Multiple sequence alignment - TraesCS7D01G248500

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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 TraesCS7D01G248500 chr7D 100.000 5673 0 0 1 5673 220273087 220278759 0.000000e+00 10477
1 TraesCS7D01G248500 chr7D 96.708 243 8 0 3510 3752 194552374 194552616 6.840000e-109 405
2 TraesCS7D01G248500 chr7D 95.935 246 10 0 3508 3753 155292309 155292554 3.180000e-107 399
3 TraesCS7D01G248500 chr7D 93.822 259 15 1 3511 3768 210295766 210295508 6.890000e-104 388
4 TraesCS7D01G248500 chr7B 93.882 3563 124 30 1 3502 179259711 179256182 0.000000e+00 5286
5 TraesCS7D01G248500 chr7B 98.283 1922 27 3 3752 5673 179256135 179254220 0.000000e+00 3362
6 TraesCS7D01G248500 chr7A 94.719 2367 79 16 1163 3511 232585988 232588326 0.000000e+00 3637
7 TraesCS7D01G248500 chr7A 94.166 1954 76 17 3752 5673 232588328 232590275 0.000000e+00 2942
8 TraesCS7D01G248500 chr7A 91.047 726 32 20 1 708 232584731 232585441 0.000000e+00 950
9 TraesCS7D01G248500 chr7A 93.573 389 23 1 779 1165 232585519 232585907 3.810000e-161 579
10 TraesCS7D01G248500 chr2D 96.721 244 7 1 3509 3752 347496441 347496683 6.840000e-109 405
11 TraesCS7D01G248500 chr2B 96.327 245 9 0 3507 3751 464038315 464038559 2.460000e-108 403
12 TraesCS7D01G248500 chr5B 96.680 241 8 0 3513 3753 131081182 131080942 8.850000e-108 401
13 TraesCS7D01G248500 chr5B 89.796 98 10 0 3355 3452 457123194 457123291 5.970000e-25 126
14 TraesCS7D01G248500 chr4A 95.951 247 9 1 3508 3753 150384287 150384041 3.180000e-107 399
15 TraesCS7D01G248500 chr6B 95.918 245 10 0 3509 3753 427455709 427455465 1.150000e-106 398
16 TraesCS7D01G248500 chr4D 95.918 245 9 1 3509 3753 338268120 338268363 4.120000e-106 396


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 TraesCS7D01G248500 chr7D 220273087 220278759 5672 False 10477 10477 100.00000 1 5673 1 chr7D.!!$F3 5672
1 TraesCS7D01G248500 chr7B 179254220 179259711 5491 True 4324 5286 96.08250 1 5673 2 chr7B.!!$R1 5672
2 TraesCS7D01G248500 chr7A 232584731 232590275 5544 False 2027 3637 93.37625 1 5673 4 chr7A.!!$F1 5672

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
871 926 0.539518 GGCTTCCTCCTTCTCCTCAC 59.460 60.000 0.0 0.0 0.00 3.51 F
1397 1539 0.527113 CATCATTTTCCAGCACCGCA 59.473 50.000 0.0 0.0 0.00 5.69 F
2751 2919 1.132453 GTCAGCTTAATCCCGCAAACC 59.868 52.381 0.0 0.0 0.00 3.27 F
3568 3774 0.186630 TGCCTGCCATCCTGCAATAT 59.813 50.000 0.0 0.0 41.51 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 2434 0.171903 AAAAGGCAGCATAGCAAGCG 59.828 50.000 0.00 0.00 37.01 4.68 R
2996 3164 1.491563 GAGTTTGCAGTACACCGCG 59.508 57.895 0.00 0.00 0.00 6.46 R
3624 3830 0.031010 GAGAGGGGTGTGGGTATCCT 60.031 60.000 0.00 0.00 0.00 3.24 R
5349 5587 0.106769 TTTGGTGTTCCTGCAGAGCA 60.107 50.000 17.39 8.22 36.92 4.26 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 96 7.041098 AGGTCATGGCTGAATTTCGAAATATAC 60.041 37.037 22.99 16.77 31.85 1.47
143 153 0.614812 TCCATCTTGCAGCTGCTGTA 59.385 50.000 36.61 23.01 42.66 2.74
267 279 3.878667 GGAGGAATCGGCAGGGGG 61.879 72.222 0.00 0.00 0.00 5.40
435 459 0.889186 TTGCTTCTTTGGCCTCCGTC 60.889 55.000 3.32 0.00 0.00 4.79
436 460 2.041115 GCTTCTTTGGCCTCCGTCC 61.041 63.158 3.32 0.00 0.00 4.79
439 463 2.725203 TTCTTTGGCCTCCGTCCGTG 62.725 60.000 3.32 0.00 0.00 4.94
440 464 4.323477 TTTGGCCTCCGTCCGTGG 62.323 66.667 3.32 0.00 0.00 4.94
445 469 3.760035 CCTCCGTCCGTGGGTCAG 61.760 72.222 0.00 0.00 0.00 3.51
490 515 0.619832 ATCCTTGGCTGCTCCTCTCA 60.620 55.000 0.00 0.00 35.26 3.27
629 657 2.751166 TGGCTCTTGCTTGTCTCTAC 57.249 50.000 0.00 0.00 39.59 2.59
655 683 1.985473 TGTCCAGCAAAACTCTGCAT 58.015 45.000 0.00 0.00 45.18 3.96
672 700 6.707608 ACTCTGCATTTTTCCTTCCAATTTTC 59.292 34.615 0.00 0.00 0.00 2.29
730 758 2.366167 CTGGAGCTGGGAGGGAGA 59.634 66.667 0.00 0.00 0.00 3.71
777 805 0.758734 CCGGACCAGGCTGATCAATA 59.241 55.000 17.94 0.00 0.00 1.90
853 908 5.139435 TCATTAGCCGAGTGATTAGATGG 57.861 43.478 0.00 0.00 0.00 3.51
857 912 2.139118 GCCGAGTGATTAGATGGCTTC 58.861 52.381 0.00 0.00 39.38 3.86
858 913 2.760374 CCGAGTGATTAGATGGCTTCC 58.240 52.381 0.00 0.00 0.00 3.46
867 922 1.506025 AGATGGCTTCCTCCTTCTCC 58.494 55.000 0.00 0.00 36.28 3.71
868 923 1.009429 AGATGGCTTCCTCCTTCTCCT 59.991 52.381 0.00 0.00 36.28 3.69
871 926 0.539518 GGCTTCCTCCTTCTCCTCAC 59.460 60.000 0.00 0.00 0.00 3.51
965 1020 1.079127 GCACGGGCTAAGCAGAAGA 60.079 57.895 0.00 0.00 36.96 2.87
1075 1130 3.247442 CGAAGGTTAGTATGCACACGAA 58.753 45.455 0.00 0.00 0.00 3.85
1076 1131 3.303495 CGAAGGTTAGTATGCACACGAAG 59.697 47.826 0.00 0.00 0.00 3.79
1095 1152 3.863142 AGCAATCTTTTCAGCATGGTC 57.137 42.857 0.00 0.00 36.16 4.02
1101 1158 6.338146 CAATCTTTTCAGCATGGTCATCATT 58.662 36.000 0.00 0.00 36.16 2.57
1144 1201 3.604582 CTCCAGGGTAAGCTCTTTCTTG 58.395 50.000 0.00 0.00 0.00 3.02
1186 1326 8.789762 TGGTAAAAAGGTATAAAGAGCAGTTTC 58.210 33.333 0.00 0.00 0.00 2.78
1235 1375 6.127366 ACAATTCTGGCCGTTTTGATCAATAT 60.127 34.615 9.40 0.00 0.00 1.28
1262 1404 7.016361 ACGTATTTTCTGCCAATCTTACATC 57.984 36.000 0.00 0.00 0.00 3.06
1266 1408 9.547753 GTATTTTCTGCCAATCTTACATCTAGA 57.452 33.333 0.00 0.00 0.00 2.43
1350 1492 5.185828 CCTTCTTTTCTGAATGTAAAGGGGG 59.814 44.000 10.89 5.86 34.92 5.40
1396 1538 0.527565 ACATCATTTTCCAGCACCGC 59.472 50.000 0.00 0.00 0.00 5.68
1397 1539 0.527113 CATCATTTTCCAGCACCGCA 59.473 50.000 0.00 0.00 0.00 5.69
1411 1553 4.754618 CAGCACCGCATATGTTTCCTAATA 59.245 41.667 4.29 0.00 0.00 0.98
1412 1554 4.755123 AGCACCGCATATGTTTCCTAATAC 59.245 41.667 4.29 0.00 0.00 1.89
1443 1585 3.130340 TCTTGCAAGTCCTTTTGACCAAC 59.870 43.478 25.19 0.00 45.68 3.77
1815 1972 9.766277 CTAAGTTATTTTTCTCTGTCATGCTTC 57.234 33.333 0.00 0.00 0.00 3.86
1870 2027 4.834406 TCCCCATAGGAGATACTCACTT 57.166 45.455 0.00 0.00 40.93 3.16
2162 2319 2.561419 GCCATGAGCCATGATTATGCTT 59.439 45.455 14.52 0.00 43.81 3.91
2169 2326 6.938507 TGAGCCATGATTATGCTTTCTTTTT 58.061 32.000 0.00 0.00 32.79 1.94
2375 2542 1.132643 CTTGAGGAGGAAGTCGTACGG 59.867 57.143 16.52 0.00 0.00 4.02
2505 2672 8.893563 AGGATTTCAATGTTGGGACTTTATAA 57.106 30.769 0.00 0.00 0.00 0.98
2691 2858 1.335810 TCGTAGACATGTATGGACGGC 59.664 52.381 13.98 0.00 35.01 5.68
2726 2894 6.652900 TCGTTCATTCAGTATTCACCATCAAA 59.347 34.615 0.00 0.00 0.00 2.69
2751 2919 1.132453 GTCAGCTTAATCCCGCAAACC 59.868 52.381 0.00 0.00 0.00 3.27
2773 2941 5.898972 ACCCATGCCAATGTTATCTAAACAT 59.101 36.000 0.00 0.00 42.19 2.71
2839 3007 5.250543 TGATGAAACCTCCCAAAGTGAGATA 59.749 40.000 0.00 0.00 31.26 1.98
2907 3075 4.313020 AGATCAACTTCAGGGCATTCTT 57.687 40.909 0.00 0.00 0.00 2.52
2996 3164 5.240403 GGAGGACATTCTAAGATGCATTTCC 59.760 44.000 0.00 0.00 0.00 3.13
3092 3260 3.247006 TCTGCATCGAGTACCTTTTCC 57.753 47.619 0.00 0.00 0.00 3.13
3327 3496 8.345565 ACAATAAACAACTCTTCATCTCAACAC 58.654 33.333 0.00 0.00 0.00 3.32
3508 3714 6.834168 ATGTTCATGTTAACCTCGGAAAAT 57.166 33.333 2.48 0.16 0.00 1.82
3509 3715 7.931578 ATGTTCATGTTAACCTCGGAAAATA 57.068 32.000 2.48 0.00 0.00 1.40
3510 3716 7.931578 TGTTCATGTTAACCTCGGAAAATAT 57.068 32.000 2.48 0.00 0.00 1.28
3511 3717 7.981142 TGTTCATGTTAACCTCGGAAAATATC 58.019 34.615 2.48 0.00 0.00 1.63
3512 3718 7.827236 TGTTCATGTTAACCTCGGAAAATATCT 59.173 33.333 2.48 0.00 0.00 1.98
3513 3719 8.336080 GTTCATGTTAACCTCGGAAAATATCTC 58.664 37.037 2.48 0.00 0.00 2.75
3514 3720 7.792032 TCATGTTAACCTCGGAAAATATCTCT 58.208 34.615 2.48 0.00 0.00 3.10
3515 3721 8.920174 TCATGTTAACCTCGGAAAATATCTCTA 58.080 33.333 2.48 0.00 0.00 2.43
3516 3722 8.979574 CATGTTAACCTCGGAAAATATCTCTAC 58.020 37.037 2.48 0.00 0.00 2.59
3517 3723 8.302515 TGTTAACCTCGGAAAATATCTCTACT 57.697 34.615 2.48 0.00 0.00 2.57
3518 3724 8.411683 TGTTAACCTCGGAAAATATCTCTACTC 58.588 37.037 2.48 0.00 0.00 2.59
3519 3725 8.631797 GTTAACCTCGGAAAATATCTCTACTCT 58.368 37.037 0.00 0.00 0.00 3.24
3520 3726 7.663043 AACCTCGGAAAATATCTCTACTCTT 57.337 36.000 0.00 0.00 0.00 2.85
3521 3727 8.763984 AACCTCGGAAAATATCTCTACTCTTA 57.236 34.615 0.00 0.00 0.00 2.10
3522 3728 8.943594 ACCTCGGAAAATATCTCTACTCTTAT 57.056 34.615 0.00 0.00 0.00 1.73
3546 3752 5.458041 AAAAACAGAGTTGGTGATGATGG 57.542 39.130 0.00 0.00 0.00 3.51
3547 3753 3.795688 AACAGAGTTGGTGATGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
3548 3754 3.063510 ACAGAGTTGGTGATGATGGTG 57.936 47.619 0.00 0.00 0.00 4.17
3549 3755 2.373169 ACAGAGTTGGTGATGATGGTGT 59.627 45.455 0.00 0.00 0.00 4.16
3550 3756 2.745821 CAGAGTTGGTGATGATGGTGTG 59.254 50.000 0.00 0.00 0.00 3.82
3551 3757 1.470098 GAGTTGGTGATGATGGTGTGC 59.530 52.381 0.00 0.00 0.00 4.57
3552 3758 0.527565 GTTGGTGATGATGGTGTGCC 59.472 55.000 0.00 0.00 0.00 5.01
3553 3759 0.405198 TTGGTGATGATGGTGTGCCT 59.595 50.000 0.00 0.00 35.27 4.75
3554 3760 0.322726 TGGTGATGATGGTGTGCCTG 60.323 55.000 0.00 0.00 35.27 4.85
3555 3761 1.660560 GGTGATGATGGTGTGCCTGC 61.661 60.000 0.00 0.00 35.27 4.85
3556 3762 1.378911 TGATGATGGTGTGCCTGCC 60.379 57.895 0.00 0.00 35.27 4.85
3557 3763 1.378911 GATGATGGTGTGCCTGCCA 60.379 57.895 0.00 0.00 39.33 4.92
3560 3766 2.043652 ATGGTGTGCCTGCCATCC 60.044 61.111 0.00 0.00 41.24 3.51
3561 3767 2.619446 ATGGTGTGCCTGCCATCCT 61.619 57.895 0.00 0.00 41.24 3.24
3562 3768 2.753043 GGTGTGCCTGCCATCCTG 60.753 66.667 0.00 0.00 0.00 3.86
3563 3769 3.446570 GTGTGCCTGCCATCCTGC 61.447 66.667 0.00 0.00 0.00 4.85
3564 3770 3.969119 TGTGCCTGCCATCCTGCA 61.969 61.111 0.00 0.00 39.37 4.41
3565 3771 2.677524 GTGCCTGCCATCCTGCAA 60.678 61.111 0.00 0.00 41.51 4.08
3566 3772 2.056223 GTGCCTGCCATCCTGCAAT 61.056 57.895 0.00 0.00 41.51 3.56
3567 3773 0.752743 GTGCCTGCCATCCTGCAATA 60.753 55.000 0.00 0.00 41.51 1.90
3568 3774 0.186630 TGCCTGCCATCCTGCAATAT 59.813 50.000 0.00 0.00 41.51 1.28
3569 3775 1.424684 TGCCTGCCATCCTGCAATATA 59.575 47.619 0.00 0.00 41.51 0.86
3570 3776 2.089980 GCCTGCCATCCTGCAATATAG 58.910 52.381 0.00 0.00 41.51 1.31
3571 3777 2.719739 CCTGCCATCCTGCAATATAGG 58.280 52.381 0.00 0.00 41.51 2.57
3572 3778 2.089980 CTGCCATCCTGCAATATAGGC 58.910 52.381 9.23 9.23 41.51 3.93
3573 3779 1.272092 TGCCATCCTGCAATATAGGCC 60.272 52.381 12.50 0.00 38.56 5.19
3574 3780 1.742761 CCATCCTGCAATATAGGCCG 58.257 55.000 0.00 0.00 35.23 6.13
3575 3781 1.003580 CCATCCTGCAATATAGGCCGT 59.996 52.381 0.00 0.00 35.23 5.68
3576 3782 2.350522 CATCCTGCAATATAGGCCGTC 58.649 52.381 0.00 0.00 35.23 4.79
3577 3783 0.685097 TCCTGCAATATAGGCCGTCC 59.315 55.000 0.00 0.00 35.23 4.79
3578 3784 0.670546 CCTGCAATATAGGCCGTCCG 60.671 60.000 0.00 0.00 37.47 4.79
3579 3785 0.317160 CTGCAATATAGGCCGTCCGA 59.683 55.000 0.00 0.00 37.47 4.55
3580 3786 0.973632 TGCAATATAGGCCGTCCGAT 59.026 50.000 0.00 0.00 37.47 4.18
3581 3787 1.346395 TGCAATATAGGCCGTCCGATT 59.654 47.619 0.00 0.00 37.47 3.34
3582 3788 2.224426 TGCAATATAGGCCGTCCGATTT 60.224 45.455 0.00 0.00 37.47 2.17
3583 3789 3.007074 TGCAATATAGGCCGTCCGATTTA 59.993 43.478 0.00 0.00 37.47 1.40
3584 3790 3.998341 GCAATATAGGCCGTCCGATTTAA 59.002 43.478 0.00 0.00 37.47 1.52
3585 3791 4.453136 GCAATATAGGCCGTCCGATTTAAA 59.547 41.667 0.00 0.00 37.47 1.52
3586 3792 5.123344 GCAATATAGGCCGTCCGATTTAAAT 59.877 40.000 0.00 0.00 37.47 1.40
3587 3793 6.674760 GCAATATAGGCCGTCCGATTTAAATC 60.675 42.308 16.79 16.79 37.47 2.17
3588 3794 4.618920 ATAGGCCGTCCGATTTAAATCT 57.381 40.909 22.52 7.00 37.47 2.40
3589 3795 2.561569 AGGCCGTCCGATTTAAATCTG 58.438 47.619 22.52 17.39 37.47 2.90
3590 3796 2.169769 AGGCCGTCCGATTTAAATCTGA 59.830 45.455 22.52 19.16 37.47 3.27
3591 3797 2.287103 GGCCGTCCGATTTAAATCTGAC 59.713 50.000 28.94 28.94 42.58 3.51
3598 3804 5.779922 TCCGATTTAAATCTGACGGATAGG 58.220 41.667 22.52 14.11 43.30 2.57
3599 3805 5.537295 TCCGATTTAAATCTGACGGATAGGA 59.463 40.000 22.52 15.81 43.30 2.94
3600 3806 6.041182 TCCGATTTAAATCTGACGGATAGGAA 59.959 38.462 22.52 3.51 43.30 3.36
3601 3807 6.366332 CCGATTTAAATCTGACGGATAGGAAG 59.634 42.308 22.52 5.18 42.40 3.46
3602 3808 6.366332 CGATTTAAATCTGACGGATAGGAAGG 59.634 42.308 22.52 1.49 33.71 3.46
3603 3809 6.801718 TTTAAATCTGACGGATAGGAAGGA 57.198 37.500 0.00 0.00 33.71 3.36
3604 3810 6.801718 TTAAATCTGACGGATAGGAAGGAA 57.198 37.500 0.00 0.00 33.71 3.36
3605 3811 5.693769 AAATCTGACGGATAGGAAGGAAA 57.306 39.130 0.00 0.00 33.71 3.13
3606 3812 4.674281 ATCTGACGGATAGGAAGGAAAC 57.326 45.455 0.00 0.00 32.04 2.78
3607 3813 4.290942 ATCTGACGGATAGGAAGGAAACT 58.709 43.478 0.00 0.00 35.69 2.66
3608 3814 4.863548 TCTGACGGATAGGAAGGAAACTA 58.136 43.478 0.00 0.00 42.68 2.24
3609 3815 5.455872 TCTGACGGATAGGAAGGAAACTAT 58.544 41.667 0.00 0.00 42.68 2.12
3610 3816 5.302059 TCTGACGGATAGGAAGGAAACTATG 59.698 44.000 0.00 0.00 42.68 2.23
3611 3817 4.344102 TGACGGATAGGAAGGAAACTATGG 59.656 45.833 0.00 0.00 42.68 2.74
3612 3818 3.071167 ACGGATAGGAAGGAAACTATGGC 59.929 47.826 0.00 0.00 42.68 4.40
3613 3819 3.071023 CGGATAGGAAGGAAACTATGGCA 59.929 47.826 0.00 0.00 42.68 4.92
3614 3820 4.444306 CGGATAGGAAGGAAACTATGGCAA 60.444 45.833 0.00 0.00 42.68 4.52
3615 3821 5.635120 GGATAGGAAGGAAACTATGGCAAT 58.365 41.667 0.00 0.00 42.68 3.56
3616 3822 6.071320 GGATAGGAAGGAAACTATGGCAATT 58.929 40.000 0.00 0.00 42.68 2.32
3617 3823 6.551227 GGATAGGAAGGAAACTATGGCAATTT 59.449 38.462 0.00 0.00 42.68 1.82
3618 3824 7.069950 GGATAGGAAGGAAACTATGGCAATTTT 59.930 37.037 0.00 0.00 42.68 1.82
3619 3825 6.041423 AGGAAGGAAACTATGGCAATTTTG 57.959 37.500 0.00 0.00 42.68 2.44
3620 3826 5.543790 AGGAAGGAAACTATGGCAATTTTGT 59.456 36.000 0.00 0.00 42.68 2.83
3621 3827 6.723977 AGGAAGGAAACTATGGCAATTTTGTA 59.276 34.615 0.00 0.00 42.68 2.41
3622 3828 7.234577 AGGAAGGAAACTATGGCAATTTTGTAA 59.765 33.333 0.00 0.00 42.68 2.41
3623 3829 7.875554 GGAAGGAAACTATGGCAATTTTGTAAA 59.124 33.333 0.00 0.00 42.68 2.01
3624 3830 9.267084 GAAGGAAACTATGGCAATTTTGTAAAA 57.733 29.630 0.00 0.00 42.68 1.52
3625 3831 8.831715 AGGAAACTATGGCAATTTTGTAAAAG 57.168 30.769 0.00 0.00 40.61 2.27
3626 3832 7.877612 AGGAAACTATGGCAATTTTGTAAAAGG 59.122 33.333 0.00 0.00 40.61 3.11
3627 3833 7.875554 GGAAACTATGGCAATTTTGTAAAAGGA 59.124 33.333 0.00 0.00 0.00 3.36
3628 3834 9.435688 GAAACTATGGCAATTTTGTAAAAGGAT 57.564 29.630 0.00 0.00 0.00 3.24
3630 3836 9.869757 AACTATGGCAATTTTGTAAAAGGATAC 57.130 29.630 0.00 0.00 0.00 2.24
3631 3837 8.474831 ACTATGGCAATTTTGTAAAAGGATACC 58.525 33.333 0.00 0.00 37.17 2.73
3632 3838 6.043854 TGGCAATTTTGTAAAAGGATACCC 57.956 37.500 0.00 0.00 37.17 3.69
3633 3839 5.544176 TGGCAATTTTGTAAAAGGATACCCA 59.456 36.000 0.00 0.00 33.88 4.51
3634 3840 5.872617 GGCAATTTTGTAAAAGGATACCCAC 59.127 40.000 0.00 0.00 33.88 4.61
3635 3841 6.459923 GCAATTTTGTAAAAGGATACCCACA 58.540 36.000 0.00 0.00 33.88 4.17
3636 3842 6.367695 GCAATTTTGTAAAAGGATACCCACAC 59.632 38.462 0.00 0.00 33.88 3.82
3637 3843 6.599356 ATTTTGTAAAAGGATACCCACACC 57.401 37.500 0.00 0.00 33.88 4.16
3638 3844 3.724732 TGTAAAAGGATACCCACACCC 57.275 47.619 0.00 0.00 33.88 4.61
3639 3845 2.309458 TGTAAAAGGATACCCACACCCC 59.691 50.000 0.00 0.00 33.88 4.95
3640 3846 1.768265 AAAAGGATACCCACACCCCT 58.232 50.000 0.00 0.00 33.88 4.79
3641 3847 1.296002 AAAGGATACCCACACCCCTC 58.704 55.000 0.00 0.00 33.88 4.30
3642 3848 0.421904 AAGGATACCCACACCCCTCT 59.578 55.000 0.00 0.00 33.88 3.69
3643 3849 0.031010 AGGATACCCACACCCCTCTC 60.031 60.000 0.00 0.00 33.88 3.20
3644 3850 1.054978 GGATACCCACACCCCTCTCC 61.055 65.000 0.00 0.00 0.00 3.71
3645 3851 0.326238 GATACCCACACCCCTCTCCA 60.326 60.000 0.00 0.00 0.00 3.86
3646 3852 0.620700 ATACCCACACCCCTCTCCAC 60.621 60.000 0.00 0.00 0.00 4.02
3647 3853 2.038545 TACCCACACCCCTCTCCACA 62.039 60.000 0.00 0.00 0.00 4.17
3648 3854 1.925455 CCCACACCCCTCTCCACAT 60.925 63.158 0.00 0.00 0.00 3.21
3649 3855 1.500783 CCCACACCCCTCTCCACATT 61.501 60.000 0.00 0.00 0.00 2.71
3650 3856 0.405585 CCACACCCCTCTCCACATTT 59.594 55.000 0.00 0.00 0.00 2.32
3651 3857 1.538047 CACACCCCTCTCCACATTTG 58.462 55.000 0.00 0.00 0.00 2.32
3652 3858 0.251341 ACACCCCTCTCCACATTTGC 60.251 55.000 0.00 0.00 0.00 3.68
3653 3859 0.251297 CACCCCTCTCCACATTTGCA 60.251 55.000 0.00 0.00 0.00 4.08
3654 3860 0.482446 ACCCCTCTCCACATTTGCAA 59.518 50.000 0.00 0.00 0.00 4.08
3655 3861 1.133199 ACCCCTCTCCACATTTGCAAA 60.133 47.619 15.44 15.44 0.00 3.68
3656 3862 2.181975 CCCCTCTCCACATTTGCAAAT 58.818 47.619 18.99 18.99 0.00 2.32
3657 3863 3.245586 ACCCCTCTCCACATTTGCAAATA 60.246 43.478 23.69 8.18 0.00 1.40
3658 3864 3.382546 CCCCTCTCCACATTTGCAAATAG 59.617 47.826 23.69 17.07 0.00 1.73
3659 3865 3.382546 CCCTCTCCACATTTGCAAATAGG 59.617 47.826 23.69 24.96 0.00 2.57
3660 3866 3.382546 CCTCTCCACATTTGCAAATAGGG 59.617 47.826 28.64 26.83 0.00 3.53
3661 3867 2.760092 TCTCCACATTTGCAAATAGGGC 59.240 45.455 28.64 0.00 0.00 5.19
3662 3868 1.830477 TCCACATTTGCAAATAGGGCC 59.170 47.619 28.64 0.00 0.00 5.80
3663 3869 1.832998 CCACATTTGCAAATAGGGCCT 59.167 47.619 23.69 12.58 0.00 5.19
3664 3870 2.236893 CCACATTTGCAAATAGGGCCTT 59.763 45.455 23.69 0.00 0.00 4.35
3665 3871 3.524541 CACATTTGCAAATAGGGCCTTC 58.475 45.455 23.69 0.00 0.00 3.46
3666 3872 2.501316 ACATTTGCAAATAGGGCCTTCC 59.499 45.455 23.69 0.00 0.00 3.46
3676 3882 4.542075 GGCCTTCCCTCGTTCATC 57.458 61.111 0.00 0.00 0.00 2.92
3677 3883 1.153147 GGCCTTCCCTCGTTCATCC 60.153 63.158 0.00 0.00 0.00 3.51
3678 3884 1.627297 GGCCTTCCCTCGTTCATCCT 61.627 60.000 0.00 0.00 0.00 3.24
3679 3885 0.253327 GCCTTCCCTCGTTCATCCTT 59.747 55.000 0.00 0.00 0.00 3.36
3680 3886 1.340114 GCCTTCCCTCGTTCATCCTTT 60.340 52.381 0.00 0.00 0.00 3.11
3681 3887 2.880167 GCCTTCCCTCGTTCATCCTTTT 60.880 50.000 0.00 0.00 0.00 2.27
3682 3888 3.010420 CCTTCCCTCGTTCATCCTTTTC 58.990 50.000 0.00 0.00 0.00 2.29
3683 3889 3.307762 CCTTCCCTCGTTCATCCTTTTCT 60.308 47.826 0.00 0.00 0.00 2.52
3684 3890 3.611766 TCCCTCGTTCATCCTTTTCTC 57.388 47.619 0.00 0.00 0.00 2.87
3685 3891 3.173965 TCCCTCGTTCATCCTTTTCTCT 58.826 45.455 0.00 0.00 0.00 3.10
3686 3892 3.583086 TCCCTCGTTCATCCTTTTCTCTT 59.417 43.478 0.00 0.00 0.00 2.85
3687 3893 4.775780 TCCCTCGTTCATCCTTTTCTCTTA 59.224 41.667 0.00 0.00 0.00 2.10
3688 3894 4.870991 CCCTCGTTCATCCTTTTCTCTTAC 59.129 45.833 0.00 0.00 0.00 2.34
3689 3895 5.479306 CCTCGTTCATCCTTTTCTCTTACA 58.521 41.667 0.00 0.00 0.00 2.41
3690 3896 5.932303 CCTCGTTCATCCTTTTCTCTTACAA 59.068 40.000 0.00 0.00 0.00 2.41
3691 3897 6.091441 CCTCGTTCATCCTTTTCTCTTACAAG 59.909 42.308 0.00 0.00 0.00 3.16
3692 3898 6.755206 TCGTTCATCCTTTTCTCTTACAAGA 58.245 36.000 0.00 0.00 0.00 3.02
3693 3899 7.386851 TCGTTCATCCTTTTCTCTTACAAGAT 58.613 34.615 0.00 0.00 33.93 2.40
3694 3900 8.528643 TCGTTCATCCTTTTCTCTTACAAGATA 58.471 33.333 0.00 0.00 33.93 1.98
3695 3901 9.151471 CGTTCATCCTTTTCTCTTACAAGATAA 57.849 33.333 0.00 0.00 33.93 1.75
3713 3919 9.448438 ACAAGATAAACTACTCATACAAATGCA 57.552 29.630 0.00 0.00 32.76 3.96
3719 3925 8.565896 AAACTACTCATACAAATGCATCTTGA 57.434 30.769 20.96 10.81 32.76 3.02
3720 3926 8.743085 AACTACTCATACAAATGCATCTTGAT 57.257 30.769 20.96 11.48 32.76 2.57
3721 3927 8.151141 ACTACTCATACAAATGCATCTTGATG 57.849 34.615 20.96 18.39 32.76 3.07
3722 3928 7.772292 ACTACTCATACAAATGCATCTTGATGT 59.228 33.333 20.96 14.21 32.76 3.06
3723 3929 7.400599 ACTCATACAAATGCATCTTGATGTT 57.599 32.000 20.96 1.04 32.76 2.71
3724 3930 7.478322 ACTCATACAAATGCATCTTGATGTTC 58.522 34.615 20.96 0.00 32.76 3.18
3725 3931 6.798482 TCATACAAATGCATCTTGATGTTCC 58.202 36.000 20.96 0.00 32.76 3.62
3726 3932 4.100707 ACAAATGCATCTTGATGTTCCG 57.899 40.909 20.96 1.56 0.00 4.30
3727 3933 3.507233 ACAAATGCATCTTGATGTTCCGT 59.493 39.130 20.96 2.07 0.00 4.69
3728 3934 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
3729 3935 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34
3730 3936 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
3731 3937 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
3732 3938 2.855180 CATCTTGATGTTCCGTGCAAC 58.145 47.619 0.00 0.00 0.00 4.17
3745 3951 3.737172 GCAACGCACGGGCATCTT 61.737 61.111 11.77 0.00 41.24 2.40
3746 3952 2.176546 CAACGCACGGGCATCTTG 59.823 61.111 11.77 3.62 41.24 3.02
3747 3953 3.737172 AACGCACGGGCATCTTGC 61.737 61.111 11.77 0.00 44.08 4.01
3748 3954 4.704833 ACGCACGGGCATCTTGCT 62.705 61.111 11.77 0.00 44.28 3.91
3749 3955 2.511373 CGCACGGGCATCTTGCTA 60.511 61.111 11.77 0.00 44.28 3.49
3750 3956 2.528743 CGCACGGGCATCTTGCTAG 61.529 63.158 11.77 0.00 44.28 3.42
3889 4099 7.834881 ATTTGAATGGCTCTATTGTCATCAT 57.165 32.000 0.00 0.00 0.00 2.45
4113 4323 0.029433 GGCGCTAACAAGCTAATGGC 59.971 55.000 7.64 0.00 42.19 4.40
4304 4514 7.744087 ACTGCAAAATGAACACATTACTCTA 57.256 32.000 0.00 0.00 34.38 2.43
4749 4985 1.535028 ACTTGTGTGTGTGTGTGTGTG 59.465 47.619 0.00 0.00 0.00 3.82
4765 5001 5.526111 GTGTGTGTGACTGTGTAATTAGGTT 59.474 40.000 0.00 0.00 0.00 3.50
4769 5005 8.084073 GTGTGTGACTGTGTAATTAGGTTACTA 58.916 37.037 0.00 0.00 42.58 1.82
5110 5348 5.470098 GGCAAACTTCTTCTGATTACAGTCA 59.530 40.000 0.00 0.00 43.81 3.41
5212 5450 3.704566 GGTGAAAGAATTGGGGGTAATCC 59.295 47.826 0.00 0.00 0.00 3.01
5349 5587 2.842496 TCTGATCCTTGCTGAATCCAGT 59.158 45.455 0.00 0.00 42.35 4.00
5521 5759 3.928992 CGATGCTGTATCCCATGATGTAC 59.071 47.826 0.00 0.00 31.82 2.90
5545 5783 3.963733 CTTGGTCAGGATCTTGCCA 57.036 52.632 14.17 14.17 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 8.522830 CAGCCATGACCTAATTTTTAGAAAAGA 58.477 33.333 0.00 0.00 0.00 2.52
70 72 7.587757 GTGATGTGTATATTTCGAAATTCAGCC 59.412 37.037 27.10 13.75 0.00 4.85
71 73 8.122330 TGTGATGTGTATATTTCGAAATTCAGC 58.878 33.333 27.10 19.21 0.00 4.26
143 153 0.834612 TGAGAGGTTTTGGTGACGGT 59.165 50.000 0.00 0.00 0.00 4.83
178 188 2.213499 GAAGTGGACGCAATGATAGGG 58.787 52.381 0.00 0.00 0.00 3.53
267 279 2.035632 CTATCAGTGTGTCTCCCTCCC 58.964 57.143 0.00 0.00 0.00 4.30
268 280 2.035632 CCTATCAGTGTGTCTCCCTCC 58.964 57.143 0.00 0.00 0.00 4.30
364 388 3.887335 TACGGTGCGGTGAAAGGGC 62.887 63.158 0.00 0.00 0.00 5.19
406 430 2.397549 CAAAGAAGCAAAGGGAAAGCG 58.602 47.619 0.00 0.00 0.00 4.68
440 464 2.930562 AGGTGAGGTGGGCTGACC 60.931 66.667 0.00 0.00 40.81 4.02
442 466 2.997315 CGAGGTGAGGTGGGCTGA 60.997 66.667 0.00 0.00 0.00 4.26
443 467 3.302347 GACGAGGTGAGGTGGGCTG 62.302 68.421 0.00 0.00 0.00 4.85
444 468 2.997897 GACGAGGTGAGGTGGGCT 60.998 66.667 0.00 0.00 0.00 5.19
445 469 4.083862 GGACGAGGTGAGGTGGGC 62.084 72.222 0.00 0.00 0.00 5.36
490 515 6.995091 GCAGGAGATGGTATTTAAGACTCAAT 59.005 38.462 0.00 0.00 0.00 2.57
601 629 0.914644 AGCAAGAGCCAATGGAGCTA 59.085 50.000 2.05 0.00 41.75 3.32
629 657 0.248866 GTTTTGCTGGACAACGGTGG 60.249 55.000 4.97 0.00 38.23 4.61
655 683 5.669904 AGGGAAGGAAAATTGGAAGGAAAAA 59.330 36.000 0.00 0.00 0.00 1.94
672 700 2.376855 AGAAGACAAAGGGAAGGGAAGG 59.623 50.000 0.00 0.00 0.00 3.46
755 783 1.760875 GATCAGCCTGGTCCGGGTA 60.761 63.158 18.58 4.90 32.55 3.69
777 805 3.750371 TGTGTACTACAAGCTGCCAATT 58.250 40.909 0.00 0.00 36.06 2.32
853 908 0.539518 GGTGAGGAGAAGGAGGAAGC 59.460 60.000 0.00 0.00 0.00 3.86
857 912 1.063266 AGCTAGGTGAGGAGAAGGAGG 60.063 57.143 0.00 0.00 0.00 4.30
858 913 2.452600 AGCTAGGTGAGGAGAAGGAG 57.547 55.000 0.00 0.00 0.00 3.69
867 922 3.320541 CCAGTTCTCCATAGCTAGGTGAG 59.679 52.174 14.15 14.15 31.08 3.51
868 923 3.052869 TCCAGTTCTCCATAGCTAGGTGA 60.053 47.826 4.27 7.17 0.00 4.02
871 926 5.184864 CAGTATCCAGTTCTCCATAGCTAGG 59.815 48.000 0.00 0.00 0.00 3.02
915 970 0.321653 GAACCTGCCAACCATCGAGT 60.322 55.000 0.00 0.00 0.00 4.18
965 1020 0.327591 CTCCTTCTCCTTGGCTGCTT 59.672 55.000 0.00 0.00 0.00 3.91
1075 1130 3.159472 TGACCATGCTGAAAAGATTGCT 58.841 40.909 0.00 0.00 0.00 3.91
1076 1131 3.581024 TGACCATGCTGAAAAGATTGC 57.419 42.857 0.00 0.00 0.00 3.56
1101 1158 6.879458 GGAGGACTGCTAGAAGAACAAATTTA 59.121 38.462 4.16 0.00 0.00 1.40
1122 1179 2.192263 AGAAAGAGCTTACCCTGGAGG 58.808 52.381 0.00 0.00 43.78 4.30
1144 1201 0.249489 ACCAGTTATCATCTCGCCGC 60.249 55.000 0.00 0.00 0.00 6.53
1218 1358 5.575019 ACGTAAATATTGATCAAAACGGCC 58.425 37.500 22.70 0.00 33.65 6.13
1235 1375 8.325421 TGTAAGATTGGCAGAAAATACGTAAA 57.675 30.769 0.00 0.00 0.00 2.01
1350 1492 6.034161 AGTACAACTGTCTACATTGGTACC 57.966 41.667 4.43 4.43 31.50 3.34
1351 1493 6.128634 GCAAGTACAACTGTCTACATTGGTAC 60.129 42.308 9.13 9.13 0.00 3.34
1361 1503 4.071961 TGATGTGCAAGTACAACTGTCT 57.928 40.909 0.00 0.00 33.69 3.41
1396 1538 8.668510 ACTGCAAGAGTATTAGGAAACATATG 57.331 34.615 0.00 0.00 37.43 1.78
1397 1539 8.709308 AGACTGCAAGAGTATTAGGAAACATAT 58.291 33.333 0.00 0.00 37.43 1.78
1427 1569 4.340617 TGTTCTGTTGGTCAAAAGGACTT 58.659 39.130 12.18 0.00 46.16 3.01
1474 1616 9.703892 TGTTCTGTCATTTGAAAAAGAAAAGAA 57.296 25.926 4.21 4.53 0.00 2.52
1475 1617 9.874205 ATGTTCTGTCATTTGAAAAAGAAAAGA 57.126 25.926 4.21 0.00 0.00 2.52
1767 1910 5.542779 AGCAAGAACGTAGAATCTGAACTT 58.457 37.500 0.00 0.00 0.00 2.66
1815 1972 0.729116 GGTTGTCTGCACGATCATGG 59.271 55.000 0.00 0.00 0.00 3.66
1870 2027 4.283467 TCTTGAAACTGCTCTGCTAGGTTA 59.717 41.667 0.00 0.00 0.00 2.85
2169 2326 5.481615 AGATAGGCAATTTAAAGGGGGAA 57.518 39.130 0.00 0.00 0.00 3.97
2170 2327 5.195756 AGAAGATAGGCAATTTAAAGGGGGA 59.804 40.000 0.00 0.00 0.00 4.81
2252 2418 9.793245 CATAGCAAGCGTGTATAATTAACTTAC 57.207 33.333 0.59 0.00 0.00 2.34
2268 2434 0.171903 AAAAGGCAGCATAGCAAGCG 59.828 50.000 0.00 0.00 37.01 4.68
2375 2542 2.669391 CGAAAGCAAATGCAGTTCCCTC 60.669 50.000 8.28 0.00 45.16 4.30
2505 2672 6.654161 GGTCTGCTATCTGAATTTCTATGCAT 59.346 38.462 3.79 3.79 0.00 3.96
2691 2858 9.535270 GAATACTGAATGAACGAAGAAGAAAAG 57.465 33.333 0.00 0.00 0.00 2.27
2745 2913 2.758736 TAACATTGGCATGGGTTTGC 57.241 45.000 0.00 0.00 42.01 3.68
2751 2919 8.721019 AAAATGTTTAGATAACATTGGCATGG 57.279 30.769 14.49 0.00 46.62 3.66
2816 2984 4.021102 TCTCACTTTGGGAGGTTTCATC 57.979 45.455 0.00 0.00 33.18 2.92
2839 3007 7.230712 TCAATGATATGAAAGCTGCATCAGATT 59.769 33.333 14.06 0.00 42.09 2.40
2907 3075 4.098349 AGCACTCAAGAAATTTGCAAGACA 59.902 37.500 0.00 0.00 35.57 3.41
2996 3164 1.491563 GAGTTTGCAGTACACCGCG 59.508 57.895 0.00 0.00 0.00 6.46
3092 3260 2.159282 ACTATCGACACGGTGCTTTAGG 60.159 50.000 8.30 0.00 0.00 2.69
3327 3496 1.879380 TGAGACCAAGACAAAATGCGG 59.121 47.619 0.00 0.00 0.00 5.69
3476 3645 7.494625 CGAGGTTAACATGAACATATGTAAGGT 59.505 37.037 9.21 5.89 40.24 3.50
3524 3730 4.895297 ACCATCATCACCAACTCTGTTTTT 59.105 37.500 0.00 0.00 0.00 1.94
3525 3731 4.279169 CACCATCATCACCAACTCTGTTTT 59.721 41.667 0.00 0.00 0.00 2.43
3526 3732 3.822735 CACCATCATCACCAACTCTGTTT 59.177 43.478 0.00 0.00 0.00 2.83
3527 3733 3.181440 ACACCATCATCACCAACTCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
3528 3734 2.373169 ACACCATCATCACCAACTCTGT 59.627 45.455 0.00 0.00 0.00 3.41
3529 3735 2.745821 CACACCATCATCACCAACTCTG 59.254 50.000 0.00 0.00 0.00 3.35
3530 3736 2.877300 GCACACCATCATCACCAACTCT 60.877 50.000 0.00 0.00 0.00 3.24
3531 3737 1.470098 GCACACCATCATCACCAACTC 59.530 52.381 0.00 0.00 0.00 3.01
3532 3738 1.538047 GCACACCATCATCACCAACT 58.462 50.000 0.00 0.00 0.00 3.16
3533 3739 0.527565 GGCACACCATCATCACCAAC 59.472 55.000 0.00 0.00 35.26 3.77
3534 3740 0.405198 AGGCACACCATCATCACCAA 59.595 50.000 0.00 0.00 39.06 3.67
3535 3741 0.322726 CAGGCACACCATCATCACCA 60.323 55.000 0.00 0.00 39.06 4.17
3536 3742 1.660560 GCAGGCACACCATCATCACC 61.661 60.000 0.00 0.00 39.06 4.02
3537 3743 1.660560 GGCAGGCACACCATCATCAC 61.661 60.000 0.00 0.00 39.06 3.06
3538 3744 1.378911 GGCAGGCACACCATCATCA 60.379 57.895 0.00 0.00 39.06 3.07
3539 3745 0.754217 ATGGCAGGCACACCATCATC 60.754 55.000 0.00 0.00 42.69 2.92
3540 3746 1.308666 ATGGCAGGCACACCATCAT 59.691 52.632 0.00 0.00 42.69 2.45
3541 3747 2.765279 ATGGCAGGCACACCATCA 59.235 55.556 0.00 0.00 42.69 3.07
3544 3750 3.259314 AGGATGGCAGGCACACCA 61.259 61.111 19.51 0.00 41.01 4.17
3545 3751 2.753043 CAGGATGGCAGGCACACC 60.753 66.667 12.37 12.37 0.00 4.16
3546 3752 3.446570 GCAGGATGGCAGGCACAC 61.447 66.667 0.00 0.00 35.86 3.82
3547 3753 2.791613 ATTGCAGGATGGCAGGCACA 62.792 55.000 0.00 0.00 45.88 4.57
3548 3754 0.752743 TATTGCAGGATGGCAGGCAC 60.753 55.000 0.00 0.00 45.88 5.01
3549 3755 0.186630 ATATTGCAGGATGGCAGGCA 59.813 50.000 0.00 0.00 45.88 4.75
3550 3756 2.089980 CTATATTGCAGGATGGCAGGC 58.910 52.381 0.00 0.00 45.88 4.85
3551 3757 2.719739 CCTATATTGCAGGATGGCAGG 58.280 52.381 0.00 0.00 45.88 4.85
3552 3758 2.089980 GCCTATATTGCAGGATGGCAG 58.910 52.381 12.68 0.00 45.88 4.85
3553 3759 1.272092 GGCCTATATTGCAGGATGGCA 60.272 52.381 17.22 0.00 43.19 4.92
3554 3760 1.467920 GGCCTATATTGCAGGATGGC 58.532 55.000 0.00 10.13 34.91 4.40
3555 3761 1.003580 ACGGCCTATATTGCAGGATGG 59.996 52.381 0.00 0.00 34.91 3.51
3556 3762 2.350522 GACGGCCTATATTGCAGGATG 58.649 52.381 0.00 0.00 34.91 3.51
3557 3763 1.279271 GGACGGCCTATATTGCAGGAT 59.721 52.381 0.00 0.00 34.91 3.24
3558 3764 0.685097 GGACGGCCTATATTGCAGGA 59.315 55.000 0.00 0.00 34.91 3.86
3559 3765 0.670546 CGGACGGCCTATATTGCAGG 60.671 60.000 5.33 0.00 36.16 4.85
3560 3766 0.317160 TCGGACGGCCTATATTGCAG 59.683 55.000 5.33 0.00 0.00 4.41
3561 3767 0.973632 ATCGGACGGCCTATATTGCA 59.026 50.000 5.33 0.00 0.00 4.08
3562 3768 2.094762 AATCGGACGGCCTATATTGC 57.905 50.000 5.33 0.00 0.00 3.56
3563 3769 6.594159 AGATTTAAATCGGACGGCCTATATTG 59.406 38.462 19.86 0.00 40.35 1.90
3564 3770 6.594159 CAGATTTAAATCGGACGGCCTATATT 59.406 38.462 19.84 0.00 40.35 1.28
3565 3771 6.070995 TCAGATTTAAATCGGACGGCCTATAT 60.071 38.462 22.22 0.00 40.35 0.86
3566 3772 5.244402 TCAGATTTAAATCGGACGGCCTATA 59.756 40.000 22.22 2.64 40.35 1.31
3567 3773 4.039973 TCAGATTTAAATCGGACGGCCTAT 59.960 41.667 22.22 0.00 40.35 2.57
3568 3774 3.385433 TCAGATTTAAATCGGACGGCCTA 59.615 43.478 22.22 0.00 40.35 3.93
3569 3775 2.169769 TCAGATTTAAATCGGACGGCCT 59.830 45.455 22.22 2.40 40.35 5.19
3570 3776 2.287103 GTCAGATTTAAATCGGACGGCC 59.713 50.000 31.74 17.93 45.64 6.13
3571 3777 3.587403 GTCAGATTTAAATCGGACGGC 57.413 47.619 31.74 18.20 45.64 5.68
3576 3782 5.779922 TCCTATCCGTCAGATTTAAATCGG 58.220 41.667 19.86 19.33 40.35 4.18
3577 3783 6.366332 CCTTCCTATCCGTCAGATTTAAATCG 59.634 42.308 19.86 15.23 40.35 3.34
3578 3784 7.442656 TCCTTCCTATCCGTCAGATTTAAATC 58.557 38.462 18.70 18.70 36.33 2.17
3579 3785 7.374975 TCCTTCCTATCCGTCAGATTTAAAT 57.625 36.000 0.00 0.00 36.33 1.40
3580 3786 6.801718 TCCTTCCTATCCGTCAGATTTAAA 57.198 37.500 0.00 0.00 36.33 1.52
3581 3787 6.801718 TTCCTTCCTATCCGTCAGATTTAA 57.198 37.500 0.00 0.00 36.33 1.52
3582 3788 6.383147 AGTTTCCTTCCTATCCGTCAGATTTA 59.617 38.462 0.00 0.00 36.33 1.40
3583 3789 5.189934 AGTTTCCTTCCTATCCGTCAGATTT 59.810 40.000 0.00 0.00 36.33 2.17
3584 3790 4.717280 AGTTTCCTTCCTATCCGTCAGATT 59.283 41.667 0.00 0.00 36.33 2.40
3585 3791 4.290942 AGTTTCCTTCCTATCCGTCAGAT 58.709 43.478 0.00 0.00 39.15 2.90
3586 3792 3.709587 AGTTTCCTTCCTATCCGTCAGA 58.290 45.455 0.00 0.00 0.00 3.27
3587 3793 5.509840 CCATAGTTTCCTTCCTATCCGTCAG 60.510 48.000 0.00 0.00 0.00 3.51
3588 3794 4.344102 CCATAGTTTCCTTCCTATCCGTCA 59.656 45.833 0.00 0.00 0.00 4.35
3589 3795 4.799917 GCCATAGTTTCCTTCCTATCCGTC 60.800 50.000 0.00 0.00 0.00 4.79
3590 3796 3.071167 GCCATAGTTTCCTTCCTATCCGT 59.929 47.826 0.00 0.00 0.00 4.69
3591 3797 3.071023 TGCCATAGTTTCCTTCCTATCCG 59.929 47.826 0.00 0.00 0.00 4.18
3592 3798 4.706842 TGCCATAGTTTCCTTCCTATCC 57.293 45.455 0.00 0.00 0.00 2.59
3593 3799 7.588497 AAATTGCCATAGTTTCCTTCCTATC 57.412 36.000 0.00 0.00 0.00 2.08
3594 3800 7.400052 ACAAAATTGCCATAGTTTCCTTCCTAT 59.600 33.333 0.00 0.00 0.00 2.57
3595 3801 6.723977 ACAAAATTGCCATAGTTTCCTTCCTA 59.276 34.615 0.00 0.00 0.00 2.94
3596 3802 5.543790 ACAAAATTGCCATAGTTTCCTTCCT 59.456 36.000 0.00 0.00 0.00 3.36
3597 3803 5.793817 ACAAAATTGCCATAGTTTCCTTCC 58.206 37.500 0.00 0.00 0.00 3.46
3598 3804 8.825667 TTTACAAAATTGCCATAGTTTCCTTC 57.174 30.769 0.00 0.00 0.00 3.46
3599 3805 9.271828 CTTTTACAAAATTGCCATAGTTTCCTT 57.728 29.630 0.00 0.00 0.00 3.36
3600 3806 7.877612 CCTTTTACAAAATTGCCATAGTTTCCT 59.122 33.333 0.00 0.00 0.00 3.36
3601 3807 7.875554 TCCTTTTACAAAATTGCCATAGTTTCC 59.124 33.333 0.00 0.00 0.00 3.13
3602 3808 8.825667 TCCTTTTACAAAATTGCCATAGTTTC 57.174 30.769 0.00 0.00 0.00 2.78
3604 3810 9.869757 GTATCCTTTTACAAAATTGCCATAGTT 57.130 29.630 0.00 0.00 0.00 2.24
3605 3811 8.474831 GGTATCCTTTTACAAAATTGCCATAGT 58.525 33.333 0.00 0.00 0.00 2.12
3606 3812 7.926018 GGGTATCCTTTTACAAAATTGCCATAG 59.074 37.037 0.00 0.00 0.00 2.23
3607 3813 7.400339 TGGGTATCCTTTTACAAAATTGCCATA 59.600 33.333 0.00 0.00 0.00 2.74
3608 3814 6.214412 TGGGTATCCTTTTACAAAATTGCCAT 59.786 34.615 0.00 0.00 0.00 4.40
3609 3815 5.544176 TGGGTATCCTTTTACAAAATTGCCA 59.456 36.000 0.00 0.00 0.00 4.92
3610 3816 5.872617 GTGGGTATCCTTTTACAAAATTGCC 59.127 40.000 0.00 0.00 0.00 4.52
3611 3817 6.367695 GTGTGGGTATCCTTTTACAAAATTGC 59.632 38.462 0.00 0.00 0.00 3.56
3612 3818 6.871492 GGTGTGGGTATCCTTTTACAAAATTG 59.129 38.462 0.00 0.00 0.00 2.32
3613 3819 6.014070 GGGTGTGGGTATCCTTTTACAAAATT 60.014 38.462 0.00 0.00 0.00 1.82
3614 3820 5.482526 GGGTGTGGGTATCCTTTTACAAAAT 59.517 40.000 0.00 0.00 0.00 1.82
3615 3821 4.833938 GGGTGTGGGTATCCTTTTACAAAA 59.166 41.667 0.00 0.00 0.00 2.44
3616 3822 4.409187 GGGTGTGGGTATCCTTTTACAAA 58.591 43.478 0.00 0.00 0.00 2.83
3617 3823 3.245336 GGGGTGTGGGTATCCTTTTACAA 60.245 47.826 0.00 0.00 0.00 2.41
3618 3824 2.309458 GGGGTGTGGGTATCCTTTTACA 59.691 50.000 0.00 0.00 0.00 2.41
3619 3825 2.579400 AGGGGTGTGGGTATCCTTTTAC 59.421 50.000 0.00 0.00 0.00 2.01
3620 3826 2.848071 GAGGGGTGTGGGTATCCTTTTA 59.152 50.000 0.00 0.00 0.00 1.52
3621 3827 1.639108 GAGGGGTGTGGGTATCCTTTT 59.361 52.381 0.00 0.00 0.00 2.27
3622 3828 1.203570 AGAGGGGTGTGGGTATCCTTT 60.204 52.381 0.00 0.00 0.00 3.11
3623 3829 0.421904 AGAGGGGTGTGGGTATCCTT 59.578 55.000 0.00 0.00 0.00 3.36
3624 3830 0.031010 GAGAGGGGTGTGGGTATCCT 60.031 60.000 0.00 0.00 0.00 3.24
3625 3831 1.054978 GGAGAGGGGTGTGGGTATCC 61.055 65.000 0.00 0.00 0.00 2.59
3626 3832 0.326238 TGGAGAGGGGTGTGGGTATC 60.326 60.000 0.00 0.00 0.00 2.24
3627 3833 0.620700 GTGGAGAGGGGTGTGGGTAT 60.621 60.000 0.00 0.00 0.00 2.73
3628 3834 1.229400 GTGGAGAGGGGTGTGGGTA 60.229 63.158 0.00 0.00 0.00 3.69
3629 3835 2.529389 GTGGAGAGGGGTGTGGGT 60.529 66.667 0.00 0.00 0.00 4.51
3630 3836 1.500783 AATGTGGAGAGGGGTGTGGG 61.501 60.000 0.00 0.00 0.00 4.61
3631 3837 0.405585 AAATGTGGAGAGGGGTGTGG 59.594 55.000 0.00 0.00 0.00 4.17
3632 3838 1.538047 CAAATGTGGAGAGGGGTGTG 58.462 55.000 0.00 0.00 0.00 3.82
3633 3839 0.251341 GCAAATGTGGAGAGGGGTGT 60.251 55.000 0.00 0.00 0.00 4.16
3634 3840 0.251297 TGCAAATGTGGAGAGGGGTG 60.251 55.000 0.00 0.00 0.00 4.61
3635 3841 0.482446 TTGCAAATGTGGAGAGGGGT 59.518 50.000 0.00 0.00 0.00 4.95
3636 3842 1.631405 TTTGCAAATGTGGAGAGGGG 58.369 50.000 8.05 0.00 0.00 4.79
3637 3843 3.382546 CCTATTTGCAAATGTGGAGAGGG 59.617 47.826 30.43 15.92 0.00 4.30
3638 3844 3.382546 CCCTATTTGCAAATGTGGAGAGG 59.617 47.826 30.80 26.61 0.00 3.69
3639 3845 3.181483 GCCCTATTTGCAAATGTGGAGAG 60.181 47.826 30.70 21.21 0.00 3.20
3640 3846 2.760092 GCCCTATTTGCAAATGTGGAGA 59.240 45.455 30.70 14.94 0.00 3.71
3641 3847 2.159057 GGCCCTATTTGCAAATGTGGAG 60.159 50.000 30.70 22.03 0.00 3.86
3642 3848 1.830477 GGCCCTATTTGCAAATGTGGA 59.170 47.619 30.70 15.82 0.00 4.02
3643 3849 1.832998 AGGCCCTATTTGCAAATGTGG 59.167 47.619 30.43 27.81 0.00 4.17
3644 3850 3.524541 GAAGGCCCTATTTGCAAATGTG 58.475 45.455 30.43 22.20 0.00 3.21
3645 3851 2.501316 GGAAGGCCCTATTTGCAAATGT 59.499 45.455 30.43 12.33 0.00 2.71
3646 3852 3.183793 GGAAGGCCCTATTTGCAAATG 57.816 47.619 30.43 20.32 0.00 2.32
3659 3865 1.153147 GGATGAACGAGGGAAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
3660 3866 0.253327 AAGGATGAACGAGGGAAGGC 59.747 55.000 0.00 0.00 0.00 4.35
3661 3867 2.789409 AAAGGATGAACGAGGGAAGG 57.211 50.000 0.00 0.00 0.00 3.46
3662 3868 3.935828 GAGAAAAGGATGAACGAGGGAAG 59.064 47.826 0.00 0.00 0.00 3.46
3663 3869 3.583086 AGAGAAAAGGATGAACGAGGGAA 59.417 43.478 0.00 0.00 0.00 3.97
3664 3870 3.173965 AGAGAAAAGGATGAACGAGGGA 58.826 45.455 0.00 0.00 0.00 4.20
3665 3871 3.618690 AGAGAAAAGGATGAACGAGGG 57.381 47.619 0.00 0.00 0.00 4.30
3666 3872 5.479306 TGTAAGAGAAAAGGATGAACGAGG 58.521 41.667 0.00 0.00 0.00 4.63
3667 3873 6.868864 TCTTGTAAGAGAAAAGGATGAACGAG 59.131 38.462 0.00 0.00 0.00 4.18
3668 3874 6.755206 TCTTGTAAGAGAAAAGGATGAACGA 58.245 36.000 0.00 0.00 0.00 3.85
3669 3875 7.602517 ATCTTGTAAGAGAAAAGGATGAACG 57.397 36.000 0.51 0.00 38.66 3.95
3687 3893 9.448438 TGCATTTGTATGAGTAGTTTATCTTGT 57.552 29.630 0.00 0.00 33.37 3.16
3693 3899 9.665719 TCAAGATGCATTTGTATGAGTAGTTTA 57.334 29.630 0.00 0.00 33.37 2.01
3694 3900 8.565896 TCAAGATGCATTTGTATGAGTAGTTT 57.434 30.769 0.00 0.00 33.37 2.66
3695 3901 8.618677 CATCAAGATGCATTTGTATGAGTAGTT 58.381 33.333 0.00 0.00 33.37 2.24
3696 3902 7.772292 ACATCAAGATGCATTTGTATGAGTAGT 59.228 33.333 22.17 13.08 42.39 2.73
3697 3903 8.151141 ACATCAAGATGCATTTGTATGAGTAG 57.849 34.615 22.17 12.72 42.39 2.57
3698 3904 8.510243 AACATCAAGATGCATTTGTATGAGTA 57.490 30.769 22.17 8.59 42.39 2.59
3699 3905 7.400599 AACATCAAGATGCATTTGTATGAGT 57.599 32.000 22.17 12.92 42.39 3.41
3700 3906 6.916387 GGAACATCAAGATGCATTTGTATGAG 59.084 38.462 22.17 12.56 42.39 2.90
3701 3907 6.458615 CGGAACATCAAGATGCATTTGTATGA 60.459 38.462 22.17 15.31 42.39 2.15
3702 3908 5.684184 CGGAACATCAAGATGCATTTGTATG 59.316 40.000 9.85 13.57 42.39 2.39
3703 3909 5.357878 ACGGAACATCAAGATGCATTTGTAT 59.642 36.000 9.85 1.80 42.39 2.29
3704 3910 4.699735 ACGGAACATCAAGATGCATTTGTA 59.300 37.500 9.85 0.00 42.39 2.41
3705 3911 3.507233 ACGGAACATCAAGATGCATTTGT 59.493 39.130 9.85 0.00 42.39 2.83
3706 3912 3.855379 CACGGAACATCAAGATGCATTTG 59.145 43.478 9.85 7.88 42.39 2.32
3707 3913 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
3708 3914 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
3709 3915 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
3710 3916 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
3711 3917 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
3712 3918 2.725759 CGTTGCACGGAACATCAAGATG 60.726 50.000 8.45 8.45 40.19 2.90
3713 3919 1.464608 CGTTGCACGGAACATCAAGAT 59.535 47.619 2.31 0.00 38.08 2.40
3714 3920 0.865111 CGTTGCACGGAACATCAAGA 59.135 50.000 2.31 0.00 38.08 3.02
3715 3921 0.725784 GCGTTGCACGGAACATCAAG 60.726 55.000 10.02 0.00 42.82 3.02
3716 3922 1.281353 GCGTTGCACGGAACATCAA 59.719 52.632 10.02 0.00 42.82 2.57
3717 3923 1.889573 TGCGTTGCACGGAACATCA 60.890 52.632 10.02 0.00 39.47 3.07
3718 3924 2.942879 TGCGTTGCACGGAACATC 59.057 55.556 10.02 0.00 39.47 3.06
3728 3934 3.737172 AAGATGCCCGTGCGTTGC 61.737 61.111 0.00 0.00 41.78 4.17
3729 3935 2.176546 CAAGATGCCCGTGCGTTG 59.823 61.111 0.00 0.00 41.78 4.10
3730 3936 3.737172 GCAAGATGCCCGTGCGTT 61.737 61.111 0.00 0.00 40.20 4.84
3733 3939 1.026718 AACTAGCAAGATGCCCGTGC 61.027 55.000 6.11 6.11 46.52 5.34
3734 3940 1.009829 GAACTAGCAAGATGCCCGTG 58.990 55.000 0.00 0.00 46.52 4.94
3735 3941 0.613260 TGAACTAGCAAGATGCCCGT 59.387 50.000 0.00 0.00 46.52 5.28
3736 3942 1.600957 CATGAACTAGCAAGATGCCCG 59.399 52.381 0.00 0.00 46.52 6.13
3737 3943 2.615912 GACATGAACTAGCAAGATGCCC 59.384 50.000 0.00 0.00 46.52 5.36
3738 3944 3.539604 AGACATGAACTAGCAAGATGCC 58.460 45.455 0.00 0.00 46.52 4.40
3739 3945 5.007136 GGTTAGACATGAACTAGCAAGATGC 59.993 44.000 0.00 0.00 45.46 3.91
3740 3946 5.525378 GGGTTAGACATGAACTAGCAAGATG 59.475 44.000 0.00 0.00 0.00 2.90
3741 3947 5.675538 GGGTTAGACATGAACTAGCAAGAT 58.324 41.667 0.00 0.00 0.00 2.40
3742 3948 4.381612 CGGGTTAGACATGAACTAGCAAGA 60.382 45.833 0.00 0.00 0.00 3.02
3743 3949 3.865745 CGGGTTAGACATGAACTAGCAAG 59.134 47.826 0.00 0.13 0.00 4.01
3744 3950 3.259876 ACGGGTTAGACATGAACTAGCAA 59.740 43.478 0.00 0.00 0.00 3.91
3745 3951 2.829720 ACGGGTTAGACATGAACTAGCA 59.170 45.455 0.00 0.00 0.00 3.49
3746 3952 3.521947 ACGGGTTAGACATGAACTAGC 57.478 47.619 0.00 4.98 0.00 3.42
3747 3953 5.983720 CCATTACGGGTTAGACATGAACTAG 59.016 44.000 0.00 0.00 0.00 2.57
3748 3954 5.682990 GCCATTACGGGTTAGACATGAACTA 60.683 44.000 0.00 0.00 34.06 2.24
3749 3955 4.766375 CCATTACGGGTTAGACATGAACT 58.234 43.478 0.00 0.72 0.00 3.01
3750 3956 3.311596 GCCATTACGGGTTAGACATGAAC 59.688 47.826 0.00 0.00 34.06 3.18
3860 4070 7.669427 TGACAATAGAGCCATTCAAATTTTGT 58.331 30.769 8.89 0.00 0.00 2.83
4304 4514 6.150140 GTCAAATGCAGAGATTTCCTACAGTT 59.850 38.462 0.00 0.00 0.00 3.16
4311 4521 5.412594 TGTACAGTCAAATGCAGAGATTTCC 59.587 40.000 0.00 0.00 0.00 3.13
4765 5001 9.610104 TTACTCCCCTAAAATGCTATCATAGTA 57.390 33.333 0.00 0.00 31.46 1.82
4769 5005 7.816411 ACTTTACTCCCCTAAAATGCTATCAT 58.184 34.615 0.00 0.00 33.53 2.45
4942 5179 6.602410 TGAACATTTTGGGCATTGAGAATA 57.398 33.333 0.00 0.00 0.00 1.75
5110 5348 1.622312 TGCAGTCTCAGTGAGATGCTT 59.378 47.619 33.24 18.81 40.98 3.91
5212 5450 2.358737 GACAAGGGCGAGGTGGTG 60.359 66.667 0.00 0.00 0.00 4.17
5349 5587 0.106769 TTTGGTGTTCCTGCAGAGCA 60.107 50.000 17.39 8.22 36.92 4.26
5488 5726 1.519234 CAGCATCGACAAGCGGCTA 60.519 57.895 1.35 0.00 41.33 3.93
5545 5783 1.866015 TCGACAGGGAGGTCATGATT 58.134 50.000 0.00 0.00 37.66 2.57


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

AutoCloner maintained by Alex Coulton.