Multiple sequence alignment - TraesCS7B01G175100

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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 TraesCS7B01G175100 chr7B 100.000 3316 0 0 1 3316 246028760 246032075 0.000000e+00 6124
1 TraesCS7B01G175100 chr1D 94.996 2638 93 13 1 2602 467453128 467450494 0.000000e+00 4104
2 TraesCS7B01G175100 chr7D 94.813 2641 96 14 1 2602 602779802 602782440 0.000000e+00 4080
3 TraesCS7B01G175100 chr7A 94.011 2638 119 13 1 2602 5451586 5448952 0.000000e+00 3960
4 TraesCS7B01G175100 chr2B 94.011 2638 117 15 1 2602 773928917 773931549 0.000000e+00 3958
5 TraesCS7B01G175100 chr3B 93.975 2639 117 16 1 2602 792248822 792246189 0.000000e+00 3954
6 TraesCS7B01G175100 chr3B 93.783 2638 118 25 1 2602 792162555 792159928 0.000000e+00 3921
7 TraesCS7B01G175100 chr3B 94.264 2249 88 14 1 2214 792085431 792083189 0.000000e+00 3400
8 TraesCS7B01G175100 chr3B 94.353 2125 81 19 1 2091 792123249 792121130 0.000000e+00 3223
9 TraesCS7B01G175100 chr3B 92.971 1508 67 13 1085 2557 6345660 6344157 0.000000e+00 2161
10 TraesCS7B01G175100 chr4A 93.866 2641 116 15 1 2602 552840598 552843231 0.000000e+00 3938
11 TraesCS7B01G175100 chr6B 93.667 2637 122 16 1 2602 51114307 51116933 0.000000e+00 3903
12 TraesCS7B01G175100 chr6B 93.594 2638 126 18 1 2602 452037843 452035213 0.000000e+00 3895
13 TraesCS7B01G175100 chr3A 93.669 2638 111 20 1 2602 667230790 667228173 0.000000e+00 3895
14 TraesCS7B01G175100 chr3D 93.489 1797 76 17 845 2602 585881620 585879826 0.000000e+00 2632
15 TraesCS7B01G175100 chr3D 88.205 195 13 4 2624 2811 378194754 378194563 1.200000e-54 224
16 TraesCS7B01G175100 chr6D 89.623 530 49 5 2788 3316 460784609 460785133 0.000000e+00 669
17 TraesCS7B01G175100 chr6D 91.473 129 5 3 2624 2749 460779871 460779996 4.400000e-39 172


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 TraesCS7B01G175100 chr7B 246028760 246032075 3315 False 6124 6124 100.000 1 3316 1 chr7B.!!$F1 3315
1 TraesCS7B01G175100 chr1D 467450494 467453128 2634 True 4104 4104 94.996 1 2602 1 chr1D.!!$R1 2601
2 TraesCS7B01G175100 chr7D 602779802 602782440 2638 False 4080 4080 94.813 1 2602 1 chr7D.!!$F1 2601
3 TraesCS7B01G175100 chr7A 5448952 5451586 2634 True 3960 3960 94.011 1 2602 1 chr7A.!!$R1 2601
4 TraesCS7B01G175100 chr2B 773928917 773931549 2632 False 3958 3958 94.011 1 2602 1 chr2B.!!$F1 2601
5 TraesCS7B01G175100 chr3B 792246189 792248822 2633 True 3954 3954 93.975 1 2602 1 chr3B.!!$R5 2601
6 TraesCS7B01G175100 chr3B 792159928 792162555 2627 True 3921 3921 93.783 1 2602 1 chr3B.!!$R4 2601
7 TraesCS7B01G175100 chr3B 792083189 792085431 2242 True 3400 3400 94.264 1 2214 1 chr3B.!!$R2 2213
8 TraesCS7B01G175100 chr3B 792121130 792123249 2119 True 3223 3223 94.353 1 2091 1 chr3B.!!$R3 2090
9 TraesCS7B01G175100 chr3B 6344157 6345660 1503 True 2161 2161 92.971 1085 2557 1 chr3B.!!$R1 1472
10 TraesCS7B01G175100 chr4A 552840598 552843231 2633 False 3938 3938 93.866 1 2602 1 chr4A.!!$F1 2601
11 TraesCS7B01G175100 chr6B 51114307 51116933 2626 False 3903 3903 93.667 1 2602 1 chr6B.!!$F1 2601
12 TraesCS7B01G175100 chr6B 452035213 452037843 2630 True 3895 3895 93.594 1 2602 1 chr6B.!!$R1 2601
13 TraesCS7B01G175100 chr3A 667228173 667230790 2617 True 3895 3895 93.669 1 2602 1 chr3A.!!$R1 2601
14 TraesCS7B01G175100 chr3D 585879826 585881620 1794 True 2632 2632 93.489 845 2602 1 chr3D.!!$R2 1757
15 TraesCS7B01G175100 chr6D 460784609 460785133 524 False 669 669 89.623 2788 3316 1 chr6D.!!$F2 528

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
163 165 0.990374 ATGCTCTTGGCTTCTGGACT 59.010 50.000 0.00 0.00 42.39 3.85 F
226 228 2.362120 GATGCTGCACCCCTGCTT 60.362 61.111 3.57 0.00 44.57 3.91 F
781 786 2.954684 CGTGCCCCCTTACAGCTGA 61.955 63.158 23.35 0.48 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1093 1098 0.888619 TCATCCTTCACGCGAGAACT 59.111 50.000 15.93 0.00 0.00 3.01 R
1096 1101 0.888619 AACTCATCCTTCACGCGAGA 59.111 50.000 15.93 7.99 0.00 4.04 R
2682 2739 1.133513 ACTGTTCCAGTTTCATGGCCA 60.134 47.619 8.56 8.56 42.59 5.36 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
163 165 0.990374 ATGCTCTTGGCTTCTGGACT 59.010 50.000 0.00 0.00 42.39 3.85
226 228 2.362120 GATGCTGCACCCCTGCTT 60.362 61.111 3.57 0.00 44.57 3.91
323 325 4.008074 ACTTGAGGTATGTGTTGACTGG 57.992 45.455 0.00 0.00 0.00 4.00
378 380 5.670792 TTCAGACGAGTGTATAAACCCAT 57.329 39.130 0.00 0.00 0.00 4.00
411 413 5.189928 TGGTCCGCATATGAGTTTAATTGT 58.810 37.500 6.97 0.00 0.00 2.71
681 686 9.167311 GGTTCAGAGCTTTTATTATCTCTTTGA 57.833 33.333 0.00 0.00 33.99 2.69
721 726 6.515272 ACTTTTCCTGTGGCATACATTTAG 57.485 37.500 0.00 0.00 38.92 1.85
781 786 2.954684 CGTGCCCCCTTACAGCTGA 61.955 63.158 23.35 0.48 0.00 4.26
1053 1058 4.699257 GTGAAGGAGGAATATGATGATGCC 59.301 45.833 0.00 0.00 0.00 4.40
1154 1159 6.891306 ATCCCGATCTGGATTTTATGGATA 57.109 37.500 12.58 0.00 42.62 2.59
1240 1247 2.640302 GCACTCTCTCGGCTGTGGA 61.640 63.158 0.00 0.00 0.00 4.02
1273 1280 1.376466 GCCAGTCAAGGAGCTCCAA 59.624 57.895 33.90 16.45 38.89 3.53
1336 1343 5.634896 CAACTACACAAATCATCTTCCTGC 58.365 41.667 0.00 0.00 0.00 4.85
1349 1356 6.344500 TCATCTTCCTGCTATTTTCTCACTC 58.656 40.000 0.00 0.00 0.00 3.51
1360 1367 7.609146 TGCTATTTTCTCACTCTTGATTCACAT 59.391 33.333 0.00 0.00 0.00 3.21
1486 1511 2.525055 TCTTGTTTGTGCGCTTGTTTC 58.475 42.857 9.73 0.00 0.00 2.78
1563 1588 4.023279 AGCATGTCGTTGTTGCTTAATTCA 60.023 37.500 0.00 0.00 43.94 2.57
1610 1635 4.472833 ACCTTGAGATTCAGGTAGAAGCAT 59.527 41.667 0.00 0.00 44.94 3.79
1611 1636 5.663106 ACCTTGAGATTCAGGTAGAAGCATA 59.337 40.000 0.00 0.00 44.94 3.14
1613 1638 7.050377 CCTTGAGATTCAGGTAGAAGCATAAA 58.950 38.462 0.00 0.00 44.94 1.40
1615 1640 9.118300 CTTGAGATTCAGGTAGAAGCATAAAAT 57.882 33.333 0.00 0.00 44.94 1.82
1616 1641 8.668510 TGAGATTCAGGTAGAAGCATAAAATC 57.331 34.615 0.00 0.00 44.94 2.17
1618 1643 7.577303 AGATTCAGGTAGAAGCATAAAATCCA 58.423 34.615 0.00 0.00 44.94 3.41
1654 1683 2.639839 ACCTGCATGTGTTCCTTAGAGT 59.360 45.455 0.00 0.00 0.00 3.24
1666 1695 7.148306 TGTGTTCCTTAGAGTGTTTGTTTTCTC 60.148 37.037 0.00 0.00 0.00 2.87
1675 1704 4.755123 AGTGTTTGTTTTCTCCATACCTCG 59.245 41.667 0.00 0.00 0.00 4.63
1853 1882 9.976511 CAATAAGCCATGATATCTTGAAATTGT 57.023 29.630 17.81 6.89 0.00 2.71
1991 2035 8.095792 TGTTTGCAACAAAATCCTGATTCATAT 58.904 29.630 0.00 0.00 38.72 1.78
2023 2071 4.981806 TTAAATGCTTGGCACATCCTAC 57.018 40.909 0.00 0.00 43.04 3.18
2043 2091 6.373216 TCCTACACAAAATCCTGATTAAACGG 59.627 38.462 0.00 0.00 0.00 4.44
2218 2272 3.127533 GATCCCACACACGGCAGC 61.128 66.667 0.00 0.00 0.00 5.25
2231 2285 4.230603 GCAGCTCTTGGCATGCTA 57.769 55.556 18.92 9.16 44.79 3.49
2358 2412 6.519679 TCTATGCCTAAAACGTCTGTAAGA 57.480 37.500 0.00 0.00 43.69 2.10
2461 2518 6.073276 TGTCTGTAAGCAACATGTTGTCATAC 60.073 38.462 33.01 29.04 42.31 2.39
2602 2659 1.154188 GCGCGATCCCGATCTAGTC 60.154 63.158 12.10 0.00 38.22 2.59
2603 2660 1.853114 GCGCGATCCCGATCTAGTCA 61.853 60.000 12.10 0.00 38.22 3.41
2604 2661 0.110147 CGCGATCCCGATCTAGTCAC 60.110 60.000 0.00 0.00 38.22 3.67
2605 2662 1.240256 GCGATCCCGATCTAGTCACT 58.760 55.000 3.35 0.00 38.22 3.41
2606 2663 2.424557 GCGATCCCGATCTAGTCACTA 58.575 52.381 3.35 0.00 38.22 2.74
2607 2664 2.812591 GCGATCCCGATCTAGTCACTAA 59.187 50.000 3.35 0.00 38.22 2.24
2608 2665 3.120130 GCGATCCCGATCTAGTCACTAAG 60.120 52.174 3.35 0.00 38.22 2.18
2609 2666 4.316645 CGATCCCGATCTAGTCACTAAGA 58.683 47.826 3.35 0.00 38.22 2.10
2610 2667 4.390603 CGATCCCGATCTAGTCACTAAGAG 59.609 50.000 3.35 0.00 38.22 2.85
2611 2668 5.553123 GATCCCGATCTAGTCACTAAGAGA 58.447 45.833 0.00 0.00 35.04 3.10
2612 2669 4.963373 TCCCGATCTAGTCACTAAGAGAG 58.037 47.826 0.00 0.00 0.00 3.20
2613 2670 3.500680 CCCGATCTAGTCACTAAGAGAGC 59.499 52.174 0.00 0.00 0.00 4.09
2614 2671 4.130857 CCGATCTAGTCACTAAGAGAGCA 58.869 47.826 0.00 0.00 0.00 4.26
2615 2672 4.576873 CCGATCTAGTCACTAAGAGAGCAA 59.423 45.833 0.00 0.00 0.00 3.91
2616 2673 5.504994 CCGATCTAGTCACTAAGAGAGCAAC 60.505 48.000 0.00 0.00 0.00 4.17
2617 2674 5.065346 CGATCTAGTCACTAAGAGAGCAACA 59.935 44.000 0.00 0.00 0.00 3.33
2618 2675 6.403746 CGATCTAGTCACTAAGAGAGCAACAA 60.404 42.308 0.00 0.00 0.00 2.83
2619 2676 6.015027 TCTAGTCACTAAGAGAGCAACAAC 57.985 41.667 0.00 0.00 0.00 3.32
2620 2677 4.672587 AGTCACTAAGAGAGCAACAACA 57.327 40.909 0.00 0.00 0.00 3.33
2621 2678 5.023533 AGTCACTAAGAGAGCAACAACAA 57.976 39.130 0.00 0.00 0.00 2.83
2622 2679 5.428253 AGTCACTAAGAGAGCAACAACAAA 58.572 37.500 0.00 0.00 0.00 2.83
2623 2680 5.294552 AGTCACTAAGAGAGCAACAACAAAC 59.705 40.000 0.00 0.00 0.00 2.93
2624 2681 5.064707 GTCACTAAGAGAGCAACAACAAACA 59.935 40.000 0.00 0.00 0.00 2.83
2625 2682 5.645929 TCACTAAGAGAGCAACAACAAACAA 59.354 36.000 0.00 0.00 0.00 2.83
2626 2683 5.739161 CACTAAGAGAGCAACAACAAACAAC 59.261 40.000 0.00 0.00 0.00 3.32
2627 2684 4.782019 AAGAGAGCAACAACAAACAACA 57.218 36.364 0.00 0.00 0.00 3.33
2628 2685 4.782019 AGAGAGCAACAACAAACAACAA 57.218 36.364 0.00 0.00 0.00 2.83
2629 2686 4.485163 AGAGAGCAACAACAAACAACAAC 58.515 39.130 0.00 0.00 0.00 3.32
2630 2687 4.022416 AGAGAGCAACAACAAACAACAACA 60.022 37.500 0.00 0.00 0.00 3.33
2631 2688 4.626042 AGAGCAACAACAAACAACAACAA 58.374 34.783 0.00 0.00 0.00 2.83
2632 2689 5.053145 AGAGCAACAACAAACAACAACAAA 58.947 33.333 0.00 0.00 0.00 2.83
2633 2690 5.177327 AGAGCAACAACAAACAACAACAAAG 59.823 36.000 0.00 0.00 0.00 2.77
2634 2691 3.905416 GCAACAACAAACAACAACAAAGC 59.095 39.130 0.00 0.00 0.00 3.51
2635 2692 4.462307 CAACAACAAACAACAACAAAGCC 58.538 39.130 0.00 0.00 0.00 4.35
2636 2693 4.001618 ACAACAAACAACAACAAAGCCT 57.998 36.364 0.00 0.00 0.00 4.58
2637 2694 4.384940 ACAACAAACAACAACAAAGCCTT 58.615 34.783 0.00 0.00 0.00 4.35
2638 2695 4.819088 ACAACAAACAACAACAAAGCCTTT 59.181 33.333 0.00 0.00 0.00 3.11
2639 2696 5.992217 ACAACAAACAACAACAAAGCCTTTA 59.008 32.000 0.00 0.00 0.00 1.85
2640 2697 6.652900 ACAACAAACAACAACAAAGCCTTTAT 59.347 30.769 0.00 0.00 0.00 1.40
2641 2698 7.819900 ACAACAAACAACAACAAAGCCTTTATA 59.180 29.630 0.00 0.00 0.00 0.98
2642 2699 7.764695 ACAAACAACAACAAAGCCTTTATAC 57.235 32.000 0.00 0.00 0.00 1.47
2643 2700 7.324178 ACAAACAACAACAAAGCCTTTATACA 58.676 30.769 0.00 0.00 0.00 2.29
2644 2701 7.984617 ACAAACAACAACAAAGCCTTTATACAT 59.015 29.630 0.00 0.00 0.00 2.29
2645 2702 7.945033 AACAACAACAAAGCCTTTATACATG 57.055 32.000 0.00 0.00 0.00 3.21
2646 2703 7.283625 ACAACAACAAAGCCTTTATACATGA 57.716 32.000 0.00 0.00 0.00 3.07
2647 2704 7.721402 ACAACAACAAAGCCTTTATACATGAA 58.279 30.769 0.00 0.00 0.00 2.57
2648 2705 8.200792 ACAACAACAAAGCCTTTATACATGAAA 58.799 29.630 0.00 0.00 0.00 2.69
2649 2706 9.039870 CAACAACAAAGCCTTTATACATGAAAA 57.960 29.630 0.00 0.00 0.00 2.29
2650 2707 9.777297 AACAACAAAGCCTTTATACATGAAAAT 57.223 25.926 0.00 0.00 0.00 1.82
2651 2708 9.423061 ACAACAAAGCCTTTATACATGAAAATC 57.577 29.630 0.00 0.00 0.00 2.17
2652 2709 8.586273 CAACAAAGCCTTTATACATGAAAATCG 58.414 33.333 0.00 0.00 0.00 3.34
2653 2710 7.257722 ACAAAGCCTTTATACATGAAAATCGG 58.742 34.615 0.00 0.00 0.00 4.18
2654 2711 7.122055 ACAAAGCCTTTATACATGAAAATCGGA 59.878 33.333 0.00 0.00 0.00 4.55
2655 2712 7.639113 AAGCCTTTATACATGAAAATCGGAA 57.361 32.000 0.00 0.00 0.00 4.30
2656 2713 7.264373 AGCCTTTATACATGAAAATCGGAAG 57.736 36.000 0.00 0.00 0.00 3.46
2657 2714 6.828785 AGCCTTTATACATGAAAATCGGAAGT 59.171 34.615 0.00 0.00 0.00 3.01
2658 2715 6.912591 GCCTTTATACATGAAAATCGGAAGTG 59.087 38.462 0.00 0.00 0.00 3.16
2659 2716 7.415206 GCCTTTATACATGAAAATCGGAAGTGT 60.415 37.037 0.00 0.00 0.00 3.55
2660 2717 9.104965 CCTTTATACATGAAAATCGGAAGTGTA 57.895 33.333 0.00 0.00 0.00 2.90
2663 2720 7.915293 ATACATGAAAATCGGAAGTGTAACA 57.085 32.000 0.00 0.00 41.43 2.41
2664 2721 6.241207 ACATGAAAATCGGAAGTGTAACAG 57.759 37.500 0.00 0.00 41.43 3.16
2665 2722 5.995282 ACATGAAAATCGGAAGTGTAACAGA 59.005 36.000 0.00 0.00 41.43 3.41
2666 2723 5.917541 TGAAAATCGGAAGTGTAACAGAC 57.082 39.130 0.00 0.00 41.43 3.51
2667 2724 4.753107 TGAAAATCGGAAGTGTAACAGACC 59.247 41.667 0.00 0.00 41.43 3.85
2668 2725 4.345859 AAATCGGAAGTGTAACAGACCA 57.654 40.909 0.00 0.00 41.43 4.02
2669 2726 4.345859 AATCGGAAGTGTAACAGACCAA 57.654 40.909 0.00 0.00 41.43 3.67
2670 2727 3.823281 TCGGAAGTGTAACAGACCAAA 57.177 42.857 0.00 0.00 41.43 3.28
2671 2728 3.724374 TCGGAAGTGTAACAGACCAAAG 58.276 45.455 0.00 0.00 41.43 2.77
2672 2729 3.385433 TCGGAAGTGTAACAGACCAAAGA 59.615 43.478 0.00 0.00 41.43 2.52
2673 2730 3.493503 CGGAAGTGTAACAGACCAAAGAC 59.506 47.826 0.00 0.00 41.43 3.01
2674 2731 4.448210 GGAAGTGTAACAGACCAAAGACA 58.552 43.478 0.00 0.00 41.43 3.41
2675 2732 4.879545 GGAAGTGTAACAGACCAAAGACAA 59.120 41.667 0.00 0.00 41.43 3.18
2676 2733 5.355910 GGAAGTGTAACAGACCAAAGACAAA 59.644 40.000 0.00 0.00 41.43 2.83
2677 2734 6.039382 GGAAGTGTAACAGACCAAAGACAAAT 59.961 38.462 0.00 0.00 41.43 2.32
2678 2735 6.377327 AGTGTAACAGACCAAAGACAAATG 57.623 37.500 0.00 0.00 41.43 2.32
2679 2736 6.119536 AGTGTAACAGACCAAAGACAAATGA 58.880 36.000 0.00 0.00 41.43 2.57
2680 2737 6.772716 AGTGTAACAGACCAAAGACAAATGAT 59.227 34.615 0.00 0.00 41.43 2.45
2681 2738 7.285401 AGTGTAACAGACCAAAGACAAATGATT 59.715 33.333 0.00 0.00 41.43 2.57
2682 2739 7.920682 GTGTAACAGACCAAAGACAAATGATTT 59.079 33.333 0.00 0.00 36.32 2.17
2683 2740 7.920151 TGTAACAGACCAAAGACAAATGATTTG 59.080 33.333 15.82 15.82 45.95 2.32
2693 2750 5.535043 GACAAATGATTTGGCCATGAAAC 57.465 39.130 20.69 0.00 42.97 2.78
2694 2751 5.231702 ACAAATGATTTGGCCATGAAACT 57.768 34.783 20.69 0.00 44.81 2.66
2695 2752 4.998672 ACAAATGATTTGGCCATGAAACTG 59.001 37.500 20.69 1.68 44.81 3.16
2696 2753 3.899052 ATGATTTGGCCATGAAACTGG 57.101 42.857 6.09 0.00 39.45 4.00
2697 2754 2.886913 TGATTTGGCCATGAAACTGGA 58.113 42.857 6.09 0.00 38.69 3.86
2698 2755 3.237746 TGATTTGGCCATGAAACTGGAA 58.762 40.909 6.09 0.00 38.69 3.53
2699 2756 3.006752 TGATTTGGCCATGAAACTGGAAC 59.993 43.478 6.09 0.00 38.69 3.62
2700 2757 2.079170 TTGGCCATGAAACTGGAACA 57.921 45.000 6.09 0.00 38.69 3.18
2717 2774 5.928976 TGGAACAGTGCATATATGTTAGCT 58.071 37.500 14.14 0.00 37.29 3.32
2718 2775 5.759763 TGGAACAGTGCATATATGTTAGCTG 59.240 40.000 14.14 16.43 37.29 4.24
2719 2776 5.180117 GGAACAGTGCATATATGTTAGCTGG 59.820 44.000 14.14 1.50 37.29 4.85
2720 2777 5.551305 ACAGTGCATATATGTTAGCTGGA 57.449 39.130 14.14 0.00 0.00 3.86
2721 2778 5.928976 ACAGTGCATATATGTTAGCTGGAA 58.071 37.500 14.14 0.00 0.00 3.53
2722 2779 6.356556 ACAGTGCATATATGTTAGCTGGAAA 58.643 36.000 14.14 0.00 0.00 3.13
2723 2780 6.828273 ACAGTGCATATATGTTAGCTGGAAAA 59.172 34.615 14.14 0.00 0.00 2.29
2724 2781 7.503566 ACAGTGCATATATGTTAGCTGGAAAAT 59.496 33.333 14.14 0.00 0.00 1.82
2725 2782 9.002600 CAGTGCATATATGTTAGCTGGAAAATA 57.997 33.333 14.14 0.00 0.00 1.40
2726 2783 9.573166 AGTGCATATATGTTAGCTGGAAAATAA 57.427 29.630 14.14 0.00 0.00 1.40
2735 2792 8.220755 TGTTAGCTGGAAAATAATGTATCACC 57.779 34.615 0.00 0.00 0.00 4.02
2736 2793 7.831690 TGTTAGCTGGAAAATAATGTATCACCA 59.168 33.333 0.00 0.00 0.00 4.17
2737 2794 8.682710 GTTAGCTGGAAAATAATGTATCACCAA 58.317 33.333 0.00 0.00 0.00 3.67
2738 2795 7.902920 AGCTGGAAAATAATGTATCACCAAT 57.097 32.000 0.00 0.00 0.00 3.16
2739 2796 7.719483 AGCTGGAAAATAATGTATCACCAATG 58.281 34.615 0.00 0.00 0.00 2.82
2740 2797 7.342799 AGCTGGAAAATAATGTATCACCAATGT 59.657 33.333 0.00 0.00 0.00 2.71
2741 2798 7.649306 GCTGGAAAATAATGTATCACCAATGTC 59.351 37.037 0.00 0.00 0.00 3.06
2742 2799 8.586879 TGGAAAATAATGTATCACCAATGTCA 57.413 30.769 0.00 0.00 0.00 3.58
2743 2800 9.199645 TGGAAAATAATGTATCACCAATGTCAT 57.800 29.630 0.00 0.00 0.00 3.06
2744 2801 9.683069 GGAAAATAATGTATCACCAATGTCATC 57.317 33.333 0.00 0.00 0.00 2.92
2748 2805 8.929260 ATAATGTATCACCAATGTCATCATGT 57.071 30.769 0.00 0.00 34.19 3.21
2749 2806 6.628919 ATGTATCACCAATGTCATCATGTG 57.371 37.500 0.00 3.96 34.19 3.21
2750 2807 4.883006 TGTATCACCAATGTCATCATGTGG 59.117 41.667 0.47 0.47 37.77 4.17
2751 2808 2.725637 TCACCAATGTCATCATGTGGG 58.274 47.619 6.29 0.00 36.97 4.61
2752 2809 2.308275 TCACCAATGTCATCATGTGGGA 59.692 45.455 6.29 0.00 36.97 4.37
2753 2810 3.090790 CACCAATGTCATCATGTGGGAA 58.909 45.455 6.29 0.00 36.97 3.97
2754 2811 3.091545 ACCAATGTCATCATGTGGGAAC 58.908 45.455 6.29 0.00 36.97 3.62
2755 2812 3.245371 ACCAATGTCATCATGTGGGAACT 60.245 43.478 6.29 0.00 36.97 3.01
2756 2813 3.379372 CCAATGTCATCATGTGGGAACTC 59.621 47.826 0.00 0.00 34.19 3.01
2757 2814 4.267536 CAATGTCATCATGTGGGAACTCT 58.732 43.478 0.00 0.00 34.19 3.24
2758 2815 4.581309 ATGTCATCATGTGGGAACTCTT 57.419 40.909 0.00 0.00 32.51 2.85
2759 2816 3.942829 TGTCATCATGTGGGAACTCTTC 58.057 45.455 0.00 0.00 0.00 2.87
2760 2817 3.327464 TGTCATCATGTGGGAACTCTTCA 59.673 43.478 0.00 0.00 0.00 3.02
2761 2818 4.019051 TGTCATCATGTGGGAACTCTTCAT 60.019 41.667 0.00 0.00 0.00 2.57
2762 2819 5.189539 TGTCATCATGTGGGAACTCTTCATA 59.810 40.000 0.00 0.00 0.00 2.15
2763 2820 6.115446 GTCATCATGTGGGAACTCTTCATAA 58.885 40.000 0.00 0.00 0.00 1.90
2764 2821 6.259608 GTCATCATGTGGGAACTCTTCATAAG 59.740 42.308 0.00 0.00 0.00 1.73
2765 2822 6.156775 TCATCATGTGGGAACTCTTCATAAGA 59.843 38.462 0.00 0.00 35.87 2.10
2766 2823 6.373005 TCATGTGGGAACTCTTCATAAGAA 57.627 37.500 0.00 0.00 37.02 2.52
2767 2824 6.962182 TCATGTGGGAACTCTTCATAAGAAT 58.038 36.000 0.00 0.00 37.02 2.40
2768 2825 7.405292 TCATGTGGGAACTCTTCATAAGAATT 58.595 34.615 0.00 0.00 37.02 2.17
2769 2826 7.890127 TCATGTGGGAACTCTTCATAAGAATTT 59.110 33.333 0.00 0.00 37.02 1.82
2770 2827 8.526147 CATGTGGGAACTCTTCATAAGAATTTT 58.474 33.333 0.00 0.00 37.02 1.82
2771 2828 9.753674 ATGTGGGAACTCTTCATAAGAATTTTA 57.246 29.630 0.00 0.00 37.02 1.52
2772 2829 9.753674 TGTGGGAACTCTTCATAAGAATTTTAT 57.246 29.630 0.00 0.00 37.02 1.40
2774 2831 9.973661 TGGGAACTCTTCATAAGAATTTTATGA 57.026 29.630 14.08 14.08 39.02 2.15
2854 2911 9.834628 AACTACATTGATTGTAACATTTAACGG 57.165 29.630 0.00 0.00 40.27 4.44
2874 2931 4.752604 ACGGTTTGCTTTTGAGTTTTTGTT 59.247 33.333 0.00 0.00 0.00 2.83
2925 2982 5.331876 AGAACTCTCTATGTGCTTGGTAC 57.668 43.478 0.00 0.00 0.00 3.34
2929 2986 4.959210 ACTCTCTATGTGCTTGGTACAGAT 59.041 41.667 0.00 0.00 42.39 2.90
2973 3030 5.435686 AGTACTAAGTGATTTCATGCCCA 57.564 39.130 0.00 0.00 0.00 5.36
2981 3038 9.683069 CTAAGTGATTTCATGCCCATAAATTAC 57.317 33.333 4.49 4.49 32.34 1.89
3029 3086 5.880332 TCATTCTTACAATAGTTCCACCAGC 59.120 40.000 0.00 0.00 0.00 4.85
3046 3103 3.758554 ACCAGCTGGATCATTTGTGTTAC 59.241 43.478 39.19 0.00 38.94 2.50
3050 3107 4.697352 AGCTGGATCATTTGTGTTACTGTC 59.303 41.667 0.00 0.00 0.00 3.51
3054 3111 7.523293 TGGATCATTTGTGTTACTGTCAATT 57.477 32.000 0.00 0.00 0.00 2.32
3062 3119 4.455533 TGTGTTACTGTCAATTCCAGCATC 59.544 41.667 2.28 0.00 33.09 3.91
3066 3123 3.771216 ACTGTCAATTCCAGCATCCTTT 58.229 40.909 2.28 0.00 33.09 3.11
3067 3124 4.922206 ACTGTCAATTCCAGCATCCTTTA 58.078 39.130 2.28 0.00 33.09 1.85
3070 3127 6.769822 ACTGTCAATTCCAGCATCCTTTATAG 59.230 38.462 2.28 0.00 33.09 1.31
3102 3159 1.679032 GCTACTCCCATGTGACCAACC 60.679 57.143 0.00 0.00 0.00 3.77
3110 3167 1.819903 CATGTGACCAACCATGCATGA 59.180 47.619 28.31 4.75 36.71 3.07
3115 3172 0.330604 ACCAACCATGCATGAGAGCT 59.669 50.000 28.31 4.36 34.99 4.09
3117 3174 2.219458 CCAACCATGCATGAGAGCTAG 58.781 52.381 28.31 11.52 34.99 3.42
3119 3176 3.538591 CAACCATGCATGAGAGCTAGAA 58.461 45.455 28.31 0.00 34.99 2.10
3123 3180 2.306341 TGCATGAGAGCTAGAACTGC 57.694 50.000 0.00 0.00 34.99 4.40
3140 3197 6.211515 AGAACTGCAATTGAAAATGAGTCAC 58.788 36.000 10.34 0.24 0.00 3.67
3144 3201 4.341806 TGCAATTGAAAATGAGTCACTGGT 59.658 37.500 10.34 0.00 0.00 4.00
3155 3212 1.032114 GTCACTGGTTGGCCCTATGC 61.032 60.000 0.00 0.00 40.16 3.14
3164 3221 2.695147 GTTGGCCCTATGCAATAGCTTT 59.305 45.455 0.00 0.00 45.64 3.51
3175 3232 5.789643 TGCAATAGCTTTTCAAAAGAGGT 57.210 34.783 14.39 0.00 42.74 3.85
3185 3242 3.812156 TCAAAAGAGGTCGAACTCACA 57.188 42.857 31.07 7.90 39.97 3.58
3202 3259 7.465379 CGAACTCACAAGATTGAAAACACACTA 60.465 37.037 0.00 0.00 0.00 2.74
3236 3293 6.760770 GGAGATATATCATCTTACCAAGCAGC 59.239 42.308 15.08 0.00 0.00 5.25
3241 3298 3.954200 TCATCTTACCAAGCAGCAATGA 58.046 40.909 0.00 0.00 0.00 2.57
3242 3299 3.943381 TCATCTTACCAAGCAGCAATGAG 59.057 43.478 0.00 0.00 0.00 2.90
3243 3300 3.701205 TCTTACCAAGCAGCAATGAGA 57.299 42.857 0.00 0.00 0.00 3.27
3245 3302 4.397420 TCTTACCAAGCAGCAATGAGAAA 58.603 39.130 0.00 0.00 0.00 2.52
3248 3305 4.612264 ACCAAGCAGCAATGAGAAAATT 57.388 36.364 0.00 0.00 0.00 1.82
3257 3314 4.463891 AGCAATGAGAAAATTACCACCCAG 59.536 41.667 0.00 0.00 0.00 4.45
3278 3335 5.182001 CCAGAAAATCATTGTTCGAACCTCT 59.818 40.000 24.78 7.15 0.00 3.69
3281 3338 2.762535 TCATTGTTCGAACCTCTCCC 57.237 50.000 24.78 0.00 0.00 4.30
3282 3339 1.974957 TCATTGTTCGAACCTCTCCCA 59.025 47.619 24.78 1.88 0.00 4.37
3283 3340 2.028112 TCATTGTTCGAACCTCTCCCAG 60.028 50.000 24.78 6.97 0.00 4.45
3308 3365 0.527565 CACTGCCCACAATGCTTACC 59.472 55.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.525199 AGGGAGCAAATAATCACCTCAGT 59.475 43.478 0.00 0.00 0.00 3.41
163 165 1.148273 GACCACCTTGAGCACCACA 59.852 57.895 0.00 0.00 0.00 4.17
243 245 5.751509 TCGTTTTCACTTATGCATACGCTAT 59.248 36.000 5.74 0.00 39.64 2.97
255 257 6.759356 TCATCTGTTTGACTCGTTTTCACTTA 59.241 34.615 0.00 0.00 0.00 2.24
323 325 8.807581 GCCACTAAAAACATAACAGCATTAATC 58.192 33.333 0.00 0.00 0.00 1.75
378 380 0.908910 ATGCGGACCATGGTCAACTA 59.091 50.000 38.83 24.59 46.20 2.24
721 726 9.289303 CAGTATACATGCAAATAACTTCCAAAC 57.711 33.333 5.50 0.00 0.00 2.93
833 838 0.889186 TCTTTCCACCAAGCGGCTTC 60.889 55.000 13.24 0.00 34.57 3.86
998 1003 1.811266 CTCGGCAACCTCCACATCG 60.811 63.158 0.00 0.00 0.00 3.84
1020 1025 3.573772 CTCCTTCACGCGAGCACCA 62.574 63.158 15.93 0.00 0.00 4.17
1053 1058 3.000819 TACCCCACGCCACTCCAG 61.001 66.667 0.00 0.00 0.00 3.86
1093 1098 0.888619 TCATCCTTCACGCGAGAACT 59.111 50.000 15.93 0.00 0.00 3.01
1096 1101 0.888619 AACTCATCCTTCACGCGAGA 59.111 50.000 15.93 7.99 0.00 4.04
1168 1174 5.607939 AAAAACTCAAACCCCTAACAAGG 57.392 39.130 0.00 0.00 0.00 3.61
1240 1247 1.518056 CTGGCCAGTTGAACGTGCAT 61.518 55.000 25.53 0.00 0.00 3.96
1430 1455 5.300286 ACAATATTATGTTCTCAGCAAGGCC 59.700 40.000 0.00 0.00 0.00 5.19
1486 1511 5.989777 CCTCTATAACCCCTGTGTTTTATCG 59.010 44.000 0.00 0.00 0.00 2.92
1563 1588 4.833478 AGAGTGACAGCCATGATTAACT 57.167 40.909 0.00 0.00 0.00 2.24
1654 1683 3.500680 GCGAGGTATGGAGAAAACAAACA 59.499 43.478 0.00 0.00 0.00 2.83
1666 1695 2.620251 TCAAGAATGGCGAGGTATGG 57.380 50.000 0.00 0.00 0.00 2.74
1675 1704 9.270640 GAGATGACCATATATATCAAGAATGGC 57.729 37.037 10.25 5.61 40.66 4.40
1991 2035 6.257630 GTGCCAAGCATTTAAAGAAAACAGAA 59.742 34.615 0.00 0.00 41.91 3.02
2000 2044 4.460948 AGGATGTGCCAAGCATTTAAAG 57.539 40.909 0.00 0.00 41.91 1.85
2023 2071 6.551736 CCTACCGTTTAATCAGGATTTTGTG 58.448 40.000 0.00 0.00 32.50 3.33
2093 2142 5.128335 GCATGGGAAAGGAATCAGAGAAATT 59.872 40.000 0.00 0.00 0.00 1.82
2218 2272 2.401967 GCCAGTAGCATGCCAAGAG 58.598 57.895 15.66 1.84 42.97 2.85
2231 2285 1.279271 GATAGTCCAAGGTGTGCCAGT 59.721 52.381 0.00 0.00 37.19 4.00
2358 2412 6.460399 GGCATAGAAGATACGACAAGAAGTCT 60.460 42.308 0.00 0.00 45.32 3.24
2362 2416 5.854010 AGGCATAGAAGATACGACAAGAA 57.146 39.130 0.00 0.00 0.00 2.52
2364 2418 6.142480 CGTTTAGGCATAGAAGATACGACAAG 59.858 42.308 0.00 0.00 0.00 3.16
2430 2487 8.359642 ACAACATGTTGCTTACAGACAATTTAT 58.640 29.630 33.23 9.18 44.03 1.40
2461 2518 6.150140 GCACCAAATATCTTAGGCATAGAAGG 59.850 42.308 0.00 0.00 0.00 3.46
2602 2659 5.484173 TGTTTGTTGTTGCTCTCTTAGTG 57.516 39.130 0.00 0.00 0.00 2.74
2603 2660 5.414454 TGTTGTTTGTTGTTGCTCTCTTAGT 59.586 36.000 0.00 0.00 0.00 2.24
2604 2661 5.879237 TGTTGTTTGTTGTTGCTCTCTTAG 58.121 37.500 0.00 0.00 0.00 2.18
2605 2662 5.888691 TGTTGTTTGTTGTTGCTCTCTTA 57.111 34.783 0.00 0.00 0.00 2.10
2606 2663 4.782019 TGTTGTTTGTTGTTGCTCTCTT 57.218 36.364 0.00 0.00 0.00 2.85
2607 2664 4.022416 TGTTGTTGTTTGTTGTTGCTCTCT 60.022 37.500 0.00 0.00 0.00 3.10
2608 2665 4.233789 TGTTGTTGTTTGTTGTTGCTCTC 58.766 39.130 0.00 0.00 0.00 3.20
2609 2666 4.250116 TGTTGTTGTTTGTTGTTGCTCT 57.750 36.364 0.00 0.00 0.00 4.09
2610 2667 4.981389 TTGTTGTTGTTTGTTGTTGCTC 57.019 36.364 0.00 0.00 0.00 4.26
2611 2668 4.319405 GCTTTGTTGTTGTTTGTTGTTGCT 60.319 37.500 0.00 0.00 0.00 3.91
2612 2669 3.905416 GCTTTGTTGTTGTTTGTTGTTGC 59.095 39.130 0.00 0.00 0.00 4.17
2613 2670 4.213059 AGGCTTTGTTGTTGTTTGTTGTTG 59.787 37.500 0.00 0.00 0.00 3.33
2614 2671 4.384940 AGGCTTTGTTGTTGTTTGTTGTT 58.615 34.783 0.00 0.00 0.00 2.83
2615 2672 4.001618 AGGCTTTGTTGTTGTTTGTTGT 57.998 36.364 0.00 0.00 0.00 3.32
2616 2673 5.355467 AAAGGCTTTGTTGTTGTTTGTTG 57.645 34.783 12.53 0.00 0.00 3.33
2617 2674 7.819900 TGTATAAAGGCTTTGTTGTTGTTTGTT 59.180 29.630 22.32 0.00 0.00 2.83
2618 2675 7.324178 TGTATAAAGGCTTTGTTGTTGTTTGT 58.676 30.769 22.32 0.00 0.00 2.83
2619 2676 7.763172 TGTATAAAGGCTTTGTTGTTGTTTG 57.237 32.000 22.32 0.00 0.00 2.93
2620 2677 8.200792 TCATGTATAAAGGCTTTGTTGTTGTTT 58.799 29.630 22.32 0.00 0.00 2.83
2621 2678 7.721402 TCATGTATAAAGGCTTTGTTGTTGTT 58.279 30.769 22.32 0.00 0.00 2.83
2622 2679 7.283625 TCATGTATAAAGGCTTTGTTGTTGT 57.716 32.000 22.32 0.00 0.00 3.32
2623 2680 8.586570 TTTCATGTATAAAGGCTTTGTTGTTG 57.413 30.769 22.32 13.55 0.00 3.33
2624 2681 9.777297 ATTTTCATGTATAAAGGCTTTGTTGTT 57.223 25.926 22.32 2.05 0.00 2.83
2625 2682 9.423061 GATTTTCATGTATAAAGGCTTTGTTGT 57.577 29.630 22.32 8.22 0.00 3.32
2626 2683 8.586273 CGATTTTCATGTATAAAGGCTTTGTTG 58.414 33.333 22.32 11.06 0.00 3.33
2627 2684 7.759433 CCGATTTTCATGTATAAAGGCTTTGTT 59.241 33.333 22.32 11.91 0.00 2.83
2628 2685 7.122055 TCCGATTTTCATGTATAAAGGCTTTGT 59.878 33.333 22.32 17.96 0.00 2.83
2629 2686 7.479980 TCCGATTTTCATGTATAAAGGCTTTG 58.520 34.615 22.32 5.37 0.00 2.77
2630 2687 7.639113 TCCGATTTTCATGTATAAAGGCTTT 57.361 32.000 17.76 17.76 0.00 3.51
2631 2688 7.339466 ACTTCCGATTTTCATGTATAAAGGCTT 59.661 33.333 0.00 0.00 0.00 4.35
2632 2689 6.828785 ACTTCCGATTTTCATGTATAAAGGCT 59.171 34.615 0.00 0.00 0.00 4.58
2633 2690 6.912591 CACTTCCGATTTTCATGTATAAAGGC 59.087 38.462 0.00 0.00 0.00 4.35
2634 2691 7.985476 ACACTTCCGATTTTCATGTATAAAGG 58.015 34.615 0.00 0.00 0.00 3.11
2637 2694 9.438228 TGTTACACTTCCGATTTTCATGTATAA 57.562 29.630 0.00 0.00 0.00 0.98
2638 2695 9.093970 CTGTTACACTTCCGATTTTCATGTATA 57.906 33.333 0.00 0.00 0.00 1.47
2639 2696 7.822334 TCTGTTACACTTCCGATTTTCATGTAT 59.178 33.333 0.00 0.00 0.00 2.29
2640 2697 7.117236 GTCTGTTACACTTCCGATTTTCATGTA 59.883 37.037 0.00 0.00 0.00 2.29
2641 2698 5.995282 TCTGTTACACTTCCGATTTTCATGT 59.005 36.000 0.00 0.00 0.00 3.21
2642 2699 6.307155 GTCTGTTACACTTCCGATTTTCATG 58.693 40.000 0.00 0.00 0.00 3.07
2643 2700 5.411669 GGTCTGTTACACTTCCGATTTTCAT 59.588 40.000 0.00 0.00 0.00 2.57
2644 2701 4.753107 GGTCTGTTACACTTCCGATTTTCA 59.247 41.667 0.00 0.00 0.00 2.69
2645 2702 4.753107 TGGTCTGTTACACTTCCGATTTTC 59.247 41.667 0.00 0.00 0.00 2.29
2646 2703 4.710324 TGGTCTGTTACACTTCCGATTTT 58.290 39.130 0.00 0.00 0.00 1.82
2647 2704 4.345859 TGGTCTGTTACACTTCCGATTT 57.654 40.909 0.00 0.00 0.00 2.17
2648 2705 4.345859 TTGGTCTGTTACACTTCCGATT 57.654 40.909 0.00 0.00 0.00 3.34
2649 2706 4.039973 TCTTTGGTCTGTTACACTTCCGAT 59.960 41.667 0.00 0.00 0.00 4.18
2650 2707 3.385433 TCTTTGGTCTGTTACACTTCCGA 59.615 43.478 0.00 0.00 0.00 4.55
2651 2708 3.493503 GTCTTTGGTCTGTTACACTTCCG 59.506 47.826 0.00 0.00 0.00 4.30
2652 2709 4.448210 TGTCTTTGGTCTGTTACACTTCC 58.552 43.478 0.00 0.00 0.00 3.46
2653 2710 6.431198 TTTGTCTTTGGTCTGTTACACTTC 57.569 37.500 0.00 0.00 0.00 3.01
2654 2711 6.601613 TCATTTGTCTTTGGTCTGTTACACTT 59.398 34.615 0.00 0.00 0.00 3.16
2655 2712 6.119536 TCATTTGTCTTTGGTCTGTTACACT 58.880 36.000 0.00 0.00 0.00 3.55
2656 2713 6.371809 TCATTTGTCTTTGGTCTGTTACAC 57.628 37.500 0.00 0.00 0.00 2.90
2657 2714 7.581213 AATCATTTGTCTTTGGTCTGTTACA 57.419 32.000 0.00 0.00 0.00 2.41
2658 2715 7.382218 CCAAATCATTTGTCTTTGGTCTGTTAC 59.618 37.037 9.31 0.00 42.48 2.50
2659 2716 7.432869 CCAAATCATTTGTCTTTGGTCTGTTA 58.567 34.615 9.31 0.00 42.48 2.41
2660 2717 6.282930 CCAAATCATTTGTCTTTGGTCTGTT 58.717 36.000 9.31 0.00 42.48 3.16
2661 2718 5.739935 GCCAAATCATTTGTCTTTGGTCTGT 60.740 40.000 9.31 0.00 46.85 3.41
2662 2719 4.687483 GCCAAATCATTTGTCTTTGGTCTG 59.313 41.667 9.31 0.00 46.85 3.51
2663 2720 4.262592 GGCCAAATCATTTGTCTTTGGTCT 60.263 41.667 9.31 0.00 46.31 3.85
2664 2721 3.996363 GGCCAAATCATTTGTCTTTGGTC 59.004 43.478 9.31 16.09 46.85 4.02
2665 2722 3.390639 TGGCCAAATCATTTGTCTTTGGT 59.609 39.130 0.61 0.00 46.85 3.67
2667 2724 5.239351 TCATGGCCAAATCATTTGTCTTTG 58.761 37.500 10.96 0.00 38.98 2.77
2668 2725 5.486735 TCATGGCCAAATCATTTGTCTTT 57.513 34.783 10.96 0.00 38.98 2.52
2669 2726 5.486735 TTCATGGCCAAATCATTTGTCTT 57.513 34.783 10.96 0.00 38.98 3.01
2670 2727 5.012354 AGTTTCATGGCCAAATCATTTGTCT 59.988 36.000 10.96 0.00 38.98 3.41
2671 2728 5.121142 CAGTTTCATGGCCAAATCATTTGTC 59.879 40.000 10.96 0.00 38.98 3.18
2672 2729 4.998672 CAGTTTCATGGCCAAATCATTTGT 59.001 37.500 10.96 0.00 38.98 2.83
2673 2730 4.393680 CCAGTTTCATGGCCAAATCATTTG 59.606 41.667 10.96 0.52 40.32 2.32
2674 2731 4.286549 TCCAGTTTCATGGCCAAATCATTT 59.713 37.500 10.96 0.00 40.41 2.32
2675 2732 3.839490 TCCAGTTTCATGGCCAAATCATT 59.161 39.130 10.96 0.00 40.41 2.57
2676 2733 3.443052 TCCAGTTTCATGGCCAAATCAT 58.557 40.909 10.96 0.00 40.41 2.45
2677 2734 2.886913 TCCAGTTTCATGGCCAAATCA 58.113 42.857 10.96 0.00 40.41 2.57
2678 2735 3.006752 TGTTCCAGTTTCATGGCCAAATC 59.993 43.478 10.96 0.00 40.41 2.17
2679 2736 2.971330 TGTTCCAGTTTCATGGCCAAAT 59.029 40.909 10.96 0.00 40.41 2.32
2680 2737 2.364970 CTGTTCCAGTTTCATGGCCAAA 59.635 45.455 10.96 0.00 40.41 3.28
2681 2738 1.962807 CTGTTCCAGTTTCATGGCCAA 59.037 47.619 10.96 0.00 40.41 4.52
2682 2739 1.133513 ACTGTTCCAGTTTCATGGCCA 60.134 47.619 8.56 8.56 42.59 5.36
2683 2740 1.270550 CACTGTTCCAGTTTCATGGCC 59.729 52.381 0.00 0.00 42.59 5.36
2684 2741 1.336240 GCACTGTTCCAGTTTCATGGC 60.336 52.381 0.00 0.00 42.59 4.40
2685 2742 1.955778 TGCACTGTTCCAGTTTCATGG 59.044 47.619 0.00 0.00 42.59 3.66
2686 2743 3.928727 ATGCACTGTTCCAGTTTCATG 57.071 42.857 0.00 0.00 42.59 3.07
2687 2744 6.830324 ACATATATGCACTGTTCCAGTTTCAT 59.170 34.615 12.79 11.31 42.59 2.57
2688 2745 6.179756 ACATATATGCACTGTTCCAGTTTCA 58.820 36.000 12.79 0.00 42.59 2.69
2689 2746 6.683974 ACATATATGCACTGTTCCAGTTTC 57.316 37.500 12.79 0.00 42.59 2.78
2690 2747 7.201732 GCTAACATATATGCACTGTTCCAGTTT 60.202 37.037 12.79 0.00 42.59 2.66
2691 2748 6.260936 GCTAACATATATGCACTGTTCCAGTT 59.739 38.462 12.79 0.00 42.59 3.16
2692 2749 5.760253 GCTAACATATATGCACTGTTCCAGT 59.240 40.000 12.79 0.00 46.51 4.00
2693 2750 5.994054 AGCTAACATATATGCACTGTTCCAG 59.006 40.000 12.79 0.00 35.00 3.86
2694 2751 5.759763 CAGCTAACATATATGCACTGTTCCA 59.240 40.000 12.79 0.00 35.00 3.53
2695 2752 5.180117 CCAGCTAACATATATGCACTGTTCC 59.820 44.000 12.79 0.00 35.00 3.62
2696 2753 5.991606 TCCAGCTAACATATATGCACTGTTC 59.008 40.000 12.79 0.00 35.00 3.18
2697 2754 5.928976 TCCAGCTAACATATATGCACTGTT 58.071 37.500 12.79 3.43 37.00 3.16
2698 2755 5.551305 TCCAGCTAACATATATGCACTGT 57.449 39.130 12.79 0.00 0.00 3.55
2699 2756 6.866010 TTTCCAGCTAACATATATGCACTG 57.134 37.500 12.79 13.39 0.00 3.66
2700 2757 9.573166 TTATTTTCCAGCTAACATATATGCACT 57.427 29.630 12.79 2.49 0.00 4.40
2709 2766 8.850156 GGTGATACATTATTTTCCAGCTAACAT 58.150 33.333 0.00 0.00 0.00 2.71
2710 2767 7.831690 TGGTGATACATTATTTTCCAGCTAACA 59.168 33.333 0.00 0.00 0.00 2.41
2711 2768 8.220755 TGGTGATACATTATTTTCCAGCTAAC 57.779 34.615 0.00 0.00 0.00 2.34
2712 2769 8.815565 TTGGTGATACATTATTTTCCAGCTAA 57.184 30.769 0.00 0.00 0.00 3.09
2713 2770 8.849168 CATTGGTGATACATTATTTTCCAGCTA 58.151 33.333 0.00 0.00 0.00 3.32
2714 2771 7.342799 ACATTGGTGATACATTATTTTCCAGCT 59.657 33.333 0.00 0.00 0.00 4.24
2715 2772 7.491682 ACATTGGTGATACATTATTTTCCAGC 58.508 34.615 0.00 0.00 0.00 4.85
2716 2773 8.685427 TGACATTGGTGATACATTATTTTCCAG 58.315 33.333 0.00 0.00 0.00 3.86
2717 2774 8.586879 TGACATTGGTGATACATTATTTTCCA 57.413 30.769 0.00 0.00 0.00 3.53
2718 2775 9.683069 GATGACATTGGTGATACATTATTTTCC 57.317 33.333 0.00 0.00 0.00 3.13
2722 2779 9.358406 ACATGATGACATTGGTGATACATTATT 57.642 29.630 0.00 0.00 34.15 1.40
2723 2780 8.789762 CACATGATGACATTGGTGATACATTAT 58.210 33.333 0.00 0.00 34.46 1.28
2724 2781 7.229106 CCACATGATGACATTGGTGATACATTA 59.771 37.037 0.00 0.00 34.46 1.90
2725 2782 6.040054 CCACATGATGACATTGGTGATACATT 59.960 38.462 0.00 0.00 34.46 2.71
2726 2783 5.533528 CCACATGATGACATTGGTGATACAT 59.466 40.000 0.00 0.00 34.46 2.29
2727 2784 4.883006 CCACATGATGACATTGGTGATACA 59.117 41.667 0.00 0.00 34.46 2.29
2728 2785 4.276678 CCCACATGATGACATTGGTGATAC 59.723 45.833 0.00 0.00 34.46 2.24
2729 2786 4.165758 TCCCACATGATGACATTGGTGATA 59.834 41.667 0.00 2.82 34.46 2.15
2730 2787 3.053470 TCCCACATGATGACATTGGTGAT 60.053 43.478 0.00 0.00 34.46 3.06
2731 2788 2.308275 TCCCACATGATGACATTGGTGA 59.692 45.455 0.00 4.65 34.46 4.02
2732 2789 2.725637 TCCCACATGATGACATTGGTG 58.274 47.619 0.00 5.85 35.24 4.17
2733 2790 3.091545 GTTCCCACATGATGACATTGGT 58.908 45.455 0.00 0.00 35.24 3.67
2734 2791 3.359033 AGTTCCCACATGATGACATTGG 58.641 45.455 0.00 0.00 35.98 3.16
2735 2792 4.267536 AGAGTTCCCACATGATGACATTG 58.732 43.478 0.00 0.00 34.15 2.82
2736 2793 4.581309 AGAGTTCCCACATGATGACATT 57.419 40.909 0.00 0.00 34.15 2.71
2737 2794 4.019051 TGAAGAGTTCCCACATGATGACAT 60.019 41.667 0.00 0.00 37.19 3.06
2738 2795 3.327464 TGAAGAGTTCCCACATGATGACA 59.673 43.478 0.00 0.00 0.00 3.58
2739 2796 3.942829 TGAAGAGTTCCCACATGATGAC 58.057 45.455 0.00 0.00 0.00 3.06
2740 2797 4.849813 ATGAAGAGTTCCCACATGATGA 57.150 40.909 0.00 0.00 0.00 2.92
2741 2798 6.351711 TCTTATGAAGAGTTCCCACATGATG 58.648 40.000 0.00 0.00 32.71 3.07
2742 2799 6.566079 TCTTATGAAGAGTTCCCACATGAT 57.434 37.500 0.00 0.00 32.71 2.45
2743 2800 6.373005 TTCTTATGAAGAGTTCCCACATGA 57.627 37.500 0.00 0.00 39.03 3.07
2744 2801 7.636150 AATTCTTATGAAGAGTTCCCACATG 57.364 36.000 0.00 0.00 39.03 3.21
2745 2802 8.655935 AAAATTCTTATGAAGAGTTCCCACAT 57.344 30.769 0.00 0.00 36.58 3.21
2746 2803 9.753674 ATAAAATTCTTATGAAGAGTTCCCACA 57.246 29.630 0.00 0.00 36.58 4.17
2748 2805 9.973661 TCATAAAATTCTTATGAAGAGTTCCCA 57.026 29.630 15.02 0.00 36.58 4.37
2818 2875 7.615582 ACAATCAATGTAGTTCACGATGAAT 57.384 32.000 0.00 0.00 41.63 2.57
2832 2889 8.973378 CAAACCGTTAAATGTTACAATCAATGT 58.027 29.630 0.00 0.00 46.36 2.71
2840 2897 7.033791 TCAAAAGCAAACCGTTAAATGTTACA 58.966 30.769 0.00 0.00 0.00 2.41
2952 3009 7.801716 TTATGGGCATGAAATCACTTAGTAC 57.198 36.000 0.00 0.00 0.00 2.73
2955 3012 9.683069 GTAATTTATGGGCATGAAATCACTTAG 57.317 33.333 0.00 0.00 0.00 2.18
3006 3063 5.882557 AGCTGGTGGAACTATTGTAAGAATG 59.117 40.000 0.00 0.00 36.74 2.67
3007 3064 5.882557 CAGCTGGTGGAACTATTGTAAGAAT 59.117 40.000 5.57 0.00 36.74 2.40
3029 3086 6.558771 TTGACAGTAACACAAATGATCCAG 57.441 37.500 0.00 0.00 0.00 3.86
3046 3103 6.293845 GCTATAAAGGATGCTGGAATTGACAG 60.294 42.308 0.00 3.03 38.95 3.51
3050 3107 6.939163 ACTAGCTATAAAGGATGCTGGAATTG 59.061 38.462 0.00 0.00 37.44 2.32
3054 3111 5.147767 TCACTAGCTATAAAGGATGCTGGA 58.852 41.667 0.00 0.00 37.44 3.86
3062 3119 7.445945 AGTAGCCAATTCACTAGCTATAAAGG 58.554 38.462 0.00 0.00 39.80 3.11
3066 3123 5.480772 GGGAGTAGCCAATTCACTAGCTATA 59.519 44.000 0.00 0.00 39.80 1.31
3067 3124 4.284746 GGGAGTAGCCAATTCACTAGCTAT 59.715 45.833 0.00 0.00 39.80 2.97
3070 3127 2.170607 TGGGAGTAGCCAATTCACTAGC 59.829 50.000 0.00 0.00 38.95 3.42
3102 3159 2.544686 GCAGTTCTAGCTCTCATGCATG 59.455 50.000 21.07 21.07 34.99 4.06
3110 3167 6.432162 TCATTTTCAATTGCAGTTCTAGCTCT 59.568 34.615 0.00 0.00 0.00 4.09
3115 3172 7.229306 AGTGACTCATTTTCAATTGCAGTTCTA 59.771 33.333 0.00 0.00 0.00 2.10
3117 3174 6.143438 CAGTGACTCATTTTCAATTGCAGTTC 59.857 38.462 0.00 0.00 0.00 3.01
3119 3176 5.508489 CCAGTGACTCATTTTCAATTGCAGT 60.508 40.000 0.00 0.00 0.00 4.40
3123 3180 5.693104 CCAACCAGTGACTCATTTTCAATTG 59.307 40.000 0.00 0.00 0.00 2.32
3140 3197 2.233271 CTATTGCATAGGGCCAACCAG 58.767 52.381 6.18 0.00 43.89 4.00
3144 3201 2.754012 AAGCTATTGCATAGGGCCAA 57.246 45.000 6.18 0.00 43.89 4.52
3155 3212 6.241207 TCGACCTCTTTTGAAAAGCTATTG 57.759 37.500 12.62 4.72 0.00 1.90
3164 3221 4.131649 TGTGAGTTCGACCTCTTTTGAA 57.868 40.909 11.53 0.00 32.50 2.69
3175 3232 5.352846 TGTGTTTTCAATCTTGTGAGTTCGA 59.647 36.000 0.00 0.00 0.00 3.71
3210 3267 7.580302 GCTGCTTGGTAAGATGATATATCTCCA 60.580 40.741 13.79 9.31 0.00 3.86
3236 3293 6.588719 TTCTGGGTGGTAATTTTCTCATTG 57.411 37.500 0.00 0.00 0.00 2.82
3241 3298 7.797121 ATGATTTTCTGGGTGGTAATTTTCT 57.203 32.000 0.00 0.00 0.00 2.52
3242 3299 7.877612 ACAATGATTTTCTGGGTGGTAATTTTC 59.122 33.333 0.00 0.00 0.00 2.29
3243 3300 7.744733 ACAATGATTTTCTGGGTGGTAATTTT 58.255 30.769 0.00 0.00 0.00 1.82
3245 3302 6.933514 ACAATGATTTTCTGGGTGGTAATT 57.066 33.333 0.00 0.00 0.00 1.40
3248 3305 4.457603 CGAACAATGATTTTCTGGGTGGTA 59.542 41.667 0.00 0.00 0.00 3.25
3257 3314 5.392057 GGGAGAGGTTCGAACAATGATTTTC 60.392 44.000 28.24 13.35 0.00 2.29


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

AutoCloner maintained by Alex Coulton.