Multiple sequence alignment - TraesCS3A01G428400

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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 TraesCS3A01G428400 chr3A 100.000 3480 0 0 1 3480 671728016 671724537 0.000000e+00 6427.0
1 TraesCS3A01G428400 chr3D 91.974 2878 135 31 98 2942 536248122 536245308 0.000000e+00 3947.0
2 TraesCS3A01G428400 chr3D 96.226 212 7 1 3269 3480 329319258 329319468 2.570000e-91 346.0
3 TraesCS3A01G428400 chr3D 89.024 82 7 2 2971 3051 536245308 536245228 2.210000e-17 100.0
4 TraesCS3A01G428400 chr3D 87.500 88 6 1 8 90 536248318 536248231 2.860000e-16 97.1
5 TraesCS3A01G428400 chr3B 90.643 2319 161 35 943 3234 708493976 708491687 0.000000e+00 3029.0
6 TraesCS3A01G428400 chr3B 89.083 229 17 3 109 329 708607430 708607658 9.510000e-71 278.0
7 TraesCS3A01G428400 chr3B 91.045 67 6 0 2243 2309 708492631 708492565 1.330000e-14 91.6
8 TraesCS3A01G428400 chr2D 96.698 212 6 1 3269 3480 517323408 517323198 5.530000e-93 351.0
9 TraesCS3A01G428400 chr5D 96.262 214 6 1 3269 3480 388416524 388416737 1.990000e-92 350.0
10 TraesCS3A01G428400 chr5D 96.244 213 7 1 3269 3480 311634960 311634748 7.150000e-92 348.0
11 TraesCS3A01G428400 chr5A 96.226 212 7 1 3269 3480 193597900 193597690 2.570000e-91 346.0
12 TraesCS3A01G428400 chr4D 96.226 212 6 2 3269 3480 401000066 400999857 2.570000e-91 346.0
13 TraesCS3A01G428400 chr4B 95.794 214 7 2 3268 3480 362457279 362457491 9.250000e-91 344.0
14 TraesCS3A01G428400 chr1D 95.392 217 9 1 3265 3480 435272834 435273050 9.250000e-91 344.0
15 TraesCS3A01G428400 chr7D 95.755 212 7 1 3269 3480 252497232 252497023 1.200000e-89 340.0


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 TraesCS3A01G428400 chr3A 671724537 671728016 3479 True 6427.000000 6427 100.000000 1 3480 1 chr3A.!!$R1 3479
1 TraesCS3A01G428400 chr3D 536245228 536248318 3090 True 1381.366667 3947 89.499333 8 3051 3 chr3D.!!$R1 3043
2 TraesCS3A01G428400 chr3B 708491687 708493976 2289 True 1560.300000 3029 90.844000 943 3234 2 chr3B.!!$R1 2291

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
714 847 0.178301 GAGCCTAGGAAAGGGGAACG 59.822 60.0 14.75 0.0 46.65 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 2803 0.179161 CCTCAACGCAGGTACTCGAG 60.179 60.0 11.84 11.84 34.6 4.04 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
32 33 8.985315 ATATGCTTACTTCTTTCATGATTCCA 57.015 30.769 0.00 0.00 0.00 3.53
39 40 7.388460 ACTTCTTTCATGATTCCATCAGAAC 57.612 36.000 0.00 0.00 43.53 3.01
47 48 6.950041 TCATGATTCCATCAGAACTTTCCTTT 59.050 34.615 0.00 0.00 43.53 3.11
90 96 4.908601 TTGAGGGTTGAAAGCTCAGATA 57.091 40.909 0.00 0.00 31.69 1.98
91 97 5.441718 TTGAGGGTTGAAAGCTCAGATAT 57.558 39.130 0.00 0.00 31.69 1.63
92 98 4.774124 TGAGGGTTGAAAGCTCAGATATG 58.226 43.478 0.00 0.00 31.69 1.78
93 99 4.225942 TGAGGGTTGAAAGCTCAGATATGT 59.774 41.667 0.00 0.00 31.69 2.29
94 100 5.425217 TGAGGGTTGAAAGCTCAGATATGTA 59.575 40.000 0.00 0.00 31.69 2.29
95 101 6.100279 TGAGGGTTGAAAGCTCAGATATGTAT 59.900 38.462 0.00 0.00 31.69 2.29
96 102 6.904626 AGGGTTGAAAGCTCAGATATGTATT 58.095 36.000 0.00 0.00 31.69 1.89
125 232 5.163622 TGAGCAAAAGGTTCAAAACTCAGAG 60.164 40.000 0.00 0.00 33.43 3.35
128 235 5.277047 CAAAAGGTTCAAAACTCAGAGAGC 58.723 41.667 3.79 0.00 32.04 4.09
130 237 2.103263 AGGTTCAAAACTCAGAGAGCGT 59.897 45.455 3.79 0.00 32.04 5.07
142 249 4.796231 GAGCGTGGCGTCGTCCAT 62.796 66.667 10.82 0.00 38.57 3.41
151 258 1.287425 GCGTCGTCCATAAAAGAGGG 58.713 55.000 0.00 0.00 0.00 4.30
170 277 0.693049 GCACCGATGGGGGAAGATAT 59.307 55.000 0.00 0.00 40.10 1.63
181 288 1.699634 GGGAAGATATGCAGCCCAGTA 59.300 52.381 0.00 0.00 38.68 2.74
218 325 2.026915 GCCCAAAAGATTTCAGCCCAAT 60.027 45.455 0.00 0.00 0.00 3.16
223 330 4.563140 AAAGATTTCAGCCCAATTGCAT 57.437 36.364 0.00 0.00 0.00 3.96
226 333 3.385755 AGATTTCAGCCCAATTGCATACC 59.614 43.478 0.00 0.00 0.00 2.73
363 475 3.237741 CCGCCTCCAGGATCCTCC 61.238 72.222 12.69 0.00 37.39 4.30
398 528 2.203832 TCCTCCACTGCAGCAGGA 60.204 61.111 26.38 22.85 35.51 3.86
433 563 2.812619 CCCGGCTCTCTCATTCCCC 61.813 68.421 0.00 0.00 0.00 4.81
434 564 1.764054 CCGGCTCTCTCATTCCCCT 60.764 63.158 0.00 0.00 0.00 4.79
435 565 1.745264 CGGCTCTCTCATTCCCCTC 59.255 63.158 0.00 0.00 0.00 4.30
436 566 0.758685 CGGCTCTCTCATTCCCCTCT 60.759 60.000 0.00 0.00 0.00 3.69
449 579 4.357918 TTCCCCTCTCTGTTTTTCTCTG 57.642 45.455 0.00 0.00 0.00 3.35
545 675 2.347490 CGGCAGCAGTAGTGGGTT 59.653 61.111 0.00 0.00 0.00 4.11
568 698 2.486548 GCTCGGCCTGTAATTGGGAATA 60.487 50.000 0.00 0.00 0.00 1.75
572 702 3.487372 GGCCTGTAATTGGGAATAGGTC 58.513 50.000 0.00 0.00 0.00 3.85
580 710 5.472301 AATTGGGAATAGGTCTGATTGGT 57.528 39.130 0.00 0.00 0.00 3.67
584 714 3.648545 GGGAATAGGTCTGATTGGTAGCT 59.351 47.826 0.00 0.00 0.00 3.32
651 781 9.130661 GTGTCTGGCTGTCTATATCTATATGAT 57.869 37.037 0.00 0.00 39.11 2.45
688 821 5.579047 TGGGAGCCTAATGAAAATTTGAGA 58.421 37.500 0.00 0.00 0.00 3.27
689 822 6.015918 TGGGAGCCTAATGAAAATTTGAGAA 58.984 36.000 0.00 0.00 0.00 2.87
690 823 6.496565 TGGGAGCCTAATGAAAATTTGAGAAA 59.503 34.615 0.00 0.00 0.00 2.52
691 824 7.180766 TGGGAGCCTAATGAAAATTTGAGAAAT 59.819 33.333 0.00 0.00 0.00 2.17
692 825 7.493645 GGGAGCCTAATGAAAATTTGAGAAATG 59.506 37.037 0.00 0.00 0.00 2.32
699 832 8.543862 AATGAAAATTTGAGAAATGAAGAGCC 57.456 30.769 0.00 0.00 0.00 4.70
701 834 8.408043 TGAAAATTTGAGAAATGAAGAGCCTA 57.592 30.769 0.00 0.00 0.00 3.93
703 836 7.401955 AAATTTGAGAAATGAAGAGCCTAGG 57.598 36.000 3.67 3.67 0.00 3.02
704 837 5.762179 TTTGAGAAATGAAGAGCCTAGGA 57.238 39.130 14.75 0.00 0.00 2.94
714 847 0.178301 GAGCCTAGGAAAGGGGAACG 59.822 60.000 14.75 0.00 46.65 3.95
751 884 9.807386 GTTGACACTATTTTGTAGTATTGTCAC 57.193 33.333 0.00 0.00 39.00 3.67
752 885 9.549078 TTGACACTATTTTGTAGTATTGTCACA 57.451 29.630 0.00 0.00 39.00 3.58
753 886 9.719355 TGACACTATTTTGTAGTATTGTCACAT 57.281 29.630 0.00 0.00 36.32 3.21
754 887 9.973246 GACACTATTTTGTAGTATTGTCACATG 57.027 33.333 0.00 0.00 33.34 3.21
755 888 9.502091 ACACTATTTTGTAGTATTGTCACATGT 57.498 29.630 0.00 0.00 0.00 3.21
773 906 4.818546 ACATGTTGTGTTCTCCTTCTCAAG 59.181 41.667 0.00 0.00 38.01 3.02
811 948 1.618837 AGCACACACTCACGTATCCTT 59.381 47.619 0.00 0.00 0.00 3.36
817 954 4.929808 ACACACTCACGTATCCTTGAATTC 59.070 41.667 0.00 0.00 0.00 2.17
825 962 5.563751 CACGTATCCTTGAATTCGTGTTTTG 59.436 40.000 0.04 0.00 41.96 2.44
886 1023 1.356938 GTCCCGTGTAACTTAGCTGC 58.643 55.000 0.00 0.00 31.75 5.25
917 1054 4.886496 AGTACTTACCTGTTCCTCAACC 57.114 45.455 0.00 0.00 0.00 3.77
922 1059 1.228124 CCTGTTCCTCAACCGGCAA 60.228 57.895 0.00 0.00 30.91 4.52
951 1088 7.118101 TGGCATTGCATTAAAGAATCAACTTTC 59.882 33.333 11.39 0.00 40.09 2.62
970 1107 7.404671 ACTTTCCTTACATGTTCTGTGTTTT 57.595 32.000 2.30 0.00 38.92 2.43
972 1109 7.122055 ACTTTCCTTACATGTTCTGTGTTTTGA 59.878 33.333 2.30 0.00 38.92 2.69
974 1111 5.007234 TCCTTACATGTTCTGTGTTTTGACG 59.993 40.000 2.30 0.00 38.92 4.35
1044 1181 0.990374 ATCTGCTCAAGAAGGCCACT 59.010 50.000 5.01 0.00 38.79 4.00
1053 1190 1.490574 AGAAGGCCACTAGCTCGAAT 58.509 50.000 5.01 0.00 43.05 3.34
1071 1208 2.666272 ATCCGACTCTCTATCAGGCA 57.334 50.000 0.00 0.00 0.00 4.75
1339 1487 4.574421 GCTGCTGTTTTGGTAATGGTTTTT 59.426 37.500 0.00 0.00 0.00 1.94
1383 1531 8.410673 TCTTTCCAGCTAAGATTATCGTAGAT 57.589 34.615 17.03 9.37 45.12 1.98
1395 1543 0.741927 TCGTAGATCGCGACACTGGA 60.742 55.000 12.93 12.82 39.67 3.86
1505 1653 6.549736 TCATAATCGGGATGAACTCTAACAGA 59.450 38.462 0.00 0.00 30.35 3.41
1510 1658 6.472887 TCGGGATGAACTCTAACAGATTTTT 58.527 36.000 0.00 0.00 0.00 1.94
1583 1731 9.312904 TGAGAAATTTCAGACCAGGATAAATTT 57.687 29.630 19.99 13.52 40.54 1.82
1584 1732 9.578439 GAGAAATTTCAGACCAGGATAAATTTG 57.422 33.333 19.99 0.00 38.92 2.32
1621 1769 2.692041 GCCCCAATTCTCTCCATCAAAG 59.308 50.000 0.00 0.00 0.00 2.77
1635 1783 7.596494 TCTCCATCAAAGCAATGTTTCTTAAG 58.404 34.615 0.00 0.00 0.00 1.85
1702 1851 3.283751 TGTTGATTGGTTGGAAGTTCGT 58.716 40.909 0.00 0.00 0.00 3.85
1734 1883 2.224843 TGGATGTCATGGCTGTGTCTTT 60.225 45.455 0.00 0.00 0.00 2.52
1748 1897 8.081633 TGGCTGTGTCTTTAATAACAAAGAATG 58.918 33.333 10.61 0.00 44.06 2.67
1916 2065 4.019321 TCTGCTAGCCTGTTAGGAAAATGT 60.019 41.667 13.29 0.00 37.67 2.71
1920 2069 6.889722 TGCTAGCCTGTTAGGAAAATGTAATT 59.110 34.615 13.29 0.00 37.67 1.40
1957 2106 6.759272 TCAGTGAGTGAGCTTACTACAATTT 58.241 36.000 11.68 0.00 39.20 1.82
2074 2228 5.659440 TTGCCCATCAACTTATTTCTTCC 57.341 39.130 0.00 0.00 0.00 3.46
2075 2229 4.934356 TGCCCATCAACTTATTTCTTCCT 58.066 39.130 0.00 0.00 0.00 3.36
2076 2230 5.332743 TGCCCATCAACTTATTTCTTCCTT 58.667 37.500 0.00 0.00 0.00 3.36
2301 2500 1.826054 CCGGCAACTTTGGTGGTGA 60.826 57.895 0.00 0.00 0.00 4.02
2303 2502 1.739667 GGCAACTTTGGTGGTGACC 59.260 57.895 0.00 0.00 43.48 4.02
2308 2507 1.153046 CTTTGGTGGTGACCGTGGT 60.153 57.895 0.00 0.00 46.62 4.16
2357 2556 3.160585 CTCCTGCAGGTTCCACCA 58.839 61.111 31.58 10.30 41.95 4.17
2377 2576 2.304180 CAGTGGTGATGAGTTCTCCCTT 59.696 50.000 0.00 0.00 37.22 3.95
2474 2673 2.484264 GACAAGTACGCCAGCAAGAATT 59.516 45.455 0.00 0.00 0.00 2.17
2571 2770 3.432378 TCCAGACCAGAGACTACTTTCC 58.568 50.000 0.00 0.00 0.00 3.13
2572 2771 2.164624 CCAGACCAGAGACTACTTTCCG 59.835 54.545 0.00 0.00 0.00 4.30
2586 2785 3.432378 ACTTTCCGGATGACTGTCTAGT 58.568 45.455 4.15 0.00 40.66 2.57
2587 2786 4.597004 ACTTTCCGGATGACTGTCTAGTA 58.403 43.478 4.15 0.00 37.25 1.82
2588 2787 4.641094 ACTTTCCGGATGACTGTCTAGTAG 59.359 45.833 4.15 0.00 37.25 2.57
2589 2788 4.498894 TTCCGGATGACTGTCTAGTAGA 57.501 45.455 4.15 0.00 37.25 2.59
2590 2789 4.074627 TCCGGATGACTGTCTAGTAGAG 57.925 50.000 0.00 0.00 37.25 2.43
2607 2806 9.107177 TCTAGTAGAGACCAAATAACTTACTCG 57.893 37.037 0.00 0.00 0.00 4.18
2664 2863 4.707030 TCAGTTTGCCTGATTTAGCATG 57.293 40.909 0.00 0.00 45.34 4.06
2670 2869 6.424812 AGTTTGCCTGATTTAGCATGTTTTTC 59.575 34.615 0.00 0.00 39.11 2.29
2671 2870 4.484236 TGCCTGATTTAGCATGTTTTTCG 58.516 39.130 0.00 0.00 33.08 3.46
2672 2871 4.022416 TGCCTGATTTAGCATGTTTTTCGT 60.022 37.500 0.00 0.00 33.08 3.85
2706 2905 7.994911 ACAAATTATCCTTCAGCAGTGATGATA 59.005 33.333 12.63 0.00 30.86 2.15
2714 2913 4.209538 TCAGCAGTGATGATATTTTGGGG 58.790 43.478 7.06 0.00 0.00 4.96
2730 2929 1.102978 GGGGATCATGTTTGGAACCG 58.897 55.000 0.00 0.00 0.00 4.44
2768 2967 1.347707 TCAACCGACCTGAAGCTCATT 59.652 47.619 0.00 0.00 0.00 2.57
2770 2969 1.270907 ACCGACCTGAAGCTCATTCT 58.729 50.000 0.00 0.00 38.83 2.40
2781 2980 4.141321 TGAAGCTCATTCTGATAATGGCCT 60.141 41.667 3.32 0.00 38.83 5.19
2790 2989 1.922447 TGATAATGGCCTGACAAGGGT 59.078 47.619 3.32 0.00 44.67 4.34
2814 3013 3.324556 ACCCAGAACAATTTGATTGGTGG 59.675 43.478 2.79 8.21 41.00 4.61
2898 3097 6.959639 TTTTGTCTGTTCTTCTTTGCCTAT 57.040 33.333 0.00 0.00 0.00 2.57
2909 3108 4.640771 TCTTTGCCTATATCCCATGACC 57.359 45.455 0.00 0.00 0.00 4.02
2921 3120 2.187958 CCCATGACCTGTTACTCCTCA 58.812 52.381 0.00 0.00 0.00 3.86
2969 3168 2.291217 TGCCTGTGTAAACCCATGCATA 60.291 45.455 0.00 0.00 29.13 3.14
2996 3196 2.030007 TGCAGGCTTTTCTGTACAATGC 60.030 45.455 0.00 0.00 37.12 3.56
3002 3202 3.420893 CTTTTCTGTACAATGCAGGGGA 58.579 45.455 0.00 0.00 34.89 4.81
3008 3208 0.465460 TACAATGCAGGGGAATCCGC 60.465 55.000 8.44 8.44 41.52 5.54
3037 3237 2.795231 TCTGCTCCTTTTCCATCCAG 57.205 50.000 0.00 0.00 0.00 3.86
3044 3244 4.626287 GCTCCTTTTCCATCCAGTCATACA 60.626 45.833 0.00 0.00 0.00 2.29
3056 3256 3.684305 CCAGTCATACAAACTCGCATTCA 59.316 43.478 0.00 0.00 0.00 2.57
3069 3269 9.519905 CAAACTCGCATTCATTTATTTGAAAAG 57.480 29.630 0.00 0.00 38.98 2.27
3071 3271 9.474920 AACTCGCATTCATTTATTTGAAAAGAA 57.525 25.926 0.00 0.00 38.98 2.52
3092 3294 4.669206 AATCAGCTCGATCAAGAGACAT 57.331 40.909 2.14 0.00 40.57 3.06
3093 3295 4.669206 ATCAGCTCGATCAAGAGACATT 57.331 40.909 2.14 0.00 40.57 2.71
3098 3300 3.681897 GCTCGATCAAGAGACATTGTTGT 59.318 43.478 2.14 0.00 40.57 3.32
3117 3319 1.032014 TTTGGCAGGTGCTTCTGAAC 58.968 50.000 10.32 3.93 41.70 3.18
3123 3325 1.542915 CAGGTGCTTCTGAACCCATTG 59.457 52.381 1.44 0.00 43.18 2.82
3133 3335 4.326826 TCTGAACCCATTGAAAGTAGCAG 58.673 43.478 0.00 0.00 0.00 4.24
3147 3349 3.922175 GCAGTTTGCGGCAGTTTC 58.078 55.556 1.67 0.00 35.86 2.78
3161 3363 3.441922 GGCAGTTTCCTGAAAGAATCTCC 59.558 47.826 0.00 0.00 41.50 3.71
3167 3369 1.373570 CTGAAAGAATCTCCACGGGC 58.626 55.000 0.00 0.00 34.07 6.13
3209 3411 5.208463 ACTGTTCCTCTCTCAAACTCTTC 57.792 43.478 0.00 0.00 0.00 2.87
3217 3419 6.778069 TCCTCTCTCAAACTCTTCAGAACTAA 59.222 38.462 0.00 0.00 0.00 2.24
3218 3420 7.287927 TCCTCTCTCAAACTCTTCAGAACTAAA 59.712 37.037 0.00 0.00 0.00 1.85
3234 3436 9.100554 TCAGAACTAAACGTATTTTCTCAACAA 57.899 29.630 0.00 0.00 0.00 2.83
3235 3437 9.710979 CAGAACTAAACGTATTTTCTCAACAAA 57.289 29.630 0.00 0.00 0.00 2.83
3263 3465 6.806388 TTGACGGGTAAAGAACTTTATTCC 57.194 37.500 9.68 12.23 37.37 3.01
3264 3466 6.117975 TGACGGGTAAAGAACTTTATTCCT 57.882 37.500 17.95 10.86 37.37 3.36
3265 3467 6.168389 TGACGGGTAAAGAACTTTATTCCTC 58.832 40.000 17.95 15.50 37.37 3.71
3266 3468 6.117975 ACGGGTAAAGAACTTTATTCCTCA 57.882 37.500 17.95 0.00 37.37 3.86
3267 3469 6.171213 ACGGGTAAAGAACTTTATTCCTCAG 58.829 40.000 17.95 11.30 37.37 3.35
3268 3470 6.013984 ACGGGTAAAGAACTTTATTCCTCAGA 60.014 38.462 17.95 0.00 37.37 3.27
3269 3471 6.313164 CGGGTAAAGAACTTTATTCCTCAGAC 59.687 42.308 17.95 5.79 37.37 3.51
3270 3472 7.395617 GGGTAAAGAACTTTATTCCTCAGACT 58.604 38.462 9.68 0.00 37.37 3.24
3271 3473 8.537858 GGGTAAAGAACTTTATTCCTCAGACTA 58.462 37.037 9.68 0.00 37.37 2.59
3272 3474 9.589111 GGTAAAGAACTTTATTCCTCAGACTAG 57.411 37.037 9.68 0.00 37.37 2.57
3273 3475 9.089601 GTAAAGAACTTTATTCCTCAGACTAGC 57.910 37.037 9.68 0.00 37.37 3.42
3274 3476 6.859112 AGAACTTTATTCCTCAGACTAGCA 57.141 37.500 0.00 0.00 0.00 3.49
3275 3477 7.246171 AGAACTTTATTCCTCAGACTAGCAA 57.754 36.000 0.00 0.00 0.00 3.91
3276 3478 7.327214 AGAACTTTATTCCTCAGACTAGCAAG 58.673 38.462 0.00 0.00 0.00 4.01
3277 3479 6.859112 ACTTTATTCCTCAGACTAGCAAGA 57.141 37.500 0.00 0.00 0.00 3.02
3278 3480 7.430760 ACTTTATTCCTCAGACTAGCAAGAT 57.569 36.000 0.00 0.00 0.00 2.40
3279 3481 7.271511 ACTTTATTCCTCAGACTAGCAAGATG 58.728 38.462 0.00 0.00 0.00 2.90
3280 3482 3.533606 TTCCTCAGACTAGCAAGATGC 57.466 47.619 0.00 0.00 45.46 3.91
3281 3483 1.759445 TCCTCAGACTAGCAAGATGCC 59.241 52.381 0.00 0.00 46.52 4.40
3282 3484 1.202627 CCTCAGACTAGCAAGATGCCC 60.203 57.143 0.00 0.00 46.52 5.36
3283 3485 0.461548 TCAGACTAGCAAGATGCCCG 59.538 55.000 0.00 0.00 46.52 6.13
3284 3486 0.176680 CAGACTAGCAAGATGCCCGT 59.823 55.000 0.00 0.00 46.52 5.28
3285 3487 0.176680 AGACTAGCAAGATGCCCGTG 59.823 55.000 0.00 0.00 46.52 4.94
3286 3488 1.432270 GACTAGCAAGATGCCCGTGC 61.432 60.000 6.11 6.11 46.52 5.34
3302 3504 2.638744 TGCATTGCACGGAACATCA 58.361 47.368 7.38 0.00 31.71 3.07
3303 3505 0.957362 TGCATTGCACGGAACATCAA 59.043 45.000 7.38 0.00 31.71 2.57
3304 3506 1.068402 TGCATTGCACGGAACATCAAG 60.068 47.619 7.38 0.00 31.71 3.02
3305 3507 1.199789 GCATTGCACGGAACATCAAGA 59.800 47.619 3.15 0.00 0.00 3.02
3306 3508 2.159338 GCATTGCACGGAACATCAAGAT 60.159 45.455 3.15 0.00 0.00 2.40
3307 3509 3.431856 CATTGCACGGAACATCAAGATG 58.568 45.455 8.45 8.45 44.15 2.90
3308 3510 0.804364 TGCACGGAACATCAAGATGC 59.196 50.000 9.85 0.00 42.39 3.91
3309 3511 0.804364 GCACGGAACATCAAGATGCA 59.196 50.000 9.85 0.00 42.39 3.96
3310 3512 1.402968 GCACGGAACATCAAGATGCAT 59.597 47.619 9.85 0.00 42.39 3.96
3311 3513 2.159338 GCACGGAACATCAAGATGCATT 60.159 45.455 9.85 0.00 42.39 3.56
3312 3514 3.674138 GCACGGAACATCAAGATGCATTT 60.674 43.478 9.85 0.00 42.39 2.32
3313 3515 4.487948 CACGGAACATCAAGATGCATTTT 58.512 39.130 9.85 0.00 42.39 1.82
3314 3516 4.925054 CACGGAACATCAAGATGCATTTTT 59.075 37.500 9.85 0.00 42.39 1.94
3342 3544 4.813346 ACCGGTTGTGATTGACCC 57.187 55.556 0.00 0.00 32.14 4.46
3343 3545 1.840598 ACCGGTTGTGATTGACCCA 59.159 52.632 0.00 0.00 32.14 4.51
3344 3546 0.404040 ACCGGTTGTGATTGACCCAT 59.596 50.000 0.00 0.00 32.14 4.00
3345 3547 0.810648 CCGGTTGTGATTGACCCATG 59.189 55.000 0.00 0.00 32.14 3.66
3346 3548 0.171007 CGGTTGTGATTGACCCATGC 59.829 55.000 0.00 0.00 32.14 4.06
3347 3549 1.255882 GGTTGTGATTGACCCATGCA 58.744 50.000 0.00 0.00 0.00 3.96
3348 3550 1.203052 GGTTGTGATTGACCCATGCAG 59.797 52.381 0.00 0.00 0.00 4.41
3349 3551 1.203052 GTTGTGATTGACCCATGCAGG 59.797 52.381 0.00 0.00 37.03 4.85
3350 3552 0.697658 TGTGATTGACCCATGCAGGA 59.302 50.000 0.00 0.00 41.22 3.86
3351 3553 1.340308 TGTGATTGACCCATGCAGGAG 60.340 52.381 0.00 0.00 41.22 3.69
3352 3554 0.994247 TGATTGACCCATGCAGGAGT 59.006 50.000 0.00 0.00 41.22 3.85
3353 3555 2.092968 GTGATTGACCCATGCAGGAGTA 60.093 50.000 0.00 0.00 41.22 2.59
3354 3556 2.575735 TGATTGACCCATGCAGGAGTAA 59.424 45.455 0.00 0.00 41.22 2.24
3355 3557 3.202818 TGATTGACCCATGCAGGAGTAAT 59.797 43.478 0.00 0.00 41.22 1.89
3356 3558 3.281727 TTGACCCATGCAGGAGTAATC 57.718 47.619 0.00 0.00 41.22 1.75
3357 3559 1.490490 TGACCCATGCAGGAGTAATCC 59.510 52.381 0.00 0.00 41.22 3.01
3358 3560 0.846693 ACCCATGCAGGAGTAATCCC 59.153 55.000 5.39 0.00 41.22 3.85
3359 3561 0.846015 CCCATGCAGGAGTAATCCCA 59.154 55.000 5.39 0.00 41.22 4.37
3360 3562 1.426598 CCCATGCAGGAGTAATCCCAT 59.573 52.381 5.39 0.10 41.22 4.00
3361 3563 2.511659 CCATGCAGGAGTAATCCCATG 58.488 52.381 16.87 16.87 41.22 3.66
3362 3564 2.158564 CCATGCAGGAGTAATCCCATGT 60.159 50.000 20.13 0.00 41.22 3.21
3363 3565 2.715749 TGCAGGAGTAATCCCATGTG 57.284 50.000 5.39 0.00 0.00 3.21
3364 3566 1.915489 TGCAGGAGTAATCCCATGTGT 59.085 47.619 5.39 0.00 0.00 3.72
3365 3567 3.111484 TGCAGGAGTAATCCCATGTGTA 58.889 45.455 5.39 0.00 0.00 2.90
3366 3568 3.521531 TGCAGGAGTAATCCCATGTGTAA 59.478 43.478 5.39 0.00 0.00 2.41
3367 3569 4.018870 TGCAGGAGTAATCCCATGTGTAAA 60.019 41.667 5.39 0.00 0.00 2.01
3368 3570 4.947388 GCAGGAGTAATCCCATGTGTAAAA 59.053 41.667 5.39 0.00 0.00 1.52
3369 3571 5.417580 GCAGGAGTAATCCCATGTGTAAAAA 59.582 40.000 5.39 0.00 0.00 1.94
3370 3572 6.625081 GCAGGAGTAATCCCATGTGTAAAAAC 60.625 42.308 5.39 0.00 0.00 2.43
3371 3573 6.659242 CAGGAGTAATCCCATGTGTAAAAACT 59.341 38.462 5.39 0.00 0.00 2.66
3372 3574 7.827236 CAGGAGTAATCCCATGTGTAAAAACTA 59.173 37.037 5.39 0.00 0.00 2.24
3373 3575 8.387813 AGGAGTAATCCCATGTGTAAAAACTAA 58.612 33.333 5.39 0.00 0.00 2.24
3374 3576 9.185680 GGAGTAATCCCATGTGTAAAAACTAAT 57.814 33.333 0.00 0.00 0.00 1.73
3376 3578 9.747898 AGTAATCCCATGTGTAAAAACTAATGA 57.252 29.630 0.00 0.00 0.00 2.57
3423 3625 8.737168 AAAATGGTATCTCGAGAATTTCATCA 57.263 30.769 20.91 9.21 0.00 3.07
3424 3626 8.737168 AAATGGTATCTCGAGAATTTCATCAA 57.263 30.769 20.91 0.00 0.00 2.57
3425 3627 8.737168 AATGGTATCTCGAGAATTTCATCAAA 57.263 30.769 20.91 0.00 0.00 2.69
3426 3628 8.737168 ATGGTATCTCGAGAATTTCATCAAAA 57.263 30.769 20.91 0.00 0.00 2.44
3427 3629 8.560355 TGGTATCTCGAGAATTTCATCAAAAA 57.440 30.769 20.91 0.00 0.00 1.94
3451 3653 9.745018 AAAAATGAAAGATGAGAGATAAGGTGA 57.255 29.630 0.00 0.00 0.00 4.02
3452 3654 8.961294 AAATGAAAGATGAGAGATAAGGTGAG 57.039 34.615 0.00 0.00 0.00 3.51
3453 3655 6.477053 TGAAAGATGAGAGATAAGGTGAGG 57.523 41.667 0.00 0.00 0.00 3.86
3454 3656 6.197903 TGAAAGATGAGAGATAAGGTGAGGA 58.802 40.000 0.00 0.00 0.00 3.71
3455 3657 6.323482 TGAAAGATGAGAGATAAGGTGAGGAG 59.677 42.308 0.00 0.00 0.00 3.69
3456 3658 4.739793 AGATGAGAGATAAGGTGAGGAGG 58.260 47.826 0.00 0.00 0.00 4.30
3457 3659 4.418526 AGATGAGAGATAAGGTGAGGAGGA 59.581 45.833 0.00 0.00 0.00 3.71
3458 3660 4.609866 TGAGAGATAAGGTGAGGAGGAA 57.390 45.455 0.00 0.00 0.00 3.36
3459 3661 5.149584 TGAGAGATAAGGTGAGGAGGAAT 57.850 43.478 0.00 0.00 0.00 3.01
3460 3662 6.281190 TGAGAGATAAGGTGAGGAGGAATA 57.719 41.667 0.00 0.00 0.00 1.75
3461 3663 6.310941 TGAGAGATAAGGTGAGGAGGAATAG 58.689 44.000 0.00 0.00 0.00 1.73
3462 3664 6.103353 TGAGAGATAAGGTGAGGAGGAATAGA 59.897 42.308 0.00 0.00 0.00 1.98
3463 3665 6.552008 AGAGATAAGGTGAGGAGGAATAGAG 58.448 44.000 0.00 0.00 0.00 2.43
3464 3666 5.083821 AGATAAGGTGAGGAGGAATAGAGC 58.916 45.833 0.00 0.00 0.00 4.09
3465 3667 1.698506 AGGTGAGGAGGAATAGAGCG 58.301 55.000 0.00 0.00 0.00 5.03
3466 3668 1.063567 AGGTGAGGAGGAATAGAGCGT 60.064 52.381 0.00 0.00 0.00 5.07
3467 3669 1.067821 GGTGAGGAGGAATAGAGCGTG 59.932 57.143 0.00 0.00 0.00 5.34
3468 3670 1.067821 GTGAGGAGGAATAGAGCGTGG 59.932 57.143 0.00 0.00 0.00 4.94
3469 3671 1.342076 TGAGGAGGAATAGAGCGTGGT 60.342 52.381 0.00 0.00 0.00 4.16
3470 3672 1.067821 GAGGAGGAATAGAGCGTGGTG 59.932 57.143 0.00 0.00 0.00 4.17
3471 3673 0.105039 GGAGGAATAGAGCGTGGTGG 59.895 60.000 0.00 0.00 0.00 4.61
3472 3674 0.824759 GAGGAATAGAGCGTGGTGGT 59.175 55.000 0.00 0.00 0.00 4.16
3473 3675 0.537188 AGGAATAGAGCGTGGTGGTG 59.463 55.000 0.00 0.00 0.00 4.17
3474 3676 0.535335 GGAATAGAGCGTGGTGGTGA 59.465 55.000 0.00 0.00 0.00 4.02
3475 3677 1.641577 GAATAGAGCGTGGTGGTGAC 58.358 55.000 0.00 0.00 0.00 3.67
3476 3678 1.204941 GAATAGAGCGTGGTGGTGACT 59.795 52.381 0.00 0.00 0.00 3.41
3477 3679 0.532573 ATAGAGCGTGGTGGTGACTG 59.467 55.000 0.00 0.00 0.00 3.51
3478 3680 1.532604 TAGAGCGTGGTGGTGACTGG 61.533 60.000 0.00 0.00 0.00 4.00
3479 3681 3.161450 AGCGTGGTGGTGACTGGT 61.161 61.111 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.880064 CATGAAAGAAGTAAGCATATTGATCTG 57.120 33.333 0.00 0.00 0.00 2.90
1 2 9.842775 TCATGAAAGAAGTAAGCATATTGATCT 57.157 29.630 0.00 0.00 0.00 2.75
6 7 9.412460 TGGAATCATGAAAGAAGTAAGCATATT 57.588 29.630 0.00 0.00 0.00 1.28
29 30 5.694995 ACTCAAAAGGAAAGTTCTGATGGA 58.305 37.500 0.00 0.00 0.00 3.41
30 31 6.396829 AACTCAAAAGGAAAGTTCTGATGG 57.603 37.500 0.00 0.00 0.00 3.51
58 64 2.714250 TCAACCCTCAAAAGGAGCCTTA 59.286 45.455 1.54 0.00 46.67 2.69
125 232 2.877360 TTATGGACGACGCCACGCTC 62.877 60.000 12.22 0.00 41.56 5.03
128 235 0.368907 CTTTTATGGACGACGCCACG 59.631 55.000 12.22 0.00 41.56 4.94
130 237 1.404986 CCTCTTTTATGGACGACGCCA 60.405 52.381 12.33 12.33 43.23 5.69
142 249 0.254747 CCCATCGGTGCCCTCTTTTA 59.745 55.000 0.00 0.00 0.00 1.52
151 258 0.693049 ATATCTTCCCCCATCGGTGC 59.307 55.000 0.00 0.00 0.00 5.01
170 277 2.298729 GGTTGAAATTTACTGGGCTGCA 59.701 45.455 0.50 0.00 0.00 4.41
181 288 2.043227 TGGGCTTTCGGGTTGAAATTT 58.957 42.857 0.00 0.00 45.21 1.82
218 325 2.292016 CACTTGTTTCGTGGGTATGCAA 59.708 45.455 0.00 0.00 0.00 4.08
223 330 1.485480 TGGACACTTGTTTCGTGGGTA 59.515 47.619 0.00 0.00 36.71 3.69
226 333 1.597663 GACTGGACACTTGTTTCGTGG 59.402 52.381 0.00 0.00 36.71 4.94
257 369 1.003233 TCGCTCTGAGTCTGTGACCTA 59.997 52.381 6.53 0.00 32.18 3.08
433 563 2.760374 ACGGCAGAGAAAAACAGAGAG 58.240 47.619 0.00 0.00 0.00 3.20
434 564 2.910688 ACGGCAGAGAAAAACAGAGA 57.089 45.000 0.00 0.00 0.00 3.10
435 565 3.430218 CACTACGGCAGAGAAAAACAGAG 59.570 47.826 0.00 0.00 0.00 3.35
436 566 3.181469 ACACTACGGCAGAGAAAAACAGA 60.181 43.478 0.00 0.00 0.00 3.41
449 579 3.479269 GCGAGCACACACTACGGC 61.479 66.667 0.00 0.00 0.00 5.68
560 690 4.141482 GCTACCAATCAGACCTATTCCCAA 60.141 45.833 0.00 0.00 0.00 4.12
568 698 1.273838 TGGGAGCTACCAATCAGACCT 60.274 52.381 17.88 0.00 41.20 3.85
580 710 6.889722 AGTACAAATTAGCAAATTGGGAGCTA 59.110 34.615 0.00 0.00 39.68 3.32
584 714 6.909550 ACAGTACAAATTAGCAAATTGGGA 57.090 33.333 0.00 0.00 35.46 4.37
623 753 8.911965 CATATAGATATAGACAGCCAGACACAT 58.088 37.037 0.00 0.00 0.00 3.21
624 754 8.109634 TCATATAGATATAGACAGCCAGACACA 58.890 37.037 0.00 0.00 0.00 3.72
688 821 3.053320 CCCCTTTCCTAGGCTCTTCATTT 60.053 47.826 2.96 0.00 43.27 2.32
689 822 2.511637 CCCCTTTCCTAGGCTCTTCATT 59.488 50.000 2.96 0.00 43.27 2.57
690 823 2.131023 CCCCTTTCCTAGGCTCTTCAT 58.869 52.381 2.96 0.00 43.27 2.57
691 824 1.080498 TCCCCTTTCCTAGGCTCTTCA 59.920 52.381 2.96 0.00 43.27 3.02
692 825 1.880941 TCCCCTTTCCTAGGCTCTTC 58.119 55.000 2.96 0.00 43.27 2.87
699 832 1.180029 TCGTCGTTCCCCTTTCCTAG 58.820 55.000 0.00 0.00 0.00 3.02
701 834 0.760572 TTTCGTCGTTCCCCTTTCCT 59.239 50.000 0.00 0.00 0.00 3.36
703 836 2.161012 GGATTTTCGTCGTTCCCCTTTC 59.839 50.000 0.00 0.00 0.00 2.62
704 837 2.156917 GGATTTTCGTCGTTCCCCTTT 58.843 47.619 0.00 0.00 0.00 3.11
714 847 5.526010 AATAGTGTCAACGGATTTTCGTC 57.474 39.130 0.00 0.00 43.07 4.20
751 884 5.059161 TCTTGAGAAGGAGAACACAACATG 58.941 41.667 0.00 0.00 0.00 3.21
752 885 5.296151 TCTTGAGAAGGAGAACACAACAT 57.704 39.130 0.00 0.00 0.00 2.71
753 886 4.753516 TCTTGAGAAGGAGAACACAACA 57.246 40.909 0.00 0.00 0.00 3.33
754 887 7.730364 TTATTCTTGAGAAGGAGAACACAAC 57.270 36.000 0.00 0.00 37.48 3.32
755 888 8.746052 TTTTATTCTTGAGAAGGAGAACACAA 57.254 30.769 0.00 0.00 37.48 3.33
756 889 8.746052 TTTTTATTCTTGAGAAGGAGAACACA 57.254 30.769 0.00 0.00 37.48 3.72
811 948 4.626042 CATTTCCCCAAAACACGAATTCA 58.374 39.130 6.22 0.00 0.00 2.57
817 954 0.665972 CGGCATTTCCCCAAAACACG 60.666 55.000 0.00 0.00 0.00 4.49
825 962 1.523032 CGGTAGACGGCATTTCCCC 60.523 63.158 0.00 0.00 39.42 4.81
886 1023 5.148651 ACAGGTAAGTACTTGGCACTTAG 57.851 43.478 18.56 5.61 38.74 2.18
922 1059 6.474140 TGATTCTTTAATGCAATGCCAGAT 57.526 33.333 1.53 0.00 0.00 2.90
951 1088 5.204833 CGTCAAAACACAGAACATGTAAGG 58.795 41.667 0.00 0.00 41.41 2.69
972 1109 3.274455 CTGCAGCAGGACGAGACGT 62.274 63.158 15.35 0.00 45.10 4.34
974 1111 0.108424 AATCTGCAGCAGGACGAGAC 60.108 55.000 22.62 0.00 31.51 3.36
981 1118 2.034104 TAGCTTCAATCTGCAGCAGG 57.966 50.000 22.62 6.69 39.10 4.85
1044 1181 2.623878 AGAGAGTCGGATTCGAGCTA 57.376 50.000 0.00 0.00 46.91 3.32
1053 1190 2.437085 TTGCCTGATAGAGAGTCGGA 57.563 50.000 0.00 0.00 0.00 4.55
1123 1260 6.645827 CAGATCATCAACAGAGGTATAAGCTG 59.354 42.308 0.00 0.00 35.81 4.24
1339 1487 6.593770 GGAAAGAACAAAGCAAAAAGGAAGAA 59.406 34.615 0.00 0.00 0.00 2.52
1340 1488 6.106003 GGAAAGAACAAAGCAAAAAGGAAGA 58.894 36.000 0.00 0.00 0.00 2.87
1341 1489 5.874261 TGGAAAGAACAAAGCAAAAAGGAAG 59.126 36.000 0.00 0.00 0.00 3.46
1342 1490 5.799213 TGGAAAGAACAAAGCAAAAAGGAA 58.201 33.333 0.00 0.00 0.00 3.36
1343 1491 5.413309 TGGAAAGAACAAAGCAAAAAGGA 57.587 34.783 0.00 0.00 0.00 3.36
1344 1492 4.034394 GCTGGAAAGAACAAAGCAAAAAGG 59.966 41.667 0.00 0.00 34.01 3.11
1352 1500 8.119226 CGATAATCTTAGCTGGAAAGAACAAAG 58.881 37.037 0.00 0.00 36.60 2.77
1383 1531 0.607217 TAGACCTTCCAGTGTCGCGA 60.607 55.000 3.71 3.71 36.61 5.87
1395 1543 4.455070 AAAGCCAAAACCTCTAGACCTT 57.545 40.909 0.00 0.00 0.00 3.50
1467 1615 5.761234 TCCCGATTATGATTTTACCTTTCCG 59.239 40.000 0.00 0.00 0.00 4.30
1510 1658 1.761449 TCAGAAAGCACAGCACCAAA 58.239 45.000 0.00 0.00 0.00 3.28
1557 1705 8.884124 AATTTATCCTGGTCTGAAATTTCTCA 57.116 30.769 18.64 10.62 0.00 3.27
1583 1731 6.569127 TTGGGGCAAGATATAGTTCTAACA 57.431 37.500 0.00 0.00 0.00 2.41
1584 1732 7.939588 AGAATTGGGGCAAGATATAGTTCTAAC 59.060 37.037 0.00 0.00 0.00 2.34
1600 1748 2.442236 TTGATGGAGAGAATTGGGGC 57.558 50.000 0.00 0.00 0.00 5.80
1651 1800 9.864034 GTTTCACCATCATTAATGTAGAATACG 57.136 33.333 14.97 0.00 46.99 3.06
1702 1851 4.220693 CATGACATCCAGGGAAGTACAA 57.779 45.455 0.00 0.00 0.00 2.41
1758 1907 6.238211 GGATTGCAGTGATAACTGATGTACAC 60.238 42.308 14.96 0.00 39.99 2.90
1859 2008 2.076100 TGATGTGGCAGAATTCACGAC 58.924 47.619 8.44 7.38 36.74 4.34
1916 2065 9.154847 CACTCACTGATGAACTTGACATAATTA 57.845 33.333 0.00 0.00 33.30 1.40
1920 2069 6.345096 TCACTCACTGATGAACTTGACATA 57.655 37.500 0.00 0.00 33.30 2.29
1957 2106 4.541705 TGTCAAGGGAAGGTGATGAAAAA 58.458 39.130 0.00 0.00 0.00 1.94
2073 2227 5.105957 CGTCCATGTAGATCCTGAGATAAGG 60.106 48.000 0.00 0.00 38.84 2.69
2074 2228 5.621104 GCGTCCATGTAGATCCTGAGATAAG 60.621 48.000 0.00 0.00 30.90 1.73
2075 2229 4.218635 GCGTCCATGTAGATCCTGAGATAA 59.781 45.833 0.00 0.00 30.90 1.75
2076 2230 3.759086 GCGTCCATGTAGATCCTGAGATA 59.241 47.826 0.00 0.00 30.90 1.98
2308 2507 0.821711 CAGCTGGGTTTCCACCGAAA 60.822 55.000 5.57 0.00 45.39 3.46
2357 2556 2.304180 CAAGGGAGAACTCATCACCACT 59.696 50.000 4.23 0.00 40.30 4.00
2474 2673 0.252239 TGCAGACTGGAGCCCTAGAA 60.252 55.000 4.26 0.00 0.00 2.10
2586 2785 7.934855 ACTCGAGTAAGTTATTTGGTCTCTA 57.065 36.000 18.46 0.00 0.00 2.43
2587 2786 6.837471 ACTCGAGTAAGTTATTTGGTCTCT 57.163 37.500 18.46 0.00 0.00 3.10
2588 2787 6.971756 GGTACTCGAGTAAGTTATTTGGTCTC 59.028 42.308 26.21 8.90 31.52 3.36
2589 2788 6.662663 AGGTACTCGAGTAAGTTATTTGGTCT 59.337 38.462 26.21 7.22 31.52 3.85
2590 2789 6.750963 CAGGTACTCGAGTAAGTTATTTGGTC 59.249 42.308 26.21 9.51 34.60 4.02
2592 2791 5.519206 GCAGGTACTCGAGTAAGTTATTTGG 59.481 44.000 26.21 9.80 34.60 3.28
2593 2792 5.229469 CGCAGGTACTCGAGTAAGTTATTTG 59.771 44.000 26.21 16.06 34.60 2.32
2604 2803 0.179161 CCTCAACGCAGGTACTCGAG 60.179 60.000 11.84 11.84 34.60 4.04
2605 2804 0.892358 ACCTCAACGCAGGTACTCGA 60.892 55.000 0.00 0.00 45.71 4.04
2607 2806 0.601558 TCACCTCAACGCAGGTACTC 59.398 55.000 1.16 0.00 45.81 2.59
2664 2863 8.902735 GGATAATTTGTGAAGAGAACGAAAAAC 58.097 33.333 0.00 0.00 0.00 2.43
2670 2869 7.364522 TGAAGGATAATTTGTGAAGAGAACG 57.635 36.000 0.00 0.00 0.00 3.95
2671 2870 7.094634 TGCTGAAGGATAATTTGTGAAGAGAAC 60.095 37.037 0.00 0.00 0.00 3.01
2672 2871 6.942005 TGCTGAAGGATAATTTGTGAAGAGAA 59.058 34.615 0.00 0.00 0.00 2.87
2706 2905 4.019411 GGTTCCAAACATGATCCCCAAAAT 60.019 41.667 0.00 0.00 0.00 1.82
2714 2913 5.622770 AACTAACGGTTCCAAACATGATC 57.377 39.130 0.00 0.00 31.69 2.92
2768 2967 2.173356 CCCTTGTCAGGCCATTATCAGA 59.827 50.000 5.01 0.00 39.20 3.27
2770 2969 1.922447 ACCCTTGTCAGGCCATTATCA 59.078 47.619 5.01 0.00 39.20 2.15
2790 2989 5.011533 CCACCAATCAAATTGTTCTGGGTAA 59.988 40.000 12.65 0.00 38.59 2.85
2814 3013 6.038356 CAGAAAACAATATGATCCTTGTGGC 58.962 40.000 6.27 0.00 35.82 5.01
2870 3069 9.077885 AGGCAAAGAAGAACAGACAAAATATAA 57.922 29.630 0.00 0.00 0.00 0.98
2898 3097 4.223953 GAGGAGTAACAGGTCATGGGATA 58.776 47.826 0.00 0.00 0.00 2.59
2909 3108 5.695851 AAACAGCAAATGAGGAGTAACAG 57.304 39.130 0.00 0.00 0.00 3.16
2921 3120 5.104374 CAGACACAACAGAAAACAGCAAAT 58.896 37.500 0.00 0.00 0.00 2.32
2969 3168 5.500234 TGTACAGAAAAGCCTGCATTCTAT 58.500 37.500 9.07 2.90 37.68 1.98
2981 3181 3.420893 TCCCCTGCATTGTACAGAAAAG 58.579 45.455 0.00 0.00 37.32 2.27
2996 3196 1.153086 CCTCAAGCGGATTCCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
3002 3202 1.541588 GCAGAAAACCTCAAGCGGATT 59.458 47.619 0.00 0.00 0.00 3.01
3008 3208 4.261783 GGAAAAGGAGCAGAAAACCTCAAG 60.262 45.833 0.00 0.00 33.16 3.02
3037 3237 8.841444 AATAAATGAATGCGAGTTTGTATGAC 57.159 30.769 0.00 0.00 0.00 3.06
3044 3244 9.474920 TCTTTTCAAATAAATGAATGCGAGTTT 57.525 25.926 0.00 0.00 38.98 2.66
3069 3269 4.428209 TGTCTCTTGATCGAGCTGATTTC 58.572 43.478 4.94 0.00 37.47 2.17
3071 3271 4.669206 ATGTCTCTTGATCGAGCTGATT 57.331 40.909 4.94 0.00 37.47 2.57
3073 3273 3.194329 ACAATGTCTCTTGATCGAGCTGA 59.806 43.478 4.94 3.54 0.00 4.26
3092 3294 0.901124 AAGCACCTGCCAAACAACAA 59.099 45.000 0.00 0.00 43.38 2.83
3093 3295 0.459489 GAAGCACCTGCCAAACAACA 59.541 50.000 0.00 0.00 43.38 3.33
3098 3300 1.032014 GTTCAGAAGCACCTGCCAAA 58.968 50.000 0.00 0.00 43.38 3.28
3117 3319 3.578688 GCAAACTGCTACTTTCAATGGG 58.421 45.455 0.00 0.00 40.96 4.00
3123 3325 0.591170 TGCCGCAAACTGCTACTTTC 59.409 50.000 0.00 0.00 42.25 2.62
3144 3346 3.559171 CCCGTGGAGATTCTTTCAGGAAA 60.559 47.826 10.31 0.00 0.00 3.13
3147 3349 2.014068 GCCCGTGGAGATTCTTTCAGG 61.014 57.143 0.00 0.00 0.00 3.86
3167 3369 0.689623 AGTGCAGTTTCAGAGGGAGG 59.310 55.000 0.00 0.00 0.00 4.30
3209 3411 9.710979 TTTGTTGAGAAAATACGTTTAGTTCTG 57.289 29.630 0.00 0.00 0.00 3.02
3237 3439 8.136800 GGAATAAAGTTCTTTACCCGTCAAAAA 58.863 33.333 7.09 0.00 0.00 1.94
3238 3440 7.503230 AGGAATAAAGTTCTTTACCCGTCAAAA 59.497 33.333 7.09 0.00 0.00 2.44
3239 3441 6.999871 AGGAATAAAGTTCTTTACCCGTCAAA 59.000 34.615 7.09 0.00 0.00 2.69
3240 3442 6.536447 AGGAATAAAGTTCTTTACCCGTCAA 58.464 36.000 7.09 0.00 0.00 3.18
3241 3443 6.117975 AGGAATAAAGTTCTTTACCCGTCA 57.882 37.500 7.09 0.00 0.00 4.35
3242 3444 6.168389 TGAGGAATAAAGTTCTTTACCCGTC 58.832 40.000 7.09 11.62 0.00 4.79
3243 3445 6.013984 TCTGAGGAATAAAGTTCTTTACCCGT 60.014 38.462 7.09 4.64 0.00 5.28
3244 3446 6.313164 GTCTGAGGAATAAAGTTCTTTACCCG 59.687 42.308 7.09 2.00 0.00 5.28
3245 3447 7.395617 AGTCTGAGGAATAAAGTTCTTTACCC 58.604 38.462 7.09 10.66 0.00 3.69
3246 3448 9.589111 CTAGTCTGAGGAATAAAGTTCTTTACC 57.411 37.037 7.09 5.76 0.00 2.85
3247 3449 9.089601 GCTAGTCTGAGGAATAAAGTTCTTTAC 57.910 37.037 7.09 0.00 0.00 2.01
3248 3450 8.812972 TGCTAGTCTGAGGAATAAAGTTCTTTA 58.187 33.333 7.35 7.35 0.00 1.85
3249 3451 7.680730 TGCTAGTCTGAGGAATAAAGTTCTTT 58.319 34.615 3.33 3.33 0.00 2.52
3250 3452 7.246171 TGCTAGTCTGAGGAATAAAGTTCTT 57.754 36.000 0.00 0.00 0.00 2.52
3251 3453 6.859112 TGCTAGTCTGAGGAATAAAGTTCT 57.141 37.500 0.00 0.00 0.00 3.01
3252 3454 7.324178 TCTTGCTAGTCTGAGGAATAAAGTTC 58.676 38.462 0.00 0.00 0.00 3.01
3253 3455 7.246171 TCTTGCTAGTCTGAGGAATAAAGTT 57.754 36.000 0.00 0.00 0.00 2.66
3254 3456 6.859112 TCTTGCTAGTCTGAGGAATAAAGT 57.141 37.500 0.00 0.00 0.00 2.66
3255 3457 6.202570 GCATCTTGCTAGTCTGAGGAATAAAG 59.797 42.308 0.00 0.00 40.96 1.85
3256 3458 6.051717 GCATCTTGCTAGTCTGAGGAATAAA 58.948 40.000 0.00 0.00 40.96 1.40
3257 3459 5.453903 GGCATCTTGCTAGTCTGAGGAATAA 60.454 44.000 0.00 0.00 44.28 1.40
3258 3460 4.039730 GGCATCTTGCTAGTCTGAGGAATA 59.960 45.833 0.00 0.00 44.28 1.75
3259 3461 3.181456 GGCATCTTGCTAGTCTGAGGAAT 60.181 47.826 0.00 0.00 44.28 3.01
3260 3462 2.169352 GGCATCTTGCTAGTCTGAGGAA 59.831 50.000 0.00 0.00 44.28 3.36
3261 3463 1.759445 GGCATCTTGCTAGTCTGAGGA 59.241 52.381 0.00 0.00 44.28 3.71
3262 3464 1.202627 GGGCATCTTGCTAGTCTGAGG 60.203 57.143 0.00 0.00 44.28 3.86
3263 3465 1.537776 CGGGCATCTTGCTAGTCTGAG 60.538 57.143 0.00 0.00 44.28 3.35
3264 3466 0.461548 CGGGCATCTTGCTAGTCTGA 59.538 55.000 0.00 0.00 44.28 3.27
3265 3467 0.176680 ACGGGCATCTTGCTAGTCTG 59.823 55.000 0.00 0.00 44.28 3.51
3266 3468 0.176680 CACGGGCATCTTGCTAGTCT 59.823 55.000 0.00 0.00 44.28 3.24
3267 3469 1.432270 GCACGGGCATCTTGCTAGTC 61.432 60.000 3.77 0.00 44.28 2.59
3268 3470 1.450312 GCACGGGCATCTTGCTAGT 60.450 57.895 3.77 0.00 44.28 2.57
3269 3471 3.414272 GCACGGGCATCTTGCTAG 58.586 61.111 3.77 0.00 44.28 3.42
3284 3486 0.957362 TTGATGTTCCGTGCAATGCA 59.043 45.000 2.72 2.72 35.60 3.96
3285 3487 1.199789 TCTTGATGTTCCGTGCAATGC 59.800 47.619 0.00 0.00 0.00 3.56
3286 3488 3.431856 CATCTTGATGTTCCGTGCAATG 58.568 45.455 0.00 0.00 0.00 2.82
3287 3489 2.159338 GCATCTTGATGTTCCGTGCAAT 60.159 45.455 11.61 0.00 0.00 3.56
3288 3490 1.199789 GCATCTTGATGTTCCGTGCAA 59.800 47.619 11.61 0.00 0.00 4.08
3289 3491 0.804364 GCATCTTGATGTTCCGTGCA 59.196 50.000 11.61 0.00 0.00 4.57
3290 3492 0.804364 TGCATCTTGATGTTCCGTGC 59.196 50.000 11.61 0.00 0.00 5.34
3291 3493 3.770263 AATGCATCTTGATGTTCCGTG 57.230 42.857 0.00 0.00 0.00 4.94
3292 3494 4.789012 AAAATGCATCTTGATGTTCCGT 57.211 36.364 0.00 0.00 0.00 4.69
3325 3527 0.404040 ATGGGTCAATCACAACCGGT 59.596 50.000 0.00 0.00 36.35 5.28
3326 3528 0.810648 CATGGGTCAATCACAACCGG 59.189 55.000 0.00 0.00 36.35 5.28
3327 3529 0.171007 GCATGGGTCAATCACAACCG 59.829 55.000 0.00 0.00 36.35 4.44
3328 3530 1.203052 CTGCATGGGTCAATCACAACC 59.797 52.381 0.00 0.00 31.12 3.77
3329 3531 1.203052 CCTGCATGGGTCAATCACAAC 59.797 52.381 0.00 0.00 31.12 3.32
3330 3532 1.075212 TCCTGCATGGGTCAATCACAA 59.925 47.619 0.00 0.00 36.20 3.33
3331 3533 0.697658 TCCTGCATGGGTCAATCACA 59.302 50.000 0.00 0.00 36.20 3.58
3332 3534 1.340405 ACTCCTGCATGGGTCAATCAC 60.340 52.381 0.00 0.00 36.20 3.06
3333 3535 0.994247 ACTCCTGCATGGGTCAATCA 59.006 50.000 0.00 0.00 36.20 2.57
3334 3536 3.281727 TTACTCCTGCATGGGTCAATC 57.718 47.619 0.00 0.00 36.20 2.67
3335 3537 3.435601 GGATTACTCCTGCATGGGTCAAT 60.436 47.826 0.00 0.00 38.65 2.57
3336 3538 2.092429 GGATTACTCCTGCATGGGTCAA 60.092 50.000 0.00 0.00 38.65 3.18
3337 3539 1.490490 GGATTACTCCTGCATGGGTCA 59.510 52.381 0.00 0.00 38.65 4.02
3338 3540 1.202818 GGGATTACTCCTGCATGGGTC 60.203 57.143 0.00 0.00 41.74 4.46
3339 3541 0.846693 GGGATTACTCCTGCATGGGT 59.153 55.000 0.00 0.00 41.74 4.51
3340 3542 0.846015 TGGGATTACTCCTGCATGGG 59.154 55.000 0.00 0.00 41.74 4.00
3341 3543 2.158564 ACATGGGATTACTCCTGCATGG 60.159 50.000 17.08 0.00 41.71 3.66
3342 3544 2.882761 CACATGGGATTACTCCTGCATG 59.117 50.000 13.41 13.41 42.45 4.06
3343 3545 2.511218 ACACATGGGATTACTCCTGCAT 59.489 45.455 0.00 0.00 41.74 3.96
3344 3546 1.915489 ACACATGGGATTACTCCTGCA 59.085 47.619 0.00 0.00 41.74 4.41
3345 3547 2.717639 ACACATGGGATTACTCCTGC 57.282 50.000 0.00 0.00 41.74 4.85
3346 3548 6.659242 AGTTTTTACACATGGGATTACTCCTG 59.341 38.462 0.00 0.00 41.74 3.86
3347 3549 6.790319 AGTTTTTACACATGGGATTACTCCT 58.210 36.000 0.00 0.00 41.74 3.69
3348 3550 8.570068 TTAGTTTTTACACATGGGATTACTCC 57.430 34.615 0.00 0.00 41.26 3.85
3350 3552 9.747898 TCATTAGTTTTTACACATGGGATTACT 57.252 29.630 0.00 0.12 0.00 2.24
3397 3599 9.177608 TGATGAAATTCTCGAGATACCATTTTT 57.822 29.630 17.44 10.32 0.00 1.94
3398 3600 8.737168 TGATGAAATTCTCGAGATACCATTTT 57.263 30.769 17.44 9.34 0.00 1.82
3399 3601 8.737168 TTGATGAAATTCTCGAGATACCATTT 57.263 30.769 17.44 17.95 0.00 2.32
3400 3602 8.737168 TTTGATGAAATTCTCGAGATACCATT 57.263 30.769 17.44 10.07 0.00 3.16
3401 3603 8.737168 TTTTGATGAAATTCTCGAGATACCAT 57.263 30.769 17.44 16.12 0.00 3.55
3402 3604 8.560355 TTTTTGATGAAATTCTCGAGATACCA 57.440 30.769 17.44 12.19 0.00 3.25
3425 3627 9.745018 TCACCTTATCTCTCATCTTTCATTTTT 57.255 29.630 0.00 0.00 0.00 1.94
3426 3628 9.393512 CTCACCTTATCTCTCATCTTTCATTTT 57.606 33.333 0.00 0.00 0.00 1.82
3427 3629 7.992033 CCTCACCTTATCTCTCATCTTTCATTT 59.008 37.037 0.00 0.00 0.00 2.32
3428 3630 7.346698 TCCTCACCTTATCTCTCATCTTTCATT 59.653 37.037 0.00 0.00 0.00 2.57
3429 3631 6.843333 TCCTCACCTTATCTCTCATCTTTCAT 59.157 38.462 0.00 0.00 0.00 2.57
3430 3632 6.197903 TCCTCACCTTATCTCTCATCTTTCA 58.802 40.000 0.00 0.00 0.00 2.69
3431 3633 6.239289 CCTCCTCACCTTATCTCTCATCTTTC 60.239 46.154 0.00 0.00 0.00 2.62
3432 3634 5.602145 CCTCCTCACCTTATCTCTCATCTTT 59.398 44.000 0.00 0.00 0.00 2.52
3433 3635 5.103301 TCCTCCTCACCTTATCTCTCATCTT 60.103 44.000 0.00 0.00 0.00 2.40
3434 3636 4.418526 TCCTCCTCACCTTATCTCTCATCT 59.581 45.833 0.00 0.00 0.00 2.90
3435 3637 4.735369 TCCTCCTCACCTTATCTCTCATC 58.265 47.826 0.00 0.00 0.00 2.92
3436 3638 4.823364 TCCTCCTCACCTTATCTCTCAT 57.177 45.455 0.00 0.00 0.00 2.90
3437 3639 4.609866 TTCCTCCTCACCTTATCTCTCA 57.390 45.455 0.00 0.00 0.00 3.27
3438 3640 6.548321 TCTATTCCTCCTCACCTTATCTCTC 58.452 44.000 0.00 0.00 0.00 3.20
3439 3641 6.538209 TCTATTCCTCCTCACCTTATCTCT 57.462 41.667 0.00 0.00 0.00 3.10
3440 3642 5.185056 GCTCTATTCCTCCTCACCTTATCTC 59.815 48.000 0.00 0.00 0.00 2.75
3441 3643 5.083821 GCTCTATTCCTCCTCACCTTATCT 58.916 45.833 0.00 0.00 0.00 1.98
3442 3644 4.082463 CGCTCTATTCCTCCTCACCTTATC 60.082 50.000 0.00 0.00 0.00 1.75
3443 3645 3.829601 CGCTCTATTCCTCCTCACCTTAT 59.170 47.826 0.00 0.00 0.00 1.73
3444 3646 3.223435 CGCTCTATTCCTCCTCACCTTA 58.777 50.000 0.00 0.00 0.00 2.69
3445 3647 2.035632 CGCTCTATTCCTCCTCACCTT 58.964 52.381 0.00 0.00 0.00 3.50
3446 3648 1.063567 ACGCTCTATTCCTCCTCACCT 60.064 52.381 0.00 0.00 0.00 4.00
3447 3649 1.067821 CACGCTCTATTCCTCCTCACC 59.932 57.143 0.00 0.00 0.00 4.02
3448 3650 1.067821 CCACGCTCTATTCCTCCTCAC 59.932 57.143 0.00 0.00 0.00 3.51
3449 3651 1.342076 ACCACGCTCTATTCCTCCTCA 60.342 52.381 0.00 0.00 0.00 3.86
3450 3652 1.067821 CACCACGCTCTATTCCTCCTC 59.932 57.143 0.00 0.00 0.00 3.71
3451 3653 1.115467 CACCACGCTCTATTCCTCCT 58.885 55.000 0.00 0.00 0.00 3.69
3452 3654 0.105039 CCACCACGCTCTATTCCTCC 59.895 60.000 0.00 0.00 0.00 4.30
3453 3655 0.824759 ACCACCACGCTCTATTCCTC 59.175 55.000 0.00 0.00 0.00 3.71
3454 3656 0.537188 CACCACCACGCTCTATTCCT 59.463 55.000 0.00 0.00 0.00 3.36
3455 3657 0.535335 TCACCACCACGCTCTATTCC 59.465 55.000 0.00 0.00 0.00 3.01
3456 3658 1.204941 AGTCACCACCACGCTCTATTC 59.795 52.381 0.00 0.00 0.00 1.75
3457 3659 1.066858 CAGTCACCACCACGCTCTATT 60.067 52.381 0.00 0.00 0.00 1.73
3458 3660 0.532573 CAGTCACCACCACGCTCTAT 59.467 55.000 0.00 0.00 0.00 1.98
3459 3661 1.532604 CCAGTCACCACCACGCTCTA 61.533 60.000 0.00 0.00 0.00 2.43
3460 3662 2.737180 CAGTCACCACCACGCTCT 59.263 61.111 0.00 0.00 0.00 4.09
3461 3663 2.357517 CCAGTCACCACCACGCTC 60.358 66.667 0.00 0.00 0.00 5.03
3462 3664 3.161450 ACCAGTCACCACCACGCT 61.161 61.111 0.00 0.00 0.00 5.07


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

AutoCloner maintained by Alex Coulton.