Multiple sequence alignment - TraesCS3D01G228400

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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 TraesCS3D01G228400 chr3D 100.000 4213 0 0 1 4213 310681239 310685451 0.000000e+00 7781.0
1 TraesCS3D01G228400 chr3D 80.206 778 135 18 1801 2567 129025165 129025934 2.200000e-157 566.0
2 TraesCS3D01G228400 chr3D 79.404 772 149 9 1800 2566 6023136 6022370 1.720000e-148 536.0
3 TraesCS3D01G228400 chr3D 79.216 255 49 4 2796 3048 129026029 129026281 1.560000e-39 174.0
4 TraesCS3D01G228400 chr3A 94.260 2648 82 28 34 2644 421722613 421719999 0.000000e+00 3984.0
5 TraesCS3D01G228400 chr3A 97.019 738 22 0 2761 3498 421719995 421719258 0.000000e+00 1242.0
6 TraesCS3D01G228400 chr3A 79.742 775 142 14 1801 2566 140806695 140805927 7.960000e-152 547.0
7 TraesCS3D01G228400 chr3A 79.009 767 149 11 1794 2554 15075182 15075942 8.080000e-142 514.0
8 TraesCS3D01G228400 chr3A 77.455 275 54 7 2796 3066 140805852 140805582 1.570000e-34 158.0
9 TraesCS3D01G228400 chr3A 94.505 91 4 1 3545 3635 421718824 421718735 5.680000e-29 139.0
10 TraesCS3D01G228400 chr3A 87.500 56 6 1 4158 4213 612977468 612977522 3.520000e-06 63.9
11 TraesCS3D01G228400 chr3B 91.570 2669 95 50 35 2648 410776724 410774131 0.000000e+00 3563.0
12 TraesCS3D01G228400 chr3B 97.177 744 19 2 2761 3502 410774133 410773390 0.000000e+00 1256.0
13 TraesCS3D01G228400 chr3B 83.088 680 76 27 3545 4213 410746899 410746248 2.180000e-162 582.0
14 TraesCS3D01G228400 chr3B 79.896 766 135 17 1801 2555 183083336 183084093 1.030000e-150 544.0
15 TraesCS3D01G228400 chr3B 92.481 133 8 2 2639 2770 816002632 816002763 5.560000e-44 189.0
16 TraesCS3D01G228400 chr3B 78.824 255 50 4 2796 3048 183084175 183084427 7.240000e-38 169.0
17 TraesCS3D01G228400 chr1B 88.514 740 85 0 1839 2578 622367012 622366273 0.000000e+00 896.0
18 TraesCS3D01G228400 chr1B 82.013 745 75 33 2789 3503 622365636 622364921 2.820000e-161 579.0
19 TraesCS3D01G228400 chr1B 78.452 775 150 13 1791 2555 212410386 212409619 1.360000e-134 490.0
20 TraesCS3D01G228400 chr1B 88.889 54 6 0 4160 4213 673788033 673788086 2.720000e-07 67.6
21 TraesCS3D01G228400 chr1D 79.049 778 140 18 1791 2555 137968334 137967567 2.910000e-141 512.0
22 TraesCS3D01G228400 chr1D 97.500 120 3 0 2645 2764 69194017 69193898 5.520000e-49 206.0
23 TraesCS3D01G228400 chr1D 97.436 117 3 0 2647 2763 85844632 85844748 2.570000e-47 200.0
24 TraesCS3D01G228400 chr1A 78.508 791 147 18 1788 2565 154700606 154701386 8.130000e-137 497.0
25 TraesCS3D01G228400 chr1A 77.778 729 145 14 1803 2523 578356412 578355693 2.330000e-117 433.0
26 TraesCS3D01G228400 chr2D 74.487 780 160 34 1813 2570 506792298 506791536 6.850000e-78 302.0
27 TraesCS3D01G228400 chr2D 93.478 46 1 2 3932 3976 575697273 575697317 2.720000e-07 67.6
28 TraesCS3D01G228400 chr2D 88.889 54 4 2 4160 4212 316130016 316129964 9.780000e-07 65.8
29 TraesCS3D01G228400 chr2D 85.965 57 6 2 4157 4212 372185529 372185584 4.550000e-05 60.2
30 TraesCS3D01G228400 chr2A 74.389 777 166 29 1813 2570 651609564 651608802 6.850000e-78 302.0
31 TraesCS3D01G228400 chr2A 75.263 190 29 15 3937 4115 611962282 611962464 1.620000e-09 75.0
32 TraesCS3D01G228400 chr2A 87.500 56 5 2 4158 4212 19605267 19605213 3.520000e-06 63.9
33 TraesCS3D01G228400 chr2B 73.974 780 164 34 1813 2570 594846530 594845768 3.210000e-71 279.0
34 TraesCS3D01G228400 chr2B 92.481 133 9 1 2637 2769 444543976 444544107 5.560000e-44 189.0
35 TraesCS3D01G228400 chrUn 96.124 129 3 2 2647 2774 97740183 97740056 4.270000e-50 209.0
36 TraesCS3D01G228400 chr6D 97.541 122 3 0 2646 2767 85585153 85585032 4.270000e-50 209.0
37 TraesCS3D01G228400 chr6D 97.458 118 3 0 2646 2763 231695229 231695112 7.140000e-48 202.0
38 TraesCS3D01G228400 chr6D 74.866 187 33 7 3937 4113 159234347 159234529 5.840000e-09 73.1
39 TraesCS3D01G228400 chr4D 95.833 120 5 0 2646 2765 151935919 151935800 1.200000e-45 195.0
40 TraesCS3D01G228400 chr4D 75.135 185 30 12 3936 4110 25214030 25214208 5.840000e-09 73.1
41 TraesCS3D01G228400 chr7B 90.714 140 10 3 2625 2764 503468855 503468991 2.590000e-42 183.0
42 TraesCS3D01G228400 chr7B 91.111 45 3 1 4166 4209 100731605 100731561 4.550000e-05 60.2
43 TraesCS3D01G228400 chr7B 97.059 34 1 0 4158 4191 125140453 125140486 1.640000e-04 58.4
44 TraesCS3D01G228400 chr5B 76.981 265 42 13 3939 4196 550139426 550139678 2.640000e-27 134.0
45 TraesCS3D01G228400 chr7D 78.453 181 25 11 4032 4201 153943882 153943705 5.760000e-19 106.0
46 TraesCS3D01G228400 chr5D 76.923 182 28 12 3937 4111 14005770 14005596 1.610000e-14 91.6
47 TraesCS3D01G228400 chr5D 95.238 42 1 1 3935 3976 522692840 522692800 9.780000e-07 65.8
48 TraesCS3D01G228400 chr5D 97.368 38 0 1 3937 3973 237842684 237842721 3.520000e-06 63.9
49 TraesCS3D01G228400 chr7A 90.385 52 4 1 3937 3988 105214030 105213980 2.720000e-07 67.6


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 TraesCS3D01G228400 chr3D 310681239 310685451 4212 False 7781.000000 7781 100.000000 1 4213 1 chr3D.!!$F1 4212
1 TraesCS3D01G228400 chr3D 6022370 6023136 766 True 536.000000 536 79.404000 1800 2566 1 chr3D.!!$R1 766
2 TraesCS3D01G228400 chr3D 129025165 129026281 1116 False 370.000000 566 79.711000 1801 3048 2 chr3D.!!$F2 1247
3 TraesCS3D01G228400 chr3A 421718735 421722613 3878 True 1788.333333 3984 95.261333 34 3635 3 chr3A.!!$R2 3601
4 TraesCS3D01G228400 chr3A 15075182 15075942 760 False 514.000000 514 79.009000 1794 2554 1 chr3A.!!$F1 760
5 TraesCS3D01G228400 chr3A 140805582 140806695 1113 True 352.500000 547 78.598500 1801 3066 2 chr3A.!!$R1 1265
6 TraesCS3D01G228400 chr3B 410773390 410776724 3334 True 2409.500000 3563 94.373500 35 3502 2 chr3B.!!$R2 3467
7 TraesCS3D01G228400 chr3B 410746248 410746899 651 True 582.000000 582 83.088000 3545 4213 1 chr3B.!!$R1 668
8 TraesCS3D01G228400 chr3B 183083336 183084427 1091 False 356.500000 544 79.360000 1801 3048 2 chr3B.!!$F2 1247
9 TraesCS3D01G228400 chr1B 622364921 622367012 2091 True 737.500000 896 85.263500 1839 3503 2 chr1B.!!$R2 1664
10 TraesCS3D01G228400 chr1B 212409619 212410386 767 True 490.000000 490 78.452000 1791 2555 1 chr1B.!!$R1 764
11 TraesCS3D01G228400 chr1D 137967567 137968334 767 True 512.000000 512 79.049000 1791 2555 1 chr1D.!!$R2 764
12 TraesCS3D01G228400 chr1A 154700606 154701386 780 False 497.000000 497 78.508000 1788 2565 1 chr1A.!!$F1 777
13 TraesCS3D01G228400 chr1A 578355693 578356412 719 True 433.000000 433 77.778000 1803 2523 1 chr1A.!!$R1 720
14 TraesCS3D01G228400 chr2D 506791536 506792298 762 True 302.000000 302 74.487000 1813 2570 1 chr2D.!!$R2 757
15 TraesCS3D01G228400 chr2A 651608802 651609564 762 True 302.000000 302 74.389000 1813 2570 1 chr2A.!!$R2 757
16 TraesCS3D01G228400 chr2B 594845768 594846530 762 True 279.000000 279 73.974000 1813 2570 1 chr2B.!!$R1 757

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
504 528 0.530650 ACCTTCGCGATGTATGGCAG 60.531 55.000 10.88 0.53 0.00 4.85 F
1043 1088 0.524862 GGCATGGAGTTGAGCAACAG 59.475 55.000 14.99 1.94 43.47 3.16 F
1095 1140 0.869454 GCGAGCAATCGTCCAGAGAG 60.869 60.000 0.00 0.00 35.26 3.20 F
1759 1804 2.158957 TGAACTGTGTCAGTGACCTTCC 60.159 50.000 20.43 6.60 44.62 3.46 F
2584 2656 2.589014 GTACGTAACCAACAGACTCCG 58.411 52.381 0.00 0.00 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1804 2.583593 GAGCCGTTAGCCTCAGCG 60.584 66.667 0.00 0.00 46.67 5.18 R
2647 2722 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85 R
2649 2724 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
2650 2725 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30 R
4167 5125 0.179032 TCGAGGAGCTTGTGGCAAAA 60.179 50.000 0.00 0.00 44.79 2.44 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
22 23 5.821516 TCTGTAGTTAACTCTCTGCTAGC 57.178 43.478 12.39 8.10 0.00 3.42
23 24 5.502079 TCTGTAGTTAACTCTCTGCTAGCT 58.498 41.667 17.23 0.00 0.00 3.32
24 25 6.651086 TCTGTAGTTAACTCTCTGCTAGCTA 58.349 40.000 17.23 3.10 0.00 3.32
25 26 6.764085 TCTGTAGTTAACTCTCTGCTAGCTAG 59.236 42.308 16.84 16.84 0.00 3.42
26 27 6.416415 TGTAGTTAACTCTCTGCTAGCTAGT 58.584 40.000 21.62 11.02 0.00 2.57
27 28 7.563020 TGTAGTTAACTCTCTGCTAGCTAGTA 58.437 38.462 21.62 16.60 0.00 1.82
28 29 6.930667 AGTTAACTCTCTGCTAGCTAGTAC 57.069 41.667 21.62 7.00 0.00 2.73
29 30 6.416415 AGTTAACTCTCTGCTAGCTAGTACA 58.584 40.000 21.62 11.21 0.00 2.90
30 31 6.540914 AGTTAACTCTCTGCTAGCTAGTACAG 59.459 42.308 21.62 19.38 0.00 2.74
31 32 4.497291 ACTCTCTGCTAGCTAGTACAGT 57.503 45.455 21.62 13.42 0.00 3.55
32 33 4.850680 ACTCTCTGCTAGCTAGTACAGTT 58.149 43.478 21.62 4.30 0.00 3.16
75 76 8.230486 GTGATTATTCTCGTCACAAGTCAAAAT 58.770 33.333 0.00 0.00 41.35 1.82
76 77 9.430623 TGATTATTCTCGTCACAAGTCAAAATA 57.569 29.630 0.00 0.00 0.00 1.40
112 114 4.388485 TGTGTACATGTTGCATCTTGTCT 58.612 39.130 16.91 0.70 0.00 3.41
129 131 1.972223 CTGACTGGACGGTCCGACT 60.972 63.158 20.51 6.72 40.17 4.18
253 272 5.473931 ACTCTGGTGCGTATCATATTCATC 58.526 41.667 0.00 0.00 0.00 2.92
254 273 5.011023 ACTCTGGTGCGTATCATATTCATCA 59.989 40.000 0.00 0.00 0.00 3.07
255 274 6.041423 TCTGGTGCGTATCATATTCATCAT 57.959 37.500 0.00 0.00 0.00 2.45
256 275 7.093771 ACTCTGGTGCGTATCATATTCATCATA 60.094 37.037 0.00 0.00 0.00 2.15
257 276 7.035612 TCTGGTGCGTATCATATTCATCATAC 58.964 38.462 0.00 0.00 0.00 2.39
264 283 7.044249 GCGTATCATATTCATCATACGTACACC 60.044 40.741 0.00 0.00 43.83 4.16
305 324 1.066752 GCCGGCGAACAAAAAGGTT 59.933 52.632 12.58 0.00 0.00 3.50
404 428 2.066999 GGATTGCGGAGGAGGAGGT 61.067 63.158 0.00 0.00 0.00 3.85
504 528 0.530650 ACCTTCGCGATGTATGGCAG 60.531 55.000 10.88 0.53 0.00 4.85
638 662 0.540597 GCTTTGGAGCTTTCCCACCT 60.541 55.000 0.00 0.00 45.65 4.00
688 725 4.749310 CCGAGCCGAGCTGCAACT 62.749 66.667 1.02 0.00 39.88 3.16
691 728 3.319926 GAGCCGAGCTGCAACTTGC 62.320 63.158 6.82 6.82 45.29 4.01
692 729 3.360340 GCCGAGCTGCAACTTGCT 61.360 61.111 14.78 0.00 45.31 3.91
693 730 2.034879 GCCGAGCTGCAACTTGCTA 61.035 57.895 14.78 1.18 45.31 3.49
695 732 0.671781 CCGAGCTGCAACTTGCTACT 60.672 55.000 14.78 11.28 45.31 2.57
696 733 1.151668 CGAGCTGCAACTTGCTACTT 58.848 50.000 14.78 0.00 45.31 2.24
697 734 1.127582 CGAGCTGCAACTTGCTACTTC 59.872 52.381 14.78 6.67 45.31 3.01
698 735 1.127582 GAGCTGCAACTTGCTACTTCG 59.872 52.381 14.78 0.00 45.31 3.79
701 738 2.408050 CTGCAACTTGCTACTTCGACT 58.592 47.619 14.78 0.00 45.31 4.18
753 798 4.384647 GCTTGTCCTGTTGATTAGGGAGAT 60.385 45.833 0.00 0.00 35.96 2.75
933 978 7.792374 TGATTATGTCCTTCTGCTTCATTAC 57.208 36.000 0.00 0.00 0.00 1.89
936 981 9.717942 GATTATGTCCTTCTGCTTCATTACTAT 57.282 33.333 0.00 0.00 0.00 2.12
938 983 7.798596 ATGTCCTTCTGCTTCATTACTATTG 57.201 36.000 0.00 0.00 0.00 1.90
940 985 4.811024 TCCTTCTGCTTCATTACTATTGCG 59.189 41.667 0.00 0.00 0.00 4.85
941 986 4.572389 CCTTCTGCTTCATTACTATTGCGT 59.428 41.667 0.00 0.00 0.00 5.24
942 987 5.753438 CCTTCTGCTTCATTACTATTGCGTA 59.247 40.000 0.00 0.00 0.00 4.42
943 988 6.074088 CCTTCTGCTTCATTACTATTGCGTAG 60.074 42.308 0.00 0.00 36.44 3.51
944 989 5.902681 TCTGCTTCATTACTATTGCGTAGT 58.097 37.500 6.79 6.79 45.49 2.73
945 990 5.977725 TCTGCTTCATTACTATTGCGTAGTC 59.022 40.000 5.01 0.00 42.63 2.59
946 991 5.047847 TGCTTCATTACTATTGCGTAGTCC 58.952 41.667 5.01 0.00 42.63 3.85
947 992 4.148348 GCTTCATTACTATTGCGTAGTCCG 59.852 45.833 5.01 0.00 42.63 4.79
1002 1047 7.569639 ACTGGAGTACTACTGTGTGTATATG 57.430 40.000 16.23 0.00 0.00 1.78
1026 1071 1.424493 CTGCAGGTTTCTCGATCGGC 61.424 60.000 16.41 8.50 0.00 5.54
1043 1088 0.524862 GGCATGGAGTTGAGCAACAG 59.475 55.000 14.99 1.94 43.47 3.16
1048 1093 1.762370 TGGAGTTGAGCAACAGAGACA 59.238 47.619 14.99 4.34 43.47 3.41
1095 1140 0.869454 GCGAGCAATCGTCCAGAGAG 60.869 60.000 0.00 0.00 35.26 3.20
1297 1342 3.654273 CAGATACCCTACTCCCTTTCCA 58.346 50.000 0.00 0.00 0.00 3.53
1759 1804 2.158957 TGAACTGTGTCAGTGACCTTCC 60.159 50.000 20.43 6.60 44.62 3.46
1774 1825 3.659089 TTCCGCTGAGGCTAACGGC 62.659 63.158 15.32 7.13 45.23 5.68
2584 2656 2.589014 GTACGTAACCAACAGACTCCG 58.411 52.381 0.00 0.00 0.00 4.63
2645 2720 5.345202 GCGTCGTTCCTCTGTATTTATATGG 59.655 44.000 0.00 0.00 0.00 2.74
2647 2722 7.587629 CGTCGTTCCTCTGTATTTATATGGTA 58.412 38.462 0.00 0.00 0.00 3.25
2648 2723 7.536622 CGTCGTTCCTCTGTATTTATATGGTAC 59.463 40.741 0.00 0.00 0.00 3.34
2649 2724 8.574737 GTCGTTCCTCTGTATTTATATGGTACT 58.425 37.037 0.00 0.00 0.00 2.73
2650 2725 8.790718 TCGTTCCTCTGTATTTATATGGTACTC 58.209 37.037 0.00 0.00 0.00 2.59
2651 2726 8.027771 CGTTCCTCTGTATTTATATGGTACTCC 58.972 40.741 0.00 0.00 0.00 3.85
2652 2727 8.312564 GTTCCTCTGTATTTATATGGTACTCCC 58.687 40.741 0.00 0.00 0.00 4.30
2653 2728 7.776745 TCCTCTGTATTTATATGGTACTCCCT 58.223 38.462 0.00 0.00 0.00 4.20
2654 2729 7.894364 TCCTCTGTATTTATATGGTACTCCCTC 59.106 40.741 0.00 0.00 0.00 4.30
2655 2730 7.124448 CCTCTGTATTTATATGGTACTCCCTCC 59.876 44.444 0.00 0.00 0.00 4.30
2656 2731 6.662234 TCTGTATTTATATGGTACTCCCTCCG 59.338 42.308 0.00 0.00 0.00 4.63
2657 2732 6.317312 TGTATTTATATGGTACTCCCTCCGT 58.683 40.000 0.00 0.00 0.00 4.69
2658 2733 5.997384 ATTTATATGGTACTCCCTCCGTC 57.003 43.478 0.00 0.00 0.00 4.79
2660 2735 0.179009 TATGGTACTCCCTCCGTCCG 60.179 60.000 0.00 0.00 0.00 4.79
2661 2736 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
2662 2737 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
2663 2738 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2664 2739 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2665 2740 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2666 2741 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2667 2742 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2668 2743 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2669 2744 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2670 2745 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2671 2746 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2672 2747 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2673 2748 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2674 2749 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2675 2750 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
2676 2751 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
2680 2755 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
2681 2756 3.555956 CGGAAATACTTGTCGGAGGAATG 59.444 47.826 0.00 0.00 0.00 2.67
2682 2757 3.877508 GGAAATACTTGTCGGAGGAATGG 59.122 47.826 0.00 0.00 0.00 3.16
2685 2760 2.698855 ACTTGTCGGAGGAATGGATG 57.301 50.000 0.00 0.00 0.00 3.51
2694 2769 5.010933 TCGGAGGAATGGATGTATCTAGAC 58.989 45.833 0.00 0.00 0.00 2.59
2699 2774 8.637986 GGAGGAATGGATGTATCTAGACATATC 58.362 40.741 0.00 0.00 40.18 1.63
2738 3047 9.573133 ACATTCATTTTTATCCATTTCTTCGAC 57.427 29.630 0.00 0.00 0.00 4.20
2739 3048 9.571810 CATTCATTTTTATCCATTTCTTCGACA 57.428 29.630 0.00 0.00 0.00 4.35
2741 3050 9.624697 TTCATTTTTATCCATTTCTTCGACAAG 57.375 29.630 0.00 0.00 0.00 3.16
2742 3051 8.792633 TCATTTTTATCCATTTCTTCGACAAGT 58.207 29.630 0.00 0.00 0.00 3.16
2748 3057 6.737254 TCCATTTCTTCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
2749 3058 5.350365 TCCATTTCTTCGACAAGTATTTCCG 59.650 40.000 0.00 0.00 0.00 4.30
2751 3060 4.524316 TTCTTCGACAAGTATTTCCGGA 57.476 40.909 0.00 0.00 0.00 5.14
2752 3061 3.841643 TCTTCGACAAGTATTTCCGGAC 58.158 45.455 1.83 0.00 0.00 4.79
2753 3062 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
2755 3064 2.228582 TCGACAAGTATTTCCGGACGAA 59.771 45.455 1.83 0.00 0.00 3.85
2756 3065 2.597305 CGACAAGTATTTCCGGACGAAG 59.403 50.000 1.83 0.00 0.00 3.79
2757 3066 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
2758 3067 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
2759 3068 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
2773 3082 4.139786 ACGAAGGGAGTATATGTAGCGAA 58.860 43.478 0.00 0.00 0.00 4.70
3413 3962 3.471244 GAGGCACGGAGGTCGATCG 62.471 68.421 9.36 9.36 42.43 3.69
3438 3987 7.201504 CGATCTGTGTATACGTCTACGGATATT 60.202 40.741 10.44 0.00 45.68 1.28
3479 4030 0.599558 CATTGTGTGGACCTTGCAGG 59.400 55.000 0.00 1.16 42.49 4.85
3503 4054 6.183360 GGATTGGTTGAATGATTCAGCATACA 60.183 38.462 20.82 9.21 41.94 2.29
3504 4055 6.587206 TTGGTTGAATGATTCAGCATACAA 57.413 33.333 20.82 13.76 41.94 2.41
3505 4056 5.953183 TGGTTGAATGATTCAGCATACAAC 58.047 37.500 20.82 9.27 41.94 3.32
3506 4057 5.476254 TGGTTGAATGATTCAGCATACAACA 59.524 36.000 20.82 6.63 41.94 3.33
3507 4058 6.153170 TGGTTGAATGATTCAGCATACAACAT 59.847 34.615 20.82 0.00 41.94 2.71
3510 4061 9.571810 GTTGAATGATTCAGCATACAACATTTA 57.428 29.630 15.72 0.00 41.38 1.40
3547 4409 3.465990 GCTGCAGCAGGACTAATCA 57.534 52.632 33.36 0.00 41.59 2.57
3548 4410 1.964552 GCTGCAGCAGGACTAATCAT 58.035 50.000 33.36 0.00 41.59 2.45
3582 4519 2.755655 TGCTTTTCGGTTTCTGGTTCAA 59.244 40.909 0.00 0.00 0.00 2.69
3593 4530 7.041372 TCGGTTTCTGGTTCAAAAATTAGAGAG 60.041 37.037 0.00 0.00 0.00 3.20
3595 4532 7.230712 GGTTTCTGGTTCAAAAATTAGAGAGGA 59.769 37.037 0.00 0.00 0.00 3.71
3648 4585 5.450592 TTTTTGACAAGCATGCATCACTA 57.549 34.783 21.98 8.21 0.00 2.74
3664 4601 6.595326 TGCATCACTAGTAATTTGACTTCAGG 59.405 38.462 0.00 0.00 0.00 3.86
3668 4605 5.122396 CACTAGTAATTTGACTTCAGGGTGC 59.878 44.000 0.00 0.00 0.00 5.01
3675 4612 1.980765 TGACTTCAGGGTGCATTCTCT 59.019 47.619 0.00 0.00 0.00 3.10
3677 4614 1.004044 ACTTCAGGGTGCATTCTCTGG 59.996 52.381 4.49 0.00 0.00 3.86
3678 4615 1.004044 CTTCAGGGTGCATTCTCTGGT 59.996 52.381 4.49 0.00 0.00 4.00
3689 4626 1.305201 TTCTCTGGTGAAACGTTGCC 58.695 50.000 0.00 5.69 38.12 4.52
3712 4649 0.321021 ATCGATGGGCTCTGATCTGC 59.679 55.000 0.00 0.00 0.00 4.26
3727 4664 5.826208 TCTGATCTGCAAATGACAATGCTAT 59.174 36.000 15.16 9.95 42.97 2.97
3745 4682 5.429957 GCTATGAAGAGCACCCAATTTAG 57.570 43.478 0.00 0.00 42.36 1.85
3746 4683 4.276926 GCTATGAAGAGCACCCAATTTAGG 59.723 45.833 0.00 0.00 42.36 2.69
3747 4684 3.806949 TGAAGAGCACCCAATTTAGGT 57.193 42.857 0.00 0.00 38.48 3.08
3748 4685 4.112634 TGAAGAGCACCCAATTTAGGTT 57.887 40.909 0.00 0.00 34.56 3.50
3749 4686 4.079253 TGAAGAGCACCCAATTTAGGTTC 58.921 43.478 0.00 0.00 34.56 3.62
3750 4687 3.806949 AGAGCACCCAATTTAGGTTCA 57.193 42.857 0.00 0.00 34.56 3.18
3751 4688 4.112634 AGAGCACCCAATTTAGGTTCAA 57.887 40.909 0.00 0.00 34.56 2.69
3752 4689 4.479158 AGAGCACCCAATTTAGGTTCAAA 58.521 39.130 0.00 0.00 34.56 2.69
3753 4690 4.898861 AGAGCACCCAATTTAGGTTCAAAA 59.101 37.500 0.00 0.00 34.56 2.44
3754 4691 5.365314 AGAGCACCCAATTTAGGTTCAAAAA 59.635 36.000 0.00 0.00 34.56 1.94
3784 4721 6.036626 AGAGCACCCAATTTTGTTTTTAAACG 59.963 34.615 1.35 0.00 41.74 3.60
3785 4722 5.875359 AGCACCCAATTTTGTTTTTAAACGA 59.125 32.000 0.00 0.00 41.74 3.85
3790 4727 5.899151 CCAATTTTGTTTTTAAACGAAGGCG 59.101 36.000 7.79 0.00 41.78 5.52
3791 4728 6.237861 CCAATTTTGTTTTTAAACGAAGGCGA 60.238 34.615 7.79 0.00 41.78 5.54
3809 4759 3.882888 GGCGAACCTCATCCATTAATTGA 59.117 43.478 0.00 0.00 0.00 2.57
3810 4760 4.023707 GGCGAACCTCATCCATTAATTGAG 60.024 45.833 8.19 8.19 37.27 3.02
3814 4764 6.017605 CGAACCTCATCCATTAATTGAGAAGG 60.018 42.308 14.57 14.29 39.36 3.46
3816 4766 6.599445 ACCTCATCCATTAATTGAGAAGGAG 58.401 40.000 19.17 11.87 39.36 3.69
3830 4780 5.019470 TGAGAAGGAGAATAGAGCTTGTCA 58.981 41.667 0.00 0.00 0.00 3.58
3833 4783 5.424895 AGAAGGAGAATAGAGCTTGTCACAT 59.575 40.000 0.00 0.00 0.00 3.21
3841 4791 2.899900 AGAGCTTGTCACATACCACTCA 59.100 45.455 0.00 0.00 0.00 3.41
3842 4792 3.517100 AGAGCTTGTCACATACCACTCAT 59.483 43.478 0.00 0.00 0.00 2.90
3843 4793 4.711846 AGAGCTTGTCACATACCACTCATA 59.288 41.667 0.00 0.00 0.00 2.15
3845 4795 5.994250 AGCTTGTCACATACCACTCATATT 58.006 37.500 0.00 0.00 0.00 1.28
3846 4796 7.069950 AGAGCTTGTCACATACCACTCATATTA 59.930 37.037 0.00 0.00 0.00 0.98
3847 4797 6.986817 AGCTTGTCACATACCACTCATATTAC 59.013 38.462 0.00 0.00 0.00 1.89
3848 4798 6.986817 GCTTGTCACATACCACTCATATTACT 59.013 38.462 0.00 0.00 0.00 2.24
3849 4799 7.495934 GCTTGTCACATACCACTCATATTACTT 59.504 37.037 0.00 0.00 0.00 2.24
3850 4800 8.942338 TTGTCACATACCACTCATATTACTTC 57.058 34.615 0.00 0.00 0.00 3.01
3851 4801 8.073467 TGTCACATACCACTCATATTACTTCA 57.927 34.615 0.00 0.00 0.00 3.02
3852 4802 7.979537 TGTCACATACCACTCATATTACTTCAC 59.020 37.037 0.00 0.00 0.00 3.18
3853 4803 7.167635 GTCACATACCACTCATATTACTTCACG 59.832 40.741 0.00 0.00 0.00 4.35
3868 4818 5.358298 ACTTCACGCATTCTTCTTTTACC 57.642 39.130 0.00 0.00 0.00 2.85
3879 4829 4.307432 TCTTCTTTTACCTCAAGAGCACG 58.693 43.478 0.00 0.00 31.84 5.34
3905 4855 9.853921 GTGCTCTAAAAGAAAAATTTTGTGATG 57.146 29.630 3.73 0.00 34.35 3.07
3910 4860 9.934190 CTAAAAGAAAAATTTTGTGATGTTGGG 57.066 29.630 3.73 0.00 34.35 4.12
3925 4875 1.272490 GTTGGGCCTGGAAAAACTAGC 59.728 52.381 4.53 0.00 0.00 3.42
3934 4884 4.327680 CTGGAAAAACTAGCTGGCTTACT 58.672 43.478 0.00 0.00 0.00 2.24
3968 4918 4.247380 GGCTCCCGGGCTCAGATG 62.247 72.222 18.49 0.33 37.53 2.90
3992 4942 4.702131 AGCCTGGTCATGAACAGTAAAATC 59.298 41.667 33.21 17.25 44.44 2.17
3995 4945 5.707298 CCTGGTCATGAACAGTAAAATCACT 59.293 40.000 33.21 0.00 44.44 3.41
4060 5014 3.311871 AGATGCTCAAATGCGTGATCTTC 59.688 43.478 0.00 0.00 35.36 2.87
4071 5025 2.159653 GCGTGATCTTCGTGCAAGAATT 60.160 45.455 15.52 6.60 44.66 2.17
4082 5036 5.451908 TCGTGCAAGAATTTGATGAAGTTC 58.548 37.500 0.00 0.00 36.36 3.01
4091 5045 7.855545 AGAATTTGATGAAGTTCGGATATTCG 58.144 34.615 0.00 0.00 0.00 3.34
4092 5046 7.710907 AGAATTTGATGAAGTTCGGATATTCGA 59.289 33.333 0.73 0.73 37.38 3.71
4094 5048 4.871513 TGATGAAGTTCGGATATTCGAGG 58.128 43.478 6.16 0.00 40.42 4.63
4096 5050 4.569761 TGAAGTTCGGATATTCGAGGAG 57.430 45.455 6.16 0.00 40.42 3.69
4132 5090 2.741211 GGGTGTCCGCGGAACTTC 60.741 66.667 32.93 18.54 0.00 3.01
4138 5096 0.511653 GTCCGCGGAACTTCTGAAAC 59.488 55.000 32.93 10.31 0.00 2.78
4145 5103 3.458189 CGGAACTTCTGAAACTCACACT 58.542 45.455 0.00 0.00 0.00 3.55
4146 5104 4.617959 CGGAACTTCTGAAACTCACACTA 58.382 43.478 0.00 0.00 0.00 2.74
4154 5112 5.798132 TCTGAAACTCACACTATTCATGCT 58.202 37.500 0.00 0.00 31.92 3.79
4162 5120 7.533426 ACTCACACTATTCATGCTTGATTTTC 58.467 34.615 2.75 0.00 0.00 2.29
4167 5125 8.800332 ACACTATTCATGCTTGATTTTCTCTTT 58.200 29.630 2.75 0.00 0.00 2.52
4196 5154 3.012518 CAAGCTCCTCGAATGTCCAAAT 58.987 45.455 0.00 0.00 0.00 2.32
4197 5155 2.911484 AGCTCCTCGAATGTCCAAATC 58.089 47.619 0.00 0.00 0.00 2.17
4198 5156 2.237143 AGCTCCTCGAATGTCCAAATCA 59.763 45.455 0.00 0.00 0.00 2.57
4203 5161 3.125829 CCTCGAATGTCCAAATCACACAG 59.874 47.826 0.00 0.00 0.00 3.66
4205 5163 4.384940 TCGAATGTCCAAATCACACAGAA 58.615 39.130 0.00 0.00 0.00 3.02
4209 5167 6.642131 CGAATGTCCAAATCACACAGAATTTT 59.358 34.615 0.00 0.00 0.00 1.82
4210 5168 7.358600 CGAATGTCCAAATCACACAGAATTTTG 60.359 37.037 0.00 0.00 0.00 2.44
4211 5169 5.049167 TGTCCAAATCACACAGAATTTTGC 58.951 37.500 0.00 0.00 29.05 3.68
4212 5170 5.049167 GTCCAAATCACACAGAATTTTGCA 58.951 37.500 0.00 0.00 29.05 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.502079 AGCTAGCAGAGAGTTAACTACAGA 58.498 41.667 18.83 0.00 0.00 3.41
1 2 5.828299 AGCTAGCAGAGAGTTAACTACAG 57.172 43.478 18.83 4.42 0.00 2.74
2 3 6.416415 ACTAGCTAGCAGAGAGTTAACTACA 58.584 40.000 20.91 0.00 0.00 2.74
3 4 6.930667 ACTAGCTAGCAGAGAGTTAACTAC 57.069 41.667 20.91 6.16 0.00 2.73
4 5 7.563020 TGTACTAGCTAGCAGAGAGTTAACTA 58.437 38.462 20.91 0.00 0.00 2.24
5 6 6.416415 TGTACTAGCTAGCAGAGAGTTAACT 58.584 40.000 20.91 8.13 0.00 2.24
6 7 6.316890 ACTGTACTAGCTAGCAGAGAGTTAAC 59.683 42.308 26.04 10.36 33.57 2.01
7 8 6.416415 ACTGTACTAGCTAGCAGAGAGTTAA 58.584 40.000 26.04 5.61 33.57 2.01
8 9 5.991861 ACTGTACTAGCTAGCAGAGAGTTA 58.008 41.667 26.04 7.22 33.57 2.24
9 10 4.850680 ACTGTACTAGCTAGCAGAGAGTT 58.149 43.478 26.04 8.07 33.57 3.01
10 11 4.497291 ACTGTACTAGCTAGCAGAGAGT 57.503 45.455 26.04 19.32 33.57 3.24
11 12 4.878971 TCAACTGTACTAGCTAGCAGAGAG 59.121 45.833 26.04 18.82 33.57 3.20
12 13 4.844884 TCAACTGTACTAGCTAGCAGAGA 58.155 43.478 26.04 20.65 33.57 3.10
13 14 5.559991 CGATCAACTGTACTAGCTAGCAGAG 60.560 48.000 26.04 21.11 33.57 3.35
14 15 4.273724 CGATCAACTGTACTAGCTAGCAGA 59.726 45.833 26.04 11.96 33.57 4.26
15 16 4.532276 CGATCAACTGTACTAGCTAGCAG 58.468 47.826 20.91 20.71 35.31 4.24
16 17 3.243101 GCGATCAACTGTACTAGCTAGCA 60.243 47.826 20.91 10.48 0.00 3.49
17 18 3.243101 TGCGATCAACTGTACTAGCTAGC 60.243 47.826 20.91 6.62 0.00 3.42
18 19 4.553756 TGCGATCAACTGTACTAGCTAG 57.446 45.455 19.44 19.44 0.00 3.42
19 20 4.976224 TTGCGATCAACTGTACTAGCTA 57.024 40.909 0.00 0.00 0.00 3.32
20 21 3.868757 TTGCGATCAACTGTACTAGCT 57.131 42.857 0.00 0.00 0.00 3.32
21 22 3.678072 TGTTTGCGATCAACTGTACTAGC 59.322 43.478 0.00 0.00 30.75 3.42
22 23 5.576774 TCATGTTTGCGATCAACTGTACTAG 59.423 40.000 0.00 0.00 30.75 2.57
23 24 5.347635 GTCATGTTTGCGATCAACTGTACTA 59.652 40.000 0.00 0.00 30.75 1.82
24 25 4.152402 GTCATGTTTGCGATCAACTGTACT 59.848 41.667 0.00 0.00 30.75 2.73
25 26 4.084066 TGTCATGTTTGCGATCAACTGTAC 60.084 41.667 0.00 0.00 30.75 2.90
26 27 4.061596 TGTCATGTTTGCGATCAACTGTA 58.938 39.130 0.00 0.00 30.75 2.74
27 28 2.877786 TGTCATGTTTGCGATCAACTGT 59.122 40.909 0.00 0.00 30.75 3.55
28 29 3.058708 ACTGTCATGTTTGCGATCAACTG 60.059 43.478 0.00 0.00 30.75 3.16
29 30 3.058708 CACTGTCATGTTTGCGATCAACT 60.059 43.478 0.00 0.00 30.75 3.16
30 31 3.058983 TCACTGTCATGTTTGCGATCAAC 60.059 43.478 0.00 0.00 30.75 3.18
31 32 3.137533 TCACTGTCATGTTTGCGATCAA 58.862 40.909 0.00 0.00 0.00 2.57
32 33 2.765122 TCACTGTCATGTTTGCGATCA 58.235 42.857 0.00 0.00 0.00 2.92
107 109 1.802337 CGGACCGTCCAGTCAGACAA 61.802 60.000 17.87 0.00 38.59 3.18
112 114 2.114625 AGTCGGACCGTCCAGTCA 59.885 61.111 17.87 0.00 38.59 3.41
129 131 2.676750 CGTTTACTCATGGCCAGCTACA 60.677 50.000 13.05 0.00 0.00 2.74
253 272 1.402968 AGGTACGCAGGTGTACGTATG 59.597 52.381 14.50 0.00 45.46 2.39
254 273 1.755179 AGGTACGCAGGTGTACGTAT 58.245 50.000 14.50 3.34 45.46 3.06
255 274 1.468520 GAAGGTACGCAGGTGTACGTA 59.531 52.381 15.91 0.00 44.48 3.57
256 275 0.242017 GAAGGTACGCAGGTGTACGT 59.758 55.000 14.79 13.07 44.48 3.57
257 276 0.457337 GGAAGGTACGCAGGTGTACG 60.457 60.000 14.79 0.00 44.48 3.67
264 283 0.684805 AGGGAGAGGAAGGTACGCAG 60.685 60.000 0.00 0.00 0.00 5.18
293 312 5.660460 ACAGTGGAATGAACCTTTTTGTTC 58.340 37.500 0.00 0.00 43.90 3.18
295 314 4.956075 AGACAGTGGAATGAACCTTTTTGT 59.044 37.500 0.00 0.00 0.00 2.83
305 324 3.421919 TGCATCAAGACAGTGGAATGA 57.578 42.857 0.00 0.00 0.00 2.57
608 632 0.820871 CTCCAAAGCTAGCGACTCCT 59.179 55.000 9.55 0.00 0.00 3.69
638 662 3.261897 GCTGGATTTATAGAGCTAGCCCA 59.738 47.826 12.13 7.24 0.00 5.36
933 978 6.292897 CTGGAACATACGGACTACGCAATAG 61.293 48.000 0.00 0.00 43.04 1.73
936 981 2.416296 CTGGAACATACGGACTACGCAA 60.416 50.000 0.00 0.00 43.04 4.85
938 983 1.836383 CTGGAACATACGGACTACGC 58.164 55.000 0.00 0.00 43.04 4.42
940 985 2.810650 CTGCTGGAACATACGGACTAC 58.189 52.381 0.00 0.00 38.20 2.73
941 986 1.136305 GCTGCTGGAACATACGGACTA 59.864 52.381 0.00 0.00 38.20 2.59
942 987 0.108138 GCTGCTGGAACATACGGACT 60.108 55.000 0.00 0.00 38.20 3.85
943 988 1.421410 CGCTGCTGGAACATACGGAC 61.421 60.000 0.00 0.00 38.20 4.79
944 989 1.153647 CGCTGCTGGAACATACGGA 60.154 57.895 0.00 0.00 38.20 4.69
945 990 2.813179 GCGCTGCTGGAACATACGG 61.813 63.158 0.00 0.00 38.20 4.02
946 991 1.811266 AGCGCTGCTGGAACATACG 60.811 57.895 10.39 0.00 37.57 3.06
947 992 4.208632 AGCGCTGCTGGAACATAC 57.791 55.556 10.39 0.00 37.57 2.39
1002 1047 2.386661 TCGAGAAACCTGCAGAATCC 57.613 50.000 17.39 1.47 0.00 3.01
1026 1071 2.740981 GTCTCTGTTGCTCAACTCCATG 59.259 50.000 13.16 0.00 41.67 3.66
1043 1088 3.181472 GCCCATTTGGATTTGGATGTCTC 60.181 47.826 0.00 0.00 37.39 3.36
1048 1093 1.487558 GCTGCCCATTTGGATTTGGAT 59.512 47.619 0.00 0.00 37.39 3.41
1095 1140 3.492311 GAGCAGCGACGGGAGATCC 62.492 68.421 0.00 0.00 0.00 3.36
1187 1232 1.959226 TCCTTGTTGTTCCGCTCGC 60.959 57.895 0.00 0.00 0.00 5.03
1712 1757 3.334751 TCAGACCGTTGCGTTGCG 61.335 61.111 0.00 0.00 0.00 4.85
1759 1804 2.583593 GAGCCGTTAGCCTCAGCG 60.584 66.667 0.00 0.00 46.67 5.18
1774 1825 4.319839 GCCTGAAGAAAAAGAAAGACCGAG 60.320 45.833 0.00 0.00 0.00 4.63
1776 1827 3.304726 GGCCTGAAGAAAAAGAAAGACCG 60.305 47.826 0.00 0.00 0.00 4.79
2584 2656 1.290009 GGCACATGTGGGAACAAGC 59.710 57.895 26.55 9.83 46.06 4.01
2645 2720 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
2647 2722 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2648 2723 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2649 2724 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2650 2725 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2651 2726 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2652 2727 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2653 2728 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2654 2729 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2655 2730 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
2656 2731 2.537401 CTCCGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 43.47 4.79
2657 2732 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
2658 2733 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
2660 2735 3.877508 CCATTCCTCCGACAAGTATTTCC 59.122 47.826 0.00 0.00 0.00 3.13
2661 2736 4.766375 TCCATTCCTCCGACAAGTATTTC 58.234 43.478 0.00 0.00 0.00 2.17
2662 2737 4.837093 TCCATTCCTCCGACAAGTATTT 57.163 40.909 0.00 0.00 0.00 1.40
2663 2738 4.164221 ACATCCATTCCTCCGACAAGTATT 59.836 41.667 0.00 0.00 0.00 1.89
2664 2739 3.711704 ACATCCATTCCTCCGACAAGTAT 59.288 43.478 0.00 0.00 0.00 2.12
2665 2740 3.104512 ACATCCATTCCTCCGACAAGTA 58.895 45.455 0.00 0.00 0.00 2.24
2666 2741 1.909302 ACATCCATTCCTCCGACAAGT 59.091 47.619 0.00 0.00 0.00 3.16
2667 2742 2.698855 ACATCCATTCCTCCGACAAG 57.301 50.000 0.00 0.00 0.00 3.16
2668 2743 3.967326 AGATACATCCATTCCTCCGACAA 59.033 43.478 0.00 0.00 0.00 3.18
2669 2744 3.576861 AGATACATCCATTCCTCCGACA 58.423 45.455 0.00 0.00 0.00 4.35
2670 2745 5.010933 TCTAGATACATCCATTCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
2671 2746 5.010933 GTCTAGATACATCCATTCCTCCGA 58.989 45.833 0.00 0.00 0.00 4.55
2672 2747 4.767409 TGTCTAGATACATCCATTCCTCCG 59.233 45.833 0.00 0.00 0.00 4.63
2673 2748 6.865834 ATGTCTAGATACATCCATTCCTCC 57.134 41.667 0.00 0.00 35.08 4.30
2674 2749 9.420118 AGATATGTCTAGATACATCCATTCCTC 57.580 37.037 4.30 0.00 40.52 3.71
2675 2750 9.781425 AAGATATGTCTAGATACATCCATTCCT 57.219 33.333 4.30 0.00 40.52 3.36
2716 3025 8.792633 ACTTGTCGAAGAAATGGATAAAAATGA 58.207 29.630 0.00 0.00 39.69 2.57
2717 3026 8.970691 ACTTGTCGAAGAAATGGATAAAAATG 57.029 30.769 0.00 0.00 39.69 2.32
2722 3031 8.889717 GGAAATACTTGTCGAAGAAATGGATAA 58.110 33.333 0.00 0.00 39.69 1.75
2724 3033 6.037172 CGGAAATACTTGTCGAAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
2725 3034 5.350365 CGGAAATACTTGTCGAAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
2726 3035 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
2727 3036 5.350365 TCCGGAAATACTTGTCGAAGAAATG 59.650 40.000 0.00 0.00 39.69 2.32
2728 3037 5.350640 GTCCGGAAATACTTGTCGAAGAAAT 59.649 40.000 5.23 0.00 39.69 2.17
2729 3038 4.687483 GTCCGGAAATACTTGTCGAAGAAA 59.313 41.667 5.23 0.00 39.69 2.52
2730 3039 4.240096 GTCCGGAAATACTTGTCGAAGAA 58.760 43.478 5.23 0.00 39.69 2.52
2732 3041 2.597305 CGTCCGGAAATACTTGTCGAAG 59.403 50.000 5.23 0.00 35.07 3.79
2734 3043 1.811965 TCGTCCGGAAATACTTGTCGA 59.188 47.619 5.23 4.55 0.00 4.20
2735 3044 2.267188 TCGTCCGGAAATACTTGTCG 57.733 50.000 5.23 1.58 0.00 4.35
2736 3045 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
2737 3046 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
2738 3047 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2739 3048 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
2741 3050 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
2742 3051 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
2743 3052 1.856629 TACTCCCTTCGTCCGGAAAT 58.143 50.000 5.23 0.00 33.34 2.17
2744 3053 1.856629 ATACTCCCTTCGTCCGGAAA 58.143 50.000 5.23 0.00 33.34 3.13
2747 3056 2.236766 ACATATACTCCCTTCGTCCGG 58.763 52.381 0.00 0.00 0.00 5.14
2748 3057 3.119919 GCTACATATACTCCCTTCGTCCG 60.120 52.174 0.00 0.00 0.00 4.79
2749 3058 3.119919 CGCTACATATACTCCCTTCGTCC 60.120 52.174 0.00 0.00 0.00 4.79
2751 3060 3.748083 TCGCTACATATACTCCCTTCGT 58.252 45.455 0.00 0.00 0.00 3.85
2752 3061 4.761235 TTCGCTACATATACTCCCTTCG 57.239 45.455 0.00 0.00 0.00 3.79
2753 3062 6.151312 TCAGATTCGCTACATATACTCCCTTC 59.849 42.308 0.00 0.00 0.00 3.46
2755 3064 5.571285 TCAGATTCGCTACATATACTCCCT 58.429 41.667 0.00 0.00 0.00 4.20
2756 3065 5.899120 TCAGATTCGCTACATATACTCCC 57.101 43.478 0.00 0.00 0.00 4.30
2757 3066 7.815068 ACAAATCAGATTCGCTACATATACTCC 59.185 37.037 0.00 0.00 0.00 3.85
2758 3067 8.642885 CACAAATCAGATTCGCTACATATACTC 58.357 37.037 0.00 0.00 0.00 2.59
2759 3068 8.144478 ACACAAATCAGATTCGCTACATATACT 58.856 33.333 0.00 0.00 0.00 2.12
2773 3082 6.589135 TGCTCATCATAGACACAAATCAGAT 58.411 36.000 0.00 0.00 0.00 2.90
3413 3962 5.859521 ATCCGTAGACGTATACACAGATC 57.140 43.478 19.46 0.00 37.74 2.75
3479 4030 6.798482 TGTATGCTGAATCATTCAACCAATC 58.202 36.000 0.75 1.48 39.58 2.67
3533 4395 5.643348 TGTTGTTACATGATTAGTCCTGCTG 59.357 40.000 0.00 0.00 0.00 4.41
3547 4409 3.004315 CGAAAAGCAGGGTGTTGTTACAT 59.996 43.478 0.00 0.00 36.50 2.29
3548 4410 2.356382 CGAAAAGCAGGGTGTTGTTACA 59.644 45.455 0.00 0.00 0.00 2.41
3582 4519 5.814705 CGACTGCTTCATCCTCTCTAATTTT 59.185 40.000 0.00 0.00 0.00 1.82
3593 4530 1.416813 CGCTGACGACTGCTTCATCC 61.417 60.000 13.87 0.00 43.93 3.51
3595 4532 1.446792 CCGCTGACGACTGCTTCAT 60.447 57.895 13.87 0.00 43.93 2.57
3648 4585 4.098914 TGCACCCTGAAGTCAAATTACT 57.901 40.909 0.00 0.00 0.00 2.24
3664 4601 1.197721 CGTTTCACCAGAGAATGCACC 59.802 52.381 0.00 0.00 0.00 5.01
3668 4605 2.350772 GGCAACGTTTCACCAGAGAATG 60.351 50.000 0.00 0.00 0.00 2.67
3689 4626 2.687425 AGATCAGAGCCCATCGATATCG 59.313 50.000 19.14 19.14 41.45 2.92
3702 4639 4.096532 AGCATTGTCATTTGCAGATCAGAG 59.903 41.667 10.03 0.00 41.35 3.35
3727 4664 3.806949 ACCTAAATTGGGTGCTCTTCA 57.193 42.857 0.00 0.00 35.51 3.02
3755 4692 6.832520 AAAACAAAATTGGGTGCTCTTTTT 57.167 29.167 0.00 0.00 0.00 1.94
3756 4693 6.832520 AAAAACAAAATTGGGTGCTCTTTT 57.167 29.167 0.00 0.00 0.00 2.27
3757 4694 7.929941 TTAAAAACAAAATTGGGTGCTCTTT 57.070 28.000 0.00 0.00 0.00 2.52
3758 4695 7.413548 CGTTTAAAAACAAAATTGGGTGCTCTT 60.414 33.333 6.41 0.00 38.81 2.85
3759 4696 6.036626 CGTTTAAAAACAAAATTGGGTGCTCT 59.963 34.615 6.41 0.00 38.81 4.09
3760 4697 6.036191 TCGTTTAAAAACAAAATTGGGTGCTC 59.964 34.615 6.41 0.00 38.81 4.26
3761 4698 5.875359 TCGTTTAAAAACAAAATTGGGTGCT 59.125 32.000 6.41 0.00 38.81 4.40
3762 4699 6.108097 TCGTTTAAAAACAAAATTGGGTGC 57.892 33.333 6.41 0.00 38.81 5.01
3763 4700 7.183433 CCTTCGTTTAAAAACAAAATTGGGTG 58.817 34.615 6.41 0.00 38.81 4.61
3764 4701 6.183360 GCCTTCGTTTAAAAACAAAATTGGGT 60.183 34.615 6.41 0.00 38.81 4.51
3765 4702 6.195868 GCCTTCGTTTAAAAACAAAATTGGG 58.804 36.000 6.41 0.00 38.81 4.12
3766 4703 5.899151 CGCCTTCGTTTAAAAACAAAATTGG 59.101 36.000 6.41 0.97 38.81 3.16
3767 4704 6.697152 TCGCCTTCGTTTAAAAACAAAATTG 58.303 32.000 6.41 0.00 38.81 2.32
3768 4705 6.889019 TCGCCTTCGTTTAAAAACAAAATT 57.111 29.167 6.41 0.00 38.81 1.82
3769 4706 6.237888 GGTTCGCCTTCGTTTAAAAACAAAAT 60.238 34.615 6.41 0.00 38.81 1.82
3770 4707 5.061933 GGTTCGCCTTCGTTTAAAAACAAAA 59.938 36.000 6.41 0.00 38.81 2.44
3771 4708 4.562000 GGTTCGCCTTCGTTTAAAAACAAA 59.438 37.500 6.41 0.00 38.81 2.83
3772 4709 4.104066 GGTTCGCCTTCGTTTAAAAACAA 58.896 39.130 6.41 0.06 38.81 2.83
3773 4710 3.693654 GGTTCGCCTTCGTTTAAAAACA 58.306 40.909 6.41 0.00 38.81 2.83
3790 4727 7.056635 TCCTTCTCAATTAATGGATGAGGTTC 58.943 38.462 15.93 0.00 40.71 3.62
3791 4728 6.973642 TCCTTCTCAATTAATGGATGAGGTT 58.026 36.000 15.93 0.00 40.71 3.50
3800 4750 9.558396 AAGCTCTATTCTCCTTCTCAATTAATG 57.442 33.333 0.00 0.00 0.00 1.90
3809 4759 4.774726 TGTGACAAGCTCTATTCTCCTTCT 59.225 41.667 0.00 0.00 0.00 2.85
3810 4760 5.078411 TGTGACAAGCTCTATTCTCCTTC 57.922 43.478 0.00 0.00 0.00 3.46
3814 4764 5.751028 GTGGTATGTGACAAGCTCTATTCTC 59.249 44.000 0.00 0.00 0.00 2.87
3816 4766 5.665459 AGTGGTATGTGACAAGCTCTATTC 58.335 41.667 0.00 0.00 0.00 1.75
3830 4780 5.983720 GCGTGAAGTAATATGAGTGGTATGT 59.016 40.000 0.00 0.00 0.00 2.29
3833 4783 5.585820 TGCGTGAAGTAATATGAGTGGTA 57.414 39.130 0.00 0.00 0.00 3.25
3842 4792 8.662141 GGTAAAAGAAGAATGCGTGAAGTAATA 58.338 33.333 0.00 0.00 0.00 0.98
3843 4793 7.390718 AGGTAAAAGAAGAATGCGTGAAGTAAT 59.609 33.333 0.00 0.00 0.00 1.89
3845 4795 6.228258 AGGTAAAAGAAGAATGCGTGAAGTA 58.772 36.000 0.00 0.00 0.00 2.24
3846 4796 5.063880 AGGTAAAAGAAGAATGCGTGAAGT 58.936 37.500 0.00 0.00 0.00 3.01
3847 4797 5.179368 TGAGGTAAAAGAAGAATGCGTGAAG 59.821 40.000 0.00 0.00 0.00 3.02
3848 4798 5.060506 TGAGGTAAAAGAAGAATGCGTGAA 58.939 37.500 0.00 0.00 0.00 3.18
3849 4799 4.637276 TGAGGTAAAAGAAGAATGCGTGA 58.363 39.130 0.00 0.00 0.00 4.35
3850 4800 5.179368 TCTTGAGGTAAAAGAAGAATGCGTG 59.821 40.000 0.00 0.00 30.79 5.34
3851 4801 5.305585 TCTTGAGGTAAAAGAAGAATGCGT 58.694 37.500 0.00 0.00 30.79 5.24
3852 4802 5.672321 GCTCTTGAGGTAAAAGAAGAATGCG 60.672 44.000 0.00 0.00 33.40 4.73
3853 4803 5.182001 TGCTCTTGAGGTAAAAGAAGAATGC 59.818 40.000 0.00 0.00 33.40 3.56
3879 4829 9.853921 CATCACAAAATTTTTCTTTTAGAGCAC 57.146 29.630 0.00 0.00 0.00 4.40
3884 4834 9.934190 CCCAACATCACAAAATTTTTCTTTTAG 57.066 29.630 0.00 0.00 0.00 1.85
3894 4844 2.038820 CCAGGCCCAACATCACAAAATT 59.961 45.455 0.00 0.00 0.00 1.82
3895 4845 1.624813 CCAGGCCCAACATCACAAAAT 59.375 47.619 0.00 0.00 0.00 1.82
3896 4846 1.047002 CCAGGCCCAACATCACAAAA 58.953 50.000 0.00 0.00 0.00 2.44
3905 4855 1.272490 GCTAGTTTTTCCAGGCCCAAC 59.728 52.381 0.00 0.00 0.00 3.77
3910 4860 0.528017 GCCAGCTAGTTTTTCCAGGC 59.472 55.000 0.00 0.00 0.00 4.85
3925 4875 1.293924 CCGCATCTCAAGTAAGCCAG 58.706 55.000 0.00 0.00 0.00 4.85
3934 4884 1.992233 GCCAAATCGCCGCATCTCAA 61.992 55.000 0.00 0.00 0.00 3.02
3968 4918 3.334583 TTACTGTTCATGACCAGGCTC 57.665 47.619 22.52 0.00 0.00 4.70
3973 4923 8.684386 TTTAGTGATTTTACTGTTCATGACCA 57.316 30.769 0.00 0.00 32.19 4.02
4010 4960 8.180920 GCTTGCCAGAAAATCAACTTTTAAAAA 58.819 29.630 1.66 0.00 37.18 1.94
4019 4969 3.981211 TCTTGCTTGCCAGAAAATCAAC 58.019 40.909 0.00 0.00 0.00 3.18
4020 4970 4.562082 CATCTTGCTTGCCAGAAAATCAA 58.438 39.130 0.58 0.00 0.00 2.57
4021 4971 3.615592 GCATCTTGCTTGCCAGAAAATCA 60.616 43.478 0.58 0.00 40.96 2.57
4024 4974 2.443887 GCATCTTGCTTGCCAGAAAA 57.556 45.000 0.58 0.00 40.96 2.29
4060 5014 4.319115 CGAACTTCATCAAATTCTTGCACG 59.681 41.667 0.00 0.00 32.14 5.34
4071 5025 5.068591 TCCTCGAATATCCGAACTTCATCAA 59.931 40.000 0.00 0.00 38.17 2.57
4115 5069 2.741211 GAAGTTCCGCGGACACCC 60.741 66.667 31.19 16.10 0.00 4.61
4116 5070 2.027625 CAGAAGTTCCGCGGACACC 61.028 63.158 31.19 18.84 0.00 4.16
4117 5071 0.599204 TTCAGAAGTTCCGCGGACAC 60.599 55.000 31.19 26.69 0.00 3.67
4119 5073 0.511653 GTTTCAGAAGTTCCGCGGAC 59.488 55.000 31.19 22.52 0.00 4.79
4120 5074 0.391597 AGTTTCAGAAGTTCCGCGGA 59.608 50.000 27.28 27.28 0.00 5.54
4121 5075 0.790814 GAGTTTCAGAAGTTCCGCGG 59.209 55.000 22.12 22.12 0.00 6.46
4122 5076 1.192534 GTGAGTTTCAGAAGTTCCGCG 59.807 52.381 0.00 0.00 0.00 6.46
4124 5078 3.458189 AGTGTGAGTTTCAGAAGTTCCG 58.542 45.455 0.00 0.00 0.00 4.30
4126 5080 7.715265 TGAATAGTGTGAGTTTCAGAAGTTC 57.285 36.000 0.00 0.00 0.00 3.01
4132 5090 6.148315 TCAAGCATGAATAGTGTGAGTTTCAG 59.852 38.462 0.00 0.00 32.13 3.02
4138 5096 7.759465 AGAAAATCAAGCATGAATAGTGTGAG 58.241 34.615 0.00 0.00 39.49 3.51
4167 5125 0.179032 TCGAGGAGCTTGTGGCAAAA 60.179 50.000 0.00 0.00 44.79 2.44
4176 5134 2.859165 TTTGGACATTCGAGGAGCTT 57.141 45.000 0.00 0.00 0.00 3.74
4184 5142 4.747540 TTCTGTGTGATTTGGACATTCG 57.252 40.909 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.