Multiple sequence alignment - TraesCS1D01G204200

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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 TraesCS1D01G204200 chr1D 100.000 8146 0 0 1 8146 289389074 289397219 0.000000e+00 15043.0
1 TraesCS1D01G204200 chr1D 84.615 650 75 10 6094 6718 94051976 94052625 2.500000e-174 623.0
2 TraesCS1D01G204200 chr1D 90.000 70 5 2 7802 7870 332573071 332573003 1.130000e-13 89.8
3 TraesCS1D01G204200 chr1B 94.118 3349 132 16 3161 6475 390619503 390622820 0.000000e+00 5033.0
4 TraesCS1D01G204200 chr1B 93.315 2154 55 22 273 2401 390616206 390618295 0.000000e+00 3097.0
5 TraesCS1D01G204200 chr1B 95.760 1085 34 7 6492 7568 390623183 390624263 0.000000e+00 1738.0
6 TraesCS1D01G204200 chr1B 97.313 707 16 3 2398 3103 390618524 390619228 0.000000e+00 1197.0
7 TraesCS1D01G204200 chr1B 91.964 224 14 4 21 244 390613621 390613840 2.210000e-80 311.0
8 TraesCS1D01G204200 chr1B 83.193 119 10 9 284 402 108192446 108192338 5.200000e-17 100.0
9 TraesCS1D01G204200 chr1B 87.500 88 6 3 7784 7870 345311232 345311149 6.730000e-16 97.1
10 TraesCS1D01G204200 chr1B 86.842 76 7 2 7784 7856 453344495 453344420 1.880000e-11 82.4
11 TraesCS1D01G204200 chr1A 95.885 2503 49 17 395 2867 361351779 361354257 0.000000e+00 4002.0
12 TraesCS1D01G204200 chr1A 93.793 2046 76 20 4575 6603 361356060 361358071 0.000000e+00 3027.0
13 TraesCS1D01G204200 chr1A 96.068 1704 44 5 2858 4545 361354363 361356059 0.000000e+00 2754.0
14 TraesCS1D01G204200 chr1A 96.209 1187 37 6 6630 7810 361358071 361359255 0.000000e+00 1936.0
15 TraesCS1D01G204200 chr1A 84.356 652 73 13 6094 6718 226157101 226156452 5.400000e-171 612.0
16 TraesCS1D01G204200 chr1A 83.242 549 55 20 3267 3806 272313914 272313394 3.440000e-128 470.0
17 TraesCS1D01G204200 chr1A 89.474 361 19 8 7798 8146 361360831 361361184 9.710000e-119 438.0
18 TraesCS1D01G204200 chr1A 90.184 163 12 2 5945 6103 91162335 91162173 8.280000e-50 209.0
19 TraesCS1D01G204200 chr4A 88.317 796 87 2 5143 5938 533012806 533013595 0.000000e+00 950.0
20 TraesCS1D01G204200 chr4A 85.661 809 95 9 5143 5941 238400240 238399443 0.000000e+00 832.0
21 TraesCS1D01G204200 chr4A 83.738 535 69 13 3369 3895 116140416 116139892 2.640000e-134 490.0
22 TraesCS1D01G204200 chr4A 78.157 293 51 11 2353 2638 719207677 719207963 3.020000e-39 174.0
23 TraesCS1D01G204200 chr4A 88.435 147 11 4 5966 6109 612428991 612429134 1.090000e-38 172.0
24 TraesCS1D01G204200 chr4A 85.227 88 8 3 7784 7870 498697563 498697480 1.460000e-12 86.1
25 TraesCS1D01G204200 chr7A 87.940 796 96 0 5143 5938 432350806 432351601 0.000000e+00 939.0
26 TraesCS1D01G204200 chr7A 87.218 798 95 6 5143 5938 467854470 467855262 0.000000e+00 902.0
27 TraesCS1D01G204200 chr7A 86.608 799 101 4 5143 5938 540664763 540665558 0.000000e+00 878.0
28 TraesCS1D01G204200 chr7A 84.308 650 77 10 6094 6718 232385341 232385990 5.400000e-171 612.0
29 TraesCS1D01G204200 chr7A 83.643 538 68 13 3369 3895 266636871 266636343 9.500000e-134 488.0
30 TraesCS1D01G204200 chr7A 80.251 319 53 7 2281 2596 717753032 717752721 1.770000e-56 231.0
31 TraesCS1D01G204200 chr5B 87.406 802 97 3 5143 5941 391231275 391230475 0.000000e+00 918.0
32 TraesCS1D01G204200 chr5B 82.857 455 62 9 3447 3895 339631537 339631981 2.130000e-105 394.0
33 TraesCS1D01G204200 chr5B 92.053 151 12 0 5947 6097 665744469 665744619 6.400000e-51 213.0
34 TraesCS1D01G204200 chr5B 86.538 156 17 3 5957 6109 693662787 693662941 1.410000e-37 169.0
35 TraesCS1D01G204200 chr2B 86.625 800 98 7 5143 5941 546948962 546948171 0.000000e+00 876.0
36 TraesCS1D01G204200 chr2B 83.146 89 11 4 7784 7870 748431762 748431848 2.440000e-10 78.7
37 TraesCS1D01G204200 chr3B 86.426 803 98 7 5143 5938 424127935 424128733 0.000000e+00 869.0
38 TraesCS1D01G204200 chr3B 82.897 497 69 10 4649 5140 377429271 377428786 4.520000e-117 433.0
39 TraesCS1D01G204200 chr3B 90.506 158 13 1 5945 6100 396271877 396272034 2.980000e-49 207.0
40 TraesCS1D01G204200 chr3B 89.172 157 10 4 5958 6109 404830461 404830307 1.080000e-43 189.0
41 TraesCS1D01G204200 chr3B 88.889 63 6 1 281 343 177649976 177649915 8.770000e-10 76.8
42 TraesCS1D01G204200 chr5A 84.615 650 75 10 6094 6718 359108444 359109093 2.500000e-174 623.0
43 TraesCS1D01G204200 chr5A 82.258 496 70 9 4653 5144 502805147 502804666 5.880000e-111 412.0
44 TraesCS1D01G204200 chr5A 92.053 151 12 0 5947 6097 656872285 656872435 6.400000e-51 213.0
45 TraesCS1D01G204200 chr5A 86.452 155 16 2 5957 6109 382069974 382070125 1.820000e-36 165.0
46 TraesCS1D01G204200 chr5A 78.995 219 35 9 2428 2638 688006320 688006535 1.100000e-28 139.0
47 TraesCS1D01G204200 chr5A 89.815 108 5 2 8034 8141 454073387 454073286 5.130000e-27 134.0
48 TraesCS1D01G204200 chr5A 87.640 89 8 3 7784 7870 353851353 353851266 5.200000e-17 100.0
49 TraesCS1D01G204200 chr5A 84.270 89 11 3 7784 7870 353851260 353851347 5.240000e-12 84.2
50 TraesCS1D01G204200 chr6A 84.462 650 76 10 6094 6718 462834224 462834873 1.160000e-172 617.0
51 TraesCS1D01G204200 chr6A 84.154 650 78 10 6094 6718 440835388 440834739 2.510000e-169 606.0
52 TraesCS1D01G204200 chr6A 85.531 546 64 10 3267 3804 173599410 173599948 2.570000e-154 556.0
53 TraesCS1D01G204200 chr6A 81.911 492 75 7 4651 5140 487969341 487968862 3.540000e-108 403.0
54 TraesCS1D01G204200 chr6A 97.368 38 1 0 6724 6761 160434259 160434296 1.900000e-06 65.8
55 TraesCS1D01G204200 chr4D 84.308 650 77 10 6094 6718 48072307 48071658 5.400000e-171 612.0
56 TraesCS1D01G204200 chr4D 82.424 660 86 16 6094 6728 210455201 210455855 4.300000e-152 549.0
57 TraesCS1D01G204200 chr4D 86.695 466 49 8 3348 3806 144439320 144439779 9.440000e-139 505.0
58 TraesCS1D01G204200 chr4D 84.549 466 51 8 6094 6538 439674640 439674175 7.500000e-120 442.0
59 TraesCS1D01G204200 chr4D 82.299 548 51 23 3267 3806 196642297 196642806 4.520000e-117 433.0
60 TraesCS1D01G204200 chr4D 87.179 78 6 2 7784 7857 281181932 281181855 1.460000e-12 86.1
61 TraesCS1D01G204200 chr5D 83.692 650 80 11 6094 6718 469491522 469492170 2.530000e-164 590.0
62 TraesCS1D01G204200 chr5D 83.023 483 68 8 4660 5140 219772587 219772117 7.560000e-115 425.0
63 TraesCS1D01G204200 chr5D 92.053 151 12 0 5947 6097 528717278 528717428 6.400000e-51 213.0
64 TraesCS1D01G204200 chr5D 87.179 156 16 3 5957 6109 559421087 559421241 3.020000e-39 174.0
65 TraesCS1D01G204200 chr5D 82.653 98 10 4 7784 7874 446265290 446265193 6.780000e-11 80.5
66 TraesCS1D01G204200 chr2D 83.692 650 77 11 6094 6718 364092658 364093303 3.280000e-163 586.0
67 TraesCS1D01G204200 chr2D 82.705 584 68 19 6162 6718 131769047 131769624 9.500000e-134 488.0
68 TraesCS1D01G204200 chr2A 85.219 548 66 9 3267 3806 137518762 137518222 4.300000e-152 549.0
69 TraesCS1D01G204200 chr2A 81.413 651 81 20 6094 6718 425904489 425903853 5.680000e-136 496.0
70 TraesCS1D01G204200 chr2A 82.556 493 72 8 4650 5140 160834910 160834430 9.770000e-114 422.0
71 TraesCS1D01G204200 chr2A 92.308 39 3 0 6723 6761 123554573 123554535 1.000000e-03 56.5
72 TraesCS1D01G204200 chr4B 82.273 660 87 16 6094 6728 253687251 253687905 2.000000e-150 544.0
73 TraesCS1D01G204200 chr4B 84.171 537 65 13 3369 3895 222353370 222352844 3.390000e-138 503.0
74 TraesCS1D01G204200 chr4B 82.482 548 59 19 3267 3806 414689945 414690463 5.800000e-121 446.0
75 TraesCS1D01G204200 chr4B 82.130 554 61 15 3369 3895 269974482 269973940 2.700000e-119 440.0
76 TraesCS1D01G204200 chr4B 86.792 53 6 1 8037 8088 94346599 94346547 3.180000e-04 58.4
77 TraesCS1D01G204200 chr3A 84.730 537 59 12 3369 3895 340913931 340914454 4.360000e-142 516.0
78 TraesCS1D01G204200 chr3A 87.952 166 11 6 5949 6109 414818199 414818038 3.880000e-43 187.0
79 TraesCS1D01G204200 chr6B 84.201 538 66 12 3369 3895 193813387 193812858 9.440000e-139 505.0
80 TraesCS1D01G204200 chr6B 83.836 464 63 7 4677 5140 319929227 319928776 1.620000e-116 431.0
81 TraesCS1D01G204200 chr7B 83.955 536 65 12 3369 3895 499465523 499466046 2.040000e-135 494.0
82 TraesCS1D01G204200 chr7B 89.222 167 14 3 5943 6106 505937311 505937476 1.070000e-48 206.0
83 TraesCS1D01G204200 chr6D 84.211 494 64 7 4649 5140 160204397 160204878 1.240000e-127 468.0
84 TraesCS1D01G204200 chr6D 84.173 417 54 6 3482 3895 248584383 248584790 2.130000e-105 394.0
85 TraesCS1D01G204200 chr6D 88.679 53 6 0 8035 8087 101900435 101900487 1.900000e-06 65.8
86 TraesCS1D01G204200 chr3D 84.362 486 62 8 4657 5140 262995665 262995192 1.600000e-126 464.0
87 TraesCS1D01G204200 chr3D 90.506 158 13 1 5945 6100 322435290 322435447 2.980000e-49 207.0
88 TraesCS1D01G204200 chr3D 89.809 157 12 3 5944 6096 315480422 315480578 1.790000e-46 198.0
89 TraesCS1D01G204200 chrUn 82.389 494 71 8 4649 5140 83943896 83943417 4.550000e-112 416.0
90 TraesCS1D01G204200 chr7D 79.567 323 54 9 2281 2598 622045599 622045284 3.830000e-53 220.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G204200 chr1D 289389074 289397219 8145 False 15043.0 15043 100.0000 1 8146 1 chr1D.!!$F2 8145
1 TraesCS1D01G204200 chr1D 94051976 94052625 649 False 623.0 623 84.6150 6094 6718 1 chr1D.!!$F1 624
2 TraesCS1D01G204200 chr1B 390613621 390624263 10642 False 2275.2 5033 94.4940 21 7568 5 chr1B.!!$F1 7547
3 TraesCS1D01G204200 chr1A 361351779 361361184 9405 False 2431.4 4002 94.2858 395 8146 5 chr1A.!!$F1 7751
4 TraesCS1D01G204200 chr1A 226156452 226157101 649 True 612.0 612 84.3560 6094 6718 1 chr1A.!!$R2 624
5 TraesCS1D01G204200 chr1A 272313394 272313914 520 True 470.0 470 83.2420 3267 3806 1 chr1A.!!$R3 539
6 TraesCS1D01G204200 chr4A 533012806 533013595 789 False 950.0 950 88.3170 5143 5938 1 chr4A.!!$F1 795
7 TraesCS1D01G204200 chr4A 238399443 238400240 797 True 832.0 832 85.6610 5143 5941 1 chr4A.!!$R2 798
8 TraesCS1D01G204200 chr4A 116139892 116140416 524 True 490.0 490 83.7380 3369 3895 1 chr4A.!!$R1 526
9 TraesCS1D01G204200 chr7A 432350806 432351601 795 False 939.0 939 87.9400 5143 5938 1 chr7A.!!$F2 795
10 TraesCS1D01G204200 chr7A 467854470 467855262 792 False 902.0 902 87.2180 5143 5938 1 chr7A.!!$F3 795
11 TraesCS1D01G204200 chr7A 540664763 540665558 795 False 878.0 878 86.6080 5143 5938 1 chr7A.!!$F4 795
12 TraesCS1D01G204200 chr7A 232385341 232385990 649 False 612.0 612 84.3080 6094 6718 1 chr7A.!!$F1 624
13 TraesCS1D01G204200 chr7A 266636343 266636871 528 True 488.0 488 83.6430 3369 3895 1 chr7A.!!$R1 526
14 TraesCS1D01G204200 chr5B 391230475 391231275 800 True 918.0 918 87.4060 5143 5941 1 chr5B.!!$R1 798
15 TraesCS1D01G204200 chr2B 546948171 546948962 791 True 876.0 876 86.6250 5143 5941 1 chr2B.!!$R1 798
16 TraesCS1D01G204200 chr3B 424127935 424128733 798 False 869.0 869 86.4260 5143 5938 1 chr3B.!!$F2 795
17 TraesCS1D01G204200 chr5A 359108444 359109093 649 False 623.0 623 84.6150 6094 6718 1 chr5A.!!$F2 624
18 TraesCS1D01G204200 chr6A 462834224 462834873 649 False 617.0 617 84.4620 6094 6718 1 chr6A.!!$F3 624
19 TraesCS1D01G204200 chr6A 440834739 440835388 649 True 606.0 606 84.1540 6094 6718 1 chr6A.!!$R1 624
20 TraesCS1D01G204200 chr6A 173599410 173599948 538 False 556.0 556 85.5310 3267 3804 1 chr6A.!!$F2 537
21 TraesCS1D01G204200 chr4D 48071658 48072307 649 True 612.0 612 84.3080 6094 6718 1 chr4D.!!$R1 624
22 TraesCS1D01G204200 chr4D 210455201 210455855 654 False 549.0 549 82.4240 6094 6728 1 chr4D.!!$F3 634
23 TraesCS1D01G204200 chr4D 196642297 196642806 509 False 433.0 433 82.2990 3267 3806 1 chr4D.!!$F2 539
24 TraesCS1D01G204200 chr5D 469491522 469492170 648 False 590.0 590 83.6920 6094 6718 1 chr5D.!!$F1 624
25 TraesCS1D01G204200 chr2D 364092658 364093303 645 False 586.0 586 83.6920 6094 6718 1 chr2D.!!$F2 624
26 TraesCS1D01G204200 chr2D 131769047 131769624 577 False 488.0 488 82.7050 6162 6718 1 chr2D.!!$F1 556
27 TraesCS1D01G204200 chr2A 137518222 137518762 540 True 549.0 549 85.2190 3267 3806 1 chr2A.!!$R2 539
28 TraesCS1D01G204200 chr2A 425903853 425904489 636 True 496.0 496 81.4130 6094 6718 1 chr2A.!!$R4 624
29 TraesCS1D01G204200 chr4B 253687251 253687905 654 False 544.0 544 82.2730 6094 6728 1 chr4B.!!$F1 634
30 TraesCS1D01G204200 chr4B 222352844 222353370 526 True 503.0 503 84.1710 3369 3895 1 chr4B.!!$R2 526
31 TraesCS1D01G204200 chr4B 414689945 414690463 518 False 446.0 446 82.4820 3267 3806 1 chr4B.!!$F2 539
32 TraesCS1D01G204200 chr4B 269973940 269974482 542 True 440.0 440 82.1300 3369 3895 1 chr4B.!!$R3 526
33 TraesCS1D01G204200 chr3A 340913931 340914454 523 False 516.0 516 84.7300 3369 3895 1 chr3A.!!$F1 526
34 TraesCS1D01G204200 chr6B 193812858 193813387 529 True 505.0 505 84.2010 3369 3895 1 chr6B.!!$R1 526
35 TraesCS1D01G204200 chr7B 499465523 499466046 523 False 494.0 494 83.9550 3369 3895 1 chr7B.!!$F1 526

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
182 183 0.250124 CACAACTCGTAACTGGGGCA 60.250 55.000 0.00 0.0 0.00 5.36 F
1186 3550 0.393132 GCTTGTAAGTCTGCCCTCCC 60.393 60.000 0.00 0.0 0.00 4.30 F
2301 4671 0.538977 AGTGCATATGATGGCTGGGC 60.539 55.000 6.97 0.0 0.00 5.36 F
3032 5752 1.226746 GTGGTGGAAACCAGTTCGAG 58.773 55.000 0.00 0.0 41.00 4.04 F
4138 7126 2.159393 TGCATTTGATAAAGCGGCTGAC 60.159 45.455 1.81 0.0 0.00 3.51 F
4998 8001 0.040058 TCGGTGCTACCCCAACTCTA 59.960 55.000 0.00 0.0 33.75 2.43 F
6311 9357 0.031616 AGAGCCTCCCTGACCTTAGG 60.032 60.000 0.00 0.0 37.59 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1223 3587 1.217882 GTAATCACAGAATCCGGGCG 58.782 55.000 0.0 0.0 0.0 6.13 R
3091 5811 1.575922 CCCGCATTCACACACACAG 59.424 57.895 0.0 0.0 0.0 3.66 R
3926 6914 1.200020 GTGACATAGCCAACCTGCAAC 59.800 52.381 0.0 0.0 0.0 4.17 R
4923 7926 0.747852 TCGGGCATATACAACGCAGA 59.252 50.000 0.0 0.0 0.0 4.26 R
5437 8462 0.529119 GTCGCCAATAATCGGACGGT 60.529 55.000 0.0 0.0 0.0 4.83 R
6561 9975 0.034089 AAGCAAGGGGTCAGGCATAC 60.034 55.000 0.0 0.0 0.0 2.39 R
7420 10847 0.670546 CGGTGCAGACTACAAGGTGG 60.671 60.000 0.0 0.0 0.0 4.61 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
18 19 1.790387 GCTAGTTGCAAGCTCACCG 59.210 57.895 0.00 0.00 42.31 4.94
19 20 0.951040 GCTAGTTGCAAGCTCACCGT 60.951 55.000 0.00 0.00 42.31 4.83
74 75 1.581954 CCACTCTCGACTCGCAACT 59.418 57.895 0.00 0.00 0.00 3.16
79 80 1.803519 CTCGACTCGCAACTGGAGC 60.804 63.158 0.00 0.00 34.87 4.70
113 114 3.838244 TCTAGTTGCAAGTCCACACTT 57.162 42.857 10.78 0.00 44.26 3.16
125 126 1.765904 TCCACACTTGGCTCACAACTA 59.234 47.619 0.00 0.00 43.56 2.24
128 129 1.072331 ACACTTGGCTCACAACTAGGG 59.928 52.381 0.00 0.00 34.76 3.53
131 132 2.137177 TTGGCTCACAACTAGGGCCC 62.137 60.000 16.46 16.46 41.84 5.80
132 133 2.125106 GCTCACAACTAGGGCCCG 60.125 66.667 18.44 5.44 0.00 6.13
133 134 2.656069 GCTCACAACTAGGGCCCGA 61.656 63.158 18.44 11.19 0.00 5.14
134 135 1.218316 CTCACAACTAGGGCCCGAC 59.782 63.158 18.44 0.00 0.00 4.79
135 136 1.534476 TCACAACTAGGGCCCGACA 60.534 57.895 18.44 4.67 0.00 4.35
136 137 0.907704 TCACAACTAGGGCCCGACAT 60.908 55.000 18.44 0.00 0.00 3.06
177 178 0.506932 CCACGCACAACTCGTAACTG 59.493 55.000 0.00 0.00 38.19 3.16
182 183 0.250124 CACAACTCGTAACTGGGGCA 60.250 55.000 0.00 0.00 0.00 5.36
225 226 2.029020 TGCAAGTCTATGCTCAACTCGT 60.029 45.455 0.67 0.00 46.54 4.18
228 229 4.031878 GCAAGTCTATGCTCAACTCGTAAC 59.968 45.833 0.00 0.00 43.06 2.50
229 230 4.373348 AGTCTATGCTCAACTCGTAACC 57.627 45.455 0.00 0.00 0.00 2.85
230 231 3.762288 AGTCTATGCTCAACTCGTAACCA 59.238 43.478 0.00 0.00 0.00 3.67
248 287 2.526110 GGGCTGACCTTTTGGGGT 59.474 61.111 0.00 0.00 46.08 4.95
252 291 0.536460 GCTGACCTTTTGGGGTTCGA 60.536 55.000 0.00 0.00 46.08 3.71
263 302 2.741211 GGTTCGACCTTGGGCGAC 60.741 66.667 18.02 12.24 34.73 5.19
266 305 0.953960 GTTCGACCTTGGGCGACAAT 60.954 55.000 18.02 0.00 38.65 2.71
267 306 0.609151 TTCGACCTTGGGCGACAATA 59.391 50.000 18.02 0.00 38.65 1.90
270 309 2.014128 CGACCTTGGGCGACAATAAAT 58.986 47.619 9.67 0.00 38.65 1.40
272 311 3.623960 CGACCTTGGGCGACAATAAATAA 59.376 43.478 9.67 0.00 38.65 1.40
274 313 5.220970 CGACCTTGGGCGACAATAAATAAAT 60.221 40.000 9.67 0.00 38.65 1.40
275 314 6.017770 CGACCTTGGGCGACAATAAATAAATA 60.018 38.462 9.67 0.00 38.65 1.40
308 347 7.727331 ACAAAACAAACAATACAATGATGGG 57.273 32.000 0.00 0.00 0.00 4.00
341 2679 4.289245 TCTACTGATGTGGGATGATGTCA 58.711 43.478 0.00 0.00 0.00 3.58
343 2681 7.093596 TATCTACTGATGTGGGATGATGTCATC 60.094 40.741 13.34 13.34 41.33 2.92
682 3026 2.125912 CCTCGCTCCTGTGTTCCG 60.126 66.667 0.00 0.00 0.00 4.30
1186 3550 0.393132 GCTTGTAAGTCTGCCCTCCC 60.393 60.000 0.00 0.00 0.00 4.30
1223 3587 1.945354 TTCCGATCTGTCACGCCCTC 61.945 60.000 0.00 0.00 0.00 4.30
1412 3781 3.873361 TCCAATTGATCAGAATCGAGTGC 59.127 43.478 7.12 0.00 39.17 4.40
1799 4168 4.752879 TGGTAGACCGGCTTGCGC 62.753 66.667 0.00 0.00 39.43 6.09
2187 4557 3.877508 AGCTACGACCAATCAAATTAGCC 59.122 43.478 0.00 0.00 0.00 3.93
2297 4667 5.047164 TGTTTTGAAAGTGCATATGATGGCT 60.047 36.000 6.97 0.00 0.00 4.75
2301 4671 0.538977 AGTGCATATGATGGCTGGGC 60.539 55.000 6.97 0.00 0.00 5.36
2676 5280 4.657039 TCCCTAGAGCCCGTTGTATAAAAT 59.343 41.667 0.00 0.00 0.00 1.82
2679 5283 3.886123 AGAGCCCGTTGTATAAAATGCT 58.114 40.909 0.00 0.00 0.00 3.79
2698 5302 2.416202 GCTGCACTTGTTTTGTTTGCTT 59.584 40.909 0.00 0.00 34.18 3.91
2807 5411 2.234661 TCTTGATTGCACCGAGATGTCT 59.765 45.455 0.00 0.00 0.00 3.41
2902 5622 5.827666 TGATCATGCTCTATGTTGCATTTG 58.172 37.500 0.00 0.00 46.29 2.32
3032 5752 1.226746 GTGGTGGAAACCAGTTCGAG 58.773 55.000 0.00 0.00 41.00 4.04
3091 5811 7.486232 GGTAAAATACTTGCTTCATTTGCTCTC 59.514 37.037 0.00 0.00 0.00 3.20
3128 5851 2.268076 GGCGGGTGAGCATGTGTTT 61.268 57.895 0.00 0.00 39.27 2.83
3373 6312 6.978659 GGGAGGTAATGCTTTTAATAAACTGC 59.021 38.462 0.00 3.87 0.00 4.40
3641 6587 5.277058 GGCGCAGAAAGTACAATAAGAGATG 60.277 44.000 10.83 0.00 0.00 2.90
3757 6726 5.616204 CGTTTTCCCGTAGAATCAAAAGGAC 60.616 44.000 0.00 0.00 33.44 3.85
3853 6828 5.766174 CCTAGTCTTGGAGGAGTGTCTATAC 59.234 48.000 0.00 0.00 34.46 1.47
3917 6905 4.040755 AGGAGGCTTGTATGGTAATGACT 58.959 43.478 0.00 0.00 0.00 3.41
3926 6914 6.433847 TGTATGGTAATGACTTATCCCCTG 57.566 41.667 0.00 0.00 0.00 4.45
3956 6944 3.374764 TGGCTATGTCACTACCATCTGT 58.625 45.455 0.00 0.00 0.00 3.41
4062 7050 5.626116 CGCTATTCTACCACCAACTTAGGTT 60.626 44.000 0.00 0.00 40.77 3.50
4132 7120 5.228635 GTGTCTCAATGCATTTGATAAAGCG 59.771 40.000 9.83 0.00 43.30 4.68
4138 7126 2.159393 TGCATTTGATAAAGCGGCTGAC 60.159 45.455 1.81 0.00 0.00 3.51
4256 7244 9.745880 ATCATCTTATGCAATTTGACTTGAATC 57.254 29.630 0.00 0.00 0.00 2.52
4483 7471 9.130312 CTTTATGAGTAGACAGACAAGTTGTAC 57.870 37.037 8.88 2.24 0.00 2.90
4531 7519 8.028354 GTCTTCAGATGACATAGGTGATAGATG 58.972 40.741 10.85 0.00 34.80 2.90
4534 7522 5.868258 CAGATGACATAGGTGATAGATGCAC 59.132 44.000 0.00 0.00 35.56 4.57
4596 7585 5.822519 TGAGGAATTCCATCATTAACTTCCG 59.177 40.000 26.22 0.00 36.61 4.30
4646 7635 7.903431 GCCAATGTAATCTAAGTGTTAGAAACG 59.097 37.037 0.66 0.00 44.75 3.60
4652 7641 7.417496 AATCTAAGTGTTAGAAACGGACAAC 57.583 36.000 0.66 0.00 44.75 3.32
4653 7642 5.904941 TCTAAGTGTTAGAAACGGACAACA 58.095 37.500 0.00 0.00 39.21 3.33
4655 7644 6.987992 TCTAAGTGTTAGAAACGGACAACAAT 59.012 34.615 0.00 0.00 39.21 2.71
4760 7763 4.672587 TCTGTCACATGGATAGCTAACC 57.327 45.455 12.98 12.98 34.93 2.85
4836 7839 6.488683 CCTTCAGATCTATCTTAACGGACTCT 59.511 42.308 0.00 0.00 34.22 3.24
4852 7855 5.012354 ACGGACTCTTCCCATGTAAAGTTTA 59.988 40.000 0.00 0.00 38.99 2.01
4853 7856 6.113411 CGGACTCTTCCCATGTAAAGTTTAT 58.887 40.000 0.00 0.00 38.99 1.40
4855 7858 7.414098 CGGACTCTTCCCATGTAAAGTTTATTG 60.414 40.741 0.00 0.75 38.99 1.90
4862 7865 5.952947 CCCATGTAAAGTTTATTGTACCCCA 59.047 40.000 0.00 0.00 0.00 4.96
4907 7910 2.287009 GCTTTAACCATCCGCTATGCAC 60.287 50.000 0.00 0.00 33.92 4.57
4923 7926 2.526873 ACTGGCGGTTCTGGAGGT 60.527 61.111 0.00 0.00 0.00 3.85
4954 7957 1.135094 ATGCCCGAACCATCTCAGAT 58.865 50.000 0.00 0.00 0.00 2.90
4960 7963 2.224233 CCGAACCATCTCAGATGATGCT 60.224 50.000 16.90 0.00 41.65 3.79
4996 7999 0.252197 AATCGGTGCTACCCCAACTC 59.748 55.000 0.00 0.00 33.75 3.01
4997 8000 0.617820 ATCGGTGCTACCCCAACTCT 60.618 55.000 0.00 0.00 33.75 3.24
4998 8001 0.040058 TCGGTGCTACCCCAACTCTA 59.960 55.000 0.00 0.00 33.75 2.43
4999 8002 1.120530 CGGTGCTACCCCAACTCTAT 58.879 55.000 0.00 0.00 33.75 1.98
5000 8003 1.485066 CGGTGCTACCCCAACTCTATT 59.515 52.381 0.00 0.00 33.75 1.73
5001 8004 2.696707 CGGTGCTACCCCAACTCTATTA 59.303 50.000 0.00 0.00 33.75 0.98
5002 8005 3.492137 CGGTGCTACCCCAACTCTATTAC 60.492 52.174 0.00 0.00 33.75 1.89
5003 8006 3.453353 GGTGCTACCCCAACTCTATTACA 59.547 47.826 0.00 0.00 30.04 2.41
5004 8007 4.102681 GGTGCTACCCCAACTCTATTACAT 59.897 45.833 0.00 0.00 30.04 2.29
5005 8008 5.306160 GGTGCTACCCCAACTCTATTACATA 59.694 44.000 0.00 0.00 30.04 2.29
5006 8009 6.013639 GGTGCTACCCCAACTCTATTACATAT 60.014 42.308 0.00 0.00 30.04 1.78
5007 8010 7.179694 GGTGCTACCCCAACTCTATTACATATA 59.820 40.741 0.00 0.00 30.04 0.86
5008 8011 8.759782 GTGCTACCCCAACTCTATTACATATAT 58.240 37.037 0.00 0.00 0.00 0.86
5009 8012 8.758829 TGCTACCCCAACTCTATTACATATATG 58.241 37.037 11.29 11.29 0.00 1.78
5127 8136 0.961019 TCAGTTGGCCAACATTCAGC 59.039 50.000 41.88 19.96 43.47 4.26
5150 8159 5.277779 GCGCCATACAACATCATAGCTTTTA 60.278 40.000 0.00 0.00 0.00 1.52
5186 8196 4.335874 GTCATAGAGGACGTCAGAAGCTTA 59.664 45.833 18.91 0.14 0.00 3.09
5243 8253 5.761726 GGCTCACATCTTCATTGATATCACA 59.238 40.000 4.48 0.00 0.00 3.58
5253 8263 9.246670 TCTTCATTGATATCACAATCCTTTTGT 57.753 29.630 4.48 0.00 38.25 2.83
5328 8351 1.346479 GGCTAACTTCCCCCTCCTCC 61.346 65.000 0.00 0.00 0.00 4.30
5338 8361 0.264955 CCCCTCCTCCTGCCTAGTAA 59.735 60.000 0.00 0.00 0.00 2.24
5437 8462 6.540914 CCGCCAATCTAACTTTCTATTAACCA 59.459 38.462 0.00 0.00 0.00 3.67
5446 8471 4.161001 ACTTTCTATTAACCACCGTCCGAT 59.839 41.667 0.00 0.00 0.00 4.18
5452 8477 2.032680 AACCACCGTCCGATTATTGG 57.967 50.000 0.00 0.00 0.00 3.16
5549 8574 5.349543 CCATCACCAAAGCAAAAAGATAAGC 59.650 40.000 0.00 0.00 0.00 3.09
5712 8751 3.873361 ACATGACATTCCGCAGTATCTTG 59.127 43.478 0.00 0.00 0.00 3.02
5714 8753 4.729227 TGACATTCCGCAGTATCTTGTA 57.271 40.909 0.00 0.00 0.00 2.41
5775 8816 6.227522 GTCCTTCTTTTGCTCCCTATATCTC 58.772 44.000 0.00 0.00 0.00 2.75
5776 8817 5.308237 TCCTTCTTTTGCTCCCTATATCTCC 59.692 44.000 0.00 0.00 0.00 3.71
5954 8995 8.854117 ACGGTAATTACTAATTAGTACCCTCTG 58.146 37.037 22.22 18.49 38.43 3.35
5972 9013 6.879458 ACCCTCTGTGTTCACAAATATAAGAC 59.121 38.462 7.07 0.00 0.00 3.01
6089 9135 9.316730 CCAAAACATCTTATATTTGTGAATGGG 57.683 33.333 0.00 0.00 32.29 4.00
6172 9218 3.428045 CCATTCTTCGGGCATCTTGTTTC 60.428 47.826 0.00 0.00 0.00 2.78
6188 9234 5.945784 TCTTGTTTCCCTGAAATATGAGGTG 59.054 40.000 0.00 0.00 33.97 4.00
6311 9357 0.031616 AGAGCCTCCCTGACCTTAGG 60.032 60.000 0.00 0.00 37.59 2.69
6341 9387 1.197036 TCGTCGCACAAAACACACAAA 59.803 42.857 0.00 0.00 0.00 2.83
6554 9968 1.659211 CGTGTTTAAACGCTGGCAGAC 60.659 52.381 24.99 8.81 36.65 3.51
6561 9975 3.114616 CGCTGGCAGACGTCCTTG 61.115 66.667 20.86 6.16 0.00 3.61
6657 10071 8.664669 TGTATGCACTCCTATCCAATTATAGA 57.335 34.615 0.00 0.00 32.13 1.98
6658 10072 9.271921 TGTATGCACTCCTATCCAATTATAGAT 57.728 33.333 0.00 0.00 32.13 1.98
6781 10199 0.721718 GACACGAATCCGAAAGCAGG 59.278 55.000 0.00 0.00 39.50 4.85
6790 10208 5.163754 CGAATCCGAAAGCAGGAAGTTAAAT 60.164 40.000 0.00 0.00 41.69 1.40
6835 10255 0.390866 CGCATGTGGAGAGAGCAAGT 60.391 55.000 0.00 0.00 0.00 3.16
7196 10616 6.426937 GGTACAGACAAATGCTTCTTACAGAA 59.573 38.462 0.00 0.00 32.50 3.02
7420 10847 8.834749 ATACCTTTGTTCTTCTCAGTACTTTC 57.165 34.615 0.00 0.00 0.00 2.62
7425 10852 4.654262 TGTTCTTCTCAGTACTTTCCACCT 59.346 41.667 0.00 0.00 0.00 4.00
7463 10890 3.987404 AGCAATCACGGCTGGAAC 58.013 55.556 0.00 0.00 40.80 3.62
7541 10968 1.487976 TCAGCAATCAGTGGATCCTCC 59.512 52.381 14.23 3.45 36.96 4.30
7573 11001 0.838987 AACGGCAGGAGAACCCCTTA 60.839 55.000 0.00 0.00 33.38 2.69
7577 11005 2.168496 GGCAGGAGAACCCCTTAAAAC 58.832 52.381 0.00 0.00 33.38 2.43
7628 11056 1.398390 CCCGAGTAAATTGCAGCAGTC 59.602 52.381 0.00 0.00 0.00 3.51
7662 11090 7.338710 TGGTCTAAGAATCTTGGAATTAGTGG 58.661 38.462 10.64 0.00 0.00 4.00
7665 11093 7.496263 GTCTAAGAATCTTGGAATTAGTGGTCC 59.504 40.741 10.64 0.00 0.00 4.46
7755 11183 1.153628 CCGTCTTCCGTCCATGGAC 60.154 63.158 31.59 31.59 37.89 4.02
7764 11192 1.883084 GTCCATGGACGATGACGCC 60.883 63.158 28.52 3.15 43.96 5.68
7796 11225 4.204799 GGTGTGTTTTACTCCCTCTGTTT 58.795 43.478 0.00 0.00 37.04 2.83
7867 12892 2.294512 GGGACAAGCTTTTTCAGACAGG 59.705 50.000 0.00 0.00 0.00 4.00
7872 12900 4.816925 ACAAGCTTTTTCAGACAGGAGTAC 59.183 41.667 0.00 0.00 0.00 2.73
7903 12931 5.532032 CCTTTTTCCTTTTTGGACATGCATT 59.468 36.000 0.00 0.00 46.14 3.56
7904 12932 6.039605 CCTTTTTCCTTTTTGGACATGCATTT 59.960 34.615 0.00 0.00 46.14 2.32
7960 12989 2.482374 GCATCGGCAGTGTTCAGC 59.518 61.111 0.00 0.00 40.72 4.26
7961 12990 2.780643 CATCGGCAGTGTTCAGCG 59.219 61.111 0.00 0.00 0.00 5.18
7970 12999 2.661537 TGTTCAGCGGTGCGTCAG 60.662 61.111 10.38 0.00 0.00 3.51
7994 13023 4.022676 GCATAGTCTAGCTAGGTGACTTCC 60.023 50.000 20.58 13.08 43.67 3.46
8028 13057 7.095816 CGGTTTTAGCTTGGTTTCCTTTTAATG 60.096 37.037 0.00 0.00 0.00 1.90
8090 13119 7.095270 TGCTAGTGATAATGATATGCTCACAG 58.905 38.462 0.00 0.00 38.90 3.66
8091 13120 7.095910 GCTAGTGATAATGATATGCTCACAGT 58.904 38.462 0.00 0.00 38.90 3.55
8092 13121 7.275341 GCTAGTGATAATGATATGCTCACAGTC 59.725 40.741 0.00 0.00 38.90 3.51
8093 13122 7.059202 AGTGATAATGATATGCTCACAGTCA 57.941 36.000 0.00 0.00 38.90 3.41
8094 13123 6.927936 AGTGATAATGATATGCTCACAGTCAC 59.072 38.462 0.00 0.00 39.48 3.67
8095 13124 6.703165 GTGATAATGATATGCTCACAGTCACA 59.297 38.462 0.00 0.00 39.25 3.58
8118 13147 9.580916 CACATGCATAGTTATCGTTTGTTATAC 57.419 33.333 0.00 0.00 0.00 1.47
8139 13168 7.953158 ATACTTGTAAGATTCATGGTCATCG 57.047 36.000 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.951040 ACGGTGAGCTTGCAACTAGC 60.951 55.000 0.00 0.00 45.96 3.42
1 2 0.792640 CACGGTGAGCTTGCAACTAG 59.207 55.000 0.74 0.00 0.00 2.57
2 3 1.227999 GCACGGTGAGCTTGCAACTA 61.228 55.000 13.29 0.00 36.22 2.24
3 4 2.546494 GCACGGTGAGCTTGCAACT 61.546 57.895 13.29 0.00 36.22 3.16
4 5 2.050985 GCACGGTGAGCTTGCAAC 60.051 61.111 13.29 0.00 36.22 4.17
5 6 2.203195 AGCACGGTGAGCTTGCAA 60.203 55.556 15.36 0.00 39.87 4.08
6 7 2.974148 CAGCACGGTGAGCTTGCA 60.974 61.111 15.36 0.00 41.14 4.08
7 8 3.730761 CCAGCACGGTGAGCTTGC 61.731 66.667 13.29 4.87 41.14 4.01
8 9 3.052082 CCCAGCACGGTGAGCTTG 61.052 66.667 13.29 4.07 41.14 4.01
18 19 3.513750 AAAGGTCAGGGCCCAGCAC 62.514 63.158 27.56 16.88 0.00 4.40
19 20 2.310930 AAAAAGGTCAGGGCCCAGCA 62.311 55.000 27.56 3.33 0.00 4.41
93 94 3.838244 AAGTGTGGACTTGCAACTAGA 57.162 42.857 0.00 0.00 41.12 2.43
113 114 2.602676 GGGCCCTAGTTGTGAGCCA 61.603 63.158 17.04 0.00 45.72 4.75
115 116 2.125106 CGGGCCCTAGTTGTGAGC 60.125 66.667 22.43 0.00 0.00 4.26
119 120 0.696501 AAATGTCGGGCCCTAGTTGT 59.303 50.000 22.43 0.00 0.00 3.32
143 144 1.376609 CGTGGGATTGCAACTAGGCC 61.377 60.000 0.00 0.00 0.00 5.19
153 154 1.227999 ACGAGTTGTGCGTGGGATTG 61.228 55.000 0.00 0.00 40.94 2.67
177 178 3.118992 GGACAAAAAGAAGATCATGCCCC 60.119 47.826 0.00 0.00 0.00 5.80
182 183 5.279156 GCAACTGGGACAAAAAGAAGATCAT 60.279 40.000 0.00 0.00 38.70 2.45
225 226 1.203001 CCAAAAGGTCAGCCCTGGTTA 60.203 52.381 0.00 0.00 45.47 2.85
228 229 1.607467 CCCAAAAGGTCAGCCCTGG 60.607 63.158 0.00 0.00 45.47 4.45
229 230 1.607467 CCCCAAAAGGTCAGCCCTG 60.607 63.158 0.00 0.00 45.47 4.45
248 287 0.609151 TATTGTCGCCCAAGGTCGAA 59.391 50.000 0.00 0.00 36.25 3.71
252 291 7.648039 TTATTTATTTATTGTCGCCCAAGGT 57.352 32.000 0.00 0.00 36.25 3.50
282 321 9.265901 CCCATCATTGTATTGTTTGTTTTGTTA 57.734 29.630 0.00 0.00 0.00 2.41
307 346 8.383175 TCCCACATCAGTAGATAAATAAATCCC 58.617 37.037 0.00 0.00 31.88 3.85
308 347 9.965902 ATCCCACATCAGTAGATAAATAAATCC 57.034 33.333 0.00 0.00 31.88 3.01
322 2660 4.082665 GATGACATCATCCCACATCAGT 57.917 45.455 10.67 0.00 45.24 3.41
327 2665 5.635278 AACTATGATGACATCATCCCACA 57.365 39.130 29.70 14.26 46.62 4.17
374 2712 9.344772 GGTCCGACTATGTCATATCTAAGATAT 57.655 37.037 0.00 0.00 32.09 1.63
375 2713 7.774157 GGGTCCGACTATGTCATATCTAAGATA 59.226 40.741 0.00 0.00 32.09 1.98
376 2714 6.603997 GGGTCCGACTATGTCATATCTAAGAT 59.396 42.308 0.00 0.00 32.09 2.40
377 2715 5.944599 GGGTCCGACTATGTCATATCTAAGA 59.055 44.000 0.00 0.00 32.09 2.10
378 2716 5.163744 CGGGTCCGACTATGTCATATCTAAG 60.164 48.000 2.83 0.00 42.83 2.18
379 2717 4.698780 CGGGTCCGACTATGTCATATCTAA 59.301 45.833 2.83 0.00 42.83 2.10
381 2719 3.082548 CGGGTCCGACTATGTCATATCT 58.917 50.000 2.83 0.00 42.83 1.98
382 2720 3.079578 TCGGGTCCGACTATGTCATATC 58.920 50.000 8.14 0.00 44.01 1.63
383 2721 3.150458 TCGGGTCCGACTATGTCATAT 57.850 47.619 8.14 0.00 44.01 1.78
384 2722 2.643995 TCGGGTCCGACTATGTCATA 57.356 50.000 8.14 0.00 44.01 2.15
385 2723 3.507675 TCGGGTCCGACTATGTCAT 57.492 52.632 8.14 0.00 44.01 3.06
1186 3550 3.047877 GGTGTTTCGGGTCAGGCG 61.048 66.667 0.00 0.00 0.00 5.52
1223 3587 1.217882 GTAATCACAGAATCCGGGCG 58.782 55.000 0.00 0.00 0.00 6.13
1799 4168 5.048713 GGGAACACCACAAGAAACTATGAAG 60.049 44.000 0.00 0.00 39.85 3.02
1828 4198 4.318071 CACAAATTAACAGATGCAACGACG 59.682 41.667 0.00 0.00 0.00 5.12
1978 4348 8.043113 ACATGAGCTTAACTGAATCAAGTCATA 58.957 33.333 0.00 0.00 0.00 2.15
2187 4557 7.023575 GGTCATAGCAACAAAACAGATACAAG 58.976 38.462 0.00 0.00 0.00 3.16
2278 4648 2.953648 CCAGCCATCATATGCACTTTCA 59.046 45.455 0.00 0.00 0.00 2.69
2459 5062 8.650143 AGAAAAGGCCATTTTAATCTCTGTAA 57.350 30.769 7.50 0.00 41.24 2.41
2638 5242 3.650942 TCTAGGGAGCCTGTTTTTCAAGA 59.349 43.478 0.00 0.00 34.61 3.02
2676 5280 1.731160 GCAAACAAAACAAGTGCAGCA 59.269 42.857 0.00 0.00 35.28 4.41
2679 5283 4.512944 TCAAAAGCAAACAAAACAAGTGCA 59.487 33.333 0.00 0.00 37.68 4.57
2807 5411 7.041644 CGGTTCTCTAAACAAAAGGACACATTA 60.042 37.037 0.00 0.00 0.00 1.90
2902 5622 3.976942 GCATGTGTCAATTGAACAGTCAC 59.023 43.478 10.35 13.64 31.90 3.67
3032 5752 7.807977 ACATCTTGGACAATATGACCATAAC 57.192 36.000 14.77 0.00 41.46 1.89
3091 5811 1.575922 CCCGCATTCACACACACAG 59.424 57.895 0.00 0.00 0.00 3.66
3118 5838 8.836268 ATTTACATTGAATTGAAACACATGCT 57.164 26.923 0.00 0.00 0.00 3.79
3128 5851 6.867816 GGACACTGCAATTTACATTGAATTGA 59.132 34.615 5.78 0.00 43.71 2.57
3217 6154 2.201732 TGTGCTTCACAGTTTCTCGAC 58.798 47.619 0.00 0.00 39.62 4.20
3373 6312 3.008330 AGTCTAGCATTGCAGAAAGCTG 58.992 45.455 11.91 0.00 45.94 4.24
3493 6438 2.352651 CCAGTTCACCATGCGACTAATG 59.647 50.000 0.00 0.00 0.00 1.90
3641 6587 3.686726 GCTAGCCATAGTGCATACATTCC 59.313 47.826 2.29 0.00 0.00 3.01
3757 6726 1.394917 CTCCTGCAATTTCTTCCGTCG 59.605 52.381 0.00 0.00 0.00 5.12
3853 6828 5.552178 ACAAGCCTCCAAAAGTAAGACTAG 58.448 41.667 0.00 0.00 0.00 2.57
3926 6914 1.200020 GTGACATAGCCAACCTGCAAC 59.800 52.381 0.00 0.00 0.00 4.17
3956 6944 8.902806 ACACATCTGATCAAGAAACAAGTAAAA 58.097 29.630 0.00 0.00 38.79 1.52
4024 7012 8.133627 TGGTAGAATAGCGTAGATCAAAGTAAC 58.866 37.037 0.00 0.00 43.27 2.50
4062 7050 7.411808 AGTTAGTAGATTCCTCTAACTCACCA 58.588 38.462 17.71 0.00 45.72 4.17
4089 7077 5.356190 AGACACATCTGGAAATTACATGCTG 59.644 40.000 0.00 0.00 32.29 4.41
4132 7120 2.354259 CTCAGAACATCAAGGTCAGCC 58.646 52.381 0.00 0.00 35.97 4.85
4138 7126 2.295885 GGATGGCTCAGAACATCAAGG 58.704 52.381 13.87 0.00 44.01 3.61
4256 7244 9.158364 GTTTATCATAGCAAAATACACATCACG 57.842 33.333 0.00 0.00 0.00 4.35
4483 7471 5.644644 ACAAACCTAACTAACCTCGATACG 58.355 41.667 0.00 0.00 0.00 3.06
4534 7522 3.006756 ATGTGAGCGAGGTGGACCG 62.007 63.158 0.00 0.00 42.08 4.79
4596 7585 6.624423 GCATGCATATCCATGTTCTTGATACC 60.624 42.308 14.21 0.00 43.46 2.73
4646 7635 6.952935 TTGTTGTTGTTGTTATTGTTGTCC 57.047 33.333 0.00 0.00 0.00 4.02
4652 7641 4.026145 CGGGCTTTGTTGTTGTTGTTATTG 60.026 41.667 0.00 0.00 0.00 1.90
4653 7642 4.116238 CGGGCTTTGTTGTTGTTGTTATT 58.884 39.130 0.00 0.00 0.00 1.40
4655 7644 2.159226 CCGGGCTTTGTTGTTGTTGTTA 60.159 45.455 0.00 0.00 0.00 2.41
4695 7698 4.534500 TCTTATGGGTTTCAACTCTAGCCA 59.466 41.667 0.00 0.00 42.93 4.75
4760 7763 4.394712 GGACAGGGGTGCGTGGAG 62.395 72.222 0.00 0.00 0.00 3.86
4836 7839 6.664384 GGGGTACAATAAACTTTACATGGGAA 59.336 38.462 0.00 0.00 0.00 3.97
4852 7855 3.009143 GTCAAGAGAGGTTGGGGTACAAT 59.991 47.826 0.00 0.00 41.95 2.71
4853 7856 2.370849 GTCAAGAGAGGTTGGGGTACAA 59.629 50.000 0.00 0.00 36.54 2.41
4855 7858 1.975680 TGTCAAGAGAGGTTGGGGTAC 59.024 52.381 0.00 0.00 0.00 3.34
4862 7865 5.181748 GCACTCATAATGTCAAGAGAGGTT 58.818 41.667 0.00 0.00 32.59 3.50
4907 7910 2.266055 GACCTCCAGAACCGCCAG 59.734 66.667 0.00 0.00 0.00 4.85
4923 7926 0.747852 TCGGGCATATACAACGCAGA 59.252 50.000 0.00 0.00 0.00 4.26
4960 7963 3.329386 CGATTGAAGAGAAGCTTGTCCA 58.671 45.455 19.26 8.99 36.83 4.02
5004 8007 9.607333 GGGTCCAGAATGAGGATATATCATATA 57.393 37.037 14.60 1.11 39.69 0.86
5005 8008 7.234371 CGGGTCCAGAATGAGGATATATCATAT 59.766 40.741 14.60 2.96 39.69 1.78
5006 8009 6.551227 CGGGTCCAGAATGAGGATATATCATA 59.449 42.308 14.60 0.70 39.69 2.15
5007 8010 5.365025 CGGGTCCAGAATGAGGATATATCAT 59.635 44.000 14.60 7.37 39.69 2.45
5008 8011 4.711846 CGGGTCCAGAATGAGGATATATCA 59.288 45.833 14.60 0.00 39.69 2.15
5009 8012 4.956700 TCGGGTCCAGAATGAGGATATATC 59.043 45.833 3.96 3.96 39.69 1.63
5057 8060 3.679361 GCAGAGATGAGCATGTTGAGACT 60.679 47.826 0.00 0.00 0.00 3.24
5058 8061 2.608546 GCAGAGATGAGCATGTTGAGAC 59.391 50.000 0.00 0.00 0.00 3.36
5127 8136 4.818534 AAAGCTATGATGTTGTATGGCG 57.181 40.909 0.00 0.00 36.12 5.69
5150 8159 6.015856 CGTCCTCTATGACAAGAGAATACCAT 60.016 42.308 13.17 0.00 44.93 3.55
5186 8196 0.994247 TGGATGGATGAAGTGGTGCT 59.006 50.000 0.00 0.00 0.00 4.40
5243 8253 3.198417 GGGATCAATGCCACAAAAGGATT 59.802 43.478 0.00 0.00 38.30 3.01
5253 8263 2.905736 TCGATATCTGGGATCAATGCCA 59.094 45.455 3.06 3.06 46.64 4.92
5328 8351 3.802685 GCGGTTTCAGTATTACTAGGCAG 59.197 47.826 0.00 0.00 0.00 4.85
5338 8361 2.027192 ACATGAGGTGCGGTTTCAGTAT 60.027 45.455 0.00 0.00 0.00 2.12
5382 8407 6.839134 AGACTTTGGAATTGGAAGGTTTTAGT 59.161 34.615 0.00 0.00 0.00 2.24
5437 8462 0.529119 GTCGCCAATAATCGGACGGT 60.529 55.000 0.00 0.00 0.00 4.83
5452 8477 1.084370 GGTGATGTGGTGCTAGTCGC 61.084 60.000 0.00 0.00 39.77 5.19
5712 8751 3.097614 TGACTTGGAGAAGGCCTACTAC 58.902 50.000 5.16 0.00 36.19 2.73
5714 8753 2.327325 TGACTTGGAGAAGGCCTACT 57.673 50.000 5.16 0.00 36.19 2.57
5954 8995 9.737025 GTTAGAACGTCTTATATTTGTGAACAC 57.263 33.333 0.00 0.00 0.00 3.32
6089 9135 2.882761 GGTGTTCAAAGTTGTACTCCCC 59.117 50.000 9.50 1.82 36.64 4.81
6172 9218 4.098501 GCTTTTCCACCTCATATTTCAGGG 59.901 45.833 0.00 0.00 33.57 4.45
6311 9357 2.167861 GTGCGACGAATCCAGGAGC 61.168 63.158 0.00 0.00 0.00 4.70
6341 9387 4.246458 GAGAACTCTACCATTGAGCGTTT 58.754 43.478 0.00 0.00 35.12 3.60
6554 9968 0.462047 GGGTCAGGCATACAAGGACG 60.462 60.000 0.00 0.00 0.00 4.79
6561 9975 0.034089 AAGCAAGGGGTCAGGCATAC 60.034 55.000 0.00 0.00 0.00 2.39
6658 10072 9.698309 CTATTAAGAAGAAGACTGTTTCAGACA 57.302 33.333 3.70 0.00 35.18 3.41
6676 10094 6.517362 CGATGATGTCCAGAAGGCTATTAAGA 60.517 42.308 0.00 0.00 33.74 2.10
6790 10208 2.026262 GGGGCCTGAGTGATACTTTTCA 60.026 50.000 0.84 0.00 0.00 2.69
6819 10239 2.255406 ACTGACTTGCTCTCTCCACAT 58.745 47.619 0.00 0.00 0.00 3.21
6835 10255 4.687769 GCCCCGATTATCCCTTTTAACTGA 60.688 45.833 0.00 0.00 0.00 3.41
7187 10607 9.042450 TCTCCTGTATTTACCAATTCTGTAAGA 57.958 33.333 0.00 0.00 44.68 2.10
7196 10616 5.450818 TTGCCTCTCCTGTATTTACCAAT 57.549 39.130 0.00 0.00 0.00 3.16
7420 10847 0.670546 CGGTGCAGACTACAAGGTGG 60.671 60.000 0.00 0.00 0.00 4.61
7425 10852 2.736995 GCGCGGTGCAGACTACAA 60.737 61.111 8.83 0.00 45.45 2.41
7463 10890 4.566360 GTGGGTCAAAAATCAAATATGCGG 59.434 41.667 0.00 0.00 0.00 5.69
7573 11001 2.416701 CCAGACCTGCAACGTTTGTTTT 60.417 45.455 0.00 0.00 35.72 2.43
7577 11005 1.101049 ACCCAGACCTGCAACGTTTG 61.101 55.000 0.00 0.00 0.00 2.93
7628 11056 5.428184 AGATTCTTAGACCAAAGTGAGGG 57.572 43.478 0.00 0.00 0.00 4.30
7662 11090 4.976116 CACCAAAATGAAGAGTTTTCGGAC 59.024 41.667 0.00 0.00 0.00 4.79
7665 11093 4.207019 GTGCACCAAAATGAAGAGTTTTCG 59.793 41.667 5.22 0.00 0.00 3.46
7755 11183 1.300465 CCATCCAGAGGCGTCATCG 60.300 63.158 9.41 0.00 40.37 3.84
7759 11187 3.083997 ACCCCATCCAGAGGCGTC 61.084 66.667 0.00 0.00 0.00 5.19
7764 11192 2.292828 AAAACACACCCCATCCAGAG 57.707 50.000 0.00 0.00 0.00 3.35
7821 12840 7.332926 CCTCAAATGGATGTATCTAGCACATAC 59.667 40.741 10.93 10.93 36.76 2.39
7822 12841 7.389232 CCTCAAATGGATGTATCTAGCACATA 58.611 38.462 9.10 0.00 36.76 2.29
7838 12857 4.202243 TGAAAAAGCTTGTCCCTCAAATGG 60.202 41.667 0.00 0.00 35.48 3.16
7843 12862 3.214328 GTCTGAAAAAGCTTGTCCCTCA 58.786 45.455 0.00 0.00 0.00 3.86
7867 12892 8.869897 CAAAAAGGAAAAAGGAAAACAGTACTC 58.130 33.333 0.00 0.00 0.00 2.59
7904 12932 3.067461 AGCACGATACAAACAGGCAAAAA 59.933 39.130 0.00 0.00 0.00 1.94
7911 12939 2.805671 TGGACAAGCACGATACAAACAG 59.194 45.455 0.00 0.00 0.00 3.16
7952 12981 2.943345 CTGACGCACCGCTGAACAC 61.943 63.158 0.00 0.00 0.00 3.32
7970 12999 3.492337 AGTCACCTAGCTAGACTATGCC 58.508 50.000 22.70 4.95 40.59 4.40
8013 13042 5.711698 AGAACCTCCATTAAAAGGAAACCA 58.288 37.500 8.46 0.00 36.46 3.67
8028 13057 5.998363 ACAAGAACTAAACATGAGAACCTCC 59.002 40.000 0.00 0.00 0.00 4.30
8090 13119 6.106877 ACAAACGATAACTATGCATGTGAC 57.893 37.500 10.16 1.16 0.00 3.67
8091 13120 6.735678 AACAAACGATAACTATGCATGTGA 57.264 33.333 10.16 0.00 0.00 3.58
8092 13121 9.580916 GTATAACAAACGATAACTATGCATGTG 57.419 33.333 10.16 4.66 0.00 3.21
8093 13122 9.542462 AGTATAACAAACGATAACTATGCATGT 57.458 29.630 10.16 2.51 0.00 3.21
8118 13147 4.813161 AGCGATGACCATGAATCTTACAAG 59.187 41.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.