Multiple sequence alignment - TraesCS6D01G098300

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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 TraesCS6D01G098300 chr6D 100.000 2811 0 0 1 2811 61814022 61811212 0.000000e+00 5192
1 TraesCS6D01G098300 chr6D 98.433 1340 17 2 220 1555 65307826 65309165 0.000000e+00 2355
2 TraesCS6D01G098300 chr6D 97.996 998 13 3 1551 2545 65317487 65318480 0.000000e+00 1725
3 TraesCS6D01G098300 chr2D 96.075 2548 88 5 1 2539 226333155 226335699 0.000000e+00 4141
4 TraesCS6D01G098300 chr2D 87.346 2268 220 45 1 2225 621361713 621363956 0.000000e+00 2536
5 TraesCS6D01G098300 chr2D 93.680 269 16 1 2544 2811 7209488 7209220 4.360000e-108 401
6 TraesCS6D01G098300 chr5B 94.751 2572 97 22 1 2542 567869111 567866548 0.000000e+00 3967
7 TraesCS6D01G098300 chr5B 89.227 724 46 18 1844 2544 41904443 41903729 0.000000e+00 876
8 TraesCS6D01G098300 chr5B 87.568 370 17 16 2172 2540 542676793 542677134 4.360000e-108 401
9 TraesCS6D01G098300 chr3D 97.144 2241 36 6 1 2234 535143552 535145771 0.000000e+00 3759
10 TraesCS6D01G098300 chr3D 98.800 250 3 0 2295 2544 535145759 535146008 1.990000e-121 446
11 TraesCS6D01G098300 chr3D 94.424 269 14 1 2544 2811 12222973 12222705 2.010000e-111 412
12 TraesCS6D01G098300 chr3B 93.557 2561 101 33 1 2539 106957261 106954743 0.000000e+00 3757
13 TraesCS6D01G098300 chr3B 94.012 2288 86 29 1 2268 8785063 8787319 0.000000e+00 3419
14 TraesCS6D01G098300 chr3B 95.760 283 11 1 2261 2543 8788127 8788408 3.300000e-124 455
15 TraesCS6D01G098300 chr7A 87.901 2149 212 30 1 2113 683510169 683508033 0.000000e+00 2484
16 TraesCS6D01G098300 chr7A 88.983 2015 183 23 1 1984 683625665 683627671 0.000000e+00 2455
17 TraesCS6D01G098300 chr7A 93.680 269 16 1 2544 2811 47252326 47252594 4.360000e-108 401
18 TraesCS6D01G098300 chr7A 93.680 269 16 1 2544 2811 721581550 721581818 4.360000e-108 401
19 TraesCS6D01G098300 chr1B 90.438 1893 153 16 1 1871 7321299 7319413 0.000000e+00 2468
20 TraesCS6D01G098300 chr5D 95.235 1343 37 9 1203 2538 43163527 43162205 0.000000e+00 2100
21 TraesCS6D01G098300 chr4A 87.554 1165 94 27 1 1123 649887669 649888824 0.000000e+00 1301
22 TraesCS6D01G098300 chr4B 91.678 709 47 7 1 699 38607820 38608526 0.000000e+00 972
23 TraesCS6D01G098300 chrUn 81.046 765 77 33 1795 2539 15859136 15859852 5.290000e-152 547
24 TraesCS6D01G098300 chrUn 93.309 269 17 1 2544 2811 230009276 230009544 2.030000e-106 396
25 TraesCS6D01G098300 chrUn 93.309 269 17 1 2544 2811 291012960 291013228 2.030000e-106 396
26 TraesCS6D01G098300 chr6B 94.118 272 16 0 2540 2811 135714382 135714111 5.600000e-112 414
27 TraesCS6D01G098300 chr7D 93.680 269 16 1 2544 2811 566880345 566880077 4.360000e-108 401
28 TraesCS6D01G098300 chr7B 93.680 269 16 1 2544 2811 677183267 677183535 4.360000e-108 401


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 TraesCS6D01G098300 chr6D 61811212 61814022 2810 True 5192.0 5192 100.000 1 2811 1 chr6D.!!$R1 2810
1 TraesCS6D01G098300 chr6D 65307826 65309165 1339 False 2355.0 2355 98.433 220 1555 1 chr6D.!!$F1 1335
2 TraesCS6D01G098300 chr6D 65317487 65318480 993 False 1725.0 1725 97.996 1551 2545 1 chr6D.!!$F2 994
3 TraesCS6D01G098300 chr2D 226333155 226335699 2544 False 4141.0 4141 96.075 1 2539 1 chr2D.!!$F1 2538
4 TraesCS6D01G098300 chr2D 621361713 621363956 2243 False 2536.0 2536 87.346 1 2225 1 chr2D.!!$F2 2224
5 TraesCS6D01G098300 chr5B 567866548 567869111 2563 True 3967.0 3967 94.751 1 2542 1 chr5B.!!$R2 2541
6 TraesCS6D01G098300 chr5B 41903729 41904443 714 True 876.0 876 89.227 1844 2544 1 chr5B.!!$R1 700
7 TraesCS6D01G098300 chr3D 535143552 535146008 2456 False 2102.5 3759 97.972 1 2544 2 chr3D.!!$F1 2543
8 TraesCS6D01G098300 chr3B 106954743 106957261 2518 True 3757.0 3757 93.557 1 2539 1 chr3B.!!$R1 2538
9 TraesCS6D01G098300 chr3B 8785063 8788408 3345 False 1937.0 3419 94.886 1 2543 2 chr3B.!!$F1 2542
10 TraesCS6D01G098300 chr7A 683508033 683510169 2136 True 2484.0 2484 87.901 1 2113 1 chr7A.!!$R1 2112
11 TraesCS6D01G098300 chr7A 683625665 683627671 2006 False 2455.0 2455 88.983 1 1984 1 chr7A.!!$F2 1983
12 TraesCS6D01G098300 chr1B 7319413 7321299 1886 True 2468.0 2468 90.438 1 1871 1 chr1B.!!$R1 1870
13 TraesCS6D01G098300 chr5D 43162205 43163527 1322 True 2100.0 2100 95.235 1203 2538 1 chr5D.!!$R1 1335
14 TraesCS6D01G098300 chr4A 649887669 649888824 1155 False 1301.0 1301 87.554 1 1123 1 chr4A.!!$F1 1122
15 TraesCS6D01G098300 chr4B 38607820 38608526 706 False 972.0 972 91.678 1 699 1 chr4B.!!$F1 698
16 TraesCS6D01G098300 chrUn 15859136 15859852 716 False 547.0 547 81.046 1795 2539 1 chrUn.!!$F1 744

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
405 407 3.420893 CAGGTAACATGTGTCCATTGGT 58.579 45.455 17.91 0.0 41.41 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2084 3.130869 ACAACAGCAGCACTTTTCATCAA 59.869 39.13 0.0 0.0 0.0 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
169 171 4.910304 AGGAAGATATTACCTGGCTGATGT 59.090 41.667 0.00 0.00 32.39 3.06
405 407 3.420893 CAGGTAACATGTGTCCATTGGT 58.579 45.455 17.91 0.00 41.41 3.67
413 415 5.115480 ACATGTGTCCATTGGTTTTTCAAC 58.885 37.500 0.00 0.00 0.00 3.18
524 533 4.183223 TGCAAGGGATAGGCAACATATT 57.817 40.909 0.00 0.00 41.41 1.28
747 759 5.587289 TGATGTCTTTTGCTTTTGTGGTAC 58.413 37.500 0.00 0.00 0.00 3.34
2005 2084 7.568199 AAGTGCTGTTGTTTATAAGAGTTGT 57.432 32.000 0.00 0.00 0.00 3.32
2079 2266 2.558378 ACATGTGCTGCTGCTGTATAG 58.442 47.619 17.00 4.75 40.48 1.31
2084 2271 1.162800 GCTGCTGCTGTATAGGTGCC 61.163 60.000 8.53 0.00 36.03 5.01
2128 2358 6.816136 TGTATAAGTGCTGCTGTATATGTGT 58.184 36.000 0.00 0.00 0.00 3.72
2169 2447 6.655003 AGTGCTGCTGTATAAGTTATGTTGTT 59.345 34.615 5.61 0.00 0.00 2.83
2170 2448 6.742718 GTGCTGCTGTATAAGTTATGTTGTTG 59.257 38.462 5.61 0.00 0.00 3.33
2171 2449 6.429692 TGCTGCTGTATAAGTTATGTTGTTGT 59.570 34.615 5.61 0.00 0.00 3.32
2544 3642 2.226437 ACATCCAAACAAAGCGCTAGTG 59.774 45.455 12.05 15.29 0.00 2.74
2545 3643 2.248280 TCCAAACAAAGCGCTAGTGA 57.752 45.000 23.61 11.35 0.00 3.41
2546 3644 2.778299 TCCAAACAAAGCGCTAGTGAT 58.222 42.857 23.61 12.03 0.00 3.06
2547 3645 2.742053 TCCAAACAAAGCGCTAGTGATC 59.258 45.455 23.61 0.00 0.00 2.92
2548 3646 2.744202 CCAAACAAAGCGCTAGTGATCT 59.256 45.455 23.61 8.13 0.00 2.75
2549 3647 3.189287 CCAAACAAAGCGCTAGTGATCTT 59.811 43.478 23.61 12.54 0.00 2.40
2550 3648 4.320494 CCAAACAAAGCGCTAGTGATCTTT 60.320 41.667 23.61 12.93 0.00 2.52
2551 3649 4.410492 AACAAAGCGCTAGTGATCTTTG 57.590 40.909 23.61 23.60 46.34 2.77
2552 3650 2.744202 ACAAAGCGCTAGTGATCTTTGG 59.256 45.455 26.38 15.80 45.64 3.28
2553 3651 2.744202 CAAAGCGCTAGTGATCTTTGGT 59.256 45.455 12.05 0.00 40.76 3.67
2554 3652 2.301577 AGCGCTAGTGATCTTTGGTC 57.698 50.000 8.99 0.00 0.00 4.02
2555 3653 1.134670 AGCGCTAGTGATCTTTGGTCC 60.135 52.381 8.99 0.00 0.00 4.46
2556 3654 1.134670 GCGCTAGTGATCTTTGGTCCT 60.135 52.381 7.68 0.00 0.00 3.85
2557 3655 2.815478 CGCTAGTGATCTTTGGTCCTC 58.185 52.381 0.00 0.00 0.00 3.71
2558 3656 2.166459 CGCTAGTGATCTTTGGTCCTCA 59.834 50.000 0.00 0.00 0.00 3.86
2559 3657 3.368427 CGCTAGTGATCTTTGGTCCTCAA 60.368 47.826 0.00 0.00 0.00 3.02
2560 3658 4.579869 GCTAGTGATCTTTGGTCCTCAAA 58.420 43.478 0.00 0.00 42.50 2.69
2568 3666 1.981256 TTGGTCCTCAAAGTGAAGGC 58.019 50.000 0.00 0.00 31.46 4.35
2569 3667 0.110486 TGGTCCTCAAAGTGAAGGCC 59.890 55.000 0.00 0.00 0.00 5.19
2570 3668 0.609406 GGTCCTCAAAGTGAAGGCCC 60.609 60.000 0.00 0.00 0.00 5.80
2571 3669 0.110486 GTCCTCAAAGTGAAGGCCCA 59.890 55.000 0.00 0.00 0.00 5.36
2572 3670 0.850100 TCCTCAAAGTGAAGGCCCAA 59.150 50.000 0.00 0.00 0.00 4.12
2573 3671 1.216678 TCCTCAAAGTGAAGGCCCAAA 59.783 47.619 0.00 0.00 0.00 3.28
2574 3672 1.341209 CCTCAAAGTGAAGGCCCAAAC 59.659 52.381 0.00 0.00 0.00 2.93
2575 3673 2.310538 CTCAAAGTGAAGGCCCAAACT 58.689 47.619 0.00 0.00 0.00 2.66
2576 3674 2.695147 CTCAAAGTGAAGGCCCAAACTT 59.305 45.455 0.00 3.63 34.40 2.66
2577 3675 3.103742 TCAAAGTGAAGGCCCAAACTTT 58.896 40.909 17.28 17.28 42.13 2.66
2578 3676 3.132111 TCAAAGTGAAGGCCCAAACTTTC 59.868 43.478 19.23 8.40 40.05 2.62
2579 3677 1.704641 AGTGAAGGCCCAAACTTTCC 58.295 50.000 0.00 0.00 0.00 3.13
2580 3678 1.217942 AGTGAAGGCCCAAACTTTCCT 59.782 47.619 0.00 0.00 0.00 3.36
2581 3679 1.341209 GTGAAGGCCCAAACTTTCCTG 59.659 52.381 0.00 0.00 0.00 3.86
2582 3680 0.969149 GAAGGCCCAAACTTTCCTGG 59.031 55.000 0.00 0.00 0.00 4.45
2583 3681 0.560688 AAGGCCCAAACTTTCCTGGA 59.439 50.000 0.00 0.00 34.35 3.86
2584 3682 0.113190 AGGCCCAAACTTTCCTGGAG 59.887 55.000 0.00 0.00 34.35 3.86
2585 3683 0.112412 GGCCCAAACTTTCCTGGAGA 59.888 55.000 0.00 0.00 34.35 3.71
2586 3684 1.480498 GGCCCAAACTTTCCTGGAGAA 60.480 52.381 0.00 0.00 34.35 2.87
2587 3685 1.889170 GCCCAAACTTTCCTGGAGAAG 59.111 52.381 13.56 13.56 35.40 2.85
2588 3686 2.753168 GCCCAAACTTTCCTGGAGAAGT 60.753 50.000 14.51 14.51 35.40 3.01
2589 3687 3.149981 CCCAAACTTTCCTGGAGAAGTC 58.850 50.000 18.24 0.00 35.40 3.01
2590 3688 3.435026 CCCAAACTTTCCTGGAGAAGTCA 60.435 47.826 18.24 0.00 35.40 3.41
2591 3689 4.401925 CCAAACTTTCCTGGAGAAGTCAT 58.598 43.478 18.24 11.39 35.40 3.06
2592 3690 4.457257 CCAAACTTTCCTGGAGAAGTCATC 59.543 45.833 18.24 0.00 35.40 2.92
2593 3691 4.982241 AACTTTCCTGGAGAAGTCATCA 57.018 40.909 18.24 0.00 35.40 3.07
2594 3692 4.982241 ACTTTCCTGGAGAAGTCATCAA 57.018 40.909 14.51 0.00 35.40 2.57
2595 3693 5.511386 ACTTTCCTGGAGAAGTCATCAAT 57.489 39.130 14.51 0.00 35.40 2.57
2596 3694 6.627087 ACTTTCCTGGAGAAGTCATCAATA 57.373 37.500 14.51 0.00 35.40 1.90
2597 3695 7.020827 ACTTTCCTGGAGAAGTCATCAATAA 57.979 36.000 14.51 0.00 35.40 1.40
2598 3696 7.461749 ACTTTCCTGGAGAAGTCATCAATAAA 58.538 34.615 14.51 0.00 35.40 1.40
2599 3697 7.944554 ACTTTCCTGGAGAAGTCATCAATAAAA 59.055 33.333 14.51 0.00 35.40 1.52
2600 3698 7.928307 TTCCTGGAGAAGTCATCAATAAAAG 57.072 36.000 0.00 0.00 0.00 2.27
2601 3699 7.020827 TCCTGGAGAAGTCATCAATAAAAGT 57.979 36.000 0.00 0.00 0.00 2.66
2602 3700 7.106239 TCCTGGAGAAGTCATCAATAAAAGTC 58.894 38.462 0.00 0.00 0.00 3.01
2603 3701 6.881065 CCTGGAGAAGTCATCAATAAAAGTCA 59.119 38.462 0.00 0.00 0.00 3.41
2604 3702 7.148340 CCTGGAGAAGTCATCAATAAAAGTCAC 60.148 40.741 0.00 0.00 0.00 3.67
2605 3703 7.223584 TGGAGAAGTCATCAATAAAAGTCACA 58.776 34.615 0.00 0.00 0.00 3.58
2606 3704 7.719193 TGGAGAAGTCATCAATAAAAGTCACAA 59.281 33.333 0.00 0.00 0.00 3.33
2607 3705 8.567948 GGAGAAGTCATCAATAAAAGTCACAAA 58.432 33.333 0.00 0.00 0.00 2.83
2608 3706 9.604626 GAGAAGTCATCAATAAAAGTCACAAAG 57.395 33.333 0.00 0.00 0.00 2.77
2609 3707 9.125026 AGAAGTCATCAATAAAAGTCACAAAGT 57.875 29.630 0.00 0.00 0.00 2.66
2612 3710 9.561069 AGTCATCAATAAAAGTCACAAAGTACT 57.439 29.630 0.00 0.00 0.00 2.73
2619 3717 8.843885 ATAAAAGTCACAAAGTACTTAGGACC 57.156 34.615 21.26 7.95 34.91 4.46
2620 3718 5.881923 AAGTCACAAAGTACTTAGGACCA 57.118 39.130 21.26 1.01 34.23 4.02
2621 3719 5.211174 AGTCACAAAGTACTTAGGACCAC 57.789 43.478 21.26 10.51 0.00 4.16
2622 3720 4.040095 AGTCACAAAGTACTTAGGACCACC 59.960 45.833 21.26 6.19 0.00 4.61
2623 3721 3.968649 TCACAAAGTACTTAGGACCACCA 59.031 43.478 8.92 0.00 38.94 4.17
2624 3722 4.409574 TCACAAAGTACTTAGGACCACCAA 59.590 41.667 8.92 0.00 38.94 3.67
2625 3723 4.755123 CACAAAGTACTTAGGACCACCAAG 59.245 45.833 8.92 0.00 38.94 3.61
2626 3724 4.657039 ACAAAGTACTTAGGACCACCAAGA 59.343 41.667 8.92 0.00 38.94 3.02
2627 3725 5.221661 ACAAAGTACTTAGGACCACCAAGAG 60.222 44.000 8.92 0.00 38.94 2.85
2628 3726 4.399483 AGTACTTAGGACCACCAAGAGA 57.601 45.455 7.33 0.00 38.94 3.10
2629 3727 4.949121 AGTACTTAGGACCACCAAGAGAT 58.051 43.478 7.33 0.00 38.94 2.75
2630 3728 4.957327 AGTACTTAGGACCACCAAGAGATC 59.043 45.833 7.33 0.00 38.94 2.75
2631 3729 4.067944 ACTTAGGACCACCAAGAGATCT 57.932 45.455 0.00 0.00 38.94 2.75
2632 3730 4.430441 ACTTAGGACCACCAAGAGATCTT 58.570 43.478 0.00 0.00 38.94 2.40
2633 3731 5.590818 ACTTAGGACCACCAAGAGATCTTA 58.409 41.667 0.00 0.00 38.94 2.10
2634 3732 5.422650 ACTTAGGACCACCAAGAGATCTTAC 59.577 44.000 0.00 0.00 38.94 2.34
2635 3733 3.108376 AGGACCACCAAGAGATCTTACC 58.892 50.000 0.00 0.00 38.94 2.85
2636 3734 2.159085 GGACCACCAAGAGATCTTACCG 60.159 54.545 0.00 0.00 34.28 4.02
2637 3735 2.758979 GACCACCAAGAGATCTTACCGA 59.241 50.000 0.00 0.00 34.28 4.69
2638 3736 2.496470 ACCACCAAGAGATCTTACCGAC 59.504 50.000 0.00 0.00 34.28 4.79
2639 3737 2.496070 CCACCAAGAGATCTTACCGACA 59.504 50.000 0.00 0.00 34.28 4.35
2640 3738 3.429547 CCACCAAGAGATCTTACCGACAG 60.430 52.174 0.00 0.00 34.28 3.51
2641 3739 3.193691 CACCAAGAGATCTTACCGACAGT 59.806 47.826 0.00 0.00 34.28 3.55
2642 3740 3.833070 ACCAAGAGATCTTACCGACAGTT 59.167 43.478 0.00 0.00 34.28 3.16
2643 3741 4.283722 ACCAAGAGATCTTACCGACAGTTT 59.716 41.667 0.00 0.00 34.28 2.66
2644 3742 4.627467 CCAAGAGATCTTACCGACAGTTTG 59.373 45.833 0.00 0.00 34.28 2.93
2645 3743 3.851098 AGAGATCTTACCGACAGTTTGC 58.149 45.455 0.00 0.00 0.00 3.68
2646 3744 3.258372 AGAGATCTTACCGACAGTTTGCA 59.742 43.478 0.00 0.00 0.00 4.08
2647 3745 3.994392 GAGATCTTACCGACAGTTTGCAA 59.006 43.478 0.00 0.00 0.00 4.08
2648 3746 4.385825 AGATCTTACCGACAGTTTGCAAA 58.614 39.130 8.05 8.05 0.00 3.68
2649 3747 3.955771 TCTTACCGACAGTTTGCAAAC 57.044 42.857 30.63 30.63 39.17 2.93
2650 3748 3.271729 TCTTACCGACAGTTTGCAAACA 58.728 40.909 36.46 16.86 41.30 2.83
2651 3749 3.880490 TCTTACCGACAGTTTGCAAACAT 59.120 39.130 36.46 26.62 41.30 2.71
2652 3750 2.774439 ACCGACAGTTTGCAAACATC 57.226 45.000 36.46 30.42 41.30 3.06
2653 3751 2.020720 ACCGACAGTTTGCAAACATCA 58.979 42.857 36.46 4.24 41.30 3.07
2654 3752 2.033299 ACCGACAGTTTGCAAACATCAG 59.967 45.455 36.46 27.38 41.30 2.90
2655 3753 2.290367 CCGACAGTTTGCAAACATCAGA 59.710 45.455 36.46 2.66 41.30 3.27
2656 3754 3.243035 CCGACAGTTTGCAAACATCAGAA 60.243 43.478 36.46 1.86 41.30 3.02
2657 3755 4.539870 CGACAGTTTGCAAACATCAGAAT 58.460 39.130 36.46 16.86 41.30 2.40
2658 3756 4.380678 CGACAGTTTGCAAACATCAGAATG 59.619 41.667 36.46 26.94 41.30 2.67
2660 3758 6.389830 ACAGTTTGCAAACATCAGAATGTA 57.610 33.333 36.46 0.00 45.48 2.29
2661 3759 6.985117 ACAGTTTGCAAACATCAGAATGTAT 58.015 32.000 36.46 14.37 45.48 2.29
2662 3760 7.086376 ACAGTTTGCAAACATCAGAATGTATC 58.914 34.615 36.46 11.11 45.48 2.24
2663 3761 7.085746 CAGTTTGCAAACATCAGAATGTATCA 58.914 34.615 36.46 0.00 45.48 2.15
2664 3762 7.595875 CAGTTTGCAAACATCAGAATGTATCAA 59.404 33.333 36.46 0.00 45.48 2.57
2665 3763 7.811236 AGTTTGCAAACATCAGAATGTATCAAG 59.189 33.333 36.46 0.00 45.48 3.02
2666 3764 6.822667 TGCAAACATCAGAATGTATCAAGT 57.177 33.333 0.00 0.00 45.48 3.16
2667 3765 6.845302 TGCAAACATCAGAATGTATCAAGTC 58.155 36.000 0.00 0.00 45.48 3.01
2668 3766 6.127925 TGCAAACATCAGAATGTATCAAGTCC 60.128 38.462 0.00 0.00 45.48 3.85
2669 3767 6.127925 GCAAACATCAGAATGTATCAAGTCCA 60.128 38.462 0.00 0.00 45.48 4.02
2670 3768 7.575532 GCAAACATCAGAATGTATCAAGTCCAA 60.576 37.037 0.00 0.00 45.48 3.53
2671 3769 6.992063 ACATCAGAATGTATCAAGTCCAAC 57.008 37.500 0.00 0.00 44.38 3.77
2672 3770 6.475504 ACATCAGAATGTATCAAGTCCAACA 58.524 36.000 0.00 0.00 44.38 3.33
2673 3771 7.114754 ACATCAGAATGTATCAAGTCCAACAT 58.885 34.615 0.00 0.00 44.38 2.71
2674 3772 7.281774 ACATCAGAATGTATCAAGTCCAACATC 59.718 37.037 0.00 0.00 44.38 3.06
2675 3773 6.950842 TCAGAATGTATCAAGTCCAACATCT 58.049 36.000 0.00 0.00 37.40 2.90
2676 3774 7.397221 TCAGAATGTATCAAGTCCAACATCTT 58.603 34.615 0.00 0.00 37.40 2.40
2677 3775 8.539544 TCAGAATGTATCAAGTCCAACATCTTA 58.460 33.333 0.00 0.00 37.40 2.10
2678 3776 8.824781 CAGAATGTATCAAGTCCAACATCTTAG 58.175 37.037 0.00 0.00 31.53 2.18
2679 3777 7.989741 AGAATGTATCAAGTCCAACATCTTAGG 59.010 37.037 0.00 0.00 31.53 2.69
2680 3778 5.428253 TGTATCAAGTCCAACATCTTAGGC 58.572 41.667 0.00 0.00 0.00 3.93
2681 3779 4.851639 ATCAAGTCCAACATCTTAGGCT 57.148 40.909 0.00 0.00 0.00 4.58
2682 3780 4.640771 TCAAGTCCAACATCTTAGGCTT 57.359 40.909 0.00 0.00 0.00 4.35
2683 3781 4.579869 TCAAGTCCAACATCTTAGGCTTC 58.420 43.478 0.00 0.00 0.00 3.86
2684 3782 4.287067 TCAAGTCCAACATCTTAGGCTTCT 59.713 41.667 0.00 0.00 0.00 2.85
2685 3783 4.917906 AGTCCAACATCTTAGGCTTCTT 57.082 40.909 0.00 0.00 0.00 2.52
2686 3784 4.583871 AGTCCAACATCTTAGGCTTCTTG 58.416 43.478 0.00 0.00 0.00 3.02
2687 3785 4.042187 AGTCCAACATCTTAGGCTTCTTGT 59.958 41.667 0.00 0.00 0.00 3.16
2688 3786 4.154918 GTCCAACATCTTAGGCTTCTTGTG 59.845 45.833 0.00 0.00 0.00 3.33
2689 3787 4.041567 TCCAACATCTTAGGCTTCTTGTGA 59.958 41.667 0.00 0.00 0.00 3.58
2690 3788 4.394300 CCAACATCTTAGGCTTCTTGTGAG 59.606 45.833 0.00 0.00 0.00 3.51
2691 3789 4.213564 ACATCTTAGGCTTCTTGTGAGG 57.786 45.455 0.00 0.00 0.00 3.86
2692 3790 3.840666 ACATCTTAGGCTTCTTGTGAGGA 59.159 43.478 0.00 0.00 0.00 3.71
2693 3791 4.081198 ACATCTTAGGCTTCTTGTGAGGAG 60.081 45.833 0.00 0.00 0.00 3.69
2694 3792 2.834549 TCTTAGGCTTCTTGTGAGGAGG 59.165 50.000 0.00 0.00 0.00 4.30
2695 3793 2.327325 TAGGCTTCTTGTGAGGAGGT 57.673 50.000 0.00 0.00 0.00 3.85
2696 3794 2.327325 AGGCTTCTTGTGAGGAGGTA 57.673 50.000 0.00 0.00 0.00 3.08
2697 3795 2.183679 AGGCTTCTTGTGAGGAGGTAG 58.816 52.381 0.00 0.00 0.00 3.18
2698 3796 2.180276 GGCTTCTTGTGAGGAGGTAGA 58.820 52.381 0.00 0.00 0.00 2.59
2699 3797 2.167487 GGCTTCTTGTGAGGAGGTAGAG 59.833 54.545 0.00 0.00 0.00 2.43
2700 3798 2.829120 GCTTCTTGTGAGGAGGTAGAGT 59.171 50.000 0.00 0.00 0.00 3.24
2701 3799 3.119280 GCTTCTTGTGAGGAGGTAGAGTC 60.119 52.174 0.00 0.00 0.00 3.36
2702 3800 4.340617 CTTCTTGTGAGGAGGTAGAGTCT 58.659 47.826 0.00 0.00 0.00 3.24
2703 3801 4.390129 TCTTGTGAGGAGGTAGAGTCTT 57.610 45.455 0.00 0.00 0.00 3.01
2704 3802 4.082845 TCTTGTGAGGAGGTAGAGTCTTG 58.917 47.826 0.00 0.00 0.00 3.02
2705 3803 3.808834 TGTGAGGAGGTAGAGTCTTGA 57.191 47.619 0.00 0.00 0.00 3.02
2706 3804 4.114015 TGTGAGGAGGTAGAGTCTTGAA 57.886 45.455 0.00 0.00 0.00 2.69
2707 3805 4.082845 TGTGAGGAGGTAGAGTCTTGAAG 58.917 47.826 0.00 0.00 0.00 3.02
2708 3806 3.445805 GTGAGGAGGTAGAGTCTTGAAGG 59.554 52.174 0.00 0.00 0.00 3.46
2709 3807 2.429250 GAGGAGGTAGAGTCTTGAAGGC 59.571 54.545 0.00 0.00 0.00 4.35
2710 3808 2.180276 GGAGGTAGAGTCTTGAAGGCA 58.820 52.381 0.00 0.00 0.00 4.75
2711 3809 2.567615 GGAGGTAGAGTCTTGAAGGCAA 59.432 50.000 0.00 0.00 0.00 4.52
2712 3810 3.591023 GAGGTAGAGTCTTGAAGGCAAC 58.409 50.000 0.00 0.00 0.00 4.17
2727 3825 3.364889 GGCAACTTTGTGTTACTTCCC 57.635 47.619 0.00 0.00 37.07 3.97
2728 3826 2.035449 GGCAACTTTGTGTTACTTCCCC 59.965 50.000 0.00 0.00 37.07 4.81
2729 3827 2.287368 GCAACTTTGTGTTACTTCCCCG 60.287 50.000 0.00 0.00 37.07 5.73
2730 3828 1.601166 ACTTTGTGTTACTTCCCCGC 58.399 50.000 0.00 0.00 0.00 6.13
2731 3829 1.142262 ACTTTGTGTTACTTCCCCGCT 59.858 47.619 0.00 0.00 0.00 5.52
2732 3830 2.369532 ACTTTGTGTTACTTCCCCGCTA 59.630 45.455 0.00 0.00 0.00 4.26
2733 3831 2.754946 TTGTGTTACTTCCCCGCTAG 57.245 50.000 0.00 0.00 0.00 3.42
2734 3832 1.927487 TGTGTTACTTCCCCGCTAGA 58.073 50.000 0.00 0.00 0.00 2.43
2735 3833 1.547372 TGTGTTACTTCCCCGCTAGAC 59.453 52.381 0.00 0.00 0.00 2.59
2736 3834 1.547372 GTGTTACTTCCCCGCTAGACA 59.453 52.381 0.00 0.00 0.00 3.41
2737 3835 2.028748 GTGTTACTTCCCCGCTAGACAA 60.029 50.000 0.00 0.00 0.00 3.18
2738 3836 2.835764 TGTTACTTCCCCGCTAGACAAT 59.164 45.455 0.00 0.00 0.00 2.71
2739 3837 3.118884 TGTTACTTCCCCGCTAGACAATC 60.119 47.826 0.00 0.00 0.00 2.67
2740 3838 1.867363 ACTTCCCCGCTAGACAATCT 58.133 50.000 0.00 0.00 0.00 2.40
2741 3839 2.188817 ACTTCCCCGCTAGACAATCTT 58.811 47.619 0.00 0.00 0.00 2.40
2742 3840 3.371965 ACTTCCCCGCTAGACAATCTTA 58.628 45.455 0.00 0.00 0.00 2.10
2743 3841 3.773119 ACTTCCCCGCTAGACAATCTTAA 59.227 43.478 0.00 0.00 0.00 1.85
2744 3842 3.814005 TCCCCGCTAGACAATCTTAAC 57.186 47.619 0.00 0.00 0.00 2.01
2745 3843 3.101437 TCCCCGCTAGACAATCTTAACA 58.899 45.455 0.00 0.00 0.00 2.41
2746 3844 3.709653 TCCCCGCTAGACAATCTTAACAT 59.290 43.478 0.00 0.00 0.00 2.71
2747 3845 4.058817 CCCCGCTAGACAATCTTAACATC 58.941 47.826 0.00 0.00 0.00 3.06
2748 3846 4.202264 CCCCGCTAGACAATCTTAACATCT 60.202 45.833 0.00 0.00 0.00 2.90
2749 3847 4.985409 CCCGCTAGACAATCTTAACATCTC 59.015 45.833 0.00 0.00 0.00 2.75
2750 3848 5.221342 CCCGCTAGACAATCTTAACATCTCT 60.221 44.000 0.00 0.00 0.00 3.10
2751 3849 6.276847 CCGCTAGACAATCTTAACATCTCTT 58.723 40.000 0.00 0.00 0.00 2.85
2752 3850 6.199908 CCGCTAGACAATCTTAACATCTCTTG 59.800 42.308 0.00 0.00 0.00 3.02
2753 3851 6.975197 CGCTAGACAATCTTAACATCTCTTGA 59.025 38.462 0.00 0.00 0.00 3.02
2754 3852 7.651304 CGCTAGACAATCTTAACATCTCTTGAT 59.349 37.037 0.00 0.00 0.00 2.57
2767 3865 6.419980 CATCTCTTGATGTGAACTCCTTTC 57.580 41.667 0.00 0.00 43.68 2.62
2768 3866 5.551305 TCTCTTGATGTGAACTCCTTTCA 57.449 39.130 0.00 0.00 42.26 2.69
2776 3874 3.208747 TGAACTCCTTTCACACCCTTC 57.791 47.619 0.00 0.00 39.45 3.46
2777 3875 2.507886 TGAACTCCTTTCACACCCTTCA 59.492 45.455 0.00 0.00 39.45 3.02
2778 3876 3.053991 TGAACTCCTTTCACACCCTTCAA 60.054 43.478 0.00 0.00 39.45 2.69
2779 3877 2.932261 ACTCCTTTCACACCCTTCAAC 58.068 47.619 0.00 0.00 0.00 3.18
2780 3878 2.241176 ACTCCTTTCACACCCTTCAACA 59.759 45.455 0.00 0.00 0.00 3.33
2781 3879 3.287222 CTCCTTTCACACCCTTCAACAA 58.713 45.455 0.00 0.00 0.00 2.83
2782 3880 3.699038 CTCCTTTCACACCCTTCAACAAA 59.301 43.478 0.00 0.00 0.00 2.83
2783 3881 4.090090 TCCTTTCACACCCTTCAACAAAA 58.910 39.130 0.00 0.00 0.00 2.44
2784 3882 4.714308 TCCTTTCACACCCTTCAACAAAAT 59.286 37.500 0.00 0.00 0.00 1.82
2785 3883 5.188751 TCCTTTCACACCCTTCAACAAAATT 59.811 36.000 0.00 0.00 0.00 1.82
2786 3884 5.879777 CCTTTCACACCCTTCAACAAAATTT 59.120 36.000 0.00 0.00 0.00 1.82
2787 3885 6.374053 CCTTTCACACCCTTCAACAAAATTTT 59.626 34.615 0.00 0.00 0.00 1.82
2788 3886 6.976636 TTCACACCCTTCAACAAAATTTTC 57.023 33.333 0.00 0.00 0.00 2.29
2789 3887 6.293004 TCACACCCTTCAACAAAATTTTCT 57.707 33.333 0.00 0.00 0.00 2.52
2790 3888 6.706295 TCACACCCTTCAACAAAATTTTCTT 58.294 32.000 0.00 0.00 0.00 2.52
2791 3889 6.816140 TCACACCCTTCAACAAAATTTTCTTC 59.184 34.615 0.00 0.00 0.00 2.87
2792 3890 6.593382 CACACCCTTCAACAAAATTTTCTTCA 59.407 34.615 0.00 0.00 0.00 3.02
2793 3891 6.593770 ACACCCTTCAACAAAATTTTCTTCAC 59.406 34.615 0.00 0.00 0.00 3.18
2794 3892 6.818142 CACCCTTCAACAAAATTTTCTTCACT 59.182 34.615 0.00 0.00 0.00 3.41
2795 3893 7.978975 CACCCTTCAACAAAATTTTCTTCACTA 59.021 33.333 0.00 0.00 0.00 2.74
2796 3894 8.197439 ACCCTTCAACAAAATTTTCTTCACTAG 58.803 33.333 0.00 0.00 0.00 2.57
2797 3895 7.169813 CCCTTCAACAAAATTTTCTTCACTAGC 59.830 37.037 0.00 0.00 0.00 3.42
2798 3896 7.706179 CCTTCAACAAAATTTTCTTCACTAGCA 59.294 33.333 0.00 0.00 0.00 3.49
2799 3897 7.985634 TCAACAAAATTTTCTTCACTAGCAC 57.014 32.000 0.00 0.00 0.00 4.40
2800 3898 7.771183 TCAACAAAATTTTCTTCACTAGCACT 58.229 30.769 0.00 0.00 0.00 4.40
2801 3899 7.701924 TCAACAAAATTTTCTTCACTAGCACTG 59.298 33.333 0.00 0.00 0.00 3.66
2802 3900 7.100458 ACAAAATTTTCTTCACTAGCACTGT 57.900 32.000 0.00 0.00 0.00 3.55
2803 3901 7.196331 ACAAAATTTTCTTCACTAGCACTGTC 58.804 34.615 0.00 0.00 0.00 3.51
2804 3902 6.942532 AAATTTTCTTCACTAGCACTGTCA 57.057 33.333 0.00 0.00 0.00 3.58
2805 3903 5.931441 ATTTTCTTCACTAGCACTGTCAC 57.069 39.130 0.00 0.00 0.00 3.67
2806 3904 3.386768 TTCTTCACTAGCACTGTCACC 57.613 47.619 0.00 0.00 0.00 4.02
2807 3905 1.618837 TCTTCACTAGCACTGTCACCC 59.381 52.381 0.00 0.00 0.00 4.61
2808 3906 0.685097 TTCACTAGCACTGTCACCCC 59.315 55.000 0.00 0.00 0.00 4.95
2809 3907 0.178932 TCACTAGCACTGTCACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
2810 3908 0.687354 CACTAGCACTGTCACCCCTT 59.313 55.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.857217 CATCTTGGCGATCAGTTCTCG 59.143 52.381 0.00 0.00 39.11 4.04
72 73 4.080919 ACAAAAAGCCAAGAGAAAAAGCCT 60.081 37.500 0.00 0.00 0.00 4.58
159 161 1.464608 CGTGTAACCAACATCAGCCAG 59.535 52.381 0.00 0.00 41.10 4.85
169 171 2.551287 CCAGGTCCATTCGTGTAACCAA 60.551 50.000 0.00 0.00 32.25 3.67
405 407 9.409312 CACTATGTTATGCATCTTGTTGAAAAA 57.591 29.630 0.19 0.00 38.94 1.94
524 533 3.535280 TGCAGCAATAAGTCGTCCATA 57.465 42.857 0.00 0.00 0.00 2.74
747 759 6.528321 TCATCTTGCTAATCCAACATCTAGG 58.472 40.000 0.00 0.00 0.00 3.02
797 809 4.755629 CAGAACATCCAGCTAATCCATCAG 59.244 45.833 0.00 0.00 0.00 2.90
1201 1251 1.128809 TCCCAACCAAACCCGCTCTA 61.129 55.000 0.00 0.00 0.00 2.43
2005 2084 3.130869 ACAACAGCAGCACTTTTCATCAA 59.869 39.130 0.00 0.00 0.00 2.57
2079 2266 4.332637 CACTTGCACAGCGGCACC 62.333 66.667 1.45 0.00 44.86 5.01
2128 2358 4.512944 GCAGCACTTATTCTATAGCAGCAA 59.487 41.667 0.00 0.00 35.09 3.91
2548 3646 2.306847 GCCTTCACTTTGAGGACCAAA 58.693 47.619 0.00 0.00 42.07 3.28
2549 3647 1.478654 GGCCTTCACTTTGAGGACCAA 60.479 52.381 0.00 0.00 0.00 3.67
2550 3648 0.110486 GGCCTTCACTTTGAGGACCA 59.890 55.000 0.00 0.00 0.00 4.02
2551 3649 0.609406 GGGCCTTCACTTTGAGGACC 60.609 60.000 0.84 0.00 36.28 4.46
2552 3650 0.110486 TGGGCCTTCACTTTGAGGAC 59.890 55.000 4.53 0.00 0.00 3.85
2553 3651 0.850100 TTGGGCCTTCACTTTGAGGA 59.150 50.000 4.53 0.00 0.00 3.71
2554 3652 1.341209 GTTTGGGCCTTCACTTTGAGG 59.659 52.381 4.53 0.00 0.00 3.86
2555 3653 2.310538 AGTTTGGGCCTTCACTTTGAG 58.689 47.619 4.53 0.00 0.00 3.02
2556 3654 2.452600 AGTTTGGGCCTTCACTTTGA 57.547 45.000 4.53 0.00 0.00 2.69
2557 3655 3.457234 GAAAGTTTGGGCCTTCACTTTG 58.543 45.455 24.03 0.00 39.13 2.77
2558 3656 2.434336 GGAAAGTTTGGGCCTTCACTTT 59.566 45.455 21.01 21.01 41.19 2.66
2559 3657 2.039418 GGAAAGTTTGGGCCTTCACTT 58.961 47.619 4.53 7.41 0.00 3.16
2560 3658 1.217942 AGGAAAGTTTGGGCCTTCACT 59.782 47.619 4.53 0.49 0.00 3.41
2561 3659 1.341209 CAGGAAAGTTTGGGCCTTCAC 59.659 52.381 4.53 0.00 0.00 3.18
2562 3660 1.703411 CAGGAAAGTTTGGGCCTTCA 58.297 50.000 4.53 0.00 0.00 3.02
2563 3661 0.969149 CCAGGAAAGTTTGGGCCTTC 59.031 55.000 4.53 0.00 0.00 3.46
2564 3662 0.560688 TCCAGGAAAGTTTGGGCCTT 59.439 50.000 4.53 0.00 35.13 4.35
2565 3663 0.113190 CTCCAGGAAAGTTTGGGCCT 59.887 55.000 4.53 0.00 35.13 5.19
2566 3664 0.112412 TCTCCAGGAAAGTTTGGGCC 59.888 55.000 0.00 0.00 35.13 5.80
2567 3665 1.889170 CTTCTCCAGGAAAGTTTGGGC 59.111 52.381 0.00 0.00 35.13 5.36
2568 3666 3.149981 GACTTCTCCAGGAAAGTTTGGG 58.850 50.000 14.61 0.00 35.13 4.12
2569 3667 3.820557 TGACTTCTCCAGGAAAGTTTGG 58.179 45.455 14.61 0.00 33.07 3.28
2570 3668 5.065914 TGATGACTTCTCCAGGAAAGTTTG 58.934 41.667 14.61 0.00 33.07 2.93
2571 3669 5.310409 TGATGACTTCTCCAGGAAAGTTT 57.690 39.130 14.61 8.48 33.07 2.66
2572 3670 4.982241 TGATGACTTCTCCAGGAAAGTT 57.018 40.909 14.61 4.40 33.07 2.66
2573 3671 4.982241 TTGATGACTTCTCCAGGAAAGT 57.018 40.909 13.77 13.77 33.07 2.66
2574 3672 7.928307 TTTATTGATGACTTCTCCAGGAAAG 57.072 36.000 8.90 8.90 33.07 2.62
2575 3673 7.944554 ACTTTTATTGATGACTTCTCCAGGAAA 59.055 33.333 0.00 0.00 33.07 3.13
2576 3674 7.461749 ACTTTTATTGATGACTTCTCCAGGAA 58.538 34.615 0.00 0.00 0.00 3.36
2577 3675 7.020827 ACTTTTATTGATGACTTCTCCAGGA 57.979 36.000 0.00 0.00 0.00 3.86
2578 3676 6.881065 TGACTTTTATTGATGACTTCTCCAGG 59.119 38.462 0.00 0.00 0.00 4.45
2579 3677 7.388776 TGTGACTTTTATTGATGACTTCTCCAG 59.611 37.037 0.00 0.00 0.00 3.86
2580 3678 7.223584 TGTGACTTTTATTGATGACTTCTCCA 58.776 34.615 0.00 0.00 0.00 3.86
2581 3679 7.672983 TGTGACTTTTATTGATGACTTCTCC 57.327 36.000 0.00 0.00 0.00 3.71
2582 3680 9.604626 CTTTGTGACTTTTATTGATGACTTCTC 57.395 33.333 0.00 0.00 0.00 2.87
2583 3681 9.125026 ACTTTGTGACTTTTATTGATGACTTCT 57.875 29.630 0.00 0.00 0.00 2.85
2586 3684 9.561069 AGTACTTTGTGACTTTTATTGATGACT 57.439 29.630 0.00 0.00 0.00 3.41
2593 3691 9.281371 GGTCCTAAGTACTTTGTGACTTTTATT 57.719 33.333 23.58 0.82 37.16 1.40
2594 3692 8.434392 TGGTCCTAAGTACTTTGTGACTTTTAT 58.566 33.333 23.58 1.16 37.16 1.40
2595 3693 7.712205 GTGGTCCTAAGTACTTTGTGACTTTTA 59.288 37.037 23.58 13.51 37.16 1.52
2596 3694 6.541278 GTGGTCCTAAGTACTTTGTGACTTTT 59.459 38.462 23.58 1.72 37.16 2.27
2597 3695 6.053650 GTGGTCCTAAGTACTTTGTGACTTT 58.946 40.000 23.58 2.30 37.16 2.66
2598 3696 5.454329 GGTGGTCCTAAGTACTTTGTGACTT 60.454 44.000 23.58 4.30 39.25 3.01
2599 3697 4.040095 GGTGGTCCTAAGTACTTTGTGACT 59.960 45.833 23.58 3.44 0.00 3.41
2600 3698 4.202284 TGGTGGTCCTAAGTACTTTGTGAC 60.202 45.833 14.49 18.16 34.23 3.67
2601 3699 3.968649 TGGTGGTCCTAAGTACTTTGTGA 59.031 43.478 14.49 8.52 34.23 3.58
2602 3700 4.345859 TGGTGGTCCTAAGTACTTTGTG 57.654 45.455 14.49 6.35 34.23 3.33
2603 3701 4.657039 TCTTGGTGGTCCTAAGTACTTTGT 59.343 41.667 14.49 0.00 34.23 2.83
2604 3702 5.011738 TCTCTTGGTGGTCCTAAGTACTTTG 59.988 44.000 14.49 11.84 34.23 2.77
2605 3703 5.152934 TCTCTTGGTGGTCCTAAGTACTTT 58.847 41.667 14.49 0.00 34.23 2.66
2606 3704 4.748701 TCTCTTGGTGGTCCTAAGTACTT 58.251 43.478 13.68 13.68 34.23 2.24
2607 3705 4.399483 TCTCTTGGTGGTCCTAAGTACT 57.601 45.455 0.00 0.00 34.23 2.73
2608 3706 4.957327 AGATCTCTTGGTGGTCCTAAGTAC 59.043 45.833 0.00 0.00 34.23 2.73
2609 3707 5.208294 AGATCTCTTGGTGGTCCTAAGTA 57.792 43.478 0.00 0.00 34.23 2.24
2610 3708 4.067944 AGATCTCTTGGTGGTCCTAAGT 57.932 45.455 0.00 0.00 34.23 2.24
2611 3709 5.163395 GGTAAGATCTCTTGGTGGTCCTAAG 60.163 48.000 0.00 0.00 37.40 2.18
2612 3710 4.715297 GGTAAGATCTCTTGGTGGTCCTAA 59.285 45.833 0.00 0.00 37.40 2.69
2613 3711 4.287552 GGTAAGATCTCTTGGTGGTCCTA 58.712 47.826 0.00 0.00 37.40 2.94
2614 3712 3.108376 GGTAAGATCTCTTGGTGGTCCT 58.892 50.000 0.00 0.00 37.40 3.85
2615 3713 2.159085 CGGTAAGATCTCTTGGTGGTCC 60.159 54.545 0.00 0.00 37.40 4.46
2616 3714 2.758979 TCGGTAAGATCTCTTGGTGGTC 59.241 50.000 0.00 0.00 37.40 4.02
2617 3715 2.496470 GTCGGTAAGATCTCTTGGTGGT 59.504 50.000 0.00 0.00 37.40 4.16
2618 3716 2.496070 TGTCGGTAAGATCTCTTGGTGG 59.504 50.000 0.00 0.00 37.40 4.61
2619 3717 3.193691 ACTGTCGGTAAGATCTCTTGGTG 59.806 47.826 0.00 0.00 37.40 4.17
2620 3718 3.432378 ACTGTCGGTAAGATCTCTTGGT 58.568 45.455 0.00 0.00 37.40 3.67
2621 3719 4.457834 AACTGTCGGTAAGATCTCTTGG 57.542 45.455 0.00 0.00 37.40 3.61
2622 3720 4.092091 GCAAACTGTCGGTAAGATCTCTTG 59.908 45.833 0.00 0.00 37.40 3.02
2623 3721 4.246458 GCAAACTGTCGGTAAGATCTCTT 58.754 43.478 0.00 0.00 39.85 2.85
2624 3722 3.258372 TGCAAACTGTCGGTAAGATCTCT 59.742 43.478 0.00 0.00 0.00 3.10
2625 3723 3.585862 TGCAAACTGTCGGTAAGATCTC 58.414 45.455 0.00 0.00 0.00 2.75
2626 3724 3.678056 TGCAAACTGTCGGTAAGATCT 57.322 42.857 0.00 0.00 0.00 2.75
2627 3725 4.024387 TGTTTGCAAACTGTCGGTAAGATC 60.024 41.667 35.09 10.99 39.59 2.75
2628 3726 3.880490 TGTTTGCAAACTGTCGGTAAGAT 59.120 39.130 35.09 0.00 39.59 2.40
2629 3727 3.271729 TGTTTGCAAACTGTCGGTAAGA 58.728 40.909 35.09 14.26 39.59 2.10
2630 3728 3.684103 TGTTTGCAAACTGTCGGTAAG 57.316 42.857 35.09 0.00 39.59 2.34
2631 3729 3.628032 TGATGTTTGCAAACTGTCGGTAA 59.372 39.130 35.09 18.05 39.59 2.85
2632 3730 3.206964 TGATGTTTGCAAACTGTCGGTA 58.793 40.909 35.09 18.71 39.59 4.02
2633 3731 2.020720 TGATGTTTGCAAACTGTCGGT 58.979 42.857 35.09 18.09 39.59 4.69
2634 3732 2.290367 TCTGATGTTTGCAAACTGTCGG 59.710 45.455 35.09 32.41 39.59 4.79
2635 3733 3.607422 TCTGATGTTTGCAAACTGTCG 57.393 42.857 35.09 25.97 39.59 4.35
2636 3734 5.284079 ACATTCTGATGTTTGCAAACTGTC 58.716 37.500 35.09 30.54 43.92 3.51
2637 3735 5.266733 ACATTCTGATGTTTGCAAACTGT 57.733 34.783 35.09 26.91 43.92 3.55
2638 3736 7.085746 TGATACATTCTGATGTTTGCAAACTG 58.914 34.615 35.09 26.36 43.92 3.16
2639 3737 7.218228 TGATACATTCTGATGTTTGCAAACT 57.782 32.000 35.09 23.64 43.92 2.66
2640 3738 7.596248 ACTTGATACATTCTGATGTTTGCAAAC 59.404 33.333 30.95 30.95 43.92 2.93
2641 3739 7.660112 ACTTGATACATTCTGATGTTTGCAAA 58.340 30.769 8.05 8.05 43.92 3.68
2642 3740 7.218228 ACTTGATACATTCTGATGTTTGCAA 57.782 32.000 0.00 0.00 43.92 4.08
2643 3741 6.127925 GGACTTGATACATTCTGATGTTTGCA 60.128 38.462 0.00 0.00 43.92 4.08
2644 3742 6.127925 TGGACTTGATACATTCTGATGTTTGC 60.128 38.462 0.00 0.00 43.92 3.68
2645 3743 7.381766 TGGACTTGATACATTCTGATGTTTG 57.618 36.000 0.00 0.00 43.92 2.93
2646 3744 7.448161 TGTTGGACTTGATACATTCTGATGTTT 59.552 33.333 0.00 0.00 43.92 2.83
2647 3745 6.942005 TGTTGGACTTGATACATTCTGATGTT 59.058 34.615 0.00 0.00 43.92 2.71
2649 3747 6.990341 TGTTGGACTTGATACATTCTGATG 57.010 37.500 0.00 0.00 39.25 3.07
2650 3748 7.571919 AGATGTTGGACTTGATACATTCTGAT 58.428 34.615 0.00 0.00 31.76 2.90
2651 3749 6.950842 AGATGTTGGACTTGATACATTCTGA 58.049 36.000 0.00 0.00 31.76 3.27
2652 3750 7.621428 AAGATGTTGGACTTGATACATTCTG 57.379 36.000 0.00 0.00 31.76 3.02
2653 3751 7.989741 CCTAAGATGTTGGACTTGATACATTCT 59.010 37.037 0.00 0.00 31.76 2.40
2654 3752 7.254932 GCCTAAGATGTTGGACTTGATACATTC 60.255 40.741 0.00 0.00 31.76 2.67
2655 3753 6.543831 GCCTAAGATGTTGGACTTGATACATT 59.456 38.462 0.00 0.00 31.76 2.71
2656 3754 6.058183 GCCTAAGATGTTGGACTTGATACAT 58.942 40.000 0.00 0.00 34.14 2.29
2657 3755 5.189736 AGCCTAAGATGTTGGACTTGATACA 59.810 40.000 0.00 0.00 0.00 2.29
2658 3756 5.675538 AGCCTAAGATGTTGGACTTGATAC 58.324 41.667 0.00 0.00 0.00 2.24
2659 3757 5.957771 AGCCTAAGATGTTGGACTTGATA 57.042 39.130 0.00 0.00 0.00 2.15
2660 3758 4.851639 AGCCTAAGATGTTGGACTTGAT 57.148 40.909 0.00 0.00 0.00 2.57
2661 3759 4.287067 AGAAGCCTAAGATGTTGGACTTGA 59.713 41.667 0.00 0.00 0.00 3.02
2662 3760 4.583871 AGAAGCCTAAGATGTTGGACTTG 58.416 43.478 0.00 0.00 0.00 3.16
2663 3761 4.917906 AGAAGCCTAAGATGTTGGACTT 57.082 40.909 0.00 0.00 0.00 3.01
2664 3762 4.042187 ACAAGAAGCCTAAGATGTTGGACT 59.958 41.667 0.00 0.00 0.00 3.85
2665 3763 4.154918 CACAAGAAGCCTAAGATGTTGGAC 59.845 45.833 0.00 0.00 0.00 4.02
2666 3764 4.041567 TCACAAGAAGCCTAAGATGTTGGA 59.958 41.667 0.00 0.00 0.00 3.53
2667 3765 4.326826 TCACAAGAAGCCTAAGATGTTGG 58.673 43.478 0.00 0.00 0.00 3.77
2668 3766 4.394300 CCTCACAAGAAGCCTAAGATGTTG 59.606 45.833 0.00 0.00 0.00 3.33
2669 3767 4.287067 TCCTCACAAGAAGCCTAAGATGTT 59.713 41.667 0.00 0.00 0.00 2.71
2670 3768 3.840666 TCCTCACAAGAAGCCTAAGATGT 59.159 43.478 0.00 0.00 0.00 3.06
2671 3769 4.440880 CTCCTCACAAGAAGCCTAAGATG 58.559 47.826 0.00 0.00 0.00 2.90
2672 3770 3.454082 CCTCCTCACAAGAAGCCTAAGAT 59.546 47.826 0.00 0.00 0.00 2.40
2673 3771 2.834549 CCTCCTCACAAGAAGCCTAAGA 59.165 50.000 0.00 0.00 0.00 2.10
2674 3772 2.569404 ACCTCCTCACAAGAAGCCTAAG 59.431 50.000 0.00 0.00 0.00 2.18
2675 3773 2.621070 ACCTCCTCACAAGAAGCCTAA 58.379 47.619 0.00 0.00 0.00 2.69
2676 3774 2.327325 ACCTCCTCACAAGAAGCCTA 57.673 50.000 0.00 0.00 0.00 3.93
2677 3775 2.183679 CTACCTCCTCACAAGAAGCCT 58.816 52.381 0.00 0.00 0.00 4.58
2678 3776 2.167487 CTCTACCTCCTCACAAGAAGCC 59.833 54.545 0.00 0.00 0.00 4.35
2679 3777 2.829120 ACTCTACCTCCTCACAAGAAGC 59.171 50.000 0.00 0.00 0.00 3.86
2680 3778 4.340617 AGACTCTACCTCCTCACAAGAAG 58.659 47.826 0.00 0.00 0.00 2.85
2681 3779 4.390129 AGACTCTACCTCCTCACAAGAA 57.610 45.455 0.00 0.00 0.00 2.52
2682 3780 4.082845 CAAGACTCTACCTCCTCACAAGA 58.917 47.826 0.00 0.00 0.00 3.02
2683 3781 4.082845 TCAAGACTCTACCTCCTCACAAG 58.917 47.826 0.00 0.00 0.00 3.16
2684 3782 4.114015 TCAAGACTCTACCTCCTCACAA 57.886 45.455 0.00 0.00 0.00 3.33
2685 3783 3.808834 TCAAGACTCTACCTCCTCACA 57.191 47.619 0.00 0.00 0.00 3.58
2686 3784 3.445805 CCTTCAAGACTCTACCTCCTCAC 59.554 52.174 0.00 0.00 0.00 3.51
2687 3785 3.702792 CCTTCAAGACTCTACCTCCTCA 58.297 50.000 0.00 0.00 0.00 3.86
2688 3786 2.429250 GCCTTCAAGACTCTACCTCCTC 59.571 54.545 0.00 0.00 0.00 3.71
2689 3787 2.225394 TGCCTTCAAGACTCTACCTCCT 60.225 50.000 0.00 0.00 0.00 3.69
2690 3788 2.180276 TGCCTTCAAGACTCTACCTCC 58.820 52.381 0.00 0.00 0.00 4.30
2691 3789 3.259625 AGTTGCCTTCAAGACTCTACCTC 59.740 47.826 0.00 0.00 31.93 3.85
2692 3790 3.243724 AGTTGCCTTCAAGACTCTACCT 58.756 45.455 0.00 0.00 31.93 3.08
2693 3791 3.686916 AGTTGCCTTCAAGACTCTACC 57.313 47.619 0.00 0.00 31.93 3.18
2694 3792 4.816925 ACAAAGTTGCCTTCAAGACTCTAC 59.183 41.667 0.00 0.00 31.93 2.59
2695 3793 4.816385 CACAAAGTTGCCTTCAAGACTCTA 59.184 41.667 0.00 0.00 31.93 2.43
2696 3794 3.629398 CACAAAGTTGCCTTCAAGACTCT 59.371 43.478 0.00 0.00 31.93 3.24
2697 3795 3.378427 ACACAAAGTTGCCTTCAAGACTC 59.622 43.478 0.00 0.00 31.93 3.36
2698 3796 3.356290 ACACAAAGTTGCCTTCAAGACT 58.644 40.909 0.00 0.00 31.93 3.24
2699 3797 3.782889 ACACAAAGTTGCCTTCAAGAC 57.217 42.857 0.00 0.00 31.93 3.01
2700 3798 4.947388 AGTAACACAAAGTTGCCTTCAAGA 59.053 37.500 0.00 0.00 42.99 3.02
2701 3799 5.248870 AGTAACACAAAGTTGCCTTCAAG 57.751 39.130 0.00 0.00 42.99 3.02
2702 3800 5.393678 GGAAGTAACACAAAGTTGCCTTCAA 60.394 40.000 16.66 0.00 43.74 2.69
2703 3801 4.097286 GGAAGTAACACAAAGTTGCCTTCA 59.903 41.667 16.66 0.00 43.74 3.02
2704 3802 4.499188 GGGAAGTAACACAAAGTTGCCTTC 60.499 45.833 10.90 10.90 42.99 3.46
2705 3803 3.383505 GGGAAGTAACACAAAGTTGCCTT 59.616 43.478 0.00 0.00 42.99 4.35
2706 3804 2.956333 GGGAAGTAACACAAAGTTGCCT 59.044 45.455 0.00 0.00 42.99 4.75
2707 3805 2.035449 GGGGAAGTAACACAAAGTTGCC 59.965 50.000 0.00 0.00 42.99 4.52
2708 3806 2.287368 CGGGGAAGTAACACAAAGTTGC 60.287 50.000 0.00 0.00 41.50 4.17
2709 3807 2.287368 GCGGGGAAGTAACACAAAGTTG 60.287 50.000 0.00 0.00 41.50 3.16
2710 3808 1.951602 GCGGGGAAGTAACACAAAGTT 59.048 47.619 0.00 0.00 44.27 2.66
2711 3809 1.142262 AGCGGGGAAGTAACACAAAGT 59.858 47.619 0.00 0.00 0.00 2.66
2712 3810 1.892209 AGCGGGGAAGTAACACAAAG 58.108 50.000 0.00 0.00 0.00 2.77
2713 3811 2.633967 TCTAGCGGGGAAGTAACACAAA 59.366 45.455 0.00 0.00 0.00 2.83
2714 3812 2.028748 GTCTAGCGGGGAAGTAACACAA 60.029 50.000 0.00 0.00 0.00 3.33
2715 3813 1.547372 GTCTAGCGGGGAAGTAACACA 59.453 52.381 0.00 0.00 0.00 3.72
2716 3814 1.547372 TGTCTAGCGGGGAAGTAACAC 59.453 52.381 0.00 0.00 0.00 3.32
2717 3815 1.927487 TGTCTAGCGGGGAAGTAACA 58.073 50.000 0.00 0.00 0.00 2.41
2718 3816 3.132467 AGATTGTCTAGCGGGGAAGTAAC 59.868 47.826 0.00 0.00 0.00 2.50
2719 3817 3.371965 AGATTGTCTAGCGGGGAAGTAA 58.628 45.455 0.00 0.00 0.00 2.24
2720 3818 3.028094 AGATTGTCTAGCGGGGAAGTA 57.972 47.619 0.00 0.00 0.00 2.24
2721 3819 1.867363 AGATTGTCTAGCGGGGAAGT 58.133 50.000 0.00 0.00 0.00 3.01
2722 3820 2.990066 AAGATTGTCTAGCGGGGAAG 57.010 50.000 0.00 0.00 0.00 3.46
2723 3821 3.516300 TGTTAAGATTGTCTAGCGGGGAA 59.484 43.478 0.00 0.00 0.00 3.97
2724 3822 3.101437 TGTTAAGATTGTCTAGCGGGGA 58.899 45.455 0.00 0.00 0.00 4.81
2725 3823 3.536956 TGTTAAGATTGTCTAGCGGGG 57.463 47.619 0.00 0.00 0.00 5.73
2726 3824 4.950050 AGATGTTAAGATTGTCTAGCGGG 58.050 43.478 0.00 0.00 0.00 6.13
2727 3825 5.837437 AGAGATGTTAAGATTGTCTAGCGG 58.163 41.667 0.00 0.00 0.00 5.52
2728 3826 6.975197 TCAAGAGATGTTAAGATTGTCTAGCG 59.025 38.462 0.51 0.00 0.00 4.26
2729 3827 8.763356 CATCAAGAGATGTTAAGATTGTCTAGC 58.237 37.037 0.00 0.00 45.28 3.42
2744 3842 5.936372 TGAAAGGAGTTCACATCAAGAGATG 59.064 40.000 4.06 4.06 44.07 2.90
2745 3843 6.119240 TGAAAGGAGTTCACATCAAGAGAT 57.881 37.500 0.00 0.00 41.47 2.75
2746 3844 5.551305 TGAAAGGAGTTCACATCAAGAGA 57.449 39.130 0.00 0.00 41.47 3.10
2756 3854 2.507886 TGAAGGGTGTGAAAGGAGTTCA 59.492 45.455 0.00 0.00 44.20 3.18
2757 3855 3.208747 TGAAGGGTGTGAAAGGAGTTC 57.791 47.619 0.00 0.00 36.70 3.01
2758 3856 3.288092 GTTGAAGGGTGTGAAAGGAGTT 58.712 45.455 0.00 0.00 0.00 3.01
2759 3857 2.241176 TGTTGAAGGGTGTGAAAGGAGT 59.759 45.455 0.00 0.00 0.00 3.85
2760 3858 2.930950 TGTTGAAGGGTGTGAAAGGAG 58.069 47.619 0.00 0.00 0.00 3.69
2761 3859 3.374042 TTGTTGAAGGGTGTGAAAGGA 57.626 42.857 0.00 0.00 0.00 3.36
2762 3860 4.464069 TTTTGTTGAAGGGTGTGAAAGG 57.536 40.909 0.00 0.00 0.00 3.11
2763 3861 6.983474 AAATTTTGTTGAAGGGTGTGAAAG 57.017 33.333 0.00 0.00 0.00 2.62
2764 3862 7.164803 AGAAAATTTTGTTGAAGGGTGTGAAA 58.835 30.769 8.47 0.00 0.00 2.69
2765 3863 6.706295 AGAAAATTTTGTTGAAGGGTGTGAA 58.294 32.000 8.47 0.00 0.00 3.18
2766 3864 6.293004 AGAAAATTTTGTTGAAGGGTGTGA 57.707 33.333 8.47 0.00 0.00 3.58
2767 3865 6.593382 TGAAGAAAATTTTGTTGAAGGGTGTG 59.407 34.615 17.17 0.00 0.00 3.82
2768 3866 6.593770 GTGAAGAAAATTTTGTTGAAGGGTGT 59.406 34.615 17.17 0.00 0.00 4.16
2769 3867 6.818142 AGTGAAGAAAATTTTGTTGAAGGGTG 59.182 34.615 17.17 0.00 0.00 4.61
2770 3868 6.946340 AGTGAAGAAAATTTTGTTGAAGGGT 58.054 32.000 17.17 0.00 0.00 4.34
2771 3869 7.169813 GCTAGTGAAGAAAATTTTGTTGAAGGG 59.830 37.037 17.17 6.66 0.00 3.95
2772 3870 7.706179 TGCTAGTGAAGAAAATTTTGTTGAAGG 59.294 33.333 17.17 4.98 0.00 3.46
2773 3871 8.534778 GTGCTAGTGAAGAAAATTTTGTTGAAG 58.465 33.333 17.17 6.37 0.00 3.02
2774 3872 8.250332 AGTGCTAGTGAAGAAAATTTTGTTGAA 58.750 29.630 17.17 3.78 0.00 2.69
2775 3873 7.701924 CAGTGCTAGTGAAGAAAATTTTGTTGA 59.298 33.333 17.17 6.94 0.00 3.18
2776 3874 7.489113 ACAGTGCTAGTGAAGAAAATTTTGTTG 59.511 33.333 17.17 4.70 0.00 3.33
2777 3875 7.547227 ACAGTGCTAGTGAAGAAAATTTTGTT 58.453 30.769 12.70 12.70 0.00 2.83
2778 3876 7.100458 ACAGTGCTAGTGAAGAAAATTTTGT 57.900 32.000 8.47 0.47 0.00 2.83
2779 3877 7.166473 GTGACAGTGCTAGTGAAGAAAATTTTG 59.834 37.037 8.47 0.00 0.00 2.44
2780 3878 7.196331 GTGACAGTGCTAGTGAAGAAAATTTT 58.804 34.615 2.28 2.28 0.00 1.82
2781 3879 6.238759 GGTGACAGTGCTAGTGAAGAAAATTT 60.239 38.462 0.00 0.00 0.00 1.82
2782 3880 5.239525 GGTGACAGTGCTAGTGAAGAAAATT 59.760 40.000 0.00 0.00 0.00 1.82
2783 3881 4.757149 GGTGACAGTGCTAGTGAAGAAAAT 59.243 41.667 0.00 0.00 0.00 1.82
2784 3882 4.127171 GGTGACAGTGCTAGTGAAGAAAA 58.873 43.478 0.00 0.00 0.00 2.29
2785 3883 3.494398 GGGTGACAGTGCTAGTGAAGAAA 60.494 47.826 0.00 0.00 0.00 2.52
2786 3884 2.037251 GGGTGACAGTGCTAGTGAAGAA 59.963 50.000 0.00 0.00 0.00 2.52
2787 3885 1.618837 GGGTGACAGTGCTAGTGAAGA 59.381 52.381 0.00 0.00 0.00 2.87
2788 3886 1.338200 GGGGTGACAGTGCTAGTGAAG 60.338 57.143 0.00 0.00 0.00 3.02
2789 3887 0.685097 GGGGTGACAGTGCTAGTGAA 59.315 55.000 0.00 0.00 0.00 3.18
2790 3888 0.178932 AGGGGTGACAGTGCTAGTGA 60.179 55.000 0.00 0.00 0.00 3.41
2791 3889 0.687354 AAGGGGTGACAGTGCTAGTG 59.313 55.000 0.00 0.00 0.00 2.74
2792 3890 3.165657 AAGGGGTGACAGTGCTAGT 57.834 52.632 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.