Multiple sequence alignment - TraesCS4D01G208400

Loading Multiple Alignment...

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 TraesCS4D01G208400 chr4D 100.000 5125 0 0 1 5125 359117269 359122393 0.000000e+00 9465.0
1 TraesCS4D01G208400 chr4D 84.615 91 9 3 2731 2821 375432498 375432583 9.140000e-13 86.1
2 TraesCS4D01G208400 chr4B 93.583 2353 105 21 401 2729 443446005 443448335 0.000000e+00 3467.0
3 TraesCS4D01G208400 chr4B 93.619 1097 44 18 3438 4517 443449461 443450548 0.000000e+00 1615.0
4 TraesCS4D01G208400 chr4B 90.180 611 38 8 4515 5125 443450808 443451396 0.000000e+00 776.0
5 TraesCS4D01G208400 chr4B 90.476 504 28 11 2828 3327 443448322 443448809 0.000000e+00 647.0
6 TraesCS4D01G208400 chr4B 92.424 330 17 4 79 402 443445512 443445839 1.010000e-126 464.0
7 TraesCS4D01G208400 chr4B 97.030 101 2 1 3435 3534 443448850 443448950 8.830000e-38 169.0
8 TraesCS4D01G208400 chr4B 98.750 80 1 0 1 80 443445271 443445350 5.350000e-30 143.0
9 TraesCS4D01G208400 chr4A 93.257 2195 100 19 565 2729 106347035 106344859 0.000000e+00 3190.0
10 TraesCS4D01G208400 chr4A 95.053 1516 53 15 3622 5125 106343607 106342102 0.000000e+00 2364.0
11 TraesCS4D01G208400 chr4A 94.433 503 26 2 2831 3332 106344869 106344368 0.000000e+00 773.0
12 TraesCS4D01G208400 chr4A 86.174 622 28 16 1 579 106358136 106357530 2.030000e-173 619.0
13 TraesCS4D01G208400 chr4A 97.576 165 3 1 3438 3602 106343979 106343816 1.090000e-71 281.0
14 TraesCS4D01G208400 chr4A 90.805 174 9 2 3435 3602 106344332 106344160 5.160000e-55 226.0
15 TraesCS4D01G208400 chr6B 89.011 91 6 3 2731 2821 678929303 678929217 5.430000e-20 110.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G208400 chr4D 359117269 359122393 5124 False 9465.000000 9465 100.000000 1 5125 1 chr4D.!!$F1 5124
1 TraesCS4D01G208400 chr4B 443445271 443451396 6125 False 1040.142857 3467 93.723143 1 5125 7 chr4B.!!$F1 5124
2 TraesCS4D01G208400 chr4A 106342102 106347035 4933 True 1366.800000 3190 94.224800 565 5125 5 chr4A.!!$R2 4560
3 TraesCS4D01G208400 chr4A 106357530 106358136 606 True 619.000000 619 86.174000 1 579 1 chr4A.!!$R1 578

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
720 1098 1.026182 TGAATCACATGGACGCAGGC 61.026 55.0 0.0 0.0 0.00 4.85 F
1303 1716 0.313672 GGCTGGTTGATTTTGCACGA 59.686 50.0 0.0 0.0 0.00 4.35 F
2190 2613 0.040204 CTCCACATTTCCAGCCCCTT 59.960 55.0 0.0 0.0 0.00 3.95 F
2226 2649 0.250901 TGAAGGTTGCTCTTGAGGCC 60.251 55.0 0.0 0.0 0.00 5.19 F
2762 3189 0.322816 TTTGGTCTCCAGGCTCATGC 60.323 55.0 0.0 0.0 33.81 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2530 0.110238 CCAACAGCACGAATGGAACG 60.110 55.0 0.00 0.00 34.82 3.95 R
3268 3699 0.111061 TGATGGCTTGCCTCAGTGTT 59.889 50.0 13.18 0.00 0.00 3.32 R
3269 3700 0.330604 ATGATGGCTTGCCTCAGTGT 59.669 50.0 13.18 0.00 0.00 3.55 R
3270 3701 0.738975 CATGATGGCTTGCCTCAGTG 59.261 55.0 13.18 9.72 0.00 3.66 R
4421 5673 0.740868 TCTCAGCATTAGCACGCACC 60.741 55.0 0.00 0.00 45.49 5.01 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
100 264 2.898705 CAGTACTCAGATGAGCCCAAC 58.101 52.381 9.75 3.95 45.79 3.77
105 269 2.224523 ACTCAGATGAGCCCAACGAAAA 60.225 45.455 9.75 0.00 45.79 2.29
114 281 6.249035 TGAGCCCAACGAAAATTACTAAAG 57.751 37.500 0.00 0.00 0.00 1.85
209 378 4.274602 TGTAGGTACATTCGGCTTTGAA 57.725 40.909 0.00 0.00 0.00 2.69
301 498 1.302511 GGAGAAGAACCGCTGCCAA 60.303 57.895 0.00 0.00 0.00 4.52
304 501 2.597510 AAGAACCGCTGCCAACCC 60.598 61.111 0.00 0.00 0.00 4.11
305 502 3.429372 AAGAACCGCTGCCAACCCA 62.429 57.895 0.00 0.00 0.00 4.51
523 896 1.681780 CCAAAGGAGGCCAGCGATAAA 60.682 52.381 5.01 0.00 0.00 1.40
534 907 3.858238 GCCAGCGATAAAGATACGGTATC 59.142 47.826 18.31 18.31 36.06 2.24
536 909 5.163683 GCCAGCGATAAAGATACGGTATCTA 60.164 44.000 26.32 15.12 44.44 1.98
537 910 6.459848 GCCAGCGATAAAGATACGGTATCTAT 60.460 42.308 26.32 18.58 44.44 1.98
589 962 1.709147 GCTGTGCTGAATAGGCCACG 61.709 60.000 5.01 0.00 0.00 4.94
654 1031 8.532819 ACGAACTTAAGTATCATTCTCCTTCTT 58.467 33.333 8.92 0.00 0.00 2.52
655 1032 9.026074 CGAACTTAAGTATCATTCTCCTTCTTC 57.974 37.037 8.92 0.00 0.00 2.87
672 1049 5.107065 CCTTCTTCGTGACATGGAAGTTTAC 60.107 44.000 14.96 0.00 40.36 2.01
676 1053 3.322541 TCGTGACATGGAAGTTTACTCCA 59.677 43.478 0.00 0.00 37.99 3.86
713 1091 6.457355 CAAGAAACCAAATGAATCACATGGA 58.543 36.000 19.23 0.00 39.39 3.41
719 1097 1.671979 ATGAATCACATGGACGCAGG 58.328 50.000 0.00 0.00 37.87 4.85
720 1098 1.026182 TGAATCACATGGACGCAGGC 61.026 55.000 0.00 0.00 0.00 4.85
721 1099 2.040213 GAATCACATGGACGCAGGCG 62.040 60.000 12.71 12.71 46.03 5.52
722 1100 4.758251 TCACATGGACGCAGGCGG 62.758 66.667 18.63 1.97 44.69 6.13
723 1101 4.758251 CACATGGACGCAGGCGGA 62.758 66.667 18.63 1.70 44.69 5.54
766 1149 2.276201 TGTCGTTCATTAATGAGGCGG 58.724 47.619 28.12 16.70 38.19 6.13
852 1253 3.635268 AACCTAGCAGGCAGGCAGC 62.635 63.158 2.72 2.72 39.63 5.25
904 1305 1.225426 CAGCCAGCCAAGCCATAGA 59.775 57.895 0.00 0.00 0.00 1.98
938 1339 2.074547 GCCACTAGCTACAACGAACA 57.925 50.000 0.00 0.00 38.99 3.18
940 1341 2.412089 GCCACTAGCTACAACGAACAAG 59.588 50.000 0.00 0.00 38.99 3.16
1076 1484 1.149288 TCCCAACACCTCAGGTACTCT 59.851 52.381 0.00 0.00 34.60 3.24
1077 1485 2.380932 TCCCAACACCTCAGGTACTCTA 59.619 50.000 0.00 0.00 34.60 2.43
1078 1486 2.496470 CCCAACACCTCAGGTACTCTAC 59.504 54.545 0.00 0.00 34.60 2.59
1092 1500 1.340211 ACTCTACCACTCTACTGCGCT 60.340 52.381 9.73 0.00 0.00 5.92
1144 1552 2.434331 CTTTCCAGGCCCCGTTCA 59.566 61.111 0.00 0.00 0.00 3.18
1145 1553 1.228429 CTTTCCAGGCCCCGTTCAA 60.228 57.895 0.00 0.00 0.00 2.69
1146 1554 1.524008 CTTTCCAGGCCCCGTTCAAC 61.524 60.000 0.00 0.00 0.00 3.18
1178 1589 2.065993 TAACTTCGTGTGCTCTGCTC 57.934 50.000 0.00 0.00 0.00 4.26
1214 1627 2.223572 GCGATTTGGCCCTGTCAATTAG 60.224 50.000 0.00 0.00 0.00 1.73
1233 1646 1.022735 GTCGGAGTAGGAATGAGCGA 58.977 55.000 0.00 0.00 0.00 4.93
1234 1647 1.002251 GTCGGAGTAGGAATGAGCGAG 60.002 57.143 0.00 0.00 0.00 5.03
1303 1716 0.313672 GGCTGGTTGATTTTGCACGA 59.686 50.000 0.00 0.00 0.00 4.35
1329 1742 0.602562 TTTCCGCTTTGGGCTTCATG 59.397 50.000 0.00 0.00 38.76 3.07
1431 1845 0.541764 AGGGCGAATTTTGCTCCCAA 60.542 50.000 4.81 0.00 39.42 4.12
1474 1888 6.520792 TCTTCAAGTTAGCGTGAGTTTTAC 57.479 37.500 0.00 0.00 34.79 2.01
1483 1897 1.459592 CGTGAGTTTTACCAGCGAAGG 59.540 52.381 0.00 0.00 0.00 3.46
1675 2089 1.346062 AGCTGAGAAGCTCCACAAGA 58.654 50.000 0.00 0.00 42.12 3.02
1828 2242 0.468029 ACAGTTTCCAGGGGCACAAG 60.468 55.000 0.00 0.00 0.00 3.16
1844 2258 0.604578 CAAGGAATGGCTGGTTGGTG 59.395 55.000 0.00 0.00 0.00 4.17
1892 2306 2.884639 GCCTGTTTGAGCTGAAGGTTTA 59.115 45.455 0.00 0.00 0.00 2.01
1954 2369 0.331616 GGTCAATTACCTGGGGCAGT 59.668 55.000 0.00 0.00 45.75 4.40
1956 2371 1.818674 GTCAATTACCTGGGGCAGTTG 59.181 52.381 0.00 0.00 0.00 3.16
2081 2496 6.624352 TTTCAGGAGTGAGTTTCTCAAATG 57.376 37.500 0.88 0.00 42.46 2.32
2113 2528 3.249320 GTGATATGCTCATTGTGCACGAT 59.751 43.478 14.16 14.16 43.59 3.73
2115 2530 4.448732 TGATATGCTCATTGTGCACGATAC 59.551 41.667 19.30 12.15 43.59 2.24
2158 2581 1.160137 GGGTGAGTGACAGTGCAATC 58.840 55.000 7.69 7.69 33.77 2.67
2190 2613 0.040204 CTCCACATTTCCAGCCCCTT 59.960 55.000 0.00 0.00 0.00 3.95
2226 2649 0.250901 TGAAGGTTGCTCTTGAGGCC 60.251 55.000 0.00 0.00 0.00 5.19
2253 2676 2.619074 GGGACTTGCTTTCCTGCATAGT 60.619 50.000 0.00 0.00 42.96 2.12
2259 2682 3.538591 TGCTTTCCTGCATAGTGATGAG 58.461 45.455 0.00 0.00 38.12 2.90
2292 2715 6.732896 ATATACCGTGATTTCAAGACCTCT 57.267 37.500 0.00 0.00 0.00 3.69
2341 2766 8.016229 GCATGCAAATTCAGTCTCTTATCTATG 58.984 37.037 14.21 0.00 0.00 2.23
2351 2776 7.013750 TCAGTCTCTTATCTATGCACTAAGTGG 59.986 40.741 0.00 0.00 33.64 4.00
2387 2812 5.860716 GCTCTGGTCTAAAGATTTGCTTTTG 59.139 40.000 0.00 0.00 44.24 2.44
2404 2829 5.037385 GCTTTTGTTGTCCTTCTTTGACTC 58.963 41.667 0.00 0.00 33.83 3.36
2722 3149 3.066621 TGTGGTTCAATGTTCAAGACAGC 59.933 43.478 0.00 0.00 42.62 4.40
2723 3150 3.066621 GTGGTTCAATGTTCAAGACAGCA 59.933 43.478 0.00 0.00 42.62 4.41
2724 3151 3.890756 TGGTTCAATGTTCAAGACAGCAT 59.109 39.130 0.00 0.00 42.62 3.79
2725 3152 4.341806 TGGTTCAATGTTCAAGACAGCATT 59.658 37.500 0.00 0.00 42.62 3.56
2726 3153 4.682860 GGTTCAATGTTCAAGACAGCATTG 59.317 41.667 9.13 9.13 45.45 2.82
2727 3154 3.904571 TCAATGTTCAAGACAGCATTGC 58.095 40.909 0.00 0.00 44.41 3.56
2728 3155 3.570975 TCAATGTTCAAGACAGCATTGCT 59.429 39.130 5.03 5.03 44.41 3.91
2729 3156 3.844577 ATGTTCAAGACAGCATTGCTC 57.155 42.857 8.54 0.00 42.62 4.26
2730 3157 2.854963 TGTTCAAGACAGCATTGCTCT 58.145 42.857 8.54 0.95 36.40 4.09
2731 3158 3.216800 TGTTCAAGACAGCATTGCTCTT 58.783 40.909 8.54 7.73 36.40 2.85
2732 3159 3.004002 TGTTCAAGACAGCATTGCTCTTG 59.996 43.478 24.25 24.25 40.22 3.02
2733 3160 2.854963 TCAAGACAGCATTGCTCTTGT 58.145 42.857 26.79 17.19 40.03 3.16
2734 3161 4.006780 TCAAGACAGCATTGCTCTTGTA 57.993 40.909 26.79 17.19 40.03 2.41
2735 3162 3.748048 TCAAGACAGCATTGCTCTTGTAC 59.252 43.478 26.79 12.33 40.03 2.90
2736 3163 3.692257 AGACAGCATTGCTCTTGTACT 57.308 42.857 8.54 2.62 36.40 2.73
2737 3164 3.332919 AGACAGCATTGCTCTTGTACTG 58.667 45.455 8.54 0.00 36.40 2.74
2738 3165 2.417933 GACAGCATTGCTCTTGTACTGG 59.582 50.000 8.54 0.00 36.40 4.00
2739 3166 2.038952 ACAGCATTGCTCTTGTACTGGA 59.961 45.455 8.54 0.00 36.40 3.86
2740 3167 2.417933 CAGCATTGCTCTTGTACTGGAC 59.582 50.000 8.54 0.00 36.40 4.02
2741 3168 1.740025 GCATTGCTCTTGTACTGGACC 59.260 52.381 0.16 0.00 0.00 4.46
2742 3169 2.616510 GCATTGCTCTTGTACTGGACCT 60.617 50.000 0.16 0.00 0.00 3.85
2743 3170 3.679389 CATTGCTCTTGTACTGGACCTT 58.321 45.455 0.00 0.00 0.00 3.50
2744 3171 3.857157 TTGCTCTTGTACTGGACCTTT 57.143 42.857 0.00 0.00 0.00 3.11
2745 3172 3.857157 TGCTCTTGTACTGGACCTTTT 57.143 42.857 0.00 0.00 0.00 2.27
2746 3173 3.476552 TGCTCTTGTACTGGACCTTTTG 58.523 45.455 0.00 0.00 0.00 2.44
2758 3185 3.256281 CCTTTTGGTCTCCAGGCTC 57.744 57.895 0.00 0.00 33.81 4.70
2759 3186 0.401738 CCTTTTGGTCTCCAGGCTCA 59.598 55.000 0.00 0.00 33.81 4.26
2760 3187 1.005215 CCTTTTGGTCTCCAGGCTCAT 59.995 52.381 0.00 0.00 33.81 2.90
2761 3188 2.089980 CTTTTGGTCTCCAGGCTCATG 58.910 52.381 0.00 0.00 33.81 3.07
2762 3189 0.322816 TTTGGTCTCCAGGCTCATGC 60.323 55.000 0.00 0.00 33.81 4.06
2780 3207 8.961294 GCTCATGCCTGTTTGAAATATATAAG 57.039 34.615 0.00 0.00 0.00 1.73
2781 3208 8.025445 GCTCATGCCTGTTTGAAATATATAAGG 58.975 37.037 0.00 0.00 0.00 2.69
2782 3209 8.995027 TCATGCCTGTTTGAAATATATAAGGT 57.005 30.769 0.00 0.00 0.00 3.50
2786 3213 9.778741 TGCCTGTTTGAAATATATAAGGTAGAG 57.221 33.333 0.00 0.00 0.00 2.43
2787 3214 9.998106 GCCTGTTTGAAATATATAAGGTAGAGA 57.002 33.333 0.00 0.00 0.00 3.10
3026 3455 5.362430 TGGTTTTATATGGCATGGTTCTTCC 59.638 40.000 10.98 5.45 0.00 3.46
3069 3498 8.950007 TTTTATTTAAAGGGGTGTGATTCTCT 57.050 30.769 0.00 0.00 0.00 3.10
3086 3515 3.982516 TCTCTTATAGCAGTGAGGGTGT 58.017 45.455 0.00 0.00 0.00 4.16
3114 3543 8.483307 AAAATAATCATTTAGCAGCAAAGTGG 57.517 30.769 0.00 0.00 33.09 4.00
3140 3569 3.343972 GCAAGAGCCACGAAGCAA 58.656 55.556 0.00 0.00 34.23 3.91
3155 3584 3.562505 GAAGCAAAGCATGTCTGAACAG 58.437 45.455 0.00 0.00 39.20 3.16
3177 3606 6.094048 ACAGTCCATTTTAGATTGACGATTGG 59.906 38.462 0.00 0.00 0.00 3.16
3185 3614 7.447374 TTTAGATTGACGATTGGTGTTTCAT 57.553 32.000 0.00 0.00 0.00 2.57
3214 3643 8.759481 TGTGATGCCTATGATTACCAATTTTA 57.241 30.769 0.00 0.00 0.00 1.52
3215 3644 9.194972 TGTGATGCCTATGATTACCAATTTTAA 57.805 29.630 0.00 0.00 0.00 1.52
3268 3699 3.366396 TGACACCCTGTAAAAGGCAAAA 58.634 40.909 0.00 0.00 45.89 2.44
3269 3700 3.769844 TGACACCCTGTAAAAGGCAAAAA 59.230 39.130 0.00 0.00 45.89 1.94
3270 3701 4.116961 GACACCCTGTAAAAGGCAAAAAC 58.883 43.478 0.00 0.00 45.89 2.43
3271 3702 3.515901 ACACCCTGTAAAAGGCAAAAACA 59.484 39.130 0.00 0.00 45.89 2.83
3272 3703 3.868661 CACCCTGTAAAAGGCAAAAACAC 59.131 43.478 0.00 0.00 45.89 3.32
3328 3759 5.560966 ATTGGTACTTTATGCTTTCCACG 57.439 39.130 0.00 0.00 0.00 4.94
3332 3763 3.343941 ACTTTATGCTTTCCACGCCTA 57.656 42.857 0.00 0.00 0.00 3.93
3333 3764 3.681593 ACTTTATGCTTTCCACGCCTAA 58.318 40.909 0.00 0.00 0.00 2.69
3334 3765 4.076394 ACTTTATGCTTTCCACGCCTAAA 58.924 39.130 0.00 0.00 0.00 1.85
3335 3766 4.521256 ACTTTATGCTTTCCACGCCTAAAA 59.479 37.500 0.00 0.00 30.75 1.52
3336 3767 5.010213 ACTTTATGCTTTCCACGCCTAAAAA 59.990 36.000 0.00 0.00 30.75 1.94
3360 3791 9.492973 AAAACAGATTATTGTGGAAAAAGGATG 57.507 29.630 0.00 0.00 0.00 3.51
3361 3792 8.421249 AACAGATTATTGTGGAAAAAGGATGA 57.579 30.769 0.00 0.00 0.00 2.92
3362 3793 7.830739 ACAGATTATTGTGGAAAAAGGATGAC 58.169 34.615 0.00 0.00 0.00 3.06
3363 3794 7.671398 ACAGATTATTGTGGAAAAAGGATGACT 59.329 33.333 0.00 0.00 0.00 3.41
3364 3795 8.526147 CAGATTATTGTGGAAAAAGGATGACTT 58.474 33.333 0.00 0.00 42.52 3.01
3365 3796 8.526147 AGATTATTGTGGAAAAAGGATGACTTG 58.474 33.333 0.00 0.00 39.96 3.16
3366 3797 7.831691 TTATTGTGGAAAAAGGATGACTTGA 57.168 32.000 0.00 0.00 39.96 3.02
3367 3798 6.923199 ATTGTGGAAAAAGGATGACTTGAT 57.077 33.333 0.00 0.00 39.96 2.57
3374 3805 6.239289 GGAAAAAGGATGACTTGATGTGGAAA 60.239 38.462 0.00 0.00 39.96 3.13
3396 3827 7.418483 GGAAAAAGGATGACTAGATACTCAGCT 60.418 40.741 0.00 0.00 0.00 4.24
3397 3828 6.403866 AAAGGATGACTAGATACTCAGCTG 57.596 41.667 7.63 7.63 0.00 4.24
3398 3829 4.406456 AGGATGACTAGATACTCAGCTGG 58.594 47.826 15.13 7.28 0.00 4.85
3399 3830 4.141041 AGGATGACTAGATACTCAGCTGGT 60.141 45.833 15.13 13.13 34.21 4.00
3400 3831 4.217550 GGATGACTAGATACTCAGCTGGTC 59.782 50.000 15.13 10.91 45.80 4.02
3401 3832 4.511786 TGACTAGATACTCAGCTGGTCT 57.488 45.455 15.13 14.12 45.79 3.85
3402 3833 4.456535 TGACTAGATACTCAGCTGGTCTC 58.543 47.826 15.13 12.31 45.79 3.36
3403 3834 4.080299 TGACTAGATACTCAGCTGGTCTCA 60.080 45.833 15.13 5.09 45.79 3.27
3404 3835 5.060427 ACTAGATACTCAGCTGGTCTCAT 57.940 43.478 15.13 1.59 22.57 2.90
3405 3836 4.826733 ACTAGATACTCAGCTGGTCTCATG 59.173 45.833 15.13 11.05 22.57 3.07
3406 3837 2.364970 AGATACTCAGCTGGTCTCATGC 59.635 50.000 15.13 0.00 0.00 4.06
3407 3838 1.560505 TACTCAGCTGGTCTCATGCA 58.439 50.000 15.13 0.00 0.00 3.96
3408 3839 0.036577 ACTCAGCTGGTCTCATGCAC 60.037 55.000 15.13 0.00 0.00 4.57
3409 3840 0.036671 CTCAGCTGGTCTCATGCACA 60.037 55.000 15.13 0.00 0.00 4.57
3410 3841 0.397564 TCAGCTGGTCTCATGCACAA 59.602 50.000 15.13 0.00 0.00 3.33
3411 3842 1.202794 TCAGCTGGTCTCATGCACAAA 60.203 47.619 15.13 0.00 0.00 2.83
3412 3843 1.068748 CAGCTGGTCTCATGCACAAAC 60.069 52.381 5.57 0.00 0.00 2.93
3413 3844 1.202855 AGCTGGTCTCATGCACAAACT 60.203 47.619 0.00 0.00 0.00 2.66
3414 3845 1.068748 GCTGGTCTCATGCACAAACTG 60.069 52.381 0.00 0.00 0.00 3.16
3416 3847 0.242017 GGTCTCATGCACAAACTGCC 59.758 55.000 0.00 0.00 46.51 4.85
3417 3848 1.242076 GTCTCATGCACAAACTGCCT 58.758 50.000 0.00 0.00 46.51 4.75
3418 3849 2.426522 GTCTCATGCACAAACTGCCTA 58.573 47.619 0.00 0.00 46.51 3.93
3419 3850 2.813754 GTCTCATGCACAAACTGCCTAA 59.186 45.455 0.00 0.00 46.51 2.69
3420 3851 3.253188 GTCTCATGCACAAACTGCCTAAA 59.747 43.478 0.00 0.00 46.51 1.85
3421 3852 3.888323 TCTCATGCACAAACTGCCTAAAA 59.112 39.130 0.00 0.00 46.51 1.52
3422 3853 4.340666 TCTCATGCACAAACTGCCTAAAAA 59.659 37.500 0.00 0.00 46.51 1.94
3423 3854 5.010922 TCTCATGCACAAACTGCCTAAAAAT 59.989 36.000 0.00 0.00 46.51 1.82
3424 3855 5.229423 TCATGCACAAACTGCCTAAAAATC 58.771 37.500 0.00 0.00 46.51 2.17
3425 3856 4.662468 TGCACAAACTGCCTAAAAATCA 57.338 36.364 0.00 0.00 46.51 2.57
3426 3857 4.619973 TGCACAAACTGCCTAAAAATCAG 58.380 39.130 0.00 0.00 46.51 2.90
3427 3858 4.340666 TGCACAAACTGCCTAAAAATCAGA 59.659 37.500 0.00 0.00 46.51 3.27
3428 3859 5.010922 TGCACAAACTGCCTAAAAATCAGAT 59.989 36.000 0.00 0.00 46.51 2.90
3429 3860 5.928264 GCACAAACTGCCTAAAAATCAGATT 59.072 36.000 0.00 0.00 40.42 2.40
3430 3861 7.090173 GCACAAACTGCCTAAAAATCAGATTA 58.910 34.615 0.00 0.00 40.42 1.75
3431 3862 7.761249 GCACAAACTGCCTAAAAATCAGATTAT 59.239 33.333 0.00 0.00 40.42 1.28
3432 3863 9.643693 CACAAACTGCCTAAAAATCAGATTATT 57.356 29.630 0.00 0.00 0.00 1.40
3433 3864 9.643693 ACAAACTGCCTAAAAATCAGATTATTG 57.356 29.630 0.00 0.00 0.00 1.90
3534 4594 3.137360 GCCCCATCTTGTTCTCTAATCCT 59.863 47.826 0.00 0.00 0.00 3.24
3546 4606 8.193953 TGTTCTCTAATCCTGATATGCACATA 57.806 34.615 0.00 0.00 0.00 2.29
3606 4828 7.048512 ACTGATTGTGGCTAGTTAATAGTTCC 58.951 38.462 0.00 0.00 33.65 3.62
3718 4967 7.129622 TGTTCTTTACTCTAAATTTGTGCACG 58.870 34.615 13.13 0.00 0.00 5.34
3998 5247 1.557443 GGTCGCAATATTCGCTCCCG 61.557 60.000 7.83 0.00 0.00 5.14
4172 5421 2.768527 TCCTTTACCTCTCTGGAGCATG 59.231 50.000 0.00 0.00 38.21 4.06
4173 5422 2.559440 CTTTACCTCTCTGGAGCATGC 58.441 52.381 10.51 10.51 38.21 4.06
4174 5423 1.571955 TTACCTCTCTGGAGCATGCA 58.428 50.000 21.98 0.00 38.21 3.96
4175 5424 1.798626 TACCTCTCTGGAGCATGCAT 58.201 50.000 21.98 4.75 34.26 3.96
4176 5425 0.469070 ACCTCTCTGGAGCATGCATC 59.531 55.000 21.98 13.95 34.26 3.91
4177 5426 0.468648 CCTCTCTGGAGCATGCATCA 59.531 55.000 21.98 15.91 34.26 3.07
4178 5427 1.072489 CCTCTCTGGAGCATGCATCAT 59.928 52.381 21.98 0.00 34.26 2.45
4179 5428 2.418692 CTCTCTGGAGCATGCATCATC 58.581 52.381 21.98 8.38 34.26 2.92
4180 5429 1.071857 TCTCTGGAGCATGCATCATCC 59.928 52.381 21.98 18.05 34.26 3.51
4221 5470 4.602340 TCAGGGAGTAGAAACAGTGAAC 57.398 45.455 0.00 0.00 0.00 3.18
4406 5658 3.443681 ACAGTTTTGTGTCTTGGTCTTGG 59.556 43.478 0.00 0.00 35.83 3.61
4417 5669 2.099141 TGGTCTTGGAAGCATTCTCG 57.901 50.000 0.00 0.00 46.56 4.04
4421 5673 0.649475 CTTGGAAGCATTCTCGCTCG 59.351 55.000 0.00 0.00 46.56 5.03
4482 5734 2.476619 ACTCTGCACGAGAAATGAAACG 59.523 45.455 16.81 0.00 42.62 3.60
4490 5742 6.077838 GCACGAGAAATGAAACGAATTAAGT 58.922 36.000 0.00 0.00 0.00 2.24
4557 6071 7.751732 TCTGTCATTCGAAACCATAAAGAATG 58.248 34.615 0.00 9.43 45.48 2.67
4583 6097 7.308435 CCAGAACCAGAAACAAAGATCATTAC 58.692 38.462 0.00 0.00 0.00 1.89
4584 6098 7.040478 CCAGAACCAGAAACAAAGATCATTACA 60.040 37.037 0.00 0.00 0.00 2.41
4586 6100 9.082313 AGAACCAGAAACAAAGATCATTACAAT 57.918 29.630 0.00 0.00 0.00 2.71
4588 6102 9.696917 AACCAGAAACAAAGATCATTACAATTC 57.303 29.630 0.00 0.00 0.00 2.17
4635 6151 7.698836 AAAAATGAAGTGTTCACATTGCTAC 57.301 32.000 5.74 0.00 43.48 3.58
4660 6176 9.060347 ACGATGATAATATTTCATTGCAAGACT 57.940 29.630 18.29 0.00 38.17 3.24
4739 6256 3.927555 ACACCCACATAGTGTTCCG 57.072 52.632 0.00 0.00 46.07 4.30
4744 6261 3.058501 CACCCACATAGTGTTCCGTTTTC 60.059 47.826 0.00 0.00 0.00 2.29
4746 6263 3.408634 CCACATAGTGTTCCGTTTTCCT 58.591 45.455 0.00 0.00 0.00 3.36
4747 6264 3.435671 CCACATAGTGTTCCGTTTTCCTC 59.564 47.826 0.00 0.00 0.00 3.71
4748 6265 4.315803 CACATAGTGTTCCGTTTTCCTCT 58.684 43.478 0.00 0.00 0.00 3.69
4749 6266 5.475719 CACATAGTGTTCCGTTTTCCTCTA 58.524 41.667 0.00 0.00 0.00 2.43
4750 6267 5.347907 CACATAGTGTTCCGTTTTCCTCTAC 59.652 44.000 0.00 0.00 0.00 2.59
4857 6378 4.635765 CGGGCTACTGAAGAAAATGATCAA 59.364 41.667 0.00 0.00 0.00 2.57
4858 6379 5.297776 CGGGCTACTGAAGAAAATGATCAAT 59.702 40.000 0.00 0.00 0.00 2.57
4880 6401 3.441922 TGCTTGAATAAATAGCGGCACAA 59.558 39.130 1.45 0.00 37.73 3.33
5080 6602 1.484653 CCAGGGTATTGATGACCACGA 59.515 52.381 0.00 0.00 38.86 4.35
5098 6620 3.127376 CACGATGCTCAAAACCATGATCA 59.873 43.478 0.00 0.00 30.81 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.736719 CGTTGGGCTCATCTGAGTACTG 60.737 54.545 0.00 0.00 43.85 2.74
114 281 4.624452 AGCCAAACGTACGAAGAATAAGAC 59.376 41.667 24.41 0.56 0.00 3.01
122 289 6.793479 TTTTTAAAAGCCAAACGTACGAAG 57.207 33.333 24.41 10.64 0.00 3.79
209 378 7.065085 TGTCTTCGTACGTTCTAAGCTTAGTAT 59.935 37.037 28.31 16.48 32.61 2.12
218 415 3.119388 CCCCATGTCTTCGTACGTTCTAA 60.119 47.826 16.05 0.72 0.00 2.10
305 502 4.508976 ATGTCAACATCAACGGGACCGT 62.509 50.000 11.15 11.15 43.23 4.83
443 816 2.094494 ACGTGACTATCAGTCCAAGCAG 60.094 50.000 3.97 0.00 44.44 4.24
523 896 5.510430 TCATGCCTGATAGATACCGTATCT 58.490 41.667 21.87 21.87 46.67 1.98
553 926 4.736168 GCACAGCATTTTTGAACCTGTACA 60.736 41.667 0.00 0.00 35.20 2.90
589 962 0.886490 CTCATAGTGATTGCCCCGGC 60.886 60.000 0.00 0.00 42.35 6.13
654 1031 3.322541 TGGAGTAAACTTCCATGTCACGA 59.677 43.478 0.00 0.00 0.00 4.35
655 1032 3.659786 TGGAGTAAACTTCCATGTCACG 58.340 45.455 0.00 0.00 0.00 4.35
672 1049 7.014230 TGGTTTCTTGGAAAATTTAGACTGGAG 59.986 37.037 0.00 0.00 0.00 3.86
676 1053 9.546428 CATTTGGTTTCTTGGAAAATTTAGACT 57.454 29.630 0.00 0.00 0.00 3.24
720 1098 2.895426 TTCTCCTCCTCTCCGCTCCG 62.895 65.000 0.00 0.00 0.00 4.63
721 1099 0.684805 TTTCTCCTCCTCTCCGCTCC 60.685 60.000 0.00 0.00 0.00 4.70
722 1100 1.136110 CTTTTCTCCTCCTCTCCGCTC 59.864 57.143 0.00 0.00 0.00 5.03
723 1101 1.190643 CTTTTCTCCTCCTCTCCGCT 58.809 55.000 0.00 0.00 0.00 5.52
852 1253 3.437049 GGTGTCATTCTTTCCCTTCTTCG 59.563 47.826 0.00 0.00 0.00 3.79
901 1302 1.621622 GGCTAGGACTGGGGTTGTCTA 60.622 57.143 0.00 0.00 35.04 2.59
904 1305 1.151899 TGGCTAGGACTGGGGTTGT 60.152 57.895 0.00 0.00 0.00 3.32
938 1339 3.076092 CTGGCTGGGTCTGAGCTT 58.924 61.111 6.83 0.00 36.63 3.74
940 1341 4.792804 GGCTGGCTGGGTCTGAGC 62.793 72.222 0.00 0.00 35.57 4.26
1076 1484 0.450583 CGAAGCGCAGTAGAGTGGTA 59.549 55.000 11.47 0.00 0.00 3.25
1077 1485 1.213013 CGAAGCGCAGTAGAGTGGT 59.787 57.895 11.47 0.00 0.00 4.16
1078 1486 4.079090 CGAAGCGCAGTAGAGTGG 57.921 61.111 11.47 0.00 0.00 4.00
1097 1505 1.070786 AACCAAGAAGCGAGGCGAA 59.929 52.632 0.00 0.00 0.00 4.70
1144 1552 4.395542 ACGAAGTTATCTAGCTCAGACGTT 59.604 41.667 0.00 0.00 37.78 3.99
1145 1553 3.940221 ACGAAGTTATCTAGCTCAGACGT 59.060 43.478 0.00 0.00 37.78 4.34
1146 1554 4.201832 ACACGAAGTTATCTAGCTCAGACG 60.202 45.833 0.00 0.00 41.61 4.18
1178 1589 1.742761 ATCGCCACATGAAGTTGAGG 58.257 50.000 0.00 0.00 0.00 3.86
1214 1627 1.002251 CTCGCTCATTCCTACTCCGAC 60.002 57.143 0.00 0.00 0.00 4.79
1233 1646 5.981915 GCAGCAGAAGAAAAATCAAGAAACT 59.018 36.000 0.00 0.00 0.00 2.66
1234 1647 5.750067 TGCAGCAGAAGAAAAATCAAGAAAC 59.250 36.000 0.00 0.00 0.00 2.78
1303 1716 3.313012 GCCCAAAGCGGAAAACTAAAT 57.687 42.857 0.00 0.00 36.56 1.40
1329 1742 1.152881 CTAGTGGCCTTGGCCATCC 60.153 63.158 32.67 21.90 42.29 3.51
1431 1845 5.070823 AGATATCAATCCCACTGCCATTT 57.929 39.130 5.32 0.00 31.98 2.32
1459 1873 2.063266 CGCTGGTAAAACTCACGCTAA 58.937 47.619 0.00 0.00 0.00 3.09
1675 2089 0.250338 GGCTGTCAGTCCGGAAGTTT 60.250 55.000 5.23 0.00 0.00 2.66
1828 2242 0.251341 AGTCACCAACCAGCCATTCC 60.251 55.000 0.00 0.00 0.00 3.01
1844 2258 1.604278 GGAAGTGCAACAAGGTCAGTC 59.396 52.381 0.00 0.00 41.43 3.51
1892 2306 7.913674 TTTGCAGAAACAAATTAAAACCACT 57.086 28.000 0.00 0.00 34.68 4.00
1954 2369 2.092158 TCACAAGATTGGGGTGTGACAA 60.092 45.455 1.74 0.00 45.02 3.18
1956 2371 2.270352 TCACAAGATTGGGGTGTGAC 57.730 50.000 1.74 0.00 45.02 3.67
2016 2431 2.951457 TCGGCATGAATTCGTAGACA 57.049 45.000 0.00 0.00 34.32 3.41
2081 2496 7.854422 CACAATGAGCATATCACACAAGATAAC 59.146 37.037 0.00 0.00 41.91 1.89
2113 2528 1.795872 CAACAGCACGAATGGAACGTA 59.204 47.619 0.00 0.00 42.07 3.57
2115 2530 0.110238 CCAACAGCACGAATGGAACG 60.110 55.000 0.00 0.00 34.82 3.95
2158 2581 1.153745 GTGGAGCTCCTGCAGTACG 60.154 63.158 32.28 1.22 42.74 3.67
2190 2613 5.505780 ACCTTCATCCGTAAATTCCATGAA 58.494 37.500 0.00 0.00 33.48 2.57
2226 2649 2.282462 AAAGCAAGTCCCCTGGCG 60.282 61.111 0.00 0.00 42.94 5.69
2253 2676 7.231925 TCACGGTATATAACTTTAGCCTCATCA 59.768 37.037 0.00 0.00 0.00 3.07
2259 2682 8.597662 TGAAATCACGGTATATAACTTTAGCC 57.402 34.615 0.00 0.00 0.00 3.93
2292 2715 4.562757 CCCACCGAGTCAAGAAGAACATTA 60.563 45.833 0.00 0.00 0.00 1.90
2341 2766 4.093556 GCTCATTGTACTTCCACTTAGTGC 59.906 45.833 6.88 0.00 31.34 4.40
2351 2776 4.464069 AGACCAGAGCTCATTGTACTTC 57.536 45.455 17.77 0.58 0.00 3.01
2387 2812 5.305585 TGTATGGAGTCAAAGAAGGACAAC 58.694 41.667 0.00 0.00 37.74 3.32
2404 2829 9.071276 AGAGTTTTGCATTATATTCCTGTATGG 57.929 33.333 0.00 0.00 37.10 2.74
2640 3065 3.911868 TCATTTGCCCTTTTCATGAACG 58.088 40.909 7.89 2.24 0.00 3.95
2722 3149 3.340814 AGGTCCAGTACAAGAGCAATG 57.659 47.619 14.40 0.00 32.93 2.82
2723 3150 4.373156 AAAGGTCCAGTACAAGAGCAAT 57.627 40.909 14.40 3.15 32.93 3.56
2724 3151 3.857157 AAAGGTCCAGTACAAGAGCAA 57.143 42.857 14.40 0.00 32.93 3.91
2725 3152 3.476552 CAAAAGGTCCAGTACAAGAGCA 58.523 45.455 14.40 0.00 32.93 4.26
2726 3153 2.814336 CCAAAAGGTCCAGTACAAGAGC 59.186 50.000 6.31 6.31 0.00 4.09
2727 3154 4.065789 GACCAAAAGGTCCAGTACAAGAG 58.934 47.826 3.27 0.00 33.21 2.85
2728 3155 3.714798 AGACCAAAAGGTCCAGTACAAGA 59.285 43.478 10.84 0.00 39.49 3.02
2729 3156 4.065789 GAGACCAAAAGGTCCAGTACAAG 58.934 47.826 10.84 0.00 39.49 3.16
2730 3157 3.181448 GGAGACCAAAAGGTCCAGTACAA 60.181 47.826 10.84 0.00 39.49 2.41
2731 3158 2.370849 GGAGACCAAAAGGTCCAGTACA 59.629 50.000 10.84 0.00 39.49 2.90
2732 3159 2.370849 TGGAGACCAAAAGGTCCAGTAC 59.629 50.000 10.84 0.00 39.49 2.73
2733 3160 2.696775 TGGAGACCAAAAGGTCCAGTA 58.303 47.619 10.84 0.00 39.49 2.74
2734 3161 1.518367 TGGAGACCAAAAGGTCCAGT 58.482 50.000 10.84 0.00 39.49 4.00
2736 3163 0.771127 CCTGGAGACCAAAAGGTCCA 59.229 55.000 10.84 3.31 39.49 4.02
2737 3164 0.609406 GCCTGGAGACCAAAAGGTCC 60.609 60.000 10.84 3.34 39.49 4.46
2738 3165 0.402121 AGCCTGGAGACCAAAAGGTC 59.598 55.000 6.55 6.55 39.01 3.85
2739 3166 0.402121 GAGCCTGGAGACCAAAAGGT 59.598 55.000 0.00 0.00 30.80 3.50
2740 3167 0.401738 TGAGCCTGGAGACCAAAAGG 59.598 55.000 0.00 0.00 30.80 3.11
2741 3168 2.089980 CATGAGCCTGGAGACCAAAAG 58.910 52.381 0.00 0.00 30.80 2.27
2742 3169 1.887956 GCATGAGCCTGGAGACCAAAA 60.888 52.381 0.00 0.00 30.80 2.44
2743 3170 0.322816 GCATGAGCCTGGAGACCAAA 60.323 55.000 0.00 0.00 30.80 3.28
2744 3171 1.300963 GCATGAGCCTGGAGACCAA 59.699 57.895 0.00 0.00 30.80 3.67
2745 3172 2.993008 GCATGAGCCTGGAGACCA 59.007 61.111 0.00 0.00 33.58 4.02
2755 3182 8.025445 CCTTATATATTTCAAACAGGCATGAGC 58.975 37.037 4.84 0.00 41.10 4.26
2756 3183 9.071276 ACCTTATATATTTCAAACAGGCATGAG 57.929 33.333 4.84 0.00 0.00 2.90
2757 3184 8.995027 ACCTTATATATTTCAAACAGGCATGA 57.005 30.769 4.84 0.00 0.00 3.07
2760 3187 9.778741 CTCTACCTTATATATTTCAAACAGGCA 57.221 33.333 0.00 0.00 0.00 4.75
2761 3188 9.998106 TCTCTACCTTATATATTTCAAACAGGC 57.002 33.333 0.00 0.00 0.00 4.85
2832 3259 1.005394 GCAACTTGCCAGCAATGCT 60.005 52.632 18.91 0.00 38.30 3.79
2833 3260 1.289109 CTGCAACTTGCCAGCAATGC 61.289 55.000 19.22 19.22 44.23 3.56
2948 3377 9.014297 AGTTGGTTATGTCTCTTAAAAAGGATG 57.986 33.333 0.00 0.00 0.00 3.51
3026 3455 1.089920 AAGGCGCATCTAAGCACAAG 58.910 50.000 10.83 0.00 34.54 3.16
3072 3501 8.710239 TGATTATTTTATACACCCTCACTGCTA 58.290 33.333 0.00 0.00 0.00 3.49
3140 3569 2.936919 TGGACTGTTCAGACATGCTT 57.063 45.000 6.83 0.00 34.72 3.91
3155 3584 6.128007 ACACCAATCGTCAATCTAAAATGGAC 60.128 38.462 0.00 0.00 0.00 4.02
3177 3606 4.445452 AGGCATCACATGAATGAAACAC 57.555 40.909 14.36 0.24 30.82 3.32
3185 3614 5.939447 TGGTAATCATAGGCATCACATGAA 58.061 37.500 0.00 0.00 32.73 2.57
3215 3644 5.538433 TCCCCGACAATCTTTTGAGATTTTT 59.462 36.000 0.00 0.00 36.48 1.94
3223 3652 3.696051 ACATCATCCCCGACAATCTTTTG 59.304 43.478 0.00 0.00 38.86 2.44
3232 3661 2.548067 GGTGTCATACATCATCCCCGAC 60.548 54.545 0.00 0.00 0.00 4.79
3233 3662 1.691976 GGTGTCATACATCATCCCCGA 59.308 52.381 0.00 0.00 0.00 5.14
3234 3663 1.270839 GGGTGTCATACATCATCCCCG 60.271 57.143 0.00 0.00 28.66 5.73
3268 3699 0.111061 TGATGGCTTGCCTCAGTGTT 59.889 50.000 13.18 0.00 0.00 3.32
3269 3700 0.330604 ATGATGGCTTGCCTCAGTGT 59.669 50.000 13.18 0.00 0.00 3.55
3270 3701 0.738975 CATGATGGCTTGCCTCAGTG 59.261 55.000 13.18 9.72 0.00 3.66
3271 3702 1.035932 GCATGATGGCTTGCCTCAGT 61.036 55.000 13.18 0.00 38.77 3.41
3272 3703 0.752009 AGCATGATGGCTTGCCTCAG 60.752 55.000 13.18 8.77 42.71 3.35
3307 3738 3.189702 GCGTGGAAAGCATAAAGTACCAA 59.810 43.478 0.00 0.00 42.41 3.67
3308 3739 2.745281 GCGTGGAAAGCATAAAGTACCA 59.255 45.455 0.00 0.00 42.41 3.25
3334 3765 9.492973 CATCCTTTTTCCACAATAATCTGTTTT 57.507 29.630 0.00 0.00 0.00 2.43
3335 3766 8.869109 TCATCCTTTTTCCACAATAATCTGTTT 58.131 29.630 0.00 0.00 0.00 2.83
3336 3767 8.306761 GTCATCCTTTTTCCACAATAATCTGTT 58.693 33.333 0.00 0.00 0.00 3.16
3337 3768 7.671398 AGTCATCCTTTTTCCACAATAATCTGT 59.329 33.333 0.00 0.00 0.00 3.41
3338 3769 8.059798 AGTCATCCTTTTTCCACAATAATCTG 57.940 34.615 0.00 0.00 0.00 2.90
3339 3770 8.526147 CAAGTCATCCTTTTTCCACAATAATCT 58.474 33.333 0.00 0.00 0.00 2.40
3340 3771 8.522830 TCAAGTCATCCTTTTTCCACAATAATC 58.477 33.333 0.00 0.00 0.00 1.75
3341 3772 8.421249 TCAAGTCATCCTTTTTCCACAATAAT 57.579 30.769 0.00 0.00 0.00 1.28
3342 3773 7.831691 TCAAGTCATCCTTTTTCCACAATAA 57.168 32.000 0.00 0.00 0.00 1.40
3343 3774 7.451255 ACATCAAGTCATCCTTTTTCCACAATA 59.549 33.333 0.00 0.00 0.00 1.90
3344 3775 6.268387 ACATCAAGTCATCCTTTTTCCACAAT 59.732 34.615 0.00 0.00 0.00 2.71
3345 3776 5.598005 ACATCAAGTCATCCTTTTTCCACAA 59.402 36.000 0.00 0.00 0.00 3.33
3346 3777 5.009911 CACATCAAGTCATCCTTTTTCCACA 59.990 40.000 0.00 0.00 0.00 4.17
3347 3778 5.464168 CACATCAAGTCATCCTTTTTCCAC 58.536 41.667 0.00 0.00 0.00 4.02
3348 3779 4.523943 CCACATCAAGTCATCCTTTTTCCA 59.476 41.667 0.00 0.00 0.00 3.53
3349 3780 4.766891 TCCACATCAAGTCATCCTTTTTCC 59.233 41.667 0.00 0.00 0.00 3.13
3350 3781 5.964958 TCCACATCAAGTCATCCTTTTTC 57.035 39.130 0.00 0.00 0.00 2.29
3351 3782 6.729690 TTTCCACATCAAGTCATCCTTTTT 57.270 33.333 0.00 0.00 0.00 1.94
3352 3783 6.729690 TTTTCCACATCAAGTCATCCTTTT 57.270 33.333 0.00 0.00 0.00 2.27
3353 3784 6.239402 CCTTTTTCCACATCAAGTCATCCTTT 60.239 38.462 0.00 0.00 0.00 3.11
3354 3785 5.244626 CCTTTTTCCACATCAAGTCATCCTT 59.755 40.000 0.00 0.00 0.00 3.36
3355 3786 4.768968 CCTTTTTCCACATCAAGTCATCCT 59.231 41.667 0.00 0.00 0.00 3.24
3356 3787 4.766891 TCCTTTTTCCACATCAAGTCATCC 59.233 41.667 0.00 0.00 0.00 3.51
3357 3788 5.964958 TCCTTTTTCCACATCAAGTCATC 57.035 39.130 0.00 0.00 0.00 2.92
3358 3789 6.012113 TCATCCTTTTTCCACATCAAGTCAT 58.988 36.000 0.00 0.00 0.00 3.06
3359 3790 5.241506 GTCATCCTTTTTCCACATCAAGTCA 59.758 40.000 0.00 0.00 0.00 3.41
3360 3791 5.474876 AGTCATCCTTTTTCCACATCAAGTC 59.525 40.000 0.00 0.00 0.00 3.01
3361 3792 5.388654 AGTCATCCTTTTTCCACATCAAGT 58.611 37.500 0.00 0.00 0.00 3.16
3362 3793 5.972107 AGTCATCCTTTTTCCACATCAAG 57.028 39.130 0.00 0.00 0.00 3.02
3363 3794 6.778821 TCTAGTCATCCTTTTTCCACATCAA 58.221 36.000 0.00 0.00 0.00 2.57
3364 3795 6.373005 TCTAGTCATCCTTTTTCCACATCA 57.627 37.500 0.00 0.00 0.00 3.07
3365 3796 8.207545 AGTATCTAGTCATCCTTTTTCCACATC 58.792 37.037 0.00 0.00 0.00 3.06
3366 3797 8.095452 AGTATCTAGTCATCCTTTTTCCACAT 57.905 34.615 0.00 0.00 0.00 3.21
3367 3798 7.180229 TGAGTATCTAGTCATCCTTTTTCCACA 59.820 37.037 0.00 0.00 34.92 4.17
3374 3805 5.304101 CCAGCTGAGTATCTAGTCATCCTTT 59.696 44.000 17.39 0.00 35.30 3.11
3406 3837 9.643693 AATAATCTGATTTTTAGGCAGTTTGTG 57.356 29.630 8.38 0.00 0.00 3.33
3407 3838 9.643693 CAATAATCTGATTTTTAGGCAGTTTGT 57.356 29.630 8.38 0.00 0.00 2.83
3408 3839 9.643693 ACAATAATCTGATTTTTAGGCAGTTTG 57.356 29.630 8.38 0.00 0.00 2.93
3409 3840 9.643693 CACAATAATCTGATTTTTAGGCAGTTT 57.356 29.630 8.38 0.00 0.00 2.66
3410 3841 8.253113 CCACAATAATCTGATTTTTAGGCAGTT 58.747 33.333 8.38 0.00 0.00 3.16
3411 3842 7.397192 ACCACAATAATCTGATTTTTAGGCAGT 59.603 33.333 8.38 0.00 0.00 4.40
3412 3843 7.775120 ACCACAATAATCTGATTTTTAGGCAG 58.225 34.615 8.38 0.00 0.00 4.85
3413 3844 7.716799 ACCACAATAATCTGATTTTTAGGCA 57.283 32.000 8.38 0.00 0.00 4.75
3414 3845 9.736023 CTAACCACAATAATCTGATTTTTAGGC 57.264 33.333 8.38 0.00 0.00 3.93
3423 3854 9.787435 AGTGTTTAACTAACCACAATAATCTGA 57.213 29.630 0.00 0.00 37.36 3.27
3430 3861 9.181061 AGTGTTAAGTGTTTAACTAACCACAAT 57.819 29.630 10.45 0.00 45.71 2.71
3431 3862 8.564509 AGTGTTAAGTGTTTAACTAACCACAA 57.435 30.769 10.45 0.00 45.71 3.33
3432 3863 9.097257 GTAGTGTTAAGTGTTTAACTAACCACA 57.903 33.333 10.45 0.00 45.71 4.17
3433 3864 8.268738 CGTAGTGTTAAGTGTTTAACTAACCAC 58.731 37.037 10.45 0.00 45.71 4.16
3546 4606 7.442969 TCGTCATTGACTTTTTACCATTACAGT 59.557 33.333 14.54 0.00 0.00 3.55
3606 4828 8.573885 AGATGTAACTATGCAAATCATCATTGG 58.426 33.333 14.81 0.00 36.63 3.16
3718 4967 6.734137 TCATTGACTTTCACCATTACAACAC 58.266 36.000 0.00 0.00 0.00 3.32
4097 5346 4.651778 TGTATGTTTTCTTCACCTCTGGG 58.348 43.478 0.00 0.00 38.88 4.45
4100 5349 7.162082 CCTACTTGTATGTTTTCTTCACCTCT 58.838 38.462 0.00 0.00 0.00 3.69
4172 5421 2.615912 GCTTACAAGGAGTGGATGATGC 59.384 50.000 0.00 0.00 0.00 3.91
4173 5422 3.877559 TGCTTACAAGGAGTGGATGATG 58.122 45.455 0.00 0.00 0.00 3.07
4174 5423 4.263462 TGTTGCTTACAAGGAGTGGATGAT 60.263 41.667 0.00 0.00 36.16 2.45
4175 5424 3.072330 TGTTGCTTACAAGGAGTGGATGA 59.928 43.478 0.00 0.00 36.16 2.92
4176 5425 3.189287 GTGTTGCTTACAAGGAGTGGATG 59.811 47.826 0.00 0.00 38.80 3.51
4177 5426 3.073062 AGTGTTGCTTACAAGGAGTGGAT 59.927 43.478 0.00 0.00 38.80 3.41
4178 5427 2.438021 AGTGTTGCTTACAAGGAGTGGA 59.562 45.455 0.00 0.00 38.80 4.02
4179 5428 2.851195 AGTGTTGCTTACAAGGAGTGG 58.149 47.619 0.00 0.00 38.80 4.00
4180 5429 3.876914 TGAAGTGTTGCTTACAAGGAGTG 59.123 43.478 0.00 0.00 38.80 3.51
4221 5470 1.153289 CCCTCAAGTCCGGCATCTG 60.153 63.158 0.00 0.00 0.00 2.90
4282 5531 1.560923 CTAGCTGTACACATGGCGAC 58.439 55.000 0.00 0.00 0.00 5.19
4417 5669 2.703409 CATTAGCACGCACCGAGC 59.297 61.111 0.00 0.00 43.14 5.03
4421 5673 0.740868 TCTCAGCATTAGCACGCACC 60.741 55.000 0.00 0.00 45.49 5.01
4454 5706 1.160989 TCTCGTGCAGAGTGAGAGTC 58.839 55.000 11.37 0.00 46.86 3.36
4460 5712 3.662713 CGTTTCATTTCTCGTGCAGAGTG 60.663 47.826 11.37 5.12 46.86 3.51
4482 5734 7.136772 AGGCGACAAACTAACAAACTTAATTC 58.863 34.615 0.00 0.00 0.00 2.17
4490 5742 4.260866 GCACTAAGGCGACAAACTAACAAA 60.261 41.667 0.00 0.00 0.00 2.83
4557 6071 3.569701 TGATCTTTGTTTCTGGTTCTGGC 59.430 43.478 0.00 0.00 0.00 4.85
4616 6132 3.723260 TCGTAGCAATGTGAACACTTCA 58.277 40.909 6.51 0.00 37.33 3.02
4620 6136 4.864916 ATCATCGTAGCAATGTGAACAC 57.135 40.909 0.00 0.00 0.00 3.32
4634 6150 9.060347 AGTCTTGCAATGAAATATTATCATCGT 57.940 29.630 0.00 0.00 36.53 3.73
4635 6151 9.888878 AAGTCTTGCAATGAAATATTATCATCG 57.111 29.630 0.00 4.77 36.53 3.84
4660 6176 4.905429 TGGCTTATCTGCTGTTAACTCAA 58.095 39.130 7.22 0.00 0.00 3.02
4739 6256 7.605410 TTGGATTCGTAATGTAGAGGAAAAC 57.395 36.000 0.00 0.00 0.00 2.43
4744 6261 5.116180 TGCTTTGGATTCGTAATGTAGAGG 58.884 41.667 0.00 0.00 0.00 3.69
4746 6263 5.935206 TGTTGCTTTGGATTCGTAATGTAGA 59.065 36.000 0.00 0.00 0.00 2.59
4747 6264 6.021596 GTGTTGCTTTGGATTCGTAATGTAG 58.978 40.000 0.00 0.00 0.00 2.74
4748 6265 5.703592 AGTGTTGCTTTGGATTCGTAATGTA 59.296 36.000 0.00 0.00 0.00 2.29
4749 6266 4.518970 AGTGTTGCTTTGGATTCGTAATGT 59.481 37.500 0.00 0.00 0.00 2.71
4750 6267 4.853196 CAGTGTTGCTTTGGATTCGTAATG 59.147 41.667 0.00 0.00 0.00 1.90
4794 6315 2.094234 TCAACTCTTGCGCATGTAGCTA 60.094 45.455 21.14 0.00 42.61 3.32
4857 6378 3.631686 TGTGCCGCTATTTATTCAAGCAT 59.368 39.130 0.00 0.00 35.98 3.79
4858 6379 3.013219 TGTGCCGCTATTTATTCAAGCA 58.987 40.909 0.00 0.00 35.98 3.91
4880 6401 7.815549 ACACTTGTAAAACCTGTTTTTCGATTT 59.184 29.630 12.73 0.00 42.22 2.17
5080 6602 2.424601 CCGTGATCATGGTTTTGAGCAT 59.575 45.455 23.76 0.00 43.24 3.79


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

AutoCloner maintained by Alex Coulton.