Multiple sequence alignment - TraesCS5B01G152000

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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 TraesCS5B01G152000 chr5B 100.000 5818 0 0 1 5818 281102423 281108240 0.000000e+00 10744.0
1 TraesCS5B01G152000 chr5B 93.365 1055 51 7 4770 5818 64625605 64624564 0.000000e+00 1543.0
2 TraesCS5B01G152000 chr5B 92.015 1052 69 7 4770 5818 594134645 594133606 0.000000e+00 1463.0
3 TraesCS5B01G152000 chr5D 96.013 1530 61 0 3242 4771 246656824 246658353 0.000000e+00 2488.0
4 TraesCS5B01G152000 chr5D 83.439 942 136 12 2 929 551451727 551450792 0.000000e+00 857.0
5 TraesCS5B01G152000 chr5D 82.655 934 140 17 17 931 91875735 91874805 0.000000e+00 808.0
6 TraesCS5B01G152000 chr5D 85.417 624 49 23 931 1531 246653310 246653914 1.390000e-170 610.0
7 TraesCS5B01G152000 chr5D 86.804 485 42 15 2191 2658 246655697 246656176 6.680000e-144 521.0
8 TraesCS5B01G152000 chr5D 81.569 548 50 20 2680 3213 246656160 246656670 7.020000e-109 405.0
9 TraesCS5B01G152000 chr5D 82.110 218 22 12 1913 2120 246654050 246654260 2.790000e-38 171.0
10 TraesCS5B01G152000 chr5A 94.430 1562 80 3 3217 4771 330504376 330505937 0.000000e+00 2396.0
11 TraesCS5B01G152000 chr5A 86.805 1637 97 40 1609 3214 330502683 330504231 0.000000e+00 1716.0
12 TraesCS5B01G152000 chr5A 92.145 662 29 9 928 1581 330502046 330502692 0.000000e+00 913.0
13 TraesCS5B01G152000 chr5A 89.249 679 64 5 4 677 634469928 634470602 0.000000e+00 841.0
14 TraesCS5B01G152000 chr6B 92.688 1053 61 4 4770 5818 123229130 123228090 0.000000e+00 1504.0
15 TraesCS5B01G152000 chr6B 92.308 1053 64 5 4770 5818 93410146 93409107 0.000000e+00 1480.0
16 TraesCS5B01G152000 chr4A 91.761 1056 72 6 4766 5818 190802722 190803765 0.000000e+00 1454.0
17 TraesCS5B01G152000 chr4A 91.825 1052 71 7 4770 5818 96321081 96320042 0.000000e+00 1452.0
18 TraesCS5B01G152000 chr4A 79.298 570 115 2 3261 3827 709717809 709717240 4.220000e-106 396.0
19 TraesCS5B01G152000 chr4A 87.225 227 29 0 1269 1495 709720363 709720137 5.780000e-65 259.0
20 TraesCS5B01G152000 chr4A 87.225 227 29 0 1269 1495 709721361 709721135 5.780000e-65 259.0
21 TraesCS5B01G152000 chr2A 91.825 1052 71 7 4770 5818 759255551 759256590 0.000000e+00 1452.0
22 TraesCS5B01G152000 chr6A 91.730 1052 72 6 4770 5818 105052714 105051675 0.000000e+00 1447.0
23 TraesCS5B01G152000 chr6A 91.643 1053 73 6 4769 5818 564670622 564669582 0.000000e+00 1443.0
24 TraesCS5B01G152000 chr6A 93.333 45 2 1 2733 2777 594508029 594507986 1.350000e-06 65.8
25 TraesCS5B01G152000 chr7B 91.263 1053 75 5 4770 5818 130513688 130512649 0.000000e+00 1419.0
26 TraesCS5B01G152000 chr7B 80.887 947 154 22 2 929 370274453 370275391 0.000000e+00 721.0
27 TraesCS5B01G152000 chr3A 90.399 1052 86 4 4770 5818 109879758 109878719 0.000000e+00 1369.0
28 TraesCS5B01G152000 chr2B 85.181 938 122 15 4 931 25455848 25456778 0.000000e+00 946.0
29 TraesCS5B01G152000 chr7A 84.395 942 124 17 4 928 222288711 222289646 0.000000e+00 904.0
30 TraesCS5B01G152000 chr7A 77.770 1471 271 38 3263 4719 26241110 26239682 0.000000e+00 854.0
31 TraesCS5B01G152000 chr7A 86.784 227 30 0 1269 1495 26242934 26242708 2.690000e-63 254.0
32 TraesCS5B01G152000 chr7A 81.928 83 10 1 3136 3213 52460712 52460794 1.350000e-06 65.8
33 TraesCS5B01G152000 chr3D 84.560 829 117 9 2 825 98534617 98535439 0.000000e+00 811.0
34 TraesCS5B01G152000 chr2D 82.260 947 143 17 2 934 94726576 94727511 0.000000e+00 795.0
35 TraesCS5B01G152000 chr2D 84.549 809 116 7 2 804 155417712 155416907 0.000000e+00 793.0
36 TraesCS5B01G152000 chr7D 82.003 739 108 13 3983 4719 25336151 25335436 6.450000e-169 604.0
37 TraesCS5B01G152000 chr7D 79.787 564 111 1 3263 3823 25336884 25336321 1.950000e-109 407.0
38 TraesCS5B01G152000 chr7D 89.868 227 23 0 1269 1495 25338528 25338302 5.700000e-75 292.0
39 TraesCS5B01G152000 chr7D 95.238 42 2 0 3172 3213 49686574 49686615 3.760000e-07 67.6
40 TraesCS5B01G152000 chr1D 77.922 154 23 4 2945 3092 426886431 426886283 1.040000e-12 86.1
41 TraesCS5B01G152000 chr6D 97.500 40 1 0 3174 3213 86373937 86373898 1.050000e-07 69.4
42 TraesCS5B01G152000 chr6D 93.333 45 2 1 2733 2777 448050691 448050648 1.350000e-06 65.8


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 TraesCS5B01G152000 chr5B 281102423 281108240 5817 False 10744.000000 10744 100.000000 1 5818 1 chr5B.!!$F1 5817
1 TraesCS5B01G152000 chr5B 64624564 64625605 1041 True 1543.000000 1543 93.365000 4770 5818 1 chr5B.!!$R1 1048
2 TraesCS5B01G152000 chr5B 594133606 594134645 1039 True 1463.000000 1463 92.015000 4770 5818 1 chr5B.!!$R2 1048
3 TraesCS5B01G152000 chr5D 551450792 551451727 935 True 857.000000 857 83.439000 2 929 1 chr5D.!!$R2 927
4 TraesCS5B01G152000 chr5D 246653310 246658353 5043 False 839.000000 2488 86.382600 931 4771 5 chr5D.!!$F1 3840
5 TraesCS5B01G152000 chr5D 91874805 91875735 930 True 808.000000 808 82.655000 17 931 1 chr5D.!!$R1 914
6 TraesCS5B01G152000 chr5A 330502046 330505937 3891 False 1675.000000 2396 91.126667 928 4771 3 chr5A.!!$F2 3843
7 TraesCS5B01G152000 chr5A 634469928 634470602 674 False 841.000000 841 89.249000 4 677 1 chr5A.!!$F1 673
8 TraesCS5B01G152000 chr6B 123228090 123229130 1040 True 1504.000000 1504 92.688000 4770 5818 1 chr6B.!!$R2 1048
9 TraesCS5B01G152000 chr6B 93409107 93410146 1039 True 1480.000000 1480 92.308000 4770 5818 1 chr6B.!!$R1 1048
10 TraesCS5B01G152000 chr4A 190802722 190803765 1043 False 1454.000000 1454 91.761000 4766 5818 1 chr4A.!!$F1 1052
11 TraesCS5B01G152000 chr4A 96320042 96321081 1039 True 1452.000000 1452 91.825000 4770 5818 1 chr4A.!!$R1 1048
12 TraesCS5B01G152000 chr4A 709717240 709721361 4121 True 304.666667 396 84.582667 1269 3827 3 chr4A.!!$R2 2558
13 TraesCS5B01G152000 chr2A 759255551 759256590 1039 False 1452.000000 1452 91.825000 4770 5818 1 chr2A.!!$F1 1048
14 TraesCS5B01G152000 chr6A 105051675 105052714 1039 True 1447.000000 1447 91.730000 4770 5818 1 chr6A.!!$R1 1048
15 TraesCS5B01G152000 chr6A 564669582 564670622 1040 True 1443.000000 1443 91.643000 4769 5818 1 chr6A.!!$R2 1049
16 TraesCS5B01G152000 chr7B 130512649 130513688 1039 True 1419.000000 1419 91.263000 4770 5818 1 chr7B.!!$R1 1048
17 TraesCS5B01G152000 chr7B 370274453 370275391 938 False 721.000000 721 80.887000 2 929 1 chr7B.!!$F1 927
18 TraesCS5B01G152000 chr3A 109878719 109879758 1039 True 1369.000000 1369 90.399000 4770 5818 1 chr3A.!!$R1 1048
19 TraesCS5B01G152000 chr2B 25455848 25456778 930 False 946.000000 946 85.181000 4 931 1 chr2B.!!$F1 927
20 TraesCS5B01G152000 chr7A 222288711 222289646 935 False 904.000000 904 84.395000 4 928 1 chr7A.!!$F2 924
21 TraesCS5B01G152000 chr7A 26239682 26242934 3252 True 554.000000 854 82.277000 1269 4719 2 chr7A.!!$R1 3450
22 TraesCS5B01G152000 chr3D 98534617 98535439 822 False 811.000000 811 84.560000 2 825 1 chr3D.!!$F1 823
23 TraesCS5B01G152000 chr2D 94726576 94727511 935 False 795.000000 795 82.260000 2 934 1 chr2D.!!$F1 932
24 TraesCS5B01G152000 chr2D 155416907 155417712 805 True 793.000000 793 84.549000 2 804 1 chr2D.!!$R1 802
25 TraesCS5B01G152000 chr7D 25335436 25338528 3092 True 434.333333 604 83.886000 1269 4719 3 chr7D.!!$R1 3450

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
152 153 0.161024 GTCGCTTTTCGGTCAAGTCG 59.839 55.0 0.00 0.00 39.05 4.18 F
854 870 0.180642 TCTGGGGCAACGTTGTGTTA 59.819 50.0 27.78 12.51 39.29 2.41 F
1060 1115 0.032316 AGGCAGAGATGGAGAGCTCA 60.032 55.0 17.77 0.00 37.06 4.26 F
1602 3919 0.240945 AAAATGCGAACGGAAGCCTG 59.759 50.0 0.00 0.00 0.00 4.85 F
2627 6383 0.393808 ACAACGTCCATGGGTATGCC 60.394 55.0 13.02 0.00 32.79 4.40 F
3539 8155 0.390860 CTTCCTTCCTGATCGGCGAT 59.609 55.0 24.26 24.26 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1042 1097 0.104671 GTGAGCTCTCCATCTCTGCC 59.895 60.000 16.19 0.0 0.00 4.85 R
2042 4362 0.251209 ACCTCTAGTGCGAGTGGTCA 60.251 55.000 1.22 0.0 38.65 4.02 R
2736 6509 0.252761 ACGGTGCATGTGATCCATCA 59.747 50.000 0.00 0.0 0.00 3.07 R
3509 8125 1.826096 AGGAAGGAAGCGTAGAGGAAC 59.174 52.381 0.00 0.0 0.00 3.62 R
3946 8581 0.532862 GACGCATCATCCATCGGGTT 60.533 55.000 0.00 0.0 34.93 4.11 R
5179 9819 0.404040 CAGGGCAGTCCAAAAGGGTA 59.596 55.000 0.00 0.0 38.24 3.69 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
84 85 1.743996 GCTTACTGCCTTCTTCCCTG 58.256 55.000 0.00 0.00 35.15 4.45
93 94 1.938657 CTTCTTCCCTGCGCTCTCGA 61.939 60.000 9.73 0.00 38.10 4.04
112 113 3.195698 GAATGCGGACTCGGTGGC 61.196 66.667 0.00 0.00 36.79 5.01
152 153 0.161024 GTCGCTTTTCGGTCAAGTCG 59.839 55.000 0.00 0.00 39.05 4.18
217 218 0.391263 CAGGTTTGGAGGGCTCGTAC 60.391 60.000 0.00 0.00 0.00 3.67
272 273 2.035940 AGAGGTCGTCTTCCCGCT 59.964 61.111 0.00 0.00 27.07 5.52
351 359 5.297029 GGTGCCCTGAAAGACACTATATTTC 59.703 44.000 0.00 0.00 39.70 2.17
369 377 4.799564 TTTCTTTCACTGTGTTTTGGCT 57.200 36.364 7.79 0.00 0.00 4.75
577 585 2.111582 GCTAAGCCTGCTGACTGCC 61.112 63.158 1.50 0.00 42.00 4.85
745 755 1.439679 CCTTCGACTAGTTGTTGGCC 58.560 55.000 10.00 0.00 0.00 5.36
804 815 1.227102 GCCTGGGTGCCATGTATCA 59.773 57.895 0.00 0.00 30.82 2.15
809 820 2.700371 CTGGGTGCCATGTATCACTCTA 59.300 50.000 10.08 0.74 34.86 2.43
817 833 7.715249 GGTGCCATGTATCACTCTATCTAAAAA 59.285 37.037 9.03 0.00 33.91 1.94
824 840 9.667107 TGTATCACTCTATCTAAAAACTTTGGG 57.333 33.333 0.00 0.00 0.00 4.12
854 870 0.180642 TCTGGGGCAACGTTGTGTTA 59.819 50.000 27.78 12.51 39.29 2.41
869 901 3.537580 TGTGTTAGTTGGTCTGGTTGTC 58.462 45.455 0.00 0.00 0.00 3.18
872 913 3.452990 TGTTAGTTGGTCTGGTTGTCTGA 59.547 43.478 0.00 0.00 0.00 3.27
903 944 5.010282 CCTGGTGGCTTCACTTATAAAGTT 58.990 41.667 0.00 0.00 40.46 2.66
910 951 2.004017 TCACTTATAAAGTTGGGCGCG 58.996 47.619 0.00 0.00 40.46 6.86
915 956 0.321298 ATAAAGTTGGGCGCGTGTCT 60.321 50.000 8.43 0.00 0.00 3.41
951 993 1.211457 AGCTATCCAACCCAGCAAGAG 59.789 52.381 0.00 0.00 37.78 2.85
959 1001 1.258445 ACCCAGCAAGAGACCCTACG 61.258 60.000 0.00 0.00 0.00 3.51
977 1022 6.499350 ACCCTACGTCCATTTGGTACATATAT 59.501 38.462 0.00 0.00 39.30 0.86
978 1023 7.675195 ACCCTACGTCCATTTGGTACATATATA 59.325 37.037 0.00 0.00 39.30 0.86
1042 1097 0.680280 AGCTTGGAGCAATGGCAGAG 60.680 55.000 0.00 0.00 45.56 3.35
1060 1115 0.032316 AGGCAGAGATGGAGAGCTCA 60.032 55.000 17.77 0.00 37.06 4.26
1080 1135 0.539051 CCGAGATCTCAGCCCAAACT 59.461 55.000 22.31 0.00 0.00 2.66
1089 1144 2.503356 CTCAGCCCAAACTATCAGACCT 59.497 50.000 0.00 0.00 0.00 3.85
1100 1155 7.978975 CCAAACTATCAGACCTAGAAGAAGAAG 59.021 40.741 0.00 0.00 0.00 2.85
1108 1163 2.026822 CCTAGAAGAAGAAGGGCAAGCA 60.027 50.000 0.00 0.00 0.00 3.91
1112 1167 3.706086 AGAAGAAGAAGGGCAAGCAAAAA 59.294 39.130 0.00 0.00 0.00 1.94
1164 1219 1.480954 TCCCTTCATAGCTGGTTCGTC 59.519 52.381 0.00 0.00 0.00 4.20
1180 1235 4.442706 GTTCGTCATCTCTCTCTCTCTCT 58.557 47.826 0.00 0.00 0.00 3.10
1181 1236 4.322080 TCGTCATCTCTCTCTCTCTCTC 57.678 50.000 0.00 0.00 0.00 3.20
1182 1237 3.704061 TCGTCATCTCTCTCTCTCTCTCA 59.296 47.826 0.00 0.00 0.00 3.27
1183 1238 3.804325 CGTCATCTCTCTCTCTCTCTCAC 59.196 52.174 0.00 0.00 0.00 3.51
1184 1239 4.442052 CGTCATCTCTCTCTCTCTCTCACT 60.442 50.000 0.00 0.00 0.00 3.41
1185 1240 5.431765 GTCATCTCTCTCTCTCTCTCACTT 58.568 45.833 0.00 0.00 0.00 3.16
1186 1241 5.525378 GTCATCTCTCTCTCTCTCTCACTTC 59.475 48.000 0.00 0.00 0.00 3.01
1187 1242 4.487714 TCTCTCTCTCTCTCTCACTTCC 57.512 50.000 0.00 0.00 0.00 3.46
1215 1270 4.651778 TCTTCCCCACACAATTAACTCTG 58.348 43.478 0.00 0.00 0.00 3.35
1556 3873 7.123997 TGTGCAGTATACATTTTGGGATTTGAT 59.876 33.333 5.50 0.00 0.00 2.57
1570 3887 3.503748 GGATTTGATGTAGTGCATAGGCC 59.496 47.826 0.00 0.00 38.06 5.19
1576 3893 1.457643 TAGTGCATAGGCCGGAGCT 60.458 57.895 5.05 0.00 40.13 4.09
1577 3894 1.748329 TAGTGCATAGGCCGGAGCTG 61.748 60.000 5.05 0.00 40.13 4.24
1578 3895 2.763710 TGCATAGGCCGGAGCTGA 60.764 61.111 5.05 0.00 40.13 4.26
1579 3896 2.142761 TGCATAGGCCGGAGCTGAT 61.143 57.895 5.05 0.00 40.13 2.90
1580 3897 1.375268 GCATAGGCCGGAGCTGATC 60.375 63.158 5.05 0.00 39.73 2.92
1581 3898 1.080230 CATAGGCCGGAGCTGATCG 60.080 63.158 5.05 0.00 39.73 3.69
1589 3906 0.305922 CGGAGCTGATCGGAAAATGC 59.694 55.000 5.48 0.00 0.00 3.56
1590 3907 0.305922 GGAGCTGATCGGAAAATGCG 59.694 55.000 5.48 0.00 0.00 4.73
1591 3908 1.290203 GAGCTGATCGGAAAATGCGA 58.710 50.000 5.48 0.00 45.91 5.10
1592 3909 1.665679 GAGCTGATCGGAAAATGCGAA 59.334 47.619 5.48 0.00 44.81 4.70
1593 3910 1.398390 AGCTGATCGGAAAATGCGAAC 59.602 47.619 5.48 0.00 44.81 3.95
1594 3911 1.852077 GCTGATCGGAAAATGCGAACG 60.852 52.381 5.48 0.00 44.81 3.95
1595 3912 0.724549 TGATCGGAAAATGCGAACGG 59.275 50.000 0.00 0.00 44.81 4.44
1596 3913 1.003851 GATCGGAAAATGCGAACGGA 58.996 50.000 0.00 0.00 44.81 4.69
1597 3914 1.395608 GATCGGAAAATGCGAACGGAA 59.604 47.619 0.00 0.00 44.81 4.30
1598 3915 0.793861 TCGGAAAATGCGAACGGAAG 59.206 50.000 0.00 0.00 37.25 3.46
1599 3916 0.793104 CGGAAAATGCGAACGGAAGC 60.793 55.000 0.00 0.00 30.86 3.86
1600 3917 0.456142 GGAAAATGCGAACGGAAGCC 60.456 55.000 0.00 0.00 0.00 4.35
1601 3918 0.521735 GAAAATGCGAACGGAAGCCT 59.478 50.000 0.00 0.00 0.00 4.58
1602 3919 0.240945 AAAATGCGAACGGAAGCCTG 59.759 50.000 0.00 0.00 0.00 4.85
1603 3920 2.200170 AAATGCGAACGGAAGCCTGC 62.200 55.000 0.00 0.00 0.00 4.85
1604 3921 3.899981 ATGCGAACGGAAGCCTGCA 62.900 57.895 0.00 0.00 36.69 4.41
1605 3922 4.090057 GCGAACGGAAGCCTGCAC 62.090 66.667 0.00 0.00 0.00 4.57
1606 3923 2.357517 CGAACGGAAGCCTGCACT 60.358 61.111 0.00 0.00 0.00 4.40
1607 3924 2.383527 CGAACGGAAGCCTGCACTC 61.384 63.158 0.00 0.00 0.00 3.51
1608 3925 2.357517 AACGGAAGCCTGCACTCG 60.358 61.111 0.00 0.00 0.00 4.18
1609 3926 3.883744 AACGGAAGCCTGCACTCGG 62.884 63.158 0.00 0.00 0.00 4.63
1610 3927 4.069232 CGGAAGCCTGCACTCGGA 62.069 66.667 0.00 0.00 0.00 4.55
1611 3928 2.125350 GGAAGCCTGCACTCGGAG 60.125 66.667 2.83 2.83 0.00 4.63
1612 3929 2.817396 GAAGCCTGCACTCGGAGC 60.817 66.667 4.58 0.00 0.00 4.70
1613 3930 3.308014 GAAGCCTGCACTCGGAGCT 62.308 63.158 4.58 0.00 0.00 4.09
1734 4051 7.040823 GGACATAGGTAGTACGTAGCAAACTAT 60.041 40.741 8.55 0.00 0.00 2.12
1737 4054 9.212641 CATAGGTAGTACGTAGCAAACTATCTA 57.787 37.037 14.68 14.68 41.35 1.98
1787 4104 6.042777 GTCGAGGTGATTTATCTCATTGTGA 58.957 40.000 0.00 0.00 36.24 3.58
1793 4110 8.680903 AGGTGATTTATCTCATTGTGATCAAAC 58.319 33.333 0.00 1.43 37.11 2.93
1798 4115 8.996024 TTTATCTCATTGTGATCAAACGACTA 57.004 30.769 0.00 0.00 37.11 2.59
1805 4122 4.951254 TGTGATCAAACGACTAACTTGGA 58.049 39.130 0.00 0.00 0.00 3.53
1868 4186 5.409826 CGGAAGCATGAAAGAACTCTTTAGT 59.590 40.000 4.71 0.00 45.37 2.24
1869 4187 6.401581 CGGAAGCATGAAAGAACTCTTTAGTC 60.402 42.308 4.71 0.00 45.37 2.59
1872 4190 5.866633 AGCATGAAAGAACTCTTTAGTCGAG 59.133 40.000 4.71 0.00 45.37 4.04
1892 4210 9.877178 AGTCGAGTGATAAAAGAGTGAAATATT 57.123 29.630 0.00 0.00 0.00 1.28
2000 4319 4.527427 TGTCATCAATGAGGCCAAAAATGA 59.473 37.500 5.01 2.82 37.51 2.57
2004 4323 6.596106 TCATCAATGAGGCCAAAAATGATTTG 59.404 34.615 5.01 0.00 32.11 2.32
2042 4362 3.645212 CCATCCACATGTCTATCAGGTCT 59.355 47.826 0.00 0.00 39.11 3.85
2060 4390 0.453793 CTGACCACTCGCACTAGAGG 59.546 60.000 0.00 0.00 42.31 3.69
2073 4403 4.130118 GCACTAGAGGTCATGTTTATGGG 58.870 47.826 0.00 0.00 34.97 4.00
2074 4404 4.708177 CACTAGAGGTCATGTTTATGGGG 58.292 47.826 0.00 0.00 34.97 4.96
2079 4409 4.772100 AGAGGTCATGTTTATGGGGTTTTG 59.228 41.667 0.00 0.00 34.97 2.44
2086 4416 5.203060 TGTTTATGGGGTTTTGTACAAGC 57.797 39.130 8.56 6.09 0.00 4.01
2088 4418 6.069331 TGTTTATGGGGTTTTGTACAAGCTA 58.931 36.000 8.56 0.00 0.00 3.32
2198 5894 2.381589 GCAGAACGCAAAGTGGTTTAC 58.618 47.619 0.00 0.00 41.79 2.01
2232 5929 6.366332 CGGGTTACATAAGTATTCTGATGAGC 59.634 42.308 3.78 0.00 36.34 4.26
2312 6013 5.829924 TCCAAAGCTCAACTTTCATTTCTCT 59.170 36.000 0.00 0.00 45.78 3.10
2340 6041 2.362077 AGCAAAATTTGGTTGAGCGAGT 59.638 40.909 4.40 0.00 38.40 4.18
2360 6061 6.455913 GCGAGTAGGTTTTCATAATTTACGCA 60.456 38.462 0.00 0.00 38.89 5.24
2365 6066 9.349145 GTAGGTTTTCATAATTTACGCAAATGT 57.651 29.630 0.00 0.00 34.53 2.71
2379 6080 4.761739 ACGCAAATGTCAATATGGATAGGG 59.238 41.667 0.00 0.00 0.00 3.53
2516 6232 3.951775 AGTTGTCATGTCTCACTCTCC 57.048 47.619 0.00 0.00 0.00 3.71
2517 6233 3.234353 AGTTGTCATGTCTCACTCTCCA 58.766 45.455 0.00 0.00 0.00 3.86
2565 6285 6.489700 ACAAACATGACCACTTGACATTGATA 59.510 34.615 0.00 0.00 0.00 2.15
2627 6383 0.393808 ACAACGTCCATGGGTATGCC 60.394 55.000 13.02 0.00 32.79 4.40
2678 6434 8.950208 TTTTATTTATTTATTTTGCGGGGGAG 57.050 30.769 0.00 0.00 0.00 4.30
2730 6503 7.047891 CCATTTCAATCCAACACTAGCTAGTA 58.952 38.462 25.63 10.83 34.13 1.82
2736 6509 7.560262 TCAATCCAACACTAGCTAGTACAGTAT 59.440 37.037 25.63 13.74 34.13 2.12
2830 6839 0.748005 GTGTGGCTCACAGTGGTGTT 60.748 55.000 14.37 0.00 45.43 3.32
2915 6924 5.887598 TCTTGAGCATTGCCATTTATAGTGT 59.112 36.000 4.70 0.00 0.00 3.55
2940 6949 9.878599 GTATATCACATGGAAATAAAGTTTCGG 57.121 33.333 0.00 0.00 0.00 4.30
2941 6950 6.834168 ATCACATGGAAATAAAGTTTCGGT 57.166 33.333 0.00 0.00 0.00 4.69
2942 6951 6.007936 TCACATGGAAATAAAGTTTCGGTG 57.992 37.500 0.00 9.98 32.25 4.94
2943 6952 5.765677 TCACATGGAAATAAAGTTTCGGTGA 59.234 36.000 0.00 12.77 34.95 4.02
2944 6953 6.263392 TCACATGGAAATAAAGTTTCGGTGAA 59.737 34.615 13.68 0.00 34.69 3.18
2945 6954 6.920758 CACATGGAAATAAAGTTTCGGTGAAA 59.079 34.615 0.00 0.00 32.47 2.69
2946 6955 7.436673 CACATGGAAATAAAGTTTCGGTGAAAA 59.563 33.333 0.00 0.00 33.14 2.29
2947 6956 7.436970 ACATGGAAATAAAGTTTCGGTGAAAAC 59.563 33.333 0.00 0.00 39.03 2.43
2948 6957 6.274579 TGGAAATAAAGTTTCGGTGAAAACC 58.725 36.000 0.00 0.00 39.46 3.27
3094 7188 8.303156 TCCCAAACACATTATCATGTACAAAAG 58.697 33.333 0.00 0.00 42.14 2.27
3108 7202 7.809331 TCATGTACAAAAGAATCAGCATTGAAC 59.191 33.333 0.00 0.00 36.78 3.18
3132 7226 3.778718 GCGTCGTGCAGTAATTAAACATG 59.221 43.478 0.00 0.00 45.45 3.21
3168 7262 5.423015 TGAATTCGCTCTTTTCATAGCTCT 58.577 37.500 0.04 0.00 36.56 4.09
3214 7321 2.158769 TCGCATGGCAATAGAACATCCT 60.159 45.455 0.00 0.00 0.00 3.24
3254 7867 7.900782 AGAGCAGTGTTAATTAATTACGTGT 57.099 32.000 7.43 0.00 0.00 4.49
3266 7879 4.963276 AATTACGTGTCCATCCAATGTG 57.037 40.909 0.00 0.00 0.00 3.21
3509 8125 4.881850 ACCTTCTTCAACTGGTACTTTGTG 59.118 41.667 0.00 0.00 0.00 3.33
3539 8155 0.390860 CTTCCTTCCTGATCGGCGAT 59.609 55.000 24.26 24.26 0.00 4.58
3626 8242 1.079750 GGCGTTCAGTCTGGTCCTC 60.080 63.158 0.00 0.00 0.00 3.71
3843 8459 1.164041 GGTGCCATTCCCGTATTCCG 61.164 60.000 0.00 0.00 0.00 4.30
3874 8493 2.279517 GGATGAGCGCTGGTACGG 60.280 66.667 18.48 0.00 38.10 4.02
3902 8537 1.647545 CCGCGTTCATGCCATCTTGT 61.648 55.000 4.92 0.00 0.00 3.16
3946 8581 0.036483 CATGATCACCACCACCGACA 60.036 55.000 0.00 0.00 0.00 4.35
3951 8586 4.244463 ACCACCACCGACAACCCG 62.244 66.667 0.00 0.00 0.00 5.28
3966 8601 2.023771 CCCGATGGATGATGCGTCG 61.024 63.158 19.64 19.64 45.01 5.12
3972 8607 2.186903 GATGATGCGTCGGGTGGT 59.813 61.111 0.58 0.00 0.00 4.16
3979 8614 3.422303 CGTCGGGTGGTCGTCGTA 61.422 66.667 0.00 0.00 37.05 3.43
4044 8679 0.677098 AGTCTCTGCTCGGCGTCTTA 60.677 55.000 6.85 0.00 0.00 2.10
4200 8835 2.185350 CTCGTGGCCTTCATCGCT 59.815 61.111 3.32 0.00 0.00 4.93
4569 9204 0.472925 TGGGGTTCTACCTCAGCACA 60.473 55.000 0.00 0.00 45.61 4.57
4572 9207 1.066787 GGGTTCTACCTCAGCACAGTC 60.067 57.143 0.00 0.00 38.64 3.51
4671 9306 3.349006 GTGGCTGTGGCAGTGACG 61.349 66.667 0.00 0.00 39.19 4.35
4731 9366 8.974408 CGATATAAGTATCAAAACCAATCGACA 58.026 33.333 0.00 0.00 37.20 4.35
4735 9370 5.067273 AGTATCAAAACCAATCGACAACCA 58.933 37.500 0.00 0.00 0.00 3.67
4756 9391 6.833041 ACCATGGTGATGTAAATACGGATTA 58.167 36.000 18.99 0.00 0.00 1.75
4778 9413 9.589111 GATTAGTAGGTTGAGTCTTTTTAGAGG 57.411 37.037 0.00 0.00 0.00 3.69
4840 9475 4.821805 CAGAGTTACACCAACAGAACCAAT 59.178 41.667 0.00 0.00 39.81 3.16
4858 9494 7.343574 AGAACCAATACCCAAACAAGTTTAACT 59.656 33.333 0.00 0.00 0.00 2.24
5012 9650 8.131100 CGTAGATTTCATTTTGGATAGCATGTT 58.869 33.333 0.00 0.00 0.00 2.71
5028 9666 2.613026 TGTTGTCGAAAGCCTGAAGA 57.387 45.000 0.00 0.00 0.00 2.87
5030 9668 3.476552 TGTTGTCGAAAGCCTGAAGATT 58.523 40.909 0.00 0.00 0.00 2.40
5066 9704 4.708726 ATAATCTCCACTGCTGCAAAAC 57.291 40.909 3.02 0.00 0.00 2.43
5128 9768 6.378582 GGAAAAATGTGTTCAATCGAGCTTA 58.621 36.000 0.00 0.00 0.00 3.09
5179 9819 0.257039 CAGCCCAGCCCACTAAGAAT 59.743 55.000 0.00 0.00 0.00 2.40
5325 9965 9.017669 GCAATGAAAGAAAATATGATCAGTGTC 57.982 33.333 0.09 0.00 35.86 3.67
5330 9970 8.503458 AAAGAAAATATGATCAGTGTCCTCAG 57.497 34.615 0.09 0.00 0.00 3.35
5364 10004 0.902984 ACACACCTATCAGTGCCCGA 60.903 55.000 0.00 0.00 41.67 5.14
5371 10011 1.546589 TATCAGTGCCCGACCCGTTT 61.547 55.000 0.00 0.00 0.00 3.60
5380 10020 1.429463 CCGACCCGTTTCTCTTCTTG 58.571 55.000 0.00 0.00 0.00 3.02
5490 10131 3.726517 CTTCACCAAGCGGCCACG 61.727 66.667 2.24 0.00 44.63 4.94
5629 10271 2.537143 TCTTCCAACTCTACAGGGGAC 58.463 52.381 0.00 0.00 29.45 4.46
5630 10272 2.111972 TCTTCCAACTCTACAGGGGACT 59.888 50.000 0.00 0.00 46.44 3.85
5631 10273 2.233305 TCCAACTCTACAGGGGACTC 57.767 55.000 0.00 0.00 40.21 3.36
5632 10274 1.717077 TCCAACTCTACAGGGGACTCT 59.283 52.381 0.00 0.00 40.21 3.24
5633 10275 2.924302 TCCAACTCTACAGGGGACTCTA 59.076 50.000 0.00 0.00 40.21 2.43
5634 10276 3.025262 CCAACTCTACAGGGGACTCTAC 58.975 54.545 0.00 0.00 40.21 2.59
5635 10277 3.563697 CCAACTCTACAGGGGACTCTACA 60.564 52.174 0.00 0.00 40.21 2.74
5636 10278 3.655615 ACTCTACAGGGGACTCTACAG 57.344 52.381 0.00 0.00 40.21 2.74
5637 10279 2.242708 ACTCTACAGGGGACTCTACAGG 59.757 54.545 0.00 0.00 40.21 4.00
5638 10280 1.569548 TCTACAGGGGACTCTACAGGG 59.430 57.143 0.00 0.00 40.21 4.45
5639 10281 0.635009 TACAGGGGACTCTACAGGGG 59.365 60.000 0.00 0.00 40.21 4.79
5640 10282 1.153695 ACAGGGGACTCTACAGGGGA 61.154 60.000 0.00 0.00 40.21 4.81
5655 10297 2.202810 GGAAAGAGAGCGCCGGAG 60.203 66.667 5.05 1.55 0.00 4.63
5683 10325 1.481056 CCCAACCCTGAACCGAGAGT 61.481 60.000 0.00 0.00 0.00 3.24
5726 10368 6.150140 AGGATCAACACAATAAGAGAACAAGC 59.850 38.462 0.00 0.00 0.00 4.01
5794 10437 2.551032 CCAAAAACGAGTGGACTTACCC 59.449 50.000 0.00 0.00 37.03 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.629739 CGGAAGGCTAAGTTCCAGTTATTAGT 60.630 42.308 3.98 0.00 43.35 2.24
84 85 2.617762 CGCATTCTTCGAGAGCGC 59.382 61.111 0.00 0.00 41.95 5.92
93 94 1.079127 CCACCGAGTCCGCATTCTT 60.079 57.895 0.00 0.00 0.00 2.52
112 113 2.158842 CCAGAGGAAGTATGAGGCCAAG 60.159 54.545 5.01 0.00 0.00 3.61
272 273 2.343101 CTCTTACGAATTTGGTCCGCA 58.657 47.619 0.00 0.00 0.00 5.69
351 359 4.044426 GCTTAGCCAAAACACAGTGAAAG 58.956 43.478 7.81 0.00 0.00 2.62
369 377 4.634012 AACACAACTCCATACCAGCTTA 57.366 40.909 0.00 0.00 0.00 3.09
415 423 3.591079 AGCTCAGAAAAGGAAGAGGGATT 59.409 43.478 0.00 0.00 0.00 3.01
550 558 1.006400 AGCAGGCTTAGCAGGGAAAAT 59.994 47.619 6.53 0.00 0.00 1.82
714 722 0.883370 GTCGAAGGGGACGCAAAAGT 60.883 55.000 0.00 0.00 0.00 2.66
745 755 2.520979 GGAGAGAAGAACGACGACATG 58.479 52.381 0.00 0.00 0.00 3.21
804 815 7.610692 GGCTAACCCAAAGTTTTTAGATAGAGT 59.389 37.037 8.95 0.00 40.05 3.24
834 850 1.101049 AACACAACGTTGCCCCAGAG 61.101 55.000 27.61 11.24 36.12 3.35
854 870 3.279434 GTTTCAGACAACCAGACCAACT 58.721 45.455 0.00 0.00 0.00 3.16
869 901 2.334307 CCACCAGGCAGTGTTTCAG 58.666 57.895 6.89 0.00 35.93 3.02
891 932 1.735571 ACGCGCCCAACTTTATAAGTG 59.264 47.619 5.73 0.00 41.91 3.16
893 934 1.735571 ACACGCGCCCAACTTTATAAG 59.264 47.619 5.73 0.00 0.00 1.73
903 944 1.503818 GAGAAAAAGACACGCGCCCA 61.504 55.000 5.73 0.00 0.00 5.36
951 993 2.234414 TGTACCAAATGGACGTAGGGTC 59.766 50.000 6.42 0.00 45.31 4.46
977 1022 3.747529 TGTGCTACGCGTATATAGCTGTA 59.252 43.478 26.65 13.65 43.54 2.74
978 1023 2.551032 TGTGCTACGCGTATATAGCTGT 59.449 45.455 26.65 0.00 43.54 4.40
1042 1097 0.104671 GTGAGCTCTCCATCTCTGCC 59.895 60.000 16.19 0.00 0.00 4.85
1060 1115 0.250513 GTTTGGGCTGAGATCTCGGT 59.749 55.000 28.23 0.00 38.23 4.69
1080 1135 4.896482 GCCCTTCTTCTTCTAGGTCTGATA 59.104 45.833 0.00 0.00 0.00 2.15
1089 1144 3.788227 TTGCTTGCCCTTCTTCTTCTA 57.212 42.857 0.00 0.00 0.00 2.10
1100 1155 1.068954 CGTCTCTCTTTTTGCTTGCCC 60.069 52.381 0.00 0.00 0.00 5.36
1108 1163 4.061596 CTCCTTGCTTCGTCTCTCTTTTT 58.938 43.478 0.00 0.00 0.00 1.94
1112 1167 1.181786 CCTCCTTGCTTCGTCTCTCT 58.818 55.000 0.00 0.00 0.00 3.10
1144 1199 1.480954 GACGAACCAGCTATGAAGGGA 59.519 52.381 0.00 0.00 0.00 4.20
1164 1219 4.818546 GGAAGTGAGAGAGAGAGAGAGATG 59.181 50.000 0.00 0.00 0.00 2.90
1180 1235 1.273324 GGGGAAGAGAGGAGGAAGTGA 60.273 57.143 0.00 0.00 0.00 3.41
1181 1236 1.199615 GGGGAAGAGAGGAGGAAGTG 58.800 60.000 0.00 0.00 0.00 3.16
1182 1237 0.793617 TGGGGAAGAGAGGAGGAAGT 59.206 55.000 0.00 0.00 0.00 3.01
1183 1238 1.199615 GTGGGGAAGAGAGGAGGAAG 58.800 60.000 0.00 0.00 0.00 3.46
1184 1239 0.491823 TGTGGGGAAGAGAGGAGGAA 59.508 55.000 0.00 0.00 0.00 3.36
1185 1240 0.252284 GTGTGGGGAAGAGAGGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
1186 1241 0.545309 TGTGTGGGGAAGAGAGGAGG 60.545 60.000 0.00 0.00 0.00 4.30
1187 1242 1.352083 TTGTGTGGGGAAGAGAGGAG 58.648 55.000 0.00 0.00 0.00 3.69
1237 1299 3.313803 TCACACAAAACACACGCATGTAT 59.686 39.130 0.00 0.00 36.72 2.29
1474 2539 1.180029 GCACCAGAACATTGATGGCT 58.820 50.000 7.07 0.00 37.64 4.75
1509 2574 3.151912 AGCTTTGAACAGAGGAAGCAT 57.848 42.857 9.28 0.00 45.17 3.79
1556 3873 2.028125 GCTCCGGCCTATGCACTACA 62.028 60.000 0.00 0.00 40.13 2.74
1570 3887 0.305922 GCATTTTCCGATCAGCTCCG 59.694 55.000 0.00 0.00 0.00 4.63
1576 3893 0.724549 CCGTTCGCATTTTCCGATCA 59.275 50.000 0.00 0.00 34.35 2.92
1577 3894 1.003851 TCCGTTCGCATTTTCCGATC 58.996 50.000 0.00 0.00 34.35 3.69
1578 3895 1.396996 CTTCCGTTCGCATTTTCCGAT 59.603 47.619 0.00 0.00 34.35 4.18
1579 3896 0.793861 CTTCCGTTCGCATTTTCCGA 59.206 50.000 0.00 0.00 0.00 4.55
1580 3897 0.793104 GCTTCCGTTCGCATTTTCCG 60.793 55.000 0.00 0.00 0.00 4.30
1581 3898 0.456142 GGCTTCCGTTCGCATTTTCC 60.456 55.000 0.00 0.00 0.00 3.13
1582 3899 0.521735 AGGCTTCCGTTCGCATTTTC 59.478 50.000 0.00 0.00 0.00 2.29
1583 3900 0.240945 CAGGCTTCCGTTCGCATTTT 59.759 50.000 0.00 0.00 0.00 1.82
1584 3901 1.875963 CAGGCTTCCGTTCGCATTT 59.124 52.632 0.00 0.00 0.00 2.32
1585 3902 2.690778 GCAGGCTTCCGTTCGCATT 61.691 57.895 0.00 0.00 0.00 3.56
1586 3903 3.127533 GCAGGCTTCCGTTCGCAT 61.128 61.111 0.00 0.00 0.00 4.73
1587 3904 4.617520 TGCAGGCTTCCGTTCGCA 62.618 61.111 0.00 0.00 0.00 5.10
1588 3905 4.090057 GTGCAGGCTTCCGTTCGC 62.090 66.667 0.00 0.00 0.00 4.70
1589 3906 2.357517 AGTGCAGGCTTCCGTTCG 60.358 61.111 0.00 0.00 0.00 3.95
1590 3907 2.383527 CGAGTGCAGGCTTCCGTTC 61.384 63.158 0.00 0.00 0.00 3.95
1591 3908 2.357517 CGAGTGCAGGCTTCCGTT 60.358 61.111 0.00 0.00 0.00 4.44
1592 3909 4.379243 CCGAGTGCAGGCTTCCGT 62.379 66.667 0.00 0.00 0.00 4.69
1593 3910 3.997064 CTCCGAGTGCAGGCTTCCG 62.997 68.421 0.00 0.00 0.00 4.30
1594 3911 2.125350 CTCCGAGTGCAGGCTTCC 60.125 66.667 0.00 0.00 0.00 3.46
1595 3912 2.817396 GCTCCGAGTGCAGGCTTC 60.817 66.667 0.00 0.00 0.00 3.86
1596 3913 3.317571 AGCTCCGAGTGCAGGCTT 61.318 61.111 0.00 0.00 0.00 4.35
1597 3914 4.079850 CAGCTCCGAGTGCAGGCT 62.080 66.667 0.00 0.00 0.00 4.58
1598 3915 3.382803 ATCAGCTCCGAGTGCAGGC 62.383 63.158 0.00 0.00 0.00 4.85
1599 3916 1.227205 GATCAGCTCCGAGTGCAGG 60.227 63.158 0.00 0.00 0.00 4.85
1600 3917 1.227205 GGATCAGCTCCGAGTGCAG 60.227 63.158 0.00 0.00 33.29 4.41
1601 3918 2.895680 GGATCAGCTCCGAGTGCA 59.104 61.111 0.00 0.00 33.29 4.57
1608 3925 5.753721 AAGGATTATAGTGGATCAGCTCC 57.246 43.478 0.00 0.00 45.19 4.70
1609 3926 6.816140 GCTAAAGGATTATAGTGGATCAGCTC 59.184 42.308 0.00 0.00 0.00 4.09
1610 3927 6.270927 TGCTAAAGGATTATAGTGGATCAGCT 59.729 38.462 0.00 0.00 0.00 4.24
1611 3928 6.467677 TGCTAAAGGATTATAGTGGATCAGC 58.532 40.000 0.00 0.00 0.00 4.26
1612 3929 8.908786 TTTGCTAAAGGATTATAGTGGATCAG 57.091 34.615 0.00 0.00 0.00 2.90
1683 4000 8.458843 CCCATAATGTAAGACGATTTTCAGTTT 58.541 33.333 0.00 0.00 0.00 2.66
1693 4010 5.836898 ACCTATGTCCCATAATGTAAGACGA 59.163 40.000 0.00 0.00 0.00 4.20
1695 4012 8.191534 ACTACCTATGTCCCATAATGTAAGAC 57.808 38.462 0.00 0.00 0.00 3.01
1707 4024 3.480470 TGCTACGTACTACCTATGTCCC 58.520 50.000 0.00 0.00 0.00 4.46
1712 4029 9.956640 ATAGATAGTTTGCTACGTACTACCTAT 57.043 33.333 4.20 4.20 29.97 2.57
1741 4058 9.613428 TCGACAAAATGATATCAAACCTAATCT 57.387 29.630 9.99 0.00 0.00 2.40
1766 4083 8.442632 TTGATCACAATGAGATAAATCACCTC 57.557 34.615 0.00 0.00 30.46 3.85
1787 4104 5.978814 AGCTATCCAAGTTAGTCGTTTGAT 58.021 37.500 0.00 0.00 0.00 2.57
1793 4110 9.915629 ATAGAAATAAGCTATCCAAGTTAGTCG 57.084 33.333 0.00 0.00 0.00 4.18
1805 4122 9.799106 AGGCATGTTACAATAGAAATAAGCTAT 57.201 29.630 0.00 0.00 0.00 2.97
1821 4138 5.220605 CGAGGCTACTTTTTAGGCATGTTAC 60.221 44.000 7.51 0.00 41.88 2.50
1899 4217 7.367285 TGTGCAAATACTTTGAGTTAATGGAC 58.633 34.615 3.87 0.00 43.26 4.02
1971 4290 7.894753 TTTGGCCTCATTGATGACATAAATA 57.105 32.000 3.32 0.00 32.50 1.40
2031 4351 2.644676 CGAGTGGTCAGACCTGATAGA 58.355 52.381 20.82 0.00 42.18 1.98
2034 4354 0.900182 TGCGAGTGGTCAGACCTGAT 60.900 55.000 20.82 6.32 42.18 2.90
2035 4355 1.530655 TGCGAGTGGTCAGACCTGA 60.531 57.895 20.82 0.00 39.58 3.86
2042 4362 0.251209 ACCTCTAGTGCGAGTGGTCA 60.251 55.000 1.22 0.00 38.65 4.02
2060 4390 6.334102 TGTACAAAACCCCATAAACATGAC 57.666 37.500 0.00 0.00 0.00 3.06
2073 4403 4.679654 GCACATGTTAGCTTGTACAAAACC 59.320 41.667 15.59 6.00 32.61 3.27
2074 4404 5.277825 TGCACATGTTAGCTTGTACAAAAC 58.722 37.500 10.03 11.59 32.61 2.43
2079 4409 3.745975 TGTCTGCACATGTTAGCTTGTAC 59.254 43.478 9.33 3.75 32.61 2.90
2138 4468 3.498927 TCCTTAAGGCGTAGTTTCGAG 57.501 47.619 17.32 0.00 34.44 4.04
2140 4470 3.370061 CCTTTCCTTAAGGCGTAGTTTCG 59.630 47.826 17.32 0.00 46.66 3.46
2141 4471 4.941325 CCTTTCCTTAAGGCGTAGTTTC 57.059 45.455 17.32 0.00 46.66 2.78
2187 5883 5.418524 ACCCGTTTTACAAGTAAACCACTTT 59.581 36.000 4.97 0.00 45.54 2.66
2189 5885 4.525996 ACCCGTTTTACAAGTAAACCACT 58.474 39.130 4.97 0.00 40.05 4.00
2198 5894 9.977762 GAATACTTATGTAACCCGTTTTACAAG 57.022 33.333 9.43 6.79 43.47 3.16
2206 5902 7.356089 TCATCAGAATACTTATGTAACCCGT 57.644 36.000 0.00 0.00 31.81 5.28
2312 6013 6.073873 CGCTCAACCAAATTTTGCTCATTTAA 60.074 34.615 3.50 0.00 0.00 1.52
2317 6018 2.360483 TCGCTCAACCAAATTTTGCTCA 59.640 40.909 3.50 0.00 0.00 4.26
2340 6041 9.562583 GACATTTGCGTAAATTATGAAAACCTA 57.437 29.630 8.88 0.00 34.34 3.08
2360 6061 9.354673 CAACTAACCCTATCCATATTGACATTT 57.645 33.333 0.00 0.00 0.00 2.32
2365 6066 5.071250 ACGCAACTAACCCTATCCATATTGA 59.929 40.000 0.00 0.00 0.00 2.57
2376 6077 2.812011 GTGATTTCACGCAACTAACCCT 59.188 45.455 0.00 0.00 37.10 4.34
2516 6232 8.283992 TGTATAATTACGTGTGGTTGTTTTCTG 58.716 33.333 0.00 0.00 0.00 3.02
2517 6233 8.380743 TGTATAATTACGTGTGGTTGTTTTCT 57.619 30.769 0.00 0.00 0.00 2.52
2627 6383 3.191078 TGGTTGTTGCAAATGAAAGGG 57.809 42.857 0.00 0.00 0.00 3.95
2730 6503 4.132336 GTGCATGTGATCCATCATACTGT 58.868 43.478 0.00 0.00 39.30 3.55
2736 6509 0.252761 ACGGTGCATGTGATCCATCA 59.747 50.000 0.00 0.00 0.00 3.07
2830 6839 7.815840 TGGTTTGAAGTCTGATTTTGATACA 57.184 32.000 0.00 0.00 0.00 2.29
2915 6924 9.621629 ACCGAAACTTTATTTCCATGTGATATA 57.378 29.630 0.00 0.00 0.00 0.86
2938 6947 9.251348 GTTTCCATCAAAACTTGGTTTTCACCG 62.251 40.741 5.55 0.00 42.78 4.94
2939 6948 5.017294 TCCATCAAAACTTGGTTTTCACC 57.983 39.130 5.55 0.00 42.78 4.02
2940 6949 6.183360 GGTTTCCATCAAAACTTGGTTTTCAC 60.183 38.462 5.55 0.00 42.78 3.18
2941 6950 5.877564 GGTTTCCATCAAAACTTGGTTTTCA 59.122 36.000 5.55 0.00 42.78 2.69
2942 6951 5.006261 CGGTTTCCATCAAAACTTGGTTTTC 59.994 40.000 5.55 0.00 42.78 2.29
2943 6952 4.873259 CGGTTTCCATCAAAACTTGGTTTT 59.127 37.500 2.99 2.99 45.06 2.43
2944 6953 4.438148 CGGTTTCCATCAAAACTTGGTTT 58.562 39.130 0.00 0.00 38.81 3.27
2945 6954 3.181470 CCGGTTTCCATCAAAACTTGGTT 60.181 43.478 0.00 0.00 38.81 3.67
2946 6955 2.364002 CCGGTTTCCATCAAAACTTGGT 59.636 45.455 0.00 0.00 38.81 3.67
2947 6956 2.364002 ACCGGTTTCCATCAAAACTTGG 59.636 45.455 0.00 8.66 38.81 3.61
2948 6957 3.067461 TCACCGGTTTCCATCAAAACTTG 59.933 43.478 2.97 0.00 38.81 3.16
3047 7132 8.359875 TGGGAATTTCACATGCTAATAGAAAA 57.640 30.769 0.00 0.00 32.65 2.29
3048 7133 7.953005 TGGGAATTTCACATGCTAATAGAAA 57.047 32.000 0.00 0.00 33.33 2.52
3094 7188 2.778659 GACGCTGTTCAATGCTGATTC 58.221 47.619 0.00 0.00 0.00 2.52
3108 7202 3.120820 TGTTTAATTACTGCACGACGCTG 60.121 43.478 0.00 0.00 44.66 5.18
3132 7226 5.180868 AGAGCGAATTCAGCAATGAATATCC 59.819 40.000 19.45 0.00 37.52 2.59
3151 7245 6.920758 ACATTACTAGAGCTATGAAAAGAGCG 59.079 38.462 0.00 0.00 43.72 5.03
3236 7846 7.976826 TGGATGGACACGTAATTAATTAACAC 58.023 34.615 9.48 1.24 0.00 3.32
3254 7867 4.676109 ACTGGAAAATCACATTGGATGGA 58.324 39.130 0.00 0.00 33.60 3.41
3266 7879 2.160417 CAGCACGAAGGACTGGAAAATC 59.840 50.000 0.00 0.00 0.00 2.17
3509 8125 1.826096 AGGAAGGAAGCGTAGAGGAAC 59.174 52.381 0.00 0.00 0.00 3.62
3843 8459 3.559242 CGCTCATCCTTCTTCCAGAAATC 59.441 47.826 0.00 0.00 33.19 2.17
3874 8493 4.980805 TGAACGCGGGTGTCAGCC 62.981 66.667 12.47 11.25 0.00 4.85
3902 8537 3.564511 GCACGATTAAGAAAGCTGCAAA 58.435 40.909 1.02 0.00 30.54 3.68
3946 8581 0.532862 GACGCATCATCCATCGGGTT 60.533 55.000 0.00 0.00 34.93 4.11
3951 8586 1.069765 ACCCGACGCATCATCCATC 59.930 57.895 0.00 0.00 0.00 3.51
3966 8601 1.735559 GCTTGTACGACGACCACCC 60.736 63.158 0.00 0.00 0.00 4.61
3972 8607 2.126618 CAGCCGCTTGTACGACGA 60.127 61.111 0.00 0.00 34.06 4.20
4200 8835 2.122769 TCAAGGACCGGGGTGACA 60.123 61.111 6.32 0.00 0.00 3.58
4395 9030 1.487142 CACAATACGGACATGGGGGTA 59.513 52.381 0.00 0.00 0.00 3.69
4569 9204 1.162181 TCACCACGTCGACGAAGACT 61.162 55.000 41.52 18.59 43.02 3.24
4572 9207 1.442184 CCTCACCACGTCGACGAAG 60.442 63.158 41.52 31.39 43.02 3.79
4671 9306 4.079253 TGAGGAAATAGCCAAAGTTCACC 58.921 43.478 0.00 0.00 0.00 4.02
4731 9366 5.105567 TCCGTATTTACATCACCATGGTT 57.894 39.130 16.84 2.78 33.82 3.67
4735 9370 8.311836 CCTACTAATCCGTATTTACATCACCAT 58.688 37.037 0.00 0.00 0.00 3.55
4756 9391 7.613551 TTCCTCTAAAAAGACTCAACCTACT 57.386 36.000 0.00 0.00 0.00 2.57
4785 9420 6.932960 GGCTTTATTTATAAAGTCGGGCTCTA 59.067 38.462 18.51 0.00 46.78 2.43
4816 9451 3.452990 TGGTTCTGTTGGTGTAACTCTGA 59.547 43.478 0.00 0.00 40.05 3.27
4840 9475 4.279145 TGGCAGTTAAACTTGTTTGGGTA 58.721 39.130 8.79 0.00 0.00 3.69
4858 9494 3.712016 TGCTACTTATGTTCCTTGGCA 57.288 42.857 0.00 0.00 0.00 4.92
4963 9601 1.450312 CTTCCCTTCTTCGGCGCAT 60.450 57.895 10.83 0.00 0.00 4.73
5012 9650 2.615493 GGGAATCTTCAGGCTTTCGACA 60.615 50.000 0.00 0.00 0.00 4.35
5028 9666 7.350921 TGGAGATTATTGACTAAGGAAGGGAAT 59.649 37.037 0.00 0.00 0.00 3.01
5030 9668 6.099845 GTGGAGATTATTGACTAAGGAAGGGA 59.900 42.308 0.00 0.00 0.00 4.20
5066 9704 4.500477 GCTGCTTATTTAAAGCCAATGTCG 59.500 41.667 7.23 0.00 42.36 4.35
5128 9768 2.688958 GTCGCTGTGGACTACTAGGAAT 59.311 50.000 0.00 0.00 34.09 3.01
5179 9819 0.404040 CAGGGCAGTCCAAAAGGGTA 59.596 55.000 0.00 0.00 38.24 3.69
5364 10004 4.714632 TCAAATCAAGAAGAGAAACGGGT 58.285 39.130 0.00 0.00 0.00 5.28
5371 10011 4.186926 CGGCTGATCAAATCAAGAAGAGA 58.813 43.478 0.00 0.00 39.11 3.10
5380 10020 1.095228 TTCCGGCGGCTGATCAAATC 61.095 55.000 23.83 0.00 0.00 2.17
5404 10044 3.088500 CTAGCAAGCTGTTCGCCGC 62.089 63.158 4.53 0.00 40.39 6.53
5490 10131 6.915349 TCGGCTTATTCTAAGCTTATCTCTC 58.085 40.000 16.10 0.00 42.62 3.20
5629 10271 1.407258 CGCTCTCTTTCCCCTGTAGAG 59.593 57.143 0.00 0.00 37.37 2.43
5630 10272 1.475403 CGCTCTCTTTCCCCTGTAGA 58.525 55.000 0.00 0.00 0.00 2.59
5631 10273 0.179097 GCGCTCTCTTTCCCCTGTAG 60.179 60.000 0.00 0.00 0.00 2.74
5632 10274 1.614241 GGCGCTCTCTTTCCCCTGTA 61.614 60.000 7.64 0.00 0.00 2.74
5633 10275 2.665603 GCGCTCTCTTTCCCCTGT 59.334 61.111 0.00 0.00 0.00 4.00
5634 10276 2.124942 GGCGCTCTCTTTCCCCTG 60.125 66.667 7.64 0.00 0.00 4.45
5635 10277 3.775654 CGGCGCTCTCTTTCCCCT 61.776 66.667 7.64 0.00 0.00 4.79
5636 10278 4.840005 CCGGCGCTCTCTTTCCCC 62.840 72.222 7.64 0.00 0.00 4.81
5637 10279 3.724914 CTCCGGCGCTCTCTTTCCC 62.725 68.421 7.64 0.00 0.00 3.97
5638 10280 2.022240 ATCTCCGGCGCTCTCTTTCC 62.022 60.000 7.64 0.00 0.00 3.13
5639 10281 0.596341 GATCTCCGGCGCTCTCTTTC 60.596 60.000 7.64 0.00 0.00 2.62
5640 10282 1.040339 AGATCTCCGGCGCTCTCTTT 61.040 55.000 7.64 0.00 0.00 2.52
5655 10297 3.762288 GGTTCAGGGTTGGGTTTTAGATC 59.238 47.826 0.00 0.00 0.00 2.75
5770 10413 4.260907 GGTAAGTCCACTCGTTTTTGGTTC 60.261 45.833 0.00 0.00 34.19 3.62
5794 10437 6.817270 CTTGTCAAATTTGTTGTCAGGAAG 57.183 37.500 17.47 6.13 0.00 3.46


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

AutoCloner maintained by Alex Coulton.