Multiple sequence alignment - TraesCS2D01G222400

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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 TraesCS2D01G222400 chr2D 100.000 7672 0 0 1 7672 189529389 189521718 0.000000e+00 14168.0
1 TraesCS2D01G222400 chr7D 98.056 3961 48 12 2447 6392 169031885 169027939 0.000000e+00 6861.0
2 TraesCS2D01G222400 chr7D 97.621 3952 55 11 2447 6392 616751322 616747404 0.000000e+00 6741.0
3 TraesCS2D01G222400 chr7D 97.928 724 14 1 1725 2448 169033211 169032489 0.000000e+00 1253.0
4 TraesCS2D01G222400 chr7D 98.331 599 10 0 1725 2323 616752811 616752213 0.000000e+00 1051.0
5 TraesCS2D01G222400 chr7D 98.305 118 2 0 1606 1723 169033379 169033262 2.810000e-49 207.0
6 TraesCS2D01G222400 chr7D 96.552 87 3 0 1591 1677 169033563 169033477 2.230000e-30 145.0
7 TraesCS2D01G222400 chr7D 96.512 86 3 0 1592 1677 616752976 616752891 8.030000e-30 143.0
8 TraesCS2D01G222400 chr7D 100.000 46 0 0 1678 1723 169033243 169033198 1.370000e-12 86.1
9 TraesCS2D01G222400 chr7D 97.826 46 1 0 1678 1723 169033429 169033384 6.380000e-11 80.5
10 TraesCS2D01G222400 chr6A 97.745 3947 71 10 2449 6391 561612951 561609019 0.000000e+00 6780.0
11 TraesCS2D01G222400 chr6A 97.492 3948 81 11 2447 6391 561440929 561444861 0.000000e+00 6726.0
12 TraesCS2D01G222400 chr6A 97.256 656 17 1 1794 2448 561614182 561613527 0.000000e+00 1110.0
13 TraesCS2D01G222400 chr6A 96.799 656 20 1 1794 2448 561439700 561440355 0.000000e+00 1094.0
14 TraesCS2D01G222400 chr6A 96.992 133 4 0 1591 1723 561439474 561439606 2.790000e-54 224.0
15 TraesCS2D01G222400 chr6A 95.489 133 6 0 1591 1723 561614408 561614276 6.030000e-51 213.0
16 TraesCS2D01G222400 chr6A 91.241 137 5 2 1335 1468 200245953 200245821 6.120000e-41 180.0
17 TraesCS2D01G222400 chr6A 98.020 101 1 1 1373 1473 61597805 61597904 2.850000e-39 174.0
18 TraesCS2D01G222400 chr6A 100.000 46 0 0 1678 1723 561614257 561614212 1.370000e-12 86.1
19 TraesCS2D01G222400 chr6A 100.000 39 0 0 1729 1767 561439661 561439699 1.070000e-08 73.1
20 TraesCS2D01G222400 chr5D 97.624 3957 70 14 2447 6392 64655250 64659193 0.000000e+00 6765.0
21 TraesCS2D01G222400 chr5D 94.118 867 14 6 1583 2448 64653844 64654674 0.000000e+00 1284.0
22 TraesCS2D01G222400 chr3B 97.544 3950 80 10 2447 6393 71551238 71547303 0.000000e+00 6741.0
23 TraesCS2D01G222400 chr3B 97.561 656 15 1 1794 2448 71553443 71552788 0.000000e+00 1122.0
24 TraesCS2D01G222400 chr3B 96.909 647 19 1 1803 2448 71552458 71551812 0.000000e+00 1083.0
25 TraesCS2D01G222400 chr3B 97.015 134 4 0 1590 1723 71553670 71553537 7.750000e-55 226.0
26 TraesCS2D01G222400 chr3B 91.391 151 7 2 1319 1465 732905447 732905299 1.310000e-47 202.0
27 TraesCS2D01G222400 chr3B 95.146 103 3 1 1373 1473 283473991 283474093 2.220000e-35 161.0
28 TraesCS2D01G222400 chr7B 97.518 3948 82 9 2447 6392 350691115 350687182 0.000000e+00 6734.0
29 TraesCS2D01G222400 chr7B 96.693 635 20 1 1815 2448 350692323 350691689 0.000000e+00 1055.0
30 TraesCS2D01G222400 chr7B 96.241 133 5 0 1591 1723 350693656 350693524 1.300000e-52 219.0
31 TraesCS2D01G222400 chr7B 86.335 161 15 7 1328 1484 593418009 593418166 1.320000e-37 169.0
32 TraesCS2D01G222400 chr7B 94.340 106 1 1 1373 1473 624570254 624570149 2.870000e-34 158.0
33 TraesCS2D01G222400 chr7B 100.000 46 0 0 1678 1723 350693505 350693460 1.370000e-12 86.1
34 TraesCS2D01G222400 chr4A 96.960 3947 99 12 2447 6391 488009653 488005726 0.000000e+00 6604.0
35 TraesCS2D01G222400 chr4A 94.737 133 7 0 1591 1723 488011234 488011102 2.810000e-49 207.0
36 TraesCS2D01G222400 chr5B 96.860 3790 78 13 2447 6231 651222562 651226315 0.000000e+00 6301.0
37 TraesCS2D01G222400 chr5B 97.403 2811 57 9 3583 6391 292188494 292185698 0.000000e+00 4772.0
38 TraesCS2D01G222400 chr5B 97.104 656 18 1 1794 2448 292194197 292193542 0.000000e+00 1105.0
39 TraesCS2D01G222400 chr5B 96.992 133 4 0 1591 1723 292194423 292194291 2.790000e-54 224.0
40 TraesCS2D01G222400 chr5B 100.000 46 0 0 1678 1723 292194272 292194227 1.370000e-12 86.1
41 TraesCS2D01G222400 chr2B 97.063 1328 25 7 1 1320 245821991 245820670 0.000000e+00 2224.0
42 TraesCS2D01G222400 chr2B 89.441 644 37 7 7032 7671 245820033 245819417 0.000000e+00 784.0
43 TraesCS2D01G222400 chr2B 97.449 392 10 0 6391 6782 245820530 245820139 0.000000e+00 669.0
44 TraesCS2D01G222400 chr2B 95.385 130 5 1 1464 1592 245820659 245820530 1.010000e-48 206.0
45 TraesCS2D01G222400 chr2B 94.949 99 1 1 1318 1416 715814806 715814712 1.330000e-32 152.0
46 TraesCS2D01G222400 chr2B 94.845 97 4 1 1320 1415 101490640 101490544 4.800000e-32 150.0
47 TraesCS2D01G222400 chr2B 93.939 99 6 0 6899 6997 245820136 245820038 4.800000e-32 150.0
48 TraesCS2D01G222400 chr2A 96.830 1325 31 6 1 1322 203327590 203326274 0.000000e+00 2204.0
49 TraesCS2D01G222400 chr2A 93.942 1139 42 4 6391 7526 203326136 203325022 0.000000e+00 1696.0
50 TraesCS2D01G222400 chr2A 88.614 202 21 2 7472 7671 203324755 203324554 2.140000e-60 244.0
51 TraesCS2D01G222400 chr2A 96.923 130 3 1 1464 1592 203326265 203326136 4.660000e-52 217.0
52 TraesCS2D01G222400 chr2A 94.595 37 2 0 7438 7474 203325022 203324986 2.990000e-04 58.4
53 TraesCS2D01G222400 chr3D 97.797 1271 14 8 5124 6392 606630861 606632119 0.000000e+00 2180.0
54 TraesCS2D01G222400 chr3A 88.221 849 59 13 1591 2414 202966931 202967763 0.000000e+00 976.0
55 TraesCS2D01G222400 chr1D 91.275 149 6 3 1317 1463 494045183 494045040 6.070000e-46 196.0
56 TraesCS2D01G222400 chr1D 77.251 211 42 5 887 1095 481557584 481557378 1.350000e-22 119.0
57 TraesCS2D01G222400 chr7A 87.097 155 10 7 1317 1465 493700368 493700518 4.760000e-37 167.0
58 TraesCS2D01G222400 chr6D 97.917 96 1 1 1374 1468 129156600 129156505 1.710000e-36 165.0
59 TraesCS2D01G222400 chr6D 94.898 98 3 1 1319 1416 312136255 312136350 1.330000e-32 152.0
60 TraesCS2D01G222400 chr1A 95.918 98 2 1 1321 1416 276575262 276575165 2.870000e-34 158.0


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 TraesCS2D01G222400 chr2D 189521718 189529389 7671 True 14168.000000 14168 100.000000 1 7672 1 chr2D.!!$R1 7671
1 TraesCS2D01G222400 chr7D 616747404 616752976 5572 True 2645.000000 6741 97.488000 1592 6392 3 chr7D.!!$R2 4800
2 TraesCS2D01G222400 chr7D 169027939 169033563 5624 True 1438.766667 6861 98.111167 1591 6392 6 chr7D.!!$R1 4801
3 TraesCS2D01G222400 chr6A 561609019 561614408 5389 True 2047.275000 6780 97.622500 1591 6391 4 chr6A.!!$R2 4800
4 TraesCS2D01G222400 chr6A 561439474 561444861 5387 False 2029.275000 6726 97.820750 1591 6391 4 chr6A.!!$F2 4800
5 TraesCS2D01G222400 chr5D 64653844 64659193 5349 False 4024.500000 6765 95.871000 1583 6392 2 chr5D.!!$F1 4809
6 TraesCS2D01G222400 chr3B 71547303 71553670 6367 True 2293.000000 6741 97.257250 1590 6393 4 chr3B.!!$R2 4803
7 TraesCS2D01G222400 chr7B 350687182 350693656 6474 True 2023.525000 6734 97.613000 1591 6392 4 chr7B.!!$R2 4801
8 TraesCS2D01G222400 chr4A 488005726 488011234 5508 True 3405.500000 6604 95.848500 1591 6391 2 chr4A.!!$R1 4800
9 TraesCS2D01G222400 chr5B 651222562 651226315 3753 False 6301.000000 6301 96.860000 2447 6231 1 chr5B.!!$F1 3784
10 TraesCS2D01G222400 chr5B 292185698 292188494 2796 True 4772.000000 4772 97.403000 3583 6391 1 chr5B.!!$R1 2808
11 TraesCS2D01G222400 chr5B 292193542 292194423 881 True 471.700000 1105 98.032000 1591 2448 3 chr5B.!!$R2 857
12 TraesCS2D01G222400 chr2B 245819417 245821991 2574 True 806.600000 2224 94.655400 1 7671 5 chr2B.!!$R3 7670
13 TraesCS2D01G222400 chr2A 203324554 203327590 3036 True 883.880000 2204 94.180800 1 7671 5 chr2A.!!$R1 7670
14 TraesCS2D01G222400 chr3D 606630861 606632119 1258 False 2180.000000 2180 97.797000 5124 6392 1 chr3D.!!$F1 1268
15 TraesCS2D01G222400 chr3A 202966931 202967763 832 False 976.000000 976 88.221000 1591 2414 1 chr3A.!!$F1 823

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
375 376 3.762288 ACTGAATCAGCTGCACAATGAAT 59.238 39.130 9.47 0.0 34.37 2.57 F
1336 1346 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.0 0.00 4.12 F
1337 1347 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.00 3.28 F
1465 1475 0.323451 AATTTTGGGACGGAGGGAGC 60.323 55.000 0.00 0.0 0.00 4.70 F
2249 3718 0.889186 ACTTTGCAACCTCGCCGAAT 60.889 50.000 0.00 0.0 0.00 3.34 F
2901 6161 1.001633 TCAGGTAAACCTTGAGCGACC 59.998 52.381 0.00 0.0 46.09 4.79 F
4297 7557 1.808945 GCATATCTTGCCTAAGCGCAT 59.191 47.619 11.47 0.0 46.15 4.73 F
6182 9453 0.671251 GGCCATACTGGAGTCTCTCG 59.329 60.000 0.00 0.0 40.96 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1456 0.323451 GCTCCCTCCGTCCCAAAATT 60.323 55.000 0.00 0.00 0.00 1.82 R
2901 6161 3.059868 AGTTCGCGAAAACATACTGTGTG 60.060 43.478 25.24 2.78 41.14 3.82 R
3571 6831 9.991906 TTATTATGCTAACTGGGATTGTAGTAC 57.008 33.333 0.00 0.00 0.00 2.73 R
3993 7253 5.032327 TCTGCATCATAGCATCAAGAAGT 57.968 39.130 0.00 0.00 44.68 3.01 R
4494 7755 2.288763 TGTAAGCACGAGCAGATGTTCA 60.289 45.455 7.77 0.00 45.49 3.18 R
5322 8590 0.744874 ATCACTTGGATGCATGCAGC 59.255 50.000 27.38 27.38 45.96 5.25 R
6503 9774 1.802365 CGTGGTGGCTGTAGTTTTACC 59.198 52.381 0.00 0.00 0.00 2.85 R
7390 10666 1.321474 TTTTGGAGCTGGCACTTCAG 58.679 50.000 0.00 0.00 37.79 3.02 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
375 376 3.762288 ACTGAATCAGCTGCACAATGAAT 59.238 39.130 9.47 0.00 34.37 2.57
523 524 5.756918 TGGTAATTTCATCCGGAATTACCA 58.243 37.500 34.60 34.60 45.18 3.25
536 537 4.552767 CGGAATTACCAATCGAGCATGAAC 60.553 45.833 0.00 0.00 38.90 3.18
537 538 4.335315 GGAATTACCAATCGAGCATGAACA 59.665 41.667 0.00 0.00 38.79 3.18
596 598 4.853924 ATTGTCCGTGCTCTGAAAATTT 57.146 36.364 0.00 0.00 0.00 1.82
597 599 4.647424 TTGTCCGTGCTCTGAAAATTTT 57.353 36.364 2.28 2.28 0.00 1.82
734 741 9.547753 TGTGATAAGACCAAGAAATATTAGAGC 57.452 33.333 0.00 0.00 0.00 4.09
927 934 6.494835 GGAATTGCCAAGGGAATATTGTATCT 59.505 38.462 6.26 0.00 35.12 1.98
928 935 7.015584 GGAATTGCCAAGGGAATATTGTATCTT 59.984 37.037 6.26 0.00 35.12 2.40
1005 1012 4.771590 TTTGCTGGATGAGAACATGAAC 57.228 40.909 0.00 0.00 36.82 3.18
1014 1021 6.723515 TGGATGAGAACATGAACCCAAAAATA 59.276 34.615 0.00 0.00 36.82 1.40
1050 1057 1.573108 CAAGGCTGTTAGGAGGAGGA 58.427 55.000 0.00 0.00 0.00 3.71
1322 1332 6.637658 GTGAATCTCCTAAGCGATGTAAGTAC 59.362 42.308 0.00 0.00 0.00 2.73
1324 1334 6.563222 ATCTCCTAAGCGATGTAAGTACTC 57.437 41.667 0.00 0.00 0.00 2.59
1326 1336 3.887716 TCCTAAGCGATGTAAGTACTCCC 59.112 47.826 0.00 0.00 0.00 4.30
1328 1338 4.023021 CCTAAGCGATGTAAGTACTCCCTC 60.023 50.000 0.00 0.00 0.00 4.30
1330 1340 1.001597 GCGATGTAAGTACTCCCTCCG 60.002 57.143 0.00 0.00 0.00 4.63
1331 1341 2.295885 CGATGTAAGTACTCCCTCCGT 58.704 52.381 0.00 0.00 0.00 4.69
1333 1343 2.134789 TGTAAGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
1334 1344 1.341383 TGTAAGTACTCCCTCCGTCCC 60.341 57.143 0.00 0.00 0.00 4.46
1335 1345 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1336 1346 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1337 1347 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1338 1348 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
1339 1349 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
1340 1350 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1341 1351 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1342 1352 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1343 1353 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1344 1354 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1345 1355 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1346 1356 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1347 1357 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1348 1358 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1349 1359 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1350 1360 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1351 1361 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1352 1362 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1353 1363 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1354 1364 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
1355 1365 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
1356 1366 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1357 1367 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1358 1368 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1366 1376 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
1367 1377 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
1368 1378 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
1369 1379 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
1370 1380 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
1371 1381 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
1374 1384 8.410673 AGATTTGTCTAGATACGGATGTATGT 57.589 34.615 0.00 0.00 41.37 2.29
1375 1385 8.516234 AGATTTGTCTAGATACGGATGTATGTC 58.484 37.037 0.00 0.00 41.37 3.06
1376 1386 6.570672 TTGTCTAGATACGGATGTATGTCC 57.429 41.667 0.00 0.00 41.37 4.02
1377 1387 5.008331 TGTCTAGATACGGATGTATGTCCC 58.992 45.833 0.00 0.00 41.37 4.46
1378 1388 5.008331 GTCTAGATACGGATGTATGTCCCA 58.992 45.833 0.00 0.00 41.37 4.37
1379 1389 5.475909 GTCTAGATACGGATGTATGTCCCAA 59.524 44.000 0.00 0.00 41.37 4.12
1380 1390 6.015688 GTCTAGATACGGATGTATGTCCCAAA 60.016 42.308 0.00 0.00 41.37 3.28
1381 1391 5.623956 AGATACGGATGTATGTCCCAAAA 57.376 39.130 0.00 0.00 41.37 2.44
1382 1392 6.187727 AGATACGGATGTATGTCCCAAAAT 57.812 37.500 0.00 0.00 41.37 1.82
1383 1393 6.601332 AGATACGGATGTATGTCCCAAAATT 58.399 36.000 0.00 0.00 41.37 1.82
1384 1394 6.710744 AGATACGGATGTATGTCCCAAAATTC 59.289 38.462 0.00 0.00 41.37 2.17
1385 1395 4.855340 ACGGATGTATGTCCCAAAATTCT 58.145 39.130 0.00 0.00 34.67 2.40
1386 1396 5.261216 ACGGATGTATGTCCCAAAATTCTT 58.739 37.500 0.00 0.00 34.67 2.52
1387 1397 5.125417 ACGGATGTATGTCCCAAAATTCTTG 59.875 40.000 0.00 0.00 34.67 3.02
1388 1398 5.125417 CGGATGTATGTCCCAAAATTCTTGT 59.875 40.000 0.00 0.00 34.67 3.16
1389 1399 6.564328 GGATGTATGTCCCAAAATTCTTGTC 58.436 40.000 0.00 0.00 31.82 3.18
1390 1400 6.378280 GGATGTATGTCCCAAAATTCTTGTCT 59.622 38.462 0.00 0.00 31.82 3.41
1391 1401 7.093771 GGATGTATGTCCCAAAATTCTTGTCTT 60.094 37.037 0.00 0.00 31.82 3.01
1392 1402 8.877864 ATGTATGTCCCAAAATTCTTGTCTTA 57.122 30.769 0.00 0.00 0.00 2.10
1393 1403 8.335532 TGTATGTCCCAAAATTCTTGTCTTAG 57.664 34.615 0.00 0.00 0.00 2.18
1394 1404 8.160765 TGTATGTCCCAAAATTCTTGTCTTAGA 58.839 33.333 0.00 0.00 0.00 2.10
1395 1405 9.178758 GTATGTCCCAAAATTCTTGTCTTAGAT 57.821 33.333 0.00 0.00 0.00 1.98
1396 1406 8.655935 ATGTCCCAAAATTCTTGTCTTAGATT 57.344 30.769 0.00 0.00 0.00 2.40
1397 1407 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
1398 1408 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
1399 1409 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1400 1410 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1401 1411 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1409 1419 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
1410 1420 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
1411 1421 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
1412 1422 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
1413 1423 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
1414 1424 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
1418 1428 9.516546 AGATTTGTCTAGATACGGATGTATACA 57.483 33.333 8.27 8.27 41.37 2.29
1437 1447 9.516546 TGTATACATCCGTATCTAGACAAATCT 57.483 33.333 0.08 0.00 39.17 2.40
1441 1451 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
1442 1452 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
1443 1453 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
1444 1454 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
1445 1455 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
1446 1456 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
1454 1464 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1455 1465 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1456 1466 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1457 1467 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1458 1468 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1459 1469 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1460 1470 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1461 1471 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1462 1472 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1463 1473 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
1464 1474 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1465 1475 0.323451 AATTTTGGGACGGAGGGAGC 60.323 55.000 0.00 0.00 0.00 4.70
1547 1557 3.909995 TGCCAGGTATATAACTGCTGGAT 59.090 43.478 20.56 0.00 38.94 3.41
1723 1902 2.876645 CGTCCGCTGCGAGAGAAC 60.877 66.667 25.45 11.75 0.00 3.01
2249 3718 0.889186 ACTTTGCAACCTCGCCGAAT 60.889 50.000 0.00 0.00 0.00 3.34
2901 6161 1.001633 TCAGGTAAACCTTGAGCGACC 59.998 52.381 0.00 0.00 46.09 4.79
3571 6831 8.204836 AGTATAGTACTGTTATCCTGCCTTTTG 58.795 37.037 5.39 0.00 37.69 2.44
3993 7253 6.351711 AGTGCTTCTTGATGCTATGATACAA 58.648 36.000 9.36 0.00 0.00 2.41
4212 7472 5.446143 ACACAATTTACATGGCTTTCGAA 57.554 34.783 0.00 0.00 0.00 3.71
4297 7557 1.808945 GCATATCTTGCCTAAGCGCAT 59.191 47.619 11.47 0.00 46.15 4.73
4319 7579 4.451379 GCTTAAGCAATGCGTTTTGTTT 57.549 36.364 22.59 6.74 41.59 2.83
4494 7755 7.757624 CAGTGTATTTTAAAACACACACTTGGT 59.242 33.333 32.74 16.13 46.71 3.67
4579 7840 3.627577 GCTCCTTTTGAACAGTTGTCAGA 59.372 43.478 0.00 0.00 0.00 3.27
4795 8056 8.401709 CCTCTTCTATTAATGCAAAAAGGAGAC 58.598 37.037 0.00 0.00 0.00 3.36
5235 8496 3.750130 ACAGCTAAGCATGTCACTTTCTG 59.250 43.478 0.00 3.88 34.96 3.02
5564 8834 6.409524 AATTTCAGAGAAAAGGACATGCAA 57.590 33.333 0.00 0.00 0.00 4.08
5573 8843 6.240894 AGAAAAGGACATGCAATTCAGTAGA 58.759 36.000 0.00 0.00 0.00 2.59
5778 9049 2.840038 CCATATCCTAGGCCTACATGCA 59.160 50.000 8.91 0.00 0.00 3.96
5892 9163 8.149647 TCATGGTTGAAATACTTTTCTGCAATT 58.850 29.630 0.00 0.00 41.54 2.32
6168 9439 7.008021 ACATATTTGTTTTCTCTTTGGCCAT 57.992 32.000 6.09 0.00 29.55 4.40
6169 9440 8.133024 ACATATTTGTTTTCTCTTTGGCCATA 57.867 30.769 6.09 0.00 29.55 2.74
6170 9441 8.034804 ACATATTTGTTTTCTCTTTGGCCATAC 58.965 33.333 6.09 0.00 29.55 2.39
6171 9442 6.670695 ATTTGTTTTCTCTTTGGCCATACT 57.329 33.333 6.09 0.00 0.00 2.12
6172 9443 5.452078 TTGTTTTCTCTTTGGCCATACTG 57.548 39.130 6.09 0.00 0.00 2.74
6174 9445 4.079253 GTTTTCTCTTTGGCCATACTGGA 58.921 43.478 6.09 0.00 40.96 3.86
6175 9446 3.634397 TTCTCTTTGGCCATACTGGAG 57.366 47.619 6.09 10.17 40.96 3.86
6176 9447 2.551270 TCTCTTTGGCCATACTGGAGT 58.449 47.619 6.09 0.00 40.96 3.85
6177 9448 2.501723 TCTCTTTGGCCATACTGGAGTC 59.498 50.000 6.09 0.00 40.96 3.36
6178 9449 2.503356 CTCTTTGGCCATACTGGAGTCT 59.497 50.000 6.09 0.00 40.96 3.24
6179 9450 2.501723 TCTTTGGCCATACTGGAGTCTC 59.498 50.000 6.09 0.00 40.96 3.36
6180 9451 2.254152 TTGGCCATACTGGAGTCTCT 57.746 50.000 6.09 0.00 40.96 3.10
6181 9452 1.781786 TGGCCATACTGGAGTCTCTC 58.218 55.000 0.00 0.00 40.96 3.20
6182 9453 0.671251 GGCCATACTGGAGTCTCTCG 59.329 60.000 0.00 0.00 40.96 4.04
6183 9454 1.681538 GCCATACTGGAGTCTCTCGA 58.318 55.000 0.00 0.00 40.96 4.04
6184 9455 2.025155 GCCATACTGGAGTCTCTCGAA 58.975 52.381 0.00 0.00 40.96 3.71
6185 9456 2.223618 GCCATACTGGAGTCTCTCGAAC 60.224 54.545 0.00 0.00 40.96 3.95
6466 9737 1.339610 GGATCCAGATGACAGACCGAG 59.660 57.143 6.95 0.00 0.00 4.63
6503 9774 0.824109 TCATGCTAACCCGAGACAGG 59.176 55.000 0.00 0.00 0.00 4.00
6796 10068 4.900684 TGCACATGCCTAAACTTGTAGTA 58.099 39.130 0.49 0.00 41.18 1.82
6823 10095 7.855375 TCCAATGGGTGCAATTTTTAATATGA 58.145 30.769 0.00 0.00 34.93 2.15
6865 10137 3.567478 AGAACCATCCACCTAAGATGC 57.433 47.619 0.00 0.00 39.87 3.91
6872 10144 4.384056 CATCCACCTAAGATGCAGGTTAG 58.616 47.826 9.83 9.83 44.18 2.34
6874 10146 3.451178 TCCACCTAAGATGCAGGTTAGAC 59.549 47.826 16.06 0.00 44.18 2.59
6890 10162 5.758924 GGTTAGACATGAAAACCTGAACAC 58.241 41.667 16.30 0.00 39.66 3.32
6897 10169 5.299279 ACATGAAAACCTGAACACGAGAAAT 59.701 36.000 0.00 0.00 0.00 2.17
6916 10188 7.042456 CGAGAAATGTTGAGTATCGATCCAAAT 60.042 37.037 0.00 0.39 38.61 2.32
6992 10264 6.887626 TCTTTTGTACATAAAGGTGGGTTC 57.112 37.500 20.57 0.00 34.22 3.62
7010 10282 7.260603 GTGGGTTCTCATCAATCTTAAATTGG 58.739 38.462 9.18 0.00 0.00 3.16
7060 10332 4.282703 TGAGGAGGTCTAAACTGGTGTAAC 59.717 45.833 0.00 0.00 0.00 2.50
7070 10342 7.546667 GTCTAAACTGGTGTAACGATCCAATAA 59.453 37.037 0.00 0.00 38.12 1.40
7205 10479 5.156804 AGCTCCGCAATAAGTTAAATTCG 57.843 39.130 0.00 0.00 0.00 3.34
7416 10692 0.598065 GCCAGCTCCAAAAATCGTGT 59.402 50.000 0.00 0.00 0.00 4.49
7444 10720 7.822161 TCACATGAATGGAATAATAGGTTGG 57.178 36.000 0.00 0.00 0.00 3.77
7471 10747 5.070001 TGTGGGTTTGTCTAAGAAAGATGG 58.930 41.667 0.00 0.00 36.36 3.51
7547 11144 9.797642 TGGTTGATATGATAGCTTATTGATGTT 57.202 29.630 0.00 0.00 0.00 2.71
7570 11169 8.607713 TGTTGTAGGGTTTGATAAGAATAAGGA 58.392 33.333 0.00 0.00 0.00 3.36
7628 11227 1.250840 TTAGCTGCCTCACTCGAGCA 61.251 55.000 13.61 3.97 38.00 4.26
7639 11238 1.007271 CTCGAGCAACACGTGTCCT 60.007 57.895 23.61 20.49 0.00 3.85
7643 11243 1.498865 GAGCAACACGTGTCCTGTGG 61.499 60.000 23.61 8.66 41.64 4.17
7663 11263 0.983378 GGCCCACTCACTACATCCCT 60.983 60.000 0.00 0.00 0.00 4.20
7665 11265 1.134371 GCCCACTCACTACATCCCTTC 60.134 57.143 0.00 0.00 0.00 3.46
7667 11267 2.472029 CCACTCACTACATCCCTTCCT 58.528 52.381 0.00 0.00 0.00 3.36
7671 11271 3.246167 ACTCACTACATCCCTTCCTTCCT 60.246 47.826 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 304 1.884579 CACTGCCACTTCTTGCTCATT 59.115 47.619 0.00 0.00 0.00 2.57
375 376 1.067516 GAGCTGAGCCAAAACTTGCAA 59.932 47.619 0.00 0.00 0.00 4.08
523 524 3.896648 AAAACGTGTTCATGCTCGATT 57.103 38.095 0.00 0.00 0.00 3.34
536 537 7.906010 TGACAAGTTAGTTATGACAAAAACGTG 59.094 33.333 11.60 11.60 34.34 4.49
537 538 7.976826 TGACAAGTTAGTTATGACAAAAACGT 58.023 30.769 0.00 0.00 0.00 3.99
608 610 9.420118 TCCTTATGCACATTACAAATTATTCCT 57.580 29.630 0.00 0.00 0.00 3.36
632 639 8.693542 AGATTCGAAATCAACAAATTCATTCC 57.306 30.769 0.00 0.00 0.00 3.01
734 741 9.961265 AATGATGATGATGCACTTAAAATACAG 57.039 29.630 0.00 0.00 0.00 2.74
927 934 6.398095 TCTTATGCTCGAGTCTTCATGAAAA 58.602 36.000 15.13 0.00 0.00 2.29
928 935 5.965922 TCTTATGCTCGAGTCTTCATGAAA 58.034 37.500 15.13 0.79 0.00 2.69
1005 1012 2.423538 CCCGAAGTCTGCTATTTTTGGG 59.576 50.000 3.53 3.53 37.77 4.12
1014 1021 2.032681 GCCAACCCGAAGTCTGCT 59.967 61.111 0.00 0.00 0.00 4.24
1050 1057 3.169099 AGCTGTCTTGGTCTGAGTATGT 58.831 45.455 0.00 0.00 0.00 2.29
1084 1091 6.595716 AGTCAATCTGTTTCCACTTACTATGC 59.404 38.462 0.00 0.00 0.00 3.14
1322 1332 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
1324 1334 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1326 1336 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1328 1338 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1330 1340 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1331 1341 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1340 1350 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
1341 1351 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
1342 1352 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
1343 1353 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
1344 1354 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
1345 1355 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
1348 1358 9.516546 ACATACATCCGTATCTAGACAAATCTA 57.483 33.333 0.00 0.00 36.11 1.98
1349 1359 8.410673 ACATACATCCGTATCTAGACAAATCT 57.589 34.615 0.00 0.00 36.11 2.40
1350 1360 7.755822 GGACATACATCCGTATCTAGACAAATC 59.244 40.741 0.00 0.00 36.11 2.17
1351 1361 7.309867 GGGACATACATCCGTATCTAGACAAAT 60.310 40.741 0.00 0.00 39.97 2.32
1352 1362 6.015688 GGGACATACATCCGTATCTAGACAAA 60.016 42.308 0.00 0.00 39.97 2.83
1353 1363 5.475909 GGGACATACATCCGTATCTAGACAA 59.524 44.000 0.00 0.00 39.97 3.18
1354 1364 5.008331 GGGACATACATCCGTATCTAGACA 58.992 45.833 0.00 0.00 39.97 3.41
1355 1365 5.008331 TGGGACATACATCCGTATCTAGAC 58.992 45.833 0.00 0.00 39.97 2.59
1356 1366 5.251182 TGGGACATACATCCGTATCTAGA 57.749 43.478 0.00 0.00 39.97 2.43
1357 1367 5.977489 TTGGGACATACATCCGTATCTAG 57.023 43.478 0.00 0.00 39.97 2.43
1358 1368 6.734502 TTTTGGGACATACATCCGTATCTA 57.265 37.500 0.00 0.00 39.97 1.98
1359 1369 5.623956 TTTTGGGACATACATCCGTATCT 57.376 39.130 0.00 0.00 39.97 1.98
1360 1370 6.710744 AGAATTTTGGGACATACATCCGTATC 59.289 38.462 0.00 0.00 39.97 2.24
1361 1371 6.601332 AGAATTTTGGGACATACATCCGTAT 58.399 36.000 0.00 0.00 39.97 3.06
1362 1372 5.996644 AGAATTTTGGGACATACATCCGTA 58.003 37.500 0.00 0.00 39.97 4.02
1363 1373 4.855340 AGAATTTTGGGACATACATCCGT 58.145 39.130 0.00 0.00 39.97 4.69
1364 1374 5.125417 ACAAGAATTTTGGGACATACATCCG 59.875 40.000 5.68 0.00 39.97 4.18
1365 1375 6.378280 AGACAAGAATTTTGGGACATACATCC 59.622 38.462 5.68 0.00 39.30 3.51
1366 1376 7.396540 AGACAAGAATTTTGGGACATACATC 57.603 36.000 5.68 0.00 39.30 3.06
1367 1377 7.781324 AAGACAAGAATTTTGGGACATACAT 57.219 32.000 5.68 0.00 39.30 2.29
1368 1378 8.160765 TCTAAGACAAGAATTTTGGGACATACA 58.839 33.333 5.68 0.00 39.30 2.29
1369 1379 8.561738 TCTAAGACAAGAATTTTGGGACATAC 57.438 34.615 5.68 0.00 39.30 2.39
1370 1380 9.753674 AATCTAAGACAAGAATTTTGGGACATA 57.246 29.630 5.68 0.00 39.30 2.29
1371 1381 8.655935 AATCTAAGACAAGAATTTTGGGACAT 57.344 30.769 5.68 0.00 39.30 3.06
1372 1382 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
1373 1383 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1374 1384 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1375 1385 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1383 1393 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
1384 1394 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
1385 1395 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
1386 1396 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
1387 1397 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
1388 1398 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
1392 1402 9.516546 TGTATACATCCGTATCTAGACAAATCT 57.483 33.333 0.08 0.00 39.17 2.40
1411 1421 9.516546 AGATTTGTCTAGATACGGATGTATACA 57.483 33.333 8.27 8.27 41.37 2.29
1415 1425 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
1416 1426 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
1417 1427 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
1418 1428 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
1419 1429 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
1420 1430 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
1428 1438 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1429 1439 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1430 1440 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1431 1441 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
1432 1442 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
1433 1443 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1434 1444 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1435 1445 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1436 1446 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1437 1447 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1438 1448 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1439 1449 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1440 1450 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1441 1451 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1442 1452 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1443 1453 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1444 1454 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1445 1455 1.751437 CTCCCTCCGTCCCAAAATTC 58.249 55.000 0.00 0.00 0.00 2.17
1446 1456 0.323451 GCTCCCTCCGTCCCAAAATT 60.323 55.000 0.00 0.00 0.00 1.82
1447 1457 1.303282 GCTCCCTCCGTCCCAAAAT 59.697 57.895 0.00 0.00 0.00 1.82
1448 1458 2.150719 TGCTCCCTCCGTCCCAAAA 61.151 57.895 0.00 0.00 0.00 2.44
1449 1459 2.528127 TGCTCCCTCCGTCCCAAA 60.528 61.111 0.00 0.00 0.00 3.28
1450 1460 3.319198 GTGCTCCCTCCGTCCCAA 61.319 66.667 0.00 0.00 0.00 4.12
1451 1461 3.846405 AAGTGCTCCCTCCGTCCCA 62.846 63.158 0.00 0.00 0.00 4.37
1452 1462 1.262640 TAAAGTGCTCCCTCCGTCCC 61.263 60.000 0.00 0.00 0.00 4.46
1453 1463 0.831307 ATAAAGTGCTCCCTCCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
1454 1464 2.694109 ACTATAAAGTGCTCCCTCCGTC 59.306 50.000 0.00 0.00 33.57 4.79
1455 1465 2.431057 CACTATAAAGTGCTCCCTCCGT 59.569 50.000 0.00 0.00 46.28 4.69
1456 1466 3.099267 CACTATAAAGTGCTCCCTCCG 57.901 52.381 0.00 0.00 46.28 4.63
1723 1902 1.795286 GATATTTTCTCTCGCAGCGGG 59.205 52.381 16.42 12.93 0.00 6.13
1905 3220 1.965754 GCAGCTCTCCGGGTTCATCT 61.966 60.000 0.00 0.00 0.00 2.90
1957 3272 1.302192 CGAAACTCCCCTTCGCCAA 60.302 57.895 0.00 0.00 39.22 4.52
2249 3718 6.537301 CAGTACCTTTCAGTTCAGTAACACAA 59.463 38.462 0.00 0.00 38.12 3.33
2352 4012 9.632807 CTAATACTCTACAGATGCTGGAATTAC 57.367 37.037 0.00 0.00 35.51 1.89
2394 5030 5.865013 ACAAAAACCCAGAAAACAAACTACG 59.135 36.000 0.00 0.00 0.00 3.51
2622 5875 9.884636 TCATGTTTCTCGGAAGATATTTTTAGA 57.115 29.630 0.00 0.00 40.84 2.10
2901 6161 3.059868 AGTTCGCGAAAACATACTGTGTG 60.060 43.478 25.24 2.78 41.14 3.82
3571 6831 9.991906 TTATTATGCTAACTGGGATTGTAGTAC 57.008 33.333 0.00 0.00 0.00 2.73
3993 7253 5.032327 TCTGCATCATAGCATCAAGAAGT 57.968 39.130 0.00 0.00 44.68 3.01
4212 7472 6.668133 TTCCCTGGTCCTAAATAAAAGGAT 57.332 37.500 0.00 0.00 44.79 3.24
4494 7755 2.288763 TGTAAGCACGAGCAGATGTTCA 60.289 45.455 7.77 0.00 45.49 3.18
4579 7840 2.670148 GGGATCTGCCGGTGAGGTT 61.670 63.158 1.90 0.00 43.70 3.50
5235 8496 3.251004 ACATTCCAGTCAAGCGTCTTTTC 59.749 43.478 0.00 0.00 0.00 2.29
5322 8590 0.744874 ATCACTTGGATGCATGCAGC 59.255 50.000 27.38 27.38 45.96 5.25
5892 9163 4.717233 AACTGAAGCAAATGTGTCACAA 57.283 36.364 10.28 0.00 0.00 3.33
5981 9252 5.672194 AGGAACCATATCCATTCAAGTAGGT 59.328 40.000 0.00 0.00 42.27 3.08
6086 9357 8.978874 AAATAGCATCCAGTATAACATGAACA 57.021 30.769 0.00 0.00 0.00 3.18
6168 9439 4.765339 TCATTTGTTCGAGAGACTCCAGTA 59.235 41.667 0.00 0.00 41.84 2.74
6169 9440 3.574396 TCATTTGTTCGAGAGACTCCAGT 59.426 43.478 0.00 0.00 41.84 4.00
6170 9441 4.179926 TCATTTGTTCGAGAGACTCCAG 57.820 45.455 0.00 0.00 41.84 3.86
6171 9442 4.464244 AGATCATTTGTTCGAGAGACTCCA 59.536 41.667 0.00 0.00 41.84 3.86
6172 9443 5.004922 AGATCATTTGTTCGAGAGACTCC 57.995 43.478 0.00 0.00 41.84 3.85
6174 9445 6.146837 CACAAAGATCATTTGTTCGAGAGACT 59.853 38.462 15.99 0.00 40.30 3.24
6175 9446 6.302615 CACAAAGATCATTTGTTCGAGAGAC 58.697 40.000 15.99 0.00 40.30 3.36
6176 9447 5.106948 GCACAAAGATCATTTGTTCGAGAGA 60.107 40.000 15.99 0.00 40.30 3.10
6177 9448 5.084722 GCACAAAGATCATTTGTTCGAGAG 58.915 41.667 15.99 8.65 40.30 3.20
6178 9449 4.514816 TGCACAAAGATCATTTGTTCGAGA 59.485 37.500 15.99 0.56 40.30 4.04
6179 9450 4.786507 TGCACAAAGATCATTTGTTCGAG 58.213 39.130 15.99 9.38 40.30 4.04
6180 9451 4.827304 TGCACAAAGATCATTTGTTCGA 57.173 36.364 15.99 0.00 40.30 3.71
6181 9452 8.839947 TTATATGCACAAAGATCATTTGTTCG 57.160 30.769 15.99 10.11 40.30 3.95
6466 9737 4.024218 GCATGAGAACAACTGAGGATATGC 60.024 45.833 0.00 0.00 0.00 3.14
6503 9774 1.802365 CGTGGTGGCTGTAGTTTTACC 59.198 52.381 0.00 0.00 0.00 2.85
6823 10095 9.783256 GTTCTTCGCAAAACAATATATAACCTT 57.217 29.630 0.00 0.00 0.00 3.50
6872 10144 3.807622 TCTCGTGTTCAGGTTTTCATGTC 59.192 43.478 0.00 0.00 33.00 3.06
6874 10146 4.811555 TTCTCGTGTTCAGGTTTTCATG 57.188 40.909 0.00 0.00 0.00 3.07
6890 10162 5.281727 TGGATCGATACTCAACATTTCTCG 58.718 41.667 9.52 0.00 0.00 4.04
6897 10169 4.769688 AGCATTTGGATCGATACTCAACA 58.230 39.130 9.52 2.26 0.00 3.33
6962 10234 7.872483 CCACCTTTATGTACAAAAGAAAGCATT 59.128 33.333 21.80 7.50 36.27 3.56
6992 10264 8.284945 TCAAGACCCAATTTAAGATTGATGAG 57.715 34.615 10.22 2.58 0.00 2.90
7030 10302 6.003950 CCAGTTTAGACCTCCTCAATCAAAA 58.996 40.000 0.00 0.00 0.00 2.44
7060 10332 7.439356 TGTCTCTAAGCATTCTTTATTGGATCG 59.561 37.037 0.00 0.00 33.85 3.69
7284 10559 9.944376 ATAGTGAGCTAATCTTTTGTACAAGAA 57.056 29.630 8.56 5.84 36.36 2.52
7326 10601 5.163754 GCATGCTTACCTATTATTTAGGCGG 60.164 44.000 11.37 0.00 38.25 6.13
7390 10666 1.321474 TTTTGGAGCTGGCACTTCAG 58.679 50.000 0.00 0.00 37.79 3.02
7444 10720 5.763204 TCTTTCTTAGACAAACCCACATCAC 59.237 40.000 0.00 0.00 0.00 3.06
7535 11132 6.509418 TCAAACCCTACAACATCAATAAGC 57.491 37.500 0.00 0.00 0.00 3.09
7628 11227 2.508928 CCCCACAGGACACGTGTT 59.491 61.111 24.26 4.55 38.24 3.32
7643 11243 1.527370 GGATGTAGTGAGTGGGCCC 59.473 63.158 17.59 17.59 0.00 5.80
7651 11251 3.491766 AGGAAGGAAGGGATGTAGTGA 57.508 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.