Multiple sequence alignment - TraesCS7B01G365700

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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 TraesCS7B01G365700 chr7B 100.000 2839 0 0 2220 5058 629581589 629578751 0.000000e+00 5243.0
1 TraesCS7B01G365700 chr7B 100.000 1774 0 0 1 1774 629583808 629582035 0.000000e+00 3277.0
2 TraesCS7B01G365700 chr7B 78.528 163 26 8 4581 4740 699363190 699363034 1.160000e-16 99.0
3 TraesCS7B01G365700 chr7A 95.466 1213 42 7 2915 4123 661594032 661595235 0.000000e+00 1923.0
4 TraesCS7B01G365700 chr7A 93.139 787 26 11 991 1761 661589226 661590000 0.000000e+00 1129.0
5 TraesCS7B01G365700 chr7A 92.751 676 38 10 18 686 661588144 661588815 0.000000e+00 966.0
6 TraesCS7B01G365700 chr7A 77.899 828 118 33 4134 4923 661596358 661597158 5.970000e-124 455.0
7 TraesCS7B01G365700 chr7A 92.910 268 14 3 2220 2482 661590350 661590617 7.940000e-103 385.0
8 TraesCS7B01G365700 chr7A 91.707 205 14 3 684 886 661588910 661589113 1.070000e-71 281.0
9 TraesCS7B01G365700 chr7A 91.960 199 14 2 2708 2906 661591501 661591697 1.390000e-70 278.0
10 TraesCS7B01G365700 chr7A 88.261 230 20 6 2494 2717 661590902 661591130 8.350000e-68 268.0
11 TraesCS7B01G365700 chr7A 95.902 122 4 1 841 961 661589109 661589230 3.990000e-46 196.0
12 TraesCS7B01G365700 chr7D 95.317 1153 38 5 2972 4123 572553692 572554829 0.000000e+00 1816.0
13 TraesCS7B01G365700 chr7D 95.690 928 21 6 841 1767 572548792 572549701 0.000000e+00 1474.0
14 TraesCS7B01G365700 chr7D 94.712 832 33 9 34 860 572547940 572548765 0.000000e+00 1282.0
15 TraesCS7B01G365700 chr7D 97.660 470 10 1 2509 2977 572550548 572551017 0.000000e+00 806.0
16 TraesCS7B01G365700 chr7D 81.091 825 103 29 4135 4923 572562496 572563303 1.200000e-170 610.0
17 TraesCS7B01G365700 chr7D 98.859 263 3 0 2220 2482 572549805 572550067 2.130000e-128 470.0
18 TraesCS7B01G365700 chr7D 74.805 385 65 23 4388 4754 5318754 5318384 1.470000e-30 145.0
19 TraesCS7B01G365700 chr7D 73.976 415 79 18 4360 4754 145910527 145910122 1.900000e-29 141.0
20 TraesCS7B01G365700 chr7D 73.243 441 95 15 4327 4750 47425851 47425417 6.830000e-29 139.0
21 TraesCS7B01G365700 chr7D 78.075 187 34 6 4571 4754 610795416 610795598 1.490000e-20 111.0
22 TraesCS7B01G365700 chr4A 86.915 1559 156 30 2535 4064 140978140 140979679 0.000000e+00 1705.0
23 TraesCS7B01G365700 chr4A 79.837 734 110 21 934 1634 140975952 140976680 7.560000e-138 501.0
24 TraesCS7B01G365700 chr4A 90.055 362 36 0 2977 3338 253273855 253274216 2.130000e-128 470.0
25 TraesCS7B01G365700 chr4A 87.981 208 21 3 2220 2424 140977198 140977404 5.060000e-60 243.0
26 TraesCS7B01G365700 chr4A 88.235 85 6 3 1664 1748 140976975 140977055 1.160000e-16 99.0
27 TraesCS7B01G365700 chr4D 86.120 1585 170 29 2514 4067 329138818 329137253 0.000000e+00 1663.0
28 TraesCS7B01G365700 chr4D 84.054 671 74 20 1092 1748 329140312 329139661 2.590000e-172 616.0
29 TraesCS7B01G365700 chr4D 92.913 127 9 0 2226 2352 329139513 329139387 8.650000e-43 185.0
30 TraesCS7B01G365700 chr4D 73.394 436 90 20 4324 4741 344128374 344128801 6.830000e-29 139.0
31 TraesCS7B01G365700 chr4D 81.379 145 17 6 4 141 6475652 6475793 5.350000e-20 110.0
32 TraesCS7B01G365700 chr1B 86.176 1577 169 29 2514 4059 135815951 135817509 0.000000e+00 1659.0
33 TraesCS7B01G365700 chr1B 83.432 676 82 19 1083 1748 135814422 135815077 7.250000e-168 601.0
34 TraesCS7B01G365700 chr1B 85.818 275 25 7 2220 2482 135815198 135815470 3.860000e-71 279.0
35 TraesCS7B01G365700 chr4B 87.050 1112 117 18 2963 4062 408980681 408979585 0.000000e+00 1230.0
36 TraesCS7B01G365700 chr4B 83.735 664 81 18 1092 1748 408984260 408983617 2.010000e-168 603.0
37 TraesCS7B01G365700 chr4B 87.409 413 44 5 2514 2922 408982804 408982396 7.670000e-128 468.0
38 TraesCS7B01G365700 chr4B 93.333 120 8 0 2233 2352 408983462 408983343 1.450000e-40 178.0
39 TraesCS7B01G365700 chr2B 81.609 174 32 0 4576 4749 393475399 393475226 1.470000e-30 145.0
40 TraesCS7B01G365700 chr2B 78.977 176 28 8 4571 4741 653584452 653584623 1.490000e-20 111.0
41 TraesCS7B01G365700 chr5A 82.069 145 22 4 4918 5058 545051658 545051802 2.470000e-23 121.0
42 TraesCS7B01G365700 chr2D 73.048 397 75 21 4331 4709 546780088 546780470 1.490000e-20 111.0
43 TraesCS7B01G365700 chr3B 80.690 145 16 11 3 141 586432407 586432545 8.960000e-18 102.0
44 TraesCS7B01G365700 chr6B 80.137 146 17 8 5 141 712129552 712129694 1.160000e-16 99.0
45 TraesCS7B01G365700 chr5D 77.966 118 21 3 4920 5034 356322751 356322636 9.090000e-08 69.4
46 TraesCS7B01G365700 chr2A 95.238 42 2 0 4918 4959 371345370 371345329 3.270000e-07 67.6
47 TraesCS7B01G365700 chr1A 100.000 33 0 0 5 37 52835817 52835785 1.520000e-05 62.1


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 TraesCS7B01G365700 chr7B 629578751 629583808 5057 True 4260.000000 5243 100.000000 1 5058 2 chr7B.!!$R2 5057
1 TraesCS7B01G365700 chr7A 661588144 661597158 9014 False 653.444444 1923 91.110556 18 4923 9 chr7A.!!$F1 4905
2 TraesCS7B01G365700 chr7D 572547940 572554829 6889 False 1169.600000 1816 96.447600 34 4123 5 chr7D.!!$F3 4089
3 TraesCS7B01G365700 chr7D 572562496 572563303 807 False 610.000000 610 81.091000 4135 4923 1 chr7D.!!$F1 788
4 TraesCS7B01G365700 chr4A 140975952 140979679 3727 False 637.000000 1705 85.742000 934 4064 4 chr4A.!!$F2 3130
5 TraesCS7B01G365700 chr4D 329137253 329140312 3059 True 821.333333 1663 87.695667 1092 4067 3 chr4D.!!$R1 2975
6 TraesCS7B01G365700 chr1B 135814422 135817509 3087 False 846.333333 1659 85.142000 1083 4059 3 chr1B.!!$F1 2976
7 TraesCS7B01G365700 chr4B 408979585 408984260 4675 True 619.750000 1230 87.881750 1092 4062 4 chr4B.!!$R1 2970


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
966 1124 0.756070 CTCTCCTAACTCCCCCGTCC 60.756 65.000 0.00 0.0 0.00 4.79 F
1188 1390 0.179018 AAGTCGAGCAACCTTTGGCT 60.179 50.000 0.00 0.0 44.48 4.75 F
1767 2240 1.652124 GCGCACATGCTCATTCTTTTG 59.348 47.619 0.30 0.0 39.32 2.44 F
1769 2242 2.659757 CGCACATGCTCATTCTTTTGTG 59.340 45.455 1.82 0.0 39.32 3.33 F
3691 11928 0.553819 TCTCCAGAGGGTCTAGAGGC 59.446 60.000 0.00 0.0 33.84 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2683 3861 2.238395 GGGAGAAGAGGCATTCTGAACT 59.762 50.000 9.4 0.0 39.63 3.01 R
3164 11398 2.555199 CAGCAGTACCAGTAGGATTGC 58.445 52.381 0.0 0.0 38.42 3.56 R
3691 11928 0.667993 TTCAAAGCACGGAAAGCCTG 59.332 50.000 0.0 0.0 0.00 4.85 R
3695 11932 6.205784 TGTAAAGATTTCAAAGCACGGAAAG 58.794 36.000 0.0 0.0 36.55 2.62 R
4617 14018 0.036388 CCAGAAGGGCAGCGTTTAGA 60.036 55.000 0.0 0.0 0.00 2.10 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
413 425 1.716826 CCGTCCTACCTCTGACTCGC 61.717 65.000 0.00 0.00 0.00 5.03
583 595 3.192422 GCTTCAGTTCTGTCTCTGCTCTA 59.808 47.826 0.00 0.00 0.00 2.43
651 663 5.456822 GCTTGTGAATTTATTTCGGAGATGC 59.543 40.000 0.00 0.00 37.13 3.91
716 825 6.245408 AGATAAGTGCACAATGGAGGTTAAA 58.755 36.000 21.04 0.00 0.00 1.52
717 826 4.584327 AAGTGCACAATGGAGGTTAAAC 57.416 40.909 21.04 0.00 0.00 2.01
737 846 9.739786 GTTAAACATTTGCATAGCATTTGTAAC 57.260 29.630 7.46 6.36 38.76 2.50
799 908 9.205719 TCATACGCTGTGTAGTTTGTTTATTTA 57.794 29.630 7.21 0.00 36.25 1.40
929 1087 1.030457 GACTATCCGACCCGACACAT 58.970 55.000 0.00 0.00 0.00 3.21
954 1112 1.759445 GCCAATCTGAGTGCTCTCCTA 59.241 52.381 13.00 1.84 39.75 2.94
961 1119 1.116308 GAGTGCTCTCCTAACTCCCC 58.884 60.000 4.37 0.00 35.36 4.81
965 1123 1.393487 GCTCTCCTAACTCCCCCGTC 61.393 65.000 0.00 0.00 0.00 4.79
966 1124 0.756070 CTCTCCTAACTCCCCCGTCC 60.756 65.000 0.00 0.00 0.00 4.79
1002 1160 3.323403 GGTACTGATTCTCCCTCCTCATG 59.677 52.174 0.00 0.00 0.00 3.07
1036 1208 1.407618 CGATGATGACGGGAACTACCA 59.592 52.381 0.00 0.00 41.20 3.25
1144 1346 9.593134 GTAGTTCAATGAGTTATTCTGATGACT 57.407 33.333 0.00 0.00 35.06 3.41
1145 1347 8.489990 AGTTCAATGAGTTATTCTGATGACTG 57.510 34.615 0.00 0.00 32.76 3.51
1147 1349 6.950842 TCAATGAGTTATTCTGATGACTGGT 58.049 36.000 0.00 0.00 32.76 4.00
1148 1350 6.820152 TCAATGAGTTATTCTGATGACTGGTG 59.180 38.462 0.00 0.00 32.76 4.17
1149 1351 6.550938 ATGAGTTATTCTGATGACTGGTGA 57.449 37.500 0.00 0.00 32.76 4.02
1150 1352 5.724328 TGAGTTATTCTGATGACTGGTGAC 58.276 41.667 0.00 0.00 32.76 3.67
1151 1353 5.245977 TGAGTTATTCTGATGACTGGTGACA 59.754 40.000 0.00 0.00 32.76 3.58
1152 1354 6.070596 TGAGTTATTCTGATGACTGGTGACAT 60.071 38.462 0.00 0.00 41.51 3.06
1153 1355 6.111382 AGTTATTCTGATGACTGGTGACATG 58.889 40.000 0.00 0.00 41.51 3.21
1154 1356 2.391616 TCTGATGACTGGTGACATGC 57.608 50.000 0.00 0.00 41.51 4.06
1188 1390 0.179018 AAGTCGAGCAACCTTTGGCT 60.179 50.000 0.00 0.00 44.48 4.75
1283 1489 3.012518 CTCCAACACCCTGCTTCTAATG 58.987 50.000 0.00 0.00 0.00 1.90
1302 1508 9.691362 TTCTAATGCTTTCAAATTTCAACCTAC 57.309 29.630 0.00 0.00 0.00 3.18
1303 1509 9.077885 TCTAATGCTTTCAAATTTCAACCTACT 57.922 29.630 0.00 0.00 0.00 2.57
1403 1610 2.559440 CTCCAAGCAGGCTATCTGTTC 58.441 52.381 0.00 0.00 45.08 3.18
1642 1850 6.817641 GGCAGAGGTATCTCATCATTCATAAG 59.182 42.308 5.64 0.00 42.34 1.73
1645 1853 9.993454 CAGAGGTATCTCATCATTCATAAGAAA 57.007 33.333 5.64 0.00 42.34 2.52
1649 1857 8.386606 GGTATCTCATCATTCATAAGAAATCGC 58.613 37.037 0.00 0.00 37.29 4.58
1650 1858 9.149225 GTATCTCATCATTCATAAGAAATCGCT 57.851 33.333 0.00 0.00 37.29 4.93
1655 1863 9.276590 TCATCATTCATAAGAAATCGCTATTGT 57.723 29.630 0.00 0.00 37.29 2.71
1656 1864 9.326339 CATCATTCATAAGAAATCGCTATTGTG 57.674 33.333 0.00 0.00 37.29 3.33
1657 1865 8.437360 TCATTCATAAGAAATCGCTATTGTGT 57.563 30.769 0.00 0.00 37.29 3.72
1661 1869 8.942338 TCATAAGAAATCGCTATTGTGTTACT 57.058 30.769 0.00 0.00 0.00 2.24
1767 2240 1.652124 GCGCACATGCTCATTCTTTTG 59.348 47.619 0.30 0.00 39.32 2.44
1769 2242 2.659757 CGCACATGCTCATTCTTTTGTG 59.340 45.455 1.82 0.00 39.32 3.33
1771 2244 3.427528 GCACATGCTCATTCTTTTGTGTG 59.572 43.478 0.00 0.00 37.40 3.82
2588 3766 9.179909 TGAATTGTTTTGTACAGAAACTAAGGA 57.820 29.630 22.55 9.17 38.19 3.36
2683 3861 6.073276 CCAAATGTGACATTTCTCGTCTACAA 60.073 38.462 19.77 0.00 34.37 2.41
3164 11398 7.161773 ACATCATATTCTTTTGTTCACCCAG 57.838 36.000 0.00 0.00 0.00 4.45
3246 11480 6.037830 CGAAGGACAACGGTTCCATAATATTT 59.962 38.462 0.00 0.00 0.00 1.40
3388 11622 8.850454 TTTGAAATTTCTAAAGAGTTTCCACG 57.150 30.769 18.64 0.00 33.44 4.94
3427 11664 8.246180 CCAGTGTTCTGAGCATTAACAAATTAT 58.754 33.333 0.00 0.00 43.76 1.28
3465 11702 8.668510 ATGACAAACTAGACCTGCATAATTAG 57.331 34.615 0.00 0.00 0.00 1.73
3691 11928 0.553819 TCTCCAGAGGGTCTAGAGGC 59.446 60.000 0.00 0.00 33.84 4.70
3695 11932 1.075600 AGAGGGTCTAGAGGCAGGC 60.076 63.158 0.00 0.00 0.00 4.85
3841 12085 2.676342 GTTTACATCGCTCGGGTTCAAT 59.324 45.455 0.00 0.00 0.00 2.57
3855 12099 2.423538 GGTTCAATGTCTATGGTGCCAC 59.576 50.000 0.00 0.00 0.00 5.01
3910 12154 3.312697 GCCGTAATTCTTGGGATGTCTTC 59.687 47.826 0.00 0.00 0.00 2.87
3969 12213 1.273495 TGGCATTGGATTTGGGCCTAA 60.273 47.619 4.53 3.27 44.85 2.69
4036 12280 1.730501 TCATTGAAGCTGCGAGAAGG 58.269 50.000 0.00 0.00 0.00 3.46
4069 12313 8.297426 CAGCTATACAAATGAGCATTGATTCAT 58.703 33.333 0.00 0.00 38.73 2.57
4070 12314 8.512956 AGCTATACAAATGAGCATTGATTCATC 58.487 33.333 0.00 0.00 38.73 2.92
4071 12315 8.294577 GCTATACAAATGAGCATTGATTCATCA 58.705 33.333 0.00 0.00 36.20 3.07
4091 12335 1.187087 ACCCGTGTCATTCTCTCCTC 58.813 55.000 0.00 0.00 0.00 3.71
4123 12367 2.203669 TGCCCAGCAGCATTTGGT 60.204 55.556 0.00 0.00 38.00 3.67
4129 12373 2.344535 AGCAGCATTTGGTGTCACC 58.655 52.632 15.64 15.64 44.70 4.02
4140 13496 0.173708 GGTGTCACCATCGAGAGGAC 59.826 60.000 17.59 7.81 38.42 3.85
4174 13530 1.804151 TCAATGCTAGCAACGACCAAC 59.196 47.619 23.54 0.00 0.00 3.77
4176 13532 1.442769 ATGCTAGCAACGACCAACTG 58.557 50.000 23.54 0.00 0.00 3.16
4184 13540 2.226437 GCAACGACCAACTGAATCATGT 59.774 45.455 0.00 0.00 0.00 3.21
4199 13555 3.829886 TCATGTCGTGGCATTCTTTTC 57.170 42.857 0.00 0.00 0.00 2.29
4204 13560 4.606961 TGTCGTGGCATTCTTTTCTTTTC 58.393 39.130 0.00 0.00 0.00 2.29
4208 13564 6.255670 GTCGTGGCATTCTTTTCTTTTCTTTT 59.744 34.615 0.00 0.00 0.00 2.27
4209 13565 6.816140 TCGTGGCATTCTTTTCTTTTCTTTTT 59.184 30.769 0.00 0.00 0.00 1.94
4306 13664 4.647564 ACATTGAGATTTCTGGACCACT 57.352 40.909 0.00 0.00 0.00 4.00
4320 13678 1.612463 GACCACTGAACGACCACTACT 59.388 52.381 0.00 0.00 0.00 2.57
4321 13679 2.035576 GACCACTGAACGACCACTACTT 59.964 50.000 0.00 0.00 0.00 2.24
4325 13694 2.102588 ACTGAACGACCACTACTTTGCT 59.897 45.455 0.00 0.00 0.00 3.91
4327 13707 1.194772 GAACGACCACTACTTTGCTGC 59.805 52.381 0.00 0.00 0.00 5.25
4329 13709 1.616865 ACGACCACTACTTTGCTGCTA 59.383 47.619 0.00 0.00 0.00 3.49
4333 13713 1.594862 CCACTACTTTGCTGCTATCGC 59.405 52.381 0.00 0.00 0.00 4.58
4338 13718 0.875908 CTTTGCTGCTATCGCCGCTA 60.876 55.000 7.14 0.00 45.29 4.26
4340 13720 2.027605 GCTGCTATCGCCGCTACA 59.972 61.111 0.00 0.00 42.29 2.74
4344 13724 1.200252 CTGCTATCGCCGCTACACTAT 59.800 52.381 0.00 0.00 34.43 2.12
4345 13725 1.199327 TGCTATCGCCGCTACACTATC 59.801 52.381 0.00 0.00 34.43 2.08
4350 13730 1.504647 CGCCGCTACACTATCGGAGA 61.505 60.000 3.91 0.00 45.53 3.71
4352 13732 1.306148 CCGCTACACTATCGGAGACA 58.694 55.000 0.00 0.00 45.53 3.41
4356 13736 1.609555 CTACACTATCGGAGACAGCCC 59.390 57.143 0.00 0.00 42.51 5.19
4383 13763 5.596268 TTGTCGATGACAATTGAGAAGTG 57.404 39.130 13.59 0.00 45.88 3.16
4384 13764 3.433274 TGTCGATGACAATTGAGAAGTGC 59.567 43.478 13.59 0.00 39.78 4.40
4389 13770 4.077300 TGACAATTGAGAAGTGCTCTGT 57.923 40.909 13.59 0.00 44.27 3.41
4397 13778 1.344942 GAAGTGCTCTGTACGTGCCG 61.345 60.000 0.00 0.00 0.00 5.69
4408 13789 1.940883 TACGTGCCGCTAAGGACCAG 61.941 60.000 0.00 0.00 45.00 4.00
4415 13796 2.432300 GCTAAGGACCAGCGCCCTA 61.432 63.158 2.29 0.00 31.36 3.53
4418 13799 0.105658 TAAGGACCAGCGCCCTAGAT 60.106 55.000 2.29 0.00 31.36 1.98
4435 13817 1.390123 AGATCGCAATTGTCGTCGTTG 59.610 47.619 17.57 0.00 0.00 4.10
4448 13830 2.407026 TCGTCGTTGAACACATGAATCG 59.593 45.455 0.00 0.00 0.00 3.34
4475 13857 4.897670 TGAAGTGCCTGATATCAGATCTCA 59.102 41.667 30.40 20.74 46.59 3.27
4478 13860 2.560105 TGCCTGATATCAGATCTCACCG 59.440 50.000 30.40 14.08 46.59 4.94
4513 13895 2.169769 ACGAGAAACTCAAACCTCACCA 59.830 45.455 0.00 0.00 0.00 4.17
4520 13902 2.176798 ACTCAAACCTCACCATCCCAAA 59.823 45.455 0.00 0.00 0.00 3.28
4527 13909 2.356535 CCTCACCATCCCAAAGAGAAGG 60.357 54.545 0.00 0.00 0.00 3.46
4529 13912 1.075601 ACCATCCCAAAGAGAAGGCA 58.924 50.000 0.00 0.00 0.00 4.75
4530 13913 1.642762 ACCATCCCAAAGAGAAGGCAT 59.357 47.619 0.00 0.00 0.00 4.40
4539 13922 5.188434 CCAAAGAGAAGGCATGAATCTACA 58.812 41.667 0.00 0.00 0.00 2.74
4540 13923 5.649395 CCAAAGAGAAGGCATGAATCTACAA 59.351 40.000 0.00 0.00 0.00 2.41
4550 13933 3.784701 TGAATCTACAACGGAGCTCTC 57.215 47.619 14.64 2.76 0.00 3.20
4557 13940 4.544001 ACGGAGCTCTCTCGGTAG 57.456 61.111 14.64 0.00 46.73 3.18
4560 13958 0.871722 CGGAGCTCTCTCGGTAGATG 59.128 60.000 14.64 0.00 40.26 2.90
4578 13976 3.194542 AGATGAACAAACTCGAGGAGGAG 59.805 47.826 18.41 4.31 39.97 3.69
4580 13978 2.296471 TGAACAAACTCGAGGAGGAGTC 59.704 50.000 18.41 7.29 46.21 3.36
4581 13979 1.258676 ACAAACTCGAGGAGGAGTCC 58.741 55.000 18.41 0.00 46.21 3.85
4600 14001 2.363038 TCCGAAAGACCAACTCGAAGAA 59.637 45.455 0.00 0.00 34.09 2.52
4653 14054 5.281558 CCTTCTGGGGACTAAAAACCCTAAT 60.282 44.000 0.00 0.00 44.97 1.73
4659 14060 7.177184 TGGGGACTAAAAACCCTAATCTAAAC 58.823 38.462 0.00 0.00 44.97 2.01
4660 14061 6.604795 GGGGACTAAAAACCCTAATCTAAACC 59.395 42.308 0.00 0.00 44.97 3.27
4674 14075 1.555075 CTAAACCACTAGCTGGAGCCA 59.445 52.381 15.59 0.00 43.95 4.75
4695 14096 2.273619 AGGCACCAGAATTCTCCTCTT 58.726 47.619 4.57 0.00 0.00 2.85
4696 14097 2.646798 AGGCACCAGAATTCTCCTCTTT 59.353 45.455 4.57 0.00 0.00 2.52
4746 14147 1.272147 GGGAGGTGAATCCACAAGCTT 60.272 52.381 0.00 0.00 44.93 3.74
4750 14151 0.961019 GTGAATCCACAAGCTTGCCA 59.039 50.000 26.27 10.58 42.72 4.92
4754 14155 0.178981 ATCCACAAGCTTGCCAGTGT 60.179 50.000 26.27 3.15 0.00 3.55
4757 14158 1.134729 CCACAAGCTTGCCAGTGTTTT 60.135 47.619 26.27 0.04 0.00 2.43
4789 14190 2.649816 AGGAAAGATGCAACCCTAACCT 59.350 45.455 0.00 0.00 0.00 3.50
4792 14193 1.668826 AGATGCAACCCTAACCTCCA 58.331 50.000 0.00 0.00 0.00 3.86
4793 14194 1.282157 AGATGCAACCCTAACCTCCAC 59.718 52.381 0.00 0.00 0.00 4.02
4794 14195 0.331616 ATGCAACCCTAACCTCCACC 59.668 55.000 0.00 0.00 0.00 4.61
4829 14230 4.647654 GTGAACTTCACGCCGAGA 57.352 55.556 6.16 0.00 37.67 4.04
4835 14236 0.317160 ACTTCACGCCGAGACATTCA 59.683 50.000 0.00 0.00 0.00 2.57
4839 14240 0.163788 CACGCCGAGACATTCAACAC 59.836 55.000 0.00 0.00 0.00 3.32
4844 14245 1.670087 CCGAGACATTCAACACGCTCT 60.670 52.381 0.00 0.00 0.00 4.09
4859 14260 1.000385 CGCTCTTTGGTTTGGATGCAA 60.000 47.619 0.00 0.00 0.00 4.08
4865 14266 6.372381 GCTCTTTGGTTTGGATGCAATAAATT 59.628 34.615 0.00 0.00 0.00 1.82
4867 14268 6.654161 TCTTTGGTTTGGATGCAATAAATTGG 59.346 34.615 0.00 0.00 38.21 3.16
4923 14324 4.894784 TGAAGGATGTTCTACAAGACCAC 58.105 43.478 0.00 0.00 0.00 4.16
4924 14325 4.346709 TGAAGGATGTTCTACAAGACCACA 59.653 41.667 0.00 0.00 0.00 4.17
4925 14326 4.543590 AGGATGTTCTACAAGACCACAG 57.456 45.455 0.00 0.00 0.00 3.66
4926 14327 3.904339 AGGATGTTCTACAAGACCACAGT 59.096 43.478 0.00 0.00 0.00 3.55
4927 14328 4.021016 AGGATGTTCTACAAGACCACAGTC 60.021 45.833 0.00 0.00 43.89 3.51
4935 14336 4.192000 GACCACAGTCTGCATCCG 57.808 61.111 0.00 0.00 40.10 4.18
4936 14337 1.293498 GACCACAGTCTGCATCCGT 59.707 57.895 0.00 0.00 40.10 4.69
4937 14338 0.320771 GACCACAGTCTGCATCCGTT 60.321 55.000 0.00 0.00 40.10 4.44
4938 14339 0.320771 ACCACAGTCTGCATCCGTTC 60.321 55.000 0.00 0.00 0.00 3.95
4939 14340 1.021390 CCACAGTCTGCATCCGTTCC 61.021 60.000 0.00 0.00 0.00 3.62
4940 14341 0.036952 CACAGTCTGCATCCGTTCCT 60.037 55.000 0.00 0.00 0.00 3.36
4941 14342 1.204704 CACAGTCTGCATCCGTTCCTA 59.795 52.381 0.00 0.00 0.00 2.94
4942 14343 1.478510 ACAGTCTGCATCCGTTCCTAG 59.521 52.381 0.00 0.00 0.00 3.02
4943 14344 1.751351 CAGTCTGCATCCGTTCCTAGA 59.249 52.381 0.00 0.00 0.00 2.43
4944 14345 1.751924 AGTCTGCATCCGTTCCTAGAC 59.248 52.381 0.00 0.00 35.88 2.59
4945 14346 1.751924 GTCTGCATCCGTTCCTAGACT 59.248 52.381 0.00 0.00 33.58 3.24
4946 14347 2.950309 GTCTGCATCCGTTCCTAGACTA 59.050 50.000 0.00 0.00 33.58 2.59
4947 14348 2.950309 TCTGCATCCGTTCCTAGACTAC 59.050 50.000 0.00 0.00 0.00 2.73
4948 14349 2.029623 TGCATCCGTTCCTAGACTACC 58.970 52.381 0.00 0.00 0.00 3.18
4949 14350 2.308690 GCATCCGTTCCTAGACTACCT 58.691 52.381 0.00 0.00 0.00 3.08
4950 14351 2.293955 GCATCCGTTCCTAGACTACCTC 59.706 54.545 0.00 0.00 0.00 3.85
4951 14352 2.725221 TCCGTTCCTAGACTACCTCC 57.275 55.000 0.00 0.00 0.00 4.30
4952 14353 1.213926 TCCGTTCCTAGACTACCTCCC 59.786 57.143 0.00 0.00 0.00 4.30
4953 14354 1.064166 CCGTTCCTAGACTACCTCCCA 60.064 57.143 0.00 0.00 0.00 4.37
4954 14355 2.622452 CCGTTCCTAGACTACCTCCCAA 60.622 54.545 0.00 0.00 0.00 4.12
4955 14356 2.688958 CGTTCCTAGACTACCTCCCAAG 59.311 54.545 0.00 0.00 0.00 3.61
4956 14357 2.431419 GTTCCTAGACTACCTCCCAAGC 59.569 54.545 0.00 0.00 0.00 4.01
4957 14358 1.930914 TCCTAGACTACCTCCCAAGCT 59.069 52.381 0.00 0.00 0.00 3.74
4958 14359 2.315155 TCCTAGACTACCTCCCAAGCTT 59.685 50.000 0.00 0.00 0.00 3.74
4959 14360 3.108376 CCTAGACTACCTCCCAAGCTTT 58.892 50.000 0.00 0.00 0.00 3.51
4960 14361 3.118592 CCTAGACTACCTCCCAAGCTTTG 60.119 52.174 0.00 0.00 0.00 2.77
4961 14362 2.339769 AGACTACCTCCCAAGCTTTGT 58.660 47.619 0.00 0.00 0.00 2.83
4962 14363 2.039084 AGACTACCTCCCAAGCTTTGTG 59.961 50.000 0.00 0.00 0.00 3.33
4963 14364 1.774856 ACTACCTCCCAAGCTTTGTGT 59.225 47.619 0.00 0.00 0.00 3.72
4964 14365 2.224548 ACTACCTCCCAAGCTTTGTGTC 60.225 50.000 0.00 0.00 0.00 3.67
4965 14366 0.535102 ACCTCCCAAGCTTTGTGTCG 60.535 55.000 0.00 0.00 0.00 4.35
4966 14367 0.250295 CCTCCCAAGCTTTGTGTCGA 60.250 55.000 0.00 0.00 0.00 4.20
4967 14368 0.868406 CTCCCAAGCTTTGTGTCGAC 59.132 55.000 9.11 9.11 0.00 4.20
4968 14369 0.878523 TCCCAAGCTTTGTGTCGACG 60.879 55.000 11.62 0.00 0.00 5.12
4969 14370 1.082756 CCAAGCTTTGTGTCGACGC 60.083 57.895 22.00 22.00 0.00 5.19
4970 14371 1.498865 CCAAGCTTTGTGTCGACGCT 61.499 55.000 27.76 18.37 0.00 5.07
4971 14372 0.383491 CAAGCTTTGTGTCGACGCTG 60.383 55.000 27.76 18.51 0.00 5.18
4972 14373 0.529773 AAGCTTTGTGTCGACGCTGA 60.530 50.000 27.76 14.92 0.00 4.26
4973 14374 0.529773 AGCTTTGTGTCGACGCTGAA 60.530 50.000 27.76 20.35 0.00 3.02
4974 14375 0.111089 GCTTTGTGTCGACGCTGAAG 60.111 55.000 27.76 27.24 0.00 3.02
4975 14376 1.487482 CTTTGTGTCGACGCTGAAGA 58.513 50.000 27.76 6.33 0.00 2.87
4976 14377 1.858458 CTTTGTGTCGACGCTGAAGAA 59.142 47.619 27.76 12.13 0.00 2.52
4977 14378 1.487482 TTGTGTCGACGCTGAAGAAG 58.513 50.000 27.76 0.00 0.00 2.85
4990 14391 2.414481 CTGAAGAAGCCTCATCACAACG 59.586 50.000 0.00 0.00 0.00 4.10
4991 14392 2.037121 TGAAGAAGCCTCATCACAACGA 59.963 45.455 0.00 0.00 0.00 3.85
4992 14393 3.265791 GAAGAAGCCTCATCACAACGAT 58.734 45.455 0.00 0.00 33.27 3.73
4999 14400 3.465990 CATCACAACGATGGAGCCT 57.534 52.632 0.00 0.00 46.73 4.58
5000 14401 2.602257 CATCACAACGATGGAGCCTA 57.398 50.000 0.00 0.00 46.73 3.93
5001 14402 2.905075 CATCACAACGATGGAGCCTAA 58.095 47.619 0.00 0.00 46.73 2.69
5002 14403 3.470709 CATCACAACGATGGAGCCTAAT 58.529 45.455 0.00 0.00 46.73 1.73
5003 14404 2.905075 TCACAACGATGGAGCCTAATG 58.095 47.619 0.00 0.00 0.00 1.90
5004 14405 2.499693 TCACAACGATGGAGCCTAATGA 59.500 45.455 0.00 0.00 0.00 2.57
5005 14406 2.609459 CACAACGATGGAGCCTAATGAC 59.391 50.000 0.00 0.00 0.00 3.06
5006 14407 2.236146 ACAACGATGGAGCCTAATGACA 59.764 45.455 0.00 0.00 0.00 3.58
5007 14408 3.118261 ACAACGATGGAGCCTAATGACAT 60.118 43.478 0.00 0.00 0.00 3.06
5008 14409 4.100963 ACAACGATGGAGCCTAATGACATA 59.899 41.667 0.00 0.00 0.00 2.29
5009 14410 4.955811 ACGATGGAGCCTAATGACATAA 57.044 40.909 0.00 0.00 0.00 1.90
5010 14411 4.887748 ACGATGGAGCCTAATGACATAAG 58.112 43.478 0.00 0.00 0.00 1.73
5011 14412 4.345257 ACGATGGAGCCTAATGACATAAGT 59.655 41.667 0.00 0.00 0.00 2.24
5012 14413 4.926238 CGATGGAGCCTAATGACATAAGTC 59.074 45.833 0.00 0.00 45.19 3.01
5013 14414 4.689612 TGGAGCCTAATGACATAAGTCC 57.310 45.455 0.00 0.00 44.33 3.85
5014 14415 4.037222 TGGAGCCTAATGACATAAGTCCA 58.963 43.478 0.00 0.00 44.33 4.02
5015 14416 4.141711 TGGAGCCTAATGACATAAGTCCAC 60.142 45.833 0.00 0.00 44.33 4.02
5016 14417 4.381411 GAGCCTAATGACATAAGTCCACC 58.619 47.826 0.00 0.00 44.33 4.61
5017 14418 3.780294 AGCCTAATGACATAAGTCCACCA 59.220 43.478 0.00 0.00 44.33 4.17
5018 14419 4.413520 AGCCTAATGACATAAGTCCACCAT 59.586 41.667 0.00 0.00 44.33 3.55
5019 14420 5.606749 AGCCTAATGACATAAGTCCACCATA 59.393 40.000 0.00 0.00 44.33 2.74
5020 14421 6.273260 AGCCTAATGACATAAGTCCACCATAT 59.727 38.462 0.00 0.00 44.33 1.78
5021 14422 6.372659 GCCTAATGACATAAGTCCACCATATG 59.627 42.308 0.00 0.00 44.33 1.78
5030 14431 3.672293 CACCATATGGATGCCGCC 58.328 61.111 28.77 0.00 38.94 6.13
5031 14432 2.032528 ACCATATGGATGCCGCCG 59.967 61.111 28.77 0.00 38.94 6.46
5032 14433 3.434319 CCATATGGATGCCGCCGC 61.434 66.667 17.49 0.00 37.39 6.53
5033 14434 3.434319 CATATGGATGCCGCCGCC 61.434 66.667 0.00 0.00 0.00 6.13
5034 14435 3.952508 ATATGGATGCCGCCGCCA 61.953 61.111 4.01 4.01 35.91 5.69
5035 14436 4.927782 TATGGATGCCGCCGCCAC 62.928 66.667 3.64 0.00 33.93 5.01
5043 14444 3.679738 CCGCCGCCACACCATTTT 61.680 61.111 0.00 0.00 0.00 1.82
5044 14445 2.126502 CGCCGCCACACCATTTTC 60.127 61.111 0.00 0.00 0.00 2.29
5045 14446 2.126502 GCCGCCACACCATTTTCG 60.127 61.111 0.00 0.00 0.00 3.46
5046 14447 2.126502 CCGCCACACCATTTTCGC 60.127 61.111 0.00 0.00 0.00 4.70
5047 14448 2.625823 CCGCCACACCATTTTCGCT 61.626 57.895 0.00 0.00 0.00 4.93
5048 14449 1.285641 CGCCACACCATTTTCGCTT 59.714 52.632 0.00 0.00 0.00 4.68
5049 14450 1.003262 CGCCACACCATTTTCGCTTG 61.003 55.000 0.00 0.00 0.00 4.01
5050 14451 0.313672 GCCACACCATTTTCGCTTGA 59.686 50.000 0.00 0.00 0.00 3.02
5051 14452 1.269517 GCCACACCATTTTCGCTTGAA 60.270 47.619 0.00 0.00 0.00 2.69
5052 14453 2.393764 CCACACCATTTTCGCTTGAAC 58.606 47.619 0.00 0.00 0.00 3.18
5053 14454 2.223688 CCACACCATTTTCGCTTGAACA 60.224 45.455 0.00 0.00 0.00 3.18
5054 14455 3.044986 CACACCATTTTCGCTTGAACAG 58.955 45.455 0.00 0.00 0.00 3.16
5055 14456 2.948979 ACACCATTTTCGCTTGAACAGA 59.051 40.909 0.00 0.00 0.00 3.41
5056 14457 3.243068 ACACCATTTTCGCTTGAACAGAC 60.243 43.478 0.00 0.00 0.00 3.51
5057 14458 3.003689 CACCATTTTCGCTTGAACAGACT 59.996 43.478 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
372 383 2.034048 GCGGAGAAGATGGGGAGGAC 62.034 65.000 0.00 0.00 0.00 3.85
583 595 2.715046 TGAAAAGCATCGAATCTGGCT 58.285 42.857 0.00 0.00 38.45 4.75
665 677 6.183360 CCTCAAATTTATCCATTGCAAGCAAC 60.183 38.462 9.97 0.00 38.88 4.17
716 825 9.874205 AATAAGTTACAAATGCTATGCAAATGT 57.126 25.926 14.56 14.56 43.62 2.71
799 908 2.106683 GGCTCGCCAACGCACTAAT 61.107 57.895 2.41 0.00 39.84 1.73
904 1061 1.821258 GGGTCGGATAGTCCACCAC 59.179 63.158 14.96 2.21 38.58 4.16
929 1087 1.219124 GCACTCAGATTGGCCGAGA 59.781 57.895 11.11 0.00 0.00 4.04
961 1119 4.222847 GCTTAGCCCTCCGGACGG 62.223 72.222 14.64 14.64 0.00 4.79
965 1123 1.760875 TACCAGCTTAGCCCTCCGG 60.761 63.158 0.00 0.00 0.00 5.14
966 1124 1.043673 AGTACCAGCTTAGCCCTCCG 61.044 60.000 0.00 0.00 0.00 4.63
1002 1160 4.148825 ATCGGCGGCAGTGAGTCC 62.149 66.667 10.53 0.00 0.00 3.85
1036 1208 3.491598 CTTTGGTGGCGGGTGAGGT 62.492 63.158 0.00 0.00 0.00 3.85
1144 1346 1.180456 CCCTGCAAAGCATGTCACCA 61.180 55.000 0.00 0.00 38.13 4.17
1145 1347 1.588082 CCCTGCAAAGCATGTCACC 59.412 57.895 0.00 0.00 38.13 4.02
1147 1349 1.531128 TGCCCTGCAAAGCATGTCA 60.531 52.632 6.22 0.00 38.13 3.58
1148 1350 3.368822 TGCCCTGCAAAGCATGTC 58.631 55.556 6.22 0.00 38.13 3.06
1152 1354 1.588824 CTTCGATGCCCTGCAAAGCA 61.589 55.000 12.28 12.28 43.62 3.91
1153 1355 1.138247 CTTCGATGCCCTGCAAAGC 59.862 57.895 0.67 0.67 43.62 3.51
1154 1356 0.449388 GACTTCGATGCCCTGCAAAG 59.551 55.000 0.00 0.00 43.62 2.77
1188 1390 4.069232 CGGGCTGCCTTCTCGTCA 62.069 66.667 19.68 0.00 0.00 4.35
1200 1402 0.248289 ACAGCGTACATTAACGGGCT 59.752 50.000 0.00 0.00 43.06 5.19
1283 1489 9.000486 ACTACTAGTAGGTTGAAATTTGAAAGC 58.000 33.333 29.05 0.00 37.49 3.51
1403 1610 2.158813 ACGGCACAATTATACCTCAGGG 60.159 50.000 0.00 0.00 38.88 4.45
1642 1850 9.474249 GTCTAAAAGTAACACAATAGCGATTTC 57.526 33.333 0.00 0.00 0.00 2.17
1645 1853 7.328737 AGGTCTAAAAGTAACACAATAGCGAT 58.671 34.615 0.00 0.00 0.00 4.58
1646 1854 6.694447 AGGTCTAAAAGTAACACAATAGCGA 58.306 36.000 0.00 0.00 0.00 4.93
1647 1855 6.963049 AGGTCTAAAAGTAACACAATAGCG 57.037 37.500 0.00 0.00 0.00 4.26
1649 1857 7.390718 AGCCAAGGTCTAAAAGTAACACAATAG 59.609 37.037 0.00 0.00 0.00 1.73
1650 1858 7.174253 CAGCCAAGGTCTAAAAGTAACACAATA 59.826 37.037 0.00 0.00 0.00 1.90
1655 1863 5.298989 TCAGCCAAGGTCTAAAAGTAACA 57.701 39.130 0.00 0.00 0.00 2.41
1656 1864 6.174049 AGATCAGCCAAGGTCTAAAAGTAAC 58.826 40.000 0.00 0.00 0.00 2.50
1657 1865 6.013725 TGAGATCAGCCAAGGTCTAAAAGTAA 60.014 38.462 0.00 0.00 0.00 2.24
1659 1867 4.287067 TGAGATCAGCCAAGGTCTAAAAGT 59.713 41.667 0.00 0.00 0.00 2.66
1660 1868 4.836825 TGAGATCAGCCAAGGTCTAAAAG 58.163 43.478 0.00 0.00 0.00 2.27
1661 1869 4.323792 CCTGAGATCAGCCAAGGTCTAAAA 60.324 45.833 4.23 0.00 42.47 1.52
2482 3044 9.807649 GAGCCAATCAAATATTTTTAGTGATGT 57.192 29.630 0.00 0.00 0.00 3.06
2683 3861 2.238395 GGGAGAAGAGGCATTCTGAACT 59.762 50.000 9.40 0.00 39.63 3.01
3164 11398 2.555199 CAGCAGTACCAGTAGGATTGC 58.445 52.381 0.00 0.00 38.42 3.56
3246 11480 6.545298 TGTACATGGCATAAGCACAATCATAA 59.455 34.615 0.00 0.00 44.61 1.90
3388 11622 4.682860 CAGAACACTGGCATCAAATGTTTC 59.317 41.667 0.00 0.00 34.40 2.78
3393 11627 2.490903 GCTCAGAACACTGGCATCAAAT 59.509 45.455 0.00 0.00 32.38 2.32
3398 11632 2.211250 AATGCTCAGAACACTGGCAT 57.789 45.000 15.04 15.04 43.32 4.40
3465 11702 3.057104 GCAACCTACACATTACCAAACCC 60.057 47.826 0.00 0.00 0.00 4.11
3691 11928 0.667993 TTCAAAGCACGGAAAGCCTG 59.332 50.000 0.00 0.00 0.00 4.85
3695 11932 6.205784 TGTAAAGATTTCAAAGCACGGAAAG 58.794 36.000 0.00 0.00 36.55 2.62
3776 12020 5.677319 TTCTCCTTGTAGAATCCGACAAT 57.323 39.130 0.00 0.00 37.30 2.71
3841 12085 2.011548 GCATTCGTGGCACCATAGACA 61.012 52.381 12.86 0.00 0.00 3.41
3855 12099 1.586422 CCACACATAGGGAGCATTCG 58.414 55.000 0.00 0.00 0.00 3.34
3910 12154 3.264666 CTTCTCAAGGATCTCGGCG 57.735 57.895 0.00 0.00 0.00 6.46
3969 12213 3.883744 CTCACAAAGCCCTCGCCGT 62.884 63.158 0.00 0.00 34.57 5.68
4069 12313 1.275291 GGAGAGAATGACACGGGTTGA 59.725 52.381 0.00 0.00 0.00 3.18
4070 12314 1.276421 AGGAGAGAATGACACGGGTTG 59.724 52.381 0.00 0.00 0.00 3.77
4071 12315 1.550976 GAGGAGAGAATGACACGGGTT 59.449 52.381 0.00 0.00 0.00 4.11
4091 12335 1.365999 GGCACTTTTTGGTTCCCCG 59.634 57.895 0.00 0.00 0.00 5.73
4102 12346 0.034337 CAAATGCTGCTGGGCACTTT 59.966 50.000 0.00 3.06 45.36 2.66
4106 12350 2.203669 ACCAAATGCTGCTGGGCA 60.204 55.556 10.67 2.54 46.63 5.36
4124 12368 0.099082 GTCGTCCTCTCGATGGTGAC 59.901 60.000 12.69 12.69 41.78 3.67
4125 12369 1.366854 CGTCGTCCTCTCGATGGTGA 61.367 60.000 4.79 2.59 41.37 4.02
4126 12370 1.062685 CGTCGTCCTCTCGATGGTG 59.937 63.158 4.79 0.61 41.37 4.17
4127 12371 3.499050 CGTCGTCCTCTCGATGGT 58.501 61.111 4.79 0.00 41.37 3.55
4129 12373 0.170561 AAACCGTCGTCCTCTCGATG 59.829 55.000 0.00 0.00 43.66 3.84
4130 12374 1.742761 TAAACCGTCGTCCTCTCGAT 58.257 50.000 0.00 0.00 41.78 3.59
4131 12375 1.742761 ATAAACCGTCGTCCTCTCGA 58.257 50.000 0.00 0.00 37.51 4.04
4132 12376 2.159476 TGAATAAACCGTCGTCCTCTCG 60.159 50.000 0.00 0.00 0.00 4.04
4140 13496 4.536364 AGCATTGATGAATAAACCGTCG 57.464 40.909 0.00 0.00 0.00 5.12
4174 13530 2.941064 AGAATGCCACGACATGATTCAG 59.059 45.455 0.00 0.00 28.32 3.02
4176 13532 4.361451 AAAGAATGCCACGACATGATTC 57.639 40.909 0.00 0.00 0.00 2.52
4184 13540 5.514274 AAGAAAAGAAAAGAATGCCACGA 57.486 34.783 0.00 0.00 0.00 4.35
4215 13571 8.181904 TCAATAGTTCTGGATGCTTTCTTTTT 57.818 30.769 0.00 0.00 0.00 1.94
4216 13572 7.765695 TCAATAGTTCTGGATGCTTTCTTTT 57.234 32.000 0.00 0.00 0.00 2.27
4217 13573 7.765695 TTCAATAGTTCTGGATGCTTTCTTT 57.234 32.000 0.00 0.00 0.00 2.52
4220 13576 8.084684 ACTTTTTCAATAGTTCTGGATGCTTTC 58.915 33.333 0.00 0.00 0.00 2.62
4289 13647 3.554960 CGTTCAGTGGTCCAGAAATCTCA 60.555 47.826 0.00 0.00 0.00 3.27
4293 13651 2.550208 GGTCGTTCAGTGGTCCAGAAAT 60.550 50.000 0.00 0.00 0.00 2.17
4295 13653 0.391597 GGTCGTTCAGTGGTCCAGAA 59.608 55.000 0.00 0.00 0.00 3.02
4306 13664 2.479837 CAGCAAAGTAGTGGTCGTTCA 58.520 47.619 0.00 0.00 0.00 3.18
4327 13707 2.160918 CGATAGTGTAGCGGCGATAG 57.839 55.000 12.98 0.00 33.31 2.08
4338 13718 2.506065 GGGCTGTCTCCGATAGTGT 58.494 57.895 0.00 0.00 0.00 3.55
4352 13732 4.473520 CATCGACAAGGCCGGGCT 62.474 66.667 27.45 27.45 0.00 5.19
4356 13736 4.277239 TTGTCATCGACAAGGCCG 57.723 55.556 5.47 0.00 45.88 6.13
4373 13753 3.579709 CACGTACAGAGCACTTCTCAAT 58.420 45.455 0.00 0.00 44.35 2.57
4375 13755 1.335964 GCACGTACAGAGCACTTCTCA 60.336 52.381 0.00 0.00 44.35 3.27
4377 13757 0.038159 GGCACGTACAGAGCACTTCT 60.038 55.000 0.00 0.00 38.23 2.85
4415 13796 1.390123 CAACGACGACAATTGCGATCT 59.610 47.619 22.87 6.47 0.00 2.75
4418 13799 1.071107 GTTCAACGACGACAATTGCGA 60.071 47.619 22.87 3.16 0.00 5.10
4423 13805 3.127589 TCATGTGTTCAACGACGACAAT 58.872 40.909 0.00 0.00 0.00 2.71
4425 13807 2.211353 TCATGTGTTCAACGACGACA 57.789 45.000 0.00 0.00 0.00 4.35
4435 13817 5.726138 GCACTTCAGATCGATTCATGTGTTC 60.726 44.000 0.00 0.00 0.00 3.18
4448 13830 5.465532 TCTGATATCAGGCACTTCAGATC 57.534 43.478 28.30 0.00 41.81 2.75
4490 13872 3.002348 GGTGAGGTTTGAGTTTCTCGTTG 59.998 47.826 0.00 0.00 32.35 4.10
4491 13873 3.203716 GGTGAGGTTTGAGTTTCTCGTT 58.796 45.455 0.00 0.00 32.35 3.85
4492 13874 2.169769 TGGTGAGGTTTGAGTTTCTCGT 59.830 45.455 0.00 0.00 32.35 4.18
4503 13885 2.716424 TCTCTTTGGGATGGTGAGGTTT 59.284 45.455 0.00 0.00 0.00 3.27
4513 13895 3.744940 TTCATGCCTTCTCTTTGGGAT 57.255 42.857 0.00 0.00 34.68 3.85
4520 13902 4.437239 CGTTGTAGATTCATGCCTTCTCT 58.563 43.478 0.00 0.00 0.00 3.10
4527 13909 2.541762 GAGCTCCGTTGTAGATTCATGC 59.458 50.000 0.87 0.00 0.00 4.06
4529 13912 3.957497 AGAGAGCTCCGTTGTAGATTCAT 59.043 43.478 10.93 0.00 0.00 2.57
4530 13913 3.357203 AGAGAGCTCCGTTGTAGATTCA 58.643 45.455 10.93 0.00 0.00 2.57
4539 13922 0.252479 TCTACCGAGAGAGCTCCGTT 59.748 55.000 10.93 0.00 37.91 4.44
4540 13923 0.470766 ATCTACCGAGAGAGCTCCGT 59.529 55.000 10.93 0.00 37.91 4.69
4550 13933 4.092771 TCGAGTTTGTTCATCTACCGAG 57.907 45.455 0.00 0.00 0.00 4.63
4556 13939 3.165875 TCCTCCTCGAGTTTGTTCATCT 58.834 45.455 12.31 0.00 0.00 2.90
4557 13940 3.056465 ACTCCTCCTCGAGTTTGTTCATC 60.056 47.826 12.31 0.00 40.23 2.92
4560 13958 2.352912 GGACTCCTCCTCGAGTTTGTTC 60.353 54.545 12.31 0.41 43.22 3.18
4578 13976 2.059541 CTTCGAGTTGGTCTTTCGGAC 58.940 52.381 0.00 0.00 43.79 4.79
4579 13977 1.958579 TCTTCGAGTTGGTCTTTCGGA 59.041 47.619 0.00 0.00 35.21 4.55
4580 13978 2.433868 TCTTCGAGTTGGTCTTTCGG 57.566 50.000 0.00 0.00 35.21 4.30
4581 13979 3.639538 TCTTCTTCGAGTTGGTCTTTCG 58.360 45.455 0.00 0.00 35.76 3.46
4582 13980 4.084276 GCTTCTTCTTCGAGTTGGTCTTTC 60.084 45.833 0.00 0.00 0.00 2.62
4584 13982 3.394719 GCTTCTTCTTCGAGTTGGTCTT 58.605 45.455 0.00 0.00 0.00 3.01
4585 13983 2.608261 CGCTTCTTCTTCGAGTTGGTCT 60.608 50.000 0.00 0.00 0.00 3.85
4586 13984 1.721926 CGCTTCTTCTTCGAGTTGGTC 59.278 52.381 0.00 0.00 0.00 4.02
4588 13986 0.440371 GCGCTTCTTCTTCGAGTTGG 59.560 55.000 0.00 0.00 0.00 3.77
4589 13987 0.440371 GGCGCTTCTTCTTCGAGTTG 59.560 55.000 7.64 0.00 0.00 3.16
4591 13989 1.444553 CGGCGCTTCTTCTTCGAGT 60.445 57.895 7.64 0.00 0.00 4.18
4592 13990 2.793322 GCGGCGCTTCTTCTTCGAG 61.793 63.158 26.86 0.00 0.00 4.04
4593 13991 2.809601 GCGGCGCTTCTTCTTCGA 60.810 61.111 26.86 0.00 0.00 3.71
4617 14018 0.036388 CCAGAAGGGCAGCGTTTAGA 60.036 55.000 0.00 0.00 0.00 2.10
4631 14032 5.554350 AGATTAGGGTTTTTAGTCCCCAGAA 59.446 40.000 0.00 0.00 44.40 3.02
4660 14061 1.451028 GCCTTGGCTCCAGCTAGTG 60.451 63.158 4.11 0.00 41.70 2.74
4674 14075 2.273619 AGAGGAGAATTCTGGTGCCTT 58.726 47.619 14.00 1.94 0.00 4.35
4682 14083 2.616510 CGGTGGCAAAGAGGAGAATTCT 60.617 50.000 7.95 7.95 0.00 2.40
4711 14112 3.655211 CCCCTCTGCCAGCCACTT 61.655 66.667 0.00 0.00 0.00 3.16
4732 14133 1.250328 CTGGCAAGCTTGTGGATTCA 58.750 50.000 26.55 14.06 0.00 2.57
4762 14163 3.966665 AGGGTTGCATCTTTCCTCAAAAA 59.033 39.130 0.00 0.00 0.00 1.94
4763 14164 3.575805 AGGGTTGCATCTTTCCTCAAAA 58.424 40.909 0.00 0.00 0.00 2.44
4764 14165 3.243359 AGGGTTGCATCTTTCCTCAAA 57.757 42.857 0.00 0.00 0.00 2.69
4765 14166 2.978156 AGGGTTGCATCTTTCCTCAA 57.022 45.000 0.00 0.00 0.00 3.02
4766 14167 3.561313 GGTTAGGGTTGCATCTTTCCTCA 60.561 47.826 0.00 0.00 0.00 3.86
4789 14190 1.850345 AGTGTTTCTTTCCCTGGTGGA 59.150 47.619 0.00 0.00 43.18 4.02
4792 14193 3.447229 CACAAAGTGTTTCTTTCCCTGGT 59.553 43.478 0.00 0.00 43.57 4.00
4793 14194 3.699038 TCACAAAGTGTTTCTTTCCCTGG 59.301 43.478 0.00 0.00 43.57 4.45
4794 14195 4.981806 TCACAAAGTGTTTCTTTCCCTG 57.018 40.909 0.00 0.00 43.57 4.45
4816 14217 0.317160 TGAATGTCTCGGCGTGAAGT 59.683 50.000 13.70 2.48 0.00 3.01
4822 14223 1.416049 CGTGTTGAATGTCTCGGCG 59.584 57.895 0.00 0.00 0.00 6.46
4829 14230 2.297701 ACCAAAGAGCGTGTTGAATGT 58.702 42.857 0.00 0.00 0.00 2.71
4835 14236 1.757682 TCCAAACCAAAGAGCGTGTT 58.242 45.000 0.00 0.00 0.00 3.32
4839 14240 0.597568 TGCATCCAAACCAAAGAGCG 59.402 50.000 0.00 0.00 0.00 5.03
4844 14245 6.302269 ACCAATTTATTGCATCCAAACCAAA 58.698 32.000 0.00 0.00 36.48 3.28
4859 14260 9.941325 TGAAATCACAATTTGCTACCAATTTAT 57.059 25.926 0.00 0.00 35.21 1.40
4865 14266 5.337410 CCCATGAAATCACAATTTGCTACCA 60.337 40.000 0.00 0.00 35.21 3.25
4867 14268 5.964758 TCCCATGAAATCACAATTTGCTAC 58.035 37.500 0.00 0.00 35.21 3.58
4923 14324 1.751351 TCTAGGAACGGATGCAGACTG 59.249 52.381 0.00 0.00 0.00 3.51
4924 14325 1.751924 GTCTAGGAACGGATGCAGACT 59.248 52.381 0.00 0.00 31.77 3.24
4925 14326 1.751924 AGTCTAGGAACGGATGCAGAC 59.248 52.381 0.00 0.00 34.07 3.51
4926 14327 2.145397 AGTCTAGGAACGGATGCAGA 57.855 50.000 0.00 0.00 0.00 4.26
4927 14328 2.034812 GGTAGTCTAGGAACGGATGCAG 59.965 54.545 0.00 0.00 0.00 4.41
4928 14329 2.029623 GGTAGTCTAGGAACGGATGCA 58.970 52.381 0.00 0.00 0.00 3.96
4929 14330 2.293955 GAGGTAGTCTAGGAACGGATGC 59.706 54.545 0.00 0.00 0.00 3.91
4930 14331 2.885894 GGAGGTAGTCTAGGAACGGATG 59.114 54.545 0.00 0.00 0.00 3.51
4931 14332 2.158490 GGGAGGTAGTCTAGGAACGGAT 60.158 54.545 0.00 0.00 0.00 4.18
4932 14333 1.213926 GGGAGGTAGTCTAGGAACGGA 59.786 57.143 0.00 0.00 0.00 4.69
4933 14334 1.064166 TGGGAGGTAGTCTAGGAACGG 60.064 57.143 0.00 0.00 0.00 4.44
4934 14335 2.431954 TGGGAGGTAGTCTAGGAACG 57.568 55.000 0.00 0.00 0.00 3.95
4935 14336 2.431419 GCTTGGGAGGTAGTCTAGGAAC 59.569 54.545 0.00 0.00 0.00 3.62
4936 14337 2.315155 AGCTTGGGAGGTAGTCTAGGAA 59.685 50.000 0.00 0.00 0.00 3.36
4937 14338 1.930914 AGCTTGGGAGGTAGTCTAGGA 59.069 52.381 0.00 0.00 0.00 2.94
4938 14339 2.463047 AGCTTGGGAGGTAGTCTAGG 57.537 55.000 0.00 0.00 0.00 3.02
4939 14340 3.515901 ACAAAGCTTGGGAGGTAGTCTAG 59.484 47.826 5.66 0.00 32.23 2.43
4940 14341 3.260884 CACAAAGCTTGGGAGGTAGTCTA 59.739 47.826 5.66 0.00 35.62 2.59
4941 14342 2.039084 CACAAAGCTTGGGAGGTAGTCT 59.961 50.000 5.66 0.00 35.62 3.24
4942 14343 2.224548 ACACAAAGCTTGGGAGGTAGTC 60.225 50.000 5.66 0.00 37.55 2.59
4943 14344 1.774856 ACACAAAGCTTGGGAGGTAGT 59.225 47.619 5.66 0.00 37.55 2.73
4944 14345 2.427506 GACACAAAGCTTGGGAGGTAG 58.572 52.381 5.66 0.00 37.55 3.18
4945 14346 1.270625 CGACACAAAGCTTGGGAGGTA 60.271 52.381 5.66 0.00 37.55 3.08
4946 14347 0.535102 CGACACAAAGCTTGGGAGGT 60.535 55.000 5.66 0.07 37.55 3.85
4947 14348 0.250295 TCGACACAAAGCTTGGGAGG 60.250 55.000 5.66 0.00 37.55 4.30
4948 14349 0.868406 GTCGACACAAAGCTTGGGAG 59.132 55.000 11.55 0.00 37.55 4.30
4949 14350 0.878523 CGTCGACACAAAGCTTGGGA 60.879 55.000 17.16 0.00 37.55 4.37
4950 14351 1.569493 CGTCGACACAAAGCTTGGG 59.431 57.895 17.16 1.04 40.79 4.12
4951 14352 1.082756 GCGTCGACACAAAGCTTGG 60.083 57.895 17.16 0.00 34.12 3.61
4952 14353 0.383491 CAGCGTCGACACAAAGCTTG 60.383 55.000 17.16 6.85 35.82 4.01
4953 14354 0.529773 TCAGCGTCGACACAAAGCTT 60.530 50.000 17.16 0.00 35.82 3.74
4954 14355 0.529773 TTCAGCGTCGACACAAAGCT 60.530 50.000 17.16 12.59 38.90 3.74
4955 14356 0.111089 CTTCAGCGTCGACACAAAGC 60.111 55.000 17.16 10.31 0.00 3.51
4956 14357 1.487482 TCTTCAGCGTCGACACAAAG 58.513 50.000 17.16 13.26 0.00 2.77
4957 14358 1.858458 CTTCTTCAGCGTCGACACAAA 59.142 47.619 17.16 3.95 0.00 2.83
4958 14359 1.487482 CTTCTTCAGCGTCGACACAA 58.513 50.000 17.16 1.00 0.00 3.33
4959 14360 0.939577 GCTTCTTCAGCGTCGACACA 60.940 55.000 17.16 0.00 39.29 3.72
4960 14361 1.775962 GCTTCTTCAGCGTCGACAC 59.224 57.895 17.16 5.80 39.29 3.67
4961 14362 4.245054 GCTTCTTCAGCGTCGACA 57.755 55.556 17.16 0.00 39.29 4.35
4969 14370 2.414481 CGTTGTGATGAGGCTTCTTCAG 59.586 50.000 13.76 0.48 37.94 3.02
4970 14371 2.037121 TCGTTGTGATGAGGCTTCTTCA 59.963 45.455 9.96 9.96 35.74 3.02
4971 14372 2.688507 TCGTTGTGATGAGGCTTCTTC 58.311 47.619 4.92 4.92 0.00 2.87
4972 14373 2.839486 TCGTTGTGATGAGGCTTCTT 57.161 45.000 0.00 0.00 0.00 2.52
4982 14383 3.134623 TCATTAGGCTCCATCGTTGTGAT 59.865 43.478 0.00 0.00 38.01 3.06
4983 14384 2.499693 TCATTAGGCTCCATCGTTGTGA 59.500 45.455 0.00 0.00 0.00 3.58
4984 14385 2.609459 GTCATTAGGCTCCATCGTTGTG 59.391 50.000 0.00 0.00 0.00 3.33
4985 14386 2.236146 TGTCATTAGGCTCCATCGTTGT 59.764 45.455 0.00 0.00 0.00 3.32
4986 14387 2.905075 TGTCATTAGGCTCCATCGTTG 58.095 47.619 0.00 0.00 0.00 4.10
4987 14388 3.845781 ATGTCATTAGGCTCCATCGTT 57.154 42.857 0.00 0.00 0.00 3.85
4988 14389 4.345257 ACTTATGTCATTAGGCTCCATCGT 59.655 41.667 4.00 0.00 0.00 3.73
4989 14390 4.887748 ACTTATGTCATTAGGCTCCATCG 58.112 43.478 4.00 0.00 0.00 3.84
4990 14391 5.221722 TGGACTTATGTCATTAGGCTCCATC 60.222 44.000 10.60 0.00 44.61 3.51
4991 14392 4.660303 TGGACTTATGTCATTAGGCTCCAT 59.340 41.667 10.60 0.00 44.61 3.41
4992 14393 4.037222 TGGACTTATGTCATTAGGCTCCA 58.963 43.478 10.60 5.99 44.61 3.86
4993 14394 4.381411 GTGGACTTATGTCATTAGGCTCC 58.619 47.826 10.60 3.68 44.61 4.70
4994 14395 4.141711 TGGTGGACTTATGTCATTAGGCTC 60.142 45.833 10.60 0.00 44.61 4.70
4995 14396 3.780294 TGGTGGACTTATGTCATTAGGCT 59.220 43.478 10.60 0.00 44.61 4.58
4996 14397 4.150897 TGGTGGACTTATGTCATTAGGC 57.849 45.455 10.60 0.00 44.61 3.93
4997 14398 7.912056 CATATGGTGGACTTATGTCATTAGG 57.088 40.000 10.60 0.00 44.61 2.69
5013 14414 2.327343 CGGCGGCATCCATATGGTG 61.327 63.158 21.28 18.12 36.34 4.17
5014 14415 2.032528 CGGCGGCATCCATATGGT 59.967 61.111 21.28 6.34 36.34 3.55
5015 14416 3.434319 GCGGCGGCATCCATATGG 61.434 66.667 16.25 16.25 39.62 2.74
5016 14417 3.434319 GGCGGCGGCATCCATATG 61.434 66.667 29.41 0.00 42.47 1.78
5017 14418 3.952508 TGGCGGCGGCATCCATAT 61.953 61.111 33.02 0.00 42.47 1.78
5018 14419 4.927782 GTGGCGGCGGCATCCATA 62.928 66.667 38.08 12.56 40.92 2.74
5026 14427 3.625082 GAAAATGGTGTGGCGGCGG 62.625 63.158 9.78 0.00 0.00 6.13
5027 14428 2.126502 GAAAATGGTGTGGCGGCG 60.127 61.111 0.51 0.51 0.00 6.46
5028 14429 2.126502 CGAAAATGGTGTGGCGGC 60.127 61.111 0.00 0.00 0.00 6.53
5029 14430 2.126502 GCGAAAATGGTGTGGCGG 60.127 61.111 0.00 0.00 0.00 6.13
5030 14431 1.003262 CAAGCGAAAATGGTGTGGCG 61.003 55.000 0.00 0.00 0.00 5.69
5031 14432 0.313672 TCAAGCGAAAATGGTGTGGC 59.686 50.000 0.00 0.00 0.00 5.01
5032 14433 2.223688 TGTTCAAGCGAAAATGGTGTGG 60.224 45.455 0.00 0.00 31.43 4.17
5033 14434 3.044986 CTGTTCAAGCGAAAATGGTGTG 58.955 45.455 0.00 0.00 31.43 3.82
5034 14435 2.948979 TCTGTTCAAGCGAAAATGGTGT 59.051 40.909 0.00 0.00 31.43 4.16
5035 14436 3.003689 AGTCTGTTCAAGCGAAAATGGTG 59.996 43.478 0.00 0.00 31.43 4.17
5036 14437 3.214328 AGTCTGTTCAAGCGAAAATGGT 58.786 40.909 0.00 0.00 31.43 3.55
5037 14438 3.904136 AGTCTGTTCAAGCGAAAATGG 57.096 42.857 0.00 0.00 31.43 3.16



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

AutoCloner maintained by Alex Coulton.