAA 58.990 45.455 0.42 0.00 0.00 2.52
3290 4311 4.437930 GCATTCGGATCTGTGGAAAGAAAG 60.438 45.833 0.42 0.00 0.00 2.62
3291 4312 4.617253 TTCGGATCTGTGGAAAGAAAGA 57.383 40.909 0.42 0.00 0.00 2.52
3292 4313 3.926616 TCGGATCTGTGGAAAGAAAGAC 58.073 45.455 0.42 0.00 0.00 3.01
3293 4314 2.668457 CGGATCTGTGGAAAGAAAGACG 59.332 50.000 0.00 0.00 0.00 4.18
3317 4338 3.005791 GGGGAAAAGGAACATGACAAGTG 59.994 47.826 0.00 0.00 0.00 3.16
3320 4341 4.518970 GGAAAAGGAACATGACAAGTGCTA 59.481 41.667 0.00 0.00 0.00 3.49
3321 4342 5.183904 GGAAAAGGAACATGACAAGTGCTAT 59.816 40.000 0.00 0.00 0.00 2.97
3340 4361 5.042593 GCTATGAGCATATTCGATCTCCTG 58.957 45.833 0.00 0.00 41.89 3.86
3383 4409 4.732285 TTTCACGAGCAACTGAAATCTC 57.268 40.909 0.00 0.00 32.62 2.75
3389 4415 3.748048 CGAGCAACTGAAATCTCTTCCAA 59.252 43.478 0.00 0.00 0.00 3.53
3392 4418 4.518211 AGCAACTGAAATCTCTTCCAACAG 59.482 41.667 0.00 0.00 0.00 3.16
3444 4471 6.488769 TTTTGGTCTCCAAGTAACAGTAGA 57.511 37.500 1.53 0.00 44.84 2.59
3445 4472 6.488769 TTTGGTCTCCAAGTAACAGTAGAA 57.511 37.500 1.53 0.00 44.84 2.10
3446 4473 6.681729 TTGGTCTCCAAGTAACAGTAGAAT 57.318 37.500 0.00 0.00 38.75 2.40
3447 4474 6.681729 TGGTCTCCAAGTAACAGTAGAATT 57.318 37.500 0.00 0.00 0.00 2.17
3448 4475 6.464222 TGGTCTCCAAGTAACAGTAGAATTG 58.536 40.000 0.00 0.00 0.00 2.32
3449 4476 6.042781 TGGTCTCCAAGTAACAGTAGAATTGT 59.957 38.462 0.00 0.00 0.00 2.71
3450 4477 6.935208 GGTCTCCAAGTAACAGTAGAATTGTT 59.065 38.462 0.00 0.00 41.36 2.83
3451 4478 7.095187 GGTCTCCAAGTAACAGTAGAATTGTTG 60.095 40.741 1.18 0.00 39.03 3.33
3452 4479 6.426937 TCTCCAAGTAACAGTAGAATTGTTGC 59.573 38.462 1.18 0.07 39.03 4.17
3453 4480 6.058833 TCCAAGTAACAGTAGAATTGTTGCA 58.941 36.000 8.48 0.00 41.64 4.08
3454 4481 6.544197 TCCAAGTAACAGTAGAATTGTTGCAA 59.456 34.615 0.00 0.00 41.64 4.08
3455 4482 6.636850 CCAAGTAACAGTAGAATTGTTGCAAC 59.363 38.462 22.83 22.83 41.64 4.17
3456 4483 6.313744 AGTAACAGTAGAATTGTTGCAACC 57.686 37.500 26.14 11.07 41.64 3.77
3457 4484 5.825679 AGTAACAGTAGAATTGTTGCAACCA 59.174 36.000 26.14 16.65 41.64 3.67
3458 4485 5.789643 AACAGTAGAATTGTTGCAACCAT 57.210 34.783 26.14 18.27 37.38 3.55
3459 4486 6.892658 AACAGTAGAATTGTTGCAACCATA 57.107 33.333 26.14 12.32 37.38 2.74
3460 4487 6.892658 ACAGTAGAATTGTTGCAACCATAA 57.107 33.333 26.14 14.60 0.00 1.90
3461 4488 7.466746 ACAGTAGAATTGTTGCAACCATAAT 57.533 32.000 26.14 16.19 0.00 1.28
3462 4489 7.895759 ACAGTAGAATTGTTGCAACCATAATT 58.104 30.769 26.14 22.77 0.00 1.40
3463 4490 8.367156 ACAGTAGAATTGTTGCAACCATAATTT 58.633 29.630 26.14 16.05 0.00 1.82
3464 4491 8.863049 CAGTAGAATTGTTGCAACCATAATTTC 58.137 33.333 26.14 17.33 0.00 2.17
3465 4492 6.949578 AGAATTGTTGCAACCATAATTTCG 57.050 33.333 26.14 0.00 0.00 3.46
3466 4493 6.686630 AGAATTGTTGCAACCATAATTTCGA 58.313 32.000 26.14 0.76 0.00 3.71
3467 4494 6.586082 AGAATTGTTGCAACCATAATTTCGAC 59.414 34.615 26.14 12.70 0.00 4.20
3468 4495 5.446143 TTGTTGCAACCATAATTTCGACT 57.554 34.783 26.14 0.00 0.00 4.18
3469 4496 4.793071 TGTTGCAACCATAATTTCGACTG 58.207 39.130 26.14 0.00 0.00 3.51
3481 4510 7.535258 CCATAATTTCGACTGTTTTCTGTCTTG 59.465 37.037 0.00 0.00 43.48 3.02
3483 4512 7.548196 AATTTCGACTGTTTTCTGTCTTGTA 57.452 32.000 0.00 0.00 43.48 2.41
3491 4520 8.691661 ACTGTTTTCTGTCTTGTACCATTATT 57.308 30.769 0.00 0.00 0.00 1.40
3492 4521 9.787435 ACTGTTTTCTGTCTTGTACCATTATTA 57.213 29.630 0.00 0.00 0.00 0.98
3510 4542 2.559698 TATGTAATCATGTGGGCCCG 57.440 50.000 19.37 1.86 35.70 6.13
3553 4585 3.305516 CCCCACTTGCAGGTTGCC 61.306 66.667 0.00 0.00 44.23 4.52
3558 4590 1.833934 ACTTGCAGGTTGCCAAGGG 60.834 57.895 0.00 0.00 44.23 3.95
3579 4633 3.660343 AAAAAGAGGAGGAGCAGCC 57.340 52.632 0.00 0.00 0.00 4.85
3623 4677 2.776536 CAGTCCAGGAAATCAGGGATCT 59.223 50.000 0.00 0.00 0.00 2.75
3704 4765 2.024080 CCCAGATTCCCAAATTCCTCCA 60.024 50.000 0.00 0.00 0.00 3.86
3705 4766 3.374540 CCCAGATTCCCAAATTCCTCCAT 60.375 47.826 0.00 0.00 0.00 3.41
3708 4769 3.459598 AGATTCCCAAATTCCTCCATCGA 59.540 43.478 0.00 0.00 0.00 3.59
3710 4771 1.211949 TCCCAAATTCCTCCATCGACC 59.788 52.381 0.00 0.00 0.00 4.79
3711 4772 1.212935 CCCAAATTCCTCCATCGACCT 59.787 52.381 0.00 0.00 0.00 3.85
3712 4773 2.292267 CCAAATTCCTCCATCGACCTG 58.708 52.381 0.00 0.00 0.00 4.00
3713 4774 1.672881 CAAATTCCTCCATCGACCTGC 59.327 52.381 0.00 0.00 0.00 4.85
3762 4829 2.738846 CTCCACAACAACCATCGAGAAG 59.261 50.000 0.00 0.00 0.00 2.85
3763 4830 1.806542 CCACAACAACCATCGAGAAGG 59.193 52.381 0.00 0.00 0.00 3.46
3818 4885 4.954118 TCTCGCCCACCCACCACT 62.954 66.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 4.377431 CGTCAAGAAACTAACAGTGCATCC 60.377 45.833 0.00 0.00 0.00 3.51
191 193 2.817258 TGGTAAAAACCAATGCTCGGAG 59.183 45.455 0.00 0.00 36.74 4.63
222 224 8.235359 TCATAACAAATATGCATGATGGAACA 57.765 30.769 10.16 0.00 41.77 3.18
301 303 3.699411 TTTCATTTGCCCCATTCCTTG 57.301 42.857 0.00 0.00 0.00 3.61
363 793 3.843422 AGTGAATGTTGGAATTCCCACA 58.157 40.909 28.14 28.14 46.62 4.17
364 794 4.559153 CAAGTGAATGTTGGAATTCCCAC 58.441 43.478 21.90 20.59 46.62 4.61
365 795 3.577848 CCAAGTGAATGTTGGAATTCCCA 59.422 43.478 21.90 13.53 46.53 4.37
399 829 6.907741 TGTTCATCGTGCATAGAAATTTGAA 58.092 32.000 0.00 0.00 0.00 2.69
402 839 6.324819 CCTTGTTCATCGTGCATAGAAATTT 58.675 36.000 0.00 0.00 0.00 1.82
474 911 9.699703 GCATCCTTTACCAATAAAGTTAAAACA 57.300 29.630 6.17 0.00 44.02 2.83
475 912 9.699703 TGCATCCTTTACCAATAAAGTTAAAAC 57.300 29.630 6.17 0.00 44.02 2.43
476 913 9.921637 CTGCATCCTTTACCAATAAAGTTAAAA 57.078 29.630 6.17 0.00 44.02 1.52
477 914 8.032451 GCTGCATCCTTTACCAATAAAGTTAAA 58.968 33.333 0.00 0.00 44.02 1.52
478 915 7.543756 GCTGCATCCTTTACCAATAAAGTTAA 58.456 34.615 0.00 0.00 44.02 2.01
479 916 6.183360 CGCTGCATCCTTTACCAATAAAGTTA 60.183 38.462 0.00 0.00 44.02 2.24
480 917 5.393027 CGCTGCATCCTTTACCAATAAAGTT 60.393 40.000 0.00 0.00 44.02 2.66
481 918 4.096382 CGCTGCATCCTTTACCAATAAAGT 59.904 41.667 0.00 0.00 44.02 2.66
482 919 4.498009 CCGCTGCATCCTTTACCAATAAAG 60.498 45.833 0.00 0.67 44.78 1.85
483 920 3.380004 CCGCTGCATCCTTTACCAATAAA 59.620 43.478 0.00 0.00 0.00 1.40
484 921 2.948979 CCGCTGCATCCTTTACCAATAA 59.051 45.455 0.00 0.00 0.00 1.40
485 922 2.092646 ACCGCTGCATCCTTTACCAATA 60.093 45.455 0.00 0.00 0.00 1.90
486 923 1.340991 ACCGCTGCATCCTTTACCAAT 60.341 47.619 0.00 0.00 0.00 3.16
487 924 0.037590 ACCGCTGCATCCTTTACCAA 59.962 50.000 0.00 0.00 0.00 3.67
488 925 0.906066 TACCGCTGCATCCTTTACCA 59.094 50.000 0.00 0.00 0.00 3.25
489 926 1.296727 GTACCGCTGCATCCTTTACC 58.703 55.000 0.00 0.00 0.00 2.85
490 927 0.928229 CGTACCGCTGCATCCTTTAC 59.072 55.000 0.00 0.00 0.00 2.01
491 928 0.818938 TCGTACCGCTGCATCCTTTA 59.181 50.000 0.00 0.00 0.00 1.85
492 929 0.460284 CTCGTACCGCTGCATCCTTT 60.460 55.000 0.00 0.00 0.00 3.11
493 930 1.141881 CTCGTACCGCTGCATCCTT 59.858 57.895 0.00 0.00 0.00 3.36
494 931 2.808315 CTCGTACCGCTGCATCCT 59.192 61.111 0.00 0.00 0.00 3.24
495 932 2.962253 GCTCGTACCGCTGCATCC 60.962 66.667 0.00 0.00 0.00 3.51
496 933 2.071844 TAGGCTCGTACCGCTGCATC 62.072 60.000 0.00 0.00 33.69 3.91
497 934 1.464376 ATAGGCTCGTACCGCTGCAT 61.464 55.000 0.00 0.00 33.69 3.96
498 935 0.820482 TATAGGCTCGTACCGCTGCA 60.820 55.000 0.00 0.00 33.69 4.41
499 936 0.109689 CTATAGGCTCGTACCGCTGC 60.110 60.000 0.00 0.00 33.69 5.25
500 937 1.520494 TCTATAGGCTCGTACCGCTG 58.480 55.000 0.00 0.00 33.69 5.18
501 938 1.878734 GTTCTATAGGCTCGTACCGCT 59.121 52.381 0.00 0.00 33.69 5.52
502 939 1.605710 TGTTCTATAGGCTCGTACCGC 59.394 52.381 0.00 0.00 33.69 5.68
503 940 3.136763 TCTGTTCTATAGGCTCGTACCG 58.863 50.000 0.00 0.00 33.69 4.02
504 941 4.156373 GGATCTGTTCTATAGGCTCGTACC 59.844 50.000 0.00 0.00 0.00 3.34
505 942 5.005094 AGGATCTGTTCTATAGGCTCGTAC 58.995 45.833 0.00 0.00 0.00 3.67
506 943 5.004448 CAGGATCTGTTCTATAGGCTCGTA 58.996 45.833 0.00 0.00 0.00 3.43
507 944 3.823873 CAGGATCTGTTCTATAGGCTCGT 59.176 47.826 0.00 0.00 0.00 4.18
508 945 3.823873 ACAGGATCTGTTCTATAGGCTCG 59.176 47.826 0.00 0.00 42.59 5.03
521 958 4.177026 CGACCTTACTTGAACAGGATCTG 58.823 47.826 0.00 0.00 37.52 2.90
522 959 3.833070 ACGACCTTACTTGAACAGGATCT 59.167 43.478 0.00 0.00 0.00 2.75
523 960 4.189639 ACGACCTTACTTGAACAGGATC 57.810 45.455 0.00 0.00 0.00 3.36
524 961 4.618920 AACGACCTTACTTGAACAGGAT 57.381 40.909 0.00 0.00 0.00 3.24
525 962 5.011329 ACATAACGACCTTACTTGAACAGGA 59.989 40.000 0.00 0.00 0.00 3.86
526 963 5.120208 CACATAACGACCTTACTTGAACAGG 59.880 44.000 0.00 0.00 0.00 4.00
527 964 5.694910 ACACATAACGACCTTACTTGAACAG 59.305 40.000 0.00 0.00 0.00 3.16
528 965 5.603596 ACACATAACGACCTTACTTGAACA 58.396 37.500 0.00 0.00 0.00 3.18
529 966 6.535274 AACACATAACGACCTTACTTGAAC 57.465 37.500 0.00 0.00 0.00 3.18
530 967 7.280428 TCAAAACACATAACGACCTTACTTGAA 59.720 33.333 0.00 0.00 0.00 2.69
531 968 6.762187 TCAAAACACATAACGACCTTACTTGA 59.238 34.615 0.00 0.00 0.00 3.02
532 969 6.849305 GTCAAAACACATAACGACCTTACTTG 59.151 38.462 0.00 0.00 0.00 3.16
533 970 6.764560 AGTCAAAACACATAACGACCTTACTT 59.235 34.615 0.00 0.00 0.00 2.24
534 971 6.285990 AGTCAAAACACATAACGACCTTACT 58.714 36.000 0.00 0.00 0.00 2.24
535 972 6.535274 AGTCAAAACACATAACGACCTTAC 57.465 37.500 0.00 0.00 0.00 2.34
536 973 7.280428 TCAAAGTCAAAACACATAACGACCTTA 59.720 33.333 0.00 0.00 0.00 2.69
537 974 6.094325 TCAAAGTCAAAACACATAACGACCTT 59.906 34.615 0.00 0.00 0.00 3.50
538 975 5.587043 TCAAAGTCAAAACACATAACGACCT 59.413 36.000 0.00 0.00 0.00 3.85
539 976 5.812652 TCAAAGTCAAAACACATAACGACC 58.187 37.500 0.00 0.00 0.00 4.79
540 977 7.908193 AATCAAAGTCAAAACACATAACGAC 57.092 32.000 0.00 0.00 0.00 4.34
541 978 8.184848 TCAAATCAAAGTCAAAACACATAACGA 58.815 29.630 0.00 0.00 0.00 3.85
542 979 8.334016 TCAAATCAAAGTCAAAACACATAACG 57.666 30.769 0.00 0.00 0.00 3.18
585 1023 2.292292 ACGGGAATTGGAAAAGAACGTG 59.708 45.455 0.00 0.00 0.00 4.49
587 1025 2.351350 CCACGGGAATTGGAAAAGAACG 60.351 50.000 0.00 0.00 36.02 3.95
602 1040 2.046285 GGATGCTTTGGTCCACGGG 61.046 63.158 0.00 0.00 34.57 5.28
608 1046 4.022068 TCTGTCAATTTGGATGCTTTGGTC 60.022 41.667 0.00 0.00 0.00 4.02
682 1221 5.371115 TTTGGTTCGCAGGATTCTAAAAG 57.629 39.130 0.00 0.00 0.00 2.27
697 1236 4.081642 GGAATTTTAGGGCTCCTTTGGTTC 60.082 45.833 0.00 1.47 34.61 3.62
702 1241 4.488770 TGTTGGAATTTTAGGGCTCCTTT 58.511 39.130 0.00 0.00 34.61 3.11
705 1244 4.023291 TGATGTTGGAATTTTAGGGCTCC 58.977 43.478 0.00 0.00 0.00 4.70
760 1305 5.947228 TGTCAGAATTTGAACATCCTCAC 57.053 39.130 0.00 0.00 37.61 3.51
809 1354 0.323178 AAGAGAAGGCCAGCCACATG 60.323 55.000 12.03 0.00 38.92 3.21
901 1448 2.486982 TCTTCTCTCTTACGTGAACGGG 59.513 50.000 7.86 0.00 44.95 5.28
908 1455 3.946558 AGGCGTATTCTTCTCTCTTACGT 59.053 43.478 0.00 0.00 38.26 3.57
914 1461 2.952978 TGAGGAGGCGTATTCTTCTCTC 59.047 50.000 0.00 0.00 37.67 3.20
915 1462 2.955660 CTGAGGAGGCGTATTCTTCTCT 59.044 50.000 0.00 0.00 37.67 3.10
916 1463 2.544903 GCTGAGGAGGCGTATTCTTCTC 60.545 54.545 0.00 0.00 37.38 2.87
921 1468 4.327885 CGCTGAGGAGGCGTATTC 57.672 61.111 0.00 0.00 46.37 1.75
937 1484 3.726517 CTTGGCGGGCAGTTGACG 61.727 66.667 3.91 0.00 0.00 4.35
1170 1719 2.121832 TTGAGGAGGCGGGAGGAA 59.878 61.111 0.00 0.00 0.00 3.36
1239 1788 2.047179 GTGAGGTGGTCGAAGGGC 60.047 66.667 0.00 0.00 0.00 5.19
1503 2386 4.680237 TGGTCGAACAGCTGGCGG 62.680 66.667 24.57 11.53 0.00 6.13
1527 2410 3.119096 GAAACGAGGTCCCGCTGC 61.119 66.667 0.00 0.00 0.00 5.25
1542 2425 2.027192 GGACAGCATGGAGTTGTAGGAA 60.027 50.000 0.00 0.00 42.13 3.36
1598 2481 2.005451 GCATCTGATCGAACAGCTGTT 58.995 47.619 31.57 31.57 41.64 3.16
1599 2482 1.649664 GCATCTGATCGAACAGCTGT 58.350 50.000 22.34 15.25 36.69 4.40
1636 2519 0.392193 CCAAGCATCGAGTTCCAGCT 60.392 55.000 0.00 0.00 37.08 4.24
1637 2520 0.674895 ACCAAGCATCGAGTTCCAGC 60.675 55.000 0.00 0.00 0.00 4.85
1653 2536 1.183030 CGAGGCGGGTATATCCACCA 61.183 60.000 11.75 0.00 40.65 4.17
1655 2538 1.590147 CCGAGGCGGGTATATCCAC 59.410 63.158 2.20 0.00 44.15 4.02
1656 2539 4.107029 CCGAGGCGGGTATATCCA 57.893 61.111 2.20 0.00 44.15 3.41
1731 2614 1.078759 CGTCCAGCATCGAGTTCCAC 61.079 60.000 0.00 0.00 0.00 4.02
2196 3079 2.975075 CTCCTCTCCATCTCCAGGAAT 58.025 52.381 0.00 0.00 34.53 3.01
2223 3106 2.027625 GGTCGTCTCGTTTGGCCTG 61.028 63.158 3.32 0.00 0.00 4.85
2304 3187 0.252421 AGAGCCTGACCATCCTGTCA 60.252 55.000 0.00 0.00 42.75 3.58
2352 3235 1.225426 GAGGTCCATCATGCAGCCA 59.775 57.895 0.00 0.00 0.00 4.75
2390 3273 2.232298 GAGGTTCTCCGAGCCTGTGG 62.232 65.000 3.91 0.00 43.17 4.17
2626 3515 2.579738 GTCCTTCTCAGCCCCGTC 59.420 66.667 0.00 0.00 0.00 4.79
2631 3520 2.266055 CCCACGTCCTTCTCAGCC 59.734 66.667 0.00 0.00 0.00 4.85
2678 3570 1.616865 CTTCAGTACCAAGACGGGTCA 59.383 52.381 1.17 0.00 42.42 4.02
2760 3703 3.628646 CTTGGGCTCCTGGGGTTCG 62.629 68.421 0.00 0.00 0.00 3.95
2796 3739 2.425592 CAACAGGTCCTCGTGGCA 59.574 61.111 0.00 0.00 34.26 4.92
2799 3742 2.310233 CGCACAACAGGTCCTCGTG 61.310 63.158 7.87 7.87 35.82 4.35
2823 3766 2.202440 CATGCTCTGCGTTGCTGC 60.202 61.111 0.00 0.00 0.00 5.25
2830 3775 1.374343 ATCCTGCAACATGCTCTGCG 61.374 55.000 9.64 5.63 45.31 5.18
2844 3789 0.318784 GGCGAGGCGTAGTAATCCTG 60.319 60.000 0.00 0.00 0.00 3.86
2846 3791 1.371389 CGGCGAGGCGTAGTAATCC 60.371 63.158 0.00 0.00 0.00 3.01
2847 3792 0.248784 AACGGCGAGGCGTAGTAATC 60.249 55.000 24.07 0.00 0.00 1.75
2868 3813 3.766068 AATCTGATGCTCCGTGATGAT 57.234 42.857 0.00 0.00 0.00 2.45
2870 3815 2.547211 GGAAATCTGATGCTCCGTGATG 59.453 50.000 3.93 0.00 0.00 3.07
2886 3831 1.228245 ACACGCACCAGCAGGAAAT 60.228 52.632 0.35 0.00 42.27 2.17
2887 3832 2.186160 CACACGCACCAGCAGGAAA 61.186 57.895 0.35 0.00 42.27 3.13
2900 3845 1.081376 GACGACAGAGGACCACACG 60.081 63.158 0.00 0.00 0.00 4.49
2922 3867 4.772231 AATGCTGGCCCTGGCTGG 62.772 66.667 8.29 2.96 41.60 4.85
2954 3901 0.036294 GCTACCCCTCGTCTTGCTTT 60.036 55.000 0.00 0.00 0.00 3.51
2962 3909 1.757340 GCAGTAGGCTACCCCTCGT 60.757 63.158 20.67 0.00 44.96 4.18
2979 3926 3.138798 CATCAGCCAGCACCCAGC 61.139 66.667 0.00 0.00 46.19 4.85
2980 3927 1.451567 CTCATCAGCCAGCACCCAG 60.452 63.158 0.00 0.00 0.00 4.45
2981 3928 2.672908 CTCATCAGCCAGCACCCA 59.327 61.111 0.00 0.00 0.00 4.51
2982 3929 2.827642 GCTCATCAGCCAGCACCC 60.828 66.667 0.00 0.00 40.14 4.61
2983 3930 1.654954 CTTGCTCATCAGCCAGCACC 61.655 60.000 0.00 0.00 45.37 5.01
2984 3931 1.801332 CTTGCTCATCAGCCAGCAC 59.199 57.895 0.00 0.00 45.37 4.40
3015 3962 2.844122 AGTCCAAACGTGTTTTCTGC 57.156 45.000 0.00 0.00 0.00 4.26
3033 3980 0.251742 TCATTGGCCCACCTCCAAAG 60.252 55.000 0.00 0.00 45.63 2.77
3034 3981 0.189574 TTCATTGGCCCACCTCCAAA 59.810 50.000 0.00 0.00 45.63 3.28
3036 3983 0.324552 CATTCATTGGCCCACCTCCA 60.325 55.000 0.00 0.00 36.63 3.86
3039 3986 4.792066 CCATTCATTGGCCCACCT 57.208 55.556 0.00 0.00 39.09 4.00
3052 4035 1.407437 GCACCTTCTCCATCGACCATT 60.407 52.381 0.00 0.00 0.00 3.16
3085 4069 2.268920 GCCGGCCAGATCAGTTGA 59.731 61.111 18.11 0.00 0.00 3.18
3086 4070 2.930385 ATCGCCGGCCAGATCAGTTG 62.930 60.000 23.46 1.99 0.00 3.16
3087 4071 2.735772 ATCGCCGGCCAGATCAGTT 61.736 57.895 23.46 0.00 0.00 3.16
3088 4072 3.157252 ATCGCCGGCCAGATCAGT 61.157 61.111 23.46 0.00 0.00 3.41
3089 4073 2.664185 CATCGCCGGCCAGATCAG 60.664 66.667 23.46 4.61 0.00 2.90
3090 4074 3.469970 ACATCGCCGGCCAGATCA 61.470 61.111 23.46 0.00 0.00 2.92
3091 4075 2.721971 ATCACATCGCCGGCCAGATC 62.722 60.000 23.46 0.00 0.00 2.75
3092 4076 2.811514 ATCACATCGCCGGCCAGAT 61.812 57.895 23.46 16.29 0.00 2.90
3093 4077 3.469970 ATCACATCGCCGGCCAGA 61.470 61.111 23.46 14.41 0.00 3.86
3094 4078 3.274586 CATCACATCGCCGGCCAG 61.275 66.667 23.46 13.61 0.00 4.85
3095 4079 3.620419 AACATCACATCGCCGGCCA 62.620 57.895 23.46 9.24 0.00 5.36
3096 4080 2.824041 AACATCACATCGCCGGCC 60.824 61.111 23.46 2.84 0.00 6.13
3097 4081 2.404789 CAACATCACATCGCCGGC 59.595 61.111 19.07 19.07 0.00 6.13
3098 4082 2.040213 GAGCAACATCACATCGCCGG 62.040 60.000 0.00 0.00 0.00 6.13
3099 4083 1.086067 AGAGCAACATCACATCGCCG 61.086 55.000 0.00 0.00 0.00 6.46
3100 4084 0.376152 CAGAGCAACATCACATCGCC 59.624 55.000 0.00 0.00 0.00 5.54
3101 4085 0.247974 GCAGAGCAACATCACATCGC 60.248 55.000 0.00 0.00 0.00 4.58
3102 4086 1.326852 GAGCAGAGCAACATCACATCG 59.673 52.381 0.00 0.00 0.00 3.84
3103 4087 2.352034 CAGAGCAGAGCAACATCACATC 59.648 50.000 0.00 0.00 0.00 3.06
3104 4088 2.357075 CAGAGCAGAGCAACATCACAT 58.643 47.619 0.00 0.00 0.00 3.21
3105 4089 1.804601 CAGAGCAGAGCAACATCACA 58.195 50.000 0.00 0.00 0.00 3.58
3106 4090 0.447011 GCAGAGCAGAGCAACATCAC 59.553 55.000 0.00 0.00 0.00 3.06
3107 4091 0.323957 AGCAGAGCAGAGCAACATCA 59.676 50.000 0.00 0.00 0.00 3.07
3108 4092 1.008329 GAGCAGAGCAGAGCAACATC 58.992 55.000 0.00 0.00 0.00 3.06
3109 4093 0.323957 TGAGCAGAGCAGAGCAACAT 59.676 50.000 0.00 0.00 0.00 2.71
3110 4094 0.107268 TTGAGCAGAGCAGAGCAACA 59.893 50.000 0.00 0.00 0.00 3.33
3111 4095 0.516439 GTTGAGCAGAGCAGAGCAAC 59.484 55.000 0.00 0.00 0.00 4.17
3112 4096 0.395686 AGTTGAGCAGAGCAGAGCAA 59.604 50.000 0.00 0.00 0.00 3.91
3113 4097 0.320508 CAGTTGAGCAGAGCAGAGCA 60.321 55.000 0.00 0.00 0.00 4.26
3114 4098 0.037512 TCAGTTGAGCAGAGCAGAGC 60.038 55.000 0.00 0.00 0.00 4.09
3115 4099 1.672441 GGTCAGTTGAGCAGAGCAGAG 60.672 57.143 6.46 0.00 41.81 3.35
3134 4118 4.552365 ATCACATCGCCGGCCAGG 62.552 66.667 23.46 13.78 44.97 4.45
3156 4140 3.496130 CACCATCTTCACTTGTCACAGAC 59.504 47.826 0.00 0.00 0.00 3.51
3157 4141 3.387699 TCACCATCTTCACTTGTCACAGA 59.612 43.478 0.00 0.00 0.00 3.41
3158 4142 3.496130 GTCACCATCTTCACTTGTCACAG 59.504 47.826 0.00 0.00 0.00 3.66
3159 4143 3.466836 GTCACCATCTTCACTTGTCACA 58.533 45.455 0.00 0.00 0.00 3.58
3160 4144 2.476619 CGTCACCATCTTCACTTGTCAC 59.523 50.000 0.00 0.00 0.00 3.67
3161 4145 2.364002 TCGTCACCATCTTCACTTGTCA 59.636 45.455 0.00 0.00 0.00 3.58
3162 4146 3.026630 TCGTCACCATCTTCACTTGTC 57.973 47.619 0.00 0.00 0.00 3.18
3163 4147 3.006859 TCATCGTCACCATCTTCACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
3193 4177 2.088674 GACACCACGGTCAGCTGACT 62.089 60.000 38.17 22.46 44.20 3.41
3194 4178 1.664965 GACACCACGGTCAGCTGAC 60.665 63.158 34.25 34.25 44.04 3.51
3195 4179 2.734591 GACACCACGGTCAGCTGA 59.265 61.111 13.74 13.74 37.73 4.26
3196 4180 2.734723 CGACACCACGGTCAGCTG 60.735 66.667 7.63 7.63 37.66 4.24
3197 4181 3.991051 CCGACACCACGGTCAGCT 61.991 66.667 0.00 0.00 46.70 4.24
3220 4204 3.898509 CGCTCTCGCCTCTCCCTG 61.899 72.222 0.00 0.00 0.00 4.45
3285 4306 2.335933 TCCTTTTCCCCTCGTCTTTCT 58.664 47.619 0.00 0.00 0.00 2.52
3288 4309 1.772453 TGTTCCTTTTCCCCTCGTCTT 59.228 47.619 0.00 0.00 0.00 3.01
3290 4311 2.084546 CATGTTCCTTTTCCCCTCGTC 58.915 52.381 0.00 0.00 0.00 4.20
3291 4312 1.702957 TCATGTTCCTTTTCCCCTCGT 59.297 47.619 0.00 0.00 0.00 4.18
3292 4313 2.084546 GTCATGTTCCTTTTCCCCTCG 58.915 52.381 0.00 0.00 0.00 4.63
3293 4314 3.154827 TGTCATGTTCCTTTTCCCCTC 57.845 47.619 0.00 0.00 0.00 4.30
3317 4338 5.042593 CAGGAGATCGAATATGCTCATAGC 58.957 45.833 0.00 0.00 42.82 2.97
3320 4341 3.369261 GCCAGGAGATCGAATATGCTCAT 60.369 47.826 0.00 0.00 0.00 2.90
3321 4342 2.028658 GCCAGGAGATCGAATATGCTCA 60.029 50.000 0.00 0.00 0.00 4.26
3340 4361 2.024918 CTGGACGCATATGGTTGCC 58.975 57.895 4.56 0.85 39.52 4.52
3370 4396 4.320788 CCTGTTGGAAGAGATTTCAGTTGC 60.321 45.833 0.00 0.00 34.57 4.17
3422 4449 6.488769 TTCTACTGTTACTTGGAGACCAAA 57.511 37.500 4.78 0.00 43.44 3.28
3423 4450 6.681729 ATTCTACTGTTACTTGGAGACCAA 57.318 37.500 3.21 3.21 41.69 3.67
3424 4451 6.042781 ACAATTCTACTGTTACTTGGAGACCA 59.957 38.462 0.00 0.00 0.00 4.02
3427 4454 6.426937 GCAACAATTCTACTGTTACTTGGAGA 59.573 38.462 0.00 0.00 35.26 3.71
3428 4455 6.204688 TGCAACAATTCTACTGTTACTTGGAG 59.795 38.462 0.00 0.00 35.26 3.86
3429 4456 6.058833 TGCAACAATTCTACTGTTACTTGGA 58.941 36.000 0.00 0.00 35.26 3.53
3430 4457 6.312399 TGCAACAATTCTACTGTTACTTGG 57.688 37.500 0.00 0.00 35.26 3.61
3431 4458 6.636850 GGTTGCAACAATTCTACTGTTACTTG 59.363 38.462 29.55 0.00 35.26 3.16
3432 4459 6.320164 TGGTTGCAACAATTCTACTGTTACTT 59.680 34.615 29.55 0.00 35.26 2.24
3434 4461 6.067263 TGGTTGCAACAATTCTACTGTTAC 57.933 37.500 29.55 8.61 35.26 2.50
3435 4462 6.892658 ATGGTTGCAACAATTCTACTGTTA 57.107 33.333 29.55 0.00 35.26 2.41
3436 4463 5.789643 ATGGTTGCAACAATTCTACTGTT 57.210 34.783 29.55 0.00 37.49 3.16
3437 4464 6.892658 TTATGGTTGCAACAATTCTACTGT 57.107 33.333 29.55 4.83 0.00 3.55
3438 4465 8.761575 AAATTATGGTTGCAACAATTCTACTG 57.238 30.769 29.55 0.00 0.00 2.74
3439 4466 7.754924 CGAAATTATGGTTGCAACAATTCTACT 59.245 33.333 29.55 12.27 0.00 2.57
3440 4467 7.753132 TCGAAATTATGGTTGCAACAATTCTAC 59.247 33.333 29.55 17.88 0.00 2.59
3441 4468 7.753132 GTCGAAATTATGGTTGCAACAATTCTA 59.247 33.333 29.55 13.83 0.00 2.10
3442 4469 6.586082 GTCGAAATTATGGTTGCAACAATTCT 59.414 34.615 29.55 16.13 0.00 2.40
3443 4470 6.586082 AGTCGAAATTATGGTTGCAACAATTC 59.414 34.615 29.55 17.71 0.00 2.17
3444 4471 6.365789 CAGTCGAAATTATGGTTGCAACAATT 59.634 34.615 29.55 22.22 0.00 2.32
3445 4472 5.863397 CAGTCGAAATTATGGTTGCAACAAT 59.137 36.000 29.55 26.10 0.00 2.71
3446 4473 5.218885 CAGTCGAAATTATGGTTGCAACAA 58.781 37.500 29.55 20.93 0.00 2.83
3447 4474 4.277174 ACAGTCGAAATTATGGTTGCAACA 59.723 37.500 29.55 16.61 0.00 3.33
3448 4475 4.794169 ACAGTCGAAATTATGGTTGCAAC 58.206 39.130 21.59 21.59 0.00 4.17
3449 4476 5.446143 AACAGTCGAAATTATGGTTGCAA 57.554 34.783 0.00 0.00 0.00 4.08
3450 4477 5.446143 AAACAGTCGAAATTATGGTTGCA 57.554 34.783 0.00 0.00 0.00 4.08
3451 4478 6.088085 CAGAAAACAGTCGAAATTATGGTTGC 59.912 38.462 0.00 0.00 0.00 4.17
3452 4479 7.138736 ACAGAAAACAGTCGAAATTATGGTTG 58.861 34.615 0.00 0.00 0.00 3.77
3453 4480 7.228706 AGACAGAAAACAGTCGAAATTATGGTT 59.771 33.333 0.00 0.00 39.67 3.67
3454 4481 6.710744 AGACAGAAAACAGTCGAAATTATGGT 59.289 34.615 0.00 0.00 39.67 3.55
3455 4482 7.133891 AGACAGAAAACAGTCGAAATTATGG 57.866 36.000 0.00 0.00 39.67 2.74
3456 4483 8.070171 ACAAGACAGAAAACAGTCGAAATTATG 58.930 33.333 0.00 0.00 39.67 1.90
3457 4484 8.154649 ACAAGACAGAAAACAGTCGAAATTAT 57.845 30.769 0.00 0.00 39.67 1.28
3458 4485 7.548196 ACAAGACAGAAAACAGTCGAAATTA 57.452 32.000 0.00 0.00 39.67 1.40
3459 4486 6.436843 ACAAGACAGAAAACAGTCGAAATT 57.563 33.333 0.00 0.00 39.67 1.82
3460 4487 6.018180 GGTACAAGACAGAAAACAGTCGAAAT 60.018 38.462 0.00 0.00 39.67 2.17
3461 4488 5.292589 GGTACAAGACAGAAAACAGTCGAAA 59.707 40.000 0.00 0.00 39.67 3.46
3462 4489 4.807304 GGTACAAGACAGAAAACAGTCGAA 59.193 41.667 0.00 0.00 39.67 3.71
3463 4490 4.142116 TGGTACAAGACAGAAAACAGTCGA 60.142 41.667 0.00 0.00 39.67 4.20
3464 4491 4.116961 TGGTACAAGACAGAAAACAGTCG 58.883 43.478 0.00 0.00 39.67 4.18
3481 4510 8.458843 GCCCACATGATTACATAATAATGGTAC 58.541 37.037 11.93 0.00 38.37 3.34
3483 4512 6.437162 GGCCCACATGATTACATAATAATGGT 59.563 38.462 11.93 0.00 38.37 3.55
3491 4520 2.050918 TCGGGCCCACATGATTACATA 58.949 47.619 24.92 0.00 35.09 2.29
3492 4521 0.843309 TCGGGCCCACATGATTACAT 59.157 50.000 24.92 0.00 37.19 2.29
3493 4522 0.107410 GTCGGGCCCACATGATTACA 60.107 55.000 24.92 0.00 0.00 2.41
3494 4523 0.818040 GGTCGGGCCCACATGATTAC 60.818 60.000 24.92 5.82 0.00 1.89
3576 4630 3.764466 CTGGCCTCGTCTTCGGCT 61.764 66.667 3.32 0.00 45.57 5.52
3579 4633 3.997064 CTGCCTGGCCTCGTCTTCG 62.997 68.421 17.53 0.00 38.55 3.79
3591 4645 4.340246 TGGACTGCTGCCTGCCTG 62.340 66.667 0.00 0.00 42.00 4.85
3605 4659 3.834813 CGATAGATCCCTGATTTCCTGGA 59.165 47.826 0.00 0.00 35.25 3.86
3609 4663 5.017294 GATCCGATAGATCCCTGATTTCC 57.983 47.826 0.00 0.00 45.00 3.13
3679 4733 1.678101 GAATTTGGGAATCTGGGCGAG 59.322 52.381 0.00 0.00 0.00 5.03
3680 4734 1.684869 GGAATTTGGGAATCTGGGCGA 60.685 52.381 0.00 0.00 0.00 5.54
3688 4749 3.555966 GTCGATGGAGGAATTTGGGAAT 58.444 45.455 0.00 0.00 0.00 3.01
3704 4765 4.479993 GCAGGCAGGCAGGTCGAT 62.480 66.667 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.