Multiple sequence alignment - TraesCS7B01G407300

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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 TraesCS7B01G407300 chr7B 100.000 2103 0 0 1847 3949 676411269 676413371 0.000000e+00 3884.0
1 TraesCS7B01G407300 chr7B 100.000 1365 0 0 1 1365 676409423 676410787 0.000000e+00 2521.0
2 TraesCS7B01G407300 chr7B 90.998 511 29 5 2583 3078 632037009 632036501 0.000000e+00 673.0
3 TraesCS7B01G407300 chr7B 93.548 217 11 3 1152 1365 412244870 412245086 1.770000e-83 320.0
4 TraesCS7B01G407300 chr7B 95.522 67 3 0 634 700 663837774 663837840 1.500000e-19 108.0
5 TraesCS7B01G407300 chr7D 91.191 1226 70 18 1864 3073 597683651 597682448 0.000000e+00 1631.0
6 TraesCS7B01G407300 chr7D 91.399 686 34 5 3231 3912 597681948 597681284 0.000000e+00 917.0
7 TraesCS7B01G407300 chr7D 90.909 605 14 15 771 1365 597684360 597683787 0.000000e+00 774.0
8 TraesCS7B01G407300 chr7D 88.889 558 41 11 89 635 597684914 597684367 0.000000e+00 667.0
9 TraesCS7B01G407300 chr7D 82.888 187 26 3 251 437 89471605 89471425 3.160000e-36 163.0
10 TraesCS7B01G407300 chr7D 98.485 66 1 0 634 699 41258342 41258407 2.490000e-22 117.0
11 TraesCS7B01G407300 chr7D 95.522 67 3 0 634 700 133500526 133500460 1.500000e-19 108.0
12 TraesCS7B01G407300 chr7D 95.522 67 3 0 634 700 133603975 133604041 1.500000e-19 108.0
13 TraesCS7B01G407300 chr7D 100.000 38 0 0 3912 3949 597681189 597681152 1.970000e-08 71.3
14 TraesCS7B01G407300 chr7D 91.667 48 4 0 3526 3573 597681620 597681573 2.550000e-07 67.6
15 TraesCS7B01G407300 chr7A 85.024 1262 75 38 1862 3078 690362945 690364137 0.000000e+00 1179.0
16 TraesCS7B01G407300 chr7A 91.792 597 11 9 771 1365 690362278 690362838 0.000000e+00 797.0
17 TraesCS7B01G407300 chr7A 94.072 388 19 3 251 636 690361887 690362272 1.580000e-163 586.0
18 TraesCS7B01G407300 chr7A 87.336 458 29 11 3360 3817 690364546 690364974 7.620000e-137 497.0
19 TraesCS7B01G407300 chr7A 90.991 333 29 1 2490 2821 143841229 143841561 7.780000e-122 448.0
20 TraesCS7B01G407300 chr7A 95.420 131 4 2 3817 3946 690368634 690368763 1.440000e-49 207.0
21 TraesCS7B01G407300 chrUn 89.366 536 46 6 830 1365 60959551 60959027 0.000000e+00 664.0
22 TraesCS7B01G407300 chrUn 87.847 288 31 3 252 536 60960455 60960169 6.320000e-88 335.0
23 TraesCS7B01G407300 chrUn 94.286 70 3 1 630 699 88582973 88582905 5.400000e-19 106.0
24 TraesCS7B01G407300 chr4B 88.540 541 31 16 828 1365 5537362 5536850 9.320000e-176 627.0
25 TraesCS7B01G407300 chr4B 81.844 716 42 24 1847 2539 656436905 656437555 4.520000e-144 521.0
26 TraesCS7B01G407300 chr4B 87.404 389 43 3 251 636 5537779 5537394 3.620000e-120 442.0
27 TraesCS7B01G407300 chr4B 94.949 198 9 1 1169 1365 188424909 188424712 3.830000e-80 309.0
28 TraesCS7B01G407300 chr1B 84.844 640 48 20 1862 2481 603632573 603633183 2.030000e-167 599.0
29 TraesCS7B01G407300 chr1B 82.403 699 40 19 1862 2541 169145719 169145085 2.090000e-147 532.0
30 TraesCS7B01G407300 chr1B 81.667 720 41 35 1847 2541 546901081 546900428 7.570000e-142 514.0
31 TraesCS7B01G407300 chr4A 86.034 537 31 22 830 1365 601197663 601197170 1.610000e-148 536.0
32 TraesCS7B01G407300 chr3A 84.495 574 37 17 1847 2396 731695944 731696489 1.630000e-143 520.0
33 TraesCS7B01G407300 chr3A 90.582 361 34 0 3232 3592 329506626 329506986 2.760000e-131 479.0
34 TraesCS7B01G407300 chr2D 92.814 334 23 1 2489 2821 10247652 10247319 2.130000e-132 483.0
35 TraesCS7B01G407300 chr2D 91.746 315 23 3 2489 2802 274432414 274432102 6.060000e-118 435.0
36 TraesCS7B01G407300 chr2D 96.970 66 2 0 634 699 422077422 422077357 1.160000e-20 111.0
37 TraesCS7B01G407300 chr3B 92.515 334 25 0 3259 3592 344300991 344300658 2.760000e-131 479.0
38 TraesCS7B01G407300 chr3B 90.691 333 30 1 2490 2821 778204758 778204426 3.620000e-120 442.0
39 TraesCS7B01G407300 chr3B 90.090 333 32 1 2490 2821 778177830 778177498 7.840000e-117 431.0
40 TraesCS7B01G407300 chr3B 92.273 220 11 5 1152 1365 646451398 646451617 1.380000e-79 307.0
41 TraesCS7B01G407300 chr3B 95.522 67 3 0 634 700 119949863 119949797 1.500000e-19 108.0
42 TraesCS7B01G407300 chr3B 90.000 60 6 0 713 772 566831873 566831932 1.180000e-10 78.7
43 TraesCS7B01G407300 chr3B 96.774 31 1 0 746 776 659302527 659302557 7.000000e-03 52.8
44 TraesCS7B01G407300 chr3D 92.216 334 25 1 2489 2821 443996384 443996717 4.620000e-129 472.0
45 TraesCS7B01G407300 chr3D 90.060 332 33 0 3261 3592 228187261 228186930 7.840000e-117 431.0
46 TraesCS7B01G407300 chr3D 95.522 67 3 0 634 700 247879472 247879406 1.500000e-19 108.0
47 TraesCS7B01G407300 chr6B 83.567 499 35 14 2047 2540 69398955 69399411 1.310000e-114 424.0
48 TraesCS7B01G407300 chr6B 80.590 644 38 27 1847 2467 628550457 628551036 2.200000e-112 416.0
49 TraesCS7B01G407300 chr5D 92.558 215 12 3 1155 1365 444011908 444011694 4.960000e-79 305.0
50 TraesCS7B01G407300 chr5D 85.075 67 8 2 709 773 561625412 561625478 2.550000e-07 67.6
51 TraesCS7B01G407300 chr1A 95.522 67 3 0 634 700 189955752 189955686 1.500000e-19 108.0
52 TraesCS7B01G407300 chr1A 87.671 73 8 1 693 765 518935629 518935700 2.530000e-12 84.2
53 TraesCS7B01G407300 chr5B 85.185 81 9 2 693 773 638765904 638765981 3.270000e-11 80.5


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 TraesCS7B01G407300 chr7B 676409423 676413371 3948 False 3202.500000 3884 100.0000 1 3949 2 chr7B.!!$F3 3948
1 TraesCS7B01G407300 chr7B 632036501 632037009 508 True 673.000000 673 90.9980 2583 3078 1 chr7B.!!$R1 495
2 TraesCS7B01G407300 chr7D 597681152 597684914 3762 True 687.983333 1631 92.3425 89 3949 6 chr7D.!!$R3 3860
3 TraesCS7B01G407300 chr7A 690361887 690368763 6876 False 653.200000 1179 90.7288 251 3946 5 chr7A.!!$F2 3695
4 TraesCS7B01G407300 chrUn 60959027 60960455 1428 True 499.500000 664 88.6065 252 1365 2 chrUn.!!$R2 1113
5 TraesCS7B01G407300 chr4B 5536850 5537779 929 True 534.500000 627 87.9720 251 1365 2 chr4B.!!$R2 1114
6 TraesCS7B01G407300 chr4B 656436905 656437555 650 False 521.000000 521 81.8440 1847 2539 1 chr4B.!!$F1 692
7 TraesCS7B01G407300 chr1B 603632573 603633183 610 False 599.000000 599 84.8440 1862 2481 1 chr1B.!!$F1 619
8 TraesCS7B01G407300 chr1B 169145085 169145719 634 True 532.000000 532 82.4030 1862 2541 1 chr1B.!!$R1 679
9 TraesCS7B01G407300 chr1B 546900428 546901081 653 True 514.000000 514 81.6670 1847 2541 1 chr1B.!!$R2 694
10 TraesCS7B01G407300 chr3A 731695944 731696489 545 False 520.000000 520 84.4950 1847 2396 1 chr3A.!!$F2 549
11 TraesCS7B01G407300 chr6B 628550457 628551036 579 False 416.000000 416 80.5900 1847 2467 1 chr6B.!!$F2 620

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
81 82 0.031449 GTCACCGAGAGCTCCTATGC 59.969 60.0 10.93 0.00 0.00 3.14 F
760 1268 0.035056 CCCTCTGACCATCCAACCAC 60.035 60.0 0.00 0.00 0.00 4.16 F
2512 3103 0.179124 GATCTCACTCGGCCTGTGTC 60.179 60.0 20.31 10.72 36.83 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 2448 0.179029 CCGACTGACCCCAAAACAGT 60.179 55.0 0.0 0.0 45.62 3.55 R
2591 3182 0.747283 GCTGGCTGGAGTGGATTGAG 60.747 60.0 0.0 0.0 0.00 3.02 R
3464 4521 0.533491 CCCTACGACATTCCGGTTGA 59.467 55.0 13.0 0.0 0.00 3.18 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
20 21 1.993370 GCAACTAATATAGCGAGCGGG 59.007 52.381 0.00 0.00 0.00 6.13
21 22 2.352421 GCAACTAATATAGCGAGCGGGA 60.352 50.000 0.00 0.00 0.00 5.14
22 23 3.859627 GCAACTAATATAGCGAGCGGGAA 60.860 47.826 0.00 0.00 0.00 3.97
23 24 4.495422 CAACTAATATAGCGAGCGGGAAT 58.505 43.478 0.00 0.00 0.00 3.01
24 25 4.373348 ACTAATATAGCGAGCGGGAATC 57.627 45.455 0.00 0.00 0.00 2.52
25 26 2.674796 AATATAGCGAGCGGGAATCC 57.325 50.000 0.00 0.00 0.00 3.01
26 27 0.824759 ATATAGCGAGCGGGAATCCC 59.175 55.000 8.64 8.64 41.09 3.85
37 38 1.826385 GGGAATCCCGATGCTAATGG 58.174 55.000 0.90 0.00 32.13 3.16
38 39 1.351017 GGGAATCCCGATGCTAATGGA 59.649 52.381 0.90 0.00 32.13 3.41
39 40 2.025887 GGGAATCCCGATGCTAATGGAT 60.026 50.000 0.90 0.00 39.26 3.41
40 41 3.199946 GGGAATCCCGATGCTAATGGATA 59.800 47.826 0.90 0.00 36.60 2.59
41 42 4.446371 GGAATCCCGATGCTAATGGATAG 58.554 47.826 0.00 0.00 36.60 2.08
42 43 4.446371 GAATCCCGATGCTAATGGATAGG 58.554 47.826 0.00 0.00 36.60 2.57
43 44 3.184382 TCCCGATGCTAATGGATAGGA 57.816 47.619 0.00 0.00 38.65 2.94
44 45 3.724478 TCCCGATGCTAATGGATAGGAT 58.276 45.455 0.00 0.00 44.50 3.24
45 46 3.452264 TCCCGATGCTAATGGATAGGATG 59.548 47.826 0.00 0.00 42.17 3.51
46 47 3.432749 CCCGATGCTAATGGATAGGATGG 60.433 52.174 0.00 0.00 42.17 3.51
47 48 3.452264 CCGATGCTAATGGATAGGATGGA 59.548 47.826 1.63 0.00 42.17 3.41
48 49 4.102210 CCGATGCTAATGGATAGGATGGAT 59.898 45.833 1.63 0.00 42.17 3.41
49 50 5.397221 CCGATGCTAATGGATAGGATGGATT 60.397 44.000 1.63 0.00 42.17 3.01
50 51 6.183361 CCGATGCTAATGGATAGGATGGATTA 60.183 42.308 1.63 0.00 42.17 1.75
51 52 6.703607 CGATGCTAATGGATAGGATGGATTAC 59.296 42.308 0.00 0.00 42.17 1.89
52 53 6.950860 TGCTAATGGATAGGATGGATTACA 57.049 37.500 0.00 0.00 31.83 2.41
53 54 6.950842 TGCTAATGGATAGGATGGATTACAG 58.049 40.000 0.00 0.00 31.83 2.74
54 55 6.501805 TGCTAATGGATAGGATGGATTACAGT 59.498 38.462 0.00 0.00 31.83 3.55
55 56 6.820656 GCTAATGGATAGGATGGATTACAGTG 59.179 42.308 0.00 0.00 31.83 3.66
56 57 7.310671 GCTAATGGATAGGATGGATTACAGTGA 60.311 40.741 0.00 0.00 31.83 3.41
57 58 6.617782 ATGGATAGGATGGATTACAGTGAG 57.382 41.667 0.00 0.00 0.00 3.51
58 59 4.284490 TGGATAGGATGGATTACAGTGAGC 59.716 45.833 0.00 0.00 0.00 4.26
59 60 2.898729 AGGATGGATTACAGTGAGCG 57.101 50.000 0.00 0.00 0.00 5.03
60 61 2.111384 AGGATGGATTACAGTGAGCGT 58.889 47.619 0.00 0.00 0.00 5.07
61 62 3.296854 AGGATGGATTACAGTGAGCGTA 58.703 45.455 0.00 0.00 0.00 4.42
62 63 3.319405 AGGATGGATTACAGTGAGCGTAG 59.681 47.826 0.00 0.00 0.00 3.51
63 64 3.068307 GGATGGATTACAGTGAGCGTAGT 59.932 47.826 0.00 0.00 0.00 2.73
64 65 3.777465 TGGATTACAGTGAGCGTAGTC 57.223 47.619 0.00 0.00 0.00 2.59
65 66 3.086282 TGGATTACAGTGAGCGTAGTCA 58.914 45.455 0.00 0.00 29.70 3.41
66 67 3.119602 TGGATTACAGTGAGCGTAGTCAC 60.120 47.826 0.00 6.60 46.22 3.67
67 68 3.436496 GATTACAGTGAGCGTAGTCACC 58.564 50.000 0.00 0.00 46.94 4.02
68 69 0.800631 TACAGTGAGCGTAGTCACCG 59.199 55.000 0.00 4.38 46.94 4.94
69 70 0.887836 ACAGTGAGCGTAGTCACCGA 60.888 55.000 0.00 0.00 46.94 4.69
70 71 0.179187 CAGTGAGCGTAGTCACCGAG 60.179 60.000 10.04 0.32 46.94 4.63
71 72 0.321387 AGTGAGCGTAGTCACCGAGA 60.321 55.000 10.04 0.00 46.94 4.04
72 73 0.097325 GTGAGCGTAGTCACCGAGAG 59.903 60.000 4.01 0.00 40.96 3.20
73 74 1.062845 GAGCGTAGTCACCGAGAGC 59.937 63.158 0.00 0.00 0.00 4.09
74 75 1.370587 GAGCGTAGTCACCGAGAGCT 61.371 60.000 0.00 0.00 36.06 4.09
75 76 1.062845 GCGTAGTCACCGAGAGCTC 59.937 63.158 5.27 5.27 0.00 4.09
76 77 1.722677 CGTAGTCACCGAGAGCTCC 59.277 63.158 10.93 0.68 0.00 4.70
77 78 0.745128 CGTAGTCACCGAGAGCTCCT 60.745 60.000 10.93 0.47 0.00 3.69
78 79 1.472904 CGTAGTCACCGAGAGCTCCTA 60.473 57.143 10.93 0.00 0.00 2.94
79 80 2.807472 CGTAGTCACCGAGAGCTCCTAT 60.807 54.545 10.93 0.00 0.00 2.57
80 81 1.686355 AGTCACCGAGAGCTCCTATG 58.314 55.000 10.93 4.30 0.00 2.23
81 82 0.031449 GTCACCGAGAGCTCCTATGC 59.969 60.000 10.93 0.00 0.00 3.14
82 83 0.395724 TCACCGAGAGCTCCTATGCA 60.396 55.000 10.93 0.00 34.99 3.96
83 84 0.461548 CACCGAGAGCTCCTATGCAA 59.538 55.000 10.93 0.00 34.99 4.08
84 85 1.069823 CACCGAGAGCTCCTATGCAAT 59.930 52.381 10.93 0.00 34.99 3.56
85 86 1.765314 ACCGAGAGCTCCTATGCAATT 59.235 47.619 10.93 0.00 34.99 2.32
86 87 2.171448 ACCGAGAGCTCCTATGCAATTT 59.829 45.455 10.93 0.00 34.99 1.82
87 88 2.805099 CCGAGAGCTCCTATGCAATTTC 59.195 50.000 10.93 0.00 34.99 2.17
98 99 7.412346 GCTCCTATGCAATTTCGATACATGTAG 60.412 40.741 11.91 0.00 0.00 2.74
172 176 3.426917 CCCCCTACATTGCACCCT 58.573 61.111 0.00 0.00 0.00 4.34
199 203 6.471146 CCTATATTCCAACTGGAGATCCAAG 58.529 44.000 2.65 0.48 46.97 3.61
213 217 3.199946 AGATCCAAGCACCCTTTTATCGA 59.800 43.478 0.00 0.00 30.40 3.59
217 221 4.398044 TCCAAGCACCCTTTTATCGAATTC 59.602 41.667 0.00 0.00 0.00 2.17
218 222 4.399303 CCAAGCACCCTTTTATCGAATTCT 59.601 41.667 3.52 0.00 0.00 2.40
219 223 5.335127 CAAGCACCCTTTTATCGAATTCTG 58.665 41.667 3.52 0.00 0.00 3.02
220 224 3.947834 AGCACCCTTTTATCGAATTCTGG 59.052 43.478 3.52 0.00 0.00 3.86
221 225 3.489229 GCACCCTTTTATCGAATTCTGGC 60.489 47.826 3.52 0.00 0.00 4.85
222 226 3.694072 CACCCTTTTATCGAATTCTGGCA 59.306 43.478 3.52 0.00 0.00 4.92
223 227 4.339247 CACCCTTTTATCGAATTCTGGCAT 59.661 41.667 3.52 0.00 0.00 4.40
224 228 5.530915 CACCCTTTTATCGAATTCTGGCATA 59.469 40.000 3.52 0.00 0.00 3.14
303 307 1.591863 GCGGCGAGTTGGGATCTAC 60.592 63.158 12.98 0.00 0.00 2.59
508 528 2.388310 TTTAATGTCGGACGATGGCA 57.612 45.000 3.34 0.00 0.00 4.92
509 529 2.613026 TTAATGTCGGACGATGGCAT 57.387 45.000 0.00 0.00 0.00 4.40
556 1064 5.592282 TGGTCAAAGCTTGTCACAAATTCTA 59.408 36.000 0.00 0.00 0.00 2.10
572 1080 7.549488 CACAAATTCTAAGAGGAGGTTTCGTAT 59.451 37.037 0.00 0.00 0.00 3.06
636 1144 0.530744 TGAGATACGTCCACTGCACC 59.469 55.000 0.00 0.00 0.00 5.01
637 1145 0.525668 GAGATACGTCCACTGCACCG 60.526 60.000 0.00 0.00 0.00 4.94
638 1146 1.214589 GATACGTCCACTGCACCGT 59.785 57.895 0.00 0.00 37.33 4.83
639 1147 0.452987 GATACGTCCACTGCACCGTA 59.547 55.000 0.00 0.00 39.74 4.02
640 1148 1.066605 GATACGTCCACTGCACCGTAT 59.933 52.381 0.00 3.50 45.94 3.06
641 1149 0.171679 TACGTCCACTGCACCGTATG 59.828 55.000 0.00 0.00 34.95 2.39
650 1158 4.088421 CACCGTATGCACCTCGTC 57.912 61.111 0.00 0.00 0.00 4.20
651 1159 1.872234 CACCGTATGCACCTCGTCG 60.872 63.158 0.00 0.00 0.00 5.12
652 1160 2.338015 ACCGTATGCACCTCGTCGT 61.338 57.895 0.00 0.00 0.00 4.34
653 1161 1.153901 CCGTATGCACCTCGTCGTT 60.154 57.895 0.00 0.00 0.00 3.85
654 1162 1.410737 CCGTATGCACCTCGTCGTTG 61.411 60.000 0.00 0.00 0.00 4.10
655 1163 0.455464 CGTATGCACCTCGTCGTTGA 60.455 55.000 0.00 0.00 0.00 3.18
656 1164 0.989890 GTATGCACCTCGTCGTTGAC 59.010 55.000 0.00 0.00 0.00 3.18
676 1184 3.516578 GGAACGTCTTCTCCCACTG 57.483 57.895 0.00 0.00 0.00 3.66
677 1185 0.966920 GGAACGTCTTCTCCCACTGA 59.033 55.000 0.00 0.00 0.00 3.41
678 1186 1.343465 GGAACGTCTTCTCCCACTGAA 59.657 52.381 0.00 0.00 0.00 3.02
679 1187 2.028020 GGAACGTCTTCTCCCACTGAAT 60.028 50.000 0.00 0.00 0.00 2.57
680 1188 2.751166 ACGTCTTCTCCCACTGAATG 57.249 50.000 0.00 0.00 0.00 2.67
681 1189 1.338200 ACGTCTTCTCCCACTGAATGC 60.338 52.381 0.00 0.00 0.00 3.56
682 1190 1.363744 GTCTTCTCCCACTGAATGCG 58.636 55.000 0.00 0.00 0.00 4.73
683 1191 0.391661 TCTTCTCCCACTGAATGCGC 60.392 55.000 0.00 0.00 0.00 6.09
684 1192 0.674581 CTTCTCCCACTGAATGCGCA 60.675 55.000 14.96 14.96 0.00 6.09
685 1193 0.035152 TTCTCCCACTGAATGCGCAT 60.035 50.000 19.28 19.28 0.00 4.73
686 1194 0.462581 TCTCCCACTGAATGCGCATC 60.463 55.000 25.53 17.12 0.00 3.91
687 1195 1.769098 CTCCCACTGAATGCGCATCG 61.769 60.000 25.53 17.09 0.00 3.84
698 1206 2.588877 CGCATCGCCGGAAATCCT 60.589 61.111 5.05 0.00 0.00 3.24
699 1207 1.300620 CGCATCGCCGGAAATCCTA 60.301 57.895 5.05 0.00 0.00 2.94
700 1208 1.284982 CGCATCGCCGGAAATCCTAG 61.285 60.000 5.05 0.00 0.00 3.02
701 1209 1.569479 GCATCGCCGGAAATCCTAGC 61.569 60.000 5.05 0.00 0.00 3.42
702 1210 0.249868 CATCGCCGGAAATCCTAGCA 60.250 55.000 5.05 1.18 33.96 3.49
703 1211 0.249911 ATCGCCGGAAATCCTAGCAC 60.250 55.000 5.05 0.00 33.96 4.40
704 1212 1.887707 CGCCGGAAATCCTAGCACC 60.888 63.158 5.05 0.00 33.96 5.01
705 1213 1.223487 GCCGGAAATCCTAGCACCA 59.777 57.895 5.05 0.00 34.34 4.17
706 1214 0.815615 GCCGGAAATCCTAGCACCAG 60.816 60.000 5.05 0.00 34.34 4.00
707 1215 0.179045 CCGGAAATCCTAGCACCAGG 60.179 60.000 0.00 0.00 37.00 4.45
714 1222 2.550277 TCCTAGCACCAGGATCTGAA 57.450 50.000 0.00 0.00 39.89 3.02
715 1223 2.111384 TCCTAGCACCAGGATCTGAAC 58.889 52.381 0.00 0.00 39.89 3.18
716 1224 1.139853 CCTAGCACCAGGATCTGAACC 59.860 57.143 0.00 0.00 38.00 3.62
717 1225 1.139853 CTAGCACCAGGATCTGAACCC 59.860 57.143 0.00 0.00 32.44 4.11
718 1226 0.548682 AGCACCAGGATCTGAACCCT 60.549 55.000 0.00 0.00 32.44 4.34
738 1246 3.431415 CTGATGGGATCGGGATACTACA 58.569 50.000 0.00 0.00 31.92 2.74
739 1247 3.431415 TGATGGGATCGGGATACTACAG 58.569 50.000 0.00 0.00 0.00 2.74
740 1248 3.181422 TGATGGGATCGGGATACTACAGT 60.181 47.826 0.00 0.00 0.00 3.55
741 1249 2.872732 TGGGATCGGGATACTACAGTC 58.127 52.381 0.00 0.00 0.00 3.51
742 1250 2.169330 GGGATCGGGATACTACAGTCC 58.831 57.143 0.00 0.00 0.00 3.85
750 1258 3.224269 GGATACTACAGTCCCTCTGACC 58.776 54.545 1.79 0.00 45.68 4.02
751 1259 3.372784 GGATACTACAGTCCCTCTGACCA 60.373 52.174 1.79 0.00 45.68 4.02
752 1260 2.930109 ACTACAGTCCCTCTGACCAT 57.070 50.000 1.79 0.00 45.68 3.55
753 1261 2.741145 ACTACAGTCCCTCTGACCATC 58.259 52.381 1.79 0.00 45.68 3.51
754 1262 2.035632 CTACAGTCCCTCTGACCATCC 58.964 57.143 1.79 0.00 45.68 3.51
755 1263 0.117140 ACAGTCCCTCTGACCATCCA 59.883 55.000 1.79 0.00 45.68 3.41
756 1264 1.279496 CAGTCCCTCTGACCATCCAA 58.721 55.000 0.00 0.00 45.68 3.53
757 1265 1.065854 CAGTCCCTCTGACCATCCAAC 60.066 57.143 0.00 0.00 45.68 3.77
758 1266 0.253327 GTCCCTCTGACCATCCAACC 59.747 60.000 0.00 0.00 38.09 3.77
759 1267 0.178876 TCCCTCTGACCATCCAACCA 60.179 55.000 0.00 0.00 0.00 3.67
760 1268 0.035056 CCCTCTGACCATCCAACCAC 60.035 60.000 0.00 0.00 0.00 4.16
761 1269 0.692476 CCTCTGACCATCCAACCACA 59.308 55.000 0.00 0.00 0.00 4.17
762 1270 1.339438 CCTCTGACCATCCAACCACAG 60.339 57.143 0.00 0.00 0.00 3.66
763 1271 1.625315 CTCTGACCATCCAACCACAGA 59.375 52.381 0.00 0.00 34.13 3.41
764 1272 2.238144 CTCTGACCATCCAACCACAGAT 59.762 50.000 0.00 0.00 34.64 2.90
765 1273 2.644299 TCTGACCATCCAACCACAGATT 59.356 45.455 0.00 0.00 31.02 2.40
766 1274 2.751259 CTGACCATCCAACCACAGATTG 59.249 50.000 0.00 0.00 0.00 2.67
767 1275 2.108075 TGACCATCCAACCACAGATTGT 59.892 45.455 0.00 0.00 0.00 2.71
768 1276 3.157087 GACCATCCAACCACAGATTGTT 58.843 45.455 0.00 0.00 0.00 2.83
769 1277 3.573967 GACCATCCAACCACAGATTGTTT 59.426 43.478 0.00 0.00 0.00 2.83
770 1278 3.573967 ACCATCCAACCACAGATTGTTTC 59.426 43.478 0.00 0.00 0.00 2.78
771 1279 3.366273 CCATCCAACCACAGATTGTTTCG 60.366 47.826 0.00 0.00 0.00 3.46
772 1280 1.606668 TCCAACCACAGATTGTTTCGC 59.393 47.619 0.00 0.00 0.00 4.70
776 1284 0.950836 CCACAGATTGTTTCGCCACA 59.049 50.000 0.00 0.00 0.00 4.17
798 1306 7.069826 CCACAGGGATGGTTTTTGAATGTATAT 59.930 37.037 0.00 0.00 34.77 0.86
799 1307 9.130661 CACAGGGATGGTTTTTGAATGTATATA 57.869 33.333 0.00 0.00 0.00 0.86
881 1398 4.361783 TGAGGGTTAATGGACTCAGATGA 58.638 43.478 0.00 0.00 35.24 2.92
1009 1526 1.324014 TCCATCTCTTCTCCCCCTCT 58.676 55.000 0.00 0.00 0.00 3.69
1012 1529 0.565674 ATCTCTTCTCCCCCTCTCCC 59.434 60.000 0.00 0.00 0.00 4.30
1048 1565 1.720694 CGTCTCCTCCTCCTCTTCGC 61.721 65.000 0.00 0.00 0.00 4.70
1049 1566 1.076632 TCTCCTCCTCCTCTTCGCC 60.077 63.158 0.00 0.00 0.00 5.54
1050 1567 2.440430 TCCTCCTCCTCTTCGCCG 60.440 66.667 0.00 0.00 0.00 6.46
1051 1568 4.214327 CCTCCTCCTCTTCGCCGC 62.214 72.222 0.00 0.00 0.00 6.53
1052 1569 3.144193 CTCCTCCTCTTCGCCGCT 61.144 66.667 0.00 0.00 0.00 5.52
1053 1570 3.132481 CTCCTCCTCTTCGCCGCTC 62.132 68.421 0.00 0.00 0.00 5.03
1910 2448 5.827267 TGGTGAAGTTCTTTGATGTGATTCA 59.173 36.000 4.17 0.00 0.00 2.57
2006 2568 1.213537 CGGTTTTGGCTGCTCCATG 59.786 57.895 0.00 0.00 46.04 3.66
2028 2590 3.976942 GTGTGCTGATAGTTTTTGTGCAG 59.023 43.478 0.00 0.00 0.00 4.41
2029 2591 3.631686 TGTGCTGATAGTTTTTGTGCAGT 59.368 39.130 0.00 0.00 0.00 4.40
2030 2592 3.976942 GTGCTGATAGTTTTTGTGCAGTG 59.023 43.478 0.00 0.00 0.00 3.66
2031 2593 3.631686 TGCTGATAGTTTTTGTGCAGTGT 59.368 39.130 0.00 0.00 0.00 3.55
2045 2607 1.875157 GCAGTGTGTGTGATGCTCAGA 60.875 52.381 0.00 0.00 35.78 3.27
2105 2667 4.024556 GCATAGCGTCATAGAAATTGCACT 60.025 41.667 0.00 0.00 0.00 4.40
2128 2690 4.492791 TCTGATTTTGACATGTGCAGTG 57.507 40.909 1.15 0.00 0.00 3.66
2151 2713 7.940137 AGTGTACCCATGTTTAGTGTAATTTGA 59.060 33.333 0.00 0.00 0.00 2.69
2177 2739 7.822334 ACATCACCATTGATTCGTAGAGTTAAA 59.178 33.333 0.00 0.00 40.79 1.52
2198 2761 6.834168 AAACGTTGATTCATGGAGGTAATT 57.166 33.333 0.00 0.00 0.00 1.40
2302 2889 8.454106 GCCATATTATTAGATTGCAACTGTAGG 58.546 37.037 0.00 0.00 0.00 3.18
2318 2909 2.835156 TGTAGGATCATGGGACGAAACA 59.165 45.455 0.00 0.00 0.00 2.83
2319 2910 3.454447 TGTAGGATCATGGGACGAAACAT 59.546 43.478 0.00 0.00 0.00 2.71
2351 2942 8.402798 TGTTGGTCTATGAATTGTTAACATGT 57.597 30.769 9.56 0.00 0.00 3.21
2381 2972 0.817229 TTGATGTGTGCACGGCAAGA 60.817 50.000 13.13 2.34 41.47 3.02
2421 3012 1.596260 CATGTATGTCTGCGCTTCCTG 59.404 52.381 9.73 0.00 0.00 3.86
2512 3103 0.179124 GATCTCACTCGGCCTGTGTC 60.179 60.000 20.31 10.72 36.83 3.67
2576 3167 1.768077 GGACCTGATGGAGAGGGGG 60.768 68.421 0.00 0.00 34.56 5.40
2591 3182 1.453669 GGGGCTCATCAGGATGGTC 59.546 63.158 9.25 2.36 39.24 4.02
2835 3426 7.610305 CCTTATATATTGCCGTATTGGGTCTTT 59.390 37.037 0.00 0.00 38.63 2.52
2879 3470 4.043200 GCTGTTCCTGGGCGCAAC 62.043 66.667 10.83 5.00 0.00 4.17
2959 3557 2.157738 GCTGTGAGGCTGATCTTGTTT 58.842 47.619 0.00 0.00 0.00 2.83
2994 3592 5.053140 TCTTGAGATAGCGCTGTATGATC 57.947 43.478 22.90 14.75 0.00 2.92
3003 3601 1.069823 CGCTGTATGATCCTTGAGGCT 59.930 52.381 0.00 0.00 34.44 4.58
3040 3644 6.127730 GCCTGTAGTTTTTATACACCTGCATT 60.128 38.462 0.00 0.00 0.00 3.56
3062 3669 1.080498 AGTGGGGTCTTGATACCTGGA 59.920 52.381 0.00 0.00 39.65 3.86
3073 3680 2.170397 TGATACCTGGATGTCGCACATT 59.830 45.455 0.00 0.00 39.27 2.71
3075 3682 2.779755 ACCTGGATGTCGCACATTAA 57.220 45.000 0.00 0.00 39.27 1.40
3076 3683 2.356135 ACCTGGATGTCGCACATTAAC 58.644 47.619 0.00 0.33 39.27 2.01
3077 3684 2.290008 ACCTGGATGTCGCACATTAACA 60.290 45.455 0.00 3.88 39.27 2.41
3078 3685 2.352651 CCTGGATGTCGCACATTAACAG 59.647 50.000 14.80 14.80 39.27 3.16
3079 3686 2.352651 CTGGATGTCGCACATTAACAGG 59.647 50.000 14.38 0.00 39.27 4.00
3081 3688 2.356135 GATGTCGCACATTAACAGGGT 58.644 47.619 3.76 0.00 39.27 4.34
3100 3912 4.646492 AGGGTACTTGCATCAATTGGATTC 59.354 41.667 5.42 0.00 32.57 2.52
3106 3918 7.605410 ACTTGCATCAATTGGATTCAAAATC 57.395 32.000 5.42 0.00 38.41 2.17
3112 3924 7.384115 GCATCAATTGGATTCAAAATCGATGAT 59.616 33.333 16.36 7.16 36.36 2.45
3117 3929 7.408756 TTGGATTCAAAATCGATGATCCTTT 57.591 32.000 18.02 6.44 31.44 3.11
3150 3962 9.100554 TCAATTGGATTAAATTGATGTGATTGC 57.899 29.630 5.42 0.00 46.51 3.56
3151 3963 9.104965 CAATTGGATTAAATTGATGTGATTGCT 57.895 29.630 0.00 0.00 46.13 3.91
3152 3964 8.657074 ATTGGATTAAATTGATGTGATTGCTG 57.343 30.769 0.00 0.00 0.00 4.41
3160 3972 0.745845 ATGTGATTGCTGCTCGTCCC 60.746 55.000 0.00 0.00 0.00 4.46
3168 3980 1.889530 GCTGCTCGTCCCAAGTACCT 61.890 60.000 0.00 0.00 0.00 3.08
3171 3983 0.606604 GCTCGTCCCAAGTACCTGAA 59.393 55.000 0.00 0.00 0.00 3.02
3196 4032 4.399303 CAGGGTCAATCAAGTCATTTACCC 59.601 45.833 7.29 7.29 45.37 3.69
3229 4173 1.078143 GCGATGTTGGGCTCCTTCT 60.078 57.895 0.00 0.00 0.00 2.85
3248 4225 4.802051 GCTGCCCGGAAGCCATGA 62.802 66.667 16.00 0.00 34.45 3.07
3284 4261 2.493675 ACAAGCGCTCTTCTGTATCTCA 59.506 45.455 12.06 0.00 0.00 3.27
3288 4265 3.445450 AGCGCTCTTCTGTATCTCAAGAA 59.555 43.478 2.64 0.00 0.00 2.52
3289 4266 3.796178 GCGCTCTTCTGTATCTCAAGAAG 59.204 47.826 0.00 6.16 39.12 2.85
3290 4267 3.796178 CGCTCTTCTGTATCTCAAGAAGC 59.204 47.826 7.41 0.00 38.05 3.86
3291 4268 4.439974 CGCTCTTCTGTATCTCAAGAAGCT 60.440 45.833 7.41 0.00 38.05 3.74
3292 4269 5.043248 GCTCTTCTGTATCTCAAGAAGCTC 58.957 45.833 7.41 0.00 38.05 4.09
3341 4318 5.060662 TGTATCTCTGTTCTTCAGGTTCG 57.939 43.478 0.00 0.00 43.76 3.95
3372 4429 7.204604 TGTTCTTTCGTCAGTACTATGTTTCA 58.795 34.615 0.00 0.00 0.00 2.69
3381 4438 7.358435 CGTCAGTACTATGTTTCAGTCAAAGTG 60.358 40.741 0.00 0.00 0.00 3.16
3419 4476 3.252215 CGCCTCAATGTAACACTTCCAAA 59.748 43.478 0.00 0.00 0.00 3.28
3464 4521 4.864247 GGATAATTGCAACTGCGTGATTTT 59.136 37.500 0.00 0.00 45.83 1.82
3478 4535 3.488489 GTGATTTTCAACCGGAATGTCG 58.512 45.455 9.46 0.00 34.91 4.35
3505 4562 4.704833 ACAATCCAGCGCGCCACT 62.705 61.111 30.33 6.46 0.00 4.00
3588 4645 8.531982 ACTTGAAGCTATCTGAACTATTGTGTA 58.468 33.333 0.00 0.00 0.00 2.90
3593 4654 8.934507 AGCTATCTGAACTATTGTGTAGTTTC 57.065 34.615 2.38 0.00 37.83 2.78
3610 4671 6.588756 TGTAGTTTCGGAACTATGTCATGTTC 59.411 38.462 19.11 14.67 46.80 3.18
3622 4683 4.898829 TGTCATGTTCAACTTGAAGGTG 57.101 40.909 3.28 3.28 37.00 4.00
3629 4690 8.859090 TCATGTTCAACTTGAAGGTGATTTATT 58.141 29.630 14.44 0.00 42.30 1.40
3646 4707 1.032014 ATTCGCATGTGGTTATGGCC 58.968 50.000 6.39 0.00 0.00 5.36
3683 4744 6.641314 ACGTGTATATCCATGAAATCTTCGAC 59.359 38.462 0.00 0.00 0.00 4.20
3749 4810 2.934553 GCCTTTACCTAACAGCTTACCG 59.065 50.000 0.00 0.00 0.00 4.02
3906 8627 3.445805 TGGTTTCTTTCAGTTGGTTGGTC 59.554 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.993370 CCCGCTCGCTATATTAGTTGC 59.007 52.381 0.00 0.00 0.00 4.17
1 2 3.570926 TCCCGCTCGCTATATTAGTTG 57.429 47.619 0.00 0.00 0.00 3.16
2 3 4.381718 GGATTCCCGCTCGCTATATTAGTT 60.382 45.833 0.00 0.00 0.00 2.24
3 4 3.130693 GGATTCCCGCTCGCTATATTAGT 59.869 47.826 0.00 0.00 0.00 2.24
4 5 3.491104 GGGATTCCCGCTCGCTATATTAG 60.491 52.174 5.84 0.00 32.13 1.73
5 6 2.429610 GGGATTCCCGCTCGCTATATTA 59.570 50.000 5.84 0.00 32.13 0.98
6 7 1.207329 GGGATTCCCGCTCGCTATATT 59.793 52.381 5.84 0.00 32.13 1.28
7 8 0.824759 GGGATTCCCGCTCGCTATAT 59.175 55.000 5.84 0.00 32.13 0.86
8 9 2.273908 GGGATTCCCGCTCGCTATA 58.726 57.895 5.84 0.00 32.13 1.31
9 10 3.060866 GGGATTCCCGCTCGCTAT 58.939 61.111 5.84 0.00 32.13 2.97
18 19 1.351017 TCCATTAGCATCGGGATTCCC 59.649 52.381 12.14 12.14 41.09 3.97
19 20 2.859165 TCCATTAGCATCGGGATTCC 57.141 50.000 0.00 0.00 0.00 3.01
20 21 4.162320 TCCTATCCATTAGCATCGGGATTC 59.838 45.833 5.49 0.00 40.49 2.52
21 22 4.104086 TCCTATCCATTAGCATCGGGATT 58.896 43.478 5.49 0.00 40.49 3.01
22 23 3.724478 TCCTATCCATTAGCATCGGGAT 58.276 45.455 0.00 0.00 42.55 3.85
23 24 3.184382 TCCTATCCATTAGCATCGGGA 57.816 47.619 0.00 0.00 0.00 5.14
24 25 3.432749 CCATCCTATCCATTAGCATCGGG 60.433 52.174 0.00 0.00 0.00 5.14
25 26 3.452264 TCCATCCTATCCATTAGCATCGG 59.548 47.826 0.00 0.00 0.00 4.18
26 27 4.743057 TCCATCCTATCCATTAGCATCG 57.257 45.455 0.00 0.00 0.00 3.84
27 28 7.568349 TGTAATCCATCCTATCCATTAGCATC 58.432 38.462 0.00 0.00 0.00 3.91
28 29 7.183475 ACTGTAATCCATCCTATCCATTAGCAT 59.817 37.037 0.00 0.00 0.00 3.79
29 30 6.501805 ACTGTAATCCATCCTATCCATTAGCA 59.498 38.462 0.00 0.00 0.00 3.49
30 31 6.820656 CACTGTAATCCATCCTATCCATTAGC 59.179 42.308 0.00 0.00 0.00 3.09
31 32 8.138928 TCACTGTAATCCATCCTATCCATTAG 57.861 38.462 0.00 0.00 0.00 1.73
32 33 7.310671 GCTCACTGTAATCCATCCTATCCATTA 60.311 40.741 0.00 0.00 0.00 1.90
33 34 6.521427 GCTCACTGTAATCCATCCTATCCATT 60.521 42.308 0.00 0.00 0.00 3.16
34 35 5.046014 GCTCACTGTAATCCATCCTATCCAT 60.046 44.000 0.00 0.00 0.00 3.41
35 36 4.284490 GCTCACTGTAATCCATCCTATCCA 59.716 45.833 0.00 0.00 0.00 3.41
36 37 4.619394 CGCTCACTGTAATCCATCCTATCC 60.619 50.000 0.00 0.00 0.00 2.59
37 38 4.021894 ACGCTCACTGTAATCCATCCTATC 60.022 45.833 0.00 0.00 0.00 2.08
38 39 3.898123 ACGCTCACTGTAATCCATCCTAT 59.102 43.478 0.00 0.00 0.00 2.57
39 40 3.296854 ACGCTCACTGTAATCCATCCTA 58.703 45.455 0.00 0.00 0.00 2.94
40 41 2.111384 ACGCTCACTGTAATCCATCCT 58.889 47.619 0.00 0.00 0.00 3.24
41 42 2.604046 ACGCTCACTGTAATCCATCC 57.396 50.000 0.00 0.00 0.00 3.51
42 43 4.202020 TGACTACGCTCACTGTAATCCATC 60.202 45.833 0.00 0.00 0.00 3.51
43 44 3.699538 TGACTACGCTCACTGTAATCCAT 59.300 43.478 0.00 0.00 0.00 3.41
44 45 3.086282 TGACTACGCTCACTGTAATCCA 58.914 45.455 0.00 0.00 0.00 3.41
45 46 3.436496 GTGACTACGCTCACTGTAATCC 58.564 50.000 0.00 0.00 38.05 3.01
46 47 3.436496 GGTGACTACGCTCACTGTAATC 58.564 50.000 4.09 0.00 40.50 1.75
47 48 2.159421 CGGTGACTACGCTCACTGTAAT 60.159 50.000 4.82 0.00 41.09 1.89
48 49 1.198408 CGGTGACTACGCTCACTGTAA 59.802 52.381 4.82 0.00 41.09 2.41
49 50 0.800631 CGGTGACTACGCTCACTGTA 59.199 55.000 4.82 0.00 41.09 2.74
50 51 0.887836 TCGGTGACTACGCTCACTGT 60.888 55.000 11.24 0.00 44.75 3.55
51 52 0.179187 CTCGGTGACTACGCTCACTG 60.179 60.000 6.35 6.35 45.51 3.66
52 53 0.321387 TCTCGGTGACTACGCTCACT 60.321 55.000 4.09 0.00 40.50 3.41
53 54 0.097325 CTCTCGGTGACTACGCTCAC 59.903 60.000 0.00 0.00 40.02 3.51
54 55 1.645704 GCTCTCGGTGACTACGCTCA 61.646 60.000 0.00 0.00 0.00 4.26
55 56 1.062845 GCTCTCGGTGACTACGCTC 59.937 63.158 0.00 0.00 0.00 5.03
56 57 1.370587 GAGCTCTCGGTGACTACGCT 61.371 60.000 6.43 0.00 0.00 5.07
57 58 1.062845 GAGCTCTCGGTGACTACGC 59.937 63.158 6.43 0.00 0.00 4.42
58 59 0.745128 AGGAGCTCTCGGTGACTACG 60.745 60.000 14.64 0.00 0.00 3.51
59 60 2.328819 TAGGAGCTCTCGGTGACTAC 57.671 55.000 14.64 0.00 0.00 2.73
60 61 2.852449 CATAGGAGCTCTCGGTGACTA 58.148 52.381 14.64 4.90 0.00 2.59
61 62 1.686355 CATAGGAGCTCTCGGTGACT 58.314 55.000 14.64 2.54 0.00 3.41
62 63 0.031449 GCATAGGAGCTCTCGGTGAC 59.969 60.000 14.64 0.00 0.00 3.67
63 64 0.395724 TGCATAGGAGCTCTCGGTGA 60.396 55.000 14.64 0.00 34.99 4.02
64 65 0.461548 TTGCATAGGAGCTCTCGGTG 59.538 55.000 14.64 8.86 34.99 4.94
65 66 1.418334 ATTGCATAGGAGCTCTCGGT 58.582 50.000 14.64 0.00 34.99 4.69
66 67 2.540265 AATTGCATAGGAGCTCTCGG 57.460 50.000 14.64 2.35 34.99 4.63
67 68 2.474359 CGAAATTGCATAGGAGCTCTCG 59.526 50.000 14.64 6.98 34.99 4.04
68 69 3.722147 TCGAAATTGCATAGGAGCTCTC 58.278 45.455 14.64 3.76 34.99 3.20
69 70 3.827008 TCGAAATTGCATAGGAGCTCT 57.173 42.857 14.64 2.18 34.99 4.09
70 71 4.991056 TGTATCGAAATTGCATAGGAGCTC 59.009 41.667 4.71 4.71 34.99 4.09
71 72 4.960938 TGTATCGAAATTGCATAGGAGCT 58.039 39.130 0.00 0.00 34.99 4.09
72 73 5.180117 ACATGTATCGAAATTGCATAGGAGC 59.820 40.000 0.00 0.00 0.00 4.70
73 74 6.791887 ACATGTATCGAAATTGCATAGGAG 57.208 37.500 0.00 0.00 0.00 3.69
74 75 6.368791 GCTACATGTATCGAAATTGCATAGGA 59.631 38.462 5.91 0.00 0.00 2.94
75 76 6.402550 GGCTACATGTATCGAAATTGCATAGG 60.403 42.308 5.91 0.00 0.00 2.57
76 77 6.147656 TGGCTACATGTATCGAAATTGCATAG 59.852 38.462 5.91 0.00 0.00 2.23
77 78 5.994668 TGGCTACATGTATCGAAATTGCATA 59.005 36.000 5.91 0.00 0.00 3.14
78 79 4.821260 TGGCTACATGTATCGAAATTGCAT 59.179 37.500 5.91 0.00 0.00 3.96
79 80 4.195416 TGGCTACATGTATCGAAATTGCA 58.805 39.130 5.91 0.00 0.00 4.08
80 81 4.811555 TGGCTACATGTATCGAAATTGC 57.188 40.909 5.91 3.54 0.00 3.56
84 85 9.549078 TGTTTATATTGGCTACATGTATCGAAA 57.451 29.630 5.91 1.32 0.00 3.46
85 86 9.549078 TTGTTTATATTGGCTACATGTATCGAA 57.451 29.630 5.91 6.32 0.00 3.71
86 87 9.719355 ATTGTTTATATTGGCTACATGTATCGA 57.281 29.630 5.91 0.00 0.00 3.59
119 121 5.299279 CCCCTCATACGAGCAAAATGTATTT 59.701 40.000 0.00 0.00 38.00 1.40
126 128 3.873781 CCCCCTCATACGAGCAAAA 57.126 52.632 0.00 0.00 38.00 2.44
169 173 3.138283 TCCAGTTGGAATATAGGCAAGGG 59.862 47.826 0.00 0.00 42.18 3.95
170 174 4.103153 TCTCCAGTTGGAATATAGGCAAGG 59.897 45.833 1.99 0.00 44.91 3.61
171 175 5.296151 TCTCCAGTTGGAATATAGGCAAG 57.704 43.478 1.99 0.00 44.91 4.01
172 176 5.221925 GGATCTCCAGTTGGAATATAGGCAA 60.222 44.000 1.99 0.00 44.91 4.52
199 203 3.489229 GCCAGAATTCGATAAAAGGGTGC 60.489 47.826 0.00 0.00 0.00 5.01
303 307 2.124983 CACTCAGGCACCCGGATG 60.125 66.667 0.73 0.00 0.00 3.51
310 314 0.610174 TCTCATCCACACTCAGGCAC 59.390 55.000 0.00 0.00 0.00 5.01
362 373 1.480137 CCCAGACAAACAACAAGGCAA 59.520 47.619 0.00 0.00 0.00 4.52
483 499 6.706716 TGCCATCGTCCGACATTAAATTAATA 59.293 34.615 0.00 0.00 0.00 0.98
556 1064 4.030913 TCCATCATACGAAACCTCCTCTT 58.969 43.478 0.00 0.00 0.00 2.85
572 1080 1.673767 AGGGAAAAGAGGCTCCATCA 58.326 50.000 11.71 0.00 32.95 3.07
636 1144 0.455464 TCAACGACGAGGTGCATACG 60.455 55.000 0.00 0.00 37.50 3.06
637 1145 0.989890 GTCAACGACGAGGTGCATAC 59.010 55.000 0.00 0.00 37.50 2.39
638 1146 3.411808 GTCAACGACGAGGTGCATA 57.588 52.632 0.00 0.00 37.50 3.14
639 1147 4.261888 GTCAACGACGAGGTGCAT 57.738 55.556 0.00 0.00 37.50 3.96
658 1166 0.966920 TCAGTGGGAGAAGACGTTCC 59.033 55.000 0.00 0.00 32.48 3.62
659 1167 2.814280 TTCAGTGGGAGAAGACGTTC 57.186 50.000 0.00 0.00 0.00 3.95
660 1168 2.872038 GCATTCAGTGGGAGAAGACGTT 60.872 50.000 0.00 0.00 0.00 3.99
661 1169 1.338200 GCATTCAGTGGGAGAAGACGT 60.338 52.381 0.00 0.00 0.00 4.34
662 1170 1.363744 GCATTCAGTGGGAGAAGACG 58.636 55.000 0.00 0.00 0.00 4.18
663 1171 1.363744 CGCATTCAGTGGGAGAAGAC 58.636 55.000 0.00 0.00 43.02 3.01
664 1172 0.391661 GCGCATTCAGTGGGAGAAGA 60.392 55.000 0.30 0.00 43.02 2.87
665 1173 0.674581 TGCGCATTCAGTGGGAGAAG 60.675 55.000 5.66 0.00 43.02 2.85
666 1174 0.035152 ATGCGCATTCAGTGGGAGAA 60.035 50.000 19.28 0.00 43.02 2.87
667 1175 0.462581 GATGCGCATTCAGTGGGAGA 60.463 55.000 26.12 0.00 43.02 3.71
668 1176 1.769098 CGATGCGCATTCAGTGGGAG 61.769 60.000 26.12 4.12 43.02 4.30
669 1177 1.815003 CGATGCGCATTCAGTGGGA 60.815 57.895 26.12 0.00 43.02 4.37
670 1178 2.711311 CGATGCGCATTCAGTGGG 59.289 61.111 26.12 4.47 43.21 4.61
681 1189 1.284982 CTAGGATTTCCGGCGATGCG 61.285 60.000 9.30 0.00 42.08 4.73
682 1190 1.569479 GCTAGGATTTCCGGCGATGC 61.569 60.000 9.30 0.00 42.08 3.91
683 1191 0.249868 TGCTAGGATTTCCGGCGATG 60.250 55.000 9.30 0.00 40.53 3.84
684 1192 0.249911 GTGCTAGGATTTCCGGCGAT 60.250 55.000 9.30 0.00 40.53 4.58
685 1193 1.143183 GTGCTAGGATTTCCGGCGA 59.857 57.895 9.30 0.00 40.53 5.54
686 1194 1.887707 GGTGCTAGGATTTCCGGCG 60.888 63.158 0.00 0.00 40.53 6.46
687 1195 0.815615 CTGGTGCTAGGATTTCCGGC 60.816 60.000 0.00 9.56 42.08 6.13
688 1196 0.179045 CCTGGTGCTAGGATTTCCGG 60.179 60.000 0.00 0.00 40.42 5.14
689 1197 0.830648 TCCTGGTGCTAGGATTTCCG 59.169 55.000 0.00 0.00 41.85 4.30
696 1204 1.139853 GGTTCAGATCCTGGTGCTAGG 59.860 57.143 0.00 0.00 39.29 3.02
697 1205 1.139853 GGGTTCAGATCCTGGTGCTAG 59.860 57.143 0.00 0.00 31.51 3.42
698 1206 1.204146 GGGTTCAGATCCTGGTGCTA 58.796 55.000 0.00 0.00 31.51 3.49
699 1207 0.548682 AGGGTTCAGATCCTGGTGCT 60.549 55.000 0.00 0.00 31.51 4.40
700 1208 0.393537 CAGGGTTCAGATCCTGGTGC 60.394 60.000 10.92 0.00 44.99 5.01
701 1209 3.869623 CAGGGTTCAGATCCTGGTG 57.130 57.895 10.92 0.00 44.99 4.17
716 1224 1.944177 AGTATCCCGATCCCATCAGG 58.056 55.000 0.00 0.00 0.00 3.86
717 1225 3.431415 TGTAGTATCCCGATCCCATCAG 58.569 50.000 0.00 0.00 0.00 2.90
718 1226 3.181422 ACTGTAGTATCCCGATCCCATCA 60.181 47.826 0.00 0.00 0.00 3.07
719 1227 3.432378 ACTGTAGTATCCCGATCCCATC 58.568 50.000 0.00 0.00 0.00 3.51
720 1228 3.432378 GACTGTAGTATCCCGATCCCAT 58.568 50.000 0.00 0.00 0.00 4.00
721 1229 2.490351 GGACTGTAGTATCCCGATCCCA 60.490 54.545 0.00 0.00 0.00 4.37
722 1230 2.169330 GGACTGTAGTATCCCGATCCC 58.831 57.143 0.00 0.00 0.00 3.85
723 1231 2.169330 GGGACTGTAGTATCCCGATCC 58.831 57.143 0.00 0.00 45.26 3.36
729 1237 3.224269 GGTCAGAGGGACTGTAGTATCC 58.776 54.545 0.00 0.00 46.16 2.59
730 1238 3.899726 TGGTCAGAGGGACTGTAGTATC 58.100 50.000 0.00 0.00 46.16 2.24
731 1239 4.475345 GATGGTCAGAGGGACTGTAGTAT 58.525 47.826 0.00 0.00 46.16 2.12
732 1240 3.372784 GGATGGTCAGAGGGACTGTAGTA 60.373 52.174 0.00 0.00 46.16 1.82
733 1241 2.624557 GGATGGTCAGAGGGACTGTAGT 60.625 54.545 0.00 0.00 46.16 2.73
734 1242 2.035632 GGATGGTCAGAGGGACTGTAG 58.964 57.143 0.00 0.00 46.16 2.74
735 1243 1.361197 TGGATGGTCAGAGGGACTGTA 59.639 52.381 0.00 0.00 46.16 2.74
736 1244 0.117140 TGGATGGTCAGAGGGACTGT 59.883 55.000 0.00 0.00 46.16 3.55
737 1245 1.065854 GTTGGATGGTCAGAGGGACTG 60.066 57.143 0.00 0.00 46.16 3.51
738 1246 1.280457 GTTGGATGGTCAGAGGGACT 58.720 55.000 0.00 0.00 46.16 3.85
739 1247 0.253327 GGTTGGATGGTCAGAGGGAC 59.747 60.000 0.00 0.00 46.20 4.46
740 1248 0.178876 TGGTTGGATGGTCAGAGGGA 60.179 55.000 0.00 0.00 0.00 4.20
741 1249 0.035056 GTGGTTGGATGGTCAGAGGG 60.035 60.000 0.00 0.00 0.00 4.30
742 1250 0.692476 TGTGGTTGGATGGTCAGAGG 59.308 55.000 0.00 0.00 0.00 3.69
743 1251 1.625315 TCTGTGGTTGGATGGTCAGAG 59.375 52.381 0.00 0.00 0.00 3.35
744 1252 1.728323 TCTGTGGTTGGATGGTCAGA 58.272 50.000 0.00 0.00 0.00 3.27
745 1253 2.751259 CAATCTGTGGTTGGATGGTCAG 59.249 50.000 0.00 0.00 0.00 3.51
746 1254 2.108075 ACAATCTGTGGTTGGATGGTCA 59.892 45.455 0.00 0.00 0.00 4.02
747 1255 2.795329 ACAATCTGTGGTTGGATGGTC 58.205 47.619 0.00 0.00 0.00 4.02
748 1256 2.978156 ACAATCTGTGGTTGGATGGT 57.022 45.000 0.00 0.00 0.00 3.55
749 1257 3.366273 CGAAACAATCTGTGGTTGGATGG 60.366 47.826 0.00 0.00 37.24 3.51
750 1258 3.825308 CGAAACAATCTGTGGTTGGATG 58.175 45.455 0.00 0.00 37.24 3.51
751 1259 2.228822 GCGAAACAATCTGTGGTTGGAT 59.771 45.455 0.00 0.00 37.24 3.41
752 1260 1.606668 GCGAAACAATCTGTGGTTGGA 59.393 47.619 0.00 0.00 37.24 3.53
753 1261 1.335872 GGCGAAACAATCTGTGGTTGG 60.336 52.381 0.00 0.00 37.24 3.77
754 1262 1.336440 TGGCGAAACAATCTGTGGTTG 59.664 47.619 0.00 0.00 37.24 3.77
755 1263 1.336755 GTGGCGAAACAATCTGTGGTT 59.663 47.619 0.00 0.00 40.99 3.67
756 1264 0.951558 GTGGCGAAACAATCTGTGGT 59.048 50.000 0.00 0.00 0.00 4.16
757 1265 0.950836 TGTGGCGAAACAATCTGTGG 59.049 50.000 0.00 0.00 0.00 4.17
758 1266 1.069022 CCTGTGGCGAAACAATCTGTG 60.069 52.381 0.00 0.00 0.00 3.66
759 1267 1.238439 CCTGTGGCGAAACAATCTGT 58.762 50.000 0.00 0.00 0.00 3.41
760 1268 0.523072 CCCTGTGGCGAAACAATCTG 59.477 55.000 0.00 0.00 0.00 2.90
761 1269 0.400213 TCCCTGTGGCGAAACAATCT 59.600 50.000 0.00 0.00 0.00 2.40
762 1270 1.133025 CATCCCTGTGGCGAAACAATC 59.867 52.381 0.00 0.00 0.00 2.67
763 1271 1.176527 CATCCCTGTGGCGAAACAAT 58.823 50.000 0.00 0.00 0.00 2.71
764 1272 0.893270 CCATCCCTGTGGCGAAACAA 60.893 55.000 0.00 0.00 31.43 2.83
765 1273 1.303236 CCATCCCTGTGGCGAAACA 60.303 57.895 0.00 0.00 31.43 2.83
766 1274 0.893727 AACCATCCCTGTGGCGAAAC 60.894 55.000 0.00 0.00 43.27 2.78
767 1275 0.178975 AAACCATCCCTGTGGCGAAA 60.179 50.000 0.00 0.00 43.27 3.46
768 1276 0.178975 AAAACCATCCCTGTGGCGAA 60.179 50.000 0.00 0.00 43.27 4.70
769 1277 0.178975 AAAAACCATCCCTGTGGCGA 60.179 50.000 0.00 0.00 43.27 5.54
770 1278 0.038343 CAAAAACCATCCCTGTGGCG 60.038 55.000 0.00 0.00 43.27 5.69
771 1279 1.337118 TCAAAAACCATCCCTGTGGC 58.663 50.000 0.00 0.00 43.27 5.01
772 1280 3.324556 ACATTCAAAAACCATCCCTGTGG 59.675 43.478 0.00 0.00 45.04 4.17
881 1398 2.000447 GCTCGTTCTGCGGAGTTTATT 59.000 47.619 3.10 0.00 41.72 1.40
1854 2375 3.716601 CGCATCACACACATATCCTACA 58.283 45.455 0.00 0.00 0.00 2.74
1910 2448 0.179029 CCGACTGACCCCAAAACAGT 60.179 55.000 0.00 0.00 45.62 3.55
2006 2568 3.963665 TGCACAAAAACTATCAGCACAC 58.036 40.909 0.00 0.00 0.00 3.82
2028 2590 4.092529 CACTAATCTGAGCATCACACACAC 59.907 45.833 0.00 0.00 42.56 3.82
2029 2591 4.248058 CACTAATCTGAGCATCACACACA 58.752 43.478 0.00 0.00 42.56 3.72
2030 2592 3.063180 GCACTAATCTGAGCATCACACAC 59.937 47.826 0.00 0.00 42.56 3.82
2031 2593 3.264947 GCACTAATCTGAGCATCACACA 58.735 45.455 0.00 0.00 42.56 3.72
2045 2607 5.198965 AGCAAAATCTGAGGATGCACTAAT 58.801 37.500 12.03 0.00 31.75 1.73
2088 2650 7.649370 ATCAGATAGTGCAATTTCTATGACG 57.351 36.000 6.80 0.00 0.00 4.35
2105 2667 5.706833 ACACTGCACATGTCAAAATCAGATA 59.293 36.000 0.00 0.00 0.00 1.98
2128 2690 8.101654 TGTCAAATTACACTAAACATGGGTAC 57.898 34.615 0.00 0.00 0.00 3.34
2151 2713 5.344743 ACTCTACGAATCAATGGTGATGT 57.655 39.130 0.00 0.00 44.02 3.06
2177 2739 5.125417 CCAAATTACCTCCATGAATCAACGT 59.875 40.000 0.00 0.00 0.00 3.99
2198 2761 0.950836 CAACAGCATCGACCAACCAA 59.049 50.000 0.00 0.00 0.00 3.67
2268 2847 9.910267 TGCAATCTAATAATATGGCATGTAGAT 57.090 29.630 10.98 5.86 0.00 1.98
2269 2848 9.737844 TTGCAATCTAATAATATGGCATGTAGA 57.262 29.630 10.98 3.53 0.00 2.59
2270 2849 9.778993 GTTGCAATCTAATAATATGGCATGTAG 57.221 33.333 10.98 0.00 0.00 2.74
2271 2850 9.519191 AGTTGCAATCTAATAATATGGCATGTA 57.481 29.630 10.98 2.59 0.00 2.29
2351 2942 6.478673 CCGTGCACACATCAATAGTTCTAATA 59.521 38.462 18.64 0.00 0.00 0.98
2481 3072 3.615937 CGAGTGAGATCATCAGGTTTGTG 59.384 47.826 0.00 0.00 39.07 3.33
2512 3103 3.305676 CCCGTTGATCTGCAGGTAGATAG 60.306 52.174 15.13 0.00 37.53 2.08
2576 3167 2.996249 TTGAGACCATCCTGATGAGC 57.004 50.000 8.69 0.71 41.20 4.26
2591 3182 0.747283 GCTGGCTGGAGTGGATTGAG 60.747 60.000 0.00 0.00 0.00 3.02
2823 3414 7.655732 ACAGCAACAAATAAAAAGACCCAATAC 59.344 33.333 0.00 0.00 0.00 1.89
2835 3426 2.621055 AGCGTGGACAGCAACAAATAAA 59.379 40.909 0.00 0.00 37.01 1.40
2879 3470 4.695217 ACCATACACCGCAACAAAATAG 57.305 40.909 0.00 0.00 0.00 1.73
2959 3557 3.404869 TCTCAAGAGCCTTATCCTCCA 57.595 47.619 0.00 0.00 0.00 3.86
3040 3644 3.112263 CCAGGTATCAAGACCCCACTTA 58.888 50.000 0.00 0.00 40.74 2.24
3062 3669 2.489938 ACCCTGTTAATGTGCGACAT 57.510 45.000 0.00 0.00 41.31 3.06
3073 3680 4.704540 CCAATTGATGCAAGTACCCTGTTA 59.295 41.667 7.12 0.00 0.00 2.41
3075 3682 3.091545 CCAATTGATGCAAGTACCCTGT 58.908 45.455 7.12 0.00 0.00 4.00
3076 3683 3.355378 TCCAATTGATGCAAGTACCCTG 58.645 45.455 7.12 0.00 0.00 4.45
3077 3684 3.737559 TCCAATTGATGCAAGTACCCT 57.262 42.857 7.12 0.00 0.00 4.34
3078 3685 4.402155 TGAATCCAATTGATGCAAGTACCC 59.598 41.667 7.12 0.00 35.98 3.69
3079 3686 5.581126 TGAATCCAATTGATGCAAGTACC 57.419 39.130 7.12 0.00 35.98 3.34
3135 3947 3.192001 ACGAGCAGCAATCACATCAATTT 59.808 39.130 0.00 0.00 0.00 1.82
3137 3949 2.353889 GACGAGCAGCAATCACATCAAT 59.646 45.455 0.00 0.00 0.00 2.57
3138 3950 1.733912 GACGAGCAGCAATCACATCAA 59.266 47.619 0.00 0.00 0.00 2.57
3139 3951 1.362768 GACGAGCAGCAATCACATCA 58.637 50.000 0.00 0.00 0.00 3.07
3140 3952 0.654683 GGACGAGCAGCAATCACATC 59.345 55.000 0.00 0.00 0.00 3.06
3141 3953 0.745845 GGGACGAGCAGCAATCACAT 60.746 55.000 0.00 0.00 0.00 3.21
3142 3954 1.375908 GGGACGAGCAGCAATCACA 60.376 57.895 0.00 0.00 0.00 3.58
3143 3955 0.955428 TTGGGACGAGCAGCAATCAC 60.955 55.000 0.00 0.00 0.00 3.06
3144 3956 0.674581 CTTGGGACGAGCAGCAATCA 60.675 55.000 0.00 0.00 0.00 2.57
3145 3957 0.674895 ACTTGGGACGAGCAGCAATC 60.675 55.000 0.00 0.00 0.00 2.67
3146 3958 0.613260 TACTTGGGACGAGCAGCAAT 59.387 50.000 0.00 0.00 0.00 3.56
3147 3959 0.320421 GTACTTGGGACGAGCAGCAA 60.320 55.000 0.00 0.00 0.00 3.91
3148 3960 1.292223 GTACTTGGGACGAGCAGCA 59.708 57.895 0.00 0.00 0.00 4.41
3149 3961 1.448013 GGTACTTGGGACGAGCAGC 60.448 63.158 0.00 0.00 0.00 5.25
3150 3962 0.108615 CAGGTACTTGGGACGAGCAG 60.109 60.000 0.00 0.00 34.60 4.24
3151 3963 0.541063 TCAGGTACTTGGGACGAGCA 60.541 55.000 5.01 0.00 34.60 4.26
3152 3964 0.606604 TTCAGGTACTTGGGACGAGC 59.393 55.000 5.01 0.00 34.60 5.03
3168 3980 2.106338 TGACTTGATTGACCCTGCTTCA 59.894 45.455 0.00 0.00 0.00 3.02
3171 3983 3.446442 AATGACTTGATTGACCCTGCT 57.554 42.857 0.00 0.00 0.00 4.24
3248 4225 1.331214 CTTGTTCCCCAACTGCACAT 58.669 50.000 0.00 0.00 33.17 3.21
3289 4266 1.202582 TCGTTCCTGTTGAGCTAGAGC 59.797 52.381 0.00 0.00 42.49 4.09
3290 4267 3.143807 CTCGTTCCTGTTGAGCTAGAG 57.856 52.381 0.00 0.00 0.00 2.43
3341 4318 4.569564 AGTACTGACGAAAGAACAACAACC 59.430 41.667 0.00 0.00 0.00 3.77
3381 4438 1.607148 AGGCGAAACAAAAGTAGGCAC 59.393 47.619 0.00 0.00 0.00 5.01
3391 4448 3.880490 AGTGTTACATTGAGGCGAAACAA 59.120 39.130 0.00 0.00 0.00 2.83
3419 4476 8.710749 ATCCATTAACTATATGGCAAACACAT 57.289 30.769 0.00 0.00 41.90 3.21
3464 4521 0.533491 CCCTACGACATTCCGGTTGA 59.467 55.000 13.00 0.00 0.00 3.18
3478 4535 1.940613 CGCTGGATTGTTTAGCCCTAC 59.059 52.381 0.00 0.00 34.02 3.18
3530 4587 8.870160 TGACATAGTTCCAAATTTGACAAAAG 57.130 30.769 19.86 1.73 0.00 2.27
3553 4610 8.721478 GTTCAGATAGCTTCAAGTTAAACATGA 58.279 33.333 0.00 0.00 0.00 3.07
3593 4654 5.408299 TCAAGTTGAACATGACATAGTTCCG 59.592 40.000 19.29 9.37 42.57 4.30
3610 4671 5.698832 TGCGAATAAATCACCTTCAAGTTG 58.301 37.500 0.00 0.00 0.00 3.16
3622 4683 4.917415 GCCATAACCACATGCGAATAAATC 59.083 41.667 0.00 0.00 0.00 2.17
3629 4690 0.747644 CTGGCCATAACCACATGCGA 60.748 55.000 5.51 0.00 35.33 5.10
3646 4707 2.264109 ATACACGTCGACTGCTTCTG 57.736 50.000 14.70 4.44 0.00 3.02
3683 4744 3.692101 AGTGTGCTAGAGTGTGCTACTAG 59.308 47.826 0.00 0.00 40.53 2.57
3729 4790 3.930848 CACGGTAAGCTGTTAGGTAAAGG 59.069 47.826 0.00 0.00 30.42 3.11
3863 8584 7.559590 ACCAAATGCTTAACTGATGATAGTC 57.440 36.000 0.00 0.00 0.00 2.59
3873 8594 7.112452 ACTGAAAGAAACCAAATGCTTAACT 57.888 32.000 0.00 0.00 37.43 2.24
3906 8627 8.712363 CCGATGGTCATGTCTAAAATTGTATAG 58.288 37.037 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.