Multiple sequence alignment - TraesCS4B01G141400

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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 TraesCS4B01G141400 chr4B 100.000 4031 0 0 1 4031 186593967 186589937 0.000000e+00 7444
1 TraesCS4B01G141400 chr4B 83.862 2144 272 46 998 3110 185911019 185908919 0.000000e+00 1975
2 TraesCS4B01G141400 chr4B 94.531 128 7 0 3102 3229 34580025 34580152 8.840000e-47 198
3 TraesCS4B01G141400 chr4B 70.136 1105 277 46 1948 3024 185222348 185221269 3.220000e-36 163
4 TraesCS4B01G141400 chr4D 93.408 2412 97 21 739 3116 122287683 122285300 0.000000e+00 3517
5 TraesCS4B01G141400 chr4D 83.947 2118 269 45 991 3076 122275090 122273012 0.000000e+00 1962
6 TraesCS4B01G141400 chr4D 92.237 438 17 11 3227 3655 122285303 122284874 4.460000e-169 604
7 TraesCS4B01G141400 chr4D 87.119 295 16 4 3749 4031 122284832 122284548 8.410000e-82 315
8 TraesCS4B01G141400 chr4D 70.428 1099 284 40 1948 3024 122170600 122169521 1.480000e-44 191
9 TraesCS4B01G141400 chr4D 93.204 103 6 1 560 662 122298184 122298083 2.510000e-32 150
10 TraesCS4B01G141400 chr4A 92.946 2424 115 27 696 3092 447791388 447793782 0.000000e+00 3478
11 TraesCS4B01G141400 chr4A 84.096 2119 263 45 992 3076 448092098 448094176 0.000000e+00 1978
12 TraesCS4B01G141400 chr4A 86.850 327 19 12 3675 3980 447794158 447794481 1.070000e-90 344
13 TraesCS4B01G141400 chr4A 70.824 922 227 38 2124 3024 448528358 448529258 1.490000e-39 174
14 TraesCS4B01G141400 chr4A 90.385 104 7 3 561 664 447791293 447791393 2.530000e-27 134
15 TraesCS4B01G141400 chr3D 88.628 554 55 6 1 547 467735072 467734520 0.000000e+00 667
16 TraesCS4B01G141400 chr3D 87.189 562 60 7 1 552 545795811 545796370 2.640000e-176 628
17 TraesCS4B01G141400 chr2A 88.909 541 51 9 1 533 5385388 5385927 0.000000e+00 658
18 TraesCS4B01G141400 chr2A 96.639 119 4 0 3113 3231 451004895 451004777 8.840000e-47 198
19 TraesCS4B01G141400 chr2A 96.639 119 4 0 3111 3229 613004708 613004590 8.840000e-47 198
20 TraesCS4B01G141400 chr7B 88.267 554 57 6 2 548 507226325 507226877 0.000000e+00 656
21 TraesCS4B01G141400 chr7B 95.868 121 5 0 3112 3232 92290917 92291037 3.180000e-46 196
22 TraesCS4B01G141400 chr3A 87.726 554 58 8 1 547 610341738 610341188 4.390000e-179 638
23 TraesCS4B01G141400 chr1D 87.189 562 59 6 1 549 383180253 383180814 9.510000e-176 627
24 TraesCS4B01G141400 chr5B 86.809 561 61 8 1 548 361013515 361014075 7.400000e-172 614
25 TraesCS4B01G141400 chr2D 86.106 547 57 10 1 533 194805872 194806413 4.520000e-159 571
26 TraesCS4B01G141400 chr1A 86.381 536 58 10 1 523 337814742 337815275 4.520000e-159 571
27 TraesCS4B01G141400 chr5A 93.893 131 5 3 3113 3241 39114815 39114686 1.140000e-45 195
28 TraesCS4B01G141400 chr5A 93.130 131 6 3 3113 3241 38997755 38997626 5.320000e-44 189
29 TraesCS4B01G141400 chr3B 96.581 117 4 0 3114 3230 173375685 173375801 1.140000e-45 195
30 TraesCS4B01G141400 chr7D 93.023 129 9 0 3111 3239 55371554 55371426 5.320000e-44 189
31 TraesCS4B01G141400 chr7A 92.308 130 10 0 3110 3239 481189954 481190083 6.880000e-43 185


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 TraesCS4B01G141400 chr4B 186589937 186593967 4030 True 7444.000000 7444 100.000000 1 4031 1 chr4B.!!$R3 4030
1 TraesCS4B01G141400 chr4B 185908919 185911019 2100 True 1975.000000 1975 83.862000 998 3110 1 chr4B.!!$R2 2112
2 TraesCS4B01G141400 chr4D 122273012 122275090 2078 True 1962.000000 1962 83.947000 991 3076 1 chr4D.!!$R2 2085
3 TraesCS4B01G141400 chr4D 122284548 122287683 3135 True 1478.666667 3517 90.921333 739 4031 3 chr4D.!!$R4 3292
4 TraesCS4B01G141400 chr4A 448092098 448094176 2078 False 1978.000000 1978 84.096000 992 3076 1 chr4A.!!$F1 2084
5 TraesCS4B01G141400 chr4A 447791293 447794481 3188 False 1318.666667 3478 90.060333 561 3980 3 chr4A.!!$F3 3419
6 TraesCS4B01G141400 chr3D 467734520 467735072 552 True 667.000000 667 88.628000 1 547 1 chr3D.!!$R1 546
7 TraesCS4B01G141400 chr3D 545795811 545796370 559 False 628.000000 628 87.189000 1 552 1 chr3D.!!$F1 551
8 TraesCS4B01G141400 chr2A 5385388 5385927 539 False 658.000000 658 88.909000 1 533 1 chr2A.!!$F1 532
9 TraesCS4B01G141400 chr7B 507226325 507226877 552 False 656.000000 656 88.267000 2 548 1 chr7B.!!$F2 546
10 TraesCS4B01G141400 chr3A 610341188 610341738 550 True 638.000000 638 87.726000 1 547 1 chr3A.!!$R1 546
11 TraesCS4B01G141400 chr1D 383180253 383180814 561 False 627.000000 627 87.189000 1 549 1 chr1D.!!$F1 548
12 TraesCS4B01G141400 chr5B 361013515 361014075 560 False 614.000000 614 86.809000 1 548 1 chr5B.!!$F1 547
13 TraesCS4B01G141400 chr2D 194805872 194806413 541 False 571.000000 571 86.106000 1 533 1 chr2D.!!$F1 532
14 TraesCS4B01G141400 chr1A 337814742 337815275 533 False 571.000000 571 86.381000 1 523 1 chr1A.!!$F1 522

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
253 258 0.234625 TTTCATCGTGAGTTGCGTGC 59.765 50.0 0.0 0.0 0.00 5.34 F
1832 1932 0.605589 AACGGTGAGCCAGAGAAGAG 59.394 55.0 0.0 0.0 34.09 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 1962 0.100682 CTCACTATCGTCCACGGTGG 59.899 60.0 21.27 21.27 40.29 4.61 R
3206 3311 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 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
133 134 8.223177 TGTGATCATGCACAATATGATTGTTA 57.777 30.769 0.00 0.00 45.08 2.41
173 178 6.933514 ATGTATGACCAAGGGTTTGATTTT 57.066 33.333 0.00 0.00 35.25 1.82
192 197 4.437682 TTTCAGGGTGAGAATGTTGAGT 57.562 40.909 0.00 0.00 0.00 3.41
196 201 1.676014 GGGTGAGAATGTTGAGTCGGG 60.676 57.143 0.00 0.00 0.00 5.14
253 258 0.234625 TTTCATCGTGAGTTGCGTGC 59.765 50.000 0.00 0.00 0.00 5.34
324 329 4.021719 GGGATCACATTGGCAATCAATAGG 60.022 45.833 10.36 0.30 43.70 2.57
364 372 4.190001 TCCGTGTGCACAAACTTTAAGTA 58.810 39.130 23.59 0.00 0.00 2.24
468 483 7.796958 AACTATTTTTGCTATGCTTCGTTTC 57.203 32.000 0.00 0.00 0.00 2.78
549 565 1.399984 GGCCAACGCAAATGCAAATTG 60.400 47.619 0.00 10.38 42.21 2.32
551 567 2.141517 CCAACGCAAATGCAAATTGGA 58.858 42.857 20.29 0.00 44.44 3.53
552 568 2.158058 CCAACGCAAATGCAAATTGGAG 59.842 45.455 20.29 0.00 44.44 3.86
553 569 2.801679 CAACGCAAATGCAAATTGGAGT 59.198 40.909 15.03 0.00 42.21 3.85
554 570 3.110447 ACGCAAATGCAAATTGGAGTT 57.890 38.095 15.03 0.00 42.21 3.01
555 571 2.801679 ACGCAAATGCAAATTGGAGTTG 59.198 40.909 20.28 20.28 44.56 3.16
556 572 2.158058 CGCAAATGCAAATTGGAGTTGG 59.842 45.455 24.23 13.40 42.57 3.77
557 573 2.095617 GCAAATGCAAATTGGAGTTGGC 60.096 45.455 24.23 14.97 42.57 4.52
558 574 2.477845 AATGCAAATTGGAGTTGGCC 57.522 45.000 0.00 0.00 0.00 5.36
559 575 1.648116 ATGCAAATTGGAGTTGGCCT 58.352 45.000 3.32 0.00 0.00 5.19
560 576 0.968405 TGCAAATTGGAGTTGGCCTC 59.032 50.000 3.32 0.00 39.67 4.70
561 577 0.968405 GCAAATTGGAGTTGGCCTCA 59.032 50.000 3.32 0.00 42.40 3.86
562 578 1.551883 GCAAATTGGAGTTGGCCTCAT 59.448 47.619 3.32 0.00 42.40 2.90
563 579 2.675889 GCAAATTGGAGTTGGCCTCATG 60.676 50.000 3.32 0.00 42.40 3.07
564 580 1.856629 AATTGGAGTTGGCCTCATGG 58.143 50.000 3.32 0.00 42.40 3.66
565 581 0.706433 ATTGGAGTTGGCCTCATGGT 59.294 50.000 3.32 0.00 42.40 3.55
591 607 2.420022 AGCATATGCAACCGAGTCAAAC 59.580 45.455 28.62 0.00 45.16 2.93
620 636 2.749621 GCTACCTCCCAACAGAATTGTG 59.250 50.000 0.13 0.13 37.67 3.33
621 637 3.810743 GCTACCTCCCAACAGAATTGTGT 60.811 47.826 1.68 1.68 37.67 3.72
624 640 3.636764 ACCTCCCAACAGAATTGTGTTTC 59.363 43.478 17.63 0.00 38.65 2.78
625 641 3.891366 CCTCCCAACAGAATTGTGTTTCT 59.109 43.478 17.63 0.00 38.65 2.52
626 642 4.342092 CCTCCCAACAGAATTGTGTTTCTT 59.658 41.667 17.63 0.00 38.65 2.52
627 643 5.507985 CCTCCCAACAGAATTGTGTTTCTTC 60.508 44.000 17.63 0.00 38.65 2.87
628 644 4.952957 TCCCAACAGAATTGTGTTTCTTCA 59.047 37.500 17.63 0.00 38.65 3.02
644 660 6.712095 TGTTTCTTCAGAGTATGCATTTGAGT 59.288 34.615 3.54 0.00 0.00 3.41
664 680 6.753180 TGAGTCTGGATGCAAAGATAGATAC 58.247 40.000 0.00 0.00 0.00 2.24
665 681 6.552725 TGAGTCTGGATGCAAAGATAGATACT 59.447 38.462 0.00 0.00 0.00 2.12
666 682 7.725844 TGAGTCTGGATGCAAAGATAGATACTA 59.274 37.037 0.00 0.00 0.00 1.82
667 683 8.121305 AGTCTGGATGCAAAGATAGATACTAG 57.879 38.462 0.00 0.00 0.00 2.57
668 684 7.947332 AGTCTGGATGCAAAGATAGATACTAGA 59.053 37.037 0.00 0.00 0.00 2.43
669 685 8.748412 GTCTGGATGCAAAGATAGATACTAGAT 58.252 37.037 0.00 0.00 0.00 1.98
670 686 9.981460 TCTGGATGCAAAGATAGATACTAGATA 57.019 33.333 0.00 0.00 0.00 1.98
685 701 9.760926 AGATACTAGATATAGTCTGGATGCAAA 57.239 33.333 2.64 0.00 37.62 3.68
687 703 9.760926 ATACTAGATATAGTCTGGATGCAAAGA 57.239 33.333 2.64 0.00 37.62 2.52
688 704 8.663209 ACTAGATATAGTCTGGATGCAAAGAT 57.337 34.615 0.00 0.00 37.62 2.40
689 705 9.760926 ACTAGATATAGTCTGGATGCAAAGATA 57.239 33.333 0.00 0.00 37.62 1.98
691 707 8.891985 AGATATAGTCTGGATGCAAAGATAGA 57.108 34.615 0.00 0.00 35.31 1.98
692 708 9.491406 AGATATAGTCTGGATGCAAAGATAGAT 57.509 33.333 0.00 0.00 35.31 1.98
695 711 6.992664 AGTCTGGATGCAAAGATAGATACT 57.007 37.500 0.00 0.00 0.00 2.12
696 712 9.760926 ATAGTCTGGATGCAAAGATAGATACTA 57.239 33.333 0.00 0.00 0.00 1.82
697 713 8.121305 AGTCTGGATGCAAAGATAGATACTAG 57.879 38.462 0.00 0.00 0.00 2.57
698 714 7.947332 AGTCTGGATGCAAAGATAGATACTAGA 59.053 37.037 0.00 0.00 0.00 2.43
699 715 8.748412 GTCTGGATGCAAAGATAGATACTAGAT 58.252 37.037 0.00 0.00 0.00 1.98
700 716 9.981460 TCTGGATGCAAAGATAGATACTAGATA 57.019 33.333 0.00 0.00 0.00 1.98
821 841 2.234414 GGGCCAGCTTCATTCATTTTGA 59.766 45.455 4.39 0.00 0.00 2.69
844 864 2.169561 GTCCTCCTCCTCCATTTCTCAC 59.830 54.545 0.00 0.00 0.00 3.51
849 869 2.776536 CCTCCTCCATTTCTCACCTCAT 59.223 50.000 0.00 0.00 0.00 2.90
879 908 3.742730 GGAACCTTCCCTCCTCCC 58.257 66.667 0.00 0.00 41.62 4.30
890 919 3.092511 TCCTCCCTGCCCATGCTC 61.093 66.667 0.00 0.00 38.71 4.26
903 932 1.133262 CCATGCTCCCATTCCATCCTT 60.133 52.381 0.00 0.00 0.00 3.36
914 943 6.212589 TCCCATTCCATCCTTTCCTTTTAAAC 59.787 38.462 0.00 0.00 0.00 2.01
917 947 6.664428 TTCCATCCTTTCCTTTTAAACAGG 57.336 37.500 9.08 9.08 0.00 4.00
934 964 2.335712 GGAGAAAAGCAGCGGGGTG 61.336 63.158 0.00 0.00 0.00 4.61
935 965 1.302511 GAGAAAAGCAGCGGGGTGA 60.303 57.895 1.43 0.00 0.00 4.02
936 966 0.678048 GAGAAAAGCAGCGGGGTGAT 60.678 55.000 1.43 0.00 0.00 3.06
937 967 0.962356 AGAAAAGCAGCGGGGTGATG 60.962 55.000 1.43 0.00 36.94 3.07
949 979 2.496942 GGTGATGCCCTTCCATGTG 58.503 57.895 0.00 0.00 0.00 3.21
961 991 2.039974 CCATGTGCAACGCAGCCTA 61.040 57.895 0.00 0.00 42.39 3.93
983 1024 3.383185 AGATAGCTACTCCAGTGTCAAGC 59.617 47.826 0.00 0.00 0.00 4.01
1360 1424 3.289834 CCAGCACCGCAACTGCTT 61.290 61.111 0.00 0.00 42.54 3.91
1361 1425 2.253452 CAGCACCGCAACTGCTTC 59.747 61.111 0.00 0.00 42.54 3.86
1362 1426 3.349006 AGCACCGCAACTGCTTCG 61.349 61.111 0.00 0.00 42.54 3.79
1364 1428 4.389576 CACCGCAACTGCTTCGGC 62.390 66.667 0.00 0.00 46.49 5.54
1414 1484 2.362503 TCCAGATCTCACGCCCGT 60.363 61.111 0.00 0.00 0.00 5.28
1425 1495 3.524606 CGCCCGTCCTACACCGAT 61.525 66.667 0.00 0.00 0.00 4.18
1461 1531 2.674754 GCCTCCCCGGACAATCAA 59.325 61.111 0.73 0.00 33.16 2.57
1498 1568 2.785258 GCGACGAGATGGCCAAAC 59.215 61.111 10.96 7.46 0.00 2.93
1685 1767 1.179174 AAGAAAAAGAGGGCCGCACC 61.179 55.000 10.70 0.00 37.93 5.01
1802 1893 3.582208 GAGATATGCATGAAGGGGACTCT 59.418 47.826 10.16 0.00 42.68 3.24
1803 1894 3.979347 AGATATGCATGAAGGGGACTCTT 59.021 43.478 10.16 0.00 42.68 2.85
1812 1903 1.650528 AGGGGACTCTTCAGAACCTG 58.349 55.000 0.00 0.00 32.90 4.00
1826 1926 1.837051 ACCTGAACGGTGAGCCAGA 60.837 57.895 0.00 0.00 46.80 3.86
1832 1932 0.605589 AACGGTGAGCCAGAGAAGAG 59.394 55.000 0.00 0.00 34.09 2.85
1861 1961 1.885163 GAAGGGCCGGTCGAGAAAGA 61.885 60.000 1.90 0.00 0.00 2.52
1862 1962 2.125633 GGGCCGGTCGAGAAAGAC 60.126 66.667 1.90 0.00 40.25 3.01
1872 1972 0.666577 CGAGAAAGACCACCGTGGAC 60.667 60.000 24.80 17.95 40.96 4.02
1923 2023 2.047465 CTCAACTGCGCTCAGGCT 60.047 61.111 9.73 0.00 44.54 4.58
1989 2089 4.115199 AGGCAGCATTCGTCCCCC 62.115 66.667 0.00 0.00 0.00 5.40
2193 2293 0.798776 CCGACAAGACCATCTGCAAC 59.201 55.000 0.00 0.00 0.00 4.17
2238 2338 3.244875 TGCACATTGTGGACTATGGTCTT 60.245 43.478 18.05 0.00 41.82 3.01
2247 2347 5.487488 TGTGGACTATGGTCTTAATCAAGGT 59.513 40.000 9.27 0.00 41.82 3.50
2259 2359 0.842030 ATCAAGGTCTCCAGTGGCCA 60.842 55.000 0.00 0.00 0.00 5.36
2268 2368 2.567497 CCAGTGGCCAGGTTTGCTG 61.567 63.158 5.11 8.98 0.00 4.41
2376 2476 1.194781 ACATTGAGGAGACAGGGCGT 61.195 55.000 0.00 0.00 0.00 5.68
2585 2685 3.855255 TCAGGTCCTCAACAACATCAA 57.145 42.857 0.00 0.00 0.00 2.57
2892 2992 1.806542 CCGTTGAATCCAGAGGTTGTG 59.193 52.381 0.00 0.00 0.00 3.33
2901 3001 1.876156 CCAGAGGTTGTGAAGCTTGTC 59.124 52.381 2.10 0.00 39.77 3.18
2907 3007 2.508526 GTTGTGAAGCTTGTCCTGGAT 58.491 47.619 2.10 0.00 0.00 3.41
3083 3188 5.828859 AGACATAGATAGATATACCCACGCC 59.171 44.000 0.00 0.00 0.00 5.68
3119 3224 5.595133 AGTAGCACTTATCTCTTGTACTCCC 59.405 44.000 0.00 0.00 0.00 4.30
3120 3225 3.381908 AGCACTTATCTCTTGTACTCCCG 59.618 47.826 0.00 0.00 0.00 5.14
3121 3226 3.707793 CACTTATCTCTTGTACTCCCGC 58.292 50.000 0.00 0.00 0.00 6.13
3122 3227 2.694109 ACTTATCTCTTGTACTCCCGCC 59.306 50.000 0.00 0.00 0.00 6.13
3123 3228 1.315690 TATCTCTTGTACTCCCGCCG 58.684 55.000 0.00 0.00 0.00 6.46
3124 3229 0.683504 ATCTCTTGTACTCCCGCCGT 60.684 55.000 0.00 0.00 0.00 5.68
3125 3230 1.139095 CTCTTGTACTCCCGCCGTC 59.861 63.158 0.00 0.00 0.00 4.79
3126 3231 2.183555 CTTGTACTCCCGCCGTCC 59.816 66.667 0.00 0.00 0.00 4.79
3127 3232 3.695022 CTTGTACTCCCGCCGTCCG 62.695 68.421 0.00 0.00 0.00 4.79
3136 3241 4.507879 CGCCGTCCGGAAATACTT 57.492 55.556 5.23 0.00 37.50 2.24
3137 3242 2.003672 CGCCGTCCGGAAATACTTG 58.996 57.895 5.23 0.00 37.50 3.16
3138 3243 0.738412 CGCCGTCCGGAAATACTTGT 60.738 55.000 5.23 0.00 37.50 3.16
3139 3244 1.004595 GCCGTCCGGAAATACTTGTC 58.995 55.000 5.23 0.00 37.50 3.18
3140 3245 1.648504 CCGTCCGGAAATACTTGTCC 58.351 55.000 5.23 0.00 37.50 4.02
3141 3246 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
3142 3247 2.537401 CGTCCGGAAATACTTGTCCTC 58.463 52.381 5.23 0.00 0.00 3.71
3143 3248 2.094390 CGTCCGGAAATACTTGTCCTCA 60.094 50.000 5.23 0.00 0.00 3.86
3144 3249 3.615592 CGTCCGGAAATACTTGTCCTCAA 60.616 47.826 5.23 0.00 0.00 3.02
3145 3250 4.320870 GTCCGGAAATACTTGTCCTCAAA 58.679 43.478 5.23 0.00 32.87 2.69
3146 3251 4.758165 GTCCGGAAATACTTGTCCTCAAAA 59.242 41.667 5.23 0.00 32.87 2.44
3147 3252 5.414765 GTCCGGAAATACTTGTCCTCAAAAT 59.585 40.000 5.23 0.00 32.87 1.82
3148 3253 5.414454 TCCGGAAATACTTGTCCTCAAAATG 59.586 40.000 0.00 0.00 32.87 2.32
3149 3254 5.393027 CCGGAAATACTTGTCCTCAAAATGG 60.393 44.000 0.00 0.00 32.87 3.16
3150 3255 5.414454 CGGAAATACTTGTCCTCAAAATGGA 59.586 40.000 0.00 0.00 32.87 3.41
3151 3256 6.095440 CGGAAATACTTGTCCTCAAAATGGAT 59.905 38.462 0.00 0.00 35.87 3.41
3152 3257 7.282224 CGGAAATACTTGTCCTCAAAATGGATA 59.718 37.037 0.00 0.00 35.87 2.59
3153 3258 8.966868 GGAAATACTTGTCCTCAAAATGGATAA 58.033 33.333 0.00 0.00 35.87 1.75
3158 3263 7.614494 ACTTGTCCTCAAAATGGATAAAATGG 58.386 34.615 0.00 0.00 34.98 3.16
3159 3264 7.454380 ACTTGTCCTCAAAATGGATAAAATGGA 59.546 33.333 0.00 0.00 34.98 3.41
3160 3265 7.976414 TGTCCTCAAAATGGATAAAATGGAT 57.024 32.000 0.00 0.00 35.87 3.41
3161 3266 7.784037 TGTCCTCAAAATGGATAAAATGGATG 58.216 34.615 0.00 0.00 35.87 3.51
3162 3267 7.399765 TGTCCTCAAAATGGATAAAATGGATGT 59.600 33.333 0.00 0.00 35.87 3.06
3163 3268 8.912988 GTCCTCAAAATGGATAAAATGGATGTA 58.087 33.333 0.00 0.00 35.87 2.29
3164 3269 9.659135 TCCTCAAAATGGATAAAATGGATGTAT 57.341 29.630 0.00 0.00 0.00 2.29
3165 3270 9.918630 CCTCAAAATGGATAAAATGGATGTATC 57.081 33.333 0.00 0.00 0.00 2.24
3201 3306 9.751542 AATAAGTCTAGATACAACCATTTCGAG 57.248 33.333 0.00 0.00 0.00 4.04
3202 3307 6.150396 AGTCTAGATACAACCATTTCGAGG 57.850 41.667 0.00 0.00 0.00 4.63
3203 3308 5.892119 AGTCTAGATACAACCATTTCGAGGA 59.108 40.000 0.00 0.00 0.00 3.71
3204 3309 5.978322 GTCTAGATACAACCATTTCGAGGAC 59.022 44.000 0.00 0.00 0.00 3.85
3205 3310 4.819105 AGATACAACCATTTCGAGGACA 57.181 40.909 0.00 0.00 0.00 4.02
3206 3311 5.160607 AGATACAACCATTTCGAGGACAA 57.839 39.130 0.00 0.00 0.00 3.18
3207 3312 5.178797 AGATACAACCATTTCGAGGACAAG 58.821 41.667 0.00 0.00 0.00 3.16
3208 3313 3.208747 ACAACCATTTCGAGGACAAGT 57.791 42.857 0.00 0.00 0.00 3.16
3209 3314 4.345859 ACAACCATTTCGAGGACAAGTA 57.654 40.909 0.00 0.00 0.00 2.24
3210 3315 4.906618 ACAACCATTTCGAGGACAAGTAT 58.093 39.130 0.00 0.00 0.00 2.12
3211 3316 5.313712 ACAACCATTTCGAGGACAAGTATT 58.686 37.500 0.00 0.00 0.00 1.89
3212 3317 5.768164 ACAACCATTTCGAGGACAAGTATTT 59.232 36.000 0.00 0.00 0.00 1.40
3213 3318 6.072673 ACAACCATTTCGAGGACAAGTATTTC 60.073 38.462 0.00 0.00 0.00 2.17
3214 3319 4.941873 ACCATTTCGAGGACAAGTATTTCC 59.058 41.667 0.00 0.00 0.00 3.13
3215 3320 4.034048 CCATTTCGAGGACAAGTATTTCCG 59.966 45.833 0.00 0.00 36.95 4.30
3216 3321 2.953466 TCGAGGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 36.95 5.14
3217 3322 2.449464 TCGAGGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 36.95 5.14
3218 3323 2.165030 TCGAGGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 36.95 4.79
3219 3324 2.537401 GAGGACAAGTATTTCCGGACG 58.463 52.381 1.83 0.00 36.95 4.79
3220 3325 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
3221 3326 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
3222 3327 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3223 3328 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3224 3329 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3225 3330 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3243 3348 3.421844 GGGAGTACCTGACAAGCAATTT 58.578 45.455 0.00 0.00 35.85 1.82
3278 3383 9.035607 ACATGCGTTAAATTGTTTATTTGTTGA 57.964 25.926 0.00 0.00 37.07 3.18
3317 3422 2.549754 TCTAAACTTCAGTTGCTGCTGC 59.450 45.455 8.89 8.89 38.44 5.25
3397 3503 5.376625 AGTTGAGCAATAAAGTTGGACTGA 58.623 37.500 0.00 0.00 0.00 3.41
3451 3559 5.546526 TGCTGTCTATGATTTGTGTGTGTA 58.453 37.500 0.00 0.00 0.00 2.90
3459 3575 6.801539 ATGATTTGTGTGTGTAGACGATTT 57.198 33.333 0.00 0.00 0.00 2.17
3483 3599 3.319122 AGATGTTTCCCACAAGTTTCAGC 59.681 43.478 0.00 0.00 39.50 4.26
3495 3612 6.369005 CACAAGTTTCAGCTTCTTGTAGATG 58.631 40.000 17.15 7.07 46.27 2.90
3514 3631 9.725019 TGTAGATGTAATTTTCTTCAGTGTCAT 57.275 29.630 0.00 0.00 0.00 3.06
3557 3674 4.609301 AGAAGAGGTCAGAAGATGCTACT 58.391 43.478 0.00 0.00 0.00 2.57
3558 3675 5.761205 AGAAGAGGTCAGAAGATGCTACTA 58.239 41.667 0.00 0.00 0.00 1.82
3559 3676 5.827797 AGAAGAGGTCAGAAGATGCTACTAG 59.172 44.000 0.00 0.00 0.00 2.57
3643 3760 9.755804 TTTCATGCAAGTTCAAACACATAAATA 57.244 25.926 0.00 0.00 0.00 1.40
3644 3761 9.755804 TTCATGCAAGTTCAAACACATAAATAA 57.244 25.926 0.00 0.00 0.00 1.40
3645 3762 9.755804 TCATGCAAGTTCAAACACATAAATAAA 57.244 25.926 0.00 0.00 0.00 1.40
3677 3794 4.417426 TTTTTGCGGGGGATAAACAAAA 57.583 36.364 0.00 0.00 38.16 2.44
3713 3830 4.202264 ACGATGACAAGTGGAAAGAAGTCT 60.202 41.667 0.00 0.00 0.00 3.24
3727 3844 8.840321 TGGAAAGAAGTCTATGAGTTCAAAAAG 58.160 33.333 14.95 0.00 42.52 2.27
3728 3845 9.057089 GGAAAGAAGTCTATGAGTTCAAAAAGA 57.943 33.333 14.95 0.00 42.52 2.52
3730 3847 9.838339 AAAGAAGTCTATGAGTTCAAAAAGAGA 57.162 29.630 14.95 0.00 42.52 3.10
3731 3848 9.487790 AAGAAGTCTATGAGTTCAAAAAGAGAG 57.512 33.333 14.95 0.00 42.52 3.20
3732 3849 8.865090 AGAAGTCTATGAGTTCAAAAAGAGAGA 58.135 33.333 14.95 0.00 42.52 3.10
3733 3850 9.139174 GAAGTCTATGAGTTCAAAAAGAGAGAG 57.861 37.037 9.49 0.00 40.53 3.20
3734 3851 8.415950 AGTCTATGAGTTCAAAAAGAGAGAGA 57.584 34.615 0.00 0.00 0.00 3.10
3735 3852 8.522830 AGTCTATGAGTTCAAAAAGAGAGAGAG 58.477 37.037 0.00 0.00 0.00 3.20
3736 3853 8.519526 GTCTATGAGTTCAAAAAGAGAGAGAGA 58.480 37.037 0.00 0.00 0.00 3.10
3737 3854 9.083422 TCTATGAGTTCAAAAAGAGAGAGAGAA 57.917 33.333 0.00 0.00 0.00 2.87
3738 3855 9.703892 CTATGAGTTCAAAAAGAGAGAGAGAAA 57.296 33.333 0.00 0.00 0.00 2.52
3739 3856 8.970859 ATGAGTTCAAAAAGAGAGAGAGAAAA 57.029 30.769 0.00 0.00 0.00 2.29
3740 3857 8.970859 TGAGTTCAAAAAGAGAGAGAGAAAAT 57.029 30.769 0.00 0.00 0.00 1.82
3747 3864 9.890352 CAAAAAGAGAGAGAGAAAATAAACTGG 57.110 33.333 0.00 0.00 0.00 4.00
3893 4039 2.356069 GCTTATTGCCTGGCTGAGTTAC 59.644 50.000 21.03 0.30 35.15 2.50
3926 4079 4.098416 GCAAGTTTGATTCGCCACTTATC 58.902 43.478 0.00 0.00 0.00 1.75
3931 4084 6.407202 AGTTTGATTCGCCACTTATCTAAGT 58.593 36.000 0.00 0.00 46.76 2.24
3969 4123 0.732538 GAACGGGAAAAAGCGCCATG 60.733 55.000 2.29 0.00 0.00 3.66
3997 4151 6.922247 TTTTTGAATGCATTGCTCAAAGAA 57.078 29.167 18.59 13.78 39.51 2.52
4017 4171 1.256812 GGCAAAGCCCAAGTGTACAT 58.743 50.000 0.00 0.00 44.06 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 7.603180 ACATACTGCTATCTCATCCTTAACA 57.397 36.000 0.00 0.00 0.00 2.41
133 134 7.093552 GGTCATACATACTGCTATCTCATCCTT 60.094 40.741 0.00 0.00 0.00 3.36
144 149 3.115390 ACCCTTGGTCATACATACTGCT 58.885 45.455 0.00 0.00 0.00 4.24
173 178 2.029020 CGACTCAACATTCTCACCCTGA 60.029 50.000 0.00 0.00 0.00 3.86
196 201 2.203480 TTGCAGAAGGTGGGTGCC 60.203 61.111 0.00 0.00 36.31 5.01
207 212 5.083533 ACAAATTGTTCAAAGGTTGCAGA 57.916 34.783 0.00 0.00 0.00 4.26
253 258 4.208047 GCAGCTATGTATGAGTGTTTCGAG 59.792 45.833 0.00 0.00 0.00 4.04
324 329 7.241376 CACACGGAAAGATTAAACCAATAGAC 58.759 38.462 0.00 0.00 0.00 2.59
343 349 3.414549 ACTTAAAGTTTGTGCACACGG 57.585 42.857 21.56 6.07 0.00 4.94
464 479 1.534163 GGAGGCCAAGTACAACGAAAC 59.466 52.381 5.01 0.00 0.00 2.78
468 483 1.740296 CCGGAGGCCAAGTACAACG 60.740 63.158 5.01 0.00 46.14 4.10
488 503 0.309302 ATCTTCGGCTCATCTCGTCG 59.691 55.000 0.00 0.00 0.00 5.12
541 557 0.968405 GAGGCCAACTCCAATTTGCA 59.032 50.000 5.01 0.00 40.49 4.08
542 558 0.968405 TGAGGCCAACTCCAATTTGC 59.032 50.000 5.01 0.00 46.01 3.68
549 565 1.450312 CGACCATGAGGCCAACTCC 60.450 63.158 5.01 0.00 46.01 3.85
551 567 1.488705 TTCCGACCATGAGGCCAACT 61.489 55.000 5.01 0.00 39.06 3.16
552 568 1.002624 TTCCGACCATGAGGCCAAC 60.003 57.895 5.01 0.00 39.06 3.77
553 569 1.299648 CTTCCGACCATGAGGCCAA 59.700 57.895 5.01 0.00 39.06 4.52
554 570 2.989639 CTTCCGACCATGAGGCCA 59.010 61.111 5.01 0.00 39.06 5.36
555 571 2.514824 GCTTCCGACCATGAGGCC 60.515 66.667 0.00 0.00 39.06 5.19
556 572 0.106708 TATGCTTCCGACCATGAGGC 59.893 55.000 0.00 0.00 39.06 4.70
557 573 2.420642 CATATGCTTCCGACCATGAGG 58.579 52.381 0.00 0.00 42.21 3.86
558 574 1.802960 GCATATGCTTCCGACCATGAG 59.197 52.381 20.64 0.00 38.21 2.90
559 575 1.140652 TGCATATGCTTCCGACCATGA 59.859 47.619 27.13 0.47 42.66 3.07
560 576 1.596603 TGCATATGCTTCCGACCATG 58.403 50.000 27.13 0.00 42.66 3.66
561 577 1.949525 GTTGCATATGCTTCCGACCAT 59.050 47.619 27.13 0.00 42.66 3.55
562 578 1.378531 GTTGCATATGCTTCCGACCA 58.621 50.000 27.13 2.54 42.66 4.02
563 579 0.663153 GGTTGCATATGCTTCCGACC 59.337 55.000 27.13 20.61 42.66 4.79
591 607 2.301870 TGTTGGGAGGTAGCACTACAAG 59.698 50.000 9.87 0.00 37.78 3.16
620 636 7.118971 AGACTCAAATGCATACTCTGAAGAAAC 59.881 37.037 0.00 0.00 0.00 2.78
621 637 7.118825 CAGACTCAAATGCATACTCTGAAGAAA 59.881 37.037 0.00 0.00 0.00 2.52
624 640 5.293814 CCAGACTCAAATGCATACTCTGAAG 59.706 44.000 0.00 0.00 0.00 3.02
625 641 5.046376 TCCAGACTCAAATGCATACTCTGAA 60.046 40.000 0.00 0.00 0.00 3.02
626 642 4.467438 TCCAGACTCAAATGCATACTCTGA 59.533 41.667 0.00 0.03 0.00 3.27
627 643 4.763073 TCCAGACTCAAATGCATACTCTG 58.237 43.478 0.00 5.90 0.00 3.35
628 644 5.366460 CATCCAGACTCAAATGCATACTCT 58.634 41.667 0.00 0.00 0.00 3.24
644 660 8.891985 ATCTAGTATCTATCTTTGCATCCAGA 57.108 34.615 0.00 0.00 0.00 3.86
665 681 9.981460 TCTATCTTTGCATCCAGACTATATCTA 57.019 33.333 0.00 0.00 35.15 1.98
666 682 8.891985 TCTATCTTTGCATCCAGACTATATCT 57.108 34.615 0.00 0.00 38.66 1.98
669 685 9.760926 AGTATCTATCTTTGCATCCAGACTATA 57.239 33.333 0.00 0.00 0.00 1.31
670 686 8.663209 AGTATCTATCTTTGCATCCAGACTAT 57.337 34.615 0.00 0.00 0.00 2.12
671 687 9.237187 CTAGTATCTATCTTTGCATCCAGACTA 57.763 37.037 0.00 0.00 0.00 2.59
672 688 6.992664 AGTATCTATCTTTGCATCCAGACT 57.007 37.500 0.00 0.00 0.00 3.24
673 689 8.116651 TCTAGTATCTATCTTTGCATCCAGAC 57.883 38.462 0.00 0.00 0.00 3.51
674 690 8.891985 ATCTAGTATCTATCTTTGCATCCAGA 57.108 34.615 0.00 0.00 0.00 3.86
683 699 9.581289 CCGGGATCATATCTAGTATCTATCTTT 57.419 37.037 0.00 0.00 0.00 2.52
684 700 8.167392 CCCGGGATCATATCTAGTATCTATCTT 58.833 40.741 18.48 0.00 0.00 2.40
685 701 7.257235 CCCCGGGATCATATCTAGTATCTATCT 60.257 44.444 26.32 0.00 0.00 1.98
686 702 6.887545 CCCCGGGATCATATCTAGTATCTATC 59.112 46.154 26.32 0.00 0.00 2.08
687 703 6.566870 TCCCCGGGATCATATCTAGTATCTAT 59.433 42.308 26.32 0.00 0.00 1.98
688 704 5.915308 TCCCCGGGATCATATCTAGTATCTA 59.085 44.000 26.32 0.00 0.00 1.98
689 705 4.732443 TCCCCGGGATCATATCTAGTATCT 59.268 45.833 26.32 0.00 0.00 1.98
690 706 5.063017 TCCCCGGGATCATATCTAGTATC 57.937 47.826 26.32 0.00 0.00 2.24
691 707 5.209659 GTTCCCCGGGATCATATCTAGTAT 58.790 45.833 26.32 0.00 0.00 2.12
692 708 4.607239 GTTCCCCGGGATCATATCTAGTA 58.393 47.826 26.32 0.00 0.00 1.82
693 709 3.442076 GTTCCCCGGGATCATATCTAGT 58.558 50.000 26.32 0.00 0.00 2.57
694 710 2.427453 CGTTCCCCGGGATCATATCTAG 59.573 54.545 26.32 0.00 0.00 2.43
695 711 2.453521 CGTTCCCCGGGATCATATCTA 58.546 52.381 26.32 0.00 0.00 1.98
696 712 1.267121 CGTTCCCCGGGATCATATCT 58.733 55.000 26.32 0.00 0.00 1.98
697 713 0.391263 GCGTTCCCCGGGATCATATC 60.391 60.000 26.32 3.88 36.94 1.63
698 714 1.677552 GCGTTCCCCGGGATCATAT 59.322 57.895 26.32 0.00 36.94 1.78
699 715 3.144285 GCGTTCCCCGGGATCATA 58.856 61.111 26.32 0.00 36.94 2.15
821 841 3.044894 GAGAAATGGAGGAGGAGGACAT 58.955 50.000 0.00 0.00 0.00 3.06
844 864 1.445095 CAGGAAGGAGCCGATGAGG 59.555 63.158 0.00 0.00 44.97 3.86
879 908 1.831286 GGAATGGGAGCATGGGCAG 60.831 63.158 0.00 0.00 44.61 4.85
890 919 6.013812 TGTTTAAAAGGAAAGGATGGAATGGG 60.014 38.462 0.00 0.00 0.00 4.00
903 932 6.682861 GCTGCTTTTCTCCTGTTTAAAAGGAA 60.683 38.462 5.28 0.00 43.27 3.36
914 943 2.042831 CCCCGCTGCTTTTCTCCTG 61.043 63.158 0.00 0.00 0.00 3.86
917 947 0.678048 ATCACCCCGCTGCTTTTCTC 60.678 55.000 0.00 0.00 0.00 2.87
934 964 0.174162 GTTGCACATGGAAGGGCATC 59.826 55.000 0.00 0.00 35.98 3.91
935 965 1.597797 CGTTGCACATGGAAGGGCAT 61.598 55.000 0.00 0.00 35.98 4.40
936 966 2.267351 CGTTGCACATGGAAGGGCA 61.267 57.895 0.00 0.00 0.00 5.36
937 967 2.568090 CGTTGCACATGGAAGGGC 59.432 61.111 0.00 0.00 0.00 5.19
938 968 2.203972 CTGCGTTGCACATGGAAGGG 62.204 60.000 7.74 0.00 33.79 3.95
939 969 1.210931 CTGCGTTGCACATGGAAGG 59.789 57.895 0.00 1.91 33.79 3.46
940 970 1.443194 GCTGCGTTGCACATGGAAG 60.443 57.895 0.00 0.00 33.79 3.46
941 971 2.644418 GCTGCGTTGCACATGGAA 59.356 55.556 0.00 0.00 33.79 3.53
942 972 2.462125 TAGGCTGCGTTGCACATGGA 62.462 55.000 0.00 0.00 33.79 3.41
943 973 1.985447 CTAGGCTGCGTTGCACATGG 61.985 60.000 0.00 0.00 33.79 3.66
944 974 1.020861 TCTAGGCTGCGTTGCACATG 61.021 55.000 0.00 0.00 33.79 3.21
949 979 0.249657 AGCTATCTAGGCTGCGTTGC 60.250 55.000 0.00 0.00 38.73 4.17
961 991 3.383185 GCTTGACACTGGAGTAGCTATCT 59.617 47.826 0.00 0.00 0.00 1.98
983 1024 0.387622 CATTGCGCTTCTGGTTGGTG 60.388 55.000 9.73 0.00 0.00 4.17
1300 1349 3.687828 AAGAGGAGGAGGGCGAGGG 62.688 68.421 0.00 0.00 0.00 4.30
1362 1426 3.730761 GATGCCGATGCCGATGCC 61.731 66.667 0.00 0.00 38.22 4.40
1363 1427 4.081030 CGATGCCGATGCCGATGC 62.081 66.667 0.00 0.00 38.22 3.91
1364 1428 4.081030 GCGATGCCGATGCCGATG 62.081 66.667 0.00 0.00 38.22 3.84
1414 1484 0.528924 CCGTTGACATCGGTGTAGGA 59.471 55.000 15.45 0.00 42.62 2.94
1498 1568 0.320247 AACAAGTCAGAGCTCGGCTG 60.320 55.000 9.22 8.61 39.88 4.85
1812 1903 0.603569 TCTTCTCTGGCTCACCGTTC 59.396 55.000 0.00 0.00 39.70 3.95
1824 1924 0.613292 TCTTCCGGCTGCTCTTCTCT 60.613 55.000 0.00 0.00 0.00 3.10
1826 1926 0.248843 CTTCTTCCGGCTGCTCTTCT 59.751 55.000 0.00 0.00 0.00 2.85
1861 1961 0.609957 TCACTATCGTCCACGGTGGT 60.610 55.000 25.53 9.98 45.01 4.16
1862 1962 0.100682 CTCACTATCGTCCACGGTGG 59.899 60.000 21.27 21.27 40.29 4.61
1864 1964 1.676529 CATCTCACTATCGTCCACGGT 59.323 52.381 0.00 0.00 40.29 4.83
1872 1972 2.035193 CAGGTCCACCATCTCACTATCG 59.965 54.545 0.00 0.00 38.89 2.92
2193 2293 0.737715 GTCTCTTACCTGCCACAGCG 60.738 60.000 0.00 0.00 44.31 5.18
2238 2338 1.559682 GGCCACTGGAGACCTTGATTA 59.440 52.381 0.00 0.00 0.00 1.75
2247 2347 1.455849 CAAACCTGGCCACTGGAGA 59.544 57.895 17.65 0.00 38.91 3.71
2376 2476 1.610624 CGGGCAAAGTTTCTGAGCCTA 60.611 52.381 12.84 0.00 44.60 3.93
2385 2485 1.065109 GAACACGCGGGCAAAGTTT 59.935 52.632 9.12 0.00 0.00 2.66
2454 2554 1.605058 CGATGTTCAGGTCCTCCGGT 61.605 60.000 0.00 0.00 39.05 5.28
2585 2685 1.552337 ACACATCAGGACGCATCTTCT 59.448 47.619 0.00 0.00 0.00 2.85
2598 2698 2.510928 TGCCATGGATGAACACATCA 57.489 45.000 18.40 0.00 41.28 3.07
2775 2875 1.200716 CCTTCACATGCGAGCACATTT 59.799 47.619 0.00 0.00 0.00 2.32
2907 3007 3.968649 TGTGGTAGTTGTCCTTGACCTTA 59.031 43.478 0.00 0.00 0.00 2.69
3057 3158 7.041235 GGCGTGGGTATATCTATCTATGTCTAC 60.041 44.444 0.00 0.00 0.00 2.59
3076 3181 6.544931 TGCTACTATTACTATATAGGCGTGGG 59.455 42.308 14.25 2.83 33.33 4.61
3093 3198 7.449086 GGGAGTACAAGAGATAAGTGCTACTAT 59.551 40.741 0.00 0.00 30.66 2.12
3116 3221 2.759149 TATTTCCGGACGGCGGGA 60.759 61.111 14.61 14.61 41.25 5.14
3117 3222 2.582734 AAGTATTTCCGGACGGCGGG 62.583 60.000 13.24 8.96 35.92 6.13
3119 3224 0.738412 ACAAGTATTTCCGGACGGCG 60.738 55.000 1.83 4.80 34.68 6.46
3120 3225 1.004595 GACAAGTATTTCCGGACGGC 58.995 55.000 1.83 0.00 34.68 5.68
3121 3226 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
3122 3227 2.094390 TGAGGACAAGTATTTCCGGACG 60.094 50.000 1.83 0.00 36.95 4.79
3123 3228 3.604875 TGAGGACAAGTATTTCCGGAC 57.395 47.619 1.83 0.00 36.95 4.79
3124 3229 4.627284 TTTGAGGACAAGTATTTCCGGA 57.373 40.909 0.00 0.00 36.95 5.14
3125 3230 5.393027 CCATTTTGAGGACAAGTATTTCCGG 60.393 44.000 0.00 0.00 36.95 5.14
3126 3231 5.414454 TCCATTTTGAGGACAAGTATTTCCG 59.586 40.000 0.00 0.00 36.95 4.30
3127 3232 6.834168 TCCATTTTGAGGACAAGTATTTCC 57.166 37.500 0.00 0.00 37.32 3.13
3132 3237 8.748412 CCATTTTATCCATTTTGAGGACAAGTA 58.252 33.333 0.00 0.00 38.13 2.24
3133 3238 7.454380 TCCATTTTATCCATTTTGAGGACAAGT 59.546 33.333 0.00 0.00 38.13 3.16
3134 3239 7.839907 TCCATTTTATCCATTTTGAGGACAAG 58.160 34.615 0.00 0.00 38.13 3.16
3135 3240 7.789202 TCCATTTTATCCATTTTGAGGACAA 57.211 32.000 0.00 0.00 38.13 3.18
3136 3241 7.399765 ACATCCATTTTATCCATTTTGAGGACA 59.600 33.333 0.00 0.00 38.13 4.02
3137 3242 7.785033 ACATCCATTTTATCCATTTTGAGGAC 58.215 34.615 0.00 0.00 38.13 3.85
3138 3243 7.976414 ACATCCATTTTATCCATTTTGAGGA 57.024 32.000 0.00 0.00 39.97 3.71
3139 3244 9.918630 GATACATCCATTTTATCCATTTTGAGG 57.081 33.333 0.00 0.00 0.00 3.86
3175 3280 9.751542 CTCGAAATGGTTGTATCTAGACTTATT 57.248 33.333 0.00 0.00 0.00 1.40
3176 3281 8.361139 CCTCGAAATGGTTGTATCTAGACTTAT 58.639 37.037 0.00 0.00 0.00 1.73
3177 3282 7.558807 TCCTCGAAATGGTTGTATCTAGACTTA 59.441 37.037 0.00 0.00 0.00 2.24
3178 3283 6.380274 TCCTCGAAATGGTTGTATCTAGACTT 59.620 38.462 0.00 0.00 0.00 3.01
3179 3284 5.892119 TCCTCGAAATGGTTGTATCTAGACT 59.108 40.000 0.00 0.00 0.00 3.24
3180 3285 5.978322 GTCCTCGAAATGGTTGTATCTAGAC 59.022 44.000 0.00 0.00 0.00 2.59
3181 3286 5.655090 TGTCCTCGAAATGGTTGTATCTAGA 59.345 40.000 0.00 0.00 0.00 2.43
3182 3287 5.902681 TGTCCTCGAAATGGTTGTATCTAG 58.097 41.667 0.00 0.00 0.00 2.43
3183 3288 5.925506 TGTCCTCGAAATGGTTGTATCTA 57.074 39.130 0.00 0.00 0.00 1.98
3184 3289 4.819105 TGTCCTCGAAATGGTTGTATCT 57.181 40.909 0.00 0.00 0.00 1.98
3185 3290 4.935808 ACTTGTCCTCGAAATGGTTGTATC 59.064 41.667 0.00 0.00 0.00 2.24
3186 3291 4.906618 ACTTGTCCTCGAAATGGTTGTAT 58.093 39.130 0.00 0.00 0.00 2.29
3187 3292 4.345859 ACTTGTCCTCGAAATGGTTGTA 57.654 40.909 0.00 0.00 0.00 2.41
3188 3293 3.208747 ACTTGTCCTCGAAATGGTTGT 57.791 42.857 0.00 0.00 0.00 3.32
3189 3294 5.880054 AATACTTGTCCTCGAAATGGTTG 57.120 39.130 0.00 0.00 0.00 3.77
3190 3295 5.414765 GGAAATACTTGTCCTCGAAATGGTT 59.585 40.000 0.00 0.00 0.00 3.67
3191 3296 4.941873 GGAAATACTTGTCCTCGAAATGGT 59.058 41.667 0.00 0.00 0.00 3.55
3192 3297 4.034048 CGGAAATACTTGTCCTCGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
3193 3298 4.034048 CCGGAAATACTTGTCCTCGAAATG 59.966 45.833 0.00 0.00 0.00 2.32
3194 3299 4.081309 TCCGGAAATACTTGTCCTCGAAAT 60.081 41.667 0.00 0.00 0.00 2.17
3195 3300 3.258872 TCCGGAAATACTTGTCCTCGAAA 59.741 43.478 0.00 0.00 0.00 3.46
3196 3301 2.827322 TCCGGAAATACTTGTCCTCGAA 59.173 45.455 0.00 0.00 0.00 3.71
3197 3302 2.165030 GTCCGGAAATACTTGTCCTCGA 59.835 50.000 5.23 0.00 0.00 4.04
3198 3303 2.537401 GTCCGGAAATACTTGTCCTCG 58.463 52.381 5.23 0.00 0.00 4.63
3199 3304 2.537401 CGTCCGGAAATACTTGTCCTC 58.463 52.381 5.23 0.00 0.00 3.71
3200 3305 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
3201 3306 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
3202 3307 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3203 3308 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3204 3309 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3205 3310 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3206 3311 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3207 3312 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3208 3313 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3209 3314 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3210 3315 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3211 3316 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3212 3317 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
3213 3318 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
3214 3319 2.119655 CAGGTACTCCCTCCGTCCG 61.120 68.421 0.00 0.00 43.86 4.79
3215 3320 1.036481 GTCAGGTACTCCCTCCGTCC 61.036 65.000 0.00 0.00 43.86 4.79
3216 3321 0.323178 TGTCAGGTACTCCCTCCGTC 60.323 60.000 0.00 0.00 43.86 4.79
3217 3322 0.113776 TTGTCAGGTACTCCCTCCGT 59.886 55.000 0.00 0.00 43.86 4.69
3218 3323 0.818296 CTTGTCAGGTACTCCCTCCG 59.182 60.000 0.00 0.00 43.86 4.63
3219 3324 0.537653 GCTTGTCAGGTACTCCCTCC 59.462 60.000 0.00 0.00 43.86 4.30
3220 3325 1.267121 TGCTTGTCAGGTACTCCCTC 58.733 55.000 0.00 0.00 43.86 4.30
3222 3327 2.789409 ATTGCTTGTCAGGTACTCCC 57.211 50.000 0.00 0.00 34.60 4.30
3223 3328 4.072131 TGAAATTGCTTGTCAGGTACTCC 58.928 43.478 0.00 0.00 34.60 3.85
3224 3329 4.515191 TGTGAAATTGCTTGTCAGGTACTC 59.485 41.667 0.00 0.00 34.60 2.59
3225 3330 4.460263 TGTGAAATTGCTTGTCAGGTACT 58.540 39.130 0.00 0.00 43.88 2.73
3243 3348 9.847706 AAACAATTTAACGCATGTAATATGTGA 57.152 25.926 7.38 0.00 34.00 3.58
3276 3381 2.749280 AGACACGCACATCTTCATCA 57.251 45.000 0.00 0.00 0.00 3.07
3317 3422 9.294030 GAAAGCTTATCTAACAATTTGATGGTG 57.706 33.333 0.00 0.00 0.00 4.17
3397 3503 3.436704 ACGAATCAAACGATGCAAGTCAT 59.563 39.130 0.00 0.00 38.32 3.06
3436 3542 6.801539 AAATCGTCTACACACACAAATCAT 57.198 33.333 0.00 0.00 0.00 2.45
3451 3559 5.556915 TGTGGGAAACATCTTAAATCGTCT 58.443 37.500 0.00 0.00 32.36 4.18
3459 3575 5.009610 GCTGAAACTTGTGGGAAACATCTTA 59.990 40.000 0.00 0.00 38.99 2.10
3656 3773 4.417426 TTTTGTTTATCCCCCGCAAAAA 57.583 36.364 0.00 0.00 36.50 1.94
3657 3774 4.417426 TTTTTGTTTATCCCCCGCAAAA 57.583 36.364 0.00 0.00 37.29 2.44
3677 3794 6.090358 CACTTGTCATCGTCGGTAACTATTTT 59.910 38.462 0.00 0.00 0.00 1.82
3693 3810 7.009179 TCATAGACTTCTTTCCACTTGTCAT 57.991 36.000 0.00 0.00 0.00 3.06
3697 3814 6.931281 TGAACTCATAGACTTCTTTCCACTTG 59.069 38.462 0.00 0.00 0.00 3.16
3727 3844 6.155393 TCCTCCCAGTTTATTTTCTCTCTCTC 59.845 42.308 0.00 0.00 0.00 3.20
3728 3845 6.026186 TCCTCCCAGTTTATTTTCTCTCTCT 58.974 40.000 0.00 0.00 0.00 3.10
3729 3846 6.301169 TCCTCCCAGTTTATTTTCTCTCTC 57.699 41.667 0.00 0.00 0.00 3.20
3730 3847 6.273495 ACTTCCTCCCAGTTTATTTTCTCTCT 59.727 38.462 0.00 0.00 0.00 3.10
3731 3848 6.477253 ACTTCCTCCCAGTTTATTTTCTCTC 58.523 40.000 0.00 0.00 0.00 3.20
3732 3849 6.455690 ACTTCCTCCCAGTTTATTTTCTCT 57.544 37.500 0.00 0.00 0.00 3.10
3733 3850 5.648526 GGACTTCCTCCCAGTTTATTTTCTC 59.351 44.000 0.00 0.00 31.83 2.87
3734 3851 5.074515 TGGACTTCCTCCCAGTTTATTTTCT 59.925 40.000 0.00 0.00 38.49 2.52
3735 3852 5.321927 TGGACTTCCTCCCAGTTTATTTTC 58.678 41.667 0.00 0.00 38.49 2.29
3736 3853 5.333566 TGGACTTCCTCCCAGTTTATTTT 57.666 39.130 0.00 0.00 38.49 1.82
3737 3854 5.333566 TTGGACTTCCTCCCAGTTTATTT 57.666 39.130 0.00 0.00 38.49 1.40
3738 3855 5.333566 TTTGGACTTCCTCCCAGTTTATT 57.666 39.130 0.00 0.00 38.49 1.40
3739 3856 5.333566 TTTTGGACTTCCTCCCAGTTTAT 57.666 39.130 0.00 0.00 38.49 1.40
3740 3857 4.799715 TTTTGGACTTCCTCCCAGTTTA 57.200 40.909 0.00 0.00 38.49 2.01
3741 3858 3.680777 TTTTGGACTTCCTCCCAGTTT 57.319 42.857 0.00 0.00 38.49 2.66
3742 3859 3.680777 TTTTTGGACTTCCTCCCAGTT 57.319 42.857 0.00 0.00 38.49 3.16
3771 3905 9.656040 TGACTAACGGTTAACAACATATAACAT 57.344 29.630 8.10 0.00 34.44 2.71
3893 4039 5.060077 CGAATCAAACTTGCAAGCACATAAG 59.940 40.000 26.27 9.43 0.00 1.73
3931 4084 6.183360 CCCGTTCGAAATATACAAAACATGGA 60.183 38.462 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.