Multiple sequence alignment - TraesCS3D01G305200

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 TraesCS3D01G305200 chr3D 100.000 2250 0 0 1 2250 419385596 419387845 0.000000e+00 4156.0
1 TraesCS3D01G305200 chr3D 83.538 1464 152 40 822 2250 418875503 418876912 0.000000e+00 1286.0
2 TraesCS3D01G305200 chr3D 83.538 1464 152 40 822 2250 418890802 418892211 0.000000e+00 1286.0
3 TraesCS3D01G305200 chr3D 100.000 636 0 0 2538 3173 419388133 419388768 0.000000e+00 1175.0
4 TraesCS3D01G305200 chr3D 78.163 664 80 37 721 1372 419515176 419515786 2.330000e-96 363.0
5 TraesCS3D01G305200 chr3D 80.833 480 53 20 903 1372 419463808 419464258 1.090000e-89 340.0
6 TraesCS3D01G305200 chr3D 95.455 44 2 0 649 692 325742775 325742732 1.580000e-08 71.3
7 TraesCS3D01G305200 chr3B 92.393 1525 65 28 768 2250 545432417 545433932 0.000000e+00 2126.0
8 TraesCS3D01G305200 chr3B 91.622 1504 80 25 783 2250 545562158 545563651 0.000000e+00 2037.0
9 TraesCS3D01G305200 chr3B 91.920 1448 71 25 839 2250 545667688 545669125 0.000000e+00 1984.0
10 TraesCS3D01G305200 chr3B 92.022 1103 50 21 1177 2250 545494443 545495536 0.000000e+00 1515.0
11 TraesCS3D01G305200 chr3B 89.684 601 40 4 2538 3118 545563722 545564320 0.000000e+00 747.0
12 TraesCS3D01G305200 chr3B 89.015 528 42 11 2538 3065 545495599 545496110 9.600000e-180 640.0
13 TraesCS3D01G305200 chr3B 89.426 331 19 11 72 398 545561543 545561861 1.370000e-108 403.0
14 TraesCS3D01G305200 chr3B 90.196 306 22 5 72 373 545667391 545667692 2.970000e-105 392.0
15 TraesCS3D01G305200 chr3B 89.434 265 21 6 857 1115 545493494 545493757 8.490000e-86 327.0
16 TraesCS3D01G305200 chr3B 94.203 207 12 0 2538 2744 545433999 545434205 1.840000e-82 316.0
17 TraesCS3D01G305200 chr3B 92.342 222 16 1 2746 2967 545448197 545448417 6.610000e-82 315.0
18 TraesCS3D01G305200 chr3B 93.229 192 13 0 22 213 545429857 545430048 1.860000e-72 283.0
19 TraesCS3D01G305200 chr3B 93.229 192 13 0 22 213 545482587 545482778 1.860000e-72 283.0
20 TraesCS3D01G305200 chr3B 89.796 196 17 2 396 588 13103813 13103618 6.800000e-62 248.0
21 TraesCS3D01G305200 chr3B 94.667 150 5 2 246 393 545432027 545432175 2.460000e-56 230.0
22 TraesCS3D01G305200 chr3B 94.667 150 5 2 246 393 545484774 545484922 2.460000e-56 230.0
23 TraesCS3D01G305200 chr3B 83.556 225 20 8 81 296 546200214 546199998 8.980000e-46 195.0
24 TraesCS3D01G305200 chr3B 93.103 116 8 0 3002 3117 545453554 545453669 1.510000e-38 171.0
25 TraesCS3D01G305200 chr3B 91.228 114 8 2 2538 2650 54544372 54544484 1.520000e-33 154.0
26 TraesCS3D01G305200 chr3B 91.000 100 3 3 768 861 545485164 545485263 2.570000e-26 130.0
27 TraesCS3D01G305200 chr3B 93.333 75 5 0 691 765 545562026 545562100 9.300000e-21 111.0
28 TraesCS3D01G305200 chr3B 98.361 61 1 0 3113 3173 545507778 545507838 1.200000e-19 108.0
29 TraesCS3D01G305200 chr3B 98.361 61 1 0 3113 3173 545565284 545565344 1.200000e-19 108.0
30 TraesCS3D01G305200 chr3B 98.361 61 1 0 3113 3173 545568576 545568636 1.200000e-19 108.0
31 TraesCS3D01G305200 chr3B 90.667 75 1 1 691 765 545432312 545432380 9.370000e-16 95.3
32 TraesCS3D01G305200 chr3B 95.000 60 2 1 3059 3118 545507181 545507239 3.370000e-15 93.5
33 TraesCS3D01G305200 chr3B 95.000 60 2 1 3059 3118 545567977 545568035 3.370000e-15 93.5
34 TraesCS3D01G305200 chr3B 89.333 75 2 1 691 765 545485059 545485127 4.360000e-14 89.8
35 TraesCS3D01G305200 chr3B 89.333 75 3 2 1 70 545667015 545667089 4.360000e-14 89.8
36 TraesCS3D01G305200 chr3A 91.700 1494 96 22 783 2250 531945075 531943584 0.000000e+00 2047.0
37 TraesCS3D01G305200 chr3A 84.191 1379 166 30 889 2245 531897546 531896198 0.000000e+00 1291.0
38 TraesCS3D01G305200 chr3A 84.183 1353 171 23 904 2245 531702688 531701368 0.000000e+00 1273.0
39 TraesCS3D01G305200 chr3A 89.320 412 25 9 1 398 531946401 531945995 1.700000e-137 499.0
40 TraesCS3D01G305200 chr3A 95.283 106 4 1 294 398 531945585 531945480 1.960000e-37 167.0
41 TraesCS3D01G305200 chr3A 95.918 49 2 0 717 765 531945178 531945130 2.620000e-11 80.5
42 TraesCS3D01G305200 chr5D 88.075 1434 126 26 822 2230 442012143 442010730 0.000000e+00 1659.0
43 TraesCS3D01G305200 chr5D 94.652 187 10 0 402 588 105860408 105860594 1.110000e-74 291.0
44 TraesCS3D01G305200 chr5D 94.118 187 11 0 402 588 85697368 85697182 5.180000e-73 285.0
45 TraesCS3D01G305200 chr5D 94.118 187 11 0 402 588 531505445 531505631 5.180000e-73 285.0
46 TraesCS3D01G305200 chr5D 89.552 201 19 2 390 588 100288668 100288868 1.460000e-63 254.0
47 TraesCS3D01G305200 chr5D 90.206 194 18 1 396 588 536387266 536387459 5.250000e-63 252.0
48 TraesCS3D01G305200 chr5D 78.740 127 26 1 2541 2666 404192567 404192693 2.030000e-12 84.2
49 TraesCS3D01G305200 chr5D 80.870 115 7 7 578 692 339984316 339984217 3.390000e-10 76.8
50 TraesCS3D01G305200 chr5D 95.455 44 2 0 649 692 105860643 105860600 1.580000e-08 71.3
51 TraesCS3D01G305200 chr5D 95.455 44 2 0 649 692 277564813 277564856 1.580000e-08 71.3
52 TraesCS3D01G305200 chr5D 94.872 39 2 0 2604 2642 446512244 446512282 9.500000e-06 62.1
53 TraesCS3D01G305200 chr5B 88.574 1339 118 19 909 2230 538039243 538037923 0.000000e+00 1592.0
54 TraesCS3D01G305200 chr5B 89.055 201 20 2 402 601 237047923 237048122 6.800000e-62 248.0
55 TraesCS3D01G305200 chr5B 78.059 237 39 11 2541 2772 544432208 544432436 1.530000e-28 137.0
56 TraesCS3D01G305200 chr4A 91.787 828 64 2 1427 2250 544381463 544382290 0.000000e+00 1149.0
57 TraesCS3D01G305200 chr4A 83.128 569 51 17 822 1372 544380764 544381305 7.960000e-131 477.0
58 TraesCS3D01G305200 chr4A 95.455 44 2 0 649 692 188192443 188192400 1.580000e-08 71.3
59 TraesCS3D01G305200 chr4A 88.679 53 1 2 578 630 258953293 258953340 3.420000e-05 60.2
60 TraesCS3D01G305200 chr7A 81.159 621 59 34 783 1348 669771256 669771873 2.250000e-121 446.0
61 TraesCS3D01G305200 chr7A 94.652 187 10 0 402 588 317629926 317630112 1.110000e-74 291.0
62 TraesCS3D01G305200 chr7A 92.000 125 10 0 2682 2806 661846119 661845995 3.250000e-40 176.0
63 TraesCS3D01G305200 chr7A 91.406 128 7 2 2539 2662 661847199 661847072 4.210000e-39 172.0
64 TraesCS3D01G305200 chr7A 86.441 59 3 2 571 629 410994462 410994515 3.420000e-05 60.2
65 TraesCS3D01G305200 chr7B 79.599 598 74 35 770 1345 641141154 641141725 4.960000e-103 385.0
66 TraesCS3D01G305200 chr7B 92.537 268 18 1 2541 2806 630104305 630104038 1.790000e-102 383.0
67 TraesCS3D01G305200 chr7B 91.837 49 3 1 578 626 248553814 248553861 2.040000e-07 67.6
68 TraesCS3D01G305200 chr7B 88.679 53 1 2 577 629 662291330 662291377 3.420000e-05 60.2
69 TraesCS3D01G305200 chr7D 79.383 616 72 41 770 1348 577703255 577703852 1.790000e-102 383.0
70 TraesCS3D01G305200 chr7D 87.925 265 19 3 2542 2806 572685306 572685055 1.850000e-77 300.0
71 TraesCS3D01G305200 chr7D 94.118 187 11 0 402 588 561578650 561578836 5.180000e-73 285.0
72 TraesCS3D01G305200 chr7D 89.691 194 19 1 396 588 254193881 254194074 2.440000e-61 246.0
73 TraesCS3D01G305200 chr7D 89.691 194 19 1 396 588 452453211 452453018 2.440000e-61 246.0
74 TraesCS3D01G305200 chr7D 100.000 36 0 0 649 684 104588276 104588311 2.040000e-07 67.6
75 TraesCS3D01G305200 chr2D 94.652 187 10 0 402 588 478093539 478093725 1.110000e-74 291.0
76 TraesCS3D01G305200 chr2D 94.652 187 10 0 402 588 647791033 647791219 1.110000e-74 291.0
77 TraesCS3D01G305200 chr2D 88.679 53 1 2 578 630 159381170 159381123 3.420000e-05 60.2
78 TraesCS3D01G305200 chr1D 93.814 194 11 1 396 588 446802766 446802959 1.110000e-74 291.0
79 TraesCS3D01G305200 chr1D 90.050 201 18 2 390 588 100123600 100123400 3.140000e-65 259.0
80 TraesCS3D01G305200 chr4D 94.624 186 10 0 402 587 307364749 307364564 4.000000e-74 289.0
81 TraesCS3D01G305200 chr4D 95.455 44 2 0 649 692 307364515 307364558 1.580000e-08 71.3
82 TraesCS3D01G305200 chr2B 92.574 202 13 2 2541 2741 728268222 728268422 4.000000e-74 289.0
83 TraesCS3D01G305200 chr2B 95.455 44 2 0 649 692 242229052 242229095 1.580000e-08 71.3
84 TraesCS3D01G305200 chr4B 91.282 195 16 1 396 589 491123135 491123329 6.750000e-67 265.0
85 TraesCS3D01G305200 chr5A 90.769 195 16 2 396 588 450507629 450507823 3.140000e-65 259.0
86 TraesCS3D01G305200 chr5A 80.682 88 17 0 2602 2689 509996389 509996302 5.680000e-08 69.4
87 TraesCS3D01G305200 chr1A 87.143 210 20 5 402 604 243740022 243740231 6.840000e-57 231.0
88 TraesCS3D01G305200 chr6D 95.455 44 2 0 649 692 82644385 82644428 1.580000e-08 71.3
89 TraesCS3D01G305200 chr6D 91.111 45 4 0 1301 1345 448595543 448595587 9.500000e-06 62.1
90 TraesCS3D01G305200 chr6D 88.679 53 1 2 578 630 295227390 295227343 3.420000e-05 60.2
91 TraesCS3D01G305200 chr6B 95.455 44 1 1 648 690 227713466 227713509 5.680000e-08 69.4
92 TraesCS3D01G305200 chr2A 86.441 59 3 2 571 629 599896306 599896359 3.420000e-05 60.2


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 TraesCS3D01G305200 chr3D 419385596 419388768 3172 False 2665.500000 4156 100.000000 1 3173 2 chr3D.!!$F5 3172
1 TraesCS3D01G305200 chr3D 418875503 418876912 1409 False 1286.000000 1286 83.538000 822 2250 1 chr3D.!!$F1 1428
2 TraesCS3D01G305200 chr3D 418890802 418892211 1409 False 1286.000000 1286 83.538000 822 2250 1 chr3D.!!$F2 1428
3 TraesCS3D01G305200 chr3D 419515176 419515786 610 False 363.000000 363 78.163000 721 1372 1 chr3D.!!$F4 651
4 TraesCS3D01G305200 chr3B 545493494 545496110 2616 False 827.333333 1515 90.157000 857 3065 3 chr3B.!!$F6 2208
5 TraesCS3D01G305200 chr3B 545667015 545669125 2110 False 821.933333 1984 90.483000 1 2250 3 chr3B.!!$F9 2249
6 TraesCS3D01G305200 chr3B 545429857 545434205 4348 False 610.060000 2126 93.031800 22 2744 5 chr3B.!!$F4 2722
7 TraesCS3D01G305200 chr3B 545561543 545568636 7093 False 515.357143 2037 93.683857 72 3173 7 chr3B.!!$F8 3101
8 TraesCS3D01G305200 chr3A 531896198 531897546 1348 True 1291.000000 1291 84.191000 889 2245 1 chr3A.!!$R2 1356
9 TraesCS3D01G305200 chr3A 531701368 531702688 1320 True 1273.000000 1273 84.183000 904 2245 1 chr3A.!!$R1 1341
10 TraesCS3D01G305200 chr3A 531943584 531946401 2817 True 698.375000 2047 93.055250 1 2250 4 chr3A.!!$R3 2249
11 TraesCS3D01G305200 chr5D 442010730 442012143 1413 True 1659.000000 1659 88.075000 822 2230 1 chr5D.!!$R4 1408
12 TraesCS3D01G305200 chr5B 538037923 538039243 1320 True 1592.000000 1592 88.574000 909 2230 1 chr5B.!!$R1 1321
13 TraesCS3D01G305200 chr4A 544380764 544382290 1526 False 813.000000 1149 87.457500 822 2250 2 chr4A.!!$F2 1428
14 TraesCS3D01G305200 chr7A 669771256 669771873 617 False 446.000000 446 81.159000 783 1348 1 chr7A.!!$F3 565
15 TraesCS3D01G305200 chr7B 641141154 641141725 571 False 385.000000 385 79.599000 770 1345 1 chr7B.!!$F2 575
16 TraesCS3D01G305200 chr7D 577703255 577703852 597 False 383.000000 383 79.383000 770 1348 1 chr7D.!!$F4 578

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
295 2551 0.322187 ACGCGGTATCCCAGCTTTTT 60.322 50.000 12.47 0.0 0.0 1.94 F
1348 4973 1.005867 TGCTTCGTTCGGGTACACC 60.006 57.895 0.00 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 4976 0.032130 AATCGACGAGCAGTGTGTGT 59.968 50.000 3.01 0.00 0.00 3.72 R
3011 6832 1.000396 GGAGCATTGGCAACCTCCT 60.000 57.895 28.32 13.52 44.61 3.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.680237 TCGCCAGGAGCACAACCG 62.680 66.667 0.00 0.00 44.04 4.44
259 2515 5.612351 AGAAACTTGACTCTTTAGGTCACC 58.388 41.667 0.00 0.00 42.41 4.02
287 2543 1.007336 CGCTAATCACGCGGTATCCC 61.007 60.000 12.47 0.00 46.32 3.85
295 2551 0.322187 ACGCGGTATCCCAGCTTTTT 60.322 50.000 12.47 0.00 0.00 1.94
398 2662 2.942804 TGTCAAAGGAAACCTGCATGA 58.057 42.857 0.00 0.00 32.13 3.07
400 2664 3.703556 TGTCAAAGGAAACCTGCATGAAA 59.296 39.130 0.00 0.00 32.13 2.69
402 2666 5.538053 TGTCAAAGGAAACCTGCATGAAATA 59.462 36.000 0.00 0.00 32.13 1.40
404 2668 6.366061 GTCAAAGGAAACCTGCATGAAATAAC 59.634 38.462 0.00 0.00 32.13 1.89
405 2669 6.041409 TCAAAGGAAACCTGCATGAAATAACA 59.959 34.615 0.00 0.00 32.13 2.41
406 2670 6.610075 AAGGAAACCTGCATGAAATAACAT 57.390 33.333 0.00 0.00 32.13 2.71
407 2671 7.716799 AAGGAAACCTGCATGAAATAACATA 57.283 32.000 0.00 0.00 32.13 2.29
408 2672 7.338800 AGGAAACCTGCATGAAATAACATAG 57.661 36.000 0.00 0.00 29.57 2.23
409 2673 6.322201 AGGAAACCTGCATGAAATAACATAGG 59.678 38.462 0.00 0.00 34.19 2.57
410 2674 6.096846 GGAAACCTGCATGAAATAACATAGGT 59.903 38.462 0.00 0.00 39.47 3.08
411 2675 7.284489 GGAAACCTGCATGAAATAACATAGGTA 59.716 37.037 0.00 0.00 37.90 3.08
413 2677 6.900194 ACCTGCATGAAATAACATAGGTAGT 58.100 36.000 0.00 0.00 37.42 2.73
414 2678 8.029782 ACCTGCATGAAATAACATAGGTAGTA 57.970 34.615 0.00 0.00 37.42 1.82
416 2680 9.507329 CCTGCATGAAATAACATAGGTAGTAAT 57.493 33.333 0.00 0.00 0.00 1.89
428 2692 9.982651 AACATAGGTAGTAATATCACACACATC 57.017 33.333 0.00 0.00 0.00 3.06
429 2693 9.368416 ACATAGGTAGTAATATCACACACATCT 57.632 33.333 0.00 0.00 0.00 2.90
433 2697 9.815306 AGGTAGTAATATCACACACATCTAGAT 57.185 33.333 0.00 0.00 0.00 1.98
451 2715 7.839680 TCTAGATAAAGTAGATGATGTGGCA 57.160 36.000 0.00 0.00 0.00 4.92
452 2716 8.250143 TCTAGATAAAGTAGATGATGTGGCAA 57.750 34.615 0.00 0.00 0.00 4.52
453 2717 8.704668 TCTAGATAAAGTAGATGATGTGGCAAA 58.295 33.333 0.00 0.00 0.00 3.68
456 2720 7.611467 AGATAAAGTAGATGATGTGGCAAACAA 59.389 33.333 0.00 0.00 43.61 2.83
457 2721 6.594788 AAAGTAGATGATGTGGCAAACAAT 57.405 33.333 0.00 0.00 43.61 2.71
459 2723 7.701539 AAGTAGATGATGTGGCAAACAATAA 57.298 32.000 0.00 0.00 43.61 1.40
462 2726 9.407380 AGTAGATGATGTGGCAAACAATAAATA 57.593 29.630 0.00 0.00 43.61 1.40
492 2756 9.476928 AAAGAGAGGAAAGTAGTAACATAGCTA 57.523 33.333 0.00 0.00 0.00 3.32
493 2757 9.476928 AAGAGAGGAAAGTAGTAACATAGCTAA 57.523 33.333 0.00 0.00 0.00 3.09
494 2758 9.649316 AGAGAGGAAAGTAGTAACATAGCTAAT 57.351 33.333 0.00 0.00 0.00 1.73
528 2792 9.755804 AGTATGAGTAACATCACACATATCAAG 57.244 33.333 0.00 0.00 40.07 3.02
530 2794 5.817296 TGAGTAACATCACACATATCAAGGC 59.183 40.000 0.00 0.00 0.00 4.35
531 2795 5.744171 AGTAACATCACACATATCAAGGCA 58.256 37.500 0.00 0.00 0.00 4.75
533 2797 5.571784 AACATCACACATATCAAGGCAAG 57.428 39.130 0.00 0.00 0.00 4.01
534 2798 4.847198 ACATCACACATATCAAGGCAAGA 58.153 39.130 0.00 0.00 0.00 3.02
536 2800 5.298527 ACATCACACATATCAAGGCAAGATG 59.701 40.000 0.00 0.00 36.24 2.90
542 2806 5.744171 ACATATCAAGGCAAGATGTGTGTA 58.256 37.500 16.54 0.00 43.33 2.90
543 2807 6.359804 ACATATCAAGGCAAGATGTGTGTAT 58.640 36.000 16.54 0.00 43.33 2.29
544 2808 7.508687 ACATATCAAGGCAAGATGTGTGTATA 58.491 34.615 16.54 0.00 43.33 1.47
545 2809 7.658982 ACATATCAAGGCAAGATGTGTGTATAG 59.341 37.037 16.54 0.00 43.33 1.31
546 2810 4.191544 TCAAGGCAAGATGTGTGTATAGC 58.808 43.478 0.00 0.00 0.00 2.97
547 2811 3.912496 AGGCAAGATGTGTGTATAGCA 57.088 42.857 0.00 0.00 0.00 3.49
548 2812 4.428294 AGGCAAGATGTGTGTATAGCAT 57.572 40.909 0.00 0.00 0.00 3.79
549 2813 5.551305 AGGCAAGATGTGTGTATAGCATA 57.449 39.130 0.00 0.00 0.00 3.14
550 2814 5.928976 AGGCAAGATGTGTGTATAGCATAA 58.071 37.500 0.00 0.00 0.00 1.90
551 2815 6.537355 AGGCAAGATGTGTGTATAGCATAAT 58.463 36.000 0.00 0.00 0.00 1.28
552 2816 7.679783 AGGCAAGATGTGTGTATAGCATAATA 58.320 34.615 0.00 0.00 0.00 0.98
553 2817 8.156820 AGGCAAGATGTGTGTATAGCATAATAA 58.843 33.333 0.00 0.00 0.00 1.40
554 2818 8.783093 GGCAAGATGTGTGTATAGCATAATAAA 58.217 33.333 0.00 0.00 0.00 1.40
570 2834 9.874205 AGCATAATAAATAAAGTGTTGCATGTT 57.126 25.926 0.00 0.00 0.00 2.71
577 2841 8.519492 AAATAAAGTGTTGCATGTTATCACAC 57.481 30.769 7.36 7.36 35.03 3.82
578 2842 5.512753 AAAGTGTTGCATGTTATCACACA 57.487 34.783 15.74 0.00 35.03 3.72
579 2843 5.710513 AAGTGTTGCATGTTATCACACAT 57.289 34.783 15.74 3.42 37.93 3.21
580 2844 6.816134 AAGTGTTGCATGTTATCACACATA 57.184 33.333 15.74 0.00 35.51 2.29
581 2845 7.395190 AAGTGTTGCATGTTATCACACATAT 57.605 32.000 15.74 1.87 35.51 1.78
582 2846 6.788243 AGTGTTGCATGTTATCACACATATG 58.212 36.000 15.74 0.00 35.51 1.78
583 2847 6.375174 AGTGTTGCATGTTATCACACATATGT 59.625 34.615 15.74 1.41 40.80 2.29
584 2848 7.028962 GTGTTGCATGTTATCACACATATGTT 58.971 34.615 5.37 0.00 36.72 2.71
586 2850 8.180920 TGTTGCATGTTATCACACATATGTTAC 58.819 33.333 5.37 0.00 36.72 2.50
587 2851 8.397906 GTTGCATGTTATCACACATATGTTACT 58.602 33.333 5.37 0.00 36.72 2.24
589 2853 9.260002 TGCATGTTATCACACATATGTTACTAG 57.740 33.333 5.37 0.00 36.72 2.57
590 2854 9.261180 GCATGTTATCACACATATGTTACTAGT 57.739 33.333 5.37 0.00 36.72 2.57
620 2884 9.646522 TGTTACTACCTTACCTTTATAGTAGGG 57.353 37.037 7.62 0.00 41.47 3.53
623 2887 8.123843 ACTACCTTACCTTTATAGTAGGGAGT 57.876 38.462 6.14 0.00 38.82 3.85
624 2888 9.242549 ACTACCTTACCTTTATAGTAGGGAGTA 57.757 37.037 2.03 0.00 38.82 2.59
628 2892 9.377238 CCTTACCTTTATAGTAGGGAGTAACAT 57.623 37.037 7.62 0.00 38.82 2.71
630 2894 7.063934 ACCTTTATAGTAGGGAGTAACATGC 57.936 40.000 0.00 0.00 37.09 4.06
631 2895 6.042897 ACCTTTATAGTAGGGAGTAACATGCC 59.957 42.308 0.00 0.00 37.09 4.40
632 2896 6.042781 CCTTTATAGTAGGGAGTAACATGCCA 59.957 42.308 0.00 0.00 31.99 4.92
633 2897 4.957684 ATAGTAGGGAGTAACATGCCAC 57.042 45.455 0.00 0.00 31.99 5.01
635 2899 2.910319 AGTAGGGAGTAACATGCCACAA 59.090 45.455 0.00 0.00 31.99 3.33
637 2901 2.726821 AGGGAGTAACATGCCACAATG 58.273 47.619 0.00 0.00 31.99 2.82
638 2902 2.308570 AGGGAGTAACATGCCACAATGA 59.691 45.455 0.00 0.00 31.99 2.57
639 2903 3.088532 GGGAGTAACATGCCACAATGAA 58.911 45.455 0.00 0.00 0.00 2.57
641 2905 4.887071 GGGAGTAACATGCCACAATGAATA 59.113 41.667 0.00 0.00 0.00 1.75
642 2906 5.009010 GGGAGTAACATGCCACAATGAATAG 59.991 44.000 0.00 0.00 0.00 1.73
646 2910 7.985476 AGTAACATGCCACAATGAATAGTAAC 58.015 34.615 0.00 0.00 0.00 2.50
648 2912 7.408756 AACATGCCACAATGAATAGTAACAT 57.591 32.000 0.00 0.00 0.00 2.71
649 2913 8.518430 AACATGCCACAATGAATAGTAACATA 57.482 30.769 0.00 0.00 0.00 2.29
650 2914 8.158169 ACATGCCACAATGAATAGTAACATAG 57.842 34.615 0.00 0.00 0.00 2.23
652 2916 9.271828 CATGCCACAATGAATAGTAACATAGTA 57.728 33.333 0.00 0.00 0.00 1.82
654 2918 9.104965 TGCCACAATGAATAGTAACATAGTAAC 57.895 33.333 0.00 0.00 0.00 2.50
655 2919 9.104965 GCCACAATGAATAGTAACATAGTAACA 57.895 33.333 0.00 0.00 0.00 2.41
672 2936 9.627395 CATAGTAACATAGACTAGTAACATGCC 57.373 37.037 0.00 0.00 33.03 4.40
673 2937 7.052142 AGTAACATAGACTAGTAACATGCCC 57.948 40.000 0.00 0.00 0.00 5.36
674 2938 5.950544 AACATAGACTAGTAACATGCCCA 57.049 39.130 0.00 0.00 0.00 5.36
675 2939 6.500589 AACATAGACTAGTAACATGCCCAT 57.499 37.500 0.00 0.00 0.00 4.00
676 2940 7.612065 AACATAGACTAGTAACATGCCCATA 57.388 36.000 0.00 0.00 0.00 2.74
677 2941 7.798710 ACATAGACTAGTAACATGCCCATAT 57.201 36.000 0.00 0.00 0.00 1.78
678 2942 8.207350 ACATAGACTAGTAACATGCCCATATT 57.793 34.615 0.00 0.00 0.00 1.28
679 2943 9.321532 ACATAGACTAGTAACATGCCCATATTA 57.678 33.333 0.00 0.00 0.00 0.98
681 2945 7.857404 AGACTAGTAACATGCCCATATTACT 57.143 36.000 14.28 14.28 42.00 2.24
682 2946 8.951614 AGACTAGTAACATGCCCATATTACTA 57.048 34.615 14.83 14.83 38.74 1.82
685 3491 7.733501 ACTAGTAACATGCCCATATTACTACCT 59.266 37.037 12.67 2.45 38.74 3.08
688 3494 8.940982 AGTAACATGCCCATATTACTACCTTTA 58.059 33.333 9.53 0.00 38.74 1.85
689 3495 9.734984 GTAACATGCCCATATTACTACCTTTAT 57.265 33.333 2.96 0.00 30.30 1.40
715 3521 3.173167 AACGGTCAACCTCCCCACG 62.173 63.158 0.00 0.00 0.00 4.94
1004 3935 2.352960 GCTAGTGCGAAAAGAAGATGGG 59.647 50.000 0.00 0.00 0.00 4.00
1263 4888 3.083997 GGGATCGTGAGGGGTGCT 61.084 66.667 0.00 0.00 0.00 4.40
1348 4973 1.005867 TGCTTCGTTCGGGTACACC 60.006 57.895 0.00 0.00 0.00 4.16
1372 5006 0.729478 ACACACTGCTCGTCGATTCG 60.729 55.000 0.00 0.00 0.00 3.34
1394 5116 5.636121 TCGTTCGAATACTAACTGCATTGTT 59.364 36.000 0.00 0.00 0.00 2.83
1395 5117 5.952064 CGTTCGAATACTAACTGCATTGTTC 59.048 40.000 0.00 0.00 0.00 3.18
1396 5118 6.400621 CGTTCGAATACTAACTGCATTGTTCA 60.401 38.462 0.00 0.00 0.00 3.18
1400 5122 8.817100 TCGAATACTAACTGCATTGTTCATTAG 58.183 33.333 0.00 0.00 0.00 1.73
1401 5123 8.604035 CGAATACTAACTGCATTGTTCATTAGT 58.396 33.333 0.00 0.00 36.90 2.24
1402 5124 9.922305 GAATACTAACTGCATTGTTCATTAGTC 57.078 33.333 0.00 0.00 35.21 2.59
1403 5125 6.743575 ACTAACTGCATTGTTCATTAGTCC 57.256 37.500 0.00 0.00 29.08 3.85
1404 5126 6.476378 ACTAACTGCATTGTTCATTAGTCCT 58.524 36.000 0.00 0.00 29.08 3.85
1405 5127 6.942576 ACTAACTGCATTGTTCATTAGTCCTT 59.057 34.615 0.00 0.00 29.08 3.36
1406 5128 8.100791 ACTAACTGCATTGTTCATTAGTCCTTA 58.899 33.333 0.00 0.00 29.08 2.69
1408 5130 6.476378 ACTGCATTGTTCATTAGTCCTTACT 58.524 36.000 0.00 0.00 39.91 2.24
1409 5131 6.942576 ACTGCATTGTTCATTAGTCCTTACTT 59.057 34.615 0.00 0.00 37.15 2.24
1415 5158 7.905604 TGTTCATTAGTCCTTACTTCATGTG 57.094 36.000 0.00 0.00 37.15 3.21
1596 5389 2.863853 CTCATGCGCCGACATCGTG 61.864 63.158 4.18 0.00 37.74 4.35
1734 5527 0.038166 GGCCCTTCTCCAATGTCACA 59.962 55.000 0.00 0.00 0.00 3.58
1833 5626 1.499056 CGCTCGCTGCATGTTCTTT 59.501 52.632 0.00 0.00 43.06 2.52
1863 5656 0.909610 TCTCTGAAATGGACCCGGCT 60.910 55.000 0.00 0.00 0.00 5.52
1929 5722 1.779569 ACGTGAACCAAGACGATGTC 58.220 50.000 0.00 0.00 38.94 3.06
1932 5725 2.755650 GTGAACCAAGACGATGTCACT 58.244 47.619 0.00 0.00 34.60 3.41
2116 5909 1.064017 TGGGGAAAATCGGGATCAAGG 60.064 52.381 0.00 0.00 0.00 3.61
2582 6384 0.108186 TGGCCTCAGCTACGACAATG 60.108 55.000 3.32 0.00 39.73 2.82
2608 6410 9.661563 GTCACAAATATAATCCGGTGGAATATA 57.338 33.333 0.00 3.72 35.38 0.86
2621 6423 6.824704 CCGGTGGAATATAAAACCAAGTCTTA 59.175 38.462 0.00 0.00 35.40 2.10
2650 6452 2.425143 TTCAGGCAGCCATTTCTAGG 57.575 50.000 15.80 0.00 0.00 3.02
2659 6461 5.239525 GGCAGCCATTTCTAGGTAGTTTATG 59.760 44.000 6.55 0.00 0.00 1.90
2687 6489 3.003480 AGAATTTGCAGTTCGACTAGCC 58.997 45.455 7.89 0.00 0.00 3.93
2768 6570 0.247736 CATACCGGGATCTAGCCAGC 59.752 60.000 6.32 0.00 0.00 4.85
2772 6574 2.925262 CGGGATCTAGCCAGCTCCG 61.925 68.421 0.00 0.00 37.87 4.63
2797 6599 1.242076 GACAAAGCCTGCATGACACT 58.758 50.000 0.00 0.00 0.00 3.55
2799 6601 1.202855 ACAAAGCCTGCATGACACTCT 60.203 47.619 0.00 0.00 0.00 3.24
2808 6610 2.632512 TGCATGACACTCTGGTTGTCTA 59.367 45.455 0.00 0.00 34.03 2.59
2816 6618 3.440522 CACTCTGGTTGTCTATCTCGACA 59.559 47.826 0.00 0.00 41.82 4.35
2878 6680 3.289834 CCTGCACGCCAACAGCTT 61.290 61.111 0.00 0.00 40.39 3.74
2894 6696 1.244019 GCTTTGCATGTTCCGGGTCT 61.244 55.000 0.00 0.00 0.00 3.85
2900 6702 1.671054 ATGTTCCGGGTCTGCAACG 60.671 57.895 0.00 0.00 0.00 4.10
2939 6741 1.187567 AAGCCTCCCACAAACATGCC 61.188 55.000 0.00 0.00 0.00 4.40
2945 6747 3.289836 CTCCCACAAACATGCCATGATA 58.710 45.455 12.53 0.00 0.00 2.15
2986 6807 2.002586 CTTCGACGTTGCTCCATCAAT 58.997 47.619 0.00 0.00 0.00 2.57
3011 6832 1.992557 ACCTTTAGCCATCCTTGGACA 59.007 47.619 0.00 0.00 46.92 4.02
3024 6845 0.482446 TTGGACAGGAGGTTGCCAAT 59.518 50.000 0.00 0.00 32.85 3.16
3066 6887 0.908910 TGTGGTTATCGGTGAGGCAT 59.091 50.000 0.00 0.00 0.00 4.40
3096 6917 2.676748 CCCATTCCTCTAGCAGTCTCT 58.323 52.381 0.00 0.00 0.00 3.10
3159 7949 2.574322 CTTGTTTTGTCGCATTCCTCG 58.426 47.619 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.160329 CCCATCTGCCGATTCGTTCC 61.160 60.000 5.20 0.00 0.00 3.62
103 409 5.297776 ACACATTATGCATACCAGCTCTTTC 59.702 40.000 5.74 0.00 34.99 2.62
259 2515 1.258982 GCGTGATTAGCGATGACCTTG 59.741 52.381 0.00 0.00 0.00 3.61
295 2551 4.757657 TGAGTTAGGCGAAACAAGCATAAA 59.242 37.500 8.20 0.00 41.49 1.40
402 2666 9.982651 GATGTGTGTGATATTACTACCTATGTT 57.017 33.333 0.00 0.00 0.00 2.71
407 2671 9.815306 ATCTAGATGTGTGTGATATTACTACCT 57.185 33.333 3.89 0.00 0.00 3.08
418 2682 9.408648 TCATCTACTTTATCTAGATGTGTGTGA 57.591 33.333 15.79 12.46 44.29 3.58
424 2688 8.310382 GCCACATCATCTACTTTATCTAGATGT 58.690 37.037 15.79 7.41 44.29 3.06
425 2689 8.309656 TGCCACATCATCTACTTTATCTAGATG 58.690 37.037 15.79 8.54 44.89 2.90
426 2690 8.427902 TGCCACATCATCTACTTTATCTAGAT 57.572 34.615 10.73 10.73 32.13 1.98
427 2691 7.839680 TGCCACATCATCTACTTTATCTAGA 57.160 36.000 0.00 0.00 0.00 2.43
428 2692 8.768955 GTTTGCCACATCATCTACTTTATCTAG 58.231 37.037 0.00 0.00 0.00 2.43
429 2693 8.264347 TGTTTGCCACATCATCTACTTTATCTA 58.736 33.333 0.00 0.00 0.00 1.98
430 2694 7.112122 TGTTTGCCACATCATCTACTTTATCT 58.888 34.615 0.00 0.00 0.00 1.98
432 2696 7.701539 TTGTTTGCCACATCATCTACTTTAT 57.298 32.000 0.00 0.00 34.43 1.40
433 2697 7.701539 ATTGTTTGCCACATCATCTACTTTA 57.298 32.000 0.00 0.00 34.43 1.85
434 2698 6.594788 ATTGTTTGCCACATCATCTACTTT 57.405 33.333 0.00 0.00 34.43 2.66
436 2700 7.701539 TTTATTGTTTGCCACATCATCTACT 57.298 32.000 0.00 0.00 34.43 2.57
465 2729 9.476928 AGCTATGTTACTACTTTCCTCTCTTTA 57.523 33.333 0.00 0.00 0.00 1.85
466 2730 8.368962 AGCTATGTTACTACTTTCCTCTCTTT 57.631 34.615 0.00 0.00 0.00 2.52
467 2731 7.964666 AGCTATGTTACTACTTTCCTCTCTT 57.035 36.000 0.00 0.00 0.00 2.85
468 2732 9.649316 ATTAGCTATGTTACTACTTTCCTCTCT 57.351 33.333 0.00 0.00 0.00 3.10
495 2759 9.895138 TGTGTGATGTTACTCATACTACTAGTA 57.105 33.333 1.89 1.89 37.92 1.82
496 2760 8.803397 TGTGTGATGTTACTCATACTACTAGT 57.197 34.615 0.00 0.00 37.92 2.57
502 2766 9.755804 CTTGATATGTGTGATGTTACTCATACT 57.244 33.333 10.75 3.32 38.84 2.12
503 2767 8.982685 CCTTGATATGTGTGATGTTACTCATAC 58.017 37.037 0.00 5.35 38.84 2.39
506 2770 5.817296 GCCTTGATATGTGTGATGTTACTCA 59.183 40.000 0.00 0.00 0.00 3.41
508 2772 5.744171 TGCCTTGATATGTGTGATGTTACT 58.256 37.500 0.00 0.00 0.00 2.24
510 2774 6.413892 TCTTGCCTTGATATGTGTGATGTTA 58.586 36.000 0.00 0.00 0.00 2.41
512 2776 4.847198 TCTTGCCTTGATATGTGTGATGT 58.153 39.130 0.00 0.00 0.00 3.06
513 2777 5.298527 ACATCTTGCCTTGATATGTGTGATG 59.701 40.000 0.00 0.00 35.23 3.07
514 2778 5.298527 CACATCTTGCCTTGATATGTGTGAT 59.701 40.000 0.00 0.00 41.46 3.06
515 2779 4.637091 CACATCTTGCCTTGATATGTGTGA 59.363 41.667 0.00 0.00 41.46 3.58
516 2780 4.916870 CACATCTTGCCTTGATATGTGTG 58.083 43.478 0.00 0.00 41.46 3.82
519 2783 4.592942 ACACACATCTTGCCTTGATATGT 58.407 39.130 0.00 0.00 32.52 2.29
520 2784 6.872628 ATACACACATCTTGCCTTGATATG 57.127 37.500 0.00 0.00 0.00 1.78
523 2787 4.818546 GCTATACACACATCTTGCCTTGAT 59.181 41.667 0.00 0.00 0.00 2.57
524 2788 4.191544 GCTATACACACATCTTGCCTTGA 58.808 43.478 0.00 0.00 0.00 3.02
525 2789 3.940852 TGCTATACACACATCTTGCCTTG 59.059 43.478 0.00 0.00 0.00 3.61
526 2790 4.220693 TGCTATACACACATCTTGCCTT 57.779 40.909 0.00 0.00 0.00 4.35
528 2792 6.808008 ATTATGCTATACACACATCTTGCC 57.192 37.500 0.00 0.00 0.00 4.52
544 2808 9.874205 AACATGCAACACTTTATTTATTATGCT 57.126 25.926 0.00 0.00 32.74 3.79
551 2815 9.619316 GTGTGATAACATGCAACACTTTATTTA 57.381 29.630 8.05 0.00 33.41 1.40
552 2816 8.140628 TGTGTGATAACATGCAACACTTTATTT 58.859 29.630 14.68 0.00 33.41 1.40
553 2817 7.656412 TGTGTGATAACATGCAACACTTTATT 58.344 30.769 14.68 0.00 33.41 1.40
554 2818 7.213216 TGTGTGATAACATGCAACACTTTAT 57.787 32.000 14.68 3.55 33.41 1.40
555 2819 6.625873 TGTGTGATAACATGCAACACTTTA 57.374 33.333 14.68 0.00 33.41 1.85
556 2820 5.512753 TGTGTGATAACATGCAACACTTT 57.487 34.783 14.68 0.00 33.41 2.66
561 2825 8.397906 AGTAACATATGTGTGATAACATGCAAC 58.602 33.333 9.63 0.00 40.93 4.17
594 2858 9.646522 CCCTACTATAAAGGTAAGGTAGTAACA 57.353 37.037 0.00 0.00 30.15 2.41
595 2859 9.868160 TCCCTACTATAAAGGTAAGGTAGTAAC 57.132 37.037 0.00 0.00 30.15 2.50
600 2864 9.868160 GTTACTCCCTACTATAAAGGTAAGGTA 57.132 37.037 1.22 0.00 31.70 3.08
602 2866 8.773033 TGTTACTCCCTACTATAAAGGTAAGG 57.227 38.462 1.22 0.00 31.70 2.69
604 2868 8.645110 GCATGTTACTCCCTACTATAAAGGTAA 58.355 37.037 0.00 0.00 31.70 2.85
605 2869 7.234166 GGCATGTTACTCCCTACTATAAAGGTA 59.766 40.741 0.00 0.00 31.70 3.08
606 2870 6.042897 GGCATGTTACTCCCTACTATAAAGGT 59.957 42.308 0.00 0.00 31.70 3.50
608 2872 6.929606 GTGGCATGTTACTCCCTACTATAAAG 59.070 42.308 0.00 0.00 0.00 1.85
612 2876 4.295201 TGTGGCATGTTACTCCCTACTAT 58.705 43.478 0.00 0.00 0.00 2.12
614 2878 2.546899 TGTGGCATGTTACTCCCTACT 58.453 47.619 0.00 0.00 0.00 2.57
615 2879 3.343941 TTGTGGCATGTTACTCCCTAC 57.656 47.619 0.00 0.00 0.00 3.18
616 2880 3.521531 TCATTGTGGCATGTTACTCCCTA 59.478 43.478 0.00 0.00 0.00 3.53
617 2881 2.308570 TCATTGTGGCATGTTACTCCCT 59.691 45.455 0.00 0.00 0.00 4.20
618 2882 2.722094 TCATTGTGGCATGTTACTCCC 58.278 47.619 0.00 0.00 0.00 4.30
619 2883 4.989279 ATTCATTGTGGCATGTTACTCC 57.011 40.909 0.00 0.00 0.00 3.85
620 2884 6.683974 ACTATTCATTGTGGCATGTTACTC 57.316 37.500 0.00 0.00 0.00 2.59
622 2886 7.757526 TGTTACTATTCATTGTGGCATGTTAC 58.242 34.615 0.00 0.00 0.00 2.50
623 2887 7.929941 TGTTACTATTCATTGTGGCATGTTA 57.070 32.000 0.00 0.00 0.00 2.41
624 2888 6.832520 TGTTACTATTCATTGTGGCATGTT 57.167 33.333 0.00 0.00 0.00 2.71
625 2889 7.775093 ACTATGTTACTATTCATTGTGGCATGT 59.225 33.333 0.00 0.00 31.40 3.21
628 2892 9.104965 GTTACTATGTTACTATTCATTGTGGCA 57.895 33.333 0.00 0.00 33.68 4.92
629 2893 9.104965 TGTTACTATGTTACTATTCATTGTGGC 57.895 33.333 0.00 0.00 33.68 5.01
646 2910 9.627395 GGCATGTTACTAGTCTATGTTACTATG 57.373 37.037 0.00 0.00 0.00 2.23
648 2912 7.781219 TGGGCATGTTACTAGTCTATGTTACTA 59.219 37.037 0.00 0.00 0.00 1.82
649 2913 6.610020 TGGGCATGTTACTAGTCTATGTTACT 59.390 38.462 0.00 0.00 0.00 2.24
650 2914 6.812998 TGGGCATGTTACTAGTCTATGTTAC 58.187 40.000 0.00 0.00 0.00 2.50
652 2916 5.950544 TGGGCATGTTACTAGTCTATGTT 57.049 39.130 0.00 0.00 0.00 2.71
654 2918 9.587772 GTAATATGGGCATGTTACTAGTCTATG 57.412 37.037 0.00 4.16 40.21 2.23
655 2919 9.548631 AGTAATATGGGCATGTTACTAGTCTAT 57.451 33.333 0.00 0.00 46.68 1.98
656 2920 8.951614 AGTAATATGGGCATGTTACTAGTCTA 57.048 34.615 0.00 0.00 46.68 2.59
657 2921 7.857404 AGTAATATGGGCATGTTACTAGTCT 57.143 36.000 0.00 0.00 46.68 3.24
661 2925 8.500667 AAGGTAGTAATATGGGCATGTTACTA 57.499 34.615 6.41 6.41 46.68 1.82
663 2927 9.734984 ATAAAGGTAGTAATATGGGCATGTTAC 57.265 33.333 0.00 0.00 42.23 2.50
666 2930 8.047310 GCTATAAAGGTAGTAATATGGGCATGT 58.953 37.037 0.00 0.00 0.00 3.21
667 2931 8.046708 TGCTATAAAGGTAGTAATATGGGCATG 58.953 37.037 0.00 0.00 0.00 4.06
668 2932 8.158025 TGCTATAAAGGTAGTAATATGGGCAT 57.842 34.615 0.00 0.00 0.00 4.40
670 2934 9.110502 GAATGCTATAAAGGTAGTAATATGGGC 57.889 37.037 0.00 0.00 0.00 5.36
675 2939 9.701098 CCGTTGAATGCTATAAAGGTAGTAATA 57.299 33.333 0.00 0.00 0.00 0.98
676 2940 8.208903 ACCGTTGAATGCTATAAAGGTAGTAAT 58.791 33.333 0.00 0.00 35.03 1.89
677 2941 7.558604 ACCGTTGAATGCTATAAAGGTAGTAA 58.441 34.615 0.00 0.00 35.03 2.24
678 2942 7.116075 ACCGTTGAATGCTATAAAGGTAGTA 57.884 36.000 0.00 0.00 35.03 1.82
679 2943 5.985911 ACCGTTGAATGCTATAAAGGTAGT 58.014 37.500 0.00 0.00 35.03 2.73
681 2945 5.979993 TGACCGTTGAATGCTATAAAGGTA 58.020 37.500 0.00 0.00 36.53 3.08
682 2946 4.839121 TGACCGTTGAATGCTATAAAGGT 58.161 39.130 0.00 0.00 38.56 3.50
685 3491 5.250200 AGGTTGACCGTTGAATGCTATAAA 58.750 37.500 0.00 0.00 42.08 1.40
688 3494 3.270877 GAGGTTGACCGTTGAATGCTAT 58.729 45.455 0.00 0.00 42.08 2.97
689 3495 2.614481 GGAGGTTGACCGTTGAATGCTA 60.614 50.000 0.00 0.00 42.08 3.49
761 3568 0.615331 ATGCCATGTCTCCTGTCGTT 59.385 50.000 0.00 0.00 0.00 3.85
765 3572 1.524002 CGGATGCCATGTCTCCTGT 59.476 57.895 0.00 0.00 0.00 4.00
824 3673 1.066143 AGATGGACGCGAATTTCCACT 60.066 47.619 17.32 13.36 44.80 4.00
1195 4820 1.068055 CCTGTTGTCGTAGTAGCCGTT 60.068 52.381 0.00 0.00 0.00 4.44
1348 4973 1.327988 CGACGAGCAGTGTGTGTACG 61.328 60.000 0.00 0.00 34.61 3.67
1349 4974 0.040692 TCGACGAGCAGTGTGTGTAC 60.041 55.000 0.00 0.00 0.00 2.90
1350 4975 0.879090 ATCGACGAGCAGTGTGTGTA 59.121 50.000 3.01 0.00 0.00 2.90
1351 4976 0.032130 AATCGACGAGCAGTGTGTGT 59.968 50.000 3.01 0.00 0.00 3.72
1352 4977 0.710567 GAATCGACGAGCAGTGTGTG 59.289 55.000 3.01 0.00 0.00 3.82
1372 5006 6.827641 TGAACAATGCAGTTAGTATTCGAAC 58.172 36.000 0.00 0.00 29.42 3.95
1394 5116 6.048732 TGCACATGAAGTAAGGACTAATGA 57.951 37.500 0.00 0.00 35.15 2.57
1395 5117 6.932356 ATGCACATGAAGTAAGGACTAATG 57.068 37.500 0.00 0.00 36.56 1.90
1396 5118 9.060347 CATAATGCACATGAAGTAAGGACTAAT 57.940 33.333 0.00 0.00 33.58 1.73
1400 5122 6.925610 TCATAATGCACATGAAGTAAGGAC 57.074 37.500 9.77 0.00 29.55 3.85
1401 5123 6.712095 GGATCATAATGCACATGAAGTAAGGA 59.288 38.462 14.85 0.00 36.08 3.36
1402 5124 6.487668 TGGATCATAATGCACATGAAGTAAGG 59.512 38.462 14.85 0.00 36.08 2.69
1403 5125 7.308408 CCTGGATCATAATGCACATGAAGTAAG 60.308 40.741 14.85 10.63 36.08 2.34
1404 5126 6.487668 CCTGGATCATAATGCACATGAAGTAA 59.512 38.462 14.85 3.63 36.08 2.24
1405 5127 5.999600 CCTGGATCATAATGCACATGAAGTA 59.000 40.000 14.85 5.58 36.08 2.24
1406 5128 4.825634 CCTGGATCATAATGCACATGAAGT 59.174 41.667 14.85 2.31 36.08 3.01
1408 5130 4.146564 CCCTGGATCATAATGCACATGAA 58.853 43.478 14.85 1.24 36.08 2.57
1409 5131 3.499021 CCCCTGGATCATAATGCACATGA 60.499 47.826 13.60 13.60 36.86 3.07
1415 5158 1.251251 GCACCCCTGGATCATAATGC 58.749 55.000 0.00 0.00 0.00 3.56
1734 5527 1.594310 GAAAGTCGCCTGGAGCTCT 59.406 57.895 14.64 0.00 40.39 4.09
1767 5560 2.366533 GTGACCATCTCGTCTGAGGTA 58.633 52.381 0.00 0.00 42.79 3.08
1818 5611 1.536766 CTGGAAAAGAACATGCAGCGA 59.463 47.619 0.00 0.00 0.00 4.93
1833 5626 0.396435 TTTCAGAGAAGCGGCTGGAA 59.604 50.000 1.81 0.30 33.05 3.53
1863 5656 1.363443 CCTGAGCTTTGCGGCAAAA 59.637 52.632 26.28 12.59 32.75 2.44
1872 5665 2.348998 CACTCGGCCCTGAGCTTT 59.651 61.111 7.51 0.00 43.05 3.51
1929 5722 2.359981 TATCCAGGACGTAGGGAGTG 57.640 55.000 8.13 0.00 33.47 3.51
1932 5725 1.063492 TGCTTATCCAGGACGTAGGGA 60.063 52.381 4.96 4.96 34.70 4.20
2582 6384 6.877611 ATTCCACCGGATTATATTTGTGAC 57.122 37.500 9.46 0.00 0.00 3.67
2621 6423 4.235079 TGGCTGCCTGAATAAGTTATGT 57.765 40.909 21.03 0.00 0.00 2.29
2625 6427 4.347607 AGAAATGGCTGCCTGAATAAGTT 58.652 39.130 21.03 3.34 0.00 2.66
2650 6452 4.616181 AATTCTGCGGCACATAAACTAC 57.384 40.909 0.00 0.00 0.00 2.73
2675 6477 1.053424 TGGTTTGGGCTAGTCGAACT 58.947 50.000 10.73 0.00 0.00 3.01
2682 6484 4.764823 TGAATTTACTGTGGTTTGGGCTAG 59.235 41.667 0.00 0.00 0.00 3.42
2687 6489 6.587226 CACATGATGAATTTACTGTGGTTTGG 59.413 38.462 0.00 0.00 32.41 3.28
2768 6570 1.532868 CAGGCTTTGTCAAGTTCGGAG 59.467 52.381 0.00 0.00 31.86 4.63
2772 6574 2.294233 TCATGCAGGCTTTGTCAAGTTC 59.706 45.455 0.00 0.00 31.86 3.01
2808 6610 2.418746 CCCGGAAGATTGTTGTCGAGAT 60.419 50.000 0.73 0.00 0.00 2.75
2816 6618 1.304134 GGGTGCCCGGAAGATTGTT 60.304 57.895 0.73 0.00 0.00 2.83
2838 6640 2.811514 GGATCCAGCTGGCCATCGA 61.812 63.158 28.91 10.24 34.44 3.59
2878 6680 1.971167 GCAGACCCGGAACATGCAA 60.971 57.895 0.73 0.00 36.88 4.08
2920 6722 1.187567 GGCATGTTTGTGGGAGGCTT 61.188 55.000 0.00 0.00 0.00 4.35
2939 6741 1.200483 GGTCGTGCGTGACTATCATG 58.800 55.000 7.90 0.00 38.91 3.07
2945 6747 4.702081 GAGCGGTCGTGCGTGACT 62.702 66.667 0.00 0.00 40.67 3.41
2986 6807 3.620488 CAAGGATGGCTAAAGGTAAGCA 58.380 45.455 0.00 0.00 41.93 3.91
3011 6832 1.000396 GGAGCATTGGCAACCTCCT 60.000 57.895 28.32 13.52 44.61 3.69
3024 6845 1.302511 GAGGAAAGCCAACGGAGCA 60.303 57.895 0.00 0.00 36.29 4.26
3066 6887 2.551270 AGAGGAATGGGCTAGTGTTCA 58.449 47.619 0.00 0.00 0.00 3.18
3096 6917 3.777478 GATCCTTGGTCGATCGTGTTTA 58.223 45.455 15.94 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.