Multiple sequence alignment - TraesCS3A01G411700

Loading Multiple Alignment...

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 TraesCS3A01G411700 chr3A 100.000 2626 0 0 881 3506 655637450 655634825 0.000000e+00 4850.0
1 TraesCS3A01G411700 chr3A 83.200 1250 168 26 1269 2494 703304281 703303050 0.000000e+00 1107.0
2 TraesCS3A01G411700 chr3A 79.540 1696 220 67 881 2487 703394754 703396411 0.000000e+00 1092.0
3 TraesCS3A01G411700 chr3A 81.342 1222 194 22 1286 2487 703270318 703271525 0.000000e+00 963.0
4 TraesCS3A01G411700 chr3A 100.000 439 0 0 1 439 655638330 655637892 0.000000e+00 811.0
5 TraesCS3A01G411700 chr3A 91.089 101 8 1 339 439 677890707 677890806 6.100000e-28 135.0
6 TraesCS3A01G411700 chr3B 95.361 1660 62 7 881 2538 685039627 685037981 0.000000e+00 2625.0
7 TraesCS3A01G411700 chr3B 83.610 1263 155 25 1265 2489 757807636 757808884 0.000000e+00 1138.0
8 TraesCS3A01G411700 chr3B 82.857 1225 165 28 1297 2494 757739782 757738576 0.000000e+00 1057.0
9 TraesCS3A01G411700 chr3B 81.384 1257 192 28 1256 2487 757734154 757735393 0.000000e+00 987.0
10 TraesCS3A01G411700 chr3B 80.515 1242 202 27 1269 2487 757773415 757772191 0.000000e+00 917.0
11 TraesCS3A01G411700 chr3B 88.496 226 10 7 125 339 685041386 685041166 3.470000e-65 259.0
12 TraesCS3A01G411700 chr3B 94.059 101 5 1 339 439 42716438 42716537 6.060000e-33 152.0
13 TraesCS3A01G411700 chr3B 87.931 58 7 0 2770 2827 624882383 624882326 6.280000e-08 69.4
14 TraesCS3A01G411700 chr3B 88.679 53 5 1 2773 2825 14248889 14248940 2.920000e-06 63.9
15 TraesCS3A01G411700 chr3D 93.420 1535 45 18 1240 2774 520191930 520190452 0.000000e+00 2224.0
16 TraesCS3A01G411700 chr3D 83.228 1264 158 30 1265 2489 570559197 570560445 0.000000e+00 1110.0
17 TraesCS3A01G411700 chr3D 81.997 1222 186 24 1286 2487 570393721 570394928 0.000000e+00 1007.0
18 TraesCS3A01G411700 chr3D 90.799 663 37 5 2825 3464 140787814 140787153 0.000000e+00 865.0
19 TraesCS3A01G411700 chr3D 79.740 1229 205 28 1269 2475 570496372 570495166 0.000000e+00 850.0
20 TraesCS3A01G411700 chr3D 79.125 1212 189 41 1266 2454 570379598 570380768 0.000000e+00 778.0
21 TraesCS3A01G411700 chr3D 79.112 1216 177 47 1270 2454 570281055 570282224 0.000000e+00 767.0
22 TraesCS3A01G411700 chr3D 86.906 695 75 15 2828 3506 523168141 523167447 0.000000e+00 765.0
23 TraesCS3A01G411700 chr3D 81.915 658 88 17 1860 2494 570400565 570399916 8.620000e-146 527.0
24 TraesCS3A01G411700 chr3D 91.961 311 20 4 881 1190 520192336 520192030 6.950000e-117 431.0
25 TraesCS3A01G411700 chr3D 92.661 218 12 3 125 339 520192592 520192376 9.450000e-81 311.0
26 TraesCS3A01G411700 chr7A 91.412 687 53 5 2825 3506 514864176 514864861 0.000000e+00 937.0
27 TraesCS3A01G411700 chr7A 97.297 37 1 0 2773 2809 219029706 219029742 2.920000e-06 63.9
28 TraesCS3A01G411700 chrUn 90.870 701 42 2 2828 3506 21562022 21561322 0.000000e+00 920.0
29 TraesCS3A01G411700 chr7D 91.454 667 34 3 2862 3506 593671580 593670915 0.000000e+00 894.0
30 TraesCS3A01G411700 chr7D 84.940 664 84 11 2834 3482 13469167 13469829 0.000000e+00 658.0
31 TraesCS3A01G411700 chr5D 89.592 711 41 12 2829 3506 396427016 396426306 0.000000e+00 872.0
32 TraesCS3A01G411700 chr5D 85.778 668 80 13 2827 3482 22427039 22427703 0.000000e+00 693.0
33 TraesCS3A01G411700 chr5D 93.069 101 6 1 339 439 73768911 73769010 2.820000e-31 147.0
34 TraesCS3A01G411700 chr5D 90.769 65 5 1 339 403 476721221 476721158 6.240000e-13 86.1
35 TraesCS3A01G411700 chr4D 87.204 633 73 3 2829 3453 365219530 365218898 0.000000e+00 713.0
36 TraesCS3A01G411700 chr4D 94.059 101 5 1 339 439 51610836 51610935 6.060000e-33 152.0
37 TraesCS3A01G411700 chr4D 85.455 55 4 3 2775 2827 447915004 447914952 2.000000e-03 54.7
38 TraesCS3A01G411700 chr7B 85.180 695 85 14 2829 3506 522040973 522041666 0.000000e+00 697.0
39 TraesCS3A01G411700 chr7B 87.356 609 72 5 2855 3460 721690618 721690012 0.000000e+00 693.0
40 TraesCS3A01G411700 chr6A 97.030 101 1 2 339 439 135006100 135006198 6.020000e-38 169.0
41 TraesCS3A01G411700 chr6A 92.000 50 4 0 2772 2821 565388205 565388254 1.750000e-08 71.3
42 TraesCS3A01G411700 chr2A 96.040 101 3 1 339 439 252096080 252096179 2.800000e-36 163.0
43 TraesCS3A01G411700 chr2A 92.727 55 4 0 2773 2827 667967751 667967805 2.900000e-11 80.5
44 TraesCS3A01G411700 chr2B 95.050 101 4 1 339 439 636653833 636653734 1.300000e-34 158.0
45 TraesCS3A01G411700 chr2B 86.792 53 7 0 2775 2827 746130090 746130142 3.780000e-05 60.2
46 TraesCS3A01G411700 chr2B 84.906 53 8 0 2775 2827 6543662 6543610 2.000000e-03 54.7
47 TraesCS3A01G411700 chr4B 93.069 101 6 1 339 439 586336976 586336877 2.820000e-31 147.0
48 TraesCS3A01G411700 chr4B 94.118 34 2 0 2775 2808 666588856 666588823 6.000000e-03 52.8
49 TraesCS3A01G411700 chr5A 92.079 101 7 1 339 439 491936318 491936417 1.310000e-29 141.0
50 TraesCS3A01G411700 chr5A 92.708 96 6 1 339 434 491705222 491705128 1.700000e-28 137.0
51 TraesCS3A01G411700 chr5A 87.755 49 5 1 2761 2808 514048121 514048169 4.890000e-04 56.5
52 TraesCS3A01G411700 chr6B 92.308 91 6 1 339 429 52978133 52978044 1.020000e-25 128.0
53 TraesCS3A01G411700 chr2D 89.109 101 9 2 339 439 555961575 555961477 1.320000e-24 124.0
54 TraesCS3A01G411700 chr4A 97.143 35 1 0 2775 2809 553465033 553465067 3.780000e-05 60.2
55 TraesCS3A01G411700 chr1D 100.000 28 0 0 339 366 425861271 425861298 6.000000e-03 52.8


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 TraesCS3A01G411700 chr3A 655634825 655638330 3505 True 2830.500000 4850 100.000000 1 3506 2 chr3A.!!$R2 3505
1 TraesCS3A01G411700 chr3A 703303050 703304281 1231 True 1107.000000 1107 83.200000 1269 2494 1 chr3A.!!$R1 1225
2 TraesCS3A01G411700 chr3A 703394754 703396411 1657 False 1092.000000 1092 79.540000 881 2487 1 chr3A.!!$F3 1606
3 TraesCS3A01G411700 chr3A 703270318 703271525 1207 False 963.000000 963 81.342000 1286 2487 1 chr3A.!!$F2 1201
4 TraesCS3A01G411700 chr3B 685037981 685041386 3405 True 1442.000000 2625 91.928500 125 2538 2 chr3B.!!$R4 2413
5 TraesCS3A01G411700 chr3B 757807636 757808884 1248 False 1138.000000 1138 83.610000 1265 2489 1 chr3B.!!$F4 1224
6 TraesCS3A01G411700 chr3B 757738576 757739782 1206 True 1057.000000 1057 82.857000 1297 2494 1 chr3B.!!$R2 1197
7 TraesCS3A01G411700 chr3B 757734154 757735393 1239 False 987.000000 987 81.384000 1256 2487 1 chr3B.!!$F3 1231
8 TraesCS3A01G411700 chr3B 757772191 757773415 1224 True 917.000000 917 80.515000 1269 2487 1 chr3B.!!$R3 1218
9 TraesCS3A01G411700 chr3D 570559197 570560445 1248 False 1110.000000 1110 83.228000 1265 2489 1 chr3D.!!$F4 1224
10 TraesCS3A01G411700 chr3D 570393721 570394928 1207 False 1007.000000 1007 81.997000 1286 2487 1 chr3D.!!$F3 1201
11 TraesCS3A01G411700 chr3D 520190452 520192592 2140 True 988.666667 2224 92.680667 125 2774 3 chr3D.!!$R5 2649
12 TraesCS3A01G411700 chr3D 140787153 140787814 661 True 865.000000 865 90.799000 2825 3464 1 chr3D.!!$R1 639
13 TraesCS3A01G411700 chr3D 570495166 570496372 1206 True 850.000000 850 79.740000 1269 2475 1 chr3D.!!$R4 1206
14 TraesCS3A01G411700 chr3D 570379598 570380768 1170 False 778.000000 778 79.125000 1266 2454 1 chr3D.!!$F2 1188
15 TraesCS3A01G411700 chr3D 570281055 570282224 1169 False 767.000000 767 79.112000 1270 2454 1 chr3D.!!$F1 1184
16 TraesCS3A01G411700 chr3D 523167447 523168141 694 True 765.000000 765 86.906000 2828 3506 1 chr3D.!!$R2 678
17 TraesCS3A01G411700 chr3D 570399916 570400565 649 True 527.000000 527 81.915000 1860 2494 1 chr3D.!!$R3 634
18 TraesCS3A01G411700 chr7A 514864176 514864861 685 False 937.000000 937 91.412000 2825 3506 1 chr7A.!!$F2 681
19 TraesCS3A01G411700 chrUn 21561322 21562022 700 True 920.000000 920 90.870000 2828 3506 1 chrUn.!!$R1 678
20 TraesCS3A01G411700 chr7D 593670915 593671580 665 True 894.000000 894 91.454000 2862 3506 1 chr7D.!!$R1 644
21 TraesCS3A01G411700 chr7D 13469167 13469829 662 False 658.000000 658 84.940000 2834 3482 1 chr7D.!!$F1 648
22 TraesCS3A01G411700 chr5D 396426306 396427016 710 True 872.000000 872 89.592000 2829 3506 1 chr5D.!!$R1 677
23 TraesCS3A01G411700 chr5D 22427039 22427703 664 False 693.000000 693 85.778000 2827 3482 1 chr5D.!!$F1 655
24 TraesCS3A01G411700 chr4D 365218898 365219530 632 True 713.000000 713 87.204000 2829 3453 1 chr4D.!!$R1 624
25 TraesCS3A01G411700 chr7B 522040973 522041666 693 False 697.000000 697 85.180000 2829 3506 1 chr7B.!!$F1 677
26 TraesCS3A01G411700 chr7B 721690012 721690618 606 True 693.000000 693 87.356000 2855 3460 1 chr7B.!!$R1 605

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
344 356 0.107459 GGCAACTCCTCCTAGCTTGG 60.107 60.0 8.03 8.03 0.0 3.61 F
345 357 0.107459 GCAACTCCTCCTAGCTTGGG 60.107 60.0 14.51 6.72 0.0 4.12 F
361 1513 0.251742 TGGGCTGAATTTGTGGAGGG 60.252 55.0 0.00 0.00 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 3471 0.526211 TGTCGTAGCACAGCTCGAAT 59.474 50.000 12.53 0.00 40.44 3.34 R
2433 3738 3.382832 AGCCTGACGAACCCGAGG 61.383 66.667 0.00 0.00 39.50 4.63 R
2580 3888 0.392336 AGCATCCAGTAGCAGCTAGC 59.608 55.000 6.62 6.62 46.19 3.42 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
21 22 4.622701 CAGCCTAAACCAAGCTATCAAC 57.377 45.455 0.00 0.00 34.38 3.18
22 23 3.063997 CAGCCTAAACCAAGCTATCAACG 59.936 47.826 0.00 0.00 34.38 4.10
23 24 3.007635 GCCTAAACCAAGCTATCAACGT 58.992 45.455 0.00 0.00 0.00 3.99
24 25 3.063588 GCCTAAACCAAGCTATCAACGTC 59.936 47.826 0.00 0.00 0.00 4.34
25 26 4.250464 CCTAAACCAAGCTATCAACGTCA 58.750 43.478 0.00 0.00 0.00 4.35
26 27 4.876107 CCTAAACCAAGCTATCAACGTCAT 59.124 41.667 0.00 0.00 0.00 3.06
27 28 5.354234 CCTAAACCAAGCTATCAACGTCATT 59.646 40.000 0.00 0.00 0.00 2.57
28 29 6.537301 CCTAAACCAAGCTATCAACGTCATTA 59.463 38.462 0.00 0.00 0.00 1.90
29 30 7.226720 CCTAAACCAAGCTATCAACGTCATTAT 59.773 37.037 0.00 0.00 0.00 1.28
30 31 9.256477 CTAAACCAAGCTATCAACGTCATTATA 57.744 33.333 0.00 0.00 0.00 0.98
31 32 7.478520 AACCAAGCTATCAACGTCATTATAC 57.521 36.000 0.00 0.00 0.00 1.47
32 33 6.578944 ACCAAGCTATCAACGTCATTATACA 58.421 36.000 0.00 0.00 0.00 2.29
33 34 7.217200 ACCAAGCTATCAACGTCATTATACAT 58.783 34.615 0.00 0.00 0.00 2.29
34 35 7.715249 ACCAAGCTATCAACGTCATTATACATT 59.285 33.333 0.00 0.00 0.00 2.71
35 36 8.559536 CCAAGCTATCAACGTCATTATACATTT 58.440 33.333 0.00 0.00 0.00 2.32
36 37 9.935682 CAAGCTATCAACGTCATTATACATTTT 57.064 29.630 0.00 0.00 0.00 1.82
37 38 9.935682 AAGCTATCAACGTCATTATACATTTTG 57.064 29.630 0.00 0.00 0.00 2.44
38 39 9.325198 AGCTATCAACGTCATTATACATTTTGA 57.675 29.630 0.00 0.00 0.00 2.69
39 40 9.586150 GCTATCAACGTCATTATACATTTTGAG 57.414 33.333 0.00 0.00 0.00 3.02
44 45 9.864034 CAACGTCATTATACATTTTGAGATACC 57.136 33.333 0.00 0.00 0.00 2.73
45 46 8.294341 ACGTCATTATACATTTTGAGATACCG 57.706 34.615 0.00 0.00 0.00 4.02
46 47 8.139350 ACGTCATTATACATTTTGAGATACCGA 58.861 33.333 0.00 0.00 0.00 4.69
47 48 8.639428 CGTCATTATACATTTTGAGATACCGAG 58.361 37.037 0.00 0.00 0.00 4.63
48 49 8.436200 GTCATTATACATTTTGAGATACCGAGC 58.564 37.037 0.00 0.00 0.00 5.03
49 50 8.147704 TCATTATACATTTTGAGATACCGAGCA 58.852 33.333 0.00 0.00 0.00 4.26
50 51 8.939929 CATTATACATTTTGAGATACCGAGCAT 58.060 33.333 0.00 0.00 0.00 3.79
51 52 8.534333 TTATACATTTTGAGATACCGAGCATC 57.466 34.615 0.00 0.00 0.00 3.91
52 53 5.028549 ACATTTTGAGATACCGAGCATCT 57.971 39.130 0.00 0.00 35.43 2.90
53 54 5.053145 ACATTTTGAGATACCGAGCATCTC 58.947 41.667 11.65 11.65 45.76 2.75
57 58 3.829886 GAGATACCGAGCATCTCAGAG 57.170 52.381 12.98 0.00 45.17 3.35
58 59 3.407698 GAGATACCGAGCATCTCAGAGA 58.592 50.000 1.54 1.54 45.17 3.10
59 60 4.009675 GAGATACCGAGCATCTCAGAGAT 58.990 47.826 7.15 7.15 45.17 2.75
60 61 5.172687 AGATACCGAGCATCTCAGAGATA 57.827 43.478 12.88 0.00 32.12 1.98
61 62 4.941263 AGATACCGAGCATCTCAGAGATAC 59.059 45.833 12.88 7.58 32.12 2.24
62 63 2.235016 ACCGAGCATCTCAGAGATACC 58.765 52.381 12.88 7.29 32.12 2.73
63 64 1.198867 CCGAGCATCTCAGAGATACCG 59.801 57.143 12.88 14.70 32.12 4.02
64 65 2.147150 CGAGCATCTCAGAGATACCGA 58.853 52.381 12.88 0.00 32.12 4.69
65 66 2.159430 CGAGCATCTCAGAGATACCGAG 59.841 54.545 12.88 1.66 32.12 4.63
66 67 3.146066 GAGCATCTCAGAGATACCGAGT 58.854 50.000 12.88 0.00 32.12 4.18
67 68 3.146066 AGCATCTCAGAGATACCGAGTC 58.854 50.000 12.88 0.00 32.12 3.36
68 69 2.095969 GCATCTCAGAGATACCGAGTCG 60.096 54.545 12.88 5.29 32.12 4.18
69 70 2.482336 CATCTCAGAGATACCGAGTCGG 59.518 54.545 29.80 29.80 42.40 4.79
70 71 5.201701 CATCTCAGAGATACCGAGTCGGC 62.202 56.522 31.22 15.31 41.18 5.54
78 79 2.047274 CCGAGTCGGCACACCATT 60.047 61.111 20.50 0.00 41.17 3.16
79 80 1.671054 CCGAGTCGGCACACCATTT 60.671 57.895 20.50 0.00 41.17 2.32
80 81 1.234615 CCGAGTCGGCACACCATTTT 61.235 55.000 20.50 0.00 41.17 1.82
81 82 1.434555 CGAGTCGGCACACCATTTTA 58.565 50.000 4.10 0.00 34.57 1.52
82 83 1.801771 CGAGTCGGCACACCATTTTAA 59.198 47.619 4.10 0.00 34.57 1.52
83 84 2.159707 CGAGTCGGCACACCATTTTAAG 60.160 50.000 4.10 0.00 34.57 1.85
84 85 3.071479 GAGTCGGCACACCATTTTAAGA 58.929 45.455 0.00 0.00 34.57 2.10
85 86 3.074412 AGTCGGCACACCATTTTAAGAG 58.926 45.455 0.00 0.00 34.57 2.85
86 87 2.812011 GTCGGCACACCATTTTAAGAGT 59.188 45.455 0.00 0.00 34.57 3.24
87 88 2.811431 TCGGCACACCATTTTAAGAGTG 59.189 45.455 0.00 0.00 34.57 3.51
88 89 2.811431 CGGCACACCATTTTAAGAGTGA 59.189 45.455 0.00 0.00 34.57 3.41
89 90 3.440173 CGGCACACCATTTTAAGAGTGAT 59.560 43.478 0.00 0.00 34.57 3.06
90 91 4.672542 CGGCACACCATTTTAAGAGTGATG 60.673 45.833 0.00 0.00 34.57 3.07
91 92 4.458989 GGCACACCATTTTAAGAGTGATGA 59.541 41.667 0.00 0.00 35.26 2.92
92 93 5.048083 GGCACACCATTTTAAGAGTGATGAA 60.048 40.000 0.00 0.00 35.26 2.57
93 94 6.088824 GCACACCATTTTAAGAGTGATGAAG 58.911 40.000 0.00 0.00 34.33 3.02
94 95 6.294176 GCACACCATTTTAAGAGTGATGAAGT 60.294 38.462 0.00 0.00 34.33 3.01
95 96 7.301054 CACACCATTTTAAGAGTGATGAAGTC 58.699 38.462 0.00 0.00 34.33 3.01
96 97 6.998074 ACACCATTTTAAGAGTGATGAAGTCA 59.002 34.615 0.00 0.00 34.33 3.41
97 98 7.667219 ACACCATTTTAAGAGTGATGAAGTCAT 59.333 33.333 0.00 0.00 39.48 3.06
106 107 2.772739 ATGAAGTCATCACAGCCGC 58.227 52.632 0.00 0.00 41.93 6.53
107 108 0.745845 ATGAAGTCATCACAGCCGCC 60.746 55.000 0.00 0.00 41.93 6.13
108 109 1.078848 GAAGTCATCACAGCCGCCT 60.079 57.895 0.00 0.00 0.00 5.52
109 110 1.078848 AAGTCATCACAGCCGCCTC 60.079 57.895 0.00 0.00 0.00 4.70
110 111 2.842394 AAGTCATCACAGCCGCCTCG 62.842 60.000 0.00 0.00 0.00 4.63
111 112 3.381983 TCATCACAGCCGCCTCGT 61.382 61.111 0.00 0.00 0.00 4.18
112 113 3.190849 CATCACAGCCGCCTCGTG 61.191 66.667 0.00 0.00 0.00 4.35
113 114 4.457496 ATCACAGCCGCCTCGTGG 62.457 66.667 0.00 0.00 36.10 4.94
124 125 4.742201 CTCGTGGTCGGTGGGCAG 62.742 72.222 0.00 0.00 37.69 4.85
126 127 4.308458 CGTGGTCGGTGGGCAGAA 62.308 66.667 0.00 0.00 0.00 3.02
127 128 2.112297 GTGGTCGGTGGGCAGAAA 59.888 61.111 0.00 0.00 0.00 2.52
128 129 1.303317 GTGGTCGGTGGGCAGAAAT 60.303 57.895 0.00 0.00 0.00 2.17
129 130 1.303236 TGGTCGGTGGGCAGAAATG 60.303 57.895 0.00 0.00 0.00 2.32
130 131 2.700773 GGTCGGTGGGCAGAAATGC 61.701 63.158 0.00 0.00 0.00 3.56
172 174 1.507140 TGACTTGAACCTGGTGGACT 58.493 50.000 0.00 0.00 37.04 3.85
199 211 3.947834 CCCACAATGAACCTAACCATCTC 59.052 47.826 0.00 0.00 0.00 2.75
339 351 1.950909 CTACTCGGCAACTCCTCCTAG 59.049 57.143 0.00 0.00 0.00 3.02
340 352 1.324005 ACTCGGCAACTCCTCCTAGC 61.324 60.000 0.00 0.00 0.00 3.42
341 353 1.000486 TCGGCAACTCCTCCTAGCT 60.000 57.895 0.00 0.00 0.00 3.32
342 354 0.614979 TCGGCAACTCCTCCTAGCTT 60.615 55.000 0.00 0.00 0.00 3.74
344 356 0.107459 GGCAACTCCTCCTAGCTTGG 60.107 60.000 8.03 8.03 0.00 3.61
345 357 0.107459 GCAACTCCTCCTAGCTTGGG 60.107 60.000 14.51 6.72 0.00 4.12
346 358 0.107459 CAACTCCTCCTAGCTTGGGC 60.107 60.000 14.51 0.00 39.06 5.36
358 1510 0.968405 GCTTGGGCTGAATTTGTGGA 59.032 50.000 0.00 0.00 35.22 4.02
359 1511 1.067354 GCTTGGGCTGAATTTGTGGAG 60.067 52.381 0.00 0.00 35.22 3.86
360 1512 1.547372 CTTGGGCTGAATTTGTGGAGG 59.453 52.381 0.00 0.00 0.00 4.30
361 1513 0.251742 TGGGCTGAATTTGTGGAGGG 60.252 55.000 0.00 0.00 0.00 4.30
363 1515 1.607801 GGCTGAATTTGTGGAGGGGC 61.608 60.000 0.00 0.00 0.00 5.80
365 1517 1.631405 CTGAATTTGTGGAGGGGCAA 58.369 50.000 0.00 0.00 0.00 4.52
370 1522 0.835543 TTTGTGGAGGGGCAAATGGG 60.836 55.000 0.00 0.00 30.68 4.00
371 1523 3.076916 GTGGAGGGGCAAATGGGC 61.077 66.667 0.00 0.00 42.44 5.36
372 1524 3.275271 TGGAGGGGCAAATGGGCT 61.275 61.111 0.00 0.00 42.84 5.19
373 1525 2.761213 GGAGGGGCAAATGGGCTG 60.761 66.667 0.00 0.00 42.84 4.85
378 1530 2.761213 GGCAAATGGGCTGGAGGG 60.761 66.667 0.00 0.00 39.42 4.30
383 1535 2.399600 AAATGGGCTGGAGGGGCAAA 62.400 55.000 0.00 0.00 0.00 3.68
384 1536 2.399600 AATGGGCTGGAGGGGCAAAA 62.400 55.000 0.00 0.00 0.00 2.44
385 1537 2.203773 GGGCTGGAGGGGCAAAAA 60.204 61.111 0.00 0.00 0.00 1.94
410 1562 8.601845 AAACATAACTTTGGGCTGATTTTAAC 57.398 30.769 0.00 0.00 0.00 2.01
411 1563 7.539034 ACATAACTTTGGGCTGATTTTAACT 57.461 32.000 0.00 0.00 0.00 2.24
412 1564 7.378181 ACATAACTTTGGGCTGATTTTAACTG 58.622 34.615 0.00 0.00 0.00 3.16
413 1565 4.871933 ACTTTGGGCTGATTTTAACTGG 57.128 40.909 0.00 0.00 0.00 4.00
414 1566 4.479158 ACTTTGGGCTGATTTTAACTGGA 58.521 39.130 0.00 0.00 0.00 3.86
415 1567 4.280929 ACTTTGGGCTGATTTTAACTGGAC 59.719 41.667 0.00 0.00 0.00 4.02
416 1568 3.517296 TGGGCTGATTTTAACTGGACA 57.483 42.857 0.00 0.00 0.00 4.02
417 1569 4.046286 TGGGCTGATTTTAACTGGACAT 57.954 40.909 0.00 0.00 0.00 3.06
421 1573 5.010012 GGGCTGATTTTAACTGGACATATGG 59.990 44.000 7.80 0.00 0.00 2.74
422 1574 5.010012 GGCTGATTTTAACTGGACATATGGG 59.990 44.000 7.80 0.00 0.00 4.00
423 1575 5.507985 GCTGATTTTAACTGGACATATGGGC 60.508 44.000 7.80 0.00 0.00 5.36
425 1577 5.593909 TGATTTTAACTGGACATATGGGCTG 59.406 40.000 7.80 0.00 0.00 4.85
426 1578 4.853468 TTTAACTGGACATATGGGCTGA 57.147 40.909 7.80 0.00 0.00 4.26
427 1579 4.853468 TTAACTGGACATATGGGCTGAA 57.147 40.909 7.80 0.00 0.00 3.02
429 1581 6.508030 TTAACTGGACATATGGGCTGAATA 57.492 37.500 7.80 0.00 0.00 1.75
430 1582 4.357918 ACTGGACATATGGGCTGAATAC 57.642 45.455 7.80 0.00 0.00 1.89
432 1584 5.155161 ACTGGACATATGGGCTGAATACTA 58.845 41.667 7.80 0.00 0.00 1.82
433 1585 5.247110 ACTGGACATATGGGCTGAATACTAG 59.753 44.000 7.80 0.00 0.00 2.57
434 1586 4.532126 TGGACATATGGGCTGAATACTAGG 59.468 45.833 7.80 0.00 0.00 3.02
435 1587 4.080863 GGACATATGGGCTGAATACTAGGG 60.081 50.000 7.80 0.00 0.00 3.53
436 1588 3.846588 ACATATGGGCTGAATACTAGGGG 59.153 47.826 7.80 0.00 0.00 4.79
437 1589 2.815357 ATGGGCTGAATACTAGGGGA 57.185 50.000 0.00 0.00 0.00 4.81
993 2145 1.696336 CCACAGGGATGGACAGATAGG 59.304 57.143 0.00 0.00 43.02 2.57
1038 2211 1.232621 ATCGATCACGCCCATGCATG 61.233 55.000 20.19 20.19 39.58 4.06
1111 2297 1.742761 TAACTACTCCTCACCGTCGG 58.257 55.000 10.48 10.48 0.00 4.79
1157 2359 0.667993 CGAGAGATCTCACCTCCAGC 59.332 60.000 24.39 2.86 43.00 4.85
1163 2365 0.980231 ATCTCACCTCCAGCCTCCAC 60.980 60.000 0.00 0.00 0.00 4.02
1164 2366 1.915266 CTCACCTCCAGCCTCCACA 60.915 63.158 0.00 0.00 0.00 4.17
1214 2437 2.659291 GCAAGTCGCAAGTTACAGTTCG 60.659 50.000 0.00 0.00 41.79 3.95
1245 2499 1.675641 CCCTGCGAACCCAGAAAGG 60.676 63.158 0.00 0.00 34.77 3.11
1255 2509 1.005215 ACCCAGAAAGGAAGATGGCAG 59.995 52.381 0.00 0.00 41.22 4.85
1256 2510 1.101331 CCAGAAAGGAAGATGGCAGC 58.899 55.000 0.00 0.00 41.22 5.25
1257 2511 1.615116 CCAGAAAGGAAGATGGCAGCA 60.615 52.381 5.19 0.00 41.22 4.41
1389 2664 3.771160 CCCTTCCACTACGGCGCT 61.771 66.667 6.90 0.00 33.14 5.92
1504 2779 4.243008 TCGCCAACGCCTTCCACA 62.243 61.111 0.00 0.00 39.84 4.17
1569 2850 3.075005 AGGACCTGCACCGCGTAT 61.075 61.111 4.92 0.00 0.00 3.06
1984 3265 2.277373 CGCACTACGTCTCGCTCC 60.277 66.667 0.00 0.00 36.87 4.70
2494 3802 3.636300 CCACTTCAATTTCACCAAGACCA 59.364 43.478 0.00 0.00 0.00 4.02
2495 3803 4.499696 CCACTTCAATTTCACCAAGACCAC 60.500 45.833 0.00 0.00 0.00 4.16
2496 3804 3.636764 ACTTCAATTTCACCAAGACCACC 59.363 43.478 0.00 0.00 0.00 4.61
2567 3875 8.927675 AAATATGTACCTCCTCTACTCTACTG 57.072 38.462 0.00 0.00 0.00 2.74
2570 3878 5.743117 TGTACCTCCTCTACTCTACTGAAC 58.257 45.833 0.00 0.00 0.00 3.18
2571 3879 5.488203 TGTACCTCCTCTACTCTACTGAACT 59.512 44.000 0.00 0.00 0.00 3.01
2572 3880 6.671340 TGTACCTCCTCTACTCTACTGAACTA 59.329 42.308 0.00 0.00 0.00 2.24
2573 3881 6.639590 ACCTCCTCTACTCTACTGAACTAA 57.360 41.667 0.00 0.00 0.00 2.24
2574 3882 6.655930 ACCTCCTCTACTCTACTGAACTAAG 58.344 44.000 0.00 0.00 0.00 2.18
2575 3883 5.529800 CCTCCTCTACTCTACTGAACTAAGC 59.470 48.000 0.00 0.00 0.00 3.09
2576 3884 6.063496 TCCTCTACTCTACTGAACTAAGCA 57.937 41.667 0.00 0.00 0.00 3.91
2577 3885 5.881443 TCCTCTACTCTACTGAACTAAGCAC 59.119 44.000 0.00 0.00 0.00 4.40
2578 3886 5.883673 CCTCTACTCTACTGAACTAAGCACT 59.116 44.000 0.00 0.00 0.00 4.40
2579 3887 7.049133 CCTCTACTCTACTGAACTAAGCACTA 58.951 42.308 0.00 0.00 0.00 2.74
2580 3888 7.225931 CCTCTACTCTACTGAACTAAGCACTAG 59.774 44.444 0.00 0.00 0.00 2.57
2581 3889 5.570234 ACTCTACTGAACTAAGCACTAGC 57.430 43.478 0.00 0.00 42.56 3.42
2606 3914 4.133078 GCTGCTACTGGATGCTAAGAATT 58.867 43.478 0.00 0.00 0.00 2.17
2607 3915 5.070981 AGCTGCTACTGGATGCTAAGAATTA 59.929 40.000 0.00 0.00 31.71 1.40
2608 3916 5.760253 GCTGCTACTGGATGCTAAGAATTAA 59.240 40.000 0.00 0.00 0.00 1.40
2609 3917 6.429385 GCTGCTACTGGATGCTAAGAATTAAT 59.571 38.462 0.00 0.00 0.00 1.40
2628 3936 1.164411 TGTTGTTGATCATGGCGGTC 58.836 50.000 0.00 0.00 0.00 4.79
2647 3955 2.180017 CCAGCAGCGGCATTTGTC 59.820 61.111 12.44 0.00 44.61 3.18
2648 3956 2.628696 CCAGCAGCGGCATTTGTCA 61.629 57.895 12.44 0.00 44.61 3.58
2649 3957 1.443194 CAGCAGCGGCATTTGTCAC 60.443 57.895 12.44 0.00 44.61 3.67
2650 3958 2.502510 GCAGCGGCATTTGTCACG 60.503 61.111 3.18 0.00 40.72 4.35
2655 3963 2.642700 GGCATTTGTCACGCCGTT 59.357 55.556 0.00 0.00 35.79 4.44
2656 3964 1.442017 GGCATTTGTCACGCCGTTC 60.442 57.895 0.00 0.00 35.79 3.95
2657 3965 1.442017 GCATTTGTCACGCCGTTCC 60.442 57.895 0.00 0.00 0.00 3.62
2658 3966 1.945522 CATTTGTCACGCCGTTCCA 59.054 52.632 0.00 0.00 0.00 3.53
2659 3967 0.521291 CATTTGTCACGCCGTTCCAT 59.479 50.000 0.00 0.00 0.00 3.41
2660 3968 0.802494 ATTTGTCACGCCGTTCCATC 59.198 50.000 0.00 0.00 0.00 3.51
2661 3969 0.250124 TTTGTCACGCCGTTCCATCT 60.250 50.000 0.00 0.00 0.00 2.90
2662 3970 0.669318 TTGTCACGCCGTTCCATCTC 60.669 55.000 0.00 0.00 0.00 2.75
2663 3971 1.080093 GTCACGCCGTTCCATCTCA 60.080 57.895 0.00 0.00 0.00 3.27
2664 3972 0.460284 GTCACGCCGTTCCATCTCAT 60.460 55.000 0.00 0.00 0.00 2.90
2665 3973 0.179111 TCACGCCGTTCCATCTCATC 60.179 55.000 0.00 0.00 0.00 2.92
2666 3974 0.179100 CACGCCGTTCCATCTCATCT 60.179 55.000 0.00 0.00 0.00 2.90
2667 3975 0.537188 ACGCCGTTCCATCTCATCTT 59.463 50.000 0.00 0.00 0.00 2.40
2668 3976 0.933097 CGCCGTTCCATCTCATCTTG 59.067 55.000 0.00 0.00 0.00 3.02
2669 3977 0.659957 GCCGTTCCATCTCATCTTGC 59.340 55.000 0.00 0.00 0.00 4.01
2670 3978 2.013563 GCCGTTCCATCTCATCTTGCA 61.014 52.381 0.00 0.00 0.00 4.08
2718 4026 6.595326 TGTGTGATATGGATTCAGAGTTTCAC 59.405 38.462 0.00 0.00 33.37 3.18
2743 4051 3.817084 TCAGAGCAAAACCATTCACTCTG 59.183 43.478 10.76 10.76 43.31 3.35
2745 4053 1.267806 AGCAAAACCATTCACTCTGCG 59.732 47.619 0.00 0.00 33.61 5.18
2760 4068 3.238441 CTCTGCGAGACAAGAAGTACAC 58.762 50.000 0.00 0.00 0.00 2.90
2777 4085 3.870606 CGGGTTGGCACGTTAGAG 58.129 61.111 0.00 0.00 36.64 2.43
2778 4086 2.388232 CGGGTTGGCACGTTAGAGC 61.388 63.158 0.00 0.00 36.64 4.09
2779 4087 1.302192 GGGTTGGCACGTTAGAGCA 60.302 57.895 0.00 0.00 35.61 4.26
2780 4088 0.887387 GGGTTGGCACGTTAGAGCAA 60.887 55.000 0.00 0.00 35.61 3.91
2781 4089 0.237498 GGTTGGCACGTTAGAGCAAC 59.763 55.000 0.00 0.00 35.61 4.17
2782 4090 1.226746 GTTGGCACGTTAGAGCAACT 58.773 50.000 0.00 0.00 35.61 3.16
2783 4091 1.194772 GTTGGCACGTTAGAGCAACTC 59.805 52.381 0.00 0.00 35.61 3.01
2784 4092 0.320421 TGGCACGTTAGAGCAACTCC 60.320 55.000 0.00 0.00 35.61 3.85
2785 4093 0.320421 GGCACGTTAGAGCAACTCCA 60.320 55.000 0.00 0.00 35.61 3.86
2786 4094 1.508632 GCACGTTAGAGCAACTCCAA 58.491 50.000 0.00 0.00 34.77 3.53
2787 4095 2.076863 GCACGTTAGAGCAACTCCAAT 58.923 47.619 0.00 0.00 34.77 3.16
2788 4096 2.159653 GCACGTTAGAGCAACTCCAATG 60.160 50.000 0.00 0.00 34.77 2.82
2789 4097 3.325870 CACGTTAGAGCAACTCCAATGA 58.674 45.455 2.65 0.00 34.77 2.57
2790 4098 3.369147 CACGTTAGAGCAACTCCAATGAG 59.631 47.826 2.65 0.00 44.62 2.90
2791 4099 2.932614 CGTTAGAGCAACTCCAATGAGG 59.067 50.000 0.00 0.00 43.29 3.86
2792 4100 2.680339 GTTAGAGCAACTCCAATGAGGC 59.320 50.000 0.00 0.00 43.29 4.70
2793 4101 0.392193 AGAGCAACTCCAATGAGGCG 60.392 55.000 0.00 0.00 43.29 5.52
2794 4102 0.391661 GAGCAACTCCAATGAGGCGA 60.392 55.000 0.00 0.00 43.29 5.54
2795 4103 0.254178 AGCAACTCCAATGAGGCGAT 59.746 50.000 0.00 0.00 43.29 4.58
2796 4104 0.659957 GCAACTCCAATGAGGCGATC 59.340 55.000 0.00 0.00 43.29 3.69
2797 4105 1.303309 CAACTCCAATGAGGCGATCC 58.697 55.000 0.00 0.00 43.29 3.36
2798 4106 0.911769 AACTCCAATGAGGCGATCCA 59.088 50.000 0.00 0.00 43.29 3.41
2799 4107 1.135094 ACTCCAATGAGGCGATCCAT 58.865 50.000 0.00 0.00 43.29 3.41
2800 4108 1.492176 ACTCCAATGAGGCGATCCATT 59.508 47.619 0.00 0.00 43.29 3.16
2801 4109 2.092212 ACTCCAATGAGGCGATCCATTT 60.092 45.455 0.00 0.00 43.29 2.32
2802 4110 2.551459 CTCCAATGAGGCGATCCATTTC 59.449 50.000 0.00 0.00 37.29 2.17
2803 4111 2.092484 TCCAATGAGGCGATCCATTTCA 60.092 45.455 0.00 0.00 37.29 2.69
2804 4112 2.889045 CCAATGAGGCGATCCATTTCAT 59.111 45.455 0.00 0.00 31.25 2.57
2805 4113 3.057736 CCAATGAGGCGATCCATTTCATC 60.058 47.826 0.00 0.00 31.25 2.92
2806 4114 2.260844 TGAGGCGATCCATTTCATCC 57.739 50.000 0.00 0.00 33.74 3.51
2807 4115 1.151668 GAGGCGATCCATTTCATCCG 58.848 55.000 0.00 0.00 33.74 4.18
2808 4116 0.886490 AGGCGATCCATTTCATCCGC 60.886 55.000 0.00 0.00 33.74 5.54
2809 4117 1.205064 GCGATCCATTTCATCCGCG 59.795 57.895 0.00 0.00 0.00 6.46
2810 4118 1.862123 CGATCCATTTCATCCGCGG 59.138 57.895 22.12 22.12 0.00 6.46
2811 4119 1.576421 GATCCATTTCATCCGCGGC 59.424 57.895 23.51 0.00 0.00 6.53
2812 4120 1.856265 GATCCATTTCATCCGCGGCC 61.856 60.000 23.51 0.00 0.00 6.13
2813 4121 3.952675 CCATTTCATCCGCGGCCG 61.953 66.667 24.05 24.05 0.00 6.13
2814 4122 3.202001 CATTTCATCCGCGGCCGT 61.202 61.111 28.70 2.82 0.00 5.68
2815 4123 2.437716 ATTTCATCCGCGGCCGTT 60.438 55.556 28.70 6.61 0.00 4.44
2816 4124 2.469516 ATTTCATCCGCGGCCGTTC 61.470 57.895 28.70 10.21 0.00 3.95
2821 4129 3.646023 ATCCGCGGCCGTTCGTTTA 62.646 57.895 28.70 10.43 0.00 2.01
2822 4130 3.845472 CCGCGGCCGTTCGTTTAG 61.845 66.667 28.70 5.89 0.00 1.85
2823 4131 3.845472 CGCGGCCGTTCGTTTAGG 61.845 66.667 28.70 1.07 0.00 2.69
2824 4132 2.739671 GCGGCCGTTCGTTTAGGT 60.740 61.111 28.70 0.00 0.00 3.08
2825 4133 2.733671 GCGGCCGTTCGTTTAGGTC 61.734 63.158 28.70 0.32 0.00 3.85
2826 4134 2.438954 CGGCCGTTCGTTTAGGTCG 61.439 63.158 19.50 0.00 46.78 4.79
2838 4146 7.043192 CGTTCGTTTAGGTCGTAAAATGGATAT 60.043 37.037 0.00 0.00 32.22 1.63
3071 4383 3.522731 CCTCGCGTCCCTCTCCAG 61.523 72.222 5.77 0.00 0.00 3.86
3075 4387 2.442272 GCGTCCCTCTCCAGCCTA 60.442 66.667 0.00 0.00 0.00 3.93
3104 4416 1.374343 TAGAACTGGCGCTCGTCGAT 61.374 55.000 7.64 0.00 41.67 3.59
3112 4424 1.064134 CGCTCGTCGATGATGTCCA 59.936 57.895 7.99 0.00 41.67 4.02
3141 4453 0.458889 GTTCGCGCTACACCACCATA 60.459 55.000 5.56 0.00 0.00 2.74
3165 4477 1.652563 CACGTCCATCTCGGCGATA 59.347 57.895 11.27 2.89 37.61 2.92
3188 4500 4.752879 GTAACGCTGCCGCCTCCA 62.753 66.667 0.00 0.00 38.22 3.86
3386 4747 1.874345 GAGGAGAAGGCGTCGGAACA 61.874 60.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.063997 CGTTGATAGCTTGGTTTAGGCTG 59.936 47.826 0.00 0.00 42.36 4.85
4 5 6.422776 AATGACGTTGATAGCTTGGTTTAG 57.577 37.500 0.00 0.00 0.00 1.85
6 7 7.551262 TGTATAATGACGTTGATAGCTTGGTTT 59.449 33.333 0.00 0.00 0.00 3.27
7 8 7.045416 TGTATAATGACGTTGATAGCTTGGTT 58.955 34.615 0.00 0.00 0.00 3.67
8 9 6.578944 TGTATAATGACGTTGATAGCTTGGT 58.421 36.000 0.00 0.00 0.00 3.67
9 10 7.658179 ATGTATAATGACGTTGATAGCTTGG 57.342 36.000 0.00 0.00 0.00 3.61
10 11 9.935682 AAAATGTATAATGACGTTGATAGCTTG 57.064 29.630 0.00 0.00 0.00 4.01
11 12 9.935682 CAAAATGTATAATGACGTTGATAGCTT 57.064 29.630 0.00 0.00 0.00 3.74
12 13 9.325198 TCAAAATGTATAATGACGTTGATAGCT 57.675 29.630 0.00 0.00 0.00 3.32
13 14 9.586150 CTCAAAATGTATAATGACGTTGATAGC 57.414 33.333 0.00 0.00 0.00 2.97
18 19 9.864034 GGTATCTCAAAATGTATAATGACGTTG 57.136 33.333 0.00 0.00 0.00 4.10
19 20 8.761497 CGGTATCTCAAAATGTATAATGACGTT 58.239 33.333 0.00 0.00 0.00 3.99
20 21 8.139350 TCGGTATCTCAAAATGTATAATGACGT 58.861 33.333 0.00 0.00 0.00 4.34
21 22 8.515473 TCGGTATCTCAAAATGTATAATGACG 57.485 34.615 0.00 0.00 0.00 4.35
22 23 8.436200 GCTCGGTATCTCAAAATGTATAATGAC 58.564 37.037 0.00 0.00 0.00 3.06
23 24 8.147704 TGCTCGGTATCTCAAAATGTATAATGA 58.852 33.333 0.00 0.00 0.00 2.57
24 25 8.310406 TGCTCGGTATCTCAAAATGTATAATG 57.690 34.615 0.00 0.00 0.00 1.90
25 26 9.155975 GATGCTCGGTATCTCAAAATGTATAAT 57.844 33.333 0.00 0.00 0.00 1.28
26 27 8.367911 AGATGCTCGGTATCTCAAAATGTATAA 58.632 33.333 0.00 0.00 29.39 0.98
27 28 7.896811 AGATGCTCGGTATCTCAAAATGTATA 58.103 34.615 0.00 0.00 29.39 1.47
28 29 6.763355 AGATGCTCGGTATCTCAAAATGTAT 58.237 36.000 0.00 0.00 29.39 2.29
29 30 6.161855 AGATGCTCGGTATCTCAAAATGTA 57.838 37.500 0.00 0.00 29.39 2.29
30 31 5.028549 AGATGCTCGGTATCTCAAAATGT 57.971 39.130 0.00 0.00 29.39 2.71
31 32 5.588568 GAGATGCTCGGTATCTCAAAATG 57.411 43.478 19.48 0.00 46.16 2.32
37 38 3.407698 TCTCTGAGATGCTCGGTATCTC 58.592 50.000 18.35 18.35 46.74 2.75
38 39 3.500448 TCTCTGAGATGCTCGGTATCT 57.500 47.619 2.58 4.62 37.68 1.98
39 40 4.095782 GGTATCTCTGAGATGCTCGGTATC 59.904 50.000 27.29 11.29 37.47 2.24
40 41 4.013728 GGTATCTCTGAGATGCTCGGTAT 58.986 47.826 27.29 6.34 37.47 2.73
41 42 3.413327 GGTATCTCTGAGATGCTCGGTA 58.587 50.000 27.29 7.62 37.47 4.02
42 43 2.235016 GGTATCTCTGAGATGCTCGGT 58.765 52.381 27.29 7.62 37.47 4.69
43 44 1.198867 CGGTATCTCTGAGATGCTCGG 59.801 57.143 27.29 16.80 37.47 4.63
44 45 2.147150 TCGGTATCTCTGAGATGCTCG 58.853 52.381 27.29 26.18 37.47 5.03
62 63 1.434555 TAAAATGGTGTGCCGACTCG 58.565 50.000 0.00 0.00 37.67 4.18
63 64 3.071479 TCTTAAAATGGTGTGCCGACTC 58.929 45.455 0.00 0.00 37.67 3.36
64 65 3.074412 CTCTTAAAATGGTGTGCCGACT 58.926 45.455 0.00 0.00 37.67 4.18
65 66 2.812011 ACTCTTAAAATGGTGTGCCGAC 59.188 45.455 0.00 0.00 37.67 4.79
66 67 2.811431 CACTCTTAAAATGGTGTGCCGA 59.189 45.455 0.00 0.00 37.67 5.54
67 68 2.811431 TCACTCTTAAAATGGTGTGCCG 59.189 45.455 0.00 0.00 37.67 5.69
68 69 4.458989 TCATCACTCTTAAAATGGTGTGCC 59.541 41.667 0.00 0.00 0.00 5.01
69 70 5.627499 TCATCACTCTTAAAATGGTGTGC 57.373 39.130 0.00 0.00 0.00 4.57
70 71 7.041167 TGACTTCATCACTCTTAAAATGGTGTG 60.041 37.037 0.00 0.00 29.99 3.82
71 72 6.998074 TGACTTCATCACTCTTAAAATGGTGT 59.002 34.615 0.00 0.00 29.99 4.16
72 73 7.439157 TGACTTCATCACTCTTAAAATGGTG 57.561 36.000 0.00 0.00 29.99 4.17
88 89 0.745845 GGCGGCTGTGATGACTTCAT 60.746 55.000 0.00 0.00 36.54 2.57
89 90 1.375908 GGCGGCTGTGATGACTTCA 60.376 57.895 0.00 0.00 0.00 3.02
90 91 1.078848 AGGCGGCTGTGATGACTTC 60.079 57.895 12.25 0.00 0.00 3.01
91 92 1.078848 GAGGCGGCTGTGATGACTT 60.079 57.895 19.63 0.00 0.00 3.01
92 93 2.581354 GAGGCGGCTGTGATGACT 59.419 61.111 19.63 0.00 0.00 3.41
93 94 2.887568 CGAGGCGGCTGTGATGAC 60.888 66.667 19.63 0.00 0.00 3.06
94 95 3.381983 ACGAGGCGGCTGTGATGA 61.382 61.111 19.63 0.00 0.00 2.92
95 96 3.190849 CACGAGGCGGCTGTGATG 61.191 66.667 26.20 12.86 35.66 3.07
96 97 4.457496 CCACGAGGCGGCTGTGAT 62.457 66.667 29.54 5.35 35.66 3.06
107 108 4.742201 CTGCCCACCGACCACGAG 62.742 72.222 0.00 0.00 42.66 4.18
109 110 3.818121 TTTCTGCCCACCGACCACG 62.818 63.158 0.00 0.00 39.43 4.94
110 111 1.303317 ATTTCTGCCCACCGACCAC 60.303 57.895 0.00 0.00 0.00 4.16
111 112 1.303236 CATTTCTGCCCACCGACCA 60.303 57.895 0.00 0.00 0.00 4.02
112 113 2.700773 GCATTTCTGCCCACCGACC 61.701 63.158 0.00 0.00 42.88 4.79
113 114 2.877691 GCATTTCTGCCCACCGAC 59.122 61.111 0.00 0.00 42.88 4.79
114 115 2.745884 CGCATTTCTGCCCACCGA 60.746 61.111 0.00 0.00 46.07 4.69
115 116 4.481112 GCGCATTTCTGCCCACCG 62.481 66.667 0.30 0.00 46.07 4.94
116 117 2.824071 CTTGCGCATTTCTGCCCACC 62.824 60.000 12.75 0.00 46.07 4.61
117 118 1.444895 CTTGCGCATTTCTGCCCAC 60.445 57.895 12.75 0.00 46.07 4.61
118 119 2.964174 CTTGCGCATTTCTGCCCA 59.036 55.556 12.75 0.00 46.07 5.36
119 120 2.507769 GCTTGCGCATTTCTGCCC 60.508 61.111 12.75 0.00 46.07 5.36
120 121 1.804326 CTGCTTGCGCATTTCTGCC 60.804 57.895 12.75 0.00 46.74 4.85
121 122 2.442188 GCTGCTTGCGCATTTCTGC 61.442 57.895 12.75 14.78 46.74 4.26
122 123 1.071019 CTGCTGCTTGCGCATTTCTG 61.071 55.000 12.75 8.66 46.74 3.02
123 124 1.211969 CTGCTGCTTGCGCATTTCT 59.788 52.632 12.75 0.00 46.74 2.52
124 125 2.442188 GCTGCTGCTTGCGCATTTC 61.442 57.895 12.75 3.76 46.74 2.17
125 126 2.431942 GCTGCTGCTTGCGCATTT 60.432 55.556 12.75 0.00 46.74 2.32
126 127 4.771356 CGCTGCTGCTTGCGCATT 62.771 61.111 22.06 0.00 46.74 3.56
192 196 3.191078 GCTGAATGTAGCTGAGATGGT 57.809 47.619 0.00 0.00 40.52 3.55
235 247 8.670922 TTCACACCTTGATTGGCAACTTATGC 62.671 42.308 0.00 0.00 43.90 3.14
339 351 0.968405 TCCACAAATTCAGCCCAAGC 59.032 50.000 0.00 0.00 40.32 4.01
340 352 1.547372 CCTCCACAAATTCAGCCCAAG 59.453 52.381 0.00 0.00 0.00 3.61
341 353 1.631405 CCTCCACAAATTCAGCCCAA 58.369 50.000 0.00 0.00 0.00 4.12
342 354 0.251742 CCCTCCACAAATTCAGCCCA 60.252 55.000 0.00 0.00 0.00 5.36
344 356 1.607801 GCCCCTCCACAAATTCAGCC 61.608 60.000 0.00 0.00 0.00 4.85
345 357 0.899717 TGCCCCTCCACAAATTCAGC 60.900 55.000 0.00 0.00 0.00 4.26
346 358 1.631405 TTGCCCCTCCACAAATTCAG 58.369 50.000 0.00 0.00 0.00 3.02
347 359 2.094100 TTTGCCCCTCCACAAATTCA 57.906 45.000 0.00 0.00 31.09 2.57
348 360 2.355007 CCATTTGCCCCTCCACAAATTC 60.355 50.000 0.00 0.00 42.34 2.17
351 363 0.835543 CCCATTTGCCCCTCCACAAA 60.836 55.000 0.00 0.00 39.87 2.83
358 1510 3.275271 TCCAGCCCATTTGCCCCT 61.275 61.111 0.00 0.00 0.00 4.79
359 1511 2.761213 CTCCAGCCCATTTGCCCC 60.761 66.667 0.00 0.00 0.00 5.80
360 1512 2.761213 CCTCCAGCCCATTTGCCC 60.761 66.667 0.00 0.00 0.00 5.36
361 1513 2.761213 CCCTCCAGCCCATTTGCC 60.761 66.667 0.00 0.00 0.00 4.52
363 1515 2.761213 GCCCCTCCAGCCCATTTG 60.761 66.667 0.00 0.00 0.00 2.32
365 1517 2.399600 TTTTGCCCCTCCAGCCCATT 62.400 55.000 0.00 0.00 0.00 3.16
383 1535 9.620259 TTAAAATCAGCCCAAAGTTATGTTTTT 57.380 25.926 0.00 0.00 31.42 1.94
384 1536 9.051679 GTTAAAATCAGCCCAAAGTTATGTTTT 57.948 29.630 0.00 0.00 0.00 2.43
385 1537 8.428852 AGTTAAAATCAGCCCAAAGTTATGTTT 58.571 29.630 0.00 0.00 0.00 2.83
386 1538 7.872483 CAGTTAAAATCAGCCCAAAGTTATGTT 59.128 33.333 0.00 0.00 0.00 2.71
387 1539 7.378181 CAGTTAAAATCAGCCCAAAGTTATGT 58.622 34.615 0.00 0.00 0.00 2.29
388 1540 6.813152 CCAGTTAAAATCAGCCCAAAGTTATG 59.187 38.462 0.00 0.00 0.00 1.90
391 1543 4.898861 TCCAGTTAAAATCAGCCCAAAGTT 59.101 37.500 0.00 0.00 0.00 2.66
393 1545 4.280677 TGTCCAGTTAAAATCAGCCCAAAG 59.719 41.667 0.00 0.00 0.00 2.77
394 1546 4.219115 TGTCCAGTTAAAATCAGCCCAAA 58.781 39.130 0.00 0.00 0.00 3.28
398 1550 5.010012 CCCATATGTCCAGTTAAAATCAGCC 59.990 44.000 1.24 0.00 0.00 4.85
399 1551 5.507985 GCCCATATGTCCAGTTAAAATCAGC 60.508 44.000 1.24 0.00 0.00 4.26
400 1552 5.829924 AGCCCATATGTCCAGTTAAAATCAG 59.170 40.000 1.24 0.00 0.00 2.90
401 1553 5.593909 CAGCCCATATGTCCAGTTAAAATCA 59.406 40.000 1.24 0.00 0.00 2.57
402 1554 5.827797 TCAGCCCATATGTCCAGTTAAAATC 59.172 40.000 1.24 0.00 0.00 2.17
403 1555 5.765510 TCAGCCCATATGTCCAGTTAAAAT 58.234 37.500 1.24 0.00 0.00 1.82
404 1556 5.186256 TCAGCCCATATGTCCAGTTAAAA 57.814 39.130 1.24 0.00 0.00 1.52
405 1557 4.853468 TCAGCCCATATGTCCAGTTAAA 57.147 40.909 1.24 0.00 0.00 1.52
406 1558 4.853468 TTCAGCCCATATGTCCAGTTAA 57.147 40.909 1.24 0.00 0.00 2.01
407 1559 5.606749 AGTATTCAGCCCATATGTCCAGTTA 59.393 40.000 1.24 0.00 0.00 2.24
408 1560 3.959495 ATTCAGCCCATATGTCCAGTT 57.041 42.857 1.24 0.00 0.00 3.16
410 1562 4.630644 AGTATTCAGCCCATATGTCCAG 57.369 45.455 1.24 0.00 0.00 3.86
411 1563 4.532126 CCTAGTATTCAGCCCATATGTCCA 59.468 45.833 1.24 0.00 0.00 4.02
412 1564 4.080863 CCCTAGTATTCAGCCCATATGTCC 60.081 50.000 1.24 0.00 0.00 4.02
413 1565 4.080863 CCCCTAGTATTCAGCCCATATGTC 60.081 50.000 1.24 0.00 0.00 3.06
414 1566 3.846588 CCCCTAGTATTCAGCCCATATGT 59.153 47.826 1.24 0.00 0.00 2.29
415 1567 4.104086 TCCCCTAGTATTCAGCCCATATG 58.896 47.826 0.00 0.00 0.00 1.78
416 1568 4.435977 TCCCCTAGTATTCAGCCCATAT 57.564 45.455 0.00 0.00 0.00 1.78
417 1569 3.935240 TCCCCTAGTATTCAGCCCATA 57.065 47.619 0.00 0.00 0.00 2.74
1038 2211 4.832608 CGGCGTACTGGGGAAGGC 62.833 72.222 0.00 0.00 0.00 4.35
1128 2314 0.970937 AGATCTCTCGGCACCGGAAA 60.971 55.000 9.46 0.00 40.25 3.13
1157 2359 7.014134 TGTGGCATTGTTTATATATTGTGGAGG 59.986 37.037 0.00 0.00 0.00 4.30
1163 2365 7.862372 GTGGAGTGTGGCATTGTTTATATATTG 59.138 37.037 0.00 0.00 0.00 1.90
1164 2366 7.779798 AGTGGAGTGTGGCATTGTTTATATATT 59.220 33.333 0.00 0.00 0.00 1.28
1214 2437 1.586154 CGCAGGGGATGTTTGGTGTC 61.586 60.000 0.00 0.00 0.00 3.67
1245 2499 2.437359 AGCCGTGCTGCCATCTTC 60.437 61.111 0.00 0.00 37.57 2.87
1569 2850 2.573083 GGTGACGGGGTTGTACGGA 61.573 63.158 0.00 0.00 0.00 4.69
1984 3265 2.202797 CTCCACGGCGATGGACTG 60.203 66.667 21.66 12.75 44.14 3.51
2169 3471 0.526211 TGTCGTAGCACAGCTCGAAT 59.474 50.000 12.53 0.00 40.44 3.34
2433 3738 3.382832 AGCCTGACGAACCCGAGG 61.383 66.667 0.00 0.00 39.50 4.63
2580 3888 0.392336 AGCATCCAGTAGCAGCTAGC 59.608 55.000 6.62 6.62 46.19 3.42
2581 3889 3.571828 TCTTAGCATCCAGTAGCAGCTAG 59.428 47.826 1.02 0.00 38.81 3.42
2582 3890 3.566351 TCTTAGCATCCAGTAGCAGCTA 58.434 45.455 0.00 0.00 36.80 3.32
2583 3891 2.392662 TCTTAGCATCCAGTAGCAGCT 58.607 47.619 0.00 0.00 39.22 4.24
2584 3892 2.898729 TCTTAGCATCCAGTAGCAGC 57.101 50.000 0.00 0.00 0.00 5.25
2585 3893 7.443575 ACATTAATTCTTAGCATCCAGTAGCAG 59.556 37.037 0.00 0.00 0.00 4.24
2606 3914 3.351740 ACCGCCATGATCAACAACATTA 58.648 40.909 0.00 0.00 0.00 1.90
2607 3915 2.164219 GACCGCCATGATCAACAACATT 59.836 45.455 0.00 0.00 0.00 2.71
2608 3916 1.745087 GACCGCCATGATCAACAACAT 59.255 47.619 0.00 0.00 0.00 2.71
2609 3917 1.164411 GACCGCCATGATCAACAACA 58.836 50.000 0.00 0.00 0.00 3.33
2639 3947 1.442017 GGAACGGCGTGACAAATGC 60.442 57.895 15.70 0.00 40.36 3.56
2640 3948 0.521291 ATGGAACGGCGTGACAAATG 59.479 50.000 15.70 0.00 0.00 2.32
2641 3949 0.802494 GATGGAACGGCGTGACAAAT 59.198 50.000 15.70 8.76 0.00 2.32
2642 3950 0.250124 AGATGGAACGGCGTGACAAA 60.250 50.000 15.70 4.02 0.00 2.83
2643 3951 0.669318 GAGATGGAACGGCGTGACAA 60.669 55.000 15.70 5.00 0.00 3.18
2644 3952 1.080093 GAGATGGAACGGCGTGACA 60.080 57.895 15.70 16.66 0.00 3.58
2645 3953 0.460284 ATGAGATGGAACGGCGTGAC 60.460 55.000 15.70 10.59 0.00 3.67
2646 3954 0.179111 GATGAGATGGAACGGCGTGA 60.179 55.000 15.70 0.19 0.00 4.35
2647 3955 0.179100 AGATGAGATGGAACGGCGTG 60.179 55.000 15.70 0.00 0.00 5.34
2648 3956 0.537188 AAGATGAGATGGAACGGCGT 59.463 50.000 6.77 6.77 0.00 5.68
2649 3957 0.933097 CAAGATGAGATGGAACGGCG 59.067 55.000 4.80 4.80 0.00 6.46
2650 3958 0.659957 GCAAGATGAGATGGAACGGC 59.340 55.000 0.00 0.00 0.00 5.68
2651 3959 2.028420 TGCAAGATGAGATGGAACGG 57.972 50.000 0.00 0.00 0.00 4.44
2652 3960 4.083110 ACTTTTGCAAGATGAGATGGAACG 60.083 41.667 0.00 0.00 33.72 3.95
2653 3961 5.382618 ACTTTTGCAAGATGAGATGGAAC 57.617 39.130 0.00 0.00 33.72 3.62
2654 3962 5.775686 CAACTTTTGCAAGATGAGATGGAA 58.224 37.500 0.00 0.00 35.31 3.53
2655 3963 5.381174 CAACTTTTGCAAGATGAGATGGA 57.619 39.130 0.00 0.00 35.31 3.41
2684 3992 7.988737 TGAATCCATATCACACACAAAAGATC 58.011 34.615 0.00 0.00 0.00 2.75
2685 3993 7.830697 TCTGAATCCATATCACACACAAAAGAT 59.169 33.333 0.00 0.00 0.00 2.40
2688 3996 6.942005 ACTCTGAATCCATATCACACACAAAA 59.058 34.615 0.00 0.00 0.00 2.44
2689 3997 6.475504 ACTCTGAATCCATATCACACACAAA 58.524 36.000 0.00 0.00 0.00 2.83
2690 3998 6.053632 ACTCTGAATCCATATCACACACAA 57.946 37.500 0.00 0.00 0.00 3.33
2691 3999 5.682234 ACTCTGAATCCATATCACACACA 57.318 39.130 0.00 0.00 0.00 3.72
2718 4026 5.048224 AGAGTGAATGGTTTTGCTCTGAATG 60.048 40.000 0.00 0.00 32.79 2.67
2743 4051 1.337821 CCGTGTACTTCTTGTCTCGC 58.662 55.000 0.00 0.00 0.00 5.03
2745 4053 3.057734 CAACCCGTGTACTTCTTGTCTC 58.942 50.000 0.00 0.00 0.00 3.36
2760 4068 2.388232 GCTCTAACGTGCCAACCCG 61.388 63.158 0.00 0.00 0.00 5.28
2774 4082 0.392193 CGCCTCATTGGAGTTGCTCT 60.392 55.000 0.00 0.00 39.64 4.09
2775 4083 0.391661 TCGCCTCATTGGAGTTGCTC 60.392 55.000 0.00 0.00 39.64 4.26
2776 4084 0.254178 ATCGCCTCATTGGAGTTGCT 59.746 50.000 0.00 0.00 39.64 3.91
2777 4085 0.659957 GATCGCCTCATTGGAGTTGC 59.340 55.000 0.00 0.00 39.64 4.17
2778 4086 1.303309 GGATCGCCTCATTGGAGTTG 58.697 55.000 0.00 0.00 39.64 3.16
2779 4087 0.911769 TGGATCGCCTCATTGGAGTT 59.088 50.000 0.00 0.00 39.64 3.01
2780 4088 1.135094 ATGGATCGCCTCATTGGAGT 58.865 50.000 0.00 0.00 39.64 3.85
2781 4089 2.267174 AATGGATCGCCTCATTGGAG 57.733 50.000 0.00 0.00 41.02 3.86
2782 4090 2.092484 TGAAATGGATCGCCTCATTGGA 60.092 45.455 0.00 0.00 38.35 3.53
2783 4091 2.300433 TGAAATGGATCGCCTCATTGG 58.700 47.619 0.00 0.00 34.28 3.16
2784 4092 3.057736 GGATGAAATGGATCGCCTCATTG 60.058 47.826 0.00 0.00 34.28 2.82
2785 4093 3.152341 GGATGAAATGGATCGCCTCATT 58.848 45.455 0.00 0.00 35.37 2.57
2786 4094 2.787994 GGATGAAATGGATCGCCTCAT 58.212 47.619 0.00 0.00 31.39 2.90
2787 4095 1.541015 CGGATGAAATGGATCGCCTCA 60.541 52.381 0.00 0.00 34.31 3.86
2788 4096 1.151668 CGGATGAAATGGATCGCCTC 58.848 55.000 0.00 0.00 34.31 4.70
2789 4097 0.886490 GCGGATGAAATGGATCGCCT 60.886 55.000 0.00 0.00 37.62 5.52
2790 4098 1.576421 GCGGATGAAATGGATCGCC 59.424 57.895 0.00 0.00 37.62 5.54
2791 4099 1.205064 CGCGGATGAAATGGATCGC 59.795 57.895 0.00 0.00 39.79 4.58
2792 4100 1.862123 CCGCGGATGAAATGGATCG 59.138 57.895 24.07 0.00 0.00 3.69
2793 4101 1.576421 GCCGCGGATGAAATGGATC 59.424 57.895 33.48 1.41 0.00 3.36
2794 4102 1.898574 GGCCGCGGATGAAATGGAT 60.899 57.895 33.48 0.00 0.00 3.41
2795 4103 2.515991 GGCCGCGGATGAAATGGA 60.516 61.111 33.48 0.00 0.00 3.41
2796 4104 3.952675 CGGCCGCGGATGAAATGG 61.953 66.667 33.48 3.40 0.00 3.16
2797 4105 2.646799 GAACGGCCGCGGATGAAATG 62.647 60.000 33.48 11.63 0.00 2.32
2798 4106 2.437716 AACGGCCGCGGATGAAAT 60.438 55.556 33.48 5.99 0.00 2.17
2799 4107 3.122323 GAACGGCCGCGGATGAAA 61.122 61.111 33.48 0.00 0.00 2.69
2803 4111 3.646023 TAAACGAACGGCCGCGGAT 62.646 57.895 33.48 16.48 0.00 4.18
2804 4112 4.354939 TAAACGAACGGCCGCGGA 62.355 61.111 33.48 8.76 0.00 5.54
2805 4113 3.845472 CTAAACGAACGGCCGCGG 61.845 66.667 28.58 24.05 0.00 6.46
2806 4114 3.845472 CCTAAACGAACGGCCGCG 61.845 66.667 28.58 24.34 0.00 6.46
2807 4115 2.733671 GACCTAAACGAACGGCCGC 61.734 63.158 28.58 9.25 0.00 6.53
2808 4116 2.438954 CGACCTAAACGAACGGCCG 61.439 63.158 26.86 26.86 0.00 6.13
2809 4117 0.109319 TACGACCTAAACGAACGGCC 60.109 55.000 0.00 0.00 34.70 6.13
2810 4118 1.696988 TTACGACCTAAACGAACGGC 58.303 50.000 0.00 0.00 34.70 5.68
2811 4119 4.434593 CCATTTTACGACCTAAACGAACGG 60.435 45.833 0.00 0.00 34.70 4.44
2812 4120 4.385447 TCCATTTTACGACCTAAACGAACG 59.615 41.667 0.00 0.00 34.70 3.95
2813 4121 5.844301 TCCATTTTACGACCTAAACGAAC 57.156 39.130 0.00 0.00 34.70 3.95
2814 4122 9.985730 ATATATCCATTTTACGACCTAAACGAA 57.014 29.630 0.00 0.00 34.70 3.85
2914 4225 1.475403 ACATTCAGACGTCGGAGGAT 58.525 50.000 17.70 7.68 0.00 3.24
3071 4383 4.320275 GCCAGTTCTACAAACAAAGTAGGC 60.320 45.833 0.00 0.00 39.48 3.93
3075 4387 2.032924 GCGCCAGTTCTACAAACAAAGT 59.967 45.455 0.00 0.00 0.00 2.66
3104 4416 2.268920 GCTTCCCGCTGGACATCA 59.731 61.111 0.00 0.00 41.57 3.07
3130 4442 1.206132 CGTGGAAGCTATGGTGGTGTA 59.794 52.381 0.00 0.00 0.00 2.90
3141 4453 1.513158 CGAGATGGACGTGGAAGCT 59.487 57.895 0.00 0.00 0.00 3.74
3188 4500 2.181584 GAGGATCGTCGTGTCCACT 58.818 57.895 17.43 2.77 36.96 4.00
3245 4557 3.454587 AACGTGTTGAGCCAGCGGA 62.455 57.895 0.00 0.00 0.00 5.54
3394 4755 1.447140 CGGATTTTCGCGGAGTCCA 60.447 57.895 17.84 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.