Multiple sequence alignment - TraesCS7D01G108000

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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 TraesCS7D01G108000 chr7D 100.000 3435 0 0 1 3435 64810600 64807166 0.000000e+00 6344
1 TraesCS7D01G108000 chr7D 84.160 2582 324 59 231 2762 64831320 64828774 0.000000e+00 2423
2 TraesCS7D01G108000 chr7D 83.051 1062 169 9 749 1805 73621117 73620062 0.000000e+00 953
3 TraesCS7D01G108000 chr7D 83.333 1038 158 11 750 1781 73363089 73364117 0.000000e+00 944
4 TraesCS7D01G108000 chr7D 85.176 850 91 21 1821 2660 73620016 73619192 0.000000e+00 839
5 TraesCS7D01G108000 chr7D 84.941 850 93 22 1821 2660 73547082 73547906 0.000000e+00 828
6 TraesCS7D01G108000 chr7D 84.824 850 91 23 1821 2660 73364187 73365008 0.000000e+00 821
7 TraesCS7D01G108000 chr7D 95.473 243 11 0 3193 3435 181032044 181032286 4.160000e-104 388
8 TraesCS7D01G108000 chr7D 95.455 242 11 0 3194 3435 78495190 78494949 1.500000e-103 387
9 TraesCS7D01G108000 chr7B 94.800 2769 121 16 1 2763 6403688 6400937 0.000000e+00 4294
10 TraesCS7D01G108000 chr7B 82.441 1065 165 17 748 1801 16514782 16515835 0.000000e+00 911
11 TraesCS7D01G108000 chr7B 82.037 1041 165 17 750 1781 16707327 16708354 0.000000e+00 867
12 TraesCS7D01G108000 chr7B 84.000 850 102 21 1821 2660 16515884 16516709 0.000000e+00 785
13 TraesCS7D01G108000 chr7B 91.275 149 13 0 2768 2916 6400906 6400758 1.620000e-48 204
14 TraesCS7D01G108000 chr7A 94.004 2785 98 16 1 2763 68917527 68914790 0.000000e+00 4154
15 TraesCS7D01G108000 chr7A 83.065 1057 167 9 749 1800 78142716 78141667 0.000000e+00 950
16 TraesCS7D01G108000 chr7A 82.801 1064 168 12 750 1805 77877151 77878207 0.000000e+00 937
17 TraesCS7D01G108000 chr7A 85.059 850 92 23 1821 2660 78141616 78140792 0.000000e+00 833
18 TraesCS7D01G108000 chr7A 84.335 849 101 18 1821 2660 77999851 78000676 0.000000e+00 802
19 TraesCS7D01G108000 chr7A 84.416 231 21 6 2768 2996 68914759 68914542 2.690000e-51 213
20 TraesCS7D01G108000 chr7A 93.333 120 5 2 3076 3194 68914300 68914183 1.270000e-39 174
21 TraesCS7D01G108000 chr3D 96.296 243 9 0 3193 3435 608130633 608130875 1.920000e-107 399
22 TraesCS7D01G108000 chr3D 95.868 242 10 0 3194 3435 580182492 580182733 3.210000e-105 392
23 TraesCS7D01G108000 chr3B 95.473 243 11 0 3193 3435 42782480 42782238 4.160000e-104 388
24 TraesCS7D01G108000 chr5D 95.455 242 11 0 3194 3435 546413544 546413785 1.500000e-103 387
25 TraesCS7D01G108000 chr4D 95.455 242 11 0 3194 3435 486520574 486520333 1.500000e-103 387
26 TraesCS7D01G108000 chr1A 95.455 242 11 0 3194 3435 580891171 580890930 1.500000e-103 387
27 TraesCS7D01G108000 chr6A 94.694 245 13 0 3191 3435 69342796 69342552 6.960000e-102 381


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 TraesCS7D01G108000 chr7D 64807166 64810600 3434 True 6344.000000 6344 100.000000 1 3435 1 chr7D.!!$R1 3434
1 TraesCS7D01G108000 chr7D 64828774 64831320 2546 True 2423.000000 2423 84.160000 231 2762 1 chr7D.!!$R2 2531
2 TraesCS7D01G108000 chr7D 73619192 73621117 1925 True 896.000000 953 84.113500 749 2660 2 chr7D.!!$R4 1911
3 TraesCS7D01G108000 chr7D 73363089 73365008 1919 False 882.500000 944 84.078500 750 2660 2 chr7D.!!$F3 1910
4 TraesCS7D01G108000 chr7D 73547082 73547906 824 False 828.000000 828 84.941000 1821 2660 1 chr7D.!!$F1 839
5 TraesCS7D01G108000 chr7B 6400758 6403688 2930 True 2249.000000 4294 93.037500 1 2916 2 chr7B.!!$R1 2915
6 TraesCS7D01G108000 chr7B 16707327 16708354 1027 False 867.000000 867 82.037000 750 1781 1 chr7B.!!$F1 1031
7 TraesCS7D01G108000 chr7B 16514782 16516709 1927 False 848.000000 911 83.220500 748 2660 2 chr7B.!!$F2 1912
8 TraesCS7D01G108000 chr7A 68914183 68917527 3344 True 1513.666667 4154 90.584333 1 3194 3 chr7A.!!$R1 3193
9 TraesCS7D01G108000 chr7A 77877151 77878207 1056 False 937.000000 937 82.801000 750 1805 1 chr7A.!!$F1 1055
10 TraesCS7D01G108000 chr7A 78140792 78142716 1924 True 891.500000 950 84.062000 749 2660 2 chr7A.!!$R2 1911
11 TraesCS7D01G108000 chr7A 77999851 78000676 825 False 802.000000 802 84.335000 1821 2660 1 chr7A.!!$F2 839

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
267 268 4.826733 TCACATGGCAAGTTGAATAGTGTT 59.173 37.5 7.16 0.0 0.0 3.32 F
1080 1108 2.198827 TCGATGGGCTCAACAACAAT 57.801 45.0 0.00 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1409 1438 0.944386 CTCCAACACCACCTTGTTCG 59.056 55.0 0.0 0.0 37.62 3.95 R
3057 3361 0.038599 ACCAACTGGCATGATGAGCA 59.961 50.0 0.0 0.0 39.32 4.26 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
257 258 6.071952 CCTTTTACACTATCACATGGCAAGTT 60.072 38.462 0.00 0.00 0.00 2.66
267 268 4.826733 TCACATGGCAAGTTGAATAGTGTT 59.173 37.500 7.16 0.00 0.00 3.32
476 491 6.494835 AGAATTTTTGGTGCTCTAATGAAGGT 59.505 34.615 0.00 0.00 0.00 3.50
583 606 4.953667 ACATCTATACTGCACACCATGAG 58.046 43.478 0.00 0.00 0.00 2.90
643 666 5.130350 ACTTACCATGTGTTAGCAACAACT 58.870 37.500 3.74 0.00 44.16 3.16
663 686 8.079211 ACAACTCTGTCACACTATTATACCAT 57.921 34.615 0.00 0.00 0.00 3.55
689 712 7.013274 TGGCATACTAGTTAATCATTTTCCAGC 59.987 37.037 0.00 0.00 0.00 4.85
782 805 5.566623 TGTGAGTCTCGATACGTCATAAAC 58.433 41.667 0.00 0.00 0.00 2.01
1080 1108 2.198827 TCGATGGGCTCAACAACAAT 57.801 45.000 0.00 0.00 0.00 2.71
1128 1156 5.645067 TGGTAAGAACAAGAAGCATGAGATG 59.355 40.000 0.00 0.00 0.00 2.90
1135 1163 3.109044 AGAAGCATGAGATGATGGACG 57.891 47.619 0.00 0.00 0.00 4.79
1205 1233 3.346315 TGTATGTTGATCTTGGTGCAGG 58.654 45.455 0.00 0.00 0.00 4.85
1535 1568 9.396022 GTTTCATCCTAATTTTCCATGAGACTA 57.604 33.333 0.00 0.00 29.96 2.59
1579 1612 6.517605 TGATTATTCGTATGGAAATGTCGGA 58.482 36.000 0.00 0.00 38.36 4.55
1588 1621 4.235939 TGGAAATGTCGGATGTGTTTTG 57.764 40.909 0.00 0.00 0.00 2.44
1641 1674 4.260948 GGATTTTCATTCTCATGAGACGGC 60.261 45.833 25.07 8.54 40.66 5.68
1781 1815 8.850156 GTGCTTCCATTAATAAGTGAATACCAT 58.150 33.333 0.00 0.00 0.00 3.55
2363 2438 3.694043 TGCAATCTACAGTTGGTGCTA 57.306 42.857 10.99 0.00 33.19 3.49
2715 2801 5.685520 AAGAAGTCTAGATTTGGTCCCTC 57.314 43.478 5.06 0.00 0.00 4.30
2765 2851 5.323371 TGAACTCTTCAAACCAAACTTGG 57.677 39.130 6.95 6.95 44.71 3.61
2859 2973 5.167845 GTGGTCATTTTGTCAAACACTTGT 58.832 37.500 0.00 0.00 33.94 3.16
2861 2975 4.032786 GGTCATTTTGTCAAACACTTGTGC 59.967 41.667 0.00 0.00 33.94 4.57
2867 2981 1.007580 TCAAACACTTGTGCGCGTTA 58.992 45.000 8.43 0.00 33.94 3.18
2905 3019 1.056660 ACACCACCTCCGTCTTGATT 58.943 50.000 0.00 0.00 0.00 2.57
2916 3030 3.058293 TCCGTCTTGATTCAATGTTGCAC 60.058 43.478 0.00 0.00 0.00 4.57
2930 3044 3.181367 GCACTTGCAGGTCATCGG 58.819 61.111 0.00 0.00 41.59 4.18
2950 3064 2.178273 TCGAGTCACGCGACATGG 59.822 61.111 15.93 0.00 45.23 3.66
2953 3067 1.213013 GAGTCACGCGACATGGAGT 59.787 57.895 15.93 4.79 45.23 3.85
2954 3068 1.073216 GAGTCACGCGACATGGAGTG 61.073 60.000 15.93 0.00 45.23 3.51
2955 3069 1.372997 GTCACGCGACATGGAGTGT 60.373 57.895 15.93 0.00 45.83 3.55
2970 3084 2.203139 TGTCAGTGTGGCAACCGG 60.203 61.111 0.00 0.00 0.00 5.28
2972 3086 4.947147 TCAGTGTGGCAACCGGGC 62.947 66.667 6.32 0.00 43.73 6.13
2993 3107 1.204062 GATGGCGTTCACACACACG 59.796 57.895 0.00 0.00 39.49 4.49
2998 3112 4.307908 GTTCACACACACGCCGGC 62.308 66.667 19.07 19.07 0.00 6.13
3016 3130 3.279116 GCACCAGCTCGCACACAA 61.279 61.111 0.00 0.00 37.91 3.33
3019 3133 2.591429 CCAGCTCGCACACAACCA 60.591 61.111 0.00 0.00 0.00 3.67
3021 3135 1.889105 CAGCTCGCACACAACCAGT 60.889 57.895 0.00 0.00 0.00 4.00
3022 3136 1.595382 AGCTCGCACACAACCAGTC 60.595 57.895 0.00 0.00 0.00 3.51
3023 3137 2.943345 GCTCGCACACAACCAGTCG 61.943 63.158 0.00 0.00 0.00 4.18
3024 3138 1.591594 CTCGCACACAACCAGTCGT 60.592 57.895 0.00 0.00 0.00 4.34
3025 3139 1.821241 CTCGCACACAACCAGTCGTG 61.821 60.000 0.00 0.00 39.10 4.35
3026 3140 2.327940 GCACACAACCAGTCGTGC 59.672 61.111 0.00 0.00 43.04 5.34
3028 3142 1.817520 CACACAACCAGTCGTGCCA 60.818 57.895 0.00 0.00 36.57 4.92
3040 3344 2.279918 GTGCCACGCCGGGTATAG 60.280 66.667 2.18 0.00 34.06 1.31
3047 3351 3.692406 GCCGGGTATAGGGGAGCG 61.692 72.222 2.18 0.00 0.00 5.03
3048 3352 3.692406 CCGGGTATAGGGGAGCGC 61.692 72.222 0.00 0.00 0.00 5.92
3049 3353 2.600769 CGGGTATAGGGGAGCGCT 60.601 66.667 11.27 11.27 0.00 5.92
3050 3354 2.932234 CGGGTATAGGGGAGCGCTG 61.932 68.421 18.48 0.00 0.00 5.18
3051 3355 1.837499 GGGTATAGGGGAGCGCTGT 60.837 63.158 18.48 0.00 0.00 4.40
3052 3356 1.367840 GGTATAGGGGAGCGCTGTG 59.632 63.158 18.48 0.00 0.00 3.66
3053 3357 1.113517 GGTATAGGGGAGCGCTGTGA 61.114 60.000 18.48 0.00 0.00 3.58
3054 3358 0.969894 GTATAGGGGAGCGCTGTGAT 59.030 55.000 18.48 3.16 0.00 3.06
3055 3359 1.067495 GTATAGGGGAGCGCTGTGATC 60.067 57.143 18.48 0.00 0.00 2.92
3060 3364 2.186384 GAGCGCTGTGATCCTGCT 59.814 61.111 18.48 0.00 38.89 4.24
3061 3365 1.882167 GAGCGCTGTGATCCTGCTC 60.882 63.158 18.48 0.00 44.37 4.26
3062 3366 2.125391 GCGCTGTGATCCTGCTCA 60.125 61.111 0.00 0.00 35.98 4.26
3063 3367 1.523258 GCGCTGTGATCCTGCTCAT 60.523 57.895 0.00 0.00 35.98 2.90
3064 3368 1.497223 GCGCTGTGATCCTGCTCATC 61.497 60.000 0.00 0.00 35.98 2.92
3065 3369 0.179092 CGCTGTGATCCTGCTCATCA 60.179 55.000 9.96 0.00 35.98 3.07
3066 3370 1.540580 CGCTGTGATCCTGCTCATCAT 60.541 52.381 9.96 0.00 35.98 2.45
3067 3371 1.874231 GCTGTGATCCTGCTCATCATG 59.126 52.381 0.00 0.00 32.86 3.07
3068 3372 1.874231 CTGTGATCCTGCTCATCATGC 59.126 52.381 0.00 0.00 32.86 4.06
3069 3373 1.236628 GTGATCCTGCTCATCATGCC 58.763 55.000 0.00 0.00 32.86 4.40
3070 3374 0.841289 TGATCCTGCTCATCATGCCA 59.159 50.000 0.00 0.00 0.00 4.92
3071 3375 1.202770 TGATCCTGCTCATCATGCCAG 60.203 52.381 0.00 0.00 0.00 4.85
3072 3376 0.844660 ATCCTGCTCATCATGCCAGT 59.155 50.000 4.93 0.00 0.00 4.00
3073 3377 0.622136 TCCTGCTCATCATGCCAGTT 59.378 50.000 4.93 0.00 0.00 3.16
3074 3378 0.738975 CCTGCTCATCATGCCAGTTG 59.261 55.000 4.93 0.00 0.00 3.16
3136 3440 2.943690 CAAACCCAGAGATCTCATGCAG 59.056 50.000 24.39 14.23 0.00 4.41
3160 3464 1.980772 GGTGCAGCCAAGCCTTCAT 60.981 57.895 4.03 0.00 37.17 2.57
3167 3471 0.109597 GCCAAGCCTTCATGTCGTTG 60.110 55.000 0.00 0.00 0.00 4.10
3194 3498 0.388520 CTTGTCGACATCAGCGTCCA 60.389 55.000 20.80 0.00 31.91 4.02
3195 3499 0.666274 TTGTCGACATCAGCGTCCAC 60.666 55.000 20.80 0.00 31.91 4.02
3196 3500 1.213013 GTCGACATCAGCGTCCACT 59.787 57.895 11.55 0.00 31.91 4.00
3197 3501 0.450583 GTCGACATCAGCGTCCACTA 59.549 55.000 11.55 0.00 31.91 2.74
3198 3502 0.733150 TCGACATCAGCGTCCACTAG 59.267 55.000 0.00 0.00 31.91 2.57
3199 3503 0.867753 CGACATCAGCGTCCACTAGC 60.868 60.000 0.00 0.00 31.91 3.42
3200 3504 0.173481 GACATCAGCGTCCACTAGCA 59.827 55.000 0.00 0.00 35.48 3.49
3201 3505 0.174389 ACATCAGCGTCCACTAGCAG 59.826 55.000 0.00 0.00 35.48 4.24
3202 3506 0.457443 CATCAGCGTCCACTAGCAGA 59.543 55.000 0.00 0.00 35.48 4.26
3203 3507 1.134995 CATCAGCGTCCACTAGCAGAA 60.135 52.381 0.00 0.00 32.84 3.02
3204 3508 0.966179 TCAGCGTCCACTAGCAGAAA 59.034 50.000 0.00 0.00 35.48 2.52
3205 3509 1.343142 TCAGCGTCCACTAGCAGAAAA 59.657 47.619 0.00 0.00 35.48 2.29
3206 3510 2.143122 CAGCGTCCACTAGCAGAAAAA 58.857 47.619 0.00 0.00 35.48 1.94
3207 3511 2.158449 CAGCGTCCACTAGCAGAAAAAG 59.842 50.000 0.00 0.00 35.48 2.27
3208 3512 1.464997 GCGTCCACTAGCAGAAAAAGG 59.535 52.381 0.00 0.00 0.00 3.11
3209 3513 2.076863 CGTCCACTAGCAGAAAAAGGG 58.923 52.381 0.00 0.00 0.00 3.95
3210 3514 1.813178 GTCCACTAGCAGAAAAAGGGC 59.187 52.381 0.00 0.00 0.00 5.19
3211 3515 1.177401 CCACTAGCAGAAAAAGGGCC 58.823 55.000 0.00 0.00 0.00 5.80
3212 3516 1.547675 CCACTAGCAGAAAAAGGGCCA 60.548 52.381 6.18 0.00 0.00 5.36
3213 3517 2.450476 CACTAGCAGAAAAAGGGCCAT 58.550 47.619 6.18 0.00 0.00 4.40
3214 3518 2.827921 CACTAGCAGAAAAAGGGCCATT 59.172 45.455 6.18 0.00 0.00 3.16
3215 3519 3.259123 CACTAGCAGAAAAAGGGCCATTT 59.741 43.478 10.16 10.16 0.00 2.32
3216 3520 2.845363 AGCAGAAAAAGGGCCATTTG 57.155 45.000 17.44 5.60 0.00 2.32
3217 3521 2.049372 AGCAGAAAAAGGGCCATTTGT 58.951 42.857 17.44 11.46 0.00 2.83
3218 3522 2.037641 AGCAGAAAAAGGGCCATTTGTC 59.962 45.455 22.82 22.82 0.00 3.18
3219 3523 2.871637 GCAGAAAAAGGGCCATTTGTCC 60.872 50.000 25.73 13.74 28.13 4.02
3220 3524 1.977854 AGAAAAAGGGCCATTTGTCCC 59.022 47.619 25.73 11.52 42.94 4.46
3224 3528 2.283604 GGGCCATTTGTCCCGGTT 60.284 61.111 4.39 0.00 32.00 4.44
3225 3529 2.348104 GGGCCATTTGTCCCGGTTC 61.348 63.158 4.39 0.00 32.00 3.62
3226 3530 2.696759 GGCCATTTGTCCCGGTTCG 61.697 63.158 0.00 0.00 0.00 3.95
3227 3531 1.969589 GCCATTTGTCCCGGTTCGT 60.970 57.895 0.00 0.00 0.00 3.85
3228 3532 0.674269 GCCATTTGTCCCGGTTCGTA 60.674 55.000 0.00 0.00 0.00 3.43
3229 3533 1.810959 CCATTTGTCCCGGTTCGTAA 58.189 50.000 0.00 0.00 0.00 3.18
3230 3534 1.735571 CCATTTGTCCCGGTTCGTAAG 59.264 52.381 0.00 0.00 0.00 2.34
3231 3535 1.735571 CATTTGTCCCGGTTCGTAAGG 59.264 52.381 0.00 0.00 38.47 2.69
3232 3536 0.603439 TTTGTCCCGGTTCGTAAGGC 60.603 55.000 0.00 0.00 38.47 4.35
3233 3537 2.125391 GTCCCGGTTCGTAAGGCC 60.125 66.667 0.00 0.00 38.47 5.19
3234 3538 3.393106 TCCCGGTTCGTAAGGCCC 61.393 66.667 0.00 0.00 38.47 5.80
3235 3539 3.708544 CCCGGTTCGTAAGGCCCA 61.709 66.667 0.00 0.00 38.47 5.36
3236 3540 2.587889 CCGGTTCGTAAGGCCCAT 59.412 61.111 0.00 0.00 38.47 4.00
3237 3541 1.078001 CCGGTTCGTAAGGCCCATT 60.078 57.895 0.00 0.00 38.47 3.16
3238 3542 0.678684 CCGGTTCGTAAGGCCCATTT 60.679 55.000 0.00 0.00 38.47 2.32
3239 3543 0.450184 CGGTTCGTAAGGCCCATTTG 59.550 55.000 0.00 0.00 38.47 2.32
3240 3544 1.541379 GGTTCGTAAGGCCCATTTGT 58.459 50.000 0.00 0.00 38.47 2.83
3241 3545 1.471287 GGTTCGTAAGGCCCATTTGTC 59.529 52.381 0.00 0.00 38.47 3.18
3242 3546 1.471287 GTTCGTAAGGCCCATTTGTCC 59.529 52.381 0.00 0.00 38.47 4.02
3243 3547 0.034863 TCGTAAGGCCCATTTGTCCC 60.035 55.000 0.00 0.00 38.47 4.46
3244 3548 1.373590 CGTAAGGCCCATTTGTCCCG 61.374 60.000 0.00 0.00 0.00 5.14
3245 3549 1.035385 GTAAGGCCCATTTGTCCCGG 61.035 60.000 0.00 0.00 0.00 5.73
3246 3550 1.502527 TAAGGCCCATTTGTCCCGGT 61.503 55.000 0.00 0.00 0.00 5.28
3247 3551 2.283604 GGCCCATTTGTCCCGGTT 60.284 61.111 0.00 0.00 0.00 4.44
3248 3552 2.645192 GGCCCATTTGTCCCGGTTG 61.645 63.158 0.00 0.00 0.00 3.77
3249 3553 2.645192 GCCCATTTGTCCCGGTTGG 61.645 63.158 0.00 0.00 0.00 3.77
3267 3571 1.605992 GGGAACCGGGACTAAAGGG 59.394 63.158 6.32 0.00 40.86 3.95
3268 3572 1.203441 GGGAACCGGGACTAAAGGGT 61.203 60.000 6.32 0.00 40.86 4.34
3269 3573 0.251354 GGAACCGGGACTAAAGGGTC 59.749 60.000 6.32 0.00 40.88 4.46
3270 3574 0.108472 GAACCGGGACTAAAGGGTCG 60.108 60.000 6.32 0.00 37.12 4.79
3271 3575 1.547472 AACCGGGACTAAAGGGTCGG 61.547 60.000 6.32 0.00 42.69 4.79
3272 3576 1.986210 CCGGGACTAAAGGGTCGGT 60.986 63.158 0.00 0.00 37.12 4.69
3273 3577 0.684153 CCGGGACTAAAGGGTCGGTA 60.684 60.000 0.00 0.00 37.12 4.02
3274 3578 0.457443 CGGGACTAAAGGGTCGGTAC 59.543 60.000 0.00 0.00 37.12 3.34
3275 3579 1.857965 GGGACTAAAGGGTCGGTACT 58.142 55.000 0.00 0.00 37.12 2.73
3276 3580 2.683742 CGGGACTAAAGGGTCGGTACTA 60.684 54.545 0.00 0.00 37.12 1.82
3277 3581 3.365472 GGGACTAAAGGGTCGGTACTAA 58.635 50.000 0.00 0.00 37.12 2.24
3278 3582 3.769300 GGGACTAAAGGGTCGGTACTAAA 59.231 47.826 0.00 0.00 37.12 1.85
3279 3583 4.142071 GGGACTAAAGGGTCGGTACTAAAG 60.142 50.000 0.00 0.00 37.12 1.85
3280 3584 4.428209 GACTAAAGGGTCGGTACTAAAGC 58.572 47.826 0.00 0.00 0.00 3.51
3281 3585 2.775911 AAAGGGTCGGTACTAAAGCC 57.224 50.000 0.00 0.00 0.00 4.35
3282 3586 0.907486 AAGGGTCGGTACTAAAGCCC 59.093 55.000 0.00 0.00 36.46 5.19
3283 3587 0.042281 AGGGTCGGTACTAAAGCCCT 59.958 55.000 0.00 0.00 41.31 5.19
3284 3588 1.288932 AGGGTCGGTACTAAAGCCCTA 59.711 52.381 10.66 0.00 44.00 3.53
3285 3589 2.090887 AGGGTCGGTACTAAAGCCCTAT 60.091 50.000 10.66 0.00 44.00 2.57
3286 3590 3.140895 AGGGTCGGTACTAAAGCCCTATA 59.859 47.826 10.66 0.00 44.00 1.31
3287 3591 3.256879 GGGTCGGTACTAAAGCCCTATAC 59.743 52.174 0.00 0.00 33.58 1.47
3288 3592 3.256879 GGTCGGTACTAAAGCCCTATACC 59.743 52.174 0.00 0.00 33.35 2.73
3289 3593 4.148079 GTCGGTACTAAAGCCCTATACCT 58.852 47.826 0.00 0.00 34.34 3.08
3290 3594 4.586421 GTCGGTACTAAAGCCCTATACCTT 59.414 45.833 0.00 0.00 34.34 3.50
3291 3595 5.069648 GTCGGTACTAAAGCCCTATACCTTT 59.930 44.000 0.00 0.00 34.34 3.11
3292 3596 6.265422 GTCGGTACTAAAGCCCTATACCTTTA 59.735 42.308 0.00 0.00 34.34 1.85
3297 3601 6.111669 CTAAAGCCCTATACCTTTAGTCCC 57.888 45.833 10.46 0.00 42.49 4.46
3298 3602 2.606378 AGCCCTATACCTTTAGTCCCG 58.394 52.381 0.00 0.00 0.00 5.14
3299 3603 1.622312 GCCCTATACCTTTAGTCCCGG 59.378 57.143 0.00 0.00 0.00 5.73
3300 3604 2.968271 CCCTATACCTTTAGTCCCGGT 58.032 52.381 0.00 0.00 34.86 5.28
3301 3605 3.311990 CCCTATACCTTTAGTCCCGGTT 58.688 50.000 0.00 0.00 32.36 4.44
3302 3606 3.713248 CCCTATACCTTTAGTCCCGGTTT 59.287 47.826 0.00 0.00 32.36 3.27
3303 3607 4.164796 CCCTATACCTTTAGTCCCGGTTTT 59.835 45.833 0.00 0.00 32.36 2.43
3304 3608 5.339447 CCCTATACCTTTAGTCCCGGTTTTT 60.339 44.000 0.00 0.00 32.36 1.94
3305 3609 6.126796 CCCTATACCTTTAGTCCCGGTTTTTA 60.127 42.308 0.00 0.00 32.36 1.52
3306 3610 6.763135 CCTATACCTTTAGTCCCGGTTTTTAC 59.237 42.308 0.00 0.00 32.36 2.01
3307 3611 4.436113 ACCTTTAGTCCCGGTTTTTACA 57.564 40.909 0.00 0.00 0.00 2.41
3308 3612 4.136796 ACCTTTAGTCCCGGTTTTTACAC 58.863 43.478 0.00 0.00 0.00 2.90
3309 3613 3.503363 CCTTTAGTCCCGGTTTTTACACC 59.497 47.826 0.00 0.00 0.00 4.16
3310 3614 3.853355 TTAGTCCCGGTTTTTACACCA 57.147 42.857 0.00 0.00 36.49 4.17
3311 3615 2.732844 AGTCCCGGTTTTTACACCAA 57.267 45.000 0.00 0.00 36.49 3.67
3312 3616 2.300433 AGTCCCGGTTTTTACACCAAC 58.700 47.619 0.00 0.00 36.49 3.77
3313 3617 1.337703 GTCCCGGTTTTTACACCAACC 59.662 52.381 0.00 0.00 39.38 3.77
3317 3621 0.675083 GGTTTTTACACCAACCGGGG 59.325 55.000 6.32 0.00 43.84 5.73
3318 3622 0.032403 GTTTTTACACCAACCGGGGC 59.968 55.000 6.32 0.00 40.67 5.80
3319 3623 0.396695 TTTTTACACCAACCGGGGCA 60.397 50.000 6.32 0.00 40.67 5.36
3320 3624 0.824182 TTTTACACCAACCGGGGCAG 60.824 55.000 6.32 0.00 40.67 4.85
3321 3625 1.706995 TTTACACCAACCGGGGCAGA 61.707 55.000 6.32 0.00 40.67 4.26
3322 3626 1.493854 TTACACCAACCGGGGCAGAT 61.494 55.000 6.32 0.00 40.67 2.90
3323 3627 2.191786 TACACCAACCGGGGCAGATG 62.192 60.000 6.32 0.00 40.67 2.90
3324 3628 4.047125 ACCAACCGGGGCAGATGG 62.047 66.667 6.32 6.76 42.91 3.51
3325 3629 4.820744 CCAACCGGGGCAGATGGG 62.821 72.222 6.32 0.00 0.00 4.00
3342 3646 2.124403 GCCTCCATGTGGCCTCTG 60.124 66.667 14.04 0.70 44.32 3.35
3343 3647 2.124403 CCTCCATGTGGCCTCTGC 60.124 66.667 3.32 0.00 34.44 4.26
3344 3648 2.513204 CTCCATGTGGCCTCTGCG 60.513 66.667 3.32 0.00 38.85 5.18
3345 3649 4.100084 TCCATGTGGCCTCTGCGG 62.100 66.667 3.32 2.76 38.85 5.69
3354 3658 4.504916 CCTCTGCGGCGAGTCCAG 62.505 72.222 12.98 8.68 34.01 3.86
3355 3659 4.504916 CTCTGCGGCGAGTCCAGG 62.505 72.222 12.98 0.00 34.01 4.45
3372 3676 2.361737 GCAGGAGGGCCTTTGGTC 60.362 66.667 7.89 0.00 43.90 4.02
3378 3682 2.526110 GGGCCTTTGGTCCTGGTT 59.474 61.111 0.84 0.00 45.53 3.67
3379 3683 1.908299 GGGCCTTTGGTCCTGGTTG 60.908 63.158 0.84 0.00 45.53 3.77
3380 3684 1.908299 GGCCTTTGGTCCTGGTTGG 60.908 63.158 0.00 0.00 37.10 3.77
3381 3685 1.152546 GCCTTTGGTCCTGGTTGGT 60.153 57.895 0.00 0.00 37.07 3.67
3382 3686 0.111639 GCCTTTGGTCCTGGTTGGTA 59.888 55.000 0.00 0.00 37.07 3.25
3383 3687 1.886655 GCCTTTGGTCCTGGTTGGTAG 60.887 57.143 0.00 0.00 37.07 3.18
3384 3688 1.534729 CTTTGGTCCTGGTTGGTAGC 58.465 55.000 0.00 0.00 37.07 3.58
3385 3689 0.847373 TTTGGTCCTGGTTGGTAGCA 59.153 50.000 0.00 0.00 37.07 3.49
3386 3690 0.109723 TTGGTCCTGGTTGGTAGCAC 59.890 55.000 0.00 0.00 37.07 4.40
3387 3691 1.002502 GGTCCTGGTTGGTAGCACC 60.003 63.158 0.00 0.12 39.22 5.01
3396 3700 2.046604 GGTAGCACCAACCGGGAC 60.047 66.667 6.32 0.00 38.42 4.46
3397 3701 2.046604 GTAGCACCAACCGGGACC 60.047 66.667 6.32 0.00 41.15 4.46
3398 3702 2.527123 TAGCACCAACCGGGACCA 60.527 61.111 6.32 0.00 41.15 4.02
3399 3703 2.148052 TAGCACCAACCGGGACCAA 61.148 57.895 6.32 0.00 41.15 3.67
3400 3704 1.706995 TAGCACCAACCGGGACCAAA 61.707 55.000 6.32 0.00 41.15 3.28
3401 3705 2.128507 GCACCAACCGGGACCAAAA 61.129 57.895 6.32 0.00 41.15 2.44
3402 3706 2.037871 CACCAACCGGGACCAAAAG 58.962 57.895 6.32 0.00 41.15 2.27
3403 3707 1.152631 ACCAACCGGGACCAAAAGG 60.153 57.895 6.32 0.00 41.15 3.11
3404 3708 2.570284 CCAACCGGGACCAAAAGGC 61.570 63.158 6.32 0.00 40.01 4.35
3405 3709 1.830408 CAACCGGGACCAAAAGGCA 60.830 57.895 6.32 0.00 0.00 4.75
3406 3710 1.155155 AACCGGGACCAAAAGGCAT 59.845 52.632 6.32 0.00 0.00 4.40
3407 3711 0.898326 AACCGGGACCAAAAGGCATC 60.898 55.000 6.32 0.00 0.00 3.91
3408 3712 2.052104 CCGGGACCAAAAGGCATCC 61.052 63.158 0.00 0.00 0.00 3.51
3409 3713 1.304052 CGGGACCAAAAGGCATCCA 60.304 57.895 0.00 0.00 32.45 3.41
3410 3714 1.315257 CGGGACCAAAAGGCATCCAG 61.315 60.000 0.00 0.00 32.45 3.86
3411 3715 0.972471 GGGACCAAAAGGCATCCAGG 60.972 60.000 0.00 0.00 32.45 4.45
3412 3716 1.607801 GGACCAAAAGGCATCCAGGC 61.608 60.000 0.00 0.00 44.61 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 6.664978 CATTTAGATATGCATTGCGTTGAC 57.335 37.500 3.54 1.62 0.00 3.18
257 258 6.752815 TGTCGTAATATTGCGAACACTATTCA 59.247 34.615 26.69 16.16 46.20 2.57
267 268 4.924462 TCACTGTTTGTCGTAATATTGCGA 59.076 37.500 22.36 22.36 42.79 5.10
476 491 9.775854 GACTACTCACATAGTGGATTACTACTA 57.224 37.037 0.00 0.00 44.30 1.82
521 536 4.643334 AGTGCATGCATATCAACAGACATT 59.357 37.500 25.64 0.00 0.00 2.71
583 606 5.048224 TGAGAGTAGTGGTTAGCTTGTACAC 60.048 44.000 0.00 0.00 0.00 2.90
643 666 5.365314 TGCCATGGTATAATAGTGTGACAGA 59.635 40.000 14.67 0.00 0.00 3.41
663 686 7.013274 GCTGGAAAATGATTAACTAGTATGCCA 59.987 37.037 0.00 0.00 0.00 4.92
1080 1108 3.278574 GCTGGTGCCATCATTGTAGTAA 58.721 45.455 0.00 0.00 0.00 2.24
1288 1317 7.725251 TCTTGCAATCCAAAGTTTTTACTCAT 58.275 30.769 0.00 0.00 31.94 2.90
1409 1438 0.944386 CTCCAACACCACCTTGTTCG 59.056 55.000 0.00 0.00 37.62 3.95
1566 1599 4.522405 TCAAAACACATCCGACATTTCCAT 59.478 37.500 0.00 0.00 0.00 3.41
1571 1604 5.766150 TCTTTCAAAACACATCCGACATT 57.234 34.783 0.00 0.00 0.00 2.71
1705 1739 7.676043 TCCCAAACAAAATTTATACATCCTGGA 59.324 33.333 0.00 0.00 0.00 3.86
1781 1815 4.764050 TGGTTGTAAGGACAAGAGTCAA 57.236 40.909 0.00 0.00 46.20 3.18
1786 1820 5.502079 TCACTTTTGGTTGTAAGGACAAGA 58.498 37.500 0.00 0.00 46.20 3.02
2089 2164 8.090788 AGAGCCTAGATTAAACAGGAAACATA 57.909 34.615 0.00 0.00 0.00 2.29
2104 2179 2.371510 GCCATGGAGAAAGAGCCTAGAT 59.628 50.000 18.40 0.00 0.00 1.98
2363 2438 8.711457 CAAATCGAAGCTTGAATTTTGGTTATT 58.289 29.630 2.10 0.00 0.00 1.40
2504 2583 0.976641 TCACTTGCCCCTACTGTGAG 59.023 55.000 0.00 0.00 33.45 3.51
2667 2752 9.947433 TTAATAGTTGAGGGTCGAAAAATAGAA 57.053 29.630 0.00 0.00 0.00 2.10
2715 2801 7.272084 GCTGCAAATTCTATGGCTTTATATTCG 59.728 37.037 0.00 0.00 0.00 3.34
2770 2882 5.479724 TCAAAACCATGCCACATCATCTAAA 59.520 36.000 0.00 0.00 0.00 1.85
2817 2930 4.191662 CACGCCGTGGAAAAATAGATAC 57.808 45.455 9.90 0.00 0.00 2.24
2859 2973 1.124462 GCAACAACAAATAACGCGCA 58.876 45.000 5.73 0.00 0.00 6.09
2861 2975 1.713404 CAGGCAACAACAAATAACGCG 59.287 47.619 3.53 3.53 41.41 6.01
2893 3007 3.189080 TGCAACATTGAATCAAGACGGAG 59.811 43.478 1.10 0.00 0.00 4.63
2898 3012 4.300803 GCAAGTGCAACATTGAATCAAGA 58.699 39.130 10.77 0.00 41.43 3.02
2916 3030 2.434884 ACGCCGATGACCTGCAAG 60.435 61.111 0.00 0.00 0.00 4.01
2937 3051 1.372997 ACACTCCATGTCGCGTGAC 60.373 57.895 22.00 22.00 45.71 3.67
2950 3064 1.498865 CGGTTGCCACACTGACACTC 61.499 60.000 0.00 0.00 0.00 3.51
2953 3067 2.203139 CCGGTTGCCACACTGACA 60.203 61.111 0.00 0.00 0.00 3.58
2954 3068 2.978010 CCCGGTTGCCACACTGAC 60.978 66.667 0.00 0.00 0.00 3.51
2955 3069 4.947147 GCCCGGTTGCCACACTGA 62.947 66.667 0.00 0.00 0.00 3.41
2970 3084 2.434185 TGTGAACGCCATCTCGCC 60.434 61.111 0.00 0.00 0.00 5.54
2972 3086 0.943835 TGTGTGTGAACGCCATCTCG 60.944 55.000 0.00 0.00 0.00 4.04
2980 3094 3.995669 CCGGCGTGTGTGTGAACG 61.996 66.667 6.01 0.00 42.61 3.95
3000 3114 2.633657 GTTGTGTGCGAGCTGGTG 59.366 61.111 0.00 0.00 0.00 4.17
3002 3116 2.591429 TGGTTGTGTGCGAGCTGG 60.591 61.111 0.00 0.00 0.00 4.85
3003 3117 1.835483 GACTGGTTGTGTGCGAGCTG 61.835 60.000 0.00 0.00 0.00 4.24
3005 3119 2.939022 GACTGGTTGTGTGCGAGC 59.061 61.111 0.00 0.00 0.00 5.03
3006 3120 1.591594 ACGACTGGTTGTGTGCGAG 60.592 57.895 0.00 0.00 0.00 5.03
3007 3121 1.880796 CACGACTGGTTGTGTGCGA 60.881 57.895 11.73 0.00 39.54 5.10
3009 3123 2.327940 GCACGACTGGTTGTGTGC 59.672 61.111 18.68 13.93 44.76 4.57
3010 3124 1.817520 TGGCACGACTGGTTGTGTG 60.818 57.895 18.68 9.21 44.76 3.82
3011 3125 1.817941 GTGGCACGACTGGTTGTGT 60.818 57.895 18.68 0.00 44.76 3.72
3012 3126 2.881266 CGTGGCACGACTGGTTGTG 61.881 63.158 34.85 14.75 46.05 3.33
3014 3128 4.012895 GCGTGGCACGACTGGTTG 62.013 66.667 40.94 12.28 46.05 3.77
3022 3136 4.210093 TATACCCGGCGTGGCACG 62.210 66.667 33.96 33.96 45.88 5.34
3023 3137 2.279918 CTATACCCGGCGTGGCAC 60.280 66.667 7.79 7.79 35.87 5.01
3024 3138 3.542676 CCTATACCCGGCGTGGCA 61.543 66.667 6.01 0.00 35.87 4.92
3025 3139 4.309950 CCCTATACCCGGCGTGGC 62.310 72.222 6.01 0.00 35.87 5.01
3026 3140 3.622826 CCCCTATACCCGGCGTGG 61.623 72.222 6.01 9.63 37.55 4.94
3028 3142 2.203596 CTCCCCTATACCCGGCGT 60.204 66.667 6.01 0.00 0.00 5.68
3037 3341 1.476007 GGATCACAGCGCTCCCCTAT 61.476 60.000 7.13 0.00 0.00 2.57
3040 3344 3.474570 AGGATCACAGCGCTCCCC 61.475 66.667 7.13 4.31 0.00 4.81
3047 3351 1.874231 CATGATGAGCAGGATCACAGC 59.126 52.381 0.00 0.00 32.68 4.40
3048 3352 1.874231 GCATGATGAGCAGGATCACAG 59.126 52.381 0.00 0.00 32.68 3.66
3049 3353 1.476291 GGCATGATGAGCAGGATCACA 60.476 52.381 0.00 0.00 32.68 3.58
3050 3354 1.236628 GGCATGATGAGCAGGATCAC 58.763 55.000 0.00 0.00 32.68 3.06
3051 3355 0.841289 TGGCATGATGAGCAGGATCA 59.159 50.000 0.00 0.00 34.37 2.92
3052 3356 1.202782 ACTGGCATGATGAGCAGGATC 60.203 52.381 0.00 0.00 0.00 3.36
3053 3357 0.844660 ACTGGCATGATGAGCAGGAT 59.155 50.000 0.00 0.00 0.00 3.24
3054 3358 0.622136 AACTGGCATGATGAGCAGGA 59.378 50.000 0.00 0.00 0.00 3.86
3055 3359 0.738975 CAACTGGCATGATGAGCAGG 59.261 55.000 0.00 0.00 0.00 4.85
3056 3360 0.738975 CCAACTGGCATGATGAGCAG 59.261 55.000 0.00 0.00 0.00 4.24
3057 3361 0.038599 ACCAACTGGCATGATGAGCA 59.961 50.000 0.00 0.00 39.32 4.26
3058 3362 1.133790 GAACCAACTGGCATGATGAGC 59.866 52.381 0.00 0.00 39.32 4.26
3059 3363 1.747355 GGAACCAACTGGCATGATGAG 59.253 52.381 0.00 0.00 39.32 2.90
3060 3364 1.075212 TGGAACCAACTGGCATGATGA 59.925 47.619 0.00 0.00 39.32 2.92
3061 3365 1.548081 TGGAACCAACTGGCATGATG 58.452 50.000 0.00 0.00 39.32 3.07
3062 3366 2.104967 CATGGAACCAACTGGCATGAT 58.895 47.619 0.00 0.00 36.14 2.45
3063 3367 1.075212 TCATGGAACCAACTGGCATGA 59.925 47.619 11.36 11.36 38.78 3.07
3064 3368 1.475280 CTCATGGAACCAACTGGCATG 59.525 52.381 7.96 7.96 39.32 4.06
3065 3369 1.617804 CCTCATGGAACCAACTGGCAT 60.618 52.381 0.00 0.00 35.09 4.40
3066 3370 0.251297 CCTCATGGAACCAACTGGCA 60.251 55.000 0.00 0.00 35.09 4.92
3067 3371 1.598701 GCCTCATGGAACCAACTGGC 61.599 60.000 14.53 14.53 35.09 4.85
3068 3372 0.251297 TGCCTCATGGAACCAACTGG 60.251 55.000 0.00 0.00 36.98 4.00
3069 3373 1.475280 CATGCCTCATGGAACCAACTG 59.525 52.381 0.00 0.00 38.11 3.16
3070 3374 1.076024 ACATGCCTCATGGAACCAACT 59.924 47.619 11.01 0.00 45.16 3.16
3071 3375 1.203052 CACATGCCTCATGGAACCAAC 59.797 52.381 11.01 0.00 45.16 3.77
3072 3376 1.548081 CACATGCCTCATGGAACCAA 58.452 50.000 11.01 0.00 45.16 3.67
3073 3377 0.323633 CCACATGCCTCATGGAACCA 60.324 55.000 11.01 0.00 45.16 3.67
3074 3378 1.669999 GCCACATGCCTCATGGAACC 61.670 60.000 11.01 0.00 45.16 3.62
3110 3414 1.630878 GAGATCTCTGGGTTTGGTGGT 59.369 52.381 15.80 0.00 0.00 4.16
3113 3417 2.356535 GCATGAGATCTCTGGGTTTGGT 60.357 50.000 22.95 0.00 0.00 3.67
3151 3455 0.877071 CTGCAACGACATGAAGGCTT 59.123 50.000 0.00 0.00 0.00 4.35
3152 3456 0.957395 CCTGCAACGACATGAAGGCT 60.957 55.000 0.00 0.00 39.30 4.58
3153 3457 1.503542 CCTGCAACGACATGAAGGC 59.496 57.895 0.00 0.00 39.30 4.35
3160 3464 2.186160 CAAGGTGCCTGCAACGACA 61.186 57.895 0.82 0.00 38.94 4.35
3167 3471 1.639298 GATGTCGACAAGGTGCCTGC 61.639 60.000 24.13 0.13 0.00 4.85
3194 3498 2.907458 ATGGCCCTTTTTCTGCTAGT 57.093 45.000 0.00 0.00 0.00 2.57
3195 3499 3.259123 ACAAATGGCCCTTTTTCTGCTAG 59.741 43.478 2.87 0.00 0.00 3.42
3196 3500 3.238597 ACAAATGGCCCTTTTTCTGCTA 58.761 40.909 2.87 0.00 0.00 3.49
3197 3501 2.037641 GACAAATGGCCCTTTTTCTGCT 59.962 45.455 11.20 0.00 0.00 4.24
3198 3502 2.416747 GACAAATGGCCCTTTTTCTGC 58.583 47.619 11.20 0.00 0.00 4.26
3199 3503 3.044235 GGACAAATGGCCCTTTTTCTG 57.956 47.619 16.22 4.55 37.19 3.02
3208 3512 2.696759 CGAACCGGGACAAATGGCC 61.697 63.158 6.32 0.00 44.61 5.36
3209 3513 0.674269 TACGAACCGGGACAAATGGC 60.674 55.000 6.32 0.00 0.00 4.40
3210 3514 1.735571 CTTACGAACCGGGACAAATGG 59.264 52.381 6.32 0.00 0.00 3.16
3211 3515 1.735571 CCTTACGAACCGGGACAAATG 59.264 52.381 6.32 0.00 0.00 2.32
3212 3516 1.947212 GCCTTACGAACCGGGACAAAT 60.947 52.381 6.32 0.00 0.00 2.32
3213 3517 0.603439 GCCTTACGAACCGGGACAAA 60.603 55.000 6.32 0.00 0.00 2.83
3214 3518 1.004679 GCCTTACGAACCGGGACAA 60.005 57.895 6.32 0.00 0.00 3.18
3215 3519 2.658422 GCCTTACGAACCGGGACA 59.342 61.111 6.32 0.00 0.00 4.02
3216 3520 2.125391 GGCCTTACGAACCGGGAC 60.125 66.667 6.32 0.00 0.00 4.46
3217 3521 3.393106 GGGCCTTACGAACCGGGA 61.393 66.667 6.32 0.00 0.00 5.14
3218 3522 2.546114 AATGGGCCTTACGAACCGGG 62.546 60.000 6.32 0.00 0.00 5.73
3219 3523 0.678684 AAATGGGCCTTACGAACCGG 60.679 55.000 4.53 0.00 0.00 5.28
3220 3524 0.450184 CAAATGGGCCTTACGAACCG 59.550 55.000 4.53 0.00 0.00 4.44
3221 3525 1.471287 GACAAATGGGCCTTACGAACC 59.529 52.381 4.53 0.00 0.00 3.62
3222 3526 1.471287 GGACAAATGGGCCTTACGAAC 59.529 52.381 4.53 0.00 0.00 3.95
3223 3527 1.614850 GGGACAAATGGGCCTTACGAA 60.615 52.381 4.53 0.00 0.00 3.85
3224 3528 0.034863 GGGACAAATGGGCCTTACGA 60.035 55.000 4.53 0.00 0.00 3.43
3225 3529 1.373590 CGGGACAAATGGGCCTTACG 61.374 60.000 4.53 0.00 0.00 3.18
3226 3530 1.035385 CCGGGACAAATGGGCCTTAC 61.035 60.000 4.53 0.00 0.00 2.34
3227 3531 1.304952 CCGGGACAAATGGGCCTTA 59.695 57.895 4.53 0.00 0.00 2.69
3228 3532 2.037208 CCGGGACAAATGGGCCTT 59.963 61.111 4.53 0.00 0.00 4.35
3229 3533 2.852281 AACCGGGACAAATGGGCCT 61.852 57.895 6.32 0.00 0.00 5.19
3230 3534 2.283604 AACCGGGACAAATGGGCC 60.284 61.111 6.32 0.00 0.00 5.80
3231 3535 2.645192 CCAACCGGGACAAATGGGC 61.645 63.158 6.32 0.00 40.01 5.36
3232 3536 3.693411 CCAACCGGGACAAATGGG 58.307 61.111 6.32 0.00 40.01 4.00
3245 3549 0.401356 TTTAGTCCCGGTTCCCCAAC 59.599 55.000 0.00 0.00 0.00 3.77
3246 3550 0.694196 CTTTAGTCCCGGTTCCCCAA 59.306 55.000 0.00 0.00 0.00 4.12
3247 3551 1.202769 CCTTTAGTCCCGGTTCCCCA 61.203 60.000 0.00 0.00 0.00 4.96
3248 3552 1.605992 CCTTTAGTCCCGGTTCCCC 59.394 63.158 0.00 0.00 0.00 4.81
3249 3553 1.203441 ACCCTTTAGTCCCGGTTCCC 61.203 60.000 0.00 0.00 0.00 3.97
3250 3554 0.251354 GACCCTTTAGTCCCGGTTCC 59.749 60.000 0.00 0.00 0.00 3.62
3251 3555 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 32.91 3.62
3252 3556 1.547472 CCGACCCTTTAGTCCCGGTT 61.547 60.000 0.00 0.00 32.91 4.44
3253 3557 1.986210 CCGACCCTTTAGTCCCGGT 60.986 63.158 0.00 0.00 32.91 5.28
3254 3558 0.684153 TACCGACCCTTTAGTCCCGG 60.684 60.000 0.00 0.00 42.30 5.73
3255 3559 0.457443 GTACCGACCCTTTAGTCCCG 59.543 60.000 0.00 0.00 32.91 5.14
3256 3560 1.857965 AGTACCGACCCTTTAGTCCC 58.142 55.000 0.00 0.00 32.91 4.46
3257 3561 4.679106 GCTTTAGTACCGACCCTTTAGTCC 60.679 50.000 0.00 0.00 32.91 3.85
3258 3562 4.428209 GCTTTAGTACCGACCCTTTAGTC 58.572 47.826 0.00 0.00 0.00 2.59
3259 3563 3.196469 GGCTTTAGTACCGACCCTTTAGT 59.804 47.826 0.00 0.00 0.00 2.24
3260 3564 3.431346 GGGCTTTAGTACCGACCCTTTAG 60.431 52.174 0.00 0.00 34.34 1.85
3261 3565 2.501316 GGGCTTTAGTACCGACCCTTTA 59.499 50.000 0.00 0.00 34.34 1.85
3262 3566 1.280133 GGGCTTTAGTACCGACCCTTT 59.720 52.381 0.00 0.00 34.34 3.11
3263 3567 0.907486 GGGCTTTAGTACCGACCCTT 59.093 55.000 0.00 0.00 34.34 3.95
3264 3568 0.042281 AGGGCTTTAGTACCGACCCT 59.958 55.000 4.22 4.22 42.97 4.34
3265 3569 1.780503 TAGGGCTTTAGTACCGACCC 58.219 55.000 0.00 0.00 37.63 4.46
3266 3570 3.256879 GGTATAGGGCTTTAGTACCGACC 59.743 52.174 0.00 0.00 0.00 4.79
3267 3571 4.148079 AGGTATAGGGCTTTAGTACCGAC 58.852 47.826 0.00 0.00 39.74 4.79
3268 3572 4.459852 AGGTATAGGGCTTTAGTACCGA 57.540 45.455 0.00 0.00 39.74 4.69
3269 3573 5.541953 AAAGGTATAGGGCTTTAGTACCG 57.458 43.478 0.00 0.00 39.74 4.02
3270 3574 7.256119 GGACTAAAGGTATAGGGCTTTAGTACC 60.256 44.444 6.31 6.49 46.28 3.34
3271 3575 7.256119 GGGACTAAAGGTATAGGGCTTTAGTAC 60.256 44.444 6.99 6.99 46.28 2.73
3272 3576 6.784473 GGGACTAAAGGTATAGGGCTTTAGTA 59.216 42.308 6.31 0.00 46.28 1.82
3274 3578 5.279356 CGGGACTAAAGGTATAGGGCTTTAG 60.279 48.000 1.97 1.97 42.08 1.85
3275 3579 4.590222 CGGGACTAAAGGTATAGGGCTTTA 59.410 45.833 0.00 0.00 0.00 1.85
3276 3580 3.390311 CGGGACTAAAGGTATAGGGCTTT 59.610 47.826 0.00 0.00 0.00 3.51
3277 3581 2.970640 CGGGACTAAAGGTATAGGGCTT 59.029 50.000 0.00 0.00 0.00 4.35
3278 3582 2.606378 CGGGACTAAAGGTATAGGGCT 58.394 52.381 0.00 0.00 0.00 5.19
3279 3583 1.622312 CCGGGACTAAAGGTATAGGGC 59.378 57.143 0.00 0.00 0.00 5.19
3280 3584 2.968271 ACCGGGACTAAAGGTATAGGG 58.032 52.381 6.32 0.00 36.34 3.53
3281 3585 5.363562 AAAACCGGGACTAAAGGTATAGG 57.636 43.478 6.32 0.00 37.26 2.57
3282 3586 7.278646 GTGTAAAAACCGGGACTAAAGGTATAG 59.721 40.741 6.32 0.00 37.26 1.31
3283 3587 7.102993 GTGTAAAAACCGGGACTAAAGGTATA 58.897 38.462 6.32 0.00 37.26 1.47
3284 3588 5.939883 GTGTAAAAACCGGGACTAAAGGTAT 59.060 40.000 6.32 0.00 37.26 2.73
3285 3589 5.304778 GTGTAAAAACCGGGACTAAAGGTA 58.695 41.667 6.32 0.00 37.26 3.08
3286 3590 4.136796 GTGTAAAAACCGGGACTAAAGGT 58.863 43.478 6.32 0.00 40.50 3.50
3287 3591 3.503363 GGTGTAAAAACCGGGACTAAAGG 59.497 47.826 6.32 0.00 0.00 3.11
3288 3592 4.136051 TGGTGTAAAAACCGGGACTAAAG 58.864 43.478 6.32 0.00 43.73 1.85
3289 3593 4.162040 TGGTGTAAAAACCGGGACTAAA 57.838 40.909 6.32 0.00 43.73 1.85
3290 3594 3.853355 TGGTGTAAAAACCGGGACTAA 57.147 42.857 6.32 0.00 43.73 2.24
3291 3595 3.475575 GTTGGTGTAAAAACCGGGACTA 58.524 45.455 6.32 0.00 43.73 2.59
3292 3596 2.300433 GTTGGTGTAAAAACCGGGACT 58.700 47.619 6.32 0.00 43.73 3.85
3293 3597 1.337703 GGTTGGTGTAAAAACCGGGAC 59.662 52.381 6.32 0.00 43.73 4.46
3294 3598 1.689984 GGTTGGTGTAAAAACCGGGA 58.310 50.000 6.32 0.00 43.73 5.14
3298 3602 0.675083 CCCCGGTTGGTGTAAAAACC 59.325 55.000 0.00 0.00 42.07 3.27
3299 3603 0.032403 GCCCCGGTTGGTGTAAAAAC 59.968 55.000 0.00 0.00 0.00 2.43
3300 3604 0.396695 TGCCCCGGTTGGTGTAAAAA 60.397 50.000 0.00 0.00 0.00 1.94
3301 3605 0.824182 CTGCCCCGGTTGGTGTAAAA 60.824 55.000 0.00 0.00 0.00 1.52
3302 3606 1.228306 CTGCCCCGGTTGGTGTAAA 60.228 57.895 0.00 0.00 0.00 2.01
3303 3607 1.493854 ATCTGCCCCGGTTGGTGTAA 61.494 55.000 0.00 0.00 0.00 2.41
3304 3608 1.921346 ATCTGCCCCGGTTGGTGTA 60.921 57.895 0.00 0.00 0.00 2.90
3305 3609 3.256960 ATCTGCCCCGGTTGGTGT 61.257 61.111 0.00 0.00 0.00 4.16
3306 3610 2.751436 CATCTGCCCCGGTTGGTG 60.751 66.667 0.00 0.00 0.00 4.17
3307 3611 4.047125 CCATCTGCCCCGGTTGGT 62.047 66.667 0.00 0.00 0.00 3.67
3308 3612 4.820744 CCCATCTGCCCCGGTTGG 62.821 72.222 0.00 0.00 31.38 3.77
3326 3630 2.124403 GCAGAGGCCACATGGAGG 60.124 66.667 5.01 0.00 37.39 4.30
3327 3631 2.513204 CGCAGAGGCCACATGGAG 60.513 66.667 5.01 0.00 37.39 3.86
3328 3632 4.100084 CCGCAGAGGCCACATGGA 62.100 66.667 5.01 0.00 37.39 3.41
3337 3641 4.504916 CTGGACTCGCCGCAGAGG 62.505 72.222 14.07 0.00 42.31 3.69
3338 3642 4.504916 CCTGGACTCGCCGCAGAG 62.505 72.222 9.69 9.69 43.56 3.35
3344 3648 4.154347 CTCCTGCCTGGACTCGCC 62.154 72.222 0.00 0.00 40.56 5.54
3345 3649 4.154347 CCTCCTGCCTGGACTCGC 62.154 72.222 0.00 0.00 40.56 5.03
3346 3650 3.465403 CCCTCCTGCCTGGACTCG 61.465 72.222 0.00 0.00 40.56 4.18
3347 3651 3.791586 GCCCTCCTGCCTGGACTC 61.792 72.222 0.00 0.00 40.56 3.36
3355 3659 2.361737 GACCAAAGGCCCTCCTGC 60.362 66.667 0.00 0.00 43.40 4.85
3356 3660 2.234296 AGGACCAAAGGCCCTCCTG 61.234 63.158 0.00 0.00 43.40 3.86
3358 3662 2.356667 CAGGACCAAAGGCCCTCC 59.643 66.667 0.00 0.00 0.00 4.30
3359 3663 2.081585 AACCAGGACCAAAGGCCCTC 62.082 60.000 0.00 0.00 0.00 4.30
3360 3664 2.091283 AACCAGGACCAAAGGCCCT 61.091 57.895 0.00 0.00 0.00 5.19
3361 3665 1.908299 CAACCAGGACCAAAGGCCC 60.908 63.158 0.00 0.00 0.00 5.80
3362 3666 1.908299 CCAACCAGGACCAAAGGCC 60.908 63.158 0.00 0.00 41.22 5.19
3363 3667 0.111639 TACCAACCAGGACCAAAGGC 59.888 55.000 0.00 0.00 41.22 4.35
3364 3668 1.886655 GCTACCAACCAGGACCAAAGG 60.887 57.143 0.00 0.00 41.22 3.11
3365 3669 1.202879 TGCTACCAACCAGGACCAAAG 60.203 52.381 0.00 0.00 41.22 2.77
3366 3670 0.847373 TGCTACCAACCAGGACCAAA 59.153 50.000 0.00 0.00 41.22 3.28
3367 3671 0.109723 GTGCTACCAACCAGGACCAA 59.890 55.000 0.00 0.00 41.22 3.67
3368 3672 1.758592 GTGCTACCAACCAGGACCA 59.241 57.895 0.00 0.00 41.22 4.02
3369 3673 1.002502 GGTGCTACCAACCAGGACC 60.003 63.158 0.00 0.00 45.61 4.46
3370 3674 4.716003 GGTGCTACCAACCAGGAC 57.284 61.111 0.00 0.00 41.22 3.85
3379 3683 2.046604 GTCCCGGTTGGTGCTACC 60.047 66.667 0.00 0.00 39.22 3.18
3380 3684 2.046604 GGTCCCGGTTGGTGCTAC 60.047 66.667 0.00 0.00 34.77 3.58
3381 3685 1.706995 TTTGGTCCCGGTTGGTGCTA 61.707 55.000 0.00 0.00 34.77 3.49
3382 3686 2.575455 TTTTGGTCCCGGTTGGTGCT 62.575 55.000 0.00 0.00 34.77 4.40
3383 3687 2.082629 CTTTTGGTCCCGGTTGGTGC 62.083 60.000 0.00 0.00 34.77 5.01
3384 3688 1.460273 CCTTTTGGTCCCGGTTGGTG 61.460 60.000 0.00 0.00 34.77 4.17
3385 3689 1.152631 CCTTTTGGTCCCGGTTGGT 60.153 57.895 0.00 0.00 34.77 3.67
3386 3690 2.570284 GCCTTTTGGTCCCGGTTGG 61.570 63.158 0.00 0.00 42.99 3.77
3387 3691 1.184970 ATGCCTTTTGGTCCCGGTTG 61.185 55.000 0.00 0.00 42.99 3.77
3388 3692 0.898326 GATGCCTTTTGGTCCCGGTT 60.898 55.000 0.00 0.00 42.99 4.44
3389 3693 1.304134 GATGCCTTTTGGTCCCGGT 60.304 57.895 0.00 0.00 42.99 5.28
3390 3694 2.052104 GGATGCCTTTTGGTCCCGG 61.052 63.158 0.00 0.00 42.99 5.73
3391 3695 1.304052 TGGATGCCTTTTGGTCCCG 60.304 57.895 0.00 0.00 42.99 5.14
3392 3696 0.972471 CCTGGATGCCTTTTGGTCCC 60.972 60.000 0.00 0.00 42.99 4.46
3393 3697 1.607801 GCCTGGATGCCTTTTGGTCC 61.608 60.000 0.00 0.00 42.99 4.46
3394 3698 1.893062 GCCTGGATGCCTTTTGGTC 59.107 57.895 0.00 0.00 42.99 4.02
3395 3699 1.978617 CGCCTGGATGCCTTTTGGT 60.979 57.895 0.00 0.00 42.99 3.67
3396 3700 1.937546 GACGCCTGGATGCCTTTTGG 61.938 60.000 0.00 0.00 44.18 3.28
3397 3701 1.243342 TGACGCCTGGATGCCTTTTG 61.243 55.000 0.00 0.00 0.00 2.44
3398 3702 0.962356 CTGACGCCTGGATGCCTTTT 60.962 55.000 0.00 0.00 0.00 2.27
3399 3703 1.377725 CTGACGCCTGGATGCCTTT 60.378 57.895 0.00 0.00 0.00 3.11
3400 3704 2.270205 CTGACGCCTGGATGCCTT 59.730 61.111 0.00 0.00 0.00 4.35
3401 3705 4.479993 GCTGACGCCTGGATGCCT 62.480 66.667 0.00 0.00 0.00 4.75
3402 3706 4.783621 TGCTGACGCCTGGATGCC 62.784 66.667 0.00 0.00 34.43 4.40
3403 3707 3.200593 CTGCTGACGCCTGGATGC 61.201 66.667 0.00 0.00 34.43 3.91
3404 3708 3.200593 GCTGCTGACGCCTGGATG 61.201 66.667 0.00 0.00 34.43 3.51
3405 3709 3.397439 AGCTGCTGACGCCTGGAT 61.397 61.111 0.00 0.00 34.43 3.41
3406 3710 4.383861 CAGCTGCTGACGCCTGGA 62.384 66.667 24.88 0.00 32.44 3.86
3412 3716 4.383861 TCCTGCCAGCTGCTGACG 62.384 66.667 30.10 15.66 41.11 4.35
3413 3717 2.436292 CTCCTGCCAGCTGCTGAC 60.436 66.667 30.10 20.18 41.11 3.51
3414 3718 4.405671 GCTCCTGCCAGCTGCTGA 62.406 66.667 30.10 10.97 41.11 4.26


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

AutoCloner maintained by Alex Coulton.