Multiple sequence alignment - TraesCS7D01G446300

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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 TraesCS7D01G446300 chr7D 100.000 4481 0 0 1 4481 566574598 566570118 0.000000e+00 8275
1 TraesCS7D01G446300 chr7A 97.126 2644 59 8 895 3527 652759929 652757292 0.000000e+00 4446
2 TraesCS7D01G446300 chr7A 91.823 746 41 8 3601 4328 652757296 652756553 0.000000e+00 1022
3 TraesCS7D01G446300 chr6D 90.743 875 69 9 27 897 115009536 115010402 0.000000e+00 1157
4 TraesCS7D01G446300 chr5B 85.073 891 89 20 27 897 202383526 202382660 0.000000e+00 869
5 TraesCS7D01G446300 chr7B 82.899 345 42 8 27 360 483916610 483916948 1.220000e-75 294
6 TraesCS7D01G446300 chr7B 98.387 124 2 0 3325 3448 42841306 42841429 7.550000e-53 219
7 TraesCS7D01G446300 chr7B 74.824 425 49 22 499 893 483917123 483917519 6.040000e-29 139
8 TraesCS7D01G446300 chr1A 80.332 361 58 8 27 381 559622863 559623216 1.240000e-65 261
9 TraesCS7D01G446300 chr1A 75.743 404 54 25 512 897 559623381 559623758 3.590000e-36 163
10 TraesCS7D01G446300 chr2A 90.090 111 11 0 3065 3175 760693918 760693808 1.300000e-30 145
11 TraesCS7D01G446300 chr5D 86.066 122 15 2 776 897 434352243 434352362 3.640000e-26 130
12 TraesCS7D01G446300 chr2B 85.039 127 18 1 515 641 40844035 40844160 1.310000e-25 128


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 TraesCS7D01G446300 chr7D 566570118 566574598 4480 True 8275.0 8275 100.0000 1 4481 1 chr7D.!!$R1 4480
1 TraesCS7D01G446300 chr7A 652756553 652759929 3376 True 2734.0 4446 94.4745 895 4328 2 chr7A.!!$R1 3433
2 TraesCS7D01G446300 chr6D 115009536 115010402 866 False 1157.0 1157 90.7430 27 897 1 chr6D.!!$F1 870
3 TraesCS7D01G446300 chr5B 202382660 202383526 866 True 869.0 869 85.0730 27 897 1 chr5B.!!$R1 870
4 TraesCS7D01G446300 chr7B 483916610 483917519 909 False 216.5 294 78.8615 27 893 2 chr7B.!!$F2 866
5 TraesCS7D01G446300 chr1A 559622863 559623758 895 False 212.0 261 78.0375 27 897 2 chr1A.!!$F1 870

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
137 138 0.098376 CGATGCAAAAGCTCTCAGCC 59.902 55.0 0.00 0.00 43.77 4.85 F
143 144 0.112025 AAAAGCTCTCAGCCAGGCTT 59.888 50.0 12.86 0.00 43.77 4.35 F
899 1025 0.252479 AGATCAGCCTGGCAAGAGTG 59.748 55.0 22.65 10.07 0.00 3.51 F
2535 2661 0.533755 CCGATGTGAAGGGCTCCATC 60.534 60.0 0.00 0.00 32.55 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1817 0.443869 CCTCAAAACTCCATCACGCG 59.556 55.000 3.53 3.53 0.00 6.01 R
2052 2178 1.541233 GCACTATGGCGGCTAGTCATT 60.541 52.381 11.43 0.00 43.84 2.57 R
2891 3017 0.038159 AACTCTCCTTGCTTCCGACG 60.038 55.000 0.00 0.00 0.00 5.12 R
3593 3730 0.041238 TGACCAGACGGAGGAGGATT 59.959 55.000 0.00 0.00 35.59 3.01 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
55 56 1.077140 TTGTGTTGCACCTGGCTCA 60.077 52.632 0.00 0.00 45.15 4.26
66 67 1.812922 CTGGCTCACACCTCGCATC 60.813 63.158 0.00 0.00 0.00 3.91
92 93 0.459585 TCGATGCGTTTGGTAGCCTC 60.460 55.000 0.00 0.00 0.00 4.70
130 131 3.443045 CGGCCCGATGCAAAAGCT 61.443 61.111 0.00 0.00 43.89 3.74
131 132 2.491621 GGCCCGATGCAAAAGCTC 59.508 61.111 0.00 0.00 43.89 4.09
132 133 2.048603 GGCCCGATGCAAAAGCTCT 61.049 57.895 0.00 0.00 43.89 4.09
134 135 1.308069 GCCCGATGCAAAAGCTCTCA 61.308 55.000 0.00 0.00 40.77 3.27
135 136 0.731417 CCCGATGCAAAAGCTCTCAG 59.269 55.000 0.00 0.00 0.00 3.35
137 138 0.098376 CGATGCAAAAGCTCTCAGCC 59.902 55.000 0.00 0.00 43.77 4.85
138 139 1.171308 GATGCAAAAGCTCTCAGCCA 58.829 50.000 0.00 0.00 43.77 4.75
139 140 1.132643 GATGCAAAAGCTCTCAGCCAG 59.867 52.381 0.00 0.00 43.77 4.85
142 143 0.608582 CAAAAGCTCTCAGCCAGGCT 60.609 55.000 8.70 8.70 43.77 4.58
143 144 0.112025 AAAAGCTCTCAGCCAGGCTT 59.888 50.000 12.86 0.00 43.77 4.35
144 145 0.987294 AAAGCTCTCAGCCAGGCTTA 59.013 50.000 12.86 2.25 43.77 3.09
145 146 0.540923 AAGCTCTCAGCCAGGCTTAG 59.459 55.000 12.86 14.59 43.77 2.18
146 147 1.145819 GCTCTCAGCCAGGCTTAGG 59.854 63.158 20.68 13.10 36.40 2.69
147 148 1.828768 CTCTCAGCCAGGCTTAGGG 59.171 63.158 20.68 15.04 36.40 3.53
167 168 0.608035 CAGGCTTAGGGGAACGCAAA 60.608 55.000 0.00 0.00 46.88 3.68
180 181 3.246619 GAACGCAAAAATCGGGCATTTA 58.753 40.909 0.00 0.00 33.16 1.40
244 246 3.370978 CGAAACGGTATGTGAGATTGCTT 59.629 43.478 0.00 0.00 0.00 3.91
257 259 6.936335 TGTGAGATTGCTTCTGATGTTTTCTA 59.064 34.615 0.00 0.00 33.74 2.10
311 315 4.367450 CCTATCGCTCTTTCCTCTTTCTG 58.633 47.826 0.00 0.00 0.00 3.02
319 323 5.337491 GCTCTTTCCTCTTTCTGTCTCTCAT 60.337 44.000 0.00 0.00 0.00 2.90
325 339 0.737367 TTTCTGTCTCTCATGCGCCG 60.737 55.000 4.18 0.00 0.00 6.46
529 614 2.034879 GCGTGCAGCCTGCTAGAAA 61.035 57.895 18.96 0.00 45.31 2.52
689 806 2.022035 TCCCTCTCCTGTCCACCAATAT 60.022 50.000 0.00 0.00 0.00 1.28
694 811 3.197766 TCTCCTGTCCACCAATATGTGTC 59.802 47.826 0.00 0.00 34.35 3.67
756 881 1.304713 CTGGCATGGGAGGCACTTT 60.305 57.895 0.00 0.00 41.55 2.66
757 882 1.601419 CTGGCATGGGAGGCACTTTG 61.601 60.000 0.00 0.00 41.55 2.77
792 918 4.225042 TGGGAAGCAGCTCACTAATTTCTA 59.775 41.667 0.00 0.00 0.00 2.10
800 926 6.590292 GCAGCTCACTAATTTCTAGTACAACA 59.410 38.462 0.00 0.00 0.00 3.33
803 929 9.804758 AGCTCACTAATTTCTAGTACAACATAC 57.195 33.333 0.00 0.00 0.00 2.39
893 1019 0.547553 TGCATTAGATCAGCCTGGCA 59.452 50.000 22.65 0.22 0.00 4.92
897 1023 2.996249 TTAGATCAGCCTGGCAAGAG 57.004 50.000 22.65 7.76 0.00 2.85
898 1024 1.871418 TAGATCAGCCTGGCAAGAGT 58.129 50.000 22.65 11.76 0.00 3.24
899 1025 0.252479 AGATCAGCCTGGCAAGAGTG 59.748 55.000 22.65 10.07 0.00 3.51
900 1026 0.747283 GATCAGCCTGGCAAGAGTGG 60.747 60.000 22.65 1.10 0.00 4.00
908 1034 1.675641 GGCAAGAGTGGCCGTGATT 60.676 57.895 0.00 0.00 44.47 2.57
1059 1185 2.229792 TCAACAACATCCTTCCTGCAC 58.770 47.619 0.00 0.00 0.00 4.57
1070 1196 0.833409 TTCCTGCACCAGCTGAGAGA 60.833 55.000 17.39 1.53 41.71 3.10
1218 1344 4.661461 GGCTTCTTGGCTGCAAAC 57.339 55.556 0.50 0.00 38.32 2.93
1233 1359 5.696724 GGCTGCAAACGTGTTATCTATATCT 59.303 40.000 0.50 0.00 0.00 1.98
1356 1482 2.344025 CCAGTTACTTCCTACAACGGC 58.656 52.381 0.00 0.00 0.00 5.68
1457 1583 2.119801 ACCATCTCCAGTGATGTTGC 57.880 50.000 8.44 0.00 41.47 4.17
1590 1716 4.398988 TCTGATGCCGAAACAAATGCTATT 59.601 37.500 0.00 0.00 0.00 1.73
1663 1789 1.580658 TCCCCCTAGACATGGATGACT 59.419 52.381 0.00 0.00 36.76 3.41
1669 1795 4.406972 CCCTAGACATGGATGACTCAAAGA 59.593 45.833 0.00 0.00 34.76 2.52
1860 1986 4.025647 GCTTCGGAAAGGAAGAACGATATG 60.026 45.833 6.50 0.00 44.93 1.78
1944 2070 8.631695 GCTTTTCTATACGATATCTTCTTCACG 58.368 37.037 0.34 0.00 0.00 4.35
2013 2139 1.334419 GCATTCGCTTCATTCATCGGG 60.334 52.381 0.00 0.00 34.30 5.14
2052 2178 3.731728 GCTGCCATCCCTGGGACA 61.732 66.667 19.82 11.04 43.36 4.02
2152 2278 1.136329 ATTGGTGTCCCTGGCTCTGT 61.136 55.000 0.00 0.00 0.00 3.41
2216 2342 1.881973 GAGAGTTGCATTTGCCTGTGA 59.118 47.619 0.00 0.00 41.18 3.58
2326 2452 5.172687 TGACAAATACCTGTGGCAAGATA 57.827 39.130 0.00 0.00 26.90 1.98
2461 2587 1.014564 GCAGTACGTTGGAGAGGTGC 61.015 60.000 0.00 0.00 0.00 5.01
2463 2589 1.000955 CAGTACGTTGGAGAGGTGCTT 59.999 52.381 0.00 0.00 37.04 3.91
2535 2661 0.533755 CCGATGTGAAGGGCTCCATC 60.534 60.000 0.00 0.00 32.55 3.51
2568 2694 3.985008 TGGTCGGGTTCATAATGATACG 58.015 45.455 0.00 0.00 0.00 3.06
2654 2780 1.796617 GCATTTCGACAATCCTGCAGC 60.797 52.381 8.66 0.00 0.00 5.25
2766 2892 2.435586 CAGAAGGAGCGCACAGGG 60.436 66.667 11.47 0.00 0.00 4.45
2845 2971 3.923864 TGTCAGCGCCGGAGTTGT 61.924 61.111 20.54 0.00 0.00 3.32
2853 2979 1.376812 GCCGGAGTTGTTACCTGGG 60.377 63.158 5.05 0.00 0.00 4.45
2873 2999 2.226674 GGACGCTTCAGAAAAGGAAAGG 59.773 50.000 0.00 0.00 0.00 3.11
2877 3003 3.315191 CGCTTCAGAAAAGGAAAGGAACA 59.685 43.478 0.00 0.00 0.00 3.18
2886 3012 5.859205 AAAGGAAAGGAACATATGATGGC 57.141 39.130 10.38 0.00 33.60 4.40
2891 3017 1.949525 AGGAACATATGATGGCGTTGC 59.050 47.619 10.38 0.00 33.60 4.17
2906 3032 2.048222 TGCGTCGGAAGCAAGGAG 60.048 61.111 16.13 0.00 42.18 3.69
2913 3039 1.273606 TCGGAAGCAAGGAGAGTTCTG 59.726 52.381 0.00 0.00 0.00 3.02
2945 3071 0.455633 GACAAGCTTGAGGCAATGCG 60.456 55.000 32.50 2.31 44.79 4.73
3000 3126 0.321653 GCATCTTCTGGGACGGTGTT 60.322 55.000 0.00 0.00 35.30 3.32
3018 3144 2.223249 TGTTCGTCTTGCAAAGCAACTC 60.223 45.455 0.00 0.00 45.70 3.01
3031 3157 0.310854 GCAACTCTTTTGTGGGGACG 59.689 55.000 0.00 0.00 0.00 4.79
3187 3313 0.533491 GTACCACGCCCACATCTACA 59.467 55.000 0.00 0.00 0.00 2.74
3222 3348 1.694169 GAGATGGGGAGGGAAGCCA 60.694 63.158 0.00 0.00 0.00 4.75
3300 3426 2.289565 GGTGACCAGCTTAATACCTGC 58.710 52.381 0.00 0.00 0.00 4.85
3325 3451 2.685106 AGCAGAGGATAATCCGAGGA 57.315 50.000 0.00 0.00 42.75 3.71
3353 3479 0.250295 CCTCTTCAAAGTGCCACCGA 60.250 55.000 0.00 0.00 0.00 4.69
3456 3582 6.423182 TCCGAATAGGATTTCAATTCCTGTT 58.577 36.000 10.63 10.00 45.98 3.16
3468 3594 4.828939 TCAATTCCTGTTCAAGCTGACATT 59.171 37.500 0.00 0.00 0.00 2.71
3481 3607 3.062763 GCTGACATTCGATGGATGTAGG 58.937 50.000 1.29 0.14 33.60 3.18
3482 3608 3.243873 GCTGACATTCGATGGATGTAGGA 60.244 47.826 1.29 0.00 33.60 2.94
3483 3609 4.302455 CTGACATTCGATGGATGTAGGAC 58.698 47.826 1.29 0.00 33.60 3.85
3519 3656 6.326843 AGAGGACTTTAGTTCCTGTTTACAGT 59.673 38.462 8.91 0.00 42.27 3.55
3527 3664 1.347707 TCCTGTTTACAGTGGCTCAGG 59.652 52.381 15.13 15.13 42.27 3.86
3528 3665 1.347707 CCTGTTTACAGTGGCTCAGGA 59.652 52.381 15.81 0.00 43.28 3.86
3529 3666 2.417719 CTGTTTACAGTGGCTCAGGAC 58.582 52.381 1.69 0.00 39.09 3.85
3530 3667 1.071699 TGTTTACAGTGGCTCAGGACC 59.928 52.381 0.00 0.00 0.00 4.46
3531 3668 1.071699 GTTTACAGTGGCTCAGGACCA 59.928 52.381 0.00 0.00 33.84 4.02
3532 3669 0.976641 TTACAGTGGCTCAGGACCAG 59.023 55.000 0.00 0.00 38.04 4.00
3533 3670 1.544825 TACAGTGGCTCAGGACCAGC 61.545 60.000 0.00 0.00 38.04 4.85
3534 3671 3.699894 AGTGGCTCAGGACCAGCG 61.700 66.667 0.00 0.00 38.04 5.18
3535 3672 3.695606 GTGGCTCAGGACCAGCGA 61.696 66.667 0.00 0.00 38.04 4.93
3536 3673 2.922503 TGGCTCAGGACCAGCGAA 60.923 61.111 0.00 0.00 37.81 4.70
3537 3674 2.293318 TGGCTCAGGACCAGCGAAT 61.293 57.895 0.00 0.00 37.81 3.34
3538 3675 1.522580 GGCTCAGGACCAGCGAATC 60.523 63.158 0.00 0.00 37.81 2.52
3539 3676 1.219124 GCTCAGGACCAGCGAATCA 59.781 57.895 0.00 0.00 0.00 2.57
3540 3677 0.809241 GCTCAGGACCAGCGAATCAG 60.809 60.000 0.00 0.00 0.00 2.90
3541 3678 0.534412 CTCAGGACCAGCGAATCAGT 59.466 55.000 0.00 0.00 0.00 3.41
3542 3679 0.976641 TCAGGACCAGCGAATCAGTT 59.023 50.000 0.00 0.00 0.00 3.16
3543 3680 1.066858 TCAGGACCAGCGAATCAGTTC 60.067 52.381 0.00 0.00 0.00 3.01
3552 3689 2.002127 GAATCAGTTCGAGCGCAGG 58.998 57.895 11.47 0.00 0.00 4.85
3553 3690 0.458543 GAATCAGTTCGAGCGCAGGA 60.459 55.000 11.47 2.53 0.00 3.86
3554 3691 0.737715 AATCAGTTCGAGCGCAGGAC 60.738 55.000 11.47 8.36 0.00 3.85
3570 3707 4.320456 ACGCAGCTGGGTCACCTG 62.320 66.667 29.00 4.22 36.39 4.00
3571 3708 4.007644 CGCAGCTGGGTCACCTGA 62.008 66.667 21.92 0.00 37.89 3.86
3572 3709 2.046507 GCAGCTGGGTCACCTGAG 60.047 66.667 17.12 0.00 37.89 3.35
3573 3710 2.046507 CAGCTGGGTCACCTGAGC 60.047 66.667 5.57 9.74 41.50 4.26
3579 3716 3.161557 GGTCACCTGAGCCCTTGT 58.838 61.111 0.00 0.00 36.62 3.16
3580 3717 2.372852 GGTCACCTGAGCCCTTGTA 58.627 57.895 0.00 0.00 36.62 2.41
3581 3718 0.690762 GGTCACCTGAGCCCTTGTAA 59.309 55.000 0.00 0.00 36.62 2.41
3582 3719 1.073284 GGTCACCTGAGCCCTTGTAAA 59.927 52.381 0.00 0.00 36.62 2.01
3583 3720 2.152016 GTCACCTGAGCCCTTGTAAAC 58.848 52.381 0.00 0.00 0.00 2.01
3584 3721 1.771854 TCACCTGAGCCCTTGTAAACA 59.228 47.619 0.00 0.00 0.00 2.83
3585 3722 2.154462 CACCTGAGCCCTTGTAAACAG 58.846 52.381 0.00 0.00 0.00 3.16
3586 3723 1.774856 ACCTGAGCCCTTGTAAACAGT 59.225 47.619 0.00 0.00 0.00 3.55
3587 3724 2.976882 ACCTGAGCCCTTGTAAACAGTA 59.023 45.455 0.00 0.00 0.00 2.74
3588 3725 3.393278 ACCTGAGCCCTTGTAAACAGTAA 59.607 43.478 0.00 0.00 0.00 2.24
3589 3726 3.751698 CCTGAGCCCTTGTAAACAGTAAC 59.248 47.826 0.00 0.00 0.00 2.50
3590 3727 4.505039 CCTGAGCCCTTGTAAACAGTAACT 60.505 45.833 0.00 0.00 0.00 2.24
3591 3728 5.279809 CCTGAGCCCTTGTAAACAGTAACTA 60.280 44.000 0.00 0.00 0.00 2.24
3592 3729 6.177310 TGAGCCCTTGTAAACAGTAACTAA 57.823 37.500 0.00 0.00 0.00 2.24
3593 3730 6.593807 TGAGCCCTTGTAAACAGTAACTAAA 58.406 36.000 0.00 0.00 0.00 1.85
3594 3731 7.055378 TGAGCCCTTGTAAACAGTAACTAAAA 58.945 34.615 0.00 0.00 0.00 1.52
3595 3732 7.722285 TGAGCCCTTGTAAACAGTAACTAAAAT 59.278 33.333 0.00 0.00 0.00 1.82
3596 3733 8.107399 AGCCCTTGTAAACAGTAACTAAAATC 57.893 34.615 0.00 0.00 0.00 2.17
3597 3734 7.176165 AGCCCTTGTAAACAGTAACTAAAATCC 59.824 37.037 0.00 0.00 0.00 3.01
3598 3735 7.176165 GCCCTTGTAAACAGTAACTAAAATCCT 59.824 37.037 0.00 0.00 0.00 3.24
3599 3736 8.727910 CCCTTGTAAACAGTAACTAAAATCCTC 58.272 37.037 0.00 0.00 0.00 3.71
3600 3737 8.727910 CCTTGTAAACAGTAACTAAAATCCTCC 58.272 37.037 0.00 0.00 0.00 4.30
3601 3738 9.503399 CTTGTAAACAGTAACTAAAATCCTCCT 57.497 33.333 0.00 0.00 0.00 3.69
3602 3739 9.498176 TTGTAAACAGTAACTAAAATCCTCCTC 57.502 33.333 0.00 0.00 0.00 3.71
3603 3740 8.098912 TGTAAACAGTAACTAAAATCCTCCTCC 58.901 37.037 0.00 0.00 0.00 4.30
3604 3741 5.340439 ACAGTAACTAAAATCCTCCTCCG 57.660 43.478 0.00 0.00 0.00 4.63
3668 3805 8.937884 GTTTTCTCTCAGATTTTAAGGTACTCC 58.062 37.037 0.00 0.00 38.49 3.85
3689 3826 3.507233 CCCAAATGAATATGGACCATCCG 59.493 47.826 11.17 0.00 40.17 4.18
3703 3840 1.544691 CCATCCGTCGGAGGTAATAGG 59.455 57.143 23.23 10.42 34.05 2.57
3706 3843 0.590195 CCGTCGGAGGTAATAGGTCG 59.410 60.000 4.91 0.00 0.00 4.79
3771 3911 6.842676 AGTTAGGATGCTTAAGATTAAGGGG 58.157 40.000 6.67 0.00 40.31 4.79
3792 3932 3.064931 GCTTAAGCGTTTCTACACCTGT 58.935 45.455 12.53 0.00 0.00 4.00
3801 3941 4.279659 GTTTCTACACCTGTTTTGAAGCG 58.720 43.478 0.00 0.00 0.00 4.68
3822 3962 3.687698 CGAAATGGTGATTTTACCCTCGT 59.312 43.478 0.00 0.00 40.09 4.18
3901 4041 0.036577 CCTGCTCTGTGAAGTCCCTG 60.037 60.000 0.00 0.00 0.00 4.45
3940 4095 1.836802 TGCCCATACGTTTTTACCCC 58.163 50.000 0.00 0.00 0.00 4.95
3950 4105 7.756272 CCATACGTTTTTACCCCTGTTTTATTC 59.244 37.037 0.00 0.00 0.00 1.75
3975 4130 9.762381 TCTGATATTTGTGTTTTTACCCCTATT 57.238 29.630 0.00 0.00 0.00 1.73
4008 4163 0.179936 CAGCTGATGGGGAAGGACTC 59.820 60.000 8.42 0.00 0.00 3.36
4069 4224 4.083862 GGAAGAAGGGCTCGCCGT 62.084 66.667 1.24 0.00 36.85 5.68
4090 4245 4.821589 CGTCGGGGAAGGAGCTGC 62.822 72.222 0.00 0.00 0.00 5.25
4163 4318 4.193334 CATCCGTGCGAGGCGAGA 62.193 66.667 0.00 0.00 0.00 4.04
4178 4333 1.599240 GAGATCGCATGGGGAAGGC 60.599 63.158 10.21 0.00 0.00 4.35
4233 4388 1.750399 GGCCATCAACGCCATCACT 60.750 57.895 0.00 0.00 46.27 3.41
4245 4400 2.216148 CATCACTGGAGGGAGGGAC 58.784 63.158 0.00 0.00 0.00 4.46
4246 4401 1.381872 ATCACTGGAGGGAGGGACG 60.382 63.158 0.00 0.00 0.00 4.79
4277 4432 3.564027 CGCGGCGGTGGAATCTTC 61.564 66.667 15.84 0.00 0.00 2.87
4292 4447 1.677966 CTTCGACCAGACGGAGGGA 60.678 63.158 0.00 0.00 35.51 4.20
4323 4478 0.323629 CTGGAGTTAAAGGCCCGTCA 59.676 55.000 0.00 0.00 0.00 4.35
4328 4483 1.092348 GTTAAAGGCCCGTCATCACC 58.908 55.000 0.00 0.00 0.00 4.02
4329 4484 0.391927 TTAAAGGCCCGTCATCACCG 60.392 55.000 0.00 0.00 0.00 4.94
4330 4485 1.546589 TAAAGGCCCGTCATCACCGT 61.547 55.000 0.00 0.00 0.00 4.83
4331 4486 3.605749 AAGGCCCGTCATCACCGTG 62.606 63.158 0.00 0.00 0.00 4.94
4333 4488 4.077184 GCCCGTCATCACCGTGGA 62.077 66.667 0.00 0.00 0.00 4.02
4334 4489 2.900273 CCCGTCATCACCGTGGAT 59.100 61.111 0.00 0.00 0.00 3.41
4335 4490 1.521457 CCCGTCATCACCGTGGATG 60.521 63.158 7.11 7.11 44.78 3.51
4336 4491 2.173669 CCGTCATCACCGTGGATGC 61.174 63.158 8.29 4.21 43.44 3.91
4337 4492 1.447663 CGTCATCACCGTGGATGCA 60.448 57.895 8.29 0.00 43.44 3.96
4338 4493 1.018752 CGTCATCACCGTGGATGCAA 61.019 55.000 8.29 0.00 43.44 4.08
4339 4494 0.729116 GTCATCACCGTGGATGCAAG 59.271 55.000 8.29 0.00 43.44 4.01
4340 4495 0.392863 TCATCACCGTGGATGCAAGG 60.393 55.000 17.32 17.32 43.44 3.61
4341 4496 0.392863 CATCACCGTGGATGCAAGGA 60.393 55.000 25.03 4.59 38.35 3.36
4342 4497 0.107508 ATCACCGTGGATGCAAGGAG 60.108 55.000 25.03 17.35 0.00 3.69
4343 4498 2.045926 ACCGTGGATGCAAGGAGC 60.046 61.111 25.03 0.00 45.96 4.70
4344 4499 2.825836 CCGTGGATGCAAGGAGCC 60.826 66.667 13.94 0.00 44.83 4.70
4345 4500 2.825836 CGTGGATGCAAGGAGCCC 60.826 66.667 0.00 0.00 44.83 5.19
4346 4501 2.679716 GTGGATGCAAGGAGCCCT 59.320 61.111 0.00 0.00 44.83 5.19
4347 4502 1.452833 GTGGATGCAAGGAGCCCTC 60.453 63.158 0.00 0.00 44.83 4.30
4348 4503 2.203126 GGATGCAAGGAGCCCTCG 60.203 66.667 0.00 0.00 44.83 4.63
4349 4504 2.586792 GATGCAAGGAGCCCTCGT 59.413 61.111 0.00 0.00 44.83 4.18
4350 4505 1.522580 GATGCAAGGAGCCCTCGTC 60.523 63.158 0.00 0.00 44.83 4.20
4351 4506 3.376935 ATGCAAGGAGCCCTCGTCG 62.377 63.158 0.00 0.00 44.83 5.12
4352 4507 4.821589 GCAAGGAGCCCTCGTCGG 62.822 72.222 0.00 0.00 37.23 4.79
4371 4526 4.436998 GCCGTCGGTGGTGAGGAG 62.437 72.222 13.94 0.00 0.00 3.69
4372 4527 3.760035 CCGTCGGTGGTGAGGAGG 61.760 72.222 2.08 0.00 0.00 4.30
4373 4528 4.436998 CGTCGGTGGTGAGGAGGC 62.437 72.222 0.00 0.00 0.00 4.70
4374 4529 4.083862 GTCGGTGGTGAGGAGGCC 62.084 72.222 0.00 0.00 0.00 5.19
4448 4603 4.816984 GAGGGCGACGAGGAGGGA 62.817 72.222 0.00 0.00 0.00 4.20
4449 4604 4.824515 AGGGCGACGAGGAGGGAG 62.825 72.222 0.00 0.00 0.00 4.30
4450 4605 4.816984 GGGCGACGAGGAGGGAGA 62.817 72.222 0.00 0.00 0.00 3.71
4451 4606 3.213402 GGCGACGAGGAGGGAGAG 61.213 72.222 0.00 0.00 0.00 3.20
4452 4607 3.894947 GCGACGAGGAGGGAGAGC 61.895 72.222 0.00 0.00 0.00 4.09
4453 4608 3.213402 CGACGAGGAGGGAGAGCC 61.213 72.222 0.00 0.00 0.00 4.70
4454 4609 3.213402 GACGAGGAGGGAGAGCCG 61.213 72.222 0.00 0.00 33.83 5.52
4474 4629 4.748144 GCCCCTGGTCCTGCCTTG 62.748 72.222 0.00 0.00 38.35 3.61
4475 4630 4.052518 CCCCTGGTCCTGCCTTGG 62.053 72.222 0.00 0.00 38.35 3.61
4476 4631 3.260100 CCCTGGTCCTGCCTTGGT 61.260 66.667 0.00 0.00 38.35 3.67
4477 4632 2.352805 CCTGGTCCTGCCTTGGTC 59.647 66.667 0.00 0.00 38.35 4.02
4478 4633 2.227036 CCTGGTCCTGCCTTGGTCT 61.227 63.158 0.00 0.00 38.35 3.85
4479 4634 1.763770 CTGGTCCTGCCTTGGTCTT 59.236 57.895 0.00 0.00 38.35 3.01
4480 4635 0.111253 CTGGTCCTGCCTTGGTCTTT 59.889 55.000 0.00 0.00 38.35 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.676195 CAACCAAACATTTTCTTTTTGTCTTTT 57.324 25.926 0.00 0.00 0.00 2.27
10 11 8.296000 CCAACCAAACATTTTCTTTTTGTCTTT 58.704 29.630 0.00 0.00 0.00 2.52
11 12 7.446931 ACCAACCAAACATTTTCTTTTTGTCTT 59.553 29.630 0.00 0.00 0.00 3.01
12 13 6.939730 ACCAACCAAACATTTTCTTTTTGTCT 59.060 30.769 0.00 0.00 0.00 3.41
13 14 7.139896 ACCAACCAAACATTTTCTTTTTGTC 57.860 32.000 0.00 0.00 0.00 3.18
14 15 7.013750 ACAACCAACCAAACATTTTCTTTTTGT 59.986 29.630 0.00 0.00 0.00 2.83
15 16 7.325579 CACAACCAACCAAACATTTTCTTTTTG 59.674 33.333 0.00 0.00 0.00 2.44
16 17 7.013750 ACACAACCAACCAAACATTTTCTTTTT 59.986 29.630 0.00 0.00 0.00 1.94
17 18 6.488344 ACACAACCAACCAAACATTTTCTTTT 59.512 30.769 0.00 0.00 0.00 2.27
18 19 6.000840 ACACAACCAACCAAACATTTTCTTT 58.999 32.000 0.00 0.00 0.00 2.52
19 20 5.555966 ACACAACCAACCAAACATTTTCTT 58.444 33.333 0.00 0.00 0.00 2.52
20 21 5.159273 ACACAACCAACCAAACATTTTCT 57.841 34.783 0.00 0.00 0.00 2.52
21 22 5.626211 CAACACAACCAACCAAACATTTTC 58.374 37.500 0.00 0.00 0.00 2.29
22 23 4.083057 GCAACACAACCAACCAAACATTTT 60.083 37.500 0.00 0.00 0.00 1.82
23 24 3.438434 GCAACACAACCAACCAAACATTT 59.562 39.130 0.00 0.00 0.00 2.32
24 25 3.006247 GCAACACAACCAACCAAACATT 58.994 40.909 0.00 0.00 0.00 2.71
25 26 2.027745 TGCAACACAACCAACCAAACAT 60.028 40.909 0.00 0.00 0.00 2.71
55 56 1.468520 CGAATTTTGGATGCGAGGTGT 59.531 47.619 0.00 0.00 0.00 4.16
130 131 2.370445 GCCCTAAGCCTGGCTGAGA 61.370 63.158 31.09 15.10 39.42 3.27
131 132 2.191641 GCCCTAAGCCTGGCTGAG 59.808 66.667 24.12 24.12 44.46 3.35
137 138 0.179034 CTAAGCCTGCCCTAAGCCTG 60.179 60.000 0.00 0.00 42.71 4.85
138 139 1.348775 CCTAAGCCTGCCCTAAGCCT 61.349 60.000 0.00 0.00 42.71 4.58
139 140 1.149401 CCTAAGCCTGCCCTAAGCC 59.851 63.158 0.00 0.00 42.71 4.35
142 143 0.253441 TTCCCCTAAGCCTGCCCTAA 60.253 55.000 0.00 0.00 0.00 2.69
143 144 0.986550 GTTCCCCTAAGCCTGCCCTA 60.987 60.000 0.00 0.00 0.00 3.53
144 145 2.127297 TTCCCCTAAGCCTGCCCT 59.873 61.111 0.00 0.00 0.00 5.19
145 146 2.275748 GTTCCCCTAAGCCTGCCC 59.724 66.667 0.00 0.00 0.00 5.36
146 147 2.124695 CGTTCCCCTAAGCCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
147 148 2.824489 GCGTTCCCCTAAGCCTGC 60.824 66.667 0.00 0.00 0.00 4.85
154 155 1.455248 CCGATTTTTGCGTTCCCCTA 58.545 50.000 0.00 0.00 0.00 3.53
216 218 5.827568 TCTCACATACCGTTTCGTTTAAC 57.172 39.130 0.00 0.00 0.00 2.01
257 259 5.106752 GCGGTGGCAATTTCAACATAATTTT 60.107 36.000 0.00 0.00 39.62 1.82
311 315 1.663074 GATCCGGCGCATGAGAGAC 60.663 63.158 10.83 0.00 0.00 3.36
325 339 1.300233 GGTGTGCTCGATCCGATCC 60.300 63.158 2.69 0.00 34.61 3.36
360 381 2.433145 CGAGCTCGAAAGGCAGCA 60.433 61.111 32.06 0.00 43.02 4.41
689 806 1.293179 CTCACCATCCTGCGACACA 59.707 57.895 0.00 0.00 0.00 3.72
694 811 2.821366 GTGCCTCACCATCCTGCG 60.821 66.667 0.00 0.00 0.00 5.18
756 881 3.758973 TTCCCAAAGCACGACGGCA 62.759 57.895 10.28 0.00 35.83 5.69
757 882 2.966309 CTTCCCAAAGCACGACGGC 61.966 63.158 0.00 0.00 0.00 5.68
792 918 4.402829 TGCATGTTTGGGTATGTTGTACT 58.597 39.130 0.00 0.00 0.00 2.73
800 926 3.053395 ACCTGAGATGCATGTTTGGGTAT 60.053 43.478 2.46 0.00 0.00 2.73
803 929 1.747355 GACCTGAGATGCATGTTTGGG 59.253 52.381 2.46 6.53 0.00 4.12
893 1019 1.207329 GTAGGAATCACGGCCACTCTT 59.793 52.381 2.24 0.00 0.00 2.85
897 1023 1.139058 AGATGTAGGAATCACGGCCAC 59.861 52.381 2.24 0.00 0.00 5.01
898 1024 1.496060 AGATGTAGGAATCACGGCCA 58.504 50.000 2.24 0.00 0.00 5.36
899 1025 2.628657 AGTAGATGTAGGAATCACGGCC 59.371 50.000 0.00 0.00 0.00 6.13
900 1026 5.646577 ATAGTAGATGTAGGAATCACGGC 57.353 43.478 0.00 0.00 0.00 5.68
901 1027 8.237949 CACTAATAGTAGATGTAGGAATCACGG 58.762 40.741 3.83 0.00 0.00 4.94
902 1028 9.000486 TCACTAATAGTAGATGTAGGAATCACG 58.000 37.037 3.83 0.00 0.00 4.35
969 1095 7.480810 GGTAATCCACCTTTAAACATGATGAC 58.519 38.462 0.00 0.00 44.79 3.06
1005 1131 3.312828 CGAGTAGTGCTGCTCCATATTC 58.687 50.000 10.82 0.00 38.81 1.75
1007 1133 1.000283 GCGAGTAGTGCTGCTCCATAT 60.000 52.381 10.82 0.00 38.81 1.78
1059 1185 1.482954 TCCACAGATCTCTCAGCTGG 58.517 55.000 15.13 4.77 34.05 4.85
1070 1196 0.622665 CCTTGGGCTCTTCCACAGAT 59.377 55.000 0.00 0.00 36.38 2.90
1095 1221 3.056749 CCAAAGCCTCTACACGAAGTACT 60.057 47.826 0.00 0.00 41.61 2.73
1218 1344 7.215719 TGTCCCAAGAGATATAGATAACACG 57.784 40.000 0.00 0.00 0.00 4.49
1233 1359 5.030147 AGACCAATACTGTATGTCCCAAGA 58.970 41.667 12.21 0.00 0.00 3.02
1457 1583 1.867233 GCACACCGATGGCTATGTTAG 59.133 52.381 0.00 0.00 0.00 2.34
1590 1716 7.596621 GCGTAGTCATAATCATCAAGATCTGAA 59.403 37.037 0.00 0.00 37.67 3.02
1614 1740 5.833082 ACTACCAAGTCTGATACTATTGCG 58.167 41.667 0.00 0.00 37.50 4.85
1669 1795 7.072030 CGCGCTAATATTGAATAAAAGCTCTT 58.928 34.615 5.56 0.00 0.00 2.85
1691 1817 0.443869 CCTCAAAACTCCATCACGCG 59.556 55.000 3.53 3.53 0.00 6.01
1860 1986 6.760298 TGAAGTCTGAAGCAATCTGATATGAC 59.240 38.462 0.00 0.00 38.16 3.06
1944 2070 4.781934 AGTAGTGAAGGAATGCATTACCC 58.218 43.478 18.34 13.17 30.32 3.69
2013 2139 2.416701 CGCCACCCCAACAAAACATATC 60.417 50.000 0.00 0.00 0.00 1.63
2052 2178 1.541233 GCACTATGGCGGCTAGTCATT 60.541 52.381 11.43 0.00 43.84 2.57
2216 2342 3.058160 GCATGTTCCTGGCGTGCT 61.058 61.111 10.23 0.00 43.37 4.40
2461 2587 1.152567 TGCCCACCAGTTCCCAAAG 60.153 57.895 0.00 0.00 0.00 2.77
2463 2589 2.520458 CTGCCCACCAGTTCCCAA 59.480 61.111 0.00 0.00 36.79 4.12
2535 2661 2.809601 CGACCAAGGAACTCGGCG 60.810 66.667 0.00 0.00 38.49 6.46
2542 2668 3.264706 TCATTATGAACCCGACCAAGGAA 59.735 43.478 0.00 0.00 0.00 3.36
2568 2694 1.682323 GACGACCAACTCTCCCCTATC 59.318 57.143 0.00 0.00 0.00 2.08
2759 2885 0.600057 CTTTTCTTCTGCCCCTGTGC 59.400 55.000 0.00 0.00 0.00 4.57
2766 2892 0.799393 GCCGACTCTTTTCTTCTGCC 59.201 55.000 0.00 0.00 0.00 4.85
2796 2922 2.009042 GCGCAATACTTGGACAGAGCT 61.009 52.381 0.30 0.00 0.00 4.09
2838 2964 0.672711 GCGTCCCAGGTAACAACTCC 60.673 60.000 0.00 0.00 41.41 3.85
2845 2971 1.344065 TTCTGAAGCGTCCCAGGTAA 58.656 50.000 0.00 0.00 0.00 2.85
2853 2979 3.139077 TCCTTTCCTTTTCTGAAGCGTC 58.861 45.455 0.00 0.00 0.00 5.19
2873 2999 1.330521 ACGCAACGCCATCATATGTTC 59.669 47.619 1.90 0.00 0.00 3.18
2877 3003 1.221466 CCGACGCAACGCCATCATAT 61.221 55.000 0.00 0.00 0.00 1.78
2886 3012 2.170985 CTTGCTTCCGACGCAACG 59.829 61.111 8.14 2.34 41.97 4.10
2891 3017 0.038159 AACTCTCCTTGCTTCCGACG 60.038 55.000 0.00 0.00 0.00 5.12
2906 3032 0.827507 TTTGGCCCCTTGCAGAACTC 60.828 55.000 0.00 0.00 43.89 3.01
2913 3039 1.667722 CTTGTCTTTGGCCCCTTGC 59.332 57.895 0.00 0.00 40.16 4.01
2945 3071 4.664188 GAGATCGATATAGGGTTCGCTTC 58.336 47.826 0.00 0.00 35.39 3.86
2956 3082 5.216918 GCTAGGGCTGTCGAGATCGATATA 61.217 50.000 8.34 0.00 42.07 0.86
3018 3144 1.460273 CCCCAACGTCCCCACAAAAG 61.460 60.000 0.00 0.00 0.00 2.27
3187 3313 4.081198 CCATCTCTCTACAGTTTTCCAGCT 60.081 45.833 0.00 0.00 0.00 4.24
3222 3348 2.234908 CTCCTCGGTCTCCAACTTCATT 59.765 50.000 0.00 0.00 0.00 2.57
3267 3393 0.765510 GGTCACCCTTGAACTGTCCT 59.234 55.000 0.00 0.00 36.41 3.85
3287 3413 4.335416 TGCTTTTGAGCAGGTATTAAGCT 58.665 39.130 0.00 0.00 40.23 3.74
3288 3414 4.701956 TGCTTTTGAGCAGGTATTAAGC 57.298 40.909 0.00 0.00 40.23 3.09
3300 3426 4.697514 TCGGATTATCCTCTGCTTTTGAG 58.302 43.478 9.78 0.00 33.30 3.02
3312 3438 4.998033 GGAATTGAACTCCTCGGATTATCC 59.002 45.833 0.14 0.14 0.00 2.59
3325 3451 4.279420 GGCACTTTGAAGAGGAATTGAACT 59.721 41.667 0.00 0.00 0.00 3.01
3353 3479 5.026121 TGTCCATGGAGTTCTCTTCTATGT 58.974 41.667 16.81 0.00 0.00 2.29
3448 3574 3.438087 CGAATGTCAGCTTGAACAGGAAT 59.562 43.478 0.00 0.00 0.00 3.01
3456 3582 3.200483 CATCCATCGAATGTCAGCTTGA 58.800 45.455 0.00 0.00 0.00 3.02
3468 3594 2.952310 CTGTCTGTCCTACATCCATCGA 59.048 50.000 0.00 0.00 0.00 3.59
3481 3607 2.790433 AGTCCTCTCAGTCTGTCTGTC 58.210 52.381 0.00 0.00 43.97 3.51
3482 3608 2.969821 AGTCCTCTCAGTCTGTCTGT 57.030 50.000 0.00 0.00 43.97 3.41
3483 3609 4.764823 ACTAAAGTCCTCTCAGTCTGTCTG 59.235 45.833 0.00 0.00 44.85 3.51
3519 3656 2.244117 GATTCGCTGGTCCTGAGCCA 62.244 60.000 0.00 0.00 32.41 4.75
3534 3671 0.458543 TCCTGCGCTCGAACTGATTC 60.459 55.000 9.73 0.00 0.00 2.52
3535 3672 0.737715 GTCCTGCGCTCGAACTGATT 60.738 55.000 9.73 0.00 0.00 2.57
3536 3673 1.153745 GTCCTGCGCTCGAACTGAT 60.154 57.895 9.73 0.00 0.00 2.90
3537 3674 2.258591 GTCCTGCGCTCGAACTGA 59.741 61.111 9.73 0.00 0.00 3.41
3538 3675 3.175240 CGTCCTGCGCTCGAACTG 61.175 66.667 9.73 0.00 0.00 3.16
3549 3686 4.007644 TGACCCAGCTGCGTCCTG 62.008 66.667 24.93 3.87 0.00 3.86
3550 3687 4.008933 GTGACCCAGCTGCGTCCT 62.009 66.667 24.93 0.00 0.00 3.85
3552 3689 4.008933 AGGTGACCCAGCTGCGTC 62.009 66.667 22.06 22.06 40.87 5.19
3557 3694 3.325753 GGCTCAGGTGACCCAGCT 61.326 66.667 19.34 0.94 43.33 4.24
3558 3695 4.416738 GGGCTCAGGTGACCCAGC 62.417 72.222 13.45 13.45 43.64 4.85
3559 3696 2.227036 AAGGGCTCAGGTGACCCAG 61.227 63.158 15.71 0.00 46.88 4.45
3560 3697 2.121963 AAGGGCTCAGGTGACCCA 60.122 61.111 15.71 0.00 46.88 4.51
3561 3698 1.198759 TACAAGGGCTCAGGTGACCC 61.199 60.000 0.00 8.73 44.62 4.46
3562 3699 0.690762 TTACAAGGGCTCAGGTGACC 59.309 55.000 0.00 0.00 0.00 4.02
3563 3700 2.152016 GTTTACAAGGGCTCAGGTGAC 58.848 52.381 0.00 0.00 0.00 3.67
3564 3701 1.771854 TGTTTACAAGGGCTCAGGTGA 59.228 47.619 0.00 0.00 0.00 4.02
3565 3702 2.154462 CTGTTTACAAGGGCTCAGGTG 58.846 52.381 0.00 0.00 0.00 4.00
3566 3703 1.774856 ACTGTTTACAAGGGCTCAGGT 59.225 47.619 0.00 0.00 0.00 4.00
3567 3704 2.568623 ACTGTTTACAAGGGCTCAGG 57.431 50.000 0.00 0.00 0.00 3.86
3568 3705 4.642429 AGTTACTGTTTACAAGGGCTCAG 58.358 43.478 0.00 0.00 0.00 3.35
3569 3706 4.699925 AGTTACTGTTTACAAGGGCTCA 57.300 40.909 0.00 0.00 0.00 4.26
3570 3707 7.500720 TTTTAGTTACTGTTTACAAGGGCTC 57.499 36.000 0.00 0.00 0.00 4.70
3571 3708 7.176165 GGATTTTAGTTACTGTTTACAAGGGCT 59.824 37.037 0.00 0.00 0.00 5.19
3572 3709 7.176165 AGGATTTTAGTTACTGTTTACAAGGGC 59.824 37.037 0.00 0.00 0.00 5.19
3573 3710 8.631480 AGGATTTTAGTTACTGTTTACAAGGG 57.369 34.615 0.00 0.00 0.00 3.95
3574 3711 8.727910 GGAGGATTTTAGTTACTGTTTACAAGG 58.272 37.037 0.00 0.00 0.00 3.61
3575 3712 9.503399 AGGAGGATTTTAGTTACTGTTTACAAG 57.497 33.333 0.00 0.00 0.00 3.16
3576 3713 9.498176 GAGGAGGATTTTAGTTACTGTTTACAA 57.502 33.333 0.00 0.00 0.00 2.41
3577 3714 8.098912 GGAGGAGGATTTTAGTTACTGTTTACA 58.901 37.037 0.00 0.00 0.00 2.41
3578 3715 7.277319 CGGAGGAGGATTTTAGTTACTGTTTAC 59.723 40.741 0.00 0.00 0.00 2.01
3579 3716 7.038799 ACGGAGGAGGATTTTAGTTACTGTTTA 60.039 37.037 0.00 0.00 0.00 2.01
3580 3717 6.171213 CGGAGGAGGATTTTAGTTACTGTTT 58.829 40.000 0.00 0.00 0.00 2.83
3581 3718 5.247792 ACGGAGGAGGATTTTAGTTACTGTT 59.752 40.000 0.00 0.00 0.00 3.16
3582 3719 4.776308 ACGGAGGAGGATTTTAGTTACTGT 59.224 41.667 0.00 0.00 0.00 3.55
3583 3720 5.127356 AGACGGAGGAGGATTTTAGTTACTG 59.873 44.000 0.00 0.00 0.00 2.74
3584 3721 5.127356 CAGACGGAGGAGGATTTTAGTTACT 59.873 44.000 0.00 0.00 0.00 2.24
3585 3722 5.349809 CAGACGGAGGAGGATTTTAGTTAC 58.650 45.833 0.00 0.00 0.00 2.50
3586 3723 4.404715 CCAGACGGAGGAGGATTTTAGTTA 59.595 45.833 0.00 0.00 0.00 2.24
3587 3724 3.197983 CCAGACGGAGGAGGATTTTAGTT 59.802 47.826 0.00 0.00 0.00 2.24
3588 3725 2.766828 CCAGACGGAGGAGGATTTTAGT 59.233 50.000 0.00 0.00 0.00 2.24
3589 3726 2.766828 ACCAGACGGAGGAGGATTTTAG 59.233 50.000 0.00 0.00 35.59 1.85
3590 3727 2.764572 GACCAGACGGAGGAGGATTTTA 59.235 50.000 0.00 0.00 35.59 1.52
3591 3728 1.555533 GACCAGACGGAGGAGGATTTT 59.444 52.381 0.00 0.00 35.59 1.82
3592 3729 1.196012 GACCAGACGGAGGAGGATTT 58.804 55.000 0.00 0.00 35.59 2.17
3593 3730 0.041238 TGACCAGACGGAGGAGGATT 59.959 55.000 0.00 0.00 35.59 3.01
3594 3731 0.684805 GTGACCAGACGGAGGAGGAT 60.685 60.000 0.00 0.00 35.59 3.24
3595 3732 1.304217 GTGACCAGACGGAGGAGGA 60.304 63.158 0.00 0.00 35.59 3.71
3596 3733 2.352032 GGTGACCAGACGGAGGAGG 61.352 68.421 0.00 0.00 35.59 4.30
3597 3734 1.304547 AGGTGACCAGACGGAGGAG 60.305 63.158 3.63 0.00 35.59 3.69
3598 3735 1.606601 CAGGTGACCAGACGGAGGA 60.607 63.158 3.63 0.00 35.59 3.71
3599 3736 1.599606 CTCAGGTGACCAGACGGAGG 61.600 65.000 3.63 0.00 35.59 4.30
3600 3737 0.609406 TCTCAGGTGACCAGACGGAG 60.609 60.000 3.63 2.78 35.59 4.63
3601 3738 0.894184 GTCTCAGGTGACCAGACGGA 60.894 60.000 3.63 0.00 32.73 4.69
3602 3739 1.587054 GTCTCAGGTGACCAGACGG 59.413 63.158 3.63 0.00 32.73 4.79
3625 3762 9.145865 GAGAGAAAACATTACTTAGAAGACTGG 57.854 37.037 0.00 0.00 0.00 4.00
3668 3805 4.144297 ACGGATGGTCCATATTCATTTGG 58.856 43.478 3.72 0.00 35.91 3.28
3689 3826 0.313357 GGCGACCTATTACCTCCGAC 59.687 60.000 0.00 0.00 0.00 4.79
3734 3871 8.822652 AAGCATCCTAACTTTTCAAATTGAAG 57.177 30.769 8.51 0.97 37.70 3.02
3737 3874 9.912634 TCTTAAGCATCCTAACTTTTCAAATTG 57.087 29.630 0.00 0.00 0.00 2.32
3771 3911 3.064931 ACAGGTGTAGAAACGCTTAAGC 58.935 45.455 17.83 17.83 36.33 3.09
3792 3932 6.422400 GGTAAAATCACCATTTCGCTTCAAAA 59.578 34.615 0.00 0.00 38.55 2.44
3801 3941 5.638596 AACGAGGGTAAAATCACCATTTC 57.361 39.130 0.00 0.00 40.65 2.17
3830 3970 8.080363 TGTAGGGGTAAAATCACAAAGTTTTT 57.920 30.769 0.00 0.00 34.45 1.94
3831 3971 7.663043 TGTAGGGGTAAAATCACAAAGTTTT 57.337 32.000 0.00 0.00 0.00 2.43
3832 3972 7.663043 TTGTAGGGGTAAAATCACAAAGTTT 57.337 32.000 0.00 0.00 0.00 2.66
3840 3980 7.868415 CGTTTTGAAATTGTAGGGGTAAAATCA 59.132 33.333 0.00 0.00 0.00 2.57
3901 4041 3.057526 GCAAGTTGTCATTTGGTCCCTAC 60.058 47.826 4.48 0.00 0.00 3.18
3909 4063 3.057596 ACGTATGGGCAAGTTGTCATTTG 60.058 43.478 10.13 9.39 0.00 2.32
3968 4123 5.675538 CTGTCCTTTGTCTAGAAATAGGGG 58.324 45.833 16.85 6.58 0.00 4.79
3975 4130 4.323028 CCATCAGCTGTCCTTTGTCTAGAA 60.323 45.833 14.67 0.00 0.00 2.10
4046 4201 1.819905 GAGCCCTTCTTCCTCCGAG 59.180 63.158 0.00 0.00 0.00 4.63
4069 4224 2.749044 CTCCTTCCCCGACGACGA 60.749 66.667 9.28 0.00 42.66 4.20
4090 4245 1.079127 CTAGCCACACCTTCCACGG 60.079 63.158 0.00 0.00 0.00 4.94
4159 4314 1.301244 CCTTCCCCATGCGATCTCG 60.301 63.158 0.00 0.00 43.27 4.04
4163 4318 2.194056 CAGCCTTCCCCATGCGAT 59.806 61.111 0.00 0.00 0.00 4.58
4222 4377 1.903877 CTCCCTCCAGTGATGGCGTT 61.904 60.000 0.00 0.00 0.00 4.84
4268 4423 0.530744 CCGTCTGGTCGAAGATTCCA 59.469 55.000 0.00 0.00 40.67 3.53
4277 4432 3.812019 CGTCCCTCCGTCTGGTCG 61.812 72.222 0.00 0.00 36.30 4.79
4323 4478 0.107508 CTCCTTGCATCCACGGTGAT 60.108 55.000 10.28 0.00 32.48 3.06
4328 4483 2.825836 GGGCTCCTTGCATCCACG 60.826 66.667 0.00 0.00 45.15 4.94
4329 4484 1.452833 GAGGGCTCCTTGCATCCAC 60.453 63.158 0.00 0.00 45.15 4.02
4330 4485 3.001514 GAGGGCTCCTTGCATCCA 58.998 61.111 0.00 0.00 45.15 3.41
4331 4486 2.203126 CGAGGGCTCCTTGCATCC 60.203 66.667 0.00 0.00 45.15 3.51
4332 4487 1.522580 GACGAGGGCTCCTTGCATC 60.523 63.158 8.07 0.00 45.15 3.91
4333 4488 2.586792 GACGAGGGCTCCTTGCAT 59.413 61.111 8.07 0.00 45.15 3.96
4334 4489 4.069232 CGACGAGGGCTCCTTGCA 62.069 66.667 8.07 0.00 45.15 4.08
4335 4490 4.821589 CCGACGAGGGCTCCTTGC 62.822 72.222 0.00 2.19 38.56 4.01
4354 4509 4.436998 CTCCTCACCACCGACGGC 62.437 72.222 15.39 0.00 0.00 5.68
4355 4510 3.760035 CCTCCTCACCACCGACGG 61.760 72.222 13.61 13.61 0.00 4.79
4356 4511 4.436998 GCCTCCTCACCACCGACG 62.437 72.222 0.00 0.00 0.00 5.12
4357 4512 4.083862 GGCCTCCTCACCACCGAC 62.084 72.222 0.00 0.00 0.00 4.79
4431 4586 4.816984 TCCCTCCTCGTCGCCCTC 62.817 72.222 0.00 0.00 0.00 4.30
4432 4587 4.824515 CTCCCTCCTCGTCGCCCT 62.825 72.222 0.00 0.00 0.00 5.19
4433 4588 4.816984 TCTCCCTCCTCGTCGCCC 62.817 72.222 0.00 0.00 0.00 6.13
4434 4589 3.213402 CTCTCCCTCCTCGTCGCC 61.213 72.222 0.00 0.00 0.00 5.54
4435 4590 3.894947 GCTCTCCCTCCTCGTCGC 61.895 72.222 0.00 0.00 0.00 5.19
4436 4591 3.213402 GGCTCTCCCTCCTCGTCG 61.213 72.222 0.00 0.00 0.00 5.12
4437 4592 3.213402 CGGCTCTCCCTCCTCGTC 61.213 72.222 0.00 0.00 0.00 4.20
4457 4612 4.748144 CAAGGCAGGACCAGGGGC 62.748 72.222 0.00 0.00 43.14 5.80
4458 4613 4.052518 CCAAGGCAGGACCAGGGG 62.053 72.222 0.00 0.00 43.14 4.79
4459 4614 3.260100 ACCAAGGCAGGACCAGGG 61.260 66.667 2.81 0.00 43.14 4.45
4460 4615 1.783250 AAGACCAAGGCAGGACCAGG 61.783 60.000 2.81 0.00 43.14 4.45
4461 4616 0.111253 AAAGACCAAGGCAGGACCAG 59.889 55.000 2.81 0.00 43.14 4.00
4462 4617 2.240510 AAAGACCAAGGCAGGACCA 58.759 52.632 2.81 0.00 43.14 4.02


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

AutoCloner maintained by Alex Coulton.