Multiple sequence alignment - TraesCS1B01G172200

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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 TraesCS1B01G172200 chr1B 100.000 3616 0 0 1 3616 307169842 307173457 0.000000e+00 6678
1 TraesCS1B01G172200 chr1B 82.079 279 40 9 2985 3260 171104543 171104814 2.810000e-56 230
2 TraesCS1B01G172200 chr1D 93.818 2103 77 14 850 2909 214266524 214268616 0.000000e+00 3114
3 TraesCS1B01G172200 chr1D 88.343 875 61 19 1 845 214265039 214265902 0.000000e+00 1013
4 TraesCS1B01G172200 chr1D 82.051 351 54 9 2919 3263 426388467 426388814 1.270000e-74 291
5 TraesCS1B01G172200 chr1D 86.636 217 18 5 3397 3612 214269135 214269341 2.810000e-56 230
6 TraesCS1B01G172200 chr1D 72.642 424 86 20 2035 2443 18210261 18210669 2.950000e-21 113
7 TraesCS1B01G172200 chr2A 81.768 1459 215 25 1101 2539 156481327 156482754 0.000000e+00 1173
8 TraesCS1B01G172200 chr2D 80.643 1524 224 30 1039 2539 145733148 145731673 0.000000e+00 1114
9 TraesCS1B01G172200 chr6B 75.806 868 148 37 1071 1914 683486909 683487738 2.040000e-102 383
10 TraesCS1B01G172200 chr1A 85.263 285 16 14 2552 2811 272212529 272212812 1.650000e-68 270
11 TraesCS1B01G172200 chr1A 88.670 203 19 2 3219 3418 272598279 272598480 1.000000e-60 244
12 TraesCS1B01G172200 chr6A 79.016 305 49 11 2967 3263 493746819 493746522 1.020000e-45 195
13 TraesCS1B01G172200 chr3A 78.738 301 52 7 2961 3252 724027134 724027431 1.330000e-44 191
14 TraesCS1B01G172200 chr3D 87.248 149 16 3 3095 3240 458315028 458315176 2.230000e-37 167
15 TraesCS1B01G172200 chrUn 79.468 263 31 12 2949 3189 113054265 113054526 8.030000e-37 165
16 TraesCS1B01G172200 chr3B 83.660 153 22 2 3097 3246 605504189 605504341 1.350000e-29 141
17 TraesCS1B01G172200 chr7D 80.982 163 26 3 3101 3263 38205544 38205387 1.360000e-24 124
18 TraesCS1B01G172200 chr4A 89.773 88 9 0 3101 3188 642180768 642180855 2.950000e-21 113


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 TraesCS1B01G172200 chr1B 307169842 307173457 3615 False 6678.000000 6678 100.000 1 3616 1 chr1B.!!$F2 3615
1 TraesCS1B01G172200 chr1D 214265039 214269341 4302 False 1452.333333 3114 89.599 1 3612 3 chr1D.!!$F3 3611
2 TraesCS1B01G172200 chr2A 156481327 156482754 1427 False 1173.000000 1173 81.768 1101 2539 1 chr2A.!!$F1 1438
3 TraesCS1B01G172200 chr2D 145731673 145733148 1475 True 1114.000000 1114 80.643 1039 2539 1 chr2D.!!$R1 1500
4 TraesCS1B01G172200 chr6B 683486909 683487738 829 False 383.000000 383 75.806 1071 1914 1 chr6B.!!$F1 843

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
688 716 0.029834 CCACTGCTGCAACTGAACAC 59.97 55.0 3.02 0.0 0.00 3.32 F
723 751 0.250467 ATCGGCTCAACTGTGCAACT 60.25 50.0 6.14 0.0 38.04 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 3010 0.109319 GTGTTGGCGCGAATCCAATT 60.109 50.0 17.76 0.0 44.49 2.32 R
2708 3436 0.371645 CGTTCTGGCTTGAATCGCTC 59.628 55.0 0.00 0.0 0.00 5.03 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
26 27 7.171678 GCTAAGAACAATAGAGTGTCACTTGTT 59.828 37.037 16.91 16.91 41.36 2.83
29 30 3.815401 ACAATAGAGTGTCACTTGTTGCC 59.185 43.478 7.00 0.00 0.00 4.52
32 33 3.113260 AGAGTGTCACTTGTTGCCTAC 57.887 47.619 7.00 0.00 0.00 3.18
41 42 4.278170 TCACTTGTTGCCTACCTTTTGATG 59.722 41.667 0.00 0.00 0.00 3.07
43 44 4.037923 ACTTGTTGCCTACCTTTTGATGTG 59.962 41.667 0.00 0.00 0.00 3.21
53 54 6.370442 CCTACCTTTTGATGTGTAAATCGTGA 59.630 38.462 0.00 0.00 0.00 4.35
61 62 3.822940 TGTGTAAATCGTGACCCCTTTT 58.177 40.909 0.00 0.00 0.00 2.27
62 63 3.566322 TGTGTAAATCGTGACCCCTTTTG 59.434 43.478 0.00 0.00 0.00 2.44
64 65 3.816523 TGTAAATCGTGACCCCTTTTGTC 59.183 43.478 0.00 0.00 0.00 3.18
65 66 2.951229 AATCGTGACCCCTTTTGTCT 57.049 45.000 0.00 0.00 33.83 3.41
66 67 2.185004 ATCGTGACCCCTTTTGTCTG 57.815 50.000 0.00 0.00 33.83 3.51
67 68 0.834612 TCGTGACCCCTTTTGTCTGT 59.165 50.000 0.00 0.00 33.83 3.41
68 69 1.202604 TCGTGACCCCTTTTGTCTGTC 60.203 52.381 0.00 0.00 33.83 3.51
70 71 0.107831 TGACCCCTTTTGTCTGTCGG 59.892 55.000 0.00 0.00 33.83 4.79
71 72 0.108019 GACCCCTTTTGTCTGTCGGT 59.892 55.000 0.00 0.00 0.00 4.69
73 74 0.107831 CCCCTTTTGTCTGTCGGTGA 59.892 55.000 0.00 0.00 0.00 4.02
97 98 3.406361 GCCTCACGCAGTCACACG 61.406 66.667 0.00 0.00 41.61 4.49
101 102 0.040336 CTCACGCAGTCACACGTAGT 60.040 55.000 0.00 0.00 41.61 2.73
104 105 1.213094 ACGCAGTCACACGTAGTTGC 61.213 55.000 0.00 0.00 32.01 4.17
118 119 5.513849 CACGTAGTTGCGATGTCTTGTAATA 59.486 40.000 0.00 0.00 41.61 0.98
121 122 6.129168 CGTAGTTGCGATGTCTTGTAATATCC 60.129 42.308 0.00 0.00 0.00 2.59
159 161 2.741985 CCTTCATGCGACGCCACA 60.742 61.111 18.69 0.00 0.00 4.17
172 174 1.901085 GCCACACCCTCTCGATCTT 59.099 57.895 0.00 0.00 0.00 2.40
175 177 1.134965 CCACACCCTCTCGATCTTCAC 60.135 57.143 0.00 0.00 0.00 3.18
180 182 1.479709 CCTCTCGATCTTCACTGGGT 58.520 55.000 0.00 0.00 0.00 4.51
233 235 7.939784 AAAGTAAAGGTTCTCTTGTTTGTCT 57.060 32.000 0.00 0.00 35.55 3.41
234 236 9.457436 AAAAGTAAAGGTTCTCTTGTTTGTCTA 57.543 29.630 0.00 0.00 35.55 2.59
243 245 9.452065 GGTTCTCTTGTTTGTCTATTCTTTTTC 57.548 33.333 0.00 0.00 0.00 2.29
259 261 8.697507 ATTCTTTTTCTTAGAGAACCACACAT 57.302 30.769 0.00 0.00 33.26 3.21
321 323 5.427481 TGGTTATACCTAGAAAAGACCAGGG 59.573 44.000 0.00 0.00 39.58 4.45
328 330 1.072965 AGAAAAGACCAGGGCTGACAG 59.927 52.381 0.00 0.00 0.00 3.51
332 334 3.909086 GACCAGGGCTGACAGGTGC 62.909 68.421 4.26 0.00 33.77 5.01
346 348 4.134563 GACAGGTGCCTAGAAAACTTTGA 58.865 43.478 0.00 0.00 0.00 2.69
404 407 0.181350 CCTCAAGGTCCCTGCATACC 59.819 60.000 5.15 5.15 35.91 2.73
420 423 3.198068 CATACCACCAGATCTGAAACCG 58.802 50.000 24.62 9.25 0.00 4.44
425 428 1.303309 CCAGATCTGAAACCGCCATC 58.697 55.000 24.62 0.00 0.00 3.51
439 442 1.221566 CCATCGTCCACCAGCATCA 59.778 57.895 0.00 0.00 0.00 3.07
441 444 0.107993 CATCGTCCACCAGCATCACT 60.108 55.000 0.00 0.00 0.00 3.41
442 445 0.615331 ATCGTCCACCAGCATCACTT 59.385 50.000 0.00 0.00 0.00 3.16
446 449 0.036732 TCCACCAGCATCACTTGGAC 59.963 55.000 0.00 0.00 31.50 4.02
455 458 3.345808 CACTTGGACGCACACCCG 61.346 66.667 0.00 0.00 0.00 5.28
476 479 3.269178 GAGGAAGAGGTGAAGCATCAAG 58.731 50.000 0.00 0.00 37.30 3.02
486 489 5.104982 AGGTGAAGCATCAAGAAACCAAAAA 60.105 36.000 0.00 0.00 37.30 1.94
515 543 1.810031 GCGCCATAGCCAGACATGTAA 60.810 52.381 0.00 0.00 34.57 2.41
521 549 5.677091 GCCATAGCCAGACATGTAAAAACAG 60.677 44.000 0.00 0.00 0.00 3.16
548 576 2.202756 GATGTGGCGAGTCGGTCC 60.203 66.667 15.52 8.48 0.00 4.46
558 586 1.669211 CGAGTCGGTCCAGAAAGTTCC 60.669 57.143 4.10 0.00 0.00 3.62
598 626 2.361438 AGATCTAACGAATCCCACGACC 59.639 50.000 0.00 0.00 34.70 4.79
630 658 0.459585 GAACGCCTAATCTGTCGCCA 60.460 55.000 0.00 0.00 0.00 5.69
656 684 2.614734 GCTACCAACCTTGTACCAGGAC 60.615 54.545 19.49 0.00 37.39 3.85
673 701 1.203013 GGACCAAACCTAAAGCCCACT 60.203 52.381 0.00 0.00 0.00 4.00
685 713 2.195567 GCCCACTGCTGCAACTGAA 61.196 57.895 3.02 0.00 36.87 3.02
687 715 1.102809 CCCACTGCTGCAACTGAACA 61.103 55.000 3.02 0.00 0.00 3.18
688 716 0.029834 CCACTGCTGCAACTGAACAC 59.970 55.000 3.02 0.00 0.00 3.32
723 751 0.250467 ATCGGCTCAACTGTGCAACT 60.250 50.000 6.14 0.00 38.04 3.16
724 752 0.391228 TCGGCTCAACTGTGCAACTA 59.609 50.000 6.14 0.00 38.04 2.24
738 766 0.982673 CAACTAGGAAGAACGTCGCG 59.017 55.000 0.00 0.00 0.00 5.87
746 774 3.103911 GAACGTCGCGGTGGTGAG 61.104 66.667 6.13 0.00 32.31 3.51
758 786 1.028905 GTGGTGAGGGAGAGATCGAG 58.971 60.000 0.00 0.00 0.00 4.04
775 803 6.533730 AGATCGAGGCCATATTATTTGACAA 58.466 36.000 5.01 0.00 0.00 3.18
776 804 6.998074 AGATCGAGGCCATATTATTTGACAAA 59.002 34.615 5.01 2.48 0.00 2.83
794 822 3.245229 ACAAATAGCACCATCCTCACCAA 60.245 43.478 0.00 0.00 0.00 3.67
803 831 3.267812 ACCATCCTCACCAAACTGATGAT 59.732 43.478 0.00 0.00 35.89 2.45
804 832 4.474651 ACCATCCTCACCAAACTGATGATA 59.525 41.667 0.00 0.00 35.89 2.15
805 833 4.818546 CCATCCTCACCAAACTGATGATAC 59.181 45.833 0.00 0.00 35.89 2.24
826 854 7.966753 TGATACTACTACATGAAAACGAGACAC 59.033 37.037 0.00 0.00 0.00 3.67
833 863 5.305585 ACATGAAAACGAGACACAACCTAT 58.694 37.500 0.00 0.00 0.00 2.57
837 867 4.553330 AAACGAGACACAACCTATGGAT 57.447 40.909 0.00 0.00 0.00 3.41
842 872 4.568359 CGAGACACAACCTATGGATCAAAG 59.432 45.833 0.00 0.00 0.00 2.77
845 875 3.333680 ACACAACCTATGGATCAAAGGGT 59.666 43.478 10.85 2.72 34.52 4.34
846 876 4.202673 ACACAACCTATGGATCAAAGGGTT 60.203 41.667 10.85 7.87 37.51 4.11
847 877 5.014755 ACACAACCTATGGATCAAAGGGTTA 59.985 40.000 9.03 0.00 35.62 2.85
848 878 5.357032 CACAACCTATGGATCAAAGGGTTAC 59.643 44.000 9.03 0.00 35.62 2.50
852 1500 5.163374 ACCTATGGATCAAAGGGTTACGTAC 60.163 44.000 10.85 0.00 34.52 3.67
873 1521 3.056821 ACAGAATCGTCAGTCAAATCCGA 60.057 43.478 0.00 0.00 0.00 4.55
897 1545 3.181501 TGCAGGTTCTGAAACAAAAGTCG 60.182 43.478 8.34 0.00 37.10 4.18
905 1553 6.565999 GTTCTGAAACAAAAGTCGAATCCGAT 60.566 38.462 0.00 0.00 39.96 4.18
945 1593 0.453390 AGTTCCCGTCCGTATCGAAC 59.547 55.000 0.00 0.00 0.00 3.95
956 1604 0.461961 GTATCGAACTGCTCCTGCCT 59.538 55.000 0.00 0.00 38.71 4.75
960 1608 0.749649 CGAACTGCTCCTGCCTATCT 59.250 55.000 0.00 0.00 38.71 1.98
961 1609 1.537776 CGAACTGCTCCTGCCTATCTG 60.538 57.143 0.00 0.00 38.71 2.90
962 1610 1.484240 GAACTGCTCCTGCCTATCTGT 59.516 52.381 0.00 0.00 38.71 3.41
963 1611 2.461300 ACTGCTCCTGCCTATCTGTA 57.539 50.000 0.00 0.00 38.71 2.74
1018 1691 4.335647 CCAGCCACCGGTTCTGCT 62.336 66.667 22.18 19.04 33.52 4.24
1019 1692 2.281761 CAGCCACCGGTTCTGCTT 60.282 61.111 17.91 4.12 30.08 3.91
1113 1789 2.487428 CTCTCCGACGACCTGCTG 59.513 66.667 0.00 0.00 0.00 4.41
1250 1926 3.186345 TACTCCCGCCAGAGTACAG 57.814 57.895 6.44 0.00 45.31 2.74
1293 1969 2.203294 AACTTGCCGGGTGACACC 60.203 61.111 16.86 16.86 37.60 4.16
1451 2145 0.871163 TTTTTCTCCGCGAACGACGT 60.871 50.000 8.23 0.00 43.93 4.34
1567 2264 4.436998 GTGACGCGCCAGCCTACT 62.437 66.667 5.73 0.00 41.18 2.57
1578 2275 2.272471 GCCTACTGCTTCCCCCAC 59.728 66.667 0.00 0.00 36.87 4.61
1579 2276 2.584608 CCTACTGCTTCCCCCACG 59.415 66.667 0.00 0.00 0.00 4.94
1580 2277 1.987855 CCTACTGCTTCCCCCACGA 60.988 63.158 0.00 0.00 0.00 4.35
1581 2278 1.517832 CTACTGCTTCCCCCACGAG 59.482 63.158 0.00 0.00 0.00 4.18
1582 2279 1.961180 CTACTGCTTCCCCCACGAGG 61.961 65.000 0.00 0.00 0.00 4.63
1645 2345 0.322277 CTGACTCTGGGCAACTGCAT 60.322 55.000 3.76 0.00 44.36 3.96
1679 2379 1.306642 ACACCTACGAGGCTCTCACG 61.307 60.000 13.50 1.97 39.63 4.35
1988 2689 4.664688 AAACCTCACATTCTGGGAAGAT 57.335 40.909 0.00 0.00 0.00 2.40
1990 2691 3.184628 ACCTCACATTCTGGGAAGATGA 58.815 45.455 0.00 0.00 0.00 2.92
2250 2951 2.503356 CCAGGAGAGGATATATGGTGGC 59.497 54.545 0.00 0.00 0.00 5.01
2303 3010 2.420547 GCACATGAAGGAGCTGGTCATA 60.421 50.000 9.30 0.00 30.85 2.15
2318 3025 1.601903 GTCATAATTGGATTCGCGCCA 59.398 47.619 0.00 0.00 0.00 5.69
2337 3044 4.389576 CACCGCGCCAGAAACTGC 62.390 66.667 0.00 0.00 0.00 4.40
2474 3181 0.031314 CGTGGAGCGCTGATGATACT 59.969 55.000 18.48 0.00 0.00 2.12
2508 3215 2.306341 ACTGATCAAGTCTGCATCCG 57.694 50.000 0.00 0.00 31.64 4.18
2562 3282 0.179015 TTTTCCACTTAGGCGTGCCA 60.179 50.000 14.29 0.00 38.92 4.92
2708 3436 2.982470 GCGGATTTCTTTCAGTGCAAAG 59.018 45.455 0.00 8.09 35.06 2.77
2760 3488 7.332678 TGTTGTCATATATGTATGCTCTCATGC 59.667 37.037 12.42 0.00 38.05 4.06
2771 3499 1.713597 CTCTCATGCACGCTGTTACA 58.286 50.000 0.00 0.00 0.00 2.41
2800 3528 6.090129 GCTTTTGGTTTTGTCTCGCAATATA 58.910 36.000 0.00 0.00 36.89 0.86
2843 3571 3.592059 CACCCATGAGGCAATGAAAAAG 58.408 45.455 0.00 0.00 40.58 2.27
2851 3579 4.281688 TGAGGCAATGAAAAAGGAGAAAGG 59.718 41.667 0.00 0.00 0.00 3.11
2852 3580 4.226384 AGGCAATGAAAAAGGAGAAAGGT 58.774 39.130 0.00 0.00 0.00 3.50
2859 3587 6.445357 TGAAAAAGGAGAAAGGTGTAACAC 57.555 37.500 0.00 0.00 39.98 3.32
2860 3588 6.184789 TGAAAAAGGAGAAAGGTGTAACACT 58.815 36.000 0.00 0.00 39.98 3.55
2861 3589 6.317893 TGAAAAAGGAGAAAGGTGTAACACTC 59.682 38.462 0.00 0.00 39.98 3.51
2862 3590 4.353383 AAGGAGAAAGGTGTAACACTCC 57.647 45.455 0.00 0.00 41.27 3.85
2863 3591 2.299297 AGGAGAAAGGTGTAACACTCCG 59.701 50.000 0.00 0.00 43.58 4.63
2864 3592 2.036862 GGAGAAAGGTGTAACACTCCGT 59.963 50.000 0.00 0.00 39.98 4.69
2865 3593 3.057734 GAGAAAGGTGTAACACTCCGTG 58.942 50.000 0.00 0.00 39.98 4.94
2867 3595 0.250166 AAGGTGTAACACTCCGTGGC 60.250 55.000 0.00 0.00 39.98 5.01
2868 3596 2.025418 GGTGTAACACTCCGTGGCG 61.025 63.158 0.00 0.00 39.98 5.69
2869 3597 1.007038 GTGTAACACTCCGTGGCGA 60.007 57.895 0.00 0.00 37.94 5.54
2870 3598 1.007038 TGTAACACTCCGTGGCGAC 60.007 57.895 0.00 0.00 37.94 5.19
2871 3599 1.735559 GTAACACTCCGTGGCGACC 60.736 63.158 0.00 0.00 37.94 4.79
2872 3600 2.934570 TAACACTCCGTGGCGACCC 61.935 63.158 0.00 0.00 37.94 4.46
2874 3602 3.066190 CACTCCGTGGCGACCCTA 61.066 66.667 0.00 0.00 0.00 3.53
2875 3603 3.066814 ACTCCGTGGCGACCCTAC 61.067 66.667 0.00 0.00 0.00 3.18
2876 3604 3.066190 CTCCGTGGCGACCCTACA 61.066 66.667 0.00 0.00 0.00 2.74
2877 3605 3.352338 CTCCGTGGCGACCCTACAC 62.352 68.421 0.00 0.00 0.00 2.90
2878 3606 3.379445 CCGTGGCGACCCTACACT 61.379 66.667 0.00 0.00 33.13 3.55
2879 3607 2.181021 CGTGGCGACCCTACACTC 59.819 66.667 0.00 0.00 33.13 3.51
2880 3608 2.577593 GTGGCGACCCTACACTCC 59.422 66.667 0.00 0.00 32.58 3.85
2881 3609 2.682494 TGGCGACCCTACACTCCC 60.682 66.667 0.00 0.00 0.00 4.30
2882 3610 2.682494 GGCGACCCTACACTCCCA 60.682 66.667 0.00 0.00 0.00 4.37
2883 3611 2.064581 GGCGACCCTACACTCCCAT 61.065 63.158 0.00 0.00 0.00 4.00
2884 3612 0.757935 GGCGACCCTACACTCCCATA 60.758 60.000 0.00 0.00 0.00 2.74
2885 3613 1.117150 GCGACCCTACACTCCCATAA 58.883 55.000 0.00 0.00 0.00 1.90
2886 3614 1.483415 GCGACCCTACACTCCCATAAA 59.517 52.381 0.00 0.00 0.00 1.40
2887 3615 2.740904 GCGACCCTACACTCCCATAAAC 60.741 54.545 0.00 0.00 0.00 2.01
2888 3616 2.498481 CGACCCTACACTCCCATAAACA 59.502 50.000 0.00 0.00 0.00 2.83
2889 3617 3.430374 CGACCCTACACTCCCATAAACAG 60.430 52.174 0.00 0.00 0.00 3.16
2890 3618 3.518303 GACCCTACACTCCCATAAACAGT 59.482 47.826 0.00 0.00 0.00 3.55
2891 3619 4.691238 ACCCTACACTCCCATAAACAGTA 58.309 43.478 0.00 0.00 0.00 2.74
2892 3620 5.095809 ACCCTACACTCCCATAAACAGTAA 58.904 41.667 0.00 0.00 0.00 2.24
2893 3621 5.548836 ACCCTACACTCCCATAAACAGTAAA 59.451 40.000 0.00 0.00 0.00 2.01
2894 3622 6.216868 ACCCTACACTCCCATAAACAGTAAAT 59.783 38.462 0.00 0.00 0.00 1.40
2895 3623 7.116736 CCCTACACTCCCATAAACAGTAAATT 58.883 38.462 0.00 0.00 0.00 1.82
2896 3624 7.282450 CCCTACACTCCCATAAACAGTAAATTC 59.718 40.741 0.00 0.00 0.00 2.17
2897 3625 7.827236 CCTACACTCCCATAAACAGTAAATTCA 59.173 37.037 0.00 0.00 0.00 2.57
2898 3626 9.396022 CTACACTCCCATAAACAGTAAATTCAT 57.604 33.333 0.00 0.00 0.00 2.57
2900 3628 9.747898 ACACTCCCATAAACAGTAAATTCATAA 57.252 29.630 0.00 0.00 0.00 1.90
2933 3661 3.780516 TTACACCCCTACACCCTCATA 57.219 47.619 0.00 0.00 0.00 2.15
2939 3667 2.421529 CCCCTACACCCTCATAAACAGC 60.422 54.545 0.00 0.00 0.00 4.40
2941 3669 3.308117 CCCTACACCCTCATAAACAGCAA 60.308 47.826 0.00 0.00 0.00 3.91
2946 3674 4.082787 ACACCCTCATAAACAGCAAATTCG 60.083 41.667 0.00 0.00 0.00 3.34
2947 3675 4.079253 ACCCTCATAAACAGCAAATTCGT 58.921 39.130 0.00 0.00 0.00 3.85
2955 3683 9.906660 TCATAAACAGCAAATTCGTAAAAGAAT 57.093 25.926 0.00 0.00 42.13 2.40
2956 3684 9.941991 CATAAACAGCAAATTCGTAAAAGAATG 57.058 29.630 0.00 0.00 40.39 2.67
2958 3686 8.641499 AAACAGCAAATTCGTAAAAGAATGAA 57.359 26.923 0.00 0.00 40.39 2.57
2959 3687 7.623268 ACAGCAAATTCGTAAAAGAATGAAC 57.377 32.000 0.00 0.00 40.39 3.18
2960 3688 7.425606 ACAGCAAATTCGTAAAAGAATGAACT 58.574 30.769 0.00 0.00 40.39 3.01
2961 3689 7.920682 ACAGCAAATTCGTAAAAGAATGAACTT 59.079 29.630 0.00 0.00 40.39 2.66
2962 3690 8.755018 CAGCAAATTCGTAAAAGAATGAACTTT 58.245 29.630 0.00 0.00 40.39 2.66
2963 3691 8.968242 AGCAAATTCGTAAAAGAATGAACTTTC 58.032 29.630 0.00 0.00 40.39 2.62
2979 3719 7.387119 TGAACTTTCAGGATCAAAGATGATG 57.613 36.000 10.16 0.00 38.26 3.07
3003 3743 8.356533 TGAAAGATTTGATGTTTTTGAGAAGC 57.643 30.769 0.00 0.00 0.00 3.86
3027 3767 6.966632 GCTTCAGCAACAAATAATATTCGTGA 59.033 34.615 0.00 0.00 41.59 4.35
3123 3868 5.888161 AGGGCTCCTCAAATGTTATTTGTAG 59.112 40.000 12.44 10.10 0.00 2.74
3148 3893 6.070897 TGAAACTTTGCAAGATCATCGAAA 57.929 33.333 0.00 0.00 0.00 3.46
3253 3999 0.755327 GGCACCTGGGTGTTGAAAGT 60.755 55.000 19.28 0.00 46.90 2.66
3255 4001 2.021723 GCACCTGGGTGTTGAAAGTCA 61.022 52.381 19.28 0.00 46.90 3.41
3256 4002 2.586425 CACCTGGGTGTTGAAAGTCAT 58.414 47.619 11.29 0.00 40.91 3.06
3277 4023 9.288576 AGTCATGTCTCAGTGAAAAATATTCAA 57.711 29.630 0.00 0.00 0.00 2.69
3286 4032 7.448161 TCAGTGAAAAATATTCAAGAGCCAAGA 59.552 33.333 0.00 0.00 0.00 3.02
3289 4035 8.031277 GTGAAAAATATTCAAGAGCCAAGACAT 58.969 33.333 0.00 0.00 0.00 3.06
3300 4046 2.094675 GCCAAGACATTAGTGCCACAT 58.905 47.619 0.00 0.00 0.00 3.21
3301 4047 2.159338 GCCAAGACATTAGTGCCACATG 60.159 50.000 0.00 0.00 0.00 3.21
3307 4053 4.119862 GACATTAGTGCCACATGTATCGT 58.880 43.478 0.00 0.00 31.10 3.73
3315 4061 1.131771 CACATGTATCGTGCGCTAGG 58.868 55.000 9.73 0.71 0.00 3.02
3316 4062 0.032130 ACATGTATCGTGCGCTAGGG 59.968 55.000 9.73 1.65 0.00 3.53
3318 4064 1.037493 ATGTATCGTGCGCTAGGGAA 58.963 50.000 11.61 0.00 0.00 3.97
3321 4067 1.591619 GTATCGTGCGCTAGGGAAAAC 59.408 52.381 11.61 4.48 0.00 2.43
3323 4069 0.669318 TCGTGCGCTAGGGAAAACTG 60.669 55.000 11.61 2.99 0.00 3.16
3324 4070 0.949105 CGTGCGCTAGGGAAAACTGT 60.949 55.000 11.61 0.00 0.00 3.55
3326 4072 1.069227 GTGCGCTAGGGAAAACTGTTG 60.069 52.381 11.61 0.00 0.00 3.33
3327 4073 1.235724 GCGCTAGGGAAAACTGTTGT 58.764 50.000 11.61 0.00 0.00 3.32
3329 4075 2.350484 GCGCTAGGGAAAACTGTTGTTC 60.350 50.000 11.61 0.87 34.96 3.18
3330 4076 3.139077 CGCTAGGGAAAACTGTTGTTCT 58.861 45.455 0.00 0.00 34.96 3.01
3331 4077 4.312443 CGCTAGGGAAAACTGTTGTTCTA 58.688 43.478 0.00 0.00 34.96 2.10
3332 4078 4.151867 CGCTAGGGAAAACTGTTGTTCTAC 59.848 45.833 0.00 0.00 34.96 2.59
3333 4079 4.454847 GCTAGGGAAAACTGTTGTTCTACC 59.545 45.833 0.00 0.00 34.96 3.18
3334 4080 3.828921 AGGGAAAACTGTTGTTCTACCC 58.171 45.455 0.00 0.00 40.02 3.69
3337 4083 4.457466 GGAAAACTGTTGTTCTACCCAGA 58.543 43.478 0.00 0.00 34.96 3.86
3348 4094 7.286546 TGTTGTTCTACCCAGATGATTTTTCAA 59.713 33.333 0.00 0.00 0.00 2.69
3355 4101 9.401058 CTACCCAGATGATTTTTCAAACTAGAT 57.599 33.333 0.00 0.00 0.00 1.98
3386 4170 6.507900 TCTCCTGATCGTAGTTGATTTCATC 58.492 40.000 0.00 0.00 0.00 2.92
3398 4185 8.973378 GTAGTTGATTTCATCTGCACTAGATAC 58.027 37.037 0.00 0.00 44.34 2.24
3403 4190 8.043113 TGATTTCATCTGCACTAGATACTTTGT 58.957 33.333 0.00 0.00 44.34 2.83
3411 4198 8.474831 TCTGCACTAGATACTTTGTTAGCATTA 58.525 33.333 0.00 0.00 0.00 1.90
3430 4241 2.808906 AGACATACCCAAAAGAGCCC 57.191 50.000 0.00 0.00 0.00 5.19
3446 4257 1.026718 GCCCAGACAATTCGGTCCAG 61.027 60.000 0.00 0.00 38.59 3.86
3458 4269 1.905512 GGTCCAGCCTAATGTCGGT 59.094 57.895 0.00 0.00 0.00 4.69
3463 4274 0.469917 CAGCCTAATGTCGGTCCCAT 59.530 55.000 0.00 0.00 0.00 4.00
3471 4282 2.812836 TGTCGGTCCCATAGTCTGTA 57.187 50.000 0.00 0.00 0.00 2.74
3481 4292 6.380560 GGTCCCATAGTCTGTAACTAAGAAGT 59.619 42.308 0.00 0.00 43.61 3.01
3483 4294 8.312564 GTCCCATAGTCTGTAACTAAGAAGTTT 58.687 37.037 0.00 0.00 43.60 2.66
3484 4295 8.877195 TCCCATAGTCTGTAACTAAGAAGTTTT 58.123 33.333 0.00 0.00 43.60 2.43
3485 4296 8.936864 CCCATAGTCTGTAACTAAGAAGTTTTG 58.063 37.037 0.00 0.00 43.60 2.44
3486 4297 8.936864 CCATAGTCTGTAACTAAGAAGTTTTGG 58.063 37.037 0.00 0.00 43.60 3.28
3487 4298 6.862711 AGTCTGTAACTAAGAAGTTTTGGC 57.137 37.500 0.00 0.00 43.60 4.52
3488 4299 5.763698 AGTCTGTAACTAAGAAGTTTTGGCC 59.236 40.000 0.00 0.00 43.60 5.36
3489 4300 5.763698 GTCTGTAACTAAGAAGTTTTGGCCT 59.236 40.000 3.32 0.00 43.60 5.19
3569 4380 2.695147 CCCATCCCCATCAAGCTTAAAC 59.305 50.000 0.00 0.00 0.00 2.01
3580 4391 1.971695 GCTTAAACAGCGGCCACCT 60.972 57.895 2.24 0.00 39.29 4.00
3590 4401 2.280186 GGCCACCTATTCGCCTCG 60.280 66.667 0.00 0.00 39.70 4.63
3596 4407 0.739561 ACCTATTCGCCTCGTCTCAC 59.260 55.000 0.00 0.00 0.00 3.51
3604 4415 2.022240 GCCTCGTCTCACCATCCTCC 62.022 65.000 0.00 0.00 0.00 4.30
3612 4423 0.834261 TCACCATCCTCCCGTTGTCA 60.834 55.000 0.00 0.00 0.00 3.58
3613 4424 0.253044 CACCATCCTCCCGTTGTCAT 59.747 55.000 0.00 0.00 0.00 3.06
3614 4425 0.541863 ACCATCCTCCCGTTGTCATC 59.458 55.000 0.00 0.00 0.00 2.92
3615 4426 0.530650 CCATCCTCCCGTTGTCATCG 60.531 60.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.123186 CGATTTACACATCAAAAGGTAGGCA 59.877 40.000 0.00 0.00 0.00 4.75
29 30 7.234384 GTCACGATTTACACATCAAAAGGTAG 58.766 38.462 0.00 0.00 0.00 3.18
32 33 5.390613 GGTCACGATTTACACATCAAAAGG 58.609 41.667 0.00 0.00 0.00 3.11
41 42 3.566742 ACAAAAGGGGTCACGATTTACAC 59.433 43.478 0.00 0.00 0.00 2.90
43 44 4.070009 AGACAAAAGGGGTCACGATTTAC 58.930 43.478 0.00 0.00 37.74 2.01
53 54 0.179029 CACCGACAGACAAAAGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
62 63 1.071605 GCATGTCTTCACCGACAGAC 58.928 55.000 0.00 0.00 46.07 3.51
64 65 0.036952 AGGCATGTCTTCACCGACAG 60.037 55.000 0.00 0.00 46.07 3.51
65 66 0.037326 GAGGCATGTCTTCACCGACA 60.037 55.000 0.00 0.00 46.82 4.35
66 67 0.037326 TGAGGCATGTCTTCACCGAC 60.037 55.000 0.00 0.00 34.52 4.79
67 68 0.037326 GTGAGGCATGTCTTCACCGA 60.037 55.000 16.28 0.00 0.00 4.69
68 69 1.354337 CGTGAGGCATGTCTTCACCG 61.354 60.000 19.21 13.53 0.00 4.94
70 71 1.790387 GCGTGAGGCATGTCTTCAC 59.210 57.895 16.81 16.81 42.87 3.18
71 72 4.284123 GCGTGAGGCATGTCTTCA 57.716 55.556 0.00 0.00 42.87 3.02
93 94 2.058798 CAAGACATCGCAACTACGTGT 58.941 47.619 0.00 0.00 32.62 4.49
95 96 2.433868 ACAAGACATCGCAACTACGT 57.566 45.000 0.00 0.00 0.00 3.57
97 98 6.129168 CGGATATTACAAGACATCGCAACTAC 60.129 42.308 0.00 0.00 0.00 2.73
101 102 4.055360 CCGGATATTACAAGACATCGCAA 58.945 43.478 0.00 0.00 0.00 4.85
104 105 5.047847 ACAACCGGATATTACAAGACATCG 58.952 41.667 9.46 0.00 0.00 3.84
118 119 0.321298 AAAGCACGCTACAACCGGAT 60.321 50.000 9.46 0.00 0.00 4.18
121 122 1.206578 CCAAAGCACGCTACAACCG 59.793 57.895 0.00 0.00 0.00 4.44
153 155 1.949847 AAGATCGAGAGGGTGTGGCG 61.950 60.000 0.00 0.00 0.00 5.69
159 161 1.479709 CCAGTGAAGATCGAGAGGGT 58.520 55.000 0.00 0.00 0.00 4.34
175 177 2.738521 CAACCGCTCACGACCCAG 60.739 66.667 0.00 0.00 43.93 4.45
180 182 3.758973 TTTGGCCAACCGCTCACGA 62.759 57.895 20.35 0.00 43.93 4.35
233 235 9.793259 ATGTGTGGTTCTCTAAGAAAAAGAATA 57.207 29.630 0.00 0.00 35.75 1.75
234 236 8.697507 ATGTGTGGTTCTCTAAGAAAAAGAAT 57.302 30.769 0.00 0.00 35.75 2.40
292 294 7.181305 TGGTCTTTTCTAGGTATAACCACATGA 59.819 37.037 0.00 0.00 41.95 3.07
313 315 2.205462 ACCTGTCAGCCCTGGTCT 59.795 61.111 0.00 0.00 31.72 3.85
321 323 1.807142 GTTTTCTAGGCACCTGTCAGC 59.193 52.381 0.00 0.00 0.00 4.26
328 330 6.569780 TCTTTTTCAAAGTTTTCTAGGCACC 58.430 36.000 0.00 0.00 0.00 5.01
332 334 7.782049 AGGGTTCTTTTTCAAAGTTTTCTAGG 58.218 34.615 0.00 0.00 0.00 3.02
369 371 7.027874 ACCTTGAGGGACTTATTTGTGATAA 57.972 36.000 1.54 0.00 41.55 1.75
404 407 0.321564 TGGCGGTTTCAGATCTGGTG 60.322 55.000 22.42 9.10 0.00 4.17
420 423 2.124570 ATGCTGGTGGACGATGGC 60.125 61.111 0.00 0.00 0.00 4.40
425 428 1.300971 CCAAGTGATGCTGGTGGACG 61.301 60.000 0.00 0.00 28.63 4.79
439 442 3.515316 CTCGGGTGTGCGTCCAAGT 62.515 63.158 0.00 0.00 0.00 3.16
441 444 4.308458 CCTCGGGTGTGCGTCCAA 62.308 66.667 0.00 0.00 0.00 3.53
446 449 2.125912 CTCTTCCTCGGGTGTGCG 60.126 66.667 0.00 0.00 0.00 5.34
455 458 3.055530 TCTTGATGCTTCACCTCTTCCTC 60.056 47.826 1.02 0.00 0.00 3.71
476 479 1.537348 GCTGACCCGGTTTTTGGTTTC 60.537 52.381 0.00 0.00 34.20 2.78
486 489 3.849951 CTATGGCGCTGACCCGGT 61.850 66.667 7.64 0.00 0.00 5.28
515 543 2.033299 CACATCGTCAAGTGCCTGTTTT 59.967 45.455 0.00 0.00 0.00 2.43
521 549 2.870372 GCCACATCGTCAAGTGCC 59.130 61.111 0.00 0.00 34.48 5.01
548 576 0.322456 TCGGCATGGGGAACTTTCTG 60.322 55.000 0.00 0.00 0.00 3.02
558 586 1.895707 GGATCTTGCTCGGCATGGG 60.896 63.158 10.39 1.79 38.76 4.00
630 658 1.208776 GTACAAGGTTGGTAGCCCGAT 59.791 52.381 0.00 0.00 0.00 4.18
656 684 0.603065 GCAGTGGGCTTTAGGTTTGG 59.397 55.000 0.00 0.00 40.25 3.28
673 701 1.302366 CTCAGTGTTCAGTTGCAGCA 58.698 50.000 2.55 0.00 0.00 4.41
685 713 2.289532 GGCCTCCTCTGCTCAGTGT 61.290 63.158 0.00 0.00 0.00 3.55
687 715 1.306825 ATGGCCTCCTCTGCTCAGT 60.307 57.895 3.32 0.00 0.00 3.41
688 716 1.446791 GATGGCCTCCTCTGCTCAG 59.553 63.158 3.32 0.00 0.00 3.35
723 751 1.210931 CACCGCGACGTTCTTCCTA 59.789 57.895 8.23 0.00 0.00 2.94
724 752 2.049433 CACCGCGACGTTCTTCCT 60.049 61.111 8.23 0.00 0.00 3.36
738 766 0.395862 TCGATCTCTCCCTCACCACC 60.396 60.000 0.00 0.00 0.00 4.61
746 774 1.859302 ATATGGCCTCGATCTCTCCC 58.141 55.000 3.32 0.00 0.00 4.30
758 786 6.868339 GGTGCTATTTGTCAAATAATATGGCC 59.132 38.462 16.80 0.00 33.26 5.36
775 803 3.010584 AGTTTGGTGAGGATGGTGCTATT 59.989 43.478 0.00 0.00 0.00 1.73
776 804 2.578021 AGTTTGGTGAGGATGGTGCTAT 59.422 45.455 0.00 0.00 0.00 2.97
794 822 9.302345 CGTTTTCATGTAGTAGTATCATCAGTT 57.698 33.333 0.00 0.00 0.00 3.16
803 831 7.205737 TGTGTCTCGTTTTCATGTAGTAGTA 57.794 36.000 0.00 0.00 0.00 1.82
804 832 6.080648 TGTGTCTCGTTTTCATGTAGTAGT 57.919 37.500 0.00 0.00 0.00 2.73
805 833 6.128902 GGTTGTGTCTCGTTTTCATGTAGTAG 60.129 42.308 0.00 0.00 0.00 2.57
826 854 4.574828 CGTAACCCTTTGATCCATAGGTTG 59.425 45.833 14.33 0.05 32.04 3.77
833 863 3.833650 TCTGTACGTAACCCTTTGATCCA 59.166 43.478 0.00 0.00 0.00 3.41
837 867 4.022068 ACGATTCTGTACGTAACCCTTTGA 60.022 41.667 0.00 0.00 40.92 2.69
842 872 3.119708 ACTGACGATTCTGTACGTAACCC 60.120 47.826 0.00 0.00 42.74 4.11
845 875 5.361135 TTGACTGACGATTCTGTACGTAA 57.639 39.130 0.00 0.00 42.74 3.18
846 876 5.361135 TTTGACTGACGATTCTGTACGTA 57.639 39.130 0.00 0.00 42.74 3.57
847 877 3.909776 TTGACTGACGATTCTGTACGT 57.090 42.857 0.00 0.00 45.32 3.57
848 878 4.265556 GGATTTGACTGACGATTCTGTACG 59.734 45.833 0.00 0.00 34.27 3.67
852 1500 3.511699 TCGGATTTGACTGACGATTCTG 58.488 45.455 0.00 0.00 0.00 3.02
873 1521 5.343307 ACTTTTGTTTCAGAACCTGCAAT 57.657 34.783 0.00 0.00 34.80 3.56
897 1545 1.268234 CGAAGCCTTGCAATCGGATTC 60.268 52.381 20.23 20.23 41.13 2.52
922 1570 1.386533 GATACGGACGGGAACTGAGA 58.613 55.000 0.00 0.00 38.67 3.27
945 1593 6.975196 ATATATACAGATAGGCAGGAGCAG 57.025 41.667 0.00 0.00 44.61 4.24
956 1604 7.621683 TGTGGGTGGTGCATATATATACAGATA 59.378 37.037 0.00 0.00 0.00 1.98
960 1608 6.443527 AGATGTGGGTGGTGCATATATATACA 59.556 38.462 0.00 0.00 0.00 2.29
961 1609 6.889198 AGATGTGGGTGGTGCATATATATAC 58.111 40.000 0.00 0.00 0.00 1.47
962 1610 6.183360 CGAGATGTGGGTGGTGCATATATATA 60.183 42.308 0.00 0.00 0.00 0.86
963 1611 5.395657 CGAGATGTGGGTGGTGCATATATAT 60.396 44.000 0.00 0.00 0.00 0.86
1113 1789 1.593750 CCTGCTCACTATGAGGCGC 60.594 63.158 0.00 0.00 44.43 6.53
1250 1926 2.126031 GAAGGTCGACGGTCTGGC 60.126 66.667 9.92 1.52 0.00 4.85
1451 2145 4.950062 GGCGATCGATGCAGGCGA 62.950 66.667 21.57 15.47 42.48 5.54
1454 2148 2.664185 CCAGGCGATCGATGCAGG 60.664 66.667 21.57 8.65 0.00 4.85
1575 2272 4.436998 GAGGTCGTGGCCTCGTGG 62.437 72.222 25.10 0.00 44.64 4.94
1679 2379 1.775962 GTCTTGCAAGACGAGCGTC 59.224 57.895 36.44 17.61 45.11 5.19
1988 2689 1.477685 GGAAGTCCAGGGGTTCGTCA 61.478 60.000 0.00 0.00 35.64 4.35
1990 2691 1.152096 AGGAAGTCCAGGGGTTCGT 60.152 57.895 0.00 0.00 38.89 3.85
2250 2951 2.349886 GCAGCTTCTTCCGTATGTTCAG 59.650 50.000 0.00 0.00 0.00 3.02
2303 3010 0.109319 GTGTTGGCGCGAATCCAATT 60.109 50.000 17.76 0.00 44.49 2.32
2318 3025 2.203153 AGTTTCTGGCGCGGTGTT 60.203 55.556 8.83 0.00 0.00 3.32
2337 3044 1.471684 GCTCAAAGCATCCTTCACCAG 59.528 52.381 0.00 0.00 41.89 4.00
2474 3181 2.552599 TCAGTTTTGTCACCGCCATA 57.447 45.000 0.00 0.00 0.00 2.74
2508 3215 2.699846 AGATCACATCAAGGAGAGGCTC 59.300 50.000 6.34 6.34 0.00 4.70
2595 3323 2.857748 CACAGATCGCACGTGCTTATTA 59.142 45.455 35.27 17.13 39.32 0.98
2596 3324 1.660607 CACAGATCGCACGTGCTTATT 59.339 47.619 35.27 18.42 39.32 1.40
2597 3325 1.280982 CACAGATCGCACGTGCTTAT 58.719 50.000 35.27 27.66 39.32 1.73
2602 3330 3.722555 ATTTTACACAGATCGCACGTG 57.277 42.857 12.28 12.28 36.70 4.49
2701 3429 1.611043 GCTTGAATCGCTCTTTGCAC 58.389 50.000 0.00 0.00 43.06 4.57
2708 3436 0.371645 CGTTCTGGCTTGAATCGCTC 59.628 55.000 0.00 0.00 0.00 5.03
2760 3488 2.686558 AAGCATGTTGTAACAGCGTG 57.313 45.000 1.66 1.66 43.04 5.34
2771 3499 4.111916 CGAGACAAAACCAAAAGCATGTT 58.888 39.130 0.00 0.00 0.00 2.71
2800 3528 6.942576 GGTGCATCCCAAATATTCTAGTGTAT 59.057 38.462 0.00 0.00 0.00 2.29
2830 3558 4.039609 CACCTTTCTCCTTTTTCATTGCCT 59.960 41.667 0.00 0.00 0.00 4.75
2831 3559 4.202253 ACACCTTTCTCCTTTTTCATTGCC 60.202 41.667 0.00 0.00 0.00 4.52
2843 3571 2.036862 ACGGAGTGTTACACCTTTCTCC 59.963 50.000 12.28 10.81 42.51 3.71
2859 3587 3.066190 TGTAGGGTCGCCACGGAG 61.066 66.667 0.00 0.00 0.00 4.63
2860 3588 3.376078 GTGTAGGGTCGCCACGGA 61.376 66.667 0.00 0.00 0.00 4.69
2861 3589 3.352338 GAGTGTAGGGTCGCCACGG 62.352 68.421 0.00 0.00 34.34 4.94
2862 3590 2.181021 GAGTGTAGGGTCGCCACG 59.819 66.667 0.00 0.00 34.34 4.94
2863 3591 2.577593 GGAGTGTAGGGTCGCCAC 59.422 66.667 0.00 0.00 0.00 5.01
2864 3592 2.682494 GGGAGTGTAGGGTCGCCA 60.682 66.667 0.00 0.00 0.00 5.69
2865 3593 0.757935 TATGGGAGTGTAGGGTCGCC 60.758 60.000 0.00 0.00 0.00 5.54
2867 3595 2.498481 TGTTTATGGGAGTGTAGGGTCG 59.502 50.000 0.00 0.00 0.00 4.79
2868 3596 3.518303 ACTGTTTATGGGAGTGTAGGGTC 59.482 47.826 0.00 0.00 0.00 4.46
2869 3597 3.527937 ACTGTTTATGGGAGTGTAGGGT 58.472 45.455 0.00 0.00 0.00 4.34
2870 3598 5.687166 TTACTGTTTATGGGAGTGTAGGG 57.313 43.478 0.00 0.00 0.00 3.53
2871 3599 7.827236 TGAATTTACTGTTTATGGGAGTGTAGG 59.173 37.037 0.00 0.00 0.00 3.18
2872 3600 8.786826 TGAATTTACTGTTTATGGGAGTGTAG 57.213 34.615 0.00 0.00 0.00 2.74
2874 3602 9.747898 TTATGAATTTACTGTTTATGGGAGTGT 57.252 29.630 0.00 0.00 0.00 3.55
2899 3627 9.536510 TGTAGGGGTGTAAAGCTATTTATTTTT 57.463 29.630 0.00 0.00 33.57 1.94
2900 3628 8.963725 GTGTAGGGGTGTAAAGCTATTTATTTT 58.036 33.333 0.00 0.00 33.57 1.82
2901 3629 7.558807 GGTGTAGGGGTGTAAAGCTATTTATTT 59.441 37.037 0.00 0.00 33.57 1.40
2902 3630 7.058525 GGTGTAGGGGTGTAAAGCTATTTATT 58.941 38.462 0.00 0.00 33.57 1.40
2903 3631 6.410041 GGGTGTAGGGGTGTAAAGCTATTTAT 60.410 42.308 0.00 0.00 33.57 1.40
2904 3632 5.104402 GGGTGTAGGGGTGTAAAGCTATTTA 60.104 44.000 0.00 0.00 0.00 1.40
2905 3633 4.324797 GGGTGTAGGGGTGTAAAGCTATTT 60.325 45.833 0.00 0.00 0.00 1.40
2906 3634 3.201487 GGGTGTAGGGGTGTAAAGCTATT 59.799 47.826 0.00 0.00 0.00 1.73
2907 3635 2.775960 GGGTGTAGGGGTGTAAAGCTAT 59.224 50.000 0.00 0.00 0.00 2.97
2908 3636 2.190538 GGGTGTAGGGGTGTAAAGCTA 58.809 52.381 0.00 0.00 0.00 3.32
2909 3637 0.989602 GGGTGTAGGGGTGTAAAGCT 59.010 55.000 0.00 0.00 0.00 3.74
2910 3638 0.989602 AGGGTGTAGGGGTGTAAAGC 59.010 55.000 0.00 0.00 0.00 3.51
2911 3639 2.262637 TGAGGGTGTAGGGGTGTAAAG 58.737 52.381 0.00 0.00 0.00 1.85
2912 3640 2.419457 TGAGGGTGTAGGGGTGTAAA 57.581 50.000 0.00 0.00 0.00 2.01
2913 3641 2.653543 ATGAGGGTGTAGGGGTGTAA 57.346 50.000 0.00 0.00 0.00 2.41
2914 3642 3.776417 GTTTATGAGGGTGTAGGGGTGTA 59.224 47.826 0.00 0.00 0.00 2.90
2915 3643 2.574824 GTTTATGAGGGTGTAGGGGTGT 59.425 50.000 0.00 0.00 0.00 4.16
2916 3644 2.574369 TGTTTATGAGGGTGTAGGGGTG 59.426 50.000 0.00 0.00 0.00 4.61
2917 3645 2.844348 CTGTTTATGAGGGTGTAGGGGT 59.156 50.000 0.00 0.00 0.00 4.95
2933 3661 8.539674 GTTCATTCTTTTACGAATTTGCTGTTT 58.460 29.630 0.00 0.00 31.52 2.83
2941 3669 8.846211 TCCTGAAAGTTCATTCTTTTACGAATT 58.154 29.630 0.00 0.00 37.70 2.17
2946 3674 9.965824 TTTGATCCTGAAAGTTCATTCTTTTAC 57.034 29.630 0.00 0.00 37.70 2.01
2955 3683 7.170277 TCATCATCTTTGATCCTGAAAGTTCA 58.830 34.615 4.48 0.00 40.70 3.18
2956 3684 7.621428 TCATCATCTTTGATCCTGAAAGTTC 57.379 36.000 4.48 0.00 40.70 3.01
2958 3686 7.886970 TCTTTCATCATCTTTGATCCTGAAAGT 59.113 33.333 23.19 0.00 45.71 2.66
2959 3687 8.277490 TCTTTCATCATCTTTGATCCTGAAAG 57.723 34.615 20.97 20.97 46.24 2.62
2960 3688 8.818622 ATCTTTCATCATCTTTGATCCTGAAA 57.181 30.769 10.75 10.75 40.70 2.69
2961 3689 8.818622 AATCTTTCATCATCTTTGATCCTGAA 57.181 30.769 0.00 0.00 40.70 3.02
2962 3690 8.683615 CAAATCTTTCATCATCTTTGATCCTGA 58.316 33.333 0.00 0.00 40.70 3.86
2963 3691 8.683615 TCAAATCTTTCATCATCTTTGATCCTG 58.316 33.333 0.00 0.00 40.70 3.86
2979 3719 8.585189 AGCTTCTCAAAAACATCAAATCTTTC 57.415 30.769 0.00 0.00 0.00 2.62
2994 3734 4.717233 TTTGTTGCTGAAGCTTCTCAAA 57.283 36.364 26.09 21.81 42.66 2.69
2998 3738 7.912250 CGAATATTATTTGTTGCTGAAGCTTCT 59.088 33.333 26.09 6.18 42.66 2.85
2999 3739 7.698130 ACGAATATTATTTGTTGCTGAAGCTTC 59.302 33.333 19.89 19.89 42.66 3.86
3003 3743 8.894409 TTCACGAATATTATTTGTTGCTGAAG 57.106 30.769 6.57 0.00 0.00 3.02
3057 3802 5.786311 ACATGCTTCAAAGTTTATGTGCAT 58.214 33.333 9.99 9.99 38.49 3.96
3102 3847 6.094048 TCAGCTACAAATAACATTTGAGGAGC 59.906 38.462 16.36 17.91 35.51 4.70
3109 3854 8.764287 GCAAAGTTTCAGCTACAAATAACATTT 58.236 29.630 0.00 0.00 0.00 2.32
3120 3865 5.362556 TGATCTTGCAAAGTTTCAGCTAC 57.637 39.130 0.00 0.00 46.34 3.58
3123 3868 3.850273 CGATGATCTTGCAAAGTTTCAGC 59.150 43.478 0.00 3.45 46.34 4.26
3148 3893 5.910614 TGAGACATCAAACATGATCGATCT 58.089 37.500 25.02 9.01 30.61 2.75
3238 3984 2.554032 GACATGACTTTCAACACCCAGG 59.446 50.000 0.00 0.00 0.00 4.45
3253 3999 9.506018 TCTTGAATATTTTTCACTGAGACATGA 57.494 29.630 0.00 0.00 0.00 3.07
3255 4001 8.457261 GCTCTTGAATATTTTTCACTGAGACAT 58.543 33.333 16.08 0.00 34.25 3.06
3256 4002 7.094634 GGCTCTTGAATATTTTTCACTGAGACA 60.095 37.037 16.08 0.00 37.30 3.41
3277 4023 1.630369 TGGCACTAATGTCTTGGCTCT 59.370 47.619 0.00 0.00 36.77 4.09
3286 4032 3.871006 CACGATACATGTGGCACTAATGT 59.129 43.478 22.29 22.29 38.32 2.71
3289 4035 2.276201 GCACGATACATGTGGCACTAA 58.724 47.619 19.83 0.00 37.80 2.24
3300 4046 0.818938 TTTCCCTAGCGCACGATACA 59.181 50.000 11.47 0.00 0.00 2.29
3301 4047 1.591619 GTTTTCCCTAGCGCACGATAC 59.408 52.381 11.47 0.00 0.00 2.24
3307 4053 1.234821 CAACAGTTTTCCCTAGCGCA 58.765 50.000 11.47 0.00 0.00 6.09
3315 4061 4.457466 TCTGGGTAGAACAACAGTTTTCC 58.543 43.478 0.00 0.00 32.92 3.13
3316 4062 5.763204 TCATCTGGGTAGAACAACAGTTTTC 59.237 40.000 0.00 0.00 36.32 2.29
3318 4064 5.304686 TCATCTGGGTAGAACAACAGTTT 57.695 39.130 0.00 0.00 36.32 2.66
3321 4067 6.824305 AAAATCATCTGGGTAGAACAACAG 57.176 37.500 0.00 0.00 36.32 3.16
3323 4069 7.214467 TGAAAAATCATCTGGGTAGAACAAC 57.786 36.000 0.00 0.00 36.32 3.32
3324 4070 7.831691 TTGAAAAATCATCTGGGTAGAACAA 57.168 32.000 0.00 0.00 36.32 2.83
3326 4072 7.886338 AGTTTGAAAAATCATCTGGGTAGAAC 58.114 34.615 0.00 0.00 36.32 3.01
3327 4073 9.231297 CTAGTTTGAAAAATCATCTGGGTAGAA 57.769 33.333 0.00 0.00 36.32 2.10
3329 4075 8.792830 TCTAGTTTGAAAAATCATCTGGGTAG 57.207 34.615 0.00 0.00 0.00 3.18
3331 4077 9.927081 ATATCTAGTTTGAAAAATCATCTGGGT 57.073 29.630 0.00 0.00 0.00 4.51
3386 4170 7.545362 AATGCTAACAAAGTATCTAGTGCAG 57.455 36.000 0.00 0.00 29.12 4.41
3398 4185 7.624360 TTGGGTATGTCTAATGCTAACAAAG 57.376 36.000 0.00 0.00 0.00 2.77
3403 4190 6.542370 GCTCTTTTGGGTATGTCTAATGCTAA 59.458 38.462 0.00 0.00 0.00 3.09
3411 4198 1.992557 TGGGCTCTTTTGGGTATGTCT 59.007 47.619 0.00 0.00 0.00 3.41
3430 4241 0.036010 AGGCTGGACCGAATTGTCTG 60.036 55.000 0.00 0.00 46.52 3.51
3446 4257 1.692519 ACTATGGGACCGACATTAGGC 59.307 52.381 0.00 0.00 0.00 3.93
3458 4269 8.431910 AAACTTCTTAGTTACAGACTATGGGA 57.568 34.615 0.00 0.00 43.74 4.37
3463 4274 6.932960 GGCCAAAACTTCTTAGTTACAGACTA 59.067 38.462 0.00 0.00 43.74 2.59
3471 4282 5.670485 CCAAAAGGCCAAAACTTCTTAGTT 58.330 37.500 5.01 0.00 46.44 2.24
3481 4292 1.139853 ACGATTGCCAAAAGGCCAAAA 59.860 42.857 5.01 0.00 0.00 2.44
3482 4293 0.755686 ACGATTGCCAAAAGGCCAAA 59.244 45.000 5.01 0.00 0.00 3.28
3483 4294 1.621992 TACGATTGCCAAAAGGCCAA 58.378 45.000 5.01 0.00 0.00 4.52
3484 4295 1.476085 CATACGATTGCCAAAAGGCCA 59.524 47.619 5.01 0.00 0.00 5.36
3485 4296 1.748493 TCATACGATTGCCAAAAGGCC 59.252 47.619 3.77 0.00 0.00 5.19
3486 4297 3.374745 CATCATACGATTGCCAAAAGGC 58.625 45.455 0.00 0.00 0.00 4.35
3487 4298 3.381272 ACCATCATACGATTGCCAAAAGG 59.619 43.478 0.00 0.00 0.00 3.11
3488 4299 4.637483 ACCATCATACGATTGCCAAAAG 57.363 40.909 0.00 0.00 0.00 2.27
3489 4300 5.825151 TCATACCATCATACGATTGCCAAAA 59.175 36.000 0.00 0.00 0.00 2.44
3496 4307 3.368427 CGGGCTCATACCATCATACGATT 60.368 47.826 0.00 0.00 0.00 3.34
3500 4311 1.623811 ACCGGGCTCATACCATCATAC 59.376 52.381 6.32 0.00 0.00 2.39
3506 4317 1.382009 TGCTACCGGGCTCATACCA 60.382 57.895 6.32 0.00 0.00 3.25
3569 4380 3.272334 GCGAATAGGTGGCCGCTG 61.272 66.667 17.49 0.78 43.75 5.18
3580 4391 1.337071 GATGGTGAGACGAGGCGAATA 59.663 52.381 0.00 0.00 0.00 1.75
3590 4401 0.108138 CAACGGGAGGATGGTGAGAC 60.108 60.000 0.00 0.00 0.00 3.36
3596 4407 0.530650 CGATGACAACGGGAGGATGG 60.531 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.