Multiple sequence alignment - TraesCS1D01G111800

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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 TraesCS1D01G111800 chr1D 100.000 4253 0 0 1 4253 107198842 107194590 0.000000e+00 7854.0
1 TraesCS1D01G111800 chr1B 97.127 2750 72 3 632 3378 159395904 159398649 0.000000e+00 4634.0
2 TraesCS1D01G111800 chr1B 95.725 538 20 3 3707 4243 159406290 159406825 0.000000e+00 863.0
3 TraesCS1D01G111800 chr1B 84.874 119 15 3 3364 3481 159405917 159406033 2.690000e-22 117.0
4 TraesCS1D01G111800 chr5D 96.724 580 18 1 1 580 335908913 335909491 0.000000e+00 965.0
5 TraesCS1D01G111800 chr5B 92.282 596 44 2 1 594 127694150 127694745 0.000000e+00 845.0
6 TraesCS1D01G111800 chr5B 87.973 582 65 3 6 586 689098576 689099153 0.000000e+00 682.0
7 TraesCS1D01G111800 chr5B 85.838 579 81 1 12 589 611075114 611075692 7.820000e-172 614.0
8 TraesCS1D01G111800 chr5B 91.765 85 5 2 3627 3709 679585745 679585829 2.690000e-22 117.0
9 TraesCS1D01G111800 chr4B 90.988 577 48 2 12 588 510852592 510852020 0.000000e+00 774.0
10 TraesCS1D01G111800 chr1A 90.210 572 52 2 17 585 13926916 13926346 0.000000e+00 743.0
11 TraesCS1D01G111800 chr2B 90.141 568 55 1 16 582 141741953 141741386 0.000000e+00 737.0
12 TraesCS1D01G111800 chr2B 86.135 577 76 2 12 588 142552367 142551795 1.680000e-173 619.0
13 TraesCS1D01G111800 chr2B 75.468 909 190 28 2533 3428 451455578 451456466 3.060000e-111 412.0
14 TraesCS1D01G111800 chr7B 87.370 578 68 3 12 589 719726931 719726359 0.000000e+00 658.0
15 TraesCS1D01G111800 chr2A 75.578 909 189 29 2533 3428 515303884 515304772 6.580000e-113 418.0
16 TraesCS1D01G111800 chr2A 91.176 68 5 1 3643 3709 740053794 740053727 1.630000e-14 91.6
17 TraesCS1D01G111800 chr2D 75.330 908 193 27 2533 3428 380079647 380080535 1.420000e-109 407.0
18 TraesCS1D01G111800 chr2D 94.118 68 3 1 3643 3709 11162555 11162488 7.520000e-18 102.0
19 TraesCS1D01G111800 chr2D 86.364 88 10 2 3627 3712 639519659 639519572 1.260000e-15 95.3
20 TraesCS1D01G111800 chr3B 92.857 70 2 2 3643 3709 765735276 765735207 9.730000e-17 99.0
21 TraesCS1D01G111800 chr3B 97.143 35 1 0 3625 3659 14964589 14964623 4.590000e-05 60.2
22 TraesCS1D01G111800 chr3D 97.059 34 1 0 1157 1190 544778708 544778741 1.650000e-04 58.4


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 TraesCS1D01G111800 chr1D 107194590 107198842 4252 True 7854 7854 100.0000 1 4253 1 chr1D.!!$R1 4252
1 TraesCS1D01G111800 chr1B 159395904 159398649 2745 False 4634 4634 97.1270 632 3378 1 chr1B.!!$F1 2746
2 TraesCS1D01G111800 chr1B 159405917 159406825 908 False 490 863 90.2995 3364 4243 2 chr1B.!!$F2 879
3 TraesCS1D01G111800 chr5D 335908913 335909491 578 False 965 965 96.7240 1 580 1 chr5D.!!$F1 579
4 TraesCS1D01G111800 chr5B 127694150 127694745 595 False 845 845 92.2820 1 594 1 chr5B.!!$F1 593
5 TraesCS1D01G111800 chr5B 689098576 689099153 577 False 682 682 87.9730 6 586 1 chr5B.!!$F4 580
6 TraesCS1D01G111800 chr5B 611075114 611075692 578 False 614 614 85.8380 12 589 1 chr5B.!!$F2 577
7 TraesCS1D01G111800 chr4B 510852020 510852592 572 True 774 774 90.9880 12 588 1 chr4B.!!$R1 576
8 TraesCS1D01G111800 chr1A 13926346 13926916 570 True 743 743 90.2100 17 585 1 chr1A.!!$R1 568
9 TraesCS1D01G111800 chr2B 141741386 141741953 567 True 737 737 90.1410 16 582 1 chr2B.!!$R1 566
10 TraesCS1D01G111800 chr2B 142551795 142552367 572 True 619 619 86.1350 12 588 1 chr2B.!!$R2 576
11 TraesCS1D01G111800 chr2B 451455578 451456466 888 False 412 412 75.4680 2533 3428 1 chr2B.!!$F1 895
12 TraesCS1D01G111800 chr7B 719726359 719726931 572 True 658 658 87.3700 12 589 1 chr7B.!!$R1 577
13 TraesCS1D01G111800 chr2A 515303884 515304772 888 False 418 418 75.5780 2533 3428 1 chr2A.!!$F1 895
14 TraesCS1D01G111800 chr2D 380079647 380080535 888 False 407 407 75.3300 2533 3428 1 chr2D.!!$F1 895

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
414 415 0.114560 AAGGAAGTCCGAGGGAGTCA 59.885 55.0 0.00 0.00 42.08 3.41 F
704 711 0.250467 CCAGTCACCCAACCTGACAG 60.250 60.0 0.00 0.00 40.56 3.51 F
1052 1062 0.333993 ATGCCTCTTGTTGCCATCCT 59.666 50.0 0.00 0.00 0.00 3.24 F
1081 1091 0.614697 TCTCATCTCCGCCTTCCACA 60.615 55.0 0.00 0.00 0.00 4.17 F
2405 2415 0.723981 GCTACTACTGCTGCAAGTGC 59.276 55.0 15.37 12.73 42.50 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1639 0.251787 GGAATTGGCCAGGACCAGTT 60.252 55.0 5.11 9.50 41.86 3.16 R
2130 2140 0.668401 GCATTGCAGGCAGTTTGACC 60.668 55.0 3.15 0.00 0.00 4.02 R
2466 2476 0.673644 ACATGCCGGTAGTGTGCTTC 60.674 55.0 1.90 0.00 0.00 3.86 R
2798 2808 2.988010 ATTGCTGCGGAAGAGATGTA 57.012 45.0 0.00 0.00 0.00 2.29 R
3845 3972 0.334676 AGAGACTCCTGCAGGCTAGT 59.665 55.0 28.91 25.86 42.72 2.57 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
135 136 2.903547 GAGCTTTTCCGGCGTGCAA 61.904 57.895 6.01 0.00 34.52 4.08
199 200 7.695480 TCATATCAAAAAGGGTCAAATTCGA 57.305 32.000 0.00 0.00 0.00 3.71
388 389 2.736682 CGTACCCGGCGCTCAAAAG 61.737 63.158 7.64 0.00 0.00 2.27
414 415 0.114560 AAGGAAGTCCGAGGGAGTCA 59.885 55.000 0.00 0.00 42.08 3.41
519 523 2.505982 CCACCTTCCGGCGATCAT 59.494 61.111 9.30 0.00 0.00 2.45
603 610 4.570663 CCCGCTCGGCTCCGTTAG 62.571 72.222 8.28 0.55 40.74 2.34
613 620 2.831742 TCCGTTAGCTCGCCGGAT 60.832 61.111 5.05 0.00 45.20 4.18
614 621 2.354773 CCGTTAGCTCGCCGGATC 60.355 66.667 5.05 0.00 44.41 3.36
615 622 2.354773 CGTTAGCTCGCCGGATCC 60.355 66.667 5.05 0.00 0.00 3.36
616 623 2.812499 GTTAGCTCGCCGGATCCA 59.188 61.111 13.41 0.00 0.00 3.41
617 624 1.143183 GTTAGCTCGCCGGATCCAA 59.857 57.895 13.41 0.00 0.00 3.53
618 625 0.876342 GTTAGCTCGCCGGATCCAAG 60.876 60.000 13.41 3.20 0.00 3.61
619 626 1.040893 TTAGCTCGCCGGATCCAAGA 61.041 55.000 13.41 6.59 0.00 3.02
620 627 0.827925 TAGCTCGCCGGATCCAAGAT 60.828 55.000 13.41 4.58 0.00 2.40
621 628 1.227674 GCTCGCCGGATCCAAGATT 60.228 57.895 13.41 0.00 0.00 2.40
622 629 1.224722 GCTCGCCGGATCCAAGATTC 61.225 60.000 13.41 0.00 0.00 2.52
623 630 0.601311 CTCGCCGGATCCAAGATTCC 60.601 60.000 13.41 0.00 0.00 3.01
624 631 1.598130 CGCCGGATCCAAGATTCCC 60.598 63.158 13.41 0.00 0.00 3.97
625 632 1.839894 GCCGGATCCAAGATTCCCT 59.160 57.895 13.41 0.00 0.00 4.20
626 633 0.536006 GCCGGATCCAAGATTCCCTG 60.536 60.000 13.41 0.00 0.00 4.45
627 634 0.839946 CCGGATCCAAGATTCCCTGT 59.160 55.000 13.41 0.00 0.00 4.00
628 635 1.202698 CCGGATCCAAGATTCCCTGTC 60.203 57.143 13.41 0.00 0.00 3.51
629 636 1.765314 CGGATCCAAGATTCCCTGTCT 59.235 52.381 13.41 0.00 0.00 3.41
630 637 2.224161 CGGATCCAAGATTCCCTGTCTC 60.224 54.545 13.41 0.00 0.00 3.36
646 653 5.123227 CCTGTCTCTTGTTTGACCAGTTAA 58.877 41.667 0.00 0.00 32.67 2.01
649 656 5.355910 TGTCTCTTGTTTGACCAGTTAAACC 59.644 40.000 13.60 1.09 38.00 3.27
660 667 9.802039 TTTGACCAGTTAAACCATTCTATAGTT 57.198 29.630 0.00 0.00 0.00 2.24
669 676 6.903883 AACCATTCTATAGTTTACACAGCG 57.096 37.500 0.00 0.00 0.00 5.18
676 683 6.967135 TCTATAGTTTACACAGCGGTCATAG 58.033 40.000 0.00 0.00 0.00 2.23
703 710 1.705002 CCCAGTCACCCAACCTGACA 61.705 60.000 1.67 0.00 40.56 3.58
704 711 0.250467 CCAGTCACCCAACCTGACAG 60.250 60.000 0.00 0.00 40.56 3.51
706 713 1.148273 GTCACCCAACCTGACAGCA 59.852 57.895 0.00 0.00 38.36 4.41
730 737 5.545723 AGGGCAGCACAGTAGAATATTCTAT 59.454 40.000 24.42 12.94 41.43 1.98
828 838 3.208594 TCCAGATTTCAGAATGGATGCG 58.791 45.455 0.40 0.00 36.92 4.73
830 840 3.003068 CCAGATTTCAGAATGGATGCGTC 59.997 47.826 0.00 0.00 36.16 5.19
832 842 3.624861 AGATTTCAGAATGGATGCGTCAC 59.375 43.478 8.47 0.00 36.16 3.67
834 844 2.299993 TCAGAATGGATGCGTCACTC 57.700 50.000 8.47 0.80 36.16 3.51
847 857 0.452585 GTCACTCGCCAGTCCTAGTC 59.547 60.000 0.00 0.00 0.00 2.59
931 941 5.121105 CCATGAATTAGCAGTGAGATGACA 58.879 41.667 0.00 0.00 0.00 3.58
932 942 5.236695 CCATGAATTAGCAGTGAGATGACAG 59.763 44.000 0.00 0.00 0.00 3.51
933 943 5.665916 TGAATTAGCAGTGAGATGACAGA 57.334 39.130 0.00 0.00 0.00 3.41
989 999 2.661176 ATAGGACTCTTCACCCCCAA 57.339 50.000 0.00 0.00 0.00 4.12
1052 1062 0.333993 ATGCCTCTTGTTGCCATCCT 59.666 50.000 0.00 0.00 0.00 3.24
1081 1091 0.614697 TCTCATCTCCGCCTTCCACA 60.615 55.000 0.00 0.00 0.00 4.17
1353 1363 3.809832 CCGATGATGGTAACCTTGTCATC 59.190 47.826 11.64 11.64 40.92 2.92
1505 1515 3.459598 TGGCAGAGCTTTGATTACCCTAT 59.540 43.478 8.73 0.00 0.00 2.57
1546 1556 1.133025 CAAAGCAAGGCGTGGATAAGG 59.867 52.381 1.91 0.00 0.00 2.69
1559 1569 2.574369 TGGATAAGGTCACCGGTTTGAT 59.426 45.455 2.97 0.00 0.00 2.57
1629 1639 6.259167 GCCGTTATTGTGTGGAATTAGATACA 59.741 38.462 0.00 0.00 0.00 2.29
1682 1692 9.239551 ACTATGCAACTCGTCCATAGTATATTA 57.760 33.333 15.64 0.00 45.77 0.98
1683 1693 9.504710 CTATGCAACTCGTCCATAGTATATTAC 57.495 37.037 0.00 0.00 35.73 1.89
1739 1749 2.287427 CGATGCCAGAAATGAATGGAGC 60.287 50.000 0.00 0.00 39.02 4.70
1752 1762 6.855763 ATGAATGGAGCCAATCTTTTTACA 57.144 33.333 6.18 0.00 0.00 2.41
2026 2036 2.846827 AGGTCACCTAAGGATTGGAAGG 59.153 50.000 0.00 0.00 35.14 3.46
2030 2040 4.470304 GTCACCTAAGGATTGGAAGGTAGT 59.530 45.833 0.00 0.00 40.39 2.73
2130 2140 4.398319 ACAAGTTCTACCCCATGACAAAG 58.602 43.478 0.00 0.00 0.00 2.77
2236 2246 3.553904 TGCATTGCATATTCCTACAGCA 58.446 40.909 7.38 0.00 31.71 4.41
2283 2293 5.359576 TGACTTGCTTAACATCAAACAAGGT 59.640 36.000 0.00 0.00 38.99 3.50
2392 2402 3.154546 AGGGGGTTATTTGGGCTACTA 57.845 47.619 0.00 0.00 0.00 1.82
2405 2415 0.723981 GCTACTACTGCTGCAAGTGC 59.276 55.000 15.37 12.73 42.50 4.40
2416 2426 4.324424 CAAGTGCCGTTGCTTTGG 57.676 55.556 0.00 0.00 38.71 3.28
2448 2458 2.620115 AGTTGTCATGTGGTTTCTGCTG 59.380 45.455 0.00 0.00 0.00 4.41
2463 2473 2.773661 TCTGCTGATATGGAGGAGCAAA 59.226 45.455 0.00 0.00 40.80 3.68
2466 2476 2.883386 GCTGATATGGAGGAGCAAAAGG 59.117 50.000 0.00 0.00 0.00 3.11
2798 2808 2.290896 TGCCAAATCTTTCCCTCGATGT 60.291 45.455 0.00 0.00 0.00 3.06
2976 2986 6.206634 CCTCATTTGTACCTAAAGTTGCAGAA 59.793 38.462 0.00 0.00 0.00 3.02
3015 3025 2.706190 TCTAGGGAGGGATTTTAGCAGC 59.294 50.000 0.00 0.00 0.00 5.25
3112 3122 1.749063 TGGATGTCTACAGCTACGGTG 59.251 52.381 0.00 0.00 37.06 4.94
3141 3151 5.339008 TGCTTGAAATAGTATCAGGTCGT 57.661 39.130 0.00 0.00 0.00 4.34
3187 3197 1.730501 CAGCACTGGTGATCATTCGT 58.269 50.000 0.00 0.00 32.22 3.85
3189 3199 1.276138 AGCACTGGTGATCATTCGTCA 59.724 47.619 0.00 0.00 0.00 4.35
3244 3254 4.397832 GGGGACGTTGCGGGCTTA 62.398 66.667 0.00 0.00 0.00 3.09
3245 3255 2.124860 GGGACGTTGCGGGCTTAT 60.125 61.111 0.00 0.00 0.00 1.73
3307 3317 2.856000 AGGGTCTGCAAGGTGGCT 60.856 61.111 0.00 0.00 34.04 4.75
3352 3362 1.520192 CAATCGACCGACCATGGGA 59.480 57.895 18.09 2.24 0.00 4.37
3370 3380 3.244911 TGGGAGAAGTGGTTCAAATCCTC 60.245 47.826 0.00 0.00 34.82 3.71
3403 3413 6.272792 TGTTAGAACTTGAAGTACCCCCAATA 59.727 38.462 0.00 0.00 0.00 1.90
3436 3447 3.954200 TCAAGCTATTGCATGAAGGTCA 58.046 40.909 4.60 0.00 42.83 4.02
3440 3451 2.754552 GCTATTGCATGAAGGTCACCAA 59.245 45.455 0.00 0.00 39.41 3.67
3441 3452 3.382546 GCTATTGCATGAAGGTCACCAAT 59.617 43.478 0.00 9.53 36.39 3.16
3442 3453 4.498682 GCTATTGCATGAAGGTCACCAATC 60.499 45.833 0.00 0.00 35.08 2.67
3445 3456 1.474077 GCATGAAGGTCACCAATCACC 59.526 52.381 4.56 0.00 0.00 4.02
3446 3457 2.094675 CATGAAGGTCACCAATCACCC 58.905 52.381 4.56 0.00 32.45 4.61
3449 3460 2.983192 TGAAGGTCACCAATCACCCTAA 59.017 45.455 0.00 0.00 32.45 2.69
3450 3461 3.396276 TGAAGGTCACCAATCACCCTAAA 59.604 43.478 0.00 0.00 32.45 1.85
3451 3462 3.434940 AGGTCACCAATCACCCTAAAC 57.565 47.619 0.00 0.00 32.45 2.01
3458 3469 7.202102 GGTCACCAATCACCCTAAACTATATCT 60.202 40.741 0.00 0.00 0.00 1.98
3460 3471 6.868864 CACCAATCACCCTAAACTATATCTCG 59.131 42.308 0.00 0.00 0.00 4.04
3464 3475 5.950023 TCACCCTAAACTATATCTCGGTCT 58.050 41.667 0.00 0.00 0.00 3.85
3477 3488 0.603707 TCGGTCTGAAGGCAAAGCAG 60.604 55.000 0.00 0.00 0.00 4.24
3481 3492 1.807142 GTCTGAAGGCAAAGCAGTACC 59.193 52.381 0.00 0.00 0.00 3.34
3488 3614 3.356290 AGGCAAAGCAGTACCCATTAAG 58.644 45.455 0.00 0.00 0.00 1.85
3500 3626 8.154856 GCAGTACCCATTAAGGTTAAGATATGA 58.845 37.037 0.00 0.00 41.58 2.15
3526 3653 7.865706 ACTTATGAGAACAACATTATGGACC 57.134 36.000 0.00 0.00 0.00 4.46
3528 3655 8.109634 ACTTATGAGAACAACATTATGGACCTT 58.890 33.333 0.00 0.00 0.00 3.50
3533 3660 6.784031 AGAACAACATTATGGACCTTCTTCT 58.216 36.000 0.00 0.00 0.00 2.85
3548 3675 6.831976 ACCTTCTTCTATGGTCCATAATCAC 58.168 40.000 12.73 0.00 29.71 3.06
3551 3678 5.858381 TCTTCTATGGTCCATAATCACTGC 58.142 41.667 12.73 0.00 0.00 4.40
3554 3681 6.191657 TCTATGGTCCATAATCACTGCAAT 57.808 37.500 12.73 0.00 0.00 3.56
3555 3682 6.604171 TCTATGGTCCATAATCACTGCAATT 58.396 36.000 12.73 0.00 0.00 2.32
3556 3683 7.062322 TCTATGGTCCATAATCACTGCAATTT 58.938 34.615 12.73 0.00 0.00 1.82
3557 3684 5.327616 TGGTCCATAATCACTGCAATTTG 57.672 39.130 0.00 0.00 0.00 2.32
3558 3685 4.771577 TGGTCCATAATCACTGCAATTTGT 59.228 37.500 0.00 0.00 0.00 2.83
3559 3686 5.948758 TGGTCCATAATCACTGCAATTTGTA 59.051 36.000 0.00 0.00 0.00 2.41
3560 3687 6.435591 TGGTCCATAATCACTGCAATTTGTAA 59.564 34.615 0.00 0.00 0.00 2.41
3561 3688 6.751888 GGTCCATAATCACTGCAATTTGTAAC 59.248 38.462 0.00 0.00 0.00 2.50
3629 3756 3.571590 GGAGAGACTGATCCCATGTACT 58.428 50.000 0.00 0.00 0.00 2.73
3630 3757 3.572255 GGAGAGACTGATCCCATGTACTC 59.428 52.174 0.00 0.00 0.00 2.59
3631 3758 3.571590 AGAGACTGATCCCATGTACTCC 58.428 50.000 0.00 0.00 0.00 3.85
3632 3759 2.630580 GAGACTGATCCCATGTACTCCC 59.369 54.545 0.00 0.00 0.00 4.30
3633 3760 2.248686 AGACTGATCCCATGTACTCCCT 59.751 50.000 0.00 0.00 0.00 4.20
3634 3761 2.630580 GACTGATCCCATGTACTCCCTC 59.369 54.545 0.00 0.00 0.00 4.30
3635 3762 1.974236 CTGATCCCATGTACTCCCTCC 59.026 57.143 0.00 0.00 0.00 4.30
3636 3763 0.969894 GATCCCATGTACTCCCTCCG 59.030 60.000 0.00 0.00 0.00 4.63
3637 3764 0.264955 ATCCCATGTACTCCCTCCGT 59.735 55.000 0.00 0.00 0.00 4.69
3638 3765 0.396695 TCCCATGTACTCCCTCCGTC 60.397 60.000 0.00 0.00 0.00 4.79
3639 3766 1.400530 CCCATGTACTCCCTCCGTCC 61.401 65.000 0.00 0.00 0.00 4.79
3640 3767 0.397254 CCATGTACTCCCTCCGTCCT 60.397 60.000 0.00 0.00 0.00 3.85
3641 3768 1.133575 CCATGTACTCCCTCCGTCCTA 60.134 57.143 0.00 0.00 0.00 2.94
3642 3769 2.662866 CATGTACTCCCTCCGTCCTAA 58.337 52.381 0.00 0.00 0.00 2.69
3643 3770 2.905415 TGTACTCCCTCCGTCCTAAA 57.095 50.000 0.00 0.00 0.00 1.85
3644 3771 3.393426 TGTACTCCCTCCGTCCTAAAT 57.607 47.619 0.00 0.00 0.00 1.40
3645 3772 4.524802 TGTACTCCCTCCGTCCTAAATA 57.475 45.455 0.00 0.00 0.00 1.40
3646 3773 5.070823 TGTACTCCCTCCGTCCTAAATAT 57.929 43.478 0.00 0.00 0.00 1.28
3647 3774 6.204852 TGTACTCCCTCCGTCCTAAATATA 57.795 41.667 0.00 0.00 0.00 0.86
3648 3775 6.613699 TGTACTCCCTCCGTCCTAAATATAA 58.386 40.000 0.00 0.00 0.00 0.98
3649 3776 6.718454 TGTACTCCCTCCGTCCTAAATATAAG 59.282 42.308 0.00 0.00 0.00 1.73
3650 3777 5.713807 ACTCCCTCCGTCCTAAATATAAGT 58.286 41.667 0.00 0.00 0.00 2.24
3651 3778 5.774184 ACTCCCTCCGTCCTAAATATAAGTC 59.226 44.000 0.00 0.00 0.00 3.01
3652 3779 4.763793 TCCCTCCGTCCTAAATATAAGTCG 59.236 45.833 0.00 0.00 0.00 4.18
3653 3780 4.522022 CCCTCCGTCCTAAATATAAGTCGT 59.478 45.833 0.00 0.00 0.00 4.34
3654 3781 5.010415 CCCTCCGTCCTAAATATAAGTCGTT 59.990 44.000 0.00 0.00 0.00 3.85
3655 3782 6.462067 CCCTCCGTCCTAAATATAAGTCGTTT 60.462 42.308 0.00 0.00 0.00 3.60
3656 3783 6.982724 CCTCCGTCCTAAATATAAGTCGTTTT 59.017 38.462 0.00 0.00 0.00 2.43
3657 3784 8.137437 CCTCCGTCCTAAATATAAGTCGTTTTA 58.863 37.037 0.00 0.00 0.00 1.52
3658 3785 9.178427 CTCCGTCCTAAATATAAGTCGTTTTAG 57.822 37.037 0.00 0.00 33.47 1.85
3659 3786 7.649306 TCCGTCCTAAATATAAGTCGTTTTAGC 59.351 37.037 0.00 0.00 32.72 3.09
3660 3787 7.436080 CCGTCCTAAATATAAGTCGTTTTAGCA 59.564 37.037 0.00 0.00 32.72 3.49
3661 3788 8.810427 CGTCCTAAATATAAGTCGTTTTAGCAA 58.190 33.333 0.00 0.00 32.72 3.91
3663 3790 8.823818 TCCTAAATATAAGTCGTTTTAGCAAGC 58.176 33.333 0.00 0.00 32.72 4.01
3664 3791 8.827677 CCTAAATATAAGTCGTTTTAGCAAGCT 58.172 33.333 0.00 0.00 32.72 3.74
3669 3796 5.358298 AAGTCGTTTTAGCAAGCTAAAGG 57.642 39.130 22.02 18.51 45.56 3.11
3670 3797 4.638304 AGTCGTTTTAGCAAGCTAAAGGA 58.362 39.130 22.02 19.97 45.56 3.36
3671 3798 4.691216 AGTCGTTTTAGCAAGCTAAAGGAG 59.309 41.667 22.02 17.67 45.56 3.69
3685 3812 3.898517 AAAGGAGCTTGCTAAAACGAC 57.101 42.857 0.00 0.00 0.00 4.34
3686 3813 1.809684 AGGAGCTTGCTAAAACGACC 58.190 50.000 0.00 0.00 0.00 4.79
3687 3814 1.348036 AGGAGCTTGCTAAAACGACCT 59.652 47.619 0.00 0.00 0.00 3.85
3688 3815 2.565834 AGGAGCTTGCTAAAACGACCTA 59.434 45.455 0.00 0.00 0.00 3.08
3689 3816 3.197983 AGGAGCTTGCTAAAACGACCTAT 59.802 43.478 0.00 0.00 0.00 2.57
3690 3817 4.404715 AGGAGCTTGCTAAAACGACCTATA 59.595 41.667 0.00 0.00 0.00 1.31
3691 3818 5.070580 AGGAGCTTGCTAAAACGACCTATAT 59.929 40.000 0.00 0.00 0.00 0.86
3692 3819 5.758784 GGAGCTTGCTAAAACGACCTATATT 59.241 40.000 0.00 0.00 0.00 1.28
3693 3820 6.260271 GGAGCTTGCTAAAACGACCTATATTT 59.740 38.462 0.00 0.00 0.00 1.40
3694 3821 7.201705 GGAGCTTGCTAAAACGACCTATATTTT 60.202 37.037 0.00 0.00 0.00 1.82
3695 3822 7.472543 AGCTTGCTAAAACGACCTATATTTTG 58.527 34.615 0.00 0.00 0.00 2.44
3696 3823 6.691388 GCTTGCTAAAACGACCTATATTTTGG 59.309 38.462 0.00 0.00 0.00 3.28
3697 3824 7.414762 GCTTGCTAAAACGACCTATATTTTGGA 60.415 37.037 0.00 0.00 0.00 3.53
3698 3825 7.925043 TGCTAAAACGACCTATATTTTGGAA 57.075 32.000 0.00 0.00 0.00 3.53
3699 3826 7.754625 TGCTAAAACGACCTATATTTTGGAAC 58.245 34.615 0.00 0.00 0.00 3.62
3700 3827 7.390996 TGCTAAAACGACCTATATTTTGGAACA 59.609 33.333 0.00 0.00 0.00 3.18
3701 3828 7.908601 GCTAAAACGACCTATATTTTGGAACAG 59.091 37.037 0.00 0.00 42.39 3.16
3702 3829 7.989416 AAAACGACCTATATTTTGGAACAGA 57.011 32.000 0.00 0.00 42.39 3.41
3703 3830 7.611213 AAACGACCTATATTTTGGAACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
3704 3831 6.540438 ACGACCTATATTTTGGAACAGAGA 57.460 37.500 0.00 0.00 42.39 3.10
3705 3832 6.942976 ACGACCTATATTTTGGAACAGAGAA 58.057 36.000 0.00 0.00 42.39 2.87
3706 3833 7.042335 ACGACCTATATTTTGGAACAGAGAAG 58.958 38.462 0.00 0.00 42.39 2.85
3707 3834 7.042335 CGACCTATATTTTGGAACAGAGAAGT 58.958 38.462 0.00 0.00 42.39 3.01
3708 3835 8.195436 CGACCTATATTTTGGAACAGAGAAGTA 58.805 37.037 0.00 0.00 42.39 2.24
3736 3863 1.149401 GGACCTGCTTCTATGGCCC 59.851 63.158 0.00 0.00 0.00 5.80
3754 3881 3.118665 GGCCCATAATCACTGCAATTTGT 60.119 43.478 0.00 0.00 0.00 2.83
3755 3882 3.866910 GCCCATAATCACTGCAATTTGTG 59.133 43.478 0.00 0.00 35.68 3.33
3768 3895 7.590322 CACTGCAATTTGTGAGCATATATCTTC 59.410 37.037 0.00 0.00 37.68 2.87
3845 3972 8.944138 TGATCCCACAATTATTTCATACTAGGA 58.056 33.333 0.00 0.00 0.00 2.94
3879 4006 6.708054 CAGGAGTCTCTGTTAAATCTGTTTGT 59.292 38.462 0.00 0.00 0.00 2.83
3949 4076 5.634859 GCAATTTAGTTGGTGAATGACCTTG 59.365 40.000 0.00 0.00 46.32 3.61
3950 4077 6.738453 GCAATTTAGTTGGTGAATGACCTTGT 60.738 38.462 0.00 0.00 46.32 3.16
3965 4092 6.187727 TGACCTTGTCAAAACCTAGAATCT 57.812 37.500 0.00 0.00 39.78 2.40
3977 4104 6.969828 AACCTAGAATCTCAAACACGATTC 57.030 37.500 0.00 0.00 43.56 2.52
3978 4105 6.037786 ACCTAGAATCTCAAACACGATTCA 57.962 37.500 12.74 1.43 44.90 2.57
3979 4106 5.869888 ACCTAGAATCTCAAACACGATTCAC 59.130 40.000 12.74 0.00 44.90 3.18
3990 4117 4.415881 ACACGATTCACCCATATTGCTA 57.584 40.909 0.00 0.00 0.00 3.49
3994 4121 5.527214 CACGATTCACCCATATTGCTAAAGA 59.473 40.000 0.00 0.00 0.00 2.52
4012 4139 1.602377 AGAAAAAGGACAACGAAGCCG 59.398 47.619 0.00 0.00 42.50 5.52
4245 4372 3.209410 CATCAAGTATGCTTCCAGTCCC 58.791 50.000 0.00 0.00 31.49 4.46
4246 4373 1.207089 TCAAGTATGCTTCCAGTCCCG 59.793 52.381 0.00 0.00 31.49 5.14
4247 4374 0.541863 AAGTATGCTTCCAGTCCCGG 59.458 55.000 0.00 0.00 0.00 5.73
4248 4375 0.617820 AGTATGCTTCCAGTCCCGGT 60.618 55.000 0.00 0.00 0.00 5.28
4249 4376 0.462047 GTATGCTTCCAGTCCCGGTG 60.462 60.000 0.00 0.00 0.00 4.94
4250 4377 1.622607 TATGCTTCCAGTCCCGGTGG 61.623 60.000 0.00 1.00 36.28 4.61
4251 4378 4.410400 GCTTCCAGTCCCGGTGGG 62.410 72.222 9.56 0.00 46.11 4.61
4252 4379 2.928396 CTTCCAGTCCCGGTGGGT 60.928 66.667 9.56 0.00 44.74 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.764851 CGATTCAGATCAGAGACGCC 58.235 55.000 0.00 0.00 32.33 5.68
135 136 5.019785 ACTTTGGTGAAGAGACGTAAGTT 57.980 39.130 0.00 0.00 45.04 2.66
199 200 5.193679 GTCCATTGCCTAAGGTATGTCTTT 58.806 41.667 0.00 0.00 0.00 2.52
388 389 1.281899 CTCGGACTTCCTTTGCGATC 58.718 55.000 0.00 0.00 36.17 3.69
414 415 3.771160 GCCGTCTCCACCATCGGT 61.771 66.667 0.00 0.00 44.07 4.69
598 605 2.354773 GGATCCGGCGAGCTAACG 60.355 66.667 9.30 0.00 0.00 3.18
599 606 0.876342 CTTGGATCCGGCGAGCTAAC 60.876 60.000 9.30 0.00 0.00 2.34
600 607 1.040893 TCTTGGATCCGGCGAGCTAA 61.041 55.000 9.30 0.57 0.00 3.09
601 608 0.827925 ATCTTGGATCCGGCGAGCTA 60.828 55.000 9.30 0.00 0.00 3.32
602 609 1.690219 AATCTTGGATCCGGCGAGCT 61.690 55.000 9.30 0.00 0.00 4.09
603 610 1.224722 GAATCTTGGATCCGGCGAGC 61.225 60.000 9.30 0.00 0.00 5.03
604 611 0.601311 GGAATCTTGGATCCGGCGAG 60.601 60.000 9.30 0.00 0.00 5.03
605 612 1.445942 GGAATCTTGGATCCGGCGA 59.554 57.895 9.30 3.53 0.00 5.54
606 613 1.598130 GGGAATCTTGGATCCGGCG 60.598 63.158 7.39 0.00 36.54 6.46
607 614 0.536006 CAGGGAATCTTGGATCCGGC 60.536 60.000 7.39 0.00 36.54 6.13
608 615 0.839946 ACAGGGAATCTTGGATCCGG 59.160 55.000 7.39 0.00 36.54 5.14
609 616 1.765314 AGACAGGGAATCTTGGATCCG 59.235 52.381 7.39 0.00 36.54 4.18
610 617 3.044894 AGAGACAGGGAATCTTGGATCC 58.955 50.000 4.20 4.20 34.85 3.36
611 618 4.450053 CAAGAGACAGGGAATCTTGGATC 58.550 47.826 6.32 0.00 43.94 3.36
612 619 4.500499 CAAGAGACAGGGAATCTTGGAT 57.500 45.455 6.32 0.00 43.94 3.41
613 620 3.988976 CAAGAGACAGGGAATCTTGGA 57.011 47.619 6.32 0.00 43.94 3.53
616 623 5.066593 GTCAAACAAGAGACAGGGAATCTT 58.933 41.667 0.00 0.00 34.93 2.40
617 624 4.505742 GGTCAAACAAGAGACAGGGAATCT 60.506 45.833 0.00 0.00 36.50 2.40
618 625 3.753797 GGTCAAACAAGAGACAGGGAATC 59.246 47.826 0.00 0.00 36.50 2.52
619 626 3.138283 TGGTCAAACAAGAGACAGGGAAT 59.862 43.478 0.00 0.00 36.50 3.01
620 627 2.507886 TGGTCAAACAAGAGACAGGGAA 59.492 45.455 0.00 0.00 36.50 3.97
621 628 2.104792 CTGGTCAAACAAGAGACAGGGA 59.895 50.000 0.00 0.00 36.50 4.20
622 629 2.158755 ACTGGTCAAACAAGAGACAGGG 60.159 50.000 0.00 0.00 36.50 4.45
623 630 3.199880 ACTGGTCAAACAAGAGACAGG 57.800 47.619 0.00 0.00 36.50 4.00
624 631 6.458342 GGTTTAACTGGTCAAACAAGAGACAG 60.458 42.308 2.50 0.00 36.56 3.51
625 632 5.355910 GGTTTAACTGGTCAAACAAGAGACA 59.644 40.000 2.50 0.00 36.56 3.41
626 633 5.355910 TGGTTTAACTGGTCAAACAAGAGAC 59.644 40.000 2.50 0.00 36.56 3.36
627 634 5.502079 TGGTTTAACTGGTCAAACAAGAGA 58.498 37.500 2.50 0.00 36.56 3.10
628 635 5.828299 TGGTTTAACTGGTCAAACAAGAG 57.172 39.130 2.50 0.00 36.56 2.85
629 636 6.605594 AGAATGGTTTAACTGGTCAAACAAGA 59.394 34.615 2.50 0.00 36.56 3.02
630 637 6.805713 AGAATGGTTTAACTGGTCAAACAAG 58.194 36.000 2.50 0.00 36.56 3.16
646 653 5.815740 CCGCTGTGTAAACTATAGAATGGTT 59.184 40.000 6.78 0.00 35.32 3.67
649 656 6.040247 TGACCGCTGTGTAAACTATAGAATG 58.960 40.000 6.78 0.00 0.00 2.67
660 667 0.828022 CCCCTATGACCGCTGTGTAA 59.172 55.000 0.00 0.00 0.00 2.41
667 674 1.526225 GGAAAGCCCCTATGACCGC 60.526 63.158 0.00 0.00 0.00 5.68
687 694 1.344953 TGCTGTCAGGTTGGGTGACT 61.345 55.000 1.14 0.00 44.02 3.41
689 696 1.451504 CTGCTGTCAGGTTGGGTGA 59.548 57.895 1.14 0.00 36.68 4.02
703 710 1.483595 TTCTACTGTGCTGCCCTGCT 61.484 55.000 0.00 0.00 0.00 4.24
704 711 0.393537 ATTCTACTGTGCTGCCCTGC 60.394 55.000 0.00 0.00 0.00 4.85
706 713 3.713764 AGAATATTCTACTGTGCTGCCCT 59.286 43.478 16.50 0.00 35.34 5.19
708 715 6.589523 CAGATAGAATATTCTACTGTGCTGCC 59.410 42.308 24.17 7.91 42.13 4.85
730 737 2.017668 AACCACATGGGGGTTGCAGA 62.018 55.000 20.68 0.00 46.53 4.26
783 790 0.179171 GACGACGACATGGACGACAT 60.179 55.000 18.41 3.89 41.57 3.06
828 838 0.452585 GACTAGGACTGGCGAGTGAC 59.547 60.000 5.94 0.00 30.16 3.67
830 840 0.965866 TGGACTAGGACTGGCGAGTG 60.966 60.000 5.94 0.00 30.16 3.51
832 842 0.965866 TGTGGACTAGGACTGGCGAG 60.966 60.000 0.00 0.00 0.00 5.03
834 844 1.513158 CTGTGGACTAGGACTGGCG 59.487 63.158 0.00 0.00 0.00 5.69
836 846 0.904865 TGGCTGTGGACTAGGACTGG 60.905 60.000 0.00 0.00 0.00 4.00
841 851 1.488705 TTGGGTGGCTGTGGACTAGG 61.489 60.000 0.00 0.00 0.00 3.02
847 857 1.741525 CAAAGTTGGGTGGCTGTGG 59.258 57.895 0.00 0.00 0.00 4.17
931 941 7.780271 TGTGATATGGTGACTGATACTACTTCT 59.220 37.037 0.00 0.00 0.00 2.85
932 942 7.863375 GTGTGATATGGTGACTGATACTACTTC 59.137 40.741 0.00 0.00 0.00 3.01
933 943 7.561722 AGTGTGATATGGTGACTGATACTACTT 59.438 37.037 0.00 0.00 0.00 2.24
989 999 3.508402 GTCCCGGGTCATGTTTTAACATT 59.492 43.478 22.86 0.00 46.95 2.71
1052 1062 5.080337 AGGCGGAGATGAGAAGTATGAATA 58.920 41.667 0.00 0.00 0.00 1.75
1081 1091 0.896940 CTTGCTGCAGAACATGGGGT 60.897 55.000 20.43 0.00 0.00 4.95
1353 1363 9.840427 ATTGTCGATTTGGTGTCTTTATTTAAG 57.160 29.630 0.00 0.00 35.04 1.85
1505 1515 0.842030 ACCAGGGAGCAGACCATCAA 60.842 55.000 0.00 0.00 0.00 2.57
1629 1639 0.251787 GGAATTGGCCAGGACCAGTT 60.252 55.000 5.11 9.50 41.86 3.16
1682 1692 2.780010 CCATTCCATTCCCCACTAGAGT 59.220 50.000 0.00 0.00 0.00 3.24
1683 1693 2.780010 ACCATTCCATTCCCCACTAGAG 59.220 50.000 0.00 0.00 0.00 2.43
2026 2036 1.065928 CGCCAGATCGGTCCACTAC 59.934 63.158 0.00 0.00 36.97 2.73
2130 2140 0.668401 GCATTGCAGGCAGTTTGACC 60.668 55.000 3.15 0.00 0.00 4.02
2236 2246 2.254152 TACCAGAGGGAGCATCTGTT 57.746 50.000 0.00 0.00 42.18 3.16
2392 2402 2.516930 AACGGCACTTGCAGCAGT 60.517 55.556 3.15 0.00 44.36 4.40
2405 2415 1.663135 CCAACAAAACCAAAGCAACGG 59.337 47.619 0.00 0.00 0.00 4.44
2416 2426 3.306703 CACATGACAACTGCCAACAAAAC 59.693 43.478 0.00 0.00 0.00 2.43
2448 2458 3.567585 GCTTCCTTTTGCTCCTCCATATC 59.432 47.826 0.00 0.00 0.00 1.63
2463 2473 1.003718 GCCGGTAGTGTGCTTCCTT 60.004 57.895 1.90 0.00 30.89 3.36
2466 2476 0.673644 ACATGCCGGTAGTGTGCTTC 60.674 55.000 1.90 0.00 0.00 3.86
2798 2808 2.988010 ATTGCTGCGGAAGAGATGTA 57.012 45.000 0.00 0.00 0.00 2.29
3015 3025 7.653767 AGTTCCTCTAAATGTAGTCAAAACG 57.346 36.000 0.00 0.00 0.00 3.60
3112 3122 7.066284 ACCTGATACTATTTCAAGCAACATCAC 59.934 37.037 0.00 0.00 0.00 3.06
3141 3151 9.764363 CTATTCTCCTTACATGTATTGTTGCTA 57.236 33.333 6.36 0.00 39.87 3.49
3187 3197 3.442273 GCAACTTGAACCGGGAAATATGA 59.558 43.478 6.32 0.00 0.00 2.15
3189 3199 3.426615 TGCAACTTGAACCGGGAAATAT 58.573 40.909 6.32 0.00 0.00 1.28
3239 3249 3.193267 TGCAACTTGTCATCCAATAAGCC 59.807 43.478 0.00 0.00 31.20 4.35
3244 3254 3.056393 CACCATGCAACTTGTCATCCAAT 60.056 43.478 0.00 0.00 31.20 3.16
3245 3255 2.296752 CACCATGCAACTTGTCATCCAA 59.703 45.455 0.00 0.00 0.00 3.53
3352 3362 3.307059 CCTCGAGGATTTGAACCACTTCT 60.307 47.826 28.21 0.00 37.39 2.85
3370 3380 4.814771 ACTTCAAGTTCTAACAAACCCTCG 59.185 41.667 0.00 0.00 0.00 4.63
3403 3413 3.710209 ATAGCTTGAAGCAGTCTTGGT 57.290 42.857 20.45 0.00 45.56 3.67
3433 3444 7.736893 AGATATAGTTTAGGGTGATTGGTGAC 58.263 38.462 0.00 0.00 0.00 3.67
3436 3447 6.014499 CCGAGATATAGTTTAGGGTGATTGGT 60.014 42.308 0.00 0.00 0.00 3.67
3440 3451 6.434652 CAGACCGAGATATAGTTTAGGGTGAT 59.565 42.308 0.00 0.00 0.00 3.06
3441 3452 5.768662 CAGACCGAGATATAGTTTAGGGTGA 59.231 44.000 0.00 0.00 0.00 4.02
3442 3453 5.768662 TCAGACCGAGATATAGTTTAGGGTG 59.231 44.000 0.00 0.00 0.00 4.61
3445 3456 6.570764 GCCTTCAGACCGAGATATAGTTTAGG 60.571 46.154 0.00 0.00 0.00 2.69
3446 3457 6.016192 TGCCTTCAGACCGAGATATAGTTTAG 60.016 42.308 0.00 0.00 0.00 1.85
3449 3460 4.215908 TGCCTTCAGACCGAGATATAGTT 58.784 43.478 0.00 0.00 0.00 2.24
3450 3461 3.833732 TGCCTTCAGACCGAGATATAGT 58.166 45.455 0.00 0.00 0.00 2.12
3451 3462 4.855715 TTGCCTTCAGACCGAGATATAG 57.144 45.455 0.00 0.00 0.00 1.31
3458 3469 0.603707 CTGCTTTGCCTTCAGACCGA 60.604 55.000 0.00 0.00 0.00 4.69
3460 3471 1.807142 GTACTGCTTTGCCTTCAGACC 59.193 52.381 0.00 0.00 0.00 3.85
3464 3475 0.476338 TGGGTACTGCTTTGCCTTCA 59.524 50.000 0.00 0.00 0.00 3.02
3500 3626 9.561069 GGTCCATAATGTTGTTCTCATAAGTAT 57.439 33.333 0.00 0.00 0.00 2.12
3505 3631 7.861629 AGAAGGTCCATAATGTTGTTCTCATA 58.138 34.615 0.00 0.00 0.00 2.15
3506 3632 6.725364 AGAAGGTCCATAATGTTGTTCTCAT 58.275 36.000 0.00 0.00 0.00 2.90
3513 3640 7.056635 ACCATAGAAGAAGGTCCATAATGTTG 58.943 38.462 0.00 0.00 0.00 3.33
3526 3653 6.426328 GCAGTGATTATGGACCATAGAAGAAG 59.574 42.308 13.88 6.50 0.00 2.85
3528 3655 5.366477 TGCAGTGATTATGGACCATAGAAGA 59.634 40.000 13.88 0.30 0.00 2.87
3533 3660 6.606796 ACAAATTGCAGTGATTATGGACCATA 59.393 34.615 10.31 10.31 0.00 2.74
3548 3675 8.296799 TGCAGAAAATAAGTTACAAATTGCAG 57.703 30.769 8.35 0.00 33.35 4.41
3566 3693 6.330004 TGCATCAAAGATAAGTTGCAGAAA 57.670 33.333 0.00 0.00 36.03 2.52
3628 3755 5.106237 CGACTTATATTTAGGACGGAGGGAG 60.106 48.000 0.00 0.00 0.00 4.30
3629 3756 4.763793 CGACTTATATTTAGGACGGAGGGA 59.236 45.833 0.00 0.00 0.00 4.20
3630 3757 4.522022 ACGACTTATATTTAGGACGGAGGG 59.478 45.833 0.00 0.00 0.00 4.30
3631 3758 5.702349 ACGACTTATATTTAGGACGGAGG 57.298 43.478 0.00 0.00 0.00 4.30
3632 3759 7.998753 AAAACGACTTATATTTAGGACGGAG 57.001 36.000 0.00 0.00 0.00 4.63
3633 3760 7.649306 GCTAAAACGACTTATATTTAGGACGGA 59.351 37.037 0.00 0.00 36.39 4.69
3634 3761 7.436080 TGCTAAAACGACTTATATTTAGGACGG 59.564 37.037 0.00 0.00 36.39 4.79
3635 3762 8.343974 TGCTAAAACGACTTATATTTAGGACG 57.656 34.615 0.00 0.00 36.39 4.79
3637 3764 8.823818 GCTTGCTAAAACGACTTATATTTAGGA 58.176 33.333 0.00 0.00 36.39 2.94
3638 3765 8.827677 AGCTTGCTAAAACGACTTATATTTAGG 58.172 33.333 0.00 0.00 36.39 2.69
3643 3770 8.827677 CCTTTAGCTTGCTAAAACGACTTATAT 58.172 33.333 22.76 0.00 0.00 0.86
3644 3771 8.036575 TCCTTTAGCTTGCTAAAACGACTTATA 58.963 33.333 22.76 3.52 0.00 0.98
3645 3772 6.877322 TCCTTTAGCTTGCTAAAACGACTTAT 59.123 34.615 22.76 0.00 0.00 1.73
3646 3773 6.225318 TCCTTTAGCTTGCTAAAACGACTTA 58.775 36.000 22.76 4.69 0.00 2.24
3647 3774 5.061179 TCCTTTAGCTTGCTAAAACGACTT 58.939 37.500 22.76 0.00 0.00 3.01
3648 3775 4.638304 TCCTTTAGCTTGCTAAAACGACT 58.362 39.130 22.76 0.00 0.00 4.18
3649 3776 4.959149 CTCCTTTAGCTTGCTAAAACGAC 58.041 43.478 22.76 0.00 0.00 4.34
3663 3790 4.142881 GGTCGTTTTAGCAAGCTCCTTTAG 60.143 45.833 0.00 0.00 0.00 1.85
3664 3791 3.749609 GGTCGTTTTAGCAAGCTCCTTTA 59.250 43.478 0.00 0.00 0.00 1.85
3665 3792 2.552743 GGTCGTTTTAGCAAGCTCCTTT 59.447 45.455 0.00 0.00 0.00 3.11
3666 3793 2.152016 GGTCGTTTTAGCAAGCTCCTT 58.848 47.619 0.00 0.00 0.00 3.36
3667 3794 1.348036 AGGTCGTTTTAGCAAGCTCCT 59.652 47.619 0.00 0.00 0.00 3.69
3668 3795 1.809684 AGGTCGTTTTAGCAAGCTCC 58.190 50.000 0.00 0.00 0.00 4.70
3669 3796 6.846325 AATATAGGTCGTTTTAGCAAGCTC 57.154 37.500 0.00 0.00 0.00 4.09
3670 3797 7.415206 CCAAAATATAGGTCGTTTTAGCAAGCT 60.415 37.037 0.00 0.00 0.00 3.74
3671 3798 6.691388 CCAAAATATAGGTCGTTTTAGCAAGC 59.309 38.462 0.00 0.00 0.00 4.01
3672 3799 7.981142 TCCAAAATATAGGTCGTTTTAGCAAG 58.019 34.615 0.00 0.00 0.00 4.01
3673 3800 7.925043 TCCAAAATATAGGTCGTTTTAGCAA 57.075 32.000 0.00 0.00 0.00 3.91
3674 3801 7.390996 TGTTCCAAAATATAGGTCGTTTTAGCA 59.609 33.333 0.00 0.00 0.00 3.49
3675 3802 7.754625 TGTTCCAAAATATAGGTCGTTTTAGC 58.245 34.615 0.00 0.00 0.00 3.09
3676 3803 9.158233 TCTGTTCCAAAATATAGGTCGTTTTAG 57.842 33.333 0.00 0.00 0.00 1.85
3677 3804 9.158233 CTCTGTTCCAAAATATAGGTCGTTTTA 57.842 33.333 0.00 0.00 0.00 1.52
3678 3805 7.881232 TCTCTGTTCCAAAATATAGGTCGTTTT 59.119 33.333 0.00 0.00 0.00 2.43
3679 3806 7.391620 TCTCTGTTCCAAAATATAGGTCGTTT 58.608 34.615 0.00 0.00 0.00 3.60
3680 3807 6.942976 TCTCTGTTCCAAAATATAGGTCGTT 58.057 36.000 0.00 0.00 0.00 3.85
3681 3808 6.540438 TCTCTGTTCCAAAATATAGGTCGT 57.460 37.500 0.00 0.00 0.00 4.34
3682 3809 7.042335 ACTTCTCTGTTCCAAAATATAGGTCG 58.958 38.462 0.00 0.00 0.00 4.79
3693 3820 9.613428 CCATACAAATATACTTCTCTGTTCCAA 57.387 33.333 0.00 0.00 0.00 3.53
3694 3821 8.988060 TCCATACAAATATACTTCTCTGTTCCA 58.012 33.333 0.00 0.00 0.00 3.53
3695 3822 9.262358 GTCCATACAAATATACTTCTCTGTTCC 57.738 37.037 0.00 0.00 0.00 3.62
3696 3823 9.262358 GGTCCATACAAATATACTTCTCTGTTC 57.738 37.037 0.00 0.00 0.00 3.18
3697 3824 8.993424 AGGTCCATACAAATATACTTCTCTGTT 58.007 33.333 0.00 0.00 0.00 3.16
3698 3825 8.424918 CAGGTCCATACAAATATACTTCTCTGT 58.575 37.037 0.00 0.00 0.00 3.41
3699 3826 7.386299 GCAGGTCCATACAAATATACTTCTCTG 59.614 40.741 0.00 0.00 0.00 3.35
3700 3827 7.291182 AGCAGGTCCATACAAATATACTTCTCT 59.709 37.037 0.00 0.00 0.00 3.10
3701 3828 7.445945 AGCAGGTCCATACAAATATACTTCTC 58.554 38.462 0.00 0.00 0.00 2.87
3702 3829 7.380423 AGCAGGTCCATACAAATATACTTCT 57.620 36.000 0.00 0.00 0.00 2.85
3703 3830 7.934120 AGAAGCAGGTCCATACAAATATACTTC 59.066 37.037 0.00 0.00 0.00 3.01
3704 3831 7.806180 AGAAGCAGGTCCATACAAATATACTT 58.194 34.615 0.00 0.00 0.00 2.24
3705 3832 7.380423 AGAAGCAGGTCCATACAAATATACT 57.620 36.000 0.00 0.00 0.00 2.12
3706 3833 9.155975 CATAGAAGCAGGTCCATACAAATATAC 57.844 37.037 0.00 0.00 0.00 1.47
3707 3834 8.321353 CCATAGAAGCAGGTCCATACAAATATA 58.679 37.037 0.00 0.00 0.00 0.86
3708 3835 7.170965 CCATAGAAGCAGGTCCATACAAATAT 58.829 38.462 0.00 0.00 0.00 1.28
3736 3863 5.404096 TGCTCACAAATTGCAGTGATTATG 58.596 37.500 6.94 0.00 43.18 1.90
3768 3895 7.630242 TGCTTCCCTCAAAGATAATTAACAG 57.370 36.000 0.00 0.00 0.00 3.16
3845 3972 0.334676 AGAGACTCCTGCAGGCTAGT 59.665 55.000 28.91 25.86 42.72 2.57
3859 3986 5.909610 GCACACAAACAGATTTAACAGAGAC 59.090 40.000 0.00 0.00 0.00 3.36
3949 4076 6.202188 TCGTGTTTGAGATTCTAGGTTTTGAC 59.798 38.462 0.00 0.00 0.00 3.18
3950 4077 6.285224 TCGTGTTTGAGATTCTAGGTTTTGA 58.715 36.000 0.00 0.00 0.00 2.69
3965 4092 4.142491 GCAATATGGGTGAATCGTGTTTGA 60.142 41.667 0.00 0.00 0.00 2.69
3977 4104 7.035612 GTCCTTTTTCTTTAGCAATATGGGTG 58.964 38.462 0.00 0.00 0.00 4.61
3978 4105 6.723977 TGTCCTTTTTCTTTAGCAATATGGGT 59.276 34.615 0.00 0.00 0.00 4.51
3979 4106 7.169158 TGTCCTTTTTCTTTAGCAATATGGG 57.831 36.000 0.00 0.00 0.00 4.00
3990 4117 3.488553 CGGCTTCGTTGTCCTTTTTCTTT 60.489 43.478 0.00 0.00 0.00 2.52
3994 4121 1.602377 CTCGGCTTCGTTGTCCTTTTT 59.398 47.619 0.00 0.00 35.06 1.94
4012 4139 0.463833 ATCCAAATCGCGGAACCCTC 60.464 55.000 6.13 0.00 35.77 4.30
4094 4221 2.136196 GAGCGAGCCTGATACCGGAG 62.136 65.000 9.46 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.